From 6d6b4a3d0adf36f336285b102754a62bc26c284d Mon Sep 17 00:00:00 2001
From: Niki Zadeh <Niki.Zadeh@noaa.gov>
Date: Tue, 6 Jan 2015 16:16:11 -0500
Subject: [PATCH 001/361] Merge updates from diomond brnach since riga

- Diamond development branch has updates that were missed to come to releases since siena.
- These do not change answers if not turned on.
- Bug fix for bilin function. Turn it on by old_bug_bilin = .false.  it is off by default to reproduce answers.
- Adding grounding_fraction and clipping_depth parameters.
- Adding optional argument to pass ocean depth.
- Adding some new diagnostics.
- Adding some checksums and functional unit test.
---
 icebergs.F90           | 54 +++++++++++++++++++-------
 icebergs_framework.F90 | 88 +++++++++++++++++++++++++++++++++++++-----
 2 files changed, 118 insertions(+), 24 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 51f8a80..2569967 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -26,7 +26,7 @@ module ice_bergs
 use ice_bergs_framework, only: icebergs_gridded, xyt, iceberg, icebergs, buffer
 use ice_bergs_framework, only: verbose, really_debug,debug,old_bug_rotated_weights,budget,use_roundoff_fix
 use ice_bergs_framework, only: find_cell,find_cell_by_search,count_bergs,is_point_in_cell,pos_within_cell
-use ice_bergs_framework, only: nclasses
+use ice_bergs_framework, only: nclasses,old_bug_bilin
 use ice_bergs_framework, only: sum_mass,sum_heat,bilin,yearday,count_bergs,bergs_chksum
 use ice_bergs_framework, only: checksum_gridded,add_new_berg_to_list
 use ice_bergs_framework, only: send_bergs_to_other_pes,move_trajectory
@@ -69,17 +69,19 @@ module ice_bergs
 subroutine icebergs_init(bergs, &
              gni, gnj, layout, io_layout, axes, dom_x_flags, dom_y_flags, &
              dt, Time, ice_lon, ice_lat, ice_wet, ice_dx, ice_dy, ice_area, &
-             cos_rot, sin_rot, maskmap)
+             cos_rot, sin_rot, ocean_depth, maskmap)
 ! Arguments
 type(icebergs), pointer :: bergs
 integer, intent(in) :: gni, gnj, layout(2), io_layout(2), axes(2)
-logical, intent(in), optional :: maskmap(:,:)
 integer, intent(in) :: dom_x_flags, dom_y_flags
 real, intent(in) :: dt
 type (time_type), intent(in) :: Time ! current time
 real, dimension(:,:), intent(in) :: ice_lon, ice_lat, ice_wet
 real, dimension(:,:), intent(in) :: ice_dx, ice_dy, ice_area
 real, dimension(:,:), intent(in) :: cos_rot, sin_rot
+real, dimension(:,:), intent(in), optional :: ocean_depth
+logical, intent(in), optional :: maskmap(:,:)
+
 integer :: stdlogunit, stderrunit
 
   ! Get the stderr and stdlog unit numbers
@@ -90,7 +92,7 @@ subroutine icebergs_init(bergs, &
   call ice_bergs_framework_init(bergs, &
              gni, gnj, layout, io_layout, axes, dom_x_flags, dom_y_flags, &
              dt, Time, ice_lon, ice_lat, ice_wet, ice_dx, ice_dy, ice_area, &
-             cos_rot, sin_rot, maskmap)
+             cos_rot, sin_rot, ocean_depth=ocean_depth, maskmap=maskmap)
 
   call mpp_clock_begin(bergs%clock_ior)
   call ice_bergs_io_init(bergs,io_layout)
@@ -402,7 +404,7 @@ subroutine thermodynamics(bergs)
 type(icebergs_gridded), pointer :: grd
 real :: M, T, W, L, SST, Vol, Ln, Wn, Tn, nVol, IC, Dn
 real :: Mv, Me, Mb, melt, dvo, dva, dM, Ss, dMe, dMb, dMv
-real :: Mnew, Mnew1, Mnew2
+real :: Mnew, Mnew1, Mnew2, Hocean
 real :: Mbits, nMbits, dMbitsE, dMbitsM, Lbits, Abits, Mbb
 integer :: i,j, stderrunit
 type(iceberg), pointer :: this, next
@@ -541,6 +543,7 @@ subroutine thermodynamics(bergs)
           T=Tn
           Tn=Wn
           Wn=T
+          Dn=(bergs%rho_bergs/rho_seawater)*Tn ! re-calculate draught (keel depth) for grounding
       end if
     endif
 
@@ -565,8 +568,13 @@ subroutine thermodynamics(bergs)
            & grd%mass(i,j)=grd%mass(i,j)+Mnew/grd%area(i,j)*this%mass_scaling ! kg/m2
       if (grd%id_bergy_mass>0 .or. bergs%add_weight_to_ocean)&
            & grd%bergy_mass(i,j)=grd%bergy_mass(i,j)+nMbits/grd%area(i,j)*this%mass_scaling ! kg/m2
-      if (bergs%add_weight_to_ocean .and. .not. bergs%time_average_weight) &
-         call spread_mass_across_ocean_cells(grd, i, j, this%xi, this%yj, Mnew, nMbits, this%mass_scaling)
+      if (bergs%add_weight_to_ocean .and. .not. bergs%time_average_weight) then
+        if (bergs%grounding_fraction>0.) then
+          Hocean=bergs%grounding_fraction*(grd%ocean_depth(i,j)+grd%ssh(i,j))
+          if (Dn>Hocean) Mnew=Mnew*min(1.,Hocean/Dn)
+        endif
+        call spread_mass_across_ocean_cells(grd, i, j, this%xi, this%yj, Mnew, nMbits, this%mass_scaling)
+      endif
     endif
   
     this=>next
@@ -584,8 +592,13 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
   ! Local variables
   real :: xL, xC, xR, yD, yC, yU, Mass
   real :: yDxL, yDxC, yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR
+  real, parameter :: rho_seawater=1035.
   
   Mass=(Mberg+Mbits)*scaling
+  ! This line attempts to "clip" the weight felt by the ocean. The concept of
+  ! clipping is non-physical and this step should be replaced by grounding.
+  if (grd%clipping_depth>0.) Mass=min(Mass,grd%clipping_depth*grd%area(i,j)*rho_seawater)
+
   xL=min(0.5, max(0., 0.5-x))
   xR=min(0.5, max(0., x-0.5))
   xC=max(0., 1.-(xL+xR))
@@ -631,7 +644,7 @@ subroutine interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y,
 real :: hxm, hxp
 real, parameter :: ssh_coast=0.00
 
-  cos_rot=bilin(grd, grd%cos, i, j, xi, yj)
+  cos_rot=bilin(grd, grd%cos, i, j, xi, yj) ! If true, uses the inverted bilin function
   sin_rot=bilin(grd, grd%sin, i, j, xi, yj)
 
   uo=bilin(grd, grd%uo, i, j, xi, yj)
@@ -991,6 +1004,13 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     lerr=send_data(grd%id_stored_ice, grd%stored_ice(grd%isc:grd%iec,grd%jsc:grd%jec,:), Time)
   if (grd%id_real_calving>0) &
     lerr=send_data(grd%id_real_calving, grd%real_calving(grd%isc:grd%iec,grd%jsc:grd%jec,:), Time)
+  if (grd%id_ssh>0) &
+    lerr=send_data(grd%id_ssh, grd%ssh(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_fax>0) &
+    lerr=send_data(grd%id_fax, tauxa(:,:), Time)
+  if (grd%id_fay>0) &
+    lerr=send_data(grd%id_fay, tauya(:,:), Time)
+
 
   ! Dump icebergs to screen
   if (really_debug) call print_bergs(stderrunit,bergs,'icebergs_run, status')
@@ -1231,14 +1251,16 @@ end subroutine icebergs_run
 
 ! ##############################################################################
 
-subroutine icebergs_incr_mass(bergs, mass)
+subroutine icebergs_incr_mass(bergs, mass, Time)
 ! Arguments
 type(icebergs), pointer :: bergs
 real, dimension(bergs%grd%isc:bergs%grd%iec,bergs%grd%jsc:bergs%grd%jec), intent(inout) :: mass
+type(time_type), intent(in), optional :: Time
 ! Local variables
 integer :: i, j
 type(icebergs_gridded), pointer :: grd
 real :: dmda
+logical :: lerr
 
   if (.not. associated(bergs)) return
 
@@ -1256,8 +1278,8 @@ subroutine icebergs_incr_mass(bergs, mass)
 
 
   if (debug) then
-    bergs%grd%tmp(:,:)=0.; bergs%grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec)=mass
-    call grd_chksum2(bergs%grd, bergs%grd%tmp, 'mass in (incr)')
+    grd%tmp(:,:)=0.; grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec)=mass
+    call grd_chksum2(grd, grd%tmp, 'mass in (incr)')
   endif
 
   call mpp_update_domains(grd%mass_on_ocean, grd%domain)
@@ -1283,12 +1305,15 @@ subroutine icebergs_incr_mass(bergs, mass)
          +     (grd%mass_on_ocean(i  ,j-1,8)+grd%mass_on_ocean(i  ,j+1,2)) ) )
     if (grd%area(i,j)>0) dmda=dmda/grd%area(i,j)*grd%msk(i,j)
     if (.not. bergs%passive_mode) mass(i,j)=mass(i,j)+dmda
+    if (grd%id_mass_on_ocn>0) grd%tmp(i,j)=dmda
   enddo; enddo
+  if (present(Time).and. (grd%id_mass_on_ocn>0)) &
+    lerr=send_data(grd%id_mass_on_ocn, grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
 
   if (debug) then
-    call grd_chksum3(bergs%grd, bergs%grd%mass_on_ocean, 'mass bergs (incr)')
-    bergs%grd%tmp(:,:)=0.; bergs%grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec)=mass
-    call grd_chksum2(bergs%grd, bergs%grd%tmp, 'mass out (incr)')
+    grd%tmp(:,:)=0.; grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec)=mass
+    call grd_chksum3(grd, grd%mass_on_ocean, 'mass bergs (incr)')
+    call grd_chksum2(grd, grd%tmp, 'mass out (incr)')
   endif
 
   call mpp_clock_end(bergs%clock_int)
@@ -2162,6 +2187,7 @@ subroutine icebergs_end(bergs)
   deallocate(bergs%grd%msk)
   deallocate(bergs%grd%cos)
   deallocate(bergs%grd%sin)
+  deallocate(bergs%grd%ocean_depth)
   deallocate(bergs%grd%calving)
   deallocate(bergs%grd%calving_hflx)
   deallocate(bergs%grd%stored_heat)
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 3988990..b94c42c 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -33,15 +33,16 @@ module ice_bergs_framework
 logical :: use_roundoff_fix=.true. ! Use a "fix" for the round-off discrepancy between is_point_in_cell() and pos_within_cell()
 logical :: old_bug_rotated_weights=.false. ! Skip the rotation of off-center weights for rotated halo updates
 logical :: make_calving_reproduce=.false. ! Make the calving.res.nc file reproduce across pe count changes.
+logical :: old_bug_bilin=.true. ! If true, uses the inverted bilin function (use False to get correct answer)
 character(len=10) :: restart_input_dir = 'INPUT/'
 integer, parameter :: delta_buf=25 ! Size by which to increment buffers
 real, parameter :: pi_180=pi/180. ! Converts degrees to radians
 logical :: fix_restart_dates=.true. ! After a restart, check that bergs were created before the current model date
-
+logical :: do_unit_tests=.false. ! Conduct some unit tests
 
 !Public params !Niki: write a subroutine to expose these
 public nclasses,buffer_width,buffer_width_traj
-public verbose, really_debug, debug, restart_input_dir,make_calving_reproduce,use_roundoff_fix
+public verbose, really_debug, debug, restart_input_dir,make_calving_reproduce,old_bug_bilin,use_roundoff_fix
 public ignore_ij_restart, use_slow_find,generate_test_icebergs,old_bug_rotated_weights,budget
 public orig_read
 
@@ -81,6 +82,7 @@ module ice_bergs_framework
   real, dimension(:,:), pointer :: msk=>null() ! Ocean-land mask (1=ocean)
   real, dimension(:,:), pointer :: cos=>null() ! Cosine from rotation matrix to lat-lon coords
   real, dimension(:,:), pointer :: sin=>null() ! Sine from rotation matrix to lat-lon coords
+  real, dimension(:,:), pointer :: ocean_depth=>NULL() ! Depth of ocean (m)
   real, dimension(:,:), pointer :: uo=>null() ! Ocean zonal flow (m/s)
   real, dimension(:,:), pointer :: vo=>null() ! Ocean meridional flow (m/s)
   real, dimension(:,:), pointer :: ui=>null() ! Ice zonal flow (m/s)
@@ -118,6 +120,10 @@ module ice_bergs_framework
   integer :: id_calving_hflx_in=-1, id_stored_heat=-1, id_melt_hflx=-1, id_heat_content=-1
   integer :: id_mass=-1, id_ui=-1, id_vi=-1, id_ua=-1, id_va=-1, id_sst=-1, id_cn=-1, id_hi=-1
   integer :: id_bergy_src=-1, id_bergy_melt=-1, id_bergy_mass=-1, id_berg_melt=-1
+  integer :: id_mass_on_ocn=-1, id_ssh=-1, id_fax=-1, id_fay=-1
+
+  real :: clipping_depth=0. ! The effective depth at which to clip the weight felt by the ocean [m].
+
 end type icebergs_gridded
 
 type :: xyt
@@ -158,7 +164,7 @@ module ice_bergs_framework
   integer :: traj_sample_hrs
   integer :: verbose_hrs
   integer :: clock, clock_mom, clock_the, clock_int, clock_cal, clock_com, clock_ini, clock_ior, clock_iow, clock_dia ! ids for fms timers
-  real :: rho_bergs ! Density of icebergs
+  real :: rho_bergs ! Density of icebergs [kg/m^3]
   real :: LoW_ratio ! Initial ratio L/W for newly calved icebergs
   real :: bergy_bit_erosion_fraction ! Fraction of erosion melt flux to divert to bergy bits
   real :: sicn_shift ! Shift of sea-ice concentration in erosion flux modulation (0<sicn_shift<1)
@@ -169,7 +175,8 @@ module ice_bergs_framework
   logical :: add_weight_to_ocean=.true. ! Add weight of bergs to ocean
   logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
   logical :: time_average_weight=.false. ! Time average the weight on the ocean
-  real :: speed_limit=0. ! CFL speed limit for a berg
+  real :: speed_limit=0. ! CFL speed limit for a berg [m/s]
+  real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
   type(buffer), pointer :: obuffer_n=>null(), ibuffer_n=>null()
   type(buffer), pointer :: obuffer_s=>null(), ibuffer_s=>null()
   type(buffer), pointer :: obuffer_e=>null(), ibuffer_e=>null()
@@ -212,7 +219,7 @@ module ice_bergs_framework
 subroutine ice_bergs_framework_init(bergs, &
              gni, gnj, layout, io_layout, axes, dom_x_flags, dom_y_flags, &
              dt, Time, ice_lon, ice_lat, ice_wet, ice_dx, ice_dy, ice_area, &
-             cos_rot, sin_rot, maskmap)
+             cos_rot, sin_rot, ocean_depth, maskmap)
 
 use mpp_parameter_mod, only: SCALAR_PAIR, CGRID_NE, BGRID_NE, CORNER, AGRID
 use mpp_domains_mod, only: mpp_update_domains, mpp_define_domains
@@ -233,13 +240,15 @@ subroutine ice_bergs_framework_init(bergs, &
 ! Arguments
 type(icebergs), pointer :: bergs
 integer, intent(in) :: gni, gnj, layout(2), io_layout(2), axes(2)
-logical, intent(in), optional :: maskmap(:,:)
 integer, intent(in) :: dom_x_flags, dom_y_flags
 real, intent(in) :: dt
 type (time_type), intent(in) :: Time ! current time
 real, dimension(:,:), intent(in) :: ice_lon, ice_lat, ice_wet
 real, dimension(:,:), intent(in) :: ice_dx, ice_dy, ice_area
 real, dimension(:,:), intent(in) :: cos_rot, sin_rot
+real, dimension(:,:), intent(in),optional :: ocean_depth
+logical, intent(in), optional :: maskmap(:,:)
+
 ! Namelist parameters (and defaults)
 integer :: halo=4 ! Width of halo region
 integer :: traj_sample_hrs=24 ! Period between sampling of position for trajectory storage
@@ -253,6 +262,8 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
 logical :: time_average_weight=.false. ! Time average the weight on the ocean
 real :: speed_limit=0. ! CFL speed limit for a berg
+real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
+logical :: do_unit_tests=.false. ! Conduct some unit tests
 real, dimension(nclasses) :: initial_mass=(/8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11/) ! Mass thresholds between iceberg classes (kg)
 real, dimension(nclasses) :: distribution=(/0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02/) ! Fraction of calving to apply to this class (non-dim)
 real, dimension(nclasses) :: mass_scaling=(/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) ! Ratio between effective and real iceberg mass (non-dim)
@@ -262,7 +273,7 @@ subroutine ice_bergs_framework_init(bergs, &
          rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, &
          time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, &
-         old_bug_rotated_weights, make_calving_reproduce, restart_input_dir, orig_read
+         old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -353,6 +364,7 @@ subroutine ice_bergs_framework_init(bergs, &
   allocate( grd%msk(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%msk(:,:)=0.
   allocate( grd%cos(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%cos(:,:)=1.
   allocate( grd%sin(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%sin(:,:)=0.
+  allocate( grd%ocean_depth(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%ocean_depth(:,:)=0.
   allocate( grd%calving(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%calving(:,:)=0.
   allocate( grd%calving_hflx(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%calving_hflx(:,:)=0.
   allocate( grd%stored_heat(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%stored_heat(:,:)=0.
@@ -391,6 +403,8 @@ subroutine ice_bergs_framework_init(bergs, &
   grd%lon(is:ie,js:je)=ice_lon(:,:)
   grd%lat(is:ie,js:je)=ice_lat(:,:)
   grd%area(is:ie,js:je)=ice_area(:,:) !sis2 has *(4.*pi*radius*radius)
+  if(present(ocean_depth)) grd%ocean_depth(is:ie,js:je)=ocean_depth(:,:)
+
   ! Copy data declared on ice model data domain
   is=grd%isc-1; ie=grd%iec+1; js=grd%jsc-1; je=grd%jec+1
   grd%dx(is:ie,js:je)=ice_dx(:,:)
@@ -406,6 +420,7 @@ subroutine ice_bergs_framework_init(bergs, &
   call mpp_update_domains(grd%msk, grd%domain)
   call mpp_update_domains(grd%cos, grd%domain, position=CORNER)
   call mpp_update_domains(grd%sin, grd%domain, position=CORNER)
+  call mpp_update_domains(grd%ocean_depth, grd%domain)
   call mpp_update_domains(grd%parity_x, grd%parity_y, grd%domain, gridtype=AGRID) ! If either parity_x/y is -ve, we need rotation of vectors
 
   ! Sanitize lon and lat at the SW edges
@@ -485,6 +500,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%passive_mode=passive_mode
   bergs%time_average_weight=time_average_weight
   bergs%speed_limit=speed_limit
+  bergs%grounding_fraction=grounding_fraction
   bergs%add_weight_to_ocean=add_weight_to_ocean
   allocate( bergs%initial_mass(nclasses) ); bergs%initial_mass(:)=initial_mass(:)
   allocate( bergs%distribution(nclasses) ); bergs%distribution(:)=distribution(:)
@@ -528,6 +544,8 @@ subroutine ice_bergs_framework_init(bergs, &
      'Virtual coverage by icebergs', 'm^2')
   grd%id_mass=register_diag_field('icebergs', 'mass', axes, Time, &
      'Iceberg density field', 'kg/(m^2)')
+  grd%id_mass_on_ocn=register_diag_field('icebergs', 'mass_on_ocean', axes, Time, &
+     'Iceberg density field felt by ocean', 'kg/(m^2)')
   grd%id_stored_ice=register_diag_field('icebergs', 'stored_ice', axes3d, Time, &
      'Accumulated ice mass by class', 'kg')
   grd%id_real_calving=register_diag_field('icebergs', 'real_calving', axes3d, Time, &
@@ -550,6 +568,12 @@ subroutine ice_bergs_framework_init(bergs, &
      'Sea ice concentration', '(fraction)')
   grd%id_hi=register_diag_field('icebergs', 'hi', axes, Time, &
      'Sea ice thickness', 'm')
+  grd%id_ssh=register_diag_field('icebergs', 'ssh', axes, Time, &
+     'Sea surface hieght', 'm')
+  grd%id_fax=register_diag_field('icebergs', 'taux', axes, Time, &
+     'X-stress on ice from atmosphere', 'N m^-2')
+  grd%id_fay=register_diag_field('icebergs', 'tauy', axes, Time, &
+     'Y-stress on ice from atmosphere', 'N m^-2')
 
   ! Static fields
   id_class=register_static_field('icebergs', 'lon', axes, &
@@ -564,6 +588,9 @@ subroutine ice_bergs_framework_init(bergs, &
   id_class=register_static_field('icebergs', 'mask', axes, &
                'wet point mask', 'none')
   if (id_class>0) lerr=send_data(id_class, grd%msk(grd%isc:grd%iec,grd%jsc:grd%jec))
+  id_class=register_static_field('icebergs', 'ocean_depth', axes, &
+               'ocean depth', 'm')
+  if (id_class>0) lerr=send_data(id_class, grd%ocean_depth(grd%isc:grd%iec,grd%jsc:grd%jec))
 
   if (debug) then
     call grd_chksum2(grd, grd%lon, 'init lon')
@@ -574,6 +601,11 @@ subroutine ice_bergs_framework_init(bergs, &
     call grd_chksum2(grd, grd%msk, 'init msk')
     call grd_chksum2(grd, grd%cos, 'init cos')
     call grd_chksum2(grd, grd%sin, 'init sin')
+    call grd_chksum2(grd, grd%ocean_depth, 'init ocean_depth')
+  endif
+
+  if (do_unit_tests) then
+   if (unitTests(bergs)) call error_mesg('diamonds, icebergs_init', 'Unit tests failed!', FATAL)
   endif
 
  !write(stderrunit,*) 'diamonds: done'
@@ -2428,6 +2460,7 @@ subroutine checksum_gridded(grd, label)
   call grd_chksum2(grd, grd%msk, 'msk')
   call grd_chksum2(grd, grd%cos, 'cos')
   call grd_chksum2(grd, grd%sin, 'sin')
+  call grd_chksum2(grd, grd%ocean_depth, 'depth')
 
 end subroutine checksum_gridded
 
@@ -2714,9 +2747,13 @@ real function bilin(grd, fld, i, j, xi, yj)
 integer, intent(in) :: i, j
 ! Local variables
 
-  bilin=(fld(i,j  )*(1.-xi)+fld(i-1,j  )*xi)*(1.-yj) &
-       +(fld(i,j-1)*(1.-xi)+fld(i-1,j-1)*xi)*yj
-
+  if (old_bug_bilin) then
+    bilin=(fld(i,j  )*(1.-xi)+fld(i-1,j  )*xi)*(1.-yj) &
+         +(fld(i,j-1)*(1.-xi)+fld(i-1,j-1)*xi)*yj
+  else
+    bilin=(fld(i,j  )*xi+fld(i-1,j  )*(1.-xi))*yj &
+         +(fld(i,j-1)*xi+fld(i-1,j-1)*(1.-xi))*(1.-yj)
+  endif
 end function bilin
 
 ! ##############################################################################
@@ -2740,4 +2777,35 @@ subroutine print_fld(grd, fld, label)
 
 end subroutine print_fld
 
+! ##############################################################################
+
+logical function unitTests(bergs)
+  type(icebergs), pointer :: bergs
+  type(icebergs_gridded), pointer :: grd
+  ! Local variables
+  integer :: stderrunit,i,j
+
+  ! This function returns True is a unit test fails
+  unitTests=.false.
+  ! For convenience
+  grd=>bergs%grd
+  stderrunit=stderr()
+  
+  i=grd%isc; j=grd%jsc
+  call localTest( bilin(grd, grd%lon, i, j, 0., 1.), grd%lon(i-1,j) )
+  call localTest( bilin(grd, grd%lon, i, j, 1., 1.), grd%lon(i,j) )
+  call localTest( bilin(grd, grd%lat, i, j, 1., 0.), grd%lat(i,j-1) )
+  call localTest( bilin(grd, grd%lat, i, j, 1., 1.), grd%lat(i,j) )
+
+  contains
+  subroutine localTest(answer, rightAnswer)
+  real, intent(in) :: answer, rightAnswer
+  if (answer==rightAnswer) return
+  unitTests=.true.
+  write(stderrunit,*) 'a=',answer,'b=',rightAnswer
+  end subroutine localTest
+end function unitTests
+
+! ##############################################################################
+
 end module

From 93467eb168a5d879e8d244a21f0b6206d4926f9c Mon Sep 17 00:00:00 2001
From: Niki Zadeh <Niki.Zadeh@noaa.gov>
Date: Thu, 15 Jan 2015 13:07:01 -0500
Subject: [PATCH 002/361] Make interfaces compatible with SIS

- The icebergs_init interface needed a minor modification to make it compatible
  with SIS without changing answers.
---
 icebergs.F90           | 5 +++--
 icebergs_framework.F90 | 7 ++++++-
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 51f8a80..17d2492 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -69,11 +69,12 @@ module ice_bergs
 subroutine icebergs_init(bergs, &
              gni, gnj, layout, io_layout, axes, dom_x_flags, dom_y_flags, &
              dt, Time, ice_lon, ice_lat, ice_wet, ice_dx, ice_dy, ice_area, &
-             cos_rot, sin_rot, maskmap)
+             cos_rot, sin_rot, maskmap, fractional_area)
 ! Arguments
 type(icebergs), pointer :: bergs
 integer, intent(in) :: gni, gnj, layout(2), io_layout(2), axes(2)
 logical, intent(in), optional :: maskmap(:,:)
+logical, intent(in), optional :: fractional_area
 integer, intent(in) :: dom_x_flags, dom_y_flags
 real, intent(in) :: dt
 type (time_type), intent(in) :: Time ! current time
@@ -90,7 +91,7 @@ subroutine icebergs_init(bergs, &
   call ice_bergs_framework_init(bergs, &
              gni, gnj, layout, io_layout, axes, dom_x_flags, dom_y_flags, &
              dt, Time, ice_lon, ice_lat, ice_wet, ice_dx, ice_dy, ice_area, &
-             cos_rot, sin_rot, maskmap)
+             cos_rot, sin_rot, maskmap, fractional_area)
 
   call mpp_clock_begin(bergs%clock_ior)
   call ice_bergs_io_init(bergs,io_layout)
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 3988990..b8a0328 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -212,7 +212,7 @@ module ice_bergs_framework
 subroutine ice_bergs_framework_init(bergs, &
              gni, gnj, layout, io_layout, axes, dom_x_flags, dom_y_flags, &
              dt, Time, ice_lon, ice_lat, ice_wet, ice_dx, ice_dy, ice_area, &
-             cos_rot, sin_rot, maskmap)
+             cos_rot, sin_rot, maskmap, fractional_area)
 
 use mpp_parameter_mod, only: SCALAR_PAIR, CGRID_NE, BGRID_NE, CORNER, AGRID
 use mpp_domains_mod, only: mpp_update_domains, mpp_define_domains
@@ -234,6 +234,7 @@ subroutine ice_bergs_framework_init(bergs, &
 type(icebergs), pointer :: bergs
 integer, intent(in) :: gni, gnj, layout(2), io_layout(2), axes(2)
 logical, intent(in), optional :: maskmap(:,:)
+logical, intent(in), optional :: fractional_area
 integer, intent(in) :: dom_x_flags, dom_y_flags
 real, intent(in) :: dt
 type (time_type), intent(in) :: Time ! current time
@@ -391,6 +392,10 @@ subroutine ice_bergs_framework_init(bergs, &
   grd%lon(is:ie,js:je)=ice_lon(:,:)
   grd%lat(is:ie,js:je)=ice_lat(:,:)
   grd%area(is:ie,js:je)=ice_area(:,:) !sis2 has *(4.*pi*radius*radius)
+  !For SIS not to change answers
+  if(present(fractional_area)) then
+    if(fractional_area) grd%area(is:ie,js:je)=ice_area(:,:) *(4.*pi*radius*radius)
+  endif
   ! Copy data declared on ice model data domain
   is=grd%isc-1; ie=grd%iec+1; js=grd%jsc-1; je=grd%jec+1
   grd%dx(is:ie,js:je)=ice_dx(:,:)

From fd86d0a0a836a035b29013f477c152f8141608ad Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Wed, 22 Apr 2015 10:06:38 -0400
Subject: [PATCH 003/361] Added License and README following DOC guidance

- In preparation for pushing to GitHub
---
 LICENSE.md | 553 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 README.md  |  15 ++
 2 files changed, 568 insertions(+)
 create mode 100644 LICENSE.md
 create mode 100644 README.md

diff --git a/LICENSE.md b/LICENSE.md
new file mode 100644
index 0000000..a05d37a
--- /dev/null
+++ b/LICENSE.md
@@ -0,0 +1,553 @@
+This file is part of the NOAA-GFDL iceberg model, referred to as
+NOAA-GFDL/icebergs. The majority of this code was written by authors at
+Princeton University who originally provided this software under version 3 of
+the Gnu General Public License, which is provided below.
+
+The intent of this license is to ensure free and unrestricted access to the
+iceberg software, and to pass on those rights to modified versions this
+software.
+
+
+GNU GENERAL PUBLIC LICENSE
+==========================
+
+Version 3, 29 June 2007
+
+Copyright &copy; 2007 Free Software Foundation, Inc. http://fsf.org/
+
+Everyone is permitted to copy and distribute verbatim copies of this license
+document, but changing it is not allowed.
+
+## Preamble
+
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+kinds of works.
+
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+Software Foundation, use the GNU General Public License for most of our software; it
+applies also to any other work released this way by its authors. You can apply it to
+your programs, too.
+
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+Public Licenses are designed to make sure that you have the freedom to distribute
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+
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+indicate your acceptance of this License to do so.
+
+### 10. Automatic Licensing of Downstream Recipients.
+
+Each time you convey a covered work, the recipient automatically receives a license
+from the original licensors, to run, modify and propagate that work, subject to this
+License. You are not responsible for enforcing compliance by third parties with this
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+An "entity transaction" is a transaction transferring control of an
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+merging organizations. If propagation of a covered work results from an entity
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+receives whatever licenses to the work the party's predecessor in interest had or
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+You may not impose any further restrictions on the exercise of the rights granted or
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+initiate litigation (including a cross-claim or counterclaim in a lawsuit) alleging
+that any patent claim is infringed by making, using, selling, offering for sale, or
+importing the Program or any portion of it.
+
+### 11. Patents.
+
+A "contributor" is a copyright holder who authorizes use under this
+License of the Program or a work on which the Program is based. The work thus
+licensed is called the contributor's "contributor version".
+
+A contributor's "essential patent claims" are all patent claims owned or
+controlled by the contributor, whether already acquired or hereafter acquired, that
+would be infringed by some manner, permitted by this License, of making, using, or
+selling its contributor version, but do not include claims that would be infringed
+only as a consequence of further modification of the contributor version. For
+purposes of this definition, "control" includes the right to grant patent
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+
+Each contributor grants you a non-exclusive, worldwide, royalty-free patent license
+under the contributor's essential patent claims, to make, use, sell, offer for sale,
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+In the following three paragraphs, a "patent license" is any express
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+express permission to practice a patent or covenant not to sue for patent
+infringement). To "grant" such a patent license to a party means to make
+such an agreement or commitment not to enforce a patent against the party.
+
+If you convey a covered work, knowingly relying on a patent license, and the
+Corresponding Source of the work is not available for anyone to copy, free of charge
+and under the terms of this License, through a publicly available network server or
+other readily accessible means, then you must either (1) cause the Corresponding
+Source to be so available, or (2) arrange to deprive yourself of the benefit of the
+patent license for this particular work, or (3) arrange, in a manner consistent with
+the requirements of this License, to extend the patent license to downstream
+recipients. "Knowingly relying" means you have actual knowledge that, but
+for the patent license, your conveying the covered work in a country, or your
+recipient's use of the covered work in a country, would infringe one or more
+identifiable patents in that country that you have reason to believe are valid.
+
+If, pursuant to or in connection with a single transaction or arrangement, you
+convey, or propagate by procuring conveyance of, a covered work, and grant a patent
+license to some of the parties receiving the covered work authorizing them to use,
+propagate, modify or convey a specific copy of the covered work, then the patent
+license you grant is automatically extended to all recipients of the covered work and
+works based on it.
+
+A patent license is "discriminatory" if it does not include within the
+scope of its coverage, prohibits the exercise of, or is conditioned on the
+non-exercise of one or more of the rights that are specifically granted under this
+License. You may not convey a covered work if you are a party to an arrangement with
+a third party that is in the business of distributing software, under which you make
+payment to the third party based on the extent of your activity of conveying the
+work, and under which the third party grants, to any of the parties who would receive
+the covered work from you, a discriminatory patent license (a) in connection with
+copies of the covered work conveyed by you (or copies made from those copies), or (b)
+primarily for and in connection with specific products or compilations that contain
+the covered work, unless you entered into that arrangement, or that patent license
+was granted, prior to 28 March 2007.
+
+Nothing in this License shall be construed as excluding or limiting any implied
+license or other defenses to infringement that may otherwise be available to you
+under applicable patent law.
+
+### 12. No Surrender of Others' Freedom.
+
+If conditions are imposed on you (whether by court order, agreement or otherwise)
+that contradict the conditions of this License, they do not excuse you from the
+conditions of this License. If you cannot convey a covered work so as to satisfy
+simultaneously your obligations under this License and any other pertinent
+obligations, then as a consequence you may not convey it at all. For example, if you
+agree to terms that obligate you to collect a royalty for further conveying from
+those to whom you convey the Program, the only way you could satisfy both those terms
+and this License would be to refrain entirely from conveying the Program.
+
+### 13. Use with the GNU Affero General Public License.
+
+Notwithstanding any other provision of this License, you have permission to link or
+combine any covered work with a work licensed under version 3 of the GNU Affero
+General Public License into a single combined work, and to convey the resulting work.
+The terms of this License will continue to apply to the part which is the covered
+work, but the special requirements of the GNU Affero General Public License, section
+13, concerning interaction through a network will apply to the combination as such.
+
+### 14. Revised Versions of this License.
+
+The Free Software Foundation may publish revised and/or new versions of the GNU
+General Public License from time to time. Such new versions will be similar in spirit
+to the present version, but may differ in detail to address new problems or concerns.
+
+Each version is given a distinguishing version number. If the Program specifies that
+a certain numbered version of the GNU General Public License "or any later
+version" applies to it, you have the option of following the terms and
+conditions either of that numbered version or of any later version published by the
+Free Software Foundation. If the Program does not specify a version number of the GNU
+General Public License, you may choose any version ever published by the Free
+Software Foundation.
+
+If the Program specifies that a proxy can decide which future versions of the GNU
+General Public License can be used, that proxy's public statement of acceptance of a
+version permanently authorizes you to choose that version for the Program.
+
+Later license versions may give you additional or different permissions. However, no
+additional obligations are imposed on any author or copyright holder as a result of
+your choosing to follow a later version.
+
+### 15. Disclaimer of Warranty.
+
+THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.
+EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
+PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER
+EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE
+QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE
+DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+### 16. Limitation of Liability.
+
+IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY
+COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS
+PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL,
+INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE
+PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE
+OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE
+WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+### 17. Interpretation of Sections 15 and 16.
+
+If the disclaimer of warranty and limitation of liability provided above cannot be
+given local legal effect according to their terms, reviewing courts shall apply local
+law that most closely approximates an absolute waiver of all civil liability in
+connection with the Program, unless a warranty or assumption of liability accompanies
+a copy of the Program in return for a fee.
+
+END OF TERMS AND CONDITIONS
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..bfd98be
--- /dev/null
+++ b/README.md
@@ -0,0 +1,15 @@
+Disclaimer
+==========
+
+The United States Department of Commerce (DOC) GitHub project code is provided
+on an "as is" basis and the user assumes responsibility for its use. DOC has
+relinquished control of the information and no longer has responsibility to
+protect the integrity, confidentiality, or availability of the information. Any
+claims against the Department of Commerce stemming from the use of its GitHub
+project will be governed by all applicable Federal law. Any reference to
+specific commercial products, processes, or services by service mark,
+trademark, manufacturer, or otherwise, does not constitute or imply their
+endorsement, recommendation or favoring by the Department of Commerce. The
+Department of Commerce seal and logo, or the seal and logo of a DOC bureau,
+shall not be used in any manner to imply endorsement of any commercial product
+or activity by DOC or the United States Government.

From 319be1311f81b7579ea504d659dee75ee727cb59 Mon Sep 17 00:00:00 2001
From: "Alistair Adcroft (Work account)" <Alistair.Adcroft@noaa.gov>
Date: Tue, 26 May 2015 22:13:05 -0400
Subject: [PATCH 004/361] Updated README.md

- With link to gitlab, following DOC guidance.
---
 README.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/README.md b/README.md
index bfd98be..fd73b8a 100644
--- a/README.md
+++ b/README.md
@@ -13,3 +13,6 @@ endorsement, recommendation or favoring by the Department of Commerce. The
 Department of Commerce seal and logo, or the seal and logo of a DOC bureau,
 shall not be used in any manner to imply endorsement of any commercial product
 or activity by DOC or the United States Government.
+
+This project code is made available through GitHub but is managed by NOAA-GFDL
+at https://gitlab.gfdl.noaa.gov.

From b01c65bf43324b14fe574fdfd39a60abc1fdcd81 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Mon, 1 Jun 2015 15:43:47 -0400
Subject: [PATCH 005/361] Commented out call to save restart in icebergs_end()

- icebergs_save_restart() is called directly by SIS1 and SIS2 so we do not need
  to call it a second time. If icebergs were controlled by the coupler then the
  icebergs would need to take responsibility for the restarts at the end of the
  run.
- Fixes warnings of form "icebergs.res.nc is already registered with other
  restart_file_type data"
- No answer changes.
---
 icebergs.F90 | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 33e5c2d..4c0965a 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -2164,7 +2164,11 @@ subroutine icebergs_end(bergs)
 
   if (.not.associated(bergs)) return
 
-  call icebergs_save_restart(bergs)
+  ! icebergs_save_restart() is called directly by SIS1 and SIS2 so
+  ! we do not need to call it a second time. If icebergs were controlled
+  ! by the coupler then the icebergs would need to take responsibility for
+  ! the restarts at the end of the run.
+  !call icebergs_save_restart(bergs)
 
   call mpp_clock_begin(bergs%clock_ini)
   ! Delete bergs and structures

From 85fa3c18769a31355bde7dd28b9e0ba7a4647cb7 Mon Sep 17 00:00:00 2001
From: Alon Stern <Alon.Stern@gaea6.ncrc.gov>
Date: Fri, 22 May 2015 14:39:01 -0400
Subject: [PATCH 006/361] Added explicit accelerations output to the accel
 subrouting Also added axe, aye (1,2,3,4) to evolve subrouting inside the
 accel calls (to make the changes consistant)

---
 icebergs.F90 | 51 ++++++++++++++++++++++++++++++---------------------
 1 file changed, 30 insertions(+), 21 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 4c0965a..7f5fea6 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -112,13 +112,15 @@ subroutine icebergs_init(bergs, &
 
 end subroutine icebergs_init
 
-subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, debug_flag)
+subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, axe, aye, debug_flag) !Seperated total acceleration (ax, ay) and implicit part (bx ,by) accelerations - Alon
+!subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, debug_flag) !old version commmented out by Alon
 ! Arguments
 type(icebergs), pointer :: bergs
 type(iceberg), pointer :: berg
 integer, intent(in) :: i, j
 real, intent(in) :: xi, yj, lat, uvel, vvel, uvel0, vvel0, dt
-real, intent(inout) :: ax, ay
+!real, intent(inout) :: ax, ay  !old version - Alon
+real, intent(inout) :: ax, ay, axe, aye ! Added explicit accelerations to output -Alon
 logical, optional :: debug_flag
 ! Local variables
 type(icebergs_gridded), pointer :: grd
@@ -128,7 +130,8 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 real :: c_ocn, c_atm, c_ice
 real :: ampl, wmod, Cr, Lwavelength, Lcutoff, Ltop
 real, parameter :: alpha=0.0, beta=1.0, accel_lim=1.e-2, Cr0=0.06, vel_lim=15.
-real :: lambda, detA, A11, A12, axe, aye, D_hi
+real :: lambda, detA, A11, A12, D_hi ! Removed axe, aye from line - Alon
+!real :: lambda, detA, A11, A12, axe, aye, D_hi !old version - Alon
 real :: uveln, vveln, us, vs, speed, loc_dx, new_speed
 logical :: dumpit
 integer :: itloop
@@ -189,6 +192,12 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
     drag_atm=c_atm*sqrt( (us-ua)**2+(vs-va)**2 )
     drag_ice=c_ice*sqrt( (us-ui)**2+(vs-vi)**2 )
 
+!Alon's proposed change - This would change it to Bob's improved scheme.
+!    !us=uveln; vs=vveln     This line is no longer needed
+!    drag_ocn=c_ocn*0.5*(sqrt( (uveln-uo)**2+(vveln-vo)**2 )+sqrt( (uvel-uo)**2+(vvel-vo)**2 ))
+!    drag_atm=c_atm*0.5*(sqrt( (uveln-ua)**2+(vveln-va)**2 )+sqrt( (uvel-ua)**2+(vvel-va)**2 ))
+!    drag_ice=c_ice*0.5*(sqrt( (uveln-ui)**2+(vveln-vi)**2 )+sqrt( (uvel-ui)**2+(vvel-vi)**2 ))
+
     ! Explicit accelerations
    !axe= f_cori*vvel -gravity*ssh_x +wave_rad*uwave &
    !    -drag_ocn*(uvel-uo) -drag_atm*(uvel-ua) -drag_ice*(uvel-ui)
@@ -1477,10 +1486,10 @@ subroutine evolve_icebergs(bergs)
 type(icebergs), pointer :: bergs
 ! Local variables
 type(icebergs_gridded), pointer :: grd
-real :: uvel1, vvel1, lon1, lat1, u1, v1, dxdl1, ax1, ay1
-real :: uvel2, vvel2, lon2, lat2, u2, v2, dxdl2, ax2, ay2
-real :: uvel3, vvel3, lon3, lat3, u3, v3, dxdl3, ax3, ay3
-real :: uvel4, vvel4, lon4, lat4, u4, v4, dxdl4, ax4, ay4
+real :: uvel1, vvel1, lon1, lat1, u1, v1, dxdl1, ax1, ay1, axe1, aye1 !axe1 and aye1 added by Alon 
+real :: uvel2, vvel2, lon2, lat2, u2, v2, dxdl2, ax2, ay2, axe2, aye2 !axe2 and aye2 added by Alon 
+real :: uvel3, vvel3, lon3, lat3, u3, v3, dxdl3, ax3, ay3, axe3, aye3 !axe3 and aye3 added by Alon
+real :: uvel4, vvel4, lon4, lat4, u4, v4, dxdl4, ax4, ay4, axe4, aye4 !axe4 and aye4 added by Alon
 real :: uveln, vveln, lonn, latn
 real :: x1, xdot1, xddot1, y1, ydot1, yddot1
 real :: x2, xdot2, xddot2, y2, ydot2, yddot2
@@ -1561,7 +1570,7 @@ subroutine evolve_icebergs(bergs)
   uvel1=berg%uvel; vvel1=berg%vvel
   if (on_tangential_plane) call rotvec_to_tang(lon1,uvel1,vvel1,xdot1,ydot1)
   u1=uvel1*dxdl1; v1=vvel1*dydl
-  call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1)
+  call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axe1, aye1) !axe1, aye1 - Added by Alon
   if (on_tangential_plane) call rotvec_to_tang(lon1,ax1,ay1,xddot1,yddot1)
   
   !  X2 = X1+dt/2*V1 ; V2 = V1+dt/2*A1; A2=A(X2)
@@ -1605,7 +1614,7 @@ subroutine evolve_icebergs(bergs)
    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2 (deg)=',dt*v1,dt*v2
    write(stderrunit,*) 'Acceleration terms for position 1'
    error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, debug_flag=.true.)
+   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axe1, aye1, debug_flag=.true.) !axe1, aye1 - Added by Alon
     call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 2')
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos2 i,j,lon,lat,xi,yj=',i,j,lon2,lat2,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos2 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
@@ -1614,7 +1623,7 @@ subroutine evolve_icebergs(bergs)
   endif
   dxdl2=r180_pi/(Rearth*cos(lat2*pi_180))
   u2=uvel2*dxdl2; v2=vvel2*dydl
-  call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2)
+  call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axe2, aye2) !axe2, aye2 - Added by Alon
   if (on_tangential_plane) call rotvec_to_tang(lon2,ax2,ay2,xddot2,yddot2)
   
   !  X3 = X1+dt/2*V2 ; V3 = V1+dt/2*A2; A3=A(X3)
@@ -1658,10 +1667,10 @@ subroutine evolve_icebergs(bergs)
    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3 (deg)=',dt*v1,dt*v2,dt*v3
    write(stderrunit,*) 'Acceleration terms for position 1'
    error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, debug_flag=.true.)
+   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axe1, aye1, debug_flag=.true.) !axe1, aye1 - Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 2'
    error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
-   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, debug_flag=.true.)
+   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axe2, aye2, debug_flag=.true.) !axe2, aye2 - Added by Alon
     call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 3')
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos3 i,j,lon,lat,xi,yj=',i,j,lon3,lat3,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos3 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
@@ -1670,7 +1679,7 @@ subroutine evolve_icebergs(bergs)
   endif
   dxdl3=r180_pi/(Rearth*cos(lat3*pi_180))
   u3=uvel3*dxdl3; v3=vvel3*dydl
-  call accel(bergs, berg, i, j, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3)
+  call accel(bergs, berg, i, j, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axe3, aye3) !axe3, aye3 - Added by Alon
   if (on_tangential_plane) call rotvec_to_tang(lon3,ax3,ay3,xddot3,yddot3)
   
   !  X4 = X1+dt*V3 ; V4 = V1+dt*A3; A4=A(X4)
@@ -1712,13 +1721,13 @@ subroutine evolve_icebergs(bergs)
    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v4 (deg)=',dt*v1,dt*v2,dt*v3,dt*v4
    write(stderrunit,*) 'Acceleration terms for position 1'
    error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, debug_flag=.true.)
+   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axe1, aye1, debug_flag=.true.) !axe1, aye1 - Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 2'
    error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
-   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, debug_flag=.true.)
+   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axe2, aye2, debug_flag=.true.) !axe2, aye2 - Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 3'
    error_flag=pos_within_cell(grd, lon3, lat3, i3, j3, xi, yj)
-   call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, debug_flag=.true.)
+   call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axe3, aye3, debug_flag=.true.) !axe3, aye3 - Added by Alon
     call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 4')
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos4 i,j,lon,lat,xi,yj=',i,j,lon4,lat4,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos4 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
@@ -1727,7 +1736,7 @@ subroutine evolve_icebergs(bergs)
   endif
   dxdl4=r180_pi/(Rearth*cos(lat4*pi_180))
   u4=uvel4*dxdl4; v4=vvel4*dydl
-  call accel(bergs, berg, i, j, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4)
+  call accel(bergs, berg, i, j, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axe4, aye4) !axe4, aye4 - Added by Alon
   if (on_tangential_plane) call rotvec_to_tang(lon4,ax4,ay4,xddot4,yddot4)
   
   !  Xn = X1+dt*(V1+2*V2+2*V3+V4)/6
@@ -1781,16 +1790,16 @@ subroutine evolve_icebergs(bergs)
    write(stderrunit,*) 'diamonds, evolve_iceberg: on_tangential_plane=',on_tangential_plane
    write(stderrunit,*) 'Acceleration terms for position 1'
    error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, debug_flag=.true.)
+   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axe1, aye1, debug_flag=.true.)  !axe1, aye1 - Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 2'
    error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
-   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, debug_flag=.true.)
+   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axe2, aye2, debug_flag=.true.)  !axe2, aye2 - Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 3'
    error_flag=pos_within_cell(grd, lon3, lat3, i3, j3, xi, yj)
-   call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, debug_flag=.true.)
+   call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axe3, aye3, debug_flag=.true.)  !axe3, aye3 - Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 4'
    error_flag=pos_within_cell(grd, lon4, lat4, i4, j4, xi, yj)
-   call accel(bergs, berg, i4, j4, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, debug_flag=.true.)
+   call accel(bergs, berg, i4, j4, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axe4, aye4, debug_flag=.true.)  !axe4, aye4 - Added by Alon
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'posn i,j,lon,lat,xi,yj=',i,j,lonn,latn,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'posn box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
     call print_berg(stderrunit, berg, 'evolve_iceberg, out of cell at end!')

From 413726aa121b3f52d2885d2a7ae3e8b29e52f4bf Mon Sep 17 00:00:00 2001
From: Alon Stern <Alon.Stern@gaea6.ncrc.gov>
Date: Mon, 1 Jun 2015 10:30:39 -0400
Subject: [PATCH 007/361] Added an if statement for choosing Range Katta or
 Verlet. Does not change the answers.

---
 icebergs.F90 | 28 ++++++++++++++++++++++------
 1 file changed, 22 insertions(+), 6 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 7f5fea6..52142ae 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -112,7 +112,7 @@ subroutine icebergs_init(bergs, &
 
 end subroutine icebergs_init
 
-subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, axe, aye, debug_flag) !Seperated total acceleration (ax, ay) and implicit part (bx ,by) accelerations - Alon
+subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, axn, ayn, debug_flag) !Saving exp acceleration for Verlet - Alon
 !subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, debug_flag) !old version commmented out by Alon
 ! Arguments
 type(icebergs), pointer :: bergs
@@ -120,7 +120,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 integer, intent(in) :: i, j
 real, intent(in) :: xi, yj, lat, uvel, vvel, uvel0, vvel0, dt
 !real, intent(inout) :: ax, ay  !old version - Alon
-real, intent(inout) :: ax, ay, axe, aye ! Added explicit accelerations to output -Alon
+real, intent(inout) :: ax, ay, axn, ayn ! Added explicit accelerations to output -Alon
 logical, optional :: debug_flag
 ! Local variables
 type(icebergs_gridded), pointer :: grd
@@ -130,8 +130,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 real :: c_ocn, c_atm, c_ice
 real :: ampl, wmod, Cr, Lwavelength, Lcutoff, Ltop
 real, parameter :: alpha=0.0, beta=1.0, accel_lim=1.e-2, Cr0=0.06, vel_lim=15.
-real :: lambda, detA, A11, A12, D_hi ! Removed axe, aye from line - Alon
-!real :: lambda, detA, A11, A12, axe, aye, D_hi !old version - Alon
+real :: lambda, detA, A11, A12, axe, aye, D_hi 
 real :: uveln, vveln, us, vs, speed, loc_dx, new_speed
 logical :: dumpit
 integer :: itloop
@@ -236,7 +235,14 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
     vveln=vvel0+dt*ay
 
   enddo ! itloop
-  
+ 
+!Saving the totally explicit part of the acceleration to use in finding the next position and u_star -Alon
+    axn=-gravity*ssh_x +wave_rad*uwave !Alon
+    ayn=-gravity*ssh_y +wave_rad*vwave !Alon
+
+
+
+ 
   ! Limit speed of bergs based on a CFL criteria
   if (bergs%speed_limit>0.) then
     speed=sqrt(uveln*uveln+vveln*vveln) ! Speed of berg
@@ -1501,6 +1507,7 @@ subroutine evolve_icebergs(bergs)
 integer :: i1,j1,i2,j2,i3,j3,i4,j4
 real :: xi, yj
 logical :: bounced, on_tangential_plane, error_flag
+logical :: Ranga_not_verlet  ! Ranga_not_verlet=1 for Range Katta, =0 for Verlet method. Added by Alon
 type(iceberg), pointer :: berg
 integer :: stderrunit
 
@@ -1530,6 +1537,10 @@ subroutine evolve_icebergs(bergs)
   dt_6=dt/6.
   Rearth=6360.e3
 
+  !Choosing time stepping scheme - Alon
+   Ranga_not_verlet=.true.    !true=Ranga Katta, False=Verlet   , Alon
+
+
   berg=>bergs%first
   do while (associated(berg)) ! loop over all bergs
 
@@ -1562,7 +1573,9 @@ subroutine evolve_icebergs(bergs)
   if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
     call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling)
 
-  ! A1 = A(X1)
+  if (Ranga_not_verlet) then !Start of the Range Katta Loop -Added by Alon
+
+ ! A1 = A(X1)
   lon1=berg%lon; lat1=berg%lat
   if (on_tangential_plane) call rotpos_to_tang(lon1,lat1,x1,y1)
   dxdl1=r180_pi/(Rearth*cos(lat1*pi_180))
@@ -1814,6 +1827,9 @@ subroutine evolve_icebergs(bergs)
       write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lat(i,j),i=grd%isd,grd%ied)
     enddo
   endif
+ 
+  endif ! End of the Range Katta Loop -added by Alon  
+
 
   berg%lon=lonn
   berg%lat=latn

From ba1d7d8f96a0bb99a36a56b7d872cb9ee00ea339 Mon Sep 17 00:00:00 2001
From: Alon Stern <Alon.Stern@gaea6.ncrc.gov>
Date: Mon, 1 Jun 2015 11:25:08 -0400
Subject: [PATCH 008/361] Flag for verlet vs Ranga Katta added. Not changes to
 the answers.

---
 icebergs.F90 | 38 +++++++++++++++++++++++---------------
 1 file changed, 23 insertions(+), 15 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 52142ae..d40b05f 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -112,7 +112,7 @@ subroutine icebergs_init(bergs, &
 
 end subroutine icebergs_init
 
-subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, axn, ayn, debug_flag) !Saving exp acceleration for Verlet - Alon
+subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, axn, ayn, Ranga_not_verlet, debug_flag) !Saving exp acceleration for Verlet, Adding Verlet flag - Alon
 !subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, debug_flag) !old version commmented out by Alon
 ! Arguments
 type(icebergs), pointer :: bergs
@@ -133,9 +133,11 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 real :: lambda, detA, A11, A12, axe, aye, D_hi 
 real :: uveln, vveln, us, vs, speed, loc_dx, new_speed
 logical :: dumpit
+logical, intent(in) :: Ranga_not_verlet  ! Flag to specify whether it is Range Katta or Verlet
 integer :: itloop
 integer :: stderrunit
 
+
   ! Get the stderr unit number.
   stderrunit = stderr()
 
@@ -204,6 +206,12 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
    !    -drag_ocn*(vvel-vo) -drag_atm*(vvel-va) -drag_ice*(vvel-vi)
     axe=-gravity*ssh_x +wave_rad*uwave
     aye=-gravity*ssh_y +wave_rad*vwave
+
+    if (.not.Ranga_not_verlet) then  ! When using Verlet, use only half the explicit acceleration,  Added by Alon
+       axe=axe/2  
+       aye=aye/2  
+    endif 
+
     if (alpha>0.) then ! If implicit, use time-level (n) rather than RK4 latest
       axe=axe+f_cori*vvel0
       aye=aye-f_cori*uvel0
@@ -1583,7 +1591,7 @@ subroutine evolve_icebergs(bergs)
   uvel1=berg%uvel; vvel1=berg%vvel
   if (on_tangential_plane) call rotvec_to_tang(lon1,uvel1,vvel1,xdot1,ydot1)
   u1=uvel1*dxdl1; v1=vvel1*dydl
-  call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axe1, aye1) !axe1, aye1 - Added by Alon
+  call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axe1, aye1, Ranga_not_verlet) !axe1, aye1 ,Ranga_not_verlet  - Added by Alon
   if (on_tangential_plane) call rotvec_to_tang(lon1,ax1,ay1,xddot1,yddot1)
   
   !  X2 = X1+dt/2*V1 ; V2 = V1+dt/2*A1; A2=A(X2)
@@ -1627,7 +1635,7 @@ subroutine evolve_icebergs(bergs)
    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2 (deg)=',dt*v1,dt*v2
    write(stderrunit,*) 'Acceleration terms for position 1'
    error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axe1, aye1, debug_flag=.true.) !axe1, aye1 - Added by Alon
+   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axe1, aye1, Ranga_not_verlet, debug_flag=.true.) !axe1, aye1, Ranga_not_verlet - Added by Alon
     call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 2')
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos2 i,j,lon,lat,xi,yj=',i,j,lon2,lat2,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos2 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
@@ -1636,7 +1644,7 @@ subroutine evolve_icebergs(bergs)
   endif
   dxdl2=r180_pi/(Rearth*cos(lat2*pi_180))
   u2=uvel2*dxdl2; v2=vvel2*dydl
-  call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axe2, aye2) !axe2, aye2 - Added by Alon
+  call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axe2, aye2, Ranga_not_verlet) !axe2, aye2, Ranga_not_verlet - Added by Alon
   if (on_tangential_plane) call rotvec_to_tang(lon2,ax2,ay2,xddot2,yddot2)
   
   !  X3 = X1+dt/2*V2 ; V3 = V1+dt/2*A2; A3=A(X3)
@@ -1680,10 +1688,10 @@ subroutine evolve_icebergs(bergs)
    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3 (deg)=',dt*v1,dt*v2,dt*v3
    write(stderrunit,*) 'Acceleration terms for position 1'
    error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axe1, aye1, debug_flag=.true.) !axe1, aye1 - Added by Alon
+   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axe1, aye1, Ranga_not_verlet, debug_flag=.true.) !axe1, aye1, Ranga_not_verlet- Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 2'
    error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
-   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axe2, aye2, debug_flag=.true.) !axe2, aye2 - Added by Alon
+   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axe2, aye2, Ranga_not_verlet, debug_flag=.true.) !axe2, aye2, Ranga_not_verlet   - Added by Alon
     call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 3')
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos3 i,j,lon,lat,xi,yj=',i,j,lon3,lat3,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos3 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
@@ -1692,7 +1700,7 @@ subroutine evolve_icebergs(bergs)
   endif
   dxdl3=r180_pi/(Rearth*cos(lat3*pi_180))
   u3=uvel3*dxdl3; v3=vvel3*dydl
-  call accel(bergs, berg, i, j, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axe3, aye3) !axe3, aye3 - Added by Alon
+  call accel(bergs, berg, i, j, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axe3, aye3, Ranga_not_verlet) !axe3, aye3, Ranga_not_verlet   - Added by Alon
   if (on_tangential_plane) call rotvec_to_tang(lon3,ax3,ay3,xddot3,yddot3)
   
   !  X4 = X1+dt*V3 ; V4 = V1+dt*A3; A4=A(X4)
@@ -1734,13 +1742,13 @@ subroutine evolve_icebergs(bergs)
    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v4 (deg)=',dt*v1,dt*v2,dt*v3,dt*v4
    write(stderrunit,*) 'Acceleration terms for position 1'
    error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axe1, aye1, debug_flag=.true.) !axe1, aye1 - Added by Alon
+   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axe1, aye1, Ranga_not_verlet, debug_flag=.true.) !axe1, aye1, Ranga_not_verlet   - Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 2'
    error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
-   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axe2, aye2, debug_flag=.true.) !axe2, aye2 - Added by Alon
+   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axe2, aye2, Ranga_not_verlet, debug_flag=.true.) !axe2, aye2, Ranga_not_verlet    - Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 3'
    error_flag=pos_within_cell(grd, lon3, lat3, i3, j3, xi, yj)
-   call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axe3, aye3, debug_flag=.true.) !axe3, aye3 - Added by Alon
+   call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axe3, aye3, Ranga_not_verlet, debug_flag=.true.) !axe3, aye3, Ranga_not_verlet - Added by Alon
     call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 4')
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos4 i,j,lon,lat,xi,yj=',i,j,lon4,lat4,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos4 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
@@ -1749,7 +1757,7 @@ subroutine evolve_icebergs(bergs)
   endif
   dxdl4=r180_pi/(Rearth*cos(lat4*pi_180))
   u4=uvel4*dxdl4; v4=vvel4*dydl
-  call accel(bergs, berg, i, j, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axe4, aye4) !axe4, aye4 - Added by Alon
+  call accel(bergs, berg, i, j, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axe4, aye4, Ranga_not_verlet) !axe4, aye4, Ranga_not_verlet - Added by Alon
   if (on_tangential_plane) call rotvec_to_tang(lon4,ax4,ay4,xddot4,yddot4)
   
   !  Xn = X1+dt*(V1+2*V2+2*V3+V4)/6
@@ -1803,16 +1811,16 @@ subroutine evolve_icebergs(bergs)
    write(stderrunit,*) 'diamonds, evolve_iceberg: on_tangential_plane=',on_tangential_plane
    write(stderrunit,*) 'Acceleration terms for position 1'
    error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axe1, aye1, debug_flag=.true.)  !axe1, aye1 - Added by Alon
+   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axe1, aye1, Ranga_not_verlet, debug_flag=.true.)  !axe1, aye1, Ranga_not_verlet   - Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 2'
    error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
-   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axe2, aye2, debug_flag=.true.)  !axe2, aye2 - Added by Alon
+   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axe2, aye2, Ranga_not_verlet, debug_flag=.true.)  !axe2, aye2, Ranga_not_verlet  - Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 3'
    error_flag=pos_within_cell(grd, lon3, lat3, i3, j3, xi, yj)
-   call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axe3, aye3, debug_flag=.true.)  !axe3, aye3 - Added by Alon
+   call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axe3, aye3, Ranga_not_verlet, debug_flag=.true.)  !axe3, aye3, Ranga_not_verlet   - Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 4'
    error_flag=pos_within_cell(grd, lon4, lat4, i4, j4, xi, yj)
-   call accel(bergs, berg, i4, j4, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axe4, aye4, debug_flag=.true.)  !axe4, aye4 - Added by Alon
+   call accel(bergs, berg, i4, j4, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axe4, aye4, Ranga_not_verlet, debug_flag=.true.)  !axe4, aye4, Ranga_not_verlet    - Added by Alon
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'posn i,j,lon,lat,xi,yj=',i,j,lonn,latn,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'posn box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
     call print_berg(stderrunit, berg, 'evolve_iceberg, out of cell at end!')

From a3a1bc001fc6c9769b74e43fc13d95490b6e33c3 Mon Sep 17 00:00:00 2001
From: Alon Stern <Alon.Stern@gaea3.ncrc.gov>
Date: Mon, 1 Jun 2015 17:35:55 -0400
Subject: [PATCH 009/361] Added in Velocity Verlet time stepping option into
 the evolve routine. It is not quite working yet, as I have not saved the
 implicit and explicit accelerations from the previous step yet. This will
 involve editing many subroutines. This commit only has changes to evolve and
 accel

---
 icebergs.F90 | 118 ++++++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 117 insertions(+), 1 deletion(-)

diff --git a/icebergs.F90 b/icebergs.F90
index d40b05f..8add4b2 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1505,11 +1505,13 @@ subroutine evolve_icebergs(bergs)
 real :: uvel3, vvel3, lon3, lat3, u3, v3, dxdl3, ax3, ay3, axe3, aye3 !axe3 and aye3 added by Alon
 real :: uvel4, vvel4, lon4, lat4, u4, v4, dxdl4, ax4, ay4, axe4, aye4 !axe4 and aye4 added by Alon
 real :: uveln, vveln, lonn, latn
-real :: x1, xdot1, xddot1, y1, ydot1, yddot1
+real :: x1, xdot1, xddot1, y1, ydot1, yddot1 
 real :: x2, xdot2, xddot2, y2, ydot2, yddot2
 real :: x3, xdot3, xddot3, y3, ydot3, yddot3
 real :: x4, xdot4, xddot4, y4, ydot4, yddot4
 real :: xn, xdotn, yn, ydotn
+real :: bxddot, byddot                                               ! Added by Alon
+real :: axn, ayn, bxn, byn                                           ! Added by Alon - explicit and implicit accelations from the previous step
 real :: r180_pi, dt, dt_2, dt_6, dydl, Rearth
 integer :: i, j
 integer :: i1,j1,i2,j2,i3,j3,i4,j4
@@ -1838,6 +1840,120 @@ subroutine evolve_icebergs(bergs)
  
   endif ! End of the Range Katta Loop -added by Alon  
 
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+  if (.not.Ranga_not_verlet) then !Start of the Verlet time_stepping -Whole loop added by Alon
+
+ ! In this scheme a_n and b_n are saved from the previous timestep, giving the explicit and implicit parts of the acceleration, and a_np1, b_np1 are for the next time step
+ ! Note that ax1=a_np1/2 +b_np1, as calculated by the acceleration subrouting
+ ! Positions and velocity is updated by
+ ! X2 = X1+dt*V1+((dt^2)/2)*a_n +((dt^2)/2)*b_n = X1+dt*u_star +((dt^2)/2)*b_n 
+ ! V2 = V1+dt/2*a_n +dt/2*a_np1 +dt*b_n = u_star + dt/2*a_np1 + dt*b_np1 = u_star +dt*ax
+
+lon1=berg%lon; lat1=berg%lat
+  if (on_tangential_plane) call rotpos_to_tang(lon1,lat1,x1,y1)
+  dxdl1=r180_pi/(Rearth*cos(lat1*pi_180))
+  dydl=r180_pi/Rearth
+  uvel1=berg%uvel; vvel1=berg%vvel
+
+!Temporary, remember to remove!!!!
+axn=0.0
+ayn=0.0
+bxn=0.0
+byn=0.0
+
+
+! Turn the velocities into u_star, v_star. - Alon (not sure how this works with tangent plane)
+  uvel1=uvel1+dt_2*axn                                              !Alon
+  vvel1=vvel1+dt_2*ayn                                              !Alon
+
+if (on_tangential_plane) call rotvec_to_tang(lon1,uvel1,vvel1,xdot1,ydot1)
+  u1=uvel1*dxdl1; v1=vvel1*dydl
+
+  if (on_tangential_plane) call rotvec_to_tang(lon1,bxn,byn,bxddot,byddot)    !Added by Alon  -rotation of implicit velocity.
+
+!Solving for new position
+  if (on_tangential_plane) then
+    xn=x1+dt_2*xdot1+(dt*dt*(bxddot)/2) ; yn=y1+dt_2*ydot1+(dt*dt*(byddot/2))             !Alon
+    call rotpos_from_tang(xn,yn,lonn,latn)
+  else
+    lonn=lon1+dt_2*u1+(dt*dt*(bxn)/2) ; latn=lat1+dt_2*v1+(dt*dt*(byn/2))  !Alon
+    uvel2=uvel1+dt*ax1; vvel2=vvel1+dt*ay1    !Alon , we call it uvel2, vvel2 until it is put into lat/long co-ordinates, where it becomes uveln, vveln
+  endif
+  dxdl2=r180_pi/(Rearth*cos(latn*pi_180))
+
+
+!Solving for the new velocity
+  call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axe1, aye1, Ranga_not_verlet) !axe1, aye1 ,Ranga_not_verlet  - Added by Alon
+  if (on_tangential_plane) call rotvec_to_tang(lon1,ax1,ay1,xddot1,yddot1)
+  if (on_tangential_plane) then
+    xdotn=xdot1+dt*xddot1; ydotn=ydot1+dt*yddot1                                    !Alon
+    call rotvec_from_tang(lonn,xdotn,ydotn,uveln,vveln)
+  else
+    uvel2=uvel1+dt*ax1; vvel2=vvel1+dt*ay1    !Alon , we call it uvel2, vvel2 until it is put into lat/long co-ordinates, where it becomes uveln, vveln
+  endif
+  uveln=uvel2*dxdl2; vveln=vvel2*dydl    !Converted to degrees.
+
+!Adjusting mass...
+  i=i1;j=j1;xi=berg%xi;yj=berg%yj
+  call adjust_index_and_ground(grd, lonn, latn, uveln, vveln, i, j, xi, yj, bounced, error_flag)
+  i2=i; j2=j
+  if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
+    call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling)
+
+!Debugging
+  if (.not.error_flag) then
+    if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j)) error_flag=.true.
+  endif
+  if (error_flag) then
+   call print_fld(grd, grd%msk, 'msk')
+   call print_fld(grd, grd%ssh, 'ssh')
+   call print_fld(grd, grd%sst, 'sst')
+   call print_fld(grd, grd%hi, 'hi')
+   write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
+   write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
+   write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: i1,i2,i=',i1,i2,i
+   write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: j1,j2,j=',j1,j2,j
+   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lon1,lonn=',lon1,lonn,berg%lon
+   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lat1,latn=',lat1,latn,berg%lat
+   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u1,un,u0=',uvel1,uveln,berg%uvel
+   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v1,vn,v0=',vvel1,vveln,berg%vvel
+   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1=',&
+        & dt*ax1
+   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ay1=',&
+        & dt*ay1
+   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,un,u0=',&
+        & dt*uvel1,dt*uvel2,dt*berg%uvel
+   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,vn,v0=',&
+        & dt*vvel1,dt*vvel2,dt*berg%vvel
+   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u_n (deg)=',&
+        & dt*u1,dt*uveln
+   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v_n (deg)=',&
+        & dt*v1,dt*vveln
+   write(stderrunit,*) 'diamonds, evolve_iceberg: on_tangential_plane=',on_tangential_plane
+   write(stderrunit,*) 'Acceleration terms for position 1'
+   error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
+   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axe1, aye1, Ranga_not_verlet, debug_flag=.true.)  !axe1, aye1, Ranga_not_verlet   - Added by Alon
+   
+    write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'posn i,j,lon,lat,xi,yj=',i,j,lonn,latn,xi,yj
+    write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'posn box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
+    call print_berg(stderrunit, berg, 'evolve_iceberg, out of cell at end!')
+    bounced=is_point_in_cell(bergs%grd, lonn, latn, i, j, explain=.true.)
+    if (debug) call error_mesg('diamonds, evolve_iceberg','berg is out of posn at end!',FATAL)
+    write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lon',(i,i=grd%isd,grd%ied)
+    do j=grd%jed,grd%jsd,-1
+      write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lon(i,j),i=grd%isd,grd%ied)
+    enddo
+    write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lat',(i,i=grd%isd,grd%ied)
+    do j=grd%jed,grd%jsd,-1
+      write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lat(i,j),i=grd%isd,grd%ied)
+    enddo
+  endif
+
+
+
+  endif ! End of the Verlet Stepiing -added by Alon  
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
   berg%lon=lonn
   berg%lat=latn

From cc107b35913b833cdd0582f5e019b903570675e2 Mon Sep 17 00:00:00 2001
From: Alon Stern <Alon.Stern@c1-batch2.ncrc.gov>
Date: Tue, 2 Jun 2015 13:48:15 -0400
Subject: [PATCH 010/361] Add explicit and implicit accelerations (axn, ayn,
 bxn, byn) to the iceberg type. This will be used for the Verlet stepping
 scheme. The Runge-Kutta scheme is working and this change does not change the
 answers. The Verlet scheme is not working yet.

---
 icebergs.F90           | 88 +++++++++++++++++++++++------------------
 icebergs_framework.F90 | 72 ++++++++++++++++++++++++++--------
 icebergs_io.F90        | 89 +++++++++++++++++++++++++++++++++++++++++-
 3 files changed, 193 insertions(+), 56 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 8add4b2..b1e528e 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -112,15 +112,15 @@ subroutine icebergs_init(bergs, &
 
 end subroutine icebergs_init
 
-subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, axn, ayn, Ranga_not_verlet, debug_flag) !Saving exp acceleration for Verlet, Adding Verlet flag - Alon
+subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, axn, ayn, bxn, byn, Runge_not_verlet, debug_flag) !Saving  acceleration for Verlet, Adding Verlet flag - Alon
 !subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, debug_flag) !old version commmented out by Alon
 ! Arguments
 type(icebergs), pointer :: bergs
 type(iceberg), pointer :: berg
 integer, intent(in) :: i, j
 real, intent(in) :: xi, yj, lat, uvel, vvel, uvel0, vvel0, dt
-!real, intent(inout) :: ax, ay  !old version - Alon
-real, intent(inout) :: ax, ay, axn, ayn ! Added explicit accelerations to output -Alon
+real, intent(inout) :: ax, ay
+real, intent(inout) :: axn, ayn, bxn, byn ! Added implicit and explicit accelerations to output -Alon
 logical, optional :: debug_flag
 ! Local variables
 type(icebergs_gridded), pointer :: grd
@@ -133,7 +133,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 real :: lambda, detA, A11, A12, axe, aye, D_hi 
 real :: uveln, vveln, us, vs, speed, loc_dx, new_speed
 logical :: dumpit
-logical, intent(in) :: Ranga_not_verlet  ! Flag to specify whether it is Range Katta or Verlet
+logical, intent(in) :: Runge_not_verlet  ! Flag to specify whether it is Runge-Kutta or Verlet
 integer :: itloop
 integer :: stderrunit
 
@@ -156,6 +156,12 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
   W=berg%width
   L=berg%length
 
+!Initializing accelerations - Alon. (I am not 100% sure this is needed). I'm not sure what is output if variable is not defined in the subroutine.
+  axn=0.
+  ayn=0.
+  bxn=0.
+  byn=0.
+
   hi=min(hi,D)
   D_hi=max(0.,D-hi)
 
@@ -207,7 +213,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
     axe=-gravity*ssh_x +wave_rad*uwave
     aye=-gravity*ssh_y +wave_rad*vwave
 
-    if (.not.Ranga_not_verlet) then  ! When using Verlet, use only half the explicit acceleration,  Added by Alon
+    if (.not.Runge_not_verlet) then  ! When using Verlet, use only half the explicit acceleration,  Added by Alon
        axe=axe/2  
        aye=aye/2  
     endif 
@@ -247,7 +253,8 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 !Saving the totally explicit part of the acceleration to use in finding the next position and u_star -Alon
     axn=-gravity*ssh_x +wave_rad*uwave !Alon
     ayn=-gravity*ssh_y +wave_rad*vwave !Alon
-
+    bxn= ax-(axn/2) !Alon
+    byn= ay-(ayn/2) !Alon
 
 
  
@@ -1454,6 +1461,10 @@ subroutine calve_icebergs(bergs)
           newberg%yj=yj
           newberg%uvel=0.
           newberg%vvel=0.
+          newberg%axn=0. !Added by Alon
+          newberg%ayn=0. !Added by Alon
+          newberg%bxn=0. !Added by Alon
+          newberg%byn=0. !Added by Alon
           newberg%mass=bergs%initial_mass(k)
           newberg%thickness=bergs%initial_thickness(k)
           newberg%width=bergs%initial_width(k)
@@ -1500,11 +1511,11 @@ subroutine evolve_icebergs(bergs)
 type(icebergs), pointer :: bergs
 ! Local variables
 type(icebergs_gridded), pointer :: grd
-real :: uvel1, vvel1, lon1, lat1, u1, v1, dxdl1, ax1, ay1, axe1, aye1 !axe1 and aye1 added by Alon 
-real :: uvel2, vvel2, lon2, lat2, u2, v2, dxdl2, ax2, ay2, axe2, aye2 !axe2 and aye2 added by Alon 
-real :: uvel3, vvel3, lon3, lat3, u3, v3, dxdl3, ax3, ay3, axe3, aye3 !axe3 and aye3 added by Alon
-real :: uvel4, vvel4, lon4, lat4, u4, v4, dxdl4, ax4, ay4, axe4, aye4 !axe4 and aye4 added by Alon
-real :: uveln, vveln, lonn, latn
+real :: uvel1, vvel1, lon1, lat1, u1, v1, dxdl1, ax1, ay1 
+real :: uvel2, vvel2, lon2, lat2, u2, v2, dxdl2, ax2, ay2 
+real :: uvel3, vvel3, lon3, lat3, u3, v3, dxdl3, ax3, ay3
+real :: uvel4, vvel4, lon4, lat4, u4, v4, dxdl4, ax4, ay4
+real :: uveln, vveln, lonn, latn, un, vn, dxdln
 real :: x1, xdot1, xddot1, y1, ydot1, yddot1 
 real :: x2, xdot2, xddot2, y2, ydot2, yddot2
 real :: x3, xdot3, xddot3, y3, ydot3, yddot3
@@ -1517,7 +1528,7 @@ subroutine evolve_icebergs(bergs)
 integer :: i1,j1,i2,j2,i3,j3,i4,j4
 real :: xi, yj
 logical :: bounced, on_tangential_plane, error_flag
-logical :: Ranga_not_verlet  ! Ranga_not_verlet=1 for Range Katta, =0 for Verlet method. Added by Alon
+logical :: Runge_not_verlet  ! Runge_not_verlet=1 for Runge Kutta, =0 for Verlet method. Added by Alon
 type(iceberg), pointer :: berg
 integer :: stderrunit
 
@@ -1548,7 +1559,7 @@ subroutine evolve_icebergs(bergs)
   Rearth=6360.e3
 
   !Choosing time stepping scheme - Alon
-   Ranga_not_verlet=.true.    !true=Ranga Katta, False=Verlet   , Alon
+   Runge_not_verlet=.true.    !true=Runge Kutta, False=Verlet   , Alon
 
 
   berg=>bergs%first
@@ -1583,7 +1594,7 @@ subroutine evolve_icebergs(bergs)
   if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
     call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling)
 
-  if (Ranga_not_verlet) then !Start of the Range Katta Loop -Added by Alon
+  if (Runge_not_verlet) then !Start of the Runge-Kutta Loop -Added by Alon
 
  ! A1 = A(X1)
   lon1=berg%lon; lat1=berg%lat
@@ -1593,7 +1604,7 @@ subroutine evolve_icebergs(bergs)
   uvel1=berg%uvel; vvel1=berg%vvel
   if (on_tangential_plane) call rotvec_to_tang(lon1,uvel1,vvel1,xdot1,ydot1)
   u1=uvel1*dxdl1; v1=vvel1*dydl
-  call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axe1, aye1, Ranga_not_verlet) !axe1, aye1 ,Ranga_not_verlet  - Added by Alon
+  call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, Runge_not_verlet) !axn,ayn, bxn, byn ,Runge_not_verlet  - Added by Alon
   if (on_tangential_plane) call rotvec_to_tang(lon1,ax1,ay1,xddot1,yddot1)
   
   !  X2 = X1+dt/2*V1 ; V2 = V1+dt/2*A1; A2=A(X2)
@@ -1637,7 +1648,7 @@ subroutine evolve_icebergs(bergs)
    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2 (deg)=',dt*v1,dt*v2
    write(stderrunit,*) 'Acceleration terms for position 1'
    error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axe1, aye1, Ranga_not_verlet, debug_flag=.true.) !axe1, aye1, Ranga_not_verlet - Added by Alon
+   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, Runge_not_verlet, debug_flag=.true.) !axn, ayn, bxn, byn, Runge_not_verlet - Added by Alon
     call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 2')
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos2 i,j,lon,lat,xi,yj=',i,j,lon2,lat2,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos2 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
@@ -1646,7 +1657,7 @@ subroutine evolve_icebergs(bergs)
   endif
   dxdl2=r180_pi/(Rearth*cos(lat2*pi_180))
   u2=uvel2*dxdl2; v2=vvel2*dydl
-  call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axe2, aye2, Ranga_not_verlet) !axe2, aye2, Ranga_not_verlet - Added by Alon
+  call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn, ayn, bxn, byn, Runge_not_verlet) !axn, ayn, bxn, byn, Runge_not_verlet - Added by Alon
   if (on_tangential_plane) call rotvec_to_tang(lon2,ax2,ay2,xddot2,yddot2)
   
   !  X3 = X1+dt/2*V2 ; V3 = V1+dt/2*A2; A3=A(X3)
@@ -1690,10 +1701,10 @@ subroutine evolve_icebergs(bergs)
    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3 (deg)=',dt*v1,dt*v2,dt*v3
    write(stderrunit,*) 'Acceleration terms for position 1'
    error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axe1, aye1, Ranga_not_verlet, debug_flag=.true.) !axe1, aye1, Ranga_not_verlet- Added by Alon
+   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, Runge_not_verlet, debug_flag=.true.) !ax, aye1, Runge_not_verlet- Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 2'
    error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
-   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axe2, aye2, Ranga_not_verlet, debug_flag=.true.) !axe2, aye2, Ranga_not_verlet   - Added by Alon
+   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn, ayn, bxn, byn, Runge_not_verlet, debug_flag=.true.) !axn, ayn, bxn, byn, Runge_not_verlet   - Added by Alon
     call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 3')
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos3 i,j,lon,lat,xi,yj=',i,j,lon3,lat3,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos3 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
@@ -1702,7 +1713,7 @@ subroutine evolve_icebergs(bergs)
   endif
   dxdl3=r180_pi/(Rearth*cos(lat3*pi_180))
   u3=uvel3*dxdl3; v3=vvel3*dydl
-  call accel(bergs, berg, i, j, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axe3, aye3, Ranga_not_verlet) !axe3, aye3, Ranga_not_verlet   - Added by Alon
+  call accel(bergs, berg, i, j, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn, ayn, bxn, byn, Runge_not_verlet) !axn, ayn, bxn, byn, Runge_not_verlet   - Added by Alon
   if (on_tangential_plane) call rotvec_to_tang(lon3,ax3,ay3,xddot3,yddot3)
   
   !  X4 = X1+dt*V3 ; V4 = V1+dt*A3; A4=A(X4)
@@ -1744,13 +1755,13 @@ subroutine evolve_icebergs(bergs)
    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v4 (deg)=',dt*v1,dt*v2,dt*v3,dt*v4
    write(stderrunit,*) 'Acceleration terms for position 1'
    error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axe1, aye1, Ranga_not_verlet, debug_flag=.true.) !axe1, aye1, Ranga_not_verlet   - Added by Alon
+   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, Runge_not_verlet, debug_flag=.true.) !axn, ayn, bxn, byn, Runge_not_verlet   - Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 2'
    error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
-   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axe2, aye2, Ranga_not_verlet, debug_flag=.true.) !axe2, aye2, Ranga_not_verlet    - Added by Alon
+   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn, ayn, bxn, byn, Runge_not_verlet, debug_flag=.true.) !axn, ayn, bxn, byn, Runge_not_verlet    - Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 3'
    error_flag=pos_within_cell(grd, lon3, lat3, i3, j3, xi, yj)
-   call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axe3, aye3, Ranga_not_verlet, debug_flag=.true.) !axe3, aye3, Ranga_not_verlet - Added by Alon
+   call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn, ayn, bxn, byn, Runge_not_verlet, debug_flag=.true.) !axn, ayn, bxn, byn, Runge_not_verlet - Added by Alon
     call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 4')
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos4 i,j,lon,lat,xi,yj=',i,j,lon4,lat4,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos4 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
@@ -1759,7 +1770,7 @@ subroutine evolve_icebergs(bergs)
   endif
   dxdl4=r180_pi/(Rearth*cos(lat4*pi_180))
   u4=uvel4*dxdl4; v4=vvel4*dydl
-  call accel(bergs, berg, i, j, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axe4, aye4, Ranga_not_verlet) !axe4, aye4, Ranga_not_verlet - Added by Alon
+  call accel(bergs, berg, i, j, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axn, ayn, bxn, byn, Runge_not_verlet) !axn, ayn, bxn, byn, Runge_not_verlet - Added by Alon
   if (on_tangential_plane) call rotvec_to_tang(lon4,ax4,ay4,xddot4,yddot4)
   
   !  Xn = X1+dt*(V1+2*V2+2*V3+V4)/6
@@ -1813,16 +1824,16 @@ subroutine evolve_icebergs(bergs)
    write(stderrunit,*) 'diamonds, evolve_iceberg: on_tangential_plane=',on_tangential_plane
    write(stderrunit,*) 'Acceleration terms for position 1'
    error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axe1, aye1, Ranga_not_verlet, debug_flag=.true.)  !axe1, aye1, Ranga_not_verlet   - Added by Alon
+   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, Runge_not_verlet, debug_flag=.true.)  !axn, ayn, Runge_not_verlet   - Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 2'
    error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
-   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axe2, aye2, Ranga_not_verlet, debug_flag=.true.)  !axe2, aye2, Ranga_not_verlet  - Added by Alon
+   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn, ayn, bxn, byn, Runge_not_verlet, debug_flag=.true.)  !axn, ayn, Runge_not_verlet  - Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 3'
    error_flag=pos_within_cell(grd, lon3, lat3, i3, j3, xi, yj)
-   call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axe3, aye3, Ranga_not_verlet, debug_flag=.true.)  !axe3, aye3, Ranga_not_verlet   - Added by Alon
+   call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn, ayn, bxn, byn, Runge_not_verlet, debug_flag=.true.)  !axn, ayn, Runge_not_verlet   - Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 4'
    error_flag=pos_within_cell(grd, lon4, lat4, i4, j4, xi, yj)
-   call accel(bergs, berg, i4, j4, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axe4, aye4, Ranga_not_verlet, debug_flag=.true.)  !axe4, aye4, Ranga_not_verlet    - Added by Alon
+   call accel(bergs, berg, i4, j4, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axn, ayn, bxn, byn, Runge_not_verlet, debug_flag=.true.)  !axn, ayn, Runge_not_verlet    - Added by Alon
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'posn i,j,lon,lat,xi,yj=',i,j,lonn,latn,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'posn box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
     call print_berg(stderrunit, berg, 'evolve_iceberg, out of cell at end!')
@@ -1838,11 +1849,11 @@ subroutine evolve_icebergs(bergs)
     enddo
   endif
  
-  endif ! End of the Range Katta Loop -added by Alon  
+  endif ! End of the Runge-Kutta Loop -added by Alon  
 
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
-  if (.not.Ranga_not_verlet) then !Start of the Verlet time_stepping -Whole loop added by Alon
+  if (.not.Runge_not_verlet) then !Start of the Verlet time_stepping -Whole loop added by Alon
 
  ! In this scheme a_n and b_n are saved from the previous timestep, giving the explicit and implicit parts of the acceleration, and a_np1, b_np1 are for the next time step
  ! Note that ax1=a_np1/2 +b_np1, as calculated by the acceleration subrouting
@@ -1856,12 +1867,9 @@ subroutine evolve_icebergs(bergs)
   dydl=r180_pi/Rearth
   uvel1=berg%uvel; vvel1=berg%vvel
 
-!Temporary, remember to remove!!!!
-axn=0.0
-ayn=0.0
-bxn=0.0
-byn=0.0
-
+!Loading past acceleartions - Alon
+  axn=berg%axn; ayn=berg%ayn !Alon
+  byn=berg%bxn; byn=berg%byn !Alon
 
 ! Turn the velocities into u_star, v_star. - Alon (not sure how this works with tangent plane)
   uvel1=uvel1+dt_2*axn                                              !Alon
@@ -1884,7 +1892,7 @@ subroutine evolve_icebergs(bergs)
 
 
 !Solving for the new velocity
-  call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axe1, aye1, Ranga_not_verlet) !axe1, aye1 ,Ranga_not_verlet  - Added by Alon
+  call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, Runge_not_verlet) !axn, ayn, bxn, byn ,Runge_not_verlet  - Added by Alon
   if (on_tangential_plane) call rotvec_to_tang(lon1,ax1,ay1,xddot1,yddot1)
   if (on_tangential_plane) then
     xdotn=xdot1+dt*xddot1; ydotn=ydot1+dt*yddot1                                    !Alon
@@ -1933,7 +1941,7 @@ subroutine evolve_icebergs(bergs)
    write(stderrunit,*) 'diamonds, evolve_iceberg: on_tangential_plane=',on_tangential_plane
    write(stderrunit,*) 'Acceleration terms for position 1'
    error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axe1, aye1, Ranga_not_verlet, debug_flag=.true.)  !axe1, aye1, Ranga_not_verlet   - Added by Alon
+   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, Runge_not_verlet, debug_flag=.true.)  !axn, ayn, bxn, byn, Runge_not_verlet   - Added by Alon
    
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'posn i,j,lon,lat,xi,yj=',i,j,lonn,latn,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'posn box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
@@ -1959,6 +1967,10 @@ subroutine evolve_icebergs(bergs)
   berg%lat=latn
   berg%uvel=uveln
   berg%vvel=vveln
+  berg%axn=axn !Alon
+  berg%ayn=ayn !Alon
+  berg%bxn=bxn !Alon
+  berg%byn=byn !Alon
   berg%ine=i
   berg%jne=j
   berg%xi=xi
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 48dfe14..ecc3efd 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -15,8 +15,8 @@ module ice_bergs_framework
 
 implicit none ; private
 
-integer, parameter :: buffer_width=20
-integer, parameter :: buffer_width_traj=23
+integer, parameter :: buffer_width=24 !Changed from 20 to 24 by Alon 
+integer, parameter :: buffer_width_traj=27  !Changed from 23 by Alon
 integer, parameter :: nclasses=10 ! Number of ice bergs classes
 
 !Local Vars
@@ -129,6 +129,7 @@ module ice_bergs_framework
 type :: xyt
   real :: lon, lat, day
   real :: mass, thickness, width, length, uvel, vvel
+  real :: axn, ayn, bxn, byn  !Explicit and implicit accelerations !Alon 
   real :: uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, cn, hi
   real :: mass_of_bits, heat_density
   integer :: year
@@ -139,6 +140,7 @@ module ice_bergs_framework
   type(iceberg), pointer :: prev=>null(), next=>null()
   ! State variables (specific to the iceberg, needed for restarts)
   real :: lon, lat, uvel, vvel, mass, thickness, width, length
+  real :: axn, ayn, bxn, byn  !Explicit and implicit accelerations !Alon 
   real :: start_lon, start_lat, start_day, start_mass, mass_scaling
   real :: mass_of_bits, heat_density
   integer :: start_year
@@ -932,6 +934,10 @@ subroutine pack_berg_into_buffer2(berg, buff, n)
     buff%data(18,n)=berg%heat_density
     buff%data(19,n)=berg%ine
     buff%data(20,n)=berg%jne
+    buff%data(21,n)=berg%axn  !Alon
+    buff%data(22,n)=berg%ayn  !Alon
+    buff%data(23,n)=berg%bxn  !Alon
+    buff%data(24,n)=berg%byn  !Alon
 
   end subroutine pack_berg_into_buffer2
 
@@ -970,6 +976,7 @@ subroutine unpack_berg_from_buffer2(first, buff, n,grd, force_append)
   logical, optional :: force_append
  ! Local variables
  !real :: lon, lat, uvel, vvel, xi, yj
+
  !real :: start_lon, start_lat, start_day, start_mass
  !integer :: ine, jne, start_year
   logical :: lres
@@ -1006,7 +1013,12 @@ subroutine unpack_berg_from_buffer2(first, buff, n,grd, force_append)
        call add_new_berg_to_list(first, localberg) 
     else
        
-    lres=find_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
+    localberg%axn=buff%data(21,n) !Alon
+    localberg%ayn=buff%data(22,n) !Alon
+    localberg%bxn=buff%data(23,n) !Alon
+    localberg%byn=buff%data(24,n) !Alon
+   
+     lres=find_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
     if (lres) then
       lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
       call add_new_berg_to_list(first, localberg)
@@ -1020,6 +1032,8 @@ subroutine unpack_berg_from_buffer2(first, buff, n,grd, force_append)
              & mpp_pe(),') Failed to find i,j=',localberg%ine,localberg%jne,' for lon,lat=',localberg%lon,localberg%lat
         write(stderrunit,*) localberg%lon,localberg%lat
         write(stderrunit,*) localberg%uvel,localberg%vvel
+        write(stderrunit,*) localberg%axn,localberg%ayn !Alon
+        write(stderrunit,*) localberg%bxn,localberg%byn !Alon
         write(stderrunit,*) grd%isc,grd%iec,grd%jsc,grd%jec
         write(stderrunit,*) grd%isd,grd%ied,grd%jsd,grd%jed
         write(stderrunit,*) grd%lon(grd%isc-1,grd%jsc-1),grd%lon(grd%iec,grd%jsc)
@@ -1163,6 +1177,10 @@ subroutine pack_traj_into_buffer2(traj, buff, n)
     buff%data(21,n)=traj%sst
     buff%data(22,n)=traj%cn
     buff%data(23,n)=traj%hi
+    buff%data(24,n)=traj%axn !Alon
+    buff%data(25,n)=traj%ayn !Alon
+    buff%data(26,n)=traj%bxn !Alon
+    buff%data(27,n)=traj%byn !Alon
 
   end subroutine pack_traj_into_buffer2
 
@@ -1200,6 +1218,10 @@ subroutine unpack_traj_from_buffer2(first, buff, n)
     traj%sst=buff%data(21,n)
     traj%cn=buff%data(22,n)
     traj%hi=buff%data(23,n)
+    traj%axn=buff%data(24,n) !Alon
+    traj%ayn=buff%data(25,n) !Alon
+    traj%bxn=buff%data(26,n) !Alon
+    traj%byn=buff%data(27,n) !Alon
 
     call append_posn(first, traj) 
 
@@ -1448,6 +1470,10 @@ logical function sameberg(berg1, berg2)
   if (berg1%thickness.ne.berg2%thickness) return
   if (berg1%width.ne.berg2%width) return
   if (berg1%length.ne.berg2%length) return
+  if (berg1%axn.ne.berg2%axn) return  !Alon
+  if (berg1%ayn.ne.berg2%ayn) return  !Alon
+  if (berg1%bxn.ne.berg2%bxn) return  !Alon
+  if (berg1%byn.ne.berg2%byn) return  !Alon
   sameberg=.true. ! passing the above tests mean that bergs 1 and 2 are identical
 end function sameberg
 
@@ -1533,10 +1559,12 @@ subroutine print_berg(iochan, berg, label)
     ' xi,yj=', berg%xi, berg%yj, &
     ' lon,lat=', berg%lon, berg%lat, &
     ' u,v=', berg%uvel, berg%vvel, &
+    ' axn,ayn=', berg%axn, berg%ayn, &
+    ' bxn,byn=', berg%bxn, berg%byn, &
     ' p,n=', associated(berg%prev), associated(berg%next)
   write(iochan,'("diamonds, print_berg: ",a," pe=(",i3,") ",6(a,2f10.4))') &
     label, mpp_pe(), 'uo,vo=', berg%uo, berg%vo, 'ua,va=', berg%ua, berg%va, 'ui,vi=', berg%ui, berg%vi
-
+!Two lines above added by Alon
 end subroutine print_berg
 
 ! ##############################################################################
@@ -1613,6 +1641,10 @@ subroutine record_posn(bergs)
     posn%sst=this%sst
     posn%cn=this%cn
     posn%hi=this%hi
+    posn%axn=this%axn
+    posn%ayn=this%ayn
+    posn%bxn=this%bxn
+    posn%byn=this%byn
 
     call push_posn(this%trajectory, posn)
 
@@ -2619,8 +2651,8 @@ subroutine bergs_chksum(bergs, txt, ignore_halo_violation)
 
   nbergs=count_bergs(bergs)
   call mpp_max(nbergs)
-  allocate( fld( nbergs, 11 ) )
-  allocate( fld2( nbergs, 11 ) )
+  allocate( fld( nbergs, 15 ) ) !Changed from 11 to 15 by Alon
+  allocate( fld2( nbergs, 15 ) ) !Changed from 11 to 15 by Alon
   allocate( icnt( grd%isd:grd%ied, grd%jsd:grd%jed ) )
   fld(:,:)=0.
   fld2(:,:)=0.
@@ -2640,9 +2672,13 @@ subroutine bergs_chksum(bergs, txt, ignore_halo_violation)
     fld(i,6) = this%thickness
     fld(i,7) = this%width
     fld(i,8) = this%length
-    fld(i,9) = time_hash(this)
-    fld(i,10) = pos_hash(this)
-    fld(i,11) = float(iberg)
+    fld(i,9) = this%axn !added by Alon
+    fld(i,10) = this%ayn !added by Alon
+    fld(i,11) = this%bxn !added by Alon
+    fld(i,12) = this%byn !added by Alon
+    fld(i,13) = time_hash(this) !Changed from 9 to 13 by Alon
+    fld(i,14) = pos_hash(this) !Changed from 10 to 12 by Alon
+    fld(i,15) = float(iberg) !Changed from 11 to 15 by Alon
     icnt(this%ine,this%jne)=icnt(this%ine,this%jne)+1
     fld2(i,:) = fld(i,:)*float( icnt(this%ine,this%jne) ) !*float( i )
     grd%tmp(this%ine,this%jne)=grd%tmp(this%ine,this%jne)+time_hash(this)*pos_hash(this)+log(this%mass)
@@ -2695,8 +2731,8 @@ integer function berg_chksum(berg )
 ! Arguments
 type(iceberg), pointer :: berg
 ! Local variables
-real :: rtmp(28)
-integer :: itmp(28+3), i8=0, ichk1, ichk2, ichk3
+real :: rtmp(32) !Changed from 28 to 32 by Alon
+integer :: itmp(32+3), i8=0, ichk1, ichk2, ichk3 !Changed from 28 to 32 by Alon
 integer :: i
 
   rtmp(:)=0.
@@ -2727,14 +2763,18 @@ integer function berg_chksum(berg )
   rtmp(26)=berg%ssh_y
   rtmp(27)=berg%cn
   rtmp(28)=berg%hi
+  rtmp(29)=berg%axn !Added by Alon
+  rtmp(30)=berg%ayn !Added by Alon
+  rtmp(31)=berg%bxn !Added by Alon
+  rtmp(32)=berg%byn !Added by Alon
 
-  itmp(1:28)=transfer(rtmp,i8)
-  itmp(29)=berg%start_year
-  itmp(30)=berg%ine
-  itmp(31)=berg%jne
+  itmp(1:32)=transfer(rtmp,i8) !Changed from 28 to 32 by Alon
+  itmp(33)=berg%start_year !Changed from 29 to 33 by Alon
+  itmp(34)=berg%ine !Changed from 30 to 34 by Alon
+  itmp(35)=berg%jne !Changed from 31 to 35 by Alon
 
   ichk1=0; ichk2=0; ichk3=0
-  do i=1,28+3
+  do i=1,32+3 !Changd from 28 to 32 by Alon
    ichk1=ichk1+itmp(i)
    ichk2=ichk2+itmp(i)*i
    ichk3=ichk3+itmp(i)*i*i
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 154fca6..21bc0bd 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -103,6 +103,10 @@ subroutine write_restart(bergs)
                                    uvel,         &
                                    vvel,         &
                                    mass,         &
+                                   axn,          &
+                                   ayn,          &
+                                   bxn,          &
+                                   byn,          &
                                    thickness,    &
                                    width,        &
                                    length,       &
@@ -140,6 +144,10 @@ subroutine write_restart(bergs)
    allocate(uvel(nbergs))
    allocate(vvel(nbergs))
    allocate(mass(nbergs))
+   allocate(axn(nbergs))
+   allocate(ayn(nbergs))
+   allocate(bxn(nbergs))
+   allocate(byn(nbergs))
    allocate(thickness(nbergs))
    allocate(width(nbergs))
    allocate(length(nbergs))
@@ -170,6 +178,10 @@ subroutine write_restart(bergs)
   id = register_restart_field(bergs_restart,filename,'uvel',uvel,longname='zonal velocity',units='m/s')
   id = register_restart_field(bergs_restart,filename,'vvel',vvel,longname='meridional velocity',units='m/s')
   id = register_restart_field(bergs_restart,filename,'mass',mass,longname='mass',units='kg')
+  id = register_restart_field(bergs_restart,filename,'axn',mass,longname='explicit zonal acceleration',units='m/s^2') !Alon
+  id = register_restart_field(bergs_restart,filename,'ayn',mass,longname='explicit meridional acceleration',units='m/s^2') !Alon
+  id = register_restart_field(bergs_restart,filename,'bxn',mass,longname='inplicit zonal acceleration',units='m/s^2') !Alon
+  id = register_restart_field(bergs_restart,filename,'byn',mass,longname='implicit meridional acceleration',units='m/s^2') !Alon
   id = register_restart_field(bergs_restart,filename,'ine',ine,longname='i index',units='none')
   id = register_restart_field(bergs_restart,filename,'jne',jne,longname='j index',units='none')
   id = register_restart_field(bergs_restart,filename,'thickness',thickness,longname='thickness',units='m')
@@ -200,6 +212,8 @@ subroutine write_restart(bergs)
     uvel(i) = this%uvel; vvel(i) = this%vvel
     ine(i) = this%ine; jne(i) = this%jne
     mass(i) = this%mass; thickness(i) = this%thickness
+    axn(i) = this%axn; ayn(i) = this%ayn !Added by Alon
+    bxn(i) = this%bxn; byn(i) = this%byn !Added by Alon
     width(i) = this%width; length(i) = this%length
     start_lon(i) = this%start_lon; start_lat(i) = this%start_lat
     start_year(i) = this%start_year; start_day(i) = this%start_day
@@ -217,6 +231,10 @@ subroutine write_restart(bergs)
              uvel,         &
              vvel,         &
              mass,         &
+             axn,          &
+             ayn,          &
+             bxn,          &
+             byn,          &
              thickness,    &
              width,        &
              length,       &
@@ -227,6 +245,7 @@ subroutine write_restart(bergs)
              mass_scaling, &
              mass_of_bits, &
              heat_density )
+!axn, ayn, bxn, byn above added by Alon
 
   deallocate(           &
              ine,       &
@@ -270,6 +289,7 @@ subroutine read_restart_bergs_orig(bergs,Time)
 integer, dimension(:), allocatable :: found_restart_int
 integer :: k, ierr, ncid, dimid, nbergs_in_file
 integer :: lonid, latid, uvelid, vvelid, ineid, jneid
+integer :: axnid, aynid, bxnid, bynid !Added by Alon
 integer :: massid, thicknessid, widthid, lengthid
 integer :: start_lonid, start_latid, start_yearid, start_dayid, start_massid
 integer :: scaling_id, mass_of_bits_id, heat_density_id
@@ -332,6 +352,10 @@ subroutine read_restart_bergs_orig(bergs,Time)
   uvelid=inq_var(ncid, 'uvel')
   vvelid=inq_var(ncid, 'vvel')
   massid=inq_var(ncid, 'mass')
+  axnid=inq_var(ncid, 'axn') !Alon
+  aynid=inq_var(ncid, 'ayn') !Alon
+  bxnid=inq_var(ncid, 'bxn') !Alon
+  bynid=inq_var(ncid, 'byn') !Alon
   thicknessid=inq_var(ncid, 'thickness')
   widthid=inq_var(ncid, 'width')
   lengthid=inq_var(ncid, 'length')
@@ -381,6 +405,10 @@ subroutine read_restart_bergs_orig(bergs,Time)
       localberg%uvel=get_double(ncid, uvelid, k)
       localberg%vvel=get_double(ncid, vvelid, k)
       localberg%mass=get_double(ncid, massid, k)
+      localberg%axn=get_double(ncid, axnid, k) !Alon
+      localberg%ayn=get_double(ncid, aynid, k) !Alon
+      localberg%bxn=get_double(ncid, bxnid, k) !Alon
+      localberg%byn=get_double(ncid, bynid, k) !Alon
       localberg%thickness=get_double(ncid, thicknessid, k)
       localberg%width=get_double(ncid, widthid, k)
       localberg%length=get_double(ncid, lengthid, k)
@@ -478,15 +506,31 @@ subroutine generate_bergs(bergs,Time)
         localberg%heat_density=0.
         localberg%uvel=1.
         localberg%vvel=0.
+        localberg%axn=0. !Alon
+        localberg%ayn=0. !Alon
+        localberg%bxn=0. !Alon
+        localberg%byn=0. !Alon
         call add_new_berg_to_list(bergs%first, localberg)
         localberg%uvel=-1.
         localberg%vvel=0.
+        localberg%axn=0. !Alon
+        localberg%ayn=0. !Alon
+        localberg%bxn=0. !Alon
+        localberg%byn=0. !Alon
         call add_new_berg_to_list(bergs%first, localberg)
         localberg%uvel=0.
         localberg%vvel=1.
+        localberg%axn=0. !Alon
+        localberg%ayn=0. !Alon
+        localberg%bxn=0. !Alon
+        localberg%byn=0. !Alon
         call add_new_berg_to_list(bergs%first, localberg)
         localberg%uvel=0.
         localberg%vvel=-1.
+        localberg%axn=0. !Alon
+        localberg%ayn=0. !Alon
+        localberg%bxn=0. !Alon
+        localberg%byn=0. !Alon
         call add_new_berg_to_list(bergs%first, localberg)
       endif
     enddo; enddo
@@ -521,6 +565,10 @@ subroutine read_restart_bergs(bergs,Time)
                                    uvel,         &
                                    vvel,         &
                                    mass,         &
+                                   axn,          &
+                                   ayn,          &
+                                   bxn,          &
+                                   byn,          &
                                    thickness,    &
                                    width,        &
                                    length,       &
@@ -531,7 +579,7 @@ subroutine read_restart_bergs(bergs,Time)
                                    mass_scaling, &
                                    mass_of_bits, &
                                    heat_density
-
+!axn, ayn, bxn, byn added by Alon
 integer, allocatable, dimension(:) :: ine,       &
                                       jne,       &
                                       start_year
@@ -560,6 +608,10 @@ subroutine read_restart_bergs(bergs,Time)
      allocate(uvel(nbergs_in_file))
      allocate(vvel(nbergs_in_file))
      allocate(mass(nbergs_in_file))
+     allocate(axn(nbergs_in_file)) !Alon
+     allocate(ayn(nbergs_in_file)) !Alon
+     allocate(bxn(nbergs_in_file)) !Alon
+     allocate(byn(nbergs_in_file)) !Alon
      allocate(thickness(nbergs_in_file))
      allocate(width(nbergs_in_file))
      allocate(length(nbergs_in_file))
@@ -580,6 +632,10 @@ subroutine read_restart_bergs(bergs,Time)
      call read_unlimited_axis(filename,'uvel',uvel,domain=grd%domain)
      call read_unlimited_axis(filename,'vvel',vvel,domain=grd%domain)
      call read_unlimited_axis(filename,'mass',mass,domain=grd%domain)
+     call read_unlimited_axis(filename,'axn',axn,domain=grd%domain) !Alon
+     call read_unlimited_axis(filename,'ayn',ayn,domain=grd%domain) !Alon
+     call read_unlimited_axis(filename,'bxn',bxn,domain=grd%domain) !Alon
+     call read_unlimited_axis(filename,'byn',byn,domain=grd%domain) !Alon
      call read_unlimited_axis(filename,'thickness',thickness,domain=grd%domain)
      call read_unlimited_axis(filename,'width',width,domain=grd%domain)
      call read_unlimited_axis(filename,'length',length,domain=grd%domain)
@@ -628,6 +684,10 @@ subroutine read_restart_bergs(bergs,Time)
          localberg%uvel=uvel(k)
          localberg%vvel=vvel(k)
          localberg%mass=mass(k)
+         localberg%axn=axn(k) !Alon
+         localberg%ayn=ayn(k) !Alon
+         localberg%bxn=bxn(k) !Alon
+         localberg%byn=byn(k) !Alon
          localberg%thickness=thickness(k)
          localberg%width=width(k)
          localberg%length=length(k)
@@ -654,6 +714,10 @@ subroutine read_restart_bergs(bergs,Time)
                 uvel,         &
                 vvel,         &
                 mass,         &
+                axn,          &
+                ayn,          &
+                bxn,          &
+                byn,          &
                 thickness,    &
                 width,        &
                 length,       &
@@ -664,7 +728,7 @@ subroutine read_restart_bergs(bergs,Time)
                 mass_scaling, &
                 mass_of_bits, &
                 heat_density )
-
+!axn, ayn, bxn, byn above added by Alon.
      deallocate(           &
                 ine,       &
                 jne,       &
@@ -719,15 +783,31 @@ subroutine generate_bergs(bergs,Time)
         localberg%heat_density=0.
         localberg%uvel=1.
         localberg%vvel=0.
+        localberg%axn=0. !Alon
+        localberg%ayn=0. !Alon
+        localberg%bxn=0. !Alon
+        localberg%byn=0. !Alon
         call add_new_berg_to_list(bergs%first, localberg)
         localberg%uvel=-1.
         localberg%vvel=0.
+        localberg%axn=0. !Alon
+        localberg%ayn=0. !Alon
+        localberg%bxn=0. !Alon
+        localberg%byn=0. !Alon
         call add_new_berg_to_list(bergs%first, localberg)
         localberg%uvel=0.
         localberg%vvel=1.
+        localberg%axn=0. !Alon
+        localberg%ayn=0. !Alon
+        localberg%bxn=0. !Alon
+        localberg%byn=0. !Alon
         call add_new_berg_to_list(bergs%first, localberg)
         localberg%uvel=0.
         localberg%vvel=-1.
+        localberg%axn=0. !Alon
+        localberg%ayn=0. !Alon
+        localberg%bxn=0. !Alon
+        localberg%byn=0. !Alon
         call add_new_berg_to_list(bergs%first, localberg)
       endif
     enddo; enddo
@@ -820,6 +900,7 @@ subroutine write_trajectory(trajectory)
 ! Local variables
 integer :: iret, ncid, i_dim, i
 integer :: lonid, latid, yearid, dayid, uvelid, vvelid
+!integer :: axnid, aynid, bxnid, bynid !Added by Alon 
 integer :: uoid, void, uiid, viid, uaid, vaid, sshxid, sshyid, sstid
 integer :: cnid, hiid
 integer :: mid, did, wid, lid, mbid, hdid
@@ -923,6 +1004,10 @@ subroutine write_trajectory(trajectory)
   dayid = def_var(ncid, 'day', NF_DOUBLE, i_dim)
   uvelid = def_var(ncid, 'uvel', NF_DOUBLE, i_dim)
   vvelid = def_var(ncid, 'vvel', NF_DOUBLE, i_dim)
+  !axnid = def_var(ncid, 'axn', NF_DOUBLE, i_dim) !Alon
+  !aynid = def_var(ncid, 'ayn', NF_DOUBLE, i_dim) !Alon
+  !bxnid = def_var(ncid, 'bxn', NF_DOUBLE, i_dim) !Alon
+  !bynid = def_var(ncid, 'byn', NF_DOUBLE, i_dim) !Alon
   uoid = def_var(ncid, 'uo', NF_DOUBLE, i_dim)
   void = def_var(ncid, 'vo', NF_DOUBLE, i_dim)
   uiid = def_var(ncid, 'ui', NF_DOUBLE, i_dim)

From 4312f7090956a90e6794ca39f14fd0a78b345237 Mon Sep 17 00:00:00 2001
From: Alon Stern <Alon.Stern@gaea8.ncrc.gov>
Date: Tue, 2 Jun 2015 14:28:07 -0400
Subject: [PATCH 011/361] Changed the submodule accel. The predictive
 corrective step when calculating the accelerations has been changed so that
 in the second iteration, it uses 0.5*(|u_o-u_n|+|u_o-u_star|). Previously it
 used |u_o-0.5*(u_n+u_star)|. This change does change the answers.

---
 icebergs.F90 | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index b1e528e..91e6393 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -194,16 +194,17 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
   uveln=uvel; vveln=vvel ! Copy starting uvel, vvel
   do itloop=1,2 ! Iterate on drag coefficients
 
-    us=0.5*(uveln+uvel); vs=0.5*(vveln+vvel)
-    drag_ocn=c_ocn*sqrt( (us-uo)**2+(vs-vo)**2 )
-    drag_atm=c_atm*sqrt( (us-ua)**2+(vs-va)**2 )
-    drag_ice=c_ice*sqrt( (us-ui)**2+(vs-vi)**2 )
+! These four lines commented out by Alon to use Bob's scheme rather than Alistairs. (will change answers)
+ !   us=0.5*(uveln+uvel); vs=0.5*(vveln+vvel)
+ !   drag_ocn=c_ocn*sqrt( (us-uo)**2+(vs-vo)**2 )
+ !   drag_atm=c_atm*sqrt( (us-ua)**2+(vs-va)**2 )
+ !   drag_ice=c_ice*sqrt( (us-ui)**2+(vs-vi)**2 )
 
 !Alon's proposed change - This would change it to Bob's improved scheme.
-!    !us=uveln; vs=vveln     This line is no longer needed
-!    drag_ocn=c_ocn*0.5*(sqrt( (uveln-uo)**2+(vveln-vo)**2 )+sqrt( (uvel-uo)**2+(vvel-vo)**2 ))
-!    drag_atm=c_atm*0.5*(sqrt( (uveln-ua)**2+(vveln-va)**2 )+sqrt( (uvel-ua)**2+(vvel-va)**2 ))
-!    drag_ice=c_ice*0.5*(sqrt( (uveln-ui)**2+(vveln-vi)**2 )+sqrt( (uvel-ui)**2+(vvel-vi)**2 ))
+    !us=uveln; vs=vveln     This line is no longer needed
+    drag_ocn=c_ocn*0.5*(sqrt( (uveln-uo)**2+(vveln-vo)**2 )+sqrt( (uvel-uo)**2+(vvel-vo)**2 ))
+    drag_atm=c_atm*0.5*(sqrt( (uveln-ua)**2+(vveln-va)**2 )+sqrt( (uvel-ua)**2+(vvel-va)**2 ))
+    drag_ice=c_ice*0.5*(sqrt( (uveln-ui)**2+(vveln-vi)**2 )+sqrt( (uvel-ui)**2+(vvel-vi)**2 ))
 
     ! Explicit accelerations
    !axe= f_cori*vvel -gravity*ssh_x +wave_rad*uwave &

From 6ffda6c16e2a8115b94b8dfc95dd15cdf4850f45 Mon Sep 17 00:00:00 2001
From: Alon Stern <Alon.Stern@gaea6.ncrc.gov>
Date: Wed, 3 Jun 2015 15:16:21 -0400
Subject: [PATCH 012/361] Verlet algorithm now seems to be working. I have not
 yet tested it thoughouly though.

---
 icebergs.F90 | 80 ++++++++++++++++++++++++++++++----------------------
 1 file changed, 46 insertions(+), 34 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 91e6393..95ee614 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -191,7 +191,9 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
   c_ice=rho_ice     /M*(0.5*Cd_iv*W*hi              )
   if (abs(ui)+abs(vi).eq.0.) c_ice=0.
 
-  uveln=uvel; vveln=vvel ! Copy starting uvel, vvel
+!  uveln=uvel; vveln=vvel ! Copy starting uvel, vvel  !Commented out by Alon
+  uveln=uvel0; vveln=vvel0 ! Copy starting uvel, vvel !Added by Alon 
+ 
   do itloop=1,2 ! Iterate on drag coefficients
 
 ! These four lines commented out by Alon to use Bob's scheme rather than Alistairs. (will change answers)
@@ -202,9 +204,9 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 
 !Alon's proposed change - This would change it to Bob's improved scheme.
     !us=uveln; vs=vveln     This line is no longer needed
-    drag_ocn=c_ocn*0.5*(sqrt( (uveln-uo)**2+(vveln-vo)**2 )+sqrt( (uvel-uo)**2+(vvel-vo)**2 ))
-    drag_atm=c_atm*0.5*(sqrt( (uveln-ua)**2+(vveln-va)**2 )+sqrt( (uvel-ua)**2+(vvel-va)**2 ))
-    drag_ice=c_ice*0.5*(sqrt( (uveln-ui)**2+(vveln-vi)**2 )+sqrt( (uvel-ui)**2+(vvel-vi)**2 ))
+    drag_ocn=c_ocn*0.5*(sqrt( (uveln-uo)**2+(vveln-vo)**2 )+sqrt( (uvel0-uo)**2+(vvel0-vo)**2 ))
+    drag_atm=c_atm*0.5*(sqrt( (uveln-ua)**2+(vveln-va)**2 )+sqrt( (uvel0-ua)**2+(vvel0-va)**2 ))
+    drag_ice=c_ice*0.5*(sqrt( (uveln-ui)**2+(vveln-vi)**2 )+sqrt( (uvel0-ui)**2+(vvel0-vi)**2 ))
 
     ! Explicit accelerations
    !axe= f_cori*vvel -gravity*ssh_x +wave_rad*uwave &
@@ -1560,7 +1562,7 @@ subroutine evolve_icebergs(bergs)
   Rearth=6360.e3
 
   !Choosing time stepping scheme - Alon
-   Runge_not_verlet=.true.    !true=Runge Kutta, False=Verlet   , Alon
+   Runge_not_verlet=.False.    !true=Runge Kutta, False=Verlet   , Alon
 
 
   berg=>bergs%first
@@ -1862,6 +1864,8 @@ subroutine evolve_icebergs(bergs)
  ! X2 = X1+dt*V1+((dt^2)/2)*a_n +((dt^2)/2)*b_n = X1+dt*u_star +((dt^2)/2)*b_n 
  ! V2 = V1+dt/2*a_n +dt/2*a_np1 +dt*b_n = u_star + dt/2*a_np1 + dt*b_np1 = u_star +dt*ax
 
+!print *, 'you are here!'
+
 lon1=berg%lon; lat1=berg%lat
   if (on_tangential_plane) call rotpos_to_tang(lon1,lat1,x1,y1)
   dxdl1=r180_pi/(Rearth*cos(lat1*pi_180))
@@ -1870,45 +1874,52 @@ subroutine evolve_icebergs(bergs)
 
 !Loading past acceleartions - Alon
   axn=berg%axn; ayn=berg%ayn !Alon
-  byn=berg%bxn; byn=berg%byn !Alon
+  bxn=berg%bxn; byn=berg%byn !Alon
 
-! Turn the velocities into u_star, v_star. - Alon (not sure how this works with tangent plane)
-  uvel1=uvel1+dt_2*axn                                              !Alon
-  vvel1=vvel1+dt_2*ayn                                              !Alon
+! Velocities used to update the position
+  uvel2=uvel1+(dt_2*axn)+(dt_2*bxn)                    !Alon
+  vvel2=vvel1+(dt_2*ayn)+(dt_2*byn)                    !Alon
 
-if (on_tangential_plane) call rotvec_to_tang(lon1,uvel1,vvel1,xdot1,ydot1)
-  u1=uvel1*dxdl1; v1=vvel1*dydl
+if (on_tangential_plane) call rotvec_to_tang(lon1,uvel2,vvel2,xdot2,ydot2)
+  u2=uvel2*dxdl1; v2=vvel2*dydl
 
-  if (on_tangential_plane) call rotvec_to_tang(lon1,bxn,byn,bxddot,byddot)    !Added by Alon  -rotation of implicit velocity.
 
 !Solving for new position
   if (on_tangential_plane) then
-    xn=x1+dt_2*xdot1+(dt*dt*(bxddot)/2) ; yn=y1+dt_2*ydot1+(dt*dt*(byddot/2))             !Alon
+    xn=x1+(dt*xdot2) ; yn=y1+(dt*ydot2)             !Alon
     call rotpos_from_tang(xn,yn,lonn,latn)
   else
-    lonn=lon1+dt_2*u1+(dt*dt*(bxn)/2) ; latn=lat1+dt_2*v1+(dt*dt*(byn/2))  !Alon
-    uvel2=uvel1+dt*ax1; vvel2=vvel1+dt*ay1    !Alon , we call it uvel2, vvel2 until it is put into lat/long co-ordinates, where it becomes uveln, vveln
+    lonn=lon1+(dt*u2) ; latn=lat1+(dt*v2)  !Alon
   endif
-  dxdl2=r180_pi/(Rearth*cos(latn*pi_180))
+  dxdln=r180_pi/(Rearth*cos(latn*pi_180))
+
+! Turn the velocities into u_star, v_star.(uvel3 is v_star) - Alon (not sure how this works with tangent plane)
+  uvel3=uvel1+(dt_2*axn)                  !Alon
+  vvel3=vvel1+(dt_2*ayn)                  !Alon
+
 
+!Adjusting mass...                      Alon decided to move this before calculating the new velocities (so that acceleration can be a fn(r_np1)
+  i=i1;j=j1;xi=berg%xi;yj=berg%yj
+  call adjust_index_and_ground(grd, lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
+  i2=i; j2=j
+  if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
+    call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling)
+
+
+!Calling the acceleration
+  call accel(bergs, berg, i, j, xi, yj, latn, uvel3, vvel3, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, Runge_not_verlet) !axn, ayn, bxn, byn ,Runge_not_verlet  - Added by Alon
 
 !Solving for the new velocity
-  call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, Runge_not_verlet) !axn, ayn, bxn, byn ,Runge_not_verlet  - Added by Alon
-  if (on_tangential_plane) call rotvec_to_tang(lon1,ax1,ay1,xddot1,yddot1)
   if (on_tangential_plane) then
-    xdotn=xdot1+dt*xddot1; ydotn=ydot1+dt*yddot1                                    !Alon
+    call rotvec_to_tang(lonn,uvel3,vvel3,xdot3,ydot3)
+    call rotvec_to_tang(lon1,ax1,ay1,xddot1,yddot1)
+    xdotn=xdot3+(dt*xddot1); ydotn=ydot3+(dt*yddot1)                                    !Alon
     call rotvec_from_tang(lonn,xdotn,ydotn,uveln,vveln)
   else
-    uvel2=uvel1+dt*ax1; vvel2=vvel1+dt*ay1    !Alon , we call it uvel2, vvel2 until it is put into lat/long co-ordinates, where it becomes uveln, vveln
+    uvel4=uvel3+dt*ax1; vvel4=vvel3+dt*ay1    !Alon , we call it uvel3, vvel3 until it is put into lat/long co-ordinates, where it becomes uveln, vveln
   endif
-  uveln=uvel2*dxdl2; vveln=vvel2*dydl    !Converted to degrees.
+  uveln=uvel4*dxdln; vveln=vvel4*dydl    !Converted to degrees.
 
-!Adjusting mass...
-  i=i1;j=j1;xi=berg%xi;yj=berg%yj
-  call adjust_index_and_ground(grd, lonn, latn, uveln, vveln, i, j, xi, yj, bounced, error_flag)
-  i2=i; j2=j
-  if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-    call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling)
 
 !Debugging
   if (.not.error_flag) then
@@ -1925,16 +1936,16 @@ subroutine evolve_icebergs(bergs)
    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: j1,j2,j=',j1,j2,j
    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lon1,lonn=',lon1,lonn,berg%lon
    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lat1,latn=',lat1,latn,berg%lat
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u1,un,u0=',uvel1,uveln,berg%uvel
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v1,vn,v0=',vvel1,vveln,berg%vvel
+   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u3,un,u0=',uvel3,uveln,berg%uvel
+   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v3,vn,v0=',vvel3,vveln,berg%vvel
    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1=',&
         & dt*ax1
    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ay1=',&
         & dt*ay1
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,un,u0=',&
-        & dt*uvel1,dt*uvel2,dt*berg%uvel
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,vn,v0=',&
-        & dt*vvel1,dt*vvel2,dt*berg%vvel
+   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u3,un,u0=',&
+        & dt*uvel3,dt*uveln,dt*berg%uvel
+   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v3,vn,v0=',&
+        & dt*vvel3,dt*vveln,dt*berg%vvel
    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u_n (deg)=',&
         & dt*u1,dt*uveln
    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v_n (deg)=',&
@@ -1942,7 +1953,7 @@ subroutine evolve_icebergs(bergs)
    write(stderrunit,*) 'diamonds, evolve_iceberg: on_tangential_plane=',on_tangential_plane
    write(stderrunit,*) 'Acceleration terms for position 1'
    error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, Runge_not_verlet, debug_flag=.true.)  !axn, ayn, bxn, byn, Runge_not_verlet   - Added by Alon
+   call accel(bergs, berg, i2, j2, xi, yj, latn, uvel3, vvel3, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, Runge_not_verlet, debug_flag=.true.)  !axn, ayn, bxn, byn, Runge_not_verlet   - Added by Alon
    
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'posn i,j,lon,lat,xi,yj=',i,j,lonn,latn,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'posn box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
@@ -1964,6 +1975,7 @@ subroutine evolve_icebergs(bergs)
   endif ! End of the Verlet Stepiing -added by Alon  
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
+!print *, 'you are here again!';
   berg%lon=lonn
   berg%lat=latn
   berg%uvel=uveln

From 717d0ef0645ec5fdf11488f69247a76ed5c4073c Mon Sep 17 00:00:00 2001
From: Alon Stern <Alon.Stern@gaea8.ncrc.gov>
Date: Wed, 3 Jun 2015 16:19:49 -0400
Subject: [PATCH 013/361] Runge_not_Verlet added to name list so that you can
 choose which time stepping scheme to use at runtime.

---
 icebergs.F90           | 4 ++--
 icebergs_framework.F90 | 6 +++++-
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 95ee614..014ae56 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1562,8 +1562,8 @@ subroutine evolve_icebergs(bergs)
   Rearth=6360.e3
 
   !Choosing time stepping scheme - Alon
-   Runge_not_verlet=.False.    !true=Runge Kutta, False=Verlet   , Alon
-
+   !Runge_not_verlet=.False.    !Loading manually: true=Runge Kutta, False=Verlet   , Alon
+   Runge_not_verlet=bergs%Runge_not_Verlet  ! Loading directly from namelist/default , Alon
 
   berg=>bergs%first
   do while (associated(berg)) ! loop over all bergs
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index ecc3efd..c6eff4b 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -177,6 +177,7 @@ module ice_bergs_framework
   logical :: add_weight_to_ocean=.true. ! Add weight of bergs to ocean
   logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
   logical :: time_average_weight=.false. ! Time average the weight on the ocean
+  logical :: Runge_not_Verlet=.false.  !True=Runge Kuttai, False=Verlet.  - Added by Alon 
   real :: speed_limit=0. ! CFL speed limit for a berg [m/s]
   real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
   type(buffer), pointer :: obuffer_n=>null(), ibuffer_n=>null()
@@ -266,6 +267,7 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: time_average_weight=.false. ! Time average the weight on the ocean
 real :: speed_limit=0. ! CFL speed limit for a berg
 real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
+logical :: Runge_not_Verlet=.false.  !True=Runge Kuttai, False=Verlet.  - Added by Alon 
 logical :: do_unit_tests=.false. ! Conduct some unit tests
 real, dimension(nclasses) :: initial_mass=(/8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11/) ! Mass thresholds between iceberg classes (kg)
 real, dimension(nclasses) :: distribution=(/0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02/) ! Fraction of calving to apply to this class (non-dim)
@@ -275,7 +277,7 @@ subroutine ice_bergs_framework_init(bergs, &
          distribution, mass_scaling, initial_thickness, verbose_hrs, &
          rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, &
-         time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, &
+         time_average_weight, generate_test_icebergs, speed_limit, Runge_not_Verlet, fix_restart_dates, use_roundoff_fix, &
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction
 
 ! Local variables
@@ -494,6 +496,7 @@ subroutine ice_bergs_framework_init(bergs, &
  !  enddo
  !endif
 
+
  ! Parameters
   bergs%dt=dt
   bergs%traj_sample_hrs=traj_sample_hrs
@@ -507,6 +510,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%passive_mode=passive_mode
   bergs%time_average_weight=time_average_weight
   bergs%speed_limit=speed_limit
+  bergs%Runge_not_Verlet=Runge_not_Verlet   !Alon
   bergs%grounding_fraction=grounding_fraction
   bergs%add_weight_to_ocean=add_weight_to_ocean
   allocate( bergs%initial_mass(nclasses) ); bergs%initial_mass(:)=initial_mass(:)

From 9dff46b367ecb58068106625f46127926ce1c046 Mon Sep 17 00:00:00 2001
From: Alon Stern <Alon.Stern@gaea7.ncrc.gov>
Date: Mon, 8 Jun 2015 17:53:41 -0400
Subject: [PATCH 014/361] Flag added which allows the user to input a calving
 freq distribution rather than a mass flux distribution. If this flag is on,
 the code converts the input freq distribution into a mass flux distribution.

---
 icebergs_framework.F90 | 21 +++++++++++++++++++--
 1 file changed, 19 insertions(+), 2 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 48dfe14..7a3edb6 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -265,8 +265,9 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: speed_limit=0. ! CFL speed limit for a berg
 real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
 logical :: do_unit_tests=.false. ! Conduct some unit tests
+logical :: input_freq_distribution=.false. ! Alon: flag to show if input distribution is freq or mass dist (=1 if input is a freq dist, =0 to use an input mass dist)
 real, dimension(nclasses) :: initial_mass=(/8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11/) ! Mass thresholds between iceberg classes (kg)
-real, dimension(nclasses) :: distribution=(/0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02/) ! Fraction of calving to apply to this class (non-dim)
+real, dimension(nclasses) :: distribution=(/0.25, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02/) ! Fraction of calving to apply to this class (non-dim) , Also 0.24 changed to 0.25 by Alon
 real, dimension(nclasses) :: mass_scaling=(/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) ! Ratio between effective and real iceberg mass (non-dim)
 real, dimension(nclasses) :: initial_thickness=(/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) ! Total thickness of newly calved bergs (m)
 namelist /icebergs_nml/ verbose, budget, halo, traj_sample_hrs, initial_mass, &
@@ -274,7 +275,7 @@ subroutine ice_bergs_framework_init(bergs, &
          rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, &
          time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, &
-         old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction
+         old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -282,6 +283,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: minl
 logical :: lerr
 integer :: stdlogunit, stderrunit
+real :: Total_mass  !Added by Alon 
 
   ! Get the stderr and stdlog unit numbers
   stderrunit=stderr()
@@ -492,6 +494,21 @@ subroutine ice_bergs_framework_init(bergs, &
  !  enddo
  !endif
 
+
+!Added by Alon  - If a freq distribution is input, we have to convert the freq distribution to a mass flux distribution)
+if (input_freq_distribution) then
+     Total_mass=0.
+     do j=1:nclasses
+          Total_mass=Total_mass+(distribution(j)*initial_mass(j))
+     enddo
+     do j=1:nclasses
+           distribution(j)=(distribution(j)*initial_mass(j))/Total_mass
+     enddo
+endif 
+
+
+
+
  ! Parameters
   bergs%dt=dt
   bergs%traj_sample_hrs=traj_sample_hrs

From 15f3388c0ab1c8fc3faeea1f12b3b6fa9a7c4fc2 Mon Sep 17 00:00:00 2001
From: Alon Stern <Alon.Stern@gaea7.ncrc.gov>
Date: Tue, 9 Jun 2015 09:10:27 -0400
Subject: [PATCH 015/361] Flag for using mass vs freq distribution has been
 included.

---
 icebergs_framework.F90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 7a3edb6..1917e4a 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -498,10 +498,10 @@ subroutine ice_bergs_framework_init(bergs, &
 !Added by Alon  - If a freq distribution is input, we have to convert the freq distribution to a mass flux distribution)
 if (input_freq_distribution) then
      Total_mass=0.
-     do j=1:nclasses
+     do j=1,nclasses
           Total_mass=Total_mass+(distribution(j)*initial_mass(j))
      enddo
-     do j=1:nclasses
+     do j=1,nclasses
            distribution(j)=(distribution(j)*initial_mass(j))/Total_mass
      enddo
 endif 

From 93329cba647751c95cf062c1f1aa9fa04cb0f9c8 Mon Sep 17 00:00:00 2001
From: Alon Stern <Alon.Stern@gaea7.ncrc.gov>
Date: Tue, 9 Jun 2015 10:16:30 -0400
Subject: [PATCH 016/361] RK and Verlet schemes are giving different answers.
 Fixed one bug in Verlet scheme. Still need to test it further.

---
 icebergs.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 014ae56..b160b06 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1907,7 +1907,7 @@ subroutine evolve_icebergs(bergs)
 
 
 !Calling the acceleration
-  call accel(bergs, berg, i, j, xi, yj, latn, uvel3, vvel3, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, Runge_not_verlet) !axn, ayn, bxn, byn ,Runge_not_verlet  - Added by Alon
+  call accel(bergs, berg, i, j, xi, yj, latn, uvel3, vvel3, uvel1, vvel1, dt, ax1, ay1, axn, ayn, bxn, byn, Runge_not_verlet) !axn, ayn, bxn, byn ,Runge_not_verlet  - Added by Alon
 
 !Solving for the new velocity
   if (on_tangential_plane) then

From 603171613491d19dc58496896531f715e938f461 Mon Sep 17 00:00:00 2001
From: Alon Stern <Alon.Stern@gaea7.ncrc.gov>
Date: Tue, 9 Jun 2015 10:28:04 -0400
Subject: [PATCH 017/361] Changed 0.25 back to 0.24 on the smallest category of
 the iceberg distribution since I was getting the error messaged "Calving is
 Over distributed".

---
 icebergs_framework.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 1917e4a..944dad0 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -267,7 +267,7 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: do_unit_tests=.false. ! Conduct some unit tests
 logical :: input_freq_distribution=.false. ! Alon: flag to show if input distribution is freq or mass dist (=1 if input is a freq dist, =0 to use an input mass dist)
 real, dimension(nclasses) :: initial_mass=(/8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11/) ! Mass thresholds between iceberg classes (kg)
-real, dimension(nclasses) :: distribution=(/0.25, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02/) ! Fraction of calving to apply to this class (non-dim) , Also 0.24 changed to 0.25 by Alon
+real, dimension(nclasses) :: distribution=(/0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02/) ! Fraction of calving to apply to this class (non-dim) , 
 real, dimension(nclasses) :: mass_scaling=(/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) ! Ratio between effective and real iceberg mass (non-dim)
 real, dimension(nclasses) :: initial_thickness=(/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) ! Total thickness of newly calved bergs (m)
 namelist /icebergs_nml/ verbose, budget, halo, traj_sample_hrs, initial_mass, &

From cebcdb4ce17dd9a8593bfaa3f84eeadd3754519e Mon Sep 17 00:00:00 2001
From: Alon Stern <Alon.Stern@gaea3.ncrc.gov>
Date: Tue, 9 Jun 2015 15:58:14 -0400
Subject: [PATCH 018/361] Alpha set = 1 in the accel scheme (to make the drag
 implicit).:wq

---
 icebergs.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/icebergs.F90 b/icebergs.F90
index b160b06..2cff261 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -129,7 +129,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 real :: drag_ocn, drag_atm, drag_ice, wave_rad
 real :: c_ocn, c_atm, c_ice
 real :: ampl, wmod, Cr, Lwavelength, Lcutoff, Ltop
-real, parameter :: alpha=0.0, beta=1.0, accel_lim=1.e-2, Cr0=0.06, vel_lim=15.
+real, parameter :: alpha=1.0, beta=1.0, accel_lim=1.e-2, Cr0=0.06, vel_lim=15.
 real :: lambda, detA, A11, A12, axe, aye, D_hi 
 real :: uveln, vveln, us, vs, speed, loc_dx, new_speed
 logical :: dumpit

From b5604eb3fc5b3da8017ecf3b4780b06902257cef Mon Sep 17 00:00:00 2001
From: Alon Stern <Alon.Stern@gaea3.ncrc.gov>
Date: Thu, 11 Jun 2015 16:54:34 -0400
Subject: [PATCH 019/361] Changes to acceleration and evolve subroutines in
 order to make them resemble Alon's code more closely. Trying to get Verlet
 and RK to agree. Introduced Crank Nicolson Coriolis. Introduced axn, ayn into
 RK algorthim.

---
 icebergs.F90 | 181 ++++++++++++++++++++++++++++++---------------------
 1 file changed, 106 insertions(+), 75 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 2cff261..a52ff16 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -129,14 +129,17 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 real :: drag_ocn, drag_atm, drag_ice, wave_rad
 real :: c_ocn, c_atm, c_ice
 real :: ampl, wmod, Cr, Lwavelength, Lcutoff, Ltop
-real, parameter :: alpha=1.0, beta=1.0, accel_lim=1.e-2, Cr0=0.06, vel_lim=15.
-real :: lambda, detA, A11, A12, axe, aye, D_hi 
+real, parameter :: alpha=1.0, beta=1.0, C_N=1.0, accel_lim=1.e-2, Cr0=0.06, vel_lim=15.
+real :: lambda, detA, A11, A12, RHS_x, RHS_y, D_hi 
 real :: uveln, vveln, us, vs, speed, loc_dx, new_speed
+real :: u_star, v_star    !Added by Alon
 logical :: dumpit
 logical, intent(in) :: Runge_not_verlet  ! Flag to specify whether it is Runge-Kutta or Verlet
 integer :: itloop
 integer :: stderrunit
 
+  u_star=uvel0+(dt/2.*axn)  !Alon
+  v_star=vvel0+(dt/2.*ayn)  !Alon
 
   ! Get the stderr unit number.
   stderrunit = stderr()
@@ -191,75 +194,90 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
   c_ice=rho_ice     /M*(0.5*Cd_iv*W*hi              )
   if (abs(ui)+abs(vi).eq.0.) c_ice=0.
 
-!  uveln=uvel; vveln=vvel ! Copy starting uvel, vvel  !Commented out by Alon
-  uveln=uvel0; vveln=vvel0 ! Copy starting uvel, vvel !Added by Alon 
+
+    ! Half half accelerations  - axn, ayn
+    if (.not.Runge_not_verlet) then  
+        axn=-gravity*ssh_x +wave_rad*uwave
+        ayn=-gravity*ssh_y +wave_rad*vwave
+    else
+    ! Not half half accelerations  - for RK
+        bxn=-gravity*ssh_x +wave_rad*uwave
+        byn=-gravity*ssh_y +wave_rad*vwave
+     endif
+
+  if (alpha>0.) then ! If implicit Coriolis, use u_star rather than RK4 latest  !Alon
+        if (C_N>0.) then !  C_N=1 for Crank Nicolson Coriolis, C_N=0 for full implicit Coriolis !Alon  
+           axn=axn+f_cori*v_star
+           ayn=ayn-f_cori*u_star
+        else
+           bxn=bxn+f_cori*v_star
+           byn=byn-f_cori*u_star
+        endif
+  else
+           bxn=bxn+f_cori*vvel
+           byn=byn-f_cori*uvel
+  endif
+
+  us=uvel0; vs=vvel0 ! us, vs are equivolent to u_pred in Alon's code. It is the variable that changes in the loop.
  
   do itloop=1,2 ! Iterate on drag coefficients
 
-! These four lines commented out by Alon to use Bob's scheme rather than Alistairs. (will change answers)
- !   us=0.5*(uveln+uvel); vs=0.5*(vveln+vvel)
- !   drag_ocn=c_ocn*sqrt( (us-uo)**2+(vs-vo)**2 )
- !   drag_atm=c_atm*sqrt( (us-ua)**2+(vs-va)**2 )
- !   drag_ice=c_ice*sqrt( (us-ui)**2+(vs-vi)**2 )
-
-!Alon's proposed change - This would change it to Bob's improved scheme.
-    !us=uveln; vs=vveln     This line is no longer needed
-    drag_ocn=c_ocn*0.5*(sqrt( (uveln-uo)**2+(vveln-vo)**2 )+sqrt( (uvel0-uo)**2+(vvel0-vo)**2 ))
-    drag_atm=c_atm*0.5*(sqrt( (uveln-ua)**2+(vveln-va)**2 )+sqrt( (uvel0-ua)**2+(vvel0-va)**2 ))
-    drag_ice=c_ice*0.5*(sqrt( (uveln-ui)**2+(vveln-vi)**2 )+sqrt( (uvel0-ui)**2+(vvel0-vi)**2 ))
-
-    ! Explicit accelerations
-   !axe= f_cori*vvel -gravity*ssh_x +wave_rad*uwave &
-   !    -drag_ocn*(uvel-uo) -drag_atm*(uvel-ua) -drag_ice*(uvel-ui)
-   !aye=-f_cori*uvel -gravity*ssh_y +wave_rad*vwave &
-   !    -drag_ocn*(vvel-vo) -drag_atm*(vvel-va) -drag_ice*(vvel-vi)
-    axe=-gravity*ssh_x +wave_rad*uwave
-    aye=-gravity*ssh_y +wave_rad*vwave
-
-    if (.not.Runge_not_verlet) then  ! When using Verlet, use only half the explicit acceleration,  Added by Alon
-       axe=axe/2  
-       aye=aye/2  
-    endif 
-
-    if (alpha>0.) then ! If implicit, use time-level (n) rather than RK4 latest
-      axe=axe+f_cori*vvel0
-      aye=aye-f_cori*uvel0
-    else
-      axe=axe+f_cori*vvel
-      aye=aye-f_cori*uvel
-    endif
-    if (beta>0.) then ! If implicit, use time-level (n) rather than RK4 latest
-      axe=axe-drag_ocn*(uvel0-uo) -drag_atm*(uvel0-ua) -drag_ice*(uvel0-ui)
-      aye=aye-drag_ocn*(vvel0-vo) -drag_atm*(vvel0-va) -drag_ice*(vvel0-vi)
+    !Alon's proposed change - using Bob's improved scheme.
+    drag_ocn=c_ocn*0.5*(sqrt( (us-uo)**2+(vs-vo)**2 )+sqrt( (uvel0-uo)**2+(vvel0-vo)**2 ))
+    drag_atm=c_atm*0.5*(sqrt( (us-ua)**2+(vs-va)**2 )+sqrt( (uvel0-ua)**2+(vvel0-va)**2 ))
+    drag_ice=c_ice*0.5*(sqrt( (us-ui)**2+(vs-vi)**2 )+sqrt( (uvel0-ui)**2+(vvel0-vi)**2 ))
+
+
+!     RHS_x=(axn/2) + bxn- drag_ocn*(u_star-uo) -drag_atm*(u_star-ua) -drag_ice*(u_star-ui)
+!     RHS_y=(ayn/2) + byn -drag_ocn*(v_star-vo) -drag_atm*(v_star-va) -drag_ice*(v_star-vi)
+
+
+     RHS_x=(axn/2) + bxn
+     RHS_y=(ayn/2) + byn
+
+     if (beta>0.) then ! If implicit, use u_star, v_star rather than RK4 latest
+         RHS_x=RHS_x - drag_ocn*(u_star-uo) -drag_atm*(u_star-ua) -drag_ice*(u_star-ui)
+         RHS_y=RHS_y - drag_ocn*(v_star-vo) -drag_atm*(v_star-va) -drag_ice*(v_star-vi)
     else
-      axe=axe-drag_ocn*(uvel-uo) -drag_atm*(uvel-ua) -drag_ice*(uvel-ui)
-      aye=aye-drag_ocn*(vvel-vo) -drag_atm*(vvel-va) -drag_ice*(vvel-vi)
+         RHS_x=RHS_x - drag_ocn*(uvel-uo) -drag_atm*(uvel-ua) -drag_ice*(uvel-ui)
+         RHS_y=RHS_y - drag_ocn*(vvel-vo) -drag_atm*(vvel-va) -drag_ice*(vvel-vi)
     endif
 
-    ! Solve for implicit accelerations
+  ! Solve for implicit accelerations
     if (alpha+beta.gt.0.) then
       lambda=drag_ocn+drag_atm+drag_ice
-      A11=1.+beta*dt*lambda
-      A12=alpha*dt*f_cori
+      A11=1.+dt*lambda
+      A12=dt/2.*f_cori  !Think about this more for non-Crank Nicolson.  Why use dt_2?
       detA=1./(A11**2+A12**2)
-      ax=detA*(A11*axe+A12*aye)
-      ay=detA*(A11*aye-A12*axe)
+      ax=detA*(A11*RHS_x+A12*RHS_y)
+      ay=detA*(A11*RHS_y-A12*RHS_x)
     else
-      ax=axe; ay=aye
+      ax=RHS_x; ay=RHS_x
     endif
 
-    uveln=uvel0+dt*ax
-    vveln=vvel0+dt*ay
+      us=u_star+dt*ax        ! Alon
+      vs=v_star+dt*ay        ! Alon
 
   enddo ! itloop
  
+      uveln=us  !Updated velocities
+      vveln=vs  !Updated velocities
+
+
 !Saving the totally explicit part of the acceleration to use in finding the next position and u_star -Alon
-    axn=-gravity*ssh_x +wave_rad*uwave !Alon
-    ayn=-gravity*ssh_y +wave_rad*vwave !Alon
+    axn=0.
+    ayn=0.
+    if (.not.Runge_not_verlet) then
+        axn=-gravity*ssh_x +wave_rad*uwave
+        ayn=-gravity*ssh_y +wave_rad*vwave
+    endif
+    if (C_N>0.) then !  C_N=1 for Crank Nicolson Coriolis, C_N=0 for full implicit Coriolis !Alon 
+      axn=axn+f_cori*vveln
+      ayn=ayn-f_cori*uveln
+    endif
     bxn= ax-(axn/2) !Alon
     byn= ay-(ayn/2) !Alon
 
-
  
   ! Limit speed of bergs based on a CFL criteria
   if (bergs%speed_limit>0.) then
@@ -308,7 +326,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
       'd*(u-ua)=',-drag_atm*(uvel-ua), &
       'd*(u-ui)=',-drag_ice*(uvel-ui)
     write(stderrunit,100) mpp_pe(),'U accel.', &
-      'axe=',axe, &
+      'RHS_x=',RHS_x, &
       'ax=',ax, &
       'ax(cori)=',detA*(A11*(f_cori*vvel)+A12*(-f_cori*uvel)), &
       'ax(grav)=',detA*(A11*(-gravity*ssh_x)+A12*(-gravity*ssh_y)), &
@@ -326,7 +344,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
       'd*(v-va)=',-drag_atm*(vvel-va), &
       'd*(v-vi)=',-drag_ice*(vvel-vi)
     write(stderrunit,100) mpp_pe(),'V accel. pe=', &
-      'aye=',aye, &
+      'RHS_y=',RHS_y, &
       'ay=',ay, &
       'ay(cori)=',detA*(-A12*(f_cori*vvel)+A11*(-f_cori*uvel)), &
       'ay(grav)=',detA*(-A12*(-gravity*ssh_x)+A11*(-gravity*ssh_y)), &
@@ -1514,16 +1532,16 @@ subroutine evolve_icebergs(bergs)
 type(icebergs), pointer :: bergs
 ! Local variables
 type(icebergs_gridded), pointer :: grd
-real :: uvel1, vvel1, lon1, lat1, u1, v1, dxdl1, ax1, ay1 
-real :: uvel2, vvel2, lon2, lat2, u2, v2, dxdl2, ax2, ay2 
-real :: uvel3, vvel3, lon3, lat3, u3, v3, dxdl3, ax3, ay3
-real :: uvel4, vvel4, lon4, lat4, u4, v4, dxdl4, ax4, ay4
+real :: uvel1, vvel1, lon1, lat1, u1, v1, dxdl1, ax1, ay1, axn1, ayn1 
+real :: uvel2, vvel2, lon2, lat2, u2, v2, dxdl2, ax2, ay2, axn2, ayn2
+real :: uvel3, vvel3, lon3, lat3, u3, v3, dxdl3, ax3, ay3, axn3, ayn3
+real :: uvel4, vvel4, lon4, lat4, u4, v4, dxdl4, ax4, ay4, axn4, ayn4
 real :: uveln, vveln, lonn, latn, un, vn, dxdln
-real :: x1, xdot1, xddot1, y1, ydot1, yddot1 
-real :: x2, xdot2, xddot2, y2, ydot2, yddot2
-real :: x3, xdot3, xddot3, y3, ydot3, yddot3
-real :: x4, xdot4, xddot4, y4, ydot4, yddot4
-real :: xn, xdotn, yn, ydotn
+real :: x1, xdot1, xddot1, y1, ydot1, yddot1, xddot1n, yddot1n 
+real :: x2, xdot2, xddot2, y2, ydot2, yddot2, xddot2n, yddot2n
+real :: x3, xdot3, xddot3, y3, ydot3, yddot3, xddot3n, yddot3n
+real :: x4, xdot4, xddot4, y4, ydot4, yddot4, xddot4n, yddot4n
+real :: xn, xdotn, yn, ydotn, xddotn, yddotn
 real :: bxddot, byddot                                               ! Added by Alon
 real :: axn, ayn, bxn, byn                                           ! Added by Alon - explicit and implicit accelations from the previous step
 real :: r180_pi, dt, dt_2, dt_6, dydl, Rearth
@@ -1607,8 +1625,9 @@ subroutine evolve_icebergs(bergs)
   uvel1=berg%uvel; vvel1=berg%vvel
   if (on_tangential_plane) call rotvec_to_tang(lon1,uvel1,vvel1,xdot1,ydot1)
   u1=uvel1*dxdl1; v1=vvel1*dydl
-  call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, Runge_not_verlet) !axn,ayn, bxn, byn ,Runge_not_verlet  - Added by Alon
+  call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, Runge_not_verlet) !axn,ayn, bxn, byn ,Runge_not_verlet  - Added by Alon
   if (on_tangential_plane) call rotvec_to_tang(lon1,ax1,ay1,xddot1,yddot1)
+  if (on_tangential_plane) call rotvec_to_tang(lon1,axn1,ayn1,xddot1n,yddot1n) !Alon
   
   !  X2 = X1+dt/2*V1 ; V2 = V1+dt/2*A1; A2=A(X2)
  !if (debug) write(stderr(),*) 'diamonds, evolve: x2=...'
@@ -1651,7 +1670,7 @@ subroutine evolve_icebergs(bergs)
    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2 (deg)=',dt*v1,dt*v2
    write(stderrunit,*) 'Acceleration terms for position 1'
    error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, Runge_not_verlet, debug_flag=.true.) !axn, ayn, bxn, byn, Runge_not_verlet - Added by Alon
+   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, Runge_not_verlet, debug_flag=.true.) !axn, ayn, bxn, byn, Runge_not_verlet - Added by Alon
     call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 2')
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos2 i,j,lon,lat,xi,yj=',i,j,lon2,lat2,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos2 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
@@ -1660,8 +1679,9 @@ subroutine evolve_icebergs(bergs)
   endif
   dxdl2=r180_pi/(Rearth*cos(lat2*pi_180))
   u2=uvel2*dxdl2; v2=vvel2*dydl
-  call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn, ayn, bxn, byn, Runge_not_verlet) !axn, ayn, bxn, byn, Runge_not_verlet - Added by Alon
+  call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn, Runge_not_verlet) !axn, ayn, bxn, byn, Runge_not_verlet - Added by Alon
   if (on_tangential_plane) call rotvec_to_tang(lon2,ax2,ay2,xddot2,yddot2)
+  if (on_tangential_plane) call rotvec_to_tang(lon2,axn2,ayn2,xddot2n,yddot2n)
   
   !  X3 = X1+dt/2*V2 ; V3 = V1+dt/2*A2; A3=A(X3)
  !if (debug) write(stderr(),*) 'diamonds, evolve: x3=...'
@@ -1704,10 +1724,10 @@ subroutine evolve_icebergs(bergs)
    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3 (deg)=',dt*v1,dt*v2,dt*v3
    write(stderrunit,*) 'Acceleration terms for position 1'
    error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, Runge_not_verlet, debug_flag=.true.) !ax, aye1, Runge_not_verlet- Added by Alon
+   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, Runge_not_verlet, debug_flag=.true.) !axn, ayn, Runge_not_verlet- Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 2'
    error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
-   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn, ayn, bxn, byn, Runge_not_verlet, debug_flag=.true.) !axn, ayn, bxn, byn, Runge_not_verlet   - Added by Alon
+   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn, Runge_not_verlet, debug_flag=.true.) !axn, ayn, bxn, byn, Runge_not_verlet   - Added by Alon
     call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 3')
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos3 i,j,lon,lat,xi,yj=',i,j,lon3,lat3,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos3 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
@@ -1716,8 +1736,9 @@ subroutine evolve_icebergs(bergs)
   endif
   dxdl3=r180_pi/(Rearth*cos(lat3*pi_180))
   u3=uvel3*dxdl3; v3=vvel3*dydl
-  call accel(bergs, berg, i, j, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn, ayn, bxn, byn, Runge_not_verlet) !axn, ayn, bxn, byn, Runge_not_verlet   - Added by Alon
+  call accel(bergs, berg, i, j, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn3, ayn3, bxn, byn, Runge_not_verlet) !axn, ayn, bxn, byn, Runge_not_verlet   - Added by Alon
   if (on_tangential_plane) call rotvec_to_tang(lon3,ax3,ay3,xddot3,yddot3)
+  if (on_tangential_plane) call rotvec_to_tang(lon3,axn3,ayn3,xddot3n,yddot3n)
   
   !  X4 = X1+dt*V3 ; V4 = V1+dt*A3; A4=A(X4)
  !if (debug) write(stderr(),*) 'diamonds, evolve: x4=...'
@@ -1758,13 +1779,13 @@ subroutine evolve_icebergs(bergs)
    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v4 (deg)=',dt*v1,dt*v2,dt*v3,dt*v4
    write(stderrunit,*) 'Acceleration terms for position 1'
    error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, Runge_not_verlet, debug_flag=.true.) !axn, ayn, bxn, byn, Runge_not_verlet   - Added by Alon
+   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, Runge_not_verlet, debug_flag=.true.) !axn, ayn, bxn, byn, Runge_not_verlet   - Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 2'
    error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
-   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn, ayn, bxn, byn, Runge_not_verlet, debug_flag=.true.) !axn, ayn, bxn, byn, Runge_not_verlet    - Added by Alon
+   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn, Runge_not_verlet, debug_flag=.true.) !axn, ayn, bxn, byn, Runge_not_verlet    - Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 3'
    error_flag=pos_within_cell(grd, lon3, lat3, i3, j3, xi, yj)
-   call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn, ayn, bxn, byn, Runge_not_verlet, debug_flag=.true.) !axn, ayn, bxn, byn, Runge_not_verlet - Added by Alon
+   call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn3, ayn3, bxn, byn, Runge_not_verlet, debug_flag=.true.) !axn, ayn, bxn, byn, Runge_not_verlet - Added by Alon
     call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 4')
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos4 i,j,lon,lat,xi,yj=',i,j,lon4,lat4,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos4 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
@@ -1773,8 +1794,9 @@ subroutine evolve_icebergs(bergs)
   endif
   dxdl4=r180_pi/(Rearth*cos(lat4*pi_180))
   u4=uvel4*dxdl4; v4=vvel4*dydl
-  call accel(bergs, berg, i, j, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axn, ayn, bxn, byn, Runge_not_verlet) !axn, ayn, bxn, byn, Runge_not_verlet - Added by Alon
+  call accel(bergs, berg, i, j, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axn4, ayn4, bxn, byn, Runge_not_verlet) !axn, ayn, bxn, byn, Runge_not_verlet - Added by Alon
   if (on_tangential_plane) call rotvec_to_tang(lon4,ax4,ay4,xddot4,yddot4)
+  if (on_tangential_plane) call rotvec_to_tang(lon4,axn4,ayn4,xddot4n,yddot4n)
   
   !  Xn = X1+dt*(V1+2*V2+2*V3+V4)/6
   !  Vn = V1+dt*(A1+2*A2+2*A3+A4)/6
@@ -1783,14 +1805,22 @@ subroutine evolve_icebergs(bergs)
     yn=y1+dt_6*( (ydot1+ydot4)+2.*(ydot2+ydot3) )
     xdotn=xdot1+dt_6*( (xddot1+xddot4)+2.*(xddot2+xddot3) )
     ydotn=ydot1+dt_6*( (yddot1+yddot4)+2.*(yddot2+yddot3) )
+    xddotn=( (xddot1n+xddot4n)+2.*(xddot2n+xddot3n) )/6.  !Alon  
+    yddotn=( (yddot1n+yddot4n)+2.*(yddot2n+yddot3n) )/6.  !Alon  
     call rotpos_from_tang(xn,yn,lonn,latn)
     call rotvec_from_tang(lonn,xdotn,ydotn,uveln,vveln)
+    call rotvec_from_tang(lonn,xddotn,yddotn,axn,ayn) !Alon
   else
     lonn=berg%lon+dt_6*( (u1+u4)+2.*(u2+u3) )
     latn=berg%lat+dt_6*( (v1+v4)+2.*(v2+v3) )
     uveln=berg%uvel+dt_6*( (ax1+ax4)+2.*(ax2+ax3) )
     vveln=berg%vvel+dt_6*( (ay1+ay4)+2.*(ay2+ay3) )
+    axn=( (axn1+axn4)+2.*(axn2+axn3) )/6. !Alon
+    ayn=( (ayn1+ayn4)+2.*(ayn2+ayn3) )/6. !Alon
   endif
+
+
+
   i=i1;j=j1;xi=berg%xi;yj=berg%yj
   call adjust_index_and_ground(grd, lonn, latn, uveln, vveln, i, j, xi, yj, bounced, error_flag)
   if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
@@ -1906,8 +1936,9 @@ subroutine evolve_icebergs(bergs)
     call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling)
 
 
-!Calling the acceleration
-  call accel(bergs, berg, i, j, xi, yj, latn, uvel3, vvel3, uvel1, vvel1, dt, ax1, ay1, axn, ayn, bxn, byn, Runge_not_verlet) !axn, ayn, bxn, byn ,Runge_not_verlet  - Added by Alon
+!Calling the acceleration   (note that the velocity is converted to u_star inside the accel script)
+!  call accel(bergs, berg, i, j, xi, yj, latn, uvel3, vvel3, uvel1, vvel1, dt, ax1, ay1, axn, ayn, bxn, byn, Runge_not_verlet) !axn, ayn, bxn, byn ,Runge_not_verlet  - Added by Alon
+  call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn, ayn, bxn, byn, Runge_not_verlet) !axn, ayn, bxn, byn ,Runge_not_verlet  - Added by Alon
 
 !Solving for the new velocity
   if (on_tangential_plane) then

From c6412ed35edf3435c1b6f9ba383641c1f7e6a7f1 Mon Sep 17 00:00:00 2001
From: Alon Stern <Alon.Stern@gaea3.ncrc.gov>
Date: Thu, 11 Jun 2015 17:45:47 -0400
Subject: [PATCH 020/361] A few more corrections. RK now works when Crank
 Nicolson is off, but crashes when CN is on.

---
 icebergs.F90 | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index a52ff16..d44164e 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -129,7 +129,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 real :: drag_ocn, drag_atm, drag_ice, wave_rad
 real :: c_ocn, c_atm, c_ice
 real :: ampl, wmod, Cr, Lwavelength, Lcutoff, Ltop
-real, parameter :: alpha=1.0, beta=1.0, C_N=1.0, accel_lim=1.e-2, Cr0=0.06, vel_lim=15.
+real, parameter :: alpha=1.0, beta=1.0, C_N=0.0, accel_lim=1.e-2, Cr0=0.06, vel_lim=15.
 real :: lambda, detA, A11, A12, RHS_x, RHS_y, D_hi 
 real :: uveln, vveln, us, vs, speed, loc_dx, new_speed
 real :: u_star, v_star    !Added by Alon
@@ -247,7 +247,11 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
     if (alpha+beta.gt.0.) then
       lambda=drag_ocn+drag_atm+drag_ice
       A11=1.+dt*lambda
-      A12=dt/2.*f_cori  !Think about this more for non-Crank Nicolson.  Why use dt_2?
+      A12=dt*f_cori  
+      if (C_N>0.) then   !For Crank-Nicolson Coriolis term.   
+          A12=A12/2.
+      endif
+
       detA=1./(A11**2+A12**2)
       ax=detA*(A11*RHS_x+A12*RHS_y)
       ay=detA*(A11*RHS_y-A12*RHS_x)
@@ -1681,7 +1685,7 @@ subroutine evolve_icebergs(bergs)
   u2=uvel2*dxdl2; v2=vvel2*dydl
   call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn, Runge_not_verlet) !axn, ayn, bxn, byn, Runge_not_verlet - Added by Alon
   if (on_tangential_plane) call rotvec_to_tang(lon2,ax2,ay2,xddot2,yddot2)
-  if (on_tangential_plane) call rotvec_to_tang(lon2,axn2,ayn2,xddot2n,yddot2n)
+  if (on_tangential_plane) call rotvec_to_tang(lon2,axn2,ayn2,xddot2n,yddot2n) !Alon
   
   !  X3 = X1+dt/2*V2 ; V3 = V1+dt/2*A2; A3=A(X3)
  !if (debug) write(stderr(),*) 'diamonds, evolve: x3=...'
@@ -1738,7 +1742,7 @@ subroutine evolve_icebergs(bergs)
   u3=uvel3*dxdl3; v3=vvel3*dydl
   call accel(bergs, berg, i, j, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn3, ayn3, bxn, byn, Runge_not_verlet) !axn, ayn, bxn, byn, Runge_not_verlet   - Added by Alon
   if (on_tangential_plane) call rotvec_to_tang(lon3,ax3,ay3,xddot3,yddot3)
-  if (on_tangential_plane) call rotvec_to_tang(lon3,axn3,ayn3,xddot3n,yddot3n)
+  if (on_tangential_plane) call rotvec_to_tang(lon3,axn3,ayn3,xddot3n,yddot3n) !Alon
   
   !  X4 = X1+dt*V3 ; V4 = V1+dt*A3; A4=A(X4)
  !if (debug) write(stderr(),*) 'diamonds, evolve: x4=...'

From 4b08f7a9caa58184cf2f9006d301d2efbc5c6f0e Mon Sep 17 00:00:00 2001
From: Alon Stern <Alon.Stern@gaea7.ncrc.gov>
Date: Fri, 12 Jun 2015 16:30:00 -0400
Subject: [PATCH 021/361] Another bug fixed. RK and Verlet are still not
 matching, but it is looking better.

---
 icebergs.F90 | 88 ++++++++++++++++++++++++++++++----------------------
 1 file changed, 51 insertions(+), 37 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index d44164e..5877b14 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -112,7 +112,7 @@ subroutine icebergs_init(bergs, &
 
 end subroutine icebergs_init
 
-subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, axn, ayn, bxn, byn, Runge_not_verlet, debug_flag) !Saving  acceleration for Verlet, Adding Verlet flag - Alon
+subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, axn, ayn, bxn, byn, Runge_not_Verlet, debug_flag) !Saving  acceleration for Verlet, Adding Verlet flag - Alon
 !subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, debug_flag) !old version commmented out by Alon
 ! Arguments
 type(icebergs), pointer :: bergs
@@ -129,17 +129,18 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 real :: drag_ocn, drag_atm, drag_ice, wave_rad
 real :: c_ocn, c_atm, c_ice
 real :: ampl, wmod, Cr, Lwavelength, Lcutoff, Ltop
-real, parameter :: alpha=1.0, beta=1.0, C_N=0.0, accel_lim=1.e-2, Cr0=0.06, vel_lim=15.
+real, parameter :: alpha=1.0, beta=1.0, C_N=1.0, accel_lim=1.e-2, Cr0=0.06, vel_lim=15.
 real :: lambda, detA, A11, A12, RHS_x, RHS_y, D_hi 
 real :: uveln, vveln, us, vs, speed, loc_dx, new_speed
 real :: u_star, v_star    !Added by Alon
 logical :: dumpit
-logical, intent(in) :: Runge_not_verlet  ! Flag to specify whether it is Runge-Kutta or Verlet
+logical, intent(in) :: Runge_not_Verlet  ! Flag to specify whether it is Runge-Kutta or Verlet
 integer :: itloop
 integer :: stderrunit
 
-  u_star=uvel0+(dt/2.*axn)  !Alon
-  v_star=vvel0+(dt/2.*ayn)  !Alon
+!print *, 'axn=',axn,'ayn=',ayn
+  u_star=uvel0+(axn*(dt/2.))  !Alon
+  v_star=vvel0+(ayn*(dt/2.))  !Alon
 
   ! Get the stderr unit number.
   stderrunit = stderr()
@@ -150,7 +151,8 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
   ! Interpolate gridded fields to berg 
   call interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, cn, hi)
 
-  f_cori=(2.*omega)*sin(pi_180*lat)
+   f_cori=(2.*omega)*sin(pi_180*lat)
+!  f_cori=0.
 
   M=berg%mass
   T=berg%thickness ! total thickness
@@ -194,9 +196,13 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
   c_ice=rho_ice     /M*(0.5*Cd_iv*W*hi              )
   if (abs(ui)+abs(vi).eq.0.) c_ice=0.
 
+!Turning drag off for testing - Alon
+!c_ocn=0.
+!c_atm=0.
+!c_ice=0.
 
     ! Half half accelerations  - axn, ayn
-    if (.not.Runge_not_verlet) then  
+    if (.not.Runge_not_Verlet) then  
         axn=-gravity*ssh_x +wave_rad*uwave
         ayn=-gravity*ssh_y +wave_rad*vwave
     else
@@ -228,10 +234,6 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
     drag_ice=c_ice*0.5*(sqrt( (us-ui)**2+(vs-vi)**2 )+sqrt( (uvel0-ui)**2+(vvel0-vi)**2 ))
 
 
-!     RHS_x=(axn/2) + bxn- drag_ocn*(u_star-uo) -drag_atm*(u_star-ua) -drag_ice*(u_star-ui)
-!     RHS_y=(ayn/2) + byn -drag_ocn*(v_star-vo) -drag_atm*(v_star-va) -drag_ice*(v_star-vi)
-
-
      RHS_x=(axn/2) + bxn
      RHS_y=(ayn/2) + byn
 
@@ -271,7 +273,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 !Saving the totally explicit part of the acceleration to use in finding the next position and u_star -Alon
     axn=0.
     ayn=0.
-    if (.not.Runge_not_verlet) then
+    if (.not.Runge_not_Verlet) then
         axn=-gravity*ssh_x +wave_rad*uwave
         ayn=-gravity*ssh_y +wave_rad*vwave
     endif
@@ -1553,7 +1555,7 @@ subroutine evolve_icebergs(bergs)
 integer :: i1,j1,i2,j2,i3,j3,i4,j4
 real :: xi, yj
 logical :: bounced, on_tangential_plane, error_flag
-logical :: Runge_not_verlet  ! Runge_not_verlet=1 for Runge Kutta, =0 for Verlet method. Added by Alon
+logical :: Runge_not_Verlet  ! Runge_not_Verlet=1 for Runge Kutta, =0 for Verlet method. Added by Alon
 type(iceberg), pointer :: berg
 integer :: stderrunit
 
@@ -1584,8 +1586,8 @@ subroutine evolve_icebergs(bergs)
   Rearth=6360.e3
 
   !Choosing time stepping scheme - Alon
-   !Runge_not_verlet=.False.    !Loading manually: true=Runge Kutta, False=Verlet   , Alon
-   Runge_not_verlet=bergs%Runge_not_Verlet  ! Loading directly from namelist/default , Alon
+   !Runge_not_Verlet=.False.    !Loading manually: true=Runge Kutta, False=Verlet   , Alon
+   Runge_not_Verlet=bergs%Runge_not_Verlet  ! Loading directly from namelist/default , Alon
 
   berg=>bergs%first
   do while (associated(berg)) ! loop over all bergs
@@ -1619,7 +1621,16 @@ subroutine evolve_icebergs(bergs)
   if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
     call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling)
 
-  if (Runge_not_verlet) then !Start of the Runge-Kutta Loop -Added by Alon
+
+
+  if (Runge_not_Verlet) then !Start of the Runge-Kutta Loop -Added by Alon, MP2
+
+ !Loading past acceleartions - Alon
+  axn=berg%axn; ayn=berg%ayn !Alon
+  axn1=axn; axn2=axn; axn3=axn; axn4=axn
+  ayn1=ayn; ayn2=ayn; ayn3=ayn; ayn4=ayn
+
+
 
  ! A1 = A(X1)
   lon1=berg%lon; lat1=berg%lat
@@ -1629,7 +1640,8 @@ subroutine evolve_icebergs(bergs)
   uvel1=berg%uvel; vvel1=berg%vvel
   if (on_tangential_plane) call rotvec_to_tang(lon1,uvel1,vvel1,xdot1,ydot1)
   u1=uvel1*dxdl1; v1=vvel1*dydl
-  call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, Runge_not_verlet) !axn,ayn, bxn, byn ,Runge_not_verlet  - Added by Alon
+  !call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, Runge_not_Verlet) !axn,ayn, bxn, byn ,Runge_not_Verlet  - Added by Alon
+  call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn1, ayn1, bxn, byn, Runge_not_Verlet) !Note change to dt. Markpoint_1
   if (on_tangential_plane) call rotvec_to_tang(lon1,ax1,ay1,xddot1,yddot1)
   if (on_tangential_plane) call rotvec_to_tang(lon1,axn1,ayn1,xddot1n,yddot1n) !Alon
   
@@ -1674,7 +1686,7 @@ subroutine evolve_icebergs(bergs)
    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2 (deg)=',dt*v1,dt*v2
    write(stderrunit,*) 'Acceleration terms for position 1'
    error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, Runge_not_verlet, debug_flag=.true.) !axn, ayn, bxn, byn, Runge_not_verlet - Added by Alon
+   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, Runge_not_Verlet, debug_flag=.true.) !axn, ayn, bxn, byn, Runge_not_Verlet - Added by Alon
     call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 2')
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos2 i,j,lon,lat,xi,yj=',i,j,lon2,lat2,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos2 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
@@ -1683,7 +1695,8 @@ subroutine evolve_icebergs(bergs)
   endif
   dxdl2=r180_pi/(Rearth*cos(lat2*pi_180))
   u2=uvel2*dxdl2; v2=vvel2*dydl
-  call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn, Runge_not_verlet) !axn, ayn, bxn, byn, Runge_not_verlet - Added by Alon
+  !call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn, Runge_not_Verlet) !axn, ayn, bxn, byn, Runge_not_Verlet - Added by Alon
+  call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt, ax2, ay2, axn2, ayn2, bxn, byn, Runge_not_Verlet) !Note change to dt. Markpoint_1
   if (on_tangential_plane) call rotvec_to_tang(lon2,ax2,ay2,xddot2,yddot2)
   if (on_tangential_plane) call rotvec_to_tang(lon2,axn2,ayn2,xddot2n,yddot2n) !Alon
   
@@ -1728,10 +1741,10 @@ subroutine evolve_icebergs(bergs)
    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3 (deg)=',dt*v1,dt*v2,dt*v3
    write(stderrunit,*) 'Acceleration terms for position 1'
    error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, Runge_not_verlet, debug_flag=.true.) !axn, ayn, Runge_not_verlet- Added by Alon
+   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, Runge_not_Verlet, debug_flag=.true.) !axn, ayn, Runge_not_Verlet- Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 2'
    error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
-   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn, Runge_not_verlet, debug_flag=.true.) !axn, ayn, bxn, byn, Runge_not_verlet   - Added by Alon
+   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn, Runge_not_Verlet, debug_flag=.true.) !axn, ayn, bxn, byn, Runge_not_Verlet   - Added by Alon
     call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 3')
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos3 i,j,lon,lat,xi,yj=',i,j,lon3,lat3,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos3 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
@@ -1740,7 +1753,7 @@ subroutine evolve_icebergs(bergs)
   endif
   dxdl3=r180_pi/(Rearth*cos(lat3*pi_180))
   u3=uvel3*dxdl3; v3=vvel3*dydl
-  call accel(bergs, berg, i, j, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn3, ayn3, bxn, byn, Runge_not_verlet) !axn, ayn, bxn, byn, Runge_not_verlet   - Added by Alon
+  call accel(bergs, berg, i, j, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn3, ayn3, bxn, byn, Runge_not_Verlet) !axn, ayn, bxn, byn, Runge_not_Verlet   - Added by Alon
   if (on_tangential_plane) call rotvec_to_tang(lon3,ax3,ay3,xddot3,yddot3)
   if (on_tangential_plane) call rotvec_to_tang(lon3,axn3,ayn3,xddot3n,yddot3n) !Alon
   
@@ -1783,13 +1796,13 @@ subroutine evolve_icebergs(bergs)
    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v4 (deg)=',dt*v1,dt*v2,dt*v3,dt*v4
    write(stderrunit,*) 'Acceleration terms for position 1'
    error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, Runge_not_verlet, debug_flag=.true.) !axn, ayn, bxn, byn, Runge_not_verlet   - Added by Alon
+   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, Runge_not_Verlet, debug_flag=.true.) !axn, ayn, bxn, byn, Runge_not_Verlet   - Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 2'
    error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
-   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn, Runge_not_verlet, debug_flag=.true.) !axn, ayn, bxn, byn, Runge_not_verlet    - Added by Alon
+   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn, Runge_not_Verlet, debug_flag=.true.) !axn, ayn, bxn, byn, Runge_not_Verlet    - Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 3'
    error_flag=pos_within_cell(grd, lon3, lat3, i3, j3, xi, yj)
-   call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn3, ayn3, bxn, byn, Runge_not_verlet, debug_flag=.true.) !axn, ayn, bxn, byn, Runge_not_verlet - Added by Alon
+   call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn3, ayn3, bxn, byn, Runge_not_Verlet, debug_flag=.true.) !axn, ayn, bxn, byn, Runge_not_Verlet - Added by Alon
     call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 4')
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos4 i,j,lon,lat,xi,yj=',i,j,lon4,lat4,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos4 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
@@ -1798,7 +1811,7 @@ subroutine evolve_icebergs(bergs)
   endif
   dxdl4=r180_pi/(Rearth*cos(lat4*pi_180))
   u4=uvel4*dxdl4; v4=vvel4*dydl
-  call accel(bergs, berg, i, j, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axn4, ayn4, bxn, byn, Runge_not_verlet) !axn, ayn, bxn, byn, Runge_not_verlet - Added by Alon
+  call accel(bergs, berg, i, j, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axn4, ayn4, bxn, byn, Runge_not_Verlet) !axn, ayn, bxn, byn, Runge_not_Verlet - Added by Alon
   if (on_tangential_plane) call rotvec_to_tang(lon4,ax4,ay4,xddot4,yddot4)
   if (on_tangential_plane) call rotvec_to_tang(lon4,axn4,ayn4,xddot4n,yddot4n)
   
@@ -1861,16 +1874,16 @@ subroutine evolve_icebergs(bergs)
    write(stderrunit,*) 'diamonds, evolve_iceberg: on_tangential_plane=',on_tangential_plane
    write(stderrunit,*) 'Acceleration terms for position 1'
    error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, Runge_not_verlet, debug_flag=.true.)  !axn, ayn, Runge_not_verlet   - Added by Alon
+   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, Runge_not_Verlet, debug_flag=.true.)  !axn, ayn, Runge_not_Verlet   - Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 2'
    error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
-   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn, ayn, bxn, byn, Runge_not_verlet, debug_flag=.true.)  !axn, ayn, Runge_not_verlet  - Added by Alon
+   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn, ayn, bxn, byn, Runge_not_Verlet, debug_flag=.true.)  !axn, ayn, Runge_not_Verlet  - Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 3'
    error_flag=pos_within_cell(grd, lon3, lat3, i3, j3, xi, yj)
-   call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn, ayn, bxn, byn, Runge_not_verlet, debug_flag=.true.)  !axn, ayn, Runge_not_verlet   - Added by Alon
+   call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn, ayn, bxn, byn, Runge_not_Verlet, debug_flag=.true.)  !axn, ayn, Runge_not_Verlet   - Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 4'
    error_flag=pos_within_cell(grd, lon4, lat4, i4, j4, xi, yj)
-   call accel(bergs, berg, i4, j4, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axn, ayn, bxn, byn, Runge_not_verlet, debug_flag=.true.)  !axn, ayn, Runge_not_verlet    - Added by Alon
+   call accel(bergs, berg, i4, j4, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axn, ayn, bxn, byn, Runge_not_Verlet, debug_flag=.true.)  !axn, ayn, Runge_not_Verlet    - Added by Alon
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'posn i,j,lon,lat,xi,yj=',i,j,lonn,latn,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'posn box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
     call print_berg(stderrunit, berg, 'evolve_iceberg, out of cell at end!')
@@ -1890,7 +1903,7 @@ subroutine evolve_icebergs(bergs)
 
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
-  if (.not.Runge_not_verlet) then !Start of the Verlet time_stepping -Whole loop added by Alon
+  if (.not.Runge_not_Verlet) then !Start of the Verlet time_stepping -Whole loop added by Alon
 
  ! In this scheme a_n and b_n are saved from the previous timestep, giving the explicit and implicit parts of the acceleration, and a_np1, b_np1 are for the next time step
  ! Note that ax1=a_np1/2 +b_np1, as calculated by the acceleration subrouting
@@ -1935,14 +1948,14 @@ subroutine evolve_icebergs(bergs)
 !Adjusting mass...                      Alon decided to move this before calculating the new velocities (so that acceleration can be a fn(r_np1)
   i=i1;j=j1;xi=berg%xi;yj=berg%yj
   call adjust_index_and_ground(grd, lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
+!  call adjust_index_and_ground(grd, lonn, latn, uvel1, vvel1, i, j, xi, yj, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
   i2=i; j2=j
   if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
     call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling)
 
 
 !Calling the acceleration   (note that the velocity is converted to u_star inside the accel script)
-!  call accel(bergs, berg, i, j, xi, yj, latn, uvel3, vvel3, uvel1, vvel1, dt, ax1, ay1, axn, ayn, bxn, byn, Runge_not_verlet) !axn, ayn, bxn, byn ,Runge_not_verlet  - Added by Alon
-  call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn, ayn, bxn, byn, Runge_not_verlet) !axn, ayn, bxn, byn ,Runge_not_verlet  - Added by Alon
+  call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn, ayn, bxn, byn, Runge_not_Verlet) !axn, ayn, bxn, byn ,Runge_not_Verlet  - Added by Alon
 
 !Solving for the new velocity
   if (on_tangential_plane) then
@@ -1951,10 +1964,11 @@ subroutine evolve_icebergs(bergs)
     xdotn=xdot3+(dt*xddot1); ydotn=ydot3+(dt*yddot1)                                    !Alon
     call rotvec_from_tang(lonn,xdotn,ydotn,uveln,vveln)
   else
-    uvel4=uvel3+dt*ax1; vvel4=vvel3+dt*ay1    !Alon , we call it uvel3, vvel3 until it is put into lat/long co-ordinates, where it becomes uveln, vveln
+    uvel4=uvel3+(dt*ax1); vvel4=vvel3+(dt*ay1)    !Alon , we call it uvel3, vvel3 until it is put into lat/long co-ordinates, where it becomes uveln, vveln
   endif
-  uveln=uvel4*dxdln; vveln=vvel4*dydl    !Converted to degrees.
-
+!  uveln=uvel4*dxdln; vveln=vvel4*dydl    !Converted to degrees.  (Perhaps this should not be here)
+  uveln=uvel4
+  vveln=vvel4 
 
 !Debugging
   if (.not.error_flag) then
@@ -1988,7 +2002,7 @@ subroutine evolve_icebergs(bergs)
    write(stderrunit,*) 'diamonds, evolve_iceberg: on_tangential_plane=',on_tangential_plane
    write(stderrunit,*) 'Acceleration terms for position 1'
    error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i2, j2, xi, yj, latn, uvel3, vvel3, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, Runge_not_verlet, debug_flag=.true.)  !axn, ayn, bxn, byn, Runge_not_verlet   - Added by Alon
+   call accel(bergs, berg, i2, j2, xi, yj, latn, uvel3, vvel3, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, Runge_not_Verlet, debug_flag=.true.)  !axn, ayn, bxn, byn, Runge_not_Verlet   - Added by Alon
    
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'posn i,j,lon,lat,xi,yj=',i,j,lonn,latn,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'posn box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)

From 1711492f928ce63ab665744bd03003a2062776ec Mon Sep 17 00:00:00 2001
From: Niki Zadeh <Niki.Zadeh@noaa.gov>
Date: Thu, 18 Jun 2015 18:45:06 -0400
Subject: [PATCH 022/361] Fix issue #1 the apparent hang in writing the
 trajectories

- Model run apparently hangs at the end when trying to write icebergs trajectories
  This is not an i/o issue but due to the root pe (or io_tile_root_pes) traversing
  a linked list of millions of nodes. It just take a long long time.
- This fix "push"es the nodes at the top of the list instead of trying to find the tail to append it.
  The list will be in reverse order and has to be reversed before writing to file.
---
 icebergs_framework.F90 | 29 ++++++++++++++++++++++++++++-
 icebergs_io.F90        |  7 +++++--
 2 files changed, 33 insertions(+), 3 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 48dfe14..148cde2 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -65,6 +65,7 @@ module ice_bergs_framework
 public checksum_gridded
 public grd_chksum2,grd_chksum3
 public fix_restart_dates, offset_berg_dates
+public reverse_list
 
 type :: icebergs_gridded
   type(domain2D), pointer :: domain ! MPP domain
@@ -1201,7 +1202,9 @@ subroutine unpack_traj_from_buffer2(first, buff, n)
     traj%cn=buff%data(22,n)
     traj%hi=buff%data(23,n)
 
-    call append_posn(first, traj) 
+!    call append_posn(first, traj) !This call could take a very long time (as if the run hangs) if there are millions of nodes in the list. Use push_posn instead and reverse the list later before writing the file.
+! 
+    call push_posn(first, traj) 
 
   end subroutine unpack_traj_from_buffer2
 
@@ -1623,6 +1626,30 @@ end subroutine record_posn
 
 ! ##############################################################################
 
+subroutine reverse_list(list)
+  ! Arguments
+  type(xyt), pointer :: list
+  
+  ! Local variables
+  type(xyt), pointer :: head,tail,node
+  integer :: i
+
+  i=0
+  head=>list
+  tail=>list
+  node=>list%next
+  list%next=>null()
+  do while (associated(node))  
+     head=>node
+     node=>node%next
+     head%next=>tail
+     tail=>head
+     i=i+1
+  enddo
+  list=>head
+  print*,'reverse_list number of nodes= ',i
+end subroutine reverse_list
+
 subroutine push_posn(trajectory, posn_vals)
 ! Arguments
 type(xyt), pointer :: trajectory
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 154fca6..48b4c36 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -22,6 +22,7 @@ module ice_bergs_io
 use ice_bergs_framework, only: pack_berg_into_buffer2,unpack_berg_from_buffer2
 use ice_bergs_framework, only: pack_traj_into_buffer2,unpack_traj_from_buffer2
 use ice_bergs_framework, only: find_cell,find_cell_by_search,count_bergs,is_point_in_cell,pos_within_cell,append_posn
+use ice_bergs_framework, only: push_posn
 use ice_bergs_framework, only: add_new_berg_to_list,destroy_iceberg
 use ice_bergs_framework, only: increase_ibuffer,increase_ibuffer_traj,grd_chksum2,grd_chksum3
 use ice_bergs_framework, only: sum_mass,sum_heat,bilin
@@ -29,7 +30,7 @@ module ice_bergs_io
 use ice_bergs_framework, only: nclasses, buffer_width, buffer_width_traj
 use ice_bergs_framework, only: verbose, really_debug, debug, restart_input_dir,make_calving_reproduce
 use ice_bergs_framework, only: ignore_ij_restart, use_slow_find,generate_test_icebergs,print_berg
-
+use ice_bergs_framework, only: reverse_list
 
 implicit none ; private
 
@@ -844,7 +845,7 @@ subroutine write_trajectory(trajectory)
      if(associated(trajectory)) then
         this=>trajectory
         do while (associated(this))
-           call append_posn(traj4io, this)
+           call push_posn(traj4io, this)
            this=>this%next
         enddo
      endif
@@ -854,6 +855,7 @@ subroutine write_trajectory(trajectory)
   ntrajs_sent_io =0
   ntrajs_rcvd_io =0 
 
+
   if(is_io_tile_root_pe) then
      !Receive trajs from all pes in this I/O tile !FRAGILE!SCARY!
      do np=2,size(io_tile_pelist) ! Note: np starts from 2 to exclude self
@@ -867,6 +869,7 @@ subroutine write_trajectory(trajectory)
            enddo
        endif
      enddo
+     call reverse_list(traj4io)
   else
      !Pack and Send trajs to the root pe for this I/O tile
      if (associated(trajectory)) then

From 34783215c04328be28cfd628e5d838bec9ddceb8 Mon Sep 17 00:00:00 2001
From: Alon Stern <Alon.Stern@gaea1.ncrc.gov>
Date: Mon, 22 Jun 2015 16:24:24 -0400
Subject: [PATCH 023/361] Included a spring force between icebergs. Damping has
 not been included yet. Have not looked closely to see if it works, but it
 does run.

---
 icebergs.F90 | 156 ++++++++++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 149 insertions(+), 7 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 5877b14..5e0a896 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -112,6 +112,138 @@ subroutine icebergs_init(bergs, &
 
 end subroutine icebergs_init
 
+
+! ##############################################################################
+
+subroutine interactive_force(bergs,berg,IA_x, IA_y) !Calculating interactive force between icebergs. Alon,  Markpoint_4
+type(icebergs), pointer :: bergs
+type(iceberg), pointer :: berg
+type(iceberg), pointer :: other_berg
+real :: T1, L1, W1, lon1, lat1, x1, y1, R1, A1   !Current iceberg
+real :: T2, L2, W2, lon2, lat2, x2, y2, R2, A2   !Other iceberg
+real :: L_crit, r_dist_x, r_dist_y, r_dist, A_o, trapped, T_min
+real :: Rearth
+real :: kappa_s, accel_spring
+real, intent(inout) :: IA_x, IA_y 
+integer :: stderrunit
+
+Rearth=6360.e3
+kappa_s=1.e-4
+
+! Get the stderr unit number.  Not sure what this does
+  stderrunit = stderr()
+
+IA_x=0.
+IA_y=0.
+
+L1=berg%length
+W1=berg%width
+T1=berg%thickness 
+A1=L1*W1 
+R1=sqrt(A1/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
+lon1=berg%lon; lat1=berg%lat
+call rotpos_to_tang(lon1,lat1,x1,y1)
+
+  other_berg=>bergs%first
+  do while (associated(other_berg)) ! loop over all other bergs    - Need to think about which icebergs to loop over
+       L2=other_berg%length
+       W2=other_berg%width
+       T2=other_berg%thickness 
+       A2=L2*W2
+       R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
+       L_crit=(R1+R2)
+       lon2=berg%lon; lat2=berg%lat
+       call rotpos_to_tang(lon2,lat2,x2,y2)
+
+       r_dist_x=x1-x2 ; r_dist_y=y1-y2
+       r_dist=sqrt( ((x1-x2)**2) + ((y1-y2)**2) )
+
+      call overlap_area(R1,R2,r_dist,A_o,trapped)
+      T_min=min(T1,T2)
+      accel_spring=kappa_s*(T_min/T1)*(A_o/A1)
+
+      if (r_dist>0) then
+          IA_x=IA_x+(accel_spring*(r_dist_x/r_dist))
+          IA_y=IA_y+(accel_spring*(r_dist_y/r_dist))
+      endif
+
+       other_berg=>other_berg%next
+  enddo ! loop over all bergs
+
+  contains
+
+
+   subroutine overlap_area(R1,R2,d,A,trapped)
+        real, intent(in) :: R1, R2, d
+        real, intent(out) :: A, Trapped
+        real :: R1_sq, R2_sq, d_sq  
+        R1_sq=R1**2
+        R2_sq=R2**2
+        d_sq=d**2
+        Trapped=0.
+
+if (d>0) then
+        if (d<(R1+R2)) then
+             if (d>abs(R1-R2)) then
+                  A= (R1_sq*acos((d_sq+R1_sq-R2_sq)/(2.*d*R1)))  +  (R2_sq*acos((d_sq+R2_sq-R1_sq)/(2.*d*R2)))  - (0.5*sqrt((-d+R1+R2)*(d+R1-R2)*(d-R1+R2)*(d+R1+R2)))
+             else
+                  A=min(pi*R1_sq,pi*R2_sq) 
+                  Trapped=1.
+             endif
+       else
+             A=0.
+       endif
+else
+       A=0.     ! No area of perfectly overlapping bergs (ie: a berg interacting with itself)
+endif
+
+   end subroutine overlap_area
+
+
+  subroutine rotpos_to_tang(lon, lat, x, y)
+  ! Arguments
+  real, intent(in) :: lon, lat
+  real, intent(out) :: x, y
+  ! Local variables
+  real :: r,colat,clon,slon
+
+    if (lat>90.) then
+      write(stderrunit,*) 'diamonds, rotpos_to_tang: lat>90 already!',lat
+      call error_mesg('diamonds, rotpos_to_tang','Something went very wrong!',FATAL)
+    endif
+    if (lat==90.) then
+      write(stderrunit,*) 'diamonds, rotpos_to_tang: lat==90 already!',lat
+      call error_mesg('diamonds, rotpos_to_tang','Something went wrong!',FATAL)
+    endif
+
+    colat=90.-lat
+    r=Rearth*(colat*pi_180)
+    clon=cos(lon*pi_180)
+    slon=sin(lon*pi_180)
+    x=r*clon
+    y=r*slon
+
+  end subroutine rotpos_to_tang
+
+
+
+end subroutine interactive_force
+
+
+! ##############################################################################
+
+
+!call Interactive_damping(bergs,berg, P_11, P_12, P_21, P_22, P_times_u_x, P_times_u_y) ! Damping forces, Made by Alon.
+
+
+
+
+
+
+!end subroutine interactive_force
+
+! ##############################################################################
+
 subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, axn, ayn, bxn, byn, Runge_not_Verlet, debug_flag) !Saving  acceleration for Verlet, Adding Verlet flag - Alon
 !subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, debug_flag) !old version commmented out by Alon
 ! Arguments
@@ -133,6 +265,8 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 real :: lambda, detA, A11, A12, RHS_x, RHS_y, D_hi 
 real :: uveln, vveln, us, vs, speed, loc_dx, new_speed
 real :: u_star, v_star    !Added by Alon
+real :: IA_x, IA_y    !Added by Alon
+real :: P_11, P_12, P_21, P_22, P_time_u_x, P_times_u_y    !Added by Alon
 logical :: dumpit
 logical, intent(in) :: Runge_not_Verlet  ! Flag to specify whether it is Runge-Kutta or Verlet
 integer :: itloop
@@ -148,7 +282,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
   ! For convenience
   grd=>bergs%grd
 
-  ! Interpolate gridded fields to berg 
+  ! Interpolate gridded fields to berg     - Note: It should be possible to move this to evolve, so that it only needs to be called once. !!!!
   call interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, cn, hi)
 
    f_cori=(2.*omega)*sin(pi_180*lat)
@@ -167,6 +301,13 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
   bxn=0.
   byn=0.
 
+! Interactive spring acceleration - Note: It should be possible to move this to evolve, so that it only needs to be called once. !!!!
+  call Interactive_force(bergs,berg,IA_x, IA_y) ! Spring forces, Made by Alon.
+
+!IA_x=0.
+!IA_y=0.
+
+
   hi=min(hi,D)
   D_hi=max(0.,D-hi)
 
@@ -203,12 +344,12 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 
     ! Half half accelerations  - axn, ayn
     if (.not.Runge_not_Verlet) then  
-        axn=-gravity*ssh_x +wave_rad*uwave
-        ayn=-gravity*ssh_y +wave_rad*vwave
+        axn=-gravity*ssh_x +wave_rad*uwave + IA_x
+        ayn=-gravity*ssh_y +wave_rad*vwave + IA_y
     else
     ! Not half half accelerations  - for RK
-        bxn=-gravity*ssh_x +wave_rad*uwave
-        byn=-gravity*ssh_y +wave_rad*vwave
+        bxn=-gravity*ssh_x +wave_rad*uwave + IA_x
+        byn=-gravity*ssh_y +wave_rad*vwave + IA_y
      endif
 
   if (alpha>0.) then ! If implicit Coriolis, use u_star rather than RK4 latest  !Alon
@@ -233,6 +374,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
     drag_atm=c_atm*0.5*(sqrt( (us-ua)**2+(vs-va)**2 )+sqrt( (uvel0-ua)**2+(vvel0-va)**2 ))
     drag_ice=c_ice*0.5*(sqrt( (us-ui)**2+(vs-vi)**2 )+sqrt( (uvel0-ui)**2+(vvel0-vi)**2 ))
 
+!    call Interactive_damping(bergs,berg, P_11, P_12, P_21, P_22, P_times_u_x, P_times_u_y) ! Damping forces, Made by Alon.
 
      RHS_x=(axn/2) + bxn
      RHS_y=(ayn/2) + byn
@@ -274,8 +416,8 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
     axn=0.
     ayn=0.
     if (.not.Runge_not_Verlet) then
-        axn=-gravity*ssh_x +wave_rad*uwave
-        ayn=-gravity*ssh_y +wave_rad*vwave
+        axn=-gravity*ssh_x +wave_rad*uwave + IA_x
+        ayn=-gravity*ssh_y +wave_rad*vwave + IA_y
     endif
     if (C_N>0.) then !  C_N=1 for Crank Nicolson Coriolis, C_N=0 for full implicit Coriolis !Alon 
       axn=axn+f_cori*vveln

From 6f02e55dc7d4f8675b251dbe4e4decc0c6d6d0ee Mon Sep 17 00:00:00 2001
From: Alon Stern <Alon.Stern@gaea7.ncrc.gov>
Date: Tue, 23 Jun 2015 10:12:10 -0400
Subject: [PATCH 024/361] Interactive force and damping on relative motion have
 been included. As it stands, each iceberg looks at all other icebergs in its
 list (which I think only includes icebergs on the same tile). This needs to
 be thought through. The current scheme is also not order independent, and has
 not been tested.

---
 icebergs.F90 | 83 +++++++++++++++++++++++++++++++++++-----------------
 1 file changed, 56 insertions(+), 27 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 5e0a896..e90ca55 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -115,26 +115,35 @@ end subroutine icebergs_init
 
 ! ##############################################################################
 
-subroutine interactive_force(bergs,berg,IA_x, IA_y) !Calculating interactive force between icebergs. Alon,  Markpoint_4
+subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y) !Calculating interactive force between icebergs. Alon,  Markpoint_4
 type(icebergs), pointer :: bergs
 type(iceberg), pointer :: berg
 type(iceberg), pointer :: other_berg
 real :: T1, L1, W1, lon1, lat1, x1, y1, R1, A1   !Current iceberg
 real :: T2, L2, W2, lon2, lat2, x2, y2, R2, A2   !Other iceberg
-real :: L_crit, r_dist_x, r_dist_y, r_dist, A_o, trapped, T_min
+real :: r_dist_x, r_dist_y, r_dist, A_o, trapped, T_min
+real, intent(in) :: u0,v0, u1, v1
+real :: P_11, P_12, P_21, P_22
+real :: u2, v2
 real :: Rearth
-real :: kappa_s, accel_spring
-real, intent(inout) :: IA_x, IA_y 
+real :: kappa_s, accel_spring, p_ia, p_ia_coef, q_ia
+real, intent(out) :: IA_x, IA_y 
+real, intent(out) :: P_ia_11, P_ia_12, P_ia_22, P_ia_21, P_ia_times_u_x, P_ia_times_u_y
 integer :: stderrunit
 
 Rearth=6360.e3
 kappa_s=1.e-4
+p_ia=2.*sqrt(kappa_s)  ! Critical damping  
+q_ia=(2.*sqrt(kappa_s)/5)  ! Critical damping  /5   (just a guess)
 
 ! Get the stderr unit number.  Not sure what this does
   stderrunit = stderr()
 
 IA_x=0.
 IA_y=0.
+P_ia_11=0. ; P_ia_12=0.  ;  P_ia_22=0. 
+P_ia_times_u_x=0. ; P_ia_times_u_y=0.
+
 
 L1=berg%length
 W1=berg%width
@@ -149,9 +158,10 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y) !Calculating interactive for
        L2=other_berg%length
        W2=other_berg%width
        T2=other_berg%thickness 
+       u2=other_berg%uvel 
+       v2=other_berg%vvel 
        A2=L2*W2
        R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
-       L_crit=(R1+R2)
        lon2=berg%lon; lat2=berg%lat
        call rotpos_to_tang(lon2,lat2,x2,y2)
 
@@ -160,13 +170,46 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y) !Calculating interactive for
 
       call overlap_area(R1,R2,r_dist,A_o,trapped)
       T_min=min(T1,T2)
-      accel_spring=kappa_s*(T_min/T1)*(A_o/A1)
 
-      if (r_dist>0) then
+      !Calculating spring force  (later this should only be done on the first time around)
+      accel_spring=kappa_s*(T_min/T1)*(A_o/A1)
+      if ((r_dist>0) .AND. (r_dist< (R1+R2)) ) then
           IA_x=IA_x+(accel_spring*(r_dist_x/r_dist))
           IA_y=IA_y+(accel_spring*(r_dist_y/r_dist))
       endif
 
+
+      !Working out the damping
+
+       !Paralel velocity
+       P_11=(r_dist_x*r_dist_x)/(r_dist**2)
+       P_12=(r_dist_x*r_dist_y)/(r_dist**2)
+       P_22=(r_dist_y*r_dist_y)/(r_dist**2)
+     
+       p_ia_coef=p_ia*(T_min/T1)*(A_o/A1)
+       p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2))+sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
+
+       P_ia_11=P_ia_11+p_ia_coef*P_11
+       P_ia_12=P_ia_12+p_ia_coef*P_12
+       P_ia_21=P_ia_21+p_ia_coef*P_21
+       P_ia_22=P_ia_22+p_ia_coef*P_22
+       P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
+       P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
+
+
+       !Normal velocities
+       P_11=1-P_11  ;  P_12=-P_12 ; P_22=1-P_22
+       p_ia_coef=q_ia*(T_min/T1)*(A_o/A1)
+       p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2))+sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
+
+       P_ia_11=P_ia_11+p_ia_coef*P_11
+       P_ia_12=P_ia_12+p_ia_coef*P_12
+       P_ia_21=P_ia_21+p_ia_coef*P_21
+       P_ia_22=P_ia_22+p_ia_coef*P_22
+       P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
+       P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
+
+
        other_berg=>other_berg%next
   enddo ! loop over all bergs
 
@@ -225,25 +268,12 @@ subroutine rotpos_to_tang(lon, lat, x, y)
 
   end subroutine rotpos_to_tang
 
-
-
 end subroutine interactive_force
 
 
 ! ##############################################################################
 
 
-!call Interactive_damping(bergs,berg, P_11, P_12, P_21, P_22, P_times_u_x, P_times_u_y) ! Damping forces, Made by Alon.
-
-
-
-
-
-
-!end subroutine interactive_force
-
-! ##############################################################################
-
 subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, axn, ayn, bxn, byn, Runge_not_Verlet, debug_flag) !Saving  acceleration for Verlet, Adding Verlet flag - Alon
 !subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, debug_flag) !old version commmented out by Alon
 ! Arguments
@@ -266,7 +296,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 real :: uveln, vveln, us, vs, speed, loc_dx, new_speed
 real :: u_star, v_star    !Added by Alon
 real :: IA_x, IA_y    !Added by Alon
-real :: P_11, P_12, P_21, P_22, P_time_u_x, P_times_u_y    !Added by Alon
+real :: P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y    !Added by Alon
 logical :: dumpit
 logical, intent(in) :: Runge_not_Verlet  ! Flag to specify whether it is Runge-Kutta or Verlet
 integer :: itloop
@@ -302,11 +332,8 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
   byn=0.
 
 ! Interactive spring acceleration - Note: It should be possible to move this to evolve, so that it only needs to be called once. !!!!
-  call Interactive_force(bergs,berg,IA_x, IA_y) ! Spring forces, Made by Alon.
-
-!IA_x=0.
-!IA_y=0.
-
+!P_ia_11=0. ; P_ia_12=0.  ; P_ia_21=0.  ; P_ia22=0.  ; P_times_u_x=0.   P_times_u_y=0. ; IA_x=0.  ;  IA_y=0.
+call Interactive_force(bergs, berg, IA_x, IA_y, uvel0, vvel0, uvel0, vvel0, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y) ! Spring forces, Made by Alon.
 
   hi=min(hi,D)
   D_hi=max(0.,D-hi)
@@ -374,7 +401,9 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
     drag_atm=c_atm*0.5*(sqrt( (us-ua)**2+(vs-va)**2 )+sqrt( (uvel0-ua)**2+(vvel0-va)**2 ))
     drag_ice=c_ice*0.5*(sqrt( (us-ui)**2+(vs-vi)**2 )+sqrt( (uvel0-ui)**2+(vvel0-vi)**2 ))
 
-!    call Interactive_damping(bergs,berg, P_11, P_12, P_21, P_22, P_times_u_x, P_times_u_y) ! Damping forces, Made by Alon.
+    if (itloop>1) then
+        call Interactive_force(bergs, berg, IA_x, IA_y, us, vs, uvel0, vvel0, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y) ! Spring forces, Made by Alon.
+    endif
 
      RHS_x=(axn/2) + bxn
      RHS_y=(ayn/2) + byn

From c4c94c1a1c7324b4395a2eea3b27fb7bce084885 Mon Sep 17 00:00:00 2001
From: Alon Stern <Alon.Stern@gaea7.ncrc.gov>
Date: Tue, 23 Jun 2015 14:56:46 -0400
Subject: [PATCH 025/361] Small change - bxn byn are now calculated correctly
 in RK.

---
 icebergs.F90 | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/icebergs.F90 b/icebergs.F90
index e90ca55..96891b2 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -2005,6 +2005,9 @@ subroutine evolve_icebergs(bergs)
     vveln=berg%vvel+dt_6*( (ay1+ay4)+2.*(ay2+ay3) )
     axn=( (axn1+axn4)+2.*(axn2+axn3) )/6. !Alon
     ayn=( (ayn1+ayn4)+2.*(ayn2+ayn3) )/6. !Alon
+    bxn=(((ax1+ax4)+2.*(ax2+ax3) )/6)  - (axn/2)
+    byn=(((ay1+ay4)+2.*(ay2+ay3) )/6)  - (ayn/2)
+
   endif
 
 

From da6038755cbed5847d7d5db835a0b049939e90b3 Mon Sep 17 00:00:00 2001
From: Alon Stern <Alon.Stern@gaea7.ncrc.gov>
Date: Wed, 24 Jun 2015 15:37:43 -0400
Subject: [PATCH 026/361] The interactive damping has been added.

---
 icebergs.F90 | 57 +++++++++++++++++++++++++++++++++++++---------------
 1 file changed, 41 insertions(+), 16 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 96891b2..ae147f4 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -298,10 +298,13 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 real :: IA_x, IA_y    !Added by Alon
 real :: P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y    !Added by Alon
 logical :: dumpit
+logical :: interactive_icebergs_on  ! Flag to decide whether to use forces between icebergs.
 logical, intent(in) :: Runge_not_Verlet  ! Flag to specify whether it is Runge-Kutta or Verlet
 integer :: itloop
 integer :: stderrunit
 
+interactive_icebergs_on=.true.
+
 !print *, 'axn=',axn,'ayn=',ayn
   u_star=uvel0+(axn*(dt/2.))  !Alon
   v_star=vvel0+(ayn*(dt/2.))  !Alon
@@ -331,10 +334,6 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
   bxn=0.
   byn=0.
 
-! Interactive spring acceleration - Note: It should be possible to move this to evolve, so that it only needs to be called once. !!!!
-!P_ia_11=0. ; P_ia_12=0.  ; P_ia_21=0.  ; P_ia22=0.  ; P_times_u_x=0.   P_times_u_y=0. ; IA_x=0.  ;  IA_y=0.
-call Interactive_force(bergs, berg, IA_x, IA_y, uvel0, vvel0, uvel0, vvel0, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y) ! Spring forces, Made by Alon.
-
   hi=min(hi,D)
   D_hi=max(0.,D-hi)
 
@@ -371,14 +370,28 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 
     ! Half half accelerations  - axn, ayn
     if (.not.Runge_not_Verlet) then  
-        axn=-gravity*ssh_x +wave_rad*uwave + IA_x
-        ayn=-gravity*ssh_y +wave_rad*vwave + IA_y
+        axn=-gravity*ssh_x +wave_rad*uwave 
+        ayn=-gravity*ssh_y +wave_rad*vwave 
     else
     ! Not half half accelerations  - for RK
-        bxn=-gravity*ssh_x +wave_rad*uwave + IA_x
-        byn=-gravity*ssh_y +wave_rad*vwave + IA_y
+        bxn=-gravity*ssh_x +wave_rad*uwave 
+        byn=-gravity*ssh_y +wave_rad*vwave 
      endif
 
+
+! Interactive spring acceleration - (Does the spring part need to be called twice?)
+if (interactive_icebergs_on) then
+           call Interactive_force(bergs, berg, IA_x, IA_y, uvel0, vvel0, uvel0, vvel0, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y) ! Spring forces, Made by Alon.
+           if (.not.Runge_not_Verlet) then
+               axn=axn + IA_x
+               ayn=ayn + IA_y
+           else
+               bxn=bxn + IA_x
+               byn=byn + IA_y
+           endif
+endif
+
+
   if (alpha>0.) then ! If implicit Coriolis, use u_star rather than RK4 latest  !Alon
         if (C_N>0.) then !  C_N=1 for Crank Nicolson Coriolis, C_N=0 for full implicit Coriolis !Alon  
            axn=axn+f_cori*v_star
@@ -401,21 +414,33 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
     drag_atm=c_atm*0.5*(sqrt( (us-ua)**2+(vs-va)**2 )+sqrt( (uvel0-ua)**2+(vvel0-va)**2 ))
     drag_ice=c_ice*0.5*(sqrt( (us-ui)**2+(vs-vi)**2 )+sqrt( (uvel0-ui)**2+(vvel0-vi)**2 ))
 
-    if (itloop>1) then
-        call Interactive_force(bergs, berg, IA_x, IA_y, us, vs, uvel0, vvel0, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y) ! Spring forces, Made by Alon.
-    endif
-
      RHS_x=(axn/2) + bxn
      RHS_y=(ayn/2) + byn
 
      if (beta>0.) then ! If implicit, use u_star, v_star rather than RK4 latest
-         RHS_x=RHS_x - drag_ocn*(u_star-uo) -drag_atm*(u_star-ua) -drag_ice*(u_star-ui)
-         RHS_y=RHS_y - drag_ocn*(v_star-vo) -drag_atm*(v_star-va) -drag_ice*(v_star-vi)
+         RHS_x=RHS_x - drag_ocn*(u_star-uo) -drag_atm*(u_star-ua) -drag_ice*(u_star-ui) 
+         RHS_y=RHS_y - drag_ocn*(v_star-vo) -drag_atm*(v_star-va) -drag_ice*(v_star-vi)  
     else
-         RHS_x=RHS_x - drag_ocn*(uvel-uo) -drag_atm*(uvel-ua) -drag_ice*(uvel-ui)
-         RHS_y=RHS_y - drag_ocn*(vvel-vo) -drag_atm*(vvel-va) -drag_ice*(vvel-vi)
+         RHS_x=RHS_x - drag_ocn*(uvel-uo) -drag_atm*(uvel-ua) -drag_ice*(uvel-ui)  
+         RHS_y=RHS_y - drag_ocn*(vvel-vo) -drag_atm*(vvel-va) -drag_ice*(vvel-vi)  
     endif
 
+if (interactive_icebergs_on) then
+   if (itloop>1) then
+        call Interactive_force(bergs, berg, IA_x, IA_y, us, vs, uvel0, vvel0, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y) ! Spring forces, Made by Alon.
+    endif
+     if (beta>0.) then ! If implicit, use u_star, v_star rather than RK4 latest
+         RHS_x=RHS_x -(((P_ia_11*u_star)+(P_ia_12*v_star))-P_ia_times_u_x) 
+         RHS_y=RHS_y -(((P_ia_21*u_star)+(P_ia_22*v_star))-P_ia_times_u_y) 
+    else
+         RHS_x=RHS_x - (((P_ia_11*uvel)+(P_ia_12*vvel))-P_ia_times_u_x)
+         RHS_y=RHS_y - (((P_ia_21*uvel)+(P_ia_22*vvel))-P_ia_times_u_y)       
+    endif
+endif
+
+
+
+
   ! Solve for implicit accelerations
     if (alpha+beta.gt.0.) then
       lambda=drag_ocn+drag_atm+drag_ice

From 78556e57cab3dc7448b749da561881d7b9475151 Mon Sep 17 00:00:00 2001
From: Alon Stern <Alon.Stern@gaea7.ncrc.gov>
Date: Wed, 24 Jun 2015 15:44:27 -0400
Subject: [PATCH 027/361] Removed the Runge_not_Verlet flag from the
 acceleration calls, and loaded it instead inside the accel subroutine.

---
 icebergs.F90 | 41 +++++++++++++++++++++--------------------
 1 file changed, 21 insertions(+), 20 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index ae147f4..89170d4 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -274,7 +274,7 @@ end subroutine interactive_force
 ! ##############################################################################
 
 
-subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, axn, ayn, bxn, byn, Runge_not_Verlet, debug_flag) !Saving  acceleration for Verlet, Adding Verlet flag - Alon
+subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, axn, ayn, bxn, byn, debug_flag) !Saving  acceleration for Verlet, Adding Verlet flag - Alon
 !subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, debug_flag) !old version commmented out by Alon
 ! Arguments
 type(icebergs), pointer :: bergs
@@ -299,11 +299,12 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 real :: P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y    !Added by Alon
 logical :: dumpit
 logical :: interactive_icebergs_on  ! Flag to decide whether to use forces between icebergs.
-logical, intent(in) :: Runge_not_Verlet  ! Flag to specify whether it is Runge-Kutta or Verlet
+logical :: Runge_not_Verlet  ! Flag to specify whether it is Runge-Kutta or Verlet
 integer :: itloop
 integer :: stderrunit
 
 interactive_icebergs_on=.true.
+Runge_not_Verlet=bergs%Runge_not_Verlet  ! Loading directly from namelist/default , Alon
 
 !print *, 'axn=',axn,'ayn=',ayn
   u_star=uvel0+(axn*(dt/2.))  !Alon
@@ -1836,8 +1837,8 @@ subroutine evolve_icebergs(bergs)
   uvel1=berg%uvel; vvel1=berg%vvel
   if (on_tangential_plane) call rotvec_to_tang(lon1,uvel1,vvel1,xdot1,ydot1)
   u1=uvel1*dxdl1; v1=vvel1*dydl
-  !call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, Runge_not_Verlet) !axn,ayn, bxn, byn ,Runge_not_Verlet  - Added by Alon
-  call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn1, ayn1, bxn, byn, Runge_not_Verlet) !Note change to dt. Markpoint_1
+  !call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn) !axn,ayn, bxn, byn  - Added by Alon
+  call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn1, ayn1, bxn, byn) !Note change to dt. Markpoint_1
   if (on_tangential_plane) call rotvec_to_tang(lon1,ax1,ay1,xddot1,yddot1)
   if (on_tangential_plane) call rotvec_to_tang(lon1,axn1,ayn1,xddot1n,yddot1n) !Alon
   
@@ -1882,7 +1883,7 @@ subroutine evolve_icebergs(bergs)
    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2 (deg)=',dt*v1,dt*v2
    write(stderrunit,*) 'Acceleration terms for position 1'
    error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, Runge_not_Verlet, debug_flag=.true.) !axn, ayn, bxn, byn, Runge_not_Verlet - Added by Alon
+   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn,- Added by Alon
     call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 2')
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos2 i,j,lon,lat,xi,yj=',i,j,lon2,lat2,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos2 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
@@ -1891,8 +1892,8 @@ subroutine evolve_icebergs(bergs)
   endif
   dxdl2=r180_pi/(Rearth*cos(lat2*pi_180))
   u2=uvel2*dxdl2; v2=vvel2*dydl
-  !call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn, Runge_not_Verlet) !axn, ayn, bxn, byn, Runge_not_Verlet - Added by Alon
-  call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt, ax2, ay2, axn2, ayn2, bxn, byn, Runge_not_Verlet) !Note change to dt. Markpoint_1
+  !call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
+  call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt, ax2, ay2, axn2, ayn2, bxn, byn) !Note change to dt. Markpoint_1
   if (on_tangential_plane) call rotvec_to_tang(lon2,ax2,ay2,xddot2,yddot2)
   if (on_tangential_plane) call rotvec_to_tang(lon2,axn2,ayn2,xddot2n,yddot2n) !Alon
   
@@ -1937,10 +1938,10 @@ subroutine evolve_icebergs(bergs)
    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3 (deg)=',dt*v1,dt*v2,dt*v3
    write(stderrunit,*) 'Acceleration terms for position 1'
    error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, Runge_not_Verlet, debug_flag=.true.) !axn, ayn, Runge_not_Verlet- Added by Alon
+   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, debug_flag=.true.) !axn, ayn - Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 2'
    error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
-   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn, Runge_not_Verlet, debug_flag=.true.) !axn, ayn, bxn, byn, Runge_not_Verlet   - Added by Alon
+   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
     call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 3')
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos3 i,j,lon,lat,xi,yj=',i,j,lon3,lat3,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos3 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
@@ -1949,7 +1950,7 @@ subroutine evolve_icebergs(bergs)
   endif
   dxdl3=r180_pi/(Rearth*cos(lat3*pi_180))
   u3=uvel3*dxdl3; v3=vvel3*dydl
-  call accel(bergs, berg, i, j, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn3, ayn3, bxn, byn, Runge_not_Verlet) !axn, ayn, bxn, byn, Runge_not_Verlet   - Added by Alon
+  call accel(bergs, berg, i, j, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn3, ayn3, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
   if (on_tangential_plane) call rotvec_to_tang(lon3,ax3,ay3,xddot3,yddot3)
   if (on_tangential_plane) call rotvec_to_tang(lon3,axn3,ayn3,xddot3n,yddot3n) !Alon
   
@@ -1992,13 +1993,13 @@ subroutine evolve_icebergs(bergs)
    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v4 (deg)=',dt*v1,dt*v2,dt*v3,dt*v4
    write(stderrunit,*) 'Acceleration terms for position 1'
    error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, Runge_not_Verlet, debug_flag=.true.) !axn, ayn, bxn, byn, Runge_not_Verlet   - Added by Alon
+   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 2'
    error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
-   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn, Runge_not_Verlet, debug_flag=.true.) !axn, ayn, bxn, byn, Runge_not_Verlet    - Added by Alon
+   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 3'
    error_flag=pos_within_cell(grd, lon3, lat3, i3, j3, xi, yj)
-   call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn3, ayn3, bxn, byn, Runge_not_Verlet, debug_flag=.true.) !axn, ayn, bxn, byn, Runge_not_Verlet - Added by Alon
+   call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn3, ayn3, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
     call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 4')
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos4 i,j,lon,lat,xi,yj=',i,j,lon4,lat4,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos4 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
@@ -2007,7 +2008,7 @@ subroutine evolve_icebergs(bergs)
   endif
   dxdl4=r180_pi/(Rearth*cos(lat4*pi_180))
   u4=uvel4*dxdl4; v4=vvel4*dydl
-  call accel(bergs, berg, i, j, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axn4, ayn4, bxn, byn, Runge_not_Verlet) !axn, ayn, bxn, byn, Runge_not_Verlet - Added by Alon
+  call accel(bergs, berg, i, j, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axn4, ayn4, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
   if (on_tangential_plane) call rotvec_to_tang(lon4,ax4,ay4,xddot4,yddot4)
   if (on_tangential_plane) call rotvec_to_tang(lon4,axn4,ayn4,xddot4n,yddot4n)
   
@@ -2073,16 +2074,16 @@ subroutine evolve_icebergs(bergs)
    write(stderrunit,*) 'diamonds, evolve_iceberg: on_tangential_plane=',on_tangential_plane
    write(stderrunit,*) 'Acceleration terms for position 1'
    error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, Runge_not_Verlet, debug_flag=.true.)  !axn, ayn, Runge_not_Verlet   - Added by Alon
+   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 2'
    error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
-   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn, ayn, bxn, byn, Runge_not_Verlet, debug_flag=.true.)  !axn, ayn, Runge_not_Verlet  - Added by Alon
+   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 3'
    error_flag=pos_within_cell(grd, lon3, lat3, i3, j3, xi, yj)
-   call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn, ayn, bxn, byn, Runge_not_Verlet, debug_flag=.true.)  !axn, ayn, Runge_not_Verlet   - Added by Alon
+   call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
    write(stderrunit,*) 'Acceleration terms for position 4'
    error_flag=pos_within_cell(grd, lon4, lat4, i4, j4, xi, yj)
-   call accel(bergs, berg, i4, j4, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axn, ayn, bxn, byn, Runge_not_Verlet, debug_flag=.true.)  !axn, ayn, Runge_not_Verlet    - Added by Alon
+   call accel(bergs, berg, i4, j4, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'posn i,j,lon,lat,xi,yj=',i,j,lonn,latn,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'posn box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
     call print_berg(stderrunit, berg, 'evolve_iceberg, out of cell at end!')
@@ -2154,7 +2155,7 @@ subroutine evolve_icebergs(bergs)
 
 
 !Calling the acceleration   (note that the velocity is converted to u_star inside the accel script)
-  call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn, ayn, bxn, byn, Runge_not_Verlet) !axn, ayn, bxn, byn ,Runge_not_Verlet  - Added by Alon
+  call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn, ayn, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
 
 !Solving for the new velocity
   if (on_tangential_plane) then
@@ -2201,7 +2202,7 @@ subroutine evolve_icebergs(bergs)
    write(stderrunit,*) 'diamonds, evolve_iceberg: on_tangential_plane=',on_tangential_plane
    write(stderrunit,*) 'Acceleration terms for position 1'
    error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i2, j2, xi, yj, latn, uvel3, vvel3, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, Runge_not_Verlet, debug_flag=.true.)  !axn, ayn, bxn, byn, Runge_not_Verlet   - Added by Alon
+   call accel(bergs, berg, i2, j2, xi, yj, latn, uvel3, vvel3, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn, bxn, byn - Added by Alon
    
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'posn i,j,lon,lat,xi,yj=',i,j,lonn,latn,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'posn box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)

From 408e0873c8be2e39f3dde1e2df036cc6c8eee31d Mon Sep 17 00:00:00 2001
From: Alon Stern <Alon.Stern@gaea7.ncrc.gov>
Date: Wed, 24 Jun 2015 15:56:44 -0400
Subject: [PATCH 028/361] interactive_icebergs_on flag has been added to the
 namelist. This allows the user to turn on and off the spring and damping
 forces between icebergs.

---
 icebergs.F90           | 2 +-
 icebergs_framework.F90 | 5 ++++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 89170d4..54ecff6 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -303,8 +303,8 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 integer :: itloop
 integer :: stderrunit
 
-interactive_icebergs_on=.true.
 Runge_not_Verlet=bergs%Runge_not_Verlet  ! Loading directly from namelist/default , Alon
+interactive_icebergs_on=bergs%interactive_icebergs_on  ! Loading directly from namelist/default , Alon
 
 !print *, 'axn=',axn,'ayn=',ayn
   u_star=uvel0+(axn*(dt/2.))  !Alon
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index c6eff4b..b53f504 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -178,6 +178,7 @@ module ice_bergs_framework
   logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
   logical :: time_average_weight=.false. ! Time average the weight on the ocean
   logical :: Runge_not_Verlet=.false.  !True=Runge Kuttai, False=Verlet.  - Added by Alon 
+  logical :: interactive_icebergs_on=.false.  !Turn on/off interactions between icebergs  - Added by Alon 
   real :: speed_limit=0. ! CFL speed limit for a berg [m/s]
   real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
   type(buffer), pointer :: obuffer_n=>null(), ibuffer_n=>null()
@@ -268,6 +269,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: speed_limit=0. ! CFL speed limit for a berg
 real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
 logical :: Runge_not_Verlet=.false.  !True=Runge Kuttai, False=Verlet.  - Added by Alon 
+logical :: interactive_icebergs_on=.false.  !Turn on/off interactions between icebergs  - Added by Alon 
 logical :: do_unit_tests=.false. ! Conduct some unit tests
 real, dimension(nclasses) :: initial_mass=(/8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11/) ! Mass thresholds between iceberg classes (kg)
 real, dimension(nclasses) :: distribution=(/0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02/) ! Fraction of calving to apply to this class (non-dim)
@@ -277,7 +279,7 @@ subroutine ice_bergs_framework_init(bergs, &
          distribution, mass_scaling, initial_thickness, verbose_hrs, &
          rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, &
-         time_average_weight, generate_test_icebergs, speed_limit, Runge_not_Verlet, fix_restart_dates, use_roundoff_fix, &
+         time_average_weight, generate_test_icebergs, speed_limit, Runge_not_Verlet, interactive_icebergs_on, fix_restart_dates, use_roundoff_fix, &
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction
 
 ! Local variables
@@ -511,6 +513,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%time_average_weight=time_average_weight
   bergs%speed_limit=speed_limit
   bergs%Runge_not_Verlet=Runge_not_Verlet   !Alon
+  bergs%interactive_icebergs_on=interactive_icebergs_on   !Alon
   bergs%grounding_fraction=grounding_fraction
   bergs%add_weight_to_ocean=add_weight_to_ocean
   allocate( bergs%initial_mass(nclasses) ); bergs%initial_mass(:)=initial_mass(:)

From a153bd63870c8ca5f75d267c4d3a197d8e7fb641 Mon Sep 17 00:00:00 2001
From: Alon Stern <Alon.Stern@gaea1.ncrc.gov>
Date: Wed, 24 Jun 2015 18:37:38 -0400
Subject: [PATCH 029/361] Fixed a number of bugs in the iceberg code. The
 iceberg interactions are now working. The model can run for a few days (have
 not tested for longer). Still need to make the code order invarient, and also
 to limit the amount of interactions to nearest neighbours.

---
 icebergs.F90           | 121 ++++++++++++++++++++++++++---------------
 icebergs_framework.F90 |  11 +++-
 2 files changed, 88 insertions(+), 44 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 54ecff6..bca9ac9 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -126,22 +126,32 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
 real :: P_11, P_12, P_21, P_22
 real :: u2, v2
 real :: Rearth
-real :: kappa_s, accel_spring, p_ia, p_ia_coef, q_ia
+real :: spring_coef, accel_spring, radial_damping_coef, p_ia_coef, tangental_damping_coef
 real, intent(out) :: IA_x, IA_y 
 real, intent(out) :: P_ia_11, P_ia_12, P_ia_22, P_ia_21, P_ia_times_u_x, P_ia_times_u_y
 integer :: stderrunit
 
 Rearth=6360.e3
-kappa_s=1.e-4
-p_ia=2.*sqrt(kappa_s)  ! Critical damping  
-q_ia=(2.*sqrt(kappa_s)/5)  ! Critical damping  /5   (just a guess)
+!spring_coef=1.e-4
+spring_coef=bergs%spring_coef
+!radial_damping_coef=bergs%radial_damping_coef
+!tangental_damping_coef=bergs%tangental_damping_coef
+
+!Using critical values for damping rather than manually setting the damping.
+radial_damping_coef=2.*sqrt(spring_coef)  ! Critical damping  
+tangental_damping_coef=(2.*sqrt(spring_coef)/5)  ! Critical damping  /5   (just a guess)
+
+!radial_damping_coef=1.e-4
+!tangental_damping_coef=1.e-4
+
+
 
 ! Get the stderr unit number.  Not sure what this does
   stderrunit = stderr()
 
 IA_x=0.
 IA_y=0.
-P_ia_11=0. ; P_ia_12=0.  ;  P_ia_22=0. 
+P_ia_11=0. ; P_ia_12=0. ;  P_ia_21=0.;  P_ia_22=0. 
 P_ia_times_u_x=0. ; P_ia_times_u_y=0.
 
 
@@ -172,43 +182,46 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
       T_min=min(T1,T2)
 
       !Calculating spring force  (later this should only be done on the first time around)
-      accel_spring=kappa_s*(T_min/T1)*(A_o/A1)
-      if ((r_dist>0) .AND. (r_dist< (R1+R2)) ) then
-          IA_x=IA_x+(accel_spring*(r_dist_x/r_dist))
-          IA_y=IA_y+(accel_spring*(r_dist_y/r_dist))
-      endif
+      accel_spring=spring_coef*(T_min/T1)*(A_o/A1)
+      if ((r_dist>0.) .AND. (r_dist< (R1+R2)) ) then
+        IA_x=IA_x+(accel_spring*(r_dist_x/r_dist))
+        IA_y=IA_y+(accel_spring*(r_dist_y/r_dist))
 
 
-      !Working out the damping
+       !Working out the damping
 
        !Paralel velocity
-       P_11=(r_dist_x*r_dist_x)/(r_dist**2)
-       P_12=(r_dist_x*r_dist_y)/(r_dist**2)
-       P_22=(r_dist_y*r_dist_y)/(r_dist**2)
-     
-       p_ia_coef=p_ia*(T_min/T1)*(A_o/A1)
-       p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2))+sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
-
-       P_ia_11=P_ia_11+p_ia_coef*P_11
-       P_ia_12=P_ia_12+p_ia_coef*P_12
-       P_ia_21=P_ia_21+p_ia_coef*P_21
-       P_ia_22=P_ia_22+p_ia_coef*P_22
-       P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
-       P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
-
-
-       !Normal velocities
-       P_11=1-P_11  ;  P_12=-P_12 ; P_22=1-P_22
-       p_ia_coef=q_ia*(T_min/T1)*(A_o/A1)
-       p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2))+sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
-
-       P_ia_11=P_ia_11+p_ia_coef*P_11
-       P_ia_12=P_ia_12+p_ia_coef*P_12
-       P_ia_21=P_ia_21+p_ia_coef*P_21
-       P_ia_22=P_ia_22+p_ia_coef*P_22
-       P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
-       P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
+        P_11=(r_dist_x*r_dist_x)/(r_dist**2)
+        P_12=(r_dist_x*r_dist_y)/(r_dist**2)
+        P_21=(r_dist_x*r_dist_y)/(r_dist**2)
+        P_22=(r_dist_y*r_dist_y)/(r_dist**2)
+        p_ia_coef=radial_damping_coef*(T_min/T1)*(A_o/A1)
+        p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2))+sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
+        P_ia_11=P_ia_11+p_ia_coef*P_11
+        P_ia_12=P_ia_12+p_ia_coef*P_12
+        P_ia_21=P_ia_21+p_ia_coef*P_21
+        P_ia_22=P_ia_22+p_ia_coef*P_22
+        P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
+        P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
+
+
+        !Normal velocities
+        P_11=1-P_11  ;  P_12=-P_12 ; P_22=1-P_22
+        p_ia_coef=tangental_damping_coef*(T_min/T1)*(A_o/A1)
+        p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2))+sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
+        P_ia_11=P_ia_11+p_ia_coef*P_11
+        P_ia_12=P_ia_12+p_ia_coef*P_12
+        P_ia_21=P_ia_21+p_ia_coef*P_21
+        P_ia_22=P_ia_22+p_ia_coef*P_22
+        P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
+        P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
+
+!print *, 'P_11',P_11
+!print *, 'P_21',P_21
+!print *, 'P_12',P_12
+!print *, 'P_22',P_22
 
+    endif
 
        other_berg=>other_berg%next
   enddo ! loop over all bergs
@@ -225,7 +238,7 @@ subroutine overlap_area(R1,R2,d,A,trapped)
         d_sq=d**2
         Trapped=0.
 
-if (d>0) then
+if (d>0.) then
         if (d<(R1+R2)) then
              if (d>abs(R1-R2)) then
                   A= (R1_sq*acos((d_sq+R1_sq-R2_sq)/(2.*d*R1)))  +  (R2_sq*acos((d_sq+R2_sq-R1_sq)/(2.*d*R2)))  - (0.5*sqrt((-d+R1+R2)*(d+R1-R2)*(d-R1+R2)*(d+R1+R2)))
@@ -292,7 +305,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 real :: c_ocn, c_atm, c_ice
 real :: ampl, wmod, Cr, Lwavelength, Lcutoff, Ltop
 real, parameter :: alpha=1.0, beta=1.0, C_N=1.0, accel_lim=1.e-2, Cr0=0.06, vel_lim=15.
-real :: lambda, detA, A11, A12, RHS_x, RHS_y, D_hi 
+real :: lambda, detA, A11, A12, A21, A22, RHS_x, RHS_y, D_hi 
 real :: uveln, vveln, us, vs, speed, loc_dx, new_speed
 real :: u_star, v_star    !Added by Alon
 real :: IA_x, IA_y    !Added by Alon
@@ -390,6 +403,11 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
                bxn=bxn + IA_x
                byn=byn + IA_y
            endif
+!print *,'IA_x=',IA_x
+!print *,'IA_x=',IA_x,'IA_y',IA_y
+!print *,'P_ia_11',P_ia_11,'P_ia_12',P_ia_12, 'P_ia_21',P_ia_21,'P_ia_22', P_ia_22
+!print *, 'P_ia_times_u_x', P_ia_times_u_x, 'P_ia_times_u_y', P_ia_times_u_y
+
 endif
 
 
@@ -446,14 +464,31 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
     if (alpha+beta.gt.0.) then
       lambda=drag_ocn+drag_atm+drag_ice
       A11=1.+dt*lambda
-      A12=dt*f_cori  
+      A22=1.+dt*lambda
+      A12=-dt*f_cori  
+      A21=dt*f_cori  
+      !A12=dt*f_cori  !Removed by ALon (in order to have the entire matrix. I hope the sign is correct)
+
       if (C_N>0.) then   !For Crank-Nicolson Coriolis term.   
           A12=A12/2.
+          A21=A21/2.
       endif
 
-      detA=1./(A11**2+A12**2)
-      ax=detA*(A11*RHS_x+A12*RHS_y)
-      ay=detA*(A11*RHS_y-A12*RHS_x)
+      if (interactive_icebergs_on) then
+            A11=A11+P_ia_11
+            A12=A12+P_ia_12
+            A21=A21+P_ia_21
+            A22=A22+P_ia_22
+     endif
+
+      detA=1./((A11*A22)-(A12*A21))
+      ax=detA*(A22*RHS_x-A12*RHS_y)
+      ay=detA*(A11*RHS_y-A21*RHS_x)
+
+!Alistair's version removed by Alon
+!      detA=1./(A11**2+A12**2)
+!      ax=detA*(A11*RHS_x+A12*RHS_y)
+!      ay=detA*(A11*RHS_y-A12*RHS_x)
     else
       ax=RHS_x; ay=RHS_x
     endif
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index b53f504..ae836b5 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -167,6 +167,9 @@ module ice_bergs_framework
   integer :: verbose_hrs
   integer :: clock, clock_mom, clock_the, clock_int, clock_cal, clock_com, clock_ini, clock_ior, clock_iow, clock_dia ! ids for fms timers
   real :: rho_bergs ! Density of icebergs [kg/m^3]
+  real :: spring_coef  ! Spring contant for iceberg interactions - Alon
+  real :: radial_damping_coef     ! Coef for relative iceberg motion damping (radial component) -Alon
+  real :: tangental_damping_coef     ! Coef for relative iceberg motion damping (tangental component) -Alon
   real :: LoW_ratio ! Initial ratio L/W for newly calved icebergs
   real :: bergy_bit_erosion_fraction ! Fraction of erosion melt flux to divert to bergy bits
   real :: sicn_shift ! Shift of sea-ice concentration in erosion flux modulation (0<sicn_shift<1)
@@ -259,6 +262,9 @@ subroutine ice_bergs_framework_init(bergs, &
 integer :: traj_sample_hrs=24 ! Period between sampling of position for trajectory storage
 integer :: verbose_hrs=24 ! Period between verbose messages
 real :: rho_bergs=850. ! Density of icebergs
+real :: spring_coef=1.e-4  ! Spring contant for iceberg interactions - Alon
+real :: radial_damping_coef=1.e-4     ! Coef for relative iceberg motion damping (radial component) -Alon
+real :: tangental_damping_coef=2.e-5     ! Coef for relative iceberg motion damping (tangental component) -Alon
 real :: LoW_ratio=1.5 ! Initial ratio L/W for newly calved icebergs
 real :: bergy_bit_erosion_fraction=0. ! Fraction of erosion melt flux to divert to bergy bits
 real :: sicn_shift=0. ! Shift of sea-ice concentration in erosion flux modulation (0<sicn_shift<1)
@@ -276,7 +282,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real, dimension(nclasses) :: mass_scaling=(/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) ! Ratio between effective and real iceberg mass (non-dim)
 real, dimension(nclasses) :: initial_thickness=(/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) ! Total thickness of newly calved bergs (m)
 namelist /icebergs_nml/ verbose, budget, halo, traj_sample_hrs, initial_mass, &
-         distribution, mass_scaling, initial_thickness, verbose_hrs, &
+         distribution, spring_coef, radial_damping_coef, tangental_damping_coef , mass_scaling, initial_thickness, verbose_hrs, &
          rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, &
          time_average_weight, generate_test_icebergs, speed_limit, Runge_not_Verlet, interactive_icebergs_on, fix_restart_dates, use_roundoff_fix, &
@@ -505,6 +511,9 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%verbose_hrs=verbose_hrs
   bergs%grd%halo=halo
   bergs%rho_bergs=rho_bergs
+  bergs%spring_coef=spring_coef
+  bergs%radial_damping_coef=radial_damping_coef
+  bergs%tangental_damping_coef=tangental_damping_coef
   bergs%LoW_ratio=LoW_ratio
   bergs%use_operator_splitting=use_operator_splitting
   bergs%bergy_bit_erosion_fraction=bergy_bit_erosion_fraction

From 43ad7aaed99609f6cef0b62f04e16bd9b75486e4 Mon Sep 17 00:00:00 2001
From: Alon Stern <Alon.Stern@gaea1.ncrc.gov>
Date: Thu, 25 Jun 2015 18:00:49 -0400
Subject: [PATCH 030/361] Saving before attempting to make the iceberg action
 order invarient

---
 icebergs.F90           | 21 ++++++++++++---------
 icebergs_framework.F90 |  5 ++++-
 2 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index bca9ac9..0c69411 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -126,6 +126,7 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
 real :: P_11, P_12, P_21, P_22
 real :: u2, v2
 real :: Rearth
+logical :: critical_interaction_damping_on
 real :: spring_coef, accel_spring, radial_damping_coef, p_ia_coef, tangental_damping_coef
 real, intent(out) :: IA_x, IA_y 
 real, intent(out) :: P_ia_11, P_ia_12, P_ia_22, P_ia_21, P_ia_times_u_x, P_ia_times_u_y
@@ -134,16 +135,15 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
 Rearth=6360.e3
 !spring_coef=1.e-4
 spring_coef=bergs%spring_coef
-!radial_damping_coef=bergs%radial_damping_coef
-!tangental_damping_coef=bergs%tangental_damping_coef
+radial_damping_coef=bergs%radial_damping_coef
+tangental_damping_coef=bergs%tangental_damping_coef
+critical_interaction_damping_on=bergs%critical_interaction_damping_on
 
 !Using critical values for damping rather than manually setting the damping.
-radial_damping_coef=2.*sqrt(spring_coef)  ! Critical damping  
-tangental_damping_coef=(2.*sqrt(spring_coef)/5)  ! Critical damping  /5   (just a guess)
-
-!radial_damping_coef=1.e-4
-!tangental_damping_coef=1.e-4
-
+if (critical_interaction_damping_on) then
+     radial_damping_coef=2.*sqrt(spring_coef)  ! Critical damping  
+     tangental_damping_coef=(2.*sqrt(spring_coef)/5)  ! Critical damping  /5   (just a guess)
+endif
 
 
 ! Get the stderr unit number.  Not sure what this does
@@ -164,7 +164,10 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
 call rotpos_to_tang(lon1,lat1,x1,y1)
 
   other_berg=>bergs%first
-  do while (associated(other_berg)) ! loop over all other bergs    - Need to think about which icebergs to loop over
+
+!Note: This summing should be made order invarient. 
+!Note: Need to limit how many icebergs we search over
+  do while (associated(other_berg)) ! loop over all other bergs  
        L2=other_berg%length
        W2=other_berg%width
        T2=other_berg%thickness 
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index ae836b5..d388d26 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -182,6 +182,7 @@ module ice_bergs_framework
   logical :: time_average_weight=.false. ! Time average the weight on the ocean
   logical :: Runge_not_Verlet=.false.  !True=Runge Kuttai, False=Verlet.  - Added by Alon 
   logical :: interactive_icebergs_on=.false.  !Turn on/off interactions between icebergs  - Added by Alon 
+  logical :: critical_interaction_damping_on=.true.  !Sets the damping on relative iceberg velocity to critical value - Added by Alon 
   real :: speed_limit=0. ! CFL speed limit for a berg [m/s]
   real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
   type(buffer), pointer :: obuffer_n=>null(), ibuffer_n=>null()
@@ -276,6 +277,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
 logical :: Runge_not_Verlet=.false.  !True=Runge Kuttai, False=Verlet.  - Added by Alon 
 logical :: interactive_icebergs_on=.false.  !Turn on/off interactions between icebergs  - Added by Alon 
+logical :: critical_interaction_damping_on=.true.  !Sets the damping on relative iceberg velocity to critical value - Added by Alon 
 logical :: do_unit_tests=.false. ! Conduct some unit tests
 real, dimension(nclasses) :: initial_mass=(/8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11/) ! Mass thresholds between iceberg classes (kg)
 real, dimension(nclasses) :: distribution=(/0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02/) ! Fraction of calving to apply to this class (non-dim)
@@ -285,7 +287,7 @@ subroutine ice_bergs_framework_init(bergs, &
          distribution, spring_coef, radial_damping_coef, tangental_damping_coef , mass_scaling, initial_thickness, verbose_hrs, &
          rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, &
-         time_average_weight, generate_test_icebergs, speed_limit, Runge_not_Verlet, interactive_icebergs_on, fix_restart_dates, use_roundoff_fix, &
+         time_average_weight, generate_test_icebergs, speed_limit, Runge_not_Verlet, interactive_icebergs_on, critical_interaction_damping_on, fix_restart_dates, use_roundoff_fix, &
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction
 
 ! Local variables
@@ -522,6 +524,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%time_average_weight=time_average_weight
   bergs%speed_limit=speed_limit
   bergs%Runge_not_Verlet=Runge_not_Verlet   !Alon
+  bergs%critical_interaction_damping_on=critical_interaction_damping_on   !Alon
   bergs%interactive_icebergs_on=interactive_icebergs_on   !Alon
   bergs%grounding_fraction=grounding_fraction
   bergs%add_weight_to_ocean=add_weight_to_ocean

From 6854f3a6c4efd158de835c3943df3b48b8b1bf90 Mon Sep 17 00:00:00 2001
From: Niki Zadeh <Niki.Zadeh@noaa.gov>
Date: Fri, 26 Jun 2015 17:11:02 -0400
Subject: [PATCH 031/361] Add capabality to write one traj file per core

- Timings show that in long run simulations writing one trajectory file
  per tile io has a sever impact on model timing. Specifically Termination time
  can become larger than the Main loop time.
- This update bypasses using the io_layout for trajectory files and forces
  one file per processor (the way old iceberg model behaved till ulm) by
  setting a namelist  icebergs_nml: force_all_pes_traj = .true.
- This is a temporary fix to let people run long run simulations until we find a proper fix.
---
 icebergs_framework.F90 |  9 +++++++--
 icebergs_io.F90        | 35 +++++++++++++++++++++++++++++------
 2 files changed, 36 insertions(+), 8 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 148cde2..239b8ac 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -39,12 +39,14 @@ module ice_bergs_framework
 real, parameter :: pi_180=pi/180. ! Converts degrees to radians
 logical :: fix_restart_dates=.true. ! After a restart, check that bergs were created before the current model date
 logical :: do_unit_tests=.false. ! Conduct some unit tests
+logical :: force_all_pes_traj=.false. ! Force all pes write trajectory files regardless of io_layout
+logical :: reverse_traj=.false. ! Force trajectories to be written in reverse order into files to save time
 
 !Public params !Niki: write a subroutine to expose these
 public nclasses,buffer_width,buffer_width_traj
 public verbose, really_debug, debug, restart_input_dir,make_calving_reproduce,old_bug_bilin,use_roundoff_fix
 public ignore_ij_restart, use_slow_find,generate_test_icebergs,old_bug_rotated_weights,budget
-public orig_read
+public orig_read, force_all_pes_traj, reverse_traj
 
 
 !Public types
@@ -165,6 +167,7 @@ module ice_bergs_framework
   integer :: traj_sample_hrs
   integer :: verbose_hrs
   integer :: clock, clock_mom, clock_the, clock_int, clock_cal, clock_com, clock_ini, clock_ior, clock_iow, clock_dia ! ids for fms timers
+  integer :: clock_trw, clock_trp
   real :: rho_bergs ! Density of icebergs [kg/m^3]
   real :: LoW_ratio ! Initial ratio L/W for newly calved icebergs
   real :: bergy_bit_erosion_fraction ! Fraction of erosion melt flux to divert to bergy bits
@@ -275,7 +278,8 @@ subroutine ice_bergs_framework_init(bergs, &
          rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, &
          time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, &
-         old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction
+         old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction,&
+         force_all_pes_traj, reverse_traj
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -324,6 +328,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%clock_ior=mpp_clock_id( 'Icebergs-I/O read', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
   bergs%clock_iow=mpp_clock_id( 'Icebergs-I/O write', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
   bergs%clock_dia=mpp_clock_id( 'Icebergs-diagnostics', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+
   call mpp_clock_begin(bergs%clock)
   call mpp_clock_begin(bergs%clock_ini)
 
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 48b4c36..3a4bdc6 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -16,6 +16,10 @@ module ice_bergs_io
 use fms_io_mod, only : register_restart_axis, register_restart_field, set_domain, nullify_domain
 use fms_io_mod, only : read_unlimited_axis =>read_compressed, field_exist, get_field_size
 
+use mpp_mod,    only : mpp_clock_begin, mpp_clock_end, mpp_clock_id
+use mpp_mod,    only : CLOCK_COMPONENT, CLOCK_SUBCOMPONENT, CLOCK_LOOP
+use fms_mod,    only : clock_flag_default
+
 use time_manager_mod, only: time_type, get_date, get_time, set_date, operator(-)
 
 use ice_bergs_framework, only: icebergs_gridded, xyt, iceberg, icebergs, buffer
@@ -30,7 +34,7 @@ module ice_bergs_io
 use ice_bergs_framework, only: nclasses, buffer_width, buffer_width_traj
 use ice_bergs_framework, only: verbose, really_debug, debug, restart_input_dir,make_calving_reproduce
 use ice_bergs_framework, only: ignore_ij_restart, use_slow_find,generate_test_icebergs,print_berg
-use ice_bergs_framework, only: reverse_list
+use ice_bergs_framework, only: reverse_list, force_all_pes_traj, reverse_traj
 
 implicit none ; private
 
@@ -49,6 +53,8 @@ module ice_bergs_io
 integer, allocatable,save :: io_tile_pelist(:)
 logical :: is_io_tile_root_pe = .true.
 
+integer :: clock_trw,clock_trp
+
 #ifdef _FILE_VERSION
   character(len=128) :: version = _FILE_VERSION
 #else
@@ -82,6 +88,9 @@ subroutine ice_bergs_io_init(bergs, io_layout)
      io_npes = io_layout(1)*io_layout(2)
   endif
 
+  clock_trw=mpp_clock_id( 'Icebergs-traj write', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+  clock_trp=mpp_clock_id( 'Icebergs-traj prepare', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+
 end subroutine ice_bergs_io_init
 
 ! ##############################################################################
@@ -839,9 +848,10 @@ subroutine write_trajectory(trajectory)
   stderrunit=stderr()
 
   !Assemble the list of trajectories from all pes in this I/O tile
+  call mpp_clock_begin(clock_trp)
 
   !First add the trajs on the io_tile_root_pe (if any) to the I/O list
-  if(is_io_tile_root_pe) then
+  if(is_io_tile_root_pe .OR. force_all_pes_traj ) then
      if(associated(trajectory)) then
         this=>trajectory
         do while (associated(this))
@@ -851,11 +861,12 @@ subroutine write_trajectory(trajectory)
      endif
   endif
 
+  if(.NOT. force_all_pes_traj ) then
+
   !Now gather and append the bergs from all pes in the io_tile to the list on corresponding io_tile_root_pe
   ntrajs_sent_io =0
   ntrajs_rcvd_io =0 
 
-
   if(is_io_tile_root_pe) then
      !Receive trajs from all pes in this I/O tile !FRAGILE!SCARY!
      do np=2,size(io_tile_pelist) ! Note: np starts from 2 to exclude self
@@ -869,7 +880,7 @@ subroutine write_trajectory(trajectory)
            enddo
        endif
      enddo
-     call reverse_list(traj4io)
+!     if(.NOT. reverse_traj .AND. associated(traj4io)) call reverse_list(traj4io)
   else
      !Pack and Send trajs to the root pe for this I/O tile
      if (associated(trajectory)) then
@@ -888,14 +899,25 @@ subroutine write_trajectory(trajectory)
      endif
   endif
 
+  endif !.NOT. force_all_pes_traj
+
+  !Here traj4io has all the trajectories in completely reverse order (last position of the last berg first)
+  !If a correct order is prefered in the trajectory file then reverse the linked list
+  !This may increase the the termination time of the model by a lot!!!
+  if(is_io_tile_root_pe .OR. force_all_pes_traj ) then
+    if(.NOT. reverse_traj .AND. associated(traj4io)) call reverse_list(traj4io)
+  endif
+
+  call mpp_clock_end(clock_trp)
 
 
   !Now start writing in the io_tile_root_pe if there are any bergs in the I/O list
+  call mpp_clock_begin(clock_trw)
 
-  if(is_io_tile_root_pe .AND. associated(traj4io)) then
+  if((force_all_pes_traj .OR. is_io_tile_root_pe) .AND. associated(traj4io)) then
  
   call get_instance_filename("iceberg_trajectories.nc", filename)
-    if(io_tile_id(1) .ge. 0) then !io_tile_root_pes write
+    if(io_tile_id(1) .ge. 0 .AND. .NOT. force_all_pes_traj) then !io_tile_root_pes write
        if(io_npes .gt. 1) then !attach tile_id  to filename only if there is more than one I/O pe
           if (io_tile_id(1)<10000) then
              write(filename,'(A,".",I4.4)') trim(filename), io_tile_id(1) 
@@ -1034,6 +1056,7 @@ subroutine write_trajectory(trajectory)
   if (iret .ne. NF_NOERR) write(stderrunit,*) 'diamonds, write_trajectory: nf_close failed',mpp_pe(),filename
 
   endif !(is_io_tile_root_pe .AND. associated(traj4io))
+  call mpp_clock_end(clock_trw)
 
 end subroutine write_trajectory
 

From 59e3853de10e53ad1e0ab43c998bc08e41e2976b Mon Sep 17 00:00:00 2001
From: Alon Stern <Alon.Stern@gaea3.ncrc.gov>
Date: Tue, 7 Jul 2015 13:42:23 -0400
Subject: [PATCH 032/361] Iceberg interactions are now order invarient, and
 icebergs interact with the positions of other icebergs at time n

---
 icebergs.F90           | 43 +++++++++++++++-----
 icebergs_framework.F90 | 68 +++++++++++++++++++++++--------
 icebergs_io.F90        | 91 +++++++++++++++++++++++++++++++++++++-----
 3 files changed, 165 insertions(+), 37 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 0c69411..5071421 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -171,11 +171,11 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
        L2=other_berg%length
        W2=other_berg%width
        T2=other_berg%thickness 
-       u2=other_berg%uvel 
-       v2=other_berg%vvel 
+       u2=other_berg%uvel_old !Old values are used to make it order invariant 
+       v2=other_berg%vvel_old !Old values are used to make it order invariant 
        A2=L2*W2
        R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
-       lon2=berg%lon; lat2=berg%lat
+       lon2=berg%lon_old; lat2=berg%lat_old !Old values are used to make it order invariant
        call rotpos_to_tang(lon2,lat2,x2,y2)
 
        r_dist_x=x1-x2 ; r_dist_y=y1-y2
@@ -1793,6 +1793,7 @@ subroutine evolve_icebergs(bergs)
 logical :: Runge_not_Verlet  ! Runge_not_Verlet=1 for Runge Kutta, =0 for Verlet method. Added by Alon
 type(iceberg), pointer :: berg
 integer :: stderrunit
+logical :: interactive_icebergs_on  ! Flag to decide whether to use forces between icebergs.
 
   ! 4th order Runge-Kutta to solve:
   !    d/dt X = V,  d/dt V = A
@@ -1813,6 +1814,8 @@ subroutine evolve_icebergs(bergs)
   ! For convenience
   grd=>bergs%grd
 
+  interactive_icebergs_on=bergs%interactive_icebergs_on  ! Loading directly from namelist/default , Alon
+
   ! Common constants
   r180_pi=1./pi_180
   dt=bergs%dt
@@ -2161,6 +2164,8 @@ subroutine evolve_icebergs(bergs)
   axn=berg%axn; ayn=berg%ayn !Alon
   bxn=berg%bxn; byn=berg%byn !Alon
 
+
+
 ! Velocities used to update the position
   uvel2=uvel1+(dt_2*axn)+(dt_2*bxn)                    !Alon
   vvel2=vvel1+(dt_2*ayn)+(dt_2*byn)                    !Alon
@@ -2262,27 +2267,43 @@ subroutine evolve_icebergs(bergs)
   endif ! End of the Verlet Stepiing -added by Alon  
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
-!print *, 'you are here again!';
-  berg%lon=lonn
-  berg%lat=latn
-  berg%uvel=uveln
-  berg%vvel=vveln
+!Saving all the iceberg variables.
   berg%axn=axn !Alon
   berg%ayn=ayn !Alon
   berg%bxn=bxn !Alon
   berg%byn=byn !Alon
+  berg%lon=lonn
+  berg%lat=latn
+  berg%uvel=uveln
+  berg%vvel=vveln
   berg%ine=i
   berg%jne=j
   berg%xi=xi
   berg%yj=yj
- !call interp_flds(grd, i, j, xi, yj, berg%uo, berg%vo, berg%ui, berg%vi, berg%ua, berg%va, berg%ssh_x, berg%ssh_y, berg%sst)
-
- !if (debug) call print_berg(stderr(), berg, 'evolve_iceberg, final posn.')
+  !call interp_flds(grd, i, j, xi, yj, berg%uo, berg%vo, berg%ui, berg%vi, berg%ua, berg%va, berg%ssh_x, berg%ssh_y, berg%sst)
+  !if (debug) call print_berg(stderr(), berg, 'evolve_iceberg, final posn.')
   if (debug) call check_position(grd, berg, 'evolve_iceberg (bot)')
 
+
   berg=>berg%next
   enddo ! loop over all bergs
 
+! When we are using interactive icebergs, we update the (old) iceberg positions and velocities in a second loop, all together (to make code order invarient)
+ if (interactive_icebergs_on) then
+  berg=>bergs%first
+  do while (associated(berg)) ! loop over all bergs
+
+      !Updating iceberg positions and velocities
+      berg%lon_old=berg%lon
+      berg%lat_old=berg%lat
+      berg%uvel_old=berg%uvel
+      berg%vvel_old=berg%vvel
+
+      berg=>berg%next
+  enddo ! loop over all bergs
+
+
+ endif
   contains
 
   subroutine rotpos_to_tang(lon, lat, x, y)
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index d388d26..70c09c9 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -15,8 +15,8 @@ module ice_bergs_framework
 
 implicit none ; private
 
-integer, parameter :: buffer_width=24 !Changed from 20 to 24 by Alon 
-integer, parameter :: buffer_width_traj=27  !Changed from 23 by Alon
+integer, parameter :: buffer_width=28 !Changed from 20 to 28 by Alon 
+integer, parameter :: buffer_width_traj=31  !Changed from 23 by Alon
 integer, parameter :: nclasses=10 ! Number of ice bergs classes
 
 !Local Vars
@@ -129,7 +129,7 @@ module ice_bergs_framework
 type :: xyt
   real :: lon, lat, day
   real :: mass, thickness, width, length, uvel, vvel
-  real :: axn, ayn, bxn, byn  !Explicit and implicit accelerations !Alon 
+  real :: axn, ayn, bxn, byn, uvel_old, vvel_old, lat_old, lon_old  !Explicit and implicit accelerations !Alon 
   real :: uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, cn, hi
   real :: mass_of_bits, heat_density
   integer :: year
@@ -140,7 +140,7 @@ module ice_bergs_framework
   type(iceberg), pointer :: prev=>null(), next=>null()
   ! State variables (specific to the iceberg, needed for restarts)
   real :: lon, lat, uvel, vvel, mass, thickness, width, length
-  real :: axn, ayn, bxn, byn  !Explicit and implicit accelerations !Alon 
+  real :: axn, ayn, bxn, byn, uvel_old, vvel_old, lon_old, lat_old !Explicit and implicit accelerations !Alon 
   real :: start_lon, start_lat, start_day, start_mass, mass_scaling
   real :: mass_of_bits, heat_density
   integer :: start_year
@@ -957,6 +957,10 @@ subroutine pack_berg_into_buffer2(berg, buff, n)
     buff%data(22,n)=berg%ayn  !Alon
     buff%data(23,n)=berg%bxn  !Alon
     buff%data(24,n)=berg%byn  !Alon
+    buff%data(25,n)=berg%uvel_old  !Alon
+    buff%data(26,n)=berg%vvel_old  !Alon
+    buff%data(27,n)=berg%lon_old  !Alon
+    buff%data(28,n)=berg%lat_old  !Alon
 
   end subroutine pack_berg_into_buffer2
 
@@ -1036,6 +1040,10 @@ subroutine unpack_berg_from_buffer2(first, buff, n,grd, force_append)
     localberg%ayn=buff%data(22,n) !Alon
     localberg%bxn=buff%data(23,n) !Alon
     localberg%byn=buff%data(24,n) !Alon
+    localberg%uvel_old=buff%data(25,n) !Alon
+    localberg%vvel_old=buff%data(26,n) !Alon
+    localberg%lon_old=buff%data(27,n) !Alon
+    localberg%lat_old=buff%data(28,n) !Alon
    
      lres=find_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
     if (lres) then
@@ -1053,6 +1061,8 @@ subroutine unpack_berg_from_buffer2(first, buff, n,grd, force_append)
         write(stderrunit,*) localberg%uvel,localberg%vvel
         write(stderrunit,*) localberg%axn,localberg%ayn !Alon
         write(stderrunit,*) localberg%bxn,localberg%byn !Alon
+        write(stderrunit,*) localberg%uvel_old,localberg%vvel_old !Alon
+        write(stderrunit,*) localberg%lon_old,localberg%lat_old !Alon
         write(stderrunit,*) grd%isc,grd%iec,grd%jsc,grd%jec
         write(stderrunit,*) grd%isd,grd%ied,grd%jsd,grd%jed
         write(stderrunit,*) grd%lon(grd%isc-1,grd%jsc-1),grd%lon(grd%iec,grd%jsc)
@@ -1200,6 +1210,10 @@ subroutine pack_traj_into_buffer2(traj, buff, n)
     buff%data(25,n)=traj%ayn !Alon
     buff%data(26,n)=traj%bxn !Alon
     buff%data(27,n)=traj%byn !Alon
+    buff%data(28,n)=traj%uvel_old !Alon
+    buff%data(29,n)=traj%vvel_old !Alon
+    buff%data(30,n)=traj%lon_old !Alon
+    buff%data(31,n)=traj%lat_old !Alon
 
   end subroutine pack_traj_into_buffer2
 
@@ -1241,6 +1255,10 @@ subroutine unpack_traj_from_buffer2(first, buff, n)
     traj%ayn=buff%data(25,n) !Alon
     traj%bxn=buff%data(26,n) !Alon
     traj%byn=buff%data(27,n) !Alon
+    traj%uvel_old=buff%data(28,n) !Alon
+    traj%vvel_old=buff%data(29,n) !Alon
+    traj%lon_old=buff%data(30,n) !Alon
+    traj%lat_old=buff%data(31,n) !Alon
 
     call append_posn(first, traj) 
 
@@ -1493,6 +1511,10 @@ logical function sameberg(berg1, berg2)
   if (berg1%ayn.ne.berg2%ayn) return  !Alon
   if (berg1%bxn.ne.berg2%bxn) return  !Alon
   if (berg1%byn.ne.berg2%byn) return  !Alon
+  if (berg1%uvel_old.ne.berg2%uvel_old) return  !Alon
+  if (berg1%vvel_old.ne.berg2%vvel_old) return  !Alon
+  if (berg1%lon_old.ne.berg2%lon_old) return  !Alon
+  if (berg1%lat_old.ne.berg2%lat_old) return  !Alon
   sameberg=.true. ! passing the above tests mean that bergs 1 and 2 are identical
 end function sameberg
 
@@ -1580,6 +1602,8 @@ subroutine print_berg(iochan, berg, label)
     ' u,v=', berg%uvel, berg%vvel, &
     ' axn,ayn=', berg%axn, berg%ayn, &
     ' bxn,byn=', berg%bxn, berg%byn, &
+    ' uvel_old,vvel_old=', berg%uvel_old, berg%vvel_old, &
+    ' lon_old,lat_old=', berg%lon_old, berg%lat_old, &
     ' p,n=', associated(berg%prev), associated(berg%next)
   write(iochan,'("diamonds, print_berg: ",a," pe=(",i3,") ",6(a,2f10.4))') &
     label, mpp_pe(), 'uo,vo=', berg%uo, berg%vo, 'ua,va=', berg%ua, berg%va, 'ui,vi=', berg%ui, berg%vi
@@ -1664,6 +1688,10 @@ subroutine record_posn(bergs)
     posn%ayn=this%ayn
     posn%bxn=this%bxn
     posn%byn=this%byn
+    posn%uvel_old=this%uvel_old
+    posn%vvel_old=this%vvel_old
+    posn%lon_old=this%lon_old
+    posn%lat_old=this%lat_old
 
     call push_posn(this%trajectory, posn)
 
@@ -2670,8 +2698,8 @@ subroutine bergs_chksum(bergs, txt, ignore_halo_violation)
 
   nbergs=count_bergs(bergs)
   call mpp_max(nbergs)
-  allocate( fld( nbergs, 15 ) ) !Changed from 11 to 15 by Alon
-  allocate( fld2( nbergs, 15 ) ) !Changed from 11 to 15 by Alon
+  allocate( fld( nbergs, 19 ) ) !Changed from 11 to 19 by Alon
+  allocate( fld2( nbergs, 19 ) ) !Changed from 11 to 19 by Alon
   allocate( icnt( grd%isd:grd%ied, grd%jsd:grd%jed ) )
   fld(:,:)=0.
   fld2(:,:)=0.
@@ -2695,9 +2723,13 @@ subroutine bergs_chksum(bergs, txt, ignore_halo_violation)
     fld(i,10) = this%ayn !added by Alon
     fld(i,11) = this%bxn !added by Alon
     fld(i,12) = this%byn !added by Alon
-    fld(i,13) = time_hash(this) !Changed from 9 to 13 by Alon
-    fld(i,14) = pos_hash(this) !Changed from 10 to 12 by Alon
-    fld(i,15) = float(iberg) !Changed from 11 to 15 by Alon
+    fld(i,13) = this%uvel_old !added by Alon
+    fld(i,14) = this%vvel_old !added by Alon
+    fld(i,15) = this%lon_old !added by Alon
+    fld(i,16) = this%lat_old !added by Alon
+    fld(i,17) = time_hash(this) !Changed from 9 to 17 by Alon
+    fld(i,18) = pos_hash(this) !Changed from 10 to 18 by Alon
+    fld(i,19) = float(iberg) !Changed from 11 to 19 by Alon
     icnt(this%ine,this%jne)=icnt(this%ine,this%jne)+1
     fld2(i,:) = fld(i,:)*float( icnt(this%ine,this%jne) ) !*float( i )
     grd%tmp(this%ine,this%jne)=grd%tmp(this%ine,this%jne)+time_hash(this)*pos_hash(this)+log(this%mass)
@@ -2750,8 +2782,8 @@ integer function berg_chksum(berg )
 ! Arguments
 type(iceberg), pointer :: berg
 ! Local variables
-real :: rtmp(32) !Changed from 28 to 32 by Alon
-integer :: itmp(32+3), i8=0, ichk1, ichk2, ichk3 !Changed from 28 to 32 by Alon
+real :: rtmp(34) !Changed from 28 to 34 by Alon
+integer :: itmp(34+3), i8=0, ichk1, ichk2, ichk3 !Changed from 28 to 34 by Alon
 integer :: i
 
   rtmp(:)=0.
@@ -2786,14 +2818,18 @@ integer function berg_chksum(berg )
   rtmp(30)=berg%ayn !Added by Alon
   rtmp(31)=berg%bxn !Added by Alon
   rtmp(32)=berg%byn !Added by Alon
+  rtmp(33)=berg%uvel_old !Added by Alon
+  rtmp(34)=berg%vvel_old !Added by Alon
+  rtmp(35)=berg%lat_old !Added by Alon
+  rtmp(36)=berg%lon_old !Added by Alon
 
-  itmp(1:32)=transfer(rtmp,i8) !Changed from 28 to 32 by Alon
-  itmp(33)=berg%start_year !Changed from 29 to 33 by Alon
-  itmp(34)=berg%ine !Changed from 30 to 34 by Alon
-  itmp(35)=berg%jne !Changed from 31 to 35 by Alon
+  itmp(1:36)=transfer(rtmp,i8) !Changed from 28 to 36 by Alon
+  itmp(37)=berg%start_year !Changed from 29 to 37 by Alon
+  itmp(38)=berg%ine !Changed from 30 to 38 by Alon
+  itmp(39)=berg%jne !Changed from 31 to 39 by Alon
 
   ichk1=0; ichk2=0; ichk3=0
-  do i=1,32+3 !Changd from 28 to 32 by Alon
+  do i=1,36+3 !Changd from 28 to 36 by Alon
    ichk1=ichk1+itmp(i)
    ichk2=ichk2+itmp(i)*i
    ichk3=ichk3+itmp(i)*i*i
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 21bc0bd..9f6410c 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -100,11 +100,15 @@ subroutine write_restart(bergs)
 type(icebergs_gridded), pointer :: grd
 real, allocatable, dimension(:) :: lon,          &
                                    lat,          &
+                                   lon_old,      &
+                                   lat_old,      &
                                    uvel,         &
                                    vvel,         &
                                    mass,         &
                                    axn,          &
                                    ayn,          &
+                                   uvel_old,     &
+                                   vvel_old,     &
                                    bxn,          &
                                    byn,          &
                                    thickness,    &
@@ -122,6 +126,7 @@ subroutine write_restart(bergs)
                                       jne,       &
                                       start_year
 
+!uvel_old, vvel_old, lon_old, lat_old, axn, ayn, bxn, byn added by Alon.
 
   ! For convenience
   grd=>bergs%grd
@@ -141,13 +146,17 @@ subroutine write_restart(bergs)
 
    allocate(lon(nbergs))
    allocate(lat(nbergs))
+   allocate(lon_old(nbergs))  !Alon
+   allocate(lat_old(nbergs))  !Alon
    allocate(uvel(nbergs))
    allocate(vvel(nbergs))
    allocate(mass(nbergs))
-   allocate(axn(nbergs))
-   allocate(ayn(nbergs))
-   allocate(bxn(nbergs))
-   allocate(byn(nbergs))
+   allocate(axn(nbergs))    !Alon
+   allocate(ayn(nbergs))    !Alon
+   allocate(uvel_old(nbergs)) !Alon
+   allocate(vvel_old(nbergs)) !Alon
+   allocate(bxn(nbergs)) !Alon
+   allocate(byn(nbergs)) !Alon
    allocate(thickness(nbergs))
    allocate(width(nbergs))
    allocate(length(nbergs))
@@ -175,11 +184,15 @@ subroutine write_restart(bergs)
   ! Define Variables
   id = register_restart_field(bergs_restart,filename,'lon',lon,longname='longitude',units='degrees_E')
   id = register_restart_field(bergs_restart,filename,'lat',lat,longname='latitude',units='degrees_N')
+  id = register_restart_field(bergs_restart,filename,'lon_old',lon_old,longname='longitude',units='degrees_E') !Alon
+  id = register_restart_field(bergs_restart,filename,'lat_old',lat_old,longname='latitude',units='degrees_N') !Alon
   id = register_restart_field(bergs_restart,filename,'uvel',uvel,longname='zonal velocity',units='m/s')
   id = register_restart_field(bergs_restart,filename,'vvel',vvel,longname='meridional velocity',units='m/s')
   id = register_restart_field(bergs_restart,filename,'mass',mass,longname='mass',units='kg')
   id = register_restart_field(bergs_restart,filename,'axn',mass,longname='explicit zonal acceleration',units='m/s^2') !Alon
   id = register_restart_field(bergs_restart,filename,'ayn',mass,longname='explicit meridional acceleration',units='m/s^2') !Alon
+  id = register_restart_field(bergs_restart,filename,'uvel_old',mass,longname='old explicit zonal acceleration',units='m/s^2') !Alon
+  id = register_restart_field(bergs_restart,filename,'vvel_old',mass,longname='old explicit meridional acceleration',units='m/s^2') !Alon
   id = register_restart_field(bergs_restart,filename,'bxn',mass,longname='inplicit zonal acceleration',units='m/s^2') !Alon
   id = register_restart_field(bergs_restart,filename,'byn',mass,longname='implicit meridional acceleration',units='m/s^2') !Alon
   id = register_restart_field(bergs_restart,filename,'ine',ine,longname='i index',units='none')
@@ -209,10 +222,12 @@ subroutine write_restart(bergs)
   if(associated(bergs%first)) this=>bergs%first
   do i=1,nbergs
     lon(i) = this%lon; lat(i) = this%lat
+    lon_old(i) = this%lon_old; lat_old(i) = this%lat_old  !Alon
     uvel(i) = this%uvel; vvel(i) = this%vvel
     ine(i) = this%ine; jne(i) = this%jne
     mass(i) = this%mass; thickness(i) = this%thickness
     axn(i) = this%axn; ayn(i) = this%ayn !Added by Alon
+    uvel_old(i) = this%uvel_old; vvel_old(i) = this%vvel_old !Added by Alon
     bxn(i) = this%bxn; byn(i) = this%byn !Added by Alon
     width(i) = this%width; length(i) = this%length
     start_lon(i) = this%start_lon; start_lat(i) = this%start_lat
@@ -228,11 +243,15 @@ subroutine write_restart(bergs)
   deallocate(              &
              lon,          &
              lat,          &
+             lon_old,      &
+             lat_old,      &
              uvel,         &
              vvel,         &
              mass,         &
              axn,          &
              ayn,          &
+             uvel_old,     &
+             vvel_old,     &
              bxn,          &
              byn,          &
              thickness,    &
@@ -245,7 +264,7 @@ subroutine write_restart(bergs)
              mass_scaling, &
              mass_of_bits, &
              heat_density )
-!axn, ayn, bxn, byn above added by Alon
+!axn, ayn, uvel_old, vvel_old, lat_old, lon_old, bxn, byn above added by Alon
 
   deallocate(           &
              ine,       &
@@ -288,8 +307,8 @@ subroutine read_restart_bergs_orig(bergs,Time)
 ! Local variables
 integer, dimension(:), allocatable :: found_restart_int
 integer :: k, ierr, ncid, dimid, nbergs_in_file
-integer :: lonid, latid, uvelid, vvelid, ineid, jneid
-integer :: axnid, aynid, bxnid, bynid !Added by Alon
+integer :: lonid, latid,  uvelid, vvelid, ineid, jneid
+integer :: axnid, aynid, uvel_oldid, vvel_oldid, bxnid, bynid, lon_oldid, lat_oldid !Added by Alon
 integer :: massid, thicknessid, widthid, lengthid
 integer :: start_lonid, start_latid, start_yearid, start_dayid, start_massid
 integer :: scaling_id, mass_of_bits_id, heat_density_id
@@ -349,11 +368,15 @@ subroutine read_restart_bergs_orig(bergs,Time)
 
   lonid=inq_var(ncid, 'lon')
   latid=inq_var(ncid, 'lat')
+  lon_oldid=inq_var(ncid, 'lon_old') !Alon
+  lat_oldid=inq_var(ncid, 'lat_old') !Alon
   uvelid=inq_var(ncid, 'uvel')
   vvelid=inq_var(ncid, 'vvel')
   massid=inq_var(ncid, 'mass')
   axnid=inq_var(ncid, 'axn') !Alon
   aynid=inq_var(ncid, 'ayn') !Alon
+  uvel_oldid=inq_var(ncid, 'uvel_old') !Alon
+  vvel_oldid=inq_var(ncid, 'vvel_old') !Alon
   bxnid=inq_var(ncid, 'bxn') !Alon
   bynid=inq_var(ncid, 'byn') !Alon
   thicknessid=inq_var(ncid, 'thickness')
@@ -407,6 +430,10 @@ subroutine read_restart_bergs_orig(bergs,Time)
       localberg%mass=get_double(ncid, massid, k)
       localberg%axn=get_double(ncid, axnid, k) !Alon
       localberg%ayn=get_double(ncid, aynid, k) !Alon
+      localberg%uvel_old=get_double(ncid, uvel_oldid, k) !Alon
+      localberg%vvel_old=get_double(ncid, vvel_oldid, k) !Alon
+      localberg%lon_old=get_double(ncid, lon_oldid, k) !Alon
+      localberg%lat_old=get_double(ncid, lat_oldid, k) !Alon
       localberg%bxn=get_double(ncid, bxnid, k) !Alon
       localberg%byn=get_double(ncid, bynid, k) !Alon
       localberg%thickness=get_double(ncid, thicknessid, k)
@@ -492,6 +519,8 @@ subroutine generate_bergs(bergs,Time)
         localberg%jne=j
         localberg%lon=bilin(grd, grd%lon, i, j, localberg%xi, localberg%yj)
         localberg%lat=bilin(grd, grd%lat, i, j, localberg%xi, localberg%yj)
+        localberg%lon_old=bilin(grd, grd%lon, i, j, localberg%xi, localberg%yj) !Alon
+        localberg%lat_old=bilin(grd, grd%lat, i, j, localberg%xi, localberg%yj) !Alon
         localberg%mass=bergs%initial_mass(1)
         localberg%thickness=bergs%initial_thickness(1)
         localberg%width=bergs%initial_width(1)
@@ -508,6 +537,8 @@ subroutine generate_bergs(bergs,Time)
         localberg%vvel=0.
         localberg%axn=0. !Alon
         localberg%ayn=0. !Alon
+        localberg%uvel_old=0. !Alon
+        localberg%vvel_old=0. !Alon
         localberg%bxn=0. !Alon
         localberg%byn=0. !Alon
         call add_new_berg_to_list(bergs%first, localberg)
@@ -515,6 +546,8 @@ subroutine generate_bergs(bergs,Time)
         localberg%vvel=0.
         localberg%axn=0. !Alon
         localberg%ayn=0. !Alon
+        localberg%uvel_old=0. !Alon
+        localberg%vvel_old=0. !Alon
         localberg%bxn=0. !Alon
         localberg%byn=0. !Alon
         call add_new_berg_to_list(bergs%first, localberg)
@@ -522,6 +555,8 @@ subroutine generate_bergs(bergs,Time)
         localberg%vvel=1.
         localberg%axn=0. !Alon
         localberg%ayn=0. !Alon
+        localberg%uvel_old=0. !Alon
+        localberg%vvel_old=0. !Alon
         localberg%bxn=0. !Alon
         localberg%byn=0. !Alon
         call add_new_berg_to_list(bergs%first, localberg)
@@ -529,6 +564,8 @@ subroutine generate_bergs(bergs,Time)
         localberg%vvel=-1.
         localberg%axn=0. !Alon
         localberg%ayn=0. !Alon
+        localberg%uvel_old=0. !Alon
+        localberg%vvel_old=0. !Alon
         localberg%bxn=0. !Alon
         localberg%byn=0. !Alon
         call add_new_berg_to_list(bergs%first, localberg)
@@ -562,11 +599,15 @@ subroutine read_restart_bergs(bergs,Time)
 
 real, allocatable, dimension(:) :: lon,          &
                                    lat,          &
+                                   lon_old,      &
+                                   lat_old,      &
                                    uvel,         &
                                    vvel,         &
                                    mass,         &
                                    axn,          &
                                    ayn,          &
+                                   uvel_old,     &
+                                   vvel_old,     &
                                    bxn,          &
                                    byn,          &
                                    thickness,    &
@@ -579,7 +620,7 @@ subroutine read_restart_bergs(bergs,Time)
                                    mass_scaling, &
                                    mass_of_bits, &
                                    heat_density
-!axn, ayn, bxn, byn added by Alon
+!axn, ayn, uvel_old, vvel_old, lon_old, lat_old, bxn, byn added by Alon
 integer, allocatable, dimension(:) :: ine,       &
                                       jne,       &
                                       start_year
@@ -605,11 +646,15 @@ subroutine read_restart_bergs(bergs,Time)
   if(nbergs_in_file > 0) then
      allocate(lon(nbergs_in_file))
      allocate(lat(nbergs_in_file))
+     allocate(lon_old(nbergs_in_file)) !Alon
+     allocate(lat_old(nbergs_in_file)) !Alon
      allocate(uvel(nbergs_in_file))
      allocate(vvel(nbergs_in_file))
      allocate(mass(nbergs_in_file))
      allocate(axn(nbergs_in_file)) !Alon
      allocate(ayn(nbergs_in_file)) !Alon
+     allocate(uvel_old(nbergs_in_file)) !Alon
+     allocate(vvel_old(nbergs_in_file)) !Alon
      allocate(bxn(nbergs_in_file)) !Alon
      allocate(byn(nbergs_in_file)) !Alon
      allocate(thickness(nbergs_in_file))
@@ -629,11 +674,15 @@ subroutine read_restart_bergs(bergs,Time)
 
      call read_unlimited_axis(filename,'lon',lon,domain=grd%domain)
      call read_unlimited_axis(filename,'lat',lat,domain=grd%domain)
+     call read_unlimited_axis(filename,'lon_old',lon_old,domain=grd%domain) !Alon
+     call read_unlimited_axis(filename,'lat_old',lat_old,domain=grd%domain) !Alon
      call read_unlimited_axis(filename,'uvel',uvel,domain=grd%domain)
      call read_unlimited_axis(filename,'vvel',vvel,domain=grd%domain)
      call read_unlimited_axis(filename,'mass',mass,domain=grd%domain)
      call read_unlimited_axis(filename,'axn',axn,domain=grd%domain) !Alon
      call read_unlimited_axis(filename,'ayn',ayn,domain=grd%domain) !Alon
+     call read_unlimited_axis(filename,'uvel_old',uvel_old,domain=grd%domain) !Alon
+     call read_unlimited_axis(filename,'vvel_old',vvel_old,domain=grd%domain) !Alon
      call read_unlimited_axis(filename,'bxn',bxn,domain=grd%domain) !Alon
      call read_unlimited_axis(filename,'byn',byn,domain=grd%domain) !Alon
      call read_unlimited_axis(filename,'thickness',thickness,domain=grd%domain)
@@ -686,6 +735,10 @@ subroutine read_restart_bergs(bergs,Time)
          localberg%mass=mass(k)
          localberg%axn=axn(k) !Alon
          localberg%ayn=ayn(k) !Alon
+         localberg%uvel_old=uvel_old(k) !Alon
+         localberg%vvel_old=vvel_old(k) !Alon
+         localberg%lon_old=lon_old(k) !Alon
+         localberg%lat_old=lat_old(k) !Alon
          localberg%bxn=bxn(k) !Alon
          localberg%byn=byn(k) !Alon
          localberg%thickness=thickness(k)
@@ -711,11 +764,15 @@ subroutine read_restart_bergs(bergs,Time)
      deallocate(              &
                 lon,          &
                 lat,          &
+                lon_old,      &
+                lat_old,      &
                 uvel,         &
                 vvel,         &
                 mass,         &
                 axn,          &
                 ayn,          &
+                uvel_old,     &
+                vvel_old,     &
                 bxn,          &
                 byn,          &
                 thickness,    &
@@ -728,7 +785,7 @@ subroutine read_restart_bergs(bergs,Time)
                 mass_scaling, &
                 mass_of_bits, &
                 heat_density )
-!axn, ayn, bxn, byn above added by Alon.
+!axn, ayn, uvel_old, vvel_old, lat_old, lon_old, bxn, byn above added by Alon.
      deallocate(           &
                 ine,       &
                 jne,       &
@@ -769,6 +826,8 @@ subroutine generate_bergs(bergs,Time)
         localberg%jne=j
         localberg%lon=bilin(grd, grd%lon, i, j, localberg%xi, localberg%yj)
         localberg%lat=bilin(grd, grd%lat, i, j, localberg%xi, localberg%yj)
+        localberg%lon_old=bilin(grd, grd%lon, i, j, localberg%xi, localberg%yj) !Alon
+        localberg%lat_old=bilin(grd, grd%lat, i, j, localberg%xi, localberg%yj) !Alon
         localberg%mass=bergs%initial_mass(1)
         localberg%thickness=bergs%initial_thickness(1)
         localberg%width=bergs%initial_width(1)
@@ -785,6 +844,8 @@ subroutine generate_bergs(bergs,Time)
         localberg%vvel=0.
         localberg%axn=0. !Alon
         localberg%ayn=0. !Alon
+        localberg%uvel_old=0. !Alon
+        localberg%vvel_old=0. !Alon
         localberg%bxn=0. !Alon
         localberg%byn=0. !Alon
         call add_new_berg_to_list(bergs%first, localberg)
@@ -792,6 +853,8 @@ subroutine generate_bergs(bergs,Time)
         localberg%vvel=0.
         localberg%axn=0. !Alon
         localberg%ayn=0. !Alon
+        localberg%uvel_old=0. !Alon
+        localberg%vvel_old=0. !Alon
         localberg%bxn=0. !Alon
         localberg%byn=0. !Alon
         call add_new_berg_to_list(bergs%first, localberg)
@@ -799,6 +862,8 @@ subroutine generate_bergs(bergs,Time)
         localberg%vvel=1.
         localberg%axn=0. !Alon
         localberg%ayn=0. !Alon
+        localberg%uvel_old=0. !Alon
+        localberg%vvel_old=0. !Alon
         localberg%bxn=0. !Alon
         localberg%byn=0. !Alon
         call add_new_berg_to_list(bergs%first, localberg)
@@ -806,6 +871,8 @@ subroutine generate_bergs(bergs,Time)
         localberg%vvel=-1.
         localberg%axn=0. !Alon
         localberg%ayn=0. !Alon
+        localberg%uvel_old=0. !Alon
+        localberg%vvel_old=0. !Alon
         localberg%bxn=0. !Alon
         localberg%byn=0. !Alon
         call add_new_berg_to_list(bergs%first, localberg)
@@ -900,7 +967,7 @@ subroutine write_trajectory(trajectory)
 ! Local variables
 integer :: iret, ncid, i_dim, i
 integer :: lonid, latid, yearid, dayid, uvelid, vvelid
-!integer :: axnid, aynid, bxnid, bynid !Added by Alon 
+!integer :: axnid, aynid, uvel_oldid, vvel_oldid, lat_oldid, lon_oldid, bxnid, bynid !Added by Alon 
 integer :: uoid, void, uiid, viid, uaid, vaid, sshxid, sshyid, sstid
 integer :: cnid, hiid
 integer :: mid, did, wid, lid, mbid, hdid
@@ -1006,6 +1073,10 @@ subroutine write_trajectory(trajectory)
   vvelid = def_var(ncid, 'vvel', NF_DOUBLE, i_dim)
   !axnid = def_var(ncid, 'axn', NF_DOUBLE, i_dim) !Alon
   !aynid = def_var(ncid, 'ayn', NF_DOUBLE, i_dim) !Alon
+  !uvel_oldid = def_var(ncid, 'uvel_old', NF_DOUBLE, i_dim) !Alon
+  !vvel_oldid = def_var(ncid, 'vvel_old', NF_DOUBLE, i_dim) !Alon
+  !lon_oldid = def_var(ncid, 'lon_old', NF_DOUBLE, i_dim) !Alon
+  !lat_oldid = def_var(ncid, 'lat_old', NF_DOUBLE, i_dim) !Alon
   !bxnid = def_var(ncid, 'bxn', NF_DOUBLE, i_dim) !Alon
   !bynid = def_var(ncid, 'byn', NF_DOUBLE, i_dim) !Alon
   uoid = def_var(ncid, 'uo', NF_DOUBLE, i_dim)

From 19107e7d38c1c518b916f0b4b4c7b960cc4e1cc5 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Thu, 16 Jul 2015 10:36:18 -0400
Subject: [PATCH 033/361] Updated write_trajectory() to not clobber existing
 file

- write_trajectory() now appends data to an existing file. This
  is a pre-requisite to being able to write trajectories mid-run
  and thereby reduce the extreme i/o buffer sizes and i/o PE memory
  requirements when writing trajectories only at the end of the run.
- Relevant to issue #1.
- No answer changes.
---
 icebergs_io.F90 | 225 ++++++++++++++++++++++++++++++------------------
 1 file changed, 143 insertions(+), 82 deletions(-)

diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 154fca6..6e763c4 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -833,6 +833,7 @@ subroutine write_trajectory(trajectory)
 integer :: ntrajs_sent_io,ntrajs_rcvd_io
 integer :: from_pe,np
 type(buffer), pointer :: obuffer_io=>null(), ibuffer_io=>null()
+logical :: io_is_in_append_mode
 
   ! Get the stderr unit number
   stderrunit=stderr()
@@ -909,93 +910,132 @@ subroutine write_trajectory(trajectory)
     endif
   if (verbose) write(*,'(2a)') 'diamonds, write_trajectory: creating ',filename
 
-  iret = nf_create(filename, NF_CLOBBER, ncid)
-  if (iret .ne. NF_NOERR) write(stderrunit,*) 'diamonds, write_trajectory: nf_create failed'
-
-  ! Dimensions
-  iret = nf_def_dim(ncid, 'i', NF_UNLIMITED, i_dim)
-  if (iret .ne. NF_NOERR) write(stderrunit,*) 'diamonds, write_trajectory: nf_def_dim i failed'
-
-  ! Variables
-  lonid = def_var(ncid, 'lon', NF_DOUBLE, i_dim)
-  latid = def_var(ncid, 'lat', NF_DOUBLE, i_dim)
-  yearid = def_var(ncid, 'year', NF_INT, i_dim)
-  dayid = def_var(ncid, 'day', NF_DOUBLE, i_dim)
-  uvelid = def_var(ncid, 'uvel', NF_DOUBLE, i_dim)
-  vvelid = def_var(ncid, 'vvel', NF_DOUBLE, i_dim)
-  uoid = def_var(ncid, 'uo', NF_DOUBLE, i_dim)
-  void = def_var(ncid, 'vo', NF_DOUBLE, i_dim)
-  uiid = def_var(ncid, 'ui', NF_DOUBLE, i_dim)
-  viid = def_var(ncid, 'vi', NF_DOUBLE, i_dim)
-  uaid = def_var(ncid, 'ua', NF_DOUBLE, i_dim)
-  vaid = def_var(ncid, 'va', NF_DOUBLE, i_dim)
-  mid = def_var(ncid, 'mass', NF_DOUBLE, i_dim)
-  mbid = def_var(ncid, 'mass_of_bits', NF_DOUBLE, i_dim)
-  hdid = def_var(ncid, 'heat_density', NF_DOUBLE, i_dim)
-  did = def_var(ncid, 'thickness', NF_DOUBLE, i_dim)
-  wid = def_var(ncid, 'width', NF_DOUBLE, i_dim)
-  lid = def_var(ncid, 'length', NF_DOUBLE, i_dim)
-  sshxid = def_var(ncid, 'ssh_x', NF_DOUBLE, i_dim)
-  sshyid = def_var(ncid, 'ssh_y', NF_DOUBLE, i_dim)
-  sstid = def_var(ncid, 'sst', NF_DOUBLE, i_dim)
-  cnid = def_var(ncid, 'cn', NF_DOUBLE, i_dim)
-  hiid = def_var(ncid, 'hi', NF_DOUBLE, i_dim)
-
-  ! Attributes
-  iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_major_version', NF_INT, 1, 0)
-  iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_minor_version', NF_INT, 1, 1)
-  call put_att(ncid, lonid, 'long_name', 'longitude')
-  call put_att(ncid, lonid, 'units', 'degrees_E')
-  call put_att(ncid, latid, 'long_name', 'latitude')
-  call put_att(ncid, latid, 'units', 'degrees_N')
-  call put_att(ncid, yearid, 'long_name', 'year')
-  call put_att(ncid, yearid, 'units', 'years')
-  call put_att(ncid, dayid, 'long_name', 'year day')
-  call put_att(ncid, dayid, 'units', 'days')
-  call put_att(ncid, uvelid, 'long_name', 'zonal spped')
-  call put_att(ncid, uvelid, 'units', 'm/s')
-  call put_att(ncid, vvelid, 'long_name', 'meridional spped')
-  call put_att(ncid, vvelid, 'units', 'm/s')
-  call put_att(ncid, uoid, 'long_name', 'ocean zonal spped')
-  call put_att(ncid, uoid, 'units', 'm/s')
-  call put_att(ncid, void, 'long_name', 'ocean meridional spped')
-  call put_att(ncid, void, 'units', 'm/s')
-  call put_att(ncid, uiid, 'long_name', 'ice zonal spped')
-  call put_att(ncid, uiid, 'units', 'm/s')
-  call put_att(ncid, viid, 'long_name', 'ice meridional spped')
-  call put_att(ncid, viid, 'units', 'm/s')
-  call put_att(ncid, uaid, 'long_name', 'atmos zonal spped')
-  call put_att(ncid, uaid, 'units', 'm/s')
-  call put_att(ncid, vaid, 'long_name', 'atmos meridional spped')
-  call put_att(ncid, vaid, 'units', 'm/s')
-  call put_att(ncid, mid, 'long_name', 'mass')
-  call put_att(ncid, mid, 'units', 'kg')
-  call put_att(ncid, mbid, 'long_name', 'mass_of_bits')
-  call put_att(ncid, mbid, 'units', 'kg')
-  call put_att(ncid, hdid, 'long_name', 'heat_density')
-  call put_att(ncid, hdid, 'units', 'J/kg')
-  call put_att(ncid, did, 'long_name', 'thickness')
-  call put_att(ncid, did, 'units', 'm')
-  call put_att(ncid, wid, 'long_name', 'width')
-  call put_att(ncid, wid, 'units', 'm')
-  call put_att(ncid, lid, 'long_name', 'length')
-  call put_att(ncid, lid, 'units', 'm')
-  call put_att(ncid, sshxid, 'long_name', 'sea surface height gradient_x')
-  call put_att(ncid, sshxid, 'units', 'non-dim')
-  call put_att(ncid, sshyid, 'long_name', 'sea surface height gradient_y')
-  call put_att(ncid, sshyid, 'units', 'non-dim')
-  call put_att(ncid, sstid, 'long_name', 'sea surface temperature')
-  call put_att(ncid, sstid, 'units', 'degrees_C')
-  call put_att(ncid, cnid, 'long_name', 'sea ice concentration')
-  call put_att(ncid, cnid, 'units', 'none')
-  call put_att(ncid, hiid, 'long_name', 'sea ice thickness')
-  call put_att(ncid, hiid, 'units', 'm')
+  io_is_in_append_mode = .false.
+  iret = nf_create(filename, NF_NOCLOBBER, ncid)
+  if (iret .ne. NF_NOERR) then
+    iret = nf_open(filename, NF_WRITE, ncid)
+    io_is_in_append_mode = .true.
+    if (iret .ne. NF_NOERR) write(stderrunit,*) 'diamonds, write_trajectory: nf_open failed'
+  endif
+
+  if (io_is_in_append_mode) then
+    iret = nf_inq_dimid(ncid, 'i', i_dim)
+    if (iret .ne. NF_NOERR) write(stderrunit,*) 'diamonds, write_trajectory: nf_inq_dimid i failed'
+    lonid = inq_varid(ncid, 'lon')
+    latid = inq_varid(ncid, 'lat')
+    yearid = inq_varid(ncid, 'year')
+    dayid = inq_varid(ncid, 'day')
+    uvelid = inq_varid(ncid, 'uvel')
+    vvelid = inq_varid(ncid, 'vvel')
+    uoid = inq_varid(ncid, 'uo')
+    void = inq_varid(ncid, 'vo')
+    uiid = inq_varid(ncid, 'ui')
+    viid = inq_varid(ncid, 'vi')
+    uaid = inq_varid(ncid, 'ua')
+    vaid = inq_varid(ncid, 'va')
+    mid = inq_varid(ncid, 'mass')
+    mbid = inq_varid(ncid, 'mass_of_bits')
+    hdid = inq_varid(ncid, 'heat_density')
+    did = inq_varid(ncid, 'thickness')
+    wid = inq_varid(ncid, 'width')
+    lid = inq_varid(ncid, 'length')
+    sshxid = inq_varid(ncid, 'ssh_x')
+    sshyid = inq_varid(ncid, 'ssh_y')
+    sstid = inq_varid(ncid, 'sst')
+    cnid = inq_varid(ncid, 'cn')
+    hiid = inq_varid(ncid, 'hi')
+  else
+    ! Dimensions
+    iret = nf_def_dim(ncid, 'i', NF_UNLIMITED, i_dim)
+    if (iret .ne. NF_NOERR) write(stderrunit,*) 'diamonds, write_trajectory: nf_def_dim i failed'
+
+    ! Variables
+    lonid = def_var(ncid, 'lon', NF_DOUBLE, i_dim)
+    latid = def_var(ncid, 'lat', NF_DOUBLE, i_dim)
+    yearid = def_var(ncid, 'year', NF_INT, i_dim)
+    dayid = def_var(ncid, 'day', NF_DOUBLE, i_dim)
+    uvelid = def_var(ncid, 'uvel', NF_DOUBLE, i_dim)
+    vvelid = def_var(ncid, 'vvel', NF_DOUBLE, i_dim)
+    uoid = def_var(ncid, 'uo', NF_DOUBLE, i_dim)
+    void = def_var(ncid, 'vo', NF_DOUBLE, i_dim)
+    uiid = def_var(ncid, 'ui', NF_DOUBLE, i_dim)
+    viid = def_var(ncid, 'vi', NF_DOUBLE, i_dim)
+    uaid = def_var(ncid, 'ua', NF_DOUBLE, i_dim)
+    vaid = def_var(ncid, 'va', NF_DOUBLE, i_dim)
+    mid = def_var(ncid, 'mass', NF_DOUBLE, i_dim)
+    mbid = def_var(ncid, 'mass_of_bits', NF_DOUBLE, i_dim)
+    hdid = def_var(ncid, 'heat_density', NF_DOUBLE, i_dim)
+    did = def_var(ncid, 'thickness', NF_DOUBLE, i_dim)
+    wid = def_var(ncid, 'width', NF_DOUBLE, i_dim)
+    lid = def_var(ncid, 'length', NF_DOUBLE, i_dim)
+    sshxid = def_var(ncid, 'ssh_x', NF_DOUBLE, i_dim)
+    sshyid = def_var(ncid, 'ssh_y', NF_DOUBLE, i_dim)
+    sstid = def_var(ncid, 'sst', NF_DOUBLE, i_dim)
+    cnid = def_var(ncid, 'cn', NF_DOUBLE, i_dim)
+    hiid = def_var(ncid, 'hi', NF_DOUBLE, i_dim)
+
+    ! Attributes
+    iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_major_version', NF_INT, 1, 0)
+    iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_minor_version', NF_INT, 1, 1)
+    call put_att(ncid, lonid, 'long_name', 'longitude')
+    call put_att(ncid, lonid, 'units', 'degrees_E')
+    call put_att(ncid, latid, 'long_name', 'latitude')
+    call put_att(ncid, latid, 'units', 'degrees_N')
+    call put_att(ncid, yearid, 'long_name', 'year')
+    call put_att(ncid, yearid, 'units', 'years')
+    call put_att(ncid, dayid, 'long_name', 'year day')
+    call put_att(ncid, dayid, 'units', 'days')
+    call put_att(ncid, uvelid, 'long_name', 'zonal spped')
+    call put_att(ncid, uvelid, 'units', 'm/s')
+    call put_att(ncid, vvelid, 'long_name', 'meridional spped')
+    call put_att(ncid, vvelid, 'units', 'm/s')
+    call put_att(ncid, uoid, 'long_name', 'ocean zonal spped')
+    call put_att(ncid, uoid, 'units', 'm/s')
+    call put_att(ncid, void, 'long_name', 'ocean meridional spped')
+    call put_att(ncid, void, 'units', 'm/s')
+    call put_att(ncid, uiid, 'long_name', 'ice zonal spped')
+    call put_att(ncid, uiid, 'units', 'm/s')
+    call put_att(ncid, viid, 'long_name', 'ice meridional spped')
+    call put_att(ncid, viid, 'units', 'm/s')
+    call put_att(ncid, uaid, 'long_name', 'atmos zonal spped')
+    call put_att(ncid, uaid, 'units', 'm/s')
+    call put_att(ncid, vaid, 'long_name', 'atmos meridional spped')
+    call put_att(ncid, vaid, 'units', 'm/s')
+    call put_att(ncid, mid, 'long_name', 'mass')
+    call put_att(ncid, mid, 'units', 'kg')
+    call put_att(ncid, mbid, 'long_name', 'mass_of_bits')
+    call put_att(ncid, mbid, 'units', 'kg')
+    call put_att(ncid, hdid, 'long_name', 'heat_density')
+    call put_att(ncid, hdid, 'units', 'J/kg')
+    call put_att(ncid, did, 'long_name', 'thickness')
+    call put_att(ncid, did, 'units', 'm')
+    call put_att(ncid, wid, 'long_name', 'width')
+    call put_att(ncid, wid, 'units', 'm')
+    call put_att(ncid, lid, 'long_name', 'length')
+    call put_att(ncid, lid, 'units', 'm')
+    call put_att(ncid, sshxid, 'long_name', 'sea surface height gradient_x')
+    call put_att(ncid, sshxid, 'units', 'non-dim')
+    call put_att(ncid, sshyid, 'long_name', 'sea surface height gradient_y')
+    call put_att(ncid, sshyid, 'units', 'non-dim')
+    call put_att(ncid, sstid, 'long_name', 'sea surface temperature')
+    call put_att(ncid, sstid, 'units', 'degrees_C')
+    call put_att(ncid, cnid, 'long_name', 'sea ice concentration')
+    call put_att(ncid, cnid, 'units', 'none')
+    call put_att(ncid, hiid, 'long_name', 'sea ice thickness')
+    call put_att(ncid, hiid, 'units', 'm')
+  endif
 
   ! End define mode
   iret = nf_enddef(ncid)
        
   ! Write variables
-  this=>traj4io; i=0
+  this=>traj4io
+  if (io_is_in_append_mode) then
+    iret = nf_inq_dimlen(ncid, i_dim, i)
+    if (iret .ne. NF_NOERR) write(stderrunit,*) 'diamonds, write_trajectory: nf_inq_dimlen i failed'
+  else
+    i = 0
+  endif
   do while (associated(this))
     i=i+1
     call put_double(ncid, lonid, i, this%lon)
@@ -1086,6 +1126,27 @@ end function def_var
 
 ! ##############################################################################
 
+integer function inq_varid(ncid, var)
+! Arguments
+integer, intent(in) :: ncid
+character(len=*), intent(in) :: var
+! Local variables
+integer :: iret
+integer :: stderrunit
+
+  ! Get the stderr unit number
+  stderrunit=stderr()
+
+  iret = nf_inq_varid(ncid, var, inq_varid)
+  if (iret .ne. NF_NOERR) then
+    write(stderrunit,*) 'diamonds, inq_varid: nf_inq_varid failed for ',trim(var)
+    call error_mesg('diamonds, inq_varid', 'netcdf function returned a failure!', FATAL)
+  endif
+
+end function inq_varid
+
+! ##############################################################################
+
 subroutine put_att(ncid, id, att, attval)
 ! Arguments
 integer, intent(in) :: ncid, id

From 150ae95810e35ad44505fe2e28c7175404a0518c Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Thu, 16 Jul 2015 11:33:34 -0400
Subject: [PATCH 034/361] Ensure that trajectory memory is deallocated

- We now deallocate the links in the trajectory chain when packing
  into the i/o buffer. This is in preparation for repeatedly
  calling write_trajectory(), see issue #1.
- No answer changes.
---
 icebergs_io.F90 | 22 ++++++++++------------
 1 file changed, 10 insertions(+), 12 deletions(-)

diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 6e763c4..a895e79 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -848,6 +848,7 @@ subroutine write_trajectory(trajectory)
            call append_posn(traj4io, this)
            this=>this%next
         enddo
+        trajectory => null()
      endif
   endif
 
@@ -869,16 +870,14 @@ subroutine write_trajectory(trajectory)
        endif
      enddo
   else
-     !Pack and Send trajs to the root pe for this I/O tile
-     if (associated(trajectory)) then
-        this=>trajectory
-        do while (associated(this))
-           ntrajs_sent_io = ntrajs_sent_io +1
-           call pack_traj_into_buffer2(this, obuffer_io, ntrajs_sent_io)
-
-           this=>this%next
-        enddo
-     endif
+     ! Pack and send trajectories to the root PE for this I/O tile
+     do while (associated(trajectory))
+       ntrajs_sent_io = ntrajs_sent_io +1
+       call pack_traj_into_buffer2(trajectory, obuffer_io, ntrajs_sent_io)
+       this => trajectory ! Need to keep pointer in order to free up the links memory
+       trajectory => trajectory%next ! This will eventually result in trajectory => null()
+       deallocate(this) ! Delete the link from memory
+     enddo
         
      call mpp_send(ntrajs_sent_io, plen=1, to_pe=io_tile_root_pe, tag=COMM_TAG_11)
      if (ntrajs_sent_io .gt. 0) then
@@ -1064,8 +1063,7 @@ subroutine write_trajectory(trajectory)
     deallocate(this)
     this=>next
   enddo
-  trajectory=>null()
-       
+
   ! Finish up
   iret = nf_close(ncid)
   if (iret .ne. NF_NOERR) write(stderrunit,*) 'diamonds, write_trajectory: nf_close failed',mpp_pe(),filename

From cea20742b3d88a6a8588d50edb57c3d780f71833 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Thu, 16 Jul 2015 16:32:14 -0400
Subject: [PATCH 035/361] Nullify pointers on repeated calls to
 write_trajectory()

- When calling write_trajectory() a second time, the declaration
    type(buffer), pointer :: obuffer_io=>null()
  does not nullify the pointer. Added explicit nullification
  in the code in addition.
- No answer changes.
---
 icebergs_io.F90 | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/icebergs_io.F90 b/icebergs_io.F90
index a895e79..38314d7 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -829,7 +829,7 @@ subroutine write_trajectory(trajectory)
 integer :: stderrunit
 
 !I/O vars
-type(xyt), pointer :: traj4io=>NULL()
+type(xyt), pointer :: traj4io=>null()
 integer :: ntrajs_sent_io,ntrajs_rcvd_io
 integer :: from_pe,np
 type(buffer), pointer :: obuffer_io=>null(), ibuffer_io=>null()
@@ -837,6 +837,9 @@ subroutine write_trajectory(trajectory)
 
   ! Get the stderr unit number
   stderrunit=stderr()
+  traj4io=>null()
+  obuffer_io=>null()
+  ibuffer_io=>null()
 
   !Assemble the list of trajectories from all pes in this I/O tile
 

From 6af1a8027ffff02a39b39a913782de464cf4538a Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Thu, 16 Jul 2015 16:34:02 -0400
Subject: [PATCH 036/361] Corrected terminal message for creating trajectory
 file

- Message used to say "creating" even when appending.
- No answer changes.
---
 icebergs_io.F90 | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 38314d7..cfff9ca 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -910,7 +910,6 @@ subroutine write_trajectory(trajectory)
           write(filename,'(A,".",I6.6)') trim(filename), mpp_pe() 
        endif
     endif
-  if (verbose) write(*,'(2a)') 'diamonds, write_trajectory: creating ',filename
 
   io_is_in_append_mode = .false.
   iret = nf_create(filename, NF_NOCLOBBER, ncid)
@@ -919,6 +918,13 @@ subroutine write_trajectory(trajectory)
     io_is_in_append_mode = .true.
     if (iret .ne. NF_NOERR) write(stderrunit,*) 'diamonds, write_trajectory: nf_open failed'
   endif
+  if (verbose) then
+    if (io_is_in_append_mode) then
+      write(*,'(2a)') 'diamonds, write_trajectory: appending to ',filename
+    else
+      write(*,'(2a)') 'diamonds, write_trajectory: creating ',filename
+    endif
+  endif
 
   if (io_is_in_append_mode) then
     iret = nf_inq_dimid(ncid, 'i', i_dim)

From a3913a7bf23c3c22d8fcc57ba47d17fcfe559f0c Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Thu, 16 Jul 2015 16:35:19 -0400
Subject: [PATCH 037/361] Added ability to frequently write trajectories

- traj_write_hrs controls interval between writing trajectories.
- Should help with issue #1.
- No answer changes.
---
 icebergs.F90           | 20 +++++++++++---------
 icebergs_framework.F90 | 30 +++++++++++++++++++++++++++---
 2 files changed, 38 insertions(+), 12 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 4c0965a..fa60754 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -29,7 +29,7 @@ module ice_bergs
 use ice_bergs_framework, only: nclasses,old_bug_bilin
 use ice_bergs_framework, only: sum_mass,sum_heat,bilin,yearday,count_bergs,bergs_chksum
 use ice_bergs_framework, only: checksum_gridded,add_new_berg_to_list
-use ice_bergs_framework, only: send_bergs_to_other_pes,move_trajectory
+use ice_bergs_framework, only: send_bergs_to_other_pes,move_trajectory,move_all_trajectories
 use ice_bergs_framework, only: record_posn,check_position,print_berg,print_bergs,print_fld
 use ice_bergs_framework, only: add_new_berg_to_list,delete_iceberg_from_list,destroy_iceberg
 use ice_bergs_framework, only: grd_chksum2,grd_chksum3
@@ -762,7 +762,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 ! Local variables
 integer :: iyr, imon, iday, ihr, imin, isec, k
 type(icebergs_gridded), pointer :: grd
-logical :: lerr, sample_traj, lbudget, lverbose
+logical :: lerr, sample_traj, write_traj, lbudget, lverbose
 real :: unused_calving, tmpsum, grdd_berg_mass, grdd_bergy_mass
 integer :: i, j, Iu, ju, iv, Jv, Iu_off, ju_off, iv_off, Jv_off
 real :: mask
@@ -804,6 +804,10 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   if (bergs%traj_sample_hrs>0) then
      if (mod(24*iday+ihr,bergs%traj_sample_hrs).eq.0) sample_traj=.true.
   end if
+  write_traj=.false.
+  if (bergs%traj_write_hrs>0) then
+     if (mod(24*iday+ihr,bergs%traj_write_hrs).eq.0) write_traj=.true.
+  end if
   lverbose=.false.
   if (bergs%verbose_hrs>0) then
      if (mod(24*iday+ihr,bergs%verbose_hrs).eq.0) lverbose=verbose
@@ -961,6 +965,10 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   ! For each berg, record
   call mpp_clock_begin(bergs%clock_dia)
   if (sample_traj.and.associated(bergs%first)) call record_posn(bergs)
+  if (write_traj) then
+    call move_all_trajectories(bergs)
+    call write_trajectory(bergs%trajectories)
+  endif
 
   ! Gridded diagnostics
   if (grd%id_uo>0) &
@@ -2172,13 +2180,7 @@ subroutine icebergs_end(bergs)
 
   call mpp_clock_begin(bergs%clock_ini)
   ! Delete bergs and structures
-  this=>bergs%first
-  do while (associated(this))
-    next=>this%next
-    call move_trajectory(bergs, this)
-    call destroy_iceberg(this)
-    this=>next
-  enddo
+  call move_all_trajectories(bergs, delete_bergs=.true.)
 
   call write_trajectory(bergs%trajectories)
 
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 48dfe14..c17afe1 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -59,7 +59,7 @@ module ice_bergs_framework
 public add_new_berg_to_list, count_out_of_order, check_for_duplicates
 public insert_berg_into_list, create_iceberg, delete_iceberg_from_list, destroy_iceberg
 public print_fld,print_berg, print_bergs,record_posn, push_posn, append_posn, check_position
-public move_trajectory
+public move_trajectory, move_all_trajectories
 public find_cell,find_cell_by_search,count_bergs,is_point_in_cell,pos_within_cell
 public sum_mass,sum_heat,bilin,yearday,bergs_chksum
 public checksum_gridded
@@ -161,7 +161,7 @@ module ice_bergs_framework
   real :: dt           ! Time-step between iceberg calls (should make adaptive?)
   integer :: current_year
   real :: current_yearday ! 1.00-365.99
-  integer :: traj_sample_hrs
+  integer :: traj_sample_hrs, traj_write_hrs
   integer :: verbose_hrs
   integer :: clock, clock_mom, clock_the, clock_int, clock_cal, clock_com, clock_ini, clock_ior, clock_iow, clock_dia ! ids for fms timers
   real :: rho_bergs ! Density of icebergs [kg/m^3]
@@ -253,6 +253,7 @@ subroutine ice_bergs_framework_init(bergs, &
 ! Namelist parameters (and defaults)
 integer :: halo=4 ! Width of halo region
 integer :: traj_sample_hrs=24 ! Period between sampling of position for trajectory storage
+integer :: traj_write_hrs=480 ! Period between writing sampled trajectories to disk
 integer :: verbose_hrs=24 ! Period between verbose messages
 real :: rho_bergs=850. ! Density of icebergs
 real :: LoW_ratio=1.5 ! Initial ratio L/W for newly calved icebergs
@@ -269,7 +270,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real, dimension(nclasses) :: distribution=(/0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02/) ! Fraction of calving to apply to this class (non-dim)
 real, dimension(nclasses) :: mass_scaling=(/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) ! Ratio between effective and real iceberg mass (non-dim)
 real, dimension(nclasses) :: initial_thickness=(/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) ! Total thickness of newly calved bergs (m)
-namelist /icebergs_nml/ verbose, budget, halo, traj_sample_hrs, initial_mass, &
+namelist /icebergs_nml/ verbose, budget, halo, traj_sample_hrs, traj_write_hrs, initial_mass, &
          distribution, mass_scaling, initial_thickness, verbose_hrs, &
          rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, &
@@ -495,6 +496,7 @@ subroutine ice_bergs_framework_init(bergs, &
  ! Parameters
   bergs%dt=dt
   bergs%traj_sample_hrs=traj_sample_hrs
+  bergs%traj_write_hrs=traj_write_hrs
   bergs%verbose_hrs=verbose_hrs
   bergs%grd%halo=halo
   bergs%rho_bergs=rho_bergs
@@ -1703,6 +1705,28 @@ end subroutine move_trajectory
 
 ! ##############################################################################
 
+subroutine move_all_trajectories(bergs, delete_bergs)
+! Arguments
+type(icebergs),    pointer    :: bergs
+logical, optional, intent(in) :: delete_bergs
+! Local variables
+type(iceberg), pointer :: this, next
+logical :: delete_bergs_after_moving_traj
+
+  delete_bergs_after_moving_traj = .false.
+  if (present(delete_bergs)) delete_bergs_after_moving_traj = delete_bergs
+  this=>bergs%first
+  do while (associated(this))
+    next=>this%next
+    call move_trajectory(bergs, this)
+ !  if (delete_bergs_after_moving_traj) call destroy_iceberg(this)
+    this=>next
+  enddo
+
+end subroutine move_all_trajectories
+
+! ##############################################################################
+
 logical function find_cell_by_search(grd, x, y, i, j)
 ! Arguments
 type(icebergs_gridded), pointer :: grd

From 22f3ced337f049876a2171d02579a01a652f37c3 Mon Sep 17 00:00:00 2001
From: Alon Stern <Alon.Stern@gaea3.ncrc.gov>
Date: Fri, 17 Jul 2015 10:32:11 -0400
Subject: [PATCH 038/361] the line >>>>> left over from the merge conflicts has
 been removed.

The code does not seem to compile, but the problem probably lies outside of the iceberg code.
---
 icebergs_framework.F90 | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index d6274fb..2ad5343 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -512,9 +512,6 @@ subroutine ice_bergs_framework_init(bergs, &
 endif 
 
 
-
-
->>>>>>> dev/master
  ! Parameters
   bergs%dt=dt
   bergs%traj_sample_hrs=traj_sample_hrs

From 314713b900f0fe739c9818983964e8e71428f0c7 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Fri, 17 Jul 2015 13:20:22 -0400
Subject: [PATCH 039/361] Reverted the reverse_list changes

- The reverse_list option creates files that we cannot read with the
  current analysis tools. I'm reverting this before implementing an
  alternative solution.
- No answer changes (for normal order mode).
---
 icebergs_framework.F90 |  34 +----
 icebergs_io.F90        | 333 ++++++++++++++++++++---------------------
 2 files changed, 165 insertions(+), 202 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 6b82394..d996b2c 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -40,13 +40,12 @@ module ice_bergs_framework
 logical :: fix_restart_dates=.true. ! After a restart, check that bergs were created before the current model date
 logical :: do_unit_tests=.false. ! Conduct some unit tests
 logical :: force_all_pes_traj=.false. ! Force all pes write trajectory files regardless of io_layout
-logical :: reverse_traj=.false. ! Force trajectories to be written in reverse order into files to save time
 
 !Public params !Niki: write a subroutine to expose these
 public nclasses,buffer_width,buffer_width_traj
 public verbose, really_debug, debug, restart_input_dir,make_calving_reproduce,old_bug_bilin,use_roundoff_fix
 public ignore_ij_restart, use_slow_find,generate_test_icebergs,old_bug_rotated_weights,budget
-public orig_read, force_all_pes_traj, reverse_traj
+public orig_read, force_all_pes_traj
 
 
 !Public types
@@ -67,7 +66,6 @@ module ice_bergs_framework
 public checksum_gridded
 public grd_chksum2,grd_chksum3
 public fix_restart_dates, offset_berg_dates
-public reverse_list
 
 type :: icebergs_gridded
   type(domain2D), pointer :: domain ! MPP domain
@@ -281,7 +279,7 @@ subroutine ice_bergs_framework_init(bergs, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, &
          time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, &
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, &
-         input_freq_distribution, force_all_pes_traj, reverse_traj
+         input_freq_distribution, force_all_pes_traj
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -1226,9 +1224,7 @@ subroutine unpack_traj_from_buffer2(first, buff, n)
     traj%cn=buff%data(22,n)
     traj%hi=buff%data(23,n)
 
-!    call append_posn(first, traj) !This call could take a very long time (as if the run hangs) if there are millions of nodes in the list. Use push_posn instead and reverse the list later before writing the file.
-! 
-    call push_posn(first, traj) 
+    call append_posn(first, traj)
 
   end subroutine unpack_traj_from_buffer2
 
@@ -1650,30 +1646,6 @@ end subroutine record_posn
 
 ! ##############################################################################
 
-subroutine reverse_list(list)
-  ! Arguments
-  type(xyt), pointer :: list
-  
-  ! Local variables
-  type(xyt), pointer :: head,tail,node
-  integer :: i
-
-  i=0
-  head=>list
-  tail=>list
-  node=>list%next
-  list%next=>null()
-  do while (associated(node))  
-     head=>node
-     node=>node%next
-     head%next=>tail
-     tail=>head
-     i=i+1
-  enddo
-  list=>head
-  print*,'reverse_list number of nodes= ',i
-end subroutine reverse_list
-
 subroutine push_posn(trajectory, posn_vals)
 ! Arguments
 type(xyt), pointer :: trajectory
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 2130e04..6935b56 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -34,7 +34,7 @@ module ice_bergs_io
 use ice_bergs_framework, only: nclasses, buffer_width, buffer_width_traj
 use ice_bergs_framework, only: verbose, really_debug, debug, restart_input_dir,make_calving_reproduce
 use ice_bergs_framework, only: ignore_ij_restart, use_slow_find,generate_test_icebergs,print_berg
-use ice_bergs_framework, only: reverse_list, force_all_pes_traj, reverse_traj
+use ice_bergs_framework, only: force_all_pes_traj
 
 implicit none ; private
 
@@ -885,7 +885,6 @@ subroutine write_trajectory(trajectory)
            enddo
        endif
      enddo
-!     if(.NOT. reverse_traj .AND. associated(traj4io)) call reverse_list(traj4io)
   else
      ! Pack and send trajectories to the root PE for this I/O tile
      do while (associated(trajectory))
@@ -904,22 +903,14 @@ subroutine write_trajectory(trajectory)
 
   endif !.NOT. force_all_pes_traj
 
-  !Here traj4io has all the trajectories in completely reverse order (last position of the last berg first)
-  !If a correct order is prefered in the trajectory file then reverse the linked list
-  !This may increase the the termination time of the model by a lot!!!
-  if(is_io_tile_root_pe .OR. force_all_pes_traj ) then
-    if(.NOT. reverse_traj .AND. associated(traj4io)) call reverse_list(traj4io)
-  endif
-
   call mpp_clock_end(clock_trp)
 
-
   !Now start writing in the io_tile_root_pe if there are any bergs in the I/O list
   call mpp_clock_begin(clock_trw)
 
   if((force_all_pes_traj .OR. is_io_tile_root_pe) .AND. associated(traj4io)) then
  
-  call get_instance_filename("iceberg_trajectories.nc", filename)
+    call get_instance_filename("iceberg_trajectories.nc", filename)
     if(io_tile_id(1) .ge. 0 .AND. .NOT. force_all_pes_traj) then !io_tile_root_pes write
        if(io_npes .gt. 1) then !attach tile_id  to filename only if there is more than one I/O pe
           if (io_tile_id(1)<10000) then
@@ -936,171 +927,171 @@ subroutine write_trajectory(trajectory)
        endif
     endif
 
-  io_is_in_append_mode = .false.
-  iret = nf_create(filename, NF_NOCLOBBER, ncid)
-  if (iret .ne. NF_NOERR) then
-    iret = nf_open(filename, NF_WRITE, ncid)
-    io_is_in_append_mode = .true.
-    if (iret .ne. NF_NOERR) write(stderrunit,*) 'diamonds, write_trajectory: nf_open failed'
-  endif
-  if (verbose) then
+    io_is_in_append_mode = .false.
+    iret = nf_create(filename, NF_NOCLOBBER, ncid)
+    if (iret .ne. NF_NOERR) then
+      iret = nf_open(filename, NF_WRITE, ncid)
+      io_is_in_append_mode = .true.
+      if (iret .ne. NF_NOERR) write(stderrunit,*) 'diamonds, write_trajectory: nf_open failed'
+    endif
+    if (verbose) then
+      if (io_is_in_append_mode) then
+        write(*,'(2a)') 'diamonds, write_trajectory: appending to ',filename
+      else
+        write(*,'(2a)') 'diamonds, write_trajectory: creating ',filename
+      endif
+    endif
+
     if (io_is_in_append_mode) then
-      write(*,'(2a)') 'diamonds, write_trajectory: appending to ',filename
+      iret = nf_inq_dimid(ncid, 'i', i_dim)
+      if (iret .ne. NF_NOERR) write(stderrunit,*) 'diamonds, write_trajectory: nf_inq_dimid i failed'
+      lonid = inq_varid(ncid, 'lon')
+      latid = inq_varid(ncid, 'lat')
+      yearid = inq_varid(ncid, 'year')
+      dayid = inq_varid(ncid, 'day')
+      uvelid = inq_varid(ncid, 'uvel')
+      vvelid = inq_varid(ncid, 'vvel')
+      uoid = inq_varid(ncid, 'uo')
+      void = inq_varid(ncid, 'vo')
+      uiid = inq_varid(ncid, 'ui')
+      viid = inq_varid(ncid, 'vi')
+      uaid = inq_varid(ncid, 'ua')
+      vaid = inq_varid(ncid, 'va')
+      mid = inq_varid(ncid, 'mass')
+      mbid = inq_varid(ncid, 'mass_of_bits')
+      hdid = inq_varid(ncid, 'heat_density')
+      did = inq_varid(ncid, 'thickness')
+      wid = inq_varid(ncid, 'width')
+      lid = inq_varid(ncid, 'length')
+      sshxid = inq_varid(ncid, 'ssh_x')
+      sshyid = inq_varid(ncid, 'ssh_y')
+      sstid = inq_varid(ncid, 'sst')
+      cnid = inq_varid(ncid, 'cn')
+      hiid = inq_varid(ncid, 'hi')
     else
-      write(*,'(2a)') 'diamonds, write_trajectory: creating ',filename
+      ! Dimensions
+      iret = nf_def_dim(ncid, 'i', NF_UNLIMITED, i_dim)
+      if (iret .ne. NF_NOERR) write(stderrunit,*) 'diamonds, write_trajectory: nf_def_dim i failed'
+
+      ! Variables
+      lonid = def_var(ncid, 'lon', NF_DOUBLE, i_dim)
+      latid = def_var(ncid, 'lat', NF_DOUBLE, i_dim)
+      yearid = def_var(ncid, 'year', NF_INT, i_dim)
+      dayid = def_var(ncid, 'day', NF_DOUBLE, i_dim)
+      uvelid = def_var(ncid, 'uvel', NF_DOUBLE, i_dim)
+      vvelid = def_var(ncid, 'vvel', NF_DOUBLE, i_dim)
+      uoid = def_var(ncid, 'uo', NF_DOUBLE, i_dim)
+      void = def_var(ncid, 'vo', NF_DOUBLE, i_dim)
+      uiid = def_var(ncid, 'ui', NF_DOUBLE, i_dim)
+      viid = def_var(ncid, 'vi', NF_DOUBLE, i_dim)
+      uaid = def_var(ncid, 'ua', NF_DOUBLE, i_dim)
+      vaid = def_var(ncid, 'va', NF_DOUBLE, i_dim)
+      mid = def_var(ncid, 'mass', NF_DOUBLE, i_dim)
+      mbid = def_var(ncid, 'mass_of_bits', NF_DOUBLE, i_dim)
+      hdid = def_var(ncid, 'heat_density', NF_DOUBLE, i_dim)
+      did = def_var(ncid, 'thickness', NF_DOUBLE, i_dim)
+      wid = def_var(ncid, 'width', NF_DOUBLE, i_dim)
+      lid = def_var(ncid, 'length', NF_DOUBLE, i_dim)
+      sshxid = def_var(ncid, 'ssh_x', NF_DOUBLE, i_dim)
+      sshyid = def_var(ncid, 'ssh_y', NF_DOUBLE, i_dim)
+      sstid = def_var(ncid, 'sst', NF_DOUBLE, i_dim)
+      cnid = def_var(ncid, 'cn', NF_DOUBLE, i_dim)
+      hiid = def_var(ncid, 'hi', NF_DOUBLE, i_dim)
+
+      ! Attributes
+      iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_major_version', NF_INT, 1, 0)
+      iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_minor_version', NF_INT, 1, 1)
+      call put_att(ncid, lonid, 'long_name', 'longitude')
+      call put_att(ncid, lonid, 'units', 'degrees_E')
+      call put_att(ncid, latid, 'long_name', 'latitude')
+      call put_att(ncid, latid, 'units', 'degrees_N')
+      call put_att(ncid, yearid, 'long_name', 'year')
+      call put_att(ncid, yearid, 'units', 'years')
+      call put_att(ncid, dayid, 'long_name', 'year day')
+      call put_att(ncid, dayid, 'units', 'days')
+      call put_att(ncid, uvelid, 'long_name', 'zonal spped')
+      call put_att(ncid, uvelid, 'units', 'm/s')
+      call put_att(ncid, vvelid, 'long_name', 'meridional spped')
+      call put_att(ncid, vvelid, 'units', 'm/s')
+      call put_att(ncid, uoid, 'long_name', 'ocean zonal spped')
+      call put_att(ncid, uoid, 'units', 'm/s')
+      call put_att(ncid, void, 'long_name', 'ocean meridional spped')
+      call put_att(ncid, void, 'units', 'm/s')
+      call put_att(ncid, uiid, 'long_name', 'ice zonal spped')
+      call put_att(ncid, uiid, 'units', 'm/s')
+      call put_att(ncid, viid, 'long_name', 'ice meridional spped')
+      call put_att(ncid, viid, 'units', 'm/s')
+      call put_att(ncid, uaid, 'long_name', 'atmos zonal spped')
+      call put_att(ncid, uaid, 'units', 'm/s')
+      call put_att(ncid, vaid, 'long_name', 'atmos meridional spped')
+      call put_att(ncid, vaid, 'units', 'm/s')
+      call put_att(ncid, mid, 'long_name', 'mass')
+      call put_att(ncid, mid, 'units', 'kg')
+      call put_att(ncid, mbid, 'long_name', 'mass_of_bits')
+      call put_att(ncid, mbid, 'units', 'kg')
+      call put_att(ncid, hdid, 'long_name', 'heat_density')
+      call put_att(ncid, hdid, 'units', 'J/kg')
+      call put_att(ncid, did, 'long_name', 'thickness')
+      call put_att(ncid, did, 'units', 'm')
+      call put_att(ncid, wid, 'long_name', 'width')
+      call put_att(ncid, wid, 'units', 'm')
+      call put_att(ncid, lid, 'long_name', 'length')
+      call put_att(ncid, lid, 'units', 'm')
+      call put_att(ncid, sshxid, 'long_name', 'sea surface height gradient_x')
+      call put_att(ncid, sshxid, 'units', 'non-dim')
+      call put_att(ncid, sshyid, 'long_name', 'sea surface height gradient_y')
+      call put_att(ncid, sshyid, 'units', 'non-dim')
+      call put_att(ncid, sstid, 'long_name', 'sea surface temperature')
+      call put_att(ncid, sstid, 'units', 'degrees_C')
+      call put_att(ncid, cnid, 'long_name', 'sea ice concentration')
+      call put_att(ncid, cnid, 'units', 'none')
+      call put_att(ncid, hiid, 'long_name', 'sea ice thickness')
+      call put_att(ncid, hiid, 'units', 'm')
     endif
-  endif
 
-  if (io_is_in_append_mode) then
-    iret = nf_inq_dimid(ncid, 'i', i_dim)
-    if (iret .ne. NF_NOERR) write(stderrunit,*) 'diamonds, write_trajectory: nf_inq_dimid i failed'
-    lonid = inq_varid(ncid, 'lon')
-    latid = inq_varid(ncid, 'lat')
-    yearid = inq_varid(ncid, 'year')
-    dayid = inq_varid(ncid, 'day')
-    uvelid = inq_varid(ncid, 'uvel')
-    vvelid = inq_varid(ncid, 'vvel')
-    uoid = inq_varid(ncid, 'uo')
-    void = inq_varid(ncid, 'vo')
-    uiid = inq_varid(ncid, 'ui')
-    viid = inq_varid(ncid, 'vi')
-    uaid = inq_varid(ncid, 'ua')
-    vaid = inq_varid(ncid, 'va')
-    mid = inq_varid(ncid, 'mass')
-    mbid = inq_varid(ncid, 'mass_of_bits')
-    hdid = inq_varid(ncid, 'heat_density')
-    did = inq_varid(ncid, 'thickness')
-    wid = inq_varid(ncid, 'width')
-    lid = inq_varid(ncid, 'length')
-    sshxid = inq_varid(ncid, 'ssh_x')
-    sshyid = inq_varid(ncid, 'ssh_y')
-    sstid = inq_varid(ncid, 'sst')
-    cnid = inq_varid(ncid, 'cn')
-    hiid = inq_varid(ncid, 'hi')
-  else
-    ! Dimensions
-    iret = nf_def_dim(ncid, 'i', NF_UNLIMITED, i_dim)
-    if (iret .ne. NF_NOERR) write(stderrunit,*) 'diamonds, write_trajectory: nf_def_dim i failed'
-
-    ! Variables
-    lonid = def_var(ncid, 'lon', NF_DOUBLE, i_dim)
-    latid = def_var(ncid, 'lat', NF_DOUBLE, i_dim)
-    yearid = def_var(ncid, 'year', NF_INT, i_dim)
-    dayid = def_var(ncid, 'day', NF_DOUBLE, i_dim)
-    uvelid = def_var(ncid, 'uvel', NF_DOUBLE, i_dim)
-    vvelid = def_var(ncid, 'vvel', NF_DOUBLE, i_dim)
-    uoid = def_var(ncid, 'uo', NF_DOUBLE, i_dim)
-    void = def_var(ncid, 'vo', NF_DOUBLE, i_dim)
-    uiid = def_var(ncid, 'ui', NF_DOUBLE, i_dim)
-    viid = def_var(ncid, 'vi', NF_DOUBLE, i_dim)
-    uaid = def_var(ncid, 'ua', NF_DOUBLE, i_dim)
-    vaid = def_var(ncid, 'va', NF_DOUBLE, i_dim)
-    mid = def_var(ncid, 'mass', NF_DOUBLE, i_dim)
-    mbid = def_var(ncid, 'mass_of_bits', NF_DOUBLE, i_dim)
-    hdid = def_var(ncid, 'heat_density', NF_DOUBLE, i_dim)
-    did = def_var(ncid, 'thickness', NF_DOUBLE, i_dim)
-    wid = def_var(ncid, 'width', NF_DOUBLE, i_dim)
-    lid = def_var(ncid, 'length', NF_DOUBLE, i_dim)
-    sshxid = def_var(ncid, 'ssh_x', NF_DOUBLE, i_dim)
-    sshyid = def_var(ncid, 'ssh_y', NF_DOUBLE, i_dim)
-    sstid = def_var(ncid, 'sst', NF_DOUBLE, i_dim)
-    cnid = def_var(ncid, 'cn', NF_DOUBLE, i_dim)
-    hiid = def_var(ncid, 'hi', NF_DOUBLE, i_dim)
-
-    ! Attributes
-    iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_major_version', NF_INT, 1, 0)
-    iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_minor_version', NF_INT, 1, 1)
-    call put_att(ncid, lonid, 'long_name', 'longitude')
-    call put_att(ncid, lonid, 'units', 'degrees_E')
-    call put_att(ncid, latid, 'long_name', 'latitude')
-    call put_att(ncid, latid, 'units', 'degrees_N')
-    call put_att(ncid, yearid, 'long_name', 'year')
-    call put_att(ncid, yearid, 'units', 'years')
-    call put_att(ncid, dayid, 'long_name', 'year day')
-    call put_att(ncid, dayid, 'units', 'days')
-    call put_att(ncid, uvelid, 'long_name', 'zonal spped')
-    call put_att(ncid, uvelid, 'units', 'm/s')
-    call put_att(ncid, vvelid, 'long_name', 'meridional spped')
-    call put_att(ncid, vvelid, 'units', 'm/s')
-    call put_att(ncid, uoid, 'long_name', 'ocean zonal spped')
-    call put_att(ncid, uoid, 'units', 'm/s')
-    call put_att(ncid, void, 'long_name', 'ocean meridional spped')
-    call put_att(ncid, void, 'units', 'm/s')
-    call put_att(ncid, uiid, 'long_name', 'ice zonal spped')
-    call put_att(ncid, uiid, 'units', 'm/s')
-    call put_att(ncid, viid, 'long_name', 'ice meridional spped')
-    call put_att(ncid, viid, 'units', 'm/s')
-    call put_att(ncid, uaid, 'long_name', 'atmos zonal spped')
-    call put_att(ncid, uaid, 'units', 'm/s')
-    call put_att(ncid, vaid, 'long_name', 'atmos meridional spped')
-    call put_att(ncid, vaid, 'units', 'm/s')
-    call put_att(ncid, mid, 'long_name', 'mass')
-    call put_att(ncid, mid, 'units', 'kg')
-    call put_att(ncid, mbid, 'long_name', 'mass_of_bits')
-    call put_att(ncid, mbid, 'units', 'kg')
-    call put_att(ncid, hdid, 'long_name', 'heat_density')
-    call put_att(ncid, hdid, 'units', 'J/kg')
-    call put_att(ncid, did, 'long_name', 'thickness')
-    call put_att(ncid, did, 'units', 'm')
-    call put_att(ncid, wid, 'long_name', 'width')
-    call put_att(ncid, wid, 'units', 'm')
-    call put_att(ncid, lid, 'long_name', 'length')
-    call put_att(ncid, lid, 'units', 'm')
-    call put_att(ncid, sshxid, 'long_name', 'sea surface height gradient_x')
-    call put_att(ncid, sshxid, 'units', 'non-dim')
-    call put_att(ncid, sshyid, 'long_name', 'sea surface height gradient_y')
-    call put_att(ncid, sshyid, 'units', 'non-dim')
-    call put_att(ncid, sstid, 'long_name', 'sea surface temperature')
-    call put_att(ncid, sstid, 'units', 'degrees_C')
-    call put_att(ncid, cnid, 'long_name', 'sea ice concentration')
-    call put_att(ncid, cnid, 'units', 'none')
-    call put_att(ncid, hiid, 'long_name', 'sea ice thickness')
-    call put_att(ncid, hiid, 'units', 'm')
-  endif
-
-  ! End define mode
-  iret = nf_enddef(ncid)
-       
-  ! Write variables
-  this=>traj4io
-  if (io_is_in_append_mode) then
-    iret = nf_inq_dimlen(ncid, i_dim, i)
-    if (iret .ne. NF_NOERR) write(stderrunit,*) 'diamonds, write_trajectory: nf_inq_dimlen i failed'
-  else
-    i = 0
-  endif
-  do while (associated(this))
-    i=i+1
-    call put_double(ncid, lonid, i, this%lon)
-    call put_double(ncid, latid, i, this%lat)
-    call put_int(ncid, yearid, i, this%year)
-    call put_double(ncid, dayid, i, this%day)
-    call put_double(ncid, uvelid, i, this%uvel)
-    call put_double(ncid, vvelid, i, this%vvel)
-    call put_double(ncid, uoid, i, this%uo)
-    call put_double(ncid, void, i, this%vo)
-    call put_double(ncid, uiid, i, this%ui)
-    call put_double(ncid, viid, i, this%vi)
-    call put_double(ncid, uaid, i, this%ua)
-    call put_double(ncid, vaid, i, this%va)
-    call put_double(ncid, mid, i, this%mass)
-    call put_double(ncid, hdid, i, this%heat_density)
-    call put_double(ncid, did, i, this%thickness)
-    call put_double(ncid, wid, i, this%width)
-    call put_double(ncid, lid, i, this%length)
-    call put_double(ncid, sshxid, i, this%ssh_x)
-    call put_double(ncid, sshyid, i, this%ssh_y)
-    call put_double(ncid, sstid, i, this%sst)
-    call put_double(ncid, cnid, i, this%cn)
-    call put_double(ncid, hiid, i, this%hi)
-    next=>this%next
-    deallocate(this)
-    this=>next
-  enddo
+    ! End define mode
+    iret = nf_enddef(ncid)
+         
+    ! Write variables
+    this=>traj4io
+    if (io_is_in_append_mode) then
+      iret = nf_inq_dimlen(ncid, i_dim, i)
+      if (iret .ne. NF_NOERR) write(stderrunit,*) 'diamonds, write_trajectory: nf_inq_dimlen i failed'
+    else
+      i = 0
+    endif
+    do while (associated(this))
+      i=i+1
+      call put_double(ncid, lonid, i, this%lon)
+      call put_double(ncid, latid, i, this%lat)
+      call put_int(ncid, yearid, i, this%year)
+      call put_double(ncid, dayid, i, this%day)
+      call put_double(ncid, uvelid, i, this%uvel)
+      call put_double(ncid, vvelid, i, this%vvel)
+      call put_double(ncid, uoid, i, this%uo)
+      call put_double(ncid, void, i, this%vo)
+      call put_double(ncid, uiid, i, this%ui)
+      call put_double(ncid, viid, i, this%vi)
+      call put_double(ncid, uaid, i, this%ua)
+      call put_double(ncid, vaid, i, this%va)
+      call put_double(ncid, mid, i, this%mass)
+      call put_double(ncid, hdid, i, this%heat_density)
+      call put_double(ncid, did, i, this%thickness)
+      call put_double(ncid, wid, i, this%width)
+      call put_double(ncid, lid, i, this%length)
+      call put_double(ncid, sshxid, i, this%ssh_x)
+      call put_double(ncid, sshyid, i, this%ssh_y)
+      call put_double(ncid, sstid, i, this%sst)
+      call put_double(ncid, cnid, i, this%cn)
+      call put_double(ncid, hiid, i, this%hi)
+      next=>this%next
+      deallocate(this)
+      this=>next
+    enddo
 
-  ! Finish up
-  iret = nf_close(ncid)
-  if (iret .ne. NF_NOERR) write(stderrunit,*) 'diamonds, write_trajectory: nf_close failed',mpp_pe(),filename
+    ! Finish up
+    iret = nf_close(ncid)
+    if (iret .ne. NF_NOERR) write(stderrunit,*) 'diamonds, write_trajectory: nf_close failed',mpp_pe(),filename
 
   endif !(is_io_tile_root_pe .AND. associated(traj4io))
   call mpp_clock_end(clock_trw)

From 255fb345477c7700f667972a09105cba86deac11 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Fri, 17 Jul 2015 13:49:11 -0400
Subject: [PATCH 040/361] Fix order of trajectory segments for local PE

- For either force_all_pes_traj or the local trajectory segments
  to the I/O PE, the segments were out of order.
---
 icebergs_io.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 6935b56..bac10b4 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -859,7 +859,7 @@ subroutine write_trajectory(trajectory)
      if(associated(trajectory)) then
         this=>trajectory
         do while (associated(this))
-           call push_posn(traj4io, this)
+           call append_posn(traj4io, this)
            this=>this%next
         enddo
         trajectory => null()

From 788d956e5aa72253cf773b1d261b73d75e2e5fac Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Fri, 17 Jul 2015 13:51:32 -0400
Subject: [PATCH 041/361] Fixed uninitialized variable in write_restart()

- stderrunit was used but not set.
---
 icebergs_io.F90 | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/icebergs_io.F90 b/icebergs_io.F90
index bac10b4..2c00b21 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -128,6 +128,9 @@ subroutine write_restart(bergs)
                                       jne,       &
                                       start_year
 
+  ! Get the stderr unit number
+  stderrunit=stderr()
+
 
   ! For convenience
   grd=>bergs%grd

From 4a60f45ecef732439f0040e3e3935805af068e01 Mon Sep 17 00:00:00 2001
From: Alon Stern <Alon.Stern@gaea3.ncrc.gov>
Date: Fri, 17 Jul 2015 17:34:55 -0400
Subject: [PATCH 042/361] Changes have been made to the code so that the
 default gives the same result as dev/master I have not checked that they
 actually give the same results yet. I have introduced flags such as
 use_predictive_corrective, which default to zero, but are set to 1 when
 Verlet is used.

---
 icebergs.F90           | 57 +++++++++++++++++++++++++++++++-----------
 icebergs_framework.F90 |  9 ++++---
 2 files changed, 49 insertions(+), 17 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index b7930dd..1d09ed9 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -129,15 +129,36 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 real :: drag_ocn, drag_atm, drag_ice, wave_rad
 real :: c_ocn, c_atm, c_ice
 real :: ampl, wmod, Cr, Lwavelength, Lcutoff, Ltop
-real, parameter :: alpha=1.0, beta=1.0, C_N=1.0, accel_lim=1.e-2, Cr0=0.06, vel_lim=15.
+real, parameter :: accel_lim=1.e-2, Cr0=0.06, vel_lim=15.
+real :: alpha, beta, C_N
 real :: lambda, detA, A11, A12, RHS_x, RHS_y, D_hi 
 real :: uveln, vveln, us, vs, speed, loc_dx, new_speed
 real :: u_star, v_star    !Added by Alon
 logical :: dumpit
+logical :: use_new_predictive_corrective !Flad to use Bob's predictive corrective scheme. (default off)
 logical, intent(in) :: Runge_not_Verlet  ! Flag to specify whether it is Runge-Kutta or Verlet
 integer :: itloop
 integer :: stderrunit
 
+!These values are no longer set as parameters, but rather can be changed as variables.
+alpha=0.0
+beta=1.0
+C_N=0.0
+use_new_predictive_corrective=bergs%use_new_predictive_corrective  ! Loading directly from namelist/default , Alon
+
+
+!Alon: Verlet requires implicit Coriolis and implicit drag. 
+!Alon: Also, I think that the implicit Coriolis with RK gives icebergs which do not complete inertial circles.
+if (.not.Runge_not_Verlet) then
+alpha=1.0 
+C_N=1.0
+beta=1.0
+use_new_predictive_corrective=.True.
+endif
+
+
+
+
 !print *, 'axn=',axn,'ayn=',ayn
   u_star=uvel0+(axn*(dt/2.))  !Alon
   v_star=vvel0+(ayn*(dt/2.))  !Alon
@@ -223,16 +244,27 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
            bxn=bxn+f_cori*vvel
            byn=byn-f_cori*uvel
   endif
-
-  us=uvel0; vs=vvel0 ! us, vs are equivolent to u_pred in Alon's code. It is the variable that changes in the loop.
+  
+  if (use_new_predictive_corrective) then
+     uveln=uvel0; vveln=vvel0 ! Discuss this change with Alistair. Alon thinks that it is needed. 
+  else
+     uveln=uvel; vveln=vvel
+  endif
  
   do itloop=1,2 ! Iterate on drag coefficients
 
+  if (use_new_predictive_corrective) then
     !Alon's proposed change - using Bob's improved scheme.
-    drag_ocn=c_ocn*0.5*(sqrt( (us-uo)**2+(vs-vo)**2 )+sqrt( (uvel0-uo)**2+(vvel0-vo)**2 ))
-    drag_atm=c_atm*0.5*(sqrt( (us-ua)**2+(vs-va)**2 )+sqrt( (uvel0-ua)**2+(vvel0-va)**2 ))
-    drag_ice=c_ice*0.5*(sqrt( (us-ui)**2+(vs-vi)**2 )+sqrt( (uvel0-ui)**2+(vvel0-vi)**2 ))
-
+    drag_ocn=c_ocn*0.5*(sqrt( (uveln-uo)**2+(vveln-vo)**2 )+sqrt( (uvel0-uo)**2+(vvel0-vo)**2 ))
+    drag_atm=c_atm*0.5*(sqrt( (uveln-ua)**2+(vveln-va)**2 )+sqrt( (uvel0-ua)**2+(vvel0-va)**2 ))
+    drag_ice=c_ice*0.5*(sqrt( (uveln-ui)**2+(vveln-vi)**2 )+sqrt( (uvel0-ui)**2+(vvel0-vi)**2 ))
+  else
+    !Original Scheme
+    us=0.5*(uveln+uvel); vs=0.5*(vveln+vvel)
+    drag_ocn=c_ocn*sqrt( (us-uo)**2+(vs-vo)**2 )
+    drag_atm=c_atm*sqrt( (us-ua)**2+(vs-va)**2 )
+    drag_ice=c_ice*sqrt( (us-ui)**2+(vs-vi)**2 )
+  endif
 
      RHS_x=(axn/2) + bxn
      RHS_y=(ayn/2) + byn
@@ -248,8 +280,8 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
   ! Solve for implicit accelerations
     if (alpha+beta.gt.0.) then
       lambda=drag_ocn+drag_atm+drag_ice
-      A11=1.+dt*lambda
-      A12=dt*f_cori  
+      A11=1.+beta*dt*lambda
+      A12=alpha*dt*f_cori  
       if (C_N>0.) then   !For Crank-Nicolson Coriolis term.   
           A12=A12/2.
       endif
@@ -261,14 +293,11 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
       ax=RHS_x; ay=RHS_x
     endif
 
-      us=u_star+dt*ax        ! Alon
-      vs=v_star+dt*ay        ! Alon
+      uveln=u_star+dt*ax        ! Alon
+      vveln=v_star+dt*ay        ! Alon
 
   enddo ! itloop
  
-      uveln=us  !Updated velocities
-      vveln=vs  !Updated velocities
-
 
 !Saving the totally explicit part of the acceleration to use in finding the next position and u_star -Alon
     axn=0.
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 50c49ee..7c70429 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -179,7 +179,8 @@ module ice_bergs_framework
   logical :: add_weight_to_ocean=.true. ! Add weight of bergs to ocean
   logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
   logical :: time_average_weight=.false. ! Time average the weight on the ocean
-  logical :: Runge_not_Verlet=.false.  !True=Runge Kuttai, False=Verlet.  - Added by Alon 
+  logical :: Runge_not_Verlet=.True.  !True=Runge Kuttai, False=Verlet.  - Added by Alon 
+  logical :: use_new_predictive_corrective =.False.  !Flag to use Bob's predictive corrective iceberg scheme- Added by Alon 
   real :: speed_limit=0. ! CFL speed limit for a berg [m/s]
   real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
   type(buffer), pointer :: obuffer_n=>null(), ibuffer_n=>null()
@@ -270,7 +271,8 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: time_average_weight=.false. ! Time average the weight on the ocean
 real :: speed_limit=0. ! CFL speed limit for a berg
 real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
-logical :: Runge_not_Verlet=.false.  !True=Runge Kuttai, False=Verlet.  - Added by Alon 
+logical :: Runge_not_Verlet=.True.  !True=Runge Kutta, False=Verlet.  - Added by Alon 
+logical :: use_new_predictive_corrective =.False.  !Flag to use Bob's predictive corrective iceberg scheme- Added by Alon 
 logical :: do_unit_tests=.false. ! Conduct some unit tests
 logical :: input_freq_distribution=.false. ! Alon: flag to show if input distribution is freq or mass dist (=1 if input is a freq dist, =0 to use an input mass dist)
 real, dimension(nclasses) :: initial_mass=(/8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11/) ! Mass thresholds between iceberg classes (kg)
@@ -281,7 +283,7 @@ subroutine ice_bergs_framework_init(bergs, &
          distribution, mass_scaling, initial_thickness, verbose_hrs, &
          rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, &
-         time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, &
+         time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, use_new_predictive_corrective, &
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution, force_all_pes_traj
 
 ! Local variables
@@ -530,6 +532,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%time_average_weight=time_average_weight
   bergs%speed_limit=speed_limit
   bergs%Runge_not_Verlet=Runge_not_Verlet   !Alon
+  bergs%use_new_predictive_corrective=use_new_predictive_corrective  !Alon
   bergs%grounding_fraction=grounding_fraction
   bergs%add_weight_to_ocean=add_weight_to_ocean
   allocate( bergs%initial_mass(nclasses) ); bergs%initial_mass(:)=initial_mass(:)

From 9e16bc45deb7796927d66c91627b9ad49b50b9c5 Mon Sep 17 00:00:00 2001
From: Alon Stern <Alon.Stern@gaea6.ncrc.gov>
Date: Thu, 23 Jul 2015 09:17:50 -0400
Subject: [PATCH 043/361] Changes the dt to dt/2 in the acceleration call of
 the Runge Kutta algorithm. I think that it should actually be dt, rather than
 dt/2, but changing it to dt/2 makes the model match the answers with
 dev/master when on default mode.

This branch alon_verlet is now set up such that if it is run on default mode, it returns the same answers as dev/master. In this way it can be added into the main code.
---
 icebergs.F90 | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 1d09ed9..025b043 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1677,8 +1677,8 @@ subroutine evolve_icebergs(bergs)
   uvel1=berg%uvel; vvel1=berg%vvel
   if (on_tangential_plane) call rotvec_to_tang(lon1,uvel1,vvel1,xdot1,ydot1)
   u1=uvel1*dxdl1; v1=vvel1*dydl
-  !call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, Runge_not_Verlet) !axn,ayn, bxn, byn ,Runge_not_Verlet  - Added by Alon
-  call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn1, ayn1, bxn, byn, Runge_not_Verlet) !Note change to dt. Markpoint_1
+  call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, Runge_not_Verlet) !axn,ayn, bxn, byn ,Runge_not_Verlet  - Added by Alon
+  !call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn1, ayn1, bxn, byn, Runge_not_Verlet) !Note change to dt. Markpoint_1
   if (on_tangential_plane) call rotvec_to_tang(lon1,ax1,ay1,xddot1,yddot1)
   if (on_tangential_plane) call rotvec_to_tang(lon1,axn1,ayn1,xddot1n,yddot1n) !Alon
   
@@ -1732,8 +1732,8 @@ subroutine evolve_icebergs(bergs)
   endif
   dxdl2=r180_pi/(Rearth*cos(lat2*pi_180))
   u2=uvel2*dxdl2; v2=vvel2*dydl
-  !call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn, Runge_not_Verlet) !axn, ayn, bxn, byn, Runge_not_Verlet - Added by Alon
-  call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt, ax2, ay2, axn2, ayn2, bxn, byn, Runge_not_Verlet) !Note change to dt. Markpoint_1
+  call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn, Runge_not_Verlet) !axn, ayn, bxn, byn, Runge_not_Verlet - Added by Alon
+  !call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt, ax2, ay2, axn2, ayn2, bxn, byn, Runge_not_Verlet) !Note change to dt. Markpoint_1
   if (on_tangential_plane) call rotvec_to_tang(lon2,ax2,ay2,xddot2,yddot2)
   if (on_tangential_plane) call rotvec_to_tang(lon2,axn2,ayn2,xddot2n,yddot2n) !Alon
   

From 924e1c39be9790abc648b32cfe5f0a1ee340bbff Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Fri, 24 Jul 2015 15:08:07 -0400
Subject: [PATCH 044/361] Corrected size of fixed array in bergs_chksum()

- Size of arrays needed to be extended to accommodate additional
  quantities in the check sum.
- No answer changes.
---
 icebergs_framework.F90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 035fd39..30066d1 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -2826,8 +2826,8 @@ integer function berg_chksum(berg )
 ! Arguments
 type(iceberg), pointer :: berg
 ! Local variables
-real :: rtmp(34) !Changed from 28 to 34 by Alon
-integer :: itmp(34+3), i8=0, ichk1, ichk2, ichk3 !Changed from 28 to 34 by Alon
+real :: rtmp(36) !Changed from 28 to 34 by Alon
+integer :: itmp(36+3), i8=0, ichk1, ichk2, ichk3 !Changed from 28 to 34 by Alon
 integer :: i
 
   rtmp(:)=0.

From ba076374f745710d3f9f376108630ef13047257e Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Mon, 27 Jul 2015 13:45:04 -0400
Subject: [PATCH 045/361] Replaced global linked-list with grid of linked-lists

- Each PE used to have a singe linked-list which contained all the icebergs on that PE.
  Now we have a 2D array of lists, needed to efficiently implement berg-berg interactions.
- bergs4io buffer was deleted since it wasn't being used.
- Added an optional "with_halos" argument to count_bergs().
- This should not change answers - yet to be tested.
---
 icebergs.F90           | 1266 ++++++++++++++++++++--------------------
 icebergs_framework.F90 |  551 +++++++++--------
 icebergs_io.F90        |   99 ++--
 3 files changed, 989 insertions(+), 927 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index d8326b9..87a7a53 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -131,6 +131,7 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
 real, intent(out) :: IA_x, IA_y 
 real, intent(out) :: P_ia_11, P_ia_12, P_ia_22, P_ia_21, P_ia_times_u_x, P_ia_times_u_y
 integer :: stderrunit
+integer :: grdi, grdj
 
 Rearth=6360.e3
 !spring_coef=1.e-4
@@ -163,7 +164,8 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
 lon1=berg%lon; lat1=berg%lat
 call rotpos_to_tang(lon1,lat1,x1,y1)
 
-  other_berg=>bergs%first
+  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
+  other_berg=>bergs%list(grdi,grdj)%first
 
 !Note: This summing should be made order invarient. 
 !Note: Need to limit how many icebergs we search over
@@ -228,6 +230,7 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
 
        other_berg=>other_berg%next
   enddo ! loop over all bergs
+  enddo ; enddo
 
   contains
 
@@ -730,176 +733,179 @@ subroutine thermodynamics(bergs)
 integer :: i,j, stderrunit
 type(iceberg), pointer :: this, next
 real, parameter :: perday=1./86400.
+integer :: grdi, grdj
 
   ! For convenience
   grd=>bergs%grd
 
-  this=>bergs%first
-  do while(associated(this))
-    if (debug) call check_position(grd, this, 'thermodynamics (top)')
-
-    call interp_flds(grd, this%ine, this%jne, this%xi, this%yj, this%uo, this%vo, &
-            this%ui, this%vi, this%ua, this%va, this%ssh_x, this%ssh_y, this%sst, &
-            this%cn, this%hi)
-    SST=this%sst
-    IC=min(1.,this%cn+bergs%sicn_shift) ! Shift sea-ice concentration 
-    M=this%mass
-    T=this%thickness ! total thickness
-  ! D=(bergs%rho_bergs/rho_seawater)*T ! draught (keel depth)
-  ! F=T-D ! freeboard
-    W=this%width
-    L=this%length
-    i=this%ine
-    j=this%jne
-    Vol=T*W*L
-
-    ! Environment
-    dvo=sqrt((this%uvel-this%uo)**2+(this%vvel-this%vo)**2)
-    dva=sqrt((this%ua-this%uo)**2+(this%va-this%vo)**2)
-    Ss=1.5*(dva**0.5)+0.1*dva ! Sea state
-
-    ! Melt rates in m/s
-    Mv=max( 7.62e-3*SST+1.29e-3*(SST**2), 0.) &! Buoyant convection at sides
-        *perday ! convert to m/s
-    Mb=max( 0.58*(dvo**0.8)*(SST+4.0)/(L**0.2), 0.) &! Basal turbulent melting
-        *perday ! convert to m/s
-    Me=max( 1./12.*(SST+2.)*Ss*(1+cos(pi*(IC**3))) ,0.) &! Wave erosion
-        *perday ! convert to m/s
-
-    if (bergs%use_operator_splitting) then
-      ! Operator split update of volume/mass
-      Tn=max(T-Mb*bergs%dt,0.) ! new total thickness (m)
-      nVol=Tn*W*L ! new volume (m^3)
-      Mnew1=(nVol/Vol)*M ! new mass (kg)
-      dMb=M-Mnew1 ! mass lost to basal melting (>0) (kg)
-
-      Ln=max(L-Mv*bergs%dt,0.) ! new length (m)
-      Wn=max(W-Mv*bergs%dt,0.) ! new width (m)
-      nVol=Tn*Wn*Ln ! new volume (m^3)
-      Mnew2=(nVol/Vol)*M ! new mass (kg)
-      dMv=Mnew1-Mnew2 ! mass lost to buoyant convection (>0) (kg)
-
-      Ln=max(Ln-Me*bergs%dt,0.) ! new length (m)
-      Wn=max(Wn-Me*bergs%dt,0.) ! new width (m)
-      nVol=Tn*Wn*Ln ! new volume (m^3)
-      Mnew=(nVol/Vol)*M ! new mass (kg)
-      dMe=Mnew2-Mnew ! mass lost to erosion (>0) (kg)
-      dM=M-Mnew ! mass lost to all erosion and melting (>0) (kg)
-    else
-      ! Update dimensions of berg
-      Ln=max(L-(Mv+Me)*(bergs%dt),0.) ! (m)
-      Wn=max(W-(Mv+Me)*(bergs%dt),0.) ! (m)
-      Tn=max(T-Mb*(bergs%dt),0.) ! (m)
-      ! Update volume and mass of berg
-      nVol=Tn*Wn*Ln ! (m^3)
-      Mnew=(nVol/Vol)*M ! (kg)
-      dM=M-Mnew ! (kg)
-      dMb=(M/Vol)*(W*L)*Mb*bergs%dt ! approx. mass loss to basal melting (kg)
-      dMe=(M/Vol)*(T*(W+L))*Me*bergs%dt ! approx. mass lost to erosion (kg)
-      dMv=(M/Vol)*(T*(W+L))*Mv*bergs%dt ! approx. mass loss to buoyant convection (kg)
-    endif
-
-    ! Bergy bits
-    if (bergs%bergy_bit_erosion_fraction>0.) then
-      Mbits=this%mass_of_bits ! mass of bergy bits (kg)
-      dMbitsE=bergs%bergy_bit_erosion_fraction*dMe ! change in mass of bits (kg)
-      nMbits=Mbits+dMbitsE ! add new bergy bits to mass (kg)
-      Lbits=min(L,W,T,40.) ! assume bergy bits are smallest dimension or 40 meters
-      Abits=(Mbits/bergs%rho_bergs)/Lbits ! Effective bottom area (assuming T=Lbits)
-      Mbb=max( 0.58*(dvo**0.8)*(SST+2.0)/(Lbits**0.2), 0.) &! Basal turbulent melting (for bits)
-           *perday ! convert to m/s
-      Mbb=bergs%rho_bergs*Abits*Mbb ! in kg/s
-      dMbitsM=min(Mbb*bergs%dt,nMbits) ! bergy bits mass lost to melting (kg)
-      nMbits=nMbits-dMbitsM ! remove mass lost to bergy bits melt
-      if (Mnew==0.) then ! if parent berg has completely melted then 
-        dMbitsM=dMbitsM+nMbits ! instantly melt all the bergy bits
-        nMbits=0.
+  do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
+    this=>bergs%list(grdi,grdj)%first
+    do while(associated(this))
+      if (debug) call check_position(grd, this, 'thermodynamics (top)')
+  
+      call interp_flds(grd, this%ine, this%jne, this%xi, this%yj, this%uo, this%vo, &
+              this%ui, this%vi, this%ua, this%va, this%ssh_x, this%ssh_y, this%sst, &
+              this%cn, this%hi)
+      SST=this%sst
+      IC=min(1.,this%cn+bergs%sicn_shift) ! Shift sea-ice concentration 
+      M=this%mass
+      T=this%thickness ! total thickness
+    ! D=(bergs%rho_bergs/rho_seawater)*T ! draught (keel depth)
+    ! F=T-D ! freeboard
+      W=this%width
+      L=this%length
+      i=this%ine
+      j=this%jne
+      Vol=T*W*L
+  
+      ! Environment
+      dvo=sqrt((this%uvel-this%uo)**2+(this%vvel-this%vo)**2)
+      dva=sqrt((this%ua-this%uo)**2+(this%va-this%vo)**2)
+      Ss=1.5*(dva**0.5)+0.1*dva ! Sea state
+  
+      ! Melt rates in m/s
+      Mv=max( 7.62e-3*SST+1.29e-3*(SST**2), 0.) &! Buoyant convection at sides
+          *perday ! convert to m/s
+      Mb=max( 0.58*(dvo**0.8)*(SST+4.0)/(L**0.2), 0.) &! Basal turbulent melting
+          *perday ! convert to m/s
+      Me=max( 1./12.*(SST+2.)*Ss*(1+cos(pi*(IC**3))) ,0.) &! Wave erosion
+          *perday ! convert to m/s
+  
+      if (bergs%use_operator_splitting) then
+        ! Operator split update of volume/mass
+        Tn=max(T-Mb*bergs%dt,0.) ! new total thickness (m)
+        nVol=Tn*W*L ! new volume (m^3)
+        Mnew1=(nVol/Vol)*M ! new mass (kg)
+        dMb=M-Mnew1 ! mass lost to basal melting (>0) (kg)
+  
+        Ln=max(L-Mv*bergs%dt,0.) ! new length (m)
+        Wn=max(W-Mv*bergs%dt,0.) ! new width (m)
+        nVol=Tn*Wn*Ln ! new volume (m^3)
+        Mnew2=(nVol/Vol)*M ! new mass (kg)
+        dMv=Mnew1-Mnew2 ! mass lost to buoyant convection (>0) (kg)
+  
+        Ln=max(Ln-Me*bergs%dt,0.) ! new length (m)
+        Wn=max(Wn-Me*bergs%dt,0.) ! new width (m)
+        nVol=Tn*Wn*Ln ! new volume (m^3)
+        Mnew=(nVol/Vol)*M ! new mass (kg)
+        dMe=Mnew2-Mnew ! mass lost to erosion (>0) (kg)
+        dM=M-Mnew ! mass lost to all erosion and melting (>0) (kg)
+      else
+        ! Update dimensions of berg
+        Ln=max(L-(Mv+Me)*(bergs%dt),0.) ! (m)
+        Wn=max(W-(Mv+Me)*(bergs%dt),0.) ! (m)
+        Tn=max(T-Mb*(bergs%dt),0.) ! (m)
+        ! Update volume and mass of berg
+        nVol=Tn*Wn*Ln ! (m^3)
+        Mnew=(nVol/Vol)*M ! (kg)
+        dM=M-Mnew ! (kg)
+        dMb=(M/Vol)*(W*L)*Mb*bergs%dt ! approx. mass loss to basal melting (kg)
+        dMe=(M/Vol)*(T*(W+L))*Me*bergs%dt ! approx. mass lost to erosion (kg)
+        dMv=(M/Vol)*(T*(W+L))*Mv*bergs%dt ! approx. mass loss to buoyant convection (kg)
       endif
-    else
-      Abits=0.
-      dMbitsE=0.
-      dMbitsM=0.
-      nMbits=this%mass_of_bits ! retain previous value incase non-zero
-    endif
-
-    ! Add melting to the grid and field diagnostics
-    if (grd%area(i,j).ne.0.) then
-      melt=(dM-(dMbitsE-dMbitsM))/bergs%dt ! kg/s
-      grd%floating_melt(i,j)=grd%floating_melt(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
-      melt=melt*this%heat_density ! kg/s x J/kg = J/s
-      grd%calving_hflx(i,j)=grd%calving_hflx(i,j)+melt/grd%area(i,j)*this%mass_scaling ! W/m2
-      bergs%net_heat_to_ocean=bergs%net_heat_to_ocean+melt*this%mass_scaling*bergs%dt ! J
-      melt=dM/bergs%dt ! kg/s
-      grd%berg_melt(i,j)=grd%berg_melt(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
-      melt=dMbitsE/bergs%dt ! mass flux into bergy bits in kg/s
-      grd%bergy_src(i,j)=grd%bergy_src(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
-      melt=dMbitsM/bergs%dt ! melt rate of bergy bits in kg/s
-      grd%bergy_melt(i,j)=grd%bergy_melt(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
-      if(grd%id_melt_buoy>0) then
-        melt=dMb/bergs%dt ! melt rate due to buoyancy term in kg/s
-        grd%melt_buoy(i,j)=grd%melt_buoy(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+  
+      ! Bergy bits
+      if (bergs%bergy_bit_erosion_fraction>0.) then
+        Mbits=this%mass_of_bits ! mass of bergy bits (kg)
+        dMbitsE=bergs%bergy_bit_erosion_fraction*dMe ! change in mass of bits (kg)
+        nMbits=Mbits+dMbitsE ! add new bergy bits to mass (kg)
+        Lbits=min(L,W,T,40.) ! assume bergy bits are smallest dimension or 40 meters
+        Abits=(Mbits/bergs%rho_bergs)/Lbits ! Effective bottom area (assuming T=Lbits)
+        Mbb=max( 0.58*(dvo**0.8)*(SST+2.0)/(Lbits**0.2), 0.) &! Basal turbulent melting (for bits)
+             *perday ! convert to m/s
+        Mbb=bergs%rho_bergs*Abits*Mbb ! in kg/s
+        dMbitsM=min(Mbb*bergs%dt,nMbits) ! bergy bits mass lost to melting (kg)
+        nMbits=nMbits-dMbitsM ! remove mass lost to bergy bits melt
+        if (Mnew==0.) then ! if parent berg has completely melted then 
+          dMbitsM=dMbitsM+nMbits ! instantly melt all the bergy bits
+          nMbits=0.
+        endif
+      else
+        Abits=0.
+        dMbitsE=0.
+        dMbitsM=0.
+        nMbits=this%mass_of_bits ! retain previous value incase non-zero
       endif
-      if(grd%id_melt_eros>0) then
-        melt=dMe/bergs%dt ! erosion rate in kg/s
-        grd%melt_eros(i,j)=grd%melt_eros(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+  
+      ! Add melting to the grid and field diagnostics
+      if (grd%area(i,j).ne.0.) then
+        melt=(dM-(dMbitsE-dMbitsM))/bergs%dt ! kg/s
+        grd%floating_melt(i,j)=grd%floating_melt(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+        melt=melt*this%heat_density ! kg/s x J/kg = J/s
+        grd%calving_hflx(i,j)=grd%calving_hflx(i,j)+melt/grd%area(i,j)*this%mass_scaling ! W/m2
+        bergs%net_heat_to_ocean=bergs%net_heat_to_ocean+melt*this%mass_scaling*bergs%dt ! J
+        melt=dM/bergs%dt ! kg/s
+        grd%berg_melt(i,j)=grd%berg_melt(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+        melt=dMbitsE/bergs%dt ! mass flux into bergy bits in kg/s
+        grd%bergy_src(i,j)=grd%bergy_src(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+        melt=dMbitsM/bergs%dt ! melt rate of bergy bits in kg/s
+        grd%bergy_melt(i,j)=grd%bergy_melt(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+        if(grd%id_melt_buoy>0) then
+          melt=dMb/bergs%dt ! melt rate due to buoyancy term in kg/s
+          grd%melt_buoy(i,j)=grd%melt_buoy(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+        endif
+        if(grd%id_melt_eros>0) then
+          melt=dMe/bergs%dt ! erosion rate in kg/s
+          grd%melt_eros(i,j)=grd%melt_eros(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+        endif
+        if(grd%id_melt_conv>0) then
+          melt=dMv/bergs%dt ! melt rate due to convection term in kg/s
+          grd%melt_conv(i,j)=grd%melt_conv(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+        endif
+      else
+        stderrunit = stderr()
+        write(stderrunit,*) 'diamonds, thermodynamics: berg appears to have grounded!!!! PE=',mpp_pe(),i,j
+        call print_berg(stderrunit,this,'thermodynamics, grounded')
+        if (associated(this%trajectory)) &
+          write(stderrunit,*) 'traj=',this%trajectory%lon,this%trajectory%lat
+        write(stderrunit,*) 'msk=',grd%msk(i,j),grd%area(i,j)
+        call error_mesg('diamonds, thermodynamics', 'berg appears to have grounded!', FATAL)
       endif
-      if(grd%id_melt_conv>0) then
-        melt=dMv/bergs%dt ! melt rate due to convection term in kg/s
-        grd%melt_conv(i,j)=grd%melt_conv(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+  
+      ! Rolling
+      Dn=(bergs%rho_bergs/rho_seawater)*Tn ! draught (keel depth)
+      if ( Dn>0. ) then
+         if ( max(Wn,Ln)<sqrt(0.92*(Dn**2)+58.32*Dn) ) then
+            T=Tn
+            Tn=Wn
+            Wn=T
+            Dn=(bergs%rho_bergs/rho_seawater)*Tn ! re-calculate draught (keel depth) for grounding
+        end if
       endif
-    else
-      stderrunit = stderr()
-      write(stderrunit,*) 'diamonds, thermodynamics: berg appears to have grounded!!!! PE=',mpp_pe(),i,j
-      call print_berg(stderrunit,this,'thermodynamics, grounded')
-      if (associated(this%trajectory)) &
-        write(stderrunit,*) 'traj=',this%trajectory%lon,this%trajectory%lat
-      write(stderrunit,*) 'msk=',grd%msk(i,j),grd%area(i,j)
-      call error_mesg('diamonds, thermodynamics', 'berg appears to have grounded!', FATAL)
-    endif
-
-    ! Rolling
-    Dn=(bergs%rho_bergs/rho_seawater)*Tn ! draught (keel depth)
-    if ( Dn>0. ) then
-       if ( max(Wn,Ln)<sqrt(0.92*(Dn**2)+58.32*Dn) ) then
-          T=Tn
-          Tn=Wn
-          Wn=T
-          Dn=(bergs%rho_bergs/rho_seawater)*Tn ! re-calculate draught (keel depth) for grounding
-      end if
-    endif
-
-    ! Store the new state of iceberg (with L>W)
-    this%mass=Mnew
-    this%mass_of_bits=nMbits
-    this%thickness=Tn
-    this%width=min(Wn,Ln)
-    this%length=max(Wn,Ln)
-
-    next=>this%next
-
-    ! Did berg completely melt?
-    if (Mnew<=0.) then ! Delete the berg
-      call move_trajectory(bergs, this)
-      call delete_iceberg_from_list(bergs%first, this)
-      bergs%nbergs_melted=bergs%nbergs_melted+1
-    else ! Diagnose mass distribution on grid
-      if (grd%id_virtual_area>0)&
-           & grd%virtual_area(i,j)=grd%virtual_area(i,j)+(Wn*Ln+Abits)*this%mass_scaling ! m^2
-      if (grd%id_mass>0 .or. bergs%add_weight_to_ocean)&
-           & grd%mass(i,j)=grd%mass(i,j)+Mnew/grd%area(i,j)*this%mass_scaling ! kg/m2
-      if (grd%id_bergy_mass>0 .or. bergs%add_weight_to_ocean)&
-           & grd%bergy_mass(i,j)=grd%bergy_mass(i,j)+nMbits/grd%area(i,j)*this%mass_scaling ! kg/m2
-      if (bergs%add_weight_to_ocean .and. .not. bergs%time_average_weight) then
-        if (bergs%grounding_fraction>0.) then
-          Hocean=bergs%grounding_fraction*(grd%ocean_depth(i,j)+grd%ssh(i,j))
-          if (Dn>Hocean) Mnew=Mnew*min(1.,Hocean/Dn)
+  
+      ! Store the new state of iceberg (with L>W)
+      this%mass=Mnew
+      this%mass_of_bits=nMbits
+      this%thickness=Tn
+      this%width=min(Wn,Ln)
+      this%length=max(Wn,Ln)
+  
+      next=>this%next
+  
+      ! Did berg completely melt?
+      if (Mnew<=0.) then ! Delete the berg
+        call move_trajectory(bergs, this)
+        call delete_iceberg_from_list(bergs%list(grdi,grdj)%first, this)
+        bergs%nbergs_melted=bergs%nbergs_melted+1
+      else ! Diagnose mass distribution on grid
+        if (grd%id_virtual_area>0)&
+             & grd%virtual_area(i,j)=grd%virtual_area(i,j)+(Wn*Ln+Abits)*this%mass_scaling ! m^2
+        if (grd%id_mass>0 .or. bergs%add_weight_to_ocean)&
+             & grd%mass(i,j)=grd%mass(i,j)+Mnew/grd%area(i,j)*this%mass_scaling ! kg/m2
+        if (grd%id_bergy_mass>0 .or. bergs%add_weight_to_ocean)&
+             & grd%bergy_mass(i,j)=grd%bergy_mass(i,j)+nMbits/grd%area(i,j)*this%mass_scaling ! kg/m2
+        if (bergs%add_weight_to_ocean .and. .not. bergs%time_average_weight) then
+          if (bergs%grounding_fraction>0.) then
+            Hocean=bergs%grounding_fraction*(grd%ocean_depth(i,j)+grd%ssh(i,j))
+            if (Dn>Hocean) Mnew=Mnew*min(1.,Hocean/Dn)
+          endif
+          call spread_mass_across_ocean_cells(grd, i, j, this%xi, this%yj, Mnew, nMbits, this%mass_scaling)
         endif
-        call spread_mass_across_ocean_cells(grd, i, j, this%xi, this%yj, Mnew, nMbits, this%mass_scaling)
       endif
-    endif
-  
-    this=>next
-  enddo
+    
+      this=>next
+    enddo
+  enddo ; enddo
 
 end subroutine thermodynamics
 
@@ -1263,7 +1269,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 
   ! For each berg, evolve
   call mpp_clock_begin(bergs%clock_mom)
-  if (associated(bergs%first)) call evolve_icebergs(bergs)
+  call evolve_icebergs(bergs)
   if (debug) call bergs_chksum(bergs, 'run bergs (evolved)',ignore_halo_violation=.true.)
   if (debug) call checksum_gridded(bergs%grd, 's/r run after evolve')
   call mpp_clock_end(bergs%clock_mom)
@@ -1277,14 +1283,14 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 
   ! Iceberg thermodynamics (melting) + rolling
   call mpp_clock_begin(bergs%clock_the)
-  if (associated(bergs%first)) call thermodynamics(bergs)
+  call thermodynamics(bergs)
   if (debug) call bergs_chksum(bergs, 'run bergs (thermo)')
   if (debug) call checksum_gridded(bergs%grd, 's/r run after thermodynamics')
   call mpp_clock_end(bergs%clock_the)
 
   ! For each berg, record
   call mpp_clock_begin(bergs%clock_dia)
-  if (sample_traj.and.associated(bergs%first)) call record_posn(bergs)
+  if (sample_traj) call record_posn(bergs)
   if (write_traj) then
     call move_all_trajectories(bergs)
     call write_trajectory(bergs%trajectories)
@@ -1376,10 +1382,10 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   if (lbudget) then
     bergs%stored_end=sum( grd%stored_ice(grd%isc:grd%iec,grd%jsc:grd%jec,:) )
     bergs%stored_heat_end=sum( grd%stored_heat(grd%isc:grd%iec,grd%jsc:grd%jec) )
-    bergs%floating_mass_end=sum_mass(bergs%first)
-    bergs%icebergs_mass_end=sum_mass(bergs%first,justbergs=.true.)
-    bergs%bergy_mass_end=sum_mass(bergs%first,justbits=.true.)
-    bergs%floating_heat_end=sum_heat(bergs%first)
+    bergs%floating_mass_end=sum_mass(bergs)
+    bergs%icebergs_mass_end=sum_mass(bergs,justbergs=.true.)
+    bergs%bergy_mass_end=sum_mass(bergs,justbits=.true.)
+    bergs%floating_heat_end=sum_heat(bergs)
     grd%tmpc(:,:)=0.;
     call mpp_clock_end(bergs%clock); call mpp_clock_end(bergs%clock_dia) ! To enable calling of public s/r
     call icebergs_incr_mass(bergs, grd%tmpc)
@@ -1775,7 +1781,7 @@ subroutine calve_icebergs(bergs)
           newberg%mass_scaling=bergs%mass_scaling(k)
           newberg%mass_of_bits=0.
           newberg%heat_density=grd%stored_heat(i,j)/grd%stored_ice(i,j,k) ! This is in J/kg
-          call add_new_berg_to_list(bergs%first, newberg)
+          call add_new_berg_to_list(bergs%list(i,j)%first, newberg)
           calved_to_berg=bergs%initial_mass(k)*bergs%mass_scaling(k) ! Units of kg
           ! Heat content
           heat_to_berg=calved_to_berg*newberg%heat_density ! Units of J
@@ -1830,6 +1836,7 @@ subroutine evolve_icebergs(bergs)
 type(iceberg), pointer :: berg
 integer :: stderrunit
 logical :: interactive_icebergs_on  ! Flag to decide whether to use forces between icebergs.
+integer :: grdi, grdj
 
   ! 4th order Runge-Kutta to solve:
   !    d/dt X = V,  d/dt V = A
@@ -1860,487 +1867,488 @@ subroutine evolve_icebergs(bergs)
   Rearth=6360.e3
 
   !Choosing time stepping scheme - Alon
-   !Runge_not_Verlet=.False.    !Loading manually: true=Runge Kutta, False=Verlet   , Alon
-   Runge_not_Verlet=bergs%Runge_not_Verlet  ! Loading directly from namelist/default , Alon
+ !Runge_not_Verlet=.False.    !Loading manually: true=Runge Kutta, False=Verlet   , Alon
+  Runge_not_Verlet=bergs%Runge_not_Verlet  ! Loading directly from namelist/default , Alon
 
-  berg=>bergs%first
-  do while (associated(berg)) ! loop over all bergs
-
-  if (.not. is_point_in_cell(bergs%grd, berg%lon, berg%lat, berg%ine, berg%jne) ) then
-    write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lon',(i,i=grd%isd,grd%ied)
-    do j=grd%jed,grd%jsd,-1
-      write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lon(i,j),i=grd%isd,grd%ied)
-    enddo
-    write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lat',(i,i=grd%isd,grd%ied)
-    do j=grd%jed,grd%jsd,-1
-      write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lat(i,j),i=grd%isd,grd%ied)
-    enddo
-    call print_berg(stderrunit, berg, 'evolve_iceberg, berg is not in proper starting cell')
-    write(stderrunit,'(a,i3,2(i4,3f8.2))') 'evolve_iceberg: pe,lon/lat(i,j)=', mpp_pe(), &
-             berg%ine,berg%lon,grd%lon(berg%ine-1,berg%jne-1),grd%lon(berg%ine,berg%jne), &
-             berg%jne,berg%lat,grd%lat(berg%ine-1,berg%jne-1),grd%lat(berg%ine,berg%jne)
-    if (debug) call error_mesg('diamonds, evolve_iceberg','berg is in wrong starting cell!',FATAL)
-  endif
-
-  if (debug) call check_position(grd, berg, 'evolve_iceberg (top)')
-
-  i=berg%ine
-  j=berg%jne
-  xi=berg%xi
-  yj=berg%yj
-  bounced=.false.
-  on_tangential_plane=.false.
-  if (berg%lat>89.) on_tangential_plane=.true.
-  i1=i;j1=j
-  if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-    call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling)
+  do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
+    berg=>bergs%list(grdi,grdj)%first
+    do while (associated(berg)) ! loop over all bergs
 
+      if (.not. is_point_in_cell(bergs%grd, berg%lon, berg%lat, berg%ine, berg%jne) ) then
+        write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lon',(i,i=grd%isd,grd%ied)
+        do j=grd%jed,grd%jsd,-1
+          write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lon(i,j),i=grd%isd,grd%ied)
+        enddo
+        write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lat',(i,i=grd%isd,grd%ied)
+        do j=grd%jed,grd%jsd,-1
+          write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lat(i,j),i=grd%isd,grd%ied)
+        enddo
+        call print_berg(stderrunit, berg, 'evolve_iceberg, berg is not in proper starting cell')
+        write(stderrunit,'(a,i3,2(i4,3f8.2))') 'evolve_iceberg: pe,lon/lat(i,j)=', mpp_pe(), &
+                 berg%ine,berg%lon,grd%lon(berg%ine-1,berg%jne-1),grd%lon(berg%ine,berg%jne), &
+                 berg%jne,berg%lat,grd%lat(berg%ine-1,berg%jne-1),grd%lat(berg%ine,berg%jne)
+        if (debug) call error_mesg('diamonds, evolve_iceberg','berg is in wrong starting cell!',FATAL)
+      endif
 
+      if (debug) call check_position(grd, berg, 'evolve_iceberg (top)')
 
-  if (Runge_not_Verlet) then !Start of the Runge-Kutta Loop -Added by Alon, MP2
+      i=berg%ine
+      j=berg%jne
+      xi=berg%xi
+      yj=berg%yj
+      bounced=.false.
+      on_tangential_plane=.false.
+      if (berg%lat>89.) on_tangential_plane=.true.
+      i1=i;j1=j
+      if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
+        call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling)
 
- !Loading past acceleartions - Alon
-  axn=berg%axn; ayn=berg%ayn !Alon
-  axn1=axn; axn2=axn; axn3=axn; axn4=axn
-  ayn1=ayn; ayn2=ayn; ayn3=ayn; ayn4=ayn
 
 
+      if (Runge_not_Verlet) then !Start of the Runge-Kutta Loop -Added by Alon, MP2
 
- ! A1 = A(X1)
-  lon1=berg%lon; lat1=berg%lat
-  if (on_tangential_plane) call rotpos_to_tang(lon1,lat1,x1,y1)
-  dxdl1=r180_pi/(Rearth*cos(lat1*pi_180))
-  dydl=r180_pi/Rearth
-  uvel1=berg%uvel; vvel1=berg%vvel
-  if (on_tangential_plane) call rotvec_to_tang(lon1,uvel1,vvel1,xdot1,ydot1)
-  u1=uvel1*dxdl1; v1=vvel1*dydl
-  call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn) !axn,ayn, bxn, byn  - Added by Alon
-  !call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn1, ayn1, bxn, byn) !Note change to dt. Markpoint_1
-  if (on_tangential_plane) call rotvec_to_tang(lon1,ax1,ay1,xddot1,yddot1)
-  if (on_tangential_plane) call rotvec_to_tang(lon1,axn1,ayn1,xddot1n,yddot1n) !Alon
+        ! Loading past accelerations - Alon
+        axn=berg%axn; ayn=berg%ayn !Alon
+        axn1=axn; axn2=axn; axn3=axn; axn4=axn
+        ayn1=ayn; ayn2=ayn; ayn3=ayn; ayn4=ayn
   
-  !  X2 = X1+dt/2*V1 ; V2 = V1+dt/2*A1; A2=A(X2)
- !if (debug) write(stderr(),*) 'diamonds, evolve: x2=...'
-  if (on_tangential_plane) then
-    x2=x1+dt_2*xdot1; y2=y1+dt_2*ydot1
-    xdot2=xdot1+dt_2*xddot1; ydot2=ydot1+dt_2*yddot1
-    call rotpos_from_tang(x2,y2,lon2,lat2)
-    call rotvec_from_tang(lon2,xdot2,ydot2,uvel2,vvel2)
-  else
-    lon2=lon1+dt_2*u1; lat2=lat1+dt_2*v1
-    uvel2=uvel1+dt_2*ax1; vvel2=vvel1+dt_2*ay1
-  endif
-  i=i1;j=j1;xi=berg%xi;yj=berg%yj
-  call adjust_index_and_ground(grd, lon2, lat2, uvel2, vvel2, i, j, xi, yj, bounced, error_flag)
-  i2=i; j2=j
-  if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-    call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling)
-  ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon2,lat2,x2,y2)
-  if (.not.error_flag) then
-    if (debug .and. .not. is_point_in_cell(bergs%grd, lon2, lat2, i, j)) error_flag=.true.
-  endif
-  if (error_flag) then
-   call print_fld(grd, grd%msk, 'msk')
-   call print_fld(grd, grd%ssh, 'ssh')
-   call print_fld(grd, grd%sst, 'sst')
-   call print_fld(grd, grd%hi, 'hi')
-   write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
-   write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
-   write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: i1,i2,i=',i1,i2,i
-   write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: j1,j2,j=',j1,j2,j
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lon1,lon2=',lon1,lon2,berg%lon
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lat1,lat2=',lat1,lat2,berg%lat
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u1,u2,u0=',uvel1,uvel2,berg%uvel
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v1,v2,v0=',vvel1,vvel2,berg%vvel
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1,ax2=',dt*ax1,dt*ax2
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ay1,ay2=',dt*ay1,dt*ay2
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u0=',dt*uvel1,dt*uvel2,dt*berg%uvel
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v0=',dt*vvel1,dt*vvel2,dt*berg%vvel
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2 (deg)=',dt*u1,dt*u2
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2 (deg)=',dt*v1,dt*v2
-   write(stderrunit,*) 'Acceleration terms for position 1'
-   error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn,- Added by Alon
-    call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 2')
-    write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos2 i,j,lon,lat,xi,yj=',i,j,lon2,lat2,xi,yj
-    write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos2 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
-    bounced=is_point_in_cell(bergs%grd, lon2, lat2, i, j, explain=.true.)
-    call error_mesg('diamonds, evolve_iceberg','berg is out of posn at 2!',FATAL)
-  endif
-  dxdl2=r180_pi/(Rearth*cos(lat2*pi_180))
-  u2=uvel2*dxdl2; v2=vvel2*dydl
-  call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
-  !call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt, ax2, ay2, axn2, ayn2, bxn, byn) !Note change to dt. Markpoint_1
-  if (on_tangential_plane) call rotvec_to_tang(lon2,ax2,ay2,xddot2,yddot2)
-  if (on_tangential_plane) call rotvec_to_tang(lon2,axn2,ayn2,xddot2n,yddot2n) !Alon
   
-  !  X3 = X1+dt/2*V2 ; V3 = V1+dt/2*A2; A3=A(X3)
- !if (debug) write(stderr(),*) 'diamonds, evolve: x3=...'
-  if (on_tangential_plane) then
-    x3=x1+dt_2*xdot2; y3=y1+dt_2*ydot2
-    xdot3=xdot1+dt_2*xddot2; ydot3=ydot1+dt_2*yddot2
-    call rotpos_from_tang(x3,y3,lon3,lat3)
-    call rotvec_from_tang(lon3,xdot3,ydot3,uvel3,vvel3)
-  else
-    lon3=lon1+dt_2*u2; lat3=lat1+dt_2*v2
-    uvel3=uvel1+dt_2*ax2; vvel3=vvel1+dt_2*ay2
-  endif
-  i=i1;j=j1;xi=berg%xi;yj=berg%yj
-  call adjust_index_and_ground(grd, lon3, lat3, uvel3, vvel3, i, j, xi, yj, bounced, error_flag)
-  i3=i; j3=j
-  if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-    call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling)
-  ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon3,lat3,x3,y3)
-  if (.not.error_flag) then
-    if (debug .and. .not. is_point_in_cell(bergs%grd, lon3, lat3, i, j)) error_flag=.true.
-  endif
-  if (error_flag) then
-   call print_fld(grd, grd%msk, 'msk')
-   call print_fld(grd, grd%ssh, 'ssh')
-   call print_fld(grd, grd%sst, 'sst')
-   call print_fld(grd, grd%hi, 'hi')
-   write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
-   write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
-   write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: i1,i2,i3,i=',i1,i2,i3,i
-   write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: j1,j2,j3,j=',j1,j2,j3,j
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lon1,lon2,lon3=',lon1,lon2,lon3,berg%lon
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lat1,lat2,lat3=',lat1,lat2,lat3,berg%lat
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u1,u2,u3,u0=',uvel1,uvel2,uvel3,berg%uvel
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v1,v2,v3,v0=',vvel1,vvel2,vvel3,berg%vvel
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1,ax2,ax3=',dt*ax1,dt*ax2,dt*ax3
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ay1,ay2,ay3=',dt*ay1,dt*ay2,dt*ay3
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3,u0=',dt*uvel1,dt*uvel2,dt*uvel3,dt*berg%uvel
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v0=',dt*vvel1,dt*vvel2,dt*vvel3,dt*berg%vvel
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3 (deg)=',dt*u1,dt*u2,dt*u3
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3 (deg)=',dt*v1,dt*v2,dt*v3
-   write(stderrunit,*) 'Acceleration terms for position 1'
-   error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, debug_flag=.true.) !axn, ayn - Added by Alon
-   write(stderrunit,*) 'Acceleration terms for position 2'
-   error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
-   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
-    call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 3')
-    write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos3 i,j,lon,lat,xi,yj=',i,j,lon3,lat3,xi,yj
-    write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos3 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
-    bounced=is_point_in_cell(bergs%grd, lon2, lat2, i, j, explain=.true.)
-    call error_mesg('diamonds, evolve_iceberg','berg is out of posn at 3!',FATAL)
-  endif
-  dxdl3=r180_pi/(Rearth*cos(lat3*pi_180))
-  u3=uvel3*dxdl3; v3=vvel3*dydl
-  call accel(bergs, berg, i, j, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn3, ayn3, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
-  if (on_tangential_plane) call rotvec_to_tang(lon3,ax3,ay3,xddot3,yddot3)
-  if (on_tangential_plane) call rotvec_to_tang(lon3,axn3,ayn3,xddot3n,yddot3n) !Alon
   
-  !  X4 = X1+dt*V3 ; V4 = V1+dt*A3; A4=A(X4)
- !if (debug) write(stderr(),*) 'diamonds, evolve: x4=...'
-  if (on_tangential_plane) then
-    x4=x1+dt*xdot3; y4=y1+dt*ydot3
-    xdot4=xdot1+dt*xddot3; ydot4=ydot1+dt*yddot3
-    call rotpos_from_tang(x4,y4,lon4,lat4)
-    call rotvec_from_tang(lon4,xdot4,ydot4,uvel4,vvel4)
-  else
-    lon4=lon1+dt*u3; lat4=lat1+dt*v3
-    uvel4=uvel1+dt*ax3; vvel4=vvel1+dt*ay3
-  endif
-  i=i1;j=j1;xi=berg%xi;yj=berg%yj
-  call adjust_index_and_ground(grd, lon4, lat4, uvel4, vvel4, i, j, xi, yj, bounced, error_flag)
-  i4=i; j4=j
-  ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon4,lat4,x4,y4)
-  if (.not.error_flag) then
-    if (debug .and. .not. is_point_in_cell(bergs%grd, lon4, lat4, i, j)) error_flag=.true.
-  endif
-  if (error_flag) then
-   call print_fld(grd, grd%msk, 'msk')
-   call print_fld(grd, grd%ssh, 'ssh')
-   call print_fld(grd, grd%sst, 'sst')
-   call print_fld(grd, grd%hi, 'hi')
-   write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
-   write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
-   write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: i1,i2,i3,i4,i=',i1,i2,i3,i4,i
-   write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: j1,j2,j3,j4,j=',j1,j2,j3,j4,j
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lon1,lon2,lon3,lon4=',lon1,lon2,lon3,lon4,berg%lon
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lat1,lat2,lat3,lat4=',lat1,lat2,lat3,lat4,berg%lat
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u1,u2,u3,u4,u0=',uvel1,uvel2,uvel3,uvel4,berg%uvel
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v1,v2,v3,v4,v0=',vvel1,vvel2,vvel3,vvel4,berg%vvel
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1,ax2,ax3,ax4=',dt*ax1,dt*ax2,dt*ax3,dt*ax4
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ay1,ay2,ay3,ay4=',dt*ay1,dt*ay2,dt*ay3,dt*ay4
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3,u4,u0=',dt*uvel1,dt*uvel2,dt*uvel3,dt*uvel4,dt*berg%uvel
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v4,v0=',dt*vvel1,dt*vvel2,dt*vvel3,dt*vvel4,dt*berg%vvel
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3,u4 (deg)=',dt*u1,dt*u2,dt*u3,dt*u4
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v4 (deg)=',dt*v1,dt*v2,dt*v3,dt*v4
-   write(stderrunit,*) 'Acceleration terms for position 1'
-   error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
-   write(stderrunit,*) 'Acceleration terms for position 2'
-   error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
-   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
-   write(stderrunit,*) 'Acceleration terms for position 3'
-   error_flag=pos_within_cell(grd, lon3, lat3, i3, j3, xi, yj)
-   call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn3, ayn3, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
-    call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 4')
-    write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos4 i,j,lon,lat,xi,yj=',i,j,lon4,lat4,xi,yj
-    write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos4 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
-    bounced=is_point_in_cell(bergs%grd, lon2, lat2, i, j, explain=.true.)
-    call error_mesg('diamonds, evolve_iceberg','berg is out of posn at 4!',FATAL)
-  endif
-  dxdl4=r180_pi/(Rearth*cos(lat4*pi_180))
-  u4=uvel4*dxdl4; v4=vvel4*dydl
-  call accel(bergs, berg, i, j, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axn4, ayn4, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
-  if (on_tangential_plane) call rotvec_to_tang(lon4,ax4,ay4,xddot4,yddot4)
-  if (on_tangential_plane) call rotvec_to_tang(lon4,axn4,ayn4,xddot4n,yddot4n)
+        ! A1 = A(X1)
+        lon1=berg%lon; lat1=berg%lat
+        if (on_tangential_plane) call rotpos_to_tang(lon1,lat1,x1,y1)
+        dxdl1=r180_pi/(Rearth*cos(lat1*pi_180))
+        dydl=r180_pi/Rearth
+        uvel1=berg%uvel; vvel1=berg%vvel
+        if (on_tangential_plane) call rotvec_to_tang(lon1,uvel1,vvel1,xdot1,ydot1)
+        u1=uvel1*dxdl1; v1=vvel1*dydl
+        call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn) !axn,ayn, bxn, byn  - Added by Alon
+        !call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn1, ayn1, bxn, byn) !Note change to dt. Markpoint_1
+        if (on_tangential_plane) call rotvec_to_tang(lon1,ax1,ay1,xddot1,yddot1)
+        if (on_tangential_plane) call rotvec_to_tang(lon1,axn1,ayn1,xddot1n,yddot1n) !Alon
+        
+        !  X2 = X1+dt/2*V1 ; V2 = V1+dt/2*A1; A2=A(X2)
+       !if (debug) write(stderr(),*) 'diamonds, evolve: x2=...'
+        if (on_tangential_plane) then
+          x2=x1+dt_2*xdot1; y2=y1+dt_2*ydot1
+          xdot2=xdot1+dt_2*xddot1; ydot2=ydot1+dt_2*yddot1
+          call rotpos_from_tang(x2,y2,lon2,lat2)
+          call rotvec_from_tang(lon2,xdot2,ydot2,uvel2,vvel2)
+        else
+          lon2=lon1+dt_2*u1; lat2=lat1+dt_2*v1
+          uvel2=uvel1+dt_2*ax1; vvel2=vvel1+dt_2*ay1
+        endif
+        i=i1;j=j1;xi=berg%xi;yj=berg%yj
+        call adjust_index_and_ground(grd, lon2, lat2, uvel2, vvel2, i, j, xi, yj, bounced, error_flag)
+        i2=i; j2=j
+        if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
+          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling)
+        ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon2,lat2,x2,y2)
+        if (.not.error_flag) then
+          if (debug .and. .not. is_point_in_cell(bergs%grd, lon2, lat2, i, j)) error_flag=.true.
+        endif
+        if (error_flag) then
+         call print_fld(grd, grd%msk, 'msk')
+         call print_fld(grd, grd%ssh, 'ssh')
+         call print_fld(grd, grd%sst, 'sst')
+         call print_fld(grd, grd%hi, 'hi')
+         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
+         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
+         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: i1,i2,i=',i1,i2,i
+         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: j1,j2,j=',j1,j2,j
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lon1,lon2=',lon1,lon2,berg%lon
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lat1,lat2=',lat1,lat2,berg%lat
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u1,u2,u0=',uvel1,uvel2,berg%uvel
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v1,v2,v0=',vvel1,vvel2,berg%vvel
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1,ax2=',dt*ax1,dt*ax2
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ay1,ay2=',dt*ay1,dt*ay2
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u0=',dt*uvel1,dt*uvel2,dt*berg%uvel
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v0=',dt*vvel1,dt*vvel2,dt*berg%vvel
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2 (deg)=',dt*u1,dt*u2
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2 (deg)=',dt*v1,dt*v2
+         write(stderrunit,*) 'Acceleration terms for position 1'
+         error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
+         call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn,- Added by Alon
+          call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 2')
+          write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos2 i,j,lon,lat,xi,yj=',i,j,lon2,lat2,xi,yj
+          write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos2 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
+          bounced=is_point_in_cell(bergs%grd, lon2, lat2, i, j, explain=.true.)
+          call error_mesg('diamonds, evolve_iceberg','berg is out of posn at 2!',FATAL)
+        endif
+        dxdl2=r180_pi/(Rearth*cos(lat2*pi_180))
+        u2=uvel2*dxdl2; v2=vvel2*dydl
+        call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
+        !call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt, ax2, ay2, axn2, ayn2, bxn, byn) !Note change to dt. Markpoint_1
+        if (on_tangential_plane) call rotvec_to_tang(lon2,ax2,ay2,xddot2,yddot2)
+        if (on_tangential_plane) call rotvec_to_tang(lon2,axn2,ayn2,xddot2n,yddot2n) !Alon
+        
+        !  X3 = X1+dt/2*V2 ; V3 = V1+dt/2*A2; A3=A(X3)
+       !if (debug) write(stderr(),*) 'diamonds, evolve: x3=...'
+        if (on_tangential_plane) then
+          x3=x1+dt_2*xdot2; y3=y1+dt_2*ydot2
+          xdot3=xdot1+dt_2*xddot2; ydot3=ydot1+dt_2*yddot2
+          call rotpos_from_tang(x3,y3,lon3,lat3)
+          call rotvec_from_tang(lon3,xdot3,ydot3,uvel3,vvel3)
+        else
+          lon3=lon1+dt_2*u2; lat3=lat1+dt_2*v2
+          uvel3=uvel1+dt_2*ax2; vvel3=vvel1+dt_2*ay2
+        endif
+        i=i1;j=j1;xi=berg%xi;yj=berg%yj
+        call adjust_index_and_ground(grd, lon3, lat3, uvel3, vvel3, i, j, xi, yj, bounced, error_flag)
+        i3=i; j3=j
+        if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
+          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling)
+        ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon3,lat3,x3,y3)
+        if (.not.error_flag) then
+          if (debug .and. .not. is_point_in_cell(bergs%grd, lon3, lat3, i, j)) error_flag=.true.
+        endif
+        if (error_flag) then
+         call print_fld(grd, grd%msk, 'msk')
+         call print_fld(grd, grd%ssh, 'ssh')
+         call print_fld(grd, grd%sst, 'sst')
+         call print_fld(grd, grd%hi, 'hi')
+         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
+         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
+         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: i1,i2,i3,i=',i1,i2,i3,i
+         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: j1,j2,j3,j=',j1,j2,j3,j
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lon1,lon2,lon3=',lon1,lon2,lon3,berg%lon
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lat1,lat2,lat3=',lat1,lat2,lat3,berg%lat
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u1,u2,u3,u0=',uvel1,uvel2,uvel3,berg%uvel
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v1,v2,v3,v0=',vvel1,vvel2,vvel3,berg%vvel
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1,ax2,ax3=',dt*ax1,dt*ax2,dt*ax3
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ay1,ay2,ay3=',dt*ay1,dt*ay2,dt*ay3
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3,u0=',dt*uvel1,dt*uvel2,dt*uvel3,dt*berg%uvel
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v0=',dt*vvel1,dt*vvel2,dt*vvel3,dt*berg%vvel
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3 (deg)=',dt*u1,dt*u2,dt*u3
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3 (deg)=',dt*v1,dt*v2,dt*v3
+         write(stderrunit,*) 'Acceleration terms for position 1'
+         error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
+         call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, debug_flag=.true.) !axn, ayn - Added by Alon
+         write(stderrunit,*) 'Acceleration terms for position 2'
+         error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
+         call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
+          call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 3')
+          write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos3 i,j,lon,lat,xi,yj=',i,j,lon3,lat3,xi,yj
+          write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos3 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
+          bounced=is_point_in_cell(bergs%grd, lon2, lat2, i, j, explain=.true.)
+          call error_mesg('diamonds, evolve_iceberg','berg is out of posn at 3!',FATAL)
+        endif
+        dxdl3=r180_pi/(Rearth*cos(lat3*pi_180))
+        u3=uvel3*dxdl3; v3=vvel3*dydl
+        call accel(bergs, berg, i, j, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn3, ayn3, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
+        if (on_tangential_plane) call rotvec_to_tang(lon3,ax3,ay3,xddot3,yddot3)
+        if (on_tangential_plane) call rotvec_to_tang(lon3,axn3,ayn3,xddot3n,yddot3n) !Alon
+        
+        !  X4 = X1+dt*V3 ; V4 = V1+dt*A3; A4=A(X4)
+       !if (debug) write(stderr(),*) 'diamonds, evolve: x4=...'
+        if (on_tangential_plane) then
+          x4=x1+dt*xdot3; y4=y1+dt*ydot3
+          xdot4=xdot1+dt*xddot3; ydot4=ydot1+dt*yddot3
+          call rotpos_from_tang(x4,y4,lon4,lat4)
+          call rotvec_from_tang(lon4,xdot4,ydot4,uvel4,vvel4)
+        else
+          lon4=lon1+dt*u3; lat4=lat1+dt*v3
+          uvel4=uvel1+dt*ax3; vvel4=vvel1+dt*ay3
+        endif
+        i=i1;j=j1;xi=berg%xi;yj=berg%yj
+        call adjust_index_and_ground(grd, lon4, lat4, uvel4, vvel4, i, j, xi, yj, bounced, error_flag)
+        i4=i; j4=j
+        ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon4,lat4,x4,y4)
+        if (.not.error_flag) then
+          if (debug .and. .not. is_point_in_cell(bergs%grd, lon4, lat4, i, j)) error_flag=.true.
+        endif
+        if (error_flag) then
+         call print_fld(grd, grd%msk, 'msk')
+         call print_fld(grd, grd%ssh, 'ssh')
+         call print_fld(grd, grd%sst, 'sst')
+         call print_fld(grd, grd%hi, 'hi')
+         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
+         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
+         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: i1,i2,i3,i4,i=',i1,i2,i3,i4,i
+         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: j1,j2,j3,j4,j=',j1,j2,j3,j4,j
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lon1,lon2,lon3,lon4=',lon1,lon2,lon3,lon4,berg%lon
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lat1,lat2,lat3,lat4=',lat1,lat2,lat3,lat4,berg%lat
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u1,u2,u3,u4,u0=',uvel1,uvel2,uvel3,uvel4,berg%uvel
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v1,v2,v3,v4,v0=',vvel1,vvel2,vvel3,vvel4,berg%vvel
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1,ax2,ax3,ax4=',dt*ax1,dt*ax2,dt*ax3,dt*ax4
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ay1,ay2,ay3,ay4=',dt*ay1,dt*ay2,dt*ay3,dt*ay4
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3,u4,u0=',dt*uvel1,dt*uvel2,dt*uvel3,dt*uvel4,dt*berg%uvel
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v4,v0=',dt*vvel1,dt*vvel2,dt*vvel3,dt*vvel4,dt*berg%vvel
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3,u4 (deg)=',dt*u1,dt*u2,dt*u3,dt*u4
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v4 (deg)=',dt*v1,dt*v2,dt*v3,dt*v4
+         write(stderrunit,*) 'Acceleration terms for position 1'
+         error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
+         call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
+         write(stderrunit,*) 'Acceleration terms for position 2'
+         error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
+         call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
+         write(stderrunit,*) 'Acceleration terms for position 3'
+         error_flag=pos_within_cell(grd, lon3, lat3, i3, j3, xi, yj)
+         call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn3, ayn3, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
+          call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 4')
+          write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos4 i,j,lon,lat,xi,yj=',i,j,lon4,lat4,xi,yj
+          write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos4 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
+          bounced=is_point_in_cell(bergs%grd, lon2, lat2, i, j, explain=.true.)
+          call error_mesg('diamonds, evolve_iceberg','berg is out of posn at 4!',FATAL)
+        endif
+        dxdl4=r180_pi/(Rearth*cos(lat4*pi_180))
+        u4=uvel4*dxdl4; v4=vvel4*dydl
+        call accel(bergs, berg, i, j, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axn4, ayn4, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
+        if (on_tangential_plane) call rotvec_to_tang(lon4,ax4,ay4,xddot4,yddot4)
+        if (on_tangential_plane) call rotvec_to_tang(lon4,axn4,ayn4,xddot4n,yddot4n)
+        
+        !  Xn = X1+dt*(V1+2*V2+2*V3+V4)/6
+        !  Vn = V1+dt*(A1+2*A2+2*A3+A4)/6
+        if (on_tangential_plane) then
+          xn=x1+dt_6*( (xdot1+xdot4)+2.*(xdot2+xdot3) )
+          yn=y1+dt_6*( (ydot1+ydot4)+2.*(ydot2+ydot3) )
+          xdotn=xdot1+dt_6*( (xddot1+xddot4)+2.*(xddot2+xddot3) )
+          ydotn=ydot1+dt_6*( (yddot1+yddot4)+2.*(yddot2+yddot3) )
+          xddotn=( (xddot1n+xddot4n)+2.*(xddot2n+xddot3n) )/6.  !Alon  
+          yddotn=( (yddot1n+yddot4n)+2.*(yddot2n+yddot3n) )/6.  !Alon  
+          call rotpos_from_tang(xn,yn,lonn,latn)
+          call rotvec_from_tang(lonn,xdotn,ydotn,uveln,vveln)
+          call rotvec_from_tang(lonn,xddotn,yddotn,axn,ayn) !Alon
+        else
+          lonn=berg%lon+dt_6*( (u1+u4)+2.*(u2+u3) )
+          latn=berg%lat+dt_6*( (v1+v4)+2.*(v2+v3) )
+          uveln=berg%uvel+dt_6*( (ax1+ax4)+2.*(ax2+ax3) )
+          vveln=berg%vvel+dt_6*( (ay1+ay4)+2.*(ay2+ay3) )
+          axn=( (axn1+axn4)+2.*(axn2+axn3) )/6. !Alon
+          ayn=( (ayn1+ayn4)+2.*(ayn2+ayn3) )/6. !Alon
+          bxn=(((ax1+ax4)+2.*(ax2+ax3) )/6)  - (axn/2)
+          byn=(((ay1+ay4)+2.*(ay2+ay3) )/6)  - (ayn/2)
   
-  !  Xn = X1+dt*(V1+2*V2+2*V3+V4)/6
-  !  Vn = V1+dt*(A1+2*A2+2*A3+A4)/6
-  if (on_tangential_plane) then
-    xn=x1+dt_6*( (xdot1+xdot4)+2.*(xdot2+xdot3) )
-    yn=y1+dt_6*( (ydot1+ydot4)+2.*(ydot2+ydot3) )
-    xdotn=xdot1+dt_6*( (xddot1+xddot4)+2.*(xddot2+xddot3) )
-    ydotn=ydot1+dt_6*( (yddot1+yddot4)+2.*(yddot2+yddot3) )
-    xddotn=( (xddot1n+xddot4n)+2.*(xddot2n+xddot3n) )/6.  !Alon  
-    yddotn=( (yddot1n+yddot4n)+2.*(yddot2n+yddot3n) )/6.  !Alon  
-    call rotpos_from_tang(xn,yn,lonn,latn)
-    call rotvec_from_tang(lonn,xdotn,ydotn,uveln,vveln)
-    call rotvec_from_tang(lonn,xddotn,yddotn,axn,ayn) !Alon
-  else
-    lonn=berg%lon+dt_6*( (u1+u4)+2.*(u2+u3) )
-    latn=berg%lat+dt_6*( (v1+v4)+2.*(v2+v3) )
-    uveln=berg%uvel+dt_6*( (ax1+ax4)+2.*(ax2+ax3) )
-    vveln=berg%vvel+dt_6*( (ay1+ay4)+2.*(ay2+ay3) )
-    axn=( (axn1+axn4)+2.*(axn2+axn3) )/6. !Alon
-    ayn=( (ayn1+ayn4)+2.*(ayn2+ayn3) )/6. !Alon
-    bxn=(((ax1+ax4)+2.*(ax2+ax3) )/6)  - (axn/2)
-    byn=(((ay1+ay4)+2.*(ay2+ay3) )/6)  - (ayn/2)
-
-  endif
-
-
-
-  i=i1;j=j1;xi=berg%xi;yj=berg%yj
-  call adjust_index_and_ground(grd, lonn, latn, uveln, vveln, i, j, xi, yj, bounced, error_flag)
-  if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-    call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling)
-
-  if (.not.error_flag) then
-    if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j)) error_flag=.true.
-  endif
-  if (error_flag) then
-   call print_fld(grd, grd%msk, 'msk')
-   call print_fld(grd, grd%ssh, 'ssh')
-   call print_fld(grd, grd%sst, 'sst')
-   call print_fld(grd, grd%hi, 'hi')
-   write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
-   write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
-   write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: i1,i2,i3,i4,i=',i1,i2,i3,i4,i
-   write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: j1,j2,j3,j4,j=',j1,j2,j3,j4,j
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lon1,lon2,lon3,lon4,lonn=',lon1,lon2,lon3,lon4,lonn,berg%lon
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lat1,lat2,lat3,lat4,latn=',lat1,lat2,lat3,lat4,latn,berg%lat
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u1,u2,u3,u4,un,u0=',uvel1,uvel2,uvel3,uvel4,uveln,berg%uvel
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v1,v2,v3,v4,vn,v0=',vvel1,vvel2,vvel3,vvel4,vveln,berg%vvel
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1,ax2,ax3,ax4,axn=',&
-        & dt*ax1,dt*ax2,dt*ax3,dt*ax4,dt_6*( (ax1+ax4)+2.*(ax2+ax3) )
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ay1,ay2,ay3,ay4,ayn=',&
-        & dt*ay1,dt*ay2,dt*ay3,dt*ay4,dt_6*( (ay1+ay4)+2.*(ay2+ay3) )
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3,u4,un,u0=',&
-        & dt*uvel1,dt*uvel2,dt*uvel3,dt*uvel4,dt*uveln,dt*berg%uvel
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v4,vn,v0=',&
-        & dt*vvel1,dt*vvel2,dt*vvel3,dt*vvel4,dt*vveln,dt*berg%vvel
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3,u4,u_rk (deg)=',&
-        & dt*u1,dt*u2,dt*u3,dt*u4,dt_6*( (u1+u4)+2.*(u2+u3) )
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v4,v_rk (deg)=',&
-        & dt*v1,dt*v2,dt*v3,dt*v4,dt_6*( (v1+v4)+2.*(v2+v3) )
-   write(stderrunit,*) 'diamonds, evolve_iceberg: on_tangential_plane=',on_tangential_plane
-   write(stderrunit,*) 'Acceleration terms for position 1'
-   error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
-   write(stderrunit,*) 'Acceleration terms for position 2'
-   error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
-   call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
-   write(stderrunit,*) 'Acceleration terms for position 3'
-   error_flag=pos_within_cell(grd, lon3, lat3, i3, j3, xi, yj)
-   call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
-   write(stderrunit,*) 'Acceleration terms for position 4'
-   error_flag=pos_within_cell(grd, lon4, lat4, i4, j4, xi, yj)
-   call accel(bergs, berg, i4, j4, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
-    write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'posn i,j,lon,lat,xi,yj=',i,j,lonn,latn,xi,yj
-    write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'posn box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
-    call print_berg(stderrunit, berg, 'evolve_iceberg, out of cell at end!')
-    bounced=is_point_in_cell(bergs%grd, lonn, latn, i, j, explain=.true.)
-    if (debug) call error_mesg('diamonds, evolve_iceberg','berg is out of posn at end!',FATAL)
-    write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lon',(i,i=grd%isd,grd%ied)
-    do j=grd%jed,grd%jsd,-1
-      write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lon(i,j),i=grd%isd,grd%ied)
-    enddo
-    write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lat',(i,i=grd%isd,grd%ied)
-    do j=grd%jed,grd%jsd,-1
-      write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lat(i,j),i=grd%isd,grd%ied)
-    enddo
-  endif
- 
-  endif ! End of the Runge-Kutta Loop -added by Alon  
+        endif
+  
+  
+  
+        i=i1;j=j1;xi=berg%xi;yj=berg%yj
+        call adjust_index_and_ground(grd, lonn, latn, uveln, vveln, i, j, xi, yj, bounced, error_flag)
+        if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
+          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling)
+  
+        if (.not.error_flag) then
+          if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j)) error_flag=.true.
+        endif
+        if (error_flag) then
+         call print_fld(grd, grd%msk, 'msk')
+         call print_fld(grd, grd%ssh, 'ssh')
+         call print_fld(grd, grd%sst, 'sst')
+         call print_fld(grd, grd%hi, 'hi')
+         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
+         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
+         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: i1,i2,i3,i4,i=',i1,i2,i3,i4,i
+         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: j1,j2,j3,j4,j=',j1,j2,j3,j4,j
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lon1,lon2,lon3,lon4,lonn=',lon1,lon2,lon3,lon4,lonn,berg%lon
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lat1,lat2,lat3,lat4,latn=',lat1,lat2,lat3,lat4,latn,berg%lat
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u1,u2,u3,u4,un,u0=',uvel1,uvel2,uvel3,uvel4,uveln,berg%uvel
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v1,v2,v3,v4,vn,v0=',vvel1,vvel2,vvel3,vvel4,vveln,berg%vvel
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1,ax2,ax3,ax4,axn=',&
+              & dt*ax1,dt*ax2,dt*ax3,dt*ax4,dt_6*( (ax1+ax4)+2.*(ax2+ax3) )
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ay1,ay2,ay3,ay4,ayn=',&
+              & dt*ay1,dt*ay2,dt*ay3,dt*ay4,dt_6*( (ay1+ay4)+2.*(ay2+ay3) )
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3,u4,un,u0=',&
+              & dt*uvel1,dt*uvel2,dt*uvel3,dt*uvel4,dt*uveln,dt*berg%uvel
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v4,vn,v0=',&
+              & dt*vvel1,dt*vvel2,dt*vvel3,dt*vvel4,dt*vveln,dt*berg%vvel
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3,u4,u_rk (deg)=',&
+              & dt*u1,dt*u2,dt*u3,dt*u4,dt_6*( (u1+u4)+2.*(u2+u3) )
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v4,v_rk (deg)=',&
+              & dt*v1,dt*v2,dt*v3,dt*v4,dt_6*( (v1+v4)+2.*(v2+v3) )
+         write(stderrunit,*) 'diamonds, evolve_iceberg: on_tangential_plane=',on_tangential_plane
+         write(stderrunit,*) 'Acceleration terms for position 1'
+         error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
+         call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
+         write(stderrunit,*) 'Acceleration terms for position 2'
+         error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
+         call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
+         write(stderrunit,*) 'Acceleration terms for position 3'
+         error_flag=pos_within_cell(grd, lon3, lat3, i3, j3, xi, yj)
+         call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
+         write(stderrunit,*) 'Acceleration terms for position 4'
+         error_flag=pos_within_cell(grd, lon4, lat4, i4, j4, xi, yj)
+         call accel(bergs, berg, i4, j4, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
+          write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'posn i,j,lon,lat,xi,yj=',i,j,lonn,latn,xi,yj
+          write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'posn box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
+          call print_berg(stderrunit, berg, 'evolve_iceberg, out of cell at end!')
+          bounced=is_point_in_cell(bergs%grd, lonn, latn, i, j, explain=.true.)
+          if (debug) call error_mesg('diamonds, evolve_iceberg','berg is out of posn at end!',FATAL)
+          write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lon',(i,i=grd%isd,grd%ied)
+          do j=grd%jed,grd%jsd,-1
+            write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lon(i,j),i=grd%isd,grd%ied)
+          enddo
+          write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lat',(i,i=grd%isd,grd%ied)
+          do j=grd%jed,grd%jsd,-1
+            write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lat(i,j),i=grd%isd,grd%ied)
+          enddo
+        endif
+     
+      endif ! End of the Runge-Kutta Loop -added by Alon  
 
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
-  if (.not.Runge_not_Verlet) then !Start of the Verlet time_stepping -Whole loop added by Alon
-
- ! In this scheme a_n and b_n are saved from the previous timestep, giving the explicit and implicit parts of the acceleration, and a_np1, b_np1 are for the next time step
- ! Note that ax1=a_np1/2 +b_np1, as calculated by the acceleration subrouting
- ! Positions and velocity is updated by
- ! X2 = X1+dt*V1+((dt^2)/2)*a_n +((dt^2)/2)*b_n = X1+dt*u_star +((dt^2)/2)*b_n 
- ! V2 = V1+dt/2*a_n +dt/2*a_np1 +dt*b_n = u_star + dt/2*a_np1 + dt*b_np1 = u_star +dt*ax
-
-!print *, 'you are here!'
-
-lon1=berg%lon; lat1=berg%lat
-  if (on_tangential_plane) call rotpos_to_tang(lon1,lat1,x1,y1)
-  dxdl1=r180_pi/(Rearth*cos(lat1*pi_180))
-  dydl=r180_pi/Rearth
-  uvel1=berg%uvel; vvel1=berg%vvel
-
-!Loading past acceleartions - Alon
-  axn=berg%axn; ayn=berg%ayn !Alon
-  bxn=berg%bxn; byn=berg%byn !Alon
-
-
-
-! Velocities used to update the position
-  uvel2=uvel1+(dt_2*axn)+(dt_2*bxn)                    !Alon
-  vvel2=vvel1+(dt_2*ayn)+(dt_2*byn)                    !Alon
-
-if (on_tangential_plane) call rotvec_to_tang(lon1,uvel2,vvel2,xdot2,ydot2)
-  u2=uvel2*dxdl1; v2=vvel2*dydl
-
-
-!Solving for new position
-  if (on_tangential_plane) then
-    xn=x1+(dt*xdot2) ; yn=y1+(dt*ydot2)             !Alon
-    call rotpos_from_tang(xn,yn,lonn,latn)
-  else
-    lonn=lon1+(dt*u2) ; latn=lat1+(dt*v2)  !Alon
-  endif
-  dxdln=r180_pi/(Rearth*cos(latn*pi_180))
-
-! Turn the velocities into u_star, v_star.(uvel3 is v_star) - Alon (not sure how this works with tangent plane)
-  uvel3=uvel1+(dt_2*axn)                  !Alon
-  vvel3=vvel1+(dt_2*ayn)                  !Alon
-
-
-!Adjusting mass...                      Alon decided to move this before calculating the new velocities (so that acceleration can be a fn(r_np1)
-  i=i1;j=j1;xi=berg%xi;yj=berg%yj
-  call adjust_index_and_ground(grd, lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
-!  call adjust_index_and_ground(grd, lonn, latn, uvel1, vvel1, i, j, xi, yj, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
-  i2=i; j2=j
-  if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-    call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling)
-
-
-!Calling the acceleration   (note that the velocity is converted to u_star inside the accel script)
-  call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn, ayn, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
-
-!Solving for the new velocity
-  if (on_tangential_plane) then
-    call rotvec_to_tang(lonn,uvel3,vvel3,xdot3,ydot3)
-    call rotvec_to_tang(lon1,ax1,ay1,xddot1,yddot1)
-    xdotn=xdot3+(dt*xddot1); ydotn=ydot3+(dt*yddot1)                                    !Alon
-    call rotvec_from_tang(lonn,xdotn,ydotn,uveln,vveln)
-  else
-    uvel4=uvel3+(dt*ax1); vvel4=vvel3+(dt*ay1)    !Alon , we call it uvel3, vvel3 until it is put into lat/long co-ordinates, where it becomes uveln, vveln
-  endif
-!  uveln=uvel4*dxdln; vveln=vvel4*dydl    !Converted to degrees.  (Perhaps this should not be here)
-  uveln=uvel4
-  vveln=vvel4 
-
-!Debugging
-  if (.not.error_flag) then
-    if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j)) error_flag=.true.
-  endif
-  if (error_flag) then
-   call print_fld(grd, grd%msk, 'msk')
-   call print_fld(grd, grd%ssh, 'ssh')
-   call print_fld(grd, grd%sst, 'sst')
-   call print_fld(grd, grd%hi, 'hi')
-   write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
-   write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
-   write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: i1,i2,i=',i1,i2,i
-   write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: j1,j2,j=',j1,j2,j
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lon1,lonn=',lon1,lonn,berg%lon
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lat1,latn=',lat1,latn,berg%lat
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u3,un,u0=',uvel3,uveln,berg%uvel
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v3,vn,v0=',vvel3,vveln,berg%vvel
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1=',&
-        & dt*ax1
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ay1=',&
-        & dt*ay1
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u3,un,u0=',&
-        & dt*uvel3,dt*uveln,dt*berg%uvel
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v3,vn,v0=',&
-        & dt*vvel3,dt*vveln,dt*berg%vvel
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u_n (deg)=',&
-        & dt*u1,dt*uveln
-   write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v_n (deg)=',&
-        & dt*v1,dt*vveln
-   write(stderrunit,*) 'diamonds, evolve_iceberg: on_tangential_plane=',on_tangential_plane
-   write(stderrunit,*) 'Acceleration terms for position 1'
-   error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-   call accel(bergs, berg, i2, j2, xi, yj, latn, uvel3, vvel3, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn, bxn, byn - Added by Alon
-   
-    write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'posn i,j,lon,lat,xi,yj=',i,j,lonn,latn,xi,yj
-    write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'posn box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
-    call print_berg(stderrunit, berg, 'evolve_iceberg, out of cell at end!')
-    bounced=is_point_in_cell(bergs%grd, lonn, latn, i, j, explain=.true.)
-    if (debug) call error_mesg('diamonds, evolve_iceberg','berg is out of posn at end!',FATAL)
-    write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lon',(i,i=grd%isd,grd%ied)
-    do j=grd%jed,grd%jsd,-1
-      write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lon(i,j),i=grd%isd,grd%ied)
-    enddo
-    write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lat',(i,i=grd%isd,grd%ied)
-    do j=grd%jed,grd%jsd,-1
-      write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lat(i,j),i=grd%isd,grd%ied)
-    enddo
-  endif
-
+      if (.not.Runge_not_Verlet) then !Start of the Verlet time_stepping -Whole loop added by Alon
 
+       ! In this scheme a_n and b_n are saved from the previous timestep, giving the explicit and implicit parts of the acceleration, and a_np1, b_np1 are for the next time step
+       ! Note that ax1=a_np1/2 +b_np1, as calculated by the acceleration subrouting
+       ! Positions and velocity is updated by
+       ! X2 = X1+dt*V1+((dt^2)/2)*a_n +((dt^2)/2)*b_n = X1+dt*u_star +((dt^2)/2)*b_n 
+       ! V2 = V1+dt/2*a_n +dt/2*a_np1 +dt*b_n = u_star + dt/2*a_np1 + dt*b_np1 = u_star +dt*ax
+  
+       !print *, 'you are here!'
+  
+        lon1=berg%lon; lat1=berg%lat
+        if (on_tangential_plane) call rotpos_to_tang(lon1,lat1,x1,y1)
+        dxdl1=r180_pi/(Rearth*cos(lat1*pi_180))
+        dydl=r180_pi/Rearth
+        uvel1=berg%uvel; vvel1=berg%vvel
+  
+        ! Loading past acceleartions - Alon
+        axn=berg%axn; ayn=berg%ayn !Alon
+        bxn=berg%bxn; byn=berg%byn !Alon
+  
+  
+  
+        ! Velocities used to update the position
+        uvel2=uvel1+(dt_2*axn)+(dt_2*bxn)                    !Alon
+        vvel2=vvel1+(dt_2*ayn)+(dt_2*byn)                    !Alon
+  
+        if (on_tangential_plane) call rotvec_to_tang(lon1,uvel2,vvel2,xdot2,ydot2)
+        u2=uvel2*dxdl1; v2=vvel2*dydl
+  
+  
+        ! Solving for new position
+        if (on_tangential_plane) then
+          xn=x1+(dt*xdot2) ; yn=y1+(dt*ydot2)             !Alon
+          call rotpos_from_tang(xn,yn,lonn,latn)
+        else
+          lonn=lon1+(dt*u2) ; latn=lat1+(dt*v2)  !Alon
+        endif
+        dxdln=r180_pi/(Rearth*cos(latn*pi_180))
+  
+        ! Turn the velocities into u_star, v_star.(uvel3 is v_star) - Alon (not sure how this works with tangent plane)
+        uvel3=uvel1+(dt_2*axn)                  !Alon
+        vvel3=vvel1+(dt_2*ayn)                  !Alon
+  
+  
+        ! Adjusting mass...                      Alon decided to move this before calculating the new velocities (so that acceleration can be a fn(r_np1)
+        i=i1;j=j1;xi=berg%xi;yj=berg%yj
+        call adjust_index_and_ground(grd, lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
+     !  call adjust_index_and_ground(grd, lonn, latn, uvel1, vvel1, i, j, xi, yj, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
+        i2=i; j2=j
+        if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
+          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling)
+  
+  
+        ! Calling the acceleration   (note that the velocity is converted to u_star inside the accel script)
+        call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn, ayn, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
+  
+  !Solving for the new velocity
+        if (on_tangential_plane) then
+          call rotvec_to_tang(lonn,uvel3,vvel3,xdot3,ydot3)
+          call rotvec_to_tang(lon1,ax1,ay1,xddot1,yddot1)
+          xdotn=xdot3+(dt*xddot1); ydotn=ydot3+(dt*yddot1)                                    !Alon
+          call rotvec_from_tang(lonn,xdotn,ydotn,uveln,vveln)
+        else
+          uvel4=uvel3+(dt*ax1); vvel4=vvel3+(dt*ay1)    !Alon , we call it uvel3, vvel3 until it is put into lat/long co-ordinates, where it becomes uveln, vveln
+        endif
+     !  uveln=uvel4*dxdln; vveln=vvel4*dydl    !Converted to degrees.  (Perhaps this should not be here)
+        uveln=uvel4
+        vveln=vvel4 
+  
+        ! Debugging
+        if (.not.error_flag) then
+          if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j)) error_flag=.true.
+        endif
+        if (error_flag) then
+         call print_fld(grd, grd%msk, 'msk')
+         call print_fld(grd, grd%ssh, 'ssh')
+         call print_fld(grd, grd%sst, 'sst')
+         call print_fld(grd, grd%hi, 'hi')
+         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
+         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
+         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: i1,i2,i=',i1,i2,i
+         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: j1,j2,j=',j1,j2,j
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lon1,lonn=',lon1,lonn,berg%lon
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lat1,latn=',lat1,latn,berg%lat
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u3,un,u0=',uvel3,uveln,berg%uvel
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v3,vn,v0=',vvel3,vveln,berg%vvel
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1=',&
+              & dt*ax1
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ay1=',&
+              & dt*ay1
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u3,un,u0=',&
+              & dt*uvel3,dt*uveln,dt*berg%uvel
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v3,vn,v0=',&
+              & dt*vvel3,dt*vveln,dt*berg%vvel
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u_n (deg)=',&
+              & dt*u1,dt*uveln
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v_n (deg)=',&
+              & dt*v1,dt*vveln
+         write(stderrunit,*) 'diamonds, evolve_iceberg: on_tangential_plane=',on_tangential_plane
+         write(stderrunit,*) 'Acceleration terms for position 1'
+         error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
+         call accel(bergs, berg, i2, j2, xi, yj, latn, uvel3, vvel3, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn, bxn, byn - Added by Alon
+         
+          write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'posn i,j,lon,lat,xi,yj=',i,j,lonn,latn,xi,yj
+          write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'posn box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
+          call print_berg(stderrunit, berg, 'evolve_iceberg, out of cell at end!')
+          bounced=is_point_in_cell(bergs%grd, lonn, latn, i, j, explain=.true.)
+          if (debug) call error_mesg('diamonds, evolve_iceberg','berg is out of posn at end!',FATAL)
+          write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lon',(i,i=grd%isd,grd%ied)
+          do j=grd%jed,grd%jsd,-1
+            write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lon(i,j),i=grd%isd,grd%ied)
+          enddo
+          write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lat',(i,i=grd%isd,grd%ied)
+          do j=grd%jed,grd%jsd,-1
+            write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lat(i,j),i=grd%isd,grd%ied)
+          enddo
+        endif
 
-  endif ! End of the Verlet Stepiing -added by Alon  
+      endif ! End of the Verlet Stepiing -added by Alon  
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
-!Saving all the iceberg variables.
-  berg%axn=axn !Alon
-  berg%ayn=ayn !Alon
-  berg%bxn=bxn !Alon
-  berg%byn=byn !Alon
-  berg%lon=lonn
-  berg%lat=latn
-  berg%uvel=uveln
-  berg%vvel=vveln
-  berg%ine=i
-  berg%jne=j
-  berg%xi=xi
-  berg%yj=yj
-  !call interp_flds(grd, i, j, xi, yj, berg%uo, berg%vo, berg%ui, berg%vi, berg%ua, berg%va, berg%ssh_x, berg%ssh_y, berg%sst)
-  !if (debug) call print_berg(stderr(), berg, 'evolve_iceberg, final posn.')
-  if (debug) call check_position(grd, berg, 'evolve_iceberg (bot)')
-
-
-  berg=>berg%next
-  enddo ! loop over all bergs
-
-! When we are using interactive icebergs, we update the (old) iceberg positions and velocities in a second loop, all together (to make code order invarient)
- if (interactive_icebergs_on) then
-  berg=>bergs%first
-  do while (associated(berg)) ! loop over all bergs
+      ! Saving all the iceberg variables.
+      berg%axn=axn !Alon
+      berg%ayn=ayn !Alon
+      berg%bxn=bxn !Alon
+      berg%byn=byn !Alon
+      berg%lon=lonn
+      berg%lat=latn
+      berg%uvel=uveln
+      berg%vvel=vveln
+      berg%ine=i
+      berg%jne=j
+      berg%xi=xi
+      berg%yj=yj
+      !call interp_flds(grd, i, j, xi, yj, berg%uo, berg%vo, berg%ui, berg%vi, berg%ua, berg%va, berg%ssh_x, berg%ssh_y, berg%sst)
+      !if (debug) call print_berg(stderr(), berg, 'evolve_iceberg, final posn.')
+      if (debug) call check_position(grd, berg, 'evolve_iceberg (bot)')
 
-      !Updating iceberg positions and velocities
-      berg%lon_old=berg%lon
-      berg%lat_old=berg%lat
-      berg%uvel_old=berg%uvel
-      berg%vvel_old=berg%vvel
 
       berg=>berg%next
-  enddo ! loop over all bergs
-
+    enddo ! loop over all bergs
+  enddo ; enddo
+
+  ! When we are using interactive icebergs, we update the (old) iceberg positions and velocities in a second loop, all together (to make code order invarient)
+  if (interactive_icebergs_on) then
+    do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
+      berg=>bergs%list(grdi,grdj)%first
+      do while (associated(berg)) ! loop over all bergs
+
+        !Updating iceberg positions and velocities
+        berg%lon_old=berg%lon
+        berg%lat_old=berg%lat
+        berg%uvel_old=berg%uvel
+        berg%vvel_old=berg%vvel
+
+        berg=>berg%next
+      enddo ! loop over all bergs
+    enddo ; enddo
+  endif
 
- endif
-  contains
+contains
 
   subroutine rotpos_to_tang(lon, lat, x, y)
   ! Arguments
@@ -2640,12 +2648,12 @@ subroutine icebergs_stock_pe(bergs, index, value)
 select case (index)
 
   case (ISTOCK_WATER)
-    berg_mass=sum_mass(bergs%first)
+    berg_mass=sum_mass(bergs)
     stored_mass=sum( grd%stored_ice(grd%isc:grd%iec,grd%jsc:grd%jec,:) )
     value=stored_mass+berg_mass
 
   case (ISTOCK_HEAT)
-    berg_mass=sum_mass(bergs%first)
+    berg_mass=sum_mass(bergs)
     stored_mass=sum( grd%stored_ice(grd%isc:grd%iec,grd%jsc:grd%jec,:) )
     value=-(stored_mass+berg_mass)*HLF ! HLF is in (J/kg) from constants_mod
 
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 30066d1..2766f65 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -157,9 +157,13 @@ module ice_bergs_framework
   real, dimension(:,:), pointer :: data
 end type buffer
 
+type :: linked_list
+  type(iceberg), pointer :: first=>null()
+end type linked_list
+
 type :: icebergs !; private!Niki: Ask Alistair why this is private. ice_bergs_io cannot compile if this is private!
   type(icebergs_gridded), pointer :: grd
-  type(iceberg), pointer :: first=>null()
+  type(linked_list), dimension(:,:), allocatable :: list
   type(xyt), pointer :: trajectories=>null()
   real :: dt           ! Time-step between iceberg calls (should make adaptive?)
   integer :: current_year
@@ -375,6 +379,11 @@ subroutine ice_bergs_framework_init(bergs, &
  !     ' [lon|lat][min|max]=', minval(ice_lon),maxval(ice_lon),minval(ice_lat),maxval(ice_lat)
  !write(stderrunit,*) 'diamonds, int args = ', mpp_pe(),gni, gnj, layout, axes
 
+ ! Allocate grid of pointers
+  allocate( bergs%list(grd%isd:grd%ied, grd%jsd:grd%jed) )
+  do j = grd%jsd,grd%jed ; do i = grd%isd,grd%ied
+    bergs%list(i,j)%first => null()
+  enddo ; enddo
 
  !write(stderrunit,*) 'diamonds: allocating grid'
   allocate( grd%lon(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%lon(:,:)=999.
@@ -672,19 +681,19 @@ subroutine offset_berg_dates(bergs,Time)
 type(iceberg), pointer :: this
 integer :: iyr, imon, iday, ihr, imin, isec, yr_offset
 real :: latest_start_year, berg_start_year
+integer :: grdi, grdj
 
   call get_date(Time, iyr, imon, iday, ihr, imin, isec)
-  latest_start_year=iyr-99999
+  latest_start_year=iyr-999999.
 
-  this=>bergs%first
-  if (associated(this)) then
-   latest_start_year=float(this%start_year)+this%start_day/367.
-  endif
-  do while (associated(this))
-    berg_start_year=float(this%start_year)+this%start_day/367.
-    if (berg_start_year>latest_start_year) latest_start_year=berg_start_year
-    this=>this%next
-  enddo
+  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this))
+      berg_start_year=float(this%start_year)+this%start_day/367.
+      if (berg_start_year>latest_start_year) latest_start_year=berg_start_year
+      this=>this%next
+    enddo
+  enddo ; enddo
   call mpp_max(latest_start_year)
 
   if (latest_start_year<=float(iyr)+yearday(imon, iday, ihr, imin, isec)/367.) return ! No conflicts!
@@ -693,11 +702,13 @@ subroutine offset_berg_dates(bergs,Time)
   if (mpp_pe().eq.mpp_root_pe()) write(*,'(a,i8,a)') &
     'diamonds: Bergs found with creation dates after model date! Adjusting berg dates by ',yr_offset,' years'
   call bergs_chksum(bergs, 'before adjusting start dates')
-  this=>bergs%first
-  do while (associated(this))
-    this%start_year=this%start_year-yr_offset
-    this=>this%next
-  enddo
+  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this))
+      this%start_year=this%start_year-yr_offset
+      this=>this%next
+    enddo
+  enddo ; enddo
   call bergs_chksum(bergs, 'after adjusting start dates')
 
 end subroutine offset_berg_dates
@@ -716,6 +727,7 @@ subroutine send_bergs_to_other_pes(bergs)
 type(icebergs_gridded), pointer :: grd
 integer :: i, nbergs_start, nbergs_end
 integer :: stderrunit
+integer :: grdi, grdj
 
   ! Get the stderr unit number
   stderrunit = stderr()
@@ -730,8 +742,8 @@ subroutine send_bergs_to_other_pes(bergs)
   ! Find number of bergs that headed east/west
   nbergs_to_send_e=0
   nbergs_to_send_w=0
-  if (associated(bergs%first)) then
-    this=>bergs%first
+  do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+    this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
       if (this%ine.gt.bergs%grd%iec) then
         kick_the_bucket=>this
@@ -739,19 +751,19 @@ subroutine send_bergs_to_other_pes(bergs)
         nbergs_to_send_e=nbergs_to_send_e+1
         call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_e, nbergs_to_send_e)
         call move_trajectory(bergs, kick_the_bucket)
-        call delete_iceberg_from_list(bergs%first,kick_the_bucket)
+        call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
       elseif (this%ine.lt.bergs%grd%isc) then
         kick_the_bucket=>this
         this=>this%next
         nbergs_to_send_w=nbergs_to_send_w+1
         call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_w, nbergs_to_send_w)
         call move_trajectory(bergs, kick_the_bucket)
-        call delete_iceberg_from_list(bergs%first,kick_the_bucket)
+        call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
       else
         this=>this%next
       endif
     enddo
-  endif
+  enddo ; enddo
 
   ! Send bergs east
   if (grd%pe_E.ne.NULL_PE) then
@@ -780,7 +792,7 @@ subroutine send_bergs_to_other_pes(bergs)
       call increase_ibuffer(bergs%ibuffer_w, nbergs_rcvd_from_w)
       call mpp_recv(bergs%ibuffer_w%data, nbergs_rcvd_from_w*buffer_width, grd%pe_W, tag=COMM_TAG_2)
       do i=1, nbergs_rcvd_from_w
-        call unpack_berg_from_buffer2(bergs%first, bergs%ibuffer_w, i, grd)
+        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_w, i, grd)
       enddo
     endif
   else
@@ -798,7 +810,7 @@ subroutine send_bergs_to_other_pes(bergs)
       call increase_ibuffer(bergs%ibuffer_e, nbergs_rcvd_from_e)
       call mpp_recv(bergs%ibuffer_e%data, nbergs_rcvd_from_e*buffer_width, grd%pe_E, tag=COMM_TAG_4)
       do i=1, nbergs_rcvd_from_e
-        call unpack_berg_from_buffer2(bergs%first, bergs%ibuffer_e, i, grd)
+        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_e, i, grd)
       enddo
     endif
   else
@@ -811,8 +823,8 @@ subroutine send_bergs_to_other_pes(bergs)
   !  here to accomodate diagonal transfer of bergs between PEs -AJA)
   nbergs_to_send_n=0
   nbergs_to_send_s=0
-  if (associated(bergs%first)) then
-    this=>bergs%first
+  do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
+    this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
       if (this%jne.gt.bergs%grd%jec) then
         kick_the_bucket=>this
@@ -820,19 +832,19 @@ subroutine send_bergs_to_other_pes(bergs)
         nbergs_to_send_n=nbergs_to_send_n+1
         call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_n, nbergs_to_send_n)
         call move_trajectory(bergs, kick_the_bucket)
-        call delete_iceberg_from_list(bergs%first,kick_the_bucket)
+        call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
       elseif (this%jne.lt.bergs%grd%jsc) then
         kick_the_bucket=>this
         this=>this%next
         nbergs_to_send_s=nbergs_to_send_s+1
         call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_s, nbergs_to_send_s)
         call move_trajectory(bergs, kick_the_bucket)
-        call delete_iceberg_from_list(bergs%first,kick_the_bucket)
+        call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
       else
         this=>this%next
       endif
     enddo
-  endif
+  enddo ; enddo
 
   ! Send bergs north
   if (grd%pe_N.ne.NULL_PE) then
@@ -869,7 +881,7 @@ subroutine send_bergs_to_other_pes(bergs)
       call increase_ibuffer(bergs%ibuffer_s, nbergs_rcvd_from_s)
       call mpp_recv(bergs%ibuffer_s%data, nbergs_rcvd_from_s*buffer_width, grd%pe_S, tag=COMM_TAG_6)
       do i=1, nbergs_rcvd_from_s
-        call unpack_berg_from_buffer2(bergs%first, bergs%ibuffer_s, i, grd) 
+        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_s, i, grd) 
       enddo
     endif
   else
@@ -895,7 +907,7 @@ subroutine send_bergs_to_other_pes(bergs)
          call mpp_recv(bergs%ibuffer_n%data, nbergs_rcvd_from_n*buffer_width, grd%pe_N, tag=COMM_TAG_8)
       endif
       do i=1, nbergs_rcvd_from_n
-        call unpack_berg_from_buffer2(bergs%first, bergs%ibuffer_n, i, grd)
+        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_n, i, grd)
       enddo
     endif
   else
@@ -925,15 +937,17 @@ subroutine send_bergs_to_other_pes(bergs)
 
   if (debug) then
     i=0
-    this=>bergs%first
-    do while (associated(this))
-      call check_position(grd, this, 'exchange (bot)')
-      if (this%ine.lt.bergs%grd%isc .or. &
-          this%ine.gt.bergs%grd%iec .or. &
-          this%jne.lt.bergs%grd%jsc .or. &
-          this%jne.gt.bergs%grd%jec) i=i+1
-      this=>this%next
-    enddo ! while
+    do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
+      this=>bergs%list(grdi,grdj)%first
+      do while (associated(this))
+        call check_position(grd, this, 'exchange (bot)')
+        if (this%ine.lt.bergs%grd%isc .or. &
+            this%ine.gt.bergs%grd%iec .or. &
+            this%jne.lt.bergs%grd%jsc .or. &
+            this%jne.gt.bergs%grd%jec) i=i+1
+        this=>this%next
+      enddo ! while
+    enddo ; enddo
     call mpp_sum(i)
     if (i>0 .and. mpp_pe()==mpp_root_pe()) then
       write(stderrunit,'(a,i4)') 'diamonds, send_bergs_to_other_pes: # of bergs outside computational domain = ',i
@@ -1012,13 +1026,12 @@ subroutine increase_buffer(old,delta)
 
   end subroutine increase_buffer
 
-  subroutine unpack_berg_from_buffer2(first, buff, n,grd, force_append)
+  subroutine unpack_berg_from_buffer2(bergs, buff, n,grd)
   ! Arguments
-  type(iceberg), pointer :: first
+  type(icebergs), pointer :: bergs
   type(buffer), pointer :: buff
   integer, intent(in) :: n
   type(icebergs_gridded), pointer :: grd  
-  logical, optional :: force_append
  ! Local variables
  !real :: lon, lat, uvel, vvel, xi, yj
 
@@ -1031,71 +1044,63 @@ subroutine unpack_berg_from_buffer2(first, buff, n,grd, force_append)
   ! Get the stderr unit number
   stderrunit = stderr()
 
-  if(present(force_append)) force_app = force_append
-     
-    localberg%lon=buff%data(1,n)
-    localberg%lat=buff%data(2,n)
-    localberg%uvel=buff%data(3,n)
-    localberg%vvel=buff%data(4,n)
-    localberg%xi=buff%data(5,n)
-    localberg%yj=buff%data(6,n)
-    localberg%start_lon=buff%data(7,n)
-    localberg%start_lat=buff%data(8,n)
-    localberg%start_year=nint(buff%data(9,n))
-    localberg%start_day=buff%data(10,n)
-    localberg%start_mass=buff%data(11,n)
-    localberg%mass=buff%data(12,n)
-    localberg%thickness=buff%data(13,n)
-    localberg%width=buff%data(14,n)
-    localberg%length=buff%data(15,n)
-    localberg%mass_scaling=buff%data(16,n)
-    localberg%mass_of_bits=buff%data(17,n)
-    localberg%heat_density=buff%data(18,n)
-
-    if(force_app) then !force append with origin ine,jne (for I/O)
-       localberg%ine=buff%data(19,n) 
-       localberg%jne=buff%data(20,n) 
-       call add_new_berg_to_list(first, localberg) 
-    else
-       
-    localberg%axn=buff%data(21,n) !Alon
-    localberg%ayn=buff%data(22,n) !Alon
-    localberg%bxn=buff%data(23,n) !Alon
-    localberg%byn=buff%data(24,n) !Alon
-    localberg%uvel_old=buff%data(25,n) !Alon
-    localberg%vvel_old=buff%data(26,n) !Alon
-    localberg%lon_old=buff%data(27,n) !Alon
-    localberg%lat_old=buff%data(28,n) !Alon
-   
-     lres=find_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
+  localberg%lon=buff%data(1,n)
+  localberg%lat=buff%data(2,n)
+  localberg%uvel=buff%data(3,n)
+  localberg%vvel=buff%data(4,n)
+  localberg%xi=buff%data(5,n)
+  localberg%yj=buff%data(6,n)
+  localberg%start_lon=buff%data(7,n)
+  localberg%start_lat=buff%data(8,n)
+  localberg%start_year=nint(buff%data(9,n))
+  localberg%start_day=buff%data(10,n)
+  localberg%start_mass=buff%data(11,n)
+  localberg%mass=buff%data(12,n)
+  localberg%thickness=buff%data(13,n)
+  localberg%width=buff%data(14,n)
+  localberg%length=buff%data(15,n)
+  localberg%mass_scaling=buff%data(16,n)
+  localberg%mass_of_bits=buff%data(17,n)
+  localberg%heat_density=buff%data(18,n)
+  localberg%ine=buff%data(19,n) 
+  localberg%jne=buff%data(20,n) 
+  localberg%axn=buff%data(21,n) !Alon
+  localberg%ayn=buff%data(22,n) !Alon
+  localberg%bxn=buff%data(23,n) !Alon
+  localberg%byn=buff%data(24,n) !Alon
+  localberg%uvel_old=buff%data(25,n) !Alon
+  localberg%vvel_old=buff%data(26,n) !Alon
+  localberg%lon_old=buff%data(27,n) !Alon
+  localberg%lat_old=buff%data(28,n) !Alon
+ 
+  lres=find_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
+  if (lres) then
+    lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
+    call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg)
+  else
+    lres=find_cell_wide(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
     if (lres) then
       lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
-      call add_new_berg_to_list(first, localberg)
+      call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg)
     else
-      lres=find_cell_wide(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
-      if (lres) then
-        lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
-        call add_new_berg_to_list(first, localberg)
-      else
-        write(stderrunit,'("diamonds, unpack_berg_from_buffer pe=(",i3,a,2i4,a,2f8.2)')&
-             & mpp_pe(),') Failed to find i,j=',localberg%ine,localberg%jne,' for lon,lat=',localberg%lon,localberg%lat
-        write(stderrunit,*) localberg%lon,localberg%lat
-        write(stderrunit,*) localberg%uvel,localberg%vvel
-        write(stderrunit,*) localberg%axn,localberg%ayn !Alon
-        write(stderrunit,*) localberg%bxn,localberg%byn !Alon
-        write(stderrunit,*) localberg%uvel_old,localberg%vvel_old !Alon
-        write(stderrunit,*) localberg%lon_old,localberg%lat_old !Alon
-        write(stderrunit,*) grd%isc,grd%iec,grd%jsc,grd%jec
-        write(stderrunit,*) grd%isd,grd%ied,grd%jsd,grd%jed
-        write(stderrunit,*) grd%lon(grd%isc-1,grd%jsc-1),grd%lon(grd%iec,grd%jsc)
-        write(stderrunit,*) grd%lat(grd%isc-1,grd%jsc-1),grd%lat(grd%iec,grd%jec)
-        write(stderrunit,*) grd%lon(grd%isd,grd%jsd),grd%lon(grd%ied,grd%jsd)
-        write(stderrunit,*) grd%lat(grd%isd,grd%jsd),grd%lat(grd%ied,grd%jed)
-        write(stderrunit,*) lres
-        call error_mesg('diamonds, unpack_berg_from_buffer', 'can not find a cell to place berg in!', FATAL)
-      endif
-    endif
+      write(stderrunit,'("diamonds, unpack_berg_from_buffer pe=(",i3,a,2i4,a,2f8.2)')&
+           & mpp_pe(),') Failed to find i,j=',localberg%ine,localberg%jne,' for lon,lat=',localberg%lon,localberg%lat
+      write(stderrunit,*) localberg%lon,localberg%lat
+      write(stderrunit,*) localberg%uvel,localberg%vvel
+      write(stderrunit,*) localberg%axn,localberg%ayn !Alon
+      write(stderrunit,*) localberg%bxn,localberg%byn !Alon
+      write(stderrunit,*) localberg%uvel_old,localberg%vvel_old !Alon
+      write(stderrunit,*) localberg%lon_old,localberg%lat_old !Alon
+      write(stderrunit,*) grd%isc,grd%iec,grd%jsc,grd%jec
+      write(stderrunit,*) grd%isd,grd%ied,grd%jsd,grd%jed
+      write(stderrunit,*) grd%lon(grd%isc-1,grd%jsc-1),grd%lon(grd%iec,grd%jsc)
+      write(stderrunit,*) grd%lat(grd%isc-1,grd%jsc-1),grd%lat(grd%iec,grd%jec)
+      write(stderrunit,*) grd%lon(grd%isd,grd%jsd),grd%lon(grd%ied,grd%jsd)
+      write(stderrunit,*) grd%lat(grd%isd,grd%jsd),grd%lat(grd%ied,grd%jed)
+      write(stderrunit,*) lres
+      call error_mesg('diamonds, unpack_berg_from_buffer', 'can not find a cell to place berg in!', FATAL)
     endif
+  endif
 
   end subroutine unpack_berg_from_buffer2
 
@@ -1320,35 +1325,40 @@ subroutine count_out_of_order(bergs,label)
 ! Local variables
 type(iceberg), pointer :: this, next
 integer :: i, icnt1, icnt2, icnt3
+integer :: grdi, grdj
 
   icnt1=0; icnt3=0
-  this=>bergs%first
-  next=>null()
-  if (associated(this)) then
-    if (associated(this%next)) next=>this%next
-  endif
-  do while (associated(next))
-    if (.not. inorder(this,next)) icnt1=icnt1+1
-    if (inorder(this,next).and.inorder(next,this)) icnt3=icnt3+1
-    this=>next
-    next=>next%next
-  enddo
+  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
+    this=>bergs%list(grdi,grdj)%first
+    next=>null()
+    if (associated(this)) then
+      if (associated(this%next)) next=>this%next
+    endif
+    do while (associated(next))
+      if (.not. inorder(this,next)) icnt1=icnt1+1
+      if (inorder(this,next).and.inorder(next,this)) icnt3=icnt3+1
+      this=>next
+      next=>next%next
+    enddo
+  enddo;enddo
   call mpp_sum(icnt1)
 
   i=0;
   icnt2=0
-  this=>bergs%first
-  do while (associated(this))
-    i=1
-    if (this%ine<bergs%grd%isc .or. &
-        this%ine>bergs%grd%iec .or. &
-        this%jne<bergs%grd%jsc .or. &
-        this%jne>bergs%grd%jec) icnt2=icnt2+1
-    this=>this%next
-    if (i>1.and..not.associated(this%prev)) then
-      call error_mesg('diamonds, count_out_of_order', 'Pointer %prev is unassociated. This should not happen!', FATAL)
-    endif
-  enddo
+  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this))
+      i=1
+      if (this%ine<bergs%grd%isc .or. &
+          this%ine>bergs%grd%iec .or. &
+          this%jne<bergs%grd%jsc .or. &
+          this%jne>bergs%grd%jec) icnt2=icnt2+1
+      this=>this%next
+      if (i>1.and..not.associated(this%prev)) then
+        call error_mesg('diamonds, count_out_of_order', 'Pointer %prev is unassociated. This should not happen!', FATAL)
+      endif
+    enddo
+  enddo; enddo
   call mpp_sum(icnt2)
 
   if ((debug.or.icnt1.ne.0).and.mpp_pe().eq.mpp_root_pe()) then
@@ -1369,19 +1379,31 @@ subroutine check_for_duplicates(bergs,label)
 ! Local variables
 type(iceberg), pointer :: this1, next1, this2, next2
 integer :: icnt_id, icnt_same
+integer :: grdi, grdj
+integer :: grdi_inner, grdj_inner
 
   icnt_id=0
   icnt_same=0
-  this1=>bergs%first
-  do while (associated(this1))
-    this2=>this1%next
-    do while (associated(this2))
-      if (sameid(this1,this2)) icnt_id=icnt_id+1
-      if (sameberg(this1,this2)) icnt_same=icnt_same+1
-      this2=>this2%next
+  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
+    this1=>bergs%list(grdi,grdj)%first
+    do while (associated(this1))
+      do grdj_inner = grdj,bergs%grd%jec ; do grdi_inner = bergs%grd%isc,bergs%grd%iec
+        if ( .not.(grdj_inner==grdj .and. grdi_inner<grdi) ) then
+          if (grdj_inner==grdj .and. grdi_inner==grdi ) then
+            this2=>this1%next
+          else
+            this2=>bergs%list(grdi_inner,grdj_inner)%first
+          endif
+          do while (associated(this2))
+            if (sameid(this1,this2)) icnt_id=icnt_id+1
+            if (sameberg(this1,this2)) icnt_same=icnt_same+1
+            this2=>this2%next
+          enddo
+        endif
+      enddo ; enddo
+      this1=>this1%next
     enddo
-    this1=>this1%next
-  enddo
+  enddo ; enddo
   call mpp_sum(icnt_id)
   call mpp_sum(icnt_same)
 
@@ -1642,12 +1664,15 @@ subroutine print_bergs(iochan, bergs, label)
 ! Local variables
 integer :: nbergs, nnbergs
 type(iceberg), pointer :: this
+integer :: grdi, grdj
 
-  this=>bergs%first
-  do while(associated(this))
-    call print_berg(iochan, this, label)
-    this=>this%next
-  enddo
+  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
+    this=>bergs%list(grdi,grdj)%first
+    do while(associated(this))
+      call print_berg(iochan, this, label)
+      this=>this%next
+    enddo
+  enddo ; enddo
   nbergs=count_bergs(bergs)
   nnbergs=nbergs
   call mpp_sum(nnbergs)
@@ -1657,18 +1682,31 @@ end subroutine print_bergs
 
 ! ##############################################################################
 
-integer function count_bergs(bergs)
+integer function count_bergs(bergs, with_halos)
 ! Arguments
 type(icebergs), pointer :: bergs
+logical, optional :: with_halos
 ! Local variables
 type(iceberg), pointer :: this
+integer :: grdi, grdj, is, ie, js, je
+logical :: include_halos
+
+  include_halos = .false.
+  if (present(with_halos)) include_halos = with_halos
+  if (include_halos) then
+   is = bergs%grd%isd ; ie = bergs%grd%ied ; js = bergs%grd%jsd ; je = bergs%grd%jed
+  else
+   is = bergs%grd%isc ; ie = bergs%grd%iec ; js = bergs%grd%jsc ; je = bergs%grd%jec
+  endif
 
   count_bergs=0
-  this=>bergs%first
-  do while(associated(this))
-    count_bergs=count_bergs+1
-    this=>this%next
-  enddo
+  do grdj = js,je ; do grdi = is,ie
+    this=>bergs%list(grdi,grdj)%first
+    do while(associated(this))
+      count_bergs=count_bergs+1
+      this=>this%next
+    enddo
+  enddo ; enddo
 
 end function count_bergs
 
@@ -1680,45 +1718,48 @@ subroutine record_posn(bergs)
 ! Local variables
 type(xyt) :: posn
 type(iceberg), pointer :: this
+integer :: grdi, grdj
 
-  this=>bergs%first
-  do while (associated(this))
-    posn%lon=this%lon
-    posn%lat=this%lat
-    posn%year=bergs%current_year
-    posn%day=bergs%current_yearday
-    posn%uvel=this%uvel
-    posn%vvel=this%vvel
-    posn%mass=this%mass
-    posn%mass_of_bits=this%mass_of_bits
-    posn%heat_density=this%heat_density
-    posn%thickness=this%thickness
-    posn%width=this%width
-    posn%length=this%length
-    posn%uo=this%uo
-    posn%vo=this%vo
-    posn%ui=this%ui
-    posn%vi=this%vi
-    posn%ua=this%ua
-    posn%va=this%va
-    posn%ssh_x=this%ssh_x
-    posn%ssh_y=this%ssh_y
-    posn%sst=this%sst
-    posn%cn=this%cn
-    posn%hi=this%hi
-    posn%axn=this%axn
-    posn%ayn=this%ayn
-    posn%bxn=this%bxn
-    posn%byn=this%byn
-    posn%uvel_old=this%uvel_old
-    posn%vvel_old=this%vvel_old
-    posn%lon_old=this%lon_old
-    posn%lat_old=this%lat_old
-
-    call push_posn(this%trajectory, posn)
-
-    this=>this%next
-  enddo
+  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this))
+      posn%lon=this%lon
+      posn%lat=this%lat
+      posn%year=bergs%current_year
+      posn%day=bergs%current_yearday
+      posn%uvel=this%uvel
+      posn%vvel=this%vvel
+      posn%mass=this%mass
+      posn%mass_of_bits=this%mass_of_bits
+      posn%heat_density=this%heat_density
+      posn%thickness=this%thickness
+      posn%width=this%width
+      posn%length=this%length
+      posn%uo=this%uo
+      posn%vo=this%vo
+      posn%ui=this%ui
+      posn%vi=this%vi
+      posn%ua=this%ua
+      posn%va=this%va
+      posn%ssh_x=this%ssh_x
+      posn%ssh_y=this%ssh_y
+      posn%sst=this%sst
+      posn%cn=this%cn
+      posn%hi=this%hi
+      posn%axn=this%axn
+      posn%ayn=this%ayn
+      posn%bxn=this%bxn
+      posn%byn=this%byn
+      posn%uvel_old=this%uvel_old
+      posn%vvel_old=this%vvel_old
+      posn%lon_old=this%lon_old
+      posn%lat_old=this%lat_old
+  
+      call push_posn(this%trajectory, posn)
+  
+      this=>this%next
+    enddo
+  enddo ; enddo
 
 end subroutine record_posn
 
@@ -1811,16 +1852,19 @@ subroutine move_all_trajectories(bergs, delete_bergs)
 ! Local variables
 type(iceberg), pointer :: this, next
 logical :: delete_bergs_after_moving_traj
+integer :: grdi, grdj
 
   delete_bergs_after_moving_traj = .false.
   if (present(delete_bergs)) delete_bergs_after_moving_traj = delete_bergs
-  this=>bergs%first
-  do while (associated(this))
-    next=>this%next
-    call move_trajectory(bergs, this)
- !  if (delete_bergs_after_moving_traj) call destroy_iceberg(this)
-    this=>next
-  enddo
+  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this))
+      next=>this%next
+      call move_trajectory(bergs, this)
+   !  if (delete_bergs_after_moving_traj) call destroy_iceberg(this)
+      this=>next
+    enddo
+  enddo ; enddo
 
 end subroutine move_all_trajectories
 
@@ -2468,52 +2512,58 @@ end subroutine check_position
 
 ! ##############################################################################
 
-real function sum_mass(first,justbits,justbergs)
+real function sum_mass(bergs,justbits,justbergs)
 ! Arguments
-type(iceberg), pointer :: first
+type(icebergs), pointer :: bergs
 logical, intent(in), optional :: justbits, justbergs
 ! Local variables
 type(iceberg), pointer :: this
+integer :: grdi, grdj
 
   sum_mass=0.
-  this=>first
-  do while(associated(this))
-    if (present(justbergs)) then
-      sum_mass=sum_mass+this%mass*this%mass_scaling
-    elseif (present(justbits)) then
-      sum_mass=sum_mass+this%mass_of_bits*this%mass_scaling
-    else
-      sum_mass=sum_mass+(this%mass+this%mass_of_bits)*this%mass_scaling
-    endif
-    this=>this%next
-  enddo
+  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
+    this=>bergs%list(grdi,grdj)%first
+    do while(associated(this))
+      if (present(justbergs)) then
+        sum_mass=sum_mass+this%mass*this%mass_scaling
+      elseif (present(justbits)) then
+        sum_mass=sum_mass+this%mass_of_bits*this%mass_scaling
+      else
+        sum_mass=sum_mass+(this%mass+this%mass_of_bits)*this%mass_scaling
+      endif
+      this=>this%next
+    enddo
+  enddo ; enddo
 
 end function sum_mass
 
 ! ##############################################################################
 
-real function sum_heat(first,justbits,justbergs)
+real function sum_heat(bergs,justbits,justbergs)
 ! Arguments
-type(iceberg), pointer :: first
+type(icebergs), pointer :: bergs
 logical, intent(in), optional :: justbits, justbergs
 ! Local variables
 type(iceberg), pointer :: this
 real :: dm
+integer :: grdi, grdj
 
   sum_heat=0.
-  this=>first
-  do while(associated(this))
-    dm=0.
-    if (present(justbergs)) then
-      dm=this%mass*this%mass_scaling
-    elseif (present(justbits)) then
-      dm=this%mass_of_bits*this%mass_scaling
-    else
-      dm=(this%mass+this%mass_of_bits)*this%mass_scaling
-    endif
-    sum_heat=sum_heat+dm*this%heat_density
-    this=>this%next
-  enddo
+  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
+    this=>bergs%list(grdi,grdj)%first
+    do while(associated(this))
+      dm=0.
+      if (present(justbergs)) then
+        dm=this%mass*this%mass_scaling
+      elseif (present(justbits)) then
+        dm=this%mass_of_bits*this%mass_scaling
+      else
+        dm=(this%mass+this%mass_of_bits)*this%mass_scaling
+      endif
+      sum_heat=sum_heat+dm*this%heat_density
+      this=>this%next
+    enddo
+  enddo ; enddo
 
 end function sum_heat
 
@@ -2736,6 +2786,7 @@ subroutine bergs_chksum(bergs, txt, ignore_halo_violation)
 type(iceberg), pointer :: this
 type(icebergs_gridded), pointer :: grd
 logical :: check_halo
+integer :: grdi, grdj
 
 ! For convenience
   grd=>bergs%grd
@@ -2750,36 +2801,38 @@ subroutine bergs_chksum(bergs, txt, ignore_halo_violation)
   icnt(:,:)=0
   grd%tmp(:,:)=0.
 
-  this=>bergs%first
-  i=0; ichk5=0
-  do while(associated(this))
-    i=i+1
-    iberg=berg_chksum(this)
-    fld(i,1) = this%lon
-    fld(i,2) = this%lat
-    fld(i,3) = this%uvel
-    fld(i,4) = this%vvel
-    fld(i,5) = this%mass
-    fld(i,6) = this%thickness
-    fld(i,7) = this%width
-    fld(i,8) = this%length
-    fld(i,9) = this%axn !added by Alon
-    fld(i,10) = this%ayn !added by Alon
-    fld(i,11) = this%bxn !added by Alon
-    fld(i,12) = this%byn !added by Alon
-    fld(i,13) = this%uvel_old !added by Alon
-    fld(i,14) = this%vvel_old !added by Alon
-    fld(i,15) = this%lon_old !added by Alon
-    fld(i,16) = this%lat_old !added by Alon
-    fld(i,17) = time_hash(this) !Changed from 9 to 17 by Alon
-    fld(i,18) = pos_hash(this) !Changed from 10 to 18 by Alon
-    fld(i,19) = float(iberg) !Changed from 11 to 19 by Alon
-    icnt(this%ine,this%jne)=icnt(this%ine,this%jne)+1
-    fld2(i,:) = fld(i,:)*float( icnt(this%ine,this%jne) ) !*float( i )
-    grd%tmp(this%ine,this%jne)=grd%tmp(this%ine,this%jne)+time_hash(this)*pos_hash(this)+log(this%mass)
-    ichk5=ichk5+iberg
-    this=>this%next
-  enddo
+  do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
+    this=>bergs%list(grdi,grdj)%first
+    i=0; ichk5=0
+    do while(associated(this))
+      i=i+1
+      iberg=berg_chksum(this)
+      fld(i,1) = this%lon
+      fld(i,2) = this%lat
+      fld(i,3) = this%uvel
+      fld(i,4) = this%vvel
+      fld(i,5) = this%mass
+      fld(i,6) = this%thickness
+      fld(i,7) = this%width
+      fld(i,8) = this%length
+      fld(i,9) = this%axn !added by Alon
+      fld(i,10) = this%ayn !added by Alon
+      fld(i,11) = this%bxn !added by Alon
+      fld(i,12) = this%byn !added by Alon
+      fld(i,13) = this%uvel_old !added by Alon
+      fld(i,14) = this%vvel_old !added by Alon
+      fld(i,15) = this%lon_old !added by Alon
+      fld(i,16) = this%lat_old !added by Alon
+      fld(i,17) = time_hash(this) !Changed from 9 to 17 by Alon
+      fld(i,18) = pos_hash(this) !Changed from 10 to 18 by Alon
+      fld(i,19) = float(iberg) !Changed from 11 to 19 by Alon
+      icnt(this%ine,this%jne)=icnt(this%ine,this%jne)+1
+      fld2(i,:) = fld(i,:)*float( icnt(this%ine,this%jne) ) !*float( i )
+      grd%tmp(this%ine,this%jne)=grd%tmp(this%ine,this%jne)+time_hash(this)*pos_hash(this)+log(this%mass)
+      ichk5=ichk5+iberg
+      this=>this%next
+    enddo
+  enddo ; enddo
 
   ichk1=mpp_chksum( fld )
   ichk2=mpp_chksum( fld2 )
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 3449158..9f9ca58 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -105,7 +105,6 @@ subroutine write_restart(bergs)
 integer :: stderrunit
 !I/O vars
 type(restart_file_type) :: bergs_restart
-type(iceberg), pointer :: bergs4io=>NULL()
 integer :: nbergs
 type(icebergs_gridded), pointer :: grd
 real, allocatable, dimension(:) :: lon,          &
@@ -136,6 +135,7 @@ subroutine write_restart(bergs)
                                       jne,       &
                                       start_year
 !uvel_old, vvel_old, lon_old, lat_old, axn, ayn, bxn, byn added by Alon.
+integer :: grdi, grdj
   
 ! Get the stderr unit number
  stderrunit=stderr()
@@ -145,17 +145,14 @@ subroutine write_restart(bergs)
   grd=>bergs%grd
  
   !First add the bergs on the io_tile_root_pe (if any) to the I/O list
-   nbergs = 0
-   if(associated(bergs%first)) then
-        !bergs4io => bergs%first !This would modify the bergs and cause them to grow to include all bergs in the tile.
-        !Alternatively, create a new list, slow
-        this=>bergs%first
-        do while (associated(this))
-           nbergs = nbergs +1
-           call add_new_berg_to_list(bergs4io, this)
-           this=>this%next
-        enddo
-   endif
+  nbergs = 0
+  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this))
+      nbergs = nbergs +1
+      this=>this%next
+    enddo
+  enddo ; enddo
 
    allocate(lon(nbergs))
    allocate(lat(nbergs))
@@ -232,24 +229,28 @@ subroutine write_restart(bergs)
 
   ! Write variables
 
-  if(associated(bergs%first)) this=>bergs%first
-  do i=1,nbergs
-    lon(i) = this%lon; lat(i) = this%lat
-    lon_old(i) = this%lon_old; lat_old(i) = this%lat_old  !Alon
-    uvel(i) = this%uvel; vvel(i) = this%vvel
-    ine(i) = this%ine; jne(i) = this%jne
-    mass(i) = this%mass; thickness(i) = this%thickness
-    axn(i) = this%axn; ayn(i) = this%ayn !Added by Alon
-    uvel_old(i) = this%uvel_old; vvel_old(i) = this%vvel_old !Added by Alon
-    bxn(i) = this%bxn; byn(i) = this%byn !Added by Alon
-    width(i) = this%width; length(i) = this%length
-    start_lon(i) = this%start_lon; start_lat(i) = this%start_lat
-    start_year(i) = this%start_year; start_day(i) = this%start_day
-    start_mass(i) = this%start_mass; mass_scaling(i) = this%mass_scaling
-    mass_of_bits(i) = this%mass_of_bits; heat_density(i) = this%heat_density
-    this=>this%next
-  enddo
-    
+  i = 0
+  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
+    this=>bergs%list(grdi,grdj)%first
+    do while(associated(this))
+      i = i + 1
+      lon(i) = this%lon; lat(i) = this%lat
+      lon_old(i) = this%lon_old; lat_old(i) = this%lat_old  !Alon
+      uvel(i) = this%uvel; vvel(i) = this%vvel
+      ine(i) = this%ine; jne(i) = this%jne
+      mass(i) = this%mass; thickness(i) = this%thickness
+      axn(i) = this%axn; ayn(i) = this%ayn !Added by Alon
+      uvel_old(i) = this%uvel_old; vvel_old(i) = this%vvel_old !Added by Alon
+      bxn(i) = this%bxn; byn(i) = this%byn !Added by Alon
+      width(i) = this%width; length(i) = this%length
+      start_lon(i) = this%start_lon; start_lat(i) = this%start_lat
+      start_year(i) = this%start_year; start_day(i) = this%start_day
+      start_mass(i) = this%start_mass; mass_scaling(i) = this%mass_scaling
+      mass_of_bits(i) = this%mass_of_bits; heat_density(i) = this%heat_density
+      this=>this%next
+    enddo
+  enddo ; enddo
+
   call save_restart(bergs_restart)
   call free_restart_type(bergs_restart)
 
@@ -471,8 +472,8 @@ subroutine read_restart_bergs_orig(bergs,Time)
       if (really_debug) lres=is_point_in_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, explain=.true.)
       lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
      !call add_new_berg_to_list(bergs%first, localberg, quick=.true.)
-      call add_new_berg_to_list(bergs%first, localberg)
-      if (really_debug) call print_berg(stderrunit, bergs%first, 'read_restart_bergs, add_new_berg_to_list')
+      call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg)
+      if (really_debug) call print_berg(stderrunit, bergs%list(localberg%ine,localberg%jne)%first, 'read_restart_bergs, add_new_berg_to_list')
     elseif (multiPErestart .and. io_tile_id(1) .lt. 0) then
       call error_mesg('diamonds, read_restart_bergs', 'berg in PE file was not on PE!', FATAL)
     endif
@@ -500,11 +501,11 @@ subroutine read_restart_bergs_orig(bergs,Time)
 
   if (.not. found_restart .and. bergs%nbergs_start==0 .and. generate_test_icebergs) call generate_bergs(bergs,Time)
 
-  bergs%floating_mass_start=sum_mass(bergs%first)
+  bergs%floating_mass_start=sum_mass(bergs)
   call mpp_sum( bergs%floating_mass_start )
-  bergs%icebergs_mass_start=sum_mass(bergs%first,justbergs=.true.)
+  bergs%icebergs_mass_start=sum_mass(bergs,justbergs=.true.)
   call mpp_sum( bergs%icebergs_mass_start )
-  bergs%bergy_mass_start=sum_mass(bergs%first,justbits=.true.)
+  bergs%bergy_mass_start=sum_mass(bergs,justbits=.true.)
   call mpp_sum( bergs%bergy_mass_start )
   if (mpp_pe().eq.mpp_root_pe().and.verbose) write(*,'(a)') 'diamonds, read_restart_bergs: completed'
 
@@ -554,7 +555,7 @@ subroutine generate_bergs(bergs,Time)
         localberg%vvel_old=0. !Alon
         localberg%bxn=0. !Alon
         localberg%byn=0. !Alon
-        call add_new_berg_to_list(bergs%first, localberg)
+        call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
         localberg%uvel=-1.
         localberg%vvel=0.
         localberg%axn=0. !Alon
@@ -563,7 +564,7 @@ subroutine generate_bergs(bergs,Time)
         localberg%vvel_old=0. !Alon
         localberg%bxn=0. !Alon
         localberg%byn=0. !Alon
-        call add_new_berg_to_list(bergs%first, localberg)
+        call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
         localberg%uvel=0.
         localberg%vvel=1.
         localberg%axn=0. !Alon
@@ -572,7 +573,7 @@ subroutine generate_bergs(bergs,Time)
         localberg%vvel_old=0. !Alon
         localberg%bxn=0. !Alon
         localberg%byn=0. !Alon
-        call add_new_berg_to_list(bergs%first, localberg)
+        call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
         localberg%uvel=0.
         localberg%vvel=-1.
         localberg%axn=0. !Alon
@@ -581,7 +582,7 @@ subroutine generate_bergs(bergs,Time)
         localberg%vvel_old=0. !Alon
         localberg%bxn=0. !Alon
         localberg%byn=0. !Alon
-        call add_new_berg_to_list(bergs%first, localberg)
+        call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
       endif
     enddo; enddo
 
@@ -768,8 +769,8 @@ subroutine read_restart_bergs(bergs,Time)
          if (really_debug) lres=is_point_in_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, explain=.true.)
          lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
         !call add_new_berg_to_list(bergs%first, localberg, quick=.true.)
-         call add_new_berg_to_list(bergs%first, localberg)
-         if (really_debug) call print_berg(stderrunit, bergs%first, 'read_restart_bergs, add_new_berg_to_list')
+         call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg)
+         if (really_debug) call print_berg(stderrunit, bergs%list(localberg%ine,localberg%jne)%first, 'read_restart_bergs, add_new_berg_to_list')
        elseif (multiPErestart .and. io_tile_id(1) .lt. 0) then
          call error_mesg('diamonds, read_restart_bergs', 'berg in PE file was not on PE!', FATAL)
        endif
@@ -807,11 +808,11 @@ subroutine read_restart_bergs(bergs,Time)
      call generate_bergs(bergs,Time)
   endif
 
-  bergs%floating_mass_start=sum_mass(bergs%first)
+  bergs%floating_mass_start=sum_mass(bergs)
   call mpp_sum( bergs%floating_mass_start )
-  bergs%icebergs_mass_start=sum_mass(bergs%first,justbergs=.true.)
+  bergs%icebergs_mass_start=sum_mass(bergs,justbergs=.true.)
   call mpp_sum( bergs%icebergs_mass_start )
-  bergs%bergy_mass_start=sum_mass(bergs%first,justbits=.true.)
+  bergs%bergy_mass_start=sum_mass(bergs,justbits=.true.)
   call mpp_sum( bergs%bergy_mass_start )
   if (mpp_pe().eq.mpp_root_pe().and.verbose) write(*,'(a)') 'diamonds, read_restart_bergs: completed'
 
@@ -861,7 +862,7 @@ subroutine generate_bergs(bergs,Time)
         localberg%vvel_old=0. !Alon
         localberg%bxn=0. !Alon
         localberg%byn=0. !Alon
-        call add_new_berg_to_list(bergs%first, localberg)
+        call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
         localberg%uvel=-1.
         localberg%vvel=0.
         localberg%axn=0. !Alon
@@ -870,7 +871,7 @@ subroutine generate_bergs(bergs,Time)
         localberg%vvel_old=0. !Alon
         localberg%bxn=0. !Alon
         localberg%byn=0. !Alon
-        call add_new_berg_to_list(bergs%first, localberg)
+        call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
         localberg%uvel=0.
         localberg%vvel=1.
         localberg%axn=0. !Alon
@@ -879,7 +880,7 @@ subroutine generate_bergs(bergs,Time)
         localberg%vvel_old=0. !Alon
         localberg%bxn=0. !Alon
         localberg%byn=0. !Alon
-        call add_new_berg_to_list(bergs%first, localberg)
+        call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
         localberg%uvel=0.
         localberg%vvel=-1.
         localberg%axn=0. !Alon
@@ -888,7 +889,7 @@ subroutine generate_bergs(bergs,Time)
         localberg%vvel_old=0. !Alon
         localberg%bxn=0. !Alon
         localberg%byn=0. !Alon
-        call add_new_berg_to_list(bergs%first, localberg)
+        call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
       endif
     enddo; enddo
 
@@ -967,7 +968,7 @@ subroutine read_restart_calving(bergs)
   call mpp_sum( bergs%stored_start )
   bergs%stored_heat_start=sum( grd%stored_heat(grd%isc:grd%iec,grd%jsc:grd%jec) )
   call mpp_sum( bergs%stored_heat_start )
-  bergs%floating_heat_start=sum_heat(bergs%first)
+  bergs%floating_heat_start=sum_heat(bergs)
   call mpp_sum( bergs%floating_heat_start )
 
 end subroutine read_restart_calving

From a01fd33c37f7c35b425cd20d9f881a742482ebce Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Wed, 29 Jul 2015 17:29:20 -0400
Subject: [PATCH 046/361] Bug fix for restarts (post Verlet)

- A few new variables (axn, any, bxn, bny, ...) added for the Verlet
  algorithm were being assigned the value of "mass" in the restart file.
---
 icebergs_io.F90 | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 3449158..5017f67 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -202,12 +202,12 @@ subroutine write_restart(bergs)
   id = register_restart_field(bergs_restart,filename,'uvel',uvel,longname='zonal velocity',units='m/s')
   id = register_restart_field(bergs_restart,filename,'vvel',vvel,longname='meridional velocity',units='m/s')
   id = register_restart_field(bergs_restart,filename,'mass',mass,longname='mass',units='kg')
-  id = register_restart_field(bergs_restart,filename,'axn',mass,longname='explicit zonal acceleration',units='m/s^2') !Alon
-  id = register_restart_field(bergs_restart,filename,'ayn',mass,longname='explicit meridional acceleration',units='m/s^2') !Alon
-  id = register_restart_field(bergs_restart,filename,'uvel_old',mass,longname='old explicit zonal acceleration',units='m/s^2') !Alon
-  id = register_restart_field(bergs_restart,filename,'vvel_old',mass,longname='old explicit meridional acceleration',units='m/s^2') !Alon
-  id = register_restart_field(bergs_restart,filename,'bxn',mass,longname='inplicit zonal acceleration',units='m/s^2') !Alon
-  id = register_restart_field(bergs_restart,filename,'byn',mass,longname='implicit meridional acceleration',units='m/s^2') !Alon
+  id = register_restart_field(bergs_restart,filename,'axn',axn,longname='explicit zonal acceleration',units='m/s^2') !Alon
+  id = register_restart_field(bergs_restart,filename,'ayn',ayn,longname='explicit meridional acceleration',units='m/s^2') !Alon
+  id = register_restart_field(bergs_restart,filename,'uvel_old',uvel_old,longname='old explicit zonal acceleration',units='m/s^2') !Alon
+  id = register_restart_field(bergs_restart,filename,'vvel_old',vvel_old,longname='old explicit meridional acceleration',units='m/s^2') !Alon
+  id = register_restart_field(bergs_restart,filename,'bxn',bxn,longname='inplicit zonal acceleration',units='m/s^2') !Alon
+  id = register_restart_field(bergs_restart,filename,'byn',byn,longname='implicit meridional acceleration',units='m/s^2') !Alon
   id = register_restart_field(bergs_restart,filename,'ine',ine,longname='i index',units='none')
   id = register_restart_field(bergs_restart,filename,'jne',jne,longname='j index',units='none')
   id = register_restart_field(bergs_restart,filename,'thickness',thickness,longname='thickness',units='m')

From 6185016de0860fdc8d48d3def027e558e4a1facd Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Tue, 4 Aug 2015 11:27:00 -0400
Subject: [PATCH 047/361] Found a small bug in the subroutine which sends bergs
 to other PE's. The search for bergs moving north to south should be on the
 entire domain including the halos. This bug has been fixed.

---
 icebergs_framework.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 2766f65..e04ff8a 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -823,7 +823,7 @@ subroutine send_bergs_to_other_pes(bergs)
   !  here to accomodate diagonal transfer of bergs between PEs -AJA)
   nbergs_to_send_n=0
   nbergs_to_send_s=0
-  do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
+  do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
     this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
       if (this%jne.gt.bergs%grd%jec) then

From 154dcbdf403d2e6faaa5a5b51f6efa9197f86a58 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Tue, 4 Aug 2015 15:14:31 -0400
Subject: [PATCH 048/361] Added a routine called move_berg_between_cells which
 makes sure that the icebergs are on the correct lists after the icebergs have
 been evolved. The routine checks if ine=grdi and jne=grdj, and if not, moves
 the berg to the correct list.

I have not fully tested whether this works.
---
 icebergs.F90           |  4 +++-
 icebergs_framework.F90 | 27 +++++++++++++++++++++++++++
 2 files changed, 30 insertions(+), 1 deletion(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 87a7a53..410cbb7 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -30,6 +30,7 @@ module ice_bergs
 use ice_bergs_framework, only: sum_mass,sum_heat,bilin,yearday,count_bergs,bergs_chksum
 use ice_bergs_framework, only: checksum_gridded,add_new_berg_to_list
 use ice_bergs_framework, only: send_bergs_to_other_pes,move_trajectory,move_all_trajectories
+use ice_bergs_framework, only: move_berg_between_cells
 use ice_bergs_framework, only: record_posn,check_position,print_berg,print_bergs,print_fld
 use ice_bergs_framework, only: add_new_berg_to_list,delete_iceberg_from_list,destroy_iceberg
 use ice_bergs_framework, only: grd_chksum2,grd_chksum3
@@ -1270,6 +1271,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   ! For each berg, evolve
   call mpp_clock_begin(bergs%clock_mom)
   call evolve_icebergs(bergs)
+  !call move_berg_between_cells(bergs)  !Markpoint6
   if (debug) call bergs_chksum(bergs, 'run bergs (evolved)',ignore_halo_violation=.true.)
   if (debug) call checksum_gridded(bergs%grd, 's/r run after evolve')
   call mpp_clock_end(bergs%clock_mom)
@@ -2342,12 +2344,12 @@ subroutine evolve_icebergs(bergs)
         berg%lat_old=berg%lat
         berg%uvel_old=berg%uvel
         berg%vvel_old=berg%vvel
-
         berg=>berg%next
       enddo ! loop over all bergs
     enddo ; enddo
   endif
 
+
 contains
 
   subroutine rotpos_to_tang(lon, lat, x, y)
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index e04ff8a..a4cd57e 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -66,6 +66,7 @@ module ice_bergs_framework
 public checksum_gridded
 public grd_chksum2,grd_chksum3
 public fix_restart_dates, offset_berg_dates
+public move_berg_between_cells
 
 type :: icebergs_gridded
   type(domain2D), pointer :: domain ! MPP domain
@@ -715,6 +716,32 @@ end subroutine offset_berg_dates
 
 ! #############################################################################
 
+subroutine move_berg_between_cells(bergs)  !Move icebergs onto the correct lists if they have moved from cell to cell.
+! Arguments
+type(icebergs), pointer :: bergs
+type(icebergs_gridded), pointer :: grd
+type(iceberg), pointer :: moving_berg, this
+integer :: grdi, grdj
+
+do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this))
+      if ((this%ine.ne.grdi) .or. (this%jne.ne.grdj))  then
+        moving_berg=>this
+        this=>this%next
+        !call move_trajectory(bergs, kick_the_bucket)
+        call add_new_berg_to_list(bergs%list(moving_berg%ine,moving_berg%jne)%first,moving_berg)
+        call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,moving_berg)
+      else
+        this=>this%next
+      endif
+    enddo
+enddo ; enddo
+
+end subroutine move_berg_between_cells
+
+! #############################################################################
+
 subroutine send_bergs_to_other_pes(bergs)
 ! Arguments
 type(icebergs), pointer :: bergs

From 8977c627f4e5702d6376ca372fd40cc4f99b2216 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Thu, 6 Aug 2015 11:51:42 -0400
Subject: [PATCH 049/361] Fixed the icebergs moving between cell lists
 subroutine.    -Added initialization for grd and this pointers.    -Do not
 allocate or deallocate memory when moving bergs from cell to cell.

- This is not working quite yet. There is still a bug
---
 icebergs.F90           |  2 +-
 icebergs_framework.F90 | 27 ++++++++++++++++++++++-----
 2 files changed, 23 insertions(+), 6 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 410cbb7..3621ad1 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1271,7 +1271,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   ! For each berg, evolve
   call mpp_clock_begin(bergs%clock_mom)
   call evolve_icebergs(bergs)
-  !call move_berg_between_cells(bergs)  !Markpoint6
+  call move_berg_between_cells(bergs)  !Markpoint6
   if (debug) call bergs_chksum(bergs, 'run bergs (evolved)',ignore_halo_violation=.true.)
   if (debug) call checksum_gridded(bergs%grd, 's/r run after evolve')
   call mpp_clock_end(bergs%clock_mom)
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index a4cd57e..9f3adeb 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -719,9 +719,12 @@ end subroutine offset_berg_dates
 subroutine move_berg_between_cells(bergs)  !Move icebergs onto the correct lists if they have moved from cell to cell.
 ! Arguments
 type(icebergs), pointer :: bergs
-type(icebergs_gridded), pointer :: grd
-type(iceberg), pointer :: moving_berg, this
+type(icebergs_gridded), pointer :: grd => null()
+type(iceberg), pointer :: moving_berg => null(), this => null()
 integer :: grdi, grdj
+logical :: quick
+! For convenience
+grd=>bergs%grd
 
 do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
     this=>bergs%list(grdi,grdj)%first
@@ -729,9 +732,23 @@ subroutine move_berg_between_cells(bergs)  !Move icebergs onto the correct lists
       if ((this%ine.ne.grdi) .or. (this%jne.ne.grdj))  then
         moving_berg=>this
         this=>this%next
-        !call move_trajectory(bergs, kick_the_bucket)
-        call add_new_berg_to_list(bergs%list(moving_berg%ine,moving_berg%jne)%first,moving_berg)
-        call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,moving_berg)
+        
+        !Removing the iceberg from the old list
+        if (associated(moving_berg%prev)) then
+           moving_berg%prev%next=>moving_berg%next
+        else
+            bergs%list(grdi,grdj)%first=>moving_berg%next
+        endif
+        if (associated(moving_berg%next)) moving_berg%next%prev=>moving_berg%prev
+
+        !Inserting the iceberg into the new list 
+!        call insert_berg_into_list(bergs%list(moving_berg%ine,moving_berg%jne)%first,moving_berg,quick=.true.)
+!        call insert_berg_into_list(bergs%list(grdi,grdj)%first,moving_berg)
+        call insert_berg_into_list(bergs%list(moving_berg%ine,moving_berg%jne)%first,moving_berg)
+
+        !Clear moving_berg
+        moving_berg=>null()
+
       else
         this=>this%next
       endif

From 277e41b27d8a0eb4ff06a0bda5f5fb0aca2e0c61 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Fri, 7 Aug 2015 11:45:18 -0400
Subject: [PATCH 050/361] Fixed a bug which was allowing the icebergs to enter
 an infinite loop. The problem was that when an iceberg moved onto a new list,
 and the new list was empty, the iceberg was assigned to first, but the next
 and previous of the berg were not set to null. The error has been corrected.

The routine which moves icebergs between lists corresponding to cells, should now be working.

The model passes a 10 day regression test.
---
 icebergs_framework.F90 | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 9f3adeb..66c1bd1 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -729,21 +729,20 @@ subroutine move_berg_between_cells(bergs)  !Move icebergs onto the correct lists
 do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
     this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
+
       if ((this%ine.ne.grdi) .or. (this%jne.ne.grdj))  then
         moving_berg=>this
         this=>this%next
         
         !Removing the iceberg from the old list
         if (associated(moving_berg%prev)) then
-           moving_berg%prev%next=>moving_berg%next
+          moving_berg%prev%next=>moving_berg%next
         else
-            bergs%list(grdi,grdj)%first=>moving_berg%next
+          bergs%list(grdi,grdj)%first=>moving_berg%next
         endif
         if (associated(moving_berg%next)) moving_berg%next%prev=>moving_berg%prev
 
         !Inserting the iceberg into the new list 
-!        call insert_berg_into_list(bergs%list(moving_berg%ine,moving_berg%jne)%first,moving_berg,quick=.true.)
-!        call insert_berg_into_list(bergs%list(grdi,grdj)%first,moving_berg)
         call insert_berg_into_list(bergs%list(moving_berg%ine,moving_berg%jne)%first,moving_berg)
 
         !Clear moving_berg
@@ -1468,17 +1467,18 @@ subroutine insert_berg_into_list(first, newberg, quick)
 type(iceberg), pointer :: this, prev
 logical :: quickly = .false.
 
-if(present(quick)) quickly = quick
 
   if (associated(first)) then
     if (.not. parallel_reprod .or. quickly) then
       newberg%next=>first
+      newberg%prev=>null()
       first%prev=>newberg
       first=>newberg
     else
       if (inorder(newberg,first)) then
         ! Insert at front of list
         newberg%next=>first
+        newberg%prev=>null()
         first%prev=>newberg
         first=>newberg
       else
@@ -1500,6 +1500,8 @@ subroutine insert_berg_into_list(first, newberg, quick)
   else
     ! list is empty so create it
     first=>newberg
+    first%next=>null()
+    first%prev=>null()
   endif
 
 end subroutine insert_berg_into_list

From 597bf993fe3e8ab48b59bca58dc00bf792458f89 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Mon, 17 Aug 2015 16:39:19 -0400
Subject: [PATCH 051/361] Minor fix for generate_test_icebergs, used in
 debugging

- generate_test_icebergs=.true. creates 4 icebergs in every cell poleward
  of +-60, moving in the cardinal directions. The start location was the
  center of cell which meant that they were indistinguishable from each
  other. The insertion into the list was not determinate.
- I have offset each of the four bergs within the cell in order to
  make each berg identifiable.
- This only affects this debugging option (generate_test_icebergs).
---
 icebergs_io.F90 | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/icebergs_io.F90 b/icebergs_io.F90
index b81888c..144af01 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -863,6 +863,7 @@ subroutine generate_bergs(bergs,Time)
         localberg%bxn=0. !Alon
         localberg%byn=0. !Alon
         call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
+        localberg%start_lon=localberg%lon-0.001
         localberg%uvel=-1.
         localberg%vvel=0.
         localberg%axn=0. !Alon
@@ -872,6 +873,7 @@ subroutine generate_bergs(bergs,Time)
         localberg%bxn=0. !Alon
         localberg%byn=0. !Alon
         call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
+        localberg%start_lat=localberg%lat+0.001
         localberg%uvel=0.
         localberg%vvel=1.
         localberg%axn=0. !Alon
@@ -881,6 +883,7 @@ subroutine generate_bergs(bergs,Time)
         localberg%bxn=0. !Alon
         localberg%byn=0. !Alon
         call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
+        localberg%start_lat=localberg%lat-0.001
         localberg%uvel=0.
         localberg%vvel=-1.
         localberg%axn=0. !Alon

From 2327b5696d12f103e5b51def5616eb6f930ceb44 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Mon, 17 Aug 2015 16:51:17 -0400
Subject: [PATCH 052/361] Added debugging diagnostics "bergs_per_cell" and
 "list_chksum"

- Implemented count_bergs_in_list() and list_chksum()
- count_bergs() uses count_bergs_in_list()
---
 icebergs.F90           | 22 +++++++++++++++---
 icebergs_framework.F90 | 52 +++++++++++++++++++++++++++++++++++-------
 2 files changed, 63 insertions(+), 11 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 3621ad1..eec7028 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -27,8 +27,8 @@ module ice_bergs
 use ice_bergs_framework, only: verbose, really_debug,debug,old_bug_rotated_weights,budget,use_roundoff_fix
 use ice_bergs_framework, only: find_cell,find_cell_by_search,count_bergs,is_point_in_cell,pos_within_cell
 use ice_bergs_framework, only: nclasses,old_bug_bilin
-use ice_bergs_framework, only: sum_mass,sum_heat,bilin,yearday,count_bergs,bergs_chksum
-use ice_bergs_framework, only: checksum_gridded,add_new_berg_to_list
+use ice_bergs_framework, only: sum_mass,sum_heat,bilin,yearday,count_bergs,bergs_chksum,count_bergs_in_list
+use ice_bergs_framework, only: checksum_gridded,add_new_berg_to_list,list_chksum
 use ice_bergs_framework, only: send_bergs_to_other_pes,move_trajectory,move_all_trajectories
 use ice_bergs_framework, only: move_berg_between_cells
 use ice_bergs_framework, only: record_posn,check_position,print_berg,print_bergs,print_fld
@@ -1095,6 +1095,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 real :: mask
 real, dimension(:,:), allocatable :: uC_tmp, vC_tmp
 integer :: vel_stagger, str_stagger
+real, dimension(:,:), allocatable :: iCount
 
 integer :: stderrunit
 
@@ -1347,7 +1348,22 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     lerr=send_data(grd%id_fax, tauxa(:,:), Time)
   if (grd%id_fay>0) &
     lerr=send_data(grd%id_fay, tauya(:,:), Time)
-
+  if (grd%id_count>0) then
+    allocate( iCount(grd%isc:grd%iec,grd%jsc:grd%jec) ); iCount(:,:)=0
+    do j = grd%jsc, grd%jec ; do i = grd%isc, grd%iec
+      iCount(i,j) = count_bergs_in_list(bergs%list(i,j)%first)
+    enddo ; enddo
+    lerr=send_data(grd%id_count, iCount(:,:), Time)
+    deallocate( iCount )
+  endif
+  if (grd%id_chksum>0) then
+    allocate( iCount(grd%isc:grd%iec,grd%jsc:grd%jec) ); iCount(:,:)=0
+    do j = grd%jsc, grd%jec ; do i = grd%isc, grd%iec
+      iCount(i,j) = list_chksum(bergs%list(i,j)%first)
+    enddo ; enddo
+    lerr=send_data(grd%id_chksum, iCount(:,:), Time)
+    deallocate( iCount )
+  endif
 
   ! Dump icebergs to screen
   if (really_debug) call print_bergs(stderrunit,bergs,'icebergs_run, status')
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 66c1bd1..2296ba6 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -62,7 +62,7 @@ module ice_bergs_framework
 public print_fld,print_berg, print_bergs,record_posn, push_posn, append_posn, check_position
 public move_trajectory, move_all_trajectories
 public find_cell,find_cell_by_search,count_bergs,is_point_in_cell,pos_within_cell
-public sum_mass,sum_heat,bilin,yearday,bergs_chksum
+public sum_mass,sum_heat,bilin,yearday,bergs_chksum,list_chksum,count_bergs_in_list
 public checksum_gridded
 public grd_chksum2,grd_chksum3
 public fix_restart_dates, offset_berg_dates
@@ -123,6 +123,7 @@ module ice_bergs_framework
   integer :: id_mass=-1, id_ui=-1, id_vi=-1, id_ua=-1, id_va=-1, id_sst=-1, id_cn=-1, id_hi=-1
   integer :: id_bergy_src=-1, id_bergy_melt=-1, id_bergy_mass=-1, id_berg_melt=-1
   integer :: id_mass_on_ocn=-1, id_ssh=-1, id_fax=-1, id_fay=-1
+  integer :: id_count=-1, id_chksum=-1
 
   real :: clipping_depth=0. ! The effective depth at which to clip the weight felt by the ocean [m].
 
@@ -608,6 +609,10 @@ subroutine ice_bergs_framework_init(bergs, &
      'Accumulated ice mass by class', 'kg')
   grd%id_real_calving=register_diag_field('icebergs', 'real_calving', axes3d, Time, &
      'Calving into iceberg class', 'kg/s')
+  grd%id_count=register_diag_field('icebergs', 'bergs_per_cell', axes, Time, &
+     'Number of bergs per cell', '#')
+  grd%id_chksum=register_diag_field('icebergs', 'list_chksum', axes, Time, &
+     'mpp_chksum on bergs in each cell', '#')
   grd%id_uo=register_diag_field('icebergs', 'uo', axes, Time, &
      'Ocean zonal component of velocity', 'm s^-1')
   grd%id_vo=register_diag_field('icebergs', 'vo', axes, Time, &
@@ -1733,7 +1738,6 @@ integer function count_bergs(bergs, with_halos)
 type(icebergs), pointer :: bergs
 logical, optional :: with_halos
 ! Local variables
-type(iceberg), pointer :: this
 integer :: grdi, grdj, is, ie, js, je
 logical :: include_halos
 
@@ -1747,17 +1751,30 @@ integer function count_bergs(bergs, with_halos)
 
   count_bergs=0
   do grdj = js,je ; do grdi = is,ie
-    this=>bergs%list(grdi,grdj)%first
-    do while(associated(this))
-      count_bergs=count_bergs+1
-      this=>this%next
-    enddo
+    count_bergs=count_bergs+count_bergs_in_list(bergs%list(grdi,grdj)%first)
   enddo ; enddo
 
 end function count_bergs
 
 ! ##############################################################################
 
+integer function count_bergs_in_list(first)
+! Arguments
+type(iceberg), pointer :: first
+! Local variables
+type(iceberg), pointer :: this
+
+  count_bergs_in_list=0
+  this=>first
+  do while(associated(this))
+    count_bergs_in_list=count_bergs_in_list+1
+    this=>this%next
+  enddo
+
+end function count_bergs_in_list
+
+! ##############################################################################
+
 subroutine record_posn(bergs)
 ! Arguments
 type(icebergs), pointer :: bergs
@@ -2921,7 +2938,26 @@ end subroutine bergs_chksum
 
 ! ##############################################################################
 
-integer function berg_chksum(berg )
+integer function list_chksum(first)
+! Arguments
+type(iceberg), pointer :: first
+! Local variables
+integer :: i
+type(iceberg), pointer :: this
+
+  this=>first
+  i=0; list_chksum=0
+  do while(associated(this))
+    i=i+1
+    list_chksum=list_chksum+berg_chksum(this)*i
+    this=>this%next
+  enddo
+
+end function list_chksum
+
+! ##############################################################################
+
+integer function berg_chksum(berg)
 ! Arguments
 type(iceberg), pointer :: berg
 ! Local variables

From f720e15b3c4e4581953926b76b79068655397302 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Fri, 11 Sep 2015 15:28:32 -0400
Subject: [PATCH 053/361] For the interactive forces, I have changed the loop
 so that icebergs only interact with other icebergs which are in the nine grid
 cells immediately adjacent.

The icebergs are not get stored correctly in the halos (or at all). So this will not work well at the edge of a processor. This will be done next.
---
 icebergs.F90 | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 3621ad1..d2a75d0 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -165,11 +165,10 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
 lon1=berg%lon; lat1=berg%lat
 call rotpos_to_tang(lon1,lat1,x1,y1)
 
-  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
+  do grdj = berg%jne-1,berg%jne+1 ; do grdi = berg%ine-1,berg%ine+1
   other_berg=>bergs%list(grdi,grdj)%first
 
 !Note: This summing should be made order invarient. 
-!Note: Need to limit how many icebergs we search over
   do while (associated(other_berg)) ! loop over all other bergs  
        L2=other_berg%length
        W2=other_berg%width

From 1f0146659394a9382eaf8734702b6f8319447e4b Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Fri, 11 Sep 2015 17:46:26 -0400
Subject: [PATCH 054/361] A new routine called update_halo has been included.

This routine works in two steps.
First the halos are cleared (ie: all the bergs are deleted from cells in the halos).
Second, the icebergs near the the edge of the processor are copied into the halos of the other processor.

The code compiles, but has not yet been tested.

Also, I am not sure that the icebergs which are being moved into the halos of the other processor are being sent to the correct grid list. This will be the next update.
---
 icebergs.F90           |   3 +-
 icebergs_framework.F90 | 243 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 245 insertions(+), 1 deletion(-)

diff --git a/icebergs.F90 b/icebergs.F90
index d2a75d0..5afee1d 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -30,7 +30,7 @@ module ice_bergs
 use ice_bergs_framework, only: sum_mass,sum_heat,bilin,yearday,count_bergs,bergs_chksum
 use ice_bergs_framework, only: checksum_gridded,add_new_berg_to_list
 use ice_bergs_framework, only: send_bergs_to_other_pes,move_trajectory,move_all_trajectories
-use ice_bergs_framework, only: move_berg_between_cells
+use ice_bergs_framework, only: move_berg_between_cells, update_halo
 use ice_bergs_framework, only: record_posn,check_position,print_berg,print_bergs,print_fld
 use ice_bergs_framework, only: add_new_berg_to_list,delete_iceberg_from_list,destroy_iceberg
 use ice_bergs_framework, only: grd_chksum2,grd_chksum3
@@ -1278,6 +1278,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   ! Send bergs to other PEs
   call mpp_clock_begin(bergs%clock_com)
   call send_bergs_to_other_pes(bergs)
+  call update_halo(bergs)
   if (debug) call bergs_chksum(bergs, 'run bergs (exchanged)')
   if (debug) call checksum_gridded(bergs%grd, 's/r run after exchange')
   call mpp_clock_end(bergs%clock_com)
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 66c1bd1..afad18a 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -54,6 +54,7 @@ module ice_bergs_framework
 !Public subs
 public ice_bergs_framework_init
 public send_bergs_to_other_pes
+public update_halo
 public pack_berg_into_buffer2, unpack_berg_from_buffer2
 public pack_traj_into_buffer2, unpack_traj_from_buffer2
 public increase_buffer, increase_ibuffer, increase_ibuffer_traj, increase_buffer_traj
@@ -756,6 +757,248 @@ subroutine move_berg_between_cells(bergs)  !Move icebergs onto the correct lists
 
 end subroutine move_berg_between_cells
 
+
+! #############################################################################
+
+subroutine update_halo(bergs)
+! Arguments
+type(icebergs), pointer :: bergs
+! Local variables
+type(iceberg), pointer :: kick_the_bucket, this
+integer :: nbergs_to_send_e, nbergs_to_send_w
+integer :: nbergs_to_send_n, nbergs_to_send_s
+integer :: nbergs_rcvd_from_e, nbergs_rcvd_from_w
+integer :: nbergs_rcvd_from_n, nbergs_rcvd_from_s
+type(icebergs_gridded), pointer :: grd
+integer :: i, nbergs_start, nbergs_end
+integer :: stderrunit
+integer :: grdi, grdj
+integer :: halo_width
+
+  halo_width=2  ! Must be less than current halo value used for updating weight.
+
+! Step 1: Clear the current halos
+  do grdj = grd%jsd,grd%jsc-1 ;  do grdi = grd%isd,grd%ied
+    call delete_all_bergs_in_list(bergs, grdj, grdi)
+  enddo ; enddo
+
+  do grdj = grd%jec+1,grd%jed ;  do grdi = grd%isd,grd%ied
+    call delete_all_bergs_in_list(bergs,grdj,grdi)
+  enddo ; enddo
+
+  do grdj = grd%jsd,grd%jed ;    do grdi = grd%isd,grd%isc-1
+    call delete_all_bergs_in_list(bergs,grdj,grdi)
+  enddo ; enddo
+
+  do grdj = grd%jsd,grd%jed ;    do grdi = grd%iec+1,grd%ied
+    call delete_all_bergs_in_list(bergs,grdj,grdi)
+  enddo ; enddo
+
+
+! Step 2: Updating the halos  - This code is mostly copied from send_to_other_pes
+
+  ! Get the stderr unit number
+  stderrunit = stderr()
+
+  ! For convenience
+  grd=>bergs%grd
+
+  if (debug) then
+    nbergs_start=count_bergs(bergs)
+  endif
+
+  ! Find number of bergs that headed east/west
+  nbergs_to_send_e=0
+  nbergs_to_send_w=0
+
+  !Bergs on eastern side of the processor
+  do grdj = grd%jsc,grd%jec ; do grdi = grd%iec+1,grd%iec+halo_width  
+    this=>bergs%list(grdi,grdj)%first
+    kick_the_bucket=>this
+    this=>this%next
+    nbergs_to_send_e=nbergs_to_send_e+1
+    call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_e, nbergs_to_send_e)
+  enddo; enddo
+
+  !Bergs on the western side of the processor
+  do grdj = grd%jsc,grd%jec ; do grdi = grd%isc-halo_width,grd%isc-1 
+    kick_the_bucket=>this
+    this=>this%next
+    nbergs_to_send_w=nbergs_to_send_w+1
+    call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_w, nbergs_to_send_w) 
+  enddo; enddo
+
+
+
+  ! Send bergs east
+  if (grd%pe_E.ne.NULL_PE) then
+    call mpp_send(nbergs_to_send_e, plen=1, to_pe=grd%pe_E, tag=COMM_TAG_1)
+    if (nbergs_to_send_e.gt.0) then
+      call mpp_send(bergs%obuffer_e%data, nbergs_to_send_e*buffer_width, grd%pe_E, tag=COMM_TAG_2)
+    endif
+  endif
+
+  ! Send bergs west
+  if (grd%pe_W.ne.NULL_PE) then
+    call mpp_send(nbergs_to_send_w, plen=1, to_pe=grd%pe_W, tag=COMM_TAG_3)
+    if (nbergs_to_send_w.gt.0) then
+      call mpp_send(bergs%obuffer_w%data, nbergs_to_send_w*buffer_width, grd%pe_W, tag=COMM_TAG_4)
+    endif
+  endif
+
+  ! Receive bergs from west
+  if (grd%pe_W.ne.NULL_PE) then
+    nbergs_rcvd_from_w=-999
+    call mpp_recv(nbergs_rcvd_from_w, glen=1, from_pe=grd%pe_W, tag=COMM_TAG_1)
+    if (nbergs_rcvd_from_w.lt.0) then
+      write(stderrunit,*) 'pe=',mpp_pe(),' received a bad number',nbergs_rcvd_from_w,' from',grd%pe_W,' (W) !!!!!!!!!!!!!!!!!!!!!!'
+    endif
+    if (nbergs_rcvd_from_w.gt.0) then
+      call increase_ibuffer(bergs%ibuffer_w, nbergs_rcvd_from_w)
+      call mpp_recv(bergs%ibuffer_w%data, nbergs_rcvd_from_w*buffer_width, grd%pe_W, tag=COMM_TAG_2)
+      do i=1, nbergs_rcvd_from_w
+        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_w, i, grd)
+      enddo
+    endif
+  else
+    nbergs_rcvd_from_w=0
+  endif
+
+  ! Receive bergs from east
+  if (grd%pe_E.ne.NULL_PE) then
+    nbergs_rcvd_from_e=-999
+    call mpp_recv(nbergs_rcvd_from_e, glen=1, from_pe=grd%pe_E, tag=COMM_TAG_3)
+    if (nbergs_rcvd_from_e.lt.0) then
+      write(stderrunit,*) 'pe=',mpp_pe(),' received a bad number',nbergs_rcvd_from_e,' from',grd%pe_E,' (E) !!!!!!!!!!!!!!!!!!!!!!'
+    endif
+    if (nbergs_rcvd_from_e.gt.0) then
+      call increase_ibuffer(bergs%ibuffer_e, nbergs_rcvd_from_e)
+      call mpp_recv(bergs%ibuffer_e%data, nbergs_rcvd_from_e*buffer_width, grd%pe_E, tag=COMM_TAG_4)
+      do i=1, nbergs_rcvd_from_e
+        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_e, i, grd)
+      enddo
+    endif
+  else
+    nbergs_rcvd_from_e=0
+  endif
+
+
+
+ ! Find number of bergs that headed north/south
+  nbergs_to_send_n=0
+  nbergs_to_send_s=0
+  
+
+  !Bergs on north side of the processor
+  do grdj = grd%jec-halo_width,grd%jec-1 ; do grdi = grd%isd,grd%ied
+    kick_the_bucket=>this
+    this=>this%next
+    nbergs_to_send_n=nbergs_to_send_n+1
+    call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_n, nbergs_to_send_n)
+  enddo; enddo
+
+
+  !Bergs on south side of the processor
+  do grdj = grd%jsc+1,grd%jsc+halo_width ; do grdi = grd%isd,grd%ied
+    kick_the_bucket=>this
+    this=>this%next
+    nbergs_to_send_s=nbergs_to_send_s+1
+    call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_s, nbergs_to_send_s)
+   enddo; enddo
+
+
+ ! Send bergs north
+  if (grd%pe_N.ne.NULL_PE) then
+    if(folded_north_on_pe) then
+       call mpp_send(nbergs_to_send_n, plen=1, to_pe=grd%pe_N, tag=COMM_TAG_9)
+    else
+       call mpp_send(nbergs_to_send_n, plen=1, to_pe=grd%pe_N, tag=COMM_TAG_5)
+    endif
+    if (nbergs_to_send_n.gt.0) then
+       if(folded_north_on_pe) then
+          call mpp_send(bergs%obuffer_n%data, nbergs_to_send_n*buffer_width, grd%pe_N, tag=COMM_TAG_10)
+       else
+          call mpp_send(bergs%obuffer_n%data, nbergs_to_send_n*buffer_width, grd%pe_N, tag=COMM_TAG_6)
+       endif
+    endif
+  endif
+
+  ! Send bergs south
+  if (grd%pe_S.ne.NULL_PE) then
+    call mpp_send(nbergs_to_send_s, plen=1, to_pe=grd%pe_S, tag=COMM_TAG_7)
+    if (nbergs_to_send_s.gt.0) then
+      call mpp_send(bergs%obuffer_s%data, nbergs_to_send_s*buffer_width, grd%pe_S, tag=COMM_TAG_8)
+    endif
+  endif
+
+
+  ! Receive bergs from south
+  if (grd%pe_S.ne.NULL_PE) then
+    nbergs_rcvd_from_s=-999
+    call mpp_recv(nbergs_rcvd_from_s, glen=1, from_pe=grd%pe_S, tag=COMM_TAG_5)
+    if (nbergs_rcvd_from_s.lt.0) then
+      write(stderrunit,*) 'pe=',mpp_pe(),' received a bad number',nbergs_rcvd_from_s,' from',grd%pe_S,' (S) !!!!!!!!!!!!!!!!!!!!!!'
+    endif
+    if (nbergs_rcvd_from_s.gt.0) then
+      call increase_ibuffer(bergs%ibuffer_s, nbergs_rcvd_from_s)
+      call mpp_recv(bergs%ibuffer_s%data, nbergs_rcvd_from_s*buffer_width, grd%pe_S, tag=COMM_TAG_6)
+      do i=1, nbergs_rcvd_from_s
+        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_s, i, grd)
+      enddo
+    endif
+  else
+    nbergs_rcvd_from_s=0
+  endif
+
+  ! Receive bergs from north
+  if (grd%pe_N.ne.NULL_PE) then
+    nbergs_rcvd_from_n=-999
+    if(folded_north_on_pe) then
+       call mpp_recv(nbergs_rcvd_from_n, glen=1, from_pe=grd%pe_N, tag=COMM_TAG_9)
+    else
+       call mpp_recv(nbergs_rcvd_from_n, glen=1, from_pe=grd%pe_N, tag=COMM_TAG_7)
+    endif
+    if (nbergs_rcvd_from_n.lt.0) then
+      write(stderrunit,*) 'pe=',mpp_pe(),' received a bad number',nbergs_rcvd_from_n,' from',grd%pe_N,' (N) !!!!!!!!!!!!!!!!!!!!!!'
+    endif
+    if (nbergs_rcvd_from_n.gt.0) then
+      call increase_ibuffer(bergs%ibuffer_n, nbergs_rcvd_from_n)
+      if(folded_north_on_pe) then
+         call mpp_recv(bergs%ibuffer_n%data, nbergs_rcvd_from_n*buffer_width, grd%pe_N, tag=COMM_TAG_10)
+      else
+         call mpp_recv(bergs%ibuffer_n%data, nbergs_rcvd_from_n*buffer_width, grd%pe_N, tag=COMM_TAG_8)
+      endif
+      do i=1, nbergs_rcvd_from_n
+        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_n, i, grd)
+      enddo
+    endif
+  else
+    nbergs_rcvd_from_n=0
+  endif
+
+
+
+  call mpp_sync_self()
+
+
+contains
+  subroutine delete_all_bergs_in_list(bergs,grdj,grdi)
+  type(icebergs), pointer :: bergs
+  ! Local variables
+  type(iceberg), pointer :: kick_the_bucket, this
+  integer :: grdi, grdj
+  this=>bergs%list(grdi,grdj)%first
+  do while (associated(this))
+    kick_the_bucket=>this
+    this=>this%next
+    call destroy_iceberg(kick_the_bucket)
+!    call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
+  enddo
+  end  subroutine delete_all_bergs_in_list
+
+end subroutine update_halo
+
+
 ! #############################################################################
 
 subroutine send_bergs_to_other_pes(bergs)

From df8a3568dd4bfca38465a71314fb2de550238859 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Thu, 17 Sep 2015 15:57:13 -0400
Subject: [PATCH 055/361] Fixed a few bugs in the subroutine halo_update. These
 bugs were causing segmentation faults. With these changes, the model is able
 to run for one day, and it returns the same answers as dev/master.

It seems that the halos are now updating correctly.

I am going to run a longer test so that the icebergs will have time to move between processors.
---
 icebergs_framework.F90 | 75 +++++++++++++++++++++++++++---------------
 1 file changed, 48 insertions(+), 27 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index afad18a..d8af313 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -774,10 +774,21 @@ subroutine update_halo(bergs)
 integer :: stderrunit
 integer :: grdi, grdj
 integer :: halo_width
+integer :: temp1, temp2
+  
+halo_width=2  ! Must be less than current halo value used for updating weight.
+
+ ! Get the stderr unit number
+   stderrunit = stderr()
+
+ ! For convenience
+   grd=>bergs%grd
+
 
-  halo_width=2  ! Must be less than current halo value used for updating weight.
 
 ! Step 1: Clear the current halos
+
+
   do grdj = grd%jsd,grd%jsc-1 ;  do grdi = grd%isd,grd%ied
     call delete_all_bergs_in_list(bergs, grdj, grdi)
   enddo ; enddo
@@ -797,11 +808,9 @@ subroutine update_halo(bergs)
 
 ! Step 2: Updating the halos  - This code is mostly copied from send_to_other_pes
 
-  ! Get the stderr unit number
-  stderrunit = stderr()
-
-  ! For convenience
-  grd=>bergs%grd
+!  ! Get the stderr unit number
+!  stderrunit = stderr()
+!
 
   if (debug) then
     nbergs_start=count_bergs(bergs)
@@ -814,18 +823,22 @@ subroutine update_halo(bergs)
   !Bergs on eastern side of the processor
   do grdj = grd%jsc,grd%jec ; do grdi = grd%iec+1,grd%iec+halo_width  
     this=>bergs%list(grdi,grdj)%first
-    kick_the_bucket=>this
-    this=>this%next
-    nbergs_to_send_e=nbergs_to_send_e+1
-    call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_e, nbergs_to_send_e)
+    do while (associated(this))
+        kick_the_bucket=>this
+        this=>this%next
+        nbergs_to_send_e=nbergs_to_send_e+1
+        call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_e, nbergs_to_send_e)
+    enddo
   enddo; enddo
 
   !Bergs on the western side of the processor
   do grdj = grd%jsc,grd%jec ; do grdi = grd%isc-halo_width,grd%isc-1 
-    kick_the_bucket=>this
-    this=>this%next
-    nbergs_to_send_w=nbergs_to_send_w+1
-    call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_w, nbergs_to_send_w) 
+    do while (associated(this))
+      kick_the_bucket=>this
+      this=>this%next
+      nbergs_to_send_w=nbergs_to_send_w+1
+    call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_w, nbergs_to_send_w)
+    enddo 
   enddo; enddo
 
 
@@ -891,20 +904,24 @@ subroutine update_halo(bergs)
 
   !Bergs on north side of the processor
   do grdj = grd%jec-halo_width,grd%jec-1 ; do grdi = grd%isd,grd%ied
-    kick_the_bucket=>this
-    this=>this%next
-    nbergs_to_send_n=nbergs_to_send_n+1
-    call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_n, nbergs_to_send_n)
+    do while (associated(this))
+      kick_the_bucket=>this
+      this=>this%next
+      nbergs_to_send_n=nbergs_to_send_n+1
+      call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_n, nbergs_to_send_n)
+    enddo
   enddo; enddo
 
 
   !Bergs on south side of the processor
   do grdj = grd%jsc+1,grd%jsc+halo_width ; do grdi = grd%isd,grd%ied
-    kick_the_bucket=>this
-    this=>this%next
-    nbergs_to_send_s=nbergs_to_send_s+1
-    call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_s, nbergs_to_send_s)
-   enddo; enddo
+    do while (associated(this))
+      kick_the_bucket=>this
+      this=>this%next
+      nbergs_to_send_s=nbergs_to_send_s+1
+      call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_s, nbergs_to_send_s)
+    enddo
+  enddo; enddo
 
 
  ! Send bergs north
@@ -981,8 +998,13 @@ subroutine update_halo(bergs)
   call mpp_sync_self()
 
 
-contains
-  subroutine delete_all_bergs_in_list(bergs,grdj,grdi)
+end subroutine update_halo
+
+
+
+
+!contains
+subroutine delete_all_bergs_in_list(bergs,grdj,grdi)
   type(icebergs), pointer :: bergs
   ! Local variables
   type(iceberg), pointer :: kick_the_bucket, this
@@ -994,9 +1016,8 @@ subroutine delete_all_bergs_in_list(bergs,grdj,grdi)
     call destroy_iceberg(kick_the_bucket)
 !    call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
   enddo
-  end  subroutine delete_all_bergs_in_list
+end  subroutine delete_all_bergs_in_list
 
-end subroutine update_halo
 
 
 ! #############################################################################

From 08a5867919f87000789ecac09d25e2b7e1008275 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Thu, 17 Sep 2015 16:55:31 -0400
Subject: [PATCH 056/361] Added iceberg_halo to the namelist with a default =2.
 It is required that iceberg_halo < halo

---
 icebergs_framework.F90 | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index d8af313..c4df69b 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -72,6 +72,7 @@ module ice_bergs_framework
 type :: icebergs_gridded
   type(domain2D), pointer :: domain ! MPP domain
   integer :: halo ! Nominal halo width
+  integer :: iceberg_halo ! halo width used by icebergs (must be lt halo)
   integer :: isc, iec, jsc, jec ! Indices of computational domain
   integer :: isd, ied, jsd, jed ! Indices of data domain
   integer :: my_pe, pe_N, pe_S, pe_E, pe_W ! MPI PE identifiers
@@ -269,6 +270,7 @@ subroutine ice_bergs_framework_init(bergs, &
 
 ! Namelist parameters (and defaults)
 integer :: halo=4 ! Width of halo region
+integer :: iceberg_halo=2 ! Width of halo region for icebergs  (must be lt halo)
 integer :: traj_sample_hrs=24 ! Period between sampling of position for trajectory storage
 integer :: traj_write_hrs=480 ! Period between writing sampled trajectories to disk
 integer :: verbose_hrs=24 ! Period between verbose messages
@@ -295,7 +297,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real, dimension(nclasses) :: distribution=(/0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02/) ! Fraction of calving to apply to this class (non-dim) , 
 real, dimension(nclasses) :: mass_scaling=(/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) ! Ratio between effective and real iceberg mass (non-dim)
 real, dimension(nclasses) :: initial_thickness=(/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) ! Total thickness of newly calved bergs (m)
-namelist /icebergs_nml/ verbose, budget, halo, traj_sample_hrs, initial_mass, traj_write_hrs, &
+namelist /icebergs_nml/ verbose, budget, halo, iceberg_halo, traj_sample_hrs, initial_mass, traj_write_hrs, &
          distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef, radial_damping_coef, tangental_damping_coef, &
          rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, &
@@ -537,6 +539,10 @@ subroutine ice_bergs_framework_init(bergs, &
      enddo
 endif 
 
+if (iceberg_halo .gt. halo) then
+    iceberg_halo=halo
+endif
+
 
  ! Parameters
   bergs%dt=dt
@@ -544,6 +550,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%traj_write_hrs=traj_write_hrs
   bergs%verbose_hrs=verbose_hrs
   bergs%grd%halo=halo
+  bergs%grd%iceberg_halo=iceberg_halo
   bergs%rho_bergs=rho_bergs
   bergs%spring_coef=spring_coef
   bergs%radial_damping_coef=radial_damping_coef
@@ -776,7 +783,7 @@ subroutine update_halo(bergs)
 integer :: halo_width
 integer :: temp1, temp2
   
-halo_width=2  ! Must be less than current halo value used for updating weight.
+halo_width=bergs%grd%iceberg_halo  ! Must be less than current halo value used for updating weight.
 
  ! Get the stderr unit number
    stderrunit = stderr()

From 2975d34f4b71fba40708ad64ce2843e3b0942542 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Fri, 18 Sep 2015 09:11:17 -0400
Subject: [PATCH 057/361] Added an if statement that only allows you to use
 interactive forces when you are using Verlet time stepping.

Interactive forces is now working, it seems
---
 icebergs.F90           | 2 --
 icebergs_framework.F90 | 3 +++
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 5afee1d..92a26c5 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -167,7 +167,6 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
 
   do grdj = berg%jne-1,berg%jne+1 ; do grdi = berg%ine-1,berg%ine+1
   other_berg=>bergs%list(grdi,grdj)%first
-
 !Note: This summing should be made order invarient. 
   do while (associated(other_berg)) ! loop over all other bergs  
        L2=other_berg%length
@@ -343,7 +342,6 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 use_new_predictive_corrective=.True.
 endif
 
-
 !print *, 'axn=',axn,'ayn=',ayn
   u_star=uvel0+(axn*(dt/2.))  !Alon
   v_star=vvel0+(ayn*(dt/2.))  !Alon
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index c4df69b..9c6ab83 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -543,6 +543,9 @@ subroutine ice_bergs_framework_init(bergs, &
     iceberg_halo=halo
 endif
 
+if (Runge_not_Verlet) then
+  interactive_icebergs_on=.false.  ! Iceberg interactions only with Verlet
+endif
 
  ! Parameters
   bergs%dt=dt

From 26517ea4b1cba54dc00d209c505bb1e69a1169af Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Fri, 18 Sep 2015 11:12:21 -0400
Subject: [PATCH 058/361] Fixed a bug in the loops inside halo_update_icebergs
 Changed the name of halo_update to halo_update_icebergs

---
 icebergs.F90           |  4 ++--
 icebergs_framework.F90 | 14 +++++++-------
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 92a26c5..427d529 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -30,7 +30,7 @@ module ice_bergs
 use ice_bergs_framework, only: sum_mass,sum_heat,bilin,yearday,count_bergs,bergs_chksum
 use ice_bergs_framework, only: checksum_gridded,add_new_berg_to_list
 use ice_bergs_framework, only: send_bergs_to_other_pes,move_trajectory,move_all_trajectories
-use ice_bergs_framework, only: move_berg_between_cells, update_halo
+use ice_bergs_framework, only: move_berg_between_cells, update_halo_icebergs
 use ice_bergs_framework, only: record_posn,check_position,print_berg,print_bergs,print_fld
 use ice_bergs_framework, only: add_new_berg_to_list,delete_iceberg_from_list,destroy_iceberg
 use ice_bergs_framework, only: grd_chksum2,grd_chksum3
@@ -1276,7 +1276,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   ! Send bergs to other PEs
   call mpp_clock_begin(bergs%clock_com)
   call send_bergs_to_other_pes(bergs)
-  call update_halo(bergs)
+  call update_halo_icebergs(bergs)
   if (debug) call bergs_chksum(bergs, 'run bergs (exchanged)')
   if (debug) call checksum_gridded(bergs%grd, 's/r run after exchange')
   call mpp_clock_end(bergs%clock_com)
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 9c6ab83..232f454 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -54,7 +54,7 @@ module ice_bergs_framework
 !Public subs
 public ice_bergs_framework_init
 public send_bergs_to_other_pes
-public update_halo
+public update_halo_icebergs
 public pack_berg_into_buffer2, unpack_berg_from_buffer2
 public pack_traj_into_buffer2, unpack_traj_from_buffer2
 public increase_buffer, increase_ibuffer, increase_ibuffer_traj, increase_buffer_traj
@@ -770,7 +770,7 @@ end subroutine move_berg_between_cells
 
 ! #############################################################################
 
-subroutine update_halo(bergs)
+subroutine update_halo_icebergs(bergs)
 ! Arguments
 type(icebergs), pointer :: bergs
 ! Local variables
@@ -831,7 +831,7 @@ subroutine update_halo(bergs)
   nbergs_to_send_w=0
 
   !Bergs on eastern side of the processor
-  do grdj = grd%jsc,grd%jec ; do grdi = grd%iec+1,grd%iec+halo_width  
+  do grdj = grd%jsc,grd%jec ; do grdi = grd%iec-halo_width+1,grd%iec  
     this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
         kick_the_bucket=>this
@@ -842,7 +842,7 @@ subroutine update_halo(bergs)
   enddo; enddo
 
   !Bergs on the western side of the processor
-  do grdj = grd%jsc,grd%jec ; do grdi = grd%isc-halo_width,grd%isc-1 
+  do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%isc+halo_width-1 
     do while (associated(this))
       kick_the_bucket=>this
       this=>this%next
@@ -913,7 +913,7 @@ subroutine update_halo(bergs)
   
 
   !Bergs on north side of the processor
-  do grdj = grd%jec-halo_width,grd%jec-1 ; do grdi = grd%isd,grd%ied
+  do grdj = grd%jec-halo_width+1,grd%jec ; do grdi = grd%isd,grd%ied
     do while (associated(this))
       kick_the_bucket=>this
       this=>this%next
@@ -924,7 +924,7 @@ subroutine update_halo(bergs)
 
 
   !Bergs on south side of the processor
-  do grdj = grd%jsc+1,grd%jsc+halo_width ; do grdi = grd%isd,grd%ied
+  do grdj = grd%jsc,grd%jsc+halo_width-1 ; do grdi = grd%isd,grd%ied
     do while (associated(this))
       kick_the_bucket=>this
       this=>this%next
@@ -1008,7 +1008,7 @@ subroutine update_halo(bergs)
   call mpp_sync_self()
 
 
-end subroutine update_halo
+end subroutine update_halo_icebergs
 
 
 

From 76b48fe7ddf3d23318fe86622bc65b72496d197d Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Fri, 18 Sep 2015 17:07:10 -0400
Subject: [PATCH 059/361] Adding iceberg_counter for each cell called
 iceberg_counter_grd. This counts the amount of icebergs created by each cell.

This has been added to the write restart.

I tried to add it to read restart, but it is not working yet.  (And now its time for the weekend)
---
 icebergs.F90           |  4 +++-
 icebergs_framework.F90 | 21 ++++++++++++++-------
 icebergs_io.F90        | 35 +++++++++++++++++++++++++++++++----
 3 files changed, 48 insertions(+), 12 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index d8326b9..84b987c 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -582,7 +582,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
     write(stderrunit,200) mpp_pe(),'Starting pars:', &
       'yr0=',berg%start_year, 'day0=',berg%start_day, &
       'lon0=',berg%start_lon, 'lat0=',berg%start_lat, 'mass0=',berg%start_mass, &
-      'sclng=',berg%mass_scaling
+      'sclng=',berg%mass_scaling, 'num0=',berg%iceberg_num
     write(stderrunit,100) mpp_pe(),'Geometry:', &
       'M=',M, 'T=',T, 'D=',D, 'F=',F, 'W=',W, 'L=',L
     write(stderrunit,100) mpp_pe(),'delta U:', &
@@ -1770,6 +1770,7 @@ subroutine calve_icebergs(bergs)
           newberg%start_lon=newberg%lon
           newberg%start_lat=newberg%lat
           newberg%start_year=bergs%current_year
+          newberg%iceberg_num=bergs%current_year !!!! ALon: MP: Change this!!
           newberg%start_day=bergs%current_yearday+ddt/86400.
           newberg%start_mass=bergs%initial_mass(k)
           newberg%mass_scaling=bergs%mass_scaling(k)
@@ -1789,6 +1790,7 @@ subroutine calve_icebergs(bergs)
           icnt=icnt+1
           bergs%nbergs_calved=bergs%nbergs_calved+1
           bergs%nbergs_calved_by_class(k)=bergs%nbergs_calved_by_class(k)+1
+          grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
         enddo
         icntmax=max(icntmax,icnt)
       enddo
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 30066d1..1ceb47d 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -15,7 +15,7 @@ module ice_bergs_framework
 
 implicit none ; private
 
-integer, parameter :: buffer_width=28 !Changed from 20 to 28 by Alon 
+integer, parameter :: buffer_width=29 !Changed from 20 to 29 by Alon 
 integer, parameter :: buffer_width_traj=31  !Changed from 23 by Alon
 integer, parameter :: nclasses=10 ! Number of ice bergs classes
 
@@ -115,6 +115,7 @@ module ice_bergs_framework
   real, dimension(:,:), pointer :: iceberg_heat_content=>null() ! Distributed heat content of bergs (J/m^2)
   real, dimension(:,:), pointer :: parity_x=>null() ! X component of vector point from i,j to i+1,j+1 (for detecting tri-polar fold)
   real, dimension(:,:), pointer :: parity_y=>null() ! Y component of vector point from i,j to i+1,j+1 (for detecting tri-polar fold)
+  integer, dimension(:,:), pointer :: iceberg_counter_grd=>null() ! Counts icebergs created for naming purposes
   ! Diagnostics handles
   integer :: id_uo=-1, id_vo=-1, id_calving=-1, id_stored_ice=-1, id_accum=-1, id_unused=-1, id_floating_melt=-1
   integer :: id_melt_buoy=-1, id_melt_eros=-1, id_melt_conv=-1, id_virtual_area=-1, id_real_calving=-1
@@ -133,7 +134,7 @@ module ice_bergs_framework
   real :: axn, ayn, bxn, byn, uvel_old, vvel_old, lat_old, lon_old  !Explicit and implicit accelerations !Alon 
   real :: uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, cn, hi
   real :: mass_of_bits, heat_density
-  integer :: year
+  integer :: year, iceberg_num
   type(xyt), pointer :: next=>null()
 end type xyt
 
@@ -145,6 +146,7 @@ module ice_bergs_framework
   real :: start_lon, start_lat, start_day, start_mass, mass_scaling
   real :: mass_of_bits, heat_density
   integer :: start_year
+  integer :: iceberg_num
   integer :: ine, jne ! nearest index in NE direction (for convenience)
   real :: xi, yj ! Non-dimensional coords within current cell (0..1)
   ! Environment variables (as seen by the iceberg)
@@ -419,6 +421,7 @@ subroutine ice_bergs_framework_init(bergs, &
   allocate( bergs%nbergs_calved_by_class(nclasses) ); bergs%nbergs_calved_by_class(:)=0
   allocate( grd%parity_x(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%parity_x(:,:)=1.
   allocate( grd%parity_y(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%parity_y(:,:)=1.
+  allocate( grd%iceberg_counter_grd(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%iceberg_counter_grd(:,:)=0
 
  !write(stderrunit,*) 'diamonds: copying grid'
   ! Copy data declared on ice model computational domain
@@ -983,6 +986,7 @@ subroutine pack_berg_into_buffer2(berg, buff, n)
     buff%data(26,n)=berg%vvel_old  !Alon
     buff%data(27,n)=berg%lon_old  !Alon
     buff%data(28,n)=berg%lat_old  !Alon
+    buff%data(29,n)=float(berg%iceberg_num)
 
   end subroutine pack_berg_into_buffer2
 
@@ -1066,6 +1070,7 @@ subroutine unpack_berg_from_buffer2(first, buff, n,grd, force_append)
     localberg%vvel_old=buff%data(26,n) !Alon
     localberg%lon_old=buff%data(27,n) !Alon
     localberg%lat_old=buff%data(28,n) !Alon
+    localberg%iceberg_num=nint(buff%data(29,n))
    
      lres=find_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
     if (lres) then
@@ -1440,7 +1445,7 @@ end subroutine insert_berg_into_list
 
 ! ##############################################################################
 
-logical function inorder(berg1, berg2)
+logical function inorder(berg1, berg2)  !MP Alon - Change to include iceberg_num
 ! Arguments
 type(iceberg), pointer :: berg1, berg2
 ! Local variables
@@ -1484,7 +1489,7 @@ end function inorder
 
 ! ##############################################################################
 
-  real function time_hash(berg)
+  real function time_hash(berg)!  Alon: Think about removing this.
   ! Arguments
   type(iceberg), pointer :: berg
     time_hash=berg%start_day+366.*float(berg%start_year)
@@ -1500,7 +1505,7 @@ end function pos_hash
 
 ! ##############################################################################
 
-logical function sameid(berg1, berg2)
+logical function sameid(berg1, berg2) !  Alon: MP updat this.
 ! Arguments
 type(iceberg), pointer :: berg1, berg2
 ! Local variables
@@ -1616,7 +1621,7 @@ subroutine print_berg(iochan, berg, label)
 
   write(iochan,'("diamonds, print_berg: ",a," pe=(",i3,") start lon,lat,yr,day,mass=",2f10.4,i5,f7.2,es12.4)') &
     label, mpp_pe(), berg%start_lon, berg%start_lat, &
-    berg%start_year, berg%start_day, berg%start_mass
+    berg%start_year, berg%iceberg_num, berg%start_day, berg%start_mass
   write(iochan,'("diamonds, print_berg: ",a," pe=(",i3,a,2i5,3(a,2f10.4),a,2l2)') &
     label, mpp_pe(), ') i,j=',berg%ine, berg%jne, &
     ' xi,yj=', berg%xi, berg%yj, &
@@ -1779,6 +1784,7 @@ subroutine move_trajectory(bergs, berg)
   vals%lon=berg%start_lon
   vals%lat=berg%start_lat
   vals%year=berg%start_year
+  vals%iceberg_num=berg%iceberg_num
   vals%day=berg%start_day
   vals%mass=berg%start_mass
   call push_posn(berg%trajectory, vals)
@@ -2871,9 +2877,10 @@ integer function berg_chksum(berg )
   itmp(37)=berg%start_year !Changed from 29 to 37 by Alon
   itmp(38)=berg%ine !Changed from 30 to 38 by Alon
   itmp(39)=berg%jne !Changed from 31 to 39 by Alon
+  itmp(40)=berg%iceberg_num !added  by Alon
 
   ichk1=0; ichk2=0; ichk3=0
-  do i=1,36+3 !Changd from 28 to 36 by Alon
+  do i=1,37+3 !Changd from 28 to 37 by Alon
    ichk1=ichk1+itmp(i)
    ichk2=ichk2+itmp(i)*i
    ichk3=ichk3+itmp(i)*i*i
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 5017f67..2e93e75 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -99,7 +99,7 @@ subroutine write_restart(bergs)
 ! Arguments
 type(icebergs), pointer :: bergs
 ! Local variables
-integer :: i,id
+integer :: i,j,id
 character(len=35) :: filename
 type(iceberg), pointer :: this=>NULL()
 integer :: stderrunit
@@ -134,7 +134,10 @@ subroutine write_restart(bergs)
 
 integer, allocatable, dimension(:) :: ine,       &
                                       jne,       &
+                                      iceberg_num,       &
                                       start_year
+
+
 !uvel_old, vvel_old, lon_old, lat_old, axn, ayn, bxn, byn added by Alon.
   
 ! Get the stderr unit number
@@ -184,6 +187,7 @@ subroutine write_restart(bergs)
    allocate(ine(nbergs))
    allocate(jne(nbergs))
    allocate(start_year(nbergs))
+   allocate(iceberg_num(nbergs))
 
   call get_instance_filename("icebergs.res.nc", filename)
   call set_domain(bergs%grd%domain)
@@ -219,6 +223,8 @@ subroutine write_restart(bergs)
                                             longname='latitude of calving location',units='degrees_N')
   id = register_restart_field(bergs_restart,filename,'start_year',start_year, &
                                             longname='calendar year of calving event', units='years')
+  id = register_restart_field(bergs_restart,filename,'iceberg_num',iceberg_num, &
+                                            longname='identification of the iceberg', units='years')
   id = register_restart_field(bergs_restart,filename,'start_day',start_day, &
                                             longname='year day of calving event',units='days')
   id = register_restart_field(bergs_restart,filename,'start_mass',start_mass, &
@@ -245,11 +251,13 @@ subroutine write_restart(bergs)
     width(i) = this%width; length(i) = this%length
     start_lon(i) = this%start_lon; start_lat(i) = this%start_lat
     start_year(i) = this%start_year; start_day(i) = this%start_day
+    iceberg_num(i) = this%iceberg_num; 
     start_mass(i) = this%start_mass; mass_scaling(i) = this%mass_scaling
     mass_of_bits(i) = this%mass_of_bits; heat_density(i) = this%heat_density
     this=>this%next
   enddo
-    
+   
+
   call save_restart(bergs_restart)
   call free_restart_type(bergs_restart)
 
@@ -282,8 +290,10 @@ subroutine write_restart(bergs)
   deallocate(           &
              ine,       &
              jne,       &
+             iceberg_num,       &
              start_year )
 
+
   call nullify_domain()
 
   ! Write stored ice
@@ -294,7 +304,8 @@ subroutine write_restart(bergs)
   call write_data(filename, 'stored_ice', bergs%grd%stored_ice, bergs%grd%domain)
   call grd_chksum2(bergs%grd, bergs%grd%stored_heat, 'write stored_heat')
   call write_data(filename, 'stored_heat', bergs%grd%stored_heat, bergs%grd%domain)
-
+  !call grd_chksum2(bergs%grd, bergs%grd%iceberg_counter_grd, 'write iceberg_counter_grd')
+  call write_data(filename, 'iceberg_counter_grd', bergs%grd%iceberg_counter_grd, bergs%grd%domain)
   contains
 
   function last_berg(berg)
@@ -323,7 +334,7 @@ subroutine read_restart_bergs_orig(bergs,Time)
 integer :: lonid, latid,  uvelid, vvelid, ineid, jneid
 integer :: axnid, aynid, uvel_oldid, vvel_oldid, bxnid, bynid, lon_oldid, lat_oldid !Added by Alon
 integer :: massid, thicknessid, widthid, lengthid
-integer :: start_lonid, start_latid, start_yearid, start_dayid, start_massid
+integer :: start_lonid, start_latid, start_yearid, iceberg_numid, start_dayid, start_massid
 integer :: scaling_id, mass_of_bits_id, heat_density_id
 logical :: lres, found_restart, multiPErestart
 real :: lon0, lon1, lat0, lat1
@@ -398,6 +409,7 @@ subroutine read_restart_bergs_orig(bergs,Time)
   start_lonid=inq_var(ncid, 'start_lon')
   start_latid=inq_var(ncid, 'start_lat')
   start_yearid=inq_var(ncid, 'start_year')
+  iceberg_numid=inq_var(ncid, 'icberg_num')
   start_dayid=inq_var(ncid, 'start_day')
   start_massid=inq_var(ncid, 'start_mass')
   scaling_id=inq_var(ncid, 'mass_scaling')
@@ -455,6 +467,7 @@ subroutine read_restart_bergs_orig(bergs,Time)
       localberg%start_lon=get_double(ncid, start_lonid, k)
       localberg%start_lat=get_double(ncid, start_latid, k)
       localberg%start_year=get_int(ncid, start_yearid, k)
+      localberg%iceberg_num=get_int(ncid, iceberg_numid, k)
       localberg%start_day=get_double(ncid, start_dayid, k)
       localberg%start_mass=get_double(ncid, start_massid, k)
       localberg%mass_scaling=get_double(ncid, scaling_id, k)
@@ -541,6 +554,7 @@ subroutine generate_bergs(bergs,Time)
         localberg%start_lon=localberg%lon
         localberg%start_lat=localberg%lat
         localberg%start_year=iyr
+        localberg%iceberg_num=iyr   !MP1!!!!Insert complex formulae here! Alon
         localberg%start_day=float(iday)+(float(ihr)+float(imin)/60.)/24.
         localberg%start_mass=localberg%mass
         localberg%mass_scaling=bergs%mass_scaling(1)
@@ -636,8 +650,11 @@ subroutine read_restart_bergs(bergs,Time)
 !axn, ayn, uvel_old, vvel_old, lon_old, lat_old, bxn, byn added by Alon
 integer, allocatable, dimension(:) :: ine,       &
                                       jne,       &
+                                      iceberg_num,       &
                                       start_year
 
+!integer, allocatable, dimension(:,:) :: iceberg_counter_gre
+
   ! Get the stderr unit number
   stderrunit=stderr()
 
@@ -684,6 +701,7 @@ subroutine read_restart_bergs(bergs,Time)
      allocate(ine(nbergs_in_file))
      allocate(jne(nbergs_in_file))
      allocate(start_year(nbergs_in_file))
+     allocate(iceberg_num(nbergs_in_file))
 
      call read_unlimited_axis(filename,'lon',lon,domain=grd%domain)
      call read_unlimited_axis(filename,'lat',lat,domain=grd%domain)
@@ -712,6 +730,7 @@ subroutine read_restart_bergs(bergs,Time)
      call read_unlimited_axis(filename,'ine',ine,domain=grd%domain)
      call read_unlimited_axis(filename,'jne',jne,domain=grd%domain)
      call read_unlimited_axis(filename,'start_year',start_year,domain=grd%domain)
+     call read_unlimited_axis(filename,'iceberg_num',iceberg_num,domain=grd%domain)
 
      ! Find approx outer bounds for tile
      lon0=minval( grd%lon(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
@@ -760,6 +779,7 @@ subroutine read_restart_bergs(bergs,Time)
          localberg%start_lon=start_lon(k)
          localberg%start_lat=start_lat(k)
          localberg%start_year=start_year(k)
+         localberg%iceberg_num=iceberg_num(k)
          localberg%start_day=start_day(k)
          localberg%start_mass=start_mass(k)
          localberg%mass_scaling=mass_scaling(k)
@@ -802,6 +822,7 @@ subroutine read_restart_bergs(bergs,Time)
      deallocate(           &
                 ine,       &
                 jne,       &
+                iceberg_num,       &
                 start_year )
   elseif(.not. found_restart .and. bergs%nbergs_start==0 .and. generate_test_icebergs) then
      call generate_bergs(bergs,Time)
@@ -848,6 +869,7 @@ subroutine generate_bergs(bergs,Time)
         localberg%start_lon=localberg%lon
         localberg%start_lat=localberg%lat
         localberg%start_year=iyr
+        localberg%iceberg_num=iyr !Alon: MP2: insert complex formulae here!!
         localberg%start_day=float(iday)+(float(ihr)+float(imin)/60.)/24.
         localberg%start_mass=localberg%mass
         localberg%mass_scaling=bergs%mass_scaling(1)
@@ -926,10 +948,15 @@ subroutine read_restart_calving(bergs)
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
        'diamonds, read_restart_calving: reading stored_heat from restart file.'
       call read_data(filename, 'stored_heat', grd%stored_heat, grd%domain)
+                if (field_exist(filename, 'iceberg_counting_grd')) then
+                        print *, 'field exitst!!!'
+                    !call read_data(filename, 'iceberg_counting_grd', grd%iceberg_counting_grd, grd%domain) ! - why does this not work???
+                endif
     else
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
      'diamonds, read_restart_calving: stored_heat WAS NOT FOUND in the file. Setting to 0.'
       grd%stored_heat(:,:)=0.
+      grd%iceberg_counter_grd(:,:)=0
     endif
     bergs%restarted=.true.
   else

From 7d000ed2bbaf7b96c35ccd95ee3534a03d3ac17d Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Mon, 21 Sep 2015 11:47:55 -0400
Subject: [PATCH 060/361] Added a unique numbering for each iceberg. This
 number is called iceberg_num and is saved in the restart file, picksup from
 the restart file.

The iceberg counter is now working and is saved as a gridded variable which saves to the restart file, and picksup from the restart.

The iceberg num is not yet saved in the iceberg trajectory file.
---
 icebergs.F90           |  9 +++++++--
 icebergs_framework.F90 | 10 +++++++++-
 icebergs_io.F90        | 38 +++++++++++++++++++++++++++++++-------
 3 files changed, 47 insertions(+), 10 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 84b987c..14f076a 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -97,6 +97,7 @@ subroutine icebergs_init(bergs, &
 
   call mpp_clock_begin(bergs%clock_ior)
   call ice_bergs_io_init(bergs,io_layout)
+  call read_restart_calving(bergs)  !This is moved to before restart_bergs (by Alon) so that generate icebergs can have the correct counter
   if(orig_read) then
      call read_restart_bergs_orig(bergs,Time)
   else
@@ -104,7 +105,7 @@ subroutine icebergs_init(bergs, &
   endif
   call bergs_chksum(bergs, 'read_restart bergs')
   if (fix_restart_dates) call offset_berg_dates(bergs,Time)
-  call read_restart_calving(bergs)
+  !call read_restart_calving(bergs)
   call mpp_clock_end(bergs%clock_ior)
 
   if (really_debug) call print_bergs(stderrunit,bergs,'icebergs_init, initial status')
@@ -1720,6 +1721,7 @@ subroutine calve_icebergs(bergs)
 ! Local variables
 type(icebergs_gridded), pointer :: grd
 integer :: i,j,k,icnt,icntmax
+integer :: iNg, jNg  !Total number of points gloablly in i and j direction
 type(iceberg) :: newberg
 logical :: lret
 real :: xi, yj, ddt, calving_to_bergs, calved_to_berg, heat_to_bergs, heat_to_berg
@@ -1731,6 +1733,9 @@ subroutine calve_icebergs(bergs)
   ! For convenience
   grd=>bergs%grd
 
+  iNg=(grd%ieg-grd%isg+1) ! Total number of points globally in i direction
+  jNg=(grd%jeg-grd%jsg+1) ! Total number of points globally in j direction
+
   grd%real_calving(:,:,:)=0.
   calving_to_bergs=0.
   heat_to_bergs=0.
@@ -1770,7 +1775,7 @@ subroutine calve_icebergs(bergs)
           newberg%start_lon=newberg%lon
           newberg%start_lat=newberg%lat
           newberg%start_year=bergs%current_year
-          newberg%iceberg_num=bergs%current_year !!!! ALon: MP: Change this!!
+          newberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i+(iNg*(j-1)))  ! unique number for each iceberg
           newberg%start_day=bergs%current_yearday+ddt/86400.
           newberg%start_mass=bergs%initial_mass(k)
           newberg%mass_scaling=bergs%mass_scaling(k)
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 1ceb47d..fafa43d 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -72,6 +72,7 @@ module ice_bergs_framework
   integer :: halo ! Nominal halo width
   integer :: isc, iec, jsc, jec ! Indices of computational domain
   integer :: isd, ied, jsd, jed ! Indices of data domain
+  integer :: isg, ieg, jsg, jeg ! Indices of global domain
   integer :: my_pe, pe_N, pe_S, pe_E, pe_W ! MPI PE identifiers
   real, dimension(:,:), pointer :: lon=>null() ! Longitude of cell corners
   real, dimension(:,:), pointer :: lat=>null() ! Latitude of cell corners
@@ -236,7 +237,7 @@ subroutine ice_bergs_framework_init(bergs, &
 
 use mpp_parameter_mod, only: SCALAR_PAIR, CGRID_NE, BGRID_NE, CORNER, AGRID
 use mpp_domains_mod, only: mpp_update_domains, mpp_define_domains
-use mpp_domains_mod, only: mpp_get_compute_domain, mpp_get_data_domain
+use mpp_domains_mod, only: mpp_get_compute_domain, mpp_get_data_domain, mpp_get_global_domain
 use mpp_domains_mod, only: CYCLIC_GLOBAL_DOMAIN, FOLD_NORTH_EDGE
 use mpp_domains_mod, only: mpp_get_neighbor_pe, NORTH, SOUTH, EAST, WEST
 use mpp_domains_mod, only: mpp_define_io_domain
@@ -362,12 +363,14 @@ subroutine ice_bergs_framework_init(bergs, &
  !write(stderrunit,*) 'diamond: get compute domain'
   call mpp_get_compute_domain( grd%domain, grd%isc, grd%iec, grd%jsc, grd%jec )
   call mpp_get_data_domain( grd%domain, grd%isd, grd%ied, grd%jsd, grd%jed )
+  call mpp_get_global_domain( grd%domain, grd%isg, grd%ieg, grd%jsg, grd%jeg )
 
   call mpp_get_neighbor_pe(grd%domain, NORTH, grd%pe_N)
   call mpp_get_neighbor_pe(grd%domain, SOUTH, grd%pe_S)
   call mpp_get_neighbor_pe(grd%domain, EAST, grd%pe_E)
   call mpp_get_neighbor_pe(grd%domain, WEST, grd%pe_W)
 
+
   folded_north_on_pe = ((dom_y_flags == FOLD_NORTH_EDGE) .and. (grd%jec == gnj)) 
  !write(stderrunit,'(a,6i4)') 'diamonds, icebergs_init: pe,n,s,e,w =',mpp_pe(),grd%pe_N,grd%pe_S,grd%pe_E,grd%pe_W, NULL_PE
 
@@ -663,6 +666,10 @@ subroutine ice_bergs_framework_init(bergs, &
   call mpp_clock_end(bergs%clock_ini)
   call mpp_clock_end(bergs%clock)
 
+!print *, mpp_pe(), 'Alon: global', grd%isg, grd%ieg, grd%jsg, grd%jeg
+!print *, mpp_pe(), 'Alon: comp', grd%isc, grd%iec, grd%jsc, grd%jec
+!print *, mpp_pe(), 'Alon: data', grd%isd, grd%ied, grd%jsd, grd%jed
+
 end subroutine ice_bergs_framework_init
 
 ! ##############################################################################
@@ -1578,6 +1585,7 @@ subroutine create_iceberg(berg, bergvals)
 
 end subroutine create_iceberg
 
+
 ! ##############################################################################
 
 subroutine delete_iceberg_from_list(first, berg)
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 2e93e75..53df911 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -529,11 +529,14 @@ subroutine generate_bergs(bergs,Time)
   type(time_type), intent(in) :: Time
   ! Local variables
   integer :: i,j
+  integer :: iNg, jNg  !Total number of points gloablly in i and j direction
   type(iceberg) :: localberg ! NOT a pointer but an actual local variable
   integer :: iyr, imon, iday, ihr, imin, isec
 
     ! For convenience
     grd=>bergs%grd
+    iNg=(grd%ieg-grd%isg+1) ! Total number of points globally in i direction
+    jNg=(grd%jeg-grd%jsg+1) ! Total number of points globally in j direction
 
     call get_date(Time, iyr, imon, iday, ihr, imin, isec)
 
@@ -554,7 +557,6 @@ subroutine generate_bergs(bergs,Time)
         localberg%start_lon=localberg%lon
         localberg%start_lat=localberg%lat
         localberg%start_year=iyr
-        localberg%iceberg_num=iyr   !MP1!!!!Insert complex formulae here! Alon
         localberg%start_day=float(iday)+(float(ihr)+float(imin)/60.)/24.
         localberg%start_mass=localberg%mass
         localberg%mass_scaling=bergs%mass_scaling(1)
@@ -568,6 +570,8 @@ subroutine generate_bergs(bergs,Time)
         localberg%vvel_old=0. !Alon
         localberg%bxn=0. !Alon
         localberg%byn=0. !Alon
+        localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
+        grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
         call add_new_berg_to_list(bergs%first, localberg)
         localberg%uvel=-1.
         localberg%vvel=0.
@@ -577,6 +581,8 @@ subroutine generate_bergs(bergs,Time)
         localberg%vvel_old=0. !Alon
         localberg%bxn=0. !Alon
         localberg%byn=0. !Alon
+        localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
+        grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
         call add_new_berg_to_list(bergs%first, localberg)
         localberg%uvel=0.
         localberg%vvel=1.
@@ -586,6 +592,8 @@ subroutine generate_bergs(bergs,Time)
         localberg%vvel_old=0. !Alon
         localberg%bxn=0. !Alon
         localberg%byn=0. !Alon
+        localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
+        grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
         call add_new_berg_to_list(bergs%first, localberg)
         localberg%uvel=0.
         localberg%vvel=-1.
@@ -595,6 +603,8 @@ subroutine generate_bergs(bergs,Time)
         localberg%vvel_old=0. !Alon
         localberg%bxn=0. !Alon
         localberg%byn=0. !Alon
+        localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
+        grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
         call add_new_berg_to_list(bergs%first, localberg)
       endif
     enddo; enddo
@@ -653,7 +663,7 @@ subroutine read_restart_bergs(bergs,Time)
                                       iceberg_num,       &
                                       start_year
 
-!integer, allocatable, dimension(:,:) :: iceberg_counter_gre
+!integer, allocatable, dimension(:,:) :: iceberg_counter_grd
 
   ! Get the stderr unit number
   stderrunit=stderr()
@@ -844,11 +854,14 @@ subroutine generate_bergs(bergs,Time)
   type(time_type), intent(in) :: Time
   ! Local variables
   integer :: i,j
+  integer :: iNg, jNg  !Total number of points gloablly in i and j direction
   type(iceberg) :: localberg ! NOT a pointer but an actual local variable
   integer :: iyr, imon, iday, ihr, imin, isec
 
     ! For convenience
     grd=>bergs%grd
+    iNg=(grd%ieg-grd%isg+1) ! Total number of points globally in i direction
+    jNg=(grd%jeg-grd%jsg+1) ! Total number of points globally in j direction
 
     call get_date(Time, iyr, imon, iday, ihr, imin, isec)
 
@@ -869,7 +882,6 @@ subroutine generate_bergs(bergs,Time)
         localberg%start_lon=localberg%lon
         localberg%start_lat=localberg%lat
         localberg%start_year=iyr
-        localberg%iceberg_num=iyr !Alon: MP2: insert complex formulae here!!
         localberg%start_day=float(iday)+(float(ihr)+float(imin)/60.)/24.
         localberg%start_mass=localberg%mass
         localberg%mass_scaling=bergs%mass_scaling(1)
@@ -883,6 +895,8 @@ subroutine generate_bergs(bergs,Time)
         localberg%vvel_old=0. !Alon
         localberg%bxn=0. !Alon
         localberg%byn=0. !Alon
+        localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
+        grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
         call add_new_berg_to_list(bergs%first, localberg)
         localberg%uvel=-1.
         localberg%vvel=0.
@@ -892,6 +906,8 @@ subroutine generate_bergs(bergs,Time)
         localberg%vvel_old=0. !Alon
         localberg%bxn=0. !Alon
         localberg%byn=0. !Alon
+        localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
+        grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
         call add_new_berg_to_list(bergs%first, localberg)
         localberg%uvel=0.
         localberg%vvel=1.
@@ -901,6 +917,8 @@ subroutine generate_bergs(bergs,Time)
         localberg%vvel_old=0. !Alon
         localberg%bxn=0. !Alon
         localberg%byn=0. !Alon
+        localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
+        grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
         call add_new_berg_to_list(bergs%first, localberg)
         localberg%uvel=0.
         localberg%vvel=-1.
@@ -910,6 +928,8 @@ subroutine generate_bergs(bergs,Time)
         localberg%vvel_old=0. !Alon
         localberg%bxn=0. !Alon
         localberg%byn=0. !Alon
+        localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
+        grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
         call add_new_berg_to_list(bergs%first, localberg)
       endif
     enddo; enddo
@@ -948,14 +968,18 @@ subroutine read_restart_calving(bergs)
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
        'diamonds, read_restart_calving: reading stored_heat from restart file.'
       call read_data(filename, 'stored_heat', grd%stored_heat, grd%domain)
-                if (field_exist(filename, 'iceberg_counting_grd')) then
-                        print *, 'field exitst!!!'
-                    !call read_data(filename, 'iceberg_counting_grd', grd%iceberg_counting_grd, grd%domain) ! - why does this not work???
-                endif
     else
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
      'diamonds, read_restart_calving: stored_heat WAS NOT FOUND in the file. Setting to 0.'
       grd%stored_heat(:,:)=0.
+    endif
+    if (field_exist(filename, 'iceberg_counter_grd')) then
+      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+       'diamonds, read_restart_calving: reading iceberg_counter_grd from restart file.'
+      call read_data(filename, 'iceberg_counter_grd', grd%iceberg_counter_grd, grd%domain) 
+    else
+      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+     'diamonds, read_restart_calving: iceberg_counter_grd WAS NOT FOUND in the file. Setting to 0.'
       grd%iceberg_counter_grd(:,:)=0
     endif
     bergs%restarted=.true.

From 8c0eb53ab70257151b06e30db0848f63c8540f74 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Mon, 21 Sep 2015 13:49:10 -0400
Subject: [PATCH 061/361] Iceberg_num now outputs into the
 iceberg_trajectory.nc file

---
 icebergs_framework.F90 | 6 ++++--
 icebergs_io.F90        | 9 +++++++--
 2 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index fafa43d..f62d13f 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -16,7 +16,7 @@ module ice_bergs_framework
 implicit none ; private
 
 integer, parameter :: buffer_width=29 !Changed from 20 to 29 by Alon 
-integer, parameter :: buffer_width_traj=31  !Changed from 23 by Alon
+integer, parameter :: buffer_width_traj=32  !Changed from 23 by Alon
 integer, parameter :: nclasses=10 ! Number of ice bergs classes
 
 !Local Vars
@@ -424,7 +424,7 @@ subroutine ice_bergs_framework_init(bergs, &
   allocate( bergs%nbergs_calved_by_class(nclasses) ); bergs%nbergs_calved_by_class(:)=0
   allocate( grd%parity_x(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%parity_x(:,:)=1.
   allocate( grd%parity_y(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%parity_y(:,:)=1.
-  allocate( grd%iceberg_counter_grd(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%iceberg_counter_grd(:,:)=0
+  allocate( grd%iceberg_counter_grd(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%iceberg_counter_grd(:,:)=1
 
  !write(stderrunit,*) 'diamonds: copying grid'
   ! Copy data declared on ice model computational domain
@@ -1248,6 +1248,7 @@ subroutine pack_traj_into_buffer2(traj, buff, n)
     buff%data(29,n)=traj%vvel_old !Alon
     buff%data(30,n)=traj%lon_old !Alon
     buff%data(31,n)=traj%lat_old !Alon
+    buff%data(32,n)=float(traj%iceberg_num)
 
   end subroutine pack_traj_into_buffer2
 
@@ -1293,6 +1294,7 @@ subroutine unpack_traj_from_buffer2(first, buff, n)
     traj%vvel_old=buff%data(29,n) !Alon
     traj%lon_old=buff%data(30,n) !Alon
     traj%lat_old=buff%data(31,n) !Alon
+    traj%iceberg_num=nint(buff%data(32,n))
 
     call append_posn(first, traj)
 
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 53df911..9ad4b85 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -224,7 +224,7 @@ subroutine write_restart(bergs)
   id = register_restart_field(bergs_restart,filename,'start_year',start_year, &
                                             longname='calendar year of calving event', units='years')
   id = register_restart_field(bergs_restart,filename,'iceberg_num',iceberg_num, &
-                                            longname='identification of the iceberg', units='years')
+                                            longname='identification of the iceberg', units='dimensionless')
   id = register_restart_field(bergs_restart,filename,'start_day',start_day, &
                                             longname='year day of calving event',units='days')
   id = register_restart_field(bergs_restart,filename,'start_mass',start_mass, &
@@ -1030,7 +1030,7 @@ subroutine write_trajectory(trajectory)
 type(xyt), pointer :: trajectory
 ! Local variables
 integer :: iret, ncid, i_dim, i
-integer :: lonid, latid, yearid, dayid, uvelid, vvelid
+integer :: lonid, latid, yearid, dayid, uvelid, vvelid, iceberg_numid
 !integer :: axnid, aynid, uvel_oldid, vvel_oldid, lat_oldid, lon_oldid, bxnid, bynid !Added by Alon 
 integer :: uoid, void, uiid, viid, uaid, vaid, sshxid, sshyid, sstid
 integer :: cnid, hiid
@@ -1170,6 +1170,7 @@ subroutine write_trajectory(trajectory)
       sstid = inq_varid(ncid, 'sst')
       cnid = inq_varid(ncid, 'cn')
       hiid = inq_varid(ncid, 'hi')
+      iceberg_numid = inq_varid(ncid, 'iceberg_num')
     else
       ! Dimensions
       iret = nf_def_dim(ncid, 'i', NF_UNLIMITED, i_dim)
@@ -1199,6 +1200,7 @@ subroutine write_trajectory(trajectory)
       sstid = def_var(ncid, 'sst', NF_DOUBLE, i_dim)
       cnid = def_var(ncid, 'cn', NF_DOUBLE, i_dim)
       hiid = def_var(ncid, 'hi', NF_DOUBLE, i_dim)
+      iceberg_numid = def_var(ncid, 'iceberg_num', NF_INT, i_dim)
 
       ! Attributes
       iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_major_version', NF_INT, 1, 0)
@@ -1249,6 +1251,8 @@ subroutine write_trajectory(trajectory)
       call put_att(ncid, cnid, 'units', 'none')
       call put_att(ncid, hiid, 'long_name', 'sea ice thickness')
       call put_att(ncid, hiid, 'units', 'm')
+      call put_att(ncid, iceberg_numid, 'long_name', 'iceberg id number')
+      call put_att(ncid, iceberg_numid, 'units', 'dimensionless')
     endif
 
     ! End define mode
@@ -1286,6 +1290,7 @@ subroutine write_trajectory(trajectory)
       call put_double(ncid, sstid, i, this%sst)
       call put_double(ncid, cnid, i, this%cn)
       call put_double(ncid, hiid, i, this%hi)
+      call put_int(ncid, iceberg_numid, i, this%iceberg_num)
       next=>this%next
       deallocate(this)
       this=>next

From 0c6591e98e5e7d7348a7eb5e4e21e9a0b0c64aac Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Tue, 22 Sep 2015 11:44:02 -0400
Subject: [PATCH 062/361] Fixed two bugs in halo_update scheme:

1) Editted the delete_all_icebergs_in_list subroutine, to make it point the first pointer to null.

2)Added a variable called halo_iceberg, which is a flag that says whether an iceberg is a temporary iceberg copied to a halo. This prevents the temporary icebergs begin copied back the orginal processor, which causes icebergs to multiply over and over again.
---
 icebergs.F90           |   1 +
 icebergs_framework.F90 | 113 ++++++++++++++++++++++++++---------------
 icebergs_io.F90        |  17 ++++++-
 3 files changed, 88 insertions(+), 43 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 427d529..5867342 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1780,6 +1780,7 @@ subroutine calve_icebergs(bergs)
           newberg%start_mass=bergs%initial_mass(k)
           newberg%mass_scaling=bergs%mass_scaling(k)
           newberg%mass_of_bits=0.
+          newberg%halo_berg=0.
           newberg%heat_density=grd%stored_heat(i,j)/grd%stored_ice(i,j,k) ! This is in J/kg
           call add_new_berg_to_list(bergs%list(i,j)%first, newberg)
           calved_to_berg=bergs%initial_mass(k)*bergs%mass_scaling(k) ! Units of kg
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 232f454..a09745a 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -15,8 +15,8 @@ module ice_bergs_framework
 
 implicit none ; private
 
-integer, parameter :: buffer_width=28 !Changed from 20 to 28 by Alon 
-integer, parameter :: buffer_width_traj=31  !Changed from 23 by Alon
+integer, parameter :: buffer_width=29 !Changed from 20 to 29 by Alon 
+integer, parameter :: buffer_width_traj=32  !Changed from 23 by Alon
 integer, parameter :: nclasses=10 ! Number of ice bergs classes
 
 !Local Vars
@@ -134,7 +134,7 @@ module ice_bergs_framework
   real :: lon, lat, day
   real :: mass, thickness, width, length, uvel, vvel
   real :: axn, ayn, bxn, byn, uvel_old, vvel_old, lat_old, lon_old  !Explicit and implicit accelerations !Alon 
-  real :: uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, cn, hi
+  real :: uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, cn, hi, halo_berg
   real :: mass_of_bits, heat_density
   integer :: year
   type(xyt), pointer :: next=>null()
@@ -147,6 +147,7 @@ module ice_bergs_framework
   real :: axn, ayn, bxn, byn, uvel_old, vvel_old, lon_old, lat_old !Explicit and implicit accelerations !Alon 
   real :: start_lon, start_lat, start_day, start_mass, mass_scaling
   real :: mass_of_bits, heat_density
+  real :: halo_berg  ! Equal to zero for bergs on computational domain, and =1 for bergs on the halo
   integer :: start_year
   integer :: ine, jne ! nearest index in NE direction (for convenience)
   real :: xi, yj ! Non-dimensional coords within current cell (0..1)
@@ -785,6 +786,7 @@ subroutine update_halo_icebergs(bergs)
 integer :: grdi, grdj
 integer :: halo_width
 integer :: temp1, temp2
+real :: current_halo_status
   
 halo_width=bergs%grd%iceberg_halo  ! Must be less than current halo value used for updating weight.
 
@@ -837,7 +839,10 @@ subroutine update_halo_icebergs(bergs)
         kick_the_bucket=>this
         this=>this%next
         nbergs_to_send_e=nbergs_to_send_e+1
+        current_halo_status=kick_the_bucket%halo_berg
+        kick_the_bucket%halo_berg=1.
         call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_e, nbergs_to_send_e)
+        kick_the_bucket%halo_berg=current_halo_status
     enddo
   enddo; enddo
 
@@ -847,7 +852,10 @@ subroutine update_halo_icebergs(bergs)
       kick_the_bucket=>this
       this=>this%next
       nbergs_to_send_w=nbergs_to_send_w+1
-    call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_w, nbergs_to_send_w)
+       current_halo_status=kick_the_bucket%halo_berg
+       kick_the_bucket%halo_berg=1.
+       call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_w, nbergs_to_send_w)
+       kick_the_bucket%halo_berg=current_halo_status
     enddo 
   enddo; enddo
 
@@ -918,7 +926,10 @@ subroutine update_halo_icebergs(bergs)
       kick_the_bucket=>this
       this=>this%next
       nbergs_to_send_n=nbergs_to_send_n+1
+      current_halo_status=kick_the_bucket%halo_berg
+      kick_the_bucket%halo_berg=1.
       call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_n, nbergs_to_send_n)
+      kick_the_bucket%halo_berg=current_halo_status
     enddo
   enddo; enddo
 
@@ -929,7 +940,10 @@ subroutine update_halo_icebergs(bergs)
       kick_the_bucket=>this
       this=>this%next
       nbergs_to_send_s=nbergs_to_send_s+1
-      call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_s, nbergs_to_send_s)
+       current_halo_status=kick_the_bucket%halo_berg
+       kick_the_bucket%halo_berg=1.
+       call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_s, nbergs_to_send_s)
+       kick_the_bucket%halo_berg=current_halo_status
     enddo
   enddo; enddo
 
@@ -1026,6 +1040,7 @@ subroutine delete_all_bergs_in_list(bergs,grdj,grdi)
     call destroy_iceberg(kick_the_bucket)
 !    call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
   enddo
+  bergs%list(grdi,grdj)%first=>null()
 end  subroutine delete_all_bergs_in_list
 
 
@@ -1062,22 +1077,26 @@ subroutine send_bergs_to_other_pes(bergs)
   do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
     this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
-      if (this%ine.gt.bergs%grd%iec) then
-        kick_the_bucket=>this
-        this=>this%next
-        nbergs_to_send_e=nbergs_to_send_e+1
-        call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_e, nbergs_to_send_e)
-        call move_trajectory(bergs, kick_the_bucket)
-        call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
-      elseif (this%ine.lt.bergs%grd%isc) then
-        kick_the_bucket=>this
-        this=>this%next
-        nbergs_to_send_w=nbergs_to_send_w+1
-        call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_w, nbergs_to_send_w)
-        call move_trajectory(bergs, kick_the_bucket)
-        call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
+      if (this%halo_berg .lt. 0.5) then
+        if (this%ine.gt.bergs%grd%iec) then
+          kick_the_bucket=>this
+          this=>this%next
+          nbergs_to_send_e=nbergs_to_send_e+1
+          call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_e, nbergs_to_send_e)
+          call move_trajectory(bergs, kick_the_bucket)
+          call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
+        elseif (this%ine.lt.bergs%grd%isc) then
+          kick_the_bucket=>this
+          this=>this%next
+          nbergs_to_send_w=nbergs_to_send_w+1
+          call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_w, nbergs_to_send_w)
+          call move_trajectory(bergs, kick_the_bucket)
+          call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
+        else
+          this=>this%next
+        endif
       else
-        this=>this%next
+         this=>this%next
       endif
     enddo
   enddo ; enddo
@@ -1143,22 +1162,26 @@ subroutine send_bergs_to_other_pes(bergs)
   do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
     this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
-      if (this%jne.gt.bergs%grd%jec) then
-        kick_the_bucket=>this
-        this=>this%next
-        nbergs_to_send_n=nbergs_to_send_n+1
-        call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_n, nbergs_to_send_n)
-        call move_trajectory(bergs, kick_the_bucket)
-        call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
-      elseif (this%jne.lt.bergs%grd%jsc) then
-        kick_the_bucket=>this
-        this=>this%next
-        nbergs_to_send_s=nbergs_to_send_s+1
-        call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_s, nbergs_to_send_s)
-        call move_trajectory(bergs, kick_the_bucket)
-        call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
+      if (this%halo_berg .lt. 0.5) then
+        if (this%jne.gt.bergs%grd%jec) then
+          kick_the_bucket=>this
+          this=>this%next
+          nbergs_to_send_n=nbergs_to_send_n+1
+          call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_n, nbergs_to_send_n)
+          call move_trajectory(bergs, kick_the_bucket)
+          call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
+        elseif (this%jne.lt.bergs%grd%jsc) then
+          kick_the_bucket=>this
+          this=>this%next
+          nbergs_to_send_s=nbergs_to_send_s+1
+          call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_s, nbergs_to_send_s)
+          call move_trajectory(bergs, kick_the_bucket)
+          call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
+        else
+          this=>this%next
+        endif
       else
-        this=>this%next
+          this=>this%next
       endif
     enddo
   enddo ; enddo
@@ -1314,6 +1337,7 @@ subroutine pack_berg_into_buffer2(berg, buff, n)
     buff%data(26,n)=berg%vvel_old  !Alon
     buff%data(27,n)=berg%lon_old  !Alon
     buff%data(28,n)=berg%lat_old  !Alon
+    buff%data(29,n)=berg%halo_berg  
 
   end subroutine pack_berg_into_buffer2
 
@@ -1389,6 +1413,7 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n,grd)
   localberg%vvel_old=buff%data(26,n) !Alon
   localberg%lon_old=buff%data(27,n) !Alon
   localberg%lat_old=buff%data(28,n) !Alon
+  localberg%halo_berg=buff%data(29,n) !Alon
  
   lres=find_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
   if (lres) then
@@ -1558,6 +1583,7 @@ subroutine pack_traj_into_buffer2(traj, buff, n)
     buff%data(29,n)=traj%vvel_old !Alon
     buff%data(30,n)=traj%lon_old !Alon
     buff%data(31,n)=traj%lat_old !Alon
+    buff%data(32,n)=traj%halo_berg !Alon
 
   end subroutine pack_traj_into_buffer2
 
@@ -1603,6 +1629,7 @@ subroutine unpack_traj_from_buffer2(first, buff, n)
     traj%vvel_old=buff%data(29,n) !Alon
     traj%lon_old=buff%data(30,n) !Alon
     traj%lat_old=buff%data(31,n) !Alon
+    traj%halo_berg=buff%data(32,n) !Alon
 
     call append_posn(first, traj)
 
@@ -2074,6 +2101,7 @@ subroutine record_posn(bergs)
       posn%vvel_old=this%vvel_old
       posn%lon_old=this%lon_old
       posn%lat_old=this%lat_old
+      posn%halo_berg=this%halo_berg
   
       call push_posn(this%trajectory, posn)
   
@@ -3199,8 +3227,8 @@ integer function berg_chksum(berg )
 ! Arguments
 type(iceberg), pointer :: berg
 ! Local variables
-real :: rtmp(36) !Changed from 28 to 34 by Alon
-integer :: itmp(36+3), i8=0, ichk1, ichk2, ichk3 !Changed from 28 to 34 by Alon
+real :: rtmp(37) !Changed from 28 to 34 by Alon
+integer :: itmp(37+3), i8=0, ichk1, ichk2, ichk3 !Changed from 28 to 34 by Alon
 integer :: i
 
   rtmp(:)=0.
@@ -3239,14 +3267,15 @@ integer function berg_chksum(berg )
   rtmp(34)=berg%vvel_old !Added by Alon
   rtmp(35)=berg%lat_old !Added by Alon
   rtmp(36)=berg%lon_old !Added by Alon
+  itmp(37)=berg%halo_berg !Changed from 31 to 40 by Alon
 
-  itmp(1:36)=transfer(rtmp,i8) !Changed from 28 to 36 by Alon
-  itmp(37)=berg%start_year !Changed from 29 to 37 by Alon
-  itmp(38)=berg%ine !Changed from 30 to 38 by Alon
-  itmp(39)=berg%jne !Changed from 31 to 39 by Alon
+  itmp(1:37)=transfer(rtmp,i8) !Changed from 28 to 37 by Alon
+  itmp(38)=berg%start_year !Changed from 29 to 38 by Alon
+  itmp(39)=berg%ine !Changed from 30 to 39 by Alon
+  itmp(40)=berg%jne !Changed from 31 to 40 by Alon
 
   ichk1=0; ichk2=0; ichk3=0
-  do i=1,36+3 !Changd from 28 to 36 by Alon
+  do i=1,37+3 !Changd from 28 to 36 by Alon
    ichk1=ichk1+itmp(i)
    ichk2=ichk2+itmp(i)*i
    ichk3=ichk3+itmp(i)*i*i
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 144af01..d5d4c89 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -129,6 +129,7 @@ subroutine write_restart(bergs)
                                    start_mass,   &
                                    mass_scaling, &
                                    mass_of_bits, &
+                                   halo_berg,    &
                                    heat_density
 
 integer, allocatable, dimension(:) :: ine,       &
@@ -177,6 +178,7 @@ subroutine write_restart(bergs)
    allocate(mass_scaling(nbergs))
    allocate(mass_of_bits(nbergs))
    allocate(heat_density(nbergs))
+   allocate(halo_berg(nbergs))
 
    allocate(ine(nbergs))
    allocate(jne(nbergs))
@@ -226,6 +228,8 @@ subroutine write_restart(bergs)
                                             longname='mass of bergy bits',units='kg')
   id = register_restart_field(bergs_restart,filename,'heat_density',heat_density, &
                                             longname='heat density',units='J/kg')
+  id = register_restart_field(bergs_restart,filename,'halo_berg',halo_berg, &
+                                            longname='halo_berg',units='dimensionless')
 
   ! Write variables
 
@@ -246,6 +250,7 @@ subroutine write_restart(bergs)
       start_lon(i) = this%start_lon; start_lat(i) = this%start_lat
       start_year(i) = this%start_year; start_day(i) = this%start_day
       start_mass(i) = this%start_mass; mass_scaling(i) = this%mass_scaling
+      halo_berg(i) = this%halo_berg 
       mass_of_bits(i) = this%mass_of_bits; heat_density(i) = this%heat_density
       this=>this%next
     enddo
@@ -277,6 +282,7 @@ subroutine write_restart(bergs)
              start_mass,   &
              mass_scaling, &
              mass_of_bits, &
+             halo_berg,    &
              heat_density )
 !axn, ayn, uvel_old, vvel_old, lat_old, lon_old, bxn, byn above added by Alon
 
@@ -325,7 +331,7 @@ subroutine read_restart_bergs_orig(bergs,Time)
 integer :: axnid, aynid, uvel_oldid, vvel_oldid, bxnid, bynid, lon_oldid, lat_oldid !Added by Alon
 integer :: massid, thicknessid, widthid, lengthid
 integer :: start_lonid, start_latid, start_yearid, start_dayid, start_massid
-integer :: scaling_id, mass_of_bits_id, heat_density_id
+integer :: scaling_id, mass_of_bits_id, heat_density_id, halo_bergid
 logical :: lres, found_restart, multiPErestart
 real :: lon0, lon1, lat0, lat1
 character(len=33) :: filename, filename_base
@@ -402,6 +408,7 @@ subroutine read_restart_bergs_orig(bergs,Time)
   start_dayid=inq_var(ncid, 'start_day')
   start_massid=inq_var(ncid, 'start_mass')
   scaling_id=inq_var(ncid, 'mass_scaling')
+  halo_bergid=inq_var(ncid, 'halo_berg')
   mass_of_bits_id=inq_var(ncid, 'mass_of_bits',unsafe=.true.)
   heat_density_id=inq_var(ncid, 'heat_density',unsafe=.true.)
   ineid=inq_var(ncid, 'ine',unsafe=.true.)
@@ -459,6 +466,7 @@ subroutine read_restart_bergs_orig(bergs,Time)
       localberg%start_day=get_double(ncid, start_dayid, k)
       localberg%start_mass=get_double(ncid, start_massid, k)
       localberg%mass_scaling=get_double(ncid, scaling_id, k)
+      localberg%halo_berg=get_double(ncid, halo_bergid, k)
       if (mass_of_bits_id>0) then ! Allow reading of older restart with no bergy bits
         localberg%mass_of_bits=get_double(ncid, mass_of_bits_id, k)
       else
@@ -546,6 +554,7 @@ subroutine generate_bergs(bergs,Time)
         localberg%start_mass=localberg%mass
         localberg%mass_scaling=bergs%mass_scaling(1)
         localberg%mass_of_bits=0.
+        localberg%halo_berg=0.
         localberg%heat_density=0.
         localberg%uvel=1.
         localberg%vvel=0.
@@ -633,6 +642,7 @@ subroutine read_restart_bergs(bergs,Time)
                                    start_mass,   &
                                    mass_scaling, &
                                    mass_of_bits, &
+                                   halo_berg,    &
                                    heat_density
 !axn, ayn, uvel_old, vvel_old, lon_old, lat_old, bxn, byn added by Alon
 integer, allocatable, dimension(:) :: ine,       &
@@ -680,6 +690,7 @@ subroutine read_restart_bergs(bergs,Time)
      allocate(start_mass(nbergs_in_file))
      allocate(mass_scaling(nbergs_in_file))
      allocate(mass_of_bits(nbergs_in_file))
+     allocate(halo_berg(nbergs_in_file))
      allocate(heat_density(nbergs_in_file))
 
      allocate(ine(nbergs_in_file))
@@ -708,6 +719,7 @@ subroutine read_restart_bergs(bergs,Time)
      call read_unlimited_axis(filename,'start_mass',start_mass,domain=grd%domain)
      call read_unlimited_axis(filename,'mass_scaling',mass_scaling,domain=grd%domain)
      call read_unlimited_axis(filename,'mass_of_bits',mass_of_bits,domain=grd%domain)
+     call read_unlimited_axis(filename,'halo_berg',halo_berg,domain=grd%domain)
      call read_unlimited_axis(filename,'heat_density',heat_density,domain=grd%domain)
 
      call read_unlimited_axis(filename,'ine',ine,domain=grd%domain)
@@ -765,6 +777,7 @@ subroutine read_restart_bergs(bergs,Time)
          localberg%start_mass=start_mass(k)
          localberg%mass_scaling=mass_scaling(k)
          localberg%mass_of_bits=mass_of_bits(k)
+         localberg%halo_berg=halo_berg(k)
          localberg%heat_density=heat_density(k)
          if (really_debug) lres=is_point_in_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, explain=.true.)
          lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
@@ -798,6 +811,7 @@ subroutine read_restart_bergs(bergs,Time)
                 start_mass,   &
                 mass_scaling, &
                 mass_of_bits, &
+                halo_berg,    &
                 heat_density )
 !axn, ayn, uvel_old, vvel_old, lat_old, lon_old, bxn, byn above added by Alon.
      deallocate(           &
@@ -853,6 +867,7 @@ subroutine generate_bergs(bergs,Time)
         localberg%start_mass=localberg%mass
         localberg%mass_scaling=bergs%mass_scaling(1)
         localberg%mass_of_bits=0.
+        localberg%halo_berg=0.
         localberg%heat_density=0.
         localberg%uvel=1.
         localberg%vvel=0.

From 82b58d9ccfd8ebf012433ca99e356df2204905b1 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Tue, 22 Sep 2015 11:51:14 -0400
Subject: [PATCH 063/361] I am not sure if the changes I commited in the
 previous commit, actually got saved. This is a repeat of the previous commit.

---
 icebergs_framework.F90 | 1 -
 1 file changed, 1 deletion(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index a09745a..a8eb46e 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -1040,7 +1040,6 @@ subroutine delete_all_bergs_in_list(bergs,grdj,grdi)
     call destroy_iceberg(kick_the_bucket)
 !    call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
   enddo
-  bergs%list(grdi,grdj)%first=>null()
 end  subroutine delete_all_bergs_in_list
 
 

From cdd81cc98fdc3156fee165f9da16cd96e4f8f5d8 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Tue, 22 Sep 2015 11:58:48 -0400
Subject: [PATCH 064/361] I tried to commit this before, but the wrong files
 got included. Here I repeat this commit:

Fixed two bugs in halo_update scheme:

    1) Editted the delete_all_icebergs_in_list subroutine, to make it point the first pointer to null.

    2)Added a variable called halo_iceberg, which is a flag that says whether an iceberg is a temporary iceberg copied to a halo. This prevents the temporary icebergs begin copied back the orginal
processor, which causes icebergs to multiply over and over again.
---
 icebergs_framework.F90 | 1 +
 1 file changed, 1 insertion(+)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index a8eb46e..c76ec82 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -1039,6 +1039,7 @@ subroutine delete_all_bergs_in_list(bergs,grdj,grdi)
     this=>this%next
     call destroy_iceberg(kick_the_bucket)
 !    call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
+    bergs%list(grdi,grdj)%first=>null()
   enddo
 end  subroutine delete_all_bergs_in_list
 

From 720361d5c10b400031b372f70761a6a3bd3a0911 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 23 Sep 2015 17:52:33 -0400
Subject: [PATCH 065/361] Added a new type called bond, which corresponds to
 bonds between icebergs

Created a submodule which initially established bonds between icebergs close to one another (for testing purposes)

Created a submodule which checks whether the bonds are health, and can also count the total number of bounds.

There are still some bugs, and everyone is not quite working, but it is now time to go home.
---
 icebergs.F90           | 280 +++++++++++++++++++++++++++++------------
 icebergs_framework.F90 |  18 ++-
 2 files changed, 219 insertions(+), 79 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 2c2fe69..8642781 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -23,7 +23,7 @@ module ice_bergs
 use diag_manager_mod, only: diag_axis_init
 
 use ice_bergs_framework, only: ice_bergs_framework_init
-use ice_bergs_framework, only: icebergs_gridded, xyt, iceberg, icebergs, buffer
+use ice_bergs_framework, only: icebergs_gridded, xyt, iceberg, icebergs, buffer, bond
 use ice_bergs_framework, only: verbose, really_debug,debug,old_bug_rotated_weights,budget,use_roundoff_fix
 use ice_bergs_framework, only: find_cell,find_cell_by_search,count_bergs,is_point_in_cell,pos_within_cell
 use ice_bergs_framework, only: nclasses,old_bug_bilin
@@ -111,10 +111,155 @@ subroutine icebergs_init(bergs, &
 
   if (really_debug) call print_bergs(stderrunit,bergs,'icebergs_init, initial status')
 
+  if (bergs%iceberg_bonds_on)  call initialize_iceberg_bonds(bergs)
+
 
 end subroutine icebergs_init
 
 
+! ##############################################################################
+
+subroutine initialize_iceberg_bonds(bergs)
+
+type(icebergs), pointer :: bergs
+type(iceberg), pointer :: berg
+type(iceberg), pointer :: other_berg
+type(icebergs_gridded), pointer :: grd
+    
+
+
+real :: T1, L1, W1, lon1, lat1, x1, y1, R1, A1   !Current iceberg
+real :: T2, L2, W2, lon2, lat2, x2, y2, R2, A2   !Other iceberg
+real :: r_dist_x, r_dist_y, r_dist
+integer :: grdi_outer, grdj_outer
+integer :: grdi_inner, grdj_inner
+
+  ! For convenience
+    grd=>bergs%grd
+    !Should update halos before doing this 
+  do grdj_outer = grd%jsc,grd%jec ; do grdi_outer = grd%isc,grd%iec  !Should you be on the data domain??
+    berg=>bergs%list(grdi_outer,grdj_outer)%first
+    do while (associated(berg)) ! loop over all bergs
+    
+      lon1=berg%lon; lat1=berg%lat
+      call rotpos_to_tang(lon1,lat1,x1,y1)
+
+      do grdj_inner = berg%jne-1,berg%jne+1 ; do grdi_inner = berg%ine-1,berg%ine+1   !Only looping through adjacent cells.
+        other_berg=>bergs%list(grdi_inner,grdj_inner)%first
+        do while (associated(other_berg)) ! loop over all other bergs  
+          
+          if (berg%iceberg_num .ne. other_berg%iceberg_num) then
+            lon2=other_berg%lon; lat2=other_berg%lat
+            call rotpos_to_tang(lon2,lat2,x2,y2)
+            r_dist_x=x1-x2 ; r_dist_y=y1-y2
+            r_dist=sqrt( ((x1-x2)**2) + ((y1-y2)**2) )
+        
+            !if (r_dist.gt.1000.) then  ! If the bergs are close together, then form a bond
+              call form_a_bond(berg, other_berg)
+            !endif       
+            other_berg=>other_berg%next
+          endif
+        enddo  ! End of looping through all other bergs in the inner list
+      enddo ; enddo;  !End of inner loop
+      berg=>berg%next
+    enddo ! End of looping through all bergs in the outer list
+  enddo ; enddo; !End of outer loop.
+
+  call check_if_all_bonds_are_present(bergs)
+
+
+
+end subroutine initialize_iceberg_bonds
+
+! ##############################################################################
+
+subroutine form_a_bond(berg, other_berg)
+
+type(iceberg), pointer :: berg
+type(iceberg), pointer :: other_berg
+type(bond) , pointer :: new_bond, first_bond
+print *, 'Forming a bond!!!'
+    
+
+! Step 1: Create a new bond
+allocate(new_bond)
+new_bond%berg_num_of_current_bond=other_berg%iceberg_num
+new_bond%berg_in_current_bond=>other_berg
+
+! Step 2: Put this new bond at the start of the bond list
+   first_bond=>berg%first_bond
+   if (associated(first_bond)) then
+        new_bond%next_bond=>first_bond
+        new_bond%prev_bond=>null()  !This should not be needed
+        first_bond%prev_bond=>new_bond
+        berg%first_bond=>new_bond
+   else
+       new_bond%next_bond=>null()  !This should not be needed
+       new_bond%prev_bond=>null()  !This should not be needed
+       berg%first_bond=>new_bond
+   endif
+
+end subroutine form_a_bond
+
+! #############################################################################
+
+subroutine check_if_all_bonds_are_present(bergs)
+
+type(icebergs), pointer :: bergs
+type(iceberg), pointer :: berg
+type(iceberg), pointer :: other_berg
+type(icebergs_gridded), pointer :: grd
+type(bond) , pointer :: current_bond, other_berg_bond
+integer :: grdi, grdj
+logical :: bond_is_good
+
+print *, "starting bond_check"
+
+ ! For convenience
+  grd=>bergs%grd
+
+  do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
+    berg=>bergs%list(grdi,grdj)%first
+    do while (associated(berg)) ! loop over all bergs
+      current_bond=>berg%first_bond
+      do while (associated(current_bond)) ! loop over all bonds
+        bond_is_good=.False.
+        other_berg=>current_bond%berg_in_current_bond
+        if (associated(other_berg)) then
+          other_berg_bond=>other_berg%first_bond
+          
+          do while (associated(other_berg_bond))  !loops over the icebergs in the other icebergs bond list            
+            if (associated(other_berg_bond%berg_in_current_bond)) then
+              if (other_berg_bond%berg_in_current_bond%iceberg_num==berg%iceberg_num) then
+                bond_is_good=.True.  !Bond_is_good becomes true when the corresponding bond is found
+              endif
+            endif                 
+            if (bond_is_good) then
+              other_berg_bond=>null()
+            else
+              other_berg_bond=>other_berg_bond%next_bond
+            endif
+          enddo  ! End of loop over the other berg's bonds.
+
+          ! Now we assess how we did
+
+          if (bond_is_good) then
+            print*, 'Perfect quality Bond:', berg%iceberg_num, current_bond%berg_num_of_current_bond
+          else
+            print*, 'Non-matching bond...:', berg%iceberg_num, current_bond%berg_num_of_current_bond
+          endif
+        
+        else
+           print *, 'Opposite berg is not assosiated:', berg%iceberg_num, current_bond%berg_in_current_bond%iceberg_num    
+        endif
+        current_bond=>current_bond%next_bond
+      enddo !End of loop over current bonds
+    enddo ! End of loop over all bergs
+  enddo; enddo !End of loop over all grid cells
+
+print *, "starting bond_check"
+end subroutine check_if_all_bonds_are_present
+
 ! ##############################################################################
 
 subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y) !Calculating interactive force between icebergs. Alon,  Markpoint_4
@@ -167,28 +312,29 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
 call rotpos_to_tang(lon1,lat1,x1,y1)
 
   do grdj = berg%jne-1,berg%jne+1 ; do grdi = berg%ine-1,berg%ine+1
-  other_berg=>bergs%list(grdi,grdj)%first
-!Note: This summing should be made order invarient. 
-  do while (associated(other_berg)) ! loop over all other bergs  
-       L2=other_berg%length
-       W2=other_berg%width
-       T2=other_berg%thickness 
-       u2=other_berg%uvel_old !Old values are used to make it order invariant 
-       v2=other_berg%vvel_old !Old values are used to make it order invariant 
-       A2=L2*W2
-       R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
-       lon2=berg%lon_old; lat2=berg%lat_old !Old values are used to make it order invariant
-       call rotpos_to_tang(lon2,lat2,x2,y2)
-
-       r_dist_x=x1-x2 ; r_dist_y=y1-y2
-       r_dist=sqrt( ((x1-x2)**2) + ((y1-y2)**2) )
-
-      call overlap_area(R1,R2,r_dist,A_o,trapped)
-      T_min=min(T1,T2)
-
-      !Calculating spring force  (later this should only be done on the first time around)
-      accel_spring=spring_coef*(T_min/T1)*(A_o/A1)
-      if ((r_dist>0.) .AND. (r_dist< (R1+R2)) ) then
+    other_berg=>bergs%list(grdi,grdj)%first
+    !Note: This summing should be made order invarient. 
+    do while (associated(other_berg)) ! loop over all other bergs  
+      if (berg%iceberg_num .ne. other_berg%iceberg_num) then
+        L2=other_berg%length
+        W2=other_berg%width
+        T2=other_berg%thickness 
+        u2=other_berg%uvel_old !Old values are used to make it order invariant 
+        v2=other_berg%vvel_old !Old values are used to make it order invariant 
+        A2=L2*W2
+        R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
+        lon2=other_berg%lon_old; lat2=other_berg%lat_old !Old values are used to make it order invariant
+        call rotpos_to_tang(lon2,lat2,x2,y2)
+
+        r_dist_x=x1-x2 ; r_dist_y=y1-y2
+        r_dist=sqrt( ((x1-x2)**2) + ((y1-y2)**2) )
+
+       call overlap_area(R1,R2,r_dist,A_o,trapped)
+       T_min=min(T1,T2)
+
+       !Calculating spring force  (later this should only be done on the first time around)
+       accel_spring=spring_coef*(T_min/T1)*(A_o/A1)
+       if ((r_dist>0.) .AND. (r_dist< (R1+R2)) ) then
         IA_x=IA_x+(accel_spring*(r_dist_x/r_dist))
         IA_y=IA_y+(accel_spring*(r_dist_y/r_dist))
 
@@ -225,12 +371,11 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
 !print *, 'P_21',P_21
 !print *, 'P_12',P_12
 !print *, 'P_22',P_22
-
+      endif
     endif
-
-       other_berg=>other_berg%next
+    other_berg=>other_berg%next
   enddo ! loop over all bergs
-  enddo ; enddo
+enddo ; enddo
 
   contains
 
@@ -262,30 +407,6 @@ subroutine overlap_area(R1,R2,d,A,trapped)
    end subroutine overlap_area
 
 
-  subroutine rotpos_to_tang(lon, lat, x, y)
-  ! Arguments
-  real, intent(in) :: lon, lat
-  real, intent(out) :: x, y
-  ! Local variables
-  real :: r,colat,clon,slon
-
-    if (lat>90.) then
-      write(stderrunit,*) 'diamonds, rotpos_to_tang: lat>90 already!',lat
-      call error_mesg('diamonds, rotpos_to_tang','Something went very wrong!',FATAL)
-    endif
-    if (lat==90.) then
-      write(stderrunit,*) 'diamonds, rotpos_to_tang: lat==90 already!',lat
-      call error_mesg('diamonds, rotpos_to_tang','Something went wrong!',FATAL)
-    endif
-
-    colat=90.-lat
-    r=Rearth*(colat*pi_180)
-    clon=cos(lon*pi_180)
-    slon=sin(lon*pi_180)
-    x=r*clon
-    y=r*slon
-
-  end subroutine rotpos_to_tang
 
 end subroutine interactive_force
 
@@ -2358,31 +2479,6 @@ subroutine evolve_icebergs(bergs)
 
 contains
 
-  subroutine rotpos_to_tang(lon, lat, x, y)
-  ! Arguments
-  real, intent(in) :: lon, lat
-  real, intent(out) :: x, y
-  ! Local variables
-  real :: r,colat,clon,slon
-
-    if (lat>90.) then
-      write(stderrunit,*) 'diamonds, rotpos_to_tang: lat>90 already!',lat
-      call error_mesg('diamonds, rotpos_to_tang','Something went very wrong!',FATAL)
-    endif
-    if (lat==90.) then
-      write(stderrunit,*) 'diamonds, rotpos_to_tang: lat==90 already!',lat
-      call error_mesg('diamonds, rotpos_to_tang','Something went wrong!',FATAL)
-    endif
-
-    colat=90.-lat
-    r=Rearth*(colat*pi_180)
-    clon=cos(lon*pi_180)
-    slon=sin(lon*pi_180)
-    x=r*clon
-    y=r*slon
-
-  end subroutine rotpos_to_tang
-
   subroutine rotpos_from_tang(x, y, lon, lat)
   ! Arguments
   real, intent(in) :: x, y
@@ -2631,11 +2727,41 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
     if (debug) error=.true.
   endif
 
-end subroutine adjust_index_and_ground
+ end subroutine adjust_index_and_ground
 
 end subroutine evolve_icebergs
 
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+subroutine rotpos_to_tang(lon, lat, x, y)
+  ! Arguments
+  real, intent(in) :: lon, lat
+  real, intent(out) :: x, y
+  ! Local variables
+  real :: r,colat,clon,slon
+  real :: Rearth
+  integer :: stderrunit
+
+  stderrunit = stderr()
+  Rearth=6360.e3
+
+  if (lat>90.) then
+      write(stderrunit,*) 'diamonds, rotpos_to_tang: lat>90 already!',lat
+      call error_mesg('diamonds, rotpos_to_tang','Something went very wrong!',FATAL)
+    endif
+    if (lat==90.) then
+      write(stderrunit,*) 'diamonds, rotpos_to_tang: lat==90 already!',lat
+      call error_mesg('diamonds, rotpos_to_tang','Something went wrong!',FATAL)
+    endif
+
+    colat=90.-lat
+    r=Rearth*(colat*pi_180)
+    clon=cos(lon*pi_180)
+    slon=sin(lon*pi_180)
+    x=r*clon
+    y=r*slon
 
+  end subroutine rotpos_to_tang
 
 ! ##############################################################################
 
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 4ab69cf..45c4fd4 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -49,7 +49,7 @@ module ice_bergs_framework
 
 
 !Public types
-public icebergs_gridded, xyt, iceberg, icebergs, buffer 
+public icebergs_gridded, xyt, iceberg, icebergs, buffer, bond 
 
 !Public subs
 public ice_bergs_framework_init
@@ -157,8 +157,15 @@ module ice_bergs_framework
   ! Environment variables (as seen by the iceberg)
   real :: uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, cn, hi
   type(xyt), pointer :: trajectory=>null()
+  type(bond), pointer :: first_bond=>null()  !First element of bond list.
 end type iceberg
 
+type :: bond
+  type(bond), pointer :: prev_bond=>null(), next_bond=>null()
+  type(iceberg), pointer :: berg_in_current_bond=>null()
+  integer :: berg_num_of_current_bond
+end type bond
+
 type :: buffer
   integer :: size=0
   real, dimension(:,:), pointer :: data
@@ -194,6 +201,7 @@ module ice_bergs_framework
   logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
   logical :: time_average_weight=.false. ! Time average the weight on the ocean
   logical :: Runge_not_Verlet=.True.  !True=Runge Kuttai, False=Verlet.  - Added by Alon 
+  logical :: iceberg_bonds_on=.False.  !True=Allow icebergs to have bonds, False=don't allow. 
   logical :: use_new_predictive_corrective =.False.  !Flag to use Bob's predictive corrective iceberg scheme- Added by Alon 
   logical :: interactive_icebergs_on=.false.  !Turn on/off interactions between icebergs  - Added by Alon 
   logical :: critical_interaction_damping_on=.true.  !Sets the damping on relative iceberg velocity to critical value - Added by Alon 
@@ -292,6 +300,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: speed_limit=0. ! CFL speed limit for a berg
 real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
 logical :: Runge_not_Verlet=.True.  !True=Runge Kutta, False=Verlet.  - Added by Alon 
+logical :: iceberg_bonds_on=.False.  !True=Allow icebergs to have bonds, False=don't allow. 
 logical :: use_new_predictive_corrective =.False.  !Flag to use Bob's predictive corrective iceberg scheme- Added by Alon 
 logical :: interactive_icebergs_on=.false.  !Turn on/off interactions between icebergs  - Added by Alon 
 logical :: critical_interaction_damping_on=.true.  !Sets the damping on relative iceberg velocity to critical value - Added by Alon 
@@ -303,7 +312,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real, dimension(nclasses) :: initial_thickness=(/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) ! Total thickness of newly calved bergs (m)
 namelist /icebergs_nml/ verbose, budget, halo, iceberg_halo, traj_sample_hrs, initial_mass, traj_write_hrs, &
          distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef, radial_damping_coef, tangental_damping_coef, &
-         rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, &
+         rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, iceberg_bonds_on, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, &
          time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, interactive_icebergs_on, critical_interaction_damping_on, &
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution, force_all_pes_traj
@@ -553,6 +562,10 @@ subroutine ice_bergs_framework_init(bergs, &
 if (Runge_not_Verlet) then
   interactive_icebergs_on=.false.  ! Iceberg interactions only with Verlet
 endif
+if (.not.interactive_icebergs_on) then
+  !iceberg_bonds_on=.false.  ! This line needs to included later, but is omitted for testing
+endif
+
 
  ! Parameters
   bergs%dt=dt
@@ -573,6 +586,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%time_average_weight=time_average_weight
   bergs%speed_limit=speed_limit
   bergs%Runge_not_Verlet=Runge_not_Verlet   !Alon
+  bergs%iceberg_bonds_on=iceberg_bonds_on   !Alon
   bergs%critical_interaction_damping_on=critical_interaction_damping_on   !Alon
   bergs%interactive_icebergs_on=interactive_icebergs_on   !Alon
   bergs%use_new_predictive_corrective=use_new_predictive_corrective  !Alon

From 6feebfb42c75a00c9c1c5823bab4e493863c286a Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 23 Sep 2015 18:08:02 -0400
Subject: [PATCH 066/361] Found a couple of bugs which were putting the code
 into an infinite loop. These have been corrected.

---
 icebergs.F90 | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 8642781..c28773c 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -157,8 +157,8 @@ subroutine initialize_iceberg_bonds(bergs)
             !if (r_dist.gt.1000.) then  ! If the bergs are close together, then form a bond
               call form_a_bond(berg, other_berg)
             !endif       
-            other_berg=>other_berg%next
           endif
+          other_berg=>other_berg%next
         enddo  ! End of looping through all other bergs in the inner list
       enddo ; enddo;  !End of inner loop
       berg=>berg%next
@@ -213,7 +213,7 @@ subroutine check_if_all_bonds_are_present(bergs)
 integer :: grdi, grdj
 logical :: bond_is_good
 
-print *, "starting bond_check"
+!print *, "starting bond_check"
 
  ! For convenience
   grd=>bergs%grd
@@ -254,10 +254,11 @@ subroutine check_if_all_bonds_are_present(bergs)
         endif
         current_bond=>current_bond%next_bond
       enddo !End of loop over current bonds
+      berg=>berg%next
     enddo ! End of loop over all bergs
   enddo; enddo !End of loop over all grid cells
 
-print *, "starting bond_check"
+!  print *, "ending bond_check"
 end subroutine check_if_all_bonds_are_present
 
 ! ##############################################################################

From aa62514524a10994cb36f032cc65e53e9e57b6c8 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Thu, 24 Sep 2015 10:59:33 -0400
Subject: [PATCH 067/361] The bond counter and bond quality control submodules
 are not working.

The bond counter counts up the number of bonds.
The bond quality control makes sure that each bond matches up with the corresponding bond saved on the bonded berg.
---
 icebergs.F90           | 90 ++++++++++++++++++++++++++++++------------
 icebergs_framework.F90 |  1 +
 2 files changed, 65 insertions(+), 26 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index c28773c..dd098e6 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -133,6 +133,8 @@ subroutine initialize_iceberg_bonds(bergs)
 real :: r_dist_x, r_dist_y, r_dist
 integer :: grdi_outer, grdj_outer
 integer :: grdi_inner, grdj_inner
+logical :: check_bond_quality
+
 
   ! For convenience
     grd=>bergs%grd
@@ -144,7 +146,8 @@ subroutine initialize_iceberg_bonds(bergs)
       lon1=berg%lon; lat1=berg%lat
       call rotpos_to_tang(lon1,lat1,x1,y1)
 
-      do grdj_inner = berg%jne-1,berg%jne+1 ; do grdi_inner = berg%ine-1,berg%ine+1   !Only looping through adjacent cells.
+      do grdj_inner = grd%jsc,grd%jec ; do grdi_inner = grd%isc,grd%iec  !This line uses n^2 steps
+!     do grdj_inner = berg%jne-1,berg%jne+1 ; do grdi_inner = berg%ine-1,berg%ine+1   !Only looping through adjacent cells.
         other_berg=>bergs%list(grdi_inner,grdj_inner)%first
         do while (associated(other_berg)) ! loop over all other bergs  
           
@@ -165,7 +168,9 @@ subroutine initialize_iceberg_bonds(bergs)
     enddo ! End of looping through all bergs in the outer list
   enddo ; enddo; !End of outer loop.
 
-  call check_if_all_bonds_are_present(bergs)
+
+  check_bond_quality=.True.
+  call check_if_all_bonds_are_present(bergs,check_bond_quality)
 
 
 
@@ -203,62 +208,95 @@ end subroutine form_a_bond
 
 ! #############################################################################
 
-subroutine check_if_all_bonds_are_present(bergs)
+subroutine check_if_all_bonds_are_present(bergs, check_bond_quality)
 
 type(icebergs), pointer :: bergs
 type(iceberg), pointer :: berg
 type(iceberg), pointer :: other_berg
 type(icebergs_gridded), pointer :: grd
 type(bond) , pointer :: current_bond, other_berg_bond
+!integer, intent(out) :: number_of_bonds 
+integer :: number_of_bonds, number_of_bonds_all_pe
 integer :: grdi, grdj
 logical :: bond_is_good
+logical, optional :: check_bond_quality
+logical :: quality_check
+logical :: all_bonds_matching
+integer :: stderrunit
 
-!print *, "starting bond_check"
+ print *, "starting bond_check"
+ quality_check=.false.
+ if(present(check_bond_quality)) quality_check = check_bond_quality
 
  ! For convenience
   grd=>bergs%grd
 
+  number_of_bonds=0  ! This is a bond counter.
+
   do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
     berg=>bergs%list(grdi,grdj)%first
     do while (associated(berg)) ! loop over all bergs
       current_bond=>berg%first_bond
       do while (associated(current_bond)) ! loop over all bonds
-        bond_is_good=.False.
-        other_berg=>current_bond%berg_in_current_bond
-        if (associated(other_berg)) then
-          other_berg_bond=>other_berg%first_bond
+        number_of_bonds=number_of_bonds+1
+
+        ! ##### Beginning Quality Check on Bonds ######
+        if (quality_check) then
+          all_bonds_matching=.True.
+          bond_is_good=.False.
+          other_berg=>current_bond%berg_in_current_bond
+          if (associated(other_berg)) then
+            other_berg_bond=>other_berg%first_bond
           
-          do while (associated(other_berg_bond))  !loops over the icebergs in the other icebergs bond list            
-            if (associated(other_berg_bond%berg_in_current_bond)) then
-              if (other_berg_bond%berg_in_current_bond%iceberg_num==berg%iceberg_num) then
-                bond_is_good=.True.  !Bond_is_good becomes true when the corresponding bond is found
+            do while (associated(other_berg_bond))  !loops over the icebergs in the other icebergs bond list            
+              if (associated(other_berg_bond%berg_in_current_bond)) then
+                if (other_berg_bond%berg_in_current_bond%iceberg_num==berg%iceberg_num) then
+                  bond_is_good=.True.  !Bond_is_good becomes true when the corresponding bond is found
+                endif
+              endif                 
+              if (bond_is_good) then
+                other_berg_bond=>null()
+              else
+                other_berg_bond=>other_berg_bond%next_bond
               endif
-            endif                 
+            enddo  ! End of loop over the other berg's bonds.
+
             if (bond_is_good) then
-              other_berg_bond=>null()
+              print*, 'Perfect quality Bond:', berg%iceberg_num, current_bond%berg_num_of_current_bond
             else
-              other_berg_bond=>other_berg_bond%next_bond
+              print*, 'Non-matching bond...:', berg%iceberg_num, current_bond%berg_num_of_current_bond
+              all_bonds_matching=.false.
             endif
-          enddo  ! End of loop over the other berg's bonds.
-
-          ! Now we assess how we did
-
-          if (bond_is_good) then
-            print*, 'Perfect quality Bond:', berg%iceberg_num, current_bond%berg_num_of_current_bond
           else
-            print*, 'Non-matching bond...:', berg%iceberg_num, current_bond%berg_num_of_current_bond
+             print *, 'Opposite berg is not assosiated:', berg%iceberg_num, current_bond%berg_in_current_bond%iceberg_num    
+             all_bonds_matching=.false.
           endif
-        
-        else
-           print *, 'Opposite berg is not assosiated:', berg%iceberg_num, current_bond%berg_in_current_bond%iceberg_num    
         endif
+        ! ##### Ending Quality Check on Bonds ######
+
         current_bond=>current_bond%next_bond
       enddo !End of loop over current bonds
       berg=>berg%next
     enddo ! End of loop over all bergs
   enddo; enddo !End of loop over all grid cells
 
-!  print *, "ending bond_check"
+   number_of_bonds_all_pe=number_of_bonds
+   call mpp_sum(number_of_bonds_all_pe)
+   
+  bergs%nbonds=number_of_bonds_all_pe  !Total number of bonds across all pe's
+  if (number_of_bonds .gt. 0) then
+    print *, "Number of bonds on pe, out of a total of: ", number_of_bonds, number_of_bonds_all_pe
+  endif
+
+  if (quality_check) then
+    if (.not. all_bonds_matching) then
+        stderrunit = stderr()
+        write(stderrunit,*) 'diamonds, Bonds are not matching!!!! PE=',mpp_pe()
+        call error_mesg('diamonds, bonds', 'Bonds are not matching!', FATAL)
+    endif
+  endif
+
+  print *, "ending bond_check"
 end subroutine check_if_all_bonds_are_present
 
 ! ##############################################################################
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 45c4fd4..4780300 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -228,6 +228,7 @@ module ice_bergs_framework
   real :: net_melt=0., berg_melt=0., bergy_src=0., bergy_melt=0.
   integer :: nbergs_calved=0, nbergs_melted=0, nbergs_start=0, nbergs_end=0
   integer :: nspeeding_tickets=0
+  integer :: nbonds=0
   integer, dimension(:), pointer :: nbergs_calved_by_class=>null()
 end type icebergs
 

From 2c8a08c3ddc9ee2f096cec187bab52476f2a779d Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Thu, 24 Sep 2015 18:46:32 -0400
Subject: [PATCH 068/361] Iceberg bonds can now be initialized, saved to a
 restart file.

Some of the code for reading bonds from the restart file has been written, but this needs a little more work.
---
 icebergs.F90           | 141 +++------------------------
 icebergs_framework.F90 | 142 ++++++++++++++++++++++++++-
 icebergs_io.F90        | 215 +++++++++++++++++++++++++++++++++++++++--
 3 files changed, 361 insertions(+), 137 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index dd098e6..0f51e60 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -26,6 +26,7 @@ module ice_bergs
 use ice_bergs_framework, only: icebergs_gridded, xyt, iceberg, icebergs, buffer, bond
 use ice_bergs_framework, only: verbose, really_debug,debug,old_bug_rotated_weights,budget,use_roundoff_fix
 use ice_bergs_framework, only: find_cell,find_cell_by_search,count_bergs,is_point_in_cell,pos_within_cell
+use ice_bergs_framework, only: count_bonds, form_a_bond
 use ice_bergs_framework, only: nclasses,old_bug_bilin
 use ice_bergs_framework, only: sum_mass,sum_heat,bilin,yearday,count_bergs,bergs_chksum
 use ice_bergs_framework, only: checksum_gridded,add_new_berg_to_list
@@ -39,6 +40,7 @@ module ice_bergs
 
 use ice_bergs_io,        only: ice_bergs_io_init,write_restart,write_trajectory
 use ice_bergs_io,        only: read_restart_bergs,read_restart_bergs_orig,read_restart_calving
+use ice_bergs_io,        only: read_restart_bonds
 
 implicit none ; private
 
@@ -111,8 +113,13 @@ subroutine icebergs_init(bergs, &
 
   if (really_debug) call print_bergs(stderrunit,bergs,'icebergs_init, initial status')
 
-  if (bergs%iceberg_bonds_on)  call initialize_iceberg_bonds(bergs)
-
+  if (bergs%iceberg_bonds_on) then
+    if (bergs%manually_initialize_bonds) then
+      call initialize_iceberg_bonds(bergs)
+    else
+      call read_restart_bonds(bergs,Time)
+    endif
+  endif
 
 end subroutine icebergs_init
 
@@ -125,7 +132,7 @@ subroutine initialize_iceberg_bonds(bergs)
 type(iceberg), pointer :: berg
 type(iceberg), pointer :: other_berg
 type(icebergs_gridded), pointer :: grd
-    
+   
 
 
 real :: T1, L1, W1, lon1, lat1, x1, y1, R1, A1   !Current iceberg
@@ -133,6 +140,7 @@ subroutine initialize_iceberg_bonds(bergs)
 real :: r_dist_x, r_dist_y, r_dist
 integer :: grdi_outer, grdj_outer
 integer :: grdi_inner, grdj_inner
+integer :: nbonds
 logical :: check_bond_quality
 
 
@@ -158,7 +166,7 @@ subroutine initialize_iceberg_bonds(bergs)
             r_dist=sqrt( ((x1-x2)**2) + ((y1-y2)**2) )
         
             !if (r_dist.gt.1000.) then  ! If the bergs are close together, then form a bond
-              call form_a_bond(berg, other_berg)
+              call form_a_bond(berg, other_berg%iceberg_num, other_berg)
             !endif       
           endif
           other_berg=>other_berg%next
@@ -170,7 +178,7 @@ subroutine initialize_iceberg_bonds(bergs)
 
 
   check_bond_quality=.True.
-  call check_if_all_bonds_are_present(bergs,check_bond_quality)
+  call count_bonds(bergs, nbonds,check_bond_quality)
 
 
 
@@ -178,129 +186,6 @@ end subroutine initialize_iceberg_bonds
 
 ! ##############################################################################
 
-subroutine form_a_bond(berg, other_berg)
-
-type(iceberg), pointer :: berg
-type(iceberg), pointer :: other_berg
-type(bond) , pointer :: new_bond, first_bond
-print *, 'Forming a bond!!!'
-    
-
-! Step 1: Create a new bond
-allocate(new_bond)
-new_bond%berg_num_of_current_bond=other_berg%iceberg_num
-new_bond%berg_in_current_bond=>other_berg
-
-! Step 2: Put this new bond at the start of the bond list
-   first_bond=>berg%first_bond
-   if (associated(first_bond)) then
-        new_bond%next_bond=>first_bond
-        new_bond%prev_bond=>null()  !This should not be needed
-        first_bond%prev_bond=>new_bond
-        berg%first_bond=>new_bond
-   else
-       new_bond%next_bond=>null()  !This should not be needed
-       new_bond%prev_bond=>null()  !This should not be needed
-       berg%first_bond=>new_bond
-   endif
-
-end subroutine form_a_bond
-
-! #############################################################################
-
-subroutine check_if_all_bonds_are_present(bergs, check_bond_quality)
-
-type(icebergs), pointer :: bergs
-type(iceberg), pointer :: berg
-type(iceberg), pointer :: other_berg
-type(icebergs_gridded), pointer :: grd
-type(bond) , pointer :: current_bond, other_berg_bond
-!integer, intent(out) :: number_of_bonds 
-integer :: number_of_bonds, number_of_bonds_all_pe
-integer :: grdi, grdj
-logical :: bond_is_good
-logical, optional :: check_bond_quality
-logical :: quality_check
-logical :: all_bonds_matching
-integer :: stderrunit
-
- print *, "starting bond_check"
- quality_check=.false.
- if(present(check_bond_quality)) quality_check = check_bond_quality
-
- ! For convenience
-  grd=>bergs%grd
-
-  number_of_bonds=0  ! This is a bond counter.
-
-  do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
-    berg=>bergs%list(grdi,grdj)%first
-    do while (associated(berg)) ! loop over all bergs
-      current_bond=>berg%first_bond
-      do while (associated(current_bond)) ! loop over all bonds
-        number_of_bonds=number_of_bonds+1
-
-        ! ##### Beginning Quality Check on Bonds ######
-        if (quality_check) then
-          all_bonds_matching=.True.
-          bond_is_good=.False.
-          other_berg=>current_bond%berg_in_current_bond
-          if (associated(other_berg)) then
-            other_berg_bond=>other_berg%first_bond
-          
-            do while (associated(other_berg_bond))  !loops over the icebergs in the other icebergs bond list            
-              if (associated(other_berg_bond%berg_in_current_bond)) then
-                if (other_berg_bond%berg_in_current_bond%iceberg_num==berg%iceberg_num) then
-                  bond_is_good=.True.  !Bond_is_good becomes true when the corresponding bond is found
-                endif
-              endif                 
-              if (bond_is_good) then
-                other_berg_bond=>null()
-              else
-                other_berg_bond=>other_berg_bond%next_bond
-              endif
-            enddo  ! End of loop over the other berg's bonds.
-
-            if (bond_is_good) then
-              print*, 'Perfect quality Bond:', berg%iceberg_num, current_bond%berg_num_of_current_bond
-            else
-              print*, 'Non-matching bond...:', berg%iceberg_num, current_bond%berg_num_of_current_bond
-              all_bonds_matching=.false.
-            endif
-          else
-             print *, 'Opposite berg is not assosiated:', berg%iceberg_num, current_bond%berg_in_current_bond%iceberg_num    
-             all_bonds_matching=.false.
-          endif
-        endif
-        ! ##### Ending Quality Check on Bonds ######
-
-        current_bond=>current_bond%next_bond
-      enddo !End of loop over current bonds
-      berg=>berg%next
-    enddo ! End of loop over all bergs
-  enddo; enddo !End of loop over all grid cells
-
-   number_of_bonds_all_pe=number_of_bonds
-   call mpp_sum(number_of_bonds_all_pe)
-   
-  bergs%nbonds=number_of_bonds_all_pe  !Total number of bonds across all pe's
-  if (number_of_bonds .gt. 0) then
-    print *, "Number of bonds on pe, out of a total of: ", number_of_bonds, number_of_bonds_all_pe
-  endif
-
-  if (quality_check) then
-    if (.not. all_bonds_matching) then
-        stderrunit = stderr()
-        write(stderrunit,*) 'diamonds, Bonds are not matching!!!! PE=',mpp_pe()
-        call error_mesg('diamonds, bonds', 'Bonds are not matching!', FATAL)
-    endif
-  endif
-
-  print *, "ending bond_check"
-end subroutine check_if_all_bonds_are_present
-
-! ##############################################################################
-
 subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y) !Calculating interactive force between icebergs. Alon,  Markpoint_4
 type(icebergs), pointer :: bergs
 type(iceberg), pointer :: berg
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 4780300..cd2dd54 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -62,7 +62,8 @@ module ice_bergs_framework
 public insert_berg_into_list, create_iceberg, delete_iceberg_from_list, destroy_iceberg
 public print_fld,print_berg, print_bergs,record_posn, push_posn, append_posn, check_position
 public move_trajectory, move_all_trajectories
-public find_cell,find_cell_by_search,count_bergs,is_point_in_cell,pos_within_cell
+public form_a_bond
+public find_cell,find_cell_by_search,count_bergs,is_point_in_cell,pos_within_cell, count_bonds
 public sum_mass,sum_heat,bilin,yearday,bergs_chksum
 public checksum_gridded
 public grd_chksum2,grd_chksum3
@@ -202,6 +203,7 @@ module ice_bergs_framework
   logical :: time_average_weight=.false. ! Time average the weight on the ocean
   logical :: Runge_not_Verlet=.True.  !True=Runge Kuttai, False=Verlet.  - Added by Alon 
   logical :: iceberg_bonds_on=.False.  !True=Allow icebergs to have bonds, False=don't allow. 
+  logical :: manually_initialize_bonds=.False.  !True= Bonds are initialize manually. 
   logical :: use_new_predictive_corrective =.False.  !Flag to use Bob's predictive corrective iceberg scheme- Added by Alon 
   logical :: interactive_icebergs_on=.false.  !Turn on/off interactions between icebergs  - Added by Alon 
   logical :: critical_interaction_damping_on=.true.  !Sets the damping on relative iceberg velocity to critical value - Added by Alon 
@@ -302,6 +304,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
 logical :: Runge_not_Verlet=.True.  !True=Runge Kutta, False=Verlet.  - Added by Alon 
 logical :: iceberg_bonds_on=.False.  !True=Allow icebergs to have bonds, False=don't allow. 
+logical :: manually_initialize_bonds=.False.  !True= Bonds are initialize manually. 
 logical :: use_new_predictive_corrective =.False.  !Flag to use Bob's predictive corrective iceberg scheme- Added by Alon 
 logical :: interactive_icebergs_on=.false.  !Turn on/off interactions between icebergs  - Added by Alon 
 logical :: critical_interaction_damping_on=.true.  !Sets the damping on relative iceberg velocity to critical value - Added by Alon 
@@ -313,7 +316,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real, dimension(nclasses) :: initial_thickness=(/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) ! Total thickness of newly calved bergs (m)
 namelist /icebergs_nml/ verbose, budget, halo, iceberg_halo, traj_sample_hrs, initial_mass, traj_write_hrs, &
          distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef, radial_damping_coef, tangental_damping_coef, &
-         rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, iceberg_bonds_on, &
+         rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, iceberg_bonds_on, manually_initialize_bonds, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, &
          time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, interactive_icebergs_on, critical_interaction_damping_on, &
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution, force_all_pes_traj
@@ -588,6 +591,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%speed_limit=speed_limit
   bergs%Runge_not_Verlet=Runge_not_Verlet   !Alon
   bergs%iceberg_bonds_on=iceberg_bonds_on   !Alon
+  bergs%manually_initialize_bonds=manually_initialize_bonds   !Alon
   bergs%critical_interaction_damping_on=critical_interaction_damping_on   !Alon
   bergs%interactive_icebergs_on=interactive_icebergs_on   !Alon
   bergs%use_new_predictive_corrective=use_new_predictive_corrective  !Alon
@@ -2065,6 +2069,140 @@ subroutine print_bergs(iochan, bergs, label)
 
 end subroutine print_bergs
 
+
+! ##############################################################################
+
+subroutine form_a_bond(berg, other_berg_num, other_berg)
+
+type(iceberg), pointer :: berg
+type(iceberg), optional,  pointer :: other_berg
+type(bond) , pointer :: new_bond, first_bond
+integer, intent(in) :: other_berg_num
+print *, 'Forming a bond!!!'
+    
+
+! Step 1: Create a new bond
+allocate(new_bond)
+new_bond%berg_num_of_current_bond=other_berg_num
+if(present(other_berg)) then
+  new_bond%berg_in_current_bond=>other_berg
+else
+  new_bond%berg_in_current_bond=>null()
+endif
+
+! Step 2: Put this new bond at the start of the bond list
+   first_bond=>berg%first_bond
+   if (associated(first_bond)) then
+        new_bond%next_bond=>first_bond
+        new_bond%prev_bond=>null()  !This should not be needed
+        first_bond%prev_bond=>new_bond
+        berg%first_bond=>new_bond
+   else
+       new_bond%next_bond=>null()  !This should not be needed
+       new_bond%prev_bond=>null()  !This should not be needed
+       berg%first_bond=>new_bond
+   endif
+
+end subroutine form_a_bond
+
+! #############################################################################
+! #############################################################################
+subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
+
+type(icebergs), pointer :: bergs
+type(iceberg), pointer :: berg
+type(iceberg), pointer :: other_berg
+type(icebergs_gridded), pointer :: grd
+type(bond) , pointer :: current_bond, other_berg_bond
+!integer, intent(out) :: number_of_bonds 
+integer, intent(out) :: number_of_bonds
+integer :: number_of_bonds_all_pe
+integer :: grdi, grdj
+logical :: bond_is_good
+logical, optional :: check_bond_quality
+logical :: quality_check
+logical :: all_bonds_matching
+integer :: stderrunit
+
+ print *, "starting bond_check"
+ quality_check=.false.
+ all_bonds_matching=.True.
+ if(present(check_bond_quality)) quality_check = check_bond_quality
+
+ ! For convenience
+  grd=>bergs%grd
+
+  number_of_bonds=0  ! This is a bond counter.
+
+  do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
+    berg=>bergs%list(grdi,grdj)%first
+    do while (associated(berg)) ! loop over all bergs
+      current_bond=>berg%first_bond
+      do while (associated(current_bond)) ! loop over all bonds
+        number_of_bonds=number_of_bonds+1
+
+        ! ##### Beginning Quality Check on Bonds ######
+        if (quality_check) then
+          all_bonds_matching=.True.
+          bond_is_good=.False.
+          other_berg=>current_bond%berg_in_current_bond
+          if (associated(other_berg)) then
+            other_berg_bond=>other_berg%first_bond
+          
+            do while (associated(other_berg_bond))  !loops over the icebergs in the other icebergs bond list            
+              if (associated(other_berg_bond%berg_in_current_bond)) then
+                if (other_berg_bond%berg_in_current_bond%iceberg_num==berg%iceberg_num) then
+                  bond_is_good=.True.  !Bond_is_good becomes true when the corresponding bond is found
+                endif
+              endif                 
+              if (bond_is_good) then
+                other_berg_bond=>null()
+              else
+                other_berg_bond=>other_berg_bond%next_bond
+              endif
+            enddo  ! End of loop over the other berg's bonds.
+
+            if (bond_is_good) then
+              print*, 'Perfect quality Bond:', berg%iceberg_num, current_bond%berg_num_of_current_bond
+            else  
+              print*, 'Non-matching bond...:', berg%iceberg_num, current_bond%berg_num_of_current_bond
+              all_bonds_matching=.false.
+            endif
+          else
+            print *, 'Opposite berg is not assosiated:', berg%iceberg_num, current_bond%berg_in_current_bond%iceberg_num    
+            all_bonds_matching=.false.
+          endif
+        endif
+        ! ##### Ending Quality Check on Bonds ######
+
+        current_bond=>current_bond%next_bond
+        enddo !End of loop over current bonds
+        berg=>berg%next
+      enddo ! End of loop over all bergs
+    enddo; enddo !End of loop over all grid cells
+
+    number_of_bonds_all_pe=number_of_bonds
+    call mpp_sum(number_of_bonds_all_pe)
+
+    bergs%nbonds=number_of_bonds_all_pe !Total number of bonds across all pe's
+    if (number_of_bonds .gt. 0) then
+      print *, "Number of bonds on pe, out of a total of: ", number_of_bonds, number_of_bonds_all_pe
+    endif
+
+    if (quality_check) then
+      if (.not.all_bonds_matching) then
+        stderrunit = stderr()
+        write(stderrunit,*) 'diamonds, Bonds are not matching!!!! PE=',mpp_pe()
+        call error_mesg('diamonds, bonds', 'Bonds are not matching!', FATAL)
+      endif
+    endif
+
+    print *, "ending bond_check"
+
+end subroutine count_bonds
+
+
+
 ! ##############################################################################
 
 integer function count_bergs(bergs, with_halos)
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index c093c6a..6044c6c 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -22,10 +22,11 @@ module ice_bergs_io
 
 use time_manager_mod, only: time_type, get_date, get_time, set_date, operator(-)
 
-use ice_bergs_framework, only: icebergs_gridded, xyt, iceberg, icebergs, buffer
+use ice_bergs_framework, only: icebergs_gridded, xyt, iceberg, icebergs, buffer, bond
 use ice_bergs_framework, only: pack_berg_into_buffer2,unpack_berg_from_buffer2
 use ice_bergs_framework, only: pack_traj_into_buffer2,unpack_traj_from_buffer2
 use ice_bergs_framework, only: find_cell,find_cell_by_search,count_bergs,is_point_in_cell,pos_within_cell,append_posn
+use ice_bergs_framework, only: count_bonds, form_a_bond
 use ice_bergs_framework, only: push_posn
 use ice_bergs_framework, only: add_new_berg_to_list,destroy_iceberg
 use ice_bergs_framework, only: increase_ibuffer,increase_ibuffer_traj,grd_chksum2,grd_chksum3
@@ -42,7 +43,7 @@ module ice_bergs_io
 
 public ice_bergs_io_init
 public read_restart_bergs,read_restart_bergs_orig,write_restart,write_trajectory
-public read_restart_calving
+public read_restart_calving, read_restart_bonds
 
 !Local Vars
 integer, parameter :: file_format_major_version=0
@@ -98,14 +99,17 @@ end subroutine ice_bergs_io_init
 subroutine write_restart(bergs)
 ! Arguments
 type(icebergs), pointer :: bergs
+type(bond), pointer :: current_bond
 ! Local variables
 integer :: i,j,id
 character(len=35) :: filename
+character(len=35) :: filename_bonds
 type(iceberg), pointer :: this=>NULL()
 integer :: stderrunit
 !I/O vars
 type(restart_file_type) :: bergs_restart
-integer :: nbergs
+type(restart_file_type) :: bergs_bond_restart
+integer :: nbergs, nbonds
 type(icebergs_gridded), pointer :: grd
 real, allocatable, dimension(:) :: lon,          &
                                    lat,          &
@@ -132,10 +136,16 @@ subroutine write_restart(bergs)
                                    halo_berg,    &
                                    heat_density
 
-integer, allocatable, dimension(:) :: ine,       &
-                                      jne,       &
-                                      iceberg_num,       &
-                                      start_year
+integer, allocatable, dimension(:) :: ine,              &
+                                      jne,              &
+                                      iceberg_num,      &
+                                      start_year,       &
+                                      bond_first_num,   &
+                                      bond_second_num,  &
+                                      bond_first_jne,         &
+                                      bond_first_ine,         &
+                                      bond_second_jne,         &
+                                      bond_second_ine
 
 
 !uvel_old, vvel_old, lon_old, lat_old, axn, ayn, bxn, byn added by Alon.
@@ -188,6 +198,7 @@ subroutine write_restart(bergs)
    allocate(start_year(nbergs))
    allocate(iceberg_num(nbergs))
 
+
   call get_instance_filename("icebergs.res.nc", filename)
   call set_domain(bergs%grd%domain)
   call register_restart_axis(bergs_restart,filename,'i',nbergs)
@@ -237,6 +248,7 @@ subroutine write_restart(bergs)
   id = register_restart_field(bergs_restart,filename,'halo_berg',halo_berg, &
                                             longname='halo_berg',units='dimensionless')
 
+
   ! Write variables
    
   i = 0
@@ -263,6 +275,7 @@ subroutine write_restart(bergs)
     enddo
   enddo ; enddo
 
+
   call save_restart(bergs_restart)
   call free_restart_type(bergs_restart)
 
@@ -299,9 +312,79 @@ subroutine write_restart(bergs)
              iceberg_num,       &
              start_year )
 
+  call nullify_domain()
+
+!########## Creating bond restart file ######################
+
+   !Allocating restart memory for bond related variables.
+   nbonds=0
+   if (bergs%iceberg_bonds_on) then
+     call count_bonds(bergs, nbonds)
+   endif
+
+   allocate(bond_first_num(nbonds))
+   allocate(bond_second_num(nbonds))
+   allocate(bond_first_ine(nbonds))
+   allocate(bond_first_jne(nbonds))
+   allocate(bond_second_ine(nbonds))
+   allocate(bond_second_jne(nbonds))
+
+  call get_instance_filename("bonds_iceberg.res.nc", filename_bonds)
+  call set_domain(bergs%grd%domain)
+  call register_restart_axis(bergs_bond_restart,filename,'i',nbonds)
+  call set_meta_global(bergs_bond_restart,'file_format_major_version',ival=(/file_format_major_version/))
+  call set_meta_global(bergs_bond_restart,'file_format_minor_version',ival=(/file_format_minor_version/))
+  call set_meta_global(bergs_bond_restart,'time_axis',ival=(/0/))
+
+  !Now start writing in the io_tile_root_pe if there are any bergs in the I/O list
+
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'bond_first_ine',bond_first_ine,longname='iceberg ine of first berg in bond',units='dimensionless')
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'bond_first_jne',bond_first_jne,longname='iceberg jne of first berg in bond',units='dimensionless')
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'bond_second_ine',bond_second_ine,longname='iceberg ine of second berg in bond',units='dimensionless')
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'bond_second_jne',bond_second_jne,longname='iceberg jne of second berg in bond',units='dimensionless')
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'bond_first_num',bond_first_num,longname='iceberg id first berg in bond',units='dimensionless')
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'bond_second_num',bond_second_num,longname='iceberg id second berg in bond',units='dimensionless')
+  
+  
+  ! Write variables
+   
+  i = 0
+  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
+    this=>bergs%list(grdi,grdj)%first
+    do while(associated(this)) !Loops over all bergs
+      current_bond=>this%first_bond
+      do while (associated(current_bond)) ! loop over all bonds
+        i = i + 1
+        bond_first_ine(i)=this%ine
+        bond_first_jne(i)=this%jne
+        bond_first_num(i)= this%iceberg_num
+        bond_second_num(i)=current_bond%berg_num_of_current_bond
+        bond_second_ine(i)=current_bond%berg_in_current_bond%ine
+        bond_second_jne(i)=current_bond%berg_in_current_bond%jne
+
+        current_bond=>current_bond%next_bond
+      enddo !End of loop over bonds
+      this=>this%next
+    enddo!End of loop over bergs
+  enddo; enddo !End of loop over grid
+
+  call save_restart(bergs_bond_restart)
+  call free_restart_type(bergs_bond_restart)
+
+
+  deallocate(                 &
+             bond_first_num,  &
+             bond_second_num, &
+             bond_first_ine,        &
+             bond_first_jne,        &
+             bond_second_ine,        &
+             bond_second_jne )
+
 
   call nullify_domain()
 
+!#############################################################################################
+
   ! Write stored ice
   filename='RESTART/calving.res.nc'
   if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(stderrunit,'(2a)') 'diamonds, write_restart: writing ',filename
@@ -960,6 +1043,124 @@ subroutine generate_bergs(bergs,Time)
   end subroutine generate_bergs
   
 end subroutine read_restart_bergs
+
+
+! ##############################################################################
+subroutine read_restart_bonds(bergs,Time)
+! Arguments
+type(icebergs), pointer :: bergs
+type(time_type), intent(in) :: Time
+! Local variables
+integer :: k, siz(4), nbonds_in_file
+logical :: lres, found_restart, found
+logical :: first_berg_found, second_berg_found
+logical :: multiPErestart  ! Not needed with new restart read; currently kept for compatibility
+real :: lon0, lon1, lat0, lat1
+character(len=33) :: filename, filename_base
+type(icebergs_gridded), pointer :: grd
+type(iceberg) :: localberg ! NOT a pointer but an actual local variable
+type(iceberg) , pointer :: this, first_berg, second_berg
+type(bond) , pointer :: current_bond
+integer :: stderrunit
+
+integer, allocatable, dimension(:) :: bond_first_num,   &
+                                      bond_second_num,  &
+                                      bond_first_jne,   &
+                                      bond_first_ine,   &
+                                      bond_second_jne,   &
+                                      bond_second_ine
+!integer, allocatable, dimension(:,:) :: iceberg_counter_grd
+
+  ! Get the stderr unit number
+  stderrunit=stderr()
+
+  ! For convenience
+  grd=>bergs%grd
+
+  ! Zero out nbergs_in_file
+  nbonds_in_file = 0
+
+  filename_base=trim(restart_input_dir)//'bonds_iceberg.res.nc'
+
+  found_restart = find_restart_file(filename_base, filename, multiPErestart, io_tile_id(1))
+  call error_mesg('read_restart_bonds_bergs_new', 'Using new icebergs restart read', NOTE)
+
+  filename = filename_base
+  call get_field_size(filename,'i',siz, field_found=found, domain=bergs%grd%domain)
+  nbonds_in_file = siz(1)
+
+  if (nbonds_in_file .gt. 0) then
+
+     allocate(bond_first_num(nbonds_in_file))
+     allocate(bond_second_num(nbonds_in_file))
+     allocate(bond_first_jne(nbonds_in_file))
+     allocate(bond_first_ine(nbonds_in_file))
+     allocate(bond_second_ine(nbonds_in_file))
+     allocate(bond_second_jne(nbonds_in_file))
+
+
+     call read_unlimited_axis(filename,'bond_first_num',bond_first_num,domain=grd%domain)
+     call read_unlimited_axis(filename,'bond_second_num',bond_second_num,domain=grd%domain)
+     call read_unlimited_axis(filename,'bond_first_jne',bond_first_jne,domain=grd%domain)
+     call read_unlimited_axis(filename,'bond_first_ine',bond_first_ine,domain=grd%domain)
+     call read_unlimited_axis(filename,'bond_second_jne',bond_second_jne,domain=grd%domain)
+     call read_unlimited_axis(filename,'bond_second_ine',bond_second_ine,domain=grd%domain)
+
+     ! Find approx outer bounds for tile
+     lon0=minval( grd%lon(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
+     lon1=maxval( grd%lon(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
+     lat0=minval( grd%lat(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
+     lat1=maxval( grd%lat(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
+     do k=1, nbonds_in_file
+        
+     
+       ! Search for the first berg, which the bond belongs to
+       first_berg_found=.false.
+       first_berg=>null()
+       this=>bergs%list(bond_first_ine(k),bond_first_jne(k))%first
+       do while(associated(this))
+         if (this%iceberg_num == bond_first_num(k)) then
+           first_berg_found=.true.
+           first_berg=>this
+           this=>null()
+         else  
+           this=>this%next
+         endif
+       enddo
+      
+       ! Search for the second berg, which the bond belongs to
+       second_berg_found=.false.
+       second_berg=>null()
+       this=>bergs%list(bond_second_ine(k),bond_second_jne(k))%first
+       do while(associated(this))
+         if (this%iceberg_num == bond_second_num(k)) then
+           second_berg_found=.true.
+           second_berg=>this
+           this=>null()
+         else  
+           this=>this%next
+         endif
+       enddo
+      
+       if (first_berg_found .and. second_berg_found) then
+           call form_a_bond(first_berg, bond_second_num(k),second_berg)
+               
+       else
+            !I need to create an option to slowly search for the icebergs
+           print *, 'The bergs and bonds do not match!!!', k, nbonds_in_file
+           call error_mesg('read_restart_bonds_bergs_new', 'Failure with reading bonds: bergs and bonds do not match', FATAL)
+       endif
+     enddo
+
+     deallocate(               &
+             bond_first_num,   &
+             bond_second_num,  &
+             bond_first_ine,   &
+             bond_first_jne,   &
+             bond_second_ine,  &
+             bond_second_jne )
+   endif
+end subroutine read_restart_bonds
 ! ##############################################################################
 
 subroutine read_restart_calving(bergs)

From 5f3bb1aaf8af92154e2d5b2a7dd6b7e232f4a442 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Fri, 25 Sep 2015 10:57:42 -0400
Subject: [PATCH 069/361] Iceberg bonds can now be read from a restart file.
 This seems to be working well.

---
 icebergs_io.F90 | 173 +++++++++++++++++++++++++++++-------------------
 1 file changed, 106 insertions(+), 67 deletions(-)

diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 6044c6c..3752e84 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -1062,7 +1062,12 @@ subroutine read_restart_bonds(bergs,Time)
 type(iceberg) , pointer :: this, first_berg, second_berg
 type(bond) , pointer :: current_bond
 integer :: stderrunit
-
+integer :: number_first_bonds_matched !How many first bond bergs found on pe
+integer :: number_second_bonds_matched !How many second bond bergs found on pe
+integer :: number_perfect_bonds ! How many complete bonds formed
+integer :: number_partial_bonds ! How many either complete/partial bonds formed.
+integer :: all_pe_number_perfect_bonds, all_pe_number_partial_bonds
+integer :: all_pe_number_first_bonds_matched, all_pe_number_second_bonds_matched
 integer, allocatable, dimension(:) :: bond_first_num,   &
                                       bond_second_num,  &
                                       bond_first_jne,   &
@@ -1091,75 +1096,109 @@ subroutine read_restart_bonds(bergs,Time)
 
   if (nbonds_in_file .gt. 0) then
 
-     allocate(bond_first_num(nbonds_in_file))
-     allocate(bond_second_num(nbonds_in_file))
-     allocate(bond_first_jne(nbonds_in_file))
-     allocate(bond_first_ine(nbonds_in_file))
-     allocate(bond_second_ine(nbonds_in_file))
-     allocate(bond_second_jne(nbonds_in_file))
-
-
-     call read_unlimited_axis(filename,'bond_first_num',bond_first_num,domain=grd%domain)
-     call read_unlimited_axis(filename,'bond_second_num',bond_second_num,domain=grd%domain)
-     call read_unlimited_axis(filename,'bond_first_jne',bond_first_jne,domain=grd%domain)
-     call read_unlimited_axis(filename,'bond_first_ine',bond_first_ine,domain=grd%domain)
-     call read_unlimited_axis(filename,'bond_second_jne',bond_second_jne,domain=grd%domain)
-     call read_unlimited_axis(filename,'bond_second_ine',bond_second_ine,domain=grd%domain)
-
-     ! Find approx outer bounds for tile
-     lon0=minval( grd%lon(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
-     lon1=maxval( grd%lon(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
-     lat0=minval( grd%lat(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
-     lat1=maxval( grd%lat(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
-     do k=1, nbonds_in_file
-        
+    allocate(bond_first_num(nbonds_in_file))
+    allocate(bond_second_num(nbonds_in_file))
+    allocate(bond_first_jne(nbonds_in_file))
+    allocate(bond_first_ine(nbonds_in_file))
+    allocate(bond_second_ine(nbonds_in_file))
+    allocate(bond_second_jne(nbonds_in_file))
+
+
+    call read_unlimited_axis(filename,'bond_first_num',bond_first_num,domain=grd%domain)
+    call read_unlimited_axis(filename,'bond_second_num',bond_second_num,domain=grd%domain)
+    call read_unlimited_axis(filename,'bond_first_jne',bond_first_jne,domain=grd%domain)
+    call read_unlimited_axis(filename,'bond_first_ine',bond_first_ine,domain=grd%domain)
+    call read_unlimited_axis(filename,'bond_second_jne',bond_second_jne,domain=grd%domain)
+    call read_unlimited_axis(filename,'bond_second_ine',bond_second_ine,domain=grd%domain)
+
+    number_first_bonds_matched=0
+    number_second_bonds_matched=0
+    number_perfect_bonds=0
+    number_partial_bonds=0
+    do k=1, nbonds_in_file
+       
+      ! Decide whether the first iceberg is on the processeor
+      if ( bond_first_ine(k)>=grd%isc .and. bond_first_ine(k)<=grd%iec .and. &
+        bond_first_jne(k)>=grd%jsc .and.bond_first_jne(k)<=grd%jec ) then
+        number_first_bonds_matched=number_first_bonds_matched+1
      
-       ! Search for the first berg, which the bond belongs to
-       first_berg_found=.false.
-       first_berg=>null()
-       this=>bergs%list(bond_first_ine(k),bond_first_jne(k))%first
-       do while(associated(this))
-         if (this%iceberg_num == bond_first_num(k)) then
-           first_berg_found=.true.
-           first_berg=>this
-           this=>null()
-         else  
-           this=>this%next
-         endif
-       enddo
-      
-       ! Search for the second berg, which the bond belongs to
-       second_berg_found=.false.
-       second_berg=>null()
-       this=>bergs%list(bond_second_ine(k),bond_second_jne(k))%first
-       do while(associated(this))
-         if (this%iceberg_num == bond_second_num(k)) then
-           second_berg_found=.true.
-           second_berg=>this
-           this=>null()
-         else  
-           this=>this%next
-         endif
-       enddo
+        ! Search for the first berg, which the bond belongs to
+        first_berg_found=.false.
+        first_berg=>null()
+        this=>bergs%list(bond_first_ine(k),bond_first_jne(k))%first
+        do while(associated(this))
+          if (this%iceberg_num == bond_first_num(k)) then
+            first_berg_found=.true.
+            first_berg=>this
+            this=>null()
+          else  
+            this=>this%next
+          endif
+        enddo
       
-       if (first_berg_found .and. second_berg_found) then
-           call form_a_bond(first_berg, bond_second_num(k),second_berg)
-               
-       else
-            !I need to create an option to slowly search for the icebergs
-           print *, 'The bergs and bonds do not match!!!', k, nbonds_in_file
-           call error_mesg('read_restart_bonds_bergs_new', 'Failure with reading bonds: bergs and bonds do not match', FATAL)
-       endif
-     enddo
+        ! Decide whether the second iceberg is on the processeor (data domain)
+        second_berg_found=.false.
+        if ( bond_second_ine(k)>=grd%isd .and. bond_second_ine(k)<=grd%ied .and. &
+          bond_second_jne(k)>=grd%jsd .and.bond_second_jne(k)<=grd%jed ) then
+          number_second_bonds_matched=number_second_bonds_matched+1
+
+          ! Search for the second berg, which the bond belongs to
+          second_berg=>null()
+          this=>bergs%list(bond_second_ine(k),bond_second_jne(k))%first
+          do while(associated(this))
+            if (this%iceberg_num == bond_second_num(k)) then
+              second_berg_found=.true.
+              second_berg=>this
+              this=>null()
+            else  
+              this=>this%next
+            endif
+          enddo
+        endif
+         
+        if (first_berg_found) then
+          number_partial_bonds=number_partial_bonds+1
+          if (second_berg_found) then
+            call form_a_bond(first_berg, bond_second_num(k),second_berg)
+            number_perfect_bonds=number_perfect_bonds+1
+          else
+            call form_a_bond(first_berg, bond_second_num(k))
+          endif
+        else
+          write(*,'(a,i8,a)') 'diamonds, bond read restart : ','Not enough partial bonds formed', k, mpp_pe(), nbonds_in_file
+          call error_mesg('read_restart_bonds_bergs_new', 'Failure with reading bonds: First bond not found on pe', FATAL)
+        endif
+      endif
+    enddo
 
-     deallocate(               &
-             bond_first_num,   &
-             bond_second_num,  &
-             bond_first_ine,   &
-             bond_first_jne,   &
-             bond_second_ine,  &
-             bond_second_jne )
-   endif
+    !Analyse how many bonds were created and take appropriate action
+    all_pe_number_perfect_bonds=number_perfect_bonds
+    all_pe_number_partial_bonds=number_partial_bonds
+    all_pe_number_first_bonds_matched=number_first_bonds_matched
+    all_pe_number_second_bonds_matched=number_second_bonds_matched
+    call mpp_sum(all_pe_number_perfect_bonds)
+    call mpp_sum(all_pe_number_partial_bonds)
+    call mpp_sum(all_pe_number_first_bonds_matched)
+    call mpp_sum(all_pe_number_second_bonds_matched)
+
+    if (all_pe_number_partial_bonds .lt. nbonds_in_file) then
+      write(*,'(a,i8,a)') 'diamonds, bond read restart : ','Not enough partial bonds formed', all_pe_number_partial_bonds , nbonds_in_file
+      call error_mesg('read_restart_bonds_bergs_new', 'Not enough partial bonds formed', FATAL)
+    endif
+    
+    if (all_pe_number_perfect_bonds .lt. nbonds_in_file) then
+      write(*,'(a,i8,a)') 'diamonds, bond read restart : ','Warning, some bonds are not fully formed', all_pe_number_perfect_bonds , nbonds_in_file
+      call error_mesg('read_restart_bonds_bergs_new', 'Not enough perfect bonds formed', NOTE)
+    endif
+
+    deallocate(               &
+            bond_first_num,   &
+            bond_second_num,  &
+            bond_first_ine,   &
+            bond_first_jne,   &
+            bond_second_ine,  &
+            bond_second_jne )
+  endif
 end subroutine read_restart_bonds
 ! ##############################################################################
 

From 97933556c1abca30a0d0553b25dcf526d5245dad Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Fri, 25 Sep 2015 16:27:14 -0400
Subject: [PATCH 070/361] Icebergs bonds can now move from one processor to
 another. After the bond has moved, it is reconstructed on the other
 processor.

I still need to write a scheme which locates the partner bergs on the other processor. However, this will be simple, since the berg stores the address of the partner berg in the bond, and moves it to the other processor.

I have also introduced a namelist parameter called max_bonds, which is the maximum amount of bonds that one iceberg can have when it is moved from one processor to another.

This all seems to be working for now.
---
 icebergs.F90           |   2 +-
 icebergs_framework.F90 | 160 ++++++++++++++++++++++++++++++-----------
 icebergs_io.F90        | 137 +++++++++++++++++------------------
 3 files changed, 189 insertions(+), 110 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 0f51e60..43f3610 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -166,7 +166,7 @@ subroutine initialize_iceberg_bonds(bergs)
             r_dist=sqrt( ((x1-x2)**2) + ((y1-y2)**2) )
         
             !if (r_dist.gt.1000.) then  ! If the bergs are close together, then form a bond
-              call form_a_bond(berg, other_berg%iceberg_num, other_berg)
+              call form_a_bond(berg, other_berg%iceberg_num, other_berg%ine, other_berg%jne, other_berg)
             !endif       
           endif
           other_berg=>other_berg%next
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index cd2dd54..8df3610 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -163,8 +163,8 @@ module ice_bergs_framework
 
 type :: bond
   type(bond), pointer :: prev_bond=>null(), next_bond=>null()
-  type(iceberg), pointer :: berg_in_current_bond=>null()
-  integer :: berg_num_of_current_bond
+  type(iceberg), pointer :: other_berg=>null()
+  integer :: other_berg_num, other_berg_ine, other_berg_jne 
 end type bond
 
 type :: buffer
@@ -185,6 +185,7 @@ module ice_bergs_framework
   real :: current_yearday ! 1.00-365.99
   integer :: traj_sample_hrs, traj_write_hrs
   integer :: verbose_hrs
+  integer :: max_bonds
   integer :: clock, clock_mom, clock_the, clock_int, clock_cal, clock_com, clock_ini, clock_ior, clock_iow, clock_dia ! ids for fms timers
   integer :: clock_trw, clock_trp
   real :: rho_bergs ! Density of icebergs [kg/m^3]
@@ -289,6 +290,7 @@ subroutine ice_bergs_framework_init(bergs, &
 integer :: traj_sample_hrs=24 ! Period between sampling of position for trajectory storage
 integer :: traj_write_hrs=480 ! Period between writing sampled trajectories to disk
 integer :: verbose_hrs=24 ! Period between verbose messages
+integer :: max_bonds=6 ! Maximum number of iceberg bond passed between processors
 real :: rho_bergs=850. ! Density of icebergs
 real :: spring_coef=1.e-4  ! Spring contant for iceberg interactions - Alon
 real :: radial_damping_coef=1.e-4     ! Coef for relative iceberg motion damping (radial component) -Alon
@@ -314,7 +316,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real, dimension(nclasses) :: distribution=(/0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02/) ! Fraction of calving to apply to this class (non-dim) , 
 real, dimension(nclasses) :: mass_scaling=(/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) ! Ratio between effective and real iceberg mass (non-dim)
 real, dimension(nclasses) :: initial_thickness=(/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) ! Total thickness of newly calved bergs (m)
-namelist /icebergs_nml/ verbose, budget, halo, iceberg_halo, traj_sample_hrs, initial_mass, traj_write_hrs, &
+namelist /icebergs_nml/ verbose, budget, halo, iceberg_halo, traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, &
          distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef, radial_damping_coef, tangental_damping_coef, &
          rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, iceberg_bonds_on, manually_initialize_bonds, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, &
@@ -569,6 +571,9 @@ subroutine ice_bergs_framework_init(bergs, &
 if (.not.interactive_icebergs_on) then
   !iceberg_bonds_on=.false.  ! This line needs to included later, but is omitted for testing
 endif
+if (.not. iceberg_bonds_on) then
+   max_bonds=0
+endif
 
 
  ! Parameters
@@ -577,6 +582,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%traj_write_hrs=traj_write_hrs
   bergs%verbose_hrs=verbose_hrs
   bergs%grd%halo=halo
+  bergs%max_bonds=max_bonds
   bergs%grd%iceberg_halo=iceberg_halo
   bergs%rho_bergs=rho_bergs
   bergs%spring_coef=spring_coef
@@ -816,7 +822,9 @@ subroutine update_halo_icebergs(bergs)
 integer :: halo_width
 integer :: temp1, temp2
 real :: current_halo_status
-  
+logical :: force_app
+
+force_app =.false.
 halo_width=bergs%grd%iceberg_halo  ! Must be less than current halo value used for updating weight.
 
  ! Get the stderr unit number
@@ -870,7 +878,7 @@ subroutine update_halo_icebergs(bergs)
         nbergs_to_send_e=nbergs_to_send_e+1
         current_halo_status=kick_the_bucket%halo_berg
         kick_the_bucket%halo_berg=1.
-        call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_e, nbergs_to_send_e)
+        call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_e, nbergs_to_send_e, bergs%max_bonds)
         kick_the_bucket%halo_berg=current_halo_status
     enddo
   enddo; enddo
@@ -883,7 +891,7 @@ subroutine update_halo_icebergs(bergs)
       nbergs_to_send_w=nbergs_to_send_w+1
        current_halo_status=kick_the_bucket%halo_berg
        kick_the_bucket%halo_berg=1.
-       call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_w, nbergs_to_send_w)
+       call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_w, nbergs_to_send_w, bergs%max_bonds)
        kick_the_bucket%halo_berg=current_halo_status
     enddo 
   enddo; enddo
@@ -917,7 +925,7 @@ subroutine update_halo_icebergs(bergs)
       call increase_ibuffer(bergs%ibuffer_w, nbergs_rcvd_from_w)
       call mpp_recv(bergs%ibuffer_w%data, nbergs_rcvd_from_w*buffer_width, grd%pe_W, tag=COMM_TAG_2)
       do i=1, nbergs_rcvd_from_w
-        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_w, i, grd)
+        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_w, i, grd, force_app, bergs%max_bonds )
       enddo
     endif
   else
@@ -935,7 +943,7 @@ subroutine update_halo_icebergs(bergs)
       call increase_ibuffer(bergs%ibuffer_e, nbergs_rcvd_from_e)
       call mpp_recv(bergs%ibuffer_e%data, nbergs_rcvd_from_e*buffer_width, grd%pe_E, tag=COMM_TAG_4)
       do i=1, nbergs_rcvd_from_e
-        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_e, i, grd)
+        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_e, i, grd, force_app, bergs%max_bonds )
       enddo
     endif
   else
@@ -957,7 +965,7 @@ subroutine update_halo_icebergs(bergs)
       nbergs_to_send_n=nbergs_to_send_n+1
       current_halo_status=kick_the_bucket%halo_berg
       kick_the_bucket%halo_berg=1.
-      call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_n, nbergs_to_send_n)
+      call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_n, nbergs_to_send_n, bergs%max_bonds )
       kick_the_bucket%halo_berg=current_halo_status
     enddo
   enddo; enddo
@@ -971,7 +979,7 @@ subroutine update_halo_icebergs(bergs)
       nbergs_to_send_s=nbergs_to_send_s+1
        current_halo_status=kick_the_bucket%halo_berg
        kick_the_bucket%halo_berg=1.
-       call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_s, nbergs_to_send_s)
+       call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_s, nbergs_to_send_s,bergs%max_bonds )
        kick_the_bucket%halo_berg=current_halo_status
     enddo
   enddo; enddo
@@ -1013,7 +1021,7 @@ subroutine update_halo_icebergs(bergs)
       call increase_ibuffer(bergs%ibuffer_s, nbergs_rcvd_from_s)
       call mpp_recv(bergs%ibuffer_s%data, nbergs_rcvd_from_s*buffer_width, grd%pe_S, tag=COMM_TAG_6)
       do i=1, nbergs_rcvd_from_s
-        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_s, i, grd)
+        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_s, i, grd,force_app, bergs%max_bonds  )
       enddo
     endif
   else
@@ -1039,7 +1047,7 @@ subroutine update_halo_icebergs(bergs)
          call mpp_recv(bergs%ibuffer_n%data, nbergs_rcvd_from_n*buffer_width, grd%pe_N, tag=COMM_TAG_8)
       endif
       do i=1, nbergs_rcvd_from_n
-        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_n, i, grd)
+        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_n, i, grd, force_app, bergs%max_bonds )
       enddo
     endif
   else
@@ -1089,6 +1097,9 @@ subroutine send_bergs_to_other_pes(bergs)
 integer :: i, nbergs_start, nbergs_end
 integer :: stderrunit
 integer :: grdi, grdj
+logical :: force_app
+
+force_app=.false.
 
   ! Get the stderr unit number
   stderrunit = stderr()
@@ -1111,14 +1122,14 @@ subroutine send_bergs_to_other_pes(bergs)
           kick_the_bucket=>this
           this=>this%next
           nbergs_to_send_e=nbergs_to_send_e+1
-          call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_e, nbergs_to_send_e)
+          call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_e, nbergs_to_send_e, bergs%max_bonds  )
           call move_trajectory(bergs, kick_the_bucket)
           call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
         elseif (this%ine.lt.bergs%grd%isc) then
           kick_the_bucket=>this
           this=>this%next
           nbergs_to_send_w=nbergs_to_send_w+1
-          call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_w, nbergs_to_send_w)
+          call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_w, nbergs_to_send_w, bergs%max_bonds  )
           call move_trajectory(bergs, kick_the_bucket)
           call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
         else
@@ -1157,7 +1168,7 @@ subroutine send_bergs_to_other_pes(bergs)
       call increase_ibuffer(bergs%ibuffer_w, nbergs_rcvd_from_w)
       call mpp_recv(bergs%ibuffer_w%data, nbergs_rcvd_from_w*buffer_width, grd%pe_W, tag=COMM_TAG_2)
       do i=1, nbergs_rcvd_from_w
-        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_w, i, grd)
+        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_w, i, grd, force_app, bergs%max_bonds  )
       enddo
     endif
   else
@@ -1175,7 +1186,7 @@ subroutine send_bergs_to_other_pes(bergs)
       call increase_ibuffer(bergs%ibuffer_e, nbergs_rcvd_from_e)
       call mpp_recv(bergs%ibuffer_e%data, nbergs_rcvd_from_e*buffer_width, grd%pe_E, tag=COMM_TAG_4)
       do i=1, nbergs_rcvd_from_e
-        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_e, i, grd)
+        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_e, i, grd, force_app,  bergs%max_bonds)
       enddo
     endif
   else
@@ -1196,14 +1207,14 @@ subroutine send_bergs_to_other_pes(bergs)
           kick_the_bucket=>this
           this=>this%next
           nbergs_to_send_n=nbergs_to_send_n+1
-          call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_n, nbergs_to_send_n)
+          call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_n, nbergs_to_send_n,bergs%max_bonds)
           call move_trajectory(bergs, kick_the_bucket)
           call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
         elseif (this%jne.lt.bergs%grd%jsc) then
           kick_the_bucket=>this
           this=>this%next
           nbergs_to_send_s=nbergs_to_send_s+1
-          call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_s, nbergs_to_send_s)
+          call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_s, nbergs_to_send_s,bergs%max_bonds)
           call move_trajectory(bergs, kick_the_bucket)
           call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
         else
@@ -1250,7 +1261,7 @@ subroutine send_bergs_to_other_pes(bergs)
       call increase_ibuffer(bergs%ibuffer_s, nbergs_rcvd_from_s)
       call mpp_recv(bergs%ibuffer_s%data, nbergs_rcvd_from_s*buffer_width, grd%pe_S, tag=COMM_TAG_6)
       do i=1, nbergs_rcvd_from_s
-        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_s, i, grd) 
+        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_s, i, grd, force_app, bergs%max_bonds ) 
       enddo
     endif
   else
@@ -1276,7 +1287,7 @@ subroutine send_bergs_to_other_pes(bergs)
          call mpp_recv(bergs%ibuffer_n%data, nbergs_rcvd_from_n*buffer_width, grd%pe_N, tag=COMM_TAG_8)
       endif
       do i=1, nbergs_rcvd_from_n
-        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_n, i, grd)
+        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_n, i, grd,force_app, bergs%max_bonds)
       enddo
     endif
   else
@@ -1328,12 +1339,20 @@ subroutine send_bergs_to_other_pes(bergs)
 
 end subroutine send_bergs_to_other_pes
 
-  subroutine pack_berg_into_buffer2(berg, buff, n)
+  subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
   ! Arguments
   type(iceberg), pointer :: berg
   type(buffer), pointer :: buff
   integer, intent(in) :: n
+  integer, optional :: max_bonds_in
+  !integer, intent(in) :: max_bonds  ! Change this later
   ! Local variables
+  integer :: counter, k, max_bonds
+  type(bond), pointer :: current_bond
+ 
+    max_bonds=0
+    if (present(max_bonds_in)) max_bonds=max_bonds_in
+
 
     if (.not.associated(buff)) call increase_buffer(buff,delta_buf)
     if (n>buff%size) call increase_buffer(buff,delta_buf)
@@ -1362,12 +1381,30 @@ subroutine pack_berg_into_buffer2(berg, buff, n)
     buff%data(22,n)=berg%ayn  !Alon
     buff%data(23,n)=berg%bxn  !Alon
     buff%data(24,n)=berg%byn  !Alon
-    buff%data(25,n)=berg%uvel_old  !Alon
+    buff%data(25,n)=berg%uvel_old  !Alon  
     buff%data(26,n)=berg%vvel_old  !Alon
     buff%data(27,n)=berg%lon_old  !Alon
     buff%data(28,n)=berg%lat_old  !Alon
     buff%data(29,n)=float(berg%iceberg_num)
-    buff%data(30,n)=berg%halo_berg  
+    buff%data(30,n)=berg%halo_berg 
+
+    if (max_bonds .gt. 0) then
+      counter=30 !how many data points being passed so far (must match above)
+      do k = 1,max_bonds
+        current_bond=>berg%first_bond
+        if (associated(current_bond)) then
+          buff%data(counter+(3*(k-1)+1),n)=float(current_bond%other_berg_num) 
+          buff%data(counter+(3*(k-1)+2),n)=float(current_bond%other_berg_ine)
+          buff%data(counter+(3*(k-1)+3),n)=float(current_bond%other_berg_jne)
+          current_bond=>current_bond%next_bond
+        else
+          buff%data(counter+(3*(k-1)+1),n)=0. 
+          buff%data(counter+(3*(k-1)+2),n)=0.
+          buff%data(counter+(3*(k-1)+3),n)=0.
+        endif
+      enddo
+    endif
+
 
   end subroutine pack_berg_into_buffer2
 
@@ -1397,13 +1434,14 @@ subroutine increase_buffer(old,delta)
 
   end subroutine increase_buffer
 
-  subroutine unpack_berg_from_buffer2(bergs, buff, n,grd, force_append)
+  subroutine unpack_berg_from_buffer2(bergs, buff, n,grd, force_append, max_bonds_in)
   ! Arguments
   type(icebergs), pointer :: bergs
   type(buffer), pointer :: buff
   integer, intent(in) :: n
   type(icebergs_gridded), pointer :: grd  
   logical, optional :: force_append
+  integer, optional :: max_bonds_in
  ! Local variables
  !real :: lon, lat, uvel, vvel, xi, yj
 
@@ -1411,11 +1449,19 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n,grd, force_append)
  !integer :: ine, jne, start_year
   logical :: lres
   type(iceberg) :: localberg
+  type(iceberg), pointer :: this
+  integer :: other_berg_num, other_berg_ine, other_berg_jne
+  integer :: counter, k, max_bonds
   integer :: stderrunit
   logical :: force_app = .false.
+  logical :: quick
+
   ! Get the stderr unit number
   stderrunit = stderr()
-
+ 
+  quick=.false.
+  max_bonds=0
+  if (present(max_bonds_in)) max_bonds=max_bonds_in
   if(present(force_append)) force_app = force_append
      
     localberg%lon=buff%data(1,n)
@@ -1449,19 +1495,20 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n,grd, force_append)
     localberg%halo_berg=buff%data(30,n) 
    
     if(force_app) then !force append with origin ine,jne (for I/O)
+
       localberg%ine=buff%data(19,n) 
       localberg%jne=buff%data(20,n) 
-      call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg) 
+      call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg,quick,this) 
     else
       lres=find_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
       if (lres) then
         lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
-        call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg)
+        call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg,quick,this)
       else
         lres=find_cell_wide(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
         if (lres) then
           lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
-          call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg)
+          call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg,quick,this)
         else
           write(stderrunit,'("diamonds, unpack_berg_from_buffer pe=(",i3,a,2i4,a,2f8.2)')&
            & mpp_pe(),') Failed to find i,j=',localberg%ine,localberg%jne,' for lon,lat=',localberg%lon,localberg%lat
@@ -1481,8 +1528,24 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n,grd, force_append)
           call error_mesg('diamonds, unpack_berg_from_buffer', 'can not find a cell to place berg in!', FATAL)
         endif
       endif
-  
-  endif
+    endif
+
+    !#  Do stuff to do with bonds here MP1
+
+    if (max_bonds .gt. 0) then
+      counter=30 !how many data points being passed so far (must match above)
+      do k = 1,max_bonds
+        other_berg_num=nint(buff%data(counter+(3*(k-1)+1),n))
+        other_berg_ine=nint(buff%data(counter+(3*(k-1)+2),n))
+        other_berg_jne=nint(buff%data(counter+(3*(k-1)+3),n))
+        if (other_berg_num .gt. 0) then
+          call form_a_bond(this, other_berg_num, other_berg_ine, other_berg_jne)
+        endif
+      enddo
+    endif
+
+    !##############################
+
   end subroutine unpack_berg_from_buffer2
 
   subroutine increase_ibuffer(old,delta)
@@ -1679,10 +1742,11 @@ end subroutine unpack_traj_from_buffer2
 
 ! ##############################################################################
 
-subroutine add_new_berg_to_list(first, bergvals, quick)
+subroutine add_new_berg_to_list(first, bergvals, quick, newberg_return)
 ! Arguments
 type(iceberg), pointer :: first
 type(iceberg), intent(in) :: bergvals
+type(iceberg), intent(out), pointer, optional :: newberg_return
 logical, intent(in), optional :: quick
 ! Local variables
 type(iceberg), pointer :: new=>null()
@@ -1690,12 +1754,18 @@ subroutine add_new_berg_to_list(first, bergvals, quick)
   new=>null()
   call create_iceberg(new, bergvals)
 
+  if (present(newberg_return)) then
+    newberg_return=>new
+    !newberg_return=>null()
+  endif
+
   if (present(quick)) then
     if(quick) call insert_berg_into_list(first, new, quick=.true.)
   else
     call insert_berg_into_list(first, new)
   endif
 
+
   !Clear new
   new=>null()
 
@@ -2072,22 +2142,30 @@ end subroutine print_bergs
 
 ! ##############################################################################
 
-subroutine form_a_bond(berg, other_berg_num, other_berg)
+subroutine form_a_bond(berg, other_berg_num, other_berg_ine, other_berg_jne, other_berg)
 
 type(iceberg), pointer :: berg
 type(iceberg), optional,  pointer :: other_berg
 type(bond) , pointer :: new_bond, first_bond
 integer, intent(in) :: other_berg_num
+integer, optional  :: other_berg_ine, other_berg_jne
+
 print *, 'Forming a bond!!!'
     
 
 ! Step 1: Create a new bond
 allocate(new_bond)
-new_bond%berg_num_of_current_bond=other_berg_num
+new_bond%other_berg_num=other_berg_num
 if(present(other_berg)) then
-  new_bond%berg_in_current_bond=>other_berg
+  new_bond%other_berg=>other_berg
+  new_bond%other_berg_ine=other_berg%ine
+  new_bond%other_berg_jne=other_berg%jne
 else
-  new_bond%berg_in_current_bond=>null()
+  new_bond%other_berg=>null()
+  if (present(other_berg_ine)) then
+    new_bond%other_berg_ine=other_berg_ine
+    new_bond%other_berg_jne=other_berg_jne
+  endif
 endif
 
 ! Step 2: Put this new bond at the start of the bond list
@@ -2145,13 +2223,13 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
         if (quality_check) then
           all_bonds_matching=.True.
           bond_is_good=.False.
-          other_berg=>current_bond%berg_in_current_bond
+          other_berg=>current_bond%other_berg
           if (associated(other_berg)) then
             other_berg_bond=>other_berg%first_bond
           
             do while (associated(other_berg_bond))  !loops over the icebergs in the other icebergs bond list            
-              if (associated(other_berg_bond%berg_in_current_bond)) then
-                if (other_berg_bond%berg_in_current_bond%iceberg_num==berg%iceberg_num) then
+              if (associated(other_berg_bond%other_berg)) then
+                if (other_berg_bond%other_berg%iceberg_num==berg%iceberg_num) then
                   bond_is_good=.True.  !Bond_is_good becomes true when the corresponding bond is found
                 endif
               endif                 
@@ -2163,13 +2241,13 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
             enddo  ! End of loop over the other berg's bonds.
 
             if (bond_is_good) then
-              print*, 'Perfect quality Bond:', berg%iceberg_num, current_bond%berg_num_of_current_bond
+              print*, 'Perfect quality Bond:', berg%iceberg_num, current_bond%other_berg_num
             else  
-              print*, 'Non-matching bond...:', berg%iceberg_num, current_bond%berg_num_of_current_bond
+              print*, 'Non-matching bond...:', berg%iceberg_num, current_bond%other_berg_num
               all_bonds_matching=.false.
             endif
           else
-            print *, 'Opposite berg is not assosiated:', berg%iceberg_num, current_bond%berg_in_current_bond%iceberg_num    
+            print *, 'Opposite berg is not assosiated:', berg%iceberg_num, current_bond%other_berg%iceberg_num    
             all_bonds_matching=.false.
           endif
         endif
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 3752e84..9b6d4e0 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -140,12 +140,12 @@ subroutine write_restart(bergs)
                                       jne,              &
                                       iceberg_num,      &
                                       start_year,       &
-                                      bond_first_num,   &
-                                      bond_second_num,  &
-                                      bond_first_jne,         &
-                                      bond_first_ine,         &
-                                      bond_second_jne,         &
-                                      bond_second_ine
+                                      first_berg_num,   &
+                                      other_berg_num,   &
+                                      first_berg_jne,         &
+                                      first_berg_ine,         &
+                                      other_berg_jne,         &
+                                      other_berg_ine
 
 
 !uvel_old, vvel_old, lon_old, lat_old, axn, ayn, bxn, byn added by Alon.
@@ -322,12 +322,12 @@ subroutine write_restart(bergs)
      call count_bonds(bergs, nbonds)
    endif
 
-   allocate(bond_first_num(nbonds))
-   allocate(bond_second_num(nbonds))
-   allocate(bond_first_ine(nbonds))
-   allocate(bond_first_jne(nbonds))
-   allocate(bond_second_ine(nbonds))
-   allocate(bond_second_jne(nbonds))
+   allocate(first_berg_num(nbonds))
+   allocate(other_berg_num(nbonds))
+   allocate(first_berg_ine(nbonds))
+   allocate(first_berg_jne(nbonds))
+   allocate(other_berg_ine(nbonds))
+   allocate(other_berg_jne(nbonds))
 
   call get_instance_filename("bonds_iceberg.res.nc", filename_bonds)
   call set_domain(bergs%grd%domain)
@@ -338,12 +338,12 @@ subroutine write_restart(bergs)
 
   !Now start writing in the io_tile_root_pe if there are any bergs in the I/O list
 
-  id = register_restart_field(bergs_bond_restart,filename_bonds,'bond_first_ine',bond_first_ine,longname='iceberg ine of first berg in bond',units='dimensionless')
-  id = register_restart_field(bergs_bond_restart,filename_bonds,'bond_first_jne',bond_first_jne,longname='iceberg jne of first berg in bond',units='dimensionless')
-  id = register_restart_field(bergs_bond_restart,filename_bonds,'bond_second_ine',bond_second_ine,longname='iceberg ine of second berg in bond',units='dimensionless')
-  id = register_restart_field(bergs_bond_restart,filename_bonds,'bond_second_jne',bond_second_jne,longname='iceberg jne of second berg in bond',units='dimensionless')
-  id = register_restart_field(bergs_bond_restart,filename_bonds,'bond_first_num',bond_first_num,longname='iceberg id first berg in bond',units='dimensionless')
-  id = register_restart_field(bergs_bond_restart,filename_bonds,'bond_second_num',bond_second_num,longname='iceberg id second berg in bond',units='dimensionless')
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'first_berg_ine',first_berg_ine,longname='iceberg ine of first berg in bond',units='dimensionless')
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'first_berg_jne',first_berg_jne,longname='iceberg jne of first berg in bond',units='dimensionless')
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'first_berg_num',first_berg_num,longname='iceberg id first berg in bond',units='dimensionless')
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'other_berg_ine',other_berg_ine,longname='iceberg ine of second berg in bond',units='dimensionless')
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'other_berg_jne',other_berg_jne,longname='iceberg jne of second berg in bond',units='dimensionless')
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'other_berg_num',other_berg_num,longname='iceberg id second berg in bond',units='dimensionless')
   
   
   ! Write variables
@@ -355,12 +355,12 @@ subroutine write_restart(bergs)
       current_bond=>this%first_bond
       do while (associated(current_bond)) ! loop over all bonds
         i = i + 1
-        bond_first_ine(i)=this%ine
-        bond_first_jne(i)=this%jne
-        bond_first_num(i)= this%iceberg_num
-        bond_second_num(i)=current_bond%berg_num_of_current_bond
-        bond_second_ine(i)=current_bond%berg_in_current_bond%ine
-        bond_second_jne(i)=current_bond%berg_in_current_bond%jne
+        first_berg_ine(i)=this%ine
+        first_berg_jne(i)=this%jne
+        first_berg_num(i)= this%iceberg_num
+        other_berg_num(i)=current_bond%other_berg_num
+        other_berg_ine(i)=current_bond%other_berg%ine
+        other_berg_jne(i)=current_bond%other_berg%jne
 
         current_bond=>current_bond%next_bond
       enddo !End of loop over bonds
@@ -373,12 +373,12 @@ subroutine write_restart(bergs)
 
 
   deallocate(                 &
-             bond_first_num,  &
-             bond_second_num, &
-             bond_first_ine,        &
-             bond_first_jne,        &
-             bond_second_ine,        &
-             bond_second_jne )
+             first_berg_num,  &
+             other_berg_num, &
+             first_berg_ine,        &
+             first_berg_jne,        &
+             other_berg_ine,        &
+             other_berg_jne )
 
 
   call nullify_domain()
@@ -1068,12 +1068,12 @@ subroutine read_restart_bonds(bergs,Time)
 integer :: number_partial_bonds ! How many either complete/partial bonds formed.
 integer :: all_pe_number_perfect_bonds, all_pe_number_partial_bonds
 integer :: all_pe_number_first_bonds_matched, all_pe_number_second_bonds_matched
-integer, allocatable, dimension(:) :: bond_first_num,   &
-                                      bond_second_num,  &
-                                      bond_first_jne,   &
-                                      bond_first_ine,   &
-                                      bond_second_jne,   &
-                                      bond_second_ine
+integer, allocatable, dimension(:) :: first_berg_num,   &
+                                      other_berg_num,  &
+                                      first_berg_jne,   &
+                                      first_berg_ine,   &
+                                      other_berg_jne,   &
+                                      other_berg_ine
 !integer, allocatable, dimension(:,:) :: iceberg_counter_grd
 
   ! Get the stderr unit number
@@ -1088,7 +1088,7 @@ subroutine read_restart_bonds(bergs,Time)
   filename_base=trim(restart_input_dir)//'bonds_iceberg.res.nc'
 
   found_restart = find_restart_file(filename_base, filename, multiPErestart, io_tile_id(1))
-  call error_mesg('read_restart_bonds_bergs_new', 'Using new icebergs restart read', NOTE)
+  call error_mesg('read_restart_bonds_bergs_new', 'Using new icebergs bond restart read', NOTE)
 
   filename = filename_base
   call get_field_size(filename,'i',siz, field_found=found, domain=bergs%grd%domain)
@@ -1096,20 +1096,20 @@ subroutine read_restart_bonds(bergs,Time)
 
   if (nbonds_in_file .gt. 0) then
 
-    allocate(bond_first_num(nbonds_in_file))
-    allocate(bond_second_num(nbonds_in_file))
-    allocate(bond_first_jne(nbonds_in_file))
-    allocate(bond_first_ine(nbonds_in_file))
-    allocate(bond_second_ine(nbonds_in_file))
-    allocate(bond_second_jne(nbonds_in_file))
+    allocate(first_berg_num(nbonds_in_file))
+    allocate(other_berg_num(nbonds_in_file))
+    allocate(first_berg_jne(nbonds_in_file))
+    allocate(first_berg_ine(nbonds_in_file))
+    allocate(other_berg_ine(nbonds_in_file))
+    allocate(other_berg_jne(nbonds_in_file))
 
 
-    call read_unlimited_axis(filename,'bond_first_num',bond_first_num,domain=grd%domain)
-    call read_unlimited_axis(filename,'bond_second_num',bond_second_num,domain=grd%domain)
-    call read_unlimited_axis(filename,'bond_first_jne',bond_first_jne,domain=grd%domain)
-    call read_unlimited_axis(filename,'bond_first_ine',bond_first_ine,domain=grd%domain)
-    call read_unlimited_axis(filename,'bond_second_jne',bond_second_jne,domain=grd%domain)
-    call read_unlimited_axis(filename,'bond_second_ine',bond_second_ine,domain=grd%domain)
+    call read_unlimited_axis(filename,'first_berg_num',first_berg_num,domain=grd%domain)
+    call read_unlimited_axis(filename,'other_berg_num',other_berg_num,domain=grd%domain)
+    call read_unlimited_axis(filename,'first_berg_jne',first_berg_jne,domain=grd%domain)
+    call read_unlimited_axis(filename,'first_berg_ine',first_berg_ine,domain=grd%domain)
+    call read_unlimited_axis(filename,'other_berg_jne',other_berg_jne,domain=grd%domain)
+    call read_unlimited_axis(filename,'other_berg_ine',other_berg_ine,domain=grd%domain)
 
     number_first_bonds_matched=0
     number_second_bonds_matched=0
@@ -1118,16 +1118,16 @@ subroutine read_restart_bonds(bergs,Time)
     do k=1, nbonds_in_file
        
       ! Decide whether the first iceberg is on the processeor
-      if ( bond_first_ine(k)>=grd%isc .and. bond_first_ine(k)<=grd%iec .and. &
-        bond_first_jne(k)>=grd%jsc .and.bond_first_jne(k)<=grd%jec ) then
+      if ( first_berg_ine(k)>=grd%isc .and. first_berg_ine(k)<=grd%iec .and. &
+        first_berg_jne(k)>=grd%jsc .and.first_berg_jne(k)<=grd%jec ) then
         number_first_bonds_matched=number_first_bonds_matched+1
      
         ! Search for the first berg, which the bond belongs to
         first_berg_found=.false.
         first_berg=>null()
-        this=>bergs%list(bond_first_ine(k),bond_first_jne(k))%first
+        this=>bergs%list(first_berg_ine(k),first_berg_jne(k))%first
         do while(associated(this))
-          if (this%iceberg_num == bond_first_num(k)) then
+          if (this%iceberg_num == first_berg_num(k)) then
             first_berg_found=.true.
             first_berg=>this
             this=>null()
@@ -1138,15 +1138,15 @@ subroutine read_restart_bonds(bergs,Time)
       
         ! Decide whether the second iceberg is on the processeor (data domain)
         second_berg_found=.false.
-        if ( bond_second_ine(k)>=grd%isd .and. bond_second_ine(k)<=grd%ied .and. &
-          bond_second_jne(k)>=grd%jsd .and.bond_second_jne(k)<=grd%jed ) then
+        if ( other_berg_ine(k)>=grd%isd .and. other_berg_ine(k)<=grd%ied .and. &
+          other_berg_jne(k)>=grd%jsd .and.other_berg_jne(k)<=grd%jed ) then
           number_second_bonds_matched=number_second_bonds_matched+1
 
           ! Search for the second berg, which the bond belongs to
           second_berg=>null()
-          this=>bergs%list(bond_second_ine(k),bond_second_jne(k))%first
+          this=>bergs%list(other_berg_ine(k),other_berg_jne(k))%first
           do while(associated(this))
-            if (this%iceberg_num == bond_second_num(k)) then
+            if (this%iceberg_num == other_berg_num(k)) then
               second_berg_found=.true.
               second_berg=>this
               this=>null()
@@ -1159,10 +1159,10 @@ subroutine read_restart_bonds(bergs,Time)
         if (first_berg_found) then
           number_partial_bonds=number_partial_bonds+1
           if (second_berg_found) then
-            call form_a_bond(first_berg, bond_second_num(k),second_berg)
+            call form_a_bond(first_berg, other_berg_num(k), other_berg_ine(k), other_berg_jne(k),  second_berg)
             number_perfect_bonds=number_perfect_bonds+1
           else
-            call form_a_bond(first_berg, bond_second_num(k))
+            call form_a_bond(first_berg, other_berg_num(k),other_berg_ine(k),other_berg_jne(k))
           endif
         else
           write(*,'(a,i8,a)') 'diamonds, bond read restart : ','Not enough partial bonds formed', k, mpp_pe(), nbonds_in_file
@@ -1178,8 +1178,6 @@ subroutine read_restart_bonds(bergs,Time)
     all_pe_number_second_bonds_matched=number_second_bonds_matched
     call mpp_sum(all_pe_number_perfect_bonds)
     call mpp_sum(all_pe_number_partial_bonds)
-    call mpp_sum(all_pe_number_first_bonds_matched)
-    call mpp_sum(all_pe_number_second_bonds_matched)
 
     if (all_pe_number_partial_bonds .lt. nbonds_in_file) then
       write(*,'(a,i8,a)') 'diamonds, bond read restart : ','Not enough partial bonds formed', all_pe_number_partial_bonds , nbonds_in_file
@@ -1187,17 +1185,20 @@ subroutine read_restart_bonds(bergs,Time)
     endif
     
     if (all_pe_number_perfect_bonds .lt. nbonds_in_file) then
-      write(*,'(a,i8,a)') 'diamonds, bond read restart : ','Warning, some bonds are not fully formed', all_pe_number_perfect_bonds , nbonds_in_file
+      call mpp_sum(all_pe_number_first_bonds_matched)
+      call mpp_sum(all_pe_number_second_bonds_matched)
+      write(*,'(a,i8,a)') 'diamonds, bond read restart : ','Warning, some bonds are not fully formed',  all_pe_number_first_bonds_matched , nbonds_in_file
+      write(*,'(a,i8,a)') 'diamonds, bond read restart : ','Number of first and second bonds matched:', all_pe_number_second_bonds_matched , nbonds_in_file
       call error_mesg('read_restart_bonds_bergs_new', 'Not enough perfect bonds formed', NOTE)
     endif
 
     deallocate(               &
-            bond_first_num,   &
-            bond_second_num,  &
-            bond_first_ine,   &
-            bond_first_jne,   &
-            bond_second_ine,  &
-            bond_second_jne )
+            first_berg_num,   &
+            other_berg_num,  &
+            first_berg_ine,   &
+            first_berg_jne,   &
+            other_berg_ine,  &
+            other_berg_jne )
   endif
 end subroutine read_restart_bonds
 ! ##############################################################################

From 1bb0ff17fd78d73cbe034c7b87e2b5755c131d01 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Fri, 25 Sep 2015 17:05:43 -0400
Subject: [PATCH 071/361] Written a submodule which reconnects bonds after
 bergs have been sent between processors. This seems to be working, but has
 not yet been tested properly.

---
 icebergs.F90           |  4 +++-
 icebergs_framework.F90 | 53 +++++++++++++++++++++++++++++++++++++++++-
 2 files changed, 55 insertions(+), 2 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 43f3610..2eab323 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -26,7 +26,7 @@ module ice_bergs
 use ice_bergs_framework, only: icebergs_gridded, xyt, iceberg, icebergs, buffer, bond
 use ice_bergs_framework, only: verbose, really_debug,debug,old_bug_rotated_weights,budget,use_roundoff_fix
 use ice_bergs_framework, only: find_cell,find_cell_by_search,count_bergs,is_point_in_cell,pos_within_cell
-use ice_bergs_framework, only: count_bonds, form_a_bond
+use ice_bergs_framework, only: count_bonds, form_a_bond,connect_all_bonds
 use ice_bergs_framework, only: nclasses,old_bug_bilin
 use ice_bergs_framework, only: sum_mass,sum_heat,bilin,yearday,count_bergs,bergs_chksum
 use ice_bergs_framework, only: checksum_gridded,add_new_berg_to_list
@@ -1322,7 +1322,9 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   ! Send bergs to other PEs
   call mpp_clock_begin(bergs%clock_com)
   call send_bergs_to_other_pes(bergs)
+  call connect_all_bonds(bergs)
   call update_halo_icebergs(bergs)
+  call connect_all_bonds(bergs)
   if (debug) call bergs_chksum(bergs, 'run bergs (exchanged)')
   if (debug) call checksum_gridded(bergs%grd, 's/r run after exchange')
   call mpp_clock_end(bergs%clock_com)
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 8df3610..2b93f6e 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -62,7 +62,7 @@ module ice_bergs_framework
 public insert_berg_into_list, create_iceberg, delete_iceberg_from_list, destroy_iceberg
 public print_fld,print_berg, print_bergs,record_posn, push_posn, append_posn, check_position
 public move_trajectory, move_all_trajectories
-public form_a_bond
+public form_a_bond, connect_all_bonds
 public find_cell,find_cell_by_search,count_bergs,is_point_in_cell,pos_within_cell, count_bonds
 public sum_mass,sum_heat,bilin,yearday,bergs_chksum
 public checksum_gridded
@@ -2184,6 +2184,57 @@ subroutine form_a_bond(berg, other_berg_num, other_berg_ine, other_berg_jne, oth
 end subroutine form_a_bond
 
 ! #############################################################################
+
+subroutine connect_all_bonds(bergs)
+type(icebergs), pointer :: bergs
+type(iceberg), pointer :: other_berg, berg
+type(icebergs_gridded), pointer :: grd
+integer :: grdi, grdj
+type(bond) , pointer :: current_bond, other_berg_bond
+logical :: bond_matched, missing_bond
+
+missing_bond=.false.
+
+ ! For convenience
+  grd=>bergs%grd
+
+  do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+    berg=>bergs%list(grdi,grdj)%first
+    do while (associated(berg)) ! loop over all bergs
+      current_bond=>berg%first_bond
+      do while (associated(current_bond)) ! loop over all bonds
+
+        !code to find parter bond goes here
+        if (.not.associated(current_bond%other_berg)) then
+          other_berg=>bergs%list(current_bond%other_berg_ine,current_bond%other_berg_jne)%first
+          do while (associated(current_bond)) ! loop over all bonds
+            bond_matched=.false.
+            if (other_berg%iceberg_num == current_bond%other_berg_num) then
+              current_bond%other_berg=>other_berg
+              other_berg=>null()
+              bond_matched=.true.  
+            else
+              other_berg=>other_berg%next
+            endif 
+          enddo
+          if (.not.bond_matched) then
+             if (berg%halo_berg .lt. 0.5) then
+                missing_bond=.true.     
+                call error_mesg('diamonds, connect_all_bonds', 'A non halo bond is missing!!!', WARNING)
+             endif
+          endif
+        endif
+
+        current_bond=>current_bond%next_bond
+      enddo
+      berg=>berg%next
+    enddo
+  enddo;enddo
+
+
+end subroutine connect_all_bonds
+
+
 ! #############################################################################
 subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
 

From d1d855550e065f9bb88f705db437cbc27f333150 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Tue, 29 Sep 2015 13:37:07 -0400
Subject: [PATCH 072/361] 1) Bonds quality control has been added to the code.
 This subrouting (inside count_bonds()) makes sure that all the bonds are
 connneted correctly.

2) Halos now update before bonds are formed, so that the bonds get formed correctly.

The structure is now in place for bonds. We just need to add the bonding force.
---
 icebergs.F90           | 23 +++++++++--------
 icebergs_framework.F90 | 57 ++++++++++++++++++++++++++++++------------
 icebergs_io.F90        |  4 ++-
 3 files changed, 56 insertions(+), 28 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 2eab323..d90ec41 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -85,6 +85,8 @@ subroutine icebergs_init(bergs, &
 real, dimension(:,:), intent(in), optional :: ocean_depth
 logical, intent(in), optional :: maskmap(:,:)
 logical, intent(in), optional :: fractional_area
+integer :: nbonds
+logical :: check_bond_quality
 
 integer :: stdlogunit, stderrunit
 
@@ -119,6 +121,10 @@ subroutine icebergs_init(bergs, &
     else
       call read_restart_bonds(bergs,Time)
     endif
+    call update_halo_icebergs(bergs)
+    call connect_all_bonds(bergs)
+    check_bond_quality=.True.
+    call count_bonds(bergs, nbonds,check_bond_quality)
   endif
 
 end subroutine icebergs_init
@@ -132,16 +138,11 @@ subroutine initialize_iceberg_bonds(bergs)
 type(iceberg), pointer :: berg
 type(iceberg), pointer :: other_berg
 type(icebergs_gridded), pointer :: grd
-   
-
-
 real :: T1, L1, W1, lon1, lat1, x1, y1, R1, A1   !Current iceberg
 real :: T2, L2, W2, lon2, lat2, x2, y2, R2, A2   !Other iceberg
 real :: r_dist_x, r_dist_y, r_dist
 integer :: grdi_outer, grdj_outer
 integer :: grdi_inner, grdj_inner
-integer :: nbonds
-logical :: check_bond_quality
 
 
   ! For convenience
@@ -177,11 +178,6 @@ subroutine initialize_iceberg_bonds(bergs)
   enddo ; enddo; !End of outer loop.
 
 
-  check_bond_quality=.True.
-  call count_bonds(bergs, nbonds,check_bond_quality)
-
-
-
 end subroutine initialize_iceberg_bonds
 
 ! ##############################################################################
@@ -1132,12 +1128,13 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 ! Local variables
 integer :: iyr, imon, iday, ihr, imin, isec, k
 type(icebergs_gridded), pointer :: grd
-logical :: lerr, sample_traj, write_traj, lbudget, lverbose
+logical :: lerr, sample_traj, write_traj, lbudget, lverbose, check_bond_quality 
 real :: unused_calving, tmpsum, grdd_berg_mass, grdd_bergy_mass
 integer :: i, j, Iu, ju, iv, Jv, Iu_off, ju_off, iv_off, Jv_off
 real :: mask
 real, dimension(:,:), allocatable :: uC_tmp, vC_tmp
 integer :: vel_stagger, str_stagger
+integer :: nbonds
 
 integer :: stderrunit
 
@@ -1549,6 +1546,10 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     bergs%berg_melt=0.
     bergs%bergy_melt=0.
     bergs%bergy_src=0.
+
+    check_bond_quality=.true.
+    call count_bonds(bergs, nbonds,check_bond_quality)
+    if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') 'diamonds, Bond check complete. Bonds are perfect: ',check_bond_quality
   endif
 
   if (debug) call bergs_chksum(bergs, 'run bergs (bot)')
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 2b93f6e..e00df91 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -2191,7 +2191,8 @@ subroutine connect_all_bonds(bergs)
 type(icebergs_gridded), pointer :: grd
 integer :: grdi, grdj
 type(bond) , pointer :: current_bond, other_berg_bond
-logical :: bond_matched, missing_bond
+logical :: bond_matched, missing_bond, check_bond_quality
+integer nbonds
 
 missing_bond=.false.
 
@@ -2207,7 +2208,7 @@ subroutine connect_all_bonds(bergs)
         !code to find parter bond goes here
         if (.not.associated(current_bond%other_berg)) then
           other_berg=>bergs%list(current_bond%other_berg_ine,current_bond%other_berg_jne)%first
-          do while (associated(current_bond)) ! loop over all bonds
+          do while (associated(other_berg)) ! loop over all other bergs
             bond_matched=.false.
             if (other_berg%iceberg_num == current_bond%other_berg_num) then
               current_bond%other_berg=>other_berg
@@ -2231,6 +2232,10 @@ subroutine connect_all_bonds(bergs)
     enddo
   enddo;enddo
 
+  if (debug) then
+    check_bond_quality=.true.
+    call count_bonds(bergs, nbonds,check_bond_quality)
+  endif
 
 end subroutine connect_all_bonds
 
@@ -2248,15 +2253,19 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
 integer :: number_of_bonds_all_pe
 integer :: grdi, grdj
 logical :: bond_is_good
-logical, optional :: check_bond_quality
+logical, intent(inout), optional :: check_bond_quality
 logical :: quality_check
-logical :: all_bonds_matching
+integer :: num_unmatched_bonds,num_unmatched_bonds_all_pe
+integer :: num_unassosiated_bond_pairs, num_unassosiated_bond_pairs_all_pe 
 integer :: stderrunit
 
- print *, "starting bond_check"
+!  print *, "starting bond_check"
+ stderrunit = stderr()
  quality_check=.false.
- all_bonds_matching=.True.
  if(present(check_bond_quality)) quality_check = check_bond_quality
+ check_bond_quality=.false.
+ num_unmatched_bonds=0
+ num_unassosiated_bond_pairs=0
 
  ! For convenience
   grd=>bergs%grd
@@ -2272,7 +2281,8 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
 
         ! ##### Beginning Quality Check on Bonds ######
         if (quality_check) then
-          all_bonds_matching=.True.
+          num_unmatched_bonds=0
+          num_unassosiated_bond_pairs=0
           bond_is_good=.False.
           other_berg=>current_bond%other_berg
           if (associated(other_berg)) then
@@ -2292,14 +2302,14 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
             enddo  ! End of loop over the other berg's bonds.
 
             if (bond_is_good) then
-              print*, 'Perfect quality Bond:', berg%iceberg_num, current_bond%other_berg_num
+              !if (debug) write(stderrunit,*) 'Perfect quality Bond:', berg%iceberg_num, current_bond%other_berg_num
             else  
-              print*, 'Non-matching bond...:', berg%iceberg_num, current_bond%other_berg_num
-              all_bonds_matching=.false.
+              if (debug) write(stderrunit,*) 'Non-matching bond...:', berg%iceberg_num, current_bond%other_berg_num
+              num_unmatched_bonds=num_unmatched_bonds+1
             endif
           else
-            print *, 'Opposite berg is not assosiated:', berg%iceberg_num, current_bond%other_berg%iceberg_num    
-            all_bonds_matching=.false.
+            if (debug) write(stderrunit,*) 'Opposite berg is not assosiated:', berg%iceberg_num, current_bond%other_berg%iceberg_num    
+            num_unassosiated_bond_pairs=0
           endif
         endif
         ! ##### Ending Quality Check on Bonds ######
@@ -2319,14 +2329,29 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
     endif
 
     if (quality_check) then
-      if (.not.all_bonds_matching) then
-        stderrunit = stderr()
-        write(stderrunit,*) 'diamonds, Bonds are not matching!!!! PE=',mpp_pe()
+      num_unmatched_bonds_all_pe=num_unmatched_bonds
+      num_unassosiated_bond_pairs_all_pe = num_unassosiated_bond_pairs
+      call mpp_sum(num_unmatched_bonds_all_pe)
+      call mpp_sum(num_unassosiated_bond_pairs_all_pe)
+
+      if (num_unmatched_bonds_all_pe .gt. 0) then
         call error_mesg('diamonds, bonds', 'Bonds are not matching!', FATAL)
       endif
+      if (num_unassosiated_bond_pairs_all_pe .ne. 0) then
+        call error_mesg('diamonds, bonds', 'Bonds partners not located!', Warning)
+        if (num_unassosiated_bond_pairs .ne. 0) then
+          write(*,'(2a)') 'diamonds, Bonds parnters not located!!!! PE=', mpp_pe()
+        endif
+      endif
+      if ((num_unmatched_bonds_all_pe == 0)  .and. (num_unassosiated_bond_pairs_all_pe == 0)) then
+        if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') 'diamonds: All iceberg bonds are connected and working well.'
+        check_bond_quality=.true.
+      else
+        if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') 'diamonds: Warning, Broken Bonds! '
+      endif
     endif
 
-    print *, "ending bond_check"
+!    print *, "ending bond_check"
 
 end subroutine count_bonds
 
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 9b6d4e0..b3b2c52 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -110,6 +110,7 @@ subroutine write_restart(bergs)
 type(restart_file_type) :: bergs_restart
 type(restart_file_type) :: bergs_bond_restart
 integer :: nbergs, nbonds
+logical :: check_bond_quality 
 type(icebergs_gridded), pointer :: grd
 real, allocatable, dimension(:) :: lon,          &
                                    lat,          &
@@ -319,7 +320,8 @@ subroutine write_restart(bergs)
    !Allocating restart memory for bond related variables.
    nbonds=0
    if (bergs%iceberg_bonds_on) then
-     call count_bonds(bergs, nbonds)
+     check_bond_quality=.true.
+     call count_bonds(bergs, nbonds,check_bond_quality)
    endif
 
    allocate(first_berg_num(nbonds))

From 25885a5cdaf6936c131480fa13b6e27b7e102e8c Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Tue, 29 Sep 2015 15:07:43 -0400
Subject: [PATCH 073/361] Added bond interactions.

The bond interactions only take place is the distance between the two icebergs is greater than R1+R2.
At the moment, this is a spring force, which does not depend on the mass of the icebergs. This requires that all bonds are broken before the iceberg becomes very small, or else the berg will become unstable. This should be revisited.

The iceberg bond interactions have not been tested yet. Before testing I need to find the bug in the verlet code.
---
 icebergs.F90           | 169 +++++++++++++++++++++++++----------------
 icebergs_framework.F90 |   7 +-
 2 files changed, 107 insertions(+), 69 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index d90ec41..a24e5d8 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -186,6 +186,7 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
 type(icebergs), pointer :: bergs
 type(iceberg), pointer :: berg
 type(iceberg), pointer :: other_berg
+type(bond), pointer :: current_bond
 real :: T1, L1, W1, lon1, lat1, x1, y1, R1, A1   !Current iceberg
 real :: T2, L2, W2, lon2, lat2, x2, y2, R2, A2   !Other iceberg
 real :: r_dist_x, r_dist_y, r_dist, A_o, trapped, T_min
@@ -194,18 +195,21 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
 real :: u2, v2
 real :: Rearth
 logical :: critical_interaction_damping_on
-real :: spring_coef, accel_spring, radial_damping_coef, p_ia_coef, tangental_damping_coef
+real :: spring_coef, accel_spring, radial_damping_coef, p_ia_coef, tangental_damping_coef, bond_coef
 real, intent(out) :: IA_x, IA_y 
 real, intent(out) :: P_ia_11, P_ia_12, P_ia_22, P_ia_21, P_ia_times_u_x, P_ia_times_u_y
 integer :: stderrunit
 integer :: grdi, grdj
-
+logical :: iceberg_bonds_on
 Rearth=6360.e3
 !spring_coef=1.e-4
 spring_coef=bergs%spring_coef
+bond_coef=bergs%bond_coef 
 radial_damping_coef=bergs%radial_damping_coef
 tangental_damping_coef=bergs%tangental_damping_coef
 critical_interaction_damping_on=bergs%critical_interaction_damping_on
+iceberg_bonds_on=bergs%iceberg_bonds_on
+
 
 !Using critical values for damping rather than manually setting the damping.
 if (critical_interaction_damping_on) then
@@ -255,78 +259,109 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
        !Calculating spring force  (later this should only be done on the first time around)
        accel_spring=spring_coef*(T_min/T1)*(A_o/A1)
        if ((r_dist>0.) .AND. (r_dist< (R1+R2)) ) then
-        IA_x=IA_x+(accel_spring*(r_dist_x/r_dist))
-        IA_y=IA_y+(accel_spring*(r_dist_y/r_dist))
-
-
-       !Working out the damping
-
-       !Paralel velocity
-        P_11=(r_dist_x*r_dist_x)/(r_dist**2)
-        P_12=(r_dist_x*r_dist_y)/(r_dist**2)
-        P_21=(r_dist_x*r_dist_y)/(r_dist**2)
-        P_22=(r_dist_y*r_dist_y)/(r_dist**2)
-        p_ia_coef=radial_damping_coef*(T_min/T1)*(A_o/A1)
-        p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2))+sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
-        P_ia_11=P_ia_11+p_ia_coef*P_11
-        P_ia_12=P_ia_12+p_ia_coef*P_12
-        P_ia_21=P_ia_21+p_ia_coef*P_21
-        P_ia_22=P_ia_22+p_ia_coef*P_22
-        P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
-        P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
-
-
-        !Normal velocities
-        P_11=1-P_11  ;  P_12=-P_12 ; P_22=1-P_22
-        p_ia_coef=tangental_damping_coef*(T_min/T1)*(A_o/A1)
-        p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2))+sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
-        P_ia_11=P_ia_11+p_ia_coef*P_11
-        P_ia_12=P_ia_12+p_ia_coef*P_12
-        P_ia_21=P_ia_21+p_ia_coef*P_21
-        P_ia_22=P_ia_22+p_ia_coef*P_22
-        P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
-        P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
-
-!print *, 'P_11',P_11
-!print *, 'P_21',P_21
-!print *, 'P_12',P_12
-!print *, 'P_22',P_22
+         IA_x=IA_x+(accel_spring*(r_dist_x/r_dist))
+         IA_y=IA_y+(accel_spring*(r_dist_y/r_dist))
+
+
+         !Working out the damping
+
+         !Paralel velocity
+          P_11=(r_dist_x*r_dist_x)/(r_dist**2)
+          P_12=(r_dist_x*r_dist_y)/(r_dist**2)
+          P_21=(r_dist_x*r_dist_y)/(r_dist**2)
+          P_22=(r_dist_y*r_dist_y)/(r_dist**2)
+          p_ia_coef=radial_damping_coef*(T_min/T1)*(A_o/A1)
+          p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2)) &
+          + sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
+          P_ia_11=P_ia_11+p_ia_coef*P_11
+          P_ia_12=P_ia_12+p_ia_coef*P_12
+          P_ia_21=P_ia_21+p_ia_coef*P_21
+          P_ia_22=P_ia_22+p_ia_coef*P_22
+          P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
+          P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
+
+
+          !Normal velocities
+          P_11=1-P_11  ;  P_12=-P_12 ; P_22=1-P_22
+          p_ia_coef=tangental_damping_coef*(T_min/T1)*(A_o/A1)
+          p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2))  &
+          + sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
+          P_ia_11=P_ia_11+p_ia_coef*P_11
+          P_ia_12=P_ia_12+p_ia_coef*P_12
+          P_ia_21=P_ia_21+p_ia_coef*P_21
+          P_ia_22=P_ia_22+p_ia_coef*P_22
+          P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
+          P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
+
+          !print *, 'P_11',P_11
+          !print *, 'P_21',P_21
+          !print *, 'P_12',P_12
+          !print *, 'P_22',P_22
+        endif
       endif
-    endif
-    other_berg=>other_berg%next
-  enddo ! loop over all bergs
-enddo ; enddo
+      other_berg=>other_berg%next
+    enddo ! loop over all bergs
+  enddo ; enddo
 
-  contains
+  !Interactions due to iceberg bonds
+  if (iceberg_bonds_on) then ! MP1  
+    current_bond=>berg%first_bond
+    do while (associated(current_bond)) ! loop over all bonds
+      other_berg=>current_bond%other_berg
+      if (.not. associated(current_bond)) then
+        call error_mesg('diamonds,bond interactions', 'Trying to do Bond interactions with unassosiated bond!' ,FATAL)
+      else
+        L2=other_berg%length
+        W2=other_berg%width
+        !T2=other_berg%thickness ! Note, that it is not dependent on thickness This means that it might go unstable for small icebergs
+        !u2=other_berg%uvel_old
+        !v2=other_berg%vvel_old 
+        A2=L2*W2
+        R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
+        lon2=other_berg%lon_old; lat2=other_berg%lat_old 
+        call rotpos_to_tang(lon2,lat2,x2,y2)
 
+        r_dist_x=x1-x2 ; r_dist_y=y1-y2
+        r_dist=sqrt( ((x1-x2)**2) + ((y1-y2)**2) )
 
-   subroutine overlap_area(R1,R2,d,A,trapped)
-        real, intent(in) :: R1, R2, d
-        real, intent(out) :: A, Trapped
-        real :: R1_sq, R2_sq, d_sq  
-        R1_sq=R1**2
-        R2_sq=R2**2
-        d_sq=d**2
-        Trapped=0.
-
-if (d>0.) then
-        if (d<(R1+R2)) then
-             if (d>abs(R1-R2)) then
-                  A= (R1_sq*acos((d_sq+R1_sq-R2_sq)/(2.*d*R1)))  +  (R2_sq*acos((d_sq+R2_sq-R1_sq)/(2.*d*R2)))  - (0.5*sqrt((-d+R1+R2)*(d+R1-R2)*(d-R1+R2)*(d+R1+R2)))
-             else
-                  A=min(pi*R1_sq,pi*R2_sq) 
-                  Trapped=1.
-             endif
-       else
-             A=0.
-       endif
-else
-       A=0.     ! No area of perfectly overlapping bergs (ie: a berg interacting with itself)
-endif
+        ! Think about doing bonds using an "inverse overlap area, or some type"
+        if ((r_dist>0.) .AND. (r_dist> (R1+R2)) ) then  
+          accel_spring=bond_coef*(r_dist-(R1+R2)) 
+          IA_x=IA_x+(accel_spring*(r_dist_x/r_dist))
+          IA_y=IA_y+(accel_spring*(r_dist_y/r_dist))
+        endif  !Note, no damping on bond force has been added yet    
+      endif
+      current_bond=>current_bond%next_bond
+    enddo
+  endif
 
-   end subroutine overlap_area
+  contains
 
+  subroutine overlap_area(R1,R2,d,A,trapped)
+    real, intent(in) :: R1, R2, d
+    real, intent(out) :: A, Trapped
+    real :: R1_sq, R2_sq, d_sq  
+    R1_sq=R1**2
+    R2_sq=R2**2
+    d_sq=d**2
+    Trapped=0.
+
+    if (d>0.) then
+      if (d<(R1+R2)) then
+        if (d>abs(R1-R2)) then
+          A= (R1_sq*acos((d_sq+R1_sq-R2_sq)/(2.*d*R1)))  +  (R2_sq*acos((d_sq+R2_sq-R1_sq)/(2.*d*R2)))  - (0.5*sqrt((-d+R1+R2)*(d+R1-R2)*(d-R1+R2)*(d+R1+R2)))
+        else
+          A=min(pi*R1_sq,pi*R2_sq) 
+          Trapped=1.
+        endif
+      else
+        A=0.
+      endif
+    else
+      A=0.     ! No area of perfectly overlapping bergs (ie: a berg interacting with itself)
+    endif
 
+   end subroutine overlap_area
 
 end subroutine interactive_force
 
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index e00df91..c360657 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -189,7 +189,8 @@ module ice_bergs_framework
   integer :: clock, clock_mom, clock_the, clock_int, clock_cal, clock_com, clock_ini, clock_ior, clock_iow, clock_dia ! ids for fms timers
   integer :: clock_trw, clock_trp
   real :: rho_bergs ! Density of icebergs [kg/m^3]
-  real :: spring_coef  ! Spring contant for iceberg interactions - Alon
+  real :: spring_coef  ! Spring contant for iceberg interactions 
+  real :: bond_coef  ! Spring contant for iceberg bonds 
   real :: radial_damping_coef     ! Coef for relative iceberg motion damping (radial component) -Alon
   real :: tangental_damping_coef     ! Coef for relative iceberg motion damping (tangental component) -Alon
   real :: LoW_ratio ! Initial ratio L/W for newly calved icebergs
@@ -293,6 +294,7 @@ subroutine ice_bergs_framework_init(bergs, &
 integer :: max_bonds=6 ! Maximum number of iceberg bond passed between processors
 real :: rho_bergs=850. ! Density of icebergs
 real :: spring_coef=1.e-4  ! Spring contant for iceberg interactions - Alon
+real :: bond_coef=100000.0  ! Spring contant for iceberg bonds - Alon
 real :: radial_damping_coef=1.e-4     ! Coef for relative iceberg motion damping (radial component) -Alon
 real :: tangental_damping_coef=2.e-5     ! Coef for relative iceberg motion damping (tangental component) -Alon
 real :: LoW_ratio=1.5 ! Initial ratio L/W for newly calved icebergs
@@ -317,7 +319,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real, dimension(nclasses) :: mass_scaling=(/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) ! Ratio between effective and real iceberg mass (non-dim)
 real, dimension(nclasses) :: initial_thickness=(/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) ! Total thickness of newly calved bergs (m)
 namelist /icebergs_nml/ verbose, budget, halo, iceberg_halo, traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, &
-         distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef, radial_damping_coef, tangental_damping_coef, &
+         distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,bond_coef, radial_damping_coef, tangental_damping_coef, &
          rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, iceberg_bonds_on, manually_initialize_bonds, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, &
          time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, interactive_icebergs_on, critical_interaction_damping_on, &
@@ -586,6 +588,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%grd%iceberg_halo=iceberg_halo
   bergs%rho_bergs=rho_bergs
   bergs%spring_coef=spring_coef
+  bergs%bond_coef=bond_coef
   bergs%radial_damping_coef=radial_damping_coef
   bergs%tangental_damping_coef=tangental_damping_coef
   bergs%LoW_ratio=LoW_ratio

From dfa63240e3ce7e3f1a1c0e72607953e056a843da Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 30 Sep 2015 10:40:49 -0400
Subject: [PATCH 074/361] Not too many changes. But want to change branches
 now.

---
 icebergs.F90 | 19 ++++++++++++++++---
 1 file changed, 16 insertions(+), 3 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index d8326b9..024c301 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -290,7 +290,7 @@ end subroutine interactive_force
 ! ##############################################################################
 
 
-subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, axn, ayn, bxn, byn, debug_flag) !Saving  acceleration for Verlet, Adding Verlet flag - Alon
+subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, axn, ayn, bxn, byn, debug_flag) !Saving  acceleration for Verlet, Adding Verlet flag - Alon  MP1
 !subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, debug_flag) !old version commmented out by Alon
 ! Arguments
 type(icebergs), pointer :: bergs
@@ -2200,7 +2200,7 @@ subroutine evolve_icebergs(bergs)
   axn=berg%axn; ayn=berg%ayn !Alon
   bxn=berg%bxn; byn=berg%byn !Alon
 
-
+print *, 'first', axn, bxn, lon1, lat1, uvel1, i, j ,xi, yj
 
 ! Velocities used to update the position
   uvel2=uvel1+(dt_2*axn)+(dt_2*bxn)                    !Alon
@@ -2219,7 +2219,7 @@ subroutine evolve_icebergs(bergs)
   endif
   dxdln=r180_pi/(Rearth*cos(latn*pi_180))
 
-! Turn the velocities into u_star, v_star.(uvel3 is v_star) - Alon (not sure how this works with tangent plane)
+! Turn the velocities into u_star, v_star.(uvel3 is v_star)
   uvel3=uvel1+(dt_2*axn)                  !Alon
   vvel3=vvel1+(dt_2*ayn)                  !Alon
 
@@ -2228,14 +2228,25 @@ subroutine evolve_icebergs(bergs)
   i=i1;j=j1;xi=berg%xi;yj=berg%yj
   call adjust_index_and_ground(grd, lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
 !  call adjust_index_and_ground(grd, lonn, latn, uvel1, vvel1, i, j, xi, yj, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
+
+if (bounced) then  !This is the case when the iceberg changes direction due to  topography
+  axn=0.
+  ayn=0.
+  bxn=0.
+  byn=0.
+endif
+
+
   i2=i; j2=j
   if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
     call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling)
 
 
+print *, 'second', axn, bxn, lon1, lat1, uvel1, i , j , xi, yj
 !Calling the acceleration   (note that the velocity is converted to u_star inside the accel script)
   call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn, ayn, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
 
+print *, 'third', axn, bxn, lon1, lat1, uvel1, i, j, xi, yj
 !Solving for the new velocity
   if (on_tangential_plane) then
     call rotvec_to_tang(lonn,uvel3,vvel3,xdot3,ydot3)
@@ -2249,6 +2260,7 @@ subroutine evolve_icebergs(bergs)
   uveln=uvel4
   vveln=vvel4 
 
+print *, 'forth', axn, bxn, lon1, lat1, uvel1, i, j, xi, yj, uveln
 !Debugging
   if (.not.error_flag) then
     if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j)) error_flag=.true.
@@ -2299,6 +2311,7 @@ subroutine evolve_icebergs(bergs)
   endif
 
 
+print *, 'fifth', axn, bxn, lon1, lat1, uvel1, i, j, xi, yj, uveln
 
   endif ! End of the Verlet Stepiing -added by Alon  
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

From 8eac08b5b695bceeceb0aff584df65d738fee1e7 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 30 Sep 2015 10:56:37 -0400
Subject: [PATCH 075/361] Two small changes to the verlet algorithm

1) lon1 changed to lonn. This was a typo from before

2) After iceberg is bounced in the Verlet algorithm, the acceleration and velocity is set to zero. This has not been done for the RK algorithm because I do not want to change the answers.
---
 icebergs.F90 | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index a24e5d8..2925127 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -2326,7 +2326,16 @@ subroutine evolve_icebergs(bergs)
         ! Adjusting mass...                      Alon decided to move this before calculating the new velocities (so that acceleration can be a fn(r_np1)
         i=i1;j=j1;xi=berg%xi;yj=berg%yj
         call adjust_index_and_ground(grd, lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
-     !  call adjust_index_and_ground(grd, lonn, latn, uvel1, vvel1, i, j, xi, yj, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
+        !call adjust_index_and_ground(grd, lonn, latn, uvel1, vvel1, i, j, xi, yj, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
+
+        ! If the iceberg bounces off the land, then its velocity and acceleration are set to zero
+        if (bounced) then
+                axn=0. ; ayn=0.
+                bxn=0. ; byn=0.
+                uvel3=0.; vvel3=0.
+                uvel1=0.; vvel1=0.
+        endif
+
         i2=i; j2=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
           call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling)
@@ -2338,7 +2347,7 @@ subroutine evolve_icebergs(bergs)
   !Solving for the new velocity
         if (on_tangential_plane) then
           call rotvec_to_tang(lonn,uvel3,vvel3,xdot3,ydot3)
-          call rotvec_to_tang(lon1,ax1,ay1,xddot1,yddot1)
+          call rotvec_to_tang(lonn,ax1,ay1,xddot1,yddot1)
           xdotn=xdot3+(dt*xddot1); ydotn=ydot3+(dt*yddot1)                                    !Alon
           call rotvec_from_tang(lonn,xdotn,ydotn,uveln,vveln)
         else

From f2b98720ceac8b66d8b58c4a04bfd3d1c55b79b7 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 30 Sep 2015 12:00:43 -0400
Subject: [PATCH 076/361] lat_old, lon_old, uvel_old, vvel_old do not need to
 be passed between processors, or passed to the IO.

I have removed these, which should speed things up a little.

I have also changed buffer_width so that it is no longer a parameter. This allows us to define buffer_width in terms of the namelist variable max_bonds. This assigns the correct amount of memory for passing bonds. At a later stage we will perhaps adjust the size of the buffer depending on the amount of bonds.
---
 icebergs_framework.F90 | 53 +++++++++++++++++++-----------------------
 1 file changed, 24 insertions(+), 29 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index c360657..704b8fe 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -15,8 +15,9 @@ module ice_bergs_framework
 
 implicit none ; private
 
-integer, parameter :: buffer_width=30 !Changed from 20 to 30 by Alon 
-integer, parameter :: buffer_width_traj=33  !Changed from 23 by Alon
+integer :: buffer_width=26 !Changed from 20 to 26 by Alon 
+!integer, parameter :: buffer_width=26 !Changed from 20 to 26 by Alon 
+integer, parameter :: buffer_width_traj=29  !Changed from 23 by Alon
 integer, parameter :: nclasses=10 ! Number of ice bergs classes
 
 !Local Vars
@@ -575,9 +576,12 @@ subroutine ice_bergs_framework_init(bergs, &
 endif
 if (.not. iceberg_bonds_on) then
    max_bonds=0
+else
+  buffer_width=buffer_width+(max_bonds*3) ! Increase buffer width to include bonds being passed between processors 
 endif
 
 
+
  ! Parameters
   bergs%dt=dt
   bergs%traj_sample_hrs=traj_sample_hrs
@@ -1384,15 +1388,11 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
     buff%data(22,n)=berg%ayn  !Alon
     buff%data(23,n)=berg%bxn  !Alon
     buff%data(24,n)=berg%byn  !Alon
-    buff%data(25,n)=berg%uvel_old  !Alon  
-    buff%data(26,n)=berg%vvel_old  !Alon
-    buff%data(27,n)=berg%lon_old  !Alon
-    buff%data(28,n)=berg%lat_old  !Alon
-    buff%data(29,n)=float(berg%iceberg_num)
-    buff%data(30,n)=berg%halo_berg 
+    buff%data(25,n)=float(berg%iceberg_num)
+    buff%data(26,n)=berg%halo_berg 
 
     if (max_bonds .gt. 0) then
-      counter=30 !how many data points being passed so far (must match above)
+      counter=26 !how many data points being passed so far (must match above)
       do k = 1,max_bonds
         current_bond=>berg%first_bond
         if (associated(current_bond)) then
@@ -1490,13 +1490,16 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n,grd, force_append, max_bonds_
     localberg%ayn=buff%data(22,n) !Alon
     localberg%bxn=buff%data(23,n) !Alon
     localberg%byn=buff%data(24,n) !Alon
-    localberg%uvel_old=buff%data(25,n) !Alon
-    localberg%vvel_old=buff%data(26,n) !Alon
-    localberg%lon_old=buff%data(27,n) !Alon
-    localberg%lat_old=buff%data(28,n) !Alon
-    localberg%iceberg_num=nint(buff%data(29,n))
-    localberg%halo_berg=buff%data(30,n) 
-   
+    localberg%iceberg_num=nint(buff%data(25,n))
+    localberg%halo_berg=buff%data(26,n) 
+
+    !These quantities no longer need to be passed between processors
+    localberg%uvel_old=localberg%uvel
+    localberg%vvel_old=localberg%vvel
+    localberg%lon_old=localberg%lon
+    localberg%lat_old=localberg%lat
+
+
     if(force_app) then !force append with origin ine,jne (for I/O)
 
       localberg%ine=buff%data(19,n) 
@@ -1536,7 +1539,7 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n,grd, force_append, max_bonds_
     !#  Do stuff to do with bonds here MP1
 
     if (max_bonds .gt. 0) then
-      counter=30 !how many data points being passed so far (must match above)
+      counter=26 !how many data points being passed so far (must match above)
       do k = 1,max_bonds
         other_berg_num=nint(buff%data(counter+(3*(k-1)+1),n))
         other_berg_ine=nint(buff%data(counter+(3*(k-1)+2),n))
@@ -1684,12 +1687,8 @@ subroutine pack_traj_into_buffer2(traj, buff, n)
     buff%data(25,n)=traj%ayn !Alon
     buff%data(26,n)=traj%bxn !Alon
     buff%data(27,n)=traj%byn !Alon
-    buff%data(28,n)=traj%uvel_old !Alon
-    buff%data(29,n)=traj%vvel_old !Alon
-    buff%data(30,n)=traj%lon_old !Alon
-    buff%data(31,n)=traj%lat_old !Alon
-    buff%data(32,n)=float(traj%iceberg_num)
-    buff%data(33,n)=traj%halo_berg !Alon
+    buff%data(28,n)=float(traj%iceberg_num)
+    buff%data(29,n)=traj%halo_berg !Alon
 
   end subroutine pack_traj_into_buffer2
 
@@ -1731,12 +1730,8 @@ subroutine unpack_traj_from_buffer2(first, buff, n)
     traj%ayn=buff%data(25,n) !Alon
     traj%bxn=buff%data(26,n) !Alon
     traj%byn=buff%data(27,n) !Alon
-    traj%uvel_old=buff%data(28,n) !Alon
-    traj%vvel_old=buff%data(29,n) !Alon
-    traj%lon_old=buff%data(30,n) !Alon
-    traj%lat_old=buff%data(31,n) !Alon
-    traj%iceberg_num=nint(buff%data(32,n))
-    traj%halo_berg=buff%data(33,n) !Alon
+    traj%iceberg_num=nint(buff%data(28,n))
+    traj%halo_berg=buff%data(29,n) !Alon
 
     call append_posn(first, traj)
 

From 2a5141f5701451294a87856e1ae4c098cb526927 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 30 Sep 2015 13:31:46 -0400
Subject: [PATCH 077/361] Iceberg bond health is only checked if iceberg bonds
 are active.

---
 icebergs.F90 | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 2925127..c7b93e6 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1582,9 +1582,11 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     bergs%bergy_melt=0.
     bergs%bergy_src=0.
 
-    check_bond_quality=.true.
-    call count_bonds(bergs, nbonds,check_bond_quality)
-    if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') 'diamonds, Bond check complete. Bonds are perfect: ',check_bond_quality
+    if (bergs%iceberg_bonds_on) then
+      check_bond_quality=.true.
+      call count_bonds(bergs, nbonds,check_bond_quality)
+      if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') 'diamonds, Bond check complete. Bonds are perfect: ',check_bond_quality
+    endif
   endif
 
   if (debug) call bergs_chksum(bergs, 'run bergs (bot)')

From 7ed59dddc5c9122d7812d6dacb110d18af599443 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 30 Sep 2015 15:21:50 -0400
Subject: [PATCH 078/361] Added a namelist flag called save_short_traj 
 (default to true).

When this is true, the iceberg_trajectory.nc file only keeps the lat, lon, day, year, iceberg_num.
This reduces the amount of time spent on writing this file, which may allow us to keep the trajectory files during long simulations.
---
 icebergs.F90           |   4 +-
 icebergs_framework.F90 | 121 +++++++++++++-----------
 icebergs_io.F90        | 205 +++++++++++++++++++++--------------------
 3 files changed, 174 insertions(+), 156 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index c7b93e6..598f25b 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1373,7 +1373,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   if (sample_traj) call record_posn(bergs)
   if (write_traj) then
     call move_all_trajectories(bergs)
-    call write_trajectory(bergs%trajectories)
+    call write_trajectory(bergs%trajectories, bergs%save_short_traj)
   endif
 
   ! Gridded diagnostics
@@ -2807,7 +2807,7 @@ subroutine icebergs_end(bergs)
   ! Delete bergs and structures
   call move_all_trajectories(bergs, delete_bergs=.true.)
 
-  call write_trajectory(bergs%trajectories)
+  call write_trajectory(bergs%trajectories, bergs%save_short_traj)
 
   deallocate(bergs%grd%lon)
   deallocate(bergs%grd%lat)
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 704b8fe..076eba4 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -16,8 +16,9 @@ module ice_bergs_framework
 implicit none ; private
 
 integer :: buffer_width=26 !Changed from 20 to 26 by Alon 
+integer :: buffer_width_traj=29  !Changed from 23 by Alon
 !integer, parameter :: buffer_width=26 !Changed from 20 to 26 by Alon 
-integer, parameter :: buffer_width_traj=29  !Changed from 23 by Alon
+!integer, parameter :: buffer_width_traj=29  !Changed from 23 by Alon
 integer, parameter :: nclasses=10 ! Number of ice bergs classes
 
 !Local Vars
@@ -205,6 +206,7 @@ module ice_bergs_framework
   logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
   logical :: time_average_weight=.false. ! Time average the weight on the ocean
   logical :: Runge_not_Verlet=.True.  !True=Runge Kuttai, False=Verlet.  - Added by Alon 
+  logical :: save_short_traj=.True.  !True saves only lon,lat,time,iceberg_num in iceberg_trajectory.nc 
   logical :: iceberg_bonds_on=.False.  !True=Allow icebergs to have bonds, False=don't allow. 
   logical :: manually_initialize_bonds=.False.  !True= Bonds are initialize manually. 
   logical :: use_new_predictive_corrective =.False.  !Flag to use Bob's predictive corrective iceberg scheme- Added by Alon 
@@ -308,6 +310,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: speed_limit=0. ! CFL speed limit for a berg
 real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
 logical :: Runge_not_Verlet=.True.  !True=Runge Kutta, False=Verlet.  - Added by Alon 
+logical :: save_short_traj=.True.  !True saves only lon,lat,time,iceberg_num in iceberg_trajectory.nc 
 logical :: iceberg_bonds_on=.False.  !True=Allow icebergs to have bonds, False=don't allow. 
 logical :: manually_initialize_bonds=.False.  !True= Bonds are initialize manually. 
 logical :: use_new_predictive_corrective =.False.  !Flag to use Bob's predictive corrective iceberg scheme- Added by Alon 
@@ -319,7 +322,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real, dimension(nclasses) :: distribution=(/0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02/) ! Fraction of calving to apply to this class (non-dim) , 
 real, dimension(nclasses) :: mass_scaling=(/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) ! Ratio between effective and real iceberg mass (non-dim)
 real, dimension(nclasses) :: initial_thickness=(/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) ! Total thickness of newly calved bergs (m)
-namelist /icebergs_nml/ verbose, budget, halo, iceberg_halo, traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, &
+namelist /icebergs_nml/ verbose, budget, halo, iceberg_halo, traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj, &
          distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,bond_coef, radial_damping_coef, tangental_damping_coef, &
          rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, iceberg_bonds_on, manually_initialize_bonds, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, &
@@ -579,13 +582,14 @@ subroutine ice_bergs_framework_init(bergs, &
 else
   buffer_width=buffer_width+(max_bonds*3) ! Increase buffer width to include bonds being passed between processors 
 endif
-
+if (save_short_traj) buffer_width_traj=5 ! This is the length of the short buffer used for abrevated traj
 
 
  ! Parameters
   bergs%dt=dt
   bergs%traj_sample_hrs=traj_sample_hrs
   bergs%traj_write_hrs=traj_write_hrs
+  bergs%save_short_traj=save_short_traj
   bergs%verbose_hrs=verbose_hrs
   bergs%grd%halo=halo
   bergs%max_bonds=max_bonds
@@ -1650,11 +1654,12 @@ subroutine increase_buffer_traj(old,delta)
 
   end subroutine increase_buffer_traj
 
-  subroutine pack_traj_into_buffer2(traj, buff, n)
+  subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj)
   ! Arguments
   type(xyt), pointer :: traj
   type(buffer), pointer :: buff
   integer, intent(in) :: n
+  logical, intent(in) :: save_short_traj
   ! Local variables
 
     if (.not.associated(buff)) call increase_buffer_traj(buff,delta_buf)
@@ -1664,35 +1669,37 @@ subroutine pack_traj_into_buffer2(traj, buff, n)
     buff%data(2,n)=traj%lat
     buff%data(3,n)=float(traj%year)
     buff%data(4,n)=traj%day
-    buff%data(5,n)=traj%uvel
-    buff%data(6,n)=traj%vvel
-    buff%data(7,n)=traj%mass
-    buff%data(8,n)=traj%mass_of_bits
-    buff%data(9,n)=traj%heat_density
-    buff%data(10,n)=traj%thickness
-    buff%data(11,n)=traj%width
-    buff%data(12,n)=traj%length
-    buff%data(13,n)=traj%uo
-    buff%data(14,n)=traj%vo
-    buff%data(15,n)=traj%ui
-    buff%data(16,n)=traj%vi
-    buff%data(17,n)=traj%ua
-    buff%data(18,n)=traj%va
-    buff%data(19,n)=traj%ssh_x
-    buff%data(20,n)=traj%ssh_y
-    buff%data(21,n)=traj%sst
-    buff%data(22,n)=traj%cn
-    buff%data(23,n)=traj%hi
-    buff%data(24,n)=traj%axn !Alon
-    buff%data(25,n)=traj%ayn !Alon
-    buff%data(26,n)=traj%bxn !Alon
-    buff%data(27,n)=traj%byn !Alon
-    buff%data(28,n)=float(traj%iceberg_num)
-    buff%data(29,n)=traj%halo_berg !Alon
+    buff%data(5,n)=float(traj%iceberg_num)
+    if (.not. save_short_traj) then
+      buff%data(6,n)=traj%uvel
+      buff%data(7,n)=traj%vvel
+      buff%data(8,n)=traj%mass
+      buff%data(9,n)=traj%mass_of_bits
+      buff%data(10,n)=traj%heat_density
+      buff%data(11,n)=traj%thickness
+      buff%data(12,n)=traj%width
+      buff%data(13,n)=traj%length
+      buff%data(14,n)=traj%uo
+      buff%data(15,n)=traj%vo
+      buff%data(16,n)=traj%ui
+      buff%data(17,n)=traj%vi
+      buff%data(18,n)=traj%ua
+      buff%data(19,n)=traj%va
+      buff%data(20,n)=traj%ssh_x
+      buff%data(21,n)=traj%ssh_y
+      buff%data(22,n)=traj%sst
+      buff%data(23,n)=traj%cn
+      buff%data(24,n)=traj%hi
+      buff%data(25,n)=traj%axn !Alon
+      buff%data(26,n)=traj%ayn !Alon
+      buff%data(27,n)=traj%bxn !Alon
+      buff%data(28,n)=traj%byn !Alon
+      buff%data(29,n)=traj%halo_berg !Alon
+    endif
 
   end subroutine pack_traj_into_buffer2
 
-  subroutine unpack_traj_from_buffer2(first, buff, n)
+  subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj)
   ! Arguments
   type(xyt), pointer :: first
   type(buffer), pointer :: buff
@@ -1700,6 +1707,7 @@ subroutine unpack_traj_from_buffer2(first, buff, n)
  ! Local variables
   type(xyt) :: traj
   integer :: stderrunit
+  logical, intent(in) :: save_short_traj 
   ! Get the stderr unit number
   stderrunit = stderr()
 
@@ -1707,32 +1715,33 @@ subroutine unpack_traj_from_buffer2(first, buff, n)
     traj%lat=buff%data(2,n)
     traj%year=nint(buff%data(3,n))
     traj%day=buff%data(4,n)
-    traj%uvel=buff%data(5,n)
-    traj%vvel=buff%data(6,n)
-    traj%mass=buff%data(7,n)
-    traj%mass_of_bits=buff%data(8,n)
-    traj%heat_density=buff%data(9,n)
-    traj%thickness=buff%data(10,n)
-    traj%width=buff%data(11,n)
-    traj%length=buff%data(12,n)
-    traj%uo=buff%data(13,n)
-    traj%vo=buff%data(14,n)
-    traj%ui=buff%data(15,n)
-    traj%vi=buff%data(16,n)
-    traj%ua=buff%data(17,n)
-    traj%va=buff%data(18,n)
-    traj%ssh_x=buff%data(19,n)
-    traj%ssh_y=buff%data(20,n)
-    traj%sst=buff%data(21,n)
-    traj%cn=buff%data(22,n)
-    traj%hi=buff%data(23,n)
-    traj%axn=buff%data(24,n) !Alon
-    traj%ayn=buff%data(25,n) !Alon
-    traj%bxn=buff%data(26,n) !Alon
-    traj%byn=buff%data(27,n) !Alon
-    traj%iceberg_num=nint(buff%data(28,n))
-    traj%halo_berg=buff%data(29,n) !Alon
-
+    traj%iceberg_num=nint(buff%data(5,n))
+    if (.not. save_short_traj) then
+      traj%uvel=buff%data(6,n)
+      traj%vvel=buff%data(7,n)
+      traj%mass=buff%data(8,n)
+      traj%mass_of_bits=buff%data(9,n)
+      traj%heat_density=buff%data(10,n)
+      traj%thickness=buff%data(11,n)
+      traj%width=buff%data(12,n)
+      traj%length=buff%data(13,n)
+      traj%uo=buff%data(14,n)
+      traj%vo=buff%data(15,n)
+      traj%ui=buff%data(16,n)
+      traj%vi=buff%data(17,n)
+      traj%ua=buff%data(18,n)
+      traj%va=buff%data(19,n)
+      traj%ssh_x=buff%data(20,n)
+      traj%ssh_y=buff%data(21,n)
+      traj%sst=buff%data(22,n)
+      traj%cn=buff%data(23,n)
+      traj%hi=buff%data(24,n)
+      traj%axn=buff%data(25,n) !Alon
+      traj%ayn=buff%data(26,n) !Alon
+      traj%bxn=buff%data(27,n) !Alon
+      traj%byn=buff%data(28,n) !Alon
+      traj%halo_berg=buff%data(29,n) !Alon
+    endif
     call append_posn(first, traj)
 
   end subroutine unpack_traj_from_buffer2
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index b3b2c52..d7ec695 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -1286,7 +1286,7 @@ end subroutine read_restart_calving
 
 ! ##############################################################################
 
-subroutine write_trajectory(trajectory)
+subroutine write_trajectory(trajectory, save_short_traj)
 ! Arguments
 type(xyt), pointer :: trajectory
 ! Local variables
@@ -1300,7 +1300,7 @@ subroutine write_trajectory(trajectory)
 character(len=7) :: pe_name
 type(xyt), pointer :: this, next
 integer :: stderrunit
-
+logical, intent(in) :: save_short_traj
 !I/O vars
 type(xyt), pointer :: traj4io=>null()
 integer :: ntrajs_sent_io,ntrajs_rcvd_io
@@ -1344,7 +1344,7 @@ subroutine write_trajectory(trajectory)
            call increase_ibuffer_traj(ibuffer_io, ntrajs_rcvd_io)
            call mpp_recv(ibuffer_io%data, ntrajs_rcvd_io*buffer_width_traj,from_pe=from_pe, tag=COMM_TAG_12)
            do i=1, ntrajs_rcvd_io
-              call unpack_traj_from_buffer2(traj4io, ibuffer_io, i)
+              call unpack_traj_from_buffer2(traj4io, ibuffer_io, i, save_short_traj)
            enddo
        endif
      enddo
@@ -1352,7 +1352,7 @@ subroutine write_trajectory(trajectory)
      ! Pack and send trajectories to the root PE for this I/O tile
      do while (associated(trajectory))
        ntrajs_sent_io = ntrajs_sent_io +1
-       call pack_traj_into_buffer2(trajectory, obuffer_io, ntrajs_sent_io)
+       call pack_traj_into_buffer2(trajectory, obuffer_io, ntrajs_sent_io, save_short_traj)
        this => trajectory ! Need to keep pointer in order to free up the links memory
        trajectory => trajectory%next ! This will eventually result in trajectory => null()
        deallocate(this) ! Delete the link from memory
@@ -1412,26 +1412,28 @@ subroutine write_trajectory(trajectory)
       latid = inq_varid(ncid, 'lat')
       yearid = inq_varid(ncid, 'year')
       dayid = inq_varid(ncid, 'day')
-      uvelid = inq_varid(ncid, 'uvel')
-      vvelid = inq_varid(ncid, 'vvel')
-      uoid = inq_varid(ncid, 'uo')
-      void = inq_varid(ncid, 'vo')
-      uiid = inq_varid(ncid, 'ui')
-      viid = inq_varid(ncid, 'vi')
-      uaid = inq_varid(ncid, 'ua')
-      vaid = inq_varid(ncid, 'va')
-      mid = inq_varid(ncid, 'mass')
-      mbid = inq_varid(ncid, 'mass_of_bits')
-      hdid = inq_varid(ncid, 'heat_density')
-      did = inq_varid(ncid, 'thickness')
-      wid = inq_varid(ncid, 'width')
-      lid = inq_varid(ncid, 'length')
-      sshxid = inq_varid(ncid, 'ssh_x')
-      sshyid = inq_varid(ncid, 'ssh_y')
-      sstid = inq_varid(ncid, 'sst')
-      cnid = inq_varid(ncid, 'cn')
-      hiid = inq_varid(ncid, 'hi')
       iceberg_numid = inq_varid(ncid, 'iceberg_num')
+      if (.not.save_short_traj) then
+        uvelid = inq_varid(ncid, 'uvel')
+        vvelid = inq_varid(ncid, 'vvel')
+        uoid = inq_varid(ncid, 'uo')
+        void = inq_varid(ncid, 'vo')
+        uiid = inq_varid(ncid, 'ui')
+        viid = inq_varid(ncid, 'vi')
+        uaid = inq_varid(ncid, 'ua')
+        vaid = inq_varid(ncid, 'va')
+        mid = inq_varid(ncid, 'mass')
+        mbid = inq_varid(ncid, 'mass_of_bits')
+        hdid = inq_varid(ncid, 'heat_density')
+        did = inq_varid(ncid, 'thickness')
+        wid = inq_varid(ncid, 'width')
+        lid = inq_varid(ncid, 'length')
+        sshxid = inq_varid(ncid, 'ssh_x')
+        sshyid = inq_varid(ncid, 'ssh_y')
+        sstid = inq_varid(ncid, 'sst')
+        cnid = inq_varid(ncid, 'cn')
+        hiid = inq_varid(ncid, 'hi')
+      endif
     else
       ! Dimensions
       iret = nf_def_dim(ncid, 'i', NF_UNLIMITED, i_dim)
@@ -1442,26 +1444,28 @@ subroutine write_trajectory(trajectory)
       latid = def_var(ncid, 'lat', NF_DOUBLE, i_dim)
       yearid = def_var(ncid, 'year', NF_INT, i_dim)
       dayid = def_var(ncid, 'day', NF_DOUBLE, i_dim)
-      uvelid = def_var(ncid, 'uvel', NF_DOUBLE, i_dim)
-      vvelid = def_var(ncid, 'vvel', NF_DOUBLE, i_dim)
-      uoid = def_var(ncid, 'uo', NF_DOUBLE, i_dim)
-      void = def_var(ncid, 'vo', NF_DOUBLE, i_dim)
-      uiid = def_var(ncid, 'ui', NF_DOUBLE, i_dim)
-      viid = def_var(ncid, 'vi', NF_DOUBLE, i_dim)
-      uaid = def_var(ncid, 'ua', NF_DOUBLE, i_dim)
-      vaid = def_var(ncid, 'va', NF_DOUBLE, i_dim)
-      mid = def_var(ncid, 'mass', NF_DOUBLE, i_dim)
-      mbid = def_var(ncid, 'mass_of_bits', NF_DOUBLE, i_dim)
-      hdid = def_var(ncid, 'heat_density', NF_DOUBLE, i_dim)
-      did = def_var(ncid, 'thickness', NF_DOUBLE, i_dim)
-      wid = def_var(ncid, 'width', NF_DOUBLE, i_dim)
-      lid = def_var(ncid, 'length', NF_DOUBLE, i_dim)
-      sshxid = def_var(ncid, 'ssh_x', NF_DOUBLE, i_dim)
-      sshyid = def_var(ncid, 'ssh_y', NF_DOUBLE, i_dim)
-      sstid = def_var(ncid, 'sst', NF_DOUBLE, i_dim)
-      cnid = def_var(ncid, 'cn', NF_DOUBLE, i_dim)
-      hiid = def_var(ncid, 'hi', NF_DOUBLE, i_dim)
       iceberg_numid = def_var(ncid, 'iceberg_num', NF_INT, i_dim)
+      if (.not. save_short_traj) then
+        uvelid = def_var(ncid, 'uvel', NF_DOUBLE, i_dim)
+        vvelid = def_var(ncid, 'vvel', NF_DOUBLE, i_dim)
+        uoid = def_var(ncid, 'uo', NF_DOUBLE, i_dim)
+        void = def_var(ncid, 'vo', NF_DOUBLE, i_dim)
+        uiid = def_var(ncid, 'ui', NF_DOUBLE, i_dim)
+        viid = def_var(ncid, 'vi', NF_DOUBLE, i_dim)
+        uaid = def_var(ncid, 'ua', NF_DOUBLE, i_dim)
+        vaid = def_var(ncid, 'va', NF_DOUBLE, i_dim)
+        mid = def_var(ncid, 'mass', NF_DOUBLE, i_dim)
+        mbid = def_var(ncid, 'mass_of_bits', NF_DOUBLE, i_dim)
+        hdid = def_var(ncid, 'heat_density', NF_DOUBLE, i_dim)
+        did = def_var(ncid, 'thickness', NF_DOUBLE, i_dim)
+        wid = def_var(ncid, 'width', NF_DOUBLE, i_dim)
+        lid = def_var(ncid, 'length', NF_DOUBLE, i_dim)
+        sshxid = def_var(ncid, 'ssh_x', NF_DOUBLE, i_dim)
+        sshyid = def_var(ncid, 'ssh_y', NF_DOUBLE, i_dim)
+        sstid = def_var(ncid, 'sst', NF_DOUBLE, i_dim)
+        cnid = def_var(ncid, 'cn', NF_DOUBLE, i_dim)
+        hiid = def_var(ncid, 'hi', NF_DOUBLE, i_dim)
+      endif
 
       ! Attributes
       iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_major_version', NF_INT, 1, 0)
@@ -1474,46 +1478,49 @@ subroutine write_trajectory(trajectory)
       call put_att(ncid, yearid, 'units', 'years')
       call put_att(ncid, dayid, 'long_name', 'year day')
       call put_att(ncid, dayid, 'units', 'days')
-      call put_att(ncid, uvelid, 'long_name', 'zonal spped')
-      call put_att(ncid, uvelid, 'units', 'm/s')
-      call put_att(ncid, vvelid, 'long_name', 'meridional spped')
-      call put_att(ncid, vvelid, 'units', 'm/s')
-      call put_att(ncid, uoid, 'long_name', 'ocean zonal spped')
-      call put_att(ncid, uoid, 'units', 'm/s')
-      call put_att(ncid, void, 'long_name', 'ocean meridional spped')
-      call put_att(ncid, void, 'units', 'm/s')
-      call put_att(ncid, uiid, 'long_name', 'ice zonal spped')
-      call put_att(ncid, uiid, 'units', 'm/s')
-      call put_att(ncid, viid, 'long_name', 'ice meridional spped')
-      call put_att(ncid, viid, 'units', 'm/s')
-      call put_att(ncid, uaid, 'long_name', 'atmos zonal spped')
-      call put_att(ncid, uaid, 'units', 'm/s')
-      call put_att(ncid, vaid, 'long_name', 'atmos meridional spped')
-      call put_att(ncid, vaid, 'units', 'm/s')
-      call put_att(ncid, mid, 'long_name', 'mass')
-      call put_att(ncid, mid, 'units', 'kg')
-      call put_att(ncid, mbid, 'long_name', 'mass_of_bits')
-      call put_att(ncid, mbid, 'units', 'kg')
-      call put_att(ncid, hdid, 'long_name', 'heat_density')
-      call put_att(ncid, hdid, 'units', 'J/kg')
-      call put_att(ncid, did, 'long_name', 'thickness')
-      call put_att(ncid, did, 'units', 'm')
-      call put_att(ncid, wid, 'long_name', 'width')
-      call put_att(ncid, wid, 'units', 'm')
-      call put_att(ncid, lid, 'long_name', 'length')
-      call put_att(ncid, lid, 'units', 'm')
-      call put_att(ncid, sshxid, 'long_name', 'sea surface height gradient_x')
-      call put_att(ncid, sshxid, 'units', 'non-dim')
-      call put_att(ncid, sshyid, 'long_name', 'sea surface height gradient_y')
-      call put_att(ncid, sshyid, 'units', 'non-dim')
-      call put_att(ncid, sstid, 'long_name', 'sea surface temperature')
-      call put_att(ncid, sstid, 'units', 'degrees_C')
-      call put_att(ncid, cnid, 'long_name', 'sea ice concentration')
-      call put_att(ncid, cnid, 'units', 'none')
-      call put_att(ncid, hiid, 'long_name', 'sea ice thickness')
-      call put_att(ncid, hiid, 'units', 'm')
       call put_att(ncid, iceberg_numid, 'long_name', 'iceberg id number')
       call put_att(ncid, iceberg_numid, 'units', 'dimensionless')
+      
+      if (.not. save_short_traj) then
+        call put_att(ncid, uvelid, 'long_name', 'zonal spped')
+        call put_att(ncid, uvelid, 'units', 'm/s')
+        call put_att(ncid, vvelid, 'long_name', 'meridional spped')
+        call put_att(ncid, vvelid, 'units', 'm/s')
+        call put_att(ncid, uoid, 'long_name', 'ocean zonal spped')
+        call put_att(ncid, uoid, 'units', 'm/s')
+        call put_att(ncid, void, 'long_name', 'ocean meridional spped')
+        call put_att(ncid, void, 'units', 'm/s')
+        call put_att(ncid, uiid, 'long_name', 'ice zonal spped')
+        call put_att(ncid, uiid, 'units', 'm/s')
+        call put_att(ncid, viid, 'long_name', 'ice meridional spped')
+        call put_att(ncid, viid, 'units', 'm/s')
+        call put_att(ncid, uaid, 'long_name', 'atmos zonal spped')
+        call put_att(ncid, uaid, 'units', 'm/s')
+        call put_att(ncid, vaid, 'long_name', 'atmos meridional spped')
+        call put_att(ncid, vaid, 'units', 'm/s')
+        call put_att(ncid, mid, 'long_name', 'mass')
+        call put_att(ncid, mid, 'units', 'kg')
+        call put_att(ncid, mbid, 'long_name', 'mass_of_bits')
+        call put_att(ncid, mbid, 'units', 'kg')
+        call put_att(ncid, hdid, 'long_name', 'heat_density')
+        call put_att(ncid, hdid, 'units', 'J/kg')
+        call put_att(ncid, did, 'long_name', 'thickness')
+        call put_att(ncid, did, 'units', 'm')
+        call put_att(ncid, wid, 'long_name', 'width')
+        call put_att(ncid, wid, 'units', 'm')
+        call put_att(ncid, lid, 'long_name', 'length')
+        call put_att(ncid, lid, 'units', 'm')
+        call put_att(ncid, sshxid, 'long_name', 'sea surface height gradient_x')
+        call put_att(ncid, sshxid, 'units', 'non-dim')
+        call put_att(ncid, sshyid, 'long_name', 'sea surface height gradient_y')
+        call put_att(ncid, sshyid, 'units', 'non-dim')
+        call put_att(ncid, sstid, 'long_name', 'sea surface temperature')
+        call put_att(ncid, sstid, 'units', 'degrees_C')
+        call put_att(ncid, cnid, 'long_name', 'sea ice concentration')
+        call put_att(ncid, cnid, 'units', 'none')
+        call put_att(ncid, hiid, 'long_name', 'sea ice thickness')
+        call put_att(ncid, hiid, 'units', 'm')
+      endif
     endif
 
     ! End define mode
@@ -1533,25 +1540,27 @@ subroutine write_trajectory(trajectory)
       call put_double(ncid, latid, i, this%lat)
       call put_int(ncid, yearid, i, this%year)
       call put_double(ncid, dayid, i, this%day)
-      call put_double(ncid, uvelid, i, this%uvel)
-      call put_double(ncid, vvelid, i, this%vvel)
-      call put_double(ncid, uoid, i, this%uo)
-      call put_double(ncid, void, i, this%vo)
-      call put_double(ncid, uiid, i, this%ui)
-      call put_double(ncid, viid, i, this%vi)
-      call put_double(ncid, uaid, i, this%ua)
-      call put_double(ncid, vaid, i, this%va)
-      call put_double(ncid, mid, i, this%mass)
-      call put_double(ncid, hdid, i, this%heat_density)
-      call put_double(ncid, did, i, this%thickness)
-      call put_double(ncid, wid, i, this%width)
-      call put_double(ncid, lid, i, this%length)
-      call put_double(ncid, sshxid, i, this%ssh_x)
-      call put_double(ncid, sshyid, i, this%ssh_y)
-      call put_double(ncid, sstid, i, this%sst)
-      call put_double(ncid, cnid, i, this%cn)
-      call put_double(ncid, hiid, i, this%hi)
       call put_int(ncid, iceberg_numid, i, this%iceberg_num)
+      if (.not. save_short_traj) then
+        call put_double(ncid, uvelid, i, this%uvel)
+        call put_double(ncid, vvelid, i, this%vvel)
+        call put_double(ncid, uoid, i, this%uo)
+        call put_double(ncid, void, i, this%vo)
+        call put_double(ncid, uiid, i, this%ui)
+        call put_double(ncid, viid, i, this%vi)
+        call put_double(ncid, uaid, i, this%ua)
+        call put_double(ncid, vaid, i, this%va)
+        call put_double(ncid, mid, i, this%mass)
+        call put_double(ncid, hdid, i, this%heat_density)
+        call put_double(ncid, did, i, this%thickness)
+        call put_double(ncid, wid, i, this%width)
+        call put_double(ncid, lid, i, this%length)
+        call put_double(ncid, sshxid, i, this%ssh_x)
+        call put_double(ncid, sshyid, i, this%ssh_y)
+        call put_double(ncid, sstid, i, this%sst)
+        call put_double(ncid, cnid, i, this%cn)
+        call put_double(ncid, hiid, i, this%hi)
+      endif
       next=>this%next
       deallocate(this)
       this=>next

From bca6646bd0c89c4cc94c0b12c90b85974d589136 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Thu, 1 Oct 2015 11:00:58 -0400
Subject: [PATCH 079/361] A few more changes to the iceberg interactions. Made
 bonding force proportional the mass so that it is more similar to the
 attractive force. Preliminary tests indicate that this is working, but much
 more testing is needed. Made a few other cosmetic changes.

---
 icebergs.F90           | 24 ++++++++++++++++++------
 icebergs_framework.F90 |  2 +-
 2 files changed, 19 insertions(+), 7 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 598f25b..eacf371 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -198,6 +198,7 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
 real :: spring_coef, accel_spring, radial_damping_coef, p_ia_coef, tangental_damping_coef, bond_coef
 real, intent(out) :: IA_x, IA_y 
 real, intent(out) :: P_ia_11, P_ia_12, P_ia_22, P_ia_21, P_ia_times_u_x, P_ia_times_u_y
+real :: L_dist
 integer :: stderrunit
 integer :: grdi, grdj
 logical :: iceberg_bonds_on
@@ -313,7 +314,7 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
       else
         L2=other_berg%length
         W2=other_berg%width
-        !T2=other_berg%thickness ! Note, that it is not dependent on thickness This means that it might go unstable for small icebergs
+        T2=other_berg%thickness ! Note, that it is not dependent on thickness This means that it might go unstable for small icebergs
         !u2=other_berg%uvel_old
         !v2=other_berg%vvel_old 
         A2=L2*W2
@@ -325,10 +326,14 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
         r_dist=sqrt( ((x1-x2)**2) + ((y1-y2)**2) )
 
         ! Think about doing bonds using an "inverse overlap area, or some type"
-        if ((r_dist>0.) .AND. (r_dist> (R1+R2)) ) then  
-          accel_spring=bond_coef*(r_dist-(R1+R2)) 
-          IA_x=IA_x+(accel_spring*(r_dist_x/r_dist))
-          IA_y=IA_y+(accel_spring*(r_dist_y/r_dist))
+        if ((r_dist>0.) .AND. (r_dist> (R1+R2)) ) then 
+          L_dist = min( (r_dist-(R1+R2) ),min(R1,R2) ) 
+          call overlap_area(R1,R2,L_dist,A_o,trapped)
+          T_min=min(T1,T2)
+          accel_spring=bond_coef*(T_min/T1)*(A_o/A1)
+          !accel_spring=bond_coef*(r_dist-(R1+R2)) 
+          IA_x=IA_x-(accel_spring*(r_dist_x/r_dist))  !Note: negative sign is an attractive force.
+          IA_y=IA_y-(accel_spring*(r_dist_y/r_dist))
         endif  !Note, no damping on bond force has been added yet    
       endif
       current_bond=>current_bond%next_bond
@@ -1585,7 +1590,12 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     if (bergs%iceberg_bonds_on) then
       check_bond_quality=.true.
       call count_bonds(bergs, nbonds,check_bond_quality)
-      if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') 'diamonds, Bond check complete. Bonds are perfect: ',check_bond_quality
+      if (mpp_pe().eq.mpp_root_pe()) 
+        if (check_bond_quality) then
+          write(*,'(2a)') 'diamonds, Bond check complete. Bonds are perfect'
+        else
+          write(*,'(2a)') 'diamonds, Bond check complete. Bonds are not perfect'
+        endif
     endif
   endif
 
@@ -2032,6 +2042,7 @@ subroutine evolve_icebergs(bergs)
           uvel2=uvel1+dt_2*ax1; vvel2=vvel1+dt_2*ay1
         endif
         i=i1;j=j1;xi=berg%xi;yj=berg%yj
+        !print *, 'Alon: look here!', lon2, lat2, uvel2, vvel2, i, j, xi, yj
         call adjust_index_and_ground(grd, lon2, lat2, uvel2, vvel2, i, j, xi, yj, bounced, error_flag)
         i2=i; j2=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
@@ -2327,6 +2338,7 @@ subroutine evolve_icebergs(bergs)
   
         ! Adjusting mass...                      Alon decided to move this before calculating the new velocities (so that acceleration can be a fn(r_np1)
         i=i1;j=j1;xi=berg%xi;yj=berg%yj
+        !print *, 'Alon: look here!', lonn, latn, uvel3, vvel3, i, j, xi, yj
         call adjust_index_and_ground(grd, lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
         !call adjust_index_and_ground(grd, lonn, latn, uvel1, vvel1, i, j, xi, yj, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
 
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 076eba4..e9e871c 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -297,7 +297,7 @@ subroutine ice_bergs_framework_init(bergs, &
 integer :: max_bonds=6 ! Maximum number of iceberg bond passed between processors
 real :: rho_bergs=850. ! Density of icebergs
 real :: spring_coef=1.e-4  ! Spring contant for iceberg interactions - Alon
-real :: bond_coef=100000.0  ! Spring contant for iceberg bonds - Alon
+real :: bond_coef=1.e-4  ! Spring contant for iceberg bonds - Alon
 real :: radial_damping_coef=1.e-4     ! Coef for relative iceberg motion damping (radial component) -Alon
 real :: tangental_damping_coef=2.e-5     ! Coef for relative iceberg motion damping (tangental component) -Alon
 real :: LoW_ratio=1.5 ! Initial ratio L/W for newly calved icebergs

From 47b51e96a41b5add01d11cc948dc36a7fc29caec Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Thu, 1 Oct 2015 18:02:08 -0400
Subject: [PATCH 080/361] A bug has been fixed. This bug was inside
 pack_icebergs_in_buffer, and had to do with the way the bonds were included
 in the buffer. (ie: the definition of current_bond was inside the loop and
 had to be moved outside).

There is another bond related bug which is giving rise to a segmentation fault after 72 days of the model running with bonds on. I will find this tomorrow
---
 icebergs.F90           | 12 ++++++------
 icebergs_framework.F90 | 44 ++++++++++++++++++++++++------------------
 2 files changed, 31 insertions(+), 25 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index eacf371..3d29f17 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1590,12 +1590,12 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     if (bergs%iceberg_bonds_on) then
       check_bond_quality=.true.
       call count_bonds(bergs, nbonds,check_bond_quality)
-      if (mpp_pe().eq.mpp_root_pe()) 
-        if (check_bond_quality) then
-          write(*,'(2a)') 'diamonds, Bond check complete. Bonds are perfect'
-        else
-          write(*,'(2a)') 'diamonds, Bond check complete. Bonds are not perfect'
-        endif
+      !if (mpp_pe().eq.mpp_root_pe()) then 
+        !if (check_bond_quality) then
+        !  write(*,'(2a)') 'diamonds, Bond check complete. Bonds are perfect'
+        !else
+        !  write(*,'(2a)') 'diamonds, Bond check complete. Bonds are not perfect'
+        !endif
     endif
   endif
 
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index e9e871c..7816a8a 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -1361,6 +1361,7 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
   integer :: counter, k, max_bonds
   type(bond), pointer :: current_bond
  
+    !print *, 'Packing berg', berg%iceberg_num, mpp_pe(), berg%halo_berg
     max_bonds=0
     if (present(max_bonds_in)) max_bonds=max_bonds_in
 
@@ -1397,8 +1398,8 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
 
     if (max_bonds .gt. 0) then
       counter=26 !how many data points being passed so far (must match above)
+      current_bond=>berg%first_bond
       do k = 1,max_bonds
-        current_bond=>berg%first_bond
         if (associated(current_bond)) then
           buff%data(counter+(3*(k-1)+1),n)=float(current_bond%other_berg_num) 
           buff%data(counter+(3*(k-1)+2),n)=float(current_bond%other_berg_ine)
@@ -1503,6 +1504,7 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n,grd, force_append, max_bonds_
     localberg%lon_old=localberg%lon
     localberg%lat_old=localberg%lat
 
+    !print *, 'Unpacking berg', localberg%iceberg_num, mpp_pe(), localberg%halo_berg
 
     if(force_app) then !force append with origin ine,jne (for I/O)
 
@@ -1548,11 +1550,12 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n,grd, force_append, max_bonds_
         other_berg_num=nint(buff%data(counter+(3*(k-1)+1),n))
         other_berg_ine=nint(buff%data(counter+(3*(k-1)+2),n))
         other_berg_jne=nint(buff%data(counter+(3*(k-1)+3),n))
-        if (other_berg_num .gt. 0) then
+        if (other_berg_num .gt. 1) then
           call form_a_bond(this, other_berg_num, other_berg_ine, other_berg_jne)
         endif
       enddo
     endif
+    this=>null()
 
     !##############################
 
@@ -2156,26 +2159,25 @@ subroutine form_a_bond(berg, other_berg_num, other_berg_ine, other_berg_jne, oth
 type(bond) , pointer :: new_bond, first_bond
 integer, intent(in) :: other_berg_num
 integer, optional  :: other_berg_ine, other_berg_jne
-
-print *, 'Forming a bond!!!'
     
-
-! Step 1: Create a new bond
-allocate(new_bond)
-new_bond%other_berg_num=other_berg_num
-if(present(other_berg)) then
-  new_bond%other_berg=>other_berg
-  new_bond%other_berg_ine=other_berg%ine
-  new_bond%other_berg_jne=other_berg%jne
-else
-  new_bond%other_berg=>null()
-  if (present(other_berg_ine)) then
-    new_bond%other_berg_ine=other_berg_ine
-    new_bond%other_berg_jne=other_berg_jne
+if (berg%iceberg_num .ne. other_berg_num) then
+  print *, 'Forming a bond!!!', mpp_pe(), berg%iceberg_num, other_berg_num, berg%halo_berg
+  ! Step 1: Create a new bond
+  allocate(new_bond)
+  new_bond%other_berg_num=other_berg_num
+  if(present(other_berg)) then
+    new_bond%other_berg=>other_berg
+    new_bond%other_berg_ine=other_berg%ine
+    new_bond%other_berg_jne=other_berg%jne
+  else
+    new_bond%other_berg=>null()
+    if (present(other_berg_ine)) then
+      new_bond%other_berg_ine=other_berg_ine
+      new_bond%other_berg_jne=other_berg_jne
+    endif
   endif
-endif
 
-! Step 2: Put this new bond at the start of the bond list
+  ! Step 2: Put this new bond at the start of the bond list
    first_bond=>berg%first_bond
    if (associated(first_bond)) then
         new_bond%next_bond=>first_bond
@@ -2187,6 +2189,10 @@ subroutine form_a_bond(berg, other_berg_num, other_berg_ine, other_berg_jne, oth
        new_bond%prev_bond=>null()  !This should not be needed
        berg%first_bond=>new_bond
    endif
+   new_bond=>null()
+ else
+   call error_mesg('diamonds, bonds', 'An iceberg is trying to bond with itself!!!', FATAL)
+ endif
 
 end subroutine form_a_bond
 

From d114b9155900b51648a2c16f9e1840f8a37c3524 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Mon, 5 Oct 2015 16:54:00 -0400
Subject: [PATCH 081/361] A series of corrections have been made to the way
 that bonds are passed from processor to processor in order to get rid of
 segmentation faults.

The bonds now seem to be working, although longer simulations are needed in order to properly debug the code.

We have added:

1) Iceberg addresses are clear from bonds when the partner iceberg leaves the processor
2) Iceberg search for their bonded pairs in the 9 cells around the last known location
3) The subroutine show_all_bonds(bergs) displays all the bonds for debugging purposes
4) The subroutine bond_address_update, puts the last known address inside the bonds (this actually only has to be done for icebergs near the edge of a processor)
---
 icebergs.F90           |  21 +++--
 icebergs_framework.F90 | 192 ++++++++++++++++++++++++++++++++++-------
 2 files changed, 173 insertions(+), 40 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 3d29f17..7f6dd8b 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -26,7 +26,7 @@ module ice_bergs
 use ice_bergs_framework, only: icebergs_gridded, xyt, iceberg, icebergs, buffer, bond
 use ice_bergs_framework, only: verbose, really_debug,debug,old_bug_rotated_weights,budget,use_roundoff_fix
 use ice_bergs_framework, only: find_cell,find_cell_by_search,count_bergs,is_point_in_cell,pos_within_cell
-use ice_bergs_framework, only: count_bonds, form_a_bond,connect_all_bonds
+use ice_bergs_framework, only: count_bonds, form_a_bond,connect_all_bonds,show_all_bonds, bond_address_update
 use ice_bergs_framework, only: nclasses,old_bug_bilin
 use ice_bergs_framework, only: sum_mass,sum_heat,bilin,yearday,count_bergs,bergs_chksum
 use ice_bergs_framework, only: checksum_gridded,add_new_berg_to_list
@@ -124,6 +124,7 @@ subroutine icebergs_init(bergs, &
     call update_halo_icebergs(bergs)
     call connect_all_bonds(bergs)
     check_bond_quality=.True.
+    nbonds=0
     call count_bonds(bergs, nbonds,check_bond_quality)
   endif
 
@@ -1328,6 +1329,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 
   if (debug) call bergs_chksum(bergs, 'run bergs (top)')
   if (debug) call checksum_gridded(bergs%grd, 'top of s/r run')
+  
 
   ! Accumulate ice from calving
   call accumulate_calving(bergs)
@@ -1356,12 +1358,13 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   if (debug) call checksum_gridded(bergs%grd, 's/r run after evolve')
   call mpp_clock_end(bergs%clock_mom)
 
+
   ! Send bergs to other PEs
   call mpp_clock_begin(bergs%clock_com)
+  if (bergs%iceberg_bonds_on)  call  bond_address_update(bergs)
   call send_bergs_to_other_pes(bergs)
-  call connect_all_bonds(bergs)
   call update_halo_icebergs(bergs)
-  call connect_all_bonds(bergs)
+  if (bergs%iceberg_bonds_on)  call connect_all_bonds(bergs)
   if (debug) call bergs_chksum(bergs, 'run bergs (exchanged)')
   if (debug) call checksum_gridded(bergs%grd, 's/r run after exchange')
   call mpp_clock_end(bergs%clock_com)
@@ -1373,6 +1376,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   if (debug) call checksum_gridded(bergs%grd, 's/r run after thermodynamics')
   call mpp_clock_end(bergs%clock_the)
 
+
   ! For each berg, record
   call mpp_clock_begin(bergs%clock_dia)
   if (sample_traj) call record_posn(bergs)
@@ -1434,6 +1438,10 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 
   ! Dump icebergs to screen
   if (really_debug) call print_bergs(stderrunit,bergs,'icebergs_run, status')
+  
+  ! Dump icebergs bonds to screen
+  if (really_debug)  call show_all_bonds(bergs)
+
   call mpp_clock_end(bergs%clock_dia)
 
   ! Return what ever calving we did not use and additional icebergs melt
@@ -1589,13 +1597,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 
     if (bergs%iceberg_bonds_on) then
       check_bond_quality=.true.
+      nbonds=0
       call count_bonds(bergs, nbonds,check_bond_quality)
-      !if (mpp_pe().eq.mpp_root_pe()) then 
-        !if (check_bond_quality) then
-        !  write(*,'(2a)') 'diamonds, Bond check complete. Bonds are perfect'
-        !else
-        !  write(*,'(2a)') 'diamonds, Bond check complete. Bonds are not perfect'
-        !endif
     endif
   endif
 
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 7816a8a..af6f023 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -64,7 +64,7 @@ module ice_bergs_framework
 public insert_berg_into_list, create_iceberg, delete_iceberg_from_list, destroy_iceberg
 public print_fld,print_berg, print_bergs,record_posn, push_posn, append_posn, check_position
 public move_trajectory, move_all_trajectories
-public form_a_bond, connect_all_bonds
+public form_a_bond, connect_all_bonds, show_all_bonds, bond_address_update
 public find_cell,find_cell_by_search,count_bergs,is_point_in_cell,pos_within_cell, count_bonds
 public sum_mass,sum_heat,bilin,yearday,bergs_chksum
 public checksum_gridded
@@ -724,10 +724,6 @@ subroutine ice_bergs_framework_init(bergs, &
   call mpp_clock_end(bergs%clock_ini)
   call mpp_clock_end(bergs%clock)
 
-!print *, mpp_pe(), 'Alon: global', grd%isg, grd%ieg, grd%jsg, grd%jeg
-!print *, mpp_pe(), 'Alon: comp', grd%isc, grd%iec, grd%jsc, grd%jec
-!print *, mpp_pe(), 'Alon: data', grd%isd, grd%ied, grd%jsd, grd%jed
-
 end subroutine ice_bergs_framework_init
 
 ! ##############################################################################
@@ -844,8 +840,6 @@ subroutine update_halo_icebergs(bergs)
  ! For convenience
    grd=>bergs%grd
 
-
-
 ! Step 1: Clear the current halos
 
 
@@ -896,6 +890,7 @@ subroutine update_halo_icebergs(bergs)
 
   !Bergs on the western side of the processor
   do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%isc+halo_width-1 
+    this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
       kick_the_bucket=>this
       this=>this%next
@@ -970,6 +965,7 @@ subroutine update_halo_icebergs(bergs)
 
   !Bergs on north side of the processor
   do grdj = grd%jec-halo_width+1,grd%jec ; do grdi = grd%isd,grd%ied
+    this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
       kick_the_bucket=>this
       this=>this%next
@@ -984,6 +980,7 @@ subroutine update_halo_icebergs(bergs)
 
   !Bergs on south side of the processor
   do grdj = grd%jsc,grd%jsc+halo_width-1 ; do grdi = grd%isd,grd%ied
+    this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
       kick_the_bucket=>this
       this=>this%next
@@ -1361,7 +1358,6 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
   integer :: counter, k, max_bonds
   type(bond), pointer :: current_bond
  
-    !print *, 'Packing berg', berg%iceberg_num, mpp_pe(), berg%halo_berg
     max_bonds=0
     if (present(max_bonds_in)) max_bonds=max_bonds_in
 
@@ -1412,10 +1408,47 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
         endif
       enddo
     endif
-
+   
+    ! Clearing berg pointer from partner bonds
+    !if (berg%halo_berg .lt. 0.5) then
+    !  call clear_berg_from_partners_bonds(berg)
+    !endif
 
   end subroutine pack_berg_into_buffer2
 
+
+!###########################################################################3
+
+  subroutine clear_berg_from_partners_bonds(berg) 
+  !Arguments
+  type(iceberg), intent(in), pointer :: berg
+  type(iceberg), pointer :: other_berg
+  type(bond), pointer :: current_bond, matching_bond
+  
+    current_bond=>berg%first_bond
+    do while (associated(current_bond)) !Looping over bonds
+      other_berg=>current_bond%other_berg
+      if (associated(other_berg)) then
+        matching_bond=>other_berg%first_bond
+        do while (associated(matching_bond))  ! Looping over possible matching bonds in other_berg
+          if (matching_bond%other_berg_num .eq. berg%iceberg_num) then
+            matching_bond%other_berg=>null()
+            matching_bond=>null()
+          else
+            matching_bond=>matching_bond%next_bond
+          endif
+        enddo
+      else
+       ! Note: This is meant to be unmatched after you have cleared the first berg       
+       ! call error_mesg('diamonds, clear berg from partners', 'The bond you are trying to clear is unmatched!', WARNING) 
+      endif
+      current_bond=>current_bond%next_bond
+    enddo !End loop over bonds
+
+  end subroutine clear_berg_from_partners_bonds
+
+
+
   subroutine increase_buffer(old,delta)
   ! Arguments
   type(buffer), pointer :: old
@@ -1504,8 +1537,7 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n,grd, force_append, max_bonds_
     localberg%lon_old=localberg%lon
     localberg%lat_old=localberg%lat
 
-    !print *, 'Unpacking berg', localberg%iceberg_num, mpp_pe(), localberg%halo_berg
-
+    ! force_app=.true.
     if(force_app) then !force append with origin ine,jne (for I/O)
 
       localberg%ine=buff%data(19,n) 
@@ -1544,6 +1576,7 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n,grd, force_append, max_bonds_
 
     !#  Do stuff to do with bonds here MP1
 
+    this%first_bond=>null()
     if (max_bonds .gt. 0) then
       counter=26 !how many data points being passed so far (must match above)
       do k = 1,max_bonds
@@ -1770,12 +1803,15 @@ subroutine add_new_berg_to_list(first, bergvals, quick, newberg_return)
   endif
 
   if (present(quick)) then
-    if(quick) call insert_berg_into_list(first, new, quick=.true.)
+    if(quick) then
+      call insert_berg_into_list(first, new, quick=.true.)
+    else
+      call insert_berg_into_list(first, new)
+    endif
   else
     call insert_berg_into_list(first, new)
   endif
 
-
   !Clear new
   new=>null()
 
@@ -2091,6 +2127,9 @@ subroutine destroy_iceberg(berg)
 type(iceberg), pointer :: berg
 ! Local variables
 
+  ! Clears all matching bonds before deallocint memory
+  call clear_berg_from_partners_bonds(berg)
+
   ! Bye-bye berg
   deallocate(berg)
 
@@ -2161,7 +2200,8 @@ subroutine form_a_bond(berg, other_berg_num, other_berg_ine, other_berg_jne, oth
 integer, optional  :: other_berg_ine, other_berg_jne
     
 if (berg%iceberg_num .ne. other_berg_num) then
-  print *, 'Forming a bond!!!', mpp_pe(), berg%iceberg_num, other_berg_num, berg%halo_berg
+  !print *, 'Forming a bond!!!', mpp_pe(), berg%iceberg_num, other_berg_num, berg%halo_berg, berg%ine, berg%jne
+
   ! Step 1: Create a new bond
   allocate(new_bond)
   new_bond%other_berg_num=other_berg_num
@@ -2198,47 +2238,139 @@ end subroutine form_a_bond
 
 ! #############################################################################
 
+subroutine bond_address_update(bergs)
+type(icebergs), pointer :: bergs
+type(iceberg), pointer :: other_berg, berg
+type(icebergs_gridded), pointer :: grd
+integer :: grdi, grdj, nbonds
+type(bond) , pointer :: current_bond
+
+ ! For convenience
+  grd=>bergs%grd
+
+  ! This could be done for only the bergs near the halos
+  do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+    berg=>bergs%list(grdi,grdj)%first
+    do while (associated(berg)) ! loop over all bergs
+      current_bond=>berg%first_bond
+      do while (associated(current_bond)) ! loop over all bonds
+        if  (associated(current_bond%other_berg)) then
+          current_bond%other_berg_ine=current_bond%other_berg%ine
+          current_bond%other_berg_jne=current_bond%other_berg%jne
+          current_bond=>current_bond%next_bond
+        else
+          if (berg%halo_berg .lt. 0.5) then     
+            call error_mesg('diamonds, bond address update', 'other berg in bond not assosiated!', FATAL)
+          endif
+          current_bond=>current_bond%next_bond
+        endif
+      enddo
+      berg=>berg%next
+    enddo
+  enddo; enddo
+
+  call mpp_sync_self()
+
+end subroutine bond_address_update
+
+!###################################################################################################
+
+subroutine show_all_bonds(bergs)
+type(icebergs), pointer :: bergs
+type(iceberg), pointer :: other_berg, berg
+type(icebergs_gridded), pointer :: grd
+integer :: grdi, grdj, nbonds
+type(bond) , pointer :: current_bond
+
+ ! For convenience
+  grd=>bergs%grd
+
+  do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+    berg=>bergs%list(grdi,grdj)%first
+    do while (associated(berg)) ! loop over all bergs
+      current_bond=>berg%first_bond
+      do while (associated(current_bond)) ! loop over all bonds
+
+        print *, 'Show Bond1 :', berg%iceberg_num, current_bond%other_berg_num, current_bond%other_berg_ine, current_bond%other_berg_jne,  mpp_pe()
+        if  (associated(current_bond%other_berg)) then
+        print *, 'Show Bond2 :', berg%iceberg_num, current_bond%other_berg_num, current_bond%other_berg%ine, current_bond%other_berg%jne,  mpp_pe()
+                print *, 'Bond matching', current_bond%other_berg%iceberg_num, current_bond%other_berg_num, mpp_pe()
+        endif
+       current_bond=>current_bond%next_bond
+      enddo
+      berg=>berg%next
+    enddo
+  enddo; enddo
+
+end subroutine show_all_bonds
+
+
 subroutine connect_all_bonds(bergs)
 type(icebergs), pointer :: bergs
 type(iceberg), pointer :: other_berg, berg
 type(icebergs_gridded), pointer :: grd
+integer :: i, j
 integer :: grdi, grdj
+integer :: grdi_inner, grdj_inner
 type(bond) , pointer :: current_bond, other_berg_bond
 logical :: bond_matched, missing_bond, check_bond_quality
 integer nbonds
 
 missing_bond=.false.
+bond_matched=.false.
 
- ! For convenience
+! For convenience
   grd=>bergs%grd
 
   do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+! do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec  ! Don't connect halo bergs
     berg=>bergs%list(grdi,grdj)%first
     do while (associated(berg)) ! loop over all bergs
       current_bond=>berg%first_bond
       do while (associated(current_bond)) ! loop over all bonds
-
         !code to find parter bond goes here
         if (.not.associated(current_bond%other_berg)) then
-          other_berg=>bergs%list(current_bond%other_berg_ine,current_bond%other_berg_jne)%first
+          bond_matched=.false.
+          i = current_bond%other_berg_ine ; j = current_bond%other_berg_jne
+          other_berg=>bergs%list(i,j)%first
           do while (associated(other_berg)) ! loop over all other bergs
-            bond_matched=.false.
             if (other_berg%iceberg_num == current_bond%other_berg_num) then
               current_bond%other_berg=>other_berg
               other_berg=>null()
-              bond_matched=.true.  
+              bond_matched=.true. 
             else
               other_berg=>other_berg%next
             endif 
           enddo
           if (.not.bond_matched) then
-             if (berg%halo_berg .lt. 0.5) then
-                missing_bond=.true.     
-                call error_mesg('diamonds, connect_all_bonds', 'A non halo bond is missing!!!', WARNING)
-             endif
+            ! If you are stil not matched, then search adjacent cells
+            do grdj_inner = j-1,j+1 ; do grdi_inner = i-1,i+1
+              if (.not. bond_matched) then
+                if    ((grdj_inner .gt. grd%jsd-1) .and. (grdj_inner .lt. grd%jed+1)        &
+                .and.  (grdi_inner .gt. grd%isd-1) .and. (grdi_inner .lt. grd%ied+1)      &
+                .and. ((grdi_inner .ne. i) .or. (grdj_inner .ne. j)) ) then
+                  other_berg=>bergs%list(grdi_inner,grdj_inner)%first
+                  do while (associated(other_berg)) ! loop over all other bergs
+                    if (other_berg%iceberg_num == current_bond%other_berg_num) then
+                      current_bond%other_berg=>other_berg
+                      other_berg=>null()
+                      bond_matched=.true.  
+                    else
+                      other_berg=>other_berg%next
+                    endif 
+                  enddo
+                endif
+              endif
+            enddo;enddo
+          endif
+          if (.not.bond_matched) then
+            if (berg%halo_berg .lt. 0.5) then
+              missing_bond=.true.    
+             print * , berg%iceberg_num, mpp_pe(), current_bond%other_berg_num, current_bond%other_berg_ine 
+              call error_mesg('diamonds, connect_all_bonds', 'A non-halo bond is missing!!!', FATAL)
+            endif
           endif
         endif
-
         current_bond=>current_bond%next_bond
       enddo
       berg=>berg%next
@@ -2247,6 +2379,7 @@ subroutine connect_all_bonds(bergs)
 
   if (debug) then
     check_bond_quality=.true.
+    nbonds=0
     call count_bonds(bergs, nbonds,check_bond_quality)
   endif
 
@@ -2261,7 +2394,6 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
 type(iceberg), pointer :: other_berg
 type(icebergs_gridded), pointer :: grd
 type(bond) , pointer :: current_bond, other_berg_bond
-!integer, intent(out) :: number_of_bonds 
 integer, intent(out) :: number_of_bonds
 integer :: number_of_bonds_all_pe
 integer :: grdi, grdj
@@ -2284,7 +2416,6 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
   grd=>bergs%grd
 
   number_of_bonds=0  ! This is a bond counter.
-
   do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
     berg=>bergs%list(grdi,grdj)%first
     do while (associated(berg)) ! loop over all bergs
@@ -2293,6 +2424,7 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
         number_of_bonds=number_of_bonds+1
 
         ! ##### Beginning Quality Check on Bonds ######
+!      print *, 'Quality check', mpp_pe(), berg%iceberg_num
         if (quality_check) then
           num_unmatched_bonds=0
           num_unassosiated_bond_pairs=0
@@ -2301,7 +2433,7 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
           if (associated(other_berg)) then
             other_berg_bond=>other_berg%first_bond
           
-            do while (associated(other_berg_bond))  !loops over the icebergs in the other icebergs bond list            
+            do while (associated(other_berg_bond))  !loops over the icebergs in the other icebergs bond list           
               if (associated(other_berg_bond%other_berg)) then
                 if (other_berg_bond%other_berg%iceberg_num==berg%iceberg_num) then
                   bond_is_good=.True.  !Bond_is_good becomes true when the corresponding bond is found
@@ -2315,7 +2447,7 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
             enddo  ! End of loop over the other berg's bonds.
 
             if (bond_is_good) then
-              !if (debug) write(stderrunit,*) 'Perfect quality Bond:', berg%iceberg_num, current_bond%other_berg_num
+              if (debug) write(stderrunit,*) 'Perfect quality Bond:', berg%iceberg_num, current_bond%other_berg_num
             else  
               if (debug) write(stderrunit,*) 'Non-matching bond...:', berg%iceberg_num, current_bond%other_berg_num
               num_unmatched_bonds=num_unmatched_bonds+1
@@ -2338,7 +2470,7 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
 
     bergs%nbonds=number_of_bonds_all_pe !Total number of bonds across all pe's
     if (number_of_bonds .gt. 0) then
-      print *, "Number of bonds on pe, out of a total of: ", number_of_bonds, number_of_bonds_all_pe
+      print *, "Number of bonds on pe:",  mpp_pe(), "out of a total of: ", number_of_bonds, number_of_bonds_all_pe
     endif
 
     if (quality_check) then
@@ -2364,8 +2496,6 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
       endif
     endif
 
-!    print *, "ending bond_check"
-
 end subroutine count_bonds
 
 

From ad09701241a512f84d6d54af652e119e41873feb Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Tue, 6 Oct 2015 11:15:01 -0400
Subject: [PATCH 082/361] Two bugs have been fixed:

1) The amount of memory allocated in berg_checksum has been corrected

2) IA_x and IA_y were not initialized correctly, which was causing errors sometimes.

Both of these bugs have been fixed
---
 icebergs.F90           | 13 +++++++++----
 icebergs_framework.F90 |  2 +-
 2 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 7f6dd8b..4b0a338 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -425,6 +425,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 use_new_predictive_corrective=.True.
 endif
 
+
 !print *, 'axn=',axn,'ayn=',ayn
   u_star=uvel0+(axn*(dt/2.))  !Alon
   v_star=vvel0+(ayn*(dt/2.))  !Alon
@@ -509,7 +510,6 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
                bxn=bxn + IA_x
                byn=byn + IA_y
            endif
-!print *,'IA_x=',IA_x
 !print *,'IA_x=',IA_x,'IA_y',IA_y
 !print *,'P_ia_11',P_ia_11,'P_ia_12',P_ia_12, 'P_ia_21',P_ia_21,'P_ia_22', P_ia_22
 !print *, 'P_ia_times_u_x', P_ia_times_u_x, 'P_ia_times_u_y', P_ia_times_u_y
@@ -621,8 +621,12 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
     axn=0.
     ayn=0.
     if (.not.Runge_not_Verlet) then
-        axn=-gravity*ssh_x +wave_rad*uwave + IA_x
-        ayn=-gravity*ssh_y +wave_rad*vwave + IA_y
+        axn=-gravity*ssh_x +wave_rad*uwave
+        ayn=-gravity*ssh_y +wave_rad*vwave
+        if (interactive_icebergs_on) then
+          axn=axn + IA_x
+          ayn=ayn + IA_y
+        endif
     endif
     if (C_N>0.) then !  C_N=1 for Crank Nicolson Coriolis, C_N=0 for full implicit Coriolis !Alon 
       axn=axn+f_cori*vveln
@@ -2342,11 +2346,13 @@ subroutine evolve_icebergs(bergs)
         ! Adjusting mass...                      Alon decided to move this before calculating the new velocities (so that acceleration can be a fn(r_np1)
         i=i1;j=j1;xi=berg%xi;yj=berg%yj
         !print *, 'Alon: look here!', lonn, latn, uvel3, vvel3, i, j, xi, yj
+        !print *, lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag 
         call adjust_index_and_ground(grd, lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
         !call adjust_index_and_ground(grd, lonn, latn, uvel1, vvel1, i, j, xi, yj, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
 
         ! If the iceberg bounces off the land, then its velocity and acceleration are set to zero
         if (bounced) then
+       !print *, 'you have been bounce: big time!',lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag 
                 axn=0. ; ayn=0.
                 bxn=0. ; byn=0.
                 uvel3=0.; vvel3=0.
@@ -2443,7 +2449,6 @@ subroutine evolve_icebergs(bergs)
       !if (debug) call print_berg(stderr(), berg, 'evolve_iceberg, final posn.')
       if (debug) call check_position(grd, berg, 'evolve_iceberg (bot)')
 
-
       berg=>berg%next
     enddo ! loop over all bergs
   enddo ; enddo
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index af6f023..0c7c109 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -3702,7 +3702,7 @@ integer function berg_chksum(berg )
 type(iceberg), pointer :: berg
 ! Local variables
 real :: rtmp(37) !Changed from 28 to 34 by Alon
-integer :: itmp(37+3), i8=0, ichk1, ichk2, ichk3 !Changed from 28 to 34 by Alon
+integer :: itmp(37+4), i8=0, ichk1, ichk2, ichk3 !Changed from 28 to 34 by Alon
 integer :: i
 
   rtmp(:)=0.

From 59a0dece34f5b26dee00a4e6966adf043da7b082 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Thu, 8 Oct 2015 11:21:45 -0400
Subject: [PATCH 083/361] Tabular icebergs can now be initiated by manually
 designing them in the restart file. A subroutine has been written which
 allows you to read in iceberg bonds while ignoring the ine, jne values of the
 bonds. This is done by searching through all grid boxes for the position of
 the iceberg which matched the iceberg id in the bond.

There also exists a python script to initialize tabular iceberg restart files (both for bonds and icebergs).

A small amount of work was also done on improving the bonding force (to make it stable in the limit of small icebergs). This is still work in progress.
---
 icebergs.F90           | 10 ++++--
 icebergs_framework.F90 | 76 +++++++++++++++++++++++++++++++++++++++++-
 icebergs_io.F90        | 47 ++++++++++++++++++++++++--
 3 files changed, 127 insertions(+), 6 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 4b0a338..441f728 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -197,6 +197,7 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
 real :: Rearth
 logical :: critical_interaction_damping_on
 real :: spring_coef, accel_spring, radial_damping_coef, p_ia_coef, tangental_damping_coef, bond_coef
+real :: mult_factor
 real, intent(out) :: IA_x, IA_y 
 real, intent(out) :: P_ia_11, P_ia_12, P_ia_22, P_ia_21, P_ia_times_u_x, P_ia_times_u_y
 real :: L_dist
@@ -327,11 +328,14 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
         r_dist=sqrt( ((x1-x2)**2) + ((y1-y2)**2) )
 
         ! Think about doing bonds using an "inverse overlap area, or some type"
+        mult_factor=((r_dist/(R1+R2))-1) 
         if ((r_dist>0.) .AND. (r_dist> (R1+R2)) ) then 
-          L_dist = min( (r_dist-(R1+R2) ),min(R1,R2) ) 
-          call overlap_area(R1,R2,L_dist,A_o,trapped)
           T_min=min(T1,T2)
-          accel_spring=bond_coef*(T_min/T1)*(A_o/A1)
+          A_o = min((pi*R1**R1),(pi*R2*R2))  !New idea - force increase with distance
+          !L_dist = min( (r_dist-(R1+R2) ),min(R1,R2) )
+          !call overlap_area(R1,R2,L_dist,A_o,trapped)
+          !accel_spring=bond_coef*(T_min/T1)*(A_o/A1)
+          accel_spring=bond_coef*mult_factor*(T_min/T1)*(A_o/A1)
           !accel_spring=bond_coef*(r_dist-(R1+R2)) 
           IA_x=IA_x-(accel_spring*(r_dist_x/r_dist))  !Note: negative sign is an attractive force.
           IA_y=IA_y-(accel_spring*(r_dist_y/r_dist))
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 0c7c109..3b7e87e 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -71,6 +71,8 @@ module ice_bergs_framework
 public grd_chksum2,grd_chksum3
 public fix_restart_dates, offset_berg_dates
 public move_berg_between_cells
+public find_individual_iceberg
+
 
 type :: icebergs_gridded
   type(domain2D), pointer :: domain ! MPP domain
@@ -840,6 +842,18 @@ subroutine update_halo_icebergs(bergs)
  ! For convenience
    grd=>bergs%grd
 
+
+!For debugging
+do grdj = grd%jsd,grd%jsd ;  do grdi = grd%isd,grd%ied
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this))
+      print *, 'A', this%iceberg_num, mpp_pe(), this%halo_berg
+      this=>this%next
+    enddo
+enddo; enddo
+
+
+
 ! Step 1: Clear the current halos
 
 
@@ -859,6 +873,20 @@ subroutine update_halo_icebergs(bergs)
     call delete_all_bergs_in_list(bergs,grdj,grdi)
   enddo ; enddo
 
+!##############################
+
+!For debugging
+do grdj = grd%jsd,grd%jsd ;  do grdi = grd%isd,grd%ied
+    this=>bergs%list(grdi,grdj)%first
+      do while (associated(this))
+      print *, 'B', this%iceberg_num, mpp_pe(), this%halo_berg
+    this=>this%next
+    enddo
+enddo; enddo
+
+
+!#######################################################
+
 
 ! Step 2: Updating the halos  - This code is mostly copied from send_to_other_pes
 
@@ -1067,6 +1095,18 @@ subroutine update_halo_icebergs(bergs)
   call mpp_sync_self()
 
 
+!For debugging
+do grdj = grd%jsd,grd%jsd ;  do grdi = grd%isd,grd%ied
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this))
+      print *, 'C', this%iceberg_num, mpp_pe(), this%halo_berg
+      this=>this%next
+    enddo
+enddo; enddo
+
+
+
+
 end subroutine update_halo_icebergs
 
 
@@ -2470,7 +2510,7 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
 
     bergs%nbonds=number_of_bonds_all_pe !Total number of bonds across all pe's
     if (number_of_bonds .gt. 0) then
-      print *, "Number of bonds on pe:",  mpp_pe(), "out of a total of: ", number_of_bonds, number_of_bonds_all_pe
+      print *, "Bonds on PE:",number_of_bonds, "Total bonds", number_of_bonds_all_PE, "on PE number:",  mpp_pe()
     endif
 
     if (quality_check) then
@@ -2893,6 +2933,40 @@ end function find_cell_loc
 
 end function find_cell_by_search
 
+
+! ##############################################################################
+
+subroutine find_individual_iceberg(bergs,iceberg_num, ine, jne, berg_found)
+type(icebergs), pointer :: bergs
+type(iceberg), pointer :: this
+type(icebergs_gridded), pointer :: grd
+integer :: grdi, grdj
+integer, intent(in) :: iceberg_num
+integer, intent(out) :: ine, jne
+real, intent(out) :: berg_found
+
+berg_found=0.0
+ine=999
+jne=999
+  ! For convenience
+    grd=>bergs%grd
+    
+    do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
+      this=>bergs%list(grdi,grdj)%first
+      do while (associated(this))
+        if (iceberg_num .eq. this%iceberg_num) then
+          ine=this%ine
+          jne=this%jne
+          berg_found=1.0
+          !print *, 'found this one'
+          return
+        endif
+        this=>this%next
+      enddo
+    enddo ; enddo                                                                             
+end subroutine  find_individual_iceberg 
+
+
 ! ##############################################################################
 
 logical function find_cell(grd, x, y, oi, oj)
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index d7ec695..e29006d 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -26,7 +26,7 @@ module ice_bergs_io
 use ice_bergs_framework, only: pack_berg_into_buffer2,unpack_berg_from_buffer2
 use ice_bergs_framework, only: pack_traj_into_buffer2,unpack_traj_from_buffer2
 use ice_bergs_framework, only: find_cell,find_cell_by_search,count_bergs,is_point_in_cell,pos_within_cell,append_posn
-use ice_bergs_framework, only: count_bonds, form_a_bond
+use ice_bergs_framework, only: count_bonds, form_a_bond, find_individual_iceberg
 use ice_bergs_framework, only: push_posn
 use ice_bergs_framework, only: add_new_berg_to_list,destroy_iceberg
 use ice_bergs_framework, only: increase_ibuffer,increase_ibuffer_traj,grd_chksum2,grd_chksum3
@@ -726,6 +726,7 @@ subroutine read_restart_bergs(bergs,Time)
 character(len=33) :: filename, filename_base
 type(icebergs_gridded), pointer :: grd
 type(iceberg) :: localberg ! NOT a pointer but an actual local variable
+real :: pos_is_good, pos_is_good_all_pe
 integer :: stderrunit
 
 real, allocatable, dimension(:) :: lon,          &
@@ -863,6 +864,16 @@ subroutine read_restart_bergs(bergs,Time)
            lres=find_cell_by_search(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
          endif
        endif
+       ! The next few lines are a check to see whether the icebergs are all found.
+       pos_is_good=0.0
+       if (lres) then
+         pos_is_good=1.0
+       endif
+       pos_is_good_all_pe=pos_is_good
+       call mpp_sum(pos_is_good_all_pe)
+       if (pos_is_good_all_pe .lt. 0.5) then
+         call error_mesg('diamonds, read_restart_bergs', 'One of the iceberg positions was not found', FATAL)
+       endif
        if (really_debug) then
          write(stderrunit,'(a,i8,a,2f9.4,a,i8)') 'diamonds, read_restart_bergs: berg ',k,' is at ',localberg%lon,localberg%lat,&
               & ' on PE ',mpp_pe()
@@ -1070,6 +1081,8 @@ subroutine read_restart_bonds(bergs,Time)
 integer :: number_partial_bonds ! How many either complete/partial bonds formed.
 integer :: all_pe_number_perfect_bonds, all_pe_number_partial_bonds
 integer :: all_pe_number_first_bonds_matched, all_pe_number_second_bonds_matched
+integer :: ine, jne
+real :: berg_found, berg_found_all_pe
 integer, allocatable, dimension(:) :: first_berg_num,   &
                                       other_berg_num,  &
                                       first_berg_jne,   &
@@ -1118,7 +1131,36 @@ subroutine read_restart_bonds(bergs,Time)
     number_perfect_bonds=0
     number_partial_bonds=0
     do k=1, nbonds_in_file
-       
+      
+
+       ! If i,j in restart files are not good, then we find the berg position of the bond addresses manually:
+       if (ignore_ij_restart) then 
+         !Finding first iceberg in bond
+         ine=999 ; jne=999 ; berg_found=0.0
+         call find_individual_iceberg(bergs,first_berg_num(k), ine, jne,berg_found)
+         berg_found_all_pe=berg_found
+         call mpp_sum(berg_found_all_pe)
+         !print *, mpp_pe(), berg_found_all_pe, berg_found, first_berg_num(k),'here'
+         if (berg_found_all_pe .gt. 0.5) then
+           first_berg_ine(k)=ine
+           first_berg_jne(k)=jne
+         else
+          call error_mesg('read_restart_bonds_bergs_new', 'First iceberg in bond not found on any pe', FATAL)
+         endif
+
+         !Finding other iceberg other iceberg
+         ine=999 ; jne=999 ; berg_found=0.0
+         call find_individual_iceberg(bergs,other_berg_num(k), ine, jne, berg_found)
+         call mpp_sum(berg_found)
+         if (berg_found .gt. 0.5) then
+           other_berg_ine(k)=ine
+           other_berg_jne(k)=jne
+         else
+          call error_mesg('read_restart_bonds_bergs_new', 'Other iceberg in bond not found on any pe', FATAL)
+         endif
+       endif
+
+
       ! Decide whether the first iceberg is on the processeor
       if ( first_berg_ine(k)>=grd%isc .and. first_berg_ine(k)<=grd%iec .and. &
         first_berg_jne(k)>=grd%jsc .and.first_berg_jne(k)<=grd%jec ) then
@@ -1203,6 +1245,7 @@ subroutine read_restart_bonds(bergs,Time)
             other_berg_jne )
   endif
 end subroutine read_restart_bonds
+
 ! ##############################################################################
 
 subroutine read_restart_calving(bergs)

From 734864f9f17e1e6479e870c0dabc0d0c7ce88059 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Thu, 8 Oct 2015 18:21:28 -0400
Subject: [PATCH 084/361] 1) Damping added to iceberg bonds.

2) A bug was fixed in the accel subroutine. The interactive_forces call was using a u_s,v_s, which was not defined. This has been corrected.
---
 icebergs.F90           | 95 ++++++++++++++++++++++++++++--------------
 icebergs_framework.F90 | 43 ++++++++++---------
 2 files changed, 85 insertions(+), 53 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 441f728..4058eec 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -190,14 +190,14 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
 type(bond), pointer :: current_bond
 real :: T1, L1, W1, lon1, lat1, x1, y1, R1, A1   !Current iceberg
 real :: T2, L2, W2, lon2, lat2, x2, y2, R2, A2   !Other iceberg
-real :: r_dist_x, r_dist_y, r_dist, A_o, trapped, T_min
+real :: r_dist_x, r_dist_y, r_dist, A_o, A_min, trapped, T_min
 real, intent(in) :: u0,v0, u1, v1
 real :: P_11, P_12, P_21, P_22
 real :: u2, v2
 real :: Rearth
 logical :: critical_interaction_damping_on
 real :: spring_coef, accel_spring, radial_damping_coef, p_ia_coef, tangental_damping_coef, bond_coef
-real :: mult_factor
+real :: mult_factor, damping_factor
 real, intent(out) :: IA_x, IA_y 
 real, intent(out) :: P_ia_11, P_ia_12, P_ia_22, P_ia_21, P_ia_times_u_x, P_ia_times_u_y
 real :: L_dist
@@ -213,12 +213,12 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
 critical_interaction_damping_on=bergs%critical_interaction_damping_on
 iceberg_bonds_on=bergs%iceberg_bonds_on
 
-
 !Using critical values for damping rather than manually setting the damping.
 if (critical_interaction_damping_on) then
      radial_damping_coef=2.*sqrt(spring_coef)  ! Critical damping  
-     tangental_damping_coef=(2.*sqrt(spring_coef)/5)  ! Critical damping  /5   (just a guess)
+     tangental_damping_coef=(2.*sqrt(spring_coef))  ! Critical damping   (just a guess)
 endif
+print *, radial_damping_coef
 
 
 ! Get the stderr unit number.  Not sure what this does
@@ -258,22 +258,23 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
 
        call overlap_area(R1,R2,r_dist,A_o,trapped)
        T_min=min(T1,T2)
+       A_min = min((pi*R1**R1),(pi*R2*R2)) 
 
        !Calculating spring force  (later this should only be done on the first time around)
-       accel_spring=spring_coef*(T_min/T1)*(A_o/A1)
        if ((r_dist>0.) .AND. (r_dist< (R1+R2)) ) then
+         !Spring force
+         accel_spring=spring_coef*(T_min/T1)*(A_o/A1)
          IA_x=IA_x+(accel_spring*(r_dist_x/r_dist))
          IA_y=IA_y+(accel_spring*(r_dist_y/r_dist))
-
-
          !Working out the damping
 
+         !Damping force:
          !Paralel velocity
           P_11=(r_dist_x*r_dist_x)/(r_dist**2)
           P_12=(r_dist_x*r_dist_y)/(r_dist**2)
           P_21=(r_dist_x*r_dist_y)/(r_dist**2)
           P_22=(r_dist_y*r_dist_y)/(r_dist**2)
-          p_ia_coef=radial_damping_coef*(T_min/T1)*(A_o/A1)
+          p_ia_coef=radial_damping_coef*(T_min/T1)*(A_min/A1)
           p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2)) &
           + sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
           P_ia_11=P_ia_11+p_ia_coef*P_11
@@ -286,7 +287,7 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
 
           !Normal velocities
           P_11=1-P_11  ;  P_12=-P_12 ; P_22=1-P_22
-          p_ia_coef=tangental_damping_coef*(T_min/T1)*(A_o/A1)
+          p_ia_coef=tangental_damping_coef*(T_min/T1)*(A_min/A1)
           p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2))  &
           + sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
           P_ia_11=P_ia_11+p_ia_coef*P_11
@@ -317,8 +318,8 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
         L2=other_berg%length
         W2=other_berg%width
         T2=other_berg%thickness ! Note, that it is not dependent on thickness This means that it might go unstable for small icebergs
-        !u2=other_berg%uvel_old
-        !v2=other_berg%vvel_old 
+        u2=other_berg%uvel_old
+        v2=other_berg%vvel_old 
         A2=L2*W2
         R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
         lon2=other_berg%lon_old; lat2=other_berg%lat_old 
@@ -326,25 +327,60 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
 
         r_dist_x=x1-x2 ; r_dist_y=y1-y2
         r_dist=sqrt( ((x1-x2)**2) + ((y1-y2)**2) )
-
-        ! Think about doing bonds using an "inverse overlap area, or some type"
-        mult_factor=((r_dist/(R1+R2))-1) 
-        if ((r_dist>0.) .AND. (r_dist> (R1+R2)) ) then 
-          T_min=min(T1,T2)
-          A_o = min((pi*R1**R1),(pi*R2*R2))  !New idea - force increase with distance
-          !L_dist = min( (r_dist-(R1+R2) ),min(R1,R2) )
-          !call overlap_area(R1,R2,L_dist,A_o,trapped)
-          !accel_spring=bond_coef*(T_min/T1)*(A_o/A1)
-          accel_spring=bond_coef*mult_factor*(T_min/T1)*(A_o/A1)
-          !accel_spring=bond_coef*(r_dist-(R1+R2)) 
+        T_min=min(T1,T2)
+        A_min = min((pi*R1**R1),(pi*R2*R2)) 
+       
+       !Spring force 
+        if ((r_dist>0.) .AND. (r_dist> (R1+R2)) ) then
+          mult_factor=((r_dist/(R1+R2))-1) 
+          accel_spring=bond_coef*mult_factor*(T_min/T1)*(A_min/A1)
           IA_x=IA_x-(accel_spring*(r_dist_x/r_dist))  !Note: negative sign is an attractive force.
           IA_y=IA_y-(accel_spring*(r_dist_y/r_dist))
-        endif  !Note, no damping on bond force has been added yet    
+        endif  !Note, no damping on bond force has been added yet   
+
+       damping_factor=2.0
+       !Spring damping 
+        if ((r_dist>0.) .AND. (r_dist> (R1+R2)) .AND. (r_dist< (damping_factor*(R1+R2))) ) then 
+         !Paralel velocity
+          P_11=(r_dist_x*r_dist_x)/(r_dist**2)
+          P_12=(r_dist_x*r_dist_y)/(r_dist**2)
+          P_21=(r_dist_x*r_dist_y)/(r_dist**2)
+          P_22=(r_dist_y*r_dist_y)/(r_dist**2)
+          p_ia_coef=radial_damping_coef*(T_min/T1)*(A_min/A1)
+          p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2)) &
+          + sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
+          P_ia_11=P_ia_11+p_ia_coef*P_11
+          P_ia_12=P_ia_12+p_ia_coef*P_12
+          P_ia_21=P_ia_21+p_ia_coef*P_21
+          P_ia_22=P_ia_22+p_ia_coef*P_22
+          P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
+          P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
+
+          !Normal velocities
+          P_11=1-P_11  ;  P_12=-P_12 ; P_22=1-P_22
+          p_ia_coef=tangental_damping_coef*(T_min/T1)*(A_min/A1)
+          p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2))  &
+          + sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
+          P_ia_11=P_ia_11+p_ia_coef*P_11
+          P_ia_12=P_ia_12+p_ia_coef*P_12
+          P_ia_21=P_ia_21+p_ia_coef*P_21
+          P_ia_22=P_ia_22+p_ia_coef*P_22
+          P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
+          P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
+
+        endif 
+
       endif
+
+
+
       current_bond=>current_bond%next_bond
     enddo
   endif
 
+!print *,'IA_x=',IA_x,'IA_y',IA_y
+!print *,'P_ia_11',P_ia_11,'P_ia_12',P_ia_12, 'P_ia_21',P_ia_21,'P_ia_22', P_ia_22
+!print *, 'P_ia_times_u_x', P_ia_times_u_x, 'P_ia_times_u_y', P_ia_times_u_y
   contains
 
   subroutine overlap_area(R1,R2,d,A,trapped)
@@ -514,9 +550,6 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
                bxn=bxn + IA_x
                byn=byn + IA_y
            endif
-!print *,'IA_x=',IA_x,'IA_y',IA_y
-!print *,'P_ia_11',P_ia_11,'P_ia_12',P_ia_12, 'P_ia_21',P_ia_21,'P_ia_22', P_ia_22
-!print *, 'P_ia_times_u_x', P_ia_times_u_x, 'P_ia_times_u_y', P_ia_times_u_y
 
 endif
 
@@ -540,8 +573,11 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
      uveln=uvel; vveln=vvel
   endif
  
+  us=uvel0   ; vs=vvel0
   do itloop=1,2 ! Iterate on drag coefficients
-
+    if (itloop .eq. 2) then
+      us=uveln   ; vs=vveln
+    endif
   if (use_new_predictive_corrective) then
     !Alon's proposed change - using Bob's improved scheme.
     drag_ocn=c_ocn*0.5*(sqrt( (uveln-uo)**2+(vveln-vo)**2 )+sqrt( (uvel0-uo)**2+(vvel0-vo)**2 ))
@@ -580,8 +616,6 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 endif
 
 
-
-
   ! Solve for implicit accelerations
     if (alpha+beta.gt.0.) then
       lambda=drag_ocn+drag_atm+drag_ice
@@ -2350,7 +2384,6 @@ subroutine evolve_icebergs(bergs)
         ! Adjusting mass...                      Alon decided to move this before calculating the new velocities (so that acceleration can be a fn(r_np1)
         i=i1;j=j1;xi=berg%xi;yj=berg%yj
         !print *, 'Alon: look here!', lonn, latn, uvel3, vvel3, i, j, xi, yj
-        !print *, lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag 
         call adjust_index_and_ground(grd, lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
         !call adjust_index_and_ground(grd, lonn, latn, uvel1, vvel1, i, j, xi, yj, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
 
@@ -2367,7 +2400,6 @@ subroutine evolve_icebergs(bergs)
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
           call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling)
   
-  
         ! Calling the acceleration   (note that the velocity is converted to u_star inside the accel script)
         call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn, ayn, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
   
@@ -2536,6 +2568,7 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
   lon0=lon; lat0=lat ! original position
   i0=i; j0=j ! original i,j
   lret=pos_within_cell(grd, lon, lat, i, j, xi, yj)
+!  print *, 'Alon:', lon, lat, i, j, xi, yj, lret
   xi0=xi; yj0=yj ! original xi,yj
   if (debug) then
     !Sanity check lret, xi and yj
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 3b7e87e..22b9165 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -842,15 +842,14 @@ subroutine update_halo_icebergs(bergs)
  ! For convenience
    grd=>bergs%grd
 
-
 !For debugging
-do grdj = grd%jsd,grd%jsd ;  do grdi = grd%isd,grd%ied
-    this=>bergs%list(grdi,grdj)%first
-    do while (associated(this))
-      print *, 'A', this%iceberg_num, mpp_pe(), this%halo_berg
-      this=>this%next
-    enddo
-enddo; enddo
+!do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
+!    this=>bergs%list(grdi,grdj)%first
+!    do while (associated(this))
+!      print *, 'A', this%iceberg_num, mpp_pe(), this%halo_berg, grdi, grdj
+!      this=>this%next
+!    enddo
+!enddo; enddo
 
 
 
@@ -876,13 +875,13 @@ subroutine update_halo_icebergs(bergs)
 !##############################
 
 !For debugging
-do grdj = grd%jsd,grd%jsd ;  do grdi = grd%isd,grd%ied
-    this=>bergs%list(grdi,grdj)%first
-      do while (associated(this))
-      print *, 'B', this%iceberg_num, mpp_pe(), this%halo_berg
-    this=>this%next
-    enddo
-enddo; enddo
+!do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
+!    this=>bergs%list(grdi,grdj)%first
+!      do while (associated(this))
+!      print *, 'B', this%iceberg_num, mpp_pe(), this%halo_berg, grdi, grdj
+!    this=>this%next
+!    enddo
+!enddo; enddo
 
 
 !#######################################################
@@ -1096,13 +1095,13 @@ subroutine update_halo_icebergs(bergs)
 
 
 !For debugging
-do grdj = grd%jsd,grd%jsd ;  do grdi = grd%isd,grd%ied
-    this=>bergs%list(grdi,grdj)%first
-    do while (associated(this))
-      print *, 'C', this%iceberg_num, mpp_pe(), this%halo_berg
-      this=>this%next
-    enddo
-enddo; enddo
+!do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
+!    this=>bergs%list(grdi,grdj)%first
+!    do while (associated(this))
+!      print *, 'C', this%iceberg_num, mpp_pe(), this%halo_berg,  grdi, grdj
+!      this=>this%next
+!    enddo
+!enddo; enddo
 
 
 

From 8869339f7e829b9dde6a93e11a0ee88f25d23da4 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Mon, 12 Oct 2015 17:05:16 -0400
Subject: [PATCH 085/361] A few bugs related to iceberg bonds have been fixed.

1) lat_old, lon_old, vvel_old, uvel_old have been removed from the restart files, and are initialized to equal lon,lat,vvel and uvel, respectively.

2) Interactive_forces subroutine has been edited so that it has less repitition. Also, the calculation of the distance between icebergs has been corrected.

3) A small bug has been corrected which allows iceberg bonds to form for all iceberg_num greater than 0 (rather than greater than 1).

4) The force between icebergs now depends on the distance between the icebergs rather than the overlap of the iceberg areas. This is stable in the limit of small icebergs, unlike the area overlap

The bonds appear to be working
---
 icebergs.F90           | 234 +++++++++++++++++++----------------------
 icebergs_framework.F90 |  67 ++++++------
 icebergs_io.F90        |  57 +---------
 3 files changed, 148 insertions(+), 210 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 4058eec..10eb565 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -188,93 +188,142 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
 type(iceberg), pointer :: berg
 type(iceberg), pointer :: other_berg
 type(bond), pointer :: current_bond
-real :: T1, L1, W1, lon1, lat1, x1, y1, R1, A1   !Current iceberg
-real :: T2, L2, W2, lon2, lat2, x2, y2, R2, A2   !Other iceberg
-real :: r_dist_x, r_dist_y, r_dist, A_o, A_min, trapped, T_min
 real, intent(in) :: u0,v0, u1, v1
-real :: P_11, P_12, P_21, P_22
 real :: u2, v2
-real :: Rearth
 logical :: critical_interaction_damping_on
-real :: spring_coef, accel_spring, radial_damping_coef, p_ia_coef, tangental_damping_coef, bond_coef
-real :: mult_factor, damping_factor
 real, intent(out) :: IA_x, IA_y 
 real, intent(out) :: P_ia_11, P_ia_12, P_ia_22, P_ia_21, P_ia_times_u_x, P_ia_times_u_y
-real :: L_dist
-integer :: stderrunit
 integer :: grdi, grdj
 logical :: iceberg_bonds_on
-Rearth=6360.e3
-!spring_coef=1.e-4
-spring_coef=bergs%spring_coef
-bond_coef=bergs%bond_coef 
-radial_damping_coef=bergs%radial_damping_coef
-tangental_damping_coef=bergs%tangental_damping_coef
-critical_interaction_damping_on=bergs%critical_interaction_damping_on
+logical :: bonded
 iceberg_bonds_on=bergs%iceberg_bonds_on
 
-!Using critical values for damping rather than manually setting the damping.
-if (critical_interaction_damping_on) then
-     radial_damping_coef=2.*sqrt(spring_coef)  ! Critical damping  
-     tangental_damping_coef=(2.*sqrt(spring_coef))  ! Critical damping   (just a guess)
-endif
-print *, radial_damping_coef
+  IA_x=0.
+  IA_y=0.
+  P_ia_11=0. ; P_ia_12=0. ;  P_ia_21=0.;  P_ia_22=0. 
+  P_ia_times_u_x=0. ; P_ia_times_u_y=0.
 
+  bonded=.false. !Unbonded iceberg interactions
+  do grdj = berg%jne-1,berg%jne+1 ; do grdi = berg%ine-1,berg%ine+1
+    other_berg=>bergs%list(grdi,grdj)%first
+    do while (associated(other_berg)) ! loop over all other bergs  
+      call calculate_force(bergs,berg,other_berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y, bonded) 
+      other_berg=>other_berg%next
+    enddo ! loop over all bergs
+  enddo ; enddo
 
-! Get the stderr unit number.  Not sure what this does
-  stderrunit = stderr()
+  bonded=.true.  !Interactions due to iceberg bonds
+  if (iceberg_bonds_on) then ! MP1  
+    current_bond=>berg%first_bond
+    do while (associated(current_bond)) ! loop over all bonds
+      other_berg=>current_bond%other_berg
+      if (.not. associated(current_bond)) then
+        call error_mesg('diamonds,bond interactions', 'Trying to do Bond interactions with unassosiated bond!' ,FATAL)
+      else
+        call calculate_force(bergs,berg,other_berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded) 
+      endif
+      current_bond=>current_bond%next_bond
+    enddo
+  endif
 
-IA_x=0.
-IA_y=0.
-P_ia_11=0. ; P_ia_12=0. ;  P_ia_21=0.;  P_ia_22=0. 
-P_ia_times_u_x=0. ; P_ia_times_u_y=0.
+!print *,'IA_x=',IA_x,'IA_y',IA_y, berg%iceberg_num
+!print *,'P_ia_11',P_ia_11,'P_ia_12',P_ia_12, 'P_ia_21',P_ia_21,'P_ia_22', P_ia_22
+!print *, 'P_ia_times_u_x', P_ia_times_u_x, 'P_ia_times_u_y', P_ia_times_u_y
+  contains
 
 
-L1=berg%length
-W1=berg%width
-T1=berg%thickness 
-A1=L1*W1 
-R1=sqrt(A1/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
-lon1=berg%lon; lat1=berg%lat
-call rotpos_to_tang(lon1,lat1,x1,y1)
+   subroutine calculate_force(bergs,berg,other_berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded) 
+   !Arguments
+     type(icebergs), pointer :: bergs
+     type(iceberg), pointer :: berg
+     type(iceberg), pointer :: other_berg
+     real :: T1, L1, W1, lon1, lat1, x1, y1, R1, A1   !Current iceberg
+     real :: T2, L2, W2, lon2, lat2, x2, y2, R2, A2   !Other iceberg
+     real :: dlon, dlat
+     real :: r_dist_x, r_dist_y, r_dist, A_o, A_min, trapped, T_min
+     real, intent(in) :: u0,v0, u1, v1
+     real :: P_11, P_12, P_21, P_22
+     real :: M1, M2, M_min
+     real :: u2, v2
+     real :: Rearth
+     logical :: critical_interaction_damping_on
+     real :: spring_coef, accel_spring, radial_damping_coef, p_ia_coef, tangental_damping_coef, bond_coef
+     real, intent(inout) :: IA_x, IA_y 
+     real, intent(inout) :: P_ia_11, P_ia_12, P_ia_22, P_ia_21, P_ia_times_u_x, P_ia_times_u_y
+     logical ,intent(in) :: bonded
+
+      Rearth=6360.e3
+      spring_coef=bergs%spring_coef
+      !bond_coef=bergs%bond_coef 
+      radial_damping_coef=bergs%radial_damping_coef
+      tangental_damping_coef=bergs%tangental_damping_coef
+      critical_interaction_damping_on=bergs%critical_interaction_damping_on
+
+      !Using critical values for damping rather than manually setting the damping.
+      if (critical_interaction_damping_on) then
+        radial_damping_coef=2.*sqrt(spring_coef)  ! Critical damping  
+        tangental_damping_coef=(2.*sqrt(spring_coef))  ! Critical damping   (just a guess)
+      endif
 
-  do grdj = berg%jne-1,berg%jne+1 ; do grdi = berg%ine-1,berg%ine+1
-    other_berg=>bergs%list(grdi,grdj)%first
-    !Note: This summing should be made order invarient. 
-    do while (associated(other_berg)) ! loop over all other bergs  
       if (berg%iceberg_num .ne. other_berg%iceberg_num) then
+        !From Berg 1
+        L1=berg%length
+        W1=berg%width
+        T1=berg%thickness 
+        M1=berg%mass 
+        A1=L1*W1 
+        R1=sqrt(A1/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
+        lon1=berg%lon; lat1=berg%lat
+        !call rotpos_to_tang(lon1,lat1,x1,y1)
+
+              
+        !From Berg 1
         L2=other_berg%length
         W2=other_berg%width
         T2=other_berg%thickness 
+        M2=other_berg%mass 
         u2=other_berg%uvel_old !Old values are used to make it order invariant 
         v2=other_berg%vvel_old !Old values are used to make it order invariant 
         A2=L2*W2
         R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
         lon2=other_berg%lon_old; lat2=other_berg%lat_old !Old values are used to make it order invariant
-        call rotpos_to_tang(lon2,lat2,x2,y2)
-
-        r_dist_x=x1-x2 ; r_dist_y=y1-y2
-        r_dist=sqrt( ((x1-x2)**2) + ((y1-y2)**2) )
-
-       call overlap_area(R1,R2,r_dist,A_o,trapped)
-       T_min=min(T1,T2)
-       A_min = min((pi*R1**R1),(pi*R2*R2)) 
+        !call rotpos_to_tang(lon2,lat2,x2,y2)
 
+        dlon=lon1-lon2
+        dlat=lat1-lat2
+        
+        !Note that this is not the exact distance along a great circle.
+        !Approximation for small distances. Should be fine.
+        !r_dist_x=x1-x2 ; r_dist_y=y1-y2
+        !r_dist=sqrt( ((x1-x2)**2) + ((y1-y2)**2) )
+        r_dist_x=dlon*(pi/180)*Rearth*cos(0.5*(lat1+lat2)*(pi/180))
+        r_dist_y=dlat*(pi/180)*Rearth
+        r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) )
+
+        !print *, 'outside the loop',R1, R2,r_dist, bonded
+       !call overlap_area(R1,R2,r_dist,A_o,trapped)
+       !T_min=min(T1,T2)
+       !A_min = min((pi*R1**R1),(pi*R2*R2)) 
+       M_min=min(M1,M2)
        !Calculating spring force  (later this should only be done on the first time around)
-       if ((r_dist>0.) .AND. (r_dist< (R1+R2)) ) then
+       if ((r_dist>0.) .AND. ((r_dist< (R1+R2)) .OR. ( (r_dist> (R1+R2)) .AND. (bonded) ) )) then
          !Spring force
-         accel_spring=spring_coef*(T_min/T1)*(A_o/A1)
+         !accel_spring=spring_coef*(T_min/T1)*(A_o/A1) ! Old version dependent on area
+         accel_spring=spring_coef*(M_min/M1)*(R1+R2-r_dist)
          IA_x=IA_x+(accel_spring*(r_dist_x/r_dist))
          IA_y=IA_y+(accel_spring*(r_dist_y/r_dist))
-         !Working out the damping
 
+         !MP1
+         !print *, 'in the loop1', spring_coef, (M_min/M1), accel_spring,(R1+R2-r_dist) 
+         !print *, 'in the loop2', IA_x, IA_y, R1, R2,r_dist
          !Damping force:
          !Paralel velocity
           P_11=(r_dist_x*r_dist_x)/(r_dist**2)
           P_12=(r_dist_x*r_dist_y)/(r_dist**2)
           P_21=(r_dist_x*r_dist_y)/(r_dist**2)
           P_22=(r_dist_y*r_dist_y)/(r_dist**2)
-          p_ia_coef=radial_damping_coef*(T_min/T1)*(A_min/A1)
+          !p_ia_coef=radial_damping_coef*(T_min/T1)*(A_min/A1)
+          p_ia_coef=radial_damping_coef*(M_min/M1)
           p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2)) &
           + sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
           P_ia_11=P_ia_11+p_ia_coef*P_11
@@ -287,7 +336,8 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
 
           !Normal velocities
           P_11=1-P_11  ;  P_12=-P_12 ; P_22=1-P_22
-          p_ia_coef=tangental_damping_coef*(T_min/T1)*(A_min/A1)
+          !p_ia_coef=tangental_damping_coef*(T_min/T1)*(A_min/A1)
+          p_ia_coef=tangental_damping_coef*(M_min/M1)
           p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2))  &
           + sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
           P_ia_11=P_ia_11+p_ia_coef*P_11
@@ -303,85 +353,10 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
           !print *, 'P_22',P_22
         endif
       endif
-      other_berg=>other_berg%next
-    enddo ! loop over all bergs
-  enddo ; enddo
-
-  !Interactions due to iceberg bonds
-  if (iceberg_bonds_on) then ! MP1  
-    current_bond=>berg%first_bond
-    do while (associated(current_bond)) ! loop over all bonds
-      other_berg=>current_bond%other_berg
-      if (.not. associated(current_bond)) then
-        call error_mesg('diamonds,bond interactions', 'Trying to do Bond interactions with unassosiated bond!' ,FATAL)
-      else
-        L2=other_berg%length
-        W2=other_berg%width
-        T2=other_berg%thickness ! Note, that it is not dependent on thickness This means that it might go unstable for small icebergs
-        u2=other_berg%uvel_old
-        v2=other_berg%vvel_old 
-        A2=L2*W2
-        R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
-        lon2=other_berg%lon_old; lat2=other_berg%lat_old 
-        call rotpos_to_tang(lon2,lat2,x2,y2)
-
-        r_dist_x=x1-x2 ; r_dist_y=y1-y2
-        r_dist=sqrt( ((x1-x2)**2) + ((y1-y2)**2) )
-        T_min=min(T1,T2)
-        A_min = min((pi*R1**R1),(pi*R2*R2)) 
-       
-       !Spring force 
-        if ((r_dist>0.) .AND. (r_dist> (R1+R2)) ) then
-          mult_factor=((r_dist/(R1+R2))-1) 
-          accel_spring=bond_coef*mult_factor*(T_min/T1)*(A_min/A1)
-          IA_x=IA_x-(accel_spring*(r_dist_x/r_dist))  !Note: negative sign is an attractive force.
-          IA_y=IA_y-(accel_spring*(r_dist_y/r_dist))
-        endif  !Note, no damping on bond force has been added yet   
-
-       damping_factor=2.0
-       !Spring damping 
-        if ((r_dist>0.) .AND. (r_dist> (R1+R2)) .AND. (r_dist< (damping_factor*(R1+R2))) ) then 
-         !Paralel velocity
-          P_11=(r_dist_x*r_dist_x)/(r_dist**2)
-          P_12=(r_dist_x*r_dist_y)/(r_dist**2)
-          P_21=(r_dist_x*r_dist_y)/(r_dist**2)
-          P_22=(r_dist_y*r_dist_y)/(r_dist**2)
-          p_ia_coef=radial_damping_coef*(T_min/T1)*(A_min/A1)
-          p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2)) &
-          + sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
-          P_ia_11=P_ia_11+p_ia_coef*P_11
-          P_ia_12=P_ia_12+p_ia_coef*P_12
-          P_ia_21=P_ia_21+p_ia_coef*P_21
-          P_ia_22=P_ia_22+p_ia_coef*P_22
-          P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
-          P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
-
-          !Normal velocities
-          P_11=1-P_11  ;  P_12=-P_12 ; P_22=1-P_22
-          p_ia_coef=tangental_damping_coef*(T_min/T1)*(A_min/A1)
-          p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2))  &
-          + sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
-          P_ia_11=P_ia_11+p_ia_coef*P_11
-          P_ia_12=P_ia_12+p_ia_coef*P_12
-          P_ia_21=P_ia_21+p_ia_coef*P_21
-          P_ia_22=P_ia_22+p_ia_coef*P_22
-          P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
-          P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
-
-        endif 
-
-      endif
 
 
+      end subroutine calculate_force
 
-      current_bond=>current_bond%next_bond
-    enddo
-  endif
-
-!print *,'IA_x=',IA_x,'IA_y',IA_y
-!print *,'P_ia_11',P_ia_11,'P_ia_12',P_ia_12, 'P_ia_21',P_ia_21,'P_ia_22', P_ia_22
-!print *, 'P_ia_times_u_x', P_ia_times_u_x, 'P_ia_times_u_y', P_ia_times_u_y
-  contains
 
   subroutine overlap_area(R1,R2,d,A,trapped)
     real, intent(in) :: R1, R2, d
@@ -409,6 +384,9 @@ subroutine overlap_area(R1,R2,d,A,trapped)
 
    end subroutine overlap_area
 
+
+
+
 end subroutine interactive_force
 
 
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 22b9165..cb2a16b 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -298,8 +298,8 @@ subroutine ice_bergs_framework_init(bergs, &
 integer :: verbose_hrs=24 ! Period between verbose messages
 integer :: max_bonds=6 ! Maximum number of iceberg bond passed between processors
 real :: rho_bergs=850. ! Density of icebergs
-real :: spring_coef=1.e-4  ! Spring contant for iceberg interactions - Alon
-real :: bond_coef=1.e-4  ! Spring contant for iceberg bonds - Alon
+real :: spring_coef=1.e-8  ! Spring contant for iceberg interactions - Alon
+real :: bond_coef=1.e-8  ! Spring contant for iceberg bonds - Alon
 real :: radial_damping_coef=1.e-4     ! Coef for relative iceberg motion damping (radial component) -Alon
 real :: tangental_damping_coef=2.e-5     ! Coef for relative iceberg motion damping (tangental component) -Alon
 real :: LoW_ratio=1.5 ! Initial ratio L/W for newly calved icebergs
@@ -833,7 +833,7 @@ subroutine update_halo_icebergs(bergs)
 real :: current_halo_status
 logical :: force_app
 
-force_app =.false.
+force_app =.true.
 halo_width=bergs%grd%iceberg_halo  ! Must be less than current halo value used for updating weight.
 
  ! Get the stderr unit number
@@ -846,16 +846,18 @@ subroutine update_halo_icebergs(bergs)
 !do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
 !    this=>bergs%list(grdi,grdj)%first
 !    do while (associated(this))
-!      print *, 'A', this%iceberg_num, mpp_pe(), this%halo_berg, grdi, grdj
+!      write(stderrunit,*) 'A', this%iceberg_num, mpp_pe(), this%halo_berg, grdi, grdj
 !      this=>this%next
 !    enddo
 !enddo; enddo
+! Use when debugging:
+!call show_all_bonds(bergs)
 
 
 
 ! Step 1: Clear the current halos
 
-
+  call mpp_sync_self()
   do grdj = grd%jsd,grd%jsc-1 ;  do grdi = grd%isd,grd%ied
     call delete_all_bergs_in_list(bergs, grdj, grdi)
   enddo ; enddo
@@ -872,30 +874,26 @@ subroutine update_halo_icebergs(bergs)
     call delete_all_bergs_in_list(bergs,grdj,grdi)
   enddo ; enddo
 
+  call mpp_sync_self()
 !##############################
 
 !For debugging
 !do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
 !    this=>bergs%list(grdi,grdj)%first
 !      do while (associated(this))
-!      print *, 'B', this%iceberg_num, mpp_pe(), this%halo_berg, grdi, grdj
+!      write(stderrunit,*) 'B', this%iceberg_num, mpp_pe(), this%halo_berg, grdi, grdj
 !    this=>this%next
 !    enddo
 !enddo; enddo
 
+  if (debug) then
+    nbergs_start=count_bergs(bergs)
+  endif
 
 !#######################################################
 
-
 ! Step 2: Updating the halos  - This code is mostly copied from send_to_other_pes
 
-!  ! Get the stderr unit number
-!  stderrunit = stderr()
-!
-
-  if (debug) then
-    nbergs_start=count_bergs(bergs)
-  endif
 
   ! Find number of bergs that headed east/west
   nbergs_to_send_e=0
@@ -905,6 +903,7 @@ subroutine update_halo_icebergs(bergs)
   do grdj = grd%jsc,grd%jec ; do grdi = grd%iec-halo_width+1,grd%iec  
     this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
+    !write(stderrunit,*)  'sending east', this%iceberg_num, this%ine, this%jne, mpp_pe()
         kick_the_bucket=>this
         this=>this%next
         nbergs_to_send_e=nbergs_to_send_e+1
@@ -947,6 +946,7 @@ subroutine update_halo_icebergs(bergs)
     endif
   endif
 
+  call mpp_sync_self()
   ! Receive bergs from west
   if (grd%pe_W.ne.NULL_PE) then
     nbergs_rcvd_from_w=-999
@@ -984,7 +984,6 @@ subroutine update_halo_icebergs(bergs)
   endif
 
 
-
  ! Find number of bergs that headed north/south
   nbergs_to_send_n=0
   nbergs_to_send_s=0
@@ -1089,19 +1088,17 @@ subroutine update_halo_icebergs(bergs)
     nbergs_rcvd_from_n=0
   endif
 
-
-
   call mpp_sync_self()
 
 
 !For debugging
-!do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
-!    this=>bergs%list(grdi,grdj)%first
-!    do while (associated(this))
-!      print *, 'C', this%iceberg_num, mpp_pe(), this%halo_berg,  grdi, grdj
-!      this=>this%next
-!    enddo
-!enddo; enddo
+do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this))
+      write(stderrunit,*)  'C', this%iceberg_num, mpp_pe(), this%halo_berg,  grdi, grdj
+      this=>this%next
+    enddo
+enddo; enddo
 
 
 
@@ -1123,8 +1120,8 @@ subroutine delete_all_bergs_in_list(bergs,grdj,grdi)
     this=>this%next
     call destroy_iceberg(kick_the_bucket)
 !    call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
-    bergs%list(grdi,grdj)%first=>null()
   enddo
+  bergs%list(grdi,grdj)%first=>null()
 end  subroutine delete_all_bergs_in_list
 
 
@@ -1146,7 +1143,7 @@ subroutine send_bergs_to_other_pes(bergs)
 integer :: grdi, grdj
 logical :: force_app
 
-force_app=.false.
+force_app=.true.
 
   ! Get the stderr unit number
   stderrunit = stderr()
@@ -1463,14 +1460,19 @@ subroutine clear_berg_from_partners_bonds(berg)
   type(iceberg), intent(in), pointer :: berg
   type(iceberg), pointer :: other_berg
   type(bond), pointer :: current_bond, matching_bond
-  
+  integer ::  stderrunit
+  ! Get the stderr unit number
+  stderrunit = stderr()
+
     current_bond=>berg%first_bond
     do while (associated(current_bond)) !Looping over bonds
       other_berg=>current_bond%other_berg
       if (associated(other_berg)) then
+        !write(stderrunit,*) , 'Other berg', berg%iceberg_num, other_berg%iceberg_num, mpp_pe()
         matching_bond=>other_berg%first_bond
         do while (associated(matching_bond))  ! Looping over possible matching bonds in other_berg
           if (matching_bond%other_berg_num .eq. berg%iceberg_num) then
+            !write(stderrunit,*) , 'Clearing', berg%iceberg_num, matching_bond%other_berg_num,other_berg%iceberg_num, mpp_pe()
             matching_bond%other_berg=>null()
             matching_bond=>null()
           else
@@ -1622,7 +1624,7 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n,grd, force_append, max_bonds_
         other_berg_num=nint(buff%data(counter+(3*(k-1)+1),n))
         other_berg_ine=nint(buff%data(counter+(3*(k-1)+2),n))
         other_berg_jne=nint(buff%data(counter+(3*(k-1)+3),n))
-        if (other_berg_num .gt. 1) then
+        if (other_berg_num .gt. 0.5) then
           call form_a_bond(this, other_berg_num, other_berg_ine, other_berg_jne)
         endif
       enddo
@@ -2237,9 +2239,13 @@ subroutine form_a_bond(berg, other_berg_num, other_berg_ine, other_berg_jne, oth
 type(bond) , pointer :: new_bond, first_bond
 integer, intent(in) :: other_berg_num
 integer, optional  :: other_berg_ine, other_berg_jne
+integer :: stderrunit
+
+ stderrunit = stderr()
     
 if (berg%iceberg_num .ne. other_berg_num) then
-  !print *, 'Forming a bond!!!', mpp_pe(), berg%iceberg_num, other_berg_num, berg%halo_berg, berg%ine, berg%jne
+              
+ !write (stderrunit,*) , 'Forming a bond!!!', mpp_pe(), berg%iceberg_num, other_berg_num, berg%halo_berg, berg%ine, berg%jne
 
   ! Step 1: Create a new bond
   allocate(new_bond)
@@ -2403,6 +2409,7 @@ subroutine connect_all_bonds(bergs)
             enddo;enddo
           endif
           if (.not.bond_matched) then
+             print * , berg%iceberg_num, mpp_pe(), current_bond%other_berg_num, current_bond%other_berg_ine 
             if (berg%halo_berg .lt. 0.5) then
               missing_bond=.true.    
              print * , berg%iceberg_num, mpp_pe(), current_bond%other_berg_num, current_bond%other_berg_ine 
@@ -2968,7 +2975,7 @@ end subroutine  find_individual_iceberg
 
 ! ##############################################################################
 
-logical function find_cell(grd, x, y, oi, oj)
+logical function find_cell(grd, x, y, oi, oj) !MP1
 ! Arguments
 type(icebergs_gridded), intent(in) :: grd
 real, intent(in) :: x, y
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index e29006d..b231d41 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -114,15 +114,11 @@ subroutine write_restart(bergs)
 type(icebergs_gridded), pointer :: grd
 real, allocatable, dimension(:) :: lon,          &
                                    lat,          &
-                                   lon_old,      &
-                                   lat_old,      &
                                    uvel,         &
                                    vvel,         &
                                    mass,         &
                                    axn,          &
                                    ayn,          &
-                                   uvel_old,     &
-                                   vvel_old,     &
                                    bxn,          &
                                    byn,          &
                                    thickness,    &
@@ -149,7 +145,6 @@ subroutine write_restart(bergs)
                                       other_berg_ine
 
 
-!uvel_old, vvel_old, lon_old, lat_old, axn, ayn, bxn, byn added by Alon.
 integer :: grdi, grdj
   
 ! Get the stderr unit number
@@ -171,15 +166,11 @@ subroutine write_restart(bergs)
 
    allocate(lon(nbergs))
    allocate(lat(nbergs))
-   allocate(lon_old(nbergs))  !Alon
-   allocate(lat_old(nbergs))  !Alon
    allocate(uvel(nbergs))
    allocate(vvel(nbergs))
    allocate(mass(nbergs))
    allocate(axn(nbergs))    !Alon
    allocate(ayn(nbergs))    !Alon
-   allocate(uvel_old(nbergs)) !Alon
-   allocate(vvel_old(nbergs)) !Alon
    allocate(bxn(nbergs)) !Alon
    allocate(byn(nbergs)) !Alon
    allocate(thickness(nbergs))
@@ -212,15 +203,11 @@ subroutine write_restart(bergs)
   ! Define Variables
   id = register_restart_field(bergs_restart,filename,'lon',lon,longname='longitude',units='degrees_E')
   id = register_restart_field(bergs_restart,filename,'lat',lat,longname='latitude',units='degrees_N')
-  id = register_restart_field(bergs_restart,filename,'lon_old',lon_old,longname='longitude',units='degrees_E') !Alon
-  id = register_restart_field(bergs_restart,filename,'lat_old',lat_old,longname='latitude',units='degrees_N') !Alon
   id = register_restart_field(bergs_restart,filename,'uvel',uvel,longname='zonal velocity',units='m/s')
   id = register_restart_field(bergs_restart,filename,'vvel',vvel,longname='meridional velocity',units='m/s')
   id = register_restart_field(bergs_restart,filename,'mass',mass,longname='mass',units='kg')
   id = register_restart_field(bergs_restart,filename,'axn',axn,longname='explicit zonal acceleration',units='m/s^2') !Alon
   id = register_restart_field(bergs_restart,filename,'ayn',ayn,longname='explicit meridional acceleration',units='m/s^2') !Alon
-  id = register_restart_field(bergs_restart,filename,'uvel_old',uvel_old,longname='old explicit zonal acceleration',units='m/s^2') !Alon
-  id = register_restart_field(bergs_restart,filename,'vvel_old',vvel_old,longname='old explicit meridional acceleration',units='m/s^2') !Alon
   id = register_restart_field(bergs_restart,filename,'bxn',bxn,longname='inplicit zonal acceleration',units='m/s^2') !Alon
   id = register_restart_field(bergs_restart,filename,'byn',byn,longname='implicit meridional acceleration',units='m/s^2') !Alon
   id = register_restart_field(bergs_restart,filename,'ine',ine,longname='i index',units='none')
@@ -258,12 +245,10 @@ subroutine write_restart(bergs)
     do while(associated(this))
       i = i + 1
       lon(i) = this%lon; lat(i) = this%lat
-      lon_old(i) = this%lon_old; lat_old(i) = this%lat_old  !Alon
       uvel(i) = this%uvel; vvel(i) = this%vvel
       ine(i) = this%ine; jne(i) = this%jne
       mass(i) = this%mass; thickness(i) = this%thickness
       axn(i) = this%axn; ayn(i) = this%ayn !Added by Alon
-      uvel_old(i) = this%uvel_old; vvel_old(i) = this%vvel_old !Added by Alon
       bxn(i) = this%bxn; byn(i) = this%byn !Added by Alon
       width(i) = this%width; length(i) = this%length
       start_lon(i) = this%start_lon; start_lat(i) = this%start_lat
@@ -283,15 +268,11 @@ subroutine write_restart(bergs)
   deallocate(              &
              lon,          &
              lat,          &
-             lon_old,      &
-             lat_old,      &
              uvel,         &
              vvel,         &
              mass,         &
              axn,          &
              ayn,          &
-             uvel_old,     &
-             vvel_old,     &
              bxn,          &
              byn,          &
              thickness,    &
@@ -305,7 +286,6 @@ subroutine write_restart(bergs)
              mass_of_bits, &
              halo_berg,    &
              heat_density )
-!axn, ayn, uvel_old, vvel_old, lat_old, lon_old, bxn, byn above added by Alon
 
   deallocate(           &
              ine,       &
@@ -423,7 +403,7 @@ subroutine read_restart_bergs_orig(bergs,Time)
 integer, dimension(:), allocatable :: found_restart_int
 integer :: k, ierr, ncid, dimid, nbergs_in_file
 integer :: lonid, latid,  uvelid, vvelid, ineid, jneid
-integer :: axnid, aynid, uvel_oldid, vvel_oldid, bxnid, bynid, lon_oldid, lat_oldid !Added by Alon
+integer :: axnid, aynid, uvel_oldid, vvel_oldid, bxnid, bynid
 integer :: massid, thicknessid, widthid, lengthid
 integer :: start_lonid, start_latid, start_yearid, iceberg_numid, start_dayid, start_massid
 integer :: scaling_id, mass_of_bits_id, heat_density_id, halo_bergid
@@ -483,15 +463,11 @@ subroutine read_restart_bergs_orig(bergs,Time)
 
   lonid=inq_var(ncid, 'lon')
   latid=inq_var(ncid, 'lat')
-  lon_oldid=inq_var(ncid, 'lon_old') !Alon
-  lat_oldid=inq_var(ncid, 'lat_old') !Alon
   uvelid=inq_var(ncid, 'uvel')
   vvelid=inq_var(ncid, 'vvel')
   massid=inq_var(ncid, 'mass')
   axnid=inq_var(ncid, 'axn') !Alon
   aynid=inq_var(ncid, 'ayn') !Alon
-  uvel_oldid=inq_var(ncid, 'uvel_old') !Alon
-  vvel_oldid=inq_var(ncid, 'vvel_old') !Alon
   bxnid=inq_var(ncid, 'bxn') !Alon
   bynid=inq_var(ncid, 'byn') !Alon
   thicknessid=inq_var(ncid, 'thickness')
@@ -547,10 +523,6 @@ subroutine read_restart_bergs_orig(bergs,Time)
       localberg%mass=get_double(ncid, massid, k)
       localberg%axn=get_double(ncid, axnid, k) !Alon
       localberg%ayn=get_double(ncid, aynid, k) !Alon
-      localberg%uvel_old=get_double(ncid, uvel_oldid, k) !Alon
-      localberg%vvel_old=get_double(ncid, vvel_oldid, k) !Alon
-      localberg%lon_old=get_double(ncid, lon_oldid, k) !Alon
-      localberg%lat_old=get_double(ncid, lat_oldid, k) !Alon
       localberg%bxn=get_double(ncid, bxnid, k) !Alon
       localberg%byn=get_double(ncid, bynid, k) !Alon
       localberg%thickness=get_double(ncid, thicknessid, k)
@@ -731,15 +703,11 @@ subroutine read_restart_bergs(bergs,Time)
 
 real, allocatable, dimension(:) :: lon,          &
                                    lat,          &
-                                   lon_old,      &
-                                   lat_old,      &
                                    uvel,         &
                                    vvel,         &
                                    mass,         &
                                    axn,          &
                                    ayn,          &
-                                   uvel_old,     &
-                                   vvel_old,     &
                                    bxn,          &
                                    byn,          &
                                    thickness,    &
@@ -753,7 +721,6 @@ subroutine read_restart_bergs(bergs,Time)
                                    mass_of_bits, &
                                    halo_berg,    &
                                    heat_density
-!axn, ayn, uvel_old, vvel_old, lon_old, lat_old, bxn, byn added by Alon
 integer, allocatable, dimension(:) :: ine,       &
                                       jne,       &
                                       iceberg_num,       &
@@ -782,15 +749,11 @@ subroutine read_restart_bergs(bergs,Time)
   if(nbergs_in_file > 0) then
      allocate(lon(nbergs_in_file))
      allocate(lat(nbergs_in_file))
-     allocate(lon_old(nbergs_in_file)) !Alon
-     allocate(lat_old(nbergs_in_file)) !Alon
      allocate(uvel(nbergs_in_file))
      allocate(vvel(nbergs_in_file))
      allocate(mass(nbergs_in_file))
      allocate(axn(nbergs_in_file)) !Alon
      allocate(ayn(nbergs_in_file)) !Alon
-     allocate(uvel_old(nbergs_in_file)) !Alon
-     allocate(vvel_old(nbergs_in_file)) !Alon
      allocate(bxn(nbergs_in_file)) !Alon
      allocate(byn(nbergs_in_file)) !Alon
      allocate(thickness(nbergs_in_file))
@@ -812,15 +775,11 @@ subroutine read_restart_bergs(bergs,Time)
 
      call read_unlimited_axis(filename,'lon',lon,domain=grd%domain)
      call read_unlimited_axis(filename,'lat',lat,domain=grd%domain)
-     call read_unlimited_axis(filename,'lon_old',lon_old,domain=grd%domain) !Alon
-     call read_unlimited_axis(filename,'lat_old',lat_old,domain=grd%domain) !Alon
      call read_unlimited_axis(filename,'uvel',uvel,domain=grd%domain)
      call read_unlimited_axis(filename,'vvel',vvel,domain=grd%domain)
      call read_unlimited_axis(filename,'mass',mass,domain=grd%domain)
      call read_unlimited_axis(filename,'axn',axn,domain=grd%domain) !Alon
      call read_unlimited_axis(filename,'ayn',ayn,domain=grd%domain) !Alon
-     call read_unlimited_axis(filename,'uvel_old',uvel_old,domain=grd%domain) !Alon
-     call read_unlimited_axis(filename,'vvel_old',vvel_old,domain=grd%domain) !Alon
      call read_unlimited_axis(filename,'bxn',bxn,domain=grd%domain) !Alon
      call read_unlimited_axis(filename,'byn',byn,domain=grd%domain) !Alon
      call read_unlimited_axis(filename,'thickness',thickness,domain=grd%domain)
@@ -885,10 +844,10 @@ subroutine read_restart_bergs(bergs,Time)
          localberg%mass=mass(k)
          localberg%axn=axn(k) !Alon
          localberg%ayn=ayn(k) !Alon
-         localberg%uvel_old=uvel_old(k) !Alon
-         localberg%vvel_old=vvel_old(k) !Alon
-         localberg%lon_old=lon_old(k) !Alon
-         localberg%lat_old=lat_old(k) !Alon
+         localberg%uvel_old=uvel(k) !Alon
+         localberg%vvel_old=vvel(k) !Alon
+         localberg%lon_old=lon(k) !Alon
+         localberg%lat_old=lat(k) !Alon
          localberg%bxn=bxn(k) !Alon
          localberg%byn=byn(k) !Alon
          localberg%thickness=thickness(k)
@@ -916,15 +875,11 @@ subroutine read_restart_bergs(bergs,Time)
      deallocate(              &
                 lon,          &
                 lat,          &
-                lon_old,      &
-                lat_old,      &
                 uvel,         &
                 vvel,         &
                 mass,         &
                 axn,          &
                 ayn,          &
-                uvel_old,     &
-                vvel_old,     &
                 bxn,          &
                 byn,          &
                 thickness,    &
@@ -938,7 +893,6 @@ subroutine read_restart_bergs(bergs,Time)
                 mass_of_bits, &
                 halo_berg,    &
                 heat_density )
-!axn, ayn, uvel_old, vvel_old, lat_old, lon_old, bxn, byn above added by Alon.
      deallocate(           &
                 ine,       &
                 jne,       &
@@ -1335,7 +1289,6 @@ subroutine write_trajectory(trajectory, save_short_traj)
 ! Local variables
 integer :: iret, ncid, i_dim, i
 integer :: lonid, latid, yearid, dayid, uvelid, vvelid, iceberg_numid
-!integer :: axnid, aynid, uvel_oldid, vvel_oldid, lat_oldid, lon_oldid, bxnid, bynid !Added by Alon 
 integer :: uoid, void, uiid, viid, uaid, vaid, sshxid, sshyid, sstid
 integer :: cnid, hiid
 integer :: mid, did, wid, lid, mbid, hdid

From a6c47baaeaa4d10c6d0e48b4b87e8a01e794bb75 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 14 Oct 2015 15:37:45 -0400
Subject: [PATCH 086/361] Two more bugs fixed in the never ending stream of
 bugs related to iceberg interactions:

1) A segmentation fault was removed by editing the subroutine connect_all_bonds. Here we had to  tell bergs in halos not to search for bonded bergs on other processors

2) A bug was fixed inside the interactive_forces subroutine. Icebergs were interacting with one another more than once per time step. This was fixed by specifically asking whether we are considering a bonded or unbonded interaction.

There are still more details to be worked out with the tabular icebergs. They not working yet for very large icebergs, but appear to work for icebergs made up of 4 smaller icebergs.
---
 icebergs.F90           | 10 +++--
 icebergs_framework.F90 | 92 +++++++++++++++++++++++++-----------------
 2 files changed, 62 insertions(+), 40 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 10eb565..2305a33 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -306,7 +306,7 @@ subroutine calculate_force(bergs,berg,other_berg,IA_x, IA_y, u0, v0, u1, v1, P_i
        !A_min = min((pi*R1**R1),(pi*R2*R2)) 
        M_min=min(M1,M2)
        !Calculating spring force  (later this should only be done on the first time around)
-       if ((r_dist>0.) .AND. ((r_dist< (R1+R2)) .OR. ( (r_dist> (R1+R2)) .AND. (bonded) ) )) then
+       if ((r_dist>0.) .AND. ((r_dist< (R1+R2).AND. (.not. bonded)) .OR. ( (r_dist> (R1+R2)) .AND. (bonded) ) )) then
          !Spring force
          !accel_spring=spring_coef*(T_min/T1)*(A_o/A1) ! Old version dependent on area
          accel_spring=spring_coef*(M_min/M1)*(R1+R2-r_dist)
@@ -314,8 +314,9 @@ subroutine calculate_force(bergs,berg,other_berg,IA_x, IA_y, u0, v0, u1, v1, P_i
          IA_y=IA_y+(accel_spring*(r_dist_y/r_dist))
 
          !MP1
+         !print *, 'in the loop1', berg%iceberg_num, other_berg%iceberg_num,r_dist, bonded
          !print *, 'in the loop1', spring_coef, (M_min/M1), accel_spring,(R1+R2-r_dist) 
-         !print *, 'in the loop2', IA_x, IA_y, R1, R2,r_dist
+         !print *, 'in the loop2', IA_x, IA_y, R1, R2,r_dist, berg%iceberg_num,other_berg%iceberg_num
          !Damping force:
          !Paralel velocity
           P_11=(r_dist_x*r_dist_x)/(r_dist**2)
@@ -591,6 +592,8 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
          RHS_x=RHS_x - (((P_ia_11*uvel)+(P_ia_12*vvel))-P_ia_times_u_x)
          RHS_y=RHS_y - (((P_ia_21*uvel)+(P_ia_22*vvel))-P_ia_times_u_y)       
     endif
+    !print *,'Before calculation:', berg%iceberg_num, IA_x, IA_y, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y
+    !print *,'Before calculation:', berg%iceberg_num, itloop, IA_x, IA_y
 endif
 
 
@@ -2048,6 +2051,8 @@ subroutine evolve_icebergs(bergs)
         uvel1=berg%uvel; vvel1=berg%vvel
         if (on_tangential_plane) call rotvec_to_tang(lon1,uvel1,vvel1,xdot1,ydot1)
         u1=uvel1*dxdl1; v1=vvel1*dydl
+
+
         call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn) !axn,ayn, bxn, byn  - Added by Alon
         !call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn1, ayn1, bxn, byn) !Note change to dt. Markpoint_1
         if (on_tangential_plane) call rotvec_to_tang(lon1,ax1,ay1,xddot1,yddot1)
@@ -2361,7 +2366,6 @@ subroutine evolve_icebergs(bergs)
   
         ! Adjusting mass...                      Alon decided to move this before calculating the new velocities (so that acceleration can be a fn(r_np1)
         i=i1;j=j1;xi=berg%xi;yj=berg%yj
-        !print *, 'Alon: look here!', lonn, latn, uvel3, vvel3, i, j, xi, yj
         call adjust_index_and_ground(grd, lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
         !call adjust_index_and_ground(grd, lonn, latn, uvel1, vvel1, i, j, xi, yj, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
 
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index cb2a16b..5200b3f 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -208,6 +208,7 @@ module ice_bergs_framework
   logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
   logical :: time_average_weight=.false. ! Time average the weight on the ocean
   logical :: Runge_not_Verlet=.True.  !True=Runge Kuttai, False=Verlet.  - Added by Alon 
+  logical :: halo_debugging=.False.  !Use for debugging halos (remove when its working) 
   logical :: save_short_traj=.True.  !True saves only lon,lat,time,iceberg_num in iceberg_trajectory.nc 
   logical :: iceberg_bonds_on=.False.  !True=Allow icebergs to have bonds, False=don't allow. 
   logical :: manually_initialize_bonds=.False.  !True= Bonds are initialize manually. 
@@ -298,8 +299,8 @@ subroutine ice_bergs_framework_init(bergs, &
 integer :: verbose_hrs=24 ! Period between verbose messages
 integer :: max_bonds=6 ! Maximum number of iceberg bond passed between processors
 real :: rho_bergs=850. ! Density of icebergs
-real :: spring_coef=1.e-8  ! Spring contant for iceberg interactions - Alon
-real :: bond_coef=1.e-8  ! Spring contant for iceberg bonds - Alon
+real :: spring_coef=3.e-9  ! Spring contant for iceberg interactions (this seems to be the highest stable value)
+real :: bond_coef=3.e-9  ! Spring contant for iceberg bonds - not being used right now
 real :: radial_damping_coef=1.e-4     ! Coef for relative iceberg motion damping (radial component) -Alon
 real :: tangental_damping_coef=2.e-5     ! Coef for relative iceberg motion damping (tangental component) -Alon
 real :: LoW_ratio=1.5 ! Initial ratio L/W for newly calved icebergs
@@ -312,6 +313,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: speed_limit=0. ! CFL speed limit for a berg
 real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
 logical :: Runge_not_Verlet=.True.  !True=Runge Kutta, False=Verlet.  - Added by Alon 
+logical :: halo_debugging=.False.  !Use for debugging halos (remove when its working) 
 logical :: save_short_traj=.True.  !True saves only lon,lat,time,iceberg_num in iceberg_trajectory.nc 
 logical :: iceberg_bonds_on=.False.  !True=Allow icebergs to have bonds, False=don't allow. 
 logical :: manually_initialize_bonds=.False.  !True= Bonds are initialize manually. 
@@ -327,7 +329,7 @@ subroutine ice_bergs_framework_init(bergs, &
 namelist /icebergs_nml/ verbose, budget, halo, iceberg_halo, traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj, &
          distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,bond_coef, radial_damping_coef, tangental_damping_coef, &
          rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, iceberg_bonds_on, manually_initialize_bonds, &
-         parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, &
+         parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, halo_debugging, &
          time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, interactive_icebergs_on, critical_interaction_damping_on, &
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution, force_all_pes_traj
 
@@ -609,6 +611,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%time_average_weight=time_average_weight
   bergs%speed_limit=speed_limit
   bergs%Runge_not_Verlet=Runge_not_Verlet   !Alon
+  bergs%halo_debugging=halo_debugging
   bergs%iceberg_bonds_on=iceberg_bonds_on   !Alon
   bergs%manually_initialize_bonds=manually_initialize_bonds   !Alon
   bergs%critical_interaction_damping_on=critical_interaction_damping_on   !Alon
@@ -832,9 +835,11 @@ subroutine update_halo_icebergs(bergs)
 integer :: temp1, temp2
 real :: current_halo_status
 logical :: force_app
+logical :: halo_debugging
 
 force_app =.true.
 halo_width=bergs%grd%iceberg_halo  ! Must be less than current halo value used for updating weight.
+halo_debugging=bergs%halo_debugging  ! Must be less than current halo value used for updating weight.
 
  ! Get the stderr unit number
    stderrunit = stderr()
@@ -842,16 +847,20 @@ subroutine update_halo_icebergs(bergs)
  ! For convenience
    grd=>bergs%grd
 
+
+
 !For debugging
-!do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
-!    this=>bergs%list(grdi,grdj)%first
-!    do while (associated(this))
-!      write(stderrunit,*) 'A', this%iceberg_num, mpp_pe(), this%halo_berg, grdi, grdj
-!      this=>this%next
-!    enddo
-!enddo; enddo
-! Use when debugging:
-!call show_all_bonds(bergs)
+if (halo_debugging) then
+  do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this))
+      write(stderrunit,*) 'A', this%iceberg_num, mpp_pe(), this%halo_berg, grdi, grdj
+      this=>this%next
+    enddo
+  enddo; enddo
+  ! Use when debugging:
+  call show_all_bonds(bergs)
+endif
 
 
 
@@ -878,14 +887,15 @@ subroutine update_halo_icebergs(bergs)
 !##############################
 
 !For debugging
-!do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
-!    this=>bergs%list(grdi,grdj)%first
-!      do while (associated(this))
-!      write(stderrunit,*) 'B', this%iceberg_num, mpp_pe(), this%halo_berg, grdi, grdj
-!    this=>this%next
-!    enddo
-!enddo; enddo
-
+if (halo_debugging) then
+  do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
+    this=>bergs%list(grdi,grdj)%first
+      do while (associated(this))
+      write(stderrunit,*) 'B', this%iceberg_num, mpp_pe(), this%halo_berg, grdi, grdj
+    this=>this%next
+    enddo
+  enddo; enddo
+endif
   if (debug) then
     nbergs_start=count_bergs(bergs)
   endif
@@ -1092,14 +1102,15 @@ subroutine update_halo_icebergs(bergs)
 
 
 !For debugging
-do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
+if (halo_debugging) then
+  do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
     this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
       write(stderrunit,*)  'C', this%iceberg_num, mpp_pe(), this%halo_berg,  grdi, grdj
       this=>this%next
     enddo
-enddo; enddo
-
+  enddo; enddo
+endif
 
 
 
@@ -2377,16 +2388,18 @@ subroutine connect_all_bonds(bergs)
         if (.not.associated(current_bond%other_berg)) then
           bond_matched=.false.
           i = current_bond%other_berg_ine ; j = current_bond%other_berg_jne
-          other_berg=>bergs%list(i,j)%first
-          do while (associated(other_berg)) ! loop over all other bergs
-            if (other_berg%iceberg_num == current_bond%other_berg_num) then
-              current_bond%other_berg=>other_berg
-              other_berg=>null()
-              bond_matched=.true. 
-            else
-              other_berg=>other_berg%next
-            endif 
-          enddo
+          if ( (i.gt. grd%isd-1) .and. (i .lt. grd%ied+1) .and. (j .gt. grd%jsd-1) .and. (j .lt. grd%jed+1)) then
+            other_berg=>bergs%list(i,j)%first
+            do while (associated(other_berg)) ! loop over all other bergs
+              if (other_berg%iceberg_num == current_bond%other_berg_num) then
+                current_bond%other_berg=>other_berg
+                other_berg=>null()
+                bond_matched=.true. 
+              else
+                other_berg=>other_berg%next
+              endif 
+            enddo
+          endif
           if (.not.bond_matched) then
             ! If you are stil not matched, then search adjacent cells
             do grdj_inner = j-1,j+1 ; do grdi_inner = i-1,i+1
@@ -2408,12 +2421,17 @@ subroutine connect_all_bonds(bergs)
               endif
             enddo;enddo
           endif
-          if (.not.bond_matched) then
-             print * , berg%iceberg_num, mpp_pe(), current_bond%other_berg_num, current_bond%other_berg_ine 
+          if (.not.bond_matched) then      
             if (berg%halo_berg .lt. 0.5) then
               missing_bond=.true.    
-             print * , berg%iceberg_num, mpp_pe(), current_bond%other_berg_num, current_bond%other_berg_ine 
+              print * ,'non-halo berg unmatched: ', berg%iceberg_num, mpp_pe(), current_bond%other_berg_num, current_bond%other_berg_ine 
               call error_mesg('diamonds, connect_all_bonds', 'A non-halo bond is missing!!!', FATAL)
+            else  ! This is not a problem if the partner berg is not yet in the halo
+              if (  (current_bond%other_berg_ine .gt.grd%isd-1) .and. (current_bond%other_berg_ine .lt.grd%ied+1) &
+                .and.  (current_bond%other_berg_jne .gt.grd%jsd-1) .and. (current_bond%other_berg_jne .lt.grd%jed+1) ) then      
+                print * ,'halo berg unmatched: ',mpp_pe(),  berg%iceberg_num, current_bond%other_berg_num, current_bond%other_berg_ine,current_bond%other_berg_jne 
+                call error_mesg('diamonds, connect_all_bonds', 'A halo bond is missing!!!', WARNING)
+              endif
             endif
           endif
         endif
@@ -2516,7 +2534,7 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
 
     bergs%nbonds=number_of_bonds_all_pe !Total number of bonds across all pe's
     if (number_of_bonds .gt. 0) then
-      print *, "Bonds on PE:",number_of_bonds, "Total bonds", number_of_bonds_all_PE, "on PE number:",  mpp_pe()
+      write(stderrunit,*) "Bonds on PE:",number_of_bonds, "Total bonds", number_of_bonds_all_PE, "on PE number:",  mpp_pe()
     endif
 
     if (quality_check) then

From 73f4e76244495af407285b63399b8f85015d3bd4 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Thu, 15 Oct 2015 17:19:57 -0400
Subject: [PATCH 087/361] Two bugs in the iceberg interactions fixed:

1) Damping coefitients must be multiplied by dt before entering the matrix A (which solves for the updated acceleration.

2) P_21 was not being correctly undated when applying the damping to perpendicular motion. This has been corrected.

Also, the perpendicular damping is set to 4 times less than the parralel. This is just a guess for now, and needs to be investigated further.

Also, a flag has been added whihc allows the user to use icebergs which only feel interaction forces, and do not feel the environment.

Fixing these two bugs allows the model to run with more than 4 bonded icebergs. More testing is needed to see if this is sufficiently robust
---
 icebergs.F90           | 120 ++++++++++++++++++++++++-----------------
 icebergs_framework.F90 |   7 ++-
 2 files changed, 77 insertions(+), 50 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 2305a33..6907b4c 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -262,7 +262,7 @@ subroutine calculate_force(bergs,berg,other_berg,IA_x, IA_y, u0, v0, u1, v1, P_i
       !Using critical values for damping rather than manually setting the damping.
       if (critical_interaction_damping_on) then
         radial_damping_coef=2.*sqrt(spring_coef)  ! Critical damping  
-        tangental_damping_coef=(2.*sqrt(spring_coef))  ! Critical damping   (just a guess)
+        tangental_damping_coef=(2.*sqrt(spring_coef))/4  ! Critical damping   (just a guess)
       endif
 
       if (berg%iceberg_num .ne. other_berg%iceberg_num) then
@@ -312,46 +312,50 @@ subroutine calculate_force(bergs,berg,other_berg,IA_x, IA_y, u0, v0, u1, v1, P_i
          accel_spring=spring_coef*(M_min/M1)*(R1+R2-r_dist)
          IA_x=IA_x+(accel_spring*(r_dist_x/r_dist))
          IA_y=IA_y+(accel_spring*(r_dist_y/r_dist))
+         
 
-         !MP1
-         !print *, 'in the loop1', berg%iceberg_num, other_berg%iceberg_num,r_dist, bonded
-         !print *, 'in the loop1', spring_coef, (M_min/M1), accel_spring,(R1+R2-r_dist) 
-         !print *, 'in the loop2', IA_x, IA_y, R1, R2,r_dist, berg%iceberg_num,other_berg%iceberg_num
-         !Damping force:
-         !Paralel velocity
-          P_11=(r_dist_x*r_dist_x)/(r_dist**2)
-          P_12=(r_dist_x*r_dist_y)/(r_dist**2)
-          P_21=(r_dist_x*r_dist_y)/(r_dist**2)
-          P_22=(r_dist_y*r_dist_y)/(r_dist**2)
-          !p_ia_coef=radial_damping_coef*(T_min/T1)*(A_min/A1)
-          p_ia_coef=radial_damping_coef*(M_min/M1)
-          p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2)) &
-          + sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
-          P_ia_11=P_ia_11+p_ia_coef*P_11
-          P_ia_12=P_ia_12+p_ia_coef*P_12
-          P_ia_21=P_ia_21+p_ia_coef*P_21
-          P_ia_22=P_ia_22+p_ia_coef*P_22
-          P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
-          P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
-
-
-          !Normal velocities
-          P_11=1-P_11  ;  P_12=-P_12 ; P_22=1-P_22
-          !p_ia_coef=tangental_damping_coef*(T_min/T1)*(A_min/A1)
-          p_ia_coef=tangental_damping_coef*(M_min/M1)
-          p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2))  &
-          + sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
-          P_ia_11=P_ia_11+p_ia_coef*P_11
-          P_ia_12=P_ia_12+p_ia_coef*P_12
-          P_ia_21=P_ia_21+p_ia_coef*P_21
-          P_ia_22=P_ia_22+p_ia_coef*P_22
-          P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
-          P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
-
-          !print *, 'P_11',P_11
-          !print *, 'P_21',P_21
-          !print *, 'P_12',P_12
-          !print *, 'P_22',P_22
+        if (r_dist < 5*(R1+R2)) then
+          !MP1
+          !print *, 'in the loop1', berg%iceberg_num, other_berg%iceberg_num,r_dist, bonded, IA_x, IA_y
+          !print *, 'in the loop1', spring_coef, (M_min/M1), accel_spring,(R1+R2-r_dist) 
+          !print *, 'in the loop2', IA_x, IA_y, R1, R2,r_dist, berg%iceberg_num,other_berg%iceberg_num
+          !Damping force:
+          !Paralel velocity
+           P_11=(r_dist_x*r_dist_x)/(r_dist**2)
+           P_12=(r_dist_x*r_dist_y)/(r_dist**2)
+           P_21=(r_dist_x*r_dist_y)/(r_dist**2)
+           P_22=(r_dist_y*r_dist_y)/(r_dist**2)
+           !p_ia_coef=radial_damping_coef*(T_min/T1)*(A_min/A1)
+           p_ia_coef=radial_damping_coef*(M_min/M1)
+           p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2)) &
+           + sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
+          
+           P_ia_11=P_ia_11+p_ia_coef*P_11
+           P_ia_12=P_ia_12+p_ia_coef*P_12
+           P_ia_21=P_ia_21+p_ia_coef*P_21
+           P_ia_22=P_ia_22+p_ia_coef*P_22
+           P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
+           P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
+           !print *, 'Paralel: ',berg%iceberg_num,  p_ia_coef, IA_x, P_ia_11, P_ia_21,P_ia_12, P_ia_22
+
+           !Normal velocities
+           P_11=1-P_11  ;  P_12=-P_12 ; P_21= -P_21 ;    P_22=1-P_22
+           !p_ia_coef=tangental_damping_coef*(T_min/T1)*(A_min/A1)
+           p_ia_coef=tangental_damping_coef*(M_min/M1)
+           p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2))  &
+           + sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
+           P_ia_11=P_ia_11+p_ia_coef*P_11
+           P_ia_12=P_ia_12+p_ia_coef*P_12
+           P_ia_21=P_ia_21+p_ia_coef*P_21
+           P_ia_22=P_ia_22+p_ia_coef*P_22
+           P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
+           P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
+           !print *, 'Perp: ',berg%iceberg_num,  p_ia_coef, IA_x, P_ia_11, P_ia_21,P_ia_12, P_ia_22
+           !print *, 'P_11',P_11
+           !print *, 'P_21',P_21
+           !print *, 'P_12',P_12
+           !print *, 'P_22',P_22
+          endif
         endif
       endif
 
@@ -521,7 +525,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 
 ! Interactive spring acceleration - (Does the spring part need to be called twice?)
 if (interactive_icebergs_on) then
-           call Interactive_force(bergs, berg, IA_x, IA_y, uvel0, vvel0, uvel0, vvel0, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y) ! Spring forces, Made by Alon.
+           call interactive_force(bergs, berg, IA_x, IA_y, uvel0, vvel0, uvel0, vvel0, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y) ! Spring forces, Made by Alon.
            if (.not.Runge_not_Verlet) then
                axn=axn + IA_x
                ayn=ayn + IA_y
@@ -583,7 +587,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 
 if (interactive_icebergs_on) then
    if (itloop>1) then
-        call Interactive_force(bergs, berg, IA_x, IA_y, us, vs, uvel0, vvel0, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y) ! Spring forces, Made by Alon.
+        call interactive_force(bergs, berg, IA_x, IA_y, uvel0, vvel0, us,vs, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y) ! Spring forces, Made by Alon.
     endif
      if (beta>0.) then ! If implicit, use u_star, v_star rather than RK4 latest
          RHS_x=RHS_x -(((P_ia_11*u_star)+(P_ia_12*v_star))-P_ia_times_u_x) 
@@ -593,7 +597,6 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
          RHS_y=RHS_y - (((P_ia_21*uvel)+(P_ia_22*vvel))-P_ia_times_u_y)       
     endif
     !print *,'Before calculation:', berg%iceberg_num, IA_x, IA_y, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y
-    !print *,'Before calculation:', berg%iceberg_num, itloop, IA_x, IA_y
 endif
 
 
@@ -612,12 +615,25 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
       endif
 
       if (interactive_icebergs_on) then
-            A11=A11+P_ia_11
-            A12=A12+P_ia_12
-            A21=A21+P_ia_21
-            A22=A22+P_ia_22
+            A11=A11+(dt*P_ia_11)
+            A12=A12+(dt*P_ia_12)
+            A21=A21+(dt*P_ia_21)
+            A22=A22+(dt*P_ia_22)
      endif
 
+     !This is for testing the code using only interactive forces
+     if (bergs%only_interactive_forces) then
+       RHS_x=(IA_x/2) -(((P_ia_11*u_star)+(P_ia_12*v_star))-P_ia_times_u_x) 
+       RHS_y=(IA_y/2) -(((P_ia_21*u_star)+(P_ia_22*v_star))-P_ia_times_u_y) 
+       A11=1+(dt*P_ia_11)
+       A12=(dt*P_ia_12)
+       A21=(dt*P_ia_21)
+       A22=1+(dt*P_ia_22)
+      !print *,'Other', berg%iceberg_num, P_ia_12,u_star, P_ia_times_u_x, P_ia_11, dt
+     endif
+
+
+
       detA=1./((A11*A22)-(A12*A21))
       ax=detA*(A22*RHS_x-A12*RHS_y)
       ay=detA*(A11*RHS_y-A21*RHS_x)
@@ -633,8 +649,8 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
       uveln=u_star+dt*ax        ! Alon
       vveln=v_star+dt*ay        ! Alon
 
+      !print *,'IN loop', berg%iceberg_num, RHS_x,  A11, A12, A21, A22, ax, itloop, uveln
   enddo ! itloop
- 
 
 !Saving the totally explicit part of the acceleration to use in finding the next position and u_star -Alon
     axn=0.
@@ -651,9 +667,17 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
       axn=axn+f_cori*vveln
       ayn=ayn-f_cori*uveln
     endif
+
+     !This is for testing the code using only interactive forces
+     if (bergs%only_interactive_forces) then
+       axn=IA_x/2
+       ayn=IA_y/2
+     endif
+
     bxn= ax-(axn/2) !Alon
     byn= ay-(ayn/2) !Alon
 
+    !print *,'After1', berg%iceberg_num, axn, bxn, uveln
  
   ! Limit speed of bergs based on a CFL criteria
   if (bergs%speed_limit>0.) then
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 5200b3f..6c04300 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -208,6 +208,7 @@ module ice_bergs_framework
   logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
   logical :: time_average_weight=.false. ! Time average the weight on the ocean
   logical :: Runge_not_Verlet=.True.  !True=Runge Kuttai, False=Verlet.  - Added by Alon 
+  logical :: only_interactive_forces=.False.  !Icebergs only feel interactive forces, and not ocean, wind... 
   logical :: halo_debugging=.False.  !Use for debugging halos (remove when its working) 
   logical :: save_short_traj=.True.  !True saves only lon,lat,time,iceberg_num in iceberg_trajectory.nc 
   logical :: iceberg_bonds_on=.False.  !True=Allow icebergs to have bonds, False=don't allow. 
@@ -313,6 +314,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: speed_limit=0. ! CFL speed limit for a berg
 real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
 logical :: Runge_not_Verlet=.True.  !True=Runge Kutta, False=Verlet.  - Added by Alon 
+logical :: only_interactive_forces=.False.  !Icebergs only feel interactive forces, and not ocean, wind... 
 logical :: halo_debugging=.False.  !Use for debugging halos (remove when its working) 
 logical :: save_short_traj=.True.  !True saves only lon,lat,time,iceberg_num in iceberg_trajectory.nc 
 logical :: iceberg_bonds_on=.False.  !True=Allow icebergs to have bonds, False=don't allow. 
@@ -327,7 +329,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real, dimension(nclasses) :: mass_scaling=(/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) ! Ratio between effective and real iceberg mass (non-dim)
 real, dimension(nclasses) :: initial_thickness=(/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) ! Total thickness of newly calved bergs (m)
 namelist /icebergs_nml/ verbose, budget, halo, iceberg_halo, traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj, &
-         distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,bond_coef, radial_damping_coef, tangental_damping_coef, &
+         distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,bond_coef, radial_damping_coef, tangental_damping_coef, only_interactive_forces, &
          rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, iceberg_bonds_on, manually_initialize_bonds, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, halo_debugging, &
          time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, interactive_icebergs_on, critical_interaction_damping_on, &
@@ -610,7 +612,8 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%passive_mode=passive_mode
   bergs%time_average_weight=time_average_weight
   bergs%speed_limit=speed_limit
-  bergs%Runge_not_Verlet=Runge_not_Verlet   !Alon
+  bergs%Runge_not_Verlet=Runge_not_Verlet   
+  bergs%only_interactive_forces=only_interactive_forces
   bergs%halo_debugging=halo_debugging
   bergs%iceberg_bonds_on=iceberg_bonds_on   !Alon
   bergs%manually_initialize_bonds=manually_initialize_bonds   !Alon

From f7a6a37cd256febe321572d96cf2f1397849f8af Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Fri, 16 Oct 2015 18:03:35 -0400
Subject: [PATCH 088/361] Fixed two bugs related to iceberg interactions:

1) The interactions were taking place based on old positions. They should rather use the updated position, r_np1, for stability. To do this meant updating the position at the end of the time step rather than beginning. This has been done. There are still remaining issues related to the fact that this means we have to search a wider range of grid cells to find hippy bergs. I will sort this out on Monday.

1b) lat_new and lon_new have to be passed between processor. They also have to be stored in the restart file (which has not been done yet).

2) Another bug is fixed, which related to the damping matrix, P, having to be multiplied by dt before being part of the inversion. This has been fixed.
---
 icebergs.F90           | 147 +++++++++++++++++++++++++++++++++++------
 icebergs_framework.F90 |  38 ++++++-----
 icebergs_io.F90        |  12 ++--
 3 files changed, 151 insertions(+), 46 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 6907b4c..81c7af5 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -204,7 +204,7 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
   P_ia_times_u_x=0. ; P_ia_times_u_y=0.
 
   bonded=.false. !Unbonded iceberg interactions
-  do grdj = berg%jne-1,berg%jne+1 ; do grdi = berg%ine-1,berg%ine+1
+  do grdj = berg%jne-2,berg%jne+2 ; do grdi = berg%ine-2,berg%ine+2  !Note: need  to make sure this is wide enough, but less than the halo width
     other_berg=>bergs%list(grdi,grdj)%first
     do while (associated(other_berg)) ! loop over all other bergs  
       call calculate_force(bergs,berg,other_berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y, bonded) 
@@ -273,7 +273,7 @@ subroutine calculate_force(bergs,berg,other_berg,IA_x, IA_y, u0, v0, u1, v1, P_i
         M1=berg%mass 
         A1=L1*W1 
         R1=sqrt(A1/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
-        lon1=berg%lon; lat1=berg%lat
+        lon1=berg%lon_new; lat1=berg%lat_new
         !call rotpos_to_tang(lon1,lat1,x1,y1)
 
               
@@ -286,7 +286,8 @@ subroutine calculate_force(bergs,berg,other_berg,IA_x, IA_y, u0, v0, u1, v1, P_i
         v2=other_berg%vvel_old !Old values are used to make it order invariant 
         A2=L2*W2
         R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
-        lon2=other_berg%lon_old; lat2=other_berg%lat_old !Old values are used to make it order invariant
+        lon2=other_berg%lon_new; lat2=other_berg%lat_new !Old values are used to make it order invariant
+
         !call rotpos_to_tang(lon2,lat2,x2,y2)
 
         dlon=lon1-lon2
@@ -300,6 +301,12 @@ subroutine calculate_force(bergs,berg,other_berg,IA_x, IA_y, u0, v0, u1, v1, P_i
         r_dist_y=dlat*(pi/180)*Rearth
         r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) )
 
+        
+          if (berg%iceberg_num .eq. 1) then
+            print *, 'Comparing longitudes: ', lon1, lon2, r_dist_x, dlon, r_dist
+            print *, 'Outside, iceberg_num, r_dist', berg%iceberg_num, r_dist,bonded
+            print *, 'Halo_status', berg%halo_berg,other_berg%halo_berg 
+          endif
         !print *, 'outside the loop',R1, R2,r_dist, bonded
        !call overlap_area(R1,R2,r_dist,A_o,trapped)
        !T_min=min(T1,T2)
@@ -315,8 +322,12 @@ subroutine calculate_force(bergs,berg,other_berg,IA_x, IA_y, u0, v0, u1, v1, P_i
          
 
         if (r_dist < 5*(R1+R2)) then
+          
           !MP1
-          !print *, 'in the loop1', berg%iceberg_num, other_berg%iceberg_num,r_dist, bonded, IA_x, IA_y
+          if (berg%iceberg_num .eq. 1) then
+            print *,  '************************************************************'
+            print *, 'INSIDE, r_dist', berg%iceberg_num, r_dist, bonded
+          endif
           !print *, 'in the loop1', spring_coef, (M_min/M1), accel_spring,(R1+R2-r_dist) 
           !print *, 'in the loop2', IA_x, IA_y, R1, R2,r_dist, berg%iceberg_num,other_berg%iceberg_num
           !Damping force:
@@ -629,7 +640,6 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
        A12=(dt*P_ia_12)
        A21=(dt*P_ia_21)
        A22=1+(dt*P_ia_22)
-      !print *,'Other', berg%iceberg_num, P_ia_12,u_star, P_ia_times_u_x, P_ia_11, dt
      endif
 
 
@@ -648,8 +658,15 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 
       uveln=u_star+dt*ax        ! Alon
       vveln=v_star+dt*ay        ! Alon
-
-      !print *,'IN loop', berg%iceberg_num, RHS_x,  A11, A12, A21, A22, ax, itloop, uveln
+!MP4
+  !    if (berg%iceberg_num .eq. 1) then
+  !      print *, '***************************************************'
+  !      print *,'Iceberg_num, itloop', berg%iceberg_num, itloop
+  !      print *, 'P matrix:', P_ia_11, P_ia_12,P_ia_21,P_ia_22,P_ia_times_u_x, P_ia_times_u_x 
+  !      print *,'A_matrix', A11, A12, A21, A22 
+  !      print *,'IA_x IA_y', IA_x, IA_y 
+  !      print *, 'RHS, ustar, uvel,ax: ', RHS_x, u_star,uveln, ax
+  !    endif
   enddo ! itloop
 
 !Saving the totally explicit part of the acceleration to use in finding the next position and u_star -Alon
@@ -670,14 +687,14 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 
      !This is for testing the code using only interactive forces
      if (bergs%only_interactive_forces) then
-       axn=IA_x/2
-       ayn=IA_y/2
+       axn=IA_x
+       ayn=IA_y
      endif
 
     bxn= ax-(axn/2) !Alon
     byn= ay-(ayn/2) !Alon
 
-    !print *,'After1', berg%iceberg_num, axn, bxn, uveln
+    if (berg%iceberg_num .eq. 1)   print *,'axn, bxn, uveln:', axn, bxn, uveln
  
   ! Limit speed of bergs based on a CFL criteria
   if (bergs%speed_limit>0.) then
@@ -2351,20 +2368,21 @@ subroutine evolve_icebergs(bergs)
        ! Positions and velocity is updated by
        ! X2 = X1+dt*V1+((dt^2)/2)*a_n +((dt^2)/2)*b_n = X1+dt*u_star +((dt^2)/2)*b_n 
        ! V2 = V1+dt/2*a_n +dt/2*a_np1 +dt*b_n = u_star + dt/2*a_np1 + dt*b_np1 = u_star +dt*ax
-  
+ 
+      !*************************************************************************************************** 
        !print *, 'you are here!'
-  
+!MP5
+       !call update_verlet_position(bergs,berg,i1,j1)
+
         lon1=berg%lon; lat1=berg%lat
         if (on_tangential_plane) call rotpos_to_tang(lon1,lat1,x1,y1)
         dxdl1=r180_pi/(Rearth*cos(lat1*pi_180))
         dydl=r180_pi/Rearth
         uvel1=berg%uvel; vvel1=berg%vvel
-  
+
         ! Loading past acceleartions - Alon
         axn=berg%axn; ayn=berg%ayn !Alon
-        bxn=berg%bxn; byn=berg%byn !Alon
-  
-  
+        bxn=berg%bxn; byn=berg%byn !Alon 
   
         ! Velocities used to update the position
         uvel2=uvel1+(dt_2*axn)+(dt_2*bxn)                    !Alon
@@ -2373,7 +2391,6 @@ subroutine evolve_icebergs(bergs)
         if (on_tangential_plane) call rotvec_to_tang(lon1,uvel2,vvel2,xdot2,ydot2)
         u2=uvel2*dxdl1; v2=vvel2*dydl
   
-  
         ! Solving for new position
         if (on_tangential_plane) then
           xn=x1+(dt*xdot2) ; yn=y1+(dt*ydot2)             !Alon
@@ -2382,20 +2399,24 @@ subroutine evolve_icebergs(bergs)
           lonn=lon1+(dt*u2) ; latn=lat1+(dt*v2)  !Alon
         endif
         dxdln=r180_pi/(Rearth*cos(latn*pi_180))
-  
+ 
+!       print *, 'TEST2: ', lonn, latn, berg%iceberg_num
+
         ! Turn the velocities into u_star, v_star.(uvel3 is v_star) - Alon (not sure how this works with tangent plane)
         uvel3=uvel1+(dt_2*axn)                  !Alon
         vvel3=vvel1+(dt_2*ayn)                  !Alon
   
   
         ! Adjusting mass...                      Alon decided to move this before calculating the new velocities (so that acceleration can be a fn(r_np1)
+        !MP3
+        !print *, 'before the bounce.!',mpp_pe(),berg%iceberg_num,lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag 
         i=i1;j=j1;xi=berg%xi;yj=berg%yj
         call adjust_index_and_ground(grd, lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
         !call adjust_index_and_ground(grd, lonn, latn, uvel1, vvel1, i, j, xi, yj, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
 
         ! If the iceberg bounces off the land, then its velocity and acceleration are set to zero
         if (bounced) then
-       !print *, 'you have been bounce: big time!',lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag 
+        print *, 'you have been bounce: big time!',mpp_pe(),berg%iceberg_num,lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag 
                 axn=0. ; ayn=0.
                 bxn=0. ; byn=0.
                 uvel3=0.; vvel3=0.
@@ -2421,7 +2442,10 @@ subroutine evolve_icebergs(bergs)
      !  uveln=uvel4*dxdln; vveln=vvel4*dydl    !Converted to degrees.  (Perhaps this should not be here)
         uveln=uvel4
         vveln=vvel4 
-  
+
+        print *, 'New velocity: ', uveln, vveln
+
+
         ! Debugging
         if (.not.error_flag) then
           if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j)) error_flag=.true.
@@ -2500,10 +2524,20 @@ subroutine evolve_icebergs(bergs)
     do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
       berg=>bergs%list(grdi,grdj)%first
       do while (associated(berg)) ! loop over all bergs
+      
+       lonn=0. ; latn =0.
+       call update_verlet_position(bergs,berg,lonn, latn) 
+
+       if (berg%iceberg_num .eq. 1) then
+         print *, 'TEST2:' , berg%lon, berg%lat
+         print *, 'test1: ', lonn, latn
+       endif
 
         !Updating iceberg positions and velocities
-        berg%lon_old=berg%lon
-        berg%lat_old=berg%lat
+        berg%lon_new=lonn    ! This is the t=n+1 position (one step ahead)
+        berg%lat_new=latn
+        !berg%lon_new=berg%lon
+        !berg%lat_new=berg%lat
         berg%uvel_old=berg%uvel
         berg%vvel_old=berg%vvel
         berg=>berg%next
@@ -2514,6 +2548,75 @@ subroutine evolve_icebergs(bergs)
 
 contains
 
+!#######################################################################
+!MP6
+subroutine update_verlet_position(bergs,berg,lonn, latn)
+type(icebergs), intent(in), pointer :: bergs 
+type(iceberg), intent(in), pointer :: berg 
+real, intent(out) :: lonn, latn
+!Local variable
+real :: uvel3, vvel3
+real :: lon1, lat1, dxdl1, dydl
+real :: uvel1, vvel1, uvel2, vvel2
+real :: axn, ayn, bxn, byn 
+real :: u2, v2, x1, y1, xn, yn
+integer :: i_temp, j_temp
+integer :: i1, j1
+real :: xi_temp, yj_temp, dx
+logical :: on_tangential_plane
+
+      i1=berg%ine
+      j1=berg%jne
+
+      on_tangential_plane=.false.
+      if (berg%lat>89.) on_tangential_plane=.true.
+
+
+        lon1=berg%lon; lat1=berg%lat
+        if (on_tangential_plane) call rotpos_to_tang(lon1,lat1,x1,y1)
+        dxdl1=r180_pi/(Rearth*cos(lat1*pi_180))
+        dydl=r180_pi/Rearth
+        uvel1=berg%uvel; vvel1=berg%vvel
+
+
+        ! Loading past acceleartions - Alon
+        axn=berg%axn; ayn=berg%ayn !Alon
+        bxn=berg%bxn; byn=berg%byn !Alon 
+  
+        ! Velocities used to update the position
+        uvel2=uvel1+(dt_2*axn)+(dt_2*bxn)                    !Alon
+        vvel2=vvel1+(dt_2*ayn)+(dt_2*byn)                    !Alon
+
+        dx=(dt*(uvel1+(dt_2*axn)+(dt_2*bxn)))
+        print *, 'dx= ' ,dx,  dt, dt_2
+
+
+        if (on_tangential_plane) call rotvec_to_tang(lon1,uvel2,vvel2,xdot2,ydot2)
+        u2=uvel2*dxdl1; v2=vvel2*dydl
+  
+        ! Solving for new position
+        if (on_tangential_plane) then
+          xn=x1+(dt*xdot2) ; yn=y1+(dt*ydot2)             !Alon
+          call rotpos_from_tang(xn,yn,lonn,latn)
+        else
+          lonn=lon1+(dt*u2) ; latn=lat1+(dt*v2)  !Alon
+        endif
+        dxdln=r180_pi/(Rearth*cos(latn*pi_180))
+  
+
+        ! Turn the velocities into u_star, v_star.(uvel3 is v_star) - Alon (not sure how this works with tangent plane)
+        uvel3=uvel1+(dt_2*axn)                  !Alon
+        vvel3=vvel1+(dt_2*ayn)                  !Alon
+
+        ! Adjusting mass...
+        !MP3
+        i_temp=i1;  j_temp=j1;  xi_temp = berg%xi;  yj_temp = berg%yj
+        call adjust_index_and_ground(grd, lonn, latn, uvel3, vvel3, i_temp, j_temp, xi_temp, yj_temp, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
+
+end subroutine update_verlet_position
+
+!#######################################################################
+
   subroutine rotpos_from_tang(x, y, lon, lat)
   ! Arguments
   real, intent(in) :: x, y
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 6c04300..39d36d6 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -15,7 +15,7 @@ module ice_bergs_framework
 
 implicit none ; private
 
-integer :: buffer_width=26 !Changed from 20 to 26 by Alon 
+integer :: buffer_width=28 !Changed from 20 to 28 by Alon 
 integer :: buffer_width_traj=29  !Changed from 23 by Alon
 !integer, parameter :: buffer_width=26 !Changed from 20 to 26 by Alon 
 !integer, parameter :: buffer_width_traj=29  !Changed from 23 by Alon
@@ -140,7 +140,7 @@ module ice_bergs_framework
 type :: xyt
   real :: lon, lat, day
   real :: mass, thickness, width, length, uvel, vvel
-  real :: axn, ayn, bxn, byn, uvel_old, vvel_old, lat_old, lon_old  !Explicit and implicit accelerations !Alon 
+  real :: axn, ayn, bxn, byn, uvel_old, vvel_old, lat_new, lon_new  !Explicit and implicit accelerations !Alon 
   real :: uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, cn, hi, halo_berg
   real :: mass_of_bits, heat_density
   integer :: year, iceberg_num
@@ -151,7 +151,7 @@ module ice_bergs_framework
   type(iceberg), pointer :: prev=>null(), next=>null()
   ! State variables (specific to the iceberg, needed for restarts)
   real :: lon, lat, uvel, vvel, mass, thickness, width, length
-  real :: axn, ayn, bxn, byn, uvel_old, vvel_old, lon_old, lat_old !Explicit and implicit accelerations !Alon 
+  real :: axn, ayn, bxn, byn, uvel_old, vvel_old, lon_new, lat_new !Explicit and implicit accelerations !Alon 
   real :: start_lon, start_lat, start_day, start_mass, mass_scaling
   real :: mass_of_bits, heat_density
   real :: halo_berg  ! Equal to zero for bergs on computational domain, and =1 for bergs on the halo
@@ -1441,9 +1441,11 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
     buff%data(24,n)=berg%byn  !Alon
     buff%data(25,n)=float(berg%iceberg_num)
     buff%data(26,n)=berg%halo_berg 
+    buff%data(27,n)=berg%lon_new 
+    buff%data(28,n)=berg%lat_new
 
     if (max_bonds .gt. 0) then
-      counter=26 !how many data points being passed so far (must match above)
+      counter=28 !how many data points being passed so far (must match above)
       current_bond=>berg%first_bond
       do k = 1,max_bonds
         if (associated(current_bond)) then
@@ -1585,12 +1587,12 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n,grd, force_append, max_bonds_
     localberg%byn=buff%data(24,n) !Alon
     localberg%iceberg_num=nint(buff%data(25,n))
     localberg%halo_berg=buff%data(26,n) 
+    localberg%lon_new=buff%data(27,n) 
+    localberg%lat_new=buff%data(28,n) 
 
     !These quantities no longer need to be passed between processors
     localberg%uvel_old=localberg%uvel
     localberg%vvel_old=localberg%vvel
-    localberg%lon_old=localberg%lon
-    localberg%lat_old=localberg%lat
 
     ! force_app=.true.
     if(force_app) then !force append with origin ine,jne (for I/O)
@@ -1615,8 +1617,8 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n,grd, force_append, max_bonds_
           write(stderrunit,*) localberg%uvel,localberg%vvel
           write(stderrunit,*) localberg%axn,localberg%ayn !Alon
           write(stderrunit,*) localberg%bxn,localberg%byn !Alon
-          write(stderrunit,*) localberg%uvel_old,localberg%vvel_old !Alon
-          write(stderrunit,*) localberg%lon_old,localberg%lat_old !Alon
+          write(stderrunit,*) localberg%uvel_old,localberg%vvel_old 
+          write(stderrunit,*) localberg%lon_new,localberg%lat_new 
           write(stderrunit,*) grd%isc,grd%iec,grd%jsc,grd%jec
           write(stderrunit,*) grd%isd,grd%ied,grd%jsd,grd%jed
           write(stderrunit,*) grd%lon(grd%isc-1,grd%jsc-1),grd%lon(grd%iec,grd%jsc)
@@ -1633,7 +1635,7 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n,grd, force_append, max_bonds_
 
     this%first_bond=>null()
     if (max_bonds .gt. 0) then
-      counter=26 !how many data points being passed so far (must match above)
+      counter=28 !how many data points being passed so far (must match above)
       do k = 1,max_bonds
         other_berg_num=nint(buff%data(counter+(3*(k-1)+1),n))
         other_berg_ine=nint(buff%data(counter+(3*(k-1)+2),n))
@@ -2116,8 +2118,8 @@ logical function sameberg(berg1, berg2)
   if (berg1%byn.ne.berg2%byn) return  !Alon
   if (berg1%uvel_old.ne.berg2%uvel_old) return  !Alon
   if (berg1%vvel_old.ne.berg2%vvel_old) return  !Alon
-  if (berg1%lon_old.ne.berg2%lon_old) return  !Alon
-  if (berg1%lat_old.ne.berg2%lat_old) return  !Alon
+  if (berg1%lon_new.ne.berg2%lon_new) return  !Alon
+  if (berg1%lat_new.ne.berg2%lat_new) return  !Alon
   sameberg=.true. ! passing the above tests mean that bergs 1 and 2 are identical
 end function sameberg
 
@@ -2210,7 +2212,7 @@ subroutine print_berg(iochan, berg, label)
     ' axn,ayn=', berg%axn, berg%ayn, &
     ' bxn,byn=', berg%bxn, berg%byn, &
     ' uvel_old,vvel_old=', berg%uvel_old, berg%vvel_old, &
-    ' lon_old,lat_old=', berg%lon_old, berg%lat_old, &
+    ' lon_new,lat_new=', berg%lon_new, berg%lat_new, &
     ' p,n=', associated(berg%prev), associated(berg%next)
   write(iochan,'("diamonds, print_berg: ",a," pe=(",i3,") ",6(a,2f10.4))') &
     label, mpp_pe(), 'uo,vo=', berg%uo, berg%vo, 'ua,va=', berg%ua, berg%va, 'ui,vi=', berg%ui, berg%vi
@@ -2639,8 +2641,8 @@ subroutine record_posn(bergs)
       posn%byn=this%byn
       posn%uvel_old=this%uvel_old
       posn%vvel_old=this%vvel_old
-      posn%lon_old=this%lon_old
-      posn%lat_old=this%lat_old
+      posn%lon_new=this%lon_new
+      posn%lat_new=this%lat_new
       posn%halo_berg=this%halo_berg
   
       call push_posn(this%trajectory, posn)
@@ -3744,8 +3746,8 @@ subroutine bergs_chksum(bergs, txt, ignore_halo_violation)
       fld(i,12) = this%byn !added by Alon
       fld(i,13) = this%uvel_old !added by Alon
       fld(i,14) = this%vvel_old !added by Alon
-      fld(i,15) = this%lon_old !added by Alon
-      fld(i,16) = this%lat_old !added by Alon
+      fld(i,15) = this%lon_new !added by Alon
+      fld(i,16) = this%lat_new !added by Alon
       fld(i,17) = time_hash(this) !Changed from 9 to 17 by Alon
       fld(i,18) = pos_hash(this) !Changed from 10 to 18 by Alon
       fld(i,19) = float(iberg) !Changed from 11 to 19 by Alon
@@ -3840,8 +3842,8 @@ integer function berg_chksum(berg )
   rtmp(32)=berg%byn !Added by Alon
   rtmp(33)=berg%uvel_old !Added by Alon
   rtmp(34)=berg%vvel_old !Added by Alon
-  rtmp(35)=berg%lat_old !Added by Alon
-  rtmp(36)=berg%lon_old !Added by Alon
+  rtmp(35)=berg%lat_new !Added by Alon
+  rtmp(36)=berg%lon_new !Added by Alon
   itmp(37)=berg%halo_berg !Changed from 31 to 40 by Alon
   itmp(1:37)=transfer(rtmp,i8) !Changed from 28 to 37 by Alon
   itmp(38)=berg%start_year !Changed from 29 to 38 by Alon
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index b231d41..9d291a8 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -613,8 +613,8 @@ subroutine generate_bergs(bergs,Time)
         localberg%jne=j
         localberg%lon=bilin(grd, grd%lon, i, j, localberg%xi, localberg%yj)
         localberg%lat=bilin(grd, grd%lat, i, j, localberg%xi, localberg%yj)
-        localberg%lon_old=bilin(grd, grd%lon, i, j, localberg%xi, localberg%yj) !Alon
-        localberg%lat_old=bilin(grd, grd%lat, i, j, localberg%xi, localberg%yj) !Alon
+        localberg%lon_new=bilin(grd, grd%lon, i, j, localberg%xi, localberg%yj) !Alon
+        localberg%lat_new=bilin(grd, grd%lat, i, j, localberg%xi, localberg%yj) !Alon
         localberg%mass=bergs%initial_mass(1)
         localberg%thickness=bergs%initial_thickness(1)
         localberg%width=bergs%initial_width(1)
@@ -846,8 +846,8 @@ subroutine read_restart_bergs(bergs,Time)
          localberg%ayn=ayn(k) !Alon
          localberg%uvel_old=uvel(k) !Alon
          localberg%vvel_old=vvel(k) !Alon
-         localberg%lon_old=lon(k) !Alon
-         localberg%lat_old=lat(k) !Alon
+         localberg%lon_new=lon(k) !Alon
+         localberg%lat_new=lat(k) !Alon
          localberg%bxn=bxn(k) !Alon
          localberg%byn=byn(k) !Alon
          localberg%thickness=thickness(k)
@@ -937,8 +937,8 @@ subroutine generate_bergs(bergs,Time)
         localberg%jne=j
         localberg%lon=bilin(grd, grd%lon, i, j, localberg%xi, localberg%yj)
         localberg%lat=bilin(grd, grd%lat, i, j, localberg%xi, localberg%yj)
-        localberg%lon_old=bilin(grd, grd%lon, i, j, localberg%xi, localberg%yj) !Alon
-        localberg%lat_old=bilin(grd, grd%lat, i, j, localberg%xi, localberg%yj) !Alon
+        localberg%lon_new=bilin(grd, grd%lon, i, j, localberg%xi, localberg%yj) !Alon
+        localberg%lat_new=bilin(grd, grd%lat, i, j, localberg%xi, localberg%yj) !Alon
         localberg%mass=bergs%initial_mass(1)
         localberg%thickness=bergs%initial_thickness(1)
         localberg%width=bergs%initial_width(1)

From 223184afef2cb22a5f628ddfe72390625b775b0c Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Mon, 19 Oct 2015 13:23:24 -0400
Subject: [PATCH 089/361] Verlet position is now updated at the end of each
 time step. At the end of the time step, (uvel,vvel=u_n), while lon,
 lat)=r_np1.

Making this change allows us to change the interaction distance to one grid cell in the interactive_forces  subroutine.

The verlet time stepping has been significantly cleaned up.
---
 icebergs.F90           | 223 +++++++++++++++++------------------------
 icebergs_framework.F90 |  36 ++++---
 icebergs_io.F90        |  12 +--
 3 files changed, 114 insertions(+), 157 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 81c7af5..88168fd 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -204,7 +204,7 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
   P_ia_times_u_x=0. ; P_ia_times_u_y=0.
 
   bonded=.false. !Unbonded iceberg interactions
-  do grdj = berg%jne-2,berg%jne+2 ; do grdi = berg%ine-2,berg%ine+2  !Note: need  to make sure this is wide enough, but less than the halo width
+  do grdj = berg%jne-1,berg%jne+1 ; do grdi = berg%ine-1,berg%ine+1  !Note: need  to make sure this is wide enough, but less than the halo width
     other_berg=>bergs%list(grdi,grdj)%first
     do while (associated(other_berg)) ! loop over all other bergs  
       call calculate_force(bergs,berg,other_berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y, bonded) 
@@ -273,7 +273,7 @@ subroutine calculate_force(bergs,berg,other_berg,IA_x, IA_y, u0, v0, u1, v1, P_i
         M1=berg%mass 
         A1=L1*W1 
         R1=sqrt(A1/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
-        lon1=berg%lon_new; lat1=berg%lat_new
+        lon1=berg%lon_old; lat1=berg%lat_old
         !call rotpos_to_tang(lon1,lat1,x1,y1)
 
               
@@ -286,7 +286,7 @@ subroutine calculate_force(bergs,berg,other_berg,IA_x, IA_y, u0, v0, u1, v1, P_i
         v2=other_berg%vvel_old !Old values are used to make it order invariant 
         A2=L2*W2
         R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
-        lon2=other_berg%lon_new; lat2=other_berg%lat_new !Old values are used to make it order invariant
+        lon2=other_berg%lon_old; lat2=other_berg%lat_old !Old values are used to make it order invariant
 
         !call rotpos_to_tang(lon2,lat2,x2,y2)
 
@@ -302,11 +302,12 @@ subroutine calculate_force(bergs,berg,other_berg,IA_x, IA_y, u0, v0, u1, v1, P_i
         r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) )
 
         
-          if (berg%iceberg_num .eq. 1) then
-            print *, 'Comparing longitudes: ', lon1, lon2, r_dist_x, dlon, r_dist
-            print *, 'Outside, iceberg_num, r_dist', berg%iceberg_num, r_dist,bonded
-            print *, 'Halo_status', berg%halo_berg,other_berg%halo_berg 
-          endif
+          !if (berg%iceberg_num .eq. 1) then
+            !print *, 'Comparing longitudes: ', lon1, lon2, r_dist_x, dlon, r_dist
+            !print *, 'Comparing longitudes: ', lon1, lon2, r_dist_x, dlon, r_dist
+            !print *, 'Outside, iceberg_num, r_dist', berg%iceberg_num, r_dist,bonded
+            !print *, 'Halo_status', berg%halo_berg,other_berg%halo_berg 
+          !endif
         !print *, 'outside the loop',R1, R2,r_dist, bonded
        !call overlap_area(R1,R2,r_dist,A_o,trapped)
        !T_min=min(T1,T2)
@@ -324,10 +325,10 @@ subroutine calculate_force(bergs,berg,other_berg,IA_x, IA_y, u0, v0, u1, v1, P_i
         if (r_dist < 5*(R1+R2)) then
           
           !MP1
-          if (berg%iceberg_num .eq. 1) then
-            print *,  '************************************************************'
-            print *, 'INSIDE, r_dist', berg%iceberg_num, r_dist, bonded
-          endif
+          !if (berg%iceberg_num .eq. 1) then
+          !  !print *,  '************************************************************'
+          !  print *, 'INSIDE, r_dist', berg%iceberg_num, other_berg%iceberg_num, r_dist, bonded
+          !endif
           !print *, 'in the loop1', spring_coef, (M_min/M1), accel_spring,(R1+R2-r_dist) 
           !print *, 'in the loop2', IA_x, IA_y, R1, R2,r_dist, berg%iceberg_num,other_berg%iceberg_num
           !Damping force:
@@ -416,7 +417,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 type(iceberg), pointer :: berg
 integer, intent(in) :: i, j
 real, intent(in) :: xi, yj, lat, uvel, vvel, uvel0, vvel0, dt
-real, intent(inout) :: ax, ay
+real, intent(out) :: ax, ay
 real, intent(inout) :: axn, ayn, bxn, byn ! Added implicit and explicit accelerations to output -Alon
 logical, optional :: debug_flag
 ! Local variables
@@ -694,8 +695,6 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
     bxn= ax-(axn/2) !Alon
     byn= ay-(ayn/2) !Alon
 
-    if (berg%iceberg_num .eq. 1)   print *,'axn, bxn, uveln:', axn, bxn, uveln
- 
   ! Limit speed of bergs based on a CFL criteria
   if (bergs%speed_limit>0.) then
     speed=sqrt(uveln*uveln+vveln*vveln) ! Speed of berg
@@ -2022,6 +2021,11 @@ subroutine evolve_icebergs(bergs)
   !  Vn = V1+dt*(A1+2*A2+2*A3+A4)/6
   
   ! Get the stderr unit number
+
+
+  !Initialize variables
+  ax1=0. ;ax2 =0.; ax3=0.; ax4=0.; 
+  ay1=0. ;ay2 =0.; ay3=0.; ay4=0.; 
   stderrunit = stderr()
 
   ! For convenience
@@ -2062,28 +2066,25 @@ subroutine evolve_icebergs(bergs)
 
       if (debug) call check_position(grd, berg, 'evolve_iceberg (top)')
 
-      i=berg%ine
-      j=berg%jne
-      xi=berg%xi
-      yj=berg%yj
-      bounced=.false.
-      on_tangential_plane=.false.
-      if (berg%lat>89.) on_tangential_plane=.true.
-      i1=i;j1=j
-      if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-        call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling)
-
-
-
-      if (Runge_not_Verlet) then !Start of the Runge-Kutta Loop -Added by Alon, MP2
+      !###########################################################################################################
+      if (Runge_not_Verlet) then !Start of the Runge-Kutta Loop
+
+        i=berg%ine
+        j=berg%jne
+        xi=berg%xi
+        yj=berg%yj
+        bounced=.false.
+        on_tangential_plane=.false.
+        if (berg%lat>89.) on_tangential_plane=.true.
+        i1=i;j1=j
+        if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
+          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling)
 
         ! Loading past accelerations - Alon
         axn=berg%axn; ayn=berg%ayn !Alon
         axn1=axn; axn2=axn; axn3=axn; axn4=axn
         ayn1=ayn; ayn2=ayn; ayn3=ayn; ayn4=ayn
-  
-  
-  
+       
         ! A1 = A(X1)
         lon1=berg%lon; lat1=berg%lat
         if (on_tangential_plane) call rotpos_to_tang(lon1,lat1,x1,y1)
@@ -2093,7 +2094,6 @@ subroutine evolve_icebergs(bergs)
         if (on_tangential_plane) call rotvec_to_tang(lon1,uvel1,vvel1,xdot1,ydot1)
         u1=uvel1*dxdl1; v1=vvel1*dydl
 
-
         call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn) !axn,ayn, bxn, byn  - Added by Alon
         !call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn1, ayn1, bxn, byn) !Note change to dt. Markpoint_1
         if (on_tangential_plane) call rotvec_to_tang(lon1,ax1,ay1,xddot1,yddot1)
@@ -2111,7 +2111,6 @@ subroutine evolve_icebergs(bergs)
           uvel2=uvel1+dt_2*ax1; vvel2=vvel1+dt_2*ay1
         endif
         i=i1;j=j1;xi=berg%xi;yj=berg%yj
-        !print *, 'Alon: look here!', lon2, lat2, uvel2, vvel2, i, j, xi, yj
         call adjust_index_and_ground(grd, lon2, lat2, uvel2, vvel2, i, j, xi, yj, bounced, error_flag)
         i2=i; j2=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
@@ -2369,84 +2368,40 @@ subroutine evolve_icebergs(bergs)
        ! X2 = X1+dt*V1+((dt^2)/2)*a_n +((dt^2)/2)*b_n = X1+dt*u_star +((dt^2)/2)*b_n 
        ! V2 = V1+dt/2*a_n +dt/2*a_np1 +dt*b_n = u_star + dt/2*a_np1 + dt*b_np1 = u_star +dt*ax
  
-      !*************************************************************************************************** 
-       !print *, 'you are here!'
-!MP5
-       !call update_verlet_position(bergs,berg,i1,j1)
-
-        lon1=berg%lon; lat1=berg%lat
-        if (on_tangential_plane) call rotpos_to_tang(lon1,lat1,x1,y1)
-        dxdl1=r180_pi/(Rearth*cos(lat1*pi_180))
-        dydl=r180_pi/Rearth
-        uvel1=berg%uvel; vvel1=berg%vvel
-
-        ! Loading past acceleartions - Alon
-        axn=berg%axn; ayn=berg%ayn !Alon
-        bxn=berg%bxn; byn=berg%byn !Alon 
-  
-        ! Velocities used to update the position
-        uvel2=uvel1+(dt_2*axn)+(dt_2*bxn)                    !Alon
-        vvel2=vvel1+(dt_2*ayn)+(dt_2*byn)                    !Alon
-  
-        if (on_tangential_plane) call rotvec_to_tang(lon1,uvel2,vvel2,xdot2,ydot2)
-        u2=uvel2*dxdl1; v2=vvel2*dydl
-  
-        ! Solving for new position
-        if (on_tangential_plane) then
-          xn=x1+(dt*xdot2) ; yn=y1+(dt*ydot2)             !Alon
-          call rotpos_from_tang(xn,yn,lonn,latn)
-        else
-          lonn=lon1+(dt*u2) ; latn=lat1+(dt*v2)  !Alon
-        endif
-        dxdln=r180_pi/(Rearth*cos(latn*pi_180))
- 
-!       print *, 'TEST2: ', lonn, latn, berg%iceberg_num
+      !*************************************************************************************************!MP5
+        lonn = berg%lon ;   latn = berg%lat
+        axn  = berg%axn ;   ayn  = berg%ayn
+        bxn=   berg%bxn ;   byn  = berg%byn
+        uvel1=berg%uvel ;   vvel1=berg%vvel
+        i=berg%ine     ;   j=berg%jne
+        xi=berg%xi      ;   yj=berg%yj
 
         ! Turn the velocities into u_star, v_star.(uvel3 is v_star) - Alon (not sure how this works with tangent plane)
         uvel3=uvel1+(dt_2*axn)                  !Alon
         vvel3=vvel1+(dt_2*ayn)                  !Alon
-  
-  
-        ! Adjusting mass...                      Alon decided to move this before calculating the new velocities (so that acceleration can be a fn(r_np1)
-        !MP3
-        !print *, 'before the bounce.!',mpp_pe(),berg%iceberg_num,lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag 
-        i=i1;j=j1;xi=berg%xi;yj=berg%yj
-        call adjust_index_and_ground(grd, lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
-        !call adjust_index_and_ground(grd, lonn, latn, uvel1, vvel1, i, j, xi, yj, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
 
-        ! If the iceberg bounces off the land, then its velocity and acceleration are set to zero
-        if (bounced) then
-        print *, 'you have been bounce: big time!',mpp_pe(),berg%iceberg_num,lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag 
-                axn=0. ; ayn=0.
-                bxn=0. ; byn=0.
-                uvel3=0.; vvel3=0.
-                uvel1=0.; vvel1=0.
-        endif
-
-        i2=i; j2=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
           call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling)
-  
+
         ! Calling the acceleration   (note that the velocity is converted to u_star inside the accel script)
         call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn, ayn, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
   
-  !Solving for the new velocity
+        !Solving for the new velocity
+        on_tangential_plane=.false.
+        if (berg%lat>89.) on_tangential_plane=.true.
         if (on_tangential_plane) then
           call rotvec_to_tang(lonn,uvel3,vvel3,xdot3,ydot3)
           call rotvec_to_tang(lonn,ax1,ay1,xddot1,yddot1)
           xdotn=xdot3+(dt*xddot1); ydotn=ydot3+(dt*yddot1)                                    !Alon
           call rotvec_from_tang(lonn,xdotn,ydotn,uveln,vveln)
         else
-          uvel4=uvel3+(dt*ax1); vvel4=vvel3+(dt*ay1)    !Alon , we call it uvel3, vvel3 until it is put into lat/long co-ordinates, where it becomes uveln, vveln
+          uveln=uvel3+(dt*ax1); vveln=vvel3+(dt*ay1)    !Alon , we call it uvel3, vvel3 until it is put into lat/long co-ordinates, where it becomes uveln, vveln
         endif
-     !  uveln=uvel4*dxdln; vveln=vvel4*dydl    !Converted to degrees.  (Perhaps this should not be here)
-        uveln=uvel4
-        vveln=vvel4 
-
-        print *, 'New velocity: ', uveln, vveln
 
-
-        ! Debugging
+        !if (berg%iceberg_num .eq. 1) print *, 'New velocity: ', uveln, vveln
+       !*************************************************************************************************!MP5
+        !!!!!!!!!!!!!!! Debugging  !!!!!!!!!!!!!!!!!!!!!!!!!!!
+        error_flag=.false.
         if (.not.error_flag) then
           if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j)) error_flag=.true.
         endif
@@ -2457,10 +2412,10 @@ subroutine evolve_icebergs(bergs)
          call print_fld(grd, grd%hi, 'hi')
          write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
          write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
-         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: i1,i2,i=',i1,i2,i
-         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: j1,j2,j=',j1,j2,j
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lon1,lonn=',lon1,lonn,berg%lon
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lat1,latn=',lat1,latn,berg%lat
+         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: i1,i=',i1,i
+         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: j1,j=',j1,j
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lonn=',lonn,berg%lon
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: latn=',latn,berg%lat
          write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u3,un,u0=',uvel3,uveln,berg%uvel
          write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v3,vn,v0=',vvel3,vveln,berg%vvel
          write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1=',&
@@ -2477,8 +2432,8 @@ subroutine evolve_icebergs(bergs)
               & dt*v1,dt*vveln
          write(stderrunit,*) 'diamonds, evolve_iceberg: on_tangential_plane=',on_tangential_plane
          write(stderrunit,*) 'Acceleration terms for position 1'
-         error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-         call accel(bergs, berg, i2, j2, xi, yj, latn, uvel3, vvel3, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn, bxn, byn - Added by Alon
+         error_flag=pos_within_cell(grd, lonn, latn, i1, j1, xi, yj)
+         call accel(bergs, berg, i, j, xi, yj, latn, uvel3, vvel3, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn, bxn, byn - Added by Alon
          
           write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'posn i,j,lon,lat,xi,yj=',i,j,lonn,latn,xi,yj
           write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'posn box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
@@ -2499,18 +2454,21 @@ subroutine evolve_icebergs(bergs)
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
       ! Saving all the iceberg variables.
-      berg%axn=axn !Alon
-      berg%ayn=ayn !Alon
-      berg%bxn=bxn !Alon
-      berg%byn=byn !Alon
-      berg%lon=lonn
-      berg%lat=latn
+      berg%axn=axn 
+      berg%ayn=ayn 
+      berg%bxn=bxn 
+      berg%byn=byn 
       berg%uvel=uveln
       berg%vvel=vveln
-      berg%ine=i
-      berg%jne=j
-      berg%xi=xi
-      berg%yj=yj
+
+      if (Runge_not_Verlet) then
+        berg%lon=lonn  ;   berg%lat=latn
+        berg%ine=i     ;   berg%jne=j
+        berg%xi=xi     ;   berg%yj=yj
+      else
+        if (.not. interactive_icebergs_on)  call update_verlet_position(bergs,berg) 
+      endif
+
       !call interp_flds(grd, i, j, xi, yj, berg%uo, berg%vo, berg%ui, berg%vi, berg%ua, berg%va, berg%ssh_x, berg%ssh_y, berg%sst)
       !if (debug) call print_berg(stderr(), berg, 'evolve_iceberg, final posn.')
       if (debug) call check_position(grd, berg, 'evolve_iceberg (bot)')
@@ -2525,21 +2483,14 @@ subroutine evolve_icebergs(bergs)
       berg=>bergs%list(grdi,grdj)%first
       do while (associated(berg)) ! loop over all bergs
       
-       lonn=0. ; latn =0.
-       call update_verlet_position(bergs,berg,lonn, latn) 
-
-       if (berg%iceberg_num .eq. 1) then
-         print *, 'TEST2:' , berg%lon, berg%lat
-         print *, 'test1: ', lonn, latn
-       endif
-
-        !Updating iceberg positions and velocities
-        berg%lon_new=lonn    ! This is the t=n+1 position (one step ahead)
-        berg%lat_new=latn
-        !berg%lon_new=berg%lon
-        !berg%lat_new=berg%lat
+       if (.not. Runge_not_Verlet)  call update_verlet_position(bergs,berg) 
+        
+       !Updating old velocities (for use in iceberg interactions)
         berg%uvel_old=berg%uvel
         berg%vvel_old=berg%vvel
+        berg%lon_old=berg%lon  ! lon_old, lat_old are not really needed for Verlet. But are needed for RK
+        berg%lat_old=berg%lat
+
         berg=>berg%next
       enddo ! loop over all bergs
     enddo ; enddo
@@ -2550,19 +2501,20 @@ subroutine evolve_icebergs(bergs)
 
 !#######################################################################
 !MP6
-subroutine update_verlet_position(bergs,berg,lonn, latn)
+subroutine update_verlet_position(bergs,berg)
 type(icebergs), intent(in), pointer :: bergs 
 type(iceberg), intent(in), pointer :: berg 
-real, intent(out) :: lonn, latn
 !Local variable
+real :: lonn, latn
+integer :: i_temp, j_temp
+real :: xi_temp, yj_temp
 real :: uvel3, vvel3
 real :: lon1, lat1, dxdl1, dydl
 real :: uvel1, vvel1, uvel2, vvel2
 real :: axn, ayn, bxn, byn 
 real :: u2, v2, x1, y1, xn, yn
-integer :: i_temp, j_temp
 integer :: i1, j1
-real :: xi_temp, yj_temp, dx
+real :: dx
 logical :: on_tangential_plane
 
       i1=berg%ine
@@ -2571,14 +2523,12 @@ subroutine update_verlet_position(bergs,berg,lonn, latn)
       on_tangential_plane=.false.
       if (berg%lat>89.) on_tangential_plane=.true.
 
-
         lon1=berg%lon; lat1=berg%lat
         if (on_tangential_plane) call rotpos_to_tang(lon1,lat1,x1,y1)
         dxdl1=r180_pi/(Rearth*cos(lat1*pi_180))
         dydl=r180_pi/Rearth
         uvel1=berg%uvel; vvel1=berg%vvel
 
-
         ! Loading past acceleartions - Alon
         axn=berg%axn; ayn=berg%ayn !Alon
         bxn=berg%bxn; byn=berg%byn !Alon 
@@ -2588,8 +2538,6 @@ subroutine update_verlet_position(bergs,berg,lonn, latn)
         vvel2=vvel1+(dt_2*ayn)+(dt_2*byn)                    !Alon
 
         dx=(dt*(uvel1+(dt_2*axn)+(dt_2*bxn)))
-        print *, 'dx= ' ,dx,  dt, dt_2
-
 
         if (on_tangential_plane) call rotvec_to_tang(lon1,uvel2,vvel2,xdot2,ydot2)
         u2=uvel2*dxdl1; v2=vvel2*dydl
@@ -2603,7 +2551,6 @@ subroutine update_verlet_position(bergs,berg,lonn, latn)
         endif
         dxdln=r180_pi/(Rearth*cos(latn*pi_180))
   
-
         ! Turn the velocities into u_star, v_star.(uvel3 is v_star) - Alon (not sure how this works with tangent plane)
         uvel3=uvel1+(dt_2*axn)                  !Alon
         vvel3=vvel1+(dt_2*ayn)                  !Alon
@@ -2613,6 +2560,18 @@ subroutine update_verlet_position(bergs,berg,lonn, latn)
         i_temp=i1;  j_temp=j1;  xi_temp = berg%xi;  yj_temp = berg%yj
         call adjust_index_and_ground(grd, lonn, latn, uvel3, vvel3, i_temp, j_temp, xi_temp, yj_temp, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
 
+        if (bounced) then
+          print *, 'you have been bounce: big time!',mpp_pe(),berg%iceberg_num,lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag 
+          berg%axn=0.0  ;  berg%ayn=0.0
+          berg%bxn=0.0  ;  berg%byn=0.0
+          berg%uvel=0.0 ;  berg%vvel=0.0
+        endif
+
+        !Updating positions and index
+        berg%lon=lonn      ;  berg%lat=latn
+        berg%ine=i_temp    ;  berg%jne=j_temp
+        berg%xi=xi_temp    ;  berg%yj=yj_temp
+
 end subroutine update_verlet_position
 
 !#######################################################################
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 39d36d6..f6ae90d 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -15,7 +15,7 @@ module ice_bergs_framework
 
 implicit none ; private
 
-integer :: buffer_width=28 !Changed from 20 to 28 by Alon 
+integer :: buffer_width=26 !Changed from 20 to 28 by Alon 
 integer :: buffer_width_traj=29  !Changed from 23 by Alon
 !integer, parameter :: buffer_width=26 !Changed from 20 to 26 by Alon 
 !integer, parameter :: buffer_width_traj=29  !Changed from 23 by Alon
@@ -140,7 +140,7 @@ module ice_bergs_framework
 type :: xyt
   real :: lon, lat, day
   real :: mass, thickness, width, length, uvel, vvel
-  real :: axn, ayn, bxn, byn, uvel_old, vvel_old, lat_new, lon_new  !Explicit and implicit accelerations !Alon 
+  real :: axn, ayn, bxn, byn, uvel_old, vvel_old, lat_old, lon_old  !Explicit and implicit accelerations !Alon 
   real :: uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, cn, hi, halo_berg
   real :: mass_of_bits, heat_density
   integer :: year, iceberg_num
@@ -151,7 +151,7 @@ module ice_bergs_framework
   type(iceberg), pointer :: prev=>null(), next=>null()
   ! State variables (specific to the iceberg, needed for restarts)
   real :: lon, lat, uvel, vvel, mass, thickness, width, length
-  real :: axn, ayn, bxn, byn, uvel_old, vvel_old, lon_new, lat_new !Explicit and implicit accelerations !Alon 
+  real :: axn, ayn, bxn, byn, uvel_old, vvel_old, lon_old, lat_old !Explicit and implicit accelerations !Alon 
   real :: start_lon, start_lat, start_day, start_mass, mass_scaling
   real :: mass_of_bits, heat_density
   real :: halo_berg  ! Equal to zero for bergs on computational domain, and =1 for bergs on the halo
@@ -1441,11 +1441,9 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
     buff%data(24,n)=berg%byn  !Alon
     buff%data(25,n)=float(berg%iceberg_num)
     buff%data(26,n)=berg%halo_berg 
-    buff%data(27,n)=berg%lon_new 
-    buff%data(28,n)=berg%lat_new
 
     if (max_bonds .gt. 0) then
-      counter=28 !how many data points being passed so far (must match above)
+      counter=26 !how many data points being passed so far (must match above)
       current_bond=>berg%first_bond
       do k = 1,max_bonds
         if (associated(current_bond)) then
@@ -1587,12 +1585,12 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n,grd, force_append, max_bonds_
     localberg%byn=buff%data(24,n) !Alon
     localberg%iceberg_num=nint(buff%data(25,n))
     localberg%halo_berg=buff%data(26,n) 
-    localberg%lon_new=buff%data(27,n) 
-    localberg%lat_new=buff%data(28,n) 
 
     !These quantities no longer need to be passed between processors
     localberg%uvel_old=localberg%uvel
     localberg%vvel_old=localberg%vvel
+    localberg%lon_old=localberg%lon 
+    localberg%lat_old=localberg%lat
 
     ! force_app=.true.
     if(force_app) then !force append with origin ine,jne (for I/O)
@@ -1618,7 +1616,7 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n,grd, force_append, max_bonds_
           write(stderrunit,*) localberg%axn,localberg%ayn !Alon
           write(stderrunit,*) localberg%bxn,localberg%byn !Alon
           write(stderrunit,*) localberg%uvel_old,localberg%vvel_old 
-          write(stderrunit,*) localberg%lon_new,localberg%lat_new 
+          write(stderrunit,*) localberg%lon_old,localberg%lat_old 
           write(stderrunit,*) grd%isc,grd%iec,grd%jsc,grd%jec
           write(stderrunit,*) grd%isd,grd%ied,grd%jsd,grd%jed
           write(stderrunit,*) grd%lon(grd%isc-1,grd%jsc-1),grd%lon(grd%iec,grd%jsc)
@@ -1635,7 +1633,7 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n,grd, force_append, max_bonds_
 
     this%first_bond=>null()
     if (max_bonds .gt. 0) then
-      counter=28 !how many data points being passed so far (must match above)
+      counter=26 !how many data points being passed so far (must match above)
       do k = 1,max_bonds
         other_berg_num=nint(buff%data(counter+(3*(k-1)+1),n))
         other_berg_ine=nint(buff%data(counter+(3*(k-1)+2),n))
@@ -2118,8 +2116,8 @@ logical function sameberg(berg1, berg2)
   if (berg1%byn.ne.berg2%byn) return  !Alon
   if (berg1%uvel_old.ne.berg2%uvel_old) return  !Alon
   if (berg1%vvel_old.ne.berg2%vvel_old) return  !Alon
-  if (berg1%lon_new.ne.berg2%lon_new) return  !Alon
-  if (berg1%lat_new.ne.berg2%lat_new) return  !Alon
+  if (berg1%lon_old .ne.berg2%lon_old) return  !Alon
+  if (berg1%lat_old.ne.berg2%lat_old) return  !Alon
   sameberg=.true. ! passing the above tests mean that bergs 1 and 2 are identical
 end function sameberg
 
@@ -2212,7 +2210,7 @@ subroutine print_berg(iochan, berg, label)
     ' axn,ayn=', berg%axn, berg%ayn, &
     ' bxn,byn=', berg%bxn, berg%byn, &
     ' uvel_old,vvel_old=', berg%uvel_old, berg%vvel_old, &
-    ' lon_new,lat_new=', berg%lon_new, berg%lat_new, &
+    ' lon_old,lat_old=', berg%lon_old, berg%lat_old, &
     ' p,n=', associated(berg%prev), associated(berg%next)
   write(iochan,'("diamonds, print_berg: ",a," pe=(",i3,") ",6(a,2f10.4))') &
     label, mpp_pe(), 'uo,vo=', berg%uo, berg%vo, 'ua,va=', berg%ua, berg%va, 'ui,vi=', berg%ui, berg%vi
@@ -2641,8 +2639,8 @@ subroutine record_posn(bergs)
       posn%byn=this%byn
       posn%uvel_old=this%uvel_old
       posn%vvel_old=this%vvel_old
-      posn%lon_new=this%lon_new
-      posn%lat_new=this%lat_new
+      posn%lon_old=this%lon_old
+      posn%lat_old=this%lat_old
       posn%halo_berg=this%halo_berg
   
       call push_posn(this%trajectory, posn)
@@ -3746,8 +3744,8 @@ subroutine bergs_chksum(bergs, txt, ignore_halo_violation)
       fld(i,12) = this%byn !added by Alon
       fld(i,13) = this%uvel_old !added by Alon
       fld(i,14) = this%vvel_old !added by Alon
-      fld(i,15) = this%lon_new !added by Alon
-      fld(i,16) = this%lat_new !added by Alon
+      fld(i,15) = this%lon_old !added by Alon
+      fld(i,16) = this%lat_old !added by Alon
       fld(i,17) = time_hash(this) !Changed from 9 to 17 by Alon
       fld(i,18) = pos_hash(this) !Changed from 10 to 18 by Alon
       fld(i,19) = float(iberg) !Changed from 11 to 19 by Alon
@@ -3842,8 +3840,8 @@ integer function berg_chksum(berg )
   rtmp(32)=berg%byn !Added by Alon
   rtmp(33)=berg%uvel_old !Added by Alon
   rtmp(34)=berg%vvel_old !Added by Alon
-  rtmp(35)=berg%lat_new !Added by Alon
-  rtmp(36)=berg%lon_new !Added by Alon
+  rtmp(35)=berg%lat_old !Added by Alon
+  rtmp(36)=berg%lon_old !Added by Alon
   itmp(37)=berg%halo_berg !Changed from 31 to 40 by Alon
   itmp(1:37)=transfer(rtmp,i8) !Changed from 28 to 37 by Alon
   itmp(38)=berg%start_year !Changed from 29 to 38 by Alon
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 9d291a8..b231d41 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -613,8 +613,8 @@ subroutine generate_bergs(bergs,Time)
         localberg%jne=j
         localberg%lon=bilin(grd, grd%lon, i, j, localberg%xi, localberg%yj)
         localberg%lat=bilin(grd, grd%lat, i, j, localberg%xi, localberg%yj)
-        localberg%lon_new=bilin(grd, grd%lon, i, j, localberg%xi, localberg%yj) !Alon
-        localberg%lat_new=bilin(grd, grd%lat, i, j, localberg%xi, localberg%yj) !Alon
+        localberg%lon_old=bilin(grd, grd%lon, i, j, localberg%xi, localberg%yj) !Alon
+        localberg%lat_old=bilin(grd, grd%lat, i, j, localberg%xi, localberg%yj) !Alon
         localberg%mass=bergs%initial_mass(1)
         localberg%thickness=bergs%initial_thickness(1)
         localberg%width=bergs%initial_width(1)
@@ -846,8 +846,8 @@ subroutine read_restart_bergs(bergs,Time)
          localberg%ayn=ayn(k) !Alon
          localberg%uvel_old=uvel(k) !Alon
          localberg%vvel_old=vvel(k) !Alon
-         localberg%lon_new=lon(k) !Alon
-         localberg%lat_new=lat(k) !Alon
+         localberg%lon_old=lon(k) !Alon
+         localberg%lat_old=lat(k) !Alon
          localberg%bxn=bxn(k) !Alon
          localberg%byn=byn(k) !Alon
          localberg%thickness=thickness(k)
@@ -937,8 +937,8 @@ subroutine generate_bergs(bergs,Time)
         localberg%jne=j
         localberg%lon=bilin(grd, grd%lon, i, j, localberg%xi, localberg%yj)
         localberg%lat=bilin(grd, grd%lat, i, j, localberg%xi, localberg%yj)
-        localberg%lon_new=bilin(grd, grd%lon, i, j, localberg%xi, localberg%yj) !Alon
-        localberg%lat_new=bilin(grd, grd%lat, i, j, localberg%xi, localberg%yj) !Alon
+        localberg%lon_old=bilin(grd, grd%lon, i, j, localberg%xi, localberg%yj) !Alon
+        localberg%lat_old=bilin(grd, grd%lat, i, j, localberg%xi, localberg%yj) !Alon
         localberg%mass=bergs%initial_mass(1)
         localberg%thickness=bergs%initial_thickness(1)
         localberg%width=bergs%initial_width(1)

From 5128472dc10faba21f72f02d1fdb8b4dd938e482 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Mon, 19 Oct 2015 15:30:24 -0400
Subject: [PATCH 090/361] The evolve_iceberg subroutine has been cleaned up and
 put in order.

Subroutines have been created for the verlet_stepping and Runge_Kutta_stepping to make the code easier to read. All sub-sub-routines inside evolve_icebergs have been made into subroutines, which again makes the code easier to read.

This commit should not change the answers.
---
 icebergs.F90 | 456 +++++++++++++++++++++++++++------------------------
 1 file changed, 244 insertions(+), 212 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 88168fd..6f427ae 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -47,7 +47,9 @@ module ice_bergs
 public icebergs_init, icebergs_end, icebergs_run, icebergs_stock_pe, icebergs
 public icebergs_incr_mass, icebergs_save_restart
 
-real, parameter :: pi_180=pi/180. ! Converts degrees to radians
+real, parameter :: pi_180=pi/180.  ! Converts degrees to radians
+real, parameter :: r180_pi=180./pi ! Converts radians to degrees
+real, parameter :: Rearth=6360000. ! Radius of earth (m)
 real, parameter :: rho_ice=916.7 ! Density of fresh ice @ 0oC (kg/m^3)
 real, parameter :: rho_water=999.8 ! Density of fresh water @ 0oC (kg/m^3)
 real, parameter :: rho_air=1.1 ! Density of air @ 0oC (kg/m^3) ???
@@ -245,14 +247,12 @@ subroutine calculate_force(bergs,berg,other_berg,IA_x, IA_y, u0, v0, u1, v1, P_i
      real :: P_11, P_12, P_21, P_22
      real :: M1, M2, M_min
      real :: u2, v2
-     real :: Rearth
      logical :: critical_interaction_damping_on
      real :: spring_coef, accel_spring, radial_damping_coef, p_ia_coef, tangental_damping_coef, bond_coef
      real, intent(inout) :: IA_x, IA_y 
      real, intent(inout) :: P_ia_11, P_ia_12, P_ia_22, P_ia_21, P_ia_times_u_x, P_ia_times_u_y
      logical ,intent(in) :: bonded
 
-      Rearth=6360.e3
       spring_coef=bergs%spring_coef
       !bond_coef=bergs%bond_coef 
       radial_damping_coef=bergs%radial_damping_coef
@@ -1984,70 +1984,30 @@ subroutine evolve_icebergs(bergs)
 type(icebergs), pointer :: bergs
 ! Local variables
 type(icebergs_gridded), pointer :: grd
-real :: uvel1, vvel1, lon1, lat1, u1, v1, dxdl1, ax1, ay1, axn1, ayn1 
-real :: uvel2, vvel2, lon2, lat2, u2, v2, dxdl2, ax2, ay2, axn2, ayn2
-real :: uvel3, vvel3, lon3, lat3, u3, v3, dxdl3, ax3, ay3, axn3, ayn3
-real :: uvel4, vvel4, lon4, lat4, u4, v4, dxdl4, ax4, ay4, axn4, ayn4
-real :: uveln, vveln, lonn, latn, un, vn, dxdln
-real :: x1, xdot1, xddot1, y1, ydot1, yddot1, xddot1n, yddot1n 
-real :: x2, xdot2, xddot2, y2, ydot2, yddot2, xddot2n, yddot2n
-real :: x3, xdot3, xddot3, y3, ydot3, yddot3, xddot3n, yddot3n
-real :: x4, xdot4, xddot4, y4, ydot4, yddot4, xddot4n, yddot4n
-real :: xn, xdotn, yn, ydotn, xddotn, yddotn
-real :: bxddot, byddot                                               ! Added by Alon
+type(iceberg), pointer :: berg
+real :: uveln, vveln, lonn, latn  
 real :: axn, ayn, bxn, byn                                           ! Added by Alon - explicit and implicit accelations from the previous step
-real :: r180_pi, dt, dt_2, dt_6, dydl, Rearth
-integer :: i, j
-integer :: i1,j1,i2,j2,i3,j3,i4,j4
 real :: xi, yj
-logical :: bounced, on_tangential_plane, error_flag
-logical :: Runge_not_Verlet  ! Runge_not_Verlet=1 for Runge Kutta, =0 for Verlet method. Added by Alon
-type(iceberg), pointer :: berg
-integer :: stderrunit
-logical :: interactive_icebergs_on  ! Flag to decide whether to use forces between icebergs.
+integer :: i, j
 integer :: grdi, grdj
-
-  ! 4th order Runge-Kutta to solve:
-  !    d/dt X = V,  d/dt V = A
-  ! with I.C.'s:
-  !    X=X1 and V=V1
-  !
-  !  A1 = A(X1)
-  !  X2 = X1+dt/2*V1 ; V2 = V1+dt/2*A1; A2=A(X2)
-  !  X3 = X1+dt/2*V2 ; V3 = V1+dt/2*A2; A3=A(X3)
-  !  X4 = X1+  dt*V3 ; V4 = V1+  dt*A3; A4=A(X4)
-  !
-  !  Xn = X1+dt*(V1+2*V2+2*V3+V4)/6
-  !  Vn = V1+dt*(A1+2*A2+2*A3+A4)/6
+integer :: stderrunit
+logical :: bounced, interactive_icebergs_on, Runge_not_Verlet 
   
   ! Get the stderr unit number
-
-
-  !Initialize variables
-  ax1=0. ;ax2 =0.; ax3=0.; ax4=0.; 
-  ay1=0. ;ay2 =0.; ay3=0.; ay4=0.; 
   stderrunit = stderr()
 
   ! For convenience
   grd=>bergs%grd
 
-  interactive_icebergs_on=bergs%interactive_icebergs_on  ! Loading directly from namelist/default , Alon
+  interactive_icebergs_on=bergs%interactive_icebergs_on
+  Runge_not_Verlet=bergs%Runge_not_Verlet
 
-  ! Common constants
-  r180_pi=1./pi_180
-  dt=bergs%dt
-  dt_2=0.5*dt
-  dt_6=dt/6.
-  Rearth=6360.e3
-
-  !Choosing time stepping scheme - Alon
- !Runge_not_Verlet=.False.    !Loading manually: true=Runge Kutta, False=Verlet   , Alon
-  Runge_not_Verlet=bergs%Runge_not_Verlet  ! Loading directly from namelist/default , Alon
 
   do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
     berg=>bergs%list(grdi,grdj)%first
     do while (associated(berg)) ! loop over all bergs
-
+ 
+      !Checking it everything is ok:
       if (.not. is_point_in_cell(bergs%grd, berg%lon, berg%lat, berg%ine, berg%jne) ) then
         write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lon',(i,i=grd%isd,grd%ied)
         do j=grd%jed,grd%jsd,-1
@@ -2063,11 +2023,217 @@ subroutine evolve_icebergs(bergs)
                  berg%jne,berg%lat,grd%lat(berg%ine-1,berg%jne-1),grd%lat(berg%ine,berg%jne)
         if (debug) call error_mesg('diamonds, evolve_iceberg','berg is in wrong starting cell!',FATAL)
       endif
-
       if (debug) call check_position(grd, berg, 'evolve_iceberg (top)')
 
-      !###########################################################################################################
-      if (Runge_not_Verlet) then !Start of the Runge-Kutta Loop
+
+      !Time stepping schemes:
+      if (Runge_not_Verlet) then 
+             call Runge_Kutta_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln,lonn, latn, i, j, xi, yj)
+      endif 
+      if (.not.Runge_not_Verlet) then 
+        call verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
+      endif 
+
+      ! Saving all the iceberg variables.
+      berg%axn=axn 
+      berg%ayn=ayn 
+      berg%bxn=bxn 
+      berg%byn=byn 
+      berg%uvel=uveln
+      berg%vvel=vveln
+
+      if (Runge_not_Verlet) then
+        berg%lon=lonn  ;   berg%lat=latn
+        berg%ine=i     ;   berg%jne=j
+        berg%xi=xi     ;   berg%yj=yj
+      else
+        if (.not. interactive_icebergs_on)  call update_verlet_position(bergs,berg) 
+      endif
+
+      !call interp_flds(grd, i, j, xi, yj, berg%uo, berg%vo, berg%ui, berg%vi, berg%ua, berg%va, berg%ssh_x, berg%ssh_y, berg%sst)
+      !if (debug) call print_berg(stderr(), berg, 'evolve_iceberg, final posn.')
+      if (debug) call check_position(grd, berg, 'evolve_iceberg (bot)')
+
+      berg=>berg%next
+    enddo ! loop over all bergs
+  enddo ; enddo
+
+  ! When we are using interactive icebergs, we update the (old) iceberg positions and velocities in a second loop, all together (to make code order invarient)
+  if (interactive_icebergs_on) then
+    do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
+      berg=>bergs%list(grdi,grdj)%first
+      do while (associated(berg)) ! loop over all bergs
+      
+       if (.not. Runge_not_Verlet)  call update_verlet_position(bergs,berg) 
+        
+       !Updating old velocities (for use in iceberg interactions)
+        berg%uvel_old=berg%uvel
+        berg%vvel_old=berg%vvel
+        berg%lon_old=berg%lon  ! lon_old, lat_old are not really needed for Verlet. But are needed for RK
+        berg%lat_old=berg%lat
+
+        berg=>berg%next
+      enddo ! loop over all bergs
+    enddo ; enddo
+  endif
+
+!contains
+end subroutine evolve_icebergs
+
+!######################################################################
+
+subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
+type(icebergs), pointer :: bergs
+type(iceberg), pointer, intent(inout) :: berg
+type(icebergs_gridded), pointer :: grd
+! Local variables
+real, intent(out) :: axn, ayn, bxn, byn, uveln, vveln
+real :: lonn, latn
+real :: uvel1, vvel1,  uvel2, vvel2, uvel3, vvel3
+real :: ax1, ay1 
+real :: x1,  y1, xddot1, yddot1, xi, yj 
+real :: xdot3, ydot3
+real :: xdotn, ydotn
+real :: dt, dt_2, dt_6, dydl
+logical :: bounced, on_tangential_plane, error_flag
+integer :: i, j 
+integer :: stderrunit
+
+  !Initialize variables
+
+       ! In this scheme a_n and b_n are saved from the previous timestep, giving the explicit and implicit parts of the acceleration, and a_np1, b_np1 are for the next time step
+       ! Note that ax1=a_np1/2 +b_np1, as calculated by the acceleration subrouting
+       ! Positions and velocity is updated by
+       ! X2 = X1+dt*V1+((dt^2)/2)*a_n +((dt^2)/2)*b_n = X1+dt*u_star +((dt^2)/2)*b_n 
+       ! V2 = V1+dt/2*a_n +dt/2*a_np1 +dt*b_n = u_star + dt/2*a_np1 + dt*b_np1 = u_star +dt*ax
+ 
+      !*************************************************************************************************
+
+  ! Get the stderr unit number
+    stderrunit = stderr()
+  ! For convenience
+    grd=>bergs%grd
+  ! Common constants
+    dt=bergs%dt
+    dt_2=0.5*dt
+
+        lonn = berg%lon ;   latn = berg%lat
+        axn  = berg%axn ;   ayn  = berg%ayn
+        bxn=   berg%bxn ;   byn  = berg%byn
+        uvel1=berg%uvel ;   vvel1=berg%vvel
+        i=berg%ine     ;   j=berg%jne
+        xi=berg%xi      ;   yj=berg%yj
+
+        ! Turn the velocities into u_star, v_star.(uvel3 is v_star) - Alon (not sure how this works with tangent plane)
+        uvel3=uvel1+(dt_2*axn)                  !Alon
+        vvel3=vvel1+(dt_2*ayn)                  !Alon
+
+        if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
+          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling)
+
+        ! Calling the acceleration   (note that the velocity is converted to u_star inside the accel script)
+        call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn, ayn, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
+  
+        !Solving for the new velocity
+        on_tangential_plane=.false.
+        if (berg%lat>89.) on_tangential_plane=.true.
+        if (on_tangential_plane) then
+          call rotvec_to_tang(lonn,uvel3,vvel3,xdot3,ydot3)
+          call rotvec_to_tang(lonn,ax1,ay1,xddot1,yddot1)
+          xdotn=xdot3+(dt*xddot1); ydotn=ydot3+(dt*yddot1)                                    !Alon
+          call rotvec_from_tang(lonn,xdotn,ydotn,uveln,vveln)
+        else
+          uveln=uvel3+(dt*ax1); vveln=vvel3+(dt*ay1)    !Alon , we call it uvel3, vvel3 until it is put into lat/long co-ordinates, where it becomes uveln, vveln
+        endif
+
+        !if (berg%iceberg_num .eq. 1) print *, 'New velocity: ', uveln, vveln
+
+       
+        !!!!!!!!!!!!!!! Debugging  !!!!!!!!!!!!!!!!!!!!!!!!!!!
+        error_flag=.false.
+        if (.not.error_flag) then
+          if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j)) error_flag=.true.
+        endif
+        if (error_flag) then
+         call print_fld(grd, grd%msk, 'msk')
+         call print_fld(grd, grd%ssh, 'ssh')
+         call print_fld(grd, grd%sst, 'sst')
+         call print_fld(grd, grd%hi, 'hi')
+         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
+         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lonn=',lonn,berg%lon
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: latn=',latn,berg%lat
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u3,un,u0=',uvel3,uveln,berg%uvel
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v3,vn,v0=',vvel3,vveln,berg%vvel
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1=',&
+              & dt*ax1
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ay1=',&
+              & dt*ay1
+         write(stderrunit,*) 'diamonds, evolve_iceberg: on_tangential_plane=',on_tangential_plane
+         write(stderrunit,*) 'Acceleration terms for position 1'
+         error_flag=pos_within_cell(grd, lonn, latn, i, j, xi, yj)
+         call accel(bergs, berg, i, j, xi, yj, latn, uvel3, vvel3, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn, bxn, byn - Added by Alon
+         
+          write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'posn i,j,lon,lat,xi,yj=',i,j,lonn,latn,xi,yj
+          write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'posn box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
+          call print_berg(stderrunit, berg, 'evolve_iceberg, out of cell at end!')
+          bounced=is_point_in_cell(bergs%grd, lonn, latn, i, j, explain=.true.)
+          if (debug) call error_mesg('diamonds, evolve_iceberg','berg is out of posn at end!',FATAL)
+          write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lon',(i,i=grd%isd,grd%ied)
+          do j=grd%jed,grd%jsd,-1
+            write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lon(i,j),i=grd%isd,grd%ied)
+          enddo
+          write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lat',(i,i=grd%isd,grd%ied)
+          do j=grd%jed,grd%jsd,-1
+            write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lat(i,j),i=grd%isd,grd%ied)
+          enddo
+        endif
+
+end subroutine verlet_stepping
+
+!######################################################################
+
+subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lonn, latn, i, j, xi, yj)
+type(icebergs), pointer :: bergs
+type(iceberg), pointer, intent(inout) :: berg
+type(icebergs_gridded), pointer :: grd
+real , intent(out) :: axn, ayn, bxn, byn, uveln, vveln,lonn, latn, xi, yj
+integer, intent(out) :: i, j
+real :: uvel1, vvel1, lon1, lat1, u1, v1, dxdl1, ax1, ay1, axn1, ayn1 
+real :: uvel2, vvel2, lon2, lat2, u2, v2, dxdl2, ax2, ay2, axn2, ayn2
+real :: uvel3, vvel3, lon3, lat3, u3, v3, dxdl3, ax3, ay3, axn3, ayn3
+real :: uvel4, vvel4, lon4, lat4, u4, v4, dxdl4, ax4, ay4, axn4, ayn4
+real :: x1, xdot1, xddot1, y1, ydot1, yddot1, xddot1n, yddot1n 
+real :: x2, xdot2, xddot2, y2, ydot2, yddot2, xddot2n, yddot2n
+real :: x3, xdot3, xddot3, y3, ydot3, yddot3, xddot3n, yddot3n
+real :: x4, xdot4, xddot4, y4, ydot4, yddot4, xddot4n, yddot4n
+real :: xn, xdotn, xddotn, yn, ydotn, yddotn, xddotnn, yddotnn
+real :: dt, dt_2, dt_6, dydl
+integer :: i1,j1,i2,j2,i3,j3,i4,j4
+integer :: stderrunit
+logical :: bounced, on_tangential_plane, error_flag
+  ! 4th order Runge-Kutta to solve:
+  !    d/dt X = V,  d/dt V = A
+  ! with I.C.'s:
+  !    X=X1 and V=V1
+  !
+  !  A1 = A(X1)
+  !  X2 = X1+dt/2*V1 ; V2 = V1+dt/2*A1; A2=A(X2)
+  !  X3 = X1+dt/2*V2 ; V3 = V1+dt/2*A2; A3=A(X3)
+  !  X4 = X1+  dt*V3 ; V4 = V1+  dt*A3; A4=A(X4)
+  !
+  !  Xn = X1+dt*(V1+2*V2+2*V3+V4)/6
+  !  Vn = V1+dt*(A1+2*A2+2*A3+A4)/6
+
+
+  ! Get the stderr unit number
+    stderrunit = stderr()
+  ! For convenience
+    grd=>bergs%grd
+  ! Common constants
+    dt=bergs%dt
+    dt_2=0.5*dt
+    dt_6=dt/6.
 
         i=berg%ine
         j=berg%jne
@@ -2355,170 +2521,34 @@ subroutine evolve_icebergs(bergs)
             write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lat(i,j),i=grd%isd,grd%ied)
           enddo
         endif
-     
-      endif ! End of the Runge-Kutta Loop -added by Alon  
-
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-      if (.not.Runge_not_Verlet) then !Start of the Verlet time_stepping -Whole loop added by Alon
-
-       ! In this scheme a_n and b_n are saved from the previous timestep, giving the explicit and implicit parts of the acceleration, and a_np1, b_np1 are for the next time step
-       ! Note that ax1=a_np1/2 +b_np1, as calculated by the acceleration subrouting
-       ! Positions and velocity is updated by
-       ! X2 = X1+dt*V1+((dt^2)/2)*a_n +((dt^2)/2)*b_n = X1+dt*u_star +((dt^2)/2)*b_n 
-       ! V2 = V1+dt/2*a_n +dt/2*a_np1 +dt*b_n = u_star + dt/2*a_np1 + dt*b_np1 = u_star +dt*ax
- 
-      !*************************************************************************************************!MP5
-        lonn = berg%lon ;   latn = berg%lat
-        axn  = berg%axn ;   ayn  = berg%ayn
-        bxn=   berg%bxn ;   byn  = berg%byn
-        uvel1=berg%uvel ;   vvel1=berg%vvel
-        i=berg%ine     ;   j=berg%jne
-        xi=berg%xi      ;   yj=berg%yj
-
-        ! Turn the velocities into u_star, v_star.(uvel3 is v_star) - Alon (not sure how this works with tangent plane)
-        uvel3=uvel1+(dt_2*axn)                  !Alon
-        vvel3=vvel1+(dt_2*ayn)                  !Alon
-
-        if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling)
-
-        ! Calling the acceleration   (note that the velocity is converted to u_star inside the accel script)
-        call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn, ayn, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
-  
-        !Solving for the new velocity
-        on_tangential_plane=.false.
-        if (berg%lat>89.) on_tangential_plane=.true.
-        if (on_tangential_plane) then
-          call rotvec_to_tang(lonn,uvel3,vvel3,xdot3,ydot3)
-          call rotvec_to_tang(lonn,ax1,ay1,xddot1,yddot1)
-          xdotn=xdot3+(dt*xddot1); ydotn=ydot3+(dt*yddot1)                                    !Alon
-          call rotvec_from_tang(lonn,xdotn,ydotn,uveln,vveln)
-        else
-          uveln=uvel3+(dt*ax1); vveln=vvel3+(dt*ay1)    !Alon , we call it uvel3, vvel3 until it is put into lat/long co-ordinates, where it becomes uveln, vveln
-        endif
-
-        !if (berg%iceberg_num .eq. 1) print *, 'New velocity: ', uveln, vveln
-       !*************************************************************************************************!MP5
-        !!!!!!!!!!!!!!! Debugging  !!!!!!!!!!!!!!!!!!!!!!!!!!!
-        error_flag=.false.
-        if (.not.error_flag) then
-          if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j)) error_flag=.true.
-        endif
-        if (error_flag) then
-         call print_fld(grd, grd%msk, 'msk')
-         call print_fld(grd, grd%ssh, 'ssh')
-         call print_fld(grd, grd%sst, 'sst')
-         call print_fld(grd, grd%hi, 'hi')
-         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
-         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
-         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: i1,i=',i1,i
-         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: j1,j=',j1,j
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lonn=',lonn,berg%lon
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: latn=',latn,berg%lat
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u3,un,u0=',uvel3,uveln,berg%uvel
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v3,vn,v0=',vvel3,vveln,berg%vvel
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1=',&
-              & dt*ax1
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ay1=',&
-              & dt*ay1
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u3,un,u0=',&
-              & dt*uvel3,dt*uveln,dt*berg%uvel
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v3,vn,v0=',&
-              & dt*vvel3,dt*vveln,dt*berg%vvel
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u_n (deg)=',&
-              & dt*u1,dt*uveln
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v_n (deg)=',&
-              & dt*v1,dt*vveln
-         write(stderrunit,*) 'diamonds, evolve_iceberg: on_tangential_plane=',on_tangential_plane
-         write(stderrunit,*) 'Acceleration terms for position 1'
-         error_flag=pos_within_cell(grd, lonn, latn, i1, j1, xi, yj)
-         call accel(bergs, berg, i, j, xi, yj, latn, uvel3, vvel3, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn, bxn, byn - Added by Alon
-         
-          write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'posn i,j,lon,lat,xi,yj=',i,j,lonn,latn,xi,yj
-          write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'posn box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
-          call print_berg(stderrunit, berg, 'evolve_iceberg, out of cell at end!')
-          bounced=is_point_in_cell(bergs%grd, lonn, latn, i, j, explain=.true.)
-          if (debug) call error_mesg('diamonds, evolve_iceberg','berg is out of posn at end!',FATAL)
-          write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lon',(i,i=grd%isd,grd%ied)
-          do j=grd%jed,grd%jsd,-1
-            write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lon(i,j),i=grd%isd,grd%ied)
-          enddo
-          write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lat',(i,i=grd%isd,grd%ied)
-          do j=grd%jed,grd%jsd,-1
-            write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lat(i,j),i=grd%isd,grd%ied)
-          enddo
-        endif
-
-      endif ! End of the Verlet Stepiing -added by Alon  
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-      ! Saving all the iceberg variables.
-      berg%axn=axn 
-      berg%ayn=ayn 
-      berg%bxn=bxn 
-      berg%byn=byn 
-      berg%uvel=uveln
-      berg%vvel=vveln
 
-      if (Runge_not_Verlet) then
-        berg%lon=lonn  ;   berg%lat=latn
-        berg%ine=i     ;   berg%jne=j
-        berg%xi=xi     ;   berg%yj=yj
-      else
-        if (.not. interactive_icebergs_on)  call update_verlet_position(bergs,berg) 
-      endif
-
-      !call interp_flds(grd, i, j, xi, yj, berg%uo, berg%vo, berg%ui, berg%vi, berg%ua, berg%va, berg%ssh_x, berg%ssh_y, berg%sst)
-      !if (debug) call print_berg(stderr(), berg, 'evolve_iceberg, final posn.')
-      if (debug) call check_position(grd, berg, 'evolve_iceberg (bot)')
-
-      berg=>berg%next
-    enddo ! loop over all bergs
-  enddo ; enddo
-
-  ! When we are using interactive icebergs, we update the (old) iceberg positions and velocities in a second loop, all together (to make code order invarient)
-  if (interactive_icebergs_on) then
-    do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
-      berg=>bergs%list(grdi,grdj)%first
-      do while (associated(berg)) ! loop over all bergs
-      
-       if (.not. Runge_not_Verlet)  call update_verlet_position(bergs,berg) 
-        
-       !Updating old velocities (for use in iceberg interactions)
-        berg%uvel_old=berg%uvel
-        berg%vvel_old=berg%vvel
-        berg%lon_old=berg%lon  ! lon_old, lat_old are not really needed for Verlet. But are needed for RK
-        berg%lat_old=berg%lat
-
-        berg=>berg%next
-      enddo ! loop over all bergs
-    enddo ; enddo
-  endif
-
-
-contains
+        end subroutine Runge_Kutta_stepping
 
 !#######################################################################
 !MP6
 subroutine update_verlet_position(bergs,berg)
 type(icebergs), intent(in), pointer :: bergs 
 type(iceberg), intent(in), pointer :: berg 
+type(icebergs_gridded), pointer :: grd
 !Local variable
 real :: lonn, latn
-integer :: i_temp, j_temp
-real :: xi_temp, yj_temp
+real :: xi, yj
 real :: uvel3, vvel3
 real :: lon1, lat1, dxdl1, dydl
 real :: uvel1, vvel1, uvel2, vvel2
-real :: axn, ayn, bxn, byn 
+real :: axn, ayn, bxn, byn
+real :: xdot2, ydot2, dxdln
 real :: u2, v2, x1, y1, xn, yn
-integer :: i1, j1
-real :: dx
-logical :: on_tangential_plane
+real :: dx, dt, dt_2
+integer :: i, j
+logical :: on_tangential_plane, error_flag, bounced
+
+  ! For convenience
+    grd=>bergs%grd
+  ! Common constants
+  dt=bergs%dt
+  dt_2=0.5*dt
 
-      i1=berg%ine
-      j1=berg%jne
 
       on_tangential_plane=.false.
       if (berg%lat>89.) on_tangential_plane=.true.
@@ -2557,8 +2587,8 @@ subroutine update_verlet_position(bergs,berg)
 
         ! Adjusting mass...
         !MP3
-        i_temp=i1;  j_temp=j1;  xi_temp = berg%xi;  yj_temp = berg%yj
-        call adjust_index_and_ground(grd, lonn, latn, uvel3, vvel3, i_temp, j_temp, xi_temp, yj_temp, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
+        i=berg%ine;  j=berg%jne;  xi = berg%xi;  yj = berg%yj
+        call adjust_index_and_ground(grd, lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
 
         if (bounced) then
           print *, 'you have been bounce: big time!',mpp_pe(),berg%iceberg_num,lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag 
@@ -2569,8 +2599,8 @@ subroutine update_verlet_position(bergs,berg)
 
         !Updating positions and index
         berg%lon=lonn      ;  berg%lat=latn
-        berg%ine=i_temp    ;  berg%jne=j_temp
-        berg%xi=xi_temp    ;  berg%yj=yj_temp
+        berg%ine=i    ;  berg%jne=j
+        berg%xi=xi    ;  berg%yj=yj
 
 end subroutine update_verlet_position
 
@@ -2630,6 +2660,10 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
 real, parameter :: posn_eps=0.05
 integer :: icount, i0, j0, inm, jnm
 real :: xi0, yj0, lon0, lat0
+integer :: stderrunit
+
+  ! Get the stderr unit number
+    stderrunit = stderr()
 
   bounced=.false.
   error=.false.
@@ -2827,7 +2861,7 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
 
  end subroutine adjust_index_and_ground
 
-end subroutine evolve_icebergs
+!end subroutine evolve_icebergs
 
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
@@ -2837,11 +2871,9 @@ subroutine rotpos_to_tang(lon, lat, x, y)
   real, intent(out) :: x, y
   ! Local variables
   real :: r,colat,clon,slon
-  real :: Rearth
   integer :: stderrunit
 
   stderrunit = stderr()
-  Rearth=6360.e3
 
   if (lat>90.) then
       write(stderrunit,*) 'diamonds, rotpos_to_tang: lat>90 already!',lat

From f7419054f4e768e04cbd15c34e6d5d0fe1701c72 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 21 Oct 2015 11:39:41 -0400
Subject: [PATCH 091/361] Two and a half bugs fixed:

1) Bug in the subroutine which reads the bond files. The write('  ') command was causing the model to crash when very large tabular icebergs were being loaded. The bug is fixed by using the write(stderrunit).

2) A bug is fixed involving the reading restart files of iceberg bonds where the tabular iceberg extends over more than one processor. The bug is fixed by updating the halos before reading the iceberg bonds. Then reading the bonds restart file, and forming all bonds which have one half of the bond in a processor. Note: it is neccesary to form the bonds where the first iceberg in the iceberg pair is in the halo, and the other bond is in the computational domain. This is because when the halo is cleared, all the iceberg bonds are in that halo are cleared too. If the halo bonds are not formed properly, they causes issues to the other bonds even though they are cleared.
On the other hand, halo-halo bonds, and halo-(other PE) bonds can be left unformed and this does not cause any problems.

3) A bug was occuring which caused the model to enter an infinite loop when a 10 by 10 tabular iceberg was used. After a lot of time trying to debug, this bug miraculouly disappeared by itself, and now I can not make it come back. Perhaps it will reemerge in the future, but for now it does not seem to be an issue.

The tabular icebergs now seem to be working quite well. A 10 by 10 berg can advect for a month. A 4 by 4 iceberg has been advecting for 5 months.
---
 icebergs.F90           |  1 +
 icebergs_framework.F90 | 55 ++++++++++++++++++---------------
 icebergs_io.F90        | 69 ++++++++++++++++++++++++++++--------------
 3 files changed, 78 insertions(+), 47 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 6f427ae..9cbb581 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -118,6 +118,7 @@ subroutine icebergs_init(bergs, &
   if (really_debug) call print_bergs(stderrunit,bergs,'icebergs_init, initial status')
 
   if (bergs%iceberg_bonds_on) then
+    call update_halo_icebergs(bergs)
     if (bergs%manually_initialize_bonds) then
       call initialize_iceberg_bonds(bergs)
     else
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index f6ae90d..edefdce 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -300,8 +300,8 @@ subroutine ice_bergs_framework_init(bergs, &
 integer :: verbose_hrs=24 ! Period between verbose messages
 integer :: max_bonds=6 ! Maximum number of iceberg bond passed between processors
 real :: rho_bergs=850. ! Density of icebergs
-real :: spring_coef=3.e-9  ! Spring contant for iceberg interactions (this seems to be the highest stable value)
-real :: bond_coef=3.e-9  ! Spring contant for iceberg bonds - not being used right now
+real :: spring_coef=1.e-8  ! Spring contant for iceberg interactions (this seems to be the highest stable value)
+real :: bond_coef=1.e-8 ! Spring contant for iceberg bonds - not being used right now
 real :: radial_damping_coef=1.e-4     ! Coef for relative iceberg motion damping (radial component) -Alon
 real :: tangental_damping_coef=2.e-5     ! Coef for relative iceberg motion damping (tangental component) -Alon
 real :: LoW_ratio=1.5 ! Initial ratio L/W for newly calved icebergs
@@ -851,7 +851,6 @@ subroutine update_halo_icebergs(bergs)
    grd=>bergs%grd
 
 
-
 !For debugging
 if (halo_debugging) then
   do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
@@ -866,7 +865,6 @@ subroutine update_halo_icebergs(bergs)
 endif
 
 
-
 ! Step 1: Clear the current halos
 
   call mpp_sync_self()
@@ -903,6 +901,7 @@ subroutine update_halo_icebergs(bergs)
     nbergs_start=count_bergs(bergs)
   endif
 
+  call mpp_sync_self()
 !#######################################################
 
 ! Step 2: Updating the halos  - This code is mostly copied from send_to_other_pes
@@ -911,7 +910,6 @@ subroutine update_halo_icebergs(bergs)
   ! Find number of bergs that headed east/west
   nbergs_to_send_e=0
   nbergs_to_send_w=0
-
   !Bergs on eastern side of the processor
   do grdj = grd%jsc,grd%jec ; do grdi = grd%iec-halo_width+1,grd%iec  
     this=>bergs%list(grdi,grdj)%first
@@ -927,6 +925,7 @@ subroutine update_halo_icebergs(bergs)
     enddo
   enddo; enddo
 
+
   !Bergs on the western side of the processor
   do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%isc+halo_width-1 
     this=>bergs%list(grdi,grdj)%first
@@ -942,7 +941,6 @@ subroutine update_halo_icebergs(bergs)
   enddo; enddo
 
 
-
   ! Send bergs east
   if (grd%pe_E.ne.NULL_PE) then
     call mpp_send(nbergs_to_send_e, plen=1, to_pe=grd%pe_E, tag=COMM_TAG_1)
@@ -959,7 +957,6 @@ subroutine update_halo_icebergs(bergs)
     endif
   endif
 
-  call mpp_sync_self()
   ! Receive bergs from west
   if (grd%pe_W.ne.NULL_PE) then
     nbergs_rcvd_from_w=-999
@@ -1101,11 +1098,11 @@ subroutine update_halo_icebergs(bergs)
     nbergs_rcvd_from_n=0
   endif
 
-  call mpp_sync_self()
 
 
 !For debugging
 if (halo_debugging) then
+  call mpp_sync_self()
   do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
     this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
@@ -1115,8 +1112,6 @@ subroutine update_halo_icebergs(bergs)
   enddo; enddo
 endif
 
-
-
 end subroutine update_halo_icebergs
 
 
@@ -2316,13 +2311,12 @@ subroutine bond_address_update(bergs)
         if  (associated(current_bond%other_berg)) then
           current_bond%other_berg_ine=current_bond%other_berg%ine
           current_bond%other_berg_jne=current_bond%other_berg%jne
-          current_bond=>current_bond%next_bond
         else
           if (berg%halo_berg .lt. 0.5) then     
             call error_mesg('diamonds, bond address update', 'other berg in bond not assosiated!', FATAL)
           endif
-          current_bond=>current_bond%next_bond
         endif
+        current_bond=>current_bond%next_bond
       enddo
       berg=>berg%next
     enddo
@@ -2349,13 +2343,16 @@ subroutine show_all_bonds(bergs)
     do while (associated(berg)) ! loop over all bergs
       current_bond=>berg%first_bond
       do while (associated(current_bond)) ! loop over all bonds
-
         print *, 'Show Bond1 :', berg%iceberg_num, current_bond%other_berg_num, current_bond%other_berg_ine, current_bond%other_berg_jne,  mpp_pe()
         if  (associated(current_bond%other_berg)) then
-        print *, 'Show Bond2 :', berg%iceberg_num, current_bond%other_berg_num, current_bond%other_berg%ine, current_bond%other_berg%jne,  mpp_pe()
-                print *, 'Bond matching', current_bond%other_berg%iceberg_num, current_bond%other_berg_num, mpp_pe()
+          if (current_bond%other_berg%iceberg_num .ne. current_bond%other_berg_num) then
+            print *, 'Bond matching', berg%iceberg_num,current_bond%other_berg%iceberg_num, current_bond%other_berg_num, mpp_pe()
+            call error_mesg('diamonds, show all bonds:', 'The bonds are not matching properly!', FATAL)
+          endif
+        else
+            print *, 'This bond has an non-assosiated other berg :', berg%iceberg_num, current_bond%other_berg_num, current_bond%other_berg_ine, current_bond%other_berg_jne,  mpp_pe()
         endif
-       current_bond=>current_bond%next_bond
+        current_bond=>current_bond%next_bond
       enddo
       berg=>berg%next
     enddo
@@ -2430,11 +2427,11 @@ subroutine connect_all_bonds(bergs)
               print * ,'non-halo berg unmatched: ', berg%iceberg_num, mpp_pe(), current_bond%other_berg_num, current_bond%other_berg_ine 
               call error_mesg('diamonds, connect_all_bonds', 'A non-halo bond is missing!!!', FATAL)
             else  ! This is not a problem if the partner berg is not yet in the halo
-              if (  (current_bond%other_berg_ine .gt.grd%isd-1) .and. (current_bond%other_berg_ine .lt.grd%ied+1) &
-                .and.  (current_bond%other_berg_jne .gt.grd%jsd-1) .and. (current_bond%other_berg_jne .lt.grd%jed+1) ) then      
-                print * ,'halo berg unmatched: ',mpp_pe(),  berg%iceberg_num, current_bond%other_berg_num, current_bond%other_berg_ine,current_bond%other_berg_jne 
-                call error_mesg('diamonds, connect_all_bonds', 'A halo bond is missing!!!', WARNING)
-              endif
+              !if (  (current_bond%other_berg_ine .gt.grd%isd-1) .and. (current_bond%other_berg_ine .lt.grd%ied+1) &
+                !.and.  (current_bond%other_berg_jne .gt.grd%jsd-1) .and. (current_bond%other_berg_jne .lt.grd%jed+1) ) then      
+                !print * ,'halo berg unmatched: ',mpp_pe(),  berg%iceberg_num, current_bond%other_berg_num, current_bond%other_berg_ine,current_bond%other_berg_jne 
+                !call error_mesg('diamonds, connect_all_bonds', 'A halo bond is missing!!!', WARNING)
+              !endif
             endif
           endif
         endif
@@ -2449,7 +2446,6 @@ subroutine connect_all_bonds(bergs)
     nbonds=0
     call count_bonds(bergs, nbonds,check_bond_quality)
   endif
-
 end subroutine connect_all_bonds
 
 
@@ -2963,14 +2959,16 @@ end function find_cell_by_search
 
 ! ##############################################################################
 
-subroutine find_individual_iceberg(bergs,iceberg_num, ine, jne, berg_found)
+subroutine find_individual_iceberg(bergs,iceberg_num, ine, jne, berg_found, search_data_domain)
 type(icebergs), pointer :: bergs
 type(iceberg), pointer :: this
 type(icebergs_gridded), pointer :: grd
 integer :: grdi, grdj
 integer, intent(in) :: iceberg_num
+logical, intent(in) :: search_data_domain
 integer, intent(out) :: ine, jne
 real, intent(out) :: berg_found
+integer :: ilim1, ilim2, jlim1, jlim2
 
 berg_found=0.0
 ine=999
@@ -2978,7 +2976,16 @@ subroutine find_individual_iceberg(bergs,iceberg_num, ine, jne, berg_found)
   ! For convenience
     grd=>bergs%grd
     
-    do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
+    if (search_data_domain) then
+        ilim1 = grd%isd  ; ilim2=grd%ied  ; jlim1 = grd%jsd  ; jlim2=grd%jed
+    else
+        ilim1 = grd%isc  ; ilim2=grd%iec  ; jlim1 = grd%jsc  ; jlim2=grd%jec
+    endif
+
+
+    do grdj = jlim1, jlim2 ; do grdi = ilim1, ilim2
+    !do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
+    !do grdj = bergs%grd%jsd,bergs%grd%jed ; do grdi = bergs%grd%isd,bergs%grd%ied
       this=>bergs%list(grdi,grdj)%first
       do while (associated(this))
         if (iceberg_num .eq. this%iceberg_num) then
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index b231d41..150948a 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -863,6 +863,7 @@ subroutine read_restart_bergs(bergs,Time)
          localberg%mass_of_bits=mass_of_bits(k)
          localberg%halo_berg=halo_berg(k)
          localberg%heat_density=heat_density(k)
+         localberg%first_bond=>null()
          if (really_debug) lres=is_point_in_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, explain=.true.)
          lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
         !call add_new_berg_to_list(bergs%first, localberg, quick=.true.)
@@ -1036,9 +1037,10 @@ subroutine read_restart_bonds(bergs,Time)
 integer :: all_pe_number_perfect_bonds, all_pe_number_partial_bonds
 integer :: all_pe_number_first_bonds_matched, all_pe_number_second_bonds_matched
 integer :: ine, jne
+logical :: search_data_domain
 real :: berg_found, berg_found_all_pe
 integer, allocatable, dimension(:) :: first_berg_num,   &
-                                      other_berg_num,  &
+                                      other_berg_num,   &
                                       first_berg_jne,   &
                                       first_berg_ine,   &
                                       other_berg_jne,   &
@@ -1084,40 +1086,54 @@ subroutine read_restart_bonds(bergs,Time)
     number_second_bonds_matched=0
     number_perfect_bonds=0
     number_partial_bonds=0
+
     do k=1, nbonds_in_file
       
 
        ! If i,j in restart files are not good, then we find the berg position of the bond addresses manually:
        if (ignore_ij_restart) then 
          !Finding first iceberg in bond
-         ine=999 ; jne=999 ; berg_found=0.0
-         call find_individual_iceberg(bergs,first_berg_num(k), ine, jne,berg_found)
+         ine=999 ; jne=999 ; berg_found=0.0 ; search_data_domain=.true.
+         call find_individual_iceberg(bergs,first_berg_num(k), ine, jne,berg_found,search_data_domain)
          berg_found_all_pe=berg_found
          call mpp_sum(berg_found_all_pe)
-         !print *, mpp_pe(), berg_found_all_pe, berg_found, first_berg_num(k),'here'
          if (berg_found_all_pe .gt. 0.5) then
-           first_berg_ine(k)=ine
-           first_berg_jne(k)=jne
+             first_berg_ine(k)=ine
+             first_berg_jne(k)=jne
+           !endif
          else
           call error_mesg('read_restart_bonds_bergs_new', 'First iceberg in bond not found on any pe', FATAL)
          endif
+         if (berg_found_all_pe .lt. 0.5) then
+                 print * , 'First bond berg not located: ', first_berg_num(k),berg_found, mpp_pe(),ine, jne
+             call error_mesg('read_restart_bonds_bergs_new', 'First bond iceberg not located', FATAL)
+         endif
+         !else
 
          !Finding other iceberg other iceberg
-         ine=999 ; jne=999 ; berg_found=0.0
-         call find_individual_iceberg(bergs,other_berg_num(k), ine, jne, berg_found)
-         call mpp_sum(berg_found)
-         if (berg_found .gt. 0.5) then
-           other_berg_ine(k)=ine
-           other_berg_jne(k)=jne
+         ine=999 ; jne=999 ; berg_found=0.0 ; search_data_domain =.true.
+         call find_individual_iceberg(bergs,other_berg_num(k), ine, jne, berg_found,search_data_domain)
+         berg_found_all_pe=berg_found
+         call mpp_sum(berg_found_all_pe)
+         if (berg_found_all_pe .gt. 0.5) then
+           !if (berg_found_all_pe .gt. 1.5) then
+           !  call error_mesg('read_restart_bonds_bergs_new', 'Other iceberg bond found on more than one pe', FATAL)
+           !else
+             other_berg_ine(k)=ine
+             other_berg_jne(k)=jne
+           !endif
          else
           call error_mesg('read_restart_bonds_bergs_new', 'Other iceberg in bond not found on any pe', FATAL)
          endif
+         if (berg_found_all_pe .lt. 0.5) then
+                 print * , 'First bond berg not located: ', other_berg_num(k),berg_found, mpp_pe(),ine, jne
+             call error_mesg('read_restart_bonds_bergs_new', 'First bond iceberg not located', FATAL)
+         endif
        endif
 
-
       ! Decide whether the first iceberg is on the processeor
-      if ( first_berg_ine(k)>=grd%isc .and. first_berg_ine(k)<=grd%iec .and. &
-        first_berg_jne(k)>=grd%jsc .and.first_berg_jne(k)<=grd%jec ) then
+      if ( (first_berg_ine(k)>=grd%isd) .and. (first_berg_ine(k)<=grd%ied) .and. &
+        (first_berg_jne(k)>=grd%jsd) .and. (first_berg_jne(k)<=grd%jed) ) then
         number_first_bonds_matched=number_first_bonds_matched+1
      
         ! Search for the first berg, which the bond belongs to
@@ -1128,16 +1144,21 @@ subroutine read_restart_bonds(bergs,Time)
           if (this%iceberg_num == first_berg_num(k)) then
             first_berg_found=.true.
             first_berg=>this
+            if (first_berg%halo_berg.gt.0.5) print *, 'bonding halo berg:', first_berg_num(k),  first_berg_ine(k),first_berg_jne(k) ,grd%isc, grd%iec, mpp_pe()
             this=>null()
           else  
             this=>this%next
           endif
         enddo
-      
+     
+!Note, this is a bug since there are no bergs in the halos up to here, are there?
+
         ! Decide whether the second iceberg is on the processeor (data domain)
         second_berg_found=.false.
-        if ( other_berg_ine(k)>=grd%isd .and. other_berg_ine(k)<=grd%ied .and. &
-          other_berg_jne(k)>=grd%jsd .and.other_berg_jne(k)<=grd%jed ) then
+        !if ( other_berg_ine(k)>=grd%isc-1 .and. other_berg_ine(k)<=grd%iec+1 .and. &
+        !  other_berg_jne(k)>=grd%jsc-1 .and.other_berg_jne(k)<=grd%jec+1 ) then
+        if ( (other_berg_ine(k)>=grd%isd) .and. (other_berg_ine(k)<=grd%ied) .and. &
+          (other_berg_jne(k)>=grd%jsd) .and.(other_berg_jne(k)<=grd%jed) ) then
           number_second_bonds_matched=number_second_bonds_matched+1
 
           ! Search for the second berg, which the bond belongs to
@@ -1160,10 +1181,11 @@ subroutine read_restart_bonds(bergs,Time)
             call form_a_bond(first_berg, other_berg_num(k), other_berg_ine(k), other_berg_jne(k),  second_berg)
             number_perfect_bonds=number_perfect_bonds+1
           else
-            call form_a_bond(first_berg, other_berg_num(k),other_berg_ine(k),other_berg_jne(k))
+            !print *, 'Forming a bond of the second type', mpp_pe(), first_berg_num(k),  other_berg_num(k)
+            !call form_a_bond(first_berg, other_berg_num(k),other_berg_ine(k),other_berg_jne(k))
           endif
         else
-          write(*,'(a,i8,a)') 'diamonds, bond read restart : ','Not enough partial bonds formed', k, mpp_pe(), nbonds_in_file
+          write(stderrunit,*) 'diamonds, bond read restart : ','Not enough partial bonds formed', k, mpp_pe(), nbonds_in_file
           call error_mesg('read_restart_bonds_bergs_new', 'Failure with reading bonds: First bond not found on pe', FATAL)
         endif
       endif
@@ -1178,15 +1200,15 @@ subroutine read_restart_bonds(bergs,Time)
     call mpp_sum(all_pe_number_partial_bonds)
 
     if (all_pe_number_partial_bonds .lt. nbonds_in_file) then
-      write(*,'(a,i8,a)') 'diamonds, bond read restart : ','Not enough partial bonds formed', all_pe_number_partial_bonds , nbonds_in_file
+      write(stderrunit,*) 'diamonds, bond read restart : ','Not enough partial bonds formed', all_pe_number_partial_bonds , nbonds_in_file
       call error_mesg('read_restart_bonds_bergs_new', 'Not enough partial bonds formed', FATAL)
     endif
     
     if (all_pe_number_perfect_bonds .lt. nbonds_in_file) then
       call mpp_sum(all_pe_number_first_bonds_matched)
       call mpp_sum(all_pe_number_second_bonds_matched)
-      write(*,'(a,i8,a)') 'diamonds, bond read restart : ','Warning, some bonds are not fully formed',  all_pe_number_first_bonds_matched , nbonds_in_file
-      write(*,'(a,i8,a)') 'diamonds, bond read restart : ','Number of first and second bonds matched:', all_pe_number_second_bonds_matched , nbonds_in_file
+      write(stderrunit,*)  'diamonds, bond read restart : ','Warning, some bonds are not fully formed',  all_pe_number_first_bonds_matched , nbonds_in_file
+      write(stderrunit,*)  'diamonds, bond read restart : ','Number of first and second bonds matched:', all_pe_number_second_bonds_matched , nbonds_in_file
       call error_mesg('read_restart_bonds_bergs_new', 'Not enough perfect bonds formed', NOTE)
     endif
 
@@ -1198,6 +1220,7 @@ subroutine read_restart_bonds(bergs,Time)
             other_berg_ine,  &
             other_berg_jne )
   endif
+
 end subroutine read_restart_bonds
 
 ! ##############################################################################

From 301faee463b899a335e4050fe05141c0e4d9ab71 Mon Sep 17 00:00:00 2001
From: Zhi Liang <Zhi.Liang@noaa.gov>
Date: Tue, 12 Jan 2016 16:11:55 -0500
Subject: [PATCH 092/361] fix the crash issue when reading from distributed
 file and some file has zero bergs. Fix on print format bug

---
 icebergs_framework.F90 |   2 +-
 icebergs_io.F90        | 165 +++++++++++++++++++++--------------------
 2 files changed, 85 insertions(+), 82 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 30066d1..4d255d5 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -1617,7 +1617,7 @@ subroutine print_berg(iochan, berg, label)
   write(iochan,'("diamonds, print_berg: ",a," pe=(",i3,") start lon,lat,yr,day,mass=",2f10.4,i5,f7.2,es12.4)') &
     label, mpp_pe(), berg%start_lon, berg%start_lat, &
     berg%start_year, berg%start_day, berg%start_mass
-  write(iochan,'("diamonds, print_berg: ",a," pe=(",i3,a,2i5,3(a,2f10.4),a,2l2)') &
+  write(iochan,'("diamonds, print_berg: ",a," pe=(",i3,a,2i5,7(a,2f10.4),a,2l2)') &
     label, mpp_pe(), ') i,j=',berg%ine, berg%jne, &
     ' xi,yj=', berg%xi, berg%yj, &
     ' lon,lat=', berg%lon, berg%lat, &
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 5017f67..63315ad 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -684,88 +684,89 @@ subroutine read_restart_bergs(bergs,Time)
      allocate(ine(nbergs_in_file))
      allocate(jne(nbergs_in_file))
      allocate(start_year(nbergs_in_file))
+  endif
 
-     call read_unlimited_axis(filename,'lon',lon,domain=grd%domain)
-     call read_unlimited_axis(filename,'lat',lat,domain=grd%domain)
-     call read_unlimited_axis(filename,'lon_old',lon_old,domain=grd%domain) !Alon
-     call read_unlimited_axis(filename,'lat_old',lat_old,domain=grd%domain) !Alon
-     call read_unlimited_axis(filename,'uvel',uvel,domain=grd%domain)
-     call read_unlimited_axis(filename,'vvel',vvel,domain=grd%domain)
-     call read_unlimited_axis(filename,'mass',mass,domain=grd%domain)
-     call read_unlimited_axis(filename,'axn',axn,domain=grd%domain) !Alon
-     call read_unlimited_axis(filename,'ayn',ayn,domain=grd%domain) !Alon
-     call read_unlimited_axis(filename,'uvel_old',uvel_old,domain=grd%domain) !Alon
-     call read_unlimited_axis(filename,'vvel_old',vvel_old,domain=grd%domain) !Alon
-     call read_unlimited_axis(filename,'bxn',bxn,domain=grd%domain) !Alon
-     call read_unlimited_axis(filename,'byn',byn,domain=grd%domain) !Alon
-     call read_unlimited_axis(filename,'thickness',thickness,domain=grd%domain)
-     call read_unlimited_axis(filename,'width',width,domain=grd%domain)
-     call read_unlimited_axis(filename,'length',length,domain=grd%domain)
-     call read_unlimited_axis(filename,'start_lon',start_lon,domain=grd%domain)
-     call read_unlimited_axis(filename,'start_lat',start_lat,domain=grd%domain)
-     call read_unlimited_axis(filename,'start_day',start_day,domain=grd%domain)
-     call read_unlimited_axis(filename,'start_mass',start_mass,domain=grd%domain)
-     call read_unlimited_axis(filename,'mass_scaling',mass_scaling,domain=grd%domain)
-     call read_unlimited_axis(filename,'mass_of_bits',mass_of_bits,domain=grd%domain)
-     call read_unlimited_axis(filename,'heat_density',heat_density,domain=grd%domain)
-
-     call read_unlimited_axis(filename,'ine',ine,domain=grd%domain)
-     call read_unlimited_axis(filename,'jne',jne,domain=grd%domain)
-     call read_unlimited_axis(filename,'start_year',start_year,domain=grd%domain)
-
-     ! Find approx outer bounds for tile
-     lon0=minval( grd%lon(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
-     lon1=maxval( grd%lon(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
-     lat0=minval( grd%lat(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
-     lat1=maxval( grd%lat(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
-     do k=1, nbergs_in_file
-       localberg%lon=lon(k)
-       localberg%lat=lat(k)
-       if (.not. ignore_ij_restart) then ! read i,j position and avoid the "find" step
-         localberg%ine=ine(k)
-         localberg%jne=jne(k)
-         if ( localberg%ine>=grd%isc .and. localberg%ine<=grd%iec .and. &
-              localberg%jne>=grd%jsc .and.localberg%jne<=grd%jec ) then
-           lres=.true.
-         else
-           lres=.false.
-         endif
-       else ! i,j are not available from the file so we search the grid to find out if we reside on this PE
-         if (use_slow_find) then
-           lres=find_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
-         else
-           lres=find_cell_by_search(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
-         endif
-       endif
-       if (really_debug) then
-         write(stderrunit,'(a,i8,a,2f9.4,a,i8)') 'diamonds, read_restart_bergs: berg ',k,' is at ',localberg%lon,localberg%lat,&
-              & ' on PE ',mpp_pe()
-         write(stderrunit,*) 'diamonds, read_restart_bergs: lres = ',lres
-       endif
-       if (lres) then ! true if we reside on this PE grid
-         localberg%uvel=uvel(k)
-         localberg%vvel=vvel(k)
-         localberg%mass=mass(k)
-         localberg%axn=axn(k) !Alon
-         localberg%ayn=ayn(k) !Alon
-         localberg%uvel_old=uvel_old(k) !Alon
-         localberg%vvel_old=vvel_old(k) !Alon
-         localberg%lon_old=lon_old(k) !Alon
-         localberg%lat_old=lat_old(k) !Alon
-         localberg%bxn=bxn(k) !Alon
-         localberg%byn=byn(k) !Alon
-         localberg%thickness=thickness(k)
-         localberg%width=width(k)
-         localberg%length=length(k)
-         localberg%start_lon=start_lon(k)
-         localberg%start_lat=start_lat(k)
-         localberg%start_year=start_year(k)
-         localberg%start_day=start_day(k)
-         localberg%start_mass=start_mass(k)
-         localberg%mass_scaling=mass_scaling(k)
-         localberg%mass_of_bits=mass_of_bits(k)
-         localberg%heat_density=heat_density(k)
-         if (really_debug) lres=is_point_in_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, explain=.true.)
+  call read_unlimited_axis(filename,'lon',lon,domain=grd%domain)
+  call read_unlimited_axis(filename,'lat',lat,domain=grd%domain)
+  call read_unlimited_axis(filename,'lon_old',lon_old,domain=grd%domain) !Alon
+  call read_unlimited_axis(filename,'lat_old',lat_old,domain=grd%domain) !Alon
+  call read_unlimited_axis(filename,'uvel',uvel,domain=grd%domain)
+  call read_unlimited_axis(filename,'vvel',vvel,domain=grd%domain)
+  call read_unlimited_axis(filename,'mass',mass,domain=grd%domain)
+  call read_unlimited_axis(filename,'axn',axn,domain=grd%domain) !Alon
+  call read_unlimited_axis(filename,'ayn',ayn,domain=grd%domain) !Alon
+  call read_unlimited_axis(filename,'uvel_old',uvel_old,domain=grd%domain) !Alon
+  call read_unlimited_axis(filename,'vvel_old',vvel_old,domain=grd%domain) !Alon
+  call read_unlimited_axis(filename,'bxn',bxn,domain=grd%domain) !Alon
+  call read_unlimited_axis(filename,'byn',byn,domain=grd%domain) !Alon
+  call read_unlimited_axis(filename,'thickness',thickness,domain=grd%domain)
+  call read_unlimited_axis(filename,'width',width,domain=grd%domain)
+  call read_unlimited_axis(filename,'length',length,domain=grd%domain)
+  call read_unlimited_axis(filename,'start_lon',start_lon,domain=grd%domain)
+  call read_unlimited_axis(filename,'start_lat',start_lat,domain=grd%domain)
+  call read_unlimited_axis(filename,'start_day',start_day,domain=grd%domain)
+  call read_unlimited_axis(filename,'start_mass',start_mass,domain=grd%domain)
+  call read_unlimited_axis(filename,'mass_scaling',mass_scaling,domain=grd%domain)
+  call read_unlimited_axis(filename,'mass_of_bits',mass_of_bits,domain=grd%domain)
+  call read_unlimited_axis(filename,'heat_density',heat_density,domain=grd%domain)
+
+  call read_unlimited_axis(filename,'ine',ine,domain=grd%domain)
+  call read_unlimited_axis(filename,'jne',jne,domain=grd%domain)
+  call read_unlimited_axis(filename,'start_year',start_year,domain=grd%domain)
+
+  ! Find approx outer bounds for tile
+  lon0=minval( grd%lon(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
+  lon1=maxval( grd%lon(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
+  lat0=minval( grd%lat(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
+  lat1=maxval( grd%lat(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
+  do k=1, nbergs_in_file
+    localberg%lon=lon(k)
+    localberg%lat=lat(k)
+    if (.not. ignore_ij_restart) then ! read i,j position and avoid the "find" step
+      localberg%ine=ine(k)
+      localberg%jne=jne(k)
+      if ( localberg%ine>=grd%isc .and. localberg%ine<=grd%iec .and. &
+           localberg%jne>=grd%jsc .and.localberg%jne<=grd%jec ) then
+        lres=.true.
+      else
+        lres=.false.
+      endif
+    else ! i,j are not available from the file so we search the grid to find out if we reside on this PE
+      if (use_slow_find) then
+        lres=find_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
+      else
+        lres=find_cell_by_search(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
+      endif
+    endif
+    if (really_debug) then
+      write(stderrunit,'(a,i8,a,2f9.4,a,i8)') 'diamonds, read_restart_bergs: berg ',k,' is at ',localberg%lon,localberg%lat,&
+           & ' on PE ',mpp_pe()
+      write(stderrunit,*) 'diamonds, read_restart_bergs: lres = ',lres
+    endif
+    if (lres) then ! true if we reside on this PE grid
+      localberg%uvel=uvel(k)
+      localberg%vvel=vvel(k)
+      localberg%mass=mass(k)
+      localberg%axn=axn(k) !Alon
+      localberg%ayn=ayn(k) !Alon
+      localberg%uvel_old=uvel_old(k) !Alon
+      localberg%vvel_old=vvel_old(k) !Alon
+      localberg%lon_old=lon_old(k) !Alon
+      localberg%lat_old=lat_old(k) !Alon
+      localberg%bxn=bxn(k) !Alon
+      localberg%byn=byn(k) !Alon
+      localberg%thickness=thickness(k)
+      localberg%width=width(k)
+      localberg%length=length(k)
+      localberg%start_lon=start_lon(k)
+      localberg%start_lat=start_lat(k)
+      localberg%start_year=start_year(k)
+      localberg%start_day=start_day(k)
+      localberg%start_mass=start_mass(k)
+      localberg%mass_scaling=mass_scaling(k)
+      localberg%mass_of_bits=mass_of_bits(k)
+      localberg%heat_density=heat_density(k)
+      if (really_debug) lres=is_point_in_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, explain=.true.)
          lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
         !call add_new_berg_to_list(bergs%first, localberg, quick=.true.)
          call add_new_berg_to_list(bergs%first, localberg)
@@ -774,6 +775,8 @@ subroutine read_restart_bergs(bergs,Time)
          call error_mesg('diamonds, read_restart_bergs', 'berg in PE file was not on PE!', FATAL)
        endif
      enddo
+  
+  if(nbergs_in_file > 0) then  
      deallocate(              &
                 lon,          &
                 lat,          &

From 173ed258c98b78a77ebca1673b1f473214a433f3 Mon Sep 17 00:00:00 2001
From: Zhi Liang <Zhi.Liang@noaa.gov>
Date: Wed, 13 Jan 2016 14:49:03 -0500
Subject: [PATCH 093/361] fix for cold restart of icebergs

---
 icebergs_io.F90 | 80 ++++++++++++++++++++++++++-----------------------
 1 file changed, 42 insertions(+), 38 deletions(-)

diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 63315ad..268760d 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -652,9 +652,11 @@ subroutine read_restart_bergs(bergs,Time)
   found_restart = find_restart_file(filename_base, filename, multiPErestart, io_tile_id(1))
   call error_mesg('read_restart_bergs_new', 'Using new icebergs restart read', NOTE)
 
-  filename = filename_base
-  call get_field_size(filename,'i',siz, field_found=found, domain=bergs%grd%domain)
-  nbergs_in_file = siz(1)
+  if (found_restart) then
+     filename = filename_base
+     call get_field_size(filename,'i',siz, field_found=found, domain=bergs%grd%domain)
+     nbergs_in_file = siz(1)
+  endif
 
   if(nbergs_in_file > 0) then
      allocate(lon(nbergs_in_file))
@@ -686,33 +688,35 @@ subroutine read_restart_bergs(bergs,Time)
      allocate(start_year(nbergs_in_file))
   endif
 
-  call read_unlimited_axis(filename,'lon',lon,domain=grd%domain)
-  call read_unlimited_axis(filename,'lat',lat,domain=grd%domain)
-  call read_unlimited_axis(filename,'lon_old',lon_old,domain=grd%domain) !Alon
-  call read_unlimited_axis(filename,'lat_old',lat_old,domain=grd%domain) !Alon
-  call read_unlimited_axis(filename,'uvel',uvel,domain=grd%domain)
-  call read_unlimited_axis(filename,'vvel',vvel,domain=grd%domain)
-  call read_unlimited_axis(filename,'mass',mass,domain=grd%domain)
-  call read_unlimited_axis(filename,'axn',axn,domain=grd%domain) !Alon
-  call read_unlimited_axis(filename,'ayn',ayn,domain=grd%domain) !Alon
-  call read_unlimited_axis(filename,'uvel_old',uvel_old,domain=grd%domain) !Alon
-  call read_unlimited_axis(filename,'vvel_old',vvel_old,domain=grd%domain) !Alon
-  call read_unlimited_axis(filename,'bxn',bxn,domain=grd%domain) !Alon
-  call read_unlimited_axis(filename,'byn',byn,domain=grd%domain) !Alon
-  call read_unlimited_axis(filename,'thickness',thickness,domain=grd%domain)
-  call read_unlimited_axis(filename,'width',width,domain=grd%domain)
-  call read_unlimited_axis(filename,'length',length,domain=grd%domain)
-  call read_unlimited_axis(filename,'start_lon',start_lon,domain=grd%domain)
-  call read_unlimited_axis(filename,'start_lat',start_lat,domain=grd%domain)
-  call read_unlimited_axis(filename,'start_day',start_day,domain=grd%domain)
-  call read_unlimited_axis(filename,'start_mass',start_mass,domain=grd%domain)
-  call read_unlimited_axis(filename,'mass_scaling',mass_scaling,domain=grd%domain)
-  call read_unlimited_axis(filename,'mass_of_bits',mass_of_bits,domain=grd%domain)
-  call read_unlimited_axis(filename,'heat_density',heat_density,domain=grd%domain)
-
-  call read_unlimited_axis(filename,'ine',ine,domain=grd%domain)
-  call read_unlimited_axis(filename,'jne',jne,domain=grd%domain)
-  call read_unlimited_axis(filename,'start_year',start_year,domain=grd%domain)
+  if (found_restart) then
+     call read_unlimited_axis(filename,'lon',lon,domain=grd%domain)
+     call read_unlimited_axis(filename,'lat',lat,domain=grd%domain)
+     call read_unlimited_axis(filename,'lon_old',lon_old,domain=grd%domain) !Alon
+     call read_unlimited_axis(filename,'lat_old',lat_old,domain=grd%domain) !Alon
+     call read_unlimited_axis(filename,'uvel',uvel,domain=grd%domain)
+     call read_unlimited_axis(filename,'vvel',vvel,domain=grd%domain)
+     call read_unlimited_axis(filename,'mass',mass,domain=grd%domain)
+     call read_unlimited_axis(filename,'axn',axn,domain=grd%domain) !Alon
+     call read_unlimited_axis(filename,'ayn',ayn,domain=grd%domain) !Alon
+     call read_unlimited_axis(filename,'uvel_old',uvel_old,domain=grd%domain) !Alon
+     call read_unlimited_axis(filename,'vvel_old',vvel_old,domain=grd%domain) !Alon
+     call read_unlimited_axis(filename,'bxn',bxn,domain=grd%domain) !Alon
+     call read_unlimited_axis(filename,'byn',byn,domain=grd%domain) !Alon
+     call read_unlimited_axis(filename,'thickness',thickness,domain=grd%domain)
+     call read_unlimited_axis(filename,'width',width,domain=grd%domain)
+     call read_unlimited_axis(filename,'length',length,domain=grd%domain)
+     call read_unlimited_axis(filename,'start_lon',start_lon,domain=grd%domain)
+     call read_unlimited_axis(filename,'start_lat',start_lat,domain=grd%domain)
+     call read_unlimited_axis(filename,'start_day',start_day,domain=grd%domain)
+     call read_unlimited_axis(filename,'start_mass',start_mass,domain=grd%domain)
+     call read_unlimited_axis(filename,'mass_scaling',mass_scaling,domain=grd%domain)
+     call read_unlimited_axis(filename,'mass_of_bits',mass_of_bits,domain=grd%domain)
+     call read_unlimited_axis(filename,'heat_density',heat_density,domain=grd%domain)
+
+     call read_unlimited_axis(filename,'ine',ine,domain=grd%domain)
+     call read_unlimited_axis(filename,'jne',jne,domain=grd%domain)
+     call read_unlimited_axis(filename,'start_year',start_year,domain=grd%domain)
+  endif
 
   ! Find approx outer bounds for tile
   lon0=minval( grd%lon(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
@@ -767,14 +771,14 @@ subroutine read_restart_bergs(bergs,Time)
       localberg%mass_of_bits=mass_of_bits(k)
       localberg%heat_density=heat_density(k)
       if (really_debug) lres=is_point_in_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, explain=.true.)
-         lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
-        !call add_new_berg_to_list(bergs%first, localberg, quick=.true.)
-         call add_new_berg_to_list(bergs%first, localberg)
-         if (really_debug) call print_berg(stderrunit, bergs%first, 'read_restart_bergs, add_new_berg_to_list')
-       elseif (multiPErestart .and. io_tile_id(1) .lt. 0) then
-         call error_mesg('diamonds, read_restart_bergs', 'berg in PE file was not on PE!', FATAL)
-       endif
-     enddo
+      lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
+      !call add_new_berg_to_list(bergs%first, localberg, quick=.true.)
+      call add_new_berg_to_list(bergs%first, localberg)
+      if (really_debug) call print_berg(stderrunit, bergs%first, 'read_restart_bergs, add_new_berg_to_list')
+    elseif (multiPErestart .and. io_tile_id(1) .lt. 0) then
+      call error_mesg('diamonds, read_restart_bergs', 'berg in PE file was not on PE!', FATAL)
+    endif
+  enddo
   
   if(nbergs_in_file > 0) then  
      deallocate(              &

From 0957ce0d01727ef54e8833070944b37f1d165cba Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 16 Mar 2016 16:03:50 -0400
Subject: [PATCH 094/361] There were a few bugs in the iceberg tipping sheme:

1) The icebergs should tip if their shortest horizonal length (W) is small compared to the iceberg depth  (model was using the large horizonal length L ) - this bug was copied from Bigg et al 1997
2) There was an error in copying from Bigg et al 1997. The tipping scheme used the iceberg draft instead of the iceberg thickness.
3) In the Weeks and Mellor paper, there was an error which meant that the plus sign in front of the 58.32 should have been a minus sign

Instead of correcting these errors a flag has been added so that a different rolling criteria is used where icebergs roll when W/Th>tip_parameter. The tip parameter can be added at runtime, or else is calculated directly from the iceberg and ocean density. This is the formula given in Burton et al 2012, equation 27, or equivolently it is the same as the Weeks and Mellor 1978 result, using an iceberg of constant density.

When run with the standard configuration, the old (incorrect) rolling scheme is used, and the code does not change the answers
---
 icebergs.F90           | 29 ++++++++++++++++++++++++++---
 icebergs_framework.F90 | 10 ++++++++--
 2 files changed, 34 insertions(+), 5 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 024c301..58f08ad 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -727,6 +727,7 @@ subroutine thermodynamics(bergs)
 real :: Mv, Me, Mb, melt, dvo, dva, dM, Ss, dMe, dMb, dMv
 real :: Mnew, Mnew1, Mnew2, Hocean
 real :: Mbits, nMbits, dMbitsE, dMbitsM, Lbits, Abits, Mbb
+real :: tip_parameter
 integer :: i,j, stderrunit
 type(iceberg), pointer :: this, next
 real, parameter :: perday=1./86400.
@@ -857,15 +858,37 @@ subroutine thermodynamics(bergs)
       call error_mesg('diamonds, thermodynamics', 'berg appears to have grounded!', FATAL)
     endif
 
-    ! Rolling
+    ! Rolling  - The corrected scheme has been included. The old scheme is here for legacy reasons
     Dn=(bergs%rho_bergs/rho_seawater)*Tn ! draught (keel depth)
     if ( Dn>0. ) then
-       if ( max(Wn,Ln)<sqrt(0.92*(Dn**2)+58.32*Dn) ) then
+      if (bergs%use_updated_rolling_scheme) then
+        if (bergs%tip_parameter>0.) then
+                tip_parameter=bergs%tip_parameter
+        else
+          ! Equation 27 from Burton et al 2012, or equivolently, Weeks and Mellor 1979 with constant density
+          tip_parameter=sqrt(6*(bergs%rho_bergs/rho_seawater)*(1-(bergs%rho_bergs/rho_seawater)))   !using default values gives 0.92
+        endif
+        !print *, 'tip_parameter',tip_parameter
+        if (Th<(tip_parameter* min(Wn,Ln)))  then     !note that we use the Thickness instead of the Draft
+          if (Wn<Ln) then
+            T=Tn
+            Tn=Wn
+            Wn=T
+          else
+            T=Tn
+            Tn=Ln
+            Ln=T
+          endif
+        endif
+      else     
+        !print *, 'using old tipping scheme'
+        if ( max(Wn,Ln)<sqrt(0.92*(Dn**2)+58.32*Dn) ) then
           T=Tn
           Tn=Wn
           Wn=T
-          Dn=(bergs%rho_bergs/rho_seawater)*Tn ! re-calculate draught (keel depth) for grounding
+        end if
       end if
+      Dn=(bergs%rho_bergs/rho_seawater)*Tn ! re-calculate draught (keel depth) for grounding
     endif
 
     ! Store the new state of iceberg (with L>W)
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 30066d1..ab8ea06 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -182,11 +182,13 @@ module ice_bergs_framework
   logical :: add_weight_to_ocean=.true. ! Add weight of bergs to ocean
   logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
   logical :: time_average_weight=.false. ! Time average the weight on the ocean
+  logical :: use_updated_rolling_scheme=.false. ! Use the corrected Rolling Scheme rather than the erronios one
   logical :: Runge_not_Verlet=.True.  !True=Runge Kuttai, False=Verlet.  - Added by Alon 
   logical :: use_new_predictive_corrective =.False.  !Flag to use Bob's predictive corrective iceberg scheme- Added by Alon 
   logical :: interactive_icebergs_on=.false.  !Turn on/off interactions between icebergs  - Added by Alon 
   logical :: critical_interaction_damping_on=.true.  !Sets the damping on relative iceberg velocity to critical value - Added by Alon 
   real :: speed_limit=0. ! CFL speed limit for a berg [m/s]
+  real :: tip_parameter=0. ! parameter to override iceberg rollilng critica ratio (use zero to get parameter directly from ice and seawater densities
   real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
   type(buffer), pointer :: obuffer_n=>null(), ibuffer_n=>null()
   type(buffer), pointer :: obuffer_s=>null(), ibuffer_s=>null()
@@ -278,8 +280,10 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
 logical :: time_average_weight=.false. ! Time average the weight on the ocean
 real :: speed_limit=0. ! CFL speed limit for a berg
+real :: tip_parameter=0. ! parameter to override iceberg rollilng critica ratio (use zero to get parameter directly from ice and seawater densities
 real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
 logical :: Runge_not_Verlet=.True.  !True=Runge Kutta, False=Verlet.  - Added by Alon 
+logical :: use_updated_rolling_scheme=.false. ! Use the corrected Rolling Scheme rather than the erronios one
 logical :: use_new_predictive_corrective =.False.  !Flag to use Bob's predictive corrective iceberg scheme- Added by Alon 
 logical :: interactive_icebergs_on=.false.  !Turn on/off interactions between icebergs  - Added by Alon 
 logical :: critical_interaction_damping_on=.true.  !Sets the damping on relative iceberg velocity to critical value - Added by Alon 
@@ -291,8 +295,8 @@ subroutine ice_bergs_framework_init(bergs, &
 real, dimension(nclasses) :: initial_thickness=(/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) ! Total thickness of newly calved bergs (m)
 namelist /icebergs_nml/ verbose, budget, halo, traj_sample_hrs, initial_mass, traj_write_hrs, &
          distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef, radial_damping_coef, tangental_damping_coef, &
-         rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, &
-         parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, &
+         rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, use_updated_rolling_scheme, &
+         parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, tip_parameter, &
          time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, interactive_icebergs_on, critical_interaction_damping_on, &
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution, force_all_pes_traj
 
@@ -544,7 +548,9 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%passive_mode=passive_mode
   bergs%time_average_weight=time_average_weight
   bergs%speed_limit=speed_limit
+  bergs%tip_parameter=tip_parameter
   bergs%Runge_not_Verlet=Runge_not_Verlet   !Alon
+  bergs%use_updated_rolling_scheme=use_updated_rolling_scheme  !Alon
   bergs%critical_interaction_damping_on=critical_interaction_damping_on   !Alon
   bergs%interactive_icebergs_on=interactive_icebergs_on   !Alon
   bergs%use_new_predictive_corrective=use_new_predictive_corrective  !Alon

From a2af07727ffd219945decbe6a6512d718393a318 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 16 Mar 2016 16:29:55 -0400
Subject: [PATCH 095/361] 1) Fixed a bug in the Rolling scheme by changing Th
 to Tn

2) Added the possibility of running the Rolling code using the corrected Weeks and Mellor 1978 scheme. This is done by setting run parameters
 use_updated_rolling_scheme=.false and  run_parameter=1000.
---
 icebergs.F90           | 37 +++++++++++++++++++++++++++----------
 icebergs_framework.F90 |  4 ++--
 2 files changed, 29 insertions(+), 12 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 58f08ad..71ed399 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -858,10 +858,14 @@ subroutine thermodynamics(bergs)
       call error_mesg('diamonds, thermodynamics', 'berg appears to have grounded!', FATAL)
     endif
 
-    ! Rolling  - The corrected scheme has been included. The old scheme is here for legacy reasons
+    ! Rolling 
+   !There are now 3 iceberg rolling schemes:
+   !1) Rolling based on aspect ratio threshold (iceberg of constant density)
+   !2) Rolling based on corrected Weeks and Mellor scheme
+   !3) Rolling based on incorrect Weeks and Mellor scheme - kept for legacy reasons
     Dn=(bergs%rho_bergs/rho_seawater)*Tn ! draught (keel depth)
     if ( Dn>0. ) then
-      if (bergs%use_updated_rolling_scheme) then
+      if (bergs%use_updated_rolling_scheme) then    !Use Rolling Scheme 1
         if (bergs%tip_parameter>0.) then
                 tip_parameter=bergs%tip_parameter
         else
@@ -869,7 +873,7 @@ subroutine thermodynamics(bergs)
           tip_parameter=sqrt(6*(bergs%rho_bergs/rho_seawater)*(1-(bergs%rho_bergs/rho_seawater)))   !using default values gives 0.92
         endif
         !print *, 'tip_parameter',tip_parameter
-        if (Th<(tip_parameter* min(Wn,Ln)))  then     !note that we use the Thickness instead of the Draft
+        if (Tn<(tip_parameter* min(Wn,Ln)))  then     !note that we use the Thickness instead of the Draft
           if (Wn<Ln) then
             T=Tn
             Tn=Wn
@@ -880,13 +884,26 @@ subroutine thermodynamics(bergs)
             Ln=T
           endif
         endif
-      else     
-        !print *, 'using old tipping scheme'
-        if ( max(Wn,Ln)<sqrt(0.92*(Dn**2)+58.32*Dn) ) then
-          T=Tn
-          Tn=Wn
-          Wn=T
-        end if
+      else
+        if (bergs%tip_parameter>999.) then     !Use Rolling Scheme 2
+          if ( min(Wn,Ln)<sqrt(0.92*(Tn**2)-58.32*Tn) ) then
+            if (Wn<Ln) then
+              T=Tn
+              Tn=Wn
+              Wn=T
+            else
+              T=Tn
+              Tn=Ln
+              Ln=T
+            endif
+          endif
+        else     !Use Rolling Scheme 3
+          if ( max(Wn,Ln)<sqrt(0.92*(Dn**2)+58.32*Dn) ) then
+            T=Tn
+            Tn=Wn
+            Wn=T
+          endif
+        endif
       end if
       Dn=(bergs%rho_bergs/rho_seawater)*Tn ! re-calculate draught (keel depth) for grounding
     endif
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index ab8ea06..5ee8153 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -182,13 +182,13 @@ module ice_bergs_framework
   logical :: add_weight_to_ocean=.true. ! Add weight of bergs to ocean
   logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
   logical :: time_average_weight=.false. ! Time average the weight on the ocean
-  logical :: use_updated_rolling_scheme=.false. ! Use the corrected Rolling Scheme rather than the erronios one
+  logical :: use_updated_rolling_scheme=.false. ! True to use the aspect ratio based rolling scheme rather than incorrect version of WM scheme   (set tip_parameter=1000. for correct WM scheme)
   logical :: Runge_not_Verlet=.True.  !True=Runge Kuttai, False=Verlet.  - Added by Alon 
   logical :: use_new_predictive_corrective =.False.  !Flag to use Bob's predictive corrective iceberg scheme- Added by Alon 
   logical :: interactive_icebergs_on=.false.  !Turn on/off interactions between icebergs  - Added by Alon 
   logical :: critical_interaction_damping_on=.true.  !Sets the damping on relative iceberg velocity to critical value - Added by Alon 
   real :: speed_limit=0. ! CFL speed limit for a berg [m/s]
-  real :: tip_parameter=0. ! parameter to override iceberg rollilng critica ratio (use zero to get parameter directly from ice and seawater densities
+  real :: tip_parameter=0. ! parameter to override iceberg rollilng critica ratio (use zero to get parameter directly from ice and seawater densities) 
   real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
   type(buffer), pointer :: obuffer_n=>null(), ibuffer_n=>null()
   type(buffer), pointer :: obuffer_s=>null(), ibuffer_s=>null()

From 93c56c458032eba3c5e1d9b748be832a666b78f6 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 16 Mar 2016 17:18:03 -0400
Subject: [PATCH 096/361] Add a swap functions to swap width and thickness when
 iceberg rolls  (This simplifies the code, but does not change the answers)

---
 icebergs.F90 | 31 ++++++++++++++++---------------
 1 file changed, 16 insertions(+), 15 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 71ed399..151135f 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -875,33 +875,23 @@ subroutine thermodynamics(bergs)
         !print *, 'tip_parameter',tip_parameter
         if (Tn<(tip_parameter* min(Wn,Ln)))  then     !note that we use the Thickness instead of the Draft
           if (Wn<Ln) then
-            T=Tn
-            Tn=Wn
-            Wn=T
+            call swap_variables(Tn,Wn)
           else
-            T=Tn
-            Tn=Ln
-            Ln=T
+            call swap_variables(Tn,Ln)
           endif
         endif
       else
         if (bergs%tip_parameter>999.) then     !Use Rolling Scheme 2
           if ( min(Wn,Ln)<sqrt(0.92*(Tn**2)-58.32*Tn) ) then
             if (Wn<Ln) then
-              T=Tn
-              Tn=Wn
-              Wn=T
+              call swap_variables(Tn,Wn)
             else
-              T=Tn
-              Tn=Ln
-              Ln=T
+              call swap_variables(Tn,Ln)
             endif
           endif
         else     !Use Rolling Scheme 3
           if ( max(Wn,Ln)<sqrt(0.92*(Dn**2)+58.32*Dn) ) then
-            T=Tn
-            Tn=Wn
-            Wn=T
+            call swap_variables(Tn,Wn)
           endif
         endif
       end if
@@ -941,6 +931,17 @@ subroutine thermodynamics(bergs)
     this=>next
   enddo
 
+  contains
+
+  subroutine swap_variables(x,y)
+  ! Arguments
+  real, intent(inout) :: x, y
+  real :: temp
+  temp=x
+  x=y
+  y=temp
+  end subroutine swap_variables
+
 end subroutine thermodynamics
 
 ! ##############################################################################

From 2b47f3f0072073bb91088c2604b85c9dfffbad2b Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 16 Mar 2016 17:38:17 -0400
Subject: [PATCH 097/361] Refactored the iceberg rolling code to make it
 shorter and easier to read. It should still do the same thing.

Note that the width is set to be the shortest horizontal dimension. This is down after Rolling Scheme 3 (ie the old scheme) so that the code will not have answers changed in default mode
---
 icebergs.F90 | 43 +++++++++++++++++++------------------------
 1 file changed, 19 insertions(+), 24 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 151135f..c038011 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -858,43 +858,38 @@ subroutine thermodynamics(bergs)
       call error_mesg('diamonds, thermodynamics', 'berg appears to have grounded!', FATAL)
     endif
 
-    ! Rolling 
+   ! Rolling 
    !There are now 3 iceberg rolling schemes:
    !1) Rolling based on aspect ratio threshold (iceberg of constant density)
    !2) Rolling based on corrected Weeks and Mellor scheme
    !3) Rolling based on incorrect Weeks and Mellor scheme - kept for legacy reasons
     Dn=(bergs%rho_bergs/rho_seawater)*Tn ! draught (keel depth)
     if ( Dn>0. ) then
-      if (bergs%use_updated_rolling_scheme) then    !Use Rolling Scheme 1
-        if (bergs%tip_parameter>0.) then
-                tip_parameter=bergs%tip_parameter
-        else
-          ! Equation 27 from Burton et al 2012, or equivolently, Weeks and Mellor 1979 with constant density
-          tip_parameter=sqrt(6*(bergs%rho_bergs/rho_seawater)*(1-(bergs%rho_bergs/rho_seawater)))   !using default values gives 0.92
-        endif
-        !print *, 'tip_parameter',tip_parameter
-        if (Tn<(tip_parameter* min(Wn,Ln)))  then     !note that we use the Thickness instead of the Draft
-          if (Wn<Ln) then
+      if ( (.not.bergs%use_updated_rolling_scheme) .and. (bergs%tip_parameter<999.) ) then    !Use Rolling Scheme 3
+          if ( max(Wn,Ln)<sqrt(0.92*(Dn**2)+58.32*Dn) ) then
             call swap_variables(Tn,Wn)
-          else
-            call swap_variables(Tn,Ln)
           endif
-        endif
       else
-        if (bergs%tip_parameter>999.) then     !Use Rolling Scheme 2
-          if ( min(Wn,Ln)<sqrt(0.92*(Tn**2)-58.32*Tn) ) then
-            if (Wn<Ln) then
+        if (Wn>Ln) call swap_variables(Ln,Wn)  !Make sure that Wn is the smaller dimension
+      
+        if ( (.not.bergs%use_updated_rolling_scheme) .and. (bergs%tip_parameter>=999.) ) then    !Use Rolling Scheme 2
+          if ( Wn<sqrt(0.92*(Tn**2)-58.32*Tn) ) then
               call swap_variables(Tn,Wn)
-            else
-              call swap_variables(Tn,Ln)
-            endif
           endif
-        else     !Use Rolling Scheme 3
-          if ( max(Wn,Ln)<sqrt(0.92*(Dn**2)+58.32*Dn) ) then
-            call swap_variables(Tn,Wn)
+        endif
+
+        if (bergs%use_updated_rolling_scheme) then    !Use Rolling Scheme 1
+          if (bergs%tip_parameter>0.) then
+            tip_parameter=bergs%tip_parameter
+          else
+            ! Equation 27 from Burton et al 2012, or equivolently, Weeks and Mellor 1979 with constant density
+            tip_parameter=sqrt(6*(bergs%rho_bergs/rho_seawater)*(1-(bergs%rho_bergs/rho_seawater)))   !using default values gives 0.92
+          endif
+          if (Tn<(tip_parameter* Wn))  then     !note that we use the Thickness instead of the Draft
+              call swap_variables(Tn,Wn)
           endif
         endif
-      end if
+      endif
       Dn=(bergs%rho_bergs/rho_seawater)*Tn ! re-calculate draught (keel depth) for grounding
     endif
 

From 2ef3f4f3096a6d095a61090f0f8dd5cf63dfe144 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Fri, 25 Mar 2016 17:22:39 -0400
Subject: [PATCH 098/361] Commented out one line which was printing every
 bouncing iceberg to the screen

---
 icebergs.F90 | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 9cbb581..c7b5ec3 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -2591,12 +2591,12 @@ subroutine update_verlet_position(bergs,berg)
         i=berg%ine;  j=berg%jne;  xi = berg%xi;  yj = berg%yj
         call adjust_index_and_ground(grd, lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
 
-        if (bounced) then
-          print *, 'you have been bounce: big time!',mpp_pe(),berg%iceberg_num,lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag 
-          berg%axn=0.0  ;  berg%ayn=0.0
-          berg%bxn=0.0  ;  berg%byn=0.0
-          berg%uvel=0.0 ;  berg%vvel=0.0
-        endif
+        !if (bounced) then
+        !  print *, 'you have been bounce: big time!',mpp_pe(),berg%iceberg_num,lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag 
+        !  berg%axn=0.0  ;  berg%ayn=0.0
+        !  berg%bxn=0.0  ;  berg%byn=0.0
+        !  berg%uvel=0.0 ;  berg%vvel=0.0
+        !endif
 
         !Updating positions and index
         berg%lon=lonn      ;  berg%lat=latn

From 9eddc06c592ad8822b4371f2b78ea0cdbcb9be9d Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Tue, 19 Apr 2016 10:19:10 -0400
Subject: [PATCH 099/361] 1) Added a Static_icebergs flag to the namelist. When
 this flag is true, the evolve_icebergs submodule does not get called, and the
 icebergs do not move. This is useful for construcing iceshelves

2) Added a ignore_missing_restart_bergs flag to namelist. This allows the model not to crash when the position of an iceberg in the restart file is not found.  This is useful when constructing an iceshelf, and one of the icebergs in the restart file is not in the model domain.

3) Added iceberg_num output in some error messages, which helps with debugging
---
 .icebergs.F90.swo      | Bin 0 -> 20480 bytes
 icebergs.F90           |  41 +++++++++++++++++++++++++----------------
 icebergs_framework.F90 |  13 ++++++++++---
 icebergs_io.F90        |   9 ++++++++-
 4 files changed, 43 insertions(+), 20 deletions(-)
 create mode 100644 .icebergs.F90.swo

diff --git a/.icebergs.F90.swo b/.icebergs.F90.swo
new file mode 100644
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zqAo%S@8ajWmLh-VYaeq`Ly{_;bh<DXQo~GYfn8EHGPq^#^o^Cz;cCHPSa1?89d$KX
zboc>(RjXB1pi5;dx>9Y3svzbkDA7~<baF|Sc(s-RuMP2F2nHrX=}k2S`YxdxU3N%&
zI=bJ$iP$nF%nz{vgz9X=M}0#F%?hcjh9ZB@A`;4=^$vtrQocCg70Tr3gVd-U1jKX0
zIb50ZWGk*rG7kNJaTVJ7(1pELu9TLmY8GmxON(kQ)XHXUU!n+!wqlU%cNtZ*u@;YG
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z91fpb4c#QIVy|2iQBuRbC{Ai_%@tH<9*CN*5v^f&-pAr=)N3fck;~Pt>;=}p03om<
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literal 0
HcmV?d00001

diff --git a/icebergs.F90 b/icebergs.F90
index c7b5ec3..c99b26d 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1416,7 +1416,10 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 
   ! For each berg, evolve
   call mpp_clock_begin(bergs%clock_mom)
-  call evolve_icebergs(bergs)
+
+  if (.not.bergs%Static_icebergs) then
+        call evolve_icebergs(bergs)
+  endif
   call move_berg_between_cells(bergs)  !Markpoint6
   if (debug) call bergs_chksum(bergs, 'run bergs (evolved)',ignore_halo_violation=.true.)
   if (debug) call checksum_gridded(bergs%grd, 's/r run after evolve')
@@ -2026,14 +2029,13 @@ subroutine evolve_icebergs(bergs)
       endif
       if (debug) call check_position(grd, berg, 'evolve_iceberg (top)')
 
-
-      !Time stepping schemes:
-      if (Runge_not_Verlet) then 
-             call Runge_Kutta_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln,lonn, latn, i, j, xi, yj)
-      endif 
-      if (.not.Runge_not_Verlet) then 
-        call verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
-      endif 
+        !Time stepping schemes:
+        if (Runge_not_Verlet) then 
+          call Runge_Kutta_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln,lonn, latn, i, j, xi, yj)
+        endif 
+        if (.not.Runge_not_Verlet) then 
+          call verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
+        endif 
 
       ! Saving all the iceberg variables.
       berg%axn=axn 
@@ -2059,12 +2061,14 @@ subroutine evolve_icebergs(bergs)
     enddo ! loop over all bergs
   enddo ; enddo
 
+
   ! When we are using interactive icebergs, we update the (old) iceberg positions and velocities in a second loop, all together (to make code order invarient)
   if (interactive_icebergs_on) then
     do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
       berg=>bergs%list(grdi,grdj)%first
       do while (associated(berg)) ! loop over all bergs
-      
+       
+
        if (.not. Runge_not_Verlet)  call update_verlet_position(bergs,berg) 
         
        !Updating old velocities (for use in iceberg interactions)
@@ -2555,7 +2559,7 @@ subroutine update_verlet_position(bergs,berg)
       if (berg%lat>89.) on_tangential_plane=.true.
 
         lon1=berg%lon; lat1=berg%lat
-        if (on_tangential_plane) call rotpos_to_tang(lon1,lat1,x1,y1)
+        if (on_tangential_plane) call rotpos_to_tang(lon1,lat1,x1,y1,berg%iceberg_num)
         dxdl1=r180_pi/(Rearth*cos(lat1*pi_180))
         dydl=r180_pi/Rearth
         uvel1=berg%uvel; vvel1=berg%vvel
@@ -2866,22 +2870,27 @@ end subroutine adjust_index_and_ground
 
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
-subroutine rotpos_to_tang(lon, lat, x, y)
+subroutine rotpos_to_tang(lon, lat, x, y, iceberg_num_in)
   ! Arguments
   real, intent(in) :: lon, lat
   real, intent(out) :: x, y
+  integer, intent(in) , optional :: iceberg_num_in
   ! Local variables
   real :: r,colat,clon,slon
-  integer :: stderrunit
+  integer :: stderrunit, iceberg_num
 
   stderrunit = stderr()
-
+  iceberg_num=000
+  if (present(iceberg_num_in)) then
+        iceberg_num=iceberg_num_in
+  endif
+        
   if (lat>90.) then
-      write(stderrunit,*) 'diamonds, rotpos_to_tang: lat>90 already!',lat
+      write(stderrunit,*) 'diamonds, rotpos_to_tang: lat>90 already!',lat, lon, iceberg_num
       call error_mesg('diamonds, rotpos_to_tang','Something went very wrong!',FATAL)
     endif
     if (lat==90.) then
-      write(stderrunit,*) 'diamonds, rotpos_to_tang: lat==90 already!',lat
+      write(stderrunit,*) 'diamonds, rotpos_to_tang: lat==90 already!',lat, lon
       call error_mesg('diamonds, rotpos_to_tang','Something went wrong!',FATAL)
     endif
 
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index edefdce..b76e366 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -207,7 +207,9 @@ module ice_bergs_framework
   logical :: add_weight_to_ocean=.true. ! Add weight of bergs to ocean
   logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
   logical :: time_average_weight=.false. ! Time average the weight on the ocean
-  logical :: Runge_not_Verlet=.True.  !True=Runge Kuttai, False=Verlet.  - Added by Alon 
+  logical :: Runge_not_Verlet=.True.  !True=Runge Kuttai, False=Verlet.   
+  logical :: ignore_missing_restart_bergs=.False.  !True Allows the model to ignorm icebergs missing in the restart. 
+  logical :: Static_icebergs=.False.  !True= icebergs do no move
   logical :: only_interactive_forces=.False.  !Icebergs only feel interactive forces, and not ocean, wind... 
   logical :: halo_debugging=.False.  !Use for debugging halos (remove when its working) 
   logical :: save_short_traj=.True.  !True saves only lon,lat,time,iceberg_num in iceberg_trajectory.nc 
@@ -314,6 +316,8 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: speed_limit=0. ! CFL speed limit for a berg
 real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
 logical :: Runge_not_Verlet=.True.  !True=Runge Kutta, False=Verlet.  - Added by Alon 
+logical :: ignore_missing_restart_bergs=.False.  !True Allows the model to ignorm icebergs missing in the restart. 
+logical :: Static_icebergs=.False.  !True= icebergs do no move
 logical :: only_interactive_forces=.False.  !Icebergs only feel interactive forces, and not ocean, wind... 
 logical :: halo_debugging=.False.  !Use for debugging halos (remove when its working) 
 logical :: save_short_traj=.True.  !True saves only lon,lat,time,iceberg_num in iceberg_trajectory.nc 
@@ -328,9 +332,9 @@ subroutine ice_bergs_framework_init(bergs, &
 real, dimension(nclasses) :: distribution=(/0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02/) ! Fraction of calving to apply to this class (non-dim) , 
 real, dimension(nclasses) :: mass_scaling=(/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) ! Ratio between effective and real iceberg mass (non-dim)
 real, dimension(nclasses) :: initial_thickness=(/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) ! Total thickness of newly calved bergs (m)
-namelist /icebergs_nml/ verbose, budget, halo, iceberg_halo, traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj, &
+namelist /icebergs_nml/ verbose, budget, halo, iceberg_halo, traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,Static_icebergs,  &
          distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,bond_coef, radial_damping_coef, tangental_damping_coef, only_interactive_forces, &
-         rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, iceberg_bonds_on, manually_initialize_bonds, &
+         rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, iceberg_bonds_on, manually_initialize_bonds, ignore_missing_restart_bergs, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, halo_debugging, &
          time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, interactive_icebergs_on, critical_interaction_damping_on, &
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution, force_all_pes_traj
@@ -613,6 +617,8 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%time_average_weight=time_average_weight
   bergs%speed_limit=speed_limit
   bergs%Runge_not_Verlet=Runge_not_Verlet   
+  bergs%ignore_missing_restart_bergs=ignore_missing_restart_bergs
+  bergs%Static_icebergs=Static_icebergs 
   bergs%only_interactive_forces=only_interactive_forces
   bergs%halo_debugging=halo_debugging
   bergs%iceberg_bonds_on=iceberg_bonds_on   !Alon
@@ -3260,6 +3266,7 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
   y3=grd%lat(i  ,j  )
   x4=grd%lon(i-1,j  )
   y4=grd%lat(i-1,j  )
+  
 
   if (present(explain)) then
     if(explain) then
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 150948a..216224e 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -700,6 +700,7 @@ subroutine read_restart_bergs(bergs,Time)
 type(iceberg) :: localberg ! NOT a pointer but an actual local variable
 real :: pos_is_good, pos_is_good_all_pe
 integer :: stderrunit
+integer :: grdj, grdi
 
 real, allocatable, dimension(:) :: lon,          &
                                    lat,          &
@@ -831,7 +832,12 @@ subroutine read_restart_bergs(bergs,Time)
        pos_is_good_all_pe=pos_is_good
        call mpp_sum(pos_is_good_all_pe)
        if (pos_is_good_all_pe .lt. 0.5) then
-         call error_mesg('diamonds, read_restart_bergs', 'One of the iceberg positions was not found', FATAL)
+         if (bergs%ignore_missing_restart_bergs) then
+           call error_mesg('diamonds, read_restart_bergs', 'Iceberg number', iceberg_num(k), 'positions was not found', WARNING)
+         else
+           call error_mesg('diamonds, read_restart_bergs', 'Iceberg number', iceberg_num(k), 'positions was not found', FATAL)
+         endif
+
        endif
        if (really_debug) then
          write(stderrunit,'(a,i8,a,2f9.4,a,i8)') 'diamonds, read_restart_bergs: berg ',k,' is at ',localberg%lon,localberg%lat,&
@@ -911,6 +917,7 @@ subroutine read_restart_bergs(bergs,Time)
   call mpp_sum( bergs%bergy_mass_start )
   if (mpp_pe().eq.mpp_root_pe().and.verbose) write(*,'(a)') 'diamonds, read_restart_bergs: completed'
 
+
 contains
   
   subroutine generate_bergs(bergs,Time)

From 270838e3bfedffb904b181dcf7ba89b0af797412 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Tue, 19 Apr 2016 15:24:04 -0400
Subject: [PATCH 100/361] 1) Added a flag to turn thermodynamics off 2) Changed
 the restart read routine so that the model ignores icebergs which are
 positioned in grid cells with zero area

---
 icebergs.F90           | 4 +++-
 icebergs_framework.F90 | 5 ++++-
 icebergs_io.F90        | 8 ++++++--
 3 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index c99b26d..7c1ce40 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1438,7 +1438,9 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 
   ! Iceberg thermodynamics (melting) + rolling
   call mpp_clock_begin(bergs%clock_the)
-  call thermodynamics(bergs)
+  if (.not.bergs%Thermodynamics_off) then
+          call thermodynamics(bergs)
+  endif
   if (debug) call bergs_chksum(bergs, 'run bergs (thermo)')
   if (debug) call checksum_gridded(bergs%grd, 's/r run after thermodynamics')
   call mpp_clock_end(bergs%clock_the)
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index b76e366..de5c08b 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -210,6 +210,7 @@ module ice_bergs_framework
   logical :: Runge_not_Verlet=.True.  !True=Runge Kuttai, False=Verlet.   
   logical :: ignore_missing_restart_bergs=.False.  !True Allows the model to ignorm icebergs missing in the restart. 
   logical :: Static_icebergs=.False.  !True= icebergs do no move
+  logical :: Thermodynamics_off=.False.  !True,, then icebergs do not decay
   logical :: only_interactive_forces=.False.  !Icebergs only feel interactive forces, and not ocean, wind... 
   logical :: halo_debugging=.False.  !Use for debugging halos (remove when its working) 
   logical :: save_short_traj=.True.  !True saves only lon,lat,time,iceberg_num in iceberg_trajectory.nc 
@@ -318,6 +319,7 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: Runge_not_Verlet=.True.  !True=Runge Kutta, False=Verlet.  - Added by Alon 
 logical :: ignore_missing_restart_bergs=.False.  !True Allows the model to ignorm icebergs missing in the restart. 
 logical :: Static_icebergs=.False.  !True= icebergs do no move
+logical :: Thermodynamics_off=.False.  !True,, then icebergs do not decay
 logical :: only_interactive_forces=.False.  !Icebergs only feel interactive forces, and not ocean, wind... 
 logical :: halo_debugging=.False.  !Use for debugging halos (remove when its working) 
 logical :: save_short_traj=.True.  !True saves only lon,lat,time,iceberg_num in iceberg_trajectory.nc 
@@ -335,7 +337,7 @@ subroutine ice_bergs_framework_init(bergs, &
 namelist /icebergs_nml/ verbose, budget, halo, iceberg_halo, traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,Static_icebergs,  &
          distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,bond_coef, radial_damping_coef, tangental_damping_coef, only_interactive_forces, &
          rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, iceberg_bonds_on, manually_initialize_bonds, ignore_missing_restart_bergs, &
-         parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, halo_debugging, &
+         parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, halo_debugging, Thermodynamics_off, &
          time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, interactive_icebergs_on, critical_interaction_damping_on, &
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution, force_all_pes_traj
 
@@ -619,6 +621,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%Runge_not_Verlet=Runge_not_Verlet   
   bergs%ignore_missing_restart_bergs=ignore_missing_restart_bergs
   bergs%Static_icebergs=Static_icebergs 
+  bergs%Thermodynamics_off=Thermodynamics_off 
   bergs%only_interactive_forces=only_interactive_forces
   bergs%halo_debugging=halo_debugging
   bergs%iceberg_bonds_on=iceberg_bonds_on   !Alon
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 216224e..2d34810 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -833,9 +833,9 @@ subroutine read_restart_bergs(bergs,Time)
        call mpp_sum(pos_is_good_all_pe)
        if (pos_is_good_all_pe .lt. 0.5) then
          if (bergs%ignore_missing_restart_bergs) then
-           call error_mesg('diamonds, read_restart_bergs', 'Iceberg number', iceberg_num(k), 'positions was not found', WARNING)
+           call error_mesg('diamonds, read_restart_bergs', 'Iceberg positions was not found', WARNING)
          else
-           call error_mesg('diamonds, read_restart_bergs', 'Iceberg number', iceberg_num(k), 'positions was not found', FATAL)
+           call error_mesg('diamonds, read_restart_bergs', 'Iceberg positions was not found', FATAL)
          endif
 
        endif
@@ -873,7 +873,11 @@ subroutine read_restart_bergs(bergs,Time)
          if (really_debug) lres=is_point_in_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, explain=.true.)
          lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
         !call add_new_berg_to_list(bergs%first, localberg, quick=.true.)
+        if (bergs%grd%area(localberg%ine,localberg%jne) .ne. 0)  then
          call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg)
+         else
+           call error_mesg('diamonds, read_restart_bergs', 'Iceberg not added because it is grounded', WARNING)
+         endif
          if (really_debug) call print_berg(stderrunit, bergs%list(localberg%ine,localberg%jne)%first, 'read_restart_bergs, add_new_berg_to_list')
        elseif (multiPErestart .and. io_tile_id(1) .lt. 0) then
          call error_mesg('diamonds, read_restart_bergs', 'berg in PE file was not on PE!', FATAL)

From a0fb9f09b88ad092aa1eaf40993bae0bdd836276 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Thu, 21 Apr 2016 16:48:38 -0400
Subject: [PATCH 101/361] 1) Iceberg spread mass to ocean routine has been
 edited to take into account the iceberg size. If the distance between an
 iceberg and the edge of a cell is greater than the iceberg length/2, then the
 iceberg does not share its mass with the neighbouring cell. This change
 allows icebergs which are initialized in a regular grid to interpolate their
 mass to a regular sea ice grid perfectly.

2) A piece of code has been added which initializes the iceberg halos on the edges of the domain correctly. Previously, the code only worked for a reentrant channel in the x-direction. The new code should work for non-reentrant boundary conditions and reentrant boundary conditions

3) The errors assosiated with an iceberg not being found in the restart file are changed to provide more information about which iceberg is not being found.
---
 icebergs.F90           | 67 +++++++++++++++++++++++++++---------------
 icebergs_framework.F90 | 60 +++++++++++++++++++++++++++----------
 icebergs_io.F90        | 12 ++++++--
 3 files changed, 98 insertions(+), 41 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 7c1ce40..659a1f4 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1019,12 +1019,20 @@ subroutine thermodynamics(bergs)
       endif
   
       ! Store the new state of iceberg (with L>W)
-      this%mass=Mnew
-      this%mass_of_bits=nMbits
-      this%thickness=Tn
-      this%width=min(Wn,Ln)
-      this%length=max(Wn,Ln)
-  
+      if (.not.bergs%Thermodynamics_off) then
+        this%mass=Mnew
+        this%mass_of_bits=nMbits
+        this%thickness=Tn
+        this%width=min(Wn,Ln)
+        this%length=max(Wn,Ln)
+      else
+        Mnew=this%mass
+        Wn=this%width
+        Ln=this%length
+        Tn=this%thickness
+        nMbits=this%mass_of_bits
+        Dn=(bergs%rho_bergs/rho_seawater)*Tn ! draught (keel depth)
+      endif
       next=>this%next
   
       ! Did berg completely melt?
@@ -1044,7 +1052,7 @@ subroutine thermodynamics(bergs)
             Hocean=bergs%grounding_fraction*(grd%ocean_depth(i,j)+grd%ssh(i,j))
             if (Dn>Hocean) Mnew=Mnew*min(1.,Hocean/Dn)
           endif
-          call spread_mass_across_ocean_cells(grd, i, j, this%xi, this%yj, Mnew, nMbits, this%mass_scaling)
+          call spread_mass_across_ocean_cells(grd, i, j, this%xi, this%yj, Mnew, nMbits, this%mass_scaling, this%length*this%width )
         endif
       endif
     
@@ -1056,26 +1064,41 @@ end subroutine thermodynamics
 
 ! ##############################################################################
 
-subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling)
+subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling, Area)
   ! Arguments
   type(icebergs_gridded), pointer :: grd
   integer, intent(in) :: i, j
-  real, intent(in) :: x, y, Mberg, Mbits, scaling
+  real, intent(in) :: x, y, Mberg, Mbits, scaling, Area
   ! Local variables
-  real :: xL, xC, xR, yD, yC, yU, Mass
+  real :: xL, xC, xR, yD, yC, yU, Mass, L
   real :: yDxL, yDxC, yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR
   real, parameter :: rho_seawater=1035.
-  
+
   Mass=(Mberg+Mbits)*scaling
   ! This line attempts to "clip" the weight felt by the ocean. The concept of
   ! clipping is non-physical and this step should be replaced by grounding.
   if (grd%clipping_depth>0.) Mass=min(Mass,grd%clipping_depth*grd%area(i,j)*rho_seawater)
+ 
+  !L is the non dimensional length of the iceberg [  L=(Area of berg/ Area of grid cell)^0.5  ] or something like that.
+
+  if (grd%area(i,j)>0) then
+          L=min( sqrt(Area / grd%area(i,j)),1.0)
+  else 
+        L=1.
+  endif
 
-  xL=min(0.5, max(0., 0.5-x))
-  xR=min(0.5, max(0., x-0.5))
+  !xL=min(0.5, max(0., 0.5-x))
+  !xR=min(0.5, max(0., x-0.5))
+  !xC=max(0., 1.-(xL+xR))
+  !yD=min(0.5, max(0., 0.5-y))
+  !yU=min(0.5, max(0., y-0.5))
+  !yC=max(0., 1.-(yD+yU))
+  
+  xL=min(0.5, max(0., 0.5-(x/L)))
+  xR=min(0.5, max(0., (x/L)+(0.5-(1/L) )))
   xC=max(0., 1.-(xL+xR))
-  yD=min(0.5, max(0., 0.5-y))
-  yU=min(0.5, max(0., y-0.5))
+  yD=min(0.5, max(0., 0.5-(y/L)))
+  yU=min(0.5, max(0., (y/L)+(0.5-(1/L) )))
   yC=max(0., 1.-(yD+yU))
 
   yDxL=yD*xL*grd%msk(i-1,j-1)
@@ -1438,9 +1461,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 
   ! Iceberg thermodynamics (melting) + rolling
   call mpp_clock_begin(bergs%clock_the)
-  if (.not.bergs%Thermodynamics_off) then
-          call thermodynamics(bergs)
-  endif
+  call thermodynamics(bergs)
   if (debug) call bergs_chksum(bergs, 'run bergs (thermo)')
   if (debug) call checksum_gridded(bergs%grd, 's/r run after thermodynamics')
   call mpp_clock_end(bergs%clock_the)
@@ -2136,7 +2157,7 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
         vvel3=vvel1+(dt_2*ayn)                  !Alon
 
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling)
+          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling, berg%length*berg%width )
 
         ! Calling the acceleration   (note that the velocity is converted to u_star inside the accel script)
         call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn, ayn, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
@@ -2251,7 +2272,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         if (berg%lat>89.) on_tangential_plane=.true.
         i1=i;j1=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling)
+          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width)
 
         ! Loading past accelerations - Alon
         axn=berg%axn; ayn=berg%ayn !Alon
@@ -2287,7 +2308,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         call adjust_index_and_ground(grd, lon2, lat2, uvel2, vvel2, i, j, xi, yj, bounced, error_flag)
         i2=i; j2=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling)
+          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling, berg%length*berg%width)
         ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon2,lat2,x2,y2)
         if (.not.error_flag) then
           if (debug .and. .not. is_point_in_cell(bergs%grd, lon2, lat2, i, j)) error_flag=.true.
@@ -2342,7 +2363,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         call adjust_index_and_ground(grd, lon3, lat3, uvel3, vvel3, i, j, xi, yj, bounced, error_flag)
         i3=i; j3=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling)
+          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width)
         ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon3,lat3,x3,y3)
         if (.not.error_flag) then
           if (debug .and. .not. is_point_in_cell(bergs%grd, lon3, lat3, i, j)) error_flag=.true.
@@ -2471,7 +2492,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         i=i1;j=j1;xi=berg%xi;yj=berg%yj
         call adjust_index_and_ground(grd, lonn, latn, uveln, vveln, i, j, xi, yj, bounced, error_flag)
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling)
+          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width)
   
         if (.not.error_flag) then
           if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j)) error_flag=.true.
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index de5c08b..4f6faa3 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -503,12 +503,34 @@ subroutine ice_bergs_framework_init(bergs, &
   call mpp_update_domains(grd%ocean_depth, grd%domain)
   call mpp_update_domains(grd%parity_x, grd%parity_y, grd%domain, gridtype=AGRID) ! If either parity_x/y is -ve, we need rotation of vectors
 
-  ! Sanitize lon and lat at the SW edges
+  ! Sanitize lon and lat in the southern halo
   do j=grd%jsc-1,grd%jsd,-1; do i=grd%isd,grd%ied
       if (grd%lon(i,j).gt.900.) grd%lon(i,j)=grd%lon(i,j+1)
       if (grd%lat(i,j).gt.900.) grd%lat(i,j)=2.*grd%lat(i,j+1)-grd%lat(i,j+2)
   enddo; enddo
 
+  ! fix halos on edge of the domain
+  !1) South
+  do j=grd%jsc-1,grd%jsd,-1; do i=grd%isd,grd%ied
+      if (grd%lon(i,j).gt.900.) grd%lon(i,j)=2.*grd%lon(i,j+1)-grd%lon(i,j+2)
+      if (grd%lat(i,j).gt.900.) grd%lat(i,j)=2.*grd%lat(i,j+1)-grd%lat(i,j+2)
+  enddo; enddo
+  !2) North
+  do j=grd%jec+1,grd%jed; do i=grd%isd,grd%ied
+      if (grd%lon(i,j).gt.900.) grd%lon(i,j)=2.*grd%lon(i,j-1)-grd%lon(i,j-2)
+      if (grd%lat(i,j).gt.900.) grd%lat(i,j)=2.*grd%lat(i,j-1)-grd%lat(i,j-2)
+  enddo; enddo
+  !3) West
+  do i=grd%isc-1,grd%isd,-1; do j=grd%jsd,grd%jed
+      if (grd%lon(i,j).gt.900.) grd%lon(i,j)=2.*grd%lon(i+1,j)-grd%lon(i+2,j)
+      if (grd%lat(i,j).gt.900.) grd%lat(i,j)=2.*grd%lat(i+1,j)-grd%lat(i+2,j)
+  enddo; enddo
+  !4) East
+  do i=grd%iec+1,grd%ied; do j=grd%jsd,grd%jed
+      if (grd%lon(i,j).gt.900.) grd%lon(i,j)=2.*grd%lon(i-1,j)-grd%lon(i-2,j)
+      if (grd%lat(i,j).gt.900.) grd%lat(i,j)=2.*grd%lat(i-1,j)-grd%lat(i-2,j)
+  enddo; enddo
+
   if (.not. present(maskmap)) then ! Using a maskmap causes tickles this sanity check
     do j=grd%jsd,grd%jed; do i=grd%isd,grd%ied
       if (grd%lon(i,j).gt.900.) write(stderrunit,*) 'bad lon: ',mpp_pe(),i-grd%isc+1,j-grd%jsc+1,grd%lon(i,j)
@@ -538,6 +560,11 @@ subroutine ice_bergs_framework_init(bergs, &
          grd%lon(i,j)=modulo(grd%lon(i,j)-minl,360.)+minl
   enddo; enddo
 
+
+
+
+
+
   ! lonc, latc used for searches
   do j=grd%jsd+1,grd%jed; do i=grd%isd+1,grd%ied
     grd%lonc(i,j)=0.25*( (grd%lon(i,j)+grd%lon(i-1,j-1)) &
@@ -552,20 +579,20 @@ subroutine ice_bergs_framework_init(bergs, &
          ' [lon|lat][min|max]=', minval(grd%lon),maxval(grd%lon),minval(grd%lat),maxval(grd%lat)
   endif
 
- !if (mpp_pe().eq.3) then
- !  write(stderrunit,'(a3,32i7)') 'Lon',(i,i=grd%isd,grd%ied)
- !  do j=grd%jed,grd%jsd,-1
- !    write(stderrunit,'(i3,32f7.1)') j,(grd%lon(i,j),i=grd%isd,grd%ied)
- !  enddo
- !  write(stderrunit,'(a3,32i7)') 'Lat',(i,i=grd%isd,grd%ied)
- !  do j=grd%jed,grd%jsd,-1
- !    write(stderrunit,'(i3,32f7.1)') j,(grd%lat(i,j),i=grd%isd,grd%ied)
- !  enddo
- !  write(stderrunit,'(a3,32i7)') 'Msk',(i,i=grd%isd,grd%ied)
- !  do j=grd%jed,grd%jsd,-1
- !    write(stderrunit,'(i3,32f7.1)') j,(grd%msk(i,j),i=grd%isd,grd%ied)
- !  enddo
- !endif
+ if (mpp_pe().eq.15) then
+   write(stderrunit,'(a3,32i7)') 'Lon',(i,i=grd%isd,grd%ied)
+   do j=grd%jed,grd%jsd,-1
+     write(stderrunit,'(i3,32f7.1)') j,(grd%lon(i,j),i=grd%isd,grd%ied)
+   enddo
+   write(stderrunit,'(a3,32i7)') 'Lat',(i,i=grd%isd,grd%ied)
+   do j=grd%jed,grd%jsd,-1
+     write(stderrunit,'(i3,32f7.1)') j,(grd%lat(i,j),i=grd%isd,grd%ied)
+   enddo
+   write(stderrunit,'(a3,32i7)') 'Msk',(i,i=grd%isd,grd%ied)
+   do j=grd%jed,grd%jsd,-1
+     write(stderrunit,'(i3,32f7.1)') j,(grd%msk(i,j),i=grd%isd,grd%ied)
+   enddo
+ endif
 
 
 !Added by Alon  - If a freq distribution is input, we have to convert the freq distribution to a mass flux distribution)
@@ -3086,9 +3113,12 @@ logical function is_point_in_cell(grd, x, y, i, j, explain)
            modulo(grd%lon(i  ,j-1)-(x-180.),360.)+(x-180.), &
            modulo(grd%lon(i-1,j  )-(x-180.),360.)+(x-180.), &
            modulo(grd%lon(i  ,j  )-(x-180.),360.)+(x-180.) )
+
   if (x.lt.xlo .or. x.gt.xhi) return
   ylo=min( grd%lat(i-1,j-1), grd%lat(i,j-1), grd%lat(i-1,j), grd%lat(i,j) )
   yhi=max( grd%lat(i-1,j-1), grd%lat(i,j-1), grd%lat(i-1,j), grd%lat(i,j) )
+
+
   if (y.lt.ylo .or. y.gt.yhi) return
   
   if (grd%lat(i,j).gt.89.999) then
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 2d34810..514e24d 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -833,7 +833,10 @@ subroutine read_restart_bergs(bergs,Time)
        call mpp_sum(pos_is_good_all_pe)
        if (pos_is_good_all_pe .lt. 0.5) then
          if (bergs%ignore_missing_restart_bergs) then
-           call error_mesg('diamonds, read_restart_bergs', 'Iceberg positions was not found', WARNING)
+           if (mpp_pe().eq.mpp_root_pe()) then
+                   print * , 'Iceberg not located: ', lon(k),lat(k), iceberg_num(k)
+                   call error_mesg('diamonds, read_restart_bergs', 'Iceberg positions was not found', WARNING)
+           endif
          else
            call error_mesg('diamonds, read_restart_bergs', 'Iceberg positions was not found', FATAL)
          endif
@@ -875,8 +878,11 @@ subroutine read_restart_bergs(bergs,Time)
         !call add_new_berg_to_list(bergs%first, localberg, quick=.true.)
         if (bergs%grd%area(localberg%ine,localberg%jne) .ne. 0)  then
          call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg)
-         else
-           call error_mesg('diamonds, read_restart_bergs', 'Iceberg not added because it is grounded', WARNING)
+        else
+           if (mpp_pe().eq.mpp_root_pe()) then
+             print * , 'Grounded iceberg: ', lat(k),lon(k), iceberg_num(k)
+             call error_mesg('diamonds, read_restart_bergs', 'Iceberg not added because it is grounded', WARNING)
+           endif
          endif
          if (really_debug) call print_berg(stderrunit, bergs%list(localberg%ine,localberg%jne)%first, 'read_restart_bergs, add_new_berg_to_list')
        elseif (multiPErestart .and. io_tile_id(1) .lt. 0) then

From e4019842abf30151bc3bc3f97ecd626da84c7432 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Thu, 21 Apr 2016 17:08:08 -0400
Subject: [PATCH 102/361] Commenting out the grid printout.

---
 icebergs_framework.F90 | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 4f6faa3..93a9af1 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -579,20 +579,20 @@ subroutine ice_bergs_framework_init(bergs, &
          ' [lon|lat][min|max]=', minval(grd%lon),maxval(grd%lon),minval(grd%lat),maxval(grd%lat)
   endif
 
- if (mpp_pe().eq.15) then
-   write(stderrunit,'(a3,32i7)') 'Lon',(i,i=grd%isd,grd%ied)
-   do j=grd%jed,grd%jsd,-1
-     write(stderrunit,'(i3,32f7.1)') j,(grd%lon(i,j),i=grd%isd,grd%ied)
-   enddo
-   write(stderrunit,'(a3,32i7)') 'Lat',(i,i=grd%isd,grd%ied)
-   do j=grd%jed,grd%jsd,-1
-     write(stderrunit,'(i3,32f7.1)') j,(grd%lat(i,j),i=grd%isd,grd%ied)
-   enddo
-   write(stderrunit,'(a3,32i7)') 'Msk',(i,i=grd%isd,grd%ied)
-   do j=grd%jed,grd%jsd,-1
-     write(stderrunit,'(i3,32f7.1)') j,(grd%msk(i,j),i=grd%isd,grd%ied)
-   enddo
- endif
+ !if (mpp_pe().eq.15) then
+ !  write(stderrunit,'(a3,32i7)') 'Lon',(i,i=grd%isd,grd%ied)
+ !  do j=grd%jed,grd%jsd,-1
+ !    write(stderrunit,'(i3,32f7.1)') j,(grd%lon(i,j),i=grd%isd,grd%ied)
+ !  enddo
+ !  write(stderrunit,'(a3,32i7)') 'Lat',(i,i=grd%isd,grd%ied)
+ !  do j=grd%jed,grd%jsd,-1
+ !    write(stderrunit,'(i3,32f7.1)') j,(grd%lat(i,j),i=grd%isd,grd%ied)
+ !  enddo
+ !  write(stderrunit,'(a3,32i7)') 'Msk',(i,i=grd%isd,grd%ied)
+ !  do j=grd%jed,grd%jsd,-1
+ !    write(stderrunit,'(i3,32f7.1)') j,(grd%msk(i,j),i=grd%isd,grd%ied)
+ !  enddo
+ !endif
 
 
 !Added by Alon  - If a freq distribution is input, we have to convert the freq distribution to a mass flux distribution)

From 418de89b71073221efdbf4d460271db577e0cf45 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Tue, 26 Apr 2016 18:24:27 -0400
Subject: [PATCH 103/361] Fixed a bug in the iceberg rolling scheme. The sign
 of the inequality was the wrong way, which was making the icebergs tip
 immediately.

---
 icebergs.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/icebergs.F90 b/icebergs.F90
index c038011..548903d 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -885,7 +885,7 @@ subroutine thermodynamics(bergs)
             ! Equation 27 from Burton et al 2012, or equivolently, Weeks and Mellor 1979 with constant density
             tip_parameter=sqrt(6*(bergs%rho_bergs/rho_seawater)*(1-(bergs%rho_bergs/rho_seawater)))   !using default values gives 0.92
           endif
-          if (Tn<(tip_parameter* Wn))  then     !note that we use the Thickness instead of the Draft
+          if (Tn>(tip_parameter* Wn))  then     !note that we use the Thickness instead of the Draft
               call swap_variables(Tn,Wn)
           endif
         endif

From 76dfade7266e55e4456929973515e85373e5a62a Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 27 Apr 2016 12:01:24 -0400
Subject: [PATCH 104/361] Fixed bug in the Burton icebergs tipping scheme.
 Icebergs should be stable when Wn=Tn. The tipping criteria is
 Tn*tipping_parameter>Wn where tipping_paramter<1.

---
 icebergs.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 548903d..a861f71 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -885,7 +885,7 @@ subroutine thermodynamics(bergs)
             ! Equation 27 from Burton et al 2012, or equivolently, Weeks and Mellor 1979 with constant density
             tip_parameter=sqrt(6*(bergs%rho_bergs/rho_seawater)*(1-(bergs%rho_bergs/rho_seawater)))   !using default values gives 0.92
           endif
-          if (Tn>(tip_parameter* Wn))  then     !note that we use the Thickness instead of the Draft
+          if ((tip_parameter*Tn)>Wn)  then     !note that we use the Thickness instead of the Draft
               call swap_variables(Tn,Wn)
           endif
         endif

From 6471ed915807720d9ed120751f1181980bc68e9a Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Fri, 13 May 2016 09:45:09 -0400
Subject: [PATCH 105/361] Thermodynamics_off flag has been removed, since it
 was not really working anyway. Turning thermodynamic effects off can be
 achieved by setting calving to zero in the OCN in the datatable.

---
 icebergs.F90           | 11 +----------
 icebergs_framework.F90 |  5 +----
 2 files changed, 2 insertions(+), 14 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 659a1f4..10a2e82 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1019,21 +1019,12 @@ subroutine thermodynamics(bergs)
       endif
   
       ! Store the new state of iceberg (with L>W)
-      if (.not.bergs%Thermodynamics_off) then
         this%mass=Mnew
         this%mass_of_bits=nMbits
         this%thickness=Tn
         this%width=min(Wn,Ln)
         this%length=max(Wn,Ln)
-      else
-        Mnew=this%mass
-        Wn=this%width
-        Ln=this%length
-        Tn=this%thickness
-        nMbits=this%mass_of_bits
-        Dn=(bergs%rho_bergs/rho_seawater)*Tn ! draught (keel depth)
-      endif
-      next=>this%next
+        next=>this%next
   
       ! Did berg completely melt?
       if (Mnew<=0.) then ! Delete the berg
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 93a9af1..8193f2e 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -210,7 +210,6 @@ module ice_bergs_framework
   logical :: Runge_not_Verlet=.True.  !True=Runge Kuttai, False=Verlet.   
   logical :: ignore_missing_restart_bergs=.False.  !True Allows the model to ignorm icebergs missing in the restart. 
   logical :: Static_icebergs=.False.  !True= icebergs do no move
-  logical :: Thermodynamics_off=.False.  !True,, then icebergs do not decay
   logical :: only_interactive_forces=.False.  !Icebergs only feel interactive forces, and not ocean, wind... 
   logical :: halo_debugging=.False.  !Use for debugging halos (remove when its working) 
   logical :: save_short_traj=.True.  !True saves only lon,lat,time,iceberg_num in iceberg_trajectory.nc 
@@ -319,7 +318,6 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: Runge_not_Verlet=.True.  !True=Runge Kutta, False=Verlet.  - Added by Alon 
 logical :: ignore_missing_restart_bergs=.False.  !True Allows the model to ignorm icebergs missing in the restart. 
 logical :: Static_icebergs=.False.  !True= icebergs do no move
-logical :: Thermodynamics_off=.False.  !True,, then icebergs do not decay
 logical :: only_interactive_forces=.False.  !Icebergs only feel interactive forces, and not ocean, wind... 
 logical :: halo_debugging=.False.  !Use for debugging halos (remove when its working) 
 logical :: save_short_traj=.True.  !True saves only lon,lat,time,iceberg_num in iceberg_trajectory.nc 
@@ -337,7 +335,7 @@ subroutine ice_bergs_framework_init(bergs, &
 namelist /icebergs_nml/ verbose, budget, halo, iceberg_halo, traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,Static_icebergs,  &
          distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,bond_coef, radial_damping_coef, tangental_damping_coef, only_interactive_forces, &
          rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, iceberg_bonds_on, manually_initialize_bonds, ignore_missing_restart_bergs, &
-         parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, halo_debugging, Thermodynamics_off, &
+         parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, halo_debugging,  &
          time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, interactive_icebergs_on, critical_interaction_damping_on, &
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution, force_all_pes_traj
 
@@ -648,7 +646,6 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%Runge_not_Verlet=Runge_not_Verlet   
   bergs%ignore_missing_restart_bergs=ignore_missing_restart_bergs
   bergs%Static_icebergs=Static_icebergs 
-  bergs%Thermodynamics_off=Thermodynamics_off 
   bergs%only_interactive_forces=only_interactive_forces
   bergs%halo_debugging=halo_debugging
   bergs%iceberg_bonds_on=iceberg_bonds_on   !Alon

From 23390e2bc1cc853d6cbbd890cbf61104e3111bb1 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Fri, 13 May 2016 12:11:13 -0400
Subject: [PATCH 106/361] Added a warning for icebergs being born on land

---
 icebergs.F90 | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/icebergs.F90 b/icebergs.F90
index d8326b9..7f52661 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1753,6 +1753,10 @@ subroutine calve_icebergs(bergs)
             write(stderrunit,*) 'diamonds, calve_icebergs: something went very wrong!',i,j,xi,yj
             call error_mesg('diamonds, calve_icebergs', 'berg xi,yj is not correct!', FATAL)
           endif
+          if (grd%msk(i,j)<0.5) then
+            write(stderrunit,*) 'diamonds, adjust: WARNING!!! Iceberg born in land cell',i,j,newberg%lon,newberg%lat
+            if (debug) call error_mesg('diamonds,calve_icebergs', 'Iceberg born in Land Cell!', FATAL)
+          endif
           newberg%ine=i
           newberg%jne=j
           newberg%xi=xi

From 88050d2daa28536eac024a4bc45ef8b89b6b28b1 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Fri, 13 May 2016 12:56:40 -0400
Subject: [PATCH 107/361] Fixed comment in warning message

- Warning message said it was issued from "adjust()" when it is
  actually issued from calve_icebergs().
- No answer changes.
---
 icebergs.F90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 7f52661..75dd448 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1754,8 +1754,8 @@ subroutine calve_icebergs(bergs)
             call error_mesg('diamonds, calve_icebergs', 'berg xi,yj is not correct!', FATAL)
           endif
           if (grd%msk(i,j)<0.5) then
-            write(stderrunit,*) 'diamonds, adjust: WARNING!!! Iceberg born in land cell',i,j,newberg%lon,newberg%lat
-            if (debug) call error_mesg('diamonds,calve_icebergs', 'Iceberg born in Land Cell!', FATAL)
+            write(stderrunit,*) 'diamonds, calve_icebergs: WARNING!!! Iceberg born in land cell',i,j,newberg%lon,newberg%lat
+            if (debug) call error_mesg('diamonds, calve_icebergs', 'Iceberg born in Land Cell!', FATAL)
           endif
           newberg%ine=i
           newberg%jne=j

From 10ca543baaf0d6ffa6f4b54ca13e86bdca983751 Mon Sep 17 00:00:00 2001
From: William Cooke <William.Cooke@noaa.gov>
Date: Fri, 27 May 2016 16:08:56 -0400
Subject: [PATCH 108/361] Fix for situation where no land points buffer the
 southern edge of the ocean.

A situation arose where halo points had NaNs and were introduced through the surface stress fields.
The workaround was to zero out the array before use.
Proper fix might involve adding an extra gridpoint or two at the southern edge. This may be atmospheric resolution dependent.
---
 icebergs.F90 | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/icebergs.F90 b/icebergs.F90
index 75dd448..cbbf95f 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1199,6 +1199,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     Jv_off = (size(tauya,2) - (grd%jec - grd%jsc))/2 - grd%jsc + 1
     allocate(uC_tmp(grd%isd:grd%ied,grd%jsd:grd%jed), &
              vC_tmp(grd%isd:grd%ied,grd%jsd:grd%jed))
+    uC_tmp(:,:) = 0.0
+    vC_tmp(:,:) = 0.0
     !   If the iceberg model used symmetric memory, the starting value of these
     ! copies would need to be decremented by 1.
     do I=grd%isc,grd%iec ; do j=grd%jsc,grd%jec
@@ -2615,6 +2617,12 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
   lret=pos_within_cell(grd, lon, lat, i, j, xi, yj) ! Update xi and yj
 
   if (.not. lret) then
+    write(0,*) 'i0, j0,=', i0,j0
+    write(0,*) 'xi0, yj0,=', xi0,yj0
+    write(0,*) 'grd%msk(i0, j0)=', grd%msk(i0,j0)
+    write(0,*) 'lon0, lat0,=', lon0,lat0
+    write(0,*) 'i,j,lon, lat,grd%msk(i,j)=', i,j,lon,lat,grd%msk(i,j)
+    
     write(stderrunit,*) 'diamonds, adjust: Should not get here! Berg is not in cell after adjustment'
     if (debug) error=.true.
   endif

From ec650393bfb5bdea43cfce1410aace3d2de9301c Mon Sep 17 00:00:00 2001
From: Nicholas Hannah <nchlshnnh@gmail.com>
Date: Wed, 1 Jun 2016 11:30:24 +1000
Subject: [PATCH 109/361] Merge loops over identical ranges. #303

---
 icebergs.F90 | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 75dd448..dd31a52 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1201,10 +1201,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
              vC_tmp(grd%isd:grd%ied,grd%jsd:grd%jed))
     !   If the iceberg model used symmetric memory, the starting value of these
     ! copies would need to be decremented by 1.
-    do I=grd%isc,grd%iec ; do j=grd%jsc,grd%jec
-      uC_tmp(I,j) = tauxa(I+Iu_off, j+ju_off)
-    enddo ; enddo
-    do i=grd%isc,grd%iec ; do J=grd%jsc,grd%jec
+    do i=grd%isc,grd%iec ; do j=grd%jsc,grd%jec
+      uC_tmp(i,j) = tauxa(i+Iu_off, j+ju_off)
       vC_tmp(i,J) = tauya(i+iv_off, J+Jv_off)
     enddo ; enddo
 

From 47174d093c228698c2795cd9f9026ac87f08c1de Mon Sep 17 00:00:00 2001
From: Nicholas Hannah <nchlshnnh@gmail.com>
Date: Wed, 1 Jun 2016 15:59:22 +1000
Subject: [PATCH 110/361] Introduce missing value. This prevents valgrind
 errors on masked points.

No answer changes. Closes https://github.com/NOAA-GFDL/MOM6/issues/303.
---
 icebergs.F90           | 3 +++
 icebergs_framework.F90 | 3 ++-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/icebergs.F90 b/icebergs.F90
index dd31a52..2ddf811 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -35,6 +35,7 @@ module ice_bergs
 use ice_bergs_framework, only: grd_chksum2,grd_chksum3
 use ice_bergs_framework, only: fix_restart_dates, offset_berg_dates
 use ice_bergs_framework, only: orig_read  ! Remove when backward compatibility no longer needed
+use ice_bergs_framework, only: missing_value
 
 use ice_bergs_io,        only: ice_bergs_io_init,write_restart,write_trajectory
 use ice_bergs_io,        only: read_restart_bergs,read_restart_bergs_orig,read_restart_calving
@@ -1199,6 +1200,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     Jv_off = (size(tauya,2) - (grd%jec - grd%jsc))/2 - grd%jsc + 1
     allocate(uC_tmp(grd%isd:grd%ied,grd%jsd:grd%jed), &
              vC_tmp(grd%isd:grd%ied,grd%jsd:grd%jed))
+    uC_tmp(:,:) = missing_value
+    vC_tmp(:,:) = missing_value
     !   If the iceberg model used symmetric memory, the starting value of these
     ! copies would need to be decremented by 1.
     do i=grd%isc,grd%iec ; do j=grd%jsc,grd%jec
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 4d255d5..a720096 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -18,6 +18,7 @@ module ice_bergs_framework
 integer, parameter :: buffer_width=28 !Changed from 20 to 28 by Alon 
 integer, parameter :: buffer_width_traj=31  !Changed from 23 by Alon
 integer, parameter :: nclasses=10 ! Number of ice bergs classes
+real, parameter :: missing_value = -1.0e34
 
 !Local Vars
 ! Global data (minimal for debugging)
@@ -45,7 +46,7 @@ module ice_bergs_framework
 public nclasses,buffer_width,buffer_width_traj
 public verbose, really_debug, debug, restart_input_dir,make_calving_reproduce,old_bug_bilin,use_roundoff_fix
 public ignore_ij_restart, use_slow_find,generate_test_icebergs,old_bug_rotated_weights,budget
-public orig_read, force_all_pes_traj
+public orig_read, force_all_pes_traj, missing_value
 
 
 !Public types

From 16fb3f5bffe6c83bed3a732c9420b84945169515 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Thu, 2 Jun 2016 09:28:18 -0400
Subject: [PATCH 111/361] Replaced "missing_value" in stress halos with zero

- When the wind stress is staggered the southern most edge of
  a global domain, or edge abutting a masked PE, might not be
  updated by mpp_update_domains(). A previous fix (47174d093c228)
  corrected the use of uninitialized data but set the stresses to
  hugely unphysical values in order to allow trapping. Since the
  values can be felt in cells next to these non-updated halos we
  are opting to set the stress to zero instead.
---
 icebergs.F90           | 5 ++---
 icebergs_framework.F90 | 3 +--
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 2ddf811..814debd 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -35,7 +35,6 @@ module ice_bergs
 use ice_bergs_framework, only: grd_chksum2,grd_chksum3
 use ice_bergs_framework, only: fix_restart_dates, offset_berg_dates
 use ice_bergs_framework, only: orig_read  ! Remove when backward compatibility no longer needed
-use ice_bergs_framework, only: missing_value
 
 use ice_bergs_io,        only: ice_bergs_io_init,write_restart,write_trajectory
 use ice_bergs_io,        only: read_restart_bergs,read_restart_bergs_orig,read_restart_calving
@@ -1200,8 +1199,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     Jv_off = (size(tauya,2) - (grd%jec - grd%jsc))/2 - grd%jsc + 1
     allocate(uC_tmp(grd%isd:grd%ied,grd%jsd:grd%jed), &
              vC_tmp(grd%isd:grd%ied,grd%jsd:grd%jed))
-    uC_tmp(:,:) = missing_value
-    vC_tmp(:,:) = missing_value
+    uC_tmp(:,:) = 0. ! This avoids uninitialized values that might remain in halo
+    vC_tmp(:,:) = 0. ! regions after the call to mpp_update_domains() below.
     !   If the iceberg model used symmetric memory, the starting value of these
     ! copies would need to be decremented by 1.
     do i=grd%isc,grd%iec ; do j=grd%jsc,grd%jec
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index a720096..4d255d5 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -18,7 +18,6 @@ module ice_bergs_framework
 integer, parameter :: buffer_width=28 !Changed from 20 to 28 by Alon 
 integer, parameter :: buffer_width_traj=31  !Changed from 23 by Alon
 integer, parameter :: nclasses=10 ! Number of ice bergs classes
-real, parameter :: missing_value = -1.0e34
 
 !Local Vars
 ! Global data (minimal for debugging)
@@ -46,7 +45,7 @@ module ice_bergs_framework
 public nclasses,buffer_width,buffer_width_traj
 public verbose, really_debug, debug, restart_input_dir,make_calving_reproduce,old_bug_bilin,use_roundoff_fix
 public ignore_ij_restart, use_slow_find,generate_test_icebergs,old_bug_rotated_weights,budget
-public orig_read, force_all_pes_traj, missing_value
+public orig_read, force_all_pes_traj
 
 
 !Public types

From 5ff50b2e4446f5755fb69b1b8991ade0e68c1289 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 22 Jun 2016 18:27:43 -0400
Subject: [PATCH 112/361] Added ability for icebergs to spread their mass as
 hexagons. It is not quite working yet, but is almost there.

---
 icebergs.F90           | 497 ++++++++++++++++++++++++++++++++++++++---
 icebergs_framework.F90 |   5 +-
 2 files changed, 465 insertions(+), 37 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 10a2e82..1e46be0 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1043,7 +1043,7 @@ subroutine thermodynamics(bergs)
             Hocean=bergs%grounding_fraction*(grd%ocean_depth(i,j)+grd%ssh(i,j))
             if (Dn>Hocean) Mnew=Mnew*min(1.,Hocean/Dn)
           endif
-          call spread_mass_across_ocean_cells(grd, i, j, this%xi, this%yj, Mnew, nMbits, this%mass_scaling, this%length*this%width )
+          call spread_mass_across_ocean_cells(grd, i, j, this%xi, this%yj, Mnew, nMbits, this%mass_scaling, this%length*this%width, bergs%hexagonal_icebergs )
         endif
       endif
     
@@ -1055,52 +1055,135 @@ end subroutine thermodynamics
 
 ! ##############################################################################
 
-subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling, Area)
+subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling, Area, hexagonal_icebergs)
   ! Arguments
   type(icebergs_gridded), pointer :: grd
   integer, intent(in) :: i, j
   real, intent(in) :: x, y, Mberg, Mbits, scaling, Area
+  logical, intent(in) :: hexagonal_icebergs
   ! Local variables
   real :: xL, xC, xR, yD, yC, yU, Mass, L
   real :: yDxL, yDxC, yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR
+  real :: S, H, origin_x, origin_y, x0, y0, theta
+  real :: Area_Q1,Area_Q2 , Area_Q3,Area_Q4, Area_hex
   real, parameter :: rho_seawater=1035.
+  integer :: stderrunit
+
+  ! Get the stderr unit number
+  stderrunit = stderr()
 
   Mass=(Mberg+Mbits)*scaling
   ! This line attempts to "clip" the weight felt by the ocean. The concept of
   ! clipping is non-physical and this step should be replaced by grounding.
   if (grd%clipping_depth>0.) Mass=min(Mass,grd%clipping_depth*grd%area(i,j)*rho_seawater)
  
-  !L is the non dimensional length of the iceberg [  L=(Area of berg/ Area of grid cell)^0.5  ] or something like that.
+  !Initialize weights for each cell       
+  yDxL=0.  ; yDxC=0. ; yDxR=0. ; yCxL=0. ; yCxR=0.
+  yUxL=0.  ; yUxC=0. ; yUxR=0. ; yCxC=1.
+
+  if (.not. hexagonal_icebergs) then  !Treat icebergs as rectangles of size L:
+    !L is the non dimensional length of the iceberg [  L=(Area of berg/ Area of grid cell)^0.5  ] or something like that.
+    if (grd%area(i,j)>0) then
+      L=min( sqrt(Area / grd%area(i,j)),1.0)
+    else 
+      L=1.
+    endif
+  
+    !Old version before icebergs were given size L
+    !xL=min(0.5, max(0., 0.5-x))
+    !xR=min(0.5, max(0., x-0.5))
+    !xC=max(0., 1.-(xL+xR))
+    !yD=min(0.5, max(0., 0.5-y))
+    !yU=min(0.5, max(0., y-0.5))
+    !yC=max(0., 1.-(yD+yU))
+  
+    xL=min(0.5, max(0., 0.5-(x/L)))
+    xR=min(0.5, max(0., (x/L)+(0.5-(1/L) )))
+    xC=max(0., 1.-(xL+xR))
+    yD=min(0.5, max(0., 0.5-(y/L)))
+    yU=min(0.5, max(0., (y/L)+(0.5-(1/L) )))
+    yC=max(0., 1.-(yD+yU))
+
+    yDxL=yD*xL*grd%msk(i-1,j-1)
+    yDxC=yD*xC*grd%msk(i  ,j-1)
+    yDxR=yD*xR*grd%msk(i+1,j-1)
+    yCxL=yC*xL*grd%msk(i-1,j  )
+    yCxR=yC*xR*grd%msk(i+1,j  )
+    yUxL=yU*xL*grd%msk(i-1,j+1)
+    yUxC=yU*xC*grd%msk(i  ,j+1)
+    yUxR=yU*xR*grd%msk(i+1,j+1)
+    yCxC=1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )
 
-  if (grd%area(i,j)>0) then
-          L=min( sqrt(Area / grd%area(i,j)),1.0)
-  else 
-        L=1.
-  endif
+ 
+  else !Spread mass as if elements area hexagonal
 
-  !xL=min(0.5, max(0., 0.5-x))
-  !xR=min(0.5, max(0., x-0.5))
-  !xC=max(0., 1.-(xL+xR))
-  !yD=min(0.5, max(0., 0.5-y))
-  !yU=min(0.5, max(0., y-0.5))
-  !yC=max(0., 1.-(yD+yU))
-  
-  xL=min(0.5, max(0., 0.5-(x/L)))
-  xR=min(0.5, max(0., (x/L)+(0.5-(1/L) )))
-  xC=max(0., 1.-(xL+xR))
-  yD=min(0.5, max(0., 0.5-(y/L)))
-  yU=min(0.5, max(0., (y/L)+(0.5-(1/L) )))
-  yC=max(0., 1.-(yD+yU))
-
-  yDxL=yD*xL*grd%msk(i-1,j-1)
-  yDxC=yD*xC*grd%msk(i  ,j-1)
-  yDxR=yD*xR*grd%msk(i+1,j-1)
-  yCxL=yC*xL*grd%msk(i-1,j  )
-  yCxR=yC*xR*grd%msk(i+1,j  )
-  yUxL=yU*xL*grd%msk(i-1,j+1)
-  yUxC=yU*xC*grd%msk(i  ,j+1)
-  yUxR=yU*xR*grd%msk(i+1,j+1)
-  yCxC=1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )
+    if (grd%area(i,j)>0) then
+      H = min(( (sqrt(Area/(2.*sqrt(3.)))  / sqrt(grd%area(i,j)))),1.) ;  !Non dimensionalize element length by grid area. (This gives the non-dim Apothen of the hexagon)
+    else 
+      H= (sqrt(3.)/2)*(0.49)  !Larges allowable H, since this makes S=0.49, and S has to be less than 0.5  (Not sure what the implications of this are)
+    endif
+    S=(2/sqrt(3.))*H !Side of the hexagon
+
+    if (S>0.5) then
+      !The width of an iceberg should not be greater than half the gridcell, or else it can spread over 3 cells  (i.e. S must be less than 0.5 nondimensionally)
+      !print 'Elements must be smaller than a whole gridcell', 'i.e.: S= ' , S , '>=0.5'
+      call error_mesg('diamonds, hexagonal spreading', 'Diameter of the iceberg is larger than a grid cell. Use smaller icebergs', WARNING)
+    endif
+
+    !Subtracting the position of the nearest corner from x,y  (The mass will then be spread over the 4 cells connected to that corner)
+    origin_x=1. ; origin_y=1.
+    if (x<0.5) origin_x=0.
+    if (y<0.5) origin_y=0.
+    
+    !Position of the hexagon center, relative to origin at the nearest vertex
+    x0=(x-origin_x)
+    y0=(y-origin_y)
+
+    theta=0.0
+    call Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
+    
+    if (min(min(Area_Q1,Area_Q2),min(Area_Q3, Area_Q4)) <0) then
+      call error_mesg('diamonds, hexagonal spreading', 'Intersection with hexagons should not be negative!!!', WARNING)
+    endif
+
+    Area_Q1=Area_Q1/Area_hex
+    Area_Q2=Area_Q2/Area_hex
+    Area_Q3=Area_Q3/Area_hex
+    Area_Q4=Area_Q4/Area_hex
+
+    !Now, you decide which quadrant belongs to which mass on ocean cell.
+    if ((x.ge. 0.5) .and. (y.ge. 0.5)) then !Top right vertex
+      yUxR=Area_Q1
+      yUxC=Area_Q2
+      yCxC=Area_Q3
+      yCxR=Area_Q4
+    elseif ((x .lt. 0.5) .and. (y.ge. 0.5)) then  !Top left vertex
+      yUxC=Area_Q1
+      yUxL=Area_Q2
+      yCxL=Area_Q3
+      yCxC=Area_Q4
+    elseif ((x.lt.0.5) .and. (y.lt. 0.5)) then !Bottom left vertex
+      yCxC=Area_Q1
+      yCxL=Area_Q2
+      yDxL=Area_Q3
+      yDxC=Area_Q4
+    elseif ((x.ge.0.5) .and. (y.lt. 0.5)) then!Bottom right vertex
+      yCxR=Area_Q1
+      yCxC=Area_Q2
+      yDxC=Area_Q3
+      yDxR=Area_Q4
+    endif
+                        
+
+      !Double check that all the mass is being used.
+      if (abs(yCxC-(1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )))>0.001) then
+        !call error_mesg('diamonds, hexagonal spreading', 'All the mass is not being used!!!', WARNING)
+        write(stderrunit,*) 'diamonds, hexagonal spreading, dimensions',S, H, x0 , y0
+        write(stderrunit,*) 'diamonds, hexagonal spreading, Areas',(Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,Area_Q2 , Area_Q3,Area_Q4
+        call error_mesg('diamonds, hexagonal spreading', 'All the mass is not being used!!!', FATAL)
+      endif
+
+  endif
 
   grd%mass_on_ocean(i,j,1)=grd%mass_on_ocean(i,j,1)+yDxL*Mass
   grd%mass_on_ocean(i,j,2)=grd%mass_on_ocean(i,j,2)+yDxC*Mass
@@ -1114,8 +1197,350 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
 
 end subroutine spread_mass_across_ocean_cells
 
+
+
+
+
 ! ##############################################################################
 
+real function Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy)
+  ! Arguments
+  real, intent(in) :: Ax,Ay,Bx,By,Cx,Cy
+  Area_of_triangle    =   abs(    0.5*((Ax*(By-Cy))+(Bx*(Cy-Ay))+(Cx*(Ay-By))) );
+end function Area_of_triangle
+
+
+logical function point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,qx,qy,include_boundary)
+  !This function decides whether a point (qx,qy) is inside the triangle ABC.
+  !There is also the option to include the boundary of the triangle.
+  ! Arguments
+  real, intent(in) :: Ax,Ay,Bx,By,Cx,Cy,qx,qy,include_boundary
+  real :: tol, invDenom,u,v
+  real :: v0x,v1x,v2x,v0y,v1y,v2y,dot00,dot01,dot02,dot11,dot12
+  
+  tol=0.0000000001;
+  if (include_boundary==0.) tol=-tol;  !Negative number excludes the boundary case.
+  
+  if ((Ax==qx .and. Ay==qy) .or. (Bx==qx .and. By==qy) .or. (Cx==qx .and. Cy==qy)) then  !Exclude the pathelogical case
+    if (include_boundary==0.) then
+      point_in_triangle = .False.
+    else
+      point_in_triangle = .True.
+    endif
+  else
+  
+    !Compute vectors
+    v0x=Cx-Ax;
+    v1x=Bx-Ax;
+    v2x=qx-Ax;
+    v0y=Cy-Ay;
+    v1y=By-Ay;
+    v2y=qy-Ay;
+
+    !Compute dot products
+    dot00 = (v0x*v0x)+(v0y*v0y);
+    dot01 = (v0x*v1x)+(v0y*v1y);
+    dot02 = (v0x*v2x)+(v0y*v2y);
+    dot11 = (v1x*v1x)+(v1y*v1y);
+    dot12 = (v1x*v2x)+(v1y*v2y);
+
+    !Compute barycentric coordinates
+    invDenom= 1 / ((dot00 * dot11) - (dot01*dot01));
+    u=((dot11*dot02)-(dot01*dot12))*invDenom;
+    v=((dot00*dot12)-(dot01*dot02))*invDenom;
+
+    point_in_triangle = ((  ((u+tol).ge.0.) .and. ((v+tol).ge.0)) .and. ((u+v).lt.(1+tol)))
+  endif
+end function point_in_triangle
+
+
+subroutine Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axis1,Area_positive, Area_negative)  !You should change this name a little, so that it not similar the other routine.
+!This function calculates the area of a triangle on opposited sides of an axis when the triangle is split with two points on one side, and one point on the other.
+!In this fuction, A is the point on one side of the axis, and B,C are on the opposite sides
+  ! Arguments
+  real , intent(in) :: Ax,Ay,Bx,By,Cx,Cy
+  character , intent(in) :: axis1
+  real, intent(out) :: Area_positive, Area_negative
+  real :: pABx, pABy, pACx, pACy, A0
+  real :: A_half_triangle, A_triangle
+
+  A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
+
+  call intercept_of_a_line(Ax,Ay,Bx,By,axis1,pABx, pABy);
+  call intercept_of_a_line(Ax,Ay,Cx,Cy,axis1,pACx, pACy);
+
+  if (axis1=='x')  A0=Ay; !Value used for if statements (deciding up/down vs left/right)
+  if (axis1=='y')  A0=Ax; !Value used for if statements (deciding up/down vs left/right)
+
+  A_half_triangle=Area_of_triangle(Ax,Ay,pABx,pABy,pACx,pACy);
+  if (A0>=0.) then
+    Area_positive= A_half_triangle;
+    Area_negative= A_triangle-A_half_triangle
+  else
+    Area_positive= A_triangle-A_half_triangle;
+    Area_negative= A_half_triangle;
+  endif
+
+end subroutine Area_of_triangle_across_axes
+
+subroutine intercept_of_a_line(Ax,Ay,Bx,By,axes1,x0,y0)
+!This routine returns the position (x0,y0) at which a line AB intercepts the x or y axis
+!The value No_intercept_val is returned when the line does not intercept the axis
+  !Arguments
+  real, intent(in) :: Ax,Ay,Bx,By
+  character, intent(in) ::axes1
+  real, intent(out) :: x0,y0
+  real :: No_intercept_val !Huge value used to make sure that the intercept is outside the triange in the parralel case.
+  
+
+  No_intercept_val=100000000000.; !Huge value used to make sure that the intercept is outside the triange in the parralel case. 
+  x0=No_intercept_val
+  y0=No_intercept_val
+  
+  if (axes1=='x') then  !x intercept
+    if (Ay.ne.By) then
+      x0=Ax -(((Ax-Bx)/(Ay-By))*Ay)
+      y0=0.
+    endif
+  endif
+
+  if (axes1=='y') then !y intercept
+    if (Ax.ne.Bx) then
+      x0=0.
+      y0=-(((Ay-By)/(Ax-Bx))*Ax)+Ay
+    endif
+  endif
+end subroutine intercept_of_a_line
+
+
+subroutine divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1,Area_positive, Area_negative)
+!This routine gives you the area of a triangle on opposite sides of the axis specified. 
+!It also takes care of the special case where the triangle is totally on one side
+!This routine calls Area_of_triangle_across_axes to calculate the areas when the triangles are split.
+
+  !Arguments
+  real, intent(in) :: Ax,Ay,Bx,By,Cx,Cy
+  character, intent(in) ::axes1
+  real, intent(out) :: Area_positive, Area_negative
+  real :: A0,B0,C0
+  real A_triangle 
+
+  if (axes1=='x') then  !Use the y-coordinates for if statements to see which side of the line you are on
+    A0=Ay
+    B0=By
+    C0=Cy
+  endif
+  if (axes1=='y') then  !Use the y-coordinates for if statements to see which side of the line you are on
+    A0=Ax
+    B0=Bx
+    C0=Cx
+  endif
+  
+  A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
+  if ((B0*C0)>0.) then !B and C are on the same side  (and non-zero)
+    if ((A0*B0).ge.0.) then !all three on the the same side (if it equals zero, then A0=0 and the otehrs are not)
+      if ((A0>0.)  .or.  ((A0==0.) .and.  (B0>0.))) then
+        Area_positive= A_triangle;
+        Area_negative= 0.;
+      else
+        Area_positive= 0.;
+        Area_negative= A_triangle;
+      endif
+    else  !A is on the opposite side to B and C
+      call Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1,Area_positive, Area_negative);
+    endif
+
+  elseif ((B0*C0)<0.) then !B and C are on the opposite sides
+    if ((A0*B0).ge. 0.) then !C is all alone
+      call Area_of_triangle_across_axes(Cx,Cy,Bx,By,Ax,Ay,axes1,Area_positive, Area_negative);
+    else !B is all alone
+      call Area_of_triangle_across_axes(Bx,By,Cx,Cy,Ax,Ay,axes1,Area_positive, Area_negative);
+    endif
+
+  else  !This is the case when either B or C is equal to zero (or both), A0 could be zero too.
+    if (((A0.eq.0.) .and. (B0.eq.0.)) .and. (C0.eq.0.)) then
+      Area_positive= 0.;
+      Area_negative= 0.;
+    elseif ((A0*B0<0.)  .or.  (A0*C0<0.)) then    !A, B are on opposite sides, and C is zero.  OR  A, C are on opposite sides, and B is zero.
+      call Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1,Area_positive, Area_negative);
+    elseif (((A0*B0>0.) .or. (A0*C0>0.)) .or. (((abs(A0)>0.) .and. (B0==0.)) .and. (C0==0.))) then
+      if (A0>0.) then
+        Area_positive= A_triangle;
+        Area_negative= 0.;
+      else
+        Area_positive= 0.;
+        Area_negative= A_triangle;
+      endif
+
+    elseif (A0.eq. 0.) then   !(one of B,C is zero too)
+      if ((B0>0.) .or. (C0>0.)) then
+        Area_positive= A_triangle;
+        Area_negative= 0.;
+      elseif ((B0<0.) .or. (C0<0.)) then
+        Area_positive= 0.;
+        Area_negative= A_triangle;
+      else
+        !print 'You should not get here1'
+        call error_mesg('diamonds, iceberg_run', 'Logical error inside triangle dividing routine', FATAL)
+      endif
+    else
+      !print 'You should not get here2'
+      call error_mesg('diamonds, iceberg_run', 'Another logical error inside triangle dividing routine', FATAL)
+    endif
+  endif
+end subroutine divding_triangle_across_axes
+
+
+subroutine Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy,Area_triangle, Area_Q1, Area_Q2 ,Area_Q3 ,Area_Q4)
+!This routine takes a triangle, and finds the intersection with the four quadrants
+  !Arguments
+  real, intent(in) :: Ax,Ay,Bx,By,Cx,Cy
+  real, intent(out) :: Area_triangle, Area_Q1, Area_Q2 ,Area_Q3 ,Area_Q4
+  real :: Area_Upper, Area_Lower, Area_Right, Area_Left
+  real :: px, py , qx , qy 
+  real :: Area_key_quadrant
+  integer :: Key_quadrant
+
+  Area_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
+  
+  !Calculating area across axes
+  call divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,'x',Area_Upper ,Area_Lower);
+  call divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,'y',Area_Right ,Area_Left);
+
+  !Decide if the origin is in the triangle. If so, then you have to divide the area 4 ways
+  !This is done by finding a quadrant where the intersection between the triangle and quadrant forms a new triangle
+  !(This occurs when on of the sides of the triangle  intersects both the x and y axis)
+  if (point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.,0.)) then
+    !Find a line in the triangle that cuts both axes in/on the trianlge
+    call intercept_of_a_line(Ax,Ay,Bx,By,'x',px,py); !x_intercept
+    call intercept_of_a_line(Ax,Ay,Bx,By,'y',qx,qy); !y_intercept
+    !Note that the 1. here means that we include points on the boundary of the triange.
+    if (.not.(point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,px,py,1.) .and. point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,qx,qy,1.))) then
+      call intercept_of_a_line(Ax,Ay,Cx,Cy,'x',px,py); !x_intercept
+      call intercept_of_a_line(Ax,Ay,Cx,Cy,'y',qx,qy); !y_intercept
+      if (.not.(point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,px,py,1.) .and. point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,qx,qy,1.))) then
+        call intercept_of_a_line(Bx,By,Cx,Cy,'x',px,py); !x_intercept
+        call intercept_of_a_line(Bx,By,Cx,Cy,'y',qx,qy); !y_intercept
+        if (.not.(point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,px,py,1.) .and. point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,qx,qy,1.))) then
+          !print 'Houston, we have a problem'
+          !You should not get here, but there might be some bugs in the code to do with points exactly falling on axes.
+          call error_mesg('diamonds, iceberg_run', 'Something went wrong with Triangle_divide_into_four_quadrants', FATAL)
+        endif
+      endif
+    endif
+
+    !Assigning quadrants. Key_quadrant is the quadrant with the baby triangle in it.
+    Area_key_quadrant=Area_of_triangle(px,py,qx,qy,0.,0.)
+    if ((px.ge. 0.) .and. (qy.ge. 0.)) then  !First quadrant
+      Key_quadrant=1;
+    elseif ((px.lt.0.) .and. (qy.ge. 0.)) then  !Second quadrant
+      Key_quadrant=2
+    elseif ((px.lt. 0.) .and. (qy.lt. 0.)) then !Third quadrant
+      Key_quadrant=3;  
+    else  !#Forth quadrant
+      Key_quadrant=4 
+    endif
+         
+  else  !At least one quadrant is empty, and this can be used to find the areas in the other quadrant.  Assigning quadrants. Key_quadrant is the empty quadrant.
+    Area_key_quadrant=0;
+    if      ( (.not. ((((Ax>0.) .and. (Ay>0.)) .or. ((Bx>0.) .and. (By> 0.))) .or. ((Cx>0.) .and. (Cy> 0.)))) .and. ((Area_Upper+Area_Right).le.Area_triangle) ) then
+      !No points land in this quadrant and triangle does not cross the quadrant
+      Key_quadrant=1;
+    elseif  ( (.not. ((((Ax<0.) .and. (Ay>=0)) .or. ((Bx<0.) .and. (By>=0.))) .or. ((Cx<0.) .and. (Cy>=0.)))) .and. ((Area_Upper+Area_Left).le. Area_triangle) ) then
+      Key_quadrant=2
+    elseif  ( (.not. ((((Ax<0.) .and. (Ay<0.)) .or. ((Bx<0.) .and. (By< 0.))) .or. ((Cx<0.) .and. (Cy< 0.)))) .and. ((Area_Lower+Area_Left) .le.Area_triangle) ) then
+      Key_quadrant=3;
+    else
+      Key_quadrant=4
+    endif
+  endif
+
+
+  !Assign values to quadrants
+  if (Key_quadrant .eq. 1) then
+    Area_Q1=Area_key_quadrant;
+    Area_Q2=Area_Upper-Area_Q1;
+    Area_Q4=Area_Right-Area_Q1;
+    Area_Q3=Area_Left-Area_Q2;
+  elseif (Key_quadrant .eq. 2) then
+    Area_Q2=Area_key_quadrant;
+    Area_Q1=Area_Upper-Area_Q2;
+    Area_Q4=Area_Right-Area_Q1;
+    Area_Q3=Area_Left-Area_Q2;
+  elseif (Key_quadrant==3) then
+    Area_Q3=Area_key_quadrant;
+    Area_Q2=Area_Left-Area_Q3;
+    Area_Q1=Area_Upper-Area_Q2;
+    Area_Q4=Area_Right-Area_Q1;
+  elseif (Key_quadrant==4) then
+    Area_Q4=Area_key_quadrant;
+    Area_Q1=Area_Right-Area_Q4;
+    Area_Q2=Area_Upper-Area_Q1;
+    Area_Q3=Area_Left-Area_Q2;
+  else
+    !print 'Help, I need somebody, help!'
+    call error_mesg('diamonds, iceberg_run', 'Logical error inside triangle into four quadrants. Should not get here.', FATAL)
+  endif
+
+  Area_Q1=max(Area_Q1,0.);
+  Area_Q2=max(Area_Q2,0.);
+  Area_Q3=max(Area_Q3,0.);
+  Area_Q4=max(Area_Q4,0.);
+
+
+end subroutine Triangle_divided_into_four_quadrants
+
+
+subroutine Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex ,Area_Q1, Area_Q2, Area_Q3, Area_Q4)
+  !This subroutine divides a regular hexagon centered at x0,y0 with apothen H, and orientation theta into its intersection with the 4 quadrants
+  !Theta=0 assumes that the apothen points upwards. (also the rotation is not working yet)
+  !Script works by finding the corners of the 6 triangles, and then finding the intersection of each of these with each quadrant.
+  !Arguments
+  real, intent(in) :: x0,y0,H,theta
+  real, intent(out) :: Area_hex ,Area_Q1, Area_Q2, Area_Q3, Area_Q4
+  real :: C1x, C2x, C3x, C4x, C5x, C6x
+  real :: C1y, C2y, C3y, C4y, C5y, C6y
+  real :: T12_Area, T12_Q1, T12_Q2, T12_Q3, T12_Q4
+  real :: T23_Area, T23_Q1, T23_Q2, T23_Q3, T23_Q4
+  real :: T34_Area, T34_Q1, T34_Q2, T34_Q3, T34_Q4
+  real :: T45_Area, T45_Q1, T45_Q2, T45_Q3, T45_Q4
+  real :: T56_Area, T56_Q1, T56_Q2, T56_Q3, T56_Q4
+  real :: T61_Area, T61_Q1, T61_Q2, T61_Q3, T61_Q4
+  real :: S
+
+  !Length of side of Hexagon
+  S=(2/sqrt(3.))*H
+  
+  !Finding positions of corners
+  C1x=S  +x0        ; C1y=0.+y0;  !Corner 1 (right)
+  C2x=H/sqrt(3.) +x0 ; C2y=H+y0;  !Corner 2 (top right)
+  C3x=-H/sqrt(3.)+x0 ; C3y=H+y0;  !Corner 3 (top left)
+  C4x=-S     +x0    ; C4y=0.+y0;  !Corner 4 (left)
+  C5x=-H/sqrt(3.) +x0; C5y=-H+y0; !Corner 5 (top left)
+  C6x=H/sqrt(3.) +x0 ; C6y=-H+y0; !Corner 3 (top left)
+
+  !Area of Hexagon is the sum of the triangles
+  call Triangle_divided_into_four_quadrants(x0,y0,C1x,C1y,C2x,C2y,T12_Area,T12_Q1,T12_Q2,T12_Q3,T12_Q4); !Triangle 012
+  call Triangle_divided_into_four_quadrants(x0,y0,C2x,C2y,C3x,C3y,T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4); !Triangle 023
+  call Triangle_divided_into_four_quadrants(x0,y0,C3x,C3y,C4x,C4y,T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4); !Triangle 034
+  call Triangle_divided_into_four_quadrants(x0,y0,C4x,C4y,C5x,C5y,T45_Area,T45_Q1,T45_Q2,T45_Q3,T45_Q4); !Triangle 045
+  call Triangle_divided_into_four_quadrants(x0,y0,C5x,C5y,C6x,C6y,T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4); !Triangle 056
+  call Triangle_divided_into_four_quadrants(x0,y0,C6x,C6y,C1x,C1y,T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4); !Triangle 061
+
+  !Summing up the triangles
+  Area_hex=T12_Area+T23_Area+T34_Area+T45_Area+T56_Area+T61_Area;
+  Area_Q1=T12_Q1+T23_Q1+T34_Q1+T45_Q1+T56_Q1+T61_Q1;
+  Area_Q2=T12_Q2+T23_Q2+T34_Q2+T45_Q2+T56_Q2+T61_Q2;
+  Area_Q3=T12_Q3+T23_Q3+T34_Q3+T45_Q3+T56_Q3+T61_Q3;
+  Area_Q4=T12_Q4+T23_Q4+T34_Q4+T45_Q4+T56_Q4+T61_Q4;
+
+
+end subroutine Hexagon_into_quadrants_using_triangles
+
+
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
 subroutine interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, cn, hi)
 ! Arguments
 type(icebergs_gridded), pointer :: grd
@@ -2148,7 +2573,7 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
         vvel3=vvel1+(dt_2*ayn)                  !Alon
 
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling, berg%length*berg%width )
+          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling, berg%length*berg%width ,bergs%hexagonal_icebergs )
 
         ! Calling the acceleration   (note that the velocity is converted to u_star inside the accel script)
         call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn, ayn, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
@@ -2263,7 +2688,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         if (berg%lat>89.) on_tangential_plane=.true.
         i1=i;j1=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width)
+          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, bergs%hexagonal_icebergs)
 
         ! Loading past accelerations - Alon
         axn=berg%axn; ayn=berg%ayn !Alon
@@ -2299,7 +2724,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         call adjust_index_and_ground(grd, lon2, lat2, uvel2, vvel2, i, j, xi, yj, bounced, error_flag)
         i2=i; j2=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling, berg%length*berg%width)
+          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling, berg%length*berg%width , bergs%hexagonal_icebergs)
         ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon2,lat2,x2,y2)
         if (.not.error_flag) then
           if (debug .and. .not. is_point_in_cell(bergs%grd, lon2, lat2, i, j)) error_flag=.true.
@@ -2354,7 +2779,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         call adjust_index_and_ground(grd, lon3, lat3, uvel3, vvel3, i, j, xi, yj, bounced, error_flag)
         i3=i; j3=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width)
+          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, bergs%hexagonal_icebergs)
         ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon3,lat3,x3,y3)
         if (.not.error_flag) then
           if (debug .and. .not. is_point_in_cell(bergs%grd, lon3, lat3, i, j)) error_flag=.true.
@@ -2483,7 +2908,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         i=i1;j=j1;xi=berg%xi;yj=berg%yj
         call adjust_index_and_ground(grd, lonn, latn, uveln, vveln, i, j, xi, yj, bounced, error_flag)
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width)
+          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, bergs%hexagonal_icebergs)
   
         if (.not.error_flag) then
           if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j)) error_flag=.true.
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 8193f2e..980c8f9 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -208,6 +208,7 @@ module ice_bergs_framework
   logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
   logical :: time_average_weight=.false. ! Time average the weight on the ocean
   logical :: Runge_not_Verlet=.True.  !True=Runge Kuttai, False=Verlet.   
+  logical :: hexagonal_icebergs=.False. !True treats icebergs as rectangles, False as hexagonal elements (for the purpose of mass spreading)
   logical :: ignore_missing_restart_bergs=.False.  !True Allows the model to ignorm icebergs missing in the restart. 
   logical :: Static_icebergs=.False.  !True= icebergs do no move
   logical :: only_interactive_forces=.False.  !Icebergs only feel interactive forces, and not ocean, wind... 
@@ -316,6 +317,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: speed_limit=0. ! CFL speed limit for a berg
 real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
 logical :: Runge_not_Verlet=.True.  !True=Runge Kutta, False=Verlet.  - Added by Alon 
+logical :: hexagonal_icebergs=.False. !True treats icebergs as rectangles, False as hexagonal elements (for the purpose of mass spreading)
 logical :: ignore_missing_restart_bergs=.False.  !True Allows the model to ignorm icebergs missing in the restart. 
 logical :: Static_icebergs=.False.  !True= icebergs do no move
 logical :: only_interactive_forces=.False.  !Icebergs only feel interactive forces, and not ocean, wind... 
@@ -335,7 +337,7 @@ subroutine ice_bergs_framework_init(bergs, &
 namelist /icebergs_nml/ verbose, budget, halo, iceberg_halo, traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,Static_icebergs,  &
          distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,bond_coef, radial_damping_coef, tangental_damping_coef, only_interactive_forces, &
          rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, iceberg_bonds_on, manually_initialize_bonds, ignore_missing_restart_bergs, &
-         parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, halo_debugging,  &
+         parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, halo_debugging, hexagonal_icebergs, &
          time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, interactive_icebergs_on, critical_interaction_damping_on, &
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution, force_all_pes_traj
 
@@ -644,6 +646,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%time_average_weight=time_average_weight
   bergs%speed_limit=speed_limit
   bergs%Runge_not_Verlet=Runge_not_Verlet   
+  bergs%hexagonal_icebergs=hexagonal_icebergs 
   bergs%ignore_missing_restart_bergs=ignore_missing_restart_bergs
   bergs%Static_icebergs=Static_icebergs 
   bergs%only_interactive_forces=only_interactive_forces

From c5d168e6737488e01fcbbdd30b881c22acfc798e Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Fri, 24 Jun 2016 18:08:33 -0400
Subject: [PATCH 113/361] Spreading of mass treating icebergs as hexagonal
 elements is now working.

This was done my fixing many bugs in the spreading scheme. One significant change is that we now apply thermodynamics to all the icebergs, including the halos. Before this change was made, the code did not reproduce across processors.

Hexagonal elements can not rotate yet.
---
 icebergs.F90 | 246 +++++++++++++++++++++++++++++++++++++++------------
 1 file changed, 187 insertions(+), 59 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 1e46be0..20e3e69 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -883,7 +883,8 @@ subroutine thermodynamics(bergs)
   ! For convenience
   grd=>bergs%grd
 
-  do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
+  !do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
+  do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied  ! Thermodynamics of  halos now calculated, so that spread mass to ocean works correctly
     this=>bergs%list(grdi,grdj)%first
     do while(associated(this))
       if (debug) call check_position(grd, this, 'thermodynamics (top)')
@@ -1068,6 +1069,7 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
   real :: Area_Q1,Area_Q2 , Area_Q3,Area_Q4, Area_hex
   real, parameter :: rho_seawater=1035.
   integer :: stderrunit
+  logical :: debug
 
   ! Get the stderr unit number
   stderrunit = stderr()
@@ -1081,7 +1083,8 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
   yDxL=0.  ; yDxC=0. ; yDxR=0. ; yCxL=0. ; yCxR=0.
   yUxL=0.  ; yUxC=0. ; yUxR=0. ; yCxC=1.
 
-  if (.not. hexagonal_icebergs) then  !Treat icebergs as rectangles of size L:
+  if (.not. hexagonal_icebergs) then  !Treat icebergs as rectangles of size L:  (this is the default)
+    
     !L is the non dimensional length of the iceberg [  L=(Area of berg/ Area of grid cell)^0.5  ] or something like that.
     if (grd%area(i,j)>0) then
       L=min( sqrt(Area / grd%area(i,j)),1.0)
@@ -1113,6 +1116,14 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
     yUxC=yU*xC*grd%msk(i  ,j+1)
     yUxR=yU*xR*grd%msk(i+1,j+1)
     yCxC=1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )
+    
+    !Temporary for debugging reasons.
+    if (mpp_pe()==mpp_root_pe()) then 
+            write(stderrunit,*) 'diamonds, You are in the square!!!', grd%area(i,j),L
+            write(stderrunit,*) 'diamonds, x,y', x,y
+            write(stderrunit,*) 'diamonds, xL,xC,xR', xL,xC,xR
+            write(stderrunit,*) 'diamonds, yU,yC,yD', yU,yC,yD
+    endif
 
  
   else !Spread mass as if elements area hexagonal
@@ -1142,8 +1153,9 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
     theta=0.0
     call Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
     
-    if (min(min(Area_Q1,Area_Q2),min(Area_Q3, Area_Q4)) <0) then
+    if (min(min(Area_Q1,Area_Q2),min(Area_Q3, Area_Q4)) <-0.001) then
       call error_mesg('diamonds, hexagonal spreading', 'Intersection with hexagons should not be negative!!!', WARNING)
+      write(stderrunit,*) 'diamonds, yU,yC,yD', Area_Q1, Area_Q2, Area_Q3, Area_Q4
     endif
 
     Area_Q1=Area_Q1/Area_hex
@@ -1174,26 +1186,32 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
       yDxR=Area_Q4
     endif
                         
+    !Temporary for debugging reasons.
+    if (mpp_pe()==mpp_root_pe()) then 
+            !write(stderrunit,*) 'diamonds, You are in the hexagonal domain now!!!'
+    endif
 
       !Double check that all the mass is being used.
-      if (abs(yCxC-(1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )))>0.001) then
+      if ((abs(yCxC-(1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )))>0.001) .and. (mpp_pe().eq.5)) then
         !call error_mesg('diamonds, hexagonal spreading', 'All the mass is not being used!!!', WARNING)
-        write(stderrunit,*) 'diamonds, hexagonal spreading, dimensions',S, H, x0 , y0
-        write(stderrunit,*) 'diamonds, hexagonal spreading, Areas',(Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,Area_Q2 , Area_Q3,Area_Q4
+        write(stderrunit,*) 'diamonds, hexagonal, H,x0,y0', H, x0 , y0
+        write(stderrunit,*) 'diamonds, hexagonal, Areas',(Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
+        debug=.True.
+        !call Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4, debug)
         call error_mesg('diamonds, hexagonal spreading', 'All the mass is not being used!!!', FATAL)
       endif
 
   endif
 
-  grd%mass_on_ocean(i,j,1)=grd%mass_on_ocean(i,j,1)+yDxL*Mass
-  grd%mass_on_ocean(i,j,2)=grd%mass_on_ocean(i,j,2)+yDxC*Mass
-  grd%mass_on_ocean(i,j,3)=grd%mass_on_ocean(i,j,3)+yDxR*Mass
-  grd%mass_on_ocean(i,j,4)=grd%mass_on_ocean(i,j,4)+yCxL*Mass
-  grd%mass_on_ocean(i,j,5)=grd%mass_on_ocean(i,j,5)+yCxC*Mass
-  grd%mass_on_ocean(i,j,6)=grd%mass_on_ocean(i,j,6)+yCxR*Mass
-  grd%mass_on_ocean(i,j,7)=grd%mass_on_ocean(i,j,7)+yUxL*Mass
-  grd%mass_on_ocean(i,j,8)=grd%mass_on_ocean(i,j,8)+yUxC*Mass
-  grd%mass_on_ocean(i,j,9)=grd%mass_on_ocean(i,j,9)+yUxR*Mass
+  grd%mass_on_ocean(i,j,1)=grd%mass_on_ocean(i,j,1)+(yDxL*Mass)
+  grd%mass_on_ocean(i,j,2)=grd%mass_on_ocean(i,j,2)+(yDxC*Mass)
+  grd%mass_on_ocean(i,j,3)=grd%mass_on_ocean(i,j,3)+(yDxR*Mass)
+  grd%mass_on_ocean(i,j,4)=grd%mass_on_ocean(i,j,4)+(yCxL*Mass)
+  grd%mass_on_ocean(i,j,5)=grd%mass_on_ocean(i,j,5)+(yCxC*Mass)
+  grd%mass_on_ocean(i,j,6)=grd%mass_on_ocean(i,j,6)+(yCxR*Mass)
+  grd%mass_on_ocean(i,j,7)=grd%mass_on_ocean(i,j,7)+(yUxL*Mass)
+  grd%mass_on_ocean(i,j,8)=grd%mass_on_ocean(i,j,8)+(yUxC*Mass)
+  grd%mass_on_ocean(i,j,9)=grd%mass_on_ocean(i,j,9)+(yUxR*Mass)
 
 end subroutine spread_mass_across_ocean_cells
 
@@ -1209,47 +1227,69 @@ real function Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy)
   Area_of_triangle    =   abs(    0.5*((Ax*(By-Cy))+(Bx*(Cy-Ay))+(Cx*(Ay-By))) );
 end function Area_of_triangle
 
+real function roundoff(x,sig_fig)
+  ! Arguments
+  real, intent(in) :: x
+  integer, intent(in) :: sig_fig
+    !roundoff=round(x*(10**(sig_fig))
+    roundoff=(FLOAT (INT(x * (10.**sig_fig) + 0.5)) / (10.**sig_fig))
+end function roundoff
+
+logical function point_in_interval(Ax,Ay,Bx,By,px,py)
+  ! Arguments
+  real, intent(in) :: Ax,Ay,Bx,By,px,py
+  point_in_interval=.False.
+  if ((px < max(Ax,Bx)) .and. (px > min(Ax,Bx))) then
+    if ((py < max(Ay,By)) .and. (py > min(Ay,By))) then
+      point_in_interval=.True.
+    endif
+  endif
+end function point_in_interval
+
+
+logical function point_is_on_the_line(Ax,Ay,Bx,By,qx,qy)
+  ! Arguments
+  real, intent(in) :: Ax,Ay,Bx,By,qx,qy
+  real :: tol, dxc,dyc,dxl,dyl,cross
+    tol=0.00000000000000;
+    dxc = qx - Ax;
+    dyc = qy - Ay;
+    dxl = Bx - Ax;
+    dyl = By - Ay;
+    cross = dxc * dyl - dyc * dxl;
+    if (abs(cross)<=tol) then
+      point_is_on_the_line=.True.
+    else
+     point_is_on_the_line=.False.
+    endif
+end function point_is_on_the_line
 
-logical function point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,qx,qy,include_boundary)
+logical function point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,qx,qy)
   !This function decides whether a point (qx,qy) is inside the triangle ABC.
   !There is also the option to include the boundary of the triangle.
   ! Arguments
-  real, intent(in) :: Ax,Ay,Bx,By,Cx,Cy,qx,qy,include_boundary
-  real :: tol, invDenom,u,v
+  real, intent(in) :: Ax,Ay,Bx,By,Cx,Cy,qx,qy
+  real :: l0,l1,l2,p0,p1,p2
   real :: v0x,v1x,v2x,v0y,v1y,v2y,dot00,dot01,dot02,dot11,dot12
   
-  tol=0.0000000001;
-  if (include_boundary==0.) tol=-tol;  !Negative number excludes the boundary case.
-  
+  point_in_triangle = .False.
   if ((Ax==qx .and. Ay==qy) .or. (Bx==qx .and. By==qy) .or. (Cx==qx .and. Cy==qy)) then  !Exclude the pathelogical case
-    if (include_boundary==0.) then
+      point_in_triangle = .False.
+  else
+    if (((point_is_on_the_line(Ax,Ay,Bx,By,qx,qy) .or. (point_is_on_the_line(Ax,Ay,Cx,Cy,qx,qy))) .or. (point_is_on_the_line(Bx,By,Cx,Cy,qx,qy)))) then
       point_in_triangle = .False.
     else
-      point_in_triangle = .True.
+      !Compute point in triangle using Barycentric coordinates (the same as sum_sign_dot_prod routines)
+      l0=(qx-Ax)*(By-Ay)-(qy-Ay)*(Bx-Ax)
+      l1=(qx-Bx)*(Cy-By)-(qy-By)*(Cx-Bx)
+      l2=(qx-Cx)*(Ay-Cy)-(qy-Cy)*(Ax-Cx)
+
+      p0=sign(1., l0); if (l0==0.)  p0=0.
+      p1=sign(1., l1); if (l1==0.)  p1=0.
+      p2=sign(1., l2); if (l2==0.)  p2=0.
+
+      if ( (abs(p0)+abs(p2))+(abs(p1)) == abs((p0+p2)+(p1)) )  point_in_triangle = .True.
     endif
-  else
-  
-    !Compute vectors
-    v0x=Cx-Ax;
-    v1x=Bx-Ax;
-    v2x=qx-Ax;
-    v0y=Cy-Ay;
-    v1y=By-Ay;
-    v2y=qy-Ay;
-
-    !Compute dot products
-    dot00 = (v0x*v0x)+(v0y*v0y);
-    dot01 = (v0x*v1x)+(v0y*v1y);
-    dot02 = (v0x*v2x)+(v0y*v2y);
-    dot11 = (v1x*v1x)+(v1y*v1y);
-    dot12 = (v1x*v2x)+(v1y*v2y);
-
-    !Compute barycentric coordinates
-    invDenom= 1 / ((dot00 * dot11) - (dot01*dot01));
-    u=((dot11*dot02)-(dot01*dot12))*invDenom;
-    v=((dot00*dot12)-(dot01*dot02))*invDenom;
-
-    point_in_triangle = ((  ((u+tol).ge.0.) .and. ((v+tol).ge.0)) .and. ((u+v).lt.(1+tol)))
   endif
 end function point_in_triangle
 
@@ -1398,8 +1438,23 @@ subroutine Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy,Area_triangle,
   real, intent(out) :: Area_triangle, Area_Q1, Area_Q2 ,Area_Q3 ,Area_Q4
   real :: Area_Upper, Area_Lower, Area_Right, Area_Left
   real :: px, py , qx , qy 
-  real :: Area_key_quadrant
+  real :: Area_key_quadrant,Error
   integer :: Key_quadrant
+  integer ::sig_fig
+  integer :: stderrunit
+
+  ! Get the stderr unit number
+  stderrunit = stderr()
+
+  !Round of numbers before proceeding further.
+  !sig_fig=12; !Significan figures
+  !Ax=roundoff(Ax0,sig_fig)
+  !Ay=roundoff(Ay0,sig_fig)
+  !Bx=roundoff(Bx0,sig_fig)
+  !By=roundoff(By0,sig_fig)
+  !Cx=roundoff(Cx0,sig_fig)
+  !Cy=roundoff(Cy0,sig_fig)
+ 
 
   Area_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
   
@@ -1410,20 +1465,23 @@ subroutine Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy,Area_triangle,
   !Decide if the origin is in the triangle. If so, then you have to divide the area 4 ways
   !This is done by finding a quadrant where the intersection between the triangle and quadrant forms a new triangle
   !(This occurs when on of the sides of the triangle  intersects both the x and y axis)
-  if (point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.,0.)) then
+  if (point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.)) then
     !Find a line in the triangle that cuts both axes in/on the trianlge
     call intercept_of_a_line(Ax,Ay,Bx,By,'x',px,py); !x_intercept
     call intercept_of_a_line(Ax,Ay,Bx,By,'y',qx,qy); !y_intercept
     !Note that the 1. here means that we include points on the boundary of the triange.
-    if (.not.(point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,px,py,1.) .and. point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,qx,qy,1.))) then
+    if (.not.((point_in_interval(Ax,Ay,Bx,By,px,py)) .and. (point_in_interval(Ax,Ay,Bx,By,qx,qy)))) then
       call intercept_of_a_line(Ax,Ay,Cx,Cy,'x',px,py); !x_intercept
       call intercept_of_a_line(Ax,Ay,Cx,Cy,'y',qx,qy); !y_intercept
-      if (.not.(point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,px,py,1.) .and. point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,qx,qy,1.))) then
+      if (.not.((point_in_interval(Ax,Ay,Cx,Cy,px,py)) .and. (point_in_interval(Ax,Ay,Cx,Cy,qx,qy)))) then
         call intercept_of_a_line(Bx,By,Cx,Cy,'x',px,py); !x_intercept
         call intercept_of_a_line(Bx,By,Cx,Cy,'y',qx,qy); !y_intercept
-        if (.not.(point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,px,py,1.) .and. point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,qx,qy,1.))) then
+        if (.not.((point_in_interval(Bx,By,Cx,Cy,px,py)) .and. (point_in_interval(Bx,By,Cx,Cy,qx,qy)))) then
           !print 'Houston, we have a problem'
           !You should not get here, but there might be some bugs in the code to do with points exactly falling on axes.
+          if (mpp_pe().eq.12) then
+            write(stderrunit,*) 'diamonds,corners', Ax,Ay,Bx,By,Cx,Cy
+          endif
           call error_mesg('diamonds, iceberg_run', 'Something went wrong with Triangle_divide_into_four_quadrants', FATAL)
         endif
       endif
@@ -1461,22 +1519,26 @@ subroutine Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy,Area_triangle,
     Area_Q1=Area_key_quadrant;
     Area_Q2=Area_Upper-Area_Q1;
     Area_Q4=Area_Right-Area_Q1;
-    Area_Q3=Area_Left-Area_Q2;
+    !Area_Q3=Area_Left-Area_Q2;   !These lines have been changes so that the sum of the 4 quadrants exactly matches the triangle area.
+    Area_Q3=Area_triangle-(Area_Q1+Area_Q2+Area_Q4);  
   elseif (Key_quadrant .eq. 2) then
     Area_Q2=Area_key_quadrant;
     Area_Q1=Area_Upper-Area_Q2;
     Area_Q4=Area_Right-Area_Q1;
-    Area_Q3=Area_Left-Area_Q2;
+    !Area_Q3=Area_Left-Area_Q2;
+    Area_Q3=Area_triangle-(Area_Q1+Area_Q2+Area_Q4);
   elseif (Key_quadrant==3) then
     Area_Q3=Area_key_quadrant;
     Area_Q2=Area_Left-Area_Q3;
     Area_Q1=Area_Upper-Area_Q2;
-    Area_Q4=Area_Right-Area_Q1;
+    !Area_Q4=Area_Right-Area_Q1;
+    Area_Q4=Area_triangle-(Area_Q1+Area_Q2+Area_Q3);
   elseif (Key_quadrant==4) then
     Area_Q4=Area_key_quadrant;
     Area_Q1=Area_Right-Area_Q4;
     Area_Q2=Area_Upper-Area_Q1;
-    Area_Q3=Area_Left-Area_Q2;
+    !Area_Q3=Area_Left-Area_Q2;
+    Area_Q3=Area_triangle-(Area_Q1+Area_Q2+Area_Q4);
   else
     !print 'Help, I need somebody, help!'
     call error_mesg('diamonds, iceberg_run', 'Logical error inside triangle into four quadrants. Should not get here.', FATAL)
@@ -1488,6 +1550,17 @@ subroutine Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy,Area_triangle,
   Area_Q4=max(Area_Q4,0.);
 
 
+  Error=abs(Area_Q1+Area_Q2+Area_Q3+Area_Q4-Area_triangle)
+  if (Error>0.01) then
+    call error_mesg('diamonds, triangle spreading', 'Triangle not evaluated accurately!!', WARNING)
+    if (mpp_pe().eq.mpp_root_pe()) then
+      write(stderrunit,*) 'diamonds, Triangle corners:',Ax,Ay,Bx,By,Cx,Cy
+      write(stderrunit,*) 'diamonds, Triangle, Areas', Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
+      write(stderrunit,*) 'diamonds, Triangle, Areas', Error
+    endif
+  endif
+
+
 end subroutine Triangle_divided_into_four_quadrants
 
 
@@ -1506,7 +1579,11 @@ subroutine Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex ,Area_Q
   real :: T45_Area, T45_Q1, T45_Q2, T45_Q3, T45_Q4
   real :: T56_Area, T56_Q1, T56_Q2, T56_Q3, T56_Q4
   real :: T61_Area, T61_Q1, T61_Q2, T61_Q3, T61_Q4
-  real :: S
+  real :: S, exact_hex_area, Error
+  integer :: stderrunit
+
+  ! Get the stderr unit number
+  stderrunit = stderr()
 
   !Length of side of Hexagon
   S=(2/sqrt(3.))*H
@@ -1532,8 +1609,53 @@ subroutine Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex ,Area_Q
   Area_Q1=T12_Q1+T23_Q1+T34_Q1+T45_Q1+T56_Q1+T61_Q1;
   Area_Q2=T12_Q2+T23_Q2+T34_Q2+T45_Q2+T56_Q2+T61_Q2;
   Area_Q3=T12_Q3+T23_Q3+T34_Q3+T45_Q3+T56_Q3+T61_Q3;
-  Area_Q4=T12_Q4+T23_Q4+T34_Q4+T45_Q4+T56_Q4+T61_Q4;
+  Area_Q4=T12_Q4+T23_Q4+T34_Q4+T45_Q4+T56_Q4+T61_Q4; 
+  
+  Area_Q1=max(Area_Q1,0.);
+  Area_Q2=max(Area_Q2,0.);
+  Area_Q3=max(Area_Q3,0.);
+  Area_Q4=max(Area_Q4,0.);
 
+  Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
+  if ((abs(Error)>0.01))then
+    if (mpp_pe().eq.mpp_root_pe()) then
+      call error_mesg('diamonds, hexagonal spreading', 'Hexagon error is large!!', WARNING)
+      write(stderrunit,*) 'diamonds, hex error, H,x0,y0, Error', H, x0 , y0, Error
+      write(stderrunit,*) 'diamonds, hex error, Areas',Area_hex, (Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
+      write(stderrunit,*) 'diamonds, Triangle1',C1x,C1y,C2x,C2y,T12_Area,T12_Q1,T12_Q2,T12_Q3,T12_Q4,(T12_Q1+T12_Q2+T12_Q3+T12_Q4-T12_Area)
+      write(stderrunit,*) 'diamonds, Triangle2',C2x,C2y,C3x,C3y,T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4,(T23_Q1+T23_Q2+T23_Q3+T23_Q4-T23_Area)
+      write(stderrunit,*) 'diamonds, Triangle3',C3x,C3y,C4x,C4y,T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4,(T34_Q1+T34_Q2+T34_Q3+T34_Q4-T34_Area)
+      write(stderrunit,*) 'diamonds, Triangle4',C4x,C4y,C5x,C5y,T45_Area,T45_Q1,T45_Q2,T45_Q3,T45_Q4,(T45_Q1+T45_Q2+T45_Q3+T45_Q4-T45_Area)
+      write(stderrunit,*) 'diamonds, Triangle5',C5x,C5y,C6x,C6y,T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4,(T56_Q1+T56_Q2+T56_Q3+T56_Q4-T56_Area)
+      write(stderrunit,*) 'diamonds, Triangle6',C6x,C6y,C1x,C1y,T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4,(T61_Q1+T61_Q2+T61_Q3+T61_Q4-T61_Area)
+    endif
+  endif
+
+  exact_hex_area=((3.*sqrt(3.)/2)*(S*S))
+  if (abs(Area_hex-exact_hex_area)>0.01) then
+    call error_mesg('diamonds, hexagonal spreading', 'Hexagon not evaluated accurately!!', WARNING)
+    if (mpp_pe().eq.mpp_root_pe()) then
+      write(stderrunit,*) 'diamonds, hex calculations, H,x0,y0', H, x0 , y0
+      write(stderrunit,*) 'diamonds, hex calculations, Areas',Area_hex, (Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
+    endif
+  endif
+
+  !Adjust Areas so that the error is zero by subtracting the error from the largest sector.
+   if  (((Area_Q1>=Area_Q2) .and. (Area_Q1>=Area_Q3)) .and. (Area_Q1>=Area_Q4)) then
+     Area_Q1=Area_Q1+Error
+   elseif  (((Area_Q2>=Area_Q1) .and. (Area_Q2>=Area_Q3)) .and. (Area_Q2>=Area_Q4)) then
+     Area_Q2=Area_Q2+Error
+   elseif  (((Area_Q3>=Area_Q1) .and. (Area_Q3>=Area_Q2)) .and. (Area_Q3>=Area_Q4)) then
+     Area_Q3=Area_Q3+Error
+   elseif  (((Area_Q4>=Area_Q1) .and. (Area_Q4>=Area_Q2)) .and. (Area_Q4>=Area_Q3)) then
+     Area_Q4=Area_Q4+Error
+   else
+     call error_mesg('diamonds, hexagonal spreading', 'Error in hexagon is larger than any quadrant!!', WARNING)
+     if (mpp_pe().eq.mpp_root_pe()) then
+      write(stderrunit,*) 'diamonds, hex quadrants, H,x0,y0', H, x0 , y0, Error
+      write(stderrunit,*) 'diamonds, hex quadrants, Areas',Area_hex, (Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
+     endif
+   endif
 
 end subroutine Hexagon_into_quadrants_using_triangles
 
@@ -2201,6 +2323,11 @@ subroutine icebergs_incr_mass(bergs, mass, Time)
 type(icebergs_gridded), pointer :: grd
 real :: dmda
 logical :: lerr
+integer :: stderrunit
+
+  ! Get the stderr unit number
+  stderrunit = stderr()
+      
 
   if (.not. associated(bergs)) return
 
@@ -2216,7 +2343,6 @@ subroutine icebergs_incr_mass(bergs, mass, Time)
  !mass(:,:)=mass(:,:)+( grd%mass(grd%isc:grd%iec,grd%jsc:grd%jec) &
  !                    + grd%bergy_mass(grd%isc:grd%iec,grd%jsc:grd%jec) )
 
-
   if (debug) then
     grd%tmp(:,:)=0.; grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec)=mass
     call grd_chksum2(grd, grd%tmp, 'mass in (incr)')
@@ -2572,8 +2698,10 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
         uvel3=uvel1+(dt_2*axn)                  !Alon
         vvel3=vvel1+(dt_2*ayn)                  !Alon
 
+        !Note, the mass scaling is equal to 1 (rather than 0.25 as in RK), since
+        !this is only called once in Verlet stepping.
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling, berg%length*berg%width ,bergs%hexagonal_icebergs )
+          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 1.0*berg%mass_scaling, berg%length*berg%width ,bergs%hexagonal_icebergs )
 
         ! Calling the acceleration   (note that the velocity is converted to u_star inside the accel script)
         call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn, ayn, bxn, byn) !axn, ayn, bxn, byn - Added by Alon

From 695a0de8dbe65146eb7e223c9f720f91ff393b3d Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Mon, 27 Jun 2016 15:09:43 -0400
Subject: [PATCH 114/361] A bug has been fixed, which prevented the model from
 reproducing across different layouts.

The model was copying icebergs from the restart file onto two different processors. This was because when an iceberg is placed directly on the edge of a grid cell, which is positioned on the edge of a processor, then the iceberg was determined to be in both cells, and was thus placed on both processors.

This has been fixed by editing the routine sum_sign_dot_prod4, so that it is asymtric, including points positioned on the south/west boundaries, and not including points on the north/east.
Note: This has only been done for the sum_sign_dot_prod4, and not for the sum_sign_dot_prod5 routine, which is used for icebregs near the northpole.

Two different tests have also been written to make sure that the correct amount of icebergs are read from the restart file.
---
 icebergs_framework.F90 | 10 ++++++----
 icebergs_io.F90        | 34 +++++++++++++++++++++++++++++++---
 2 files changed, 37 insertions(+), 7 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 980c8f9..eb0cc78 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -3186,10 +3186,12 @@ logical function sum_sign_dot_prod4(x0, y0, x1, y1, x2, y2, x3, y3, x, y, explai
   l2=(xx-xx2)*(y3-y2)-(y-y2)*(xx3-xx2)
   l3=(xx-xx3)*(y0-y3)-(y-y3)*(xx0-xx3)
 
-  p0=sign(1., l0); if (l0.eq.0.) p0=0.
-  p1=sign(1., l1); if (l1.eq.0.) p1=0.
-  p2=sign(1., l2); if (l2.eq.0.) p2=0.
-  p3=sign(1., l3); if (l3.eq.0.) p3=0.
+  !We use an asymerty between South and East line boundaries and North and East
+  !to avoid icebergs appearing to two cells (half values used for debugging
+  p0=sign(1., l0); if (l0.eq.0.) p0=-0.5
+  p1=sign(1., l1); if (l1.eq.0.) p1=0.5
+  p2=sign(1., l2); if (l2.eq.0.) p2=0.5
+  p3=sign(1., l3); if (l3.eq.0.) p3=-0.5
 
   if ( (abs(p0)+abs(p2))+(abs(p1)+abs(p3)) .eq. abs((p0+p2)+(p1+p3)) ) then
     sum_sign_dot_prod4=.true.
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 514e24d..8fd70ea 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -691,14 +691,15 @@ subroutine read_restart_bergs(bergs,Time)
 type(icebergs), pointer :: bergs
 type(time_type), intent(in) :: Time
 ! Local variables
-integer :: k, siz(4), nbergs_in_file
+integer :: k, siz(4), nbergs_in_file, nbergs_read
 logical :: lres, found_restart, found
+logical :: explain
 logical :: multiPErestart  ! Not needed with new restart read; currently kept for compatibility
 real :: lon0, lon1, lat0, lat1
 character(len=33) :: filename, filename_base
 type(icebergs_gridded), pointer :: grd
 type(iceberg) :: localberg ! NOT a pointer but an actual local variable
-real :: pos_is_good, pos_is_good_all_pe
+real :: pos_is_good, pos_is_good_all_pe,eps
 integer :: stderrunit
 integer :: grdj, grdi
 
@@ -831,8 +832,9 @@ subroutine read_restart_bergs(bergs,Time)
        endif
        pos_is_good_all_pe=pos_is_good
        call mpp_sum(pos_is_good_all_pe)
+       !Check to see if any iceberg in the restart file was not found
        if (pos_is_good_all_pe .lt. 0.5) then
-         if (bergs%ignore_missing_restart_bergs) then
+         if (bergs%ignore_missing_restart_bergs) then 
            if (mpp_pe().eq.mpp_root_pe()) then
                    print * , 'Iceberg not located: ', lon(k),lat(k), iceberg_num(k)
                    call error_mesg('diamonds, read_restart_bergs', 'Iceberg positions was not found', WARNING)
@@ -842,6 +844,13 @@ subroutine read_restart_bergs(bergs,Time)
          endif
 
        endif
+       !Check to see if any iceberg was found more than once.
+       if (pos_is_good_all_pe .gt. 1.5) then
+         if (mpp_pe().eq.mpp_root_pe()) then
+           print * , 'Iceberg was found more than once: ', lon(k),lat(k), iceberg_num(k)
+           call error_mesg('diamonds, read_restart_bergs', 'Iceberg copied twice', FATAL)
+         endif
+       endif
        if (really_debug) then
          write(stderrunit,'(a,i8,a,2f9.4,a,i8)') 'diamonds, read_restart_bergs: berg ',k,' is at ',localberg%lon,localberg%lat,&
               & ' on PE ',mpp_pe()
@@ -915,6 +924,25 @@ subroutine read_restart_bergs(bergs,Time)
                 jne,       &
                 iceberg_num,       &
                 start_year )
+
+     !Checking the total number of icebergs read from the restart file.
+     nbergs_read=count_bergs(bergs)
+     call mpp_sum(nbergs_read)
+     if (mpp_pe().eq.mpp_root_pe()) then
+       write(*,'(a,i8,a,i8,a)') 'diamonds, read_restart_bergs: Number of Icebergs in restart file=',nbergs_in_file,' Number of Icebergs read=', nbergs_read
+       if (nbergs_read .gt. nbergs_in_file) then
+         call error_mesg('diamonds, read_restart_bergs', 'More icebergs read than exist in restart file.', FATAL)
+       elseif (nbergs_read .lt. nbergs_in_file) then
+         if (bergs%ignore_missing_restart_bergs) then
+           call error_mesg('diamonds, read_restart_bergs', 'Some Icebergs from restart file were not found (ignore_missing flag is on)', WARNING)
+         else
+           call error_mesg('diamonds, read_restart_bergs', 'Some Icebergs from restart file were not found', FATAL)
+         endif
+       elseif (nbergs_read .eq. nbergs_in_file) then
+         write(*,'(a,i8,a,i8,a)') 'diamonds, read_restart_bergs: Number of icebergs read (#',nbergs_read,') matches the number of icebergs in the file'
+       endif
+     endif
+
   elseif(.not. found_restart .and. bergs%nbergs_start==0 .and. generate_test_icebergs) then
      call generate_bergs(bergs,Time)
   endif

From 5394e98845160d863b880ea0cc7b260200514f65 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Mon, 27 Jun 2016 17:28:59 -0400
Subject: [PATCH 115/361] Added a diagnostic within the iceberg model called
 spread_mass. This shows how iceberg mass would be spread onto the ocean if
 the spread_mass_to_ocean flag was on, and the passive mode flag was off. This
 allows us to see what the weight on the ocean would have been even for
 simuation where the iceberg is not adding weight to ocean. This is useful for
 testing.

---
 icebergs.F90           | 57 ++++++++++++++++++++++++++++++++----------
 icebergs_framework.F90 |  8 +++++-
 2 files changed, 51 insertions(+), 14 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 20e3e69..ff4be19 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1795,12 +1795,13 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 integer :: iyr, imon, iday, ihr, imin, isec, k
 type(icebergs_gridded), pointer :: grd
 logical :: lerr, sample_traj, write_traj, lbudget, lverbose, check_bond_quality 
-real :: unused_calving, tmpsum, grdd_berg_mass, grdd_bergy_mass
+real :: unused_calving, tmpsum, grdd_berg_mass, grdd_bergy_mass,grdd_spread_mass
 integer :: i, j, Iu, ju, iv, Jv, Iu_off, ju_off, iv_off, Jv_off
 real :: mask
 real, dimension(:,:), allocatable :: uC_tmp, vC_tmp
 integer :: vel_stagger, str_stagger
 integer :: nbonds
+logical :: within_iceberg_model
 
 integer :: stderrunit
 
@@ -1824,6 +1825,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   grd%bergy_src(:,:)=0.
   grd%bergy_melt(:,:)=0.
   grd%bergy_mass(:,:)=0.
+  grd%spread_mass(:,:)=0.
   grd%mass(:,:)=0.
   if (bergs%add_weight_to_ocean) grd%mass_on_ocean(:,:,:)=0.
   grd%virtual_area(:,:)=0.
@@ -2013,6 +2015,12 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     call write_trajectory(bergs%trajectories, bergs%save_short_traj)
   endif
 
+  !Update diagnostic of iceberg mass spread on ocean
+  if (grd%id_spread_mass>0) then
+          within_iceberg_model=.True.
+    call icebergs_incr_mass(bergs, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec),within_iceberg_model) 
+  endif
+
   ! Gridded diagnostics
   if (grd%id_uo>0) &
     lerr=send_data(grd%id_uo, grd%uo(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
@@ -2050,6 +2058,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     lerr=send_data(grd%id_bergy_melt, grd%bergy_melt(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   if (grd%id_bergy_mass>0) &
     lerr=send_data(grd%id_bergy_mass, grd%bergy_mass(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_spread_mass>0) &
+    lerr=send_data(grd%id_spread_mass, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   if (grd%id_mass>0) &
     lerr=send_data(grd%id_mass, grd%mass(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   if (grd%id_stored_ice>0) &
@@ -2106,6 +2116,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     bergs%floating_mass_end=sum_mass(bergs)
     bergs%icebergs_mass_end=sum_mass(bergs,justbergs=.true.)
     bergs%bergy_mass_end=sum_mass(bergs,justbits=.true.)
+    bergs%spread_mass_end=sum_mass(bergs) !Not sure what this is
     bergs%floating_heat_end=sum_heat(bergs)
     grd%tmpc(:,:)=0.;
     call mpp_clock_end(bergs%clock); call mpp_clock_end(bergs%clock_dia) ! To enable calling of public s/r
@@ -2118,6 +2129,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     call mpp_sum(bergs%floating_mass_end)
     call mpp_sum(bergs%icebergs_mass_end)
     call mpp_sum(bergs%bergy_mass_end)
+    call mpp_sum(bergs%spread_mass_end)
     call mpp_sum(bergs%floating_heat_end)
     call mpp_sum(bergs%returned_mass_on_ocean)
     call mpp_sum(bergs%nbergs_end)
@@ -2144,6 +2156,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     call mpp_sum(grdd_berg_mass)
     grdd_bergy_mass=sum( grd%bergy_mass(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
     call mpp_sum(grdd_bergy_mass)
+    grdd_spread_mass=sum( grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
+    call mpp_sum(grdd_spread_mass)
     if (mpp_pe().eq.mpp_root_pe()) then
  100 format("diamonds: ",a19,3(a18,"=",es14.7,x,a2,:,","),a12,i8)
  200 format("diamonds: ",a19,10(a18,"=",es14.7,x,a2,:,","))
@@ -2151,6 +2165,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
       call report_state('floating','kg','',bergs%floating_mass_start,'',bergs%floating_mass_end,'',bergs%nbergs_end)
       call report_state('icebergs','kg','',bergs%icebergs_mass_start,'',bergs%icebergs_mass_end,'')
       call report_state('bits','kg','',bergs%bergy_mass_start,'',bergs%bergy_mass_end,'')
+      call report_state('spread icebergs','kg','',bergs%spread_mass_start,'',bergs%spread_mass_end,'')
       call report_istate('berg #','',bergs%nbergs_start,'',bergs%nbergs_end,'')
       call report_ibudget('berg #','calved',bergs%nbergs_calved, &
                                    'melted',bergs%nbergs_melted, &
@@ -2172,6 +2187,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
                                          'net mass',bergs%stored_start+bergs%floating_mass_start, &
                                                     bergs%stored_end+bergs%floating_mass_end)
       call report_consistant('iceberg mass','kg','gridded',grdd_berg_mass,'bergs',bergs%icebergs_mass_end)
+      call report_consistant('spread mass','kg','gridded',grdd_spread_mass,'bergs',bergs%spread_mass_end)
       call report_consistant('bits mass','kg','gridded',grdd_bergy_mass,'bits',bergs%bergy_mass_end)
       call report_consistant('wieght','kg','returned',bergs%returned_mass_on_ocean,'floating',bergs%floating_mass_end)
       call report_state('net heat','J','',bergs%stored_heat_start+bergs%floating_heat_start,'',&
@@ -2207,6 +2223,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     bergs%floating_mass_start=bergs%floating_mass_end
     bergs%icebergs_mass_start=bergs%icebergs_mass_end
     bergs%bergy_mass_start=bergs%bergy_mass_end
+    bergs%spread_mass_start=bergs%spread_mass_end
     bergs%net_calving_used=0.
     bergs%net_calving_to_bergs=0.
     bergs%net_heat_to_bergs=0.
@@ -2313,11 +2330,13 @@ end subroutine icebergs_run
 
 ! ##############################################################################
 
-subroutine icebergs_incr_mass(bergs, mass, Time)
+subroutine icebergs_incr_mass(bergs, mass, within_iceberg_model, Time)
 ! Arguments
 type(icebergs), pointer :: bergs
 real, dimension(bergs%grd%isc:bergs%grd%iec,bergs%grd%jsc:bergs%grd%jec), intent(inout) :: mass
 type(time_type), intent(in), optional :: Time
+logical, intent(in), optional :: within_iceberg_model
+logical :: within_model
 ! Local variables
 integer :: i, j
 type(icebergs_gridded), pointer :: grd
@@ -2327,14 +2346,19 @@ subroutine icebergs_incr_mass(bergs, mass, Time)
 
   ! Get the stderr unit number
   stderrunit = stderr()
+  
+  
+  within_model=.False.
+  if (present(within_iceberg_model)) then 
+    within_model=within_iceberg_model
+  endif
       
-
-  if (.not. associated(bergs)) return
-
-  if (.not. bergs%add_weight_to_ocean) return
-
-  call mpp_clock_begin(bergs%clock)
-  call mpp_clock_begin(bergs%clock_int)
+  if (.not.(within_model)) then
+    if (.not. associated(bergs)) return
+    if (.not. bergs%add_weight_to_ocean) return
+    call mpp_clock_begin(bergs%clock)
+    call mpp_clock_begin(bergs%clock_int)
+  endif
 
   ! For convenience
   grd=>bergs%grd
@@ -2370,7 +2394,12 @@ subroutine icebergs_incr_mass(bergs, mass, Time)
          +   ( (grd%mass_on_ocean(i-1,j  ,6)+grd%mass_on_ocean(i+1,j  ,4))   &
          +     (grd%mass_on_ocean(i  ,j-1,8)+grd%mass_on_ocean(i  ,j+1,2)) ) )
     if (grd%area(i,j)>0) dmda=dmda/grd%area(i,j)*grd%msk(i,j)
-    if (.not. bergs%passive_mode) mass(i,j)=mass(i,j)+dmda
+
+    if (.not.(within_model)) then
+      if (.not. bergs%passive_mode) mass(i,j)=mass(i,j)+dmda
+    else
+      mass(i,j)=dmda
+    endif
     if (grd%id_mass_on_ocn>0) grd%tmp(i,j)=dmda
   enddo; enddo
   if (present(Time).and. (grd%id_mass_on_ocn>0)) &
@@ -2382,9 +2411,10 @@ subroutine icebergs_incr_mass(bergs, mass, Time)
     call grd_chksum2(grd, grd%tmp, 'mass out (incr)')
   endif
 
-  call mpp_clock_end(bergs%clock_int)
-  call mpp_clock_end(bergs%clock)
-
+  if (.not.(within_model)) then
+    call mpp_clock_end(bergs%clock_int)
+    call mpp_clock_end(bergs%clock)
+  endif
 end subroutine icebergs_incr_mass
 
 ! ##############################################################################
@@ -3565,6 +3595,7 @@ subroutine icebergs_end(bergs)
   deallocate(bergs%grd%bergy_src)
   deallocate(bergs%grd%bergy_melt)
   deallocate(bergs%grd%bergy_mass)
+  deallocate(bergs%grd%spread_mass)
   deallocate(bergs%grd%virtual_area)
   deallocate(bergs%grd%mass)
   deallocate(bergs%grd%mass_on_ocean)
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index eb0cc78..9d7736d 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -113,6 +113,7 @@ module ice_bergs_framework
   real, dimension(:,:), pointer :: bergy_src=>null() ! Mass flux from berg erosion into bergy bits (kg/s/m^2)
   real, dimension(:,:), pointer :: bergy_melt=>null() ! Melting rate of bergy bits (kg/s/m^2)
   real, dimension(:,:), pointer :: bergy_mass=>null() ! Mass distribution of bergy bits (kg/s/m^2)
+  real, dimension(:,:), pointer :: spread_mass=>null() ! Mass of icebergs after spreading (kg/s/m^2)
   real, dimension(:,:), pointer :: virtual_area=>null() ! Virtual surface coverage by icebergs (m^2)
   real, dimension(:,:), pointer :: mass=>null() ! Mass distribution (kg/m^2)
   real, dimension(:,:,:), pointer :: mass_on_ocean=>null() ! Mass distribution partitioned by neighbor (kg/m^2)
@@ -131,7 +132,7 @@ module ice_bergs_framework
   integer :: id_calving_hflx_in=-1, id_stored_heat=-1, id_melt_hflx=-1, id_heat_content=-1
   integer :: id_mass=-1, id_ui=-1, id_vi=-1, id_ua=-1, id_va=-1, id_sst=-1, id_cn=-1, id_hi=-1
   integer :: id_bergy_src=-1, id_bergy_melt=-1, id_bergy_mass=-1, id_berg_melt=-1
-  integer :: id_mass_on_ocn=-1, id_ssh=-1, id_fax=-1, id_fay=-1
+  integer :: id_mass_on_ocn=-1, id_ssh=-1, id_fax=-1, id_fay=-1,  id_spread_mass=-1
 
   real :: clipping_depth=0. ! The effective depth at which to clip the weight felt by the ocean [m].
 
@@ -238,6 +239,7 @@ module ice_bergs_framework
   real :: floating_heat_start=0., floating_heat_end=0.
   real :: icebergs_mass_start=0., icebergs_mass_end=0.
   real :: bergy_mass_start=0., bergy_mass_end=0.
+  real :: spread_mass_start=0., spread_mass_end=0.
   real :: returned_mass_on_ocean=0.
   real :: net_melt=0., berg_melt=0., bergy_src=0., bergy_melt=0.
   integer :: nbergs_calved=0, nbergs_melted=0, nbergs_start=0, nbergs_end=0
@@ -451,6 +453,7 @@ subroutine ice_bergs_framework_init(bergs, &
   allocate( grd%bergy_src(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%bergy_src(:,:)=0.
   allocate( grd%bergy_melt(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%bergy_melt(:,:)=0.
   allocate( grd%bergy_mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%bergy_mass(:,:)=0.
+  allocate( grd%spread_mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_mass(:,:)=0.
   allocate( grd%virtual_area(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%virtual_area(:,:)=0.
   allocate( grd%mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%mass(:,:)=0.
   allocate( grd%mass_on_ocean(grd%isd:grd%ied, grd%jsd:grd%jed, 9) ); grd%mass_on_ocean(:,:,:)=0.
@@ -696,6 +699,8 @@ subroutine ice_bergs_framework_init(bergs, &
      'Melt rate of bergy bits', 'kg/(m^2*s)')
   grd%id_bergy_mass=register_diag_field('icebergs', 'bergy_mass', axes, Time, &
      'Bergy bit density field', 'kg/(m^2)')
+  grd%id_spread_mass=register_diag_field('icebergs', 'spread_mass', axes, Time, &
+     'Iceberg mass after spreading', 'kg/(m^2)')
   grd%id_virtual_area=register_diag_field('icebergs', 'virtual_area', axes, Time, &
      'Virtual coverage by icebergs', 'm^2')
   grd%id_mass=register_diag_field('icebergs', 'mass', axes, Time, &
@@ -3595,6 +3600,7 @@ subroutine checksum_gridded(grd, label)
   call grd_chksum2(grd, grd%bergy_src, 'bergy_src')
   call grd_chksum2(grd, grd%bergy_melt, 'bergy_melt')
   call grd_chksum2(grd, grd%bergy_mass, 'bergy_mass')
+  call grd_chksum2(grd, grd%bergy_mass, 'spread_mass')
   call grd_chksum2(grd, grd%virtual_area, 'varea')
   call grd_chksum2(grd, grd%floating_melt, 'floating_melt')
   call grd_chksum2(grd, grd%berg_melt, 'berg_melt')

From 91a90281d4c23d6dfb3e3a1903cb64e2e6cc9284 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Mon, 27 Jun 2016 18:28:53 -0400
Subject: [PATCH 116/361] A warning has been added when Runge Kutta algorithm
 is used with interactive icebergs. This is because it is unclear whether the
 model is stable when interactive forces are used the Runge Kutta with
 interactions using the old iceberg positions and velocities (since iceberg
 interact with the positions and velocities of other icebergs at the begining
 of a time step.)

A warning has been added when iceberg bonds are used without interactive force.
---
 icebergs_framework.F90 | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 9d7736d..09e99a9 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -613,11 +613,13 @@ subroutine ice_bergs_framework_init(bergs, &
     iceberg_halo=halo
 endif
 
-if (Runge_not_Verlet) then
-  interactive_icebergs_on=.false.  ! Iceberg interactions only with Verlet
+if (interactive_icebergs_on) then
+  !Runge_not_Verlet=.false.  ! Iceberg interactions only with Verlet
+  call error_mesg('diamonds, framework', 'It is unlcear whther interactive icebergs work with Runge Kutta stepping.', WARNING) 
 endif
 if (.not.interactive_icebergs_on) then
-  !iceberg_bonds_on=.false.  ! This line needs to included later, but is omitted for testing
+  !iceberg_bonds_on=.false.  
+  call error_mesg('diamonds, framework', 'Interactive icebergs off requires iceberg bonds off (turning bonds off).', WARNING) 
 endif
 if (.not. iceberg_bonds_on) then
    max_bonds=0

From a9bf6fd44550d51d7d2902e984686d1599630c2c Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Tue, 28 Jun 2016 10:14:55 -0400
Subject: [PATCH 117/361] The WARNINGs using Runge Kutta with interactive
 icebergs, and bonds without interactions have now been implemented correctly
 (with appropriate if statements)

---
 icebergs_framework.F90 | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 09e99a9..ac9b068 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -614,12 +614,16 @@ subroutine ice_bergs_framework_init(bergs, &
 endif
 
 if (interactive_icebergs_on) then
-  !Runge_not_Verlet=.false.  ! Iceberg interactions only with Verlet
-  call error_mesg('diamonds, framework', 'It is unlcear whther interactive icebergs work with Runge Kutta stepping.', WARNING) 
+  if (Runge_not_Verlet.eq..true.) then
+    !Runge_not_Verlet=.false.  ! Iceberg interactions only with Verlet
+    call error_mesg('diamonds, framework', 'It is unlcear whther interactive icebergs work with Runge Kutta stepping.', WARNING) 
+  endif
 endif
 if (.not.interactive_icebergs_on) then
-  !iceberg_bonds_on=.false.  
-  call error_mesg('diamonds, framework', 'Interactive icebergs off requires iceberg bonds off (turning bonds off).', WARNING) 
+  if (iceberg_bonds_on.eq..true.) then  
+    !iceberg_bonds_on=.false.  
+    call error_mesg('diamonds, framework', 'Interactive icebergs off requires iceberg bonds off (turning bonds off).', WARNING) 
+  endif
 endif
 if (.not. iceberg_bonds_on) then
    max_bonds=0

From 21578ddbf282f416698174d60ddd4511dc07de1e Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Tue, 28 Jun 2016 10:55:45 -0400
Subject: [PATCH 118/361] Removing some text output which was there for
 debuggin reasons

---
 icebergs.F90 | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index ff4be19..26489cf 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1117,15 +1117,6 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
     yUxR=yU*xR*grd%msk(i+1,j+1)
     yCxC=1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )
     
-    !Temporary for debugging reasons.
-    if (mpp_pe()==mpp_root_pe()) then 
-            write(stderrunit,*) 'diamonds, You are in the square!!!', grd%area(i,j),L
-            write(stderrunit,*) 'diamonds, x,y', x,y
-            write(stderrunit,*) 'diamonds, xL,xC,xR', xL,xC,xR
-            write(stderrunit,*) 'diamonds, yU,yC,yD', yU,yC,yD
-    endif
-
- 
   else !Spread mass as if elements area hexagonal
 
     if (grd%area(i,j)>0) then

From 19773277fe11f771e0f6e258dfe8e28c9a93c366 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Tue, 28 Jun 2016 11:43:37 -0400
Subject: [PATCH 119/361] Two new flags have been added:
 1)set_melt_rates_to_zero - this sets all melt to zero for testing purposes.
 The thermodynamic routine is still run.  (Default=false)
 2)allow_bergs_to_roll  - this flag allows you to turn rolling off (Default =
 true)

---
 icebergs.F90           | 17 +++++++++++++----
 icebergs_framework.F90 |  9 ++++++++-
 2 files changed, 21 insertions(+), 5 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 26489cf..160f24c 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -916,6 +916,13 @@ subroutine thermodynamics(bergs)
           *perday ! convert to m/s
       Me=max( 1./12.*(SST+2.)*Ss*(1+cos(pi*(IC**3))) ,0.) &! Wave erosion
           *perday ! convert to m/s
+
+      if (bergs%set_melt_rates_to_zero) then
+        Mv=0.0
+        Mb=0.0
+        Me=0.0
+      endif
+
   
       if (bergs%use_operator_splitting) then
         ! Operator split update of volume/mass
@@ -1009,14 +1016,16 @@ subroutine thermodynamics(bergs)
       endif
   
       ! Rolling
-      Dn=(bergs%rho_bergs/rho_seawater)*Tn ! draught (keel depth)
-      if ( Dn>0. ) then
-         if ( max(Wn,Ln)<sqrt(0.92*(Dn**2)+58.32*Dn) ) then
+      if (bergs%allow_bergs_to_roll) then
+        Dn=(bergs%rho_bergs/rho_seawater)*Tn ! draught (keel depth)
+        if ( Dn>0. ) then
+          if ( max(Wn,Ln)<sqrt(0.92*(Dn**2)+58.32*Dn) ) then
             T=Tn
             Tn=Wn
             Wn=T
             Dn=(bergs%rho_bergs/rho_seawater)*Tn ! re-calculate draught (keel depth) for grounding
-        end if
+          end if
+        endif
       endif
   
       ! Store the new state of iceberg (with L>W)
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index ac9b068..ed21d50 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -209,7 +209,9 @@ module ice_bergs_framework
   logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
   logical :: time_average_weight=.false. ! Time average the weight on the ocean
   logical :: Runge_not_Verlet=.True.  !True=Runge Kuttai, False=Verlet.   
+  logical :: set_melt_rates_to_zero=.False.  !Sets all melt rates to zero, for testing purposes (thermodynamics routine is still run)
   logical :: hexagonal_icebergs=.False. !True treats icebergs as rectangles, False as hexagonal elements (for the purpose of mass spreading)
+  logical :: allow_bergs_to_roll=.True. !Allows icebergs to roll over when rolling conditions are met
   logical :: ignore_missing_restart_bergs=.False.  !True Allows the model to ignorm icebergs missing in the restart. 
   logical :: Static_icebergs=.False.  !True= icebergs do no move
   logical :: only_interactive_forces=.False.  !Icebergs only feel interactive forces, and not ocean, wind... 
@@ -319,6 +321,8 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: speed_limit=0. ! CFL speed limit for a berg
 real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
 logical :: Runge_not_Verlet=.True.  !True=Runge Kutta, False=Verlet.  - Added by Alon 
+logical :: set_melt_rates_to_zero=.False.  !Sets all melt rates to zero, for testing purposes (thermodynamics routine is still run)
+logical :: allow_bergs_to_roll=.True. !Allows icebergs to roll over when rolling conditions are met
 logical :: hexagonal_icebergs=.False. !True treats icebergs as rectangles, False as hexagonal elements (for the purpose of mass spreading)
 logical :: ignore_missing_restart_bergs=.False.  !True Allows the model to ignorm icebergs missing in the restart. 
 logical :: Static_icebergs=.False.  !True= icebergs do no move
@@ -341,7 +345,8 @@ subroutine ice_bergs_framework_init(bergs, &
          rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, iceberg_bonds_on, manually_initialize_bonds, ignore_missing_restart_bergs, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, halo_debugging, hexagonal_icebergs, &
          time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, interactive_icebergs_on, critical_interaction_damping_on, &
-         old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution, force_all_pes_traj
+         old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution, force_all_pes_traj, &
+         allow_bergs_to_roll,set_melt_rates_to_zero
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -655,6 +660,8 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%time_average_weight=time_average_weight
   bergs%speed_limit=speed_limit
   bergs%Runge_not_Verlet=Runge_not_Verlet   
+  bergs%set_melt_rates_to_zero=set_melt_rates_to_zero 
+  bergs%allow_bergs_to_roll=allow_bergs_to_roll 
   bergs%hexagonal_icebergs=hexagonal_icebergs 
   bergs%ignore_missing_restart_bergs=ignore_missing_restart_bergs
   bergs%Static_icebergs=Static_icebergs 

From 379d4e8cfbf5c1f926e6d71dd325eed827020628 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Tue, 28 Jun 2016 14:37:07 -0400
Subject: [PATCH 120/361] A runtime parameter called Omega_icebergs, which
 allows you to change the rotation rate.

---
 icebergs.F90           | 2 +-
 icebergs_framework.F90 | 5 ++++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 160f24c..c1d5b8d 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -475,7 +475,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
   ! Interpolate gridded fields to berg     - Note: It should be possible to move this to evolve, so that it only needs to be called once. !!!!
   call interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, cn, hi)
 
-   f_cori=(2.*omega)*sin(pi_180*lat)
+   f_cori=(2.*bergs%Omega_icebergs)*sin(pi_180*lat)
 !  f_cori=0.
 
   M=berg%mass
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index ed21d50..dfc68d9 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -201,6 +201,7 @@ module ice_bergs_framework
   real :: LoW_ratio ! Initial ratio L/W for newly calved icebergs
   real :: bergy_bit_erosion_fraction ! Fraction of erosion melt flux to divert to bergy bits
   real :: sicn_shift ! Shift of sea-ice concentration in erosion flux modulation (0<sicn_shift<1)
+  real :: Omega_icebergs=omega ! Option to override the rotation rate.
   real, dimension(:), pointer :: initial_mass, distribution, mass_scaling
   real, dimension(:), pointer :: initial_thickness, initial_width, initial_length
   logical :: restarted=.false. ! Indicate whether we read state from a restart or not
@@ -314,6 +315,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: LoW_ratio=1.5 ! Initial ratio L/W for newly calved icebergs
 real :: bergy_bit_erosion_fraction=0. ! Fraction of erosion melt flux to divert to bergy bits
 real :: sicn_shift=0. ! Shift of sea-ice concentration in erosion flux modulation (0<sicn_shift<1)
+real :: Omega_icebergs=omega ! Option to override the rotation rate.
 logical :: use_operator_splitting=.true. ! Use first order operator splitting for thermodynamics
 logical :: add_weight_to_ocean=.true. ! Add weight of icebergs + bits to ocean
 logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
@@ -346,7 +348,7 @@ subroutine ice_bergs_framework_init(bergs, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, halo_debugging, hexagonal_icebergs, &
          time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, interactive_icebergs_on, critical_interaction_damping_on, &
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution, force_all_pes_traj, &
-         allow_bergs_to_roll,set_melt_rates_to_zero
+         allow_bergs_to_roll,set_melt_rates_to_zero,Omega_icebergs
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -660,6 +662,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%time_average_weight=time_average_weight
   bergs%speed_limit=speed_limit
   bergs%Runge_not_Verlet=Runge_not_Verlet   
+  bergs%Omega_icebergs=Omega_icebergs
   bergs%set_melt_rates_to_zero=set_melt_rates_to_zero 
   bergs%allow_bergs_to_roll=allow_bergs_to_roll 
   bergs%hexagonal_icebergs=hexagonal_icebergs 

From 32bfab7ab644b8e3ab2afe9c9302b52a638e0fa3 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 29 Jun 2016 16:12:27 -0400
Subject: [PATCH 121/361] A bug has been fixed where NaN values were being
 copied into the halos of the gridded fields for simulations using
 non-periodic domains (also happened sometimes with periodic domains). This
 has been fixed by setting the gridded values equal to zero in the cases where
 the mask is equal to zero (ie: in the masked region)

---
 icebergs.F90           | 34 ++++++++++++++++++++++++++--------
 icebergs_framework.F90 | 28 ++++++++++++++--------------
 2 files changed, 40 insertions(+), 22 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index c1d5b8d..66da55f 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1676,6 +1676,10 @@ subroutine interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y,
 #endif
 real :: hxm, hxp
 real, parameter :: ssh_coast=0.00
+integer :: stderrunit
+
+  ! Get the stderr unit number
+  stderrunit = stderr()
 
   cos_rot=bilin(grd, grd%cos, i, j, xi, yj) ! If true, uses the inverted bilin function
   sin_rot=bilin(grd, grd%sin, i, j, xi, yj)
@@ -1691,7 +1695,7 @@ subroutine interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y,
   sst=grd%sst(i,j) ! A-grid
   cn=grd%cn(i,j) ! A-grid
   hi=grd%hi(i,j) ! A-grid
-
+    
   ! Estimate SSH gradient in X direction
 #ifdef USE_OLD_SSH_GRADIENT
   dxp=0.5*(grd%dx(i+1,j)+grd%dx(i+1,j-1))
@@ -1928,8 +1932,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
       ! Interpolate wind stresses from C-grid velocity-points.
       ! This masking is needed for now to prevent icebergs from running up on to land.
       mask = min(grd%msk(i,j), grd%msk(i+1,j), grd%msk(i,j+1), grd%msk(i+1,j+1))
-      grd%ua(I,J) = mask * 0.5*(uC_tmp(I,j)+uC_tmp(I,j+1))
-      grd%va(I,J) = mask * 0.5*(vC_tmp(i,J)+vC_tmp(i+1,J))
+       grd%ua(I,J) = mask * 0.5*(uC_tmp(I,j)+uC_tmp(I,j+1))
+       grd%va(I,J) = mask * 0.5*(vC_tmp(i,J)+vC_tmp(i+1,J))
     enddo ; enddo
     deallocate(uC_tmp, vC_tmp)
   else
@@ -1954,6 +1958,18 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   grd%hi(grd%isc-1:grd%iec+1,grd%jsc-1:grd%jec+1)=hi(:,:)
   call mpp_update_domains(grd%hi, grd%domain)
 
+ !Make sure that gridded values agree with mask  (to get ride of NaN values)
+  do i=grd%isd,grd%ied ; do j=grd%jsc-1,grd%jed
+  !Initializing all gridded values to zero
+    if (grd%msk(i,j).lt. 0.5) then
+      grd%ua(i,j) = 0.0 ;  grd%va(i,j) = 0.0
+      grd%uo(i,j) = 0.0 ;  grd%vo(i,j) = 0.0
+      grd%ui(i,j) = 0.0 ;  grd%vi(i,j) = 0.0
+      grd%sst(i,j) = 0.0;  grd%cn(i,j) = 0.0
+      grd%hi(i,j) = 0.0
+    endif
+  enddo; enddo
+
   if (debug) call bergs_chksum(bergs, 'run bergs (top)')
   if (debug) call checksum_gridded(bergs%grd, 'top of s/r run')
   
@@ -3144,6 +3160,10 @@ subroutine update_verlet_position(bergs,berg)
 real :: dx, dt, dt_2
 integer :: i, j
 logical :: on_tangential_plane, error_flag, bounced
+integer :: stderrunit
+
+  ! Get the stderr unit number
+    stderrunit = stderr()
 
   ! For convenience
     grd=>bergs%grd
@@ -3361,7 +3381,7 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
         if (grd%msk(i-1,j)>0.) then
           if (i>grd%isd+1) i=i-1
         else
-         !write(stderr(),'(a,6f8.3,i)') 'diamonds, adjust: bouncing berg from west',lon,lat,xi,yj,uvel,vvel,mpp_pe()
+         write(stderr(),'(a,6f8.3,i)') 'diamonds, adjust: bouncing berg from west',lon,lat,xi,yj,uvel,vvel,mpp_pe()
           bounced=.true.
         endif
       endif
@@ -3380,7 +3400,7 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
         if (grd%msk(i,j-1)>0.) then
           if (j>grd%jsd+1) j=j-1
         else
-         !write(stderr(),'(a,6f8.3,i)') 'diamonds, adjust: bouncing berg from south',lon,lat,xi,yj,uvel,vvel,mpp_pe()
+         write(stderr(),'(a,6f8.3,i)') 'diamonds, adjust: bouncing berg from south',lon,lat,xi,yj,uvel,vvel,mpp_pe()
           bounced=.true.
         endif
       endif
@@ -3389,7 +3409,7 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
         if (grd%msk(i,j+1)>0.) then
           if (j<grd%jed) j=j+1
         else
-         !write(stderr(),'(a,6f8.3,i)') 'diamonds, adjust: bouncing berg from north',lon,lat,xi,yj,uvel,vvel,mpp_pe()
+         write(stderr(),'(a,6f8.3,i)') 'diamonds, adjust: bouncing berg from north',lon,lat,xi,yj,uvel,vvel,mpp_pe()
           bounced=.true.
         endif
       endif
@@ -3407,7 +3427,6 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
     endif
     lret=pos_within_cell(grd, lon, lat, i, j, xi, yj) ! Update xi and yj
   enddo
-
  !if (debug) then
  !  if (abs(i-i0)>2) then
  !    stop 'diamonds, adjust: Moved too far in i!'
@@ -3460,7 +3479,6 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
     write(stderrunit,*) 'diamonds, adjust: Should not get here! Berg is not in cell after adjustment'
     if (debug) error=.true.
   endif
-
  end subroutine adjust_index_and_ground
 
 !end subroutine evolve_icebergs
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index dfc68d9..8fbdd2c 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -589,20 +589,20 @@ subroutine ice_bergs_framework_init(bergs, &
          ' [lon|lat][min|max]=', minval(grd%lon),maxval(grd%lon),minval(grd%lat),maxval(grd%lat)
   endif
 
- !if (mpp_pe().eq.15) then
- !  write(stderrunit,'(a3,32i7)') 'Lon',(i,i=grd%isd,grd%ied)
- !  do j=grd%jed,grd%jsd,-1
- !    write(stderrunit,'(i3,32f7.1)') j,(grd%lon(i,j),i=grd%isd,grd%ied)
- !  enddo
- !  write(stderrunit,'(a3,32i7)') 'Lat',(i,i=grd%isd,grd%ied)
- !  do j=grd%jed,grd%jsd,-1
- !    write(stderrunit,'(i3,32f7.1)') j,(grd%lat(i,j),i=grd%isd,grd%ied)
- !  enddo
- !  write(stderrunit,'(a3,32i7)') 'Msk',(i,i=grd%isd,grd%ied)
- !  do j=grd%jed,grd%jsd,-1
- !    write(stderrunit,'(i3,32f7.1)') j,(grd%msk(i,j),i=grd%isd,grd%ied)
- !  enddo
- !endif
+! if (mpp_pe().eq.3) then
+!   write(stderrunit,'(a3,32i7)') 'Lon',(i,i=grd%isd,grd%ied)
+!   do j=grd%jed,grd%jsd,-1
+!     write(stderrunit,'(i3,32f7.1)') j,(grd%lon(i,j),i=grd%isd,grd%ied)
+!   enddo
+!   write(stderrunit,'(a3,32i7)') 'Lat',(i,i=grd%isd,grd%ied)
+!   do j=grd%jed,grd%jsd,-1
+!     write(stderrunit,'(i3,32f7.1)') j,(grd%lat(i,j),i=grd%isd,grd%ied)
+!   enddo
+!   write(stderrunit,'(a3,32i7)') 'Msk',(i,i=grd%isd,grd%ied)
+!   do j=grd%jed,grd%jsd,-1
+!     write(stderrunit,'(i3,32f7.1)') j,(grd%msk(i,j),i=grd%isd,grd%ied)
+!   enddo
+! endif
 
 
 !Added by Alon  - If a freq distribution is input, we have to convert the freq distribution to a mass flux distribution)

From e8ef485ec72c780c66156eb7ada4d855b12c49d1 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Fri, 1 Jul 2016 09:46:05 -0400
Subject: [PATCH 122/361] A piece of code has been added to the routine which
 handels spreading mass to ocean. The new code reassigns mass which should be
 spread onto land points (masked points). The unused mass is assigned to the
 other grid around the iceberg in proportion to the percent of the iceberg
 which is in that grid cell. This piece of code completes the hexagonal
 spreading, and allows the hexagonal spreading to interact with boundaries.

For the square spreading, the code should not make any difference, because all of the mass is already distributed (with the center grid cell taking all the mass which would have otherwise been put onto a masked cell. At some point we may want to change the way this works (and make it work more like the hexagonal case). However, for now, we leave it as it was, so that the answers should not change.
---
 icebergs.F90 | 36 ++++++++++++++++++++++++------------
 1 file changed, 24 insertions(+), 12 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 66da55f..96298a8 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1076,6 +1076,7 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
   real :: yDxL, yDxC, yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR
   real :: S, H, origin_x, origin_y, x0, y0, theta
   real :: Area_Q1,Area_Q2 , Area_Q3,Area_Q4, Area_hex
+  real :: fraction_used
   real, parameter :: rho_seawater=1035.
   integer :: stderrunit
   logical :: debug
@@ -1202,16 +1203,22 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
       endif
 
   endif
-
-  grd%mass_on_ocean(i,j,1)=grd%mass_on_ocean(i,j,1)+(yDxL*Mass)
-  grd%mass_on_ocean(i,j,2)=grd%mass_on_ocean(i,j,2)+(yDxC*Mass)
-  grd%mass_on_ocean(i,j,3)=grd%mass_on_ocean(i,j,3)+(yDxR*Mass)
-  grd%mass_on_ocean(i,j,4)=grd%mass_on_ocean(i,j,4)+(yCxL*Mass)
-  grd%mass_on_ocean(i,j,5)=grd%mass_on_ocean(i,j,5)+(yCxC*Mass)
-  grd%mass_on_ocean(i,j,6)=grd%mass_on_ocean(i,j,6)+(yCxR*Mass)
-  grd%mass_on_ocean(i,j,7)=grd%mass_on_ocean(i,j,7)+(yUxL*Mass)
-  grd%mass_on_ocean(i,j,8)=grd%mass_on_ocean(i,j,8)+(yUxC*Mass)
-  grd%mass_on_ocean(i,j,9)=grd%mass_on_ocean(i,j,9)+(yUxR*Mass)
+        
+  !Scale each cell by (1/fraction_used) in order to redisribute ice mass which landed up on the land, back into the ocean
+  !Note that for the square elements, the mass has already been reassigned, so fraction_used shoule be equal to 1 aready
+  fraction_used= ((yDxL*grd%msk(i-1,j-1)) + (yDxC*grd%msk(i  ,j-1))  +(yDxR*grd%msk(i+1,j-1)) +(yCxL*grd%msk(i-1,j  )) +  (yCxR*grd%msk(i+1,j  ))&
+                 +(yUxL*grd%msk(i-1,j+1)) +(yUxC*grd%msk(i  ,j+1))   +(yUxR*grd%msk(i+1,j+1)) + (yCxC**grd%msk(i,j)))
+
+
+  grd%mass_on_ocean(i,j,1)=grd%mass_on_ocean(i,j,1)+(yDxL*Mass/fraction_used)
+  grd%mass_on_ocean(i,j,2)=grd%mass_on_ocean(i,j,2)+(yDxC*Mass/fraction_used)
+  grd%mass_on_ocean(i,j,3)=grd%mass_on_ocean(i,j,3)+(yDxR*Mass/fraction_used)
+  grd%mass_on_ocean(i,j,4)=grd%mass_on_ocean(i,j,4)+(yCxL*Mass/fraction_used)
+  grd%mass_on_ocean(i,j,5)=grd%mass_on_ocean(i,j,5)+(yCxC*Mass/fraction_used)
+  grd%mass_on_ocean(i,j,6)=grd%mass_on_ocean(i,j,6)+(yCxR*Mass/fraction_used)
+  grd%mass_on_ocean(i,j,7)=grd%mass_on_ocean(i,j,7)+(yUxL*Mass/fraction_used)
+  grd%mass_on_ocean(i,j,8)=grd%mass_on_ocean(i,j,8)+(yUxC*Mass/fraction_used)
+  grd%mass_on_ocean(i,j,9)=grd%mass_on_ocean(i,j,9)+(yUxR*Mass/fraction_used)
 
 end subroutine spread_mass_across_ocean_cells
 
@@ -1504,7 +1511,7 @@ subroutine Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy,Area_triangle,
     if      ( (.not. ((((Ax>0.) .and. (Ay>0.)) .or. ((Bx>0.) .and. (By> 0.))) .or. ((Cx>0.) .and. (Cy> 0.)))) .and. ((Area_Upper+Area_Right).le.Area_triangle) ) then
       !No points land in this quadrant and triangle does not cross the quadrant
       Key_quadrant=1;
-    elseif  ( (.not. ((((Ax<0.) .and. (Ay>=0)) .or. ((Bx<0.) .and. (By>=0.))) .or. ((Cx<0.) .and. (Cy>=0.)))) .and. ((Area_Upper+Area_Left).le. Area_triangle) ) then
+    elseif  ( (.not. ((((Ax<0.) .and. (Ay>0)) .or. ((Bx<0.) .and. (By>0.))) .or. ((Cx<0.) .and. (Cy>0.)))) .and. ((Area_Upper+Area_Left).le. Area_triangle) ) then
       Key_quadrant=2
     elseif  ( (.not. ((((Ax<0.) .and. (Ay<0.)) .or. ((Bx<0.) .and. (By< 0.))) .or. ((Cx<0.) .and. (Cy< 0.)))) .and. ((Area_Lower+Area_Left) .le.Area_triangle) ) then
       Key_quadrant=3;
@@ -1553,10 +1560,15 @@ subroutine Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy,Area_triangle,
   Error=abs(Area_Q1+Area_Q2+Area_Q3+Area_Q4-Area_triangle)
   if (Error>0.01) then
     call error_mesg('diamonds, triangle spreading', 'Triangle not evaluated accurately!!', WARNING)
-    if (mpp_pe().eq.mpp_root_pe()) then
+    !if (mpp_pe().eq.mpp_root_pe()) then
+    if (mpp_pe().eq. 0) then
       write(stderrunit,*) 'diamonds, Triangle corners:',Ax,Ay,Bx,By,Cx,Cy
       write(stderrunit,*) 'diamonds, Triangle, Areas', Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
       write(stderrunit,*) 'diamonds, Triangle, Areas', Error
+      write(stderrunit,*) 'diamonds, point in triangle',(point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.)),Key_quadrant
+      write(stderrunit,*) 'diamonds, halves',Area_Upper,Area_Lower,Area_Right,Area_Left
+
+
     endif
   endif
 

From 7c666e97b25c09072e00dd4bc75cc2d49b66e018 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Fri, 1 Jul 2016 13:33:47 -0400
Subject: [PATCH 123/361] An iceberg property called static_berg has been added
 to icebergs (and to restart files). If static iceberg =1, then the iceberg
 does not move. An if statement has been added to evolve_icebergs routine to
 stop the static icebergs from moving. The static_berg variable is useful for
 running ice shelf simulations.

The static_berg can later be used to simulate iceberg grounding (by letting a partially grounded iceberg have static_berg between 0 and 1.
---
 icebergs.F90           | 111 +++++++++++++++++++++--------------------
 icebergs_framework.F90 |  45 ++++++++++-------
 icebergs_io.F90        |  18 ++++++-
 3 files changed, 98 insertions(+), 76 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 96298a8..474c50b 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -2575,6 +2575,7 @@ subroutine calve_icebergs(bergs)
           newberg%mass_scaling=bergs%mass_scaling(k)
           newberg%mass_of_bits=0.
           newberg%halo_berg=0.
+          newberg%static_berg=0.
           newberg%heat_density=grd%stored_heat(i,j)/grd%stored_ice(i,j,k) ! This is in J/kg
           call add_new_berg_to_list(bergs%list(i,j)%first, newberg)
           calved_to_berg=bergs%initial_mass(k)*bergs%mass_scaling(k) ! Units of kg
@@ -2633,53 +2634,54 @@ subroutine evolve_icebergs(bergs)
   do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
     berg=>bergs%list(grdi,grdj)%first
     do while (associated(berg)) ! loop over all bergs
+      if (berg%static_berg .lt. 0.5) then  !Only allow non-static icebergs to evolve
  
-      !Checking it everything is ok:
-      if (.not. is_point_in_cell(bergs%grd, berg%lon, berg%lat, berg%ine, berg%jne) ) then
-        write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lon',(i,i=grd%isd,grd%ied)
-        do j=grd%jed,grd%jsd,-1
-          write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lon(i,j),i=grd%isd,grd%ied)
-        enddo
-        write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lat',(i,i=grd%isd,grd%ied)
-        do j=grd%jed,grd%jsd,-1
-          write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lat(i,j),i=grd%isd,grd%ied)
-        enddo
-        call print_berg(stderrunit, berg, 'evolve_iceberg, berg is not in proper starting cell')
-        write(stderrunit,'(a,i3,2(i4,3f8.2))') 'evolve_iceberg: pe,lon/lat(i,j)=', mpp_pe(), &
-                 berg%ine,berg%lon,grd%lon(berg%ine-1,berg%jne-1),grd%lon(berg%ine,berg%jne), &
-                 berg%jne,berg%lat,grd%lat(berg%ine-1,berg%jne-1),grd%lat(berg%ine,berg%jne)
-        if (debug) call error_mesg('diamonds, evolve_iceberg','berg is in wrong starting cell!',FATAL)
-      endif
-      if (debug) call check_position(grd, berg, 'evolve_iceberg (top)')
-
-        !Time stepping schemes:
-        if (Runge_not_Verlet) then 
-          call Runge_Kutta_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln,lonn, latn, i, j, xi, yj)
-        endif 
-        if (.not.Runge_not_Verlet) then 
-          call verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
-        endif 
-
-      ! Saving all the iceberg variables.
-      berg%axn=axn 
-      berg%ayn=ayn 
-      berg%bxn=bxn 
-      berg%byn=byn 
-      berg%uvel=uveln
-      berg%vvel=vveln
-
-      if (Runge_not_Verlet) then
-        berg%lon=lonn  ;   berg%lat=latn
-        berg%ine=i     ;   berg%jne=j
-        berg%xi=xi     ;   berg%yj=yj
-      else
-        if (.not. interactive_icebergs_on)  call update_verlet_position(bergs,berg) 
-      endif
-
-      !call interp_flds(grd, i, j, xi, yj, berg%uo, berg%vo, berg%ui, berg%vi, berg%ua, berg%va, berg%ssh_x, berg%ssh_y, berg%sst)
-      !if (debug) call print_berg(stderr(), berg, 'evolve_iceberg, final posn.')
-      if (debug) call check_position(grd, berg, 'evolve_iceberg (bot)')
+        !Checking it everything is ok:
+        if (.not. is_point_in_cell(bergs%grd, berg%lon, berg%lat, berg%ine, berg%jne) ) then
+          write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lon',(i,i=grd%isd,grd%ied)
+          do j=grd%jed,grd%jsd,-1
+            write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lon(i,j),i=grd%isd,grd%ied)
+          enddo
+          write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lat',(i,i=grd%isd,grd%ied)
+          do j=grd%jed,grd%jsd,-1
+            write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lat(i,j),i=grd%isd,grd%ied)
+          enddo
+          call print_berg(stderrunit, berg, 'evolve_iceberg, berg is not in proper starting cell')
+          write(stderrunit,'(a,i3,2(i4,3f8.2))') 'evolve_iceberg: pe,lon/lat(i,j)=', mpp_pe(), &
+                   berg%ine,berg%lon,grd%lon(berg%ine-1,berg%jne-1),grd%lon(berg%ine,berg%jne), &
+                   berg%jne,berg%lat,grd%lat(berg%ine-1,berg%jne-1),grd%lat(berg%ine,berg%jne)
+          if (debug) call error_mesg('diamonds, evolve_iceberg','berg is in wrong starting cell!',FATAL)
+        endif
+        if (debug) call check_position(grd, berg, 'evolve_iceberg (top)')
+
+          !Time stepping schemes:
+          if (Runge_not_Verlet) then 
+            call Runge_Kutta_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln,lonn, latn, i, j, xi, yj)
+          endif 
+          if (.not.Runge_not_Verlet) then 
+            call verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
+          endif 
+
+        ! Saving all the iceberg variables.
+        berg%axn=axn 
+        berg%ayn=ayn 
+        berg%bxn=bxn 
+        berg%byn=byn 
+        berg%uvel=uveln
+        berg%vvel=vveln
+
+        if (Runge_not_Verlet) then
+          berg%lon=lonn  ;   berg%lat=latn
+          berg%ine=i     ;   berg%jne=j
+          berg%xi=xi     ;   berg%yj=yj
+        else
+          if (.not. interactive_icebergs_on)  call update_verlet_position(bergs,berg) 
+        endif
 
+        !call interp_flds(grd, i, j, xi, yj, berg%uo, berg%vo, berg%ui, berg%vi, berg%ua, berg%va, berg%ssh_x, berg%ssh_y, berg%sst)
+        !if (debug) call print_berg(stderr(), berg, 'evolve_iceberg, final posn.')
+        if (debug) call check_position(grd, berg, 'evolve_iceberg (bot)')
+      endif
       berg=>berg%next
     enddo ! loop over all bergs
   enddo ; enddo
@@ -2690,16 +2692,15 @@ subroutine evolve_icebergs(bergs)
     do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
       berg=>bergs%list(grdi,grdj)%first
       do while (associated(berg)) ! loop over all bergs
-       
-
-       if (.not. Runge_not_Verlet)  call update_verlet_position(bergs,berg) 
-        
-       !Updating old velocities (for use in iceberg interactions)
-        berg%uvel_old=berg%uvel
-        berg%vvel_old=berg%vvel
-        berg%lon_old=berg%lon  ! lon_old, lat_old are not really needed for Verlet. But are needed for RK
-        berg%lat_old=berg%lat
-
+        if (berg%static_berg .lt. 0.5) then  !Only allow non-static icebergs to evolve
+         if (.not. Runge_not_Verlet)  call update_verlet_position(bergs,berg) 
+          
+         !Updating old velocities (for use in iceberg interactions)
+          berg%uvel_old=berg%uvel
+          berg%vvel_old=berg%vvel
+          berg%lon_old=berg%lon  ! lon_old, lat_old are not really needed for Verlet. But are needed for RK
+          berg%lat_old=berg%lat
+        endif
         berg=>berg%next
       enddo ! loop over all bergs
     enddo ; enddo
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 8fbdd2c..b3d7caa 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -15,8 +15,8 @@ module ice_bergs_framework
 
 implicit none ; private
 
-integer :: buffer_width=26 !Changed from 20 to 28 by Alon 
-integer :: buffer_width_traj=29  !Changed from 23 by Alon
+integer :: buffer_width=27 !Changed from 20 to 28 by Alon 
+integer :: buffer_width_traj=30  !Changed from 23 by Alon
 !integer, parameter :: buffer_width=26 !Changed from 20 to 26 by Alon 
 !integer, parameter :: buffer_width_traj=29  !Changed from 23 by Alon
 integer, parameter :: nclasses=10 ! Number of ice bergs classes
@@ -142,7 +142,7 @@ module ice_bergs_framework
   real :: lon, lat, day
   real :: mass, thickness, width, length, uvel, vvel
   real :: axn, ayn, bxn, byn, uvel_old, vvel_old, lat_old, lon_old  !Explicit and implicit accelerations !Alon 
-  real :: uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, cn, hi, halo_berg
+  real :: uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, cn, hi, halo_berg, static_berg
   real :: mass_of_bits, heat_density
   integer :: year, iceberg_num
   type(xyt), pointer :: next=>null()
@@ -156,6 +156,7 @@ module ice_bergs_framework
   real :: start_lon, start_lat, start_day, start_mass, mass_scaling
   real :: mass_of_bits, heat_density
   real :: halo_berg  ! Equal to zero for bergs on computational domain, and =1 for bergs on the halo
+  real :: static_berg  ! Equal to 1 for icebergs which are static (not allowed to move). Might be extended to grounding later.
   integer :: start_year
   integer :: iceberg_num
   integer :: ine, jne ! nearest index in NE direction (for convenience)
@@ -1493,9 +1494,10 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
     buff%data(24,n)=berg%byn  !Alon
     buff%data(25,n)=float(berg%iceberg_num)
     buff%data(26,n)=berg%halo_berg 
+    buff%data(27,n)=berg%static_berg 
 
     if (max_bonds .gt. 0) then
-      counter=26 !how many data points being passed so far (must match above)
+      counter=27 !how many data points being passed so far (must match above)
       current_bond=>berg%first_bond
       do k = 1,max_bonds
         if (associated(current_bond)) then
@@ -1637,6 +1639,7 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n,grd, force_append, max_bonds_
     localberg%byn=buff%data(24,n) !Alon
     localberg%iceberg_num=nint(buff%data(25,n))
     localberg%halo_berg=buff%data(26,n) 
+    localberg%static_berg=buff%data(27,n) 
 
     !These quantities no longer need to be passed between processors
     localberg%uvel_old=localberg%uvel
@@ -1838,6 +1841,7 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj)
       buff%data(27,n)=traj%bxn !Alon
       buff%data(28,n)=traj%byn !Alon
       buff%data(29,n)=traj%halo_berg !Alon
+      buff%data(30,n)=traj%static_berg !Alon
     endif
 
   end subroutine pack_traj_into_buffer2
@@ -1884,6 +1888,7 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj)
       traj%bxn=buff%data(27,n) !Alon
       traj%byn=buff%data(28,n) !Alon
       traj%halo_berg=buff%data(29,n) !Alon
+      traj%static_berg=buff%data(30,n) !Alon
     endif
     call append_posn(first, traj)
 
@@ -2695,6 +2700,7 @@ subroutine record_posn(bergs)
       posn%lon_old=this%lon_old
       posn%lat_old=this%lat_old
       posn%halo_berg=this%halo_berg
+      posn%static_berg=this%static_berg
   
       call push_posn(this%trajectory, posn)
   
@@ -3905,23 +3911,24 @@ integer function berg_chksum(berg )
   rtmp(26)=berg%ssh_y
   rtmp(27)=berg%cn
   rtmp(28)=berg%hi
-  rtmp(29)=berg%axn !Added by Alon
-  rtmp(30)=berg%ayn !Added by Alon
-  rtmp(31)=berg%bxn !Added by Alon
-  rtmp(32)=berg%byn !Added by Alon
-  rtmp(33)=berg%uvel_old !Added by Alon
-  rtmp(34)=berg%vvel_old !Added by Alon
-  rtmp(35)=berg%lat_old !Added by Alon
-  rtmp(36)=berg%lon_old !Added by Alon
-  itmp(37)=berg%halo_berg !Changed from 31 to 40 by Alon
-  itmp(1:37)=transfer(rtmp,i8) !Changed from 28 to 37 by Alon
-  itmp(38)=berg%start_year !Changed from 29 to 38 by Alon
-  itmp(39)=berg%ine !Changed from 30 to 39 by Alon
-  itmp(40)=berg%jne !Changed from 31 to 40 by Alon
-  itmp(41)=berg%iceberg_num !added  by Alon
+  rtmp(29)=berg%axn 
+  rtmp(30)=berg%ayn 
+  rtmp(31)=berg%bxn 
+  rtmp(32)=berg%byn 
+  rtmp(33)=berg%uvel_old 
+  rtmp(34)=berg%vvel_old 
+  rtmp(35)=berg%lat_old 
+  rtmp(36)=berg%lon_old 
+  itmp(37)=berg%halo_berg 
+  itmp(38)=berg%static_berg 
+  itmp(1:38)=transfer(rtmp,i8) 
+  itmp(39)=berg%start_year 
+  itmp(40)=berg%ine 
+  itmp(41)=berg%jne 
+  itmp(42)=berg%iceberg_num 
 
   ichk1=0; ichk2=0; ichk3=0
-  do i=1,37+4 !Changd from 28 to 37, 3 to 4 by Alon
+  do i=1,38+4 
    ichk1=ichk1+itmp(i)
    ichk2=ichk2+itmp(i)*i
    ichk3=ichk3+itmp(i)*i*i
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 8fd70ea..c6c686b 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -131,6 +131,7 @@ subroutine write_restart(bergs)
                                    mass_scaling, &
                                    mass_of_bits, &
                                    halo_berg,    &
+                                   static_berg,  &
                                    heat_density
 
 integer, allocatable, dimension(:) :: ine,              &
@@ -184,6 +185,7 @@ subroutine write_restart(bergs)
    allocate(mass_of_bits(nbergs))
    allocate(heat_density(nbergs))
    allocate(halo_berg(nbergs))
+   allocate(static_berg(nbergs))
 
    allocate(ine(nbergs))
    allocate(jne(nbergs))
@@ -235,6 +237,8 @@ subroutine write_restart(bergs)
                                             longname='heat density',units='J/kg')
   id = register_restart_field(bergs_restart,filename,'halo_berg',halo_berg, &
                                             longname='halo_berg',units='dimensionless')
+  id = register_restart_field(bergs_restart,filename,'static_berg',static_berg, &
+                                            longname='static_berg',units='dimensionless')
 
 
   ! Write variables
@@ -255,6 +259,7 @@ subroutine write_restart(bergs)
       start_year(i) = this%start_year; start_day(i) = this%start_day
       start_mass(i) = this%start_mass; mass_scaling(i) = this%mass_scaling
       halo_berg(i) = this%halo_berg 
+      static_berg(i) = this%static_berg 
       iceberg_num(i) = this%iceberg_num; 
       mass_of_bits(i) = this%mass_of_bits; heat_density(i) = this%heat_density
       this=>this%next
@@ -284,7 +289,7 @@ subroutine write_restart(bergs)
              start_mass,   &
              mass_scaling, &
              mass_of_bits, &
-             halo_berg,    &
+             static_berg,    &
              heat_density )
 
   deallocate(           &
@@ -406,7 +411,7 @@ subroutine read_restart_bergs_orig(bergs,Time)
 integer :: axnid, aynid, uvel_oldid, vvel_oldid, bxnid, bynid
 integer :: massid, thicknessid, widthid, lengthid
 integer :: start_lonid, start_latid, start_yearid, iceberg_numid, start_dayid, start_massid
-integer :: scaling_id, mass_of_bits_id, heat_density_id, halo_bergid
+integer :: scaling_id, mass_of_bits_id, heat_density_id, halo_bergid, static_bergid
 logical :: lres, found_restart, multiPErestart
 real :: lon0, lon1, lat0, lat1
 character(len=33) :: filename, filename_base
@@ -481,6 +486,7 @@ subroutine read_restart_bergs_orig(bergs,Time)
   start_massid=inq_var(ncid, 'start_mass')
   scaling_id=inq_var(ncid, 'mass_scaling')
   halo_bergid=inq_var(ncid, 'halo_berg')
+  static_bergid=inq_var(ncid, 'static_berg')
   mass_of_bits_id=inq_var(ncid, 'mass_of_bits',unsafe=.true.)
   heat_density_id=inq_var(ncid, 'heat_density',unsafe=.true.)
   ineid=inq_var(ncid, 'ine',unsafe=.true.)
@@ -536,6 +542,7 @@ subroutine read_restart_bergs_orig(bergs,Time)
       localberg%start_mass=get_double(ncid, start_massid, k)
       localberg%mass_scaling=get_double(ncid, scaling_id, k)
       localberg%halo_berg=get_double(ncid, halo_bergid, k)
+      localberg%static_berg=get_double(ncid, static_bergid, k)
       if (mass_of_bits_id>0) then ! Allow reading of older restart with no bergy bits
         localberg%mass_of_bits=get_double(ncid, mass_of_bits_id, k)
       else
@@ -627,6 +634,7 @@ subroutine generate_bergs(bergs,Time)
         localberg%mass_scaling=bergs%mass_scaling(1)
         localberg%mass_of_bits=0.
         localberg%halo_berg=0.
+        localberg%static_berg=0.
         localberg%heat_density=0.
         localberg%uvel=1.
         localberg%vvel=0.
@@ -722,6 +730,7 @@ subroutine read_restart_bergs(bergs,Time)
                                    mass_scaling, &
                                    mass_of_bits, &
                                    halo_berg,    &
+                                   static_berg,    &
                                    heat_density
 integer, allocatable, dimension(:) :: ine,       &
                                       jne,       &
@@ -768,6 +777,7 @@ subroutine read_restart_bergs(bergs,Time)
      allocate(mass_scaling(nbergs_in_file))
      allocate(mass_of_bits(nbergs_in_file))
      allocate(halo_berg(nbergs_in_file))
+     allocate(static_berg(nbergs_in_file))
      allocate(heat_density(nbergs_in_file))
 
      allocate(ine(nbergs_in_file))
@@ -794,6 +804,7 @@ subroutine read_restart_bergs(bergs,Time)
      call read_unlimited_axis(filename,'mass_scaling',mass_scaling,domain=grd%domain)
      call read_unlimited_axis(filename,'mass_of_bits',mass_of_bits,domain=grd%domain)
      call read_unlimited_axis(filename,'halo_berg',halo_berg,domain=grd%domain)
+     call read_unlimited_axis(filename,'static_berg',static_berg,domain=grd%domain)
      call read_unlimited_axis(filename,'heat_density',heat_density,domain=grd%domain)
 
      call read_unlimited_axis(filename,'ine',ine,domain=grd%domain)
@@ -880,6 +891,7 @@ subroutine read_restart_bergs(bergs,Time)
          localberg%mass_scaling=mass_scaling(k)
          localberg%mass_of_bits=mass_of_bits(k)
          localberg%halo_berg=halo_berg(k)
+         localberg%static_berg=static_berg(k)
          localberg%heat_density=heat_density(k)
          localberg%first_bond=>null()
          if (really_debug) lres=is_point_in_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, explain=.true.)
@@ -918,6 +930,7 @@ subroutine read_restart_bergs(bergs,Time)
                 mass_scaling, &
                 mass_of_bits, &
                 halo_berg,    &
+                static_berg,    &
                 heat_density )
      deallocate(           &
                 ine,       &
@@ -997,6 +1010,7 @@ subroutine generate_bergs(bergs,Time)
         localberg%mass_scaling=bergs%mass_scaling(1)
         localberg%mass_of_bits=0.
         localberg%halo_berg=0.
+        localberg%static_berg=0.
         localberg%heat_density=0.
         localberg%uvel=1.
         localberg%vvel=0.

From b4ad6a5bc8b13f54edb68a7a041ffe7124708002 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Tue, 5 Jul 2016 15:16:51 -0400
Subject: [PATCH 124/361] The routine initialize bonds, which initializes the
 bonds automatically when the manual flag is turned on, has been edited. The
 edits mean that the distance between the two icebergs is calculated
 correctly. However, this distance is not used. The routine should be removed
 at some point. It was created for development.

A few more lines have been adde in order to allow icebergs to have an orientation which is achieve through the positions of their bonds. However, this is not quite working yet
---
 icebergs.F90 | 74 +++++++++++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 70 insertions(+), 4 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 474c50b..447b007 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -144,6 +144,7 @@ subroutine initialize_iceberg_bonds(bergs)
 type(icebergs_gridded), pointer :: grd
 real :: T1, L1, W1, lon1, lat1, x1, y1, R1, A1   !Current iceberg
 real :: T2, L2, W2, lon2, lat2, x2, y2, R2, A2   !Other iceberg
+real :: dlon,dlat
 real :: r_dist_x, r_dist_y, r_dist
 integer :: grdi_outer, grdj_outer
 integer :: grdi_inner, grdj_inner
@@ -157,7 +158,7 @@ subroutine initialize_iceberg_bonds(bergs)
     do while (associated(berg)) ! loop over all bergs
     
       lon1=berg%lon; lat1=berg%lat
-      call rotpos_to_tang(lon1,lat1,x1,y1)
+      !call rotpos_to_tang(lon1,lat1,x1,y1)  !Is this correct? Shouldn't it only be on tangent plane?
 
       do grdj_inner = grd%jsc,grd%jec ; do grdi_inner = grd%isc,grd%iec  !This line uses n^2 steps
 !     do grdj_inner = berg%jne-1,berg%jne+1 ; do grdi_inner = berg%ine-1,berg%ine+1   !Only looping through adjacent cells.
@@ -166,9 +167,15 @@ subroutine initialize_iceberg_bonds(bergs)
           
           if (berg%iceberg_num .ne. other_berg%iceberg_num) then
             lon2=other_berg%lon; lat2=other_berg%lat
-            call rotpos_to_tang(lon2,lat2,x2,y2)
-            r_dist_x=x1-x2 ; r_dist_y=y1-y2
-            r_dist=sqrt( ((x1-x2)**2) + ((y1-y2)**2) )
+            !call rotpos_to_tang(lon2,lat2,x2,y2) !Is this correct? Shouldn't it only be on tangent plane?
+            !r_dist_x=x1-x2 ; r_dist_y=y1-y2
+            !r_dist=sqrt( ((x1-x2)**2) + ((y1-y2)**2) )
+
+            dlon=lon1-lon2
+            dlat=lat1-lat2
+            r_dist_x=dlon*(pi/180)*Rearth*cos(0.5*(lat1+lat2)*(pi/180))
+            r_dist_y=dlat*(pi/180)*Rearth
+            r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) )
         
             !if (r_dist.gt.1000.) then  ! If the bergs are close together, then form a bond
               call form_a_bond(berg, other_berg%iceberg_num, other_berg%ine, other_berg%jne, other_berg)
@@ -879,6 +886,7 @@ subroutine thermodynamics(bergs)
 type(iceberg), pointer :: this, next
 real, parameter :: perday=1./86400.
 integer :: grdi, grdj
+real :: orientation
 
   ! For convenience
   grd=>bergs%grd
@@ -1053,6 +1061,15 @@ subroutine thermodynamics(bergs)
             Hocean=bergs%grounding_fraction*(grd%ocean_depth(i,j)+grd%ssh(i,j))
             if (Dn>Hocean) Mnew=Mnew*min(1.,Hocean/Dn)
           endif
+
+          orientation=bergs%initial_orientation
+          if ((bergs%iceberg_bonds_on) .and. (bergs%rotate_icebergs_for_mass_spreading)) then
+                  orientation=find_orientation_using_iceberg_bonds(this,bergs%initial_orientation)
+                  print *, 'orientation: ', orientation, this%iceberg_num
+
+          endif
+
+
           call spread_mass_across_ocean_cells(grd, i, j, this%xi, this%yj, Mnew, nMbits, this%mass_scaling, this%length*this%width, bergs%hexagonal_icebergs )
         endif
       endif
@@ -1063,6 +1080,55 @@ subroutine thermodynamics(bergs)
 
 end subroutine thermodynamics
 
+!MPP1
+real function find_orientation_using_iceberg_bonds(berg,initial_orientation)
+  ! Arguments
+  type(iceberg) :: berg
+  real, intent(in) :: initial_orientation 
+  type(iceberg), pointer :: other_berg
+  type(bond), pointer :: current_bond
+  real :: angle, lat1,lat2,lon1,lon2,dlat,dlon
+  real :: r_dist_x, r_dist_y
+  real :: theta, bond_count, Average_angle
+    
+  bond_count=0.
+  Average_angle=0.
+  current_bond=>berg%first_bond
+  lat1=berg%lat
+  lon1=berg%lon
+  do while (associated(current_bond)) ! loop over all bonds
+      other_berg=>current_bond%other_berg
+      if (.not. associated(current_bond)) then
+        call error_mesg('diamonds,calculating orientation', 'Trying to do Bond interactions with unassosiated bond!' ,FATAL)
+      else
+        lat2=other_berg%lat
+        lon2=other_berg%lon
+
+        dlat=lat2-lat1
+        dlon=lon2-lon1
+        
+        r_dist_x=dlon*(pi/180)*Rearth*cos(0.5*(lat1+lat2)*(pi/180))
+        r_dist_y=dlat*(pi/180)*Rearth
+        if (r_dist_y .eq. 0.) then
+          angle=pi/2.
+        else
+          angle=atan(r_dist_x/r_dist_y)
+          angle= ((pi/2)  - (initial_orientation*(pi/180)))  - angle
+          angle=modulo(angle-(2*pi) ,pi/6.)
+        endif
+        bond_count=bond_count+1.
+        Average_angle=Average_angle+angle
+
+      endif
+      current_bond=>current_bond%next_bond
+    enddo
+    Average_angle =Average_angle/bond_count
+    find_orientation_using_iceberg_bonds=modulo(angle-(2*pi) ,pi/6.)
+
+end function find_orientation_using_iceberg_bonds
+
+
+
 ! ##############################################################################
 
 subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling, Area, hexagonal_icebergs)

From 4f879b0ad2e297e9ff3598753d7a293a43626651 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Tue, 5 Jul 2016 20:00:37 -0400
Subject: [PATCH 125/361] Code has been added to allow for non periodic
 domains, for periodic domains which are not of length 360, and also for grids
 which are not lat lon grids.

The periodicity of the domain (in the x-direction) is in imput variable. For non-periodic domains, this should be set to a very large number.
A flag has been added which signals whether the grid_is_latlon. The various metric terms have been adjusted according to this flag.

Period domains in the y-direction have not yet been implemented.

The code has not yet been tested, but it does compile.
---
 icebergs.F90 | 184 +++++++++++++++++++++++++++++++++------------------
 1 file changed, 118 insertions(+), 66 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 447b007..129bb31 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -145,6 +145,7 @@ subroutine initialize_iceberg_bonds(bergs)
 real :: T1, L1, W1, lon1, lat1, x1, y1, R1, A1   !Current iceberg
 real :: T2, L2, W2, lon2, lat2, x2, y2, R2, A2   !Other iceberg
 real :: dlon,dlat
+real :: dx_dlon,dy_dlat, lat_ref
 real :: r_dist_x, r_dist_y, r_dist
 integer :: grdi_outer, grdj_outer
 integer :: grdi_inner, grdj_inner
@@ -173,8 +174,10 @@ subroutine initialize_iceberg_bonds(bergs)
 
             dlon=lon1-lon2
             dlat=lat1-lat2
-            r_dist_x=dlon*(pi/180)*Rearth*cos(0.5*(lat1+lat2)*(pi/180))
-            r_dist_y=dlat*(pi/180)*Rearth
+            lat_ref=0.5*(lat1+lat2)
+            call convert_from_grid_to_meters(lat_ref,bergs%grid_is_latlon,dx_dlon,dy_dlat)
+            r_dist_x=dlon*dx_dlon
+            r_dist_y=dlat*dy_dlat
             r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) )
         
             !if (r_dist.gt.1000.) then  ! If the bergs are close together, then form a bond
@@ -191,6 +194,39 @@ subroutine initialize_iceberg_bonds(bergs)
 
 end subroutine initialize_iceberg_bonds
 
+subroutine  convert_from_grid_to_meters(lat_ref,grid_is_latlon ,dx_dlon,dy_dlat)
+  ! Arguments
+  real, intent(in) :: lat_ref
+  logical, intent(in) :: grid_is_latlon
+  real, intent(out) :: dx_dlon,dy_dlat
+
+  if (grid_is_latlon) then
+    dx_dlon=(pi/180.)*Rearth*cos((lat_ref)*(pi/180.))
+    dy_dlat=(pi/180.)*Rearth
+
+  else
+    dx_dlon=1.
+    dy_dlat=1.
+
+  endif
+end subroutine  convert_from_grid_to_meters
+
+subroutine  convert_from_meters_to_grid(lat_ref,grid_is_latlon ,dlon_dx,dlat_dy)
+  ! Arguments
+  real, intent(in) :: lat_ref
+  logical, intent(in) :: grid_is_latlon
+  real, intent(out) :: dlon_dx,dlat_dy
+
+  if (grid_is_latlon) then
+    dlon_dx=(180./pi)/(Rearth*cos((lat_ref)*(pi/180.)))
+    dlat_dy=(180./pi)/Rearth
+
+  else
+    dlon_dx=1.
+    dlat_dy=1.
+
+  endif
+end subroutine  convert_from_meters_to_grid
 ! ##############################################################################
 
 subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y) !Calculating interactive force between icebergs. Alon,  Markpoint_4
@@ -255,6 +291,7 @@ subroutine calculate_force(bergs,berg,other_berg,IA_x, IA_y, u0, v0, u1, v1, P_i
      real :: P_11, P_12, P_21, P_22
      real :: M1, M2, M_min
      real :: u2, v2
+     real :: lat_ref, dx_dlon, dy_dlat
      logical :: critical_interaction_damping_on
      real :: spring_coef, accel_spring, radial_damping_coef, p_ia_coef, tangental_damping_coef, bond_coef
      real, intent(inout) :: IA_x, IA_y 
@@ -305,10 +342,12 @@ subroutine calculate_force(bergs,berg,other_berg,IA_x, IA_y, u0, v0, u1, v1, P_i
         !Approximation for small distances. Should be fine.
         !r_dist_x=x1-x2 ; r_dist_y=y1-y2
         !r_dist=sqrt( ((x1-x2)**2) + ((y1-y2)**2) )
-        r_dist_x=dlon*(pi/180)*Rearth*cos(0.5*(lat1+lat2)*(pi/180))
-        r_dist_y=dlat*(pi/180)*Rearth
-        r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) )
+        lat_ref=0.5*(lat1+lat2)
+        call convert_from_grid_to_meters(lat_ref,bergs%grid_is_latlon,dx_dlon,dy_dlat)
 
+        r_dist_x=dlon*dx_dlon
+        r_dist_y=dlat*dy_dlat
+        r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) )
         
           !if (berg%iceberg_num .eq. 1) then
             !print *, 'Comparing longitudes: ', lon1, lon2, r_dist_x, dlon, r_dist
@@ -895,7 +934,7 @@ subroutine thermodynamics(bergs)
   do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied  ! Thermodynamics of  halos now calculated, so that spread mass to ocean works correctly
     this=>bergs%list(grdi,grdj)%first
     do while(associated(this))
-      if (debug) call check_position(grd, this, 'thermodynamics (top)')
+      if (debug) call check_position(grd, this, 'thermodynamics (top)',bergs%Lx,bergs%grid_is_latlon)
   
       call interp_flds(grd, this%ine, this%jne, this%xi, this%yj, this%uo, this%vo, &
               this%ui, this%vi, this%ua, this%va, this%ssh_x, this%ssh_y, this%sst, &
@@ -1064,7 +1103,7 @@ subroutine thermodynamics(bergs)
 
           orientation=bergs%initial_orientation
           if ((bergs%iceberg_bonds_on) .and. (bergs%rotate_icebergs_for_mass_spreading)) then
-                  orientation=find_orientation_using_iceberg_bonds(this,bergs%initial_orientation)
+                  orientation=find_orientation_using_iceberg_bonds(this,bergs%initial_orientation,bergs%grid_is_latlon)
                   print *, 'orientation: ', orientation, this%iceberg_num
 
           endif
@@ -1081,14 +1120,16 @@ subroutine thermodynamics(bergs)
 end subroutine thermodynamics
 
 !MPP1
-real function find_orientation_using_iceberg_bonds(berg,initial_orientation)
+real function find_orientation_using_iceberg_bonds(berg,initial_orientation,grid_is_latlon)
   ! Arguments
   type(iceberg) :: berg
   real, intent(in) :: initial_orientation 
+  logical, intent(in) :: grid_is_latlon
   type(iceberg), pointer :: other_berg
   type(bond), pointer :: current_bond
   real :: angle, lat1,lat2,lon1,lon2,dlat,dlon
-  real :: r_dist_x, r_dist_y
+  real :: r_dist_x, r_dist_y 
+  real :: lat_ref, dx_dlon, dy_dlat
   real :: theta, bond_count, Average_angle
     
   bond_count=0.
@@ -1107,8 +1148,11 @@ real function find_orientation_using_iceberg_bonds(berg,initial_orientation)
         dlat=lat2-lat1
         dlon=lon2-lon1
         
-        r_dist_x=dlon*(pi/180)*Rearth*cos(0.5*(lat1+lat2)*(pi/180))
-        r_dist_y=dlat*(pi/180)*Rearth
+        lat_ref=0.5*(lat1+lat2)
+        call convert_from_grid_to_meters(lat_ref,grid_is_latlon,dx_dlon,dy_dlat)
+        r_dist_x=dlon*dx_dlon
+        r_dist_y=dlat*dy_dlat
+
         if (r_dist_y .eq. 0.) then
           angle=pi/2.
         else
@@ -2609,7 +2653,7 @@ subroutine calve_icebergs(bergs)
           newberg%lon=0.25*((grd%lon(i,j)+grd%lon(i-1,j-1))+(grd%lon(i-1,j)+grd%lon(i,j-1)))
           newberg%lat=0.25*((grd%lat(i,j)+grd%lat(i-1,j-1))+(grd%lat(i-1,j)+grd%lat(i,j-1)))
          !write(stderr(),*) 'diamonds, calve_icebergs: creating new iceberg at ',newberg%lon,newberg%lat
-          lret=pos_within_cell(grd, newberg%lon, newberg%lat, i, j, xi, yj)
+          lret=pos_within_cell(grd, newberg%lon, newberg%lat, i, j, xi, yj,bergs%Lx,bergs%grid_is_latlon)
           if (.not.lret) then
             write(stderrunit,*) 'diamonds, calve_icebergs: something went very wrong!',i,j,xi,yj
             call error_mesg('diamonds, calve_icebergs', 'berg is not in the correct cell!', FATAL)
@@ -2703,7 +2747,7 @@ subroutine evolve_icebergs(bergs)
       if (berg%static_berg .lt. 0.5) then  !Only allow non-static icebergs to evolve
  
         !Checking it everything is ok:
-        if (.not. is_point_in_cell(bergs%grd, berg%lon, berg%lat, berg%ine, berg%jne) ) then
+        if (.not. is_point_in_cell(bergs%grd, berg%lon, berg%lat, berg%ine, berg%jne,bergs%Lx,bergs%grid_is_latlon) ) then
           write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lon',(i,i=grd%isd,grd%ied)
           do j=grd%jed,grd%jsd,-1
             write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lon(i,j),i=grd%isd,grd%ied)
@@ -2718,7 +2762,7 @@ subroutine evolve_icebergs(bergs)
                    berg%jne,berg%lat,grd%lat(berg%ine-1,berg%jne-1),grd%lat(berg%ine,berg%jne)
           if (debug) call error_mesg('diamonds, evolve_iceberg','berg is in wrong starting cell!',FATAL)
         endif
-        if (debug) call check_position(grd, berg, 'evolve_iceberg (top)')
+        if (debug) call check_position(grd, berg, 'evolve_iceberg (top)',bergs%Lx,bergs%grid_is_latlon)
 
           !Time stepping schemes:
           if (Runge_not_Verlet) then 
@@ -2746,7 +2790,7 @@ subroutine evolve_icebergs(bergs)
 
         !call interp_flds(grd, i, j, xi, yj, berg%uo, berg%vo, berg%ui, berg%vi, berg%ua, berg%va, berg%ssh_x, berg%ssh_y, berg%sst)
         !if (debug) call print_berg(stderr(), berg, 'evolve_iceberg, final posn.')
-        if (debug) call check_position(grd, berg, 'evolve_iceberg (bot)')
+        if (debug) call check_position(grd, berg, 'evolve_iceberg (bot)',bergs%Lx,bergs%grid_is_latlon)
       endif
       berg=>berg%next
     enddo ! loop over all bergs
@@ -2833,7 +2877,7 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
   
         !Solving for the new velocity
         on_tangential_plane=.false.
-        if (berg%lat>89.) on_tangential_plane=.true.
+        if ((berg%lat>89.) .and. (bergs%grid_is_latlon)) on_tangential_plane=.true.
         if (on_tangential_plane) then
           call rotvec_to_tang(lonn,uvel3,vvel3,xdot3,ydot3)
           call rotvec_to_tang(lonn,ax1,ay1,xddot1,yddot1)
@@ -2849,7 +2893,7 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
         !!!!!!!!!!!!!!! Debugging  !!!!!!!!!!!!!!!!!!!!!!!!!!!
         error_flag=.false.
         if (.not.error_flag) then
-          if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j)) error_flag=.true.
+          if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j,bergs%Lx,bergs%grid_is_latlon)) error_flag=.true.
         endif
         if (error_flag) then
          call print_fld(grd, grd%msk, 'msk')
@@ -2868,13 +2912,13 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
               & dt*ay1
          write(stderrunit,*) 'diamonds, evolve_iceberg: on_tangential_plane=',on_tangential_plane
          write(stderrunit,*) 'Acceleration terms for position 1'
-         error_flag=pos_within_cell(grd, lonn, latn, i, j, xi, yj)
+         error_flag=pos_within_cell(grd, lonn, latn, i, j, xi,  yj,bergs%Lx,bergs%grid_is_latlon)
          call accel(bergs, berg, i, j, xi, yj, latn, uvel3, vvel3, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn, bxn, byn - Added by Alon
          
           write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'posn i,j,lon,lat,xi,yj=',i,j,lonn,latn,xi,yj
           write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'posn box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
           call print_berg(stderrunit, berg, 'evolve_iceberg, out of cell at end!')
-          bounced=is_point_in_cell(bergs%grd, lonn, latn, i, j, explain=.true.)
+          bounced=is_point_in_cell(bergs%grd, lonn, latn, i, j,bergs%Lx,bergs%grid_is_latlon ,explain=.true.)
           if (debug) call error_mesg('diamonds, evolve_iceberg','berg is out of posn at end!',FATAL)
           write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lon',(i,i=grd%isd,grd%ied)
           do j=grd%jed,grd%jsd,-1
@@ -2938,7 +2982,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         yj=berg%yj
         bounced=.false.
         on_tangential_plane=.false.
-        if (berg%lat>89.) on_tangential_plane=.true.
+        if ((berg%lat>89.) .and. (bergs%grid_is_latlon)) on_tangential_plane=.true.
         i1=i;j1=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
           call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, bergs%hexagonal_icebergs)
@@ -2951,8 +2995,10 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         ! A1 = A(X1)
         lon1=berg%lon; lat1=berg%lat
         if (on_tangential_plane) call rotpos_to_tang(lon1,lat1,x1,y1)
-        dxdl1=r180_pi/(Rearth*cos(lat1*pi_180))
-        dydl=r180_pi/Rearth
+        
+        call  convert_from_meters_to_grid(lat1,bergs%grid_is_latlon ,dxdl1,dydl)
+        !dxdl1=r180_pi/(Rearth*cos(lat1*pi_180))
+        !dydl=r180_pi/Rearth
         uvel1=berg%uvel; vvel1=berg%vvel
         if (on_tangential_plane) call rotvec_to_tang(lon1,uvel1,vvel1,xdot1,ydot1)
         u1=uvel1*dxdl1; v1=vvel1*dydl
@@ -2974,13 +3020,13 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
           uvel2=uvel1+dt_2*ax1; vvel2=vvel1+dt_2*ay1
         endif
         i=i1;j=j1;xi=berg%xi;yj=berg%yj
-        call adjust_index_and_ground(grd, lon2, lat2, uvel2, vvel2, i, j, xi, yj, bounced, error_flag)
+        call adjust_index_and_ground(grd, lon2, lat2, uvel2, vvel2, i, j, xi, yj, bounced, error_flag,bergs%Lx,bergs%grid_is_latlon)
         i2=i; j2=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
           call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling, berg%length*berg%width , bergs%hexagonal_icebergs)
         ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon2,lat2,x2,y2)
         if (.not.error_flag) then
-          if (debug .and. .not. is_point_in_cell(bergs%grd, lon2, lat2, i, j)) error_flag=.true.
+          if (debug .and. .not. is_point_in_cell(bergs%grd, lon2, lat2, i, j,bergs%Lx,bergs%grid_is_latlon)) error_flag=.true.
         endif
         if (error_flag) then
          call print_fld(grd, grd%msk, 'msk')
@@ -3002,15 +3048,16 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
          write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2 (deg)=',dt*u1,dt*u2
          write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2 (deg)=',dt*v1,dt*v2
          write(stderrunit,*) 'Acceleration terms for position 1'
-         error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
+         error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj,bergs%Lx,bergs%grid_is_latlon)
          call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn,- Added by Alon
           call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 2')
           write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos2 i,j,lon,lat,xi,yj=',i,j,lon2,lat2,xi,yj
           write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos2 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
-          bounced=is_point_in_cell(bergs%grd, lon2, lat2, i, j, explain=.true.)
+          bounced=is_point_in_cell(bergs%grd, lon2, lat2, i, j, bergs%Lx,bergs%grid_is_latlon,explain=.true.)
           call error_mesg('diamonds, evolve_iceberg','berg is out of posn at 2!',FATAL)
         endif
-        dxdl2=r180_pi/(Rearth*cos(lat2*pi_180))
+        call  convert_from_meters_to_grid(lat2,bergs%grid_is_latlon ,dxdl2,dydl)
+        !dxdl2=r180_pi/(Rearth*cos(lat2*pi_180))
         u2=uvel2*dxdl2; v2=vvel2*dydl
         call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
         !call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt, ax2, ay2, axn2, ayn2, bxn, byn) !Note change to dt. Markpoint_1
@@ -3029,13 +3076,13 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
           uvel3=uvel1+dt_2*ax2; vvel3=vvel1+dt_2*ay2
         endif
         i=i1;j=j1;xi=berg%xi;yj=berg%yj
-        call adjust_index_and_ground(grd, lon3, lat3, uvel3, vvel3, i, j, xi, yj, bounced, error_flag)
+        call adjust_index_and_ground(grd, lon3, lat3, uvel3, vvel3, i, j, xi, yj, bounced, error_flag,bergs%Lx,bergs%grid_is_latlon)
         i3=i; j3=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
           call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, bergs%hexagonal_icebergs)
         ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon3,lat3,x3,y3)
         if (.not.error_flag) then
-          if (debug .and. .not. is_point_in_cell(bergs%grd, lon3, lat3, i, j)) error_flag=.true.
+          if (debug .and. .not. is_point_in_cell(bergs%grd, lon3, lat3, i, j,bergs%Lx,bergs%grid_is_latlon)) error_flag=.true.
         endif
         if (error_flag) then
          call print_fld(grd, grd%msk, 'msk')
@@ -3057,18 +3104,19 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
          write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3 (deg)=',dt*u1,dt*u2,dt*u3
          write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3 (deg)=',dt*v1,dt*v2,dt*v3
          write(stderrunit,*) 'Acceleration terms for position 1'
-         error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
+         error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj,bergs%Lx,bergs%grid_is_latlon)
          call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, debug_flag=.true.) !axn, ayn - Added by Alon
          write(stderrunit,*) 'Acceleration terms for position 2'
-         error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
+         error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj,bergs%Lx,bergs%grid_is_latlon)
          call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
           call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 3')
           write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos3 i,j,lon,lat,xi,yj=',i,j,lon3,lat3,xi,yj
           write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos3 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
-          bounced=is_point_in_cell(bergs%grd, lon2, lat2, i, j, explain=.true.)
+          bounced=is_point_in_cell(bergs%grd, lon2, lat2, i, j, bergs%Lx,bergs%grid_is_latlon,explain=.true.)
           call error_mesg('diamonds, evolve_iceberg','berg is out of posn at 3!',FATAL)
         endif
-        dxdl3=r180_pi/(Rearth*cos(lat3*pi_180))
+        call  convert_from_meters_to_grid(lat3,bergs%grid_is_latlon ,dxdl3,dydl)
+        !dxdl3=r180_pi/(Rearth*cos(lat3*pi_180))
         u3=uvel3*dxdl3; v3=vvel3*dydl
         call accel(bergs, berg, i, j, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn3, ayn3, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
         if (on_tangential_plane) call rotvec_to_tang(lon3,ax3,ay3,xddot3,yddot3)
@@ -3086,11 +3134,11 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
           uvel4=uvel1+dt*ax3; vvel4=vvel1+dt*ay3
         endif
         i=i1;j=j1;xi=berg%xi;yj=berg%yj
-        call adjust_index_and_ground(grd, lon4, lat4, uvel4, vvel4, i, j, xi, yj, bounced, error_flag)
+        call adjust_index_and_ground(grd, lon4, lat4, uvel4, vvel4, i, j, xi, yj, bounced, error_flag,bergs%Lx,bergs%grid_is_latlon)
         i4=i; j4=j
         ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon4,lat4,x4,y4)
         if (.not.error_flag) then
-          if (debug .and. .not. is_point_in_cell(bergs%grd, lon4, lat4, i, j)) error_flag=.true.
+          if (debug .and. .not. is_point_in_cell(bergs%grd, lon4, lat4, i, j,bergs%Lx,bergs%grid_is_latlon)) error_flag=.true.
         endif
         if (error_flag) then
          call print_fld(grd, grd%msk, 'msk')
@@ -3112,21 +3160,22 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
          write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3,u4 (deg)=',dt*u1,dt*u2,dt*u3,dt*u4
          write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v4 (deg)=',dt*v1,dt*v2,dt*v3,dt*v4
          write(stderrunit,*) 'Acceleration terms for position 1'
-         error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
+         error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj,bergs%Lx,bergs%grid_is_latlon)
          call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
          write(stderrunit,*) 'Acceleration terms for position 2'
-         error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
+         error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj,bergs%Lx,bergs%grid_is_latlon)
          call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
          write(stderrunit,*) 'Acceleration terms for position 3'
-         error_flag=pos_within_cell(grd, lon3, lat3, i3, j3, xi, yj)
+         error_flag=pos_within_cell(grd, lon3, lat3, i3, j3, xi, yj,bergs%Lx,bergs%grid_is_latlon)
          call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn3, ayn3, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
           call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 4')
           write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos4 i,j,lon,lat,xi,yj=',i,j,lon4,lat4,xi,yj
           write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos4 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
-          bounced=is_point_in_cell(bergs%grd, lon2, lat2, i, j, explain=.true.)
+          bounced=is_point_in_cell(bergs%grd, lon2, lat2, i, j,bergs%Lx,bergs%grid_is_latlon, explain=.true.)
           call error_mesg('diamonds, evolve_iceberg','berg is out of posn at 4!',FATAL)
         endif
-        dxdl4=r180_pi/(Rearth*cos(lat4*pi_180))
+        call  convert_from_meters_to_grid(lat4,bergs%grid_is_latlon ,dxdl4,dydl)
+        !dxdl4=r180_pi/(Rearth*cos(lat4*pi_180))
         u4=uvel4*dxdl4; v4=vvel4*dydl
         call accel(bergs, berg, i, j, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axn4, ayn4, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
         if (on_tangential_plane) call rotvec_to_tang(lon4,ax4,ay4,xddot4,yddot4)
@@ -3159,12 +3208,12 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
   
   
         i=i1;j=j1;xi=berg%xi;yj=berg%yj
-        call adjust_index_and_ground(grd, lonn, latn, uveln, vveln, i, j, xi, yj, bounced, error_flag)
+        call adjust_index_and_ground(grd, lonn, latn, uveln, vveln, i, j, xi, yj, bounced, error_flag,bergs%Lx,bergs%grid_is_latlon)
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
           call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, bergs%hexagonal_icebergs)
   
         if (.not.error_flag) then
-          if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j)) error_flag=.true.
+          if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j,bergs%Lx,bergs%grid_is_latlon)) error_flag=.true.
         endif
         if (error_flag) then
          call print_fld(grd, grd%msk, 'msk')
@@ -3193,21 +3242,21 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
               & dt*v1,dt*v2,dt*v3,dt*v4,dt_6*( (v1+v4)+2.*(v2+v3) )
          write(stderrunit,*) 'diamonds, evolve_iceberg: on_tangential_plane=',on_tangential_plane
          write(stderrunit,*) 'Acceleration terms for position 1'
-         error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
+         error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj,bergs%Lx,bergs%grid_is_latlon)
          call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
          write(stderrunit,*) 'Acceleration terms for position 2'
-         error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
+         error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj,bergs%Lx,bergs%grid_is_latlon)
          call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
          write(stderrunit,*) 'Acceleration terms for position 3'
-         error_flag=pos_within_cell(grd, lon3, lat3, i3, j3, xi, yj)
+         error_flag=pos_within_cell(grd, lon3, lat3, i3, j3, xi, yj,bergs%Lx,bergs%grid_is_latlon)
          call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
          write(stderrunit,*) 'Acceleration terms for position 4'
-         error_flag=pos_within_cell(grd, lon4, lat4, i4, j4, xi, yj)
+         error_flag=pos_within_cell(grd, lon4, lat4, i4, j4, xi, yj,bergs%Lx,bergs%grid_is_latlon)
          call accel(bergs, berg, i4, j4, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
           write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'posn i,j,lon,lat,xi,yj=',i,j,lonn,latn,xi,yj
           write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'posn box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
           call print_berg(stderrunit, berg, 'evolve_iceberg, out of cell at end!')
-          bounced=is_point_in_cell(bergs%grd, lonn, latn, i, j, explain=.true.)
+          bounced=is_point_in_cell(bergs%grd, lonn, latn, i, j,bergs%Lx,bergs%grid_is_latlon, explain=.true.)
           if (debug) call error_mesg('diamonds, evolve_iceberg','berg is out of posn at end!',FATAL)
           write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lon',(i,i=grd%isd,grd%ied)
           do j=grd%jed,grd%jsd,-1
@@ -3252,12 +3301,13 @@ subroutine update_verlet_position(bergs,berg)
 
 
       on_tangential_plane=.false.
-      if (berg%lat>89.) on_tangential_plane=.true.
+      if ((berg%lat>89.) .and. (bergs%grid_is_latlon)) on_tangential_plane=.true.
 
         lon1=berg%lon; lat1=berg%lat
         if (on_tangential_plane) call rotpos_to_tang(lon1,lat1,x1,y1,berg%iceberg_num)
-        dxdl1=r180_pi/(Rearth*cos(lat1*pi_180))
-        dydl=r180_pi/Rearth
+        !dxdl1=r180_pi/(Rearth*cos(lat1*pi_180))
+        !dydl=r180_pi/Rearth
+        call  convert_from_meters_to_grid(lat1,bergs%grid_is_latlon ,dxdl1,dydl)
         uvel1=berg%uvel; vvel1=berg%vvel
 
         ! Loading past acceleartions - Alon
@@ -3280,7 +3330,8 @@ subroutine update_verlet_position(bergs,berg)
         else
           lonn=lon1+(dt*u2) ; latn=lat1+(dt*v2)  !Alon
         endif
-        dxdln=r180_pi/(Rearth*cos(latn*pi_180))
+        !dxdln=r180_pi/(Rearth*cos(latn*pi_180))
+        call  convert_from_meters_to_grid(latn,bergs%grid_is_latlon ,dxdln,dydl)
   
         ! Turn the velocities into u_star, v_star.(uvel3 is v_star) - Alon (not sure how this works with tangent plane)
         uvel3=uvel1+(dt_2*axn)                  !Alon
@@ -3289,7 +3340,7 @@ subroutine update_verlet_position(bergs,berg)
         ! Adjusting mass...
         !MP3
         i=berg%ine;  j=berg%jne;  xi = berg%xi;  yj = berg%yj
-        call adjust_index_and_ground(grd, lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
+        call adjust_index_and_ground(grd, lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag,bergs%Lx,bergs%grid_is_latlon)  !Alon:"unclear which velocity to use here?"
 
         !if (bounced) then
         !  print *, 'you have been bounce: big time!',mpp_pe(),berg%iceberg_num,lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag 
@@ -3350,10 +3401,11 @@ end subroutine rotvec_from_tang
 
 ! ##############################################################################
 
-subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, bounced, error)
+subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, bounced, error, Lx,grid_is_latlon)
 ! Arguments
 type(icebergs_gridded), pointer :: grd
-real, intent(inout) :: lon, lat, uvel, vvel, xi, yj
+real, intent(inout) :: lon, lat, uvel, vvel, xi, yj, Lx
+logical, intent(in) :: grid_is_latlon
 integer, intent(inout) :: i,j
 logical, intent(out) :: bounced, error
 ! Local variables
@@ -3370,12 +3422,12 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
   error=.false.
   lon0=lon; lat0=lat ! original position
   i0=i; j0=j ! original i,j
-  lret=pos_within_cell(grd, lon, lat, i, j, xi, yj)
+  lret=pos_within_cell(grd, lon, lat, i, j, xi, yj,Lx,grid_is_latlon)
 !  print *, 'Alon:', lon, lat, i, j, xi, yj, lret
   xi0=xi; yj0=yj ! original xi,yj
   if (debug) then
     !Sanity check lret, xi and yj
-    lret=is_point_in_cell(grd, lon, lat, i, j)
+    lret=is_point_in_cell(grd, lon, lat, i, j, Lx, grid_is_latlon)
     if (xi<0. .or. xi>1. .or. yj<0. .or. yj>1.) then
       if (lret) then
         write(stderrunit,*) 'diamonds, adjust: WARNING!!! lret=T but |xi,yj|>1',mpp_pe()
@@ -3385,9 +3437,9 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
         write(stderrunit,*) 'diamonds, adjust: yi=',yj,' lat=',lat
         write(stderrunit,*) 'diamonds, adjust: y3 y2=',grd%lat(i-1,j),grd%lat(i,j)
         write(stderrunit,*) 'diamonds, adjust: y0 y1=',grd%lat(i-1,j-1),grd%lat(i,j-1)
-        lret=is_point_in_cell(grd, lon, lat, i, j, explain=.true.)
+        lret=is_point_in_cell(grd, lon, lat, i, j, Lx,grid_is_latlon,explain=.true.)
         write(stderrunit,*) 'diamonds, adjust: fn is_point_in_cell=',lret
-        lret=pos_within_cell(grd, lon, lat, i, j, xi, yj, explain=.true.)
+        lret=pos_within_cell(grd, lon, lat, i, j, xi, yj, Lx,grid_is_latlon,explain=.true.)
         write(stderrunit,*) 'diamonds, adjust: fn pos_within_cell=',lret
         write(0,*) 'This should never happen!'
         error=.true.; return
@@ -3401,15 +3453,15 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
         write(stderrunit,*) 'diamonds, adjust: yi=',yj,' lat=',lat
         write(stderrunit,*) 'diamonds, adjust: y3 y2=',grd%lat(i-1,j),grd%lat(i,j)
         write(stderrunit,*) 'diamonds, adjust: y0 y1=',grd%lat(i-1,j-1),grd%lat(i,j-1)
-        lret=is_point_in_cell(grd, lon, lat, i, j, explain=.true.)
+        lret=is_point_in_cell(grd, lon, lat, i, j, Lx, grid_is_latlon, explain=.true.)
         write(stderrunit,*) 'diamonds, adjust: fn is_point_in_cell=',lret
-        lret=pos_within_cell(grd, lon, lat, i, j, xi, yj, explain=.true.)
+        lret=pos_within_cell(grd, lon, lat, i, j, xi, yj, Lx, grid_is_latlon,explain=.true.)
         write(stderrunit,*) 'diamonds, adjust: fn pos_within_cell=',lret
         write(0,*) 'This should never happen!'
         error=.true.; return
       endif
     endif
-    lret=pos_within_cell(grd, lon, lat, i, j, xi, yj)
+    lret=pos_within_cell(grd, lon, lat, i, j, xi, yj,Lx,grid_is_latlon)
   endif ! debug
   if (lret) return ! Berg was already in cell
 
@@ -3439,7 +3491,7 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
         jnm=jnm+1
       endif
     endif
-    lret=pos_within_cell(grd, lon, lat, inm, jnm, xi, yj) ! Update xi and yj
+    lret=pos_within_cell(grd, lon, lat, inm, jnm, xi, yj,Lx,grid_is_latlon) ! Update xi and yj
   enddo
   if (abs(inm-i0)>1) then
     write(stderrunit,*) 'pe=',mpp_pe(),'diamonds, adjust: inm,i0,inm-i0=',inm,i0,inm-i0
@@ -3452,7 +3504,7 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
 
   ! Adjust i,j based on xi,yj while bouncing off of masked land cells
   icount=0
-  lret=pos_within_cell(grd, lon, lat, i0, j0, xi, yj)
+  lret=pos_within_cell(grd, lon, lat, i0, j0, xi, yj,Lx,grid_is_latlon)
   do while ( .not.lret.and. icount<4 )
     icount=icount+1
     if (xi.lt.0.) then
@@ -3504,7 +3556,7 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
     if (debug) then
       if (grd%msk(i,j)==0.) stop 'diamonds, adjust: Berg is in land! This should not happen...'
     endif
-    lret=pos_within_cell(grd, lon, lat, i, j, xi, yj) ! Update xi and yj
+    lret=pos_within_cell(grd, lon, lat, i, j, xi, yj,Lx,grid_is_latlon) ! Update xi and yj
   enddo
  !if (debug) then
  !  if (abs(i-i0)>2) then
@@ -3527,7 +3579,7 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
       write(stderrunit,*) 'diamonds, adjust: i,j=',i,j
       write(stderrunit,*) 'diamonds, adjust: inm,jnm=',inm,jnm
       write(stderrunit,*) 'diamonds, adjust: icount=',icount
-      lret=pos_within_cell(grd, lon, lat, i, j, xi, yj, explain=.true.)
+      lret=pos_within_cell(grd, lon, lat, i, j, xi, yj, Lx,grid_is_latlon,explain=.true.)
       write(stderrunit,*) 'diamonds, adjust: lret=',lret
     endif
     if (abs(i-i0)+abs(j-j0)==0) then
@@ -3552,7 +3604,7 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
   if (yj<0.) yj=posn_eps
   lon=bilin(grd, grd%lon, i, j, xi, yj)
   lat=bilin(grd, grd%lat, i, j, xi, yj)
-  lret=pos_within_cell(grd, lon, lat, i, j, xi, yj) ! Update xi and yj
+  lret=pos_within_cell(grd, lon, lat, i, j, xi, yj,Lx,grid_is_latlon) ! Update xi and yj
 
   if (.not. lret) then
     write(stderrunit,*) 'diamonds, adjust: Should not get here! Berg is not in cell after adjustment'

From 6e9e32877a5a4ae8dd0f2892cd9af84af5fbbc5f Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 6 Jul 2016 10:35:30 -0400
Subject: [PATCH 126/361] The length of the domain, Lx, and the flag
 grid_is_latlon have been included in the gridded_icebergs type, which means
 that these variables do not have to be passed around as explicitly. This
 neatens the code.

A flag has been added to allow the code to run on an f-plane. The reference latitude for the f_plane is an input parameter, lat_ref.

The option to change omega has been removed. No rotation can be achieved by setting the lat_ref to zero and using the f-plane (this is the default for when grid_is_latlon is off)

The model has been set to default to an f-plane when grid_is_latlon is off.

The periodicity in the x-direction is set by Lx. When grid_is_latlon is set to False, and Lx=360 (default), then Lx is set to a very large number which makes the model not periodic.
---
 icebergs.F90           | 121 +++++++++++-----------
 icebergs_framework.F90 | 224 ++++++++++++++++++++++++-----------------
 icebergs_io.F90        |   2 +-
 3 files changed, 193 insertions(+), 154 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 129bb31..1db6a3f 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -175,7 +175,7 @@ subroutine initialize_iceberg_bonds(bergs)
             dlon=lon1-lon2
             dlat=lat1-lat2
             lat_ref=0.5*(lat1+lat2)
-            call convert_from_grid_to_meters(lat_ref,bergs%grid_is_latlon,dx_dlon,dy_dlat)
+            call convert_from_grid_to_meters(lat_ref,grd%grid_is_latlon,dx_dlon,dy_dlat)
             r_dist_x=dlon*dx_dlon
             r_dist_y=dlat*dy_dlat
             r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) )
@@ -343,7 +343,7 @@ subroutine calculate_force(bergs,berg,other_berg,IA_x, IA_y, u0, v0, u1, v1, P_i
         !r_dist_x=x1-x2 ; r_dist_y=y1-y2
         !r_dist=sqrt( ((x1-x2)**2) + ((y1-y2)**2) )
         lat_ref=0.5*(lat1+lat2)
-        call convert_from_grid_to_meters(lat_ref,bergs%grid_is_latlon,dx_dlon,dy_dlat)
+        call convert_from_grid_to_meters(lat_ref,bergs%grd%grid_is_latlon,dx_dlon,dy_dlat)
 
         r_dist_x=dlon*dx_dlon
         r_dist_y=dlat*dy_dlat
@@ -521,7 +521,11 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
   ! Interpolate gridded fields to berg     - Note: It should be possible to move this to evolve, so that it only needs to be called once. !!!!
   call interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, cn, hi)
 
-   f_cori=(2.*bergs%Omega_icebergs)*sin(pi_180*lat)
+  if ((grd%grid_is_latlon) .and. (.not. bergs%use_f_plane)) then
+     f_cori=(2.*omega)*sin(pi_180*lat)
+  else
+     f_cori=(2.*omega)*sin(pi_180*bergs%lat_ref)
+  endif
 !  f_cori=0.
 
   M=berg%mass
@@ -934,7 +938,7 @@ subroutine thermodynamics(bergs)
   do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied  ! Thermodynamics of  halos now calculated, so that spread mass to ocean works correctly
     this=>bergs%list(grdi,grdj)%first
     do while(associated(this))
-      if (debug) call check_position(grd, this, 'thermodynamics (top)',bergs%Lx,bergs%grid_is_latlon)
+      if (debug) call check_position(grd, this, 'thermodynamics (top)')
   
       call interp_flds(grd, this%ine, this%jne, this%xi, this%yj, this%uo, this%vo, &
               this%ui, this%vi, this%ua, this%va, this%ssh_x, this%ssh_y, this%sst, &
@@ -1103,7 +1107,7 @@ subroutine thermodynamics(bergs)
 
           orientation=bergs%initial_orientation
           if ((bergs%iceberg_bonds_on) .and. (bergs%rotate_icebergs_for_mass_spreading)) then
-                  orientation=find_orientation_using_iceberg_bonds(this,bergs%initial_orientation,bergs%grid_is_latlon)
+                  orientation=find_orientation_using_iceberg_bonds(this,bergs%initial_orientation,bergs%grd%grid_is_latlon)
                   print *, 'orientation: ', orientation, this%iceberg_num
 
           endif
@@ -2653,7 +2657,7 @@ subroutine calve_icebergs(bergs)
           newberg%lon=0.25*((grd%lon(i,j)+grd%lon(i-1,j-1))+(grd%lon(i-1,j)+grd%lon(i,j-1)))
           newberg%lat=0.25*((grd%lat(i,j)+grd%lat(i-1,j-1))+(grd%lat(i-1,j)+grd%lat(i,j-1)))
          !write(stderr(),*) 'diamonds, calve_icebergs: creating new iceberg at ',newberg%lon,newberg%lat
-          lret=pos_within_cell(grd, newberg%lon, newberg%lat, i, j, xi, yj,bergs%Lx,bergs%grid_is_latlon)
+          lret=pos_within_cell(grd, newberg%lon, newberg%lat, i, j, xi, yj)
           if (.not.lret) then
             write(stderrunit,*) 'diamonds, calve_icebergs: something went very wrong!',i,j,xi,yj
             call error_mesg('diamonds, calve_icebergs', 'berg is not in the correct cell!', FATAL)
@@ -2747,7 +2751,7 @@ subroutine evolve_icebergs(bergs)
       if (berg%static_berg .lt. 0.5) then  !Only allow non-static icebergs to evolve
  
         !Checking it everything is ok:
-        if (.not. is_point_in_cell(bergs%grd, berg%lon, berg%lat, berg%ine, berg%jne,bergs%Lx,bergs%grid_is_latlon) ) then
+        if (.not. is_point_in_cell(bergs%grd, berg%lon, berg%lat, berg%ine, berg%jne) ) then
           write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lon',(i,i=grd%isd,grd%ied)
           do j=grd%jed,grd%jsd,-1
             write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lon(i,j),i=grd%isd,grd%ied)
@@ -2762,7 +2766,7 @@ subroutine evolve_icebergs(bergs)
                    berg%jne,berg%lat,grd%lat(berg%ine-1,berg%jne-1),grd%lat(berg%ine,berg%jne)
           if (debug) call error_mesg('diamonds, evolve_iceberg','berg is in wrong starting cell!',FATAL)
         endif
-        if (debug) call check_position(grd, berg, 'evolve_iceberg (top)',bergs%Lx,bergs%grid_is_latlon)
+        if (debug) call check_position(grd, berg, 'evolve_iceberg (top)')
 
           !Time stepping schemes:
           if (Runge_not_Verlet) then 
@@ -2790,7 +2794,7 @@ subroutine evolve_icebergs(bergs)
 
         !call interp_flds(grd, i, j, xi, yj, berg%uo, berg%vo, berg%ui, berg%vi, berg%ua, berg%va, berg%ssh_x, berg%ssh_y, berg%sst)
         !if (debug) call print_berg(stderr(), berg, 'evolve_iceberg, final posn.')
-        if (debug) call check_position(grd, berg, 'evolve_iceberg (bot)',bergs%Lx,bergs%grid_is_latlon)
+        if (debug) call check_position(grd, berg, 'evolve_iceberg (bot)')
       endif
       berg=>berg%next
     enddo ! loop over all bergs
@@ -2877,7 +2881,7 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
   
         !Solving for the new velocity
         on_tangential_plane=.false.
-        if ((berg%lat>89.) .and. (bergs%grid_is_latlon)) on_tangential_plane=.true.
+        if ((berg%lat>89.) .and. (bergs%grd%grid_is_latlon)) on_tangential_plane=.true.
         if (on_tangential_plane) then
           call rotvec_to_tang(lonn,uvel3,vvel3,xdot3,ydot3)
           call rotvec_to_tang(lonn,ax1,ay1,xddot1,yddot1)
@@ -2893,7 +2897,7 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
         !!!!!!!!!!!!!!! Debugging  !!!!!!!!!!!!!!!!!!!!!!!!!!!
         error_flag=.false.
         if (.not.error_flag) then
-          if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j,bergs%Lx,bergs%grid_is_latlon)) error_flag=.true.
+          if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j)) error_flag=.true.
         endif
         if (error_flag) then
          call print_fld(grd, grd%msk, 'msk')
@@ -2912,13 +2916,13 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
               & dt*ay1
          write(stderrunit,*) 'diamonds, evolve_iceberg: on_tangential_plane=',on_tangential_plane
          write(stderrunit,*) 'Acceleration terms for position 1'
-         error_flag=pos_within_cell(grd, lonn, latn, i, j, xi,  yj,bergs%Lx,bergs%grid_is_latlon)
+         error_flag=pos_within_cell(grd, lonn, latn, i, j, xi,  yj)
          call accel(bergs, berg, i, j, xi, yj, latn, uvel3, vvel3, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn, bxn, byn - Added by Alon
          
           write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'posn i,j,lon,lat,xi,yj=',i,j,lonn,latn,xi,yj
           write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'posn box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
           call print_berg(stderrunit, berg, 'evolve_iceberg, out of cell at end!')
-          bounced=is_point_in_cell(bergs%grd, lonn, latn, i, j,bergs%Lx,bergs%grid_is_latlon ,explain=.true.)
+          bounced=is_point_in_cell(bergs%grd, lonn, latn, i, j,explain=.true.)
           if (debug) call error_mesg('diamonds, evolve_iceberg','berg is out of posn at end!',FATAL)
           write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lon',(i,i=grd%isd,grd%ied)
           do j=grd%jed,grd%jsd,-1
@@ -2982,7 +2986,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         yj=berg%yj
         bounced=.false.
         on_tangential_plane=.false.
-        if ((berg%lat>89.) .and. (bergs%grid_is_latlon)) on_tangential_plane=.true.
+        if ((berg%lat>89.) .and. (bergs%grd%grid_is_latlon)) on_tangential_plane=.true.
         i1=i;j1=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
           call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, bergs%hexagonal_icebergs)
@@ -2996,7 +3000,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         lon1=berg%lon; lat1=berg%lat
         if (on_tangential_plane) call rotpos_to_tang(lon1,lat1,x1,y1)
         
-        call  convert_from_meters_to_grid(lat1,bergs%grid_is_latlon ,dxdl1,dydl)
+        call  convert_from_meters_to_grid(lat1,bergs%grd%grid_is_latlon ,dxdl1,dydl)
         !dxdl1=r180_pi/(Rearth*cos(lat1*pi_180))
         !dydl=r180_pi/Rearth
         uvel1=berg%uvel; vvel1=berg%vvel
@@ -3020,13 +3024,13 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
           uvel2=uvel1+dt_2*ax1; vvel2=vvel1+dt_2*ay1
         endif
         i=i1;j=j1;xi=berg%xi;yj=berg%yj
-        call adjust_index_and_ground(grd, lon2, lat2, uvel2, vvel2, i, j, xi, yj, bounced, error_flag,bergs%Lx,bergs%grid_is_latlon)
+        call adjust_index_and_ground(grd, lon2, lat2, uvel2, vvel2, i, j, xi, yj, bounced, error_flag)
         i2=i; j2=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
           call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling, berg%length*berg%width , bergs%hexagonal_icebergs)
         ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon2,lat2,x2,y2)
         if (.not.error_flag) then
-          if (debug .and. .not. is_point_in_cell(bergs%grd, lon2, lat2, i, j,bergs%Lx,bergs%grid_is_latlon)) error_flag=.true.
+          if (debug .and. .not. is_point_in_cell(bergs%grd, lon2, lat2, i, j)) error_flag=.true.
         endif
         if (error_flag) then
          call print_fld(grd, grd%msk, 'msk')
@@ -3048,15 +3052,15 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
          write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2 (deg)=',dt*u1,dt*u2
          write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2 (deg)=',dt*v1,dt*v2
          write(stderrunit,*) 'Acceleration terms for position 1'
-         error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj,bergs%Lx,bergs%grid_is_latlon)
+         error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
          call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn,- Added by Alon
           call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 2')
           write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos2 i,j,lon,lat,xi,yj=',i,j,lon2,lat2,xi,yj
           write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos2 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
-          bounced=is_point_in_cell(bergs%grd, lon2, lat2, i, j, bergs%Lx,bergs%grid_is_latlon,explain=.true.)
+          bounced=is_point_in_cell(bergs%grd, lon2, lat2, i, j,explain=.true.)
           call error_mesg('diamonds, evolve_iceberg','berg is out of posn at 2!',FATAL)
         endif
-        call  convert_from_meters_to_grid(lat2,bergs%grid_is_latlon ,dxdl2,dydl)
+        call  convert_from_meters_to_grid(lat2,bergs%grd%grid_is_latlon ,dxdl2,dydl)
         !dxdl2=r180_pi/(Rearth*cos(lat2*pi_180))
         u2=uvel2*dxdl2; v2=vvel2*dydl
         call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
@@ -3076,13 +3080,13 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
           uvel3=uvel1+dt_2*ax2; vvel3=vvel1+dt_2*ay2
         endif
         i=i1;j=j1;xi=berg%xi;yj=berg%yj
-        call adjust_index_and_ground(grd, lon3, lat3, uvel3, vvel3, i, j, xi, yj, bounced, error_flag,bergs%Lx,bergs%grid_is_latlon)
+        call adjust_index_and_ground(grd, lon3, lat3, uvel3, vvel3, i, j, xi, yj, bounced, error_flag)
         i3=i; j3=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
           call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, bergs%hexagonal_icebergs)
         ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon3,lat3,x3,y3)
         if (.not.error_flag) then
-          if (debug .and. .not. is_point_in_cell(bergs%grd, lon3, lat3, i, j,bergs%Lx,bergs%grid_is_latlon)) error_flag=.true.
+          if (debug .and. .not. is_point_in_cell(bergs%grd, lon3, lat3, i, j)) error_flag=.true.
         endif
         if (error_flag) then
          call print_fld(grd, grd%msk, 'msk')
@@ -3104,18 +3108,18 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
          write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3 (deg)=',dt*u1,dt*u2,dt*u3
          write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3 (deg)=',dt*v1,dt*v2,dt*v3
          write(stderrunit,*) 'Acceleration terms for position 1'
-         error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj,bergs%Lx,bergs%grid_is_latlon)
+         error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
          call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, debug_flag=.true.) !axn, ayn - Added by Alon
          write(stderrunit,*) 'Acceleration terms for position 2'
-         error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj,bergs%Lx,bergs%grid_is_latlon)
+         error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
          call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
           call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 3')
           write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos3 i,j,lon,lat,xi,yj=',i,j,lon3,lat3,xi,yj
           write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos3 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
-          bounced=is_point_in_cell(bergs%grd, lon2, lat2, i, j, bergs%Lx,bergs%grid_is_latlon,explain=.true.)
+          bounced=is_point_in_cell(bergs%grd, lon2, lat2, i, j,explain=.true.)
           call error_mesg('diamonds, evolve_iceberg','berg is out of posn at 3!',FATAL)
         endif
-        call  convert_from_meters_to_grid(lat3,bergs%grid_is_latlon ,dxdl3,dydl)
+        call  convert_from_meters_to_grid(lat3,bergs%grd%grid_is_latlon ,dxdl3,dydl)
         !dxdl3=r180_pi/(Rearth*cos(lat3*pi_180))
         u3=uvel3*dxdl3; v3=vvel3*dydl
         call accel(bergs, berg, i, j, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn3, ayn3, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
@@ -3134,11 +3138,11 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
           uvel4=uvel1+dt*ax3; vvel4=vvel1+dt*ay3
         endif
         i=i1;j=j1;xi=berg%xi;yj=berg%yj
-        call adjust_index_and_ground(grd, lon4, lat4, uvel4, vvel4, i, j, xi, yj, bounced, error_flag,bergs%Lx,bergs%grid_is_latlon)
+        call adjust_index_and_ground(grd, lon4, lat4, uvel4, vvel4, i, j, xi, yj, bounced, error_flag)
         i4=i; j4=j
         ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon4,lat4,x4,y4)
         if (.not.error_flag) then
-          if (debug .and. .not. is_point_in_cell(bergs%grd, lon4, lat4, i, j,bergs%Lx,bergs%grid_is_latlon)) error_flag=.true.
+          if (debug .and. .not. is_point_in_cell(bergs%grd, lon4, lat4, i, j)) error_flag=.true.
         endif
         if (error_flag) then
          call print_fld(grd, grd%msk, 'msk')
@@ -3160,21 +3164,21 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
          write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3,u4 (deg)=',dt*u1,dt*u2,dt*u3,dt*u4
          write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v4 (deg)=',dt*v1,dt*v2,dt*v3,dt*v4
          write(stderrunit,*) 'Acceleration terms for position 1'
-         error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj,bergs%Lx,bergs%grid_is_latlon)
+         error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
          call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
          write(stderrunit,*) 'Acceleration terms for position 2'
-         error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj,bergs%Lx,bergs%grid_is_latlon)
+         error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
          call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
          write(stderrunit,*) 'Acceleration terms for position 3'
-         error_flag=pos_within_cell(grd, lon3, lat3, i3, j3, xi, yj,bergs%Lx,bergs%grid_is_latlon)
+         error_flag=pos_within_cell(grd, lon3, lat3, i3, j3, xi, yj)
          call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn3, ayn3, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
           call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 4')
           write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos4 i,j,lon,lat,xi,yj=',i,j,lon4,lat4,xi,yj
           write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos4 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
-          bounced=is_point_in_cell(bergs%grd, lon2, lat2, i, j,bergs%Lx,bergs%grid_is_latlon, explain=.true.)
+          bounced=is_point_in_cell(bergs%grd, lon2, lat2, i, j, explain=.true.)
           call error_mesg('diamonds, evolve_iceberg','berg is out of posn at 4!',FATAL)
         endif
-        call  convert_from_meters_to_grid(lat4,bergs%grid_is_latlon ,dxdl4,dydl)
+        call  convert_from_meters_to_grid(lat4,bergs%grd%grid_is_latlon ,dxdl4,dydl)
         !dxdl4=r180_pi/(Rearth*cos(lat4*pi_180))
         u4=uvel4*dxdl4; v4=vvel4*dydl
         call accel(bergs, berg, i, j, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axn4, ayn4, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
@@ -3208,12 +3212,12 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
   
   
         i=i1;j=j1;xi=berg%xi;yj=berg%yj
-        call adjust_index_and_ground(grd, lonn, latn, uveln, vveln, i, j, xi, yj, bounced, error_flag,bergs%Lx,bergs%grid_is_latlon)
+        call adjust_index_and_ground(grd, lonn, latn, uveln, vveln, i, j, xi, yj, bounced, error_flag)
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
           call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, bergs%hexagonal_icebergs)
   
         if (.not.error_flag) then
-          if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j,bergs%Lx,bergs%grid_is_latlon)) error_flag=.true.
+          if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j)) error_flag=.true.
         endif
         if (error_flag) then
          call print_fld(grd, grd%msk, 'msk')
@@ -3242,21 +3246,21 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
               & dt*v1,dt*v2,dt*v3,dt*v4,dt_6*( (v1+v4)+2.*(v2+v3) )
          write(stderrunit,*) 'diamonds, evolve_iceberg: on_tangential_plane=',on_tangential_plane
          write(stderrunit,*) 'Acceleration terms for position 1'
-         error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj,bergs%Lx,bergs%grid_is_latlon)
+         error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
          call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
          write(stderrunit,*) 'Acceleration terms for position 2'
-         error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj,bergs%Lx,bergs%grid_is_latlon)
+         error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
          call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
          write(stderrunit,*) 'Acceleration terms for position 3'
-         error_flag=pos_within_cell(grd, lon3, lat3, i3, j3, xi, yj,bergs%Lx,bergs%grid_is_latlon)
+         error_flag=pos_within_cell(grd, lon3, lat3, i3, j3, xi, yj)
          call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
          write(stderrunit,*) 'Acceleration terms for position 4'
-         error_flag=pos_within_cell(grd, lon4, lat4, i4, j4, xi, yj,bergs%Lx,bergs%grid_is_latlon)
+         error_flag=pos_within_cell(grd, lon4, lat4, i4, j4, xi, yj)
          call accel(bergs, berg, i4, j4, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
           write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'posn i,j,lon,lat,xi,yj=',i,j,lonn,latn,xi,yj
           write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'posn box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
           call print_berg(stderrunit, berg, 'evolve_iceberg, out of cell at end!')
-          bounced=is_point_in_cell(bergs%grd, lonn, latn, i, j,bergs%Lx,bergs%grid_is_latlon, explain=.true.)
+          bounced=is_point_in_cell(bergs%grd, lonn, latn, i, j, explain=.true.)
           if (debug) call error_mesg('diamonds, evolve_iceberg','berg is out of posn at end!',FATAL)
           write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lon',(i,i=grd%isd,grd%ied)
           do j=grd%jed,grd%jsd,-1
@@ -3301,13 +3305,13 @@ subroutine update_verlet_position(bergs,berg)
 
 
       on_tangential_plane=.false.
-      if ((berg%lat>89.) .and. (bergs%grid_is_latlon)) on_tangential_plane=.true.
+      if ((berg%lat>89.) .and. (grd%grid_is_latlon)) on_tangential_plane=.true.
 
         lon1=berg%lon; lat1=berg%lat
         if (on_tangential_plane) call rotpos_to_tang(lon1,lat1,x1,y1,berg%iceberg_num)
         !dxdl1=r180_pi/(Rearth*cos(lat1*pi_180))
         !dydl=r180_pi/Rearth
-        call  convert_from_meters_to_grid(lat1,bergs%grid_is_latlon ,dxdl1,dydl)
+        call  convert_from_meters_to_grid(lat1,grd%grid_is_latlon ,dxdl1,dydl)
         uvel1=berg%uvel; vvel1=berg%vvel
 
         ! Loading past acceleartions - Alon
@@ -3331,7 +3335,7 @@ subroutine update_verlet_position(bergs,berg)
           lonn=lon1+(dt*u2) ; latn=lat1+(dt*v2)  !Alon
         endif
         !dxdln=r180_pi/(Rearth*cos(latn*pi_180))
-        call  convert_from_meters_to_grid(latn,bergs%grid_is_latlon ,dxdln,dydl)
+        call  convert_from_meters_to_grid(latn,grd%grid_is_latlon ,dxdln,dydl)
   
         ! Turn the velocities into u_star, v_star.(uvel3 is v_star) - Alon (not sure how this works with tangent plane)
         uvel3=uvel1+(dt_2*axn)                  !Alon
@@ -3340,7 +3344,7 @@ subroutine update_verlet_position(bergs,berg)
         ! Adjusting mass...
         !MP3
         i=berg%ine;  j=berg%jne;  xi = berg%xi;  yj = berg%yj
-        call adjust_index_and_ground(grd, lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag,bergs%Lx,bergs%grid_is_latlon)  !Alon:"unclear which velocity to use here?"
+        call adjust_index_and_ground(grd, lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
 
         !if (bounced) then
         !  print *, 'you have been bounce: big time!',mpp_pe(),berg%iceberg_num,lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag 
@@ -3401,11 +3405,10 @@ end subroutine rotvec_from_tang
 
 ! ##############################################################################
 
-subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, bounced, error, Lx,grid_is_latlon)
+subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, bounced, error)
 ! Arguments
 type(icebergs_gridded), pointer :: grd
-real, intent(inout) :: lon, lat, uvel, vvel, xi, yj, Lx
-logical, intent(in) :: grid_is_latlon
+real, intent(inout) :: lon, lat, uvel, vvel, xi, yj
 integer, intent(inout) :: i,j
 logical, intent(out) :: bounced, error
 ! Local variables
@@ -3422,12 +3425,12 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
   error=.false.
   lon0=lon; lat0=lat ! original position
   i0=i; j0=j ! original i,j
-  lret=pos_within_cell(grd, lon, lat, i, j, xi, yj,Lx,grid_is_latlon)
+  lret=pos_within_cell(grd, lon, lat, i, j, xi, yj)
 !  print *, 'Alon:', lon, lat, i, j, xi, yj, lret
   xi0=xi; yj0=yj ! original xi,yj
   if (debug) then
     !Sanity check lret, xi and yj
-    lret=is_point_in_cell(grd, lon, lat, i, j, Lx, grid_is_latlon)
+    lret=is_point_in_cell(grd, lon, lat, i, j)
     if (xi<0. .or. xi>1. .or. yj<0. .or. yj>1.) then
       if (lret) then
         write(stderrunit,*) 'diamonds, adjust: WARNING!!! lret=T but |xi,yj|>1',mpp_pe()
@@ -3437,9 +3440,9 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
         write(stderrunit,*) 'diamonds, adjust: yi=',yj,' lat=',lat
         write(stderrunit,*) 'diamonds, adjust: y3 y2=',grd%lat(i-1,j),grd%lat(i,j)
         write(stderrunit,*) 'diamonds, adjust: y0 y1=',grd%lat(i-1,j-1),grd%lat(i,j-1)
-        lret=is_point_in_cell(grd, lon, lat, i, j, Lx,grid_is_latlon,explain=.true.)
+        lret=is_point_in_cell(grd, lon, lat, i, j,explain=.true.)
         write(stderrunit,*) 'diamonds, adjust: fn is_point_in_cell=',lret
-        lret=pos_within_cell(grd, lon, lat, i, j, xi, yj, Lx,grid_is_latlon,explain=.true.)
+        lret=pos_within_cell(grd, lon, lat, i, j, xi, yj,explain=.true.)
         write(stderrunit,*) 'diamonds, adjust: fn pos_within_cell=',lret
         write(0,*) 'This should never happen!'
         error=.true.; return
@@ -3453,15 +3456,15 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
         write(stderrunit,*) 'diamonds, adjust: yi=',yj,' lat=',lat
         write(stderrunit,*) 'diamonds, adjust: y3 y2=',grd%lat(i-1,j),grd%lat(i,j)
         write(stderrunit,*) 'diamonds, adjust: y0 y1=',grd%lat(i-1,j-1),grd%lat(i,j-1)
-        lret=is_point_in_cell(grd, lon, lat, i, j, Lx, grid_is_latlon, explain=.true.)
+        lret=is_point_in_cell(grd, lon, lat, i, j,  explain=.true.)
         write(stderrunit,*) 'diamonds, adjust: fn is_point_in_cell=',lret
-        lret=pos_within_cell(grd, lon, lat, i, j, xi, yj, Lx, grid_is_latlon,explain=.true.)
+        lret=pos_within_cell(grd, lon, lat, i, j, xi, yj, explain=.true.)
         write(stderrunit,*) 'diamonds, adjust: fn pos_within_cell=',lret
         write(0,*) 'This should never happen!'
         error=.true.; return
       endif
     endif
-    lret=pos_within_cell(grd, lon, lat, i, j, xi, yj,Lx,grid_is_latlon)
+    lret=pos_within_cell(grd, lon, lat, i, j, xi, yj)
   endif ! debug
   if (lret) return ! Berg was already in cell
 
@@ -3491,7 +3494,7 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
         jnm=jnm+1
       endif
     endif
-    lret=pos_within_cell(grd, lon, lat, inm, jnm, xi, yj,Lx,grid_is_latlon) ! Update xi and yj
+    lret=pos_within_cell(grd, lon, lat, inm, jnm, xi, yj) ! Update xi and yj
   enddo
   if (abs(inm-i0)>1) then
     write(stderrunit,*) 'pe=',mpp_pe(),'diamonds, adjust: inm,i0,inm-i0=',inm,i0,inm-i0
@@ -3504,7 +3507,7 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
 
   ! Adjust i,j based on xi,yj while bouncing off of masked land cells
   icount=0
-  lret=pos_within_cell(grd, lon, lat, i0, j0, xi, yj,Lx,grid_is_latlon)
+  lret=pos_within_cell(grd, lon, lat, i0, j0, xi, yj)
   do while ( .not.lret.and. icount<4 )
     icount=icount+1
     if (xi.lt.0.) then
@@ -3556,7 +3559,7 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
     if (debug) then
       if (grd%msk(i,j)==0.) stop 'diamonds, adjust: Berg is in land! This should not happen...'
     endif
-    lret=pos_within_cell(grd, lon, lat, i, j, xi, yj,Lx,grid_is_latlon) ! Update xi and yj
+    lret=pos_within_cell(grd, lon, lat, i, j, xi, yj) ! Update xi and yj
   enddo
  !if (debug) then
  !  if (abs(i-i0)>2) then
@@ -3579,7 +3582,7 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
       write(stderrunit,*) 'diamonds, adjust: i,j=',i,j
       write(stderrunit,*) 'diamonds, adjust: inm,jnm=',inm,jnm
       write(stderrunit,*) 'diamonds, adjust: icount=',icount
-      lret=pos_within_cell(grd, lon, lat, i, j, xi, yj, Lx,grid_is_latlon,explain=.true.)
+      lret=pos_within_cell(grd, lon, lat, i, j, xi, yj,explain=.true.)
       write(stderrunit,*) 'diamonds, adjust: lret=',lret
     endif
     if (abs(i-i0)+abs(j-j0)==0) then
@@ -3604,7 +3607,7 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
   if (yj<0.) yj=posn_eps
   lon=bilin(grd, grd%lon, i, j, xi, yj)
   lat=bilin(grd, grd%lat, i, j, xi, yj)
-  lret=pos_within_cell(grd, lon, lat, i, j, xi, yj,Lx,grid_is_latlon) ! Update xi and yj
+  lret=pos_within_cell(grd, lon, lat, i, j, xi, yj) ! Update xi and yj
 
   if (.not. lret) then
     write(stderrunit,*) 'diamonds, adjust: Should not get here! Berg is not in cell after adjustment'
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index b3d7caa..d886856 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -81,7 +81,9 @@ module ice_bergs_framework
   integer :: isc, iec, jsc, jec ! Indices of computational domain
   integer :: isd, ied, jsd, jed ! Indices of data domain
   integer :: isg, ieg, jsg, jeg ! Indices of global domain
-  integer :: my_pe, pe_N, pe_S, pe_E, pe_W ! MPI PE identifiers
+  integer :: my_pe, pe_N, pe_S, pe_E, pe_W ! MPI PE idenLx ! Length of domain, for periodic boundary condition (Ly to be adde later if needed)
+  logical :: grid_is_latlon !Flag to say whether the coordinate is in lat lon degrees, or meters
+  real :: Lx !Length of the domain in x direction
   real, dimension(:,:), pointer :: lon=>null() ! Longitude of cell corners
   real, dimension(:,:), pointer :: lat=>null() ! Latitude of cell corners
   real, dimension(:,:), pointer :: lonc=>null() ! Longitude of cell centers
@@ -202,7 +204,8 @@ module ice_bergs_framework
   real :: LoW_ratio ! Initial ratio L/W for newly calved icebergs
   real :: bergy_bit_erosion_fraction ! Fraction of erosion melt flux to divert to bergy bits
   real :: sicn_shift ! Shift of sea-ice concentration in erosion flux modulation (0<sicn_shift<1)
-  real :: Omega_icebergs=omega ! Option to override the rotation rate.
+  real :: lat_ref=0. ! Reference latitude for f-plane (when this option is on)
+  real :: initial_orientation=0. ! Iceberg orientaion relative to this angle (in degrees). Used for hexagonal mass spreading.
   real, dimension(:), pointer :: initial_mass, distribution, mass_scaling
   real, dimension(:), pointer :: initial_thickness, initial_width, initial_length
   logical :: restarted=.false. ! Indicate whether we read state from a restart or not
@@ -211,6 +214,8 @@ module ice_bergs_framework
   logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
   logical :: time_average_weight=.false. ! Time average the weight on the ocean
   logical :: Runge_not_Verlet=.True.  !True=Runge Kuttai, False=Verlet.   
+  logical :: use_f_plane=.False.  !Flag to use a f-plane for the rotation
+  logical :: rotate_icebergs_for_mass_spreading=.True.  !Flag allows icebergs to rotate for spreading their mass (in hexagonal spreading mode)
   logical :: set_melt_rates_to_zero=.False.  !Sets all melt rates to zero, for testing purposes (thermodynamics routine is still run)
   logical :: hexagonal_icebergs=.False. !True treats icebergs as rectangles, False as hexagonal elements (for the purpose of mass spreading)
   logical :: allow_bergs_to_roll=.True. !Allows icebergs to roll over when rolling conditions are met
@@ -316,7 +321,9 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: LoW_ratio=1.5 ! Initial ratio L/W for newly calved icebergs
 real :: bergy_bit_erosion_fraction=0. ! Fraction of erosion melt flux to divert to bergy bits
 real :: sicn_shift=0. ! Shift of sea-ice concentration in erosion flux modulation (0<sicn_shift<1)
-real :: Omega_icebergs=omega ! Option to override the rotation rate.
+real :: lat_ref=0. ! Reference latitude for f-plane (when this option is on)
+real :: Lx=360. ! Length of domain in x direction, used for periodicity (use a huge number for non-periodic)
+real :: initial_orientation=0. ! Iceberg orientaion relative to this angle (in degrees). Used for hexagonal mass spreading.
 logical :: use_operator_splitting=.true. ! Use first order operator splitting for thermodynamics
 logical :: add_weight_to_ocean=.true. ! Add weight of icebergs + bits to ocean
 logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
@@ -324,6 +331,9 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: speed_limit=0. ! CFL speed limit for a berg
 real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
 logical :: Runge_not_Verlet=.True.  !True=Runge Kutta, False=Verlet.  - Added by Alon 
+logical :: use_f_plane=.False.  !Flag to use a f-plane for the rotation
+logical :: grid_is_latlon=.True.  !True means that the grid is specified in lat lon, and uses to radius of the earth to convert to distance
+logical :: rotate_icebergs_for_mass_spreading=.True.  !Flag allows icebergs to rotate for spreading their mass (in hexagonal spreading mode)
 logical :: set_melt_rates_to_zero=.False.  !Sets all melt rates to zero, for testing purposes (thermodynamics routine is still run)
 logical :: allow_bergs_to_roll=.True. !Allows icebergs to roll over when rolling conditions are met
 logical :: hexagonal_icebergs=.False. !True treats icebergs as rectangles, False as hexagonal elements (for the purpose of mass spreading)
@@ -349,12 +359,12 @@ subroutine ice_bergs_framework_init(bergs, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, halo_debugging, hexagonal_icebergs, &
          time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, interactive_icebergs_on, critical_interaction_damping_on, &
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution, force_all_pes_traj, &
-         allow_bergs_to_roll,set_melt_rates_to_zero,Omega_icebergs
+         allow_bergs_to_roll,set_melt_rates_to_zero,lat_ref,initial_orientation,rotate_icebergs_for_mass_spreading,grid_is_latlon,Lx,use_f_plane
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
 type(icebergs_gridded), pointer :: grd
-real :: minl
+real :: minl, big_number
 logical :: lerr
 integer :: stdlogunit, stderrunit
 real :: Total_mass  !Added by Alon 
@@ -438,11 +448,12 @@ subroutine ice_bergs_framework_init(bergs, &
     bergs%list(i,j)%first => null()
   enddo ; enddo
 
+  big_number=1.0E30
  !write(stderrunit,*) 'diamonds: allocating grid'
-  allocate( grd%lon(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%lon(:,:)=999.
-  allocate( grd%lat(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%lat(:,:)=999.
-  allocate( grd%lonc(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%lon(:,:)=999.
-  allocate( grd%latc(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%lat(:,:)=999.
+  allocate( grd%lon(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%lon(:,:)=big_number
+  allocate( grd%lat(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%lat(:,:)=big_number
+  allocate( grd%lonc(grd%isd:grd%ied, grd%jsd:grd%jed) );grd%lon(:,:)=big_number
+  allocate( grd%latc(grd%isd:grd%ied, grd%jsd:grd%jed) );grd%lat(:,:)=big_number
   allocate( grd%dx(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%dx(:,:)=0.
   allocate( grd%dy(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%dy(:,:)=0.
   allocate( grd%area(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%area(:,:)=0.
@@ -516,59 +527,59 @@ subroutine ice_bergs_framework_init(bergs, &
 
   ! Sanitize lon and lat in the southern halo
   do j=grd%jsc-1,grd%jsd,-1; do i=grd%isd,grd%ied
-      if (grd%lon(i,j).gt.900.) grd%lon(i,j)=grd%lon(i,j+1)
-      if (grd%lat(i,j).gt.900.) grd%lat(i,j)=2.*grd%lat(i,j+1)-grd%lat(i,j+2)
+      if (grd%lon(i,j).ge.big_number) grd%lon(i,j)=grd%lon(i,j+1)
+      if (grd%lat(i,j).ge.big_number) grd%lat(i,j)=2.*grd%lat(i,j+1)-grd%lat(i,j+2)
   enddo; enddo
 
   ! fix halos on edge of the domain
   !1) South
   do j=grd%jsc-1,grd%jsd,-1; do i=grd%isd,grd%ied
-      if (grd%lon(i,j).gt.900.) grd%lon(i,j)=2.*grd%lon(i,j+1)-grd%lon(i,j+2)
-      if (grd%lat(i,j).gt.900.) grd%lat(i,j)=2.*grd%lat(i,j+1)-grd%lat(i,j+2)
+      if (grd%lon(i,j).ge.big_number) grd%lon(i,j)=2.*grd%lon(i,j+1)-grd%lon(i,j+2)
+      if (grd%lat(i,j).ge.big_number) grd%lat(i,j)=2.*grd%lat(i,j+1)-grd%lat(i,j+2)
   enddo; enddo
   !2) North
   do j=grd%jec+1,grd%jed; do i=grd%isd,grd%ied
-      if (grd%lon(i,j).gt.900.) grd%lon(i,j)=2.*grd%lon(i,j-1)-grd%lon(i,j-2)
-      if (grd%lat(i,j).gt.900.) grd%lat(i,j)=2.*grd%lat(i,j-1)-grd%lat(i,j-2)
+      if (grd%lon(i,j).ge.big_number) grd%lon(i,j)=2.*grd%lon(i,j-1)-grd%lon(i,j-2)
+      if (grd%lat(i,j).ge.big_number) grd%lat(i,j)=2.*grd%lat(i,j-1)-grd%lat(i,j-2)
   enddo; enddo
   !3) West
   do i=grd%isc-1,grd%isd,-1; do j=grd%jsd,grd%jed
-      if (grd%lon(i,j).gt.900.) grd%lon(i,j)=2.*grd%lon(i+1,j)-grd%lon(i+2,j)
-      if (grd%lat(i,j).gt.900.) grd%lat(i,j)=2.*grd%lat(i+1,j)-grd%lat(i+2,j)
+      if (grd%lon(i,j).ge.big_number) grd%lon(i,j)=2.*grd%lon(i+1,j)-grd%lon(i+2,j)
+      if (grd%lat(i,j).ge.big_number) grd%lat(i,j)=2.*grd%lat(i+1,j)-grd%lat(i+2,j)
   enddo; enddo
   !4) East
   do i=grd%iec+1,grd%ied; do j=grd%jsd,grd%jed
-      if (grd%lon(i,j).gt.900.) grd%lon(i,j)=2.*grd%lon(i-1,j)-grd%lon(i-2,j)
-      if (grd%lat(i,j).gt.900.) grd%lat(i,j)=2.*grd%lat(i-1,j)-grd%lat(i-2,j)
+      if (grd%lon(i,j).ge.big_number) grd%lon(i,j)=2.*grd%lon(i-1,j)-grd%lon(i-2,j)
+      if (grd%lat(i,j).ge.big_number) grd%lat(i,j)=2.*grd%lat(i-1,j)-grd%lat(i-2,j)
   enddo; enddo
 
   if (.not. present(maskmap)) then ! Using a maskmap causes tickles this sanity check
     do j=grd%jsd,grd%jed; do i=grd%isd,grd%ied
-      if (grd%lon(i,j).gt.900.) write(stderrunit,*) 'bad lon: ',mpp_pe(),i-grd%isc+1,j-grd%jsc+1,grd%lon(i,j)
-      if (grd%lat(i,j).gt.900.) write(stderrunit,*) 'bad lat: ',mpp_pe(),i-grd%isc+1,j-grd%jsc+1,grd%lat(i,j)
+      if (grd%lon(i,j).ge.big_number) write(stderrunit,*) 'bad lon: ',mpp_pe(),i-grd%isc+1,j-grd%jsc+1,grd%lon(i,j)
+      if (grd%lat(i,j).ge.big_number) write(stderrunit,*) 'bad lat: ',mpp_pe(),i-grd%isc+1,j-grd%jsc+1,grd%lat(i,j)
     enddo; enddo
   endif
 
  !The fix to reproduce across PE layout change, from AJA
   j=grd%jsc; do i=grd%isc+1,grd%ied
-    minl=grd%lon(i-1,j)-180.
-    if (abs(grd%lon(i,j)-(modulo(grd%lon(i,j)-minl,360.)+minl))>180.) &
-       grd%lon(i,j)=modulo(grd%lon(i,j)-minl,360.)+minl
+  minl=grd%lon(i-1,j)-(Lx/2.)
+    if (abs(grd%lon(i,j)-(modulo(grd%lon(i,j)-minl,Lx)+minl))>(Lx/2.)) &
+    grd%lon(i,j)=modulo(grd%lon(i,j)-minl,Lx)+minl
   enddo
   j=grd%jsc; do i=grd%isc-1,grd%isd,-1
-    minl=grd%lon(i+1,j)-180.
-    if (abs(grd%lon(i,j)-(modulo(grd%lon(i,j)-minl,360.)+minl))>180.) &
-       grd%lon(i,j)=modulo(grd%lon(i,j)-minl,360.)+minl
+    minl=grd%lon(i+1,j)-(Lx/2.)
+    if (abs(grd%lon(i,j)-(modulo(grd%lon(i,j)-minl,Lx)+minl))>(Lx/2.)) &
+    grd%lon(i,j)=modulo(grd%lon(i,j)-minl,Lx)+minl
   enddo
   do j=grd%jsc+1,grd%jed; do i=grd%isd,grd%ied
-      minl=grd%lon(i,j-1)-180.
-      if (abs(grd%lon(i,j)-(modulo(grd%lon(i,j)-minl,360.)+minl))>180.) &
-         grd%lon(i,j)=modulo(grd%lon(i,j)-minl,360.)+minl
+      minl=grd%lon(i,j-1)-(Lx/2.)
+      if (abs(grd%lon(i,j)-(modulo(grd%lon(i,j)-minl,Lx)+minl))>(Lx/2.)) &
+      grd%lon(i,j)=modulo(grd%lon(i,j)-minl,Lx)+minl
   enddo; enddo
   do j=grd%jsc-1,grd%jsd,-1; do i=grd%isd,grd%ied
-      minl=grd%lon(i,j+1)-180.
-      if (abs(grd%lon(i,j)-(modulo(grd%lon(i,j)-minl,360.)+minl))>180.) &
-         grd%lon(i,j)=modulo(grd%lon(i,j)-minl,360.)+minl
+      minl=grd%lon(i,j+1)-(Lx/2.)
+      if (abs(grd%lon(i,j)-(modulo(grd%lon(i,j)-minl,Lx)+minl))>(Lx/2.)) &
+      grd%lon(i,j)=modulo(grd%lon(i,j)-minl,Lx)+minl
   enddo; enddo
 
 
@@ -640,6 +651,10 @@ subroutine ice_bergs_framework_init(bergs, &
 endif
 if (save_short_traj) buffer_width_traj=5 ! This is the length of the short buffer used for abrevated traj
 
+if ((.not. grid_is_latlon) .and. (Lx.eq.360.)) then
+  call error_mesg('diamonds, framework', 'Since the lat/lon grid is off, the x-direction is being set as non-periodic. Set Lx not equal to 360 override.', WARNING) 
+  Lx=1E31
+endif
 
  ! Parameters
   bergs%dt=dt
@@ -648,6 +663,8 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%save_short_traj=save_short_traj
   bergs%verbose_hrs=verbose_hrs
   bergs%grd%halo=halo
+  bergs%grd%Lx=Lx
+  bergs%grd%grid_is_latlon=grid_is_latlon  
   bergs%max_bonds=max_bonds
   bergs%grd%iceberg_halo=iceberg_halo
   bergs%rho_bergs=rho_bergs
@@ -663,7 +680,10 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%time_average_weight=time_average_weight
   bergs%speed_limit=speed_limit
   bergs%Runge_not_Verlet=Runge_not_Verlet   
-  bergs%Omega_icebergs=Omega_icebergs
+  bergs%use_f_plane=use_f_plane 
+  bergs%rotate_icebergs_for_mass_spreading=rotate_icebergs_for_mass_spreading 
+  bergs%lat_ref=lat_ref
+  bergs%initial_orientation=initial_orientation
   bergs%set_melt_rates_to_zero=set_melt_rates_to_zero 
   bergs%allow_bergs_to_roll=allow_bergs_to_roll 
   bergs%hexagonal_icebergs=hexagonal_icebergs 
@@ -2827,17 +2847,19 @@ logical function find_cell_by_search(grd, x, y, i, j)
 integer :: is,ie,js,je,di,dj,io,jo,icnt
 real :: d0,d1,d2,d3,d4,d5,d6,d7,d8,dmin
 logical :: explain=.false.
-
+real :: Lx
+ 
 911 continue
 
+  Lx=grd%Lx  
   find_cell_by_search=.false.
   is=grd%isc; ie=grd%iec; js=grd%jsc; je=grd%jec
 
   ! Start at nearest corner
-  d1=dcost(x,y,grd%lonc(is+1,js+1),grd%latc(is+1,js+1))
-  d2=dcost(x,y,grd%lonc(ie-1,js+1),grd%latc(ie-1,js+1))
-  d3=dcost(x,y,grd%lonc(ie-1,je-1),grd%latc(ie-1,je-1))
-  d4=dcost(x,y,grd%lonc(is+1,je-1),grd%latc(is+1,je-1))
+  d1=dcost(x,y,grd%lonc(is+1,js+1),grd%latc(is+1,js+1),Lx)
+  d2=dcost(x,y,grd%lonc(ie-1,js+1),grd%latc(ie-1,js+1),Lx)
+  d3=dcost(x,y,grd%lonc(ie-1,je-1),grd%latc(ie-1,je-1),Lx)
+  d4=dcost(x,y,grd%lonc(is+1,je-1),grd%latc(is+1,je-1),Lx)
   dmin=min(d1,d2,d3,d4)
   if (d1==dmin) then; i=is+1; j=js+1
   elseif (d2==dmin) then; i=ie-1; j=js+1
@@ -2861,15 +2883,15 @@ logical function find_cell_by_search(grd, x, y, i, j)
   do icnt=1, 1*(ie-is+je-js)
     io=i; jo=j
 
-    d0=dcost(x,y,grd%lonc(io,jo),grd%latc(io,jo))
-    d1=dcost(x,y,grd%lonc(io,jo+1),grd%latc(io,jo+1))
-    d2=dcost(x,y,grd%lonc(io-1,jo+1),grd%latc(io-1,jo+1))
-    d3=dcost(x,y,grd%lonc(io-1,jo),grd%latc(io-1,jo))
-    d4=dcost(x,y,grd%lonc(io-1,jo-1),grd%latc(io-1,jo-1))
-    d5=dcost(x,y,grd%lonc(io,jo-1),grd%latc(io,jo-1))
-    d6=dcost(x,y,grd%lonc(io+1,jo-1),grd%latc(io+1,jo-1))
-    d7=dcost(x,y,grd%lonc(io+1,jo),grd%latc(io+1,jo))
-    d8=dcost(x,y,grd%lonc(io+1,jo+1),grd%latc(io+1,jo+1))
+    d0=dcost(x,y,grd%lonc(io,jo),grd%latc(io,jo),Lx)
+    d1=dcost(x,y,grd%lonc(io,jo+1),grd%latc(io,jo+1),Lx)
+    d2=dcost(x,y,grd%lonc(io-1,jo+1),grd%latc(io-1,jo+1),Lx)
+    d3=dcost(x,y,grd%lonc(io-1,jo),grd%latc(io-1,jo),Lx)
+    d4=dcost(x,y,grd%lonc(io-1,jo-1),grd%latc(io-1,jo-1),Lx)
+    d5=dcost(x,y,grd%lonc(io,jo-1),grd%latc(io,jo-1),Lx)
+    d6=dcost(x,y,grd%lonc(io+1,jo-1),grd%latc(io+1,jo-1),Lx)
+    d7=dcost(x,y,grd%lonc(io+1,jo),grd%latc(io+1,jo),Lx)
+    d8=dcost(x,y,grd%lonc(io+1,jo+1),grd%latc(io+1,jo+1),Lx)
 
   ! dmin=min(d0,d1,d3,d5,d7)
     dmin=min(d0,d1,d2,d3,d4,d5,d6,d7,d8)
@@ -2950,13 +2972,13 @@ logical function find_cell_by_search(grd, x, y, i, j)
 
 ! # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
 
-  real function dcost(x1, y1, x2, y2)
+  real function dcost(x1, y1, x2, y2,Lx)
   ! Arguments
-  real, intent(in) :: x1, x2, y1, y2
+  real, intent(in) :: x1, x2, y1, y2,Lx
   ! Local variables
   real :: x1m
 
-    x1m=modulo(x1-(x2-180.),360.)+(x2-180.)
+    x1m=modulo(x1-(x2-(Lx/2.)),Lx)+(x2-(Lx/2.))
   ! dcost=(x2-x1)**2+(y2-y1)**2
     dcost=(x2-x1m)**2+(y2-y1)**2
   end function dcost
@@ -2972,6 +2994,9 @@ logical function find_better_min(grd, x, y, w, oi, oj)
   ! Local variables
   integer :: i,j,xs,xe,ys,ye
   real :: dmin, dcst
+  real :: Lx
+
+  Lx=grd%Lx
 
   xs=max(grd%isc, oi-w)
   xe=min(grd%iec, oi+w)
@@ -2979,9 +3004,9 @@ logical function find_better_min(grd, x, y, w, oi, oj)
   ye=min(grd%jec, oj+w)
 
   find_better_min=.false.
-  dmin=dcost(x,y,grd%lonc(oi,oj),grd%latc(oi,oj))
+  dmin=dcost(x,y,grd%lonc(oi,oj),grd%latc(oi,oj),Lx)
   do j=ys,ye; do i=xs,xe
-      dcst=dcost(x,y,grd%lonc(i,j),grd%latc(i,j))
+      dcst=dcost(x,y,grd%lonc(i,j),grd%latc(i,j),Lx)
       if (dcst<dmin) then
         find_better_min=.true.
         dmin=dcst
@@ -3116,10 +3141,14 @@ logical function is_point_in_cell(grd, x, y, i, j, explain)
 logical, intent(in), optional :: explain
 ! Local variables
 real :: xlo, xhi, ylo, yhi
+real :: Lx_2
 integer :: stderrunit
+real :: Lx
 
   ! Get the stderr unit number
   stderrunit=stderr()
+  Lx=grd%Lx
+  Lx_2=Lx/2.
 
   ! Safety check index bounds
   if (i-1.lt.grd%isd.or.i.gt.grd%ied.or.j-1.lt.grd%jsd.or.j.gt.grd%jed) then
@@ -3132,14 +3161,14 @@ logical function is_point_in_cell(grd, x, y, i, j, explain)
   is_point_in_cell=.false.
 
   ! Test crude bounds
-  xlo=min( modulo(grd%lon(i-1,j-1)-(x-180.),360.)+(x-180.), &
-           modulo(grd%lon(i  ,j-1)-(x-180.),360.)+(x-180.), &
-           modulo(grd%lon(i-1,j  )-(x-180.),360.)+(x-180.), &
-           modulo(grd%lon(i  ,j  )-(x-180.),360.)+(x-180.) )
-  xhi=max( modulo(grd%lon(i-1,j-1)-(x-180.),360.)+(x-180.), &
-           modulo(grd%lon(i  ,j-1)-(x-180.),360.)+(x-180.), &
-           modulo(grd%lon(i-1,j  )-(x-180.),360.)+(x-180.), &
-           modulo(grd%lon(i  ,j  )-(x-180.),360.)+(x-180.) )
+  xlo=min( modulo(grd%lon(i-1,j-1)-(x-Lx_2),Lx)+(x-Lx_2), &
+           modulo(grd%lon(i  ,j-1)-(x-Lx_2),Lx)+(x-Lx_2), &
+           modulo(grd%lon(i-1,j  )-(x-Lx_2),Lx)+(x-Lx_2), &
+           modulo(grd%lon(i  ,j  )-(x-Lx_2),Lx)+(x-Lx_2) )
+  xhi=max( modulo(grd%lon(i-1,j-1)-(x-Lx_2),Lx)+(x-Lx_2), &
+           modulo(grd%lon(i  ,j-1)-(x-Lx_2),Lx)+(x-Lx_2), &
+           modulo(grd%lon(i-1,j  )-(x-Lx_2),Lx)+(x-Lx_2), &
+           modulo(grd%lon(i  ,j  )-(x-Lx_2),Lx)+(x-Lx_2) )
 
   if (x.lt.xlo .or. x.gt.xhi) return
   ylo=min( grd%lat(i-1,j-1), grd%lat(i,j-1), grd%lat(i-1,j), grd%lat(i,j) )
@@ -3148,65 +3177,67 @@ logical function is_point_in_cell(grd, x, y, i, j, explain)
 
   if (y.lt.ylo .or. y.gt.yhi) return
   
-  if (grd%lat(i,j).gt.89.999) then
+  if ((grd%lat(i,j).gt.89.999).and. (grd%grid_is_latlon))   then
     is_point_in_cell=sum_sign_dot_prod5(grd%lon(i-1,j-1),grd%lat(i-1,j-1), &
                                         grd%lon(i  ,j-1),grd%lat(i  ,j-1), &
                                         grd%lon(i  ,j-1),grd%lat(i  ,j  ), &
                                         grd%lon(i-1,j  ),grd%lat(i  ,j  ), &
                                         grd%lon(i-1,j  ),grd%lat(i-1,j  ), &
-                                        x, y, explain=explain) 
-  elseif (grd%lat(i-1,j).gt.89.999) then
+                                        x, y, Lx,explain=explain) 
+  elseif ((grd%lat(i-1,j).gt.89.999) .and. (grd%grid_is_latlon))  then
     is_point_in_cell=sum_sign_dot_prod5(grd%lon(i-1,j-1),grd%lat(i-1,j-1), &
                                         grd%lon(i  ,j-1),grd%lat(i  ,j-1), &
                                         grd%lon(i  ,j  ),grd%lat(i  ,j  ), &
                                         grd%lon(i  ,j  ),grd%lat(i-1,j  ), &
                                         grd%lon(i-1,j-1),grd%lat(i-1,j  ), &
-                                        x, y, explain=explain) 
-  elseif (grd%lat(i-1,j-1).gt.89.999) then
+                                        x, y,Lx, explain=explain) 
+  elseif ((grd%lat(i-1,j-1).gt.89.999) .and. (grd%grid_is_latlon))  then
     is_point_in_cell=sum_sign_dot_prod5(grd%lon(i-1,j  ),grd%lat(i-1,j-1), &
                                         grd%lon(i  ,j-1),grd%lat(i-1,j-1), &
                                         grd%lon(i  ,j-1),grd%lat(i  ,j-1), &
                                         grd%lon(i  ,j  ),grd%lat(i  ,j  ), &
                                         grd%lon(i-1,j  ),grd%lat(i-1,j  ), &
-                                        x, y, explain=explain) 
-  elseif (grd%lat(i,j-1).gt.89.999) then
+                                        x, y,Lx, explain=explain) 
+  elseif ((grd%lat(i,j-1).gt.89.999) .and. (grd%grid_is_latlon)) then
     is_point_in_cell=sum_sign_dot_prod5(grd%lon(i-1,j-1),grd%lat(i-1,j-1), &
                                         grd%lon(i-1,j-1),grd%lat(i  ,j-1), &
                                         grd%lon(i  ,j  ),grd%lat(i  ,j-1), &
                                         grd%lon(i  ,j  ),grd%lat(i  ,j  ), &
                                         grd%lon(i-1,j  ),grd%lat(i-1,j  ), &
-                                        x, y, explain=explain) 
+                                        x, y, Lx,explain=explain) 
   else
   is_point_in_cell=sum_sign_dot_prod4(grd%lon(i-1,j-1),grd%lat(i-1,j-1), &
                                       grd%lon(i  ,j-1),grd%lat(i  ,j-1), &
                                       grd%lon(i  ,j  ),grd%lat(i  ,j  ), &
                                       grd%lon(i-1,j  ),grd%lat(i-1,j  ), &
-                                      x, y, explain=explain) 
+                                      x, y,Lx, explain=explain) 
   endif
 
 end function is_point_in_cell
 
 ! ##############################################################################
 
-logical function sum_sign_dot_prod4(x0, y0, x1, y1, x2, y2, x3, y3, x, y, explain)
+logical function sum_sign_dot_prod4(x0, y0, x1, y1, x2, y2, x3, y3, x, y,Lx, explain)
 ! Arguments
-real, intent(in) :: x0, y0, x1, y1, x2, y2, x3, y3, x, y
+real, intent(in) :: x0, y0, x1, y1, x2, y2, x3, y3, x, y, Lx
 logical, intent(in), optional :: explain
 ! Local variables
 real :: p0,p1,p2,p3,xx
 real :: l0,l1,l2,l3
 real :: xx0,xx1,xx2,xx3
 integer :: stderrunit
+real :: Lx_2
 
   ! Get the stderr unit number
   stderrunit=stderr()
+  Lx_2=Lx/2.
 
   sum_sign_dot_prod4=.false.
-  xx=modulo(x-(x0-180.),360.)+(x0-180.) ! Reference x to within 180 of x0
-  xx0=modulo(x0-(x0-180.),360.)+(x0-180.) ! Reference x0 to within 180 of xx
-  xx1=modulo(x1-(x0-180.),360.)+(x0-180.) ! Reference x1 to within 180 of xx
-  xx2=modulo(x2-(x0-180.),360.)+(x0-180.) ! Reference x2 to within 180 of xx
-  xx3=modulo(x3-(x0-180.),360.)+(x0-180.) ! Reference x3 to within 180 of xx
+  xx=modulo(x-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x to within Lx_2of x0
+  xx0=modulo(x0-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x0 to within Lx_2of xx
+  xx1=modulo(x1-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x1 to within Lx_2of xx
+  xx2=modulo(x2-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x2 to within Lx_2of xx
+  xx3=modulo(x3-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x3 to within Lx_2of xx
 
   l0=(xx-xx0)*(y1-y0)-(y-y0)*(xx1-xx0)
   l1=(xx-xx1)*(y2-y1)-(y-y1)*(xx2-xx1)
@@ -3244,26 +3275,28 @@ end function sum_sign_dot_prod4
 
 ! ##############################################################################
 
-logical function sum_sign_dot_prod5(x0, y0, x1, y1, x2, y2, x3, y3, x4, y4, x, y, explain)
+logical function sum_sign_dot_prod5(x0, y0, x1, y1, x2, y2, x3, y3, x4, y4, x, y, Lx, explain)
 ! Arguments
-real, intent(in) :: x0, y0, x1, y1, x2, y2, x3, y3, x4, y4, x, y
+real, intent(in) :: x0, y0, x1, y1, x2, y2, x3, y3, x4, y4, x, y, Lx
 logical, intent(in), optional :: explain
 ! Local variables
 real :: p0,p1,p2,p3,p4,xx
 real :: l0,l1,l2,l3,l4
 real :: xx0,xx1,xx2,xx3,xx4
 integer :: stderrunit
+real :: Lx_2
 
   ! Get the stderr unit number
   stderrunit=stderr()
+  Lx_2=Lx/2.
 
   sum_sign_dot_prod5=.false.
-  xx=modulo(x-(x0-180.),360.)+(x0-180.) ! Reference x to within 180 of x0
-  xx0=modulo(x0-(x0-180.),360.)+(x0-180.) ! Reference x0 to within 180 of xx
-  xx1=modulo(x1-(x0-180.),360.)+(x0-180.) ! Reference x1 to within 180 of xx
-  xx2=modulo(x2-(x0-180.),360.)+(x0-180.) ! Reference x2 to within 180 of xx
-  xx3=modulo(x3-(x0-180.),360.)+(x0-180.) ! Reference x3 to within 180 of xx
-  xx4=modulo(x4-(x0-180.),360.)+(x0-180.) ! Reference x4 to within 180 of xx
+  xx=modulo(x-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x to within Lx_2of x0
+  xx0=modulo(x0-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x0 to within Lx_2of xx
+  xx1=modulo(x1-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x1 to within Lx_2of xx
+  xx2=modulo(x2-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x2 to within Lx_2of xx
+  xx3=modulo(x3-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x3 to within Lx_2of xx
+  xx4=modulo(x4-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x4 to within Lx_2of xx
 
   l0=(xx-xx0)*(y1-y0)-(y-y0)*(xx1-xx0)
   l1=(xx-xx1)*(y2-y1)-(y-y1)*(xx2-xx1)
@@ -3310,10 +3343,11 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
 ! Local variables
 real :: x1,y1,x2,y2,x3,y3,x4,y4,xx,yy,fac
 integer :: stderrunit
+real :: Lx
 
   ! Get the stderr unit number
   stderrunit=stderr()
-
+  Lx=grd%Lx
   pos_within_cell=.false.; xi=-999.; yj=-999.
   if (i-1<grd%isd) return
   if (j-1<grd%jsd) return
@@ -3339,8 +3373,8 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
     endif
   endif
 
-  if (max(y1,y2,y3,y4)<89.999) then
-    call calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x, y, xi, yj, explain=explain)
+  if ((max(y1,y2,y3,y4)<89.999).or. (.not. grd%grid_is_latlon) ) then
+    call calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x, y, xi, yj, Lx, explain=explain)
   else
     if (debug) write(stderrunit,*) 'diamonds, pos_within_cell: working in tangential plane!'
     xx=(90.-y)*cos(x*pi_180)
@@ -3361,7 +3395,7 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
       write(stderrunit,'(a,2f12.6)') 'pos_within_cell: y',yy
       endif
     endif
-    call calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, xx, yy, xi, yj, explain=explain)
+    call calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, xx, yy, xi, yj, Lx,explain=explain)
     if (is_point_in_cell(grd, x, y, i, j)) then
       if (abs(xi-0.5)>0.5.or.abs(yj-0.5)>0.5) then
         ! Scale internal coordinates to be consistent with is_point_in_cell()
@@ -3380,7 +3414,7 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
   endif
 
   if (present(explain)) then
-	if(explain) write(stderrunit,'(a,2f12.6)') 'pos_within_cell: xi,yj=',xi,yj
+    if(explain) write(stderrunit,'(a,2f12.6)') 'pos_within_cell: xi,yj=',xi,yj
   endif
 
  !if (.not. is_point_in_cell(grd, x, y, i, j) ) then
@@ -3389,7 +3423,7 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
  !endif
 
   if (xi.ge.0. .and. xi.le.1. .and. yj.ge.0. .and. yj.le.1.) then
-    pos_within_cell=is_point_in_cell(grd, x, y, i, j, explain=explain)
+    pos_within_cell=is_point_in_cell(grd, x, y, i, j,explain=explain)
     if (.not. pos_within_cell .and. verbose) then
       if (debug) call error_mesg('diamonds, pos_within_cell', 'pos_within_cell is in cell BUT is_point_in_cell disagrees!', WARNING)
     endif
@@ -3398,18 +3432,20 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
 
   contains
 
-  subroutine calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x, y, xi, yj, explain)
+  subroutine calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x, y, xi, yj,Lx, explain)
   ! Arguments
-  real,  intent(in) :: x1, x2, x3, x4, y1, y2, y3, y4, x, y
+  real,  intent(in) :: x1, x2, x3, x4, y1, y2, y3, y4, x, y, Lx
   real, intent(out) :: xi, yj
   logical, intent(in), optional :: explain
   ! Local variables
   real :: alpha, beta, gamma, delta, epsilon, kappa, a, b, c, d, dx, dy, yy1, yy2
   logical :: expl=.false.
   integer :: stderrunit
+  real :: Lx_2
 
   ! Get the stderr unit number
   stderrunit=stderr()
+  Lx_2=Lx/2.
 
   expl=.false.
   if (present(explain)) then
@@ -3425,7 +3461,7 @@ subroutine calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x, y, xi, yj, explain)
   if (expl) write(stderrunit,'(a,1p6e12.4)') 'calc_xiyj: coeffs delta,epsilon,kappa',alpha,beta,gamma,delta,epsilon,kappa
 
   a=(kappa*beta-gamma*epsilon)
-  dx=modulo(x-(x1-180.),360.)+(x1-180.)-x1
+  dx=modulo(x-(x1-Lx_2),Lx)+(x1-Lx_2)-x1
   dy=y-y1
   b=(delta*beta-alpha*epsilon)-(kappa*dx-gamma*dy)
   c=(alpha*dy-delta*dx)
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index c6c686b..5157350 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -894,7 +894,7 @@ subroutine read_restart_bergs(bergs,Time)
          localberg%static_berg=static_berg(k)
          localberg%heat_density=heat_density(k)
          localberg%first_bond=>null()
-         if (really_debug) lres=is_point_in_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, explain=.true.)
+         if (really_debug) lres=is_point_in_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne,explain=.true.)
          lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
         !call add_new_berg_to_list(bergs%first, localberg, quick=.true.)
         if (bergs%grd%area(localberg%ine,localberg%jne) .ne. 0)  then

From 634913c1d025070223d47d6a412c67e6dca223de Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 6 Jul 2016 16:02:43 -0400
Subject: [PATCH 127/361] Finite domains have been tested a bit more, and
 appear to be working (there were a few bugs)

---
 icebergs.F90           | 15 +++++----------
 icebergs_framework.F90 | 13 ++++++++-----
 2 files changed, 13 insertions(+), 15 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 1db6a3f..52f855c 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1161,7 +1161,7 @@ real function find_orientation_using_iceberg_bonds(berg,initial_orientation,grid
           angle=pi/2.
         else
           angle=atan(r_dist_x/r_dist_y)
-          angle= ((pi/2)  - (initial_orientation*(pi/180)))  - angle
+          angle= ((pi/2)  - (initial_orientation*(pi/180.)))  - angle
           angle=modulo(angle-(2*pi) ,pi/6.)
         endif
         bond_count=bond_count+1.
@@ -1323,7 +1323,6 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
   fraction_used= ((yDxL*grd%msk(i-1,j-1)) + (yDxC*grd%msk(i  ,j-1))  +(yDxR*grd%msk(i+1,j-1)) +(yCxL*grd%msk(i-1,j  )) +  (yCxR*grd%msk(i+1,j  ))&
                  +(yUxL*grd%msk(i-1,j+1)) +(yUxC*grd%msk(i  ,j+1))   +(yUxR*grd%msk(i+1,j+1)) + (yCxC**grd%msk(i,j)))
 
-
   grd%mass_on_ocean(i,j,1)=grd%mass_on_ocean(i,j,1)+(yDxL*Mass/fraction_used)
   grd%mass_on_ocean(i,j,2)=grd%mass_on_ocean(i,j,2)+(yDxC*Mass/fraction_used)
   grd%mass_on_ocean(i,j,3)=grd%mass_on_ocean(i,j,3)+(yDxR*Mass/fraction_used)
@@ -1541,11 +1540,9 @@ subroutine divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1,Area_positive, A
         Area_positive= 0.;
         Area_negative= A_triangle;
       else
-        !print 'You should not get here1'
         call error_mesg('diamonds, iceberg_run', 'Logical error inside triangle dividing routine', FATAL)
       endif
     else
-      !print 'You should not get here2'
       call error_mesg('diamonds, iceberg_run', 'Another logical error inside triangle dividing routine', FATAL)
     endif
   endif
@@ -1598,7 +1595,6 @@ subroutine Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy,Area_triangle,
         call intercept_of_a_line(Bx,By,Cx,Cy,'x',px,py); !x_intercept
         call intercept_of_a_line(Bx,By,Cx,Cy,'y',qx,qy); !y_intercept
         if (.not.((point_in_interval(Bx,By,Cx,Cy,px,py)) .and. (point_in_interval(Bx,By,Cx,Cy,qx,qy)))) then
-          !print 'Houston, we have a problem'
           !You should not get here, but there might be some bugs in the code to do with points exactly falling on axes.
           if (mpp_pe().eq.12) then
             write(stderrunit,*) 'diamonds,corners', Ax,Ay,Bx,By,Cx,Cy
@@ -1661,7 +1657,6 @@ subroutine Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy,Area_triangle,
     !Area_Q3=Area_Left-Area_Q2;
     Area_Q3=Area_triangle-(Area_Q1+Area_Q2+Area_Q4);
   else
-    !print 'Help, I need somebody, help!'
     call error_mesg('diamonds, iceberg_run', 'Logical error inside triangle into four quadrants. Should not get here.', FATAL)
   endif
 
@@ -1957,6 +1952,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   grd%bergy_mass(:,:)=0.
   grd%spread_mass(:,:)=0.
   grd%mass(:,:)=0.
+
   if (bergs%add_weight_to_ocean) grd%mass_on_ocean(:,:,:)=0.
   grd%virtual_area(:,:)=0.
 
@@ -2748,6 +2744,7 @@ subroutine evolve_icebergs(bergs)
   do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
     berg=>bergs%list(grdi,grdj)%first
     do while (associated(berg)) ! loop over all bergs
+
       if (berg%static_berg .lt. 0.5) then  !Only allow non-static icebergs to evolve
  
         !Checking it everything is ok:
@@ -3287,7 +3284,7 @@ subroutine update_verlet_position(bergs,berg)
 real :: lon1, lat1, dxdl1, dydl
 real :: uvel1, vvel1, uvel2, vvel2
 real :: axn, ayn, bxn, byn
-real :: xdot2, ydot2, dxdln
+real :: xdot2, ydot2
 real :: u2, v2, x1, y1, xn, yn
 real :: dx, dt, dt_2
 integer :: i, j
@@ -3322,7 +3319,7 @@ subroutine update_verlet_position(bergs,berg)
         uvel2=uvel1+(dt_2*axn)+(dt_2*bxn)                    !Alon
         vvel2=vvel1+(dt_2*ayn)+(dt_2*byn)                    !Alon
 
-        dx=(dt*(uvel1+(dt_2*axn)+(dt_2*bxn)))
+        !dx=(dt*(uvel1+(dt_2*axn)+(dt_2*bxn)))
 
         if (on_tangential_plane) call rotvec_to_tang(lon1,uvel2,vvel2,xdot2,ydot2)
         u2=uvel2*dxdl1; v2=vvel2*dydl
@@ -3334,8 +3331,6 @@ subroutine update_verlet_position(bergs,berg)
         else
           lonn=lon1+(dt*u2) ; latn=lat1+(dt*v2)  !Alon
         endif
-        !dxdln=r180_pi/(Rearth*cos(latn*pi_180))
-        call  convert_from_meters_to_grid(latn,grd%grid_is_latlon ,dxdln,dydl)
   
         ! Turn the velocities into u_star, v_star.(uvel3 is v_star) - Alon (not sure how this works with tangent plane)
         uvel3=uvel1+(dt_2*axn)                  !Alon
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index d886856..3f4ec26 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -560,6 +560,14 @@ subroutine ice_bergs_framework_init(bergs, &
     enddo; enddo
   endif
 
+  if (Lx.gt.1E15 ) then
+          call error_mesg('diamonds, framework', 'Model does not enjoy the domain being larger than 1E15. Not sure why. Probably to do with floating point precision.', WARNING) 
+  endif
+  if ((.not. grid_is_latlon) .and. (Lx.eq.360.)) then
+    call error_mesg('diamonds, framework', 'Since the lat/lon grid is off, the x-direction is being set as non-periodic. Set Lx not equal to 360 override.', WARNING) 
+    Lx=1E14
+  endif
+
  !The fix to reproduce across PE layout change, from AJA
   j=grd%jsc; do i=grd%isc+1,grd%ied
   minl=grd%lon(i-1,j)-(Lx/2.)
@@ -651,11 +659,6 @@ subroutine ice_bergs_framework_init(bergs, &
 endif
 if (save_short_traj) buffer_width_traj=5 ! This is the length of the short buffer used for abrevated traj
 
-if ((.not. grid_is_latlon) .and. (Lx.eq.360.)) then
-  call error_mesg('diamonds, framework', 'Since the lat/lon grid is off, the x-direction is being set as non-periodic. Set Lx not equal to 360 override.', WARNING) 
-  Lx=1E31
-endif
-
  ! Parameters
   bergs%dt=dt
   bergs%traj_sample_hrs=traj_sample_hrs

From 8d45d45eb4629f5b485d69cea544fab1a244ab5f Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 6 Jul 2016 18:43:26 -0400
Subject: [PATCH 128/361] A bug has been fixed by setting all NaN's in
 ua,va,uo,vo,ui,ui,sst,hi and cn to zero. I believe that NaN's can enter these
 variables if the iceberg grid does not match the atmospheric grid (for
 example). We need to think further on how to properly handle undefined
 quanties. Setting them to zero stops the model from crashing.

---
 icebergs.F90           | 58 ++++++++++++++++++++++++++++++++++++------
 icebergs_framework.F90 |  6 +++--
 2 files changed, 54 insertions(+), 10 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 52f855c..86c3de5 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1798,6 +1798,7 @@ subroutine interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y,
 real :: hxm, hxp
 real, parameter :: ssh_coast=0.00
 integer :: stderrunit
+integer :: ii, jj
 
   ! Get the stderr unit number
   stderrunit = stderr()
@@ -1811,6 +1812,29 @@ subroutine interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y,
   vi=bilin(grd, grd%vi, i, j, xi, yj)
   ua=bilin(grd, grd%ua, i, j, xi, yj)
   va=bilin(grd, grd%va, i, j, xi, yj)
+
+  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+  if (ua.ne.ua) then
+    if (mpp_pe().eq.9) then
+      write(stderrunit,'(a3,32i7)') 'ua',(ii,ii=grd%isd,grd%ied)
+      do jj=grd%jed,grd%jsd,-1
+        write(stderrunit,'(i3,32f7.1)') jj,(grd%ua(ii,jj),ii=grd%isd,grd%ied)
+      enddo
+  !   write(stderrunit,'(a3,32i7)') 'Lat',(i,i=grd%isd,grd%ied)
+  !   do j=grd%jed,grd%jsd,-1
+  !     write(stderrunit,'(i3,32f7.1)') j,(grd%lat(i,j),i=grd%isd,grd%ied)
+  !   enddo
+  !   write(stderrunit,'(a3,32i7)') 'Msk',(i,i=grd%isd,grd%ied)
+  !   do j=grd%jed,grd%jsd,-1
+  !     write(stderrunit,'(i3,32f7.1)') j,(grd%msk(i,j),i=grd%isd,grd%ied)
+  !   enddo
+  ! endif
+      call error_mesg('diamonds, interp fields', 'ua is NaNs', FATAL)
+    endif
+  endif
+  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+
   ! These fields are cell centered (A-grid) and would
   ! best be interpolated using PLM. For now we use PCM!
   sst=grd%sst(i,j) ! A-grid
@@ -1865,6 +1889,14 @@ subroutine interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y,
   call rotate(ua, va, cos_rot, sin_rot)
   call rotate(ssh_x, ssh_y, cos_rot, sin_rot)
 
+  if (((((uo.ne.uo) .or. (vo.ne.vo)) .or. ((ui.ne.ui) .or. (vi.ne.vi))) .or. (((ua.ne.ua) .or. (va.ne.va)) .or. ((ssh_x.ne.ssh_x) .or.  (ssh_y.ne.ssh_y)))) .or. \
+  (((sst.ne. sst) .or. (cn.ne.cn)) .or. (hi.ne. hi))) then
+    write(stderrunit,*) 'diamonds, Error in interpolate: uo,vo,ui,vi',uo, vo, ui, vi
+    write(stderrunit,*) 'diamonds, Error in interpolate: ua,va,ssh_x,ssh_y', ua, va, ssh_x, ssh_y
+    write(stderrunit,*) 'diamonds, Error in interpolate: sst,cn,hi', sst, cn, hi, mpp_pe()
+    call error_mesg('diamonds, interp fields', 'field interpaolations has NaNs', FATAL)
+
+  endif 
   contains
 
   real function ddx_ssh(grd,i,j)
@@ -2081,7 +2113,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   call mpp_update_domains(grd%hi, grd%domain)
 
  !Make sure that gridded values agree with mask  (to get ride of NaN values)
-  do i=grd%isd,grd%ied ; do j=grd%jsc-1,grd%jed
+  do i=grd%isd,grd%ied ; do j=grd%jsd,grd%jed
   !Initializing all gridded values to zero
     if (grd%msk(i,j).lt. 0.5) then
       grd%ua(i,j) = 0.0 ;  grd%va(i,j) = 0.0
@@ -2090,6 +2122,15 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
       grd%sst(i,j) = 0.0;  grd%cn(i,j) = 0.0
       grd%hi(i,j) = 0.0
     endif
+    if (grd%ua(i,j) .ne. grd%ua(i,j)) grd%ua(i,j)=0.
+    if (grd%va(i,j) .ne. grd%va(i,j)) grd%va(i,j)=0.
+    if (grd%uo(i,j) .ne. grd%uo(i,j)) grd%uo(i,j)=0.
+    if (grd%vo(i,j) .ne. grd%vo(i,j)) grd%vo(i,j)=0.
+    if (grd%ui(i,j) .ne. grd%ui(i,j)) grd%ui(i,j)=0.
+    if (grd%vi(i,j) .ne. grd%vi(i,j)) grd%vi(i,j)=0.
+    if (grd%sst(i,j) .ne. grd%sst(i,j)) grd%sst(i,j)=0.
+    if (grd%cn(i,j) .ne. grd%cn(i,j)) grd%cn(i,j)=0.
+    if (grd%hi(i,j) .ne. grd%hi(i,j)) grd%hi(i,j)=0.
   enddo; enddo
 
   if (debug) call bergs_chksum(bergs, 'run bergs (top)')
@@ -3021,7 +3062,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
           uvel2=uvel1+dt_2*ax1; vvel2=vvel1+dt_2*ay1
         endif
         i=i1;j=j1;xi=berg%xi;yj=berg%yj
-        call adjust_index_and_ground(grd, lon2, lat2, uvel2, vvel2, i, j, xi, yj, bounced, error_flag)
+        call adjust_index_and_ground(grd, lon2, lat2, uvel2, vvel2, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)
         i2=i; j2=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
           call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling, berg%length*berg%width , bergs%hexagonal_icebergs)
@@ -3077,7 +3118,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
           uvel3=uvel1+dt_2*ax2; vvel3=vvel1+dt_2*ay2
         endif
         i=i1;j=j1;xi=berg%xi;yj=berg%yj
-        call adjust_index_and_ground(grd, lon3, lat3, uvel3, vvel3, i, j, xi, yj, bounced, error_flag)
+        call adjust_index_and_ground(grd, lon3, lat3, uvel3, vvel3, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)
         i3=i; j3=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
           call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, bergs%hexagonal_icebergs)
@@ -3135,7 +3176,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
           uvel4=uvel1+dt*ax3; vvel4=vvel1+dt*ay3
         endif
         i=i1;j=j1;xi=berg%xi;yj=berg%yj
-        call adjust_index_and_ground(grd, lon4, lat4, uvel4, vvel4, i, j, xi, yj, bounced, error_flag)
+        call adjust_index_and_ground(grd, lon4, lat4, uvel4, vvel4, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)
         i4=i; j4=j
         ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon4,lat4,x4,y4)
         if (.not.error_flag) then
@@ -3209,7 +3250,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
   
   
         i=i1;j=j1;xi=berg%xi;yj=berg%yj
-        call adjust_index_and_ground(grd, lonn, latn, uveln, vveln, i, j, xi, yj, bounced, error_flag)
+        call adjust_index_and_ground(grd, lonn, latn, uveln, vveln, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
           call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, bergs%hexagonal_icebergs)
   
@@ -3339,7 +3380,7 @@ subroutine update_verlet_position(bergs,berg)
         ! Adjusting mass...
         !MP3
         i=berg%ine;  j=berg%jne;  xi = berg%xi;  yj = berg%yj
-        call adjust_index_and_ground(grd, lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag)  !Alon:"unclear which velocity to use here?"
+        call adjust_index_and_ground(grd, lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)  !Alon:"unclear which velocity to use here?"
 
         !if (bounced) then
         !  print *, 'you have been bounce: big time!',mpp_pe(),berg%iceberg_num,lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag 
@@ -3400,11 +3441,12 @@ end subroutine rotvec_from_tang
 
 ! ##############################################################################
 
-subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, bounced, error)
+subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, bounced, error, iceberg_num)
 ! Arguments
 type(icebergs_gridded), pointer :: grd
 real, intent(inout) :: lon, lat, uvel, vvel, xi, yj
 integer, intent(inout) :: i,j
+integer, intent(in) :: iceberg_num
 logical, intent(out) :: bounced, error
 ! Local variables
 logical lret, lpos
@@ -3605,7 +3647,7 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
   lret=pos_within_cell(grd, lon, lat, i, j, xi, yj) ! Update xi and yj
 
   if (.not. lret) then
-    write(stderrunit,*) 'diamonds, adjust: Should not get here! Berg is not in cell after adjustment'
+    write(stderrunit,*) 'diamonds, adjust: Should not get here! Berg is not in cell after adjustment', iceberg_num, mpp_pe()
     if (debug) error=.true.
   endif
  end subroutine adjust_index_and_ground
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 3f4ec26..82b9aa4 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -560,11 +560,13 @@ subroutine ice_bergs_framework_init(bergs, &
     enddo; enddo
   endif
 
-  if (Lx.gt.1E15 ) then
+  if ((Lx.gt.1E15 ) .and. (mpp_pe().eq.mpp_root_pe())) then
           call error_mesg('diamonds, framework', 'Model does not enjoy the domain being larger than 1E15. Not sure why. Probably to do with floating point precision.', WARNING) 
   endif
   if ((.not. grid_is_latlon) .and. (Lx.eq.360.)) then
-    call error_mesg('diamonds, framework', 'Since the lat/lon grid is off, the x-direction is being set as non-periodic. Set Lx not equal to 360 override.', WARNING) 
+    if (mpp_pe().eq.mpp_root_pe())  then
+            call error_mesg('diamonds, framework', 'Since the lat/lon grid is off, the x-direction is being set as non-periodic. Set Lx not equal to 360 override.', WARNING) 
+    endif
     Lx=1E14
   endif
 

From c4b68edf3961cf8a3b9c370451979ed24297dc57 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Thu, 7 Jul 2016 17:52:18 -0400
Subject: [PATCH 129/361] 1) Fixed a bug in the calculation of hexagon areas
 (the case where the point lies on the x-axis)

2) Added some new diagnostic output for loading bonds from a restart file.

3) Changed some code in the adjust_indext rountine which excludes the north and east boundary of the cell. I am not 100% sure that this is correct, but it does seem right. The code runs after these changes. This might change the answers in certain setups

4)Still working on rotating the hexagons. The finding the orientation part is almost done.
---
 icebergs.F90           | 75 +++++++++++++++++++++++++++++------------
 icebergs_framework.F90 | 76 ++++++++++++++++++++++++++++++------------
 icebergs_io.F90        | 11 +++++-
 3 files changed, 117 insertions(+), 45 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 86c3de5..f85dd8f 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -747,16 +747,23 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
     byn= ay-(ayn/2) !Alon
 
   ! Limit speed of bergs based on a CFL criteria
-  if (bergs%speed_limit>0.) then
+  if ((bergs%speed_limit>0.) .or. (bergs%speed_limit .eq.-1.)) then
     speed=sqrt(uveln*uveln+vveln*vveln) ! Speed of berg
     if (speed>0.) then
       loc_dx=min(0.5*(grd%dx(i,j)+grd%dx(i,j-1)),0.5*(grd%dy(i,j)+grd%dy(i-1,j))) ! min(dx,dy)
-     !new_speed=min(loc_dx/dt*bergs%speed_limit,speed) ! Restrict speed to dx/dt x factor
+      !new_speed=min(loc_dx/dt*bergs%speed_limit,speed) ! Restrict speed to dx/dt x factor
       new_speed=loc_dx/dt*bergs%speed_limit ! Speed limit as a factor of dx / dt 
       if (new_speed<speed) then
-        uveln=uveln*(new_speed/speed) ! Scale velocity to reduce speed
-        vveln=vveln*(new_speed/speed) ! without changing the direction
-        bergs%nspeeding_tickets=bergs%nspeeding_tickets+1
+        if (bergs%speed_limit>0.) then
+          uveln=uveln*(new_speed/speed) ! Scale velocity to reduce speed
+          vveln=vveln*(new_speed/speed) ! without changing the direction
+          bergs%nspeeding_tickets=bergs%nspeeding_tickets+1
+        else 
+          call error_mesg('diamonds, Speeding icebergs', 'Faster than the CFL!', WARNING)
+          write(stderrunit,*) 'diamonds, Speeding berg1! =',mpp_pe(), berg%iceberg_num
+          write(stderrunit,*) 'diamonds, Speeding berg2, speed =',speed, loc_dx/dt
+          write(stderrunit,*) 'diamonds, Speeding berg3, lat, lon =',lat,xi,yj
+        endif
       endif
     endif
   endif
@@ -1105,10 +1112,13 @@ subroutine thermodynamics(bergs)
             if (Dn>Hocean) Mnew=Mnew*min(1.,Hocean/Dn)
           endif
 
+          !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!1
+          !call show_all_bonds(bergs)
+          !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
           orientation=bergs%initial_orientation
           if ((bergs%iceberg_bonds_on) .and. (bergs%rotate_icebergs_for_mass_spreading)) then
                   orientation=find_orientation_using_iceberg_bonds(this,bergs%initial_orientation,bergs%grd%grid_is_latlon)
-                  print *, 'orientation: ', orientation, this%iceberg_num
+                  print *, 'orientation: ', (180/pi)*orientation, this%iceberg_num
 
           endif
 
@@ -1141,6 +1151,7 @@ real function find_orientation_using_iceberg_bonds(berg,initial_orientation,grid
   current_bond=>berg%first_bond
   lat1=berg%lat
   lon1=berg%lon
+  print *, 'Looking for orientation: '
   do while (associated(current_bond)) ! loop over all bonds
       other_berg=>current_bond%other_berg
       if (.not. associated(current_bond)) then
@@ -1160,10 +1171,12 @@ real function find_orientation_using_iceberg_bonds(berg,initial_orientation,grid
         if (r_dist_y .eq. 0.) then
           angle=pi/2.
         else
-          angle=atan(r_dist_x/r_dist_y)
+          angle=atan(r_dist_y/r_dist_x)
           angle= ((pi/2)  - (initial_orientation*(pi/180.)))  - angle
-          angle=modulo(angle-(2*pi) ,pi/6.)
+          print *, 'angle: ', angle, initial_orientation
+          angle=modulo(angle ,pi/6.)
         endif
+        print *, 'angle2: ', angle
         bond_count=bond_count+1.
         Average_angle=Average_angle+angle
 
@@ -1171,7 +1184,8 @@ real function find_orientation_using_iceberg_bonds(berg,initial_orientation,grid
       current_bond=>current_bond%next_bond
     enddo
     Average_angle =Average_angle/bond_count
-    find_orientation_using_iceberg_bonds=modulo(angle-(2*pi) ,pi/6.)
+    find_orientation_using_iceberg_bonds=modulo(angle ,pi/3.)
+    print *, 'Finished looking: '
 
 end function find_orientation_using_iceberg_bonds
 
@@ -1359,8 +1373,8 @@ logical function point_in_interval(Ax,Ay,Bx,By,px,py)
   ! Arguments
   real, intent(in) :: Ax,Ay,Bx,By,px,py
   point_in_interval=.False.
-  if ((px < max(Ax,Bx)) .and. (px > min(Ax,Bx))) then
-    if ((py < max(Ay,By)) .and. (py > min(Ay,By))) then
+  if ((px <= max(Ax,Bx)) .and. (px >= min(Ax,Bx))) then
+    if ((py <= max(Ay,By)) .and. (py >= min(Ay,By))) then
       point_in_interval=.True.
     endif
   endif
@@ -1596,9 +1610,9 @@ subroutine Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy,Area_triangle,
         call intercept_of_a_line(Bx,By,Cx,Cy,'y',qx,qy); !y_intercept
         if (.not.((point_in_interval(Bx,By,Cx,Cy,px,py)) .and. (point_in_interval(Bx,By,Cx,Cy,qx,qy)))) then
           !You should not get here, but there might be some bugs in the code to do with points exactly falling on axes.
-          if (mpp_pe().eq.12) then
+          !if (mpp_pe().eq.12) then
             write(stderrunit,*) 'diamonds,corners', Ax,Ay,Bx,By,Cx,Cy
-          endif
+          !endif
           call error_mesg('diamonds, iceberg_run', 'Something went wrong with Triangle_divide_into_four_quadrants', FATAL)
         endif
       endif
@@ -2948,6 +2962,7 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
          write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: latn=',latn,berg%lat
          write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u3,un,u0=',uvel3,uveln,berg%uvel
          write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v3,vn,v0=',vvel3,vveln,berg%vvel
+         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: iceberg_num=',berg%iceberg_num
          write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1=',&
               & dt*ax1
          write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ay1=',&
@@ -3465,6 +3480,9 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
   lret=pos_within_cell(grd, lon, lat, i, j, xi, yj)
 !  print *, 'Alon:', lon, lat, i, j, xi, yj, lret
   xi0=xi; yj0=yj ! original xi,yj
+
+
+  !Removing this while debuggin
   if (debug) then
     !Sanity check lret, xi and yj
     lret=is_point_in_cell(grd, lon, lat, i, j)
@@ -3503,6 +3521,7 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
     endif
     lret=pos_within_cell(grd, lon, lat, i, j, xi, yj)
   endif ! debug
+
   if (lret) return ! Berg was already in cell
 
   ! Find inm, jnm (as if adjusting i,j) based on xi,yj
@@ -3518,6 +3537,7 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
         inm=inm-1
       endif
     elseif (xi.gt.1.) then
+!    elseif (xi.ge.1.) then   !Alon: maybe it should be .ge.
       if (inm<grd%ied) then
         inm=inm+1
       endif
@@ -3527,6 +3547,7 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
         jnm=jnm-1
       endif
     elseif (yj.gt.1.) then
+!    elseif (yj.ge.1.) then   !Alon:maybe it should be .ge.
       if (jnm<grd%jed) then
         jnm=jnm+1
       endif
@@ -3552,11 +3573,12 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
         if (grd%msk(i-1,j)>0.) then
           if (i>grd%isd+1) i=i-1
         else
-         write(stderr(),'(a,6f8.3,i)') 'diamonds, adjust: bouncing berg from west',lon,lat,xi,yj,uvel,vvel,mpp_pe()
+         !write(stderr(),'(a,6f8.3,i)') 'diamonds, adjust: bouncing berg from west',lon,lat,xi,yj,uvel,vvel,mpp_pe()
           bounced=.true.
         endif
       endif
-    elseif (xi.gt.1.) then
+    elseif (xi.ge.1.) then    !Alon!!!!
+!    elseif (xi.gt.1.) then
       if (i<grd%ied) then
         if (grd%msk(i+1,j)>0.) then
           if (i<grd%ied) i=i+1
@@ -3571,24 +3593,27 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
         if (grd%msk(i,j-1)>0.) then
           if (j>grd%jsd+1) j=j-1
         else
-         write(stderr(),'(a,6f8.3,i)') 'diamonds, adjust: bouncing berg from south',lon,lat,xi,yj,uvel,vvel,mpp_pe()
+         !write(stderr(),'(a,6f8.3,i)') 'diamonds, adjust: bouncing berg from south',lon,lat,xi,yj,uvel,vvel,mpp_pe()
           bounced=.true.
         endif
       endif
-    elseif (yj.gt.1.) then
+    elseif (yj.ge.1.) then     !Alon.
+!    elseif (yj.gt.1.) then
       if (j<grd%jed) then
         if (grd%msk(i,j+1)>0.) then
           if (j<grd%jed) j=j+1
         else
-         write(stderr(),'(a,6f8.3,i)') 'diamonds, adjust: bouncing berg from north',lon,lat,xi,yj,uvel,vvel,mpp_pe()
+         !write(stderr(),'(a,6f8.3,i)') 'diamonds, adjust: bouncing berg from north',lon,lat,xi,yj,uvel,vvel,mpp_pe()
           bounced=.true.
         endif
       endif
     endif
     if (bounced) then
-      if (xi>1.) xi=1.-posn_eps
+      if (xi>=1.) xi=1.-posn_eps   !Alon.
+!      if (xi>1.) xi=1.-posn_eps   !
       if (xi<0.) xi=posn_eps
-      if (yj>1.) yj=1.-posn_eps
+      if (yj>=1.) yj=1.-posn_eps  !Alon.
+!      if (yj>1.) yj=1.-posn_eps
       if (yj<0.) yj=posn_eps
       lon=bilin(grd, grd%lon, i, j, xi, yj)
       lat=bilin(grd, grd%lat, i, j, xi, yj)
@@ -3634,14 +3659,20 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
         yj=(yj-0.5)*(1.-posn_eps)+0.5
       endif
       call error_mesg('diamonds, adjust', 'Berg did not move or bounce during iterations AND was not in cell. Adjusting!', WARNING)
+      write(stderrunit,*) 'diamonds, adjust: The adjusting iceberg is: ', iceberg_num,  mpp_pe()
+      write(stderrunit,*) 'diamonds, adjust: The adjusting lon,lat,u,v: ', lon, lat, uvel, vvel
+      write(stderrunit,*) 'diamonds, adjust: The adjusting xi,ji: ', xi, yj
+      lret=pos_within_cell(grd, lon, lat, inm, jnm, xi, yj,explain=.true.)
     else
       call error_mesg('diamonds, adjust', 'Berg iterated many times without bouncing!', WARNING)
     endif
   endif
-  if (xi>1.) xi=1.-posn_eps
+!  if (xi>1.) xi=1.-posn_eps    !Alon
+  if (xi>=1.) xi=1.-posn_eps
   if (xi<0.) xi=posn_eps
   if (yj>1.) yj=1.-posn_eps
-  if (yj<0.) yj=posn_eps
+!  if (yj>1.) yj=1.-posn_eps
+  if (yj<=0.) yj=posn_eps        !Alon
   lon=bilin(grd, grd%lon, i, j, xi, yj)
   lat=bilin(grd, grd%lat, i, j, xi, yj)
   lret=pos_within_cell(grd, lon, lat, i, j, xi, yj) ! Update xi and yj
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 82b9aa4..736e472 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -448,7 +448,7 @@ subroutine ice_bergs_framework_init(bergs, &
     bergs%list(i,j)%first => null()
   enddo ; enddo
 
-  big_number=1.0E30
+  big_number=1.0E15
  !write(stderrunit,*) 'diamonds: allocating grid'
   allocate( grd%lon(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%lon(:,:)=big_number
   allocate( grd%lat(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%lat(:,:)=big_number
@@ -501,6 +501,24 @@ subroutine ice_bergs_framework_init(bergs, &
   grd%lon(is:ie,js:je)=ice_lon(:,:)
   grd%lat(is:ie,js:je)=ice_lat(:,:)
   grd%area(is:ie,js:je)=ice_area(:,:) !sis2 has *(4.*pi*radius*radius)
+
+  !!!!!!!!!!!!!!!debugging!!!!!!!!!!!!!!!!!!
+  !if (mpp_pe().eq.5) then
+  ! write(stderrunit,'(a3,32i7)') 'LB',(i,i=grd%isd,grd%ied)
+  ! do j=grd%jed,grd%jsd,-1
+  !   write(stderrunit,'(i3,32f7.1)') j,(grd%lon(i,j),i=grd%isd,grd%ied)
+  ! enddo
+  ! write(stderrunit,'(a3,32i7)') 'Ice lon',(i,i=grd%isd,grd%ied)
+  ! do j=grd%jed,grd%jsd,-1
+  !   write(stderrunit,'(i3,32f7.1)') j,(ice_lon(i,j),i=grd%isd,grd%ied)
+  ! enddo
+  ! write(stderrunit,'(a3,32i7)') 'LA',(i,i=grd%isd,grd%ied)
+  ! do j=grd%jed,grd%jsd,-1
+  !   write(stderrunit,'(i3,32f7.1)') j,(grd%lon(i,j),i=grd%isd,grd%ied)
+  ! enddo
+  !endif
+  !!!!!!!!!!!!!!!debugging!!!!!!!!!!!!!!!!!!
+
   !For SIS not to change answers
   if(present(fractional_area)) then
     if(fractional_area) grd%area(is:ie,js:je)=ice_area(:,:) *(4.*pi*radius*radius)
@@ -555,8 +573,8 @@ subroutine ice_bergs_framework_init(bergs, &
 
   if (.not. present(maskmap)) then ! Using a maskmap causes tickles this sanity check
     do j=grd%jsd,grd%jed; do i=grd%isd,grd%ied
-      if (grd%lon(i,j).ge.big_number) write(stderrunit,*) 'bad lon: ',mpp_pe(),i-grd%isc+1,j-grd%jsc+1,grd%lon(i,j)
-      if (grd%lat(i,j).ge.big_number) write(stderrunit,*) 'bad lat: ',mpp_pe(),i-grd%isc+1,j-grd%jsc+1,grd%lat(i,j)
+      !if (grd%lon(i,j).ge.big_number) write(stderrunit,*) 'bad lon: ',mpp_pe(),i-grd%isc+1,j-grd%jsc+1,grd%lon(i,j)
+      !if (grd%lat(i,j).ge.big_number) write(stderrunit,*) 'bad lat: ',mpp_pe(),i-grd%isc+1,j-grd%jsc+1,grd%lat(i,j)
     enddo; enddo
   endif
 
@@ -611,20 +629,32 @@ subroutine ice_bergs_framework_init(bergs, &
          ' [lon|lat][min|max]=', minval(grd%lon),maxval(grd%lon),minval(grd%lat),maxval(grd%lat)
   endif
 
-! if (mpp_pe().eq.3) then
-!   write(stderrunit,'(a3,32i7)') 'Lon',(i,i=grd%isd,grd%ied)
-!   do j=grd%jed,grd%jsd,-1
-!     write(stderrunit,'(i3,32f7.1)') j,(grd%lon(i,j),i=grd%isd,grd%ied)
-!   enddo
-!   write(stderrunit,'(a3,32i7)') 'Lat',(i,i=grd%isd,grd%ied)
-!   do j=grd%jed,grd%jsd,-1
-!     write(stderrunit,'(i3,32f7.1)') j,(grd%lat(i,j),i=grd%isd,grd%ied)
-!   enddo
-!   write(stderrunit,'(a3,32i7)') 'Msk',(i,i=grd%isd,grd%ied)
-!   do j=grd%jed,grd%jsd,-1
-!     write(stderrunit,'(i3,32f7.1)') j,(grd%msk(i,j),i=grd%isd,grd%ied)
-!   enddo
-! endif
+ !if (mpp_pe().eq.5) then
+ !  write(stderrunit,'(a3,32i7)') 'Lon',(i,i=grd%isd,grd%ied)
+ !  do j=grd%jed,grd%jsd,-1
+ !    write(stderrunit,'(i3,32f7.1)') j,(grd%lon(i,j),i=grd%isd,grd%ied)
+ !  enddo
+ !  write(stderrunit,'(a3,32i7)') 'Lat',(i,i=grd%isd,grd%ied)
+ !  do j=grd%jed,grd%jsd,-1
+ !    write(stderrunit,'(i3,32f7.1)') j,(grd%lat(i,j),i=grd%isd,grd%ied)
+ !  enddo
+ !  write(stderrunit,'(a3,32i7)') 'Msk',(i,i=grd%isd,grd%ied)
+ !  do j=grd%jed,grd%jsd,-1
+ !    write(stderrunit,'(i3,32f7.1)') j,(grd%msk(i,j),i=grd%isd,grd%ied)
+ !  enddo
+ !endif
+
+! Final check for NaN's in the latlon grid:
+  do j=grd%jsd+1,grd%jed; do i=grd%isd+1,grd%ied
+    if (grd%lat(i,j) .ne. grd%lat(i,j)) then
+      write(stderrunit,*) 'Lat not defined properly', mpp_pe(),i,j,grd%lat(i,j)
+      call error_mesg('diamonds,grid defining', 'Latitude contains NaNs', FATAL)
+    endif
+    if (grd%lon(i,j) .ne. grd%lon(i,j)) then
+      write(stderrunit,*) 'Lon not defined properly', mpp_pe(),i,j,grd%lon(i,j)
+      call error_mesg('diamonds, grid defining', 'Longatudes contains NaNs', FATAL)
+    endif
+  enddo; enddo
 
 
 !Added by Alon  - If a freq distribution is input, we have to convert the freq distribution to a mass flux distribution)
@@ -3238,7 +3268,7 @@ logical function sum_sign_dot_prod4(x0, y0, x1, y1, x2, y2, x3, y3, x, y,Lx, exp
   Lx_2=Lx/2.
 
   sum_sign_dot_prod4=.false.
-  xx=modulo(x-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x to within Lx_2of x0
+  xx=modulo(x-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x to within Lx_2 of x0
   xx0=modulo(x0-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x0 to within Lx_2of xx
   xx1=modulo(x1-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x1 to within Lx_2of xx
   xx2=modulo(x2-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x2 to within Lx_2of xx
@@ -3249,8 +3279,10 @@ logical function sum_sign_dot_prod4(x0, y0, x1, y1, x2, y2, x3, y3, x, y,Lx, exp
   l2=(xx-xx2)*(y3-y2)-(y-y2)*(xx3-xx2)
   l3=(xx-xx3)*(y0-y3)-(y-y3)*(xx0-xx3)
 
-  !We use an asymerty between South and East line boundaries and North and East
-  !to avoid icebergs appearing to two cells (half values used for debugging
+  !We use an assymerty between South and East line boundaries and North and East
+  !to avoid icebergs appearing to two cells (half values used for debugging)
+  !This is intended to make the South and East boundaries be part of the
+  !cell, while the North and West are not part of the cell.
   p0=sign(1., l0); if (l0.eq.0.) p0=-0.5
   p1=sign(1., l1); if (l1.eq.0.) p1=0.5
   p2=sign(1., l2); if (l2.eq.0.) p2=0.5
@@ -3920,8 +3952,8 @@ integer function berg_chksum(berg )
 ! Arguments
 type(iceberg), pointer :: berg
 ! Local variables
-real :: rtmp(37) !Changed from 28 to 34 by Alon
-integer :: itmp(37+4), i8=0, ichk1, ichk2, ichk3 !Changed from 28 to 34 by Alon
+real :: rtmp(38) !Changed from 28 to 34 by Alon
+integer :: itmp(38+4), i8=0, ichk1, ichk2, ichk3 !Changed from 28 to 34 by Alon
 integer :: i
 
   rtmp(:)=0.
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 5157350..b134249 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -1114,15 +1114,20 @@ subroutine read_restart_bonds(bergs,Time)
 
   ! Zero out nbergs_in_file
   nbonds_in_file = 0
+  all_pe_number_perfect_bonds=0
 
   filename_base=trim(restart_input_dir)//'bonds_iceberg.res.nc'
 
   found_restart = find_restart_file(filename_base, filename, multiPErestart, io_tile_id(1))
-  call error_mesg('read_restart_bonds_bergs_new', 'Using new icebergs bond restart read', NOTE)
+  call error_mesg('read_restart_bonds_bergs_new', 'Using icebergs bond restart read', NOTE)
 
   filename = filename_base
   call get_field_size(filename,'i',siz, field_found=found, domain=bergs%grd%domain)
   nbonds_in_file = siz(1)
+  
+    if (mpp_pe() .eq. mpp_root_pe()) then
+      write(stderrunit,*)  'diamonds, bond read restart : ','Number of bonds in file',  nbonds_in_file
+    endif
 
   if (nbonds_in_file .gt. 0) then
 
@@ -1279,6 +1284,10 @@ subroutine read_restart_bonds(bergs,Time)
             other_berg_ine,  &
             other_berg_jne )
   endif
+    
+  if (mpp_pe() .eq. mpp_root_pe()) then
+    write(stderrunit,*)  'diamonds, bond read restart : ','Number of bonds created',  all_pe_number_perfect_bonds
+  endif
 
 end subroutine read_restart_bonds
 

From 9ba6aeec55f1975d93f196381dc402e01024c617 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Tue, 19 Jul 2016 11:10:22 -0400
Subject: [PATCH 130/361] A bug has been fixed in the code which calculates the
 orientation of an icebergs by the average position of the icebergs it is
 bonded to. This is now working.

Code has been added which allows icebergs to distribute their mass as hexigons which are oriented according to the angle calculated above. This code has not yet been tested.
---
 icebergs.F90 | 82 +++++++++++++++++++++++++++++++++-------------------
 1 file changed, 52 insertions(+), 30 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index f85dd8f..521fa30 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1112,18 +1112,14 @@ subroutine thermodynamics(bergs)
             if (Dn>Hocean) Mnew=Mnew*min(1.,Hocean/Dn)
           endif
 
-          !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!1
-          !call show_all_bonds(bergs)
-          !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
           orientation=bergs%initial_orientation
           if ((bergs%iceberg_bonds_on) .and. (bergs%rotate_icebergs_for_mass_spreading)) then
-                  orientation=find_orientation_using_iceberg_bonds(this,bergs%initial_orientation,bergs%grd%grid_is_latlon)
-                  print *, 'orientation: ', (180/pi)*orientation, this%iceberg_num
-
+            orientation=find_orientation_using_iceberg_bonds(this,bergs%initial_orientation,bergs%grd%grid_is_latlon)
+            !print *, 'orientation: ', (180/pi)*orientation, this%iceberg_num
+          else
+            orientation=0.0
           endif
-
-
-          call spread_mass_across_ocean_cells(grd, i, j, this%xi, this%yj, Mnew, nMbits, this%mass_scaling, this%length*this%width, bergs%hexagonal_icebergs )
+          call spread_mass_across_ocean_cells(grd, i, j, this%xi, this%yj, Mnew, nMbits, this%mass_scaling, this%length*this%width, bergs%hexagonal_icebergs,orientation)
         endif
       endif
     
@@ -1133,7 +1129,7 @@ subroutine thermodynamics(bergs)
 
 end subroutine thermodynamics
 
-!MPP1
+
 real function find_orientation_using_iceberg_bonds(berg,initial_orientation,grid_is_latlon)
   ! Arguments
   type(iceberg) :: berg
@@ -1167,44 +1163,43 @@ real function find_orientation_using_iceberg_bonds(berg,initial_orientation,grid
         call convert_from_grid_to_meters(lat_ref,grid_is_latlon,dx_dlon,dy_dlat)
         r_dist_x=dlon*dx_dlon
         r_dist_y=dlat*dy_dlat
+        !print *, 'r_dist_x,r_dist_y: ', r_dist_x,r_dist_y
 
-        if (r_dist_y .eq. 0.) then
+        if (r_dist_x .eq. 0.) then
           angle=pi/2.
         else
           angle=atan(r_dist_y/r_dist_x)
-          angle= ((pi/2)  - (initial_orientation*(pi/180.)))  - angle
-          print *, 'angle: ', angle, initial_orientation
-          angle=modulo(angle ,pi/6.)
+          angle= ((pi/2.)  - (initial_orientation*(pi/180.)))  - angle
+          !print *, 'angle: ', angle*(180/pi), initial_orientation
+          angle=modulo(angle ,pi/3.)
         endif
-        print *, 'angle2: ', angle
+        !print *, 'angle2: ', angle*(180/pi)
         bond_count=bond_count+1.
         Average_angle=Average_angle+angle
-
       endif
       current_bond=>current_bond%next_bond
     enddo
     Average_angle =Average_angle/bond_count
+    !print *, 'Average angle', Average_angle*(180/pi), bond_count
     find_orientation_using_iceberg_bonds=modulo(angle ,pi/3.)
-    print *, 'Finished looking: '
+    !print *, 'Finished looking: '
 
 end function find_orientation_using_iceberg_bonds
 
-
-
-! ##############################################################################
-
-subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling, Area, hexagonal_icebergs)
+subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling, Area, hexagonal_icebergs,theta_in)
   ! Arguments
   type(icebergs_gridded), pointer :: grd
   integer, intent(in) :: i, j
   real, intent(in) :: x, y, Mberg, Mbits, scaling, Area
   logical, intent(in) :: hexagonal_icebergs
+  real, optional, intent(in) :: theta_in
   ! Local variables
   real :: xL, xC, xR, yD, yC, yU, Mass, L
   real :: yDxL, yDxC, yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR
-  real :: S, H, origin_x, origin_y, x0, y0, theta
+  real :: S, H, origin_x, origin_y, x0, y0
   real :: Area_Q1,Area_Q2 , Area_Q3,Area_Q4, Area_hex
   real :: fraction_used
+  real :: theta
   real, parameter :: rho_seawater=1035.
   integer :: stderrunit
   logical :: debug
@@ -1212,6 +1207,12 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
   ! Get the stderr unit number
   stderrunit = stderr()
 
+  theta=0.0
+  !This is here because the findinding orientaion scheme is not coded when spread mass to ocean is called directly from the time stepping scheme.
+  if (present(theta_in)) then
+    theta=theta_in
+  endif
+
   Mass=(Mberg+Mbits)*scaling
   ! This line attempts to "clip" the weight felt by the ocean. The concept of
   ! clipping is non-physical and this step should be replaced by grounding.
@@ -1279,7 +1280,6 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
     x0=(x-origin_x)
     y0=(y-origin_y)
 
-    theta=0.0
     call Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
     
     if (min(min(Area_Q1,Area_Q2),min(Area_Q3, Area_Q4)) <-0.001) then
@@ -1698,6 +1698,20 @@ subroutine Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy,Area_triangle,
 
 end subroutine Triangle_divided_into_four_quadrants
 
+subroutine rotate_and_translate(px,py,theta,x0,y0)
+  !This function takes a point px,py, and rotates it clockwise around the origin by theta degrees, and then translates by (x0,y0)
+  ! Arguments
+  real, intent(in) :: x0,y0,theta
+  real, intent(inout) :: px,py
+
+  !Rotation
+  px = ( cos(theta*pi/180)*px) + (sin(theta*pi/180)*py)
+  py = (-sin(theta*pi/180)*px) + (cos(theta*pi/180)*py)
+ 
+  !Translation
+  px= px + x0
+  py= py + y0
+end subroutine rotate_and_translate
 
 subroutine Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex ,Area_Q1, Area_Q2, Area_Q3, Area_Q4)
   !This subroutine divides a regular hexagon centered at x0,y0 with apothen H, and orientation theta into its intersection with the 4 quadrants
@@ -1724,12 +1738,20 @@ subroutine Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex ,Area_Q
   S=(2/sqrt(3.))*H
   
   !Finding positions of corners
-  C1x=S  +x0        ; C1y=0.+y0;  !Corner 1 (right)
-  C2x=H/sqrt(3.) +x0 ; C2y=H+y0;  !Corner 2 (top right)
-  C3x=-H/sqrt(3.)+x0 ; C3y=H+y0;  !Corner 3 (top left)
-  C4x=-S     +x0    ; C4y=0.+y0;  !Corner 4 (left)
-  C5x=-H/sqrt(3.) +x0; C5y=-H+y0; !Corner 5 (top left)
-  C6x=H/sqrt(3.) +x0 ; C6y=-H+y0; !Corner 3 (top left)
+  C1x=S           ; C1y=0.  !Corner 1 (right)
+  C2x=H/sqrt(3.)  ; C2y=H;  !Corner 2 (top right)
+  C3x=-H/sqrt(3.) ; C3y=H;  !Corner 3 (top left)
+  C4x=-S          ; C4y=0.; !Corner 4 (left)
+  C5x=-H/sqrt(3.) ; C5y=-H; !Corner 5 (bottom left)
+  C6x=H/sqrt(3.)  ; C6y=-H; !Corner 6 (bottom right)
+
+  !Finding positions of corners
+  call rotate_and_translate(C1x,C1y,theta,x0,y0)
+  call rotate_and_translate(C2x,C2y,theta,x0,y0)
+  call rotate_and_translate(C3x,C3y,theta,x0,y0)
+  call rotate_and_translate(C4x,C4y,theta,x0,y0)
+  call rotate_and_translate(C5x,C5y,theta,x0,y0)
+  call rotate_and_translate(C6x,C6y,theta,x0,y0)
 
   !Area of Hexagon is the sum of the triangles
   call Triangle_divided_into_four_quadrants(x0,y0,C1x,C1y,C2x,C2y,T12_Area,T12_Q1,T12_Q2,T12_Q3,T12_Q4); !Triangle 012

From 54017536e56e533fa0688fe603521e1fead299bb Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Tue, 19 Jul 2016 11:14:18 -0400
Subject: [PATCH 131/361] A print statement has been removed.

---
 icebergs.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 521fa30..0192950 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1147,7 +1147,7 @@ real function find_orientation_using_iceberg_bonds(berg,initial_orientation,grid
   current_bond=>berg%first_bond
   lat1=berg%lat
   lon1=berg%lon
-  print *, 'Looking for orientation: '
+  !print *, 'Looking for orientation: '
   do while (associated(current_bond)) ! loop over all bonds
       other_berg=>current_bond%other_berg
       if (.not. associated(current_bond)) then

From 90e9f2c506f30ac3ca99a053e26ab0ce63685b2e Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Tue, 19 Jul 2016 13:36:10 -0400
Subject: [PATCH 132/361] Fixed a bug to do with iceberg bonds being moved
 betweeen proceesors. The numbering for packing and unpacking icebergs must be
 the same. This bug was introuduced when the Static_berg property was added.
 With this correction, the bonds can move accross processors

---
 icebergs_framework.F90 | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 736e472..1086178 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -1688,13 +1688,14 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n,grd, force_append, max_bonds_
     localberg%mass_of_bits=buff%data(17,n)
     localberg%heat_density=buff%data(18,n)
 
-    localberg%axn=buff%data(21,n) !Alon
-    localberg%ayn=buff%data(22,n) !Alon
-    localberg%bxn=buff%data(23,n) !Alon
-    localberg%byn=buff%data(24,n) !Alon
+    localberg%axn=buff%data(21,n) 
+    localberg%ayn=buff%data(22,n) 
+    localberg%bxn=buff%data(23,n) 
+    localberg%byn=buff%data(24,n) 
     localberg%iceberg_num=nint(buff%data(25,n))
     localberg%halo_berg=buff%data(26,n) 
     localberg%static_berg=buff%data(27,n) 
+    counter=27 !how many data points being passed so far (must match largest number directly above)
 
     !These quantities no longer need to be passed between processors
     localberg%uvel_old=localberg%uvel
@@ -1743,7 +1744,6 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n,grd, force_append, max_bonds_
 
     this%first_bond=>null()
     if (max_bonds .gt. 0) then
-      counter=26 !how many data points being passed so far (must match above)
       do k = 1,max_bonds
         other_berg_num=nint(buff%data(counter+(3*(k-1)+1),n))
         other_berg_ine=nint(buff%data(counter+(3*(k-1)+2),n))

From 1432626bbdf18f96e68238bb51b005175d265d25 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Tue, 19 Jul 2016 15:46:49 -0400
Subject: [PATCH 133/361] Code has been added which allows the radius for
 interactions between icebergs to depend on the iceberg packing. In
 particular, when the icebergs are packed as hexagons, and the
 bergs%hexagonal_icebergs flag is true, then the radius is calculated
 appropriately.

With this change, icebergs which are perfectly packed and bonded together, do not move (in a test with no forcing)
---
 icebergs.F90 | 38 +++++++++++++++++++++++---------------
 1 file changed, 23 insertions(+), 15 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 0192950..db19f90 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -272,9 +272,9 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
     enddo
   endif
 
-!print *,'IA_x=',IA_x,'IA_y',IA_y, berg%iceberg_num
-!print *,'P_ia_11',P_ia_11,'P_ia_12',P_ia_12, 'P_ia_21',P_ia_21,'P_ia_22', P_ia_22
-!print *, 'P_ia_times_u_x', P_ia_times_u_x, 'P_ia_times_u_y', P_ia_times_u_y
+  !print *,'IA_x=',IA_x,'IA_y',IA_y, berg%iceberg_num
+  !print *,'P_ia_11',P_ia_11,'P_ia_12',P_ia_12, 'P_ia_21',P_ia_21,'P_ia_22', P_ia_22
+  !print *, 'P_ia_times_u_x', P_ia_times_u_x, 'P_ia_times_u_y', P_ia_times_u_y
   contains
 
 
@@ -317,11 +317,9 @@ subroutine calculate_force(bergs,berg,other_berg,IA_x, IA_y, u0, v0, u1, v1, P_i
         T1=berg%thickness 
         M1=berg%mass 
         A1=L1*W1 
-        R1=sqrt(A1/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
         lon1=berg%lon_old; lat1=berg%lat_old
         !call rotpos_to_tang(lon1,lat1,x1,y1)
 
-              
         !From Berg 1
         L2=other_berg%length
         W2=other_berg%width
@@ -330,7 +328,6 @@ subroutine calculate_force(bergs,berg,other_berg,IA_x, IA_y, u0, v0, u1, v1, P_i
         u2=other_berg%uvel_old !Old values are used to make it order invariant 
         v2=other_berg%vvel_old !Old values are used to make it order invariant 
         A2=L2*W2
-        R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
         lon2=other_berg%lon_old; lat2=other_berg%lat_old !Old values are used to make it order invariant
 
         !call rotpos_to_tang(lon2,lat2,x2,y2)
@@ -348,14 +345,25 @@ subroutine calculate_force(bergs,berg,other_berg,IA_x, IA_y, u0, v0, u1, v1, P_i
         r_dist_x=dlon*dx_dlon
         r_dist_y=dlat*dy_dlat
         r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) )
-        
-          !if (berg%iceberg_num .eq. 1) then
-            !print *, 'Comparing longitudes: ', lon1, lon2, r_dist_x, dlon, r_dist
-            !print *, 'Comparing longitudes: ', lon1, lon2, r_dist_x, dlon, r_dist
-            !print *, 'Outside, iceberg_num, r_dist', berg%iceberg_num, r_dist,bonded
-            !print *, 'Halo_status', berg%halo_berg,other_berg%halo_berg 
-          !endif
-        !print *, 'outside the loop',R1, R2,r_dist, bonded
+       
+        if (bergs%hexagonal_icebergs) then 
+          R1=sqrt(A1/(2.*sqrt(3.)))
+          R2=sqrt(A2/(2.*sqrt(3.)))
+        else !square packing
+          R1=sqrt(A1/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
+          R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
+        endif
+       !!!!!!!!!!!!!!!!!!!!!!!!!!!debugging!!!!!!!!!!!!!!!!!!!!!!!!!!MP1 
+       ! if (berg%iceberg_num .eq. 1) then
+       !   print *, 'Comparing longitudes: ', lon1, lon2, r_dist_x, dlon
+       !   print *, 'Comparing latitudes: ', lat1, lat2, r_dist_y, dlat
+       !   print *, 'Outside, iceberg_num, r_dist', berg%iceberg_num, r_dist,bonded
+       !   print *, 'Halo_status', berg%halo_berg,other_berg%halo_berg 
+       ! endif
+       ! print *, 'outside the loop',R1, R2,r_dist, bonded
+       !!!!!!!!!!!!!!!!!!!!!!!!!!!debugging!!!!!!!!!!!!!!!!!!!!!!!!!! 
+
+
        !call overlap_area(R1,R2,r_dist,A_o,trapped)
        !T_min=min(T1,T2)
        !A_min = min((pi*R1**R1),(pi*R2*R2)) 
@@ -1261,7 +1269,7 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
     if (grd%area(i,j)>0) then
       H = min(( (sqrt(Area/(2.*sqrt(3.)))  / sqrt(grd%area(i,j)))),1.) ;  !Non dimensionalize element length by grid area. (This gives the non-dim Apothen of the hexagon)
     else 
-      H= (sqrt(3.)/2)*(0.49)  !Larges allowable H, since this makes S=0.49, and S has to be less than 0.5  (Not sure what the implications of this are)
+      H= (sqrt(3.)/2)*(0.49)  !Largest allowable H, since this makes S=0.49, and S has to be less than 0.5  (Not sure what the implications of this are)
     endif
     S=(2/sqrt(3.))*H !Side of the hexagon
 

From 813a1c5c4aaca21e4917c128d3203a78634e5baa Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 20 Jul 2016 15:55:55 -0400
Subject: [PATCH 134/361] 1) Removed icebergs_halos width, so that the
 iceberg_halos and the gridded halos are the same. This makes the code easier
 to understand. And avoids errors assosiated with having non-matching halos. I
 can not think of any reason why we would need the iceberg halos to be
 different from the gridded halos. If this is needed, it can be added at a
 later time.

2) The second derivative of the sea surface height (used to estimate ssh_x, ssh_y) were giving NaN's close to the boundary because of masked points (when using a non-periodic domain). This has been resolved by setting ddh_x to zero when it is NaN. This works for now. At a later stage we can consider what gradients should be used at these boundaries.

3) The model can not run with iceberg bond when the halo width <2. An Warning has been added when the halo width is less than 2 and iceberg interactions are being used. The halo widths are now automatically set to 2 in this situation.

4) An error was occuring with the finding orientation code. This resulted from the fact that icebergs on the edge of the halo are not always assosiated with their bonded icebergs (since they they might not be on the halo). This means that we can not find the orientation of these icebergs using the average positions of their bonds. Luckily, we do not need the orientation of these icebergs, since if the halo has width greater than 2, these icebergs on the edge of the halos do not spread their mass onto the computational domain. (Recall that the iceberg orientation is used in the spread_mass_to_ocean calculation). This is a reason why the halos need to be >= 2 when bonds are used. This issue has been resolved using an if statement to get around this case.

5) A couple of other things have been cleaned up  (this is bad git practice)
---
 icebergs.F90           | 112 +++++++++++++++++++++++------------------
 icebergs_framework.F90 |  18 +++----
 icebergs_io.F90        |  36 +++++++++----
 3 files changed, 97 insertions(+), 69 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index db19f90..2cff5b3 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -263,8 +263,8 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
     current_bond=>berg%first_bond
     do while (associated(current_bond)) ! loop over all bonds
       other_berg=>current_bond%other_berg
-      if (.not. associated(current_bond)) then
-        call error_mesg('diamonds,bond interactions', 'Trying to do Bond interactions with unassosiated bond!' ,FATAL)
+      if (.not. associated(other_berg)) then
+        call error_mesg('diamonds,bond interactions', 'Trying to do Bond interactions with unassosiated berg!' ,FATAL)
       else
         call calculate_force(bergs,berg,other_berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded) 
       endif
@@ -951,6 +951,7 @@ subroutine thermodynamics(bergs)
 
   !do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
   do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied  ! Thermodynamics of  halos now calculated, so that spread mass to ocean works correctly
+  !do grdj = grd%jsc-1,grd%jec+1 ; do grdi = grd%isc-1,grd%iec+1  ! Thermodynamics of first halo row is calculated, so that spread mass to ocean works correctly
     this=>bergs%list(grdi,grdj)%first
     do while(associated(this))
       if (debug) call check_position(grd, this, 'thermodynamics (top)')
@@ -962,8 +963,8 @@ subroutine thermodynamics(bergs)
       IC=min(1.,this%cn+bergs%sicn_shift) ! Shift sea-ice concentration 
       M=this%mass
       T=this%thickness ! total thickness
-    ! D=(bergs%rho_bergs/rho_seawater)*T ! draught (keel depth)
-    ! F=T-D ! freeboard
+      !D=(bergs%rho_bergs/rho_seawater)*T ! draught (keel depth)
+      !F=T-D ! freeboard
       W=this%width
       L=this%length
       i=this%ine
@@ -988,7 +989,6 @@ subroutine thermodynamics(bergs)
         Mb=0.0
         Me=0.0
       endif
-
   
       if (bergs%use_operator_splitting) then
         ! Operator split update of volume/mass
@@ -1095,12 +1095,12 @@ subroutine thermodynamics(bergs)
       endif
   
       ! Store the new state of iceberg (with L>W)
-        this%mass=Mnew
-        this%mass_of_bits=nMbits
-        this%thickness=Tn
-        this%width=min(Wn,Ln)
-        this%length=max(Wn,Ln)
-        next=>this%next
+      this%mass=Mnew
+      this%mass_of_bits=nMbits
+      this%thickness=Tn
+      this%width=min(Wn,Ln)
+      this%length=max(Wn,Ln)
+      next=>this%next
   
       ! Did berg completely melt?
       if (Mnew<=0.) then ! Delete the berg
@@ -1122,10 +1122,11 @@ subroutine thermodynamics(bergs)
 
           orientation=bergs%initial_orientation
           if ((bergs%iceberg_bonds_on) .and. (bergs%rotate_icebergs_for_mass_spreading)) then
-            orientation=find_orientation_using_iceberg_bonds(this,bergs%initial_orientation,bergs%grd%grid_is_latlon)
+            !Don't check orientation of the edges of halo,  since they can contain unassosiated bonds  (this is why halo width must be larger >= 2 to use bonds)    
+            if  (  ((this%ine .gt.  grd%isd) .and. (this%ine .lt. grd%ied)) .and. ((this%jne .ge.  grd%jsd) .and. (this%jne .le. grd%jed) ) ) then  
+              orientation=find_orientation_using_iceberg_bonds(grd,this,bergs%initial_orientation)
+            endif
             !print *, 'orientation: ', (180/pi)*orientation, this%iceberg_num
-          else
-            orientation=0.0
           endif
           call spread_mass_across_ocean_cells(grd, i, j, this%xi, this%yj, Mnew, nMbits, this%mass_scaling, this%length*this%width, bergs%hexagonal_icebergs,orientation)
         endif
@@ -1138,18 +1139,20 @@ subroutine thermodynamics(bergs)
 end subroutine thermodynamics
 
 
-real function find_orientation_using_iceberg_bonds(berg,initial_orientation,grid_is_latlon)
+real function find_orientation_using_iceberg_bonds(grd,berg,initial_orientation)
   ! Arguments
-  type(iceberg) :: berg
+  type(iceberg), pointer :: berg
   real, intent(in) :: initial_orientation 
-  logical, intent(in) :: grid_is_latlon
+  type(icebergs_gridded), pointer :: grd
   type(iceberg), pointer :: other_berg
   type(bond), pointer :: current_bond
   real :: angle, lat1,lat2,lon1,lon2,dlat,dlon
   real :: r_dist_x, r_dist_y 
   real :: lat_ref, dx_dlon, dy_dlat
   real :: theta, bond_count, Average_angle
+  logical  :: grid_is_latlon
     
+  grid_is_latlon=grd%grid_is_latlon
   bond_count=0.
   Average_angle=0.
   current_bond=>berg%first_bond
@@ -1157,39 +1160,50 @@ real function find_orientation_using_iceberg_bonds(berg,initial_orientation,grid
   lon1=berg%lon
   !print *, 'Looking for orientation: '
   do while (associated(current_bond)) ! loop over all bonds
-      other_berg=>current_bond%other_berg
-      if (.not. associated(current_bond)) then
-        call error_mesg('diamonds,calculating orientation', 'Trying to do Bond interactions with unassosiated bond!' ,FATAL)
-      else
-        lat2=other_berg%lat
-        lon2=other_berg%lon
-
-        dlat=lat2-lat1
-        dlon=lon2-lon1
-        
-        lat_ref=0.5*(lat1+lat2)
-        call convert_from_grid_to_meters(lat_ref,grid_is_latlon,dx_dlon,dy_dlat)
-        r_dist_x=dlon*dx_dlon
-        r_dist_y=dlat*dy_dlat
-        !print *, 'r_dist_x,r_dist_y: ', r_dist_x,r_dist_y
+    other_berg=>current_bond%other_berg
+    if (.not. associated(other_berg)) then !good place for debugging 
+      !One valid option: current iceberg is on the edge of halo, with other berg on the next pe (not influencing mass spreading)
+        !print *, 'Iceberg bond details:',berg%iceberg_num, current_bond%other_berg_num,berg%halo_berg, mpp_pe()
+        !print *, 'Iceberg bond details2:',berg%ine, berg%jne, current_bond%other_berg_ine, current_bond%other_berg_jne
+        !print *, 'Iceberg isd,ied,jsd,jed:',grd%isd, grd%ied, grd%jsd, grd%jed
+        !print *, 'Iceberg isc,iec,jsc,jec:',grd%isc, grd%iec, grd%jsc, grd%jec
+        !call error_mesg('diamonds,calculating orientation', 'Looking at bond interactions of unassosiated berg!' ,FATAL)
+      !endif
+    else
+      lat2=other_berg%lat
+      lon2=other_berg%lon
 
-        if (r_dist_x .eq. 0.) then
-          angle=pi/2.
-        else
-          angle=atan(r_dist_y/r_dist_x)
-          angle= ((pi/2.)  - (initial_orientation*(pi/180.)))  - angle
-          !print *, 'angle: ', angle*(180/pi), initial_orientation
-          angle=modulo(angle ,pi/3.)
-        endif
-        !print *, 'angle2: ', angle*(180/pi)
-        bond_count=bond_count+1.
-        Average_angle=Average_angle+angle
+      dlat=lat2-lat1
+      dlon=lon2-lon1
+      
+      lat_ref=0.5*(lat1+lat2)
+      call convert_from_grid_to_meters(lat_ref,grid_is_latlon,dx_dlon,dy_dlat)
+      r_dist_x=dlon*dx_dlon
+      r_dist_y=dlat*dy_dlat
+      !print *, 'r_dist_x,r_dist_y: ', r_dist_x,r_dist_y
+
+      if (r_dist_x .eq. 0.) then
+        angle=pi/2.
+      else
+        angle=atan(r_dist_y/r_dist_x)
+        angle= ((pi/2.)  - (initial_orientation*(pi/180.)))  - angle
+        !print *, 'angle: ', angle*(180/pi), initial_orientation
+        angle=modulo(angle ,pi/3.)
       endif
-      current_bond=>current_bond%next_bond
-    enddo
+      !print *, 'angle2: ', angle*(180/pi)
+      bond_count=bond_count+1.
+      Average_angle=Average_angle+angle
+    endif
+    current_bond=>current_bond%next_bond
+  enddo  !End loop over bonds
+  if (bond_count.gt.0) then
     Average_angle =Average_angle/bond_count
+  else
+    Average_angle =0.
+  endif
     !print *, 'Average angle', Average_angle*(180/pi), bond_count
-    find_orientation_using_iceberg_bonds=modulo(angle ,pi/3.)
+    find_orientation_using_iceberg_bonds=modulo(Average_angle ,pi/3.)
+    !find_orientation_using_iceberg_bonds=modulo(angle ,pi/3.)
     !print *, 'Finished looking: '
 
 end function find_orientation_using_iceberg_bonds
@@ -1857,7 +1871,6 @@ subroutine interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y,
   ua=bilin(grd, grd%ua, i, j, xi, yj)
   va=bilin(grd, grd%va, i, j, xi, yj)
 
-  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
   if (ua.ne.ua) then
     if (mpp_pe().eq.9) then
       write(stderrunit,'(a3,32i7)') 'ua',(ii,ii=grd%isd,grd%ied)
@@ -1876,8 +1889,6 @@ subroutine interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y,
       call error_mesg('diamonds, interp fields', 'ua is NaNs', FATAL)
     endif
   endif
-  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
 
   ! These fields are cell centered (A-grid) and would
   ! best be interpolated using PLM. For now we use PCM!
@@ -1952,6 +1963,8 @@ real function ddx_ssh(grd,i,j)
     dxp=0.5*(grd%dx(i+1,j)+grd%dx(i+1,j-1))
     dx0=0.5*(grd%dx(i,j)+grd%dx(i,j-1))
     ddx_ssh=2.*(grd%ssh(i+1,j)-grd%ssh(i,j))/(dx0+dxp)*grd%msk(i+1,j)*grd%msk(i,j)
+
+    if (ddx_ssh .ne. ddx_ssh)  ddx_ssh=0. !This makes the model not crash for finite domains. 
   end function ddx_ssh
 
   real function ddy_ssh(grd,i,j)
@@ -1963,6 +1976,7 @@ real function ddy_ssh(grd,i,j)
     dyp=0.5*(grd%dy(i,j+1)+grd%dy(i-1,j+1))
     dy0=0.5*(grd%dy(i,j)+grd%dy(i-1,j))
     ddy_ssh=2.*(grd%ssh(i,j+1)-grd%ssh(i,j))/(dy0+dyp)*grd%msk(i,j+1)*grd%msk(i,j)
+    if (ddy_ssh .ne. ddy_ssh)  ddy_ssh=0.  !This makes the model not crash for finite domains. 
   end function ddy_ssh
 
   subroutine rotate(u, v, cos_rot, sin_rot)
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 1086178..97501cd 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -77,7 +77,6 @@ module ice_bergs_framework
 type :: icebergs_gridded
   type(domain2D), pointer :: domain ! MPP domain
   integer :: halo ! Nominal halo width
-  integer :: iceberg_halo ! halo width used by icebergs (must be lt halo)
   integer :: isc, iec, jsc, jec ! Indices of computational domain
   integer :: isd, ied, jsd, jed ! Indices of data domain
   integer :: isg, ieg, jsg, jeg ! Indices of global domain
@@ -308,7 +307,6 @@ subroutine ice_bergs_framework_init(bergs, &
 
 ! Namelist parameters (and defaults)
 integer :: halo=4 ! Width of halo region
-integer :: iceberg_halo=2 ! Width of halo region for icebergs  (must be lt halo)
 integer :: traj_sample_hrs=24 ! Period between sampling of position for trajectory storage
 integer :: traj_write_hrs=480 ! Period between writing sampled trajectories to disk
 integer :: verbose_hrs=24 ! Period between verbose messages
@@ -353,7 +351,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real, dimension(nclasses) :: distribution=(/0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02/) ! Fraction of calving to apply to this class (non-dim) , 
 real, dimension(nclasses) :: mass_scaling=(/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) ! Ratio between effective and real iceberg mass (non-dim)
 real, dimension(nclasses) :: initial_thickness=(/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) ! Total thickness of newly calved bergs (m)
-namelist /icebergs_nml/ verbose, budget, halo, iceberg_halo, traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,Static_icebergs,  &
+namelist /icebergs_nml/ verbose, budget, halo,  traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,Static_icebergs,  &
          distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,bond_coef, radial_damping_coef, tangental_damping_coef, only_interactive_forces, &
          rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, iceberg_bonds_on, manually_initialize_bonds, ignore_missing_restart_bergs, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, halo_debugging, hexagonal_icebergs, &
@@ -668,8 +666,9 @@ subroutine ice_bergs_framework_init(bergs, &
      enddo
 endif 
 
-if (iceberg_halo .gt. halo) then
-    iceberg_halo=halo
+if ((halo .lt. 2) .and. (interactive_icebergs_on .or. iceberg_bonds_on) )   then
+    halo=2
+    call error_mesg('diamonds, framework', 'Setting iceberg halos =2, since halos must be >= 2 for interactions', WARNING) 
 endif
 
 if (interactive_icebergs_on) then
@@ -701,7 +700,6 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%grd%Lx=Lx
   bergs%grd%grid_is_latlon=grid_is_latlon  
   bergs%max_bonds=max_bonds
-  bergs%grd%iceberg_halo=iceberg_halo
   bergs%rho_bergs=rho_bergs
   bergs%spring_coef=spring_coef
   bergs%bond_coef=bond_coef
@@ -954,8 +952,8 @@ subroutine update_halo_icebergs(bergs)
 logical :: halo_debugging
 
 force_app =.true.
-halo_width=bergs%grd%iceberg_halo  ! Must be less than current halo value used for updating weight.
-halo_debugging=bergs%halo_debugging  ! Must be less than current halo value used for updating weight.
+halo_width=bergs%grd%halo  
+halo_debugging=bergs%halo_debugging  
 
  ! Get the stderr unit number
    stderrunit = stderr()
@@ -964,7 +962,7 @@ subroutine update_halo_icebergs(bergs)
    grd=>bergs%grd
 
 
-!For debugging
+!For debugging, MP1
 if (halo_debugging) then
   do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
     this=>bergs%list(grdi,grdj)%first
@@ -3126,7 +3124,7 @@ end subroutine  find_individual_iceberg
 
 ! ##############################################################################
 
-logical function find_cell(grd, x, y, oi, oj) !MP1
+logical function find_cell(grd, x, y, oi, oj) 
 ! Arguments
 type(icebergs_gridded), intent(in) :: grd
 real, intent(in) :: x, y
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index b134249..84d4ff7 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -1093,8 +1093,10 @@ subroutine read_restart_bonds(bergs,Time)
 integer :: number_second_bonds_matched !How many second bond bergs found on pe
 integer :: number_perfect_bonds ! How many complete bonds formed
 integer :: number_partial_bonds ! How many either complete/partial bonds formed.
+integer :: number_perfect_bonds_with_first_on_pe ! How many bonds with first bond on the compuational domain
 integer :: all_pe_number_perfect_bonds, all_pe_number_partial_bonds
 integer :: all_pe_number_first_bonds_matched, all_pe_number_second_bonds_matched
+integer :: all_pe_number_perfect_bonds_with_first_on_pe
 integer :: ine, jne
 logical :: search_data_domain
 real :: berg_found, berg_found_all_pe
@@ -1150,6 +1152,7 @@ subroutine read_restart_bonds(bergs,Time)
     number_second_bonds_matched=0
     number_perfect_bonds=0
     number_partial_bonds=0
+    number_perfect_bonds_with_first_on_pe=0
 
     do k=1, nbonds_in_file
       
@@ -1164,13 +1167,9 @@ subroutine read_restart_bonds(bergs,Time)
          if (berg_found_all_pe .gt. 0.5) then
              first_berg_ine(k)=ine
              first_berg_jne(k)=jne
-           !endif
          else
-          call error_mesg('read_restart_bonds_bergs_new', 'First iceberg in bond not found on any pe', FATAL)
-         endif
-         if (berg_found_all_pe .lt. 0.5) then
-                 print * , 'First bond berg not located: ', first_berg_num(k),berg_found, mpp_pe(),ine, jne
-             call error_mesg('read_restart_bonds_bergs_new', 'First bond iceberg not located', FATAL)
+           print * , 'First bond berg not located: ', first_berg_num(k),berg_found, mpp_pe(),ine, jne
+           call error_mesg('read_restart_bonds_bergs_new', 'First iceberg in bond not found on any pe', FATAL)
          endif
          !else
 
@@ -1199,7 +1198,7 @@ subroutine read_restart_bonds(bergs,Time)
       if ( (first_berg_ine(k)>=grd%isd) .and. (first_berg_ine(k)<=grd%ied) .and. &
         (first_berg_jne(k)>=grd%jsd) .and. (first_berg_jne(k)<=grd%jed) ) then
         number_first_bonds_matched=number_first_bonds_matched+1
-     
+        
         ! Search for the first berg, which the bond belongs to
         first_berg_found=.false.
         first_berg=>null()
@@ -1208,14 +1207,13 @@ subroutine read_restart_bonds(bergs,Time)
           if (this%iceberg_num == first_berg_num(k)) then
             first_berg_found=.true.
             first_berg=>this
-            if (first_berg%halo_berg.gt.0.5) print *, 'bonding halo berg:', first_berg_num(k),  first_berg_ine(k),first_berg_jne(k) ,grd%isc, grd%iec, mpp_pe()
+            !if (first_berg%halo_berg.gt.0.5) print *, 'bonding halo berg:', first_berg_num(k),  first_berg_ine(k),first_berg_jne(k) ,grd%isc, grd%iec, mpp_pe()
             this=>null()
           else  
             this=>this%next
           endif
         enddo
      
-!Note, this is a bug since there are no bergs in the halos up to here, are there?
 
         ! Decide whether the second iceberg is on the processeor (data domain)
         second_berg_found=.false.
@@ -1244,6 +1242,13 @@ subroutine read_restart_bonds(bergs,Time)
           if (second_berg_found) then
             call form_a_bond(first_berg, other_berg_num(k), other_berg_ine(k), other_berg_jne(k),  second_berg)
             number_perfect_bonds=number_perfect_bonds+1
+    
+            !Counting number of bonds where the first bond is in the computational domain
+            if ( (first_berg_ine(k)>=grd%isc) .and. (first_berg_ine(k)<=grd%iec) .and. &
+              (first_berg_jne(k)>=grd%jsc) .and. (first_berg_jne(k)<=grd%jec) ) then
+               number_perfect_bonds_with_first_on_pe=number_perfect_bonds_with_first_on_pe+1
+        endif
+     
           else
             !print *, 'Forming a bond of the second type', mpp_pe(), first_berg_num(k),  other_berg_num(k)
             !call form_a_bond(first_berg, other_berg_num(k),other_berg_ine(k),other_berg_jne(k))
@@ -1257,11 +1262,13 @@ subroutine read_restart_bonds(bergs,Time)
 
     !Analyse how many bonds were created and take appropriate action
     all_pe_number_perfect_bonds=number_perfect_bonds
+    all_pe_number_perfect_bonds_with_first_on_pe=number_perfect_bonds_with_first_on_pe
     all_pe_number_partial_bonds=number_partial_bonds
     all_pe_number_first_bonds_matched=number_first_bonds_matched
     all_pe_number_second_bonds_matched=number_second_bonds_matched
     call mpp_sum(all_pe_number_perfect_bonds)
     call mpp_sum(all_pe_number_partial_bonds)
+    call mpp_sum(all_pe_number_perfect_bonds_with_first_on_pe)
 
     if (all_pe_number_partial_bonds .lt. nbonds_in_file) then
       write(stderrunit,*) 'diamonds, bond read restart : ','Not enough partial bonds formed', all_pe_number_partial_bonds , nbonds_in_file
@@ -1276,6 +1283,14 @@ subroutine read_restart_bonds(bergs,Time)
       call error_mesg('read_restart_bonds_bergs_new', 'Not enough perfect bonds formed', NOTE)
     endif
 
+    if (all_pe_number_perfect_bonds_with_first_on_pe .ne. nbonds_in_file) then
+      call mpp_sum(all_pe_number_first_bonds_matched)
+      call mpp_sum(all_pe_number_second_bonds_matched)
+      write(stderrunit,*)  'diamonds, bond read restart : ','Warning, # bonds with first bond on computational domain, does not match file',  all_pe_number_first_bonds_matched , nbonds_in_file
+      write(stderrunit,*)  'diamonds, bond read restart : ','Computational bond, first second:', all_pe_number_second_bonds_matched , nbonds_in_file
+      call error_mesg('read_restart_bonds_bergs_new', 'Computational perfect bonds do not match those in file', NOTE)
+    endif
+
     deallocate(               &
             first_berg_num,   &
             other_berg_num,  &
@@ -1286,7 +1301,8 @@ subroutine read_restart_bonds(bergs,Time)
   endif
     
   if (mpp_pe() .eq. mpp_root_pe()) then
-    write(stderrunit,*)  'diamonds, bond read restart : ','Number of bonds created',  all_pe_number_perfect_bonds
+    write(stderrunit,*)  'diamonds, bond read restart : ','Number of bonds (including halos)',  all_pe_number_perfect_bonds
+    write(stderrunit,*)  'diamonds, bond read restart : ','Number of true bonds created',  all_pe_number_perfect_bonds_with_first_on_pe
   endif
 
 end subroutine read_restart_bonds

From afd006cd75ec5df01c60acea907001be64ea4c14 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Thu, 28 Jul 2016 12:57:46 -0400
Subject: [PATCH 135/361] Added namelist flag read_old_restart

- This allows icebergs to read a restart with out the iceberg_number identifier
  entry in the restart file.
---
 icebergs_framework.F90 |  8 ++++++--
 icebergs_io.F90        | 20 +++++++++++++++++---
 2 files changed, 23 insertions(+), 5 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index ec503ca..d40dcc5 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -189,6 +189,7 @@ module ice_bergs_framework
   logical :: use_new_predictive_corrective =.False.  !Flag to use Bob's predictive corrective iceberg scheme- Added by Alon 
   logical :: interactive_icebergs_on=.false.  !Turn on/off interactions between icebergs  - Added by Alon 
   logical :: critical_interaction_damping_on=.true.  !Sets the damping on relative iceberg velocity to critical value - Added by Alon 
+  logical :: read_old_restarts=.true. ! If true, read restarts prior to grid_of_lists and iceberg_num innovation
   real :: speed_limit=0. ! CFL speed limit for a berg [m/s]
   real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
   type(buffer), pointer :: obuffer_n=>null(), ibuffer_n=>null()
@@ -287,7 +288,8 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: interactive_icebergs_on=.false.  !Turn on/off interactions between icebergs  - Added by Alon 
 logical :: critical_interaction_damping_on=.true.  !Sets the damping on relative iceberg velocity to critical value - Added by Alon 
 logical :: do_unit_tests=.false. ! Conduct some unit tests
-logical :: input_freq_distribution=.false. ! Alon: flag to show if input distribution is freq or mass dist (=1 if input is a freq dist, =0 to use an input mass dist)
+logical :: input_freq_distribution=.false. ! Flag to show if input distribution is freq or mass dist (=1 if input is a freq dist, =0 to use an input mass dist)
+logical :: read_old_restarts=.true. ! If true, read restarts prior to grid_of_lists and iceberg_num innovations
 real, dimension(nclasses) :: initial_mass=(/8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11/) ! Mass thresholds between iceberg classes (kg)
 real, dimension(nclasses) :: distribution=(/0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02/) ! Fraction of calving to apply to this class (non-dim) , 
 real, dimension(nclasses) :: mass_scaling=(/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) ! Ratio between effective and real iceberg mass (non-dim)
@@ -297,7 +299,8 @@ subroutine ice_bergs_framework_init(bergs, &
          rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, &
          time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, interactive_icebergs_on, critical_interaction_damping_on, &
-         old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution, force_all_pes_traj
+         old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution, force_all_pes_traj, &
+         read_old_restarts
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -556,6 +559,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%use_new_predictive_corrective=use_new_predictive_corrective  !Alon
   bergs%grounding_fraction=grounding_fraction
   bergs%add_weight_to_ocean=add_weight_to_ocean
+  bergs%read_old_restarts=read_old_restarts
   allocate( bergs%initial_mass(nclasses) ); bergs%initial_mass(:)=initial_mass(:)
   allocate( bergs%distribution(nclasses) ); bergs%distribution(:)=distribution(:)
   allocate( bergs%mass_scaling(nclasses) ); bergs%mass_scaling(:)=mass_scaling(:)
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 1c77753..81fbfa7 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -341,13 +341,15 @@ subroutine read_restart_bergs_orig(bergs,Time)
 character(len=33) :: filename, filename_base
 type(icebergs_gridded), pointer :: grd
 type(iceberg) :: localberg ! NOT a pointer but an actual local variable
-integer :: stderrunit
+integer :: stderrunit, iNg, jNg, i, j
 
   ! Get the stderr unit number
   stderrunit=stderr()
 
   ! For convenience
   grd=>bergs%grd
+  iNg=(grd%ieg-grd%isg+1) ! Total number of points globally in i direction, used with read_old_restarts=.true.
+  jNg=(grd%jeg-grd%jsg+1) ! Total number of points globally in j direction, used with read_old_restarts=.true.
 
   ! Find a restart file
   multiPErestart=.false.
@@ -409,7 +411,11 @@ subroutine read_restart_bergs_orig(bergs,Time)
   start_lonid=inq_var(ncid, 'start_lon')
   start_latid=inq_var(ncid, 'start_lat')
   start_yearid=inq_var(ncid, 'start_year')
-  iceberg_numid=inq_var(ncid, 'icberg_num')
+  if (bergs%read_old_restarts) then
+    iceberg_numid=-1
+  else
+    iceberg_numid=inq_var(ncid, 'icberg_num')
+  endif
   start_dayid=inq_var(ncid, 'start_day')
   start_massid=inq_var(ncid, 'start_mass')
   scaling_id=inq_var(ncid, 'mass_scaling')
@@ -467,7 +473,15 @@ subroutine read_restart_bergs_orig(bergs,Time)
       localberg%start_lon=get_double(ncid, start_lonid, k)
       localberg%start_lat=get_double(ncid, start_latid, k)
       localberg%start_year=get_int(ncid, start_yearid, k)
-      localberg%iceberg_num=get_int(ncid, iceberg_numid, k)
+      if (bergs%read_old_restarts) then
+        ! This emulates the iceberg counter used at calving sites but uses the restart position instead
+        i = localberg%ine
+        j = localberg%jne
+        localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i+(iNg*(j-1)))  ! unique number for each iceberg
+        grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
+      else
+        localberg%iceberg_num=get_int(ncid, iceberg_numid, k)
+      endif
       localberg%start_day=get_double(ncid, start_dayid, k)
       localberg%start_mass=get_double(ncid, start_massid, k)
       localberg%mass_scaling=get_double(ncid, scaling_id, k)

From 516c4168ea88acd8f330dfeaa8e75d85914a2f75 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Thu, 28 Jul 2016 13:49:44 -0400
Subject: [PATCH 136/361] Initialize *_old data when not using Verlet algorithm

- The checksums included uvle_old, vvel_old, lon_old and lat_old even
  when not using the Verlet algorithm that uses this data.
- Regression tests across restarts were passing even though the checksums
  appeared to differ across restarts. This was due to uninitialized values
  in this *_old iceberg attributes.
- Restarts and checksums now reproduce across restarts.
---
 icebergs.F90 | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/icebergs.F90 b/icebergs.F90
index 8d21f4f..9196916 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1779,6 +1779,10 @@ subroutine calve_icebergs(bergs)
           newberg%mass_scaling=bergs%mass_scaling(k)
           newberg%mass_of_bits=0.
           newberg%heat_density=grd%stored_heat(i,j)/grd%stored_ice(i,j,k) ! This is in J/kg
+          newberg%lon_old=newberg%lon
+          newberg%lat_old=newberg%lat
+          newberg%uvel_old=newberg%uvel
+          newberg%vvel_old=newberg%vvel
           call add_new_berg_to_list(bergs%first, newberg)
           calved_to_berg=bergs%initial_mass(k)*bergs%mass_scaling(k) ! Units of kg
           ! Heat content

From 0f2ac729140ab4a6e619a13be0a0596009123f0c Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Thu, 28 Jul 2016 15:13:32 -0400
Subject: [PATCH 137/361] Fixed read_old_restarts for new i/o method

- In commit afd006cd75e we forgot to update the new FMS i/o
  version of read_restarts.
---
 icebergs_framework.F90 |  1 +
 icebergs_io.F90        | 20 +++++++++++++++++---
 2 files changed, 18 insertions(+), 3 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index d40dcc5..e793967 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -569,6 +569,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%initial_width(:)=sqrt(initial_mass(:)/(LoW_ratio*rho_bergs*initial_thickness(:)))
   bergs%initial_length(:)=LoW_ratio*bergs%initial_width(:)
 
+  if (bergs%read_old_restarts) call error_mesg('diamonds, ice_bergs_framework_init', 'Setting "read_old_restarts=.true." can lead to non-reproducing checksums in restarts!', WARNING)
 
   ! Diagnostics
   id_class = diag_axis_init('mass_class', initial_mass, 'kg','Z', 'iceberg mass')
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 81fbfa7..e2633c4 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -646,7 +646,7 @@ subroutine read_restart_bergs(bergs,Time)
 character(len=33) :: filename, filename_base
 type(icebergs_gridded), pointer :: grd
 type(iceberg) :: localberg ! NOT a pointer but an actual local variable
-integer :: stderrunit
+integer :: stderrunit, iNg, jNg, i, j
 
 real, allocatable, dimension(:) :: lon,          &
                                    lat,          &
@@ -684,6 +684,8 @@ subroutine read_restart_bergs(bergs,Time)
 
   ! For convenience
   grd=>bergs%grd
+  iNg=(grd%ieg-grd%isg+1) ! Total number of points globally in i direction, used with read_old_restarts=.true.
+  jNg=(grd%jeg-grd%jsg+1) ! Total number of points globally in j direction, used with read_old_restarts=.true.
 
   ! Zero out nbergs_in_file
   nbergs_in_file = 0
@@ -756,7 +758,11 @@ subroutine read_restart_bergs(bergs,Time)
      call read_unlimited_axis(filename,'ine',ine,domain=grd%domain)
      call read_unlimited_axis(filename,'jne',jne,domain=grd%domain)
      call read_unlimited_axis(filename,'start_year',start_year,domain=grd%domain)
-     call read_unlimited_axis(filename,'iceberg_num',iceberg_num,domain=grd%domain)
+     if (bergs%read_old_restarts) then
+       iceberg_num(:)=-1
+     else
+       call read_unlimited_axis(filename,'iceberg_num',iceberg_num,domain=grd%domain)
+     endif
   endif
 
   ! Find approx outer bounds for tile
@@ -806,7 +812,15 @@ subroutine read_restart_bergs(bergs,Time)
       localberg%start_lon=start_lon(k)
       localberg%start_lat=start_lat(k)
       localberg%start_year=start_year(k)
-      localberg%iceberg_num=iceberg_num(k)
+      if (bergs%read_old_restarts) then
+        ! This emulates the iceberg counter used at calving sites but uses the restart position instead
+        i = localberg%ine
+        j = localberg%jne
+        localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i+(iNg*(j-1)))  ! unique number for each iceberg
+        grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
+      else
+        localberg%iceberg_num=iceberg_num(k)
+      endif
       localberg%start_day=start_day(k)
       localberg%start_mass=start_mass(k)
       localberg%mass_scaling=mass_scaling(k)

From 40aab7a801f2c9c8381991e35cb60ad3074a76d0 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Thu, 28 Jul 2016 15:31:14 -0400
Subject: [PATCH 138/361] Code added which sets sea surface slope gradients to
 0 if they equal NaN. This is needed when using finite domains (since they
 code which calculates gradients was written for periodic domain). This is not
 a perfect solution, but stops the model from crashing

A line of code has been added which stops the model from doing many checksums when the time step is small.
---
 icebergs.F90           | 10 ++++++----
 icebergs_framework.F90 | 10 +++++++---
 2 files changed, 13 insertions(+), 7 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 2cff5b3..3258306 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1944,6 +1944,10 @@ subroutine interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y,
   call rotate(ua, va, cos_rot, sin_rot)
   call rotate(ssh_x, ssh_y, cos_rot, sin_rot)
 
+  !There are some issues with the boundaries ssh gradient calculation in a finite domain. This is a temporary fix
+  if (ssh_x.ne.ssh_x) ssh_x=0.
+  if (ssh_y.ne.ssh_y) ssh_y=0.
+
   if (((((uo.ne.uo) .or. (vo.ne.vo)) .or. ((ui.ne.ui) .or. (vi.ne.vi))) .or. (((ua.ne.ua) .or. (va.ne.va)) .or. ((ssh_x.ne.ssh_x) .or.  (ssh_y.ne.ssh_y)))) .or. \
   (((sst.ne. sst) .or. (cn.ne.cn)) .or. (hi.ne. hi))) then
     write(stderrunit,*) 'diamonds, Error in interpolate: uo,vo,ui,vi',uo, vo, ui, vi
@@ -1963,8 +1967,6 @@ real function ddx_ssh(grd,i,j)
     dxp=0.5*(grd%dx(i+1,j)+grd%dx(i+1,j-1))
     dx0=0.5*(grd%dx(i,j)+grd%dx(i,j-1))
     ddx_ssh=2.*(grd%ssh(i+1,j)-grd%ssh(i,j))/(dx0+dxp)*grd%msk(i+1,j)*grd%msk(i,j)
-
-    if (ddx_ssh .ne. ddx_ssh)  ddx_ssh=0. !This makes the model not crash for finite domains. 
   end function ddx_ssh
 
   real function ddy_ssh(grd,i,j)
@@ -1976,7 +1978,6 @@ real function ddy_ssh(grd,i,j)
     dyp=0.5*(grd%dy(i,j+1)+grd%dy(i-1,j+1))
     dy0=0.5*(grd%dy(i,j)+grd%dy(i-1,j))
     ddy_ssh=2.*(grd%ssh(i,j+1)-grd%ssh(i,j))/(dy0+dyp)*grd%msk(i,j+1)*grd%msk(i,j)
-    if (ddy_ssh .ne. ddy_ssh)  ddy_ssh=0.  !This makes the model not crash for finite domains. 
   end function ddy_ssh
 
   subroutine rotate(u, v, cos_rot, sin_rot)
@@ -2065,7 +2066,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   end if
   lbudget=.false.
   if (bergs%verbose_hrs>0) then
-     if (mod(24*iday+ihr,bergs%verbose_hrs).eq.0) lbudget=budget
+     !if (mod(24*iday+ihr,bergs%verbose_hrs).eq.0) lbudget=budget
+     if (mod(24*iday+ihr+(imin/60.),float(bergs%verbose_hrs)).eq.0) lbudget=budget  !Added minutes, so that it does not repeat when smaller time steps are used.:q
   end if
   if (mpp_pe()==mpp_root_pe().and.lverbose) write(*,'(a,3i5,a,3i5,a,i5,f8.3)') &
        'diamonds: y,m,d=',iyr, imon, iday,' h,m,s=', ihr, imin, isec, &
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 97501cd..e7c1e9b 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -2647,8 +2647,10 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
     call mpp_sum(number_of_bonds_all_pe)
 
     bergs%nbonds=number_of_bonds_all_pe !Total number of bonds across all pe's
-    if (number_of_bonds .gt. 0) then
-      write(stderrunit,*) "Bonds on PE:",number_of_bonds, "Total bonds", number_of_bonds_all_PE, "on PE number:",  mpp_pe()
+    if (debug) then 
+      if (number_of_bonds .gt. 0) then
+        write(stderrunit,*) "Bonds on PE:",number_of_bonds, "Total bonds", number_of_bonds_all_PE, "on PE number:",  mpp_pe()
+      endif
     endif
 
     if (quality_check) then
@@ -2667,7 +2669,9 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
         endif
       endif
       if ((num_unmatched_bonds_all_pe == 0)  .and. (num_unassosiated_bond_pairs_all_pe == 0)) then
-        if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') 'diamonds: All iceberg bonds are connected and working well.'
+        if (mpp_pe().eq.mpp_root_pe()) then
+                write(stderrunit,*)  "Total number of bonds is: ", number_of_bonds_all_PE, "All iceberg bonds are connected and working well"
+        endif
         check_bond_quality=.true.
       else
         if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') 'diamonds: Warning, Broken Bonds! '

From 0b045915f79927268a8c0005b262e480cd85e4d1 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Fri, 29 Jul 2016 11:58:45 -0400
Subject: [PATCH 139/361] Added run-time parameter use_old_spreading

- use_old_spreading=.true. recovers the original implementation
  of spreading which essentially treats the icebergs as one cell wide.
---
 icebergs.F90           | 51 +++++++++++++++++++++++++-----------------
 icebergs_framework.F90 |  5 ++++-
 2 files changed, 34 insertions(+), 22 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 19a8fab..88673c6 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1128,7 +1128,8 @@ subroutine thermodynamics(bergs)
             endif
             !print *, 'orientation: ', (180/pi)*orientation, this%iceberg_num
           endif
-          call spread_mass_across_ocean_cells(grd, i, j, this%xi, this%yj, Mnew, nMbits, this%mass_scaling, this%length*this%width, bergs%hexagonal_icebergs,orientation)
+          call spread_mass_across_ocean_cells(grd, i, j, this%xi, this%yj, Mnew, nMbits, this%mass_scaling, &
+                      this%length*this%width, bergs%use_old_spreading, bergs%hexagonal_icebergs,orientation)
         endif
       endif
     
@@ -1208,12 +1209,13 @@ real function find_orientation_using_iceberg_bonds(grd,berg,initial_orientation)
 
 end function find_orientation_using_iceberg_bonds
 
-subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling, Area, hexagonal_icebergs,theta_in)
+subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling, Area, use_old_spreading, hexagonal_icebergs, theta_in)
   ! Arguments
   type(icebergs_gridded), pointer :: grd
   integer, intent(in) :: i, j
   real, intent(in) :: x, y, Mberg, Mbits, scaling, Area
   logical, intent(in) :: hexagonal_icebergs
+  logical, intent(in) :: use_old_spreading
   real, optional, intent(in) :: theta_in
   ! Local variables
   real :: xL, xC, xR, yD, yC, yU, Mass, L
@@ -1253,20 +1255,22 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
       L=1.
     endif
   
-    !Old version before icebergs were given size L
-    !xL=min(0.5, max(0., 0.5-x))
-    !xR=min(0.5, max(0., x-0.5))
-    !xC=max(0., 1.-(xL+xR))
-    !yD=min(0.5, max(0., 0.5-y))
-    !yU=min(0.5, max(0., y-0.5))
-    !yC=max(0., 1.-(yD+yU))
-  
-    xL=min(0.5, max(0., 0.5-(x/L)))
-    xR=min(0.5, max(0., (x/L)+(0.5-(1/L) )))
-    xC=max(0., 1.-(xL+xR))
-    yD=min(0.5, max(0., 0.5-(y/L)))
-    yU=min(0.5, max(0., (y/L)+(0.5-(1/L) )))
-    yC=max(0., 1.-(yD+yU))
+    if (use_old_spreading) then
+      !Old version before icebergs were given size L
+      xL=min(0.5, max(0., 0.5-x))
+      xR=min(0.5, max(0., x-0.5))
+      xC=max(0., 1.-(xL+xR))
+      yD=min(0.5, max(0., 0.5-y))
+      yU=min(0.5, max(0., y-0.5))
+      yC=max(0., 1.-(yD+yU))
+    else
+      xL=min(0.5, max(0., 0.5-(x/L)))
+      xR=min(0.5, max(0., (x/L)+(0.5-(1/L) )))
+      xC=max(0., 1.-(xL+xR))
+      yD=min(0.5, max(0., 0.5-(y/L)))
+      yU=min(0.5, max(0., (y/L)+(0.5-(1/L) )))
+      yC=max(0., 1.-(yD+yU))
+    endif
 
     yDxL=yD*xL*grd%msk(i-1,j-1)
     yDxC=yD*xC*grd%msk(i  ,j-1)
@@ -2989,7 +2993,8 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
         !Note, the mass scaling is equal to 1 (rather than 0.25 as in RK), since
         !this is only called once in Verlet stepping.
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 1.0*berg%mass_scaling, berg%length*berg%width ,bergs%hexagonal_icebergs )
+          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 1.0*berg%mass_scaling,berg%length*berg%width, &
+                         bergs%use_old_spreading, bergs%hexagonal_icebergs)
 
         ! Calling the acceleration   (note that the velocity is converted to u_star inside the accel script)
         call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn, ayn, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
@@ -3105,7 +3110,8 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         if ((berg%lat>89.) .and. (bergs%grd%grid_is_latlon)) on_tangential_plane=.true.
         i1=i;j1=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, bergs%hexagonal_icebergs)
+          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, &
+                         bergs%use_old_spreading, bergs%hexagonal_icebergs)
 
         ! Loading past accelerations - Alon
         axn=berg%axn; ayn=berg%ayn !Alon
@@ -3143,7 +3149,8 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         call adjust_index_and_ground(grd, lon2, lat2, uvel2, vvel2, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)
         i2=i; j2=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling, berg%length*berg%width , bergs%hexagonal_icebergs)
+          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, &
+                         bergs%use_old_spreading, bergs%hexagonal_icebergs)
         ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon2,lat2,x2,y2)
         if (.not.error_flag) then
           if (debug .and. .not. is_point_in_cell(bergs%grd, lon2, lat2, i, j)) error_flag=.true.
@@ -3199,7 +3206,8 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         call adjust_index_and_ground(grd, lon3, lat3, uvel3, vvel3, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)
         i3=i; j3=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, bergs%hexagonal_icebergs)
+          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, &
+                         bergs%use_old_spreading, bergs%hexagonal_icebergs)
         ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon3,lat3,x3,y3)
         if (.not.error_flag) then
           if (debug .and. .not. is_point_in_cell(bergs%grd, lon3, lat3, i, j)) error_flag=.true.
@@ -3330,7 +3338,8 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         i=i1;j=j1;xi=berg%xi;yj=berg%yj
         call adjust_index_and_ground(grd, lonn, latn, uveln, vveln, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, bergs%hexagonal_icebergs)
+          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, &
+                         bergs%use_old_spreading, bergs%hexagonal_icebergs)
   
         if (.not.error_flag) then
           if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j)) error_flag=.true.
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index bfdc391..2b08563 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -229,6 +229,7 @@ module ice_bergs_framework
   logical :: use_new_predictive_corrective =.False.  !Flag to use Bob's predictive corrective iceberg scheme- Added by Alon 
   logical :: interactive_icebergs_on=.false.  !Turn on/off interactions between icebergs  - Added by Alon 
   logical :: critical_interaction_damping_on=.true.  !Sets the damping on relative iceberg velocity to critical value - Added by Alon 
+  logical :: use_old_spreading=.true. ! If true, spreads iceberg mass as if the berg is one grid cell wide
   real :: speed_limit=0. ! CFL speed limit for a berg [m/s]
   real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
   type(buffer), pointer :: obuffer_n=>null(), ibuffer_n=>null()
@@ -348,6 +349,7 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: critical_interaction_damping_on=.true.  !Sets the damping on relative iceberg velocity to critical value - Added by Alon 
 logical :: do_unit_tests=.false. ! Conduct some unit tests
 logical :: input_freq_distribution=.false. ! Alon: flag to show if input distribution is freq or mass dist (=1 if input is a freq dist, =0 to use an input mass dist)
+logical :: use_old_spreading=.true. ! If true, spreads iceberg mass as if the berg is one grid cell wide
 real, dimension(nclasses) :: initial_mass=(/8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11/) ! Mass thresholds between iceberg classes (kg)
 real, dimension(nclasses) :: distribution=(/0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02/) ! Fraction of calving to apply to this class (non-dim) , 
 real, dimension(nclasses) :: mass_scaling=(/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) ! Ratio between effective and real iceberg mass (non-dim)
@@ -358,7 +360,7 @@ subroutine ice_bergs_framework_init(bergs, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, halo_debugging, hexagonal_icebergs, &
          time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, interactive_icebergs_on, critical_interaction_damping_on, &
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution, force_all_pes_traj, &
-         allow_bergs_to_roll,set_melt_rates_to_zero,lat_ref,initial_orientation,rotate_icebergs_for_mass_spreading,grid_is_latlon,Lx,use_f_plane
+         allow_bergs_to_roll,set_melt_rates_to_zero,lat_ref,initial_orientation,rotate_icebergs_for_mass_spreading,grid_is_latlon,Lx,use_f_plane, use_old_spreading
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -732,6 +734,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%use_new_predictive_corrective=use_new_predictive_corrective  !Alon
   bergs%grounding_fraction=grounding_fraction
   bergs%add_weight_to_ocean=add_weight_to_ocean
+  bergs%use_old_spreading=use_old_spreading
   allocate( bergs%initial_mass(nclasses) ); bergs%initial_mass(:)=initial_mass(:)
   allocate( bergs%distribution(nclasses) ); bergs%distribution(:)=distribution(:)
   allocate( bergs%mass_scaling(nclasses) ); bergs%mass_scaling(:)=mass_scaling(:)

From 04b480198bc1ecfa2a5fc8fae1574ceaf594c2cb Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Mon, 1 Aug 2016 17:46:25 -0400
Subject: [PATCH 140/361] 1) Static icebergs which have hexagonal packing now
 do not conserve mass at side boundaries. Excess mass which is in masked cells
 is discarded. This is only true for static icebergs. Dynamic icebergs still
 retain this excess mass.

2) A few unit tests have been added to test the hexagon code. These are not comprehensive, but are a start

3) A flag has been added to see if the grid is a regular cartesian grid. If it is a regular cartesian grid, then a more effitient method is used to find the position of an iceberg in a cell.

4) The tolorance values for the errors made while calculating the hexagonal mass spreading have been changed to 1.e-10, so that the code has to be more precise.
---
 icebergs.F90           | 188 +++++++++++++++++++++++++++++++++++------
 icebergs_framework.F90 |  19 ++++-
 icebergs_io.F90        |   1 +
 3 files changed, 178 insertions(+), 30 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 3258306..3696982 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -102,6 +102,8 @@ subroutine icebergs_init(bergs, &
              dt, Time, ice_lon, ice_lat, ice_wet, ice_dx, ice_dy, ice_area, &
              cos_rot, sin_rot, ocean_depth=ocean_depth, maskmap=maskmap, fractional_area=fractional_area)
 
+  call unit_testing()
+
   call mpp_clock_begin(bergs%clock_ior)
   call ice_bergs_io_init(bergs,io_layout)
   call read_restart_calving(bergs)  !This is moved to before restart_bergs (by Alon) so that generate icebergs can have the correct counter
@@ -134,6 +136,124 @@ subroutine icebergs_init(bergs, &
 end subroutine icebergs_init
 
 
+! ##############################################################################
+subroutine unit_testing()
+! Arguments
+
+call hexagon_test()
+
+end subroutine unit_testing
+
+
+subroutine hexagon_test()
+! Arguments
+real :: x0,y0  !Position of icebergs
+real :: H,theta,S !Apothen of iceberg and angle.
+real :: Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4 ! Areas of icebergs
+real :: tol
+logical :: fail_unit_test
+integer :: stderrunit
+  
+  ! Get the stderr unit number.
+  stderrunit = stderr()
+
+  fail_unit_test=.False.
+
+  tol=1.e-10
+  theta=0.0
+  H=1.
+  S=2.*H/sqrt(3.)
+
+  !Test 1: center at origin: Areas should be equal
+  x0=0.  ;  y0=0.
+  call Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
+  if (abs(Area_hex - ((3.*sqrt(3.)/2.)*(S*S)))>tol) then
+    call error_mesg('diamonds, hexagon unit testing:', 'Hexagon at origin has the wrong area!', WARNING)
+    if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'diamonds, hexagon areas =', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+    fail_unit_test=.True.
+  endif
+  if (((abs((Area_hex/4)-Area_Q1 )>tol) .or.  (abs((Area_hex/4)-Area_Q2 )>tol)) .or. ((abs((Area_hex/4)-Area_Q3 )>tol) .or. (abs((Area_hex/4)-Area_Q4 )>tol))) then
+  if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'diamonds, hexagon areas =', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+    call error_mesg('diamonds, hexagon unit testing:', 'Hexagon at origin divides into unqual parts!', WARNING)
+    fail_unit_test=.True.
+  endif
+
+  ! Test 2:  Hexagon split into two quadrants
+  !Test 2a: center on x>0 axis
+  x0=S  ;  y0=0.
+  call Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
+  if (((abs((Area_hex/2)-Area_Q1 )>tol) .or.  (abs(0-Area_Q2 )>tol)) .or. ((abs(0-Area_Q3 )>tol) .or. (abs((Area_hex/2)-Area_Q4 )>tol))) then
+  if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'diamonds, hexagon areas =', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+    call error_mesg('diamonds, hexagon unit testing:', 'Hexagon split btw 1 and 4!', WARNING)
+    fail_unit_test=.True.
+  endif
+  !Test 2b: center on x<0 axis
+  x0=-S  ;  y0=0.
+  call Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
+  if (((abs((Area_hex/2)-Area_Q2 )>tol) .or.  (abs(0-Area_Q1 )>tol)) .or. ((abs(0-Area_Q4 )>tol) .or. (abs((Area_hex/2)-Area_Q3 )>tol))) then
+  if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'diamonds, hexagon areas =', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+    call error_mesg('diamonds, hexagon unit testing:', 'Hexagon split btw 2 and 3!', WARNING)
+    fail_unit_test=.True.
+  endif
+  !Test 2c: center on y>0 axis
+  x0=0.  ;  y0=H
+  call Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
+  if (((abs((Area_hex/2)-Area_Q1 )>tol) .or.  (abs(0-Area_Q3 )>tol)) .or. ((abs(0-Area_Q4 )>tol) .or. (abs((Area_hex/2)-Area_Q2 )>tol))) then
+  if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'diamonds, hexagon areas =', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+    call error_mesg('diamonds, hexagon unit testing:', 'Hexagon split btw 1 and 2!', WARNING)
+    fail_unit_test=.True.
+  endif
+  !Test 3d: center on y<0 axis
+  x0=0.  ;  y0=-H
+  call Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
+  if (((abs((Area_hex/2)-Area_Q3 )>tol) .or.  (abs(0-Area_Q1 )>tol)) .or. ((abs(0-Area_Q2 )>tol) .or. (abs((Area_hex/2)-Area_Q4 )>tol))) then
+  if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'diamonds, hexagon areas =', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+    call error_mesg('diamonds, hexagon unit testing:', 'Hexagon split btw 3 and 4!', WARNING)
+    fail_unit_test=.True.
+  endif
+  
+  ! Test 3:  Two corners of hex on the axis
+  !Test 3a: center on x>0 axis
+  x0=S/2.  ;  y0=0.
+  call Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
+  if (((abs((2.5*Area_hex/6.)-Area_Q1 )>tol) .or.  (abs((0.5*Area_hex/6.)-Area_Q2 )>tol)) .or. ((abs((0.5*Area_hex/6.)-Area_Q3 )>tol) .or. (abs((2.5*Area_hex/6.)-Area_Q4 )>tol))) then
+  if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'diamonds, hexagon areas =', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+    call error_mesg('diamonds, hexagon unit testing:', 'Hexagon split two coners of hex (x>0)!', WARNING)
+    fail_unit_test=.True.
+  endif
+  !Test 3b: center on x<0 axis
+  x0=-S/2.  ;  y0=0.
+  call Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
+  if (((abs((2.5*Area_hex/6.)-Area_Q2 )>tol) .or.  (abs((0.5*Area_hex/6.)-Area_Q1 )>tol)) .or. ((abs((0.5*Area_hex/6.)-Area_Q4 )>tol) .or. (abs((2.5*Area_hex/6.)-Area_Q3 )>tol))) then
+  if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'diamonds, hexagon areas =', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+    call error_mesg('diamonds, hexagon unit testing:', 'Hexagon split two coners of hex (x<0)!', WARNING)
+    fail_unit_test=.True.
+  endif
+  !Test 3c: center on y>0 axis
+  !x0=0.  ;  y0=H/2.
+  !call Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
+  !if (((abs((2.5*Area_hex/6.)-Area_Q1 )>tol) .or.  (abs((0.5*Area_hex/6.)-Area_Q3 )>tol)) .or. ((abs((0.5*Area_hex/6.)-Area_Q4 )>tol) .or. (abs((2.5*Area_hex/6.)-Area_Q2 )>tol))) then
+  !if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'diamonds, hexagon areas =', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+  !if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'diamonds, hexagon errors =', (abs((2.5*Area_hex/6.)-Area_Q1 )), (abs((0.5*Area_hex/6.)-Area_Q3 )),&
+  !  call error_mesg('diamonds, hexagon unit testing:', 'Hexagon split two coners of hex (y>0)!', WARNING)
+  !  fail_unit_test=.True.
+  !endif
+  !!Test 3d: center on y<0 axis
+  !x0=0.  ;  y0=-H/2.
+  !call Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
+  !if (((abs((2.5*Area_hex/6.)-Area_Q3 )>tol) .or.  (abs((0.5*Area_hex/6.)-Area_Q2 )>tol)) .or. ((abs((0.5*Area_hex/6.)-Area_Q1 )>tol) .or. (abs((2.5*Area_hex/6.)-Area_Q4 )>tol))) then
+  !if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'diamonds, hexagon areas =', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+  !if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'diamonds, hexagon errots =', (abs((2.5*Area_hex/6.)-Area_Q3 )), (abs((0.5*Area_hex/6.)-Area_Q2 )),&
+  !  call error_mesg('diamonds, hexagon unit testing:', 'Hexagon split two coners of hex (y<0)!', WARNING)
+  !  fail_unit_test=.True.
+  !endif
+
+
+  if (fail_unit_test) call error_mesg('diamonds, hexagon unit testing:', 'Hexagon unit testing does not pass!', FATAL)
+
+
+end subroutine hexagon_test
+
 ! ##############################################################################
 
 subroutine initialize_iceberg_bonds(bergs)
@@ -944,10 +1064,13 @@ subroutine thermodynamics(bergs)
 type(iceberg), pointer :: this, next
 real, parameter :: perday=1./86400.
 integer :: grdi, grdj
-real :: orientation
+real :: orientation, static_berg
 
   ! For convenience
   grd=>bergs%grd
+  
+  !Initializing static_berg
+  static_berg=0.
 
   !do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
   do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied  ! Thermodynamics of  halos now calculated, so that spread mass to ocean works correctly
@@ -1128,7 +1251,8 @@ subroutine thermodynamics(bergs)
             endif
             !print *, 'orientation: ', (180/pi)*orientation, this%iceberg_num
           endif
-          call spread_mass_across_ocean_cells(grd, i, j, this%xi, this%yj, Mnew, nMbits, this%mass_scaling, this%length*this%width, bergs%hexagonal_icebergs,orientation)
+          if (bergs%hexagonal_icebergs) static_berg=this%static_berg  !Change this to use_old_restart=false when this is merged in
+          call spread_mass_across_ocean_cells(grd, i, j, this%xi, this%yj, Mnew, nMbits, this%mass_scaling, this%length*this%width, bergs%hexagonal_icebergs,orientation,static_berg)
         endif
       endif
     
@@ -1208,13 +1332,14 @@ real function find_orientation_using_iceberg_bonds(grd,berg,initial_orientation)
 
 end function find_orientation_using_iceberg_bonds
 
-subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling, Area, hexagonal_icebergs,theta_in)
+subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling, Area, hexagonal_icebergs,theta_in,static_berg)
   ! Arguments
   type(icebergs_gridded), pointer :: grd
   integer, intent(in) :: i, j
   real, intent(in) :: x, y, Mberg, Mbits, scaling, Area
   logical, intent(in) :: hexagonal_icebergs
   real, optional, intent(in) :: theta_in
+  real, optional, intent(in) :: static_berg
   ! Local variables
   real :: xL, xC, xR, yD, yC, yU, Mass, L
   real :: yDxL, yDxC, yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR
@@ -1222,6 +1347,7 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
   real :: Area_Q1,Area_Q2 , Area_Q3,Area_Q4, Area_hex
   real :: fraction_used
   real :: theta
+  real :: tol
   real, parameter :: rho_seawater=1035.
   integer :: stderrunit
   logical :: debug
@@ -1230,6 +1356,7 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
   stderrunit = stderr()
 
   theta=0.0
+  tol=1.e-10
   !This is here because the findinding orientaion scheme is not coded when spread mass to ocean is called directly from the time stepping scheme.
   if (present(theta_in)) then
     theta=theta_in
@@ -1304,7 +1431,7 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
 
     call Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
     
-    if (min(min(Area_Q1,Area_Q2),min(Area_Q3, Area_Q4)) <-0.001) then
+    if (min(min(Area_Q1,Area_Q2),min(Area_Q3, Area_Q4)) <-tol) then
       call error_mesg('diamonds, hexagonal spreading', 'Intersection with hexagons should not be negative!!!', WARNING)
       write(stderrunit,*) 'diamonds, yU,yC,yD', Area_Q1, Area_Q2, Area_Q3, Area_Q4
     endif
@@ -1343,7 +1470,7 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
     endif
 
       !Double check that all the mass is being used.
-      if ((abs(yCxC-(1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )))>0.001) .and. (mpp_pe().eq.5)) then
+      if ((abs(yCxC-(1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )))>tol) .and. (mpp_pe().eq. mpp_root_pe())) then
         !call error_mesg('diamonds, hexagonal spreading', 'All the mass is not being used!!!', WARNING)
         write(stderrunit,*) 'diamonds, hexagonal, H,x0,y0', H, x0 , y0
         write(stderrunit,*) 'diamonds, hexagonal, Areas',(Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
@@ -1359,6 +1486,11 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
   fraction_used= ((yDxL*grd%msk(i-1,j-1)) + (yDxC*grd%msk(i  ,j-1))  +(yDxR*grd%msk(i+1,j-1)) +(yCxL*grd%msk(i-1,j  )) +  (yCxR*grd%msk(i+1,j  ))&
                  +(yUxL*grd%msk(i-1,j+1)) +(yUxC*grd%msk(i  ,j+1))   +(yUxR*grd%msk(i+1,j+1)) + (yCxC**grd%msk(i,j)))
 
+  if ((hexagonal_icebergs) .and.  (static_berg .eq. 1)) then
+    !Change this to use_old_restart=false when this is merged in
+    fraction_used=1.  !Static icebergs do not share their mass with the boundary (this to initialize icebergs in regular arrangements against boundaries)
+  endif
+
   grd%mass_on_ocean(i,j,1)=grd%mass_on_ocean(i,j,1)+(yDxL*Mass/fraction_used)
   grd%mass_on_ocean(i,j,2)=grd%mass_on_ocean(i,j,2)+(yDxC*Mass/fraction_used)
   grd%mass_on_ocean(i,j,3)=grd%mass_on_ocean(i,j,3)+(yDxR*Mass/fraction_used)
@@ -1369,6 +1501,7 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
   grd%mass_on_ocean(i,j,8)=grd%mass_on_ocean(i,j,8)+(yUxC*Mass/fraction_used)
   grd%mass_on_ocean(i,j,9)=grd%mass_on_ocean(i,j,9)+(yUxR*Mass/fraction_used)
 
+
 end subroutine spread_mass_across_ocean_cells
 
 
@@ -1407,7 +1540,7 @@ logical function point_is_on_the_line(Ax,Ay,Bx,By,qx,qy)
   ! Arguments
   real, intent(in) :: Ax,Ay,Bx,By,qx,qy
   real :: tol, dxc,dyc,dxl,dyl,cross
-    tol=0.00000000000000;
+    tol=1.e-12;
     dxc = qx - Ax;
     dyc = qy - Ay;
     dxl = Bx - Ax;
@@ -1593,22 +1726,14 @@ subroutine Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy,Area_triangle,
   real :: Area_Upper, Area_Lower, Area_Right, Area_Left
   real :: px, py , qx , qy 
   real :: Area_key_quadrant,Error
+  real :: tol
   integer :: Key_quadrant
   integer ::sig_fig
   integer :: stderrunit
 
   ! Get the stderr unit number
   stderrunit = stderr()
-
-  !Round of numbers before proceeding further.
-  !sig_fig=12; !Significan figures
-  !Ax=roundoff(Ax0,sig_fig)
-  !Ay=roundoff(Ay0,sig_fig)
-  !Bx=roundoff(Bx0,sig_fig)
-  !By=roundoff(By0,sig_fig)
-  !Cx=roundoff(Cx0,sig_fig)
-  !Cy=roundoff(Cy0,sig_fig)
- 
+  tol=1.e-10
 
   Area_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
   
@@ -1703,7 +1828,7 @@ subroutine Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy,Area_triangle,
 
 
   Error=abs(Area_Q1+Area_Q2+Area_Q3+Area_Q4-Area_triangle)
-  if (Error>0.01) then
+  if (Error>tol) then
     call error_mesg('diamonds, triangle spreading', 'Triangle not evaluated accurately!!', WARNING)
     !if (mpp_pe().eq.mpp_root_pe()) then
     if (mpp_pe().eq. 0) then
@@ -1751,10 +1876,12 @@ subroutine Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex ,Area_Q
   real :: T56_Area, T56_Q1, T56_Q2, T56_Q3, T56_Q4
   real :: T61_Area, T61_Q1, T61_Q2, T61_Q3, T61_Q4
   real :: S, exact_hex_area, Error
+  real :: tol
   integer :: stderrunit
 
   ! Get the stderr unit number
   stderrunit = stderr()
+  tol=1.e-10
 
   !Length of side of Hexagon
   S=(2/sqrt(3.))*H
@@ -1796,7 +1923,7 @@ subroutine Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex ,Area_Q
   Area_Q4=max(Area_Q4,0.);
 
   Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
-  if ((abs(Error)>0.01))then
+  if ((abs(Error)>tol))then
     if (mpp_pe().eq.mpp_root_pe()) then
       call error_mesg('diamonds, hexagonal spreading', 'Hexagon error is large!!', WARNING)
       write(stderrunit,*) 'diamonds, hex error, H,x0,y0, Error', H, x0 , y0, Error
@@ -1811,7 +1938,7 @@ subroutine Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex ,Area_Q
   endif
 
   exact_hex_area=((3.*sqrt(3.)/2)*(S*S))
-  if (abs(Area_hex-exact_hex_area)>0.01) then
+  if (abs(Area_hex-exact_hex_area)>tol) then
     call error_mesg('diamonds, hexagonal spreading', 'Hexagon not evaluated accurately!!', WARNING)
     if (mpp_pe().eq.mpp_root_pe()) then
       write(stderrunit,*) 'diamonds, hex calculations, H,x0,y0', H, x0 , y0
@@ -1839,9 +1966,6 @@ subroutine Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex ,Area_Q
 end subroutine Hexagon_into_quadrants_using_triangles
 
 
-
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
 subroutine interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, cn, hi)
 ! Arguments
 type(icebergs_gridded), pointer :: grd
@@ -2648,6 +2772,7 @@ subroutine icebergs_incr_mass(bergs, mass, within_iceberg_model, Time)
     grd%tmp(:,:)=0.; grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec)=mass
     call grd_chksum3(grd, grd%mass_on_ocean, 'mass bergs (incr)')
     call grd_chksum2(grd, grd%tmp, 'mass out (incr)')
+
   endif
 
   if (.not.(within_model)) then
@@ -2936,6 +3061,7 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
 real :: xdot3, ydot3
 real :: xdotn, ydotn
 real :: dt, dt_2, dt_6, dydl
+real :: static_berg
 logical :: bounced, on_tangential_plane, error_flag
 integer :: i, j 
 integer :: stderrunit
@@ -2958,6 +3084,10 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
     dt=bergs%dt
     dt_2=0.5*dt
 
+    static_berg=0.  !Initializing
+    if (bergs%hexagonal_icebergs) static_berg=berg%static_berg  !Change this to use_old_restart=false when this is merged in
+    
+
         lonn = berg%lon ;   latn = berg%lat
         axn  = berg%axn ;   ayn  = berg%ayn
         bxn=   berg%bxn ;   byn  = berg%byn
@@ -2972,7 +3102,7 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
         !Note, the mass scaling is equal to 1 (rather than 0.25 as in RK), since
         !this is only called once in Verlet stepping.
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 1.0*berg%mass_scaling, berg%length*berg%width ,bergs%hexagonal_icebergs )
+          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 1.0*berg%mass_scaling, berg%length*berg%width ,bergs%hexagonal_icebergs,static_berg )
 
         ! Calling the acceleration   (note that the velocity is converted to u_star inside the accel script)
         call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn, ayn, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
@@ -3053,6 +3183,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
 real :: x4, xdot4, xddot4, y4, ydot4, yddot4, xddot4n, yddot4n
 real :: xn, xdotn, xddotn, yn, ydotn, yddotn, xddotnn, yddotnn
 real :: dt, dt_2, dt_6, dydl
+real :: static_berg
 integer :: i1,j1,i2,j2,i3,j3,i4,j4
 integer :: stderrunit
 logical :: bounced, on_tangential_plane, error_flag
@@ -3078,6 +3209,9 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
     dt=bergs%dt
     dt_2=0.5*dt
     dt_6=dt/6.
+    
+    static_berg=0.  !Initializing
+    if (bergs%hexagonal_icebergs) static_berg=berg%static_berg  !Change this to use_old_restart=false when this is merged in
 
         i=berg%ine
         j=berg%jne
@@ -3088,7 +3222,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         if ((berg%lat>89.) .and. (bergs%grd%grid_is_latlon)) on_tangential_plane=.true.
         i1=i;j1=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, bergs%hexagonal_icebergs)
+          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, bergs%hexagonal_icebergs,static_berg)
 
         ! Loading past accelerations - Alon
         axn=berg%axn; ayn=berg%ayn !Alon
@@ -3126,7 +3260,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         call adjust_index_and_ground(grd, lon2, lat2, uvel2, vvel2, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)
         i2=i; j2=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling, berg%length*berg%width , bergs%hexagonal_icebergs)
+          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling, berg%length*berg%width , bergs%hexagonal_icebergs,static_berg)
         ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon2,lat2,x2,y2)
         if (.not.error_flag) then
           if (debug .and. .not. is_point_in_cell(bergs%grd, lon2, lat2, i, j)) error_flag=.true.
@@ -3182,7 +3316,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         call adjust_index_and_ground(grd, lon3, lat3, uvel3, vvel3, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)
         i3=i; j3=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, bergs%hexagonal_icebergs)
+          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, bergs%hexagonal_icebergs,static_berg)
         ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon3,lat3,x3,y3)
         if (.not.error_flag) then
           if (debug .and. .not. is_point_in_cell(bergs%grd, lon3, lat3, i, j)) error_flag=.true.
@@ -3313,7 +3447,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         i=i1;j=j1;xi=berg%xi;yj=berg%yj
         call adjust_index_and_ground(grd, lonn, latn, uveln, vveln, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, bergs%hexagonal_icebergs)
+          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, bergs%hexagonal_icebergs,static_berg)
   
         if (.not.error_flag) then
           if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j)) error_flag=.true.
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index e7c1e9b..1aacc10 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -82,6 +82,7 @@ module ice_bergs_framework
   integer :: isg, ieg, jsg, jeg ! Indices of global domain
   integer :: my_pe, pe_N, pe_S, pe_E, pe_W ! MPI PE idenLx ! Length of domain, for periodic boundary condition (Ly to be adde later if needed)
   logical :: grid_is_latlon !Flag to say whether the coordinate is in lat lon degrees, or meters
+  logical :: grid_is_regular !Flag to say whether point in cell can be found assuming regular cartesian grid
   real :: Lx !Length of the domain in x direction
   real, dimension(:,:), pointer :: lon=>null() ! Longitude of cell corners
   real, dimension(:,:), pointer :: lat=>null() ! Latitude of cell corners
@@ -331,6 +332,7 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: Runge_not_Verlet=.True.  !True=Runge Kutta, False=Verlet.  - Added by Alon 
 logical :: use_f_plane=.False.  !Flag to use a f-plane for the rotation
 logical :: grid_is_latlon=.True.  !True means that the grid is specified in lat lon, and uses to radius of the earth to convert to distance
+logical :: grid_is_regular !Flag to say whether point in cell can be found assuming regular cartesian grid
 logical :: rotate_icebergs_for_mass_spreading=.True.  !Flag allows icebergs to rotate for spreading their mass (in hexagonal spreading mode)
 logical :: set_melt_rates_to_zero=.False.  !Sets all melt rates to zero, for testing purposes (thermodynamics routine is still run)
 logical :: allow_bergs_to_roll=.True. !Allows icebergs to roll over when rolling conditions are met
@@ -357,7 +359,7 @@ subroutine ice_bergs_framework_init(bergs, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, halo_debugging, hexagonal_icebergs, &
          time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, interactive_icebergs_on, critical_interaction_damping_on, &
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution, force_all_pes_traj, &
-         allow_bergs_to_roll,set_melt_rates_to_zero,lat_ref,initial_orientation,rotate_icebergs_for_mass_spreading,grid_is_latlon,Lx,use_f_plane
+         allow_bergs_to_roll,set_melt_rates_to_zero,lat_ref,initial_orientation,rotate_icebergs_for_mass_spreading,grid_is_regular,grid_is_latlon,Lx,use_f_plane
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -699,6 +701,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%grd%halo=halo
   bergs%grd%Lx=Lx
   bergs%grd%grid_is_latlon=grid_is_latlon  
+  bergs%grd%grid_is_regular=grid_is_regular 
   bergs%max_bonds=max_bonds
   bergs%rho_bergs=rho_bergs
   bergs%spring_coef=spring_coef
@@ -3382,7 +3385,7 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
 ! Local variables
 real :: x1,y1,x2,y2,x3,y3,x4,y4,xx,yy,fac
 integer :: stderrunit
-real :: Lx
+real :: Lx, dx,dy
 
   ! Get the stderr unit number
   stderrunit=stderr()
@@ -3412,7 +3415,16 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
     endif
   endif
 
-  if ((max(y1,y2,y3,y4)<89.999).or. (.not. grd%grid_is_latlon) ) then
+  !This part only works for a regular cartesian grid. For more complex grids, we
+  !should use calc_xiyj
+  if ((.not. grd%grid_is_latlon) .and. (grd%grid_is_regular))  then
+    dx=(grd%lon(i  ,j  )-grd%lon(i-1  ,j  ))
+    dy=(grd%lat(i  ,j  )-grd%lat(i  ,j-1  ))
+    x1=grd%lon(i  ,j  )-(dx/2)
+    y1=grd%lat(i  ,j  )-(dy/2)
+    xi=((x-x1)/dx)+0.5
+    yj=((y-y1)/dy)+0.5
+  elseif ((max(y1,y2,y3,y4)<89.999) .or.(.not. grd%grid_is_latlon)) then
     call calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x, y, xi, yj, Lx, explain=explain)
   else
     if (debug) write(stderrunit,*) 'diamonds, pos_within_cell: working in tangential plane!'
@@ -3490,6 +3502,7 @@ subroutine calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x, y, xi, yj,Lx, explain)
   if (present(explain)) then
      if(explain) expl=.true.
   endif
+
   alpha=x2-x1
   delta=y2-y1
   beta=x4-x1
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 84d4ff7..2d014f6 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -896,6 +896,7 @@ subroutine read_restart_bergs(bergs,Time)
          localberg%first_bond=>null()
          if (really_debug) lres=is_point_in_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne,explain=.true.)
          lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
+
         !call add_new_berg_to_list(bergs%first, localberg, quick=.true.)
         if (bergs%grd%area(localberg%ine,localberg%jne) .ne. 0)  then
          call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg)

From cc0138ecb5ef22468b0e03b7a800bc65f6053877 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Tue, 2 Aug 2016 12:03:36 -0400
Subject: [PATCH 141/361]  Not sure what has been changed here

---
 .icebergs.F90.swo      | Bin 20480 -> 0 bytes
 icebergs_framework.F90 |   2 +-
 2 files changed, 1 insertion(+), 1 deletion(-)
 delete mode 100644 .icebergs.F90.swo

diff --git a/.icebergs.F90.swo b/.icebergs.F90.swo
deleted file mode 100644
index ddfd693b44f034bd69bd80bd09917230ed1d2d10..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 1aacc10..4bf28e5 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -332,7 +332,7 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: Runge_not_Verlet=.True.  !True=Runge Kutta, False=Verlet.  - Added by Alon 
 logical :: use_f_plane=.False.  !Flag to use a f-plane for the rotation
 logical :: grid_is_latlon=.True.  !True means that the grid is specified in lat lon, and uses to radius of the earth to convert to distance
-logical :: grid_is_regular !Flag to say whether point in cell can be found assuming regular cartesian grid
+logical :: grid_is_regular=.True. !Flag to say whether point in cell can be found assuming regular cartesian grid
 logical :: rotate_icebergs_for_mass_spreading=.True.  !Flag allows icebergs to rotate for spreading their mass (in hexagonal spreading mode)
 logical :: set_melt_rates_to_zero=.False.  !Sets all melt rates to zero, for testing purposes (thermodynamics routine is still run)
 logical :: allow_bergs_to_roll=.True. !Allows icebergs to roll over when rolling conditions are met

From 203baad4e1aaa107eb4ec46a094b7b28a5f7e4f0 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Tue, 2 Aug 2016 13:59:13 -0400
Subject: [PATCH 142/361] Iceberg bond restart file will only be written when
 iceberg_bonds_on flag is true

---
 icebergs_io.F90 | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 84d4ff7..9dac66b 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -307,7 +307,6 @@ subroutine write_restart(bergs)
    if (bergs%iceberg_bonds_on) then
      check_bond_quality=.true.
      call count_bonds(bergs, nbonds,check_bond_quality)
-   endif
 
    allocate(first_berg_num(nbonds))
    allocate(other_berg_num(nbonds))
@@ -369,7 +368,7 @@ subroutine write_restart(bergs)
 
 
   call nullify_domain()
-
+   endif
 !#############################################################################################
 
   ! Write stored ice

From af0f7a48011373438fd1839596aea4ac2eedc446 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Tue, 2 Aug 2016 15:49:59 -0400
Subject: [PATCH 143/361] Option to find the orientation of an iceberg from its
 bonds has been added inside the Verlet Scheme. The orientaion code has not
 yet been properly tested. The code has been refactored slightly so that the
 orientation scheme can be called more easily.

---
 icebergs.F90           | 142 +++++++++++++++++++----------------------
 icebergs_framework.F90 |   5 +-
 2 files changed, 70 insertions(+), 77 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 5eaf16d..1c84f67 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1065,16 +1065,19 @@ subroutine thermodynamics(bergs)
 real, parameter :: perday=1./86400.
 integer :: grdi, grdj
 real :: orientation, static_berg
+integer :: extra_cell
 
   ! For convenience
   grd=>bergs%grd
   
   !Initializing static_berg
   static_berg=0.
+  extra_cell=0
+  if ((bergs%iceberg_bonds_on) .and. (bergs%rotate_icebergs_for_mass_spreading))  extra_cell=1
 
-  !do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
-  !do grdj = grd%jsd+2,grd%jed-1 ; do grdi = grd%isd+2,grd%ied-1  ! Thermodynamics of  halos now calculated, so that spread mass to ocean works correctly
-  do grdj = grd%jsc-1,grd%jec+1 ; do grdi = grd%isc-1,grd%iec+1  ! Thermodynamics of first halo row is calculated, so that spread mass to ocean works correctly
+  ! Thermodynamics of first halo row is calculated, so that spread mass to ocean works correctly
+  ! Thermodynamics of first second halo row is calculated if orientation is being found using bonds 
+  do grdj = grd%jsc-1-extra_cell,grd%jec+1+extra_cell ; do grdi = grd%isc-1-extra_cell,grd%iec+1+extra_cell  
     this=>bergs%list(grdi,grdj)%first
     do while(associated(this))
       if (debug) call check_position(grd, this, 'thermodynamics (top)')
@@ -1244,13 +1247,7 @@ subroutine thermodynamics(bergs)
           endif
 
           orientation=bergs%initial_orientation
-          if ((bergs%iceberg_bonds_on) .and. (bergs%rotate_icebergs_for_mass_spreading)) then
-            !Don't check orientation of the edges of halo,  since they can contain unassosiated bonds  (this is why halo width must be larger >= 2 to use bonds)    
-            if  (  ((this%ine .gt.  grd%isd) .and. (this%ine .lt. grd%ied)) .and. ((this%jne .ge.  grd%jsd) .and. (this%jne .le. grd%jed) ) ) then  
-              orientation=find_orientation_using_iceberg_bonds(grd,this,bergs%initial_orientation)
-            endif
-            !print *, 'orientation: ', (180/pi)*orientation, this%iceberg_num
-          endif
+          if ((bergs%iceberg_bonds_on) .and. (bergs%rotate_icebergs_for_mass_spreading)) call find_orientation_using_iceberg_bonds(grd,this,orientation)
           if (bergs%hexagonal_icebergs) static_berg=this%static_berg  !Change this to use_old_restart=false when this is merged in
           call spread_mass_across_ocean_cells(grd, i, j, this%xi, this%yj, Mnew, nMbits, this%mass_scaling, &
                       this%length*this%width, bergs%use_old_spreading, bergs%hexagonal_icebergs,orientation,static_berg)
@@ -1264,10 +1261,10 @@ subroutine thermodynamics(bergs)
 end subroutine thermodynamics
 
 
-real function find_orientation_using_iceberg_bonds(grd,berg,initial_orientation)
+subroutine find_orientation_using_iceberg_bonds(grd,berg,orientation)
   ! Arguments
   type(iceberg), pointer :: berg
-  real, intent(in) :: initial_orientation 
+  real, intent(inout) :: orientation 
   type(icebergs_gridded), pointer :: grd
   type(iceberg), pointer :: other_berg
   type(bond), pointer :: current_bond
@@ -1275,72 +1272,67 @@ real function find_orientation_using_iceberg_bonds(grd,berg,initial_orientation)
   real :: r_dist_x, r_dist_y 
   real :: lat_ref, dx_dlon, dy_dlat
   real :: theta, bond_count, Average_angle
-  logical  :: grid_is_latlon
     
-  grid_is_latlon=grd%grid_is_latlon
   bond_count=0.
   Average_angle=0.
-  current_bond=>berg%first_bond
-  lat1=berg%lat
-  lon1=berg%lon
-  !print *, 'Looking for orientation: '
-  do while (associated(current_bond)) ! loop over all bonds
-    other_berg=>current_bond%other_berg
-    if (.not. associated(other_berg)) then !good place for debugging 
-      !One valid option: current iceberg is on the edge of halo, with other berg on the next pe (not influencing mass spreading)
-        !print *, 'Iceberg bond details:',berg%iceberg_num, current_bond%other_berg_num,berg%halo_berg, mpp_pe()
-        !print *, 'Iceberg bond details2:',berg%ine, berg%jne, current_bond%other_berg_ine, current_bond%other_berg_jne
-        !print *, 'Iceberg isd,ied,jsd,jed:',grd%isd, grd%ied, grd%jsd, grd%jed
-        !print *, 'Iceberg isc,iec,jsc,jec:',grd%isc, grd%iec, grd%jsc, grd%jec
-        !call error_mesg('diamonds,calculating orientation', 'Looking at bond interactions of unassosiated berg!' ,FATAL)
-      !endif
-    else
-      lat2=other_berg%lat
-      lon2=other_berg%lon
-
-      dlat=lat2-lat1
-      dlon=lon2-lon1
-      
-      lat_ref=0.5*(lat1+lat2)
-      call convert_from_grid_to_meters(lat_ref,grid_is_latlon,dx_dlon,dy_dlat)
-      r_dist_x=dlon*dx_dlon
-      r_dist_y=dlat*dy_dlat
-      !print *, 'r_dist_x,r_dist_y: ', r_dist_x,r_dist_y
-
-      if (r_dist_x .eq. 0.) then
-        angle=pi/2.
+  !Don't check orientation of the edges of halo,  since they can contain unassosiated bonds  (this is why halo width must be larger >= 2 to use bonds)    
+  if  (  ((berg%ine .gt.  grd%isd) .and. (berg%ine .lt. grd%ied)) .and. ((berg%jne .ge.  grd%jsd) .and. (berg%jne .le. grd%jed) ) ) then  
+    current_bond=>berg%first_bond
+    lat1=berg%lat
+    lon1=berg%lon
+    do while (associated(current_bond)) ! loop over all bonds
+      other_berg=>current_bond%other_berg
+      if (.not. associated(other_berg)) then !good place for debugging 
+        !One valid option: current iceberg is on the edge of halo, with other berg on the next pe (not influencing mass spreading)
+          !print *, 'Iceberg bond details:',berg%iceberg_num, current_bond%other_berg_num,berg%halo_berg, mpp_pe()
+          !print *, 'Iceberg bond details2:',berg%ine, berg%jne, current_bond%other_berg_ine, current_bond%other_berg_jne
+          !print *, 'Iceberg isd,ied,jsd,jed:',grd%isd, grd%ied, grd%jsd, grd%jed
+          !print *, 'Iceberg isc,iec,jsc,jec:',grd%isc, grd%iec, grd%jsc, grd%jec
+          !call error_mesg('diamonds,calculating orientation', 'Looking at bond interactions of unassosiated berg!' ,FATAL)
+        !endif
       else
-        angle=atan(r_dist_y/r_dist_x)
-        angle= ((pi/2.)  - (initial_orientation*(pi/180.)))  - angle
-        !print *, 'angle: ', angle*(180/pi), initial_orientation
-        angle=modulo(angle ,pi/3.)
+        lat2=other_berg%lat
+        lon2=other_berg%lon
+
+        dlat=lat2-lat1
+        dlon=lon2-lon1
+        
+        lat_ref=0.5*(lat1+lat2)
+        call convert_from_grid_to_meters(lat_ref,grd%grid_is_latlon,dx_dlon,dy_dlat)
+        r_dist_x=dlon*dx_dlon
+        r_dist_y=dlat*dy_dlat
+
+        if (r_dist_x .eq. 0.) then
+          angle=pi/2.
+        else
+          angle=atan(r_dist_y/r_dist_x)
+          angle= ((pi/2.)  - (orientation*(pi/180.)))  - angle
+          !print *, 'angle: ', angle*(180/pi), initial_orientation
+          angle=modulo(angle ,pi/3.)
+        endif
+        bond_count=bond_count+1.
+        Average_angle=Average_angle+angle
       endif
-      !print *, 'angle2: ', angle*(180/pi)
-      bond_count=bond_count+1.
-      Average_angle=Average_angle+angle
+      current_bond=>current_bond%next_bond
+    enddo  !End loop over bonds
+    if (bond_count.gt.0) then
+      Average_angle =Average_angle/bond_count
+    else
+      Average_angle =0.
     endif
-    current_bond=>current_bond%next_bond
-  enddo  !End loop over bonds
-  if (bond_count.gt.0) then
-    Average_angle =Average_angle/bond_count
-  else
-    Average_angle =0.
+    orientation=modulo(Average_angle ,pi/3.)
   endif
-    !print *, 'Average angle', Average_angle*(180/pi), bond_count
-    find_orientation_using_iceberg_bonds=modulo(Average_angle ,pi/3.)
-    !find_orientation_using_iceberg_bonds=modulo(angle ,pi/3.)
-    !print *, 'Finished looking: '
 
-end function find_orientation_using_iceberg_bonds
+end subroutine find_orientation_using_iceberg_bonds
 
-subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling, Area, use_old_spreading,hexagonal_icebergs,theta_in,static_berg)
+subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling, Area, use_old_spreading,hexagonal_icebergs,theta,static_berg)
   ! Arguments
   type(icebergs_gridded), pointer :: grd
   integer, intent(in) :: i, j
   real, intent(in) :: x, y, Mberg, Mbits, scaling, Area
   logical, intent(in) :: hexagonal_icebergs
   logical, intent(in) :: use_old_spreading
-  real, optional, intent(in) :: theta_in
+  real, intent(in) :: theta
   real, optional, intent(in) :: static_berg
   ! Local variables
   real :: xL, xC, xR, yD, yC, yU, Mass, L
@@ -1348,7 +1340,6 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
   real :: S, H, origin_x, origin_y, x0, y0
   real :: Area_Q1,Area_Q2 , Area_Q3,Area_Q4, Area_hex
   real :: fraction_used
-  real :: theta
   real :: tol
   real, parameter :: rho_seawater=1035.
   integer :: stderrunit
@@ -1357,12 +1348,7 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
   ! Get the stderr unit number
   stderrunit = stderr()
 
-  theta=0.0
   tol=1.e-10
-  !This is here because the findinding orientaion scheme is not coded when spread mass to ocean is called directly from the time stepping scheme.
-  if (present(theta_in)) then
-    theta=theta_in
-  endif
 
   Mass=(Mberg+Mbits)*scaling
   ! This line attempts to "clip" the weight felt by the ocean. The concept of
@@ -3082,7 +3068,7 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
 real :: xdot3, ydot3
 real :: xdotn, ydotn
 real :: dt, dt_2, dt_6, dydl
-real :: static_berg
+real :: static_berg, orientation
 logical :: bounced, on_tangential_plane, error_flag
 integer :: i, j 
 integer :: stderrunit
@@ -3106,6 +3092,8 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
     dt_2=0.5*dt
 
     static_berg=0.  !Initializing
+    orientation=bergs%initial_orientation
+    if ((bergs%iceberg_bonds_on) .and. (bergs%rotate_icebergs_for_mass_spreading)) call find_orientation_using_iceberg_bonds(grd,berg,orientation)
     if (bergs%hexagonal_icebergs) static_berg=berg%static_berg  !Change this to use_old_restart=false when this is merged in
     
 
@@ -3124,7 +3112,7 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
         !this is only called once in Verlet stepping.
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
           call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 1.0*berg%mass_scaling,berg%length*berg%width, &
-                         bergs%use_old_spreading, bergs%hexagonal_icebergs,static_berg )
+                         bergs%use_old_spreading, bergs%hexagonal_icebergs,orientation,static_berg )
 
         ! Calling the acceleration   (note that the velocity is converted to u_star inside the accel script)
         call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn, ayn, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
@@ -3205,7 +3193,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
 real :: x4, xdot4, xddot4, y4, ydot4, yddot4, xddot4n, yddot4n
 real :: xn, xdotn, xddotn, yn, ydotn, yddotn, xddotnn, yddotnn
 real :: dt, dt_2, dt_6, dydl
-real :: static_berg
+real :: static_berg,orientation
 integer :: i1,j1,i2,j2,i3,j3,i4,j4
 integer :: stderrunit
 logical :: bounced, on_tangential_plane, error_flag
@@ -3233,6 +3221,8 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
     dt_6=dt/6.
     
     static_berg=0.  !Initializing
+    orientation=bergs%initial_orientation
+    if ((bergs%iceberg_bonds_on) .and. (bergs%rotate_icebergs_for_mass_spreading)) call find_orientation_using_iceberg_bonds(grd,berg,orientation) !Not sure if this works with Runge Kutta
     if (bergs%hexagonal_icebergs) static_berg=berg%static_berg  !Change this to use_old_restart=false when this is merged in
 
         i=berg%ine
@@ -3245,7 +3235,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         i1=i;j1=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
           call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, &
-                         bergs%use_old_spreading, bergs%hexagonal_icebergs,static_berg )
+                         bergs%use_old_spreading, bergs%hexagonal_icebergs,orientation,static_berg )
 
         ! Loading past accelerations - Alon
         axn=berg%axn; ayn=berg%ayn !Alon
@@ -3284,7 +3274,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         i2=i; j2=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
           call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, &
-                         bergs%use_old_spreading, bergs%hexagonal_icebergs,static_berg )
+                         bergs%use_old_spreading, bergs%hexagonal_icebergs,orientation,static_berg )
         ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon2,lat2,x2,y2)
         if (.not.error_flag) then
           if (debug .and. .not. is_point_in_cell(bergs%grd, lon2, lat2, i, j)) error_flag=.true.
@@ -3341,7 +3331,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         i3=i; j3=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
           call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, &
-                         bergs%use_old_spreading, bergs%hexagonal_icebergs,static_berg )
+                         bergs%use_old_spreading, bergs%hexagonal_icebergs,orientation,static_berg )
         ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon3,lat3,x3,y3)
         if (.not.error_flag) then
           if (debug .and. .not. is_point_in_cell(bergs%grd, lon3, lat3, i, j)) error_flag=.true.
@@ -3473,7 +3463,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         call adjust_index_and_ground(grd, lonn, latn, uveln, vveln, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
           call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, &
-                         bergs%use_old_spreading, bergs%hexagonal_icebergs,static_berg )
+                         bergs%use_old_spreading, bergs%hexagonal_icebergs,orientation,static_berg )
   
         if (.not.error_flag) then
           if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j)) error_flag=.true.
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index ae749f7..d221651 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -671,7 +671,10 @@ subroutine ice_bergs_framework_init(bergs, &
      enddo
 endif 
 
-if ((halo .lt. 2) .and. (interactive_icebergs_on .or. iceberg_bonds_on) )   then
+if ((halo .lt. 3) .and. (rotate_icebergs_for_mass_spreading .and. iceberg_bonds_on) )   then
+    halo=3
+    call error_mesg('diamonds, framework', 'Setting iceberg halos =3, since halos must be >= 3 for rotating icebergs for mass spreading', WARNING) 
+elseif  ((halo .lt. 2) .and. (interactive_icebergs_on .or. iceberg_bonds_on) )   then
     halo=2
     call error_mesg('diamonds, framework', 'Setting iceberg halos =2, since halos must be >= 2 for interactions', WARNING) 
 endif

From 5377f0c376c6854b5b037f4fd9721aa54930be8f Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 3 Aug 2016 16:14:39 -0400
Subject: [PATCH 144/361] Fixed a bug in the routing which rotates the hexagons
 by a prescibed angle.

---
 icebergs.F90 | 16 ++++++----------
 1 file changed, 6 insertions(+), 10 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 1c84f67..8a97485 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1065,19 +1065,15 @@ subroutine thermodynamics(bergs)
 real, parameter :: perday=1./86400.
 integer :: grdi, grdj
 real :: orientation, static_berg
-integer :: extra_cell
 
   ! For convenience
   grd=>bergs%grd
   
   !Initializing static_berg
   static_berg=0.
-  extra_cell=0
-  if ((bergs%iceberg_bonds_on) .and. (bergs%rotate_icebergs_for_mass_spreading))  extra_cell=1
 
   ! Thermodynamics of first halo row is calculated, so that spread mass to ocean works correctly
-  ! Thermodynamics of first second halo row is calculated if orientation is being found using bonds 
-  do grdj = grd%jsc-1-extra_cell,grd%jec+1+extra_cell ; do grdi = grd%isc-1-extra_cell,grd%iec+1+extra_cell  
+  do grdj = grd%jsc-1,grd%jec+1 ; do grdi = grd%isc-1,grd%iec+1  
     this=>bergs%list(grdi,grdj)%first
     do while(associated(this))
       if (debug) call check_position(grd, this, 'thermodynamics (top)')
@@ -1253,7 +1249,6 @@ subroutine thermodynamics(bergs)
                       this%length*this%width, bergs%use_old_spreading, bergs%hexagonal_icebergs,orientation,static_berg)
         endif
       endif
-    
       this=>next
     enddo
   enddo ; enddo
@@ -1840,14 +1835,15 @@ subroutine rotate_and_translate(px,py,theta,x0,y0)
   ! Arguments
   real, intent(in) :: x0,y0,theta
   real, intent(inout) :: px,py
+  real :: px_temp,py_temp
 
   !Rotation
-  px = ( cos(theta*pi/180)*px) + (sin(theta*pi/180)*py)
-  py = (-sin(theta*pi/180)*px) + (cos(theta*pi/180)*py)
+  px_temp = ( cos(theta*pi/180)*px) + (sin(theta*pi/180)*py)
+  py_temp = (-sin(theta*pi/180)*px) + (cos(theta*pi/180)*py)
  
   !Translation
-  px= px + x0
-  py= py + y0
+  px= px_temp + x0
+  py= py_temp + y0
 end subroutine rotate_and_translate
 
 subroutine Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex ,Area_Q1, Area_Q2, Area_Q3, Area_Q4)

From cfa98aa42bf84ee196bf0678fa4dbbfde593654f Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Fri, 5 Aug 2016 16:43:35 -0400
Subject: [PATCH 145/361] 1) Added an option to override the iceberg velocitiy
 and set accelerations to zero. This is useful for testing the ocean model
 with fixed iceberg velocities

2) Added a gridded diagnostic of the average (mass weighted) iceberg velocity in a grid cell. This does not account for icebergs being mass spreading across grid cells.

3) Fixed a random bug which incorrectly set the sea ice velocity incorrecly.

3) Added an if statement that sets the sea ice drag force to zero when the sea ice thinckness is equal to one.
---
 icebergs.F90           | 57 +++++++++++++++++++++++++++++++++++++++---
 icebergs_framework.F90 | 26 +++++++++++++++++--
 2 files changed, 77 insertions(+), 6 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 8a97485..7fd3140 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -649,6 +649,13 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
   ! Interpolate gridded fields to berg     - Note: It should be possible to move this to evolve, so that it only needs to be called once. !!!!
   call interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, cn, hi)
 
+
+  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+  !Temporary for messing around
+  !ssh_x=0.
+  !ssh_y=0.
+  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
   if ((grd%grid_is_latlon) .and. (.not. bergs%use_f_plane)) then
      f_cori=(2.*omega)*sin(pi_180*lat)
   else
@@ -695,7 +702,11 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
   ! Weighted drag coefficients
   c_ocn=rho_seawater/M*(0.5*Cd_wv*W*(D_hi)+Cd_wh*W*L)
   c_atm=rho_air     /M*(0.5*Cd_av*W*F     +Cd_ah*W*L)
-  c_ice=rho_ice     /M*(0.5*Cd_iv*W*hi              )
+  if (abs(hi).eq.0.) then
+    c_ice=0.
+  else
+    c_ice=rho_ice     /M*(0.5*Cd_iv*W*hi              )
+  endif
   if (abs(ui)+abs(vi).eq.0.) c_ice=0.
 
 !Turning drag off for testing - Alon
@@ -997,6 +1008,13 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
     call print_berg(stderrunit,berg,'diamonds, accel, large accel')
   endif
 
+  !Used for testing the ocean response to fixed iceberg motion.
+  if (bergs%override_iceberg_velocities) then
+    ax  = 0.0;  ay  = 0.0;
+    axn = 0.0;  ayn = 0.0;
+    bxn = 0.0;  byn = 0.0;
+  endif
+
   contains
 
   subroutine dump_locfld(grd,i0,j0,A,lbl)
@@ -1232,8 +1250,13 @@ subroutine thermodynamics(bergs)
       else ! Diagnose mass distribution on grid
         if (grd%id_virtual_area>0)&
              & grd%virtual_area(i,j)=grd%virtual_area(i,j)+(Wn*Ln+Abits)*this%mass_scaling ! m^2
-        if (grd%id_mass>0 .or. bergs%add_weight_to_ocean)&
+        if ((grd%id_mass>0 .or. bergs%add_weight_to_ocean) .or. ((grd%id_u_iceberg>0) .or. (grd%id_v_iceberg>0)))   &
              & grd%mass(i,j)=grd%mass(i,j)+Mnew/grd%area(i,j)*this%mass_scaling ! kg/m2
+        !Finding the average iceberg velocity in a grid cell (mass weighted)
+        if (grd%id_u_iceberg>0 )&
+             & grd%u_iceberg(i,j)=grd%u_iceberg(i,j)+((Mnew/grd%area(i,j)*this%mass_scaling)*this%uvel) ! kg/m2
+        if (grd%id_v_iceberg>0 )&
+             & grd%v_iceberg(i,j)=grd%v_iceberg(i,j)+((Mnew/grd%area(i,j)*this%mass_scaling)*this%vvel) ! kg/m2
         if (grd%id_bergy_mass>0 .or. bergs%add_weight_to_ocean)&
              & grd%bergy_mass(i,j)=grd%bergy_mass(i,j)+nMbits/grd%area(i,j)*this%mass_scaling ! kg/m2
         if (bergs%add_weight_to_ocean .and. .not. bergs%time_average_weight) then
@@ -1252,6 +1275,16 @@ subroutine thermodynamics(bergs)
       this=>next
     enddo
   enddo ; enddo
+  
+  !Scaling the gridded iceberg velocity by the iceberg mass
+  if ((grd%id_u_iceberg>0) .or. (grd%id_v_iceberg>0)) then
+    do j = grd%jsc,grd%jec ; do i = grd%isc,grd%iec  
+      if ((grd%id_u_iceberg>0 ).and. (grd%mass(i,j)>0.))  &
+        & grd%u_iceberg(i,j)=grd%u_iceberg(i,j)/grd%mass(i,j)
+      if ((grd%id_v_iceberg>0 ).and. (grd%mass(i,j)>0.))  &
+        & grd%v_iceberg(i,j)=grd%v_iceberg(i,j)/grd%mass(i,j)
+    enddo; enddo
+  endif
 
 end subroutine thermodynamics
 
@@ -2123,6 +2156,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 type(icebergs_gridded), pointer :: grd
 logical :: lerr, sample_traj, write_traj, lbudget, lverbose, check_bond_quality 
 real :: unused_calving, tmpsum, grdd_berg_mass, grdd_bergy_mass,grdd_spread_mass
+real :: grdd_u_iceberg, grdd_v_iceberg
 integer :: i, j, Iu, ju, iv, Jv, Iu_off, ju_off, iv_off, Jv_off
 real :: mask
 real, dimension(:,:), allocatable :: uC_tmp, vC_tmp
@@ -2154,6 +2188,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   grd%bergy_melt(:,:)=0.
   grd%bergy_mass(:,:)=0.
   grd%spread_mass(:,:)=0.
+  grd%u_iceberg(:,:)=0.
+  grd%v_iceberg(:,:)=0.
   grd%mass(:,:)=0.
 
   if (bergs%add_weight_to_ocean) grd%mass_on_ocean(:,:,:)=0.
@@ -2226,7 +2262,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
       grd%uo(I,J) = mask * 0.5*(uo(Iu,ju)+uo(Iu,ju+1))
       grd%ui(I,J) = mask * 0.5*(ui(Iu,ju)+ui(Iu,ju+1))
       grd%vo(I,J) = mask * 0.5*(vo(iv,Jv)+vo(iv+1,Jv))
-      grd%vi(I,J) = mask * 0.5*(vi(iv,Jv)+vo(iv+1,Jv))
+      grd%vi(I,J) = mask * 0.5*(vi(iv,Jv)+vi(iv+1,Jv)) !There was a bug here.
     enddo ; enddo
   else
     call error_mesg('diamonds, iceberg_run', 'Unrecognized value of stagger!', FATAL)
@@ -2411,6 +2447,10 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     lerr=send_data(grd%id_bergy_mass, grd%bergy_mass(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   if (grd%id_spread_mass>0) &
     lerr=send_data(grd%id_spread_mass, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_u_iceberg>0) &
+    lerr=send_data(grd%id_u_iceberg, grd%u_iceberg(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_v_iceberg>0) &
+    lerr=send_data(grd%id_v_iceberg, grd%v_iceberg(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   if (grd%id_mass>0) &
     lerr=send_data(grd%id_mass, grd%mass(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   if (grd%id_stored_ice>0) &
@@ -2483,6 +2523,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     bergs%icebergs_mass_end=sum_mass(bergs,justbergs=.true.)
     bergs%bergy_mass_end=sum_mass(bergs,justbits=.true.)
     bergs%spread_mass_end=sum_mass(bergs) !Not sure what this is
+    bergs%u_iceberg_end=sum_mass(bergs) !Not sure what this is
+    bergs%v_iceberg_end=sum_mass(bergs) !Not sure what this is
     bergs%floating_heat_end=sum_heat(bergs)
     grd%tmpc(:,:)=0.;
     call mpp_clock_end(bergs%clock); call mpp_clock_end(bergs%clock_dia) ! To enable calling of public s/r
@@ -2496,6 +2538,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     call mpp_sum(bergs%icebergs_mass_end)
     call mpp_sum(bergs%bergy_mass_end)
     call mpp_sum(bergs%spread_mass_end)
+    call mpp_sum(bergs%u_iceberg_end)
+    call mpp_sum(bergs%v_iceberg_end)
     call mpp_sum(bergs%floating_heat_end)
     call mpp_sum(bergs%returned_mass_on_ocean)
     call mpp_sum(bergs%nbergs_end)
@@ -2973,7 +3017,6 @@ subroutine evolve_icebergs(bergs)
   do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
     berg=>bergs%list(grdi,grdj)%first
     do while (associated(berg)) ! loop over all bergs
-
       if (berg%static_berg .lt. 0.5) then  !Only allow non-static icebergs to evolve
  
         !Checking it everything is ok:
@@ -3002,6 +3045,12 @@ subroutine evolve_icebergs(bergs)
             call verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
           endif 
 
+          !Used for testing the ocean response to fixed iceberg motion.
+          if (bergs%override_iceberg_velocities) then
+            uveln  = bergs%u_override
+            vveln  = bergs%v_override
+          endif
+
         ! Saving all the iceberg variables.
         berg%axn=axn 
         berg%ayn=ayn 
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index d221651..0edb2f8 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -116,6 +116,8 @@ module ice_bergs_framework
   real, dimension(:,:), pointer :: bergy_melt=>null() ! Melting rate of bergy bits (kg/s/m^2)
   real, dimension(:,:), pointer :: bergy_mass=>null() ! Mass distribution of bergy bits (kg/s/m^2)
   real, dimension(:,:), pointer :: spread_mass=>null() ! Mass of icebergs after spreading (kg/s/m^2)
+  real, dimension(:,:), pointer :: u_iceberg=>null() ! Average iceberg velocity in grid cell (mass weighted - but not spread mass weighted)
+  real, dimension(:,:), pointer :: v_iceberg=>null() ! Average iceberg velocity in grid cell (mass weighted - but not spread mass weighted)
   real, dimension(:,:), pointer :: virtual_area=>null() ! Virtual surface coverage by icebergs (m^2)
   real, dimension(:,:), pointer :: mass=>null() ! Mass distribution (kg/m^2)
   real, dimension(:,:,:), pointer :: mass_on_ocean=>null() ! Mass distribution partitioned by neighbor (kg/m^2)
@@ -135,7 +137,7 @@ module ice_bergs_framework
   integer :: id_mass=-1, id_ui=-1, id_vi=-1, id_ua=-1, id_va=-1, id_sst=-1, id_cn=-1, id_hi=-1
   integer :: id_bergy_src=-1, id_bergy_melt=-1, id_bergy_mass=-1, id_berg_melt=-1
   integer :: id_mass_on_ocn=-1, id_ssh=-1, id_fax=-1, id_fay=-1,  id_spread_mass=-1
-  integer :: id_count=-1, id_chksum=-1
+  integer :: id_count=-1, id_chksum=-1, id_u_iceberg=-1, id_v_iceberg=-1
 
   real :: clipping_depth=0. ! The effective depth at which to clip the weight felt by the ocean [m].
 
@@ -206,6 +208,8 @@ module ice_bergs_framework
   real :: bergy_bit_erosion_fraction ! Fraction of erosion melt flux to divert to bergy bits
   real :: sicn_shift ! Shift of sea-ice concentration in erosion flux modulation (0<sicn_shift<1)
   real :: lat_ref=0. ! Reference latitude for f-plane (when this option is on)
+  real :: u_override=0.0 ! Overrides the u velocity of icebergs (for ocean testing)
+  real :: v_override=0.0 ! Overrides the v velocity of icebergs (for ocean testing)
   real :: initial_orientation=0. ! Iceberg orientaion relative to this angle (in degrees). Used for hexagonal mass spreading.
   real, dimension(:), pointer :: initial_mass, distribution, mass_scaling
   real, dimension(:), pointer :: initial_thickness, initial_width, initial_length
@@ -215,6 +219,7 @@ module ice_bergs_framework
   logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
   logical :: time_average_weight=.false. ! Time average the weight on the ocean
   logical :: Runge_not_Verlet=.True.  !True=Runge Kuttai, False=Verlet.   
+  logical :: override_iceberg_velocities=.False.  !Allows you to set a fixed iceberg velocity for all non-static icebergs.
   logical :: use_f_plane=.False.  !Flag to use a f-plane for the rotation
   logical :: rotate_icebergs_for_mass_spreading=.True.  !Flag allows icebergs to rotate for spreading their mass (in hexagonal spreading mode)
   logical :: set_melt_rates_to_zero=.False.  !Sets all melt rates to zero, for testing purposes (thermodynamics routine is still run)
@@ -251,6 +256,8 @@ module ice_bergs_framework
   real :: icebergs_mass_start=0., icebergs_mass_end=0.
   real :: bergy_mass_start=0., bergy_mass_end=0.
   real :: spread_mass_start=0., spread_mass_end=0.
+  real :: u_iceberg_start=0., u_iceberg_end=0.
+  real :: v_iceberg_start=0., v_iceberg_end=0.
   real :: returned_mass_on_ocean=0.
   real :: net_melt=0., berg_melt=0., bergy_src=0., bergy_melt=0.
   integer :: nbergs_calved=0, nbergs_melted=0, nbergs_start=0, nbergs_end=0
@@ -323,6 +330,8 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: bergy_bit_erosion_fraction=0. ! Fraction of erosion melt flux to divert to bergy bits
 real :: sicn_shift=0. ! Shift of sea-ice concentration in erosion flux modulation (0<sicn_shift<1)
 real :: lat_ref=0. ! Reference latitude for f-plane (when this option is on)
+real :: u_override=0.0 ! Overrides the u velocity of icebergs (for ocean testing)
+real :: v_override=0.0 ! Overrides the v velocity of icebergs (for ocean testing)
 real :: Lx=360. ! Length of domain in x direction, used for periodicity (use a huge number for non-periodic)
 real :: initial_orientation=0. ! Iceberg orientaion relative to this angle (in degrees). Used for hexagonal mass spreading.
 logical :: use_operator_splitting=.true. ! Use first order operator splitting for thermodynamics
@@ -332,6 +341,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: speed_limit=0. ! CFL speed limit for a berg
 real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
 logical :: Runge_not_Verlet=.True.  !True=Runge Kutta, False=Verlet.  - Added by Alon 
+logical :: override_iceberg_velocities=.False.  !Allows you to set a fixed iceberg velocity for all non-static icebergs.
 logical :: use_f_plane=.False.  !Flag to use a f-plane for the rotation
 logical :: grid_is_latlon=.True.  !True means that the grid is specified in lat lon, and uses to radius of the earth to convert to distance
 logical :: grid_is_regular=.True. !Flag to say whether point in cell can be found assuming regular cartesian grid
@@ -362,7 +372,8 @@ subroutine ice_bergs_framework_init(bergs, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, halo_debugging, hexagonal_icebergs, &
          time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, interactive_icebergs_on, critical_interaction_damping_on, &
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution, force_all_pes_traj, &
-         allow_bergs_to_roll,set_melt_rates_to_zero,lat_ref,initial_orientation,rotate_icebergs_for_mass_spreading,grid_is_latlon,Lx,use_f_plane,use_old_spreading, grid_is_regular,Lx,use_f_plane
+         allow_bergs_to_roll,set_melt_rates_to_zero,lat_ref,initial_orientation,rotate_icebergs_for_mass_spreading,grid_is_latlon,Lx,use_f_plane,use_old_spreading, &
+         grid_is_regular,Lx,use_f_plane,override_iceberg_velocities,u_override,v_override
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -476,6 +487,8 @@ subroutine ice_bergs_framework_init(bergs, &
   allocate( grd%bergy_melt(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%bergy_melt(:,:)=0.
   allocate( grd%bergy_mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%bergy_mass(:,:)=0.
   allocate( grd%spread_mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_mass(:,:)=0.
+  allocate( grd%u_iceberg(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%u_iceberg(:,:)=0.
+  allocate( grd%v_iceberg(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%v_iceberg(:,:)=0.
   allocate( grd%virtual_area(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%virtual_area(:,:)=0.
   allocate( grd%mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%mass(:,:)=0.
   allocate( grd%mass_on_ocean(grd%isd:grd%ied, grd%jsd:grd%jed, 9) ); grd%mass_on_ocean(:,:,:)=0.
@@ -722,9 +735,12 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%time_average_weight=time_average_weight
   bergs%speed_limit=speed_limit
   bergs%Runge_not_Verlet=Runge_not_Verlet   
+  bergs%override_iceberg_velocities=override_iceberg_velocities 
   bergs%use_f_plane=use_f_plane 
   bergs%rotate_icebergs_for_mass_spreading=rotate_icebergs_for_mass_spreading 
   bergs%lat_ref=lat_ref
+  bergs%u_override=u_override
+  bergs%v_override=v_override
   bergs%initial_orientation=initial_orientation
   bergs%set_melt_rates_to_zero=set_melt_rates_to_zero 
   bergs%allow_bergs_to_roll=allow_bergs_to_roll 
@@ -781,6 +797,10 @@ subroutine ice_bergs_framework_init(bergs, &
      'Bergy bit density field', 'kg/(m^2)')
   grd%id_spread_mass=register_diag_field('icebergs', 'spread_mass', axes, Time, &
      'Iceberg mass after spreading', 'kg/(m^2)')
+  grd%id_u_iceberg=register_diag_field('icebergs', 'u_iceberg', axes, Time, &
+     'Iceberg u velocity (m/s)')
+  grd%id_v_iceberg=register_diag_field('icebergs', 'v_iceberg', axes, Time, &
+     'Iceberg v velocity (m/s)')
   grd%id_virtual_area=register_diag_field('icebergs', 'virtual_area', axes, Time, &
      'Virtual coverage by icebergs', 'm^2')
   grd%id_mass=register_diag_field('icebergs', 'mass', axes, Time, &
@@ -3732,6 +3752,8 @@ subroutine checksum_gridded(grd, label)
   call grd_chksum2(grd, grd%bergy_melt, 'bergy_melt')
   call grd_chksum2(grd, grd%bergy_mass, 'bergy_mass')
   call grd_chksum2(grd, grd%bergy_mass, 'spread_mass')
+  call grd_chksum2(grd, grd%bergy_mass, 'u_iceberg')
+  call grd_chksum2(grd, grd%bergy_mass, 'v_iceberg')
   call grd_chksum2(grd, grd%virtual_area, 'varea')
   call grd_chksum2(grd, grd%floating_melt, 'floating_melt')
   call grd_chksum2(grd, grd%berg_melt, 'berg_melt')

From 47bfb984d2355b0ede9ee6b32f28810c177f6b86 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Tue, 9 Aug 2016 11:32:21 -0400
Subject: [PATCH 146/361] 1) Fixed a bug affecting the adjust_index_and_ground
 routine (the actuall fix is in the  prod_sum_sign_dot_prod5,4 routines). The
 probelm was related to do with periodic boundary conditions. When
 non-periodic boundary conditions are being used, we let the domain size be
 periodic at length Lx where Lx is large. One unintended consiquence of this
 is that taking the modulo using Lx, rounds off the numbers. The result of
 this was that points which area in a grid cell where being found to be not in
 a grid cell (therefore the adjust_index_and_ground could not find the correct
 cell for points near the boundaries).

This is resolved by only applying the modulo when Lx<10**14.

Note that there are other places in the code where modulo Lx is used. This might cause rounding errors. Most of these seem to be rounding of the grid values rather than the iceberg location, which should not be a problem (hopefully).

2) A bug in is point_is_on_the_line routine has been fixed. Tolerence has been set to zero, so that only points which are directly on the line will be judged to be on the line. Before this was set to zero, points which were near the line where getting the wrong result, which was causing errors in the point_is_on_the_line() routine.

3) A unit test for point_in_triangle has been added.
---
 icebergs.F90           | 73 +++++++++++++++++++++++++++++++++++-----
 icebergs_framework.F90 | 76 ++++++++++++++++++++++++++++++++----------
 2 files changed, 122 insertions(+), 27 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 7fd3140..5bb3c79 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -141,9 +141,29 @@ subroutine unit_testing()
 ! Arguments
 
 call hexagon_test()
+call point_in_triangle_test()
 
 end subroutine unit_testing
 
+subroutine point_in_triangle_test()
+! Arguments
+real :: Ax,Ay,Bx,By,Cx,Cy  !Position of icebergs
+logical :: fail_unit_test
+integer :: stderrunit
+  
+  ! Get the stderr unit number.
+  stderrunit = stderr()
+  Ax= -2.695732526092343E-012
+  Ay=0.204344508198090
+  Bx=-2.695750202346321E-012
+  By= -8.433062639672301E-002
+  Cx=0.249999999997304
+  Cy=6.000694090068343E-002
+
+  fail_unit_test=(.not. point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.))
+  if (fail_unit_test) call error_mesg('diamonds, hexagon unit testing:', 'Point in triangle test does not pass!', FATAL)
+
+end subroutine point_in_triangle_test
 
 subroutine hexagon_test()
 ! Arguments
@@ -1558,7 +1578,8 @@ logical function point_is_on_the_line(Ax,Ay,Bx,By,qx,qy)
   ! Arguments
   real, intent(in) :: Ax,Ay,Bx,By,qx,qy
   real :: tol, dxc,dyc,dxl,dyl,cross
-    tol=1.e-12;
+    !tol=1.e-12;
+    tol=0.0;
     dxc = qx - Ax;
     dyc = qy - Ay;
     dxl = Bx - Ax;
@@ -1791,8 +1812,11 @@ subroutine Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy,Area_triangle,
       Key_quadrant=2
     elseif ((px.lt. 0.) .and. (qy.lt. 0.)) then !Third quadrant
       Key_quadrant=3;  
-    else  !#Forth quadrant
+    elseif ((px.ge. 0.) .and. (qy.lt. 0.)) then !Forth quadrant
       Key_quadrant=4 
+    else  !
+      call error_mesg('diamonds, iceberg_run', 'None of the quadrants are Key', WARNING)
+      write(stderrunit,*) 'diamonds, Triangle, px,qy', px,qy
     endif
          
   else  !At least one quadrant is empty, and this can be used to find the areas in the other quadrant.  Assigning quadrants. Key_quadrant is the empty quadrant.
@@ -1849,14 +1873,14 @@ subroutine Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy,Area_triangle,
   if (Error>tol) then
     call error_mesg('diamonds, triangle spreading', 'Triangle not evaluated accurately!!', WARNING)
     !if (mpp_pe().eq.mpp_root_pe()) then
-    if (mpp_pe().eq. 0) then
+    if (mpp_pe().eq. 20) then
       write(stderrunit,*) 'diamonds, Triangle corners:',Ax,Ay,Bx,By,Cx,Cy
+      write(stderrunit,*) 'diamonds, Triangle, Full Area', Area_Q1+ Area_Q2+ Area_Q3+ Area_Q4
       write(stderrunit,*) 'diamonds, Triangle, Areas', Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
       write(stderrunit,*) 'diamonds, Triangle, Areas', Error
-      write(stderrunit,*) 'diamonds, point in triangle',(point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.)),Key_quadrant
+      write(stderrunit,*) 'diamonds, Key quadrant',Key_quadrant,Area_key_quadrant
+      write(stderrunit,*) 'diamonds, point in triangle',(point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.))
       write(stderrunit,*) 'diamonds, halves',Area_Upper,Area_Lower,Area_Right,Area_Left
-
-
     endif
   endif
 
@@ -2187,7 +2211,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   grd%bergy_src(:,:)=0.
   grd%bergy_melt(:,:)=0.
   grd%bergy_mass(:,:)=0.
-  grd%spread_mass(:,:)=0.
+  !grd%spread_mass(:,:)=0.  !Don't zero this out yet, because we can first use this an add it onto the SSH
   grd%u_iceberg(:,:)=0.
   grd%v_iceberg(:,:)=0.
   grd%mass(:,:)=0.
@@ -2309,8 +2333,18 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
  !grd%ua(grd%isc:grd%iec,grd%jsc:grd%jec)=sign(sqrt(abs(tauxa(:,:))/0.01),tauxa(:,:))  ! Note rough conversion from stress to speed
  !grd%va(grd%isc:grd%iec,grd%jsc:grd%jec)=sign(sqrt(abs(tauya(:,:))/0.01),tauya(:,:))  ! Note rough conversion from stress to speed
   call mpp_update_domains(grd%ua, grd%va, grd%domain, gridtype=BGRID_NE)
+
   ! Copy sea surface height and temperature(resides on A grid)
   grd%ssh(grd%isc-1:grd%iec+1,grd%jsc-1:grd%jec+1)=ssh(:,:)
+  if (bergs%add_iceberg_thickness_to_SSH) then
+    !We might need to make sure spread_mass is defined on halos (or this might be done automatically. I need to look into this)
+    do i=grd%isd,grd%ied ; do j=grd%jsd,grd%jed
+      if (grd%area(i,j)>0) then
+        grd%ssh(i,j) =   ((grd%spread_mass(i,j)/grd%area(i,j))*(bergs%rho_bergs/rho_seawater))  !Is this an appropriate sea water density to use? Should be freezing point.
+      endif
+    enddo ;enddo
+  endif
+
   call mpp_update_domains(grd%ssh, grd%domain)
   grd%sst(grd%isc:grd%iec,grd%jsc:grd%jec)=sst(:,:)-273.15 ! Note convert from Kelvin to Celsius
   call mpp_update_domains(grd%sst, grd%domain)
@@ -2404,7 +2438,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 
   !Update diagnostic of iceberg mass spread on ocean
   if (grd%id_spread_mass>0) then
-          within_iceberg_model=.True.
+    grd%spread_mass(:,:)=0.
+    within_iceberg_model=.True.
     call icebergs_incr_mass(bergs, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec),within_iceberg_model) 
   endif
 
@@ -3863,6 +3898,7 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
       if (grd%msk(i,j)==0.) stop 'diamonds, adjust: Berg is in land! This should not happen...'
     endif
     lret=pos_within_cell(grd, lon, lat, i, j, xi, yj) ! Update xi and yj
+
   enddo
  !if (debug) then
  !  if (abs(i-i0)>2) then
@@ -3874,8 +3910,8 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
  !endif
 
   if (.not.bounced.and.lret.and.grd%msk(i,j)>0.) return ! Landed in ocean without bouncing so all is well
+
   if (.not.bounced.and..not.lret) then ! This implies the berg traveled many cells without getting far enough
-                                       ! OR that it did not move at all (round-off problem)
     if (debug) then
       write(stderrunit,*) 'diamonds, adjust: lon0, lat0=',lon0,lat0
       write(stderrunit,*) 'diamonds, adjust: xi0, yj0=',xi0,yj0
@@ -3888,6 +3924,7 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
       lret=pos_within_cell(grd, lon, lat, i, j, xi, yj,explain=.true.)
       write(stderrunit,*) 'diamonds, adjust: lret=',lret
     endif
+
     if (abs(i-i0)+abs(j-j0)==0) then
       if (use_roundoff_fix) then
         ! This is a special case due to round off where is_point_in_cell()
@@ -3906,6 +3943,24 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
       lret=pos_within_cell(grd, lon, lat, inm, jnm, xi, yj,explain=.true.)
     else
       call error_mesg('diamonds, adjust', 'Berg iterated many times without bouncing!', WARNING)
+       !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!11
+     if (iceberg_num .eq. 29217) then 
+         write(stderrunit,*) 'iceberg_num',iceberg_num, mpp_pe(), bounced
+         write(stderrunit,*) ' lon, lat',lon, lat
+         write(stderrunit,*) ' i,j',i,j
+         write(stderrunit,*) ' xi,yj',xi,yj
+      write(stderrunit,*) 'diamonds, adjust: lon0, lat0=',lon0,lat0
+      write(stderrunit,*) 'diamonds, adjust: xi0, yj0=',xi0,yj0
+      write(stderrunit,*) 'diamonds, adjust: i0,j0=',i0,j0 
+      write(stderrunit,*) 'diamonds, adjust: lon, lat=',lon,lat
+      write(stderrunit,*) 'diamonds, adjust: xi,yj=',xi,yj 
+      write(stderrunit,*) 'diamonds, adjust: i,j=',i,j
+      write(stderrunit,*) 'diamonds, adjust: inm,jnm=',inm,jnm
+      write(stderrunit,*) 'diamonds, adjust: icount=',icount
+      lret=pos_within_cell(grd, lon, lat, i, j, xi, yj,explain=.true.)
+      write(stderrunit,*) 'diamonds, adjust: lret=',lret
+    endif
+    !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!11
     endif
   endif
 !  if (xi>1.) xi=1.-posn_eps    !Alon
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 0edb2f8..1f6f305 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -219,6 +219,7 @@ module ice_bergs_framework
   logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
   logical :: time_average_weight=.false. ! Time average the weight on the ocean
   logical :: Runge_not_Verlet=.True.  !True=Runge Kuttai, False=Verlet.   
+  logical :: add_iceberg_thickness_to_SSH=.False.  !Adds the iceberg contribution to SSH.   
   logical :: override_iceberg_velocities=.False.  !Allows you to set a fixed iceberg velocity for all non-static icebergs.
   logical :: use_f_plane=.False.  !Flag to use a f-plane for the rotation
   logical :: rotate_icebergs_for_mass_spreading=.True.  !Flag allows icebergs to rotate for spreading their mass (in hexagonal spreading mode)
@@ -341,6 +342,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: speed_limit=0. ! CFL speed limit for a berg
 real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
 logical :: Runge_not_Verlet=.True.  !True=Runge Kutta, False=Verlet.  - Added by Alon 
+logical :: add_iceberg_thickness_to_SSH=.False.  !Adds the iceberg contribution to SSH.   
 logical :: override_iceberg_velocities=.False.  !Allows you to set a fixed iceberg velocity for all non-static icebergs.
 logical :: use_f_plane=.False.  !Flag to use a f-plane for the rotation
 logical :: grid_is_latlon=.True.  !True means that the grid is specified in lat lon, and uses to radius of the earth to convert to distance
@@ -373,7 +375,7 @@ subroutine ice_bergs_framework_init(bergs, &
          time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, interactive_icebergs_on, critical_interaction_damping_on, &
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution, force_all_pes_traj, &
          allow_bergs_to_roll,set_melt_rates_to_zero,lat_ref,initial_orientation,rotate_icebergs_for_mass_spreading,grid_is_latlon,Lx,use_f_plane,use_old_spreading, &
-         grid_is_regular,Lx,use_f_plane,override_iceberg_velocities,u_override,v_override
+         grid_is_regular,Lx,use_f_plane,override_iceberg_velocities,u_override,v_override,add_iceberg_thickness_to_SSH
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -735,6 +737,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%time_average_weight=time_average_weight
   bergs%speed_limit=speed_limit
   bergs%Runge_not_Verlet=Runge_not_Verlet   
+  bergs%add_iceberg_thickness_to_SSH=add_iceberg_thickness_to_SSH  
   bergs%override_iceberg_velocities=override_iceberg_velocities 
   bergs%use_f_plane=use_f_plane 
   bergs%rotate_icebergs_for_mass_spreading=rotate_icebergs_for_mass_spreading 
@@ -3314,11 +3317,19 @@ logical function sum_sign_dot_prod4(x0, y0, x1, y1, x2, y2, x3, y3, x, y,Lx, exp
   Lx_2=Lx/2.
 
   sum_sign_dot_prod4=.false.
-  xx=modulo(x-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x to within Lx_2 of x0
-  xx0=modulo(x0-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x0 to within Lx_2of xx
-  xx1=modulo(x1-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x1 to within Lx_2of xx
-  xx2=modulo(x2-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x2 to within Lx_2of xx
-  xx3=modulo(x3-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x3 to within Lx_2of xx
+  if (Lx .ge. 1E14 ) then
+    xx=x
+    xx0=x0
+    xx1=x1
+    xx2=x2
+    xx3=x3
+  else
+    xx=modulo(x-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x to within Lx_2 of x0
+    xx0=modulo(x0-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x0 to within Lx_2of xx
+    xx1=modulo(x1-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x1 to within Lx_2of xx
+    xx2=modulo(x2-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x2 to within Lx_2of xx
+    xx3=modulo(x3-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x3 to within Lx_2of xx
+  endif
 
   l0=(xx-xx0)*(y1-y0)-(y-y0)*(xx1-xx0)
   l1=(xx-xx1)*(y2-y1)-(y-y1)*(xx2-xx1)
@@ -3374,12 +3385,21 @@ logical function sum_sign_dot_prod5(x0, y0, x1, y1, x2, y2, x3, y3, x4, y4, x, y
   Lx_2=Lx/2.
 
   sum_sign_dot_prod5=.false.
-  xx=modulo(x-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x to within Lx_2of x0
-  xx0=modulo(x0-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x0 to within Lx_2of xx
-  xx1=modulo(x1-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x1 to within Lx_2of xx
-  xx2=modulo(x2-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x2 to within Lx_2of xx
-  xx3=modulo(x3-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x3 to within Lx_2of xx
-  xx4=modulo(x4-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x4 to within Lx_2of xx
+  if (Lx .ge. 1E14 ) then
+    xx=x
+    xx0=x0
+    xx1=x1
+    xx2=x2
+    xx3=x3
+    xx4=x4
+  else
+    xx=modulo(x-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x to within Lx_2of x0
+    xx0=modulo(x0-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x0 to within Lx_2 of xx
+    xx1=modulo(x1-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x1 to within Lx_2 of xx
+    xx2=modulo(x2-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x2 to within Lx_2 of xx
+    xx3=modulo(x3-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x3 to within Lx_2 of xx
+    xx4=modulo(x4-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x4 to within Lx_2 of xx
+  endif
 
   l0=(xx-xx0)*(y1-y0)-(y-y0)*(xx1-xx0)
   l1=(xx-xx1)*(y2-y1)-(y-y1)*(xx2-xx1)
@@ -3430,6 +3450,15 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
 
   ! Get the stderr unit number
   stderrunit=stderr()
+  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+  if (present(explain)) then
+    if(explain) then
+    write(stderrunit,'(a,2f12.6)') 'pos_within_cell: x ',x
+    print *,'x',x
+    write(stderrunit,'(a,2f12.6)') 'pos_within_cell: y ',y
+    endif
+  endif
+  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
   Lx=grd%Lx
   pos_within_cell=.false.; xi=-999.; yj=-999.
   if (i-1<grd%isd) return
@@ -3449,22 +3478,33 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
 
   if (present(explain)) then
     if(explain) then
-    write(stderrunit,'(a,4f12.6)') 'pos_within_cell: x1..x4 ',x1,x2,x3,x4
-    write(stderrunit,'(a,2f12.6)') 'pos_within_cell: x',x
-    write(stderrunit,'(a,4f12.6)') 'pos_within_cell: y1..y4 ',y1,y2,y3,y4
-    write(stderrunit,'(a,2f12.6)') 'pos_within_cell: y',y
+    write(stderrunit,'(a,4f12.6)') 'pos_within_cell: x1..x4 ',x1, x2, x3, x4
+    write(stderrunit,'(a,2f12.6)') 'pos_within_cell: x ',x
+    write(stderrunit,'(a,4f12.6)') 'pos_within_cell: y1..y4 ',y1, y2, y3, y4
+    write(stderrunit,'(a,2f12.6)') 'pos_within_cell: y ',y
     endif
   endif
 
   !This part only works for a regular cartesian grid. For more complex grids, we
   !should use calc_xiyj
   if ((.not. grd%grid_is_latlon) .and. (grd%grid_is_regular))  then
-    dx=(grd%lon(i  ,j  )-grd%lon(i-1  ,j  ))
-    dy=(grd%lat(i  ,j  )-grd%lat(i  ,j-1  ))
+    dx=abs((grd%lon(i  ,j  )-grd%lon(i-1  ,j  )))
+    dy=abs((grd%lat(i  ,j  )-grd%lat(i  ,j-1  )))
     x1=grd%lon(i  ,j  )-(dx/2)
     y1=grd%lat(i  ,j  )-(dy/2)
     xi=((x-x1)/dx)+0.5
     yj=((y-y1)/dy)+0.5
+
+  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+  if (present(explain)) then
+    if(explain) then
+    write(stderrunit,'(a,4f12.6)') 'One more time, xi,yi',xi,yj
+    write(stderrunit,'(a,4f12.6)') 'One more time, x1 ',x1
+    write(stderrunit,'(a,4f12.6)') 'One more time, dx,dy',dx, dy
+    write(stderrunit,'(a,4f12.6)') 'One more time, x-x1,',x-x1-1000.
+    endif
+  endif
+  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
   elseif ((max(y1,y2,y3,y4)<89.999) .or.(.not. grd%grid_is_latlon)) then
     call calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x, y, xi, yj, Lx, explain=explain)
   else

From e424b86fb55211d8720aeebefc1bb20cf54d1c7b Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 10 Aug 2016 14:41:34 -0400
Subject: [PATCH 147/361] No real changes, just a little bit of cleaning up.

---
 icebergs.F90           | 29 +-----------------------
 icebergs_framework.F90 | 51 +++++++++++++++---------------------------
 2 files changed, 19 insertions(+), 61 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 5bb3c79..9106be9 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -128,8 +128,8 @@ subroutine icebergs_init(bergs, &
     endif
     call update_halo_icebergs(bergs)
     call connect_all_bonds(bergs)
-    check_bond_quality=.True.
     nbonds=0
+    check_bond_quality=.True.
     call count_bonds(bergs, nbonds,check_bond_quality)
   endif
 
@@ -669,13 +669,6 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
   ! Interpolate gridded fields to berg     - Note: It should be possible to move this to evolve, so that it only needs to be called once. !!!!
   call interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, cn, hi)
 
-
-  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-  !Temporary for messing around
-  !ssh_x=0.
-  !ssh_y=0.
-  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
   if ((grd%grid_is_latlon) .and. (.not. bergs%use_f_plane)) then
      f_cori=(2.*omega)*sin(pi_180*lat)
   else
@@ -1308,7 +1301,6 @@ subroutine thermodynamics(bergs)
 
 end subroutine thermodynamics
 
-
 subroutine find_orientation_using_iceberg_bonds(grd,berg,orientation)
   ! Arguments
   type(iceberg), pointer :: berg
@@ -2409,7 +2401,6 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   if (debug) call checksum_gridded(bergs%grd, 's/r run after evolve')
   call mpp_clock_end(bergs%clock_mom)
 
-
   ! Send bergs to other PEs
   call mpp_clock_begin(bergs%clock_com)
   if (bergs%iceberg_bonds_on)  call  bond_address_update(bergs)
@@ -3943,24 +3934,6 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
       lret=pos_within_cell(grd, lon, lat, inm, jnm, xi, yj,explain=.true.)
     else
       call error_mesg('diamonds, adjust', 'Berg iterated many times without bouncing!', WARNING)
-       !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!11
-     if (iceberg_num .eq. 29217) then 
-         write(stderrunit,*) 'iceberg_num',iceberg_num, mpp_pe(), bounced
-         write(stderrunit,*) ' lon, lat',lon, lat
-         write(stderrunit,*) ' i,j',i,j
-         write(stderrunit,*) ' xi,yj',xi,yj
-      write(stderrunit,*) 'diamonds, adjust: lon0, lat0=',lon0,lat0
-      write(stderrunit,*) 'diamonds, adjust: xi0, yj0=',xi0,yj0
-      write(stderrunit,*) 'diamonds, adjust: i0,j0=',i0,j0 
-      write(stderrunit,*) 'diamonds, adjust: lon, lat=',lon,lat
-      write(stderrunit,*) 'diamonds, adjust: xi,yj=',xi,yj 
-      write(stderrunit,*) 'diamonds, adjust: i,j=',i,j
-      write(stderrunit,*) 'diamonds, adjust: inm,jnm=',inm,jnm
-      write(stderrunit,*) 'diamonds, adjust: icount=',icount
-      lret=pos_within_cell(grd, lon, lat, i, j, xi, yj,explain=.true.)
-      write(stderrunit,*) 'diamonds, adjust: lret=',lret
-    endif
-    !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!11
     endif
   endif
 !  if (xi>1.) xi=1.-posn_eps    !Alon
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 1f6f305..49ba07a 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -713,6 +713,7 @@ subroutine ice_bergs_framework_init(bergs, &
 endif
 if (save_short_traj) buffer_width_traj=5 ! This is the length of the short buffer used for abrevated traj
 
+
  ! Parameters
   bergs%dt=dt
   bergs%traj_sample_hrs=traj_sample_hrs
@@ -1002,7 +1003,7 @@ subroutine update_halo_icebergs(bergs)
   do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
     this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
-      write(stderrunit,*) 'A', this%iceberg_num, mpp_pe(), this%halo_berg, grdi, grdj
+        write(stderrunit,*) 'A', this%iceberg_num, mpp_pe(), this%halo_berg, grdi, grdj
       this=>this%next
     enddo
   enddo; enddo
@@ -1256,6 +1257,7 @@ subroutine update_halo_icebergs(bergs)
       this=>this%next
     enddo
   enddo; enddo
+  call show_all_bonds(bergs)
 endif
 
 end subroutine update_halo_icebergs
@@ -2494,13 +2496,16 @@ subroutine show_all_bonds(bergs)
       current_bond=>berg%first_bond
       do while (associated(current_bond)) ! loop over all bonds
         print *, 'Show Bond1 :', berg%iceberg_num, current_bond%other_berg_num, current_bond%other_berg_ine, current_bond%other_berg_jne,  mpp_pe()
+        !print *, 'Current:', berg%iceberg_num, berg%ine, berg%jne,berg%halo_berg, mpp_pe()
         if  (associated(current_bond%other_berg)) then
           if (current_bond%other_berg%iceberg_num .ne. current_bond%other_berg_num) then
-            print *, 'Bond matching', berg%iceberg_num,current_bond%other_berg%iceberg_num, current_bond%other_berg_num, mpp_pe()
+            print *, 'Bond matching', berg%iceberg_num,current_bond%other_berg%iceberg_num, current_bond%other_berg_num,\
+            berg%halo_berg,current_bond%other_berg%halo_berg ,mpp_pe()
             call error_mesg('diamonds, show all bonds:', 'The bonds are not matching properly!', FATAL)
           endif
         else
-            print *, 'This bond has an non-assosiated other berg :', berg%iceberg_num, current_bond%other_berg_num, current_bond%other_berg_ine, current_bond%other_berg_jne,  mpp_pe()
+            print *, 'This bond has an non-assosiated other berg :', berg%iceberg_num, current_bond%other_berg_num,&
+            current_bond%other_berg_ine, current_bond%other_berg_jne, berg%halo_berg,  mpp_pe()
         endif
         current_bond=>current_bond%next_bond
       enddo
@@ -2541,7 +2546,7 @@ subroutine connect_all_bonds(bergs)
           if ( (i.gt. grd%isd-1) .and. (i .lt. grd%ied+1) .and. (j .gt. grd%jsd-1) .and. (j .lt. grd%jed+1)) then
             other_berg=>bergs%list(i,j)%first
             do while (associated(other_berg)) ! loop over all other bergs
-              if (other_berg%iceberg_num == current_bond%other_berg_num) then
+              if (other_berg%iceberg_num .eq. current_bond%other_berg_num) then
                 current_bond%other_berg=>other_berg
                 other_berg=>null()
                 bond_matched=.true. 
@@ -2559,7 +2564,7 @@ subroutine connect_all_bonds(bergs)
                 .and. ((grdi_inner .ne. i) .or. (grdj_inner .ne. j)) ) then
                   other_berg=>bergs%list(grdi_inner,grdj_inner)%first
                   do while (associated(other_berg)) ! loop over all other bergs
-                    if (other_berg%iceberg_num == current_bond%other_berg_num) then
+                    if (other_berg%iceberg_num .eq. current_bond%other_berg_num) then
                       current_bond%other_berg=>other_berg
                       other_berg=>null()
                       bond_matched=.true.  
@@ -2632,12 +2637,13 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
   do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
     berg=>bergs%list(grdi,grdj)%first
     do while (associated(berg)) ! loop over all bergs
+
       current_bond=>berg%first_bond
       do while (associated(current_bond)) ! loop over all bonds
         number_of_bonds=number_of_bonds+1
 
         ! ##### Beginning Quality Check on Bonds ######
-!      print *, 'Quality check', mpp_pe(), berg%iceberg_num
+        !      print *, 'Quality check', mpp_pe(), berg%iceberg_num
         if (quality_check) then
           num_unmatched_bonds=0
           num_unassosiated_bond_pairs=0
@@ -2645,10 +2651,9 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
           other_berg=>current_bond%other_berg
           if (associated(other_berg)) then
             other_berg_bond=>other_berg%first_bond
-          
             do while (associated(other_berg_bond))  !loops over the icebergs in the other icebergs bond list           
               if (associated(other_berg_bond%other_berg)) then
-                if (other_berg_bond%other_berg%iceberg_num==berg%iceberg_num) then
+                if (other_berg_bond%other_berg%iceberg_num .eq.berg%iceberg_num) then
                   bond_is_good=.True.  !Bond_is_good becomes true when the corresponding bond is found
                 endif
               endif                 
@@ -2671,12 +2676,11 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
           endif
         endif
         ! ##### Ending Quality Check on Bonds ######
-
         current_bond=>current_bond%next_bond
-        enddo !End of loop over current bonds
-        berg=>berg%next
-      enddo ! End of loop over all bergs
-    enddo; enddo !End of loop over all grid cells
+      enddo !End of loop over current bonds
+      berg=>berg%next
+    enddo ! End of loop over all bergs
+  enddo; enddo !End of loop over all grid cells
 
     number_of_bonds_all_pe=number_of_bonds
     call mpp_sum(number_of_bonds_all_pe)
@@ -2703,7 +2707,7 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
           write(*,'(2a)') 'diamonds, Bonds parnters not located!!!! PE=', mpp_pe()
         endif
       endif
-      if ((num_unmatched_bonds_all_pe == 0)  .and. (num_unassosiated_bond_pairs_all_pe == 0)) then
+      if ((num_unmatched_bonds_all_pe .eq. 0)  .and. (num_unassosiated_bond_pairs_all_pe .eq. 0)) then
         if (mpp_pe().eq.mpp_root_pe()) then
                 write(stderrunit,*)  "Total number of bonds is: ", number_of_bonds_all_PE, "All iceberg bonds are connected and working well"
         endif
@@ -3450,15 +3454,6 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
 
   ! Get the stderr unit number
   stderrunit=stderr()
-  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-  if (present(explain)) then
-    if(explain) then
-    write(stderrunit,'(a,2f12.6)') 'pos_within_cell: x ',x
-    print *,'x',x
-    write(stderrunit,'(a,2f12.6)') 'pos_within_cell: y ',y
-    endif
-  endif
-  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
   Lx=grd%Lx
   pos_within_cell=.false.; xi=-999.; yj=-999.
   if (i-1<grd%isd) return
@@ -3495,16 +3490,6 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
     xi=((x-x1)/dx)+0.5
     yj=((y-y1)/dy)+0.5
 
-  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-  if (present(explain)) then
-    if(explain) then
-    write(stderrunit,'(a,4f12.6)') 'One more time, xi,yi',xi,yj
-    write(stderrunit,'(a,4f12.6)') 'One more time, x1 ',x1
-    write(stderrunit,'(a,4f12.6)') 'One more time, dx,dy',dx, dy
-    write(stderrunit,'(a,4f12.6)') 'One more time, x-x1,',x-x1-1000.
-    endif
-  endif
-  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
   elseif ((max(y1,y2,y3,y4)<89.999) .or.(.not. grd%grid_is_latlon)) then
     call calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x, y, xi, yj, Lx, explain=explain)
   else

From a93a94800fd47380428dc66f606f66945cc4259b Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Fri, 12 Aug 2016 11:34:30 -0400
Subject: [PATCH 148/361] A routine which implements the two equation melting
 model and three equation melting model have been added. These schemes have
 not yet been added to the thermodynamics routine, and have also not been
 properly tested. A unit test of these two schemes has been added.

---
 icebergs.F90 | 348 ++++++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 346 insertions(+), 2 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 9106be9..e9a98c7 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -77,6 +77,7 @@ subroutine icebergs_init(bergs, &
              cos_rot, sin_rot, ocean_depth, maskmap, fractional_area)
 ! Arguments
 type(icebergs), pointer :: bergs
+type(icebergs_gridded), pointer :: grd => null()
 integer, intent(in) :: gni, gnj, layout(2), io_layout(2), axes(2)
 integer, intent(in) :: dom_x_flags, dom_y_flags
 real, intent(in) :: dt
@@ -102,7 +103,7 @@ subroutine icebergs_init(bergs, &
              dt, Time, ice_lon, ice_lat, ice_wet, ice_dx, ice_dy, ice_area, &
              cos_rot, sin_rot, ocean_depth=ocean_depth, maskmap=maskmap, fractional_area=fractional_area)
 
-  call unit_testing()
+  call unit_testing(bergs)
 
   call mpp_clock_begin(bergs%clock_ior)
   call ice_bergs_io_init(bergs,io_layout)
@@ -137,14 +138,34 @@ end subroutine icebergs_init
 
 
 ! ##############################################################################
-subroutine unit_testing()
+subroutine unit_testing(bergs)
 ! Arguments
+type(icebergs), pointer :: bergs
 
 call hexagon_test()
 call point_in_triangle_test()
+call basal_melt_test(bergs)
 
 end subroutine unit_testing
 
+subroutine basal_melt_test(bergs)
+  ! Arguments
+  type(icebergs), pointer :: bergs
+  real :: dvo,lat,salt,temp, basal_melt, thickness
+  logical :: Use_three_equation_model
+
+  if (mpp_pe() .eq. mpp_root_pe() ) print *, 'Begining Basal Melting Unit Test'
+  dvo=0.2 ;lat=0.0 ; salt=35.0 ; temp=2.0 ;thickness=100.
+  Use_three_equation_model=.False.
+  call find_basal_melt(bergs,dvo,lat,salt,temp,Use_three_equation_model,thickness,basal_melt)
+  if (mpp_pe() .eq. mpp_root_pe()) print *, 'Two equation model basal_melt =',basal_melt
+
+  Use_three_equation_model=.True.
+  call find_basal_melt(bergs,dvo,lat,salt,temp,Use_three_equation_model,thickness,basal_melt)
+   if (mpp_pe() .eq. mpp_root_pe()) print *, 'Three equation model basal_melt =',basal_melt
+
+end subroutine basal_melt_test
+
 subroutine point_in_triangle_test()
 ! Arguments
 real :: Ax,Ay,Bx,By,Cx,Cy  !Position of icebergs
@@ -1301,6 +1322,329 @@ subroutine thermodynamics(bergs)
 
 end subroutine thermodynamics
 
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+subroutine find_basal_melt(bergs,dvo,lat,salt,temp,Use_three_equation_model,thickness,basal_melt)
+  ! Arguments
+  type(icebergs), pointer :: bergs
+  ! Local variables
+  real , intent(out) :: basal_melt !Melt rate underneath the icebergs
+  real , intent(in) :: dvo !Speed of iceberg relative to ocean mixed layer
+  real , intent(in) :: salt !Salinity of mixed layer
+  real , intent(in) :: temp !Temperature of mixed layer
+  real , intent(in) :: lat !Latitude (for boundary layer calculation)
+  real , intent(in) :: thickness !Ice thickness - needed to work out the pressure below the ice
+  logical , intent(in) :: Use_three_equation_model !True uses the 3 equation model, False uses the 2 equation model.
+  
+  ! Local variables
+  real :: utide, ustar_bg, ustar, f_cori, absf,tfreeze
+  real :: Hml !Mixed layer depth
+
+  !These could also be useful output variables if needed.
+  real :: t_flux, exch_vel_t, exch_vel_s,tflux_shelf,lprec 
+ 
+  real ::  Rhoml   ! Ocean mixed layer density in kg m-3.
+  real ::  p_int   ! The pressure at the ice-ocean interface, in Pa.
+
+  real, parameter :: VK    = 0.40     ! Von Karman's constant - dimensionless
+  real :: ZETA_N = 0.052   ! The fraction of the boundary layer over which the
+                           ! viscosity is linearly increasing. (Was 1/8. Why?)
+  real, parameter :: RC    = 0.20     ! critical flux Richardson number.
+  real :: I_ZETA_N  ! The inverse of ZETA_N.
+  real :: I_LF  ! Inverse of Latent Heat of fusion (J kg-1)
+  real :: I_VK      ! The inverse of VK.
+  real :: PR, SC    ! The Prandtl number and Schmidt number, nondim.
+!
+  ! 3 equation formulation variables
+  real :: Sbdry     !   Salinities in the ocean at the interface with the
+  real :: Sbdry_it  ! the ice shelf, in PSU.
+  real :: dS_it     ! The interface salinity change during an iteration, in PSU.
+  real :: hBL_neut  ! The neutral boundary layer thickness, in m.
+  real :: hBL_neut_h_molec ! The ratio of the neutral boundary layer thickness
+                           ! to the molecular boundary layer thickness, ND.
+  real :: wT_flux ! The vertical fluxes of heat and buoyancy just inside the
+  real :: wB_flux ! ocean, in C m s-1 and m2 s-3, ###CURRENTLY POSITIVE UPWARD.
+  real :: dB_dS  ! The derivative of buoyancy with salinity, in m s-2 PSU-1.
+  real :: dB_dT  ! The derivative of buoyancy with temperature, in m s-2 C-1.
+  real :: I_n_star, n_star_term
+  real :: dIns_dwB  ! The partial derivative of I_n_star with wB_flux, in ???.
+  real :: dT_ustar, dS_ustar
+  real :: ustar_h
+  real :: Gam_turb
+  real :: Gam_mol_t, Gam_mol_s
+  real :: RhoCp
+  real :: I_RhoLF
+  real :: Rho0
+  real :: ln_neut
+  real :: mass_exch
+  real :: Sb_min, Sb_max
+  real :: dS_min, dS_max
+  real :: density_ice
+!
+  ! Variables used in iterating for wB_flux.
+  real :: wB_flux_new, DwB, dDwB_dwB_in
+  real :: I_Gam_T, I_Gam_S
+  real :: dG_dwB, iDens
+  logical :: Sb_min_set, Sb_max_set
+
+  real, parameter :: c2_3 = 2.0/3.0
+  integer ::  it1, it3
+ 
+  !Parameters copied ice shelf module defaults (could be entered in the namelist later)
+  real, parameter ::  dR0_dT = -0.038357 ! Partial derivative of the mixed layer density with temperature, in units of kg m-3 K-1. 
+  real, parameter ::  dR0_dS = 0.805876 ! Partial derivative of the mixed layer density with salinity, in units of kg m-3 psu-1.
+  real, parameter ::  RHO_T0_S0 = 999.910681 ! Density of water with T=0, S=0 for linear EOS
+  real, parameter :: Salin_Ice =0.0 !Salinity of ice
+  real, parameter :: Temp_Ice = -15.0 !Salinity of ice
+  real, parameter :: kd_molec_salt=  8.02e-10 !The molecular diffusivity of salt in sea water at the freezing point
+  real, parameter :: kd_molec_temp=  1.41e-7 !The molecular diffusivity of heat in sea water at the freezing point
+  real, parameter :: kv_molec=  1.95e-6 !The molecular molecular kinimatic viscosity of sea water at the freezing point
+  real, parameter :: Cp_Ice =  2009.0 !Specific heat capacity of ice, taking from HJ99 (Holland and Jenkins 1999)
+  real, parameter :: Cp_ml =  3974.0 !Specific heat capacity of mixed layer, taking from HJ99 (Holland and Jenkins 1999)
+  real, parameter :: LF =  3.335e5 !Latent heat of fusion, taken from HJ99 (Holland and Jenkins 1999)
+  real, parameter :: cdrag =  1.5e-3 !Momentum Drag coef, taken from HJ99 (Holland and Jenkins 1999)
+  real, parameter :: gamma_t =  0.0 ! Exchange velcoity used in 2 equation model. Whn gamma_t is >0, the exchange velocity is independ of u_star. 
+                                  ! When gamma_t=0.0, then gamma_t is not used, and the exchange velocity is found using u_star.
+  real, parameter :: p_atm =  101325 ! Average atmospheric pressure (Pa) - from Google. 
+  
+  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+  density_ice = bergs%rho_bergs
+  Rho0=rho_seawater  !Note that the ice shelf code has a default of Rho0=1035
+  utide=0.     ! Tidal speeds, set to zero for now.
+  ustar_bg=0.001 !Background u_star under iceshelf. This should be linked to a value felt by the ocean boundary layer
+  Hml =10.      !Mixed layer depth. This is an approximate value. It looks like the code is not sensitive to it (since it enters in log(Hml)
+  p_int= p_atm+(gravity*thickness*density_ice)    ! The pressure at the ice-ocean interface, in Pa.
+  
+  ! Find the ocean mixed layer density in kg m-3.
+  call calculate_density(temp, salt, p_int, Rhoml, Rho_T0_S0, dR0_dT, dR0_dS)
+
+  ! This routine finds the melt at the base of the icebergs using the 2 equation
+  ! model or 3 equation model. This code is adapted from the ice shelf code. Once
+  ! the iceberg model is inside the ocean model, we should use the same code. 
+
+  I_ZETA_N = 1.0 / ZETA_N
+  I_RhoLF = 1.0/(Rho0*LF)
+  I_LF = 1.0 / LF
+  SC = kv_molec/kd_molec_salt
+  PR = kv_molec/kd_molec_temp
+  I_VK = 1.0/VK
+  RhoCp = Rho0 * Cp_ml
+
+  !first calculate molecular component  
+  Gam_mol_t = 12.5 * (PR**c2_3) - 6
+  Gam_mol_s = 12.5 * (SC**c2_3) - 6
+
+  iDens = 1.0/Rho0
+
+  !Preparing the mixed layer properties for use in both 2 and 3 equation version
+  ustar = cdrag*(dvo  + utide)
+  ustar_h = MAX(ustar_bg, ustar)
+
+  ! Estimate the neutral ocean boundary layer thickness as the minimum of the
+  ! reported ocean mixed layer thickness and the neutral Ekman depth.
+  !(Note that in Dan's code, f is spread over adjacent grid cells)
+  if ((bergs%grd%grid_is_latlon) .and. (.not. bergs%use_f_plane)) then
+     f_cori=(2.*omega)*sin(pi_180*lat)
+  else
+     f_cori=(2.*omega)*sin(pi_180*bergs%lat_ref)
+  endif
+  absf = abs(f_cori)  !Absolute value of the Coriolis parameter
+  if ((absf*Hml <= VK*ustar_h) .or. (absf.eq.0.))  then 
+    hBL_neut = Hml
+  else 
+    hBL_neut = (VK*ustar_h) / absf 
+  endif
+  hBL_neut_h_molec = ZETA_N * ((hBL_neut * ustar_h) / (5.0 * Kv_molec))
+  ln_neut = 0.0 ; if (hBL_neut_h_molec > 1.0) ln_neut = log(hBL_neut_h_molec)
+
+  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+  if (.not. Use_three_equation_model) then
+    ! In the 2-equation form, the mixed layer turbulent exchange velocity
+    ! is specified and large enough that the ocean salinity at the interface
+    ! is about the same as the boundary layer salinity.
+    ! Alon: I have adapted the code so that the turbulent exchange velocoty is not constant, but rather proportional to the frictional velocity. 
+    ! This should give you the same answers as the 3 equation model when salinity gradients in the mixed layer are zero (I think/hope)
+
+    call calculate_TFreeze(salt, p_int, tfreeze)
+
+    Gam_turb = I_VK * (ln_neut + (0.5 * I_ZETA_N - 1.0))
+    I_Gam_T = 1.0 / (Gam_mol_t + Gam_turb)
+
+    exch_vel_t= ustar_h * I_Gam_T
+    if (gamma_t>0.0) exch_vel_t = gamma_t  !Option to set the exchange to a constant, independent of the frictional velocity (as was previously coded)
+    wT_flux = exch_vel_t *(temp - tfreeze)
+
+    t_flux  = RhoCp * wT_flux
+    tflux_shelf = 0.0
+    lprec = I_LF * t_flux
+  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+  else  ! Use 3 equation model
+    ! 3 equation model solves for the melt rates iteratively. This is not working right now, because we don't have access to the mixed layer 
+    ! temperature and salinty gradients
+
+
+    ! Guess sss as the iteration starting point for the boundary salinity.
+    Sbdry = salt ; Sb_max_set = .false. ; Sb_min_set = .false.
+
+    ! Determine the mixed layer buoyancy flux, wB_flux.      
+    dB_dS = (gravity / Rhoml) * dR0_dS
+    dB_dT = (gravity / Rhoml) * dR0_dT
+
+    do it1 = 1,20
+      ! Determine the potential temperature at the ice-ocean interface.
+      call calculate_TFreeze(Sbdry, p_int, tfreeze)
+
+      dT_ustar = (temp - tfreeze) * ustar_h
+      dS_ustar = (salt - Sbdry) * ustar_h
+
+      ! First, determine the buoyancy flux assuming no effects of stability
+      ! on the turbulence.  Following H & J '99, this limit also applies
+      ! when the buoyancy flux is destabilizing.
+
+      Gam_turb = I_VK * (ln_neut + (0.5 * I_ZETA_N - 1.0))
+      I_Gam_T = 1.0 / (Gam_mol_t + Gam_turb)
+      I_Gam_S = 1.0 / (Gam_mol_s + Gam_turb)
+      wT_flux = dT_ustar * I_Gam_T
+      wB_flux = dB_dS * (dS_ustar * I_Gam_S) + dB_dT * wT_flux
+
+      if (wB_flux > 0.0) then
+        ! The buoyancy flux is stabilizing and will reduce the tubulent
+        ! fluxes, and iteration is required.
+        n_star_term = (ZETA_N/RC) * (hBL_neut * VK) / ustar_h**3
+        do it3 = 1,30
+          ! n_star <= 1.0 is the ratio of working boundary layer thickness
+          ! to the neutral thickness.
+          ! hBL = n_star*hBL_neut ; hSub = 1/8*n_star*hBL
+          I_n_star = sqrt(1.0 + n_star_term * wB_flux)
+          dIns_dwB = 0.5 * n_star_term / I_n_star
+          if (hBL_neut_h_molec > I_n_star**2) then
+            Gam_turb = I_VK * ((ln_neut - 2.0*log(I_n_star)) + &
+                       (0.5*I_ZETA_N*I_n_star - 1.0))
+            dG_dwB =  I_VK * ( -2.0 / I_n_star + (0.5 * I_ZETA_N)) * dIns_dwB
+          else
+            !   The layer dominated by molecular viscosity is smaller than
+            ! the assumed boundary layer.  This should be rare!
+            Gam_turb = I_VK * (0.5 * I_ZETA_N*I_n_star - 1.0)
+            dG_dwB = I_VK * (0.5 * I_ZETA_N) * dIns_dwB
+          endif
+
+          I_Gam_T = 1.0 / (Gam_mol_t + Gam_turb)
+          I_Gam_S = 1.0 / (Gam_mol_s + Gam_turb)
+          wT_flux = dT_ustar * I_Gam_T
+          wB_flux_new = dB_dS * (dS_ustar * I_Gam_S) + dB_dT * wT_flux
+
+          ! Find the root where dwB = 0.0
+          DwB = wB_flux_new - wB_flux
+          if (abs(wB_flux_new - wB_flux) < &
+            1e-4*(abs(wB_flux_new) + abs(wB_flux))) exit
+
+          dDwB_dwB_in = -dG_dwB * (dB_dS * (dS_ustar * I_Gam_S**2) + &
+                                         dB_dT * (dT_ustar * I_Gam_T**2)) - 1.0
+          ! This is Newton's method without any bounds. ( ### SHOULD BOUNDS BE NEEDED?)
+          wB_flux_new = wB_flux - DwB / dDwB_dwB_in
+        enddo !it3
+      endif
+
+      t_flux  = RhoCp * wT_flux
+      exch_vel_t = ustar_h * I_Gam_T
+      exch_vel_s = ustar_h * I_Gam_S
+
+      if (t_flux <= 0.0) then  ! Freezing occurs, so zero ice heat flux.
+        lprec = I_LF * t_flux
+        tflux_shelf = 0.0
+      else
+      !no conduction/perfect insulator
+      tflux_shelf = 0.0
+      lprec = I_LF * t_flux
+      ! With melting, from H&J 1999, eqs (31) & (26)...
+      !   Q_ice ~= cp_ice * (Temp_Ice-T_freeze) * lprec
+      !   RhoLF*lprec = Q_ice + t_flux
+      !   lprec = (t_flux) / (LF + cp_ice * (T_freeze-Temp_Ice))
+      !   lprec = t_flux /  (LF + Cp_ice * (tfreeze - Temp_Ice))
+      !   tflux_shelf = t_flux - LF*lprec
+      !other options: dTi/dz linear through shelf
+      !            dTi_dz = (Temp_Ice - tfreeze)/draft
+      !            tflux_shelf = - Rho_Ice * Cp_ice * KTI * dTi_dz
+      endif
+
+      mass_exch = exch_vel_s * Rho0
+      Sbdry_it = (salt * mass_exch + Salin_Ice * lprec) / (mass_exch + lprec)
+      dS_it = Sbdry_it - Sbdry
+      if (abs(dS_it) < 1e-4*(0.5*(salt + Sbdry + 1.e-10))) exit
+
+      if (dS_it < 0.0) then ! Sbdry is now the upper bound.
+        if (Sb_max_set .and. (Sbdry > Sb_max)) &
+          call error_mesg('diamonds,Find basal melt', 'shelf_calc_flux: Irregular iteration for Sbdry (max).' ,FATAL)
+        Sb_max = Sbdry ; dS_max = dS_it ; Sb_max_set = .true.
+      else ! Sbdry is now the lower bound.
+        if (Sb_min_set .and. (Sbdry < Sb_min)) &
+          call error_mesg('diamonds,Find basal melt', 'shelf_calc_flux: Irregular iteration for Sbdry (min).' ,FATAL)
+        Sb_min = Sbdry ; dS_min = dS_it ; Sb_min_set = .true.
+      endif
+      if (Sb_min_set .and. Sb_max_set) then
+        ! Use the false position method for the next iteration.
+        Sbdry = Sb_min + (Sb_max-Sb_min) * (dS_min / (dS_min - dS_max))
+      else
+        Sbdry = Sbdry_it
+      endif
+      Sbdry = Sbdry_it
+    enddo !it1
+  endif
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+  ! melt in m/s (melts of ice melted per second)
+  basal_melt = lprec /density_ice
+
+contains
+
+  subroutine calculate_TFreeze(S, pres, T_Fr)
+    !Arguments
+    real,    intent(in)  :: S, pres
+    real,    intent(out) :: T_Fr
+    real, parameter :: dTFr_dp    = -7.53E-08    !DTFREEZE_DP in MOM_input
+    real, parameter :: dTFr_dS    = -0.0573      !DTFREEZE_DS in MOM_input
+    real, parameter :: TFr_S0_P0  =0.0832        !TFREEZE_S0_P0 in MOM_input
+    !    This subroutine computes the freezing point potential temparature
+    !  (in deg C) from salinity (in psu), and pressure (in Pa) using a simple
+    !  linear expression, with coefficients passed in as arguments.
+    !  Copied from subroutine calculate_TFreeze_linear_scalar (in MOM/equation_of_state)
+    !
+    ! Arguments: S - salinity in PSU.
+    !  (in)      pres - pressure in Pa.
+    !  (out)     T_Fr - Freezing point potential temperature in deg C.
+    !  (in)      TFr_S0_P0 - The freezing point at S=0, p=0, in deg C.
+    !  (in)      dTFr_dS - The derivatives of freezing point with salinity, in
+    !                      deg C PSU-1.
+    !  (in)      dTFr_dp - The derivatives of freezing point with pressure, in
+    !                      deg C Pa-1.
+    T_Fr = (TFr_S0_P0 + dTFr_dS*S) + dTFr_dp*pres
+  end subroutine calculate_TFreeze
+
+  subroutine calculate_density(T, S, pressure, rho, Rho_T0_S0, dRho_dT, dRho_dS)
+    !Arguments
+    real,    intent(in)  :: T, S, pressure
+    real,    intent(out) :: rho
+    real,    intent(in)  :: Rho_T0_S0, dRho_dT, dRho_dS
+    ! *  This subroutine computes the density of sea water with a trivial  *
+    ! *  linear equation of state (in kg/m^3) from salinity (sal in psu),  *
+    ! *  potential temperature (T in deg C), and pressure in Pa.           *
+    !    Copied from subroutine calculate_density_scalar_linear (in MOM/equation_of_state)
+    ! *                                                                    *
+    ! * Arguments: T - potential temperature relative to the surface in C. *
+    ! *  (in)      S - salinity in PSU.                                    *
+    ! *  (in)      pressure - pressure in Pa.                              *
+    ! *  (out)     rho - in situ density in kg m-3.                        *
+    ! *  (in)      start - the starting point in the arrays.               *
+    ! *  (in)      npts - the number of values to calculate.               *
+    ! *  (in)      Rho_T0_S0 - The density at T=0, S=0, in kg m-3.         *
+    ! *  (in)      dRho_dT - The derivatives of density with temperature   *
+    ! *  (in)      dRho_dS - and salinity, in kg m-3 C-1 and kg m-3 psu-1. *
+    rho = Rho_T0_S0 + dRho_dT*T + dRho_dS*S
+  end subroutine calculate_density
+
+end subroutine find_basal_melt
+!
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
 subroutine find_orientation_using_iceberg_bonds(grd,berg,orientation)
   ! Arguments
   type(iceberg), pointer :: berg

From 5e3153f91199edcd3b61e43aae547fe1537570c1 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 17 Aug 2016 09:49:19 -0400
Subject: [PATCH 149/361] 1) Added an option to melt the icebergs without the
 icebergs changing mass. In this mode, the melt rates are calculated, the
 freshwater is fluxed into the ocean, but the icebergs do not decay. The flag
 for this mode is Iceberg_melt_without_decay=.true.

2) Added an option to melt the icebergs using the 2 or 3 equation model (instead of the usual parametrizations for iceberg melt). The flag for this option is melt_icebergs_as_ice_shelf=.true. In this mode, buoyant convection and wave erosion are set to zero. Later we should include a way to melt some icebergs as ice shelves and others as icebergs, perhaps using iceberg bonds.

3) Added an option to find the freshwater flux into the ocean using the difference in spread_mass. This allows melt water fluxes for icebergs to be spread across grid cells, and allows for smoother melt fields. The flag for this option is find_melt_using_spread_mass=.true.

Note that the three equation melt model is not working quite yet.
---
 icebergs.F90           | 60 +++++++++++++++++++++++++++++++++++-------
 icebergs_framework.F90 | 15 ++++++++++-
 2 files changed, 64 insertions(+), 11 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index e9a98c7..7fb47d3 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1117,6 +1117,7 @@ subroutine thermodynamics(bergs)
 real, parameter :: perday=1./86400.
 integer :: grdi, grdj
 real :: orientation, static_berg
+real :: SSS !Temporarily here
 
   ! For convenience
   grd=>bergs%grd
@@ -1129,7 +1130,6 @@ subroutine thermodynamics(bergs)
     this=>bergs%list(grdi,grdj)%first
     do while(associated(this))
       if (debug) call check_position(grd, this, 'thermodynamics (top)')
-  
       call interp_flds(grd, this%ine, this%jne, this%xi, this%yj, this%uo, this%vo, &
               this%ui, this%vi, this%ua, this%va, this%ssh_x, this%ssh_y, this%sst, &
               this%cn, this%hi)
@@ -1158,6 +1158,16 @@ subroutine thermodynamics(bergs)
       Me=max( 1./12.*(SST+2.)*Ss*(1+cos(pi*(IC**3))) ,0.) &! Wave erosion
           *perday ! convert to m/s
 
+      !For icebergs acting as ice shelves 
+      if (bergs%melt_icebergs_as_ice_shelf) then
+        Mv=0.0
+        Mb=0.0
+        Me=0.0
+        SSS=33.  !Temporarily here.
+        call find_basal_melt(bergs,dvo,this%lat,SSS,SST,bergs%Use_three_equation_model,T,Mb)
+        Mb=max(Mb,0.)
+      endif
+
       if (bergs%set_melt_rates_to_zero) then
         Mv=0.0
         Mb=0.0
@@ -1267,13 +1277,29 @@ subroutine thermodynamics(bergs)
           end if
         endif
       endif
-  
-      ! Store the new state of iceberg (with L>W)
-      this%mass=Mnew
-      this%mass_of_bits=nMbits
-      this%thickness=Tn
-      this%width=min(Wn,Ln)
-      this%length=max(Wn,Ln)
+ 
+
+       !This option allows iceberg melt fluxes to enter the ocean without the icebergs changing shape
+       if (bergs%Iceberg_melt_without_decay) then
+         Mnew=this%mass
+         nMbits=this%mass_of_bits
+         Tn=this%thickness
+         Wn=this%width
+         Ln=this%length
+         if (bergs%bergy_bit_erosion_fraction>0.) then
+           Mbits=this%mass_of_bits ! mass of bergy bits (kg)
+           nMbits=Mbits
+           Lbits=min(L,W,T,40.) ! assume bergy bits are smallest dimension or 40 meters
+           Abits=(Mbits/bergs%rho_bergs)/Lbits ! Effective bottom area (assuming T=Lbits)
+         endif
+      else
+        ! Store the new state of iceberg (with L>W)
+        this%mass=Mnew
+        this%mass_of_bits=nMbits
+        this%thickness=Tn
+        this%width=min(Wn,Ln)
+        this%length=max(Wn,Ln)
+      endif
       next=>this%next
   
       ! Did berg completely melt?
@@ -2771,11 +2797,25 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     call write_trajectory(bergs%trajectories, bergs%save_short_traj)
   endif
 
-  !Update diagnostic of iceberg mass spread on ocean
-  if (grd%id_spread_mass>0) then
+  !Update diagnostic of iceberg mass spread on ocean,MP1 
+  if ( (grd%id_spread_mass>0) .or. (bergs%find_melt_using_spread_mass) ) then
+    if ((bergs%find_melt_using_spread_mass) ) then
+      grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec)=grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec)  !Temporarily using the variable calving for storing old mass (not sure better way)
+    endif
     grd%spread_mass(:,:)=0.
     within_iceberg_model=.True.
     call icebergs_incr_mass(bergs, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec),within_iceberg_model) 
+    if (bergs%find_melt_using_spread_mass) then
+     do i=grd%isc,grd%iec ; do j=grd%jsc,grd%jec
+       if (grd%area(i,j)>0.0) then
+         grd%floating_melt(i,j)=max((grd%floating_melt(i,j) - grd%spread_mass(i,j))/(bergs%dt),0.0)
+         !grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)=grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec)*HLF !Not 100% sure this is correct.
+         grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)=grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec)*0.0 !Not 100% sure this is correct.
+       else
+         grd%floating_melt(i,j)=0.0
+       endif
+     enddo ;enddo
+    endif
   endif
 
   ! Gridded diagnostics
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 49ba07a..3525c47 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -219,6 +219,10 @@ module ice_bergs_framework
   logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
   logical :: time_average_weight=.false. ! Time average the weight on the ocean
   logical :: Runge_not_Verlet=.True.  !True=Runge Kuttai, False=Verlet.   
+  logical :: find_melt_using_spread_mass=.False.  !If true, then the model calculates ice loss by looping at the spread_mass before and after.
+  logical :: Use_three_equation_model=.True.  !Uses 3 equation model for melt when ice shelf type thermodynamics are used.
+  logical :: melt_icebergs_as_ice_shelf=.False.  !Uses iceshelf type thermodynamics
+  logical :: Iceberg_melt_without_decay=.False.  !Allows icebergs meltwater fluxes to enter the ocean, without the iceberg decaying or changing shape.
   logical :: add_iceberg_thickness_to_SSH=.False.  !Adds the iceberg contribution to SSH.   
   logical :: override_iceberg_velocities=.False.  !Allows you to set a fixed iceberg velocity for all non-static icebergs.
   logical :: use_f_plane=.False.  !Flag to use a f-plane for the rotation
@@ -342,6 +346,10 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: speed_limit=0. ! CFL speed limit for a berg
 real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
 logical :: Runge_not_Verlet=.True.  !True=Runge Kutta, False=Verlet.  - Added by Alon 
+logical :: find_melt_using_spread_mass=.False.  !If true, then the model calculates ice loss by looping at the spread_mass before and after.
+logical :: Use_three_equation_model=.True.  !Uses 3 equation model for melt when ice shelf type thermodynamics are used.
+logical :: melt_icebergs_as_ice_shelf=.False.  !Uses iceshelf type thermodynamics
+logical :: Iceberg_melt_without_decay=.False.  !Allows icebergs meltwater fluxes to enter the ocean, without the iceberg decaying or changing shape.
 logical :: add_iceberg_thickness_to_SSH=.False.  !Adds the iceberg contribution to SSH.   
 logical :: override_iceberg_velocities=.False.  !Allows you to set a fixed iceberg velocity for all non-static icebergs.
 logical :: use_f_plane=.False.  !Flag to use a f-plane for the rotation
@@ -375,7 +383,8 @@ subroutine ice_bergs_framework_init(bergs, &
          time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, interactive_icebergs_on, critical_interaction_damping_on, &
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution, force_all_pes_traj, &
          allow_bergs_to_roll,set_melt_rates_to_zero,lat_ref,initial_orientation,rotate_icebergs_for_mass_spreading,grid_is_latlon,Lx,use_f_plane,use_old_spreading, &
-         grid_is_regular,Lx,use_f_plane,override_iceberg_velocities,u_override,v_override,add_iceberg_thickness_to_SSH
+         grid_is_regular,Lx,use_f_plane,override_iceberg_velocities,u_override,v_override,add_iceberg_thickness_to_SSH,Iceberg_melt_without_decay,melt_icebergs_as_ice_shelf, &
+         Use_three_equation_model,find_melt_using_spread_mass 
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -738,6 +747,10 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%time_average_weight=time_average_weight
   bergs%speed_limit=speed_limit
   bergs%Runge_not_Verlet=Runge_not_Verlet   
+  bergs%find_melt_using_spread_mass=find_melt_using_spread_mass 
+  bergs%Use_three_equation_model=Use_three_equation_model 
+  bergs%melt_icebergs_as_ice_shelf=melt_icebergs_as_ice_shelf 
+  bergs%Iceberg_melt_without_decay=Iceberg_melt_without_decay 
   bergs%add_iceberg_thickness_to_SSH=add_iceberg_thickness_to_SSH  
   bergs%override_iceberg_velocities=override_iceberg_velocities 
   bergs%use_f_plane=use_f_plane 

From b2b19086f021f2f2989f4d9f00aebca328f4d632 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 17 Aug 2016 10:11:43 -0400
Subject: [PATCH 150/361] Added an optional argument to included sea surface
 salinity in the icebergs_run call.

---
 icebergs.F90 | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 522d0cd..fe06c5c 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1109,13 +1109,14 @@ end subroutine interp_flds
 ! ##############################################################################
 
 subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh, sst, calving_hflx, cn, hi, &
-                        stagger, stress_stagger)
+                        stagger, stress_stagger,sss)
 ! Arguments
 type(icebergs), pointer :: bergs
 type(time_type), intent(in) :: time
 real, dimension(:,:), intent(inout) :: calving, calving_hflx
 real, dimension(:,:), intent(in) :: uo, vo, ui, vi, tauxa, tauya, ssh, sst, cn, hi
 integer,    optional, intent(in) :: stagger, stress_stagger
+real, dimension(:,:), optional, intent(in) ::  sss
 ! Local variables
 integer :: iyr, imon, iday, ihr, imin, isec, k
 type(icebergs_gridded), pointer :: grd

From 6923967c48e13e1cbbe6dd074be7535d7458f41e Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 17 Aug 2016 10:59:27 -0400
Subject: [PATCH 151/361] Added an optional argument to included sea surface
 salinity in the icebergs_run call.

---
 icebergs.F90 | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 7fb47d3..6125f27 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -2530,13 +2530,14 @@ end subroutine interp_flds
 ! ##############################################################################
 
 subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh, sst, calving_hflx, cn, hi, &
-                        stagger, stress_stagger)
+                        stagger, stress_stagger,sss)
 ! Arguments
 type(icebergs), pointer :: bergs
 type(time_type), intent(in) :: time
 real, dimension(:,:), intent(inout) :: calving, calving_hflx
 real, dimension(:,:), intent(in) :: uo, vo, ui, vi, tauxa, tauya, ssh, sst, cn, hi
 integer,    optional, intent(in) :: stagger, stress_stagger
+real, dimension(:,:), optional, intent(in) :: sss
 ! Local variables
 integer :: iyr, imon, iday, ihr, imin, isec, k
 type(icebergs_gridded), pointer :: grd

From 4106264e6074d08b94a6cbeb7b9d6a6c99d8432c Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 17 Aug 2016 13:15:57 -0400
Subject: [PATCH 152/361] Added sea surface salinity to the iceberg code. The
 sss is added to icebergs_run as an optional argument. It is used in the
 thermodynamics when using the three equation model. The sss is set to -1 when
 no salinity is provided by the sea ice model.

---
 icebergs.F90           | 44 +++++++++++++++++++++++++++++++-----------
 icebergs_framework.F90 | 21 +++++++++++++++-----
 icebergs_io.F90        |  7 ++++++-
 3 files changed, 55 insertions(+), 17 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 6125f27..b157542 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -638,7 +638,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 logical, optional :: debug_flag
 ! Local variables
 type(icebergs_gridded), pointer :: grd
-real :: uo, vo, ui, vi, ua, va, uwave, vwave, ssh_x, ssh_y, sst, cn, hi
+real :: uo, vo, ui, vi, ua, va, uwave, vwave, ssh_x, ssh_y, sst, sss, cn, hi
 real :: f_cori, T, D, W, L, M, F
 real :: drag_ocn, drag_atm, drag_ice, wave_rad
 real :: c_ocn, c_atm, c_ice
@@ -688,7 +688,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
   grd=>bergs%grd
 
   ! Interpolate gridded fields to berg     - Note: It should be possible to move this to evolve, so that it only needs to be called once. !!!!
-  call interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, cn, hi)
+  call interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, sss, cn, hi)
 
   if ((grd%grid_is_latlon) .and. (.not. bergs%use_f_plane)) then
      f_cori=(2.*omega)*sin(pi_180*lat)
@@ -1029,6 +1029,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
     call dump_locfld(grd,i,j,grd%msk,'MSK')
     call dump_locfld(grd,i,j,grd%ssh,'SSH')
     call dump_locfld(grd,i,j,grd%sst,'SST')
+    call dump_locfld(grd,i,j,grd%sss,'SSS')
     call dump_locvel(grd,i,j,grd%uo,'Uo')
     call dump_locvel(grd,i,j,grd%vo,'Vo')
     call dump_locvel(grd,i,j,grd%ua,'Ua')
@@ -1132,8 +1133,9 @@ subroutine thermodynamics(bergs)
       if (debug) call check_position(grd, this, 'thermodynamics (top)')
       call interp_flds(grd, this%ine, this%jne, this%xi, this%yj, this%uo, this%vo, &
               this%ui, this%vi, this%ua, this%va, this%ssh_x, this%ssh_y, this%sst, &
-              this%cn, this%hi)
+              this%sss,this%cn, this%hi)
       SST=this%sst
+      SSS=this%sss
       IC=min(1.,this%cn+bergs%sicn_shift) ! Shift sea-ice concentration 
       M=this%mass
       T=this%thickness ! total thickness
@@ -1163,7 +1165,7 @@ subroutine thermodynamics(bergs)
         Mv=0.0
         Mb=0.0
         Me=0.0
-        SSS=33.  !Temporarily here.
+        if (.not. bergs%use_mixed_layer_salinity_for_thermo)  SSS=35.0  
         call find_basal_melt(bergs,dvo,this%lat,SSS,SST,bergs%Use_three_equation_model,T,Mb)
         Mb=max(Mb,0.)
       endif
@@ -2371,12 +2373,12 @@ subroutine Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex ,Area_Q
 end subroutine Hexagon_into_quadrants_using_triangles
 
 
-subroutine interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, cn, hi)
+subroutine interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, sss, cn, hi)
 ! Arguments
 type(icebergs_gridded), pointer :: grd
 integer, intent(in) :: i, j
 real, intent(in) :: xi, yj
-real, intent(out) :: uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, cn, hi
+real, intent(out) :: uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, sss, cn, hi
 ! Local variables
 real :: cos_rot, sin_rot
 #ifdef USE_OLD_SSH_GRADIENT
@@ -2422,6 +2424,7 @@ subroutine interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y,
   ! These fields are cell centered (A-grid) and would
   ! best be interpolated using PLM. For now we use PCM!
   sst=grd%sst(i,j) ! A-grid
+  sss=grd%sss(i,j) ! A-grid
   cn=grd%cn(i,j) ! A-grid
   hi=grd%hi(i,j) ! A-grid
     
@@ -2479,10 +2482,10 @@ subroutine interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y,
 
   if (((((uo.ne.uo) .or. (vo.ne.vo)) .or. ((ui.ne.ui) .or. (vi.ne.vi))) .or. &
        (((ua.ne.ua) .or. (va.ne.va)) .or. ((ssh_x.ne.ssh_x) .or. (ssh_y.ne.ssh_y)))) .or. &
-       (((sst.ne. sst) .or. (cn.ne.cn)) .or. (hi.ne. hi))) then
+       (((sst.ne. sst) .or. (sss.ne. sss) .or. (cn.ne.cn)) .or. (hi.ne. hi))) then
     write(stderrunit,*) 'diamonds, Error in interpolate: uo,vo,ui,vi',uo, vo, ui, vi
     write(stderrunit,*) 'diamonds, Error in interpolate: ua,va,ssh_x,ssh_y', ua, va, ssh_x, ssh_y
-    write(stderrunit,*) 'diamonds, Error in interpolate: sst,cn,hi', sst, cn, hi, mpp_pe()
+    write(stderrunit,*) 'diamonds, Error in interpolate: sst,cn,hi', sst, sss, cn, hi, mpp_pe()
     call error_mesg('diamonds, interp fields', 'field interpaolations has NaNs', FATAL)
 
   endif 
@@ -2530,7 +2533,7 @@ end subroutine interp_flds
 ! ##############################################################################
 
 subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh, sst, calving_hflx, cn, hi, &
-                        stagger, stress_stagger,sss)
+                        stagger, stress_stagger, sss)
 ! Arguments
 type(icebergs), pointer :: bergs
 type(time_type), intent(in) :: time
@@ -2716,6 +2719,16 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   call mpp_update_domains(grd%cn, grd%domain)
   grd%hi(grd%isc-1:grd%iec+1,grd%jsc-1:grd%jec+1)=hi(:,:)
   call mpp_update_domains(grd%hi, grd%domain)
+  
+  !Adding gridded salinity.
+  if (present(sss)) then
+    grd%sss(grd%isc:grd%iec,grd%jsc:grd%jec)=sss(:,:)
+  else
+    grd%sss(grd%isc:grd%iec,grd%jsc:grd%jec)=-1.0
+    if ((bergs%use_mixed_layer_salinity_for_thermo) .and. (bergs%melt_icebergs_as_ice_shelf))  then
+      call error_mesg('diamonds, icebergs_run', 'Can not use salinity for thermo. Ocean ML salinity not present!', FATAL)
+    endif
+  endif
 
  !Make sure that gridded values agree with mask  (to get ride of NaN values)
   do i=grd%isd,grd%ied ; do j=grd%jsd,grd%jed
@@ -2724,8 +2737,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
       grd%ua(i,j) = 0.0 ;  grd%va(i,j) = 0.0
       grd%uo(i,j) = 0.0 ;  grd%vo(i,j) = 0.0
       grd%ui(i,j) = 0.0 ;  grd%vi(i,j) = 0.0
-      grd%sst(i,j) = 0.0;  grd%cn(i,j) = 0.0
-      grd%hi(i,j) = 0.0
+      grd%sst(i,j)= 0.0;  grd%sss(i,j)= 0.0  
+      grd%cn(i,j) = 0.0 ;  grd%hi(i,j) = 0.0
     endif
     if (grd%ua(i,j) .ne. grd%ua(i,j)) grd%ua(i,j)=0.
     if (grd%va(i,j) .ne. grd%va(i,j)) grd%va(i,j)=0.
@@ -2734,6 +2747,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     if (grd%ui(i,j) .ne. grd%ui(i,j)) grd%ui(i,j)=0.
     if (grd%vi(i,j) .ne. grd%vi(i,j)) grd%vi(i,j)=0.
     if (grd%sst(i,j) .ne. grd%sst(i,j)) grd%sst(i,j)=0.
+    if (grd%sss(i,j) .ne. grd%sss(i,j)) grd%sss(i,j)=0.
     if (grd%cn(i,j) .ne. grd%cn(i,j)) grd%cn(i,j)=0.
     if (grd%hi(i,j) .ne. grd%hi(i,j)) grd%hi(i,j)=0.
   enddo; enddo
@@ -2834,6 +2848,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     lerr=send_data(grd%id_va, grd%va(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   if (grd%id_sst>0) &
     lerr=send_data(grd%id_sst, grd%sst(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_sss>0) &
+    lerr=send_data(grd%id_sss, grd%sss(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   if (grd%id_cn>0) &
     lerr=send_data(grd%id_cn, grd%cn(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   if (grd%id_hi>0) &
@@ -3597,6 +3613,7 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
          call print_fld(grd, grd%msk, 'msk')
          call print_fld(grd, grd%ssh, 'ssh')
          call print_fld(grd, grd%sst, 'sst')
+         call print_fld(grd, grd%sss, 'sss')
          call print_fld(grd, grd%hi, 'hi')
          write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
          write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
@@ -3739,6 +3756,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
          call print_fld(grd, grd%msk, 'msk')
          call print_fld(grd, grd%ssh, 'ssh')
          call print_fld(grd, grd%sst, 'sst')
+         call print_fld(grd, grd%sss, 'sss')
          call print_fld(grd, grd%hi, 'hi')
          write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
          write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
@@ -3796,6 +3814,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
          call print_fld(grd, grd%msk, 'msk')
          call print_fld(grd, grd%ssh, 'ssh')
          call print_fld(grd, grd%sst, 'sst')
+         call print_fld(grd, grd%sss, 'sss')
          call print_fld(grd, grd%hi, 'hi')
          write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
          write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
@@ -3852,6 +3871,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
          call print_fld(grd, grd%msk, 'msk')
          call print_fld(grd, grd%ssh, 'ssh')
          call print_fld(grd, grd%sst, 'sst')
+         call print_fld(grd, grd%sss, 'sss')
          call print_fld(grd, grd%hi, 'hi')
          write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
          write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
@@ -3928,6 +3948,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
          call print_fld(grd, grd%msk, 'msk')
          call print_fld(grd, grd%ssh, 'ssh')
          call print_fld(grd, grd%sst, 'sst')
+         call print_fld(grd, grd%sss, 'sss')
          call print_fld(grd, grd%hi, 'hi')
          write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
          write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
@@ -4485,6 +4506,7 @@ subroutine icebergs_end(bergs)
   deallocate(bergs%grd%va)
   deallocate(bergs%grd%ssh)
   deallocate(bergs%grd%sst)
+  deallocate(bergs%grd%sss)
   deallocate(bergs%grd%cn)
   deallocate(bergs%grd%hi)
   deallocate(bergs%grd%domain)
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 3525c47..3d158c7 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -16,7 +16,7 @@ module ice_bergs_framework
 implicit none ; private
 
 integer :: buffer_width=27 !Changed from 20 to 28 by Alon 
-integer :: buffer_width_traj=30  !Changed from 23 by Alon
+integer :: buffer_width_traj=31  !Changed from 23 by Alon
 !integer, parameter :: buffer_width=26 !Changed from 20 to 26 by Alon 
 !integer, parameter :: buffer_width_traj=29  !Changed from 23 by Alon
 integer, parameter :: nclasses=10 ! Number of ice bergs classes
@@ -103,6 +103,7 @@ module ice_bergs_framework
   real, dimension(:,:), pointer :: va=>null() ! Atmosphere meridional flow (m/s)
   real, dimension(:,:), pointer :: ssh=>null() ! Sea surface height (m)
   real, dimension(:,:), pointer :: sst=>null() ! Sea surface temperature (oC)
+  real, dimension(:,:), pointer :: sss=>null() ! Sea surface salinity (psu)
   real, dimension(:,:), pointer :: cn=>null() ! Sea-ice concentration (0 to 1)
   real, dimension(:,:), pointer :: hi=>null() ! Sea-ice thickness (m)
   real, dimension(:,:), pointer :: calving=>null() ! Calving mass rate [frozen runoff] (kg/s) (into stored ice)
@@ -137,7 +138,7 @@ module ice_bergs_framework
   integer :: id_mass=-1, id_ui=-1, id_vi=-1, id_ua=-1, id_va=-1, id_sst=-1, id_cn=-1, id_hi=-1
   integer :: id_bergy_src=-1, id_bergy_melt=-1, id_bergy_mass=-1, id_berg_melt=-1
   integer :: id_mass_on_ocn=-1, id_ssh=-1, id_fax=-1, id_fay=-1,  id_spread_mass=-1
-  integer :: id_count=-1, id_chksum=-1, id_u_iceberg=-1, id_v_iceberg=-1
+  integer :: id_count=-1, id_chksum=-1, id_u_iceberg=-1, id_v_iceberg=-1, id_sss=-1
 
   real :: clipping_depth=0. ! The effective depth at which to clip the weight felt by the ocean [m].
 
@@ -147,7 +148,7 @@ module ice_bergs_framework
   real :: lon, lat, day
   real :: mass, thickness, width, length, uvel, vvel
   real :: axn, ayn, bxn, byn, uvel_old, vvel_old, lat_old, lon_old  !Explicit and implicit accelerations !Alon 
-  real :: uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, cn, hi, halo_berg, static_berg
+  real :: uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, sss, cn, hi, halo_berg, static_berg
   real :: mass_of_bits, heat_density
   integer :: year, iceberg_num
   type(xyt), pointer :: next=>null()
@@ -167,7 +168,7 @@ module ice_bergs_framework
   integer :: ine, jne ! nearest index in NE direction (for convenience)
   real :: xi, yj ! Non-dimensional coords within current cell (0..1)
   ! Environment variables (as seen by the iceberg)
-  real :: uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, cn, hi
+  real :: uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, sss, cn, hi
   type(xyt), pointer :: trajectory=>null()
   type(bond), pointer :: first_bond=>null()  !First element of bond list.
 end type iceberg
@@ -219,6 +220,7 @@ module ice_bergs_framework
   logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
   logical :: time_average_weight=.false. ! Time average the weight on the ocean
   logical :: Runge_not_Verlet=.True.  !True=Runge Kuttai, False=Verlet.   
+  logical :: use_mixed_layer_salinity_for_thermo=.False.  !If true, then model uses ocean salinity for 3 and 2 equation melt model.
   logical :: find_melt_using_spread_mass=.False.  !If true, then the model calculates ice loss by looping at the spread_mass before and after.
   logical :: Use_three_equation_model=.True.  !Uses 3 equation model for melt when ice shelf type thermodynamics are used.
   logical :: melt_icebergs_as_ice_shelf=.False.  !Uses iceshelf type thermodynamics
@@ -346,6 +348,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: speed_limit=0. ! CFL speed limit for a berg
 real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
 logical :: Runge_not_Verlet=.True.  !True=Runge Kutta, False=Verlet.  - Added by Alon 
+logical :: use_mixed_layer_salinity_for_thermo=.False.  !If true, then model uses ocean salinity for 3 and 2 equation melt model.
 logical :: find_melt_using_spread_mass=.False.  !If true, then the model calculates ice loss by looping at the spread_mass before and after.
 logical :: Use_three_equation_model=.True.  !Uses 3 equation model for melt when ice shelf type thermodynamics are used.
 logical :: melt_icebergs_as_ice_shelf=.False.  !Uses iceshelf type thermodynamics
@@ -384,7 +387,7 @@ subroutine ice_bergs_framework_init(bergs, &
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution, force_all_pes_traj, &
          allow_bergs_to_roll,set_melt_rates_to_zero,lat_ref,initial_orientation,rotate_icebergs_for_mass_spreading,grid_is_latlon,Lx,use_f_plane,use_old_spreading, &
          grid_is_regular,Lx,use_f_plane,override_iceberg_velocities,u_override,v_override,add_iceberg_thickness_to_SSH,Iceberg_melt_without_decay,melt_icebergs_as_ice_shelf, &
-         Use_three_equation_model,find_melt_using_spread_mass 
+         Use_three_equation_model,find_melt_using_spread_mass,use_mixed_layer_salinity_for_thermo 
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -513,6 +516,7 @@ subroutine ice_bergs_framework_init(bergs, &
   allocate( grd%va(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%va(:,:)=0.
   allocate( grd%ssh(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%ssh(:,:)=0.
   allocate( grd%sst(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%sst(:,:)=0.
+  allocate( grd%sss(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%sss(:,:)=0.
   allocate( grd%cn(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%cn(:,:)=0.
   allocate( grd%hi(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%hi(:,:)=0.
   allocate( grd%tmp(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%tmp(:,:)=0.
@@ -747,6 +751,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%time_average_weight=time_average_weight
   bergs%speed_limit=speed_limit
   bergs%Runge_not_Verlet=Runge_not_Verlet   
+  bergs%use_mixed_layer_salinity_for_thermo=use_mixed_layer_salinity_for_thermo 
   bergs%find_melt_using_spread_mass=find_melt_using_spread_mass 
   bergs%Use_three_equation_model=Use_three_equation_model 
   bergs%melt_icebergs_as_ice_shelf=melt_icebergs_as_ice_shelf 
@@ -846,6 +851,8 @@ subroutine ice_bergs_framework_init(bergs, &
      'Atmos meridional component of velocity', 'm s^-1')
   grd%id_sst=register_diag_field('icebergs', 'sst', axes, Time, &
      'Sea surface temperature', 'degrees_C')
+  grd%id_sss=register_diag_field('icebergs', 'sss', axes, Time, &
+     'Sea surface salinity', 'psu')
   grd%id_cn=register_diag_field('icebergs', 'cn', axes, Time, &
      'Sea ice concentration', '(fraction)')
   grd%id_hi=register_diag_field('icebergs', 'hi', axes, Time, &
@@ -1945,6 +1952,7 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj)
       buff%data(28,n)=traj%byn !Alon
       buff%data(29,n)=traj%halo_berg !Alon
       buff%data(30,n)=traj%static_berg !Alon
+      buff%data(31,n)=traj%sss
     endif
 
   end subroutine pack_traj_into_buffer2
@@ -1992,6 +2000,7 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj)
       traj%byn=buff%data(28,n) !Alon
       traj%halo_berg=buff%data(29,n) !Alon
       traj%static_berg=buff%data(30,n) !Alon
+      traj%sss=buff%data(31,n)
     endif
     call append_posn(first, traj)
 
@@ -2810,6 +2819,7 @@ subroutine record_posn(bergs)
       posn%ssh_x=this%ssh_x
       posn%ssh_y=this%ssh_y
       posn%sst=this%sst
+      posn%sss=this%sss
       posn%cn=this%cn
       posn%hi=this%hi
       posn%axn=this%axn
@@ -3773,6 +3783,7 @@ subroutine checksum_gridded(grd, label)
   call grd_chksum2(grd, grd%vi, 'vi')
   call grd_chksum2(grd, grd%ssh, 'ssh')
   call grd_chksum2(grd, grd%sst, 'sst')
+  call grd_chksum2(grd, grd%sss, 'sss')
   call grd_chksum2(grd, grd%hi, 'hi')
   call grd_chksum2(grd, grd%cn, 'cn')
   call grd_chksum2(grd, grd%calving, 'calving')
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index d01c767..ec8017d 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -1396,7 +1396,7 @@ subroutine write_trajectory(trajectory, save_short_traj)
 ! Local variables
 integer :: iret, ncid, i_dim, i
 integer :: lonid, latid, yearid, dayid, uvelid, vvelid, iceberg_numid
-integer :: uoid, void, uiid, viid, uaid, vaid, sshxid, sshyid, sstid
+integer :: uoid, void, uiid, viid, uaid, vaid, sshxid, sshyid, sstid, sssid
 integer :: cnid, hiid
 integer :: mid, did, wid, lid, mbid, hdid
 character(len=37) :: filename
@@ -1534,6 +1534,7 @@ subroutine write_trajectory(trajectory, save_short_traj)
         sshxid = inq_varid(ncid, 'ssh_x')
         sshyid = inq_varid(ncid, 'ssh_y')
         sstid = inq_varid(ncid, 'sst')
+        sssid = inq_varid(ncid, 'sss')
         cnid = inq_varid(ncid, 'cn')
         hiid = inq_varid(ncid, 'hi')
       endif
@@ -1566,6 +1567,7 @@ subroutine write_trajectory(trajectory, save_short_traj)
         sshxid = def_var(ncid, 'ssh_x', NF_DOUBLE, i_dim)
         sshyid = def_var(ncid, 'ssh_y', NF_DOUBLE, i_dim)
         sstid = def_var(ncid, 'sst', NF_DOUBLE, i_dim)
+        sssid = def_var(ncid, 'sss', NF_DOUBLE, i_dim)
         cnid = def_var(ncid, 'cn', NF_DOUBLE, i_dim)
         hiid = def_var(ncid, 'hi', NF_DOUBLE, i_dim)
       endif
@@ -1619,6 +1621,8 @@ subroutine write_trajectory(trajectory, save_short_traj)
         call put_att(ncid, sshyid, 'units', 'non-dim')
         call put_att(ncid, sstid, 'long_name', 'sea surface temperature')
         call put_att(ncid, sstid, 'units', 'degrees_C')
+        call put_att(ncid, sssid, 'long_name', 'sea surface salinity')
+        call put_att(ncid, sssid, 'units', 'psu')
         call put_att(ncid, cnid, 'long_name', 'sea ice concentration')
         call put_att(ncid, cnid, 'units', 'none')
         call put_att(ncid, hiid, 'long_name', 'sea ice thickness')
@@ -1661,6 +1665,7 @@ subroutine write_trajectory(trajectory, save_short_traj)
         call put_double(ncid, sshxid, i, this%ssh_x)
         call put_double(ncid, sshyid, i, this%ssh_y)
         call put_double(ncid, sstid, i, this%sst)
+        call put_double(ncid, sssid, i, this%sss)
         call put_double(ncid, cnid, i, this%cn)
         call put_double(ncid, hiid, i, this%hi)
       endif

From a0d4913459afc2eea3c7305714e5f75f74d28791 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Tue, 23 Aug 2016 17:11:19 -0400
Subject: [PATCH 153/361] When using the 3 equation iceberg model, when the
 iteration does not converge, the two equation model is used instead. This
 gives an error when run in debug mode.

---
 icebergs.F90 | 81 ++++++++++++++++++++++++++++++++--------------------
 1 file changed, 50 insertions(+), 31 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index b157542..3b25127 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -152,16 +152,17 @@ subroutine basal_melt_test(bergs)
   ! Arguments
   type(icebergs), pointer :: bergs
   real :: dvo,lat,salt,temp, basal_melt, thickness
+  integer :: iceberg_num
   logical :: Use_three_equation_model
 
   if (mpp_pe() .eq. mpp_root_pe() ) print *, 'Begining Basal Melting Unit Test'
-  dvo=0.2 ;lat=0.0 ; salt=35.0 ; temp=2.0 ;thickness=100.
+  dvo=0.2 ;lat=0.0 ; salt=35.0 ; temp=2.0 ;thickness=100.; iceberg_num=0
   Use_three_equation_model=.False.
-  call find_basal_melt(bergs,dvo,lat,salt,temp,Use_three_equation_model,thickness,basal_melt)
+  call find_basal_melt(bergs,dvo,lat,salt,temp,Use_three_equation_model,thickness,basal_melt,iceberg_num)
   if (mpp_pe() .eq. mpp_root_pe()) print *, 'Two equation model basal_melt =',basal_melt
 
   Use_three_equation_model=.True.
-  call find_basal_melt(bergs,dvo,lat,salt,temp,Use_three_equation_model,thickness,basal_melt)
+  call find_basal_melt(bergs,dvo,lat,salt,temp,Use_three_equation_model,thickness,basal_melt,iceberg_num)
    if (mpp_pe() .eq. mpp_root_pe()) print *, 'Three equation model basal_melt =',basal_melt
 
 end subroutine basal_melt_test
@@ -1166,7 +1167,7 @@ subroutine thermodynamics(bergs)
         Mb=0.0
         Me=0.0
         if (.not. bergs%use_mixed_layer_salinity_for_thermo)  SSS=35.0  
-        call find_basal_melt(bergs,dvo,this%lat,SSS,SST,bergs%Use_three_equation_model,T,Mb)
+        call find_basal_melt(bergs,dvo,this%lat,SSS,SST,bergs%Use_three_equation_model,T,Mb,this%iceberg_num)
         Mb=max(Mb,0.)
       endif
 
@@ -1352,7 +1353,7 @@ end subroutine thermodynamics
 
 
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-subroutine find_basal_melt(bergs,dvo,lat,salt,temp,Use_three_equation_model,thickness,basal_melt)
+subroutine find_basal_melt(bergs,dvo,lat,salt,temp,Use_three_equation_model,thickness,basal_melt,iceberg_num)
   ! Arguments
   type(icebergs), pointer :: bergs
   ! Local variables
@@ -1361,6 +1362,7 @@ subroutine find_basal_melt(bergs,dvo,lat,salt,temp,Use_three_equation_model,thic
   real , intent(in) :: salt !Salinity of mixed layer
   real , intent(in) :: temp !Temperature of mixed layer
   real , intent(in) :: lat !Latitude (for boundary layer calculation)
+  integer , intent(in) :: iceberg_num !Iceberg number, used for debugging (error messages)
   real , intent(in) :: thickness !Ice thickness - needed to work out the pressure below the ice
   logical , intent(in) :: Use_three_equation_model !True uses the 3 equation model, False uses the 2 equation model.
   
@@ -1414,6 +1416,7 @@ subroutine find_basal_melt(bergs,dvo,lat,salt,temp,Use_three_equation_model,thic
   real :: I_Gam_T, I_Gam_S
   real :: dG_dwB, iDens
   logical :: Sb_min_set, Sb_max_set
+  logical :: out_of_bounds
 
   real, parameter :: c2_3 = 2.0/3.0
   integer ::  it1, it3
@@ -1486,33 +1489,14 @@ subroutine find_basal_melt(bergs,dvo,lat,salt,temp,Use_three_equation_model,thic
   ln_neut = 0.0 ; if (hBL_neut_h_molec > 1.0) ln_neut = log(hBL_neut_h_molec)
 
   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-  if (.not. Use_three_equation_model) then
-    ! In the 2-equation form, the mixed layer turbulent exchange velocity
-    ! is specified and large enough that the ocean salinity at the interface
-    ! is about the same as the boundary layer salinity.
-    ! Alon: I have adapted the code so that the turbulent exchange velocoty is not constant, but rather proportional to the frictional velocity. 
-    ! This should give you the same answers as the 3 equation model when salinity gradients in the mixed layer are zero (I think/hope)
-
-    call calculate_TFreeze(salt, p_int, tfreeze)
-
-    Gam_turb = I_VK * (ln_neut + (0.5 * I_ZETA_N - 1.0))
-    I_Gam_T = 1.0 / (Gam_mol_t + Gam_turb)
-
-    exch_vel_t= ustar_h * I_Gam_T
-    if (gamma_t>0.0) exch_vel_t = gamma_t  !Option to set the exchange to a constant, independent of the frictional velocity (as was previously coded)
-    wT_flux = exch_vel_t *(temp - tfreeze)
-
-    t_flux  = RhoCp * wT_flux
-    tflux_shelf = 0.0
-    lprec = I_LF * t_flux
-  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-  else  ! Use 3 equation model
+  if (Use_three_equation_model) then   ! Use 3 equation model
     ! 3 equation model solves for the melt rates iteratively. This is not working right now, because we don't have access to the mixed layer 
     ! temperature and salinty gradients
 
 
     ! Guess sss as the iteration starting point for the boundary salinity.
     Sbdry = salt ; Sb_max_set = .false. ; Sb_min_set = .false.
+    out_of_bounds=.false.
 
     ! Determine the mixed layer buoyancy flux, wB_flux.      
     dB_dS = (gravity / Rhoml) * dR0_dS
@@ -1601,12 +1585,24 @@ subroutine find_basal_melt(bergs,dvo,lat,salt,temp,Use_three_equation_model,thic
       if (abs(dS_it) < 1e-4*(0.5*(salt + Sbdry + 1.e-10))) exit
 
       if (dS_it < 0.0) then ! Sbdry is now the upper bound.
-        if (Sb_max_set .and. (Sbdry > Sb_max)) &
-          call error_mesg('diamonds,Find basal melt', 'shelf_calc_flux: Irregular iteration for Sbdry (max).' ,FATAL)
+        if (Sb_max_set .and. (Sbdry > Sb_max)) then
+          if (debug) then
+            call error_mesg('diamonds,Find basal melt', 'shelf_calc_flux: Irregular iteration for Sbdry (max).' ,WARNING)
+            print *, 'Sbdry error: iceberg_num,dvo,temp,salt,lat,thickness :',iceberg_num,dvo,temp,salt,lat,thickness
+          endif
+          out_of_bounds=.true.
+          exit
+        endif
         Sb_max = Sbdry ; dS_max = dS_it ; Sb_max_set = .true.
       else ! Sbdry is now the lower bound.
-        if (Sb_min_set .and. (Sbdry < Sb_min)) &
-          call error_mesg('diamonds,Find basal melt', 'shelf_calc_flux: Irregular iteration for Sbdry (min).' ,FATAL)
+        if (Sb_min_set .and. (Sbdry < Sb_min)) then
+          if (debug) then
+            call error_mesg('diamonds,Find basal melt', 'shelf_calc_flux: Irregular iteration for Sbdry (min).' ,WARNING)
+            print *, 'Sbdry error: iceberg_num,dvo,temp,salt,lat,thickness :',iceberg_num,dvo,temp,salt,lat,thickness
+          endif
+          out_of_bounds=.true.
+          exit
+        endif
         Sb_min = Sbdry ; dS_min = dS_it ; Sb_min_set = .true.
       endif
       if (Sb_min_set .and. Sb_max_set) then
@@ -1618,7 +1614,30 @@ subroutine find_basal_melt(bergs,dvo,lat,salt,temp,Use_three_equation_model,thic
       Sbdry = Sbdry_it
     enddo !it1
   endif
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+  if ((.not. Use_three_equation_model) .or. (out_of_bounds)) then
+    ! In the 2-equation form, the mixed layer turbulent exchange velocity
+    ! is specified and large enough that the ocean salinity at the interface
+    ! is about the same as the boundary layer salinity.
+    ! Alon: I have adapted the code so that the turbulent exchange velocoty is not constant, but rather proportional to the frictional velocity. 
+    ! This should give you the same answers as the 3 equation model when salinity gradients in the mixed layer are zero (I think/hope)
+    ! Use 2-equation model when 3 equation version fails.
+
+    call calculate_TFreeze(salt, p_int, tfreeze)
+
+    Gam_turb = I_VK * (ln_neut + (0.5 * I_ZETA_N - 1.0))
+    I_Gam_T = 1.0 / (Gam_mol_t + Gam_turb)
+
+    exch_vel_t= ustar_h * I_Gam_T
+    if (gamma_t>0.0) exch_vel_t = gamma_t  !Option to set the exchange to a constant, independent of the frictional velocity (as was previously coded)
+    wT_flux = exch_vel_t *(temp - tfreeze)
+
+    t_flux  = RhoCp * wT_flux
+    tflux_shelf = 0.0
+    lprec = I_LF * t_flux
+    endif
+    !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
   ! melt in m/s (melts of ice melted per second)
   basal_melt = lprec /density_ice
 

From 30ab56fd15a1a82e8eaab885170f9a6fa218ce77 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 24 Aug 2016 10:57:46 -0400
Subject: [PATCH 154/361] A option has been added which allows the incoming
 calving field to be smoothed over a time scale tau_calving. This is done so
 that the calving will be uncoupled from the seasonal cylce. The smoothing is
 achieved by keeping track of a running mean calving and calving heat flux.
 These running means are time stepped with a Newton cooling type relaxation
 over a time scale tau_calving. When tau_calving is set to zero, the
 instantious calving field is used, and it should revert back to the original
 scheme. This is the default option and should not change the answers.

---
 icebergs.F90           | 39 +++++++++++++++++++++++++++++++++++++++
 icebergs_framework.F90 | 19 +++++++++++++++++--
 icebergs_io.F90        | 25 +++++++++++++++++++++++++
 3 files changed, 81 insertions(+), 2 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 522d0cd..3fe3971 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1177,10 +1177,13 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
        'diamonds: y,m,d=',iyr, imon, iday,' h,m,s=', ihr, imin, isec, &
        ' yr,yrdy=', bergs%current_year, bergs%current_yearday
 
+
   ! Adapt calving flux from coupler for use here
  !call sanitize_field(grd%calving,1.e20)
   tmpsum=sum( calving(:,:)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
   bergs%net_calving_received=bergs%net_calving_received+tmpsum*bergs%dt
+  
+  call get_running_mean_calving(bergs,calving,calving_hflx)
   grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec)=calving(:,:) ! Units of kg/m2/s
   grd%calving(:,:)=grd%calving(:,:)*grd%msk(:,:)*grd%area(:,:) ! Convert to kg/s
   tmpsum=sum( grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec) )
@@ -1368,6 +1371,10 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     lerr=send_data(grd%id_mass, grd%mass(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   if (grd%id_stored_ice>0) &
     lerr=send_data(grd%id_stored_ice, grd%stored_ice(grd%isc:grd%iec,grd%jsc:grd%jec,:), Time)
+  if (grd%id_mean_calving>0) &
+    lerr=send_data(grd%id_mean_calving, grd%mean_calving(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_mean_calving_hflx>0) &
+    lerr=send_data(grd%id_mean_calving_hflx, grd%mean_calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   if (grd%id_real_calving>0) &
     lerr=send_data(grd%id_real_calving, grd%real_calving(grd%isc:grd%iec,grd%jsc:grd%jec,:), Time)
   if (grd%id_ssh>0) &
@@ -1412,6 +1419,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   bergs%net_outgoing_calving_heat=bergs%net_outgoing_calving_heat+tmpsum*bergs%dt ! Units of J
   if (lbudget) then
     bergs%stored_end=sum( grd%stored_ice(grd%isc:grd%iec,grd%jsc:grd%jec,:) )
+    bergs%mean_calving_end=sum( grd%mean_calving(grd%isc:grd%iec,grd%jsc:grd%jec) )
+    bergs%mean_calving_hflx_end=sum( grd%mean_calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec) )
     bergs%stored_heat_end=sum( grd%stored_heat(grd%isc:grd%iec,grd%jsc:grd%jec) )
     bergs%floating_mass_end=sum_mass(bergs%first)
     bergs%icebergs_mass_end=sum_mass(bergs%first,justbergs=.true.)
@@ -1613,6 +1622,35 @@ subroutine report_ibudget(budgetstr,instr,inval,outstr,outval,delstr,startval,en
   200 format("diamonds: ",a19,10(a18,"=",i14,x,:,","))
   end subroutine report_ibudget
 
+  subroutine get_running_mean_calving(bergs,calving,calving_hflx)
+  ! Arguments
+  type(icebergs), pointer :: bergs
+  real, dimension(:,:), intent(inout) :: calving, calving_hflx
+  ! Local variables
+  real ::  alpha  !Parameter used for calving relaxation time stepping.  (0<=alpha<1)
+  real ::  tau  !Relaxation timescale in seconds
+  !This subroutine takes in the new calving and calving_hflx, and uses them to time step a mean_calving value
+  !The time stepping uses a time scale tau. When tau is equal to zero, the
+  !running mean is exactly equal to the new calving value. 
+  !In the first iteration (or if the running mean is not yet set), then alpha is set to zero  (this is done using the 999. trick)
+
+  !Applying "Newton cooling" with timescale tau, to smooth out the calving field.
+  tau=bergs%tau_calving/(365.*24*60*60) !Converting time scale from years to seconds
+  alpha=tau/(tau+bergs%dt)
+  if ((maxval(bergs%grd%mean_calving).eq.999.0) .or. (maxval(bergs%grd%mean_calving_hflx).eq.999.0)) alpha=0.0  !Special case for first time step.
+  bergs%grd%mean_calving=calving + alpha*(bergs%grd%mean_calving-calving)
+  bergs%grd%mean_calving_hflx=calving + alpha*(bergs%grd%mean_calving_hflx-calving)
+  
+  !Removing negative values
+  bergs%grd%mean_calving=max(bergs%grd%mean_calving,0.)
+  bergs%grd%mean_calving_hflx=max(bergs%grd%mean_calving_hflx,0.)
+
+  !Setting calving used by the iceberg model equal to the running mean
+  calving=bergs%grd%mean_calving
+  calving_hflx=bergs%grd%mean_calving_hflx
+  
+  end subroutine get_running_mean_calving
+
 end subroutine icebergs_run
 
 ! ##############################################################################
@@ -2792,6 +2830,7 @@ subroutine icebergs_end(bergs)
   deallocate(bergs%grd%tmp)
   deallocate(bergs%grd%tmpc)
   deallocate(bergs%grd%stored_ice)
+  deallocate(bergs%grd%mean_calving)
   deallocate(bergs%grd%real_calving)
   deallocate(bergs%grd%uo)
   deallocate(bergs%grd%vo)
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index d6e6763..3940961 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -111,6 +111,8 @@ module ice_bergs_framework
   real, dimension(:,:), pointer :: tmp=>null() ! Temporary work space
   real, dimension(:,:), pointer :: tmpc=>null() ! Temporary work space
   real, dimension(:,:,:), pointer :: stored_ice=>null() ! Accumulated ice mass flux at calving locations (kg)
+  real, dimension(:,:), pointer :: mean_calving=>null() !Running mean for ice calving
+  real, dimension(:,:), pointer :: mean_calving_hflx=>null() !Running mean for ice calving
   real, dimension(:,:), pointer :: stored_heat=>null() ! Heat content of stored ice (J)
   real, dimension(:,:,:), pointer :: real_calving=>null() ! Calving rate into iceberg class at calving locations (kg/s)
   real, dimension(:,:), pointer :: iceberg_heat_content=>null() ! Distributed heat content of bergs (J/m^2)
@@ -123,7 +125,7 @@ module ice_bergs_framework
   integer :: id_calving_hflx_in=-1, id_stored_heat=-1, id_melt_hflx=-1, id_heat_content=-1
   integer :: id_mass=-1, id_ui=-1, id_vi=-1, id_ua=-1, id_va=-1, id_sst=-1, id_cn=-1, id_hi=-1
   integer :: id_bergy_src=-1, id_bergy_melt=-1, id_bergy_mass=-1, id_berg_melt=-1
-  integer :: id_mass_on_ocn=-1, id_ssh=-1, id_fax=-1, id_fay=-1
+  integer :: id_mass_on_ocn=-1, id_ssh=-1, id_fax=-1, id_fay=-1,  id_mean_calving=-1, id_mean_calving_hflx=-1
 
   real :: clipping_depth=0. ! The effective depth at which to clip the weight felt by the ocean [m].
 
@@ -192,6 +194,7 @@ module ice_bergs_framework
   logical :: critical_interaction_damping_on=.true.  !Sets the damping on relative iceberg velocity to critical value - Added by Alon 
   logical :: read_old_restarts=.true. ! If true, read restarts prior to grid_of_lists and iceberg_num innovation
   real :: speed_limit=0. ! CFL speed limit for a berg [m/s]
+  real :: tau_calving=0. ! Time scale for smoothing out calving field (years)
   real :: tip_parameter=0. ! parameter to override iceberg rollilng critica ratio (use zero to get parameter directly from ice and seawater densities) 
   real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
   type(buffer), pointer :: obuffer_n=>null(), ibuffer_n=>null()
@@ -205,6 +208,8 @@ module ice_bergs_framework
   real :: net_incoming_calving_heat=0., net_outgoing_calving_heat=0.
   real :: net_incoming_calving_heat_used=0., net_heat_to_bergs=0.
   real :: stored_start=0., stored_end=0.
+  real :: mean_calving_start=0., mean_calving_end=0.
+  real :: mean_calving_hflx_start=0., mean_calving_hflx_end=0.
   real :: stored_heat_start=0., stored_heat_end=0., net_heat_to_ocean=0.
   real :: net_calving_used=0., net_calving_to_bergs=0.
   real :: floating_mass_start=0., floating_mass_end=0.
@@ -284,6 +289,7 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
 logical :: time_average_weight=.false. ! Time average the weight on the ocean
 real :: speed_limit=0. ! CFL speed limit for a berg
+real :: tau_calving=0. ! Time scale for smoothing out calving field (years)
 real :: tip_parameter=0. ! parameter to override iceberg rollilng critica ratio (use zero to get parameter directly from ice and seawater densities
 real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
 logical :: Runge_not_Verlet=.True.  !True=Runge Kutta, False=Verlet.  - Added by Alon 
@@ -304,7 +310,7 @@ subroutine ice_bergs_framework_init(bergs, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, tip_parameter, &
          time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, interactive_icebergs_on, critical_interaction_damping_on, &
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution, force_all_pes_traj, &
-         read_old_restarts
+         read_old_restarts,tau_calving
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -415,6 +421,8 @@ subroutine ice_bergs_framework_init(bergs, &
   allocate( grd%mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%mass(:,:)=0.
   allocate( grd%mass_on_ocean(grd%isd:grd%ied, grd%jsd:grd%jed, 9) ); grd%mass_on_ocean(:,:,:)=0.
   allocate( grd%stored_ice(grd%isd:grd%ied, grd%jsd:grd%jed, nclasses) ); grd%stored_ice(:,:,:)=0.
+  allocate( grd%mean_calving(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%mean_calving(:,:)=999.
+  allocate( grd%mean_calving_hflx(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%mean_calving_hflx(:,:)=999.
   allocate( grd%real_calving(grd%isd:grd%ied, grd%jsd:grd%jed, nclasses) ); grd%real_calving(:,:,:)=0.
   allocate( grd%uo(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%uo(:,:)=0.
   allocate( grd%vo(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%vo(:,:)=0.
@@ -557,6 +565,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%passive_mode=passive_mode
   bergs%time_average_weight=time_average_weight
   bergs%speed_limit=speed_limit
+  bergs%tau_calving=tau_calving
   bergs%tip_parameter=tip_parameter
   bergs%Runge_not_Verlet=Runge_not_Verlet   !Alon
   bergs%use_updated_rolling_scheme=use_updated_rolling_scheme  !Alon
@@ -615,6 +624,10 @@ subroutine ice_bergs_framework_init(bergs, &
      'Accumulated ice mass by class', 'kg')
   grd%id_real_calving=register_diag_field('icebergs', 'real_calving', axes3d, Time, &
      'Calving into iceberg class', 'kg/s')
+  grd%id_mean_calving=register_diag_field('icebergs', 'mean_calving', axes, Time, &
+     'Running mean of calving', 'kg/s')
+  grd%id_mean_calving_hflx=register_diag_field('icebergs', 'mean_calving_hflx', axes, Time, &
+     'Running mean of calving heat flux', 'J/s')
   grd%id_uo=register_diag_field('icebergs', 'uo', axes, Time, &
      'Ocean zonal component of velocity', 'm s^-1')
   grd%id_vo=register_diag_field('icebergs', 'vo', axes, Time, &
@@ -2593,6 +2606,8 @@ subroutine checksum_gridded(grd, label)
   call grd_chksum2(grd, grd%mass, 'mass')
   call grd_chksum3(grd, grd%mass_on_ocean, 'mass_on_ocean')
   call grd_chksum3(grd, grd%stored_ice, 'stored_ice')
+  call grd_chksum2(grd, grd%mean_calving, 'mean_calving')
+  call grd_chksum2(grd, grd%mean_calving_hflx, 'mean_calving_hflx')
   call grd_chksum2(grd, grd%stored_heat, 'stored_heat')
   call grd_chksum2(grd, grd%melt_buoy, 'melt_b')
   call grd_chksum2(grd, grd%melt_eros, 'melt_e')
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index e2633c4..eea6035 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -306,6 +306,9 @@ subroutine write_restart(bergs)
   call write_data(filename, 'stored_heat', bergs%grd%stored_heat, bergs%grd%domain)
   !call grd_chksum2(bergs%grd, bergs%grd%iceberg_counter_grd, 'write iceberg_counter_grd')
   call write_data(filename, 'iceberg_counter_grd', bergs%grd%iceberg_counter_grd, bergs%grd%domain)
+  call grd_chksum2(bergs%grd, bergs%grd%stored_ice, 'write calving mean')
+  call write_data(filename, 'mean_calving', bergs%grd%mean_calving, bergs%grd%domain)
+  call write_data(filename, 'mean_calving_hflx', bergs%grd%mean_calving_hflx, bergs%grd%domain)
   contains
 
   function last_berg(berg)
@@ -1006,6 +1009,24 @@ subroutine read_restart_calving(bergs)
      'diamonds, read_restart_calving: stored_heat WAS NOT FOUND in the file. Setting to 0.'
       grd%stored_heat(:,:)=0.
     endif
+    if (field_exist(filename, 'mean_calving')) then
+      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+       'diamonds, read_restart_calving: reading mean_calving from restart file.'
+      call read_data(filename, 'mean_calving', grd%mean_calving, grd%domain)
+    else
+      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+     'diamonds, read_restart_calving: mean_calving WAS NOT FOUND in the file. Setting to 0.'
+      grd%mean_calving(:,:)=999.
+    endif
+    if (field_exist(filename, 'mean_calving_hflx')) then
+      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+       'diamonds, read_restart_calving: reading mean_calving_hflx from restart file.'
+      call read_data(filename, 'mean_calving_hflx', grd%mean_calving_hflx, grd%domain)
+    else
+      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+     'diamonds, read_restart_calving: mean_calving_hflx WAS NOT FOUND in the file. Setting to 0.'
+      grd%mean_calving_hflx(:,:)=999.
+    endif
     if (field_exist(filename, 'iceberg_counter_grd')) then
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
        'diamonds, read_restart_calving: reading iceberg_counter_grd from restart file.'
@@ -1045,9 +1066,13 @@ subroutine read_restart_calving(bergs)
   endif
 
   call grd_chksum3(bergs%grd, bergs%grd%stored_ice, 'read_restart_calving, stored_ice')
+  call grd_chksum2(bergs%grd, bergs%grd%mean_calving, 'read_restart_calving, mean_calving')
+  call grd_chksum2(bergs%grd, bergs%grd%mean_calving_hflx, 'read_restart_calving, mean_calving_hflx')
   call grd_chksum2(bergs%grd, bergs%grd%stored_heat, 'read_restart_calving, stored_heat')
 
   bergs%stored_start=sum( grd%stored_ice(grd%isc:grd%iec,grd%jsc:grd%jec,:) )
+  bergs%mean_calving_start=sum( grd%mean_calving(grd%isc:grd%iec,grd%jsc:grd%jec) )
+  bergs%mean_calving_hflx_start=sum( grd%mean_calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec) )
   call mpp_sum( bergs%stored_start )
   bergs%stored_heat_start=sum( grd%stored_heat(grd%isc:grd%iec,grd%jsc:grd%jec) )
   call mpp_sum( bergs%stored_heat_start )

From 7e257bb0f9574bc60ed579fd9be5a6cfb429b90d Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 24 Aug 2016 11:06:16 -0400
Subject: [PATCH 155/361] Deallocate mean_calving_hflx has been added

---
 icebergs.F90 | 1 +
 1 file changed, 1 insertion(+)

diff --git a/icebergs.F90 b/icebergs.F90
index 3fe3971..6c2a597 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -2831,6 +2831,7 @@ subroutine icebergs_end(bergs)
   deallocate(bergs%grd%tmpc)
   deallocate(bergs%grd%stored_ice)
   deallocate(bergs%grd%mean_calving)
+  deallocate(bergs%grd%mean_calving_hflx)
   deallocate(bergs%grd%real_calving)
   deallocate(bergs%grd%uo)
   deallocate(bergs%grd%vo)

From 83ec1c894a59c3a37f72da1b8db393f57bb9a340 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Wed, 24 Aug 2016 13:17:02 -0400
Subject: [PATCH 156/361] Renamed grd%mean_calving to grd%rmean_calving

- The field grd%mean_calving(:,:) stores the running-mean so we
  change the name to include "rmean".
- Fixed bug where rmean_calving_hflx was using calving instead of calving_hlf.
- Added explicit array syntax; a(:)=b(:) is preferred to a=b.
- Added a logical flag to catch need to initialize the running mean fields.
- Avoid doing any computation when weight alpha==0.
- Switch to a sign preserving form of the running mean expression.
---
 icebergs.F90           | 78 +++++++++++++++++++++++++++---------------
 icebergs_framework.F90 | 24 +++++++------
 icebergs_io.F90        | 35 ++++++++++---------
 3 files changed, 81 insertions(+), 56 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 6c2a597..49c280e 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1178,21 +1178,29 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
        ' yr,yrdy=', bergs%current_year, bergs%current_yearday
 
 
-  ! Adapt calving flux from coupler for use here
  !call sanitize_field(grd%calving,1.e20)
   tmpsum=sum( calving(:,:)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
   bergs%net_calving_received=bergs%net_calving_received+tmpsum*bergs%dt
+
+  ! Adapt calving heat flux from coupler
+  grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)=calving_hflx(:,:) & ! Units of W/m2
+       *grd%msk(grd%isc:grd%iec,grd%jsc:grd%jec)
   
-  call get_running_mean_calving(bergs,calving,calving_hflx)
-  grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec)=calving(:,:) ! Units of kg/m2/s
+  ! Adapt calving flux from coupler for use here
+  grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec)=calving(:,:) & ! Units of kg/m2/s
+       *grd%msk(grd%isc:grd%iec,grd%jsc:grd%jec)
+
+  ! Running means of calving and calving_hflx
+  call get_running_mean_calving(bergs, grd%calving, grd%calving_hflx)
+  calving(:,:)=grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec) ! Copy back from grd%calving if using running-mean
+  calving_hflx(:,:)=grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)
+
   grd%calving(:,:)=grd%calving(:,:)*grd%msk(:,:)*grd%area(:,:) ! Convert to kg/s
   tmpsum=sum( grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec) )
   bergs%net_incoming_calving=bergs%net_incoming_calving+tmpsum*bergs%dt
   if (grd%id_calving>0) &
     lerr=send_data(grd%id_calving, grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
 
-  ! Adapt calving heat flux from coupler
-  grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)=calving_hflx(:,:) ! Units of W/m2
   grd%calving_hflx(:,:)=grd%calving_hflx(:,:)*grd%msk(:,:) ! Mask (just in case)
   if (grd%id_calving_hflx_in>0) &
     lerr=send_data(grd%id_calving_hflx_in, grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
@@ -1371,10 +1379,10 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     lerr=send_data(grd%id_mass, grd%mass(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   if (grd%id_stored_ice>0) &
     lerr=send_data(grd%id_stored_ice, grd%stored_ice(grd%isc:grd%iec,grd%jsc:grd%jec,:), Time)
-  if (grd%id_mean_calving>0) &
-    lerr=send_data(grd%id_mean_calving, grd%mean_calving(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  if (grd%id_mean_calving_hflx>0) &
-    lerr=send_data(grd%id_mean_calving_hflx, grd%mean_calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_rmean_calving>0) &
+    lerr=send_data(grd%id_rmean_calving, grd%rmean_calving(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_rmean_calving_hflx>0) &
+    lerr=send_data(grd%id_rmean_calving_hflx, grd%rmean_calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   if (grd%id_real_calving>0) &
     lerr=send_data(grd%id_real_calving, grd%real_calving(grd%isc:grd%iec,grd%jsc:grd%jec,:), Time)
   if (grd%id_ssh>0) &
@@ -1419,8 +1427,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   bergs%net_outgoing_calving_heat=bergs%net_outgoing_calving_heat+tmpsum*bergs%dt ! Units of J
   if (lbudget) then
     bergs%stored_end=sum( grd%stored_ice(grd%isc:grd%iec,grd%jsc:grd%jec,:) )
-    bergs%mean_calving_end=sum( grd%mean_calving(grd%isc:grd%iec,grd%jsc:grd%jec) )
-    bergs%mean_calving_hflx_end=sum( grd%mean_calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec) )
+    bergs%rmean_calving_end=sum( grd%rmean_calving(grd%isc:grd%iec,grd%jsc:grd%jec) )
+    bergs%rmean_calving_hflx_end=sum( grd%rmean_calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec) )
     bergs%stored_heat_end=sum( grd%stored_heat(grd%isc:grd%iec,grd%jsc:grd%jec) )
     bergs%floating_mass_end=sum_mass(bergs%first)
     bergs%icebergs_mass_end=sum_mass(bergs%first,justbergs=.true.)
@@ -1627,28 +1635,42 @@ subroutine get_running_mean_calving(bergs,calving,calving_hflx)
   type(icebergs), pointer :: bergs
   real, dimension(:,:), intent(inout) :: calving, calving_hflx
   ! Local variables
-  real ::  alpha  !Parameter used for calving relaxation time stepping.  (0<=alpha<1)
-  real ::  tau  !Relaxation timescale in seconds
-  !This subroutine takes in the new calving and calving_hflx, and uses them to time step a mean_calving value
+  real :: alpha  !Parameter used for calving relaxation time stepping.  (0<=alpha<1)
+  real :: tau  !Relaxation timescale in seconds
+  real :: beta  ! = 1-alpha (0<=beta<1)
+  !This subroutine takes in the new calving and calving_hflx, and uses them to time step a running-mean_calving value
   !The time stepping uses a time scale tau. When tau is equal to zero, the
-  !running mean is exactly equal to the new calving value. 
-  !In the first iteration (or if the running mean is not yet set), then alpha is set to zero  (this is done using the 999. trick)
+  !running mean is exactly equal to the new calving value.
+
+  ! For the first time-step, initialize the running mean with the current data
+  if (.not. bergs%grd%rmean_calving_initialized) then
+    bergs%grd%rmean_calving(:,:)=calving(:,:)
+    bergs%grd%rmean_calving_initialized=.true.
+  endif
+  if (.not. bergs%grd%rmean_calving_hflx_initialized) then
+    bergs%grd%rmean_calving_hflx(:,:)=calving_hflx(:,:)
+    bergs%grd%rmean_calving_hflx_initialized=.true.
+  endif
 
   !Applying "Newton cooling" with timescale tau, to smooth out the calving field.
   tau=bergs%tau_calving/(365.*24*60*60) !Converting time scale from years to seconds
   alpha=tau/(tau+bergs%dt)
-  if ((maxval(bergs%grd%mean_calving).eq.999.0) .or. (maxval(bergs%grd%mean_calving_hflx).eq.999.0)) alpha=0.0  !Special case for first time step.
-  bergs%grd%mean_calving=calving + alpha*(bergs%grd%mean_calving-calving)
-  bergs%grd%mean_calving_hflx=calving + alpha*(bergs%grd%mean_calving_hflx-calving)
-  
-  !Removing negative values
-  bergs%grd%mean_calving=max(bergs%grd%mean_calving,0.)
-  bergs%grd%mean_calving_hflx=max(bergs%grd%mean_calving_hflx,0.)
+  if (alpha==0.) return ! Avoids unnecessary copying of arrays
+  if (alpha>0.5) then ! beta is small
+    beta=bergs%dt/(tau+bergs%dt)
+    alpha=1.-beta
+  else ! alpha is small
+    beta=1.-alpha
+  endif
+
+  ! For non-negative alpha and beta, these expressions for the running means are sign preserving
+  bergs%grd%rmean_calving(:,:)=beta*calving(:,:) + alpha*bergs%grd%rmean_calving(:,:)
+  bergs%grd%rmean_calving_hflx(:,:)=beta*calving_hflx(:,:) + alpha*bergs%grd%rmean_calving_hflx(:,:)
 
   !Setting calving used by the iceberg model equal to the running mean
-  calving=bergs%grd%mean_calving
-  calving_hflx=bergs%grd%mean_calving_hflx
-  
+  calving(:,:)=bergs%grd%rmean_calving(:,:)
+  calving_hflx(:,:)=bergs%grd%rmean_calving_hflx(:,:)
+
   end subroutine get_running_mean_calving
 
 end subroutine icebergs_run
@@ -2830,8 +2852,8 @@ subroutine icebergs_end(bergs)
   deallocate(bergs%grd%tmp)
   deallocate(bergs%grd%tmpc)
   deallocate(bergs%grd%stored_ice)
-  deallocate(bergs%grd%mean_calving)
-  deallocate(bergs%grd%mean_calving_hflx)
+  deallocate(bergs%grd%rmean_calving)
+  deallocate(bergs%grd%rmean_calving_hflx)
   deallocate(bergs%grd%real_calving)
   deallocate(bergs%grd%uo)
   deallocate(bergs%grd%vo)
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 3940961..3d51418 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -111,21 +111,23 @@ module ice_bergs_framework
   real, dimension(:,:), pointer :: tmp=>null() ! Temporary work space
   real, dimension(:,:), pointer :: tmpc=>null() ! Temporary work space
   real, dimension(:,:,:), pointer :: stored_ice=>null() ! Accumulated ice mass flux at calving locations (kg)
-  real, dimension(:,:), pointer :: mean_calving=>null() !Running mean for ice calving
-  real, dimension(:,:), pointer :: mean_calving_hflx=>null() !Running mean for ice calving
+  real, dimension(:,:), pointer :: rmean_calving=>null() ! Running mean for ice calving
+  real, dimension(:,:), pointer :: rmean_calving_hflx=>null() ! Running mean for ice calving
   real, dimension(:,:), pointer :: stored_heat=>null() ! Heat content of stored ice (J)
   real, dimension(:,:,:), pointer :: real_calving=>null() ! Calving rate into iceberg class at calving locations (kg/s)
   real, dimension(:,:), pointer :: iceberg_heat_content=>null() ! Distributed heat content of bergs (J/m^2)
   real, dimension(:,:), pointer :: parity_x=>null() ! X component of vector point from i,j to i+1,j+1 (for detecting tri-polar fold)
   real, dimension(:,:), pointer :: parity_y=>null() ! Y component of vector point from i,j to i+1,j+1 (for detecting tri-polar fold)
   integer, dimension(:,:), pointer :: iceberg_counter_grd=>null() ! Counts icebergs created for naming purposes
+  logical :: rmean_calving_initialized = .false. ! True if rmean_calving(:,:) has been filled with meaningful data
+  logical :: rmean_calving_hflx_initialized = .false. ! True if rmean_calving_hflx(:,:) has been filled with meaningful data
   ! Diagnostics handles
   integer :: id_uo=-1, id_vo=-1, id_calving=-1, id_stored_ice=-1, id_accum=-1, id_unused=-1, id_floating_melt=-1
   integer :: id_melt_buoy=-1, id_melt_eros=-1, id_melt_conv=-1, id_virtual_area=-1, id_real_calving=-1
   integer :: id_calving_hflx_in=-1, id_stored_heat=-1, id_melt_hflx=-1, id_heat_content=-1
   integer :: id_mass=-1, id_ui=-1, id_vi=-1, id_ua=-1, id_va=-1, id_sst=-1, id_cn=-1, id_hi=-1
   integer :: id_bergy_src=-1, id_bergy_melt=-1, id_bergy_mass=-1, id_berg_melt=-1
-  integer :: id_mass_on_ocn=-1, id_ssh=-1, id_fax=-1, id_fay=-1,  id_mean_calving=-1, id_mean_calving_hflx=-1
+  integer :: id_mass_on_ocn=-1, id_ssh=-1, id_fax=-1, id_fay=-1,  id_rmean_calving=-1, id_rmean_calving_hflx=-1
 
   real :: clipping_depth=0. ! The effective depth at which to clip the weight felt by the ocean [m].
 
@@ -208,8 +210,8 @@ module ice_bergs_framework
   real :: net_incoming_calving_heat=0., net_outgoing_calving_heat=0.
   real :: net_incoming_calving_heat_used=0., net_heat_to_bergs=0.
   real :: stored_start=0., stored_end=0.
-  real :: mean_calving_start=0., mean_calving_end=0.
-  real :: mean_calving_hflx_start=0., mean_calving_hflx_end=0.
+  real :: rmean_calving_start=0., rmean_calving_end=0.
+  real :: rmean_calving_hflx_start=0., rmean_calving_hflx_end=0.
   real :: stored_heat_start=0., stored_heat_end=0., net_heat_to_ocean=0.
   real :: net_calving_used=0., net_calving_to_bergs=0.
   real :: floating_mass_start=0., floating_mass_end=0.
@@ -421,8 +423,8 @@ subroutine ice_bergs_framework_init(bergs, &
   allocate( grd%mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%mass(:,:)=0.
   allocate( grd%mass_on_ocean(grd%isd:grd%ied, grd%jsd:grd%jed, 9) ); grd%mass_on_ocean(:,:,:)=0.
   allocate( grd%stored_ice(grd%isd:grd%ied, grd%jsd:grd%jed, nclasses) ); grd%stored_ice(:,:,:)=0.
-  allocate( grd%mean_calving(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%mean_calving(:,:)=999.
-  allocate( grd%mean_calving_hflx(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%mean_calving_hflx(:,:)=999.
+  allocate( grd%rmean_calving(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%rmean_calving(:,:)=0.
+  allocate( grd%rmean_calving_hflx(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%rmean_calving_hflx(:,:)=0.
   allocate( grd%real_calving(grd%isd:grd%ied, grd%jsd:grd%jed, nclasses) ); grd%real_calving(:,:,:)=0.
   allocate( grd%uo(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%uo(:,:)=0.
   allocate( grd%vo(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%vo(:,:)=0.
@@ -624,9 +626,9 @@ subroutine ice_bergs_framework_init(bergs, &
      'Accumulated ice mass by class', 'kg')
   grd%id_real_calving=register_diag_field('icebergs', 'real_calving', axes3d, Time, &
      'Calving into iceberg class', 'kg/s')
-  grd%id_mean_calving=register_diag_field('icebergs', 'mean_calving', axes, Time, &
+  grd%id_rmean_calving=register_diag_field('icebergs', 'running_mean_calving', axes, Time, &
      'Running mean of calving', 'kg/s')
-  grd%id_mean_calving_hflx=register_diag_field('icebergs', 'mean_calving_hflx', axes, Time, &
+  grd%id_rmean_calving_hflx=register_diag_field('icebergs', 'running_mean_calving_hflx', axes, Time, &
      'Running mean of calving heat flux', 'J/s')
   grd%id_uo=register_diag_field('icebergs', 'uo', axes, Time, &
      'Ocean zonal component of velocity', 'm s^-1')
@@ -2606,8 +2608,8 @@ subroutine checksum_gridded(grd, label)
   call grd_chksum2(grd, grd%mass, 'mass')
   call grd_chksum3(grd, grd%mass_on_ocean, 'mass_on_ocean')
   call grd_chksum3(grd, grd%stored_ice, 'stored_ice')
-  call grd_chksum2(grd, grd%mean_calving, 'mean_calving')
-  call grd_chksum2(grd, grd%mean_calving_hflx, 'mean_calving_hflx')
+  call grd_chksum2(grd, grd%rmean_calving, 'rmean_calving')
+  call grd_chksum2(grd, grd%rmean_calving_hflx, 'rmean_calving_hflx')
   call grd_chksum2(grd, grd%stored_heat, 'stored_heat')
   call grd_chksum2(grd, grd%melt_buoy, 'melt_b')
   call grd_chksum2(grd, grd%melt_eros, 'melt_e')
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index eea6035..bc0bc76 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -306,9 +306,10 @@ subroutine write_restart(bergs)
   call write_data(filename, 'stored_heat', bergs%grd%stored_heat, bergs%grd%domain)
   !call grd_chksum2(bergs%grd, bergs%grd%iceberg_counter_grd, 'write iceberg_counter_grd')
   call write_data(filename, 'iceberg_counter_grd', bergs%grd%iceberg_counter_grd, bergs%grd%domain)
-  call grd_chksum2(bergs%grd, bergs%grd%stored_ice, 'write calving mean')
-  call write_data(filename, 'mean_calving', bergs%grd%mean_calving, bergs%grd%domain)
-  call write_data(filename, 'mean_calving_hflx', bergs%grd%mean_calving_hflx, bergs%grd%domain)
+  call grd_chksum2(bergs%grd, bergs%grd%rmean_calving, 'write mean calving')
+  call write_data(filename, 'rmean_calving', bergs%grd%rmean_calving, bergs%grd%domain)
+  call grd_chksum2(bergs%grd, bergs%grd%rmean_calving_hflx, 'write mean calving_hflx')
+  call write_data(filename, 'rmean_calving_hflx', bergs%grd%rmean_calving_hflx, bergs%grd%domain)
   contains
 
   function last_berg(berg)
@@ -1009,23 +1010,23 @@ subroutine read_restart_calving(bergs)
      'diamonds, read_restart_calving: stored_heat WAS NOT FOUND in the file. Setting to 0.'
       grd%stored_heat(:,:)=0.
     endif
-    if (field_exist(filename, 'mean_calving')) then
+    if (field_exist(filename, 'rmean_calving')) then
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
-       'diamonds, read_restart_calving: reading mean_calving from restart file.'
-      call read_data(filename, 'mean_calving', grd%mean_calving, grd%domain)
+       'diamonds, read_restart_calving: reading rmean_calving from restart file.'
+      call read_data(filename, 'rmean_calving', grd%rmean_calving, grd%domain)
+      grd%rmean_calving_initialized=.true.
     else
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
-     'diamonds, read_restart_calving: mean_calving WAS NOT FOUND in the file. Setting to 0.'
-      grd%mean_calving(:,:)=999.
+     'diamonds, read_restart_calving: rmean_calving WAS NOT FOUND in the file. Setting to 0.'
     endif
-    if (field_exist(filename, 'mean_calving_hflx')) then
+    if (field_exist(filename, 'rmean_calving_hflx')) then
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
-       'diamonds, read_restart_calving: reading mean_calving_hflx from restart file.'
-      call read_data(filename, 'mean_calving_hflx', grd%mean_calving_hflx, grd%domain)
+       'diamonds, read_restart_calving: reading rmean_calving_hflx from restart file.'
+      call read_data(filename, 'rmean_calving_hflx', grd%rmean_calving_hflx, grd%domain)
+      grd%rmean_calving_hflx_initialized=.true.
     else
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
-     'diamonds, read_restart_calving: mean_calving_hflx WAS NOT FOUND in the file. Setting to 0.'
-      grd%mean_calving_hflx(:,:)=999.
+     'diamonds, read_restart_calving: rmean_calving_hflx WAS NOT FOUND in the file. Setting to 0.'
     endif
     if (field_exist(filename, 'iceberg_counter_grd')) then
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
@@ -1066,13 +1067,13 @@ subroutine read_restart_calving(bergs)
   endif
 
   call grd_chksum3(bergs%grd, bergs%grd%stored_ice, 'read_restart_calving, stored_ice')
-  call grd_chksum2(bergs%grd, bergs%grd%mean_calving, 'read_restart_calving, mean_calving')
-  call grd_chksum2(bergs%grd, bergs%grd%mean_calving_hflx, 'read_restart_calving, mean_calving_hflx')
   call grd_chksum2(bergs%grd, bergs%grd%stored_heat, 'read_restart_calving, stored_heat')
+  call grd_chksum2(bergs%grd, bergs%grd%rmean_calving, 'read_restart_calving, rmean_calving')
+  call grd_chksum2(bergs%grd, bergs%grd%rmean_calving_hflx, 'read_restart_calving, rmean_calving_hflx')
 
   bergs%stored_start=sum( grd%stored_ice(grd%isc:grd%iec,grd%jsc:grd%jec,:) )
-  bergs%mean_calving_start=sum( grd%mean_calving(grd%isc:grd%iec,grd%jsc:grd%jec) )
-  bergs%mean_calving_hflx_start=sum( grd%mean_calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec) )
+  bergs%rmean_calving_start=sum( grd%rmean_calving(grd%isc:grd%iec,grd%jsc:grd%jec) )
+  bergs%rmean_calving_hflx_start=sum( grd%rmean_calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec) )
   call mpp_sum( bergs%stored_start )
   bergs%stored_heat_start=sum( grd%stored_heat(grd%isc:grd%iec,grd%jsc:grd%jec) )
   call mpp_sum( bergs%stored_heat_start )

From a28e4abbcc5ca7b7f4aae69f719858e24baba9a5 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Wed, 24 Aug 2016 15:43:04 -0400
Subject: [PATCH 157/361] Wrapped running-mean of calving in logical if-block

- To avoid unnecessary copying of data and writing of data to restart
  files, the running-mean calculations of calving and calving_hlfx
  are now wrapped inside "if (tau_calving>0)" blocks.
- No answer changes.
---
 icebergs.F90    |  8 +++++---
 icebergs_io.F90 | 10 ++++++----
 2 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 49c280e..9cdb511 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1191,9 +1191,11 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
        *grd%msk(grd%isc:grd%iec,grd%jsc:grd%jec)
 
   ! Running means of calving and calving_hflx
-  call get_running_mean_calving(bergs, grd%calving, grd%calving_hflx)
-  calving(:,:)=grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec) ! Copy back from grd%calving if using running-mean
-  calving_hflx(:,:)=grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)
+  if (bergs%tau_calving>0.) then
+    call get_running_mean_calving(bergs, grd%calving, grd%calving_hflx)
+    calving(:,:)=grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec) ! Copy back from grd%calving if using running-mean
+    calving_hflx(:,:)=grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)
+  endif
 
   grd%calving(:,:)=grd%calving(:,:)*grd%msk(:,:)*grd%area(:,:) ! Convert to kg/s
   tmpsum=sum( grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec) )
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index bc0bc76..bd4f994 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -306,10 +306,12 @@ subroutine write_restart(bergs)
   call write_data(filename, 'stored_heat', bergs%grd%stored_heat, bergs%grd%domain)
   !call grd_chksum2(bergs%grd, bergs%grd%iceberg_counter_grd, 'write iceberg_counter_grd')
   call write_data(filename, 'iceberg_counter_grd', bergs%grd%iceberg_counter_grd, bergs%grd%domain)
-  call grd_chksum2(bergs%grd, bergs%grd%rmean_calving, 'write mean calving')
-  call write_data(filename, 'rmean_calving', bergs%grd%rmean_calving, bergs%grd%domain)
-  call grd_chksum2(bergs%grd, bergs%grd%rmean_calving_hflx, 'write mean calving_hflx')
-  call write_data(filename, 'rmean_calving_hflx', bergs%grd%rmean_calving_hflx, bergs%grd%domain)
+  if (bergs%tau_calving>0.) then
+    call grd_chksum2(bergs%grd, bergs%grd%rmean_calving, 'write mean calving')
+    call write_data(filename, 'rmean_calving', bergs%grd%rmean_calving, bergs%grd%domain)
+    call grd_chksum2(bergs%grd, bergs%grd%rmean_calving_hflx, 'write mean calving_hflx')
+    call write_data(filename, 'rmean_calving_hflx', bergs%grd%rmean_calving_hflx, bergs%grd%domain)
+  endif
   contains
 
   function last_berg(berg)

From 87317223c47fd980763def351012af137fc11048 Mon Sep 17 00:00:00 2001
From: Niki Zadeh <Niki.Zadeh@noaa.gov>
Date: Fri, 26 Aug 2016 13:30:48 -0400
Subject: [PATCH 158/361] Write bonds only if they are being used

-Fix suggested by Alon to turn off writing the bond files if they're not being used
---
 icebergs_io.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 84d4ff7..8c96195 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -307,7 +307,6 @@ subroutine write_restart(bergs)
    if (bergs%iceberg_bonds_on) then
      check_bond_quality=.true.
      call count_bonds(bergs, nbonds,check_bond_quality)
-   endif
 
    allocate(first_berg_num(nbonds))
    allocate(other_berg_num(nbonds))
@@ -369,6 +368,7 @@ subroutine write_restart(bergs)
 
 
   call nullify_domain()
+   endif
 
 !#############################################################################################
 

From 4f920fae95ba2d30e64bbc65924befbd9b203b5b Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 14 Sep 2016 11:33:44 -0400
Subject: [PATCH 159/361] 1) When read_old_restart flag is set to true, the
 model does not reproduce accross restarts. This bug is fixed by setting
 iceberg_num to -1 when read_old_restarts is true. In order to used the
 iceberg_num correctly, read_old_restarts should be set to false.

2) The model was not reproducing accross: restarts in certain situations when fix_restart_date=.true. (default). This is because a minor offset is added to the icebergs start time (to differentiate icebergs with the same start date). This minor offset can make the start date be in the future. When fix_restart_date is true, an iceberg being in the future, makes the code update the start dates, which prevents the model from reproducing across restarts. This has been fixed by making the minor offset be negative, so that iceberg start dates are always before the current date. (I hope that this does not cause any other unforeseen issues).

3) The code which generates icebergs for testing  has also been refactored slightly to remove redundant lines and to make it more readable (both in the old and new versions of the read_restart subroutine)
---
 icebergs.F90    |  6 +++++-
 icebergs_io.F90 | 55 +++++++++++++++++++------------------------------
 2 files changed, 26 insertions(+), 35 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 522d0cd..87a7f16 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1815,7 +1815,11 @@ subroutine calve_icebergs(bergs)
           newberg%start_lon=newberg%lon
           newberg%start_lat=newberg%lat
           newberg%start_year=bergs%current_year
-          newberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i+(iNg*(j-1)))  ! unique number for each iceberg
+          if (.not. bergs%read_old_restarts) then
+            newberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i+(iNg*(j-1)))  ! unique number for each iceberg
+          else
+            newberg%iceberg_num=-1
+          endif
           newberg%start_day=bergs%current_yearday+ddt/86400.
           newberg%start_mass=bergs%initial_mass(k)
           newberg%mass_scaling=bergs%mass_scaling(k)
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index e2633c4..7092cb8 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -298,7 +298,6 @@ subroutine write_restart(bergs)
 
   ! Write stored ice
   filename='RESTART/calving.res.nc'
-  if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(stderrunit,'(2a)') 'diamonds, write_restart: writing ',filename
 
   call grd_chksum3(bergs%grd, bergs%grd%stored_ice, 'write stored_ice')
   call write_data(filename, 'stored_ice', bergs%grd%stored_ice, bergs%grd%domain)
@@ -475,10 +474,11 @@ subroutine read_restart_bergs_orig(bergs,Time)
       localberg%start_year=get_int(ncid, start_yearid, k)
       if (bergs%read_old_restarts) then
         ! This emulates the iceberg counter used at calving sites but uses the restart position instead
-        i = localberg%ine
-        j = localberg%jne
-        localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i+(iNg*(j-1)))  ! unique number for each iceberg
-        grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
+        !i = localberg%ine
+        !j = localberg%jne
+        !localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i+(iNg*(j-1)))  ! unique number for each iceberg
+        !grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
+        localberg%iceberg_num=-1
       else
         localberg%iceberg_num=get_int(ncid, iceberg_numid, k)
       endif
@@ -576,47 +576,34 @@ subroutine generate_bergs(bergs,Time)
         localberg%mass_scaling=bergs%mass_scaling(1)
         localberg%mass_of_bits=0.
         localberg%heat_density=0.
-        localberg%uvel=1.
-        localberg%vvel=0.
         localberg%axn=0. !Alon
         localberg%ayn=0. !Alon
         localberg%uvel_old=0. !Alon
         localberg%vvel_old=0. !Alon
         localberg%bxn=0. !Alon
         localberg%byn=0. !Alon
+        
+        !Berg A
+        localberg%uvel=1.
+        localberg%vvel=0.
         localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
         grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
         call add_new_berg_to_list(bergs%first, localberg)
+        !Berg B
         localberg%uvel=-1.
         localberg%vvel=0.
-        localberg%axn=0. !Alon
-        localberg%ayn=0. !Alon
-        localberg%uvel_old=0. !Alon
-        localberg%vvel_old=0. !Alon
-        localberg%bxn=0. !Alon
-        localberg%byn=0. !Alon
         localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
         grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
         call add_new_berg_to_list(bergs%first, localberg)
+        !Berg C
         localberg%uvel=0.
         localberg%vvel=1.
-        localberg%axn=0. !Alon
-        localberg%ayn=0. !Alon
-        localberg%uvel_old=0. !Alon
-        localberg%vvel_old=0. !Alon
-        localberg%bxn=0. !Alon
-        localberg%byn=0. !Alon
         localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
         grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
         call add_new_berg_to_list(bergs%first, localberg)
+        !Berg D
         localberg%uvel=0.
         localberg%vvel=-1.
-        localberg%axn=0. !Alon
-        localberg%ayn=0. !Alon
-        localberg%uvel_old=0. !Alon
-        localberg%vvel_old=0. !Alon
-        localberg%bxn=0. !Alon
-        localberg%byn=0. !Alon
         localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
         grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
         call add_new_berg_to_list(bergs%first, localberg)
@@ -812,15 +799,15 @@ subroutine read_restart_bergs(bergs,Time)
       localberg%start_lon=start_lon(k)
       localberg%start_lat=start_lat(k)
       localberg%start_year=start_year(k)
-      if (bergs%read_old_restarts) then
-        ! This emulates the iceberg counter used at calving sites but uses the restart position instead
-        i = localberg%ine
-        j = localberg%jne
-        localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i+(iNg*(j-1)))  ! unique number for each iceberg
-        grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
-      else
+      !if (bergs%read_old_restarts) then
+      !  ! This emulates the iceberg counter used at calving sites but uses the restart position instead
+      !  !i = localberg%ine
+      !  !j = localberg%jne
+      !  !localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i+(iNg*(j-1)))  ! unique number for each iceberg
+      !  !grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
+      !else
         localberg%iceberg_num=iceberg_num(k)
-      endif
+      !endif
       localberg%start_day=start_day(k)
       localberg%start_mass=start_mass(k)
       localberg%mass_scaling=mass_scaling(k)
@@ -1013,7 +1000,7 @@ subroutine read_restart_calving(bergs)
     else
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
      'diamonds, read_restart_calving: iceberg_counter_grd WAS NOT FOUND in the file. Setting to 0.'
-      grd%iceberg_counter_grd(:,:)=0
+      grd%iceberg_counter_grd(:,:)=1
     endif
     bergs%restarted=.true.
   else

From 6456f11ed026c51ab5544dad0690d772fdf1da51 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 14 Sep 2016 14:57:24 -0400
Subject: [PATCH 160/361] 1) A line which writes the restart filename to the
 screen was removed by mistake before the last commit. This has been added
 again.

2) The changes made in the last commit have been cleaned up a little to remove commented out lines.
---
 icebergs.F90           |  6 +++++-
 icebergs_framework.F90 |  5 ++++-
 icebergs_io.F90        | 43 +++++++++---------------------------------
 3 files changed, 18 insertions(+), 36 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 87a7f16..3f4e762 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1839,7 +1839,11 @@ subroutine calve_icebergs(bergs)
           grd%stored_ice(i,j,k)=grd%stored_ice(i,j,k)-calved_to_berg
           calving_to_bergs=calving_to_bergs+calved_to_berg
           grd%real_calving(i,j,k)=grd%real_calving(i,j,k)+calved_to_berg/bergs%dt
-          ddt=ddt+bergs%dt*2./17. ! Minor offset to start day
+
+          !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+          ddt=ddt-bergs%dt*2./17. ! Minor offset to start day (negative offsets)
+          !ddt=ddt+bergs%dt*2./17. ! Minor offset to start day
+          !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
           icnt=icnt+1
           bergs%nbergs_calved=bergs%nbergs_calved+1
           bergs%nbergs_calved_by_class(k)=bergs%nbergs_calved_by_class(k)+1
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index d6e6763..628c6db 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -693,6 +693,7 @@ subroutine offset_berg_dates(bergs,Time)
 type(iceberg), pointer :: this
 integer :: iyr, imon, iday, ihr, imin, isec, yr_offset
 real :: latest_start_year, berg_start_year
+real :: current_time_val
 
   call get_date(Time, iyr, imon, iday, ihr, imin, isec)
   latest_start_year=iyr-99999
@@ -708,7 +709,9 @@ subroutine offset_berg_dates(bergs,Time)
   enddo
   call mpp_max(latest_start_year)
 
-  if (latest_start_year<=float(iyr)+yearday(imon, iday, ihr, imin, isec)/367.) return ! No conflicts!
+  current_time_val=float(iyr)+yearday(imon, iday, ihr, imin, isec)/367.
+  if (latest_start_year<=current_time_val) return ! No conflicts!
+  !if (latest_start_year<=float(iyr)+yearday(imon, iday, ihr, imin, isec)/367.) return ! No conflicts!
 
   yr_offset=int(latest_start_year+1.)-iyr
   if (mpp_pe().eq.mpp_root_pe()) write(*,'(a,i8,a)') &
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 7092cb8..1832374 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -298,6 +298,7 @@ subroutine write_restart(bergs)
 
   ! Write stored ice
   filename='RESTART/calving.res.nc'
+  if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(stderrunit,'(2a)') 'diamonds, write_restart: writing ',filename
 
   call grd_chksum3(bergs%grd, bergs%grd%stored_ice, 'write stored_ice')
   call write_data(filename, 'stored_ice', bergs%grd%stored_ice, bergs%grd%domain)
@@ -473,11 +474,6 @@ subroutine read_restart_bergs_orig(bergs,Time)
       localberg%start_lat=get_double(ncid, start_latid, k)
       localberg%start_year=get_int(ncid, start_yearid, k)
       if (bergs%read_old_restarts) then
-        ! This emulates the iceberg counter used at calving sites but uses the restart position instead
-        !i = localberg%ine
-        !j = localberg%jne
-        !localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i+(iNg*(j-1)))  ! unique number for each iceberg
-        !grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
         localberg%iceberg_num=-1
       else
         localberg%iceberg_num=get_int(ncid, iceberg_numid, k)
@@ -799,15 +795,7 @@ subroutine read_restart_bergs(bergs,Time)
       localberg%start_lon=start_lon(k)
       localberg%start_lat=start_lat(k)
       localberg%start_year=start_year(k)
-      !if (bergs%read_old_restarts) then
-      !  ! This emulates the iceberg counter used at calving sites but uses the restart position instead
-      !  !i = localberg%ine
-      !  !j = localberg%jne
-      !  !localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i+(iNg*(j-1)))  ! unique number for each iceberg
-      !  !grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
-      !else
-        localberg%iceberg_num=iceberg_num(k)
-      !endif
+      localberg%iceberg_num=iceberg_num(k)
       localberg%start_day=start_day(k)
       localberg%start_mass=start_mass(k)
       localberg%mass_scaling=mass_scaling(k)
@@ -907,47 +895,34 @@ subroutine generate_bergs(bergs,Time)
         localberg%mass_scaling=bergs%mass_scaling(1)
         localberg%mass_of_bits=0.
         localberg%heat_density=0.
-        localberg%uvel=1.
-        localberg%vvel=0.
         localberg%axn=0. !Alon
         localberg%ayn=0. !Alon
         localberg%uvel_old=0. !Alon
         localberg%vvel_old=0. !Alon
         localberg%bxn=0. !Alon
         localberg%byn=0. !Alon
+
+        !Berg A
+        localberg%uvel=1.
+        localberg%vvel=0.
         localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
         grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
         call add_new_berg_to_list(bergs%first, localberg)
+        !Berg B
         localberg%uvel=-1.
         localberg%vvel=0.
-        localberg%axn=0. !Alon
-        localberg%ayn=0. !Alon
-        localberg%uvel_old=0. !Alon
-        localberg%vvel_old=0. !Alon
-        localberg%bxn=0. !Alon
-        localberg%byn=0. !Alon
         localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
         grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
         call add_new_berg_to_list(bergs%first, localberg)
+        !Berg C
         localberg%uvel=0.
         localberg%vvel=1.
-        localberg%axn=0. !Alon
-        localberg%ayn=0. !Alon
-        localberg%uvel_old=0. !Alon
-        localberg%vvel_old=0. !Alon
-        localberg%bxn=0. !Alon
-        localberg%byn=0. !Alon
         localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
         grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
         call add_new_berg_to_list(bergs%first, localberg)
+        !Berg D
         localberg%uvel=0.
         localberg%vvel=-1.
-        localberg%axn=0. !Alon
-        localberg%ayn=0. !Alon
-        localberg%uvel_old=0. !Alon
-        localberg%vvel_old=0. !Alon
-        localberg%bxn=0. !Alon
-        localberg%byn=0. !Alon
         localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
         grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
         call add_new_berg_to_list(bergs%first, localberg)

From bc9cb264c50698f26163f0bf9fe703843a5e1d59 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 14 Sep 2016 15:01:55 -0400
Subject: [PATCH 161/361] A few more lines have been cleaned up to remove
 commented out lines.

---
 icebergs.F90           | 4 ----
 icebergs_framework.F90 | 1 -
 2 files changed, 5 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 3f4e762..71b710c 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1839,11 +1839,7 @@ subroutine calve_icebergs(bergs)
           grd%stored_ice(i,j,k)=grd%stored_ice(i,j,k)-calved_to_berg
           calving_to_bergs=calving_to_bergs+calved_to_berg
           grd%real_calving(i,j,k)=grd%real_calving(i,j,k)+calved_to_berg/bergs%dt
-
-          !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
           ddt=ddt-bergs%dt*2./17. ! Minor offset to start day (negative offsets)
-          !ddt=ddt+bergs%dt*2./17. ! Minor offset to start day
-          !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
           icnt=icnt+1
           bergs%nbergs_calved=bergs%nbergs_calved+1
           bergs%nbergs_calved_by_class(k)=bergs%nbergs_calved_by_class(k)+1
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 628c6db..00b54ac 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -711,7 +711,6 @@ subroutine offset_berg_dates(bergs,Time)
 
   current_time_val=float(iyr)+yearday(imon, iday, ihr, imin, isec)/367.
   if (latest_start_year<=current_time_val) return ! No conflicts!
-  !if (latest_start_year<=float(iyr)+yearday(imon, iday, ihr, imin, isec)/367.) return ! No conflicts!
 
   yr_offset=int(latest_start_year+1.)-iyr
   if (mpp_pe().eq.mpp_root_pe()) write(*,'(a,i8,a)') &

From 05f7b6a52dbb13f7c390320127dc04cd9c95e231 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Thu, 15 Sep 2016 16:04:37 -0400
Subject: [PATCH 162/361] A variable grd%spread_area has been added to the
 model and diagnostics. This variable gives the percent of a grid cell which
 is covered by icebergs. This area covered by icebergs is calculated within
 the spread_mass_to_ocean subroutine, and the icebergs_incr_mass subrouting
 (using an optional flag).

---
 icebergs.F90           | 151 +++++++++++++++++++++++++++++------------
 icebergs_framework.F90 |  25 +++++--
 2 files changed, 126 insertions(+), 50 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 3b25127..c27c5a0 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1766,7 +1766,7 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
   real, intent(in) :: theta
   real, optional, intent(in) :: static_berg
   ! Local variables
-  real :: xL, xC, xR, yD, yC, yU, Mass, L
+  real :: xL, xC, xR, yD, yC, yU, Mass, L, Area_scaled
   real :: yDxL, yDxC, yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR
   real :: S, H, origin_x, origin_y, x0, y0
   real :: Area_Q1,Area_Q2 , Area_Q3,Area_Q4, Area_hex
@@ -1912,6 +1912,7 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
     fraction_used=1.  !Static icebergs do not share their mass with the boundary (this to initialize icebergs in regular arrangements against boundaries)
   endif
 
+  !Spreading the iceberg mass onto the ocean
   grd%mass_on_ocean(i,j,1)=grd%mass_on_ocean(i,j,1)+(yDxL*Mass/fraction_used)
   grd%mass_on_ocean(i,j,2)=grd%mass_on_ocean(i,j,2)+(yDxC*Mass/fraction_used)
   grd%mass_on_ocean(i,j,3)=grd%mass_on_ocean(i,j,3)+(yDxR*Mass/fraction_used)
@@ -1922,6 +1923,17 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
   grd%mass_on_ocean(i,j,8)=grd%mass_on_ocean(i,j,8)+(yUxC*Mass/fraction_used)
   grd%mass_on_ocean(i,j,9)=grd%mass_on_ocean(i,j,9)+(yUxR*Mass/fraction_used)
 
+  !Spreading the iceberg area onto the ocean
+  Area_scaled=Area*scaling
+  grd%area_on_ocean(i,j,1)=grd%area_on_ocean(i,j,1)+(yDxL*Area_scaled/fraction_used)
+  grd%area_on_ocean(i,j,2)=grd%area_on_ocean(i,j,2)+(yDxC*Area_scaled/fraction_used)
+  grd%area_on_ocean(i,j,3)=grd%area_on_ocean(i,j,3)+(yDxR*Area_scaled/fraction_used)
+  grd%area_on_ocean(i,j,4)=grd%area_on_ocean(i,j,4)+(yCxL*Area_scaled/fraction_used)
+  grd%area_on_ocean(i,j,5)=grd%area_on_ocean(i,j,5)+(yCxC*Area_scaled/fraction_used)
+  grd%area_on_ocean(i,j,6)=grd%area_on_ocean(i,j,6)+(yCxR*Area_scaled/fraction_used)
+  grd%area_on_ocean(i,j,7)=grd%area_on_ocean(i,j,7)+(yUxL*Area_scaled/fraction_used)
+  grd%area_on_ocean(i,j,8)=grd%area_on_ocean(i,j,8)+(yUxC*Area_scaled/fraction_used)
+  grd%area_on_ocean(i,j,9)=grd%area_on_ocean(i,j,9)+(yUxR*Area_scaled/fraction_used)
 
 end subroutine spread_mass_across_ocean_cells
 
@@ -2564,7 +2576,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 integer :: iyr, imon, iday, ihr, imin, isec, k
 type(icebergs_gridded), pointer :: grd
 logical :: lerr, sample_traj, write_traj, lbudget, lverbose, check_bond_quality 
-real :: unused_calving, tmpsum, grdd_berg_mass, grdd_bergy_mass,grdd_spread_mass
+real :: unused_calving, tmpsum, grdd_berg_mass, grdd_bergy_mass,grdd_spread_mass, grdd_spread_area
 real :: grdd_u_iceberg, grdd_v_iceberg
 integer :: i, j, Iu, ju, iv, Jv, Iu_off, ju_off, iv_off, Jv_off
 real :: mask
@@ -2572,7 +2584,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 integer :: vel_stagger, str_stagger
 real, dimension(:,:), allocatable :: iCount
 integer :: nbonds
-logical :: within_iceberg_model
+!logical :: within_iceberg_model
 
 integer :: stderrunit
 
@@ -2597,11 +2609,13 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   grd%bergy_melt(:,:)=0.
   grd%bergy_mass(:,:)=0.
   !grd%spread_mass(:,:)=0.  !Don't zero this out yet, because we can first use this an add it onto the SSH
+  grd%spread_area(:,:)=0. 
   grd%u_iceberg(:,:)=0.
   grd%v_iceberg(:,:)=0.
   grd%mass(:,:)=0.
 
   if (bergs%add_weight_to_ocean) grd%mass_on_ocean(:,:,:)=0.
+  if (bergs%add_weight_to_ocean) grd%area_on_ocean(:,:,:)=0.
   grd%virtual_area(:,:)=0.
 
   ! Manage time
@@ -2831,25 +2845,28 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     call write_trajectory(bergs%trajectories, bergs%save_short_traj)
   endif
 
-  !Update diagnostic of iceberg mass spread on ocean,MP1 
-  if ( (grd%id_spread_mass>0) .or. (bergs%find_melt_using_spread_mass) ) then
-    if ((bergs%find_melt_using_spread_mass) ) then
-      grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec)=grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec)  !Temporarily using the variable calving for storing old mass (not sure better way)
-    endif
+  !Using spread_mass_to_ocean to calculate melt rates (if this option is chosen)
+  !within_iceberg_model=.True.
+  if (bergs%find_melt_using_spread_mass) then
+    grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec)=grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec)  !Temporarily using the variable calving for storing old mass (not sure better way)
     grd%spread_mass(:,:)=0.
-    within_iceberg_model=.True.
-    call icebergs_incr_mass(bergs, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec),within_iceberg_model) 
-    if (bergs%find_melt_using_spread_mass) then
-     do i=grd%isc,grd%iec ; do j=grd%jsc,grd%jec
-       if (grd%area(i,j)>0.0) then
-         grd%floating_melt(i,j)=max((grd%floating_melt(i,j) - grd%spread_mass(i,j))/(bergs%dt),0.0)
-         !grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)=grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec)*HLF !Not 100% sure this is correct.
-         grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)=grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec)*0.0 !Not 100% sure this is correct.
-       else
-         grd%floating_melt(i,j)=0.0
-       endif
-     enddo ;enddo
-    endif
+    call icebergs_incr_mass(bergs, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec),within_iceberg_model=.True.) 
+    do i=grd%isc,grd%iec ; do j=grd%jsc,grd%jec
+      if (grd%area(i,j)>0.0) then
+        grd%floating_melt(i,j)=max((grd%floating_melt(i,j) - grd%spread_mass(i,j))/(bergs%dt),0.0)
+        !grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)=grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec)*HLF !Not 100% sure this is correct.
+        grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)=grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec)*0.0 !Not 100% sure this is correct.
+      else
+        grd%floating_melt(i,j)=0.0
+      endif
+    enddo ;enddo
+  elseif  (grd%id_spread_mass>0) then   !Update diagnostic of iceberg mass spread on ocean
+    grd%spread_mass(:,:)=0.
+    call icebergs_incr_mass(bergs, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec),within_iceberg_model=.True.) 
+  endif
+  if ( (grd%id_spread_area>0) ) then  !Update diagnostic of iceberg area spread on ocean
+    grd%spread_area(:,:)=0.
+    call icebergs_incr_mass(bergs, grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec),within_iceberg_model=.True.,spread_area_not_mass=.True.) 
   endif
 
   ! Gridded diagnostics
@@ -2893,6 +2910,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     lerr=send_data(grd%id_bergy_mass, grd%bergy_mass(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   if (grd%id_spread_mass>0) &
     lerr=send_data(grd%id_spread_mass, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_spread_area>0) &
+    lerr=send_data(grd%id_spread_area, grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   if (grd%id_u_iceberg>0) &
     lerr=send_data(grd%id_u_iceberg, grd%u_iceberg(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   if (grd%id_v_iceberg>0) &
@@ -2968,15 +2987,22 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     bergs%floating_mass_end=sum_mass(bergs)
     bergs%icebergs_mass_end=sum_mass(bergs,justbergs=.true.)
     bergs%bergy_mass_end=sum_mass(bergs,justbits=.true.)
-    bergs%spread_mass_end=sum_mass(bergs) !Not sure what this is
-    bergs%u_iceberg_end=sum_mass(bergs) !Not sure what this is
-    bergs%v_iceberg_end=sum_mass(bergs) !Not sure what this is
+    !bergs%spread_mass_end=sum_mass(bergs) !Not sure what this is
+    !bergs%spread_area_end=sum_mass(bergs) !Not sure what this is
+    !bergs%u_iceberg_end=sum_mass(bergs) !Not sure what this is
+    !bergs%v_iceberg_end=sum_mass(bergs) !Not sure what this is
     bergs%floating_heat_end=sum_heat(bergs)
     grd%tmpc(:,:)=0.;
+    !Finding spread mass
     call mpp_clock_end(bergs%clock); call mpp_clock_end(bergs%clock_dia) ! To enable calling of public s/r
     call icebergs_incr_mass(bergs, grd%tmpc)
     call mpp_clock_begin(bergs%clock_dia); call mpp_clock_begin(bergs%clock) ! To enable calling of public s/r
     bergs%returned_mass_on_ocean=sum( grd%tmpc(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
+    !Finding spread area
+    call mpp_clock_end(bergs%clock); call mpp_clock_end(bergs%clock_dia) ! To enable calling of public s/r
+    call icebergs_incr_mass(bergs, grd%tmpc,spread_area_not_mass=.true.)
+    call mpp_clock_begin(bergs%clock_dia); call mpp_clock_begin(bergs%clock) ! To enable calling of public s/r
+    bergs%returned_area_on_ocean=sum( grd%tmpc(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
     bergs%nbergs_end=count_bergs(bergs)
     call mpp_sum(bergs%stored_end)
     call mpp_sum(bergs%stored_heat_end)
@@ -2984,6 +3010,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     call mpp_sum(bergs%icebergs_mass_end)
     call mpp_sum(bergs%bergy_mass_end)
     call mpp_sum(bergs%spread_mass_end)
+    call mpp_sum(bergs%spread_area_end)
     call mpp_sum(bergs%u_iceberg_end)
     call mpp_sum(bergs%v_iceberg_end)
     call mpp_sum(bergs%floating_heat_end)
@@ -3014,6 +3041,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     call mpp_sum(grdd_bergy_mass)
     grdd_spread_mass=sum( grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
     call mpp_sum(grdd_spread_mass)
+    grdd_spread_area=sum( grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
+    call mpp_sum(grdd_spread_area)
     if (mpp_pe().eq.mpp_root_pe()) then
  100 format("diamonds: ",a19,3(a18,"=",es14.7,x,a2,:,","),a12,i8)
  200 format("diamonds: ",a19,10(a18,"=",es14.7,x,a2,:,","))
@@ -3022,6 +3051,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
       call report_state('icebergs','kg','',bergs%icebergs_mass_start,'',bergs%icebergs_mass_end,'')
       call report_state('bits','kg','',bergs%bergy_mass_start,'',bergs%bergy_mass_end,'')
       call report_state('spread icebergs','kg','',bergs%spread_mass_start,'',bergs%spread_mass_end,'')
+      call report_state('spread icebergs','m^2','',bergs%spread_area_start,'',bergs%spread_area_end,'')
       call report_istate('berg #','',bergs%nbergs_start,'',bergs%nbergs_end,'')
       call report_ibudget('berg #','calved',bergs%nbergs_calved, &
                                    'melted',bergs%nbergs_melted, &
@@ -3044,6 +3074,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
                                                     bergs%stored_end+bergs%floating_mass_end)
       call report_consistant('iceberg mass','kg','gridded',grdd_berg_mass,'bergs',bergs%icebergs_mass_end)
       call report_consistant('spread mass','kg','gridded',grdd_spread_mass,'bergs',bergs%spread_mass_end)
+      call report_consistant('spread area','kg','gridded',grdd_spread_area,'bergs',bergs%spread_area_end)
       call report_consistant('bits mass','kg','gridded',grdd_bergy_mass,'bits',bergs%bergy_mass_end)
       call report_consistant('wieght','kg','returned',bergs%returned_mass_on_ocean,'floating',bergs%floating_mass_end)
       call report_state('net heat','J','',bergs%stored_heat_start+bergs%floating_heat_start,'',&
@@ -3080,6 +3111,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     bergs%icebergs_mass_start=bergs%icebergs_mass_end
     bergs%bergy_mass_start=bergs%bergy_mass_end
     bergs%spread_mass_start=bergs%spread_mass_end
+    bergs%spread_area_start=bergs%spread_area_end
     bergs%net_calving_used=0.
     bergs%net_calving_to_bergs=0.
     bergs%net_heat_to_bergs=0.
@@ -3186,23 +3218,43 @@ end subroutine icebergs_run
 
 ! ##############################################################################
 
-subroutine icebergs_incr_mass(bergs, mass, within_iceberg_model, Time)
+subroutine icebergs_incr_mass(bergs, mass, within_iceberg_model, Time, spread_area_not_mass)
 ! Arguments
 type(icebergs), pointer :: bergs
 real, dimension(bergs%grd%isc:bergs%grd%iec,bergs%grd%jsc:bergs%grd%jec), intent(inout) :: mass
 type(time_type), intent(in), optional :: Time
 logical, intent(in), optional :: within_iceberg_model
-logical :: within_model
+logical, intent(in), optional :: spread_area_not_mass
 ! Local variables
+logical :: within_model
+logical :: spread_area !Logical flag which allows you to spread area over ocean (instead of mass)
 integer :: i, j
 type(icebergs_gridded), pointer :: grd
 real :: dmda
 logical :: lerr
+real, dimension(bergs%grd%isd:bergs%grd%ied, bergs%grd%jsd:bergs%grd%jed,9) :: var_on_ocean   !Variable being spread onto the ocean  (mass or area)
 integer :: stderrunit
 
   ! Get the stderr unit number
   stderrunit = stderr()
+  ! For convenience
+  grd=>bergs%grd
+
+  !var_on_ocean(:,:,:)=0.
   
+  !Decide whether area of mass are being spread across grid cells (default spread mass)
+  spread_area=.False. 
+  if (present(spread_area_not_mass)) then 
+    if (spread_area_not_mass) then 
+      spread_area=.True. 
+    endif
+  endif
+  if (spread_area) then 
+    var_on_ocean(:,:,:)=grd%area_on_ocean(:,:,:)
+  else
+    var_on_ocean(:,:,:)=grd%mass_on_ocean(:,:,:)
+  endif
+
   
   within_model=.False.
   if (present(within_iceberg_model)) then 
@@ -3216,8 +3268,6 @@ subroutine icebergs_incr_mass(bergs, mass, within_iceberg_model, Time)
     call mpp_clock_begin(bergs%clock_int)
   endif
 
-  ! For convenience
-  grd=>bergs%grd
 
   ! Add iceberg+bits mass field to non-haloed SIS field (kg/m^2)
  !mass(:,:)=mass(:,:)+( grd%mass(grd%isc:grd%iec,grd%jsc:grd%jec) &
@@ -3228,7 +3278,7 @@ subroutine icebergs_incr_mass(bergs, mass, within_iceberg_model, Time)
     call grd_chksum2(grd, grd%tmp, 'mass in (incr)')
   endif
 
-  call mpp_update_domains(grd%mass_on_ocean, grd%domain)
+  call mpp_update_domains(var_on_ocean, grd%domain)
   if (.not. old_bug_rotated_weights) then
     do j=grd%jsd, grd%jed; do i=grd%isd, grd%ied
       if (grd%parity_x(i,j)<0.) then
@@ -3236,19 +3286,19 @@ subroutine icebergs_incr_mass(bergs, mass, within_iceberg_model, Time)
         ! (i.e. a 180 degree rotation). In general, we should handle
         ! +/- 90 degree rotations as well but in CM2*-class models
         ! this is not necessary. -aja
-        dmda=grd%mass_on_ocean(i,j,9); grd%mass_on_ocean(i,j,9)=grd%mass_on_ocean(i,j,1); grd%mass_on_ocean(i,j,1)=dmda
-        dmda=grd%mass_on_ocean(i,j,8); grd%mass_on_ocean(i,j,8)=grd%mass_on_ocean(i,j,2); grd%mass_on_ocean(i,j,2)=dmda
-        dmda=grd%mass_on_ocean(i,j,7); grd%mass_on_ocean(i,j,7)=grd%mass_on_ocean(i,j,3); grd%mass_on_ocean(i,j,3)=dmda
-        dmda=grd%mass_on_ocean(i,j,6); grd%mass_on_ocean(i,j,6)=grd%mass_on_ocean(i,j,4); grd%mass_on_ocean(i,j,4)=dmda
+        dmda=var_on_ocean(i,j,9); var_on_ocean(i,j,9)=var_on_ocean(i,j,1); var_on_ocean(i,j,1)=dmda
+        dmda=var_on_ocean(i,j,8); var_on_ocean(i,j,8)=var_on_ocean(i,j,2); var_on_ocean(i,j,2)=dmda
+        dmda=var_on_ocean(i,j,7); var_on_ocean(i,j,7)=var_on_ocean(i,j,3); var_on_ocean(i,j,3)=dmda
+        dmda=var_on_ocean(i,j,6); var_on_ocean(i,j,6)=var_on_ocean(i,j,4); var_on_ocean(i,j,4)=dmda
       endif
     enddo; enddo
   endif
   do j=grd%jsc, grd%jec; do i=grd%isc, grd%iec
-    dmda=grd%mass_on_ocean(i,j,5) &
-         + ( ( (grd%mass_on_ocean(i-1,j-1,9)+grd%mass_on_ocean(i+1,j+1,1))   &
-         +     (grd%mass_on_ocean(i+1,j-1,7)+grd%mass_on_ocean(i-1,j+1,3)) ) &
-         +   ( (grd%mass_on_ocean(i-1,j  ,6)+grd%mass_on_ocean(i+1,j  ,4))   &
-         +     (grd%mass_on_ocean(i  ,j-1,8)+grd%mass_on_ocean(i  ,j+1,2)) ) )
+    dmda=var_on_ocean(i,j,5) &
+         + ( ( (var_on_ocean(i-1,j-1,9)+var_on_ocean(i+1,j+1,1))   &
+         +     (var_on_ocean(i+1,j-1,7)+var_on_ocean(i-1,j+1,3)) ) &
+         +   ( (var_on_ocean(i-1,j  ,6)+var_on_ocean(i+1,j  ,4))   &
+         +     (var_on_ocean(i  ,j-1,8)+var_on_ocean(i  ,j+1,2)) ) )
     if (grd%area(i,j)>0) dmda=dmda/grd%area(i,j)*grd%msk(i,j)
 
     if (.not.(within_model)) then
@@ -3256,16 +3306,27 @@ subroutine icebergs_incr_mass(bergs, mass, within_iceberg_model, Time)
     else
       mass(i,j)=dmda
     endif
-    if (grd%id_mass_on_ocn>0) grd%tmp(i,j)=dmda
+    if ((grd%id_area_on_ocn>0).and.(spread_area)) grd%tmp(i,j)=dmda
+    if ((grd%id_mass_on_ocn>0).and.(.not. spread_area)) grd%tmp(i,j)=dmda
   enddo; enddo
-  if (present(Time).and. (grd%id_mass_on_ocn>0)) &
-    lerr=send_data(grd%id_mass_on_ocn, grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  
+  if (spread_area) then
+    if (present(Time).and. (grd%id_area_on_ocn>0)) &
+      lerr=send_data(grd%id_area_on_ocn, grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  else
+    if (present(Time).and. (grd%id_mass_on_ocn>0)) &
+      lerr=send_data(grd%id_mass_on_ocn, grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  endif
 
   if (debug) then
     grd%tmp(:,:)=0.; grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec)=mass
-    call grd_chksum3(grd, grd%mass_on_ocean, 'mass bergs (incr)')
-    call grd_chksum2(grd, grd%tmp, 'mass out (incr)')
-
+    if (.not. spread_area) then
+      call grd_chksum3(grd, grd%mass_on_ocean, 'mass bergs (incr)')
+      call grd_chksum2(grd, grd%tmp, 'mass out (incr)')
+    else
+      call grd_chksum3(grd, grd%area_on_ocean, 'area bergs (incr)')
+      call grd_chksum2(grd, grd%tmp, 'area out (incr)')
+    endif
   endif
 
   if (.not.(within_model)) then
@@ -4510,9 +4571,11 @@ subroutine icebergs_end(bergs)
   deallocate(bergs%grd%bergy_melt)
   deallocate(bergs%grd%bergy_mass)
   deallocate(bergs%grd%spread_mass)
+  deallocate(bergs%grd%spread_area)
   deallocate(bergs%grd%virtual_area)
   deallocate(bergs%grd%mass)
   deallocate(bergs%grd%mass_on_ocean)
+  deallocate(bergs%grd%area_on_ocean)
   deallocate(bergs%grd%tmp)
   deallocate(bergs%grd%tmpc)
   deallocate(bergs%grd%stored_ice)
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 3d158c7..b8b5f28 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -117,11 +117,13 @@ module ice_bergs_framework
   real, dimension(:,:), pointer :: bergy_melt=>null() ! Melting rate of bergy bits (kg/s/m^2)
   real, dimension(:,:), pointer :: bergy_mass=>null() ! Mass distribution of bergy bits (kg/s/m^2)
   real, dimension(:,:), pointer :: spread_mass=>null() ! Mass of icebergs after spreading (kg/s/m^2)
+  real, dimension(:,:), pointer :: spread_area=>null() ! Area of icebergs after spreading (m^2/s/m^2)
   real, dimension(:,:), pointer :: u_iceberg=>null() ! Average iceberg velocity in grid cell (mass weighted - but not spread mass weighted)
   real, dimension(:,:), pointer :: v_iceberg=>null() ! Average iceberg velocity in grid cell (mass weighted - but not spread mass weighted)
   real, dimension(:,:), pointer :: virtual_area=>null() ! Virtual surface coverage by icebergs (m^2)
   real, dimension(:,:), pointer :: mass=>null() ! Mass distribution (kg/m^2)
-  real, dimension(:,:,:), pointer :: mass_on_ocean=>null() ! Mass distribution partitioned by neighbor (kg/m^2)
+  real, dimension(:,:,:), pointer :: mass_on_ocean=>null() ! Mass distribution partitioned by neighbor (kg/m^2)   - Alon:I think that this actually has units of kg
+  real, dimension(:,:,:), pointer :: area_on_ocean=>null() ! Area distribution partitioned by neighbor (m^2/m^2)  - Alon:I think that this actually has units of m^2
   real, dimension(:,:), pointer :: tmp=>null() ! Temporary work space
   real, dimension(:,:), pointer :: tmpc=>null() ! Temporary work space
   real, dimension(:,:,:), pointer :: stored_ice=>null() ! Accumulated ice mass flux at calving locations (kg)
@@ -136,8 +138,9 @@ module ice_bergs_framework
   integer :: id_melt_buoy=-1, id_melt_eros=-1, id_melt_conv=-1, id_virtual_area=-1, id_real_calving=-1
   integer :: id_calving_hflx_in=-1, id_stored_heat=-1, id_melt_hflx=-1, id_heat_content=-1
   integer :: id_mass=-1, id_ui=-1, id_vi=-1, id_ua=-1, id_va=-1, id_sst=-1, id_cn=-1, id_hi=-1
-  integer :: id_bergy_src=-1, id_bergy_melt=-1, id_bergy_mass=-1, id_berg_melt=-1
-  integer :: id_mass_on_ocn=-1, id_ssh=-1, id_fax=-1, id_fay=-1,  id_spread_mass=-1
+  integer :: id_bergy_src=-1,   id_bergy_melt=-1, id_bergy_mass=-1, id_berg_melt=-1
+  integer :: id_mass_on_ocn=-1, id_area_on_ocn=-1, id_spread_mass=-1, id_spread_area=-1
+  integer :: id_ssh=-1, id_fax=-1, id_fay=-1
   integer :: id_count=-1, id_chksum=-1, id_u_iceberg=-1, id_v_iceberg=-1, id_sss=-1
 
   real :: clipping_depth=0. ! The effective depth at which to clip the weight felt by the ocean [m].
@@ -263,9 +266,11 @@ module ice_bergs_framework
   real :: icebergs_mass_start=0., icebergs_mass_end=0.
   real :: bergy_mass_start=0., bergy_mass_end=0.
   real :: spread_mass_start=0., spread_mass_end=0.
+  real :: spread_area_start=0., spread_area_end=0.
   real :: u_iceberg_start=0., u_iceberg_end=0.
   real :: v_iceberg_start=0., v_iceberg_end=0.
   real :: returned_mass_on_ocean=0.
+  real :: returned_area_on_ocean=0.
   real :: net_melt=0., berg_melt=0., bergy_src=0., bergy_melt=0.
   integer :: nbergs_calved=0, nbergs_melted=0, nbergs_start=0, nbergs_end=0
   integer :: nspeeding_tickets=0
@@ -501,11 +506,13 @@ subroutine ice_bergs_framework_init(bergs, &
   allocate( grd%bergy_melt(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%bergy_melt(:,:)=0.
   allocate( grd%bergy_mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%bergy_mass(:,:)=0.
   allocate( grd%spread_mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_mass(:,:)=0.
+  allocate( grd%spread_area(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_area(:,:)=0.
   allocate( grd%u_iceberg(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%u_iceberg(:,:)=0.
   allocate( grd%v_iceberg(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%v_iceberg(:,:)=0.
   allocate( grd%virtual_area(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%virtual_area(:,:)=0.
   allocate( grd%mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%mass(:,:)=0.
   allocate( grd%mass_on_ocean(grd%isd:grd%ied, grd%jsd:grd%jed, 9) ); grd%mass_on_ocean(:,:,:)=0.
+  allocate( grd%area_on_ocean(grd%isd:grd%ied, grd%jsd:grd%jed, 9) ); grd%area_on_ocean(:,:,:)=0.
   allocate( grd%stored_ice(grd%isd:grd%ied, grd%jsd:grd%jed, nclasses) ); grd%stored_ice(:,:,:)=0.
   allocate( grd%real_calving(grd%isd:grd%ied, grd%jsd:grd%jed, nclasses) ); grd%real_calving(:,:,:)=0.
   allocate( grd%uo(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%uo(:,:)=0.
@@ -819,6 +826,8 @@ subroutine ice_bergs_framework_init(bergs, &
      'Bergy bit density field', 'kg/(m^2)')
   grd%id_spread_mass=register_diag_field('icebergs', 'spread_mass', axes, Time, &
      'Iceberg mass after spreading', 'kg/(m^2)')
+  grd%id_spread_area=register_diag_field('icebergs', 'spread_area', axes, Time, &
+     'Iceberg area after spreading', 'm^2/(m^2)')
   grd%id_u_iceberg=register_diag_field('icebergs', 'u_iceberg', axes, Time, &
      'Iceberg u velocity (m/s)')
   grd%id_v_iceberg=register_diag_field('icebergs', 'v_iceberg', axes, Time, &
@@ -829,6 +838,8 @@ subroutine ice_bergs_framework_init(bergs, &
      'Iceberg density field', 'kg/(m^2)')
   grd%id_mass_on_ocn=register_diag_field('icebergs', 'mass_on_ocean', axes, Time, &
      'Iceberg density field felt by ocean', 'kg/(m^2)')
+  grd%id_area_on_ocn=register_diag_field('icebergs', 'area_on_ocean', axes, Time, &
+     'Iceberg area field felt by ocean', 'm^2/(m^2)')
   grd%id_stored_ice=register_diag_field('icebergs', 'stored_ice', axes3d, Time, &
      'Accumulated ice mass by class', 'kg')
   grd%id_real_calving=register_diag_field('icebergs', 'real_calving', axes3d, Time, &
@@ -3792,6 +3803,7 @@ subroutine checksum_gridded(grd, label)
   ! state
   call grd_chksum2(grd, grd%mass, 'mass')
   call grd_chksum3(grd, grd%mass_on_ocean, 'mass_on_ocean')
+  call grd_chksum3(grd, grd%area_on_ocean, 'area_on_ocean')
   call grd_chksum3(grd, grd%stored_ice, 'stored_ice')
   call grd_chksum2(grd, grd%stored_heat, 'stored_heat')
   call grd_chksum2(grd, grd%melt_buoy, 'melt_b')
@@ -3800,9 +3812,10 @@ subroutine checksum_gridded(grd, label)
   call grd_chksum2(grd, grd%bergy_src, 'bergy_src')
   call grd_chksum2(grd, grd%bergy_melt, 'bergy_melt')
   call grd_chksum2(grd, grd%bergy_mass, 'bergy_mass')
-  call grd_chksum2(grd, grd%bergy_mass, 'spread_mass')
-  call grd_chksum2(grd, grd%bergy_mass, 'u_iceberg')
-  call grd_chksum2(grd, grd%bergy_mass, 'v_iceberg')
+  call grd_chksum2(grd, grd%spread_mass, 'spread_mass')
+  call grd_chksum2(grd, grd%spread_area, 'spread_area')
+  call grd_chksum2(grd, grd%u_iceberg, 'u_iceberg')
+  call grd_chksum2(grd, grd%v_iceberg, 'v_iceberg')
   call grd_chksum2(grd, grd%virtual_area, 'varea')
   call grd_chksum2(grd, grd%floating_melt, 'floating_melt')
   call grd_chksum2(grd, grd%berg_melt, 'berg_melt')

From 959bf0e713f821fbab1e88c2689cf62e91d51c8f Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Mon, 19 Sep 2016 12:59:58 -0400
Subject: [PATCH 163/361] A variable u_star_icebergs has been added to the
 iceberg model. This provides the frictional velcoity that should be felt by
 the ocean boundary layer beneath the icebergs. The u_star_icebergs is a
 gridded quantity. It is based on the (mass weighted) velocity difference
 between the iceberg and ocean. The calculation for u_star currently uses the
 mass rather than the spread_mass to do the velocity weighting. It should used
 the spread mass. This can be done at a later stage if it is found cause
 problems.

The next step is to pass u_star through the coupler so that it can be felt by the ocean. This has not been done yet.
---
 icebergs.F90           | 48 ++++++++++++++++++++++++------------------
 icebergs_framework.F90 | 19 +++++++++++++++--
 2 files changed, 45 insertions(+), 22 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index c27c5a0..9fae040 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1114,6 +1114,7 @@ subroutine thermodynamics(bergs)
 real :: Mv, Me, Mb, melt, dvo, dva, dM, Ss, dMe, dMb, dMv
 real :: Mnew, Mnew1, Mnew2, Hocean
 real :: Mbits, nMbits, dMbitsE, dMbitsM, Lbits, Abits, Mbb
+real :: ustar_h, ustar
 integer :: i,j, stderrunit
 type(iceberg), pointer :: this, next
 real, parameter :: perday=1./86400.
@@ -1316,10 +1317,8 @@ subroutine thermodynamics(bergs)
         if ((grd%id_mass>0 .or. bergs%add_weight_to_ocean) .or. ((grd%id_u_iceberg>0) .or. (grd%id_v_iceberg>0)))   &
              & grd%mass(i,j)=grd%mass(i,j)+Mnew/grd%area(i,j)*this%mass_scaling ! kg/m2
         !Finding the average iceberg velocity in a grid cell (mass weighted)
-        if (grd%id_u_iceberg>0 )&
-             & grd%u_iceberg(i,j)=grd%u_iceberg(i,j)+((Mnew/grd%area(i,j)*this%mass_scaling)*this%uvel) ! kg/m2
-        if (grd%id_v_iceberg>0 )&
-             & grd%v_iceberg(i,j)=grd%v_iceberg(i,j)+((Mnew/grd%area(i,j)*this%mass_scaling)*this%vvel) ! kg/m2
+        grd%u_iceberg(i,j)=grd%u_iceberg(i,j)+((Mnew/grd%area(i,j)*this%mass_scaling)*this%uvel) ! kg/m2
+        grd%v_iceberg(i,j)=grd%v_iceberg(i,j)+((Mnew/grd%area(i,j)*this%mass_scaling)*this%vvel) ! kg/m2
         if (grd%id_bergy_mass>0 .or. bergs%add_weight_to_ocean)&
              & grd%bergy_mass(i,j)=grd%bergy_mass(i,j)+nMbits/grd%area(i,j)*this%mass_scaling ! kg/m2
         if (bergs%add_weight_to_ocean .and. .not. bergs%time_average_weight) then
@@ -1339,15 +1338,23 @@ subroutine thermodynamics(bergs)
     enddo
   enddo ; enddo
   
-  !Scaling the gridded iceberg velocity by the iceberg mass
-  if ((grd%id_u_iceberg>0) .or. (grd%id_v_iceberg>0)) then
-    do j = grd%jsc,grd%jec ; do i = grd%isc,grd%iec  
-      if ((grd%id_u_iceberg>0 ).and. (grd%mass(i,j)>0.))  &
-        & grd%u_iceberg(i,j)=grd%u_iceberg(i,j)/grd%mass(i,j)
-      if ((grd%id_v_iceberg>0 ).and. (grd%mass(i,j)>0.))  &
-        & grd%v_iceberg(i,j)=grd%v_iceberg(i,j)/grd%mass(i,j)
-    enddo; enddo
-  endif
+  !Scaling the gridded iceberg velocity by the iceberg mass 
+  do j = grd%jsc,grd%jec ; do i = grd%isc,grd%iec  
+    if (grd%mass(i,j)>0.) then
+      grd%u_iceberg(i,j)=grd%u_iceberg(i,j)/grd%mass(i,j)
+      grd%v_iceberg(i,j)=grd%v_iceberg(i,j)/grd%mass(i,j)
+    else
+      grd%u_iceberg(i,j)=0. ; grd%v_iceberg(i,j)=0.
+    endif
+  enddo; enddo
+  
+  !Calculating ustar_iceberg (gridded)
+  do j = grd%jsc,grd%jec ; do i = grd%isc,grd%iec  
+    dvo=sqrt((grd%u_iceberg(i,j)-grd%uo(i,j))**2+(grd%v_iceberg(i,j)-grd%vo(i,j))**2)
+    ustar = sqrt(bergs%cdrag_icebergs*(dvo**2  + bergs%utide_icebergs**2))
+    ustar_h = max(bergs%ustar_icebergs_bg, ustar)
+    grd%ustar_iceberg(i,j)=ustar_h
+  enddo; enddo
 
 end subroutine thermodynamics
 
@@ -1367,7 +1374,7 @@ subroutine find_basal_melt(bergs,dvo,lat,salt,temp,Use_three_equation_model,thic
   logical , intent(in) :: Use_three_equation_model !True uses the 3 equation model, False uses the 2 equation model.
   
   ! Local variables
-  real :: utide, ustar_bg, ustar, f_cori, absf,tfreeze
+  real :: ustar, f_cori, absf,tfreeze
   real :: Hml !Mixed layer depth
 
   !These could also be useful output variables if needed.
@@ -1433,7 +1440,6 @@ subroutine find_basal_melt(bergs,dvo,lat,salt,temp,Use_three_equation_model,thic
   real, parameter :: Cp_Ice =  2009.0 !Specific heat capacity of ice, taking from HJ99 (Holland and Jenkins 1999)
   real, parameter :: Cp_ml =  3974.0 !Specific heat capacity of mixed layer, taking from HJ99 (Holland and Jenkins 1999)
   real, parameter :: LF =  3.335e5 !Latent heat of fusion, taken from HJ99 (Holland and Jenkins 1999)
-  real, parameter :: cdrag =  1.5e-3 !Momentum Drag coef, taken from HJ99 (Holland and Jenkins 1999)
   real, parameter :: gamma_t =  0.0 ! Exchange velcoity used in 2 equation model. Whn gamma_t is >0, the exchange velocity is independ of u_star. 
                                   ! When gamma_t=0.0, then gamma_t is not used, and the exchange velocity is found using u_star.
   real, parameter :: p_atm =  101325 ! Average atmospheric pressure (Pa) - from Google. 
@@ -1441,8 +1447,6 @@ subroutine find_basal_melt(bergs,dvo,lat,salt,temp,Use_three_equation_model,thic
   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
   density_ice = bergs%rho_bergs
   Rho0=rho_seawater  !Note that the ice shelf code has a default of Rho0=1035
-  utide=0.     ! Tidal speeds, set to zero for now.
-  ustar_bg=0.001 !Background u_star under iceshelf. This should be linked to a value felt by the ocean boundary layer
   Hml =10.      !Mixed layer depth. This is an approximate value. It looks like the code is not sensitive to it (since it enters in log(Hml)
   p_int= p_atm+(gravity*thickness*density_ice)    ! The pressure at the ice-ocean interface, in Pa.
   
@@ -1468,8 +1472,8 @@ subroutine find_basal_melt(bergs,dvo,lat,salt,temp,Use_three_equation_model,thic
   iDens = 1.0/Rho0
 
   !Preparing the mixed layer properties for use in both 2 and 3 equation version
-  ustar = cdrag*(dvo  + utide)
-  ustar_h = MAX(ustar_bg, ustar)
+  ustar = bergs%cdrag_icebergs*(dvo  + bergs%utide_icebergs)
+  ustar_h = max(bergs%ustar_icebergs_bg, ustar)
 
   ! Estimate the neutral ocean boundary layer thickness as the minimum of the
   ! reported ocean mixed layer thickness and the neutral Ekman depth.
@@ -2577,7 +2581,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 type(icebergs_gridded), pointer :: grd
 logical :: lerr, sample_traj, write_traj, lbudget, lverbose, check_bond_quality 
 real :: unused_calving, tmpsum, grdd_berg_mass, grdd_bergy_mass,grdd_spread_mass, grdd_spread_area
-real :: grdd_u_iceberg, grdd_v_iceberg
+real :: grdd_u_iceberg, grdd_v_iceberg, grdd_ustar_iceberg
 integer :: i, j, Iu, ju, iv, Jv, Iu_off, ju_off, iv_off, Jv_off
 real :: mask
 real, dimension(:,:), allocatable :: uC_tmp, vC_tmp
@@ -2612,6 +2616,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   grd%spread_area(:,:)=0. 
   grd%u_iceberg(:,:)=0.
   grd%v_iceberg(:,:)=0.
+  grd%ustar_iceberg(:,:)=0.
   grd%mass(:,:)=0.
 
   if (bergs%add_weight_to_ocean) grd%mass_on_ocean(:,:,:)=0.
@@ -2916,6 +2921,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     lerr=send_data(grd%id_u_iceberg, grd%u_iceberg(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   if (grd%id_v_iceberg>0) &
     lerr=send_data(grd%id_v_iceberg, grd%v_iceberg(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_ustar_iceberg>0) &
+    lerr=send_data(grd%id_ustar_iceberg, grd%ustar_iceberg(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   if (grd%id_mass>0) &
     lerr=send_data(grd%id_mass, grd%mass(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   if (grd%id_stored_ice>0) &
@@ -3013,6 +3020,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     call mpp_sum(bergs%spread_area_end)
     call mpp_sum(bergs%u_iceberg_end)
     call mpp_sum(bergs%v_iceberg_end)
+    call mpp_sum(bergs%ustar_iceberg_end)
     call mpp_sum(bergs%floating_heat_end)
     call mpp_sum(bergs%returned_mass_on_ocean)
     call mpp_sum(bergs%nbergs_end)
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index b8b5f28..5e46ee1 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -120,6 +120,7 @@ module ice_bergs_framework
   real, dimension(:,:), pointer :: spread_area=>null() ! Area of icebergs after spreading (m^2/s/m^2)
   real, dimension(:,:), pointer :: u_iceberg=>null() ! Average iceberg velocity in grid cell (mass weighted - but not spread mass weighted)
   real, dimension(:,:), pointer :: v_iceberg=>null() ! Average iceberg velocity in grid cell (mass weighted - but not spread mass weighted)
+  real, dimension(:,:), pointer :: ustar_iceberg=>null() ! Frictional velocity below icebergs to be passed to ocean (mass weighted - but not spread mass weighted)
   real, dimension(:,:), pointer :: virtual_area=>null() ! Virtual surface coverage by icebergs (m^2)
   real, dimension(:,:), pointer :: mass=>null() ! Mass distribution (kg/m^2)
   real, dimension(:,:,:), pointer :: mass_on_ocean=>null() ! Mass distribution partitioned by neighbor (kg/m^2)   - Alon:I think that this actually has units of kg
@@ -141,7 +142,7 @@ module ice_bergs_framework
   integer :: id_bergy_src=-1,   id_bergy_melt=-1, id_bergy_mass=-1, id_berg_melt=-1
   integer :: id_mass_on_ocn=-1, id_area_on_ocn=-1, id_spread_mass=-1, id_spread_area=-1
   integer :: id_ssh=-1, id_fax=-1, id_fay=-1
-  integer :: id_count=-1, id_chksum=-1, id_u_iceberg=-1, id_v_iceberg=-1, id_sss=-1
+  integer :: id_count=-1, id_chksum=-1, id_u_iceberg=-1, id_v_iceberg=-1, id_sss=-1, id_ustar_iceberg
 
   real :: clipping_depth=0. ! The effective depth at which to clip the weight felt by the ocean [m].
 
@@ -214,6 +215,9 @@ module ice_bergs_framework
   real :: lat_ref=0. ! Reference latitude for f-plane (when this option is on)
   real :: u_override=0.0 ! Overrides the u velocity of icebergs (for ocean testing)
   real :: v_override=0.0 ! Overrides the v velocity of icebergs (for ocean testing)
+  real :: utide_icebergs= 0.      ! Tidal speeds, set to zero for now.
+  real :: ustar_icebergs_bg=0.001 ! Background u_star under icebergs. This should be linked to a value felt by the ocean boundary layer
+  real :: cdrag_icebergs =  1.5e-3 !Momentum Drag coef, taken from HJ99  (Holland and Jenkins 1999)
   real :: initial_orientation=0. ! Iceberg orientaion relative to this angle (in degrees). Used for hexagonal mass spreading.
   real, dimension(:), pointer :: initial_mass, distribution, mass_scaling
   real, dimension(:), pointer :: initial_thickness, initial_width, initial_length
@@ -269,6 +273,7 @@ module ice_bergs_framework
   real :: spread_area_start=0., spread_area_end=0.
   real :: u_iceberg_start=0., u_iceberg_end=0.
   real :: v_iceberg_start=0., v_iceberg_end=0.
+  real :: ustar_iceberg_start=0., ustar_iceberg_end=0.
   real :: returned_mass_on_ocean=0.
   real :: returned_area_on_ocean=0.
   real :: net_melt=0., berg_melt=0., bergy_src=0., bergy_melt=0.
@@ -346,6 +351,9 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: v_override=0.0 ! Overrides the v velocity of icebergs (for ocean testing)
 real :: Lx=360. ! Length of domain in x direction, used for periodicity (use a huge number for non-periodic)
 real :: initial_orientation=0. ! Iceberg orientaion relative to this angle (in degrees). Used for hexagonal mass spreading.
+real :: utide_icebergs= 0.      ! Tidal speeds, set to zero for now.
+real :: ustar_icebergs_bg=0.001 ! Background u_star under icebergs. This should be linked to a value felt by the ocean boundary layer
+real :: cdrag_icebergs =  1.5e-3 !Momentum Drag coef, taken from HJ99  (Holland and Jenkins 1999)
 logical :: use_operator_splitting=.true. ! Use first order operator splitting for thermodynamics
 logical :: add_weight_to_ocean=.true. ! Add weight of icebergs + bits to ocean
 logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
@@ -392,7 +400,7 @@ subroutine ice_bergs_framework_init(bergs, &
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution, force_all_pes_traj, &
          allow_bergs_to_roll,set_melt_rates_to_zero,lat_ref,initial_orientation,rotate_icebergs_for_mass_spreading,grid_is_latlon,Lx,use_f_plane,use_old_spreading, &
          grid_is_regular,Lx,use_f_plane,override_iceberg_velocities,u_override,v_override,add_iceberg_thickness_to_SSH,Iceberg_melt_without_decay,melt_icebergs_as_ice_shelf, &
-         Use_three_equation_model,find_melt_using_spread_mass,use_mixed_layer_salinity_for_thermo 
+         Use_three_equation_model,find_melt_using_spread_mass,use_mixed_layer_salinity_for_thermo,utide_icebergs,ustar_icebergs_bg,cdrag_icebergs
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -509,6 +517,7 @@ subroutine ice_bergs_framework_init(bergs, &
   allocate( grd%spread_area(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_area(:,:)=0.
   allocate( grd%u_iceberg(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%u_iceberg(:,:)=0.
   allocate( grd%v_iceberg(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%v_iceberg(:,:)=0.
+  allocate( grd%ustar_iceberg(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%ustar_iceberg(:,:)=0.
   allocate( grd%virtual_area(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%virtual_area(:,:)=0.
   allocate( grd%mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%mass(:,:)=0.
   allocate( grd%mass_on_ocean(grd%isd:grd%ied, grd%jsd:grd%jed, 9) ); grd%mass_on_ocean(:,:,:)=0.
@@ -758,6 +767,9 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%time_average_weight=time_average_weight
   bergs%speed_limit=speed_limit
   bergs%Runge_not_Verlet=Runge_not_Verlet   
+  bergs%ustar_icebergs_bg=ustar_icebergs_bg   
+  bergs%utide_icebergs=utide_icebergs  
+  bergs%cdrag_icebergs=cdrag_icebergs  
   bergs%use_mixed_layer_salinity_for_thermo=use_mixed_layer_salinity_for_thermo 
   bergs%find_melt_using_spread_mass=find_melt_using_spread_mass 
   bergs%Use_three_equation_model=Use_three_equation_model 
@@ -832,6 +844,8 @@ subroutine ice_bergs_framework_init(bergs, &
      'Iceberg u velocity (m/s)')
   grd%id_v_iceberg=register_diag_field('icebergs', 'v_iceberg', axes, Time, &
      'Iceberg v velocity (m/s)')
+  grd%id_ustar_iceberg=register_diag_field('icebergs', 'ustar_iceberg', axes, Time, &
+     'Iceberg frictional velocity (m/s)')
   grd%id_virtual_area=register_diag_field('icebergs', 'virtual_area', axes, Time, &
      'Virtual coverage by icebergs', 'm^2')
   grd%id_mass=register_diag_field('icebergs', 'mass', axes, Time, &
@@ -3816,6 +3830,7 @@ subroutine checksum_gridded(grd, label)
   call grd_chksum2(grd, grd%spread_area, 'spread_area')
   call grd_chksum2(grd, grd%u_iceberg, 'u_iceberg')
   call grd_chksum2(grd, grd%v_iceberg, 'v_iceberg')
+  call grd_chksum2(grd, grd%ustar_iceberg, 'ustar_iceberg')
   call grd_chksum2(grd, grd%virtual_area, 'varea')
   call grd_chksum2(grd, grd%floating_melt, 'floating_melt')
   call grd_chksum2(grd, grd%berg_melt, 'berg_melt')

From 495efb7a341e0e640f90400f8a869c25bb3b5f45 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Tue, 20 Sep 2016 16:11:57 -0400
Subject: [PATCH 164/361] Added "debug iceberg with id" capability

- Setting namelist parameter debug_iceberg_with_id=##### to the iceberg_num
  of a particular berg allows "tracking" of a single berg.
  - Only two calls to monitor_a_berg() have been added so far.
- print_berg() and check_positions() now have optional arguments for
  the i,j of the gridded-list they belong to.
- Updated error messages in check_position().
- Corrected formatting in print_berg(); id was being formatted as a float.
- No answer changes.
---
 icebergs_framework.F90 | 58 +++++++++++++++++++++++++++++++++++++-----
 1 file changed, 51 insertions(+), 7 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 37188b1..d366327 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -231,6 +231,7 @@ module ice_bergs_framework
   logical :: interactive_icebergs_on=.false.  !Turn on/off interactions between icebergs  - Added by Alon 
   logical :: critical_interaction_damping_on=.true.  !Sets the damping on relative iceberg velocity to critical value - Added by Alon 
   logical :: use_old_spreading=.true. ! If true, spreads iceberg mass as if the berg is one grid cell wide
+  integer :: debug_iceberg_with_id = -1 ! If positive, monitors a berg with this id
   real :: speed_limit=0. ! CFL speed limit for a berg [m/s]
   real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
   type(buffer), pointer :: obuffer_n=>null(), ibuffer_n=>null()
@@ -356,13 +357,15 @@ subroutine ice_bergs_framework_init(bergs, &
 real, dimension(nclasses) :: distribution=(/0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02/) ! Fraction of calving to apply to this class (non-dim) , 
 real, dimension(nclasses) :: mass_scaling=(/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) ! Ratio between effective and real iceberg mass (non-dim)
 real, dimension(nclasses) :: initial_thickness=(/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) ! Total thickness of newly calved bergs (m)
+integer :: debug_iceberg_with_id = -1 ! If positive, monitors a berg with this id
 namelist /icebergs_nml/ verbose, budget, halo,  traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,Static_icebergs,  &
          distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,bond_coef, radial_damping_coef, tangental_damping_coef, only_interactive_forces, &
          rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, iceberg_bonds_on, manually_initialize_bonds, ignore_missing_restart_bergs, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, halo_debugging, hexagonal_icebergs, &
          time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, interactive_icebergs_on, critical_interaction_damping_on, &
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution, force_all_pes_traj, &
-         allow_bergs_to_roll,set_melt_rates_to_zero,lat_ref,initial_orientation,rotate_icebergs_for_mass_spreading,grid_is_regular,grid_is_latlon,Lx,use_f_plane, use_old_spreading
+         allow_bergs_to_roll,set_melt_rates_to_zero,lat_ref,initial_orientation,rotate_icebergs_for_mass_spreading,grid_is_regular,grid_is_latlon,Lx,use_f_plane, use_old_spreading, &
+         debug_iceberg_with_id
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -738,6 +741,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%grounding_fraction=grounding_fraction
   bergs%add_weight_to_ocean=add_weight_to_ocean
   bergs%use_old_spreading=use_old_spreading
+  bergs%debug_iceberg_with_id=debug_iceberg_with_id
   allocate( bergs%initial_mass(nclasses) ); bergs%initial_mass(:)=initial_mass(:)
   allocate( bergs%distribution(nclasses) ); bergs%distribution(:)=distribution(:)
   allocate( bergs%mass_scaling(nclasses) ); bergs%mass_scaling(:)=mass_scaling(:)
@@ -1284,6 +1288,8 @@ subroutine send_bergs_to_other_pes(bergs)
     nbergs_start=count_bergs(bergs)
   endif
 
+  if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'send_bergs_to_other_pes (top)')
+
   ! Find number of bergs that headed east/west
   nbergs_to_send_e=0
   nbergs_to_send_w=0
@@ -1467,6 +1473,8 @@ subroutine send_bergs_to_other_pes(bergs)
     nbergs_rcvd_from_n=0
   endif
 
+  if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'send_bergs_to_other_pes (end)')
+
   if (debug) then
     nbergs_end=count_bergs(bergs)
     i=nbergs_rcvd_from_n+nbergs_rcvd_from_s+nbergs_rcvd_from_e+nbergs_rcvd_from_w &
@@ -2091,6 +2099,32 @@ end subroutine check_for_duplicates
 
 ! ##############################################################################
 
+subroutine monitor_a_berg(bergs, label)
+! Arguments
+type(icebergs), pointer :: bergs
+character(len=*) :: label
+! Local variables
+type(iceberg), pointer :: this
+integer :: grdi, grdj
+integer :: stderrunit
+
+  if (bergs%debug_iceberg_with_id<0) return
+  stderrunit=stderr() ! Get the stderr unit number
+
+  do grdj = bergs%grd%jsd,bergs%grd%jed ; do grdi = bergs%grd%isd,bergs%grd%ied
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this))
+      if (this%iceberg_num == bergs%debug_iceberg_with_id) then
+        call print_berg(stderrunit, this, 'MONITOR: '//label, grdi, grdj)
+      endif
+      this=>this%next
+    enddo
+  enddo ; enddo
+
+end subroutine monitor_a_berg
+
+! ##############################################################################
+
 subroutine insert_berg_into_list(first, newberg, quick)
 ! Arguments
 type(iceberg), pointer :: first, newberg
@@ -2311,16 +2345,21 @@ end subroutine destroy_iceberg
 
 ! ##############################################################################
 
-subroutine print_berg(iochan, berg, label)
+subroutine print_berg(iochan, berg, label, il, jl)
 ! Arguments
 integer, intent(in) :: iochan
 type(iceberg), pointer :: berg
 character(len=*) :: label
+integer, optional, intent(in) :: il, jl !< Indices of cell berg should be in
 ! Local variables
 
-  write(iochan,'("diamonds, print_berg: ",a," pe=(",i3,") start lon,lat,yr,day,mass=",2f10.4,i5,f7.2,es12.4)') &
+  write(iochan,'("diamonds, print_berg: ",a," pe=(",i3,") start lon,lat,yr,#,day,mass,hb=",2f10.4,i5,i12,f7.2,es12.4,f5.1)') &
     label, mpp_pe(), berg%start_lon, berg%start_lat, &
-    berg%start_year, berg%iceberg_num, berg%start_day, berg%start_mass
+    berg%start_year, berg%iceberg_num, berg%start_day, berg%start_mass, berg%halo_berg
+  if (present(il).and.present(jl)) then
+    write(iochan,'("diamonds, print_berg: ",a," pe=(",i3,a,2i5,3(a,2f10.4),a,2l2)') &
+      label, mpp_pe(), ') List i,j=',il,jl
+  endif
   write(iochan,'("diamonds, print_berg: ",a," pe=(",i3,a,2i5,3(a,2f10.4),a,2l2)') &
     label, mpp_pe(), ') i,j=',berg%ine, berg%jne, &
     ' xi,yj=', berg%xi, berg%yj, &
@@ -3592,11 +3631,12 @@ end function pos_within_cell
 
 ! ##############################################################################
 
-subroutine check_position(grd, berg, label)
+subroutine check_position(grd, berg, label, il, jl)
 ! Arguments
 type(icebergs_gridded), pointer :: grd
 type(iceberg), pointer :: berg
 character(len=*) :: label
+integer, optional, intent(in) :: il, jl !< Indices of cell berg should be in
 ! Local variables
 real :: xi, yj
 logical :: lret
@@ -3609,8 +3649,12 @@ subroutine check_position(grd, berg, label)
   if (xi.ne.berg%xi.or.yj.ne.berg%yj) then
     write(stderrunit,'("diamonds: check_position (",i4,") b%x,x,-=",3(es12.4,x),a)') mpp_pe(),berg%xi,xi,berg%xi-xi,label
     write(stderrunit,'("diamonds: check_position (",i4,") b%y,y,-=",3(es12.4,x),a)') mpp_pe(),berg%yj,yj,berg%yj-yj,label
-    call print_berg(stderrunit, berg, 'check_position')
-    call error_mesg('diamonds, check_position','berg has inconsistent xi,yj!',FATAL)
+    call print_berg(stderrunit, berg, 'check_position', il, jl)
+    call error_mesg('diamonds, check_position, '//trim(label),'berg has inconsistent xi,yj!',FATAL)
+  endif
+  if (grd%msk(berg%ine, berg%jne)==0.) then
+    call print_berg(stderrunit, berg, 'check_position, '//trim(label), il, jl)
+    call error_mesg('diamonds, check_position, '//trim(label),'berg is in a land cell!',FATAL)
   endif
 
 end subroutine check_position

From 2b9cfd7b0a9fe1f00cb9fc3cc790d5a8830ef827 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Tue, 20 Sep 2016 16:18:39 -0400
Subject: [PATCH 165/361] Corrected debugging of halo updates

- With debug=true, the existence of persistent bergs in halos needed
  the budget of bergs within send_bergs_to_other_pes() to include halos.
- Also updated args to call check_posiiton().
- No answer changes.
---
 icebergs_framework.F90 | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index d366327..3f51efe 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -1285,7 +1285,7 @@ subroutine send_bergs_to_other_pes(bergs)
   grd=>bergs%grd
 
   if (debug) then
-    nbergs_start=count_bergs(bergs)
+    nbergs_start=count_bergs(bergs, with_halos=.true.)
   endif
 
   if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'send_bergs_to_other_pes (top)')
@@ -1476,7 +1476,7 @@ subroutine send_bergs_to_other_pes(bergs)
   if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'send_bergs_to_other_pes (end)')
 
   if (debug) then
-    nbergs_end=count_bergs(bergs)
+    nbergs_end=count_bergs(bergs, with_halos=.true.)
     i=nbergs_rcvd_from_n+nbergs_rcvd_from_s+nbergs_rcvd_from_e+nbergs_rcvd_from_w &
      -nbergs_to_send_n-nbergs_to_send_s-nbergs_to_send_e-nbergs_to_send_w
     if (nbergs_end-(nbergs_start+i).ne.0) then
@@ -1501,7 +1501,7 @@ subroutine send_bergs_to_other_pes(bergs)
     do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
       this=>bergs%list(grdi,grdj)%first
       do while (associated(this))
-        call check_position(grd, this, 'exchange (bot)')
+        call check_position(grd, this, 'exchange (bot)', grdi, grdj)
         if (this%ine.lt.bergs%grd%isc .or. &
             this%ine.gt.bergs%grd%iec .or. &
             this%jne.lt.bergs%grd%jsc .or. &

From d5577377b2da0fb70dd8dcd9d88eeae7785e5361 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Tue, 20 Sep 2016 16:44:28 -0400
Subject: [PATCH 166/361] Removed "force append" from send_bergs_to_other_pes()

- When unpacking bergs during communication we do not want to use
  the append method for adding bergs to lists.
- Also avoid using of "initial values" in insert_berg_into_list()
  and unpack_berg_into_buffer(). Initial values automatically add
  the save attribute and the value is not initialized on second calls.
- Avoid potential allocation error with nbergs=0.
- No answer changes.
---
 icebergs_framework.F90 | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 3f51efe..923d7e7 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -1274,9 +1274,6 @@ subroutine send_bergs_to_other_pes(bergs)
 integer :: i, nbergs_start, nbergs_end
 integer :: stderrunit
 integer :: grdi, grdj
-logical :: force_app
-
-force_app=.true.
 
   ! Get the stderr unit number
   stderrunit = stderr()
@@ -1347,7 +1344,7 @@ subroutine send_bergs_to_other_pes(bergs)
       call increase_ibuffer(bergs%ibuffer_w, nbergs_rcvd_from_w)
       call mpp_recv(bergs%ibuffer_w%data, nbergs_rcvd_from_w*buffer_width, grd%pe_W, tag=COMM_TAG_2)
       do i=1, nbergs_rcvd_from_w
-        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_w, i, grd, force_app, bergs%max_bonds  )
+        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_w, i, grd, max_bonds_in=bergs%max_bonds  )
       enddo
     endif
   else
@@ -1365,7 +1362,7 @@ subroutine send_bergs_to_other_pes(bergs)
       call increase_ibuffer(bergs%ibuffer_e, nbergs_rcvd_from_e)
       call mpp_recv(bergs%ibuffer_e%data, nbergs_rcvd_from_e*buffer_width, grd%pe_E, tag=COMM_TAG_4)
       do i=1, nbergs_rcvd_from_e
-        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_e, i, grd, force_app,  bergs%max_bonds)
+        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_e, i, grd, max_bonds_in=bergs%max_bonds)
       enddo
     endif
   else
@@ -1440,7 +1437,7 @@ subroutine send_bergs_to_other_pes(bergs)
       call increase_ibuffer(bergs%ibuffer_s, nbergs_rcvd_from_s)
       call mpp_recv(bergs%ibuffer_s%data, nbergs_rcvd_from_s*buffer_width, grd%pe_S, tag=COMM_TAG_6)
       do i=1, nbergs_rcvd_from_s
-        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_s, i, grd, force_app, bergs%max_bonds ) 
+        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_s, i, grd, max_bonds_in=bergs%max_bonds )
       enddo
     endif
   else
@@ -1466,7 +1463,7 @@ subroutine send_bergs_to_other_pes(bergs)
          call mpp_recv(bergs%ibuffer_n%data, nbergs_rcvd_from_n*buffer_width, grd%pe_N, tag=COMM_TAG_8)
       endif
       do i=1, nbergs_rcvd_from_n
-        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_n, i, grd,force_app, bergs%max_bonds)
+        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_n, i, grd, max_bonds_in=bergs%max_bonds)
       enddo
     endif
   else
@@ -1673,7 +1670,7 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n,grd, force_append, max_bonds_
   integer :: other_berg_num, other_berg_ine, other_berg_jne
   integer :: counter, k, max_bonds
   integer :: stderrunit
-  logical :: force_app = .false.
+  logical :: force_app
   logical :: quick
 
   ! Get the stderr unit number
@@ -1682,6 +1679,7 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n,grd, force_append, max_bonds_
   quick=.false.
   max_bonds=0
   if (present(max_bonds_in)) max_bonds=max_bonds_in
+  force_app = .false.
   if(present(force_append)) force_app = force_append
      
     localberg%lon=buff%data(1,n)
@@ -2131,8 +2129,9 @@ subroutine insert_berg_into_list(first, newberg, quick)
 logical, intent(in), optional :: quick
 ! Local variables
 type(iceberg), pointer :: this, prev
-logical :: quickly = .false.
+logical :: quickly
 
+  quickly = .false.
 
   if (associated(first)) then
     if (.not. parallel_reprod .or. quickly) then
@@ -3943,6 +3942,7 @@ subroutine bergs_chksum(bergs, txt, ignore_halo_violation)
 
   nbergs=count_bergs(bergs)
   call mpp_max(nbergs)
+  nbergs = max(nbergs, 1)
   allocate( fld( nbergs, 19 ) ) !Changed from 11 to 19 by Alon
   allocate( fld2( nbergs, 19 ) ) !Changed from 11 to 19 by Alon
   allocate( icnt( grd%isd:grd%ied, grd%jsd:grd%jed ) )

From d48eb2fce33aafa5b7d4c8cb2f2dbb5f314ebf50 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Fri, 23 Sep 2016 16:43:01 -0400
Subject: [PATCH 167/361] 1) Added spread_uvel and spread_vvel fields, which
 are the gridded average iceberg velocity. These fields are calculated using
 the spread_mass_to_ocean routine. These fields are used in order to calculate
 ustar, which is then passed through to the ocean model.

2) the spread_mass_to_ocean routine has been refactored to allow mass, area, uvel and vvel to be spread across cells.

3) The iceberg_incr_mass routine has been reworked so that it can spread mass, area, uvel and vvel. This is done by taking in an optional argument (string), which tells the routine which variable to update.

4) A flag PASSS_FIELDS_TO_OCEAN_MODEL has been added. When this is true, the spread_area, ustar, and spread_mass are calculated so that they can be passed to the ocean model.

5) The variable spread_mass_old has been added to the icebergs_run routine. This is a temporary variable used when differencing old and new iceberg masses to work out melting (when find_melt_using_spread_mass=.true.)
---
 icebergs.F90           | 177 +++++++++++++++++++++++++----------------
 icebergs_framework.F90 |  42 +++++++---
 2 files changed, 140 insertions(+), 79 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 9fae040..d34ba3d 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1127,6 +1127,8 @@ subroutine thermodynamics(bergs)
   
   !Initializing static_berg
   static_berg=0.
+  grd%Uvel_on_ocean(:,:,:)=0.
+  grd%Vvel_on_ocean(:,:,:)=0.
 
   ! Thermodynamics of first halo row is calculated, so that spread mass to ocean works correctly
   do grdj = grd%jsc-1,grd%jec+1 ; do grdi = grd%isc-1,grd%iec+1  
@@ -1331,14 +1333,22 @@ subroutine thermodynamics(bergs)
           if ((bergs%iceberg_bonds_on) .and. (bergs%rotate_icebergs_for_mass_spreading)) call find_orientation_using_iceberg_bonds(grd,this,orientation)
           if (bergs%hexagonal_icebergs) static_berg=this%static_berg  !Change this to use_old_restart=false when this is merged in
           call spread_mass_across_ocean_cells(grd, i, j, this%xi, this%yj, Mnew, nMbits, this%mass_scaling, &
-                      this%length*this%width, bergs%use_old_spreading, bergs%hexagonal_icebergs,orientation,static_berg)
+                      this%length*this%width, bergs%use_old_spreading, bergs%hexagonal_icebergs,orientation,static_berg,this%uvel,this%vvel)
         endif
       endif
       this=>next
     enddo
   enddo ; enddo
   
-  !Scaling the gridded iceberg velocity by the iceberg mass 
+  !Finding the average iceberg velocity in a cell to calculate u_star  
+  grd%spread_uvel(:,:)=0.
+  call icebergs_incr_mass(bergs, grd%spread_uvel(grd%isc:grd%iec,grd%jsc:grd%jec),within_iceberg_model=.True.,field_name_in='Uvel') 
+  grd%spread_vvel(:,:)=0.
+  call icebergs_incr_mass(bergs, grd%spread_vvel(grd%isc:grd%iec,grd%jsc:grd%jec),within_iceberg_model=.True.,field_name_in='Vvel') 
+  grd%spread_area(:,:)=0.
+  call icebergs_incr_mass(bergs, grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec),within_iceberg_model=.True.,field_name_in='area') 
+  
+  !Divdind the gridded iceberg momentum by the iceberg mass to get velocities
   do j = grd%jsc,grd%jec ; do i = grd%isc,grd%iec  
     if (grd%mass(i,j)>0.) then
       grd%u_iceberg(i,j)=grd%u_iceberg(i,j)/grd%mass(i,j)
@@ -1349,12 +1359,17 @@ subroutine thermodynamics(bergs)
   enddo; enddo
   
   !Calculating ustar_iceberg (gridded)
-  do j = grd%jsc,grd%jec ; do i = grd%isc,grd%iec  
-    dvo=sqrt((grd%u_iceberg(i,j)-grd%uo(i,j))**2+(grd%v_iceberg(i,j)-grd%vo(i,j))**2)
-    ustar = sqrt(bergs%cdrag_icebergs*(dvo**2  + bergs%utide_icebergs**2))
-    ustar_h = max(bergs%ustar_icebergs_bg, ustar)
-    grd%ustar_iceberg(i,j)=ustar_h
-  enddo; enddo
+  grd%ustar_iceberg(:,:)=0.
+  if  ((grd%id_ustar_iceberg>0) .or. (bergs%pass_fields_to_ocean_model)) then   !Update diagnostic of iceberg mass spread on ocean
+    do j = grd%jsc,grd%jec ; do i = grd%isc,grd%iec  
+      !dvo=sqrt((grd%u_iceberg(i,j)-grd%uo(i,j))**2+(grd%v_iceberg(i,j)-grd%vo(i,j))**2)
+      dvo=sqrt((grd%spread_uvel(i,j)-grd%uo(i,j))**2+(grd%spread_vvel(i,j)-grd%vo(i,j))**2)
+      ustar = sqrt(bergs%cdrag_icebergs*(dvo**2  + bergs%utide_icebergs**2))
+      ustar_h = max(bergs%ustar_icebergs_bg, ustar)
+      if (grd%spread_area(i,j) ==0.0) ustar_h=0.
+        grd%ustar_iceberg(i,j)=ustar_h
+    enddo; enddo
+  endif
 
 end subroutine thermodynamics
 
@@ -1760,17 +1775,17 @@ subroutine find_orientation_using_iceberg_bonds(grd,berg,orientation)
 
 end subroutine find_orientation_using_iceberg_bonds
 
-subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling, Area, use_old_spreading,hexagonal_icebergs,theta,static_berg)
+subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling, Area, use_old_spreading,hexagonal_icebergs,theta,static_berg,uvel,vvel)
   ! Arguments
   type(icebergs_gridded), pointer :: grd
   integer, intent(in) :: i, j
-  real, intent(in) :: x, y, Mberg, Mbits, scaling, Area
+  real, intent(in) :: x, y, Mberg, Mbits, scaling, Area,uvel,vvel
   logical, intent(in) :: hexagonal_icebergs
   logical, intent(in) :: use_old_spreading
   real, intent(in) :: theta
   real, optional, intent(in) :: static_berg
   ! Local variables
-  real :: xL, xC, xR, yD, yC, yU, Mass, L, Area_scaled
+  real :: xL, xC, xR, yD, yC, yU, Mass, L
   real :: yDxL, yDxC, yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR
   real :: S, H, origin_x, origin_y, x0, y0
   real :: Area_Q1,Area_Q2 , Area_Q3,Area_Q4, Area_hex
@@ -1917,32 +1932,42 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
   endif
 
   !Spreading the iceberg mass onto the ocean
-  grd%mass_on_ocean(i,j,1)=grd%mass_on_ocean(i,j,1)+(yDxL*Mass/fraction_used)
-  grd%mass_on_ocean(i,j,2)=grd%mass_on_ocean(i,j,2)+(yDxC*Mass/fraction_used)
-  grd%mass_on_ocean(i,j,3)=grd%mass_on_ocean(i,j,3)+(yDxR*Mass/fraction_used)
-  grd%mass_on_ocean(i,j,4)=grd%mass_on_ocean(i,j,4)+(yCxL*Mass/fraction_used)
-  grd%mass_on_ocean(i,j,5)=grd%mass_on_ocean(i,j,5)+(yCxC*Mass/fraction_used)
-  grd%mass_on_ocean(i,j,6)=grd%mass_on_ocean(i,j,6)+(yCxR*Mass/fraction_used)
-  grd%mass_on_ocean(i,j,7)=grd%mass_on_ocean(i,j,7)+(yUxL*Mass/fraction_used)
-  grd%mass_on_ocean(i,j,8)=grd%mass_on_ocean(i,j,8)+(yUxC*Mass/fraction_used)
-  grd%mass_on_ocean(i,j,9)=grd%mass_on_ocean(i,j,9)+(yUxR*Mass/fraction_used)
-
+  call spread_variable_across_cells(grd, grd%mass_on_ocean, Mass, i ,j, &
+             yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR, fraction_used)
   !Spreading the iceberg area onto the ocean
-  Area_scaled=Area*scaling
-  grd%area_on_ocean(i,j,1)=grd%area_on_ocean(i,j,1)+(yDxL*Area_scaled/fraction_used)
-  grd%area_on_ocean(i,j,2)=grd%area_on_ocean(i,j,2)+(yDxC*Area_scaled/fraction_used)
-  grd%area_on_ocean(i,j,3)=grd%area_on_ocean(i,j,3)+(yDxR*Area_scaled/fraction_used)
-  grd%area_on_ocean(i,j,4)=grd%area_on_ocean(i,j,4)+(yCxL*Area_scaled/fraction_used)
-  grd%area_on_ocean(i,j,5)=grd%area_on_ocean(i,j,5)+(yCxC*Area_scaled/fraction_used)
-  grd%area_on_ocean(i,j,6)=grd%area_on_ocean(i,j,6)+(yCxR*Area_scaled/fraction_used)
-  grd%area_on_ocean(i,j,7)=grd%area_on_ocean(i,j,7)+(yUxL*Area_scaled/fraction_used)
-  grd%area_on_ocean(i,j,8)=grd%area_on_ocean(i,j,8)+(yUxC*Area_scaled/fraction_used)
-  grd%area_on_ocean(i,j,9)=grd%area_on_ocean(i,j,9)+(yUxR*Area_scaled/fraction_used)
-
+  call spread_variable_across_cells(grd, grd%area_on_ocean, Area*scaling , i ,j, &
+             yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR,fraction_used)
+  !Spreading the iceberg x momentum onto the ocean
+  call spread_variable_across_cells(grd,grd%Uvel_on_ocean, uvel*Area*scaling , i ,j, &
+             yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR, fraction_used)
+  !Spreading the iceberg y momentum onto the ocean
+  call spread_variable_across_cells(grd,grd%Vvel_on_ocean, vvel*Area*scaling , i ,j, &
+             yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR, fraction_used)
+  
 end subroutine spread_mass_across_ocean_cells
 
+subroutine spread_variable_across_cells(grd, variable_on_ocean, Var,i,j, &
+           yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR,fraction_used)
+  ! Arguments
+  type(icebergs_gridded), pointer, intent(in) :: grd
+  real, dimension(grd%isd:grd%ied, grd%jsd:grd%jed, 9), intent(inout) :: variable_on_ocean 
+  real, intent(in) :: Var !Variable to be spread accross cell
+  real, intent(in) :: yDxL, yDxC, yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR !Weights
+  real, intent(in) :: fraction_used !Amount of iceberg used
+  integer, intent(in) :: i, j
 
+  !Spreading the iceberg mass onto the ocean
+  variable_on_ocean(i,j,1)=variable_on_ocean(i,j,1)+(yDxL*Var/fraction_used)
+  variable_on_ocean(i,j,2)=variable_on_ocean(i,j,2)+(yDxC*Var/fraction_used)
+  variable_on_ocean(i,j,3)=variable_on_ocean(i,j,3)+(yDxR*Var/fraction_used)
+  variable_on_ocean(i,j,4)=variable_on_ocean(i,j,4)+(yCxL*Var/fraction_used)
+  variable_on_ocean(i,j,5)=variable_on_ocean(i,j,5)+(yCxC*Var/fraction_used)
+  variable_on_ocean(i,j,6)=variable_on_ocean(i,j,6)+(yCxR*Var/fraction_used)
+  variable_on_ocean(i,j,7)=variable_on_ocean(i,j,7)+(yUxL*Var/fraction_used)
+  variable_on_ocean(i,j,8)=variable_on_ocean(i,j,8)+(yUxC*Var/fraction_used)
+  variable_on_ocean(i,j,9)=variable_on_ocean(i,j,9)+(yUxR*Var/fraction_used)
 
+end subroutine spread_variable_across_cells
 
 
 ! ##############################################################################
@@ -2581,12 +2606,13 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 type(icebergs_gridded), pointer :: grd
 logical :: lerr, sample_traj, write_traj, lbudget, lverbose, check_bond_quality 
 real :: unused_calving, tmpsum, grdd_berg_mass, grdd_bergy_mass,grdd_spread_mass, grdd_spread_area
-real :: grdd_u_iceberg, grdd_v_iceberg, grdd_ustar_iceberg
+real :: grdd_u_iceberg, grdd_v_iceberg, grdd_ustar_iceberg, grdd_spread_uvel, grdd_spread_vvel
 integer :: i, j, Iu, ju, iv, Jv, Iu_off, ju_off, iv_off, Jv_off
 real :: mask
 real, dimension(:,:), allocatable :: uC_tmp, vC_tmp
 integer :: vel_stagger, str_stagger
 real, dimension(:,:), allocatable :: iCount
+real, dimension(bergs%grd%isc:bergs%grd%iec,bergs%grd%jsc:bergs%grd%jec)  :: ustar_berg, area_berg, spread_mass_old
 integer :: nbonds
 !logical :: within_iceberg_model
 
@@ -2616,8 +2642,13 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   grd%spread_area(:,:)=0. 
   grd%u_iceberg(:,:)=0.
   grd%v_iceberg(:,:)=0.
+  grd%spread_uvel(:,:)=0.
+  grd%spread_vvel(:,:)=0.
   grd%ustar_iceberg(:,:)=0.
   grd%mass(:,:)=0.
+ 
+  ustar_berg(:,:)=0.
+  area_berg(:,:)=0.
 
   if (bergs%add_weight_to_ocean) grd%mass_on_ocean(:,:,:)=0.
   if (bergs%add_weight_to_ocean) grd%area_on_ocean(:,:,:)=0.
@@ -2853,25 +2884,24 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   !Using spread_mass_to_ocean to calculate melt rates (if this option is chosen)
   !within_iceberg_model=.True.
   if (bergs%find_melt_using_spread_mass) then
-    grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec)=grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec)  !Temporarily using the variable calving for storing old mass (not sure better way)
+    spread_mass_old=grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec)
     grd%spread_mass(:,:)=0.
     call icebergs_incr_mass(bergs, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec),within_iceberg_model=.True.) 
     do i=grd%isc,grd%iec ; do j=grd%jsc,grd%jec
       if (grd%area(i,j)>0.0) then
-        grd%floating_melt(i,j)=max((grd%floating_melt(i,j) - grd%spread_mass(i,j))/(bergs%dt),0.0)
-        !grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)=grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec)*HLF !Not 100% sure this is correct.
-        grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)=grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec)*0.0 !Not 100% sure this is correct.
+        grd%floating_melt(i,j)=max((spread_mass_old(i,j) - grd%spread_mass(i,j))/(bergs%dt),0.0)
+        grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)=grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec)*HLF !Not 100% sure this is correct.
       else
         grd%floating_melt(i,j)=0.0
       endif
     enddo ;enddo
-  elseif  (grd%id_spread_mass>0) then   !Update diagnostic of iceberg mass spread on ocean
+  elseif  ((grd%id_spread_mass>0) .or. (bergs%pass_fields_to_ocean_model)) then   !Update diagnostic of iceberg mass spread on ocean
     grd%spread_mass(:,:)=0.
     call icebergs_incr_mass(bergs, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec),within_iceberg_model=.True.) 
   endif
-  if ( (grd%id_spread_area>0) ) then  !Update diagnostic of iceberg area spread on ocean
+  if ( (grd%id_spread_area>0)  .or. (bergs%pass_fields_to_ocean_model)) then  !Update diagnostic of iceberg area spread on ocean
     grd%spread_area(:,:)=0.
-    call icebergs_incr_mass(bergs, grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec),within_iceberg_model=.True.,spread_area_not_mass=.True.) 
+    call icebergs_incr_mass(bergs, grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec),within_iceberg_model=.True.,field_name_in='area') 
   endif
 
   ! Gridded diagnostics
@@ -2921,6 +2951,10 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     lerr=send_data(grd%id_u_iceberg, grd%u_iceberg(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   if (grd%id_v_iceberg>0) &
     lerr=send_data(grd%id_v_iceberg, grd%v_iceberg(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_spread_uvel>0) &
+    lerr=send_data(grd%id_spread_uvel, grd%spread_uvel(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_spread_vvel>0) &
+    lerr=send_data(grd%id_spread_vvel, grd%spread_vvel(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   if (grd%id_ustar_iceberg>0) &
     lerr=send_data(grd%id_ustar_iceberg, grd%ustar_iceberg(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   if (grd%id_mass>0) &
@@ -2966,8 +3000,12 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     where (grd%area(grd%isc:grd%iec,grd%jsc:grd%jec)>0.)
       calving(:,:)=grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec)/grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) &
                   +grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec)
+      ustar_berg(:,:)=grd%ustar_iceberg(grd%isc:grd%iec,grd%jsc:grd%jec)
+      area_berg(:,:)=grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec)
     elsewhere
       calving(:,:)=0.
+      ustar_berg(:,:)=0.
+      area_berg(:,:)=0.
     end where
     calving_hflx(:,:)=grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)
   endif
@@ -3007,7 +3045,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     bergs%returned_mass_on_ocean=sum( grd%tmpc(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
     !Finding spread area
     call mpp_clock_end(bergs%clock); call mpp_clock_end(bergs%clock_dia) ! To enable calling of public s/r
-    call icebergs_incr_mass(bergs, grd%tmpc,spread_area_not_mass=.true.)
+    call icebergs_incr_mass(bergs, grd%tmpc,field_name_in='area')
     call mpp_clock_begin(bergs%clock_dia); call mpp_clock_begin(bergs%clock) ! To enable calling of public s/r
     bergs%returned_area_on_ocean=sum( grd%tmpc(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
     bergs%nbergs_end=count_bergs(bergs)
@@ -3020,6 +3058,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     call mpp_sum(bergs%spread_area_end)
     call mpp_sum(bergs%u_iceberg_end)
     call mpp_sum(bergs%v_iceberg_end)
+    call mpp_sum(bergs%spread_uvel_end)
+    call mpp_sum(bergs%spread_vvel_end)
     call mpp_sum(bergs%ustar_iceberg_end)
     call mpp_sum(bergs%floating_heat_end)
     call mpp_sum(bergs%returned_mass_on_ocean)
@@ -3226,16 +3266,16 @@ end subroutine icebergs_run
 
 ! ##############################################################################
 
-subroutine icebergs_incr_mass(bergs, mass, within_iceberg_model, Time, spread_area_not_mass)
+subroutine icebergs_incr_mass(bergs, mass, within_iceberg_model, Time,field_name_in)
 ! Arguments
 type(icebergs), pointer :: bergs
 real, dimension(bergs%grd%isc:bergs%grd%iec,bergs%grd%jsc:bergs%grd%jec), intent(inout) :: mass
 type(time_type), intent(in), optional :: Time
 logical, intent(in), optional :: within_iceberg_model
-logical, intent(in), optional :: spread_area_not_mass
+character(len=4), intent(in), optional :: field_name_in
 ! Local variables
 logical :: within_model
-logical :: spread_area !Logical flag which allows you to spread area over ocean (instead of mass)
+character(len=4) :: field_name
 integer :: i, j
 type(icebergs_gridded), pointer :: grd
 real :: dmda
@@ -3250,18 +3290,14 @@ subroutine icebergs_incr_mass(bergs, mass, within_iceberg_model, Time, spread_ar
 
   !var_on_ocean(:,:,:)=0.
   
-  !Decide whether area of mass are being spread across grid cells (default spread mass)
-  spread_area=.False. 
-  if (present(spread_area_not_mass)) then 
-    if (spread_area_not_mass) then 
-      spread_area=.True. 
-    endif
-  endif
-  if (spread_area) then 
-    var_on_ocean(:,:,:)=grd%area_on_ocean(:,:,:)
-  else
-    var_on_ocean(:,:,:)=grd%mass_on_ocean(:,:,:)
-  endif
+  !Deciding which varibale to spread across cells across grid cells (default spread mass)
+  field_name='mass'
+  if (present(field_name_in)) field_name=field_name_in 
+  if (field_name=='mass') var_on_ocean(:,:,:)=grd%mass_on_ocean(:,:,:)
+  if (field_name=='area') var_on_ocean(:,:,:)=grd%area_on_ocean(:,:,:)
+  if (field_name=='Uvel') var_on_ocean(:,:,:)=grd%Uvel_on_ocean(:,:,:)
+  if (field_name=='Vvel') var_on_ocean(:,:,:)=grd%Vvel_on_ocean(:,:,:)
+
 
   
   within_model=.False.
@@ -3309,29 +3345,32 @@ subroutine icebergs_incr_mass(bergs, mass, within_iceberg_model, Time, spread_ar
          +     (var_on_ocean(i  ,j-1,8)+var_on_ocean(i  ,j+1,2)) ) )
     if (grd%area(i,j)>0) dmda=dmda/grd%area(i,j)*grd%msk(i,j)
 
+    !Make sure that area <=1.0
+    if (field_name=='area') dmda=min(dmda,1.0)
+
     if (.not.(within_model)) then
       if (.not. bergs%passive_mode) mass(i,j)=mass(i,j)+dmda
     else
       mass(i,j)=dmda
     endif
-    if ((grd%id_area_on_ocn>0).and.(spread_area)) grd%tmp(i,j)=dmda
-    if ((grd%id_mass_on_ocn>0).and.(.not. spread_area)) grd%tmp(i,j)=dmda
+    if ((grd%id_area_on_ocn>0).and.(field_name=='area')) grd%tmp(i,j)=dmda
+    if ((grd%id_mass_on_ocn>0).and.(field_name=='mass')) grd%tmp(i,j)=dmda
   enddo; enddo
   
-  if (spread_area) then
-    if (present(Time).and. (grd%id_area_on_ocn>0)) &
-      lerr=send_data(grd%id_area_on_ocn, grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  else
+  if (field_name=='mass') then
     if (present(Time).and. (grd%id_mass_on_ocn>0)) &
       lerr=send_data(grd%id_mass_on_ocn, grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  elseif (field_name=='area') then
+    if (present(Time).and. (grd%id_area_on_ocn>0)) &
+      lerr=send_data(grd%id_area_on_ocn, grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   endif
 
   if (debug) then
     grd%tmp(:,:)=0.; grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec)=mass
-    if (.not. spread_area) then
+    if (field_name=='mass') then
       call grd_chksum3(grd, grd%mass_on_ocean, 'mass bergs (incr)')
       call grd_chksum2(grd, grd%tmp, 'mass out (incr)')
-    else
+  elseif (field_name=='area') then
       call grd_chksum3(grd, grd%area_on_ocean, 'area bergs (incr)')
       call grd_chksum2(grd, grd%tmp, 'area out (incr)')
     endif
@@ -3672,7 +3711,7 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
         !this is only called once in Verlet stepping.
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
           call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 1.0*berg%mass_scaling,berg%length*berg%width, &
-                         bergs%use_old_spreading, bergs%hexagonal_icebergs,orientation,static_berg )
+                         bergs%use_old_spreading, bergs%hexagonal_icebergs,orientation,static_berg, berg%uvel, berg%vvel)
 
         ! Calling the acceleration   (note that the velocity is converted to u_star inside the accel script)
         call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn, ayn, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
@@ -3796,7 +3835,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         i1=i;j1=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
           call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, &
-                         bergs%use_old_spreading, bergs%hexagonal_icebergs,orientation,static_berg )
+                         bergs%use_old_spreading, bergs%hexagonal_icebergs,orientation,static_berg, berg%uvel, berg%vvel)
 
         ! Loading past accelerations - Alon
         axn=berg%axn; ayn=berg%ayn !Alon
@@ -3835,7 +3874,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         i2=i; j2=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
           call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, &
-                         bergs%use_old_spreading, bergs%hexagonal_icebergs,orientation,static_berg )
+                         bergs%use_old_spreading, bergs%hexagonal_icebergs,orientation,static_berg, berg%uvel, berg%vvel)
         ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon2,lat2,x2,y2)
         if (.not.error_flag) then
           if (debug .and. .not. is_point_in_cell(bergs%grd, lon2, lat2, i, j)) error_flag=.true.
@@ -3893,7 +3932,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         i3=i; j3=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
           call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, &
-                         bergs%use_old_spreading, bergs%hexagonal_icebergs,orientation,static_berg )
+                         bergs%use_old_spreading, bergs%hexagonal_icebergs,orientation,static_berg, berg%uvel, berg%vvel)
         ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon3,lat3,x3,y3)
         if (.not.error_flag) then
           if (debug .and. .not. is_point_in_cell(bergs%grd, lon3, lat3, i, j)) error_flag=.true.
@@ -4027,7 +4066,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         call adjust_index_and_ground(grd, lonn, latn, uveln, vveln, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
           call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, &
-                         bergs%use_old_spreading, bergs%hexagonal_icebergs,orientation,static_berg )
+                         bergs%use_old_spreading, bergs%hexagonal_icebergs,orientation,static_berg, berg%uvel, berg%vvel)
   
         if (.not.error_flag) then
           if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j)) error_flag=.true.
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 5e46ee1..24477e9 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -116,15 +116,19 @@ module ice_bergs_framework
   real, dimension(:,:), pointer :: bergy_src=>null() ! Mass flux from berg erosion into bergy bits (kg/s/m^2)
   real, dimension(:,:), pointer :: bergy_melt=>null() ! Melting rate of bergy bits (kg/s/m^2)
   real, dimension(:,:), pointer :: bergy_mass=>null() ! Mass distribution of bergy bits (kg/s/m^2)
-  real, dimension(:,:), pointer :: spread_mass=>null() ! Mass of icebergs after spreading (kg/s/m^2)
-  real, dimension(:,:), pointer :: spread_area=>null() ! Area of icebergs after spreading (m^2/s/m^2)
+  real, dimension(:,:), pointer :: spread_mass=>null() ! Mass of icebergs after spreading (kg/m^2)
+  real, dimension(:,:), pointer :: spread_area=>null() ! Area of icebergs after spreading (m^2/m^2)
   real, dimension(:,:), pointer :: u_iceberg=>null() ! Average iceberg velocity in grid cell (mass weighted - but not spread mass weighted)
   real, dimension(:,:), pointer :: v_iceberg=>null() ! Average iceberg velocity in grid cell (mass weighted - but not spread mass weighted)
-  real, dimension(:,:), pointer :: ustar_iceberg=>null() ! Frictional velocity below icebergs to be passed to ocean (mass weighted - but not spread mass weighted)
+  real, dimension(:,:), pointer :: spread_uvel=>null() ! Average iceberg velocity in grid cell (spread area weighted)
+  real, dimension(:,:), pointer :: spread_vvel=>null() ! Average iceberg velocity in grid cell (spread area weighted)
+  real, dimension(:,:), pointer :: ustar_iceberg=>null() ! Frictional velocity below icebergs to be passed to ocean
   real, dimension(:,:), pointer :: virtual_area=>null() ! Virtual surface coverage by icebergs (m^2)
   real, dimension(:,:), pointer :: mass=>null() ! Mass distribution (kg/m^2)
-  real, dimension(:,:,:), pointer :: mass_on_ocean=>null() ! Mass distribution partitioned by neighbor (kg/m^2)   - Alon:I think that this actually has units of kg
-  real, dimension(:,:,:), pointer :: area_on_ocean=>null() ! Area distribution partitioned by neighbor (m^2/m^2)  - Alon:I think that this actually has units of m^2
+  real, dimension(:,:,:), pointer :: mass_on_ocean=>null() ! Mass distribution partitioned by neighbor (kg)  
+  real, dimension(:,:,:), pointer :: area_on_ocean=>null() ! Area distribution partitioned by neighbor (m^2)  
+  real, dimension(:,:,:), pointer :: Uvel_on_ocean=>null() ! zonal velocity distribution partitioned by neighbor (m^2* m/s)  
+  real, dimension(:,:,:), pointer :: Vvel_on_ocean=>null() ! meridional momentum distribution partitioned by neighbor (m^2 m/s)  
   real, dimension(:,:), pointer :: tmp=>null() ! Temporary work space
   real, dimension(:,:), pointer :: tmpc=>null() ! Temporary work space
   real, dimension(:,:,:), pointer :: stored_ice=>null() ! Accumulated ice mass flux at calving locations (kg)
@@ -143,6 +147,7 @@ module ice_bergs_framework
   integer :: id_mass_on_ocn=-1, id_area_on_ocn=-1, id_spread_mass=-1, id_spread_area=-1
   integer :: id_ssh=-1, id_fax=-1, id_fay=-1
   integer :: id_count=-1, id_chksum=-1, id_u_iceberg=-1, id_v_iceberg=-1, id_sss=-1, id_ustar_iceberg
+  integer :: id_spread_uvel=-1, id_spread_vvel=-1
 
   real :: clipping_depth=0. ! The effective depth at which to clip the weight felt by the ocean [m].
 
@@ -227,6 +232,7 @@ module ice_bergs_framework
   logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
   logical :: time_average_weight=.false. ! Time average the weight on the ocean
   logical :: Runge_not_Verlet=.True.  !True=Runge Kuttai, False=Verlet.   
+  logical :: pass_fields_to_ocean_model=.False. !Iceberg area, mass and ustar fields are prepared to pass to ocean model
   logical :: use_mixed_layer_salinity_for_thermo=.False.  !If true, then model uses ocean salinity for 3 and 2 equation melt model.
   logical :: find_melt_using_spread_mass=.False.  !If true, then the model calculates ice loss by looping at the spread_mass before and after.
   logical :: Use_three_equation_model=.True.  !Uses 3 equation model for melt when ice shelf type thermodynamics are used.
@@ -273,6 +279,8 @@ module ice_bergs_framework
   real :: spread_area_start=0., spread_area_end=0.
   real :: u_iceberg_start=0., u_iceberg_end=0.
   real :: v_iceberg_start=0., v_iceberg_end=0.
+  real :: spread_uvel_start=0., spread_uvel_end=0.
+  real :: spread_vvel_start=0., spread_vvel_end=0.
   real :: ustar_iceberg_start=0., ustar_iceberg_end=0.
   real :: returned_mass_on_ocean=0.
   real :: returned_area_on_ocean=0.
@@ -361,6 +369,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: speed_limit=0. ! CFL speed limit for a berg
 real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
 logical :: Runge_not_Verlet=.True.  !True=Runge Kutta, False=Verlet.  - Added by Alon 
+logical :: pass_fields_to_ocean_model=.False. !Iceberg area, mass and ustar fields are prepared to pass to ocean model
 logical :: use_mixed_layer_salinity_for_thermo=.False.  !If true, then model uses ocean salinity for 3 and 2 equation melt model.
 logical :: find_melt_using_spread_mass=.False.  !If true, then the model calculates ice loss by looping at the spread_mass before and after.
 logical :: Use_three_equation_model=.True.  !Uses 3 equation model for melt when ice shelf type thermodynamics are used.
@@ -400,7 +409,7 @@ subroutine ice_bergs_framework_init(bergs, &
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution, force_all_pes_traj, &
          allow_bergs_to_roll,set_melt_rates_to_zero,lat_ref,initial_orientation,rotate_icebergs_for_mass_spreading,grid_is_latlon,Lx,use_f_plane,use_old_spreading, &
          grid_is_regular,Lx,use_f_plane,override_iceberg_velocities,u_override,v_override,add_iceberg_thickness_to_SSH,Iceberg_melt_without_decay,melt_icebergs_as_ice_shelf, &
-         Use_three_equation_model,find_melt_using_spread_mass,use_mixed_layer_salinity_for_thermo,utide_icebergs,ustar_icebergs_bg,cdrag_icebergs
+         Use_three_equation_model,find_melt_using_spread_mass,use_mixed_layer_salinity_for_thermo,utide_icebergs,ustar_icebergs_bg,cdrag_icebergs, pass_fields_to_ocean_model
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -517,11 +526,15 @@ subroutine ice_bergs_framework_init(bergs, &
   allocate( grd%spread_area(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_area(:,:)=0.
   allocate( grd%u_iceberg(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%u_iceberg(:,:)=0.
   allocate( grd%v_iceberg(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%v_iceberg(:,:)=0.
+  allocate( grd%spread_uvel(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_uvel(:,:)=0.
+  allocate( grd%spread_vvel(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_vvel(:,:)=0.
   allocate( grd%ustar_iceberg(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%ustar_iceberg(:,:)=0.
   allocate( grd%virtual_area(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%virtual_area(:,:)=0.
   allocate( grd%mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%mass(:,:)=0.
   allocate( grd%mass_on_ocean(grd%isd:grd%ied, grd%jsd:grd%jed, 9) ); grd%mass_on_ocean(:,:,:)=0.
   allocate( grd%area_on_ocean(grd%isd:grd%ied, grd%jsd:grd%jed, 9) ); grd%area_on_ocean(:,:,:)=0.
+  allocate( grd%Uvel_on_ocean(grd%isd:grd%ied, grd%jsd:grd%jed, 9) ); grd%Uvel_on_ocean(:,:,:)=0.
+  allocate( grd%Vvel_on_ocean(grd%isd:grd%ied, grd%jsd:grd%jed, 9) ); grd%Vvel_on_ocean(:,:,:)=0.
   allocate( grd%stored_ice(grd%isd:grd%ied, grd%jsd:grd%jed, nclasses) ); grd%stored_ice(:,:,:)=0.
   allocate( grd%real_calving(grd%isd:grd%ied, grd%jsd:grd%jed, nclasses) ); grd%real_calving(:,:,:)=0.
   allocate( grd%uo(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%uo(:,:)=0.
@@ -767,6 +780,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%time_average_weight=time_average_weight
   bergs%speed_limit=speed_limit
   bergs%Runge_not_Verlet=Runge_not_Verlet   
+  bergs%pass_fields_to_ocean_model=pass_fields_to_ocean_model 
   bergs%ustar_icebergs_bg=ustar_icebergs_bg   
   bergs%utide_icebergs=utide_icebergs  
   bergs%cdrag_icebergs=cdrag_icebergs  
@@ -844,16 +858,20 @@ subroutine ice_bergs_framework_init(bergs, &
      'Iceberg u velocity (m/s)')
   grd%id_v_iceberg=register_diag_field('icebergs', 'v_iceberg', axes, Time, &
      'Iceberg v velocity (m/s)')
+  grd%id_spread_uvel=register_diag_field('icebergs', 'spread_uvel', axes, Time, &
+     'Iceberg u velocity spread (m/s)')
+  grd%id_spread_vvel=register_diag_field('icebergs', 'spread_vvel', axes, Time, &
+     'Iceberg v velocity spread (m/s)')
   grd%id_ustar_iceberg=register_diag_field('icebergs', 'ustar_iceberg', axes, Time, &
      'Iceberg frictional velocity (m/s)')
   grd%id_virtual_area=register_diag_field('icebergs', 'virtual_area', axes, Time, &
      'Virtual coverage by icebergs', 'm^2')
   grd%id_mass=register_diag_field('icebergs', 'mass', axes, Time, &
      'Iceberg density field', 'kg/(m^2)')
-  grd%id_mass_on_ocn=register_diag_field('icebergs', 'mass_on_ocean', axes, Time, &
-     'Iceberg density field felt by ocean', 'kg/(m^2)')
-  grd%id_area_on_ocn=register_diag_field('icebergs', 'area_on_ocean', axes, Time, &
-     'Iceberg area field felt by ocean', 'm^2/(m^2)')
+!  grd%id_mass_on_ocn=register_diag_field('icebergs', 'mass_on_ocean', axes, Time, &
+!     'Iceberg density field felt by ocean', 'kg/(m^2)')
+!  grd%id_area_on_ocn=register_diag_field('icebergs', 'area_on_ocean', axes, Time, &
+!     'Iceberg area field felt by ocean', 'm^2/(m^2)')
   grd%id_stored_ice=register_diag_field('icebergs', 'stored_ice', axes3d, Time, &
      'Accumulated ice mass by class', 'kg')
   grd%id_real_calving=register_diag_field('icebergs', 'real_calving', axes3d, Time, &
@@ -3818,6 +3836,8 @@ subroutine checksum_gridded(grd, label)
   call grd_chksum2(grd, grd%mass, 'mass')
   call grd_chksum3(grd, grd%mass_on_ocean, 'mass_on_ocean')
   call grd_chksum3(grd, grd%area_on_ocean, 'area_on_ocean')
+  call grd_chksum3(grd, grd%Uvel_on_ocean, 'Uvel_on_ocean')
+  call grd_chksum3(grd, grd%Vvel_on_ocean, 'Vvel_on_ocean')
   call grd_chksum3(grd, grd%stored_ice, 'stored_ice')
   call grd_chksum2(grd, grd%stored_heat, 'stored_heat')
   call grd_chksum2(grd, grd%melt_buoy, 'melt_b')
@@ -3830,6 +3850,8 @@ subroutine checksum_gridded(grd, label)
   call grd_chksum2(grd, grd%spread_area, 'spread_area')
   call grd_chksum2(grd, grd%u_iceberg, 'u_iceberg')
   call grd_chksum2(grd, grd%v_iceberg, 'v_iceberg')
+  call grd_chksum2(grd, grd%spread_uvel, 'spread_uvel')
+  call grd_chksum2(grd, grd%spread_vvel, 'spread_vvel')
   call grd_chksum2(grd, grd%ustar_iceberg, 'ustar_iceberg')
   call grd_chksum2(grd, grd%virtual_area, 'varea')
   call grd_chksum2(grd, grd%floating_melt, 'floating_melt')

From 504779ede5250920db2e619dcdb4762ae8969dee Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Fri, 23 Sep 2016 17:18:16 -0400
Subject: [PATCH 168/361] Fields spread_mass, spread_area and ustar_iceberg
 have been added to the icebergs_gridded type and allocated. This change will
 allow SIS2 to compile when the new code which passes fields from the icebergs
 model to the ocean model (through the sea ice model) is added.

---
 icebergs_framework.F90 | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index d2b6899..85bd6d2 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -105,6 +105,9 @@ module ice_bergs_framework
   real, dimension(:,:), pointer :: bergy_src=>null() ! Mass flux from berg erosion into bergy bits (kg/s/m^2)
   real, dimension(:,:), pointer :: bergy_melt=>null() ! Melting rate of bergy bits (kg/s/m^2)
   real, dimension(:,:), pointer :: bergy_mass=>null() ! Mass distribution of bergy bits (kg/s/m^2)
+  real, dimension(:,:), pointer :: spread_mass=>null() ! Mass of icebergs after spreading (kg/m^2)
+  real, dimension(:,:), pointer :: spread_area=>null() ! Area of icebergs  after spreading (m^2/m^2)
+  real, dimension(:,:), pointer :: ustar_iceberg=>null() ! Frictional velocity below icebergs to be passed to ocean
   real, dimension(:,:), pointer :: virtual_area=>null() ! Virtual surface coverage by icebergs (m^2)
   real, dimension(:,:), pointer :: mass=>null() ! Mass distribution (kg/m^2)
   real, dimension(:,:,:), pointer :: mass_on_ocean=>null() ! Mass distribution partitioned by neighbor (kg/m^2)
@@ -419,6 +422,9 @@ subroutine ice_bergs_framework_init(bergs, &
   allocate( grd%bergy_src(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%bergy_src(:,:)=0.
   allocate( grd%bergy_melt(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%bergy_melt(:,:)=0.
   allocate( grd%bergy_mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%bergy_mass(:,:)=0.
+  allocate( grd%spread_mass(grd%isd:grd%ied, grd%jsd:grd%jed) );  grd%spread_mass(:,:)=0.
+  allocate( grd%spread_area(grd%isd:grd%ied, grd%jsd:grd%jed) );  grd%spread_area(:,:)=0.
+  allocate( grd%ustar_iceberg(grd%isd:grd%ied, grd%jsd:grd%jed) );grd%ustar_iceberg(:,:)=0.
   allocate( grd%virtual_area(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%virtual_area(:,:)=0.
   allocate( grd%mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%mass(:,:)=0.
   allocate( grd%mass_on_ocean(grd%isd:grd%ied, grd%jsd:grd%jed, 9) ); grd%mass_on_ocean(:,:,:)=0.

From 142b593eac25c29bad09c09f6c94dc932f5e05da Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Thu, 29 Sep 2016 13:32:40 -0400
Subject: [PATCH 169/361] 1) Added an option in the three equation model to use
 a fixed value for gamma_T, following what is done in the ice shelf code. (It
 now looks similar to the ice shelf code, however, I have not explored whether
 this option gives reasonable answers)

2) The dimensions of ustar_berg, area_berg and spread_mass_old have been changed. This fixed a bug in the calculating melt through spread mass option.

3) Added a diagnostic for melt which has units of m/yr, so that it is more easily comparible with the melt fields in the ocean model
---
 icebergs.F90           | 36 ++++++++++++++++++++++++++----------
 icebergs_framework.F90 | 12 +++++++++++-
 2 files changed, 37 insertions(+), 11 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index d34ba3d..e161cd8 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1532,9 +1532,14 @@ subroutine find_basal_melt(bergs,dvo,lat,salt,temp,Use_three_equation_model,thic
       ! on the turbulence.  Following H & J '99, this limit also applies
       ! when the buoyancy flux is destabilizing.
 
-      Gam_turb = I_VK * (ln_neut + (0.5 * I_ZETA_N - 1.0))
-      I_Gam_T = 1.0 / (Gam_mol_t + Gam_turb)
-      I_Gam_S = 1.0 / (Gam_mol_s + Gam_turb)
+      if (bergs%const_gamma) then ! if using a constant gamma_T
+        I_Gam_T = bergs%Gamma_T_3EQ
+        I_Gam_S = bergs%Gamma_T_3EQ/35.
+      else
+        Gam_turb = I_VK * (ln_neut + (0.5 * I_ZETA_N - 1.0))
+        I_Gam_T = 1.0 / (Gam_mol_t + Gam_turb)
+        I_Gam_S = 1.0 / (Gam_mol_s + Gam_turb)
+      endif
       wT_flux = dT_ustar * I_Gam_T
       wB_flux = dB_dS * (dS_ustar * I_Gam_S) + dB_dT * wT_flux
 
@@ -1559,8 +1564,14 @@ subroutine find_basal_melt(bergs,dvo,lat,salt,temp,Use_three_equation_model,thic
             dG_dwB = I_VK * (0.5 * I_ZETA_N) * dIns_dwB
           endif
 
-          I_Gam_T = 1.0 / (Gam_mol_t + Gam_turb)
-          I_Gam_S = 1.0 / (Gam_mol_s + Gam_turb)
+          if (bergs%const_gamma) then ! if using a constant gamma_T
+            I_Gam_T = bergs%Gamma_T_3EQ
+            I_Gam_S = bergs%Gamma_T_3EQ/35.
+          else
+            I_Gam_T = 1.0 / (Gam_mol_t + Gam_turb)
+            I_Gam_S = 1.0 / (Gam_mol_s + Gam_turb)
+          endif
+
           wT_flux = dT_ustar * I_Gam_T
           wB_flux_new = dB_dS * (dS_ustar * I_Gam_S) + dB_dT * wT_flux
 
@@ -2612,7 +2623,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 real, dimension(:,:), allocatable :: uC_tmp, vC_tmp
 integer :: vel_stagger, str_stagger
 real, dimension(:,:), allocatable :: iCount
-real, dimension(bergs%grd%isc:bergs%grd%iec,bergs%grd%jsc:bergs%grd%jec)  :: ustar_berg, area_berg, spread_mass_old
+real, dimension(bergs%grd%isd:bergs%grd%ied,bergs%grd%jsd:bergs%grd%jed)  :: ustar_berg, area_berg, spread_mass_old
 integer :: nbonds
 !logical :: within_iceberg_model
 
@@ -2884,10 +2895,11 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   !Using spread_mass_to_ocean to calculate melt rates (if this option is chosen)
   !within_iceberg_model=.True.
   if (bergs%find_melt_using_spread_mass) then
-    spread_mass_old=grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec)
+    !spread_mass_old=grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec)
+    spread_mass_old(:,:)=grd%spread_mass(:,:)
     grd%spread_mass(:,:)=0.
     call icebergs_incr_mass(bergs, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec),within_iceberg_model=.True.) 
-    do i=grd%isc,grd%iec ; do j=grd%jsc,grd%jec
+    do i=grd%isd,grd%ied ; do j=grd%jsd,grd%jed
       if (grd%area(i,j)>0.0) then
         grd%floating_melt(i,j)=max((spread_mass_old(i,j) - grd%spread_mass(i,j))/(bergs%dt),0.0)
         grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)=grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec)*HLF !Not 100% sure this is correct.
@@ -2927,6 +2939,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     lerr=send_data(grd%id_hi, grd%hi(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   if (grd%id_floating_melt>0) &
     lerr=send_data(grd%id_floating_melt, grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_melt_m_per_year>0) &
+    lerr=send_data(grd%id_melt_m_per_year, grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec)* (86400.0*365.0/bergs%rho_bergs), Time)
   if (grd%id_berg_melt>0) &
     lerr=send_data(grd%id_berg_melt, grd%berg_melt(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   if (grd%id_melt_buoy>0) &
@@ -3000,8 +3014,10 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     where (grd%area(grd%isc:grd%iec,grd%jsc:grd%jec)>0.)
       calving(:,:)=grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec)/grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) &
                   +grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec)
-      ustar_berg(:,:)=grd%ustar_iceberg(grd%isc:grd%iec,grd%jsc:grd%jec)
-      area_berg(:,:)=grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec)
+      !ustar_berg(:,:)=grd%ustar_iceberg(grd%isc:grd%iec,grd%jsc:grd%jec)
+      !area_berg(:,:)=grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec)
+      ustar_berg(:,:)=grd%ustar_iceberg(:,:)
+      area_berg(:,:)=grd%spread_area(:,:)
     elsewhere
       calving(:,:)=0.
       ustar_berg(:,:)=0.
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 24477e9..96652d6 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -148,6 +148,7 @@ module ice_bergs_framework
   integer :: id_ssh=-1, id_fax=-1, id_fay=-1
   integer :: id_count=-1, id_chksum=-1, id_u_iceberg=-1, id_v_iceberg=-1, id_sss=-1, id_ustar_iceberg
   integer :: id_spread_uvel=-1, id_spread_vvel=-1
+  integer :: id_melt_m_per_year=-1
 
   real :: clipping_depth=0. ! The effective depth at which to clip the weight felt by the ocean [m].
 
@@ -224,6 +225,8 @@ module ice_bergs_framework
   real :: ustar_icebergs_bg=0.001 ! Background u_star under icebergs. This should be linked to a value felt by the ocean boundary layer
   real :: cdrag_icebergs =  1.5e-3 !Momentum Drag coef, taken from HJ99  (Holland and Jenkins 1999)
   real :: initial_orientation=0. ! Iceberg orientaion relative to this angle (in degrees). Used for hexagonal mass spreading.
+  real :: Gamma_T_3EQ=0.022 ! Nondimensional heat-transfer coefficient
+  logical :: const_gamma=.True. !If true uses a constant heat tranfer coefficient, from which the salt transfer is calculated
   real, dimension(:), pointer :: initial_mass, distribution, mass_scaling
   real, dimension(:), pointer :: initial_thickness, initial_width, initial_length
   logical :: restarted=.false. ! Indicate whether we read state from a restart or not
@@ -362,6 +365,8 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: utide_icebergs= 0.      ! Tidal speeds, set to zero for now.
 real :: ustar_icebergs_bg=0.001 ! Background u_star under icebergs. This should be linked to a value felt by the ocean boundary layer
 real :: cdrag_icebergs =  1.5e-3 !Momentum Drag coef, taken from HJ99  (Holland and Jenkins 1999)
+real :: Gamma_T_3EQ=0.022 ! Nondimensional heat-transfer coefficient
+logical :: const_gamma=.True. !If true uses a constant heat tranfer coefficient, from which the salt transfer is calculated
 logical :: use_operator_splitting=.true. ! Use first order operator splitting for thermodynamics
 logical :: add_weight_to_ocean=.true. ! Add weight of icebergs + bits to ocean
 logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
@@ -409,7 +414,8 @@ subroutine ice_bergs_framework_init(bergs, &
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution, force_all_pes_traj, &
          allow_bergs_to_roll,set_melt_rates_to_zero,lat_ref,initial_orientation,rotate_icebergs_for_mass_spreading,grid_is_latlon,Lx,use_f_plane,use_old_spreading, &
          grid_is_regular,Lx,use_f_plane,override_iceberg_velocities,u_override,v_override,add_iceberg_thickness_to_SSH,Iceberg_melt_without_decay,melt_icebergs_as_ice_shelf, &
-         Use_three_equation_model,find_melt_using_spread_mass,use_mixed_layer_salinity_for_thermo,utide_icebergs,ustar_icebergs_bg,cdrag_icebergs, pass_fields_to_ocean_model
+         Use_three_equation_model,find_melt_using_spread_mass,use_mixed_layer_salinity_for_thermo,utide_icebergs,ustar_icebergs_bg,cdrag_icebergs, pass_fields_to_ocean_model, &
+         const_gamma, Gamma_T_3EQ
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -780,6 +786,8 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%time_average_weight=time_average_weight
   bergs%speed_limit=speed_limit
   bergs%Runge_not_Verlet=Runge_not_Verlet   
+  bergs%const_gamma=const_gamma 
+  bergs%Gamma_T_3EQ=Gamma_T_3EQ
   bergs%pass_fields_to_ocean_model=pass_fields_to_ocean_model 
   bergs%ustar_icebergs_bg=ustar_icebergs_bg   
   bergs%utide_icebergs=utide_icebergs  
@@ -836,6 +844,8 @@ subroutine ice_bergs_framework_init(bergs, &
      'Unused calving mass rate', 'kg/s')
   grd%id_floating_melt=register_diag_field('icebergs', 'melt', axes, Time, &
      'Melt rate of icebergs + bits', 'kg/(m^2*s)')
+  grd%id_melt_m_per_year=register_diag_field('icebergs', 'melt_m_per_year', axes, Time, &
+     'Melt rate of icebergs + bits (m/yr)', 'm/yr')
   grd%id_berg_melt=register_diag_field('icebergs', 'berg_melt', axes, Time, &
      'Melt rate of icebergs', 'kg/(m^2*s)')
   grd%id_melt_buoy=register_diag_field('icebergs', 'melt_buoy', axes, Time, &

From 1bd85a643998f024cbf98dc3820d8791603d0856 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Fri, 30 Sep 2016 15:13:29 -0400
Subject: [PATCH 170/361] 1) A bug was identified which made the model run
 slower and slower the longer it ran. This was beceause the model was
 assigning extra memory in the increase_ibuffer routine (and also in the
 increase_ibuffer_traj). This bug was resolved by correcting the line in the
 ibuffer routine so that if the amount of space in the buffer is sufficient,
 then the buffer size is not increased.

2) The routine increase_ibuffer was also refactored slightly so that it is easier to read. In particular, the variable delta, was renamed nbergs. The routine checks to see if the buffer size is greater than nbergs, and if not the buffer size is increased.

3) The routines increase_buffer, increase_buffer_traj and increase_ibuffer_traj have been removed. The routine increase_ibuffer has been slightly edited so that it can be used instead of these three other routines.This was achievd by the following:
     i) The buffer_width has been added to the inputs of the routine. This allows the trajetories and the bergs buffers to be increased with the same routine.
     ii)The role of the increase_buffer routine was to increase the buffer size by a fixed value delta. It was noticed that the increase_ibuffer routine would do the same thing if the size of the buffer was smaller than the current number of bergs.

4) A new flag IGNORE_TRAJ was added. When this flag is true, then iceberg trajectories are not stored at all. This is to make the model run faster when trajectories are not needed.

5) The update_halo() routine is only called when iceberg interactions or iceberg bonds are on. This makes the icebergs module run faster when interactions are not needed. I am 95% sure that this change makes sense, but there could be issues that I am not seeing.

6) Some debugging lines have been added to update_halo() which will display data when the flag debug=.true.

6) An if (save_short_traj)=.true. line has been added to the record_position routine, so that only the relavent variables are record (since save_short_traj means that only a few of the trajectory variables are saved).
---
 icebergs.F90           |   7 +-
 icebergs_framework.F90 | 253 ++++++++++++++++++-----------------------
 icebergs_io.F90        |   4 +-
 3 files changed, 117 insertions(+), 147 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index e161cd8..15b5c02 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -2671,11 +2671,11 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   bergs%current_yearday=yearday(imon, iday, ihr, imin, isec)
   ! Turn on sampling of trajectories, verbosity, budgets
   sample_traj=.false.
-  if (bergs%traj_sample_hrs>0) then
+  if ( (bergs%traj_sample_hrs>0)  .and. (.not. bergs%ignore_traj) ) then
      if (mod(24*iday+ihr,bergs%traj_sample_hrs).eq.0) sample_traj=.true.
   end if
   write_traj=.false.
-  if (bergs%traj_write_hrs>0) then
+  if ((bergs%traj_write_hrs>0) .and. (.not. bergs%ignore_traj))  then
      if (mod(24*iday+ihr,bergs%traj_write_hrs).eq.0) write_traj=.true.
   end if
   lverbose=.false.
@@ -2869,7 +2869,9 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   ! Send bergs to other PEs
   call mpp_clock_begin(bergs%clock_com)
   if (bergs%iceberg_bonds_on)  call  bond_address_update(bergs)
+
   call send_bergs_to_other_pes(bergs)
+  if ((bergs%interactive_icebergs_on) .or. (bergs%iceberg_bonds_on)) &
   call update_halo_icebergs(bergs)
   if (bergs%iceberg_bonds_on)  call connect_all_bonds(bergs)
   if (debug) call bergs_chksum(bergs, 'run bergs (exchanged)')
@@ -4609,6 +4611,7 @@ subroutine icebergs_end(bergs)
   ! Delete bergs and structures
   call move_all_trajectories(bergs, delete_bergs=.true.)
 
+  if (.not. bergs%ignore_traj) &
   call write_trajectory(bergs%trajectories, bergs%save_short_traj)
 
   deallocate(bergs%grd%lon)
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 96652d6..8d18fcd 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -59,7 +59,7 @@ module ice_bergs_framework
 public update_halo_icebergs
 public pack_berg_into_buffer2, unpack_berg_from_buffer2
 public pack_traj_into_buffer2, unpack_traj_from_buffer2
-public increase_buffer, increase_ibuffer, increase_ibuffer_traj, increase_buffer_traj
+public increase_ibuffer 
 public add_new_berg_to_list, count_out_of_order, check_for_duplicates
 public insert_berg_into_list, create_iceberg, delete_iceberg_from_list, destroy_iceberg
 public print_fld,print_berg, print_bergs,record_posn, push_posn, append_posn, check_position
@@ -253,6 +253,7 @@ module ice_bergs_framework
   logical :: only_interactive_forces=.False.  !Icebergs only feel interactive forces, and not ocean, wind... 
   logical :: halo_debugging=.False.  !Use for debugging halos (remove when its working) 
   logical :: save_short_traj=.True.  !True saves only lon,lat,time,iceberg_num in iceberg_trajectory.nc 
+  logical :: ignore_traj=.False.  !If true, then model does not traj trajectory data at all 
   logical :: iceberg_bonds_on=.False.  !True=Allow icebergs to have bonds, False=don't allow. 
   logical :: manually_initialize_bonds=.False.  !True= Bonds are initialize manually. 
   logical :: use_new_predictive_corrective =.False.  !Flag to use Bob's predictive corrective iceberg scheme- Added by Alon 
@@ -394,6 +395,7 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: only_interactive_forces=.False.  !Icebergs only feel interactive forces, and not ocean, wind... 
 logical :: halo_debugging=.False.  !Use for debugging halos (remove when its working) 
 logical :: save_short_traj=.True.  !True saves only lon,lat,time,iceberg_num in iceberg_trajectory.nc 
+logical :: ignore_traj=.False.  !If true, then model does not traj trajectory data at all 
 logical :: iceberg_bonds_on=.False.  !True=Allow icebergs to have bonds, False=don't allow. 
 logical :: manually_initialize_bonds=.False.  !True= Bonds are initialize manually. 
 logical :: use_new_predictive_corrective =.False.  !Flag to use Bob's predictive corrective iceberg scheme- Added by Alon 
@@ -415,7 +417,7 @@ subroutine ice_bergs_framework_init(bergs, &
          allow_bergs_to_roll,set_melt_rates_to_zero,lat_ref,initial_orientation,rotate_icebergs_for_mass_spreading,grid_is_latlon,Lx,use_f_plane,use_old_spreading, &
          grid_is_regular,Lx,use_f_plane,override_iceberg_velocities,u_override,v_override,add_iceberg_thickness_to_SSH,Iceberg_melt_without_decay,melt_icebergs_as_ice_shelf, &
          Use_three_equation_model,find_melt_using_spread_mass,use_mixed_layer_salinity_for_thermo,utide_icebergs,ustar_icebergs_bg,cdrag_icebergs, pass_fields_to_ocean_model, &
-         const_gamma, Gamma_T_3EQ
+         const_gamma, Gamma_T_3EQ, ignore_traj
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -760,6 +762,7 @@ subroutine ice_bergs_framework_init(bergs, &
   buffer_width=buffer_width+(max_bonds*3) ! Increase buffer width to include bonds being passed between processors 
 endif
 if (save_short_traj) buffer_width_traj=5 ! This is the length of the short buffer used for abrevated traj
+if (ignore_traj) buffer_width_traj=0 ! If this is true, then all traj files should be ignored
 
 
  ! Parameters
@@ -767,6 +770,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%traj_sample_hrs=traj_sample_hrs
   bergs%traj_write_hrs=traj_write_hrs
   bergs%save_short_traj=save_short_traj
+  bergs%ignore_traj=ignore_traj
   bergs%verbose_hrs=verbose_hrs
   bergs%grd%halo=halo
   bergs%grd%Lx=Lx
@@ -1070,7 +1074,6 @@ subroutine update_halo_icebergs(bergs)
  ! For convenience
    grd=>bergs%grd
 
-
 !For debugging, MP1
 if (halo_debugging) then
   do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
@@ -1185,7 +1188,7 @@ subroutine update_halo_icebergs(bergs)
       write(stderrunit,*) 'pe=',mpp_pe(),' received a bad number',nbergs_rcvd_from_w,' from',grd%pe_W,' (W) !!!!!!!!!!!!!!!!!!!!!!'
     endif
     if (nbergs_rcvd_from_w.gt.0) then
-      call increase_ibuffer(bergs%ibuffer_w, nbergs_rcvd_from_w)
+      call increase_ibuffer(bergs%ibuffer_w, nbergs_rcvd_from_w,buffer_width)
       call mpp_recv(bergs%ibuffer_w%data, nbergs_rcvd_from_w*buffer_width, grd%pe_W, tag=COMM_TAG_2)
       do i=1, nbergs_rcvd_from_w
         call unpack_berg_from_buffer2(bergs, bergs%ibuffer_w, i, grd, max_bonds_in=bergs%max_bonds )
@@ -1203,7 +1206,7 @@ subroutine update_halo_icebergs(bergs)
       write(stderrunit,*) 'pe=',mpp_pe(),' received a bad number',nbergs_rcvd_from_e,' from',grd%pe_E,' (E) !!!!!!!!!!!!!!!!!!!!!!'
     endif
     if (nbergs_rcvd_from_e.gt.0) then
-      call increase_ibuffer(bergs%ibuffer_e, nbergs_rcvd_from_e)
+      call increase_ibuffer(bergs%ibuffer_e, nbergs_rcvd_from_e,buffer_width)
       call mpp_recv(bergs%ibuffer_e%data, nbergs_rcvd_from_e*buffer_width, grd%pe_E, tag=COMM_TAG_4)
       do i=1, nbergs_rcvd_from_e
         call unpack_berg_from_buffer2(bergs, bergs%ibuffer_e, i, grd, max_bonds_in=bergs%max_bonds )
@@ -1282,7 +1285,7 @@ subroutine update_halo_icebergs(bergs)
       write(stderrunit,*) 'pe=',mpp_pe(),' received a bad number',nbergs_rcvd_from_s,' from',grd%pe_S,' (S) !!!!!!!!!!!!!!!!!!!!!!'
     endif
     if (nbergs_rcvd_from_s.gt.0) then
-      call increase_ibuffer(bergs%ibuffer_s, nbergs_rcvd_from_s)
+      call increase_ibuffer(bergs%ibuffer_s, nbergs_rcvd_from_s,buffer_width)
       call mpp_recv(bergs%ibuffer_s%data, nbergs_rcvd_from_s*buffer_width, grd%pe_S, tag=COMM_TAG_6)
       do i=1, nbergs_rcvd_from_s
         call unpack_berg_from_buffer2(bergs, bergs%ibuffer_s, i, grd, max_bonds_in=bergs%max_bonds  )
@@ -1304,7 +1307,7 @@ subroutine update_halo_icebergs(bergs)
       write(stderrunit,*) 'pe=',mpp_pe(),' received a bad number',nbergs_rcvd_from_n,' from',grd%pe_N,' (N) !!!!!!!!!!!!!!!!!!!!!!'
     endif
     if (nbergs_rcvd_from_n.gt.0) then
-      call increase_ibuffer(bergs%ibuffer_n, nbergs_rcvd_from_n)
+      call increase_ibuffer(bergs%ibuffer_n, nbergs_rcvd_from_n,buffer_width)
       if(folded_north_on_pe) then
          call mpp_recv(bergs%ibuffer_n%data, nbergs_rcvd_from_n*buffer_width, grd%pe_N, tag=COMM_TAG_10)
       else
@@ -1333,12 +1336,54 @@ subroutine update_halo_icebergs(bergs)
   call show_all_bonds(bergs)
 endif
 
-end subroutine update_halo_icebergs
 
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!Debugging!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!111
+  if (debug) then
+    nbergs_end=count_bergs(bergs)
+    i=nbergs_rcvd_from_n+nbergs_rcvd_from_s+nbergs_rcvd_from_e+nbergs_rcvd_from_w &
+     -nbergs_to_send_n-nbergs_to_send_s-nbergs_to_send_e-nbergs_to_send_w
+    if (nbergs_end-(nbergs_start+i).ne.0) then
+      write(stderrunit,'(a,i4,a,i4)') 'diamonds, update_halos: nbergs_end=',nbergs_end,' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'diamonds, update_halos: nbergs_start=',nbergs_start,' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'diamonds, update_halos: delta=',i,' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'diamonds, update_halos: error=',nbergs_end-(nbergs_start+i),' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'diamonds, update_halos: nbergs_to_send_n=',nbergs_to_send_n,' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'diamonds, update_halos: nbergs_to_send_s=',nbergs_to_send_s,' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'diamonds, update_halos: nbergs_to_send_e=',nbergs_to_send_e,' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'diamonds, update_halos: nbergs_to_send_w=',nbergs_to_send_w,' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'diamonds, update_halos: nbergs_rcvd_from_n=',nbergs_rcvd_from_n,' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'diamonds, update_halos: nbergs_rcvd_from_s=',nbergs_rcvd_from_s,' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'diamonds, update_halos: nbergs_rcvd_from_e=',nbergs_rcvd_from_e,' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'diamonds, update_halos: nbergs_rcvd_from_w=',nbergs_rcvd_from_w,' on PE',mpp_pe()
+      !call error_mesg('diamonds, update_halos:', 'We lost some bergs!', FATAL)
+    endif
+  endif
+  if (debug) then
+    i=0
+    do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
+      this=>bergs%list(grdi,grdj)%first
+      do while (associated(this))
+        call check_position(grd, this, 'exchange (bot)')
+        if (this%ine.lt.bergs%grd%isc .or. &
+            this%ine.gt.bergs%grd%iec .or. &
+            this%jne.lt.bergs%grd%jsc .or. &
+            this%jne.gt.bergs%grd%jec) i=i+1
+        this=>this%next
+      enddo ! while
+    enddo ; enddo
+    call mpp_sum(i)
+    if (i>0 .and. mpp_pe()==mpp_root_pe()) then
+      write(stderrunit,'(a,i4)') 'diamonds, update_halos: # of bergs outside computational domain = ',i
+      call error_mesg('diamonds, update_halos:', 'there are bergs still in halos!', FATAL)
+    endif ! root_pe
+  endif ! debug
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!Debugging!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!111
+
+end subroutine update_halo_icebergs
 
 
 
-!contains
 subroutine delete_all_bergs_in_list(bergs,grdj,grdi)
   type(icebergs), pointer :: bergs
   ! Local variables
@@ -1355,7 +1400,6 @@ subroutine delete_all_bergs_in_list(bergs,grdj,grdi)
 end  subroutine delete_all_bergs_in_list
 
 
-
 ! #############################################################################
 
 subroutine send_bergs_to_other_pes(bergs)
@@ -1439,7 +1483,7 @@ subroutine send_bergs_to_other_pes(bergs)
       write(stderrunit,*) 'pe=',mpp_pe(),' received a bad number',nbergs_rcvd_from_w,' from',grd%pe_W,' (W) !!!!!!!!!!!!!!!!!!!!!!'
     endif
     if (nbergs_rcvd_from_w.gt.0) then
-      call increase_ibuffer(bergs%ibuffer_w, nbergs_rcvd_from_w)
+      call increase_ibuffer(bergs%ibuffer_w, nbergs_rcvd_from_w,buffer_width)
       call mpp_recv(bergs%ibuffer_w%data, nbergs_rcvd_from_w*buffer_width, grd%pe_W, tag=COMM_TAG_2)
       do i=1, nbergs_rcvd_from_w
         call unpack_berg_from_buffer2(bergs, bergs%ibuffer_w, i, grd, force_app, bergs%max_bonds  )
@@ -1457,7 +1501,7 @@ subroutine send_bergs_to_other_pes(bergs)
       write(stderrunit,*) 'pe=',mpp_pe(),' received a bad number',nbergs_rcvd_from_e,' from',grd%pe_E,' (E) !!!!!!!!!!!!!!!!!!!!!!'
     endif
     if (nbergs_rcvd_from_e.gt.0) then
-      call increase_ibuffer(bergs%ibuffer_e, nbergs_rcvd_from_e)
+      call increase_ibuffer(bergs%ibuffer_e, nbergs_rcvd_from_e,buffer_width)
       call mpp_recv(bergs%ibuffer_e%data, nbergs_rcvd_from_e*buffer_width, grd%pe_E, tag=COMM_TAG_4)
       do i=1, nbergs_rcvd_from_e
         call unpack_berg_from_buffer2(bergs, bergs%ibuffer_e, i, grd, force_app,  bergs%max_bonds)
@@ -1532,7 +1576,7 @@ subroutine send_bergs_to_other_pes(bergs)
       write(stderrunit,*) 'pe=',mpp_pe(),' received a bad number',nbergs_rcvd_from_s,' from',grd%pe_S,' (S) !!!!!!!!!!!!!!!!!!!!!!'
     endif
     if (nbergs_rcvd_from_s.gt.0) then
-      call increase_ibuffer(bergs%ibuffer_s, nbergs_rcvd_from_s)
+      call increase_ibuffer(bergs%ibuffer_s, nbergs_rcvd_from_s,buffer_width)
       call mpp_recv(bergs%ibuffer_s%data, nbergs_rcvd_from_s*buffer_width, grd%pe_S, tag=COMM_TAG_6)
       do i=1, nbergs_rcvd_from_s
         call unpack_berg_from_buffer2(bergs, bergs%ibuffer_s, i, grd, force_app, bergs%max_bonds ) 
@@ -1554,7 +1598,7 @@ subroutine send_bergs_to_other_pes(bergs)
       write(stderrunit,*) 'pe=',mpp_pe(),' received a bad number',nbergs_rcvd_from_n,' from',grd%pe_N,' (N) !!!!!!!!!!!!!!!!!!!!!!'
     endif
     if (nbergs_rcvd_from_n.gt.0) then
-      call increase_ibuffer(bergs%ibuffer_n, nbergs_rcvd_from_n)
+      call increase_ibuffer(bergs%ibuffer_n, nbergs_rcvd_from_n,buffer_width)
       if(folded_north_on_pe) then
          call mpp_recv(bergs%ibuffer_n%data, nbergs_rcvd_from_n*buffer_width, grd%pe_N, tag=COMM_TAG_10)
       else
@@ -1628,8 +1672,8 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
     if (present(max_bonds_in)) max_bonds=max_bonds_in
 
 
-    if (.not.associated(buff)) call increase_buffer(buff,delta_buf)
-    if (n>buff%size) call increase_buffer(buff,delta_buf)
+    if (.not.associated(buff)) call increase_ibuffer(buff,n,buffer_width)
+    if (n>buff%size) call increase_ibuffer(buff,n,buffer_width)
 
     buff%data(1,n)=berg%lon
     buff%data(2,n)=berg%lat
@@ -1720,33 +1764,6 @@ subroutine clear_berg_from_partners_bonds(berg)
   end subroutine clear_berg_from_partners_bonds
 
 
-
-  subroutine increase_buffer(old,delta)
-  ! Arguments
-  type(buffer), pointer :: old
-  integer, intent(in) :: delta
-  ! Local variables
-  type(buffer), pointer :: new
-  integer :: new_size
-
-    if (.not.associated(old)) then
-      new_size=delta
-    else
-      new_size=old%size+delta
-    endif
-    allocate(new)
-    allocate(new%data(buffer_width,new_size))
-    new%size=new_size
-    if (associated(old)) then
-      new%data(:,1:old%size)=old%data(:,1:old%size)
-      deallocate(old%data)
-      deallocate(old)
-    endif
-    old=>new
-   !write(stderr(),*) 'diamonds, increase_buffer',mpp_pe(),' increased to',new_size
-
-  end subroutine increase_buffer
-
   subroutine unpack_berg_from_buffer2(bergs, buff, n,grd, force_append, max_bonds_in)
   ! Arguments
   type(icebergs), pointer :: bergs
@@ -1867,29 +1884,33 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n,grd, force_append, max_bonds_
 
   end subroutine unpack_berg_from_buffer2
 
-  subroutine increase_ibuffer(old,delta)
+  subroutine increase_ibuffer(old,num_bergs,width)
   ! Arguments
   type(buffer), pointer :: old
-  integer, intent(in) :: delta
+  integer, intent(in) :: num_bergs,width
   ! Local variables
   type(buffer), pointer :: new
   integer :: new_size, old_size
+  !This routine checks if the buffer size is smaller than nbergs
+  !If it is, the buffer size is increased by delta_buf
+  !The buffer increases by more than 1 so that the buffer does not have to increase every time
 
     if (.not.associated(old)) then
-      new_size=delta+delta_buf
+      new_size=num_bergs+delta_buf
       old_size=0
     else
       old_size=old%size
-      if (delta<old%size) then
-        new_size=old%size+delta
+      if (num_bergs<old%size) then
+        new_size=old%size
       else
-        new_size=delta+delta_buf
+        new_size=num_bergs+delta_buf
       endif
     endif
 
     if (old_size.ne.new_size) then
       allocate(new)
-      allocate(new%data(buffer_width,new_size))
+      !allocate(new%data(buffer_width,new_size))
+      allocate(new%data(width,new_size))
       new%size=new_size
       if (associated(old)) then
         new%data(:,1:old%size)=old%data(:,1:old%size)
@@ -1902,67 +1923,6 @@ subroutine increase_ibuffer(old,delta)
 
   end subroutine increase_ibuffer
 
-  subroutine increase_ibuffer_traj(old,delta)
-  ! Arguments
-  type(buffer), pointer :: old
-  integer, intent(in) :: delta
-  ! Local variables
-  type(buffer), pointer :: new
-  integer :: new_size, old_size
-
-    if (.not.associated(old)) then
-      new_size=delta+delta_buf
-      old_size=0
-    else
-      old_size=old%size
-      if (delta<old%size) then
-        new_size=old%size+delta
-      else
-        new_size=delta+delta_buf
-      endif
-    endif
-
-    if (old_size.ne.new_size) then
-      allocate(new)
-      allocate(new%data(buffer_width_traj,new_size))
-      new%size=new_size
-      if (associated(old)) then
-        new%data(:,1:old%size)=old%data(:,1:old%size)
-        deallocate(old%data)
-        deallocate(old)
-      endif
-      old=>new
-     !write(stderr(),*) 'diamonds, increase_ibuffer',mpp_pe(),' increased to',new_size
-    endif
-
-  end subroutine increase_ibuffer_traj
-
-  subroutine increase_buffer_traj(old,delta)
-  ! Arguments
-  type(buffer), pointer :: old
-  integer, intent(in) :: delta
-  ! Local variables
-  type(buffer), pointer :: new
-  integer :: new_size
-
-    if (.not.associated(old)) then
-      new_size=delta
-    else
-      new_size=old%size+delta
-    endif
-    allocate(new)
-    allocate(new%data(buffer_width_traj,new_size))
-    new%size=new_size
-    if (associated(old)) then
-      new%data(:,1:old%size)=old%data(:,1:old%size)
-      deallocate(old%data)
-      deallocate(old)
-    endif
-    old=>new
-   !write(stderr(),*) 'diamonds, increase_buffer',mpp_pe(),' increased to',new_size
-
-  end subroutine increase_buffer_traj
-
   subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj)
   ! Arguments
   type(xyt), pointer :: traj
@@ -1971,8 +1931,8 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj)
   logical, intent(in) :: save_short_traj
   ! Local variables
 
-    if (.not.associated(buff)) call increase_buffer_traj(buff,delta_buf)
-    if (n>buff%size) call increase_buffer_traj(buff,delta_buf)
+    if (.not.associated(buff)) call increase_ibuffer(buff,n,buffer_width_traj)
+    if (n>buff%size) call increase_ibuffer(buff,n,buffer_width_traj)
 
     buff%data(1,n)=traj%lon
     buff%data(2,n)=traj%lat
@@ -2855,36 +2815,39 @@ subroutine record_posn(bergs)
       posn%lat=this%lat
       posn%year=bergs%current_year
       posn%day=bergs%current_yearday
-      posn%uvel=this%uvel
-      posn%vvel=this%vvel
-      posn%mass=this%mass
-      posn%mass_of_bits=this%mass_of_bits
-      posn%heat_density=this%heat_density
-      posn%thickness=this%thickness
-      posn%width=this%width
-      posn%length=this%length
-      posn%uo=this%uo
-      posn%vo=this%vo
-      posn%ui=this%ui
-      posn%vi=this%vi
-      posn%ua=this%ua
-      posn%va=this%va
-      posn%ssh_x=this%ssh_x
-      posn%ssh_y=this%ssh_y
-      posn%sst=this%sst
-      posn%sss=this%sss
-      posn%cn=this%cn
-      posn%hi=this%hi
-      posn%axn=this%axn
-      posn%ayn=this%ayn
-      posn%bxn=this%bxn
-      posn%byn=this%byn
-      posn%uvel_old=this%uvel_old
-      posn%vvel_old=this%vvel_old
-      posn%lon_old=this%lon_old
-      posn%lat_old=this%lat_old
-      posn%halo_berg=this%halo_berg
-      posn%static_berg=this%static_berg
+      posn%iceberg_num=posn%iceberg_num
+      if (.not. bergs%save_short_traj) then !Not totally sure that this is correct
+        posn%uvel=this%uvel
+        posn%vvel=this%vvel
+        posn%mass=this%mass
+        posn%mass_of_bits=this%mass_of_bits
+        posn%heat_density=this%heat_density
+        posn%thickness=this%thickness
+        posn%width=this%width
+        posn%length=this%length
+        posn%uo=this%uo
+        posn%vo=this%vo
+        posn%ui=this%ui
+        posn%vi=this%vi
+        posn%ua=this%ua
+        posn%va=this%va
+        posn%ssh_x=this%ssh_x
+        posn%ssh_y=this%ssh_y
+        posn%sst=this%sst
+        posn%sss=this%sss
+        posn%cn=this%cn
+        posn%hi=this%hi
+        posn%axn=this%axn
+        posn%ayn=this%ayn
+        posn%bxn=this%bxn
+        posn%byn=this%byn
+        posn%uvel_old=this%uvel_old
+        posn%vvel_old=this%vvel_old
+        posn%lon_old=this%lon_old
+        posn%lat_old=this%lat_old
+        posn%halo_berg=this%halo_berg
+        posn%static_berg=this%static_berg
+      endif
   
       call push_posn(this%trajectory, posn)
   
@@ -2944,6 +2907,8 @@ subroutine move_trajectory(bergs, berg)
 type(xyt), pointer :: next, last
 type(xyt) :: vals
 
+  if (bergs%ignore_traj) return
+
   ! If the trajectory is empty, ignore it
   if (.not.associated(berg%trajectory)) return
 
@@ -2985,6 +2950,8 @@ subroutine move_all_trajectories(bergs, delete_bergs)
 type(iceberg), pointer :: this, next
 logical :: delete_bergs_after_moving_traj
 integer :: grdi, grdj
+  
+  if (bergs%ignore_traj) return
 
   delete_bergs_after_moving_traj = .false.
   if (present(delete_bergs)) delete_bergs_after_moving_traj = delete_bergs
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index ec8017d..8f7ff67 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -29,7 +29,7 @@ module ice_bergs_io
 use ice_bergs_framework, only: count_bonds, form_a_bond, find_individual_iceberg
 use ice_bergs_framework, only: push_posn
 use ice_bergs_framework, only: add_new_berg_to_list,destroy_iceberg
-use ice_bergs_framework, only: increase_ibuffer,increase_ibuffer_traj,grd_chksum2,grd_chksum3
+use ice_bergs_framework, only: increase_ibuffer,grd_chksum2,grd_chksum3
 use ice_bergs_framework, only: sum_mass,sum_heat,bilin
 !params !Niki: write a subroutine to get these
 use ice_bergs_framework, only: nclasses, buffer_width, buffer_width_traj
@@ -1444,7 +1444,7 @@ subroutine write_trajectory(trajectory, save_short_traj)
         from_pe=io_tile_pelist(np)
         call mpp_recv(ntrajs_rcvd_io, glen=1, from_pe=from_pe, tag=COMM_TAG_11)
         if (ntrajs_rcvd_io .gt. 0) then
-           call increase_ibuffer_traj(ibuffer_io, ntrajs_rcvd_io)
+           call increase_ibuffer(ibuffer_io, ntrajs_rcvd_io,buffer_width_traj)
            call mpp_recv(ibuffer_io%data, ntrajs_rcvd_io*buffer_width_traj,from_pe=from_pe, tag=COMM_TAG_12)
            do i=1, ntrajs_rcvd_io
               call unpack_traj_from_buffer2(traj4io, ibuffer_io, i, save_short_traj)

From cb4b2cc00b332a30e0f62a79980d21512f93f3e6 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 5 Oct 2016 13:28:12 -0400
Subject: [PATCH 171/361] 1) Iceberg module now reads in the bottom topography
 from a file called topog.nc (when the flag is set to true)

2) The bottom topography is used to calculate the thickness of the ocean below the icebergs. When the ocean thickness is less than melt_cutoff, then the icebergs basal melt M_b is set to zero.

3) There is an option to set the basal melt to zero based on the thickness of the iceberg, or based on the average thickness of icebergs in the grid cell.
---
 icebergs.F90           | 30 ++++++++++++++++++++++++++++--
 icebergs_framework.F90 | 25 ++++++++++++++++++++-----
 icebergs_io.F90        | 31 +++++++++++++++++++++++++++++++
 3 files changed, 79 insertions(+), 7 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 3c9b467..9abf81c 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -41,6 +41,7 @@ module ice_bergs
 use ice_bergs_io,        only: ice_bergs_io_init,write_restart,write_trajectory
 use ice_bergs_io,        only: read_restart_bergs,read_restart_bergs_orig,read_restart_calving
 use ice_bergs_io,        only: read_restart_bonds
+use ice_bergs_io,        only: read_ocean_depth
 
 implicit none ; private
 
@@ -119,6 +120,9 @@ subroutine icebergs_init(bergs, &
   call mpp_clock_end(bergs%clock_ior)
 
   if (really_debug) call print_bergs(stderrunit,bergs,'icebergs_init, initial status')
+  
+  !Reading ocean depth from a file
+  if (bergs%read_ocean_depth_from_file) call read_ocean_depth(bergs%grd)
 
   if (bergs%iceberg_bonds_on) then
     call update_halo_icebergs(bergs)
@@ -1172,9 +1176,15 @@ subroutine thermodynamics(bergs)
         Me=0.0
         if (.not. bergs%use_mixed_layer_salinity_for_thermo)  SSS=35.0  
         call find_basal_melt(bergs,dvo,this%lat,SSS,SST,bergs%Use_three_equation_model,T,Mb,this%iceberg_num)
-        Mb=max(Mb,0.)
+        Mb=max(Mb,0.) !No refreezing allowed for now
+        !Set melt to zero if ocean is too thin.
+        if ((bergs%melt_cutoff >=0.) .and. (bergs%apply_thickness_cutoff_to_bergs_melt)) then
+          if ((grd%ocean_depth(i,j)-this%thickness) < bergs%melt_cutoff) then
+            Mb=0.
+          endif
+        endif
       endif
-
+            
       if (bergs%set_melt_rates_to_zero) then
         Mv=0.0
         Mb=0.0
@@ -2656,6 +2666,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 real :: grdd_u_iceberg, grdd_v_iceberg, grdd_ustar_iceberg, grdd_spread_uvel, grdd_spread_vvel
 integer :: i, j, Iu, ju, iv, Jv, Iu_off, ju_off, iv_off, Jv_off
 real :: mask
+real :: ave_thickness
 real, dimension(:,:), allocatable :: uC_tmp, vC_tmp
 integer :: vel_stagger, str_stagger
 real, dimension(:,:), allocatable :: iCount
@@ -2759,6 +2770,9 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   tmpsum=sum( grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
   bergs%net_incoming_calving_heat=bergs%net_incoming_calving_heat+tmpsum*bergs%dt ! Units of J
 
+  if (grd%id_ocean_depth>0) &
+    lerr=send_data(grd%id_ocean_depth, grd%ocean_depth(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+
   if (vel_stagger == BGRID_NE) then
     ! Copy ocean and ice velocities. They are already on B-grid u-points.
     grd%uo(grd%isc-1:grd%iec+1,grd%jsc-1:grd%jec+1) = uo(:,:)
@@ -2966,6 +2980,18 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     grd%spread_area(:,:)=0.
     call icebergs_incr_mass(bergs, grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec),within_iceberg_model=.True.,field_name_in='area') 
   endif
+  if (bergs%apply_thickness_cutoff_to_gridded_melt) then
+    do i=grd%isd,grd%ied ; do j=grd%jsd,grd%jed
+      if ((bergs%melt_cutoff >=0.) .and. (grd%spread_area(i,j)>0.)) then
+        ave_thickness=grd%spread_mass(i,j)/(grd%spread_area(i,j)*bergs%rho_bergs) 
+        if ((grd%ocean_depth(i,j)-ave_thickness) < bergs%melt_cutoff) then
+          grd%floating_melt(i,j)=0.0
+          grd%calving_hflx(i,j)=0.0
+        endif
+      endif
+    enddo ;enddo
+  endif
+
 
   ! Gridded diagnostics
   if (grd%id_uo>0) &
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 045bf52..071dfaa 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -154,6 +154,7 @@ module ice_bergs_framework
   integer :: id_count=-1, id_chksum=-1, id_u_iceberg=-1, id_v_iceberg=-1, id_sss=-1, id_ustar_iceberg
   integer :: id_spread_uvel=-1, id_spread_vvel=-1
   integer :: id_melt_m_per_year=-1
+  integer :: id_ocean_depth=-1
 
   real :: clipping_depth=0. ! The effective depth at which to clip the weight felt by the ocean [m].
 
@@ -231,6 +232,7 @@ module ice_bergs_framework
   real :: cdrag_icebergs =  1.5e-3 !Momentum Drag coef, taken from HJ99  (Holland and Jenkins 1999)
   real :: initial_orientation=0. ! Iceberg orientaion relative to this angle (in degrees). Used for hexagonal mass spreading.
   real :: Gamma_T_3EQ=0.022 ! Nondimensional heat-transfer coefficient
+  real :: melt_cutoff=-1.0 !Minimum ocean thickness for melting to occur (is not applied for values < 0)
   logical :: const_gamma=.True. !If true uses a constant heat tranfer coefficient, from which the salt transfer is calculated
   real, dimension(:), pointer :: initial_mass, distribution, mass_scaling
   real, dimension(:), pointer :: initial_thickness, initial_width, initial_length
@@ -240,6 +242,8 @@ module ice_bergs_framework
   logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
   logical :: time_average_weight=.false. ! Time average the weight on the ocean
   logical :: Runge_not_Verlet=.True.  !True=Runge Kuttai, False=Verlet.  - Added by Alon 
+  logical :: apply_thickness_cutoff_to_gridded_melt=.False.  !Prevents melt for ocean thickness below melt_cuttoff (applied to gridded melt fields)
+  logical :: apply_thickness_cutoff_to_bergs_melt=.False.  !Prevents melt for ocean thickness below melt_cuttoff (applied to bergs)
   logical :: use_updated_rolling_scheme=.false. ! True to use the aspect ratio based rolling scheme rather than incorrect version of WM scheme   (set tip_parameter=1000. for correct WM scheme)
   logical :: read_old_restarts=.true. ! If true, read restarts prior to grid_of_lists and iceberg_num innovation
   logical :: pass_fields_to_ocean_model=.False. !Iceberg area, mass and ustar fields are prepared to pass to ocean model
@@ -267,6 +271,7 @@ module ice_bergs_framework
   logical :: interactive_icebergs_on=.false.  !Turn on/off interactions between icebergs  - Added by Alon 
   logical :: critical_interaction_damping_on=.true.  !Sets the damping on relative iceberg velocity to critical value - Added by Alon 
   logical :: use_old_spreading=.true. ! If true, spreads iceberg mass as if the berg is one grid cell wide
+  logical :: read_ocean_depth_from_file=.false. ! If true, ocean depth is read from a file.
   integer :: debug_iceberg_with_id = -1 ! If positive, monitors a berg with this id
 
   real :: speed_limit=0. ! CFL speed limit for a berg [m/s]
@@ -380,6 +385,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: ustar_icebergs_bg=0.001 ! Background u_star under icebergs. This should be linked to a value felt by the ocean boundary layer
 real :: cdrag_icebergs =  1.5e-3 !Momentum Drag coef, taken from HJ99  (Holland and Jenkins 1999)
 real :: Gamma_T_3EQ=0.022 ! Nondimensional heat-transfer coefficient
+real :: melt_cutoff=-1.0 !Minimum ocean thickness for melting to occur (is not applied for values < 0)
 logical :: const_gamma=.True. !If true uses a constant heat tranfer coefficient, from which the salt transfer is calculated
 logical :: use_operator_splitting=.true. ! Use first order operator splitting for thermodynamics
 logical :: add_weight_to_ocean=.true. ! Add weight of icebergs + bits to ocean
@@ -390,6 +396,8 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: tip_parameter=0. ! parameter to override iceberg rollilng critica ratio (use zero to get parameter directly from ice and seawater densities
 real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
 logical :: Runge_not_Verlet=.True.  !True=Runge Kutta, False=Verlet.  - Added by Alon 
+logical :: apply_thickness_cutoff_to_gridded_melt=.False.  !Prevents melt for ocean thickness below melt_cuttoff (applied to gridded melt fields)
+logical :: apply_thickness_cutoff_to_bergs_melt=.False.  !Prevents melt for ocean thickness below melt_cuttoff (applied to bergs)
 logical :: use_updated_rolling_scheme=.false. ! Use the corrected Rolling Scheme rather than the erronios one
 logical :: pass_fields_to_ocean_model=.False. !Iceberg area, mass and ustar fields are prepared to pass to ocean model
 logical :: use_mixed_layer_salinity_for_thermo=.False.  !If true, then model uses ocean salinity for 3 and 2 equation melt model.
@@ -421,6 +429,7 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: input_freq_distribution=.false. ! Flag to show if input distribution is freq or mass dist (=1 if input is a freq dist, =0 to use an input mass dist)
 logical :: read_old_restarts=.true. ! If true, read restarts prior to grid_of_lists and iceberg_num innovations
 logical :: use_old_spreading=.true. ! If true, spreads iceberg mass as if the berg is one grid cell wide
+logical :: read_ocean_depth_from_file=.false. ! If true, ocean depth is read from a file.
 real, dimension(nclasses) :: initial_mass=(/8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11/) ! Mass thresholds between iceberg classes (kg)
 real, dimension(nclasses) :: distribution=(/0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02/) ! Fraction of calving to apply to this class (non-dim) , 
 real, dimension(nclasses) :: mass_scaling=(/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) ! Ratio between effective and real iceberg mass (non-dim)
@@ -437,7 +446,8 @@ subroutine ice_bergs_framework_init(bergs, &
          allow_bergs_to_roll,set_melt_rates_to_zero,lat_ref,initial_orientation,rotate_icebergs_for_mass_spreading,grid_is_latlon,Lx,use_f_plane,use_old_spreading, &
          grid_is_regular,override_iceberg_velocities,u_override,v_override,add_iceberg_thickness_to_SSH,Iceberg_melt_without_decay,melt_icebergs_as_ice_shelf, &
          Use_three_equation_model,find_melt_using_spread_mass,use_mixed_layer_salinity_for_thermo,utide_icebergs,ustar_icebergs_bg,cdrag_icebergs, pass_fields_to_ocean_model, &
-         const_gamma, Gamma_T_3EQ, ignore_traj, debug_iceberg_with_id,use_updated_rolling_scheme, tip_parameter, read_old_restarts, tau_calving
+         const_gamma, Gamma_T_3EQ, ignore_traj, debug_iceberg_with_id,use_updated_rolling_scheme, tip_parameter, read_old_restarts, tau_calving, read_ocean_depth_from_file, melt_cutoff,&
+         apply_thickness_cutoff_to_gridded_melt, apply_thickness_cutoff_to_bergs_melt
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -614,7 +624,7 @@ subroutine ice_bergs_framework_init(bergs, &
     if(fractional_area) grd%area(is:ie,js:je)=ice_area(:,:) *(4.*pi*radius*radius)
   endif
   if(present(ocean_depth)) grd%ocean_depth(is:ie,js:je)=ocean_depth(:,:)
-
+  
   ! Copy data declared on ice model data domain
   is=grd%isc-1; ie=grd%iec+1; js=grd%jsc-1; je=grd%jec+1
   grd%dx(is:ie,js:je)=ice_dx(:,:)
@@ -815,6 +825,10 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%tip_parameter=tip_parameter
   bergs%use_updated_rolling_scheme=use_updated_rolling_scheme  !Alon
   bergs%Runge_not_Verlet=Runge_not_Verlet   
+  bergs%apply_thickness_cutoff_to_bergs_melt=apply_thickness_cutoff_to_bergs_melt
+  bergs%apply_thickness_cutoff_to_gridded_melt=apply_thickness_cutoff_to_gridded_melt
+  bergs%melt_cutoff=melt_cutoff 
+  bergs%read_ocean_depth_from_file=read_ocean_depth_from_file
   bergs%const_gamma=const_gamma 
   bergs%Gamma_T_3EQ=Gamma_T_3EQ
   bergs%pass_fields_to_ocean_model=pass_fields_to_ocean_model 
@@ -952,6 +966,8 @@ subroutine ice_bergs_framework_init(bergs, &
      'X-stress on ice from atmosphere', 'N m^-2')
   grd%id_fay=register_diag_field('icebergs', 'tauy', axes, Time, &
      'Y-stress on ice from atmosphere', 'N m^-2')
+  grd%id_ocean_depth=register_diag_field('icebergs', 'Depth', axes, Time, &
+     'Ocean Depth', 'm')
 
   ! Static fields
   id_class=register_static_field('icebergs', 'lon', axes, &
@@ -966,8 +982,8 @@ subroutine ice_bergs_framework_init(bergs, &
   id_class=register_static_field('icebergs', 'mask', axes, &
                'wet point mask', 'none')
   if (id_class>0) lerr=send_data(id_class, grd%msk(grd%isc:grd%iec,grd%jsc:grd%jec))
-  id_class=register_static_field('icebergs', 'ocean_depth', axes, &
-               'ocean depth', 'm')
+  id_class=register_static_field('icebergs', 'ocean_depth_static', axes, &
+               'ocean depth static', 'm')
   if (id_class>0) lerr=send_data(id_class, grd%ocean_depth(grd%isc:grd%iec,grd%jsc:grd%jec))
 
   if (debug) then
@@ -991,7 +1007,6 @@ subroutine ice_bergs_framework_init(bergs, &
   call mpp_clock_end(bergs%clock)
 
 end subroutine ice_bergs_framework_init
-
 ! ##############################################################################
 
 subroutine offset_berg_dates(bergs,Time)
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index d53cd9f..0971c06 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -44,6 +44,7 @@ module ice_bergs_io
 public ice_bergs_io_init
 public read_restart_bergs,read_restart_bergs_orig,write_restart,write_trajectory
 public read_restart_calving, read_restart_bonds
+public read_ocean_depth
 
 !Local Vars
 integer, parameter :: file_format_major_version=0
@@ -1418,6 +1419,36 @@ end subroutine read_restart_calving
 
 ! ##############################################################################
 
+subroutine read_ocean_depth(grd)
+! Arguments
+! Local variables
+character(len=37) :: filename 
+type(icebergs_gridded), pointer :: grd
+
+  ! Read stored ice
+  filename=trim(restart_input_dir)//'topog.nc'
+  if (file_exist(filename)) then
+    if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') &
+     'diamonds, read_ocean_depth: reading ',filename
+    if (field_exist(filename, 'depth')) then
+      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+       'diamonds, read_restart_calving: reading stored_heat from restart file.'
+      call read_data(filename, 'depth', grd%ocean_depth, grd%domain)
+    else
+      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+     'diamonds, read_restart_calving: stored_heat WAS NOT FOUND in the file. Setting to 0.'
+      !grd%ocean_depth(:,:)=0.
+    endif
+  else
+    if (mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+     'diamonds, read_ocean_depth: Ocean depth file (topog.nc) not present)'
+  endif
+
+  !call grd_chksum2(bergs%grd, bergs%grd%ocean_depth, 'read_ocean_depth, ocean_depth')
+end subroutine read_ocean_depth
+
+! ##############################################################################
+
 subroutine write_trajectory(trajectory, save_short_traj)
 ! Arguments
 type(xyt), pointer :: trajectory

From 20cdf780b2b41e55807a52043fd0afe7cd96d277 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 5 Oct 2016 16:34:53 -0400
Subject: [PATCH 172/361] Added optional arguments in the icebergs_run call
 which allow the mass_berg, area_berg and ustar_berg to be passed to the sea
 ice model.

---
 icebergs.F90 | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/icebergs.F90 b/icebergs.F90
index d31f9ca..4d8f1d6 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1109,7 +1109,7 @@ end subroutine interp_flds
 ! ##############################################################################
 
 subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh, sst, calving_hflx, cn, hi, &
-                        stagger, stress_stagger,sss)
+                        stagger, stress_stagger,sss,mass_berg, ustar_berg, area_berg)
 ! Arguments
 type(icebergs), pointer :: bergs
 type(time_type), intent(in) :: time
@@ -1117,6 +1117,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 real, dimension(:,:), intent(in) :: uo, vo, ui, vi, tauxa, tauya, ssh, sst, cn, hi
 integer,    optional, intent(in) :: stagger, stress_stagger
 real, dimension(:,:), optional, intent(in) ::  sss
+real, dimension(:,:), optional, intent(inout) ::  mass_berg, ustar_berg, area_berg
 ! Local variables
 integer :: iyr, imon, iday, ihr, imin, isec, k
 type(icebergs_gridded), pointer :: grd
@@ -1153,6 +1154,10 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   if (bergs%add_weight_to_ocean) grd%mass_on_ocean(:,:,:)=0.
   grd%virtual_area(:,:)=0.
 
+  mass_berg(:,:)=3.0
+  ustar_berg(:,:)=2.0
+  area_berg(:,:)=1.0
+
   ! Manage time
   call get_date(time, iyr, imon, iday, ihr, imin, isec)
   bergs%current_year=iyr

From 86782d15ece6c01fd2c8c78db0241c4671ce30d6 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 5 Oct 2016 17:22:49 -0400
Subject: [PATCH 173/361] Optional arguments have been added to icebergs_run so
 that it can pass the iceberg mass, area and ustar to the sea ice model. These
 changes have been made in such a way that the sea ice model does not need to
 call the function icebergs_incr_mass.

The fields area_berg and area_berg0, ustar_berg and ustar_berg0 are approximately the same. One of these will be removed later
---
 icebergs.F90 | 36 ++++++++++++++++++++++++------------
 1 file changed, 24 insertions(+), 12 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 9abf81c..5176c42 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -2650,7 +2650,7 @@ end subroutine interp_flds
 ! ##############################################################################
 
 subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh, sst, calving_hflx, cn, hi, &
-                        stagger, stress_stagger,sss)
+                        stagger, stress_stagger,sss,mass_berg, ustar_berg, area_berg)
 ! Arguments
 type(icebergs), pointer :: bergs
 type(time_type), intent(in) :: time
@@ -2658,6 +2658,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 real, dimension(:,:), intent(in) :: uo, vo, ui, vi, tauxa, tauya, ssh, sst, cn, hi
 integer,    optional, intent(in) :: stagger, stress_stagger
 real, dimension(:,:), optional, intent(in) :: sss
+real, dimension(:,:), optional, intent(inout) ::  mass_berg, ustar_berg, area_berg
+
 ! Local variables
 integer :: iyr, imon, iday, ihr, imin, isec, k
 type(icebergs_gridded), pointer :: grd
@@ -2670,7 +2672,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 real, dimension(:,:), allocatable :: uC_tmp, vC_tmp
 integer :: vel_stagger, str_stagger
 real, dimension(:,:), allocatable :: iCount
-real, dimension(bergs%grd%isd:bergs%grd%ied,bergs%grd%jsd:bergs%grd%jed)  :: ustar_berg, area_berg, spread_mass_old
+real, dimension(bergs%grd%isd:bergs%grd%ied,bergs%grd%jsd:bergs%grd%jed)  :: ustar_berg0, area_berg0, spread_mass_old
 integer :: nbonds
 !logical :: within_iceberg_model
 
@@ -2705,8 +2707,13 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   grd%ustar_iceberg(:,:)=0.
   grd%mass(:,:)=0.
  
-  ustar_berg(:,:)=0.
-  area_berg(:,:)=0.
+  ustar_berg0(:,:)=0.
+  area_berg0(:,:)=0.
+
+  mass_berg(:,:)=3.0
+  ustar_berg(:,:)=2.0
+  area_berg(:,:)=1.0
+
 
   if (bergs%add_weight_to_ocean) grd%mass_on_ocean(:,:,:)=0.
   if (bergs%add_weight_to_ocean) grd%area_on_ocean(:,:,:)=0.
@@ -2972,10 +2979,12 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
         grd%floating_melt(i,j)=0.0
       endif
     enddo ;enddo
-  elseif  ((grd%id_spread_mass>0) .or. (bergs%pass_fields_to_ocean_model)) then   !Update diagnostic of iceberg mass spread on ocean
+  !elseif  ((grd%id_spread_mass>0) .or. (bergs%pass_fields_to_ocean_model)) then   !Update diagnostic of iceberg mass spread on ocean
+  else   !Update iceberg mass spread on ocean
     grd%spread_mass(:,:)=0.
     call icebergs_incr_mass(bergs, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec),within_iceberg_model=.True.) 
   endif
+
   if ( (grd%id_spread_area>0)  .or. (bergs%pass_fields_to_ocean_model)) then  !Update diagnostic of iceberg area spread on ocean
     grd%spread_area(:,:)=0.
     call icebergs_incr_mass(bergs, grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec),within_iceberg_model=.True.,field_name_in='area') 
@@ -2991,7 +3000,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
       endif
     enddo ;enddo
   endif
-
+   
 
   ! Gridded diagnostics
   if (grd%id_uo>0) &
@@ -3095,16 +3104,19 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     where (grd%area(grd%isc:grd%iec,grd%jsc:grd%jec)>0.)
       calving(:,:)=grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec)/grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) &
                   +grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec)
-      !ustar_berg(:,:)=grd%ustar_iceberg(grd%isc:grd%iec,grd%jsc:grd%jec)
-      !area_berg(:,:)=grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec)
-      ustar_berg(:,:)=grd%ustar_iceberg(:,:)
-      area_berg(:,:)=grd%spread_area(:,:)
+      !ustar_berg0(:,:)=grd%ustar_iceberg(grd%isc:grd%iec,grd%jsc:grd%jec)
+      !area_berg0(:,:)=grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec)
+      ustar_berg0(:,:)=grd%ustar_iceberg(:,:)
+      area_berg0(:,:)=grd%spread_area(:,:)
     elsewhere
       calving(:,:)=0.
-      ustar_berg(:,:)=0.
-      area_berg(:,:)=0.
+      ustar_berg0(:,:)=0.
+      area_berg0(:,:)=0.
     end where
     calving_hflx(:,:)=grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)
+    mass_berg(:,:)=grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec)
+    area_berg(:,:)=grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec)
+    ustar_berg(:,:)=grd%ustar_iceberg(grd%isc:grd%iec,grd%jsc:grd%jec)
   endif
   call mpp_clock_end(bergs%clock_int)
 

From d03aa8e1efc1242fc23a845c21ca4c530cbebd4d Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 5 Oct 2016 17:28:07 -0400
Subject: [PATCH 174/361] Initializing mass, area and ustar to zero

---
 icebergs.F90 | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 5176c42..2fc2855 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -2710,9 +2710,9 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   ustar_berg0(:,:)=0.
   area_berg0(:,:)=0.
 
-  mass_berg(:,:)=3.0
-  ustar_berg(:,:)=2.0
-  area_berg(:,:)=1.0
+  mass_berg(:,:)=0.0
+  ustar_berg(:,:)=0.0
+  area_berg(:,:)=0.0
 
 
   if (bergs%add_weight_to_ocean) grd%mass_on_ocean(:,:,:)=0.

From 8d248ae2d64f7628ffcfeb36d470f474d2ae1c75 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 5 Oct 2016 18:23:00 -0400
Subject: [PATCH 175/361] Edited incr_mass rountine so that it can be called
 from inside the iceberg model and out

---
 icebergs.F90 | 51 ++++++++++++++++++++++++++++++++++++++++++---------
 1 file changed, 42 insertions(+), 9 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 4d8f1d6..f24ab94 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1154,9 +1154,9 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   if (bergs%add_weight_to_ocean) grd%mass_on_ocean(:,:,:)=0.
   grd%virtual_area(:,:)=0.
 
-  mass_berg(:,:)=3.0
-  ustar_berg(:,:)=2.0
-  area_berg(:,:)=1.0
+  mass_berg(:,:)=0.0
+  ustar_berg(:,:)=1.0
+  area_berg(:,:)=2.0
 
   ! Manage time
   call get_date(time, iyr, imon, iday, ihr, imin, isec)
@@ -1405,6 +1405,10 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   if (really_debug) call print_bergs(stderrunit,bergs,'icebergs_run, status')
   call mpp_clock_end(bergs%clock_dia)
 
+  !Making sure that spread_mass has the correct mass
+  grd%spread_mass(:,:)=0.0
+  call icebergs_incr_mass(bergs, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec), within_iceberg_model=.True.)
+
   ! Return what ever calving we did not use and additional icebergs melt
   call mpp_clock_begin(bergs%clock_int)
   if (.not. bergs%passive_mode) then
@@ -1415,6 +1419,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
       calving(:,:)=0.
     end where
     calving_hflx(:,:)=grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)
+    mass_berg(:,:)=grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec)
   endif
   call mpp_clock_end(bergs%clock_int)
 
@@ -1685,23 +1690,37 @@ end subroutine icebergs_run
 
 ! ##############################################################################
 
-subroutine icebergs_incr_mass(bergs, mass, Time)
+subroutine icebergs_incr_mass(bergs, mass,  within_iceberg_model,Time)
 ! Arguments
 type(icebergs), pointer :: bergs
 real, dimension(bergs%grd%isc:bergs%grd%iec,bergs%grd%jsc:bergs%grd%jec), intent(inout) :: mass
+logical, intent(in), optional :: within_iceberg_model
 type(time_type), intent(in), optional :: Time
 ! Local variables
 integer :: i, j
 type(icebergs_gridded), pointer :: grd
 real :: dmda
 logical :: lerr
+logical :: within_model
 
   if (.not. associated(bergs)) return
 
   if (.not. bergs%add_weight_to_ocean) return
 
-  call mpp_clock_begin(bergs%clock)
-  call mpp_clock_begin(bergs%clock_int)
+  within_model=.False.
+  if (present(within_iceberg_model)) then 
+    within_model=within_iceberg_model
+  endif
+
+  if (.not.(within_model)) then
+    if (.not. associated(bergs)) return
+      if (.not. bergs%add_weight_to_ocean) return
+        call mpp_clock_begin(bergs%clock)
+        call mpp_clock_begin(bergs%clock_int)
+  endif
+
+  !call mpp_clock_begin(bergs%clock)
+  !call mpp_clock_begin(bergs%clock_int)
 
   ! For convenience
   grd=>bergs%grd
@@ -1738,7 +1757,16 @@ subroutine icebergs_incr_mass(bergs, mass, Time)
          +   ( (grd%mass_on_ocean(i-1,j  ,6)+grd%mass_on_ocean(i+1,j  ,4))   &
          +     (grd%mass_on_ocean(i  ,j-1,8)+grd%mass_on_ocean(i  ,j+1,2)) ) )
     if (grd%area(i,j)>0) dmda=dmda/grd%area(i,j)*grd%msk(i,j)
-    if (.not. bergs%passive_mode) mass(i,j)=mass(i,j)+dmda
+
+    if (.not.(within_model)) then
+      if (.not. bergs%passive_mode) then
+              mass(i,j)=mass(i,j)+dmda
+      else 
+              mass(i,j)=dmda
+      endif
+    endif
+
+    !if (.not. bergs%passive_mode) mass(i,j)=mass(i,j)+dmda
     if (grd%id_mass_on_ocn>0) grd%tmp(i,j)=dmda
   enddo; enddo
   if (present(Time).and. (grd%id_mass_on_ocn>0)) &
@@ -1750,8 +1778,13 @@ subroutine icebergs_incr_mass(bergs, mass, Time)
     call grd_chksum2(grd, grd%tmp, 'mass out (incr)')
   endif
 
-  call mpp_clock_end(bergs%clock_int)
-  call mpp_clock_end(bergs%clock)
+  !call mpp_clock_end(bergs%clock_int)
+  !call mpp_clock_end(bergs%clock)
+ 
+  if (.not.(within_model)) then
+    call mpp_clock_end(bergs%clock_int)
+    call mpp_clock_end(bergs%clock)
+  endif
 
 end subroutine icebergs_incr_mass
 

From cc9a7a8b3e42f2b1c17357f6fe933ee7b2c4f067 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 5 Oct 2016 18:49:52 -0400
Subject: [PATCH 176/361] mass_berg, area_berg and ustar_berg only edited when
 they are present

---
 icebergs.F90 | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index f24ab94..7afdc28 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1154,9 +1154,15 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   if (bergs%add_weight_to_ocean) grd%mass_on_ocean(:,:,:)=0.
   grd%virtual_area(:,:)=0.
 
-  mass_berg(:,:)=0.0
-  ustar_berg(:,:)=1.0
-  area_berg(:,:)=2.0
+  if (present(mass_berg)) then
+          mass_berg(:,:)=0.0
+  endif
+  if (present(ustar_berg)) then
+          ustar_berg(:,:)=1.0
+  endif
+  if (present(area_berg)) then
+          area_berg(:,:)=2.0
+  endif
 
   ! Manage time
   call get_date(time, iyr, imon, iday, ihr, imin, isec)
@@ -1419,7 +1425,9 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
       calving(:,:)=0.
     end where
     calving_hflx(:,:)=grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)
-    mass_berg(:,:)=grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec)
+    if (present(mass_berg)) then
+            mass_berg(:,:)=grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec)
+    endif
   endif
   call mpp_clock_end(bergs%clock_int)
 

From 68a764463b5d8969576460ef818a71c7959785dd Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 5 Oct 2016 20:18:02 -0400
Subject: [PATCH 177/361] Setting a value for ustar_berg, area_berg and
 mass_berg. Area_berg must be less than or equal to 1.

Note that when these fields are passed through the coupler in the global model, they have a different value on the ocean side, so something is not being done correctly.
---
 icebergs.F90 | 21 +++++++++++----------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 7afdc28..c1b16e3 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1154,16 +1154,6 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   if (bergs%add_weight_to_ocean) grd%mass_on_ocean(:,:,:)=0.
   grd%virtual_area(:,:)=0.
 
-  if (present(mass_berg)) then
-          mass_berg(:,:)=0.0
-  endif
-  if (present(ustar_berg)) then
-          ustar_berg(:,:)=1.0
-  endif
-  if (present(area_berg)) then
-          area_berg(:,:)=2.0
-  endif
-
   ! Manage time
   call get_date(time, iyr, imon, iday, ihr, imin, isec)
   bergs%current_year=iyr
@@ -1429,6 +1419,17 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
             mass_berg(:,:)=grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec)
     endif
   endif
+  
+  if (present(area_berg)) then
+    area_berg(:,:)=0.5
+  endif
+  !if (present(mass_berg)) then
+  !  mass_berg(:,:)=0.0
+  !endif
+  if (present(ustar_berg)) then
+    ustar_berg(:,:)=0.02
+  endif
+  
   call mpp_clock_end(bergs%clock_int)
 
   ! Diagnose budgets

From c3a585f97ed8d653cb2b10124c8e1524c42044e7 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Thu, 6 Oct 2016 13:33:25 -0400
Subject: [PATCH 178/361] 1) Added if present() qualifier before the optional
 arguments ustar_berg, mass_berg and area_berg, so that if they are not
 defined, the road does not try to access them. Note that if allocated
 qualifier is not included since these are not allocatable fields.

2) The variables ustar_berg0 and area_berg0 have been removed since they are not needed.
---
 icebergs.F90 | 42 +++++++++++++++++++++++++++---------------
 1 file changed, 27 insertions(+), 15 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 2fc2855..f867a62 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -2672,7 +2672,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 real, dimension(:,:), allocatable :: uC_tmp, vC_tmp
 integer :: vel_stagger, str_stagger
 real, dimension(:,:), allocatable :: iCount
-real, dimension(bergs%grd%isd:bergs%grd%ied,bergs%grd%jsd:bergs%grd%jed)  :: ustar_berg0, area_berg0, spread_mass_old
+real, dimension(bergs%grd%isd:bergs%grd%ied,bergs%grd%jsd:bergs%grd%jed)  :: spread_mass_old
+!real, dimension(bergs%grd%isd:bergs%grd%ied,bergs%grd%jsd:bergs%grd%jed)  :: ustar_berg0, area_berg0
 integer :: nbonds
 !logical :: within_iceberg_model
 
@@ -2707,12 +2708,19 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   grd%ustar_iceberg(:,:)=0.
   grd%mass(:,:)=0.
  
-  ustar_berg0(:,:)=0.
-  area_berg0(:,:)=0.
+  !I belive that ustar_berg0 and area_berg0 are no longer needed
+  !ustar_berg0(:,:)=0.
+  !area_berg0(:,:)=0.
 
-  mass_berg(:,:)=0.0
-  ustar_berg(:,:)=0.0
-  area_berg(:,:)=0.0
+  if (present(mass_berg)) then !; if (allocated(mass_berg)) then
+    mass_berg(:,:)=0.0
+  endif !; endif
+  if (present(ustar_berg)) then !; if (allocated(ustar_berg)) then
+    ustar_berg(:,:)=0.0
+  endif !; endif
+  if (present(area_berg)) then !; if (allocated(area_berg)) then
+    area_berg(:,:)=0.0
+  endif !; endif
 
 
   if (bergs%add_weight_to_ocean) grd%mass_on_ocean(:,:,:)=0.
@@ -3104,19 +3112,23 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     where (grd%area(grd%isc:grd%iec,grd%jsc:grd%jec)>0.)
       calving(:,:)=grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec)/grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) &
                   +grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec)
-      !ustar_berg0(:,:)=grd%ustar_iceberg(grd%isc:grd%iec,grd%jsc:grd%jec)
-      !area_berg0(:,:)=grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec)
-      ustar_berg0(:,:)=grd%ustar_iceberg(:,:)
-      area_berg0(:,:)=grd%spread_area(:,:)
+      !ustar_berg0(:,:)=grd%ustar_iceberg(:,:)
+      !area_berg0(:,:)=grd%spread_area(:,:)
     elsewhere
       calving(:,:)=0.
-      ustar_berg0(:,:)=0.
-      area_berg0(:,:)=0.
+      !ustar_berg0(:,:)=0.
+      !area_berg0(:,:)=0.
     end where
     calving_hflx(:,:)=grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)
-    mass_berg(:,:)=grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec)
-    area_berg(:,:)=grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec)
-    ustar_berg(:,:)=grd%ustar_iceberg(grd%isc:grd%iec,grd%jsc:grd%jec)
+    if (present(mass_berg)) then !; if (allocated(mass_berg)) then
+      mass_berg(:,:)=grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec)
+    endif !; endif
+    if (present(ustar_berg)) then !; if (allocated(ustar_berg)) then
+      ustar_berg(:,:)=grd%ustar_iceberg(grd%isc:grd%iec,grd%jsc:grd%jec)
+    endif !; endif
+    if (present(area_berg)) then !; if (allocated(area_berg)) then
+      area_berg(:,:)=grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec)
+    endif !; endif
   endif
   call mpp_clock_end(bergs%clock_int)
 

From 7a2f25e21590e71e224f7626a021fb91687e2d8f Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Fri, 7 Oct 2016 13:04:09 -0400
Subject: [PATCH 179/361] Cleaned up logical for passive_mode

- Logical for clocks inside icebergs_incr_mass() was simplified and
  corrected for passive_mode.
- Tidied up some white space.
- No answer changes.
---
 icebergs.F90 | 42 ++++++++++++------------------------------
 1 file changed, 12 insertions(+), 30 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index c1b16e3..72b1f87 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1109,7 +1109,7 @@ end subroutine interp_flds
 ! ##############################################################################
 
 subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh, sst, calving_hflx, cn, hi, &
-                        stagger, stress_stagger,sss,mass_berg, ustar_berg, area_berg)
+                        stagger, stress_stagger, sss, mass_berg, ustar_berg, area_berg)
 ! Arguments
 type(icebergs), pointer :: bergs
 type(time_type), intent(in) :: time
@@ -1117,7 +1117,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 real, dimension(:,:), intent(in) :: uo, vo, ui, vi, tauxa, tauya, ssh, sst, cn, hi
 integer,    optional, intent(in) :: stagger, stress_stagger
 real, dimension(:,:), optional, intent(in) ::  sss
-real, dimension(:,:), optional, intent(inout) ::  mass_berg, ustar_berg, area_berg
+real, dimension(:,:), optional, pointer ::  mass_berg, ustar_berg, area_berg
 ! Local variables
 integer :: iyr, imon, iday, ihr, imin, isec, k
 type(icebergs_gridded), pointer :: grd
@@ -1416,20 +1416,12 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     end where
     calving_hflx(:,:)=grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)
     if (present(mass_berg)) then
-            mass_berg(:,:)=grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec)
+      if (associated(mass_berg) .and. .not.bergs%passive_mode) then
+        mass_berg(:,:)=grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec)
+      endif
     endif
   endif
   
-  if (present(area_berg)) then
-    area_berg(:,:)=0.5
-  endif
-  !if (present(mass_berg)) then
-  !  mass_berg(:,:)=0.0
-  !endif
-  if (present(ustar_berg)) then
-    ustar_berg(:,:)=0.02
-  endif
-  
   call mpp_clock_end(bergs%clock_int)
 
   ! Diagnose budgets
@@ -1699,7 +1691,7 @@ end subroutine icebergs_run
 
 ! ##############################################################################
 
-subroutine icebergs_incr_mass(bergs, mass,  within_iceberg_model,Time)
+subroutine icebergs_incr_mass(bergs, mass, within_iceberg_model, Time)
 ! Arguments
 type(icebergs), pointer :: bergs
 real, dimension(bergs%grd%isc:bergs%grd%iec,bergs%grd%jsc:bergs%grd%jec), intent(inout) :: mass
@@ -1722,15 +1714,10 @@ subroutine icebergs_incr_mass(bergs, mass,  within_iceberg_model,Time)
   endif
 
   if (.not.(within_model)) then
-    if (.not. associated(bergs)) return
-      if (.not. bergs%add_weight_to_ocean) return
-        call mpp_clock_begin(bergs%clock)
-        call mpp_clock_begin(bergs%clock_int)
+    call mpp_clock_begin(bergs%clock)
+    call mpp_clock_begin(bergs%clock_int)
   endif
 
-  !call mpp_clock_begin(bergs%clock)
-  !call mpp_clock_begin(bergs%clock_int)
-
   ! For convenience
   grd=>bergs%grd
 
@@ -1767,12 +1754,10 @@ subroutine icebergs_incr_mass(bergs, mass,  within_iceberg_model,Time)
          +     (grd%mass_on_ocean(i  ,j-1,8)+grd%mass_on_ocean(i  ,j+1,2)) ) )
     if (grd%area(i,j)>0) dmda=dmda/grd%area(i,j)*grd%msk(i,j)
 
-    if (.not.(within_model)) then
-      if (.not. bergs%passive_mode) then
-              mass(i,j)=mass(i,j)+dmda
-      else 
-              mass(i,j)=dmda
-      endif
+    if (within_model) then
+      mass(i,j)=mass(i,j)+dmda
+    else
+      if (.not. bergs%passive_mode) mass(i,j)=mass(i,j)+dmda
     endif
 
     !if (.not. bergs%passive_mode) mass(i,j)=mass(i,j)+dmda
@@ -1787,9 +1772,6 @@ subroutine icebergs_incr_mass(bergs, mass,  within_iceberg_model,Time)
     call grd_chksum2(grd, grd%tmp, 'mass out (incr)')
   endif
 
-  !call mpp_clock_end(bergs%clock_int)
-  !call mpp_clock_end(bergs%clock)
- 
   if (.not.(within_model)) then
     call mpp_clock_end(bergs%clock_int)
     call mpp_clock_end(bergs%clock)

From c87016df664b51b4d54ef7d2852a7e75dedfbed4 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Mon, 10 Oct 2016 11:38:48 -0400
Subject: [PATCH 180/361] Corrected the ustar calaculation inside the iceberg
 melt procedure

---
 icebergs.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/icebergs.F90 b/icebergs.F90
index f867a62..a757e8d 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1533,7 +1533,7 @@ subroutine find_basal_melt(bergs,dvo,lat,salt,temp,Use_three_equation_model,thic
   iDens = 1.0/Rho0
 
   !Preparing the mixed layer properties for use in both 2 and 3 equation version
-  ustar = bergs%cdrag_icebergs*(dvo  + bergs%utide_icebergs)
+  ustar = sqrt(bergs%cdrag_icebergs*(dvo**2  + bergs%utide_icebergs**2))
   ustar_h = max(bergs%ustar_icebergs_bg, ustar)
 
   ! Estimate the neutral ocean boundary layer thickness as the minimum of the

From d7bf5c30c7095494884bb57892be93293ea58f2d Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Tue, 11 Oct 2016 09:56:34 -0400
Subject: [PATCH 181/361] 1) print_berg routine has been edited so that more
 decimal places are displayed for the iceberg fields

2) The spread_mass_across_ocean_cells has been edited so that it is more likely to reproduce. In particular, fraction_used is set equal to exactly 1 when the icebergs spread their mass as rectangles. Previously, fraction_used was equal to the sum of a few terms which added to 1, but now it is set to exactly 1. Also, instead of dividing by fraction_used, we introduce I_fraction_used, which is the invers of fraction_used. This allows us to multiply by I_fraction used which distributing the fields.

3) A routine has been added which calculates the mass on the ocean. This routine is used to calculate the spread_mass_old, which is the spread_mass after the icebergs have been evolved, but before the thermodynamics have been applied. This allows us to correctly differnce these fields to find melt rates. (Previously find_melt_from_spread_mass option did not account for the iceberg movement (since the spread_mass_old was calculated before the iceberg_evolve.
---
 icebergs.F90           | 104 ++++++++++++++++++++++++++++++-----------
 icebergs_framework.F90 |   6 +--
 2 files changed, 80 insertions(+), 30 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index a757e8d..a3ff6c8 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1846,7 +1846,8 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
   real :: yDxL, yDxC, yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR
   real :: S, H, origin_x, origin_y, x0, y0
   real :: Area_Q1,Area_Q2 , Area_Q3,Area_Q4, Area_hex
-  real :: fraction_used
+  real :: fraction_used !fraction of iceberg mass included (part of the mass near the boundary is discarded sometimes)
+  real :: I_fraction_used !Inverse of fraction used
   real :: tol
   real, parameter :: rho_seawater=1035.
   integer :: stderrunit
@@ -1902,6 +1903,8 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
     yUxR=yU*xR*grd%msk(i+1,j+1)
     yCxC=1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )
     
+    fraction_used=1.  !rectangular bergs do share mass with boundaries (all mass is included in cells)
+
   else !Spread mass as if elements area hexagonal
 
     if (grd%area(i,j)>0) then
@@ -1976,53 +1979,51 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
         call error_mesg('diamonds, hexagonal spreading', 'All the mass is not being used!!!', FATAL)
       endif
 
-  endif
         
-  !Scale each cell by (1/fraction_used) in order to redisribute ice mass which landed up on the land, back into the ocean
-  !Note that for the square elements, the mass has already been reassigned, so fraction_used shoule be equal to 1 aready
-  fraction_used= ((yDxL*grd%msk(i-1,j-1)) + (yDxC*grd%msk(i  ,j-1))  +(yDxR*grd%msk(i+1,j-1)) +(yCxL*grd%msk(i-1,j  )) +  (yCxR*grd%msk(i+1,j  ))&
-                 +(yUxL*grd%msk(i-1,j+1)) +(yUxC*grd%msk(i  ,j+1))   +(yUxR*grd%msk(i+1,j+1)) + (yCxC**grd%msk(i,j)))
-
-  if ((hexagonal_icebergs) .and.  (static_berg .eq. 1)) then
-    !Change this to use_old_restart=false when this is merged in
-    fraction_used=1.  !Static icebergs do not share their mass with the boundary (this to initialize icebergs in regular arrangements against boundaries)
+    !Scale each cell by (1/fraction_used) in order to redisribute ice mass which landed up on the land, back into the ocean
+    !Note that for the square elements, the mass has already been reassigned, so fraction_used shoule be equal to 1 aready
+    fraction_used= ((yDxL*grd%msk(i-1,j-1)) + (yDxC*grd%msk(i  ,j-1))  +(yDxR*grd%msk(i+1,j-1)) +(yCxL*grd%msk(i-1,j  )) +  (yCxR*grd%msk(i+1,j  ))&
+                   +(yUxL*grd%msk(i-1,j+1)) +(yUxC*grd%msk(i  ,j+1))   +(yUxR*grd%msk(i+1,j+1)) + (yCxC**grd%msk(i,j)))
+    if  (static_berg .eq. 1)  fraction_used=1.  !Static icebergs do not share their mass with the boundary
+                                                ! (this allows us to easily  initialize hexagonal icebergs in regular arrangements against boundaries)
   endif
+  I_fraction_used=1./fraction_used !Invert this so that the arithmatec reprocudes
 
   !Spreading the iceberg mass onto the ocean
   call spread_variable_across_cells(grd, grd%mass_on_ocean, Mass, i ,j, &
-             yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR, fraction_used)
+             yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR, I_fraction_used)
   !Spreading the iceberg area onto the ocean
   call spread_variable_across_cells(grd, grd%area_on_ocean, Area*scaling , i ,j, &
-             yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR,fraction_used)
+             yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR,I_fraction_used)
   !Spreading the iceberg x momentum onto the ocean
   call spread_variable_across_cells(grd,grd%Uvel_on_ocean, uvel*Area*scaling , i ,j, &
-             yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR, fraction_used)
+             yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR, I_fraction_used)
   !Spreading the iceberg y momentum onto the ocean
   call spread_variable_across_cells(grd,grd%Vvel_on_ocean, vvel*Area*scaling , i ,j, &
-             yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR, fraction_used)
+             yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR, I_fraction_used)
   
 end subroutine spread_mass_across_ocean_cells
 
 subroutine spread_variable_across_cells(grd, variable_on_ocean, Var,i,j, &
-           yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR,fraction_used)
+           yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR,I_fraction_used)
   ! Arguments
   type(icebergs_gridded), pointer, intent(in) :: grd
   real, dimension(grd%isd:grd%ied, grd%jsd:grd%jed, 9), intent(inout) :: variable_on_ocean 
   real, intent(in) :: Var !Variable to be spread accross cell
   real, intent(in) :: yDxL, yDxC, yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR !Weights
-  real, intent(in) :: fraction_used !Amount of iceberg used
+  real, intent(in) :: I_fraction_used !Amount of iceberg used (inverse)
   integer, intent(in) :: i, j
 
   !Spreading the iceberg mass onto the ocean
-  variable_on_ocean(i,j,1)=variable_on_ocean(i,j,1)+(yDxL*Var/fraction_used)
-  variable_on_ocean(i,j,2)=variable_on_ocean(i,j,2)+(yDxC*Var/fraction_used)
-  variable_on_ocean(i,j,3)=variable_on_ocean(i,j,3)+(yDxR*Var/fraction_used)
-  variable_on_ocean(i,j,4)=variable_on_ocean(i,j,4)+(yCxL*Var/fraction_used)
-  variable_on_ocean(i,j,5)=variable_on_ocean(i,j,5)+(yCxC*Var/fraction_used)
-  variable_on_ocean(i,j,6)=variable_on_ocean(i,j,6)+(yCxR*Var/fraction_used)
-  variable_on_ocean(i,j,7)=variable_on_ocean(i,j,7)+(yUxL*Var/fraction_used)
-  variable_on_ocean(i,j,8)=variable_on_ocean(i,j,8)+(yUxC*Var/fraction_used)
-  variable_on_ocean(i,j,9)=variable_on_ocean(i,j,9)+(yUxR*Var/fraction_used)
+  variable_on_ocean(i,j,1)=variable_on_ocean(i,j,1)+(yDxL*Var*I_fraction_used)
+  variable_on_ocean(i,j,2)=variable_on_ocean(i,j,2)+(yDxC*Var*I_fraction_used)
+  variable_on_ocean(i,j,3)=variable_on_ocean(i,j,3)+(yDxR*Var*I_fraction_used)
+  variable_on_ocean(i,j,4)=variable_on_ocean(i,j,4)+(yCxL*Var*I_fraction_used)
+  variable_on_ocean(i,j,5)=variable_on_ocean(i,j,5)+(yCxC*Var*I_fraction_used)
+  variable_on_ocean(i,j,6)=variable_on_ocean(i,j,6)+(yCxR*Var*I_fraction_used)
+  variable_on_ocean(i,j,7)=variable_on_ocean(i,j,7)+(yUxL*Var*I_fraction_used)
+  variable_on_ocean(i,j,8)=variable_on_ocean(i,j,8)+(yUxC*Var*I_fraction_used)
+  variable_on_ocean(i,j,9)=variable_on_ocean(i,j,9)+(yUxR*Var*I_fraction_used)
 
 end subroutine spread_variable_across_cells
 
@@ -2647,6 +2648,51 @@ end subroutine rotate
 end subroutine interp_flds
 
 
+subroutine calculate_mass_on_ocean(bergs, spread_mass_old)
+! Arguments
+type(icebergs), pointer :: bergs
+type(iceberg), pointer :: berg
+type(icebergs_gridded), pointer :: grd
+real, dimension(:,:), optional, intent(out) :: spread_mass_old
+! Local variables
+integer :: grdj, grdi   
+real :: orientation
+
+  ! For convenience
+  grd=>bergs%grd
+
+  !Initialize fields
+  grd%mass_on_ocean(:,:,:)=0.
+  grd%area_on_ocean(:,:,:)=0.
+  grd%Uvel_on_ocean(:,:,:)=0.
+  grd%Vvel_on_ocean(:,:,:)=0.
+
+  do grdj = grd%jsc-1,grd%jec+1 ; do grdi = grd%isc-1,grd%iec+1  
+    berg=>bergs%list(grdi,grdj)%first
+    do while(associated(berg))
+    orientation=bergs%initial_orientation
+    if ((bergs%iceberg_bonds_on) .and. (bergs%rotate_icebergs_for_mass_spreading)) call find_orientation_using_iceberg_bonds(grd,berg,orientation)
+      call spread_mass_across_ocean_cells(grd, grdi, grdj, berg%xi, berg%yj, berg%mass,berg%mass_of_bits, berg%mass_scaling, &
+                berg%length*berg%width, bergs%use_old_spreading, bergs%hexagonal_icebergs,orientation,berg%static_berg,berg%uvel,berg%vvel)
+
+      berg=>berg%next
+    enddo
+  enddo ;enddo
+  call mpp_sync_self()
+
+  grd%spread_mass(:,:)=0.
+  call icebergs_incr_mass(bergs, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec),within_iceberg_model=.True.) 
+  spread_mass_old(:,:)=grd%spread_mass(:,:)
+
+  !Reset fields
+  grd%mass_on_ocean(:,:,:)=0.
+  grd%area_on_ocean(:,:,:)=0.
+  grd%Uvel_on_ocean(:,:,:)=0.
+  grd%Vvel_on_ocean(:,:,:)=0.
+
+end subroutine calculate_mass_on_ocean
+
+
 ! ##############################################################################
 
 subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh, sst, calving_hflx, cn, hi, &
@@ -2956,6 +3002,12 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   if (debug) call checksum_gridded(bergs%grd, 's/r run after exchange')
   call mpp_clock_end(bergs%clock_com)
 
+  
+  if (bergs%find_melt_using_spread_mass) then 
+    spread_mass_old(:,:)=0.
+    call calculate_mass_on_ocean(bergs, spread_mass_old)
+  endif
+
   ! Iceberg thermodynamics (melting) + rolling
   call mpp_clock_begin(bergs%clock_the)
   call thermodynamics(bergs)
@@ -2975,8 +3027,6 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   !Using spread_mass_to_ocean to calculate melt rates (if this option is chosen)
   !within_iceberg_model=.True.
   if (bergs%find_melt_using_spread_mass) then
-    !spread_mass_old=grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec)
-    spread_mass_old(:,:)=grd%spread_mass(:,:)
     grd%spread_mass(:,:)=0.
     call icebergs_incr_mass(bergs, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec),within_iceberg_model=.True.) 
     do i=grd%isd,grd%ied ; do j=grd%jsd,grd%jed
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 071dfaa..123eee0 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -2464,10 +2464,10 @@ subroutine print_berg(iochan, berg, label, il, jl)
     label, mpp_pe(), berg%start_lon, berg%start_lat, &
     berg%start_year, berg%iceberg_num, berg%start_day, berg%start_mass, berg%halo_berg
   if (present(il).and.present(jl)) then
-    write(iochan,'("diamonds, print_berg: ",a," pe=(",i3,a,2i5,3(a,2f10.4),a,2l2)') &
+    write(iochan,'("diamonds, print_berg: ",a," pe=(",i3,a,2i5,3(a,2f14.8),a,2l2)') &
       label, mpp_pe(), ') List i,j=',il,jl
   endif
-  write(iochan,'("diamonds, print_berg: ",a," pe=(",i3,a,2i5,3(a,2f10.4),a,2l2)') &
+  write(iochan,'("diamonds, print_berg: ",a," pe=(",i3,a,2i5,3(a,2f14.8),a,2l2)') &
     label, mpp_pe(), ') i,j=',berg%ine, berg%jne, &
     ' xi,yj=', berg%xi, berg%yj, &
     ' lon,lat=', berg%lon, berg%lat, &
@@ -2477,7 +2477,7 @@ subroutine print_berg(iochan, berg, label, il, jl)
     ' uvel_old,vvel_old=', berg%uvel_old, berg%vvel_old, &
     ' lon_old,lat_old=', berg%lon_old, berg%lat_old, &
     ' p,n=', associated(berg%prev), associated(berg%next)
-  write(iochan,'("diamonds, print_berg: ",a," pe=(",i3,") ",6(a,2f10.4))') &
+  write(iochan,'("diamonds, print_berg: ",a," pe=(",i3,") ",6(a,2f14.8))') &
     label, mpp_pe(), 'uo,vo=', berg%uo, berg%vo, 'ua,va=', berg%ua, berg%va, 'ui,vi=', berg%ui, berg%vi
 !Two lines above added by Alon
 end subroutine print_berg

From ceb5e10b144176844708892dd0ea07658299650a Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 12 Oct 2016 15:29:25 -0400
Subject: [PATCH 182/361] Parts of the code has been slightly refactored /
 reorganized to avoid code being duplicated, and to make it easier to read.
 The changes are:

1) spread_mass_across_ocean_cells now takes in the iceberg pointer, and the bergs icebergs type pointer. This means that fewer arguments need to be passed into this subroutine. The iceberg orientation, static vs non-static and grounding fraction are now taken care of within this subroutine. This means that this code does not have to be duplicated in many places across the model. Similarly, some of the flags are now unpacked from bergs within the subroutine.

2) A subroutine called calculate_mass_on_ocean has been written. This routine loops through all the icebergs and  calls spread_mass_across_ocean_cells for each iceberg. It also has an option to calculate other diagnositics which require looping through all the icebergs.

3) A subroutine called create_gridded_icebergs_fields has been added. This subroutine contains most of the code which takes the icebergs and interpolated their data back onto the ocean/sea ice grid. Some code has been removed from the thermodynamics subroutine, and some code has been removed from the icebergs_run subroutine, and instead is called within this subroutine.

4) mass_berg, area_berg, and ustar_berg are not optional inputs for icebergs_run, and are pointers. There are only accessed with they are assosiated. These threee fields are the only way that the iceberg model sends data to the sea ice and ocean model. These are not filled in with values when we are in passive mode, or add_mass_to_ocean is set to zero (mass field).

5) A new subroutine called sum_up_spread_fields has been written. This subroutine is almost the same as what icebergs_incr_mass was. The subroutine icebergs_incr_mass has been significantly shortened. The reason for this is that icebergs_incr_mass is called directly from the SIS model. The purpose of this routine is to add the iceberg mass to the sea ice mass. The icebergs_incr_mass routine is now shorter, and just adds the field spread_mass to the inputed mass field.

The subroutine sum_up_spread_fields takes in a field (mass, area, Uvel or Vvel) and sums up the contributions to this field from adjacent grid cells. The clocks and diagnostics have been removed from this routine so that it is now simpler.

6) A spread_mass_old field has been added to the gridded fields. This field is helpful when calculating the melt from changes in spread mass

7) The find_melt_from_spread mass now has been improved in two ways:

Firstly, the calculation of the old spread_mass happens after the icebergs have been evolved. This done incorrectly previously

Secondly, when the flag melt_without_decay is set to true, the spread mass is calculated inside of the thermodynamics routine before the iceberg is restored to its original size. this means that find_melt_from_spread_mass and melt_without_decay can be used together
---
 icebergs.F90           | 524 ++++++++++++++++++++++-------------------
 icebergs_framework.F90 |   8 +-
 2 files changed, 287 insertions(+), 245 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index a3ff6c8..d4a79ef 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1119,19 +1119,16 @@ subroutine thermodynamics(bergs)
 real :: Mnew, Mnew1, Mnew2, Hocean
 real :: Mbits, nMbits, dMbitsE, dMbitsM, Lbits, Abits, Mbb
 real :: tip_parameter
-real :: ustar_h, ustar
 integer :: i,j, stderrunit
 type(iceberg), pointer :: this, next
 real, parameter :: perday=1./86400.
 integer :: grdi, grdj
-real :: orientation, static_berg
 real :: SSS !Temporarily here
 
   ! For convenience
   grd=>bergs%grd
   
-  !Initializing static_berg
-  static_berg=0.
+  !Initializing 
   grd%Uvel_on_ocean(:,:,:)=0.
   grd%Vvel_on_ocean(:,:,:)=0.
 
@@ -1322,6 +1319,16 @@ subroutine thermodynamics(bergs)
 
        !This option allows iceberg melt fluxes to enter the ocean without the icebergs changing shape
        if (bergs%Iceberg_melt_without_decay) then
+         !In this case, the iceberg dimension are reset to their values before
+         !the thermodynamics are applied. 
+         !If the spread_mass is being used to calculate melt, we calculate this
+         !before reseting 
+         if (bergs%find_melt_using_spread_mass) then
+           if (Mnew>0.) then !If the berg still exists
+             call spread_mass_across_ocean_cells(bergs,this, i, j, this%xi, this%yj,Mnew , nMbits, this%mass_scaling, Ln*Wn,  Tn)
+           endif
+         endif
+         !Reset all the values
          Mnew=this%mass
          nMbits=this%mass_of_bits
          Tn=this%thickness
@@ -1329,7 +1336,6 @@ subroutine thermodynamics(bergs)
          Ln=this%length
          if (bergs%bergy_bit_erosion_fraction>0.) then
            Mbits=this%mass_of_bits ! mass of bergy bits (kg)
-           nMbits=Mbits
            Lbits=min(L,W,T,40.) ! assume bergy bits are smallest dimension or 40 meters
            Abits=(Mbits/bergs%rho_bergs)/Lbits ! Effective bottom area (assuming T=Lbits)
          endif
@@ -1348,56 +1354,105 @@ subroutine thermodynamics(bergs)
         call move_trajectory(bergs, this)
         call delete_iceberg_from_list(bergs%list(grdi,grdj)%first, this)
         bergs%nbergs_melted=bergs%nbergs_melted+1
-      else ! Diagnose mass distribution on grid
-        if (grd%id_virtual_area>0)&
-             & grd%virtual_area(i,j)=grd%virtual_area(i,j)+(Wn*Ln+Abits)*this%mass_scaling ! m^2
-        if ((grd%id_mass>0 .or. bergs%add_weight_to_ocean) .or. ((grd%id_u_iceberg>0) .or. (grd%id_v_iceberg>0)))   &
-             & grd%mass(i,j)=grd%mass(i,j)+Mnew/grd%area(i,j)*this%mass_scaling ! kg/m2
-        !Finding the average iceberg velocity in a grid cell (mass weighted)
-        grd%u_iceberg(i,j)=grd%u_iceberg(i,j)+((Mnew/grd%area(i,j)*this%mass_scaling)*this%uvel) ! kg/m2
-        grd%v_iceberg(i,j)=grd%v_iceberg(i,j)+((Mnew/grd%area(i,j)*this%mass_scaling)*this%vvel) ! kg/m2
-        if (grd%id_bergy_mass>0 .or. bergs%add_weight_to_ocean)&
-             & grd%bergy_mass(i,j)=grd%bergy_mass(i,j)+nMbits/grd%area(i,j)*this%mass_scaling ! kg/m2
-        if (bergs%add_weight_to_ocean .and. .not. bergs%time_average_weight) then
-          if (bergs%grounding_fraction>0.) then
-            Hocean=bergs%grounding_fraction*(grd%ocean_depth(i,j)+grd%ssh(i,j))
-            if (Dn>Hocean) Mnew=Mnew*min(1.,Hocean/Dn)
-          endif
-
-          orientation=bergs%initial_orientation
-          if ((bergs%iceberg_bonds_on) .and. (bergs%rotate_icebergs_for_mass_spreading)) call find_orientation_using_iceberg_bonds(grd,this,orientation)
-          if (bergs%hexagonal_icebergs) static_berg=this%static_berg  !Change this to use_old_restart=false when this is merged in
-          call spread_mass_across_ocean_cells(grd, i, j, this%xi, this%yj, Mnew, nMbits, this%mass_scaling, &
-                      this%length*this%width, bergs%use_old_spreading, bergs%hexagonal_icebergs,orientation,static_berg,this%uvel,this%vvel)
-        endif
       endif
       this=>next
     enddo
   enddo ; enddo
+
+
+  contains
+
+  subroutine swap_variables(x,y)
+  ! Arguments
+  real, intent(inout) :: x, y
+  real :: temp
+  temp=x
+  x=y
+  y=temp
+  end subroutine swap_variables
+
+end subroutine thermodynamics
+
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+subroutine create_gridded_icebergs_fields(bergs)
+! Arguments
+type(icebergs), pointer :: bergs
+! Local variables
+type(icebergs_gridded), pointer :: grd
+type(iceberg), pointer :: this
+integer i,j
+integer :: grdi, grdj
+real :: Hocean, Dn,Tn,dvo, mass_tmp 
+real :: ustar_h, ustar
+real :: orientation
+real :: ave_thickness
+real, dimension(bergs%grd%isd:bergs%grd%ied,bergs%grd%jsd:bergs%grd%jed)  :: spread_mass_tmp
+real :: tmp
+
+  ! For convenience
+  grd=>bergs%grd
+
+  spread_mass_tmp(:,:)=0. !Initializing temporary variable to use in iceberg melt calculation 
+
+  !Special case for icebergs not decaying, but mass diffence being used for melt rates
+  if ((bergs%find_melt_using_spread_mass) .and.  (bergs%Iceberg_melt_without_decay)) then
+    call sum_up_spread_fields(bergs, spread_mass_tmp(grd%isc:grd%iec,grd%jsc:grd%jec),'mass') 
+  endif
+ 
+  !Loop through icebergs and spread mass on ocean 
+  call calculate_mass_on_ocean(bergs, with_diagnostics=.true.)
   
-  !Finding the average iceberg velocity in a cell to calculate u_star  
-  grd%spread_uvel(:,:)=0.
-  call icebergs_incr_mass(bergs, grd%spread_uvel(grd%isc:grd%iec,grd%jsc:grd%jec),within_iceberg_model=.True.,field_name_in='Uvel') 
-  grd%spread_vvel(:,:)=0.
-  call icebergs_incr_mass(bergs, grd%spread_vvel(grd%isc:grd%iec,grd%jsc:grd%jec),within_iceberg_model=.True.,field_name_in='Vvel') 
-  grd%spread_area(:,:)=0.
-  call icebergs_incr_mass(bergs, grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec),within_iceberg_model=.True.,field_name_in='area') 
+  !Finding the spread fields 
+  if ((grd%id_spread_uvel>0)  .or. (bergs%pass_fields_to_ocean_model)) then 
+    grd%spread_uvel(:,:)=0.
+    call sum_up_spread_fields(bergs, grd%spread_uvel(grd%isc:grd%iec,grd%jsc:grd%jec), 'Uvel') 
+  endif
+  if ( (grd%id_spread_vvel>0)  .or. (bergs%pass_fields_to_ocean_model)) then 
+    grd%spread_vvel(:,:)=0.
+    call sum_up_spread_fields(bergs, grd%spread_vvel(grd%isc:grd%iec,grd%jsc:grd%jec), 'Vvel') 
+  endif
+  if ( (grd%id_spread_area>0)  .or. (bergs%pass_fields_to_ocean_model)) then 
+    grd%spread_area(:,:)=0.
+    call sum_up_spread_fields(bergs, grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec), 'area') 
+  endif
+  !Always find spread_mass since it is used for so many things.  
+  grd%spread_mass(:,:)=0.
+    call sum_up_spread_fields(bergs, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec),'mass') 
   
-  !Divdind the gridded iceberg momentum by the iceberg mass to get velocities
-  do j = grd%jsc,grd%jec ; do i = grd%isc,grd%iec  
-    if (grd%mass(i,j)>0.) then
-      grd%u_iceberg(i,j)=grd%u_iceberg(i,j)/grd%mass(i,j)
-      grd%v_iceberg(i,j)=grd%v_iceberg(i,j)/grd%mass(i,j)
-    else
-      grd%u_iceberg(i,j)=0. ; grd%v_iceberg(i,j)=0.
-    endif
-  enddo; enddo
+  !Using spread_mass_to_ocean to calculate melt rates (if this option is chosen)
+  if (bergs%find_melt_using_spread_mass) then
+    if (.not. bergs%Iceberg_melt_without_decay) &
+         spread_mass_tmp(grd%isc:grd%iec,grd%jsc:grd%jec)= grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec)
+    do i=grd%isd,grd%ied ; do j=grd%jsd,grd%jed
+      if (grd%area(i,j)>0.0) then
+        grd%floating_melt(i,j)=max((grd%spread_mass_old(i,j) - spread_mass_tmp(i,j))/(bergs%dt),0.0)
+      else
+        grd%floating_melt(i,j)=0.0
+      endif
+    enddo ;enddo
+    grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)=grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec)*HLF !Not 100% sure this is correct.
+  endif
+
+  !Dividng the gridded iceberg momentum diagnostic by the iceberg mass to get velocities
+  if ((grd%id_u_iceberg>0) .or. (grd%id_v_iceberg>0)) then
+    do j = grd%jsc,grd%jec ; do i = grd%isc,grd%iec  
+      if (grd%mass(i,j)>0.) then
+        if (grd%id_u_iceberg>0) &
+          grd%u_iceberg(i,j)=grd%u_iceberg(i,j)/grd%mass(i,j)
+        if (grd%id_v_iceberg>0) &
+          grd%v_iceberg(i,j)=grd%v_iceberg(i,j)/grd%mass(i,j)
+      else
+        if (grd%id_u_iceberg>0)  grd%u_iceberg(i,j)=0. 
+        if (grd%id_v_iceberg>0)  grd%v_iceberg(i,j)=0. 
+      endif
+    enddo; enddo
+  endif
   
   !Calculating ustar_iceberg (gridded)
   grd%ustar_iceberg(:,:)=0.
   if  ((grd%id_ustar_iceberg>0) .or. (bergs%pass_fields_to_ocean_model)) then   !Update diagnostic of iceberg mass spread on ocean
     do j = grd%jsc,grd%jec ; do i = grd%isc,grd%iec  
-      !dvo=sqrt((grd%u_iceberg(i,j)-grd%uo(i,j))**2+(grd%v_iceberg(i,j)-grd%vo(i,j))**2)
       dvo=sqrt((grd%spread_uvel(i,j)-grd%uo(i,j))**2+(grd%spread_vvel(i,j)-grd%vo(i,j))**2)
       ustar = sqrt(bergs%cdrag_icebergs*(dvo**2  + bergs%utide_icebergs**2))
       ustar_h = max(bergs%ustar_icebergs_bg, ustar)
@@ -1406,19 +1461,19 @@ subroutine thermodynamics(bergs)
     enddo; enddo
   endif
 
-  contains
-
-  subroutine swap_variables(x,y)
-  ! Arguments
-  real, intent(inout) :: x, y
-  real :: temp
-  temp=x
-  x=y
-  y=temp
-  end subroutine swap_variables
-
-end subroutine thermodynamics
-
+  !Only allowing melt in ocean above a minimum cutoff thickness
+  if (bergs%apply_thickness_cutoff_to_gridded_melt) then
+    do i=grd%isd,grd%ied ; do j=grd%jsd,grd%jed
+      if ((bergs%melt_cutoff >=0.) .and. (grd%spread_area(i,j)>0.)) then
+        ave_thickness=grd%spread_mass(i,j)/(grd%spread_area(i,j)*bergs%rho_bergs) 
+        if ((grd%ocean_depth(i,j)-ave_thickness) < bergs%melt_cutoff) then
+          grd%floating_melt(i,j)=0.0
+          grd%calving_hflx(i,j)=0.0
+        endif
+      endif
+    enddo ;enddo
+  endif
+end subroutine create_gridded_icebergs_fields
 
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 subroutine find_basal_melt(bergs,dvo,lat,salt,temp,Use_three_equation_model,thickness,basal_melt,iceberg_num)
@@ -1832,15 +1887,14 @@ subroutine find_orientation_using_iceberg_bonds(grd,berg,orientation)
 
 end subroutine find_orientation_using_iceberg_bonds
 
-subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling, Area, use_old_spreading,hexagonal_icebergs,theta,static_berg,uvel,vvel)
+subroutine spread_mass_across_ocean_cells(bergs, berg, i, j, x, y, Mberg, Mbits, scaling, Area, Tn)
   ! Arguments
+  type(icebergs), pointer :: bergs
   type(icebergs_gridded), pointer :: grd
+  type(iceberg), pointer :: berg
   integer, intent(in) :: i, j
-  real, intent(in) :: x, y, Mberg, Mbits, scaling, Area,uvel,vvel
-  logical, intent(in) :: hexagonal_icebergs
-  logical, intent(in) :: use_old_spreading
-  real, intent(in) :: theta
-  real, optional, intent(in) :: static_berg
+  real, intent(in) :: x, y, Mberg, Mbits, scaling, Area
+  real, intent(in) :: Tn
   ! Local variables
   real :: xL, xC, xR, yD, yC, yU, Mass, L
   real :: yDxL, yDxC, yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR
@@ -1849,16 +1903,27 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
   real :: fraction_used !fraction of iceberg mass included (part of the mass near the boundary is discarded sometimes)
   real :: I_fraction_used !Inverse of fraction used
   real :: tol
+  real :: Dn, Hocean
   real, parameter :: rho_seawater=1035.
   integer :: stderrunit
   logical :: debug
+  real :: orientation, Mass_berg
 
   ! Get the stderr unit number
   stderrunit = stderr()
 
   tol=1.e-10
+  grd=>bergs%grd
+  Mass_berg=Mberg
 
-  Mass=(Mberg+Mbits)*scaling
+  !Trimming icebergs to account for grounded fraction.
+  if (bergs%grounding_fraction>0.) then
+    Hocean=bergs%grounding_fraction*(grd%ocean_depth(i,j)+grd%ssh(i,j))
+    Dn=(bergs%rho_bergs/rho_seawater)*Tn ! re-calculate draught (keel depth)
+    if (Dn>Hocean) Mass_berg=Mberg*min(1.,Hocean/Dn)
+  endif
+
+  Mass=(Mass_berg+Mbits)*scaling
   ! This line attempts to "clip" the weight felt by the ocean. The concept of
   ! clipping is non-physical and this step should be replaced by grounding.
   if (grd%clipping_depth>0.) Mass=min(Mass,grd%clipping_depth*grd%area(i,j)*rho_seawater)
@@ -1867,7 +1932,7 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
   yDxL=0.  ; yDxC=0. ; yDxR=0. ; yCxL=0. ; yCxR=0.
   yUxL=0.  ; yUxC=0. ; yUxR=0. ; yCxC=1.
 
-  if (.not. hexagonal_icebergs) then  !Treat icebergs as rectangles of size L:  (this is the default)
+  if (.not. bergs%hexagonal_icebergs) then  !Treat icebergs as rectangles of size L:  (this is the default)
     
     !L is the non dimensional length of the iceberg [  L=(Area of berg/ Area of grid cell)^0.5  ] or something like that.
     if (grd%area(i,j)>0) then
@@ -1876,7 +1941,7 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
       L=1.
     endif
   
-    if (use_old_spreading) then
+    if (bergs%use_old_spreading) then
       !Old version before icebergs were given size L
       xL=min(0.5, max(0., 0.5-x))
       xR=min(0.5, max(0., x-0.5))
@@ -1906,6 +1971,9 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
     fraction_used=1.  !rectangular bergs do share mass with boundaries (all mass is included in cells)
 
   else !Spread mass as if elements area hexagonal
+    
+    orientation=bergs%initial_orientation
+    if ((bergs%iceberg_bonds_on) .and. (bergs%rotate_icebergs_for_mass_spreading)) call find_orientation_using_iceberg_bonds(grd,berg,orientation)
 
     if (grd%area(i,j)>0) then
       H = min(( (sqrt(Area/(2.*sqrt(3.)))  / sqrt(grd%area(i,j)))),1.) ;  !Non dimensionalize element length by grid area. (This gives the non-dim Apothen of the hexagon)
@@ -1929,7 +1997,7 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
     x0=(x-origin_x)
     y0=(y-origin_y)
 
-    call Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
+    call Hexagon_into_quadrants_using_triangles(x0,y0,H,orientation,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
     
     if (min(min(Area_Q1,Area_Q2),min(Area_Q3, Area_Q4)) <-tol) then
       call error_mesg('diamonds, hexagonal spreading', 'Intersection with hexagons should not be negative!!!', WARNING)
@@ -1975,7 +2043,7 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
         write(stderrunit,*) 'diamonds, hexagonal, H,x0,y0', H, x0 , y0
         write(stderrunit,*) 'diamonds, hexagonal, Areas',(Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
         debug=.True.
-        !call Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4, debug)
+        !call Hexagon_into_quadrants_using_triangles(x0,y0,H,orientation,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4, debug)
         call error_mesg('diamonds, hexagonal spreading', 'All the mass is not being used!!!', FATAL)
       endif
 
@@ -1984,7 +2052,7 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
     !Note that for the square elements, the mass has already been reassigned, so fraction_used shoule be equal to 1 aready
     fraction_used= ((yDxL*grd%msk(i-1,j-1)) + (yDxC*grd%msk(i  ,j-1))  +(yDxR*grd%msk(i+1,j-1)) +(yCxL*grd%msk(i-1,j  )) +  (yCxR*grd%msk(i+1,j  ))&
                    +(yUxL*grd%msk(i-1,j+1)) +(yUxC*grd%msk(i  ,j+1))   +(yUxR*grd%msk(i+1,j+1)) + (yCxC**grd%msk(i,j)))
-    if  (static_berg .eq. 1)  fraction_used=1.  !Static icebergs do not share their mass with the boundary
+    if  (berg%static_berg .eq. 1)  fraction_used=1.  !Static icebergs do not share their mass with the boundary
                                                 ! (this allows us to easily  initialize hexagonal icebergs in regular arrangements against boundaries)
   endif
   I_fraction_used=1./fraction_used !Invert this so that the arithmatec reprocudes
@@ -1996,10 +2064,10 @@ subroutine spread_mass_across_ocean_cells(grd, i, j, x, y, Mberg, Mbits, scaling
   call spread_variable_across_cells(grd, grd%area_on_ocean, Area*scaling , i ,j, &
              yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR,I_fraction_used)
   !Spreading the iceberg x momentum onto the ocean
-  call spread_variable_across_cells(grd,grd%Uvel_on_ocean, uvel*Area*scaling , i ,j, &
+  call spread_variable_across_cells(grd,grd%Uvel_on_ocean, berg%uvel*Area*scaling , i ,j, &
              yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR, I_fraction_used)
   !Spreading the iceberg y momentum onto the ocean
-  call spread_variable_across_cells(grd,grd%Vvel_on_ocean, vvel*Area*scaling , i ,j, &
+  call spread_variable_across_cells(grd,grd%Vvel_on_ocean, berg%vvel*Area*scaling , i ,j, &
              yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR, I_fraction_used)
   
 end subroutine spread_mass_across_ocean_cells
@@ -2648,15 +2716,15 @@ end subroutine rotate
 end subroutine interp_flds
 
 
-subroutine calculate_mass_on_ocean(bergs, spread_mass_old)
+subroutine calculate_mass_on_ocean(bergs, with_diagnostics)
 ! Arguments
 type(icebergs), pointer :: bergs
 type(iceberg), pointer :: berg
 type(icebergs_gridded), pointer :: grd
-real, dimension(:,:), optional, intent(out) :: spread_mass_old
+logical, intent(in) :: with_diagnostics
 ! Local variables
 integer :: grdj, grdi   
-real :: orientation
+integer :: j, i   
 
   ! For convenience
   grd=>bergs%grd
@@ -2670,28 +2738,61 @@ subroutine calculate_mass_on_ocean(bergs, spread_mass_old)
   do grdj = grd%jsc-1,grd%jec+1 ; do grdi = grd%isc-1,grd%iec+1  
     berg=>bergs%list(grdi,grdj)%first
     do while(associated(berg))
-    orientation=bergs%initial_orientation
-    if ((bergs%iceberg_bonds_on) .and. (bergs%rotate_icebergs_for_mass_spreading)) call find_orientation_using_iceberg_bonds(grd,berg,orientation)
-      call spread_mass_across_ocean_cells(grd, grdi, grdj, berg%xi, berg%yj, berg%mass,berg%mass_of_bits, berg%mass_scaling, &
-                berg%length*berg%width, bergs%use_old_spreading, bergs%hexagonal_icebergs,orientation,berg%static_berg,berg%uvel,berg%vvel)
+      i=berg%ine  ;     j=berg%jne
+      if (grd%area(i,j) > 0.) then
+        
+        !Increasing Mass on ocean
+        if ((bergs%add_weight_to_ocean .and. .not. bergs%time_average_weight) .or.(bergs%find_melt_using_spread_mass)) then
+          call spread_mass_across_ocean_cells(bergs, berg, berg%ine, berg%jne, berg%xi, berg%yj, berg%mass,berg%mass_of_bits, berg%mass_scaling, &
+                berg%length*berg%width, berg%thickness)
+        endif
 
+        !Calculated some iceberg diagnositcs  
+        if (with_diagnostics) call calculate_sum_over_bergs_diagnositcs(bergs,grd,berg,i,j)
+
+      endif
       berg=>berg%next
     enddo
   enddo ;enddo
-  call mpp_sync_self()
 
-  grd%spread_mass(:,:)=0.
-  call icebergs_incr_mass(bergs, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec),within_iceberg_model=.True.) 
-  spread_mass_old(:,:)=grd%spread_mass(:,:)
+  contains
 
-  !Reset fields
-  grd%mass_on_ocean(:,:,:)=0.
-  grd%area_on_ocean(:,:,:)=0.
-  grd%Uvel_on_ocean(:,:,:)=0.
-  grd%Vvel_on_ocean(:,:,:)=0.
+  subroutine calculate_sum_over_bergs_diagnositcs(bergs,grd,berg,i,j)
+  ! Arguments
+  type(icebergs), pointer :: bergs
+  type(iceberg), pointer :: berg
+  type(icebergs_gridded), pointer :: grd
+  integer, intent(in) :: i, j
+  ! Local variables
+  real ::  Abits, Lbits, Mbits
+
+           !Virtual area diagnostic
+           if (grd%id_virtual_area>0) then
+             if (bergs%bergy_bit_erosion_fraction>0.) then
+               Lbits=min(berg%length,berg%width,berg%thickness,40.) ! assume bergy bits are smallest dimension or 40 meters
+               Abits=(berg%mass_of_bits/bergs%rho_bergs)/Lbits ! Effective bottom area (assuming T=Lbits)
+             else
+               Abits=0.0
+             endif
+             grd%virtual_area(i,j)=grd%virtual_area(i,j)+(berg%width*berg%length+Abits)*berg%mass_scaling ! m^2
+           endif
 
-end subroutine calculate_mass_on_ocean
+           !Mass diagnostic (also used in u_iceberg, v_iceberg
+           if ((grd%id_mass>0 ) .or. ((grd%id_u_iceberg>0) .or. (grd%id_v_iceberg>0)))   &
+                & grd%mass(i,j)=grd%mass(i,j)+berg%mass/grd%area(i,j)*berg%mass_scaling ! kg/m2
 
+           !Finding the average iceberg velocity in a grid cell (mass weighted)
+           if (grd%id_u_iceberg>0) &
+           grd%u_iceberg(i,j)=grd%u_iceberg(i,j)+((berg%mass/grd%area(i,j)*berg%mass_scaling)*berg%uvel) ! kg/m2
+           if (grd%id_v_iceberg>0) &
+           grd%v_iceberg(i,j)=grd%v_iceberg(i,j)+((berg%mass/grd%area(i,j)*berg%mass_scaling)*berg%vvel) ! kg/m2
+
+           !Mass of bergy bits
+           if (grd%id_bergy_mass>0 .or. bergs%add_weight_to_ocean)&
+                & grd%bergy_mass(i,j)=grd%bergy_mass(i,j)+berg%mass_of_bits/grd%area(i,j)*berg%mass_scaling ! kg/m2
+ end subroutine calculate_sum_over_bergs_diagnositcs
+
+end subroutine calculate_mass_on_ocean
 
 ! ##############################################################################
 
@@ -2704,7 +2805,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 real, dimension(:,:), intent(in) :: uo, vo, ui, vi, tauxa, tauya, ssh, sst, cn, hi
 integer,    optional, intent(in) :: stagger, stress_stagger
 real, dimension(:,:), optional, intent(in) :: sss
-real, dimension(:,:), optional, intent(inout) ::  mass_berg, ustar_berg, area_berg
+real, dimension(:,:), optional, pointer ::  mass_berg, ustar_berg, area_berg
 
 ! Local variables
 integer :: iyr, imon, iday, ihr, imin, isec, k
@@ -2718,11 +2819,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 real, dimension(:,:), allocatable :: uC_tmp, vC_tmp
 integer :: vel_stagger, str_stagger
 real, dimension(:,:), allocatable :: iCount
-real, dimension(bergs%grd%isd:bergs%grd%ied,bergs%grd%jsd:bergs%grd%jed)  :: spread_mass_old
-!real, dimension(bergs%grd%isd:bergs%grd%ied,bergs%grd%jsd:bergs%grd%jed)  :: ustar_berg0, area_berg0
 integer :: nbonds
-!logical :: within_iceberg_model
-
 integer :: stderrunit
 
   ! Get the stderr unit number
@@ -2745,6 +2842,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   grd%bergy_src(:,:)=0.
   grd%bergy_melt(:,:)=0.
   grd%bergy_mass(:,:)=0.
+  grd%spread_mass_old(:,:)=0.  
   !grd%spread_mass(:,:)=0.  !Don't zero this out yet, because we can first use this an add it onto the SSH
   grd%spread_area(:,:)=0. 
   grd%u_iceberg(:,:)=0.
@@ -2753,25 +2851,21 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   grd%spread_vvel(:,:)=0.
   grd%ustar_iceberg(:,:)=0.
   grd%mass(:,:)=0.
- 
-  !I belive that ustar_berg0 and area_berg0 are no longer needed
-  !ustar_berg0(:,:)=0.
-  !area_berg0(:,:)=0.
+  grd%virtual_area(:,:)=0.
+  
+  !Initializing _on_ocean_fields
+  grd%mass_on_ocean(:,:,:)=0. ;   grd%area_on_ocean(:,:,:)=0.
+  grd%Uvel_on_ocean(:,:,:)=0. ;   grd%Vvel_on_ocean(:,:,:)=0.
 
-  if (present(mass_berg)) then !; if (allocated(mass_berg)) then
+  if (present(mass_berg)) then ;  if (associated(mass_berg)) then 
     mass_berg(:,:)=0.0
-  endif !; endif
-  if (present(ustar_berg)) then !; if (allocated(ustar_berg)) then
+  endif ;  endif
+  if (present(ustar_berg)) then ; if (associated(ustar_berg)) then 
     ustar_berg(:,:)=0.0
-  endif !; endif
-  if (present(area_berg)) then !; if (allocated(area_berg)) then
+  endif ;  endif
+  if (present(area_berg)) then ;  if (associated(area_berg)) then 
     area_berg(:,:)=0.0
-  endif !; endif
-
-
-  if (bergs%add_weight_to_ocean) grd%mass_on_ocean(:,:,:)=0.
-  if (bergs%add_weight_to_ocean) grd%area_on_ocean(:,:,:)=0.
-  grd%virtual_area(:,:)=0.
+  endif ;  endif
 
   ! Manage time
   call get_date(time, iyr, imon, iday, ihr, imin, isec)
@@ -3002,10 +3096,14 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   if (debug) call checksum_gridded(bergs%grd, 's/r run after exchange')
   call mpp_clock_end(bergs%clock_com)
 
-  
+  !Caculate mass on ocean before thermodynamics, to use in melt rate calculation
   if (bergs%find_melt_using_spread_mass) then 
-    spread_mass_old(:,:)=0.
-    call calculate_mass_on_ocean(bergs, spread_mass_old)
+    call calculate_mass_on_ocean(bergs, with_diagnostics=.false.)
+    grd%spread_mass_old(:,:)=0.
+    call sum_up_spread_fields(bergs,grd%spread_mass_old(grd%isc:grd%iec,grd%jsc:grd%jec), 'mass') 
+    !Reset fields
+    grd%mass_on_ocean(:,:,:)=0.  ;  grd%area_on_ocean(:,:,:)=0.
+    grd%Uvel_on_ocean(:,:,:)=0.  ;  grd%Vvel_on_ocean(:,:,:)=0.
   endif
 
   ! Iceberg thermodynamics (melting) + rolling
@@ -3015,6 +3113,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   if (debug) call checksum_gridded(bergs%grd, 's/r run after thermodynamics')
   call mpp_clock_end(bergs%clock_the)
 
+  !Creating gridded fields from new icebergs
+  call create_gridded_icebergs_fields(bergs)
 
   ! For each berg, record
   call mpp_clock_begin(bergs%clock_dia)
@@ -3024,42 +3124,6 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     call write_trajectory(bergs%trajectories, bergs%save_short_traj)
   endif
 
-  !Using spread_mass_to_ocean to calculate melt rates (if this option is chosen)
-  !within_iceberg_model=.True.
-  if (bergs%find_melt_using_spread_mass) then
-    grd%spread_mass(:,:)=0.
-    call icebergs_incr_mass(bergs, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec),within_iceberg_model=.True.) 
-    do i=grd%isd,grd%ied ; do j=grd%jsd,grd%jed
-      if (grd%area(i,j)>0.0) then
-        grd%floating_melt(i,j)=max((spread_mass_old(i,j) - grd%spread_mass(i,j))/(bergs%dt),0.0)
-        grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)=grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec)*HLF !Not 100% sure this is correct.
-      else
-        grd%floating_melt(i,j)=0.0
-      endif
-    enddo ;enddo
-  !elseif  ((grd%id_spread_mass>0) .or. (bergs%pass_fields_to_ocean_model)) then   !Update diagnostic of iceberg mass spread on ocean
-  else   !Update iceberg mass spread on ocean
-    grd%spread_mass(:,:)=0.
-    call icebergs_incr_mass(bergs, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec),within_iceberg_model=.True.) 
-  endif
-
-  if ( (grd%id_spread_area>0)  .or. (bergs%pass_fields_to_ocean_model)) then  !Update diagnostic of iceberg area spread on ocean
-    grd%spread_area(:,:)=0.
-    call icebergs_incr_mass(bergs, grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec),within_iceberg_model=.True.,field_name_in='area') 
-  endif
-  if (bergs%apply_thickness_cutoff_to_gridded_melt) then
-    do i=grd%isd,grd%ied ; do j=grd%jsd,grd%jed
-      if ((bergs%melt_cutoff >=0.) .and. (grd%spread_area(i,j)>0.)) then
-        ave_thickness=grd%spread_mass(i,j)/(grd%spread_area(i,j)*bergs%rho_bergs) 
-        if ((grd%ocean_depth(i,j)-ave_thickness) < bergs%melt_cutoff) then
-          grd%floating_melt(i,j)=0.0
-          grd%calving_hflx(i,j)=0.0
-        endif
-      endif
-    enddo ;enddo
-  endif
-   
-
   ! Gridded diagnostics
   if (grd%id_uo>0) &
     lerr=send_data(grd%id_uo, grd%uo(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
@@ -3156,29 +3220,28 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 
   call mpp_clock_end(bergs%clock_dia)
 
-  ! Return what ever calving we did not use and additional icebergs melt
+  !This is the point in the algorithem which determines which fields get passed to the ice model
+  !Return what ever calving we did not use and additional icebergs melt
   call mpp_clock_begin(bergs%clock_int)
   if (.not. bergs%passive_mode) then
     where (grd%area(grd%isc:grd%iec,grd%jsc:grd%jec)>0.)
       calving(:,:)=grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec)/grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) &
                   +grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec)
-      !ustar_berg0(:,:)=grd%ustar_iceberg(:,:)
-      !area_berg0(:,:)=grd%spread_area(:,:)
     elsewhere
       calving(:,:)=0.
-      !ustar_berg0(:,:)=0.
-      !area_berg0(:,:)=0.
     end where
     calving_hflx(:,:)=grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)
-    if (present(mass_berg)) then !; if (allocated(mass_berg)) then
-      mass_berg(:,:)=grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec)
-    endif !; endif
-    if (present(ustar_berg)) then !; if (allocated(ustar_berg)) then
+    !Return iceberg mass, area and ustar to pass on to ocean model
+    if (present(mass_berg)) then ; if (associated(mass_berg)) then
+      if (bergs%add_weight_to_ocean) &
+        mass_berg(:,:)=grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec)
+    endif ; endif
+    if (present(ustar_berg)) then ; if (associated(ustar_berg)) then
       ustar_berg(:,:)=grd%ustar_iceberg(grd%isc:grd%iec,grd%jsc:grd%jec)
-    endif !; endif
-    if (present(area_berg)) then !; if (allocated(area_berg)) then
+    endif ; endif
+    if (present(area_berg)) then ; if (associated(area_berg)) then
       area_berg(:,:)=grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec)
-    endif !; endif
+    endif ; endif
   endif
   call mpp_clock_end(bergs%clock_int)
 
@@ -3213,12 +3276,12 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     grd%tmpc(:,:)=0.;
     !Finding spread mass
     call mpp_clock_end(bergs%clock); call mpp_clock_end(bergs%clock_dia) ! To enable calling of public s/r
-    call icebergs_incr_mass(bergs, grd%tmpc)
+    call sum_up_spread_fields(bergs, grd%tmpc, 'mass')
     call mpp_clock_begin(bergs%clock_dia); call mpp_clock_begin(bergs%clock) ! To enable calling of public s/r
     bergs%returned_mass_on_ocean=sum( grd%tmpc(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
     !Finding spread area
     call mpp_clock_end(bergs%clock); call mpp_clock_end(bergs%clock_dia) ! To enable calling of public s/r
-    call icebergs_incr_mass(bergs, grd%tmpc,field_name_in='area')
+    call sum_up_spread_fields(bergs, grd%tmpc, 'area')
     call mpp_clock_begin(bergs%clock_dia); call mpp_clock_begin(bergs%clock) ! To enable calling of public s/r
     bergs%returned_area_on_ocean=sum( grd%tmpc(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
     bergs%nbergs_end=count_bergs(bergs)
@@ -3482,21 +3545,53 @@ end subroutine icebergs_run
 
 ! ##############################################################################
 
-subroutine icebergs_incr_mass(bergs, mass, within_iceberg_model, Time,field_name_in)
+
+subroutine icebergs_incr_mass(bergs, mass, Time)
 ! Arguments
 type(icebergs), pointer :: bergs
-real, dimension(bergs%grd%isc:bergs%grd%iec,bergs%grd%jsc:bergs%grd%jec), intent(inout) :: mass
 type(time_type), intent(in), optional :: Time
-logical, intent(in), optional :: within_iceberg_model
-character(len=4), intent(in), optional :: field_name_in
+type(icebergs_gridded), pointer :: grd
+integer :: i, j
+logical :: lerr
+real, dimension(bergs%grd%isc:bergs%grd%iec,bergs%grd%jsc:bergs%grd%jec), intent(inout) :: mass
+
+!This routine is called from SIS, (and older versions of SIS2), but not within
+!the iceberg model. The routine adds the spread iceberg mass to mass provided
+!the add weight to ocean flag is on, and passive mode is off. It also appears to
+!play some role in diagnostics
+
+    if (.not. associated(bergs)) return
+    if (.not. bergs%add_weight_to_ocean) return
+  
+    ! For convenience
+    grd=>bergs%grd
+
+    !Start the clocks
+    call mpp_clock_begin(bergs%clock)
+    call mpp_clock_begin(bergs%clock_int)
+
+    do j=grd%jsc, grd%jec; do i=grd%isc, grd%iec
+      if (.not. bergs%passive_mode)   mass(i,j)=mass(i,j) + grd%spread_mass(i,j)
+    enddo  ;enddo
+    
+  !Stop the clocks
+  call mpp_clock_end(bergs%clock_int)
+  call mpp_clock_end(bergs%clock)
+
+end subroutine icebergs_incr_mass
+
+
+subroutine sum_up_spread_fields(bergs, field, field_name)
+! Arguments
+type(icebergs), pointer :: bergs
+real, dimension(bergs%grd%isc:bergs%grd%iec,bergs%grd%jsc:bergs%grd%jec), intent(out) :: field
+character(len=4), intent(in) :: field_name
 ! Local variables
-logical :: within_model
-character(len=4) :: field_name
 integer :: i, j
 type(icebergs_gridded), pointer :: grd
 real :: dmda
 logical :: lerr
-real, dimension(bergs%grd%isd:bergs%grd%ied, bergs%grd%jsd:bergs%grd%jed,9) :: var_on_ocean   !Variable being spread onto the ocean  (mass or area)
+real, dimension(bergs%grd%isd:bergs%grd%ied, bergs%grd%jsd:bergs%grd%jed,9) :: var_on_ocean   !Variable being spread onto the ocean  (mass, area, Uvel, Vvel)
 integer :: stderrunit
 
   ! Get the stderr unit number
@@ -3504,41 +3599,20 @@ subroutine icebergs_incr_mass(bergs, mass, within_iceberg_model, Time,field_name
   ! For convenience
   grd=>bergs%grd
 
-  !var_on_ocean(:,:,:)=0.
-  
-  !Deciding which varibale to spread across cells across grid cells (default spread mass)
-  field_name='mass'
-  if (present(field_name_in)) field_name=field_name_in 
+  field(:,:)=0.
+
+  !Deciding which varibale to spread across cells across grid cells
   if (field_name=='mass') var_on_ocean(:,:,:)=grd%mass_on_ocean(:,:,:)
   if (field_name=='area') var_on_ocean(:,:,:)=grd%area_on_ocean(:,:,:)
   if (field_name=='Uvel') var_on_ocean(:,:,:)=grd%Uvel_on_ocean(:,:,:)
   if (field_name=='Vvel') var_on_ocean(:,:,:)=grd%Vvel_on_ocean(:,:,:)
-
-
   
-  within_model=.False.
-  if (present(within_iceberg_model)) then 
-    within_model=within_iceberg_model
-  endif
-      
-  if (.not.(within_model)) then
-    if (.not. associated(bergs)) return
-    if (.not. bergs%add_weight_to_ocean) return
-    call mpp_clock_begin(bergs%clock)
-    call mpp_clock_begin(bergs%clock_int)
-  endif
-
-
-  ! Add iceberg+bits mass field to non-haloed SIS field (kg/m^2)
- !mass(:,:)=mass(:,:)+( grd%mass(grd%isc:grd%iec,grd%jsc:grd%jec) &
- !                    + grd%bergy_mass(grd%isc:grd%iec,grd%jsc:grd%jec) )
-
-  if (debug) then
-    grd%tmp(:,:)=0.; grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec)=mass
-    call grd_chksum2(grd, grd%tmp, 'mass in (incr)')
-  endif
+  !if (.not. bergs%add_weight_to_ocean) return
 
+  !Update the halos of the var_on_ocean
   call mpp_update_domains(var_on_ocean, grd%domain)
+
+  !Rotatine when old_bug_rotated_weights is on  - we should remove this.
   if (.not. old_bug_rotated_weights) then
     do j=grd%jsd, grd%jed; do i=grd%isd, grd%ied
       if (grd%parity_x(i,j)<0.) then
@@ -3553,6 +3627,8 @@ subroutine icebergs_incr_mass(bergs, mass, within_iceberg_model, Time,field_name
       endif
     enddo; enddo
   endif
+
+  !Here we add the contribution of the 9 cells. This is the heart of the routine.
   do j=grd%jsc, grd%jec; do i=grd%isc, grd%iec
     dmda=var_on_ocean(i,j,5) &
          + ( ( (var_on_ocean(i-1,j-1,9)+var_on_ocean(i+1,j+1,1))   &
@@ -3564,39 +3640,20 @@ subroutine icebergs_incr_mass(bergs, mass, within_iceberg_model, Time,field_name
     !Make sure that area <=1.0
     if (field_name=='area') dmda=min(dmda,1.0)
 
-    if (.not.(within_model)) then
-      if (.not. bergs%passive_mode) mass(i,j)=mass(i,j)+dmda
-    else
-      mass(i,j)=dmda
-    endif
-    if ((grd%id_area_on_ocn>0).and.(field_name=='area')) grd%tmp(i,j)=dmda
-    if ((grd%id_mass_on_ocn>0).and.(field_name=='mass')) grd%tmp(i,j)=dmda
+    field(i,j)=dmda
   enddo; enddo
   
-  if (field_name=='mass') then
-    if (present(Time).and. (grd%id_mass_on_ocn>0)) &
-      lerr=send_data(grd%id_mass_on_ocn, grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  elseif (field_name=='area') then
-    if (present(Time).and. (grd%id_area_on_ocn>0)) &
-      lerr=send_data(grd%id_area_on_ocn, grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  endif
-
   if (debug) then
-    grd%tmp(:,:)=0.; grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec)=mass
+    grd%tmp(:,:)=0.; grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec)=field
     if (field_name=='mass') then
       call grd_chksum3(grd, grd%mass_on_ocean, 'mass bergs (incr)')
       call grd_chksum2(grd, grd%tmp, 'mass out (incr)')
-  elseif (field_name=='area') then
+    elseif (field_name=='area') then
       call grd_chksum3(grd, grd%area_on_ocean, 'area bergs (incr)')
       call grd_chksum2(grd, grd%tmp, 'area out (incr)')
     endif
-  endif
-
-  if (.not.(within_model)) then
-    call mpp_clock_end(bergs%clock_int)
-    call mpp_clock_end(bergs%clock)
-  endif
-end subroutine icebergs_incr_mass
+ endif
+end subroutine sum_up_spread_fields
 
 ! ##############################################################################
 
@@ -3891,7 +3948,7 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
 real :: xdot3, ydot3
 real :: xdotn, ydotn
 real :: dt, dt_2, dt_6, dydl
-real :: static_berg, orientation
+real :: orientation
 logical :: bounced, on_tangential_plane, error_flag
 integer :: i, j 
 integer :: stderrunit
@@ -3914,11 +3971,8 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
     dt=bergs%dt
     dt_2=0.5*dt
 
-    static_berg=0.  !Initializing
     orientation=bergs%initial_orientation
     if ((bergs%iceberg_bonds_on) .and. (bergs%rotate_icebergs_for_mass_spreading)) call find_orientation_using_iceberg_bonds(grd,berg,orientation)
-    if (bergs%hexagonal_icebergs) static_berg=berg%static_berg  !Change this to use_old_restart=false when this is merged in
-    
 
         lonn = berg%lon ;   latn = berg%lat
         axn  = berg%axn ;   ayn  = berg%ayn
@@ -3934,8 +3988,7 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
         !Note, the mass scaling is equal to 1 (rather than 0.25 as in RK), since
         !this is only called once in Verlet stepping.
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 1.0*berg%mass_scaling,berg%length*berg%width, &
-                         bergs%use_old_spreading, bergs%hexagonal_icebergs,orientation,static_berg, berg%uvel, berg%vvel)
+          call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 1.0*berg%mass_scaling,berg%length*berg%width, berg%thickness)
 
         ! Calling the acceleration   (note that the velocity is converted to u_star inside the accel script)
         call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn, ayn, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
@@ -4017,7 +4070,6 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
 real :: x4, xdot4, xddot4, y4, ydot4, yddot4, xddot4n, yddot4n
 real :: xn, xdotn, xddotn, yn, ydotn, yddotn, xddotnn, yddotnn
 real :: dt, dt_2, dt_6, dydl
-real :: static_berg,orientation
 integer :: i1,j1,i2,j2,i3,j3,i4,j4
 integer :: stderrunit
 logical :: bounced, on_tangential_plane, error_flag
@@ -4044,11 +4096,6 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
     dt_2=0.5*dt
     dt_6=dt/6.
     
-    static_berg=0.  !Initializing
-    orientation=bergs%initial_orientation
-    if ((bergs%iceberg_bonds_on) .and. (bergs%rotate_icebergs_for_mass_spreading)) call find_orientation_using_iceberg_bonds(grd,berg,orientation) !Not sure if this works with Runge Kutta
-    if (bergs%hexagonal_icebergs) static_berg=berg%static_berg  !Change this to use_old_restart=false when this is merged in
-
         i=berg%ine
         j=berg%jne
         xi=berg%xi
@@ -4058,8 +4105,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         if ((berg%lat>89.) .and. (bergs%grd%grid_is_latlon)) on_tangential_plane=.true.
         i1=i;j1=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, &
-                         bergs%use_old_spreading, bergs%hexagonal_icebergs,orientation,static_berg, berg%uvel, berg%vvel)
+          call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, berg%thickness)
 
         ! Loading past accelerations - Alon
         axn=berg%axn; ayn=berg%ayn !Alon
@@ -4097,8 +4143,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         call adjust_index_and_ground(grd, lon2, lat2, uvel2, vvel2, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)
         i2=i; j2=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, &
-                         bergs%use_old_spreading, bergs%hexagonal_icebergs,orientation,static_berg, berg%uvel, berg%vvel)
+          call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, berg%thickness)
         ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon2,lat2,x2,y2)
         if (.not.error_flag) then
           if (debug .and. .not. is_point_in_cell(bergs%grd, lon2, lat2, i, j)) error_flag=.true.
@@ -4155,8 +4200,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         call adjust_index_and_ground(grd, lon3, lat3, uvel3, vvel3, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)
         i3=i; j3=j
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, &
-                         bergs%use_old_spreading, bergs%hexagonal_icebergs,orientation,static_berg, berg%uvel, berg%vvel)
+          call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, berg%thickness)
         ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon3,lat3,x3,y3)
         if (.not.error_flag) then
           if (debug .and. .not. is_point_in_cell(bergs%grd, lon3, lat3, i, j)) error_flag=.true.
@@ -4289,8 +4333,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
         i=i1;j=j1;xi=berg%xi;yj=berg%yj
         call adjust_index_and_ground(grd, lonn, latn, uveln, vveln, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)
         if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(grd, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, &
-                         bergs%use_old_spreading, bergs%hexagonal_icebergs,orientation,static_berg, berg%uvel, berg%vvel)
+          call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, berg%thickness)
   
         if (.not.error_flag) then
           if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j)) error_flag=.true.
@@ -4848,6 +4891,7 @@ subroutine icebergs_end(bergs)
   deallocate(bergs%grd%bergy_melt)
   deallocate(bergs%grd%bergy_mass)
   deallocate(bergs%grd%spread_mass)
+  deallocate(bergs%grd%spread_mass_old)
   deallocate(bergs%grd%spread_area)
   deallocate(bergs%grd%virtual_area)
   deallocate(bergs%grd%mass)
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 123eee0..b04b063 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -117,6 +117,7 @@ module ice_bergs_framework
   real, dimension(:,:), pointer :: bergy_melt=>null() ! Melting rate of bergy bits (kg/s/m^2)
   real, dimension(:,:), pointer :: bergy_mass=>null() ! Mass distribution of bergy bits (kg/s/m^2)
   real, dimension(:,:), pointer :: spread_mass=>null() ! Mass of icebergs after spreading (kg/m^2)
+  real, dimension(:,:), pointer :: spread_mass_old=>null() ! Mass of icebergs after spreading old (kg/m^2)
   real, dimension(:,:), pointer :: spread_area=>null() ! Area of icebergs after spreading (m^2/m^2)
   real, dimension(:,:), pointer :: u_iceberg=>null() ! Average iceberg velocity in grid cell (mass weighted - but not spread mass weighted)
   real, dimension(:,:), pointer :: v_iceberg=>null() ! Average iceberg velocity in grid cell (mass weighted - but not spread mass weighted)
@@ -149,7 +150,7 @@ module ice_bergs_framework
   integer :: id_mass=-1, id_ui=-1, id_vi=-1, id_ua=-1, id_va=-1, id_sst=-1, id_cn=-1, id_hi=-1
   integer :: id_bergy_src=-1, id_bergy_melt=-1, id_bergy_mass=-1, id_berg_melt=-1
   integer :: id_rmean_calving=-1, id_rmean_calving_hflx=-1
-  integer :: id_mass_on_ocn=-1, id_area_on_ocn=-1, id_spread_mass=-1, id_spread_area=-1
+  integer :: id_spread_mass=-1, id_spread_area=-1
   integer :: id_ssh=-1, id_fax=-1, id_fay=-1
   integer :: id_count=-1, id_chksum=-1, id_u_iceberg=-1, id_v_iceberg=-1, id_sss=-1, id_ustar_iceberg
   integer :: id_spread_uvel=-1, id_spread_vvel=-1
@@ -561,6 +562,7 @@ subroutine ice_bergs_framework_init(bergs, &
   allocate( grd%bergy_melt(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%bergy_melt(:,:)=0.
   allocate( grd%bergy_mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%bergy_mass(:,:)=0.
   allocate( grd%spread_mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_mass(:,:)=0.
+  allocate( grd%spread_mass_old(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_mass_old(:,:)=0.
   allocate( grd%spread_area(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_area(:,:)=0.
   allocate( grd%u_iceberg(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%u_iceberg(:,:)=0.
   allocate( grd%v_iceberg(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%v_iceberg(:,:)=0.
@@ -924,10 +926,6 @@ subroutine ice_bergs_framework_init(bergs, &
      'Virtual coverage by icebergs', 'm^2')
   grd%id_mass=register_diag_field('icebergs', 'mass', axes, Time, &
      'Iceberg density field', 'kg/(m^2)')
-!  grd%id_mass_on_ocn=register_diag_field('icebergs', 'mass_on_ocean', axes, Time, &
-!     'Iceberg density field felt by ocean', 'kg/(m^2)')
-!  grd%id_area_on_ocn=register_diag_field('icebergs', 'area_on_ocean', axes, Time, &
-!     'Iceberg area field felt by ocean', 'm^2/(m^2)')
   grd%id_stored_ice=register_diag_field('icebergs', 'stored_ice', axes3d, Time, &
      'Accumulated ice mass by class', 'kg')
   grd%id_real_calving=register_diag_field('icebergs', 'real_calving', axes3d, Time, &

From 74e5f1937b3996fa80c00442982cb3ee4fd16ce4 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Thu, 13 Oct 2016 13:38:18 -0400
Subject: [PATCH 183/361] Fixed the part of the code which restricts melting to
 ocean thicknesses less than a threshold value. The ocean thickness is now
 calculated by subtracting the ocean depth from the iceshelf draft (while
 previously we were subtracting ocean depth from ice shelf thickness)

---
 icebergs.F90 | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index d4a79ef..53162b7 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1176,7 +1176,8 @@ subroutine thermodynamics(bergs)
         Mb=max(Mb,0.) !No refreezing allowed for now
         !Set melt to zero if ocean is too thin.
         if ((bergs%melt_cutoff >=0.) .and. (bergs%apply_thickness_cutoff_to_bergs_melt)) then
-          if ((grd%ocean_depth(i,j)-this%thickness) < bergs%melt_cutoff) then
+          Dn=(bergs%rho_bergs/rho_seawater)*this%thickness ! draught (keel depth)
+          if ((grd%ocean_depth(i,j)-Dn) < bergs%melt_cutoff) then
             Mb=0.
           endif
         endif
@@ -1386,7 +1387,7 @@ subroutine create_gridded_icebergs_fields(bergs)
 real :: Hocean, Dn,Tn,dvo, mass_tmp 
 real :: ustar_h, ustar
 real :: orientation
-real :: ave_thickness
+real :: ave_thickness, ave_draft
 real, dimension(bergs%grd%isd:bergs%grd%ied,bergs%grd%jsd:bergs%grd%jed)  :: spread_mass_tmp
 real :: tmp
 
@@ -1466,7 +1467,8 @@ subroutine create_gridded_icebergs_fields(bergs)
     do i=grd%isd,grd%ied ; do j=grd%jsd,grd%jed
       if ((bergs%melt_cutoff >=0.) .and. (grd%spread_area(i,j)>0.)) then
         ave_thickness=grd%spread_mass(i,j)/(grd%spread_area(i,j)*bergs%rho_bergs) 
-        if ((grd%ocean_depth(i,j)-ave_thickness) < bergs%melt_cutoff) then
+        ave_draft=ave_thickness*(bergs%rho_bergs/rho_seawater)
+        if ((grd%ocean_depth(i,j)-ave_draft) < bergs%melt_cutoff) then
           grd%floating_melt(i,j)=0.0
           grd%calving_hflx(i,j)=0.0
         endif

From ac7556eecff13b7632db01fbbb4fe8a1f7f3f917 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Mon, 17 Oct 2016 11:16:40 -0400
Subject: [PATCH 184/361] Replaced initialization of logical force_app

- The line "logical :: force_app = .false." only set force_app=.false.
  the very first time a send_bergs_to_other_pes() was called. This is
  bad practice. Replaced with explicit line 'force_app=.false.'
- No answer changes (luckily).
---
 icebergs_framework.F90 | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 85bd6d2..f2253d6 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -1072,10 +1072,11 @@ subroutine unpack_berg_from_buffer2(first, buff, n,grd, force_append)
   logical :: lres
   type(iceberg) :: localberg
   integer :: stderrunit
-  logical :: force_app = .false.
+  logical :: force_app
   ! Get the stderr unit number
   stderrunit = stderr()
 
+  force_app = .false.
   if(present(force_append)) force_app = force_append
      
     localberg%lon=buff%data(1,n)

From 2b7b4d2275ba035903bd98d2a6a7db7dd19f94fc Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Mon, 17 Oct 2016 16:03:03 -0400
Subject: [PATCH 185/361] (*)Fixed logic for xi,yj coord calc in polar cells

- Some logic used when calculation the non-dimensional position within
  a cell with a corner at the norht pole seemed to be back to front.
  Reversed the logic and was able pass bergs over PE boundaries in
  the northern hemisphere.
- Tests do not change answers but this should matter if bergs are ever
  at the north pole.
---
 icebergs_framework.F90 | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index f2253d6..c845941 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -2350,7 +2350,7 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
   if (max(y1,y2,y3,y4)<89.999) then
     call calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x, y, xi, yj, explain=explain)
   else
-    if (debug) write(stderrunit,*) 'diamonds, pos_within_cell: working in tangential plane!'
+!   if (debug) write(stderrunit,*) 'diamonds, pos_within_cell: working in tangential plane!'
     xx=(90.-y)*cos(x*pi_180)
     yy=(90.-y)*sin(x*pi_180)
     x1=(90.-y1)*cos(grd%lon(i-1,j-1)*pi_180)
@@ -2370,7 +2370,8 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
       endif
     endif
     call calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, xx, yy, xi, yj, explain=explain)
-    if (is_point_in_cell(grd, x, y, i, j)) then
+    if (.not. is_point_in_cell(grd, x, y, i, j)) then
+!was if (is_point_in_cell(grd, x, y, i, j)) then
       if (abs(xi-0.5)>0.5.or.abs(yj-0.5)>0.5) then
         ! Scale internal coordinates to be consistent with is_point_in_cell()
         ! Note: this is intended to fix the inconsistency between the tangent plane
@@ -2378,11 +2379,11 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
         fac=2.*max( abs(xi-0.5), abs(yj-0.5) ); fac=max(1., fac)
         xi=0.5+(xi-0.5)/fac
         yj=0.5+(yj-0.5)/fac
-        if (debug) call error_mesg('diamonds, pos_within_cell', 'in cell so scaling internal coordinates!', WARNING)
+ !      if (debug) call error_mesg('diamonds, pos_within_cell', 'in cell so scaling internal coordinates!', WARNING)
       endif
     else
-      if (abs(xi-0.5)<=0.5.and.abs(yj-0.5)<=0.5) then
-        if (debug) call error_mesg('diamonds, pos_within_cell', 'out of cell but coordinates <=0.5!', WARNING)
+      if (abs(xi-0.5)>0.5.and.abs(yj-0.5)>0.5) then
+        if (debug) call error_mesg('diamonds, pos_within_cell', 'in cell but coordinates >0.5!', WARNING)
       endif
     endif
   endif

From ee793fe49b48b06f74894fc316fc469534ffcc93 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Mon, 17 Oct 2016 16:04:48 -0400
Subject: [PATCH 186/361] Modified generate_bergs() used in testing

- Cleaned up artificial generation of bergs which was not setting
  the lon.lat consistently with xi,yj.
- No answer changes since this routine is only used to generate
  lots of bergs when debugging.
---
 icebergs_io.F90 | 58 ++++++++++++++++++++++++++++++++++++-------------
 1 file changed, 43 insertions(+), 15 deletions(-)

diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 60ed182..4c12449 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -871,6 +871,7 @@ subroutine generate_bergs(bergs,Time)
   integer :: iNg, jNg  !Total number of points gloablly in i and j direction
   type(iceberg) :: localberg ! NOT a pointer but an actual local variable
   integer :: iyr, imon, iday, ihr, imin, isec
+  logical :: lres
 
     ! For convenience
     grd=>bergs%grd
@@ -880,15 +881,16 @@ subroutine generate_bergs(bergs,Time)
     call get_date(Time, iyr, imon, iday, ihr, imin, isec)
 
     do j=grd%jsc,grd%jec; do i=grd%isc,grd%iec
-      if (grd%msk(i,j)>0. .and. abs(grd%latc(i,j))>60.) then
-        localberg%xi=0.5
-        localberg%yj=0.5
+      if (grd%msk(i,j)>0. .and. abs(grd%latc(i,j))>80.0) then
+        if (max(grd%lat(i,j),grd%lat(i-1,j),grd%lat(i,j-1),grd%lat(i-1,j-1))>89.999) cycle ! Cannot use this at Pole cells
+        localberg%xi=-999.
+        localberg%yj=-999.
         localberg%ine=i
         localberg%jne=j
-        localberg%lon=bilin(grd, grd%lon, i, j, localberg%xi, localberg%yj)
-        localberg%lat=bilin(grd, grd%lat, i, j, localberg%xi, localberg%yj)
-        localberg%lon_old=bilin(grd, grd%lon, i, j, localberg%xi, localberg%yj) !Alon
-        localberg%lat_old=bilin(grd, grd%lat, i, j, localberg%xi, localberg%yj) !Alon
+        localberg%lon=grd%lonc(i,j)
+        localberg%lat=grd%latc(i,j)
+        localberg%lon_old=localberg%lon
+        localberg%lat_old=localberg%lat
         localberg%mass=bergs%initial_mass(1)
         localberg%thickness=bergs%initial_thickness(1)
         localberg%width=bergs%initial_width(1)
@@ -909,26 +911,22 @@ subroutine generate_bergs(bergs,Time)
         localberg%byn=0. !Alon
 
         !Berg A
-        localberg%uvel=1.
-        localberg%vvel=0.
+        call loc_set_berg_pos(grd, 0.9, 0.5, 1., 0., localberg)
         localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
         grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
         call add_new_berg_to_list(bergs%first, localberg)
         !Berg B
-        localberg%uvel=-1.
-        localberg%vvel=0.
+        call loc_set_berg_pos(grd, 0.1, 0.5, -1., 0., localberg)
         localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
         grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
         call add_new_berg_to_list(bergs%first, localberg)
         !Berg C
-        localberg%uvel=0.
-        localberg%vvel=1.
+        call loc_set_berg_pos(grd, 0.5, 0.9, 0., 1., localberg)
         localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
         grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
         call add_new_berg_to_list(bergs%first, localberg)
         !Berg D
-        localberg%uvel=0.
-        localberg%vvel=-1.
+        call loc_set_berg_pos(grd, 0.5, 0.1, 0., -1., localberg)
         localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
         grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
         call add_new_berg_to_list(bergs%first, localberg)
@@ -941,6 +939,36 @@ subroutine generate_bergs(bergs,Time)
       write(*,'(a,i8,a)') 'diamonds, generate_bergs: ',bergs%nbergs_start,' were generated'
 
   end subroutine generate_bergs
+
+  subroutine loc_set_berg_pos(grd, xi, yj, uvel, vvel, berg)
+    type(icebergs_gridded), pointer :: grd
+    real, intent(in) :: xi, yj, uvel, vvel
+    type(iceberg), intent(inout) :: berg
+    integer :: i, j
+    logical :: lres
+    i = berg%ine ; j = berg%jne
+    if (max(grd%lat(i,j),grd%lat(i-1,j),grd%lat(i,j-1),grd%lat(i-1,j-1))>89.999) then
+      berg%lon=grd%lonc(i,j)
+      berg%lat=grd%latc(i,j)
+      berg%xi=0.5 ; berg%yj=0.5
+    else
+      berg%lon=bilin(grd, grd%lon, i, j, xi, yj)
+      berg%lat=bilin(grd, grd%lat, i, j, xi, yj)
+      berg%xi=xi ; berg%yj=yj
+    endif
+    berg%uvel=uvel ; berg%vvel=vvel
+    berg%lon_old=berg%lon ; berg%lat_old=berg%lat
+    berg%start_lon=berg%lon ; berg%start_lat=berg%lat
+    lres=pos_within_cell(grd, berg%lon, berg%lat, berg%ine, berg%jne, berg%xi, berg%yj)
+    if (.not. lres) then
+      lres=pos_within_cell(grd, berg%lon, berg%lat, berg%ine, berg%jne, berg%xi, berg%yj, explain=.true.)
+      write(0,*) lres, i, j, xi, yj, uvel, vvel
+      write(0,*) lres, berg%ine, berg%jne, berg%xi, berg%yj
+      write(0,*) 'bx=',berg%lon, 'gx=',grd%lon(i-1,j-1), grd%lon(i,j-1), grd%lon(i,j), grd%lon(i-1,j),'cx=', grd%lonc(i,j)
+      write(0,*) 'by=',berg%lat, 'gy=',grd%lat(i-1,j-1), grd%lat(i,j-1), grd%lat(i,j), grd%lat(i-1,j),'cy=', grd%latc(i,j)
+      stop 'generate_bergs, loc_set_berg_pos(): VERY FATAL!'
+    endif
+  end subroutine loc_set_berg_pos
   
 end subroutine read_restart_bergs
 ! ##############################################################################

From aef8a359008d078c1c72d4399c1dcc83cff8e1ad Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Tue, 18 Oct 2016 11:51:13 -0400
Subject: [PATCH 187/361] *Bug fix: Interpolated ice velocity used ocean
 velocity

- Commit cfa98aa42bf84ee196bf0678fa4dbbfde593654f included a bug fix
  where the meridional ice velocity component interpolated from a C
  grid was using the ocean velocity instead of the ice velocity.
- Re-implementing on dev/master in order to merge in other branches
  which already have the fix.
- Changes answers (only detected in SIS2_bergs_cgrid).
---
 icebergs.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 72b1f87..9844826 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1233,7 +1233,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
       grd%uo(I,J) = mask * 0.5*(uo(Iu,ju)+uo(Iu,ju+1))
       grd%ui(I,J) = mask * 0.5*(ui(Iu,ju)+ui(Iu,ju+1))
       grd%vo(I,J) = mask * 0.5*(vo(iv,Jv)+vo(iv+1,Jv))
-      grd%vi(I,J) = mask * 0.5*(vi(iv,Jv)+vo(iv+1,Jv))
+      grd%vi(I,J) = mask * 0.5*(vi(iv,Jv)+vi(iv+1,Jv))
     enddo ; enddo
   else
     call error_mesg('diamonds, iceberg_run', 'Unrecognized value of stagger!', FATAL)

From 447fe502f9f42bdf68b243e7505d8109ae3931db Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Tue, 18 Oct 2016 13:13:11 -0400
Subject: [PATCH 188/361] Fixed syntax issue with PGI line continuation

- A "\" escape character was being used instead of "&" line continuation
  that gnu and intel were letting through but which PGI complained.
- No answer changes.
---
 icebergs_framework.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index e333c2e..fdf0c54 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -2618,7 +2618,7 @@ subroutine show_all_bonds(bergs)
         !print *, 'Current:', berg%iceberg_num, berg%ine, berg%jne,berg%halo_berg, mpp_pe()
         if  (associated(current_bond%other_berg)) then
           if (current_bond%other_berg%iceberg_num .ne. current_bond%other_berg_num) then
-            print *, 'Bond matching', berg%iceberg_num,current_bond%other_berg%iceberg_num, current_bond%other_berg_num,\
+            print *, 'Bond matching', berg%iceberg_num,current_bond%other_berg%iceberg_num, current_bond%other_berg_num,&
             berg%halo_berg,current_bond%other_berg%halo_berg ,mpp_pe()
             call error_mesg('diamonds, show all bonds:', 'The bonds are not matching properly!', FATAL)
           endif

From 109b1f9c2558a7c4ed1a62b2cd471c10fde27a03 Mon Sep 17 00:00:00 2001
From: Robert Hallberg <Robert.Hallberg@noaa.gov>
Date: Thu, 27 Oct 2016 15:05:02 -0400
Subject: [PATCH 189/361] +Added code to handle A-grid wind stresses

  Added code to interpolate A-grid wind stresses to the B-grid locations used
by the iceberg code.  This new option is only triggered if the optional argument
str_stagger=AGRID, which would have previously caused an error.  The answers in
all existing test cases are unchanged, but they do not use this new option.
---
 icebergs.F90 | 22 +++++++++++++++++++++-
 1 file changed, 21 insertions(+), 1 deletion(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 9844826..2a8257b 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1125,7 +1125,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 real :: unused_calving, tmpsum, grdd_berg_mass, grdd_bergy_mass
 integer :: i, j, Iu, ju, iv, Jv, Iu_off, ju_off, iv_off, Jv_off
 real :: mask
-real, dimension(:,:), allocatable :: uC_tmp, vC_tmp
+real, dimension(:,:), allocatable :: uC_tmp, vC_tmp, uA_tmp, vA_tmp
 integer :: vel_stagger, str_stagger
 
 integer :: stderrunit
@@ -1269,6 +1269,26 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
       grd%va(I,J) = mask * 0.5*(vC_tmp(i,J)+vC_tmp(i+1,J))
     enddo ; enddo
     deallocate(uC_tmp, vC_tmp)
+  elseif (str_stagger == AGRID) then
+    ! Copy into arrays with local index conventions and halos.
+    allocate(uA_tmp(grd%isd:grd%ied,grd%jsd:grd%jed), &
+             vA_tmp(grd%isd:grd%ied,grd%jsd:grd%jed))
+    uA_tmp(:,:) = 0.0 ! This avoids uninitialized values that might remain in halo
+    vA_tmp(:,:) = 0.0 ! regions after the call to mpp_update_domains() below.
+    uA_tmp(grd%isc:grd%iec,grd%jsc:grd%jec) = tauxa(:,:)
+    vA_tmp(grd%isc:grd%iec,grd%jsc:grd%jec) = tauya(:,:)
+    call mpp_update_domains(uA_tmp, vA_tmp, grd%domain, gridtype=AGRID)
+    do I=grd%isc-1,grd%iec ; do J=grd%jsc-1,grd%jec
+      ! Interpolate wind stresses from A-grid tracer points to the corner B-grid points.
+      ! This masking is needed for now to prevent icebergs from running up on to land.
+      mask = min(grd%msk(i,j), grd%msk(i+1,j), grd%msk(i,j+1), grd%msk(i+1,j+1))
+      grd%ua(I,J) = mask * 0.25*((uA_tmp(i,j) + uA_tmp(i+1,j+1)) + &
+                                 (uA_tmp(i+1,j) + uA_tmp(i,j+1)))
+      grd%va(I,J) = mask * 0.25*((vA_tmp(i,j) + vA_tmp(i+1,j+1)) + &
+                                 (vA_tmp(i+1,j) + vA_tmp(i,j+1)))
+    enddo ; enddo
+    
+    deallocate(uA_tmp, vA_tmp)
   else
     call error_mesg('diamonds, iceberg_run', 'Unrecognized value of stress_stagger!', FATAL)
   endif

From 839a09fd53a37b4bbe571ee068122f5dd460e259 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Thu, 3 Nov 2016 16:01:20 -0400
Subject: [PATCH 190/361] Added multiple points for calling monitor_a_berg()

- Run-time option debug_a_berg_with_id was only enabling debugging/
  monitoring of a berg within the send_bergs_to_other_pes() routine.
  Now we can monitor a berg at the icebergs_run() level and watch
  a berg evolve through each step of the algorithm.
- No answer changes.
---
 icebergs.F90           | 17 +++++++++++++----
 icebergs_framework.F90 |  6 +-----
 2 files changed, 14 insertions(+), 9 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index c6f7e7f..910ea95 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -37,6 +37,7 @@ module ice_bergs
 use ice_bergs_framework, only: grd_chksum2,grd_chksum3
 use ice_bergs_framework, only: fix_restart_dates, offset_berg_dates
 use ice_bergs_framework, only: orig_read  ! Remove when backward compatibility no longer needed
+use ice_bergs_framework, only: monitor_a_berg
 
 use ice_bergs_io,        only: ice_bergs_io_init,write_restart,write_trajectory
 use ice_bergs_io,        only: read_restart_bergs,read_restart_bergs_orig,read_restart_calving
@@ -3088,18 +3089,22 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 
   call mpp_clock_begin(bergs%clock_cal)
   ! Calve excess stored ice into icebergs
+  if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, before calving()   ')
   call calve_icebergs(bergs)
   if (debug) call bergs_chksum(bergs, 'run bergs (calved)')
   if (debug) call checksum_gridded(bergs%grd, 's/r run after calving')
+  if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after calving()    ')
   call mpp_clock_end(bergs%clock_cal)
 
   ! For each berg, evolve
   call mpp_clock_begin(bergs%clock_mom)
 
   if (.not.bergs%Static_icebergs) then
-        call evolve_icebergs(bergs)
+    call evolve_icebergs(bergs)
+    if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after evolve()     ')
   endif
   call move_berg_between_cells(bergs)  !Markpoint6
+  if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after move_lists() ')
   if (debug) call bergs_chksum(bergs, 'run bergs (evolved)',ignore_halo_violation=.true.)
   if (debug) call checksum_gridded(bergs%grd, 's/r run after evolve')
   call mpp_clock_end(bergs%clock_mom)
@@ -3109,9 +3114,12 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   if (bergs%iceberg_bonds_on)  call  bond_address_update(bergs)
 
   call send_bergs_to_other_pes(bergs)
-  if ((bergs%interactive_icebergs_on) .or. (bergs%iceberg_bonds_on)) &
-  call update_halo_icebergs(bergs)
-  if (bergs%iceberg_bonds_on)  call connect_all_bonds(bergs)
+  if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after send_bergs() ')
+  if ((bergs%interactive_icebergs_on) .or. (bergs%iceberg_bonds_on)) then
+    call update_halo_icebergs(bergs)
+    if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after update_halo()')
+    if (bergs%iceberg_bonds_on)  call connect_all_bonds(bergs)
+  endif
   if (debug) call bergs_chksum(bergs, 'run bergs (exchanged)')
   if (debug) call checksum_gridded(bergs%grd, 's/r run after exchange')
   call mpp_clock_end(bergs%clock_com)
@@ -3129,6 +3137,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   ! Iceberg thermodynamics (melting) + rolling
   call mpp_clock_begin(bergs%clock_the)
   call thermodynamics(bergs)
+  if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after thermodyn()  ')
   if (debug) call bergs_chksum(bergs, 'run bergs (thermo)')
   if (debug) call checksum_gridded(bergs%grd, 's/r run after thermodynamics')
   call mpp_clock_end(bergs%clock_the)
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 78ae317..4411a45 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -72,7 +72,7 @@ module ice_bergs_framework
 public fix_restart_dates, offset_berg_dates
 public move_berg_between_cells
 public find_individual_iceberg
-
+public monitor_a_berg
 
 type :: icebergs_gridded
   type(domain2D), pointer :: domain ! MPP domain
@@ -1473,8 +1473,6 @@ subroutine send_bergs_to_other_pes(bergs)
     nbergs_start=count_bergs(bergs, with_halos=.true.)
   endif
 
-  if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'send_bergs_to_other_pes (top)')
-
   ! Find number of bergs that headed east/west
   nbergs_to_send_e=0
   nbergs_to_send_w=0
@@ -1658,8 +1656,6 @@ subroutine send_bergs_to_other_pes(bergs)
     nbergs_rcvd_from_n=0
   endif
 
-  if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'send_bergs_to_other_pes (end)')
-
   if (debug) then
     nbergs_end=count_bergs(bergs, with_halos=.true.)
     i=nbergs_rcvd_from_n+nbergs_rcvd_from_s+nbergs_rcvd_from_e+nbergs_rcvd_from_w &

From 5c80ddbfc797dce7d3df781c091f8d80c34b532a Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Thu, 3 Nov 2016 16:03:15 -0400
Subject: [PATCH 191/361] Tidied up formatting of print_berg() and warnings

- print_berg() now adds %iceberg_num to every line.
- formatted diagnostics from pos_within_cell() such that
  we can cut and paste into a python window.
- No answer changes.
---
 icebergs_framework.F90 | 55 ++++++++++++++++++++++++------------------
 1 file changed, 31 insertions(+), 24 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 4411a45..77976d1 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -2455,26 +2455,35 @@ subroutine print_berg(iochan, berg, label, il, jl)
 integer, optional, intent(in) :: il, jl !< Indices of cell berg should be in
 ! Local variables
 
-  write(iochan,'("diamonds, print_berg: ",a," pe=(",i3,") start lon,lat,yr,#,day,mass,hb=",2f10.4,i5,i12,f7.2,es12.4,f5.1)') &
-    label, mpp_pe(), berg%start_lon, berg%start_lat, &
-    berg%start_year, berg%iceberg_num, berg%start_day, berg%start_mass, berg%halo_berg
+  write(iochan,'("diamonds, print_berg: ",2a,i5,a,i12,a,2f10.4,i5,f7.2,es12.4,f5.1)') &
+    label, 'pe=(', mpp_pe(), ') #=', berg%iceberg_num, ' start lon,lat,yr,day,mass,hb=', &
+    berg%start_lon, berg%start_lat, berg%start_year, berg%start_day, berg%start_mass, berg%halo_berg
   if (present(il).and.present(jl)) then
-    write(iochan,'("diamonds, print_berg: ",a," pe=(",i3,a,2i5,3(a,2f14.8),a,2l2)') &
-      label, mpp_pe(), ') List i,j=',il,jl
+    write(iochan,'("diamonds, print_berg: ",2a,i5,a,i12,a,2i5)') &
+      label, 'pe=(', mpp_pe(), ') #=', berg%iceberg_num, ' List i,j=',il,jl
   endif
-  write(iochan,'("diamonds, print_berg: ",a," pe=(",i3,a,2i5,3(a,2f14.8),a,2l2)') &
-    label, mpp_pe(), ') i,j=',berg%ine, berg%jne, &
+  write(iochan,'("diamonds, print_berg: ",2a,i5,a,i12,a,2i5,a,2l2)') &
+    label, 'pe=(', mpp_pe(), ') #=', berg%iceberg_num, &
+    ' i,j=', berg%ine, berg%jne, &
+    ' p,n=', associated(berg%prev), associated(berg%next)
+  write(iochan,'("diamonds, print_berg: ",2a,i5,a,i12,3(a,2f14.8))') &
+    label, 'pe=(', mpp_pe(), ') #=', berg%iceberg_num, &
     ' xi,yj=', berg%xi, berg%yj, &
     ' lon,lat=', berg%lon, berg%lat, &
+    ' lon_old,lat_old=', berg%lon_old, berg%lat_old
+  write(iochan,'("diamonds, print_berg: ",2a,i5,a,i12,2(a,2f14.8))') &
+    label, 'pe=(', mpp_pe(), ') #=', berg%iceberg_num, &
     ' u,v=', berg%uvel, berg%vvel, &
+    ' uvel_old,vvel_old=', berg%uvel_old, berg%vvel_old
+  write(iochan,'("diamonds, print_berg: ",2a,i5,a,i12,2(a,2f14.8))') &
+    label, 'pe=(', mpp_pe(), ') #=', berg%iceberg_num, &
     ' axn,ayn=', berg%axn, berg%ayn, &
-    ' bxn,byn=', berg%bxn, berg%byn, &
-    ' uvel_old,vvel_old=', berg%uvel_old, berg%vvel_old, &
-    ' lon_old,lat_old=', berg%lon_old, berg%lat_old, &
-    ' p,n=', associated(berg%prev), associated(berg%next)
-  write(iochan,'("diamonds, print_berg: ",a," pe=(",i3,") ",6(a,2f14.8))') &
-    label, mpp_pe(), 'uo,vo=', berg%uo, berg%vo, 'ua,va=', berg%ua, berg%va, 'ui,vi=', berg%ui, berg%vi
-!Two lines above added by Alon
+    ' bxn,byn=', berg%bxn, berg%byn
+  write(iochan,'("diamonds, print_berg: ",2a,i5,a,i12,3(a,2f14.8))') &
+    label, 'pe=(', mpp_pe(), ') #=', berg%iceberg_num, &
+    ' uo,vo=', berg%uo, berg%vo, &
+    ' ua,va=', berg%ua, berg%va, &
+    ' ui,vi=', berg%ui, berg%vi
 end subroutine print_berg
 
 ! ##############################################################################
@@ -3594,10 +3603,9 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
 
   if (present(explain)) then
     if(explain) then
-    write(stderrunit,'(a,4f12.6)') 'pos_within_cell: x1..x4 ',x1, x2, x3, x4
-    write(stderrunit,'(a,2f12.6)') 'pos_within_cell: x ',x
-    write(stderrunit,'(a,4f12.6)') 'pos_within_cell: y1..y4 ',y1, y2, y3, y4
-    write(stderrunit,'(a,2f12.6)') 'pos_within_cell: y ',y
+    write(stderrunit,'(a,4(f12.6,a))') 'pos_within_cell: lon=[',x1,',',x2,',',x3,',',x4,']'
+    write(stderrunit,'(a,4(f12.6,a))') 'pos_within_cell: lat=[',y1,',',y2,',',y3,',',y4,']'
+    write(stderrunit,'(2(a,f12.6))') 'pos_within_cell: x,y=',x,',',y
     endif
   endif
 
@@ -3627,10 +3635,9 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
     y4=(90.-y4)*sin(grd%lon(i-1,j  )*pi_180)
     if (present(explain)) then
       if(explain) then
-      write(stderrunit,'(a,4f12.6)') 'pos_within_cell: x1..x4 ',x1,x2,x3,x4
-      write(stderrunit,'(a,2f12.6)') 'pos_within_cell: x',xx
-      write(stderrunit,'(a,4f12.6)') 'pos_within_cell: y1..y4 ',y1,y2,y3,y4
-      write(stderrunit,'(a,2f12.6)') 'pos_within_cell: y',yy
+      write(stderrunit,'(a,4(f12.6,a))') 'pos_within_cell: lon=[',x1,',',x2,',',x3,',',x4,']'
+      write(stderrunit,'(a,4(f12.6,a))') 'pos_within_cell: lat=[',y1,',',y2,',',y3,',',y4,']'
+      write(stderrunit,'(2(a,f12.6))') 'pos_within_cell: x,y=',xx,',',yy
       endif
     endif
     call calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, xx, yy, xi, yj, Lx,explain=explain)
@@ -3717,9 +3724,9 @@ subroutine calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x, y, xi, yj,Lx, explain)
       if (abs(yy1-0.5).lt.abs(yy2-0.5)) then; yj=yy1; else; yj=yy2; endif
       if (expl) write(stderrunit,'(a,1p3e12.4)') 'Roots for y = ',yy1,yy2,yj
     else
-      write(stderrunit,'(a,i3,4f8.2)') 'calc_xiyj: x1..x4 ',mpp_pe(),x1,x2,x3,x4
+      write(stderrunit,'(a,i3,a,4(f8.2,a))') 'calc_xiyj: ',mpp_pe(),'lon=[',x1,',',x2,',',x3,',',x4,']'
       write(stderrunit,'(a,i3,3f8.2)') 'calc_xiyj: x2..x4 - x1',mpp_pe(),x2-x1,x3-x1,x4-x1
-      write(stderrunit,'(a,i3,4f8.2)') 'calc_xiyj: y1..y4 ',mpp_pe(),y1,y2,y3,y4
+      write(stderrunit,'(a,i3,a,4(f8.2,a))') 'calc_xiyj: ',mpp_pe(),'lat=[',y1,',',y2,',',y3,',',y4,']'
       write(stderrunit,'(a,i3,3f8.2)') 'calc_xiyj: y2..y4 - x1',mpp_pe(),y2-y1,y3-y1,y4-y1
       write(stderrunit,'(a,i3,1p6e12.4)') 'calc_xiyj: coeffs alpha..kappa',mpp_pe(),alpha,beta,gamma,delta,epsilon,kappa
       write(stderrunit,'(a,i3)') 'calc_xiyj: b<0 in quadratic root solver!!!!',mpp_pe()

From 98c2f3b40cabbe349106df45ee0bf5e979d1d720 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Fri, 4 Nov 2016 15:50:55 -0400
Subject: [PATCH 192/361] *Revert previous logic update for polar cells

- In commit 2b7b4d2275b we updated the code and broke things!
  We've reverted and added a lot more comments explaining what
  the logic is doing. It's right this time! :)
- Changes answers in ice_ocean_SIS2/SIS2_bergs_cgrid because
  we are generating bergs where as we weren't when we made
  the bad update (2b7b4d2275b).
---
 icebergs_framework.F90 | 46 ++++++++++++++++++++++++++----------------
 1 file changed, 29 insertions(+), 17 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 77976d1..d87596f 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -3599,7 +3599,6 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
   y3=grd%lat(i  ,j  )
   x4=grd%lon(i-1,j  )
   y4=grd%lat(i-1,j  )
-  
 
   if (present(explain)) then
     if(explain) then
@@ -3620,9 +3619,11 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
     yj=((y-y1)/dy)+0.5
 
   elseif ((max(y1,y2,y3,y4)<89.999) .or.(.not. grd%grid_is_latlon)) then
+    ! This returns non-dimensional position xi,yj for quad cells (not at a pole)
     call calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x, y, xi, yj, Lx, explain=explain)
   else
-!   if (debug) write(stderrunit,*) 'diamonds, pos_within_cell: working in tangential plane!'
+    ! One of the cell corners is at the north pole so we switch to a tangent plane with
+    ! co-latitude as a radial coordinate.
     xx=(90.-y)*cos(x*pi_180)
     yy=(90.-y)*sin(x*pi_180)
     x1=(90.-y1)*cos(grd%lon(i-1,j-1)*pi_180)
@@ -3640,21 +3641,29 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
       write(stderrunit,'(2(a,f12.6))') 'pos_within_cell: x,y=',xx,',',yy
       endif
     endif
+    ! Calculate non-dimensional position xi,yj within a quad in the tangent plane.
+    ! This quad has straight sides in the plane and so is not the same on the
+    ! projection of the spherical quad.
     call calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, xx, yy, xi, yj, Lx,explain=explain)
-    if (.not. is_point_in_cell(grd, x, y, i, j)) then
-!was if (is_point_in_cell(grd, x, y, i, j)) then
+    if (is_point_in_cell(grd, x, y, i, j)) then
+      ! The point is within the spherical quad
       if (abs(xi-0.5)>0.5.or.abs(yj-0.5)>0.5) then
-        ! Scale internal coordinates to be consistent with is_point_in_cell()
+        ! If the non-dimensional position is found to be outside (possible because the
+        ! projection of the spherical quad and the quad in the tangent plane are different)
+        ! then scale non-dimensional coordinates to be consistent with is_point_in_cell()
         ! Note: this is intended to fix the inconsistency between the tangent plane
-        ! and lat-lon calculations
-        fac=2.*max( abs(xi-0.5), abs(yj-0.5) ); fac=max(1., fac)
+        ! and lat-lon calculations and is a work around only for the four polar cells.
+        fac=2.1*max( abs(xi-0.5), abs(yj-0.5) ); fac=max(1., fac)
         xi=0.5+(xi-0.5)/fac
         yj=0.5+(yj-0.5)/fac
- !      if (debug) call error_mesg('diamonds, pos_within_cell', 'in cell so scaling internal coordinates!', WARNING)
+        if (debug) call error_mesg('diamonds, pos_within_cell', 'in cell but scaling internal coordinates!', WARNING)
       endif
     else
-      if (abs(xi-0.5)>0.5.and.abs(yj-0.5)>0.5) then
-        if (debug) call error_mesg('diamonds, pos_within_cell', 'in cell but coordinates >0.5!', WARNING)
+      ! The point is not inside the spherical quad
+      if (abs(xi-0.5)<0.5.and.abs(yj-0.5)<0.5) then
+        ! The projection of the spherical quad onto the tangent plane should be larger than
+        ! quad in the tangent plane so we should never be able to get here.
+        call error_mesg('diamonds, pos_within_cell', 'not in cell but coordinates <0.5!', FATAL)
       endif
     endif
   endif
@@ -3663,17 +3672,20 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
     if(explain) write(stderrunit,'(a,2f12.6)') 'pos_within_cell: xi,yj=',xi,yj
   endif
 
- !if (.not. is_point_in_cell(grd, x, y, i, j) ) then
- !   write(stderrunit,'(a,i3,a,8f8.2,a)') 'diamonds, pos_within_cell: (',mpp_pe(),') ', &
- !                   x1, y1, x2, y2, x3, y3, x4, y4, ' NOT IN CELL!'
- !endif
-
+  ! Check for consistency with test for whether point is inside a polygon
+  pos_within_cell=is_point_in_cell(grd, x, y, i, j,explain=explain)
   if (xi.ge.0. .and. xi.le.1. .and. yj.ge.0. .and. yj.le.1.) then
-    pos_within_cell=is_point_in_cell(grd, x, y, i, j,explain=explain)
+    ! Based on coordinate, the point is out of cell
+    if (pos_within_cell .and. verbose) then
+      ! Based on is_point_in_cell() the point is within cell so we have an inconsistency
+      if (debug) call error_mesg('diamonds, pos_within_cell', 'pos_within_cell is in cell BUT is_point_in_cell disagrees!', WARNING)
+    endif
+  else
+    ! Based on coordinate, the point is within cell
     if (.not. pos_within_cell .and. verbose) then
+      ! Based on is_point_in_cell() the point is out of cell so we have an inconsistency
       if (debug) call error_mesg('diamonds, pos_within_cell', 'pos_within_cell is in cell BUT is_point_in_cell disagrees!', WARNING)
     endif
-   !pos_within_cell=.true. ! commenting this out makes pos_within_cell agree with is_point_in_cell
   endif
 
   contains

From 1f201f80ec9669e23acda611550556c0dcfcdc9f Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Sun, 6 Nov 2016 11:48:33 -0500
Subject: [PATCH 193/361] Support reading of old restarts on a field-by-field
 basis

- Fields axn, ayn, bxn, byn, iceberg_num, mass_of_bits, heat_density,
  halo_berg and static_berg are now optional in the restarts and
  are filled with a default value if missing on a read.
- Fields are only written if being used.
- No answer changes.
---
 icebergs_io.F90 | 142 +++++++++++++++++++++++++++++-------------------
 1 file changed, 86 insertions(+), 56 deletions(-)

diff --git a/icebergs_io.F90 b/icebergs_io.F90
index e176b15..2fe0766 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -209,10 +209,12 @@ subroutine write_restart(bergs)
   id = register_restart_field(bergs_restart,filename,'uvel',uvel,longname='zonal velocity',units='m/s')
   id = register_restart_field(bergs_restart,filename,'vvel',vvel,longname='meridional velocity',units='m/s')
   id = register_restart_field(bergs_restart,filename,'mass',mass,longname='mass',units='kg')
-  id = register_restart_field(bergs_restart,filename,'axn',axn,longname='explicit zonal acceleration',units='m/s^2') !Alon
-  id = register_restart_field(bergs_restart,filename,'ayn',ayn,longname='explicit meridional acceleration',units='m/s^2') !Alon
-  id = register_restart_field(bergs_restart,filename,'bxn',bxn,longname='inplicit zonal acceleration',units='m/s^2') !Alon
-  id = register_restart_field(bergs_restart,filename,'byn',byn,longname='implicit meridional acceleration',units='m/s^2') !Alon
+  if (.not. bergs%Runge_not_Verlet) then
+    id = register_restart_field(bergs_restart,filename,'axn',axn,longname='explicit zonal acceleration',units='m/s^2')
+    id = register_restart_field(bergs_restart,filename,'ayn',ayn,longname='explicit meridional acceleration',units='m/s^2')
+    id = register_restart_field(bergs_restart,filename,'bxn',bxn,longname='inplicit zonal acceleration',units='m/s^2')
+    id = register_restart_field(bergs_restart,filename,'byn',byn,longname='implicit meridional acceleration',units='m/s^2')
+  endif
   id = register_restart_field(bergs_restart,filename,'ine',ine,longname='i index',units='none')
   id = register_restart_field(bergs_restart,filename,'jne',jne,longname='j index',units='none')
   id = register_restart_field(bergs_restart,filename,'thickness',thickness,longname='thickness',units='m')
@@ -236,11 +238,12 @@ subroutine write_restart(bergs)
                                             longname='mass of bergy bits',units='kg')
   id = register_restart_field(bergs_restart,filename,'heat_density',heat_density, &
                                             longname='heat density',units='J/kg')
-  id = register_restart_field(bergs_restart,filename,'halo_berg',halo_berg, &
-                                            longname='halo_berg',units='dimensionless')
-  id = register_restart_field(bergs_restart,filename,'static_berg',static_berg, &
-                                            longname='static_berg',units='dimensionless')
-
+  if (bergs%interactive_icebergs_on .or. bergs%iceberg_bonds_on) &
+    id = register_restart_field(bergs_restart,filename,'halo_berg',halo_berg, &
+                                              longname='halo_berg',units='dimensionless')
+  if (bergs%static_icebergs) &
+    id = register_restart_field(bergs_restart,filename,'static_berg',static_berg, &
+                                              longname='static_berg',units='dimensionless')
 
   ! Write variables
    
@@ -479,28 +482,24 @@ subroutine read_restart_bergs_orig(bergs,Time)
   uvelid=inq_var(ncid, 'uvel')
   vvelid=inq_var(ncid, 'vvel')
   massid=inq_var(ncid, 'mass')
-  axnid=inq_var(ncid, 'axn') !Alon
-  aynid=inq_var(ncid, 'ayn') !Alon
-  bxnid=inq_var(ncid, 'bxn') !Alon
-  bynid=inq_var(ncid, 'byn') !Alon
+  axnid=inq_var(ncid, 'axn', unsafe=.true.)
+  aynid=inq_var(ncid, 'ayn', unsafe=.true.)
+  bxnid=inq_var(ncid, 'bxn', unsafe=.true.)
+  bynid=inq_var(ncid, 'byn', unsafe=.true.)
   thicknessid=inq_var(ncid, 'thickness')
   widthid=inq_var(ncid, 'width')
   lengthid=inq_var(ncid, 'length')
   start_lonid=inq_var(ncid, 'start_lon')
   start_latid=inq_var(ncid, 'start_lat')
   start_yearid=inq_var(ncid, 'start_year')
-  if (bergs%read_old_restarts) then
-    iceberg_numid=-1
-  else
-    iceberg_numid=inq_var(ncid, 'icberg_num')
-  endif
+  iceberg_numid=inq_var(ncid, 'icberg_num', unsafe=.true.)
   start_dayid=inq_var(ncid, 'start_day')
   start_massid=inq_var(ncid, 'start_mass')
   scaling_id=inq_var(ncid, 'mass_scaling')
-  halo_bergid=inq_var(ncid, 'halo_berg')
-  static_bergid=inq_var(ncid, 'static_berg')
-  mass_of_bits_id=inq_var(ncid, 'mass_of_bits',unsafe=.true.)
-  heat_density_id=inq_var(ncid, 'heat_density',unsafe=.true.)
+  halo_bergid=inq_var(ncid, 'halo_berg', unsafe=.true.)
+  static_bergid=inq_var(ncid, 'static_berg', unsafe=.true.)
+  mass_of_bits_id=inq_var(ncid, 'mass_of_bits', unsafe=.true.)
+  heat_density_id=inq_var(ncid, 'heat_density', unsafe=.true.)
   ineid=inq_var(ncid, 'ine',unsafe=.true.)
   jneid=inq_var(ncid, 'jne',unsafe=.true.)
 
@@ -539,36 +538,29 @@ subroutine read_restart_bergs_orig(bergs,Time)
       localberg%uvel=get_double(ncid, uvelid, k)
       localberg%vvel=get_double(ncid, vvelid, k)
       localberg%mass=get_double(ncid, massid, k)
-      localberg%axn=get_double(ncid, axnid, k) !Alon
-      localberg%ayn=get_double(ncid, aynid, k) !Alon
-      localberg%bxn=get_double(ncid, bxnid, k) !Alon
-      localberg%byn=get_double(ncid, bynid, k) !Alon
+      localberg%axn=get_real_from_file(ncid, axnid, k, value_if_not_in_file=0.)
+      localberg%ayn=get_real_from_file(ncid, aynid, k, value_if_not_in_file=0.)
+      localberg%bxn=get_real_from_file(ncid, bxnid, k, value_if_not_in_file=0.)
+      localberg%byn=get_real_from_file(ncid, bynid, k, value_if_not_in_file=0.)
       localberg%thickness=get_double(ncid, thicknessid, k)
       localberg%width=get_double(ncid, widthid, k)
       localberg%length=get_double(ncid, lengthid, k)
       localberg%start_lon=get_double(ncid, start_lonid, k)
       localberg%start_lat=get_double(ncid, start_latid, k)
       localberg%start_year=get_int(ncid, start_yearid, k)
-      if (bergs%read_old_restarts) then
-        localberg%iceberg_num=-1
-      else
+      if (iceberg_numid>0) then
         localberg%iceberg_num=get_int(ncid, iceberg_numid, k)
+      else
+        localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
+        grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
       endif
       localberg%start_day=get_double(ncid, start_dayid, k)
       localberg%start_mass=get_double(ncid, start_massid, k)
       localberg%mass_scaling=get_double(ncid, scaling_id, k)
-      localberg%halo_berg=get_double(ncid, halo_bergid, k)
-      localberg%static_berg=get_double(ncid, static_bergid, k)
-      if (mass_of_bits_id>0) then ! Allow reading of older restart with no bergy bits
-        localberg%mass_of_bits=get_double(ncid, mass_of_bits_id, k)
-      else
-        localberg%mass_of_bits=0.
-      endif
-      if (heat_density_id>0) then ! Allow reading of older restart with no heat content
-        localberg%heat_density=get_double(ncid, heat_density_id, k)
-      else
-        localberg%heat_density=0.
-      endif
+      localberg%halo_berg=get_real_from_file(ncid, halo_bergid, k, value_if_not_in_file=0.)
+      localberg%static_berg=get_real_from_file(ncid, static_bergid, k, value_if_not_in_file=0.)
+      localberg%mass_of_bits=get_real_from_file(ncid, mass_of_bits_id, k, value_if_not_in_file=0.)
+      localberg%heat_density=get_real_from_file(ncid, heat_density_id, k, value_if_not_in_file=0.)
       if (really_debug) lres=is_point_in_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, explain=.true.)
       lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
      !call add_new_berg_to_list(bergs%first, localberg, quick=.true.)
@@ -610,6 +602,17 @@ subroutine read_restart_bergs_orig(bergs,Time)
   if (mpp_pe().eq.mpp_root_pe().and.verbose) write(*,'(a)') 'diamonds, read_restart_bergs: completed'
 
 contains
+
+  real function get_real_from_file(ncid, varid, k, value_if_not_in_file)
+  integer, intent(in) :: ncid, varid, k
+  real, optional :: value_if_not_in_file
+
+  if (varid<1.and.present(value_if_not_in_file)) then
+    get_real_from_file=value_if_not_in_file
+  else
+    get_real_from_file=get_double(ncid, ncid, k)
+  endif
+  end function get_real_from_file
   
   subroutine generate_bergs(bergs,Time)
   ! Arguments
@@ -797,10 +800,10 @@ subroutine read_restart_bergs(bergs,Time)
      call read_unlimited_axis(filename,'uvel',uvel,domain=grd%domain)
      call read_unlimited_axis(filename,'vvel',vvel,domain=grd%domain)
      call read_unlimited_axis(filename,'mass',mass,domain=grd%domain)
-     call read_unlimited_axis(filename,'axn',axn,domain=grd%domain) !Alon
-     call read_unlimited_axis(filename,'ayn',ayn,domain=grd%domain) !Alon
-     call read_unlimited_axis(filename,'bxn',bxn,domain=grd%domain) !Alon
-     call read_unlimited_axis(filename,'byn',byn,domain=grd%domain) !Alon
+     call read_real_vector(filename,'axn',axn,grd%domain,value_if_not_in_file=0.)
+     call read_real_vector(filename,'ayn',ayn,grd%domain,value_if_not_in_file=0.)
+     call read_real_vector(filename,'bxn',bxn,grd%domain,value_if_not_in_file=0.)
+     call read_real_vector(filename,'byn',byn,grd%domain,value_if_not_in_file=0.)
      call read_unlimited_axis(filename,'thickness',thickness,domain=grd%domain)
      call read_unlimited_axis(filename,'width',width,domain=grd%domain)
      call read_unlimited_axis(filename,'length',length,domain=grd%domain)
@@ -809,18 +812,14 @@ subroutine read_restart_bergs(bergs,Time)
      call read_unlimited_axis(filename,'start_day',start_day,domain=grd%domain)
      call read_unlimited_axis(filename,'start_mass',start_mass,domain=grd%domain)
      call read_unlimited_axis(filename,'mass_scaling',mass_scaling,domain=grd%domain)
-     call read_unlimited_axis(filename,'mass_of_bits',mass_of_bits,domain=grd%domain)
-     call read_unlimited_axis(filename,'halo_berg',halo_berg,domain=grd%domain)
-     call read_unlimited_axis(filename,'static_berg',static_berg,domain=grd%domain)
-     call read_unlimited_axis(filename,'heat_density',heat_density,domain=grd%domain)
+     call read_real_vector(filename,'mass_of_bits',mass_of_bits,domain=grd%domain,value_if_not_in_file=0.)
+     call read_real_vector(filename,'heat_density',heat_density,domain=grd%domain,value_if_not_in_file=0.)
      call read_unlimited_axis(filename,'ine',ine,domain=grd%domain)
      call read_unlimited_axis(filename,'jne',jne,domain=grd%domain)
      call read_unlimited_axis(filename,'start_year',start_year,domain=grd%domain)
-     if (bergs%read_old_restarts) then
-       iceberg_num(:)=-1
-     else
-       call read_unlimited_axis(filename,'iceberg_num',iceberg_num,domain=grd%domain)
-     endif
+     call read_real_vector(filename,'halo_berg',halo_berg,grd%domain,value_if_not_in_file=0.)
+     call read_int_vector(filename,'iceberg_num',iceberg_num,grd%domain,value_if_not_in_file=-1)
+     call read_real_vector(filename,'static_berg',static_berg,grd%domain,value_if_not_in_file=0.)
   endif
 
   ! Find approx outer bounds for tile
@@ -915,7 +914,11 @@ subroutine read_restart_bergs(bergs,Time)
       !call add_new_berg_to_list(bergs%first, localberg, quick=.true.)
 
       if (bergs%grd%area(localberg%ine,localberg%jne) .ne. 0)  then
-       call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg)
+        if (iceberg_num(k)==-1) then ! If using an old_restart then iceberg_num needs to be generated
+          localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(localberg%ine,localberg%jne))+(localberg%ine+(iNg*(localberg%jne-1)))
+          grd%iceberg_counter_grd(localberg%ine,localberg%jne)=grd%iceberg_counter_grd(localberg%ine,localberg%jne)+1
+        endif
+        call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg)
       else
         if (mpp_pe().eq.mpp_root_pe()) then
           print * , 'Grounded iceberg: ', lat(k),lon(k), iceberg_num(k)
@@ -988,8 +991,35 @@ subroutine read_restart_bergs(bergs,Time)
   call mpp_sum( bergs%bergy_mass_start )
   if (mpp_pe().eq.mpp_root_pe().and.verbose) write(*,'(a)') 'diamonds, read_restart_bergs: completed'
 
-
 contains
+
+  subroutine read_real_vector(filename, varname, values, domain, value_if_not_in_file)
+    character(len=*), intent(in)  :: filename
+    character(len=*), intent(in)  :: varname
+    real,             intent(out) :: values(:)
+    type(domain2D),   intent(in)  :: domain
+    real, optional,   intent(in)  :: value_if_not_in_file
+
+    if (present(value_if_not_in_file).and..not.field_exist(filename, varname)) then
+      values(:)=value_if_not_in_file
+    else
+      call read_unlimited_axis(filename,varname,values,domain=domain)
+    endif
+  end subroutine read_real_vector
+
+  subroutine read_int_vector(filename, varname, values, domain, value_if_not_in_file)
+    character(len=*),  intent(in)  :: filename
+    character(len=*),  intent(in)  :: varname
+    integer,           intent(out) :: values(:)
+    type(domain2D),    intent(in)  :: domain
+    integer, optional, intent(in)  :: value_if_not_in_file
+
+    if (present(value_if_not_in_file).and..not.field_exist(filename, varname)) then
+      values(:)=value_if_not_in_file
+    else
+      call read_unlimited_axis(filename,varname,values,domain=domain)
+    endif
+  end subroutine read_int_vector
   
   subroutine generate_bergs(bergs,Time)
   ! Arguments

From dbad95b3644f26ecdcdb0675540c94d0781342f7 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Sun, 6 Nov 2016 11:51:24 -0500
Subject: [PATCH 194/361] Obsoleted parameter read_old_restarts

- Now that old restarts are read/written optionally on a field-by-field
  basis, there is no need for the run-time parameter "read_old_restarts".
- The namelist is still present (for backwards compatibility) but it
  does nothing except issue a warning about being obsolete.
- No answer changes.
---
 icebergs.F90           | 6 +-----
 icebergs_framework.F90 | 6 ++----
 icebergs_io.F90        | 8 ++++----
 3 files changed, 7 insertions(+), 13 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 910ea95..f6bef1a 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -3826,11 +3826,7 @@ subroutine calve_icebergs(bergs)
           newberg%start_lon=newberg%lon
           newberg%start_lat=newberg%lat
           newberg%start_year=bergs%current_year
-          if (.not. bergs%read_old_restarts) then
-            newberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i+(iNg*(j-1)))  ! unique number for each iceberg
-          else
-            newberg%iceberg_num=-1
-          endif
+          newberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i+(iNg*(j-1)))  ! unique number for each iceberg
           newberg%start_day=bergs%current_yearday+ddt/86400.
           newberg%start_mass=bergs%initial_mass(k)
           newberg%mass_scaling=bergs%mass_scaling(k)
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index d87596f..e21e0cd 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -246,7 +246,6 @@ module ice_bergs_framework
   logical :: apply_thickness_cutoff_to_gridded_melt=.False.  !Prevents melt for ocean thickness below melt_cuttoff (applied to gridded melt fields)
   logical :: apply_thickness_cutoff_to_bergs_melt=.False.  !Prevents melt for ocean thickness below melt_cuttoff (applied to bergs)
   logical :: use_updated_rolling_scheme=.false. ! True to use the aspect ratio based rolling scheme rather than incorrect version of WM scheme   (set tip_parameter=1000. for correct WM scheme)
-  logical :: read_old_restarts=.true. ! If true, read restarts prior to grid_of_lists and iceberg_num innovation
   logical :: pass_fields_to_ocean_model=.False. !Iceberg area, mass and ustar fields are prepared to pass to ocean model
   logical :: use_mixed_layer_salinity_for_thermo=.False.  !If true, then model uses ocean salinity for 3 and 2 equation melt model.
   logical :: find_melt_using_spread_mass=.False.  !If true, then the model calculates ice loss by looping at the spread_mass before and after.
@@ -428,7 +427,7 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: critical_interaction_damping_on=.true.  !Sets the damping on relative iceberg velocity to critical value - Added by Alon 
 logical :: do_unit_tests=.false. ! Conduct some unit tests
 logical :: input_freq_distribution=.false. ! Flag to show if input distribution is freq or mass dist (=1 if input is a freq dist, =0 to use an input mass dist)
-logical :: read_old_restarts=.true. ! If true, read restarts prior to grid_of_lists and iceberg_num innovations
+logical :: read_old_restarts=.false. ! Legacy option that does nothing
 logical :: use_old_spreading=.true. ! If true, spreads iceberg mass as if the berg is one grid cell wide
 logical :: read_ocean_depth_from_file=.false. ! If true, ocean depth is read from a file.
 real, dimension(nclasses) :: initial_mass=(/8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11/) ! Mass thresholds between iceberg classes (kg)
@@ -864,7 +863,6 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%use_new_predictive_corrective=use_new_predictive_corrective  !Alon
   bergs%grounding_fraction=grounding_fraction
   bergs%add_weight_to_ocean=add_weight_to_ocean
-  bergs%read_old_restarts=read_old_restarts
   bergs%use_old_spreading=use_old_spreading
   bergs%debug_iceberg_with_id=debug_iceberg_with_id
   allocate( bergs%initial_mass(nclasses) ); bergs%initial_mass(:)=initial_mass(:)
@@ -876,7 +874,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%initial_width(:)=sqrt(initial_mass(:)/(LoW_ratio*rho_bergs*initial_thickness(:)))
   bergs%initial_length(:)=LoW_ratio*bergs%initial_width(:)
 
-  if (bergs%read_old_restarts) call error_mesg('diamonds, ice_bergs_framework_init', 'Setting "read_old_restarts=.true." can lead to non-reproducing checksums in restarts!', WARNING)
+  if (read_old_restarts) call error_mesg('diamonds, ice_bergs_framework_init', 'Setting "read_old_restarts=.true." is obsolete and does nothing!', WARNING)
 
   ! Diagnostics
   id_class = diag_axis_init('mass_class', initial_mass, 'kg','Z', 'iceberg mass')
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 2fe0766..f3eff4a 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -433,8 +433,8 @@ subroutine read_restart_bergs_orig(bergs,Time)
 
   ! For convenience
   grd=>bergs%grd
-  iNg=(grd%ieg-grd%isg+1) ! Total number of points globally in i direction, used with read_old_restarts=.true.
-  jNg=(grd%jeg-grd%jsg+1) ! Total number of points globally in j direction, used with read_old_restarts=.true.
+  iNg=(grd%ieg-grd%isg+1) ! Total number of points globally in i direction
+  jNg=(grd%jeg-grd%jsg+1) ! Total number of points globally in j direction
 
   ! Find a restart file
   multiPErestart=.false.
@@ -749,8 +749,8 @@ subroutine read_restart_bergs(bergs,Time)
 
   ! For convenience
   grd=>bergs%grd
-  iNg=(grd%ieg-grd%isg+1) ! Total number of points globally in i direction, used with read_old_restarts=.true.
-  jNg=(grd%jeg-grd%jsg+1) ! Total number of points globally in j direction, used with read_old_restarts=.true.
+  iNg=(grd%ieg-grd%isg+1) ! Total number of points globally in i direction
+  jNg=(grd%jeg-grd%jsg+1) ! Total number of points globally in j direction
 
   ! Zero out nbergs_in_file
   nbergs_in_file = 0

From dc0a56140d8d07d86f7665e0ea17a7051dec44ac Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 16 Nov 2016 19:08:31 -0500
Subject: [PATCH 195/361] Weeks and Mellor Rolling scheme has been fixed

---
 icebergs.F90 | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/icebergs.F90 b/icebergs.F90
index f6bef1a..cfa33ed 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1120,6 +1120,7 @@ subroutine thermodynamics(bergs)
 real :: Mnew, Mnew1, Mnew2, Hocean
 real :: Mbits, nMbits, dMbitsE, dMbitsM, Lbits, Abits, Mbb
 real :: tip_parameter
+real :: Delta, q
 integer :: i,j, stderrunit
 type(iceberg), pointer :: this, next
 real, parameter :: perday=1./86400.
@@ -1298,7 +1299,9 @@ subroutine thermodynamics(bergs)
           if (Wn>Ln) call swap_variables(Ln,Wn)  !Make sure that Wn is the smaller dimension
         
           if ( (.not.bergs%use_updated_rolling_scheme) .and. (bergs%tip_parameter>=999.) ) then    !Use Rolling Scheme 2
-            if ( Wn<sqrt(0.92*(Tn**2)-58.32*Tn) ) then
+            q=bergs%rho_bergs/rho_seawater
+            Delta=6.0
+            if (Wn<sqrt((6.0*q*(1-q)*(Tn**2))-(12*Delta*q*Tn))) then
                 call swap_variables(Tn,Wn)
             endif
           endif

From 256fe9ecf56f20d0ade75481a9bd453e79ce079a Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 23 Nov 2016 16:38:41 -0500
Subject: [PATCH 196/361] The model was writing to the icebergs_trajectories.nc
 file too many times. This was because the condition for sampling and writing
 the trajectory data did not account for the minutes and seconds. This means
 that when the time step is shorter than an hour, the modle sampled the
 trajectory many times.

This bug is corrected by adding the minutes and seconds to the condition for traj_sample and traj_write.
---
 icebergs.F90 | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index cfa33ed..5dc31a1 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -2878,21 +2878,20 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   ! Turn on sampling of trajectories, verbosity, budgets
   sample_traj=.false.
   if ( (bergs%traj_sample_hrs>0)  .and. (.not. bergs%ignore_traj) ) then
-     if (mod(24*iday+ihr,bergs%traj_sample_hrs).eq.0) sample_traj=.true.
-  end if
+    if (mod(60*60*24*iday+ 60*60*ihr + 60*imin + isec ,60*60*bergs%traj_sample_hrs).eq.0) &  sample_traj=.true.
+  endif
   write_traj=.false.
   if ((bergs%traj_write_hrs>0) .and. (.not. bergs%ignore_traj))  then
-     if (mod(24*iday+ihr,bergs%traj_write_hrs).eq.0) write_traj=.true.
-  end if
+     if (mod(60*60*24*iday+ 60*60*ihr + 60*imin + isec ,60*60*bergs%traj_write_hrs).eq.0) &  write_traj=.true.
+  endif
   lverbose=.false.
   if (bergs%verbose_hrs>0) then
-     if (mod(24*iday+ihr,bergs%verbose_hrs).eq.0) lverbose=verbose
-  end if
+     if (mod(24*iday+ihr+(imin/60.),float(bergs%verbose_hrs)).eq.0) lverbose=verbose
+  endif
   lbudget=.false.
   if (bergs%verbose_hrs>0) then
-     !if (mod(24*iday+ihr,bergs%verbose_hrs).eq.0) lbudget=budget
      if (mod(24*iday+ihr+(imin/60.),float(bergs%verbose_hrs)).eq.0) lbudget=budget  !Added minutes, so that it does not repeat when smaller time steps are used.:q
-  end if
+  endif
   if (mpp_pe()==mpp_root_pe().and.lverbose) write(*,'(a,3i5,a,3i5,a,i5,f8.3)') &
        'diamonds: y,m,d=',iyr, imon, iday,' h,m,s=', ihr, imin, isec, &
        ' yr,yrdy=', bergs%current_year, bergs%current_yearday

From ddbcdbc23e8c42acdad6827d5487fece53cf4be1 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Tue, 29 Nov 2016 10:39:31 -0500
Subject: [PATCH 197/361] Fixing is_point_in_cell routine for points near cell
 edge

A bug was found in the routine is_point_in_cell. For icebergs with a longitude very close to the edge of a the cell, the modulo arithemtic inside sum_sign_prod4 rounds off the berg position to be exactly on the edge of the cell. However, the one edge of the cell actually belows to the next cell over. Therefore after roundoff, the berg is found not to be inside the cell.

However, the 'crude bounds' inside is_point_in_cell mean that the adjacent cell (which the berg will be in after roundoff) does not make it through. This means that the icebergs is not found in either cell, and is not found at all.

This problem has been solved by weakening the crude bound test. A tolorance has been added to the crude bounds inside the routine is_point_in_cell. This tol=0.1 avoids excluding points which are very near to the edge of the cell.

This is a bit of an hack solution since the tolorance is in longitude coordinates. However it works for now.
---
 icebergs_framework.F90 | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index e21e0cd..fe65935 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -3360,6 +3360,7 @@ logical function is_point_in_cell(grd, x, y, i, j, explain)
 real :: Lx_2
 integer :: stderrunit
 real :: Lx
+real :: tol
 
   ! Get the stderr unit number
   stderrunit=stderr()
@@ -3386,11 +3387,14 @@ logical function is_point_in_cell(grd, x, y, i, j, explain)
            modulo(grd%lon(i-1,j  )-(x-Lx_2),Lx)+(x-Lx_2), &
            modulo(grd%lon(i  ,j  )-(x-Lx_2),Lx)+(x-Lx_2) )
 
-  if (x.lt.xlo .or. x.gt.xhi) return
+  ! The modolo function inside sum_sign_dot_prod leads to a roundoff.
+  !Adding adding a tolorance to the crude bounds avoids excluding the cell which
+  !would be correct after roundoff. This is a bit of a hack.
+  tol=0.1 
+  if (x.lt.(xlo-tol) .or. x.gt.(xhi+tol)) return
+
   ylo=min( grd%lat(i-1,j-1), grd%lat(i,j-1), grd%lat(i-1,j), grd%lat(i,j) )
   yhi=max( grd%lat(i-1,j-1), grd%lat(i,j-1), grd%lat(i-1,j), grd%lat(i,j) )
-
-
   if (y.lt.ylo .or. y.gt.yhi) return
   
   if ((grd%lat(i,j).gt.89.999).and. (grd%grid_is_latlon))   then

From 5b058b25a6d55cf5ff1884a2715672b75d1740df Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Tue, 29 Nov 2016 11:15:52 -0500
Subject: [PATCH 198/361] Added the posibility for periodic boundary conditions
 in the x-direction when using grid_is_regular.

This is done by adding modulo Lx to the routine which finds the position of an iceberg inside a cell.
---
 icebergs_framework.F90 | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index fe65935..fe57976 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -3583,10 +3583,12 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
 real :: x1,y1,x2,y2,x3,y3,x4,y4,xx,yy,fac
 integer :: stderrunit
 real :: Lx, dx,dy
+real :: Delta_x, Lx_2
 
   ! Get the stderr unit number
   stderrunit=stderr()
   Lx=grd%Lx
+  Lx_2=Lx/2
   pos_within_cell=.false.; xi=-999.; yj=-999.
   if (i-1<grd%isd) return
   if (j-1<grd%jsd) return
@@ -3617,7 +3619,9 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
     dy=abs((grd%lat(i  ,j  )-grd%lat(i  ,j-1  )))
     x1=grd%lon(i  ,j  )-(dx/2)
     y1=grd%lat(i  ,j  )-(dy/2)
-    xi=((x-x1)/dx)+0.5
+    Delta_x=modulo(x-(x1-Lx_2),Lx)+(x1-Lx_2)-x1
+    xi=((Delta_x)/dx)+0.5
+    !xi=((x-x1)/dx)+0.5
     yj=((y-y1)/dy)+0.5
 
   elseif ((max(y1,y2,y3,y4)<89.999) .or.(.not. grd%grid_is_latlon)) then

From 3b50802b4c83a3e67e7aef99ef24e55251601af3 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Thu, 1 Dec 2016 13:06:04 -0500
Subject: [PATCH 199/361] Corrected joined lines

- Code would not compile due to syntax errors!
---
 icebergs.F90 | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 5dc31a1..73077eb 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -2878,11 +2878,13 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   ! Turn on sampling of trajectories, verbosity, budgets
   sample_traj=.false.
   if ( (bergs%traj_sample_hrs>0)  .and. (.not. bergs%ignore_traj) ) then
-    if (mod(60*60*24*iday+ 60*60*ihr + 60*imin + isec ,60*60*bergs%traj_sample_hrs).eq.0) &  sample_traj=.true.
+    if (mod(60*60*24*iday+ 60*60*ihr + 60*imin + isec ,60*60*bergs%traj_sample_hrs).eq.0) &
+        sample_traj=.true.
   endif
   write_traj=.false.
   if ((bergs%traj_write_hrs>0) .and. (.not. bergs%ignore_traj))  then
-     if (mod(60*60*24*iday+ 60*60*ihr + 60*imin + isec ,60*60*bergs%traj_write_hrs).eq.0) &  write_traj=.true.
+     if (mod(60*60*24*iday+ 60*60*ihr + 60*imin + isec ,60*60*bergs%traj_write_hrs).eq.0) &
+         write_traj=.true.
   endif
   lverbose=.false.
   if (bergs%verbose_hrs>0) then
@@ -2890,7 +2892,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   endif
   lbudget=.false.
   if (bergs%verbose_hrs>0) then
-     if (mod(24*iday+ihr+(imin/60.),float(bergs%verbose_hrs)).eq.0) lbudget=budget  !Added minutes, so that it does not repeat when smaller time steps are used.:q
+     if (mod(24*iday+ihr+(imin/60.),float(bergs%verbose_hrs)).eq.0) lbudget=budget  !Added minutes, so that it does not repeat when smaller time steps are used.
   endif
   if (mpp_pe()==mpp_root_pe().and.lverbose) write(*,'(a,3i5,a,3i5,a,i5,f8.3)') &
        'diamonds: y,m,d=',iyr, imon, iday,' h,m,s=', ihr, imin, isec, &

From ec431c6c53cb54d59490ac9c2b7bfa2d4d770f38 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Thu, 8 Dec 2016 13:06:54 -0500
Subject: [PATCH 200/361] Added a flag which forces static_berg to be saved in
 the restart file.

Previously, static_berg was being saved when Static_icebergs was set to true. However, the flag Static_icebergs makes all icebergs static, while static_berg is a property of an individual iceberg, whcih makes it not move.
---
 icebergs_framework.F90 | 5 ++++-
 icebergs_io.F90        | 2 +-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index fe57976..324463b 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -261,6 +261,7 @@ module ice_bergs_framework
   logical :: allow_bergs_to_roll=.True. !Allows icebergs to roll over when rolling conditions are met
   logical :: ignore_missing_restart_bergs=.False.  !True Allows the model to ignorm icebergs missing in the restart. 
   logical :: Static_icebergs=.False.  !True= icebergs do no move
+  logical :: save_static_berg_field_in_restart=.False.  !If true, then static_berg is saved in restarts
   logical :: only_interactive_forces=.False.  !Icebergs only feel interactive forces, and not ocean, wind... 
   logical :: halo_debugging=.False.  !Use for debugging halos (remove when its working) 
   logical :: save_short_traj=.True.  !True saves only lon,lat,time,iceberg_num in iceberg_trajectory.nc 
@@ -416,6 +417,7 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: hexagonal_icebergs=.False. !True treats icebergs as rectangles, False as hexagonal elements (for the purpose of mass spreading)
 logical :: ignore_missing_restart_bergs=.False.  !True Allows the model to ignorm icebergs missing in the restart. 
 logical :: Static_icebergs=.False.  !True= icebergs do no move
+logical :: save_static_berg_field_in_restart=.False.  !If true, then static_berg is saved in restarts
 logical :: only_interactive_forces=.False.  !Icebergs only feel interactive forces, and not ocean, wind... 
 logical :: halo_debugging=.False.  !Use for debugging halos (remove when its working) 
 logical :: save_short_traj=.True.  !True saves only lon,lat,time,iceberg_num in iceberg_trajectory.nc 
@@ -447,7 +449,7 @@ subroutine ice_bergs_framework_init(bergs, &
          grid_is_regular,override_iceberg_velocities,u_override,v_override,add_iceberg_thickness_to_SSH,Iceberg_melt_without_decay,melt_icebergs_as_ice_shelf, &
          Use_three_equation_model,find_melt_using_spread_mass,use_mixed_layer_salinity_for_thermo,utide_icebergs,ustar_icebergs_bg,cdrag_icebergs, pass_fields_to_ocean_model, &
          const_gamma, Gamma_T_3EQ, ignore_traj, debug_iceberg_with_id,use_updated_rolling_scheme, tip_parameter, read_old_restarts, tau_calving, read_ocean_depth_from_file, melt_cutoff,&
-         apply_thickness_cutoff_to_gridded_melt, apply_thickness_cutoff_to_bergs_melt
+         apply_thickness_cutoff_to_gridded_melt, apply_thickness_cutoff_to_bergs_melt, save_static_berg_field_in_restart 
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -854,6 +856,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%hexagonal_icebergs=hexagonal_icebergs 
   bergs%ignore_missing_restart_bergs=ignore_missing_restart_bergs
   bergs%Static_icebergs=Static_icebergs 
+  bergs%save_static_berg_field_in_restart=save_static_berg_field_in_restart 
   bergs%only_interactive_forces=only_interactive_forces
   bergs%halo_debugging=halo_debugging
   bergs%iceberg_bonds_on=iceberg_bonds_on   !Alon
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index f3eff4a..823067f 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -241,7 +241,7 @@ subroutine write_restart(bergs)
   if (bergs%interactive_icebergs_on .or. bergs%iceberg_bonds_on) &
     id = register_restart_field(bergs_restart,filename,'halo_berg',halo_berg, &
                                               longname='halo_berg',units='dimensionless')
-  if (bergs%static_icebergs) &
+  if (bergs%save_static_berg_field_in_restart) &
     id = register_restart_field(bergs_restart,filename,'static_berg',static_berg, &
                                               longname='static_berg',units='dimensionless')
 

From 6be7dd4551048422e5904cdef1a436c5a3553158 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Mon, 12 Dec 2016 10:34:06 -0500
Subject: [PATCH 201/361] Removing halo_berg from restart_read

The variable halo_berg does not need to be read in from restart files since it should always have the value halo_berg=0 when being read in. The option to read in this variable has been removed.
---
 icebergs_io.F90 | 17 +++--------------
 1 file changed, 3 insertions(+), 14 deletions(-)

diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 823067f..64e7fbb 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -131,7 +131,6 @@ subroutine write_restart(bergs)
                                    start_mass,   &
                                    mass_scaling, &
                                    mass_of_bits, &
-                                   halo_berg,    &
                                    static_berg,  &
                                    heat_density
 
@@ -185,7 +184,6 @@ subroutine write_restart(bergs)
    allocate(mass_scaling(nbergs))
    allocate(mass_of_bits(nbergs))
    allocate(heat_density(nbergs))
-   allocate(halo_berg(nbergs))
    allocate(static_berg(nbergs))
 
    allocate(ine(nbergs))
@@ -238,9 +236,6 @@ subroutine write_restart(bergs)
                                             longname='mass of bergy bits',units='kg')
   id = register_restart_field(bergs_restart,filename,'heat_density',heat_density, &
                                             longname='heat density',units='J/kg')
-  if (bergs%interactive_icebergs_on .or. bergs%iceberg_bonds_on) &
-    id = register_restart_field(bergs_restart,filename,'halo_berg',halo_berg, &
-                                              longname='halo_berg',units='dimensionless')
   if (bergs%save_static_berg_field_in_restart) &
     id = register_restart_field(bergs_restart,filename,'static_berg',static_berg, &
                                               longname='static_berg',units='dimensionless')
@@ -262,7 +257,6 @@ subroutine write_restart(bergs)
       start_lon(i) = this%start_lon; start_lat(i) = this%start_lat
       start_year(i) = this%start_year; start_day(i) = this%start_day
       start_mass(i) = this%start_mass; mass_scaling(i) = this%mass_scaling
-      halo_berg(i) = this%halo_berg 
       static_berg(i) = this%static_berg 
       iceberg_num(i) = this%iceberg_num; 
       mass_of_bits(i) = this%mass_of_bits; heat_density(i) = this%heat_density
@@ -420,7 +414,7 @@ subroutine read_restart_bergs_orig(bergs,Time)
 integer :: axnid, aynid, uvel_oldid, vvel_oldid, bxnid, bynid
 integer :: massid, thicknessid, widthid, lengthid
 integer :: start_lonid, start_latid, start_yearid, iceberg_numid, start_dayid, start_massid
-integer :: scaling_id, mass_of_bits_id, heat_density_id, halo_bergid, static_bergid
+integer :: scaling_id, mass_of_bits_id, heat_density_id, static_bergid
 logical :: lres, found_restart, multiPErestart
 real :: lon0, lon1, lat0, lat1
 character(len=33) :: filename, filename_base
@@ -496,7 +490,6 @@ subroutine read_restart_bergs_orig(bergs,Time)
   start_dayid=inq_var(ncid, 'start_day')
   start_massid=inq_var(ncid, 'start_mass')
   scaling_id=inq_var(ncid, 'mass_scaling')
-  halo_bergid=inq_var(ncid, 'halo_berg', unsafe=.true.)
   static_bergid=inq_var(ncid, 'static_berg', unsafe=.true.)
   mass_of_bits_id=inq_var(ncid, 'mass_of_bits', unsafe=.true.)
   heat_density_id=inq_var(ncid, 'heat_density', unsafe=.true.)
@@ -557,7 +550,7 @@ subroutine read_restart_bergs_orig(bergs,Time)
       localberg%start_day=get_double(ncid, start_dayid, k)
       localberg%start_mass=get_double(ncid, start_massid, k)
       localberg%mass_scaling=get_double(ncid, scaling_id, k)
-      localberg%halo_berg=get_real_from_file(ncid, halo_bergid, k, value_if_not_in_file=0.)
+      localberg%halo_berg=0.
       localberg%static_berg=get_real_from_file(ncid, static_bergid, k, value_if_not_in_file=0.)
       localberg%mass_of_bits=get_real_from_file(ncid, mass_of_bits_id, k, value_if_not_in_file=0.)
       localberg%heat_density=get_real_from_file(ncid, heat_density_id, k, value_if_not_in_file=0.)
@@ -734,7 +727,6 @@ subroutine read_restart_bergs(bergs,Time)
                                    start_mass,   &
                                    mass_scaling, &
                                    mass_of_bits, &
-                                   halo_berg,    &
                                    static_berg,    &
                                    heat_density
 integer, allocatable, dimension(:) :: ine,       &
@@ -785,7 +777,6 @@ subroutine read_restart_bergs(bergs,Time)
      allocate(start_mass(nbergs_in_file))
      allocate(mass_scaling(nbergs_in_file))
      allocate(mass_of_bits(nbergs_in_file))
-     allocate(halo_berg(nbergs_in_file))
      allocate(static_berg(nbergs_in_file))
      allocate(heat_density(nbergs_in_file))
      allocate(ine(nbergs_in_file))
@@ -817,7 +808,6 @@ subroutine read_restart_bergs(bergs,Time)
      call read_unlimited_axis(filename,'ine',ine,domain=grd%domain)
      call read_unlimited_axis(filename,'jne',jne,domain=grd%domain)
      call read_unlimited_axis(filename,'start_year',start_year,domain=grd%domain)
-     call read_real_vector(filename,'halo_berg',halo_berg,grd%domain,value_if_not_in_file=0.)
      call read_int_vector(filename,'iceberg_num',iceberg_num,grd%domain,value_if_not_in_file=-1)
      call read_real_vector(filename,'static_berg',static_berg,grd%domain,value_if_not_in_file=0.)
   endif
@@ -904,7 +894,7 @@ subroutine read_restart_bergs(bergs,Time)
       localberg%start_mass=start_mass(k)
       localberg%mass_scaling=mass_scaling(k)
       localberg%mass_of_bits=mass_of_bits(k)
-      localberg%halo_berg=halo_berg(k)
+      localberg%halo_berg=0.
       localberg%static_berg=static_berg(k)
       localberg%heat_density=heat_density(k)
       localberg%first_bond=>null()
@@ -952,7 +942,6 @@ subroutine read_restart_bergs(bergs,Time)
                 start_mass,   &
                 mass_scaling, &
                 mass_of_bits, &
-                halo_berg,    &
                 static_berg,    &
                 heat_density )
      deallocate(           &

From b511e5ba8483beccf4ec9d4d58d8da9a01ab1fb5 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 14 Dec 2016 15:46:30 -0500
Subject: [PATCH 202/361] Applying modulo and point_within_xi_yj_bounds

When periodic boundary conditions are used, the modulo procedure is used a number of times. One consequence is that for large domains, applying modulo rounds off the iceberg position. This results in the iceberg position being found to be in a certain cell when is_point_in_cell is used, but not found to be in cell when considering xi, yi.

This bug was fixed by
A) Being more careful when looking at the inconsistancy between is_point_in_cell() and pos_within_cell()
B) Introducing code which only applies modulo (and hense roundoff) when Lx>0.

(This probably should have been two (or more) commits)

A) Addressing inconsistancy between is_point_in_cell and pos_within_cell:

1) A rountine subroutine is_point_within_xi_yj_bounds is been written which checks whether the calculated xi, yj have  0<=xi<1  and 0<=yi<1. If so, this means that the iceberg is in the cell according to its local variables.  This subroutine has been included so that we can remove if statements in other places in the code, to avoid using the wrong inequalities or strict inequalities.

1b) A few inequalities within the code have been replaced by is_point_within_xi_yj_bounds. This includes an inequality within pos_within_cell (inside the special case for the north pole), which was previously using a symetric inequality (inconsistant with in_point_in_cell).

2) Inside the pos_within_cell routine, the logic inside the check for consistancy was reversed.

2) Inside the pos_within_cell routine, the error message assosiated with an inconsistany was changed to a FATAL error, and is appied whenever debug is true. Some explanation output have also been added.

B) Addressing modulo arithemetic

1) A function has been written called apply_modulo_around_point(x, y, Lx). This function returns  modulo(x-(y-Lx_2),Lx)+(y-Lx_2) if Lx>0 , and x otherwise. (ie: gives the modula value of x within the interval [y-(Lx/2)  y+(Lx/2)]  , modulo Lx.

2) This function has been used to replace the modula arithemtic in almost all places in the code.

3) There is one remaining place where modlua arithmetic is used. This will be changed in a seperate commit to avoid making a mistake (since it is a little bit complicated). For this, we include an "if Lx>0", so that the code will run with Lx<0.

4) When grid_is_lat_lon =False, and Lx=360., Lx is set to -1, so that it will not be periodic. (Previously it was set to 1E14, which was assumed to be larger than the domain.
---
 icebergs.F90           |   8 +-
 icebergs_framework.F90 | 167 +++++++++++++++++++++++------------------
 2 files changed, 101 insertions(+), 74 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 73077eb..9b07a90 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -38,6 +38,7 @@ module ice_bergs
 use ice_bergs_framework, only: fix_restart_dates, offset_berg_dates
 use ice_bergs_framework, only: orig_read  ! Remove when backward compatibility no longer needed
 use ice_bergs_framework, only: monitor_a_berg
+use ice_bergs_framework, only: is_point_within_xi_yj_bounds
 
 use ice_bergs_io,        only: ice_bergs_io_init,write_restart,write_trajectory
 use ice_bergs_io,        only: read_restart_bergs,read_restart_bergs_orig,read_restart_calving
@@ -4579,6 +4580,7 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
 integer :: icount, i0, j0, inm, jnm
 real :: xi0, yj0, lon0, lat0
 integer :: stderrunit
+logical :: point_in_cell_using_xi_yj
 
   ! Get the stderr unit number
     stderrunit = stderr()
@@ -4596,7 +4598,9 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
   if (debug) then
     !Sanity check lret, xi and yj
     lret=is_point_in_cell(grd, lon, lat, i, j)
-    if (xi<0. .or. xi>1. .or. yj<0. .or. yj>1.) then
+    point_in_cell_using_xi_yj=is_point_within_xi_yj_bounds(xi,yj)
+    if (.not. point_in_cell_using_xi_yj) then
+
       if (lret) then
         write(stderrunit,*) 'diamonds, adjust: WARNING!!! lret=T but |xi,yj|>1',mpp_pe()
         write(stderrunit,*) 'diamonds, adjust: xi=',xi,' lon=',lon
@@ -4610,6 +4614,7 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
         lret=pos_within_cell(grd, lon, lat, i, j, xi, yj,explain=.true.)
         write(stderrunit,*) 'diamonds, adjust: fn pos_within_cell=',lret
         write(0,*) 'This should never happen!'
+        call error_mesg('adjust index, ','Iceberg is_point_in_cell=True but xi, yi are out of cell',FATAL)
         error=.true.; return
      endif
     else
@@ -4626,6 +4631,7 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
         lret=pos_within_cell(grd, lon, lat, i, j, xi, yj, explain=.true.)
         write(stderrunit,*) 'diamonds, adjust: fn pos_within_cell=',lret
         write(0,*) 'This should never happen!'
+        call error_mesg('adjust index, ','Iceberg is_point_in_cell=False but xi, yi are out of cell',FATAL)
         error=.true.; return
       endif
     endif
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 324463b..41ca386 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -73,6 +73,7 @@ module ice_bergs_framework
 public move_berg_between_cells
 public find_individual_iceberg
 public monitor_a_berg
+public is_point_within_xi_yj_bounds
 
 type :: icebergs_gridded
   type(domain2D), pointer :: domain ! MPP domain
@@ -688,33 +689,33 @@ subroutine ice_bergs_framework_init(bergs, &
     if (mpp_pe().eq.mpp_root_pe())  then
             call error_mesg('diamonds, framework', 'Since the lat/lon grid is off, the x-direction is being set as non-periodic. Set Lx not equal to 360 override.', WARNING) 
     endif
-    Lx=1E14
+    Lx=-1.
   endif
 
+
  !The fix to reproduce across PE layout change, from AJA
-  j=grd%jsc; do i=grd%isc+1,grd%ied
-  minl=grd%lon(i-1,j)-(Lx/2.)
-    if (abs(grd%lon(i,j)-(modulo(grd%lon(i,j)-minl,Lx)+minl))>(Lx/2.)) &
-    grd%lon(i,j)=modulo(grd%lon(i,j)-minl,Lx)+minl
-  enddo
-  j=grd%jsc; do i=grd%isc-1,grd%isd,-1
-    minl=grd%lon(i+1,j)-(Lx/2.)
-    if (abs(grd%lon(i,j)-(modulo(grd%lon(i,j)-minl,Lx)+minl))>(Lx/2.)) &
-    grd%lon(i,j)=modulo(grd%lon(i,j)-minl,Lx)+minl
-  enddo
-  do j=grd%jsc+1,grd%jed; do i=grd%isd,grd%ied
+  if (Lx>0.) then
+    j=grd%jsc; do i=grd%isc+1,grd%ied
+      minl=grd%lon(i-1,j)-(Lx/2.)
+      if (abs(grd%lon(i,j)-(modulo(grd%lon(i,j)-minl,Lx)+minl))>(Lx/2.)) &
+      grd%lon(i,j)=modulo(grd%lon(i,j)-minl,Lx)+minl
+    enddo
+    j=grd%jsc; do i=grd%isc-1,grd%isd,-1
+      minl=grd%lon(i+1,j)-(Lx/2.)
+      if (abs(grd%lon(i,j)-(modulo(grd%lon(i,j)-minl,Lx)+minl))>(Lx/2.)) &
+      grd%lon(i,j)=modulo(grd%lon(i,j)-minl,Lx)+minl
+    enddo
+    do j=grd%jsc+1,grd%jed; do i=grd%isd,grd%ied
       minl=grd%lon(i,j-1)-(Lx/2.)
       if (abs(grd%lon(i,j)-(modulo(grd%lon(i,j)-minl,Lx)+minl))>(Lx/2.)) &
       grd%lon(i,j)=modulo(grd%lon(i,j)-minl,Lx)+minl
-  enddo; enddo
-  do j=grd%jsc-1,grd%jsd,-1; do i=grd%isd,grd%ied
+    enddo; enddo
+    do j=grd%jsc-1,grd%jsd,-1; do i=grd%isd,grd%ied
       minl=grd%lon(i,j+1)-(Lx/2.)
       if (abs(grd%lon(i,j)-(modulo(grd%lon(i,j)-minl,Lx)+minl))>(Lx/2.)) &
       grd%lon(i,j)=modulo(grd%lon(i,j)-minl,Lx)+minl
-  enddo; enddo
-
-
-
+    enddo; enddo
+  endif
 
 
 
@@ -3197,7 +3198,7 @@ real function dcost(x1, y1, x2, y2,Lx)
   ! Local variables
   real :: x1m
 
-    x1m=modulo(x1-(x2-(Lx/2.)),Lx)+(x2-(Lx/2.))
+    x1m=apply_modulo_around_point(x1,x2,Lx)
   ! dcost=(x2-x1)**2+(y2-y1)**2
     dcost=(x2-x1m)**2+(y2-y1)**2
   end function dcost
@@ -3360,7 +3361,6 @@ logical function is_point_in_cell(grd, x, y, i, j, explain)
 logical, intent(in), optional :: explain
 ! Local variables
 real :: xlo, xhi, ylo, yhi
-real :: Lx_2
 integer :: stderrunit
 real :: Lx
 real :: tol
@@ -3368,7 +3368,6 @@ logical function is_point_in_cell(grd, x, y, i, j, explain)
   ! Get the stderr unit number
   stderrunit=stderr()
   Lx=grd%Lx
-  Lx_2=Lx/2.
 
   ! Safety check index bounds
   if (i-1.lt.grd%isd.or.i.gt.grd%ied.or.j-1.lt.grd%jsd.or.j.gt.grd%jed) then
@@ -3381,14 +3380,14 @@ logical function is_point_in_cell(grd, x, y, i, j, explain)
   is_point_in_cell=.false.
 
   ! Test crude bounds
-  xlo=min( modulo(grd%lon(i-1,j-1)-(x-Lx_2),Lx)+(x-Lx_2), &
-           modulo(grd%lon(i  ,j-1)-(x-Lx_2),Lx)+(x-Lx_2), &
-           modulo(grd%lon(i-1,j  )-(x-Lx_2),Lx)+(x-Lx_2), &
-           modulo(grd%lon(i  ,j  )-(x-Lx_2),Lx)+(x-Lx_2) )
-  xhi=max( modulo(grd%lon(i-1,j-1)-(x-Lx_2),Lx)+(x-Lx_2), &
-           modulo(grd%lon(i  ,j-1)-(x-Lx_2),Lx)+(x-Lx_2), &
-           modulo(grd%lon(i-1,j  )-(x-Lx_2),Lx)+(x-Lx_2), &
-           modulo(grd%lon(i  ,j  )-(x-Lx_2),Lx)+(x-Lx_2) )
+  xlo=min( apply_modulo_around_point(grd%lon(i-1,j-1)   ,x,  Lx), & 
+           apply_modulo_around_point(grd%lon(i  ,j-1)   ,x,  Lx), &
+           apply_modulo_around_point(grd%lon(i-1,j  )   ,x,  Lx), &
+           apply_modulo_around_point(grd%lon(i  ,j  )   ,x,  Lx) )
+  xhi=max( apply_modulo_around_point(grd%lon(i-1,j-1)   ,x,  Lx), & 
+           apply_modulo_around_point(grd%lon(i  ,j-1)   ,x,  Lx), &
+           apply_modulo_around_point(grd%lon(i-1,j  )   ,x,  Lx), &
+           apply_modulo_around_point(grd%lon(i  ,j  )   ,x,  Lx) )
 
   ! The modolo function inside sum_sign_dot_prod leads to a roundoff.
   !Adding adding a tolorance to the crude bounds avoids excluding the cell which
@@ -3449,26 +3448,17 @@ logical function sum_sign_dot_prod4(x0, y0, x1, y1, x2, y2, x3, y3, x, y,Lx, exp
 real :: l0,l1,l2,l3
 real :: xx0,xx1,xx2,xx3
 integer :: stderrunit
-real :: Lx_2
 
   ! Get the stderr unit number
   stderrunit=stderr()
-  Lx_2=Lx/2.
 
   sum_sign_dot_prod4=.false.
-  if (Lx .ge. 1E14 ) then
-    xx=x
-    xx0=x0
-    xx1=x1
-    xx2=x2
-    xx3=x3
-  else
-    xx=modulo(x-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x to within Lx_2 of x0
-    xx0=modulo(x0-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x0 to within Lx_2of xx
-    xx1=modulo(x1-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x1 to within Lx_2of xx
-    xx2=modulo(x2-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x2 to within Lx_2of xx
-    xx3=modulo(x3-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x3 to within Lx_2of xx
-  endif
+  xx= apply_modulo_around_point(x,x0,Lx)
+  xx0= apply_modulo_around_point(x0,x0,Lx)
+  xx1= apply_modulo_around_point(x1,x0,Lx)
+  xx2= apply_modulo_around_point(x2,x0,Lx)
+  xx3= apply_modulo_around_point(x3,x0,Lx)
+
 
   l0=(xx-xx0)*(y1-y0)-(y-y0)*(xx1-xx0)
   l1=(xx-xx1)*(y2-y1)-(y-y1)*(xx2-xx1)
@@ -3517,28 +3507,18 @@ logical function sum_sign_dot_prod5(x0, y0, x1, y1, x2, y2, x3, y3, x4, y4, x, y
 real :: l0,l1,l2,l3,l4
 real :: xx0,xx1,xx2,xx3,xx4
 integer :: stderrunit
-real :: Lx_2
 
   ! Get the stderr unit number
   stderrunit=stderr()
-  Lx_2=Lx/2.
 
   sum_sign_dot_prod5=.false.
-  if (Lx .ge. 1E14 ) then
-    xx=x
-    xx0=x0
-    xx1=x1
-    xx2=x2
-    xx3=x3
-    xx4=x4
-  else
-    xx=modulo(x-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x to within Lx_2of x0
-    xx0=modulo(x0-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x0 to within Lx_2 of xx
-    xx1=modulo(x1-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x1 to within Lx_2 of xx
-    xx2=modulo(x2-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x2 to within Lx_2 of xx
-    xx3=modulo(x3-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x3 to within Lx_2 of xx
-    xx4=modulo(x4-(x0-Lx_2),Lx)+(x0-Lx_2) ! Reference x4 to within Lx_2 of xx
-  endif
+  xx= apply_modulo_around_point(x,x0,Lx)
+  xx0= apply_modulo_around_point(x0,x0,Lx)
+  xx1= apply_modulo_around_point(x1,x0,Lx)
+  xx2= apply_modulo_around_point(x2,x0,Lx)
+  xx3= apply_modulo_around_point(x3,x0,Lx)
+  xx4= apply_modulo_around_point(x4,x0,Lx)
+
 
   l0=(xx-xx0)*(y1-y0)-(y-y0)*(xx1-xx0)
   l1=(xx-xx1)*(y2-y1)-(y-y1)*(xx2-xx1)
@@ -3586,12 +3566,12 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
 real :: x1,y1,x2,y2,x3,y3,x4,y4,xx,yy,fac
 integer :: stderrunit
 real :: Lx, dx,dy
-real :: Delta_x, Lx_2
+real :: Delta_x
+logical :: is_point_in_cell_using_xi_yj
 
   ! Get the stderr unit number
   stderrunit=stderr()
   Lx=grd%Lx
-  Lx_2=Lx/2
   pos_within_cell=.false.; xi=-999.; yj=-999.
   if (i-1<grd%isd) return
   if (j-1<grd%jsd) return
@@ -3622,7 +3602,9 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
     dy=abs((grd%lat(i  ,j  )-grd%lat(i  ,j-1  )))
     x1=grd%lon(i  ,j  )-(dx/2)
     y1=grd%lat(i  ,j  )-(dy/2)
-    Delta_x=modulo(x-(x1-Lx_2),Lx)+(x1-Lx_2)-x1
+
+    Delta_x= apply_modulo_around_point(x,x1,Lx)-x1
+
     xi=((Delta_x)/dx)+0.5
     !xi=((x-x1)/dx)+0.5
     yj=((y-y1)/dy)+0.5
@@ -3656,7 +3638,8 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
     call calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, xx, yy, xi, yj, Lx,explain=explain)
     if (is_point_in_cell(grd, x, y, i, j)) then
       ! The point is within the spherical quad
-      if (abs(xi-0.5)>0.5.or.abs(yj-0.5)>0.5) then
+      is_point_in_cell_using_xi_yj=is_point_within_xi_yj_bounds(xi,yj)
+      if (.not. is_point_in_cell_using_xi_yj) then
         ! If the non-dimensional position is found to be outside (possible because the
         ! projection of the spherical quad and the quad in the tangent plane are different)
         ! then scale non-dimensional coordinates to be consistent with is_point_in_cell()
@@ -3683,17 +3666,26 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
 
   ! Check for consistency with test for whether point is inside a polygon
   pos_within_cell=is_point_in_cell(grd, x, y, i, j,explain=explain)
-  if (xi.ge.0. .and. xi.le.1. .and. yj.ge.0. .and. yj.le.1.) then
+  is_point_in_cell_using_xi_yj=is_point_within_xi_yj_bounds(xi,yj)
+  if (is_point_in_cell_using_xi_yj) then
     ! Based on coordinate, the point is out of cell
-    if (pos_within_cell .and. verbose) then
+    if (.not. pos_within_cell) then
       ! Based on is_point_in_cell() the point is within cell so we have an inconsistency
-      if (debug) call error_mesg('diamonds, pos_within_cell', 'pos_within_cell is in cell BUT is_point_in_cell disagrees!', WARNING)
+      if (debug) then
+        write(stderrunit,'(a,1p6e12.4)') 'values of xi, yj ',xi, yj
+        pos_within_cell=is_point_in_cell(grd, x, y, i, j,explain=.True.)
+        call error_mesg('diamonds, pos_within_cell', 'pos_within_cell is False BUT is_point_in_cell disagrees!', FATAL)
+      endif
     endif
   else
     ! Based on coordinate, the point is within cell
-    if (.not. pos_within_cell .and. verbose) then
+    if (pos_within_cell) then
       ! Based on is_point_in_cell() the point is out of cell so we have an inconsistency
-      if (debug) call error_mesg('diamonds, pos_within_cell', 'pos_within_cell is in cell BUT is_point_in_cell disagrees!', WARNING)
+      if (debug) then
+        write(stderrunit,'(a,1p6e12.4)') 'values of xi, yj ',xi, yj
+        pos_within_cell=is_point_in_cell(grd, x, y, i, j,explain=.True.)
+        call error_mesg('diamonds, pos_within_cell', 'pos_within_cell is True BUT is_point_in_cell disagrees!', FATAL)
+      endif
     endif
   endif
 
@@ -3708,11 +3700,9 @@ subroutine calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x, y, xi, yj,Lx, explain)
   real :: alpha, beta, gamma, delta, epsilon, kappa, a, b, c, d, dx, dy, yy1, yy2
   logical :: expl=.false.
   integer :: stderrunit
-  real :: Lx_2
 
   ! Get the stderr unit number
   stderrunit=stderr()
-  Lx_2=Lx/2.
 
   expl=.false.
   if (present(explain)) then
@@ -3729,7 +3719,8 @@ subroutine calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x, y, xi, yj,Lx, explain)
   if (expl) write(stderrunit,'(a,1p6e12.4)') 'calc_xiyj: coeffs delta,epsilon,kappa',alpha,beta,gamma,delta,epsilon,kappa
 
   a=(kappa*beta-gamma*epsilon)
-  dx=modulo(x-(x1-Lx_2),Lx)+(x1-Lx_2)-x1
+  dx= apply_modulo_around_point(x,x1,Lx)-x1
+
   dy=y-y1
   b=(delta*beta-alpha*epsilon)-(kappa*dx-gamma*dy)
   c=(alpha*dy-delta*dx)
@@ -3790,6 +3781,36 @@ end function pos_within_cell
 
 ! ##############################################################################
 
+real function is_point_within_xi_yj_bounds(xi,yj)
+! Arguments
+real, intent(in) :: xi, yj
+! Local variables
+!Includes South and East boundaries, and excludes North and West  (double check this is the way that is needed)
+  is_point_within_xi_yj_bounds=.False.
+  if ((xi .ge. 0 )  .and.  (xi .lt. 1)) then
+    if ((yj .ge. 0 )  .and.  (yj .lt. 1)) then
+      is_point_within_xi_yj_bounds=.True.
+    endif
+  endif
+end function is_point_within_xi_yj_bounds
+
+real function apply_modulo_around_point(x,y,Lx)
+! Arguments
+real, intent(in) :: x ,y ,Lx
+!Local_variables
+real ::Lx_2
+!Gives the modula value of x in an interval [y-(Lx/2)  y+(Lx/2)]  , modulo Lx
+!If Lx<=0, then it returns x without applying modulo arithmetic.
+
+  if (Lx>0.) then
+    Lx_2=Lx/2.
+    apply_modulo_around_point=modulo(x-(y-Lx_2),Lx)+(y-Lx_2)
+  else
+    apply_modulo_around_point=x
+  endif
+
+end function apply_modulo_around_point
+
 subroutine check_position(grd, berg, label, il, jl)
 ! Arguments
 type(icebergs_gridded), pointer :: grd

From d73e935ac8a1a44c23a0efa5d4a7c969763e8f4a Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 14 Dec 2016 16:24:43 -0500
Subject: [PATCH 203/361] Refactoring a section of the code which uses modulo.

A small section of code has been refactored to use the apply_modulo_around_point function. The code should do exactly what it did before, but is now easier to read.
---
 icebergs_framework.F90 | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 41ca386..d034352 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -455,7 +455,7 @@ subroutine ice_bergs_framework_init(bergs, &
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
 type(icebergs_gridded), pointer :: grd
-real :: minl, big_number
+real :: lon_mod, big_number
 logical :: lerr
 integer :: stdlogunit, stderrunit
 real :: Total_mass  !Added by Alon 
@@ -696,24 +696,24 @@ subroutine ice_bergs_framework_init(bergs, &
  !The fix to reproduce across PE layout change, from AJA
   if (Lx>0.) then
     j=grd%jsc; do i=grd%isc+1,grd%ied
-      minl=grd%lon(i-1,j)-(Lx/2.)
-      if (abs(grd%lon(i,j)-(modulo(grd%lon(i,j)-minl,Lx)+minl))>(Lx/2.)) &
-      grd%lon(i,j)=modulo(grd%lon(i,j)-minl,Lx)+minl
+      lon_mod = apply_modulo_around_point(grd%lon(i,j),grd%lon(i-1,j),Lx)
+      if (abs(grd%lon(i,j)-lon_mod)>(Lx/2.)) &
+        grd%lon(i,j)= lon_mod
     enddo
     j=grd%jsc; do i=grd%isc-1,grd%isd,-1
-      minl=grd%lon(i+1,j)-(Lx/2.)
-      if (abs(grd%lon(i,j)-(modulo(grd%lon(i,j)-minl,Lx)+minl))>(Lx/2.)) &
-      grd%lon(i,j)=modulo(grd%lon(i,j)-minl,Lx)+minl
+      lon_mod = apply_modulo_around_point(grd%lon(i,j),grd%lon(i+1,j) ,Lx)
+      if (abs(grd%lon(i,j)-  lon_mod )>(Lx/2.)) &
+        grd%lon(i,j)= lon_mod
     enddo
     do j=grd%jsc+1,grd%jed; do i=grd%isd,grd%ied
-      minl=grd%lon(i,j-1)-(Lx/2.)
-      if (abs(grd%lon(i,j)-(modulo(grd%lon(i,j)-minl,Lx)+minl))>(Lx/2.)) &
-      grd%lon(i,j)=modulo(grd%lon(i,j)-minl,Lx)+minl
+      lon_mod = apply_modulo_around_point(grd%lon(i,j),grd%lon(i,j-1) ,Lx)
+      if (abs(grd%lon(i,j)-(lon_mod ))>(Lx/2.)) &
+        grd%lon(i,j)= lon_mod
     enddo; enddo
     do j=grd%jsc-1,grd%jsd,-1; do i=grd%isd,grd%ied
-      minl=grd%lon(i,j+1)-(Lx/2.)
-      if (abs(grd%lon(i,j)-(modulo(grd%lon(i,j)-minl,Lx)+minl))>(Lx/2.)) &
-      grd%lon(i,j)=modulo(grd%lon(i,j)-minl,Lx)+minl
+      lon_mod = apply_modulo_around_point(grd%lon(i,j),grd%lon(i,j+1) ,Lx)
+      if (abs(grd%lon(i,j)- lon_mod )>(Lx/2.)) &
+        grd%lon(i,j)=  lon_mod
     enddo; enddo
   endif
 

From fbb0feb58441e7c9d54915e4965b35e2303429b9 Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Thu, 15 Dec 2016 10:20:02 -0500
Subject: [PATCH 204/361] Removed the flag save_static_berg_field_in_restart

The flag save_static_berg_field_in_restart has been removed since it was frustrating to have to remember to include this flag every time in order to get a useable restart file.
Instead, the field static_berg is included in the restart file whenever there exists an iceberg which has static_berg > 0.

This means that in Production runs where this field is not being used, the field will not be saved.
---
 icebergs_framework.F90 |  5 +----
 icebergs_io.F90        | 14 +++++++++++++-
 2 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 324463b..05bfb31 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -261,7 +261,6 @@ module ice_bergs_framework
   logical :: allow_bergs_to_roll=.True. !Allows icebergs to roll over when rolling conditions are met
   logical :: ignore_missing_restart_bergs=.False.  !True Allows the model to ignorm icebergs missing in the restart. 
   logical :: Static_icebergs=.False.  !True= icebergs do no move
-  logical :: save_static_berg_field_in_restart=.False.  !If true, then static_berg is saved in restarts
   logical :: only_interactive_forces=.False.  !Icebergs only feel interactive forces, and not ocean, wind... 
   logical :: halo_debugging=.False.  !Use for debugging halos (remove when its working) 
   logical :: save_short_traj=.True.  !True saves only lon,lat,time,iceberg_num in iceberg_trajectory.nc 
@@ -417,7 +416,6 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: hexagonal_icebergs=.False. !True treats icebergs as rectangles, False as hexagonal elements (for the purpose of mass spreading)
 logical :: ignore_missing_restart_bergs=.False.  !True Allows the model to ignorm icebergs missing in the restart. 
 logical :: Static_icebergs=.False.  !True= icebergs do no move
-logical :: save_static_berg_field_in_restart=.False.  !If true, then static_berg is saved in restarts
 logical :: only_interactive_forces=.False.  !Icebergs only feel interactive forces, and not ocean, wind... 
 logical :: halo_debugging=.False.  !Use for debugging halos (remove when its working) 
 logical :: save_short_traj=.True.  !True saves only lon,lat,time,iceberg_num in iceberg_trajectory.nc 
@@ -449,7 +447,7 @@ subroutine ice_bergs_framework_init(bergs, &
          grid_is_regular,override_iceberg_velocities,u_override,v_override,add_iceberg_thickness_to_SSH,Iceberg_melt_without_decay,melt_icebergs_as_ice_shelf, &
          Use_three_equation_model,find_melt_using_spread_mass,use_mixed_layer_salinity_for_thermo,utide_icebergs,ustar_icebergs_bg,cdrag_icebergs, pass_fields_to_ocean_model, &
          const_gamma, Gamma_T_3EQ, ignore_traj, debug_iceberg_with_id,use_updated_rolling_scheme, tip_parameter, read_old_restarts, tau_calving, read_ocean_depth_from_file, melt_cutoff,&
-         apply_thickness_cutoff_to_gridded_melt, apply_thickness_cutoff_to_bergs_melt, save_static_berg_field_in_restart 
+         apply_thickness_cutoff_to_gridded_melt, apply_thickness_cutoff_to_bergs_melt 
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -856,7 +854,6 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%hexagonal_icebergs=hexagonal_icebergs 
   bergs%ignore_missing_restart_bergs=ignore_missing_restart_bergs
   bergs%Static_icebergs=Static_icebergs 
-  bergs%save_static_berg_field_in_restart=save_static_berg_field_in_restart 
   bergs%only_interactive_forces=only_interactive_forces
   bergs%halo_debugging=halo_debugging
   bergs%iceberg_bonds_on=iceberg_bonds_on   !Alon
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 64e7fbb..ef3b82d 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -111,6 +111,7 @@ subroutine write_restart(bergs)
 type(restart_file_type) :: bergs_restart
 type(restart_file_type) :: bergs_bond_restart
 integer :: nbergs, nbonds
+integer :: n_static_bergs
 logical :: check_bond_quality 
 type(icebergs_gridded), pointer :: grd
 real, allocatable, dimension(:) :: lon,          &
@@ -236,7 +237,18 @@ subroutine write_restart(bergs)
                                             longname='mass of bergy bits',units='kg')
   id = register_restart_field(bergs_restart,filename,'heat_density',heat_density, &
                                             longname='heat density',units='J/kg')
-  if (bergs%save_static_berg_field_in_restart) &
+
+  !Checking if any icebergs are static in order to decide whether to save static_berg
+  n_static_bergs = 0
+  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this))
+      n_static_bergs=n_static_bergs+this%static_berg
+      this=>this%next
+    enddo
+  enddo ; enddo
+  call mpp_sum(n_static_bergs) 
+  if (n_static_bergs .gt. 0) &
     id = register_restart_field(bergs_restart,filename,'static_berg',static_berg, &
                                               longname='static_berg',units='dimensionless')
 

From f789d232d393c33005c459355f8080baf19b7764 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Tue, 20 Dec 2016 11:51:48 -0500
Subject: [PATCH 205/361] Changed data type for is_point_within_xi_yj_bounds()

- Function is_point_within_xi_yj_bounds() was cast as a real but
  should have been/is now a logical.
---
 icebergs_framework.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 116551e..fcc4949 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -3778,7 +3778,7 @@ end function pos_within_cell
 
 ! ##############################################################################
 
-real function is_point_within_xi_yj_bounds(xi,yj)
+logical function is_point_within_xi_yj_bounds(xi,yj)
 ! Arguments
 real, intent(in) :: xi, yj
 ! Local variables

From a92391b8e380d52db6b4db4c925c62f5992b2c8c Mon Sep 17 00:00:00 2001
From: Robert Hallberg <Robert.Hallberg@noaa.gov>
Date: Tue, 20 Dec 2016 15:22:55 -0500
Subject: [PATCH 206/361] +Allow icebergs_run(sst) to be in Celsius or Kelvin

  Added code to allow the sst argument to icebergs_run to be in either degrees
Celsius or degrees Kelvin, using whether the maximum value in an array is less
than or greater than 120 degrees as a test.  All answers are bitwise identical
to the previous behavior when the sst input array is in Kelvin, and there are
no interface changes.  (Pretty cool, huh!)
---
 icebergs.F90 | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 9b07a90..86d987c 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -2820,7 +2820,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 real :: unused_calving, tmpsum, grdd_berg_mass, grdd_bergy_mass,grdd_spread_mass, grdd_spread_area
 real :: grdd_u_iceberg, grdd_v_iceberg, grdd_ustar_iceberg, grdd_spread_uvel, grdd_spread_vvel
 integer :: i, j, Iu, ju, iv, Jv, Iu_off, ju_off, iv_off, Jv_off
-real :: mask
+real :: mask, max_SST
 real, dimension(:,:), allocatable :: uC_tmp, vC_tmp, uA_tmp, vA_tmp
 integer :: vel_stagger, str_stagger
 real, dimension(:,:), allocatable :: iCount
@@ -3036,7 +3036,12 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   endif
 
   call mpp_update_domains(grd%ssh, grd%domain)
-  grd%sst(grd%isc:grd%iec,grd%jsc:grd%jec)=sst(:,:)-273.15 ! Note convert from Kelvin to Celsius
+  max_SST = maxval(sst(:,:))
+  if (max_SST > 120.0) then ! The input sst is in degrees Kelvin, otherwise the water would be boiling.
+    grd%sst(grd%isc:grd%iec,grd%jsc:grd%jec) = sst(:,:)-273.15 ! Note convert from Kelvin to Celsius
+  else  ! The input sst is already in degrees Celsius.
+    grd%sst(grd%isc:grd%iec,grd%jsc:grd%jec) = sst(:,:) ! Note no conversion necessary.
+  endif
   call mpp_update_domains(grd%sst, grd%domain)
   ! Copy sea-ice concentration and thickness (resides on A grid)
   grd%cn(grd%isc-1:grd%iec+1,grd%jsc-1:grd%jec+1)=cn(:,:)

From 4dcc6d159f5b6de6e882d2533f2b6be3d2d1c1ad Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Wed, 21 Dec 2016 17:34:42 -0500
Subject: [PATCH 207/361] Added check_for_duplicates_in_parallel()

- New function check_for_duplicates_in_parallel() checks for
  duplicate icebergs on and between PEs.
- The above calls check_for_duplicate_ids_in_list() which
  has unit tests which are always called during initialization.
---
 icebergs.F90           |   2 +
 icebergs_framework.F90 | 128 ++++++++++++++++++++++++++++++++++++++++-
 2 files changed, 129 insertions(+), 1 deletion(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 9b07a90..e21108d 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -39,6 +39,7 @@ module ice_bergs
 use ice_bergs_framework, only: orig_read  ! Remove when backward compatibility no longer needed
 use ice_bergs_framework, only: monitor_a_berg
 use ice_bergs_framework, only: is_point_within_xi_yj_bounds
+use ice_bergs_framework, only: test_check_for_duplicate_ids_in_list
 
 use ice_bergs_io,        only: ice_bergs_io_init,write_restart,write_trajectory
 use ice_bergs_io,        only: read_restart_bergs,read_restart_bergs_orig,read_restart_calving
@@ -151,6 +152,7 @@ subroutine unit_testing(bergs)
 call hexagon_test()
 call point_in_triangle_test()
 call basal_melt_test(bergs)
+call test_check_for_duplicate_ids_in_list()
 
 end subroutine unit_testing
 
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index fcc4949..957846b 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -49,7 +49,6 @@ module ice_bergs_framework
 public ignore_ij_restart, use_slow_find,generate_test_icebergs,old_bug_rotated_weights,budget
 public orig_read, force_all_pes_traj
 
-
 !Public types
 public icebergs_gridded, xyt, iceberg, icebergs, buffer, bond 
 
@@ -74,6 +73,8 @@ module ice_bergs_framework
 public find_individual_iceberg
 public monitor_a_berg
 public is_point_within_xi_yj_bounds
+public test_check_for_duplicate_ids_in_list
+public check_for_duplicates_in_parallel
 
 type :: icebergs_gridded
   type(domain2D), pointer :: domain ! MPP domain
@@ -4366,4 +4367,129 @@ end function unitTests
 
 ! ##############################################################################
 
+!> Check for duplicates of icebergs on and across processors and issue an error
+!! if any are detected
+subroutine check_for_duplicates_in_parallel(bergs)
+  type(icebergs), pointer :: bergs !< Icebergs
+  ! Local variables
+  type(icebergs_gridded), pointer :: grd
+  type(iceberg), pointer :: this
+  integer :: stderrunit, i, j, k, nbergs, nbergs_total
+  integer, dimension(:), allocatable :: ids ! List of ids of all bergs on this processor
+
+  stderrunit=stderr()
+  grd=>bergs%grd
+  nbergs = count_bergs(bergs)
+  nbergs_total = nbergs
+  call mpp_sum(nbergs_total) ! Total number of bergs
+  if (nbergs_total==0) return ! Skip the rest of the test
+
+  k = 0
+  if (nbergs>0) then
+    allocate(ids(nbergs))
+    do j = grd%jsc,grd%jec ; do i = grd%isc,grd%iec
+      this=>bergs%list(i,j)%first
+      do while (associated(this))
+        k = k + 1
+        ids(k) = this%iceberg_num
+        this=>this%next
+      enddo
+    enddo ; enddo
+  endif
+  if (k /= nbergs) then
+    write(stderrunit,*) 'counted bergs=',k,'count_bergs()=',nbergs
+    call error_mesg('diamonds, check_for_duplicates:', 'Mismatch between concatenation of lists and count_bergs()!', FATAL)
+  endif
+  k = check_for_duplicate_ids_in_list(nbergs, ids, verbose=.true.)
+  if (k /= 0) call error_mesg('diamonds, check_for_duplicates:', 'Duplicate berg detected across PEs!', FATAL)
+  if (nbergs>0) deallocate(ids)
+end subroutine check_for_duplicates_in_parallel
+
+!> Returns error count of duplicates of integer values in a distributed list
+integer function check_for_duplicate_ids_in_list(nbergs, ids, verbose)
+  integer,               intent(in)    :: nbergs !< Length of ids
+  integer, dimension(:), intent(inout) :: ids !< List of ids
+  logical,               intent(in)    :: verbose !< True if messages should be written
+  integer :: stderrunit, i, j, k, l, nbergs_total, ii
+
+  stderrunit=stderr()
+  nbergs_total = nbergs
+  call mpp_sum(nbergs_total) ! Total number of bergs
+  ! Sort the list "ids" (largest first)
+  do j = 1, nbergs-1
+    do i = j+1, nbergs
+      if (ids(j) < ids(i)) then
+        ! Swap
+        k = ids(i)
+        ids(i) = ids(j)
+        ids(j) = k
+      endif
+    enddo
+  enddo
+  ! Check for duplicates on processor
+  check_for_duplicate_ids_in_list = 0
+  do k = 1, nbergs-1
+    if (ids(k) == ids(k+1)) then
+      if (verbose) write(stderrunit,*) 'Duplicated berg on PE with id=',ids(k),'pe=',mpp_pe()
+      check_for_duplicate_ids_in_list = check_for_duplicate_ids_in_list + 1
+    endif
+  enddo
+  ! Check for duplicates across processor
+  j = 1 ! Pointer to first berg in my list
+  do k = 1, nbergs_total
+    ! Set i to first id in my list
+    if (j <= nbergs) then
+      i = ids(j)
+    else
+      i = 0
+    endif
+    l = i
+    call mpp_max(l)
+    if (i == l) then
+      ii = 1 ! This berg is mine
+      j = j + 1
+    else
+      ii = 0 ! This berg is not mine
+    endif
+    call mpp_sum(ii)
+    if (ii > 1) then
+      if (verbose) write(stderrunit,*) 'Duplicated berg across PEs with id=',i,l,' seen',ii,' times pe=',mpp_pe(),k
+      check_for_duplicate_ids_in_list = check_for_duplicate_ids_in_list + 1
+    endif
+  enddo
+
+end function check_for_duplicate_ids_in_list
+
+subroutine test_check_for_duplicate_ids_in_list()
+  integer :: k
+  integer, dimension(:), allocatable :: ids
+  integer :: error_count
+
+  allocate(ids(5))
+  do k = 1,5
+    ids(k) = k + 5*mpp_pe()
+  enddo
+  error_count = check_for_duplicate_ids_in_list(5, ids, verbose=.false.)
+  call mpp_sum(error_count)
+  if (error_count /= 0) then
+    error_count = check_for_duplicate_ids_in_list(5, ids, verbose=.true.)
+    call error_mesg('diamonds, test_check_for_duplicate_ids_in_list:', 'Unit test for clean list failed!', FATAL)
+  endif
+  if (mpp_pe() == mpp_root_pe()) ids(5) = ids(4)
+  error_count = check_for_duplicate_ids_in_list(5, ids, verbose=.false.)
+  call mpp_sum(error_count)
+  if (error_count == 0) then
+    error_count = check_for_duplicate_ids_in_list(5, ids, verbose=.true.)
+    call error_mesg('diamonds, test_check_for_duplicate_ids_in_list:', 'Unit test for dirty list failed!', FATAL)
+  endif
+  if (mpp_pe() == mpp_root_pe()) ids(5) = 7 + 5*mpp_pe()
+  error_count = check_for_duplicate_ids_in_list(5, ids, verbose=.false.)
+  call mpp_sum(error_count)
+  if (error_count == 0) then
+    error_count = check_for_duplicate_ids_in_list(5, ids, verbose=.true.)
+    call error_mesg('diamonds, test_check_for_duplicate_ids_in_list:', 'Unit test for a really dirty list failed!', FATAL)
+  endif
+  deallocate(ids)
+end subroutine test_check_for_duplicate_ids_in_list
+
 end module

From 7be78bfc82358b0bf86f169af493741fcf4a8d2c Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Wed, 21 Dec 2016 17:37:08 -0500
Subject: [PATCH 208/361] Replaced restart sanity checks with
 check_for_duplicates_in_parallel()

- The sanity checks made after reading a restart were only correct
  for i/o layouts of 1,1 or 0,0. These have been removed.
  - Note that we don't have equivalent tests for arbitrary layouts.
- Call check_for_duplicates_in_parallel() always after reading a restart.
- Closes #47
---
 icebergs_io.F90 | 133 ++++++++++++++++++++----------------------------
 1 file changed, 55 insertions(+), 78 deletions(-)

diff --git a/icebergs_io.F90 b/icebergs_io.F90
index ef3b82d..b8bee75 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -36,6 +36,7 @@ module ice_bergs_io
 use ice_bergs_framework, only: verbose, really_debug, debug, restart_input_dir,make_calving_reproduce
 use ice_bergs_framework, only: ignore_ij_restart, use_slow_find,generate_test_icebergs,print_berg
 use ice_bergs_framework, only: force_all_pes_traj
+use ice_bergs_framework, only: check_for_duplicates_in_parallel
 
 implicit none ; private
 
@@ -845,39 +846,10 @@ subroutine read_restart_bergs(bergs,Time)
     else ! i,j are not available from the file so we search the grid to find out if we reside on this PE
       if (use_slow_find) then
         lres=find_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
-       else
-         lres=find_cell_by_search(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
-       endif
-     endif
-     ! The next few lines are a check to see whether the icebergs are all found.
-
-       ! The next few lines are a check to see whether the icebergs are all found.
-       pos_is_good=0.0
-       if (lres) then
-         pos_is_good=1.0
-       endif
-       pos_is_good_all_pe=pos_is_good
-       call mpp_sum(pos_is_good_all_pe)
-       !Check to see if any iceberg in the restart file was not found
-       if (pos_is_good_all_pe .lt. 0.5) then
-         if (bergs%ignore_missing_restart_bergs) then 
-           if (mpp_pe().eq.mpp_root_pe()) then
-                   print * , 'Iceberg not located: ', lon(k),lat(k), iceberg_num(k)
-                   call error_mesg('diamonds, read_restart_bergs', 'Iceberg positions was not found', WARNING)
-           endif
-         else
-           call error_mesg('diamonds, read_restart_bergs', 'Iceberg positions was not found', FATAL)
-         endif
-
-       endif
-       !Check to see if any iceberg was found more than once.
-       if (pos_is_good_all_pe .gt. 1.5) then
-         if (mpp_pe().eq.mpp_root_pe()) then
-           print * , 'Iceberg was found more than once: ', lon(k),lat(k), iceberg_num(k)
-           call error_mesg('diamonds, read_restart_bergs', 'Iceberg copied twice', FATAL)
-         endif
-       endif
-
+      else
+        lres=find_cell_by_search(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
+      endif
+    endif
     if (really_debug) then
       write(stderrunit,'(a,i8,a,2f9.4,a,i8)') 'diamonds, read_restart_bergs: berg ',k,' is at ',localberg%lon,localberg%lat,&
            & ' on PE ',mpp_pe()
@@ -935,55 +907,60 @@ subroutine read_restart_bergs(bergs,Time)
   enddo
   
   if(nbergs_in_file > 0) then
-     deallocate(              &
-                lon,          &
-                lat,          &
-                uvel,         &
-                vvel,         &
-                mass,         &
-                axn,          &
-                ayn,          &
-                bxn,          &
-                byn,          &
-                thickness,    &
-                width,        &
-                length,       &
-                start_lon,    &
-                start_lat,    &
-                start_day,    &
-                start_mass,   &
-                mass_scaling, &
-                mass_of_bits, &
-                static_berg,    &
-                heat_density )
-     deallocate(           &
-                ine,       &
-                jne,       &
-                iceberg_num,       &
-                start_year )
-
-     !Checking the total number of icebergs read from the restart file.
-     nbergs_read=count_bergs(bergs)
-     call mpp_sum(nbergs_read)
-     if (mpp_pe().eq.mpp_root_pe()) then
-       write(*,'(a,i8,a,i8,a)') 'diamonds, read_restart_bergs: Number of Icebergs in restart file=',nbergs_in_file,' Number of Icebergs read=', nbergs_read
-       if (nbergs_read .gt. nbergs_in_file) then
-         call error_mesg('diamonds, read_restart_bergs', 'More icebergs read than exist in restart file.', FATAL)
-       elseif (nbergs_read .lt. nbergs_in_file) then
-         if (bergs%ignore_missing_restart_bergs) then
-           call error_mesg('diamonds, read_restart_bergs', 'Some Icebergs from restart file were not found (ignore_missing flag is on)', WARNING)
-         else
-           call error_mesg('diamonds, read_restart_bergs', 'Some Icebergs from restart file were not found', FATAL)
-         endif
-       elseif (nbergs_read .eq. nbergs_in_file) then
-         write(*,'(a,i8,a,i8,a)') 'diamonds, read_restart_bergs: Number of icebergs read (#',nbergs_read,') matches the number of icebergs in the file'
-       endif
-     endif
+    deallocate(              &
+               lon,          &
+               lat,          &
+               uvel,         &
+               vvel,         &
+               mass,         &
+               axn,          &
+               ayn,          &
+               bxn,          &
+               byn,          &
+               thickness,    &
+               width,        &
+               length,       &
+               start_lon,    &
+               start_lat,    &
+               start_day,    &
+               start_mass,   &
+               mass_scaling, &
+               mass_of_bits, &
+               static_berg,  &
+               heat_density )
+    deallocate(              &
+               ine,          &
+               jne,          &
+               iceberg_num,  &
+               start_year )
+
+    ! This block only works for IO_LAYOUT=1,1 or 0,0 but not for arbitrary layouts.
+    ! I'm commenting this out until we find a way to implement the same sorts of checks
+    ! that work for all i/o layouts. -AJA
+    !Checking the total number of icebergs read from the restart file.
+    !nbergs_read=count_bergs(bergs)
+    !call mpp_sum(nbergs_read)
+    !if (mpp_pe().eq.mpp_root_pe()) then
+    !  write(*,'(a,i8,a,i8,a)') 'diamonds, read_restart_bergs: Number of Icebergs in restart file=',nbergs_in_file,' Number of Icebergs read=', nbergs_read
+    !  if (nbergs_read .gt. nbergs_in_file) then
+    !    call error_mesg('diamonds, read_restart_bergs', 'More icebergs read than exist in restart file.', FATAL)
+    !  elseif (nbergs_read .lt. nbergs_in_file) then
+    !    if (bergs%ignore_missing_restart_bergs) then
+    !      call error_mesg('diamonds, read_restart_bergs', 'Some Icebergs from restart file were not found (ignore_missing flag is on)', WARNING)
+    !    else
+    !      call error_mesg('diamonds, read_restart_bergs', 'Some Icebergs from restart file were not found', FATAL)
+    !    endif
+    !  elseif (nbergs_read .eq. nbergs_in_file) then
+    !    write(*,'(a,i8,a,i8,a)') 'diamonds, read_restart_bergs: Number of icebergs read (#',nbergs_read,') matches the number of icebergs in the file'
+    !  endif
+    !endif
 
   elseif(.not. found_restart .and. bergs%nbergs_start==0 .and. generate_test_icebergs) then
-     call generate_bergs(bergs,Time)
+    call generate_bergs(bergs,Time)
   endif
 
+  call check_for_duplicates_in_parallel(bergs)
+
   bergs%floating_mass_start=sum_mass(bergs)
   call mpp_sum( bergs%floating_mass_start )
   bergs%icebergs_mass_start=sum_mass(bergs,justbergs=.true.)

From 6009017c248745f5fb4dfb5a71b39d2fecb14724 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Wed, 18 Jan 2017 11:29:14 -0500
Subject: [PATCH 209/361] Fix for when iceberg ids are negative

- check_for_duplicates_in_parallel() was incorrectly detecting duplicates
  when an iceberg has a negative id (iceberg_num). We were assuming all
  ids were positive and using '0' as a nonexistent id. We now find the
  lowest id and subtract 1 from it to create a nonexistent id.
- Fixes restart problems in CM4
---
 icebergs_framework.F90 | 23 +++++++++++++++++++----
 1 file changed, 19 insertions(+), 4 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 957846b..61d29cc 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -4410,11 +4410,22 @@ integer function check_for_duplicate_ids_in_list(nbergs, ids, verbose)
   integer,               intent(in)    :: nbergs !< Length of ids
   integer, dimension(:), intent(inout) :: ids !< List of ids
   logical,               intent(in)    :: verbose !< True if messages should be written
-  integer :: stderrunit, i, j, k, l, nbergs_total, ii
+  integer :: stderrunit, i, j, k, l, nbergs_total, ii, lowest_id, nonexistent_id
+  logical :: have_berg
 
   stderrunit=stderr()
   nbergs_total = nbergs
   call mpp_sum(nbergs_total) ! Total number of bergs
+
+  ! Establish lowest id or 0 across all PEs
+  lowest_id = 0
+  if (nbergs>0) lowest_id = minval(ids)
+  call mpp_min(lowest_id)
+  i = lowest_id
+  nonexistent_id = lowest_id - 1
+  if (nonexistent_id >= lowest_id) then
+    write(stderrunit,*) 'Underflow in iceberg ids!',nonexistent_id,lowest_id,mpp_pe()
+  endif
   ! Sort the list "ids" (largest first)
   do j = 1, nbergs-1
     do i = j+1, nbergs
@@ -4440,12 +4451,14 @@ integer function check_for_duplicate_ids_in_list(nbergs, ids, verbose)
     ! Set i to first id in my list
     if (j <= nbergs) then
       i = ids(j)
+      have_berg = .true.
     else
-      i = 0
+      i = nonexistent_id
+      have_berg = .false.
     endif
     l = i
     call mpp_max(l)
-    if (i == l) then
+    if (have_berg .and. i == l) then
       ii = 1 ! This berg is mine
       j = j + 1
     else
@@ -4453,8 +4466,10 @@ integer function check_for_duplicate_ids_in_list(nbergs, ids, verbose)
     endif
     call mpp_sum(ii)
     if (ii > 1) then
-      if (verbose) write(stderrunit,*) 'Duplicated berg across PEs with id=',i,l,' seen',ii,' times pe=',mpp_pe(),k
+      if (verbose) write(stderrunit,*) 'Duplicated berg across PEs with id=',i,l,' seen',ii,' times pe=',mpp_pe(),k,j,nbergs
       check_for_duplicate_ids_in_list = check_for_duplicate_ids_in_list + 1
+    elseif (ii == 0) then
+      if (verbose) write(stderrunit,*) 'Berg not accounted for on all PEs with id=',i,l,' seen',ii,' times pe=',mpp_pe(),k,j,nbergs
     endif
   enddo
 

From 6e8c31cf44996e1fc0b00f59fe2aa8f2ce45caaa Mon Sep 17 00:00:00 2001
From: Alon Stern <sternalon@gmail.com>
Date: Wed, 1 Feb 2017 03:53:32 -0500
Subject: [PATCH 210/361] Mixed ice shelf / iceberg melting option

A runtime flag use_mixed_melting has been added. When this flag is true, then the iceberg melt done partly using iceberg melt parametrizations, and parly using ice shelf melt paramtrizations (3 equation model). The decision whether to melt as an ice shelf or iceberg is based on the number of bonds.
---
 icebergs.F90           | 37 +++++++++++++++++++++++++++++--------
 icebergs_framework.F90 |  5 ++++-
 2 files changed, 33 insertions(+), 9 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index aac15a0..d03e8b3 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1118,11 +1118,13 @@ subroutine thermodynamics(bergs)
 type(icebergs), pointer :: bergs
 ! Local variables
 type(icebergs_gridded), pointer :: grd
+type(bond), pointer :: current_bond
 real :: M, T, W, L, SST, Vol, Ln, Wn, Tn, nVol, IC, Dn
 real :: Mv, Me, Mb, melt, dvo, dva, dM, Ss, dMe, dMb, dMv
 real :: Mnew, Mnew1, Mnew2, Hocean
 real :: Mbits, nMbits, dMbitsE, dMbitsM, Lbits, Abits, Mbb
 real :: tip_parameter
+real :: Ms, N_bonds, N_max !Ice shelf melt, Number of bonds, Max_number of bonds
 real :: Delta, q
 integer :: i,j, stderrunit
 type(iceberg), pointer :: this, next
@@ -1170,21 +1172,40 @@ subroutine thermodynamics(bergs)
           *perday ! convert to m/s
       Me=max( 1./12.*(SST+2.)*Ss*(1+cos(pi*(IC**3))) ,0.) &! Wave erosion
           *perday ! convert to m/s
-
+       
       !For icebergs acting as ice shelves 
-      if (bergs%melt_icebergs_as_ice_shelf) then
-        Mv=0.0
-        Mb=0.0
-        Me=0.0
+      if ((bergs%melt_icebergs_as_ice_shelf) .or.(bergs%use_mixed_melting))  then
         if (.not. bergs%use_mixed_layer_salinity_for_thermo)  SSS=35.0  
-        call find_basal_melt(bergs,dvo,this%lat,SSS,SST,bergs%Use_three_equation_model,T,Mb,this%iceberg_num)
-        Mb=max(Mb,0.) !No refreezing allowed for now
+        call find_basal_melt(bergs,dvo,this%lat,SSS,SST,bergs%Use_three_equation_model,T,Ms,this%iceberg_num)
+        Ms=max(Ms,0.) !No refreezing allowed for now
         !Set melt to zero if ocean is too thin.
         if ((bergs%melt_cutoff >=0.) .and. (bergs%apply_thickness_cutoff_to_bergs_melt)) then
           Dn=(bergs%rho_bergs/rho_seawater)*this%thickness ! draught (keel depth)
           if ((grd%ocean_depth(i,j)-Dn) < bergs%melt_cutoff) then
-            Mb=0.
+            Ms=0.
+          endif
+        endif
+
+        if (bergs%use_mixed_melting) then
+          N_bonds=0.
+          N_max=4.0  !Maximum number of bonds that element can form based on shape      
+          if (bergs%hexagonal_icebergs) N_max=6.0
+          if (bergs%iceberg_bonds_on) then
+            ! Determining number of bonds
+            current_bond=>this%first_bond
+            do while (associated(current_bond)) ! loop over all bonds
+              N_bonds=N_bonds+1.0
+              current_bond=>current_bond%next_bond
+            enddo
           endif
+          if  (this%static_berg .eq. 1)  N_bonds=N_max  !Static icebergs melt  like ice shelves 
+          Me=((N_max-N_bonds)/N_max)*(Mv+Me)
+          Mv=0.0
+          Mb=(((N_max-N_bonds)/N_max)*(Mb)) + (N_bonds/N_max)*Ms
+        else  !Using Three equation model only.
+          Mv=0.0
+          Me=0.0
+          Mb=Ms
         endif
       endif
             
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 61d29cc..3477dd0 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -245,6 +245,7 @@ module ice_bergs_framework
   logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
   logical :: time_average_weight=.false. ! Time average the weight on the ocean
   logical :: Runge_not_Verlet=.True.  !True=Runge Kuttai, False=Verlet.  - Added by Alon 
+  logical :: use_mixed_melting=.False.  !If true, then the melt is determined partly using 3 eq model partly using iceberg parametrizations (according to iceberg bond number)
   logical :: apply_thickness_cutoff_to_gridded_melt=.False.  !Prevents melt for ocean thickness below melt_cuttoff (applied to gridded melt fields)
   logical :: apply_thickness_cutoff_to_bergs_melt=.False.  !Prevents melt for ocean thickness below melt_cuttoff (applied to bergs)
   logical :: use_updated_rolling_scheme=.false. ! True to use the aspect ratio based rolling scheme rather than incorrect version of WM scheme   (set tip_parameter=1000. for correct WM scheme)
@@ -398,6 +399,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: tip_parameter=0. ! parameter to override iceberg rollilng critica ratio (use zero to get parameter directly from ice and seawater densities
 real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
 logical :: Runge_not_Verlet=.True.  !True=Runge Kutta, False=Verlet.  - Added by Alon 
+logical :: use_mixed_melting=.False.  !If true, then the melt is determined partly using 3 eq model partly using iceberg parametrizations (according to iceberg bond number)
 logical :: apply_thickness_cutoff_to_gridded_melt=.False.  !Prevents melt for ocean thickness below melt_cuttoff (applied to gridded melt fields)
 logical :: apply_thickness_cutoff_to_bergs_melt=.False.  !Prevents melt for ocean thickness below melt_cuttoff (applied to bergs)
 logical :: use_updated_rolling_scheme=.false. ! Use the corrected Rolling Scheme rather than the erronios one
@@ -449,7 +451,7 @@ subroutine ice_bergs_framework_init(bergs, &
          grid_is_regular,override_iceberg_velocities,u_override,v_override,add_iceberg_thickness_to_SSH,Iceberg_melt_without_decay,melt_icebergs_as_ice_shelf, &
          Use_three_equation_model,find_melt_using_spread_mass,use_mixed_layer_salinity_for_thermo,utide_icebergs,ustar_icebergs_bg,cdrag_icebergs, pass_fields_to_ocean_model, &
          const_gamma, Gamma_T_3EQ, ignore_traj, debug_iceberg_with_id,use_updated_rolling_scheme, tip_parameter, read_old_restarts, tau_calving, read_ocean_depth_from_file, melt_cutoff,&
-         apply_thickness_cutoff_to_gridded_melt, apply_thickness_cutoff_to_bergs_melt 
+         apply_thickness_cutoff_to_gridded_melt, apply_thickness_cutoff_to_bergs_melt,use_mixed_melting 
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -828,6 +830,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%tip_parameter=tip_parameter
   bergs%use_updated_rolling_scheme=use_updated_rolling_scheme  !Alon
   bergs%Runge_not_Verlet=Runge_not_Verlet   
+  bergs%use_mixed_melting=use_mixed_melting   
   bergs%apply_thickness_cutoff_to_bergs_melt=apply_thickness_cutoff_to_bergs_melt
   bergs%apply_thickness_cutoff_to_gridded_melt=apply_thickness_cutoff_to_gridded_melt
   bergs%melt_cutoff=melt_cutoff 

From 06d2074ea8e94f131ac55dffb9e26b08466c6d56 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Thu, 2 Mar 2017 13:15:11 -0500
Subject: [PATCH 211/361] Partially doxygenized APIs

- icebergs_io APIs are fully documented.
- icebergs_framework APIs are mostly documented (some bond routines outstanding).
- icebergs are mostly undocumented but indenting has been mostly fixed.

Todo:
- Finish documentation of APIs.
- Add docs directory for building documentation.
---
 icebergs.F90           | 2629 ++++++++++++++++++++--------------------
 icebergs_framework.F90 | 2171 +++++++++++++++++----------------
 icebergs_io.F90        |  300 ++---
 3 files changed, 2616 insertions(+), 2484 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index d03e8b3..693b55d 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -1,5 +1,8 @@
+!> Top-level/entry functions that step forward the governing equations
 module ice_bergs
 
+! This file is part of NOAA-GFDL/icebergs. See LICENSE.md for the license.
+
 use constants_mod, only: pi, omega, HLF
 use fms_mod, only: open_namelist_file, check_nml_error, close_file
 use fms_mod, only: field_exist, get_global_att_value
@@ -51,20 +54,20 @@ module ice_bergs
 public icebergs_init, icebergs_end, icebergs_run, icebergs_stock_pe, icebergs
 public icebergs_incr_mass, icebergs_save_restart
 
-real, parameter :: pi_180=pi/180.  ! Converts degrees to radians
-real, parameter :: r180_pi=180./pi ! Converts radians to degrees
-real, parameter :: Rearth=6360000. ! Radius of earth (m)
-real, parameter :: rho_ice=916.7 ! Density of fresh ice @ 0oC (kg/m^3)
-real, parameter :: rho_water=999.8 ! Density of fresh water @ 0oC (kg/m^3)
-real, parameter :: rho_air=1.1 ! Density of air @ 0oC (kg/m^3) ???
-real, parameter :: rho_seawater=1025. ! Approx. density of surface sea water @ 0oC (kg/m^3)
-real, parameter :: gravity=9.8 ! Gravitational acceleratio (m/s^2)
-real, parameter :: Cd_av=1.3 ! (Vertical) Drag coefficient between bergs and atmos (?)
-real, parameter :: Cd_ah=0.0055 ! (Horizontal) Drag coefficient between bergs and atmos (?)
-real, parameter :: Cd_wv=0.9 ! (Vertical) Drag coefficient between bergs and ocean (?)
-real, parameter :: Cd_wh=0.0012 ! (Horizontal) Drag coefficient between bergs and ocean (?)
-real, parameter :: Cd_iv=0.9 ! (Vertical) Drag coefficient between bergs and sea-ice (?)
-!TOM> no horizontal drag for sea ice! real, parameter :: Cd_ih=0.0012 ! (Horizontal) Drag coefficient between bergs and sea-ice (?)
+real, parameter :: pi_180=pi/180.  !< Converts degrees to radians
+real, parameter :: r180_pi=180./pi !< Converts radians to degrees
+real, parameter :: Rearth=6360000. !< Radius of earth (m)
+real, parameter :: rho_ice=916.7 !< Density of fresh ice @ 0oC (kg/m^3)
+real, parameter :: rho_water=999.8 !< Density of fresh water @ 0oC (kg/m^3)
+real, parameter :: rho_air=1.1 !< Density of air @ 0oC (kg/m^3) ???
+real, parameter :: rho_seawater=1025. !< Approx. density of surface sea water @ 0oC (kg/m^3)
+real, parameter :: gravity=9.8 !< Gravitational acceleratio (m/s^2)
+real, parameter :: Cd_av=1.3 !< (Vertical) Drag coefficient between bergs and atmos (?)
+real, parameter :: Cd_ah=0.0055 !< (Horizontal) Drag coefficient between bergs and atmos (?)
+real, parameter :: Cd_wv=0.9 !< (Vertical) Drag coefficient between bergs and ocean (?)
+real, parameter :: Cd_wh=0.0012 !< (Horizontal) Drag coefficient between bergs and ocean (?)
+real, parameter :: Cd_iv=0.9 !< (Vertical) Drag coefficient between bergs and sea-ice (?)
+!TOM> no horizontal drag for sea ice! real, parameter :: Cd_ih=0.0012 !< (Horizontal) Drag coefficient between bergs and sea-ice (?)
 
 #ifdef _FILE_VERSION
   character(len=128) :: version = _FILE_VERSION
@@ -74,27 +77,37 @@ module ice_bergs
 
 contains
 
-! ##############################################################################
+!> Initializes icebergs container "bergs"
 subroutine icebergs_init(bergs, &
              gni, gnj, layout, io_layout, axes, dom_x_flags, dom_y_flags, &
              dt, Time, ice_lon, ice_lat, ice_wet, ice_dx, ice_dy, ice_area, &
              cos_rot, sin_rot, ocean_depth, maskmap, fractional_area)
 ! Arguments
-type(icebergs), pointer :: bergs
+type(icebergs), pointer :: bergs !< Container for all types and memory
+integer, intent(in) :: gni !< Number of global points in i-direction
+integer, intent(in) :: gnj !< Number of global points in j-direction
+integer, intent(in) :: layout(2) !< Parallel decomposition of computational processors in i/j direction
+integer, intent(in) :: io_layout(2) !< Parallel decomposition of i/o processors in i/j direction
+integer, intent(in) :: axes(2) !< Diagnostic axes
+integer, intent(in) :: dom_x_flags !< Decomposition flags for i-direction
+integer, intent(in) :: dom_y_flags !< Decomposition flags for j-direction
+real, intent(in) :: dt !< Time step (s)
+type (time_type), intent(in) :: Time !< Model time
+real, dimension(:,:), intent(in) :: ice_lon !< Longitude of cell corners using NE convention (degree E)
+real, dimension(:,:), intent(in) :: ice_lat !< Latitude of cell corners using NE conventino (degree N)
+real, dimension(:,:), intent(in) :: ice_wet !< Wet/dry mask (1 is wet, 0 is dry) of cell centers
+real, dimension(:,:), intent(in) :: ice_dx !< Zonal length of cell on northern side (m)
+real, dimension(:,:), intent(in) :: ice_dy !< Meridional length of cell on eastern side (m)
+real, dimension(:,:), intent(in) :: ice_area !< Area of cells (m^2, or non-dim is fractional_area=True)
+real, dimension(:,:), intent(in) :: cos_rot !< Cosine from rotation matrix to lat-lon coords
+real, dimension(:,:), intent(in) :: sin_rot !< Sine from rotation matrix to lat-lon coords
+real, dimension(:,:), intent(in),optional :: ocean_depth !< Depth of ocean bottom (m)
+logical, intent(in), optional :: maskmap(:,:) !< Masks out parallel cores
+logical, intent(in), optional :: fractional_area !< If true, ice_area contains cell area as fraction of entire spherical surface
+! Local variables
 type(icebergs_gridded), pointer :: grd => null()
-integer, intent(in) :: gni, gnj, layout(2), io_layout(2), axes(2)
-integer, intent(in) :: dom_x_flags, dom_y_flags
-real, intent(in) :: dt
-type (time_type), intent(in) :: Time ! current time
-real, dimension(:,:), intent(in) :: ice_lon, ice_lat, ice_wet
-real, dimension(:,:), intent(in) :: ice_dx, ice_dy, ice_area
-real, dimension(:,:), intent(in) :: cos_rot, sin_rot
-real, dimension(:,:), intent(in), optional :: ocean_depth
-logical, intent(in), optional :: maskmap(:,:)
-logical, intent(in), optional :: fractional_area
 integer :: nbonds
 logical :: check_bond_quality
-
 integer :: stdlogunit, stderrunit
 
   ! Get the stderr and stdlog unit numbers
@@ -123,7 +136,7 @@ subroutine icebergs_init(bergs, &
   call mpp_clock_end(bergs%clock_ior)
 
   if (really_debug) call print_bergs(stderrunit,bergs,'icebergs_init, initial status')
-  
+
   !Reading ocean depth from a file
   if (bergs%read_ocean_depth_from_file) call read_ocean_depth(bergs%grd)
 
@@ -143,11 +156,10 @@ subroutine icebergs_init(bergs, &
 
 end subroutine icebergs_init
 
-
-! ##############################################################################
+!> Invoke some unit testing
 subroutine unit_testing(bergs)
 ! Arguments
-type(icebergs), pointer :: bergs
+type(icebergs), pointer :: bergs !< Container for all types and memory
 
 call hexagon_test()
 call point_in_triangle_test()
@@ -156,12 +168,14 @@ subroutine unit_testing(bergs)
 
 end subroutine unit_testing
 
+!> Test find_basal_melt()
 subroutine basal_melt_test(bergs)
-  ! Arguments
-  type(icebergs), pointer :: bergs
-  real :: dvo,lat,salt,temp, basal_melt, thickness
-  integer :: iceberg_num
-  logical :: Use_three_equation_model
+! Arguments
+type(icebergs), pointer :: bergs !< Container for all types and memory
+! Local variables
+real :: dvo,lat,salt,temp, basal_melt, thickness
+integer :: iceberg_num
+logical :: Use_three_equation_model
 
   if (mpp_pe() .eq. mpp_root_pe() ) print *, 'Begining Basal Melting Unit Test'
   dvo=0.2 ;lat=0.0 ; salt=35.0 ; temp=2.0 ;thickness=100.; iceberg_num=0
@@ -175,12 +189,13 @@ subroutine basal_melt_test(bergs)
 
 end subroutine basal_melt_test
 
+!> Test point_in_triangle()
 subroutine point_in_triangle_test()
 ! Arguments
 real :: Ax,Ay,Bx,By,Cx,Cy  !Position of icebergs
 logical :: fail_unit_test
 integer :: stderrunit
-  
+
   ! Get the stderr unit number.
   stderrunit = stderr()
   Ax= -2.695732526092343E-012
@@ -195,6 +210,7 @@ subroutine point_in_triangle_test()
 
 end subroutine point_in_triangle_test
 
+!> Test Hexagon_into_quadrants_using_triangles()
 subroutine hexagon_test()
 ! Arguments
 real :: x0,y0  !Position of icebergs
@@ -203,7 +219,7 @@ subroutine hexagon_test()
 real :: tol
 logical :: fail_unit_test
 integer :: stderrunit
-  
+
   ! Get the stderr unit number.
   stderrunit = stderr()
 
@@ -261,7 +277,7 @@ subroutine hexagon_test()
     call error_mesg('diamonds, hexagon unit testing:', 'Hexagon split btw 3 and 4!', WARNING)
     fail_unit_test=.True.
   endif
-  
+
   ! Test 3:  Two corners of hex on the axis
   !Test 3a: center on x>0 axis
   x0=S/2.  ;  y0=0.
@@ -304,11 +320,11 @@ subroutine hexagon_test()
 
 end subroutine hexagon_test
 
-! ##############################################################################
-
+!> Initializes bonds
 subroutine initialize_iceberg_bonds(bergs)
-
-type(icebergs), pointer :: bergs
+! Arguments
+type(icebergs), pointer :: bergs !< Container for all types and memory
+! Local variables
 type(iceberg), pointer :: berg
 type(iceberg), pointer :: other_berg
 type(icebergs_gridded), pointer :: grd
@@ -320,22 +336,21 @@ subroutine initialize_iceberg_bonds(bergs)
 integer :: grdi_outer, grdj_outer
 integer :: grdi_inner, grdj_inner
 
-
   ! For convenience
-    grd=>bergs%grd
-    !Should update halos before doing this 
+  grd=>bergs%grd
+  !Should update halos before doing this
   do grdj_outer = grd%jsc,grd%jec ; do grdi_outer = grd%isc,grd%iec  !Should you be on the data domain??
     berg=>bergs%list(grdi_outer,grdj_outer)%first
     do while (associated(berg)) ! loop over all bergs
-    
+
       lon1=berg%lon; lat1=berg%lat
       !call rotpos_to_tang(lon1,lat1,x1,y1)  !Is this correct? Shouldn't it only be on tangent plane?
 
       do grdj_inner = grd%jsc,grd%jec ; do grdi_inner = grd%isc,grd%iec  !This line uses n^2 steps
 !     do grdj_inner = berg%jne-1,berg%jne+1 ; do grdi_inner = berg%ine-1,berg%ine+1   !Only looping through adjacent cells.
         other_berg=>bergs%list(grdi_inner,grdj_inner)%first
-        do while (associated(other_berg)) ! loop over all other bergs  
-          
+        do while (associated(other_berg)) ! loop over all other bergs
+
           if (berg%iceberg_num .ne. other_berg%iceberg_num) then
             lon2=other_berg%lon; lat2=other_berg%lat
             !call rotpos_to_tang(lon2,lat2,x2,y2) !Is this correct? Shouldn't it only be on tangent plane?
@@ -349,10 +364,10 @@ subroutine initialize_iceberg_bonds(bergs)
             r_dist_x=dlon*dx_dlon
             r_dist_y=dlat*dy_dlat
             r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) )
-        
+
             !if (r_dist.gt.1000.) then  ! If the bergs are close together, then form a bond
               call form_a_bond(berg, other_berg%iceberg_num, other_berg%ine, other_berg%jne, other_berg)
-            !endif       
+            !endif
           endif
           other_berg=>other_berg%next
         enddo  ! End of looping through all other bergs in the inner list
@@ -361,82 +376,98 @@ subroutine initialize_iceberg_bonds(bergs)
     enddo ! End of looping through all bergs in the outer list
   enddo ; enddo; !End of outer loop.
 
-
 end subroutine initialize_iceberg_bonds
 
-subroutine  convert_from_grid_to_meters(lat_ref,grid_is_latlon ,dx_dlon,dy_dlat)
-  ! Arguments
-  real, intent(in) :: lat_ref
-  logical, intent(in) :: grid_is_latlon
-  real, intent(out) :: dx_dlon,dy_dlat
+! Returns metric converting grid distances to meters
+subroutine convert_from_grid_to_meters(lat_ref, grid_is_latlon, dx_dlon, dy_dlat)
+! Arguments
+real, intent(in) :: lat_ref
+logical, intent(in) :: grid_is_latlon
+real, intent(out) :: dx_dlon
+real, intent(out) :: dy_dlat
 
   if (grid_is_latlon) then
     dx_dlon=(pi/180.)*Rearth*cos((lat_ref)*(pi/180.))
     dy_dlat=(pi/180.)*Rearth
-
   else
     dx_dlon=1.
     dy_dlat=1.
-
   endif
+
 end subroutine  convert_from_grid_to_meters
 
+! Returns metric converting distance in meters to grid distance
 subroutine  convert_from_meters_to_grid(lat_ref,grid_is_latlon ,dlon_dx,dlat_dy)
-  ! Arguments
-  real, intent(in) :: lat_ref
-  logical, intent(in) :: grid_is_latlon
-  real, intent(out) :: dlon_dx,dlat_dy
+! Arguments
+real, intent(in) :: lat_ref
+logical, intent(in) :: grid_is_latlon
+real, intent(out) :: dlon_dx
+real, intent(out) :: dlat_dy
 
   if (grid_is_latlon) then
     dlon_dx=(180./pi)/(Rearth*cos((lat_ref)*(pi/180.)))
     dlat_dy=(180./pi)/Rearth
-
   else
     dlon_dx=1.
     dlat_dy=1.
-
   endif
+
 end subroutine  convert_from_meters_to_grid
-! ##############################################################################
 
-subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y) !Calculating interactive force between icebergs. Alon,  Markpoint_4
-type(icebergs), pointer :: bergs
+subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
+                             P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y)
+!Calculating interactive force between icebergs. Alon,  Markpoint_4
+! Arguments
+type(icebergs), pointer :: bergs !< Container for all types and memory
 type(iceberg), pointer :: berg
 type(iceberg), pointer :: other_berg
 type(bond), pointer :: current_bond
-real, intent(in) :: u0,v0, u1, v1
+real, intent(in) :: u0
+real, intent(in) :: v0
+real, intent(in) :: u1
+real, intent(in) :: v1
+real, intent(out) :: IA_x
+real, intent(out) :: IA_y
+real, intent(out) :: P_ia_11
+real, intent(out) :: P_ia_12
+real, intent(out) :: P_ia_22
+real, intent(out) :: P_ia_21
+real, intent(out) :: P_ia_times_u_x
+real, intent(out) :: P_ia_times_u_y
+! Local variables
 real :: u2, v2
 logical :: critical_interaction_damping_on
-real, intent(out) :: IA_x, IA_y 
-real, intent(out) :: P_ia_11, P_ia_12, P_ia_22, P_ia_21, P_ia_times_u_x, P_ia_times_u_y
 integer :: grdi, grdj
 logical :: iceberg_bonds_on
 logical :: bonded
-iceberg_bonds_on=bergs%iceberg_bonds_on
+
+  iceberg_bonds_on=bergs%iceberg_bonds_on
 
   IA_x=0.
   IA_y=0.
-  P_ia_11=0. ; P_ia_12=0. ;  P_ia_21=0.;  P_ia_22=0. 
+  P_ia_11=0. ; P_ia_12=0. ;  P_ia_21=0.;  P_ia_22=0.
   P_ia_times_u_x=0. ; P_ia_times_u_y=0.
 
   bonded=.false. !Unbonded iceberg interactions
   do grdj = berg%jne-1,berg%jne+1 ; do grdi = berg%ine-1,berg%ine+1  !Note: need  to make sure this is wide enough, but less than the halo width
     other_berg=>bergs%list(grdi,grdj)%first
-    do while (associated(other_berg)) ! loop over all other bergs  
-      call calculate_force(bergs,berg,other_berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y, bonded) 
+    do while (associated(other_berg)) ! loop over all other bergs
+      call calculate_force(bergs,berg,other_berg, IA_x, IA_y, u0, v0, u1, v1, &
+                           P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y, bonded)
       other_berg=>other_berg%next
     enddo ! loop over all bergs
   enddo ; enddo
 
   bonded=.true.  !Interactions due to iceberg bonds
-  if (iceberg_bonds_on) then ! MP1  
+  if (iceberg_bonds_on) then ! MP1
     current_bond=>berg%first_bond
     do while (associated(current_bond)) ! loop over all bonds
       other_berg=>current_bond%other_berg
       if (.not. associated(other_berg)) then
         call error_mesg('diamonds,bond interactions', 'Trying to do Bond interactions with unassosiated berg!' ,FATAL)
       else
-        call calculate_force(bergs,berg,other_berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded) 
+        call calculate_force(bergs,berg,other_berg, IA_x, IA_y, u0, v0, u1, v1,  &
+                             P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded)
       endif
       current_bond=>current_bond%next_bond
     enddo
@@ -445,165 +476,170 @@ subroutine interactive_force(bergs,berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_i
   !print *,'IA_x=',IA_x,'IA_y',IA_y, berg%iceberg_num
   !print *,'P_ia_11',P_ia_11,'P_ia_12',P_ia_12, 'P_ia_21',P_ia_21,'P_ia_22', P_ia_22
   !print *, 'P_ia_times_u_x', P_ia_times_u_x, 'P_ia_times_u_y', P_ia_times_u_y
+
   contains
 
+  subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1, &
+                             P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded)
+  !Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  type(iceberg), pointer :: berg
+  type(iceberg), pointer :: other_berg
+  real :: T1, L1, W1, lon1, lat1, x1, y1, R1, A1   !Current iceberg
+  real :: T2, L2, W2, lon2, lat2, x2, y2, R2, A2   !Other iceberg
+  real :: dlon, dlat
+  real :: r_dist_x, r_dist_y, r_dist, A_o, A_min, trapped, T_min
+  real, intent(in) :: u0,v0, u1, v1
+  real :: P_11, P_12, P_21, P_22
+  real :: M1, M2, M_min
+  real :: u2, v2
+  real :: lat_ref, dx_dlon, dy_dlat
+  logical :: critical_interaction_damping_on
+  real :: spring_coef, accel_spring, radial_damping_coef, p_ia_coef, tangental_damping_coef, bond_coef
+  real, intent(inout) :: IA_x, IA_y
+  real, intent(inout) :: P_ia_11, P_ia_12, P_ia_22, P_ia_21, P_ia_times_u_x, P_ia_times_u_y
+  logical ,intent(in) :: bonded
+
+    spring_coef=bergs%spring_coef
+    !bond_coef=bergs%bond_coef
+    radial_damping_coef=bergs%radial_damping_coef
+    tangental_damping_coef=bergs%tangental_damping_coef
+    critical_interaction_damping_on=bergs%critical_interaction_damping_on
+
+    !Using critical values for damping rather than manually setting the damping.
+    if (critical_interaction_damping_on) then
+      radial_damping_coef=2.*sqrt(spring_coef)  ! Critical damping
+      tangental_damping_coef=(2.*sqrt(spring_coef))/4  ! Critical damping   (just a guess)
+    endif
 
-   subroutine calculate_force(bergs,berg,other_berg,IA_x, IA_y, u0, v0, u1, v1, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded) 
-   !Arguments
-     type(icebergs), pointer :: bergs
-     type(iceberg), pointer :: berg
-     type(iceberg), pointer :: other_berg
-     real :: T1, L1, W1, lon1, lat1, x1, y1, R1, A1   !Current iceberg
-     real :: T2, L2, W2, lon2, lat2, x2, y2, R2, A2   !Other iceberg
-     real :: dlon, dlat
-     real :: r_dist_x, r_dist_y, r_dist, A_o, A_min, trapped, T_min
-     real, intent(in) :: u0,v0, u1, v1
-     real :: P_11, P_12, P_21, P_22
-     real :: M1, M2, M_min
-     real :: u2, v2
-     real :: lat_ref, dx_dlon, dy_dlat
-     logical :: critical_interaction_damping_on
-     real :: spring_coef, accel_spring, radial_damping_coef, p_ia_coef, tangental_damping_coef, bond_coef
-     real, intent(inout) :: IA_x, IA_y 
-     real, intent(inout) :: P_ia_11, P_ia_12, P_ia_22, P_ia_21, P_ia_times_u_x, P_ia_times_u_y
-     logical ,intent(in) :: bonded
-
-      spring_coef=bergs%spring_coef
-      !bond_coef=bergs%bond_coef 
-      radial_damping_coef=bergs%radial_damping_coef
-      tangental_damping_coef=bergs%tangental_damping_coef
-      critical_interaction_damping_on=bergs%critical_interaction_damping_on
-
-      !Using critical values for damping rather than manually setting the damping.
-      if (critical_interaction_damping_on) then
-        radial_damping_coef=2.*sqrt(spring_coef)  ! Critical damping  
-        tangental_damping_coef=(2.*sqrt(spring_coef))/4  ! Critical damping   (just a guess)
+    if (berg%iceberg_num .ne. other_berg%iceberg_num) then
+      !From Berg 1
+      L1=berg%length
+      W1=berg%width
+      T1=berg%thickness
+      M1=berg%mass
+      A1=L1*W1
+      lon1=berg%lon_old; lat1=berg%lat_old
+      !call rotpos_to_tang(lon1,lat1,x1,y1)
+
+      !From Berg 1
+      L2=other_berg%length
+      W2=other_berg%width
+      T2=other_berg%thickness
+      M2=other_berg%mass
+      u2=other_berg%uvel_old !Old values are used to make it order invariant
+      v2=other_berg%vvel_old !Old values are used to make it order invariant
+      A2=L2*W2
+      lon2=other_berg%lon_old; lat2=other_berg%lat_old !Old values are used to make it order invariant
+
+      !call rotpos_to_tang(lon2,lat2,x2,y2)
+
+      dlon=lon1-lon2
+      dlat=lat1-lat2
+
+      !Note that this is not the exact distance along a great circle.
+      !Approximation for small distances. Should be fine.
+      !r_dist_x=x1-x2 ; r_dist_y=y1-y2
+      !r_dist=sqrt( ((x1-x2)**2) + ((y1-y2)**2) )
+      lat_ref=0.5*(lat1+lat2)
+      call convert_from_grid_to_meters(lat_ref,bergs%grd%grid_is_latlon,dx_dlon,dy_dlat)
+
+      r_dist_x=dlon*dx_dlon
+      r_dist_y=dlat*dy_dlat
+      r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) )
+
+      if (bergs%hexagonal_icebergs) then
+        R1=sqrt(A1/(2.*sqrt(3.)))
+        R2=sqrt(A2/(2.*sqrt(3.)))
+      else !square packing
+        R1=sqrt(A1/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
+        R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
       endif
+      !!!!!!!!!!!!!!!!!!!!!!!!!!!debugging!!!!!!!!!!!!!!!!!!!!!!!!!!MP1
+      ! if (berg%iceberg_num .eq. 1) then
+      !   print *, 'Comparing longitudes: ', lon1, lon2, r_dist_x, dlon
+      !   print *, 'Comparing latitudes: ', lat1, lat2, r_dist_y, dlat
+      !   print *, 'Outside, iceberg_num, r_dist', berg%iceberg_num, r_dist,bonded
+      !   print *, 'Halo_status', berg%halo_berg,other_berg%halo_berg
+      ! endif
+      ! print *, 'outside the loop',R1, R2,r_dist, bonded
+      !!!!!!!!!!!!!!!!!!!!!!!!!!!debugging!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+
+      !call overlap_area(R1,R2,r_dist,A_o,trapped)
+      !T_min=min(T1,T2)
+      !A_min = min((pi*R1**R1),(pi*R2*R2))
+      M_min=min(M1,M2)
+      !Calculating spring force  (later this should only be done on the first time around)
+      if ((r_dist>0.) .AND. ((r_dist< (R1+R2).AND. (.not. bonded)) .OR. ( (r_dist> (R1+R2)) .AND. (bonded) ) )) then
+        !Spring force
+        !accel_spring=spring_coef*(T_min/T1)*(A_o/A1) ! Old version dependent on area
+        accel_spring=spring_coef*(M_min/M1)*(R1+R2-r_dist)
+        IA_x=IA_x+(accel_spring*(r_dist_x/r_dist))
+        IA_y=IA_y+(accel_spring*(r_dist_y/r_dist))
 
-      if (berg%iceberg_num .ne. other_berg%iceberg_num) then
-        !From Berg 1
-        L1=berg%length
-        W1=berg%width
-        T1=berg%thickness 
-        M1=berg%mass 
-        A1=L1*W1 
-        lon1=berg%lon_old; lat1=berg%lat_old
-        !call rotpos_to_tang(lon1,lat1,x1,y1)
-
-        !From Berg 1
-        L2=other_berg%length
-        W2=other_berg%width
-        T2=other_berg%thickness 
-        M2=other_berg%mass 
-        u2=other_berg%uvel_old !Old values are used to make it order invariant 
-        v2=other_berg%vvel_old !Old values are used to make it order invariant 
-        A2=L2*W2
-        lon2=other_berg%lon_old; lat2=other_berg%lat_old !Old values are used to make it order invariant
-
-        !call rotpos_to_tang(lon2,lat2,x2,y2)
-
-        dlon=lon1-lon2
-        dlat=lat1-lat2
-        
-        !Note that this is not the exact distance along a great circle.
-        !Approximation for small distances. Should be fine.
-        !r_dist_x=x1-x2 ; r_dist_y=y1-y2
-        !r_dist=sqrt( ((x1-x2)**2) + ((y1-y2)**2) )
-        lat_ref=0.5*(lat1+lat2)
-        call convert_from_grid_to_meters(lat_ref,bergs%grd%grid_is_latlon,dx_dlon,dy_dlat)
-
-        r_dist_x=dlon*dx_dlon
-        r_dist_y=dlat*dy_dlat
-        r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) )
-       
-        if (bergs%hexagonal_icebergs) then 
-          R1=sqrt(A1/(2.*sqrt(3.)))
-          R2=sqrt(A2/(2.*sqrt(3.)))
-        else !square packing
-          R1=sqrt(A1/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
-          R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
-        endif
-       !!!!!!!!!!!!!!!!!!!!!!!!!!!debugging!!!!!!!!!!!!!!!!!!!!!!!!!!MP1 
-       ! if (berg%iceberg_num .eq. 1) then
-       !   print *, 'Comparing longitudes: ', lon1, lon2, r_dist_x, dlon
-       !   print *, 'Comparing latitudes: ', lat1, lat2, r_dist_y, dlat
-       !   print *, 'Outside, iceberg_num, r_dist', berg%iceberg_num, r_dist,bonded
-       !   print *, 'Halo_status', berg%halo_berg,other_berg%halo_berg 
-       ! endif
-       ! print *, 'outside the loop',R1, R2,r_dist, bonded
-       !!!!!!!!!!!!!!!!!!!!!!!!!!!debugging!!!!!!!!!!!!!!!!!!!!!!!!!! 
-
-
-       !call overlap_area(R1,R2,r_dist,A_o,trapped)
-       !T_min=min(T1,T2)
-       !A_min = min((pi*R1**R1),(pi*R2*R2)) 
-       M_min=min(M1,M2)
-       !Calculating spring force  (later this should only be done on the first time around)
-       if ((r_dist>0.) .AND. ((r_dist< (R1+R2).AND. (.not. bonded)) .OR. ( (r_dist> (R1+R2)) .AND. (bonded) ) )) then
-         !Spring force
-         !accel_spring=spring_coef*(T_min/T1)*(A_o/A1) ! Old version dependent on area
-         accel_spring=spring_coef*(M_min/M1)*(R1+R2-r_dist)
-         IA_x=IA_x+(accel_spring*(r_dist_x/r_dist))
-         IA_y=IA_y+(accel_spring*(r_dist_y/r_dist))
-         
 
         if (r_dist < 5*(R1+R2)) then
-          
+
           !MP1
           !if (berg%iceberg_num .eq. 1) then
           !  !print *,  '************************************************************'
           !  print *, 'INSIDE, r_dist', berg%iceberg_num, other_berg%iceberg_num, r_dist, bonded
           !endif
-          !print *, 'in the loop1', spring_coef, (M_min/M1), accel_spring,(R1+R2-r_dist) 
+          !print *, 'in the loop1', spring_coef, (M_min/M1), accel_spring,(R1+R2-r_dist)
           !print *, 'in the loop2', IA_x, IA_y, R1, R2,r_dist, berg%iceberg_num,other_berg%iceberg_num
           !Damping force:
           !Paralel velocity
-           P_11=(r_dist_x*r_dist_x)/(r_dist**2)
-           P_12=(r_dist_x*r_dist_y)/(r_dist**2)
-           P_21=(r_dist_x*r_dist_y)/(r_dist**2)
-           P_22=(r_dist_y*r_dist_y)/(r_dist**2)
-           !p_ia_coef=radial_damping_coef*(T_min/T1)*(A_min/A1)
-           p_ia_coef=radial_damping_coef*(M_min/M1)
-           p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2)) &
-           + sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
-          
-           P_ia_11=P_ia_11+p_ia_coef*P_11
-           P_ia_12=P_ia_12+p_ia_coef*P_12
-           P_ia_21=P_ia_21+p_ia_coef*P_21
-           P_ia_22=P_ia_22+p_ia_coef*P_22
-           P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
-           P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
-           !print *, 'Paralel: ',berg%iceberg_num,  p_ia_coef, IA_x, P_ia_11, P_ia_21,P_ia_12, P_ia_22
-
-           !Normal velocities
-           P_11=1-P_11  ;  P_12=-P_12 ; P_21= -P_21 ;    P_22=1-P_22
-           !p_ia_coef=tangental_damping_coef*(T_min/T1)*(A_min/A1)
-           p_ia_coef=tangental_damping_coef*(M_min/M1)
-           p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2))  &
-           + sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
-           P_ia_11=P_ia_11+p_ia_coef*P_11
-           P_ia_12=P_ia_12+p_ia_coef*P_12
-           P_ia_21=P_ia_21+p_ia_coef*P_21
-           P_ia_22=P_ia_22+p_ia_coef*P_22
-           P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
-           P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
-           !print *, 'Perp: ',berg%iceberg_num,  p_ia_coef, IA_x, P_ia_11, P_ia_21,P_ia_12, P_ia_22
-           !print *, 'P_11',P_11
-           !print *, 'P_21',P_21
-           !print *, 'P_12',P_12
-           !print *, 'P_22',P_22
-          endif
+          P_11=(r_dist_x*r_dist_x)/(r_dist**2)
+          P_12=(r_dist_x*r_dist_y)/(r_dist**2)
+          P_21=(r_dist_x*r_dist_y)/(r_dist**2)
+          P_22=(r_dist_y*r_dist_y)/(r_dist**2)
+          !p_ia_coef=radial_damping_coef*(T_min/T1)*(A_min/A1)
+          p_ia_coef=radial_damping_coef*(M_min/M1)
+          p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2)) &
+          + sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
+
+          P_ia_11=P_ia_11+p_ia_coef*P_11
+          P_ia_12=P_ia_12+p_ia_coef*P_12
+          P_ia_21=P_ia_21+p_ia_coef*P_21
+          P_ia_22=P_ia_22+p_ia_coef*P_22
+          P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
+          P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
+          !print *, 'Paralel: ',berg%iceberg_num,  p_ia_coef, IA_x, P_ia_11, P_ia_21,P_ia_12, P_ia_22
+
+          !Normal velocities
+          P_11=1-P_11  ;  P_12=-P_12 ; P_21= -P_21 ;    P_22=1-P_22
+          !p_ia_coef=tangental_damping_coef*(T_min/T1)*(A_min/A1)
+          p_ia_coef=tangental_damping_coef*(M_min/M1)
+          p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2))  &
+          + sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
+          P_ia_11=P_ia_11+p_ia_coef*P_11
+          P_ia_12=P_ia_12+p_ia_coef*P_12
+          P_ia_21=P_ia_21+p_ia_coef*P_21
+          P_ia_22=P_ia_22+p_ia_coef*P_22
+          P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
+          P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
+          !print *, 'Perp: ',berg%iceberg_num,  p_ia_coef, IA_x, P_ia_11, P_ia_21,P_ia_12, P_ia_22
+          !print *, 'P_11',P_11
+          !print *, 'P_21',P_21
+          !print *, 'P_12',P_12
+          !print *, 'P_22',P_22
         endif
       endif
+    endif
 
+  end subroutine calculate_force
 
-      end subroutine calculate_force
-
+  subroutine overlap_area(R1, R2, d, A, trapped)
+  ! Arguments
+  real, intent(in) :: R1
+  real, intent(in) :: R2
+  real, intent(in) :: d
+  real, intent(out) :: A
+  real, intent(out) :: Trapped
+  ! Local variables
+  real :: R1_sq, R2_sq, d_sq
 
-  subroutine overlap_area(R1,R2,d,A,trapped)
-    real, intent(in) :: R1, R2, d
-    real, intent(out) :: A, Trapped
-    real :: R1_sq, R2_sq, d_sq  
     R1_sq=R1**2
     R2_sq=R2**2
     d_sq=d**2
@@ -614,7 +650,7 @@ subroutine overlap_area(R1,R2,d,A,trapped)
         if (d>abs(R1-R2)) then
           A= (R1_sq*acos((d_sq+R1_sq-R2_sq)/(2.*d*R1)))  +  (R2_sq*acos((d_sq+R2_sq-R1_sq)/(2.*d*R2)))  - (0.5*sqrt((-d+R1+R2)*(d+R1-R2)*(d-R1+R2)*(d+R1+R2)))
         else
-          A=min(pi*R1_sq,pi*R2_sq) 
+          A=min(pi*R1_sq,pi*R2_sq)
           Trapped=1.
         endif
       else
@@ -626,25 +662,31 @@ subroutine overlap_area(R1,R2,d,A,trapped)
 
    end subroutine overlap_area
 
-
-
-
 end subroutine interactive_force
 
-
-! ##############################################################################
-
-
+!> Calculates the instantaneous acceleration of an iceberg
 subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, axn, ayn, bxn, byn, debug_flag) !Saving  acceleration for Verlet, Adding Verlet flag - Alon  MP1
 !subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, debug_flag) !old version commmented out by Alon
 ! Arguments
-type(icebergs), pointer :: bergs
-type(iceberg), pointer :: berg
-integer, intent(in) :: i, j
-real, intent(in) :: xi, yj, lat, uvel, vvel, uvel0, vvel0, dt
-real, intent(out) :: ax, ay
-real, intent(inout) :: axn, ayn, bxn, byn ! Added implicit and explicit accelerations to output -Alon
-logical, optional :: debug_flag
+type(icebergs), pointer :: bergs !< Container for all types and memory
+type(iceberg), pointer :: berg !< An iceberg
+integer, intent(in) :: i !< i-index of cell berg is in
+integer, intent(in) :: j !< j-index of cell berg is in
+real, intent(in) :: xi !< Non-dimensional x-position within cell of berg
+real, intent(in) :: yj !< Non-dimensional y-position within cell of berg
+real, intent(in) :: lat !< Latitude of berg (degree N)
+real, intent(in) :: uvel !< Zonal velocity of berg (m/s)
+real, intent(in) :: vvel !< Meridional velocity of berg (m/s)
+real, intent(in) :: uvel0
+real, intent(in) :: vvel0
+real, intent(in) :: dt !< Time step (s)
+real, intent(out) :: ax !< Zonal acceleration (m/s2)
+real, intent(out) :: ay !< Meridional acceleration (m/s2)
+real, intent(inout) :: axn
+real, intent(inout) :: ayn
+real, intent(inout) :: bxn
+real, intent(inout) :: byn ! Added implicit and explicit accelerations to output -Alon
+logical, optional :: debug_flag !< If true, print debugging
 ! Local variables
 type(icebergs_gridded), pointer :: grd
 real :: uo, vo, ui, vi, ua, va, uwave, vwave, ssh_x, ssh_y, sst, sss, cn, hi
@@ -654,7 +696,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 real :: ampl, wmod, Cr, Lwavelength, Lcutoff, Ltop
 real, parameter :: accel_lim=1.e-2, Cr0=0.06, vel_lim=15.
 real :: alpha, beta, C_N
-real :: lambda, detA, A11, A12, A21, A22, RHS_x, RHS_y, D_hi 
+real :: lambda, detA, A11, A12, A21, A22, RHS_x, RHS_y, D_hi
 real :: uveln, vveln, us, vs, speed, loc_dx, new_speed
 real :: u_star, v_star    !Added by Alon
 real :: IA_x, IA_y    !Added by Alon
@@ -666,27 +708,25 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 integer :: itloop
 integer :: stderrunit
 
-Runge_not_Verlet=bergs%Runge_not_Verlet  ! Loading directly from namelist/default , Alon
-interactive_icebergs_on=bergs%interactive_icebergs_on  ! Loading directly from namelist/default , Alon
-use_new_predictive_corrective=bergs%use_new_predictive_corrective  ! Loading directly from namelist/default , Alon
-
-!These values are no longer set as parameters, but rather can be changed as variables.
-alpha=0.0
-beta=1.0
-C_N=0.0
-
-
-!Alon: Verlet requires implicit Coriolis and implicit drag. 
-!Alon: Also, I think that the implicit Coriolis with RK gives icebergs which do not complete inertial circles.
-if (.not.Runge_not_Verlet) then
-alpha=1.0 
-C_N=1.0
-beta=1.0
-use_new_predictive_corrective=.True.
-endif
-
+  Runge_not_Verlet=bergs%Runge_not_Verlet  ! Loading directly from namelist/default , Alon
+  interactive_icebergs_on=bergs%interactive_icebergs_on  ! Loading directly from namelist/default , Alon
+  use_new_predictive_corrective=bergs%use_new_predictive_corrective  ! Loading directly from namelist/default , Alon
+
+  !These values are no longer set as parameters, but rather can be changed as variables.
+  alpha=0.0
+  beta=1.0
+  C_N=0.0
+
+  !Alon: Verlet requires implicit Coriolis and implicit drag.
+  !Alon: Also, I think that the implicit Coriolis with RK gives icebergs which do not complete inertial circles.
+  if (.not.Runge_not_Verlet) then
+    alpha=1.0
+    C_N=1.0
+    beta=1.0
+    use_new_predictive_corrective=.True.
+  endif
 
-!print *, 'axn=',axn,'ayn=',ayn
+  !print *, 'axn=',axn,'ayn=',ayn
   u_star=uvel0+(axn*(dt/2.))  !Alon
   v_star=vvel0+(ayn*(dt/2.))  !Alon
 
@@ -704,7 +744,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
   else
      f_cori=(2.*omega)*sin(pi_180*bergs%lat_ref)
   endif
-!  f_cori=0.
+  !f_cori=0.
 
   M=berg%mass
   T=berg%thickness ! total thickness
@@ -713,7 +753,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
   W=berg%width
   L=berg%length
 
-!Initializing accelerations - Alon. (I am not 100% sure this is needed). I'm not sure what is output if variable is not defined in the subroutine.
+  ! Initializing accelerations - Alon. (I am not 100% sure this is needed). I'm not sure what is output if variable is not defined in the subroutine.
   axn=0.
   ayn=0.
   bxn=0.
@@ -725,14 +765,14 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
   ! Wave radiation
   uwave=ua-uo; vwave=va-vo  ! Use wind speed rel. to ocean for wave model (aja)?
   wmod=uwave*uwave+vwave*vwave ! The wave amplitude and length depend on the wind speed relative to the ocean current;
-                               !  actually wmod is wmod**2 here.
+                               ! actually wmod is wmod**2 here.
   ampl=0.5*0.02025*wmod ! This is "a", the wave amplitude
   Lwavelength=0.32*wmod ! Surface wave length fitted to data in table at
-  !      http://www4.ncsu.edu/eos/users/c/ceknowle/public/chapter10/part2.html
+                        ! http://www4.ncsu.edu/eos/users/c/ceknowle/public/chapter10/part2.html
   Lcutoff=0.125*Lwavelength
   Ltop=0.25*Lwavelength
-  Cr=Cr0*min(max(0.,(L-Lcutoff)/((Ltop-Lcutoff)+1.e-30)),1.) ! Wave radiation coefficient
-  !     fitted to graph from Carrieres et al.,  POAC Drift Model.
+  Cr=Cr0*min(max(0.,(L-Lcutoff)/((Ltop-Lcutoff)+1.e-30)),1.) ! Wave radiation coefficient fitted to
+                                                             ! graph from Carrieres et al.,  POAC Drift Model.
   wave_rad=0.5*rho_seawater/M*Cr*gravity*ampl*min(ampl,F)*(2.*W*L)/(W+L)
   wmod = sqrt(ua*ua+va*va) ! Wind speed
   if (wmod.ne.0.) then
@@ -758,53 +798,50 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 !c_ice=0.
 
     ! Half half accelerations  - axn, ayn
-    if (.not.Runge_not_Verlet) then  
-        axn=-gravity*ssh_x +wave_rad*uwave 
-        ayn=-gravity*ssh_y +wave_rad*vwave 
+    if (.not.Runge_not_Verlet) then
+      axn=-gravity*ssh_x +wave_rad*uwave
+      ayn=-gravity*ssh_y +wave_rad*vwave
     else
-    ! Not half half accelerations  - for RK
-        bxn=-gravity*ssh_x +wave_rad*uwave 
-        byn=-gravity*ssh_y +wave_rad*vwave 
-     endif
-
-
-! Interactive spring acceleration - (Does the spring part need to be called twice?)
-if (interactive_icebergs_on) then
-           call interactive_force(bergs, berg, IA_x, IA_y, uvel0, vvel0, uvel0, vvel0, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y) ! Spring forces, Made by Alon.
-           if (.not.Runge_not_Verlet) then
-               axn=axn + IA_x
-               ayn=ayn + IA_y
-           else
-               bxn=bxn + IA_x
-               byn=byn + IA_y
-           endif
-
-endif
+      ! Not half half accelerations  - for RK
+      bxn=-gravity*ssh_x +wave_rad*uwave
+      byn=-gravity*ssh_y +wave_rad*vwave
+    endif
 
+  ! Interactive spring acceleration - (Does the spring part need to be called twice?)
+  if (interactive_icebergs_on) then
+    call interactive_force(bergs, berg, IA_x, IA_y, uvel0, vvel0, uvel0, vvel0, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y) ! Spring forces, Made by Alon.
+    if (.not.Runge_not_Verlet) then
+      axn=axn + IA_x
+      ayn=ayn + IA_y
+    else
+      bxn=bxn + IA_x
+      byn=byn + IA_y
+    endif
+  endif
 
   if (alpha>0.) then ! If implicit Coriolis, use u_star rather than RK4 latest  !Alon
-        if (C_N>0.) then !  C_N=1 for Crank Nicolson Coriolis, C_N=0 for full implicit Coriolis !Alon  
-           axn=axn+f_cori*v_star
-           ayn=ayn-f_cori*u_star
-        else
-           bxn=bxn+f_cori*v_star
-           byn=byn-f_cori*u_star
-        endif
+    if (C_N>0.) then !  C_N=1 for Crank Nicolson Coriolis, C_N=0 for full implicit Coriolis !Alon
+      axn=axn+f_cori*v_star
+      ayn=ayn-f_cori*u_star
+    else
+      bxn=bxn+f_cori*v_star
+      byn=byn-f_cori*u_star
+    endif
   else
-           bxn=bxn+f_cori*vvel
-           byn=byn-f_cori*uvel
+    bxn=bxn+f_cori*vvel
+    byn=byn-f_cori*uvel
   endif
-  
+
   if (use_new_predictive_corrective) then
-     uveln=uvel0; vveln=vvel0 ! Discuss this change with Alistair. Alon thinks that it is needed. 
+    uveln=uvel0; vveln=vvel0 ! Discuss this change with Alistair. Alon thinks that it is needed.
   else
-     uveln=uvel; vveln=vvel
+    uveln=uvel; vveln=vvel
   endif
- 
+
   us=uvel0   ; vs=vvel0
   do itloop=1,2 ! Iterate on drag coefficients
     if (itloop .eq. 2) then
-      us=uveln   ; vs=vveln
+      us=uveln ; vs=vveln
     endif
   if (use_new_predictive_corrective) then
     !Alon's proposed change - using Bob's improved scheme.
@@ -819,68 +856,66 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
     drag_ice=c_ice*sqrt( (us-ui)**2+(vs-vi)**2 )
   endif
 
-     RHS_x=(axn/2) + bxn
-     RHS_y=(ayn/2) + byn
+  RHS_x=(axn/2) + bxn
+  RHS_y=(ayn/2) + byn
 
-     if (beta>0.) then ! If implicit, use u_star, v_star rather than RK4 latest
-         RHS_x=RHS_x - drag_ocn*(u_star-uo) -drag_atm*(u_star-ua) -drag_ice*(u_star-ui) 
-         RHS_y=RHS_y - drag_ocn*(v_star-vo) -drag_atm*(v_star-va) -drag_ice*(v_star-vi)  
-    else
-         RHS_x=RHS_x - drag_ocn*(uvel-uo) -drag_atm*(uvel-ua) -drag_ice*(uvel-ui)  
-         RHS_y=RHS_y - drag_ocn*(vvel-vo) -drag_atm*(vvel-va) -drag_ice*(vvel-vi)  
-    endif
+  if (beta>0.) then ! If implicit, use u_star, v_star rather than RK4 latest
+    RHS_x=RHS_x - drag_ocn*(u_star-uo) -drag_atm*(u_star-ua) -drag_ice*(u_star-ui)
+    RHS_y=RHS_y - drag_ocn*(v_star-vo) -drag_atm*(v_star-va) -drag_ice*(v_star-vi)
+  else
+    RHS_x=RHS_x - drag_ocn*(uvel-uo) -drag_atm*(uvel-ua) -drag_ice*(uvel-ui)
+    RHS_y=RHS_y - drag_ocn*(vvel-vo) -drag_atm*(vvel-va) -drag_ice*(vvel-vi)
+  endif
 
-if (interactive_icebergs_on) then
-   if (itloop>1) then
-        call interactive_force(bergs, berg, IA_x, IA_y, uvel0, vvel0, us,vs, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y) ! Spring forces, Made by Alon.
+  if (interactive_icebergs_on) then
+    if (itloop>1) then
+      call interactive_force(bergs, berg, IA_x, IA_y, uvel0, vvel0, us,vs, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y) ! Spring forces, Made by Alon.
     endif
-     if (beta>0.) then ! If implicit, use u_star, v_star rather than RK4 latest
-         RHS_x=RHS_x -(((P_ia_11*u_star)+(P_ia_12*v_star))-P_ia_times_u_x) 
-         RHS_y=RHS_y -(((P_ia_21*u_star)+(P_ia_22*v_star))-P_ia_times_u_y) 
+    if (beta>0.) then ! If implicit, use u_star, v_star rather than RK4 latest
+      RHS_x=RHS_x -(((P_ia_11*u_star)+(P_ia_12*v_star))-P_ia_times_u_x)
+      RHS_y=RHS_y -(((P_ia_21*u_star)+(P_ia_22*v_star))-P_ia_times_u_y)
     else
-         RHS_x=RHS_x - (((P_ia_11*uvel)+(P_ia_12*vvel))-P_ia_times_u_x)
-         RHS_y=RHS_y - (((P_ia_21*uvel)+(P_ia_22*vvel))-P_ia_times_u_y)       
+      RHS_x=RHS_x - (((P_ia_11*uvel)+(P_ia_12*vvel))-P_ia_times_u_x)
+      RHS_y=RHS_y - (((P_ia_21*uvel)+(P_ia_22*vvel))-P_ia_times_u_y)
     endif
     !print *,'Before calculation:', berg%iceberg_num, IA_x, IA_y, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y
-endif
+  endif
 
 
   ! Solve for implicit accelerations
-    if (alpha+beta.gt.0.) then
-      lambda=drag_ocn+drag_atm+drag_ice
-      A11=1.+beta*dt*lambda
-      A22=1.+beta*dt*lambda
-      A12=-alpha*dt*f_cori  
-      A21=alpha*dt*f_cori  
-      !A12=dt*f_cori  !Removed by ALon (in order to have the entire matrix. I hope the sign is correct)
-
-      if (C_N>0.) then   !For Crank-Nicolson Coriolis term.   
-          A12=A12/2.
-          A21=A21/2.
-      endif
+  if (alpha+beta.gt.0.) then
+    lambda=drag_ocn+drag_atm+drag_ice
+    A11=1.+beta*dt*lambda
+    A22=1.+beta*dt*lambda
+    A12=-alpha*dt*f_cori
+    A21=alpha*dt*f_cori
+    !A12=dt*f_cori  !Removed by ALon (in order to have the entire matrix. I hope the sign is correct)
+
+    if (C_N>0.) then ! For Crank-Nicolson Coriolis term.
+        A12=A12/2.
+        A21=A21/2.
+    endif
 
-      if (interactive_icebergs_on) then
-            A11=A11+(dt*P_ia_11)
-            A12=A12+(dt*P_ia_12)
-            A21=A21+(dt*P_ia_21)
-            A22=A22+(dt*P_ia_22)
-     endif
+    if (interactive_icebergs_on) then
+          A11=A11+(dt*P_ia_11)
+          A12=A12+(dt*P_ia_12)
+          A21=A21+(dt*P_ia_21)
+          A22=A22+(dt*P_ia_22)
+    endif
 
-     !This is for testing the code using only interactive forces
-     if (bergs%only_interactive_forces) then
-       RHS_x=(IA_x/2) -(((P_ia_11*u_star)+(P_ia_12*v_star))-P_ia_times_u_x) 
-       RHS_y=(IA_y/2) -(((P_ia_21*u_star)+(P_ia_22*v_star))-P_ia_times_u_y) 
+    ! This is for testing the code using only interactive forces
+    if (bergs%only_interactive_forces) then
+       RHS_x=(IA_x/2) -(((P_ia_11*u_star)+(P_ia_12*v_star))-P_ia_times_u_x)
+       RHS_y=(IA_y/2) -(((P_ia_21*u_star)+(P_ia_22*v_star))-P_ia_times_u_y)
        A11=1+(dt*P_ia_11)
        A12=(dt*P_ia_12)
        A21=(dt*P_ia_21)
        A22=1+(dt*P_ia_22)
-     endif
-
-
+    endif
 
-      detA=1./((A11*A22)-(A12*A21))
-      ax=detA*(A22*RHS_x-A12*RHS_y)
-      ay=detA*(A11*RHS_y-A21*RHS_x)
+    detA=1./((A11*A22)-(A12*A21))
+    ax=detA*(A22*RHS_x-A12*RHS_y)
+    ay=detA*(A11*RHS_y-A21*RHS_x)
 
 !Alistair's version removed by Alon
 !      detA=1./(A11**2+A12**2)
@@ -890,43 +925,43 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
       ax=RHS_x; ay=RHS_y
     endif
 
-      uveln=u_star+dt*ax        ! Alon
-      vveln=v_star+dt*ay        ! Alon
+    uveln=u_star+dt*ax        ! Alon
+    vveln=v_star+dt*ay        ! Alon
 !MP4
   !    if (berg%iceberg_num .eq. 1) then
   !      print *, '***************************************************'
   !      print *,'Iceberg_num, itloop', berg%iceberg_num, itloop
-  !      print *, 'P matrix:', P_ia_11, P_ia_12,P_ia_21,P_ia_22,P_ia_times_u_x, P_ia_times_u_x 
-  !      print *,'A_matrix', A11, A12, A21, A22 
-  !      print *,'IA_x IA_y', IA_x, IA_y 
+  !      print *, 'P matrix:', P_ia_11, P_ia_12,P_ia_21,P_ia_22,P_ia_times_u_x, P_ia_times_u_x
+  !      print *,'A_matrix', A11, A12, A21, A22
+  !      print *,'IA_x IA_y', IA_x, IA_y
   !      print *, 'RHS, ustar, uvel,ax: ', RHS_x, u_star,uveln, ax
   !    endif
   enddo ! itloop
 
-!Saving the totally explicit part of the acceleration to use in finding the next position and u_star -Alon
-    axn=0.
-    ayn=0.
-    if (.not.Runge_not_Verlet) then
-        axn=-gravity*ssh_x +wave_rad*uwave
-        ayn=-gravity*ssh_y +wave_rad*vwave
-        if (interactive_icebergs_on) then
-          axn=axn + IA_x
-          ayn=ayn + IA_y
-        endif
-    endif
-    if (C_N>0.) then !  C_N=1 for Crank Nicolson Coriolis, C_N=0 for full implicit Coriolis !Alon 
-      axn=axn+f_cori*vveln
-      ayn=ayn-f_cori*uveln
+  !Saving the totally explicit part of the acceleration to use in finding the next position and u_star -Alon
+  axn=0.
+  ayn=0.
+  if (.not.Runge_not_Verlet) then
+    axn=-gravity*ssh_x +wave_rad*uwave
+    ayn=-gravity*ssh_y +wave_rad*vwave
+    if (interactive_icebergs_on) then
+      axn=axn + IA_x
+      ayn=ayn + IA_y
     endif
+  endif
+  if (C_N>0.) then !  C_N=1 for Crank Nicolson Coriolis, C_N=0 for full implicit Coriolis !Alon
+    axn=axn+f_cori*vveln
+    ayn=ayn-f_cori*uveln
+  endif
 
-     !This is for testing the code using only interactive forces
-     if (bergs%only_interactive_forces) then
-       axn=IA_x
-       ayn=IA_y
-     endif
+  !This is for testing the code using only interactive forces
+  if (bergs%only_interactive_forces) then
+    axn=IA_x
+    ayn=IA_y
+  endif
 
-    bxn= ax-(axn/2) !Alon
-    byn= ay-(ayn/2) !Alon
+  bxn= ax-(axn/2) !Alon
+  byn= ay-(ayn/2) !Alon
 
   ! Limit speed of bergs based on a CFL criteria
   if ((bergs%speed_limit>0.) .or. (bergs%speed_limit .eq.-1.)) then
@@ -934,13 +969,13 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
     if (speed>0.) then
       loc_dx=min(0.5*(grd%dx(i,j)+grd%dx(i,j-1)),0.5*(grd%dy(i,j)+grd%dy(i-1,j))) ! min(dx,dy)
       !new_speed=min(loc_dx/dt*bergs%speed_limit,speed) ! Restrict speed to dx/dt x factor
-      new_speed=loc_dx/dt*bergs%speed_limit ! Speed limit as a factor of dx / dt 
+      new_speed=loc_dx/dt*bergs%speed_limit ! Speed limit as a factor of dx / dt
       if (new_speed<speed) then
         if (bergs%speed_limit>0.) then
           uveln=uveln*(new_speed/speed) ! Scale velocity to reduce speed
           vveln=vveln*(new_speed/speed) ! without changing the direction
           bergs%nspeeding_tickets=bergs%nspeeding_tickets+1
-        else 
+        else
           call error_mesg('diamonds, Speeding icebergs', 'Faster than the CFL!', WARNING)
           write(stderrunit,*) 'diamonds, Speeding berg1! =',mpp_pe(), berg%iceberg_num
           write(stderrunit,*) 'diamonds, Speeding berg2, speed =',speed, loc_dx/dt
@@ -1084,7 +1119,7 @@ subroutine dump_locfld(grd,i0,j0,A,lbl)
     write(stderrunit,'("pe=",i3,x,i8,3es12.4)') mpp_pe(),j0+jj,(B(ii,jj),ii=-1,1)
   enddo
   end subroutine dump_locfld
-  
+
   subroutine dump_locvel(grd,i0,j0,A,lbl)
   ! Arguments
   type(icebergs_gridded), pointer :: grd
@@ -1108,14 +1143,14 @@ subroutine dump_locvel(grd,i0,j0,A,lbl)
     write(stderrunit,'("pe=",i3,x,i8,3es12.4)') mpp_pe(),j0+jj,(B(ii,jj),ii=-1,0)
   enddo
   end subroutine dump_locvel
-  
+
 end subroutine accel
 
 ! ##############################################################################
 
 subroutine thermodynamics(bergs)
 ! Arguments
-type(icebergs), pointer :: bergs
+type(icebergs), pointer :: bergs !< Container for all types and memory
 ! Local variables
 type(icebergs_gridded), pointer :: grd
 type(bond), pointer :: current_bond
@@ -1134,13 +1169,13 @@ subroutine thermodynamics(bergs)
 
   ! For convenience
   grd=>bergs%grd
-  
-  !Initializing 
+
+  !Initializing
   grd%Uvel_on_ocean(:,:,:)=0.
   grd%Vvel_on_ocean(:,:,:)=0.
 
   ! Thermodynamics of first halo row is calculated, so that spread mass to ocean works correctly
-  do grdj = grd%jsc-1,grd%jec+1 ; do grdi = grd%isc-1,grd%iec+1  
+  do grdj = grd%jsc-1,grd%jec+1 ; do grdi = grd%isc-1,grd%iec+1
     this=>bergs%list(grdi,grdj)%first
     do while(associated(this))
       if (debug) call check_position(grd, this, 'thermodynamics (top)')
@@ -1149,7 +1184,7 @@ subroutine thermodynamics(bergs)
               this%sss,this%cn, this%hi)
       SST=this%sst
       SSS=this%sss
-      IC=min(1.,this%cn+bergs%sicn_shift) ! Shift sea-ice concentration 
+      IC=min(1.,this%cn+bergs%sicn_shift) ! Shift sea-ice concentration
       M=this%mass
       T=this%thickness ! total thickness
       !D=(bergs%rho_bergs/rho_seawater)*T ! draught (keel depth)
@@ -1159,12 +1194,12 @@ subroutine thermodynamics(bergs)
       i=this%ine
       j=this%jne
       Vol=T*W*L
-  
+
       ! Environment
       dvo=sqrt((this%uvel-this%uo)**2+(this%vvel-this%vo)**2)
       dva=sqrt((this%ua-this%uo)**2+(this%va-this%vo)**2)
       Ss=1.5*(dva**0.5)+0.1*dva ! Sea state
-  
+
       ! Melt rates in m/s
       Mv=max( 7.62e-3*SST+1.29e-3*(SST**2), 0.) &! Buoyant convection at sides
           *perday ! convert to m/s
@@ -1172,10 +1207,10 @@ subroutine thermodynamics(bergs)
           *perday ! convert to m/s
       Me=max( 1./12.*(SST+2.)*Ss*(1+cos(pi*(IC**3))) ,0.) &! Wave erosion
           *perday ! convert to m/s
-       
-      !For icebergs acting as ice shelves 
+
+      !For icebergs acting as ice shelves
       if ((bergs%melt_icebergs_as_ice_shelf) .or.(bergs%use_mixed_melting))  then
-        if (.not. bergs%use_mixed_layer_salinity_for_thermo)  SSS=35.0  
+        if (.not. bergs%use_mixed_layer_salinity_for_thermo)  SSS=35.0
         call find_basal_melt(bergs,dvo,this%lat,SSS,SST,bergs%Use_three_equation_model,T,Ms,this%iceberg_num)
         Ms=max(Ms,0.) !No refreezing allowed for now
         !Set melt to zero if ocean is too thin.
@@ -1188,7 +1223,7 @@ subroutine thermodynamics(bergs)
 
         if (bergs%use_mixed_melting) then
           N_bonds=0.
-          N_max=4.0  !Maximum number of bonds that element can form based on shape      
+          N_max=4.0  !Maximum number of bonds that element can form based on shape
           if (bergs%hexagonal_icebergs) N_max=6.0
           if (bergs%iceberg_bonds_on) then
             ! Determining number of bonds
@@ -1198,7 +1233,7 @@ subroutine thermodynamics(bergs)
               current_bond=>current_bond%next_bond
             enddo
           endif
-          if  (this%static_berg .eq. 1)  N_bonds=N_max  !Static icebergs melt  like ice shelves 
+          if  (this%static_berg .eq. 1)  N_bonds=N_max  !Static icebergs melt  like ice shelves
           Me=((N_max-N_bonds)/N_max)*(Mv+Me)
           Mv=0.0
           Mb=(((N_max-N_bonds)/N_max)*(Mb)) + (N_bonds/N_max)*Ms
@@ -1208,26 +1243,26 @@ subroutine thermodynamics(bergs)
           Mb=Ms
         endif
       endif
-            
+
       if (bergs%set_melt_rates_to_zero) then
         Mv=0.0
         Mb=0.0
         Me=0.0
       endif
-  
+
       if (bergs%use_operator_splitting) then
         ! Operator split update of volume/mass
         Tn=max(T-Mb*bergs%dt,0.) ! new total thickness (m)
         nVol=Tn*W*L ! new volume (m^3)
         Mnew1=(nVol/Vol)*M ! new mass (kg)
         dMb=M-Mnew1 ! mass lost to basal melting (>0) (kg)
-  
+
         Ln=max(L-Mv*bergs%dt,0.) ! new length (m)
         Wn=max(W-Mv*bergs%dt,0.) ! new width (m)
         nVol=Tn*Wn*Ln ! new volume (m^3)
         Mnew2=(nVol/Vol)*M ! new mass (kg)
         dMv=Mnew1-Mnew2 ! mass lost to buoyant convection (>0) (kg)
-  
+
         Ln=max(Ln-Me*bergs%dt,0.) ! new length (m)
         Wn=max(Wn-Me*bergs%dt,0.) ! new width (m)
         nVol=Tn*Wn*Ln ! new volume (m^3)
@@ -1247,7 +1282,7 @@ subroutine thermodynamics(bergs)
         dMe=(M/Vol)*(T*(W+L))*Me*bergs%dt ! approx. mass lost to erosion (kg)
         dMv=(M/Vol)*(T*(W+L))*Mv*bergs%dt ! approx. mass loss to buoyant convection (kg)
       endif
-  
+
       ! Bergy bits
       if (bergs%bergy_bit_erosion_fraction>0.) then
         Mbits=this%mass_of_bits ! mass of bergy bits (kg)
@@ -1260,7 +1295,7 @@ subroutine thermodynamics(bergs)
         Mbb=bergs%rho_bergs*Abits*Mbb ! in kg/s
         dMbitsM=min(Mbb*bergs%dt,nMbits) ! bergy bits mass lost to melting (kg)
         nMbits=nMbits-dMbitsM ! remove mass lost to bergy bits melt
-        if (Mnew==0.) then ! if parent berg has completely melted then 
+        if (Mnew==0.) then ! if parent berg has completely melted then
           dMbitsM=dMbitsM+nMbits ! instantly melt all the bergy bits
           nMbits=0.
         endif
@@ -1270,7 +1305,7 @@ subroutine thermodynamics(bergs)
         dMbitsM=0.
         nMbits=this%mass_of_bits ! retain previous value incase non-zero
       endif
-  
+
       ! Add melting to the grid and field diagnostics
       if (grd%area(i,j).ne.0.) then
         melt=(dM-(dMbitsE-dMbitsM))/bergs%dt ! kg/s
@@ -1305,69 +1340,68 @@ subroutine thermodynamics(bergs)
         write(stderrunit,*) 'msk=',grd%msk(i,j),grd%area(i,j)
         call error_mesg('diamonds, thermodynamics', 'berg appears to have grounded!', FATAL)
       endif
-  
- 
-   ! Rolling 
-   !There are now 3 iceberg rolling schemes:
-   !1) Rolling based on aspect ratio threshold (iceberg of constant density)
-   !2) Rolling based on corrected Weeks and Mellor scheme
-   !3) Rolling based on incorrect Weeks and Mellor scheme - kept for legacy reasons
-    if (bergs%allow_bergs_to_roll) then
-      Dn=(bergs%rho_bergs/rho_seawater)*Tn ! draught (keel depth)
-      if ( Dn>0. ) then
-        if ( (.not.bergs%use_updated_rolling_scheme) .and. (bergs%tip_parameter<999.) ) then    !Use Rolling Scheme 3
-            if ( max(Wn,Ln)<sqrt(0.92*(Dn**2)+58.32*Dn) ) then
-              call swap_variables(Tn,Wn)
-            endif
-        else
-          if (Wn>Ln) call swap_variables(Ln,Wn)  !Make sure that Wn is the smaller dimension
-        
-          if ( (.not.bergs%use_updated_rolling_scheme) .and. (bergs%tip_parameter>=999.) ) then    !Use Rolling Scheme 2
-            q=bergs%rho_bergs/rho_seawater
-            Delta=6.0
-            if (Wn<sqrt((6.0*q*(1-q)*(Tn**2))-(12*Delta*q*Tn))) then
+
+      ! Rolling
+      !There are now 3 iceberg rolling schemes:
+      !1) Rolling based on aspect ratio threshold (iceberg of constant density)
+      !2) Rolling based on corrected Weeks and Mellor scheme
+      !3) Rolling based on incorrect Weeks and Mellor scheme - kept for legacy reasons
+      if (bergs%allow_bergs_to_roll) then
+        Dn=(bergs%rho_bergs/rho_seawater)*Tn ! draught (keel depth)
+        if ( Dn>0. ) then
+          if ( (.not.bergs%use_updated_rolling_scheme) .and. (bergs%tip_parameter<999.) ) then    !Use Rolling Scheme 3
+              if ( max(Wn,Ln)<sqrt(0.92*(Dn**2)+58.32*Dn) ) then
                 call swap_variables(Tn,Wn)
+              endif
+          else
+            if (Wn>Ln) call swap_variables(Ln,Wn)  !Make sure that Wn is the smaller dimension
+
+            if ( (.not.bergs%use_updated_rolling_scheme) .and. (bergs%tip_parameter>=999.) ) then    !Use Rolling Scheme 2
+              q=bergs%rho_bergs/rho_seawater
+              Delta=6.0
+              if (Wn<sqrt((6.0*q*(1-q)*(Tn**2))-(12*Delta*q*Tn))) then
+                  call swap_variables(Tn,Wn)
+              endif
             endif
-          endif
 
-          if (bergs%use_updated_rolling_scheme) then    !Use Rolling Scheme 1
-            if (bergs%tip_parameter>0.) then
-              tip_parameter=bergs%tip_parameter
-            else
-              ! Equation 27 from Burton et al 2012, or equivolently, Weeks and Mellor 1979 with constant density
-              tip_parameter=sqrt(6*(bergs%rho_bergs/rho_seawater)*(1-(bergs%rho_bergs/rho_seawater)))   !using default values gives 0.92
-            endif
-            if ((tip_parameter*Tn)>Wn)  then     !note that we use the Thickness instead of the Draft
-                call swap_variables(Tn,Wn)
+            if (bergs%use_updated_rolling_scheme) then    !Use Rolling Scheme 1
+              if (bergs%tip_parameter>0.) then
+                tip_parameter=bergs%tip_parameter
+              else
+                ! Equation 27 from Burton et al 2012, or equivolently, Weeks and Mellor 1979 with constant density
+                tip_parameter=sqrt(6*(bergs%rho_bergs/rho_seawater)*(1-(bergs%rho_bergs/rho_seawater)))   !using default values gives 0.92
+              endif
+              if ((tip_parameter*Tn)>Wn)  then     !note that we use the Thickness instead of the Draft
+                  call swap_variables(Tn,Wn)
+              endif
             endif
           endif
+          Dn=(bergs%rho_bergs/rho_seawater)*Tn ! re-calculate draught (keel depth) for grounding
         endif
-        Dn=(bergs%rho_bergs/rho_seawater)*Tn ! re-calculate draught (keel depth) for grounding
       endif
-    endif
 
-       !This option allows iceberg melt fluxes to enter the ocean without the icebergs changing shape
-       if (bergs%Iceberg_melt_without_decay) then
-         !In this case, the iceberg dimension are reset to their values before
-         !the thermodynamics are applied. 
-         !If the spread_mass is being used to calculate melt, we calculate this
-         !before reseting 
-         if (bergs%find_melt_using_spread_mass) then
-           if (Mnew>0.) then !If the berg still exists
-             call spread_mass_across_ocean_cells(bergs,this, i, j, this%xi, this%yj,Mnew , nMbits, this%mass_scaling, Ln*Wn,  Tn)
-           endif
-         endif
-         !Reset all the values
-         Mnew=this%mass
-         nMbits=this%mass_of_bits
-         Tn=this%thickness
-         Wn=this%width
-         Ln=this%length
-         if (bergs%bergy_bit_erosion_fraction>0.) then
-           Mbits=this%mass_of_bits ! mass of bergy bits (kg)
-           Lbits=min(L,W,T,40.) ! assume bergy bits are smallest dimension or 40 meters
-           Abits=(Mbits/bergs%rho_bergs)/Lbits ! Effective bottom area (assuming T=Lbits)
-         endif
+      !This option allows iceberg melt fluxes to enter the ocean without the icebergs changing shape
+      if (bergs%Iceberg_melt_without_decay) then
+        !In this case, the iceberg dimension are reset to their values before
+        !the thermodynamics are applied.
+        !If the spread_mass is being used to calculate melt, we calculate this
+        !before reseting
+        if (bergs%find_melt_using_spread_mass) then
+          if (Mnew>0.) then !If the berg still exists
+            call spread_mass_across_ocean_cells(bergs,this, i, j, this%xi, this%yj,Mnew , nMbits, this%mass_scaling, Ln*Wn,  Tn)
+          endif
+        endif
+        !Reset all the values
+        Mnew=this%mass
+        nMbits=this%mass_of_bits
+        Tn=this%thickness
+        Wn=this%width
+        Ln=this%length
+        if (bergs%bergy_bit_erosion_fraction>0.) then
+          Mbits=this%mass_of_bits ! mass of bergy bits (kg)
+          Lbits=min(L,W,T,40.) ! assume bergy bits are smallest dimension or 40 meters
+          Abits=(Mbits/bergs%rho_bergs)/Lbits ! Effective bottom area (assuming T=Lbits)
+        endif
       else
         ! Store the new state of iceberg (with L>W)
         this%mass=Mnew
@@ -1377,7 +1411,7 @@ subroutine thermodynamics(bergs)
         this%length=max(Wn,Ln)
       endif
       next=>this%next
-  
+
       ! Did berg completely melt?
       if (Mnew<=0.) then ! Delete the berg
         call move_trajectory(bergs, this)
@@ -1388,31 +1422,28 @@ subroutine thermodynamics(bergs)
     enddo
   enddo ; enddo
 
-
   contains
 
   subroutine swap_variables(x,y)
   ! Arguments
   real, intent(inout) :: x, y
   real :: temp
-  temp=x
-  x=y
-  y=temp
+    temp=x
+    x=y
+    y=temp
   end subroutine swap_variables
 
 end subroutine thermodynamics
 
-
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 subroutine create_gridded_icebergs_fields(bergs)
 ! Arguments
-type(icebergs), pointer :: bergs
+type(icebergs), pointer :: bergs !< Container for all types and memory
 ! Local variables
 type(icebergs_gridded), pointer :: grd
 type(iceberg), pointer :: this
 integer i,j
 integer :: grdi, grdj
-real :: Hocean, Dn,Tn,dvo, mass_tmp 
+real :: Hocean, Dn,Tn,dvo, mass_tmp
 real :: ustar_h, ustar
 real :: orientation
 real :: ave_thickness, ave_draft
@@ -1422,33 +1453,33 @@ subroutine create_gridded_icebergs_fields(bergs)
   ! For convenience
   grd=>bergs%grd
 
-  spread_mass_tmp(:,:)=0. !Initializing temporary variable to use in iceberg melt calculation 
+  spread_mass_tmp(:,:)=0. !Initializing temporary variable to use in iceberg melt calculation
 
   !Special case for icebergs not decaying, but mass diffence being used for melt rates
   if ((bergs%find_melt_using_spread_mass) .and.  (bergs%Iceberg_melt_without_decay)) then
-    call sum_up_spread_fields(bergs, spread_mass_tmp(grd%isc:grd%iec,grd%jsc:grd%jec),'mass') 
+    call sum_up_spread_fields(bergs, spread_mass_tmp(grd%isc:grd%iec,grd%jsc:grd%jec),'mass')
   endif
- 
-  !Loop through icebergs and spread mass on ocean 
+
+  !Loop through icebergs and spread mass on ocean
   call calculate_mass_on_ocean(bergs, with_diagnostics=.true.)
-  
-  !Finding the spread fields 
-  if ((grd%id_spread_uvel>0)  .or. (bergs%pass_fields_to_ocean_model)) then 
+
+  !Finding the spread fields
+  if ((grd%id_spread_uvel>0)  .or. (bergs%pass_fields_to_ocean_model)) then
     grd%spread_uvel(:,:)=0.
-    call sum_up_spread_fields(bergs, grd%spread_uvel(grd%isc:grd%iec,grd%jsc:grd%jec), 'Uvel') 
+    call sum_up_spread_fields(bergs, grd%spread_uvel(grd%isc:grd%iec,grd%jsc:grd%jec), 'Uvel')
   endif
-  if ( (grd%id_spread_vvel>0)  .or. (bergs%pass_fields_to_ocean_model)) then 
+  if ( (grd%id_spread_vvel>0)  .or. (bergs%pass_fields_to_ocean_model)) then
     grd%spread_vvel(:,:)=0.
-    call sum_up_spread_fields(bergs, grd%spread_vvel(grd%isc:grd%iec,grd%jsc:grd%jec), 'Vvel') 
+    call sum_up_spread_fields(bergs, grd%spread_vvel(grd%isc:grd%iec,grd%jsc:grd%jec), 'Vvel')
   endif
-  if ( (grd%id_spread_area>0)  .or. (bergs%pass_fields_to_ocean_model)) then 
+  if ( (grd%id_spread_area>0)  .or. (bergs%pass_fields_to_ocean_model)) then
     grd%spread_area(:,:)=0.
-    call sum_up_spread_fields(bergs, grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec), 'area') 
+    call sum_up_spread_fields(bergs, grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec), 'area')
   endif
-  !Always find spread_mass since it is used for so many things.  
+  !Always find spread_mass since it is used for so many things.
   grd%spread_mass(:,:)=0.
-    call sum_up_spread_fields(bergs, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec),'mass') 
-  
+    call sum_up_spread_fields(bergs, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec),'mass')
+
   !Using spread_mass_to_ocean to calculate melt rates (if this option is chosen)
   if (bergs%find_melt_using_spread_mass) then
     if (.not. bergs%Iceberg_melt_without_decay) &
@@ -1463,25 +1494,25 @@ subroutine create_gridded_icebergs_fields(bergs)
     grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)=grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec)*HLF !Not 100% sure this is correct.
   endif
 
-  !Dividng the gridded iceberg momentum diagnostic by the iceberg mass to get velocities
+  ! Dividing the gridded iceberg momentum diagnostic by the iceberg mass to get velocities
   if ((grd%id_u_iceberg>0) .or. (grd%id_v_iceberg>0)) then
-    do j = grd%jsc,grd%jec ; do i = grd%isc,grd%iec  
+    do j = grd%jsc,grd%jec ; do i = grd%isc,grd%iec
       if (grd%mass(i,j)>0.) then
         if (grd%id_u_iceberg>0) &
           grd%u_iceberg(i,j)=grd%u_iceberg(i,j)/grd%mass(i,j)
         if (grd%id_v_iceberg>0) &
           grd%v_iceberg(i,j)=grd%v_iceberg(i,j)/grd%mass(i,j)
       else
-        if (grd%id_u_iceberg>0)  grd%u_iceberg(i,j)=0. 
-        if (grd%id_v_iceberg>0)  grd%v_iceberg(i,j)=0. 
+        if (grd%id_u_iceberg>0)  grd%u_iceberg(i,j)=0.
+        if (grd%id_v_iceberg>0)  grd%v_iceberg(i,j)=0.
       endif
     enddo; enddo
   endif
-  
+
   !Calculating ustar_iceberg (gridded)
   grd%ustar_iceberg(:,:)=0.
   if  ((grd%id_ustar_iceberg>0) .or. (bergs%pass_fields_to_ocean_model)) then   !Update diagnostic of iceberg mass spread on ocean
-    do j = grd%jsc,grd%jec ; do i = grd%isc,grd%iec  
+    do j = grd%jsc,grd%jec ; do i = grd%isc,grd%iec
       dvo=sqrt((grd%spread_uvel(i,j)-grd%uo(i,j))**2+(grd%spread_vvel(i,j)-grd%vo(i,j))**2)
       ustar = sqrt(bergs%cdrag_icebergs*(dvo**2  + bergs%utide_icebergs**2))
       ustar_h = max(bergs%ustar_icebergs_bg, ustar)
@@ -1494,7 +1525,7 @@ subroutine create_gridded_icebergs_fields(bergs)
   if (bergs%apply_thickness_cutoff_to_gridded_melt) then
     do i=grd%isd,grd%ied ; do j=grd%jsd,grd%jed
       if ((bergs%melt_cutoff >=0.) .and. (grd%spread_area(i,j)>0.)) then
-        ave_thickness=grd%spread_mass(i,j)/(grd%spread_area(i,j)*bergs%rho_bergs) 
+        ave_thickness=grd%spread_mass(i,j)/(grd%spread_area(i,j)*bergs%rho_bergs)
         ave_draft=ave_thickness*(bergs%rho_bergs/rho_seawater)
         if ((grd%ocean_depth(i,j)-ave_draft) < bergs%melt_cutoff) then
           grd%floating_melt(i,j)=0.0
@@ -1505,103 +1536,100 @@ subroutine create_gridded_icebergs_fields(bergs)
   endif
 end subroutine create_gridded_icebergs_fields
 
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-subroutine find_basal_melt(bergs,dvo,lat,salt,temp,Use_three_equation_model,thickness,basal_melt,iceberg_num)
-  ! Arguments
-  type(icebergs), pointer :: bergs
-  ! Local variables
-  real , intent(out) :: basal_melt !Melt rate underneath the icebergs
-  real , intent(in) :: dvo !Speed of iceberg relative to ocean mixed layer
-  real , intent(in) :: salt !Salinity of mixed layer
-  real , intent(in) :: temp !Temperature of mixed layer
-  real , intent(in) :: lat !Latitude (for boundary layer calculation)
-  integer , intent(in) :: iceberg_num !Iceberg number, used for debugging (error messages)
-  real , intent(in) :: thickness !Ice thickness - needed to work out the pressure below the ice
-  logical , intent(in) :: Use_three_equation_model !True uses the 3 equation model, False uses the 2 equation model.
-  
-  ! Local variables
-  real :: ustar, f_cori, absf,tfreeze
-  real :: Hml !Mixed layer depth
-
-  !These could also be useful output variables if needed.
-  real :: t_flux, exch_vel_t, exch_vel_s,tflux_shelf,lprec 
- 
-  real ::  Rhoml   ! Ocean mixed layer density in kg m-3.
-  real ::  p_int   ! The pressure at the ice-ocean interface, in Pa.
-
-  real, parameter :: VK    = 0.40     ! Von Karman's constant - dimensionless
-  real :: ZETA_N = 0.052   ! The fraction of the boundary layer over which the
-                           ! viscosity is linearly increasing. (Was 1/8. Why?)
-  real, parameter :: RC    = 0.20     ! critical flux Richardson number.
-  real :: I_ZETA_N  ! The inverse of ZETA_N.
-  real :: I_LF  ! Inverse of Latent Heat of fusion (J kg-1)
-  real :: I_VK      ! The inverse of VK.
-  real :: PR, SC    ! The Prandtl number and Schmidt number, nondim.
-!
-  ! 3 equation formulation variables
-  real :: Sbdry     !   Salinities in the ocean at the interface with the
-  real :: Sbdry_it  ! the ice shelf, in PSU.
-  real :: dS_it     ! The interface salinity change during an iteration, in PSU.
-  real :: hBL_neut  ! The neutral boundary layer thickness, in m.
-  real :: hBL_neut_h_molec ! The ratio of the neutral boundary layer thickness
-                           ! to the molecular boundary layer thickness, ND.
-  real :: wT_flux ! The vertical fluxes of heat and buoyancy just inside the
-  real :: wB_flux ! ocean, in C m s-1 and m2 s-3, ###CURRENTLY POSITIVE UPWARD.
-  real :: dB_dS  ! The derivative of buoyancy with salinity, in m s-2 PSU-1.
-  real :: dB_dT  ! The derivative of buoyancy with temperature, in m s-2 C-1.
-  real :: I_n_star, n_star_term
-  real :: dIns_dwB  ! The partial derivative of I_n_star with wB_flux, in ???.
-  real :: dT_ustar, dS_ustar
-  real :: ustar_h
-  real :: Gam_turb
-  real :: Gam_mol_t, Gam_mol_s
-  real :: RhoCp
-  real :: I_RhoLF
-  real :: Rho0
-  real :: ln_neut
-  real :: mass_exch
-  real :: Sb_min, Sb_max
-  real :: dS_min, dS_max
-  real :: density_ice
-!
-  ! Variables used in iterating for wB_flux.
-  real :: wB_flux_new, DwB, dDwB_dwB_in
-  real :: I_Gam_T, I_Gam_S
-  real :: dG_dwB, iDens
-  logical :: Sb_min_set, Sb_max_set
-  logical :: out_of_bounds
-
-  real, parameter :: c2_3 = 2.0/3.0
-  integer ::  it1, it3
- 
-  !Parameters copied ice shelf module defaults (could be entered in the namelist later)
-  real, parameter ::  dR0_dT = -0.038357 ! Partial derivative of the mixed layer density with temperature, in units of kg m-3 K-1. 
-  real, parameter ::  dR0_dS = 0.805876 ! Partial derivative of the mixed layer density with salinity, in units of kg m-3 psu-1.
-  real, parameter ::  RHO_T0_S0 = 999.910681 ! Density of water with T=0, S=0 for linear EOS
-  real, parameter :: Salin_Ice =0.0 !Salinity of ice
-  real, parameter :: Temp_Ice = -15.0 !Salinity of ice
-  real, parameter :: kd_molec_salt=  8.02e-10 !The molecular diffusivity of salt in sea water at the freezing point
-  real, parameter :: kd_molec_temp=  1.41e-7 !The molecular diffusivity of heat in sea water at the freezing point
-  real, parameter :: kv_molec=  1.95e-6 !The molecular molecular kinimatic viscosity of sea water at the freezing point
-  real, parameter :: Cp_Ice =  2009.0 !Specific heat capacity of ice, taking from HJ99 (Holland and Jenkins 1999)
-  real, parameter :: Cp_ml =  3974.0 !Specific heat capacity of mixed layer, taking from HJ99 (Holland and Jenkins 1999)
-  real, parameter :: LF =  3.335e5 !Latent heat of fusion, taken from HJ99 (Holland and Jenkins 1999)
-  real, parameter :: gamma_t =  0.0 ! Exchange velcoity used in 2 equation model. Whn gamma_t is >0, the exchange velocity is independ of u_star. 
-                                  ! When gamma_t=0.0, then gamma_t is not used, and the exchange velocity is found using u_star.
-  real, parameter :: p_atm =  101325 ! Average atmospheric pressure (Pa) - from Google. 
-  
+subroutine find_basal_melt(bergs, dvo, lat, salt, temp, Use_three_equation_model, thickness, basal_melt, iceberg_num)
+! Arguments
+type(icebergs), pointer :: bergs !< Container for all types and memory
+real, intent(in) :: dvo !< Speed of iceberg relative to ocean mixed layer
+real, intent(in) :: lat !< Latitude (for boundary layer calculation)
+real, intent(in) :: salt !< Salinity of mixed layer
+real, intent(in) :: temp !< Temperature of mixed layer
+logical, intent(in) :: Use_three_equation_model !< True uses the 3 equation model, False uses the 2 equation model.
+real, intent(in) :: thickness !< Ice thickness - needed to work out the pressure below the ice
+real, intent(out) :: basal_melt !< Melt rate underneath the icebergs
+integer, intent(in) :: iceberg_num !< Iceberg number, used for debugging (error messages)
+! Local variables
+real :: ustar, f_cori, absf,tfreeze
+real :: Hml !Mixed layer depth
+
+!These could also be useful output variables if needed.
+real :: t_flux, exch_vel_t, exch_vel_s,tflux_shelf,lprec
+
+real ::  Rhoml   ! Ocean mixed layer density in kg m-3.
+real ::  p_int   ! The pressure at the ice-ocean interface, in Pa.
+
+real, parameter :: VK    = 0.40     ! Von Karman's constant - dimensionless
+real :: ZETA_N = 0.052   ! The fraction of the boundary layer over which the
+                         ! viscosity is linearly increasing. (Was 1/8. Why?)
+real, parameter :: RC    = 0.20     ! critical flux Richardson number.
+real :: I_ZETA_N  ! The inverse of ZETA_N.
+real :: I_LF  ! Inverse of Latent Heat of fusion (J kg-1)
+real :: I_VK      ! The inverse of VK.
+real :: PR, SC    ! The Prandtl number and Schmidt number, nondim.
+
+! 3 equation formulation variables
+real :: Sbdry     !   Salinities in the ocean at the interface with the
+real :: Sbdry_it  ! the ice shelf, in PSU.
+real :: dS_it     ! The interface salinity change during an iteration, in PSU.
+real :: hBL_neut  ! The neutral boundary layer thickness, in m.
+real :: hBL_neut_h_molec ! The ratio of the neutral boundary layer thickness
+                         ! to the molecular boundary layer thickness, ND.
+real :: wT_flux ! The vertical fluxes of heat and buoyancy just inside the
+real :: wB_flux ! ocean, in C m s-1 and m2 s-3, ###CURRENTLY POSITIVE UPWARD.
+real :: dB_dS  ! The derivative of buoyancy with salinity, in m s-2 PSU-1.
+real :: dB_dT  ! The derivative of buoyancy with temperature, in m s-2 C-1.
+real :: I_n_star, n_star_term
+real :: dIns_dwB  ! The partial derivative of I_n_star with wB_flux, in ???.
+real :: dT_ustar, dS_ustar
+real :: ustar_h
+real :: Gam_turb
+real :: Gam_mol_t, Gam_mol_s
+real :: RhoCp
+real :: I_RhoLF
+real :: Rho0
+real :: ln_neut
+real :: mass_exch
+real :: Sb_min, Sb_max
+real :: dS_min, dS_max
+real :: density_ice
+
+! Variables used in iterating for wB_flux.
+real :: wB_flux_new, DwB, dDwB_dwB_in
+real :: I_Gam_T, I_Gam_S
+real :: dG_dwB, iDens
+logical :: Sb_min_set, Sb_max_set
+logical :: out_of_bounds
+
+real, parameter :: c2_3 = 2.0/3.0
+integer ::  it1, it3
+
+!Parameters copied ice shelf module defaults (could be entered in the namelist later)
+real, parameter :: dR0_dT = -0.038357 ! Partial derivative of the mixed layer density with temperature, in units of kg m-3 K-1.
+real, parameter :: dR0_dS = 0.805876 ! Partial derivative of the mixed layer density with salinity, in units of kg m-3 psu-1.
+real, parameter :: RHO_T0_S0 = 999.910681 ! Density of water with T=0, S=0 for linear EOS
+real, parameter :: Salin_Ice =0.0 !Salinity of ice
+real, parameter :: Temp_Ice = -15.0 !Salinity of ice
+real, parameter :: kd_molec_salt=  8.02e-10 !The molecular diffusivity of salt in sea water at the freezing point
+real, parameter :: kd_molec_temp=  1.41e-7 !The molecular diffusivity of heat in sea water at the freezing point
+real, parameter :: kv_molec=  1.95e-6 !The molecular molecular kinematic viscosity of sea water at the freezing point
+real, parameter :: Cp_Ice =  2009.0 !Specific heat capacity of ice, taking from HJ99 (Holland and Jenkins 1999)
+real, parameter :: Cp_ml =  3974.0 !Specific heat capacity of mixed layer, taking from HJ99 (Holland and Jenkins 1999)
+real, parameter :: LF =  3.335e5 !Latent heat of fusion, taken from HJ99 (Holland and Jenkins 1999)
+real, parameter :: gamma_t =  0.0 ! Exchange velocity used in 2 equation model. Whn gamma_t is >0, the exchange velocity is independent of u_star.
+                                ! When gamma_t=0.0, then gamma_t is not used, and the exchange velocity is found using u_star.
+real, parameter :: p_atm =  101325 ! Average atmospheric pressure (Pa) - from Google.
+
   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
   density_ice = bergs%rho_bergs
   Rho0=rho_seawater  !Note that the ice shelf code has a default of Rho0=1035
   Hml =10.      !Mixed layer depth. This is an approximate value. It looks like the code is not sensitive to it (since it enters in log(Hml)
   p_int= p_atm+(gravity*thickness*density_ice)    ! The pressure at the ice-ocean interface, in Pa.
-  
+
   ! Find the ocean mixed layer density in kg m-3.
   call calculate_density(temp, salt, p_int, Rhoml, Rho_T0_S0, dR0_dT, dR0_dS)
 
   ! This routine finds the melt at the base of the icebergs using the 2 equation
   ! model or 3 equation model. This code is adapted from the ice shelf code. Once
-  ! the iceberg model is inside the ocean model, we should use the same code. 
+  ! the iceberg model is inside the ocean model, we should use the same code.
 
   I_ZETA_N = 1.0 / ZETA_N
   I_RhoLF = 1.0/(Rho0*LF)
@@ -1611,7 +1639,7 @@ subroutine find_basal_melt(bergs,dvo,lat,salt,temp,Use_three_equation_model,thic
   I_VK = 1.0/VK
   RhoCp = Rho0 * Cp_ml
 
-  !first calculate molecular component  
+  !first calculate molecular component
   Gam_mol_t = 12.5 * (PR**c2_3) - 6
   Gam_mol_s = 12.5 * (SC**c2_3) - 6
 
@@ -1630,25 +1658,24 @@ subroutine find_basal_melt(bergs,dvo,lat,salt,temp,Use_three_equation_model,thic
      f_cori=(2.*omega)*sin(pi_180*bergs%lat_ref)
   endif
   absf = abs(f_cori)  !Absolute value of the Coriolis parameter
-  if ((absf*Hml <= VK*ustar_h) .or. (absf.eq.0.))  then 
+  if ((absf*Hml <= VK*ustar_h) .or. (absf.eq.0.))  then
     hBL_neut = Hml
-  else 
-    hBL_neut = (VK*ustar_h) / absf 
+  else
+    hBL_neut = (VK*ustar_h) / absf
   endif
   hBL_neut_h_molec = ZETA_N * ((hBL_neut * ustar_h) / (5.0 * Kv_molec))
   ln_neut = 0.0 ; if (hBL_neut_h_molec > 1.0) ln_neut = log(hBL_neut_h_molec)
 
   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
   if (Use_three_equation_model) then   ! Use 3 equation model
-    ! 3 equation model solves for the melt rates iteratively. This is not working right now, because we don't have access to the mixed layer 
-    ! temperature and salinty gradients
-
+    ! 3 equation model solves for the melt rates iteratively. This is not working right now, because we don't have access to the mixed layer
+    ! temperature and salinity gradients
 
     ! Guess sss as the iteration starting point for the boundary salinity.
     Sbdry = salt ; Sb_max_set = .false. ; Sb_min_set = .false.
     out_of_bounds=.false.
 
-    ! Determine the mixed layer buoyancy flux, wB_flux.      
+    ! Determine the mixed layer buoyancy flux, wB_flux.
     dB_dS = (gravity / Rhoml) * dR0_dS
     dB_dT = (gravity / Rhoml) * dR0_dT
 
@@ -1781,7 +1808,7 @@ subroutine find_basal_melt(bergs,dvo,lat,salt,temp,Use_three_equation_model,thic
     ! In the 2-equation form, the mixed layer turbulent exchange velocity
     ! is specified and large enough that the ocean salinity at the interface
     ! is about the same as the boundary layer salinity.
-    ! Alon: I have adapted the code so that the turbulent exchange velocoty is not constant, but rather proportional to the frictional velocity. 
+    ! Alon: I have adapted the code so that the turbulent exchange velocoty is not constant, but rather proportional to the frictional velocity.
     ! This should give you the same answers as the 3 equation model when salinity gradients in the mixed layer are zero (I think/hope)
     ! Use 2-equation model when 3 equation version fails.
 
@@ -1850,37 +1877,36 @@ subroutine calculate_density(T, S, pressure, rho, Rho_T0_S0, dRho_dT, dRho_dS)
   end subroutine calculate_density
 
 end subroutine find_basal_melt
-!
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
-subroutine find_orientation_using_iceberg_bonds(grd,berg,orientation)
-  ! Arguments
-  type(iceberg), pointer :: berg
-  real, intent(inout) :: orientation 
-  type(icebergs_gridded), pointer :: grd
-  type(iceberg), pointer :: other_berg
-  type(bond), pointer :: current_bond
-  real :: angle, lat1,lat2,lon1,lon2,dlat,dlon
-  real :: r_dist_x, r_dist_y 
-  real :: lat_ref, dx_dlon, dy_dlat
-  real :: theta, bond_count, Average_angle
-    
+subroutine find_orientation_using_iceberg_bonds(grd, berg, orientation)
+! Arguments
+type(icebergs_gridded), pointer :: grd
+type(iceberg), pointer :: berg
+real, intent(inout) :: orientation
+! Local variables
+type(iceberg), pointer :: other_berg
+type(bond), pointer :: current_bond
+real :: angle, lat1,lat2,lon1,lon2,dlat,dlon
+real :: r_dist_x, r_dist_y
+real :: lat_ref, dx_dlon, dy_dlat
+real :: theta, bond_count, Average_angle
+
   bond_count=0.
   Average_angle=0.
-  !Don't check orientation of the edges of halo,  since they can contain unassosiated bonds  (this is why halo width must be larger >= 2 to use bonds)    
-  if  (  ((berg%ine .gt.  grd%isd) .and. (berg%ine .lt. grd%ied)) .and. ((berg%jne .ge.  grd%jsd) .and. (berg%jne .le. grd%jed) ) ) then  
+  !Don't check orientation of the edges of halo,  since they can contain unassosiated bonds  (this is why halo width must be larger >= 2 to use bonds)
+  if  (  ((berg%ine .gt.  grd%isd) .and. (berg%ine .lt. grd%ied)) .and. ((berg%jne .ge.  grd%jsd) .and. (berg%jne .le. grd%jed) ) ) then
     current_bond=>berg%first_bond
     lat1=berg%lat
     lon1=berg%lon
     do while (associated(current_bond)) ! loop over all bonds
       other_berg=>current_bond%other_berg
-      if (.not. associated(other_berg)) then !good place for debugging 
+      if (.not. associated(other_berg)) then !good place for debugging
         !One valid option: current iceberg is on the edge of halo, with other berg on the next pe (not influencing mass spreading)
-          !print *, 'Iceberg bond details:',berg%iceberg_num, current_bond%other_berg_num,berg%halo_berg, mpp_pe()
-          !print *, 'Iceberg bond details2:',berg%ine, berg%jne, current_bond%other_berg_ine, current_bond%other_berg_jne
-          !print *, 'Iceberg isd,ied,jsd,jed:',grd%isd, grd%ied, grd%jsd, grd%jed
-          !print *, 'Iceberg isc,iec,jsc,jec:',grd%isc, grd%iec, grd%jsc, grd%jec
-          !call error_mesg('diamonds,calculating orientation', 'Looking at bond interactions of unassosiated berg!' ,FATAL)
+        !print *, 'Iceberg bond details:',berg%iceberg_num, current_bond%other_berg_num,berg%halo_berg, mpp_pe()
+        !print *, 'Iceberg bond details2:',berg%ine, berg%jne, current_bond%other_berg_ine, current_bond%other_berg_jne
+        !print *, 'Iceberg isd,ied,jsd,jed:',grd%isd, grd%ied, grd%jsd, grd%jed
+        !print *, 'Iceberg isc,iec,jsc,jec:',grd%isc, grd%iec, grd%jsc, grd%jec
+        !call error_mesg('diamonds,calculating orientation', 'Looking at bond interactions of unassosiated berg!' ,FATAL)
         !endif
       else
         lat2=other_berg%lat
@@ -1888,7 +1914,7 @@ subroutine find_orientation_using_iceberg_bonds(grd,berg,orientation)
 
         dlat=lat2-lat1
         dlon=lon2-lon1
-        
+
         lat_ref=0.5*(lat1+lat2)
         call convert_from_grid_to_meters(lat_ref,grd%grid_is_latlon,dx_dlon,dy_dlat)
         r_dist_x=dlon*dx_dlon
@@ -1918,26 +1944,26 @@ subroutine find_orientation_using_iceberg_bonds(grd,berg,orientation)
 end subroutine find_orientation_using_iceberg_bonds
 
 subroutine spread_mass_across_ocean_cells(bergs, berg, i, j, x, y, Mberg, Mbits, scaling, Area, Tn)
-  ! Arguments
-  type(icebergs), pointer :: bergs
-  type(icebergs_gridded), pointer :: grd
-  type(iceberg), pointer :: berg
-  integer, intent(in) :: i, j
-  real, intent(in) :: x, y, Mberg, Mbits, scaling, Area
-  real, intent(in) :: Tn
-  ! Local variables
-  real :: xL, xC, xR, yD, yC, yU, Mass, L
-  real :: yDxL, yDxC, yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR
-  real :: S, H, origin_x, origin_y, x0, y0
-  real :: Area_Q1,Area_Q2 , Area_Q3,Area_Q4, Area_hex
-  real :: fraction_used !fraction of iceberg mass included (part of the mass near the boundary is discarded sometimes)
-  real :: I_fraction_used !Inverse of fraction used
-  real :: tol
-  real :: Dn, Hocean
-  real, parameter :: rho_seawater=1035.
-  integer :: stderrunit
-  logical :: debug
-  real :: orientation, Mass_berg
+! Arguments
+type(icebergs), pointer :: bergs !< Container for all types and memory
+type(icebergs_gridded), pointer :: grd
+type(iceberg), pointer :: berg
+integer, intent(in) :: i, j
+real, intent(in) :: x, y, Mberg, Mbits, scaling, Area
+real, intent(in) :: Tn
+! Local variables
+real :: xL, xC, xR, yD, yC, yU, Mass, L
+real :: yDxL, yDxC, yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR
+real :: S, H, origin_x, origin_y, x0, y0
+real :: Area_Q1,Area_Q2 , Area_Q3,Area_Q4, Area_hex
+real :: fraction_used !fraction of iceberg mass included (part of the mass near the boundary is discarded sometimes)
+real :: I_fraction_used !Inverse of fraction used
+real :: tol
+real :: Dn, Hocean
+real, parameter :: rho_seawater=1035.
+integer :: stderrunit
+logical :: debug
+real :: orientation, Mass_berg
 
   ! Get the stderr unit number
   stderrunit = stderr()
@@ -1957,20 +1983,20 @@ subroutine spread_mass_across_ocean_cells(bergs, berg, i, j, x, y, Mberg, Mbits,
   ! This line attempts to "clip" the weight felt by the ocean. The concept of
   ! clipping is non-physical and this step should be replaced by grounding.
   if (grd%clipping_depth>0.) Mass=min(Mass,grd%clipping_depth*grd%area(i,j)*rho_seawater)
- 
-  !Initialize weights for each cell       
+
+  !Initialize weights for each cell
   yDxL=0.  ; yDxC=0. ; yDxR=0. ; yCxL=0. ; yCxR=0.
   yUxL=0.  ; yUxC=0. ; yUxR=0. ; yCxC=1.
 
   if (.not. bergs%hexagonal_icebergs) then  !Treat icebergs as rectangles of size L:  (this is the default)
-    
+
     !L is the non dimensional length of the iceberg [  L=(Area of berg/ Area of grid cell)^0.5  ] or something like that.
     if (grd%area(i,j)>0) then
       L=min( sqrt(Area / grd%area(i,j)),1.0)
-    else 
+    else
       L=1.
     endif
-  
+
     if (bergs%use_old_spreading) then
       !Old version before icebergs were given size L
       xL=min(0.5, max(0., 0.5-x))
@@ -1997,17 +2023,17 @@ subroutine spread_mass_across_ocean_cells(bergs, berg, i, j, x, y, Mberg, Mbits,
     yUxC=yU*xC*grd%msk(i  ,j+1)
     yUxR=yU*xR*grd%msk(i+1,j+1)
     yCxC=1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )
-    
+
     fraction_used=1.  !rectangular bergs do share mass with boundaries (all mass is included in cells)
 
   else !Spread mass as if elements area hexagonal
-    
+
     orientation=bergs%initial_orientation
     if ((bergs%iceberg_bonds_on) .and. (bergs%rotate_icebergs_for_mass_spreading)) call find_orientation_using_iceberg_bonds(grd,berg,orientation)
 
     if (grd%area(i,j)>0) then
       H = min(( (sqrt(Area/(2.*sqrt(3.)))  / sqrt(grd%area(i,j)))),1.) ;  !Non dimensionalize element length by grid area. (This gives the non-dim Apothen of the hexagon)
-    else 
+    else
       H= (sqrt(3.)/2)*(0.49)  !Largest allowable H, since this makes S=0.49, and S has to be less than 0.5  (Not sure what the implications of this are)
     endif
     S=(2/sqrt(3.))*H !Side of the hexagon
@@ -2022,13 +2048,13 @@ subroutine spread_mass_across_ocean_cells(bergs, berg, i, j, x, y, Mberg, Mbits,
     origin_x=1. ; origin_y=1.
     if (x<0.5) origin_x=0.
     if (y<0.5) origin_y=0.
-    
+
     !Position of the hexagon center, relative to origin at the nearest vertex
     x0=(x-origin_x)
     y0=(y-origin_y)
 
     call Hexagon_into_quadrants_using_triangles(x0,y0,H,orientation,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
-    
+
     if (min(min(Area_Q1,Area_Q2),min(Area_Q3, Area_Q4)) <-tol) then
       call error_mesg('diamonds, hexagonal spreading', 'Intersection with hexagons should not be negative!!!', WARNING)
       write(stderrunit,*) 'diamonds, yU,yC,yD', Area_Q1, Area_Q2, Area_Q3, Area_Q4
@@ -2061,23 +2087,22 @@ subroutine spread_mass_across_ocean_cells(bergs, berg, i, j, x, y, Mberg, Mbits,
       yDxC=Area_Q3
       yDxR=Area_Q4
     endif
-                        
+
     !Temporary for debugging reasons.
-    if (mpp_pe()==mpp_root_pe()) then 
-            !write(stderrunit,*) 'diamonds, You are in the hexagonal domain now!!!'
+    if (mpp_pe()==mpp_root_pe()) then
+      !write(stderrunit,*) 'diamonds, You are in the hexagonal domain now!!!'
     endif
 
-      !Double check that all the mass is being used.
-      if ((abs(yCxC-(1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )))>tol) .and. (mpp_pe().eq. mpp_root_pe())) then
-        !call error_mesg('diamonds, hexagonal spreading', 'All the mass is not being used!!!', WARNING)
-        write(stderrunit,*) 'diamonds, hexagonal, H,x0,y0', H, x0 , y0
-        write(stderrunit,*) 'diamonds, hexagonal, Areas',(Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
-        debug=.True.
-        !call Hexagon_into_quadrants_using_triangles(x0,y0,H,orientation,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4, debug)
-        call error_mesg('diamonds, hexagonal spreading', 'All the mass is not being used!!!', FATAL)
-      endif
+    !Double check that all the mass is being used.
+    if ((abs(yCxC-(1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )))>tol) .and. (mpp_pe().eq. mpp_root_pe())) then
+      !call error_mesg('diamonds, hexagonal spreading', 'All the mass is not being used!!!', WARNING)
+      write(stderrunit,*) 'diamonds, hexagonal, H,x0,y0', H, x0 , y0
+      write(stderrunit,*) 'diamonds, hexagonal, Areas',(Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
+      debug=.True.
+      !call Hexagon_into_quadrants_using_triangles(x0,y0,H,orientation,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4, debug)
+      call error_mesg('diamonds, hexagonal spreading', 'All the mass is not being used!!!', FATAL)
+    endif
 
-        
     !Scale each cell by (1/fraction_used) in order to redisribute ice mass which landed up on the land, back into the ocean
     !Note that for the square elements, the mass has already been reassigned, so fraction_used shoule be equal to 1 aready
     fraction_used= ((yDxL*grd%msk(i-1,j-1)) + (yDxC*grd%msk(i  ,j-1))  +(yDxR*grd%msk(i+1,j-1)) +(yCxL*grd%msk(i-1,j  )) +  (yCxR*grd%msk(i+1,j  ))&
@@ -2099,14 +2124,14 @@ subroutine spread_mass_across_ocean_cells(bergs, berg, i, j, x, y, Mberg, Mbits,
   !Spreading the iceberg y momentum onto the ocean
   call spread_variable_across_cells(grd,grd%Vvel_on_ocean, berg%vvel*Area*scaling , i ,j, &
              yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR, I_fraction_used)
-  
+
 end subroutine spread_mass_across_ocean_cells
 
 subroutine spread_variable_across_cells(grd, variable_on_ocean, Var,i,j, &
            yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR,I_fraction_used)
   ! Arguments
   type(icebergs_gridded), pointer, intent(in) :: grd
-  real, dimension(grd%isd:grd%ied, grd%jsd:grd%jed, 9), intent(inout) :: variable_on_ocean 
+  real, dimension(grd%isd:grd%ied, grd%jsd:grd%jed, 9), intent(inout) :: variable_on_ocean
   real, intent(in) :: Var !Variable to be spread accross cell
   real, intent(in) :: yDxL, yDxC, yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR !Weights
   real, intent(in) :: I_fraction_used !Amount of iceberg used (inverse)
@@ -2125,26 +2150,23 @@ subroutine spread_variable_across_cells(grd, variable_on_ocean, Var,i,j, &
 
 end subroutine spread_variable_across_cells
 
-
-! ##############################################################################
-
-real function Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy)
-  ! Arguments
-  real, intent(in) :: Ax,Ay,Bx,By,Cx,Cy
+real function Area_of_triangle(Ax, Ay, Bx, By, Cx, Cy)
+! Arguments
+real, intent(in) :: Ax,Ay,Bx,By,Cx,Cy
   Area_of_triangle    =   abs(    0.5*((Ax*(By-Cy))+(Bx*(Cy-Ay))+(Cx*(Ay-By))) );
 end function Area_of_triangle
 
 real function roundoff(x,sig_fig)
-  ! Arguments
-  real, intent(in) :: x
-  integer, intent(in) :: sig_fig
-    !roundoff=round(x*(10**(sig_fig))
-    roundoff=(FLOAT (INT(x * (10.**sig_fig) + 0.5)) / (10.**sig_fig))
+! Arguments
+real, intent(in) :: x
+integer, intent(in) :: sig_fig
+  !roundoff=round(x*(10**(sig_fig))
+  roundoff=(FLOAT (INT(x * (10.**sig_fig) + 0.5)) / (10.**sig_fig))
 end function roundoff
 
-logical function point_in_interval(Ax,Ay,Bx,By,px,py)
-  ! Arguments
-  real, intent(in) :: Ax,Ay,Bx,By,px,py
+logical function point_in_interval(Ax, Ay, Bx, By, px, py)
+! Arguments
+real, intent(in) :: Ax,Ay,Bx,By,px,py
   point_in_interval=.False.
   if ((px <= max(Ax,Bx)) .and. (px >= min(Ax,Bx))) then
     if ((py <= max(Ay,By)) .and. (py >= min(Ay,By))) then
@@ -2153,33 +2175,33 @@ logical function point_in_interval(Ax,Ay,Bx,By,px,py)
   endif
 end function point_in_interval
 
-
 logical function point_is_on_the_line(Ax,Ay,Bx,By,qx,qy)
-  ! Arguments
-  real, intent(in) :: Ax,Ay,Bx,By,qx,qy
-  real :: tol, dxc,dyc,dxl,dyl,cross
-    !tol=1.e-12;
-    tol=0.0;
-    dxc = qx - Ax;
-    dyc = qy - Ay;
-    dxl = Bx - Ax;
-    dyl = By - Ay;
-    cross = dxc * dyl - dyc * dxl;
-    if (abs(cross)<=tol) then
-      point_is_on_the_line=.True.
-    else
-     point_is_on_the_line=.False.
-    endif
+! Arguments
+real, intent(in) :: Ax,Ay,Bx,By,qx,qy
+real :: tol, dxc,dyc,dxl,dyl,cross
+  !tol=1.e-12;
+  tol=0.0;
+  dxc = qx - Ax;
+  dyc = qy - Ay;
+  dxl = Bx - Ax;
+  dyl = By - Ay;
+  cross = dxc * dyl - dyc * dxl;
+  if (abs(cross)<=tol) then
+    point_is_on_the_line=.True.
+  else
+   point_is_on_the_line=.False.
+  endif
 end function point_is_on_the_line
 
 logical function point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,qx,qy)
-  !This function decides whether a point (qx,qy) is inside the triangle ABC.
-  !There is also the option to include the boundary of the triangle.
-  ! Arguments
-  real, intent(in) :: Ax,Ay,Bx,By,Cx,Cy,qx,qy
-  real :: l0,l1,l2,p0,p1,p2
-  real :: v0x,v1x,v2x,v0y,v1y,v2y,dot00,dot01,dot02,dot11,dot12
-  
+!This function decides whether a point (qx,qy) is inside the triangle ABC.
+!There is also the option to include the boundary of the triangle.
+! Arguments
+real, intent(in) :: Ax,Ay,Bx,By,Cx,Cy,qx,qy
+! Local variables
+real :: l0,l1,l2,p0,p1,p2
+real :: v0x,v1x,v2x,v0y,v1y,v2y,dot00,dot01,dot02,dot11,dot12
+
   point_in_triangle = .False.
   if ((Ax==qx .and. Ay==qy) .or. (Bx==qx .and. By==qy) .or. (Cx==qx .and. Cy==qy)) then  !Exclude the pathelogical case
       point_in_triangle = .False.
@@ -2201,16 +2223,15 @@ logical function point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,qx,qy)
   endif
 end function point_in_triangle
 
-
 subroutine Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axis1,Area_positive, Area_negative)  !You should change this name a little, so that it not similar the other routine.
 !This function calculates the area of a triangle on opposited sides of an axis when the triangle is split with two points on one side, and one point on the other.
 !In this fuction, A is the point on one side of the axis, and B,C are on the opposite sides
-  ! Arguments
-  real , intent(in) :: Ax,Ay,Bx,By,Cx,Cy
-  character , intent(in) :: axis1
-  real, intent(out) :: Area_positive, Area_negative
-  real :: pABx, pABy, pACx, pACy, A0
-  real :: A_half_triangle, A_triangle
+! Arguments
+real , intent(in) :: Ax,Ay,Bx,By,Cx,Cy
+character , intent(in) :: axis1
+real, intent(out) :: Area_positive, Area_negative
+real :: pABx, pABy, pACx, pACy, A0
+real :: A_half_triangle, A_triangle
 
   A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
 
@@ -2234,17 +2255,16 @@ end subroutine Area_of_triangle_across_axes
 subroutine intercept_of_a_line(Ax,Ay,Bx,By,axes1,x0,y0)
 !This routine returns the position (x0,y0) at which a line AB intercepts the x or y axis
 !The value No_intercept_val is returned when the line does not intercept the axis
-  !Arguments
-  real, intent(in) :: Ax,Ay,Bx,By
-  character, intent(in) ::axes1
-  real, intent(out) :: x0,y0
-  real :: No_intercept_val !Huge value used to make sure that the intercept is outside the triange in the parralel case.
-  
+!Arguments
+real, intent(in) :: Ax,Ay,Bx,By
+character, intent(in) ::axes1
+real, intent(out) :: x0,y0
+real :: No_intercept_val !Huge value used to make sure that the intercept is outside the triange in the parralel case.
 
-  No_intercept_val=100000000000.; !Huge value used to make sure that the intercept is outside the triange in the parralel case. 
+  No_intercept_val=100000000000.; !Huge value used to make sure that the intercept is outside the triange in the parralel case.
   x0=No_intercept_val
   y0=No_intercept_val
-  
+
   if (axes1=='x') then  !x intercept
     if (Ay.ne.By) then
       x0=Ax -(((Ax-Bx)/(Ay-By))*Ay)
@@ -2260,18 +2280,16 @@ subroutine intercept_of_a_line(Ax,Ay,Bx,By,axes1,x0,y0)
   endif
 end subroutine intercept_of_a_line
 
-
 subroutine divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1,Area_positive, Area_negative)
-!This routine gives you the area of a triangle on opposite sides of the axis specified. 
+!This routine gives you the area of a triangle on opposite sides of the axis specified.
 !It also takes care of the special case where the triangle is totally on one side
 !This routine calls Area_of_triangle_across_axes to calculate the areas when the triangles are split.
-
-  !Arguments
-  real, intent(in) :: Ax,Ay,Bx,By,Cx,Cy
-  character, intent(in) ::axes1
-  real, intent(out) :: Area_positive, Area_negative
-  real :: A0,B0,C0
-  real A_triangle 
+!Arguments
+real, intent(in) :: Ax,Ay,Bx,By,Cx,Cy
+character, intent(in) ::axes1
+real, intent(out) :: Area_positive, Area_negative
+real :: A0,B0,C0
+real A_triangle
 
   if (axes1=='x') then  !Use the y-coordinates for if statements to see which side of the line you are on
     A0=Ay
@@ -2283,7 +2301,7 @@ subroutine divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1,Area_positive, A
     B0=Bx
     C0=Cx
   endif
-  
+
   A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
   if ((B0*C0)>0.) then !B and C are on the same side  (and non-zero)
     if ((A0*B0).ge.0.) then !all three on the the same side (if it equals zero, then A0=0 and the otehrs are not)
@@ -2339,23 +2357,23 @@ end subroutine divding_triangle_across_axes
 
 subroutine Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy,Area_triangle, Area_Q1, Area_Q2 ,Area_Q3 ,Area_Q4)
 !This routine takes a triangle, and finds the intersection with the four quadrants
-  !Arguments
-  real, intent(in) :: Ax,Ay,Bx,By,Cx,Cy
-  real, intent(out) :: Area_triangle, Area_Q1, Area_Q2 ,Area_Q3 ,Area_Q4
-  real :: Area_Upper, Area_Lower, Area_Right, Area_Left
-  real :: px, py , qx , qy 
-  real :: Area_key_quadrant,Error
-  real :: tol
-  integer :: Key_quadrant
-  integer ::sig_fig
-  integer :: stderrunit
+!Arguments
+real, intent(in) :: Ax,Ay,Bx,By,Cx,Cy
+real, intent(out) :: Area_triangle, Area_Q1, Area_Q2 ,Area_Q3 ,Area_Q4
+real :: Area_Upper, Area_Lower, Area_Right, Area_Left
+real :: px, py , qx , qy
+real :: Area_key_quadrant,Error
+real :: tol
+integer :: Key_quadrant
+integer ::sig_fig
+integer :: stderrunit
 
   ! Get the stderr unit number
   stderrunit = stderr()
   tol=1.e-10
 
   Area_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
-  
+
   !Calculating area across axes
   call divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,'x',Area_Upper ,Area_Lower);
   call divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,'y',Area_Right ,Area_Left);
@@ -2391,14 +2409,14 @@ subroutine Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy,Area_triangle,
     elseif ((px.lt.0.) .and. (qy.ge. 0.)) then  !Second quadrant
       Key_quadrant=2
     elseif ((px.lt. 0.) .and. (qy.lt. 0.)) then !Third quadrant
-      Key_quadrant=3;  
+      Key_quadrant=3;
     elseif ((px.ge. 0.) .and. (qy.lt. 0.)) then !Forth quadrant
-      Key_quadrant=4 
+      Key_quadrant=4
     else  !
       call error_mesg('diamonds, iceberg_run', 'None of the quadrants are Key', WARNING)
       write(stderrunit,*) 'diamonds, Triangle, px,qy', px,qy
     endif
-         
+
   else  !At least one quadrant is empty, and this can be used to find the areas in the other quadrant.  Assigning quadrants. Key_quadrant is the empty quadrant.
     Area_key_quadrant=0;
     if      ( (.not. ((((Ax>0.) .and. (Ay>0.)) .or. ((Bx>0.) .and. (By> 0.))) .or. ((Cx>0.) .and. (Cy> 0.)))) .and. ((Area_Upper+Area_Right).le.Area_triangle) ) then
@@ -2420,7 +2438,7 @@ subroutine Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy,Area_triangle,
     Area_Q2=Area_Upper-Area_Q1;
     Area_Q4=Area_Right-Area_Q1;
     !Area_Q3=Area_Left-Area_Q2;   !These lines have been changes so that the sum of the 4 quadrants exactly matches the triangle area.
-    Area_Q3=Area_triangle-(Area_Q1+Area_Q2+Area_Q4);  
+    Area_Q3=Area_triangle-(Area_Q1+Area_Q2+Area_Q4);
   elseif (Key_quadrant .eq. 2) then
     Area_Q2=Area_key_quadrant;
     Area_Q1=Area_Upper-Area_Q2;
@@ -2464,7 +2482,6 @@ subroutine Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy,Area_triangle,
     endif
   endif
 
-
 end subroutine Triangle_divided_into_four_quadrants
 
 subroutine rotate_and_translate(px,py,theta,x0,y0)
@@ -2477,7 +2494,7 @@ subroutine rotate_and_translate(px,py,theta,x0,y0)
   !Rotation
   px_temp = ( cos(theta*pi/180)*px) + (sin(theta*pi/180)*py)
   py_temp = (-sin(theta*pi/180)*px) + (cos(theta*pi/180)*py)
- 
+
   !Translation
   px= px_temp + x0
   py= py_temp + y0
@@ -2508,7 +2525,7 @@ subroutine Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex ,Area_Q
 
   !Length of side of Hexagon
   S=(2/sqrt(3.))*H
-  
+
   !Finding positions of corners
   C1x=S           ; C1y=0.  !Corner 1 (right)
   C2x=H/sqrt(3.)  ; C2y=H;  !Corner 2 (top right)
@@ -2538,8 +2555,8 @@ subroutine Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex ,Area_Q
   Area_Q1=T12_Q1+T23_Q1+T34_Q1+T45_Q1+T56_Q1+T61_Q1;
   Area_Q2=T12_Q2+T23_Q2+T34_Q2+T45_Q2+T56_Q2+T61_Q2;
   Area_Q3=T12_Q3+T23_Q3+T34_Q3+T45_Q3+T56_Q3+T61_Q3;
-  Area_Q4=T12_Q4+T23_Q4+T34_Q4+T45_Q4+T56_Q4+T61_Q4; 
-  
+  Area_Q4=T12_Q4+T23_Q4+T34_Q4+T45_Q4+T56_Q4+T61_Q4;
+
   Area_Q1=max(Area_Q1,0.);
   Area_Q2=max(Area_Q2,0.);
   Area_Q3=max(Area_Q3,0.);
@@ -2588,7 +2605,6 @@ subroutine Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex ,Area_Q
 
 end subroutine Hexagon_into_quadrants_using_triangles
 
-
 subroutine interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, sss, cn, hi)
 ! Arguments
 type(icebergs_gridded), pointer :: grd
@@ -2643,7 +2659,7 @@ subroutine interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y,
   sss=grd%sss(i,j) ! A-grid
   cn=grd%cn(i,j) ! A-grid
   hi=grd%hi(i,j) ! A-grid
-    
+
   ! Estimate SSH gradient in X direction
 #ifdef USE_OLD_SSH_GRADIENT
   dxp=0.5*(grd%dx(i+1,j)+grd%dx(i+1,j-1))
@@ -2685,7 +2701,7 @@ subroutine interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y,
 #endif
   ! ssh_y is at the v-point on a C-grid
   ssh_y=yj*hxp+(1.-yj)*hxm
-  
+
   ! Rotate vectors from local grid to lat/lon coordinates
   call rotate(uo, vo, cos_rot, sin_rot)
   call rotate(ui, vi, cos_rot, sin_rot)
@@ -2704,7 +2720,7 @@ subroutine interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y,
     write(stderrunit,*) 'diamonds, Error in interpolate: sst,cn,hi', sst, sss, cn, hi, mpp_pe()
     call error_mesg('diamonds, interp fields', 'field interpaolations has NaNs', FATAL)
 
-  endif 
+  endif
   contains
 
   real function ddx_ssh(grd,i,j)
@@ -2748,13 +2764,13 @@ end subroutine interp_flds
 
 subroutine calculate_mass_on_ocean(bergs, with_diagnostics)
 ! Arguments
-type(icebergs), pointer :: bergs
+type(icebergs), pointer :: bergs !< Container for all types and memory
 type(iceberg), pointer :: berg
 type(icebergs_gridded), pointer :: grd
 logical, intent(in) :: with_diagnostics
 ! Local variables
-integer :: grdj, grdi   
-integer :: j, i   
+integer :: grdj, grdi
+integer :: j, i
 
   ! For convenience
   grd=>bergs%grd
@@ -2765,19 +2781,19 @@ subroutine calculate_mass_on_ocean(bergs, with_diagnostics)
   grd%Uvel_on_ocean(:,:,:)=0.
   grd%Vvel_on_ocean(:,:,:)=0.
 
-  do grdj = grd%jsc-1,grd%jec+1 ; do grdi = grd%isc-1,grd%iec+1  
+  do grdj = grd%jsc-1,grd%jec+1 ; do grdi = grd%isc-1,grd%iec+1
     berg=>bergs%list(grdi,grdj)%first
     do while(associated(berg))
       i=berg%ine  ;     j=berg%jne
       if (grd%area(i,j) > 0.) then
-        
+
         !Increasing Mass on ocean
         if ((bergs%add_weight_to_ocean .and. .not. bergs%time_average_weight) .or.(bergs%find_melt_using_spread_mass)) then
           call spread_mass_across_ocean_cells(bergs, berg, berg%ine, berg%jne, berg%xi, berg%yj, berg%mass,berg%mass_of_bits, berg%mass_scaling, &
                 berg%length*berg%width, berg%thickness)
         endif
 
-        !Calculated some iceberg diagnositcs  
+        !Calculated some iceberg diagnositcs
         if (with_diagnostics) call calculate_sum_over_bergs_diagnositcs(bergs,grd,berg,i,j)
 
       endif
@@ -2789,47 +2805,45 @@ subroutine calculate_mass_on_ocean(bergs, with_diagnostics)
 
   subroutine calculate_sum_over_bergs_diagnositcs(bergs,grd,berg,i,j)
   ! Arguments
-  type(icebergs), pointer :: bergs
+  type(icebergs), pointer :: bergs !< Container for all types and memory
   type(iceberg), pointer :: berg
   type(icebergs_gridded), pointer :: grd
   integer, intent(in) :: i, j
   ! Local variables
   real ::  Abits, Lbits, Mbits
 
-           !Virtual area diagnostic
-           if (grd%id_virtual_area>0) then
-             if (bergs%bergy_bit_erosion_fraction>0.) then
-               Lbits=min(berg%length,berg%width,berg%thickness,40.) ! assume bergy bits are smallest dimension or 40 meters
-               Abits=(berg%mass_of_bits/bergs%rho_bergs)/Lbits ! Effective bottom area (assuming T=Lbits)
-             else
-               Abits=0.0
-             endif
-             grd%virtual_area(i,j)=grd%virtual_area(i,j)+(berg%width*berg%length+Abits)*berg%mass_scaling ! m^2
-           endif
-
-           !Mass diagnostic (also used in u_iceberg, v_iceberg
-           if ((grd%id_mass>0 ) .or. ((grd%id_u_iceberg>0) .or. (grd%id_v_iceberg>0)))   &
-                & grd%mass(i,j)=grd%mass(i,j)+berg%mass/grd%area(i,j)*berg%mass_scaling ! kg/m2
-
-           !Finding the average iceberg velocity in a grid cell (mass weighted)
-           if (grd%id_u_iceberg>0) &
-           grd%u_iceberg(i,j)=grd%u_iceberg(i,j)+((berg%mass/grd%area(i,j)*berg%mass_scaling)*berg%uvel) ! kg/m2
-           if (grd%id_v_iceberg>0) &
-           grd%v_iceberg(i,j)=grd%v_iceberg(i,j)+((berg%mass/grd%area(i,j)*berg%mass_scaling)*berg%vvel) ! kg/m2
-
-           !Mass of bergy bits
-           if (grd%id_bergy_mass>0 .or. bergs%add_weight_to_ocean)&
-                & grd%bergy_mass(i,j)=grd%bergy_mass(i,j)+berg%mass_of_bits/grd%area(i,j)*berg%mass_scaling ! kg/m2
+   !Virtual area diagnostic
+   if (grd%id_virtual_area>0) then
+     if (bergs%bergy_bit_erosion_fraction>0.) then
+       Lbits=min(berg%length,berg%width,berg%thickness,40.) ! assume bergy bits are smallest dimension or 40 meters
+       Abits=(berg%mass_of_bits/bergs%rho_bergs)/Lbits ! Effective bottom area (assuming T=Lbits)
+     else
+       Abits=0.0
+     endif
+     grd%virtual_area(i,j)=grd%virtual_area(i,j)+(berg%width*berg%length+Abits)*berg%mass_scaling ! m^2
+   endif
+
+   !Mass diagnostic (also used in u_iceberg, v_iceberg
+   if ((grd%id_mass>0 ) .or. ((grd%id_u_iceberg>0) .or. (grd%id_v_iceberg>0)))   &
+        & grd%mass(i,j)=grd%mass(i,j)+berg%mass/grd%area(i,j)*berg%mass_scaling ! kg/m2
+
+   !Finding the average iceberg velocity in a grid cell (mass weighted)
+   if (grd%id_u_iceberg>0) &
+   grd%u_iceberg(i,j)=grd%u_iceberg(i,j)+((berg%mass/grd%area(i,j)*berg%mass_scaling)*berg%uvel) ! kg/m2
+   if (grd%id_v_iceberg>0) &
+   grd%v_iceberg(i,j)=grd%v_iceberg(i,j)+((berg%mass/grd%area(i,j)*berg%mass_scaling)*berg%vvel) ! kg/m2
+
+   !Mass of bergy bits
+   if (grd%id_bergy_mass>0 .or. bergs%add_weight_to_ocean)&
+        & grd%bergy_mass(i,j)=grd%bergy_mass(i,j)+berg%mass_of_bits/grd%area(i,j)*berg%mass_scaling ! kg/m2
  end subroutine calculate_sum_over_bergs_diagnositcs
 
 end subroutine calculate_mass_on_ocean
 
-! ##############################################################################
-
 subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh, sst, calving_hflx, cn, hi, &
                         stagger, stress_stagger, sss, mass_berg, ustar_berg, area_berg)
 ! Arguments
-type(icebergs), pointer :: bergs
+type(icebergs), pointer :: bergs !< Container for all types and memory
 type(time_type), intent(in) :: time
 real, dimension(:,:), intent(inout) :: calving, calving_hflx
 real, dimension(:,:), intent(in) :: uo, vo, ui, vi, tauxa, tauya, ssh, sst, cn, hi
@@ -2839,7 +2853,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 ! Local variables
 integer :: iyr, imon, iday, ihr, imin, isec, k
 type(icebergs_gridded), pointer :: grd
-logical :: lerr, sample_traj, write_traj, lbudget, lverbose, check_bond_quality 
+logical :: lerr, sample_traj, write_traj, lbudget, lverbose, check_bond_quality
 real :: unused_calving, tmpsum, grdd_berg_mass, grdd_bergy_mass,grdd_spread_mass, grdd_spread_area
 real :: grdd_u_iceberg, grdd_v_iceberg, grdd_ustar_iceberg, grdd_spread_uvel, grdd_spread_vvel
 integer :: i, j, Iu, ju, iv, Jv, Iu_off, ju_off, iv_off, Jv_off
@@ -2870,9 +2884,9 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   grd%bergy_src(:,:)=0.
   grd%bergy_melt(:,:)=0.
   grd%bergy_mass(:,:)=0.
-  grd%spread_mass_old(:,:)=0.  
+  grd%spread_mass_old(:,:)=0.
   !grd%spread_mass(:,:)=0.  !Don't zero this out yet, because we can first use this an add it onto the SSH
-  grd%spread_area(:,:)=0. 
+  grd%spread_area(:,:)=0.
   grd%u_iceberg(:,:)=0.
   grd%v_iceberg(:,:)=0.
   grd%spread_uvel(:,:)=0.
@@ -2880,18 +2894,18 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   grd%ustar_iceberg(:,:)=0.
   grd%mass(:,:)=0.
   grd%virtual_area(:,:)=0.
-  
+
   !Initializing _on_ocean_fields
   grd%mass_on_ocean(:,:,:)=0. ;   grd%area_on_ocean(:,:,:)=0.
   grd%Uvel_on_ocean(:,:,:)=0. ;   grd%Vvel_on_ocean(:,:,:)=0.
 
-  if (present(mass_berg)) then ;  if (associated(mass_berg)) then 
+  if (present(mass_berg)) then ;  if (associated(mass_berg)) then
     mass_berg(:,:)=0.0
   endif ;  endif
-  if (present(ustar_berg)) then ; if (associated(ustar_berg)) then 
+  if (present(ustar_berg)) then ; if (associated(ustar_berg)) then
     ustar_berg(:,:)=0.0
   endif ;  endif
-  if (present(area_berg)) then ;  if (associated(area_berg)) then 
+  if (present(area_berg)) then ;  if (associated(area_berg)) then
     area_berg(:,:)=0.0
   endif ;  endif
 
@@ -2930,7 +2944,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   ! Adapt calving heat flux from coupler
   grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)=calving_hflx(:,:) & ! Units of W/m2
        *grd%msk(grd%isc:grd%iec,grd%jsc:grd%jec)
-  
+
   ! Adapt calving flux from coupler for use here
   grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec)=calving(:,:) & ! Units of kg/m2/s
        *grd%msk(grd%isc:grd%iec,grd%jsc:grd%jec)
@@ -3033,7 +3047,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
       grd%va(I,J) = mask * 0.25*((vA_tmp(i,j) + vA_tmp(i+1,j+1)) + &
                                  (vA_tmp(i+1,j) + vA_tmp(i,j+1)))
     enddo ; enddo
-    
+
     deallocate(uA_tmp, vA_tmp)
   else
     call error_mesg('diamonds, iceberg_run', 'Unrecognized value of stress_stagger!', FATAL)
@@ -3071,7 +3085,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   call mpp_update_domains(grd%cn, grd%domain)
   grd%hi(grd%isc-1:grd%iec+1,grd%jsc-1:grd%jec+1)=hi(:,:)
   call mpp_update_domains(grd%hi, grd%domain)
-  
+
   !Adding gridded salinity.
   if (present(sss)) then
     grd%sss(grd%isc:grd%iec,grd%jsc:grd%jec)=sss(:,:)
@@ -3089,7 +3103,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
       grd%ua(i,j) = 0.0 ;  grd%va(i,j) = 0.0
       grd%uo(i,j) = 0.0 ;  grd%vo(i,j) = 0.0
       grd%ui(i,j) = 0.0 ;  grd%vi(i,j) = 0.0
-      grd%sst(i,j)= 0.0;  grd%sss(i,j)= 0.0  
+      grd%sst(i,j)= 0.0;  grd%sss(i,j)= 0.0
       grd%cn(i,j) = 0.0 ;  grd%hi(i,j) = 0.0
     endif
     if (grd%ua(i,j) .ne. grd%ua(i,j)) grd%ua(i,j)=0.
@@ -3106,7 +3120,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 
   if (debug) call bergs_chksum(bergs, 'run bergs (top)')
   if (debug) call checksum_gridded(bergs%grd, 'top of s/r run')
-  
+
 
   ! Accumulate ice from calving
   call accumulate_calving(bergs)
@@ -3158,10 +3172,10 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   call mpp_clock_end(bergs%clock_com)
 
   !Caculate mass on ocean before thermodynamics, to use in melt rate calculation
-  if (bergs%find_melt_using_spread_mass) then 
+  if (bergs%find_melt_using_spread_mass) then
     call calculate_mass_on_ocean(bergs, with_diagnostics=.false.)
     grd%spread_mass_old(:,:)=0.
-    call sum_up_spread_fields(bergs,grd%spread_mass_old(grd%isc:grd%iec,grd%jsc:grd%jec), 'mass') 
+    call sum_up_spread_fields(bergs,grd%spread_mass_old(grd%isc:grd%iec,grd%jsc:grd%jec), 'mass')
     !Reset fields
     grd%mass_on_ocean(:,:,:)=0.  ;  grd%area_on_ocean(:,:,:)=0.
     grd%Uvel_on_ocean(:,:,:)=0.  ;  grd%Vvel_on_ocean(:,:,:)=0.
@@ -3276,7 +3290,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 
   ! Dump icebergs to screen
   if (really_debug) call print_bergs(stderrunit,bergs,'icebergs_run, status')
-  
+
   ! Dump icebergs bonds to screen
   if (really_debug)  call show_all_bonds(bergs)
 
@@ -3284,7 +3298,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 
   !This is the point in the algorithem which determines which fields get passed to the ice model
   !Return what ever calving we did not use and additional icebergs melt
-  
+
   !Making sure that spread_mass has the correct mass
   !grd%spread_mass(:,:)=0.0
   !call icebergs_incr_mass(bergs, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec), within_iceberg_model=.True.)
@@ -3301,24 +3315,24 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     end where
     calving_hflx(:,:)=grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)
     !Return iceberg mass, area and ustar to pass on to ocean model
-    if (present(mass_berg)) then 
+    if (present(mass_berg)) then
       if (associated(mass_berg)) then
         if (bergs%add_weight_to_ocean) &
           mass_berg(:,:)=grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec)
       endif
     endif
-    if (present(ustar_berg)) then 
+    if (present(ustar_berg)) then
       if (associated(ustar_berg)) then
         ustar_berg(:,:)=grd%ustar_iceberg(grd%isc:grd%iec,grd%jsc:grd%jec)
-      endif 
+      endif
     endif
-    if (present(area_berg)) then 
+    if (present(area_berg)) then
       if (associated(area_berg)) then
         area_berg(:,:)=grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec)
-      endif 
+      endif
     endif
   endif
-  
+
   call mpp_clock_end(bergs%clock_int)
 
   ! Diagnose budgets
@@ -3576,7 +3590,7 @@ end subroutine report_ibudget
 
   subroutine get_running_mean_calving(bergs,calving,calving_hflx)
   ! Arguments
-  type(icebergs), pointer :: bergs
+  type(icebergs), pointer :: bergs !< Container for all types and memory
   real, dimension(:,:), intent(inout) :: calving, calving_hflx
   ! Local variables
   real :: alpha  !Parameter used for calving relaxation time stepping.  (0<=alpha<1)
@@ -3619,11 +3633,9 @@ end subroutine get_running_mean_calving
 
 end subroutine icebergs_run
 
-! ##############################################################################
-
 subroutine icebergs_incr_mass(bergs, mass, Time)
 ! Arguments
-type(icebergs), pointer :: bergs
+type(icebergs), pointer :: bergs !< Container for all types and memory
 type(time_type), intent(in), optional :: Time
 type(icebergs_gridded), pointer :: grd
 integer :: i, j
@@ -3635,30 +3647,29 @@ subroutine icebergs_incr_mass(bergs, mass, Time)
 !the add weight to ocean flag is on, and passive mode is off. It also appears to
 !play some role in diagnostics
 
-    if (.not. associated(bergs)) return
-    if (.not. bergs%add_weight_to_ocean) return
-  
-    ! For convenience
-    grd=>bergs%grd
+  if (.not. associated(bergs)) return
+  if (.not. bergs%add_weight_to_ocean) return
+
+  ! For convenience
+  grd=>bergs%grd
+
+  !Start the clocks
+  call mpp_clock_begin(bergs%clock)
+  call mpp_clock_begin(bergs%clock_int)
 
-    !Start the clocks
-    call mpp_clock_begin(bergs%clock)
-    call mpp_clock_begin(bergs%clock_int)
+  do j=grd%jsc, grd%jec; do i=grd%isc, grd%iec
+    if (.not. bergs%passive_mode)   mass(i,j)=mass(i,j) + grd%spread_mass(i,j)
+  enddo  ;enddo
 
-    do j=grd%jsc, grd%jec; do i=grd%isc, grd%iec
-      if (.not. bergs%passive_mode)   mass(i,j)=mass(i,j) + grd%spread_mass(i,j)
-    enddo  ;enddo
-    
   !Stop the clocks
   call mpp_clock_end(bergs%clock_int)
   call mpp_clock_end(bergs%clock)
 
 end subroutine icebergs_incr_mass
 
-
 subroutine sum_up_spread_fields(bergs, field, field_name)
 ! Arguments
-type(icebergs), pointer :: bergs
+type(icebergs), pointer :: bergs !< Container for all types and memory
 real, dimension(bergs%grd%isc:bergs%grd%iec,bergs%grd%jsc:bergs%grd%jec), intent(out) :: field
 character(len=4), intent(in) :: field_name
 ! Local variables
@@ -3681,7 +3692,7 @@ subroutine sum_up_spread_fields(bergs, field, field_name)
   if (field_name=='area') var_on_ocean(:,:,:)=grd%area_on_ocean(:,:,:)
   if (field_name=='Uvel') var_on_ocean(:,:,:)=grd%Uvel_on_ocean(:,:,:)
   if (field_name=='Vvel') var_on_ocean(:,:,:)=grd%Vvel_on_ocean(:,:,:)
-  
+
   !This line has been removed, for that routine can be used for other fields
   !if (.not. bergs%add_weight_to_ocean) return
 
@@ -3718,7 +3729,7 @@ subroutine sum_up_spread_fields(bergs, field, field_name)
 
     field(i,j)=dmda
   enddo; enddo
-  
+
   if (debug) then
     grd%tmp(:,:)=0.; grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec)=field
     if (field_name=='mass') then
@@ -3735,7 +3746,7 @@ end subroutine sum_up_spread_fields
 
 subroutine accumulate_calving(bergs)
 ! Arguments
-type(icebergs), pointer :: bergs
+type(icebergs), pointer :: bergs !< Container for all types and memory
 ! Local variables
 type(icebergs_gridded), pointer :: grd
 real :: remaining_dist, net_calving_used
@@ -3797,7 +3808,7 @@ end subroutine accumulate_calving
 
 subroutine calve_icebergs(bergs)
 ! Arguments
-type(icebergs), pointer :: bergs
+type(icebergs), pointer :: bergs !< Container for all types and memory
 ! Local variables
 type(icebergs_gridded), pointer :: grd
 integer :: i,j,k,icnt,icntmax
@@ -3895,22 +3906,20 @@ subroutine calve_icebergs(bergs)
 
 end subroutine calve_icebergs
 
-! ##############################################################################
-
 subroutine evolve_icebergs(bergs)
 ! Arguments
-type(icebergs), pointer :: bergs
+type(icebergs), pointer :: bergs !< Container for all types and memory
 ! Local variables
 type(icebergs_gridded), pointer :: grd
 type(iceberg), pointer :: berg
-real :: uveln, vveln, lonn, latn  
+real :: uveln, vveln, lonn, latn
 real :: axn, ayn, bxn, byn                                           ! Added by Alon - explicit and implicit accelations from the previous step
 real :: xi, yj
 integer :: i, j
 integer :: grdi, grdj
 integer :: stderrunit
-logical :: bounced, interactive_icebergs_on, Runge_not_Verlet 
-  
+logical :: bounced, interactive_icebergs_on, Runge_not_Verlet
+
   ! Get the stderr unit number
   stderrunit = stderr()
 
@@ -3925,7 +3934,7 @@ subroutine evolve_icebergs(bergs)
     berg=>bergs%list(grdi,grdj)%first
     do while (associated(berg)) ! loop over all bergs
       if (berg%static_berg .lt. 0.5) then  !Only allow non-static icebergs to evolve
- 
+
         !Checking it everything is ok:
         if (.not. is_point_in_cell(bergs%grd, berg%lon, berg%lat, berg%ine, berg%jne) ) then
           write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lon',(i,i=grd%isd,grd%ied)
@@ -3945,12 +3954,12 @@ subroutine evolve_icebergs(bergs)
         if (debug) call check_position(grd, berg, 'evolve_iceberg (top)')
 
           !Time stepping schemes:
-          if (Runge_not_Verlet) then 
+          if (Runge_not_Verlet) then
             call Runge_Kutta_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln,lonn, latn, i, j, xi, yj)
-          endif 
-          if (.not.Runge_not_Verlet) then 
+          endif
+          if (.not.Runge_not_Verlet) then
             call verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
-          endif 
+          endif
 
           !Used for testing the ocean response to fixed iceberg motion.
           if (bergs%override_iceberg_velocities) then
@@ -3959,10 +3968,10 @@ subroutine evolve_icebergs(bergs)
           endif
 
         ! Saving all the iceberg variables.
-        berg%axn=axn 
-        berg%ayn=ayn 
-        berg%bxn=bxn 
-        berg%byn=byn 
+        berg%axn=axn
+        berg%ayn=ayn
+        berg%bxn=bxn
+        berg%byn=byn
         berg%uvel=uveln
         berg%vvel=vveln
 
@@ -3971,7 +3980,7 @@ subroutine evolve_icebergs(bergs)
           berg%ine=i     ;   berg%jne=j
           berg%xi=xi     ;   berg%yj=yj
         else
-          if (.not. interactive_icebergs_on)  call update_verlet_position(bergs,berg) 
+          if (.not. interactive_icebergs_on)  call update_verlet_position(bergs,berg)
         endif
 
         !call interp_flds(grd, i, j, xi, yj, berg%uo, berg%vo, berg%ui, berg%vi, berg%ua, berg%va, berg%ssh_x, berg%ssh_y, berg%sst)
@@ -3982,15 +3991,14 @@ subroutine evolve_icebergs(bergs)
     enddo ! loop over all bergs
   enddo ; enddo
 
-
   ! When we are using interactive icebergs, we update the (old) iceberg positions and velocities in a second loop, all together (to make code order invarient)
   if (interactive_icebergs_on) then
     do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
       berg=>bergs%list(grdi,grdj)%first
       do while (associated(berg)) ! loop over all bergs
         if (berg%static_berg .lt. 0.5) then  !Only allow non-static icebergs to evolve
-         if (.not. Runge_not_Verlet)  call update_verlet_position(bergs,berg) 
-          
+         if (.not. Runge_not_Verlet)  call update_verlet_position(bergs,berg)
+
          !Updating old velocities (for use in iceberg interactions)
           berg%uvel_old=berg%uvel
           berg%vvel_old=berg%vvel
@@ -4005,138 +4013,134 @@ subroutine evolve_icebergs(bergs)
 !contains
 end subroutine evolve_icebergs
 
-!######################################################################
-
 subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
-type(icebergs), pointer :: bergs
+type(icebergs), pointer :: bergs !< Container for all types and memory
 type(iceberg), pointer, intent(inout) :: berg
 type(icebergs_gridded), pointer :: grd
 ! Local variables
 real, intent(out) :: axn, ayn, bxn, byn, uveln, vveln
 real :: lonn, latn
 real :: uvel1, vvel1,  uvel2, vvel2, uvel3, vvel3
-real :: ax1, ay1 
-real :: x1,  y1, xddot1, yddot1, xi, yj 
+real :: ax1, ay1
+real :: x1,  y1, xddot1, yddot1, xi, yj
 real :: xdot3, ydot3
 real :: xdotn, ydotn
 real :: dt, dt_2, dt_6, dydl
 real :: orientation
 logical :: bounced, on_tangential_plane, error_flag
-integer :: i, j 
+integer :: i, j
 integer :: stderrunit
 
   !Initialize variables
 
-       ! In this scheme a_n and b_n are saved from the previous timestep, giving the explicit and implicit parts of the acceleration, and a_np1, b_np1 are for the next time step
-       ! Note that ax1=a_np1/2 +b_np1, as calculated by the acceleration subrouting
-       ! Positions and velocity is updated by
-       ! X2 = X1+dt*V1+((dt^2)/2)*a_n +((dt^2)/2)*b_n = X1+dt*u_star +((dt^2)/2)*b_n 
-       ! V2 = V1+dt/2*a_n +dt/2*a_np1 +dt*b_n = u_star + dt/2*a_np1 + dt*b_np1 = u_star +dt*ax
- 
-      !*************************************************************************************************
+  ! In this scheme a_n and b_n are saved from the previous timestep, giving the explicit and implicit parts of the acceleration, and a_np1, b_np1 are for the next time step
+  ! Note that ax1=a_np1/2 +b_np1, as calculated by the acceleration subrouting
+  ! Positions and velocity is updated by
+  ! X2 = X1+dt*V1+((dt^2)/2)*a_n +((dt^2)/2)*b_n = X1+dt*u_star +((dt^2)/2)*b_n
+  ! V2 = V1+dt/2*a_n +dt/2*a_np1 +dt*b_n = u_star + dt/2*a_np1 + dt*b_np1 = u_star +dt*ax
+
+  !*************************************************************************************************
 
   ! Get the stderr unit number
-    stderrunit = stderr()
+  stderrunit = stderr()
   ! For convenience
-    grd=>bergs%grd
+  grd=>bergs%grd
   ! Common constants
-    dt=bergs%dt
-    dt_2=0.5*dt
+  dt=bergs%dt
+  dt_2=0.5*dt
 
-    orientation=bergs%initial_orientation
-    if ((bergs%iceberg_bonds_on) .and. (bergs%rotate_icebergs_for_mass_spreading)) call find_orientation_using_iceberg_bonds(grd,berg,orientation)
+  orientation=bergs%initial_orientation
+  if ((bergs%iceberg_bonds_on) .and. (bergs%rotate_icebergs_for_mass_spreading)) call find_orientation_using_iceberg_bonds(grd,berg,orientation)
+
+  lonn = berg%lon ;   latn = berg%lat
+  axn  = berg%axn ;   ayn  = berg%ayn
+  bxn=   berg%bxn ;   byn  = berg%byn
+  uvel1=berg%uvel ;   vvel1=berg%vvel
+  i=berg%ine     ;   j=berg%jne
+  xi=berg%xi      ;   yj=berg%yj
+
+  ! Turn the velocities into u_star, v_star.(uvel3 is v_star) - Alon (not sure how this works with tangent plane)
+  uvel3=uvel1+(dt_2*axn)                  !Alon
+  vvel3=vvel1+(dt_2*ayn)                  !Alon
+
+  !Note, the mass scaling is equal to 1 (rather than 0.25 as in RK), since
+  !this is only called once in Verlet stepping.
+  if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
+    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 1.0*berg%mass_scaling,berg%length*berg%width, berg%thickness)
+
+  ! Calling the acceleration   (note that the velocity is converted to u_star inside the accel script)
+  call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn, ayn, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
+
+  !Solving for the new velocity
+  on_tangential_plane=.false.
+  if ((berg%lat>89.) .and. (bergs%grd%grid_is_latlon)) on_tangential_plane=.true.
+  if (on_tangential_plane) then
+    call rotvec_to_tang(lonn,uvel3,vvel3,xdot3,ydot3)
+    call rotvec_to_tang(lonn,ax1,ay1,xddot1,yddot1)
+    xdotn=xdot3+(dt*xddot1); ydotn=ydot3+(dt*yddot1)                                    !Alon
+    call rotvec_from_tang(lonn,xdotn,ydotn,uveln,vveln)
+  else
+    uveln=uvel3+(dt*ax1); vveln=vvel3+(dt*ay1)    !Alon , we call it uvel3, vvel3 until it is put into lat/long co-ordinates, where it becomes uveln, vveln
+  endif
 
-        lonn = berg%lon ;   latn = berg%lat
-        axn  = berg%axn ;   ayn  = berg%ayn
-        bxn=   berg%bxn ;   byn  = berg%byn
-        uvel1=berg%uvel ;   vvel1=berg%vvel
-        i=berg%ine     ;   j=berg%jne
-        xi=berg%xi      ;   yj=berg%yj
-
-        ! Turn the velocities into u_star, v_star.(uvel3 is v_star) - Alon (not sure how this works with tangent plane)
-        uvel3=uvel1+(dt_2*axn)                  !Alon
-        vvel3=vvel1+(dt_2*ayn)                  !Alon
-
-        !Note, the mass scaling is equal to 1 (rather than 0.25 as in RK), since
-        !this is only called once in Verlet stepping.
-        if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 1.0*berg%mass_scaling,berg%length*berg%width, berg%thickness)
-
-        ! Calling the acceleration   (note that the velocity is converted to u_star inside the accel script)
-        call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn, ayn, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
-  
-        !Solving for the new velocity
-        on_tangential_plane=.false.
-        if ((berg%lat>89.) .and. (bergs%grd%grid_is_latlon)) on_tangential_plane=.true.
-        if (on_tangential_plane) then
-          call rotvec_to_tang(lonn,uvel3,vvel3,xdot3,ydot3)
-          call rotvec_to_tang(lonn,ax1,ay1,xddot1,yddot1)
-          xdotn=xdot3+(dt*xddot1); ydotn=ydot3+(dt*yddot1)                                    !Alon
-          call rotvec_from_tang(lonn,xdotn,ydotn,uveln,vveln)
-        else
-          uveln=uvel3+(dt*ax1); vveln=vvel3+(dt*ay1)    !Alon , we call it uvel3, vvel3 until it is put into lat/long co-ordinates, where it becomes uveln, vveln
-        endif
+  !if (berg%iceberg_num .eq. 1) print *, 'New velocity: ', uveln, vveln
 
-        !if (berg%iceberg_num .eq. 1) print *, 'New velocity: ', uveln, vveln
 
-       
-        !!!!!!!!!!!!!!! Debugging  !!!!!!!!!!!!!!!!!!!!!!!!!!!
-        error_flag=.false.
-        if (.not.error_flag) then
-          if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j)) error_flag=.true.
-        endif
-        if (error_flag) then
-         call print_fld(grd, grd%msk, 'msk')
-         call print_fld(grd, grd%ssh, 'ssh')
-         call print_fld(grd, grd%sst, 'sst')
-         call print_fld(grd, grd%sss, 'sss')
-         call print_fld(grd, grd%hi, 'hi')
-         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
-         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lonn=',lonn,berg%lon
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: latn=',latn,berg%lat
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u3,un,u0=',uvel3,uveln,berg%uvel
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v3,vn,v0=',vvel3,vveln,berg%vvel
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: iceberg_num=',berg%iceberg_num
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1=',&
-              & dt*ax1
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ay1=',&
-              & dt*ay1
-         write(stderrunit,*) 'diamonds, evolve_iceberg: on_tangential_plane=',on_tangential_plane
-         write(stderrunit,*) 'Acceleration terms for position 1'
-         error_flag=pos_within_cell(grd, lonn, latn, i, j, xi,  yj)
-         call accel(bergs, berg, i, j, xi, yj, latn, uvel3, vvel3, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn, bxn, byn - Added by Alon
-         
-          write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'posn i,j,lon,lat,xi,yj=',i,j,lonn,latn,xi,yj
-          write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'posn box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
-          call print_berg(stderrunit, berg, 'evolve_iceberg, out of cell at end!')
-          bounced=is_point_in_cell(bergs%grd, lonn, latn, i, j,explain=.true.)
-          if (debug) call error_mesg('diamonds, evolve_iceberg','berg is out of posn at end!',FATAL)
-          write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lon',(i,i=grd%isd,grd%ied)
-          do j=grd%jed,grd%jsd,-1
-            write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lon(i,j),i=grd%isd,grd%ied)
-          enddo
-          write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lat',(i,i=grd%isd,grd%ied)
-          do j=grd%jed,grd%jsd,-1
-            write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lat(i,j),i=grd%isd,grd%ied)
-          enddo
-        endif
+  !!!!!!!!!!!!!!! Debugging  !!!!!!!!!!!!!!!!!!!!!!!!!!!
+  error_flag=.false.
+  if (.not.error_flag) then
+    if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j)) error_flag=.true.
+  endif
+  if (error_flag) then
+    call print_fld(grd, grd%msk, 'msk')
+    call print_fld(grd, grd%ssh, 'ssh')
+    call print_fld(grd, grd%sst, 'sst')
+    call print_fld(grd, grd%sss, 'sss')
+    call print_fld(grd, grd%hi, 'hi')
+    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
+    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lonn=',lonn,berg%lon
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: latn=',latn,berg%lat
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u3,un,u0=',uvel3,uveln,berg%uvel
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v3,vn,v0=',vvel3,vveln,berg%vvel
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: iceberg_num=',berg%iceberg_num
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1=',&
+         & dt*ax1
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ay1=',&
+         & dt*ay1
+    write(stderrunit,*) 'diamonds, evolve_iceberg: on_tangential_plane=',on_tangential_plane
+    write(stderrunit,*) 'Acceleration terms for position 1'
+    error_flag=pos_within_cell(grd, lonn, latn, i, j, xi,  yj)
+    call accel(bergs, berg, i, j, xi, yj, latn, uvel3, vvel3, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn, bxn, byn - Added by Alon
+
+    write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'posn i,j,lon,lat,xi,yj=',i,j,lonn,latn,xi,yj
+    write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'posn box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
+    call print_berg(stderrunit, berg, 'evolve_iceberg, out of cell at end!')
+    bounced=is_point_in_cell(bergs%grd, lonn, latn, i, j,explain=.true.)
+    if (debug) call error_mesg('diamonds, evolve_iceberg','berg is out of posn at end!',FATAL)
+    write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lon',(i,i=grd%isd,grd%ied)
+    do j=grd%jed,grd%jsd,-1
+      write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lon(i,j),i=grd%isd,grd%ied)
+    enddo
+    write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lat',(i,i=grd%isd,grd%ied)
+    do j=grd%jed,grd%jsd,-1
+      write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lat(i,j),i=grd%isd,grd%ied)
+    enddo
+  endif
 
 end subroutine verlet_stepping
 
-!######################################################################
-
 subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lonn, latn, i, j, xi, yj)
-type(icebergs), pointer :: bergs
+type(icebergs), pointer :: bergs !< Container for all types and memory
 type(iceberg), pointer, intent(inout) :: berg
 type(icebergs_gridded), pointer :: grd
 real , intent(out) :: axn, ayn, bxn, byn, uveln, vveln,lonn, latn, xi, yj
 integer, intent(out) :: i, j
-real :: uvel1, vvel1, lon1, lat1, u1, v1, dxdl1, ax1, ay1, axn1, ayn1 
+real :: uvel1, vvel1, lon1, lat1, u1, v1, dxdl1, ax1, ay1, axn1, ayn1
 real :: uvel2, vvel2, lon2, lat2, u2, v2, dxdl2, ax2, ay2, axn2, ayn2
 real :: uvel3, vvel3, lon3, lat3, u3, v3, dxdl3, ax3, ay3, axn3, ayn3
 real :: uvel4, vvel4, lon4, lat4, u4, v4, dxdl4, ax4, ay4, axn4, ayn4
-real :: x1, xdot1, xddot1, y1, ydot1, yddot1, xddot1n, yddot1n 
+real :: x1, xdot1, xddot1, y1, ydot1, yddot1, xddot1n, yddot1n
 real :: x2, xdot2, xddot2, y2, ydot2, yddot2, xddot2n, yddot2n
 real :: x3, xdot3, xddot3, y3, ydot3, yddot3, xddot3n, yddot3n
 real :: x4, xdot4, xddot4, y4, ydot4, yddot4, xddot4n, yddot4n
@@ -4160,317 +4164,313 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
 
 
   ! Get the stderr unit number
-    stderrunit = stderr()
+  stderrunit = stderr()
   ! For convenience
-    grd=>bergs%grd
+  grd=>bergs%grd
   ! Common constants
-    dt=bergs%dt
-    dt_2=0.5*dt
-    dt_6=dt/6.
-    
-        i=berg%ine
-        j=berg%jne
-        xi=berg%xi
-        yj=berg%yj
-        bounced=.false.
-        on_tangential_plane=.false.
-        if ((berg%lat>89.) .and. (bergs%grd%grid_is_latlon)) on_tangential_plane=.true.
-        i1=i;j1=j
-        if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, berg%thickness)
-
-        ! Loading past accelerations - Alon
-        axn=berg%axn; ayn=berg%ayn !Alon
-        axn1=axn; axn2=axn; axn3=axn; axn4=axn
-        ayn1=ayn; ayn2=ayn; ayn3=ayn; ayn4=ayn
-       
-        ! A1 = A(X1)
-        lon1=berg%lon; lat1=berg%lat
-        if (on_tangential_plane) call rotpos_to_tang(lon1,lat1,x1,y1)
-        
-        call  convert_from_meters_to_grid(lat1,bergs%grd%grid_is_latlon ,dxdl1,dydl)
-        !dxdl1=r180_pi/(Rearth*cos(lat1*pi_180))
-        !dydl=r180_pi/Rearth
-        uvel1=berg%uvel; vvel1=berg%vvel
-        if (on_tangential_plane) call rotvec_to_tang(lon1,uvel1,vvel1,xdot1,ydot1)
-        u1=uvel1*dxdl1; v1=vvel1*dydl
-
-        call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn) !axn,ayn, bxn, byn  - Added by Alon
-        !call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn1, ayn1, bxn, byn) !Note change to dt. Markpoint_1
-        if (on_tangential_plane) call rotvec_to_tang(lon1,ax1,ay1,xddot1,yddot1)
-        if (on_tangential_plane) call rotvec_to_tang(lon1,axn1,ayn1,xddot1n,yddot1n) !Alon
-        
-        !  X2 = X1+dt/2*V1 ; V2 = V1+dt/2*A1; A2=A(X2)
-       !if (debug) write(stderr(),*) 'diamonds, evolve: x2=...'
-        if (on_tangential_plane) then
-          x2=x1+dt_2*xdot1; y2=y1+dt_2*ydot1
-          xdot2=xdot1+dt_2*xddot1; ydot2=ydot1+dt_2*yddot1
-          call rotpos_from_tang(x2,y2,lon2,lat2)
-          call rotvec_from_tang(lon2,xdot2,ydot2,uvel2,vvel2)
-        else
-          lon2=lon1+dt_2*u1; lat2=lat1+dt_2*v1
-          uvel2=uvel1+dt_2*ax1; vvel2=vvel1+dt_2*ay1
-        endif
-        i=i1;j=j1;xi=berg%xi;yj=berg%yj
-        call adjust_index_and_ground(grd, lon2, lat2, uvel2, vvel2, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)
-        i2=i; j2=j
-        if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, berg%thickness)
-        ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon2,lat2,x2,y2)
-        if (.not.error_flag) then
-          if (debug .and. .not. is_point_in_cell(bergs%grd, lon2, lat2, i, j)) error_flag=.true.
-        endif
-        if (error_flag) then
-         call print_fld(grd, grd%msk, 'msk')
-         call print_fld(grd, grd%ssh, 'ssh')
-         call print_fld(grd, grd%sst, 'sst')
-         call print_fld(grd, grd%sss, 'sss')
-         call print_fld(grd, grd%hi, 'hi')
-         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
-         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
-         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: i1,i2,i=',i1,i2,i
-         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: j1,j2,j=',j1,j2,j
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lon1,lon2=',lon1,lon2,berg%lon
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lat1,lat2=',lat1,lat2,berg%lat
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u1,u2,u0=',uvel1,uvel2,berg%uvel
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v1,v2,v0=',vvel1,vvel2,berg%vvel
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1,ax2=',dt*ax1,dt*ax2
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ay1,ay2=',dt*ay1,dt*ay2
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u0=',dt*uvel1,dt*uvel2,dt*berg%uvel
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v0=',dt*vvel1,dt*vvel2,dt*berg%vvel
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2 (deg)=',dt*u1,dt*u2
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2 (deg)=',dt*v1,dt*v2
-         write(stderrunit,*) 'Acceleration terms for position 1'
-         error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-         call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn,- Added by Alon
-          call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 2')
-          write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos2 i,j,lon,lat,xi,yj=',i,j,lon2,lat2,xi,yj
-          write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos2 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
-          bounced=is_point_in_cell(bergs%grd, lon2, lat2, i, j,explain=.true.)
-          call error_mesg('diamonds, evolve_iceberg','berg is out of posn at 2!',FATAL)
-        endif
-        call  convert_from_meters_to_grid(lat2,bergs%grd%grid_is_latlon ,dxdl2,dydl)
-        !dxdl2=r180_pi/(Rearth*cos(lat2*pi_180))
-        u2=uvel2*dxdl2; v2=vvel2*dydl
-        call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
-        !call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt, ax2, ay2, axn2, ayn2, bxn, byn) !Note change to dt. Markpoint_1
-        if (on_tangential_plane) call rotvec_to_tang(lon2,ax2,ay2,xddot2,yddot2)
-        if (on_tangential_plane) call rotvec_to_tang(lon2,axn2,ayn2,xddot2n,yddot2n) !Alon
-        
-        !  X3 = X1+dt/2*V2 ; V3 = V1+dt/2*A2; A3=A(X3)
-       !if (debug) write(stderr(),*) 'diamonds, evolve: x3=...'
-        if (on_tangential_plane) then
-          x3=x1+dt_2*xdot2; y3=y1+dt_2*ydot2
-          xdot3=xdot1+dt_2*xddot2; ydot3=ydot1+dt_2*yddot2
-          call rotpos_from_tang(x3,y3,lon3,lat3)
-          call rotvec_from_tang(lon3,xdot3,ydot3,uvel3,vvel3)
-        else
-          lon3=lon1+dt_2*u2; lat3=lat1+dt_2*v2
-          uvel3=uvel1+dt_2*ax2; vvel3=vvel1+dt_2*ay2
-        endif
-        i=i1;j=j1;xi=berg%xi;yj=berg%yj
-        call adjust_index_and_ground(grd, lon3, lat3, uvel3, vvel3, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)
-        i3=i; j3=j
-        if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, berg%thickness)
-        ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon3,lat3,x3,y3)
-        if (.not.error_flag) then
-          if (debug .and. .not. is_point_in_cell(bergs%grd, lon3, lat3, i, j)) error_flag=.true.
-        endif
-        if (error_flag) then
-         call print_fld(grd, grd%msk, 'msk')
-         call print_fld(grd, grd%ssh, 'ssh')
-         call print_fld(grd, grd%sst, 'sst')
-         call print_fld(grd, grd%sss, 'sss')
-         call print_fld(grd, grd%hi, 'hi')
-         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
-         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
-         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: i1,i2,i3,i=',i1,i2,i3,i
-         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: j1,j2,j3,j=',j1,j2,j3,j
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lon1,lon2,lon3=',lon1,lon2,lon3,berg%lon
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lat1,lat2,lat3=',lat1,lat2,lat3,berg%lat
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u1,u2,u3,u0=',uvel1,uvel2,uvel3,berg%uvel
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v1,v2,v3,v0=',vvel1,vvel2,vvel3,berg%vvel
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1,ax2,ax3=',dt*ax1,dt*ax2,dt*ax3
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ay1,ay2,ay3=',dt*ay1,dt*ay2,dt*ay3
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3,u0=',dt*uvel1,dt*uvel2,dt*uvel3,dt*berg%uvel
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v0=',dt*vvel1,dt*vvel2,dt*vvel3,dt*berg%vvel
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3 (deg)=',dt*u1,dt*u2,dt*u3
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3 (deg)=',dt*v1,dt*v2,dt*v3
-         write(stderrunit,*) 'Acceleration terms for position 1'
-         error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-         call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, debug_flag=.true.) !axn, ayn - Added by Alon
-         write(stderrunit,*) 'Acceleration terms for position 2'
-         error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
-         call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
-          call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 3')
-          write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos3 i,j,lon,lat,xi,yj=',i,j,lon3,lat3,xi,yj
-          write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos3 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
-          bounced=is_point_in_cell(bergs%grd, lon2, lat2, i, j,explain=.true.)
-          call error_mesg('diamonds, evolve_iceberg','berg is out of posn at 3!',FATAL)
-        endif
-        call  convert_from_meters_to_grid(lat3,bergs%grd%grid_is_latlon ,dxdl3,dydl)
-        !dxdl3=r180_pi/(Rearth*cos(lat3*pi_180))
-        u3=uvel3*dxdl3; v3=vvel3*dydl
-        call accel(bergs, berg, i, j, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn3, ayn3, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
-        if (on_tangential_plane) call rotvec_to_tang(lon3,ax3,ay3,xddot3,yddot3)
-        if (on_tangential_plane) call rotvec_to_tang(lon3,axn3,ayn3,xddot3n,yddot3n) !Alon
-        
-        !  X4 = X1+dt*V3 ; V4 = V1+dt*A3; A4=A(X4)
-       !if (debug) write(stderr(),*) 'diamonds, evolve: x4=...'
-        if (on_tangential_plane) then
-          x4=x1+dt*xdot3; y4=y1+dt*ydot3
-          xdot4=xdot1+dt*xddot3; ydot4=ydot1+dt*yddot3
-          call rotpos_from_tang(x4,y4,lon4,lat4)
-          call rotvec_from_tang(lon4,xdot4,ydot4,uvel4,vvel4)
-        else
-          lon4=lon1+dt*u3; lat4=lat1+dt*v3
-          uvel4=uvel1+dt*ax3; vvel4=vvel1+dt*ay3
-        endif
-        i=i1;j=j1;xi=berg%xi;yj=berg%yj
-        call adjust_index_and_ground(grd, lon4, lat4, uvel4, vvel4, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)
-        i4=i; j4=j
-        ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon4,lat4,x4,y4)
-        if (.not.error_flag) then
-          if (debug .and. .not. is_point_in_cell(bergs%grd, lon4, lat4, i, j)) error_flag=.true.
-        endif
-        if (error_flag) then
-         call print_fld(grd, grd%msk, 'msk')
-         call print_fld(grd, grd%ssh, 'ssh')
-         call print_fld(grd, grd%sst, 'sst')
-         call print_fld(grd, grd%sss, 'sss')
-         call print_fld(grd, grd%hi, 'hi')
-         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
-         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
-         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: i1,i2,i3,i4,i=',i1,i2,i3,i4,i
-         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: j1,j2,j3,j4,j=',j1,j2,j3,j4,j
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lon1,lon2,lon3,lon4=',lon1,lon2,lon3,lon4,berg%lon
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lat1,lat2,lat3,lat4=',lat1,lat2,lat3,lat4,berg%lat
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u1,u2,u3,u4,u0=',uvel1,uvel2,uvel3,uvel4,berg%uvel
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v1,v2,v3,v4,v0=',vvel1,vvel2,vvel3,vvel4,berg%vvel
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1,ax2,ax3,ax4=',dt*ax1,dt*ax2,dt*ax3,dt*ax4
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ay1,ay2,ay3,ay4=',dt*ay1,dt*ay2,dt*ay3,dt*ay4
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3,u4,u0=',dt*uvel1,dt*uvel2,dt*uvel3,dt*uvel4,dt*berg%uvel
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v4,v0=',dt*vvel1,dt*vvel2,dt*vvel3,dt*vvel4,dt*berg%vvel
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3,u4 (deg)=',dt*u1,dt*u2,dt*u3,dt*u4
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v4 (deg)=',dt*v1,dt*v2,dt*v3,dt*v4
-         write(stderrunit,*) 'Acceleration terms for position 1'
-         error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-         call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
-         write(stderrunit,*) 'Acceleration terms for position 2'
-         error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
-         call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
-         write(stderrunit,*) 'Acceleration terms for position 3'
-         error_flag=pos_within_cell(grd, lon3, lat3, i3, j3, xi, yj)
-         call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn3, ayn3, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
-          call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 4')
-          write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos4 i,j,lon,lat,xi,yj=',i,j,lon4,lat4,xi,yj
-          write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos4 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
-          bounced=is_point_in_cell(bergs%grd, lon2, lat2, i, j, explain=.true.)
-          call error_mesg('diamonds, evolve_iceberg','berg is out of posn at 4!',FATAL)
-        endif
-        call  convert_from_meters_to_grid(lat4,bergs%grd%grid_is_latlon ,dxdl4,dydl)
-        !dxdl4=r180_pi/(Rearth*cos(lat4*pi_180))
-        u4=uvel4*dxdl4; v4=vvel4*dydl
-        call accel(bergs, berg, i, j, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axn4, ayn4, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
-        if (on_tangential_plane) call rotvec_to_tang(lon4,ax4,ay4,xddot4,yddot4)
-        if (on_tangential_plane) call rotvec_to_tang(lon4,axn4,ayn4,xddot4n,yddot4n)
-        
-        !  Xn = X1+dt*(V1+2*V2+2*V3+V4)/6
-        !  Vn = V1+dt*(A1+2*A2+2*A3+A4)/6
-        if (on_tangential_plane) then
-          xn=x1+dt_6*( (xdot1+xdot4)+2.*(xdot2+xdot3) )
-          yn=y1+dt_6*( (ydot1+ydot4)+2.*(ydot2+ydot3) )
-          xdotn=xdot1+dt_6*( (xddot1+xddot4)+2.*(xddot2+xddot3) )
-          ydotn=ydot1+dt_6*( (yddot1+yddot4)+2.*(yddot2+yddot3) )
-          xddotn=( (xddot1n+xddot4n)+2.*(xddot2n+xddot3n) )/6.  !Alon  
-          yddotn=( (yddot1n+yddot4n)+2.*(yddot2n+yddot3n) )/6.  !Alon  
-          call rotpos_from_tang(xn,yn,lonn,latn)
-          call rotvec_from_tang(lonn,xdotn,ydotn,uveln,vveln)
-          call rotvec_from_tang(lonn,xddotn,yddotn,axn,ayn) !Alon
-        else
-          lonn=berg%lon+dt_6*( (u1+u4)+2.*(u2+u3) )
-          latn=berg%lat+dt_6*( (v1+v4)+2.*(v2+v3) )
-          uveln=berg%uvel+dt_6*( (ax1+ax4)+2.*(ax2+ax3) )
-          vveln=berg%vvel+dt_6*( (ay1+ay4)+2.*(ay2+ay3) )
-          axn=( (axn1+axn4)+2.*(axn2+axn3) )/6. !Alon
-          ayn=( (ayn1+ayn4)+2.*(ayn2+ayn3) )/6. !Alon
-          bxn=(((ax1+ax4)+2.*(ax2+ax3) )/6)  - (axn/2)
-          byn=(((ay1+ay4)+2.*(ay2+ay3) )/6)  - (ayn/2)
-  
-        endif
-  
-  
-  
-        i=i1;j=j1;xi=berg%xi;yj=berg%yj
-        call adjust_index_and_ground(grd, lonn, latn, uveln, vveln, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)
-        if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-          call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, berg%thickness)
-  
-        if (.not.error_flag) then
-          if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j)) error_flag=.true.
-        endif
-        if (error_flag) then
-         call print_fld(grd, grd%msk, 'msk')
-         call print_fld(grd, grd%ssh, 'ssh')
-         call print_fld(grd, grd%sst, 'sst')
-         call print_fld(grd, grd%sss, 'sss')
-         call print_fld(grd, grd%hi, 'hi')
-         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
-         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
-         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: i1,i2,i3,i4,i=',i1,i2,i3,i4,i
-         write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: j1,j2,j3,j4,j=',j1,j2,j3,j4,j
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lon1,lon2,lon3,lon4,lonn=',lon1,lon2,lon3,lon4,lonn,berg%lon
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lat1,lat2,lat3,lat4,latn=',lat1,lat2,lat3,lat4,latn,berg%lat
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u1,u2,u3,u4,un,u0=',uvel1,uvel2,uvel3,uvel4,uveln,berg%uvel
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v1,v2,v3,v4,vn,v0=',vvel1,vvel2,vvel3,vvel4,vveln,berg%vvel
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1,ax2,ax3,ax4,axn=',&
-              & dt*ax1,dt*ax2,dt*ax3,dt*ax4,dt_6*( (ax1+ax4)+2.*(ax2+ax3) )
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ay1,ay2,ay3,ay4,ayn=',&
-              & dt*ay1,dt*ay2,dt*ay3,dt*ay4,dt_6*( (ay1+ay4)+2.*(ay2+ay3) )
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3,u4,un,u0=',&
-              & dt*uvel1,dt*uvel2,dt*uvel3,dt*uvel4,dt*uveln,dt*berg%uvel
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v4,vn,v0=',&
-              & dt*vvel1,dt*vvel2,dt*vvel3,dt*vvel4,dt*vveln,dt*berg%vvel
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3,u4,u_rk (deg)=',&
-              & dt*u1,dt*u2,dt*u3,dt*u4,dt_6*( (u1+u4)+2.*(u2+u3) )
-         write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v4,v_rk (deg)=',&
-              & dt*v1,dt*v2,dt*v3,dt*v4,dt_6*( (v1+v4)+2.*(v2+v3) )
-         write(stderrunit,*) 'diamonds, evolve_iceberg: on_tangential_plane=',on_tangential_plane
-         write(stderrunit,*) 'Acceleration terms for position 1'
-         error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-         call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
-         write(stderrunit,*) 'Acceleration terms for position 2'
-         error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
-         call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
-         write(stderrunit,*) 'Acceleration terms for position 3'
-         error_flag=pos_within_cell(grd, lon3, lat3, i3, j3, xi, yj)
-         call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
-         write(stderrunit,*) 'Acceleration terms for position 4'
-         error_flag=pos_within_cell(grd, lon4, lat4, i4, j4, xi, yj)
-         call accel(bergs, berg, i4, j4, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
-          write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'posn i,j,lon,lat,xi,yj=',i,j,lonn,latn,xi,yj
-          write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'posn box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
-          call print_berg(stderrunit, berg, 'evolve_iceberg, out of cell at end!')
-          bounced=is_point_in_cell(bergs%grd, lonn, latn, i, j, explain=.true.)
-          if (debug) call error_mesg('diamonds, evolve_iceberg','berg is out of posn at end!',FATAL)
-          write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lon',(i,i=grd%isd,grd%ied)
-          do j=grd%jed,grd%jsd,-1
-            write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lon(i,j),i=grd%isd,grd%ied)
-          enddo
-          write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lat',(i,i=grd%isd,grd%ied)
-          do j=grd%jed,grd%jsd,-1
-            write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lat(i,j),i=grd%isd,grd%ied)
-          enddo
-        endif
-end subroutine Runge_Kutta_stepping
+  dt=bergs%dt
+  dt_2=0.5*dt
+  dt_6=dt/6.
+
+  i=berg%ine
+  j=berg%jne
+  xi=berg%xi
+  yj=berg%yj
+  bounced=.false.
+  on_tangential_plane=.false.
+  if ((berg%lat>89.) .and. (bergs%grd%grid_is_latlon)) on_tangential_plane=.true.
+  i1=i;j1=j
+  if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
+    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, berg%thickness)
+
+  ! Loading past accelerations - Alon
+  axn=berg%axn; ayn=berg%ayn !Alon
+  axn1=axn; axn2=axn; axn3=axn; axn4=axn
+  ayn1=ayn; ayn2=ayn; ayn3=ayn; ayn4=ayn
+
+  ! A1 = A(X1)
+  lon1=berg%lon; lat1=berg%lat
+  if (on_tangential_plane) call rotpos_to_tang(lon1,lat1,x1,y1)
+
+  call  convert_from_meters_to_grid(lat1,bergs%grd%grid_is_latlon ,dxdl1,dydl)
+  !dxdl1=r180_pi/(Rearth*cos(lat1*pi_180))
+  !dydl=r180_pi/Rearth
+  uvel1=berg%uvel; vvel1=berg%vvel
+  if (on_tangential_plane) call rotvec_to_tang(lon1,uvel1,vvel1,xdot1,ydot1)
+  u1=uvel1*dxdl1; v1=vvel1*dydl
+
+  call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn) !axn,ayn, bxn, byn  - Added by Alon
+  !call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn1, ayn1, bxn, byn) !Note change to dt. Markpoint_1
+  if (on_tangential_plane) call rotvec_to_tang(lon1,ax1,ay1,xddot1,yddot1)
+  if (on_tangential_plane) call rotvec_to_tang(lon1,axn1,ayn1,xddot1n,yddot1n) !Alon
+
+  !  X2 = X1+dt/2*V1 ; V2 = V1+dt/2*A1; A2=A(X2)
+  !if (debug) write(stderr(),*) 'diamonds, evolve: x2=...'
+  if (on_tangential_plane) then
+    x2=x1+dt_2*xdot1; y2=y1+dt_2*ydot1
+    xdot2=xdot1+dt_2*xddot1; ydot2=ydot1+dt_2*yddot1
+    call rotpos_from_tang(x2,y2,lon2,lat2)
+    call rotvec_from_tang(lon2,xdot2,ydot2,uvel2,vvel2)
+  else
+    lon2=lon1+dt_2*u1; lat2=lat1+dt_2*v1
+    uvel2=uvel1+dt_2*ax1; vvel2=vvel1+dt_2*ay1
+  endif
+  i=i1;j=j1;xi=berg%xi;yj=berg%yj
+  call adjust_index_and_ground(grd, lon2, lat2, uvel2, vvel2, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)
+  i2=i; j2=j
+  if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
+    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, berg%thickness)
+  ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon2,lat2,x2,y2)
+  if (.not.error_flag) then
+    if (debug .and. .not. is_point_in_cell(bergs%grd, lon2, lat2, i, j)) error_flag=.true.
+  endif
+  if (error_flag) then
+    call print_fld(grd, grd%msk, 'msk')
+    call print_fld(grd, grd%ssh, 'ssh')
+    call print_fld(grd, grd%sst, 'sst')
+    call print_fld(grd, grd%sss, 'sss')
+    call print_fld(grd, grd%hi, 'hi')
+    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
+    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
+    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: i1,i2,i=',i1,i2,i
+    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: j1,j2,j=',j1,j2,j
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lon1,lon2=',lon1,lon2,berg%lon
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lat1,lat2=',lat1,lat2,berg%lat
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u1,u2,u0=',uvel1,uvel2,berg%uvel
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v1,v2,v0=',vvel1,vvel2,berg%vvel
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1,ax2=',dt*ax1,dt*ax2
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ay1,ay2=',dt*ay1,dt*ay2
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u0=',dt*uvel1,dt*uvel2,dt*berg%uvel
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v0=',dt*vvel1,dt*vvel2,dt*berg%vvel
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2 (deg)=',dt*u1,dt*u2
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2 (deg)=',dt*v1,dt*v2
+    write(stderrunit,*) 'Acceleration terms for position 1'
+    error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
+    call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn,- Added by Alon
+    call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 2')
+    write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos2 i,j,lon,lat,xi,yj=',i,j,lon2,lat2,xi,yj
+    write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos2 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
+    bounced=is_point_in_cell(bergs%grd, lon2, lat2, i, j,explain=.true.)
+    call error_mesg('diamonds, evolve_iceberg','berg is out of posn at 2!',FATAL)
+  endif
+  call  convert_from_meters_to_grid(lat2,bergs%grd%grid_is_latlon ,dxdl2,dydl)
+  !dxdl2=r180_pi/(Rearth*cos(lat2*pi_180))
+  u2=uvel2*dxdl2; v2=vvel2*dydl
+  call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
+  !call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt, ax2, ay2, axn2, ayn2, bxn, byn) !Note change to dt. Markpoint_1
+  if (on_tangential_plane) call rotvec_to_tang(lon2,ax2,ay2,xddot2,yddot2)
+  if (on_tangential_plane) call rotvec_to_tang(lon2,axn2,ayn2,xddot2n,yddot2n) !Alon
+
+  !  X3 = X1+dt/2*V2 ; V3 = V1+dt/2*A2; A3=A(X3)
+  !if (debug) write(stderr(),*) 'diamonds, evolve: x3=...'
+  if (on_tangential_plane) then
+    x3=x1+dt_2*xdot2; y3=y1+dt_2*ydot2
+    xdot3=xdot1+dt_2*xddot2; ydot3=ydot1+dt_2*yddot2
+    call rotpos_from_tang(x3,y3,lon3,lat3)
+    call rotvec_from_tang(lon3,xdot3,ydot3,uvel3,vvel3)
+  else
+    lon3=lon1+dt_2*u2; lat3=lat1+dt_2*v2
+    uvel3=uvel1+dt_2*ax2; vvel3=vvel1+dt_2*ay2
+  endif
+  i=i1;j=j1;xi=berg%xi;yj=berg%yj
+  call adjust_index_and_ground(grd, lon3, lat3, uvel3, vvel3, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)
+  i3=i; j3=j
+  if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
+    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, berg%thickness)
+  ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon3,lat3,x3,y3)
+  if (.not.error_flag) then
+    if (debug .and. .not. is_point_in_cell(bergs%grd, lon3, lat3, i, j)) error_flag=.true.
+  endif
+  if (error_flag) then
+    call print_fld(grd, grd%msk, 'msk')
+    call print_fld(grd, grd%ssh, 'ssh')
+    call print_fld(grd, grd%sst, 'sst')
+    call print_fld(grd, grd%sss, 'sss')
+    call print_fld(grd, grd%hi, 'hi')
+    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
+    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
+    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: i1,i2,i3,i=',i1,i2,i3,i
+    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: j1,j2,j3,j=',j1,j2,j3,j
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lon1,lon2,lon3=',lon1,lon2,lon3,berg%lon
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lat1,lat2,lat3=',lat1,lat2,lat3,berg%lat
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u1,u2,u3,u0=',uvel1,uvel2,uvel3,berg%uvel
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v1,v2,v3,v0=',vvel1,vvel2,vvel3,berg%vvel
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1,ax2,ax3=',dt*ax1,dt*ax2,dt*ax3
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ay1,ay2,ay3=',dt*ay1,dt*ay2,dt*ay3
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3,u0=',dt*uvel1,dt*uvel2,dt*uvel3,dt*berg%uvel
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v0=',dt*vvel1,dt*vvel2,dt*vvel3,dt*berg%vvel
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3 (deg)=',dt*u1,dt*u2,dt*u3
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3 (deg)=',dt*v1,dt*v2,dt*v3
+    write(stderrunit,*) 'Acceleration terms for position 1'
+    error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
+    call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, debug_flag=.true.) !axn, ayn - Added by Alon
+    write(stderrunit,*) 'Acceleration terms for position 2'
+    error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
+    call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
+    call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 3')
+    write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos3 i,j,lon,lat,xi,yj=',i,j,lon3,lat3,xi,yj
+    write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos3 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
+    bounced=is_point_in_cell(bergs%grd, lon2, lat2, i, j,explain=.true.)
+    call error_mesg('diamonds, evolve_iceberg','berg is out of posn at 3!',FATAL)
+  endif
+  call  convert_from_meters_to_grid(lat3,bergs%grd%grid_is_latlon ,dxdl3,dydl)
+  !dxdl3=r180_pi/(Rearth*cos(lat3*pi_180))
+  u3=uvel3*dxdl3; v3=vvel3*dydl
+  call accel(bergs, berg, i, j, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn3, ayn3, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
+  if (on_tangential_plane) call rotvec_to_tang(lon3,ax3,ay3,xddot3,yddot3)
+  if (on_tangential_plane) call rotvec_to_tang(lon3,axn3,ayn3,xddot3n,yddot3n) !Alon
+
+  !  X4 = X1+dt*V3 ; V4 = V1+dt*A3; A4=A(X4)
+  !if (debug) write(stderr(),*) 'diamonds, evolve: x4=...'
+  if (on_tangential_plane) then
+    x4=x1+dt*xdot3; y4=y1+dt*ydot3
+    xdot4=xdot1+dt*xddot3; ydot4=ydot1+dt*yddot3
+    call rotpos_from_tang(x4,y4,lon4,lat4)
+    call rotvec_from_tang(lon4,xdot4,ydot4,uvel4,vvel4)
+  else
+    lon4=lon1+dt*u3; lat4=lat1+dt*v3
+    uvel4=uvel1+dt*ax3; vvel4=vvel1+dt*ay3
+  endif
+  i=i1;j=j1;xi=berg%xi;yj=berg%yj
+  call adjust_index_and_ground(grd, lon4, lat4, uvel4, vvel4, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)
+  i4=i; j4=j
+  ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon4,lat4,x4,y4)
+  if (.not.error_flag) then
+    if (debug .and. .not. is_point_in_cell(bergs%grd, lon4, lat4, i, j)) error_flag=.true.
+  endif
+  if (error_flag) then
+    call print_fld(grd, grd%msk, 'msk')
+    call print_fld(grd, grd%ssh, 'ssh')
+    call print_fld(grd, grd%sst, 'sst')
+    call print_fld(grd, grd%sss, 'sss')
+    call print_fld(grd, grd%hi, 'hi')
+    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
+    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
+    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: i1,i2,i3,i4,i=',i1,i2,i3,i4,i
+    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: j1,j2,j3,j4,j=',j1,j2,j3,j4,j
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lon1,lon2,lon3,lon4=',lon1,lon2,lon3,lon4,berg%lon
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lat1,lat2,lat3,lat4=',lat1,lat2,lat3,lat4,berg%lat
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u1,u2,u3,u4,u0=',uvel1,uvel2,uvel3,uvel4,berg%uvel
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v1,v2,v3,v4,v0=',vvel1,vvel2,vvel3,vvel4,berg%vvel
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1,ax2,ax3,ax4=',dt*ax1,dt*ax2,dt*ax3,dt*ax4
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ay1,ay2,ay3,ay4=',dt*ay1,dt*ay2,dt*ay3,dt*ay4
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3,u4,u0=',dt*uvel1,dt*uvel2,dt*uvel3,dt*uvel4,dt*berg%uvel
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v4,v0=',dt*vvel1,dt*vvel2,dt*vvel3,dt*vvel4,dt*berg%vvel
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3,u4 (deg)=',dt*u1,dt*u2,dt*u3,dt*u4
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v4 (deg)=',dt*v1,dt*v2,dt*v3,dt*v4
+    write(stderrunit,*) 'Acceleration terms for position 1'
+    error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
+    call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
+    write(stderrunit,*) 'Acceleration terms for position 2'
+    error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
+    call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
+    write(stderrunit,*) 'Acceleration terms for position 3'
+    error_flag=pos_within_cell(grd, lon3, lat3, i3, j3, xi, yj)
+    call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn3, ayn3, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
+    call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 4')
+    write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos4 i,j,lon,lat,xi,yj=',i,j,lon4,lat4,xi,yj
+    write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos4 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
+    bounced=is_point_in_cell(bergs%grd, lon2, lat2, i, j, explain=.true.)
+    call error_mesg('diamonds, evolve_iceberg','berg is out of posn at 4!',FATAL)
+  endif
+  call  convert_from_meters_to_grid(lat4,bergs%grd%grid_is_latlon ,dxdl4,dydl)
+  !dxdl4=r180_pi/(Rearth*cos(lat4*pi_180))
+  u4=uvel4*dxdl4; v4=vvel4*dydl
+  call accel(bergs, berg, i, j, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axn4, ayn4, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
+  if (on_tangential_plane) call rotvec_to_tang(lon4,ax4,ay4,xddot4,yddot4)
+  if (on_tangential_plane) call rotvec_to_tang(lon4,axn4,ayn4,xddot4n,yddot4n)
+
+  !  Xn = X1+dt*(V1+2*V2+2*V3+V4)/6
+  !  Vn = V1+dt*(A1+2*A2+2*A3+A4)/6
+  if (on_tangential_plane) then
+    xn=x1+dt_6*( (xdot1+xdot4)+2.*(xdot2+xdot3) )
+    yn=y1+dt_6*( (ydot1+ydot4)+2.*(ydot2+ydot3) )
+    xdotn=xdot1+dt_6*( (xddot1+xddot4)+2.*(xddot2+xddot3) )
+    ydotn=ydot1+dt_6*( (yddot1+yddot4)+2.*(yddot2+yddot3) )
+    xddotn=( (xddot1n+xddot4n)+2.*(xddot2n+xddot3n) )/6.  !Alon
+    yddotn=( (yddot1n+yddot4n)+2.*(yddot2n+yddot3n) )/6.  !Alon
+    call rotpos_from_tang(xn,yn,lonn,latn)
+    call rotvec_from_tang(lonn,xdotn,ydotn,uveln,vveln)
+    call rotvec_from_tang(lonn,xddotn,yddotn,axn,ayn) !Alon
+  else
+    lonn=berg%lon+dt_6*( (u1+u4)+2.*(u2+u3) )
+    latn=berg%lat+dt_6*( (v1+v4)+2.*(v2+v3) )
+    uveln=berg%uvel+dt_6*( (ax1+ax4)+2.*(ax2+ax3) )
+    vveln=berg%vvel+dt_6*( (ay1+ay4)+2.*(ay2+ay3) )
+    axn=( (axn1+axn4)+2.*(axn2+axn3) )/6. !Alon
+    ayn=( (ayn1+ayn4)+2.*(ayn2+ayn3) )/6. !Alon
+    bxn=(((ax1+ax4)+2.*(ax2+ax3) )/6)  - (axn/2)
+    byn=(((ay1+ay4)+2.*(ay2+ay3) )/6)  - (ayn/2)
+  endif
+
+  i=i1;j=j1;xi=berg%xi;yj=berg%yj
+  call adjust_index_and_ground(grd, lonn, latn, uveln, vveln, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)
+  if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
+    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, berg%thickness)
 
+  if (.not.error_flag) then
+    if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j)) error_flag=.true.
+  endif
+  if (error_flag) then
+    call print_fld(grd, grd%msk, 'msk')
+    call print_fld(grd, grd%ssh, 'ssh')
+    call print_fld(grd, grd%sst, 'sst')
+    call print_fld(grd, grd%sss, 'sss')
+    call print_fld(grd, grd%hi, 'hi')
+    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
+    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
+    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: i1,i2,i3,i4,i=',i1,i2,i3,i4,i
+    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: j1,j2,j3,j4,j=',j1,j2,j3,j4,j
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lon1,lon2,lon3,lon4,lonn=',lon1,lon2,lon3,lon4,lonn,berg%lon
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lat1,lat2,lat3,lat4,latn=',lat1,lat2,lat3,lat4,latn,berg%lat
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u1,u2,u3,u4,un,u0=',uvel1,uvel2,uvel3,uvel4,uveln,berg%uvel
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v1,v2,v3,v4,vn,v0=',vvel1,vvel2,vvel3,vvel4,vveln,berg%vvel
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1,ax2,ax3,ax4,axn=',&
+         & dt*ax1,dt*ax2,dt*ax3,dt*ax4,dt_6*( (ax1+ax4)+2.*(ax2+ax3) )
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ay1,ay2,ay3,ay4,ayn=',&
+         & dt*ay1,dt*ay2,dt*ay3,dt*ay4,dt_6*( (ay1+ay4)+2.*(ay2+ay3) )
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3,u4,un,u0=',&
+         & dt*uvel1,dt*uvel2,dt*uvel3,dt*uvel4,dt*uveln,dt*berg%uvel
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v4,vn,v0=',&
+         & dt*vvel1,dt*vvel2,dt*vvel3,dt*vvel4,dt*vveln,dt*berg%vvel
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3,u4,u_rk (deg)=',&
+         & dt*u1,dt*u2,dt*u3,dt*u4,dt_6*( (u1+u4)+2.*(u2+u3) )
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v4,v_rk (deg)=',&
+         & dt*v1,dt*v2,dt*v3,dt*v4,dt_6*( (v1+v4)+2.*(v2+v3) )
+    write(stderrunit,*) 'diamonds, evolve_iceberg: on_tangential_plane=',on_tangential_plane
+    write(stderrunit,*) 'Acceleration terms for position 1'
+    error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
+    call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
+    write(stderrunit,*) 'Acceleration terms for position 2'
+    error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
+    call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
+    write(stderrunit,*) 'Acceleration terms for position 3'
+    error_flag=pos_within_cell(grd, lon3, lat3, i3, j3, xi, yj)
+    call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
+    write(stderrunit,*) 'Acceleration terms for position 4'
+    error_flag=pos_within_cell(grd, lon4, lat4, i4, j4, xi, yj)
+    call accel(bergs, berg, i4, j4, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
+    write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'posn i,j,lon,lat,xi,yj=',i,j,lonn,latn,xi,yj
+    write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'posn box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
+    call print_berg(stderrunit, berg, 'evolve_iceberg, out of cell at end!')
+    bounced=is_point_in_cell(bergs%grd, lonn, latn, i, j, explain=.true.)
+    if (debug) call error_mesg('diamonds, evolve_iceberg','berg is out of posn at end!',FATAL)
+    write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lon',(i,i=grd%isd,grd%ied)
+    do j=grd%jed,grd%jsd,-1
+      write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lon(i,j),i=grd%isd,grd%ied)
+    enddo
+    write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lat',(i,i=grd%isd,grd%ied)
+    do j=grd%jed,grd%jsd,-1
+      write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lat(i,j),i=grd%isd,grd%ied)
+    enddo
+  endif
+end subroutine Runge_Kutta_stepping
 
 !#######################################################################
 !MP6
 subroutine update_verlet_position(bergs,berg)
-type(icebergs), intent(in), pointer :: bergs 
-type(iceberg), intent(in), pointer :: berg 
+type(icebergs), intent(in), pointer :: bergs
+type(iceberg), intent(in), pointer :: berg
 type(icebergs_gridded), pointer :: grd
 !Local variable
 real :: lonn, latn
@@ -4487,111 +4487,111 @@ subroutine update_verlet_position(bergs,berg)
 integer :: stderrunit
 
   ! Get the stderr unit number
-    stderrunit = stderr()
+  stderrunit = stderr()
 
   ! For convenience
-    grd=>bergs%grd
+  grd=>bergs%grd
   ! Common constants
   dt=bergs%dt
   dt_2=0.5*dt
 
 
-      on_tangential_plane=.false.
-      if ((berg%lat>89.) .and. (grd%grid_is_latlon)) on_tangential_plane=.true.
-
-        lon1=berg%lon; lat1=berg%lat
-        if (on_tangential_plane) call rotpos_to_tang(lon1,lat1,x1,y1,berg%iceberg_num)
-        !dxdl1=r180_pi/(Rearth*cos(lat1*pi_180))
-        !dydl=r180_pi/Rearth
-        call  convert_from_meters_to_grid(lat1,grd%grid_is_latlon ,dxdl1,dydl)
-        uvel1=berg%uvel; vvel1=berg%vvel
-
-        ! Loading past acceleartions - Alon
-        axn=berg%axn; ayn=berg%ayn !Alon
-        bxn=berg%bxn; byn=berg%byn !Alon 
-  
-        ! Velocities used to update the position
-        uvel2=uvel1+(dt_2*axn)+(dt_2*bxn)                    !Alon
-        vvel2=vvel1+(dt_2*ayn)+(dt_2*byn)                    !Alon
-
-        !dx=(dt*(uvel1+(dt_2*axn)+(dt_2*bxn)))
-
-        if (on_tangential_plane) call rotvec_to_tang(lon1,uvel2,vvel2,xdot2,ydot2)
-        u2=uvel2*dxdl1; v2=vvel2*dydl
-  
-        ! Solving for new position
-        if (on_tangential_plane) then
-          xn=x1+(dt*xdot2) ; yn=y1+(dt*ydot2)             !Alon
-          call rotpos_from_tang(xn,yn,lonn,latn)
-        else
-          lonn=lon1+(dt*u2) ; latn=lat1+(dt*v2)  !Alon
-        endif
-  
-        ! Turn the velocities into u_star, v_star.(uvel3 is v_star) - Alon (not sure how this works with tangent plane)
-        uvel3=uvel1+(dt_2*axn)                  !Alon
-        vvel3=vvel1+(dt_2*ayn)                  !Alon
-
-        ! Adjusting mass...
-        !MP3
-        i=berg%ine;  j=berg%jne;  xi = berg%xi;  yj = berg%yj
-        call adjust_index_and_ground(grd, lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)  !Alon:"unclear which velocity to use here?"
-
-        !if (bounced) then
-        !  print *, 'you have been bounce: big time!',mpp_pe(),berg%iceberg_num,lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag 
-        !  berg%axn=0.0  ;  berg%ayn=0.0
-        !  berg%bxn=0.0  ;  berg%byn=0.0
-        !  berg%uvel=0.0 ;  berg%vvel=0.0
-        !endif
+  on_tangential_plane=.false.
+  if ((berg%lat>89.) .and. (grd%grid_is_latlon)) on_tangential_plane=.true.
+
+  lon1=berg%lon; lat1=berg%lat
+  if (on_tangential_plane) call rotpos_to_tang(lon1,lat1,x1,y1,berg%iceberg_num)
+  !dxdl1=r180_pi/(Rearth*cos(lat1*pi_180))
+  !dydl=r180_pi/Rearth
+  call  convert_from_meters_to_grid(lat1,grd%grid_is_latlon ,dxdl1,dydl)
+  uvel1=berg%uvel; vvel1=berg%vvel
+
+  ! Loading past acceleartions - Alon
+  axn=berg%axn; ayn=berg%ayn !Alon
+  bxn=berg%bxn; byn=berg%byn !Alon
+
+  ! Velocities used to update the position
+  uvel2=uvel1+(dt_2*axn)+(dt_2*bxn)                    !Alon
+  vvel2=vvel1+(dt_2*ayn)+(dt_2*byn)                    !Alon
+
+  !dx=(dt*(uvel1+(dt_2*axn)+(dt_2*bxn)))
+
+  if (on_tangential_plane) call rotvec_to_tang(lon1,uvel2,vvel2,xdot2,ydot2)
+  u2=uvel2*dxdl1; v2=vvel2*dydl
+
+  ! Solving for new position
+  if (on_tangential_plane) then
+    xn=x1+(dt*xdot2) ; yn=y1+(dt*ydot2)             !Alon
+    call rotpos_from_tang(xn,yn,lonn,latn)
+  else
+    lonn=lon1+(dt*u2) ; latn=lat1+(dt*v2)  !Alon
+  endif
+
+  ! Turn the velocities into u_star, v_star.(uvel3 is v_star) - Alon (not sure how this works with tangent plane)
+  uvel3=uvel1+(dt_2*axn)                  !Alon
+  vvel3=vvel1+(dt_2*ayn)                  !Alon
 
-        !Updating positions and index
-        berg%lon=lonn      ;  berg%lat=latn
-        berg%ine=i    ;  berg%jne=j
-        berg%xi=xi    ;  berg%yj=yj
+  ! Adjusting mass...
+  !MP3
+  i=berg%ine;  j=berg%jne;  xi = berg%xi;  yj = berg%yj
+  call adjust_index_and_ground(grd, lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)  !Alon:"unclear which velocity to use here?"
+
+  !if (bounced) then
+  !  print *, 'you have been bounce: big time!',mpp_pe(),berg%iceberg_num,lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag
+  !  berg%axn=0.0  ;  berg%ayn=0.0
+  !  berg%bxn=0.0  ;  berg%byn=0.0
+  !  berg%uvel=0.0 ;  berg%vvel=0.0
+  !endif
+
+  !Updating positions and index
+  berg%lon=lonn      ;  berg%lat=latn
+  berg%ine=i    ;  berg%jne=j
+  berg%xi=xi    ;  berg%yj=yj
 
 end subroutine update_verlet_position
 
 !#######################################################################
 
-  subroutine rotpos_from_tang(x, y, lon, lat)
+subroutine rotpos_from_tang(x, y, lon, lat)
   ! Arguments
   real, intent(in) :: x, y
   real, intent(out) :: lon, lat
   ! Local variables
   real :: r
 
-    r=sqrt(x**2+y**2)
-    lat=90.-(r180_pi*r/Rearth)
-    lon=r180_pi*acos(x/r)*sign(1.,y)
+  r=sqrt(x**2+y**2)
+  lat=90.-(r180_pi*r/Rearth)
+  lon=r180_pi*acos(x/r)*sign(1.,y)
 
-  end subroutine rotpos_from_tang
+end subroutine rotpos_from_tang
 
-  subroutine rotvec_to_tang(lon, uvel, vvel, xdot, ydot)
+subroutine rotvec_to_tang(lon, uvel, vvel, xdot, ydot)
   ! Arguments
   real, intent(in) :: lon, uvel, vvel
   real, intent(out) :: xdot, ydot
   ! Local variables
   real :: clon,slon
 
-    clon=cos(lon*pi_180)
-    slon=sin(lon*pi_180)
-    xdot=-slon*uvel-clon*vvel
-    ydot=clon*uvel-slon*vvel
+  clon=cos(lon*pi_180)
+  slon=sin(lon*pi_180)
+  xdot=-slon*uvel-clon*vvel
+  ydot=clon*uvel-slon*vvel
 
-  end subroutine rotvec_to_tang
+end subroutine rotvec_to_tang
 
-  subroutine rotvec_from_tang(lon, xdot, ydot, uvel, vvel)
+subroutine rotvec_from_tang(lon, xdot, ydot, uvel, vvel)
   ! Arguments
   real, intent(in) :: lon, xdot, ydot
   real, intent(out) :: uvel, vvel
   ! Local variables
   real :: clon,slon
 
-    clon=cos(lon*pi_180)
-    slon=sin(lon*pi_180)
-    uvel=-slon*xdot+clon*ydot
-    vvel=-clon*xdot-slon*ydot
+  clon=cos(lon*pi_180)
+  slon=sin(lon*pi_180)
+  uvel=-slon*xdot+clon*ydot
+  vvel=-clon*xdot-slon*ydot
 
-  end subroutine rotvec_from_tang
+end subroutine rotvec_from_tang
 
 ! ##############################################################################
 
@@ -4611,7 +4611,7 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
 logical :: point_in_cell_using_xi_yj
 
   ! Get the stderr unit number
-    stderrunit = stderr()
+  stderrunit = stderr()
 
   bounced=.false.
   error=.false.
@@ -4783,9 +4783,9 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
     if (debug) then
       write(stderrunit,*) 'diamonds, adjust: lon0, lat0=',lon0,lat0
       write(stderrunit,*) 'diamonds, adjust: xi0, yj0=',xi0,yj0
-      write(stderrunit,*) 'diamonds, adjust: i0,j0=',i0,j0 
+      write(stderrunit,*) 'diamonds, adjust: i0,j0=',i0,j0
       write(stderrunit,*) 'diamonds, adjust: lon, lat=',lon,lat
-      write(stderrunit,*) 'diamonds, adjust: xi,yj=',xi,yj 
+      write(stderrunit,*) 'diamonds, adjust: xi,yj=',xi,yj
       write(stderrunit,*) 'diamonds, adjust: i,j=',i,j
       write(stderrunit,*) 'diamonds, adjust: inm,jnm=',inm,jnm
       write(stderrunit,*) 'diamonds, adjust: icount=',icount
@@ -4852,24 +4852,24 @@ subroutine rotpos_to_tang(lon, lat, x, y, iceberg_num_in)
   if (present(iceberg_num_in)) then
         iceberg_num=iceberg_num_in
   endif
-        
+
   if (lat>90.) then
       write(stderrunit,*) 'diamonds, rotpos_to_tang: lat>90 already!',lat, lon, iceberg_num
       call error_mesg('diamonds, rotpos_to_tang','Something went very wrong!',FATAL)
-    endif
-    if (lat==90.) then
-      write(stderrunit,*) 'diamonds, rotpos_to_tang: lat==90 already!',lat, lon
-      call error_mesg('diamonds, rotpos_to_tang','Something went wrong!',FATAL)
-    endif
+  endif
+  if (lat==90.) then
+    write(stderrunit,*) 'diamonds, rotpos_to_tang: lat==90 already!',lat, lon
+    call error_mesg('diamonds, rotpos_to_tang','Something went wrong!',FATAL)
+  endif
 
-    colat=90.-lat
-    r=Rearth*(colat*pi_180)
-    clon=cos(lon*pi_180)
-    slon=sin(lon*pi_180)
-    x=r*clon
-    y=r*slon
+  colat=90.-lat
+  r=Rearth*(colat*pi_180)
+  clon=cos(lon*pi_180)
+  slon=sin(lon*pi_180)
+  x=r*clon
+  y=r*slon
 
-  end subroutine rotpos_to_tang
+end subroutine rotpos_to_tang
 
 ! ##############################################################################
 
@@ -4877,17 +4877,17 @@ subroutine icebergs_stock_pe(bergs, index, value)
 ! Modules
 use stock_constants_mod, only : ISTOCK_WATER, ISTOCK_HEAT
 ! Arguments
-type(icebergs), pointer :: bergs
+type(icebergs), pointer :: bergs !< Container for all types and memory
 integer, intent(in) :: index
 real, intent(out) :: value
 ! Local variables
 type(icebergs_gridded), pointer :: grd
 real :: berg_mass, stored_mass
 
-! For convenience
-grd=>bergs%grd
+  ! For convenience
+  grd=>bergs%grd
 
-select case (index)
+  select case (index)
 
   case (ISTOCK_WATER)
     berg_mass=sum_mass(bergs)
@@ -4902,7 +4902,7 @@ subroutine icebergs_stock_pe(bergs, index, value)
   case default
     value = 0.0
 
-end select
+  end select
 
 end subroutine icebergs_stock_pe
 
@@ -4910,7 +4910,7 @@ end subroutine icebergs_stock_pe
 
 subroutine icebergs_save_restart(bergs)
 ! Arguments
-type(icebergs), pointer :: bergs
+type(icebergs), pointer :: bergs !< Container for all types and memory
 ! Local variables
 
   if (.not.associated(bergs)) return
@@ -4926,7 +4926,7 @@ end subroutine icebergs_save_restart
 
 subroutine icebergs_end(bergs)
 ! Arguments
-type(icebergs), pointer :: bergs
+type(icebergs), pointer :: bergs !< Container for all types and memory
 ! Local variables
 type(iceberg), pointer :: this, next
 
@@ -5056,5 +5056,4 @@ end subroutine invert_tau_for_du
 
 ! ##############################################################################
 
-
 end module
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 3477dd0..1b71b9a 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -1,5 +1,8 @@
+!> Provides utilites for managing bergs in linked lists, and bonds between bergs
 module ice_bergs_framework
 
+! This file is part of NOAA-GFDL/icebergs. See LICENSE.md for the license.
+
 use constants_mod, only: radius, pi, omega, HLF
 
 use mpp_domains_mod, only: domain2D
@@ -15,33 +18,33 @@ module ice_bergs_framework
 
 implicit none ; private
 
-integer :: buffer_width=27 !Changed from 20 to 28 by Alon 
+integer :: buffer_width=27 !Changed from 20 to 28 by Alon
 integer :: buffer_width_traj=31  !Changed from 23 by Alon
-!integer, parameter :: buffer_width=26 !Changed from 20 to 26 by Alon 
+!integer, parameter :: buffer_width=26 !Changed from 20 to 26 by Alon
 !integer, parameter :: buffer_width_traj=29  !Changed from 23 by Alon
 integer, parameter :: nclasses=10 ! Number of ice bergs classes
 
 !Local Vars
 ! Global data (minimal for debugging)
-logical :: folded_north_on_pe = .false.
-logical :: verbose=.false. ! Be verbose to stderr
-logical :: budget=.true. ! Calculate budgets
-logical :: debug=.false. ! Turn on debugging
-logical :: really_debug=.false. ! Turn on debugging
-logical :: parallel_reprod=.true. ! Reproduce across different PE decompositions
-logical :: use_slow_find=.true. ! Use really slow (but robust) find_cell for reading restarts
-logical :: ignore_ij_restart=.false. ! Read i,j location from restart if available (needed to use restarts on different grids)
-logical :: generate_test_icebergs=.false. ! Create icebergs in absence of a restart file
-logical :: use_roundoff_fix=.true. ! Use a "fix" for the round-off discrepancy between is_point_in_cell() and pos_within_cell()
-logical :: old_bug_rotated_weights=.false. ! Skip the rotation of off-center weights for rotated halo updates
-logical :: make_calving_reproduce=.false. ! Make the calving.res.nc file reproduce across pe count changes.
-logical :: old_bug_bilin=.true. ! If true, uses the inverted bilin function (use False to get correct answer)
-character(len=10) :: restart_input_dir = 'INPUT/'
-integer, parameter :: delta_buf=25 ! Size by which to increment buffers
-real, parameter :: pi_180=pi/180. ! Converts degrees to radians
-logical :: fix_restart_dates=.true. ! After a restart, check that bergs were created before the current model date
-logical :: do_unit_tests=.false. ! Conduct some unit tests
-logical :: force_all_pes_traj=.false. ! Force all pes write trajectory files regardless of io_layout
+logical :: folded_north_on_pe = .false. !< If true, indicates the presence of the tri-polar grid
+logical :: verbose=.false. !< Be verbose to stderr
+logical :: budget=.true. !< Calculate budgets
+logical :: debug=.false. !< Turn on debugging
+logical :: really_debug=.false. !< Turn on debugging
+logical :: parallel_reprod=.true. !< Reproduce across different PE decompositions
+logical :: use_slow_find=.true. !< Use really slow (but robust) find_cell for reading restarts
+logical :: ignore_ij_restart=.false. !< Read i,j location from restart if available (needed to use restarts on different grids)
+logical :: generate_test_icebergs=.false. !< Create icebergs in absence of a restart file
+logical :: use_roundoff_fix=.true. !< Use a "fix" for the round-off discrepancy between is_point_in_cell() and pos_within_cell()
+logical :: old_bug_rotated_weights=.false. !< Skip the rotation of off-center weights for rotated halo updates
+logical :: make_calving_reproduce=.false. !< Make the calving.res.nc file reproduce across pe count changes.
+logical :: old_bug_bilin=.true. !< If true, uses the inverted bilinear function (use False to get correct answer)
+character(len=10) :: restart_input_dir = 'INPUT/' !< Directory to look for restart files
+integer, parameter :: delta_buf=25 !< Size by which to increment buffers
+real, parameter :: pi_180=pi/180. !< Converts degrees to radians
+logical :: fix_restart_dates=.true. !< After a restart, check that bergs were created before the current model date
+logical :: do_unit_tests=.false. !< Conduct some unit tests
+logical :: force_all_pes_traj=.false. !< Force all pes write trajectory files regardless of io_layout
 
 !Public params !Niki: write a subroutine to expose these
 public nclasses,buffer_width,buffer_width_traj
@@ -50,7 +53,7 @@ module ice_bergs_framework
 public orig_read, force_all_pes_traj
 
 !Public types
-public icebergs_gridded, xyt, iceberg, icebergs, buffer, bond 
+public icebergs_gridded, xyt, iceberg, icebergs, buffer, bond
 
 !Public subs
 public ice_bergs_framework_init
@@ -58,7 +61,7 @@ module ice_bergs_framework
 public update_halo_icebergs
 public pack_berg_into_buffer2, unpack_berg_from_buffer2
 public pack_traj_into_buffer2, unpack_traj_from_buffer2
-public increase_ibuffer 
+public increase_ibuffer
 public add_new_berg_to_list, count_out_of_order, check_for_duplicates
 public insert_berg_into_list, create_iceberg, delete_iceberg_from_list, destroy_iceberg
 public print_fld,print_berg, print_bergs,record_posn, push_posn, append_posn, check_position
@@ -76,76 +79,91 @@ module ice_bergs_framework
 public test_check_for_duplicate_ids_in_list
 public check_for_duplicates_in_parallel
 
+!> Container for gridded fields
 type :: icebergs_gridded
-  type(domain2D), pointer :: domain ! MPP domain
-  integer :: halo ! Nominal halo width
-  integer :: isc, iec, jsc, jec ! Indices of computational domain
-  integer :: isd, ied, jsd, jed ! Indices of data domain
-  integer :: isg, ieg, jsg, jeg ! Indices of global domain
-  integer :: my_pe, pe_N, pe_S, pe_E, pe_W ! MPI PE idenLx ! Length of domain, for periodic boundary condition (Ly to be adde later if needed)
-  logical :: grid_is_latlon !Flag to say whether the coordinate is in lat lon degrees, or meters
-  logical :: grid_is_regular !Flag to say whether point in cell can be found assuming regular cartesian grid
-  real :: Lx !Length of the domain in x direction
-  real, dimension(:,:), pointer :: lon=>null() ! Longitude of cell corners
-  real, dimension(:,:), pointer :: lat=>null() ! Latitude of cell corners
-  real, dimension(:,:), pointer :: lonc=>null() ! Longitude of cell centers
-  real, dimension(:,:), pointer :: latc=>null() ! Latitude of cell centers
-  real, dimension(:,:), pointer :: dx=>null() ! Length of cell edge (m)
-  real, dimension(:,:), pointer :: dy=>null() ! Length of cell edge (m)
-  real, dimension(:,:), pointer :: area=>null() ! Area of cell (m^2)
-  real, dimension(:,:), pointer :: msk=>null() ! Ocean-land mask (1=ocean)
-  real, dimension(:,:), pointer :: cos=>null() ! Cosine from rotation matrix to lat-lon coords
-  real, dimension(:,:), pointer :: sin=>null() ! Sine from rotation matrix to lat-lon coords
-  real, dimension(:,:), pointer :: ocean_depth=>NULL() ! Depth of ocean (m)
-  real, dimension(:,:), pointer :: uo=>null() ! Ocean zonal flow (m/s)
-  real, dimension(:,:), pointer :: vo=>null() ! Ocean meridional flow (m/s)
-  real, dimension(:,:), pointer :: ui=>null() ! Ice zonal flow (m/s)
-  real, dimension(:,:), pointer :: vi=>null() ! Ice meridional flow (m/s)
-  real, dimension(:,:), pointer :: ua=>null() ! Atmosphere zonal flow (m/s)
-  real, dimension(:,:), pointer :: va=>null() ! Atmosphere meridional flow (m/s)
-  real, dimension(:,:), pointer :: ssh=>null() ! Sea surface height (m)
-  real, dimension(:,:), pointer :: sst=>null() ! Sea surface temperature (oC)
-  real, dimension(:,:), pointer :: sss=>null() ! Sea surface salinity (psu)
-  real, dimension(:,:), pointer :: cn=>null() ! Sea-ice concentration (0 to 1)
-  real, dimension(:,:), pointer :: hi=>null() ! Sea-ice thickness (m)
-  real, dimension(:,:), pointer :: calving=>null() ! Calving mass rate [frozen runoff] (kg/s) (into stored ice)
-  real, dimension(:,:), pointer :: calving_hflx=>null() ! Calving heat flux [heat content of calving] (W/m2) (into stored ice)
-  real, dimension(:,:), pointer :: floating_melt=>null() ! Net melting rate to icebergs + bits (kg/s/m^2)
-  real, dimension(:,:), pointer :: berg_melt=>null() ! Melting+erosion rate of icebergs (kg/s/m^2)
-  real, dimension(:,:), pointer :: melt_buoy=>null() ! Buoyancy componenet of melting rate (kg/s/m^2)
-  real, dimension(:,:), pointer :: melt_eros=>null() ! Erosion component of melting rate (kg/s/m^2)
-  real, dimension(:,:), pointer :: melt_conv=>null() ! Convective component of melting rate (kg/s/m^2)
-  real, dimension(:,:), pointer :: bergy_src=>null() ! Mass flux from berg erosion into bergy bits (kg/s/m^2)
-  real, dimension(:,:), pointer :: bergy_melt=>null() ! Melting rate of bergy bits (kg/s/m^2)
-  real, dimension(:,:), pointer :: bergy_mass=>null() ! Mass distribution of bergy bits (kg/s/m^2)
-  real, dimension(:,:), pointer :: spread_mass=>null() ! Mass of icebergs after spreading (kg/m^2)
-  real, dimension(:,:), pointer :: spread_mass_old=>null() ! Mass of icebergs after spreading old (kg/m^2)
-  real, dimension(:,:), pointer :: spread_area=>null() ! Area of icebergs after spreading (m^2/m^2)
-  real, dimension(:,:), pointer :: u_iceberg=>null() ! Average iceberg velocity in grid cell (mass weighted - but not spread mass weighted)
-  real, dimension(:,:), pointer :: v_iceberg=>null() ! Average iceberg velocity in grid cell (mass weighted - but not spread mass weighted)
-  real, dimension(:,:), pointer :: spread_uvel=>null() ! Average iceberg velocity in grid cell (spread area weighted)
-  real, dimension(:,:), pointer :: spread_vvel=>null() ! Average iceberg velocity in grid cell (spread area weighted)
-  real, dimension(:,:), pointer :: ustar_iceberg=>null() ! Frictional velocity below icebergs to be passed to ocean
-  real, dimension(:,:), pointer :: virtual_area=>null() ! Virtual surface coverage by icebergs (m^2)
-  real, dimension(:,:), pointer :: mass=>null() ! Mass distribution (kg/m^2)
-  real, dimension(:,:,:), pointer :: mass_on_ocean=>null() ! Mass distribution partitioned by neighbor (kg)  
-  real, dimension(:,:,:), pointer :: area_on_ocean=>null() ! Area distribution partitioned by neighbor (m^2)  
-  real, dimension(:,:,:), pointer :: Uvel_on_ocean=>null() ! zonal velocity distribution partitioned by neighbor (m^2* m/s)  
-  real, dimension(:,:,:), pointer :: Vvel_on_ocean=>null() ! meridional momentum distribution partitioned by neighbor (m^2 m/s)  
-  real, dimension(:,:), pointer :: tmp=>null() ! Temporary work space
-  real, dimension(:,:), pointer :: tmpc=>null() ! Temporary work space
-  real, dimension(:,:,:), pointer :: stored_ice=>null() ! Accumulated ice mass flux at calving locations (kg)
-  real, dimension(:,:), pointer :: rmean_calving=>null() ! Running mean for ice calving
-  real, dimension(:,:), pointer :: rmean_calving_hflx=>null() ! Running mean for ice calving
-  real, dimension(:,:), pointer :: stored_heat=>null() ! Heat content of stored ice (J)
-  real, dimension(:,:,:), pointer :: real_calving=>null() ! Calving rate into iceberg class at calving locations (kg/s)
-  real, dimension(:,:), pointer :: iceberg_heat_content=>null() ! Distributed heat content of bergs (J/m^2)
-  real, dimension(:,:), pointer :: parity_x=>null() ! X component of vector point from i,j to i+1,j+1 (for detecting tri-polar fold)
-  real, dimension(:,:), pointer :: parity_y=>null() ! Y component of vector point from i,j to i+1,j+1 (for detecting tri-polar fold)
-  integer, dimension(:,:), pointer :: iceberg_counter_grd=>null() ! Counts icebergs created for naming purposes
-  logical :: rmean_calving_initialized = .false. ! True if rmean_calving(:,:) has been filled with meaningful data
-  logical :: rmean_calving_hflx_initialized = .false. ! True if rmean_calving_hflx(:,:) has been filled with meaningful data
-  ! Diagnostics handles
+  type(domain2D), pointer :: domain !< MPP parallel domain
+  integer :: halo !< Nominal halo width
+  integer :: isc !< Start i-index of computational domain
+  integer :: iec !< End i-index of computational domain
+  integer :: jsc !< Start j-index of computational domain
+  integer :: jec !< End j-index of computational domain
+  integer :: isd !< Start i-index of data domain
+  integer :: ied !< End i-index of data domain
+  integer :: jsd !< Start j-index of data domain
+  integer :: jed !< End j-index of data domain
+  integer :: isg !< Start i-index of global domain
+  integer :: ieg !< End i-index of global domain
+  integer :: jsg !< Start j-index of global domain
+  integer :: jeg !< End j-index of global domain
+  integer :: my_pe !< MPI PE index
+  integer :: pe_N !< MPI PE index of PE to the north
+  integer :: pe_S !< MPI PE index of PE to the south
+  integer :: pe_E !< MPI PE index of PE to the east
+  integer :: pe_W !< MPI PE index of PE to the west
+  logical :: grid_is_latlon !< Flag to say whether the coordinate is in lat-lon degrees, or meters
+  logical :: grid_is_regular !< Flag to say whether point in cell can be found assuming regular Cartesian grid
+  real :: Lx !< Length of the domain in x direction
+  real, dimension(:,:), pointer :: lon=>null() !< Longitude of cell corners (degree E)
+  real, dimension(:,:), pointer :: lat=>null() !< Latitude of cell corners (degree N)
+  real, dimension(:,:), pointer :: lonc=>null() !< Longitude of cell centers (degree E)
+  real, dimension(:,:), pointer :: latc=>null() !< Latitude of cell centers (degree N)
+  real, dimension(:,:), pointer :: dx=>null() !< Length of cell edge (m)
+  real, dimension(:,:), pointer :: dy=>null() !< Length of cell edge (m)
+  real, dimension(:,:), pointer :: area=>null() !< Area of cell (m^2)
+  real, dimension(:,:), pointer :: msk=>null() !< Ocean-land mask (1=ocean)
+  real, dimension(:,:), pointer :: cos=>null() !< Cosine from rotation matrix to lat-lon coords
+  real, dimension(:,:), pointer :: sin=>null() !< Sine from rotation matrix to lat-lon coords
+  real, dimension(:,:), pointer :: ocean_depth=>NULL() !< Depth of ocean (m)
+  real, dimension(:,:), pointer :: uo=>null() !< Ocean zonal flow (m/s)
+  real, dimension(:,:), pointer :: vo=>null() !< Ocean meridional flow (m/s)
+  real, dimension(:,:), pointer :: ui=>null() !< Ice zonal flow (m/s)
+  real, dimension(:,:), pointer :: vi=>null() !< Ice meridional flow (m/s)
+  real, dimension(:,:), pointer :: ua=>null() !< Atmosphere zonal flow (m/s)
+  real, dimension(:,:), pointer :: va=>null() !< Atmosphere meridional flow (m/s)
+  real, dimension(:,:), pointer :: ssh=>null() !< Sea surface height (m)
+  real, dimension(:,:), pointer :: sst=>null() !< Sea surface temperature (oC)
+  real, dimension(:,:), pointer :: sss=>null() !< Sea surface salinity (psu)
+  real, dimension(:,:), pointer :: cn=>null() !< Sea-ice concentration (0 to 1)
+  real, dimension(:,:), pointer :: hi=>null() !< Sea-ice thickness (m)
+  real, dimension(:,:), pointer :: calving=>null() !< Calving mass rate [frozen runoff] (kg/s) (into stored ice)
+  real, dimension(:,:), pointer :: calving_hflx=>null() !< Calving heat flux [heat content of calving] (W/m2) (into stored ice)
+  real, dimension(:,:), pointer :: floating_melt=>null() !< Net melting rate to icebergs + bits (kg/s/m^2)
+  real, dimension(:,:), pointer :: berg_melt=>null() !< Melting+erosion rate of icebergs (kg/s/m^2)
+  real, dimension(:,:), pointer :: melt_buoy=>null() !< Buoyancy component of melting rate (kg/s/m^2)
+  real, dimension(:,:), pointer :: melt_eros=>null() !< Erosion component of melting rate (kg/s/m^2)
+  real, dimension(:,:), pointer :: melt_conv=>null() !< Convective component of melting rate (kg/s/m^2)
+  real, dimension(:,:), pointer :: bergy_src=>null() !< Mass flux from berg erosion into bergy bits (kg/s/m^2)
+  real, dimension(:,:), pointer :: bergy_melt=>null() !< Melting rate of bergy bits (kg/s/m^2)
+  real, dimension(:,:), pointer :: bergy_mass=>null() !< Mass distribution of bergy bits (kg/s/m^2)
+  real, dimension(:,:), pointer :: spread_mass=>null() !< Mass of icebergs after spreading (kg/m^2)
+  real, dimension(:,:), pointer :: spread_mass_old=>null() !< Mass of icebergs after spreading old (kg/m^2)
+  real, dimension(:,:), pointer :: spread_area=>null() !< Area of icebergs after spreading (m^2/m^2)
+  real, dimension(:,:), pointer :: u_iceberg=>null() !< Average iceberg velocity in grid cell (mass weighted - but not spread mass weighted)
+  real, dimension(:,:), pointer :: v_iceberg=>null() !< Average iceberg velocity in grid cell (mass weighted - but not spread mass weighted)
+  real, dimension(:,:), pointer :: spread_uvel=>null() !< Average iceberg velocity in grid cell (spread area weighted)
+  real, dimension(:,:), pointer :: spread_vvel=>null() !< Average iceberg velocity in grid cell (spread area weighted)
+  real, dimension(:,:), pointer :: ustar_iceberg=>null() !< Frictional velocity below icebergs to be passed to ocean
+  real, dimension(:,:), pointer :: virtual_area=>null() !< Virtual surface coverage by icebergs (m^2)
+  real, dimension(:,:), pointer :: mass=>null() !< Mass distribution (kg/m^2)
+  real, dimension(:,:,:), pointer :: mass_on_ocean=>null() !< Mass distribution partitioned by neighbor (kg)
+  real, dimension(:,:,:), pointer :: area_on_ocean=>null() !< Area distribution partitioned by neighbor (m^2)
+  real, dimension(:,:,:), pointer :: Uvel_on_ocean=>null() !< zonal velocity distribution partitioned by neighbor (m^2* m/s)
+  real, dimension(:,:,:), pointer :: Vvel_on_ocean=>null() !< meridional momentum distribution partitioned by neighbor (m^2 m/s)
+  real, dimension(:,:), pointer :: tmp=>null() !< Temporary work space
+  real, dimension(:,:), pointer :: tmpc=>null() !< Temporary work space
+  real, dimension(:,:,:), pointer :: stored_ice=>null() !< Accumulated ice mass flux at calving locations (kg)
+  real, dimension(:,:), pointer :: rmean_calving=>null() !< Running mean for ice calving
+  real, dimension(:,:), pointer :: rmean_calving_hflx=>null() !< Running mean for ice calving
+  real, dimension(:,:), pointer :: stored_heat=>null() !< Heat content of stored ice (J)
+  real, dimension(:,:,:), pointer :: real_calving=>null() !< Calving rate into iceberg class at calving locations (kg/s)
+  real, dimension(:,:), pointer :: iceberg_heat_content=>null() !< Distributed heat content of bergs (J/m^2)
+  real, dimension(:,:), pointer :: parity_x=>null() !< X component of vector point from i,j to i+1,j+1 (for detecting tri-polar fold)
+  real, dimension(:,:), pointer :: parity_y=>null() !< Y component of vector point from i,j to i+1,j+1 (for detecting tri-polar fold)
+  integer, dimension(:,:), pointer :: iceberg_counter_grd=>null() !< Counts icebergs created for naming purposes
+  logical :: rmean_calving_initialized = .false. !< True if rmean_calving(:,:) has been filled with meaningful data
+  logical :: rmean_calving_hflx_initialized = .false. !< True if rmean_calving_hflx(:,:) has been filled with meaningful data
+  !>@{
+  !! Diagnostic handle
   integer :: id_uo=-1, id_vo=-1, id_calving=-1, id_stored_ice=-1, id_accum=-1, id_unused=-1, id_floating_melt=-1
   integer :: id_melt_buoy=-1, id_melt_eros=-1, id_melt_conv=-1, id_virtual_area=-1, id_real_calving=-1
   integer :: id_calving_hflx_in=-1, id_stored_heat=-1, id_melt_hflx=-1, id_heat_content=-1
@@ -158,134 +176,216 @@ module ice_bergs_framework
   integer :: id_spread_uvel=-1, id_spread_vvel=-1
   integer :: id_melt_m_per_year=-1
   integer :: id_ocean_depth=-1
+  !>@}
 
-  real :: clipping_depth=0. ! The effective depth at which to clip the weight felt by the ocean [m].
+  real :: clipping_depth=0. !< The effective depth at which to clip the weight felt by the ocean [m].
 
 end type icebergs_gridded
 
+!> A link in the trajectory record (diagnostic)
 type :: xyt
-  real :: lon, lat, day
-  real :: mass, thickness, width, length, uvel, vvel
-  real :: axn, ayn, bxn, byn, uvel_old, vvel_old, lat_old, lon_old  !Explicit and implicit accelerations !Alon 
-  real :: uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, sss, cn, hi, halo_berg, static_berg
-  real :: mass_of_bits, heat_density
-  integer :: year, iceberg_num
-  type(xyt), pointer :: next=>null()
+  real :: lon !< Longitude of berg (degree N or unit of grid coordinate)
+  real :: lat !< Latitude of berg (degree N or unit of grid coordinate)
+  real :: day !< Day of this record (days)
+  real :: mass !< Mass of berg (kg)
+  real :: thickness !< Thickness of berg (m)
+  real :: width !< Width of berg (m)
+  real :: length !< Length of berg (m)
+  real :: uvel !< Zonal velocity of berg (m/s)
+  real :: vvel !< Meridional velocity of berg (m/s)
+  real :: axn
+  real :: ayn
+  real :: bxn
+  real :: byn
+  real :: uvel_old
+  real :: vvel_old
+  real :: lat_old
+  real :: lon_old
+  real :: uo !< Zonal velocity of ocean (m/s)
+  real :: vo !< Meridional velocity of ocean (m/s)
+  real :: ui !< Zonal velocity of ice (m/s)
+  real :: vi !< Meridional velocity of ice (m/s)
+  real :: ua !< Zonal velocity of atmosphere (m/s)
+  real :: va !< Meridional velocity of atmosphere (m/s)
+  real :: ssh_x !< Zonal gradient of sea-surface height (nondim)
+  real :: ssh_y !< Meridional gradient of sea-surface height (nondim)
+  real :: sst !< Sea-surface temperature (Celsius)
+  real :: sss !< Sea-surface salinity (1e-3)
+  real :: cn !< Sea-ice concentration (nondim)
+  real :: hi !< Sea-ice thickness (m)
+  real :: halo_berg
+  real :: static_berg
+  real :: mass_of_bits !< Mass of bergy bits (kg)
+  real :: heat_density !< Heat density of berg (???)
+  integer :: year !< Year of this record (years)
+  integer :: iceberg_num !< Iceberg identifier
+  type(xyt), pointer :: next=>null() !< Next link in list
 end type xyt
 
+!> An iceberg object, used as a link in a linked list
 type :: iceberg
-  type(iceberg), pointer :: prev=>null(), next=>null()
+  type(iceberg), pointer :: prev=>null() !< Previous link in list
+  type(iceberg), pointer :: next=>null() !< Next link in list
   ! State variables (specific to the iceberg, needed for restarts)
-  real :: lon, lat, uvel, vvel, mass, thickness, width, length
-  real :: axn, ayn, bxn, byn, uvel_old, vvel_old, lon_old, lat_old !Explicit and implicit accelerations !Alon 
-  real :: start_lon, start_lat, start_day, start_mass, mass_scaling
-  real :: mass_of_bits, heat_density
+  real :: lon !< Longitude of berg (degree N or unit of grid coordinate)
+  real :: lat !< Latitude of berg (degree E or unit of grid coordinate)
+  real :: uvel !< Zonal velocity of berg (m/s)
+  real :: vvel !< Meridional velocity of berg (m/s)
+  real :: mass !< Mass of berg (kg)
+  real :: thickness !< Thickness of berg (m)
+  real :: width !< Width of berg (m)
+  real :: length !< Length of berg (m)
+  real :: axn
+  real :: ayn
+  real :: bxn
+  real :: byn
+  real :: uvel_old
+  real :: vvel_old
+  real :: lon_old
+  real :: lat_old
+  real :: start_lon !< Longitude where berg was created (degree N or unit of grid coordinate)
+  real :: start_lat !< Latitude where berg was created (degree E or unit of grid coordinate)
+  real :: start_day !< Day that berg was created (days)
+  real :: start_mass !< Mass berg had when created (kg)
+  real :: mass_scaling !< Multiplier to scale mass when interpreting berg as a cloud of bergs (nondim)
+  real :: mass_of_bits !< Mass of bergy bits following berg (kg)
+  real :: heat_density !< Heat density of berg (???)
   real :: halo_berg  ! Equal to zero for bergs on computational domain, and =1 for bergs on the halo
   real :: static_berg  ! Equal to 1 for icebergs which are static (not allowed to move). Might be extended to grounding later.
-  integer :: start_year
-  integer :: iceberg_num
-  integer :: ine, jne ! nearest index in NE direction (for convenience)
-  real :: xi, yj ! Non-dimensional coords within current cell (0..1)
+  integer :: start_year !< Year that berg was created (years)
+  integer :: iceberg_num !< Iceberg identifier
+  integer :: ine !< Nearest i-index in NE direction (for convenience)
+  integer :: jne !< Nearest j-index in NE direction (for convenience)
+  real :: xi !< Non-dimensional x-coordinate within current cell (0..1)
+  real :: yj !< Non-dimensional y-coordinate within current cell (0..1)
   ! Environment variables (as seen by the iceberg)
-  real :: uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, sss, cn, hi
-  type(xyt), pointer :: trajectory=>null()
-  type(bond), pointer :: first_bond=>null()  !First element of bond list.
+  real :: uo !< Zonal velocity of ocean (m/s)
+  real :: vo !< Meridional velocity of ocean (m/s)
+  real :: ui !< Zonal velocity of ice (m/s)
+  real :: vi !< Meridional velocity of ice (m/s)
+  real :: ua !< Zonal velocity of atmosphere (m/s)
+  real :: va !< Meridional velocity of atmosphere (m/s)
+  real :: ssh_x !< Zonal gradient of sea-surface height (nondim)
+  real :: ssh_y !< Meridional gradient of sea-surface height (nondim)
+  real :: sst !< Sea-surface temperature (Celsius)
+  real :: sss !< Sea-surface salinity (1e-3)
+  real :: cn !< Sea-ice concentration (nondim)
+  real :: hi !< Sea-ice thickness (m)
+  type(xyt), pointer :: trajectory=>null() !< Trajectory for this berg
+  type(bond), pointer :: first_bond=>null() !< First element of bond list.
 end type iceberg
 
+!> A bond object connecting two bergs, used as a link in a linked list
 type :: bond
-  type(bond), pointer :: prev_bond=>null(), next_bond=>null()
+  type(bond), pointer :: prev_bond=>null() !< Previous link in list
+  type(bond), pointer :: next_bond=>null() !< Next link in list
   type(iceberg), pointer :: other_berg=>null()
-  integer :: other_berg_num, other_berg_ine, other_berg_jne 
+  integer :: other_berg_num
+  integer :: other_berg_ine
+  integer :: other_berg_jne
 end type bond
 
+! A dynamic buffer, used for communication, that packs types into rectangular memory
 type :: buffer
-  integer :: size=0
-  real, dimension(:,:), pointer :: data
+  integer :: size=0 !< Size of buffer
+  real, dimension(:,:), pointer :: data !< Buffer memory
 end type buffer
 
+!> A wrapper for the iceberg linked list (since an array of pointers is not allowed)
 type :: linked_list
-  type(iceberg), pointer :: first=>null()
+  type(iceberg), pointer :: first=>null() !< Pointer to the beginning of a linked list of bergs
 end type linked_list
 
-type :: icebergs !; private!Niki: Ask Alistair why this is private. ice_bergs_io cannot compile if this is private!
-  type(icebergs_gridded), pointer :: grd
-  type(linked_list), dimension(:,:), allocatable :: list
-  type(xyt), pointer :: trajectories=>null()
-  real :: dt           ! Time-step between iceberg calls (should make adaptive?)
-  integer :: current_year
-  real :: current_yearday ! 1.00-365.99
-  integer :: traj_sample_hrs, traj_write_hrs
-  integer :: verbose_hrs
+!> Container for all types and memory
+type :: icebergs !; private !Niki: Ask Alistair why this is private. ice_bergs_io cannot compile if this is private!
+  type(icebergs_gridded), pointer :: grd !< Container with all gridded data
+  type(linked_list), dimension(:,:), allocatable :: list !< Linked list of icebergs
+  type(xyt), pointer :: trajectories=>null() !< A linked list for detached segments of trajectories
+  real :: dt !< Time-step between iceberg calls
+             !! \todo Should make dt adaptive?
+  integer :: current_year !< Current year (years)
+  real :: current_yearday !< Current year-day, 1.00-365.99, (days)
+  integer :: traj_sample_hrs !< Period between sampling for trajectories (hours)
+  integer :: traj_write_hrs !< Period between writing of trajectories (hours)
+  integer :: verbose_hrs !< Period between terminal status reports (hours)
   integer :: max_bonds
-  integer :: clock, clock_mom, clock_the, clock_int, clock_cal, clock_com, clock_ini, clock_ior, clock_iow, clock_dia ! ids for fms timers
+  !>@{
+  !! Handles for clocks
+  integer :: clock, clock_mom, clock_the, clock_int, clock_cal, clock_com, clock_ini, clock_ior, clock_iow, clock_dia
   integer :: clock_trw, clock_trp
-  real :: rho_bergs ! Density of icebergs [kg/m^3]
-  real :: spring_coef  ! Spring contant for iceberg interactions 
-  real :: bond_coef  ! Spring contant for iceberg bonds 
-  real :: radial_damping_coef     ! Coef for relative iceberg motion damping (radial component) -Alon
-  real :: tangental_damping_coef     ! Coef for relative iceberg motion damping (tangental component) -Alon
-  real :: LoW_ratio ! Initial ratio L/W for newly calved icebergs
-  real :: bergy_bit_erosion_fraction ! Fraction of erosion melt flux to divert to bergy bits
-  real :: sicn_shift ! Shift of sea-ice concentration in erosion flux modulation (0<sicn_shift<1)
-  real :: lat_ref=0. ! Reference latitude for f-plane (when this option is on)
-  real :: u_override=0.0 ! Overrides the u velocity of icebergs (for ocean testing)
-  real :: v_override=0.0 ! Overrides the v velocity of icebergs (for ocean testing)
-  real :: utide_icebergs= 0.      ! Tidal speeds, set to zero for now.
-  real :: ustar_icebergs_bg=0.001 ! Background u_star under icebergs. This should be linked to a value felt by the ocean boundary layer
-  real :: cdrag_icebergs =  1.5e-3 !Momentum Drag coef, taken from HJ99  (Holland and Jenkins 1999)
-  real :: initial_orientation=0. ! Iceberg orientaion relative to this angle (in degrees). Used for hexagonal mass spreading.
-  real :: Gamma_T_3EQ=0.022 ! Nondimensional heat-transfer coefficient
-  real :: melt_cutoff=-1.0 !Minimum ocean thickness for melting to occur (is not applied for values < 0)
-  logical :: const_gamma=.True. !If true uses a constant heat tranfer coefficient, from which the salt transfer is calculated
+  !>@}
+  real :: rho_bergs !< Density of icebergs [kg/m^3]
+  real :: spring_coef !< Spring constant for iceberg interactions
+  real :: bond_coef !< Spring constant for iceberg bonds
+  real :: radial_damping_coef !< Coefficient for relative iceberg motion damping (radial component) -Alon
+  real :: tangental_damping_coef !< Coefficient for relative iceberg motion damping (tangential component) -Alon
+  real :: LoW_ratio !< Initial ratio L/W for newly calved icebergs
+  real :: bergy_bit_erosion_fraction !< Fraction of erosion melt flux to divert to bergy bits
+  real :: sicn_shift !< Shift of sea-ice concentration in erosion flux modulation (0<sicn_shift<1)
+  real :: lat_ref=0. !< Reference latitude for f-plane (when this option is on)
+  real :: u_override=0.0 !< Overrides the u velocity of icebergs (for ocean testing)
+  real :: v_override=0.0 !< Overrides the v velocity of icebergs (for ocean testing)
+  real :: utide_icebergs= 0. !< Tidal speeds, set to zero for now.
+  real :: ustar_icebergs_bg=0.001 !< Background u_star under icebergs. This should be linked to a value felt by the ocean boundary layer
+  real :: cdrag_icebergs =  1.5e-3 !< Momentum Drag coef, taken from HJ99 (Holland and Jenkins 1999)
+  real :: initial_orientation=0. !< Iceberg orientation relative to this angle (in degrees). Used for hexagonal mass spreading.
+  real :: Gamma_T_3EQ=0.022 !< Non-dimensional heat-transfer coefficient
+  real :: melt_cutoff=-1.0 !< Minimum ocean thickness for melting to occur (is not applied for values < 0)
+  logical :: const_gamma=.True. !< If true uses a constant heat transfer coefficient, from which the salt transfer is calculated
   real, dimension(:), pointer :: initial_mass, distribution, mass_scaling
   real, dimension(:), pointer :: initial_thickness, initial_width, initial_length
-  logical :: restarted=.false. ! Indicate whether we read state from a restart or not
-  logical :: use_operator_splitting=.true. ! Use first order operator splitting for thermodynamics
-  logical :: add_weight_to_ocean=.true. ! Add weight of bergs to ocean
-  logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
-  logical :: time_average_weight=.false. ! Time average the weight on the ocean
-  logical :: Runge_not_Verlet=.True.  !True=Runge Kuttai, False=Verlet.  - Added by Alon 
-  logical :: use_mixed_melting=.False.  !If true, then the melt is determined partly using 3 eq model partly using iceberg parametrizations (according to iceberg bond number)
-  logical :: apply_thickness_cutoff_to_gridded_melt=.False.  !Prevents melt for ocean thickness below melt_cuttoff (applied to gridded melt fields)
-  logical :: apply_thickness_cutoff_to_bergs_melt=.False.  !Prevents melt for ocean thickness below melt_cuttoff (applied to bergs)
-  logical :: use_updated_rolling_scheme=.false. ! True to use the aspect ratio based rolling scheme rather than incorrect version of WM scheme   (set tip_parameter=1000. for correct WM scheme)
-  logical :: pass_fields_to_ocean_model=.False. !Iceberg area, mass and ustar fields are prepared to pass to ocean model
-  logical :: use_mixed_layer_salinity_for_thermo=.False.  !If true, then model uses ocean salinity for 3 and 2 equation melt model.
-  logical :: find_melt_using_spread_mass=.False.  !If true, then the model calculates ice loss by looping at the spread_mass before and after.
-  logical :: Use_three_equation_model=.True.  !Uses 3 equation model for melt when ice shelf type thermodynamics are used.
-  logical :: melt_icebergs_as_ice_shelf=.False.  !Uses iceshelf type thermodynamics
-  logical :: Iceberg_melt_without_decay=.False.  !Allows icebergs meltwater fluxes to enter the ocean, without the iceberg decaying or changing shape.
-  logical :: add_iceberg_thickness_to_SSH=.False.  !Adds the iceberg contribution to SSH.   
-  logical :: override_iceberg_velocities=.False.  !Allows you to set a fixed iceberg velocity for all non-static icebergs.
-  logical :: use_f_plane=.False.  !Flag to use a f-plane for the rotation
-  logical :: rotate_icebergs_for_mass_spreading=.True.  !Flag allows icebergs to rotate for spreading their mass (in hexagonal spreading mode)
-  logical :: set_melt_rates_to_zero=.False.  !Sets all melt rates to zero, for testing purposes (thermodynamics routine is still run)
-  logical :: hexagonal_icebergs=.False. !True treats icebergs as rectangles, False as hexagonal elements (for the purpose of mass spreading)
-  logical :: allow_bergs_to_roll=.True. !Allows icebergs to roll over when rolling conditions are met
-  logical :: ignore_missing_restart_bergs=.False.  !True Allows the model to ignorm icebergs missing in the restart. 
-  logical :: Static_icebergs=.False.  !True= icebergs do no move
-  logical :: only_interactive_forces=.False.  !Icebergs only feel interactive forces, and not ocean, wind... 
-  logical :: halo_debugging=.False.  !Use for debugging halos (remove when its working) 
-  logical :: save_short_traj=.True.  !True saves only lon,lat,time,iceberg_num in iceberg_trajectory.nc 
-  logical :: ignore_traj=.False.  !If true, then model does not traj trajectory data at all 
-  logical :: iceberg_bonds_on=.False.  !True=Allow icebergs to have bonds, False=don't allow. 
-  logical :: manually_initialize_bonds=.False.  !True= Bonds are initialize manually. 
-  logical :: use_new_predictive_corrective =.False.  !Flag to use Bob's predictive corrective iceberg scheme- Added by Alon 
-  logical :: interactive_icebergs_on=.false.  !Turn on/off interactions between icebergs  - Added by Alon 
-  logical :: critical_interaction_damping_on=.true.  !Sets the damping on relative iceberg velocity to critical value - Added by Alon 
-  logical :: use_old_spreading=.true. ! If true, spreads iceberg mass as if the berg is one grid cell wide
-  logical :: read_ocean_depth_from_file=.false. ! If true, ocean depth is read from a file.
-  integer :: debug_iceberg_with_id = -1 ! If positive, monitors a berg with this id
-
-  real :: speed_limit=0. ! CFL speed limit for a berg [m/s]
-  real :: tau_calving=0. ! Time scale for smoothing out calving field (years)
-  real :: tip_parameter=0. ! parameter to override iceberg rollilng critica ratio (use zero to get parameter directly from ice and seawater densities) 
-  real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
-  type(buffer), pointer :: obuffer_n=>null(), ibuffer_n=>null()
-  type(buffer), pointer :: obuffer_s=>null(), ibuffer_s=>null()
-  type(buffer), pointer :: obuffer_e=>null(), ibuffer_e=>null()
-  type(buffer), pointer :: obuffer_w=>null(), ibuffer_w=>null()
-  type(buffer), pointer :: obuffer_io=>null(), ibuffer_io=>null()
+  logical :: restarted=.false. !< Indicate whether we read state from a restart or not
+  logical :: use_operator_splitting=.true. !< Use first order operator splitting for thermodynamics
+  logical :: add_weight_to_ocean=.true. !< Add weight of bergs to ocean
+  logical :: passive_mode=.false. !< Add weight of icebergs + bits to ocean
+  logical :: time_average_weight=.false. !< Time average the weight on the ocean
+  logical :: Runge_not_Verlet=.True. !< True=Runge-Kutta, False=Verlet.
+  logical :: use_mixed_melting=.False. !< If true, then the melt is determined partly using 3 eq model partly using iceberg parameterizations (according to iceberg bond number)
+  logical :: apply_thickness_cutoff_to_gridded_melt=.False. !< Prevents melt for ocean thickness below melt_cuttoff (applied to gridded melt fields)
+  logical :: apply_thickness_cutoff_to_bergs_melt=.False. !< Prevents melt for ocean thickness below melt_cuttoff (applied to bergs)
+  logical :: use_updated_rolling_scheme=.false. !< True to use the aspect ratio based rolling scheme rather than incorrect version of WM scheme (set tip_parameter=1000. for correct WM scheme)
+  logical :: pass_fields_to_ocean_model=.False. !< Iceberg area, mass and ustar fields are prepared to pass to ocean model
+  logical :: use_mixed_layer_salinity_for_thermo=.False. !< If true, then model uses ocean salinity for 3 and 2 equation melt model.
+  logical :: find_melt_using_spread_mass=.False. !< If true, then the model calculates ice loss by looping at the spread_mass before and after.
+  logical :: Use_three_equation_model=.True. !< Uses 3 equation model for melt when ice shelf type thermodynamics are used.
+  logical :: melt_icebergs_as_ice_shelf=.False. !< Uses iceshelf type thermodynamics
+  logical :: Iceberg_melt_without_decay=.False. !< Allows icebergs meltwater fluxes to enter the ocean, without the iceberg decaying or changing shape.
+  logical :: add_iceberg_thickness_to_SSH=.False. !< Adds the iceberg contribution to SSH.
+  logical :: override_iceberg_velocities=.False. !< Allows you to set a fixed iceberg velocity for all non-static icebergs.
+  logical :: use_f_plane=.False. !< Flag to use a f-plane for the rotation
+  logical :: rotate_icebergs_for_mass_spreading=.True. !< Flag allows icebergs to rotate for spreading their mass (in hexagonal spreading mode)
+  logical :: set_melt_rates_to_zero=.False. !< Sets all melt rates to zero, for testing purposes (thermodynamics routine is still run)
+  logical :: hexagonal_icebergs=.False. !< True treats icebergs as rectangles, False as hexagonal elements (for the purpose of mass spreading)
+  logical :: allow_bergs_to_roll=.True. !< Allows icebergs to roll over when rolling conditions are met
+  logical :: ignore_missing_restart_bergs=.False. !< True Allows the model to ignore icebergs missing in the restart.
+  logical :: Static_icebergs=.False. !< True= icebergs do no move
+  logical :: only_interactive_forces=.False. !< Icebergs only feel interactive forces, and not ocean, wind...
+  logical :: halo_debugging=.False. !< Use for debugging halos (remove when its working)
+  logical :: save_short_traj=.True. !< True saves only lon,lat,time,iceberg_num in iceberg_trajectory.nc
+  logical :: ignore_traj=.False. !< If true, then model does not write trajectory data at all
+  logical :: iceberg_bonds_on=.False. !< True=Allow icebergs to have bonds, False=don't allow.
+  logical :: manually_initialize_bonds=.False. !< True= Bonds are initialize manually.
+  logical :: use_new_predictive_corrective =.False. !< Flag to use Bob's predictive corrective iceberg scheme- Added by Alon
+  logical :: interactive_icebergs_on=.false. !< Turn on/off interactions between icebergs  - Added by Alon
+  logical :: critical_interaction_damping_on=.true. !< Sets the damping on relative iceberg velocity to critical value - Added by Alon
+  logical :: use_old_spreading=.true. !< If true, spreads iceberg mass as if the berg is one grid cell wide
+  logical :: read_ocean_depth_from_file=.false. !< If true, ocean depth is read from a file.
+  integer :: debug_iceberg_with_id = -1 !< If positive, monitors a berg with this id
+
+  real :: speed_limit=0. !< CFL speed limit for a berg [m/s]
+  real :: tau_calving=0. !< Time scale for smoothing out calving field (years)
+  real :: tip_parameter=0. !< parameter to override iceberg rolling critical ratio (use zero to get parameter directly from ice and seawater densities)
+  real :: grounding_fraction=0. !< Fraction of water column depth at which grounding occurs
+  type(buffer), pointer :: obuffer_n=>null() !< Buffer for outgoing bergs to the north
+  type(buffer), pointer :: ibuffer_n=>null() !< Buffer for incoming bergs from the north
+  type(buffer), pointer :: obuffer_s=>null() !< Buffer for outgoing bergs to the south
+  type(buffer), pointer :: ibuffer_s=>null() !< Buffer for incoming bergs from the south
+  type(buffer), pointer :: obuffer_e=>null() !< Buffer for outgoing bergs to the east
+  type(buffer), pointer :: ibuffer_e=>null() !< Buffer for incoming bergs from the east
+  type(buffer), pointer :: obuffer_w=>null() !< Buffer for outgoing bergs to the west
+  type(buffer), pointer :: ibuffer_w=>null() !< Buffer for incoming bergs from the west
+  type(buffer), pointer :: obuffer_io=>null() !< Buffer for outgoing bergs during i/o
+  type(buffer), pointer :: ibuffer_io=>null() !< Buffer for incoming bergs during i/o
   ! Budgets
   real :: net_calving_received=0., net_calving_returned=0.
   real :: net_incoming_calving=0., net_outgoing_calving=0.
@@ -316,10 +416,11 @@ module ice_bergs_framework
   integer, dimension(:), pointer :: nbergs_calved_by_class=>null()
 end type icebergs
 
-! Needs to be module global so can be public to icebergs_mod.
-! Remove when backward compatibility no longer needed
+!> Read original restarts. Needs to be module global so can be public to icebergs_mod.
+!! \todo Remove when backward compatibility no longer needed
 logical :: orig_read=.false.
 
+!> Version of file provided by CPP macro (usually set to git hash)
 #ifdef _FILE_VERSION
   character(len=128) :: version = _FILE_VERSION
 #else
@@ -328,9 +429,7 @@ module ice_bergs_framework
 
 contains
 
-
-! ##############################################################################
-
+!> Initializes parallel framework
 subroutine ice_bergs_framework_init(bergs, &
              gni, gnj, layout, io_layout, axes, dom_x_flags, dom_y_flags, &
              dt, Time, ice_lon, ice_lat, ice_wet, ice_dx, ice_dy, ice_area, &
@@ -353,17 +452,27 @@ subroutine ice_bergs_framework_init(bergs, &
 use diag_manager_mod, only: diag_axis_init
 
 ! Arguments
-type(icebergs), pointer :: bergs
-integer, intent(in) :: gni, gnj, layout(2), io_layout(2), axes(2)
-integer, intent(in) :: dom_x_flags, dom_y_flags
-real, intent(in) :: dt
-type (time_type), intent(in) :: Time ! current time
-real, dimension(:,:), intent(in) :: ice_lon, ice_lat, ice_wet
-real, dimension(:,:), intent(in) :: ice_dx, ice_dy, ice_area
-real, dimension(:,:), intent(in) :: cos_rot, sin_rot
-real, dimension(:,:), intent(in),optional :: ocean_depth
-logical, intent(in), optional :: maskmap(:,:)
-logical, intent(in), optional :: fractional_area
+type(icebergs), pointer :: bergs !< Container for all types and memory
+integer, intent(in) :: gni !< Number grid cells in i-direction
+integer, intent(in) :: gnj !< Number grid cells in j-direction
+integer, intent(in) :: layout(2) !< Number of processing cores in i,j direction
+integer, intent(in) :: io_layout(2) !< Number of i/o cores in i,j direction
+integer, intent(in) :: axes(2) !< Diagnostic axes
+integer, intent(in) :: dom_x_flags !< Domain flags in i-direction
+integer, intent(in) :: dom_y_flags !< Domain flags in j-direction
+real, intent(in) :: dt !< Time-step (s)
+type (time_type), intent(in) :: Time ! Current model time
+real, dimension(:,:), intent(in) :: ice_lon !< Longitude of cell corners using NE convention (degree E)
+real, dimension(:,:), intent(in) :: ice_lat !< Latitude of cell corners using NE conventino (degree N)
+real, dimension(:,:), intent(in) :: ice_wet !< Wet/dry mask (1 is wet, 0 is dry) of cell centers
+real, dimension(:,:), intent(in) :: ice_dx !< Zonal length of cell on northern side (m)
+real, dimension(:,:), intent(in) :: ice_dy !< Meridional length of cell on eastern side (m)
+real, dimension(:,:), intent(in) :: ice_area !< Area of cells (m^2, or non-dim is fractional_area=True)
+real, dimension(:,:), intent(in) :: cos_rot !< Cosine from rotation matrix to lat-lon coords
+real, dimension(:,:), intent(in) :: sin_rot !< Sine from rotation matrix to lat-lon coords
+real, dimension(:,:), intent(in),optional :: ocean_depth !< Depth of ocean bottom (m)
+logical, intent(in), optional :: maskmap(:,:) !< Masks out parallel cores
+logical, intent(in), optional :: fractional_area !< If true, ice_area contains cell area as fraction of entire spherical surface
 
 ! Namelist parameters (and defaults)
 integer :: halo=4 ! Width of halo region
@@ -372,10 +481,10 @@ subroutine ice_bergs_framework_init(bergs, &
 integer :: verbose_hrs=24 ! Period between verbose messages
 integer :: max_bonds=6 ! Maximum number of iceberg bond passed between processors
 real :: rho_bergs=850. ! Density of icebergs
-real :: spring_coef=1.e-8  ! Spring contant for iceberg interactions (this seems to be the highest stable value)
-real :: bond_coef=1.e-8 ! Spring contant for iceberg bonds - not being used right now
-real :: radial_damping_coef=1.e-4     ! Coef for relative iceberg motion damping (radial component) -Alon
-real :: tangental_damping_coef=2.e-5     ! Coef for relative iceberg motion damping (tangental component) -Alon
+real :: spring_coef=1.e-8 ! Spring constant for iceberg interactions (this seems to be the highest stable value)
+real :: bond_coef=1.e-8 ! Spring constant for iceberg bonds - not being used right now
+real :: radial_damping_coef=1.e-4 ! Coefficient for relative iceberg motion damping (radial component) -Alon
+real :: tangental_damping_coef=2.e-5 ! Coefficient for relative iceberg motion damping (tangential component) -Alon
 real :: LoW_ratio=1.5 ! Initial ratio L/W for newly calved icebergs
 real :: bergy_bit_erosion_fraction=0. ! Fraction of erosion melt flux to divert to bergy bits
 real :: sicn_shift=0. ! Shift of sea-ice concentration in erosion flux modulation (0<sicn_shift<1)
@@ -383,64 +492,63 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: u_override=0.0 ! Overrides the u velocity of icebergs (for ocean testing)
 real :: v_override=0.0 ! Overrides the v velocity of icebergs (for ocean testing)
 real :: Lx=360. ! Length of domain in x direction, used for periodicity (use a huge number for non-periodic)
-real :: initial_orientation=0. ! Iceberg orientaion relative to this angle (in degrees). Used for hexagonal mass spreading.
-real :: utide_icebergs= 0.      ! Tidal speeds, set to zero for now.
+real :: initial_orientation=0. ! Iceberg orientation relative to this angle (in degrees). Used for hexagonal mass spreading.
+real :: utide_icebergs= 0. ! Tidal speeds, set to zero for now.
 real :: ustar_icebergs_bg=0.001 ! Background u_star under icebergs. This should be linked to a value felt by the ocean boundary layer
-real :: cdrag_icebergs =  1.5e-3 !Momentum Drag coef, taken from HJ99  (Holland and Jenkins 1999)
-real :: Gamma_T_3EQ=0.022 ! Nondimensional heat-transfer coefficient
-real :: melt_cutoff=-1.0 !Minimum ocean thickness for melting to occur (is not applied for values < 0)
-logical :: const_gamma=.True. !If true uses a constant heat tranfer coefficient, from which the salt transfer is calculated
+real :: cdrag_icebergs =  1.5e-3 ! Momentum Drag coef, taken from HJ99  (Holland and Jenkins 1999)
+real :: Gamma_T_3EQ=0.022 ! Non-dimensional heat-transfer coefficient
+real :: melt_cutoff=-1.0 ! Minimum ocean thickness for melting to occur (is not applied for values < 0)
+logical :: const_gamma=.True. ! If true uses a constant heat transfer coefficient, from which the salt transfer is calculated
 logical :: use_operator_splitting=.true. ! Use first order operator splitting for thermodynamics
 logical :: add_weight_to_ocean=.true. ! Add weight of icebergs + bits to ocean
 logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
 logical :: time_average_weight=.false. ! Time average the weight on the ocean
 real :: speed_limit=0. ! CFL speed limit for a berg
 real :: tau_calving=0. ! Time scale for smoothing out calving field (years)
-real :: tip_parameter=0. ! parameter to override iceberg rollilng critica ratio (use zero to get parameter directly from ice and seawater densities
+real :: tip_parameter=0. ! Parameter to override iceberg rolling critical ratio (use zero to get parameter directly from ice and seawater densities
 real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
-logical :: Runge_not_Verlet=.True.  !True=Runge Kutta, False=Verlet.  - Added by Alon 
-logical :: use_mixed_melting=.False.  !If true, then the melt is determined partly using 3 eq model partly using iceberg parametrizations (according to iceberg bond number)
-logical :: apply_thickness_cutoff_to_gridded_melt=.False.  !Prevents melt for ocean thickness below melt_cuttoff (applied to gridded melt fields)
-logical :: apply_thickness_cutoff_to_bergs_melt=.False.  !Prevents melt for ocean thickness below melt_cuttoff (applied to bergs)
-logical :: use_updated_rolling_scheme=.false. ! Use the corrected Rolling Scheme rather than the erronios one
-logical :: pass_fields_to_ocean_model=.False. !Iceberg area, mass and ustar fields are prepared to pass to ocean model
-logical :: use_mixed_layer_salinity_for_thermo=.False.  !If true, then model uses ocean salinity for 3 and 2 equation melt model.
-logical :: find_melt_using_spread_mass=.False.  !If true, then the model calculates ice loss by looping at the spread_mass before and after.
-logical :: Use_three_equation_model=.True.  !Uses 3 equation model for melt when ice shelf type thermodynamics are used.
-logical :: melt_icebergs_as_ice_shelf=.False.  !Uses iceshelf type thermodynamics
-logical :: Iceberg_melt_without_decay=.False.  !Allows icebergs meltwater fluxes to enter the ocean, without the iceberg decaying or changing shape.
-logical :: add_iceberg_thickness_to_SSH=.False.  !Adds the iceberg contribution to SSH.   
-logical :: override_iceberg_velocities=.False.  !Allows you to set a fixed iceberg velocity for all non-static icebergs.
-logical :: use_f_plane=.False.  !Flag to use a f-plane for the rotation
-logical :: grid_is_latlon=.True.  !True means that the grid is specified in lat lon, and uses to radius of the earth to convert to distance
-logical :: grid_is_regular=.True. !Flag to say whether point in cell can be found assuming regular cartesian grid
-logical :: rotate_icebergs_for_mass_spreading=.True.  !Flag allows icebergs to rotate for spreading their mass (in hexagonal spreading mode)
-logical :: set_melt_rates_to_zero=.False.  !Sets all melt rates to zero, for testing purposes (thermodynamics routine is still run)
-logical :: allow_bergs_to_roll=.True. !Allows icebergs to roll over when rolling conditions are met
-logical :: hexagonal_icebergs=.False. !True treats icebergs as rectangles, False as hexagonal elements (for the purpose of mass spreading)
-logical :: ignore_missing_restart_bergs=.False.  !True Allows the model to ignorm icebergs missing in the restart. 
-logical :: Static_icebergs=.False.  !True= icebergs do no move
-logical :: only_interactive_forces=.False.  !Icebergs only feel interactive forces, and not ocean, wind... 
-logical :: halo_debugging=.False.  !Use for debugging halos (remove when its working) 
-logical :: save_short_traj=.True.  !True saves only lon,lat,time,iceberg_num in iceberg_trajectory.nc 
-logical :: ignore_traj=.False.  !If true, then model does not traj trajectory data at all 
-logical :: iceberg_bonds_on=.False.  !True=Allow icebergs to have bonds, False=don't allow. 
-logical :: manually_initialize_bonds=.False.  !True= Bonds are initialize manually. 
-logical :: use_new_predictive_corrective =.False.  !Flag to use Bob's predictive corrective iceberg scheme- Added by Alon 
-logical :: interactive_icebergs_on=.false.  !Turn on/off interactions between icebergs  - Added by Alon 
-logical :: critical_interaction_damping_on=.true.  !Sets the damping on relative iceberg velocity to critical value - Added by Alon 
+logical :: Runge_not_Verlet=.True. ! True=Runge Kutta, False=Verlet.
+logical :: use_mixed_melting=.False. ! If true, then the melt is determined partly using 3 eq model partly using iceberg parameterizations (according to iceberg bond number)
+logical :: apply_thickness_cutoff_to_gridded_melt=.False. ! Prevents melt for ocean thickness below melt_cuttoff (applied to gridded melt fields)
+logical :: apply_thickness_cutoff_to_bergs_melt=.False. ! Prevents melt for ocean thickness below melt_cuttoff (applied to bergs)
+logical :: use_updated_rolling_scheme=.false. ! Use the corrected Rolling Scheme rather than the erroneous one
+logical :: pass_fields_to_ocean_model=.False. ! Iceberg area, mass and ustar fields are prepared to pass to ocean model
+logical :: use_mixed_layer_salinity_for_thermo=.False. ! If true, then model uses ocean salinity for 3 and 2 equation melt model.
+logical :: find_melt_using_spread_mass=.False. ! If true, then the model calculates ice loss by looping at the spread_mass before and after.
+logical :: Use_three_equation_model=.True. ! Uses 3 equation model for melt when ice shelf type thermodynamics are used.
+logical :: melt_icebergs_as_ice_shelf=.False. ! Uses iceshelf type thermodynamics
+logical :: Iceberg_melt_without_decay=.False. ! Allows icebergs meltwater fluxes to enter the ocean, without the iceberg decaying or changing shape.
+logical :: add_iceberg_thickness_to_SSH=.False. ! Adds the iceberg contribution to SSH.
+logical :: override_iceberg_velocities=.False. ! Allows you to set a fixed iceberg velocity for all non-static icebergs.
+logical :: use_f_plane=.False. ! Flag to use a f-plane for the rotation
+logical :: grid_is_latlon=.True. ! True means that the grid is specified in lat lon, and uses to radius of the earth to convert to distance
+logical :: grid_is_regular=.True. ! Flag to say whether point in cell can be found assuming regular Cartesian grid
+logical :: rotate_icebergs_for_mass_spreading=.True. ! Flag allows icebergs to rotate for spreading their mass (in hexagonal spreading mode)
+logical :: set_melt_rates_to_zero=.False. ! Sets all melt rates to zero, for testing purposes (thermodynamics routine is still run)
+logical :: allow_bergs_to_roll=.True. ! Allows icebergs to roll over when rolling conditions are met
+logical :: hexagonal_icebergs=.False. ! True treats icebergs as rectangles, False as hexagonal elements (for the purpose of mass spreading)
+logical :: ignore_missing_restart_bergs=.False. ! True Allows the model to ignore icebergs missing in the restart.
+logical :: Static_icebergs=.False. ! True= icebergs do no move
+logical :: only_interactive_forces=.False. ! Icebergs only feel interactive forces, and not ocean, wind...
+logical :: halo_debugging=.False. ! Use for debugging halos (remove when its working)
+logical :: save_short_traj=.True. ! True saves only lon,lat,time,iceberg_num in iceberg_trajectory.nc
+logical :: ignore_traj=.False. ! If true, then model does not traj trajectory data at all
+logical :: iceberg_bonds_on=.False. ! True=Allow icebergs to have bonds, False=don't allow.
+logical :: manually_initialize_bonds=.False. ! True= Bonds are initialize manually.
+logical :: use_new_predictive_corrective =.False. ! Flag to use Bob's predictive corrective iceberg scheme- Added by Alon
+logical :: interactive_icebergs_on=.false. ! Turn on/off interactions between icebergs  - Added by Alon
+logical :: critical_interaction_damping_on=.true. ! Sets the damping on relative iceberg velocity to critical value - Added by Alon
 logical :: do_unit_tests=.false. ! Conduct some unit tests
 logical :: input_freq_distribution=.false. ! Flag to show if input distribution is freq or mass dist (=1 if input is a freq dist, =0 to use an input mass dist)
 logical :: read_old_restarts=.false. ! Legacy option that does nothing
 logical :: use_old_spreading=.true. ! If true, spreads iceberg mass as if the berg is one grid cell wide
 logical :: read_ocean_depth_from_file=.false. ! If true, ocean depth is read from a file.
 real, dimension(nclasses) :: initial_mass=(/8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11/) ! Mass thresholds between iceberg classes (kg)
-real, dimension(nclasses) :: distribution=(/0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02/) ! Fraction of calving to apply to this class (non-dim) , 
+real, dimension(nclasses) :: distribution=(/0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02/) ! Fraction of calving to apply to this class (non-dim) ,
 real, dimension(nclasses) :: mass_scaling=(/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) ! Ratio between effective and real iceberg mass (non-dim)
 real, dimension(nclasses) :: initial_thickness=(/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) ! Total thickness of newly calved bergs (m)
 integer :: debug_iceberg_with_id = -1 ! If positive, monitors a berg with this id
 
-
 namelist /icebergs_nml/ verbose, budget, halo,  traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,Static_icebergs,  &
          distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,bond_coef, radial_damping_coef, tangental_damping_coef, only_interactive_forces, &
          rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, iceberg_bonds_on, manually_initialize_bonds, ignore_missing_restart_bergs, &
@@ -451,7 +559,7 @@ subroutine ice_bergs_framework_init(bergs, &
          grid_is_regular,override_iceberg_velocities,u_override,v_override,add_iceberg_thickness_to_SSH,Iceberg_melt_without_decay,melt_icebergs_as_ice_shelf, &
          Use_three_equation_model,find_melt_using_spread_mass,use_mixed_layer_salinity_for_thermo,utide_icebergs,ustar_icebergs_bg,cdrag_icebergs, pass_fields_to_ocean_model, &
          const_gamma, Gamma_T_3EQ, ignore_traj, debug_iceberg_with_id,use_updated_rolling_scheme, tip_parameter, read_old_restarts, tau_calving, read_ocean_depth_from_file, melt_cutoff,&
-         apply_thickness_cutoff_to_gridded_melt, apply_thickness_cutoff_to_bergs_melt,use_mixed_melting 
+         apply_thickness_cutoff_to_gridded_melt, apply_thickness_cutoff_to_bergs_melt,use_mixed_melting
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -459,7 +567,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: lon_mod, big_number
 logical :: lerr
 integer :: stdlogunit, stderrunit
-real :: Total_mass  !Added by Alon 
+real :: Total_mass  !Added by Alon
 
   ! Get the stderr and stdlog unit numbers
   stderrunit=stderr()
@@ -525,7 +633,7 @@ subroutine ice_bergs_framework_init(bergs, &
   call mpp_get_neighbor_pe(grd%domain, WEST, grd%pe_W)
 
 
-  folded_north_on_pe = ((dom_y_flags == FOLD_NORTH_EDGE) .and. (grd%jec == gnj)) 
+  folded_north_on_pe = ((dom_y_flags == FOLD_NORTH_EDGE) .and. (grd%jec == gnj))
  !write(stderrunit,'(a,6i4)') 'diamonds, icebergs_init: pe,n,s,e,w =',mpp_pe(),grd%pe_N,grd%pe_S,grd%pe_E,grd%pe_W, NULL_PE
 
  !if (verbose) &
@@ -629,7 +737,7 @@ subroutine ice_bergs_framework_init(bergs, &
     if(fractional_area) grd%area(is:ie,js:je)=ice_area(:,:) *(4.*pi*radius*radius)
   endif
   if(present(ocean_depth)) grd%ocean_depth(is:ie,js:je)=ocean_depth(:,:)
-  
+
   ! Copy data declared on ice model data domain
   is=grd%isc-1; ie=grd%iec+1; js=grd%jsc-1; je=grd%jec+1
   grd%dx(is:ie,js:je)=ice_dx(:,:)
@@ -684,11 +792,11 @@ subroutine ice_bergs_framework_init(bergs, &
   endif
 
   if ((Lx.gt.1E15 ) .and. (mpp_pe().eq.mpp_root_pe())) then
-          call error_mesg('diamonds, framework', 'Model does not enjoy the domain being larger than 1E15. Not sure why. Probably to do with floating point precision.', WARNING) 
+          call error_mesg('diamonds, framework', 'Model does not enjoy the domain being larger than 1E15. Not sure why. Probably to do with floating point precision.', WARNING)
   endif
   if ((.not. grid_is_latlon) .and. (Lx.eq.360.)) then
     if (mpp_pe().eq.mpp_root_pe())  then
-            call error_mesg('diamonds, framework', 'Since the lat/lon grid is off, the x-direction is being set as non-periodic. Set Lx not equal to 360 override.', WARNING) 
+            call error_mesg('diamonds, framework', 'Since the lat/lon grid is off, the x-direction is being set as non-periodic. Set Lx not equal to 360 override.', WARNING)
     endif
     Lx=-1.
   endif
@@ -771,32 +879,32 @@ subroutine ice_bergs_framework_init(bergs, &
      do j=1,nclasses
            distribution(j)=(distribution(j)*initial_mass(j))/Total_mass
      enddo
-endif 
+endif
 
 if ((halo .lt. 3) .and. (rotate_icebergs_for_mass_spreading .and. iceberg_bonds_on) )   then
     halo=3
-    call error_mesg('diamonds, framework', 'Setting iceberg halos =3, since halos must be >= 3 for rotating icebergs for mass spreading', WARNING) 
+    call error_mesg('diamonds, framework', 'Setting iceberg halos =3, since halos must be >= 3 for rotating icebergs for mass spreading', WARNING)
 elseif  ((halo .lt. 2) .and. (interactive_icebergs_on .or. iceberg_bonds_on) )   then
     halo=2
-    call error_mesg('diamonds, framework', 'Setting iceberg halos =2, since halos must be >= 2 for interactions', WARNING) 
+    call error_mesg('diamonds, framework', 'Setting iceberg halos =2, since halos must be >= 2 for interactions', WARNING)
 endif
 
 if (interactive_icebergs_on) then
   if (Runge_not_Verlet) then
     !Runge_not_Verlet=.false.  ! Iceberg interactions only with Verlet
-    call error_mesg('diamonds, framework', 'It is unlcear whther interactive icebergs work with Runge Kutta stepping.', WARNING) 
+    call error_mesg('diamonds, framework', 'It is unlcear whther interactive icebergs work with Runge Kutta stepping.', WARNING)
   endif
 endif
 if (.not.interactive_icebergs_on) then
-  if (iceberg_bonds_on) then  
-    !iceberg_bonds_on=.false.  
-    call error_mesg('diamonds, framework', 'Interactive icebergs off requires iceberg bonds off (turning bonds off).', WARNING) 
+  if (iceberg_bonds_on) then
+    !iceberg_bonds_on=.false.
+    call error_mesg('diamonds, framework', 'Interactive icebergs off requires iceberg bonds off (turning bonds off).', WARNING)
   endif
 endif
 if (.not. iceberg_bonds_on) then
    max_bonds=0
 else
-  buffer_width=buffer_width+(max_bonds*3) ! Increase buffer width to include bonds being passed between processors 
+  buffer_width=buffer_width+(max_bonds*3) ! Increase buffer width to include bonds being passed between processors
 endif
 if (save_short_traj) buffer_width_traj=5 ! This is the length of the short buffer used for abrevated traj
 if (ignore_traj) buffer_width_traj=0 ! If this is true, then all traj files should be ignored
@@ -811,8 +919,8 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%verbose_hrs=verbose_hrs
   bergs%grd%halo=halo
   bergs%grd%Lx=Lx
-  bergs%grd%grid_is_latlon=grid_is_latlon  
-  bergs%grd%grid_is_regular=grid_is_regular 
+  bergs%grd%grid_is_latlon=grid_is_latlon
+  bergs%grd%grid_is_regular=grid_is_regular
   bergs%max_bonds=max_bonds
   bergs%rho_bergs=rho_bergs
   bergs%spring_coef=spring_coef
@@ -829,36 +937,36 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%tau_calving=tau_calving
   bergs%tip_parameter=tip_parameter
   bergs%use_updated_rolling_scheme=use_updated_rolling_scheme  !Alon
-  bergs%Runge_not_Verlet=Runge_not_Verlet   
-  bergs%use_mixed_melting=use_mixed_melting   
+  bergs%Runge_not_Verlet=Runge_not_Verlet
+  bergs%use_mixed_melting=use_mixed_melting
   bergs%apply_thickness_cutoff_to_bergs_melt=apply_thickness_cutoff_to_bergs_melt
   bergs%apply_thickness_cutoff_to_gridded_melt=apply_thickness_cutoff_to_gridded_melt
-  bergs%melt_cutoff=melt_cutoff 
+  bergs%melt_cutoff=melt_cutoff
   bergs%read_ocean_depth_from_file=read_ocean_depth_from_file
-  bergs%const_gamma=const_gamma 
+  bergs%const_gamma=const_gamma
   bergs%Gamma_T_3EQ=Gamma_T_3EQ
-  bergs%pass_fields_to_ocean_model=pass_fields_to_ocean_model 
-  bergs%ustar_icebergs_bg=ustar_icebergs_bg   
-  bergs%utide_icebergs=utide_icebergs  
-  bergs%cdrag_icebergs=cdrag_icebergs  
-  bergs%use_mixed_layer_salinity_for_thermo=use_mixed_layer_salinity_for_thermo 
-  bergs%find_melt_using_spread_mass=find_melt_using_spread_mass 
-  bergs%Use_three_equation_model=Use_three_equation_model 
-  bergs%melt_icebergs_as_ice_shelf=melt_icebergs_as_ice_shelf 
-  bergs%Iceberg_melt_without_decay=Iceberg_melt_without_decay 
-  bergs%add_iceberg_thickness_to_SSH=add_iceberg_thickness_to_SSH  
-  bergs%override_iceberg_velocities=override_iceberg_velocities 
-  bergs%use_f_plane=use_f_plane 
-  bergs%rotate_icebergs_for_mass_spreading=rotate_icebergs_for_mass_spreading 
+  bergs%pass_fields_to_ocean_model=pass_fields_to_ocean_model
+  bergs%ustar_icebergs_bg=ustar_icebergs_bg
+  bergs%utide_icebergs=utide_icebergs
+  bergs%cdrag_icebergs=cdrag_icebergs
+  bergs%use_mixed_layer_salinity_for_thermo=use_mixed_layer_salinity_for_thermo
+  bergs%find_melt_using_spread_mass=find_melt_using_spread_mass
+  bergs%Use_three_equation_model=Use_three_equation_model
+  bergs%melt_icebergs_as_ice_shelf=melt_icebergs_as_ice_shelf
+  bergs%Iceberg_melt_without_decay=Iceberg_melt_without_decay
+  bergs%add_iceberg_thickness_to_SSH=add_iceberg_thickness_to_SSH
+  bergs%override_iceberg_velocities=override_iceberg_velocities
+  bergs%use_f_plane=use_f_plane
+  bergs%rotate_icebergs_for_mass_spreading=rotate_icebergs_for_mass_spreading
   bergs%lat_ref=lat_ref
   bergs%u_override=u_override
   bergs%v_override=v_override
   bergs%initial_orientation=initial_orientation
-  bergs%set_melt_rates_to_zero=set_melt_rates_to_zero 
-  bergs%allow_bergs_to_roll=allow_bergs_to_roll 
-  bergs%hexagonal_icebergs=hexagonal_icebergs 
+  bergs%set_melt_rates_to_zero=set_melt_rates_to_zero
+  bergs%allow_bergs_to_roll=allow_bergs_to_roll
+  bergs%hexagonal_icebergs=hexagonal_icebergs
   bergs%ignore_missing_restart_bergs=ignore_missing_restart_bergs
-  bergs%Static_icebergs=Static_icebergs 
+  bergs%Static_icebergs=Static_icebergs
   bergs%only_interactive_forces=only_interactive_forces
   bergs%halo_debugging=halo_debugging
   bergs%iceberg_bonds_on=iceberg_bonds_on   !Alon
@@ -1008,12 +1116,12 @@ subroutine ice_bergs_framework_init(bergs, &
   call mpp_clock_end(bergs%clock)
 
 end subroutine ice_bergs_framework_init
-! ##############################################################################
 
+!> Adjust berg dates to allow use of restarts from later dates
 subroutine offset_berg_dates(bergs,Time)
 ! Arguments
-type(icebergs), pointer :: bergs
-type(time_type), intent(in) :: Time
+type(icebergs), pointer :: bergs !< Container for all types and memory
+type(time_type), intent(in) :: Time !< Model time
 ! Local variables
 type(iceberg), pointer :: this
 integer :: iyr, imon, iday, ihr, imin, isec, yr_offset
@@ -1052,11 +1160,11 @@ subroutine offset_berg_dates(bergs,Time)
 
 end subroutine offset_berg_dates
 
-! #############################################################################
-
-subroutine move_berg_between_cells(bergs)  !Move icebergs onto the correct lists if they have moved from cell to cell.
+!> Moves icebergs between lists if they have moved from cell to cell
+subroutine move_berg_between_cells(bergs)
 ! Arguments
-type(icebergs), pointer :: bergs
+type(icebergs), pointer :: bergs !< Container for all types and memory
+! Local variables
 type(icebergs_gridded), pointer :: grd => null()
 type(iceberg), pointer :: moving_berg => null(), this => null()
 integer :: grdi, grdj
@@ -1071,7 +1179,7 @@ subroutine move_berg_between_cells(bergs)  !Move icebergs onto the correct lists
       if ((this%ine.ne.grdi) .or. (this%jne.ne.grdj))  then
         moving_berg=>this
         this=>this%next
-        
+
         !Removing the iceberg from the old list
         if (associated(moving_berg%prev)) then
           moving_berg%prev%next=>moving_berg%next
@@ -1080,7 +1188,7 @@ subroutine move_berg_between_cells(bergs)  !Move icebergs onto the correct lists
         endif
         if (associated(moving_berg%next)) moving_berg%next%prev=>moving_berg%prev
 
-        !Inserting the iceberg into the new list 
+        !Inserting the iceberg into the new list
         call insert_berg_into_list(bergs%list(moving_berg%ine,moving_berg%jne)%first,moving_berg)
 
         !Clear moving_berg
@@ -1094,12 +1202,10 @@ subroutine move_berg_between_cells(bergs)  !Move icebergs onto the correct lists
 
 end subroutine move_berg_between_cells
 
-
-! #############################################################################
-
+!> Populates the halo lists with bergs from neighbor processers
 subroutine update_halo_icebergs(bergs)
 ! Arguments
-type(icebergs), pointer :: bergs
+type(icebergs), pointer :: bergs !< Container for all types and memory
 ! Local variables
 type(iceberg), pointer :: kick_the_bucket, this
 integer :: nbergs_to_send_e, nbergs_to_send_w
@@ -1115,31 +1221,29 @@ subroutine update_halo_icebergs(bergs)
 real :: current_halo_status
 logical :: halo_debugging
 
-halo_width=bergs%grd%halo  
-halo_debugging=bergs%halo_debugging  
-
- ! Get the stderr unit number
-   stderrunit = stderr()
-
- ! For convenience
-   grd=>bergs%grd
+  halo_width=bergs%grd%halo
+  halo_debugging=bergs%halo_debugging
 
-!For debugging, MP1
-if (halo_debugging) then
-  do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
-    this=>bergs%list(grdi,grdj)%first
-    do while (associated(this))
-        write(stderrunit,*) 'A', this%iceberg_num, mpp_pe(), this%halo_berg, grdi, grdj
-      this=>this%next
-    enddo
-  enddo; enddo
-  ! Use when debugging:
-  call show_all_bonds(bergs)
-endif
+  ! Get the stderr unit number
+  stderrunit = stderr()
 
+  ! For convenience
+  grd=>bergs%grd
 
-! Step 1: Clear the current halos
+  ! For debugging, MP1
+  if (halo_debugging) then
+    do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
+      this=>bergs%list(grdi,grdj)%first
+      do while (associated(this))
+          write(stderrunit,*) 'A', this%iceberg_num, mpp_pe(), this%halo_berg, grdi, grdj
+        this=>this%next
+      enddo
+    enddo; enddo
+    ! Use when debugging:
+    call show_all_bonds(bergs)
+  endif
 
+  ! Step 1: Clear the current halos
   call mpp_sync_self()
   do grdj = grd%jsd,grd%jsc-1 ;  do grdi = grd%isd,grd%ied
     call delete_all_bergs_in_list(bergs, grdj, grdi)
@@ -1158,62 +1262,57 @@ subroutine update_halo_icebergs(bergs)
   enddo ; enddo
 
   call mpp_sync_self()
-!##############################
 
-!For debugging
-if (halo_debugging) then
-  do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
-    this=>bergs%list(grdi,grdj)%first
-      do while (associated(this))
-      write(stderrunit,*) 'B', this%iceberg_num, mpp_pe(), this%halo_berg, grdi, grdj
-    this=>this%next
-    enddo
-  enddo; enddo
-endif
+  ! For debugging
+  if (halo_debugging) then
+    do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
+      this=>bergs%list(grdi,grdj)%first
+        do while (associated(this))
+        write(stderrunit,*) 'B', this%iceberg_num, mpp_pe(), this%halo_berg, grdi, grdj
+      this=>this%next
+      enddo
+    enddo; enddo
+  endif
   if (debug) then
     nbergs_start=count_bergs(bergs)
   endif
 
   call mpp_sync_self()
-!#######################################################
-
-! Step 2: Updating the halos  - This code is mostly copied from send_to_other_pes
 
+  ! Step 2: Updating the halos  - This code is mostly copied from send_to_other_pes
 
   ! Find number of bergs that headed east/west
   nbergs_to_send_e=0
   nbergs_to_send_w=0
-  !Bergs on eastern side of the processor
-  do grdj = grd%jsc,grd%jec ; do grdi = grd%iec-halo_width+2,grd%iec  
+  ! Bergs on eastern side of the processor
+  do grdj = grd%jsc,grd%jec ; do grdi = grd%iec-halo_width+2,grd%iec
     this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
     !write(stderrunit,*)  'sending east', this%iceberg_num, this%ine, this%jne, mpp_pe()
-        kick_the_bucket=>this
-        this=>this%next
-        nbergs_to_send_e=nbergs_to_send_e+1
-        current_halo_status=kick_the_bucket%halo_berg
-        kick_the_bucket%halo_berg=1.
-        call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_e, nbergs_to_send_e, bergs%max_bonds)
-        kick_the_bucket%halo_berg=current_halo_status
+      kick_the_bucket=>this
+      this=>this%next
+      nbergs_to_send_e=nbergs_to_send_e+1
+      current_halo_status=kick_the_bucket%halo_berg
+      kick_the_bucket%halo_berg=1.
+      call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_e, nbergs_to_send_e, bergs%max_bonds)
+      kick_the_bucket%halo_berg=current_halo_status
     enddo
   enddo; enddo
 
-
-  !Bergs on the western side of the processor
-  do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%isc+halo_width-1 
+  ! Bergs on the western side of the processor
+  do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%isc+halo_width-1
     this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
       kick_the_bucket=>this
       this=>this%next
       nbergs_to_send_w=nbergs_to_send_w+1
-       current_halo_status=kick_the_bucket%halo_berg
-       kick_the_bucket%halo_berg=1.
-       call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_w, nbergs_to_send_w, bergs%max_bonds)
-       kick_the_bucket%halo_berg=current_halo_status
-    enddo 
+      current_halo_status=kick_the_bucket%halo_berg
+      kick_the_bucket%halo_berg=1.
+      call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_w, nbergs_to_send_w, bergs%max_bonds)
+      kick_the_bucket%halo_berg=current_halo_status
+    enddo
   enddo; enddo
 
-
   ! Send bergs east
   if (grd%pe_E.ne.NULL_PE) then
     call mpp_send(nbergs_to_send_e, plen=1, to_pe=grd%pe_E, tag=COMM_TAG_1)
@@ -1266,13 +1365,11 @@ subroutine update_halo_icebergs(bergs)
     nbergs_rcvd_from_e=0
   endif
 
-
- ! Find number of bergs that headed north/south
+  ! Find number of bergs that headed north/south
   nbergs_to_send_n=0
   nbergs_to_send_s=0
-  
 
-  !Bergs on north side of the processor
+  ! Bergs on north side of the processor
   do grdj = grd%jec-halo_width+2,grd%jec ; do grdi = grd%isd,grd%ied
     this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
@@ -1286,35 +1383,33 @@ subroutine update_halo_icebergs(bergs)
     enddo
   enddo; enddo
 
-
-  !Bergs on south side of the processor
+  ! Bergs on south side of the processor
   do grdj = grd%jsc,grd%jsc+halo_width-1 ; do grdi = grd%isd,grd%ied
     this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
       kick_the_bucket=>this
       this=>this%next
       nbergs_to_send_s=nbergs_to_send_s+1
-       current_halo_status=kick_the_bucket%halo_berg
-       kick_the_bucket%halo_berg=1.
-       call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_s, nbergs_to_send_s,bergs%max_bonds )
-       kick_the_bucket%halo_berg=current_halo_status
+      current_halo_status=kick_the_bucket%halo_berg
+      kick_the_bucket%halo_berg=1.
+      call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_s, nbergs_to_send_s,bergs%max_bonds )
+      kick_the_bucket%halo_berg=current_halo_status
     enddo
   enddo; enddo
 
-
  ! Send bergs north
   if (grd%pe_N.ne.NULL_PE) then
     if(folded_north_on_pe) then
-       call mpp_send(nbergs_to_send_n, plen=1, to_pe=grd%pe_N, tag=COMM_TAG_9)
+      call mpp_send(nbergs_to_send_n, plen=1, to_pe=grd%pe_N, tag=COMM_TAG_9)
     else
-       call mpp_send(nbergs_to_send_n, plen=1, to_pe=grd%pe_N, tag=COMM_TAG_5)
+      call mpp_send(nbergs_to_send_n, plen=1, to_pe=grd%pe_N, tag=COMM_TAG_5)
     endif
     if (nbergs_to_send_n.gt.0) then
-       if(folded_north_on_pe) then
-          call mpp_send(bergs%obuffer_n%data, nbergs_to_send_n*buffer_width, grd%pe_N, tag=COMM_TAG_10)
-       else
-          call mpp_send(bergs%obuffer_n%data, nbergs_to_send_n*buffer_width, grd%pe_N, tag=COMM_TAG_6)
-       endif
+      if(folded_north_on_pe) then
+        call mpp_send(bergs%obuffer_n%data, nbergs_to_send_n*buffer_width, grd%pe_N, tag=COMM_TAG_10)
+      else
+        call mpp_send(bergs%obuffer_n%data, nbergs_to_send_n*buffer_width, grd%pe_N, tag=COMM_TAG_6)
+      endif
     endif
   endif
 
@@ -1326,7 +1421,6 @@ subroutine update_halo_icebergs(bergs)
     endif
   endif
 
-
   ! Receive bergs from south
   if (grd%pe_S.ne.NULL_PE) then
     nbergs_rcvd_from_s=-999
@@ -1349,9 +1443,9 @@ subroutine update_halo_icebergs(bergs)
   if (grd%pe_N.ne.NULL_PE) then
     nbergs_rcvd_from_n=-999
     if(folded_north_on_pe) then
-       call mpp_recv(nbergs_rcvd_from_n, glen=1, from_pe=grd%pe_N, tag=COMM_TAG_9)
+      call mpp_recv(nbergs_rcvd_from_n, glen=1, from_pe=grd%pe_N, tag=COMM_TAG_9)
     else
-       call mpp_recv(nbergs_rcvd_from_n, glen=1, from_pe=grd%pe_N, tag=COMM_TAG_7)
+      call mpp_recv(nbergs_rcvd_from_n, glen=1, from_pe=grd%pe_N, tag=COMM_TAG_7)
     endif
     if (nbergs_rcvd_from_n.lt.0) then
       write(stderrunit,*) 'pe=',mpp_pe(),' received a bad number',nbergs_rcvd_from_n,' from',grd%pe_N,' (N) !!!!!!!!!!!!!!!!!!!!!!'
@@ -1359,9 +1453,9 @@ subroutine update_halo_icebergs(bergs)
     if (nbergs_rcvd_from_n.gt.0) then
       call increase_ibuffer(bergs%ibuffer_n, nbergs_rcvd_from_n,buffer_width)
       if(folded_north_on_pe) then
-         call mpp_recv(bergs%ibuffer_n%data, nbergs_rcvd_from_n*buffer_width, grd%pe_N, tag=COMM_TAG_10)
+        call mpp_recv(bergs%ibuffer_n%data, nbergs_rcvd_from_n*buffer_width, grd%pe_N, tag=COMM_TAG_10)
       else
-         call mpp_recv(bergs%ibuffer_n%data, nbergs_rcvd_from_n*buffer_width, grd%pe_N, tag=COMM_TAG_8)
+        call mpp_recv(bergs%ibuffer_n%data, nbergs_rcvd_from_n*buffer_width, grd%pe_N, tag=COMM_TAG_8)
       endif
       do i=1, nbergs_rcvd_from_n
         call unpack_berg_from_buffer2(bergs, bergs%ibuffer_n, i, grd, max_bonds_in=bergs%max_bonds )
@@ -1371,23 +1465,20 @@ subroutine update_halo_icebergs(bergs)
     nbergs_rcvd_from_n=0
   endif
 
+  ! For debugging
+  if (halo_debugging) then
+    call mpp_sync_self()
+    do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
+      this=>bergs%list(grdi,grdj)%first
+      do while (associated(this))
+        write(stderrunit,*)  'C', this%iceberg_num, mpp_pe(), this%halo_berg,  grdi, grdj
+        this=>this%next
+      enddo
+    enddo; enddo
+    call show_all_bonds(bergs)
+  endif
 
-
-!For debugging
-if (halo_debugging) then
-  call mpp_sync_self()
-  do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
-    this=>bergs%list(grdi,grdj)%first
-    do while (associated(this))
-      write(stderrunit,*)  'C', this%iceberg_num, mpp_pe(), this%halo_berg,  grdi, grdj
-      this=>this%next
-    enddo
-  enddo; enddo
-  call show_all_bonds(bergs)
-endif
-
-
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!Debugging!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!111
+  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!Debugging!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
   if (debug) then
     nbergs_end=count_bergs(bergs)
     i=nbergs_rcvd_from_n+nbergs_rcvd_from_s+nbergs_rcvd_from_e+nbergs_rcvd_from_w &
@@ -1427,34 +1518,32 @@ subroutine update_halo_icebergs(bergs)
       call error_mesg('diamonds, update_halos:', 'there are bergs still in halos!', FATAL)
     endif ! root_pe
   endif ! debug
-
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!Debugging!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!111
+  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!Debugging!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!111
 
 end subroutine update_halo_icebergs
 
-
-
-subroutine delete_all_bergs_in_list(bergs,grdj,grdi)
-  type(icebergs), pointer :: bergs
+!> Destroys all bergs in a list
+subroutine delete_all_bergs_in_list(bergs, grdj, grdi)
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  integer :: grdi !< i-index of list
+  integer :: grdj !< j-index of list
   ! Local variables
   type(iceberg), pointer :: kick_the_bucket, this
-  integer :: grdi, grdj
   this=>bergs%list(grdi,grdj)%first
   do while (associated(this))
     kick_the_bucket=>this
     this=>this%next
     call destroy_iceberg(kick_the_bucket)
-!    call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
+   !call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
   enddo
   bergs%list(grdi,grdj)%first=>null()
 end  subroutine delete_all_bergs_in_list
 
 
-! #############################################################################
-
+!> Send bergs in halo lists to other processors
 subroutine send_bergs_to_other_pes(bergs)
 ! Arguments
-type(icebergs), pointer :: bergs
+type(icebergs), pointer :: bergs !< Container for all types and memory
 ! Local variables
 type(iceberg), pointer :: kick_the_bucket, this
 integer :: nbergs_to_send_e, nbergs_to_send_w
@@ -1595,7 +1684,7 @@ subroutine send_bergs_to_other_pes(bergs)
   if (grd%pe_N.ne.NULL_PE) then
     if(folded_north_on_pe) then
        call mpp_send(nbergs_to_send_n, plen=1, to_pe=grd%pe_N, tag=COMM_TAG_9)
-    else 
+    else
        call mpp_send(nbergs_to_send_n, plen=1, to_pe=grd%pe_N, tag=COMM_TAG_5)
     endif
     if (nbergs_to_send_n.gt.0) then
@@ -1704,379 +1793,377 @@ subroutine send_bergs_to_other_pes(bergs)
 
 end subroutine send_bergs_to_other_pes
 
-  subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
-  ! Arguments
-  type(iceberg), pointer :: berg
-  type(buffer), pointer :: buff
-  integer, intent(in) :: n
-  integer, optional :: max_bonds_in
-  !integer, intent(in) :: max_bonds  ! Change this later
-  ! Local variables
-  integer :: counter, k, max_bonds
-  type(bond), pointer :: current_bond
- 
-    max_bonds=0
-    if (present(max_bonds_in)) max_bonds=max_bonds_in
-
-
-    if (.not.associated(buff)) call increase_ibuffer(buff,n,buffer_width)
-    if (n>buff%size) call increase_ibuffer(buff,n,buffer_width)
-
-    buff%data(1,n)=berg%lon
-    buff%data(2,n)=berg%lat
-    buff%data(3,n)=berg%uvel
-    buff%data(4,n)=berg%vvel
-    buff%data(5,n)=berg%xi
-    buff%data(6,n)=berg%yj
-    buff%data(7,n)=berg%start_lon
-    buff%data(8,n)=berg%start_lat
-    buff%data(9,n)=float(berg%start_year)
-    buff%data(10,n)=berg%start_day
-    buff%data(11,n)=berg%start_mass
-    buff%data(12,n)=berg%mass
-    buff%data(13,n)=berg%thickness
-    buff%data(14,n)=berg%width
-    buff%data(15,n)=berg%length
-    buff%data(16,n)=berg%mass_scaling
-    buff%data(17,n)=berg%mass_of_bits
-    buff%data(18,n)=berg%heat_density
-    buff%data(19,n)=berg%ine
-    buff%data(20,n)=berg%jne
-    buff%data(21,n)=berg%axn  !Alon
-    buff%data(22,n)=berg%ayn  !Alon
-    buff%data(23,n)=berg%bxn  !Alon
-    buff%data(24,n)=berg%byn  !Alon
-    buff%data(25,n)=float(berg%iceberg_num)
-    buff%data(26,n)=berg%halo_berg 
-    buff%data(27,n)=berg%static_berg 
-
-    if (max_bonds .gt. 0) then
-      counter=27 !how many data points being passed so far (must match above)
-      current_bond=>berg%first_bond
-      do k = 1,max_bonds
-        if (associated(current_bond)) then
-          buff%data(counter+(3*(k-1)+1),n)=float(current_bond%other_berg_num) 
-          buff%data(counter+(3*(k-1)+2),n)=float(current_bond%other_berg_ine)
-          buff%data(counter+(3*(k-1)+3),n)=float(current_bond%other_berg_jne)
-          current_bond=>current_bond%next_bond
-        else
-          buff%data(counter+(3*(k-1)+1),n)=0. 
-          buff%data(counter+(3*(k-1)+2),n)=0.
-          buff%data(counter+(3*(k-1)+3),n)=0.
-        endif
-      enddo
-    endif
-   
-    ! Clearing berg pointer from partner bonds
-    !if (berg%halo_berg .lt. 0.5) then
-    !  call clear_berg_from_partners_bonds(berg)
-    !endif
-
-  end subroutine pack_berg_into_buffer2
-
-
-!###########################################################################3
+!> Pack a berg into a buffer
+subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
+! Arguments
+type(iceberg), pointer :: berg !< Iceberg to pack into buffer
+type(buffer), pointer :: buff !< Buffer to pack berg into
+integer, intent(in) :: n !< Position in buffer to place berg
+integer, optional :: max_bonds_in !< <undocumented>
+!integer, intent(in) :: max_bonds  ! Change this later
+! Local variables
+integer :: counter, k, max_bonds
+type(bond), pointer :: current_bond
 
-  subroutine clear_berg_from_partners_bonds(berg) 
-  !Arguments
-  type(iceberg), intent(in), pointer :: berg
-  type(iceberg), pointer :: other_berg
-  type(bond), pointer :: current_bond, matching_bond
-  integer ::  stderrunit
-  ! Get the stderr unit number
-  stderrunit = stderr()
+  max_bonds=0
+  if (present(max_bonds_in)) max_bonds=max_bonds_in
 
+  if (.not.associated(buff)) call increase_ibuffer(buff,n,buffer_width)
+  if (n>buff%size) call increase_ibuffer(buff,n,buffer_width)
+
+  buff%data(1,n)=berg%lon
+  buff%data(2,n)=berg%lat
+  buff%data(3,n)=berg%uvel
+  buff%data(4,n)=berg%vvel
+  buff%data(5,n)=berg%xi
+  buff%data(6,n)=berg%yj
+  buff%data(7,n)=berg%start_lon
+  buff%data(8,n)=berg%start_lat
+  buff%data(9,n)=float(berg%start_year)
+  buff%data(10,n)=berg%start_day
+  buff%data(11,n)=berg%start_mass
+  buff%data(12,n)=berg%mass
+  buff%data(13,n)=berg%thickness
+  buff%data(14,n)=berg%width
+  buff%data(15,n)=berg%length
+  buff%data(16,n)=berg%mass_scaling
+  buff%data(17,n)=berg%mass_of_bits
+  buff%data(18,n)=berg%heat_density
+  buff%data(19,n)=berg%ine
+  buff%data(20,n)=berg%jne
+  buff%data(21,n)=berg%axn  !Alon
+  buff%data(22,n)=berg%ayn  !Alon
+  buff%data(23,n)=berg%bxn  !Alon
+  buff%data(24,n)=berg%byn  !Alon
+  buff%data(25,n)=float(berg%iceberg_num)
+  buff%data(26,n)=berg%halo_berg
+  buff%data(27,n)=berg%static_berg
+
+  if (max_bonds .gt. 0) then
+    counter=27 !how many data points being passed so far (must match above)
     current_bond=>berg%first_bond
-    do while (associated(current_bond)) !Looping over bonds
-      other_berg=>current_bond%other_berg
-      if (associated(other_berg)) then
-        !write(stderrunit,*) , 'Other berg', berg%iceberg_num, other_berg%iceberg_num, mpp_pe()
-        matching_bond=>other_berg%first_bond
-        do while (associated(matching_bond))  ! Looping over possible matching bonds in other_berg
-          if (matching_bond%other_berg_num .eq. berg%iceberg_num) then
-            !write(stderrunit,*) , 'Clearing', berg%iceberg_num, matching_bond%other_berg_num,other_berg%iceberg_num, mpp_pe()
-            matching_bond%other_berg=>null()
-            matching_bond=>null()
-          else
-            matching_bond=>matching_bond%next_bond
-          endif
-        enddo
+    do k = 1,max_bonds
+      if (associated(current_bond)) then
+        buff%data(counter+(3*(k-1)+1),n)=float(current_bond%other_berg_num)
+        buff%data(counter+(3*(k-1)+2),n)=float(current_bond%other_berg_ine)
+        buff%data(counter+(3*(k-1)+3),n)=float(current_bond%other_berg_jne)
+        current_bond=>current_bond%next_bond
       else
-       ! Note: This is meant to be unmatched after you have cleared the first berg       
-       ! call error_mesg('diamonds, clear berg from partners', 'The bond you are trying to clear is unmatched!', WARNING) 
+        buff%data(counter+(3*(k-1)+1),n)=0.
+        buff%data(counter+(3*(k-1)+2),n)=0.
+        buff%data(counter+(3*(k-1)+3),n)=0.
       endif
-      current_bond=>current_bond%next_bond
-    enddo !End loop over bonds
+    enddo
+  endif
 
-  end subroutine clear_berg_from_partners_bonds
+  ! Clearing berg pointer from partner bonds
+  !if (berg%halo_berg .lt. 0.5) then
+  !  call clear_berg_from_partners_bonds(berg)
+  !endif
 
+end subroutine pack_berg_into_buffer2
 
-  subroutine unpack_berg_from_buffer2(bergs, buff, n,grd, force_append, max_bonds_in)
-  ! Arguments
-  type(icebergs), pointer :: bergs
-  type(buffer), pointer :: buff
-  integer, intent(in) :: n
-  type(icebergs_gridded), pointer :: grd  
-  logical, optional :: force_append
-  integer, optional :: max_bonds_in
- ! Local variables
- !real :: lon, lat, uvel, vvel, xi, yj
-
- !real :: start_lon, start_lat, start_day, start_mass
- !integer :: ine, jne, start_year
-  logical :: lres
-  type(iceberg) :: localberg
-  type(iceberg), pointer :: this
-  integer :: other_berg_num, other_berg_ine, other_berg_jne
-  integer :: counter, k, max_bonds
-  integer :: stderrunit
-  logical :: force_app
-  logical :: quick
+subroutine clear_berg_from_partners_bonds(berg)
+! Arguments
+type(iceberg), intent(in), pointer :: berg
+! Local variables
+type(iceberg), pointer :: other_berg
+type(bond), pointer :: current_bond, matching_bond
+integer ::  stderrunit
+! Get the stderr unit number
+stderrunit = stderr()
+
+  current_bond=>berg%first_bond
+  do while (associated(current_bond)) !Looping over bonds
+    other_berg=>current_bond%other_berg
+    if (associated(other_berg)) then
+      !write(stderrunit,*) , 'Other berg', berg%iceberg_num, other_berg%iceberg_num, mpp_pe()
+      matching_bond=>other_berg%first_bond
+      do while (associated(matching_bond))  ! Looping over possible matching bonds in other_berg
+        if (matching_bond%other_berg_num .eq. berg%iceberg_num) then
+          !write(stderrunit,*) , 'Clearing', berg%iceberg_num, matching_bond%other_berg_num,other_berg%iceberg_num, mpp_pe()
+          matching_bond%other_berg=>null()
+          matching_bond=>null()
+        else
+          matching_bond=>matching_bond%next_bond
+        endif
+      enddo
+    else
+     ! Note: This is meant to be unmatched after you have cleared the first berg
+     ! call error_mesg('diamonds, clear berg from partners', 'The bond you are trying to clear is unmatched!', WARNING)
+    endif
+    current_bond=>current_bond%next_bond
+  enddo !End loop over bonds
+
+end subroutine clear_berg_from_partners_bonds
+
+!> Unpacks a berg entry from a buffer to a new berg
+subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds_in)
+! Arguments
+type(icebergs), pointer :: bergs !< Container for all types and memory
+type(buffer), pointer :: buff !< Buffer from which to unpack berg
+integer, intent(in) :: n !< Position in buffer to unpack
+type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+logical, optional :: force_append !< <undocumented>
+integer, optional :: max_bonds_in !< <undocumented>
+! Local variables
+!real :: lon, lat, uvel, vvel, xi, yj
+!real :: start_lon, start_lat, start_day, start_mass
+!integer :: ine, jne, start_year
+logical :: lres
+type(iceberg) :: localberg
+type(iceberg), pointer :: this
+integer :: other_berg_num, other_berg_ine, other_berg_jne
+integer :: counter, k, max_bonds
+integer :: stderrunit
+logical :: force_app
+logical :: quick
 
   ! Get the stderr unit number
   stderrunit = stderr()
- 
+
   quick=.false.
   max_bonds=0
   if (present(max_bonds_in)) max_bonds=max_bonds_in
 
   force_app = .false.
   if(present(force_append)) force_app = force_append
-     
-    localberg%lon=buff%data(1,n)
-    localberg%lat=buff%data(2,n)
-    localberg%uvel=buff%data(3,n)
-    localberg%vvel=buff%data(4,n)
-    localberg%xi=buff%data(5,n)
-    localberg%yj=buff%data(6,n)
-    localberg%start_lon=buff%data(7,n)
-    localberg%start_lat=buff%data(8,n)
-    localberg%start_year=nint(buff%data(9,n))
-    localberg%start_day=buff%data(10,n)
-    localberg%start_mass=buff%data(11,n)
-    localberg%mass=buff%data(12,n)
-    localberg%thickness=buff%data(13,n)
-    localberg%width=buff%data(14,n)
-    localberg%length=buff%data(15,n)
-    localberg%mass_scaling=buff%data(16,n)
-    localberg%mass_of_bits=buff%data(17,n)
-    localberg%heat_density=buff%data(18,n)
-
-    localberg%axn=buff%data(21,n) 
-    localberg%ayn=buff%data(22,n) 
-    localberg%bxn=buff%data(23,n) 
-    localberg%byn=buff%data(24,n) 
-    localberg%iceberg_num=nint(buff%data(25,n))
-    localberg%halo_berg=buff%data(26,n) 
-    localberg%static_berg=buff%data(27,n) 
-    counter=27 !how many data points being passed so far (must match largest number directly above)
-
-    !These quantities no longer need to be passed between processors
-    localberg%uvel_old=localberg%uvel
-    localberg%vvel_old=localberg%vvel
-    localberg%lon_old=localberg%lon 
-    localberg%lat_old=localberg%lat
-
-    ! force_app=.true.
-    if(force_app) then !force append with origin ine,jne (for I/O)
-
-      localberg%ine=buff%data(19,n) 
-      localberg%jne=buff%data(20,n) 
-      call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg,quick,this) 
+
+  localberg%lon=buff%data(1,n)
+  localberg%lat=buff%data(2,n)
+  localberg%uvel=buff%data(3,n)
+  localberg%vvel=buff%data(4,n)
+  localberg%xi=buff%data(5,n)
+  localberg%yj=buff%data(6,n)
+  localberg%start_lon=buff%data(7,n)
+  localberg%start_lat=buff%data(8,n)
+  localberg%start_year=nint(buff%data(9,n))
+  localberg%start_day=buff%data(10,n)
+  localberg%start_mass=buff%data(11,n)
+  localberg%mass=buff%data(12,n)
+  localberg%thickness=buff%data(13,n)
+  localberg%width=buff%data(14,n)
+  localberg%length=buff%data(15,n)
+  localberg%mass_scaling=buff%data(16,n)
+  localberg%mass_of_bits=buff%data(17,n)
+  localberg%heat_density=buff%data(18,n)
+
+  localberg%axn=buff%data(21,n)
+  localberg%ayn=buff%data(22,n)
+  localberg%bxn=buff%data(23,n)
+  localberg%byn=buff%data(24,n)
+  localberg%iceberg_num=nint(buff%data(25,n))
+  localberg%halo_berg=buff%data(26,n)
+  localberg%static_berg=buff%data(27,n)
+  counter=27 !how many data points being passed so far (must match largest number directly above)
+
+  !These quantities no longer need to be passed between processors
+  localberg%uvel_old=localberg%uvel
+  localberg%vvel_old=localberg%vvel
+  localberg%lon_old=localberg%lon
+  localberg%lat_old=localberg%lat
+
+  ! force_app=.true.
+  if(force_app) then !force append with origin ine,jne (for I/O)
+
+    localberg%ine=buff%data(19,n)
+    localberg%jne=buff%data(20,n)
+    call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg,quick,this)
+  else
+    lres=find_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
+    if (lres) then
+      lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
+      call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg,quick,this)
     else
-      lres=find_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
+      lres=find_cell_wide(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
       if (lres) then
         lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
         call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg,quick,this)
       else
-        lres=find_cell_wide(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
-        if (lres) then
-          lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
-          call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg,quick,this)
-        else
-          write(stderrunit,'("diamonds, unpack_berg_from_buffer pe=(",i3,a,2i4,a,2f8.2)')&
-           & mpp_pe(),') Failed to find i,j=',localberg%ine,localberg%jne,' for lon,lat=',localberg%lon,localberg%lat
-          write(stderrunit,*) localberg%lon,localberg%lat
-          write(stderrunit,*) localberg%uvel,localberg%vvel
-          write(stderrunit,*) localberg%axn,localberg%ayn !Alon
-          write(stderrunit,*) localberg%bxn,localberg%byn !Alon
-          write(stderrunit,*) localberg%uvel_old,localberg%vvel_old 
-          write(stderrunit,*) localberg%lon_old,localberg%lat_old 
-          write(stderrunit,*) grd%isc,grd%iec,grd%jsc,grd%jec
-          write(stderrunit,*) grd%isd,grd%ied,grd%jsd,grd%jed
-          write(stderrunit,*) grd%lon(grd%isc-1,grd%jsc-1),grd%lon(grd%iec,grd%jsc)
-          write(stderrunit,*) grd%lat(grd%isc-1,grd%jsc-1),grd%lat(grd%iec,grd%jec)
-          write(stderrunit,*) grd%lon(grd%isd,grd%jsd),grd%lon(grd%ied,grd%jsd)
-          write(stderrunit,*) grd%lat(grd%isd,grd%jsd),grd%lat(grd%ied,grd%jed)
-          write(stderrunit,*) lres
-          call error_mesg('diamonds, unpack_berg_from_buffer', 'can not find a cell to place berg in!', FATAL)
-        endif
+        write(stderrunit,'("diamonds, unpack_berg_from_buffer pe=(",i3,a,2i4,a,2f8.2)')&
+         & mpp_pe(),') Failed to find i,j=',localberg%ine,localberg%jne,' for lon,lat=',localberg%lon,localberg%lat
+        write(stderrunit,*) localberg%lon,localberg%lat
+        write(stderrunit,*) localberg%uvel,localberg%vvel
+        write(stderrunit,*) localberg%axn,localberg%ayn !Alon
+        write(stderrunit,*) localberg%bxn,localberg%byn !Alon
+        write(stderrunit,*) localberg%uvel_old,localberg%vvel_old
+        write(stderrunit,*) localberg%lon_old,localberg%lat_old
+        write(stderrunit,*) grd%isc,grd%iec,grd%jsc,grd%jec
+        write(stderrunit,*) grd%isd,grd%ied,grd%jsd,grd%jed
+        write(stderrunit,*) grd%lon(grd%isc-1,grd%jsc-1),grd%lon(grd%iec,grd%jsc)
+        write(stderrunit,*) grd%lat(grd%isc-1,grd%jsc-1),grd%lat(grd%iec,grd%jec)
+        write(stderrunit,*) grd%lon(grd%isd,grd%jsd),grd%lon(grd%ied,grd%jsd)
+        write(stderrunit,*) grd%lat(grd%isd,grd%jsd),grd%lat(grd%ied,grd%jed)
+        write(stderrunit,*) lres
+        call error_mesg('diamonds, unpack_berg_from_buffer', 'can not find a cell to place berg in!', FATAL)
       endif
     endif
+  endif
 
-    !#  Do stuff to do with bonds here MP1
-
-    this%first_bond=>null()
-    if (max_bonds .gt. 0) then
-      do k = 1,max_bonds
-        other_berg_num=nint(buff%data(counter+(3*(k-1)+1),n))
-        other_berg_ine=nint(buff%data(counter+(3*(k-1)+2),n))
-        other_berg_jne=nint(buff%data(counter+(3*(k-1)+3),n))
-        if (other_berg_num .gt. 0.5) then
-          call form_a_bond(this, other_berg_num, other_berg_ine, other_berg_jne)
-        endif
-      enddo
-    endif
-    this=>null()
-
-    !##############################
+  !#  Do stuff to do with bonds here MP1
+  this%first_bond=>null()
+  if (max_bonds .gt. 0) then
+    do k = 1,max_bonds
+      other_berg_num=nint(buff%data(counter+(3*(k-1)+1),n))
+      other_berg_ine=nint(buff%data(counter+(3*(k-1)+2),n))
+      other_berg_jne=nint(buff%data(counter+(3*(k-1)+3),n))
+      if (other_berg_num .gt. 0.5) then
+        call form_a_bond(this, other_berg_num, other_berg_ine, other_berg_jne)
+      endif
+    enddo
+  endif
+  this=>null()
 
-  end subroutine unpack_berg_from_buffer2
+end subroutine unpack_berg_from_buffer2
 
-  subroutine increase_ibuffer(old,num_bergs,width)
-  ! Arguments
-  type(buffer), pointer :: old
-  integer, intent(in) :: num_bergs,width
-  ! Local variables
-  type(buffer), pointer :: new
-  integer :: new_size, old_size
-  !This routine checks if the buffer size is smaller than nbergs
-  !If it is, the buffer size is increased by delta_buf
-  !The buffer increases by more than 1 so that the buffer does not have to increase every time
+!> Increase size of buffer
+!!
+!! This routine checks if the buffer size is smaller than nbergs
+!! If it is, the buffer size is increased by delta_buf.
+!! The buffer increases by more than 1 so that the buffer does not have to increase every time.
+subroutine increase_ibuffer(old, num_bergs, width)
+! Arguments
+type(buffer), pointer :: old !< Buffer to expand
+integer, intent(in) :: num_bergs !< Number of bergs
+integer, intent(in) :: width !< Width of buffer (first dimension)
+! Local variables
+type(buffer), pointer :: new
+integer :: new_size, old_size
 
-    if (.not.associated(old)) then
-      new_size=num_bergs+delta_buf
-      old_size=0
+  if (.not.associated(old)) then
+    new_size=num_bergs+delta_buf
+    old_size=0
+  else
+    old_size=old%size
+    if (num_bergs<old%size) then
+      new_size=old%size
     else
-      old_size=old%size
-      if (num_bergs<old%size) then
-        new_size=old%size
-      else
-        new_size=num_bergs+delta_buf
-      endif
-    endif
-
-    if (old_size.ne.new_size) then
-      allocate(new)
-      !allocate(new%data(buffer_width,new_size))
-      allocate(new%data(width,new_size))
-      new%size=new_size
-      if (associated(old)) then
-        new%data(:,1:old%size)=old%data(:,1:old%size)
-        deallocate(old%data)
-        deallocate(old)
-      endif
-      old=>new
-     !write(stderr(),*) 'diamonds, increase_ibuffer',mpp_pe(),' increased to',new_size
+      new_size=num_bergs+delta_buf
     endif
+  endif
 
-  end subroutine increase_ibuffer
-
-  subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj)
-  ! Arguments
-  type(xyt), pointer :: traj
-  type(buffer), pointer :: buff
-  integer, intent(in) :: n
-  logical, intent(in) :: save_short_traj
-  ! Local variables
-
-    if (.not.associated(buff)) call increase_ibuffer(buff,n,buffer_width_traj)
-    if (n>buff%size) call increase_ibuffer(buff,n,buffer_width_traj)
-
-    buff%data(1,n)=traj%lon
-    buff%data(2,n)=traj%lat
-    buff%data(3,n)=float(traj%year)
-    buff%data(4,n)=traj%day
-    buff%data(5,n)=float(traj%iceberg_num)
-    if (.not. save_short_traj) then
-      buff%data(6,n)=traj%uvel
-      buff%data(7,n)=traj%vvel
-      buff%data(8,n)=traj%mass
-      buff%data(9,n)=traj%mass_of_bits
-      buff%data(10,n)=traj%heat_density
-      buff%data(11,n)=traj%thickness
-      buff%data(12,n)=traj%width
-      buff%data(13,n)=traj%length
-      buff%data(14,n)=traj%uo
-      buff%data(15,n)=traj%vo
-      buff%data(16,n)=traj%ui
-      buff%data(17,n)=traj%vi
-      buff%data(18,n)=traj%ua
-      buff%data(19,n)=traj%va
-      buff%data(20,n)=traj%ssh_x
-      buff%data(21,n)=traj%ssh_y
-      buff%data(22,n)=traj%sst
-      buff%data(23,n)=traj%cn
-      buff%data(24,n)=traj%hi
-      buff%data(25,n)=traj%axn !Alon
-      buff%data(26,n)=traj%ayn !Alon
-      buff%data(27,n)=traj%bxn !Alon
-      buff%data(28,n)=traj%byn !Alon
-      buff%data(29,n)=traj%halo_berg !Alon
-      buff%data(30,n)=traj%static_berg !Alon
-      buff%data(31,n)=traj%sss
+  if (old_size.ne.new_size) then
+    allocate(new)
+    !allocate(new%data(buffer_width,new_size))
+    allocate(new%data(width,new_size))
+    new%size=new_size
+    if (associated(old)) then
+      new%data(:,1:old%size)=old%data(:,1:old%size)
+      deallocate(old%data)
+      deallocate(old)
     endif
+    old=>new
+   !write(stderr(),*) 'diamonds, increase_ibuffer',mpp_pe(),' increased to',new_size
+  endif
 
-  end subroutine pack_traj_into_buffer2
-
-  subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj)
-  ! Arguments
-  type(xyt), pointer :: first
-  type(buffer), pointer :: buff
-  integer, intent(in) :: n
- ! Local variables
-  type(xyt) :: traj
-  integer :: stderrunit
-  logical, intent(in) :: save_short_traj 
-  ! Get the stderr unit number
-  stderrunit = stderr()
+end subroutine increase_ibuffer
 
-    traj%lon=buff%data(1,n)
-    traj%lat=buff%data(2,n)
-    traj%year=nint(buff%data(3,n))
-    traj%day=buff%data(4,n)
-    traj%iceberg_num=nint(buff%data(5,n))
-    if (.not. save_short_traj) then
-      traj%uvel=buff%data(6,n)
-      traj%vvel=buff%data(7,n)
-      traj%mass=buff%data(8,n)
-      traj%mass_of_bits=buff%data(9,n)
-      traj%heat_density=buff%data(10,n)
-      traj%thickness=buff%data(11,n)
-      traj%width=buff%data(12,n)
-      traj%length=buff%data(13,n)
-      traj%uo=buff%data(14,n)
-      traj%vo=buff%data(15,n)
-      traj%ui=buff%data(16,n)
-      traj%vi=buff%data(17,n)
-      traj%ua=buff%data(18,n)
-      traj%va=buff%data(19,n)
-      traj%ssh_x=buff%data(20,n)
-      traj%ssh_y=buff%data(21,n)
-      traj%sst=buff%data(22,n)
-      traj%cn=buff%data(23,n)
-      traj%hi=buff%data(24,n)
-      traj%axn=buff%data(25,n) !Alon
-      traj%ayn=buff%data(26,n) !Alon
-      traj%bxn=buff%data(27,n) !Alon
-      traj%byn=buff%data(28,n) !Alon
-      traj%halo_berg=buff%data(29,n) !Alon
-      traj%static_berg=buff%data(30,n) !Alon
-      traj%sss=buff%data(31,n)
-    endif
-    call append_posn(first, traj)
+!> Packs a trajectory entry into a buffer
+subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj)
+! Arguments
+type(xyt), pointer :: traj !< Trajectory entry to pack
+type(buffer), pointer :: buff !< Buffer to pack entry into
+integer, intent(in) :: n !< Position in buffer to place entry
+logical, intent(in) :: save_short_traj !< If true, only use a subset of trajectory data
+
+  if (.not.associated(buff)) call increase_ibuffer(buff,n,buffer_width_traj)
+  if (n>buff%size) call increase_ibuffer(buff,n,buffer_width_traj)
+
+  buff%data(1,n)=traj%lon
+  buff%data(2,n)=traj%lat
+  buff%data(3,n)=float(traj%year)
+  buff%data(4,n)=traj%day
+  buff%data(5,n)=float(traj%iceberg_num)
+  if (.not. save_short_traj) then
+    buff%data(6,n)=traj%uvel
+    buff%data(7,n)=traj%vvel
+    buff%data(8,n)=traj%mass
+    buff%data(9,n)=traj%mass_of_bits
+    buff%data(10,n)=traj%heat_density
+    buff%data(11,n)=traj%thickness
+    buff%data(12,n)=traj%width
+    buff%data(13,n)=traj%length
+    buff%data(14,n)=traj%uo
+    buff%data(15,n)=traj%vo
+    buff%data(16,n)=traj%ui
+    buff%data(17,n)=traj%vi
+    buff%data(18,n)=traj%ua
+    buff%data(19,n)=traj%va
+    buff%data(20,n)=traj%ssh_x
+    buff%data(21,n)=traj%ssh_y
+    buff%data(22,n)=traj%sst
+    buff%data(23,n)=traj%cn
+    buff%data(24,n)=traj%hi
+    buff%data(25,n)=traj%axn !Alon
+    buff%data(26,n)=traj%ayn !Alon
+    buff%data(27,n)=traj%bxn !Alon
+    buff%data(28,n)=traj%byn !Alon
+    buff%data(29,n)=traj%halo_berg !Alon
+    buff%data(30,n)=traj%static_berg !Alon
+    buff%data(31,n)=traj%sss
+  endif
 
-  end subroutine unpack_traj_from_buffer2
+end subroutine pack_traj_into_buffer2
 
+!> Unpacks a trajectory entry from a buffer
+subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj)
+! Arguments
+type(xyt), pointer :: first !< Trajectory list
+type(buffer), pointer :: buff !< Buffer from which to unpack
+integer, intent(in) :: n !< Position in buffer to unpack
+logical, intent(in) :: save_short_traj !< If true, only use a subset of trajectory data
+! Local variables
+type(xyt) :: traj
+
+  traj%lon=buff%data(1,n)
+  traj%lat=buff%data(2,n)
+  traj%year=nint(buff%data(3,n))
+  traj%day=buff%data(4,n)
+  traj%iceberg_num=nint(buff%data(5,n))
+  if (.not. save_short_traj) then
+    traj%uvel=buff%data(6,n)
+    traj%vvel=buff%data(7,n)
+    traj%mass=buff%data(8,n)
+    traj%mass_of_bits=buff%data(9,n)
+    traj%heat_density=buff%data(10,n)
+    traj%thickness=buff%data(11,n)
+    traj%width=buff%data(12,n)
+    traj%length=buff%data(13,n)
+    traj%uo=buff%data(14,n)
+    traj%vo=buff%data(15,n)
+    traj%ui=buff%data(16,n)
+    traj%vi=buff%data(17,n)
+    traj%ua=buff%data(18,n)
+    traj%va=buff%data(19,n)
+    traj%ssh_x=buff%data(20,n)
+    traj%ssh_y=buff%data(21,n)
+    traj%sst=buff%data(22,n)
+    traj%cn=buff%data(23,n)
+    traj%hi=buff%data(24,n)
+    traj%axn=buff%data(25,n) !Alon
+    traj%ayn=buff%data(26,n) !Alon
+    traj%bxn=buff%data(27,n) !Alon
+    traj%byn=buff%data(28,n) !Alon
+    traj%halo_berg=buff%data(29,n) !Alon
+    traj%static_berg=buff%data(30,n) !Alon
+    traj%sss=buff%data(31,n)
+  endif
+  call append_posn(first, traj)
 
-! ##############################################################################
+end subroutine unpack_traj_from_buffer2
 
+!> Add a new berg to a list by copying values
+!!
+!! The input berg are a berg with set values whose memory is assumed to be
+!! temporary. This routine allocates memory for a new berg and copies the
+!! the input values into it. The memory for the new berg is pointed to
+!! by newberg_return (if present).
 subroutine add_new_berg_to_list(first, bergvals, quick, newberg_return)
 ! Arguments
-type(iceberg), pointer :: first
-type(iceberg), intent(in) :: bergvals
-type(iceberg), intent(out), pointer, optional :: newberg_return
-logical, intent(in), optional :: quick
+type(iceberg), pointer :: first !< List of icebergs
+type(iceberg), intent(in) :: bergvals !< Berg values to copy
+type(iceberg), intent(out), pointer, optional :: newberg_return !< New berg
+logical, intent(in), optional :: quick !< If true, use the quick insertion algorithm
 ! Local variables
 type(iceberg), pointer :: new=>null()
 
@@ -2103,12 +2190,12 @@ subroutine add_new_berg_to_list(first, bergvals, quick, newberg_return)
 
 end subroutine add_new_berg_to_list
 
-! ##############################################################################
 
+!> Scans all lists and checks that bergs are in a sorted order in each list
 subroutine count_out_of_order(bergs,label)
 ! Arguments
-type(icebergs), pointer :: bergs
-character(len=*) :: label
+type(icebergs), pointer :: bergs !< Container for all types and memory
+character(len=*) :: label !< Label to add to messages
 ! Local variables
 type(iceberg), pointer :: this, next
 integer :: i, icnt1, icnt2, icnt3
@@ -2157,12 +2244,11 @@ subroutine count_out_of_order(bergs,label)
 
 end subroutine count_out_of_order
 
-! ##############################################################################
-
+!> Scans all lists and checks for duplicate identifiers between lists
 subroutine check_for_duplicates(bergs,label)
 ! Arguments
-type(icebergs), pointer :: bergs
-character(len=*) :: label
+type(icebergs), pointer :: bergs !< Container for all types and memory
+character(len=*) :: label !< Label to add to message
 ! Local variables
 type(iceberg), pointer :: this1, next1, this2, next2
 integer :: icnt_id, icnt_same
@@ -2201,12 +2287,14 @@ subroutine check_for_duplicates(bergs,label)
 
 end subroutine check_for_duplicates
 
-! ##############################################################################
-
+!> Prints a particular berg's vitals
+!!
+!! All lists are scanned and if a berg has the identifier equal to
+!! debug_iceberg_with_id then the state of that berg is printed.
 subroutine monitor_a_berg(bergs, label)
 ! Arguments
-type(icebergs), pointer :: bergs
-character(len=*) :: label
+type(icebergs), pointer :: bergs !< Container for all types and memory
+character(len=*) :: label !< Label to add to message
 ! Local variables
 type(iceberg), pointer :: this
 integer :: grdi, grdj
@@ -2227,12 +2315,13 @@ subroutine monitor_a_berg(bergs, label)
 
 end subroutine monitor_a_berg
 
-! ##############################################################################
-
+!> Inserts a berg into a list
 subroutine insert_berg_into_list(first, newberg, quick)
 ! Arguments
-type(iceberg), pointer :: first, newberg
-logical, intent(in), optional :: quick
+type(iceberg), pointer :: first !< List of bergs
+type(iceberg), pointer :: newberg !< New berg to insert
+logical, intent(in), optional :: quick !< If true, use the quick insertion algorithm
+                                       !! \todo Delete arguments since the code does not appear to use it.
 ! Local variables
 type(iceberg), pointer :: this, prev
 logical :: quickly
@@ -2277,11 +2366,13 @@ subroutine insert_berg_into_list(first, newberg, quick)
 
 end subroutine insert_berg_into_list
 
-! ##############################################################################
-
+!> Returns True when berg1 and berg2 are in sorted order
+!! \todo inorder() should use the iceberg identifier for efficiency and simplicity
+!! instead of dates and properties
 logical function inorder(berg1, berg2)  !MP Alon - Change to include iceberg_num
 ! Arguments
-type(iceberg), pointer :: berg1, berg2
+type(iceberg), pointer :: berg1 !< An iceberg
+type(iceberg), pointer :: berg2 !< An iceberg
 ! Local variables
   if (berg1%start_year<berg2%start_year) then ! want newer first
     inorder=.true.
@@ -2321,27 +2412,30 @@ logical function inorder(berg1, berg2)  !MP Alon - Change to include iceberg_num
   inorder=.true. ! passing the above tests mean the bergs 1 and 2 are identical?
 end function inorder
 
-! ##############################################################################
-
-  real function time_hash(berg)!  Alon: Think about removing this.
-  ! Arguments
-  type(iceberg), pointer :: berg
-    time_hash=berg%start_day+366.*float(berg%start_year)
-  end function time_hash
-
-! ##############################################################################
 
-  real function pos_hash(berg)
-  ! Arguments
-  type(iceberg), pointer :: berg
-    pos_hash=berg%start_lon+360.*(berg%start_lat+90.)
-  end function pos_hash
+!> Returns a hash of a berg's start year and day
+!! \todo Should be able to remove this function if using identifiers properly
+real function time_hash(berg)!  Alon: Think about removing this.
+! Arguments
+type(iceberg), pointer :: berg
+  time_hash=berg%start_day+366.*float(berg%start_year)
+end function time_hash
 
-! ##############################################################################
+!> Returns a hash of a berg's start position
+!! \todo Should be able to remove this function if using identifiers properly
+real function pos_hash(berg)
+! Arguments
+type(iceberg), pointer :: berg !< An iceberg
+  pos_hash=berg%start_lon+360.*(berg%start_lat+90.)
+end function pos_hash
 
+!> Returns True if berg1 and berg2 have the identifying properties
+!!
+!! This function compares the start year, day, mass and position of the bergs.
 logical function sameid(berg1, berg2) !  Alon: MP updat this.
 ! Arguments
-type(iceberg), pointer :: berg1, berg2
+type(iceberg), pointer :: berg1 !< An iceberg
+type(iceberg), pointer :: berg2 !< An iceberg
 ! Local variables
   sameid=.false.
   if (berg1%start_year.ne.berg2%start_year) return
@@ -2352,11 +2446,12 @@ logical function sameid(berg1, berg2) !  Alon: MP updat this.
   sameid=.true. ! passing the above tests means that bergs 1 and 2 have the same id
 end function sameid
 
-! ##############################################################################
-
+!> Returns True if berg1 and berg2 are identical in both identifying properties
+!! and dynamic properties
 logical function sameberg(berg1, berg2)
 ! Arguments
-type(iceberg), pointer :: berg1, berg2
+type(iceberg), pointer :: berg1 !< An iceberg
+type(iceberg), pointer :: berg2 !< An iceberg
 ! Local variables
   sameberg=.false.
   if (.not. sameid(berg1, berg2)) return
@@ -2379,22 +2474,24 @@ logical function sameberg(berg1, berg2)
   sameberg=.true. ! passing the above tests mean that bergs 1 and 2 are identical
 end function sameberg
 
-! ##############################################################################
-
+!> Returns the year day (a single float for the day of the year, range 0-365.999...)
 real function yearday(imon, iday, ihr, imin, isec)
 ! Arguments
-integer, intent(in) :: imon, iday, ihr, imin, isec
+integer, intent(in) :: imon !< Month of year (1-12)
+integer, intent(in) :: iday !< Day of month (1-31)
+integer, intent(in) :: ihr !< Hour of day (0-23)
+integer, intent(in) :: imin !< Minute of hour (0-59)
+integer, intent(in) :: isec !< Second of minute (0-59)
 
   yearday=float(imon-1)*31.+float(iday-1)+(float(ihr)+(float(imin)+float(isec)/60.)/60.)/24.
 
 end function yearday
 
-! ##############################################################################
-
+!> Create a new berg with given values
 subroutine create_iceberg(berg, bergvals)
 ! Arguments
-type(iceberg), pointer :: berg
-type(iceberg), intent(in) :: bergvals
+type(iceberg), pointer :: berg !< Berg to be created
+type(iceberg), intent(in) :: bergvals !< Values to assign
 ! Local variables
 integer :: stderrunit
 
@@ -2413,11 +2510,13 @@ subroutine create_iceberg(berg, bergvals)
 end subroutine create_iceberg
 
 
-! ##############################################################################
-
+!> Delete a berg from a list and destroy the memory for the berg
+!!
+!! first is needed when berg is the first in the list
 subroutine delete_iceberg_from_list(first, berg)
 ! Arguments
-type(iceberg), pointer :: first, berg
+type(iceberg), pointer :: first !< List of bergs
+type(iceberg), pointer :: berg !< Berg to be deleted
 ! Local variables
 
   ! Connect neighbors to each other
@@ -2433,14 +2532,15 @@ subroutine delete_iceberg_from_list(first, berg)
 
 end subroutine delete_iceberg_from_list
 
-! ##############################################################################
-
+!> Destroy a berg
+!!
+!! Deallocates memory for a berg after deleting links to the berg recorded in bonds
 subroutine destroy_iceberg(berg)
 ! Arguments
 type(iceberg), pointer :: berg
 ! Local variables
 
-  ! Clears all matching bonds before deallocint memory
+  ! Clears all matching bonds before deallocating memory
   call clear_berg_from_partners_bonds(berg)
 
   ! Bye-bye berg
@@ -2448,14 +2548,14 @@ subroutine destroy_iceberg(berg)
 
 end subroutine destroy_iceberg
 
-! ##############################################################################
-
+!> Print the state of a particular berg
 subroutine print_berg(iochan, berg, label, il, jl)
 ! Arguments
-integer, intent(in) :: iochan
-type(iceberg), pointer :: berg
-character(len=*) :: label
-integer, optional, intent(in) :: il, jl !< Indices of cell berg should be in
+integer, intent(in) :: iochan !< Standard channel to use (usually stdout or stderr)
+type(iceberg), pointer :: berg !< Berg to print
+character(len=*) :: label !< Label to use in messages
+integer, optional, intent(in) :: il !< i-index of cell berg should be in
+integer, optional, intent(in) :: jl !< j-index of cell berg should be in
 ! Local variables
 
   write(iochan,'("diamonds, print_berg: ",2a,i5,a,i12,a,2f10.4,i5,f7.2,es12.4,f5.1)') &
@@ -2489,13 +2589,12 @@ subroutine print_berg(iochan, berg, label, il, jl)
     ' ui,vi=', berg%ui, berg%vi
 end subroutine print_berg
 
-! ##############################################################################
-
+!> Print the state of all bergs
 subroutine print_bergs(iochan, bergs, label)
 ! Arguments
-integer, intent(in) :: iochan
-type(icebergs), pointer :: bergs
-character(len=*) :: label
+integer, intent(in) :: iochan !< Standard channel to use (usually stdout or stderr)
+type(icebergs), pointer :: bergs !< Container for all types and memory
+character(len=*) :: label !< Label to use in messages
 ! Local variables
 integer :: nbergs, nnbergs
 type(iceberg), pointer :: this
@@ -2515,11 +2614,8 @@ subroutine print_bergs(iochan, bergs, label)
 
 end subroutine print_bergs
 
-
-! ##############################################################################
-
 subroutine form_a_bond(berg, other_berg_num, other_berg_ine, other_berg_jne, other_berg)
-
+! Arguments
 type(iceberg), pointer :: berg
 type(iceberg), optional,  pointer :: other_berg
 type(bond) , pointer :: new_bond, first_bond
@@ -2528,9 +2624,9 @@ subroutine form_a_bond(berg, other_berg_num, other_berg_ine, other_berg_jne, oth
 integer :: stderrunit
 
  stderrunit = stderr()
-    
+
 if (berg%iceberg_num .ne. other_berg_num) then
-              
+
  !write (stderrunit,*) , 'Forming a bond!!!', mpp_pe(), berg%iceberg_num, other_berg_num, berg%halo_berg, berg%ine, berg%jne
 
   ! Step 1: Create a new bond
@@ -2570,7 +2666,8 @@ end subroutine form_a_bond
 ! #############################################################################
 
 subroutine bond_address_update(bergs)
-type(icebergs), pointer :: bergs
+! Arguments
+type(icebergs), pointer :: bergs !< Container for all types and memory
 type(iceberg), pointer :: other_berg, berg
 type(icebergs_gridded), pointer :: grd
 integer :: grdi, grdj, nbonds
@@ -2589,7 +2686,7 @@ subroutine bond_address_update(bergs)
           current_bond%other_berg_ine=current_bond%other_berg%ine
           current_bond%other_berg_jne=current_bond%other_berg%jne
         else
-          if (berg%halo_berg .lt. 0.5) then     
+          if (berg%halo_berg .lt. 0.5) then
             call error_mesg('diamonds, bond address update', 'other berg in bond not assosiated!', FATAL)
           endif
         endif
@@ -2603,10 +2700,8 @@ subroutine bond_address_update(bergs)
 
 end subroutine bond_address_update
 
-!###################################################################################################
-
 subroutine show_all_bonds(bergs)
-type(icebergs), pointer :: bergs
+type(icebergs), pointer :: bergs !< Container for all types and memory
 type(iceberg), pointer :: other_berg, berg
 type(icebergs_gridded), pointer :: grd
 integer :: grdi, grdj, nbonds
@@ -2640,9 +2735,8 @@ subroutine show_all_bonds(bergs)
 
 end subroutine show_all_bonds
 
-
 subroutine connect_all_bonds(bergs)
-type(icebergs), pointer :: bergs
+type(icebergs), pointer :: bergs !< Container for all types and memory
 type(iceberg), pointer :: other_berg, berg
 type(icebergs_gridded), pointer :: grd
 integer :: i, j
@@ -2674,10 +2768,10 @@ subroutine connect_all_bonds(bergs)
               if (other_berg%iceberg_num .eq. current_bond%other_berg_num) then
                 current_bond%other_berg=>other_berg
                 other_berg=>null()
-                bond_matched=.true. 
+                bond_matched=.true.
               else
                 other_berg=>other_berg%next
-              endif 
+              endif
             enddo
           endif
           if (.not.bond_matched) then
@@ -2692,24 +2786,24 @@ subroutine connect_all_bonds(bergs)
                     if (other_berg%iceberg_num .eq. current_bond%other_berg_num) then
                       current_bond%other_berg=>other_berg
                       other_berg=>null()
-                      bond_matched=.true.  
+                      bond_matched=.true.
                     else
                       other_berg=>other_berg%next
-                    endif 
+                    endif
                   enddo
                 endif
               endif
             enddo;enddo
           endif
-          if (.not.bond_matched) then      
+          if (.not.bond_matched) then
             if (berg%halo_berg .lt. 0.5) then
-              missing_bond=.true.    
-              print * ,'non-halo berg unmatched: ', berg%iceberg_num, mpp_pe(), current_bond%other_berg_num, current_bond%other_berg_ine 
+              missing_bond=.true.
+              print * ,'non-halo berg unmatched: ', berg%iceberg_num, mpp_pe(), current_bond%other_berg_num, current_bond%other_berg_ine
               call error_mesg('diamonds, connect_all_bonds', 'A non-halo bond is missing!!!', FATAL)
             else  ! This is not a problem if the partner berg is not yet in the halo
               !if (  (current_bond%other_berg_ine .gt.grd%isd-1) .and. (current_bond%other_berg_ine .lt.grd%ied+1) &
-                !.and.  (current_bond%other_berg_jne .gt.grd%jsd-1) .and. (current_bond%other_berg_jne .lt.grd%jed+1) ) then      
-                !print * ,'halo berg unmatched: ',mpp_pe(),  berg%iceberg_num, current_bond%other_berg_num, current_bond%other_berg_ine,current_bond%other_berg_jne 
+                !.and.  (current_bond%other_berg_jne .gt.grd%jsd-1) .and. (current_bond%other_berg_jne .lt.grd%jed+1) ) then
+                !print * ,'halo berg unmatched: ',mpp_pe(),  berg%iceberg_num, current_bond%other_berg_num, current_bond%other_berg_ine,current_bond%other_berg_jne
                 !call error_mesg('diamonds, connect_all_bonds', 'A halo bond is missing!!!', WARNING)
               !endif
             endif
@@ -2728,11 +2822,9 @@ subroutine connect_all_bonds(bergs)
   endif
 end subroutine connect_all_bonds
 
-
-! #############################################################################
 subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
 
-type(icebergs), pointer :: bergs
+type(icebergs), pointer :: bergs !< Container for all types and memory
 type(iceberg), pointer :: berg
 type(iceberg), pointer :: other_berg
 type(icebergs_gridded), pointer :: grd
@@ -2744,7 +2836,7 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
 logical, intent(inout), optional :: check_bond_quality
 logical :: quality_check
 integer :: num_unmatched_bonds,num_unmatched_bonds_all_pe
-integer :: num_unassosiated_bond_pairs, num_unassosiated_bond_pairs_all_pe 
+integer :: num_unassosiated_bond_pairs, num_unassosiated_bond_pairs_all_pe
 integer :: stderrunit
 
 !  print *, "starting bond_check"
@@ -2776,12 +2868,12 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
           other_berg=>current_bond%other_berg
           if (associated(other_berg)) then
             other_berg_bond=>other_berg%first_bond
-            do while (associated(other_berg_bond))  !loops over the icebergs in the other icebergs bond list           
+            do while (associated(other_berg_bond))  !loops over the icebergs in the other icebergs bond list
               if (associated(other_berg_bond%other_berg)) then
                 if (other_berg_bond%other_berg%iceberg_num .eq.berg%iceberg_num) then
                   bond_is_good=.True.  !Bond_is_good becomes true when the corresponding bond is found
                 endif
-              endif                 
+              endif
               if (bond_is_good) then
                 other_berg_bond=>null()
               else
@@ -2791,12 +2883,12 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
 
             if (bond_is_good) then
               if (debug) write(stderrunit,*) 'Perfect quality Bond:', berg%iceberg_num, current_bond%other_berg_num
-            else  
+            else
               if (debug) write(stderrunit,*) 'Non-matching bond...:', berg%iceberg_num, current_bond%other_berg_num
               num_unmatched_bonds=num_unmatched_bonds+1
             endif
           else
-            if (debug) write(stderrunit,*) 'Opposite berg is not assosiated:', berg%iceberg_num, current_bond%other_berg%iceberg_num    
+            if (debug) write(stderrunit,*) 'Opposite berg is not assosiated:', berg%iceberg_num, current_bond%other_berg%iceberg_num
             num_unassosiated_bond_pairs=0
           endif
         endif
@@ -2811,7 +2903,7 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
     call mpp_sum(number_of_bonds_all_pe)
 
     bergs%nbonds=number_of_bonds_all_pe !Total number of bonds across all pe's
-    if (debug) then 
+    if (debug) then
       if (number_of_bonds .gt. 0) then
         write(stderrunit,*) "Bonds on PE:",number_of_bonds, "Total bonds", number_of_bonds_all_PE, "on PE number:",  mpp_pe()
       endif
@@ -2844,14 +2936,11 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
 
 end subroutine count_bonds
 
-
-
-! ##############################################################################
-
+!> Returns number of bergs across all lists
 integer function count_bergs(bergs, with_halos)
 ! Arguments
-type(icebergs), pointer :: bergs
-logical, optional :: with_halos
+type(icebergs), pointer :: bergs !< Container for all types and memory
+logical, optional :: with_halos !< If true, include halo lists
 ! Local variables
 integer :: grdi, grdj, is, ie, js, je
 logical :: include_halos
@@ -2871,11 +2960,10 @@ integer function count_bergs(bergs, with_halos)
 
 end function count_bergs
 
-! ##############################################################################
-
+!> Returns number of bergs in a list
 integer function count_bergs_in_list(first)
 ! Arguments
-type(iceberg), pointer :: first
+type(iceberg), pointer :: first !< List of bergs
 ! Local variables
 type(iceberg), pointer :: this
 
@@ -2888,11 +2976,10 @@ integer function count_bergs_in_list(first)
 
 end function count_bergs_in_list
 
-! ##############################################################################
-
+!> Add a record to the trajectory of each berg
 subroutine record_posn(bergs)
 ! Arguments
-type(icebergs), pointer :: bergs
+type(icebergs), pointer :: bergs !< Container for all types and memory
 ! Local variables
 type(xyt) :: posn
 type(iceberg), pointer :: this
@@ -2938,21 +3025,20 @@ subroutine record_posn(bergs)
         posn%halo_berg=this%halo_berg
         posn%static_berg=this%static_berg
       endif
-  
+
       call push_posn(this%trajectory, posn)
-  
+
       this=>this%next
     enddo
   enddo ; enddo
 
 end subroutine record_posn
 
-! ##############################################################################
-
+!> Add trajectory values as a new record in a trajectory
 subroutine push_posn(trajectory, posn_vals)
 ! Arguments
-type(xyt), pointer :: trajectory
-type(xyt) :: posn_vals
+type(xyt), pointer :: trajectory !< Trajectory list
+type(xyt) :: posn_vals !< Values to add
 ! Local variables
 type(xyt), pointer :: new_posn
 
@@ -2963,11 +3049,12 @@ subroutine push_posn(trajectory, posn_vals)
 
 end subroutine push_posn
 
+!> Appends trajectory values to the end of the trajectory list (slow)
+!! \todo append_posn() is very slow and should be removed a.s.a.p.
 subroutine append_posn(trajectory, posn_vals)
-! This routine appends a new position leaf to the end of the given trajectory 
 ! Arguments
-type(xyt), pointer :: trajectory
-type(xyt) :: posn_vals
+type(xyt), pointer :: trajectory !< Trajectory list
+type(xyt) :: posn_vals !< Values to add
 ! Local variables
 type(xyt), pointer :: new_posn,next,last
 
@@ -2987,12 +3074,11 @@ subroutine append_posn(trajectory, posn_vals)
   endif
 end subroutine append_posn
 
-! ##############################################################################
-
+!> Disconnect a trajectory from a berg and add it to a list of trajectory segments
 subroutine move_trajectory(bergs, berg)
 ! Arguments
-type(icebergs), pointer :: bergs
-type(iceberg), pointer :: berg
+type(icebergs), pointer :: bergs !< Container for all types and memory
+type(iceberg), pointer :: berg !< Berg containing trajectory
 ! Local variables
 type(xyt), pointer :: next, last
 type(xyt) :: vals
@@ -3030,17 +3116,17 @@ subroutine move_trajectory(bergs, berg)
 
 end subroutine move_trajectory
 
-! ##############################################################################
-
+!> Scan all bergs in a list and disconnect trajectories and more to the list of trajectory segments
+!! \todo The argument delete_bergs should be removed.
 subroutine move_all_trajectories(bergs, delete_bergs)
 ! Arguments
-type(icebergs),    pointer    :: bergs
-logical, optional, intent(in) :: delete_bergs
+type(icebergs),    pointer    :: bergs !< Container for all types and memory
+logical, optional, intent(in) :: delete_bergs !< If true, delete bergs after disconnecting its trajectory
 ! Local variables
 type(iceberg), pointer :: this, next
 logical :: delete_bergs_after_moving_traj
 integer :: grdi, grdj
-  
+
   if (bergs%ignore_traj) return
 
   delete_bergs_after_moving_traj = .false.
@@ -3057,22 +3143,23 @@ subroutine move_all_trajectories(bergs, delete_bergs)
 
 end subroutine move_all_trajectories
 
-! ##############################################################################
-
+!> Search the grid for a cell containing position x,y
 logical function find_cell_by_search(grd, x, y, i, j)
 ! Arguments
-type(icebergs_gridded), pointer :: grd
-real, intent(in) :: x, y
-integer, intent(inout) :: i, j
+type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+real, intent(in) :: x !< Longitude of position
+real, intent(in) :: y !< Latitude of position
+integer, intent(inout) :: i !< i-index of cell containing x,y
+integer, intent(inout) :: j !< j-index of cell containing x,y
 ! Local variables
 integer :: is,ie,js,je,di,dj,io,jo,icnt
 real :: d0,d1,d2,d3,d4,d5,d6,d7,d8,dmin
 logical :: explain=.false.
 real :: Lx
- 
+
 911 continue
 
-  Lx=grd%Lx  
+  Lx=grd%Lx
   find_cell_by_search=.false.
   is=grd%isc; ie=grd%iec; js=grd%jsc; je=grd%jec
 
@@ -3100,7 +3187,7 @@ logical function find_cell_by_search(grd, x, y, i, j)
     find_cell_by_search=.true.
     return
   endif
-    
+
   do icnt=1, 1*(ie-is+je-js)
     io=i; jo=j
 
@@ -3143,7 +3230,7 @@ logical function find_cell_by_search(grd, x, y, i, j)
       find_cell_by_search=.true.
       return
     endif
-    
+
     if ((i==io.and.j==jo) &
         .and. .not.find_better_min(grd, x, y, 3, i, j) &
        ) then
@@ -3191,7 +3278,7 @@ logical function find_cell_by_search(grd, x, y, i, j)
 
   contains
 
-! # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
+! # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
 
   real function dcost(x1, y1, x2, y2,Lx)
   ! Arguments
@@ -3204,11 +3291,11 @@ real function dcost(x1, y1, x2, y2,Lx)
     dcost=(x2-x1m)**2+(y2-y1)**2
   end function dcost
 
-! # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
+! # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
 
   logical function find_better_min(grd, x, y, w, oi, oj)
   ! Arguments
-  type(icebergs_gridded), intent(in) :: grd
+  type(icebergs_gridded), intent(in) :: grd !< Container for gridded fields
   real, intent(in) :: x, y
   integer, intent(in) :: w
   integer, intent(inout) :: oi, oj
@@ -3237,11 +3324,11 @@ logical function find_better_min(grd, x, y, w, oi, oj)
 
   end function find_better_min
 
-! # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
+! # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
 
   logical function find_cell_loc(grd, x, y, is, ie, js, je, w, oi, oj)
   ! Arguments
-  type(icebergs_gridded), intent(in) :: grd
+  type(icebergs_gridded), intent(in) :: grd !< Container for gridded fields
   real, intent(in) :: x, y
   integer, intent(in) :: is, ie, js, je, w
   integer, intent(inout) :: oi, oj
@@ -3265,18 +3352,19 @@ end function find_cell_loc
 
 end function find_cell_by_search
 
-
-! ##############################################################################
-
-subroutine find_individual_iceberg(bergs,iceberg_num, ine, jne, berg_found, search_data_domain)
-type(icebergs), pointer :: bergs
+!> Returns the i,j of cell containing an iceberg with the given identifier
+subroutine find_individual_iceberg(bergs, iceberg_num, ine, jne, berg_found, search_data_domain)
+! Arguments
+type(icebergs), pointer :: bergs !< Container for all types and memory
+integer, intent(in) :: iceberg_num !< Berg identifier
+integer, intent(out) :: ine !< i-index of cell containing berg
+integer, intent(out) :: jne !< j-index of cell containing berg
+logical, intent(in) :: search_data_domain !< If true, search halos too
+real, intent(out) :: berg_found !< Returns 1.0 if berg is found, 0. otherwise
+! Local variables
 type(iceberg), pointer :: this
 type(icebergs_gridded), pointer :: grd
 integer :: grdi, grdj
-integer, intent(in) :: iceberg_num
-logical, intent(in) :: search_data_domain
-integer, intent(out) :: ine, jne
-real, intent(out) :: berg_found
 integer :: ilim1, ilim2, jlim1, jlim2
 
 berg_found=0.0
@@ -3284,7 +3372,7 @@ subroutine find_individual_iceberg(bergs,iceberg_num, ine, jne, berg_found, sear
 jne=999
   ! For convenience
     grd=>bergs%grd
-    
+
     if (search_data_domain) then
         ilim1 = grd%isd  ; ilim2=grd%ied  ; jlim1 = grd%jsd  ; jlim2=grd%jed
     else
@@ -3306,17 +3394,17 @@ subroutine find_individual_iceberg(bergs,iceberg_num, ine, jne, berg_found, sear
         endif
         this=>this%next
       enddo
-    enddo ; enddo                                                                             
-end subroutine  find_individual_iceberg 
-
-
-! ##############################################################################
+    enddo ; enddo
+end subroutine  find_individual_iceberg
 
-logical function find_cell(grd, x, y, oi, oj) 
+!> Scans each computational grid cell until is_point_in_cell() is true
+logical function find_cell(grd, x, y, oi, oj)
 ! Arguments
-type(icebergs_gridded), intent(in) :: grd
-real, intent(in) :: x, y
-integer, intent(out) :: oi, oj
+type(icebergs_gridded), intent(in) :: grd !< Container for gridded fields
+real, intent(in) :: x !< Longitude of position
+real, intent(in) :: y !< Latitude of position
+integer, intent(out) :: oi !< i-index of cell containing position or -999
+integer, intent(out) :: oj !< j-index of cell containing position or -999
 ! Local variables
 integer :: i,j
 
@@ -3331,13 +3419,14 @@ logical function find_cell(grd, x, y, oi, oj)
 
 end function find_cell
 
-! ##############################################################################
-
+!> Scans each all grid cells until is_point_in_cell() is true (includes halos)
 logical function find_cell_wide(grd, x, y, oi, oj)
 ! Arguments
-type(icebergs_gridded), intent(in) :: grd
-real, intent(in) :: x, y
-integer, intent(out) :: oi, oj
+type(icebergs_gridded), intent(in) :: grd !< Container for gridded fields
+real, intent(in) :: x !< Longitude of position
+real, intent(in) :: y !< Latitude of position
+integer, intent(out) :: oi !< i-index of cell containing position or -999
+integer, intent(out) :: oj !< j-index of cell containing position or -999
 ! Local variables
 integer :: i,j
 
@@ -3352,14 +3441,15 @@ logical function find_cell_wide(grd, x, y, oi, oj)
 
 end function find_cell_wide
 
-! ##############################################################################
-
+!> Returns True if x,y is in cell i,j
 logical function is_point_in_cell(grd, x, y, i, j, explain)
 ! Arguments
-type(icebergs_gridded), intent(in) :: grd
-real, intent(in) :: x, y
-integer, intent(in) :: i, j
-logical, intent(in), optional :: explain
+type(icebergs_gridded), intent(in) :: grd !< Container for gridded fields
+real, intent(in) :: x !< Longitude of position
+real, intent(in) :: y !< Latitude of position
+integer, intent(in) :: i !< i-index of cell
+integer, intent(in) :: j !< j-index of cell
+logical, intent(in), optional :: explain !< If true, print debugging
 ! Local variables
 real :: xlo, xhi, ylo, yhi
 integer :: stderrunit
@@ -3381,11 +3471,11 @@ logical function is_point_in_cell(grd, x, y, i, j, explain)
   is_point_in_cell=.false.
 
   ! Test crude bounds
-  xlo=min( apply_modulo_around_point(grd%lon(i-1,j-1)   ,x,  Lx), & 
+  xlo=min( apply_modulo_around_point(grd%lon(i-1,j-1)   ,x,  Lx), &
            apply_modulo_around_point(grd%lon(i  ,j-1)   ,x,  Lx), &
            apply_modulo_around_point(grd%lon(i-1,j  )   ,x,  Lx), &
            apply_modulo_around_point(grd%lon(i  ,j  )   ,x,  Lx) )
-  xhi=max( apply_modulo_around_point(grd%lon(i-1,j-1)   ,x,  Lx), & 
+  xhi=max( apply_modulo_around_point(grd%lon(i-1,j-1)   ,x,  Lx), &
            apply_modulo_around_point(grd%lon(i  ,j-1)   ,x,  Lx), &
            apply_modulo_around_point(grd%lon(i-1,j  )   ,x,  Lx), &
            apply_modulo_around_point(grd%lon(i  ,j  )   ,x,  Lx) )
@@ -3393,57 +3483,66 @@ logical function is_point_in_cell(grd, x, y, i, j, explain)
   ! The modolo function inside sum_sign_dot_prod leads to a roundoff.
   !Adding adding a tolorance to the crude bounds avoids excluding the cell which
   !would be correct after roundoff. This is a bit of a hack.
-  tol=0.1 
+  tol=0.1
   if (x.lt.(xlo-tol) .or. x.gt.(xhi+tol)) return
 
   ylo=min( grd%lat(i-1,j-1), grd%lat(i,j-1), grd%lat(i-1,j), grd%lat(i,j) )
   yhi=max( grd%lat(i-1,j-1), grd%lat(i,j-1), grd%lat(i-1,j), grd%lat(i,j) )
   if (y.lt.ylo .or. y.gt.yhi) return
-  
+
   if ((grd%lat(i,j).gt.89.999).and. (grd%grid_is_latlon))   then
     is_point_in_cell=sum_sign_dot_prod5(grd%lon(i-1,j-1),grd%lat(i-1,j-1), &
                                         grd%lon(i  ,j-1),grd%lat(i  ,j-1), &
                                         grd%lon(i  ,j-1),grd%lat(i  ,j  ), &
                                         grd%lon(i-1,j  ),grd%lat(i  ,j  ), &
                                         grd%lon(i-1,j  ),grd%lat(i-1,j  ), &
-                                        x, y, Lx,explain=explain) 
+                                        x, y, Lx,explain=explain)
   elseif ((grd%lat(i-1,j).gt.89.999) .and. (grd%grid_is_latlon))  then
     is_point_in_cell=sum_sign_dot_prod5(grd%lon(i-1,j-1),grd%lat(i-1,j-1), &
                                         grd%lon(i  ,j-1),grd%lat(i  ,j-1), &
                                         grd%lon(i  ,j  ),grd%lat(i  ,j  ), &
                                         grd%lon(i  ,j  ),grd%lat(i-1,j  ), &
                                         grd%lon(i-1,j-1),grd%lat(i-1,j  ), &
-                                        x, y,Lx, explain=explain) 
+                                        x, y,Lx, explain=explain)
   elseif ((grd%lat(i-1,j-1).gt.89.999) .and. (grd%grid_is_latlon))  then
     is_point_in_cell=sum_sign_dot_prod5(grd%lon(i-1,j  ),grd%lat(i-1,j-1), &
                                         grd%lon(i  ,j-1),grd%lat(i-1,j-1), &
                                         grd%lon(i  ,j-1),grd%lat(i  ,j-1), &
                                         grd%lon(i  ,j  ),grd%lat(i  ,j  ), &
                                         grd%lon(i-1,j  ),grd%lat(i-1,j  ), &
-                                        x, y,Lx, explain=explain) 
+                                        x, y,Lx, explain=explain)
   elseif ((grd%lat(i,j-1).gt.89.999) .and. (grd%grid_is_latlon)) then
     is_point_in_cell=sum_sign_dot_prod5(grd%lon(i-1,j-1),grd%lat(i-1,j-1), &
                                         grd%lon(i-1,j-1),grd%lat(i  ,j-1), &
                                         grd%lon(i  ,j  ),grd%lat(i  ,j-1), &
                                         grd%lon(i  ,j  ),grd%lat(i  ,j  ), &
                                         grd%lon(i-1,j  ),grd%lat(i-1,j  ), &
-                                        x, y, Lx,explain=explain) 
+                                        x, y, Lx,explain=explain)
   else
   is_point_in_cell=sum_sign_dot_prod4(grd%lon(i-1,j-1),grd%lat(i-1,j-1), &
                                       grd%lon(i  ,j-1),grd%lat(i  ,j-1), &
                                       grd%lon(i  ,j  ),grd%lat(i  ,j  ), &
                                       grd%lon(i-1,j  ),grd%lat(i-1,j  ), &
-                                      x, y,Lx, explain=explain) 
+                                      x, y,Lx, explain=explain)
   endif
 
 end function is_point_in_cell
 
-! ##############################################################################
-
-logical function sum_sign_dot_prod4(x0, y0, x1, y1, x2, y2, x3, y3, x, y,Lx, explain)
+!> Returns true if point x,y is inside polygon with four corners
+logical function sum_sign_dot_prod4(x0, y0, x1, y1, x2, y2, x3, y3, x, y, Lx, explain)
 ! Arguments
-real, intent(in) :: x0, y0, x1, y1, x2, y2, x3, y3, x, y, Lx
-logical, intent(in), optional :: explain
+real, intent(in) :: x0 !< Longitude of first corner
+real, intent(in) :: y0 !< Latitude of first corner
+real, intent(in) :: x1 !< Longitude of second corner
+real, intent(in) :: y1 !< Latitude of second corner
+real, intent(in) :: x2 !< Longitude of third corner
+real, intent(in) :: y2 !< Latitude of third corner
+real, intent(in) :: x3 !< Longitude of fourth corner
+real, intent(in) :: y3 !< Latitude of fourth corner
+real, intent(in) :: x !< Longitude of point
+real, intent(in) :: y !< Latitude of point
+real, intent(in) :: Lx !< Length of domain in zonal direction
+logical, intent(in), optional :: explain !< If true, print debugging
 ! Local variables
 real :: p0,p1,p2,p3,xx
 real :: l0,l1,l2,l3
@@ -3466,7 +3565,7 @@ logical function sum_sign_dot_prod4(x0, y0, x1, y1, x2, y2, x3, y3, x, y,Lx, exp
   l2=(xx-xx2)*(y3-y2)-(y-y2)*(xx3-xx2)
   l3=(xx-xx3)*(y0-y3)-(y-y3)*(xx0-xx3)
 
-  !We use an assymerty between South and East line boundaries and North and East
+  !We use an asymmetry between South and East line boundaries and North and East
   !to avoid icebergs appearing to two cells (half values used for debugging)
   !This is intended to make the South and East boundaries be part of the
   !cell, while the North and West are not part of the cell.
@@ -3497,12 +3596,23 @@ logical function sum_sign_dot_prod4(x0, y0, x1, y1, x2, y2, x3, y3, x, y,Lx, exp
 
 end function sum_sign_dot_prod4
 
-! ##############################################################################
-
+!> Returns true if point x,y is inside polygon with five corners
 logical function sum_sign_dot_prod5(x0, y0, x1, y1, x2, y2, x3, y3, x4, y4, x, y, Lx, explain)
 ! Arguments
-real, intent(in) :: x0, y0, x1, y1, x2, y2, x3, y3, x4, y4, x, y, Lx
-logical, intent(in), optional :: explain
+real, intent(in) :: x0 !< Longitude of first corner
+real, intent(in) :: y0 !< Latitude of first corner
+real, intent(in) :: x1 !< Longitude of second corner
+real, intent(in) :: y1 !< Latitude of second corner
+real, intent(in) :: x2 !< Longitude of third corner
+real, intent(in) :: y2 !< Latitude of third corner
+real, intent(in) :: x3 !< Longitude of fourth corner
+real, intent(in) :: y3 !< Latitude of fourth corner
+real, intent(in) :: x4 !< Longitude of fifth corner
+real, intent(in) :: y4 !< Latitude of fifth corner
+real, intent(in) :: x !< Longitude of point
+real, intent(in) :: y !< Latitude of point
+real, intent(in) :: Lx !< Length of domain in zonal direction
+logical, intent(in), optional :: explain !< If true, print debugging
 ! Local variables
 real :: p0,p1,p2,p3,p4,xx
 real :: l0,l1,l2,l3,l4
@@ -3554,15 +3664,17 @@ logical function sum_sign_dot_prod5(x0, y0, x1, y1, x2, y2, x3, y3, x4, y4, x, y
 
 end function sum_sign_dot_prod5
 
-! ##############################################################################
-
+!> Calculates non-dimensional position with cell i,j and returns true if point is in cell
 logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
 ! Arguments
-type(icebergs_gridded), intent(in) :: grd
-real, intent(in) :: x, y
-integer, intent(in) :: i, j
-real, intent(out) :: xi, yj
-logical, intent(in), optional :: explain
+type(icebergs_gridded), intent(in) :: grd !< Container for gridded fields
+real, intent(in) :: x !< Longitude of position
+real, intent(in) :: y !< Latitude of position
+integer, intent(in) :: i !< i-index of cell
+integer, intent(in) :: j !< j-index of cell
+real, intent(out) :: xi !< Non-dimensional x-position within cell
+real, intent(out) :: yj !< Non-dimensional y-position within cell
+logical, intent(in), optional :: explain !< If true, print debugging
 ! Local variables
 real :: x1,y1,x2,y2,x3,y3,x4,y4,xx,yy,fac
 integer :: stderrunit
@@ -3692,11 +3804,23 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
 
   contains
 
-  subroutine calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x, y, xi, yj,Lx, explain)
+  !> Calculates non-dimension position of x,y within a polygon with four corners
+  subroutine calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x, y, xi, yj, Lx, explain)
   ! Arguments
-  real,  intent(in) :: x1, x2, x3, x4, y1, y2, y3, y4, x, y, Lx
-  real, intent(out) :: xi, yj
-  logical, intent(in), optional :: explain
+  real, intent(in) :: x1 !< Longitude of first corner
+  real, intent(in) :: y1 !< Latitude of first corner
+  real, intent(in) :: x2 !< Longitude of second corner
+  real, intent(in) :: y2 !< Latitude of second corner
+  real, intent(in) :: x3 !< Longitude of third corner
+  real, intent(in) :: y3 !< Latitude of third corner
+  real, intent(in) :: x4 !< Longitude of fourth corner
+  real, intent(in) :: y4 !< Latitude of fourth corner
+  real, intent(in) :: x !< Longitude of point
+  real, intent(in) :: y !< Latitude of point
+  real, intent(out) :: xi !< Non-dimensional x-position within cell
+  real, intent(out) :: yj !< Non-dimensional y-position within cell
+  real, intent(in) :: Lx !< Length of domain in zonal direction
+  logical, intent(in), optional :: explain !< If true, print debugging
   ! Local variables
   real :: alpha, beta, gamma, delta, epsilon, kappa, a, b, c, d, dx, dy, yy1, yy2
   logical :: expl=.false.
@@ -3780,11 +3904,14 @@ end subroutine calc_xiyj
 
 end function pos_within_cell
 
-! ##############################################################################
-
+!> Returns true if non-dimensional position xi,yj is in unit interval
+!!
+!! Includes South and East boundaries, and excludes North and West.
+!! \todo Double check definition of is_point_within_xi_yj_bounds()
 logical function is_point_within_xi_yj_bounds(xi,yj)
 ! Arguments
-real, intent(in) :: xi, yj
+real, intent(in) :: xi !< Non-dimensional x-position
+real, intent(in) :: yj !< Non-dimensional y-position
 ! Local variables
 !Includes South and East boundaries, and excludes North and West  (double check this is the way that is needed)
   is_point_within_xi_yj_bounds=.False.
@@ -3795,13 +3922,17 @@ logical function is_point_within_xi_yj_bounds(xi,yj)
   endif
 end function is_point_within_xi_yj_bounds
 
-real function apply_modulo_around_point(x,y,Lx)
+!> Modulo value of x in an interval [y-(Lx/2)  y+(Lx/2)]
+!!
+!! Gives the modulo value of x in an interval [y-(Lx/2)  y+(Lx/2)]  , modulo Lx
+!! If Lx<=0, then it returns x without applying modulo arithmetic.
+real function apply_modulo_around_point(x, y, Lx)
 ! Arguments
-real, intent(in) :: x ,y ,Lx
+real, intent(in) :: x !< Value to apply modulo arithmetic to
+real, intent(in) :: y !< Center of modulo range
+real, intent(in) :: Lx !< Modulo width
 !Local_variables
 real ::Lx_2
-!Gives the modula value of x in an interval [y-(Lx/2)  y+(Lx/2)]  , modulo Lx
-!If Lx<=0, then it returns x without applying modulo arithmetic.
 
   if (Lx>0.) then
     Lx_2=Lx/2.
@@ -3812,12 +3943,14 @@ real function apply_modulo_around_point(x,y,Lx)
 
 end function apply_modulo_around_point
 
+!> Checks that a berg's position metrics are consistent
 subroutine check_position(grd, berg, label, il, jl)
 ! Arguments
-type(icebergs_gridded), pointer :: grd
-type(iceberg), pointer :: berg
-character(len=*) :: label
-integer, optional, intent(in) :: il, jl !< Indices of cell berg should be in
+type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+type(iceberg), pointer :: berg !< Berg to check
+character(len=*) :: label !< Label to add to messages
+integer, optional, intent(in) :: il !< i-index of cell berg should be in
+integer, optional, intent(in) :: jl !< j-index of cell berg should be in
 ! Local variables
 real :: xi, yj
 logical :: lret
@@ -3840,12 +3973,12 @@ subroutine check_position(grd, berg, label, il, jl)
 
 end subroutine check_position
 
-! ##############################################################################
-
-real function sum_mass(bergs,justbits,justbergs)
+!> Add up the mass of bergs and/or bergy bits
+real function sum_mass(bergs, justbits, justbergs)
 ! Arguments
-type(icebergs), pointer :: bergs
-logical, intent(in), optional :: justbits, justbergs
+type(icebergs), pointer :: bergs !< Container for all types and memory
+logical, intent(in), optional :: justbits !< If present, add up mass of just bergy bits
+logical, intent(in), optional :: justbergs !< If present, add up mass of just bergs
 ! Local variables
 type(iceberg), pointer :: this
 integer :: grdi, grdj
@@ -3867,12 +4000,12 @@ real function sum_mass(bergs,justbits,justbergs)
 
 end function sum_mass
 
-! ##############################################################################
-
+!> Add up the heat content of bergs and/or bergy bits
 real function sum_heat(bergs,justbits,justbergs)
 ! Arguments
-type(icebergs), pointer :: bergs
-logical, intent(in), optional :: justbits, justbergs
+type(icebergs), pointer :: bergs !< Container for all types and memory
+logical, intent(in), optional :: justbits !< If present, add up heat content of just bergy bits
+logical, intent(in), optional :: justbergs !< If present, add up heat content of just bergs
 ! Local variables
 type(iceberg), pointer :: this
 real :: dm
@@ -3897,11 +4030,11 @@ real function sum_heat(bergs,justbits,justbergs)
 
 end function sum_heat
 
-
-subroutine sanitize_field(arr,val)
+!> Set elements of an array to 0. if the absolute value is larger than a given value
+subroutine sanitize_field(arr, val)
 ! Arguments
-real, dimension(:,:),intent(inout) :: arr
-real, intent(in) :: val
+real, dimension(:,:),intent(inout) :: arr !< Array to sanitize
+real, intent(in) :: val !< Threshold value to use for sanitizing
 ! Local variables
 integer :: i, j
 
@@ -3913,17 +4046,11 @@ subroutine sanitize_field(arr,val)
 
 end subroutine sanitize_field
 
-! ##############################################################################
-
-
-
-
-! ##############################################################################
-
+!> Calculates checksums for all gridded fields
 subroutine checksum_gridded(grd, label)
 ! Arguments
-type(icebergs_gridded), pointer :: grd
-character(len=*) :: label
+type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+character(len=*) :: label !< Label to use in messages
 ! Local variables
 
   if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') 'diamonds: checksumming gridded data @ ',trim(label)
@@ -3985,13 +4112,12 @@ subroutine checksum_gridded(grd, label)
 
 end subroutine checksum_gridded
 
-! ##############################################################################
-
+!> Calculates checksum for a 3d field
 subroutine grd_chksum3(grd, fld, txt)
 ! Arguments
-type(icebergs_gridded), pointer :: grd
-real, dimension(:,:,:), intent(in) :: fld
-character(len=*), intent(in) :: txt
+type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+real, dimension(:,:,:), intent(in) :: fld !< Field to checksum
+character(len=*), intent(in) :: txt !< Label to use in message
 ! Local variables
 integer :: i, j, k, halo, icount, io, jo
 real :: mean, rms, SD, minv, maxv
@@ -4057,13 +4183,12 @@ subroutine grd_chksum3(grd, fld, txt)
 
 end subroutine grd_chksum3
 
-! ##############################################################################
-
+!> Calculates checksum for a 2d field
 subroutine grd_chksum2(grd, fld, txt)
 ! Arguments
-type(icebergs_gridded), pointer :: grd
-real, dimension(grd%isd:grd%ied,grd%jsd:grd%jed), intent(in) :: fld
-character(len=*), intent(in) :: txt
+type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+real, dimension(grd%isd:grd%ied,grd%jsd:grd%jed), intent(in) :: fld !< Field to checksum
+character(len=*), intent(in) :: txt !< Label to use in message
 ! Local variables
 integer :: i, j, icount
 real :: mean, rms, SD, minv, maxv
@@ -4115,12 +4240,11 @@ subroutine grd_chksum2(grd, fld, txt)
 
 end subroutine grd_chksum2
 
-! ##############################################################################
-
+!> Calculates checksums for all bergs
 subroutine bergs_chksum(bergs, txt, ignore_halo_violation)
 ! Arguments
-type(icebergs), pointer :: bergs
-character(len=*), intent(in) :: txt
+type(icebergs), pointer :: bergs !< Container for all types and memory
+character(len=*), intent(in) :: txt !< Label to use in messages
 logical, optional :: ignore_halo_violation
 ! Local variables
 integer :: i, nbergs, ichk1, ichk2, ichk3, ichk4, ichk5, iberg
@@ -4217,11 +4341,10 @@ subroutine bergs_chksum(bergs, txt, ignore_halo_violation)
 
 end subroutine bergs_chksum
 
-! ##############################################################################
-
+!> Checksum a list of bergs
 integer function list_chksum(first)
 ! Arguments
-type(iceberg), pointer :: first
+type(iceberg), pointer :: first !< List of bergs
 ! Local variables
 integer :: i
 type(iceberg), pointer :: this
@@ -4236,11 +4359,10 @@ integer function list_chksum(first)
 
 end function list_chksum
 
-! ##############################################################################
-
+!> Checksum a berg
 integer function berg_chksum(berg)
 ! Arguments
-type(iceberg), pointer :: berg
+type(iceberg), pointer :: berg !< An iceberg
 ! Local variables
 real :: rtmp(38) !Changed from 28 to 34 by Alon
 integer :: itmp(38+4), i8=0, ichk1, ichk2, ichk3 !Changed from 28 to 34 by Alon
@@ -4274,24 +4396,24 @@ integer function berg_chksum(berg)
   rtmp(26)=berg%ssh_y
   rtmp(27)=berg%cn
   rtmp(28)=berg%hi
-  rtmp(29)=berg%axn 
-  rtmp(30)=berg%ayn 
-  rtmp(31)=berg%bxn 
-  rtmp(32)=berg%byn 
-  rtmp(33)=berg%uvel_old 
-  rtmp(34)=berg%vvel_old 
-  rtmp(35)=berg%lat_old 
-  rtmp(36)=berg%lon_old 
-  itmp(37)=berg%halo_berg 
-  itmp(38)=berg%static_berg 
-  itmp(1:38)=transfer(rtmp,i8) 
-  itmp(39)=berg%start_year 
-  itmp(40)=berg%ine 
-  itmp(41)=berg%jne 
-  itmp(42)=berg%iceberg_num 
+  rtmp(29)=berg%axn
+  rtmp(30)=berg%ayn
+  rtmp(31)=berg%bxn
+  rtmp(32)=berg%byn
+  rtmp(33)=berg%uvel_old
+  rtmp(34)=berg%vvel_old
+  rtmp(35)=berg%lat_old
+  rtmp(36)=berg%lon_old
+  itmp(37)=berg%halo_berg
+  itmp(38)=berg%static_berg
+  itmp(1:38)=transfer(rtmp,i8)
+  itmp(39)=berg%start_year
+  itmp(40)=berg%ine
+  itmp(41)=berg%jne
+  itmp(42)=berg%iceberg_num
 
   ichk1=0; ichk2=0; ichk3=0
-  do i=1,38+4 
+  do i=1,38+4
    ichk1=ichk1+itmp(i)
    ichk2=ichk2+itmp(i)*i
    ichk3=ichk3+itmp(i)*i*i
@@ -4300,13 +4422,15 @@ integer function berg_chksum(berg)
 
 end function berg_chksum
 
-! ##############################################################################
-
+!> Bi-linear interpolate a field at corners in cell i,j to non-dimensional position xi,yj
 real function bilin(grd, fld, i, j, xi, yj)
 ! Arguments
-type(icebergs_gridded), pointer :: grd
-real, intent(in) :: fld(grd%isd:grd%ied,grd%jsd:grd%jed), xi, yj
-integer, intent(in) :: i, j
+type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+real, intent(in) :: fld(grd%isd:grd%ied,grd%jsd:grd%jed) !< Field to interpolate
+real, intent(in) :: xi !< Non-dimensional x-position within cell
+real, intent(in) :: yj !< Non-dimensional y-position within cell
+integer, intent(in) :: i !< i-index of cell
+integer, intent(in) :: j !< j-index of cell
 ! Local variables
 
   if (old_bug_bilin) then
@@ -4318,13 +4442,12 @@ real function bilin(grd, fld, i, j, xi, yj)
   endif
 end function bilin
 
-! ##############################################################################
-
+!> Prints a field
 subroutine print_fld(grd, fld, label)
 ! Arguments
-type(icebergs_gridded), pointer :: grd
-real, intent(in) :: fld(grd%isd:grd%ied,grd%jsd:grd%jed)
-character(len=*) :: label
+type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+real, intent(in) :: fld(grd%isd:grd%ied,grd%jsd:grd%jed) !< Field to print
+character(len=*) :: label !< Label to use in title
 ! Local variables
 integer :: i, j
 integer :: stderrunit
@@ -4339,12 +4462,11 @@ subroutine print_fld(grd, fld, label)
 
 end subroutine print_fld
 
-! ##############################################################################
-
+!> Invoke some unit tests
 logical function unitTests(bergs)
-  type(icebergs), pointer :: bergs
-  type(icebergs_gridded), pointer :: grd
+  type(icebergs), pointer :: bergs !< Container for all types and memory
   ! Local variables
+  type(icebergs_gridded), pointer :: grd
   integer :: stderrunit,i,j
 
   ! This function returns True is a unit test fails
@@ -4352,7 +4474,7 @@ logical function unitTests(bergs)
   ! For convenience
   grd=>bergs%grd
   stderrunit=stderr()
-  
+
   i=grd%isc; j=grd%jsc
   call localTest( bilin(grd, grd%lon, i, j, 0., 1.), grd%lon(i-1,j) )
   call localTest( bilin(grd, grd%lon, i, j, 1., 1.), grd%lon(i,j) )
@@ -4360,6 +4482,8 @@ logical function unitTests(bergs)
   call localTest( bilin(grd, grd%lat, i, j, 1., 1.), grd%lat(i,j) )
 
   contains
+
+  !> Checks answer to right answer and prints results if different
   subroutine localTest(answer, rightAnswer)
   real, intent(in) :: answer, rightAnswer
   if (answer==rightAnswer) return
@@ -4368,12 +4492,11 @@ subroutine localTest(answer, rightAnswer)
   end subroutine localTest
 end function unitTests
 
-! ##############################################################################
-
 !> Check for duplicates of icebergs on and across processors and issue an error
 !! if any are detected
 subroutine check_for_duplicates_in_parallel(bergs)
-  type(icebergs), pointer :: bergs !< Icebergs
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
   ! Local variables
   type(icebergs_gridded), pointer :: grd
   type(iceberg), pointer :: this
@@ -4410,9 +4533,11 @@ end subroutine check_for_duplicates_in_parallel
 
 !> Returns error count of duplicates of integer values in a distributed list
 integer function check_for_duplicate_ids_in_list(nbergs, ids, verbose)
+  ! Arguments
   integer,               intent(in)    :: nbergs !< Length of ids
   integer, dimension(:), intent(inout) :: ids !< List of ids
   logical,               intent(in)    :: verbose !< True if messages should be written
+  ! Local variables
   integer :: stderrunit, i, j, k, l, nbergs_total, ii, lowest_id, nonexistent_id
   logical :: have_berg
 
@@ -4478,7 +4603,9 @@ integer function check_for_duplicate_ids_in_list(nbergs, ids, verbose)
 
 end function check_for_duplicate_ids_in_list
 
+!> Unit test for check_for_duplicate_ids_in_list()
 subroutine test_check_for_duplicate_ids_in_list()
+  ! Local variables
   integer :: k
   integer, dimension(:), allocatable :: ids
   integer :: error_count
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index b8bee75..b55b229 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -1,5 +1,8 @@
+!> Handles reading/writing of restart files and trajectory-based diagnostic files
 module ice_bergs_io
 
+! This file is part of NOAA-GFDL/icebergs. See LICENSE.md for the license.
+
 use mpp_domains_mod, only: domain2D
 use mpp_domains_mod, only: mpp_domain_is_tile_root_pe,mpp_get_domain_tile_root_pe
 use mpp_domains_mod, only: mpp_get_tile_pelist,mpp_get_tile_npes,mpp_get_io_domain,mpp_get_tile_id
@@ -66,9 +69,10 @@ module ice_bergs_io
 
 contains
 
+!> Initialize parallel i/o
 subroutine ice_bergs_io_init(bergs, io_layout)
-type(icebergs), pointer :: bergs
-integer, intent(in) :: io_layout(2)
+type(icebergs), pointer :: bergs !< Icebergs container
+integer, intent(in) :: io_layout(2) !< Decomposition of i/o processors
 
 integer :: np
 integer :: stdlogunit, stderrunit
@@ -78,7 +82,7 @@ subroutine ice_bergs_io_init(bergs, io_layout)
   stdlogunit=stdlog()
   write(stdlogunit,*) "ice_bergs_framework: "//trim(version)
 
-  !I/O layout init 
+  !I/O layout init
   io_tile_id=-1
   io_domain => mpp_get_io_domain(bergs%grd%domain)
   if(associated(io_domain)) then
@@ -96,13 +100,12 @@ subroutine ice_bergs_io_init(bergs, io_layout)
 
 end subroutine ice_bergs_io_init
 
-! ##############################################################################
-
+!> Write an iceberg restart file
 subroutine write_restart(bergs)
 ! Arguments
-type(icebergs), pointer :: bergs
-type(bond), pointer :: current_bond
+type(icebergs), pointer :: bergs !< Icebergs container
 ! Local variables
+type(bond), pointer :: current_bond
 integer :: i,j,id
 character(len=35) :: filename
 character(len=35) :: filename_bonds
@@ -113,7 +116,7 @@ subroutine write_restart(bergs)
 type(restart_file_type) :: bergs_bond_restart
 integer :: nbergs, nbonds
 integer :: n_static_bergs
-logical :: check_bond_quality 
+logical :: check_bond_quality
 type(icebergs_gridded), pointer :: grd
 real, allocatable, dimension(:) :: lon,          &
                                    lat,          &
@@ -149,14 +152,14 @@ subroutine write_restart(bergs)
 
 
 integer :: grdi, grdj
-  
+
 ! Get the stderr unit number
  stderrunit=stderr()
 
 
   ! For convenience
   grd=>bergs%grd
- 
+
   !First add the bergs on the io_tile_root_pe (if any) to the I/O list
   nbergs = 0
   do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
@@ -248,13 +251,13 @@ subroutine write_restart(bergs)
       this=>this%next
     enddo
   enddo ; enddo
-  call mpp_sum(n_static_bergs) 
+  call mpp_sum(n_static_bergs)
   if (n_static_bergs .gt. 0) &
     id = register_restart_field(bergs_restart,filename,'static_berg',static_berg, &
                                               longname='static_berg',units='dimensionless')
 
   ! Write variables
-   
+
   i = 0
   do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
     this=>bergs%list(grdi,grdj)%first
@@ -270,8 +273,8 @@ subroutine write_restart(bergs)
       start_lon(i) = this%start_lon; start_lat(i) = this%start_lat
       start_year(i) = this%start_year; start_day(i) = this%start_day
       start_mass(i) = this%start_mass; mass_scaling(i) = this%mass_scaling
-      static_berg(i) = this%static_berg 
-      iceberg_num(i) = this%iceberg_num; 
+      static_berg(i) = this%static_berg
+      iceberg_num(i) = this%iceberg_num
       mass_of_bits(i) = this%mass_of_bits; heat_density(i) = this%heat_density
       this=>this%next
     enddo
@@ -313,18 +316,18 @@ subroutine write_restart(bergs)
 
 !########## Creating bond restart file ######################
 
-   !Allocating restart memory for bond related variables.
-   nbonds=0
-   if (bergs%iceberg_bonds_on) then
-     check_bond_quality=.true.
-     call count_bonds(bergs, nbonds,check_bond_quality)
+  !Allocating restart memory for bond related variables.
+  nbonds=0
+  if (bergs%iceberg_bonds_on) then
+    check_bond_quality=.true.
+    call count_bonds(bergs, nbonds,check_bond_quality)
 
-   allocate(first_berg_num(nbonds))
-   allocate(other_berg_num(nbonds))
-   allocate(first_berg_ine(nbonds))
-   allocate(first_berg_jne(nbonds))
-   allocate(other_berg_ine(nbonds))
-   allocate(other_berg_jne(nbonds))
+  allocate(first_berg_num(nbonds))
+  allocate(other_berg_num(nbonds))
+  allocate(first_berg_ine(nbonds))
+  allocate(first_berg_jne(nbonds))
+  allocate(other_berg_ine(nbonds))
+  allocate(other_berg_jne(nbonds))
 
   call get_instance_filename("bonds_iceberg.res.nc", filename_bonds)
   call set_domain(bergs%grd%domain)
@@ -341,10 +344,10 @@ subroutine write_restart(bergs)
   id = register_restart_field(bergs_bond_restart,filename_bonds,'other_berg_ine',other_berg_ine,longname='iceberg ine of second berg in bond',units='dimensionless')
   id = register_restart_field(bergs_bond_restart,filename_bonds,'other_berg_jne',other_berg_jne,longname='iceberg jne of second berg in bond',units='dimensionless')
   id = register_restart_field(bergs_bond_restart,filename_bonds,'other_berg_num',other_berg_num,longname='iceberg id second berg in bond',units='dimensionless')
-  
-  
+
+
   ! Write variables
-   
+
   i = 0
   do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
     this=>bergs%list(grdi,grdj)%first
@@ -379,8 +382,7 @@ subroutine write_restart(bergs)
 
 
   call nullify_domain()
-   endif
-!#############################################################################################
+  endif
 
   ! Write stored ice
   filename='RESTART/calving.res.nc'
@@ -400,9 +402,11 @@ subroutine write_restart(bergs)
   endif
   contains
 
+  !> Find the last berg in a linked list.
   function last_berg(berg)
   ! Arguments
-  type(iceberg), pointer :: last_berg, berg
+  type(iceberg), pointer :: berg !< Pointer to an iceberg
+  type(iceberg), pointer :: last_berg
   ! Local variables
 
     last_berg=>berg
@@ -414,12 +418,11 @@ end function last_berg
 
 end subroutine write_restart
 
-! ##############################################################################
-
+!> Read an iceberg restart file (original implementation)
 subroutine read_restart_bergs_orig(bergs,Time)
 ! Arguments
-type(icebergs), pointer :: bergs
-type(time_type), intent(in) :: Time
+type(icebergs), pointer :: bergs !< Icebergs container
+type(time_type), intent(in) :: Time !< Model time
 ! Local variables
 integer, dimension(:), allocatable :: found_restart_int
 integer :: k, ierr, ncid, dimid, nbergs_in_file
@@ -471,7 +474,7 @@ subroutine read_restart_bergs_orig(bergs,Time)
 
   elseif (found_restart) then ! if (.not.found_restart)
   ! only do the following if a file was found
-  
+
   if (verbose.and.mpp_pe()==mpp_root_pe()) write(*,'(2a)') 'diamonds, read_restart_bergs: found restart file = ',filename
 
   ierr=nf_open(filename, NF_NOWRITE, ncid)
@@ -580,7 +583,7 @@ subroutine read_restart_bergs_orig(bergs,Time)
   else ! if no restart file was read on this PE
     nbergs_in_file=0
   endif ! if (.not.found_restart)
-  
+
   ! Sanity check
   k=count_bergs(bergs)
   if (verbose) write(*,'(2(a,i8))') 'diamonds, read_restart_bergs: # bergs =',k,' on PE',mpp_pe()
@@ -595,7 +598,7 @@ subroutine read_restart_bergs_orig(bergs,Time)
      k,' bergs have been read'
   endif
 
-  if (k.ne.nbergs_in_file) call error_mesg('diamonds, read_restart_bergs', 'wrong number of bergs read!', FATAL) 
+  if (k.ne.nbergs_in_file) call error_mesg('diamonds, read_restart_bergs', 'wrong number of bergs read!', FATAL)
 
   if (.not. found_restart .and. bergs%nbergs_start==0 .and. generate_test_icebergs) call generate_bergs(bergs,Time)
 
@@ -609,6 +612,7 @@ subroutine read_restart_bergs_orig(bergs,Time)
 
 contains
 
+  !> Read a real value from a file and optionally return a default value if variable is missing
   real function get_real_from_file(ncid, varid, k, value_if_not_in_file)
   integer, intent(in) :: ncid, varid, k
   real, optional :: value_if_not_in_file
@@ -619,11 +623,12 @@ real function get_real_from_file(ncid, varid, k, value_if_not_in_file)
     get_real_from_file=get_double(ncid, ncid, k)
   endif
   end function get_real_from_file
-  
+
+  !> Generate bergs for the purpose of debugging
   subroutine generate_bergs(bergs,Time)
   ! Arguments
-  type(icebergs), pointer :: bergs
-  type(time_type), intent(in) :: Time
+  type(icebergs), pointer :: bergs !< Icebergs container
+  type(time_type), intent(in) :: Time !< Model time
   ! Local variables
   integer :: i,j
   integer :: iNg, jNg  !Total number of points gloablly in i and j direction
@@ -667,7 +672,7 @@ subroutine generate_bergs(bergs,Time)
         localberg%vvel_old=0. !Alon
         localberg%bxn=0. !Alon
         localberg%byn=0. !Alon
-        
+
         !Berg A
         localberg%uvel=1.
         localberg%vvel=0.
@@ -701,15 +706,14 @@ subroutine generate_bergs(bergs,Time)
       write(*,'(a,i8,a)') 'diamonds, generate_bergs: ',bergs%nbergs_start,' were generated'
 
   end subroutine generate_bergs
-  
-end subroutine read_restart_bergs_orig
 
-! ##############################################################################
+end subroutine read_restart_bergs_orig
 
+!> Read an iceberg restart file
 subroutine read_restart_bergs(bergs,Time)
 ! Arguments
-type(icebergs), pointer :: bergs
-type(time_type), intent(in) :: Time
+type(icebergs), pointer :: bergs !< Icebergs container
+type(time_type), intent(in) :: Time !< Model time
 ! Local variables
 integer :: k, siz(4), nbergs_in_file, nbergs_read
 logical :: lres, found_restart, found
@@ -830,7 +834,7 @@ subroutine read_restart_bergs(bergs,Time)
   lon1=maxval( grd%lon(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
   lat0=minval( grd%lat(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
   lat1=maxval( grd%lat(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
-     
+
   do k=1, nbergs_in_file
     localberg%lon=lon(k)
     localberg%lat=lat(k)
@@ -905,7 +909,7 @@ subroutine read_restart_bergs(bergs,Time)
       call error_mesg('diamonds, read_restart_bergs', 'berg in PE file was not on PE!', FATAL)
     endif
   enddo
-  
+
   if(nbergs_in_file > 0) then
     deallocate(              &
                lon,          &
@@ -971,12 +975,13 @@ subroutine read_restart_bergs(bergs,Time)
 
 contains
 
+  !> Read a vector of reals from file and use a default value if variable is missing
   subroutine read_real_vector(filename, varname, values, domain, value_if_not_in_file)
-    character(len=*), intent(in)  :: filename
-    character(len=*), intent(in)  :: varname
-    real,             intent(out) :: values(:)
-    type(domain2D),   intent(in)  :: domain
-    real, optional,   intent(in)  :: value_if_not_in_file
+    character(len=*), intent(in)  :: filename !< Name of file to read from
+    character(len=*), intent(in)  :: varname !< Name of variable to read
+    real,             intent(out) :: values(:) !< Returned vector of reals
+    type(domain2D),   intent(in)  :: domain !< Parallel decomposition
+    real, optional,   intent(in)  :: value_if_not_in_file !< Value to use if variable is not in file
 
     if (present(value_if_not_in_file).and..not.field_exist(filename, varname)) then
       values(:)=value_if_not_in_file
@@ -985,12 +990,13 @@ subroutine read_real_vector(filename, varname, values, domain, value_if_not_in_f
     endif
   end subroutine read_real_vector
 
+  !> Read a vector of integers from file and use a default value if variable is missing
   subroutine read_int_vector(filename, varname, values, domain, value_if_not_in_file)
-    character(len=*),  intent(in)  :: filename
-    character(len=*),  intent(in)  :: varname
-    integer,           intent(out) :: values(:)
-    type(domain2D),    intent(in)  :: domain
-    integer, optional, intent(in)  :: value_if_not_in_file
+    character(len=*),  intent(in)  :: filename !< Name of file to read from
+    character(len=*),  intent(in)  :: varname !< Name of variable to read
+    integer,           intent(out) :: values(:) !< Returned vector of integers
+    type(domain2D),    intent(in)  :: domain !< Parallel decomposition
+    integer, optional, intent(in)  :: value_if_not_in_file !< Value to use if variable is not in file
 
     if (present(value_if_not_in_file).and..not.field_exist(filename, varname)) then
       values(:)=value_if_not_in_file
@@ -998,11 +1004,12 @@ subroutine read_int_vector(filename, varname, values, domain, value_if_not_in_fi
       call read_unlimited_axis(filename,varname,values,domain=domain)
     endif
   end subroutine read_int_vector
-  
+
+  !> Generate bergs for the purpose of debugging
   subroutine generate_bergs(bergs,Time)
   ! Arguments
-  type(icebergs), pointer :: bergs
-  type(time_type), intent(in) :: Time
+  type(icebergs), pointer :: bergs !< Icebergs container
+  type(time_type), intent(in) :: Time !< Model time
   ! Local variables
   integer :: i,j
   integer :: iNg, jNg  !Total number of points gloablly in i and j direction
@@ -1080,9 +1087,12 @@ subroutine generate_bergs(bergs,Time)
   end subroutine generate_bergs
 
   subroutine loc_set_berg_pos(grd, xi, yj, uvel, vvel, berg)
-    type(icebergs_gridded), pointer :: grd
-    real, intent(in) :: xi, yj, uvel, vvel
-    type(iceberg), intent(inout) :: berg
+    type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+    real, intent(in) :: xi !< Non-dimensional x-position within cell to give berg
+    real, intent(in) :: yj !< Non-dimensional y-position within cell to give berg
+    real, intent(in) :: uvel !< Zonal velocity to give berg
+    real, intent(in) :: vvel !< Meridional velocity to give berg
+    type(iceberg), intent(inout) :: berg !< An iceberg
     integer :: i, j
     logical :: lres
     i = berg%ine ; j = berg%jne
@@ -1108,15 +1118,15 @@ subroutine loc_set_berg_pos(grd, xi, yj, uvel, vvel, berg)
       stop 'generate_bergs, loc_set_berg_pos(): VERY FATAL!'
     endif
   end subroutine loc_set_berg_pos
-  
+
 end subroutine read_restart_bergs
 
 
-! ##############################################################################
+!> Read bond restart file
 subroutine read_restart_bonds(bergs,Time)
 ! Arguments
-type(icebergs), pointer :: bergs
-type(time_type), intent(in) :: Time
+type(icebergs), pointer :: bergs !< Icebergs container
+type(time_type), intent(in) :: Time !< Model time
 ! Local variables
 integer :: k, siz(4), nbonds_in_file
 logical :: lres, found_restart, found
@@ -1166,7 +1176,7 @@ subroutine read_restart_bonds(bergs,Time)
   filename = filename_base
   call get_field_size(filename,'i',siz, field_found=found, domain=bergs%grd%domain)
   nbonds_in_file = siz(1)
-  
+
     if (mpp_pe() .eq. mpp_root_pe()) then
       write(stderrunit,*)  'diamonds, bond read restart : ','Number of bonds in file',  nbonds_in_file
     endif
@@ -1195,10 +1205,9 @@ subroutine read_restart_bonds(bergs,Time)
     number_perfect_bonds_with_first_on_pe=0
 
     do k=1, nbonds_in_file
-      
 
        ! If i,j in restart files are not good, then we find the berg position of the bond addresses manually:
-       if (ignore_ij_restart) then 
+       if (ignore_ij_restart) then
          !Finding first iceberg in bond
          ine=999 ; jne=999 ; berg_found=0.0 ; search_data_domain=.true.
          call find_individual_iceberg(bergs,first_berg_num(k), ine, jne,berg_found,search_data_domain)
@@ -1238,7 +1247,7 @@ subroutine read_restart_bonds(bergs,Time)
       if ( (first_berg_ine(k)>=grd%isd) .and. (first_berg_ine(k)<=grd%ied) .and. &
         (first_berg_jne(k)>=grd%jsd) .and. (first_berg_jne(k)<=grd%jed) ) then
         number_first_bonds_matched=number_first_bonds_matched+1
-        
+
         ! Search for the first berg, which the bond belongs to
         first_berg_found=.false.
         first_berg=>null()
@@ -1249,11 +1258,10 @@ subroutine read_restart_bonds(bergs,Time)
             first_berg=>this
             !if (first_berg%halo_berg.gt.0.5) print *, 'bonding halo berg:', first_berg_num(k),  first_berg_ine(k),first_berg_jne(k) ,grd%isc, grd%iec, mpp_pe()
             this=>null()
-          else  
+          else
             this=>this%next
           endif
         enddo
-     
 
         ! Decide whether the second iceberg is on the processeor (data domain)
         second_berg_found=.false.
@@ -1271,24 +1279,24 @@ subroutine read_restart_bonds(bergs,Time)
               second_berg_found=.true.
               second_berg=>this
               this=>null()
-            else  
+            else
               this=>this%next
             endif
           enddo
         endif
-         
+
         if (first_berg_found) then
           number_partial_bonds=number_partial_bonds+1
           if (second_berg_found) then
             call form_a_bond(first_berg, other_berg_num(k), other_berg_ine(k), other_berg_jne(k),  second_berg)
             number_perfect_bonds=number_perfect_bonds+1
-    
+
             !Counting number of bonds where the first bond is in the computational domain
             if ( (first_berg_ine(k)>=grd%isc) .and. (first_berg_ine(k)<=grd%iec) .and. &
               (first_berg_jne(k)>=grd%jsc) .and. (first_berg_jne(k)<=grd%jec) ) then
                number_perfect_bonds_with_first_on_pe=number_perfect_bonds_with_first_on_pe+1
-        endif
-     
+            endif
+
           else
             !print *, 'Forming a bond of the second type', mpp_pe(), first_berg_num(k),  other_berg_num(k)
             !call form_a_bond(first_berg, other_berg_num(k),other_berg_ine(k),other_berg_jne(k))
@@ -1314,7 +1322,7 @@ subroutine read_restart_bonds(bergs,Time)
       write(stderrunit,*) 'diamonds, bond read restart : ','Not enough partial bonds formed', all_pe_number_partial_bonds , nbonds_in_file
       call error_mesg('read_restart_bonds_bergs_new', 'Not enough partial bonds formed', FATAL)
     endif
-    
+
     if (all_pe_number_perfect_bonds .lt. nbonds_in_file) then
       call mpp_sum(all_pe_number_first_bonds_matched)
       call mpp_sum(all_pe_number_second_bonds_matched)
@@ -1339,7 +1347,7 @@ subroutine read_restart_bonds(bergs,Time)
             other_berg_ine,  &
             other_berg_jne )
   endif
-    
+
   if (mpp_pe() .eq. mpp_root_pe()) then
     write(stderrunit,*)  'diamonds, bond read restart : ','Number of bonds (including halos)',  all_pe_number_perfect_bonds
     write(stderrunit,*)  'diamonds, bond read restart : ','Number of true bonds created',  all_pe_number_perfect_bonds_with_first_on_pe
@@ -1347,12 +1355,11 @@ subroutine read_restart_bonds(bergs,Time)
 
 end subroutine read_restart_bonds
 
-! ##############################################################################
-
+!> Reading calving and gridded restart data
 subroutine read_restart_calving(bergs)
 use random_numbers_mod, only: initializeRandomNumberStream, getRandomNumbers, randomNumberStream
 ! Arguments
-type(icebergs), pointer :: bergs
+type(icebergs), pointer :: bergs !< Icebergs container
 ! Local variables
 integer :: k,i,j
 character(len=37) :: filename, actual_filename
@@ -1399,7 +1406,7 @@ subroutine read_restart_calving(bergs)
     if (field_exist(filename, 'iceberg_counter_grd')) then
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
        'diamonds, read_restart_calving: reading iceberg_counter_grd from restart file.'
-      call read_data(filename, 'iceberg_counter_grd', grd%iceberg_counter_grd, grd%domain) 
+      call read_data(filename, 'iceberg_counter_grd', grd%iceberg_counter_grd, grd%domain)
     else
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
      'diamonds, read_restart_calving: iceberg_counter_grd WAS NOT FOUND in the file. Setting to 0.'
@@ -1450,13 +1457,12 @@ subroutine read_restart_calving(bergs)
 
 end subroutine read_restart_calving
 
-! ##############################################################################
-
+!> Read ocean depth from file
 subroutine read_ocean_depth(grd)
 ! Arguments
+type(icebergs_gridded), pointer :: grd !< Container for gridded fields
 ! Local variables
-character(len=37) :: filename 
-type(icebergs_gridded), pointer :: grd
+character(len=37) :: filename
 
   ! Read stored ice
   filename=trim(restart_input_dir)//'topog.nc'
@@ -1480,11 +1486,11 @@ subroutine read_ocean_depth(grd)
   !call grd_chksum2(bergs%grd, bergs%grd%ocean_depth, 'read_ocean_depth, ocean_depth')
 end subroutine read_ocean_depth
 
-! ##############################################################################
-
+!> Write a trajectory-based diagnostics file
 subroutine write_trajectory(trajectory, save_short_traj)
 ! Arguments
-type(xyt), pointer :: trajectory
+type(xyt), pointer :: trajectory !< An iceberg trajectory
+logical, intent(in) :: save_short_traj !< If true, record less data
 ! Local variables
 integer :: iret, ncid, i_dim, i
 integer :: lonid, latid, yearid, dayid, uvelid, vvelid, iceberg_numid
@@ -1495,7 +1501,6 @@ subroutine write_trajectory(trajectory, save_short_traj)
 character(len=7) :: pe_name
 type(xyt), pointer :: this, next
 integer :: stderrunit
-logical, intent(in) :: save_short_traj
 !I/O vars
 type(xyt), pointer :: traj4io=>null()
 integer :: ntrajs_sent_io,ntrajs_rcvd_io
@@ -1528,7 +1533,7 @@ subroutine write_trajectory(trajectory, save_short_traj)
 
   !Now gather and append the bergs from all pes in the io_tile to the list on corresponding io_tile_root_pe
   ntrajs_sent_io =0
-  ntrajs_rcvd_io =0 
+  ntrajs_rcvd_io =0
 
   if(is_io_tile_root_pe) then
      !Receive trajs from all pes in this I/O tile !FRAGILE!SCARY!
@@ -1552,7 +1557,7 @@ subroutine write_trajectory(trajectory, save_short_traj)
        trajectory => trajectory%next ! This will eventually result in trajectory => null()
        deallocate(this) ! Delete the link from memory
      enddo
-        
+
      call mpp_send(ntrajs_sent_io, plen=1, to_pe=io_tile_root_pe, tag=COMM_TAG_11)
      if (ntrajs_sent_io .gt. 0) then
         call mpp_send(obuffer_io%data, ntrajs_sent_io*buffer_width_traj, to_pe=io_tile_root_pe, tag=COMM_TAG_12)
@@ -1567,21 +1572,21 @@ subroutine write_trajectory(trajectory, save_short_traj)
   call mpp_clock_begin(clock_trw)
 
   if((force_all_pes_traj .OR. is_io_tile_root_pe) .AND. associated(traj4io)) then
- 
+
     call get_instance_filename("iceberg_trajectories.nc", filename)
     if(io_tile_id(1) .ge. 0 .AND. .NOT. force_all_pes_traj) then !io_tile_root_pes write
        if(io_npes .gt. 1) then !attach tile_id  to filename only if there is more than one I/O pe
           if (io_tile_id(1)<10000) then
-             write(filename,'(A,".",I4.4)') trim(filename), io_tile_id(1) 
+             write(filename,'(A,".",I4.4)') trim(filename), io_tile_id(1)
           else
-             write(filename,'(A,".",I6.6)') trim(filename), io_tile_id(1) 
+             write(filename,'(A,".",I6.6)') trim(filename), io_tile_id(1)
           endif
        endif
     else !All pes write, attach pe# to filename
        if (mpp_npes()<10000) then
-          write(filename,'(A,".",I4.4)') trim(filename), mpp_pe() 
+          write(filename,'(A,".",I4.4)') trim(filename), mpp_pe()
        else
-          write(filename,'(A,".",I6.6)') trim(filename), mpp_pe() 
+          write(filename,'(A,".",I6.6)') trim(filename), mpp_pe()
        endif
     endif
 
@@ -1677,7 +1682,7 @@ subroutine write_trajectory(trajectory, save_short_traj)
       call put_att(ncid, dayid, 'units', 'days')
       call put_att(ncid, iceberg_numid, 'long_name', 'iceberg id number')
       call put_att(ncid, iceberg_numid, 'units', 'dimensionless')
-      
+
       if (.not. save_short_traj) then
         call put_att(ncid, uvelid, 'long_name', 'zonal spped')
         call put_att(ncid, uvelid, 'units', 'm/s')
@@ -1724,7 +1729,7 @@ subroutine write_trajectory(trajectory, save_short_traj)
 
     ! End define mode
     iret = nf_enddef(ncid)
-         
+
     ! Write variables
     this=>traj4io
     if (io_is_in_append_mode) then
@@ -1775,20 +1780,18 @@ subroutine write_trajectory(trajectory, save_short_traj)
 
 end subroutine write_trajectory
 
-
-! ##############################################################################
-
+!> Returns netcdf id of variable
 integer function inq_var(ncid, var, unsafe)
 ! Arguments
-integer, intent(in) :: ncid
-character(len=*), intent(in) :: var
-logical, optional, intent(in) :: unsafe
+integer, intent(in) :: ncid !< Handle to netcdf file
+character(len=*), intent(in) :: var !< Name of variable
+logical, optional, intent(in) :: unsafe !< If present and true, do not fail if variable is not in file
 ! Local variables
 integer :: iret
 integer :: stderrunit
 logical :: unsafely=.false.
 
-if(present(unsafe)) unsafely=unsafe
+  if(present(unsafe)) unsafely=unsafe
   ! Get the stderr unit number
   stderrunit=stderr()
 
@@ -1804,12 +1807,13 @@ integer function inq_var(ncid, var, unsafe)
 
 end function inq_var
 
-! ##############################################################################
-
+!> Define a netcdf variable
 integer function def_var(ncid, var, ntype, idim)
 ! Arguments
-integer, intent(in) :: ncid, ntype, idim
-character(len=*), intent(in) :: var
+integer, intent(in) :: ncid !< Handle to netcdf file
+character(len=*), intent(in) :: var !< Name of variable
+integer, intent(in) :: ntype !< Netcdf type of variable
+integer, intent(in) :: idim !< Length of vector
 ! Local variables
 integer :: iret
 integer :: stderrunit
@@ -1825,12 +1829,11 @@ integer function def_var(ncid, var, ntype, idim)
 
 end function def_var
 
-! ##############################################################################
-
+!> Returns id of variable
 integer function inq_varid(ncid, var)
 ! Arguments
-integer, intent(in) :: ncid
-character(len=*), intent(in) :: var
+integer, intent(in) :: ncid !< Handle to netcdf file
+character(len=*), intent(in) :: var !< Name of variable
 ! Local variables
 integer :: iret
 integer :: stderrunit
@@ -1846,12 +1849,13 @@ integer function inq_varid(ncid, var)
 
 end function inq_varid
 
-! ##############################################################################
-
+!> Add a string attribute to a netcdf variable
 subroutine put_att(ncid, id, att, attval)
 ! Arguments
-integer, intent(in) :: ncid, id
-character(len=*), intent(in) :: att, attval
+integer, intent(in) :: ncid !< Handle to netcdf file
+integer, intent(in) :: id !< Netcdf id of variable
+character(len=*), intent(in) :: att !< Name of attribute
+character(len=*), intent(in) :: attval !< Value of attribute
 ! Local variables
 integer :: vallen, iret
 integer :: stderrunit
@@ -1869,11 +1873,12 @@ subroutine put_att(ncid, id, att, attval)
 
 end subroutine put_att
 
-! ##############################################################################
-
+!> Read a real from a netcdf file
 real function get_double(ncid, id, i)
 ! Arguments
-integer, intent(in) :: ncid, id, i
+integer, intent(in) :: ncid !< Handle to netcdf file
+integer, intent(in) :: id !< Netcdf id of variable
+integer, intent(in) :: i !< Index to read
 ! Local variables
 integer :: iret
 integer :: stderrunit
@@ -1889,11 +1894,12 @@ real function get_double(ncid, id, i)
 
 end function get_double
 
-! ##############################################################################
-
+!> Read an integer from a netcdf file
 integer function get_int(ncid, id, i)
 ! Arguments
-integer, intent(in) :: ncid, id, i
+integer, intent(in) :: ncid !< Handle to netcdf file
+integer, intent(in) :: id !< Netcdf id of variable
+integer, intent(in) :: i !< Index to read
 ! Local variables
 integer :: iret
 integer :: stderrunit
@@ -1909,12 +1915,13 @@ integer function get_int(ncid, id, i)
 
 end function get_int
 
-! ##############################################################################
-
+!> Write a real to a netcdf file
 subroutine put_double(ncid, id, i, val)
 ! Arguments
-integer, intent(in) :: ncid, id, i
-real, intent(in) :: val
+integer, intent(in) :: ncid !< Handle to netcdf file
+integer, intent(in) :: id !< Netcdf id of variable
+integer, intent(in) :: i !< Index of position to write
+real, intent(in) :: val !< Value to write
 ! Local variables
 integer :: iret
 integer :: stderrunit
@@ -1930,11 +1937,13 @@ subroutine put_double(ncid, id, i, val)
 
 end subroutine put_double
 
-! ##############################################################################
-
+!> Write an integer to a netcdf file
 subroutine put_int(ncid, id, i, val)
 ! Arguments
-integer, intent(in) :: ncid, id, i, val
+integer, intent(in) :: ncid !< Handle to netcdf file
+integer, intent(in) :: id !< Netcdf id of variable
+integer, intent(in) :: i !< Index of position to write
+integer, intent(in) :: val !< Value to write
 ! Local variables
 integer :: iret
 integer :: stderrunit
@@ -1950,14 +1959,12 @@ subroutine put_int(ncid, id, i, val)
 
 end subroutine put_int
 
-
-! ##############################################################################
-
+!> True is a restart file can be found
 logical function find_restart_file(filename, actual_file, multiPErestart, tile_id)
-  character(len=*), intent(in) :: filename
-  character(len=*), intent(out) :: actual_file
-  logical, intent(out) :: multiPErestart
-  integer, intent(in) :: tile_id
+  character(len=*), intent(in) :: filename !< Base-name of restart file
+  character(len=*), intent(out) :: actual_file !< Actual name of file, if found
+  logical, intent(out) :: multiPErestart !< True if found, false otherwise
+  integer, intent(in) :: tile_id !< Parallel tile number of file
 
   character(len=6) :: pe_name
 
@@ -1965,19 +1972,19 @@ logical function find_restart_file(filename, actual_file, multiPErestart, tile_i
 
   ! If running as ensemble, add the ensemble id string to the filename
   call get_instance_filename(filename, actual_file)
-    
+
   ! Prefer combined restart files.
   inquire(file=actual_file,exist=find_restart_file)
   if (find_restart_file) return
-    
+
   ! Uncombined restart
   if(tile_id .ge. 0) then
     write(actual_file,'(A,".",I4.4)') trim(actual_file), tile_id
   else
   if (mpp_npes()>10000) then
-     write(pe_name,'(a,i6.6)' )'.', mpp_pe()    
+     write(pe_name,'(a,i6.6)' )'.', mpp_pe()
   else
-     write(pe_name,'(a,i4.4)' )'.', mpp_pe()    
+     write(pe_name,'(a,i4.4)' )'.', mpp_pe()
   endif
   actual_file=trim(actual_file)//trim(pe_name)
   endif
@@ -1994,5 +2001,4 @@ logical function find_restart_file(filename, actual_file, multiPErestart, tile_i
 
 end function find_restart_file
 
-
 end module

From b3e877492d639bba68bcc9f1f4d87c270bd40a61 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Mon, 27 Mar 2017 16:41:14 -0400
Subject: [PATCH 212/361] More doxygenization of icebergs.F90

- More indenting and API documentation
  - Still far from complete
---
 icebergs.F90 | 622 +++++++++++++++++++++++++--------------------------
 1 file changed, 310 insertions(+), 312 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 693b55d..8853f00 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -82,33 +82,33 @@ subroutine icebergs_init(bergs, &
              gni, gnj, layout, io_layout, axes, dom_x_flags, dom_y_flags, &
              dt, Time, ice_lon, ice_lat, ice_wet, ice_dx, ice_dy, ice_area, &
              cos_rot, sin_rot, ocean_depth, maskmap, fractional_area)
-! Arguments
-type(icebergs), pointer :: bergs !< Container for all types and memory
-integer, intent(in) :: gni !< Number of global points in i-direction
-integer, intent(in) :: gnj !< Number of global points in j-direction
-integer, intent(in) :: layout(2) !< Parallel decomposition of computational processors in i/j direction
-integer, intent(in) :: io_layout(2) !< Parallel decomposition of i/o processors in i/j direction
-integer, intent(in) :: axes(2) !< Diagnostic axes
-integer, intent(in) :: dom_x_flags !< Decomposition flags for i-direction
-integer, intent(in) :: dom_y_flags !< Decomposition flags for j-direction
-real, intent(in) :: dt !< Time step (s)
-type (time_type), intent(in) :: Time !< Model time
-real, dimension(:,:), intent(in) :: ice_lon !< Longitude of cell corners using NE convention (degree E)
-real, dimension(:,:), intent(in) :: ice_lat !< Latitude of cell corners using NE conventino (degree N)
-real, dimension(:,:), intent(in) :: ice_wet !< Wet/dry mask (1 is wet, 0 is dry) of cell centers
-real, dimension(:,:), intent(in) :: ice_dx !< Zonal length of cell on northern side (m)
-real, dimension(:,:), intent(in) :: ice_dy !< Meridional length of cell on eastern side (m)
-real, dimension(:,:), intent(in) :: ice_area !< Area of cells (m^2, or non-dim is fractional_area=True)
-real, dimension(:,:), intent(in) :: cos_rot !< Cosine from rotation matrix to lat-lon coords
-real, dimension(:,:), intent(in) :: sin_rot !< Sine from rotation matrix to lat-lon coords
-real, dimension(:,:), intent(in),optional :: ocean_depth !< Depth of ocean bottom (m)
-logical, intent(in), optional :: maskmap(:,:) !< Masks out parallel cores
-logical, intent(in), optional :: fractional_area !< If true, ice_area contains cell area as fraction of entire spherical surface
-! Local variables
-type(icebergs_gridded), pointer :: grd => null()
-integer :: nbonds
-logical :: check_bond_quality
-integer :: stdlogunit, stderrunit
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  integer, intent(in) :: gni !< Number of global points in i-direction
+  integer, intent(in) :: gnj !< Number of global points in j-direction
+  integer, intent(in) :: layout(2) !< Parallel decomposition of computational processors in i/j direction
+  integer, intent(in) :: io_layout(2) !< Parallel decomposition of i/o processors in i/j direction
+  integer, intent(in) :: axes(2) !< Diagnostic axes
+  integer, intent(in) :: dom_x_flags !< Decomposition flags for i-direction
+  integer, intent(in) :: dom_y_flags !< Decomposition flags for j-direction
+  real, intent(in) :: dt !< Time step (s)
+  type (time_type), intent(in) :: Time !< Model time
+  real, dimension(:,:), intent(in) :: ice_lon !< Longitude of cell corners using NE convention (degree E)
+  real, dimension(:,:), intent(in) :: ice_lat !< Latitude of cell corners using NE conventino (degree N)
+  real, dimension(:,:), intent(in) :: ice_wet !< Wet/dry mask (1 is wet, 0 is dry) of cell centers
+  real, dimension(:,:), intent(in) :: ice_dx !< Zonal length of cell on northern side (m)
+  real, dimension(:,:), intent(in) :: ice_dy !< Meridional length of cell on eastern side (m)
+  real, dimension(:,:), intent(in) :: ice_area !< Area of cells (m^2, or non-dim is fractional_area=True)
+  real, dimension(:,:), intent(in) :: cos_rot !< Cosine from rotation matrix to lat-lon coords
+  real, dimension(:,:), intent(in) :: sin_rot !< Sine from rotation matrix to lat-lon coords
+  real, dimension(:,:), intent(in),optional :: ocean_depth !< Depth of ocean bottom (m)
+  logical, intent(in), optional :: maskmap(:,:) !< Masks out parallel cores
+  logical, intent(in), optional :: fractional_area !< If true, ice_area contains cell area as fraction of entire spherical surface
+  ! Local variables
+  type(icebergs_gridded), pointer :: grd => null()
+  integer :: nbonds
+  logical :: check_bond_quality
+  integer :: stdlogunit, stderrunit
 
   ! Get the stderr and stdlog unit numbers
   stderrunit=stderr()
@@ -158,24 +158,24 @@ end subroutine icebergs_init
 
 !> Invoke some unit testing
 subroutine unit_testing(bergs)
-! Arguments
-type(icebergs), pointer :: bergs !< Container for all types and memory
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
 
-call hexagon_test()
-call point_in_triangle_test()
-call basal_melt_test(bergs)
-call test_check_for_duplicate_ids_in_list()
+  call hexagon_test()
+  call point_in_triangle_test()
+  call basal_melt_test(bergs)
+  call test_check_for_duplicate_ids_in_list()
 
 end subroutine unit_testing
 
 !> Test find_basal_melt()
 subroutine basal_melt_test(bergs)
-! Arguments
-type(icebergs), pointer :: bergs !< Container for all types and memory
-! Local variables
-real :: dvo,lat,salt,temp, basal_melt, thickness
-integer :: iceberg_num
-logical :: Use_three_equation_model
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  ! Local variables
+  real :: dvo,lat,salt,temp, basal_melt, thickness
+  integer :: iceberg_num
+  logical :: Use_three_equation_model
 
   if (mpp_pe() .eq. mpp_root_pe() ) print *, 'Begining Basal Melting Unit Test'
   dvo=0.2 ;lat=0.0 ; salt=35.0 ; temp=2.0 ;thickness=100.; iceberg_num=0
@@ -191,10 +191,10 @@ end subroutine basal_melt_test
 
 !> Test point_in_triangle()
 subroutine point_in_triangle_test()
-! Arguments
-real :: Ax,Ay,Bx,By,Cx,Cy  !Position of icebergs
-logical :: fail_unit_test
-integer :: stderrunit
+  ! Local variables
+  real :: Ax,Ay,Bx,By,Cx,Cy  !Position of icebergs
+  logical :: fail_unit_test
+  integer :: stderrunit
 
   ! Get the stderr unit number.
   stderrunit = stderr()
@@ -212,13 +212,13 @@ end subroutine point_in_triangle_test
 
 !> Test Hexagon_into_quadrants_using_triangles()
 subroutine hexagon_test()
-! Arguments
-real :: x0,y0  !Position of icebergs
-real :: H,theta,S !Apothen of iceberg and angle.
-real :: Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4 ! Areas of icebergs
-real :: tol
-logical :: fail_unit_test
-integer :: stderrunit
+  ! Local variables
+  real :: x0,y0  !Position of icebergs
+  real :: H,theta,S !Apothen of iceberg and angle.
+  real :: Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4 ! Areas of icebergs
+  real :: tol
+  logical :: fail_unit_test
+  integer :: stderrunit
 
   ! Get the stderr unit number.
   stderrunit = stderr()
@@ -317,24 +317,23 @@ subroutine hexagon_test()
 
   if (fail_unit_test) call error_mesg('diamonds, hexagon unit testing:', 'Hexagon unit testing does not pass!', FATAL)
 
-
 end subroutine hexagon_test
 
 !> Initializes bonds
 subroutine initialize_iceberg_bonds(bergs)
-! Arguments
-type(icebergs), pointer :: bergs !< Container for all types and memory
-! Local variables
-type(iceberg), pointer :: berg
-type(iceberg), pointer :: other_berg
-type(icebergs_gridded), pointer :: grd
-real :: T1, L1, W1, lon1, lat1, x1, y1, R1, A1   !Current iceberg
-real :: T2, L2, W2, lon2, lat2, x2, y2, R2, A2   !Other iceberg
-real :: dlon,dlat
-real :: dx_dlon,dy_dlat, lat_ref
-real :: r_dist_x, r_dist_y, r_dist
-integer :: grdi_outer, grdj_outer
-integer :: grdi_inner, grdj_inner
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  ! Local variables
+  type(iceberg), pointer :: berg
+  type(iceberg), pointer :: other_berg
+  type(icebergs_gridded), pointer :: grd
+  real :: T1, L1, W1, lon1, lat1, x1, y1, R1, A1   !Current iceberg
+  real :: T2, L2, W2, lon2, lat2, x2, y2, R2, A2   !Other iceberg
+  real :: dlon,dlat
+  real :: dx_dlon,dy_dlat, lat_ref
+  real :: r_dist_x, r_dist_y, r_dist
+  integer :: grdi_outer, grdj_outer
+  integer :: grdi_inner, grdj_inner
 
   ! For convenience
   grd=>bergs%grd
@@ -380,11 +379,11 @@ end subroutine initialize_iceberg_bonds
 
 ! Returns metric converting grid distances to meters
 subroutine convert_from_grid_to_meters(lat_ref, grid_is_latlon, dx_dlon, dy_dlat)
-! Arguments
-real, intent(in) :: lat_ref
-logical, intent(in) :: grid_is_latlon
-real, intent(out) :: dx_dlon
-real, intent(out) :: dy_dlat
+  ! Arguments
+  real, intent(in) :: lat_ref !< Latitude at which to make metric conversion (degree N)
+  logical, intent(in) :: grid_is_latlon !< True if grid model grid is in lat-lon coordinates
+  real, intent(out) :: dx_dlon !< Metric dx/dlon
+  real, intent(out) :: dy_dlat !< Metric dy/dlat
 
   if (grid_is_latlon) then
     dx_dlon=(pi/180.)*Rearth*cos((lat_ref)*(pi/180.))
@@ -394,15 +393,15 @@ subroutine convert_from_grid_to_meters(lat_ref, grid_is_latlon, dx_dlon, dy_dlat
     dy_dlat=1.
   endif
 
-end subroutine  convert_from_grid_to_meters
+end subroutine convert_from_grid_to_meters
 
 ! Returns metric converting distance in meters to grid distance
 subroutine  convert_from_meters_to_grid(lat_ref,grid_is_latlon ,dlon_dx,dlat_dy)
-! Arguments
-real, intent(in) :: lat_ref
-logical, intent(in) :: grid_is_latlon
-real, intent(out) :: dlon_dx
-real, intent(out) :: dlat_dy
+  ! Arguments
+  real, intent(in) :: lat_ref !< Latitude at which to make metric conversion (degree N)
+  logical, intent(in) :: grid_is_latlon !< True if grid model grid is in lat-lon coordinates
+  real, intent(out) :: dlon_dx !< Metric dlon/dx
+  real, intent(out) :: dlat_dy !< Metric dlat/dy
 
   if (grid_is_latlon) then
     dlon_dx=(180./pi)/(Rearth*cos((lat_ref)*(pi/180.)))
@@ -412,34 +411,34 @@ subroutine  convert_from_meters_to_grid(lat_ref,grid_is_latlon ,dlon_dx,dlat_dy)
     dlat_dy=1.
   endif
 
-end subroutine  convert_from_meters_to_grid
+end subroutine convert_from_meters_to_grid
 
+!> Calculates interactive forcs between two bergs.
 subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
                              P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y)
-!Calculating interactive force between icebergs. Alon,  Markpoint_4
-! Arguments
-type(icebergs), pointer :: bergs !< Container for all types and memory
-type(iceberg), pointer :: berg
-type(iceberg), pointer :: other_berg
-type(bond), pointer :: current_bond
-real, intent(in) :: u0
-real, intent(in) :: v0
-real, intent(in) :: u1
-real, intent(in) :: v1
-real, intent(out) :: IA_x
-real, intent(out) :: IA_y
-real, intent(out) :: P_ia_11
-real, intent(out) :: P_ia_12
-real, intent(out) :: P_ia_22
-real, intent(out) :: P_ia_21
-real, intent(out) :: P_ia_times_u_x
-real, intent(out) :: P_ia_times_u_y
-! Local variables
-real :: u2, v2
-logical :: critical_interaction_damping_on
-integer :: grdi, grdj
-logical :: iceberg_bonds_on
-logical :: bonded
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  type(iceberg), pointer :: berg !< Primary iceberg
+  type(iceberg), pointer :: other_berg !< Berg that primary is interacting with
+  real, intent(in) :: u0
+  real, intent(in) :: v0
+  real, intent(in) :: u1
+  real, intent(in) :: v1
+  real, intent(out) :: IA_x
+  real, intent(out) :: IA_y
+  real, intent(out) :: P_ia_11
+  real, intent(out) :: P_ia_12
+  real, intent(out) :: P_ia_22
+  real, intent(out) :: P_ia_21
+  real, intent(out) :: P_ia_times_u_x
+  real, intent(out) :: P_ia_times_u_y
+  ! Local variables
+  type(bond), pointer :: current_bond
+  real :: u2, v2
+  logical :: critical_interaction_damping_on
+  integer :: grdi, grdj
+  logical :: iceberg_bonds_on
+  logical :: bonded
 
   iceberg_bonds_on=bergs%iceberg_bonds_on
 
@@ -480,25 +479,26 @@ subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
   contains
 
   subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1, &
-                             P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded)
-  !Arguments
-  type(icebergs), pointer :: bergs !< Container for all types and memory
-  type(iceberg), pointer :: berg
-  type(iceberg), pointer :: other_berg
-  real :: T1, L1, W1, lon1, lat1, x1, y1, R1, A1   !Current iceberg
-  real :: T2, L2, W2, lon2, lat2, x2, y2, R2, A2   !Other iceberg
-  real :: dlon, dlat
-  real :: r_dist_x, r_dist_y, r_dist, A_o, A_min, trapped, T_min
-  real, intent(in) :: u0,v0, u1, v1
-  real :: P_11, P_12, P_21, P_22
-  real :: M1, M2, M_min
-  real :: u2, v2
-  real :: lat_ref, dx_dlon, dy_dlat
-  logical :: critical_interaction_damping_on
-  real :: spring_coef, accel_spring, radial_damping_coef, p_ia_coef, tangental_damping_coef, bond_coef
-  real, intent(inout) :: IA_x, IA_y
-  real, intent(inout) :: P_ia_11, P_ia_12, P_ia_22, P_ia_21, P_ia_times_u_x, P_ia_times_u_y
-  logical ,intent(in) :: bonded
+                             P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y, bonded)
+    ! Arguments
+    type(icebergs), pointer :: bergs !< Container for all types and memory
+    type(iceberg), pointer :: berg !< Primary berg
+    type(iceberg), pointer :: other_berg !< Berg that primary is interacting with
+    real, intent(inout) :: IA_x, IA_y
+    real, intent(in) :: u0, v0, u1, v1
+    real, intent(inout) :: P_ia_11, P_ia_12, P_ia_22, P_ia_21, P_ia_times_u_x, P_ia_times_u_y
+    logical ,intent(in) :: bonded
+    ! Local variables
+    real :: T1, L1, W1, lon1, lat1, x1, y1, R1, A1   !Current iceberg
+    real :: T2, L2, W2, lon2, lat2, x2, y2, R2, A2   !Other iceberg
+    real :: dlon, dlat
+    real :: r_dist_x, r_dist_y, r_dist, A_o, A_min, trapped, T_min
+    real :: P_11, P_12, P_21, P_22
+    real :: M1, M2, M_min
+    real :: u2, v2
+    real :: lat_ref, dx_dlon, dy_dlat
+    logical :: critical_interaction_damping_on
+    real :: spring_coef, accel_spring, radial_damping_coef, p_ia_coef, tangental_damping_coef, bond_coef
 
     spring_coef=bergs%spring_coef
     !bond_coef=bergs%bond_coef
@@ -631,14 +631,14 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
   end subroutine calculate_force
 
   subroutine overlap_area(R1, R2, d, A, trapped)
-  ! Arguments
-  real, intent(in) :: R1
-  real, intent(in) :: R2
-  real, intent(in) :: d
-  real, intent(out) :: A
-  real, intent(out) :: Trapped
-  ! Local variables
-  real :: R1_sq, R2_sq, d_sq
+    ! Arguments
+    real, intent(in) :: R1
+    real, intent(in) :: R2
+    real, intent(in) :: d
+    real, intent(out) :: A
+    real, intent(out) :: Trapped
+    ! Local variables
+    real :: R1_sq, R2_sq, d_sq
 
     R1_sq=R1**2
     R2_sq=R2**2
@@ -665,48 +665,47 @@ end subroutine overlap_area
 end subroutine interactive_force
 
 !> Calculates the instantaneous acceleration of an iceberg
-subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, axn, ayn, bxn, byn, debug_flag) !Saving  acceleration for Verlet, Adding Verlet flag - Alon  MP1
-!subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, debug_flag) !old version commmented out by Alon
-! Arguments
-type(icebergs), pointer :: bergs !< Container for all types and memory
-type(iceberg), pointer :: berg !< An iceberg
-integer, intent(in) :: i !< i-index of cell berg is in
-integer, intent(in) :: j !< j-index of cell berg is in
-real, intent(in) :: xi !< Non-dimensional x-position within cell of berg
-real, intent(in) :: yj !< Non-dimensional y-position within cell of berg
-real, intent(in) :: lat !< Latitude of berg (degree N)
-real, intent(in) :: uvel !< Zonal velocity of berg (m/s)
-real, intent(in) :: vvel !< Meridional velocity of berg (m/s)
-real, intent(in) :: uvel0
-real, intent(in) :: vvel0
-real, intent(in) :: dt !< Time step (s)
-real, intent(out) :: ax !< Zonal acceleration (m/s2)
-real, intent(out) :: ay !< Meridional acceleration (m/s2)
-real, intent(inout) :: axn
-real, intent(inout) :: ayn
-real, intent(inout) :: bxn
-real, intent(inout) :: byn ! Added implicit and explicit accelerations to output -Alon
-logical, optional :: debug_flag !< If true, print debugging
-! Local variables
-type(icebergs_gridded), pointer :: grd
-real :: uo, vo, ui, vi, ua, va, uwave, vwave, ssh_x, ssh_y, sst, sss, cn, hi
-real :: f_cori, T, D, W, L, M, F
-real :: drag_ocn, drag_atm, drag_ice, wave_rad
-real :: c_ocn, c_atm, c_ice
-real :: ampl, wmod, Cr, Lwavelength, Lcutoff, Ltop
-real, parameter :: accel_lim=1.e-2, Cr0=0.06, vel_lim=15.
-real :: alpha, beta, C_N
-real :: lambda, detA, A11, A12, A21, A22, RHS_x, RHS_y, D_hi
-real :: uveln, vveln, us, vs, speed, loc_dx, new_speed
-real :: u_star, v_star    !Added by Alon
-real :: IA_x, IA_y    !Added by Alon
-real :: P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y    !Added by Alon
-logical :: dumpit
-logical :: interactive_icebergs_on  ! Flag to decide whether to use forces between icebergs.
-logical :: Runge_not_Verlet  ! Flag to specify whether it is Runge-Kutta or Verlet
-logical :: use_new_predictive_corrective !Flad to use Bob's predictive corrective scheme. (default off)
-integer :: itloop
-integer :: stderrunit
+subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, axn, ayn, bxn, byn, debug_flag)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  type(iceberg), pointer :: berg !< An iceberg
+  integer, intent(in) :: i !< i-index of cell berg is in
+  integer, intent(in) :: j !< j-index of cell berg is in
+  real, intent(in) :: xi !< Non-dimensional x-position within cell of berg
+  real, intent(in) :: yj !< Non-dimensional y-position within cell of berg
+  real, intent(in) :: lat !< Latitude of berg (degree N)
+  real, intent(in) :: uvel !< Zonal velocity of berg (m/s)
+  real, intent(in) :: vvel !< Meridional velocity of berg (m/s)
+  real, intent(in) :: uvel0 !< Zonal velocity of berg at beginning of time-step (m/s)
+  real, intent(in) :: vvel0 !< Meridional velocity of berg at beginning of time-step (m/s)
+  real, intent(in) :: dt !< Time step (s)
+  real, intent(out) :: ax !< Zonal acceleration (m/s2)
+  real, intent(out) :: ay !< Meridional acceleration (m/s2)
+  real, intent(inout) :: axn !< Explicit estimate of zonal acceleration (m/s2)
+  real, intent(inout) :: ayn !< Explicit estimate of meridional acceleration (m/s2)
+  real, intent(inout) :: bxn !< Implicit component of zonal acceleration (m/s2)
+  real, intent(inout) :: byn !< Implicit component of meridional acceleration (m/s2)
+  logical, optional :: debug_flag !< If true, print debugging
+  ! Local variables
+  type(icebergs_gridded), pointer :: grd
+  real :: uo, vo, ui, vi, ua, va, uwave, vwave, ssh_x, ssh_y, sst, sss, cn, hi
+  real :: f_cori, T, D, W, L, M, F
+  real :: drag_ocn, drag_atm, drag_ice, wave_rad
+  real :: c_ocn, c_atm, c_ice
+  real :: ampl, wmod, Cr, Lwavelength, Lcutoff, Ltop
+  real, parameter :: accel_lim=1.e-2, Cr0=0.06, vel_lim=15.
+  real :: alpha, beta, C_N
+  real :: lambda, detA, A11, A12, A21, A22, RHS_x, RHS_y, D_hi
+  real :: uveln, vveln, us, vs, speed, loc_dx, new_speed
+  real :: u_star, v_star    !Added by Alon
+  real :: IA_x, IA_y    !Added by Alon
+  real :: P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y    !Added by Alon
+  logical :: dumpit
+  logical :: interactive_icebergs_on  ! Flag to decide whether to use forces between icebergs.
+  logical :: Runge_not_Verlet  ! Flag to specify whether it is Runge-Kutta or Verlet
+  logical :: use_new_predictive_corrective !Flad to use Bob's predictive corrective scheme. (default off)
+  integer :: itloop
+  integer :: stderrunit
 
   Runge_not_Verlet=bergs%Runge_not_Verlet  ! Loading directly from namelist/default , Alon
   interactive_icebergs_on=bergs%interactive_icebergs_on  ! Loading directly from namelist/default , Alon
@@ -881,7 +880,6 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
     !print *,'Before calculation:', berg%iceberg_num, IA_x, IA_y, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y
   endif
 
-
   ! Solve for implicit accelerations
   if (alpha+beta.gt.0.) then
     lambda=drag_ocn+drag_atm+drag_ice
@@ -1097,75 +1095,74 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
   contains
 
   subroutine dump_locfld(grd,i0,j0,A,lbl)
-  ! Arguments
-  type(icebergs_gridded), pointer :: grd
-  integer, intent(in) :: i0, j0
-  real, dimension(grd%isd:grd%ied,grd%jsd:grd%jed), intent(in) :: A
-  character(len=*) :: lbl
-! Local variables
-  integer :: i, j, ii, jj
-  real :: B(-1:1,-1:1), fac
-
-  do jj=-1,1
-    j=max(grd%jsd,min(grd%jed,jj+j0))
-    do ii=-1,1
-      i=max(grd%isd,min(grd%ied,ii+i0))
-      B(ii,jj)=A(i,j)
-      if ((i.ne.ii+i0).or.(j.ne.jj+j0)) B(ii,jj)=-9.999999e-99
+    ! Arguments
+    type(icebergs_gridded), pointer :: grd
+    integer, intent(in) :: i0, j0
+    real, dimension(grd%isd:grd%ied,grd%jsd:grd%jed), intent(in) :: A
+    character(len=*) :: lbl
+    ! Local variables
+    integer :: i, j, ii, jj
+    real :: B(-1:1,-1:1), fac
+
+    do jj=-1,1
+      j=max(grd%jsd,min(grd%jed,jj+j0))
+      do ii=-1,1
+        i=max(grd%isd,min(grd%ied,ii+i0))
+        B(ii,jj)=A(i,j)
+        if ((i.ne.ii+i0).or.(j.ne.jj+j0)) B(ii,jj)=-9.999999e-99
+      enddo
+    enddo
+    write(stderrunit,'("pe=",i3,x,a8,3i12)') mpp_pe(),lbl,(i0+ii,ii=-1,1)
+    do jj=1,-1,-1
+      write(stderrunit,'("pe=",i3,x,i8,3es12.4)') mpp_pe(),j0+jj,(B(ii,jj),ii=-1,1)
     enddo
-  enddo
-  write(stderrunit,'("pe=",i3,x,a8,3i12)') mpp_pe(),lbl,(i0+ii,ii=-1,1)
-  do jj=1,-1,-1
-    write(stderrunit,'("pe=",i3,x,i8,3es12.4)') mpp_pe(),j0+jj,(B(ii,jj),ii=-1,1)
-  enddo
   end subroutine dump_locfld
 
   subroutine dump_locvel(grd,i0,j0,A,lbl)
-  ! Arguments
-  type(icebergs_gridded), pointer :: grd
-  integer, intent(in) :: i0, j0
-  real, dimension(grd%isd:grd%ied,grd%jsd:grd%jed), intent(in) :: A
-  character(len=*) :: lbl
-! Local variables
-  integer :: i, j, ii, jj
-  real :: B(-1:0,-1:0), fac
-
-  do jj=-1,0
-    j=max(grd%jsd,min(grd%jed,jj+j0))
-    do ii=-1,0
-      i=max(grd%isd,min(grd%ied,ii+i0))
-      B(ii,jj)=A(i,j)
-      if ((i.ne.ii+i0).or.(j.ne.jj+j0)) B(ii,jj)=-9.999999e-99
+    ! Arguments
+    type(icebergs_gridded), pointer :: grd
+    integer, intent(in) :: i0, j0
+    real, dimension(grd%isd:grd%ied,grd%jsd:grd%jed), intent(in) :: A
+    character(len=*) :: lbl
+    ! Local variables
+    integer :: i, j, ii, jj
+    real :: B(-1:0,-1:0), fac
+
+    do jj=-1,0
+      j=max(grd%jsd,min(grd%jed,jj+j0))
+      do ii=-1,0
+        i=max(grd%isd,min(grd%ied,ii+i0))
+        B(ii,jj)=A(i,j)
+        if ((i.ne.ii+i0).or.(j.ne.jj+j0)) B(ii,jj)=-9.999999e-99
+      enddo
+    enddo
+    write(stderrunit,'("pe=",i3,x,a8,3i12)') mpp_pe(),lbl,(i0+ii,ii=-1,0)
+    do jj=0,-1,-1
+      write(stderrunit,'("pe=",i3,x,i8,3es12.4)') mpp_pe(),j0+jj,(B(ii,jj),ii=-1,0)
     enddo
-  enddo
-  write(stderrunit,'("pe=",i3,x,a8,3i12)') mpp_pe(),lbl,(i0+ii,ii=-1,0)
-  do jj=0,-1,-1
-    write(stderrunit,'("pe=",i3,x,i8,3es12.4)') mpp_pe(),j0+jj,(B(ii,jj),ii=-1,0)
-  enddo
   end subroutine dump_locvel
 
 end subroutine accel
 
-! ##############################################################################
-
+!> Steps forward thermodynamic state of all bergs
 subroutine thermodynamics(bergs)
-! Arguments
-type(icebergs), pointer :: bergs !< Container for all types and memory
-! Local variables
-type(icebergs_gridded), pointer :: grd
-type(bond), pointer :: current_bond
-real :: M, T, W, L, SST, Vol, Ln, Wn, Tn, nVol, IC, Dn
-real :: Mv, Me, Mb, melt, dvo, dva, dM, Ss, dMe, dMb, dMv
-real :: Mnew, Mnew1, Mnew2, Hocean
-real :: Mbits, nMbits, dMbitsE, dMbitsM, Lbits, Abits, Mbb
-real :: tip_parameter
-real :: Ms, N_bonds, N_max !Ice shelf melt, Number of bonds, Max_number of bonds
-real :: Delta, q
-integer :: i,j, stderrunit
-type(iceberg), pointer :: this, next
-real, parameter :: perday=1./86400.
-integer :: grdi, grdj
-real :: SSS !Temporarily here
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  ! Local variables
+  type(icebergs_gridded), pointer :: grd
+  type(bond), pointer :: current_bond
+  real :: M, T, W, L, SST, Vol, Ln, Wn, Tn, nVol, IC, Dn
+  real :: Mv, Me, Mb, melt, dvo, dva, dM, Ss, dMe, dMb, dMv
+  real :: Mnew, Mnew1, Mnew2, Hocean
+  real :: Mbits, nMbits, dMbitsE, dMbitsM, Lbits, Abits, Mbb
+  real :: tip_parameter
+  real :: Ms, N_bonds, N_max !Ice shelf melt, Number of bonds, Max_number of bonds
+  real :: Delta, q
+  integer :: i,j, stderrunit
+  type(iceberg), pointer :: this, next
+  real, parameter :: perday=1./86400.
+  integer :: grdi, grdj
+  real :: SSS !Temporarily here
 
   ! For convenience
   grd=>bergs%grd
@@ -1425,9 +1422,9 @@ subroutine thermodynamics(bergs)
   contains
 
   subroutine swap_variables(x,y)
-  ! Arguments
-  real, intent(inout) :: x, y
-  real :: temp
+    ! Arguments
+    real, intent(inout) :: x, y
+    real :: temp
     temp=x
     x=y
     y=temp
@@ -1536,87 +1533,88 @@ subroutine create_gridded_icebergs_fields(bergs)
   endif
 end subroutine create_gridded_icebergs_fields
 
+!> Calculates basl melt for given thermodynamic properties
 subroutine find_basal_melt(bergs, dvo, lat, salt, temp, Use_three_equation_model, thickness, basal_melt, iceberg_num)
-! Arguments
-type(icebergs), pointer :: bergs !< Container for all types and memory
-real, intent(in) :: dvo !< Speed of iceberg relative to ocean mixed layer
-real, intent(in) :: lat !< Latitude (for boundary layer calculation)
-real, intent(in) :: salt !< Salinity of mixed layer
-real, intent(in) :: temp !< Temperature of mixed layer
-logical, intent(in) :: Use_three_equation_model !< True uses the 3 equation model, False uses the 2 equation model.
-real, intent(in) :: thickness !< Ice thickness - needed to work out the pressure below the ice
-real, intent(out) :: basal_melt !< Melt rate underneath the icebergs
-integer, intent(in) :: iceberg_num !< Iceberg number, used for debugging (error messages)
-! Local variables
-real :: ustar, f_cori, absf,tfreeze
-real :: Hml !Mixed layer depth
-
-!These could also be useful output variables if needed.
-real :: t_flux, exch_vel_t, exch_vel_s,tflux_shelf,lprec
-
-real ::  Rhoml   ! Ocean mixed layer density in kg m-3.
-real ::  p_int   ! The pressure at the ice-ocean interface, in Pa.
-
-real, parameter :: VK    = 0.40     ! Von Karman's constant - dimensionless
-real :: ZETA_N = 0.052   ! The fraction of the boundary layer over which the
-                         ! viscosity is linearly increasing. (Was 1/8. Why?)
-real, parameter :: RC    = 0.20     ! critical flux Richardson number.
-real :: I_ZETA_N  ! The inverse of ZETA_N.
-real :: I_LF  ! Inverse of Latent Heat of fusion (J kg-1)
-real :: I_VK      ! The inverse of VK.
-real :: PR, SC    ! The Prandtl number and Schmidt number, nondim.
-
-! 3 equation formulation variables
-real :: Sbdry     !   Salinities in the ocean at the interface with the
-real :: Sbdry_it  ! the ice shelf, in PSU.
-real :: dS_it     ! The interface salinity change during an iteration, in PSU.
-real :: hBL_neut  ! The neutral boundary layer thickness, in m.
-real :: hBL_neut_h_molec ! The ratio of the neutral boundary layer thickness
-                         ! to the molecular boundary layer thickness, ND.
-real :: wT_flux ! The vertical fluxes of heat and buoyancy just inside the
-real :: wB_flux ! ocean, in C m s-1 and m2 s-3, ###CURRENTLY POSITIVE UPWARD.
-real :: dB_dS  ! The derivative of buoyancy with salinity, in m s-2 PSU-1.
-real :: dB_dT  ! The derivative of buoyancy with temperature, in m s-2 C-1.
-real :: I_n_star, n_star_term
-real :: dIns_dwB  ! The partial derivative of I_n_star with wB_flux, in ???.
-real :: dT_ustar, dS_ustar
-real :: ustar_h
-real :: Gam_turb
-real :: Gam_mol_t, Gam_mol_s
-real :: RhoCp
-real :: I_RhoLF
-real :: Rho0
-real :: ln_neut
-real :: mass_exch
-real :: Sb_min, Sb_max
-real :: dS_min, dS_max
-real :: density_ice
-
-! Variables used in iterating for wB_flux.
-real :: wB_flux_new, DwB, dDwB_dwB_in
-real :: I_Gam_T, I_Gam_S
-real :: dG_dwB, iDens
-logical :: Sb_min_set, Sb_max_set
-logical :: out_of_bounds
-
-real, parameter :: c2_3 = 2.0/3.0
-integer ::  it1, it3
-
-!Parameters copied ice shelf module defaults (could be entered in the namelist later)
-real, parameter :: dR0_dT = -0.038357 ! Partial derivative of the mixed layer density with temperature, in units of kg m-3 K-1.
-real, parameter :: dR0_dS = 0.805876 ! Partial derivative of the mixed layer density with salinity, in units of kg m-3 psu-1.
-real, parameter :: RHO_T0_S0 = 999.910681 ! Density of water with T=0, S=0 for linear EOS
-real, parameter :: Salin_Ice =0.0 !Salinity of ice
-real, parameter :: Temp_Ice = -15.0 !Salinity of ice
-real, parameter :: kd_molec_salt=  8.02e-10 !The molecular diffusivity of salt in sea water at the freezing point
-real, parameter :: kd_molec_temp=  1.41e-7 !The molecular diffusivity of heat in sea water at the freezing point
-real, parameter :: kv_molec=  1.95e-6 !The molecular molecular kinematic viscosity of sea water at the freezing point
-real, parameter :: Cp_Ice =  2009.0 !Specific heat capacity of ice, taking from HJ99 (Holland and Jenkins 1999)
-real, parameter :: Cp_ml =  3974.0 !Specific heat capacity of mixed layer, taking from HJ99 (Holland and Jenkins 1999)
-real, parameter :: LF =  3.335e5 !Latent heat of fusion, taken from HJ99 (Holland and Jenkins 1999)
-real, parameter :: gamma_t =  0.0 ! Exchange velocity used in 2 equation model. Whn gamma_t is >0, the exchange velocity is independent of u_star.
-                                ! When gamma_t=0.0, then gamma_t is not used, and the exchange velocity is found using u_star.
-real, parameter :: p_atm =  101325 ! Average atmospheric pressure (Pa) - from Google.
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  real, intent(in) :: dvo !< Speed of iceberg relative to ocean mixed layer
+  real, intent(in) :: lat !< Latitude (for boundary layer calculation)
+  real, intent(in) :: salt !< Salinity of mixed layer
+  real, intent(in) :: temp !< Temperature of mixed layer
+  logical, intent(in) :: Use_three_equation_model !< True uses the 3 equation model, False uses the 2 equation model.
+  real, intent(in) :: thickness !< Ice thickness - needed to work out the pressure below the ice
+  real, intent(out) :: basal_melt !< Melt rate underneath the icebergs
+  integer, intent(in) :: iceberg_num !< Iceberg number, used for debugging (error messages)
+  ! Local variables
+  real :: ustar, f_cori, absf,tfreeze
+  real :: Hml !Mixed layer depth
+
+  !These could also be useful output variables if needed.
+  real :: t_flux, exch_vel_t, exch_vel_s,tflux_shelf,lprec
+
+  real ::  Rhoml   ! Ocean mixed layer density in kg m-3.
+  real ::  p_int   ! The pressure at the ice-ocean interface, in Pa.
+
+  real, parameter :: VK    = 0.40     ! Von Karman's constant - dimensionless
+  real :: ZETA_N = 0.052   ! The fraction of the boundary layer over which the
+                           ! viscosity is linearly increasing. (Was 1/8. Why?)
+  real, parameter :: RC    = 0.20     ! critical flux Richardson number.
+  real :: I_ZETA_N  ! The inverse of ZETA_N.
+  real :: I_LF  ! Inverse of Latent Heat of fusion (J kg-1)
+  real :: I_VK      ! The inverse of VK.
+  real :: PR, SC    ! The Prandtl number and Schmidt number, nondim.
+
+  ! 3 equation formulation variables
+  real :: Sbdry     !   Salinities in the ocean at the interface with the
+  real :: Sbdry_it  ! the ice shelf, in PSU.
+  real :: dS_it     ! The interface salinity change during an iteration, in PSU.
+  real :: hBL_neut  ! The neutral boundary layer thickness, in m.
+  real :: hBL_neut_h_molec ! The ratio of the neutral boundary layer thickness
+                           ! to the molecular boundary layer thickness, ND.
+  real :: wT_flux ! The vertical fluxes of heat and buoyancy just inside the
+  real :: wB_flux ! ocean, in C m s-1 and m2 s-3, ###CURRENTLY POSITIVE UPWARD.
+  real :: dB_dS  ! The derivative of buoyancy with salinity, in m s-2 PSU-1.
+  real :: dB_dT  ! The derivative of buoyancy with temperature, in m s-2 C-1.
+  real :: I_n_star, n_star_term
+  real :: dIns_dwB  ! The partial derivative of I_n_star with wB_flux, in ???.
+  real :: dT_ustar, dS_ustar
+  real :: ustar_h
+  real :: Gam_turb
+  real :: Gam_mol_t, Gam_mol_s
+  real :: RhoCp
+  real :: I_RhoLF
+  real :: Rho0
+  real :: ln_neut
+  real :: mass_exch
+  real :: Sb_min, Sb_max
+  real :: dS_min, dS_max
+  real :: density_ice
+
+  ! Variables used in iterating for wB_flux.
+  real :: wB_flux_new, DwB, dDwB_dwB_in
+  real :: I_Gam_T, I_Gam_S
+  real :: dG_dwB, iDens
+  logical :: Sb_min_set, Sb_max_set
+  logical :: out_of_bounds
+
+  real, parameter :: c2_3 = 2.0/3.0
+  integer ::  it1, it3
+
+  !Parameters copied ice shelf module defaults (could be entered in the namelist later)
+  real, parameter :: dR0_dT = -0.038357 ! Partial derivative of the mixed layer density with temperature, in units of kg m-3 K-1.
+  real, parameter :: dR0_dS = 0.805876 ! Partial derivative of the mixed layer density with salinity, in units of kg m-3 psu-1.
+  real, parameter :: RHO_T0_S0 = 999.910681 ! Density of water with T=0, S=0 for linear EOS
+  real, parameter :: Salin_Ice =0.0 !Salinity of ice
+  real, parameter :: Temp_Ice = -15.0 !Salinity of ice
+  real, parameter :: kd_molec_salt=  8.02e-10 !The molecular diffusivity of salt in sea water at the freezing point
+  real, parameter :: kd_molec_temp=  1.41e-7 !The molecular diffusivity of heat in sea water at the freezing point
+  real, parameter :: kv_molec=  1.95e-6 !The molecular molecular kinematic viscosity of sea water at the freezing point
+  real, parameter :: Cp_Ice =  2009.0 !Specific heat capacity of ice, taking from HJ99 (Holland and Jenkins 1999)
+  real, parameter :: Cp_ml =  3974.0 !Specific heat capacity of mixed layer, taking from HJ99 (Holland and Jenkins 1999)
+  real, parameter :: LF =  3.335e5 !Latent heat of fusion, taken from HJ99 (Holland and Jenkins 1999)
+  real, parameter :: gamma_t =  0.0 ! Exchange velocity used in 2 equation model. Whn gamma_t is >0, the exchange velocity is independent of u_star.
+                                  ! When gamma_t=0.0, then gamma_t is not used, and the exchange velocity is found using u_star.
+  real, parameter :: p_atm =  101325 ! Average atmospheric pressure (Pa) - from Google.
 
   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
   density_ice = bergs%rho_bergs

From 0dca7ae756b870054e34e1d6893bf7df90c6ae00 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <aadcroft@princeton.edu>
Date: Mon, 27 Mar 2017 23:58:31 -0400
Subject: [PATCH 213/361] More doxygenization of icebergs.F90

- More API documentation.
- More indenting fixes.
- This is hard work - vim says I'm only 73% of the way through the file
  and this is my second commit after hours of editing for each!
---
 icebergs.F90 | 1216 +++++++++++++++++++++++++++++---------------------
 1 file changed, 700 insertions(+), 516 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 8853f00..deba85a 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -377,7 +377,7 @@ subroutine initialize_iceberg_bonds(bergs)
 
 end subroutine initialize_iceberg_bonds
 
-! Returns metric converting grid distances to meters
+!> Returns metric converting grid distances to meters
 subroutine convert_from_grid_to_meters(lat_ref, grid_is_latlon, dx_dlon, dy_dlat)
   ! Arguments
   real, intent(in) :: lat_ref !< Latitude at which to make metric conversion (degree N)
@@ -395,7 +395,7 @@ subroutine convert_from_grid_to_meters(lat_ref, grid_is_latlon, dx_dlon, dy_dlat
 
 end subroutine convert_from_grid_to_meters
 
-! Returns metric converting distance in meters to grid distance
+!> Returns metric converting distance in meters to grid distance
 subroutine  convert_from_meters_to_grid(lat_ref,grid_is_latlon ,dlon_dx,dlat_dy)
   ! Arguments
   real, intent(in) :: lat_ref !< Latitude at which to make metric conversion (degree N)
@@ -413,19 +413,19 @@ subroutine  convert_from_meters_to_grid(lat_ref,grid_is_latlon ,dlon_dx,dlat_dy)
 
 end subroutine convert_from_meters_to_grid
 
-!> Calculates interactive forcs between two bergs.
+!> Calculates interactions between a berg and all bergs in range
 subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
                              P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
   type(iceberg), pointer :: berg !< Primary iceberg
   type(iceberg), pointer :: other_berg !< Berg that primary is interacting with
-  real, intent(in) :: u0
-  real, intent(in) :: v0
-  real, intent(in) :: u1
-  real, intent(in) :: v1
-  real, intent(out) :: IA_x
-  real, intent(out) :: IA_y
+  real, intent(in) :: u0 !< Zonal velocity of primary berg (m/s)
+  real, intent(in) :: v0 !< Meridional velocity of primary berg (m/s)
+  real, intent(in) :: u1 !< Zonal velocity of other berg (m/s)
+  real, intent(in) :: v1 !< Meridional velocity of other berg (m/s)
+  real, intent(out) :: IA_x !< Net zonal acceleration of berg due to interactions (m/s2)
+  real, intent(out) :: IA_y !< Net meridional acceleration of berg due to interactions (m/s2)
   real, intent(out) :: P_ia_11
   real, intent(out) :: P_ia_12
   real, intent(out) :: P_ia_22
@@ -447,17 +447,17 @@ subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
   P_ia_11=0. ; P_ia_12=0. ;  P_ia_21=0.;  P_ia_22=0.
   P_ia_times_u_x=0. ; P_ia_times_u_y=0.
 
-  bonded=.false. !Unbonded iceberg interactions
-  do grdj = berg%jne-1,berg%jne+1 ; do grdi = berg%ine-1,berg%ine+1  !Note: need  to make sure this is wide enough, but less than the halo width
+  bonded=.false. ! Unbonded iceberg interactions
+  do grdj = berg%jne-1,berg%jne+1 ; do grdi = berg%ine-1,berg%ine+1 ! Note: need to make sure this is wide enough, but less than the halo width
     other_berg=>bergs%list(grdi,grdj)%first
     do while (associated(other_berg)) ! loop over all other bergs
-      call calculate_force(bergs,berg,other_berg, IA_x, IA_y, u0, v0, u1, v1, &
+      call calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1, &
                            P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y, bonded)
       other_berg=>other_berg%next
     enddo ! loop over all bergs
   enddo ; enddo
 
-  bonded=.true.  !Interactions due to iceberg bonds
+  bonded=.true. ! Interactions due to iceberg bonds
   if (iceberg_bonds_on) then ! MP1
     current_bond=>berg%first_bond
     do while (associated(current_bond)) ! loop over all bonds
@@ -465,7 +465,7 @@ subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
       if (.not. associated(other_berg)) then
         call error_mesg('diamonds,bond interactions', 'Trying to do Bond interactions with unassosiated berg!' ,FATAL)
       else
-        call calculate_force(bergs,berg,other_berg, IA_x, IA_y, u0, v0, u1, v1,  &
+        call calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,  &
                              P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded)
       endif
       current_bond=>current_bond%next_bond
@@ -478,19 +478,29 @@ subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
 
   contains
 
+  !> Calculate interactive forces between two bergs
   subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1, &
                              P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y, bonded)
     ! Arguments
     type(icebergs), pointer :: bergs !< Container for all types and memory
     type(iceberg), pointer :: berg !< Primary berg
     type(iceberg), pointer :: other_berg !< Berg that primary is interacting with
-    real, intent(inout) :: IA_x, IA_y
-    real, intent(in) :: u0, v0, u1, v1
-    real, intent(inout) :: P_ia_11, P_ia_12, P_ia_22, P_ia_21, P_ia_times_u_x, P_ia_times_u_y
+    real, intent(inout) :: IA_x !< Net zonal acceleration of berg due to interactions (m/s2)
+    real, intent(inout) :: IA_y !< Net meridional acceleration of berg due to interactions (m/s2)
+    real, intent(in) :: u0 !< Zonal velocity of primary berg (m/s)
+    real, intent(in) :: v0 !< Meridional velocity of primary berg (m/s)
+    real, intent(in) :: u1 !< Zonal velocity of other berg (m/s)
+    real, intent(in) :: v1 !< Meridional velocity of other berg (m/s)
+    real, intent(inout) :: P_ia_11
+    real, intent(inout) :: P_ia_12
+    real, intent(inout) :: P_ia_22
+    real, intent(inout) :: P_ia_21
+    real, intent(inout) :: P_ia_times_u_x
+    real, intent(inout) :: P_ia_times_u_y
     logical ,intent(in) :: bonded
     ! Local variables
-    real :: T1, L1, W1, lon1, lat1, x1, y1, R1, A1   !Current iceberg
-    real :: T2, L2, W2, lon2, lat2, x2, y2, R2, A2   !Other iceberg
+    real :: T1, L1, W1, lon1, lat1, x1, y1, R1, A1 ! Current iceberg
+    real :: T2, L2, W2, lon2, lat2, x2, y2, R2, A2 ! Other iceberg
     real :: dlon, dlat
     real :: r_dist_x, r_dist_y, r_dist, A_o, A_min, trapped, T_min
     real :: P_11, P_12, P_21, P_22
@@ -506,14 +516,14 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
     tangental_damping_coef=bergs%tangental_damping_coef
     critical_interaction_damping_on=bergs%critical_interaction_damping_on
 
-    !Using critical values for damping rather than manually setting the damping.
+    ! Using critical values for damping rather than manually setting the damping.
     if (critical_interaction_damping_on) then
-      radial_damping_coef=2.*sqrt(spring_coef)  ! Critical damping
-      tangental_damping_coef=(2.*sqrt(spring_coef))/4  ! Critical damping   (just a guess)
+      radial_damping_coef=2.*sqrt(spring_coef) ! Critical damping
+      tangental_damping_coef=(2.*sqrt(spring_coef))/4 ! Critical damping (just a guess)
     endif
 
     if (berg%iceberg_num .ne. other_berg%iceberg_num) then
-      !From Berg 1
+      ! From Berg 1
       L1=berg%length
       W1=berg%width
       T1=berg%thickness
@@ -522,7 +532,7 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
       lon1=berg%lon_old; lat1=berg%lat_old
       !call rotpos_to_tang(lon1,lat1,x1,y1)
 
-      !From Berg 1
+      ! From Berg 1
       L2=other_berg%length
       W2=other_berg%width
       T2=other_berg%thickness
@@ -537,8 +547,8 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
       dlon=lon1-lon2
       dlat=lat1-lat2
 
-      !Note that this is not the exact distance along a great circle.
-      !Approximation for small distances. Should be fine.
+      ! Note that this is not the exact distance along a great circle.
+      ! Approximation for small distances. Should be fine.
       !r_dist_x=x1-x2 ; r_dist_y=y1-y2
       !r_dist=sqrt( ((x1-x2)**2) + ((y1-y2)**2) )
       lat_ref=0.5*(lat1+lat2)
@@ -572,7 +582,7 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
       M_min=min(M1,M2)
       !Calculating spring force  (later this should only be done on the first time around)
       if ((r_dist>0.) .AND. ((r_dist< (R1+R2).AND. (.not. bonded)) .OR. ( (r_dist> (R1+R2)) .AND. (bonded) ) )) then
-        !Spring force
+        ! Spring force
         !accel_spring=spring_coef*(T_min/T1)*(A_o/A1) ! Old version dependent on area
         accel_spring=spring_coef*(M_min/M1)*(R1+R2-r_dist)
         IA_x=IA_x+(accel_spring*(r_dist_x/r_dist))
@@ -588,8 +598,8 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
           !endif
           !print *, 'in the loop1', spring_coef, (M_min/M1), accel_spring,(R1+R2-r_dist)
           !print *, 'in the loop2', IA_x, IA_y, R1, R2,r_dist, berg%iceberg_num,other_berg%iceberg_num
-          !Damping force:
-          !Paralel velocity
+          ! Damping force:
+          ! Paralel velocity
           P_11=(r_dist_x*r_dist_x)/(r_dist**2)
           P_12=(r_dist_x*r_dist_y)/(r_dist**2)
           P_21=(r_dist_x*r_dist_y)/(r_dist**2)
@@ -607,7 +617,7 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
           P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
           !print *, 'Paralel: ',berg%iceberg_num,  p_ia_coef, IA_x, P_ia_11, P_ia_21,P_ia_12, P_ia_22
 
-          !Normal velocities
+          ! Normal velocities
           P_11=1-P_11  ;  P_12=-P_12 ; P_21= -P_21 ;    P_22=1-P_22
           !p_ia_coef=tangental_damping_coef*(T_min/T1)*(A_min/A1)
           p_ia_coef=tangental_damping_coef*(M_min/M1)
@@ -630,13 +640,14 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
 
   end subroutine calculate_force
 
+  !> Calculates area of overlap between two circular bergs
   subroutine overlap_area(R1, R2, d, A, trapped)
     ! Arguments
-    real, intent(in) :: R1
-    real, intent(in) :: R2
-    real, intent(in) :: d
-    real, intent(out) :: A
-    real, intent(out) :: Trapped
+    real, intent(in) :: R1 !< Radius of berg 1 (m)
+    real, intent(in) :: R2 !< Radius of berg 2 (m)
+    real, intent(in) :: d !< Separation of berg centers (m)
+    real, intent(out) :: A !< Overlap area (m2)
+    real, intent(out) :: Trapped !< =1. if one berg is completely inside the other, =0. otherwise
     ! Local variables
     real :: R1_sq, R2_sq, d_sq
 
@@ -648,7 +659,7 @@ subroutine overlap_area(R1, R2, d, A, trapped)
     if (d>0.) then
       if (d<(R1+R2)) then
         if (d>abs(R1-R2)) then
-          A= (R1_sq*acos((d_sq+R1_sq-R2_sq)/(2.*d*R1)))  +  (R2_sq*acos((d_sq+R2_sq-R1_sq)/(2.*d*R2)))  - (0.5*sqrt((-d+R1+R2)*(d+R1-R2)*(d-R1+R2)*(d+R1+R2)))
+          A=(R1_sq*acos((d_sq+R1_sq-R2_sq)/(2.*d*R1))) + (R2_sq*acos((d_sq+R2_sq-R1_sq)/(2.*d*R2))) - (0.5*sqrt((-d+R1+R2)*(d+R1-R2)*(d-R1+R2)*(d+R1+R2)))
         else
           A=min(pi*R1_sq,pi*R2_sq)
           Trapped=1.
@@ -657,7 +668,7 @@ subroutine overlap_area(R1, R2, d, A, trapped)
         A=0.
       endif
     else
-      A=0.     ! No area of perfectly overlapping bergs (ie: a berg interacting with itself)
+      A=0. ! No area of perfectly overlapping bergs (ie: a berg interacting with itself)
     endif
 
    end subroutine overlap_area
@@ -763,7 +774,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 
   ! Wave radiation
   uwave=ua-uo; vwave=va-vo  ! Use wind speed rel. to ocean for wave model (aja)?
-  wmod=uwave*uwave+vwave*vwave ! The wave amplitude and length depend on the wind speed relative to the ocean current;
+  wmod=uwave*uwave+vwave*vwave ! The wave amplitude and length depend on the wind speed relative to the ocean current
                                ! actually wmod is wmod**2 here.
   ampl=0.5*0.02025*wmod ! This is "a", the wave amplitude
   Lwavelength=0.32*wmod ! Surface wave length fitted to data in table at
@@ -1087,19 +1098,21 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 
   !Used for testing the ocean response to fixed iceberg motion.
   if (bergs%override_iceberg_velocities) then
-    ax  = 0.0;  ay  = 0.0;
-    axn = 0.0;  ayn = 0.0;
-    bxn = 0.0;  byn = 0.0;
+    ax  = 0.0;  ay  = 0.0
+    axn = 0.0;  ayn = 0.0
+    bxn = 0.0;  byn = 0.0
   endif
 
   contains
 
-  subroutine dump_locfld(grd,i0,j0,A,lbl)
+  !> Print 3x3 cells from 2d array A
+  subroutine dump_locfld(grd, i0, j0, A, lbl)
     ! Arguments
-    type(icebergs_gridded), pointer :: grd
-    integer, intent(in) :: i0, j0
-    real, dimension(grd%isd:grd%ied,grd%jsd:grd%jed), intent(in) :: A
-    character(len=*) :: lbl
+    type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+    integer, intent(in) :: i0 !< i-index of center of 3x3 patch to print
+    integer, intent(in) :: j0 !< j-index of center of 3x3 patch to print
+    real, dimension(grd%isd:grd%ied,grd%jsd:grd%jed), intent(in) :: A !< Field to print
+    character(len=*) :: lbl !< Label to add to messages
     ! Local variables
     integer :: i, j, ii, jj
     real :: B(-1:1,-1:1), fac
@@ -1118,12 +1131,14 @@ subroutine dump_locfld(grd,i0,j0,A,lbl)
     enddo
   end subroutine dump_locfld
 
-  subroutine dump_locvel(grd,i0,j0,A,lbl)
+  !> Print 2x2 cells from 2d array A
+  subroutine dump_locvel(grd, i0, j0, A, lbl)
     ! Arguments
-    type(icebergs_gridded), pointer :: grd
-    integer, intent(in) :: i0, j0
-    real, dimension(grd%isd:grd%ied,grd%jsd:grd%jed), intent(in) :: A
-    character(len=*) :: lbl
+    type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+    integer, intent(in) :: i0 !< i-index of NE-cell of 2x2 patch to print
+    integer, intent(in) :: j0 !< j-index of NE-cell of 2x2 patch to print
+    real, dimension(grd%isd:grd%ied,grd%jsd:grd%jed), intent(in) :: A !< Field to print
+    character(len=*) :: lbl !< Label to add to messages
     ! Local variables
     integer :: i, j, ii, jj
     real :: B(-1:0,-1:0), fac
@@ -1533,7 +1548,7 @@ subroutine create_gridded_icebergs_fields(bergs)
   endif
 end subroutine create_gridded_icebergs_fields
 
-!> Calculates basl melt for given thermodynamic properties
+!> Calculates basal melt for given thermodynamic properties
 subroutine find_basal_melt(bergs, dvo, lat, salt, temp, Use_three_equation_model, thickness, basal_melt, iceberg_num)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
@@ -1829,65 +1844,62 @@ subroutine find_basal_melt(bergs, dvo, lat, salt, temp, Use_three_equation_model
 
 contains
 
+  !> Calculates freezing point potential temperature of seawater using a linear relation
+  !!
+  !! This subroutine computes the freezing point potential temperature
+  !! (in deg C) from salinity (in psu), and pressure (in Pa) using a simple
+  !! linear expression, with coefficients passed in as arguments.
+  !!
+  !! Copied from subroutine calculate_TFreeze_linear_scalar (in MOM/equation_of_state)
   subroutine calculate_TFreeze(S, pres, T_Fr)
-    !Arguments
-    real,    intent(in)  :: S, pres
-    real,    intent(out) :: T_Fr
+    ! Arguments
+    real, intent(in) :: S !< Salinity (1e-3)
+    real, intent(in) :: pres !< Presure (Pa)
+    real, intent(out) :: T_Fr !< Freezing point (C)
+    ! Local variables
     real, parameter :: dTFr_dp    = -7.53E-08    !DTFREEZE_DP in MOM_input
     real, parameter :: dTFr_dS    = -0.0573      !DTFREEZE_DS in MOM_input
     real, parameter :: TFr_S0_P0  =0.0832        !TFREEZE_S0_P0 in MOM_input
-    !    This subroutine computes the freezing point potential temparature
-    !  (in deg C) from salinity (in psu), and pressure (in Pa) using a simple
-    !  linear expression, with coefficients passed in as arguments.
-    !  Copied from subroutine calculate_TFreeze_linear_scalar (in MOM/equation_of_state)
-    !
-    ! Arguments: S - salinity in PSU.
-    !  (in)      pres - pressure in Pa.
-    !  (out)     T_Fr - Freezing point potential temperature in deg C.
-    !  (in)      TFr_S0_P0 - The freezing point at S=0, p=0, in deg C.
-    !  (in)      dTFr_dS - The derivatives of freezing point with salinity, in
-    !                      deg C PSU-1.
-    !  (in)      dTFr_dp - The derivatives of freezing point with pressure, in
-    !                      deg C Pa-1.
+    ! TFr_S0_P0 - The freezing point at S=0, p=0, in deg C.
+    ! dTFr_dS - The derivatives of freezing point with salinity, in deg C PSU-1.
+    ! dTFr_dp - The derivatives of freezing point with pressure, in deg C Pa-1.
     T_Fr = (TFr_S0_P0 + dTFr_dS*S) + dTFr_dp*pres
   end subroutine calculate_TFreeze
 
+  !> Calculates density of seawater using a linear equation of state
+  !!
+  !! This subroutine computes the density of sea water with a trivial
+  !! linear equation of state (in kg/m^3) from salinity (sal in psu),
+  !! potential temperature (T in deg C), and pressure in Pa.
+  !!
+  !! Copied from subroutine calculate_density_scalar_linear (in MOM/equation_of_state)
   subroutine calculate_density(T, S, pressure, rho, Rho_T0_S0, dRho_dT, dRho_dS)
     !Arguments
-    real,    intent(in)  :: T, S, pressure
-    real,    intent(out) :: rho
-    real,    intent(in)  :: Rho_T0_S0, dRho_dT, dRho_dS
-    ! *  This subroutine computes the density of sea water with a trivial  *
-    ! *  linear equation of state (in kg/m^3) from salinity (sal in psu),  *
-    ! *  potential temperature (T in deg C), and pressure in Pa.           *
-    !    Copied from subroutine calculate_density_scalar_linear (in MOM/equation_of_state)
-    ! *                                                                    *
-    ! * Arguments: T - potential temperature relative to the surface in C. *
-    ! *  (in)      S - salinity in PSU.                                    *
-    ! *  (in)      pressure - pressure in Pa.                              *
-    ! *  (out)     rho - in situ density in kg m-3.                        *
-    ! *  (in)      start - the starting point in the arrays.               *
-    ! *  (in)      npts - the number of values to calculate.               *
-    ! *  (in)      Rho_T0_S0 - The density at T=0, S=0, in kg m-3.         *
-    ! *  (in)      dRho_dT - The derivatives of density with temperature   *
-    ! *  (in)      dRho_dS - and salinity, in kg m-3 C-1 and kg m-3 psu-1. *
+    real, intent(in)  :: T !< Potential temperature (C)
+    real, intent(in)  :: S !< Salinity (1e-3)
+    real, intent(in)  :: pressure !< Pressure (Pa)
+    real, intent(out) :: rho !< In situ density (kg/3)
+    real, intent(in)  :: Rho_T0_S0 !< Density at T=0, S=0 (kg/m3)
+    real, intent(in)  :: dRho_dT !< Derivative of density w.r.t. potential temperature (kg/m3/C)
+    real, intent(in)  :: dRho_dS !< Derivative of density w.r.t. salinity (1e3 kg/m3)
     rho = Rho_T0_S0 + dRho_dT*T + dRho_dS*S
   end subroutine calculate_density
 
 end subroutine find_basal_melt
 
+!> Returns orientation of a berg determined by its bonds
 subroutine find_orientation_using_iceberg_bonds(grd, berg, orientation)
-! Arguments
-type(icebergs_gridded), pointer :: grd
-type(iceberg), pointer :: berg
-real, intent(inout) :: orientation
-! Local variables
-type(iceberg), pointer :: other_berg
-type(bond), pointer :: current_bond
-real :: angle, lat1,lat2,lon1,lon2,dlat,dlon
-real :: r_dist_x, r_dist_y
-real :: lat_ref, dx_dlon, dy_dlat
-real :: theta, bond_count, Average_angle
+  ! Arguments
+  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+  type(iceberg), pointer :: berg !< Berg for which orientation is needed
+  real, intent(inout) :: orientation !< Angle of orientation (radians)
+  ! Local variables
+  type(iceberg), pointer :: other_berg
+  type(bond), pointer :: current_bond
+  real :: angle, lat1,lat2,lon1,lon2,dlat,dlon
+  real :: r_dist_x, r_dist_y
+  real :: lat_ref, dx_dlon, dy_dlat
+  real :: theta, bond_count, Average_angle
 
   bond_count=0.
   Average_angle=0.
@@ -1941,27 +1953,34 @@ subroutine find_orientation_using_iceberg_bonds(grd, berg, orientation)
 
 end subroutine find_orientation_using_iceberg_bonds
 
+!> Spread mass of a berg around cells centered on i,j
 subroutine spread_mass_across_ocean_cells(bergs, berg, i, j, x, y, Mberg, Mbits, scaling, Area, Tn)
-! Arguments
-type(icebergs), pointer :: bergs !< Container for all types and memory
-type(icebergs_gridded), pointer :: grd
-type(iceberg), pointer :: berg
-integer, intent(in) :: i, j
-real, intent(in) :: x, y, Mberg, Mbits, scaling, Area
-real, intent(in) :: Tn
-! Local variables
-real :: xL, xC, xR, yD, yC, yU, Mass, L
-real :: yDxL, yDxC, yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR
-real :: S, H, origin_x, origin_y, x0, y0
-real :: Area_Q1,Area_Q2 , Area_Q3,Area_Q4, Area_hex
-real :: fraction_used !fraction of iceberg mass included (part of the mass near the boundary is discarded sometimes)
-real :: I_fraction_used !Inverse of fraction used
-real :: tol
-real :: Dn, Hocean
-real, parameter :: rho_seawater=1035.
-integer :: stderrunit
-logical :: debug
-real :: orientation, Mass_berg
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  type(iceberg), pointer :: berg !< Berg whose mass is being considered
+  integer, intent(in) :: i !< i-index of cell contained center of berg
+  integer, intent(in) :: j !< j-index of cell contained center of berg
+  real, intent(in) :: x !< Longitude of berg (degree E)
+  real, intent(in) :: y !< Latitude of berg (degree N)
+  real, intent(in) :: Mberg !< Mass of berg (kg)
+  real, intent(in) :: Mbits !< Mass of bergy bits (kg)
+  real, intent(in) :: scaling !< Multiplier to scale mass (nondim)
+  real, intent(in) :: Area !< Area of berg (m2)
+  real, intent(in) :: Tn !< Thickness of berg (m)
+  ! Local variables
+  type(icebergs_gridded), pointer :: grd
+  real :: xL, xC, xR, yD, yC, yU, Mass, L
+  real :: yDxL, yDxC, yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR
+  real :: S, H, origin_x, origin_y, x0, y0
+  real :: Area_Q1,Area_Q2 , Area_Q3,Area_Q4, Area_hex
+  real :: fraction_used !fraction of iceberg mass included (part of the mass near the boundary is discarded sometimes)
+  real :: I_fraction_used !Inverse of fraction used
+  real :: tol
+  real :: Dn, Hocean
+  real, parameter :: rho_seawater=1035.
+  integer :: stderrunit
+  logical :: debug
+  real :: orientation, Mass_berg
 
   ! Get the stderr unit number
   stderrunit = stderr()
@@ -1970,7 +1989,7 @@ subroutine spread_mass_across_ocean_cells(bergs, berg, i, j, x, y, Mberg, Mbits,
   grd=>bergs%grd
   Mass_berg=Mberg
 
-  !Trimming icebergs to account for grounded fraction.
+  ! Trimming icebergs to account for grounded fraction.
   if (bergs%grounding_fraction>0.) then
     Hocean=bergs%grounding_fraction*(grd%ocean_depth(i,j)+grd%ssh(i,j))
     Dn=(bergs%rho_bergs/rho_seawater)*Tn ! re-calculate draught (keel depth)
@@ -1986,9 +2005,9 @@ subroutine spread_mass_across_ocean_cells(bergs, berg, i, j, x, y, Mberg, Mbits,
   yDxL=0.  ; yDxC=0. ; yDxR=0. ; yCxL=0. ; yCxR=0.
   yUxL=0.  ; yUxC=0. ; yUxR=0. ; yCxC=1.
 
-  if (.not. bergs%hexagonal_icebergs) then  !Treat icebergs as rectangles of size L:  (this is the default)
+  if (.not. bergs%hexagonal_icebergs) then ! Treat icebergs as rectangles of size L: (this is the default)
 
-    !L is the non dimensional length of the iceberg [  L=(Area of berg/ Area of grid cell)^0.5  ] or something like that.
+    ! L is the non dimensional length of the iceberg [ L=(Area of berg/ Area of grid cell)^0.5 ] or something like that.
     if (grd%area(i,j)>0) then
       L=min( sqrt(Area / grd%area(i,j)),1.0)
     else
@@ -1996,7 +2015,7 @@ subroutine spread_mass_across_ocean_cells(bergs, berg, i, j, x, y, Mberg, Mbits,
     endif
 
     if (bergs%use_old_spreading) then
-      !Old version before icebergs were given size L
+      ! Old version before icebergs were given size L
       xL=min(0.5, max(0., 0.5-x))
       xR=min(0.5, max(0., x-0.5))
       xC=max(0., 1.-(xL+xR))
@@ -2022,23 +2041,23 @@ subroutine spread_mass_across_ocean_cells(bergs, berg, i, j, x, y, Mberg, Mbits,
     yUxR=yU*xR*grd%msk(i+1,j+1)
     yCxC=1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )
 
-    fraction_used=1.  !rectangular bergs do share mass with boundaries (all mass is included in cells)
+    fraction_used=1. ! rectangular bergs do share mass with boundaries (all mass is included in cells)
 
-  else !Spread mass as if elements area hexagonal
+  else ! Spread mass as if elements area hexagonal
 
     orientation=bergs%initial_orientation
     if ((bergs%iceberg_bonds_on) .and. (bergs%rotate_icebergs_for_mass_spreading)) call find_orientation_using_iceberg_bonds(grd,berg,orientation)
 
     if (grd%area(i,j)>0) then
-      H = min(( (sqrt(Area/(2.*sqrt(3.)))  / sqrt(grd%area(i,j)))),1.) ;  !Non dimensionalize element length by grid area. (This gives the non-dim Apothen of the hexagon)
+      H=min(( (sqrt(Area/(2.*sqrt(3.))) / sqrt(grd%area(i,j)))),1.) ! Non-dimensionalize element length by grid area. (This gives the non-dim Apothem of the hexagon)
     else
-      H= (sqrt(3.)/2)*(0.49)  !Largest allowable H, since this makes S=0.49, and S has to be less than 0.5  (Not sure what the implications of this are)
+      H=(sqrt(3.)/2)*(0.49) ! Largest allowable H, since this makes S=0.49, and S has to be less than 0.5 (Not sure what the implications of this are)
     endif
     S=(2/sqrt(3.))*H !Side of the hexagon
 
     if (S>0.5) then
-      !The width of an iceberg should not be greater than half the gridcell, or else it can spread over 3 cells  (i.e. S must be less than 0.5 nondimensionally)
-      !print 'Elements must be smaller than a whole gridcell', 'i.e.: S= ' , S , '>=0.5'
+      ! The width of an iceberg should not be greater than half the grid cell, or else it can spread over 3 cells  (i.e. S must be less than 0.5 non-dimensionally)
+      !print 'Elements must be smaller than a whole grid cell', 'i.e.: S= ' , S , '>=0.5'
       call error_mesg('diamonds, hexagonal spreading', 'Diameter of the iceberg is larger than a grid cell. Use smaller icebergs', WARNING)
     endif
 
@@ -2125,15 +2144,25 @@ subroutine spread_mass_across_ocean_cells(bergs, berg, i, j, x, y, Mberg, Mbits,
 
 end subroutine spread_mass_across_ocean_cells
 
-subroutine spread_variable_across_cells(grd, variable_on_ocean, Var,i,j, &
-           yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR,I_fraction_used)
+!> Distribute a quantity among nine cells on a grid centered at cell i,j
+subroutine spread_variable_across_cells(grd, variable_on_ocean, Var, i, j, &
+           yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR, I_fraction_used)
   ! Arguments
-  type(icebergs_gridded), pointer, intent(in) :: grd
-  real, dimension(grd%isd:grd%ied, grd%jsd:grd%jed, 9), intent(inout) :: variable_on_ocean
-  real, intent(in) :: Var !Variable to be spread accross cell
-  real, intent(in) :: yDxL, yDxC, yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR !Weights
-  real, intent(in) :: I_fraction_used !Amount of iceberg used (inverse)
-  integer, intent(in) :: i, j
+  type(icebergs_gridded), pointer, intent(in) :: grd !< Container for gridded fields
+  real, dimension(grd%isd:grd%ied, grd%jsd:grd%jed, 9), intent(inout) :: variable_on_ocean !< Gridded field to augment
+  real, intent(in) :: Var !< Variable to be spread accross cell
+  real, intent(in) :: yDxL !< Weight for the cell at i-1,j-1
+  real, intent(in) :: yDxC !< Weight for the cell at i-1,j
+  real, intent(in) :: yDxR !< Weight for the cell at i-1,j+1
+  real, intent(in) :: yCxL !< Weight for the cell at i,j-1
+  real, intent(in) :: yCxC !< Weight for the cell at i,j
+  real, intent(in) :: yCxR !< Weight for the cell at i,j-1
+  real, intent(in) :: yUxL !< Weight for the cell at i+1,j-1
+  real, intent(in) :: yUxC !< Weight for the cell at i+1,j
+  real, intent(in) :: yUxR !< Weight for the cell at i+1,j+1
+  real, intent(in) :: I_fraction_used !< Amount of iceberg used (inverse)
+  integer, intent(in) :: i !< i-index of cell containing center of berg
+  integer, intent(in) :: j !< j-index of cell containing center of berg
 
   !Spreading the iceberg mass onto the ocean
   variable_on_ocean(i,j,1)=variable_on_ocean(i,j,1)+(yDxL*Var*I_fraction_used)
@@ -2148,23 +2177,37 @@ subroutine spread_variable_across_cells(grd, variable_on_ocean, Var,i,j, &
 
 end subroutine spread_variable_across_cells
 
+!> Returns area of a triangle
 real function Area_of_triangle(Ax, Ay, Bx, By, Cx, Cy)
-! Arguments
-real, intent(in) :: Ax,Ay,Bx,By,Cx,Cy
-  Area_of_triangle    =   abs(    0.5*((Ax*(By-Cy))+(Bx*(Cy-Ay))+(Cx*(Ay-By))) );
+  ! Arguments
+  real, intent(in) :: Ax !< x-position of corner A
+  real, intent(in) :: Ay !< y-position of corner A
+  real, intent(in) :: Bx !< x-position of corner B
+  real, intent(in) :: By !< y-position of corner B
+  real, intent(in) :: Cx !< x-position of corner C
+  real, intent(in) :: Cy !< y-position of corner C
+  Area_of_triangle    =   abs(    0.5*((Ax*(By-Cy))+(Bx*(Cy-Ay))+(Cx*(Ay-By))) )
 end function Area_of_triangle
 
+!> Returns x rounded of to sig_fig
+!! \todo What the heck is this for? -AJA
 real function roundoff(x,sig_fig)
-! Arguments
-real, intent(in) :: x
-integer, intent(in) :: sig_fig
+  ! Arguments
+  real, intent(in) :: x !< A quantity with 15 significant figures of useful information
+  integer, intent(in) :: sig_fig !< Number of significant figures to keep
   !roundoff=round(x*(10**(sig_fig))
-  roundoff=(FLOAT (INT(x * (10.**sig_fig) + 0.5)) / (10.**sig_fig))
+  roundoff=(FLOAT(INT(x * (10.**sig_fig) + 0.5)) / (10.**sig_fig))
 end function roundoff
 
+!> Returns true of a point is in or on the rectangle with opposite corners A and B
 logical function point_in_interval(Ax, Ay, Bx, By, px, py)
-! Arguments
-real, intent(in) :: Ax,Ay,Bx,By,px,py
+  ! Arguments
+  real, intent(in) :: Ax !< x-position of corner A
+  real, intent(in) :: Ay !< y-position of corner A
+  real, intent(in) :: Bx !< x-position of corner B
+  real, intent(in) :: By !< y-position of corner B
+  real, intent(in) :: px !< x-position of point
+  real, intent(in) :: py !< y-position of point
   point_in_interval=.False.
   if ((px <= max(Ax,Bx)) .and. (px >= min(Ax,Bx))) then
     if ((py <= max(Ay,By)) .and. (py >= min(Ay,By))) then
@@ -2173,17 +2216,24 @@ logical function point_in_interval(Ax, Ay, Bx, By, px, py)
   endif
 end function point_in_interval
 
-logical function point_is_on_the_line(Ax,Ay,Bx,By,qx,qy)
-! Arguments
-real, intent(in) :: Ax,Ay,Bx,By,qx,qy
-real :: tol, dxc,dyc,dxl,dyl,cross
-  !tol=1.e-12;
-  tol=0.0;
-  dxc = qx - Ax;
-  dyc = qy - Ay;
-  dxl = Bx - Ax;
-  dyl = By - Ay;
-  cross = dxc * dyl - dyc * dxl;
+!> Returns true if point q is on a line through points A and B
+logical function point_is_on_the_line(Ax, Ay, Bx, By, qx, qy)
+  ! Arguments
+  real, intent(in) :: Ax !< x-position of point A
+  real, intent(in) :: Ay !< y-position of point A
+  real, intent(in) :: Bx !< x-position of point B
+  real, intent(in) :: By !< y-position of point B
+  real, intent(in) :: qx !< x-position of point q
+  real, intent(in) :: qy !< y-position of point q
+  ! Local variables
+  real :: tol, dxc,dyc,dxl,dyl,cross
+  !tol=1.e-12
+  tol=0.0
+  dxc = qx - Ax
+  dyc = qy - Ay
+  dxl = Bx - Ax
+  dyl = By - Ay
+  cross = dxc * dyl - dyc * dxl
   if (abs(cross)<=tol) then
     point_is_on_the_line=.True.
   else
@@ -2191,23 +2241,32 @@ logical function point_is_on_the_line(Ax,Ay,Bx,By,qx,qy)
   endif
 end function point_is_on_the_line
 
-logical function point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,qx,qy)
-!This function decides whether a point (qx,qy) is inside the triangle ABC.
-!There is also the option to include the boundary of the triangle.
-! Arguments
-real, intent(in) :: Ax,Ay,Bx,By,Cx,Cy,qx,qy
-! Local variables
-real :: l0,l1,l2,p0,p1,p2
-real :: v0x,v1x,v2x,v0y,v1y,v2y,dot00,dot01,dot02,dot11,dot12
+!> Returns True if a point q is inside a triangle ABC
+!!
+!! This function decides whether a point (qx,qy) is inside the triangle ABC.
+!! There is also the option to include the boundary of the triangle.
+logical function point_in_triangle(Ax, Ay, Bx, By, Cx, Cy, qx, qy)
+  ! Arguments
+  real, intent(in) :: Ax !< x-position of corner A
+  real, intent(in) :: Ay !< y-position of corner A
+  real, intent(in) :: Bx !< x-position of corner B
+  real, intent(in) :: By !< y-position of corner B
+  real, intent(in) :: Cx !< x-position of corner C
+  real, intent(in) :: Cy !< y-position of corner C
+  real, intent(in) :: qx !< x-position of point q
+  real, intent(in) :: qy !< y-position of point q
+  ! Local variables
+  real :: l0,l1,l2,p0,p1,p2
+  real :: v0x,v1x,v2x,v0y,v1y,v2y,dot00,dot01,dot02,dot11,dot12
 
   point_in_triangle = .False.
-  if ((Ax==qx .and. Ay==qy) .or. (Bx==qx .and. By==qy) .or. (Cx==qx .and. Cy==qy)) then  !Exclude the pathelogical case
+  if ((Ax==qx .and. Ay==qy) .or. (Bx==qx .and. By==qy) .or. (Cx==qx .and. Cy==qy)) then ! Exclude the pathelogical case
       point_in_triangle = .False.
   else
     if (((point_is_on_the_line(Ax,Ay,Bx,By,qx,qy) .or. (point_is_on_the_line(Ax,Ay,Cx,Cy,qx,qy))) .or. (point_is_on_the_line(Bx,By,Cx,Cy,qx,qy)))) then
       point_in_triangle = .False.
     else
-      !Compute point in triangle using Barycentric coordinates (the same as sum_sign_dot_prod routines)
+      ! Compute point in triangle using Barycentric coordinates (the same as sum_sign_dot_prod routines)
       l0=(qx-Ax)*(By-Ay)-(qy-Ay)*(Bx-Ax)
       l1=(qx-Bx)*(Cy-By)-(qy-By)*(Cx-Bx)
       l2=(qx-Cx)*(Ay-Cy)-(qy-Cy)*(Ax-Cx)
@@ -2221,56 +2280,74 @@ logical function point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,qx,qy)
   endif
 end function point_in_triangle
 
-subroutine Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axis1,Area_positive, Area_negative)  !You should change this name a little, so that it not similar the other routine.
-!This function calculates the area of a triangle on opposited sides of an axis when the triangle is split with two points on one side, and one point on the other.
-!In this fuction, A is the point on one side of the axis, and B,C are on the opposite sides
-! Arguments
-real , intent(in) :: Ax,Ay,Bx,By,Cx,Cy
-character , intent(in) :: axis1
-real, intent(out) :: Area_positive, Area_negative
-real :: pABx, pABy, pACx, pACy, A0
-real :: A_half_triangle, A_triangle
+!> Calculates the two areas of a triangle divided by an axis line
+!!
+!! This function calculates the area of a triangle on opposite sides of an axis when the
+!! triangle is split with two points on one side, and one point on the other.
+!! In this function, A is the point on one side of the axis, and B,C are on the opposite sides.
+!! \todo You should change this name a little, so that it not similar the other routine.
+subroutine Area_of_triangle_across_axes(Ax, Ay, Bx, By, Cx, Cy, axis1, Area_positive, Area_negative)
+  ! Arguments
+  real, intent(in) :: Ax !< x-position of corner A
+  real, intent(in) :: Ay !< y-position of corner A
+  real, intent(in) :: Bx !< x-position of corner B
+  real, intent(in) :: By !< y-position of corner B
+  real, intent(in) :: Cx !< x-position of corner C
+  real, intent(in) :: Cy !< y-position of corner C
+  character, intent(in) :: axis1 !< Either 'x' or 'y'
+  real, intent(out) :: Area_positive !< Area on negative side of axis line
+  real, intent(out) :: Area_negative !< Area on positive side of axis line
+  ! Local variables
+  real :: pABx, pABy, pACx, pACy, A0
+  real :: A_half_triangle, A_triangle
 
-  A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
+  A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy)
 
-  call intercept_of_a_line(Ax,Ay,Bx,By,axis1,pABx, pABy);
-  call intercept_of_a_line(Ax,Ay,Cx,Cy,axis1,pACx, pACy);
+  call intercept_of_a_line(Ax,Ay,Bx,By,axis1,pABx, pABy)
+  call intercept_of_a_line(Ax,Ay,Cx,Cy,axis1,pACx, pACy)
 
   if (axis1=='x')  A0=Ay; !Value used for if statements (deciding up/down vs left/right)
   if (axis1=='y')  A0=Ax; !Value used for if statements (deciding up/down vs left/right)
 
-  A_half_triangle=Area_of_triangle(Ax,Ay,pABx,pABy,pACx,pACy);
+  A_half_triangle=Area_of_triangle(Ax,Ay,pABx,pABy,pACx,pACy)
   if (A0>=0.) then
-    Area_positive= A_half_triangle;
+    Area_positive= A_half_triangle
     Area_negative= A_triangle-A_half_triangle
   else
-    Area_positive= A_triangle-A_half_triangle;
-    Area_negative= A_half_triangle;
+    Area_positive= A_triangle-A_half_triangle
+    Area_negative= A_half_triangle
   endif
 
 end subroutine Area_of_triangle_across_axes
 
-subroutine intercept_of_a_line(Ax,Ay,Bx,By,axes1,x0,y0)
-!This routine returns the position (x0,y0) at which a line AB intercepts the x or y axis
-!The value No_intercept_val is returned when the line does not intercept the axis
-!Arguments
-real, intent(in) :: Ax,Ay,Bx,By
-character, intent(in) ::axes1
-real, intent(out) :: x0,y0
-real :: No_intercept_val !Huge value used to make sure that the intercept is outside the triange in the parralel case.
+!> Returns the axis intercept of a line AB
+!!
+!! This routine returns the position (x0,y0) at which a line AB intercepts the x or y axis.
+!! The value No_intercept_val is returned when the line does not intercept the axis.
+subroutine intercept_of_a_line(Ax, Ay, Bx, By, axes1, x0, y0)
+  ! Arguments
+  real, intent(in) :: Ax !< x-position of corner A
+  real, intent(in) :: Ay !< y-position of corner A
+  real, intent(in) :: Bx !< x-position of corner B
+  real, intent(in) :: By !< y-position of corner B
+  character, intent(in) :: axes1 !< Either 'x' or 'y'
+  real, intent(out) :: x0 !< x-position of intercept
+  real, intent(out) :: y0 !< y-position of intercept
+  ! Local variables
+  real :: No_intercept_val ! Huge value used to make sure that the intercept is outside the triangle in the parallel case.
 
-  No_intercept_val=100000000000.; !Huge value used to make sure that the intercept is outside the triange in the parralel case.
+  No_intercept_val=100000000000. ! Huge value used to make sure that the intercept is outside the triangle in the parallel case.
   x0=No_intercept_val
   y0=No_intercept_val
 
-  if (axes1=='x') then  !x intercept
+  if (axes1=='x') then ! x intercept
     if (Ay.ne.By) then
       x0=Ax -(((Ax-Bx)/(Ay-By))*Ay)
       y0=0.
     endif
   endif
 
-  if (axes1=='y') then !y intercept
+  if (axes1=='y') then ! y intercept
     if (Ax.ne.Bx) then
       x0=0.
       y0=-(((Ay-By)/(Ax-Bx))*Ax)+Ay
@@ -2278,71 +2355,80 @@ subroutine intercept_of_a_line(Ax,Ay,Bx,By,axes1,x0,y0)
   endif
 end subroutine intercept_of_a_line
 
-subroutine divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1,Area_positive, Area_negative)
-!This routine gives you the area of a triangle on opposite sides of the axis specified.
-!It also takes care of the special case where the triangle is totally on one side
-!This routine calls Area_of_triangle_across_axes to calculate the areas when the triangles are split.
-!Arguments
-real, intent(in) :: Ax,Ay,Bx,By,Cx,Cy
-character, intent(in) ::axes1
-real, intent(out) :: Area_positive, Area_negative
-real :: A0,B0,C0
-real A_triangle
-
-  if (axes1=='x') then  !Use the y-coordinates for if statements to see which side of the line you are on
+!> Calculates the area of a triangle on either side of an axis, if any.
+!!
+!! This routine gives you the area of a triangle on opposite sides of the axis specified.
+!! It also takes care of the special case where the triangle is totally on one side.
+!! This routine calls Area_of_triangle_across_axes to calculate the areas when the triangles are split.
+subroutine divding_triangle_across_axes(Ax, Ay, Bx, By, Cx, Cy, axes1, Area_positive, Area_negative)
+  ! Arguments
+  real, intent(in) :: Ax !< x-position of corner A
+  real, intent(in) :: Ay !< y-position of corner A
+  real, intent(in) :: Bx !< x-position of corner B
+  real, intent(in) :: By !< y-position of corner B
+  real, intent(in) :: Cx !< x-position of corner C
+  real, intent(in) :: Cy !< y-position of corner C
+  character, intent(in) :: axes1 !< Either 'x' or 'y'
+  real, intent(out) :: Area_positive !< Area on negative side of axis line
+  real, intent(out) :: Area_negative !< Area on positive side of axis line
+  ! Local variables
+  real :: A0,B0,C0
+  real A_triangle
+
+  if (axes1=='x') then ! Use the y-coordinates for if statements to see which side of the line you are on
     A0=Ay
     B0=By
     C0=Cy
   endif
-  if (axes1=='y') then  !Use the y-coordinates for if statements to see which side of the line you are on
+  if (axes1=='y') then ! Use the y-coordinates for if statements to see which side of the line you are on
     A0=Ax
     B0=Bx
     C0=Cx
   endif
 
-  A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
-  if ((B0*C0)>0.) then !B and C are on the same side  (and non-zero)
-    if ((A0*B0).ge.0.) then !all three on the the same side (if it equals zero, then A0=0 and the otehrs are not)
+  A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy)
+  if ((B0*C0)>0.) then ! B and C are on the same side  (and non-zero)
+    if ((A0*B0).ge.0.) then ! all three on the same side (if it equals zero, then A0=0 and the others are not)
       if ((A0>0.)  .or.  ((A0==0.) .and.  (B0>0.))) then
-        Area_positive= A_triangle;
-        Area_negative= 0.;
+        Area_positive= A_triangle
+        Area_negative= 0.
       else
-        Area_positive= 0.;
-        Area_negative= A_triangle;
+        Area_positive= 0.
+        Area_negative= A_triangle
       endif
     else  !A is on the opposite side to B and C
-      call Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1,Area_positive, Area_negative);
+      call Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1,Area_positive, Area_negative)
     endif
 
   elseif ((B0*C0)<0.) then !B and C are on the opposite sides
     if ((A0*B0).ge. 0.) then !C is all alone
-      call Area_of_triangle_across_axes(Cx,Cy,Bx,By,Ax,Ay,axes1,Area_positive, Area_negative);
+      call Area_of_triangle_across_axes(Cx,Cy,Bx,By,Ax,Ay,axes1,Area_positive, Area_negative)
     else !B is all alone
-      call Area_of_triangle_across_axes(Bx,By,Cx,Cy,Ax,Ay,axes1,Area_positive, Area_negative);
+      call Area_of_triangle_across_axes(Bx,By,Cx,Cy,Ax,Ay,axes1,Area_positive, Area_negative)
     endif
 
   else  !This is the case when either B or C is equal to zero (or both), A0 could be zero too.
     if (((A0.eq.0.) .and. (B0.eq.0.)) .and. (C0.eq.0.)) then
-      Area_positive= 0.;
-      Area_negative= 0.;
+      Area_positive= 0.
+      Area_negative= 0.
     elseif ((A0*B0<0.)  .or.  (A0*C0<0.)) then    !A, B are on opposite sides, and C is zero.  OR  A, C are on opposite sides, and B is zero.
-      call Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1,Area_positive, Area_negative);
+      call Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1,Area_positive, Area_negative)
     elseif (((A0*B0>0.) .or. (A0*C0>0.)) .or. (((abs(A0)>0.) .and. (B0==0.)) .and. (C0==0.))) then
       if (A0>0.) then
-        Area_positive= A_triangle;
-        Area_negative= 0.;
+        Area_positive= A_triangle
+        Area_negative= 0.
       else
-        Area_positive= 0.;
-        Area_negative= A_triangle;
+        Area_positive= 0.
+        Area_negative= A_triangle
       endif
 
     elseif (A0.eq. 0.) then   !(one of B,C is zero too)
       if ((B0>0.) .or. (C0>0.)) then
-        Area_positive= A_triangle;
-        Area_negative= 0.;
+        Area_positive= A_triangle
+        Area_negative= 0.
       elseif ((B0<0.) .or. (C0<0.)) then
-        Area_positive= 0.;
-        Area_negative= A_triangle;
+        Area_positive= 0.
+        Area_negative= A_triangle
       else
         call error_mesg('diamonds, iceberg_run', 'Logical error inside triangle dividing routine', FATAL)
       endif
@@ -2352,38 +2438,49 @@ subroutine divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1,Area_positive, A
   endif
 end subroutine divding_triangle_across_axes
 
-
-subroutine Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy,Area_triangle, Area_Q1, Area_Q2 ,Area_Q3 ,Area_Q4)
-!This routine takes a triangle, and finds the intersection with the four quadrants
-!Arguments
-real, intent(in) :: Ax,Ay,Bx,By,Cx,Cy
-real, intent(out) :: Area_triangle, Area_Q1, Area_Q2 ,Area_Q3 ,Area_Q4
-real :: Area_Upper, Area_Lower, Area_Right, Area_Left
-real :: px, py , qx , qy
-real :: Area_key_quadrant,Error
-real :: tol
-integer :: Key_quadrant
-integer ::sig_fig
-integer :: stderrunit
+!> Areas of a triangle divided into quadrants
+!!
+!! This routine takes a triangle, and finds the intersection with the four quadrants.
+subroutine Triangle_divided_into_four_quadrants(Ax, Ay, Bx, By, Cx, Cy, Area_triangle, Area_Q1, Area_Q2 ,Area_Q3 ,Area_Q4)
+  ! Arguments
+  real, intent(in) :: Ax !< x-position of corner A
+  real, intent(in) :: Ay !< y-position of corner A
+  real, intent(in) :: Bx !< x-position of corner B
+  real, intent(in) :: By !< y-position of corner B
+  real, intent(in) :: Cx !< x-position of corner C
+  real, intent(in) :: Cy !< y-position of corner C
+  real, intent(out) :: Area_triangle !< Are of triangle
+  real, intent(out) :: Area_Q1 !< Are in quadrant 1
+  real, intent(out) :: Area_Q2 !< Are in quadrant 2
+  real, intent(out) :: Area_Q3 !< Are in quadrant 2
+  real, intent(out) :: Area_Q4 !< Are in quadrant 4
+  ! Local variables
+  real :: Area_Upper, Area_Lower, Area_Right, Area_Left
+  real :: px, py , qx , qy
+  real :: Area_key_quadrant,Error
+  real :: tol
+  integer :: Key_quadrant
+  integer ::sig_fig
+  integer :: stderrunit
 
   ! Get the stderr unit number
   stderrunit = stderr()
   tol=1.e-10
 
-  Area_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
+  Area_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy)
 
-  !Calculating area across axes
-  call divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,'x',Area_Upper ,Area_Lower);
-  call divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,'y',Area_Right ,Area_Left);
+  ! Calculating area across axes
+  call divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,'x',Area_Upper ,Area_Lower)
+  call divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,'y',Area_Right ,Area_Left)
 
-  !Decide if the origin is in the triangle. If so, then you have to divide the area 4 ways
-  !This is done by finding a quadrant where the intersection between the triangle and quadrant forms a new triangle
-  !(This occurs when on of the sides of the triangle  intersects both the x and y axis)
+  ! Decide if the origin is in the triangle. If so, then you have to divide the area 4 ways
+  ! This is done by finding a quadrant where the intersection between the triangle and quadrant forms a new triangle
+  ! (This occurs when on of the sides of the triangle  intersects both the x and y axis)
   if (point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.)) then
-    !Find a line in the triangle that cuts both axes in/on the trianlge
+    ! Find a line in the triangle that cuts both axes in/on the triangle
     call intercept_of_a_line(Ax,Ay,Bx,By,'x',px,py); !x_intercept
     call intercept_of_a_line(Ax,Ay,Bx,By,'y',qx,qy); !y_intercept
-    !Note that the 1. here means that we include points on the boundary of the triange.
+    ! Note that the 1. here means that we include points on the boundary of the triangle.
     if (.not.((point_in_interval(Ax,Ay,Bx,By,px,py)) .and. (point_in_interval(Ax,Ay,Bx,By,qx,qy)))) then
       call intercept_of_a_line(Ax,Ay,Cx,Cy,'x',px,py); !x_intercept
       call intercept_of_a_line(Ax,Ay,Cx,Cy,'y',qx,qy); !y_intercept
@@ -2391,7 +2488,7 @@ subroutine Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy,Area_triangle,
         call intercept_of_a_line(Bx,By,Cx,Cy,'x',px,py); !x_intercept
         call intercept_of_a_line(Bx,By,Cx,Cy,'y',qx,qy); !y_intercept
         if (.not.((point_in_interval(Bx,By,Cx,Cy,px,py)) .and. (point_in_interval(Bx,By,Cx,Cy,qx,qy)))) then
-          !You should not get here, but there might be some bugs in the code to do with points exactly falling on axes.
+          ! You should not get here, but there might be some bugs in the code to do with points exactly falling on axes.
           !if (mpp_pe().eq.12) then
             write(stderrunit,*) 'diamonds,corners', Ax,Ay,Bx,By,Cx,Cy
           !endif
@@ -2400,14 +2497,14 @@ subroutine Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy,Area_triangle,
       endif
     endif
 
-    !Assigning quadrants. Key_quadrant is the quadrant with the baby triangle in it.
+    ! Assigning quadrants. Key_quadrant is the quadrant with the baby triangle in it.
     Area_key_quadrant=Area_of_triangle(px,py,qx,qy,0.,0.)
     if ((px.ge. 0.) .and. (qy.ge. 0.)) then  !First quadrant
-      Key_quadrant=1;
+      Key_quadrant=1
     elseif ((px.lt.0.) .and. (qy.ge. 0.)) then  !Second quadrant
       Key_quadrant=2
     elseif ((px.lt. 0.) .and. (qy.lt. 0.)) then !Third quadrant
-      Key_quadrant=3;
+      Key_quadrant=3
     elseif ((px.ge. 0.) .and. (qy.lt. 0.)) then !Forth quadrant
       Key_quadrant=4
     else  !
@@ -2415,54 +2512,53 @@ subroutine Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy,Area_triangle,
       write(stderrunit,*) 'diamonds, Triangle, px,qy', px,qy
     endif
 
-  else  !At least one quadrant is empty, and this can be used to find the areas in the other quadrant.  Assigning quadrants. Key_quadrant is the empty quadrant.
-    Area_key_quadrant=0;
+  else ! At least one quadrant is empty, and this can be used to find the areas in the other quadrant.  Assigning quadrants. Key_quadrant is the empty quadrant.
+    Area_key_quadrant=0
     if      ( (.not. ((((Ax>0.) .and. (Ay>0.)) .or. ((Bx>0.) .and. (By> 0.))) .or. ((Cx>0.) .and. (Cy> 0.)))) .and. ((Area_Upper+Area_Right).le.Area_triangle) ) then
-      !No points land in this quadrant and triangle does not cross the quadrant
-      Key_quadrant=1;
+      ! No points land in this quadrant and triangle does not cross the quadrant
+      Key_quadrant=1
     elseif  ( (.not. ((((Ax<0.) .and. (Ay>0)) .or. ((Bx<0.) .and. (By>0.))) .or. ((Cx<0.) .and. (Cy>0.)))) .and. ((Area_Upper+Area_Left).le. Area_triangle) ) then
       Key_quadrant=2
     elseif  ( (.not. ((((Ax<0.) .and. (Ay<0.)) .or. ((Bx<0.) .and. (By< 0.))) .or. ((Cx<0.) .and. (Cy< 0.)))) .and. ((Area_Lower+Area_Left) .le.Area_triangle) ) then
-      Key_quadrant=3;
+      Key_quadrant=3
     else
       Key_quadrant=4
     endif
   endif
 
-
-  !Assign values to quadrants
+  ! Assign values to quadrants
   if (Key_quadrant .eq. 1) then
-    Area_Q1=Area_key_quadrant;
-    Area_Q2=Area_Upper-Area_Q1;
-    Area_Q4=Area_Right-Area_Q1;
-    !Area_Q3=Area_Left-Area_Q2;   !These lines have been changes so that the sum of the 4 quadrants exactly matches the triangle area.
-    Area_Q3=Area_triangle-(Area_Q1+Area_Q2+Area_Q4);
+    Area_Q1=Area_key_quadrant
+    Area_Q2=Area_Upper-Area_Q1
+    Area_Q4=Area_Right-Area_Q1
+    !Area_Q3=Area_Left-Area_Q2 ! These lines have been changes so that the sum of the 4 quadrants exactly matches the triangle area.
+    Area_Q3=Area_triangle-(Area_Q1+Area_Q2+Area_Q4)
   elseif (Key_quadrant .eq. 2) then
-    Area_Q2=Area_key_quadrant;
-    Area_Q1=Area_Upper-Area_Q2;
-    Area_Q4=Area_Right-Area_Q1;
-    !Area_Q3=Area_Left-Area_Q2;
-    Area_Q3=Area_triangle-(Area_Q1+Area_Q2+Area_Q4);
+    Area_Q2=Area_key_quadrant
+    Area_Q1=Area_Upper-Area_Q2
+    Area_Q4=Area_Right-Area_Q1
+    !Area_Q3=Area_Left-Area_Q2
+    Area_Q3=Area_triangle-(Area_Q1+Area_Q2+Area_Q4)
   elseif (Key_quadrant==3) then
-    Area_Q3=Area_key_quadrant;
-    Area_Q2=Area_Left-Area_Q3;
-    Area_Q1=Area_Upper-Area_Q2;
-    !Area_Q4=Area_Right-Area_Q1;
-    Area_Q4=Area_triangle-(Area_Q1+Area_Q2+Area_Q3);
+    Area_Q3=Area_key_quadrant
+    Area_Q2=Area_Left-Area_Q3
+    Area_Q1=Area_Upper-Area_Q2
+    !Area_Q4=Area_Right-Area_Q1
+    Area_Q4=Area_triangle-(Area_Q1+Area_Q2+Area_Q3)
   elseif (Key_quadrant==4) then
-    Area_Q4=Area_key_quadrant;
-    Area_Q1=Area_Right-Area_Q4;
-    Area_Q2=Area_Upper-Area_Q1;
-    !Area_Q3=Area_Left-Area_Q2;
-    Area_Q3=Area_triangle-(Area_Q1+Area_Q2+Area_Q4);
+    Area_Q4=Area_key_quadrant
+    Area_Q1=Area_Right-Area_Q4
+    Area_Q2=Area_Upper-Area_Q1
+    !Area_Q3=Area_Left-Area_Q2
+    Area_Q3=Area_triangle-(Area_Q1+Area_Q2+Area_Q4)
   else
     call error_mesg('diamonds, iceberg_run', 'Logical error inside triangle into four quadrants. Should not get here.', FATAL)
   endif
 
-  Area_Q1=max(Area_Q1,0.);
-  Area_Q2=max(Area_Q2,0.);
-  Area_Q3=max(Area_Q3,0.);
-  Area_Q4=max(Area_Q4,0.);
+  Area_Q1=max(Area_Q1,0.)
+  Area_Q2=max(Area_Q2,0.)
+  Area_Q3=max(Area_Q3,0.)
+  Area_Q4=max(Area_Q4,0.)
 
 
   Error=abs(Area_Q1+Area_Q2+Area_Q3+Area_Q4-Area_triangle)
@@ -2482,29 +2578,44 @@ subroutine Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy,Area_triangle,
 
 end subroutine Triangle_divided_into_four_quadrants
 
-subroutine rotate_and_translate(px,py,theta,x0,y0)
-  !This function takes a point px,py, and rotates it clockwise around the origin by theta degrees, and then translates by (x0,y0)
+!> Rotates a point clockwise about origin and then translates by x0,y0
+subroutine rotate_and_translate(px, py, theta, x0, y0)
   ! Arguments
-  real, intent(in) :: x0,y0,theta
-  real, intent(inout) :: px,py
+  real, intent(in) :: x0 !< x-direction shift
+  real, intent(in) :: y0 !< y-direction shift
+  real, intent(in) :: theta !< Angle to rotate (degrees)
+  real, intent(inout) :: px !< x-coordinate of point
+  real, intent(inout) :: py !< y-coordinate of point
+  ! Local variables
   real :: px_temp,py_temp
 
-  !Rotation
+  ! Rotation
   px_temp = ( cos(theta*pi/180)*px) + (sin(theta*pi/180)*py)
   py_temp = (-sin(theta*pi/180)*px) + (cos(theta*pi/180)*py)
 
-  !Translation
+  ! Translation
   px= px_temp + x0
   py= py_temp + y0
 end subroutine rotate_and_translate
 
-subroutine Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex ,Area_Q1, Area_Q2, Area_Q3, Area_Q4)
-  !This subroutine divides a regular hexagon centered at x0,y0 with apothen H, and orientation theta into its intersection with the 4 quadrants
-  !Theta=0 assumes that the apothen points upwards. (also the rotation is not working yet)
-  !Script works by finding the corners of the 6 triangles, and then finding the intersection of each of these with each quadrant.
-  !Arguments
-  real, intent(in) :: x0,y0,H,theta
-  real, intent(out) :: Area_hex ,Area_Q1, Area_Q2, Area_Q3, Area_Q4
+!> Areas of a hexagon divided into quadrants
+!!
+!! This subroutine divides a regular hexagon centered at x0,y0 with apothem H, and orientation theta into its intersection with the 4 quadrants.
+!! Theta=0 assumes that the apothem points upwards.
+!! Routine works by finding the corners of the 6 triangles, and then finding the intersection of each of these with each quadrant.
+!! \todo (also the rotation is not working yet)
+subroutine Hexagon_into_quadrants_using_triangles(x0, y0, H, theta, Area_hex ,Area_Q1, Area_Q2, Area_Q3, Area_Q4)
+  ! Arguments
+  real, intent(in) :: x0 !< x-coordinate of center of hexagon
+  real, intent(in) :: y0 !< y-coordinate of center of hexagon
+  real, intent(in) :: H !< Apothem (inner radius of hexagon)
+  real, intent(in) :: theta !< Orientation angle of hexagon
+  real, intent(out) :: Area_hex !< Area of hexagon
+  real, intent(out) :: Area_Q1 !< Are in quadrant 1
+  real, intent(out) :: Area_Q2 !< Are in quadrant 2
+  real, intent(out) :: Area_Q3 !< Are in quadrant 2
+  real, intent(out) :: Area_Q4 !< Are in quadrant 4
+  ! Local variables
   real :: C1x, C2x, C3x, C4x, C5x, C6x
   real :: C1y, C2y, C3y, C4y, C5y, C6y
   real :: T12_Area, T12_Q1, T12_Q2, T12_Q3, T12_Q4
@@ -2521,10 +2632,10 @@ subroutine Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex ,Area_Q
   stderrunit = stderr()
   tol=1.e-10
 
-  !Length of side of Hexagon
+  ! Length of side of Hexagon
   S=(2/sqrt(3.))*H
 
-  !Finding positions of corners
+  ! Finding positions of corners
   C1x=S           ; C1y=0.  !Corner 1 (right)
   C2x=H/sqrt(3.)  ; C2y=H;  !Corner 2 (top right)
   C3x=-H/sqrt(3.) ; C3y=H;  !Corner 3 (top left)
@@ -2532,7 +2643,7 @@ subroutine Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex ,Area_Q
   C5x=-H/sqrt(3.) ; C5y=-H; !Corner 5 (bottom left)
   C6x=H/sqrt(3.)  ; C6y=-H; !Corner 6 (bottom right)
 
-  !Finding positions of corners
+  ! Finding positions of corners
   call rotate_and_translate(C1x,C1y,theta,x0,y0)
   call rotate_and_translate(C2x,C2y,theta,x0,y0)
   call rotate_and_translate(C3x,C3y,theta,x0,y0)
@@ -2540,7 +2651,7 @@ subroutine Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex ,Area_Q
   call rotate_and_translate(C5x,C5y,theta,x0,y0)
   call rotate_and_translate(C6x,C6y,theta,x0,y0)
 
-  !Area of Hexagon is the sum of the triangles
+  ! Area of Hexagon is the sum of the triangles
   call Triangle_divided_into_four_quadrants(x0,y0,C1x,C1y,C2x,C2y,T12_Area,T12_Q1,T12_Q2,T12_Q3,T12_Q4); !Triangle 012
   call Triangle_divided_into_four_quadrants(x0,y0,C2x,C2y,C3x,C3y,T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4); !Triangle 023
   call Triangle_divided_into_four_quadrants(x0,y0,C3x,C3y,C4x,C4y,T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4); !Triangle 034
@@ -2548,17 +2659,17 @@ subroutine Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex ,Area_Q
   call Triangle_divided_into_four_quadrants(x0,y0,C5x,C5y,C6x,C6y,T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4); !Triangle 056
   call Triangle_divided_into_four_quadrants(x0,y0,C6x,C6y,C1x,C1y,T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4); !Triangle 061
 
-  !Summing up the triangles
-  Area_hex=T12_Area+T23_Area+T34_Area+T45_Area+T56_Area+T61_Area;
-  Area_Q1=T12_Q1+T23_Q1+T34_Q1+T45_Q1+T56_Q1+T61_Q1;
-  Area_Q2=T12_Q2+T23_Q2+T34_Q2+T45_Q2+T56_Q2+T61_Q2;
-  Area_Q3=T12_Q3+T23_Q3+T34_Q3+T45_Q3+T56_Q3+T61_Q3;
-  Area_Q4=T12_Q4+T23_Q4+T34_Q4+T45_Q4+T56_Q4+T61_Q4;
+  ! Summing up the triangles
+  Area_hex=T12_Area+T23_Area+T34_Area+T45_Area+T56_Area+T61_Area
+  Area_Q1=T12_Q1+T23_Q1+T34_Q1+T45_Q1+T56_Q1+T61_Q1
+  Area_Q2=T12_Q2+T23_Q2+T34_Q2+T45_Q2+T56_Q2+T61_Q2
+  Area_Q3=T12_Q3+T23_Q3+T34_Q3+T45_Q3+T56_Q3+T61_Q3
+  Area_Q4=T12_Q4+T23_Q4+T34_Q4+T45_Q4+T56_Q4+T61_Q4
 
-  Area_Q1=max(Area_Q1,0.);
-  Area_Q2=max(Area_Q2,0.);
-  Area_Q3=max(Area_Q3,0.);
-  Area_Q4=max(Area_Q4,0.);
+  Area_Q1=max(Area_Q1,0.)
+  Area_Q2=max(Area_Q2,0.)
+  Area_Q3=max(Area_Q3,0.)
+  Area_Q4=max(Area_Q4,0.)
 
   Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
   if ((abs(Error)>tol))then
@@ -2584,7 +2695,7 @@ subroutine Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex ,Area_Q
     endif
   endif
 
-  !Adjust Areas so that the error is zero by subtracting the error from the largest sector.
+  ! Adjust Areas so that the error is zero by subtracting the error from the largest sector.
    if  (((Area_Q1>=Area_Q2) .and. (Area_Q1>=Area_Q3)) .and. (Area_Q1>=Area_Q4)) then
      Area_Q1=Area_Q1+Error
    elseif  (((Area_Q2>=Area_Q1) .and. (Area_Q2>=Area_Q3)) .and. (Area_Q2>=Area_Q4)) then
@@ -2604,20 +2715,33 @@ subroutine Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex ,Area_Q
 end subroutine Hexagon_into_quadrants_using_triangles
 
 subroutine interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, sss, cn, hi)
-! Arguments
-type(icebergs_gridded), pointer :: grd
-integer, intent(in) :: i, j
-real, intent(in) :: xi, yj
-real, intent(out) :: uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, sss, cn, hi
-! Local variables
-real :: cos_rot, sin_rot
+  ! Arguments
+  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+  integer, intent(in) :: i !< i-index of cell in which to interpolate
+  integer, intent(in) :: j !< j-index of cell in which to interpolate
+  real, intent(in) :: xi !< Non-dimensional x-position within cell to interpolate to
+  real, intent(in) :: yj !< Non-dimensional y-position within cell to interpolate to
+  real, intent(out) :: uo !< Ocean zonal velocity at point xi,yj (m/s)
+  real, intent(out) :: vo !< Ocean meridional velocity at point xi,yj (m/s)
+  real, intent(out) :: ui !< Ice zonal velocity at point xi,yj (m/s)
+  real, intent(out) :: vi !< Ice meridional velocity at point xi,yj (m/s)
+  real, intent(out) :: ua !< Atmospheric zonal velocity at point xi,yj (m/s)
+  real, intent(out) :: va !< Atmospheric meridional velocity at point xi,yj (m/s)
+  real, intent(out) :: ssh_x !< Zonal slope of sea-surface height (nondim)
+  real, intent(out) :: ssh_y !< Meridional slope of sea-surface height (nondim)
+  real, intent(out) :: sst !< Sea-surface temperature (C)
+  real, intent(out) :: sss !< Sea-surface salinity (1e-3)
+  real, intent(out) :: cn !< Sea-ice concentration (nondim)
+  real, intent(out) :: hi !< Sea-ice thickness (m)
+  ! Local variables
+  real :: cos_rot, sin_rot
 #ifdef USE_OLD_SSH_GRADIENT
-real :: dxm, dx0, dxp
+  real :: dxm, dx0, dxp
 #endif
-real :: hxm, hxp
-real, parameter :: ssh_coast=0.00
-integer :: stderrunit
-integer :: ii, jj
+  real :: hxm, hxp
+  real, parameter :: ssh_coast=0.00
+  integer :: stderrunit
+  integer :: ii, jj
 
   ! Get the stderr unit number
   stderrunit = stderr()
@@ -2719,36 +2843,44 @@ subroutine interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y,
     call error_mesg('diamonds, interp fields', 'field interpaolations has NaNs', FATAL)
 
   endif
+
   contains
 
+  !> Returns zonal slope of sea-surface height across the east face of cell i,j
   real function ddx_ssh(grd,i,j)
-  ! Arguments
-  type(icebergs_gridded), pointer :: grd
-  integer, intent(in) :: i, j
-  ! Local variables
-  real :: dxp,dx0
+    ! Arguments
+    type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+    integer, intent(in) :: i !< i-index of cell
+    integer, intent(in) :: j !< j-index of cell
+    ! Local variables
+    real :: dxp,dx0
     dxp=0.5*(grd%dx(i+1,j)+grd%dx(i+1,j-1))
     dx0=0.5*(grd%dx(i,j)+grd%dx(i,j-1))
     ddx_ssh=2.*(grd%ssh(i+1,j)-grd%ssh(i,j))/(dx0+dxp)*grd%msk(i+1,j)*grd%msk(i,j)
   end function ddx_ssh
 
+  !> Returns meridional slope of sea-surface height across the northern face of cell i,j
   real function ddy_ssh(grd,i,j)
-  ! Arguments
-  type(icebergs_gridded), pointer :: grd
-  integer, intent(in) :: i, j
-  ! Local variables
-  real :: dyp,dy0
+    ! Arguments
+    type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+    integer, intent(in) :: i !< i-index of cell
+    integer, intent(in) :: j !< j-index of cell
+    ! Local variables
+    real :: dyp,dy0
     dyp=0.5*(grd%dy(i,j+1)+grd%dy(i-1,j+1))
     dy0=0.5*(grd%dy(i,j)+grd%dy(i-1,j))
     ddy_ssh=2.*(grd%ssh(i,j+1)-grd%ssh(i,j))/(dy0+dyp)*grd%msk(i,j+1)*grd%msk(i,j)
   end function ddy_ssh
 
+  ! Rotates vector (u,v) using rotation matrix with elements cos_rot and sin_rot
   subroutine rotate(u, v, cos_rot, sin_rot)
-  ! Arguments
-  real, intent(inout) :: u, v
-  real, intent(in) :: cos_rot, sin_rot
-  ! Local variables
-  real :: u_old, v_old
+    ! Arguments
+    real, intent(inout) :: u !< x-component of vector
+    real, intent(inout) :: v !< y-component of vector
+    real, intent(in) :: cos_rot !< Cosine of rotation angle
+    real, intent(in) :: sin_rot !< Sine of rotation angle
+    ! Local variables
+    real :: u_old, v_old
 
     u_old=u
     v_old=v
@@ -2759,16 +2891,16 @@ end subroutine rotate
 
 end subroutine interp_flds
 
-
+!> Calculates bergs%grd%mass_on_ocean
 subroutine calculate_mass_on_ocean(bergs, with_diagnostics)
-! Arguments
-type(icebergs), pointer :: bergs !< Container for all types and memory
-type(iceberg), pointer :: berg
-type(icebergs_gridded), pointer :: grd
-logical, intent(in) :: with_diagnostics
-! Local variables
-integer :: grdj, grdi
-integer :: j, i
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  logical, intent(in) :: with_diagnostics
+  ! Local variables
+  type(iceberg), pointer :: berg
+  type(icebergs_gridded), pointer :: grd
+  integer :: grdj, grdi
+  integer :: j, i
 
   ! For convenience
   grd=>bergs%grd
@@ -2801,66 +2933,82 @@ subroutine calculate_mass_on_ocean(bergs, with_diagnostics)
 
   contains
 
-  subroutine calculate_sum_over_bergs_diagnositcs(bergs,grd,berg,i,j)
-  ! Arguments
-  type(icebergs), pointer :: bergs !< Container for all types and memory
-  type(iceberg), pointer :: berg
-  type(icebergs_gridded), pointer :: grd
-  integer, intent(in) :: i, j
-  ! Local variables
-  real ::  Abits, Lbits, Mbits
-
-   !Virtual area diagnostic
-   if (grd%id_virtual_area>0) then
-     if (bergs%bergy_bit_erosion_fraction>0.) then
-       Lbits=min(berg%length,berg%width,berg%thickness,40.) ! assume bergy bits are smallest dimension or 40 meters
-       Abits=(berg%mass_of_bits/bergs%rho_bergs)/Lbits ! Effective bottom area (assuming T=Lbits)
-     else
-       Abits=0.0
-     endif
-     grd%virtual_area(i,j)=grd%virtual_area(i,j)+(berg%width*berg%length+Abits)*berg%mass_scaling ! m^2
-   endif
+  !> Projects additional diagnostics of bergs on to the grid
+  subroutine calculate_sum_over_bergs_diagnositcs(bergs, grd, berg, i, j)
+    ! Arguments
+    type(icebergs), pointer :: bergs !< Container for all types and memory
+    type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+    type(iceberg), pointer :: berg !< An iceberg
+    integer, intent(in) :: i !< i-index of cell containing berg
+    integer, intent(in) :: j !< j-index of cell containing berg
+    ! Local variables
+    real ::  Abits, Lbits, Mbits
+
+    !Virtual area diagnostic
+    if (grd%id_virtual_area>0) then
+      if (bergs%bergy_bit_erosion_fraction>0.) then
+        Lbits=min(berg%length,berg%width,berg%thickness,40.) ! assume bergy bits are smallest dimension or 40 meters
+        Abits=(berg%mass_of_bits/bergs%rho_bergs)/Lbits ! Effective bottom area (assuming T=Lbits)
+      else
+        Abits=0.0
+      endif
+      grd%virtual_area(i,j)=grd%virtual_area(i,j)+(berg%width*berg%length+Abits)*berg%mass_scaling ! m^2
+    endif
 
-   !Mass diagnostic (also used in u_iceberg, v_iceberg
-   if ((grd%id_mass>0 ) .or. ((grd%id_u_iceberg>0) .or. (grd%id_v_iceberg>0)))   &
-        & grd%mass(i,j)=grd%mass(i,j)+berg%mass/grd%area(i,j)*berg%mass_scaling ! kg/m2
+    !Mass diagnostic (also used in u_iceberg, v_iceberg
+    if ((grd%id_mass>0 ) .or. ((grd%id_u_iceberg>0) .or. (grd%id_v_iceberg>0)))   &
+         & grd%mass(i,j)=grd%mass(i,j)+berg%mass/grd%area(i,j)*berg%mass_scaling ! kg/m2
 
-   !Finding the average iceberg velocity in a grid cell (mass weighted)
-   if (grd%id_u_iceberg>0) &
-   grd%u_iceberg(i,j)=grd%u_iceberg(i,j)+((berg%mass/grd%area(i,j)*berg%mass_scaling)*berg%uvel) ! kg/m2
-   if (grd%id_v_iceberg>0) &
-   grd%v_iceberg(i,j)=grd%v_iceberg(i,j)+((berg%mass/grd%area(i,j)*berg%mass_scaling)*berg%vvel) ! kg/m2
+    !Finding the average iceberg velocity in a grid cell (mass weighted)
+    if (grd%id_u_iceberg>0) &
+    grd%u_iceberg(i,j)=grd%u_iceberg(i,j)+((berg%mass/grd%area(i,j)*berg%mass_scaling)*berg%uvel) ! kg/m2
+    if (grd%id_v_iceberg>0) &
+    grd%v_iceberg(i,j)=grd%v_iceberg(i,j)+((berg%mass/grd%area(i,j)*berg%mass_scaling)*berg%vvel) ! kg/m2
 
-   !Mass of bergy bits
-   if (grd%id_bergy_mass>0 .or. bergs%add_weight_to_ocean)&
-        & grd%bergy_mass(i,j)=grd%bergy_mass(i,j)+berg%mass_of_bits/grd%area(i,j)*berg%mass_scaling ! kg/m2
- end subroutine calculate_sum_over_bergs_diagnositcs
+    !Mass of bergy bits
+    if (grd%id_bergy_mass>0 .or. bergs%add_weight_to_ocean)&
+         & grd%bergy_mass(i,j)=grd%bergy_mass(i,j)+berg%mass_of_bits/grd%area(i,j)*berg%mass_scaling ! kg/m2
+  end subroutine calculate_sum_over_bergs_diagnositcs
 
 end subroutine calculate_mass_on_ocean
 
+!> The main driver the steps updates icebergs
 subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh, sst, calving_hflx, cn, hi, &
                         stagger, stress_stagger, sss, mass_berg, ustar_berg, area_berg)
-! Arguments
-type(icebergs), pointer :: bergs !< Container for all types and memory
-type(time_type), intent(in) :: time
-real, dimension(:,:), intent(inout) :: calving, calving_hflx
-real, dimension(:,:), intent(in) :: uo, vo, ui, vi, tauxa, tauya, ssh, sst, cn, hi
-integer,    optional, intent(in) :: stagger, stress_stagger
-real, dimension(:,:), optional, intent(in) :: sss
-real, dimension(:,:), optional, pointer ::  mass_berg, ustar_berg, area_berg
-! Local variables
-integer :: iyr, imon, iday, ihr, imin, isec, k
-type(icebergs_gridded), pointer :: grd
-logical :: lerr, sample_traj, write_traj, lbudget, lverbose, check_bond_quality
-real :: unused_calving, tmpsum, grdd_berg_mass, grdd_bergy_mass,grdd_spread_mass, grdd_spread_area
-real :: grdd_u_iceberg, grdd_v_iceberg, grdd_ustar_iceberg, grdd_spread_uvel, grdd_spread_vvel
-integer :: i, j, Iu, ju, iv, Jv, Iu_off, ju_off, iv_off, Jv_off
-real :: mask, max_SST
-real, dimension(:,:), allocatable :: uC_tmp, vC_tmp, uA_tmp, vA_tmp
-integer :: vel_stagger, str_stagger
-real, dimension(:,:), allocatable :: iCount
-integer :: nbonds
-integer :: stderrunit
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  type(time_type), intent(in) :: time !< Model time
+  real, dimension(:,:), intent(inout) :: calving !< Calving (kg/s). This field is updated with melt by bergs.
+  real, dimension(:,:), intent(inout) :: calving_hflx !< Calving heat flux (W/m2)
+  real, dimension(:,:), intent(in) :: uo !< Ocean zonal velocity (m/s)
+  real, dimension(:,:), intent(in) :: vo !< Ocean meridional velocity (m/s)
+  real, dimension(:,:), intent(in) :: ui !< Ice zonal velocity (m/s)
+  real, dimension(:,:), intent(in) :: vi !< Ice meridional velocity (m/s)
+  real, dimension(:,:), intent(in) :: tauxa !< Zonal wind stress (Pa)
+  real, dimension(:,:), intent(in) :: tauya !< Meridional wind stress (Pa)
+  real, dimension(:,:), intent(in) :: ssh !< Effective sea-surface height (m)
+  real, dimension(:,:), intent(in) :: sst !< Sea-surface temperature (C or K)
+  real, dimension(:,:), intent(in) :: cn !< Sea-ice concentration (nondim)
+  real, dimension(:,:), intent(in) :: hi !< Sea-ice thickness (m)
+  integer, optional, intent(in) :: stagger
+  integer, optional, intent(in) :: stress_stagger
+  real, dimension(:,:), optional, intent(in) :: sss !< Sea-surface salinity (1e-3)
+  real, dimension(:,:), optional, pointer :: mass_berg !< Mass of bergs (kg)
+  real, dimension(:,:), optional, pointer :: ustar_berg !< Friction velocity on base of bergs (m/s)
+  real, dimension(:,:), optional, pointer :: area_berg !< Area of bergs (m2)
+  ! Local variables
+  integer :: iyr, imon, iday, ihr, imin, isec, k
+  type(icebergs_gridded), pointer :: grd
+  logical :: lerr, sample_traj, write_traj, lbudget, lverbose, check_bond_quality
+  real :: unused_calving, tmpsum, grdd_berg_mass, grdd_bergy_mass,grdd_spread_mass, grdd_spread_area
+  real :: grdd_u_iceberg, grdd_v_iceberg, grdd_ustar_iceberg, grdd_spread_uvel, grdd_spread_vvel
+  integer :: i, j, Iu, ju, iv, Jv, Iu_off, ju_off, iv_off, Jv_off
+  real :: mask, max_SST
+  real, dimension(:,:), allocatable :: uC_tmp, vC_tmp, uA_tmp, vA_tmp
+  integer :: vel_stagger, str_stagger
+  real, dimension(:,:), allocatable :: iCount
+  integer :: nbonds
+  integer :: stderrunit
 
   ! Get the stderr unit number
   stderrunit = stderr()
@@ -3084,7 +3232,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   grd%hi(grd%isc-1:grd%iec+1,grd%jsc-1:grd%jec+1)=hi(:,:)
   call mpp_update_domains(grd%hi, grd%domain)
 
-  !Adding gridded salinity.
+  ! Adding gridded salinity.
   if (present(sss)) then
     grd%sss(grd%isc:grd%iec,grd%jsc:grd%jec)=sss(:,:)
   else
@@ -3094,9 +3242,9 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     endif
   endif
 
- !Make sure that gridded values agree with mask  (to get ride of NaN values)
+  ! Make sure that gridded values agree with mask  (to get ride of NaN values)
   do i=grd%isd,grd%ied ; do j=grd%jsd,grd%jed
-  !Initializing all gridded values to zero
+    ! Initializing all gridded values to zero
     if (grd%msk(i,j).lt. 0.5) then
       grd%ua(i,j) = 0.0 ;  grd%va(i,j) = 0.0
       grd%uo(i,j) = 0.0 ;  grd%vo(i,j) = 0.0
@@ -3169,7 +3317,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   if (debug) call checksum_gridded(bergs%grd, 's/r run after exchange')
   call mpp_clock_end(bergs%clock_com)
 
-  !Caculate mass on ocean before thermodynamics, to use in melt rate calculation
+  ! Calculate mass on ocean before thermodynamics, to use in melt rate calculation
   if (bergs%find_melt_using_spread_mass) then
     call calculate_mass_on_ocean(bergs, with_diagnostics=.false.)
     grd%spread_mass_old(:,:)=0.
@@ -3294,10 +3442,10 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 
   call mpp_clock_end(bergs%clock_dia)
 
-  !This is the point in the algorithem which determines which fields get passed to the ice model
-  !Return what ever calving we did not use and additional icebergs melt
+  ! This is the point in the algorithm which determines which fields get passed to the ice model
+  ! Return what ever calving we did not use and additional icebergs melt
 
-  !Making sure that spread_mass has the correct mass
+  ! Making sure that spread_mass has the correct mass
   !grd%spread_mass(:,:)=0.0
   !call icebergs_incr_mass(bergs, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec), within_iceberg_model=.True.)
 
@@ -3361,7 +3509,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     !bergs%u_iceberg_end=sum_mass(bergs) !Not sure what this is
     !bergs%v_iceberg_end=sum_mass(bergs) !Not sure what this is
     bergs%floating_heat_end=sum_heat(bergs)
-    grd%tmpc(:,:)=0.;
+    grd%tmpc(:,:)=0.
     !Finding spread mass
     call mpp_clock_end(bergs%clock); call mpp_clock_end(bergs%clock_dia) ! To enable calling of public s/r
     call sum_up_spread_fields(bergs, grd%tmpc, 'mass')
@@ -3515,135 +3663,171 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 
   contains
 
-  subroutine report_state(budgetstr,budgetunits,startstr,startval,endstr,endval,delstr,nbergs)
-  ! Arguments
-  character*(*), intent(in) :: budgetstr, budgetunits, startstr, endstr, delstr
-  real, intent(in) :: startval, endval
-  integer, intent(in), optional :: nbergs
-  ! Local variables
-  if (present(nbergs)) then
-    write(*,100) budgetstr//' state:', &
-                        startstr//' start',startval,budgetunits, &
-                        endstr//' end',endval,budgetunits, &
-                        'Delta '//delstr,endval-startval,budgetunits, &
-                        '# of bergs',nbergs
-  else
-    write(*,100) budgetstr//' state:', &
-                        startstr//' start',startval,budgetunits, &
-                        endstr//' end',endval,budgetunits, &
-                        delstr//'Delta',endval-startval,budgetunits
-  endif
-  100 format("diamonds: ",a19,3(a18,"=",es14.7,x,a2,:,","),a12,i8)
+  !> Prints summary of start and end states
+  subroutine report_state(budgetstr, budgetunits, startstr, startval, endstr, endval, delstr, nbergs)
+    ! Arguments
+    character*(*), intent(in) :: budgetstr !< Budget title
+    character*(*), intent(in) :: budgetunits !< Units of budgeted quantity
+    character*(*), intent(in) :: startstr !< Start label
+    real, intent(in) :: startval !< Start value for budget
+    character*(*), intent(in) :: endstr !< End label
+    real, intent(in) :: endval !< End value for budget
+    character*(*), intent(in) :: delstr !< Delta label
+    integer, intent(in), optional :: nbergs !< Number of bergs
+    ! Local variables
+    if (present(nbergs)) then
+      write(*,100) budgetstr//' state:', &
+                          startstr//' start',startval,budgetunits, &
+                          endstr//' end',endval,budgetunits, &
+                          'Delta '//delstr,endval-startval,budgetunits, &
+                          '# of bergs',nbergs
+    else
+      write(*,100) budgetstr//' state:', &
+                          startstr//' start',startval,budgetunits, &
+                          endstr//' end',endval,budgetunits, &
+                          delstr//'Delta',endval-startval,budgetunits
+    endif
+    100 format("diamonds: ",a19,3(a18,"=",es14.7,x,a2,:,","),a12,i8)
   end subroutine report_state
 
-  subroutine report_consistant(budgetstr,budgetunits,startstr,startval,endstr,endval)
-  ! Arguments
-  character*(*), intent(in) :: budgetstr, budgetunits, startstr, endstr
-  real, intent(in) :: startval, endval
-  ! Local variables
-  write(*,200) budgetstr//' check:', &
-                      startstr,startval,budgetunits, &
-                      endstr,endval,budgetunits, &
-                      'error',(endval-startval)/((endval+startval)+1e-30),'nd'
-  200 format("diamonds: ",a19,10(a18,"=",es14.7,x,a2,:,","))
+  !> Prints consistency summary of start and end states
+  subroutine report_consistant(budgetstr, budgetunits, startstr, startval, endstr, endval)
+    ! Arguments
+    character*(*), intent(in) :: budgetstr !< Budget title
+    character*(*), intent(in) :: budgetunits !< Units of budgeted quantity
+    character*(*), intent(in) :: startstr !< Start label
+    real, intent(in) :: startval !< Start value for budget
+    character*(*), intent(in) :: endstr !< End label
+    real, intent(in) :: endval !< End value for budget
+    ! Local variables
+    write(*,200) budgetstr//' check:', &
+                        startstr,startval,budgetunits, &
+                        endstr,endval,budgetunits, &
+                        'error',(endval-startval)/((endval+startval)+1e-30),'nd'
+    200 format("diamonds: ",a19,10(a18,"=",es14.7,x,a2,:,","))
   end subroutine report_consistant
 
-  subroutine report_budget(budgetstr,budgetunits,instr,inval,outstr,outval,delstr,startval,endval)
-  ! Arguments
-  character*(*), intent(in) :: budgetstr, budgetunits, instr, outstr, delstr
-  real, intent(in) :: inval, outval, startval, endval
-  ! Local variables
-  write(*,200) budgetstr//' budget:', &
-                      instr//' in',inval,budgetunits, &
-                      outstr//' out',outval,budgetunits, &
-                      'Delta '//delstr,inval-outval,budgetunits, &
-                      'error',((endval-startval)-(inval-outval))/max(1.e-30,max(abs(endval-startval),abs(inval-outval))),'nd'
-  200 format("diamonds: ",a19,3(a18,"=",es14.7,x,a2,:,","),a8,"=",es10.3,x,a2)
+  !> Prints a budget
+  subroutine report_budget(budgetstr, budgetunits, instr, inval, outstr, outval, delstr, startval, endval)
+    ! Arguments
+    character*(*), intent(in) :: budgetstr !< Budget title
+    character*(*), intent(in) :: budgetunits !< Units of budgeted quantity
+    character*(*), intent(in) :: instr !< Incoming label
+    real, intent(in) :: inval !< Incoming value
+    character*(*), intent(in) :: outstr !< Outgoing label
+    real, intent(in) :: outval !< Outgoing value
+    character*(*), intent(in) :: delstr !< Delta label
+    real, intent(in) :: startval !< Start value for budget
+    real, intent(in) :: endval !< End value for budget
+    ! Local variables
+    write(*,200) budgetstr//' budget:', &
+                        instr//' in',inval,budgetunits, &
+                        outstr//' out',outval,budgetunits, &
+                        'Delta '//delstr,inval-outval,budgetunits, &
+                        'error',((endval-startval)-(inval-outval))/max(1.e-30,max(abs(endval-startval),abs(inval-outval))),'nd'
+    200 format("diamonds: ",a19,3(a18,"=",es14.7,x,a2,:,","),a8,"=",es10.3,x,a2)
   end subroutine report_budget
 
-  subroutine report_istate(budgetstr,startstr,startval,endstr,endval,delstr)
-  ! Arguments
-  character*(*), intent(in) :: budgetstr, startstr, endstr, delstr
-  integer, intent(in) :: startval, endval
-  ! Local variables
-  write(*,100) budgetstr//' state:', &
-                        startstr//' start',startval, &
-                        endstr//' end',endval, &
-                        delstr//'Delta',endval-startval
-  100 format("diamonds: ",a19,3(a18,"=",i14,x,:,","))
+  !> Prints summary of start and end states
+  subroutine report_istate(budgetstr, startstr, startval, endstr, endval, delstr)
+    ! Arguments
+    character*(*), intent(in) :: budgetstr !< Budget title
+    character*(*), intent(in) :: startstr !< Start label
+    integer, intent(in) :: startval !< Start value for budget
+    character*(*), intent(in) :: endstr !< End label
+    integer, intent(in) :: endval !< End value for budget
+    character*(*), intent(in) :: delstr !< Delta label
+    ! Local variables
+    write(*,100) budgetstr//' state:', &
+                          startstr//' start',startval, &
+                          endstr//' end',endval, &
+                          delstr//'Delta',endval-startval
+    100 format("diamonds: ",a19,3(a18,"=",i14,x,:,","))
   end subroutine report_istate
 
+  !> Prints a budget
   subroutine report_ibudget(budgetstr,instr,inval,outstr,outval,delstr,startval,endval)
-  ! Arguments
-  character*(*), intent(in) :: budgetstr, instr, outstr, delstr
-  integer, intent(in) :: inval, outval, startval, endval
-  ! Local variables
-  write(*,200) budgetstr//' budget:', &
-                      instr//' in',inval, &
-                      outstr//' out',outval, &
-                      'Delta '//delstr,inval-outval, &
-                      'error',((endval-startval)-(inval-outval))
-  200 format("diamonds: ",a19,10(a18,"=",i14,x,:,","))
+    ! Arguments
+    character*(*), intent(in) :: budgetstr !< Budget title
+    character*(*), intent(in) :: instr !< Incoming label
+    integer, intent(in) :: inval !< Incoming value
+    character*(*), intent(in) :: outstr !< Outgoing label
+    integer, intent(in) :: outval !< Outgoing value
+    character*(*), intent(in) :: delstr !< Delta label
+    integer, intent(in) :: startval !< Start value for budget
+    integer, intent(in) :: endval !< End value for budget
+    ! Local variables
+    write(*,200) budgetstr//' budget:', &
+                        instr//' in',inval, &
+                        outstr//' out',outval, &
+                        'Delta '//delstr,inval-outval, &
+                        'error',((endval-startval)-(inval-outval))
+    200 format("diamonds: ",a19,10(a18,"=",i14,x,:,","))
   end subroutine report_ibudget
 
-  subroutine get_running_mean_calving(bergs,calving,calving_hflx)
-  ! Arguments
-  type(icebergs), pointer :: bergs !< Container for all types and memory
-  real, dimension(:,:), intent(inout) :: calving, calving_hflx
-  ! Local variables
-  real :: alpha  !Parameter used for calving relaxation time stepping.  (0<=alpha<1)
-  real :: tau  !Relaxation timescale in seconds
-  real :: beta  ! = 1-alpha (0<=beta<1)
-  !This subroutine takes in the new calving and calving_hflx, and uses them to time step a running-mean_calving value
-  !The time stepping uses a time scale tau. When tau is equal to zero, the
-  !running mean is exactly equal to the new calving value.
-
-  ! For the first time-step, initialize the running mean with the current data
-  if (.not. bergs%grd%rmean_calving_initialized) then
-    bergs%grd%rmean_calving(:,:)=calving(:,:)
-    bergs%grd%rmean_calving_initialized=.true.
-  endif
-  if (.not. bergs%grd%rmean_calving_hflx_initialized) then
-    bergs%grd%rmean_calving_hflx(:,:)=calving_hflx(:,:)
-    bergs%grd%rmean_calving_hflx_initialized=.true.
-  endif
+  !> Time-filter calving and calving_hflx with a running mean.
+  !!
+  !! This subroutine takes in the new calving and calving_hflx, and uses them to time step a running-mean_calving value.
+  !! The time stepping uses a time scale tau. When tau is equal to zero, the
+  !! running mean is exactly equal to the new calving value.
+  subroutine get_running_mean_calving(bergs, calving, calving_hflx)
+    ! Arguments
+    type(icebergs), pointer :: bergs !< Container for all types and memory
+    real, dimension(:,:), intent(inout) :: calving !< Calving (kg/s)
+    real, dimension(:,:), intent(inout) :: calving_hflx !< Calving heat flux (W/m2)
+    ! Local variables
+    real :: alpha  !Parameter used for calving relaxation time stepping.  (0<=alpha<1)
+    real :: tau  !Relaxation timescale in seconds
+    real :: beta  ! = 1-alpha (0<=beta<1)
+
+    ! For the first time-step, initialize the running mean with the current data
+    if (.not. bergs%grd%rmean_calving_initialized) then
+      bergs%grd%rmean_calving(:,:)=calving(:,:)
+      bergs%grd%rmean_calving_initialized=.true.
+    endif
+    if (.not. bergs%grd%rmean_calving_hflx_initialized) then
+      bergs%grd%rmean_calving_hflx(:,:)=calving_hflx(:,:)
+      bergs%grd%rmean_calving_hflx_initialized=.true.
+    endif
 
-  !Applying "Newton cooling" with timescale tau, to smooth out the calving field.
-  tau=bergs%tau_calving/(365.*24*60*60) !Converting time scale from years to seconds
-  alpha=tau/(tau+bergs%dt)
-  if (alpha==0.) return ! Avoids unnecessary copying of arrays
-  if (alpha>0.5) then ! beta is small
-    beta=bergs%dt/(tau+bergs%dt)
-    alpha=1.-beta
-  else ! alpha is small
-    beta=1.-alpha
-  endif
+    !Applying "Newton cooling" with timescale tau, to smooth out the calving field.
+    tau=bergs%tau_calving/(365.*24*60*60) !Converting time scale from years to seconds
+    alpha=tau/(tau+bergs%dt)
+    if (alpha==0.) return ! Avoids unnecessary copying of arrays
+    if (alpha>0.5) then ! beta is small
+      beta=bergs%dt/(tau+bergs%dt)
+      alpha=1.-beta
+    else ! alpha is small
+      beta=1.-alpha
+    endif
 
-  ! For non-negative alpha and beta, these expressions for the running means are sign preserving
-  bergs%grd%rmean_calving(:,:)=beta*calving(:,:) + alpha*bergs%grd%rmean_calving(:,:)
-  bergs%grd%rmean_calving_hflx(:,:)=beta*calving_hflx(:,:) + alpha*bergs%grd%rmean_calving_hflx(:,:)
+    ! For non-negative alpha and beta, these expressions for the running means are sign preserving
+    bergs%grd%rmean_calving(:,:)=beta*calving(:,:) + alpha*bergs%grd%rmean_calving(:,:)
+    bergs%grd%rmean_calving_hflx(:,:)=beta*calving_hflx(:,:) + alpha*bergs%grd%rmean_calving_hflx(:,:)
 
-  !Setting calving used by the iceberg model equal to the running mean
-  calving(:,:)=bergs%grd%rmean_calving(:,:)
-  calving_hflx(:,:)=bergs%grd%rmean_calving_hflx(:,:)
+    !Setting calving used by the iceberg model equal to the running mean
+    calving(:,:)=bergs%grd%rmean_calving(:,:)
+    calving_hflx(:,:)=bergs%grd%rmean_calving_hflx(:,:)
 
   end subroutine get_running_mean_calving
 
 end subroutine icebergs_run
 
+!> Increments a gridded mass field with the mass of bergs (called from outside icebergs_run)
+!!
+!! This routine is called from SIS, (and older versions of SIS2), but not within
+!! the iceberg model. The routine adds the spread iceberg mass to mass provided
+!! the add weight to ocean flag is on, and passive mode is off. It also appears to
+!! play some role in diagnostics
 subroutine icebergs_incr_mass(bergs, mass, Time)
-! Arguments
-type(icebergs), pointer :: bergs !< Container for all types and memory
-type(time_type), intent(in), optional :: Time
-type(icebergs_gridded), pointer :: grd
-integer :: i, j
-logical :: lerr
-real, dimension(bergs%grd%isc:bergs%grd%iec,bergs%grd%jsc:bergs%grd%jec), intent(inout) :: mass
-
-!This routine is called from SIS, (and older versions of SIS2), but not within
-!the iceberg model. The routine adds the spread iceberg mass to mass provided
-!the add weight to ocean flag is on, and passive mode is off. It also appears to
-!play some role in diagnostics
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  real, dimension(bergs%grd%isc:bergs%grd%iec,bergs%grd%jsc:bergs%grd%jec), intent(inout) :: mass !< Mass field to increment
+  type(time_type), intent(in), optional :: Time !< Model time
+  ! Local variables
+  type(icebergs_gridded), pointer :: grd
+  integer :: i, j
+  logical :: lerr
 
   if (.not. associated(bergs)) return
   if (.not. bergs%add_weight_to_ocean) return
@@ -4595,7 +4779,7 @@ end subroutine rotvec_from_tang
 
 subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, bounced, error, iceberg_num)
 ! Arguments
-type(icebergs_gridded), pointer :: grd
+type(icebergs_gridded), pointer :: grd !< Container for gridded fields
 real, intent(inout) :: lon, lat, uvel, vvel, xi, yj
 integer, intent(inout) :: i,j
 integer, intent(in) :: iceberg_num

From 7b35c7ab4c2932f8e43ebb3f8b594deba589d103 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <aadcroft@princeton.edu>
Date: Tue, 28 Mar 2017 00:01:24 -0400
Subject: [PATCH 214/361] Added doxygen configuration files

- Added Doxyfile based on that for MOM6.
- Likewise layout.xml
- Placed in docs, in anticipation of hosting on RTD.
---
 docs/.gitignore |    2 +
 docs/Doxyfile   | 2434 +++++++++++++++++++++++++++++++++++++++++++++++
 docs/layout.xml |  191 ++++
 3 files changed, 2627 insertions(+)
 create mode 100644 docs/.gitignore
 create mode 100644 docs/Doxyfile
 create mode 100644 docs/layout.xml

diff --git a/docs/.gitignore b/docs/.gitignore
new file mode 100644
index 0000000..8bbe7ac
--- /dev/null
+++ b/docs/.gitignore
@@ -0,0 +1,2 @@
+html 
+doxygen.log
diff --git a/docs/Doxyfile b/docs/Doxyfile
new file mode 100644
index 0000000..40cc078
--- /dev/null
+++ b/docs/Doxyfile
@@ -0,0 +1,2434 @@
+# Doxyfile 1.8.12
+
+# This file describes the settings to be used by the documentation system
+# doxygen (www.doxygen.org) for a project.
+#
+# All text after a double hash (##) is considered a comment and is placed in
+# front of the TAG it is preceding.
+#
+# All text after a single hash (#) is considered a comment and will be ignored.
+# The format is:
+# TAG = value [value, ...]
+# For lists, items can also be appended using:
+# TAG += value [value, ...]
+# Values that contain spaces should be placed between quotes (\" \").
+
+#---------------------------------------------------------------------------
+# Project related configuration options
+#---------------------------------------------------------------------------
+
+# This tag specifies the encoding used for all characters in the config file
+# that follow. The default is UTF-8 which is also the encoding used for all text
+# before the first occurrence of this tag. Doxygen uses libiconv (or the iconv
+# built into libc) for the transcoding. See http://www.gnu.org/software/libiconv
+# for the list of possible encodings.
+# The default value is: UTF-8.
+
+DOXYFILE_ENCODING      = UTF-8
+
+# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by
+# double-quotes, unless you are using Doxywizard) that should identify the
+# project for which the documentation is generated. This name is used in the
+# title of most generated pages and in a few other places.
+# The default value is: My Project.
+
+PROJECT_NAME           = "icebergs"
+
+# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
+# could be handy for archiving the generated documentation or if some version
+# control system is used.
+
+PROJECT_NUMBER         =
+
+# Using the PROJECT_BRIEF tag one can provide an optional one line description
+# for a project that appears at the top of each page and should give viewer a
+# quick idea about the purpose of the project. Keep the description short.
+
+PROJECT_BRIEF          =
+
+# With the PROJECT_LOGO tag one can specify a logo or an icon that is included
+# in the documentation. The maximum height of the logo should not exceed 55
+# pixels and the maximum width should not exceed 200 pixels. Doxygen will copy
+# the logo to the output directory.
+
+PROJECT_LOGO           =
+
+# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
+# into which the generated documentation will be written. If a relative path is
+# entered, it will be relative to the location where doxygen was started. If
+# left blank the current directory will be used.
+
+#OUTPUT_DIRECTORY       =
+
+# If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub-
+# directories (in 2 levels) under the output directory of each output format and
+# will distribute the generated files over these directories. Enabling this
+# option can be useful when feeding doxygen a huge amount of source files, where
+# putting all generated files in the same directory would otherwise causes
+# performance problems for the file system.
+# The default value is: NO.
+
+CREATE_SUBDIRS         = NO
+
+# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII
+# characters to appear in the names of generated files. If set to NO, non-ASCII
+# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode
+# U+3044.
+# The default value is: NO.
+
+ALLOW_UNICODE_NAMES    = NO
+
+# The OUTPUT_LANGUAGE tag is used to specify the language in which all
+# documentation generated by doxygen is written. Doxygen will use this
+# information to generate all constant output in the proper language.
+# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese,
+# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States),
+# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian,
+# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages),
+# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian,
+# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian,
+# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish,
+# Ukrainian and Vietnamese.
+# The default value is: English.
+
+OUTPUT_LANGUAGE        = English
+
+# If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member
+# descriptions after the members that are listed in the file and class
+# documentation (similar to Javadoc). Set to NO to disable this.
+# The default value is: YES.
+
+BRIEF_MEMBER_DESC      = YES
+
+# If the REPEAT_BRIEF tag is set to YES, doxygen will prepend the brief
+# description of a member or function before the detailed description
+#
+# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
+# brief descriptions will be completely suppressed.
+# The default value is: YES.
+
+REPEAT_BRIEF           = YES
+
+# This tag implements a quasi-intelligent brief description abbreviator that is
+# used to form the text in various listings. Each string in this list, if found
+# as the leading text of the brief description, will be stripped from the text
+# and the result, after processing the whole list, is used as the annotated
+# text. Otherwise, the brief description is used as-is. If left blank, the
+# following values are used ($name is automatically replaced with the name of
+# the entity):The $name class, The $name widget, The $name file, is, provides,
+# specifies, contains, represents, a, an and the.
+
+ABBREVIATE_BRIEF       =
+
+# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
+# doxygen will generate a detailed section even if there is only a brief
+# description.
+# The default value is: NO.
+
+ALWAYS_DETAILED_SEC    = NO
+
+# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
+# inherited members of a class in the documentation of that class as if those
+# members were ordinary class members. Constructors, destructors and assignment
+# operators of the base classes will not be shown.
+# The default value is: NO.
+
+INLINE_INHERITED_MEMB  = NO
+
+# If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path
+# before files name in the file list and in the header files. If set to NO the
+# shortest path that makes the file name unique will be used
+# The default value is: YES.
+
+FULL_PATH_NAMES        = YES
+
+# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path.
+# Stripping is only done if one of the specified strings matches the left-hand
+# part of the path. The tag can be used to show relative paths in the file list.
+# If left blank the directory from which doxygen is run is used as the path to
+# strip.
+#
+# Note that you can specify absolute paths here, but also relative paths, which
+# will be relative from the directory where doxygen is started.
+# This tag requires that the tag FULL_PATH_NAMES is set to YES.
+
+STRIP_FROM_PATH        =
+
+# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the
+# path mentioned in the documentation of a class, which tells the reader which
+# header file to include in order to use a class. If left blank only the name of
+# the header file containing the class definition is used. Otherwise one should
+# specify the list of include paths that are normally passed to the compiler
+# using the -I flag.
+
+STRIP_FROM_INC_PATH    =
+
+# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but
+# less readable) file names. This can be useful is your file systems doesn't
+# support long names like on DOS, Mac, or CD-ROM.
+# The default value is: NO.
+
+SHORT_NAMES            = NO
+
+# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the
+# first line (until the first dot) of a Javadoc-style comment as the brief
+# description. If set to NO, the Javadoc-style will behave just like regular Qt-
+# style comments (thus requiring an explicit @brief command for a brief
+# description.)
+# The default value is: NO.
+
+JAVADOC_AUTOBRIEF      = NO
+
+# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first
+# line (until the first dot) of a Qt-style comment as the brief description. If
+# set to NO, the Qt-style will behave just like regular Qt-style comments (thus
+# requiring an explicit \brief command for a brief description.)
+# The default value is: NO.
+
+QT_AUTOBRIEF           = NO
+
+# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a
+# multi-line C++ special comment block (i.e. a block of //! or /// comments) as
+# a brief description. This used to be the default behavior. The new default is
+# to treat a multi-line C++ comment block as a detailed description. Set this
+# tag to YES if you prefer the old behavior instead.
+#
+# Note that setting this tag to YES also means that rational rose comments are
+# not recognized any more.
+# The default value is: NO.
+
+MULTILINE_CPP_IS_BRIEF = NO
+
+# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the
+# documentation from any documented member that it re-implements.
+# The default value is: YES.
+
+INHERIT_DOCS           = YES
+
+# If the SEPARATE_MEMBER_PAGES tag is set to YES then doxygen will produce a new
+# page for each member. If set to NO, the documentation of a member will be part
+# of the file/class/namespace that contains it.
+# The default value is: NO.
+
+SEPARATE_MEMBER_PAGES  = NO
+
+# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen
+# uses this value to replace tabs by spaces in code fragments.
+# Minimum value: 1, maximum value: 16, default value: 4.
+
+TAB_SIZE               = 2
+
+# This tag can be used to specify a number of aliases that act as commands in
+# the documentation. An alias has the form:
+# name=value
+# For example adding
+# "sideeffect=@par Side Effects:\n"
+# will allow you to put the command \sideeffect (or @sideeffect) in the
+# documentation, which will result in a user-defined paragraph with heading
+# "Side Effects:". You can put \n's in the value part of an alias to insert
+# newlines.
+
+ALIASES                =
+
+# This tag can be used to specify a number of word-keyword mappings (TCL only).
+# A mapping has the form "name=value". For example adding "class=itcl::class"
+# will allow you to use the command class in the itcl::class meaning.
+
+TCL_SUBST              =
+
+# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources
+# only. Doxygen will then generate output that is more tailored for C. For
+# instance, some of the names that are used will be different. The list of all
+# members will be omitted, etc.
+# The default value is: NO.
+
+OPTIMIZE_OUTPUT_FOR_C  = NO
+
+# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or
+# Python sources only. Doxygen will then generate output that is more tailored
+# for that language. For instance, namespaces will be presented as packages,
+# qualified scopes will look different, etc.
+# The default value is: NO.
+
+OPTIMIZE_OUTPUT_JAVA   = NO
+
+# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
+# sources. Doxygen will then generate output that is tailored for Fortran.
+# The default value is: NO.
+
+OPTIMIZE_FOR_FORTRAN   = YES
+
+# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
+# sources. Doxygen will then generate output that is tailored for VHDL.
+# The default value is: NO.
+
+OPTIMIZE_OUTPUT_VHDL   = NO
+
+# Doxygen selects the parser to use depending on the extension of the files it
+# parses. With this tag you can assign which parser to use for a given
+# extension. Doxygen has a built-in mapping, but you can override or extend it
+# using this tag. The format is ext=language, where ext is a file extension, and
+# language is one of the parsers supported by doxygen: IDL, Java, Javascript,
+# C#, C, C++, D, PHP, Objective-C, Python, Fortran (fixed format Fortran:
+# FortranFixed, free formatted Fortran: FortranFree, unknown formatted Fortran:
+# Fortran. In the later case the parser tries to guess whether the code is fixed
+# or free formatted code, this is the default for Fortran type files), VHDL. For
+# instance to make doxygen treat .inc files as Fortran files (default is PHP),
+# and .f files as C (default is Fortran), use: inc=Fortran f=C.
+#
+# Note: For files without extension you can use no_extension as a placeholder.
+#
+# Note that for custom extensions you also need to set FILE_PATTERNS otherwise
+# the files are not read by doxygen.
+
+EXTENSION_MAPPING      =
+
+# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments
+# according to the Markdown format, which allows for more readable
+# documentation. See http://daringfireball.net/projects/markdown/ for details.
+# The output of markdown processing is further processed by doxygen, so you can
+# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in
+# case of backward compatibilities issues.
+# The default value is: YES.
+
+MARKDOWN_SUPPORT       = YES
+
+# When the TOC_INCLUDE_HEADINGS tag is set to a non-zero value, all headings up
+# to that level are automatically included in the table of contents, even if
+# they do not have an id attribute.
+# Note: This feature currently applies only to Markdown headings.
+# Minimum value: 0, maximum value: 99, default value: 0.
+# This tag requires that the tag MARKDOWN_SUPPORT is set to YES.
+
+TOC_INCLUDE_HEADINGS   = 0
+
+# When enabled doxygen tries to link words that correspond to documented
+# classes, or namespaces to their corresponding documentation. Such a link can
+# be prevented in individual cases by putting a % sign in front of the word or
+# globally by setting AUTOLINK_SUPPORT to NO.
+# The default value is: YES.
+
+AUTOLINK_SUPPORT       = YES
+
+# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
+# to include (a tag file for) the STL sources as input, then you should set this
+# tag to YES in order to let doxygen match functions declarations and
+# definitions whose arguments contain STL classes (e.g. func(std::string);
+# versus func(std::string) {}). This also make the inheritance and collaboration
+# diagrams that involve STL classes more complete and accurate.
+# The default value is: NO.
+
+BUILTIN_STL_SUPPORT    = NO
+
+# If you use Microsoft's C++/CLI language, you should set this option to YES to
+# enable parsing support.
+# The default value is: NO.
+
+CPP_CLI_SUPPORT        = NO
+
+# Set the SIP_SUPPORT tag to YES if your project consists of sip (see:
+# http://www.riverbankcomputing.co.uk/software/sip/intro) sources only. Doxygen
+# will parse them like normal C++ but will assume all classes use public instead
+# of private inheritance when no explicit protection keyword is present.
+# The default value is: NO.
+
+SIP_SUPPORT            = NO
+
+# For Microsoft's IDL there are propget and propput attributes to indicate
+# getter and setter methods for a property. Setting this option to YES will make
+# doxygen to replace the get and set methods by a property in the documentation.
+# This will only work if the methods are indeed getting or setting a simple
+# type. If this is not the case, or you want to show the methods anyway, you
+# should set this option to NO.
+# The default value is: YES.
+
+IDL_PROPERTY_SUPPORT   = YES
+
+# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
+# tag is set to YES then doxygen will reuse the documentation of the first
+# member in the group (if any) for the other members of the group. By default
+# all members of a group must be documented explicitly.
+# The default value is: NO.
+
+DISTRIBUTE_GROUP_DOC   = YES
+
+# If one adds a struct or class to a group and this option is enabled, then also
+# any nested class or struct is added to the same group. By default this option
+# is disabled and one has to add nested compounds explicitly via \ingroup.
+# The default value is: NO.
+
+GROUP_NESTED_COMPOUNDS = NO
+
+# Set the SUBGROUPING tag to YES to allow class member groups of the same type
+# (for instance a group of public functions) to be put as a subgroup of that
+# type (e.g. under the Public Functions section). Set it to NO to prevent
+# subgrouping. Alternatively, this can be done per class using the
+# \nosubgrouping command.
+# The default value is: YES.
+
+SUBGROUPING            = YES
+
+# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions
+# are shown inside the group in which they are included (e.g. using \ingroup)
+# instead of on a separate page (for HTML and Man pages) or section (for LaTeX
+# and RTF).
+#
+# Note that this feature does not work in combination with
+# SEPARATE_MEMBER_PAGES.
+# The default value is: NO.
+
+INLINE_GROUPED_CLASSES = NO
+
+# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions
+# with only public data fields or simple typedef fields will be shown inline in
+# the documentation of the scope in which they are defined (i.e. file,
+# namespace, or group documentation), provided this scope is documented. If set
+# to NO, structs, classes, and unions are shown on a separate page (for HTML and
+# Man pages) or section (for LaTeX and RTF).
+# The default value is: NO.
+
+INLINE_SIMPLE_STRUCTS  = NO
+
+# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or
+# enum is documented as struct, union, or enum with the name of the typedef. So
+# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
+# with name TypeT. When disabled the typedef will appear as a member of a file,
+# namespace, or class. And the struct will be named TypeS. This can typically be
+# useful for C code in case the coding convention dictates that all compound
+# types are typedef'ed and only the typedef is referenced, never the tag name.
+# The default value is: NO.
+
+TYPEDEF_HIDES_STRUCT   = NO
+
+# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
+# cache is used to resolve symbols given their name and scope. Since this can be
+# an expensive process and often the same symbol appears multiple times in the
+# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small
+# doxygen will become slower. If the cache is too large, memory is wasted. The
+# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range
+# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536
+# symbols. At the end of a run doxygen will report the cache usage and suggest
+# the optimal cache size from a speed point of view.
+# Minimum value: 0, maximum value: 9, default value: 0.
+
+LOOKUP_CACHE_SIZE      = 0
+
+#---------------------------------------------------------------------------
+# Build related configuration options
+#---------------------------------------------------------------------------
+
+# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in
+# documentation are documented, even if no documentation was available. Private
+# class members and static file members will be hidden unless the
+# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES.
+# Note: This will also disable the warnings about undocumented members that are
+# normally produced when WARNINGS is set to YES.
+# The default value is: NO.
+
+EXTRACT_ALL            = YES
+
+# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
+# be included in the documentation.
+# The default value is: NO.
+
+EXTRACT_PRIVATE        = YES
+
+# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
+# scope will be included in the documentation.
+# The default value is: NO.
+
+EXTRACT_PACKAGE        = YES
+
+# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be
+# included in the documentation.
+# The default value is: NO.
+
+EXTRACT_STATIC         = YES
+
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined
+# locally in source files will be included in the documentation. If set to NO,
+# only classes defined in header files are included. Does not have any effect
+# for Java sources.
+# The default value is: YES.
+
+EXTRACT_LOCAL_CLASSES  = YES
+
+# This flag is only useful for Objective-C code. If set to YES, local methods,
+# which are defined in the implementation section but not in the interface are
+# included in the documentation. If set to NO, only methods in the interface are
+# included.
+# The default value is: NO.
+
+EXTRACT_LOCAL_METHODS  = YES
+
+# If this flag is set to YES, the members of anonymous namespaces will be
+# extracted and appear in the documentation as a namespace called
+# 'anonymous_namespace{file}', where file will be replaced with the base name of
+# the file that contains the anonymous namespace. By default anonymous namespace
+# are hidden.
+# The default value is: NO.
+
+EXTRACT_ANON_NSPACES   = YES
+
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all
+# undocumented members inside documented classes or files. If set to NO these
+# members will be included in the various overviews, but no documentation
+# section is generated. This option has no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
+
+HIDE_UNDOC_MEMBERS     = NO
+
+# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all
+# undocumented classes that are normally visible in the class hierarchy. If set
+# to NO, these classes will be included in the various overviews. This option
+# has no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
+
+HIDE_UNDOC_CLASSES     = NO
+
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend
+# (class|struct|union) declarations. If set to NO, these declarations will be
+# included in the documentation.
+# The default value is: NO.
+
+HIDE_FRIEND_COMPOUNDS  = NO
+
+# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any
+# documentation blocks found inside the body of a function. If set to NO, these
+# blocks will be appended to the function's detailed documentation block.
+# The default value is: NO.
+
+HIDE_IN_BODY_DOCS      = NO
+
+# The INTERNAL_DOCS tag determines if documentation that is typed after a
+# \internal command is included. If the tag is set to NO then the documentation
+# will be excluded. Set it to YES to include the internal documentation.
+# The default value is: NO.
+
+INTERNAL_DOCS          = YES
+
+# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file
+# names in lower-case letters. If set to YES, upper-case letters are also
+# allowed. This is useful if you have classes or files whose names only differ
+# in case and if your file system supports case sensitive file names. Windows
+# and Mac users are advised to set this option to NO.
+# The default value is: system dependent.
+
+CASE_SENSE_NAMES       = YES
+
+# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with
+# their full class and namespace scopes in the documentation. If set to YES, the
+# scope will be hidden.
+# The default value is: NO.
+
+HIDE_SCOPE_NAMES       = NO
+
+# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will
+# append additional text to a page's title, such as Class Reference. If set to
+# YES the compound reference will be hidden.
+# The default value is: NO.
+
+HIDE_COMPOUND_REFERENCE= NO
+
+# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
+# the files that are included by a file in the documentation of that file.
+# The default value is: YES.
+
+SHOW_INCLUDE_FILES     = YES
+
+# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
+# grouped member an include statement to the documentation, telling the reader
+# which file to include in order to use the member.
+# The default value is: NO.
+
+SHOW_GROUPED_MEMB_INC  = NO
+
+# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include
+# files with double quotes in the documentation rather than with sharp brackets.
+# The default value is: NO.
+
+FORCE_LOCAL_INCLUDES   = NO
+
+# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the
+# documentation for inline members.
+# The default value is: YES.
+
+INLINE_INFO            = YES
+
+# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the
+# (detailed) documentation of file and class members alphabetically by member
+# name. If set to NO, the members will appear in declaration order.
+# The default value is: YES.
+
+SORT_MEMBER_DOCS       = YES
+
+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief
+# descriptions of file, namespace and class members alphabetically by member
+# name. If set to NO, the members will appear in declaration order. Note that
+# this will also influence the order of the classes in the class list.
+# The default value is: NO.
+
+SORT_BRIEF_DOCS        = NO
+
+# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
+# (brief and detailed) documentation of class members so that constructors and
+# destructors are listed first. If set to NO the constructors will appear in the
+# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS.
+# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief
+# member documentation.
+# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting
+# detailed member documentation.
+# The default value is: NO.
+
+SORT_MEMBERS_CTORS_1ST = NO
+
+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
+# of group names into alphabetical order. If set to NO the group names will
+# appear in their defined order.
+# The default value is: NO.
+
+SORT_GROUP_NAMES       = NO
+
+# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by
+# fully-qualified names, including namespaces. If set to NO, the class list will
+# be sorted only by class name, not including the namespace part.
+# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
+# Note: This option applies only to the class list, not to the alphabetical
+# list.
+# The default value is: NO.
+
+SORT_BY_SCOPE_NAME     = NO
+
+# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper
+# type resolution of all parameters of a function it will reject a match between
+# the prototype and the implementation of a member function even if there is
+# only one candidate or it is obvious which candidate to choose by doing a
+# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still
+# accept a match between prototype and implementation in such cases.
+# The default value is: NO.
+
+STRICT_PROTO_MATCHING  = NO
+
+# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo
+# list. This list is created by putting \todo commands in the documentation.
+# The default value is: YES.
+
+GENERATE_TODOLIST      = YES
+
+# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test
+# list. This list is created by putting \test commands in the documentation.
+# The default value is: YES.
+
+GENERATE_TESTLIST      = YES
+
+# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug
+# list. This list is created by putting \bug commands in the documentation.
+# The default value is: YES.
+
+GENERATE_BUGLIST       = YES
+
+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO)
+# the deprecated list. This list is created by putting \deprecated commands in
+# the documentation.
+# The default value is: YES.
+
+GENERATE_DEPRECATEDLIST= YES
+
+# The ENABLED_SECTIONS tag can be used to enable conditional documentation
+# sections, marked by \if <section_label> ... \endif and \cond <section_label>
+# ... \endcond blocks.
+
+ENABLED_SECTIONS       =
+
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
+# initial value of a variable or macro / define can have for it to appear in the
+# documentation. If the initializer consists of more lines than specified here
+# it will be hidden. Use a value of 0 to hide initializers completely. The
+# appearance of the value of individual variables and macros / defines can be
+# controlled using \showinitializer or \hideinitializer command in the
+# documentation regardless of this setting.
+# Minimum value: 0, maximum value: 10000, default value: 30.
+
+MAX_INITIALIZER_LINES  = 30
+
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at
+# the bottom of the documentation of classes and structs. If set to YES, the
+# list will mention the files that were used to generate the documentation.
+# The default value is: YES.
+
+SHOW_USED_FILES        = YES
+
+# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
+# will remove the Files entry from the Quick Index and from the Folder Tree View
+# (if specified).
+# The default value is: YES.
+
+SHOW_FILES             = YES
+
+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
+# page. This will remove the Namespaces entry from the Quick Index and from the
+# Folder Tree View (if specified).
+# The default value is: YES.
+
+SHOW_NAMESPACES        = YES
+
+# The FILE_VERSION_FILTER tag can be used to specify a program or script that
+# doxygen should invoke to get the current version for each file (typically from
+# the version control system). Doxygen will invoke the program by executing (via
+# popen()) the command command input-file, where command is the value of the
+# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided
+# by doxygen. Whatever the program writes to standard output is used as the file
+# version. For an example see the documentation.
+
+FILE_VERSION_FILTER    =
+
+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
+# by doxygen. The layout file controls the global structure of the generated
+# output files in an output format independent way. To create the layout file
+# that represents doxygen's defaults, run doxygen with the -l option. You can
+# optionally specify a file name after the option, if omitted DoxygenLayout.xml
+# will be used as the name of the layout file.
+#
+# Note that if you run doxygen from a directory containing a file called
+# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
+# tag is left empty.
+
+LAYOUT_FILE            = layout.xml
+
+# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
+# the reference definitions. This must be a list of .bib files. The .bib
+# extension is automatically appended if omitted. This requires the bibtex tool
+# to be installed. See also http://en.wikipedia.org/wiki/BibTeX for more info.
+# For LaTeX the style of the bibliography can be controlled using
+# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
+# search path. See also \cite for info how to create references.
+
+CITE_BIB_FILES         =
+
+#---------------------------------------------------------------------------
+# Configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+
+# The QUIET tag can be used to turn on/off the messages that are generated to
+# standard output by doxygen. If QUIET is set to YES this implies that the
+# messages are off.
+# The default value is: NO.
+
+QUIET                  = NO
+
+# The WARNINGS tag can be used to turn on/off the warning messages that are
+# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES
+# this implies that the warnings are on.
+#
+# Tip: Turn warnings on while writing the documentation.
+# The default value is: YES.
+
+WARNINGS               = YES
+
+# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate
+# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag
+# will automatically be disabled.
+# The default value is: YES.
+
+WARN_IF_UNDOCUMENTED   = YES
+
+# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
+# potential errors in the documentation, such as not documenting some parameters
+# in a documented function, or documenting parameters that don't exist or using
+# markup commands wrongly.
+# The default value is: YES.
+
+WARN_IF_DOC_ERROR      = YES
+
+# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that
+# are documented, but have no documentation for their parameters or return
+# value. If set to NO, doxygen will only warn about wrong or incomplete
+# parameter documentation, but not about the absence of documentation.
+# The default value is: NO.
+
+WARN_NO_PARAMDOC       = NO
+
+# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when
+# a warning is encountered.
+# The default value is: NO.
+
+WARN_AS_ERROR          = NO
+
+# The WARN_FORMAT tag determines the format of the warning messages that doxygen
+# can produce. The string should contain the $file, $line, and $text tags, which
+# will be replaced by the file and line number from which the warning originated
+# and the warning text. Optionally the format may contain $version, which will
+# be replaced by the version of the file (if it could be obtained via
+# FILE_VERSION_FILTER)
+# The default value is: $file:$line: $text.
+
+WARN_FORMAT            = "$file:$line: $text"
+
+# The WARN_LOGFILE tag can be used to specify a file to which warning and error
+# messages should be written. If left blank the output is written to standard
+# error (stderr).
+
+WARN_LOGFILE           = doxygen.log
+
+#---------------------------------------------------------------------------
+# Configuration options related to the input files
+#---------------------------------------------------------------------------
+
+# The INPUT tag is used to specify the files and/or directories that contain
+# documented source files. You may enter file names like myfile.cpp or
+# directories like /usr/src/myproject. Separate the files or directories with
+# spaces.
+# Note: If this tag is empty the current directory is searched.
+
+INPUT                  = ../
+
+# This tag can be used to specify the character encoding of the source files
+# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
+# libiconv (or the iconv built into libc) for the transcoding. See the libiconv
+# documentation (see: http://www.gnu.org/software/libiconv) for the list of
+# possible encodings.
+# The default value is: UTF-8.
+
+INPUT_ENCODING         = UTF-8
+
+# If the value of the INPUT tag contains directories, you can use the
+# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
+# *.h) to filter out the source-files in the directories.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# read by doxygen.
+#
+# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp,
+# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h,
+# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc,
+# *.m, *.markdown, *.md, *.mm, *.dox, *.py, *.pyw, *.f90, *.f, *.for, *.tcl,
+# *.vhd, *.vhdl, *.ucf and *.qsf.
+
+FILE_PATTERNS          = *.c \
+                         *.cc \
+                         *.cxx \
+                         *.cpp \
+                         *.c++ \
+                         *.h \
+                         *.hh \
+                         *.hxx \
+                         *.hpp \
+                         *.h++ \
+                         *.inc \
+                         *.m \
+                         *.markdown \
+                         *.md \
+                         *.mm \
+                         *.dox \
+                         *.f90 \
+                         *.f \
+                         *.for \
+                         *.F90
+
+# The RECURSIVE tag can be used to specify whether or not subdirectories should
+# be searched for input files as well.
+# The default value is: NO.
+
+RECURSIVE              = YES
+
+# The EXCLUDE tag can be used to specify files and/or directories that should be
+# excluded from the INPUT source files. This way you can easily exclude a
+# subdirectory from a directory tree whose root is specified with the INPUT tag.
+#
+# Note that relative paths are relative to the directory from which doxygen is
+# run.
+
+EXCLUDE                =
+
+# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
+# directories that are symbolic links (a Unix file system feature) are excluded
+# from the input.
+# The default value is: NO.
+
+EXCLUDE_SYMLINKS       = NO
+
+# If the value of the INPUT tag contains directories, you can use the
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
+# certain files from those directories.
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories for example use the pattern */test/*
+
+EXCLUDE_PATTERNS       = makedep.py
+
+# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
+# (namespaces, classes, functions, etc.) that should be excluded from the
+# output. The symbol name can be a fully qualified name, a word, or if the
+# wildcard * is used, a substring. Examples: ANamespace, AClass,
+# AClass::ANamespace, ANamespace::*Test
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories use the pattern */test/*
+
+EXCLUDE_SYMBOLS        =
+
+# The EXAMPLE_PATH tag can be used to specify one or more files or directories
+# that contain example code fragments that are included (see the \include
+# command).
+
+EXAMPLE_PATH           =
+
+# If the value of the EXAMPLE_PATH tag contains directories, you can use the
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
+# *.h) to filter out the source-files in the directories. If left blank all
+# files are included.
+
+EXAMPLE_PATTERNS       = *
+
+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
+# searched for input files to be used with the \include or \dontinclude commands
+# irrespective of the value of the RECURSIVE tag.
+# The default value is: NO.
+
+EXAMPLE_RECURSIVE      = NO
+
+# The IMAGE_PATH tag can be used to specify one or more files or directories
+# that contain images that are to be included in the documentation (see the
+# \image command).
+
+IMAGE_PATH             =
+
+# The INPUT_FILTER tag can be used to specify a program that doxygen should
+# invoke to filter for each input file. Doxygen will invoke the filter program
+# by executing (via popen()) the command:
+#
+# <filter> <input-file>
+#
+# where <filter> is the value of the INPUT_FILTER tag, and <input-file> is the
+# name of an input file. Doxygen will then use the output that the filter
+# program writes to standard output. If FILTER_PATTERNS is specified, this tag
+# will be ignored.
+#
+# Note that the filter must not add or remove lines; it is applied before the
+# code is scanned, but not when the output code is generated. If lines are added
+# or removed, the anchors will not be placed correctly.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# properly processed by doxygen.
+
+INPUT_FILTER           =
+
+# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
+# basis. Doxygen will compare the file name with each pattern and apply the
+# filter if there is a match. The filters are a list of the form: pattern=filter
+# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how
+# filters are used. If the FILTER_PATTERNS tag is empty or if none of the
+# patterns match the file name, INPUT_FILTER is applied.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# properly processed by doxygen.
+
+FILTER_PATTERNS        =
+
+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
+# INPUT_FILTER) will also be used to filter the input files that are used for
+# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES).
+# The default value is: NO.
+
+FILTER_SOURCE_FILES    = NO
+
+# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
+# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and
+# it is also possible to disable source filtering for a specific pattern using
+# *.ext= (so without naming a filter).
+# This tag requires that the tag FILTER_SOURCE_FILES is set to YES.
+
+FILTER_SOURCE_PATTERNS =
+
+# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that
+# is part of the input, its contents will be placed on the main page
+# (index.html). This can be useful if you have a project on for instance GitHub
+# and want to reuse the introduction page also for the doxygen output.
+
+USE_MDFILE_AS_MAINPAGE = ../README.md
+
+#---------------------------------------------------------------------------
+# Configuration options related to source browsing
+#---------------------------------------------------------------------------
+
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will be
+# generated. Documented entities will be cross-referenced with these sources.
+#
+# Note: To get rid of all source code in the generated output, make sure that
+# also VERBATIM_HEADERS is set to NO.
+# The default value is: NO.
+
+SOURCE_BROWSER         = YES
+
+# Setting the INLINE_SOURCES tag to YES will include the body of functions,
+# classes and enums directly into the documentation.
+# The default value is: NO.
+
+INLINE_SOURCES         = YES
+
+# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any
+# special comment blocks from generated source code fragments. Normal C, C++ and
+# Fortran comments will always remain visible.
+# The default value is: YES.
+
+STRIP_CODE_COMMENTS    = NO
+
+# If the REFERENCED_BY_RELATION tag is set to YES then for each documented
+# function all documented functions referencing it will be listed.
+# The default value is: NO.
+
+REFERENCED_BY_RELATION = YES
+
+# If the REFERENCES_RELATION tag is set to YES then for each documented function
+# all documented entities called/used by that function will be listed.
+# The default value is: NO.
+
+REFERENCES_RELATION    = YES
+
+# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set
+# to YES then the hyperlinks from functions in REFERENCES_RELATION and
+# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will
+# link to the documentation.
+# The default value is: YES.
+
+REFERENCES_LINK_SOURCE = YES
+
+# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the
+# source code will show a tooltip with additional information such as prototype,
+# brief description and links to the definition and documentation. Since this
+# will make the HTML file larger and loading of large files a bit slower, you
+# can opt to disable this feature.
+# The default value is: YES.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
+
+SOURCE_TOOLTIPS        = YES
+
+# If the USE_HTAGS tag is set to YES then the references to source code will
+# point to the HTML generated by the htags(1) tool instead of doxygen built-in
+# source browser. The htags tool is part of GNU's global source tagging system
+# (see http://www.gnu.org/software/global/global.html). You will need version
+# 4.8.6 or higher.
+#
+# To use it do the following:
+# - Install the latest version of global
+# - Enable SOURCE_BROWSER and USE_HTAGS in the config file
+# - Make sure the INPUT points to the root of the source tree
+# - Run doxygen as normal
+#
+# Doxygen will invoke htags (and that will in turn invoke gtags), so these
+# tools must be available from the command line (i.e. in the search path).
+#
+# The result: instead of the source browser generated by doxygen, the links to
+# source code will now point to the output of htags.
+# The default value is: NO.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
+
+USE_HTAGS              = NO
+
+# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a
+# verbatim copy of the header file for each class for which an include is
+# specified. Set to NO to disable this.
+# See also: Section \class.
+# The default value is: YES.
+
+VERBATIM_HEADERS       = YES
+
+#---------------------------------------------------------------------------
+# Configuration options related to the alphabetical class index
+#---------------------------------------------------------------------------
+
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all
+# compounds will be generated. Enable this if the project contains a lot of
+# classes, structs, unions or interfaces.
+# The default value is: YES.
+
+ALPHABETICAL_INDEX     = YES
+
+# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in
+# which the alphabetical index list will be split.
+# Minimum value: 1, maximum value: 20, default value: 5.
+# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
+
+COLS_IN_ALPHA_INDEX    = 5
+
+# In case all classes in a project start with a common prefix, all classes will
+# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
+# can be used to specify a prefix (or a list of prefixes) that should be ignored
+# while generating the index headers.
+# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
+
+IGNORE_PREFIX          =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the HTML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output
+# The default value is: YES.
+
+GENERATE_HTML          = YES
+
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_OUTPUT            = html
+
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
+# generated HTML page (for example: .htm, .php, .asp).
+# The default value is: .html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_FILE_EXTENSION    = .html
+
+# The HTML_HEADER tag can be used to specify a user-defined HTML header file for
+# each generated HTML page. If the tag is left blank doxygen will generate a
+# standard header.
+#
+# To get valid HTML the header file that includes any scripts and style sheets
+# that doxygen needs, which is dependent on the configuration options used (e.g.
+# the setting GENERATE_TREEVIEW). It is highly recommended to start with a
+# default header using
+# doxygen -w html new_header.html new_footer.html new_stylesheet.css
+# YourConfigFile
+# and then modify the file new_header.html. See also section "Doxygen usage"
+# for information on how to generate the default header that doxygen normally
+# uses.
+# Note: The header is subject to change so you typically have to regenerate the
+# default header when upgrading to a newer version of doxygen. For a description
+# of the possible markers and block names see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_HEADER            =
+
+# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
+# generated HTML page. If the tag is left blank doxygen will generate a standard
+# footer. See HTML_HEADER for more information on how to generate a default
+# footer and what special commands can be used inside the footer. See also
+# section "Doxygen usage" for information on how to generate the default footer
+# that doxygen normally uses.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_FOOTER            =
+
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
+# sheet that is used by each HTML page. It can be used to fine-tune the look of
+# the HTML output. If left blank doxygen will generate a default style sheet.
+# See also section "Doxygen usage" for information on how to generate the style
+# sheet that doxygen normally uses.
+# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as
+# it is more robust and this tag (HTML_STYLESHEET) will in the future become
+# obsolete.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_STYLESHEET        =
+
+# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
+# cascading style sheets that are included after the standard style sheets
+# created by doxygen. Using this option one can overrule certain style aspects.
+# This is preferred over using HTML_STYLESHEET since it does not replace the
+# standard style sheet and is therefore more robust against future updates.
+# Doxygen will copy the style sheet files to the output directory.
+# Note: The order of the extra style sheet files is of importance (e.g. the last
+# style sheet in the list overrules the setting of the previous ones in the
+# list). For an example see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_EXTRA_STYLESHEET  =
+
+# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the HTML output directory. Note
+# that these files will be copied to the base HTML output directory. Use the
+# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
+# files. In the HTML_STYLESHEET file, use the file name only. Also note that the
+# files will be copied as-is; there are no commands or markers available.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_EXTRA_FILES       =
+
+# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
+# will adjust the colors in the style sheet and background images according to
+# this color. Hue is specified as an angle on a colorwheel, see
+# http://en.wikipedia.org/wiki/Hue for more information. For instance the value
+# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300
+# purple, and 360 is red again.
+# Minimum value: 0, maximum value: 359, default value: 220.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_HUE    = 220
+
+# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
+# in the HTML output. For a value of 0 the output will use grayscales only. A
+# value of 255 will produce the most vivid colors.
+# Minimum value: 0, maximum value: 255, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_SAT    = 100
+
+# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the
+# luminance component of the colors in the HTML output. Values below 100
+# gradually make the output lighter, whereas values above 100 make the output
+# darker. The value divided by 100 is the actual gamma applied, so 80 represents
+# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not
+# change the gamma.
+# Minimum value: 40, maximum value: 240, default value: 80.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_GAMMA  = 80
+
+# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
+# page will contain the date and time when the page was generated. Setting this
+# to YES can help to show when doxygen was last run and thus if the
+# to NO can help when comparing the output of multiple runs.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_TIMESTAMP         = NO
+
+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
+# documentation will contain sections that can be hidden and shown after the
+# page has loaded.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_DYNAMIC_SECTIONS  = NO
+
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
+# shown in the various tree structured indices initially; the user can expand
+# and collapse entries dynamically later on. Doxygen will expand the tree to
+# such a level that at most the specified number of entries are visible (unless
+# a fully collapsed tree already exceeds this amount). So setting the number of
+# entries 1 will produce a full collapsed tree by default. 0 is a special value
+# representing an infinite number of entries and will result in a full expanded
+# tree by default.
+# Minimum value: 0, maximum value: 9999, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_INDEX_NUM_ENTRIES = 900
+
+# If the GENERATE_DOCSET tag is set to YES, additional index files will be
+# generated that can be used as input for Apple's Xcode 3 integrated development
+# environment (see: http://developer.apple.com/tools/xcode/), introduced with
+# OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a
+# Makefile in the HTML output directory. Running make will produce the docset in
+# that directory and running make install will install the docset in
+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at
+# startup. See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
+# for more information.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_DOCSET        = NO
+
+# This tag determines the name of the docset feed. A documentation feed provides
+# an umbrella under which multiple documentation sets from a single provider
+# (such as a company or product suite) can be grouped.
+# The default value is: Doxygen generated docs.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_FEEDNAME        = "Doxygen generated docs"
+
+# This tag specifies a string that should uniquely identify the documentation
+# set bundle. This should be a reverse domain-name style string, e.g.
+# com.mycompany.MyDocSet. Doxygen will append .docset to the name.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_BUNDLE_ID       = org.doxygen.Project
+
+# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify
+# the documentation publisher. This should be a reverse domain-name style
+# string, e.g. com.mycompany.MyDocSet.documentation.
+# The default value is: org.doxygen.Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_PUBLISHER_ID    = org.doxygen.Publisher
+
+# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher.
+# The default value is: Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_PUBLISHER_NAME  = Publisher
+
+# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three
+# additional HTML index files: index.hhp, index.hhc, and index.hhk. The
+# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop
+# (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on
+# Windows.
+#
+# The HTML Help Workshop contains a compiler that can convert all HTML output
+# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML
+# files are now used as the Windows 98 help format, and will replace the old
+# Windows help format (.hlp) on all Windows platforms in the future. Compressed
+# HTML files also contain an index, a table of contents, and you can search for
+# words in the documentation. The HTML workshop also contains a viewer for
+# compressed HTML files.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_HTMLHELP      = NO
+
+# The CHM_FILE tag can be used to specify the file name of the resulting .chm
+# file. You can add a path in front of the file if the result should not be
+# written to the html output directory.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+CHM_FILE               =
+
+# The HHC_LOCATION tag can be used to specify the location (absolute path
+# including file name) of the HTML help compiler (hhc.exe). If non-empty,
+# doxygen will try to run the HTML help compiler on the generated index.hhp.
+# The file has to be specified with full path.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+HHC_LOCATION           =
+
+# The GENERATE_CHI flag controls if a separate .chi index file is generated
+# (YES) or that it should be included in the master .chm file (NO).
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+GENERATE_CHI           = NO
+
+# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc)
+# and project file content.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+CHM_INDEX_ENCODING     =
+
+# The BINARY_TOC flag controls whether a binary table of contents is generated
+# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it
+# enables the Previous and Next buttons.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+BINARY_TOC             = NO
+
+# The TOC_EXPAND flag can be set to YES to add extra items for group members to
+# the table of contents of the HTML help documentation and to the tree view.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+TOC_EXPAND             = NO
+
+# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
+# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that
+# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help
+# (.qch) of the generated HTML documentation.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_QHP           = NO
+
+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify
+# the file name of the resulting .qch file. The path specified is relative to
+# the HTML output folder.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QCH_FILE               =
+
+# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help
+# Project output. For more information please see Qt Help Project / Namespace
+# (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#namespace).
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_NAMESPACE          = org.doxygen.Project
+
+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt
+# Help Project output. For more information please see Qt Help Project / Virtual
+# Folders (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#virtual-
+# folders).
+# The default value is: doc.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_VIRTUAL_FOLDER     = doc
+
+# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom
+# filter to add. For more information please see Qt Help Project / Custom
+# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
+# filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_CUST_FILTER_NAME   =
+
+# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the
+# custom filter to add. For more information please see Qt Help Project / Custom
+# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
+# filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_CUST_FILTER_ATTRS  =
+
+# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
+# project's filter section matches. Qt Help Project / Filter Attributes (see:
+# http://qt-project.org/doc/qt-4.8/qthelpproject.html#filter-attributes).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_SECT_FILTER_ATTRS  =
+
+# The QHG_LOCATION tag can be used to specify the location of Qt's
+# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the
+# generated .qhp file.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHG_LOCATION           =
+
+# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be
+# generated, together with the HTML files, they form an Eclipse help plugin. To
+# install this plugin and make it available under the help contents menu in
+# Eclipse, the contents of the directory containing the HTML and XML files needs
+# to be copied into the plugins directory of eclipse. The name of the directory
+# within the plugins directory should be the same as the ECLIPSE_DOC_ID value.
+# After copying Eclipse needs to be restarted before the help appears.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_ECLIPSEHELP   = NO
+
+# A unique identifier for the Eclipse help plugin. When installing the plugin
+# the directory name containing the HTML and XML files should also have this
+# name. Each documentation set should have its own identifier.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES.
+
+ECLIPSE_DOC_ID         = org.doxygen.Project
+
+# If you want full control over the layout of the generated HTML pages it might
+# be necessary to disable the index and replace it with your own. The
+# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top
+# of each HTML page. A value of NO enables the index and the value YES disables
+# it. Since the tabs in the index contain the same information as the navigation
+# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+DISABLE_INDEX          = NO
+
+# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
+# structure should be generated to display hierarchical information. If the tag
+# value is set to YES, a side panel will be generated containing a tree-like
+# index structure (just like the one that is generated for HTML Help). For this
+# to work a browser that supports JavaScript, DHTML, CSS and frames is required
+# (i.e. any modern browser). Windows users are probably better off using the
+# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can
+# further fine-tune the look of the index. As an example, the default style
+# sheet generated by doxygen has an example that shows how to put an image at
+# the root of the tree instead of the PROJECT_NAME. Since the tree basically has
+# the same information as the tab index, you could consider setting
+# DISABLE_INDEX to YES when enabling this option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_TREEVIEW      = YES
+
+# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
+# doxygen will group on one line in the generated HTML documentation.
+#
+# Note that a value of 0 will completely suppress the enum values from appearing
+# in the overview section.
+# Minimum value: 0, maximum value: 20, default value: 4.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+ENUM_VALUES_PER_LINE   = 4
+
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used
+# to set the initial width (in pixels) of the frame in which the tree is shown.
+# Minimum value: 0, maximum value: 1500, default value: 250.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+TREEVIEW_WIDTH         = 250
+
+# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to
+# external symbols imported via tag files in a separate window.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+EXT_LINKS_IN_WINDOW    = NO
+
+# Use this tag to change the font size of LaTeX formulas included as images in
+# the HTML documentation. When you change the font size after a successful
+# doxygen run you need to manually remove any form_*.png images from the HTML
+# output directory to force them to be regenerated.
+# Minimum value: 8, maximum value: 50, default value: 10.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+FORMULA_FONTSIZE       = 10
+
+# Use the FORMULA_TRANPARENT tag to determine whether or not the images
+# generated for formulas are transparent PNGs. Transparent PNGs are not
+# supported properly for IE 6.0, but are supported on all modern browsers.
+#
+# Note that when changing this option you need to delete any form_*.png files in
+# the HTML output directory before the changes have effect.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+FORMULA_TRANSPARENT    = YES
+
+# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see
+# http://www.mathjax.org) which uses client side Javascript for the rendering
+# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX
+# installed or if you want to formulas look prettier in the HTML output. When
+# enabled you may also need to install MathJax separately and configure the path
+# to it using the MATHJAX_RELPATH option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+USE_MATHJAX            = YES
+
+# When MathJax is enabled you can set the default output format to be used for
+# the MathJax output. See the MathJax site (see:
+# http://docs.mathjax.org/en/latest/output.html) for more details.
+# Possible values are: HTML-CSS (which is slower, but has the best
+# compatibility), NativeMML (i.e. MathML) and SVG.
+# The default value is: HTML-CSS.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_FORMAT         = HTML-CSS
+
+# When MathJax is enabled you need to specify the location relative to the HTML
+# output directory using the MATHJAX_RELPATH option. The destination directory
+# should contain the MathJax.js script. For instance, if the mathjax directory
+# is located at the same level as the HTML output directory, then
+# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax
+# Content Delivery Network so you can quickly see the result without installing
+# MathJax. However, it is strongly recommended to install a local copy of
+# MathJax from http://www.mathjax.org before deployment.
+# The default value is: http://cdn.mathjax.org/mathjax/latest.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_RELPATH        = http://cdn.mathjax.org/mathjax/latest
+
+# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
+# extension names that should be enabled during MathJax rendering. For example
+# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_EXTENSIONS     =
+
+# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
+# of code that will be used on startup of the MathJax code. See the MathJax site
+# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an
+# example see the documentation.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_CODEFILE       =
+
+# When the SEARCHENGINE tag is enabled doxygen will generate a search box for
+# the HTML output. The underlying search engine uses javascript and DHTML and
+# should work on any modern browser. Note that when using HTML help
+# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET)
+# there is already a search function so this one should typically be disabled.
+# For large projects the javascript based search engine can be slow, then
+# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to
+# search using the keyboard; to jump to the search box use <access key> + S
+# (what the <access key> is depends on the OS and browser, but it is typically
+# <CTRL>, <ALT>/<option>, or both). Inside the search box use the <cursor down
+# key> to jump into the search results window, the results can be navigated
+# using the <cursor keys>. Press <Enter> to select an item or <escape> to cancel
+# the search. The filter options can be selected when the cursor is inside the
+# search box by pressing <Shift>+<cursor down>. Also here use the <cursor keys>
+# to select a filter and <Enter> or <escape> to activate or cancel the filter
+# option.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+SEARCHENGINE           = YES
+
+# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
+# implemented using a web server instead of a web client using Javascript. There
+# are two flavors of web server based searching depending on the EXTERNAL_SEARCH
+# setting. When disabled, doxygen will generate a PHP script for searching and
+# an index file used by the script. When EXTERNAL_SEARCH is enabled the indexing
+# and searching needs to be provided by external tools. See the section
+# "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SERVER_BASED_SEARCH    = NO
+
+# When EXTERNAL_SEARCH tag is enabled doxygen will no longer generate the PHP
+# script for searching. Instead the search results are written to an XML file
+# which needs to be processed by an external indexer. Doxygen will invoke an
+# external search engine pointed to by the SEARCHENGINE_URL option to obtain the
+# search results.
+#
+# Doxygen ships with an example indexer (doxyindexer) and search engine
+# (doxysearch.cgi) which are based on the open source search engine library
+# Xapian (see: http://xapian.org/).
+#
+# See the section "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTERNAL_SEARCH        = NO
+
+# The SEARCHENGINE_URL should point to a search engine hosted by a web server
+# which will return the search results when EXTERNAL_SEARCH is enabled.
+#
+# Doxygen ships with an example indexer (doxyindexer) and search engine
+# (doxysearch.cgi) which are based on the open source search engine library
+# Xapian (see: http://xapian.org/). See the section "External Indexing and
+# Searching" for details.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SEARCHENGINE_URL       =
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed
+# search data is written to a file for indexing by an external tool. With the
+# SEARCHDATA_FILE tag the name of this file can be specified.
+# The default file is: searchdata.xml.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SEARCHDATA_FILE        = searchdata.xml
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the
+# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is
+# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple
+# projects and redirect the results back to the right project.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTERNAL_SEARCH_ID     =
+
+# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen
+# projects other than the one defined by this configuration file, but that are
+# all added to the same external search index. Each project needs to have a
+# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id of
+# to a relative location where the documentation can be found. The format is:
+# EXTRA_SEARCH_MAPPINGS = tagname1=loc1 tagname2=loc2 ...
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTRA_SEARCH_MAPPINGS  =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the LaTeX output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output.
+# The default value is: YES.
+
+GENERATE_LATEX         = NO
+
+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: latex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_OUTPUT           = latex
+
+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
+# invoked.
+#
+# Note that when enabling USE_PDFLATEX this option is only used for generating
+# bitmaps for formulas in the HTML output, but not in the Makefile that is
+# written to the output directory.
+# The default file is: latex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_CMD_NAME         = latex
+
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate
+# index for LaTeX.
+# The default file is: makeindex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+MAKEINDEX_CMD_NAME     = makeindex
+
+# If the COMPACT_LATEX tag is set to YES, doxygen generates more compact LaTeX
+# documents. This may be useful for small projects and may help to save some
+# trees in general.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+COMPACT_LATEX          = NO
+
+# The PAPER_TYPE tag can be used to set the paper type that is used by the
+# printer.
+# Possible values are: a4 (210 x 297 mm), letter (8.5 x 11 inches), legal (8.5 x
+# 14 inches) and executive (7.25 x 10.5 inches).
+# The default value is: a4.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+PAPER_TYPE             = a4
+
+# The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names
+# that should be included in the LaTeX output. The package can be specified just
+# by its name or with the correct syntax as to be used with the LaTeX
+# \usepackage command. To get the times font for instance you can specify :
+# EXTRA_PACKAGES=times or EXTRA_PACKAGES={times}
+# To use the option intlimits with the amsmath package you can specify:
+# EXTRA_PACKAGES=[intlimits]{amsmath}
+# If left blank no extra packages will be included.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+EXTRA_PACKAGES         =
+
+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for the
+# generated LaTeX document. The header should contain everything until the first
+# chapter. If it is left blank doxygen will generate a standard header. See
+# section "Doxygen usage" for information on how to let doxygen write the
+# default header to a separate file.
+#
+# Note: Only use a user-defined header if you know what you are doing! The
+# following commands have a special meaning inside the header: $title,
+# $datetime, $date, $doxygenversion, $projectname, $projectnumber,
+# $projectbrief, $projectlogo. Doxygen will replace $title with the empty
+# string, for the replacement values of the other commands the user is referred
+# to HTML_HEADER.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_HEADER           =
+
+# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the
+# generated LaTeX document. The footer should contain everything after the last
+# chapter. If it is left blank doxygen will generate a standard footer. See
+# LATEX_HEADER for more information on how to generate a default footer and what
+# special commands can be used inside the footer.
+#
+# Note: Only use a user-defined footer if you know what you are doing!
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_FOOTER           =
+
+# The LATEX_EXTRA_STYLESHEET tag can be used to specify additional user-defined
+# LaTeX style sheets that are included after the standard style sheets created
+# by doxygen. Using this option one can overrule certain style aspects. Doxygen
+# will copy the style sheet files to the output directory.
+# Note: The order of the extra style sheet files is of importance (e.g. the last
+# style sheet in the list overrules the setting of the previous ones in the
+# list).
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_EXTRA_STYLESHEET =
+
+# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the LATEX_OUTPUT output
+# directory. Note that the files will be copied as-is; there are no commands or
+# markers available.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_EXTRA_FILES      =
+
+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated is
+# prepared for conversion to PDF (using ps2pdf or pdflatex). The PDF file will
+# contain links (just like the HTML output) instead of page references. This
+# makes the output suitable for online browsing using a PDF viewer.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+PDF_HYPERLINKS         = YES
+
+# If the USE_PDFLATEX tag is set to YES, doxygen will use pdflatex to generate
+# the PDF file directly from the LaTeX files. Set this option to YES, to get a
+# higher quality PDF documentation.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+USE_PDFLATEX           = YES
+
+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode
+# command to the generated LaTeX files. This will instruct LaTeX to keep running
+# if errors occur, instead of asking the user for help. This option is also used
+# when generating formulas in HTML.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_BATCHMODE        = NO
+
+# If the LATEX_HIDE_INDICES tag is set to YES then doxygen will not include the
+# index chapters (such as File Index, Compound Index, etc.) in the output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_HIDE_INDICES     = NO
+
+# If the LATEX_SOURCE_CODE tag is set to YES then doxygen will include source
+# code with syntax highlighting in the LaTeX output.
+#
+# Note that which sources are shown also depends on other settings such as
+# SOURCE_BROWSER.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_SOURCE_CODE      = NO
+
+# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
+# bibliography, e.g. plainnat, or ieeetr. See
+# http://en.wikipedia.org/wiki/BibTeX and \cite for more info.
+# The default value is: plain.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_BIB_STYLE        = plain
+
+# If the LATEX_TIMESTAMP tag is set to YES then the footer of each generated
+# page will contain the date and time when the page was generated. Setting this
+# to NO can help when comparing the output of multiple runs.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_TIMESTAMP        = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the RTF output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_RTF tag is set to YES, doxygen will generate RTF output. The
+# RTF output is optimized for Word 97 and may not look too pretty with other RTF
+# readers/editors.
+# The default value is: NO.
+
+GENERATE_RTF           = NO
+
+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: rtf.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_OUTPUT             = rtf
+
+# If the COMPACT_RTF tag is set to YES, doxygen generates more compact RTF
+# documents. This may be useful for small projects and may help to save some
+# trees in general.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+COMPACT_RTF            = NO
+
+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated will
+# contain hyperlink fields. The RTF file will contain links (just like the HTML
+# output) instead of page references. This makes the output suitable for online
+# browsing using Word or some other Word compatible readers that support those
+# fields.
+#
+# Note: WordPad (write) and others do not support links.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_HYPERLINKS         = NO
+
+# Load stylesheet definitions from file. Syntax is similar to doxygen's config
+# file, i.e. a series of assignments. You only have to provide replacements,
+# missing definitions are set to their default value.
+#
+# See also section "Doxygen usage" for information on how to generate the
+# default style sheet that doxygen normally uses.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_STYLESHEET_FILE    =
+
+# Set optional variables used in the generation of an RTF document. Syntax is
+# similar to doxygen's config file. A template extensions file can be generated
+# using doxygen -e rtf extensionFile.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_EXTENSIONS_FILE    =
+
+# If the RTF_SOURCE_CODE tag is set to YES then doxygen will include source code
+# with syntax highlighting in the RTF output.
+#
+# Note that which sources are shown also depends on other settings such as
+# SOURCE_BROWSER.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_SOURCE_CODE        = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the man page output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_MAN tag is set to YES, doxygen will generate man pages for
+# classes and files.
+# The default value is: NO.
+
+GENERATE_MAN           = NO
+
+# The MAN_OUTPUT tag is used to specify where the man pages will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it. A directory man3 will be created inside the directory specified by
+# MAN_OUTPUT.
+# The default directory is: man.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_OUTPUT             = man
+
+# The MAN_EXTENSION tag determines the extension that is added to the generated
+# man pages. In case the manual section does not start with a number, the number
+# 3 is prepended. The dot (.) at the beginning of the MAN_EXTENSION tag is
+# optional.
+# The default value is: .3.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_EXTENSION          = .3
+
+# The MAN_SUBDIR tag determines the name of the directory created within
+# MAN_OUTPUT in which the man pages are placed. If defaults to man followed by
+# MAN_EXTENSION with the initial . removed.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_SUBDIR             =
+
+# If the MAN_LINKS tag is set to YES and doxygen generates man output, then it
+# will generate one additional man file for each entity documented in the real
+# man page(s). These additional files only source the real man page, but without
+# them the man command would be unable to find the correct page.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_LINKS              = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the XML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_XML tag is set to YES, doxygen will generate an XML file that
+# captures the structure of the code including all documentation.
+# The default value is: NO.
+
+GENERATE_XML           = NO
+
+# The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: xml.
+# This tag requires that the tag GENERATE_XML is set to YES.
+
+XML_OUTPUT             = xml
+
+# If the XML_PROGRAMLISTING tag is set to YES, doxygen will dump the program
+# listings (including syntax highlighting and cross-referencing information) to
+# the XML output. Note that enabling this will significantly increase the size
+# of the XML output.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_XML is set to YES.
+
+XML_PROGRAMLISTING     = YES
+
+#---------------------------------------------------------------------------
+# Configuration options related to the DOCBOOK output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_DOCBOOK tag is set to YES, doxygen will generate Docbook files
+# that can be used to generate PDF.
+# The default value is: NO.
+
+GENERATE_DOCBOOK       = NO
+
+# The DOCBOOK_OUTPUT tag is used to specify where the Docbook pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in
+# front of it.
+# The default directory is: docbook.
+# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
+
+DOCBOOK_OUTPUT         = docbook
+
+# If the DOCBOOK_PROGRAMLISTING tag is set to YES, doxygen will include the
+# program listings (including syntax highlighting and cross-referencing
+# information) to the DOCBOOK output. Note that enabling this will significantly
+# increase the size of the DOCBOOK output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
+
+DOCBOOK_PROGRAMLISTING = NO
+
+#---------------------------------------------------------------------------
+# Configuration options for the AutoGen Definitions output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_AUTOGEN_DEF tag is set to YES, doxygen will generate an
+# AutoGen Definitions (see http://autogen.sf.net) file that captures the
+# structure of the code including all documentation. Note that this feature is
+# still experimental and incomplete at the moment.
+# The default value is: NO.
+
+GENERATE_AUTOGEN_DEF   = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the Perl module output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_PERLMOD tag is set to YES, doxygen will generate a Perl module
+# file that captures the structure of the code including all documentation.
+#
+# Note that this feature is still experimental and incomplete at the moment.
+# The default value is: NO.
+
+GENERATE_PERLMOD       = NO
+
+# If the PERLMOD_LATEX tag is set to YES, doxygen will generate the necessary
+# Makefile rules, Perl scripts and LaTeX code to be able to generate PDF and DVI
+# output from the Perl module output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_LATEX          = NO
+
+# If the PERLMOD_PRETTY tag is set to YES, the Perl module output will be nicely
+# formatted so it can be parsed by a human reader. This is useful if you want to
+# understand what is going on. On the other hand, if this tag is set to NO, the
+# size of the Perl module output will be much smaller and Perl will parse it
+# just the same.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_PRETTY         = YES
+
+# The names of the make variables in the generated doxyrules.make file are
+# prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. This is useful
+# so different doxyrules.make files included by the same Makefile don't
+# overwrite each other's variables.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_MAKEVAR_PREFIX =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the preprocessor
+#---------------------------------------------------------------------------
+
+# If the ENABLE_PREPROCESSING tag is set to YES, doxygen will evaluate all
+# C-preprocessor directives found in the sources and include files.
+# The default value is: YES.
+
+ENABLE_PREPROCESSING   = YES
+
+# If the MACRO_EXPANSION tag is set to YES, doxygen will expand all macro names
+# in the source code. If set to NO, only conditional compilation will be
+# performed. Macro expansion can be done in a controlled way by setting
+# EXPAND_ONLY_PREDEF to YES.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+MACRO_EXPANSION        = YES
+
+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
+# the macro expansion is limited to the macros specified with the PREDEFINED and
+# EXPAND_AS_DEFINED tags.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+EXPAND_ONLY_PREDEF     = YES
+
+# If the SEARCH_INCLUDES tag is set to YES, the include files in the
+# INCLUDE_PATH will be searched if a #include is found.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+SEARCH_INCLUDES        = YES
+
+# The INCLUDE_PATH tag can be used to specify one or more directories that
+# contain include files that are not input files but should be processed by the
+# preprocessor.
+# This tag requires that the tag SEARCH_INCLUDES is set to YES.
+
+INCLUDE_PATH           =
+
+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
+# patterns (like *.h and *.hpp) to filter out the header-files in the
+# directories. If left blank, the patterns specified with FILE_PATTERNS will be
+# used.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+INCLUDE_FILE_PATTERNS  =
+
+# The PREDEFINED tag can be used to specify one or more macro names that are
+# defined before the preprocessor is started (similar to the -D option of e.g.
+# gcc). The argument of the tag is a list of macros of the form: name or
+# name=definition (no spaces). If the definition and the "=" are omitted, "=1"
+# is assumed. To prevent a macro definition from being undefined via #undef or
+# recursively expanded use the := operator instead of the = operator.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+PREDEFINED             =
+
+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
+# tag can be used to specify a list of macro names that should be expanded. The
+# macro definition that is found in the sources will be used. Use the PREDEFINED
+# tag if you want to use a different macro definition that overrules the
+# definition found in the source code.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+EXPAND_AS_DEFINED      =
+
+# If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will
+# remove all references to function-like macros that are alone on a line, have
+# an all uppercase name, and do not end with a semicolon. Such function macros
+# are typically used for boiler-plate code, and will confuse the parser if not
+# removed.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+SKIP_FUNCTION_MACROS   = YES
+
+#---------------------------------------------------------------------------
+# Configuration options related to external references
+#---------------------------------------------------------------------------
+
+# The TAGFILES tag can be used to specify one or more tag files. For each tag
+# file the location of the external documentation should be added. The format of
+# a tag file without this location is as follows:
+# TAGFILES = file1 file2 ...
+# Adding location for the tag files is done as follows:
+# TAGFILES = file1=loc1 "file2 = loc2" ...
+# where loc1 and loc2 can be relative or absolute paths or URLs. See the
+# section "Linking to external documentation" for more information about the use
+# of tag files.
+# Note: Each tag file must have a unique name (where the name does NOT include
+# the path). If a tag file is not located in the directory in which doxygen is
+# run, you must also specify the path to the tagfile here.
+
+TAGFILES               =
+
+# When a file name is specified after GENERATE_TAGFILE, doxygen will create a
+# tag file that is based on the input files it reads. See section "Linking to
+# external documentation" for more information about the usage of tag files.
+
+GENERATE_TAGFILE       =
+
+# If the ALLEXTERNALS tag is set to YES, all external class will be listed in
+# the class index. If set to NO, only the inherited external classes will be
+# listed.
+# The default value is: NO.
+
+ALLEXTERNALS           = NO
+
+# If the EXTERNAL_GROUPS tag is set to YES, all external groups will be listed
+# in the modules index. If set to NO, only the current project's groups will be
+# listed.
+# The default value is: YES.
+
+EXTERNAL_GROUPS        = YES
+
+# If the EXTERNAL_PAGES tag is set to YES, all external pages will be listed in
+# the related pages index. If set to NO, only the current project's pages will
+# be listed.
+# The default value is: YES.
+
+EXTERNAL_PAGES         = YES
+
+# The PERL_PATH should be the absolute path and name of the perl script
+# interpreter (i.e. the result of 'which perl').
+# The default file (with absolute path) is: /usr/bin/perl.
+
+PERL_PATH              = /usr/bin/perl
+
+#---------------------------------------------------------------------------
+# Configuration options related to the dot tool
+#---------------------------------------------------------------------------
+
+# If the CLASS_DIAGRAMS tag is set to YES, doxygen will generate a class diagram
+# (in HTML and LaTeX) for classes with base or super classes. Setting the tag to
+# NO turns the diagrams off. Note that this option also works with HAVE_DOT
+# disabled, but it is recommended to install and use dot, since it yields more
+# powerful graphs.
+# The default value is: YES.
+
+CLASS_DIAGRAMS         = YES
+
+# You can define message sequence charts within doxygen comments using the \msc
+# command. Doxygen will then run the mscgen tool (see:
+# http://www.mcternan.me.uk/mscgen/)) to produce the chart and insert it in the
+# documentation. The MSCGEN_PATH tag allows you to specify the directory where
+# the mscgen tool resides. If left empty the tool is assumed to be found in the
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diff --git a/docs/layout.xml b/docs/layout.xml
new file mode 100644
index 0000000..b83dcee
--- /dev/null
+++ b/docs/layout.xml
@@ -0,0 +1,191 @@
+<doxygenlayout version="1.0">
+  <!-- Generated by doxygen 1.8.13 -->
+  <!-- Navigation index tabs for HTML output -->
+  <navindex>
+    <tab type="mainpage" visible="yes" title="Main page"/>
+    <tab type="pages" visible="yes" title="Pages" intro="Pages"/>
+    <tab type="modules" visible="yes" title="Modules" intro=""/>
+    <tab type="namespaces" visible="yes" title="Name Spaces">
+      <tab type="namespacelist" visible="yes" title="Name space list" intro=""/>
+      <tab type="namespacemembers" visible="yes" title="Name space members" intro=""/>
+    </tab>
+    <tab type="classes" visible="yes" title="F90 modules">
+      <tab type="classlist" visible="yes" title="F90 module list" intro="This is the list of all F90 modules. Some are expandable which shows the defined types that are provided by that module."/>
+      <tab type="classindex" visible="yes" title=""/>
+      <tab type="hierarchy" visible="yes" title="Hierarchy" intro=""/>
+      <tab type="classmembers" visible="yes" title="Module functions and variables" intro=""/>
+    </tab>
+    <tab type="files" visible="yes" title="Source files">
+      <tab type="filelist" visible="yes" title="File list" intro=""/>
+      <tab type="globals" visible="yes" title="Globals" intro=""/>
+    </tab>
+    <tab type="examples" visible="yes" title="Examples" intro=""/> 
+  </navindex>
+
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+    <detaileddescription title=""/>
+    <includes visible="$SHOW_INCLUDE_FILES"/>
+    <inheritancegraph visible="$CLASS_GRAPH"/>
+    <collaborationgraph visible="$COLLABORATION_GRAPH"/>
+    <memberdecl>
+      <nestedclasses visible="yes" title="Defined types"/>
+      <publictypes title="publictypes"/>
+      <services title="services"/>
+      <interfaces title="interfaces"/>
+      <publicslots title="publicslots"/>
+      <signals title="signals"/>
+      <publicmethods title="Public functions"/>
+      <publicstaticmethods title="publicstaticmethdso"/>
+      <publicattributes title="Public variables and constants"/>
+      <publicstaticattributes title="publicstaticattributes"/>
+      <protectedtypes title="protectedtypes"/>
+      <protectedslots title="protectedslots"/>
+      <protectedmethods title="protectedmethods"/>
+      <protectedstaticmethods title="protectedstaticmethods"/>
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+      <packagetypes title="packagetypes"/>
+      <packagemethods title="packagemethods"/>
+      <packagestaticmethods title="packagestaticmethods"/>
+      <packageattributes title="packageattributes"/>
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+      <properties title="properties"/>
+      <events title="events"/>
+      <privatetypes title="privatetypes"/>
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+      <privatemethods title="Private functions"/>
+      <privatestaticmethods title="privatestaticmethods"/>
+      <privateattributes title="Private variables and constants"/>
+      <privatestaticattributes title="privatestaticattributes"/>
+      <friends title="friends"/>
+      <related title="related" subtitle=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    <memberdef>
+      <inlineclasses title="inlineclasses"/>
+      <typedefs title="typedefs"/>
+      <enums title="enums"/>
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+      <functions title="Functions and subroutines"/>
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+    <allmemberslink visible="yes"/>
+    <usedfiles visible="$SHOW_USED_FILES"/>
+    <authorsection visible="yes"/>
+  </class>
+
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+    <detaileddescription title=""/>
+    <memberdecl>
+      <nestednamespaces visible="yes" title=""/>
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+      <classes visible="yes" title=""/>
+      <typedefs title=""/>
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+      <functions title=""/>
+      <variables title=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    <memberdef>
+      <inlineclasses title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <functions title=""/>
+      <variables title=""/>
+    </memberdef>
+    <authorsection visible="yes"/>
+  </namespace>
+
+  <!-- Layout definition for a file page -->
+  <file>
+    <detaileddescription title=""/>
+    <includes visible="$SHOW_INCLUDE_FILES"/>
+    <includegraph visible="$INCLUDE_GRAPH"/>
+    <includedbygraph visible="$INCLUDED_BY_GRAPH"/>
+    <sourcelink visible="yes"/>
+    <memberdecl>
+      <classes visible="yes" title=""/>
+      <namespaces visible="yes" title=""/>
+      <constantgroups visible="yes" title=""/>
+      <defines title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <functions title=""/>
+      <variables title=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    <memberdef>
+      <inlineclasses title=""/>
+      <defines title=""/>
+      <typedefs title=""/>
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+      <functions title=""/>
+      <variables title=""/>
+    </memberdef>
+    <authorsection/>
+  </file>
+
+  <!-- Layout definition for a group page -->
+  <group>
+    <briefdescription visible="yes"/>
+    <detaileddescription title=""/>
+    <groupgraph visible="$GROUP_GRAPHS"/>
+    <memberdecl>
+      <nestedgroups visible="yes" title=""/>
+      <dirs visible="yes" title=""/>
+      <files visible="yes" title=""/>
+      <namespaces visible="yes" title=""/>
+      <classes visible="yes" title=""/>
+      <defines title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <enumvalues title=""/>
+      <functions title=""/>
+      <variables title=""/>
+      <signals title=""/>
+      <publicslots title=""/>
+      <protectedslots title=""/>
+      <privateslots title=""/>
+      <events title=""/>
+      <properties title=""/>
+      <friends title=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    <memberdef>
+      <pagedocs/>
+      <inlineclasses title=""/>
+      <defines title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <enumvalues title=""/>
+      <functions title=""/>
+      <variables title=""/>
+      <signals title=""/>
+      <publicslots title=""/>
+      <protectedslots title=""/>
+      <privateslots title=""/>
+      <events title=""/>
+      <properties title=""/>
+      <friends title=""/>
+    </memberdef>
+    <authorsection visible="yes"/>
+  </group>
+
+  <!-- Layout definition for a directory page -->
+  <directory>
+    <briefdescription visible="yes"/>
+    <directorygraph visible="yes"/>
+    <memberdecl>
+      <dirs visible="yes"/>
+      <files visible="yes"/>
+    </memberdecl>
+    <detaileddescription title=""/>
+  </directory>
+</doxygenlayout>

From 19b5cf7f264184d5e6490b13667db998917feaf1 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Tue, 28 Mar 2017 09:42:30 -0400
Subject: [PATCH 215/361] Finished documenting APIs

- All APIs documented about from a few bond-associated function that
  @sternalon needs to do.
---
 icebergs.F90           | 369 ++++++++++++++++++++++-------------------
 icebergs_framework.F90 |   2 +-
 2 files changed, 199 insertions(+), 172 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index deba85a..e74f4c5 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -70,9 +70,9 @@ module ice_bergs
 !TOM> no horizontal drag for sea ice! real, parameter :: Cd_ih=0.0012 !< (Horizontal) Drag coefficient between bergs and sea-ice (?)
 
 #ifdef _FILE_VERSION
-  character(len=128) :: version = _FILE_VERSION
+character(len=128) :: version = _FILE_VERSION !< Version of file
 #else
-  character(len=128) :: version = 'unknown'
+character(len=128) :: version = 'unknown' !< Version of file
 #endif
 
 contains
@@ -3849,18 +3849,19 @@ subroutine icebergs_incr_mass(bergs, mass, Time)
 
 end subroutine icebergs_incr_mass
 
+!> Sums up a berg property into a gridded field
 subroutine sum_up_spread_fields(bergs, field, field_name)
-! Arguments
-type(icebergs), pointer :: bergs !< Container for all types and memory
-real, dimension(bergs%grd%isc:bergs%grd%iec,bergs%grd%jsc:bergs%grd%jec), intent(out) :: field
-character(len=4), intent(in) :: field_name
-! Local variables
-integer :: i, j
-type(icebergs_gridded), pointer :: grd
-real :: dmda
-logical :: lerr
-real, dimension(bergs%grd%isd:bergs%grd%ied, bergs%grd%jsd:bergs%grd%jed,9) :: var_on_ocean   !Variable being spread onto the ocean  (mass, area, Uvel, Vvel)
-integer :: stderrunit
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  real, dimension(bergs%grd%isc:bergs%grd%iec,bergs%grd%jsc:bergs%grd%jec), intent(out) :: field !< Gridded field
+  character(len=4), intent(in) :: field_name !< Name of field to grid
+  ! Local variables
+  integer :: i, j
+  type(icebergs_gridded), pointer :: grd
+  real :: dmda
+  logical :: lerr
+  real, dimension(bergs%grd%isd:bergs%grd%ied, bergs%grd%jsd:bergs%grd%jed,9) :: var_on_ocean   !Variable being spread onto the ocean  (mass, area, Uvel, Vvel)
+  integer :: stderrunit
 
   ! Get the stderr unit number
   stderrunit = stderr()
@@ -3924,17 +3925,16 @@ subroutine sum_up_spread_fields(bergs, field, field_name)
  endif
 end subroutine sum_up_spread_fields
 
-! ##############################################################################
-
+!> Adds calving (from driver) to the coastal "buckets"
 subroutine accumulate_calving(bergs)
-! Arguments
-type(icebergs), pointer :: bergs !< Container for all types and memory
-! Local variables
-type(icebergs_gridded), pointer :: grd
-real :: remaining_dist, net_calving_used
-integer :: k, i, j
-logical, save :: first_call=.true.
-integer :: stderrunit
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  ! Local variables
+  type(icebergs_gridded), pointer :: grd
+  real :: remaining_dist, net_calving_used
+  integer :: k, i, j
+  logical, save :: first_call=.true.
+  integer :: stderrunit
 
   ! Get the stderr unit number
   stderrunit = stderr()
@@ -3986,19 +3986,18 @@ subroutine accumulate_calving(bergs)
 
 end subroutine accumulate_calving
 
-! ##############################################################################
-
+!> Generate icebergs from overflowing "buckets"
 subroutine calve_icebergs(bergs)
-! Arguments
-type(icebergs), pointer :: bergs !< Container for all types and memory
-! Local variables
-type(icebergs_gridded), pointer :: grd
-integer :: i,j,k,icnt,icntmax
-integer :: iNg, jNg  !Total number of points gloablly in i and j direction
-type(iceberg) :: newberg
-logical :: lret
-real :: xi, yj, ddt, calving_to_bergs, calved_to_berg, heat_to_bergs, heat_to_berg
-integer :: stderrunit
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  ! Local variables
+  type(icebergs_gridded), pointer :: grd
+  integer :: i,j,k,icnt,icntmax
+  integer :: iNg, jNg ! Total number of points globally in i and j direction
+  type(iceberg) :: newberg
+  logical :: lret
+  real :: xi, yj, ddt, calving_to_bergs, calved_to_berg, heat_to_bergs, heat_to_berg
+  integer :: stderrunit
 
   ! Get the stderr unit number
   stderrunit = stderr()
@@ -4088,19 +4087,20 @@ subroutine calve_icebergs(bergs)
 
 end subroutine calve_icebergs
 
+!> Evolves icebergs forward by updating velocity and position with a time-stepping scheme
 subroutine evolve_icebergs(bergs)
-! Arguments
-type(icebergs), pointer :: bergs !< Container for all types and memory
-! Local variables
-type(icebergs_gridded), pointer :: grd
-type(iceberg), pointer :: berg
-real :: uveln, vveln, lonn, latn
-real :: axn, ayn, bxn, byn                                           ! Added by Alon - explicit and implicit accelations from the previous step
-real :: xi, yj
-integer :: i, j
-integer :: grdi, grdj
-integer :: stderrunit
-logical :: bounced, interactive_icebergs_on, Runge_not_Verlet
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  ! Local variables
+  type(icebergs_gridded), pointer :: grd
+  type(iceberg), pointer :: berg
+  real :: uveln, vveln, lonn, latn
+  real :: axn, ayn, bxn, byn          ! Added by Alon - explicit and implicit accelerations from the previous step
+  real :: xi, yj
+  integer :: i, j
+  integer :: grdi, grdj
+  integer :: stderrunit
+  logical :: bounced, interactive_icebergs_on, Runge_not_Verlet
 
   ! Get the stderr unit number
   stderrunit = stderr()
@@ -4111,7 +4111,6 @@ subroutine evolve_icebergs(bergs)
   interactive_icebergs_on=bergs%interactive_icebergs_on
   Runge_not_Verlet=bergs%Runge_not_Verlet
 
-
   do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
     berg=>bergs%list(grdi,grdj)%first
     do while (associated(berg)) ! loop over all bergs
@@ -4162,7 +4161,7 @@ subroutine evolve_icebergs(bergs)
           berg%ine=i     ;   berg%jne=j
           berg%xi=xi     ;   berg%yj=yj
         else
-          if (.not. interactive_icebergs_on)  call update_verlet_position(bergs,berg)
+          if (.not. interactive_icebergs_on) call update_verlet_position(bergs,berg)
         endif
 
         !call interp_flds(grd, i, j, xi, yj, berg%uo, berg%vo, berg%ui, berg%vi, berg%ua, berg%va, berg%ssh_x, berg%ssh_y, berg%sst)
@@ -4179,7 +4178,7 @@ subroutine evolve_icebergs(bergs)
       berg=>bergs%list(grdi,grdj)%first
       do while (associated(berg)) ! loop over all bergs
         if (berg%static_berg .lt. 0.5) then  !Only allow non-static icebergs to evolve
-         if (.not. Runge_not_Verlet)  call update_verlet_position(bergs,berg)
+         if (.not. Runge_not_Verlet) call update_verlet_position(bergs,berg)
 
          !Updating old velocities (for use in iceberg interactions)
           berg%uvel_old=berg%uvel
@@ -4192,28 +4191,33 @@ subroutine evolve_icebergs(bergs)
     enddo ; enddo
   endif
 
-!contains
 end subroutine evolve_icebergs
 
+!> Calculate explicit and implicit accelerations, and new velocity, using the Verlet method
 subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
-type(icebergs), pointer :: bergs !< Container for all types and memory
-type(iceberg), pointer, intent(inout) :: berg
-type(icebergs_gridded), pointer :: grd
-! Local variables
-real, intent(out) :: axn, ayn, bxn, byn, uveln, vveln
-real :: lonn, latn
-real :: uvel1, vvel1,  uvel2, vvel2, uvel3, vvel3
-real :: ax1, ay1
-real :: x1,  y1, xddot1, yddot1, xi, yj
-real :: xdot3, ydot3
-real :: xdotn, ydotn
-real :: dt, dt_2, dt_6, dydl
-real :: orientation
-logical :: bounced, on_tangential_plane, error_flag
-integer :: i, j
-integer :: stderrunit
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  type(iceberg), pointer, intent(inout) :: berg !< Iceberg
+  real, intent(out) :: axn !< Explicit zonal acceleration (m/s2)
+  real, intent(out) :: ayn !< Explicit meridional acceleration (m/s2)
+  real, intent(out) :: bxn !< Implicit zonal acceleration (m/s2)
+  real, intent(out) :: byn !< Implicit meridional acceleration (m/s2)
+  real, intent(out) :: uveln !< New zonal velocity (m/s)
+  real, intent(out) :: vveln !< New meridional velocity (m/s)
+  ! Local variables
+  type(icebergs_gridded), pointer :: grd
+  real :: lonn, latn
+  real :: uvel1, vvel1,  uvel2, vvel2, uvel3, vvel3
+  real :: ax1, ay1
+  real :: x1,  y1, xddot1, yddot1, xi, yj
+  real :: xdot3, ydot3
+  real :: xdotn, ydotn
+  real :: dt, dt_2, dt_6, dydl
+  real :: orientation
+  logical :: bounced, on_tangential_plane, error_flag
+  integer :: i, j
+  integer :: stderrunit
 
-  !Initialize variables
+  ! Initialize variables
 
   ! In this scheme a_n and b_n are saved from the previous timestep, giving the explicit and implicit parts of the acceleration, and a_np1, b_np1 are for the next time step
   ! Note that ax1=a_np1/2 +b_np1, as calculated by the acceleration subrouting
@@ -4245,15 +4249,15 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
   uvel3=uvel1+(dt_2*axn)                  !Alon
   vvel3=vvel1+(dt_2*ayn)                  !Alon
 
-  !Note, the mass scaling is equal to 1 (rather than 0.25 as in RK), since
-  !this is only called once in Verlet stepping.
+  ! Note, the mass scaling is equal to 1 (rather than 0.25 as in RK), since
+  ! this is only called once in Verlet stepping.
   if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
     call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 1.0*berg%mass_scaling,berg%length*berg%width, berg%thickness)
 
   ! Calling the acceleration   (note that the velocity is converted to u_star inside the accel script)
   call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn, ayn, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
 
-  !Solving for the new velocity
+  ! Solving for the new velocity
   on_tangential_plane=.false.
   if ((berg%lat>89.) .and. (bergs%grd%grid_is_latlon)) on_tangential_plane=.true.
   if (on_tangential_plane) then
@@ -4312,25 +4316,38 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
 
 end subroutine verlet_stepping
 
-subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lonn, latn, i, j, xi, yj)
-type(icebergs), pointer :: bergs !< Container for all types and memory
-type(iceberg), pointer, intent(inout) :: berg
-type(icebergs_gridded), pointer :: grd
-real , intent(out) :: axn, ayn, bxn, byn, uveln, vveln,lonn, latn, xi, yj
-integer, intent(out) :: i, j
-real :: uvel1, vvel1, lon1, lat1, u1, v1, dxdl1, ax1, ay1, axn1, ayn1
-real :: uvel2, vvel2, lon2, lat2, u2, v2, dxdl2, ax2, ay2, axn2, ayn2
-real :: uvel3, vvel3, lon3, lat3, u3, v3, dxdl3, ax3, ay3, axn3, ayn3
-real :: uvel4, vvel4, lon4, lat4, u4, v4, dxdl4, ax4, ay4, axn4, ayn4
-real :: x1, xdot1, xddot1, y1, ydot1, yddot1, xddot1n, yddot1n
-real :: x2, xdot2, xddot2, y2, ydot2, yddot2, xddot2n, yddot2n
-real :: x3, xdot3, xddot3, y3, ydot3, yddot3, xddot3n, yddot3n
-real :: x4, xdot4, xddot4, y4, ydot4, yddot4, xddot4n, yddot4n
-real :: xn, xdotn, xddotn, yn, ydotn, yddotn, xddotnn, yddotnn
-real :: dt, dt_2, dt_6, dydl
-integer :: i1,j1,i2,j2,i3,j3,i4,j4
-integer :: stderrunit
-logical :: bounced, on_tangential_plane, error_flag
+!> Calculate explicit and implicit accelerations, new velocity, and new position, using the fourth order Runge-Kutta  method
+subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, lonn, latn, i, j, xi, yj)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  type(iceberg), pointer, intent(inout) :: berg !< Iceberg
+  real, intent(out) :: axn !< Explicit zonal acceleration (m/s2)
+  real, intent(out) :: ayn !< Explicit meridional acceleration (m/s2)
+  real, intent(out) :: bxn !< Implicit zonal acceleration (m/s2)
+  real, intent(out) :: byn !< Implicit meridional acceleration (m/s2)
+  real, intent(out) :: uveln !< New zonal velocity (m/s)
+  real, intent(out) :: vveln !< New meridional velocity (m/s)
+  real, intent(out) :: lonn !< New longitude (degree E)
+  real, intent(out) :: latn !< New latitude (degree N)
+  integer, intent(out) :: i !< New i-index of containing cell
+  integer, intent(out) :: j !< New i-index of containing cell
+  real, intent(out) :: xi !< New non-dimensional x-position
+  real, intent(out) :: yj !< New non-dimensional y-position
+  ! Local variables
+  type(icebergs_gridded), pointer :: grd
+  real :: uvel1, vvel1, lon1, lat1, u1, v1, dxdl1, ax1, ay1, axn1, ayn1
+  real :: uvel2, vvel2, lon2, lat2, u2, v2, dxdl2, ax2, ay2, axn2, ayn2
+  real :: uvel3, vvel3, lon3, lat3, u3, v3, dxdl3, ax3, ay3, axn3, ayn3
+  real :: uvel4, vvel4, lon4, lat4, u4, v4, dxdl4, ax4, ay4, axn4, ayn4
+  real :: x1, xdot1, xddot1, y1, ydot1, yddot1, xddot1n, yddot1n
+  real :: x2, xdot2, xddot2, y2, ydot2, yddot2, xddot2n, yddot2n
+  real :: x3, xdot3, xddot3, y3, ydot3, yddot3, xddot3n, yddot3n
+  real :: x4, xdot4, xddot4, y4, ydot4, yddot4, xddot4n, yddot4n
+  real :: xn, xdotn, xddotn, yn, ydotn, yddotn, xddotnn, yddotnn
+  real :: dt, dt_2, dt_6, dydl
+  integer :: i1,j1,i2,j2,i3,j3,i4,j4
+  integer :: stderrunit
+  logical :: bounced, on_tangential_plane, error_flag
   ! 4th order Runge-Kutta to solve:
   !    d/dt X = V,  d/dt V = A
   ! with I.C.'s:
@@ -4648,25 +4665,26 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln,lo
   endif
 end subroutine Runge_Kutta_stepping
 
-!#######################################################################
-!MP6
-subroutine update_verlet_position(bergs,berg)
-type(icebergs), intent(in), pointer :: bergs
-type(iceberg), intent(in), pointer :: berg
-type(icebergs_gridded), pointer :: grd
-!Local variable
-real :: lonn, latn
-real :: xi, yj
-real :: uvel3, vvel3
-real :: lon1, lat1, dxdl1, dydl
-real :: uvel1, vvel1, uvel2, vvel2
-real :: axn, ayn, bxn, byn
-real :: xdot2, ydot2
-real :: u2, v2, x1, y1, xn, yn
-real :: dx, dt, dt_2
-integer :: i, j
-logical :: on_tangential_plane, error_flag, bounced
-integer :: stderrunit
+!> Updates a bergs position using the Verlet algorithm
+!!
+!! \todo The intent(in) are not consistent with usage, or are not even needed.
+subroutine update_verlet_position(bergs, berg)
+  type(icebergs), intent(in), pointer :: bergs !< Container for all types and memory
+  type(iceberg), intent(in), pointer :: berg !< Iceberg
+  !Local variable
+  type(icebergs_gridded), pointer :: grd
+  real :: lonn, latn
+  real :: xi, yj
+  real :: uvel3, vvel3
+  real :: lon1, lat1, dxdl1, dydl
+  real :: uvel1, vvel1, uvel2, vvel2
+  real :: axn, ayn, bxn, byn
+  real :: xdot2, ydot2
+  real :: u2, v2, x1, y1, xn, yn
+  real :: dx, dt, dt_2
+  integer :: i, j
+  logical :: on_tangential_plane, error_flag, bounced
+  integer :: stderrunit
 
   ! Get the stderr unit number
   stderrunit = stderr()
@@ -4732,12 +4750,13 @@ subroutine update_verlet_position(bergs,berg)
 
 end subroutine update_verlet_position
 
-!#######################################################################
-
+!> Calculate longitude-latitude from tangent plane coordinates
 subroutine rotpos_from_tang(x, y, lon, lat)
   ! Arguments
-  real, intent(in) :: x, y
-  real, intent(out) :: lon, lat
+  real, intent(in) :: x !< x-coordinate in tangent plane
+  real, intent(in) :: y !< y-coordinate in tangent plane
+  real, intent(out) :: lon !< Longitude (degree E)
+  real, intent(out) :: lat !< Latitude (degree N)
   ! Local variables
   real :: r
 
@@ -4747,10 +4766,14 @@ subroutine rotpos_from_tang(x, y, lon, lat)
 
 end subroutine rotpos_from_tang
 
+!> Calculates tangent plane velocity from velocity in velocity oriented in geographic coordinates
 subroutine rotvec_to_tang(lon, uvel, vvel, xdot, ydot)
   ! Arguments
-  real, intent(in) :: lon, uvel, vvel
-  real, intent(out) :: xdot, ydot
+  real, intent(in) :: lon !< Longitude (degree E)
+  real, intent(in) :: uvel !< Zonal velocity (m/s)
+  real, intent(in) :: vvel !< Meridional velocity (m/s)
+  real, intent(out) :: xdot !< x-component of velocity in tangent plane (m/s)
+  real, intent(out) :: ydot !< y-component of velocity in tangent plane (m/s)
   ! Local variables
   real :: clon,slon
 
@@ -4761,10 +4784,14 @@ subroutine rotvec_to_tang(lon, uvel, vvel, xdot, ydot)
 
 end subroutine rotvec_to_tang
 
+!> Calculate velocity oriented in geographic coordinates from tangent plane velocity
 subroutine rotvec_from_tang(lon, xdot, ydot, uvel, vvel)
   ! Arguments
-  real, intent(in) :: lon, xdot, ydot
-  real, intent(out) :: uvel, vvel
+  real, intent(in) :: lon !< Longitude (degree E)
+  real, intent(in) :: xdot !< x-component of velocity in tangent plane (m/s)
+  real, intent(in) :: ydot !< y-component of velocity in tangent plane (m/s)
+  real, intent(out) :: uvel !< Zonal velocity (m/s)
+  real, intent(out) :: vvel !< Meridional velocity (m/s)
   ! Local variables
   real :: clon,slon
 
@@ -4775,22 +4802,28 @@ subroutine rotvec_from_tang(lon, xdot, ydot, uvel, vvel)
 
 end subroutine rotvec_from_tang
 
-! ##############################################################################
-
+!> Moves berg's cell indexes,(i,j), checking for collisional with coasts
 subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, bounced, error, iceberg_num)
-! Arguments
-type(icebergs_gridded), pointer :: grd !< Container for gridded fields
-real, intent(inout) :: lon, lat, uvel, vvel, xi, yj
-integer, intent(inout) :: i,j
-integer, intent(in) :: iceberg_num
-logical, intent(out) :: bounced, error
-! Local variables
-logical lret, lpos
-real, parameter :: posn_eps=0.05
-integer :: icount, i0, j0, inm, jnm
-real :: xi0, yj0, lon0, lat0
-integer :: stderrunit
-logical :: point_in_cell_using_xi_yj
+  ! Arguments
+  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+  real, intent(inout) :: lon !< Longitude (degree E)
+  real, intent(inout) :: lat !< Latitude (degree N)
+  real, intent(inout) :: uvel !< Zonal velocity (m/s)
+  real, intent(inout) :: vvel !< Meridional velocity (m/s)
+  real, intent(inout) :: xi !< Non-dimension x-position within cell
+  real, intent(inout) :: yj !< Non-dimension y-position within cell
+  integer, intent(inout) :: i !< i-index of cell
+  integer, intent(inout) :: j !< j-index of cell
+  logical, intent(out) :: bounced !< True if berg collided with coast
+  logical, intent(out) :: error !< True if adjustments could not be made consistently
+  integer, intent(in) :: iceberg_num !< Berg identifier
+  ! Local variables
+  logical lret, lpos
+  real, parameter :: posn_eps=0.05
+  integer :: icount, i0, j0, inm, jnm
+  real :: xi0, yj0, lon0, lat0
+  integer :: stderrunit
+  logical :: point_in_cell_using_xi_yj
 
   ! Get the stderr unit number
   stderrunit = stderr()
@@ -5016,15 +5049,14 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
   endif
  end subroutine adjust_index_and_ground
 
-!end subroutine evolve_icebergs
-
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
+!> Calculate longitude-latitude from tangent plane coordinates
 subroutine rotpos_to_tang(lon, lat, x, y, iceberg_num_in)
   ! Arguments
-  real, intent(in) :: lon, lat
-  real, intent(out) :: x, y
-  integer, intent(in) , optional :: iceberg_num_in
+  real, intent(in) :: lon !< Longitude (degree E)
+  real, intent(in) :: lat !< Latitude (degree N)
+  real, intent(out) :: x !< x-coordinate in tangent plane
+  real, intent(out) :: y !< y-coordinate in tangent plane
+  integer, intent(in), optional :: iceberg_num_in !< Berg identifier
   ! Local variables
   real :: r,colat,clon,slon
   integer :: stderrunit, iceberg_num
@@ -5053,18 +5085,17 @@ subroutine rotpos_to_tang(lon, lat, x, y, iceberg_num_in)
 
 end subroutine rotpos_to_tang
 
-! ##############################################################################
-
+!> Calculate stocks of water and heat
 subroutine icebergs_stock_pe(bergs, index, value)
-! Modules
-use stock_constants_mod, only : ISTOCK_WATER, ISTOCK_HEAT
-! Arguments
-type(icebergs), pointer :: bergs !< Container for all types and memory
-integer, intent(in) :: index
-real, intent(out) :: value
-! Local variables
-type(icebergs_gridded), pointer :: grd
-real :: berg_mass, stored_mass
+  ! Modules
+  use stock_constants_mod, only : ISTOCK_WATER, ISTOCK_HEAT
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  integer, intent(in) :: index !< =ISTOCK_WATER or ISTOCK_HEAT
+  real, intent(out) :: value !< Amount of ice or water
+  ! Local variables
+  type(icebergs_gridded), pointer :: grd
+  real :: berg_mass, stored_mass
 
   ! For convenience
   grd=>bergs%grd
@@ -5088,12 +5119,11 @@ subroutine icebergs_stock_pe(bergs, index, value)
 
 end subroutine icebergs_stock_pe
 
-! ##############################################################################
-
+!> Write restart files
 subroutine icebergs_save_restart(bergs)
-! Arguments
-type(icebergs), pointer :: bergs !< Container for all types and memory
-! Local variables
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  ! Local variables
 
   if (.not.associated(bergs)) return
 
@@ -5104,13 +5134,12 @@ subroutine icebergs_save_restart(bergs)
 
 end subroutine icebergs_save_restart
 
-! ##############################################################################
-
+!> Deallocate all memory and disassociated pointer
 subroutine icebergs_end(bergs)
-! Arguments
-type(icebergs), pointer :: bergs !< Container for all types and memory
-! Local variables
-type(iceberg), pointer :: this, next
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  ! Local variables
+  type(iceberg), pointer :: this, next
 
   if (.not.associated(bergs)) return
 
@@ -5209,14 +5238,14 @@ end subroutine dealloc_buffer
 
 end subroutine icebergs_end
 
-! ##############################################################################
-
-subroutine invert_tau_for_du(u,v)
-! Arguments
-real, dimension(:,:),intent(inout) :: u, v
-! Local variables
-integer :: i, j
-real :: cd, cddvmod, tau2
+!> Approximately convert a wind-stress into a velocity difference
+subroutine invert_tau_for_du(u, v)
+  ! Arguments
+  real, dimension(:,:), intent(inout) :: u !< On entry, zonal wind stress (Pa). On exit, zonal velocity difference (m/s).
+  real, dimension(:,:), intent(inout) :: v !< On entry, meridional wind stress (Pa). On exit, meridional velocity difference (m/s).
+  ! Local variables
+  integer :: i, j
+  real :: cd, cddvmod, tau2
 
   cd=0.0015
 
@@ -5236,6 +5265,4 @@ subroutine invert_tau_for_du(u,v)
 
 end subroutine invert_tau_for_du
 
-! ##############################################################################
-
 end module
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 1b71b9a..934293e 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -461,7 +461,7 @@ subroutine ice_bergs_framework_init(bergs, &
 integer, intent(in) :: dom_x_flags !< Domain flags in i-direction
 integer, intent(in) :: dom_y_flags !< Domain flags in j-direction
 real, intent(in) :: dt !< Time-step (s)
-type (time_type), intent(in) :: Time ! Current model time
+type (time_type), intent(in) :: Time !< Current model time
 real, dimension(:,:), intent(in) :: ice_lon !< Longitude of cell corners using NE convention (degree E)
 real, dimension(:,:), intent(in) :: ice_lat !< Latitude of cell corners using NE conventino (degree N)
 real, dimension(:,:), intent(in) :: ice_wet !< Wet/dry mask (1 is wet, 0 is dry) of cell centers

From 7aece18dea33ba2702e5f9eed613804284508f53 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Tue, 28 Mar 2017 17:06:51 -0400
Subject: [PATCH 216/361] Removed local subroutines via "contains"

---
 icebergs.F90           | 1006 ++++++++++++++++++++--------------------
 icebergs_framework.F90 |  232 +++++----
 icebergs_io.F90        |  500 ++++++++++----------
 3 files changed, 859 insertions(+), 879 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index e74f4c5..035be60 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -476,204 +476,202 @@ subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
   !print *,'P_ia_11',P_ia_11,'P_ia_12',P_ia_12, 'P_ia_21',P_ia_21,'P_ia_22', P_ia_22
   !print *, 'P_ia_times_u_x', P_ia_times_u_x, 'P_ia_times_u_y', P_ia_times_u_y
 
-  contains
+end subroutine interactive_force
 
-  !> Calculate interactive forces between two bergs
-  subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1, &
-                             P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y, bonded)
-    ! Arguments
-    type(icebergs), pointer :: bergs !< Container for all types and memory
-    type(iceberg), pointer :: berg !< Primary berg
-    type(iceberg), pointer :: other_berg !< Berg that primary is interacting with
-    real, intent(inout) :: IA_x !< Net zonal acceleration of berg due to interactions (m/s2)
-    real, intent(inout) :: IA_y !< Net meridional acceleration of berg due to interactions (m/s2)
-    real, intent(in) :: u0 !< Zonal velocity of primary berg (m/s)
-    real, intent(in) :: v0 !< Meridional velocity of primary berg (m/s)
-    real, intent(in) :: u1 !< Zonal velocity of other berg (m/s)
-    real, intent(in) :: v1 !< Meridional velocity of other berg (m/s)
-    real, intent(inout) :: P_ia_11
-    real, intent(inout) :: P_ia_12
-    real, intent(inout) :: P_ia_22
-    real, intent(inout) :: P_ia_21
-    real, intent(inout) :: P_ia_times_u_x
-    real, intent(inout) :: P_ia_times_u_y
-    logical ,intent(in) :: bonded
-    ! Local variables
-    real :: T1, L1, W1, lon1, lat1, x1, y1, R1, A1 ! Current iceberg
-    real :: T2, L2, W2, lon2, lat2, x2, y2, R2, A2 ! Other iceberg
-    real :: dlon, dlat
-    real :: r_dist_x, r_dist_y, r_dist, A_o, A_min, trapped, T_min
-    real :: P_11, P_12, P_21, P_22
-    real :: M1, M2, M_min
-    real :: u2, v2
-    real :: lat_ref, dx_dlon, dy_dlat
-    logical :: critical_interaction_damping_on
-    real :: spring_coef, accel_spring, radial_damping_coef, p_ia_coef, tangental_damping_coef, bond_coef
-
-    spring_coef=bergs%spring_coef
-    !bond_coef=bergs%bond_coef
-    radial_damping_coef=bergs%radial_damping_coef
-    tangental_damping_coef=bergs%tangental_damping_coef
-    critical_interaction_damping_on=bergs%critical_interaction_damping_on
-
-    ! Using critical values for damping rather than manually setting the damping.
-    if (critical_interaction_damping_on) then
-      radial_damping_coef=2.*sqrt(spring_coef) ! Critical damping
-      tangental_damping_coef=(2.*sqrt(spring_coef))/4 ! Critical damping (just a guess)
-    endif
+!> Calculate interactive forces between two bergs
+subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1, &
+                           P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y, bonded)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  type(iceberg), pointer :: berg !< Primary berg
+  type(iceberg), pointer :: other_berg !< Berg that primary is interacting with
+  real, intent(inout) :: IA_x !< Net zonal acceleration of berg due to interactions (m/s2)
+  real, intent(inout) :: IA_y !< Net meridional acceleration of berg due to interactions (m/s2)
+  real, intent(in) :: u0 !< Zonal velocity of primary berg (m/s)
+  real, intent(in) :: v0 !< Meridional velocity of primary berg (m/s)
+  real, intent(in) :: u1 !< Zonal velocity of other berg (m/s)
+  real, intent(in) :: v1 !< Meridional velocity of other berg (m/s)
+  real, intent(inout) :: P_ia_11
+  real, intent(inout) :: P_ia_12
+  real, intent(inout) :: P_ia_22
+  real, intent(inout) :: P_ia_21
+  real, intent(inout) :: P_ia_times_u_x
+  real, intent(inout) :: P_ia_times_u_y
+  logical ,intent(in) :: bonded
+  ! Local variables
+  real :: T1, L1, W1, lon1, lat1, x1, y1, R1, A1 ! Current iceberg
+  real :: T2, L2, W2, lon2, lat2, x2, y2, R2, A2 ! Other iceberg
+  real :: dlon, dlat
+  real :: r_dist_x, r_dist_y, r_dist, A_o, A_min, trapped, T_min
+  real :: P_11, P_12, P_21, P_22
+  real :: M1, M2, M_min
+  real :: u2, v2
+  real :: lat_ref, dx_dlon, dy_dlat
+  logical :: critical_interaction_damping_on
+  real :: spring_coef, accel_spring, radial_damping_coef, p_ia_coef, tangental_damping_coef, bond_coef
+
+  spring_coef=bergs%spring_coef
+  !bond_coef=bergs%bond_coef
+  radial_damping_coef=bergs%radial_damping_coef
+  tangental_damping_coef=bergs%tangental_damping_coef
+  critical_interaction_damping_on=bergs%critical_interaction_damping_on
+
+  ! Using critical values for damping rather than manually setting the damping.
+  if (critical_interaction_damping_on) then
+    radial_damping_coef=2.*sqrt(spring_coef) ! Critical damping
+    tangental_damping_coef=(2.*sqrt(spring_coef))/4 ! Critical damping (just a guess)
+  endif
 
-    if (berg%iceberg_num .ne. other_berg%iceberg_num) then
-      ! From Berg 1
-      L1=berg%length
-      W1=berg%width
-      T1=berg%thickness
-      M1=berg%mass
-      A1=L1*W1
-      lon1=berg%lon_old; lat1=berg%lat_old
-      !call rotpos_to_tang(lon1,lat1,x1,y1)
-
-      ! From Berg 1
-      L2=other_berg%length
-      W2=other_berg%width
-      T2=other_berg%thickness
-      M2=other_berg%mass
-      u2=other_berg%uvel_old !Old values are used to make it order invariant
-      v2=other_berg%vvel_old !Old values are used to make it order invariant
-      A2=L2*W2
-      lon2=other_berg%lon_old; lat2=other_berg%lat_old !Old values are used to make it order invariant
-
-      !call rotpos_to_tang(lon2,lat2,x2,y2)
-
-      dlon=lon1-lon2
-      dlat=lat1-lat2
-
-      ! Note that this is not the exact distance along a great circle.
-      ! Approximation for small distances. Should be fine.
-      !r_dist_x=x1-x2 ; r_dist_y=y1-y2
-      !r_dist=sqrt( ((x1-x2)**2) + ((y1-y2)**2) )
-      lat_ref=0.5*(lat1+lat2)
-      call convert_from_grid_to_meters(lat_ref,bergs%grd%grid_is_latlon,dx_dlon,dy_dlat)
-
-      r_dist_x=dlon*dx_dlon
-      r_dist_y=dlat*dy_dlat
-      r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) )
-
-      if (bergs%hexagonal_icebergs) then
-        R1=sqrt(A1/(2.*sqrt(3.)))
-        R2=sqrt(A2/(2.*sqrt(3.)))
-      else !square packing
-        R1=sqrt(A1/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
-        R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
-      endif
-      !!!!!!!!!!!!!!!!!!!!!!!!!!!debugging!!!!!!!!!!!!!!!!!!!!!!!!!!MP1
-      ! if (berg%iceberg_num .eq. 1) then
-      !   print *, 'Comparing longitudes: ', lon1, lon2, r_dist_x, dlon
-      !   print *, 'Comparing latitudes: ', lat1, lat2, r_dist_y, dlat
-      !   print *, 'Outside, iceberg_num, r_dist', berg%iceberg_num, r_dist,bonded
-      !   print *, 'Halo_status', berg%halo_berg,other_berg%halo_berg
-      ! endif
-      ! print *, 'outside the loop',R1, R2,r_dist, bonded
-      !!!!!!!!!!!!!!!!!!!!!!!!!!!debugging!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-
-      !call overlap_area(R1,R2,r_dist,A_o,trapped)
-      !T_min=min(T1,T2)
-      !A_min = min((pi*R1**R1),(pi*R2*R2))
-      M_min=min(M1,M2)
-      !Calculating spring force  (later this should only be done on the first time around)
-      if ((r_dist>0.) .AND. ((r_dist< (R1+R2).AND. (.not. bonded)) .OR. ( (r_dist> (R1+R2)) .AND. (bonded) ) )) then
-        ! Spring force
-        !accel_spring=spring_coef*(T_min/T1)*(A_o/A1) ! Old version dependent on area
-        accel_spring=spring_coef*(M_min/M1)*(R1+R2-r_dist)
-        IA_x=IA_x+(accel_spring*(r_dist_x/r_dist))
-        IA_y=IA_y+(accel_spring*(r_dist_y/r_dist))
-
-
-        if (r_dist < 5*(R1+R2)) then
-
-          !MP1
-          !if (berg%iceberg_num .eq. 1) then
-          !  !print *,  '************************************************************'
-          !  print *, 'INSIDE, r_dist', berg%iceberg_num, other_berg%iceberg_num, r_dist, bonded
-          !endif
-          !print *, 'in the loop1', spring_coef, (M_min/M1), accel_spring,(R1+R2-r_dist)
-          !print *, 'in the loop2', IA_x, IA_y, R1, R2,r_dist, berg%iceberg_num,other_berg%iceberg_num
-          ! Damping force:
-          ! Paralel velocity
-          P_11=(r_dist_x*r_dist_x)/(r_dist**2)
-          P_12=(r_dist_x*r_dist_y)/(r_dist**2)
-          P_21=(r_dist_x*r_dist_y)/(r_dist**2)
-          P_22=(r_dist_y*r_dist_y)/(r_dist**2)
-          !p_ia_coef=radial_damping_coef*(T_min/T1)*(A_min/A1)
-          p_ia_coef=radial_damping_coef*(M_min/M1)
-          p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2)) &
-          + sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
-
-          P_ia_11=P_ia_11+p_ia_coef*P_11
-          P_ia_12=P_ia_12+p_ia_coef*P_12
-          P_ia_21=P_ia_21+p_ia_coef*P_21
-          P_ia_22=P_ia_22+p_ia_coef*P_22
-          P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
-          P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
-          !print *, 'Paralel: ',berg%iceberg_num,  p_ia_coef, IA_x, P_ia_11, P_ia_21,P_ia_12, P_ia_22
-
-          ! Normal velocities
-          P_11=1-P_11  ;  P_12=-P_12 ; P_21= -P_21 ;    P_22=1-P_22
-          !p_ia_coef=tangental_damping_coef*(T_min/T1)*(A_min/A1)
-          p_ia_coef=tangental_damping_coef*(M_min/M1)
-          p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2))  &
-          + sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
-          P_ia_11=P_ia_11+p_ia_coef*P_11
-          P_ia_12=P_ia_12+p_ia_coef*P_12
-          P_ia_21=P_ia_21+p_ia_coef*P_21
-          P_ia_22=P_ia_22+p_ia_coef*P_22
-          P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
-          P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
-          !print *, 'Perp: ',berg%iceberg_num,  p_ia_coef, IA_x, P_ia_11, P_ia_21,P_ia_12, P_ia_22
-          !print *, 'P_11',P_11
-          !print *, 'P_21',P_21
-          !print *, 'P_12',P_12
-          !print *, 'P_22',P_22
-        endif
+  if (berg%iceberg_num .ne. other_berg%iceberg_num) then
+    ! From Berg 1
+    L1=berg%length
+    W1=berg%width
+    T1=berg%thickness
+    M1=berg%mass
+    A1=L1*W1
+    lon1=berg%lon_old; lat1=berg%lat_old
+    !call rotpos_to_tang(lon1,lat1,x1,y1)
+
+    ! From Berg 1
+    L2=other_berg%length
+    W2=other_berg%width
+    T2=other_berg%thickness
+    M2=other_berg%mass
+    u2=other_berg%uvel_old !Old values are used to make it order invariant
+    v2=other_berg%vvel_old !Old values are used to make it order invariant
+    A2=L2*W2
+    lon2=other_berg%lon_old; lat2=other_berg%lat_old !Old values are used to make it order invariant
+
+    !call rotpos_to_tang(lon2,lat2,x2,y2)
+
+    dlon=lon1-lon2
+    dlat=lat1-lat2
+
+    ! Note that this is not the exact distance along a great circle.
+    ! Approximation for small distances. Should be fine.
+    !r_dist_x=x1-x2 ; r_dist_y=y1-y2
+    !r_dist=sqrt( ((x1-x2)**2) + ((y1-y2)**2) )
+    lat_ref=0.5*(lat1+lat2)
+    call convert_from_grid_to_meters(lat_ref,bergs%grd%grid_is_latlon,dx_dlon,dy_dlat)
+
+    r_dist_x=dlon*dx_dlon
+    r_dist_y=dlat*dy_dlat
+    r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) )
+
+    if (bergs%hexagonal_icebergs) then
+      R1=sqrt(A1/(2.*sqrt(3.)))
+      R2=sqrt(A2/(2.*sqrt(3.)))
+    else !square packing
+      R1=sqrt(A1/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
+      R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
+    endif
+    !!!!!!!!!!!!!!!!!!!!!!!!!!!debugging!!!!!!!!!!!!!!!!!!!!!!!!!!MP1
+    ! if (berg%iceberg_num .eq. 1) then
+    !   print *, 'Comparing longitudes: ', lon1, lon2, r_dist_x, dlon
+    !   print *, 'Comparing latitudes: ', lat1, lat2, r_dist_y, dlat
+    !   print *, 'Outside, iceberg_num, r_dist', berg%iceberg_num, r_dist,bonded
+    !   print *, 'Halo_status', berg%halo_berg,other_berg%halo_berg
+    ! endif
+    ! print *, 'outside the loop',R1, R2,r_dist, bonded
+    !!!!!!!!!!!!!!!!!!!!!!!!!!!debugging!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+
+    !call overlap_area(R1,R2,r_dist,A_o,trapped)
+    !T_min=min(T1,T2)
+    !A_min = min((pi*R1**R1),(pi*R2*R2))
+    M_min=min(M1,M2)
+    !Calculating spring force  (later this should only be done on the first time around)
+    if ((r_dist>0.) .AND. ((r_dist< (R1+R2).AND. (.not. bonded)) .OR. ( (r_dist> (R1+R2)) .AND. (bonded) ) )) then
+      ! Spring force
+      !accel_spring=spring_coef*(T_min/T1)*(A_o/A1) ! Old version dependent on area
+      accel_spring=spring_coef*(M_min/M1)*(R1+R2-r_dist)
+      IA_x=IA_x+(accel_spring*(r_dist_x/r_dist))
+      IA_y=IA_y+(accel_spring*(r_dist_y/r_dist))
+
+
+      if (r_dist < 5*(R1+R2)) then
+
+        !MP1
+        !if (berg%iceberg_num .eq. 1) then
+        !  !print *,  '************************************************************'
+        !  print *, 'INSIDE, r_dist', berg%iceberg_num, other_berg%iceberg_num, r_dist, bonded
+        !endif
+        !print *, 'in the loop1', spring_coef, (M_min/M1), accel_spring,(R1+R2-r_dist)
+        !print *, 'in the loop2', IA_x, IA_y, R1, R2,r_dist, berg%iceberg_num,other_berg%iceberg_num
+        ! Damping force:
+        ! Paralel velocity
+        P_11=(r_dist_x*r_dist_x)/(r_dist**2)
+        P_12=(r_dist_x*r_dist_y)/(r_dist**2)
+        P_21=(r_dist_x*r_dist_y)/(r_dist**2)
+        P_22=(r_dist_y*r_dist_y)/(r_dist**2)
+        !p_ia_coef=radial_damping_coef*(T_min/T1)*(A_min/A1)
+        p_ia_coef=radial_damping_coef*(M_min/M1)
+        p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2)) &
+        + sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
+
+        P_ia_11=P_ia_11+p_ia_coef*P_11
+        P_ia_12=P_ia_12+p_ia_coef*P_12
+        P_ia_21=P_ia_21+p_ia_coef*P_21
+        P_ia_22=P_ia_22+p_ia_coef*P_22
+        P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
+        P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
+        !print *, 'Paralel: ',berg%iceberg_num,  p_ia_coef, IA_x, P_ia_11, P_ia_21,P_ia_12, P_ia_22
+
+        ! Normal velocities
+        P_11=1-P_11  ;  P_12=-P_12 ; P_21= -P_21 ;    P_22=1-P_22
+        !p_ia_coef=tangental_damping_coef*(T_min/T1)*(A_min/A1)
+        p_ia_coef=tangental_damping_coef*(M_min/M1)
+        p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2))  &
+        + sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
+        P_ia_11=P_ia_11+p_ia_coef*P_11
+        P_ia_12=P_ia_12+p_ia_coef*P_12
+        P_ia_21=P_ia_21+p_ia_coef*P_21
+        P_ia_22=P_ia_22+p_ia_coef*P_22
+        P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
+        P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
+        !print *, 'Perp: ',berg%iceberg_num,  p_ia_coef, IA_x, P_ia_11, P_ia_21,P_ia_12, P_ia_22
+        !print *, 'P_11',P_11
+        !print *, 'P_21',P_21
+        !print *, 'P_12',P_12
+        !print *, 'P_22',P_22
       endif
     endif
+  endif
 
-  end subroutine calculate_force
+end subroutine calculate_force
 
-  !> Calculates area of overlap between two circular bergs
-  subroutine overlap_area(R1, R2, d, A, trapped)
-    ! Arguments
-    real, intent(in) :: R1 !< Radius of berg 1 (m)
-    real, intent(in) :: R2 !< Radius of berg 2 (m)
-    real, intent(in) :: d !< Separation of berg centers (m)
-    real, intent(out) :: A !< Overlap area (m2)
-    real, intent(out) :: Trapped !< =1. if one berg is completely inside the other, =0. otherwise
-    ! Local variables
-    real :: R1_sq, R2_sq, d_sq
-
-    R1_sq=R1**2
-    R2_sq=R2**2
-    d_sq=d**2
-    Trapped=0.
-
-    if (d>0.) then
-      if (d<(R1+R2)) then
-        if (d>abs(R1-R2)) then
-          A=(R1_sq*acos((d_sq+R1_sq-R2_sq)/(2.*d*R1))) + (R2_sq*acos((d_sq+R2_sq-R1_sq)/(2.*d*R2))) - (0.5*sqrt((-d+R1+R2)*(d+R1-R2)*(d-R1+R2)*(d+R1+R2)))
-        else
-          A=min(pi*R1_sq,pi*R2_sq)
-          Trapped=1.
-        endif
+!> Calculates area of overlap between two circular bergs
+subroutine overlap_area(R1, R2, d, A, trapped)
+  ! Arguments
+  real, intent(in) :: R1 !< Radius of berg 1 (m)
+  real, intent(in) :: R2 !< Radius of berg 2 (m)
+  real, intent(in) :: d !< Separation of berg centers (m)
+  real, intent(out) :: A !< Overlap area (m2)
+  real, intent(out) :: Trapped !< =1. if one berg is completely inside the other, =0. otherwise
+  ! Local variables
+  real :: R1_sq, R2_sq, d_sq
+
+  R1_sq=R1**2
+  R2_sq=R2**2
+  d_sq=d**2
+  Trapped=0.
+
+  if (d>0.) then
+    if (d<(R1+R2)) then
+      if (d>abs(R1-R2)) then
+        A=(R1_sq*acos((d_sq+R1_sq-R2_sq)/(2.*d*R1))) + (R2_sq*acos((d_sq+R2_sq-R1_sq)/(2.*d*R2))) - (0.5*sqrt((-d+R1+R2)*(d+R1-R2)*(d-R1+R2)*(d+R1+R2)))
       else
-        A=0.
+        A=min(pi*R1_sq,pi*R2_sq)
+        Trapped=1.
       endif
     else
-      A=0. ! No area of perfectly overlapping bergs (ie: a berg interacting with itself)
+      A=0.
     endif
+  else
+    A=0. ! No area of perfectly overlapping bergs (ie: a berg interacting with itself)
+  endif
 
-   end subroutine overlap_area
-
-end subroutine interactive_force
+end subroutine overlap_area
 
 !> Calculates the instantaneous acceleration of an iceberg
 subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, axn, ayn, bxn, byn, debug_flag)
@@ -1103,61 +1101,63 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
     bxn = 0.0;  byn = 0.0
   endif
 
-  contains
+end subroutine accel
 
-  !> Print 3x3 cells from 2d array A
-  subroutine dump_locfld(grd, i0, j0, A, lbl)
-    ! Arguments
-    type(icebergs_gridded), pointer :: grd !< Container for gridded fields
-    integer, intent(in) :: i0 !< i-index of center of 3x3 patch to print
-    integer, intent(in) :: j0 !< j-index of center of 3x3 patch to print
-    real, dimension(grd%isd:grd%ied,grd%jsd:grd%jed), intent(in) :: A !< Field to print
-    character(len=*) :: lbl !< Label to add to messages
-    ! Local variables
-    integer :: i, j, ii, jj
-    real :: B(-1:1,-1:1), fac
-
-    do jj=-1,1
-      j=max(grd%jsd,min(grd%jed,jj+j0))
-      do ii=-1,1
-        i=max(grd%isd,min(grd%ied,ii+i0))
-        B(ii,jj)=A(i,j)
-        if ((i.ne.ii+i0).or.(j.ne.jj+j0)) B(ii,jj)=-9.999999e-99
-      enddo
-    enddo
-    write(stderrunit,'("pe=",i3,x,a8,3i12)') mpp_pe(),lbl,(i0+ii,ii=-1,1)
-    do jj=1,-1,-1
-      write(stderrunit,'("pe=",i3,x,i8,3es12.4)') mpp_pe(),j0+jj,(B(ii,jj),ii=-1,1)
-    enddo
-  end subroutine dump_locfld
+!> Print 3x3 cells from 2d array A
+subroutine dump_locfld(grd, i0, j0, A, lbl)
+  ! Arguments
+  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+  integer, intent(in) :: i0 !< i-index of center of 3x3 patch to print
+  integer, intent(in) :: j0 !< j-index of center of 3x3 patch to print
+  real, dimension(grd%isd:grd%ied,grd%jsd:grd%jed), intent(in) :: A !< Field to print
+  character(len=*) :: lbl !< Label to add to messages
+  ! Local variables
+  integer :: i, j, ii, jj
+  real :: B(-1:1,-1:1), fac
+  integer :: stderrunit
+  stderrunit = stderr()
 
-  !> Print 2x2 cells from 2d array A
-  subroutine dump_locvel(grd, i0, j0, A, lbl)
-    ! Arguments
-    type(icebergs_gridded), pointer :: grd !< Container for gridded fields
-    integer, intent(in) :: i0 !< i-index of NE-cell of 2x2 patch to print
-    integer, intent(in) :: j0 !< j-index of NE-cell of 2x2 patch to print
-    real, dimension(grd%isd:grd%ied,grd%jsd:grd%jed), intent(in) :: A !< Field to print
-    character(len=*) :: lbl !< Label to add to messages
-    ! Local variables
-    integer :: i, j, ii, jj
-    real :: B(-1:0,-1:0), fac
-
-    do jj=-1,0
-      j=max(grd%jsd,min(grd%jed,jj+j0))
-      do ii=-1,0
-        i=max(grd%isd,min(grd%ied,ii+i0))
-        B(ii,jj)=A(i,j)
-        if ((i.ne.ii+i0).or.(j.ne.jj+j0)) B(ii,jj)=-9.999999e-99
-      enddo
+  do jj=-1,1
+    j=max(grd%jsd,min(grd%jed,jj+j0))
+    do ii=-1,1
+      i=max(grd%isd,min(grd%ied,ii+i0))
+      B(ii,jj)=A(i,j)
+      if ((i.ne.ii+i0).or.(j.ne.jj+j0)) B(ii,jj)=-9.999999e-99
     enddo
-    write(stderrunit,'("pe=",i3,x,a8,3i12)') mpp_pe(),lbl,(i0+ii,ii=-1,0)
-    do jj=0,-1,-1
-      write(stderrunit,'("pe=",i3,x,i8,3es12.4)') mpp_pe(),j0+jj,(B(ii,jj),ii=-1,0)
-    enddo
-  end subroutine dump_locvel
+  enddo
+  write(stderrunit,'("pe=",i3,x,a8,3i12)') mpp_pe(),lbl,(i0+ii,ii=-1,1)
+  do jj=1,-1,-1
+    write(stderrunit,'("pe=",i3,x,i8,3es12.4)') mpp_pe(),j0+jj,(B(ii,jj),ii=-1,1)
+  enddo
+end subroutine dump_locfld
 
-end subroutine accel
+!> Print 2x2 cells from 2d array A
+subroutine dump_locvel(grd, i0, j0, A, lbl)
+  ! Arguments
+  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+  integer, intent(in) :: i0 !< i-index of NE-cell of 2x2 patch to print
+  integer, intent(in) :: j0 !< j-index of NE-cell of 2x2 patch to print
+  real, dimension(grd%isd:grd%ied,grd%jsd:grd%jed), intent(in) :: A !< Field to print
+  character(len=*) :: lbl !< Label to add to messages
+  ! Local variables
+  integer :: i, j, ii, jj
+  real :: B(-1:0,-1:0), fac
+  integer :: stderrunit
+  stderrunit = stderr()
+
+  do jj=-1,0
+    j=max(grd%jsd,min(grd%jed,jj+j0))
+    do ii=-1,0
+      i=max(grd%isd,min(grd%ied,ii+i0))
+      B(ii,jj)=A(i,j)
+      if ((i.ne.ii+i0).or.(j.ne.jj+j0)) B(ii,jj)=-9.999999e-99
+    enddo
+  enddo
+  write(stderrunit,'("pe=",i3,x,a8,3i12)') mpp_pe(),lbl,(i0+ii,ii=-1,0)
+  do jj=0,-1,-1
+    write(stderrunit,'("pe=",i3,x,i8,3es12.4)') mpp_pe(),j0+jj,(B(ii,jj),ii=-1,0)
+  enddo
+end subroutine dump_locvel
 
 !> Steps forward thermodynamic state of all bergs
 subroutine thermodynamics(bergs)
@@ -1842,51 +1842,49 @@ subroutine find_basal_melt(bergs, dvo, lat, salt, temp, Use_three_equation_model
   ! melt in m/s (melts of ice melted per second)
   basal_melt = lprec /density_ice
 
-contains
-
-  !> Calculates freezing point potential temperature of seawater using a linear relation
-  !!
-  !! This subroutine computes the freezing point potential temperature
-  !! (in deg C) from salinity (in psu), and pressure (in Pa) using a simple
-  !! linear expression, with coefficients passed in as arguments.
-  !!
-  !! Copied from subroutine calculate_TFreeze_linear_scalar (in MOM/equation_of_state)
-  subroutine calculate_TFreeze(S, pres, T_Fr)
-    ! Arguments
-    real, intent(in) :: S !< Salinity (1e-3)
-    real, intent(in) :: pres !< Presure (Pa)
-    real, intent(out) :: T_Fr !< Freezing point (C)
-    ! Local variables
-    real, parameter :: dTFr_dp    = -7.53E-08    !DTFREEZE_DP in MOM_input
-    real, parameter :: dTFr_dS    = -0.0573      !DTFREEZE_DS in MOM_input
-    real, parameter :: TFr_S0_P0  =0.0832        !TFREEZE_S0_P0 in MOM_input
-    ! TFr_S0_P0 - The freezing point at S=0, p=0, in deg C.
-    ! dTFr_dS - The derivatives of freezing point with salinity, in deg C PSU-1.
-    ! dTFr_dp - The derivatives of freezing point with pressure, in deg C Pa-1.
-    T_Fr = (TFr_S0_P0 + dTFr_dS*S) + dTFr_dp*pres
-  end subroutine calculate_TFreeze
-
-  !> Calculates density of seawater using a linear equation of state
-  !!
-  !! This subroutine computes the density of sea water with a trivial
-  !! linear equation of state (in kg/m^3) from salinity (sal in psu),
-  !! potential temperature (T in deg C), and pressure in Pa.
-  !!
-  !! Copied from subroutine calculate_density_scalar_linear (in MOM/equation_of_state)
-  subroutine calculate_density(T, S, pressure, rho, Rho_T0_S0, dRho_dT, dRho_dS)
-    !Arguments
-    real, intent(in)  :: T !< Potential temperature (C)
-    real, intent(in)  :: S !< Salinity (1e-3)
-    real, intent(in)  :: pressure !< Pressure (Pa)
-    real, intent(out) :: rho !< In situ density (kg/3)
-    real, intent(in)  :: Rho_T0_S0 !< Density at T=0, S=0 (kg/m3)
-    real, intent(in)  :: dRho_dT !< Derivative of density w.r.t. potential temperature (kg/m3/C)
-    real, intent(in)  :: dRho_dS !< Derivative of density w.r.t. salinity (1e3 kg/m3)
-    rho = Rho_T0_S0 + dRho_dT*T + dRho_dS*S
-  end subroutine calculate_density
-
 end subroutine find_basal_melt
 
+!> Calculates freezing point potential temperature of seawater using a linear relation
+!!
+!! This subroutine computes the freezing point potential temperature
+!! (in deg C) from salinity (in psu), and pressure (in Pa) using a simple
+!! linear expression, with coefficients passed in as arguments.
+!!
+!! Copied from subroutine calculate_TFreeze_linear_scalar (in MOM/equation_of_state)
+subroutine calculate_TFreeze(S, pres, T_Fr)
+  ! Arguments
+  real, intent(in) :: S !< Salinity (1e-3)
+  real, intent(in) :: pres !< Presure (Pa)
+  real, intent(out) :: T_Fr !< Freezing point (C)
+  ! Local variables
+  real, parameter :: dTFr_dp    = -7.53E-08    !DTFREEZE_DP in MOM_input
+  real, parameter :: dTFr_dS    = -0.0573      !DTFREEZE_DS in MOM_input
+  real, parameter :: TFr_S0_P0  =0.0832        !TFREEZE_S0_P0 in MOM_input
+  ! TFr_S0_P0 - The freezing point at S=0, p=0, in deg C.
+  ! dTFr_dS - The derivatives of freezing point with salinity, in deg C PSU-1.
+  ! dTFr_dp - The derivatives of freezing point with pressure, in deg C Pa-1.
+  T_Fr = (TFr_S0_P0 + dTFr_dS*S) + dTFr_dp*pres
+end subroutine calculate_TFreeze
+
+!> Calculates density of seawater using a linear equation of state
+!!
+!! This subroutine computes the density of sea water with a trivial
+!! linear equation of state (in kg/m^3) from salinity (sal in psu),
+!! potential temperature (T in deg C), and pressure in Pa.
+!!
+!! Copied from subroutine calculate_density_scalar_linear (in MOM/equation_of_state)
+subroutine calculate_density(T, S, pressure, rho, Rho_T0_S0, dRho_dT, dRho_dS)
+  !Arguments
+  real, intent(in)  :: T !< Potential temperature (C)
+  real, intent(in)  :: S !< Salinity (1e-3)
+  real, intent(in)  :: pressure !< Pressure (Pa)
+  real, intent(out) :: rho !< In situ density (kg/3)
+  real, intent(in)  :: Rho_T0_S0 !< Density at T=0, S=0 (kg/m3)
+  real, intent(in)  :: dRho_dT !< Derivative of density w.r.t. potential temperature (kg/m3/C)
+  real, intent(in)  :: dRho_dS !< Derivative of density w.r.t. salinity (1e3 kg/m3)
+  rho = Rho_T0_S0 + dRho_dT*T + dRho_dS*S
+end subroutine calculate_density
+
 !> Returns orientation of a berg determined by its bonds
 subroutine find_orientation_using_iceberg_bonds(grd, berg, orientation)
   ! Arguments
@@ -2737,9 +2735,9 @@ subroutine interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y,
   real :: cos_rot, sin_rot
 #ifdef USE_OLD_SSH_GRADIENT
   real :: dxm, dx0, dxp
+  real, parameter :: ssh_coast=0.00
 #endif
   real :: hxm, hxp
-  real, parameter :: ssh_coast=0.00
   integer :: stderrunit
   integer :: ii, jj
 
@@ -2844,52 +2842,50 @@ subroutine interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y,
 
   endif
 
-  contains
+end subroutine interp_flds
 
-  !> Returns zonal slope of sea-surface height across the east face of cell i,j
-  real function ddx_ssh(grd,i,j)
-    ! Arguments
-    type(icebergs_gridded), pointer :: grd !< Container for gridded fields
-    integer, intent(in) :: i !< i-index of cell
-    integer, intent(in) :: j !< j-index of cell
-    ! Local variables
-    real :: dxp,dx0
-    dxp=0.5*(grd%dx(i+1,j)+grd%dx(i+1,j-1))
-    dx0=0.5*(grd%dx(i,j)+grd%dx(i,j-1))
-    ddx_ssh=2.*(grd%ssh(i+1,j)-grd%ssh(i,j))/(dx0+dxp)*grd%msk(i+1,j)*grd%msk(i,j)
-  end function ddx_ssh
-
-  !> Returns meridional slope of sea-surface height across the northern face of cell i,j
-  real function ddy_ssh(grd,i,j)
-    ! Arguments
-    type(icebergs_gridded), pointer :: grd !< Container for gridded fields
-    integer, intent(in) :: i !< i-index of cell
-    integer, intent(in) :: j !< j-index of cell
-    ! Local variables
-    real :: dyp,dy0
-    dyp=0.5*(grd%dy(i,j+1)+grd%dy(i-1,j+1))
-    dy0=0.5*(grd%dy(i,j)+grd%dy(i-1,j))
-    ddy_ssh=2.*(grd%ssh(i,j+1)-grd%ssh(i,j))/(dy0+dyp)*grd%msk(i,j+1)*grd%msk(i,j)
-  end function ddy_ssh
-
-  ! Rotates vector (u,v) using rotation matrix with elements cos_rot and sin_rot
-  subroutine rotate(u, v, cos_rot, sin_rot)
-    ! Arguments
-    real, intent(inout) :: u !< x-component of vector
-    real, intent(inout) :: v !< y-component of vector
-    real, intent(in) :: cos_rot !< Cosine of rotation angle
-    real, intent(in) :: sin_rot !< Sine of rotation angle
-    ! Local variables
-    real :: u_old, v_old
+!> Returns zonal slope of sea-surface height across the east face of cell i,j
+real function ddx_ssh(grd,i,j)
+  ! Arguments
+  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+  integer, intent(in) :: i !< i-index of cell
+  integer, intent(in) :: j !< j-index of cell
+  ! Local variables
+  real :: dxp,dx0
+  dxp=0.5*(grd%dx(i+1,j)+grd%dx(i+1,j-1))
+  dx0=0.5*(grd%dx(i,j)+grd%dx(i,j-1))
+  ddx_ssh=2.*(grd%ssh(i+1,j)-grd%ssh(i,j))/(dx0+dxp)*grd%msk(i+1,j)*grd%msk(i,j)
+end function ddx_ssh
 
-    u_old=u
-    v_old=v
-    u=cos_rot*u_old+sin_rot*v_old
-    v=cos_rot*v_old-sin_rot*u_old
+!> Returns meridional slope of sea-surface height across the northern face of cell i,j
+real function ddy_ssh(grd,i,j)
+  ! Arguments
+  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+  integer, intent(in) :: i !< i-index of cell
+  integer, intent(in) :: j !< j-index of cell
+  ! Local variables
+  real :: dyp,dy0
+  dyp=0.5*(grd%dy(i,j+1)+grd%dy(i-1,j+1))
+  dy0=0.5*(grd%dy(i,j)+grd%dy(i-1,j))
+  ddy_ssh=2.*(grd%ssh(i,j+1)-grd%ssh(i,j))/(dy0+dyp)*grd%msk(i,j+1)*grd%msk(i,j)
+end function ddy_ssh
+
+! Rotates vector (u,v) using rotation matrix with elements cos_rot and sin_rot
+subroutine rotate(u, v, cos_rot, sin_rot)
+  ! Arguments
+  real, intent(inout) :: u !< x-component of vector
+  real, intent(inout) :: v !< y-component of vector
+  real, intent(in) :: cos_rot !< Cosine of rotation angle
+  real, intent(in) :: sin_rot !< Sine of rotation angle
+  ! Local variables
+  real :: u_old, v_old
 
-  end subroutine rotate
+  u_old=u
+  v_old=v
+  u=cos_rot*u_old+sin_rot*v_old
+  v=cos_rot*v_old-sin_rot*u_old
 
-end subroutine interp_flds
+end subroutine rotate
 
 !> Calculates bergs%grd%mass_on_ocean
 subroutine calculate_mass_on_ocean(bergs, with_diagnostics)
@@ -2931,46 +2927,44 @@ subroutine calculate_mass_on_ocean(bergs, with_diagnostics)
     enddo
   enddo ;enddo
 
-  contains
+end subroutine calculate_mass_on_ocean
 
-  !> Projects additional diagnostics of bergs on to the grid
-  subroutine calculate_sum_over_bergs_diagnositcs(bergs, grd, berg, i, j)
-    ! Arguments
-    type(icebergs), pointer :: bergs !< Container for all types and memory
-    type(icebergs_gridded), pointer :: grd !< Container for gridded fields
-    type(iceberg), pointer :: berg !< An iceberg
-    integer, intent(in) :: i !< i-index of cell containing berg
-    integer, intent(in) :: j !< j-index of cell containing berg
-    ! Local variables
-    real ::  Abits, Lbits, Mbits
-
-    !Virtual area diagnostic
-    if (grd%id_virtual_area>0) then
-      if (bergs%bergy_bit_erosion_fraction>0.) then
-        Lbits=min(berg%length,berg%width,berg%thickness,40.) ! assume bergy bits are smallest dimension or 40 meters
-        Abits=(berg%mass_of_bits/bergs%rho_bergs)/Lbits ! Effective bottom area (assuming T=Lbits)
-      else
-        Abits=0.0
-      endif
-      grd%virtual_area(i,j)=grd%virtual_area(i,j)+(berg%width*berg%length+Abits)*berg%mass_scaling ! m^2
-    endif
+!> Projects additional diagnostics of bergs on to the grid
+subroutine calculate_sum_over_bergs_diagnositcs(bergs, grd, berg, i, j)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+  type(iceberg), pointer :: berg !< An iceberg
+  integer, intent(in) :: i !< i-index of cell containing berg
+  integer, intent(in) :: j !< j-index of cell containing berg
+  ! Local variables
+  real ::  Abits, Lbits, Mbits
 
-    !Mass diagnostic (also used in u_iceberg, v_iceberg
-    if ((grd%id_mass>0 ) .or. ((grd%id_u_iceberg>0) .or. (grd%id_v_iceberg>0)))   &
-         & grd%mass(i,j)=grd%mass(i,j)+berg%mass/grd%area(i,j)*berg%mass_scaling ! kg/m2
+  !Virtual area diagnostic
+  if (grd%id_virtual_area>0) then
+    if (bergs%bergy_bit_erosion_fraction>0.) then
+      Lbits=min(berg%length,berg%width,berg%thickness,40.) ! assume bergy bits are smallest dimension or 40 meters
+      Abits=(berg%mass_of_bits/bergs%rho_bergs)/Lbits ! Effective bottom area (assuming T=Lbits)
+    else
+      Abits=0.0
+    endif
+    grd%virtual_area(i,j)=grd%virtual_area(i,j)+(berg%width*berg%length+Abits)*berg%mass_scaling ! m^2
+  endif
 
-    !Finding the average iceberg velocity in a grid cell (mass weighted)
-    if (grd%id_u_iceberg>0) &
-    grd%u_iceberg(i,j)=grd%u_iceberg(i,j)+((berg%mass/grd%area(i,j)*berg%mass_scaling)*berg%uvel) ! kg/m2
-    if (grd%id_v_iceberg>0) &
-    grd%v_iceberg(i,j)=grd%v_iceberg(i,j)+((berg%mass/grd%area(i,j)*berg%mass_scaling)*berg%vvel) ! kg/m2
+  !Mass diagnostic (also used in u_iceberg, v_iceberg
+  if ((grd%id_mass>0 ) .or. ((grd%id_u_iceberg>0) .or. (grd%id_v_iceberg>0)))   &
+       & grd%mass(i,j)=grd%mass(i,j)+berg%mass/grd%area(i,j)*berg%mass_scaling ! kg/m2
 
-    !Mass of bergy bits
-    if (grd%id_bergy_mass>0 .or. bergs%add_weight_to_ocean)&
-         & grd%bergy_mass(i,j)=grd%bergy_mass(i,j)+berg%mass_of_bits/grd%area(i,j)*berg%mass_scaling ! kg/m2
-  end subroutine calculate_sum_over_bergs_diagnositcs
+  !Finding the average iceberg velocity in a grid cell (mass weighted)
+  if (grd%id_u_iceberg>0) &
+  grd%u_iceberg(i,j)=grd%u_iceberg(i,j)+((berg%mass/grd%area(i,j)*berg%mass_scaling)*berg%uvel) ! kg/m2
+  if (grd%id_v_iceberg>0) &
+  grd%v_iceberg(i,j)=grd%v_iceberg(i,j)+((berg%mass/grd%area(i,j)*berg%mass_scaling)*berg%vvel) ! kg/m2
 
-end subroutine calculate_mass_on_ocean
+  !Mass of bergy bits
+  if (grd%id_bergy_mass>0 .or. bergs%add_weight_to_ocean)&
+       & grd%bergy_mass(i,j)=grd%bergy_mass(i,j)+berg%mass_of_bits/grd%area(i,j)*berg%mass_scaling ! kg/m2
+end subroutine calculate_sum_over_bergs_diagnositcs
 
 !> The main driver the steps updates icebergs
 subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh, sst, calving_hflx, cn, hi, &
@@ -3661,157 +3655,155 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 
   call mpp_clock_end(bergs%clock)
 
-  contains
-
-  !> Prints summary of start and end states
-  subroutine report_state(budgetstr, budgetunits, startstr, startval, endstr, endval, delstr, nbergs)
-    ! Arguments
-    character*(*), intent(in) :: budgetstr !< Budget title
-    character*(*), intent(in) :: budgetunits !< Units of budgeted quantity
-    character*(*), intent(in) :: startstr !< Start label
-    real, intent(in) :: startval !< Start value for budget
-    character*(*), intent(in) :: endstr !< End label
-    real, intent(in) :: endval !< End value for budget
-    character*(*), intent(in) :: delstr !< Delta label
-    integer, intent(in), optional :: nbergs !< Number of bergs
-    ! Local variables
-    if (present(nbergs)) then
-      write(*,100) budgetstr//' state:', &
-                          startstr//' start',startval,budgetunits, &
-                          endstr//' end',endval,budgetunits, &
-                          'Delta '//delstr,endval-startval,budgetunits, &
-                          '# of bergs',nbergs
-    else
-      write(*,100) budgetstr//' state:', &
-                          startstr//' start',startval,budgetunits, &
-                          endstr//' end',endval,budgetunits, &
-                          delstr//'Delta',endval-startval,budgetunits
-    endif
-    100 format("diamonds: ",a19,3(a18,"=",es14.7,x,a2,:,","),a12,i8)
-  end subroutine report_state
+end subroutine icebergs_run
 
-  !> Prints consistency summary of start and end states
-  subroutine report_consistant(budgetstr, budgetunits, startstr, startval, endstr, endval)
-    ! Arguments
-    character*(*), intent(in) :: budgetstr !< Budget title
-    character*(*), intent(in) :: budgetunits !< Units of budgeted quantity
-    character*(*), intent(in) :: startstr !< Start label
-    real, intent(in) :: startval !< Start value for budget
-    character*(*), intent(in) :: endstr !< End label
-    real, intent(in) :: endval !< End value for budget
-    ! Local variables
-    write(*,200) budgetstr//' check:', &
-                        startstr,startval,budgetunits, &
-                        endstr,endval,budgetunits, &
-                        'error',(endval-startval)/((endval+startval)+1e-30),'nd'
-    200 format("diamonds: ",a19,10(a18,"=",es14.7,x,a2,:,","))
-  end subroutine report_consistant
-
-  !> Prints a budget
-  subroutine report_budget(budgetstr, budgetunits, instr, inval, outstr, outval, delstr, startval, endval)
-    ! Arguments
-    character*(*), intent(in) :: budgetstr !< Budget title
-    character*(*), intent(in) :: budgetunits !< Units of budgeted quantity
-    character*(*), intent(in) :: instr !< Incoming label
-    real, intent(in) :: inval !< Incoming value
-    character*(*), intent(in) :: outstr !< Outgoing label
-    real, intent(in) :: outval !< Outgoing value
-    character*(*), intent(in) :: delstr !< Delta label
-    real, intent(in) :: startval !< Start value for budget
-    real, intent(in) :: endval !< End value for budget
-    ! Local variables
-    write(*,200) budgetstr//' budget:', &
-                        instr//' in',inval,budgetunits, &
-                        outstr//' out',outval,budgetunits, &
-                        'Delta '//delstr,inval-outval,budgetunits, &
-                        'error',((endval-startval)-(inval-outval))/max(1.e-30,max(abs(endval-startval),abs(inval-outval))),'nd'
-    200 format("diamonds: ",a19,3(a18,"=",es14.7,x,a2,:,","),a8,"=",es10.3,x,a2)
-  end subroutine report_budget
-
-  !> Prints summary of start and end states
-  subroutine report_istate(budgetstr, startstr, startval, endstr, endval, delstr)
-    ! Arguments
-    character*(*), intent(in) :: budgetstr !< Budget title
-    character*(*), intent(in) :: startstr !< Start label
-    integer, intent(in) :: startval !< Start value for budget
-    character*(*), intent(in) :: endstr !< End label
-    integer, intent(in) :: endval !< End value for budget
-    character*(*), intent(in) :: delstr !< Delta label
-    ! Local variables
+!> Prints summary of start and end states
+subroutine report_state(budgetstr, budgetunits, startstr, startval, endstr, endval, delstr, nbergs)
+  ! Arguments
+  character*(*), intent(in) :: budgetstr !< Budget title
+  character*(*), intent(in) :: budgetunits !< Units of budgeted quantity
+  character*(*), intent(in) :: startstr !< Start label
+  real, intent(in) :: startval !< Start value for budget
+  character*(*), intent(in) :: endstr !< End label
+  real, intent(in) :: endval !< End value for budget
+  character*(*), intent(in) :: delstr !< Delta label
+  integer, intent(in), optional :: nbergs !< Number of bergs
+  ! Local variables
+  if (present(nbergs)) then
     write(*,100) budgetstr//' state:', &
-                          startstr//' start',startval, &
-                          endstr//' end',endval, &
-                          delstr//'Delta',endval-startval
-    100 format("diamonds: ",a19,3(a18,"=",i14,x,:,","))
-  end subroutine report_istate
-
-  !> Prints a budget
-  subroutine report_ibudget(budgetstr,instr,inval,outstr,outval,delstr,startval,endval)
-    ! Arguments
-    character*(*), intent(in) :: budgetstr !< Budget title
-    character*(*), intent(in) :: instr !< Incoming label
-    integer, intent(in) :: inval !< Incoming value
-    character*(*), intent(in) :: outstr !< Outgoing label
-    integer, intent(in) :: outval !< Outgoing value
-    character*(*), intent(in) :: delstr !< Delta label
-    integer, intent(in) :: startval !< Start value for budget
-    integer, intent(in) :: endval !< End value for budget
-    ! Local variables
-    write(*,200) budgetstr//' budget:', &
-                        instr//' in',inval, &
-                        outstr//' out',outval, &
-                        'Delta '//delstr,inval-outval, &
-                        'error',((endval-startval)-(inval-outval))
-    200 format("diamonds: ",a19,10(a18,"=",i14,x,:,","))
-  end subroutine report_ibudget
-
-  !> Time-filter calving and calving_hflx with a running mean.
-  !!
-  !! This subroutine takes in the new calving and calving_hflx, and uses them to time step a running-mean_calving value.
-  !! The time stepping uses a time scale tau. When tau is equal to zero, the
-  !! running mean is exactly equal to the new calving value.
-  subroutine get_running_mean_calving(bergs, calving, calving_hflx)
-    ! Arguments
-    type(icebergs), pointer :: bergs !< Container for all types and memory
-    real, dimension(:,:), intent(inout) :: calving !< Calving (kg/s)
-    real, dimension(:,:), intent(inout) :: calving_hflx !< Calving heat flux (W/m2)
-    ! Local variables
-    real :: alpha  !Parameter used for calving relaxation time stepping.  (0<=alpha<1)
-    real :: tau  !Relaxation timescale in seconds
-    real :: beta  ! = 1-alpha (0<=beta<1)
-
-    ! For the first time-step, initialize the running mean with the current data
-    if (.not. bergs%grd%rmean_calving_initialized) then
-      bergs%grd%rmean_calving(:,:)=calving(:,:)
-      bergs%grd%rmean_calving_initialized=.true.
-    endif
-    if (.not. bergs%grd%rmean_calving_hflx_initialized) then
-      bergs%grd%rmean_calving_hflx(:,:)=calving_hflx(:,:)
-      bergs%grd%rmean_calving_hflx_initialized=.true.
-    endif
+                        startstr//' start',startval,budgetunits, &
+                        endstr//' end',endval,budgetunits, &
+                        'Delta '//delstr,endval-startval,budgetunits, &
+                        '# of bergs',nbergs
+  else
+    write(*,100) budgetstr//' state:', &
+                        startstr//' start',startval,budgetunits, &
+                        endstr//' end',endval,budgetunits, &
+                        delstr//'Delta',endval-startval,budgetunits
+  endif
+  100 format("diamonds: ",a19,3(a18,"=",es14.7,x,a2,:,","),a12,i8)
+end subroutine report_state
 
-    !Applying "Newton cooling" with timescale tau, to smooth out the calving field.
-    tau=bergs%tau_calving/(365.*24*60*60) !Converting time scale from years to seconds
-    alpha=tau/(tau+bergs%dt)
-    if (alpha==0.) return ! Avoids unnecessary copying of arrays
-    if (alpha>0.5) then ! beta is small
-      beta=bergs%dt/(tau+bergs%dt)
-      alpha=1.-beta
-    else ! alpha is small
-      beta=1.-alpha
-    endif
+!> Prints consistency summary of start and end states
+subroutine report_consistant(budgetstr, budgetunits, startstr, startval, endstr, endval)
+  ! Arguments
+  character*(*), intent(in) :: budgetstr !< Budget title
+  character*(*), intent(in) :: budgetunits !< Units of budgeted quantity
+  character*(*), intent(in) :: startstr !< Start label
+  real, intent(in) :: startval !< Start value for budget
+  character*(*), intent(in) :: endstr !< End label
+  real, intent(in) :: endval !< End value for budget
+  ! Local variables
+  write(*,200) budgetstr//' check:', &
+                      startstr,startval,budgetunits, &
+                      endstr,endval,budgetunits, &
+                      'error',(endval-startval)/((endval+startval)+1e-30),'nd'
+  200 format("diamonds: ",a19,10(a18,"=",es14.7,x,a2,:,","))
+end subroutine report_consistant
+
+!> Prints a budget
+subroutine report_budget(budgetstr, budgetunits, instr, inval, outstr, outval, delstr, startval, endval)
+  ! Arguments
+  character*(*), intent(in) :: budgetstr !< Budget title
+  character*(*), intent(in) :: budgetunits !< Units of budgeted quantity
+  character*(*), intent(in) :: instr !< Incoming label
+  real, intent(in) :: inval !< Incoming value
+  character*(*), intent(in) :: outstr !< Outgoing label
+  real, intent(in) :: outval !< Outgoing value
+  character*(*), intent(in) :: delstr !< Delta label
+  real, intent(in) :: startval !< Start value for budget
+  real, intent(in) :: endval !< End value for budget
+  ! Local variables
+  write(*,200) budgetstr//' budget:', &
+                      instr//' in',inval,budgetunits, &
+                      outstr//' out',outval,budgetunits, &
+                      'Delta '//delstr,inval-outval,budgetunits, &
+                      'error',((endval-startval)-(inval-outval))/max(1.e-30,max(abs(endval-startval),abs(inval-outval))),'nd'
+  200 format("diamonds: ",a19,3(a18,"=",es14.7,x,a2,:,","),a8,"=",es10.3,x,a2)
+end subroutine report_budget
+
+!> Prints summary of start and end states
+subroutine report_istate(budgetstr, startstr, startval, endstr, endval, delstr)
+  ! Arguments
+  character*(*), intent(in) :: budgetstr !< Budget title
+  character*(*), intent(in) :: startstr !< Start label
+  integer, intent(in) :: startval !< Start value for budget
+  character*(*), intent(in) :: endstr !< End label
+  integer, intent(in) :: endval !< End value for budget
+  character*(*), intent(in) :: delstr !< Delta label
+  ! Local variables
+  write(*,100) budgetstr//' state:', &
+                        startstr//' start',startval, &
+                        endstr//' end',endval, &
+                        delstr//'Delta',endval-startval
+  100 format("diamonds: ",a19,3(a18,"=",i14,x,:,","))
+end subroutine report_istate
+
+!> Prints a budget
+subroutine report_ibudget(budgetstr,instr,inval,outstr,outval,delstr,startval,endval)
+  ! Arguments
+  character*(*), intent(in) :: budgetstr !< Budget title
+  character*(*), intent(in) :: instr !< Incoming label
+  integer, intent(in) :: inval !< Incoming value
+  character*(*), intent(in) :: outstr !< Outgoing label
+  integer, intent(in) :: outval !< Outgoing value
+  character*(*), intent(in) :: delstr !< Delta label
+  integer, intent(in) :: startval !< Start value for budget
+  integer, intent(in) :: endval !< End value for budget
+  ! Local variables
+  write(*,200) budgetstr//' budget:', &
+                      instr//' in',inval, &
+                      outstr//' out',outval, &
+                      'Delta '//delstr,inval-outval, &
+                      'error',((endval-startval)-(inval-outval))
+  200 format("diamonds: ",a19,10(a18,"=",i14,x,:,","))
+end subroutine report_ibudget
+
+!> Time-filter calving and calving_hflx with a running mean.
+!!
+!! This subroutine takes in the new calving and calving_hflx, and uses them to time step a running-mean_calving value.
+!! The time stepping uses a time scale tau. When tau is equal to zero, the
+!! running mean is exactly equal to the new calving value.
+subroutine get_running_mean_calving(bergs, calving, calving_hflx)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  real, dimension(:,:), intent(inout) :: calving !< Calving (kg/s)
+  real, dimension(:,:), intent(inout) :: calving_hflx !< Calving heat flux (W/m2)
+  ! Local variables
+  real :: alpha  !Parameter used for calving relaxation time stepping.  (0<=alpha<1)
+  real :: tau  !Relaxation timescale in seconds
+  real :: beta  ! = 1-alpha (0<=beta<1)
+
+  ! For the first time-step, initialize the running mean with the current data
+  if (.not. bergs%grd%rmean_calving_initialized) then
+    bergs%grd%rmean_calving(:,:)=calving(:,:)
+    bergs%grd%rmean_calving_initialized=.true.
+  endif
+  if (.not. bergs%grd%rmean_calving_hflx_initialized) then
+    bergs%grd%rmean_calving_hflx(:,:)=calving_hflx(:,:)
+    bergs%grd%rmean_calving_hflx_initialized=.true.
+  endif
 
-    ! For non-negative alpha and beta, these expressions for the running means are sign preserving
-    bergs%grd%rmean_calving(:,:)=beta*calving(:,:) + alpha*bergs%grd%rmean_calving(:,:)
-    bergs%grd%rmean_calving_hflx(:,:)=beta*calving_hflx(:,:) + alpha*bergs%grd%rmean_calving_hflx(:,:)
+  !Applying "Newton cooling" with timescale tau, to smooth out the calving field.
+  tau=bergs%tau_calving/(365.*24*60*60) !Converting time scale from years to seconds
+  alpha=tau/(tau+bergs%dt)
+  if (alpha==0.) return ! Avoids unnecessary copying of arrays
+  if (alpha>0.5) then ! beta is small
+    beta=bergs%dt/(tau+bergs%dt)
+    alpha=1.-beta
+  else ! alpha is small
+    beta=1.-alpha
+  endif
 
-    !Setting calving used by the iceberg model equal to the running mean
-    calving(:,:)=bergs%grd%rmean_calving(:,:)
-    calving_hflx(:,:)=bergs%grd%rmean_calving_hflx(:,:)
+  ! For non-negative alpha and beta, these expressions for the running means are sign preserving
+  bergs%grd%rmean_calving(:,:)=beta*calving(:,:) + alpha*bergs%grd%rmean_calving(:,:)
+  bergs%grd%rmean_calving_hflx(:,:)=beta*calving_hflx(:,:) + alpha*bergs%grd%rmean_calving_hflx(:,:)
 
-  end subroutine get_running_mean_calving
+  !Setting calving used by the iceberg model equal to the running mean
+  calving(:,:)=bergs%grd%rmean_calving(:,:)
+  calving_hflx(:,:)=bergs%grd%rmean_calving_hflx(:,:)
 
-end subroutine icebergs_run
+end subroutine get_running_mean_calving
 
 !> Increments a gridded mass field with the mass of bergs (called from outside icebergs_run)
 !!
@@ -5224,9 +5216,9 @@ subroutine icebergs_end(bergs)
 
   if (mpp_pe()==mpp_root_pe()) write(*,'(a,i8)') 'diamonds: icebergs_end complete',mpp_pe()
 
-  contains
+end subroutine icebergs_end
 
-  subroutine dealloc_buffer(buff)
+subroutine dealloc_buffer(buff)
   ! Arguments
   type(buffer), pointer :: buff
   ! Local variables
@@ -5234,9 +5226,7 @@ subroutine dealloc_buffer(buff)
       if (associated(buff%data)) deallocate(buff%data)
       deallocate(buff)
     endif
-  end subroutine dealloc_buffer
-
-end subroutine icebergs_end
+end subroutine dealloc_buffer
 
 !> Approximately convert a wind-stress into a velocity difference
 subroutine invert_tau_for_du(u, v)
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 934293e..f83205d 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -422,9 +422,9 @@ module ice_bergs_framework
 
 !> Version of file provided by CPP macro (usually set to git hash)
 #ifdef _FILE_VERSION
-  character(len=128) :: version = _FILE_VERSION
+character(len=128) :: version = _FILE_VERSION !< Version of file
 #else
-  character(len=128) :: version = 'unknown'
+character(len=128) :: version = 'unknown' !< Version of file
 #endif
 
 contains
@@ -3276,11 +3276,9 @@ logical function find_cell_by_search(grd, x, y, i, j)
   endif
   find_cell_by_search=.false.
 
-  contains
-
-! # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
+end function find_cell_by_search
 
-  real function dcost(x1, y1, x2, y2,Lx)
+real function dcost(x1, y1, x2, y2,Lx)
   ! Arguments
   real, intent(in) :: x1, x2, y1, y2,Lx
   ! Local variables
@@ -3289,11 +3287,9 @@ real function dcost(x1, y1, x2, y2,Lx)
     x1m=apply_modulo_around_point(x1,x2,Lx)
   ! dcost=(x2-x1)**2+(y2-y1)**2
     dcost=(x2-x1m)**2+(y2-y1)**2
-  end function dcost
-
-! # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
+end function dcost
 
-  logical function find_better_min(grd, x, y, w, oi, oj)
+logical function find_better_min(grd, x, y, w, oi, oj)
   ! Arguments
   type(icebergs_gridded), intent(in) :: grd !< Container for gridded fields
   real, intent(in) :: x, y
@@ -3322,11 +3318,9 @@ logical function find_better_min(grd, x, y, w, oi, oj)
       endif
   enddo; enddo
 
-  end function find_better_min
+end function find_better_min
 
-! # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
-
-  logical function find_cell_loc(grd, x, y, is, ie, js, je, w, oi, oj)
+logical function find_cell_loc(grd, x, y, is, ie, js, je, w, oi, oj)
   ! Arguments
   type(icebergs_gridded), intent(in) :: grd !< Container for gridded fields
   real, intent(in) :: x, y
@@ -3348,9 +3342,7 @@ logical function find_cell_loc(grd, x, y, is, ie, js, je, w, oi, oj)
         endif
     enddo; enddo
 
-  end function find_cell_loc
-
-end function find_cell_by_search
+end function find_cell_loc
 
 !> Returns the i,j of cell containing an iceberg with the given identifier
 subroutine find_individual_iceberg(bergs, iceberg_num, ine, jne, berg_found, search_data_domain)
@@ -3802,107 +3794,105 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
     endif
   endif
 
-  contains
+end function pos_within_cell
 
-  !> Calculates non-dimension position of x,y within a polygon with four corners
-  subroutine calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x, y, xi, yj, Lx, explain)
-  ! Arguments
-  real, intent(in) :: x1 !< Longitude of first corner
-  real, intent(in) :: y1 !< Latitude of first corner
-  real, intent(in) :: x2 !< Longitude of second corner
-  real, intent(in) :: y2 !< Latitude of second corner
-  real, intent(in) :: x3 !< Longitude of third corner
-  real, intent(in) :: y3 !< Latitude of third corner
-  real, intent(in) :: x4 !< Longitude of fourth corner
-  real, intent(in) :: y4 !< Latitude of fourth corner
-  real, intent(in) :: x !< Longitude of point
-  real, intent(in) :: y !< Latitude of point
-  real, intent(out) :: xi !< Non-dimensional x-position within cell
-  real, intent(out) :: yj !< Non-dimensional y-position within cell
-  real, intent(in) :: Lx !< Length of domain in zonal direction
-  logical, intent(in), optional :: explain !< If true, print debugging
-  ! Local variables
-  real :: alpha, beta, gamma, delta, epsilon, kappa, a, b, c, d, dx, dy, yy1, yy2
-  logical :: expl=.false.
-  integer :: stderrunit
+!> Calculates non-dimension position of x,y within a polygon with four corners
+subroutine calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x, y, xi, yj, Lx, explain)
+! Arguments
+real, intent(in) :: x1 !< Longitude of first corner
+real, intent(in) :: y1 !< Latitude of first corner
+real, intent(in) :: x2 !< Longitude of second corner
+real, intent(in) :: y2 !< Latitude of second corner
+real, intent(in) :: x3 !< Longitude of third corner
+real, intent(in) :: y3 !< Latitude of third corner
+real, intent(in) :: x4 !< Longitude of fourth corner
+real, intent(in) :: y4 !< Latitude of fourth corner
+real, intent(in) :: x !< Longitude of point
+real, intent(in) :: y !< Latitude of point
+real, intent(out) :: xi !< Non-dimensional x-position within cell
+real, intent(out) :: yj !< Non-dimensional y-position within cell
+real, intent(in) :: Lx !< Length of domain in zonal direction
+logical, intent(in), optional :: explain !< If true, print debugging
+! Local variables
+real :: alpha, beta, gamma, delta, epsilon, kappa, a, b, c, d, dx, dy, yy1, yy2
+logical :: expl=.false.
+integer :: stderrunit
 
-  ! Get the stderr unit number
-  stderrunit=stderr()
+! Get the stderr unit number
+stderrunit=stderr()
 
-  expl=.false.
-  if (present(explain)) then
-     if(explain) expl=.true.
-  endif
+expl=.false.
+if (present(explain)) then
+   if(explain) expl=.true.
+endif
 
-  alpha=x2-x1
-  delta=y2-y1
-  beta=x4-x1
-  epsilon=y4-y1
-  gamma=(x3-x1)-(alpha+beta)
-  kappa=(y3-y1)-(delta+epsilon)
-  if (expl) write(stderrunit,'(a,1p6e12.4)') 'calc_xiyj: coeffs alpha,beta,gamma',alpha,beta,gamma,delta,epsilon,kappa
-  if (expl) write(stderrunit,'(a,1p6e12.4)') 'calc_xiyj: coeffs delta,epsilon,kappa',alpha,beta,gamma,delta,epsilon,kappa
-
-  a=(kappa*beta-gamma*epsilon)
-  dx= apply_modulo_around_point(x,x1,Lx)-x1
-
-  dy=y-y1
-  b=(delta*beta-alpha*epsilon)-(kappa*dx-gamma*dy)
-  c=(alpha*dy-delta*dx)
-  if (expl) write(stderrunit,'(a,1p6e12.4)') 'calc_xiyj: coeffs dx,dy=',dx,dy
-  if (expl) write(stderrunit,'(a,1p6e12.4)') 'calc_xiyj: coeffs A,B,C=',a,b,c
-  if (abs(a)>1.e-12) then
-    d=0.25*(b**2)-a*c
-    if (expl) write(stderrunit,'(a,1p6e12.4)') 'calc_xiyj: coeffs D=',d
-    if (d.ge.0.) then
-      if (expl) write(stderrunit,'(a,1p3e12.4)') 'Roots for b/2a, sqrt(d) = ',-0.5*b/a,sqrt(d)/a
-      yy1=-(0.5*b+sqrt(d))/a
-      yy2=-(0.5*b-sqrt(d))/a
-      if (abs(yy1-0.5).lt.abs(yy2-0.5)) then; yj=yy1; else; yj=yy2; endif
-      if (expl) write(stderrunit,'(a,1p3e12.4)') 'Roots for y = ',yy1,yy2,yj
-    else
-      write(stderrunit,'(a,i3,a,4(f8.2,a))') 'calc_xiyj: ',mpp_pe(),'lon=[',x1,',',x2,',',x3,',',x4,']'
-      write(stderrunit,'(a,i3,3f8.2)') 'calc_xiyj: x2..x4 - x1',mpp_pe(),x2-x1,x3-x1,x4-x1
-      write(stderrunit,'(a,i3,a,4(f8.2,a))') 'calc_xiyj: ',mpp_pe(),'lat=[',y1,',',y2,',',y3,',',y4,']'
-      write(stderrunit,'(a,i3,3f8.2)') 'calc_xiyj: y2..y4 - x1',mpp_pe(),y2-y1,y3-y1,y4-y1
-      write(stderrunit,'(a,i3,1p6e12.4)') 'calc_xiyj: coeffs alpha..kappa',mpp_pe(),alpha,beta,gamma,delta,epsilon,kappa
-      write(stderrunit,'(a,i3)') 'calc_xiyj: b<0 in quadratic root solver!!!!',mpp_pe()
-      write(stderrunit,'(a,i3,1p6e12.4)') 'calc_xiyj: coeffs a,b,c,d,dx,dy',mpp_pe(),a,b,c,d,dx,dy
-      call error_mesg('diamonds, calc_xiyj', 'We have complex roots. The grid must be very distorted!', FATAL)
-    endif
+alpha=x2-x1
+delta=y2-y1
+beta=x4-x1
+epsilon=y4-y1
+gamma=(x3-x1)-(alpha+beta)
+kappa=(y3-y1)-(delta+epsilon)
+if (expl) write(stderrunit,'(a,1p6e12.4)') 'calc_xiyj: coeffs alpha,beta,gamma',alpha,beta,gamma,delta,epsilon,kappa
+if (expl) write(stderrunit,'(a,1p6e12.4)') 'calc_xiyj: coeffs delta,epsilon,kappa',alpha,beta,gamma,delta,epsilon,kappa
+
+a=(kappa*beta-gamma*epsilon)
+dx= apply_modulo_around_point(x,x1,Lx)-x1
+
+dy=y-y1
+b=(delta*beta-alpha*epsilon)-(kappa*dx-gamma*dy)
+c=(alpha*dy-delta*dx)
+if (expl) write(stderrunit,'(a,1p6e12.4)') 'calc_xiyj: coeffs dx,dy=',dx,dy
+if (expl) write(stderrunit,'(a,1p6e12.4)') 'calc_xiyj: coeffs A,B,C=',a,b,c
+if (abs(a)>1.e-12) then
+  d=0.25*(b**2)-a*c
+  if (expl) write(stderrunit,'(a,1p6e12.4)') 'calc_xiyj: coeffs D=',d
+  if (d.ge.0.) then
+    if (expl) write(stderrunit,'(a,1p3e12.4)') 'Roots for b/2a, sqrt(d) = ',-0.5*b/a,sqrt(d)/a
+    yy1=-(0.5*b+sqrt(d))/a
+    yy2=-(0.5*b-sqrt(d))/a
+    if (abs(yy1-0.5).lt.abs(yy2-0.5)) then; yj=yy1; else; yj=yy2; endif
+    if (expl) write(stderrunit,'(a,1p3e12.4)') 'Roots for y = ',yy1,yy2,yj
   else
-    if (b.ne.0.) then
-      yj=-c/b
-    else
-      yj=0.
-    endif
+    write(stderrunit,'(a,i3,a,4(f8.2,a))') 'calc_xiyj: ',mpp_pe(),'lon=[',x1,',',x2,',',x3,',',x4,']'
+    write(stderrunit,'(a,i3,3f8.2)') 'calc_xiyj: x2..x4 - x1',mpp_pe(),x2-x1,x3-x1,x4-x1
+    write(stderrunit,'(a,i3,a,4(f8.2,a))') 'calc_xiyj: ',mpp_pe(),'lat=[',y1,',',y2,',',y3,',',y4,']'
+    write(stderrunit,'(a,i3,3f8.2)') 'calc_xiyj: y2..y4 - x1',mpp_pe(),y2-y1,y3-y1,y4-y1
+    write(stderrunit,'(a,i3,1p6e12.4)') 'calc_xiyj: coeffs alpha..kappa',mpp_pe(),alpha,beta,gamma,delta,epsilon,kappa
+    write(stderrunit,'(a,i3)') 'calc_xiyj: b<0 in quadratic root solver!!!!',mpp_pe()
+    write(stderrunit,'(a,i3,1p6e12.4)') 'calc_xiyj: coeffs a,b,c,d,dx,dy',mpp_pe(),a,b,c,d,dx,dy
+    call error_mesg('diamonds, calc_xiyj', 'We have complex roots. The grid must be very distorted!', FATAL)
   endif
-
-  a=(alpha+gamma*yj)
-  b=(delta+kappa*yj)
-  if (a.ne.0.) then
-    xi=(dx-beta*yj)/a
-  elseif (b.ne.0.) then
-    xi=(dy-epsilon*yj)/b
+else
+  if (b.ne.0.) then
+    yj=-c/b
   else
-    c=(epsilon*alpha-beta*delta)+(epsilon*gamma-beta*kappa)*yj
-    if (c.ne.0.) then
-      xi=(epsilon*dx-beta*dy)/c
-    else
-      write(stderrunit,'(a,i3,4f8.2)') 'calc_xiyj: x1..x4 ',mpp_pe(),x1,x2,x3,x4
-      write(stderrunit,'(a,i3,3f8.2)') 'calc_xiyj: x2..x4 - x1',mpp_pe(),x2-x1,x3-x1,x4-x1
-      write(stderrunit,'(a,i3,4f8.2)') 'calc_xiyj: y1..y4 ',mpp_pe(),y1,y2,y3,y4
-      write(stderrunit,'(a,i3,3f8.2)') 'calc_xiyj: y2..y4 - x1',mpp_pe(),y2-y1,y3-y1,y4-y1
-      write(stderrunit,'(a,i3,1p6e12.4)') 'calc_xiyj: coeffs alpha..kappa',mpp_pe(),alpha,beta,gamma,delta,epsilon,kappa
-      write(stderrunit,'(a,i3,1p2e12.4)') 'calc_xiyj: coeffs a,b',mpp_pe(),a,b
-      call error_mesg('diamonds, calc_xiyj', 'Can not invert either linear equaton for xi! This should not happen!', FATAL)
-    endif
+    yj=0.
   endif
-  if (expl) write(stderrunit,'(a,2e12.4)') 'calc_xiyj: xi,yj=',xi,yj
+endif
 
-  end subroutine calc_xiyj
+a=(alpha+gamma*yj)
+b=(delta+kappa*yj)
+if (a.ne.0.) then
+  xi=(dx-beta*yj)/a
+elseif (b.ne.0.) then
+  xi=(dy-epsilon*yj)/b
+else
+  c=(epsilon*alpha-beta*delta)+(epsilon*gamma-beta*kappa)*yj
+  if (c.ne.0.) then
+    xi=(epsilon*dx-beta*dy)/c
+  else
+    write(stderrunit,'(a,i3,4f8.2)') 'calc_xiyj: x1..x4 ',mpp_pe(),x1,x2,x3,x4
+    write(stderrunit,'(a,i3,3f8.2)') 'calc_xiyj: x2..x4 - x1',mpp_pe(),x2-x1,x3-x1,x4-x1
+    write(stderrunit,'(a,i3,4f8.2)') 'calc_xiyj: y1..y4 ',mpp_pe(),y1,y2,y3,y4
+    write(stderrunit,'(a,i3,3f8.2)') 'calc_xiyj: y2..y4 - x1',mpp_pe(),y2-y1,y3-y1,y4-y1
+    write(stderrunit,'(a,i3,1p6e12.4)') 'calc_xiyj: coeffs alpha..kappa',mpp_pe(),alpha,beta,gamma,delta,epsilon,kappa
+    write(stderrunit,'(a,i3,1p2e12.4)') 'calc_xiyj: coeffs a,b',mpp_pe(),a,b
+    call error_mesg('diamonds, calc_xiyj', 'Can not invert either linear equaton for xi! This should not happen!', FATAL)
+  endif
+endif
+if (expl) write(stderrunit,'(a,2e12.4)') 'calc_xiyj: xi,yj=',xi,yj
 
-end function pos_within_cell
+end subroutine calc_xiyj
 
 !> Returns true if non-dimensional position xi,yj is in unit interval
 !!
@@ -4476,21 +4466,25 @@ logical function unitTests(bergs)
   stderrunit=stderr()
 
   i=grd%isc; j=grd%jsc
-  call localTest( bilin(grd, grd%lon, i, j, 0., 1.), grd%lon(i-1,j) )
-  call localTest( bilin(grd, grd%lon, i, j, 1., 1.), grd%lon(i,j) )
-  call localTest( bilin(grd, grd%lat, i, j, 1., 0.), grd%lat(i,j-1) )
-  call localTest( bilin(grd, grd%lat, i, j, 1., 1.), grd%lat(i,j) )
+  call localTest( unitTests, bilin(grd, grd%lon, i, j, 0., 1.), grd%lon(i-1,j) )
+  call localTest( unitTests, bilin(grd, grd%lon, i, j, 1., 1.), grd%lon(i,j) )
+  call localTest( unitTests, bilin(grd, grd%lat, i, j, 1., 0.), grd%lat(i,j-1) )
+  call localTest( unitTests, bilin(grd, grd%lat, i, j, 1., 1.), grd%lat(i,j) )
 
-  contains
+end function unitTests
 
-  !> Checks answer to right answer and prints results if different
-  subroutine localTest(answer, rightAnswer)
-  real, intent(in) :: answer, rightAnswer
+!> Checks answer to right answer and prints results if different
+subroutine localTest(unit_test, answer, rightAnswer)
+  logical, intent(inout) :: unit_test !< Set to true answer is wrong
+  real, intent(in) :: answer !< Calculated answer
+  real, intent(in) :: rightAnswer !< Correct answer
+  ! Local variables
+  integer :: stderrunit
+  stderrunit=stderr()
   if (answer==rightAnswer) return
-  unitTests=.true.
+  unit_test=.true.
   write(stderrunit,*) 'a=',answer,'b=',rightAnswer
-  end subroutine localTest
-end function unitTests
+end subroutine localTest
 
 !> Check for duplicates of icebergs on and across processors and issue an error
 !! if any are detected
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index b55b229..6ed119c 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -400,24 +400,23 @@ subroutine write_restart(bergs)
     call grd_chksum2(bergs%grd, bergs%grd%rmean_calving_hflx, 'write mean calving_hflx')
     call write_data(filename, 'rmean_calving_hflx', bergs%grd%rmean_calving_hflx, bergs%grd%domain)
   endif
-  contains
-
-  !> Find the last berg in a linked list.
-  function last_berg(berg)
-  ! Arguments
-  type(iceberg), pointer :: berg !< Pointer to an iceberg
-  type(iceberg), pointer :: last_berg
-  ! Local variables
-
-    last_berg=>berg
-    do while (associated(last_berg%next))
-      last_berg=>last_berg%next
-    enddo
-
-  end function last_berg
 
 end subroutine write_restart
 
+!> Find the last berg in a linked list.
+function last_berg(berg)
+! Arguments
+type(iceberg), pointer :: berg !< Pointer to an iceberg
+type(iceberg), pointer :: last_berg
+! Local variables
+
+  last_berg=>berg
+  do while (associated(last_berg%next))
+    last_berg=>last_berg%next
+  enddo
+
+end function last_berg
+
 !> Read an iceberg restart file (original implementation)
 subroutine read_restart_bergs_orig(bergs,Time)
 ! Arguments
@@ -600,7 +599,7 @@ subroutine read_restart_bergs_orig(bergs,Time)
 
   if (k.ne.nbergs_in_file) call error_mesg('diamonds, read_restart_bergs', 'wrong number of bergs read!', FATAL)
 
-  if (.not. found_restart .and. bergs%nbergs_start==0 .and. generate_test_icebergs) call generate_bergs(bergs,Time)
+  if (.not. found_restart .and. bergs%nbergs_start==0 .and. generate_test_icebergs) call generate_bergs_orig(bergs,Time)
 
   bergs%floating_mass_start=sum_mass(bergs)
   call mpp_sum( bergs%floating_mass_start )
@@ -610,104 +609,103 @@ subroutine read_restart_bergs_orig(bergs,Time)
   call mpp_sum( bergs%bergy_mass_start )
   if (mpp_pe().eq.mpp_root_pe().and.verbose) write(*,'(a)') 'diamonds, read_restart_bergs: completed'
 
-contains
+end subroutine read_restart_bergs_orig
 
-  !> Read a real value from a file and optionally return a default value if variable is missing
-  real function get_real_from_file(ncid, varid, k, value_if_not_in_file)
-  integer, intent(in) :: ncid, varid, k
-  real, optional :: value_if_not_in_file
+!> Read a real value from a file and optionally return a default value if variable is missing
+real function get_real_from_file(ncid, varid, k, value_if_not_in_file)
+integer, intent(in) :: ncid, varid, k
+real, optional :: value_if_not_in_file
 
-  if (varid<1.and.present(value_if_not_in_file)) then
-    get_real_from_file=value_if_not_in_file
-  else
-    get_real_from_file=get_double(ncid, ncid, k)
-  endif
-  end function get_real_from_file
-
-  !> Generate bergs for the purpose of debugging
-  subroutine generate_bergs(bergs,Time)
-  ! Arguments
-  type(icebergs), pointer :: bergs !< Icebergs container
-  type(time_type), intent(in) :: Time !< Model time
-  ! Local variables
-  integer :: i,j
-  integer :: iNg, jNg  !Total number of points gloablly in i and j direction
-  type(iceberg) :: localberg ! NOT a pointer but an actual local variable
-  integer :: iyr, imon, iday, ihr, imin, isec
-
-    ! For convenience
-    grd=>bergs%grd
-    iNg=(grd%ieg-grd%isg+1) ! Total number of points globally in i direction
-    jNg=(grd%jeg-grd%jsg+1) ! Total number of points globally in j direction
-
-    call get_date(Time, iyr, imon, iday, ihr, imin, isec)
-
-    do j=grd%jsc,grd%jec; do i=grd%isc,grd%iec
-      if (grd%msk(i,j)>0. .and. abs(grd%latc(i,j))>60.) then
-        localberg%xi=0.5
-        localberg%yj=0.5
-        localberg%ine=i
-        localberg%jne=j
-        localberg%lon=bilin(grd, grd%lon, i, j, localberg%xi, localberg%yj)
-        localberg%lat=bilin(grd, grd%lat, i, j, localberg%xi, localberg%yj)
-        localberg%lon_old=bilin(grd, grd%lon, i, j, localberg%xi, localberg%yj) !Alon
-        localberg%lat_old=bilin(grd, grd%lat, i, j, localberg%xi, localberg%yj) !Alon
-        localberg%mass=bergs%initial_mass(1)
-        localberg%thickness=bergs%initial_thickness(1)
-        localberg%width=bergs%initial_width(1)
-        localberg%length=bergs%initial_length(1)
-        localberg%start_lon=localberg%lon
-        localberg%start_lat=localberg%lat
-        localberg%start_year=iyr
-        localberg%start_day=float(iday)+(float(ihr)+float(imin)/60.)/24.
-        localberg%start_mass=localberg%mass
-        localberg%mass_scaling=bergs%mass_scaling(1)
-        localberg%mass_of_bits=0.
-        localberg%halo_berg=0.
-        localberg%static_berg=0.
-        localberg%heat_density=0.
-        localberg%axn=0. !Alon
-        localberg%ayn=0. !Alon
-        localberg%uvel_old=0. !Alon
-        localberg%vvel_old=0. !Alon
-        localberg%bxn=0. !Alon
-        localberg%byn=0. !Alon
-
-        !Berg A
-        localberg%uvel=1.
-        localberg%vvel=0.
-        localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
-        grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
-        call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
-        !Berg B
-        localberg%uvel=-1.
-        localberg%vvel=0.
-        localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
-        grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
-        call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
-        !Berg C
-        localberg%uvel=0.
-        localberg%vvel=1.
-        localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
-        grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
-        call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
-        !Berg D
-        localberg%uvel=0.
-        localberg%vvel=-1.
-        localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
-        grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
-        call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
-      endif
-    enddo; enddo
+if (varid<1.and.present(value_if_not_in_file)) then
+  get_real_from_file=value_if_not_in_file
+else
+  get_real_from_file=get_double(ncid, ncid, k)
+endif
+end function get_real_from_file
 
-    bergs%nbergs_start=count_bergs(bergs)
-    call mpp_sum(bergs%nbergs_start)
-    if (mpp_pe().eq.mpp_root_pe()) &
-      write(*,'(a,i8,a)') 'diamonds, generate_bergs: ',bergs%nbergs_start,' were generated'
+!> Generate bergs for the purpose of debugging
+subroutine generate_bergs_orig(bergs, Time)
+! Arguments
+type(icebergs), pointer :: bergs !< Icebergs container
+type(time_type), intent(in) :: Time !< Model time
+! Local variables
+type(icebergs_gridded), pointer :: grd
+integer :: i,j
+integer :: iNg, jNg  !Total number of points gloablly in i and j direction
+type(iceberg) :: localberg ! NOT a pointer but an actual local variable
+integer :: iyr, imon, iday, ihr, imin, isec
 
-  end subroutine generate_bergs
+  ! For convenience
+  grd=>bergs%grd
+  iNg=(grd%ieg-grd%isg+1) ! Total number of points globally in i direction
+  jNg=(grd%jeg-grd%jsg+1) ! Total number of points globally in j direction
 
-end subroutine read_restart_bergs_orig
+  call get_date(Time, iyr, imon, iday, ihr, imin, isec)
+
+  do j=grd%jsc,grd%jec; do i=grd%isc,grd%iec
+    if (grd%msk(i,j)>0. .and. abs(grd%latc(i,j))>60.) then
+      localberg%xi=0.5
+      localberg%yj=0.5
+      localberg%ine=i
+      localberg%jne=j
+      localberg%lon=bilin(grd, grd%lon, i, j, localberg%xi, localberg%yj)
+      localberg%lat=bilin(grd, grd%lat, i, j, localberg%xi, localberg%yj)
+      localberg%lon_old=bilin(grd, grd%lon, i, j, localberg%xi, localberg%yj) !Alon
+      localberg%lat_old=bilin(grd, grd%lat, i, j, localberg%xi, localberg%yj) !Alon
+      localberg%mass=bergs%initial_mass(1)
+      localberg%thickness=bergs%initial_thickness(1)
+      localberg%width=bergs%initial_width(1)
+      localberg%length=bergs%initial_length(1)
+      localberg%start_lon=localberg%lon
+      localberg%start_lat=localberg%lat
+      localberg%start_year=iyr
+      localberg%start_day=float(iday)+(float(ihr)+float(imin)/60.)/24.
+      localberg%start_mass=localberg%mass
+      localberg%mass_scaling=bergs%mass_scaling(1)
+      localberg%mass_of_bits=0.
+      localberg%halo_berg=0.
+      localberg%static_berg=0.
+      localberg%heat_density=0.
+      localberg%axn=0. !Alon
+      localberg%ayn=0. !Alon
+      localberg%uvel_old=0. !Alon
+      localberg%vvel_old=0. !Alon
+      localberg%bxn=0. !Alon
+      localberg%byn=0. !Alon
+
+      !Berg A
+      localberg%uvel=1.
+      localberg%vvel=0.
+      localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
+      grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
+      call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
+      !Berg B
+      localberg%uvel=-1.
+      localberg%vvel=0.
+      localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
+      grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
+      call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
+      !Berg C
+      localberg%uvel=0.
+      localberg%vvel=1.
+      localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
+      grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
+      call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
+      !Berg D
+      localberg%uvel=0.
+      localberg%vvel=-1.
+      localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
+      grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
+      call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
+    endif
+  enddo; enddo
+
+  bergs%nbergs_start=count_bergs(bergs)
+  call mpp_sum(bergs%nbergs_start)
+  if (mpp_pe().eq.mpp_root_pe()) &
+    write(*,'(a,i8,a)') 'diamonds, generate_bergs: ',bergs%nbergs_start,' were generated'
+
+end subroutine generate_bergs_orig
 
 !> Read an iceberg restart file
 subroutine read_restart_bergs(bergs,Time)
@@ -973,154 +971,152 @@ subroutine read_restart_bergs(bergs,Time)
   call mpp_sum( bergs%bergy_mass_start )
   if (mpp_pe().eq.mpp_root_pe().and.verbose) write(*,'(a)') 'diamonds, read_restart_bergs: completed'
 
-contains
+end subroutine read_restart_bergs
 
-  !> Read a vector of reals from file and use a default value if variable is missing
-  subroutine read_real_vector(filename, varname, values, domain, value_if_not_in_file)
-    character(len=*), intent(in)  :: filename !< Name of file to read from
-    character(len=*), intent(in)  :: varname !< Name of variable to read
-    real,             intent(out) :: values(:) !< Returned vector of reals
-    type(domain2D),   intent(in)  :: domain !< Parallel decomposition
-    real, optional,   intent(in)  :: value_if_not_in_file !< Value to use if variable is not in file
+!> Read a vector of reals from file and use a default value if variable is missing
+subroutine read_real_vector(filename, varname, values, domain, value_if_not_in_file)
+  character(len=*), intent(in)  :: filename !< Name of file to read from
+  character(len=*), intent(in)  :: varname !< Name of variable to read
+  real,             intent(out) :: values(:) !< Returned vector of reals
+  type(domain2D),   intent(in)  :: domain !< Parallel decomposition
+  real, optional,   intent(in)  :: value_if_not_in_file !< Value to use if variable is not in file
 
-    if (present(value_if_not_in_file).and..not.field_exist(filename, varname)) then
-      values(:)=value_if_not_in_file
-    else
-      call read_unlimited_axis(filename,varname,values,domain=domain)
-    endif
-  end subroutine read_real_vector
-
-  !> Read a vector of integers from file and use a default value if variable is missing
-  subroutine read_int_vector(filename, varname, values, domain, value_if_not_in_file)
-    character(len=*),  intent(in)  :: filename !< Name of file to read from
-    character(len=*),  intent(in)  :: varname !< Name of variable to read
-    integer,           intent(out) :: values(:) !< Returned vector of integers
-    type(domain2D),    intent(in)  :: domain !< Parallel decomposition
-    integer, optional, intent(in)  :: value_if_not_in_file !< Value to use if variable is not in file
-
-    if (present(value_if_not_in_file).and..not.field_exist(filename, varname)) then
-      values(:)=value_if_not_in_file
-    else
-      call read_unlimited_axis(filename,varname,values,domain=domain)
-    endif
-  end subroutine read_int_vector
-
-  !> Generate bergs for the purpose of debugging
-  subroutine generate_bergs(bergs,Time)
-  ! Arguments
-  type(icebergs), pointer :: bergs !< Icebergs container
-  type(time_type), intent(in) :: Time !< Model time
-  ! Local variables
-  integer :: i,j
-  integer :: iNg, jNg  !Total number of points gloablly in i and j direction
-  type(iceberg) :: localberg ! NOT a pointer but an actual local variable
-  integer :: iyr, imon, iday, ihr, imin, isec
-  logical :: lres
+  if (present(value_if_not_in_file).and..not.field_exist(filename, varname)) then
+    values(:)=value_if_not_in_file
+  else
+    call read_unlimited_axis(filename,varname,values,domain=domain)
+  endif
+end subroutine read_real_vector
+
+!> Read a vector of integers from file and use a default value if variable is missing
+subroutine read_int_vector(filename, varname, values, domain, value_if_not_in_file)
+  character(len=*),  intent(in)  :: filename !< Name of file to read from
+  character(len=*),  intent(in)  :: varname !< Name of variable to read
+  integer,           intent(out) :: values(:) !< Returned vector of integers
+  type(domain2D),    intent(in)  :: domain !< Parallel decomposition
+  integer, optional, intent(in)  :: value_if_not_in_file !< Value to use if variable is not in file
+
+  if (present(value_if_not_in_file).and..not.field_exist(filename, varname)) then
+    values(:)=value_if_not_in_file
+  else
+    call read_unlimited_axis(filename,varname,values,domain=domain)
+  endif
+end subroutine read_int_vector
 
-    ! For convenience
-    grd=>bergs%grd
-    iNg=(grd%ieg-grd%isg+1) ! Total number of points globally in i direction
-    jNg=(grd%jeg-grd%jsg+1) ! Total number of points globally in j direction
-
-    call get_date(Time, iyr, imon, iday, ihr, imin, isec)
-
-    do j=grd%jsc,grd%jec; do i=grd%isc,grd%iec
-      if (grd%msk(i,j)>0. .and. abs(grd%latc(i,j))>80.0) then
-        if (max(grd%lat(i,j),grd%lat(i-1,j),grd%lat(i,j-1),grd%lat(i-1,j-1))>89.999) cycle ! Cannot use this at Pole cells
-        localberg%xi=-999.
-        localberg%yj=-999.
-        localberg%ine=i
-        localberg%jne=j
-        localberg%lon=grd%lonc(i,j)
-        localberg%lat=grd%latc(i,j)
-        localberg%lon_old=localberg%lon
-        localberg%lat_old=localberg%lat
-        localberg%mass=bergs%initial_mass(1)
-        localberg%thickness=bergs%initial_thickness(1)
-        localberg%width=bergs%initial_width(1)
-        localberg%length=bergs%initial_length(1)
-        localberg%start_lon=localberg%lon
-        localberg%start_lat=localberg%lat
-        localberg%start_year=iyr
-        localberg%start_day=float(iday)+(float(ihr)+float(imin)/60.)/24.
-        localberg%start_mass=localberg%mass
-        localberg%mass_scaling=bergs%mass_scaling(1)
-        localberg%mass_of_bits=0.
-        localberg%halo_berg=0.
-        localberg%static_berg=0.
-        localberg%heat_density=0.
-        localberg%axn=0. !Alon
-        localberg%ayn=0. !Alon
-        localberg%uvel_old=0. !Alon
-        localberg%vvel_old=0. !Alon
-        localberg%bxn=0. !Alon
-        localberg%byn=0. !Alon
-
-        !Berg A
-        call loc_set_berg_pos(grd, 0.9, 0.5, 1., 0., localberg)
-        localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
-        grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
-        call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
-        !Berg B
-        call loc_set_berg_pos(grd, 0.1, 0.5, -1., 0., localberg)
-        localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
-        grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
-        call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
-        !Berg C
-        call loc_set_berg_pos(grd, 0.5, 0.9, 0., 1., localberg)
-        localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
-        grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
-        call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
-        !Berg D
-        call loc_set_berg_pos(grd, 0.5, 0.1, 0., -1., localberg)
-        localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
-        grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
-        call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
-      endif
-    enddo; enddo
-
-    bergs%nbergs_start=count_bergs(bergs)
-    call mpp_sum(bergs%nbergs_start)
-    if (mpp_pe().eq.mpp_root_pe()) &
-      write(*,'(a,i8,a)') 'diamonds, generate_bergs: ',bergs%nbergs_start,' were generated'
-
-  end subroutine generate_bergs
-
-  subroutine loc_set_berg_pos(grd, xi, yj, uvel, vvel, berg)
-    type(icebergs_gridded), pointer :: grd !< Container for gridded fields
-    real, intent(in) :: xi !< Non-dimensional x-position within cell to give berg
-    real, intent(in) :: yj !< Non-dimensional y-position within cell to give berg
-    real, intent(in) :: uvel !< Zonal velocity to give berg
-    real, intent(in) :: vvel !< Meridional velocity to give berg
-    type(iceberg), intent(inout) :: berg !< An iceberg
-    integer :: i, j
-    logical :: lres
-    i = berg%ine ; j = berg%jne
-    if (max(grd%lat(i,j),grd%lat(i-1,j),grd%lat(i,j-1),grd%lat(i-1,j-1))>89.999) then
-      berg%lon=grd%lonc(i,j)
-      berg%lat=grd%latc(i,j)
-      berg%xi=0.5 ; berg%yj=0.5
-    else
-      berg%lon=bilin(grd, grd%lon, i, j, xi, yj)
-      berg%lat=bilin(grd, grd%lat, i, j, xi, yj)
-      berg%xi=xi ; berg%yj=yj
-    endif
-    berg%uvel=uvel ; berg%vvel=vvel
-    berg%lon_old=berg%lon ; berg%lat_old=berg%lat
-    berg%start_lon=berg%lon ; berg%start_lat=berg%lat
-    lres=pos_within_cell(grd, berg%lon, berg%lat, berg%ine, berg%jne, berg%xi, berg%yj)
-    if (.not. lres) then
-      lres=pos_within_cell(grd, berg%lon, berg%lat, berg%ine, berg%jne, berg%xi, berg%yj, explain=.true.)
-      write(0,*) lres, i, j, xi, yj, uvel, vvel
-      write(0,*) lres, berg%ine, berg%jne, berg%xi, berg%yj
-      write(0,*) 'bx=',berg%lon, 'gx=',grd%lon(i-1,j-1), grd%lon(i,j-1), grd%lon(i,j), grd%lon(i-1,j),'cx=', grd%lonc(i,j)
-      write(0,*) 'by=',berg%lat, 'gy=',grd%lat(i-1,j-1), grd%lat(i,j-1), grd%lat(i,j), grd%lat(i-1,j),'cy=', grd%latc(i,j)
-      stop 'generate_bergs, loc_set_berg_pos(): VERY FATAL!'
-    endif
-  end subroutine loc_set_berg_pos
+!> Generate bergs for the purpose of debugging
+subroutine generate_bergs(bergs,Time)
+! Arguments
+type(icebergs), pointer :: bergs !< Icebergs container
+type(time_type), intent(in) :: Time !< Model time
+! Local variables
+type(icebergs_gridded), pointer :: grd
+integer :: i,j
+integer :: iNg, jNg  !Total number of points gloablly in i and j direction
+type(iceberg) :: localberg ! NOT a pointer but an actual local variable
+integer :: iyr, imon, iday, ihr, imin, isec
+logical :: lres
 
-end subroutine read_restart_bergs
+  ! For convenience
+  grd=>bergs%grd
+  iNg=(grd%ieg-grd%isg+1) ! Total number of points globally in i direction
+  jNg=(grd%jeg-grd%jsg+1) ! Total number of points globally in j direction
 
+  call get_date(Time, iyr, imon, iday, ihr, imin, isec)
+
+  do j=grd%jsc,grd%jec; do i=grd%isc,grd%iec
+    if (grd%msk(i,j)>0. .and. abs(grd%latc(i,j))>80.0) then
+      if (max(grd%lat(i,j),grd%lat(i-1,j),grd%lat(i,j-1),grd%lat(i-1,j-1))>89.999) cycle ! Cannot use this at Pole cells
+      localberg%xi=-999.
+      localberg%yj=-999.
+      localberg%ine=i
+      localberg%jne=j
+      localberg%lon=grd%lonc(i,j)
+      localberg%lat=grd%latc(i,j)
+      localberg%lon_old=localberg%lon
+      localberg%lat_old=localberg%lat
+      localberg%mass=bergs%initial_mass(1)
+      localberg%thickness=bergs%initial_thickness(1)
+      localberg%width=bergs%initial_width(1)
+      localberg%length=bergs%initial_length(1)
+      localberg%start_lon=localberg%lon
+      localberg%start_lat=localberg%lat
+      localberg%start_year=iyr
+      localberg%start_day=float(iday)+(float(ihr)+float(imin)/60.)/24.
+      localberg%start_mass=localberg%mass
+      localberg%mass_scaling=bergs%mass_scaling(1)
+      localberg%mass_of_bits=0.
+      localberg%halo_berg=0.
+      localberg%static_berg=0.
+      localberg%heat_density=0.
+      localberg%axn=0. !Alon
+      localberg%ayn=0. !Alon
+      localberg%uvel_old=0. !Alon
+      localberg%vvel_old=0. !Alon
+      localberg%bxn=0. !Alon
+      localberg%byn=0. !Alon
+
+      !Berg A
+      call loc_set_berg_pos(grd, 0.9, 0.5, 1., 0., localberg)
+      localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
+      grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
+      call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
+      !Berg B
+      call loc_set_berg_pos(grd, 0.1, 0.5, -1., 0., localberg)
+      localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
+      grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
+      call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
+      !Berg C
+      call loc_set_berg_pos(grd, 0.5, 0.9, 0., 1., localberg)
+      localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
+      grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
+      call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
+      !Berg D
+      call loc_set_berg_pos(grd, 0.5, 0.1, 0., -1., localberg)
+      localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
+      grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
+      call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
+    endif
+  enddo; enddo
+
+  bergs%nbergs_start=count_bergs(bergs)
+  call mpp_sum(bergs%nbergs_start)
+  if (mpp_pe().eq.mpp_root_pe()) &
+    write(*,'(a,i8,a)') 'diamonds, generate_bergs: ',bergs%nbergs_start,' were generated'
+
+end subroutine generate_bergs
+
+subroutine loc_set_berg_pos(grd, xi, yj, uvel, vvel, berg)
+  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+  real, intent(in) :: xi !< Non-dimensional x-position within cell to give berg
+  real, intent(in) :: yj !< Non-dimensional y-position within cell to give berg
+  real, intent(in) :: uvel !< Zonal velocity to give berg
+  real, intent(in) :: vvel !< Meridional velocity to give berg
+  type(iceberg), intent(inout) :: berg !< An iceberg
+  integer :: i, j
+  logical :: lres
+  i = berg%ine ; j = berg%jne
+  if (max(grd%lat(i,j),grd%lat(i-1,j),grd%lat(i,j-1),grd%lat(i-1,j-1))>89.999) then
+    berg%lon=grd%lonc(i,j)
+    berg%lat=grd%latc(i,j)
+    berg%xi=0.5 ; berg%yj=0.5
+  else
+    berg%lon=bilin(grd, grd%lon, i, j, xi, yj)
+    berg%lat=bilin(grd, grd%lat, i, j, xi, yj)
+    berg%xi=xi ; berg%yj=yj
+  endif
+  berg%uvel=uvel ; berg%vvel=vvel
+  berg%lon_old=berg%lon ; berg%lat_old=berg%lat
+  berg%start_lon=berg%lon ; berg%start_lat=berg%lat
+  lres=pos_within_cell(grd, berg%lon, berg%lat, berg%ine, berg%jne, berg%xi, berg%yj)
+  if (.not. lres) then
+    lres=pos_within_cell(grd, berg%lon, berg%lat, berg%ine, berg%jne, berg%xi, berg%yj, explain=.true.)
+    write(0,*) lres, i, j, xi, yj, uvel, vvel
+    write(0,*) lres, berg%ine, berg%jne, berg%xi, berg%yj
+    write(0,*) 'bx=',berg%lon, 'gx=',grd%lon(i-1,j-1), grd%lon(i,j-1), grd%lon(i,j), grd%lon(i-1,j),'cx=', grd%lonc(i,j)
+    write(0,*) 'by=',berg%lat, 'gy=',grd%lat(i-1,j-1), grd%lat(i,j-1), grd%lat(i,j), grd%lat(i-1,j),'cy=', grd%latc(i,j)
+    stop 'generate_bergs, loc_set_berg_pos(): VERY FATAL!'
+  endif
+end subroutine loc_set_berg_pos
 
 !> Read bond restart file
 subroutine read_restart_bonds(bergs,Time)

From 0348755c90bcfac0bd444dc97be1168a7b72d5c8 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Wed, 14 Jun 2017 23:21:31 -0400
Subject: [PATCH 217/361] Add functions id_from_2_ints() and split_id()

- Two new functions to cobine two 32-bit integers into a single 64-bit
  integer and back again.
  - When we wrote the iceberg_num (iceberg id code) we assumed integers
    were 64-bit but by default they are 32-bit with the compilation options
    used with FMS codes, and netcdf only supports 32-bit integers!
- Also renamed unitTests() to unit_tests().
---
 icebergs_framework.F90 | 51 ++++++++++++++++++++++++++++++++++--------
 1 file changed, 42 insertions(+), 9 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index f83205d..c8a6c81 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -1108,7 +1108,7 @@ subroutine ice_bergs_framework_init(bergs, &
   endif
 
   if (do_unit_tests) then
-   if (unitTests(bergs)) call error_mesg('diamonds, icebergs_init', 'Unit tests failed!', FATAL)
+   if (unit_tests(bergs)) call error_mesg('diamonds, icebergs_init', 'Unit tests failed!', FATAL)
   endif
 
  !write(stderrunit,*) 'diamonds: done'
@@ -4452,26 +4452,59 @@ subroutine print_fld(grd, fld, label)
 
 end subroutine print_fld
 
+!> Combine a counter and i,j hash into an id
+integer(kind=8) function id_from_2_ints(counter, ijhash)
+  integer, intent(in) :: counter !< The counter value assigned at calving
+  integer, intent(in) :: ijhash  !< A hash of i,j calving location
+
+  id_from_2_ints = int(counter,8) * (2**32) + int(ijhash,8)
+
+end function id_from_2_ints
+
+!> Split an iceberg ID into two parts
+subroutine split_id(id, counter, ijhash)
+  integer(kind=8), intent(in)  :: id      !< A unique id assigned when a berg is created
+  integer,         intent(out) :: counter !< The counter value assigned at calving
+  integer,         intent(out) :: ijhash  !< A hash of i,j calving location
+  ! Local variables
+  integer(kind=8) :: i8
+
+  counter = ishft(id,-32)
+  !counter = i8
+  ijhash = int(id,4)
+
+end subroutine split_id
+
 !> Invoke some unit tests
-logical function unitTests(bergs)
+logical function unit_tests(bergs)
   type(icebergs), pointer :: bergs !< Container for all types and memory
   ! Local variables
   type(icebergs_gridded), pointer :: grd
-  integer :: stderrunit,i,j
+  integer :: stderrunit,i,j,c1,c2
+  integer(kind=8) :: id
 
   ! This function returns True is a unit test fails
-  unitTests=.false.
+  unit_tests=.false.
   ! For convenience
   grd=>bergs%grd
   stderrunit=stderr()
 
   i=grd%isc; j=grd%jsc
-  call localTest( unitTests, bilin(grd, grd%lon, i, j, 0., 1.), grd%lon(i-1,j) )
-  call localTest( unitTests, bilin(grd, grd%lon, i, j, 1., 1.), grd%lon(i,j) )
-  call localTest( unitTests, bilin(grd, grd%lat, i, j, 1., 0.), grd%lat(i,j-1) )
-  call localTest( unitTests, bilin(grd, grd%lat, i, j, 1., 1.), grd%lat(i,j) )
+  call localTest( unit_tests, bilin(grd, grd%lon, i, j, 0., 1.), grd%lon(i-1,j) )
+  call localTest( unit_tests, bilin(grd, grd%lon, i, j, 1., 1.), grd%lon(i,j) )
+  call localTest( unit_tests, bilin(grd, grd%lat, i, j, 1., 0.), grd%lat(i,j-1) )
+  call localTest( unit_tests, bilin(grd, grd%lat, i, j, 1., 1.), grd%lat(i,j) )
+
+  ! Test 64-bit ID conversion
+  i = 1440*1080 ; c1 = 2**30 + 2**4 + 1
+  id = id_from_2_ints(c1, i)
+  call split_id(id,c2,j)
+  if (j /= i .or. c2 /= c1) then
+    write(0,*) 'i,c in:',i,c1,' id=',id,' i,c out:',j,c2
+    unit_tests=.true.
+  endif
 
-end function unitTests
+end function unit_tests
 
 !> Checks answer to right answer and prints results if different
 subroutine localTest(unit_test, answer, rightAnswer)

From 33e090d58d87de17df4d8113f1c4f7f7b69f16cc Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Thu, 15 Jun 2017 01:03:35 -0400
Subject: [PATCH 218/361] Added function generate_id()

- A new member %id is a 64-bit integer for a better constructed id.
- New function, generate_id(), returns a 64-bit integer hash of
  counter and position.
---
 icebergs_framework.F90 | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index c8a6c81..f73394c 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -78,6 +78,7 @@ module ice_bergs_framework
 public is_point_within_xi_yj_bounds
 public test_check_for_duplicate_ids_in_list
 public check_for_duplicates_in_parallel
+public split_id, id_from_2_ints, generate_id
 
 !> Container for gridded fields
 type :: icebergs_gridded
@@ -254,6 +255,7 @@ module ice_bergs_framework
   real :: static_berg  ! Equal to 1 for icebergs which are static (not allowed to move). Might be extended to grounding later.
   integer :: start_year !< Year that berg was created (years)
   integer :: iceberg_num !< Iceberg identifier
+  integer(kind=8) :: id !< Iceberg identifier
   integer :: ine !< Nearest i-index in NE direction (for convenience)
   integer :: jne !< Nearest j-index in NE direction (for convenience)
   real :: xi !< Non-dimensional x-coordinate within current cell (0..1)
@@ -281,6 +283,7 @@ module ice_bergs_framework
   type(bond), pointer :: next_bond=>null() !< Next link in list
   type(iceberg), pointer :: other_berg=>null()
   integer :: other_berg_num
+  integer(kind=8) :: other_id !< ID of other berg
   integer :: other_berg_ine
   integer :: other_berg_jne
 end type bond
@@ -2287,6 +2290,29 @@ subroutine check_for_duplicates(bergs,label)
 
 end subroutine check_for_duplicates
 
+!> Generate an iceberg id from a counter at calving-location and the calving location itself.
+!! Note that this updates grd%iceberg_counter_grd.
+!!
+!! \todo If we initialized grd%iceberg_counter_grd to 0 when the model is first run we could move
+!! this increment line to before the id generation and then the counter would be an actual count.
+integer(kind=8) function generate_id(grd, i, j)
+  type(icebergs_gridded), pointer    :: grd !< Container for gridded fields
+  integer,                intent(in) :: i   !< i-index of calving location
+  integer,                intent(in) :: j   !< j-index of calving location
+  ! Local variables
+  integer :: ij ! Hash of i,j
+  integer :: iNg ! Total number of points globally in i direction
+
+  iNg=(grd%ieg-grd%isg+1)
+  ! ij is unique number for each grid cell (32-bit integers allow for ~1/100th degree global resolution)
+  ij = i + (iNg*(j-1))
+  ! Generate a 64-bit id
+  generate_id = id_from_2_ints( grd%iceberg_counter_grd(i,j), ij )
+  ! Increment counter in calving cell
+  grd%iceberg_counter_grd(i,j) = grd%iceberg_counter_grd(i,j) + 1
+
+end function generate_id
+
 !> Prints a particular berg's vitals
 !!
 !! All lists are scanned and if a berg has the identifier equal to

From e7fc83fda9cadc6e4687a2734cf4ce2507510003 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Thu, 15 Jun 2017 01:08:01 -0400
Subject: [PATCH 219/361] Set berg%id everywhere %iceberg_num is set

- This calls the new generate_id() function and stores
  the 64-bit %id in the iceberg everywhere we first create
  %iceberg_num.
---
 icebergs.F90    |  3 ++-
 icebergs_io.F90 | 21 +++++++++++----------
 2 files changed, 13 insertions(+), 11 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 035be60..f85e15b 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -43,6 +43,7 @@ module ice_bergs
 use ice_bergs_framework, only: monitor_a_berg
 use ice_bergs_framework, only: is_point_within_xi_yj_bounds
 use ice_bergs_framework, only: test_check_for_duplicate_ids_in_list
+use ice_bergs_framework, only: generate_id
 
 use ice_bergs_io,        only: ice_bergs_io_init,write_restart,write_trajectory
 use ice_bergs_io,        only: read_restart_bergs,read_restart_bergs_orig,read_restart_calving
@@ -4044,6 +4045,7 @@ subroutine calve_icebergs(bergs)
           newberg%start_lat=newberg%lat
           newberg%start_year=bergs%current_year
           newberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i+(iNg*(j-1)))  ! unique number for each iceberg
+          newberg%id = generate_id(grd, i, j)
           newberg%start_day=bergs%current_yearday+ddt/86400.
           newberg%start_mass=bergs%initial_mass(k)
           newberg%mass_scaling=bergs%mass_scaling(k)
@@ -4065,7 +4067,6 @@ subroutine calve_icebergs(bergs)
           icnt=icnt+1
           bergs%nbergs_calved=bergs%nbergs_calved+1
           bergs%nbergs_calved_by_class(k)=bergs%nbergs_calved_by_class(k)+1
-          grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
         enddo
         icntmax=max(icntmax,icnt)
       enddo
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 6ed119c..2164895 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -40,6 +40,7 @@ module ice_bergs_io
 use ice_bergs_framework, only: ignore_ij_restart, use_slow_find,generate_test_icebergs,print_berg
 use ice_bergs_framework, only: force_all_pes_traj
 use ice_bergs_framework, only: check_for_duplicates_in_parallel
+use ice_bergs_framework, only: split_id, id_from_2_ints, generate_id
 
 implicit none ; private
 
@@ -560,7 +561,7 @@ subroutine read_restart_bergs_orig(bergs,Time)
         localberg%iceberg_num=get_int(ncid, iceberg_numid, k)
       else
         localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
-        grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
+        localberg%id = generate_id(grd, i, j)
       endif
       localberg%start_day=get_double(ncid, start_dayid, k)
       localberg%start_mass=get_double(ncid, start_massid, k)
@@ -677,25 +678,25 @@ subroutine generate_bergs_orig(bergs, Time)
       localberg%uvel=1.
       localberg%vvel=0.
       localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
-      grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
+      localberg%id = generate_id(grd, i, j)
       call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
       !Berg B
       localberg%uvel=-1.
       localberg%vvel=0.
       localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
-      grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
+      localberg%id = generate_id(grd, i, j)
       call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
       !Berg C
       localberg%uvel=0.
       localberg%vvel=1.
       localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
-      grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
+      localberg%id = generate_id(grd, i, j)
       call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
       !Berg D
       localberg%uvel=0.
       localberg%vvel=-1.
       localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
-      grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
+      localberg%id = generate_id(grd, i, j)
       call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
     endif
   enddo; enddo
@@ -892,7 +893,7 @@ subroutine read_restart_bergs(bergs,Time)
       if (bergs%grd%area(localberg%ine,localberg%jne) .ne. 0)  then
         if (iceberg_num(k)==-1) then ! If using an old_restart then iceberg_num needs to be generated
           localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(localberg%ine,localberg%jne))+(localberg%ine+(iNg*(localberg%jne-1)))
-          grd%iceberg_counter_grd(localberg%ine,localberg%jne)=grd%iceberg_counter_grd(localberg%ine,localberg%jne)+1
+          localberg%id = generate_id(grd, localberg%ine, localberg%jne)
         endif
         call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg)
       else
@@ -1058,22 +1059,22 @@ subroutine generate_bergs(bergs,Time)
       !Berg A
       call loc_set_berg_pos(grd, 0.9, 0.5, 1., 0., localberg)
       localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
-      grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
+      localberg%id = generate_id(grd, i, j)
       call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
       !Berg B
       call loc_set_berg_pos(grd, 0.1, 0.5, -1., 0., localberg)
       localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
-      grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
+      localberg%id = generate_id(grd, i, j)
       call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
       !Berg C
       call loc_set_berg_pos(grd, 0.5, 0.9, 0., 1., localberg)
       localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
-      grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
+      localberg%id = generate_id(grd, i, j)
       call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
       !Berg D
       call loc_set_berg_pos(grd, 0.5, 0.1, 0., -1., localberg)
       localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
-      grd%iceberg_counter_grd(i,j)=grd%iceberg_counter_grd(i,j)+1
+      localberg%id = generate_id(grd, i, j)
       call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
     endif
   enddo; enddo

From 04dfea1556bc51ed30970aaaa990af14ed8822b7 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Thu, 15 Jun 2017 23:36:19 -0400
Subject: [PATCH 220/361] Fix for when restart files have zero bergs

- When the restart file exists but has zero length data in then
  the model was correctly NOT allocating but was then proceeding to
  try and read into the non-allocated array. This avoids that condition.
- I thought this was fixed before but apparently not.
---
 icebergs_io.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 6ed119c..2293f18 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -800,7 +800,7 @@ subroutine read_restart_bergs(bergs,Time)
      allocate(iceberg_num(nbergs_in_file))
   endif
 
-  if (found_restart) then
+  if (found_restart .and. nbergs_in_file > 0) then
      call read_unlimited_axis(filename,'lon',lon,domain=grd%domain)
      call read_unlimited_axis(filename,'lat',lat,domain=grd%domain)
      call read_unlimited_axis(filename,'uvel',uvel,domain=grd%domain)

From 85dfb937cbdc1cb36d11b242341f2794b6157109 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Fri, 16 Jun 2017 00:11:49 -0400
Subject: [PATCH 221/361] Removed use/public lines for pack_berg_into_buffer2

- There were unnecessary use and public lines for the functions
  pack_berg_into_buffer2() and unpack_berg_from_buffer2().
---
 icebergs_framework.F90 | 1 -
 icebergs_io.F90        | 1 -
 2 files changed, 2 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index f73394c..a3efbd7 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -59,7 +59,6 @@ module ice_bergs_framework
 public ice_bergs_framework_init
 public send_bergs_to_other_pes
 public update_halo_icebergs
-public pack_berg_into_buffer2, unpack_berg_from_buffer2
 public pack_traj_into_buffer2, unpack_traj_from_buffer2
 public increase_ibuffer
 public add_new_berg_to_list, count_out_of_order, check_for_duplicates
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index b272bf6..2d0d831 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -26,7 +26,6 @@ module ice_bergs_io
 use time_manager_mod, only: time_type, get_date, get_time, set_date, operator(-)
 
 use ice_bergs_framework, only: icebergs_gridded, xyt, iceberg, icebergs, buffer, bond
-use ice_bergs_framework, only: pack_berg_into_buffer2,unpack_berg_from_buffer2
 use ice_bergs_framework, only: pack_traj_into_buffer2,unpack_traj_from_buffer2
 use ice_bergs_framework, only: find_cell,find_cell_by_search,count_bergs,is_point_in_cell,pos_within_cell,append_posn
 use ice_bergs_framework, only: count_bonds, form_a_bond, find_individual_iceberg

From c8d5b63a4bfff780544376c37cc5981eadf95e32 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Fri, 16 Jun 2017 00:43:30 -0400
Subject: [PATCH 222/361] Re-factor pack_berg_into_buffer2()

- Previously the pack_berg_into_buffer2() and unpack_berg_from_buffer2()
  routines would place particular members in the berg type into a
  particular position of a 2D array. This makes adding variables or
  re-ordering variables cumbersome since fixed integer locations have to
  be made consistent.
- Now we treat a row of the 2d array as a fifo stack so that only the
  order matters in the code, and the absolute position does not need to
  appear in the code. The order of packing and unpacking must still be
  consistent.
---
 icebergs_framework.F90 | 188 ++++++++++++++++++++++++++---------------
 1 file changed, 120 insertions(+), 68 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index a3efbd7..7977dad 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -429,6 +429,16 @@ module ice_bergs_framework
 character(len=128) :: version = 'unknown' !< Version of file
 #endif
 
+!> Set a value in the buffer at position (counter,n) after incrementing counter
+interface push_buffer_value
+  module procedure push_buffer_rvalue, push_buffer_ivalue
+end interface
+
+!> Get a value in the buffer at position (counter,n) after incrementing counter
+interface pull_buffer_value
+  module procedure pull_buffer_rvalue, pull_buffer_ivalue
+end interface
+
 contains
 
 !> Initializes parallel framework
@@ -1813,47 +1823,47 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
   if (.not.associated(buff)) call increase_ibuffer(buff,n,buffer_width)
   if (n>buff%size) call increase_ibuffer(buff,n,buffer_width)
 
-  buff%data(1,n)=berg%lon
-  buff%data(2,n)=berg%lat
-  buff%data(3,n)=berg%uvel
-  buff%data(4,n)=berg%vvel
-  buff%data(5,n)=berg%xi
-  buff%data(6,n)=berg%yj
-  buff%data(7,n)=berg%start_lon
-  buff%data(8,n)=berg%start_lat
-  buff%data(9,n)=float(berg%start_year)
-  buff%data(10,n)=berg%start_day
-  buff%data(11,n)=berg%start_mass
-  buff%data(12,n)=berg%mass
-  buff%data(13,n)=berg%thickness
-  buff%data(14,n)=berg%width
-  buff%data(15,n)=berg%length
-  buff%data(16,n)=berg%mass_scaling
-  buff%data(17,n)=berg%mass_of_bits
-  buff%data(18,n)=berg%heat_density
-  buff%data(19,n)=berg%ine
-  buff%data(20,n)=berg%jne
-  buff%data(21,n)=berg%axn  !Alon
-  buff%data(22,n)=berg%ayn  !Alon
-  buff%data(23,n)=berg%bxn  !Alon
-  buff%data(24,n)=berg%byn  !Alon
-  buff%data(25,n)=float(berg%iceberg_num)
-  buff%data(26,n)=berg%halo_berg
-  buff%data(27,n)=berg%static_berg
+  counter = 0
+  call push_buffer_value(buff%data(:,n), counter, berg%lon)
+  call push_buffer_value(buff%data(:,n), counter, berg%lat)
+  call push_buffer_value(buff%data(:,n), counter, berg%uvel)
+  call push_buffer_value(buff%data(:,n), counter, berg%vvel)
+  call push_buffer_value(buff%data(:,n), counter, berg%xi)
+  call push_buffer_value(buff%data(:,n), counter, berg%yj)
+  call push_buffer_value(buff%data(:,n), counter, berg%start_lon)
+  call push_buffer_value(buff%data(:,n), counter, berg%start_lat)
+  call push_buffer_value(buff%data(:,n), counter, berg%start_year)
+  call push_buffer_value(buff%data(:,n), counter, berg%start_day)
+  call push_buffer_value(buff%data(:,n), counter, berg%start_mass)
+  call push_buffer_value(buff%data(:,n), counter, berg%mass)
+  call push_buffer_value(buff%data(:,n), counter, berg%thickness)
+  call push_buffer_value(buff%data(:,n), counter, berg%width)
+  call push_buffer_value(buff%data(:,n), counter, berg%length)
+  call push_buffer_value(buff%data(:,n), counter, berg%mass_scaling)
+  call push_buffer_value(buff%data(:,n), counter, berg%mass_of_bits)
+  call push_buffer_value(buff%data(:,n), counter, berg%heat_density)
+  call push_buffer_value(buff%data(:,n), counter, berg%ine)
+  call push_buffer_value(buff%data(:,n), counter, berg%jne)
+  call push_buffer_value(buff%data(:,n), counter, berg%axn)
+  call push_buffer_value(buff%data(:,n), counter, berg%ayn)
+  call push_buffer_value(buff%data(:,n), counter, berg%bxn)
+  call push_buffer_value(buff%data(:,n), counter, berg%byn)
+  call push_buffer_value(buff%data(:,n), counter, berg%iceberg_num)
+  call push_buffer_value(buff%data(:,n), counter, berg%halo_berg)
+  call push_buffer_value(buff%data(:,n), counter, berg%static_berg)
 
   if (max_bonds .gt. 0) then
-    counter=27 !how many data points being passed so far (must match above)
     current_bond=>berg%first_bond
     do k = 1,max_bonds
       if (associated(current_bond)) then
-        buff%data(counter+(3*(k-1)+1),n)=float(current_bond%other_berg_num)
-        buff%data(counter+(3*(k-1)+2),n)=float(current_bond%other_berg_ine)
-        buff%data(counter+(3*(k-1)+3),n)=float(current_bond%other_berg_jne)
+        call push_buffer_value(buff%data(:,n), counter, current_bond%other_berg_num)
+        call push_buffer_value(buff%data(:,n), counter, current_bond%other_berg_ine)
+        call push_buffer_value(buff%data(:,n), counter, current_bond%other_berg_jne)
         current_bond=>current_bond%next_bond
       else
-        buff%data(counter+(3*(k-1)+1),n)=0.
-        buff%data(counter+(3*(k-1)+2),n)=0.
-        buff%data(counter+(3*(k-1)+3),n)=0.
+        call push_buffer_value(buff%data(:,n), counter, 0)
+        call push_buffer_value(buff%data(:,n), counter, 0)
+        call push_buffer_value(buff%data(:,n), counter, 0)
       endif
     enddo
   endif
@@ -1865,6 +1875,50 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
 
 end subroutine pack_berg_into_buffer2
 
+!> Set a real value in the buffer at position (counter) after incrementing counter
+subroutine push_buffer_rvalue(vbuf, counter, val)
+  real, dimension(:), intent(inout) :: vbuf    !< Buffer vector to push value into
+  integer,            intent(inout) :: counter !< Position to increment
+  real,               intent(in)    :: val     !< Value to place in buffer
+
+  counter = counter + 1
+  vbuf(counter) = val
+
+end subroutine push_buffer_rvalue
+
+!> Set an integer value in the buffer at position (counter) after incrementing counter
+subroutine push_buffer_ivalue(vbuf, counter, val)
+  real, dimension(:), intent(inout) :: vbuf    !< Buffer vector to push value into
+  integer,            intent(inout) :: counter !< Position to increment
+  integer,            intent(in)    :: val     !< Value to place in buffer
+
+  counter = counter + 1
+  vbuf(counter) = float(val)
+
+end subroutine push_buffer_ivalue
+
+!> Get a real value from the buffer at position (counter) after incrementing counter
+subroutine pull_buffer_rvalue(vbuf, counter, val)
+  real, dimension(:), intent(in)    :: vbuf    !< Buffer vector to pull value from
+  integer,            intent(inout) :: counter !< Position to increment
+  real,               intent(out)   :: val     !< Value to get from buffer
+
+  counter = counter + 1
+  val = vbuf(counter)
+
+end subroutine pull_buffer_rvalue
+
+!> Get an integer value from the buffer at position (counter) after incrementing counter
+subroutine pull_buffer_ivalue(vbuf, counter, val)
+  real, dimension(:), intent(in)    :: vbuf    !< Buffer vector to pull value from
+  integer,            intent(inout) :: counter !< Position to increment
+  integer,            intent(out)   :: val     !< Value to get from buffer
+
+  counter = counter + 1
+  val = nint(vbuf(counter))
+
+end subroutine pull_buffer_ivalue
+
 subroutine clear_berg_from_partners_bonds(berg)
 ! Arguments
 type(iceberg), intent(in), pointer :: berg
@@ -1931,33 +1985,34 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
   force_app = .false.
   if(present(force_append)) force_app = force_append
 
-  localberg%lon=buff%data(1,n)
-  localberg%lat=buff%data(2,n)
-  localberg%uvel=buff%data(3,n)
-  localberg%vvel=buff%data(4,n)
-  localberg%xi=buff%data(5,n)
-  localberg%yj=buff%data(6,n)
-  localberg%start_lon=buff%data(7,n)
-  localberg%start_lat=buff%data(8,n)
-  localberg%start_year=nint(buff%data(9,n))
-  localberg%start_day=buff%data(10,n)
-  localberg%start_mass=buff%data(11,n)
-  localberg%mass=buff%data(12,n)
-  localberg%thickness=buff%data(13,n)
-  localberg%width=buff%data(14,n)
-  localberg%length=buff%data(15,n)
-  localberg%mass_scaling=buff%data(16,n)
-  localberg%mass_of_bits=buff%data(17,n)
-  localberg%heat_density=buff%data(18,n)
-
-  localberg%axn=buff%data(21,n)
-  localberg%ayn=buff%data(22,n)
-  localberg%bxn=buff%data(23,n)
-  localberg%byn=buff%data(24,n)
-  localberg%iceberg_num=nint(buff%data(25,n))
-  localberg%halo_berg=buff%data(26,n)
-  localberg%static_berg=buff%data(27,n)
-  counter=27 !how many data points being passed so far (must match largest number directly above)
+  counter = 0
+  call pull_buffer_value(buff%data(:,n), counter, localberg%lon)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%lat)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%uvel)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%vvel)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%xi)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%yj)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%start_lon)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%start_lat)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%start_year)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%start_day)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%start_mass)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%mass)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%thickness)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%width)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%length)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%mass_scaling)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%mass_of_bits)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%heat_density)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%ine)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%jne)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%axn)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%ayn)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%bxn)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%byn)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%iceberg_num)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%halo_berg)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%static_berg)
 
   !These quantities no longer need to be passed between processors
   localberg%uvel_old=localberg%uvel
@@ -1967,10 +2022,7 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
 
   ! force_app=.true.
   if(force_app) then !force append with origin ine,jne (for I/O)
-
-    localberg%ine=buff%data(19,n)
-    localberg%jne=buff%data(20,n)
-    call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg,quick,this)
+    call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg, quick, this)
   else
     lres=find_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
     if (lres) then
@@ -2006,9 +2058,9 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
   this%first_bond=>null()
   if (max_bonds .gt. 0) then
     do k = 1,max_bonds
-      other_berg_num=nint(buff%data(counter+(3*(k-1)+1),n))
-      other_berg_ine=nint(buff%data(counter+(3*(k-1)+2),n))
-      other_berg_jne=nint(buff%data(counter+(3*(k-1)+3),n))
+      call pull_buffer_value(buff%data(:,n), counter, other_berg_num)
+      call pull_buffer_value(buff%data(:,n), counter, other_berg_ine)
+      call pull_buffer_value(buff%data(:,n), counter, other_berg_jne)
       if (other_berg_num .gt. 0.5) then
         call form_a_bond(this, other_berg_num, other_berg_ine, other_berg_jne)
       endif

From 905f4f25f578fa9893254651efde4cbd66bd3bb9 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Fri, 16 Jun 2017 12:10:11 -0400
Subject: [PATCH 223/361] Modularized generate_id(), added convert_old_id()

- In order to switch over to using the 64-bit IDs I needed to be able
  calculate new 64-bit IDs from old 32-bit IDs which involved splitting
  the generate_id() function into more modular parts.
---
 icebergs_framework.F90 | 51 +++++++++++++++++++++++++++++++++++++++---
 1 file changed, 48 insertions(+), 3 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 7977dad..89cbd0c 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -2352,11 +2352,9 @@ integer(kind=8) function generate_id(grd, i, j)
   integer,                intent(in) :: j   !< j-index of calving location
   ! Local variables
   integer :: ij ! Hash of i,j
-  integer :: iNg ! Total number of points globally in i direction
 
-  iNg=(grd%ieg-grd%isg+1)
   ! ij is unique number for each grid cell (32-bit integers allow for ~1/100th degree global resolution)
-  ij = i + (iNg*(j-1))
+  ij = ij_component_of_id(grd, i, j)
   ! Generate a 64-bit id
   generate_id = id_from_2_ints( grd%iceberg_counter_grd(i,j), ij )
   ! Increment counter in calving cell
@@ -2364,6 +2362,53 @@ integer(kind=8) function generate_id(grd, i, j)
 
 end function generate_id
 
+!> Convert an old 32-bit id to a 64-bit id
+integer(kind=8) function convert_old_id(grd, old_id)
+  type(icebergs_gridded), pointer    :: grd    !< Container for gridded fields
+  integer,                intent(in) :: old_id !< 32-bit iceberg id
+  ! Local variables
+  integer :: cnt ! Counter component
+  integer :: ij ! Hash of i,j
+  integer :: i,j ! Cell indexes
+  integer :: iNg, jNg, ncells ! Shape and size of the global grid
+
+  ! Number cells in the grid
+  iNg = grd%ieg - grd%isg + 1
+  jNg = grd%jeg - grd%jsg + 1
+  ncells = iNg * jNg
+
+  ! cnt is the cell-based counter
+  cnt = old_id / ncells
+  ! ij is the has of i,j
+  ij = mod( old_id, ncells )
+
+  ! i,j should be the cells the berg was calved in
+  j = ij / iNg
+  i = mod( ij, iNg )
+
+  ij = ij_component_of_id(grd, i, j)
+  convert_old_id = id_from_2_ints( cnt, ij )
+
+end function convert_old_id
+
+!> Calculate the location-derived component of an iceberg id which is a hash of the i,j-indexes for the cell
+integer function ij_component_of_id(grd, i, j)
+  type(icebergs_gridded), pointer    :: grd !< Container for gridded fields
+  integer,                intent(in) :: i   !< i-index of calving location
+  integer,                intent(in) :: j   !< j-index of calving location
+  ! Local variables
+  integer :: ij ! Hash of i,j
+  integer :: iNg ! Zonal size of the global grid
+
+  ! Using the current grid shape maximizes the numbers of IDs that can be represented
+  ! allowing up to 30-minute uniform global resolution, or potentially finer if non-uniform. 
+  iNg = grd%ieg - grd%isg + 1
+
+  ! ij_component_of_id is unique number for each grid cell (32-bit integers allow for ~1/100th degree global resolution)
+  ij_component_of_id = i + ( iNg * ( j - 1 ) )
+
+end function ij_component_of_id
+
 !> Prints a particular berg's vitals
 !!
 !! All lists are scanned and if a berg has the identifier equal to

From a5d3576878aa0406a73de87acc58077e3d3af08a Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Fri, 16 Jun 2017 12:47:35 -0400
Subject: [PATCH 224/361] Use push/pull_buffer_value() in
 pack_traj_into_buffer2()

- As for pack_berg_into_buffer2(), the trajectory packing and unpacking
  now uses the FIFO stack-style approach.
---
 icebergs_framework.F90 | 153 +++++++++++++++++++++--------------------
 1 file changed, 79 insertions(+), 74 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 89cbd0c..14f759d 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -2114,93 +2114,98 @@ end subroutine increase_ibuffer
 
 !> Packs a trajectory entry into a buffer
 subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj)
-! Arguments
-type(xyt), pointer :: traj !< Trajectory entry to pack
-type(buffer), pointer :: buff !< Buffer to pack entry into
-integer, intent(in) :: n !< Position in buffer to place entry
-logical, intent(in) :: save_short_traj !< If true, only use a subset of trajectory data
+  ! Arguments
+  type(xyt), pointer :: traj !< Trajectory entry to pack
+  type(buffer), pointer :: buff !< Buffer to pack entry into
+  integer, intent(in) :: n !< Position in buffer to place entry
+  logical, intent(in) :: save_short_traj !< If true, only use a subset of trajectory data
+  ! Local variables
+  integer :: counter ! Position in stack
 
   if (.not.associated(buff)) call increase_ibuffer(buff,n,buffer_width_traj)
   if (n>buff%size) call increase_ibuffer(buff,n,buffer_width_traj)
 
-  buff%data(1,n)=traj%lon
-  buff%data(2,n)=traj%lat
-  buff%data(3,n)=float(traj%year)
-  buff%data(4,n)=traj%day
-  buff%data(5,n)=float(traj%iceberg_num)
+  counter = 0
+  call push_buffer_value(buff%data(:,n),counter,traj%lon)
+  call push_buffer_value(buff%data(:,n),counter,traj%lat)
+  call push_buffer_value(buff%data(:,n),counter,traj%year)
+  call push_buffer_value(buff%data(:,n),counter,traj%day)
+  call push_buffer_value(buff%data(:,n),counter,traj%iceberg_num)
   if (.not. save_short_traj) then
-    buff%data(6,n)=traj%uvel
-    buff%data(7,n)=traj%vvel
-    buff%data(8,n)=traj%mass
-    buff%data(9,n)=traj%mass_of_bits
-    buff%data(10,n)=traj%heat_density
-    buff%data(11,n)=traj%thickness
-    buff%data(12,n)=traj%width
-    buff%data(13,n)=traj%length
-    buff%data(14,n)=traj%uo
-    buff%data(15,n)=traj%vo
-    buff%data(16,n)=traj%ui
-    buff%data(17,n)=traj%vi
-    buff%data(18,n)=traj%ua
-    buff%data(19,n)=traj%va
-    buff%data(20,n)=traj%ssh_x
-    buff%data(21,n)=traj%ssh_y
-    buff%data(22,n)=traj%sst
-    buff%data(23,n)=traj%cn
-    buff%data(24,n)=traj%hi
-    buff%data(25,n)=traj%axn !Alon
-    buff%data(26,n)=traj%ayn !Alon
-    buff%data(27,n)=traj%bxn !Alon
-    buff%data(28,n)=traj%byn !Alon
-    buff%data(29,n)=traj%halo_berg !Alon
-    buff%data(30,n)=traj%static_berg !Alon
-    buff%data(31,n)=traj%sss
+    call push_buffer_value(buff%data(:,n),counter,traj%uvel)
+    call push_buffer_value(buff%data(:,n),counter,traj%vvel)
+    call push_buffer_value(buff%data(:,n),counter,traj%mass)
+    call push_buffer_value(buff%data(:,n),counter,traj%mass_of_bits)
+    call push_buffer_value(buff%data(:,n),counter,traj%heat_density)
+    call push_buffer_value(buff%data(:,n),counter,traj%thickness)
+    call push_buffer_value(buff%data(:,n),counter,traj%width)
+    call push_buffer_value(buff%data(:,n),counter,traj%length)
+    call push_buffer_value(buff%data(:,n),counter,traj%uo)
+    call push_buffer_value(buff%data(:,n),counter,traj%vo)
+    call push_buffer_value(buff%data(:,n),counter,traj%ui)
+    call push_buffer_value(buff%data(:,n),counter,traj%vi)
+    call push_buffer_value(buff%data(:,n),counter,traj%ua)
+    call push_buffer_value(buff%data(:,n),counter,traj%va)
+    call push_buffer_value(buff%data(:,n),counter,traj%ssh_x)
+    call push_buffer_value(buff%data(:,n),counter,traj%ssh_y)
+    call push_buffer_value(buff%data(:,n),counter,traj%sst)
+    call push_buffer_value(buff%data(:,n),counter,traj%cn)
+    call push_buffer_value(buff%data(:,n),counter,traj%hi)
+    call push_buffer_value(buff%data(:,n),counter,traj%axn)
+    call push_buffer_value(buff%data(:,n),counter,traj%ayn)
+    call push_buffer_value(buff%data(:,n),counter,traj%bxn)
+    call push_buffer_value(buff%data(:,n),counter,traj%byn)
+    call push_buffer_value(buff%data(:,n),counter,traj%halo_berg)
+    call push_buffer_value(buff%data(:,n),counter,traj%static_berg)
+    call push_buffer_value(buff%data(:,n),counter,traj%sss)
   endif
 
 end subroutine pack_traj_into_buffer2
 
 !> Unpacks a trajectory entry from a buffer
 subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj)
-! Arguments
-type(xyt), pointer :: first !< Trajectory list
-type(buffer), pointer :: buff !< Buffer from which to unpack
-integer, intent(in) :: n !< Position in buffer to unpack
-logical, intent(in) :: save_short_traj !< If true, only use a subset of trajectory data
-! Local variables
-type(xyt) :: traj
+  ! Arguments
+  type(xyt), pointer :: first !< Trajectory list
+  type(buffer), pointer :: buff !< Buffer from which to unpack
+  integer, intent(in) :: n !< Position in buffer to unpack
+  logical, intent(in) :: save_short_traj !< If true, only use a subset of trajectory data
+  ! Local variables
+  type(xyt) :: traj
+  integer :: counter ! Position in stack
 
-  traj%lon=buff%data(1,n)
-  traj%lat=buff%data(2,n)
-  traj%year=nint(buff%data(3,n))
-  traj%day=buff%data(4,n)
-  traj%iceberg_num=nint(buff%data(5,n))
+  counter = 0
+  call pull_buffer_value(buff%data(:,n),counter,traj%lon)
+  call pull_buffer_value(buff%data(:,n),counter,traj%lat)
+  call pull_buffer_value(buff%data(:,n),counter,traj%year)
+  call pull_buffer_value(buff%data(:,n),counter,traj%day)
+  call pull_buffer_value(buff%data(:,n),counter,traj%iceberg_num)
   if (.not. save_short_traj) then
-    traj%uvel=buff%data(6,n)
-    traj%vvel=buff%data(7,n)
-    traj%mass=buff%data(8,n)
-    traj%mass_of_bits=buff%data(9,n)
-    traj%heat_density=buff%data(10,n)
-    traj%thickness=buff%data(11,n)
-    traj%width=buff%data(12,n)
-    traj%length=buff%data(13,n)
-    traj%uo=buff%data(14,n)
-    traj%vo=buff%data(15,n)
-    traj%ui=buff%data(16,n)
-    traj%vi=buff%data(17,n)
-    traj%ua=buff%data(18,n)
-    traj%va=buff%data(19,n)
-    traj%ssh_x=buff%data(20,n)
-    traj%ssh_y=buff%data(21,n)
-    traj%sst=buff%data(22,n)
-    traj%cn=buff%data(23,n)
-    traj%hi=buff%data(24,n)
-    traj%axn=buff%data(25,n) !Alon
-    traj%ayn=buff%data(26,n) !Alon
-    traj%bxn=buff%data(27,n) !Alon
-    traj%byn=buff%data(28,n) !Alon
-    traj%halo_berg=buff%data(29,n) !Alon
-    traj%static_berg=buff%data(30,n) !Alon
-    traj%sss=buff%data(31,n)
+    call pull_buffer_value(buff%data(:,n),counter,traj%uvel)
+    call pull_buffer_value(buff%data(:,n),counter,traj%vvel)
+    call pull_buffer_value(buff%data(:,n),counter,traj%mass)
+    call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_bits)
+    call pull_buffer_value(buff%data(:,n),counter,traj%heat_density)
+    call pull_buffer_value(buff%data(:,n),counter,traj%thickness)
+    call pull_buffer_value(buff%data(:,n),counter,traj%width)
+    call pull_buffer_value(buff%data(:,n),counter,traj%length)
+    call pull_buffer_value(buff%data(:,n),counter,traj%uo)
+    call pull_buffer_value(buff%data(:,n),counter,traj%vo)
+    call pull_buffer_value(buff%data(:,n),counter,traj%ui)
+    call pull_buffer_value(buff%data(:,n),counter,traj%vi)
+    call pull_buffer_value(buff%data(:,n),counter,traj%ua)
+    call pull_buffer_value(buff%data(:,n),counter,traj%va)
+    call pull_buffer_value(buff%data(:,n),counter,traj%ssh_x)
+    call pull_buffer_value(buff%data(:,n),counter,traj%ssh_y)
+    call pull_buffer_value(buff%data(:,n),counter,traj%sst)
+    call pull_buffer_value(buff%data(:,n),counter,traj%cn)
+    call pull_buffer_value(buff%data(:,n),counter,traj%hi)
+    call pull_buffer_value(buff%data(:,n),counter,traj%axn)
+    call pull_buffer_value(buff%data(:,n),counter,traj%ayn)
+    call pull_buffer_value(buff%data(:,n),counter,traj%bxn)
+    call pull_buffer_value(buff%data(:,n),counter,traj%byn)
+    call pull_buffer_value(buff%data(:,n),counter,traj%halo_berg)
+    call pull_buffer_value(buff%data(:,n),counter,traj%static_berg)
+    call pull_buffer_value(buff%data(:,n),counter,traj%sss)
   endif
   call append_posn(first, traj)
 

From bbde6c246895ab6fbb9cc1b85fd80083eda7ba9c Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Fri, 16 Jun 2017 13:59:11 -0400
Subject: [PATCH 225/361] Set %id everywhere %iceberg_num is set

- %id is set everywhere that %iceberg_num is set.
- When resading restarts we convert the 32-bit id to a 64-bit id.
- New bergs are assigned both a 32-bit and 64-bit id.
---
 icebergs.F90           |  4 ++--
 icebergs_framework.F90 | 30 +++++++++++++++++++++++++-----
 icebergs_io.F90        |  8 ++++++--
 3 files changed, 33 insertions(+), 9 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index f85e15b..f63aad0 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -366,7 +366,7 @@ subroutine initialize_iceberg_bonds(bergs)
             r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) )
 
             !if (r_dist.gt.1000.) then  ! If the bergs are close together, then form a bond
-              call form_a_bond(berg, other_berg%iceberg_num, other_berg%ine, other_berg%jne, other_berg)
+              call form_a_bond(berg, other_berg%iceberg_num, other_berg%id, other_berg%ine, other_berg%jne, other_berg)
             !endif
           endif
           other_berg=>other_berg%next
@@ -5055,7 +5055,7 @@ subroutine rotpos_to_tang(lon, lat, x, y, iceberg_num_in)
   integer :: stderrunit, iceberg_num
 
   stderrunit = stderr()
-  iceberg_num=000
+  iceberg_num=0
   if (present(iceberg_num_in)) then
         iceberg_num=iceberg_num_in
   endif
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 14f759d..6229406 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -77,7 +77,7 @@ module ice_bergs_framework
 public is_point_within_xi_yj_bounds
 public test_check_for_duplicate_ids_in_list
 public check_for_duplicates_in_parallel
-public split_id, id_from_2_ints, generate_id
+public split_id, id_from_2_ints, generate_id, convert_old_id
 
 !> Container for gridded fields
 type :: icebergs_gridded
@@ -219,6 +219,7 @@ module ice_bergs_framework
   real :: heat_density !< Heat density of berg (???)
   integer :: year !< Year of this record (years)
   integer :: iceberg_num !< Iceberg identifier
+  integer(kind=8) :: id !< Iceberg identifier
   type(xyt), pointer :: next=>null() !< Next link in list
 end type xyt
 
@@ -1814,7 +1815,7 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
 integer, optional :: max_bonds_in !< <undocumented>
 !integer, intent(in) :: max_bonds  ! Change this later
 ! Local variables
-integer :: counter, k, max_bonds
+integer :: counter, k, max_bonds, id_cnt, id_ij
 type(bond), pointer :: current_bond
 
   max_bonds=0
@@ -1851,12 +1852,18 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
   call push_buffer_value(buff%data(:,n), counter, berg%iceberg_num)
   call push_buffer_value(buff%data(:,n), counter, berg%halo_berg)
   call push_buffer_value(buff%data(:,n), counter, berg%static_berg)
+  call split_id(berg%id, id_cnt, id_ij)
+  call push_buffer_value(buff%data(:,n), counter, id_cnt)
+  call push_buffer_value(buff%data(:,n), counter, id_ij)
 
   if (max_bonds .gt. 0) then
     current_bond=>berg%first_bond
     do k = 1,max_bonds
       if (associated(current_bond)) then
         call push_buffer_value(buff%data(:,n), counter, current_bond%other_berg_num)
+        call split_id(current_bond%other_id, id_cnt, id_ij)
+        call push_buffer_value(buff%data(:,n), counter, id_cnt)
+        call push_buffer_value(buff%data(:,n), counter, id_ij)
         call push_buffer_value(buff%data(:,n), counter, current_bond%other_berg_ine)
         call push_buffer_value(buff%data(:,n), counter, current_bond%other_berg_jne)
         current_bond=>current_bond%next_bond
@@ -1864,6 +1871,8 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
         call push_buffer_value(buff%data(:,n), counter, 0)
         call push_buffer_value(buff%data(:,n), counter, 0)
         call push_buffer_value(buff%data(:,n), counter, 0)
+        call push_buffer_value(buff%data(:,n), counter, 0)
+        call push_buffer_value(buff%data(:,n), counter, 0)
       endif
     enddo
   endif
@@ -1970,7 +1979,8 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
 type(iceberg) :: localberg
 type(iceberg), pointer :: this
 integer :: other_berg_num, other_berg_ine, other_berg_jne
-integer :: counter, k, max_bonds
+integer :: counter, k, max_bonds, id_cnt, id_ij
+integer(kind=8) :: id
 integer :: stderrunit
 logical :: force_app
 logical :: quick
@@ -2013,6 +2023,9 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
   call pull_buffer_value(buff%data(:,n), counter, localberg%iceberg_num)
   call pull_buffer_value(buff%data(:,n), counter, localberg%halo_berg)
   call pull_buffer_value(buff%data(:,n), counter, localberg%static_berg)
+  call pull_buffer_value(buff%data(:,n), counter, id_cnt)
+  call pull_buffer_value(buff%data(:,n), counter, id_ij)
+  localberg%id = id_from_2_ints(id_cnt, id_ij)
 
   !These quantities no longer need to be passed between processors
   localberg%uvel_old=localberg%uvel
@@ -2059,10 +2072,13 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
   if (max_bonds .gt. 0) then
     do k = 1,max_bonds
       call pull_buffer_value(buff%data(:,n), counter, other_berg_num)
+      call pull_buffer_value(buff%data(:,n), counter, id_cnt)
+      call pull_buffer_value(buff%data(:,n), counter, id_ij)
+      id = id_from_2_ints(id_cnt, id_ij)
       call pull_buffer_value(buff%data(:,n), counter, other_berg_ine)
       call pull_buffer_value(buff%data(:,n), counter, other_berg_jne)
       if (other_berg_num .gt. 0.5) then
-        call form_a_bond(this, other_berg_num, other_berg_ine, other_berg_jne)
+        call form_a_bond(this, other_berg_num, id, other_berg_ine, other_berg_jne)
       endif
     enddo
   endif
@@ -2741,12 +2757,13 @@ subroutine print_bergs(iochan, bergs, label)
 
 end subroutine print_bergs
 
-subroutine form_a_bond(berg, other_berg_num, other_berg_ine, other_berg_jne, other_berg)
+subroutine form_a_bond(berg, other_berg_num, other_id, other_berg_ine, other_berg_jne, other_berg)
 ! Arguments
 type(iceberg), pointer :: berg
 type(iceberg), optional,  pointer :: other_berg
 type(bond) , pointer :: new_bond, first_bond
 integer, intent(in) :: other_berg_num
+integer(kind=8), intent(in) :: other_id
 integer, optional  :: other_berg_ine, other_berg_jne
 integer :: stderrunit
 
@@ -2759,6 +2776,7 @@ subroutine form_a_bond(berg, other_berg_num, other_berg_ine, other_berg_jne, oth
   ! Step 1: Create a new bond
   allocate(new_bond)
   new_bond%other_berg_num=other_berg_num
+  new_bond%other_id=other_id
   if(present(other_berg)) then
     new_bond%other_berg=>other_berg
     new_bond%other_berg_ine=other_berg%ine
@@ -3120,6 +3138,7 @@ subroutine record_posn(bergs)
       posn%year=bergs%current_year
       posn%day=bergs%current_yearday
       posn%iceberg_num=posn%iceberg_num
+      posn%id=posn%id
       if (.not. bergs%save_short_traj) then !Not totally sure that this is correct
         posn%uvel=this%uvel
         posn%vvel=this%vvel
@@ -3220,6 +3239,7 @@ subroutine move_trajectory(bergs, berg)
   vals%lat=berg%start_lat
   vals%year=berg%start_year
   vals%iceberg_num=berg%iceberg_num
+  vals%id=berg%id
   vals%day=berg%start_day
   vals%mass=berg%start_mass
   call push_posn(berg%trajectory, vals)
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 2d0d831..aa9b536 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -39,7 +39,7 @@ module ice_bergs_io
 use ice_bergs_framework, only: ignore_ij_restart, use_slow_find,generate_test_icebergs,print_berg
 use ice_bergs_framework, only: force_all_pes_traj
 use ice_bergs_framework, only: check_for_duplicates_in_parallel
-use ice_bergs_framework, only: split_id, id_from_2_ints, generate_id
+use ice_bergs_framework, only: split_id, id_from_2_ints, generate_id, convert_old_id
 
 implicit none ; private
 
@@ -558,6 +558,7 @@ subroutine read_restart_bergs_orig(bergs,Time)
       localberg%start_year=get_int(ncid, start_yearid, k)
       if (iceberg_numid>0) then
         localberg%iceberg_num=get_int(ncid, iceberg_numid, k)
+        localberg%id = convert_old_id(grd, localberg%iceberg_num)
       else
         localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
         localberg%id = generate_id(grd, i, j)
@@ -876,6 +877,7 @@ subroutine read_restart_bergs(bergs,Time)
       localberg%start_lat=start_lat(k)
       localberg%start_year=start_year(k)
       localberg%iceberg_num=iceberg_num(k)
+      localberg%id=convert_old_id(grd, localberg%iceberg_num)
       localberg%start_day=start_day(k)
       localberg%start_mass=start_mass(k)
       localberg%mass_scaling=mass_scaling(k)
@@ -1152,6 +1154,7 @@ subroutine read_restart_bonds(bergs,Time)
                                       first_berg_ine,   &
                                       other_berg_jne,   &
                                       other_berg_ine
+integer(kind=8) :: id
 !integer, allocatable, dimension(:,:) :: iceberg_counter_grd
 
   ! Get the stderr unit number
@@ -1284,7 +1287,8 @@ subroutine read_restart_bonds(bergs,Time)
         if (first_berg_found) then
           number_partial_bonds=number_partial_bonds+1
           if (second_berg_found) then
-            call form_a_bond(first_berg, other_berg_num(k), other_berg_ine(k), other_berg_jne(k),  second_berg)
+            id = convert_old_id(grd, other_berg_num(k))
+            call form_a_bond(first_berg, other_berg_num(k), id, other_berg_ine(k), other_berg_jne(k),  second_berg)
             number_perfect_bonds=number_perfect_bonds+1
 
             !Counting number of bonds where the first bond is in the computational domain

From 1efcdafe00a95a2fb3327e2bd9c3834d0a43ab1a Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Fri, 16 Jun 2017 13:31:50 -0400
Subject: [PATCH 226/361] Use %id in all print statements

- To reduce amount of code that needs to edited when deprecating $iceberg_num
  I've uniformly updated every print statement that uses %iceberg_num.
---
 icebergs.F90           | 30 +++++++++++++--------------
 icebergs_framework.F90 | 46 +++++++++++++++++++++---------------------
 2 files changed, 38 insertions(+), 38 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index f63aad0..b4f789b 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -473,7 +473,7 @@ subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
     enddo
   endif
 
-  !print *,'IA_x=',IA_x,'IA_y',IA_y, berg%iceberg_num
+  !print *,'IA_x=',IA_x,'IA_y',IA_y, berg%id
   !print *,'P_ia_11',P_ia_11,'P_ia_12',P_ia_12, 'P_ia_21',P_ia_21,'P_ia_22', P_ia_22
   !print *, 'P_ia_times_u_x', P_ia_times_u_x, 'P_ia_times_u_y', P_ia_times_u_y
 
@@ -570,7 +570,7 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
     ! if (berg%iceberg_num .eq. 1) then
     !   print *, 'Comparing longitudes: ', lon1, lon2, r_dist_x, dlon
     !   print *, 'Comparing latitudes: ', lat1, lat2, r_dist_y, dlat
-    !   print *, 'Outside, iceberg_num, r_dist', berg%iceberg_num, r_dist,bonded
+    !   print *, 'Outside, id, r_dist', berg%id, r_dist,bonded
     !   print *, 'Halo_status', berg%halo_berg,other_berg%halo_berg
     ! endif
     ! print *, 'outside the loop',R1, R2,r_dist, bonded
@@ -595,10 +595,10 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
         !MP1
         !if (berg%iceberg_num .eq. 1) then
         !  !print *,  '************************************************************'
-        !  print *, 'INSIDE, r_dist', berg%iceberg_num, other_berg%iceberg_num, r_dist, bonded
+        !  print *, 'INSIDE, r_dist', berg%id, other_berg%id, r_dist, bonded
         !endif
         !print *, 'in the loop1', spring_coef, (M_min/M1), accel_spring,(R1+R2-r_dist)
-        !print *, 'in the loop2', IA_x, IA_y, R1, R2,r_dist, berg%iceberg_num,other_berg%iceberg_num
+        !print *, 'in the loop2', IA_x, IA_y, R1, R2,r_dist, berg%id,other_berg%id
         ! Damping force:
         ! Paralel velocity
         P_11=(r_dist_x*r_dist_x)/(r_dist**2)
@@ -616,7 +616,7 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
         P_ia_22=P_ia_22+p_ia_coef*P_22
         P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
         P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
-        !print *, 'Paralel: ',berg%iceberg_num,  p_ia_coef, IA_x, P_ia_11, P_ia_21,P_ia_12, P_ia_22
+        !print *, 'Paralel: ',berg%id,  p_ia_coef, IA_x, P_ia_11, P_ia_21,P_ia_12, P_ia_22
 
         ! Normal velocities
         P_11=1-P_11  ;  P_12=-P_12 ; P_21= -P_21 ;    P_22=1-P_22
@@ -630,7 +630,7 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
         P_ia_22=P_ia_22+p_ia_coef*P_22
         P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
         P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
-        !print *, 'Perp: ',berg%iceberg_num,  p_ia_coef, IA_x, P_ia_11, P_ia_21,P_ia_12, P_ia_22
+        !print *, 'Perp: ',berg%id,  p_ia_coef, IA_x, P_ia_11, P_ia_21,P_ia_12, P_ia_22
         !print *, 'P_11',P_11
         !print *, 'P_21',P_21
         !print *, 'P_12',P_12
@@ -887,7 +887,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
       RHS_x=RHS_x - (((P_ia_11*uvel)+(P_ia_12*vvel))-P_ia_times_u_x)
       RHS_y=RHS_y - (((P_ia_21*uvel)+(P_ia_22*vvel))-P_ia_times_u_y)
     endif
-    !print *,'Before calculation:', berg%iceberg_num, IA_x, IA_y, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y
+    !print *,'Before calculation:', berg%id, IA_x, IA_y, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y
   endif
 
   ! Solve for implicit accelerations
@@ -938,7 +938,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
 !MP4
   !    if (berg%iceberg_num .eq. 1) then
   !      print *, '***************************************************'
-  !      print *,'Iceberg_num, itloop', berg%iceberg_num, itloop
+  !      print *,'id, itloop', berg%id, itloop
   !      print *, 'P matrix:', P_ia_11, P_ia_12,P_ia_21,P_ia_22,P_ia_times_u_x, P_ia_times_u_x
   !      print *,'A_matrix', A11, A12, A21, A22
   !      print *,'IA_x IA_y', IA_x, IA_y
@@ -985,7 +985,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
           bergs%nspeeding_tickets=bergs%nspeeding_tickets+1
         else
           call error_mesg('diamonds, Speeding icebergs', 'Faster than the CFL!', WARNING)
-          write(stderrunit,*) 'diamonds, Speeding berg1! =',mpp_pe(), berg%iceberg_num
+          write(stderrunit,*) 'diamonds, Speeding berg1! =',mpp_pe(), berg%id
           write(stderrunit,*) 'diamonds, Speeding berg2, speed =',speed, loc_dx/dt
           write(stderrunit,*) 'diamonds, Speeding berg3, lat, lon =',lat,xi,yj
         endif
@@ -1012,7 +1012,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
     write(stderrunit,200) mpp_pe(),'Starting pars:', &
       'yr0=',berg%start_year, 'day0=',berg%start_day, &
       'lon0=',berg%start_lon, 'lat0=',berg%start_lat, 'mass0=',berg%start_mass, &
-      'sclng=',berg%mass_scaling, 'num0=',berg%iceberg_num
+      'sclng=',berg%mass_scaling, 'id0=',berg%id
     write(stderrunit,100) mpp_pe(),'Geometry:', &
       'M=',M, 'T=',T, 'D=',D, 'F=',F, 'W=',W, 'L=',L
     write(stderrunit,100) mpp_pe(),'delta U:', &
@@ -1790,7 +1790,7 @@ subroutine find_basal_melt(bergs, dvo, lat, salt, temp, Use_three_equation_model
         if (Sb_max_set .and. (Sbdry > Sb_max)) then
           if (debug) then
             call error_mesg('diamonds,Find basal melt', 'shelf_calc_flux: Irregular iteration for Sbdry (max).' ,WARNING)
-            print *, 'Sbdry error: iceberg_num,dvo,temp,salt,lat,thickness :',iceberg_num,dvo,temp,salt,lat,thickness
+            print *, 'Sbdry error: id,dvo,temp,salt,lat,thickness :',iceberg_num,dvo,temp,salt,lat,thickness
           endif
           out_of_bounds=.true.
           exit
@@ -1800,7 +1800,7 @@ subroutine find_basal_melt(bergs, dvo, lat, salt, temp, Use_three_equation_model
         if (Sb_min_set .and. (Sbdry < Sb_min)) then
           if (debug) then
             call error_mesg('diamonds,Find basal melt', 'shelf_calc_flux: Irregular iteration for Sbdry (min).' ,WARNING)
-            print *, 'Sbdry error: iceberg_num,dvo,temp,salt,lat,thickness :',iceberg_num,dvo,temp,salt,lat,thickness
+            print *, 'Sbdry error: id,dvo,temp,salt,lat,thickness :',iceberg_num,dvo,temp,salt,lat,thickness
           endif
           out_of_bounds=.true.
           exit
@@ -1911,7 +1911,7 @@ subroutine find_orientation_using_iceberg_bonds(grd, berg, orientation)
       other_berg=>current_bond%other_berg
       if (.not. associated(other_berg)) then !good place for debugging
         !One valid option: current iceberg is on the edge of halo, with other berg on the next pe (not influencing mass spreading)
-        !print *, 'Iceberg bond details:',berg%iceberg_num, current_bond%other_berg_num,berg%halo_berg, mpp_pe()
+        !print *, 'Iceberg bond details:',berg%id, current_bond%other_berg_num,berg%halo_berg, mpp_pe()
         !print *, 'Iceberg bond details2:',berg%ine, berg%jne, current_bond%other_berg_ine, current_bond%other_berg_jne
         !print *, 'Iceberg isd,ied,jsd,jed:',grd%isd, grd%ied, grd%jsd, grd%jed
         !print *, 'Iceberg isc,iec,jsc,jec:',grd%isc, grd%iec, grd%jsc, grd%jec
@@ -4282,7 +4282,7 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
     write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: latn=',latn,berg%lat
     write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u3,un,u0=',uvel3,uveln,berg%uvel
     write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v3,vn,v0=',vvel3,vveln,berg%vvel
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: iceberg_num=',berg%iceberg_num
+    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: id=',berg%id
     write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1=',&
          & dt*ax1
     write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ay1=',&
@@ -4730,7 +4730,7 @@ subroutine update_verlet_position(bergs, berg)
   call adjust_index_and_ground(grd, lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)  !Alon:"unclear which velocity to use here?"
 
   !if (bounced) then
-  !  print *, 'you have been bounce: big time!',mpp_pe(),berg%iceberg_num,lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag
+  !  print *, 'you have been bounce: big time!',mpp_pe(),berg%id,lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag
   !  berg%axn=0.0  ;  berg%ayn=0.0
   !  berg%bxn=0.0  ;  berg%byn=0.0
   !  berg%uvel=0.0 ;  berg%vvel=0.0
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 6229406..337d6af 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -1248,7 +1248,7 @@ subroutine update_halo_icebergs(bergs)
     do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
       this=>bergs%list(grdi,grdj)%first
       do while (associated(this))
-          write(stderrunit,*) 'A', this%iceberg_num, mpp_pe(), this%halo_berg, grdi, grdj
+          write(stderrunit,*) 'A', this%id, mpp_pe(), this%halo_berg, grdi, grdj
         this=>this%next
       enddo
     enddo; enddo
@@ -1281,7 +1281,7 @@ subroutine update_halo_icebergs(bergs)
     do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
       this=>bergs%list(grdi,grdj)%first
         do while (associated(this))
-        write(stderrunit,*) 'B', this%iceberg_num, mpp_pe(), this%halo_berg, grdi, grdj
+        write(stderrunit,*) 'B', this%id, mpp_pe(), this%halo_berg, grdi, grdj
       this=>this%next
       enddo
     enddo; enddo
@@ -1301,7 +1301,7 @@ subroutine update_halo_icebergs(bergs)
   do grdj = grd%jsc,grd%jec ; do grdi = grd%iec-halo_width+2,grd%iec
     this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
-    !write(stderrunit,*)  'sending east', this%iceberg_num, this%ine, this%jne, mpp_pe()
+    !write(stderrunit,*)  'sending east', this%id, this%ine, this%jne, mpp_pe()
       kick_the_bucket=>this
       this=>this%next
       nbergs_to_send_e=nbergs_to_send_e+1
@@ -1484,7 +1484,7 @@ subroutine update_halo_icebergs(bergs)
     do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
       this=>bergs%list(grdi,grdj)%first
       do while (associated(this))
-        write(stderrunit,*)  'C', this%iceberg_num, mpp_pe(), this%halo_berg,  grdi, grdj
+        write(stderrunit,*)  'C', this%id, mpp_pe(), this%halo_berg,  grdi, grdj
         this=>this%next
       enddo
     enddo; enddo
@@ -1942,11 +1942,11 @@ subroutine clear_berg_from_partners_bonds(berg)
   do while (associated(current_bond)) !Looping over bonds
     other_berg=>current_bond%other_berg
     if (associated(other_berg)) then
-      !write(stderrunit,*) , 'Other berg', berg%iceberg_num, other_berg%iceberg_num, mpp_pe()
+      !write(stderrunit,*) , 'Other berg', berg%id, other_berg%id, mpp_pe()
       matching_bond=>other_berg%first_bond
       do while (associated(matching_bond))  ! Looping over possible matching bonds in other_berg
         if (matching_bond%other_berg_num .eq. berg%iceberg_num) then
-          !write(stderrunit,*) , 'Clearing', berg%iceberg_num, matching_bond%other_berg_num,other_berg%iceberg_num, mpp_pe()
+          !write(stderrunit,*) , 'Clearing', berg%id, matching_bond%other_berg_num,other_berg%id, mpp_pe()
           matching_bond%other_berg=>null()
           matching_bond=>null()
         else
@@ -2702,31 +2702,31 @@ subroutine print_berg(iochan, berg, label, il, jl)
 ! Local variables
 
   write(iochan,'("diamonds, print_berg: ",2a,i5,a,i12,a,2f10.4,i5,f7.2,es12.4,f5.1)') &
-    label, 'pe=(', mpp_pe(), ') #=', berg%iceberg_num, ' start lon,lat,yr,day,mass,hb=', &
+    label, 'pe=(', mpp_pe(), ') #=', berg%id, ' start lon,lat,yr,day,mass,hb=', &
     berg%start_lon, berg%start_lat, berg%start_year, berg%start_day, berg%start_mass, berg%halo_berg
   if (present(il).and.present(jl)) then
     write(iochan,'("diamonds, print_berg: ",2a,i5,a,i12,a,2i5)') &
-      label, 'pe=(', mpp_pe(), ') #=', berg%iceberg_num, ' List i,j=',il,jl
+      label, 'pe=(', mpp_pe(), ') #=', berg%id, ' List i,j=',il,jl
   endif
   write(iochan,'("diamonds, print_berg: ",2a,i5,a,i12,a,2i5,a,2l2)') &
-    label, 'pe=(', mpp_pe(), ') #=', berg%iceberg_num, &
+    label, 'pe=(', mpp_pe(), ') #=', berg%id, &
     ' i,j=', berg%ine, berg%jne, &
     ' p,n=', associated(berg%prev), associated(berg%next)
   write(iochan,'("diamonds, print_berg: ",2a,i5,a,i12,3(a,2f14.8))') &
-    label, 'pe=(', mpp_pe(), ') #=', berg%iceberg_num, &
+    label, 'pe=(', mpp_pe(), ') #=', berg%id, &
     ' xi,yj=', berg%xi, berg%yj, &
     ' lon,lat=', berg%lon, berg%lat, &
     ' lon_old,lat_old=', berg%lon_old, berg%lat_old
   write(iochan,'("diamonds, print_berg: ",2a,i5,a,i12,2(a,2f14.8))') &
-    label, 'pe=(', mpp_pe(), ') #=', berg%iceberg_num, &
+    label, 'pe=(', mpp_pe(), ') #=', berg%id, &
     ' u,v=', berg%uvel, berg%vvel, &
     ' uvel_old,vvel_old=', berg%uvel_old, berg%vvel_old
   write(iochan,'("diamonds, print_berg: ",2a,i5,a,i12,2(a,2f14.8))') &
-    label, 'pe=(', mpp_pe(), ') #=', berg%iceberg_num, &
+    label, 'pe=(', mpp_pe(), ') #=', berg%id, &
     ' axn,ayn=', berg%axn, berg%ayn, &
     ' bxn,byn=', berg%bxn, berg%byn
   write(iochan,'("diamonds, print_berg: ",2a,i5,a,i12,3(a,2f14.8))') &
-    label, 'pe=(', mpp_pe(), ') #=', berg%iceberg_num, &
+    label, 'pe=(', mpp_pe(), ') #=', berg%id, &
     ' uo,vo=', berg%uo, berg%vo, &
     ' ua,va=', berg%ua, berg%va, &
     ' ui,vi=', berg%ui, berg%vi
@@ -2860,16 +2860,16 @@ subroutine show_all_bonds(bergs)
     do while (associated(berg)) ! loop over all bergs
       current_bond=>berg%first_bond
       do while (associated(current_bond)) ! loop over all bonds
-        print *, 'Show Bond1 :', berg%iceberg_num, current_bond%other_berg_num, current_bond%other_berg_ine, current_bond%other_berg_jne,  mpp_pe()
-        !print *, 'Current:', berg%iceberg_num, berg%ine, berg%jne,berg%halo_berg, mpp_pe()
+        print *, 'Show Bond1 :', berg%id, current_bond%other_berg_num, current_bond%other_berg_ine, current_bond%other_berg_jne,  mpp_pe()
+        !print *, 'Current:', berg%id, berg%ine, berg%jne,berg%halo_berg, mpp_pe()
         if  (associated(current_bond%other_berg)) then
           if (current_bond%other_berg%iceberg_num .ne. current_bond%other_berg_num) then
-            print *, 'Bond matching', berg%iceberg_num,current_bond%other_berg%iceberg_num, current_bond%other_berg_num,&
+            print *, 'Bond matching', berg%id,current_bond%other_berg%id, current_bond%other_berg_num,&
             berg%halo_berg,current_bond%other_berg%halo_berg ,mpp_pe()
             call error_mesg('diamonds, show all bonds:', 'The bonds are not matching properly!', FATAL)
           endif
         else
-            print *, 'This bond has an non-assosiated other berg :', berg%iceberg_num, current_bond%other_berg_num,&
+            print *, 'This bond has an non-assosiated other berg :', berg%id, current_bond%other_berg_num,&
             current_bond%other_berg_ine, current_bond%other_berg_jne, berg%halo_berg,  mpp_pe()
         endif
         current_bond=>current_bond%next_bond
@@ -2943,12 +2943,12 @@ subroutine connect_all_bonds(bergs)
           if (.not.bond_matched) then
             if (berg%halo_berg .lt. 0.5) then
               missing_bond=.true.
-              print * ,'non-halo berg unmatched: ', berg%iceberg_num, mpp_pe(), current_bond%other_berg_num, current_bond%other_berg_ine
+              print * ,'non-halo berg unmatched: ', berg%id, mpp_pe(), current_bond%other_berg_num, current_bond%other_berg_ine
               call error_mesg('diamonds, connect_all_bonds', 'A non-halo bond is missing!!!', FATAL)
             else  ! This is not a problem if the partner berg is not yet in the halo
               !if (  (current_bond%other_berg_ine .gt.grd%isd-1) .and. (current_bond%other_berg_ine .lt.grd%ied+1) &
                 !.and.  (current_bond%other_berg_jne .gt.grd%jsd-1) .and. (current_bond%other_berg_jne .lt.grd%jed+1) ) then
-                !print * ,'halo berg unmatched: ',mpp_pe(),  berg%iceberg_num, current_bond%other_berg_num, current_bond%other_berg_ine,current_bond%other_berg_jne
+                !print * ,'halo berg unmatched: ',mpp_pe(),  berg%id, current_bond%other_berg_num, current_bond%other_berg_ine,current_bond%other_berg_jne
                 !call error_mesg('diamonds, connect_all_bonds', 'A halo bond is missing!!!', WARNING)
               !endif
             endif
@@ -3005,7 +3005,7 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
         number_of_bonds=number_of_bonds+1
 
         ! ##### Beginning Quality Check on Bonds ######
-        !      print *, 'Quality check', mpp_pe(), berg%iceberg_num
+        !      print *, 'Quality check', mpp_pe(), berg%id
         if (quality_check) then
           num_unmatched_bonds=0
           num_unassosiated_bond_pairs=0
@@ -3027,13 +3027,13 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
             enddo  ! End of loop over the other berg's bonds.
 
             if (bond_is_good) then
-              if (debug) write(stderrunit,*) 'Perfect quality Bond:', berg%iceberg_num, current_bond%other_berg_num
+              if (debug) write(stderrunit,*) 'Perfect quality Bond:', berg%id, current_bond%other_berg_num
             else
-              if (debug) write(stderrunit,*) 'Non-matching bond...:', berg%iceberg_num, current_bond%other_berg_num
+              if (debug) write(stderrunit,*) 'Non-matching bond...:', berg%id, current_bond%other_berg_num
               num_unmatched_bonds=num_unmatched_bonds+1
             endif
           else
-            if (debug) write(stderrunit,*) 'Opposite berg is not assosiated:', berg%iceberg_num, current_bond%other_berg%iceberg_num
+            if (debug) write(stderrunit,*) 'Opposite berg is not assosiated:', berg%id, current_bond%other_berg%id
             num_unassosiated_bond_pairs=0
           endif
         endif

From 04e827bc11f2def718a72419c56caa4add07aaa6 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Sat, 17 Jun 2017 18:14:15 -0400
Subject: [PATCH 227/361] Fix id_from_2_ints() for Intel and PGI

- gnu was casting a constant integer to the kind of the result, while
  intel and pgi compilers are making all constants integer*4. This commit
  forces the expression to be evaluated in integer*8 terms.
---
 icebergs_framework.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 337d6af..80cb83d 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -4604,7 +4604,7 @@ integer(kind=8) function id_from_2_ints(counter, ijhash)
   integer, intent(in) :: counter !< The counter value assigned at calving
   integer, intent(in) :: ijhash  !< A hash of i,j calving location
 
-  id_from_2_ints = int(counter,8) * (2**32) + int(ijhash,8)
+  id_from_2_ints = int(counter,8) * (int(2,8)**32) + int(ijhash,8)
 
 end function id_from_2_ints
 

From 32eba0a61008dd20be2eaeaa3c17a50e899a41f4 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Sat, 17 Jun 2017 18:45:25 -0400
Subject: [PATCH 228/361] Use %id instead of $iceberg_num

- Everywhere tests are made now uses %id instead of $iceberg_num,
  except for the restart files.
---
 icebergs.F90           |  68 +++++++++----------
 icebergs_framework.F90 | 150 +++++++++++++++++++----------------------
 icebergs_io.F90        | 103 +++++++++++++++++-----------
 3 files changed, 164 insertions(+), 157 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index b4f789b..8a58b60 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -175,17 +175,17 @@ subroutine basal_melt_test(bergs)
   type(icebergs), pointer :: bergs !< Container for all types and memory
   ! Local variables
   real :: dvo,lat,salt,temp, basal_melt, thickness
-  integer :: iceberg_num
+  integer(kind=8) :: id
   logical :: Use_three_equation_model
 
   if (mpp_pe() .eq. mpp_root_pe() ) print *, 'Begining Basal Melting Unit Test'
-  dvo=0.2 ;lat=0.0 ; salt=35.0 ; temp=2.0 ;thickness=100.; iceberg_num=0
+  dvo=0.2 ;lat=0.0 ; salt=35.0 ; temp=2.0 ;thickness=100.; id=0
   Use_three_equation_model=.False.
-  call find_basal_melt(bergs,dvo,lat,salt,temp,Use_three_equation_model,thickness,basal_melt,iceberg_num)
+  call find_basal_melt(bergs,dvo,lat,salt,temp,Use_three_equation_model,thickness,basal_melt,id)
   if (mpp_pe() .eq. mpp_root_pe()) print *, 'Two equation model basal_melt =',basal_melt
 
   Use_three_equation_model=.True.
-  call find_basal_melt(bergs,dvo,lat,salt,temp,Use_three_equation_model,thickness,basal_melt,iceberg_num)
+  call find_basal_melt(bergs,dvo,lat,salt,temp,Use_three_equation_model,thickness,basal_melt,id)
    if (mpp_pe() .eq. mpp_root_pe()) print *, 'Three equation model basal_melt =',basal_melt
 
 end subroutine basal_melt_test
@@ -351,7 +351,7 @@ subroutine initialize_iceberg_bonds(bergs)
         other_berg=>bergs%list(grdi_inner,grdj_inner)%first
         do while (associated(other_berg)) ! loop over all other bergs
 
-          if (berg%iceberg_num .ne. other_berg%iceberg_num) then
+          if (berg%id .ne. other_berg%id) then
             lon2=other_berg%lon; lat2=other_berg%lat
             !call rotpos_to_tang(lon2,lat2,x2,y2) !Is this correct? Shouldn't it only be on tangent plane?
             !r_dist_x=x1-x2 ; r_dist_y=y1-y2
@@ -366,7 +366,7 @@ subroutine initialize_iceberg_bonds(bergs)
             r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) )
 
             !if (r_dist.gt.1000.) then  ! If the bergs are close together, then form a bond
-              call form_a_bond(berg, other_berg%iceberg_num, other_berg%id, other_berg%ine, other_berg%jne, other_berg)
+              call form_a_bond(berg, other_berg%id, other_berg%ine, other_berg%jne, other_berg)
             !endif
           endif
           other_berg=>other_berg%next
@@ -523,7 +523,7 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
     tangental_damping_coef=(2.*sqrt(spring_coef))/4 ! Critical damping (just a guess)
   endif
 
-  if (berg%iceberg_num .ne. other_berg%iceberg_num) then
+  if (berg%id .ne. other_berg%id) then
     ! From Berg 1
     L1=berg%length
     W1=berg%width
@@ -567,7 +567,7 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
       R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
     endif
     !!!!!!!!!!!!!!!!!!!!!!!!!!!debugging!!!!!!!!!!!!!!!!!!!!!!!!!!MP1
-    ! if (berg%iceberg_num .eq. 1) then
+    ! if (berg%id .eq. 1) then
     !   print *, 'Comparing longitudes: ', lon1, lon2, r_dist_x, dlon
     !   print *, 'Comparing latitudes: ', lat1, lat2, r_dist_y, dlat
     !   print *, 'Outside, id, r_dist', berg%id, r_dist,bonded
@@ -593,7 +593,7 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
       if (r_dist < 5*(R1+R2)) then
 
         !MP1
-        !if (berg%iceberg_num .eq. 1) then
+        !if (berg%id .eq. 1) then
         !  !print *,  '************************************************************'
         !  print *, 'INSIDE, r_dist', berg%id, other_berg%id, r_dist, bonded
         !endif
@@ -936,7 +936,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
     uveln=u_star+dt*ax        ! Alon
     vveln=v_star+dt*ay        ! Alon
 !MP4
-  !    if (berg%iceberg_num .eq. 1) then
+  !    if (berg%id .eq. 1) then
   !      print *, '***************************************************'
   !      print *,'id, itloop', berg%id, itloop
   !      print *, 'P matrix:', P_ia_11, P_ia_12,P_ia_21,P_ia_22,P_ia_times_u_x, P_ia_times_u_x
@@ -1224,7 +1224,7 @@ subroutine thermodynamics(bergs)
       !For icebergs acting as ice shelves
       if ((bergs%melt_icebergs_as_ice_shelf) .or.(bergs%use_mixed_melting))  then
         if (.not. bergs%use_mixed_layer_salinity_for_thermo)  SSS=35.0
-        call find_basal_melt(bergs,dvo,this%lat,SSS,SST,bergs%Use_three_equation_model,T,Ms,this%iceberg_num)
+        call find_basal_melt(bergs,dvo,this%lat,SSS,SST,bergs%Use_three_equation_model,T,Ms,this%id)
         Ms=max(Ms,0.) !No refreezing allowed for now
         !Set melt to zero if ocean is too thin.
         if ((bergs%melt_cutoff >=0.) .and. (bergs%apply_thickness_cutoff_to_bergs_melt)) then
@@ -1550,7 +1550,7 @@ subroutine create_gridded_icebergs_fields(bergs)
 end subroutine create_gridded_icebergs_fields
 
 !> Calculates basal melt for given thermodynamic properties
-subroutine find_basal_melt(bergs, dvo, lat, salt, temp, Use_three_equation_model, thickness, basal_melt, iceberg_num)
+subroutine find_basal_melt(bergs, dvo, lat, salt, temp, Use_three_equation_model, thickness, basal_melt, id)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
   real, intent(in) :: dvo !< Speed of iceberg relative to ocean mixed layer
@@ -1560,7 +1560,7 @@ subroutine find_basal_melt(bergs, dvo, lat, salt, temp, Use_three_equation_model
   logical, intent(in) :: Use_three_equation_model !< True uses the 3 equation model, False uses the 2 equation model.
   real, intent(in) :: thickness !< Ice thickness - needed to work out the pressure below the ice
   real, intent(out) :: basal_melt !< Melt rate underneath the icebergs
-  integer, intent(in) :: iceberg_num !< Iceberg number, used for debugging (error messages)
+  integer(kind=8), intent(in) :: id !< Iceberg id, used for debugging (error messages)
   ! Local variables
   real :: ustar, f_cori, absf,tfreeze
   real :: Hml !Mixed layer depth
@@ -1790,7 +1790,7 @@ subroutine find_basal_melt(bergs, dvo, lat, salt, temp, Use_three_equation_model
         if (Sb_max_set .and. (Sbdry > Sb_max)) then
           if (debug) then
             call error_mesg('diamonds,Find basal melt', 'shelf_calc_flux: Irregular iteration for Sbdry (max).' ,WARNING)
-            print *, 'Sbdry error: id,dvo,temp,salt,lat,thickness :',iceberg_num,dvo,temp,salt,lat,thickness
+            print *, 'Sbdry error: id,dvo,temp,salt,lat,thickness :',id,dvo,temp,salt,lat,thickness
           endif
           out_of_bounds=.true.
           exit
@@ -1800,7 +1800,7 @@ subroutine find_basal_melt(bergs, dvo, lat, salt, temp, Use_three_equation_model
         if (Sb_min_set .and. (Sbdry < Sb_min)) then
           if (debug) then
             call error_mesg('diamonds,Find basal melt', 'shelf_calc_flux: Irregular iteration for Sbdry (min).' ,WARNING)
-            print *, 'Sbdry error: id,dvo,temp,salt,lat,thickness :',iceberg_num,dvo,temp,salt,lat,thickness
+            print *, 'Sbdry error: id,dvo,temp,salt,lat,thickness :',id,dvo,temp,salt,lat,thickness
           endif
           out_of_bounds=.true.
           exit
@@ -1911,7 +1911,7 @@ subroutine find_orientation_using_iceberg_bonds(grd, berg, orientation)
       other_berg=>current_bond%other_berg
       if (.not. associated(other_berg)) then !good place for debugging
         !One valid option: current iceberg is on the edge of halo, with other berg on the next pe (not influencing mass spreading)
-        !print *, 'Iceberg bond details:',berg%id, current_bond%other_berg_num,berg%halo_berg, mpp_pe()
+        !print *, 'Iceberg bond details:',berg%id, current_bond%other_id,berg%halo_berg, mpp_pe()
         !print *, 'Iceberg bond details2:',berg%ine, berg%jne, current_bond%other_berg_ine, current_bond%other_berg_jne
         !print *, 'Iceberg isd,ied,jsd,jed:',grd%isd, grd%ied, grd%jsd, grd%jed
         !print *, 'Iceberg isc,iec,jsc,jec:',grd%isc, grd%iec, grd%jsc, grd%jec
@@ -4262,7 +4262,7 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
     uveln=uvel3+(dt*ax1); vveln=vvel3+(dt*ay1)    !Alon , we call it uvel3, vvel3 until it is put into lat/long co-ordinates, where it becomes uveln, vveln
   endif
 
-  !if (berg%iceberg_num .eq. 1) print *, 'New velocity: ', uveln, vveln
+  !if (berg%id .eq. 1) print *, 'New velocity: ', uveln, vveln
 
 
   !!!!!!!!!!!!!!! Debugging  !!!!!!!!!!!!!!!!!!!!!!!!!!!
@@ -4408,7 +4408,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
     uvel2=uvel1+dt_2*ax1; vvel2=vvel1+dt_2*ay1
   endif
   i=i1;j=j1;xi=berg%xi;yj=berg%yj
-  call adjust_index_and_ground(grd, lon2, lat2, uvel2, vvel2, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)
+  call adjust_index_and_ground(grd, lon2, lat2, uvel2, vvel2, i, j, xi, yj, bounced, error_flag, berg%id)
   i2=i; j2=j
   if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
     call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, berg%thickness)
@@ -4465,7 +4465,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
     uvel3=uvel1+dt_2*ax2; vvel3=vvel1+dt_2*ay2
   endif
   i=i1;j=j1;xi=berg%xi;yj=berg%yj
-  call adjust_index_and_ground(grd, lon3, lat3, uvel3, vvel3, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)
+  call adjust_index_and_ground(grd, lon3, lat3, uvel3, vvel3, i, j, xi, yj, bounced, error_flag, berg%id)
   i3=i; j3=j
   if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
     call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, berg%thickness)
@@ -4524,7 +4524,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
     uvel4=uvel1+dt*ax3; vvel4=vvel1+dt*ay3
   endif
   i=i1;j=j1;xi=berg%xi;yj=berg%yj
-  call adjust_index_and_ground(grd, lon4, lat4, uvel4, vvel4, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)
+  call adjust_index_and_ground(grd, lon4, lat4, uvel4, vvel4, i, j, xi, yj, bounced, error_flag, berg%id)
   i4=i; j4=j
   ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon4,lat4,x4,y4)
   if (.not.error_flag) then
@@ -4596,7 +4596,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
   endif
 
   i=i1;j=j1;xi=berg%xi;yj=berg%yj
-  call adjust_index_and_ground(grd, lonn, latn, uveln, vveln, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)
+  call adjust_index_and_ground(grd, lonn, latn, uveln, vveln, i, j, xi, yj, bounced, error_flag, berg%id)
   if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
     call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, berg%thickness)
 
@@ -4693,7 +4693,7 @@ subroutine update_verlet_position(bergs, berg)
   if ((berg%lat>89.) .and. (grd%grid_is_latlon)) on_tangential_plane=.true.
 
   lon1=berg%lon; lat1=berg%lat
-  if (on_tangential_plane) call rotpos_to_tang(lon1,lat1,x1,y1,berg%iceberg_num)
+  if (on_tangential_plane) call rotpos_to_tang(lon1,lat1,x1,y1,berg%id)
   !dxdl1=r180_pi/(Rearth*cos(lat1*pi_180))
   !dydl=r180_pi/Rearth
   call  convert_from_meters_to_grid(lat1,grd%grid_is_latlon ,dxdl1,dydl)
@@ -4727,7 +4727,7 @@ subroutine update_verlet_position(bergs, berg)
   ! Adjusting mass...
   !MP3
   i=berg%ine;  j=berg%jne;  xi = berg%xi;  yj = berg%yj
-  call adjust_index_and_ground(grd, lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag, berg%iceberg_num)  !Alon:"unclear which velocity to use here?"
+  call adjust_index_and_ground(grd, lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag, berg%id)  !Alon:"unclear which velocity to use here?"
 
   !if (bounced) then
   !  print *, 'you have been bounce: big time!',mpp_pe(),berg%id,lonn, latn, uvel3, vvel3, i, j, xi, yj, bounced, error_flag
@@ -4796,7 +4796,7 @@ subroutine rotvec_from_tang(lon, xdot, ydot, uvel, vvel)
 end subroutine rotvec_from_tang
 
 !> Moves berg's cell indexes,(i,j), checking for collisional with coasts
-subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, bounced, error, iceberg_num)
+subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, bounced, error, id)
   ! Arguments
   type(icebergs_gridded), pointer :: grd !< Container for gridded fields
   real, intent(inout) :: lon !< Longitude (degree E)
@@ -4809,7 +4809,7 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
   integer, intent(inout) :: j !< j-index of cell
   logical, intent(out) :: bounced !< True if berg collided with coast
   logical, intent(out) :: error !< True if adjustments could not be made consistently
-  integer, intent(in) :: iceberg_num !< Berg identifier
+  integer(kind=8), intent(in) :: id !< Berg identifier
   ! Local variables
   logical lret, lpos
   real, parameter :: posn_eps=0.05
@@ -5013,7 +5013,7 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
         yj=(yj-0.5)*(1.-posn_eps)+0.5
       endif
       call error_mesg('diamonds, adjust', 'Berg did not move or bounce during iterations AND was not in cell. Adjusting!', WARNING)
-      write(stderrunit,*) 'diamonds, adjust: The adjusting iceberg is: ', iceberg_num,  mpp_pe()
+      write(stderrunit,*) 'diamonds, adjust: The adjusting iceberg is: ', id,  mpp_pe()
       write(stderrunit,*) 'diamonds, adjust: The adjusting lon,lat,u,v: ', lon, lat, uvel, vvel
       write(stderrunit,*) 'diamonds, adjust: The adjusting xi,ji: ', xi, yj
       lret=pos_within_cell(grd, lon, lat, inm, jnm, xi, yj,explain=.true.)
@@ -5037,31 +5037,31 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
     write(0,*) 'grd%msk(i0, j0)=', grd%msk(i0,j0)
     write(0,*) 'lon0, lat0,=', lon0,lat0
     write(0,*) 'i,j,lon, lat,grd%msk(i,j)=', i,j,lon,lat,grd%msk(i,j)
-    write(stderrunit,*) 'diamonds, adjust: Should not get here! Berg is not in cell after adjustment', iceberg_num, mpp_pe()
+    write(stderrunit,*) 'diamonds, adjust: Should not get here! Berg is not in cell after adjustment', id, mpp_pe()
     if (debug) error=.true.
   endif
  end subroutine adjust_index_and_ground
 
 !> Calculate longitude-latitude from tangent plane coordinates
-subroutine rotpos_to_tang(lon, lat, x, y, iceberg_num_in)
+subroutine rotpos_to_tang(lon, lat, x, y, id_in)
   ! Arguments
   real, intent(in) :: lon !< Longitude (degree E)
   real, intent(in) :: lat !< Latitude (degree N)
   real, intent(out) :: x !< x-coordinate in tangent plane
   real, intent(out) :: y !< y-coordinate in tangent plane
-  integer, intent(in), optional :: iceberg_num_in !< Berg identifier
+  integer(kind=8), intent(in), optional :: id_in !< Berg identifier
   ! Local variables
   real :: r,colat,clon,slon
-  integer :: stderrunit, iceberg_num
+  integer :: stderrunit, id
 
   stderrunit = stderr()
-  iceberg_num=0
-  if (present(iceberg_num_in)) then
-        iceberg_num=iceberg_num_in
+  id=0
+  if (present(id_in)) then
+        id=id_in
   endif
 
   if (lat>90.) then
-      write(stderrunit,*) 'diamonds, rotpos_to_tang: lat>90 already!',lat, lon, iceberg_num
+      write(stderrunit,*) 'diamonds, rotpos_to_tang: lat>90 already!',lat, lon, id
       call error_mesg('diamonds, rotpos_to_tang','Something went very wrong!',FATAL)
   endif
   if (lat==90.) then
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 80cb83d..19b3f23 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -18,10 +18,8 @@ module ice_bergs_framework
 
 implicit none ; private
 
-integer :: buffer_width=27 !Changed from 20 to 28 by Alon
-integer :: buffer_width_traj=31  !Changed from 23 by Alon
-!integer, parameter :: buffer_width=26 !Changed from 20 to 26 by Alon
-!integer, parameter :: buffer_width_traj=29  !Changed from 23 by Alon
+integer :: buffer_width=29 ! This should be a parameter
+integer :: buffer_width_traj=32 ! This should be a parameter
 integer, parameter :: nclasses=10 ! Number of ice bergs classes
 
 !Local Vars
@@ -218,8 +216,7 @@ module ice_bergs_framework
   real :: mass_of_bits !< Mass of bergy bits (kg)
   real :: heat_density !< Heat density of berg (???)
   integer :: year !< Year of this record (years)
-  integer :: iceberg_num !< Iceberg identifier
-  integer(kind=8) :: id !< Iceberg identifier
+  integer(kind=8) :: id = -1 !< Iceberg identifier
   type(xyt), pointer :: next=>null() !< Next link in list
 end type xyt
 
@@ -282,7 +279,6 @@ module ice_bergs_framework
   type(bond), pointer :: prev_bond=>null() !< Previous link in list
   type(bond), pointer :: next_bond=>null() !< Next link in list
   type(iceberg), pointer :: other_berg=>null()
-  integer :: other_berg_num
   integer(kind=8) :: other_id !< ID of other berg
   integer :: other_berg_ine
   integer :: other_berg_jne
@@ -364,7 +360,7 @@ module ice_bergs_framework
   logical :: Static_icebergs=.False. !< True= icebergs do no move
   logical :: only_interactive_forces=.False. !< Icebergs only feel interactive forces, and not ocean, wind...
   logical :: halo_debugging=.False. !< Use for debugging halos (remove when its working)
-  logical :: save_short_traj=.True. !< True saves only lon,lat,time,iceberg_num in iceberg_trajectory.nc
+  logical :: save_short_traj=.True. !< True saves only lon,lat,time,id in iceberg_trajectory.nc
   logical :: ignore_traj=.False. !< If true, then model does not write trajectory data at all
   logical :: iceberg_bonds_on=.False. !< True=Allow icebergs to have bonds, False=don't allow.
   logical :: manually_initialize_bonds=.False. !< True= Bonds are initialize manually.
@@ -373,7 +369,7 @@ module ice_bergs_framework
   logical :: critical_interaction_damping_on=.true. !< Sets the damping on relative iceberg velocity to critical value - Added by Alon
   logical :: use_old_spreading=.true. !< If true, spreads iceberg mass as if the berg is one grid cell wide
   logical :: read_ocean_depth_from_file=.false. !< If true, ocean depth is read from a file.
-  integer :: debug_iceberg_with_id = -1 !< If positive, monitors a berg with this id
+  integer(kind=8) :: debug_iceberg_with_id = -1 !< If positive, monitors a berg with this id
 
   real :: speed_limit=0. !< CFL speed limit for a berg [m/s]
   real :: tau_calving=0. !< Time scale for smoothing out calving field (years)
@@ -544,7 +540,7 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: Static_icebergs=.False. ! True= icebergs do no move
 logical :: only_interactive_forces=.False. ! Icebergs only feel interactive forces, and not ocean, wind...
 logical :: halo_debugging=.False. ! Use for debugging halos (remove when its working)
-logical :: save_short_traj=.True. ! True saves only lon,lat,time,iceberg_num in iceberg_trajectory.nc
+logical :: save_short_traj=.True. ! True saves only lon,lat,time,id in iceberg_trajectory.nc
 logical :: ignore_traj=.False. ! If true, then model does not traj trajectory data at all
 logical :: iceberg_bonds_on=.False. ! True=Allow icebergs to have bonds, False=don't allow.
 logical :: manually_initialize_bonds=.False. ! True= Bonds are initialize manually.
@@ -560,7 +556,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real, dimension(nclasses) :: distribution=(/0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02/) ! Fraction of calving to apply to this class (non-dim) ,
 real, dimension(nclasses) :: mass_scaling=(/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) ! Ratio between effective and real iceberg mass (non-dim)
 real, dimension(nclasses) :: initial_thickness=(/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) ! Total thickness of newly calved bergs (m)
-integer :: debug_iceberg_with_id = -1 ! If positive, monitors a berg with this id
+integer(kind=8) :: debug_iceberg_with_id = -1 ! If positive, monitors a berg with this id
 
 namelist /icebergs_nml/ verbose, budget, halo,  traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,Static_icebergs,  &
          distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,bond_coef, radial_damping_coef, tangental_damping_coef, only_interactive_forces, &
@@ -917,9 +913,9 @@ subroutine ice_bergs_framework_init(bergs, &
 if (.not. iceberg_bonds_on) then
    max_bonds=0
 else
-  buffer_width=buffer_width+(max_bonds*3) ! Increase buffer width to include bonds being passed between processors
+  buffer_width=buffer_width+(max_bonds*4) ! Increase buffer width to include bonds being passed between processors
 endif
-if (save_short_traj) buffer_width_traj=5 ! This is the length of the short buffer used for abrevated traj
+if (save_short_traj) buffer_width_traj=6 ! This is the length of the short buffer used for abrevated traj
 if (ignore_traj) buffer_width_traj=0 ! If this is true, then all traj files should be ignored
 
 
@@ -1860,7 +1856,6 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
     current_bond=>berg%first_bond
     do k = 1,max_bonds
       if (associated(current_bond)) then
-        call push_buffer_value(buff%data(:,n), counter, current_bond%other_berg_num)
         call split_id(current_bond%other_id, id_cnt, id_ij)
         call push_buffer_value(buff%data(:,n), counter, id_cnt)
         call push_buffer_value(buff%data(:,n), counter, id_ij)
@@ -1872,7 +1867,6 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
         call push_buffer_value(buff%data(:,n), counter, 0)
         call push_buffer_value(buff%data(:,n), counter, 0)
         call push_buffer_value(buff%data(:,n), counter, 0)
-        call push_buffer_value(buff%data(:,n), counter, 0)
       endif
     enddo
   endif
@@ -1891,6 +1885,7 @@ subroutine push_buffer_rvalue(vbuf, counter, val)
   real,               intent(in)    :: val     !< Value to place in buffer
 
   counter = counter + 1
+  if (counter > size(vbuf)) stop 'OOB in push_buffer_rvalue'
   vbuf(counter) = val
 
 end subroutine push_buffer_rvalue
@@ -1902,6 +1897,7 @@ subroutine push_buffer_ivalue(vbuf, counter, val)
   integer,            intent(in)    :: val     !< Value to place in buffer
 
   counter = counter + 1
+  if (counter > size(vbuf)) stop 'OOB in push_buffer_ivalue'
   vbuf(counter) = float(val)
 
 end subroutine push_buffer_ivalue
@@ -1913,6 +1909,7 @@ subroutine pull_buffer_rvalue(vbuf, counter, val)
   real,               intent(out)   :: val     !< Value to get from buffer
 
   counter = counter + 1
+  if (counter > size(vbuf)) stop 'OOB in pull_buffer_rvalue'
   val = vbuf(counter)
 
 end subroutine pull_buffer_rvalue
@@ -1924,6 +1921,7 @@ subroutine pull_buffer_ivalue(vbuf, counter, val)
   integer,            intent(out)   :: val     !< Value to get from buffer
 
   counter = counter + 1
+  if (counter > size(vbuf)) stop 'OOB in pull_buffer_ivalue'
   val = nint(vbuf(counter))
 
 end subroutine pull_buffer_ivalue
@@ -1945,8 +1943,8 @@ subroutine clear_berg_from_partners_bonds(berg)
       !write(stderrunit,*) , 'Other berg', berg%id, other_berg%id, mpp_pe()
       matching_bond=>other_berg%first_bond
       do while (associated(matching_bond))  ! Looping over possible matching bonds in other_berg
-        if (matching_bond%other_berg_num .eq. berg%iceberg_num) then
-          !write(stderrunit,*) , 'Clearing', berg%id, matching_bond%other_berg_num,other_berg%id, mpp_pe()
+        if (matching_bond%other_id .eq. berg%id) then
+          !write(stderrunit,*) , 'Clearing', berg%id, matching_bond%other_id,other_berg%id, mpp_pe()
           matching_bond%other_berg=>null()
           matching_bond=>null()
         else
@@ -2071,14 +2069,13 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
   this%first_bond=>null()
   if (max_bonds .gt. 0) then
     do k = 1,max_bonds
-      call pull_buffer_value(buff%data(:,n), counter, other_berg_num)
       call pull_buffer_value(buff%data(:,n), counter, id_cnt)
       call pull_buffer_value(buff%data(:,n), counter, id_ij)
       id = id_from_2_ints(id_cnt, id_ij)
       call pull_buffer_value(buff%data(:,n), counter, other_berg_ine)
       call pull_buffer_value(buff%data(:,n), counter, other_berg_jne)
-      if (other_berg_num .gt. 0.5) then
-        call form_a_bond(this, other_berg_num, id, other_berg_ine, other_berg_jne)
+      if (id_ij > 0) then
+        call form_a_bond(this, id, other_berg_ine, other_berg_jne)
       endif
     enddo
   endif
@@ -2137,6 +2134,7 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj)
   logical, intent(in) :: save_short_traj !< If true, only use a subset of trajectory data
   ! Local variables
   integer :: counter ! Position in stack
+  integer :: cnt, ij
 
   if (.not.associated(buff)) call increase_ibuffer(buff,n,buffer_width_traj)
   if (n>buff%size) call increase_ibuffer(buff,n,buffer_width_traj)
@@ -2146,7 +2144,9 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj)
   call push_buffer_value(buff%data(:,n),counter,traj%lat)
   call push_buffer_value(buff%data(:,n),counter,traj%year)
   call push_buffer_value(buff%data(:,n),counter,traj%day)
-  call push_buffer_value(buff%data(:,n),counter,traj%iceberg_num)
+  call split_id(traj%id, cnt, ij)
+  call push_buffer_value(buff%data(:,n),counter,cnt)
+  call push_buffer_value(buff%data(:,n),counter,ij)
   if (.not. save_short_traj) then
     call push_buffer_value(buff%data(:,n),counter,traj%uvel)
     call push_buffer_value(buff%data(:,n),counter,traj%vvel)
@@ -2188,13 +2188,16 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj)
   ! Local variables
   type(xyt) :: traj
   integer :: counter ! Position in stack
+  integer :: cnt, ij
 
   counter = 0
   call pull_buffer_value(buff%data(:,n),counter,traj%lon)
   call pull_buffer_value(buff%data(:,n),counter,traj%lat)
   call pull_buffer_value(buff%data(:,n),counter,traj%year)
   call pull_buffer_value(buff%data(:,n),counter,traj%day)
-  call pull_buffer_value(buff%data(:,n),counter,traj%iceberg_num)
+  call pull_buffer_value(buff%data(:,n),counter,cnt)
+  call pull_buffer_value(buff%data(:,n),counter,ij)
+  traj%id = id_from_2_ints(cnt, ij)
   if (.not. save_short_traj) then
     call pull_buffer_value(buff%data(:,n),counter,traj%uvel)
     call pull_buffer_value(buff%data(:,n),counter,traj%vvel)
@@ -2449,7 +2452,7 @@ subroutine monitor_a_berg(bergs, label)
   do grdj = bergs%grd%jsd,bergs%grd%jed ; do grdi = bergs%grd%isd,bergs%grd%ied
     this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
-      if (this%iceberg_num == bergs%debug_iceberg_with_id) then
+      if (this%id == bergs%debug_iceberg_with_id) then
         call print_berg(stderrunit, this, 'MONITOR: '//label, grdi, grdj)
       endif
       this=>this%next
@@ -2512,7 +2515,7 @@ end subroutine insert_berg_into_list
 !> Returns True when berg1 and berg2 are in sorted order
 !! \todo inorder() should use the iceberg identifier for efficiency and simplicity
 !! instead of dates and properties
-logical function inorder(berg1, berg2)  !MP Alon - Change to include iceberg_num
+logical function inorder(berg1, berg2)  !MP Alon - Change to use iceberg id
 ! Arguments
 type(iceberg), pointer :: berg1 !< An iceberg
 type(iceberg), pointer :: berg2 !< An iceberg
@@ -2757,25 +2760,23 @@ subroutine print_bergs(iochan, bergs, label)
 
 end subroutine print_bergs
 
-subroutine form_a_bond(berg, other_berg_num, other_id, other_berg_ine, other_berg_jne, other_berg)
+subroutine form_a_bond(berg, other_id, other_berg_ine, other_berg_jne, other_berg)
 ! Arguments
 type(iceberg), pointer :: berg
 type(iceberg), optional,  pointer :: other_berg
 type(bond) , pointer :: new_bond, first_bond
-integer, intent(in) :: other_berg_num
 integer(kind=8), intent(in) :: other_id
 integer, optional  :: other_berg_ine, other_berg_jne
 integer :: stderrunit
 
  stderrunit = stderr()
 
-if (berg%iceberg_num .ne. other_berg_num) then
+if (berg%id .ne. other_id) then
 
- !write (stderrunit,*) , 'Forming a bond!!!', mpp_pe(), berg%iceberg_num, other_berg_num, berg%halo_berg, berg%ine, berg%jne
+ !write (stderrunit,*) , 'Forming a bond!!!', mpp_pe(), berg%id, other_id, berg%halo_berg, berg%ine, berg%jne
 
   ! Step 1: Create a new bond
   allocate(new_bond)
-  new_bond%other_berg_num=other_berg_num
   new_bond%other_id=other_id
   if(present(other_berg)) then
     new_bond%other_berg=>other_berg
@@ -2860,16 +2861,16 @@ subroutine show_all_bonds(bergs)
     do while (associated(berg)) ! loop over all bergs
       current_bond=>berg%first_bond
       do while (associated(current_bond)) ! loop over all bonds
-        print *, 'Show Bond1 :', berg%id, current_bond%other_berg_num, current_bond%other_berg_ine, current_bond%other_berg_jne,  mpp_pe()
+        print *, 'Show Bond1 :', berg%id, current_bond%other_id, current_bond%other_berg_ine, current_bond%other_berg_jne,  mpp_pe()
         !print *, 'Current:', berg%id, berg%ine, berg%jne,berg%halo_berg, mpp_pe()
         if  (associated(current_bond%other_berg)) then
-          if (current_bond%other_berg%iceberg_num .ne. current_bond%other_berg_num) then
-            print *, 'Bond matching', berg%id,current_bond%other_berg%id, current_bond%other_berg_num,&
+          if (current_bond%other_berg%id .ne. current_bond%other_id) then
+            print *, 'Bond matching', berg%id,current_bond%other_berg%id, current_bond%other_id,&
             berg%halo_berg,current_bond%other_berg%halo_berg ,mpp_pe()
             call error_mesg('diamonds, show all bonds:', 'The bonds are not matching properly!', FATAL)
           endif
         else
-            print *, 'This bond has an non-assosiated other berg :', berg%id, current_bond%other_berg_num,&
+            print *, 'This bond has an non-assosiated other berg :', berg%id, current_bond%other_id,&
             current_bond%other_berg_ine, current_bond%other_berg_jne, berg%halo_berg,  mpp_pe()
         endif
         current_bond=>current_bond%next_bond
@@ -2910,7 +2911,7 @@ subroutine connect_all_bonds(bergs)
           if ( (i.gt. grd%isd-1) .and. (i .lt. grd%ied+1) .and. (j .gt. grd%jsd-1) .and. (j .lt. grd%jed+1)) then
             other_berg=>bergs%list(i,j)%first
             do while (associated(other_berg)) ! loop over all other bergs
-              if (other_berg%iceberg_num .eq. current_bond%other_berg_num) then
+              if (other_berg%id .eq. current_bond%other_id) then
                 current_bond%other_berg=>other_berg
                 other_berg=>null()
                 bond_matched=.true.
@@ -2928,7 +2929,7 @@ subroutine connect_all_bonds(bergs)
                 .and. ((grdi_inner .ne. i) .or. (grdj_inner .ne. j)) ) then
                   other_berg=>bergs%list(grdi_inner,grdj_inner)%first
                   do while (associated(other_berg)) ! loop over all other bergs
-                    if (other_berg%iceberg_num .eq. current_bond%other_berg_num) then
+                    if (other_berg%id .eq. current_bond%other_id) then
                       current_bond%other_berg=>other_berg
                       other_berg=>null()
                       bond_matched=.true.
@@ -2943,12 +2944,12 @@ subroutine connect_all_bonds(bergs)
           if (.not.bond_matched) then
             if (berg%halo_berg .lt. 0.5) then
               missing_bond=.true.
-              print * ,'non-halo berg unmatched: ', berg%id, mpp_pe(), current_bond%other_berg_num, current_bond%other_berg_ine
+              print * ,'non-halo berg unmatched: ', berg%id, mpp_pe(), current_bond%other_id, current_bond%other_berg_ine
               call error_mesg('diamonds, connect_all_bonds', 'A non-halo bond is missing!!!', FATAL)
             else  ! This is not a problem if the partner berg is not yet in the halo
               !if (  (current_bond%other_berg_ine .gt.grd%isd-1) .and. (current_bond%other_berg_ine .lt.grd%ied+1) &
                 !.and.  (current_bond%other_berg_jne .gt.grd%jsd-1) .and. (current_bond%other_berg_jne .lt.grd%jed+1) ) then
-                !print * ,'halo berg unmatched: ',mpp_pe(),  berg%id, current_bond%other_berg_num, current_bond%other_berg_ine,current_bond%other_berg_jne
+                !print * ,'halo berg unmatched: ',mpp_pe(),  berg%id, current_bond%other_id, current_bond%other_berg_ine,current_bond%other_berg_jne
                 !call error_mesg('diamonds, connect_all_bonds', 'A halo bond is missing!!!', WARNING)
               !endif
             endif
@@ -3015,7 +3016,7 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
             other_berg_bond=>other_berg%first_bond
             do while (associated(other_berg_bond))  !loops over the icebergs in the other icebergs bond list
               if (associated(other_berg_bond%other_berg)) then
-                if (other_berg_bond%other_berg%iceberg_num .eq.berg%iceberg_num) then
+                if (other_berg_bond%other_berg%id .eq.berg%id) then
                   bond_is_good=.True.  !Bond_is_good becomes true when the corresponding bond is found
                 endif
               endif
@@ -3027,9 +3028,9 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
             enddo  ! End of loop over the other berg's bonds.
 
             if (bond_is_good) then
-              if (debug) write(stderrunit,*) 'Perfect quality Bond:', berg%id, current_bond%other_berg_num
+              if (debug) write(stderrunit,*) 'Perfect quality Bond:', berg%id, current_bond%other_id
             else
-              if (debug) write(stderrunit,*) 'Non-matching bond...:', berg%id, current_bond%other_berg_num
+              if (debug) write(stderrunit,*) 'Non-matching bond...:', berg%id, current_bond%other_id
               num_unmatched_bonds=num_unmatched_bonds+1
             endif
           else
@@ -3137,8 +3138,7 @@ subroutine record_posn(bergs)
       posn%lat=this%lat
       posn%year=bergs%current_year
       posn%day=bergs%current_yearday
-      posn%iceberg_num=posn%iceberg_num
-      posn%id=posn%id
+      posn%id=this%id
       if (.not. bergs%save_short_traj) then !Not totally sure that this is correct
         posn%uvel=this%uvel
         posn%vvel=this%vvel
@@ -3234,22 +3234,6 @@ subroutine move_trajectory(bergs, berg)
   ! If the trajectory is empty, ignore it
   if (.not.associated(berg%trajectory)) return
 
-  ! Push identifying info into first posn (note reverse order due to stack)
-  vals%lon=berg%start_lon
-  vals%lat=berg%start_lat
-  vals%year=berg%start_year
-  vals%iceberg_num=berg%iceberg_num
-  vals%id=berg%id
-  vals%day=berg%start_day
-  vals%mass=berg%start_mass
-  call push_posn(berg%trajectory, vals)
-  vals%lon=0.
-  vals%lat=99.
-  vals%year=0
-  vals%day=0.
-  vals%mass=berg%mass_scaling
-  call push_posn(berg%trajectory, vals)
-
   ! Find end of berg trajectory and point it to start of existing trajectories
   next=>berg%trajectory
   do while (associated(next))
@@ -3492,10 +3476,10 @@ logical function find_cell_loc(grd, x, y, is, ie, js, je, w, oi, oj)
 end function find_cell_loc
 
 !> Returns the i,j of cell containing an iceberg with the given identifier
-subroutine find_individual_iceberg(bergs, iceberg_num, ine, jne, berg_found, search_data_domain)
+subroutine find_individual_iceberg(bergs, id, ine, jne, berg_found, search_data_domain)
 ! Arguments
 type(icebergs), pointer :: bergs !< Container for all types and memory
-integer, intent(in) :: iceberg_num !< Berg identifier
+integer(kind=8), intent(in) :: id !< Berg identifier
 integer, intent(out) :: ine !< i-index of cell containing berg
 integer, intent(out) :: jne !< j-index of cell containing berg
 logical, intent(in) :: search_data_domain !< If true, search halos too
@@ -3524,7 +3508,7 @@ subroutine find_individual_iceberg(bergs, iceberg_num, ine, jne, berg_found, sea
     !do grdj = bergs%grd%jsd,bergs%grd%jed ; do grdi = bergs%grd%isd,bergs%grd%ied
       this=>bergs%list(grdi,grdj)%first
       do while (associated(this))
-        if (iceberg_num .eq. this%iceberg_num) then
+        if (id .eq. this%id) then
           ine=this%ine
           jne=this%jne
           berg_found=1.0
@@ -4501,8 +4485,8 @@ integer function berg_chksum(berg)
 ! Arguments
 type(iceberg), pointer :: berg !< An iceberg
 ! Local variables
-real :: rtmp(38) !Changed from 28 to 34 by Alon
-integer :: itmp(38+4), i8=0, ichk1, ichk2, ichk3 !Changed from 28 to 34 by Alon
+real :: rtmp(36)
+integer :: itmp(36+8), i8=0, ichk1, ichk2, ichk3
 integer :: i
 
   rtmp(:)=0.
@@ -4541,16 +4525,17 @@ integer function berg_chksum(berg)
   rtmp(34)=berg%vvel_old
   rtmp(35)=berg%lat_old
   rtmp(36)=berg%lon_old
+  itmp(1:36)=transfer(rtmp,i8)
   itmp(37)=berg%halo_berg
   itmp(38)=berg%static_berg
-  itmp(1:38)=transfer(rtmp,i8)
   itmp(39)=berg%start_year
   itmp(40)=berg%ine
   itmp(41)=berg%jne
   itmp(42)=berg%iceberg_num
+  call split_id( berg%id, itmp(43), itmp(44) )
 
   ichk1=0; ichk2=0; ichk3=0
-  do i=1,38+4
+  do i=1,36+8
    ichk1=ichk1+itmp(i)
    ichk2=ichk2+itmp(i)*i
    ichk3=ichk3+itmp(i)*i*i
@@ -4675,7 +4660,7 @@ subroutine check_for_duplicates_in_parallel(bergs)
   type(icebergs_gridded), pointer :: grd
   type(iceberg), pointer :: this
   integer :: stderrunit, i, j, k, nbergs, nbergs_total
-  integer, dimension(:), allocatable :: ids ! List of ids of all bergs on this processor
+  integer(kind=8), dimension(:), allocatable :: ids ! List of ids of all bergs on this processor
 
   stderrunit=stderr()
   grd=>bergs%grd
@@ -4691,7 +4676,7 @@ subroutine check_for_duplicates_in_parallel(bergs)
       this=>bergs%list(i,j)%first
       do while (associated(this))
         k = k + 1
-        ids(k) = this%iceberg_num
+        ids(k) = this%id
         this=>this%next
       enddo
     enddo ; enddo
@@ -4708,11 +4693,12 @@ end subroutine check_for_duplicates_in_parallel
 !> Returns error count of duplicates of integer values in a distributed list
 integer function check_for_duplicate_ids_in_list(nbergs, ids, verbose)
   ! Arguments
-  integer,               intent(in)    :: nbergs !< Length of ids
-  integer, dimension(:), intent(inout) :: ids !< List of ids
-  logical,               intent(in)    :: verbose !< True if messages should be written
+  integer,                       intent(in)    :: nbergs !< Length of ids
+  integer(kind=8), dimension(:), intent(inout) :: ids !< List of ids
+  logical,                       intent(in)    :: verbose !< True if messages should be written
   ! Local variables
-  integer :: stderrunit, i, j, k, l, nbergs_total, ii, lowest_id, nonexistent_id
+  integer :: stderrunit, i, j, k, nbergs_total, ii
+  integer(kind=8) :: lowest_id, nonexistent_id, id, lid
   logical :: have_berg
 
   stderrunit=stderr()
@@ -4723,7 +4709,7 @@ integer function check_for_duplicate_ids_in_list(nbergs, ids, verbose)
   lowest_id = 0
   if (nbergs>0) lowest_id = minval(ids)
   call mpp_min(lowest_id)
-  i = lowest_id
+  id = lowest_id
   nonexistent_id = lowest_id - 1
   if (nonexistent_id >= lowest_id) then
     write(stderrunit,*) 'Underflow in iceberg ids!',nonexistent_id,lowest_id,mpp_pe()
@@ -4733,9 +4719,9 @@ integer function check_for_duplicate_ids_in_list(nbergs, ids, verbose)
     do i = j+1, nbergs
       if (ids(j) < ids(i)) then
         ! Swap
-        k = ids(i)
+        id = ids(i)
         ids(i) = ids(j)
-        ids(j) = k
+        ids(j) = id
       endif
     enddo
   enddo
@@ -4752,15 +4738,15 @@ integer function check_for_duplicate_ids_in_list(nbergs, ids, verbose)
   do k = 1, nbergs_total
     ! Set i to first id in my list
     if (j <= nbergs) then
-      i = ids(j)
+      id = ids(j)
       have_berg = .true.
     else
-      i = nonexistent_id
+      id = nonexistent_id
       have_berg = .false.
     endif
-    l = i
-    call mpp_max(l)
-    if (have_berg .and. i == l) then
+    lid = id
+    call mpp_max(lid)
+    if (have_berg .and. id == lid) then
       ii = 1 ! This berg is mine
       j = j + 1
     else
@@ -4768,10 +4754,10 @@ integer function check_for_duplicate_ids_in_list(nbergs, ids, verbose)
     endif
     call mpp_sum(ii)
     if (ii > 1) then
-      if (verbose) write(stderrunit,*) 'Duplicated berg across PEs with id=',i,l,' seen',ii,' times pe=',mpp_pe(),k,j,nbergs
+      if (verbose) write(stderrunit,*) 'Duplicated berg across PEs with id=',id,lid,' seen',ii,' times pe=',mpp_pe(),k,j,nbergs
       check_for_duplicate_ids_in_list = check_for_duplicate_ids_in_list + 1
     elseif (ii == 0) then
-      if (verbose) write(stderrunit,*) 'Berg not accounted for on all PEs with id=',i,l,' seen',ii,' times pe=',mpp_pe(),k,j,nbergs
+      if (verbose) write(stderrunit,*) 'Berg not accounted for on all PEs with id=',id,lid,' seen',ii,' times pe=',mpp_pe(),k,j,nbergs
     endif
   enddo
 
@@ -4781,7 +4767,7 @@ end function check_for_duplicate_ids_in_list
 subroutine test_check_for_duplicate_ids_in_list()
   ! Local variables
   integer :: k
-  integer, dimension(:), allocatable :: ids
+  integer(kind=8), dimension(:), allocatable :: ids
   integer :: error_count
 
   allocate(ids(5))
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index aa9b536..bce7271 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -143,8 +143,10 @@ subroutine write_restart(bergs)
                                       jne,              &
                                       iceberg_num,      &
                                       start_year,       &
-                                      first_berg_num,   &
-                                      other_berg_num,   &
+                                      first_id_cnt,     &
+                                      other_id_cnt,     &
+                                      first_id_ij,      &
+                                      other_id_ij,      &
                                       first_berg_jne,         &
                                       first_berg_ine,         &
                                       other_berg_jne,         &
@@ -322,8 +324,10 @@ subroutine write_restart(bergs)
     check_bond_quality=.true.
     call count_bonds(bergs, nbonds,check_bond_quality)
 
-  allocate(first_berg_num(nbonds))
-  allocate(other_berg_num(nbonds))
+  allocate(first_id_cnt(nbonds))
+  allocate(other_id_cnt(nbonds))
+  allocate(first_id_ij(nbonds))
+  allocate(other_id_ij(nbonds))
   allocate(first_berg_ine(nbonds))
   allocate(first_berg_jne(nbonds))
   allocate(other_berg_ine(nbonds))
@@ -340,10 +344,12 @@ subroutine write_restart(bergs)
 
   id = register_restart_field(bergs_bond_restart,filename_bonds,'first_berg_ine',first_berg_ine,longname='iceberg ine of first berg in bond',units='dimensionless')
   id = register_restart_field(bergs_bond_restart,filename_bonds,'first_berg_jne',first_berg_jne,longname='iceberg jne of first berg in bond',units='dimensionless')
-  id = register_restart_field(bergs_bond_restart,filename_bonds,'first_berg_num',first_berg_num,longname='iceberg id first berg in bond',units='dimensionless')
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'first_id_cnt',first_id_cnt,longname='counter component of iceberg id first berg in bond',units='dimensionless')
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'first_id_ij',first_id_ij,longname='position component of iceberg id first berg in bond',units='dimensionless')
   id = register_restart_field(bergs_bond_restart,filename_bonds,'other_berg_ine',other_berg_ine,longname='iceberg ine of second berg in bond',units='dimensionless')
   id = register_restart_field(bergs_bond_restart,filename_bonds,'other_berg_jne',other_berg_jne,longname='iceberg jne of second berg in bond',units='dimensionless')
-  id = register_restart_field(bergs_bond_restart,filename_bonds,'other_berg_num',other_berg_num,longname='iceberg id second berg in bond',units='dimensionless')
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'other_id_cnt',other_id_cnt,longname='counter component of iceberg id second berg in bond',units='dimensionless')
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'other_id_ij',other_id_ij,longname='position component of iceberg id second berg in bond',units='dimensionless')
 
 
   ! Write variables
@@ -357,8 +363,8 @@ subroutine write_restart(bergs)
         i = i + 1
         first_berg_ine(i)=this%ine
         first_berg_jne(i)=this%jne
-        first_berg_num(i)= this%iceberg_num
-        other_berg_num(i)=current_bond%other_berg_num
+        call split_id( this%id, first_id_cnt(i), first_id_ij(i) )
+        call split_id( current_bond%other_id, other_id_cnt(i), other_id_ij(i) )
         other_berg_ine(i)=current_bond%other_berg%ine
         other_berg_jne(i)=current_bond%other_berg%jne
 
@@ -372,9 +378,10 @@ subroutine write_restart(bergs)
   call free_restart_type(bergs_bond_restart)
 
 
-  deallocate(                 &
-             first_berg_num,  &
-             other_berg_num, &
+  deallocate(first_id_cnt,          &
+             other_id_cnt,          &
+             first_id_ij,           &
+             other_id_ij,           &
              first_berg_ine,        &
              first_berg_jne,        &
              other_berg_ine,        &
@@ -437,6 +444,7 @@ subroutine read_restart_bergs_orig(bergs,Time)
 type(iceberg) :: localberg ! NOT a pointer but an actual local variable
 integer :: stderrunit, iNg, jNg, i, j
 
+stop 'Obsolete!'
   ! Get the stderr unit number
   stderrunit=stderr()
 
@@ -899,7 +907,7 @@ subroutine read_restart_bergs(bergs,Time)
         call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg)
       else
         if (mpp_pe().eq.mpp_root_pe()) then
-          print * , 'Grounded iceberg: ', lat(k),lon(k), iceberg_num(k)
+          print * , 'Grounded iceberg: ', lat(k),lon(k), localberg%id
           call error_mesg('diamonds, read_restart_bergs', 'Iceberg not added because it is grounded', WARNING)
         endif
        endif
@@ -1148,13 +1156,13 @@ subroutine read_restart_bonds(bergs,Time)
 integer :: ine, jne
 logical :: search_data_domain
 real :: berg_found, berg_found_all_pe
-integer, allocatable, dimension(:) :: first_berg_num,   &
-                                      other_berg_num,   &
+integer, allocatable, dimension(:) :: id_cnt, id_ij,    &
                                       first_berg_jne,   &
                                       first_berg_ine,   &
                                       other_berg_jne,   &
                                       other_berg_ine
-integer(kind=8) :: id
+integer(kind=8), allocatable, dimension(:) :: first_id,   &
+                                              other_id
 !integer, allocatable, dimension(:,:) :: iceberg_counter_grd
 
   ! Get the stderr unit number
@@ -1182,16 +1190,27 @@ subroutine read_restart_bonds(bergs,Time)
 
   if (nbonds_in_file .gt. 0) then
 
-    allocate(first_berg_num(nbonds_in_file))
-    allocate(other_berg_num(nbonds_in_file))
+    allocate(first_id(nbonds_in_file))
+    allocate(other_id(nbonds_in_file))
+    allocate(id_cnt(nbonds_in_file))
+    allocate(id_ij(nbonds_in_file))
     allocate(first_berg_jne(nbonds_in_file))
     allocate(first_berg_ine(nbonds_in_file))
     allocate(other_berg_ine(nbonds_in_file))
     allocate(other_berg_jne(nbonds_in_file))
 
 
-    call read_unlimited_axis(filename,'first_berg_num',first_berg_num,domain=grd%domain)
-    call read_unlimited_axis(filename,'other_berg_num',other_berg_num,domain=grd%domain)
+    call read_unlimited_axis(filename,'first_id_cnt',id_cnt,domain=grd%domain)
+    call read_unlimited_axis(filename,'first_id_ij',id_ij,domain=grd%domain)
+    do k=1, nbonds_in_file
+      first_id(k) = id_from_2_ints( id_cnt(k), id_ij(k) )
+    enddo
+    call read_unlimited_axis(filename,'other_id_cnt',id_cnt,domain=grd%domain)
+    call read_unlimited_axis(filename,'other_id_ij',id_ij,domain=grd%domain)
+    do k=1, nbonds_in_file
+      other_id(k) = id_from_2_ints( id_cnt(k), id_ij(k) )
+    enddo
+    deallocate(id_cnt, id_ij)
     call read_unlimited_axis(filename,'first_berg_jne',first_berg_jne,domain=grd%domain)
     call read_unlimited_axis(filename,'first_berg_ine',first_berg_ine,domain=grd%domain)
     call read_unlimited_axis(filename,'other_berg_jne',other_berg_jne,domain=grd%domain)
@@ -1209,21 +1228,21 @@ subroutine read_restart_bonds(bergs,Time)
        if (ignore_ij_restart) then
          !Finding first iceberg in bond
          ine=999 ; jne=999 ; berg_found=0.0 ; search_data_domain=.true.
-         call find_individual_iceberg(bergs,first_berg_num(k), ine, jne,berg_found,search_data_domain)
+         call find_individual_iceberg(bergs,first_id(k), ine, jne,berg_found,search_data_domain)
          berg_found_all_pe=berg_found
          call mpp_sum(berg_found_all_pe)
          if (berg_found_all_pe .gt. 0.5) then
              first_berg_ine(k)=ine
              first_berg_jne(k)=jne
          else
-           print * , 'First bond berg not located: ', first_berg_num(k),berg_found, mpp_pe(),ine, jne
+           print * , 'First bond berg not located: ', first_id(k),berg_found, mpp_pe(),ine, jne
            call error_mesg('read_restart_bonds_bergs_new', 'First iceberg in bond not found on any pe', FATAL)
          endif
          !else
 
          !Finding other iceberg other iceberg
          ine=999 ; jne=999 ; berg_found=0.0 ; search_data_domain =.true.
-         call find_individual_iceberg(bergs,other_berg_num(k), ine, jne, berg_found,search_data_domain)
+         call find_individual_iceberg(bergs,other_id(k), ine, jne, berg_found,search_data_domain)
          berg_found_all_pe=berg_found
          call mpp_sum(berg_found_all_pe)
          if (berg_found_all_pe .gt. 0.5) then
@@ -1237,7 +1256,7 @@ subroutine read_restart_bonds(bergs,Time)
           call error_mesg('read_restart_bonds_bergs_new', 'Other iceberg in bond not found on any pe', FATAL)
          endif
          if (berg_found_all_pe .lt. 0.5) then
-                 print * , 'First bond berg not located: ', other_berg_num(k),berg_found, mpp_pe(),ine, jne
+                 print * , 'First bond berg not located: ', other_id(k),berg_found, mpp_pe(),ine, jne
              call error_mesg('read_restart_bonds_bergs_new', 'First bond iceberg not located', FATAL)
          endif
        endif
@@ -1252,10 +1271,10 @@ subroutine read_restart_bonds(bergs,Time)
         first_berg=>null()
         this=>bergs%list(first_berg_ine(k),first_berg_jne(k))%first
         do while(associated(this))
-          if (this%iceberg_num == first_berg_num(k)) then
+          if (this%id == first_id(k)) then
             first_berg_found=.true.
             first_berg=>this
-            !if (first_berg%halo_berg.gt.0.5) print *, 'bonding halo berg:', first_berg_num(k),  first_berg_ine(k),first_berg_jne(k) ,grd%isc, grd%iec, mpp_pe()
+            !if (first_berg%halo_berg.gt.0.5) print *, 'bonding halo berg:', first_id(k),  first_berg_ine(k),first_berg_jne(k) ,grd%isc, grd%iec, mpp_pe()
             this=>null()
           else
             this=>this%next
@@ -1274,7 +1293,7 @@ subroutine read_restart_bonds(bergs,Time)
           second_berg=>null()
           this=>bergs%list(other_berg_ine(k),other_berg_jne(k))%first
           do while(associated(this))
-            if (this%iceberg_num == other_berg_num(k)) then
+            if (this%id == other_id(k)) then
               second_berg_found=.true.
               second_berg=>this
               this=>null()
@@ -1287,8 +1306,7 @@ subroutine read_restart_bonds(bergs,Time)
         if (first_berg_found) then
           number_partial_bonds=number_partial_bonds+1
           if (second_berg_found) then
-            id = convert_old_id(grd, other_berg_num(k))
-            call form_a_bond(first_berg, other_berg_num(k), id, other_berg_ine(k), other_berg_jne(k),  second_berg)
+            call form_a_bond(first_berg, other_id(k), other_berg_ine(k), other_berg_jne(k),  second_berg)
             number_perfect_bonds=number_perfect_bonds+1
 
             !Counting number of bonds where the first bond is in the computational domain
@@ -1298,8 +1316,8 @@ subroutine read_restart_bonds(bergs,Time)
             endif
 
           else
-            !print *, 'Forming a bond of the second type', mpp_pe(), first_berg_num(k),  other_berg_num(k)
-            !call form_a_bond(first_berg, other_berg_num(k),other_berg_ine(k),other_berg_jne(k))
+            !print *, 'Forming a bond of the second type', mpp_pe(), first_id(k),  other_id(k)
+            !call form_a_bond(first_berg, other_id(k), other_berg_ine(k),other_berg_jne(k))
           endif
         else
           write(stderrunit,*) 'diamonds, bond read restart : ','Not enough partial bonds formed', k, mpp_pe(), nbonds_in_file
@@ -1340,8 +1358,6 @@ subroutine read_restart_bonds(bergs,Time)
     endif
 
     deallocate(               &
-            first_berg_num,   &
-            other_berg_num,  &
             first_berg_ine,   &
             first_berg_jne,   &
             other_berg_ine,  &
@@ -1493,14 +1509,14 @@ subroutine write_trajectory(trajectory, save_short_traj)
 logical, intent(in) :: save_short_traj !< If true, record less data
 ! Local variables
 integer :: iret, ncid, i_dim, i
-integer :: lonid, latid, yearid, dayid, uvelid, vvelid, iceberg_numid
+integer :: lonid, latid, yearid, dayid, uvelid, vvelid, idcntid, idijid
 integer :: uoid, void, uiid, viid, uaid, vaid, sshxid, sshyid, sstid, sssid
 integer :: cnid, hiid
 integer :: mid, did, wid, lid, mbid, hdid
 character(len=37) :: filename
 character(len=7) :: pe_name
 type(xyt), pointer :: this, next
-integer :: stderrunit
+integer :: stderrunit, cnt, ij
 !I/O vars
 type(xyt), pointer :: traj4io=>null()
 integer :: ntrajs_sent_io,ntrajs_rcvd_io
@@ -1612,7 +1628,8 @@ subroutine write_trajectory(trajectory, save_short_traj)
       latid = inq_varid(ncid, 'lat')
       yearid = inq_varid(ncid, 'year')
       dayid = inq_varid(ncid, 'day')
-      iceberg_numid = inq_varid(ncid, 'iceberg_num')
+      idcntid = inq_varid(ncid, 'id_cnt')
+      idijid = inq_varid(ncid, 'id_ij')
       if (.not.save_short_traj) then
         uvelid = inq_varid(ncid, 'uvel')
         vvelid = inq_varid(ncid, 'vvel')
@@ -1645,7 +1662,8 @@ subroutine write_trajectory(trajectory, save_short_traj)
       latid = def_var(ncid, 'lat', NF_DOUBLE, i_dim)
       yearid = def_var(ncid, 'year', NF_INT, i_dim)
       dayid = def_var(ncid, 'day', NF_DOUBLE, i_dim)
-      iceberg_numid = def_var(ncid, 'iceberg_num', NF_INT, i_dim)
+      idcntid = def_var(ncid, 'id_cnt', NF_INT, i_dim)
+      idijid = def_var(ncid, 'id_ij', NF_INT, i_dim)
       if (.not. save_short_traj) then
         uvelid = def_var(ncid, 'uvel', NF_DOUBLE, i_dim)
         vvelid = def_var(ncid, 'vvel', NF_DOUBLE, i_dim)
@@ -1680,8 +1698,10 @@ subroutine write_trajectory(trajectory, save_short_traj)
       call put_att(ncid, yearid, 'units', 'years')
       call put_att(ncid, dayid, 'long_name', 'year day')
       call put_att(ncid, dayid, 'units', 'days')
-      call put_att(ncid, iceberg_numid, 'long_name', 'iceberg id number')
-      call put_att(ncid, iceberg_numid, 'units', 'dimensionless')
+      call put_att(ncid, idcntid, 'long_name', 'counter component of iceberg id')
+      call put_att(ncid, idcntid, 'units', 'dimensionless')
+      call put_att(ncid, idijid, 'long_name', 'position component of iceberg id')
+      call put_att(ncid, idijid, 'units', 'dimensionless')
 
       if (.not. save_short_traj) then
         call put_att(ncid, uvelid, 'long_name', 'zonal spped')
@@ -1744,7 +1764,9 @@ subroutine write_trajectory(trajectory, save_short_traj)
       call put_double(ncid, latid, i, this%lat)
       call put_int(ncid, yearid, i, this%year)
       call put_double(ncid, dayid, i, this%day)
-      call put_int(ncid, iceberg_numid, i, this%iceberg_num)
+      call split_id(this%id, cnt, ij)
+      call put_int(ncid, idcntid, i, cnt)
+      call put_int(ncid, idijid, i, ij)
       if (.not. save_short_traj) then
         call put_double(ncid, uvelid, i, this%uvel)
         call put_double(ncid, vvelid, i, this%vvel)
@@ -1823,8 +1845,7 @@ integer function def_var(ncid, var, ntype, idim)
 
   iret = nf_def_var(ncid, var, ntype, 1, idim, def_var)
   if (iret .ne. NF_NOERR) then
-    write(stderrunit,*) 'diamonds, def_var: nf_def_var failed for ',trim(var)
-    call error_mesg('diamonds, def_var', 'netcdf function returned a failure!', FATAL)
+    call error_mesg('diamonds, def_var', nf_strerror(iret), FATAL)
   endif
 
 end function def_var

From 22bb2a04ce34790ded9a99070889fa5179c654a4 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Sat, 17 Jun 2017 19:02:20 -0400
Subject: [PATCH 229/361] Removed read_restart_bergs_orig()

- Removed code used to read legacy restarts.
- Added FATAL error message if "read_orig" is set in the namelist.
---
 icebergs.F90    |  10 +-
 icebergs_io.F90 | 282 +-----------------------------------------------
 2 files changed, 6 insertions(+), 286 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 8a58b60..8f7c2dd 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -45,8 +45,8 @@ module ice_bergs
 use ice_bergs_framework, only: test_check_for_duplicate_ids_in_list
 use ice_bergs_framework, only: generate_id
 
-use ice_bergs_io,        only: ice_bergs_io_init,write_restart,write_trajectory
-use ice_bergs_io,        only: read_restart_bergs,read_restart_bergs_orig,read_restart_calving
+use ice_bergs_io,        only: ice_bergs_io_init, write_restart, write_trajectory
+use ice_bergs_io,        only: read_restart_bergs, read_restart_calving
 use ice_bergs_io,        only: read_restart_bonds
 use ice_bergs_io,        only: read_ocean_depth
 
@@ -126,10 +126,10 @@ subroutine icebergs_init(bergs, &
   call mpp_clock_begin(bergs%clock_ior)
   call ice_bergs_io_init(bergs,io_layout)
   call read_restart_calving(bergs)  !This is moved to before restart_bergs (by Alon) so that generate icebergs can have the correct counter
-  if(orig_read) then
-     call read_restart_bergs_orig(bergs,Time)
+  if (orig_read) then
+    call error_mesg('diamonds, icebergs_init: ', 'Parameter "orig_read" is no longer supported!', FATAL)
   else
-     call read_restart_bergs(bergs,Time)
+    call read_restart_bergs(bergs,Time)
   endif
   call bergs_chksum(bergs, 'read_restart bergs')
   if (fix_restart_dates) call offset_berg_dates(bergs,Time)
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index bce7271..3370702 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -46,7 +46,7 @@ module ice_bergs_io
 include 'netcdf.inc'
 
 public ice_bergs_io_init
-public read_restart_bergs,read_restart_bergs_orig,write_restart,write_trajectory
+public read_restart_bergs, write_restart, write_trajectory
 public read_restart_calving, read_restart_bonds
 public read_ocean_depth
 
@@ -424,202 +424,6 @@ function last_berg(berg)
 
 end function last_berg
 
-!> Read an iceberg restart file (original implementation)
-subroutine read_restart_bergs_orig(bergs,Time)
-! Arguments
-type(icebergs), pointer :: bergs !< Icebergs container
-type(time_type), intent(in) :: Time !< Model time
-! Local variables
-integer, dimension(:), allocatable :: found_restart_int
-integer :: k, ierr, ncid, dimid, nbergs_in_file
-integer :: lonid, latid,  uvelid, vvelid, ineid, jneid
-integer :: axnid, aynid, uvel_oldid, vvel_oldid, bxnid, bynid
-integer :: massid, thicknessid, widthid, lengthid
-integer :: start_lonid, start_latid, start_yearid, iceberg_numid, start_dayid, start_massid
-integer :: scaling_id, mass_of_bits_id, heat_density_id, static_bergid
-logical :: lres, found_restart, multiPErestart
-real :: lon0, lon1, lat0, lat1
-character(len=33) :: filename, filename_base
-type(icebergs_gridded), pointer :: grd
-type(iceberg) :: localberg ! NOT a pointer but an actual local variable
-integer :: stderrunit, iNg, jNg, i, j
-
-stop 'Obsolete!'
-  ! Get the stderr unit number
-  stderrunit=stderr()
-
-  ! For convenience
-  grd=>bergs%grd
-  iNg=(grd%ieg-grd%isg+1) ! Total number of points globally in i direction
-  jNg=(grd%jeg-grd%jsg+1) ! Total number of points globally in j direction
-
-  ! Find a restart file
-  multiPErestart=.false.
-
-  ! Zero out nbergs_in_file
-  nbergs_in_file = 0
-
-  filename_base=trim(restart_input_dir)//'icebergs.res.nc'
-
-  found_restart = find_restart_file(filename_base, filename, multiPErestart, io_tile_id(1))
-
-  ! Check if no restart found on any pe
-  allocate(found_restart_int(mpp_npes()))
-  if (found_restart .eqv. .true.) then
-     k=1
-  else
-     k=0
-  endif
-  call mpp_gather((/k/),found_restart_int)
-  if (sum(found_restart_int)==0.and.mpp_pe()==mpp_root_pe())&
-       & write(*,'(a)') 'diamonds, read_restart_bergs: no restart file found'
-  deallocate(found_restart_int)
-
-  if (.not.found_restart) then
-
-  multiPErestart=.true. ! This is to force sanity checking in a mulit-PE mode if no file was found on this PE
-
-  elseif (found_restart) then ! if (.not.found_restart)
-  ! only do the following if a file was found
-
-  if (verbose.and.mpp_pe()==mpp_root_pe()) write(*,'(2a)') 'diamonds, read_restart_bergs: found restart file = ',filename
-
-  ierr=nf_open(filename, NF_NOWRITE, ncid)
-  if (ierr .ne. NF_NOERR) write(stderrunit,*) 'diamonds, read_restart_bergs: nf_open failed'
-
-  ierr=nf_inq_unlimdim(ncid, dimid)
-  if (ierr .ne. NF_NOERR) write(stderrunit,*) 'diamonds, read_restart_bergs: nf_inq_unlimdim failed'
-
-  ierr=nf_inq_dimlen(ncid, dimid, nbergs_in_file)
-  if (ierr .ne. NF_NOERR) write(stderrunit,*) 'diamonds, read_restart_bergs: nf_inq_dimlen failed'
- !write(stderrunit,*) 'diamonds, read_restart_bergs: nbergs in file =', nbergs_in_file
-
-  lonid=inq_var(ncid, 'lon')
-  latid=inq_var(ncid, 'lat')
-  uvelid=inq_var(ncid, 'uvel')
-  vvelid=inq_var(ncid, 'vvel')
-  massid=inq_var(ncid, 'mass')
-  axnid=inq_var(ncid, 'axn', unsafe=.true.)
-  aynid=inq_var(ncid, 'ayn', unsafe=.true.)
-  bxnid=inq_var(ncid, 'bxn', unsafe=.true.)
-  bynid=inq_var(ncid, 'byn', unsafe=.true.)
-  thicknessid=inq_var(ncid, 'thickness')
-  widthid=inq_var(ncid, 'width')
-  lengthid=inq_var(ncid, 'length')
-  start_lonid=inq_var(ncid, 'start_lon')
-  start_latid=inq_var(ncid, 'start_lat')
-  start_yearid=inq_var(ncid, 'start_year')
-  iceberg_numid=inq_var(ncid, 'icberg_num', unsafe=.true.)
-  start_dayid=inq_var(ncid, 'start_day')
-  start_massid=inq_var(ncid, 'start_mass')
-  scaling_id=inq_var(ncid, 'mass_scaling')
-  static_bergid=inq_var(ncid, 'static_berg', unsafe=.true.)
-  mass_of_bits_id=inq_var(ncid, 'mass_of_bits', unsafe=.true.)
-  heat_density_id=inq_var(ncid, 'heat_density', unsafe=.true.)
-  ineid=inq_var(ncid, 'ine',unsafe=.true.)
-  jneid=inq_var(ncid, 'jne',unsafe=.true.)
-
-  ! Find approx outer bounds for tile
-  lon0=minval( grd%lon(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
-  lon1=maxval( grd%lon(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
-  lat0=minval( grd%lat(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
-  lat1=maxval( grd%lat(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
- !write(stderrunit,'(a,i3,a,4f10.3)') 'diamonds, read_restart_bergs: (',mpp_pe(),') ',lon0,lon1,lat0,lat1
-  do k=1, nbergs_in_file
-   !write(stderrunit,*) 'diamonds, read_restart_bergs: reading berg ',k
-    localberg%lon=get_double(ncid, lonid, k)
-    localberg%lat=get_double(ncid, latid, k)
-    if (ineid>0 .and. jneid>0 .and. .not. ignore_ij_restart) then ! read i,j position and avoid the "find" step
-      localberg%ine=get_int(ncid, ineid, k)
-      localberg%jne=get_int(ncid, jneid, k)
-      if ( localberg%ine>=grd%isc .and. localberg%ine<=grd%iec .and. &
-           localberg%jne>=grd%jsc .and.localberg%jne<=grd%jec ) then
-        lres=.true.
-      else
-        lres=.false.
-      endif
-    else ! i,j are not available from the file so we search the grid to find out if we reside on this PE
-      if (use_slow_find) then
-        lres=find_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
-      else
-        lres=find_cell_by_search(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
-      endif
-    endif
-    if (really_debug) then
-      write(stderrunit,'(a,i8,a,2f9.4,a,i8)') 'diamonds, read_restart_bergs: berg ',k,' is at ',localberg%lon,localberg%lat,&
-           & ' on PE ',mpp_pe()
-      write(stderrunit,*) 'diamonds, read_restart_bergs: lres = ',lres
-    endif
-    if (lres) then ! true if we reside on this PE grid
-      localberg%uvel=get_double(ncid, uvelid, k)
-      localberg%vvel=get_double(ncid, vvelid, k)
-      localberg%mass=get_double(ncid, massid, k)
-      localberg%axn=get_real_from_file(ncid, axnid, k, value_if_not_in_file=0.)
-      localberg%ayn=get_real_from_file(ncid, aynid, k, value_if_not_in_file=0.)
-      localberg%bxn=get_real_from_file(ncid, bxnid, k, value_if_not_in_file=0.)
-      localberg%byn=get_real_from_file(ncid, bynid, k, value_if_not_in_file=0.)
-      localberg%thickness=get_double(ncid, thicknessid, k)
-      localberg%width=get_double(ncid, widthid, k)
-      localberg%length=get_double(ncid, lengthid, k)
-      localberg%start_lon=get_double(ncid, start_lonid, k)
-      localberg%start_lat=get_double(ncid, start_latid, k)
-      localberg%start_year=get_int(ncid, start_yearid, k)
-      if (iceberg_numid>0) then
-        localberg%iceberg_num=get_int(ncid, iceberg_numid, k)
-        localberg%id = convert_old_id(grd, localberg%iceberg_num)
-      else
-        localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
-        localberg%id = generate_id(grd, i, j)
-      endif
-      localberg%start_day=get_double(ncid, start_dayid, k)
-      localberg%start_mass=get_double(ncid, start_massid, k)
-      localberg%mass_scaling=get_double(ncid, scaling_id, k)
-      localberg%halo_berg=0.
-      localberg%static_berg=get_real_from_file(ncid, static_bergid, k, value_if_not_in_file=0.)
-      localberg%mass_of_bits=get_real_from_file(ncid, mass_of_bits_id, k, value_if_not_in_file=0.)
-      localberg%heat_density=get_real_from_file(ncid, heat_density_id, k, value_if_not_in_file=0.)
-      if (really_debug) lres=is_point_in_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, explain=.true.)
-      lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
-     !call add_new_berg_to_list(bergs%first, localberg, quick=.true.)
-      call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg)
-      if (really_debug) call print_berg(stderrunit, bergs%list(localberg%ine,localberg%jne)%first, 'read_restart_bergs, add_new_berg_to_list')
-    elseif (multiPErestart .and. io_tile_id(1) .lt. 0) then
-      call error_mesg('diamonds, read_restart_bergs', 'berg in PE file was not on PE!', FATAL)
-    endif
-  enddo
-
-  else ! if no restart file was read on this PE
-    nbergs_in_file=0
-  endif ! if (.not.found_restart)
-
-  ! Sanity check
-  k=count_bergs(bergs)
-  if (verbose) write(*,'(2(a,i8))') 'diamonds, read_restart_bergs: # bergs =',k,' on PE',mpp_pe()
-  if (multiPErestart)  then
-      if (.NOT. is_io_tile_root_pe) nbergs_in_file=0 !If io_layout specified only tile root pes should count bergs
-      call mpp_sum(nbergs_in_file) ! In case PE 0 didn't open a file
-  endif
-  call mpp_sum(k)
-  bergs%nbergs_start=k
-  if (mpp_pe().eq.mpp_root_pe()) then
-    write(*,'(a,i8,a,i8,a)') 'diamonds, read_restart_bergs: there were',nbergs_in_file,' bergs in the restart file and', &
-     k,' bergs have been read'
-  endif
-
-  if (k.ne.nbergs_in_file) call error_mesg('diamonds, read_restart_bergs', 'wrong number of bergs read!', FATAL)
-
-  if (.not. found_restart .and. bergs%nbergs_start==0 .and. generate_test_icebergs) call generate_bergs_orig(bergs,Time)
-
-  bergs%floating_mass_start=sum_mass(bergs)
-  call mpp_sum( bergs%floating_mass_start )
-  bergs%icebergs_mass_start=sum_mass(bergs,justbergs=.true.)
-  call mpp_sum( bergs%icebergs_mass_start )
-  bergs%bergy_mass_start=sum_mass(bergs,justbits=.true.)
-  call mpp_sum( bergs%bergy_mass_start )
-  if (mpp_pe().eq.mpp_root_pe().and.verbose) write(*,'(a)') 'diamonds, read_restart_bergs: completed'
-
-end subroutine read_restart_bergs_orig
-
 !> Read a real value from a file and optionally return a default value if variable is missing
 real function get_real_from_file(ncid, varid, k, value_if_not_in_file)
 integer, intent(in) :: ncid, varid, k
@@ -632,90 +436,6 @@ real function get_real_from_file(ncid, varid, k, value_if_not_in_file)
 endif
 end function get_real_from_file
 
-!> Generate bergs for the purpose of debugging
-subroutine generate_bergs_orig(bergs, Time)
-! Arguments
-type(icebergs), pointer :: bergs !< Icebergs container
-type(time_type), intent(in) :: Time !< Model time
-! Local variables
-type(icebergs_gridded), pointer :: grd
-integer :: i,j
-integer :: iNg, jNg  !Total number of points gloablly in i and j direction
-type(iceberg) :: localberg ! NOT a pointer but an actual local variable
-integer :: iyr, imon, iday, ihr, imin, isec
-
-  ! For convenience
-  grd=>bergs%grd
-  iNg=(grd%ieg-grd%isg+1) ! Total number of points globally in i direction
-  jNg=(grd%jeg-grd%jsg+1) ! Total number of points globally in j direction
-
-  call get_date(Time, iyr, imon, iday, ihr, imin, isec)
-
-  do j=grd%jsc,grd%jec; do i=grd%isc,grd%iec
-    if (grd%msk(i,j)>0. .and. abs(grd%latc(i,j))>60.) then
-      localberg%xi=0.5
-      localberg%yj=0.5
-      localberg%ine=i
-      localberg%jne=j
-      localberg%lon=bilin(grd, grd%lon, i, j, localberg%xi, localberg%yj)
-      localberg%lat=bilin(grd, grd%lat, i, j, localberg%xi, localberg%yj)
-      localberg%lon_old=bilin(grd, grd%lon, i, j, localberg%xi, localberg%yj) !Alon
-      localberg%lat_old=bilin(grd, grd%lat, i, j, localberg%xi, localberg%yj) !Alon
-      localberg%mass=bergs%initial_mass(1)
-      localberg%thickness=bergs%initial_thickness(1)
-      localberg%width=bergs%initial_width(1)
-      localberg%length=bergs%initial_length(1)
-      localberg%start_lon=localberg%lon
-      localberg%start_lat=localberg%lat
-      localberg%start_year=iyr
-      localberg%start_day=float(iday)+(float(ihr)+float(imin)/60.)/24.
-      localberg%start_mass=localberg%mass
-      localberg%mass_scaling=bergs%mass_scaling(1)
-      localberg%mass_of_bits=0.
-      localberg%halo_berg=0.
-      localberg%static_berg=0.
-      localberg%heat_density=0.
-      localberg%axn=0. !Alon
-      localberg%ayn=0. !Alon
-      localberg%uvel_old=0. !Alon
-      localberg%vvel_old=0. !Alon
-      localberg%bxn=0. !Alon
-      localberg%byn=0. !Alon
-
-      !Berg A
-      localberg%uvel=1.
-      localberg%vvel=0.
-      localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
-      localberg%id = generate_id(grd, i, j)
-      call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
-      !Berg B
-      localberg%uvel=-1.
-      localberg%vvel=0.
-      localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
-      localberg%id = generate_id(grd, i, j)
-      call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
-      !Berg C
-      localberg%uvel=0.
-      localberg%vvel=1.
-      localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
-      localberg%id = generate_id(grd, i, j)
-      call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
-      !Berg D
-      localberg%uvel=0.
-      localberg%vvel=-1.
-      localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
-      localberg%id = generate_id(grd, i, j)
-      call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
-    endif
-  enddo; enddo
-
-  bergs%nbergs_start=count_bergs(bergs)
-  call mpp_sum(bergs%nbergs_start)
-  if (mpp_pe().eq.mpp_root_pe()) &
-    write(*,'(a,i8,a)') 'diamonds, generate_bergs: ',bergs%nbergs_start,' were generated'
-
-end subroutine generate_bergs_orig
-
 !> Read an iceberg restart file
 subroutine read_restart_bergs(bergs,Time)
 ! Arguments

From df4e43a3120e38c3d60ba49e8400f0265a3af0eb Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Sat, 17 Jun 2017 19:23:17 -0400
Subject: [PATCH 230/361] Add id to write_restart()

- Add id (as id_cnt,id_ij) to restart files (not yet used when reading).
---
 icebergs_io.F90 | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 3370702..1ea8a7d 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -142,6 +142,8 @@ subroutine write_restart(bergs)
 integer, allocatable, dimension(:) :: ine,              &
                                       jne,              &
                                       iceberg_num,      &
+                                      id_cnt,           &
+                                      id_ij,            &
                                       start_year,       &
                                       first_id_cnt,     &
                                       other_id_cnt,     &
@@ -197,6 +199,8 @@ subroutine write_restart(bergs)
    allocate(jne(nbergs))
    allocate(start_year(nbergs))
    allocate(iceberg_num(nbergs))
+   allocate(id_cnt(nbergs))
+   allocate(id_ij(nbergs))
 
 
   call get_instance_filename("icebergs.res.nc", filename)
@@ -233,6 +237,10 @@ subroutine write_restart(bergs)
                                             longname='calendar year of calving event', units='years')
   id = register_restart_field(bergs_restart,filename,'iceberg_num',iceberg_num, &
                                             longname='identification of the iceberg', units='dimensionless')
+  id = register_restart_field(bergs_restart,filename,'id_cnt',id_cnt, &
+                                            longname='counter component of iceberg id', units='dimensionless')
+  id = register_restart_field(bergs_restart,filename,'id_ij',id_ij, &
+                                            longname='position component of iceberg id', units='dimensionless')
   id = register_restart_field(bergs_restart,filename,'start_day',start_day, &
                                             longname='year day of calving event',units='days')
   id = register_restart_field(bergs_restart,filename,'start_mass',start_mass, &
@@ -277,6 +285,7 @@ subroutine write_restart(bergs)
       start_mass(i) = this%start_mass; mass_scaling(i) = this%mass_scaling
       static_berg(i) = this%static_berg
       iceberg_num(i) = this%iceberg_num
+      call split_id(this%id, id_cnt(i), id_ij(i))
       mass_of_bits(i) = this%mass_of_bits; heat_density(i) = this%heat_density
       this=>this%next
     enddo
@@ -312,6 +321,8 @@ subroutine write_restart(bergs)
              ine,       &
              jne,       &
              iceberg_num,       &
+             id_cnt,    &
+             id_ij,     &
              start_year )
 
   call nullify_domain()

From 3038a4730ccd49caaa47f48669a8336799acb572 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Sat, 17 Jun 2017 20:23:28 -0400
Subject: [PATCH 231/361] Start grd%iceberg_counter at 0 and increment before
 generating berg

- I can not figure out why we would initialize the counter to 1 and then
  increment after generating a berg. Starting at 0 and incrementing before
  generating a berg means the counter is now a counter of how many bergs
  were calved in that cell.
---
 icebergs_framework.F90 | 6 +++---
 icebergs_io.F90        | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 19b3f23..04ee22b 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -715,7 +715,7 @@ subroutine ice_bergs_framework_init(bergs, &
   allocate( bergs%nbergs_calved_by_class(nclasses) ); bergs%nbergs_calved_by_class(:)=0
   allocate( grd%parity_x(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%parity_x(:,:)=1.
   allocate( grd%parity_y(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%parity_y(:,:)=1.
-  allocate( grd%iceberg_counter_grd(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%iceberg_counter_grd(:,:)=1
+  allocate( grd%iceberg_counter_grd(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%iceberg_counter_grd(:,:)=0
 
  !write(stderrunit,*) 'diamonds: copying grid'
   ! Copy data declared on ice model computational domain
@@ -2377,12 +2377,12 @@ integer(kind=8) function generate_id(grd, i, j)
   ! Local variables
   integer :: ij ! Hash of i,j
 
+  ! Increment counter in calving cell
+  grd%iceberg_counter_grd(i,j) = grd%iceberg_counter_grd(i,j) + 1
   ! ij is unique number for each grid cell (32-bit integers allow for ~1/100th degree global resolution)
   ij = ij_component_of_id(grd, i, j)
   ! Generate a 64-bit id
   generate_id = id_from_2_ints( grd%iceberg_counter_grd(i,j), ij )
-  ! Increment counter in calving cell
-  grd%iceberg_counter_grd(i,j) = grd%iceberg_counter_grd(i,j) + 1
 
 end function generate_id
 
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 1ea8a7d..6456ad9 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -1157,7 +1157,7 @@ subroutine read_restart_calving(bergs)
     else
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
      'diamonds, read_restart_calving: iceberg_counter_grd WAS NOT FOUND in the file. Setting to 0.'
-      grd%iceberg_counter_grd(:,:)=1
+      grd%iceberg_counter_grd(:,:) = 0
     endif
     bergs%restarted=.true.
   else

From 08ea4460c86736839dfd0c7c09707df80b462127 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Sat, 17 Jun 2017 20:31:08 -0400
Subject: [PATCH 232/361] Split convert_old_id() in cij_from_old_id()

- When reading the 32-bit iceberg_num from restarts we will need to
  recover the starting i,j for the berg.
- Also removed comments abotu moving read_restart_calving().
---
 icebergs.F90           |  3 +--
 icebergs_framework.F90 | 23 ++++++++++++++++++-----
 2 files changed, 19 insertions(+), 7 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 8f7c2dd..2695b59 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -125,7 +125,7 @@ subroutine icebergs_init(bergs, &
 
   call mpp_clock_begin(bergs%clock_ior)
   call ice_bergs_io_init(bergs,io_layout)
-  call read_restart_calving(bergs)  !This is moved to before restart_bergs (by Alon) so that generate icebergs can have the correct counter
+  call read_restart_calving(bergs)
   if (orig_read) then
     call error_mesg('diamonds, icebergs_init: ', 'Parameter "orig_read" is no longer supported!', FATAL)
   else
@@ -133,7 +133,6 @@ subroutine icebergs_init(bergs, &
   endif
   call bergs_chksum(bergs, 'read_restart bergs')
   if (fix_restart_dates) call offset_berg_dates(bergs,Time)
-  !call read_restart_calving(bergs)
   call mpp_clock_end(bergs%clock_ior)
 
   if (really_debug) call print_bergs(stderrunit,bergs,'icebergs_init, initial status')
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 04ee22b..841412a 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -75,7 +75,7 @@ module ice_bergs_framework
 public is_point_within_xi_yj_bounds
 public test_check_for_duplicate_ids_in_list
 public check_for_duplicates_in_parallel
-public split_id, id_from_2_ints, generate_id, convert_old_id
+public split_id, id_from_2_ints, generate_id, cij_from_old_id, convert_old_id
 
 !> Container for gridded fields
 type :: icebergs_gridded
@@ -2394,6 +2394,22 @@ integer(kind=8) function convert_old_id(grd, old_id)
   integer :: cnt ! Counter component
   integer :: ij ! Hash of i,j
   integer :: i,j ! Cell indexes
+
+  call cij_from_old_id(grd, old_id, cnt, i, j)
+  ij = ij_component_of_id(grd, i, j)
+  convert_old_id = id_from_2_ints( cnt, ij )
+
+end function convert_old_id
+
+!> Recover i,j an old 32-bit id
+subroutine cij_from_old_id(grd, old_id, cnt, i, j)
+  type(icebergs_gridded), pointer     :: grd    !< Container for gridded fields
+  integer,                intent(in)  :: old_id !< 32-bit iceberg id
+  integer,                intent(out) :: cnt    !< Counter component of old id
+  integer,                intent(out) :: i      !< i-index of calving cell
+  integer,                intent(out) :: j      !< j-index of calving cell
+  ! Local variables
+  integer :: ij ! Hash of i,j
   integer :: iNg, jNg, ncells ! Shape and size of the global grid
 
   ! Number cells in the grid
@@ -2410,10 +2426,7 @@ integer(kind=8) function convert_old_id(grd, old_id)
   j = ij / iNg
   i = mod( ij, iNg )
 
-  ij = ij_component_of_id(grd, i, j)
-  convert_old_id = id_from_2_ints( cnt, ij )
-
-end function convert_old_id
+end subroutine cij_from_old_id
 
 !> Calculate the location-derived component of an iceberg id which is a hash of the i,j-indexes for the cell
 integer function ij_component_of_id(grd, i, j)

From be476433d8c92cd253b98c1ac8ac760271c735ea Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Sat, 17 Jun 2017 20:39:55 -0400
Subject: [PATCH 233/361] Read id from restarts or generate ids if iceberg_num
 is present

- We now read id_cnt and id_ij to create an id, unless iceberg_num
  is present.
- No longer write iceberg_num (ever).
---
 icebergs_io.F90 | 69 ++++++++++++++++++++++++++-----------------------
 1 file changed, 36 insertions(+), 33 deletions(-)

diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 6456ad9..54f76d5 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -39,7 +39,7 @@ module ice_bergs_io
 use ice_bergs_framework, only: ignore_ij_restart, use_slow_find,generate_test_icebergs,print_berg
 use ice_bergs_framework, only: force_all_pes_traj
 use ice_bergs_framework, only: check_for_duplicates_in_parallel
-use ice_bergs_framework, only: split_id, id_from_2_ints, generate_id, convert_old_id
+use ice_bergs_framework, only: split_id, id_from_2_ints, generate_id
 
 implicit none ; private
 
@@ -141,7 +141,6 @@ subroutine write_restart(bergs)
 
 integer, allocatable, dimension(:) :: ine,              &
                                       jne,              &
-                                      iceberg_num,      &
                                       id_cnt,           &
                                       id_ij,            &
                                       start_year,       &
@@ -198,7 +197,6 @@ subroutine write_restart(bergs)
    allocate(ine(nbergs))
    allocate(jne(nbergs))
    allocate(start_year(nbergs))
-   allocate(iceberg_num(nbergs))
    allocate(id_cnt(nbergs))
    allocate(id_ij(nbergs))
 
@@ -235,8 +233,6 @@ subroutine write_restart(bergs)
                                             longname='latitude of calving location',units='degrees_N')
   id = register_restart_field(bergs_restart,filename,'start_year',start_year, &
                                             longname='calendar year of calving event', units='years')
-  id = register_restart_field(bergs_restart,filename,'iceberg_num',iceberg_num, &
-                                            longname='identification of the iceberg', units='dimensionless')
   id = register_restart_field(bergs_restart,filename,'id_cnt',id_cnt, &
                                             longname='counter component of iceberg id', units='dimensionless')
   id = register_restart_field(bergs_restart,filename,'id_ij',id_ij, &
@@ -284,7 +280,6 @@ subroutine write_restart(bergs)
       start_year(i) = this%start_year; start_day(i) = this%start_day
       start_mass(i) = this%start_mass; mass_scaling(i) = this%mass_scaling
       static_berg(i) = this%static_berg
-      iceberg_num(i) = this%iceberg_num
       call split_id(this%id, id_cnt(i), id_ij(i))
       mass_of_bits(i) = this%mass_of_bits; heat_density(i) = this%heat_density
       this=>this%next
@@ -314,13 +309,12 @@ subroutine write_restart(bergs)
              start_mass,   &
              mass_scaling, &
              mass_of_bits, &
-             static_berg,    &
+             static_berg,  &
              heat_density )
 
   deallocate(           &
              ine,       &
              jne,       &
-             iceberg_num,       &
              id_cnt,    &
              id_ij,     &
              start_year )
@@ -454,7 +448,7 @@ subroutine read_restart_bergs(bergs,Time)
 type(time_type), intent(in) :: Time !< Model time
 ! Local variables
 integer :: k, siz(4), nbergs_in_file, nbergs_read
-logical :: lres, found_restart, found
+logical :: lres, found_restart, found, replace_iceberg_num
 logical :: explain
 logical :: multiPErestart  ! Not needed with new restart read; currently kept for compatibility
 real :: lon0, lon1, lat0, lat1
@@ -462,7 +456,7 @@ subroutine read_restart_bergs(bergs,Time)
 character(len=33) :: filename, filename_base
 type(icebergs_gridded), pointer :: grd
 type(iceberg) :: localberg ! NOT a pointer but an actual local variable
-integer :: stderrunit, iNg, jNg, i, j
+integer :: stderrunit, i, j, cnt, ij
 
 real, allocatable, dimension(:) :: lon,          &
                                    lat,          &
@@ -482,11 +476,13 @@ subroutine read_restart_bergs(bergs,Time)
                                    start_mass,   &
                                    mass_scaling, &
                                    mass_of_bits, &
-                                   static_berg,    &
+                                   static_berg,  &
                                    heat_density
-integer, allocatable, dimension(:) :: ine,       &
-                                      jne,       &
-                                      iceberg_num,       &
+integer, allocatable, dimension(:) :: ine,        &
+                                      jne,        &
+                                      iceberg_num,&
+                                      id_cnt,     &
+                                      id_ij,      &
                                       start_year
 
 !integer, allocatable, dimension(:,:) :: iceberg_counter_grd
@@ -496,8 +492,6 @@ subroutine read_restart_bergs(bergs,Time)
 
   ! For convenience
   grd=>bergs%grd
-  iNg=(grd%ieg-grd%isg+1) ! Total number of points globally in i direction
-  jNg=(grd%jeg-grd%jsg+1) ! Total number of points globally in j direction
 
   ! Zero out nbergs_in_file
   nbergs_in_file = 0
@@ -505,7 +499,6 @@ subroutine read_restart_bergs(bergs,Time)
   filename_base=trim(restart_input_dir)//'icebergs.res.nc'
 
   found_restart = find_restart_file(filename_base, filename, multiPErestart, io_tile_id(1))
-  call error_mesg('read_restart_bergs_new', 'Using new icebergs restart read', NOTE)
 
   if (found_restart) then
      filename = filename_base
@@ -514,6 +507,7 @@ subroutine read_restart_bergs(bergs,Time)
   endif
 
   if(nbergs_in_file > 0) then
+     replace_iceberg_num = field_exist(filename, 'iceberg_num') ! True if using 32-bit iceberg_num in restart file
      allocate(lon(nbergs_in_file))
      allocate(lat(nbergs_in_file))
      allocate(uvel(nbergs_in_file))
@@ -537,7 +531,13 @@ subroutine read_restart_bergs(bergs,Time)
      allocate(ine(nbergs_in_file))
      allocate(jne(nbergs_in_file))
      allocate(start_year(nbergs_in_file))
-     allocate(iceberg_num(nbergs_in_file))
+     if (replace_iceberg_num) then
+       call error_mesg('read_restart_bergs', "Calculating new iceberg ID's", WARNING)
+       allocate(iceberg_num(nbergs_in_file))
+     else
+       allocate(id_cnt(nbergs_in_file))
+       allocate(id_ij(nbergs_in_file))
+     endif
   endif
 
   if (found_restart .and. nbergs_in_file > 0) then
@@ -563,7 +563,12 @@ subroutine read_restart_bergs(bergs,Time)
      call read_unlimited_axis(filename,'ine',ine,domain=grd%domain)
      call read_unlimited_axis(filename,'jne',jne,domain=grd%domain)
      call read_unlimited_axis(filename,'start_year',start_year,domain=grd%domain)
-     call read_int_vector(filename,'iceberg_num',iceberg_num,grd%domain,value_if_not_in_file=-1)
+     if (replace_iceberg_num) then
+       call read_int_vector(filename,'iceberg_num',iceberg_num,grd%domain,value_if_not_in_file=-1)
+     else
+       call read_int_vector(filename,'id_cnt',id_cnt,grd%domain)
+       call read_int_vector(filename,'id_ij',id_ij,grd%domain)
+     endif
      call read_real_vector(filename,'static_berg',static_berg,grd%domain,value_if_not_in_file=0.)
   endif
 
@@ -615,8 +620,11 @@ subroutine read_restart_bergs(bergs,Time)
       localberg%start_lon=start_lon(k)
       localberg%start_lat=start_lat(k)
       localberg%start_year=start_year(k)
-      localberg%iceberg_num=iceberg_num(k)
-      localberg%id=convert_old_id(grd, localberg%iceberg_num)
+      if (replace_iceberg_num) then
+        localberg%id = generate_id(grd, localberg%ine, localberg%jne)
+      else
+        localberg%id=id_from_2_ints(id_cnt(k), id_ij(k))
+      endif
       localberg%start_day=start_day(k)
       localberg%start_mass=start_mass(k)
       localberg%mass_scaling=mass_scaling(k)
@@ -631,10 +639,6 @@ subroutine read_restart_bergs(bergs,Time)
       !call add_new_berg_to_list(bergs%first, localberg, quick=.true.)
 
       if (bergs%grd%area(localberg%ine,localberg%jne) .ne. 0)  then
-        if (iceberg_num(k)==-1) then ! If using an old_restart then iceberg_num needs to be generated
-          localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(localberg%ine,localberg%jne))+(localberg%ine+(iNg*(localberg%jne-1)))
-          localberg%id = generate_id(grd, localberg%ine, localberg%jne)
-        endif
         call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg)
       else
         if (mpp_pe().eq.mpp_root_pe()) then
@@ -674,9 +678,15 @@ subroutine read_restart_bergs(bergs,Time)
     deallocate(              &
                ine,          &
                jne,          &
-               iceberg_num,  &
                start_year )
 
+    if (replace_iceberg_num) then
+      deallocate(iceberg_num)
+    else
+      deallocate(id_cnt)
+      deallocate(id_ij)
+    endif
+
     ! This block only works for IO_LAYOUT=1,1 or 0,0 but not for arbitrary layouts.
     ! I'm commenting this out until we find a way to implement the same sorts of checks
     ! that work for all i/o layouts. -AJA
@@ -752,15 +762,12 @@ subroutine generate_bergs(bergs,Time)
 ! Local variables
 type(icebergs_gridded), pointer :: grd
 integer :: i,j
-integer :: iNg, jNg  !Total number of points gloablly in i and j direction
 type(iceberg) :: localberg ! NOT a pointer but an actual local variable
 integer :: iyr, imon, iday, ihr, imin, isec
 logical :: lres
 
   ! For convenience
   grd=>bergs%grd
-  iNg=(grd%ieg-grd%isg+1) ! Total number of points globally in i direction
-  jNg=(grd%jeg-grd%jsg+1) ! Total number of points globally in j direction
 
   call get_date(Time, iyr, imon, iday, ihr, imin, isec)
 
@@ -798,22 +805,18 @@ subroutine generate_bergs(bergs,Time)
 
       !Berg A
       call loc_set_berg_pos(grd, 0.9, 0.5, 1., 0., localberg)
-      localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
       localberg%id = generate_id(grd, i, j)
       call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
       !Berg B
       call loc_set_berg_pos(grd, 0.1, 0.5, -1., 0., localberg)
-      localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
       localberg%id = generate_id(grd, i, j)
       call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
       !Berg C
       call loc_set_berg_pos(grd, 0.5, 0.9, 0., 1., localberg)
-      localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
       localberg%id = generate_id(grd, i, j)
       call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
       !Berg D
       call loc_set_berg_pos(grd, 0.5, 0.1, 0., -1., localberg)
-      localberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i +(iNg*(j-1)))  ! unique number for each iceberg
       localberg%id = generate_id(grd, i, j)
       call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
     endif

From f7988fe605175fd7a66fc37be97efc10ef46b818 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Sat, 17 Jun 2017 21:58:35 -0400
Subject: [PATCH 234/361] Removed last vestiges of %iceberg_num

- iceberg_num now only appears when reading an old restart with the
  32-bit reperesentation of iceberg_num.
---
 icebergs.F90           |  1 -
 icebergs_framework.F90 | 14 +++++---------
 2 files changed, 5 insertions(+), 10 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 2695b59..9f14762 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -4043,7 +4043,6 @@ subroutine calve_icebergs(bergs)
           newberg%start_lon=newberg%lon
           newberg%start_lat=newberg%lat
           newberg%start_year=bergs%current_year
-          newberg%iceberg_num=((iNg*jNg)*grd%iceberg_counter_grd(i,j))+(i+(iNg*(j-1)))  ! unique number for each iceberg
           newberg%id = generate_id(grd, i, j)
           newberg%start_day=bergs%current_yearday+ddt/86400.
           newberg%start_mass=bergs%initial_mass(k)
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 841412a..63fdab3 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -18,7 +18,7 @@ module ice_bergs_framework
 
 implicit none ; private
 
-integer :: buffer_width=29 ! This should be a parameter
+integer :: buffer_width=28 ! This should be a parameter
 integer :: buffer_width_traj=32 ! This should be a parameter
 integer, parameter :: nclasses=10 ! Number of ice bergs classes
 
@@ -251,7 +251,6 @@ module ice_bergs_framework
   real :: halo_berg  ! Equal to zero for bergs on computational domain, and =1 for bergs on the halo
   real :: static_berg  ! Equal to 1 for icebergs which are static (not allowed to move). Might be extended to grounding later.
   integer :: start_year !< Year that berg was created (years)
-  integer :: iceberg_num !< Iceberg identifier
   integer(kind=8) :: id !< Iceberg identifier
   integer :: ine !< Nearest i-index in NE direction (for convenience)
   integer :: jne !< Nearest j-index in NE direction (for convenience)
@@ -1845,7 +1844,6 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
   call push_buffer_value(buff%data(:,n), counter, berg%ayn)
   call push_buffer_value(buff%data(:,n), counter, berg%bxn)
   call push_buffer_value(buff%data(:,n), counter, berg%byn)
-  call push_buffer_value(buff%data(:,n), counter, berg%iceberg_num)
   call push_buffer_value(buff%data(:,n), counter, berg%halo_berg)
   call push_buffer_value(buff%data(:,n), counter, berg%static_berg)
   call split_id(berg%id, id_cnt, id_ij)
@@ -1976,7 +1974,7 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
 logical :: lres
 type(iceberg) :: localberg
 type(iceberg), pointer :: this
-integer :: other_berg_num, other_berg_ine, other_berg_jne
+integer :: other_berg_ine, other_berg_jne
 integer :: counter, k, max_bonds, id_cnt, id_ij
 integer(kind=8) :: id
 integer :: stderrunit
@@ -2018,7 +2016,6 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
   call pull_buffer_value(buff%data(:,n), counter, localberg%ayn)
   call pull_buffer_value(buff%data(:,n), counter, localberg%bxn)
   call pull_buffer_value(buff%data(:,n), counter, localberg%byn)
-  call pull_buffer_value(buff%data(:,n), counter, localberg%iceberg_num)
   call pull_buffer_value(buff%data(:,n), counter, localberg%halo_berg)
   call pull_buffer_value(buff%data(:,n), counter, localberg%static_berg)
   call pull_buffer_value(buff%data(:,n), counter, id_cnt)
@@ -4499,7 +4496,7 @@ integer function berg_chksum(berg)
 type(iceberg), pointer :: berg !< An iceberg
 ! Local variables
 real :: rtmp(36)
-integer :: itmp(36+8), i8=0, ichk1, ichk2, ichk3
+integer :: itmp(36+7), i8=0, ichk1, ichk2, ichk3
 integer :: i
 
   rtmp(:)=0.
@@ -4544,11 +4541,10 @@ integer function berg_chksum(berg)
   itmp(39)=berg%start_year
   itmp(40)=berg%ine
   itmp(41)=berg%jne
-  itmp(42)=berg%iceberg_num
-  call split_id( berg%id, itmp(43), itmp(44) )
+  call split_id( berg%id, itmp(42), itmp(43) )
 
   ichk1=0; ichk2=0; ichk3=0
-  do i=1,36+8
+  do i=1,36+7
    ichk1=ichk1+itmp(i)
    ichk2=ichk2+itmp(i)*i
    ichk3=ichk3+itmp(i)*i*i

From c67f4357069182ebe237bf651da56bb39bbe52e0 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Tue, 20 Jun 2017 16:34:24 -0400
Subject: [PATCH 235/361] Fixes hang when mpp_io is not called on some PEs with
 empty berg restarts

- When a restart file is empty (zero record length) we were skipping the
  read step to avoid segmentation violations when passing unallocated arrays
  to mpp. However, an mpp_sync inside mpp_io then caused some PEs to hang.
- In order to call mpp_io on all PEs we are now allocating zero-sized
  arrays which happily allows the everything to work inside mpp.
- Closes #52
- Also closes #48 which should have been closed with PRs #50 and #51 for
  which this commit is a further fix.
---
 icebergs_io.F90 | 12 +++---------
 1 file changed, 3 insertions(+), 9 deletions(-)

diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 54f76d5..04d7d90 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -504,9 +504,7 @@ subroutine read_restart_bergs(bergs,Time)
      filename = filename_base
      call get_field_size(filename,'i',siz, field_found=found, domain=bergs%grd%domain)
      nbergs_in_file = siz(1)
-  endif
 
-  if(nbergs_in_file > 0) then
      replace_iceberg_num = field_exist(filename, 'iceberg_num') ! True if using 32-bit iceberg_num in restart file
      allocate(lon(nbergs_in_file))
      allocate(lat(nbergs_in_file))
@@ -538,9 +536,7 @@ subroutine read_restart_bergs(bergs,Time)
        allocate(id_cnt(nbergs_in_file))
        allocate(id_ij(nbergs_in_file))
      endif
-  endif
 
-  if (found_restart .and. nbergs_in_file > 0) then
      call read_unlimited_axis(filename,'lon',lon,domain=grd%domain)
      call read_unlimited_axis(filename,'lat',lat,domain=grd%domain)
      call read_unlimited_axis(filename,'uvel',uvel,domain=grd%domain)
@@ -653,9 +649,8 @@ subroutine read_restart_bergs(bergs,Time)
     endif
   enddo
 
-  if(nbergs_in_file > 0) then
-    deallocate(              &
-               lon,          &
+  if (found_restart) then
+    deallocate(lon,          &
                lat,          &
                uvel,         &
                vvel,         &
@@ -674,8 +669,7 @@ subroutine read_restart_bergs(bergs,Time)
                mass_scaling, &
                mass_of_bits, &
                static_berg,  &
-               heat_density )
-    deallocate(              &
+               heat_density, &
                ine,          &
                jne,          &
                start_year )

From 6595cdd81789a67449873350ea9b69b87f44ff70 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Fri, 8 Sep 2017 15:58:00 -0400
Subject: [PATCH 236/361] Update license to LGPLv3

- License text updated to reflect change from GPLv3 to LGPLv3.
- Permission to change the license was obtained from all contributors
  to the code, up to this commit (September 8, 2017).
---
 LICENSE.md | 700 ++++++++++++-----------------------------------------
 1 file changed, 161 insertions(+), 539 deletions(-)

diff --git a/LICENSE.md b/LICENSE.md
index a05d37a..d3d7789 100644
--- a/LICENSE.md
+++ b/LICENSE.md
@@ -1,553 +1,175 @@
 This file is part of the NOAA-GFDL iceberg model, referred to as
 NOAA-GFDL/icebergs. The majority of this code was written by authors at
-Princeton University who originally provided this software under version 3 of
-the Gnu General Public License, which is provided below.
+Princeton University and is available with version 3 of the Gnu Lesser
+General Public License, which is provided below.
 
 The intent of this license is to ensure free and unrestricted access to the
 iceberg software, and to pass on those rights to modified versions this
 software.
 
 
-GNU GENERAL PUBLIC LICENSE
-==========================
+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
 
-Version 3, 29 June 2007
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
 
-Copyright &copy; 2007 Free Software Foundation, Inc. http://fsf.org/
 
-Everyone is permitted to copy and distribute verbatim copies of this license
-document, but changing it is not allowed.
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
 
-## Preamble
+  0. Additional Definitions.
 
-The GNU General Public License is a free, copyleft license for software and other
-kinds of works.
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
 
-The licenses for most software and other practical works are designed to take away
-your freedom to share and change the works. By contrast, the GNU General Public
-License is intended to guarantee your freedom to share and change all versions of a
-program--to make sure it remains free software for all its users. We, the Free
-Software Foundation, use the GNU General Public License for most of our software; it
-applies also to any other work released this way by its authors. You can apply it to
-your programs, too.
-
-When we speak of free software, we are referring to freedom, not price. Our General
-Public Licenses are designed to make sure that you have the freedom to distribute
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-
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-
-Developers that use the GNU GPL protect your rights with two steps: (1) assert
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-
-The precise terms and conditions for copying, distribution and modification follow.
-
-## TERMS AND CONDITIONS
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-### 3. Protecting Users' Legal Rights From Anti-Circumvention Law.
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-### 4. Conveying Verbatim Copies.
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-### 5. Conveying Modified Source Versions.
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-* **d)** If the work has interactive user interfaces, each must display Appropriate Legal
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-### 6. Conveying Non-Source Forms.
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-You may convey a covered work in object code form under the terms of sections 4 and
-5, provided that you also convey the machine-readable Corresponding Source under the
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-* **a)** Convey the object code in, or embodied in, a physical product (including a
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-* **e)** Convey the object code using peer-to-peer transmission, provided you inform
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-"Installation Information" for a User Product means any methods,
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-accompanied by the Installation Information. But this requirement does not apply if
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-
-### 7. Additional Terms.
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-"Additional permissions" are terms that supplement the terms of this
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-When you convey a copy of a covered work, you may at your option remove any
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-* **a)** Disclaiming warranty or limiting liability differently from the terms of
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-### 8. Termination.
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-granted under the third paragraph of section 11).
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-### 10. Automatic Licensing of Downstream Recipients.
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-was granted, prior to 28 March 2007.
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-Nothing in this License shall be construed as excluding or limiting any implied
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-under applicable patent law.
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-### 12. No Surrender of Others' Freedom.
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-### 13. Use with the GNU Affero General Public License.
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-Notwithstanding any other provision of this License, you have permission to link or
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-13, concerning interaction through a network will apply to the combination as such.
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-### 14. Revised Versions of this License.
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-Each version is given a distinguishing version number. If the Program specifies that
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-If the Program specifies that a proxy can decide which future versions of the GNU
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-### 15. Disclaimer of Warranty.
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-### 16. Limitation of Liability.
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From 87be6e99eb428a36555cc91b4e29ba3ea7101707 Mon Sep 17 00:00:00 2001
From: Niki Zadeh <Niki.Zadeh@noaa.gov>
Date: Tue, 12 Sep 2017 11:15:05 -0400
Subject: [PATCH 237/361] Fix double append of _ensNN to restart filenames in
 ensemble runs

- Fixes issue #10
- Restart tests for ensemble runs fail because the icebergs restart file names from each ensemble member has the ensemble_id appended twice like
icebergs.res.ens_01.ens_01.nc instead of
icebergs.res.ens_01.nc
and so they are ignored when the model restarts.
---
 icebergs_io.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 04d7d90..a8b4c42 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -201,7 +201,7 @@ subroutine write_restart(bergs)
    allocate(id_ij(nbergs))
 
 
-  call get_instance_filename("icebergs.res.nc", filename)
+  filename = trim("icebergs.res.nc")
   call set_domain(bergs%grd%domain)
   call register_restart_axis(bergs_restart,filename,'i',nbergs)
   call set_meta_global(bergs_restart,'file_format_major_version',ival=(/file_format_major_version/))

From 6fd6f11635953beb465f8671cd6b148aa9a1f715 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Tue, 17 Oct 2017 14:47:12 -0400
Subject: [PATCH 238/361] Adds an incentive to move away from coasts

- The CM4 model has a slow sea-level fall because mass is being locked
  up in bergs trapped in single point inlets and channels. There are
  also a larger than expected number of bergs stuck against open coasts.
  Both biases are due to the wind being masked to zero on land cells.
  This commit introduces an optional bias to drive bergs away from land-
  sea boundaries. This does not address the single-point channels bias.
---
 icebergs.F90           | 11 +++++++++++
 icebergs_framework.F90 |  5 ++++-
 2 files changed, 15 insertions(+), 1 deletion(-)

diff --git a/icebergs.F90 b/icebergs.F90
index 9f14762..f9f08dd 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -2754,6 +2754,17 @@ subroutine interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y,
   ua=bilin(grd, grd%ua, i, j, xi, yj)
   va=bilin(grd, grd%va, i, j, xi, yj)
 
+  ! The following block accelerates a berg away from coastlines towards open water
+  ! which is a bias needed to avoid piling up in coarse resolution models
+  if (grd%coastal_drift > 0.) then
+    ! If a cell to the west is land (msk=0), accelerate to the east, and vice versa.
+    uo = uo + grd%coastal_drift * ( grd%msk(i+1,j) - grd%msk(i-1,j) ) * grd%msk(i,j)
+    ui = ui + grd%coastal_drift * ( grd%msk(i+1,j) - grd%msk(i-1,j) ) * grd%msk(i,j)
+    ! If a cell to the south is land (msk=0), accelerate to the north, and vice versa.
+    vo = vo + grd%coastal_drift * ( grd%msk(i,j+1) - grd%msk(i,j-1) ) * grd%msk(i,j)
+    vi = vi + grd%coastal_drift * ( grd%msk(i,j+1) - grd%msk(i,j-1) ) * grd%msk(i,j)
+  endif
+
   if (ua.ne.ua) then
     if (mpp_pe().eq.9) then
       write(stderrunit,'(a3,32i7)') 'ua',(ii,ii=grd%isd,grd%ied)
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 63fdab3..4d3f68a 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -160,6 +160,7 @@ module ice_bergs_framework
   integer, dimension(:,:), pointer :: iceberg_counter_grd=>null() !< Counts icebergs created for naming purposes
   logical :: rmean_calving_initialized = .false. !< True if rmean_calving(:,:) has been filled with meaningful data
   logical :: rmean_calving_hflx_initialized = .false. !< True if rmean_calving_hflx(:,:) has been filled with meaningful data
+  real :: coastal_drift=0. ! A velocity added to ocean currents to cause bergs to drift away from land cells
   !>@{
   !! Diagnostic handle
   integer :: id_uo=-1, id_vo=-1, id_calving=-1, id_stored_ice=-1, id_accum=-1, id_unused=-1, id_floating_melt=-1
@@ -515,6 +516,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: tau_calving=0. ! Time scale for smoothing out calving field (years)
 real :: tip_parameter=0. ! Parameter to override iceberg rolling critical ratio (use zero to get parameter directly from ice and seawater densities
 real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
+real :: coastal_drift=0. ! A velocity added to ocean currents to cause bergs to drift away from land cells
 logical :: Runge_not_Verlet=.True. ! True=Runge Kutta, False=Verlet.
 logical :: use_mixed_melting=.False. ! If true, then the melt is determined partly using 3 eq model partly using iceberg parameterizations (according to iceberg bond number)
 logical :: apply_thickness_cutoff_to_gridded_melt=.False. ! Prevents melt for ocean thickness below melt_cuttoff (applied to gridded melt fields)
@@ -567,7 +569,7 @@ subroutine ice_bergs_framework_init(bergs, &
          grid_is_regular,override_iceberg_velocities,u_override,v_override,add_iceberg_thickness_to_SSH,Iceberg_melt_without_decay,melt_icebergs_as_ice_shelf, &
          Use_three_equation_model,find_melt_using_spread_mass,use_mixed_layer_salinity_for_thermo,utide_icebergs,ustar_icebergs_bg,cdrag_icebergs, pass_fields_to_ocean_model, &
          const_gamma, Gamma_T_3EQ, ignore_traj, debug_iceberg_with_id,use_updated_rolling_scheme, tip_parameter, read_old_restarts, tau_calving, read_ocean_depth_from_file, melt_cutoff,&
-         apply_thickness_cutoff_to_gridded_melt, apply_thickness_cutoff_to_bergs_melt,use_mixed_melting
+         apply_thickness_cutoff_to_gridded_melt, apply_thickness_cutoff_to_bergs_melt, use_mixed_melting, coastal_drift
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -994,6 +996,7 @@ subroutine ice_bergs_framework_init(bergs, &
   allocate( bergs%initial_length(nclasses) )
   bergs%initial_width(:)=sqrt(initial_mass(:)/(LoW_ratio*rho_bergs*initial_thickness(:)))
   bergs%initial_length(:)=LoW_ratio*bergs%initial_width(:)
+  grd%coastal_drift = coastal_drift
 
   if (read_old_restarts) call error_mesg('diamonds, ice_bergs_framework_init', 'Setting "read_old_restarts=.true." is obsolete and does nothing!', WARNING)
 

From b913118e05541918bb3d3b66a1e47ca830f6eda0 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Tue, 17 Oct 2017 16:19:42 -0400
Subject: [PATCH 239/361] Adds a stochastic parameterization of
 unresolved/tidal currents

- The CM4 model has a slow sea-level fall because mass is being locked
  up in bergs trapped in single point inlets and channels. This happens
  because the winds are masked out on land cells.
- This commit adds random vectors to the ocean currents in the vicinity
  of land cells so that particle dispersion can allow the bergs to
  eventually escape. The controlling parameter is a velocity amplitude.
---
 icebergs.F90           | 99 +++++++++++++++++++++++++++++-------------
 icebergs_framework.F90 |  5 ++-
 2 files changed, 73 insertions(+), 31 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index f9f08dd..dd16cab 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -13,7 +13,7 @@ module ice_bergs
 use mpp_mod, only: mpp_send, mpp_recv, mpp_sync_self, mpp_chksum
 use mpp_mod, only: mpp_clock_begin, mpp_clock_end, mpp_clock_id
 use mpp_mod, only: CLOCK_COMPONENT, CLOCK_SUBCOMPONENT, CLOCK_LOOP
-
+use random_numbers_mod, only: initializeRandomNumberStream, getRandomNumbers, randomNumberStream
 use mpp_mod, only: mpp_gather
 use fms_mod, only: clock_flag_default
 use fms_io_mod, only: get_instance_filename
@@ -674,7 +674,7 @@ subroutine overlap_area(R1, R2, d, A, trapped)
 end subroutine overlap_area
 
 !> Calculates the instantaneous acceleration of an iceberg
-subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, ax, ay, axn, ayn, bxn, byn, debug_flag)
+subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, rx, ry, ax, ay, axn, ayn, bxn, byn, debug_flag)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
   type(iceberg), pointer :: berg !< An iceberg
@@ -688,6 +688,8 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
   real, intent(in) :: uvel0 !< Zonal velocity of berg at beginning of time-step (m/s)
   real, intent(in) :: vvel0 !< Meridional velocity of berg at beginning of time-step (m/s)
   real, intent(in) :: dt !< Time step (s)
+  real, intent(in) :: rx !< Random number between -1 and 1 for use in x-component of stochastic tidal parameterization
+  real, intent(in) :: ry !< Random number between -1 and 1 for use in y-component of stochastic tidal parameterization
   real, intent(out) :: ax !< Zonal acceleration (m/s2)
   real, intent(out) :: ay !< Meridional acceleration (m/s2)
   real, intent(inout) :: axn !< Explicit estimate of zonal acceleration (m/s2)
@@ -745,7 +747,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, a
   grd=>bergs%grd
 
   ! Interpolate gridded fields to berg     - Note: It should be possible to move this to evolve, so that it only needs to be called once. !!!!
-  call interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, sss, cn, hi)
+  call interp_flds(grd, i, j, xi, yj, rx, ry, uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, sss, cn, hi)
 
   if ((grd%grid_is_latlon) .and. (.not. bergs%use_f_plane)) then
      f_cori=(2.*omega)*sin(pi_180*lat)
@@ -1191,7 +1193,7 @@ subroutine thermodynamics(bergs)
     this=>bergs%list(grdi,grdj)%first
     do while(associated(this))
       if (debug) call check_position(grd, this, 'thermodynamics (top)')
-      call interp_flds(grd, this%ine, this%jne, this%xi, this%yj, this%uo, this%vo, &
+      call interp_flds(grd, this%ine, this%jne, this%xi, this%yj, 0., 0., this%uo, this%vo, &
               this%ui, this%vi, this%ua, this%va, this%ssh_x, this%ssh_y, this%sst, &
               this%sss,this%cn, this%hi)
       SST=this%sst
@@ -2712,13 +2714,15 @@ subroutine Hexagon_into_quadrants_using_triangles(x0, y0, H, theta, Area_hex ,Ar
 
 end subroutine Hexagon_into_quadrants_using_triangles
 
-subroutine interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, sss, cn, hi)
+subroutine interp_flds(grd, i, j, xi, yj, rx, ry, uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, sss, cn, hi)
   ! Arguments
   type(icebergs_gridded), pointer :: grd !< Container for gridded fields
   integer, intent(in) :: i !< i-index of cell in which to interpolate
   integer, intent(in) :: j !< j-index of cell in which to interpolate
   real, intent(in) :: xi !< Non-dimensional x-position within cell to interpolate to
   real, intent(in) :: yj !< Non-dimensional y-position within cell to interpolate to
+  real, intent(in) :: rx !< Random number between -1 and 1 for use in x-component of stochastic tidal parameterization
+  real, intent(in) :: ry !< Random number between -1 and 1 for use in y-component of stochastic tidal parameterization
   real, intent(out) :: uo !< Ocean zonal velocity at point xi,yj (m/s)
   real, intent(out) :: vo !< Ocean meridional velocity at point xi,yj (m/s)
   real, intent(out) :: ui !< Ice zonal velocity at point xi,yj (m/s)
@@ -2732,7 +2736,7 @@ subroutine interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y,
   real, intent(out) :: cn !< Sea-ice concentration (nondim)
   real, intent(out) :: hi !< Sea-ice thickness (m)
   ! Local variables
-  real :: cos_rot, sin_rot
+  real :: cos_rot, sin_rot, du, dv
 #ifdef USE_OLD_SSH_GRADIENT
   real :: dxm, dx0, dxp
   real, parameter :: ssh_coast=0.00
@@ -2765,6 +2769,22 @@ subroutine interp_flds(grd, i, j, xi, yj, uo, vo, ui, vi, ua, va, ssh_x, ssh_y,
     vi = vi + grd%coastal_drift * ( grd%msk(i,j+1) - grd%msk(i,j-1) ) * grd%msk(i,j)
   endif
 
+  ! Stochastic acceleration to represent unresolved tidal and wave motions.
+  ! Note: this scheme should account for the time-step and have memory!
+  if (grd%tidal_drift > 0.) then
+    ! The acceleration is modulated to not move particles towards land cells.
+    du = ( min(0., rx) * grd%msk(i-1,j) + max(0., rx) * grd%msk(i+1,j) ) &
+         * ( 1. - grd%msk(i,j-1) * grd%msk(i,j+1) ) ! Do not apply in open ocean
+    dv = ( min(0., ry) * grd%msk(i,j-1) + max(0., ry) * grd%msk(i,j+1) ) &
+         * ( 1. - grd%msk(i-1,j) * grd%msk(i+1,j) ) ! Do not apply in open ocean
+    du = du * grd%tidal_drift * grd%msk(i,j)
+    dv = dv * grd%tidal_drift * grd%msk(i,j)
+    uo = uo + du
+    ui = ui + du
+    vo = vo + dv
+    vi = vi + dv
+  endif
+
   if (ua.ne.ua) then
     if (mpp_pe().eq.9) then
       write(stderrunit,'(a3,32i7)') 'ua',(ii,ii=grd%isd,grd%ied)
@@ -4098,23 +4118,30 @@ subroutine evolve_icebergs(bergs)
   type(iceberg), pointer :: berg
   real :: uveln, vveln, lonn, latn
   real :: axn, ayn, bxn, byn          ! Added by Alon - explicit and implicit accelerations from the previous step
-  real :: xi, yj
+  real :: xi, yj, rx, ry
   integer :: i, j
   integer :: grdi, grdj
   integer :: stderrunit
   logical :: bounced, interactive_icebergs_on, Runge_not_Verlet
-
+  type(randomNumberStream) :: rns ! Random numbers for stochastic tidal parameterization
   ! Get the stderr unit number
   stderrunit = stderr()
 
   ! For convenience
   grd=>bergs%grd
+  rx = 0.
+  ry = 0.
 
   interactive_icebergs_on=bergs%interactive_icebergs_on
   Runge_not_Verlet=bergs%Runge_not_Verlet
 
   do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
     berg=>bergs%list(grdi,grdj)%first
+    if (associated(berg) .and. grd%tidal_drift>0.) then
+      ! Seed random numbers based on space and "time"
+      rns = initializeRandomNumberStream( grdi + 10000*grdj + &
+                                          int( 16384.*abs( sin(262144.*grd%ssh(grdi,grdj)) ) ) )
+    endif
     do while (associated(berg)) ! loop over all bergs
       if (berg%static_berg .lt. 0.5) then  !Only allow non-static icebergs to evolve
 
@@ -4136,12 +4163,20 @@ subroutine evolve_icebergs(bergs)
         endif
         if (debug) call check_position(grd, berg, 'evolve_iceberg (top)')
 
+        if (grd%tidal_drift>0.) then
+          call getRandomNumbers(rns, rx)
+          rx = 2.*rx - 1.
+          call getRandomNumbers(rns, ry)
+          ry = 2.*ry - 1.
+        endif
+
           !Time stepping schemes:
           if (Runge_not_Verlet) then
-            call Runge_Kutta_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln,lonn, latn, i, j, xi, yj)
+            call Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, &
+                                      lonn, latn, i, j, xi, yj, rx, ry)
           endif
           if (.not.Runge_not_Verlet) then
-            call verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
+            call verlet_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, rx, ry)
           endif
 
           !Used for testing the ocean response to fixed iceberg motion.
@@ -4196,7 +4231,7 @@ subroutine evolve_icebergs(bergs)
 end subroutine evolve_icebergs
 
 !> Calculate explicit and implicit accelerations, and new velocity, using the Verlet method
-subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
+subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln, rx, ry)
   type(icebergs), pointer :: bergs !< Container for all types and memory
   type(iceberg), pointer, intent(inout) :: berg !< Iceberg
   real, intent(out) :: axn !< Explicit zonal acceleration (m/s2)
@@ -4205,6 +4240,8 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
   real, intent(out) :: byn !< Implicit meridional acceleration (m/s2)
   real, intent(out) :: uveln !< New zonal velocity (m/s)
   real, intent(out) :: vveln !< New meridional velocity (m/s)
+  real, intent(in) :: rx !< Random number between -1 and 1 for use in x-component of stochastic tidal parameterization
+  real, intent(in) :: ry !< Random number between -1 and 1 for use in y-component of stochastic tidal parameterization
   ! Local variables
   type(icebergs_gridded), pointer :: grd
   real :: lonn, latn
@@ -4257,7 +4294,7 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
     call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 1.0*berg%mass_scaling,berg%length*berg%width, berg%thickness)
 
   ! Calling the acceleration   (note that the velocity is converted to u_star inside the accel script)
-  call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn, ayn, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
+  call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, ax1, ay1, axn, ayn, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
 
   ! Solving for the new velocity
   on_tangential_plane=.false.
@@ -4299,7 +4336,7 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
     write(stderrunit,*) 'diamonds, evolve_iceberg: on_tangential_plane=',on_tangential_plane
     write(stderrunit,*) 'Acceleration terms for position 1'
     error_flag=pos_within_cell(grd, lonn, latn, i, j, xi,  yj)
-    call accel(bergs, berg, i, j, xi, yj, latn, uvel3, vvel3, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn, bxn, byn - Added by Alon
+    call accel(bergs, berg, i, j, xi, yj, latn, uvel3, vvel3, uvel1, vvel1, dt_2, rx, ry, ax1, ay1, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn, bxn, byn - Added by Alon
 
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'posn i,j,lon,lat,xi,yj=',i,j,lonn,latn,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'posn box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
@@ -4319,7 +4356,7 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln)
 end subroutine verlet_stepping
 
 !> Calculate explicit and implicit accelerations, new velocity, and new position, using the fourth order Runge-Kutta  method
-subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, lonn, latn, i, j, xi, yj)
+subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, lonn, latn, i, j, xi, yj, rx, ry)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
   type(iceberg), pointer, intent(inout) :: berg !< Iceberg
@@ -4335,6 +4372,8 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
   integer, intent(out) :: j !< New i-index of containing cell
   real, intent(out) :: xi !< New non-dimensional x-position
   real, intent(out) :: yj !< New non-dimensional y-position
+  real, intent(in) :: rx !< Random number between -1 and 1 for use in x-component of stochastic tidal parameterization
+  real, intent(in) :: ry !< Random number between -1 and 1 for use in y-component of stochastic tidal parameterization
   ! Local variables
   type(icebergs_gridded), pointer :: grd
   real :: uvel1, vvel1, lon1, lat1, u1, v1, dxdl1, ax1, ay1, axn1, ayn1
@@ -4400,8 +4439,8 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
   if (on_tangential_plane) call rotvec_to_tang(lon1,uvel1,vvel1,xdot1,ydot1)
   u1=uvel1*dxdl1; v1=vvel1*dydl
 
-  call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn) !axn,ayn, bxn, byn  - Added by Alon
-  !call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt, ax1, ay1, axn1, ayn1, bxn, byn) !Note change to dt. Markpoint_1
+  call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, rx, ry, ax1, ay1, axn1, ayn1, bxn, byn) !axn,ayn, bxn, byn  - Added by Alon
+  !call accel(bergs, berg, i, j, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, ax1, ay1, axn1, ayn1, bxn, byn) !Note change to dt. Markpoint_1
   if (on_tangential_plane) call rotvec_to_tang(lon1,ax1,ay1,xddot1,yddot1)
   if (on_tangential_plane) call rotvec_to_tang(lon1,axn1,ayn1,xddot1n,yddot1n) !Alon
 
@@ -4447,7 +4486,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
     write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2 (deg)=',dt*v1,dt*v2
     write(stderrunit,*) 'Acceleration terms for position 1'
     error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-    call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn,- Added by Alon
+    call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, rx, ry, ax1, ay1, axn1, ayn1, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn,- Added by Alon
     call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 2')
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos2 i,j,lon,lat,xi,yj=',i,j,lon2,lat2,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos2 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
@@ -4457,8 +4496,8 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
   call  convert_from_meters_to_grid(lat2,bergs%grd%grid_is_latlon ,dxdl2,dydl)
   !dxdl2=r180_pi/(Rearth*cos(lat2*pi_180))
   u2=uvel2*dxdl2; v2=vvel2*dydl
-  call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
-  !call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt, ax2, ay2, axn2, ayn2, bxn, byn) !Note change to dt. Markpoint_1
+  call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, rx, ry, ax2, ay2, axn2, ayn2, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
+  !call accel(bergs, berg, i, j, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt, rx, ry, ax2, ay2, axn2, ayn2, bxn, byn) !Note change to dt. Markpoint_1
   if (on_tangential_plane) call rotvec_to_tang(lon2,ax2,ay2,xddot2,yddot2)
   if (on_tangential_plane) call rotvec_to_tang(lon2,axn2,ayn2,xddot2n,yddot2n) !Alon
 
@@ -4504,10 +4543,10 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
     write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3 (deg)=',dt*v1,dt*v2,dt*v3
     write(stderrunit,*) 'Acceleration terms for position 1'
     error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-    call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, debug_flag=.true.) !axn, ayn - Added by Alon
+    call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, rx, ry, ax1, ay1, axn1, ayn1, bxn, byn, debug_flag=.true.) !axn, ayn - Added by Alon
     write(stderrunit,*) 'Acceleration terms for position 2'
     error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
-    call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
+    call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, rx, ry, ax2, ay2, axn2, ayn2, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
     call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 3')
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos3 i,j,lon,lat,xi,yj=',i,j,lon3,lat3,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos3 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
@@ -4517,7 +4556,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
   call  convert_from_meters_to_grid(lat3,bergs%grd%grid_is_latlon ,dxdl3,dydl)
   !dxdl3=r180_pi/(Rearth*cos(lat3*pi_180))
   u3=uvel3*dxdl3; v3=vvel3*dydl
-  call accel(bergs, berg, i, j, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn3, ayn3, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
+  call accel(bergs, berg, i, j, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, rx, ry, ax3, ay3, axn3, ayn3, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
   if (on_tangential_plane) call rotvec_to_tang(lon3,ax3,ay3,xddot3,yddot3)
   if (on_tangential_plane) call rotvec_to_tang(lon3,axn3,ayn3,xddot3n,yddot3n) !Alon
 
@@ -4561,13 +4600,13 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
     write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v4 (deg)=',dt*v1,dt*v2,dt*v3,dt*v4
     write(stderrunit,*) 'Acceleration terms for position 1'
     error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-    call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn1, ayn1, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
+    call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, rx, ry, ax1, ay1, axn1, ayn1, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
     write(stderrunit,*) 'Acceleration terms for position 2'
     error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
-    call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn2, ayn2, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
+    call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, rx, ry, ax2, ay2, axn2, ayn2, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
     write(stderrunit,*) 'Acceleration terms for position 3'
     error_flag=pos_within_cell(grd, lon3, lat3, i3, j3, xi, yj)
-    call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn3, ayn3, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
+    call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, rx, ry, ax3, ay3, axn3, ayn3, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
     call print_berg(stderrunit, berg, 'evolve_iceberg, out of position at 4')
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos4 i,j,lon,lat,xi,yj=',i,j,lon4,lat4,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos4 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
@@ -4577,7 +4616,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
   call  convert_from_meters_to_grid(lat4,bergs%grd%grid_is_latlon ,dxdl4,dydl)
   !dxdl4=r180_pi/(Rearth*cos(lat4*pi_180))
   u4=uvel4*dxdl4; v4=vvel4*dydl
-  call accel(bergs, berg, i, j, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axn4, ayn4, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
+  call accel(bergs, berg, i, j, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, rx, ry, ax4, ay4, axn4, ayn4, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
   if (on_tangential_plane) call rotvec_to_tang(lon4,ax4,ay4,xddot4,yddot4)
   if (on_tangential_plane) call rotvec_to_tang(lon4,axn4,ayn4,xddot4n,yddot4n)
 
@@ -4641,16 +4680,16 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
     write(stderrunit,*) 'diamonds, evolve_iceberg: on_tangential_plane=',on_tangential_plane
     write(stderrunit,*) 'Acceleration terms for position 1'
     error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
-    call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, ax1, ay1, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
+    call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, rx, ry, ax1, ay1, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
     write(stderrunit,*) 'Acceleration terms for position 2'
     error_flag=pos_within_cell(grd, lon2, lat2, i2, j2, xi, yj)
-    call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, ax2, ay2, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
+    call accel(bergs, berg, i2, j2, xi, yj, lat2, uvel2, vvel2, uvel1, vvel1, dt_2, rx, ry, ax2, ay2, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
     write(stderrunit,*) 'Acceleration terms for position 3'
     error_flag=pos_within_cell(grd, lon3, lat3, i3, j3, xi, yj)
-    call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, ax3, ay3, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
+    call accel(bergs, berg, i3, j3, xi, yj, lat3, uvel3, vvel3, uvel1, vvel1, dt, rx, ry, ax3, ay3, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
     write(stderrunit,*) 'Acceleration terms for position 4'
     error_flag=pos_within_cell(grd, lon4, lat4, i4, j4, xi, yj)
-    call accel(bergs, berg, i4, j4, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, ax4, ay4, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
+    call accel(bergs, berg, i4, j4, xi, yj, lat4, uvel4, vvel4, uvel1, vvel1, dt, rx, ry, ax4, ay4, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'posn i,j,lon,lat,xi,yj=',i,j,lonn,latn,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'posn box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
     call print_berg(stderrunit, berg, 'evolve_iceberg, out of cell at end!')
diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index 4d3f68a..e90ead6 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -161,6 +161,7 @@ module ice_bergs_framework
   logical :: rmean_calving_initialized = .false. !< True if rmean_calving(:,:) has been filled with meaningful data
   logical :: rmean_calving_hflx_initialized = .false. !< True if rmean_calving_hflx(:,:) has been filled with meaningful data
   real :: coastal_drift=0. ! A velocity added to ocean currents to cause bergs to drift away from land cells
+  real :: tidal_drift=0. ! Amplitude of a stochastic tidal velocity added to ocean currents to cause bergs to drift randomly
   !>@{
   !! Diagnostic handle
   integer :: id_uo=-1, id_vo=-1, id_calving=-1, id_stored_ice=-1, id_accum=-1, id_unused=-1, id_floating_melt=-1
@@ -517,6 +518,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: tip_parameter=0. ! Parameter to override iceberg rolling critical ratio (use zero to get parameter directly from ice and seawater densities
 real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
 real :: coastal_drift=0. ! A velocity added to ocean currents to cause bergs to drift away from land cells
+real :: tidal_drift=0. ! Amplitude of a stochastic tidal velocity added to ocean currents to cause bergs to drift randomly
 logical :: Runge_not_Verlet=.True. ! True=Runge Kutta, False=Verlet.
 logical :: use_mixed_melting=.False. ! If true, then the melt is determined partly using 3 eq model partly using iceberg parameterizations (according to iceberg bond number)
 logical :: apply_thickness_cutoff_to_gridded_melt=.False. ! Prevents melt for ocean thickness below melt_cuttoff (applied to gridded melt fields)
@@ -569,7 +571,7 @@ subroutine ice_bergs_framework_init(bergs, &
          grid_is_regular,override_iceberg_velocities,u_override,v_override,add_iceberg_thickness_to_SSH,Iceberg_melt_without_decay,melt_icebergs_as_ice_shelf, &
          Use_three_equation_model,find_melt_using_spread_mass,use_mixed_layer_salinity_for_thermo,utide_icebergs,ustar_icebergs_bg,cdrag_icebergs, pass_fields_to_ocean_model, &
          const_gamma, Gamma_T_3EQ, ignore_traj, debug_iceberg_with_id,use_updated_rolling_scheme, tip_parameter, read_old_restarts, tau_calving, read_ocean_depth_from_file, melt_cutoff,&
-         apply_thickness_cutoff_to_gridded_melt, apply_thickness_cutoff_to_bergs_melt, use_mixed_melting, coastal_drift
+         apply_thickness_cutoff_to_gridded_melt, apply_thickness_cutoff_to_bergs_melt, use_mixed_melting, coastal_drift, tidal_drift
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -997,6 +999,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%initial_width(:)=sqrt(initial_mass(:)/(LoW_ratio*rho_bergs*initial_thickness(:)))
   bergs%initial_length(:)=LoW_ratio*bergs%initial_width(:)
   grd%coastal_drift = coastal_drift
+  grd%tidal_drift = tidal_drift
 
   if (read_old_restarts) call error_mesg('diamonds, ice_bergs_framework_init', 'Setting "read_old_restarts=.true." is obsolete and does nothing!', WARNING)
 

From 2ee1389e28aeb87ca46b6e77c2e8a8d44375306d Mon Sep 17 00:00:00 2001
From: William Cooke <William.Cooke@noaa.gov>
Date: Tue, 6 Feb 2018 12:37:53 -0500
Subject: [PATCH 240/361] Add timestamp to intermediate iceberg restart files.

Also corrects double tagging of ensemble name to iceberg restart filename.
---
 icebergs.F90    | 5 +++--
 icebergs_io.F90 | 8 +++++---
 2 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/icebergs.F90 b/icebergs.F90
index dd16cab..38bf357 100644
--- a/icebergs.F90
+++ b/icebergs.F90
@@ -5161,16 +5161,17 @@ subroutine icebergs_stock_pe(bergs, index, value)
 end subroutine icebergs_stock_pe
 
 !> Write restart files
-subroutine icebergs_save_restart(bergs)
+subroutine icebergs_save_restart(bergs, time_stamp)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
+  character(len=*),    intent(in), optional :: time_stamp !< Timestamp for restart file
   ! Local variables
 
   if (.not.associated(bergs)) return
 
   call mpp_clock_begin(bergs%clock_iow)
   call bergs_chksum(bergs, 'write_restart bergs')
-  call write_restart(bergs)
+  call write_restart(bergs, time_stamp)
   call mpp_clock_end(bergs%clock_iow)
 
 end subroutine icebergs_save_restart
diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 04d7d90..a99893d 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -101,9 +101,11 @@ subroutine ice_bergs_io_init(bergs, io_layout)
 end subroutine ice_bergs_io_init
 
 !> Write an iceberg restart file
-subroutine write_restart(bergs)
+subroutine write_restart(bergs, time_stamp)
 ! Arguments
 type(icebergs), pointer :: bergs !< Icebergs container
+character(len=*), intent(in), optional :: time_stamp !< Timestamp for restart file
+
 ! Local variables
 type(bond), pointer :: current_bond
 integer :: i,j,id
@@ -201,7 +203,7 @@ subroutine write_restart(bergs)
    allocate(id_ij(nbergs))
 
 
-  call get_instance_filename("icebergs.res.nc", filename)
+  filename = "icebergs.res.nc"
   call set_domain(bergs%grd%domain)
   call register_restart_axis(bergs_restart,filename,'i',nbergs)
   call set_meta_global(bergs_restart,'file_format_major_version',ival=(/file_format_major_version/))
@@ -287,7 +289,7 @@ subroutine write_restart(bergs)
   enddo ; enddo
 
 
-  call save_restart(bergs_restart)
+  call save_restart(bergs_restart, time_stamp)
   call free_restart_type(bergs_restart)
 
   deallocate(              &

From 2a32d929aebc2e4dd2d1ff84b44b23135defff08 Mon Sep 17 00:00:00 2001
From: William Cooke <William.Cooke@noaa.gov>
Date: Mon, 12 Feb 2018 12:43:20 -0500
Subject: [PATCH 241/361] Add timestamp to calving restart file.

Update to icebergs timestamp capability.
If timestamps (restart_interval != 6*0) were enabled previously, the calving
restart file received multiple timesteps of data. This changed answers after
a restart.
---
 icebergs_io.F90 | 45 ++++++++++++++++++++++++++++++++++-----------
 1 file changed, 34 insertions(+), 11 deletions(-)

diff --git a/icebergs_io.F90 b/icebergs_io.F90
index a99893d..4614b19 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -116,6 +116,7 @@ subroutine write_restart(bergs, time_stamp)
 !I/O vars
 type(restart_file_type) :: bergs_restart
 type(restart_file_type) :: bergs_bond_restart
+type(restart_file_type) :: calving_restart
 integer :: nbergs, nbonds
 integer :: n_static_bergs
 logical :: check_bond_quality
@@ -381,7 +382,7 @@ subroutine write_restart(bergs, time_stamp)
     enddo!End of loop over bergs
   enddo; enddo !End of loop over grid
 
-  call save_restart(bergs_bond_restart)
+  call save_restart(bergs_bond_restart, time_stamp)
   call free_restart_type(bergs_bond_restart)
 
 
@@ -398,23 +399,45 @@ subroutine write_restart(bergs, time_stamp)
   call nullify_domain()
   endif
 
+!  ! Write stored ice
+!  filename='RESTART/calving.res.nc'
+!  if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(stderrunit,'(2a)') 'diamonds, write_restart: writing ',filename
+!
+!  call grd_chksum3(bergs%grd, bergs%grd%stored_ice, 'write stored_ice')
+!  call write_data(filename, 'stored_ice', bergs%grd%stored_ice, bergs%grd%domain)
+!  call grd_chksum2(bergs%grd, bergs%grd%stored_heat, 'write stored_heat')
+!  call write_data(filename, 'stored_heat', bergs%grd%stored_heat, bergs%grd%domain)
+!  !call grd_chksum2(bergs%grd, bergs%grd%iceberg_counter_grd, 'write iceberg_counter_grd')
+!  call write_data(filename, 'iceberg_counter_grd', bergs%grd%iceberg_counter_grd, bergs%grd%domain)
+!  if (bergs%tau_calving>0.) then
+!    call grd_chksum2(bergs%grd, bergs%grd%rmean_calving, 'write mean calving')
+!    call write_data(filename, 'rmean_calving', bergs%grd%rmean_calving, bergs%grd%domain)
+!    call grd_chksum2(bergs%grd, bergs%grd%rmean_calving_hflx, 'write mean calving_hflx')
+!    call write_data(filename, 'rmean_calving_hflx', bergs%grd%rmean_calving_hflx, bergs%grd%domain)
+!  endif
+
   ! Write stored ice
-  filename='RESTART/calving.res.nc'
+  filename='calving.res.nc'
   if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(stderrunit,'(2a)') 'diamonds, write_restart: writing ',filename
-
   call grd_chksum3(bergs%grd, bergs%grd%stored_ice, 'write stored_ice')
-  call write_data(filename, 'stored_ice', bergs%grd%stored_ice, bergs%grd%domain)
   call grd_chksum2(bergs%grd, bergs%grd%stored_heat, 'write stored_heat')
-  call write_data(filename, 'stored_heat', bergs%grd%stored_heat, bergs%grd%domain)
-  !call grd_chksum2(bergs%grd, bergs%grd%iceberg_counter_grd, 'write iceberg_counter_grd')
-  call write_data(filename, 'iceberg_counter_grd', bergs%grd%iceberg_counter_grd, bergs%grd%domain)
   if (bergs%tau_calving>0.) then
     call grd_chksum2(bergs%grd, bergs%grd%rmean_calving, 'write mean calving')
-    call write_data(filename, 'rmean_calving', bergs%grd%rmean_calving, bergs%grd%domain)
     call grd_chksum2(bergs%grd, bergs%grd%rmean_calving_hflx, 'write mean calving_hflx')
-    call write_data(filename, 'rmean_calving_hflx', bergs%grd%rmean_calving_hflx, bergs%grd%domain)
   endif
 
+  call set_domain(bergs%grd%domain)
+  id = register_restart_field(calving_restart,filename,'stored_ice',bergs%grd%stored_ice,longname='STORED_ICE',units='none')
+  id = register_restart_field(calving_restart,filename,'stored_heat',bergs%grd%stored_heat,longname='STORED_HEAT',units='none')
+  id = register_restart_field(calving_restart,filename,'iceberg_counter_grd',bergs%grd%iceberg_counter_grd,longname='ICEBERG_COUNTER_GRD',units='none')
+  if (bergs%tau_calving>0.) then
+    id = register_restart_field(calving_restart,filename,'rmean_calving',bergs%grd%rmean_calving,longname='RMEAN_CALVING',units='none')
+    id = register_restart_field(calving_restart,filename,'rmean_calving_hflx',bergs%grd%rmean_calving_hflx,longname='RMEAN_CALVING_HFLX',units='none')
+  endif
+
+  call save_restart(calving_restart, time_stamp)
+  call free_restart_type(calving_restart)
+
 end subroutine write_restart
 
 !> Find the last berg in a linked list.
@@ -1217,11 +1240,11 @@ subroutine read_ocean_depth(grd)
      'diamonds, read_ocean_depth: reading ',filename
     if (field_exist(filename, 'depth')) then
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
-       'diamonds, read_restart_calving: reading stored_heat from restart file.'
+       'diamonds, read_ocean_depth: reading depth from topog file.'
       call read_data(filename, 'depth', grd%ocean_depth, grd%domain)
     else
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
-     'diamonds, read_restart_calving: stored_heat WAS NOT FOUND in the file. Setting to 0.'
+     'diamonds, read_ocean_depth: depth WAS NOT FOUND in the file. Setting to 0.'
       !grd%ocean_depth(:,:)=0.
     endif
   else

From 9debf320ce36c68b6c310c1c94fdf799e4dfbd88 Mon Sep 17 00:00:00 2001
From: William Cooke <William.Cooke@noaa.gov>
Date: Mon, 12 Feb 2018 12:49:11 -0500
Subject: [PATCH 242/361] Cleaned up previous restart code

---
 icebergs_io.F90 | 17 -----------------
 1 file changed, 17 deletions(-)

diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 4614b19..2448196 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -399,23 +399,6 @@ subroutine write_restart(bergs, time_stamp)
   call nullify_domain()
   endif
 
-!  ! Write stored ice
-!  filename='RESTART/calving.res.nc'
-!  if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(stderrunit,'(2a)') 'diamonds, write_restart: writing ',filename
-!
-!  call grd_chksum3(bergs%grd, bergs%grd%stored_ice, 'write stored_ice')
-!  call write_data(filename, 'stored_ice', bergs%grd%stored_ice, bergs%grd%domain)
-!  call grd_chksum2(bergs%grd, bergs%grd%stored_heat, 'write stored_heat')
-!  call write_data(filename, 'stored_heat', bergs%grd%stored_heat, bergs%grd%domain)
-!  !call grd_chksum2(bergs%grd, bergs%grd%iceberg_counter_grd, 'write iceberg_counter_grd')
-!  call write_data(filename, 'iceberg_counter_grd', bergs%grd%iceberg_counter_grd, bergs%grd%domain)
-!  if (bergs%tau_calving>0.) then
-!    call grd_chksum2(bergs%grd, bergs%grd%rmean_calving, 'write mean calving')
-!    call write_data(filename, 'rmean_calving', bergs%grd%rmean_calving, bergs%grd%domain)
-!    call grd_chksum2(bergs%grd, bergs%grd%rmean_calving_hflx, 'write mean calving_hflx')
-!    call write_data(filename, 'rmean_calving_hflx', bergs%grd%rmean_calving_hflx, bergs%grd%domain)
-!  endif
-
   ! Write stored ice
   filename='calving.res.nc'
   if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(stderrunit,'(2a)') 'diamonds, write_restart: writing ',filename

From ad861df399dd26e6453b6bd08d911acc86bb08bb Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Tue, 14 Jul 2020 14:57:54 -0400
Subject: [PATCH 243/361] Fix for single-process tests

- The unit test "test_check_for_duplicate_ids_in_list" fails because
  it relies on two cores. This bypasses the test if there is only
  one core.
---
 icebergs_framework.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/icebergs_framework.F90 b/icebergs_framework.F90
index e90ead6..f8c6219 100644
--- a/icebergs_framework.F90
+++ b/icebergs_framework.F90
@@ -4805,7 +4805,7 @@ subroutine test_check_for_duplicate_ids_in_list()
   if (mpp_pe() == mpp_root_pe()) ids(5) = 7 + 5*mpp_pe()
   error_count = check_for_duplicate_ids_in_list(5, ids, verbose=.false.)
   call mpp_sum(error_count)
-  if (error_count == 0) then
+  if (error_count == 0 .and. mpp_npes()>1) then
     error_count = check_for_duplicate_ids_in_list(5, ids, verbose=.true.)
     call error_mesg('diamonds, test_check_for_duplicate_ids_in_list:', 'Unit test for a really dirty list failed!', FATAL)
   endif

From aa759b7987db19f350b8a9077e516eb06e1af215 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Tue, 14 Jul 2020 14:56:58 -0400
Subject: [PATCH 244/361] Re-structure to add solo-driver

This is incomplete in that it only calls the icebergs_init() of icebergs
so far but it does compile and run. It just doesn't do anything
significant yet (although booting FMS and getting past the missing files
was a  significant acheivement really).

- Moved .F90 files into src/ directory
- Added driver/ directory
- Added partial draft of driver/icebergs_driver.F90
- Added build/gaea-gnu-env for environment
- Added build/README.md with quick build instructions
- Added input.nml diag_table in build/ for quick testing
---
 build/.gitignore                              |   7 +
 build/README.md                               |  12 ++
 build/diag_table                              |   3 +
 build/env                                     |   4 +
 build/input.nml                               |  10 ++
 driver/icebergs_driver.F90                    | 139 ++++++++++++++++++
 icebergs.F90 => src/icebergs.F90              |   0
 .../icebergs_framework.F90                    |   0
 icebergs_io.F90 => src/icebergs_io.F90        |   0
 9 files changed, 175 insertions(+)
 create mode 100644 build/.gitignore
 create mode 100644 build/README.md
 create mode 100644 build/diag_table
 create mode 100644 build/env
 create mode 100644 build/input.nml
 create mode 100644 driver/icebergs_driver.F90
 rename icebergs.F90 => src/icebergs.F90 (100%)
 rename icebergs_framework.F90 => src/icebergs_framework.F90 (100%)
 rename icebergs_io.F90 => src/icebergs_io.F90 (100%)

diff --git a/build/.gitignore b/build/.gitignore
new file mode 100644
index 0000000..512654e
--- /dev/null
+++ b/build/.gitignore
@@ -0,0 +1,7 @@
+path_names
+Makefile
+bergs.x
+logfile.000000.out
+.bergs.x.cppdefs
+*.mod
+*.o
diff --git a/build/README.md b/build/README.md
new file mode 100644
index 0000000..9a0e3a0
--- /dev/null
+++ b/build/README.md
@@ -0,0 +1,12 @@
+To create list of files to compile:
+```
+../../mkmf/bin/list_paths ../../FMS/{mpp,diag_manager,time_manager,include,memutils,constants,platform,fms,random_numbers,mosaic,exchange} ../src/ ../driver/
+```
+To create a `Makefile`:
+```
+../../mkmf/bin/mkmf -t ../../mkmf/templates/ncrc-gnu.mk -p bergs.x path_names 
+```
+To compile a "debug" executable:
+```
+make DEBUG=1 -j
+```
diff --git a/build/diag_table b/build/diag_table
new file mode 100644
index 0000000..c1c8819
--- /dev/null
+++ b/build/diag_table
@@ -0,0 +1,3 @@
+"icebergs test"
+1 1 1 0 0 0
+
diff --git a/build/env b/build/env
new file mode 100644
index 0000000..8dc2c5c
--- /dev/null
+++ b/build/env
@@ -0,0 +1,4 @@
+source /opt/modules/default/etc/modules.sh
+module use -a /ncrc/home2/fms/local/modulefiles
+MODULEPATH=/usw/eslogin/modulefiles-c4:/sw/eslogin-c4/modulefiles:/opt/cray/pe/ari/modulefiles:/opt/cray/ari/modulefiles:/opt/cray/pe/modulefiles:/opt/cray/modulefiles:/opt/modulefiles:/sw/common/modulefiles
+module unload PrgEnv-pgi PrgEnv-intel PrgEnv-gnu darshan; module load PrgEnv-gnu; module unload netcdf gcc; module load gcc/7.3.0 cray-hdf5 cray-netcdf
diff --git a/build/input.nml b/build/input.nml
new file mode 100644
index 0000000..5ee0e8b
--- /dev/null
+++ b/build/input.nml
@@ -0,0 +1,10 @@
+&icebergs_driver_nml
+  ni=30
+  nj=20
+/
+
+&icebergs_nml
+/
+
+&diag_manager_nml
+/
diff --git a/driver/icebergs_driver.F90 b/driver/icebergs_driver.F90
new file mode 100644
index 0000000..e65bb27
--- /dev/null
+++ b/driver/icebergs_driver.F90
@@ -0,0 +1,139 @@
+program icebergs_driver
+
+use fms_mod, only : fms_init
+use fms_mod, only : fms_end
+use fms_mod, only : open_namelist_file
+use fms_mod, only : close_file
+use fms_mod, only : error_mesg
+use fms_mod, only : FATAL
+use mpp_domains_mod, only : mpp_define_layout
+use mpp_domains_mod, only : mpp_define_domains
+use mpp_domains_mod, only : mpp_define_io_domain
+use mpp_domains_mod, only : mpp_get_compute_domain
+use mpp_domains_mod, only : mpp_get_data_domain
+use mpp_domains_mod, only : domain2D
+use mpp_mod, only : mpp_npes
+use mpp_mod, only : mpp_pe
+use mpp_mod, only : mpp_root_pe
+use time_manager_mod, only : time_type
+use time_manager_mod, only : set_date
+use time_manager_mod, only : set_calendar_type
+use time_manager_mod, only : THIRTY_DAY_MONTHS
+use diag_manager_mod, only : diag_manager_init
+
+use ice_bergs, only : icebergs
+use ice_bergs, only : icebergs_init
+use ice_bergs, only : icebergs_run
+use ice_bergs, only : icebergs_end
+
+! For parallelism
+integer :: nprocs !< Number of processes
+integer :: layout(2) !< Layout of MPI processes
+integer :: io_layout(2) !< Layout of I/O processes
+integer :: iflags=0 !< For i-direction flags
+integer :: jflags=0 !< For j-direction flags
+type(domain2D) :: mpp_domain !< Parallel decomposition
+! For declarations
+integer :: isd !< Start of i-index for data domain (used in declarations)
+integer :: ied !< End of i-index for data domain (used in declarations)
+integer :: jsd !< Start of j-index for data domain (used in declarations)
+integer :: jed !< End of j-index for data domain (used in declarations)
+! I/O
+integer :: nmunit !< Namelist file unit
+integer :: axes(2) !< Diagnostic axes
+! Run-time parameters for this driver
+integer :: ni=0 !< Global number of grid cells in i-direction (mandatory input)
+integer :: nj=0 !< Global number of grid cells in j-direction (mandatory input)
+logical :: debug=.true. !< If true, do some debugging
+integer :: halo=1 !< Width of halo in parallel decomposition
+namelist /icebergs_driver_nml/ debug, ni, nj, halo
+! For loops
+integer :: isc !< Start of i-index for computational domain (used for loops)
+integer :: iec !< End of i-index for computational domain (used for loops)
+integer :: jsc !< Start of j-index for computational domain (used for loops)
+integer :: jec !< End of j-index for computational domain (used for loops)
+! For icebergs
+type(icebergs), pointer :: bergs !< Container for icebergs
+type (time_type) :: time !< Model time
+real, allocatable :: lon(:,:) !< Longitude or position in x
+real, allocatable :: lat(:,:) !< Latitude or position in y
+real, allocatable :: wet(:,:) !< Wet-dry mask to indicate ocean/land
+real, allocatable :: dx(:,:) !< Length of northern edge of cell (m)
+real, allocatable :: dy(:,:) !< Length of eatern edge of cell (m)
+real, allocatable :: area(:,:) !< Area of cell (m2)
+real, allocatable :: cos_rot(:,:) !< Cosine of angle of grid orientation
+real, allocatable :: sin_rot(:,:) !< Sine of angle of grid orientation
+real, allocatable :: depth(:,:) !< Depth of ocean (m)
+! Work variables
+integer :: i,j
+
+! Boot FMS
+call fms_init()
+
+! Read run-time parameters
+nmunit = open_namelist_file(file='input.nml')
+read(nmunit, nml=icebergs_driver_nml)
+call close_file(nmunit)
+if (min(ni,nj)<1) call error_mesg('icebergs_driver:', &
+  'Both ni,nj must be positive in icebergs_driver_nml namelist', FATAL)
+
+! Ask FMS to figure our how to decompose the global ni x nj grid
+layout = (/0,0/) ! 0,0 lets FMS find an optimal layout
+nprocs = mpp_npes() ! How many processes are we using?
+call mpp_define_layout((/1, ni, 1, nj/), nprocs, layout)
+if (debug .and. mpp_root_pe()==0) print *,'layout=',layout,'nprocs=',nprocs,'PE=',mpp_pe()
+
+! Create a decomposed domain with the given layout from above
+call mpp_define_domains((/1,ni,1,nj/), layout, mpp_domain, &
+         xflags=iflags, yflags=jflags, &
+         xhalo=halo, yhalo=halo, &
+         symmetry=.false., name='iceberg_driver')
+
+! Set up I/O
+io_layout = (/1,1/) ! 1,1 tells FMS to use just one processor for I/O
+call mpp_define_io_domain(mpp_domain, io_layout)
+
+call diag_manager_init()
+
+! Query for declaration ranges
+call mpp_get_data_domain(mpp_domain, isd, ied, jsd, jed)
+if (debug .and. mpp_root_pe()==0) print *,'isd,ied,jsc,jed=',isd,ied,jsc,jed
+
+! Query for loop ranges
+call mpp_get_compute_domain(mpp_domain, isc, iec, jsc, jec)
+if (debug .and. mpp_root_pe()==0) print *,'isd,isc,iec,ied=',isd,isc,iec,ied
+if (debug .and. mpp_root_pe()==0) print *,'jsd,jsc,jec,jed=',jsd,jsc,jec,jed
+
+allocate( lon(isd:ied,jsd:jed) )
+allocate( lat(isd:ied,jsd:jed) )
+allocate( wet(isd:ied,jsd:jed) )
+allocate( dx(isd:ied,jsd:jed) )
+allocate( dy(isd:ied,jsd:jed) )
+allocate( area(isd:ied,jsd:jed) )
+allocate( cos_rot(isd:ied,jsd:jed) )
+allocate( sin_rot(isd:ied,jsd:jed) )
+allocate( depth(isd:ied,jsd:jed) )
+
+do j = jsc, jec
+  do i = isc, iec
+    lon(i,j) = 10.e3*real(i)
+    lat(i,j) = 10.e3*real(j)
+    dx(i,j) = 10.e3
+    dy(i,j) = 10.e3
+    area(i,j) = 1.e8
+    wet(i,j) = 1.0
+    cos_rot(i,j) = 1.0
+    sin_rot(i,j) = 0.0
+    depth(i,j) = 1000.
+  enddo
+enddo
+
+call set_calendar_type(THIRTY_DAY_MONTHS)
+time = set_date(1,1,1,0,0,0)
+
+call icebergs_init(bergs, &
+                   ni, nj, layout, io_layout, axes, iflags, jflags, dt, time, &
+                   lon(isc:iec,jsc:jec), lat(isc:iec,jsc:jec), wet, dx, dy, area(isc:iec,jsc:jec), &
+                   cos_rot, sin_rot, depth(isc:iec,jsc:jec), fractional_area=.false.)
+
+end program icebergs_driver
diff --git a/icebergs.F90 b/src/icebergs.F90
similarity index 100%
rename from icebergs.F90
rename to src/icebergs.F90
diff --git a/icebergs_framework.F90 b/src/icebergs_framework.F90
similarity index 100%
rename from icebergs_framework.F90
rename to src/icebergs_framework.F90
diff --git a/icebergs_io.F90 b/src/icebergs_io.F90
similarity index 100%
rename from icebergs_io.F90
rename to src/icebergs_io.F90

From 1c80144bbad23016746c75e105ac96e5377aa1e2 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Tue, 14 Jul 2020 22:18:19 -0400
Subject: [PATCH 245/361] Corrected README with critical bit for MPI

- Certain CPP macros are required to compile with MPI
---
 build/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build/README.md b/build/README.md
index 9a0e3a0..370a51a 100644
--- a/build/README.md
+++ b/build/README.md
@@ -4,7 +4,7 @@ To create list of files to compile:
 ```
 To create a `Makefile`:
 ```
-../../mkmf/bin/mkmf -t ../../mkmf/templates/ncrc-gnu.mk -p bergs.x path_names 
+../../mkmf/bin/mkmf -t ../../mkmf/templates/ncrc-gnu.mk -c "-Duse_libMPI -Duse_netCDF" -p bergs.x path_names 
 ```
 To compile a "debug" executable:
 ```

From a7cc66bbce413d33ccad5ff3dae7f440e24a0a40 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Tue, 14 Jul 2020 22:18:58 -0400
Subject: [PATCH 246/361] Added diagnostics axes

- axes(2) was declared but set/initialized which is now done
  with diag_axis_init()
---
 driver/icebergs_driver.F90 | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/driver/icebergs_driver.F90 b/driver/icebergs_driver.F90
index e65bb27..b760f71 100644
--- a/driver/icebergs_driver.F90
+++ b/driver/icebergs_driver.F90
@@ -20,6 +20,7 @@ program icebergs_driver
 use time_manager_mod, only : set_calendar_type
 use time_manager_mod, only : THIRTY_DAY_MONTHS
 use diag_manager_mod, only : diag_manager_init
+use diag_axis_mod, only : diag_axis_init
 
 use ice_bergs, only : icebergs
 use ice_bergs, only : icebergs_init
@@ -66,6 +67,7 @@ program icebergs_driver
 real, allocatable :: depth(:,:) !< Depth of ocean (m)
 ! Work variables
 integer :: i,j
+real, allocatable :: coord(:) !< One dimensional coordinate for initializing diagnostics
 
 ! Boot FMS
 call fms_init()
@@ -93,7 +95,21 @@ program icebergs_driver
 io_layout = (/1,1/) ! 1,1 tells FMS to use just one processor for I/O
 call mpp_define_io_domain(mpp_domain, io_layout)
 
+! Diagnostics manager
 call diag_manager_init()
+! Axes for diagnostics
+allocate( coord(ni) )
+do i = 1, ni
+  coord(i) = real(i)
+enddo
+axes(1) = diag_axis_init('i', coord, 'index', 'X', 'cell index i', Domain2=mpp_domain)
+deallocate( coord )
+allocate( coord(nj) )
+do j = 1, nj
+  coord(j) = real(j)
+enddo
+axes(2) = diag_axis_init('j', coord, 'index', 'Y', 'cell index j', Domain2=mpp_domain)
+deallocate( coord )
 
 ! Query for declaration ranges
 call mpp_get_data_domain(mpp_domain, isd, ied, jsd, jed)

From 3b43d93ff09aa6705a760f2d4e28d70d949bae3f Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Fri, 14 Aug 2020 14:09:10 -0400
Subject: [PATCH 247/361] restructure for solo-driver and add initial test case

---
 build/README.md              |   10 +-
 build/env                    |   18 +-
 build/input.nml              |   10 -
 build/mkcmd                  |    1 +
 build/mkmkf                  |    3 +
 driver/icebergs_driver.F90   |  422 +++++++----
 src/icebergs_framework.F90   | 1302 +++++++++++++++++-----------------
 src/icebergs_io.F90          |    9 +-
 test/Iceberg_repository      |    1 +
 test/README                  |    4 +
 test/RUN                     |    2 +
 test/animate_trajectories.py |  114 +++
 test/diag_table              |    3 +
 test/input.nml               |   49 ++
 14 files changed, 1152 insertions(+), 796 deletions(-)
 delete mode 100644 build/input.nml
 create mode 100644 build/mkcmd
 create mode 100644 build/mkmkf
 create mode 160000 test/Iceberg_repository
 create mode 100644 test/README
 create mode 100755 test/RUN
 create mode 100755 test/animate_trajectories.py
 create mode 100644 test/diag_table
 create mode 100644 test/input.nml

diff --git a/build/README.md b/build/README.md
index 370a51a..6b5b28d 100644
--- a/build/README.md
+++ b/build/README.md
@@ -1,12 +1,20 @@
 To create list of files to compile:
+
+
+#rm -f path_names
+
 ```
 ../../mkmf/bin/list_paths ../../FMS/{mpp,diag_manager,time_manager,include,memutils,constants,platform,fms,random_numbers,mosaic,exchange} ../src/ ../driver/
 ```
 To create a `Makefile`:
 ```
-../../mkmf/bin/mkmf -t ../../mkmf/templates/ncrc-gnu.mk -c "-Duse_libMPI -Duse_netCDF" -p bergs.x path_names 
+../../mkmf/bin/mkmf -t ../../mkmf/templates/ncrc-gnu.mk -c "-Duse_libMPI -Duse_netCDF" -p bergs.x path_names
+
+
+##../../mkmf/bin/mkmf -t ../../mkmf/templates/ncrc-intel.mk -c "-Duse_libMPI -Duse_netCDF" -p bergs.x path_names 
 ```
 To compile a "debug" executable:
 ```
 make DEBUG=1 -j
+##make NETCDF=3 DEBUG=1 bergs.x -j
 ```
diff --git a/build/env b/build/env
index 8dc2c5c..8dd47c1 100644
--- a/build/env
+++ b/build/env
@@ -1,4 +1,16 @@
-source /opt/modules/default/etc/modules.sh
+#source /opt/modules/default/etc/modules.sh
 module use -a /ncrc/home2/fms/local/modulefiles
-MODULEPATH=/usw/eslogin/modulefiles-c4:/sw/eslogin-c4/modulefiles:/opt/cray/pe/ari/modulefiles:/opt/cray/ari/modulefiles:/opt/cray/pe/modulefiles:/opt/cray/modulefiles:/opt/modulefiles:/sw/common/modulefiles
-module unload PrgEnv-pgi PrgEnv-intel PrgEnv-gnu darshan; module load PrgEnv-gnu; module unload netcdf gcc; module load gcc/7.3.0 cray-hdf5 cray-netcdf
+setenv MODULEPATH /usw/eslogin/modulefiles-c4:/sw/eslogin-c4/modulefiles:/opt/cray/pe/ari/modulefiles:/opt/cray/ari/modulefiles:/opt/cray/pe/modulefiles:/opt/cray/modulefiles:/opt/modulefiles:/sw/common/modulefiles
+#module unload PrgEnv-pgi PrgEnv-intel PrgEnv-gnu darshan; module load PrgEnv-gnu; module unload netcdf gcc; module load gcc/7.3.0 cray-hdf5 cray-netcdf
+
+module unload PrgEnv-pgi
+module unload PrgEnv-pathscale
+module unload PrgEnv-intel
+module unload PrgEnv-gnu
+module unload PrgEnv-cray
+
+module load PrgEnv-intel
+module swap intel intel/18.0.6.288
+module unload netcdf
+module load cray-netcdf
+module load cray-hdf5
\ No newline at end of file
diff --git a/build/input.nml b/build/input.nml
deleted file mode 100644
index 5ee0e8b..0000000
--- a/build/input.nml
+++ /dev/null
@@ -1,10 +0,0 @@
-&icebergs_driver_nml
-  ni=30
-  nj=20
-/
-
-&icebergs_nml
-/
-
-&diag_manager_nml
-/
diff --git a/build/mkcmd b/build/mkcmd
new file mode 100644
index 0000000..426e776
--- /dev/null
+++ b/build/mkcmd
@@ -0,0 +1 @@
+make NETCDF=3 DEBUG=1 bergs.x -j
\ No newline at end of file
diff --git a/build/mkmkf b/build/mkmkf
new file mode 100644
index 0000000..7a8943e
--- /dev/null
+++ b/build/mkmkf
@@ -0,0 +1,3 @@
+rm -f path_names
+../../mkmf/bin/list_paths ../../FMS/{mpp,diag_manager,time_manager,include,memutils,constants,platform,fms,random_numbers,mosaic,exchange} ../src/ ../driver/ ../test/
+../../mkmf/bin/mkmf -t ../../mkmf/templates/ncrc-intel.mk -c "-Duse_libMPI -Duse_netCDF" -p bergs.x path_names
\ No newline at end of file
diff --git a/driver/icebergs_driver.F90 b/driver/icebergs_driver.F90
index b760f71..e39ea46 100644
--- a/driver/icebergs_driver.F90
+++ b/driver/icebergs_driver.F90
@@ -1,155 +1,281 @@
 program icebergs_driver
 
-use fms_mod, only : fms_init
-use fms_mod, only : fms_end
-use fms_mod, only : open_namelist_file
-use fms_mod, only : close_file
-use fms_mod, only : error_mesg
-use fms_mod, only : FATAL
-use mpp_domains_mod, only : mpp_define_layout
-use mpp_domains_mod, only : mpp_define_domains
-use mpp_domains_mod, only : mpp_define_io_domain
-use mpp_domains_mod, only : mpp_get_compute_domain
-use mpp_domains_mod, only : mpp_get_data_domain
-use mpp_domains_mod, only : domain2D
-use mpp_mod, only : mpp_npes
-use mpp_mod, only : mpp_pe
-use mpp_mod, only : mpp_root_pe
-use time_manager_mod, only : time_type
-use time_manager_mod, only : set_date
-use time_manager_mod, only : set_calendar_type
-use time_manager_mod, only : THIRTY_DAY_MONTHS
-use diag_manager_mod, only : diag_manager_init
-use diag_axis_mod, only : diag_axis_init
-
-use ice_bergs, only : icebergs
-use ice_bergs, only : icebergs_init
-use ice_bergs, only : icebergs_run
-use ice_bergs, only : icebergs_end
-
-! For parallelism
-integer :: nprocs !< Number of processes
-integer :: layout(2) !< Layout of MPI processes
-integer :: io_layout(2) !< Layout of I/O processes
-integer :: iflags=0 !< For i-direction flags
-integer :: jflags=0 !< For j-direction flags
-type(domain2D) :: mpp_domain !< Parallel decomposition
-! For declarations
-integer :: isd !< Start of i-index for data domain (used in declarations)
-integer :: ied !< End of i-index for data domain (used in declarations)
-integer :: jsd !< Start of j-index for data domain (used in declarations)
-integer :: jed !< End of j-index for data domain (used in declarations)
-! I/O
-integer :: nmunit !< Namelist file unit
-integer :: axes(2) !< Diagnostic axes
-! Run-time parameters for this driver
-integer :: ni=0 !< Global number of grid cells in i-direction (mandatory input)
-integer :: nj=0 !< Global number of grid cells in j-direction (mandatory input)
-logical :: debug=.true. !< If true, do some debugging
-integer :: halo=1 !< Width of halo in parallel decomposition
-namelist /icebergs_driver_nml/ debug, ni, nj, halo
-! For loops
-integer :: isc !< Start of i-index for computational domain (used for loops)
-integer :: iec !< End of i-index for computational domain (used for loops)
-integer :: jsc !< Start of j-index for computational domain (used for loops)
-integer :: jec !< End of j-index for computational domain (used for loops)
-! For icebergs
-type(icebergs), pointer :: bergs !< Container for icebergs
-type (time_type) :: time !< Model time
-real, allocatable :: lon(:,:) !< Longitude or position in x
-real, allocatable :: lat(:,:) !< Latitude or position in y
-real, allocatable :: wet(:,:) !< Wet-dry mask to indicate ocean/land
-real, allocatable :: dx(:,:) !< Length of northern edge of cell (m)
-real, allocatable :: dy(:,:) !< Length of eatern edge of cell (m)
-real, allocatable :: area(:,:) !< Area of cell (m2)
-real, allocatable :: cos_rot(:,:) !< Cosine of angle of grid orientation
-real, allocatable :: sin_rot(:,:) !< Sine of angle of grid orientation
-real, allocatable :: depth(:,:) !< Depth of ocean (m)
-! Work variables
-integer :: i,j
-real, allocatable :: coord(:) !< One dimensional coordinate for initializing diagnostics
-
-! Boot FMS
-call fms_init()
-
-! Read run-time parameters
-nmunit = open_namelist_file(file='input.nml')
-read(nmunit, nml=icebergs_driver_nml)
-call close_file(nmunit)
-if (min(ni,nj)<1) call error_mesg('icebergs_driver:', &
-  'Both ni,nj must be positive in icebergs_driver_nml namelist', FATAL)
-
-! Ask FMS to figure our how to decompose the global ni x nj grid
-layout = (/0,0/) ! 0,0 lets FMS find an optimal layout
-nprocs = mpp_npes() ! How many processes are we using?
-call mpp_define_layout((/1, ni, 1, nj/), nprocs, layout)
-if (debug .and. mpp_root_pe()==0) print *,'layout=',layout,'nprocs=',nprocs,'PE=',mpp_pe()
-
-! Create a decomposed domain with the given layout from above
-call mpp_define_domains((/1,ni,1,nj/), layout, mpp_domain, &
-         xflags=iflags, yflags=jflags, &
-         xhalo=halo, yhalo=halo, &
-         symmetry=.false., name='iceberg_driver')
-
-! Set up I/O
-io_layout = (/1,1/) ! 1,1 tells FMS to use just one processor for I/O
-call mpp_define_io_domain(mpp_domain, io_layout)
-
-! Diagnostics manager
-call diag_manager_init()
-! Axes for diagnostics
-allocate( coord(ni) )
-do i = 1, ni
-  coord(i) = real(i)
-enddo
-axes(1) = diag_axis_init('i', coord, 'index', 'X', 'cell index i', Domain2=mpp_domain)
-deallocate( coord )
-allocate( coord(nj) )
-do j = 1, nj
-  coord(j) = real(j)
-enddo
-axes(2) = diag_axis_init('j', coord, 'index', 'Y', 'cell index j', Domain2=mpp_domain)
-deallocate( coord )
-
-! Query for declaration ranges
-call mpp_get_data_domain(mpp_domain, isd, ied, jsd, jed)
-if (debug .and. mpp_root_pe()==0) print *,'isd,ied,jsc,jed=',isd,ied,jsc,jed
-
-! Query for loop ranges
-call mpp_get_compute_domain(mpp_domain, isc, iec, jsc, jec)
-if (debug .and. mpp_root_pe()==0) print *,'isd,isc,iec,ied=',isd,isc,iec,ied
-if (debug .and. mpp_root_pe()==0) print *,'jsd,jsc,jec,jed=',jsd,jsc,jec,jed
-
-allocate( lon(isd:ied,jsd:jed) )
-allocate( lat(isd:ied,jsd:jed) )
-allocate( wet(isd:ied,jsd:jed) )
-allocate( dx(isd:ied,jsd:jed) )
-allocate( dy(isd:ied,jsd:jed) )
-allocate( area(isd:ied,jsd:jed) )
-allocate( cos_rot(isd:ied,jsd:jed) )
-allocate( sin_rot(isd:ied,jsd:jed) )
-allocate( depth(isd:ied,jsd:jed) )
-
-do j = jsc, jec
-  do i = isc, iec
-    lon(i,j) = 10.e3*real(i)
-    lat(i,j) = 10.e3*real(j)
-    dx(i,j) = 10.e3
-    dy(i,j) = 10.e3
-    area(i,j) = 1.e8
-    wet(i,j) = 1.0
-    cos_rot(i,j) = 1.0
-    sin_rot(i,j) = 0.0
-    depth(i,j) = 1000.
+  use fms_mod, only : fms_init
+  use fms_mod, only : fms_end
+  use fms_mod, only : open_namelist_file
+  use fms_mod, only : close_file
+  use fms_mod, only : error_mesg
+  use fms_mod, only : FATAL
+  use mpp_domains_mod, only : mpp_define_layout
+  use mpp_domains_mod, only : mpp_define_domains
+  use mpp_domains_mod, only : mpp_define_io_domain
+  use mpp_domains_mod, only : mpp_get_compute_domain
+  use mpp_domains_mod, only : mpp_get_data_domain
+  use mpp_domains_mod, only : domain2D
+  use mpp_domains_mod, only : CYCLIC_GLOBAL_DOMAIN,GLOBAL_DATA_DOMAIN
+  use mpp_mod, only : mpp_npes
+  use mpp_mod, only : mpp_pe
+  use mpp_mod, only : mpp_root_pe
+  use time_manager_mod, only : time_type
+  use time_manager_mod, only : set_date
+  use time_manager_mod, only : set_calendar_type
+  use time_manager_mod, only : THIRTY_DAY_MONTHS
+  use time_manager_mod, only : increment_date
+  use time_manager_mod, only : real_to_time_type,time_type_to_real
+  use time_manager_mod, only : operator(+), operator(-), operator(*), operator(/)
+  use time_manager_mod, only : operator(>), operator(<), operator(>=)  
+  use diag_manager_mod, only : diag_manager_init
+  use diag_axis_mod, only : diag_axis_init
+  use ice_bergs, only : icebergs
+  use ice_bergs, only : icebergs_init
+  use ice_bergs, only : icebergs_run
+  use ice_bergs, only : icebergs_end
+  use ice_bergs, only : icebergs_save_restart
+
+
+  ! For parallelism
+  integer :: nprocs !< Number of processes
+  integer :: layout(2) !< Layout of MPI processes
+  integer :: io_layout(2) !< Layout of I/O processes
+
+  integer :: iflags= 2  !< For i-direction flags ( cyclic_global_domain)
+  integer :: jflags= 0  !< For j-direction flags
+  type(domain2D) :: mpp_domain !< Parallel decomposition
+  ! For declarations
+  integer :: isd !< Start of i-index for data domain (used in declarations)
+  integer :: ied !< End of i-index for data domain (used in declarations)
+  integer :: jsd !< Start of j-index for data domain (used in declarations)
+  integer :: jed !< End of j-index for data domain (used in declarations)
+  ! I/O
+  integer :: nmunit !< Namelist file unit 
+  integer :: axes(2) !< Diagnostic axes
+  ! Run-time parameters for this driver
+  integer :: ni=0 !< Global number of grid cells in i-direction (mandatory input)
+  integer :: nj=0 !< Global number of grid cells in j-direction (mandatory input)
+  logical :: debug=.true. !< If true, do some debugging
+  integer :: halo=1 !< Width of halo in parallel decomposition
+  real :: ibdt=3600.0
+  real :: ibuo=0.1
+  real :: ibvo=0.0
+  integer :: ibhrs=2
+  namelist /icebergs_driver_nml/ debug, ni, nj, halo, ibhrs, ibdt, ibuo, ibvo
+  ! For loops
+  integer :: isc !< Start of i-index for computational domain (used for loops)
+  integer :: iec !< End of i-index for computational domain (used for loops)
+  integer :: jsc !< Start of j-index for computational domain (used for loops)
+  integer :: jec !< End of j-index for computational domain (used for loops)
+  ! Time
+  type(time_type) :: Time !< Model time
+  type(time_type) :: Time_end  !<end time for the experiment (s)
+  real :: nmax = 2000000000 !<max number of iterations  
+  real :: dt !<time increment
+  integer :: ns !<timestep counter
+  ! For icebergs
+  type(icebergs), pointer :: bergs !< Container for icebergs
+  real, allocatable :: lon(:,:) !< Longitude or position in x
+  real, allocatable :: lat(:,:) !< Latitude or position in y
+  real, allocatable :: wet(:,:) !< Wet-dry mask to indicate ocean/land
+  real, allocatable :: dx(:,:) !< Length of northern edge of cell (m)
+  real, allocatable :: dy(:,:) !< Length of eatern edge of cell (m)
+  real, allocatable :: area(:,:) !< Area of cell (m2)
+  real, allocatable :: cos_rot(:,:) !< Cosine of angle of grid orientation
+  real, allocatable :: sin_rot(:,:) !< Sine of angle of grid orientation
+  real, allocatable :: depth(:,:) !< Depth of ocean (m)
+  ! Work variables
+  integer :: i,j
+  real, allocatable :: coord(:) !< One dimensional coordinate for initializing diagnostics
+
+  ! For icebergs_run
+  real, dimension(:,:), allocatable :: calving !<Calving (kg/s)
+  real, dimension(:,:), allocatable :: uo,vo !<zonal and meridonal ocean velocities (m/s)
+  real, dimension(:,:), allocatable :: ui,vi !<zonal and meridonal ice velocities (m/s)
+  real, dimension(:,:), allocatable :: tauxa,tauya !< Zonal and meridonal wind stress (Pa)
+  real, dimension(:,:), allocatable :: ssh !< Effective sea-surface height (m)
+  real, dimension(:,:), allocatable :: sst !< Sea-surface temperature (C or K)
+  real, dimension(:,:), allocatable :: cn !< Sea-ice concentration (nondim)
+  real, dimension(:,:), allocatable :: hi !< Sea-ice thickness (m)
+  real, dimension(:,:), allocatable :: calving_hflx !< Calving heat flux (W/m2)
+  integer :: stagger, stress_stagger
+  real, dimension(:,:), allocatable :: sss !< Sea-surface salinity (1e-3)
+  real, dimension(:,:), pointer :: mass_berg !< Mass of bergs (kg)
+  real, dimension(:,:), pointer  :: ustar_berg !< Friction velocity on base of bergs (m/s)
+  real, dimension(:,:), pointer :: area_berg !< Area of bergs (m2)
+
+
+
+  
+  ! Boot FMS
+  call fms_init()
+
+  ! Read run-time parameters
+  nmunit = open_namelist_file(file='./../test/input.nml')
+  read(nmunit, nml=icebergs_driver_nml)
+  call close_file(nmunit)
+  if (min(ni,nj)<1) call error_mesg('icebergs_driver:', &
+       'Both ni,nj must be positive in icebergs_driver_nml namelist', FATAL)
+
+
+  ! Ask FMS to figure our how to decompose the global ni x nj grid
+  layout = (/0,0/) ! 0,0 lets FMS find an optimal layout
+  nprocs = mpp_npes() ! How many processes are we using?
+  call mpp_define_layout((/1, ni, 1, nj/), nprocs, layout)
+  if (debug .and. mpp_root_pe()==0) print *,'layout=',layout,'nprocs=',nprocs,'PE=',mpp_pe()
+  
+  ! Create a decomposed domain with the given layout from above
+  call mpp_define_domains((/1,ni,1,nj/), layout, mpp_domain, &
+       xflags=cyclic_global_domain, yflags=jflags, &
+       xhalo=halo, yhalo=halo, &
+       symmetry=.false., name='iceberg_driver')
+
+  ! Set up I/O
+  io_layout = (/1,1/) ! 1,1 tells FMS to use just one processor for I/O
+  call mpp_define_io_domain(mpp_domain, io_layout)
+
+  ! Diagnostics manager
+  call diag_manager_init()
+  ! Axes for diagnostics
+  allocate( coord(ni) )
+  do i = 1, ni
+     coord(i) =  real(i)
+  enddo
+  axes(1) = diag_axis_init('i', coord, 'index', 'X', 'cell index i', Domain2=mpp_domain)
+  deallocate( coord )
+  allocate( coord(nj) )
+  do j = 1, nj
+     coord(j) = real(j)
+  enddo
+  axes(2) = diag_axis_init('j', coord, 'index', 'Y', 'cell index j', Domain2=mpp_domain)
+  deallocate( coord )
+
+  ! Query for declaration ranges
+  call mpp_get_data_domain(mpp_domain, isd, ied, jsd, jed)
+  if (debug .and. mpp_root_pe()==0) print *,'isd,ied,jsd,jed=',isd,ied,jsd,jed
+
+  ! Query for loop ranges
+  call mpp_get_compute_domain(mpp_domain, isc, iec, jsc, jec)
+  if (debug .and. mpp_root_pe()==0) print *,'isd,isc,iec,ied=',isd,isc,iec,ied
+  if (debug .and. mpp_root_pe()==0) print *,'jsd,jsc,jec,jed=',jsd,jsc,jec,jed
+
+  allocate( lon(isd:ied,jsd:jed) )
+  allocate( lat(isd:ied,jsd:jed) )
+  allocate( wet(isd:ied,jsd:jed) )
+  allocate( dx(isd:ied,jsd:jed) )
+  allocate( dy(isd:ied,jsd:jed) )
+  allocate( area(isd:ied,jsd:jed) )
+  allocate( cos_rot(isd:ied,jsd:jed) )
+  allocate( sin_rot(isd:ied,jsd:jed) )
+  allocate( depth(isd:ied,jsd:jed) )
+
+   
+  do j = jsd, jed
+     do i = isd, ied
+        lon(i,j) = 10.e3*real(i)
+        lat(i,j) = 10.e3*real(j)
+        dx(i,j) = 10.e3
+        dy(i,j) = 10.e3
+        area(i,j) = 1.e8
+        wet(i,j) = 1.0
+        cos_rot(i,j) = 1.0 
+        sin_rot(i,j) = 0.0
+        depth(i,j) = 1000.
+     enddo
   enddo
-enddo
 
-call set_calendar_type(THIRTY_DAY_MONTHS)
-time = set_date(1,1,1,0,0,0)
 
-call icebergs_init(bergs, &
-                   ni, nj, layout, io_layout, axes, iflags, jflags, dt, time, &
-                   lon(isc:iec,jsc:jec), lat(isc:iec,jsc:jec), wet, dx, dy, area(isc:iec,jsc:jec), &
-                   cos_rot, sin_rot, depth(isc:iec,jsc:jec), fractional_area=.false.)
+  call set_calendar_type(THIRTY_DAY_MONTHS)
+  time = set_date(1,1,1,0,0,0)
+  dt = ibdt !3600.0
+
+  call icebergs_init(bergs, &
+       ni, nj, layout, io_layout, axes, iflags, jflags, dt, time, &
+       lon(isc:iec,jsc:jec), lat(isc:iec,jsc:jec), wet, dx, dy, area(isc:iec,jsc:jec), &
+       cos_rot, sin_rot, depth(isc:iec,jsc:jec), fractional_area=.false.)
+
+
+  ! for icebergs_run: 
+  allocate( calving(isd:ied,jsd:jed) )
+  allocate( uo(isd:ied,jsd:jed) )
+  allocate( vo(isd:ied,jsd:jed) )
+  allocate( ui(isd:ied,jsd:jed) )
+  allocate( vi(isd:ied,jsd:jed) )
+  allocate( tauxa(isd:ied,jsd:jed) )
+  allocate( tauya(isd:ied,jsd:jed) )
+  allocate( ssh(isd:ied,jsd:jed) )
+  allocate( sst(isd:ied,jsd:jed) ) 
+  allocate( cn(isd:ied,jsd:jed) )
+  allocate( hi(isd:ied,jsd:jed) )
+  allocate( calving_hflx(isd:ied,jsd:jed) )
+
+  calving = 0.0 !"calving" flux (kg/s) due to "melt" of bergs
+  uo = ibuo !0.1 !zonal ocean velocities (m/s)
+  vo = ibvo !meridonal ocean velocities (m/s)
+  ui = 0.0 !zonal ice velocities (m/s)
+  vi = 0.0 !meridonal ice velocities (m/s)
+  tauxa = 0.0 !zonal wind stress (Pa)
+  tauya = 0.0 !meridonal wind stress (Pa)
+  ssh = 0.0 !eff sea-surf height
+  sst = -2.0 !sea surface temperature (C or K; if K, will automatically adjust to C)
+  cn = 0.0 !sea-ice concentration (nondim)
+  hi = 0.0 !sea-ice thickness (m)
+  calving_hflx = 0.0 !calving heat flux (W/m2)
+
+ 
+  ! do j = jsc, jec
+  !    do i = isc, iec
+  !       if (i == j) then
+  !          calving(i,j) = 2.0
+  !       end if
+  !    enddo
+  ! enddo
+
+  ! optional:
+  ! allocate( sss(isd:ied,jsd:jed) )
+  ! allocate( mass_berg(isd:ied,jsd:jed) )
+  ! allocate( ustar_berg(isd:ied,jsd:jed) )
+  ! allocate( area_berg(isd:ied,jsd:jed) )  
+  ! stagger =  !scalar integer
+  ! stress_stagger = !scalar integer
+  ! sss = !sea surface salinity (1e-3)
+  ! mass_berg = !mass of bergs (kg)
+  ! ustar_berg = !Friction velocity on base of bergs (m/s)
+  ! area_berg = !Area of bergs (m2)
+
+  ns = 1 !timestep counter
+  ! Time_end = increment_date(Time, years, months, days, hours, minutes, seconds)
+
+  Time_end = increment_date(Time,0,0,0,ibhrs,0,0) 
+
+  do while ((ns < nmax) .and. (Time < Time_end))
+
+     print *,''
+     print *,'----------------------------'
+     print *,''
+     print *,'ns',ns
+     print *,'time',time_type_to_real(Time)
+     print *,''
+     print *,'----------------------------'
+     print *,''
+
+     ! The main driver the steps updates icebergs
+     call icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh, sst, &
+          calving_hflx, cn, hi)
+
+     ! full form, with optional vars:
+     ! call icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh, sst, &
+     ! calving_hflx, cn, hi,stagger, stress_stagger, sss, mass_berg, ustar_berg, area_berg)       
+
+     ! if (ns == 1) then
+     !    calving = 0.0
+     ! endif
+
+
+     Time = Time + real_to_time_type(dt)
+     ns = ns+1
+  enddo
+
+!  call icebergs_save_restart(bergs)
+ 
+  !Deallocate all memory and disassociated pointer
+  call icebergs_end(bergs)
 
 end program icebergs_driver
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index f8c6219..79884da 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -440,128 +440,128 @@ module ice_bergs_framework
 contains
 
 !> Initializes parallel framework
-subroutine ice_bergs_framework_init(bergs, &
-             gni, gnj, layout, io_layout, axes, dom_x_flags, dom_y_flags, &
-             dt, Time, ice_lon, ice_lat, ice_wet, ice_dx, ice_dy, ice_area, &
-             cos_rot, sin_rot, ocean_depth, maskmap, fractional_area)
-
-use mpp_parameter_mod, only: SCALAR_PAIR, CGRID_NE, BGRID_NE, CORNER, AGRID
-use mpp_domains_mod, only: mpp_update_domains, mpp_define_domains
-use mpp_domains_mod, only: mpp_get_compute_domain, mpp_get_data_domain, mpp_get_global_domain
-use mpp_domains_mod, only: CYCLIC_GLOBAL_DOMAIN, FOLD_NORTH_EDGE
-use mpp_domains_mod, only: mpp_get_neighbor_pe, NORTH, SOUTH, EAST, WEST
-use mpp_domains_mod, only: mpp_define_io_domain
-
-use mpp_mod, only: mpp_clock_begin, mpp_clock_end, mpp_clock_id, input_nml_file
-use mpp_mod, only: CLOCK_COMPONENT, CLOCK_SUBCOMPONENT, CLOCK_LOOP
-
-use fms_mod, only: open_namelist_file, check_nml_error, close_file
-use fms_mod, only: clock_flag_default
-
-use diag_manager_mod, only: register_diag_field, register_static_field, send_data
-use diag_manager_mod, only: diag_axis_init
-
-! Arguments
-type(icebergs), pointer :: bergs !< Container for all types and memory
-integer, intent(in) :: gni !< Number grid cells in i-direction
-integer, intent(in) :: gnj !< Number grid cells in j-direction
-integer, intent(in) :: layout(2) !< Number of processing cores in i,j direction
-integer, intent(in) :: io_layout(2) !< Number of i/o cores in i,j direction
-integer, intent(in) :: axes(2) !< Diagnostic axes
-integer, intent(in) :: dom_x_flags !< Domain flags in i-direction
-integer, intent(in) :: dom_y_flags !< Domain flags in j-direction
-real, intent(in) :: dt !< Time-step (s)
-type (time_type), intent(in) :: Time !< Current model time
-real, dimension(:,:), intent(in) :: ice_lon !< Longitude of cell corners using NE convention (degree E)
-real, dimension(:,:), intent(in) :: ice_lat !< Latitude of cell corners using NE conventino (degree N)
-real, dimension(:,:), intent(in) :: ice_wet !< Wet/dry mask (1 is wet, 0 is dry) of cell centers
-real, dimension(:,:), intent(in) :: ice_dx !< Zonal length of cell on northern side (m)
-real, dimension(:,:), intent(in) :: ice_dy !< Meridional length of cell on eastern side (m)
-real, dimension(:,:), intent(in) :: ice_area !< Area of cells (m^2, or non-dim is fractional_area=True)
-real, dimension(:,:), intent(in) :: cos_rot !< Cosine from rotation matrix to lat-lon coords
-real, dimension(:,:), intent(in) :: sin_rot !< Sine from rotation matrix to lat-lon coords
-real, dimension(:,:), intent(in),optional :: ocean_depth !< Depth of ocean bottom (m)
-logical, intent(in), optional :: maskmap(:,:) !< Masks out parallel cores
-logical, intent(in), optional :: fractional_area !< If true, ice_area contains cell area as fraction of entire spherical surface
-
-! Namelist parameters (and defaults)
-integer :: halo=4 ! Width of halo region
-integer :: traj_sample_hrs=24 ! Period between sampling of position for trajectory storage
-integer :: traj_write_hrs=480 ! Period between writing sampled trajectories to disk
-integer :: verbose_hrs=24 ! Period between verbose messages
-integer :: max_bonds=6 ! Maximum number of iceberg bond passed between processors
-real :: rho_bergs=850. ! Density of icebergs
-real :: spring_coef=1.e-8 ! Spring constant for iceberg interactions (this seems to be the highest stable value)
-real :: bond_coef=1.e-8 ! Spring constant for iceberg bonds - not being used right now
-real :: radial_damping_coef=1.e-4 ! Coefficient for relative iceberg motion damping (radial component) -Alon
-real :: tangental_damping_coef=2.e-5 ! Coefficient for relative iceberg motion damping (tangential component) -Alon
-real :: LoW_ratio=1.5 ! Initial ratio L/W for newly calved icebergs
-real :: bergy_bit_erosion_fraction=0. ! Fraction of erosion melt flux to divert to bergy bits
-real :: sicn_shift=0. ! Shift of sea-ice concentration in erosion flux modulation (0<sicn_shift<1)
-real :: lat_ref=0. ! Reference latitude for f-plane (when this option is on)
-real :: u_override=0.0 ! Overrides the u velocity of icebergs (for ocean testing)
-real :: v_override=0.0 ! Overrides the v velocity of icebergs (for ocean testing)
-real :: Lx=360. ! Length of domain in x direction, used for periodicity (use a huge number for non-periodic)
-real :: initial_orientation=0. ! Iceberg orientation relative to this angle (in degrees). Used for hexagonal mass spreading.
-real :: utide_icebergs= 0. ! Tidal speeds, set to zero for now.
-real :: ustar_icebergs_bg=0.001 ! Background u_star under icebergs. This should be linked to a value felt by the ocean boundary layer
-real :: cdrag_icebergs =  1.5e-3 ! Momentum Drag coef, taken from HJ99  (Holland and Jenkins 1999)
-real :: Gamma_T_3EQ=0.022 ! Non-dimensional heat-transfer coefficient
-real :: melt_cutoff=-1.0 ! Minimum ocean thickness for melting to occur (is not applied for values < 0)
-logical :: const_gamma=.True. ! If true uses a constant heat transfer coefficient, from which the salt transfer is calculated
-logical :: use_operator_splitting=.true. ! Use first order operator splitting for thermodynamics
-logical :: add_weight_to_ocean=.true. ! Add weight of icebergs + bits to ocean
-logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
-logical :: time_average_weight=.false. ! Time average the weight on the ocean
-real :: speed_limit=0. ! CFL speed limit for a berg
-real :: tau_calving=0. ! Time scale for smoothing out calving field (years)
-real :: tip_parameter=0. ! Parameter to override iceberg rolling critical ratio (use zero to get parameter directly from ice and seawater densities
-real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
-real :: coastal_drift=0. ! A velocity added to ocean currents to cause bergs to drift away from land cells
-real :: tidal_drift=0. ! Amplitude of a stochastic tidal velocity added to ocean currents to cause bergs to drift randomly
-logical :: Runge_not_Verlet=.True. ! True=Runge Kutta, False=Verlet.
-logical :: use_mixed_melting=.False. ! If true, then the melt is determined partly using 3 eq model partly using iceberg parameterizations (according to iceberg bond number)
-logical :: apply_thickness_cutoff_to_gridded_melt=.False. ! Prevents melt for ocean thickness below melt_cuttoff (applied to gridded melt fields)
-logical :: apply_thickness_cutoff_to_bergs_melt=.False. ! Prevents melt for ocean thickness below melt_cuttoff (applied to bergs)
-logical :: use_updated_rolling_scheme=.false. ! Use the corrected Rolling Scheme rather than the erroneous one
-logical :: pass_fields_to_ocean_model=.False. ! Iceberg area, mass and ustar fields are prepared to pass to ocean model
-logical :: use_mixed_layer_salinity_for_thermo=.False. ! If true, then model uses ocean salinity for 3 and 2 equation melt model.
-logical :: find_melt_using_spread_mass=.False. ! If true, then the model calculates ice loss by looping at the spread_mass before and after.
-logical :: Use_three_equation_model=.True. ! Uses 3 equation model for melt when ice shelf type thermodynamics are used.
-logical :: melt_icebergs_as_ice_shelf=.False. ! Uses iceshelf type thermodynamics
-logical :: Iceberg_melt_without_decay=.False. ! Allows icebergs meltwater fluxes to enter the ocean, without the iceberg decaying or changing shape.
-logical :: add_iceberg_thickness_to_SSH=.False. ! Adds the iceberg contribution to SSH.
-logical :: override_iceberg_velocities=.False. ! Allows you to set a fixed iceberg velocity for all non-static icebergs.
-logical :: use_f_plane=.False. ! Flag to use a f-plane for the rotation
-logical :: grid_is_latlon=.True. ! True means that the grid is specified in lat lon, and uses to radius of the earth to convert to distance
-logical :: grid_is_regular=.True. ! Flag to say whether point in cell can be found assuming regular Cartesian grid
-logical :: rotate_icebergs_for_mass_spreading=.True. ! Flag allows icebergs to rotate for spreading their mass (in hexagonal spreading mode)
-logical :: set_melt_rates_to_zero=.False. ! Sets all melt rates to zero, for testing purposes (thermodynamics routine is still run)
-logical :: allow_bergs_to_roll=.True. ! Allows icebergs to roll over when rolling conditions are met
-logical :: hexagonal_icebergs=.False. ! True treats icebergs as rectangles, False as hexagonal elements (for the purpose of mass spreading)
-logical :: ignore_missing_restart_bergs=.False. ! True Allows the model to ignore icebergs missing in the restart.
-logical :: Static_icebergs=.False. ! True= icebergs do no move
-logical :: only_interactive_forces=.False. ! Icebergs only feel interactive forces, and not ocean, wind...
-logical :: halo_debugging=.False. ! Use for debugging halos (remove when its working)
-logical :: save_short_traj=.True. ! True saves only lon,lat,time,id in iceberg_trajectory.nc
-logical :: ignore_traj=.False. ! If true, then model does not traj trajectory data at all
-logical :: iceberg_bonds_on=.False. ! True=Allow icebergs to have bonds, False=don't allow.
-logical :: manually_initialize_bonds=.False. ! True= Bonds are initialize manually.
-logical :: use_new_predictive_corrective =.False. ! Flag to use Bob's predictive corrective iceberg scheme- Added by Alon
-logical :: interactive_icebergs_on=.false. ! Turn on/off interactions between icebergs  - Added by Alon
-logical :: critical_interaction_damping_on=.true. ! Sets the damping on relative iceberg velocity to critical value - Added by Alon
-logical :: do_unit_tests=.false. ! Conduct some unit tests
-logical :: input_freq_distribution=.false. ! Flag to show if input distribution is freq or mass dist (=1 if input is a freq dist, =0 to use an input mass dist)
-logical :: read_old_restarts=.false. ! Legacy option that does nothing
-logical :: use_old_spreading=.true. ! If true, spreads iceberg mass as if the berg is one grid cell wide
-logical :: read_ocean_depth_from_file=.false. ! If true, ocean depth is read from a file.
-real, dimension(nclasses) :: initial_mass=(/8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11/) ! Mass thresholds between iceberg classes (kg)
-real, dimension(nclasses) :: distribution=(/0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02/) ! Fraction of calving to apply to this class (non-dim) ,
-real, dimension(nclasses) :: mass_scaling=(/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) ! Ratio between effective and real iceberg mass (non-dim)
-real, dimension(nclasses) :: initial_thickness=(/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) ! Total thickness of newly calved bergs (m)
-integer(kind=8) :: debug_iceberg_with_id = -1 ! If positive, monitors a berg with this id
-
-namelist /icebergs_nml/ verbose, budget, halo,  traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,Static_icebergs,  &
+  subroutine ice_bergs_framework_init(bergs, &
+       gni, gnj, layout, io_layout, axes, dom_x_flags, dom_y_flags, &
+       dt, Time, ice_lon, ice_lat, ice_wet, ice_dx, ice_dy, ice_area, &
+       cos_rot, sin_rot, ocean_depth, maskmap, fractional_area)
+
+    use mpp_parameter_mod, only: SCALAR_PAIR, CGRID_NE, BGRID_NE, CORNER, AGRID
+    use mpp_domains_mod, only: mpp_update_domains, mpp_define_domains
+    use mpp_domains_mod, only: mpp_get_compute_domain, mpp_get_data_domain, mpp_get_global_domain
+    use mpp_domains_mod, only: CYCLIC_GLOBAL_DOMAIN, FOLD_NORTH_EDGE
+    use mpp_domains_mod, only: mpp_get_neighbor_pe, NORTH, SOUTH, EAST, WEST
+    use mpp_domains_mod, only: mpp_define_io_domain
+
+    use mpp_mod, only: mpp_clock_begin, mpp_clock_end, mpp_clock_id, input_nml_file
+    use mpp_mod, only: CLOCK_COMPONENT, CLOCK_SUBCOMPONENT, CLOCK_LOOP
+
+    use fms_mod, only: open_namelist_file, check_nml_error, close_file
+    use fms_mod, only: clock_flag_default
+
+    use diag_manager_mod, only: register_diag_field, register_static_field, send_data
+    use diag_manager_mod, only: diag_axis_init
+
+    ! Arguments
+    type(icebergs), pointer :: bergs !< Container for all types and memory
+    integer, intent(in) :: gni !< Number grid cells in i-direction
+    integer, intent(in) :: gnj !< Number grid cells in j-direction
+    integer, intent(in) :: layout(2) !< Number of processing cores in i,j direction
+    integer, intent(in) :: io_layout(2) !< Number of i/o cores in i,j direction
+    integer, intent(in) :: axes(2) !< Diagnostic axes
+    integer, intent(in) :: dom_x_flags !< Domain flags in i-direction
+    integer, intent(in) :: dom_y_flags !< Domain flags in j-direction
+    real, intent(in) :: dt !< Time-step (s)
+    type (time_type), intent(in) :: Time !< Current model time
+    real, dimension(:,:), intent(in) :: ice_lon !< Longitude of cell corners using NE convention (degree E)
+    real, dimension(:,:), intent(in) :: ice_lat !< Latitude of cell corners using NE convention (degree N)
+    real, dimension(:,:), intent(in) :: ice_wet !< Wet/dry mask (1 is wet, 0 is dry) of cell centers
+    real, dimension(:,:), intent(in) :: ice_dx !< Zonal length of cell on northern side (m)
+    real, dimension(:,:), intent(in) :: ice_dy !< Meridional length of cell on eastern side (m)
+    real, dimension(:,:), intent(in) :: ice_area !< Area of cells (m^2, or non-dim is fractional_area=True)
+    real, dimension(:,:), intent(in) :: cos_rot !< Cosine from rotation matrix to lat-lon coords
+    real, dimension(:,:), intent(in) :: sin_rot !< Sine from rotation matrix to lat-lon coords
+    real, dimension(:,:), intent(in),optional :: ocean_depth !< Depth of ocean bottom (m)
+    logical, intent(in), optional :: maskmap(:,:) !< Masks out parallel cores
+    logical, intent(in), optional :: fractional_area !< If true, ice_area contains cell area as fraction of entire spherical surface
+
+    ! Namelist parameters (and defaults)
+    integer :: halo=4 ! Width of halo region
+    integer :: traj_sample_hrs=24 ! Period between sampling of position for trajectory storage
+    integer :: traj_write_hrs=480 ! Period between writing sampled trajectories to disk
+    integer :: verbose_hrs=24 ! Period between verbose messages
+    integer :: max_bonds=6 ! Maximum number of iceberg bond passed between processors
+    real :: rho_bergs=850. ! Density of icebergs
+    real :: spring_coef=1.e-8 ! Spring constant for iceberg interactions (this seems to be the highest stable value)
+    real :: bond_coef=1.e-8 ! Spring constant for iceberg bonds - not being used right now
+    real :: radial_damping_coef=1.e-4 ! Coefficient for relative iceberg motion damping (radial component) -Alon
+    real :: tangental_damping_coef=2.e-5 ! Coefficient for relative iceberg motion damping (tangential component) -Alon
+    real :: LoW_ratio=1.5 ! Initial ratio L/W for newly calved icebergs
+    real :: bergy_bit_erosion_fraction=0. ! Fraction of erosion melt flux to divert to bergy bits
+    real :: sicn_shift=0. ! Shift of sea-ice concentration in erosion flux modulation (0<sicn_shift<1)
+    real :: lat_ref=0. ! Reference latitude for f-plane (when this option is on)
+    real :: u_override=0.0 ! Overrides the u velocity of icebergs (for ocean testing)
+    real :: v_override=0.0 ! Overrides the v velocity of icebergs (for ocean testing)
+    real :: Lx=360. ! Length of domain in x direction, used for periodicity (use a huge number for non-periodic)
+    real :: initial_orientation=0. ! Iceberg orientation relative to this angle (in degrees). Used for hexagonal mass spreading.
+    real :: utide_icebergs= 0. ! Tidal speeds, set to zero for now.
+    real :: ustar_icebergs_bg=0.001 ! Background u_star under icebergs. This should be linked to a value felt by the ocean boundary layer
+    real :: cdrag_icebergs =  1.5e-3 ! Momentum Drag coef, taken from HJ99  (Holland and Jenkins 1999)
+    real :: Gamma_T_3EQ=0.022 ! Non-dimensional heat-transfer coefficient
+    real :: melt_cutoff=-1.0 ! Minimum ocean thickness for melting to occur (is not applied for values < 0)
+    logical :: const_gamma=.True. ! If true uses a constant heat transfer coefficient, from which the salt transfer is calculated
+    logical :: use_operator_splitting=.true. ! Use first order operator splitting for thermodynamics
+    logical :: add_weight_to_ocean=.true. ! Add weight of icebergs + bits to ocean
+    logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
+    logical :: time_average_weight=.false. ! Time average the weight on the ocean
+    real :: speed_limit=0. ! CFL speed limit for a berg
+    real :: tau_calving=0. ! Time scale for smoothing out calving field (years)
+    real :: tip_parameter=0. ! Parameter to override iceberg rolling critical ratio (use zero to get parameter directly from ice and seawater densities
+    real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
+    real :: coastal_drift=0. ! A velocity added to ocean currents to cause bergs to drift away from land cells
+    real :: tidal_drift=0. ! Amplitude of a stochastic tidal velocity added to ocean currents to cause bergs to drift randomly
+    logical :: Runge_not_Verlet=.True. ! True=Runge Kutta, False=Verlet.
+    logical :: use_mixed_melting=.False. ! If true, then the melt is determined partly using 3 eq model partly using iceberg parameterizations (according to iceberg bond number)
+    logical :: apply_thickness_cutoff_to_gridded_melt=.False. ! Prevents melt for ocean thickness below melt_cuttoff (applied to gridded melt fields)
+    logical :: apply_thickness_cutoff_to_bergs_melt=.False. ! Prevents melt for ocean thickness below melt_cuttoff (applied to bergs)
+    logical :: use_updated_rolling_scheme=.false. ! Use the corrected Rolling Scheme rather than the erroneous one
+    logical :: pass_fields_to_ocean_model=.False. ! Iceberg area, mass and ustar fields are prepared to pass to ocean model
+    logical :: use_mixed_layer_salinity_for_thermo=.False. ! If true, then model uses ocean salinity for 3 and 2 equation melt model.
+    logical :: find_melt_using_spread_mass=.False. ! If true, then the model calculates ice loss by looping at the spread_mass before and after.
+    logical :: Use_three_equation_model=.True. ! Uses 3 equation model for melt when ice shelf type thermodynamics are used.
+    logical :: melt_icebergs_as_ice_shelf=.False. ! Uses iceshelf type thermodynamics
+    logical :: Iceberg_melt_without_decay=.False. ! Allows icebergs meltwater fluxes to enter the ocean, without the iceberg decaying or changing shape.
+    logical :: add_iceberg_thickness_to_SSH=.False. ! Adds the iceberg contribution to SSH.
+    logical :: override_iceberg_velocities=.False. ! Allows you to set a fixed iceberg velocity for all non-static icebergs.
+    logical :: use_f_plane=.False. ! Flag to use a f-plane for the rotation
+    logical :: grid_is_latlon=.True. ! True means that the grid is specified in lat lon, and uses to radius of the earth to convert to distance
+    logical :: grid_is_regular=.True. ! Flag to say whether point in cell can be found assuming regular Cartesian grid
+    logical :: rotate_icebergs_for_mass_spreading=.True. ! Flag allows icebergs to rotate for spreading their mass (in hexagonal spreading mode)
+    logical :: set_melt_rates_to_zero=.False. ! Sets all melt rates to zero, for testing purposes (thermodynamics routine is still run)
+    logical :: allow_bergs_to_roll=.True. ! Allows icebergs to roll over when rolling conditions are met
+    logical :: hexagonal_icebergs=.False. ! True treats icebergs as rectangles, False as hexagonal elements (for the purpose of mass spreading)
+    logical :: ignore_missing_restart_bergs=.False. ! True Allows the model to ignore icebergs missing in the restart.
+    logical :: Static_icebergs=.False. ! True= icebergs do no move
+    logical :: only_interactive_forces=.False. ! Icebergs only feel interactive forces, and not ocean, wind...
+    logical :: halo_debugging=.False. ! Use for debugging halos (remove when its working)
+    logical :: save_short_traj=.True. ! True saves only lon,lat,time,id in iceberg_trajectory.nc
+    logical :: ignore_traj=.False. ! If true, then model does not traj trajectory data at all
+    logical :: iceberg_bonds_on=.False. ! True=Allow icebergs to have bonds, False=don't allow.
+    logical :: manually_initialize_bonds=.False. ! True= Bonds are initialize manually.
+    logical :: use_new_predictive_corrective =.False. ! Flag to use Bob's predictive corrective iceberg scheme- Added by Alon
+    logical :: interactive_icebergs_on=.false. ! Turn on/off interactions between icebergs  - Added by Alon
+    logical :: critical_interaction_damping_on=.true. ! Sets the damping on relative iceberg velocity to critical value - Added by Alon
+    logical :: do_unit_tests=.false. ! Conduct some unit tests
+    logical :: input_freq_distribution=.false. ! Flag to show if input distribution is freq or mass dist (=1 if input is a freq dist, =0 to use an input mass dist)
+    logical :: read_old_restarts=.false. ! Legacy option that does nothing
+    logical :: use_old_spreading=.true. ! If true, spreads iceberg mass as if the berg is one grid cell wide
+    logical :: read_ocean_depth_from_file=.false. ! If true, ocean depth is read from a file.
+    real, dimension(nclasses) :: initial_mass=(/8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11/) ! Mass thresholds between iceberg classes (kg)
+    real, dimension(nclasses) :: distribution=(/0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02/) ! Fraction of calving to apply to this class (non-dim) ,
+    real, dimension(nclasses) :: mass_scaling=(/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) ! Ratio between effective and real iceberg mass (non-dim)
+    real, dimension(nclasses) :: initial_thickness=(/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) ! Total thickness of newly calved bergs (m)
+    integer(kind=8) :: debug_iceberg_with_id = -1 ! If positive, monitors a berg with this id
+
+    namelist /icebergs_nml/ verbose, budget, halo,  traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,Static_icebergs,  &
          distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,bond_coef, radial_damping_coef, tangental_damping_coef, only_interactive_forces, &
          rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, iceberg_bonds_on, manually_initialize_bonds, ignore_missing_restart_bergs, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, halo_debugging, hexagonal_icebergs, &
@@ -573,561 +573,598 @@ subroutine ice_bergs_framework_init(bergs, &
          const_gamma, Gamma_T_3EQ, ignore_traj, debug_iceberg_with_id,use_updated_rolling_scheme, tip_parameter, read_old_restarts, tau_calving, read_ocean_depth_from_file, melt_cutoff,&
          apply_thickness_cutoff_to_gridded_melt, apply_thickness_cutoff_to_bergs_melt, use_mixed_melting, coastal_drift, tidal_drift
 
-! Local variables
-integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
-type(icebergs_gridded), pointer :: grd
-real :: lon_mod, big_number
-logical :: lerr
-integer :: stdlogunit, stderrunit
-real :: Total_mass  !Added by Alon
-
-  ! Get the stderr and stdlog unit numbers
-  stderrunit=stderr()
-  stdlogunit=stdlog()
-  write(stdlogunit,*) "ice_bergs_framework: "//trim(version)
-
-! Read namelist parameters
- !write(stderrunit,*) 'diamonds: reading namelist'
+    ! Local variables
+    integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
+    type(icebergs_gridded), pointer :: grd
+    real :: lon_mod, big_number
+    logical :: lerr
+    integer :: stdlogunit, stderrunit
+    real :: Total_mass  !Added by Alon
+
+    ! Get the stderr and stdlog unit numbers
+    stderrunit=stderr()
+    stdlogunit=stdlog()
+    write(stdlogunit,*) "ice_bergs_framework: "//trim(version)
+
+    ! Read namelist parameters
+    !write(stderrunit,*) 'diamonds: reading namelist'
 #ifdef INTERNAL_FILE_NML
-  read (input_nml_file, nml=icebergs_nml, iostat=ierr)
+    read (input_nml_file, nml=icebergs_nml, iostat=ierr)
 #else
-  iunit = open_namelist_file()
-  read  (iunit, icebergs_nml,iostat=ierr)
-  call close_file (iunit)
+    iunit = open_namelist_file()
+    read  (iunit, icebergs_nml,iostat=ierr)
+    call close_file (iunit)
 #endif
-  ierr = check_nml_error(ierr,'icebergs_nml')
-
-  if (really_debug) debug=.true. ! One implies the other...
-
-  write (stdlogunit, icebergs_nml)
-
-
-! Allocate overall structure
- !write(stderrunit,*) 'diamonds: allocating bergs'
-  allocate(bergs)
-  allocate(bergs%grd)
-  grd=>bergs%grd ! For convenience to avoid bergs%grd%X
- !write(stderrunit,*) 'diamonds: allocating domain'
-  allocate(grd%domain)
-
-! Clocks
-  bergs%clock=mpp_clock_id( 'Icebergs', flags=clock_flag_default, grain=CLOCK_COMPONENT )
-  bergs%clock_mom=mpp_clock_id( 'Icebergs-momentum', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
-  bergs%clock_the=mpp_clock_id( 'Icebergs-thermodyn', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
-  bergs%clock_int=mpp_clock_id( 'Icebergs-interface', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
-  bergs%clock_cal=mpp_clock_id( 'Icebergs-calving', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
-  bergs%clock_com=mpp_clock_id( 'Icebergs-communication', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
-  bergs%clock_ini=mpp_clock_id( 'Icebergs-initialization', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
-  bergs%clock_ior=mpp_clock_id( 'Icebergs-I/O read', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
-  bergs%clock_iow=mpp_clock_id( 'Icebergs-I/O write', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
-  bergs%clock_dia=mpp_clock_id( 'Icebergs-diagnostics', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
-
-  call mpp_clock_begin(bergs%clock)
-  call mpp_clock_begin(bergs%clock_ini)
-
-! Set up iceberg domain
- !write(stderrunit,*) 'diamonds: defining domain'
-  call mpp_define_domains( (/1,gni,1,gnj/), layout, grd%domain, &
-                           maskmap=maskmap, &
-                           xflags=dom_x_flags, xhalo=halo,  &
-                           yflags=dom_y_flags, yhalo=halo, name='diamond')
-
-  call mpp_define_io_domain(grd%domain, io_layout)
-
- !write(stderrunit,*) 'diamond: get compute domain'
-  call mpp_get_compute_domain( grd%domain, grd%isc, grd%iec, grd%jsc, grd%jec )
-  call mpp_get_data_domain( grd%domain, grd%isd, grd%ied, grd%jsd, grd%jed )
-  call mpp_get_global_domain( grd%domain, grd%isg, grd%ieg, grd%jsg, grd%jeg )
-
-  call mpp_get_neighbor_pe(grd%domain, NORTH, grd%pe_N)
-  call mpp_get_neighbor_pe(grd%domain, SOUTH, grd%pe_S)
-  call mpp_get_neighbor_pe(grd%domain, EAST, grd%pe_E)
-  call mpp_get_neighbor_pe(grd%domain, WEST, grd%pe_W)
-
-
-  folded_north_on_pe = ((dom_y_flags == FOLD_NORTH_EDGE) .and. (grd%jec == gnj))
- !write(stderrunit,'(a,6i4)') 'diamonds, icebergs_init: pe,n,s,e,w =',mpp_pe(),grd%pe_N,grd%pe_S,grd%pe_E,grd%pe_W, NULL_PE
-
- !if (verbose) &
- !write(stderrunit,'(a,i3,a,4i4,a,4f8.2)') 'diamonds, icebergs_init: (',mpp_pe(),') [ij][se]c=', &
- !     grd%isc,grd%iec,grd%jsc,grd%jec, &
- !     ' [lon|lat][min|max]=', minval(ice_lon),maxval(ice_lon),minval(ice_lat),maxval(ice_lat)
- !write(stderrunit,*) 'diamonds, int args = ', mpp_pe(),gni, gnj, layout, axes
-
- ! Allocate grid of pointers
-  allocate( bergs%list(grd%isd:grd%ied, grd%jsd:grd%jed) )
-  do j = grd%jsd,grd%jed ; do i = grd%isd,grd%ied
-    bergs%list(i,j)%first => null()
-  enddo ; enddo
+    ierr = check_nml_error(ierr,'icebergs_nml')
+
+    if (really_debug) debug=.true. ! One implies the other...
+
+    write (stdlogunit, icebergs_nml)
+
+
+    ! Allocate overall structure
+    !write(stderrunit,*) 'diamonds: allocating bergs'
+    allocate(bergs)
+    allocate(bergs%grd)
+    grd=>bergs%grd ! For convenience to avoid bergs%grd%X
+    !write(stderrunit,*) 'diamonds: allocating domain'
+    allocate(grd%domain)
+
+    ! Clocks
+    bergs%clock=mpp_clock_id( 'Icebergs', flags=clock_flag_default, grain=CLOCK_COMPONENT )
+    bergs%clock_mom=mpp_clock_id( 'Icebergs-momentum', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+    bergs%clock_the=mpp_clock_id( 'Icebergs-thermodyn', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+    bergs%clock_int=mpp_clock_id( 'Icebergs-interface', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+    bergs%clock_cal=mpp_clock_id( 'Icebergs-calving', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+    bergs%clock_com=mpp_clock_id( 'Icebergs-communication', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+    bergs%clock_ini=mpp_clock_id( 'Icebergs-initialization', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+    bergs%clock_ior=mpp_clock_id( 'Icebergs-I/O read', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+    bergs%clock_iow=mpp_clock_id( 'Icebergs-I/O write', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+    bergs%clock_dia=mpp_clock_id( 'Icebergs-diagnostics', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+
+    call mpp_clock_begin(bergs%clock)
+    call mpp_clock_begin(bergs%clock_ini)
+
+    ! Set up iceberg domain
+    !write(stderrunit,*) 'diamonds: defining domain'
+    call mpp_define_domains( (/1,gni,1,gnj/), layout, grd%domain, &
+         maskmap=maskmap, &
+         xflags=dom_x_flags, xhalo=halo,  &
+         yflags=dom_y_flags, yhalo=halo, name='diamond')
+
+    call mpp_define_io_domain(grd%domain, io_layout)
+
+    !write(stderrunit,*) 'diamond: get compute domain'
+    call mpp_get_compute_domain( grd%domain, grd%isc, grd%iec, grd%jsc, grd%jec )
+    call mpp_get_data_domain( grd%domain, grd%isd, grd%ied, grd%jsd, grd%jed )
+    call mpp_get_global_domain( grd%domain, grd%isg, grd%ieg, grd%jsg, grd%jeg )
+
+    call mpp_get_neighbor_pe(grd%domain, NORTH, grd%pe_N)
+    call mpp_get_neighbor_pe(grd%domain, SOUTH, grd%pe_S)
+    call mpp_get_neighbor_pe(grd%domain, EAST, grd%pe_E)
+    call mpp_get_neighbor_pe(grd%domain, WEST, grd%pe_W)
+
+
+    folded_north_on_pe = ((dom_y_flags == FOLD_NORTH_EDGE) .and. (grd%jec == gnj))
+    !write(stderrunit,'(a,6i4)') 'diamonds, icebergs_init: pe,n,s,e,w =',mpp_pe(),grd%pe_N,grd%pe_S,grd%pe_E,grd%pe_W, NULL_PE
+
+    !if (verbose) &
+    !write(stderrunit,'(a,i3,a,4i4,a,4f8.2)') 'diamonds, icebergs_init: (',mpp_pe(),') [ij][se]c=', &
+    !     grd%isc,grd%iec,grd%jsc,grd%jec, &
+    !     ' [lon|lat][min|max]=', minval(ice_lon),maxval(ice_lon),minval(ice_lat),maxval(ice_lat)
+    !write(stderrunit,*) 'diamonds, int args = ', mpp_pe(),gni, gnj, layout, axes
+
+    ! Allocate grid of pointers
+    allocate( bergs%list(grd%isd:grd%ied, grd%jsd:grd%jed) )
+    do j = grd%jsd,grd%jed ; do i = grd%isd,grd%ied
+       bergs%list(i,j)%first => null()
+    enddo; enddo
 
-  big_number=1.0E15
- !write(stderrunit,*) 'diamonds: allocating grid'
-  allocate( grd%lon(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%lon(:,:)=big_number
-  allocate( grd%lat(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%lat(:,:)=big_number
-  allocate( grd%lonc(grd%isd:grd%ied, grd%jsd:grd%jed) );grd%lon(:,:)=big_number
-  allocate( grd%latc(grd%isd:grd%ied, grd%jsd:grd%jed) );grd%lat(:,:)=big_number
-  allocate( grd%dx(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%dx(:,:)=0.
-  allocate( grd%dy(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%dy(:,:)=0.
-  allocate( grd%area(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%area(:,:)=0.
-  allocate( grd%msk(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%msk(:,:)=0.
-  allocate( grd%cos(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%cos(:,:)=1.
-  allocate( grd%sin(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%sin(:,:)=0.
-  allocate( grd%ocean_depth(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%ocean_depth(:,:)=0.
-  allocate( grd%calving(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%calving(:,:)=0.
-  allocate( grd%calving_hflx(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%calving_hflx(:,:)=0.
-  allocate( grd%stored_heat(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%stored_heat(:,:)=0.
-  allocate( grd%floating_melt(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%floating_melt(:,:)=0.
-  allocate( grd%berg_melt(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%berg_melt(:,:)=0.
-  allocate( grd%melt_buoy(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%melt_buoy(:,:)=0.
-  allocate( grd%melt_eros(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%melt_eros(:,:)=0.
-  allocate( grd%melt_conv(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%melt_conv(:,:)=0.
-  allocate( grd%bergy_src(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%bergy_src(:,:)=0.
-  allocate( grd%bergy_melt(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%bergy_melt(:,:)=0.
-  allocate( grd%bergy_mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%bergy_mass(:,:)=0.
-  allocate( grd%spread_mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_mass(:,:)=0.
-  allocate( grd%spread_mass_old(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_mass_old(:,:)=0.
-  allocate( grd%spread_area(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_area(:,:)=0.
-  allocate( grd%u_iceberg(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%u_iceberg(:,:)=0.
-  allocate( grd%v_iceberg(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%v_iceberg(:,:)=0.
-  allocate( grd%spread_uvel(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_uvel(:,:)=0.
-  allocate( grd%spread_vvel(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_vvel(:,:)=0.
-  allocate( grd%ustar_iceberg(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%ustar_iceberg(:,:)=0.
-  allocate( grd%virtual_area(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%virtual_area(:,:)=0.
-  allocate( grd%mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%mass(:,:)=0.
-  allocate( grd%mass_on_ocean(grd%isd:grd%ied, grd%jsd:grd%jed, 9) ); grd%mass_on_ocean(:,:,:)=0.
-  allocate( grd%area_on_ocean(grd%isd:grd%ied, grd%jsd:grd%jed, 9) ); grd%area_on_ocean(:,:,:)=0.
-  allocate( grd%Uvel_on_ocean(grd%isd:grd%ied, grd%jsd:grd%jed, 9) ); grd%Uvel_on_ocean(:,:,:)=0.
-  allocate( grd%Vvel_on_ocean(grd%isd:grd%ied, grd%jsd:grd%jed, 9) ); grd%Vvel_on_ocean(:,:,:)=0.
-  allocate( grd%stored_ice(grd%isd:grd%ied, grd%jsd:grd%jed, nclasses) ); grd%stored_ice(:,:,:)=0.
-  allocate( grd%rmean_calving(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%rmean_calving(:,:)=0.
-  allocate( grd%rmean_calving_hflx(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%rmean_calving_hflx(:,:)=0.
-  allocate( grd%real_calving(grd%isd:grd%ied, grd%jsd:grd%jed, nclasses) ); grd%real_calving(:,:,:)=0.
-  allocate( grd%uo(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%uo(:,:)=0.
-  allocate( grd%vo(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%vo(:,:)=0.
-  allocate( grd%ui(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%ui(:,:)=0.
-  allocate( grd%vi(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%vi(:,:)=0.
-  allocate( grd%ua(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%ua(:,:)=0.
-  allocate( grd%va(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%va(:,:)=0.
-  allocate( grd%ssh(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%ssh(:,:)=0.
-  allocate( grd%sst(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%sst(:,:)=0.
-  allocate( grd%sss(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%sss(:,:)=0.
-  allocate( grd%cn(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%cn(:,:)=0.
-  allocate( grd%hi(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%hi(:,:)=0.
-  allocate( grd%tmp(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%tmp(:,:)=0.
-  allocate( grd%tmpc(grd%isc:grd%iec, grd%jsc:grd%jec) ); grd%tmpc(:,:)=0.
-  allocate( bergs%nbergs_calved_by_class(nclasses) ); bergs%nbergs_calved_by_class(:)=0
-  allocate( grd%parity_x(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%parity_x(:,:)=1.
-  allocate( grd%parity_y(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%parity_y(:,:)=1.
-  allocate( grd%iceberg_counter_grd(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%iceberg_counter_grd(:,:)=0
-
- !write(stderrunit,*) 'diamonds: copying grid'
-  ! Copy data declared on ice model computational domain
-  is=grd%isc; ie=grd%iec; js=grd%jsc; je=grd%jec
-  grd%lon(is:ie,js:je)=ice_lon(:,:)
-  grd%lat(is:ie,js:je)=ice_lat(:,:)
-  grd%area(is:ie,js:je)=ice_area(:,:) !sis2 has *(4.*pi*radius*radius)
-
-  !!!!!!!!!!!!!!!debugging!!!!!!!!!!!!!!!!!!
-  !if (mpp_pe().eq.5) then
-  ! write(stderrunit,'(a3,32i7)') 'LB',(i,i=grd%isd,grd%ied)
-  ! do j=grd%jed,grd%jsd,-1
-  !   write(stderrunit,'(i3,32f7.1)') j,(grd%lon(i,j),i=grd%isd,grd%ied)
-  ! enddo
-  ! write(stderrunit,'(a3,32i7)') 'Ice lon',(i,i=grd%isd,grd%ied)
-  ! do j=grd%jed,grd%jsd,-1
-  !   write(stderrunit,'(i3,32f7.1)') j,(ice_lon(i,j),i=grd%isd,grd%ied)
-  ! enddo
-  ! write(stderrunit,'(a3,32i7)') 'LA',(i,i=grd%isd,grd%ied)
-  ! do j=grd%jed,grd%jsd,-1
-  !   write(stderrunit,'(i3,32f7.1)') j,(grd%lon(i,j),i=grd%isd,grd%ied)
-  ! enddo
-  !endif
-  !!!!!!!!!!!!!!!debugging!!!!!!!!!!!!!!!!!!
+    big_number=1.0E15
+    !write(stderrunit,*) 'diamonds: allocating grid'
+    allocate( grd%lon(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%lon(:,:)=big_number
+    allocate( grd%lat(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%lat(:,:)=big_number
+    allocate( grd%lonc(grd%isd:grd%ied, grd%jsd:grd%jed) );grd%lon(:,:)=big_number
+    allocate( grd%latc(grd%isd:grd%ied, grd%jsd:grd%jed) );grd%lat(:,:)=big_number
+    allocate( grd%dx(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%dx(:,:)=0.
+    allocate( grd%dy(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%dy(:,:)=0.
+    allocate( grd%area(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%area(:,:)=0.
+    allocate( grd%msk(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%msk(:,:)=0.
+    allocate( grd%cos(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%cos(:,:)=1.
+    allocate( grd%sin(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%sin(:,:)=0.
+    allocate( grd%ocean_depth(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%ocean_depth(:,:)=0.
+    allocate( grd%calving(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%calving(:,:)=0.
+    allocate( grd%calving_hflx(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%calving_hflx(:,:)=0.
+    allocate( grd%stored_heat(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%stored_heat(:,:)=0.
+    allocate( grd%floating_melt(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%floating_melt(:,:)=0.
+    allocate( grd%berg_melt(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%berg_melt(:,:)=0.
+    allocate( grd%melt_buoy(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%melt_buoy(:,:)=0.
+    allocate( grd%melt_eros(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%melt_eros(:,:)=0.
+    allocate( grd%melt_conv(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%melt_conv(:,:)=0.
+    allocate( grd%bergy_src(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%bergy_src(:,:)=0.
+    allocate( grd%bergy_melt(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%bergy_melt(:,:)=0.
+    allocate( grd%bergy_mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%bergy_mass(:,:)=0.
+    allocate( grd%spread_mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_mass(:,:)=0.
+    allocate( grd%spread_mass_old(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_mass_old(:,:)=0.
+    allocate( grd%spread_area(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_area(:,:)=0.
+    allocate( grd%u_iceberg(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%u_iceberg(:,:)=0.
+    allocate( grd%v_iceberg(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%v_iceberg(:,:)=0.
+    allocate( grd%spread_uvel(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_uvel(:,:)=0.
+    allocate( grd%spread_vvel(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_vvel(:,:)=0.
+    allocate( grd%ustar_iceberg(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%ustar_iceberg(:,:)=0.
+    allocate( grd%virtual_area(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%virtual_area(:,:)=0.
+    allocate( grd%mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%mass(:,:)=0.
+    allocate( grd%mass_on_ocean(grd%isd:grd%ied, grd%jsd:grd%jed, 9) ); grd%mass_on_ocean(:,:,:)=0.
+    allocate( grd%area_on_ocean(grd%isd:grd%ied, grd%jsd:grd%jed, 9) ); grd%area_on_ocean(:,:,:)=0.
+    allocate( grd%Uvel_on_ocean(grd%isd:grd%ied, grd%jsd:grd%jed, 9) ); grd%Uvel_on_ocean(:,:,:)=0.
+    allocate( grd%Vvel_on_ocean(grd%isd:grd%ied, grd%jsd:grd%jed, 9) ); grd%Vvel_on_ocean(:,:,:)=0.
+    allocate( grd%stored_ice(grd%isd:grd%ied, grd%jsd:grd%jed, nclasses) ); grd%stored_ice(:,:,:)=0.
+    allocate( grd%rmean_calving(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%rmean_calving(:,:)=0.
+    allocate( grd%rmean_calving_hflx(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%rmean_calving_hflx(:,:)=0.
+    allocate( grd%real_calving(grd%isd:grd%ied, grd%jsd:grd%jed, nclasses) ); grd%real_calving(:,:,:)=0.
+    allocate( grd%uo(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%uo(:,:)=0.
+    allocate( grd%vo(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%vo(:,:)=0.
+    allocate( grd%ui(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%ui(:,:)=0.
+    allocate( grd%vi(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%vi(:,:)=0.
+    allocate( grd%ua(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%ua(:,:)=0.
+    allocate( grd%va(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%va(:,:)=0.
+    allocate( grd%ssh(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%ssh(:,:)=0.
+    allocate( grd%sst(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%sst(:,:)=0.
+    allocate( grd%sss(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%sss(:,:)=0.
+    allocate( grd%cn(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%cn(:,:)=0.
+    allocate( grd%hi(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%hi(:,:)=0.
+    allocate( grd%tmp(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%tmp(:,:)=0.
+    allocate( grd%tmpc(grd%isc:grd%iec, grd%jsc:grd%jec) ); grd%tmpc(:,:)=0.
+    allocate( bergs%nbergs_calved_by_class(nclasses) ); bergs%nbergs_calved_by_class(:)=0
+    allocate( grd%parity_x(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%parity_x(:,:)=1.
+    allocate( grd%parity_y(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%parity_y(:,:)=1.
+    allocate( grd%iceberg_counter_grd(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%iceberg_counter_grd(:,:)=0
+
+    !write(stderrunit,*) 'diamonds: copying grid'
+    ! Copy data declared on ice model computational domain
+    is=grd%isc; ie=grd%iec; js=grd%jsc; je=grd%jec
+    grd%lon(is:ie,js:je)=ice_lon(:,:)
+    grd%lat(is:ie,js:je)=ice_lat(:,:)
+    grd%area(is:ie,js:je)=ice_area(:,:) !sis2 has *(4.*pi*radius*radius)
+
+!!!!!!!!!!!!!!!debugging!!!!!!!!!!!!!!!!!!
+    !if (mpp_pe().eq.5) then
+    ! write(stderrunit,'(a3,32i7)') 'LB',(i,i=grd%isd,grd%ied)
+    ! do j=grd%jed,grd%jsd,-1
+    !   write(stderrunit,'(i3,32f7.1)') j,(grd%lon(i,j),i=grd%isd,grd%ied)
+    ! enddo
+    ! write(stderrunit,'(a3,32i7)') 'Ice lon',(i,i=grd%isd,grd%ied)
+    ! do j=grd%jed,grd%jsd,-1
+    !   write(stderrunit,'(i3,32f7.1)') j,(ice_lon(i,j),i=grd%isd,grd%ied)
+    ! enddo
+    ! write(stderrunit,'(a3,32i7)') 'LA',(i,i=grd%isd,grd%ied)
+    ! do j=grd%jed,grd%jsd,-1
+    !   write(stderrunit,'(i3,32f7.1)') j,(grd%lon(i,j),i=grd%isd,grd%ied)
+    ! enddo
+    !endif
+!!!!!!!!!!!!!!!debugging!!!!!!!!!!!!!!!!!!
+
+    !For SIS not to change answers
+    if(present(fractional_area)) then
+       if(fractional_area) grd%area(is:ie,js:je)=ice_area(:,:) *(4.*pi*radius*radius)
+    endif
+    if(present(ocean_depth)) grd%ocean_depth(is:ie,js:je)=ocean_depth(:,:)
+
+    ! Copy data declared on ice model data domain
+    is=grd%isc-1; ie=grd%iec+1; js=grd%jsc-1; je=grd%jec+1
+    grd%dx(is:ie,js:je)=ice_dx(:,:)
+    grd%dy(is:ie,js:je)=ice_dy(:,:)
+    grd%msk(is:ie,js:je)=ice_wet(:,:)
+    grd%cos(is:ie,js:je)=cos_rot(:,:)
+    grd%sin(is:ie,js:je)=sin_rot(:,:)
+
+    call mpp_update_domains(grd%lon, grd%domain, position=CORNER)
+    call mpp_update_domains(grd%lat, grd%domain, position=CORNER)
+    call mpp_update_domains(grd%dy, grd%dx, grd%domain, gridtype=CGRID_NE, flags=SCALAR_PAIR)
+    call mpp_update_domains(grd%area, grd%domain)
+    call mpp_update_domains(grd%msk, grd%domain)
+    call mpp_update_domains(grd%cos, grd%domain, position=CORNER)
+    call mpp_update_domains(grd%sin, grd%domain, position=CORNER)
+    call mpp_update_domains(grd%ocean_depth, grd%domain)
+    call mpp_update_domains(grd%parity_x, grd%parity_y, grd%domain, gridtype=AGRID) ! If either parity_x/y is -ve, we need rotation of vectors
+
+    ! Sanitize lon and lat in the southern halo
+    do j=grd%jsc-1,grd%jsd,-1; do i=grd%isd,grd%ied
+       if (grd%lon(i,j).ge.big_number) grd%lon(i,j)=grd%lon(i,j+1)
+       if (grd%lat(i,j).ge.big_number) grd%lat(i,j)=2.*grd%lat(i,j+1)-grd%lat(i,j+2)
+    enddo; enddo
 
-  !For SIS not to change answers
-  if(present(fractional_area)) then
-    if(fractional_area) grd%area(is:ie,js:je)=ice_area(:,:) *(4.*pi*radius*radius)
-  endif
-  if(present(ocean_depth)) grd%ocean_depth(is:ie,js:je)=ocean_depth(:,:)
-
-  ! Copy data declared on ice model data domain
-  is=grd%isc-1; ie=grd%iec+1; js=grd%jsc-1; je=grd%jec+1
-  grd%dx(is:ie,js:je)=ice_dx(:,:)
-  grd%dy(is:ie,js:je)=ice_dy(:,:)
-  grd%msk(is:ie,js:je)=ice_wet(:,:)
-  grd%cos(is:ie,js:je)=cos_rot(:,:)
-  grd%sin(is:ie,js:je)=sin_rot(:,:)
-
-  call mpp_update_domains(grd%lon, grd%domain, position=CORNER)
-  call mpp_update_domains(grd%lat, grd%domain, position=CORNER)
-  call mpp_update_domains(grd%dy, grd%dx, grd%domain, gridtype=CGRID_NE, flags=SCALAR_PAIR)
-  call mpp_update_domains(grd%area, grd%domain)
-  call mpp_update_domains(grd%msk, grd%domain)
-  call mpp_update_domains(grd%cos, grd%domain, position=CORNER)
-  call mpp_update_domains(grd%sin, grd%domain, position=CORNER)
-  call mpp_update_domains(grd%ocean_depth, grd%domain)
-  call mpp_update_domains(grd%parity_x, grd%parity_y, grd%domain, gridtype=AGRID) ! If either parity_x/y is -ve, we need rotation of vectors
-
-  ! Sanitize lon and lat in the southern halo
-  do j=grd%jsc-1,grd%jsd,-1; do i=grd%isd,grd%ied
-      if (grd%lon(i,j).ge.big_number) grd%lon(i,j)=grd%lon(i,j+1)
-      if (grd%lat(i,j).ge.big_number) grd%lat(i,j)=2.*grd%lat(i,j+1)-grd%lat(i,j+2)
-  enddo; enddo
+    ! fix halos on edge of the domain
+    !1) South
+    do j=grd%jsc-1,grd%jsd,-1; do i=grd%isd,grd%ied
+       if (grd%lon(i,j).ge.big_number) grd%lon(i,j)=2.*grd%lon(i,j+1)-grd%lon(i,j+2)
+       if (grd%lat(i,j).ge.big_number) grd%lat(i,j)=2.*grd%lat(i,j+1)-grd%lat(i,j+2)
+    enddo; enddo
+    !2) North
+    do j=grd%jec+1,grd%jed; do i=grd%isd,grd%ied
+       if (grd%lon(i,j).ge.big_number) grd%lon(i,j)=2.*grd%lon(i,j-1)-grd%lon(i,j-2)
+       if (grd%lat(i,j).ge.big_number) grd%lat(i,j)=2.*grd%lat(i,j-1)-grd%lat(i,j-2)
+    enddo; enddo
+    !3) West
+    do i=grd%isc-1,grd%isd,-1; do j=grd%jsd,grd%jed
+       if (grd%lon(i,j).ge.big_number) grd%lon(i,j)=2.*grd%lon(i+1,j)-grd%lon(i+2,j)
+       if (grd%lat(i,j).ge.big_number) grd%lat(i,j)=2.*grd%lat(i+1,j)-grd%lat(i+2,j)
+    enddo; enddo
+    !4) East
+    do i=grd%iec+1,grd%ied; do j=grd%jsd,grd%jed
+       if (grd%lon(i,j).ge.big_number) grd%lon(i,j)=2.*grd%lon(i-1,j)-grd%lon(i-2,j)
+       if (grd%lat(i,j).ge.big_number) grd%lat(i,j)=2.*grd%lat(i-1,j)-grd%lat(i-2,j)
+    enddo; enddo
 
-  ! fix halos on edge of the domain
-  !1) South
-  do j=grd%jsc-1,grd%jsd,-1; do i=grd%isd,grd%ied
-      if (grd%lon(i,j).ge.big_number) grd%lon(i,j)=2.*grd%lon(i,j+1)-grd%lon(i,j+2)
-      if (grd%lat(i,j).ge.big_number) grd%lat(i,j)=2.*grd%lat(i,j+1)-grd%lat(i,j+2)
-  enddo; enddo
-  !2) North
-  do j=grd%jec+1,grd%jed; do i=grd%isd,grd%ied
-      if (grd%lon(i,j).ge.big_number) grd%lon(i,j)=2.*grd%lon(i,j-1)-grd%lon(i,j-2)
-      if (grd%lat(i,j).ge.big_number) grd%lat(i,j)=2.*grd%lat(i,j-1)-grd%lat(i,j-2)
-  enddo; enddo
-  !3) West
-  do i=grd%isc-1,grd%isd,-1; do j=grd%jsd,grd%jed
-      if (grd%lon(i,j).ge.big_number) grd%lon(i,j)=2.*grd%lon(i+1,j)-grd%lon(i+2,j)
-      if (grd%lat(i,j).ge.big_number) grd%lat(i,j)=2.*grd%lat(i+1,j)-grd%lat(i+2,j)
-  enddo; enddo
-  !4) East
-  do i=grd%iec+1,grd%ied; do j=grd%jsd,grd%jed
-      if (grd%lon(i,j).ge.big_number) grd%lon(i,j)=2.*grd%lon(i-1,j)-grd%lon(i-2,j)
-      if (grd%lat(i,j).ge.big_number) grd%lat(i,j)=2.*grd%lat(i-1,j)-grd%lat(i-2,j)
-  enddo; enddo
 
-  if (.not. present(maskmap)) then ! Using a maskmap causes tickles this sanity check
-    do j=grd%jsd,grd%jed; do i=grd%isd,grd%ied
-      !if (grd%lon(i,j).ge.big_number) write(stderrunit,*) 'bad lon: ',mpp_pe(),i-grd%isc+1,j-grd%jsc+1,grd%lon(i,j)
-      !if (grd%lat(i,j).ge.big_number) write(stderrunit,*) 'bad lat: ',mpp_pe(),i-grd%isc+1,j-grd%jsc+1,grd%lat(i,j)
-    enddo; enddo
-  endif
+    if (mpp_pe() == 0) then
+       print *,'before'
+       print *,'grd%lon(:,1)',grd%lon(:,grd%jsd)
+       ! print *,''
+       ! print *,'grd%lat(:,1)',grd%lat(:,grd%jsd)
+       ! print *,''
+       ! print *,'grd%lon(1,:)',grd%lon(grd%isd,:)
+       ! print *,''
+       ! print *,'grd%lat(1,:)',grd%lat(grd%isd,:)
+       ! print *,''
+    end if
+
+
+    if (.not. present(maskmap)) then ! Using a maskmap causes tickles this sanity check
+       do j=grd%jsd,grd%jed; do i=grd%isd,grd%ied
+          !if (grd%lon(i,j).ge.big_number) write(stderrunit,*) 'bad lon: ',mpp_pe(),i-grd%isc+1,j-grd%jsc+1,grd%lon(i,j)
+          !if (grd%lat(i,j).ge.big_number) write(stderrunit,*) 'bad lat: ',mpp_pe(),i-grd%isc+1,j-grd%jsc+1,grd%lat(i,j)
+       enddo; enddo
+    endif
 
-  if ((Lx.gt.1E15 ) .and. (mpp_pe().eq.mpp_root_pe())) then
-          call error_mesg('diamonds, framework', 'Model does not enjoy the domain being larger than 1E15. Not sure why. Probably to do with floating point precision.', WARNING)
-  endif
-  if ((.not. grid_is_latlon) .and. (Lx.eq.360.)) then
-    if (mpp_pe().eq.mpp_root_pe())  then
-            call error_mesg('diamonds, framework', 'Since the lat/lon grid is off, the x-direction is being set as non-periodic. Set Lx not equal to 360 override.', WARNING)
+    if ((Lx.gt.1E15 ) .and. (mpp_pe().eq.mpp_root_pe())) then
+       call error_mesg('diamonds, framework', 'Model does not enjoy the domain being larger than 1E15. Not sure why. Probably to do with floating point precision.', WARNING)
+    endif
+    if ((.not. grid_is_latlon) .and. (Lx.eq.360.)) then
+       if (mpp_pe().eq.mpp_root_pe())  then
+          call error_mesg('diamonds, framework', 'Since the lat/lon grid is off, the x-direction is being set as non-periodic. Set Lx not equal to 360 override.', WARNING)
+       endif
+       Lx=-1.
     endif
-    Lx=-1.
-  endif
 
 
- !The fix to reproduce across PE layout change, from AJA
-  if (Lx>0.) then
-    j=grd%jsc; do i=grd%isc+1,grd%ied
-      lon_mod = apply_modulo_around_point(grd%lon(i,j),grd%lon(i-1,j),Lx)
-      if (abs(grd%lon(i,j)-lon_mod)>(Lx/2.)) &
-        grd%lon(i,j)= lon_mod
+    !The fix to reproduce across PE layout change, from AJA
+    if (Lx>0.) then
+       j=grd%jsc; do i=grd%isc+1,grd%ied
+       lon_mod = apply_modulo_around_point(grd%lon(i,j),grd%lon(i-1,j),Lx)
+       if (abs(grd%lon(i,j)-lon_mod)>(Lx/2.)) &
+            grd%lon(i,j)= lon_mod
     enddo
     j=grd%jsc; do i=grd%isc-1,grd%isd,-1
-      lon_mod = apply_modulo_around_point(grd%lon(i,j),grd%lon(i+1,j) ,Lx)
-      if (abs(grd%lon(i,j)-  lon_mod )>(Lx/2.)) &
-        grd%lon(i,j)= lon_mod
-    enddo
-    do j=grd%jsc+1,grd%jed; do i=grd%isd,grd%ied
-      lon_mod = apply_modulo_around_point(grd%lon(i,j),grd%lon(i,j-1) ,Lx)
-      if (abs(grd%lon(i,j)-(lon_mod ))>(Lx/2.)) &
-        grd%lon(i,j)= lon_mod
-    enddo; enddo
-    do j=grd%jsc-1,grd%jsd,-1; do i=grd%isd,grd%ied
-      lon_mod = apply_modulo_around_point(grd%lon(i,j),grd%lon(i,j+1) ,Lx)
-      if (abs(grd%lon(i,j)- lon_mod )>(Lx/2.)) &
-        grd%lon(i,j)=  lon_mod
-    enddo; enddo
-  endif
+    lon_mod = apply_modulo_around_point(grd%lon(i,j),grd%lon(i+1,j) ,Lx)
+    if (abs(grd%lon(i,j)-  lon_mod )>(Lx/2.)) &
+         grd%lon(i,j)= lon_mod
+ enddo
+ do j=grd%jsc+1,grd%jed; do i=grd%isd,grd%ied
+    lon_mod = apply_modulo_around_point(grd%lon(i,j),grd%lon(i,j-1) ,Lx)
+    if (abs(grd%lon(i,j)-(lon_mod ))>(Lx/2.)) &
+         grd%lon(i,j)= lon_mod
+ enddo; enddo
+ do j=grd%jsc-1,grd%jsd,-1; do i=grd%isd,grd%ied
+    lon_mod = apply_modulo_around_point(grd%lon(i,j),grd%lon(i,j+1) ,Lx)
+    if (abs(grd%lon(i,j)- lon_mod )>(Lx/2.)) &
+         grd%lon(i,j)=  lon_mod
+ enddo; enddo
+endif
 
 
+! lonc, latc used for searches
+do j=grd%jsd+1,grd%jed; do i=grd%isd+1,grd%ied
+ grd%lonc(i,j)=0.25*( (grd%lon(i,j)+grd%lon(i-1,j-1)) &
+      +(grd%lon(i-1,j)+grd%lon(i,j-1)) )
+ grd%latc(i,j)=0.25*( (grd%lat(i,j)+grd%lat(i-1,j-1)) &
+      +(grd%lat(i-1,j)+grd%lat(i,j-1)) )
+enddo; enddo
 
-  ! lonc, latc used for searches
-  do j=grd%jsd+1,grd%jed; do i=grd%isd+1,grd%ied
-    grd%lonc(i,j)=0.25*( (grd%lon(i,j)+grd%lon(i-1,j-1)) &
-                        +(grd%lon(i-1,j)+grd%lon(i,j-1)) )
-    grd%latc(i,j)=0.25*( (grd%lat(i,j)+grd%lat(i-1,j-1)) &
-                        +(grd%lat(i-1,j)+grd%lat(i,j-1)) )
-  enddo; enddo
+if (debug) then
+   ! Write(stderrunit,'(a,i3,a,4i4,a,4f8.2)') 'diamonds, icebergs_init: (',mpp_pe(),') [ij][se]c=', &
+   !      grd%isc,grd%iec,grd%jsc,grd%jec, &
+   !      ' [Lon|lat][min|max]=', minval(grd%lon),maxval(grd%lon),minval(grd%lat),maxval(grd%lat)
 
-  if (debug) then
-    write(stderrunit,'(a,i3,a,4i4,a,4f8.2)') 'diamonds, icebergs_init: (',mpp_pe(),') [ij][se]c=', &
-         grd%isc,grd%iec,grd%jsc,grd%jec, &
-         ' [lon|lat][min|max]=', minval(grd%lon),maxval(grd%lon),minval(grd%lat),maxval(grd%lat)
-  endif
 
- !if (mpp_pe().eq.5) then
- !  write(stderrunit,'(a3,32i7)') 'Lon',(i,i=grd%isd,grd%ied)
- !  do j=grd%jed,grd%jsd,-1
- !    write(stderrunit,'(i3,32f7.1)') j,(grd%lon(i,j),i=grd%isd,grd%ied)
- !  enddo
- !  write(stderrunit,'(a3,32i7)') 'Lat',(i,i=grd%isd,grd%ied)
- !  do j=grd%jed,grd%jsd,-1
- !    write(stderrunit,'(i3,32f7.1)') j,(grd%lat(i,j),i=grd%isd,grd%ied)
- !  enddo
- !  write(stderrunit,'(a3,32i7)') 'Msk',(i,i=grd%isd,grd%ied)
- !  do j=grd%jed,grd%jsd,-1
- !    write(stderrunit,'(i3,32f7.1)') j,(grd%msk(i,j),i=grd%isd,grd%ied)
- !  enddo
- !endif
+ Write(stderrunit,'(a,i3,a,4i4)') 'diamonds, icebergs_init: (',mpp_pe(),') [ij][se]c=', &
+      grd%isc,grd%iec,grd%jsc,grd%jec   
+
+ print *,'minval(grd%lon)',minval(grd%lon)
+ print *,'maxval(grd%lon)',maxval(grd%lon)
+ print *,'minval(grd%lat)',minval(grd%lat)
+ print *,'maxval(grd%lat)',maxval(grd%lat)    
+
+ write(stderrunit,'(a,4f10.2)') '[Lon|lat][min|max]=', &
+      minval(grd%lon),maxval(grd%lon),minval(grd%lat),maxval(grd%lat)
+endif
+
+ if (mpp_pe() == 1) then
+    print *,'after'
+    print *,'grd%lon(:,1)',grd%lon(:,grd%jsd)
+    ! print *,''
+    ! print *,'grd%lat(:,1)',grd%lat(:,grd%jsd)
+    ! print *,''
+    ! print *,'grd%lon(1,:)',grd%lon(grd%isd,:)
+    ! print *,''
+    ! print *,'grd%lat(1,:)',grd%lat(grd%isd,:)
+    ! print *,''
+ end if
+
+!if (mpp_pe().eq.5) then
+!  write(stderrunit,'(a3,32i7)') 'Lon',(i,i=grd%isd,grd%ied)
+!  do j=grd%jed,grd%jsd,-1
+!    write(stderrunit,'(i3,32f7.1)') j,(grd%lon(i,j),i=grd%isd,grd%ied)
+!  enddo
+!  write(stderrunit,'(a3,32i7)') 'Lat',(i,i=grd%isd,grd%ied)
+!  do j=grd%jed,grd%jsd,-1
+!    write(stderrunit,'(i3,32f7.1)') j,(grd%lat(i,j),i=grd%isd,grd%ied)
+!  enddo
+!  write(stderrunit,'(a3,32i7)') 'Msk',(i,i=grd%isd,grd%ied)
+!  do j=grd%jed,grd%jsd,-1
+!    write(stderrunit,'(i3,32f7.1)') j,(grd%msk(i,j),i=grd%isd,grd%ied)
+!  enddo
+!endif
 
 ! Final check for NaN's in the latlon grid:
-  do j=grd%jsd+1,grd%jed; do i=grd%isd+1,grd%ied
-    if (grd%lat(i,j) .ne. grd%lat(i,j)) then
-      write(stderrunit,*) 'Lat not defined properly', mpp_pe(),i,j,grd%lat(i,j)
-      call error_mesg('diamonds,grid defining', 'Latitude contains NaNs', FATAL)
-    endif
-    if (grd%lon(i,j) .ne. grd%lon(i,j)) then
-      write(stderrunit,*) 'Lon not defined properly', mpp_pe(),i,j,grd%lon(i,j)
-      call error_mesg('diamonds, grid defining', 'Longatudes contains NaNs', FATAL)
-    endif
-  enddo; enddo
+do j=grd%jsd+1,grd%jed; do i=grd%isd+1,grd%ied
+ if (grd%lat(i,j) .ne. grd%lat(i,j)) then
+    write(stderrunit,*) 'Lat not defined properly', mpp_pe(),i,j,grd%lat(i,j)
+    call error_mesg('diamonds,grid defining', 'Latitude contains NaNs', FATAL)
+ endif
+ if (grd%lon(i,j) .ne. grd%lon(i,j)) then
+    write(stderrunit,*) 'Lon not defined properly', mpp_pe(),i,j,grd%lon(i,j)
+    call error_mesg('diamonds, grid defining', 'Longatudes contains NaNs', FATAL)
+ endif
+enddo; enddo
 
 
 !Added by Alon  - If a freq distribution is input, we have to convert the freq distribution to a mass flux distribution)
 if (input_freq_distribution) then
-     Total_mass=0.
-     do j=1,nclasses
-          Total_mass=Total_mass+(distribution(j)*initial_mass(j))
-     enddo
-     do j=1,nclasses
-           distribution(j)=(distribution(j)*initial_mass(j))/Total_mass
-     enddo
+ Total_mass=0.
+ do j=1,nclasses
+    Total_mass=Total_mass+(distribution(j)*initial_mass(j))
+ enddo
+ do j=1,nclasses
+    distribution(j)=(distribution(j)*initial_mass(j))/Total_mass
+ enddo
 endif
 
 if ((halo .lt. 3) .and. (rotate_icebergs_for_mass_spreading .and. iceberg_bonds_on) )   then
-    halo=3
-    call error_mesg('diamonds, framework', 'Setting iceberg halos =3, since halos must be >= 3 for rotating icebergs for mass spreading', WARNING)
+ halo=3
+ call error_mesg('diamonds, framework', 'Setting iceberg halos =3, since halos must be >= 3 for rotating icebergs for mass spreading', WARNING)
 elseif  ((halo .lt. 2) .and. (interactive_icebergs_on .or. iceberg_bonds_on) )   then
-    halo=2
-    call error_mesg('diamonds, framework', 'Setting iceberg halos =2, since halos must be >= 2 for interactions', WARNING)
+ halo=2
+ call error_mesg('diamonds, framework', 'Setting iceberg halos =2, since halos must be >= 2 for interactions', WARNING)
 endif
 
 if (interactive_icebergs_on) then
-  if (Runge_not_Verlet) then
+ if (Runge_not_Verlet) then
     !Runge_not_Verlet=.false.  ! Iceberg interactions only with Verlet
     call error_mesg('diamonds, framework', 'It is unlcear whther interactive icebergs work with Runge Kutta stepping.', WARNING)
-  endif
+ endif
 endif
 if (.not.interactive_icebergs_on) then
-  if (iceberg_bonds_on) then
+ if (iceberg_bonds_on) then
     !iceberg_bonds_on=.false.
     call error_mesg('diamonds, framework', 'Interactive icebergs off requires iceberg bonds off (turning bonds off).', WARNING)
-  endif
+ endif
 endif
 if (.not. iceberg_bonds_on) then
-   max_bonds=0
+ max_bonds=0
 else
-  buffer_width=buffer_width+(max_bonds*4) ! Increase buffer width to include bonds being passed between processors
+ buffer_width=buffer_width+(max_bonds*4) ! Increase buffer width to include bonds being passed between processors
 endif
 if (save_short_traj) buffer_width_traj=6 ! This is the length of the short buffer used for abrevated traj
 if (ignore_traj) buffer_width_traj=0 ! If this is true, then all traj files should be ignored
 
 
- ! Parameters
-  bergs%dt=dt
-  bergs%traj_sample_hrs=traj_sample_hrs
-  bergs%traj_write_hrs=traj_write_hrs
-  bergs%save_short_traj=save_short_traj
-  bergs%ignore_traj=ignore_traj
-  bergs%verbose_hrs=verbose_hrs
-  bergs%grd%halo=halo
-  bergs%grd%Lx=Lx
-  bergs%grd%grid_is_latlon=grid_is_latlon
-  bergs%grd%grid_is_regular=grid_is_regular
-  bergs%max_bonds=max_bonds
-  bergs%rho_bergs=rho_bergs
-  bergs%spring_coef=spring_coef
-  bergs%bond_coef=bond_coef
-  bergs%radial_damping_coef=radial_damping_coef
-  bergs%tangental_damping_coef=tangental_damping_coef
-  bergs%LoW_ratio=LoW_ratio
-  bergs%use_operator_splitting=use_operator_splitting
-  bergs%bergy_bit_erosion_fraction=bergy_bit_erosion_fraction
-  bergs%sicn_shift=sicn_shift
-  bergs%passive_mode=passive_mode
-  bergs%time_average_weight=time_average_weight
-  bergs%speed_limit=speed_limit
-  bergs%tau_calving=tau_calving
-  bergs%tip_parameter=tip_parameter
-  bergs%use_updated_rolling_scheme=use_updated_rolling_scheme  !Alon
-  bergs%Runge_not_Verlet=Runge_not_Verlet
-  bergs%use_mixed_melting=use_mixed_melting
-  bergs%apply_thickness_cutoff_to_bergs_melt=apply_thickness_cutoff_to_bergs_melt
-  bergs%apply_thickness_cutoff_to_gridded_melt=apply_thickness_cutoff_to_gridded_melt
-  bergs%melt_cutoff=melt_cutoff
-  bergs%read_ocean_depth_from_file=read_ocean_depth_from_file
-  bergs%const_gamma=const_gamma
-  bergs%Gamma_T_3EQ=Gamma_T_3EQ
-  bergs%pass_fields_to_ocean_model=pass_fields_to_ocean_model
-  bergs%ustar_icebergs_bg=ustar_icebergs_bg
-  bergs%utide_icebergs=utide_icebergs
-  bergs%cdrag_icebergs=cdrag_icebergs
-  bergs%use_mixed_layer_salinity_for_thermo=use_mixed_layer_salinity_for_thermo
-  bergs%find_melt_using_spread_mass=find_melt_using_spread_mass
-  bergs%Use_three_equation_model=Use_three_equation_model
-  bergs%melt_icebergs_as_ice_shelf=melt_icebergs_as_ice_shelf
-  bergs%Iceberg_melt_without_decay=Iceberg_melt_without_decay
-  bergs%add_iceberg_thickness_to_SSH=add_iceberg_thickness_to_SSH
-  bergs%override_iceberg_velocities=override_iceberg_velocities
-  bergs%use_f_plane=use_f_plane
-  bergs%rotate_icebergs_for_mass_spreading=rotate_icebergs_for_mass_spreading
-  bergs%lat_ref=lat_ref
-  bergs%u_override=u_override
-  bergs%v_override=v_override
-  bergs%initial_orientation=initial_orientation
-  bergs%set_melt_rates_to_zero=set_melt_rates_to_zero
-  bergs%allow_bergs_to_roll=allow_bergs_to_roll
-  bergs%hexagonal_icebergs=hexagonal_icebergs
-  bergs%ignore_missing_restart_bergs=ignore_missing_restart_bergs
-  bergs%Static_icebergs=Static_icebergs
-  bergs%only_interactive_forces=only_interactive_forces
-  bergs%halo_debugging=halo_debugging
-  bergs%iceberg_bonds_on=iceberg_bonds_on   !Alon
-  bergs%manually_initialize_bonds=manually_initialize_bonds   !Alon
-  bergs%critical_interaction_damping_on=critical_interaction_damping_on   !Alon
-  bergs%interactive_icebergs_on=interactive_icebergs_on   !Alon
-  bergs%use_new_predictive_corrective=use_new_predictive_corrective  !Alon
-  bergs%grounding_fraction=grounding_fraction
-  bergs%add_weight_to_ocean=add_weight_to_ocean
-  bergs%use_old_spreading=use_old_spreading
-  bergs%debug_iceberg_with_id=debug_iceberg_with_id
-  allocate( bergs%initial_mass(nclasses) ); bergs%initial_mass(:)=initial_mass(:)
-  allocate( bergs%distribution(nclasses) ); bergs%distribution(:)=distribution(:)
-  allocate( bergs%mass_scaling(nclasses) ); bergs%mass_scaling(:)=mass_scaling(:)
-  allocate( bergs%initial_thickness(nclasses) ); bergs%initial_thickness(:)=initial_thickness(:)
-  allocate( bergs%initial_width(nclasses) )
-  allocate( bergs%initial_length(nclasses) )
-  bergs%initial_width(:)=sqrt(initial_mass(:)/(LoW_ratio*rho_bergs*initial_thickness(:)))
-  bergs%initial_length(:)=LoW_ratio*bergs%initial_width(:)
-  grd%coastal_drift = coastal_drift
-  grd%tidal_drift = tidal_drift
-
-  if (read_old_restarts) call error_mesg('diamonds, ice_bergs_framework_init', 'Setting "read_old_restarts=.true." is obsolete and does nothing!', WARNING)
-
-  ! Diagnostics
-  id_class = diag_axis_init('mass_class', initial_mass, 'kg','Z', 'iceberg mass')
-  axes3d(1:2)=axes
-  axes3d(3)=id_class
-  grd%id_calving=register_diag_field('icebergs', 'calving', axes, Time, &
-     'Incoming Calving mass rate', 'kg/s')
-  grd%id_calving_hflx_in=register_diag_field('icebergs', 'calving_hflx_in', axes, Time, &
-     'Incoming Calving heat flux', 'J/s')
-  grd%id_accum=register_diag_field('icebergs', 'accum_calving', axes, Time, &
-     'Accumulated calving mass rate', 'kg/s')
-  grd%id_unused=register_diag_field('icebergs', 'unused_calving', axes, Time, &
-     'Unused calving mass rate', 'kg/s')
-  grd%id_floating_melt=register_diag_field('icebergs', 'melt', axes, Time, &
-     'Melt rate of icebergs + bits', 'kg/(m^2*s)')
-  grd%id_melt_m_per_year=register_diag_field('icebergs', 'melt_m_per_year', axes, Time, &
-     'Melt rate of icebergs + bits (m/yr)', 'm/yr')
-  grd%id_berg_melt=register_diag_field('icebergs', 'berg_melt', axes, Time, &
-     'Melt rate of icebergs', 'kg/(m^2*s)')
-  grd%id_melt_buoy=register_diag_field('icebergs', 'melt_buoy', axes, Time, &
-     'Buoyancy component of iceberg melt rate', 'kg/(m^2*s)')
-  grd%id_melt_eros=register_diag_field('icebergs', 'melt_eros', axes, Time, &
-     'Erosion component of iceberg melt rate', 'kg/(m^2*s)')
-  grd%id_melt_conv=register_diag_field('icebergs', 'melt_conv', axes, Time, &
-     'Convective component of iceberg melt rate', 'kg/(m^2*s)')
-  grd%id_bergy_src=register_diag_field('icebergs', 'bergy_src', axes, Time, &
-     'Mass source of bergy bits', 'kg/(m^2*s)')
-  grd%id_bergy_melt=register_diag_field('icebergs', 'bergy_melt', axes, Time, &
-     'Melt rate of bergy bits', 'kg/(m^2*s)')
-  grd%id_bergy_mass=register_diag_field('icebergs', 'bergy_mass', axes, Time, &
-     'Bergy bit density field', 'kg/(m^2)')
-  grd%id_spread_mass=register_diag_field('icebergs', 'spread_mass', axes, Time, &
-     'Iceberg mass after spreading', 'kg/(m^2)')
-  grd%id_spread_area=register_diag_field('icebergs', 'spread_area', axes, Time, &
-     'Iceberg area after spreading', 'm^2/(m^2)')
-  grd%id_u_iceberg=register_diag_field('icebergs', 'u_iceberg', axes, Time, &
-     'Iceberg u velocity (m/s)')
-  grd%id_v_iceberg=register_diag_field('icebergs', 'v_iceberg', axes, Time, &
-     'Iceberg v velocity (m/s)')
-  grd%id_spread_uvel=register_diag_field('icebergs', 'spread_uvel', axes, Time, &
-     'Iceberg u velocity spread (m/s)')
-  grd%id_spread_vvel=register_diag_field('icebergs', 'spread_vvel', axes, Time, &
-     'Iceberg v velocity spread (m/s)')
-  grd%id_ustar_iceberg=register_diag_field('icebergs', 'ustar_iceberg', axes, Time, &
-     'Iceberg frictional velocity (m/s)')
-  grd%id_virtual_area=register_diag_field('icebergs', 'virtual_area', axes, Time, &
-     'Virtual coverage by icebergs', 'm^2')
-  grd%id_mass=register_diag_field('icebergs', 'mass', axes, Time, &
-     'Iceberg density field', 'kg/(m^2)')
-  grd%id_stored_ice=register_diag_field('icebergs', 'stored_ice', axes3d, Time, &
-     'Accumulated ice mass by class', 'kg')
-  grd%id_real_calving=register_diag_field('icebergs', 'real_calving', axes3d, Time, &
-     'Calving into iceberg class', 'kg/s')
-  grd%id_rmean_calving=register_diag_field('icebergs', 'running_mean_calving', axes, Time, &
-     'Running mean of calving', 'kg/s')
-  grd%id_rmean_calving_hflx=register_diag_field('icebergs', 'running_mean_calving_hflx', axes, Time, &
-     'Running mean of calving heat flux', 'J/s')
-  grd%id_count=register_diag_field('icebergs', 'bergs_per_cell', axes, Time, &
-     'Number of bergs per cell', '#')
-  grd%id_chksum=register_diag_field('icebergs', 'list_chksum', axes, Time, &
-     'mpp_chksum on bergs in each cell', '#')
-  grd%id_uo=register_diag_field('icebergs', 'uo', axes, Time, &
-     'Ocean zonal component of velocity', 'm s^-1')
-  grd%id_vo=register_diag_field('icebergs', 'vo', axes, Time, &
-     'Ocean meridional component of velocity', 'm s^-1')
-  grd%id_ui=register_diag_field('icebergs', 'ui', axes, Time, &
-     'Ice zonal component of velocity', 'm s^-1')
-  grd%id_vi=register_diag_field('icebergs', 'vi', axes, Time, &
-     'Ice meridional component of velocity', 'm s^-1')
-  grd%id_ua=register_diag_field('icebergs', 'ua', axes, Time, &
-     'Atmos zonal component of velocity', 'm s^-1')
-  grd%id_va=register_diag_field('icebergs', 'va', axes, Time, &
-     'Atmos meridional component of velocity', 'm s^-1')
-  grd%id_sst=register_diag_field('icebergs', 'sst', axes, Time, &
-     'Sea surface temperature', 'degrees_C')
-  grd%id_sss=register_diag_field('icebergs', 'sss', axes, Time, &
-     'Sea surface salinity', 'psu')
-  grd%id_cn=register_diag_field('icebergs', 'cn', axes, Time, &
-     'Sea ice concentration', '(fraction)')
-  grd%id_hi=register_diag_field('icebergs', 'hi', axes, Time, &
-     'Sea ice thickness', 'm')
-  grd%id_ssh=register_diag_field('icebergs', 'ssh', axes, Time, &
-     'Sea surface hieght', 'm')
-  grd%id_fax=register_diag_field('icebergs', 'taux', axes, Time, &
-     'X-stress on ice from atmosphere', 'N m^-2')
-  grd%id_fay=register_diag_field('icebergs', 'tauy', axes, Time, &
-     'Y-stress on ice from atmosphere', 'N m^-2')
-  grd%id_ocean_depth=register_diag_field('icebergs', 'Depth', axes, Time, &
-     'Ocean Depth', 'm')
-
-  ! Static fields
-  id_class=register_static_field('icebergs', 'lon', axes, &
-               'longitude (corners)', 'degrees_E')
-  if (id_class>0) lerr=send_data(id_class, grd%lon(grd%isc:grd%iec,grd%jsc:grd%jec))
-  id_class=register_static_field('icebergs', 'lat', axes, &
-               'latitude (corners)', 'degrees_N')
-  if (id_class>0) lerr=send_data(id_class, grd%lat(grd%isc:grd%iec,grd%jsc:grd%jec))
-  id_class=register_static_field('icebergs', 'area', axes, &
-               'cell area', 'm^2')
-  if (id_class>0) lerr=send_data(id_class, grd%area(grd%isc:grd%iec,grd%jsc:grd%jec))
-  id_class=register_static_field('icebergs', 'mask', axes, &
-               'wet point mask', 'none')
-  if (id_class>0) lerr=send_data(id_class, grd%msk(grd%isc:grd%iec,grd%jsc:grd%jec))
-  id_class=register_static_field('icebergs', 'ocean_depth_static', axes, &
-               'ocean depth static', 'm')
-  if (id_class>0) lerr=send_data(id_class, grd%ocean_depth(grd%isc:grd%iec,grd%jsc:grd%jec))
-
-  if (debug) then
-    call grd_chksum2(grd, grd%lon, 'init lon')
-    call grd_chksum2(grd, grd%lat, 'init lat')
-    call grd_chksum2(grd, grd%lonc, 'init lonc')
-    call grd_chksum2(grd, grd%latc, 'init latc')
-    call grd_chksum2(grd, grd%area, 'init area')
-    call grd_chksum2(grd, grd%msk, 'init msk')
-    call grd_chksum2(grd, grd%cos, 'init cos')
-    call grd_chksum2(grd, grd%sin, 'init sin')
-    call grd_chksum2(grd, grd%ocean_depth, 'init ocean_depth')
-  endif
+! Parameters
+bergs%dt=dt
+bergs%traj_sample_hrs=traj_sample_hrs
+bergs%traj_write_hrs=traj_write_hrs
+bergs%save_short_traj=save_short_traj
+bergs%ignore_traj=ignore_traj
+bergs%verbose_hrs=verbose_hrs
+bergs%grd%halo=halo
+bergs%grd%Lx=Lx
+bergs%grd%grid_is_latlon=grid_is_latlon
+bergs%grd%grid_is_regular=grid_is_regular
+bergs%max_bonds=max_bonds
+bergs%rho_bergs=rho_bergs
+bergs%spring_coef=spring_coef
+bergs%bond_coef=bond_coef
+bergs%radial_damping_coef=radial_damping_coef
+bergs%tangental_damping_coef=tangental_damping_coef
+bergs%LoW_ratio=LoW_ratio
+bergs%use_operator_splitting=use_operator_splitting
+bergs%bergy_bit_erosion_fraction=bergy_bit_erosion_fraction
+bergs%sicn_shift=sicn_shift
+bergs%passive_mode=passive_mode
+bergs%time_average_weight=time_average_weight
+bergs%speed_limit=speed_limit
+bergs%tau_calving=tau_calving
+bergs%tip_parameter=tip_parameter
+bergs%use_updated_rolling_scheme=use_updated_rolling_scheme  !Alon
+bergs%Runge_not_Verlet=Runge_not_Verlet
+bergs%use_mixed_melting=use_mixed_melting
+bergs%apply_thickness_cutoff_to_bergs_melt=apply_thickness_cutoff_to_bergs_melt
+bergs%apply_thickness_cutoff_to_gridded_melt=apply_thickness_cutoff_to_gridded_melt
+bergs%melt_cutoff=melt_cutoff
+bergs%read_ocean_depth_from_file=read_ocean_depth_from_file
+bergs%const_gamma=const_gamma
+bergs%Gamma_T_3EQ=Gamma_T_3EQ
+bergs%pass_fields_to_ocean_model=pass_fields_to_ocean_model
+bergs%ustar_icebergs_bg=ustar_icebergs_bg
+bergs%utide_icebergs=utide_icebergs
+bergs%cdrag_icebergs=cdrag_icebergs
+bergs%use_mixed_layer_salinity_for_thermo=use_mixed_layer_salinity_for_thermo
+bergs%find_melt_using_spread_mass=find_melt_using_spread_mass
+bergs%Use_three_equation_model=Use_three_equation_model
+bergs%melt_icebergs_as_ice_shelf=melt_icebergs_as_ice_shelf
+bergs%Iceberg_melt_without_decay=Iceberg_melt_without_decay
+bergs%add_iceberg_thickness_to_SSH=add_iceberg_thickness_to_SSH
+bergs%override_iceberg_velocities=override_iceberg_velocities
+bergs%use_f_plane=use_f_plane
+bergs%rotate_icebergs_for_mass_spreading=rotate_icebergs_for_mass_spreading
+bergs%lat_ref=lat_ref
+bergs%u_override=u_override
+bergs%v_override=v_override
+bergs%initial_orientation=initial_orientation
+bergs%set_melt_rates_to_zero=set_melt_rates_to_zero
+bergs%allow_bergs_to_roll=allow_bergs_to_roll
+bergs%hexagonal_icebergs=hexagonal_icebergs
+bergs%ignore_missing_restart_bergs=ignore_missing_restart_bergs
+bergs%Static_icebergs=Static_icebergs
+bergs%only_interactive_forces=only_interactive_forces
+bergs%halo_debugging=halo_debugging
+bergs%iceberg_bonds_on=iceberg_bonds_on   !Alon
+bergs%manually_initialize_bonds=manually_initialize_bonds   !Alon
+bergs%critical_interaction_damping_on=critical_interaction_damping_on   !Alon
+bergs%interactive_icebergs_on=interactive_icebergs_on   !Alon
+bergs%use_new_predictive_corrective=use_new_predictive_corrective  !Alon
+bergs%grounding_fraction=grounding_fraction
+bergs%add_weight_to_ocean=add_weight_to_ocean
+bergs%use_old_spreading=use_old_spreading
+bergs%debug_iceberg_with_id=debug_iceberg_with_id
+allocate( bergs%initial_mass(nclasses) ); bergs%initial_mass(:)=initial_mass(:)
+allocate( bergs%distribution(nclasses) ); bergs%distribution(:)=distribution(:)
+allocate( bergs%mass_scaling(nclasses) ); bergs%mass_scaling(:)=mass_scaling(:)
+allocate( bergs%initial_thickness(nclasses) ); bergs%initial_thickness(:)=initial_thickness(:)
+allocate( bergs%initial_width(nclasses) )
+allocate( bergs%initial_length(nclasses) )
+bergs%initial_width(:)=sqrt(initial_mass(:)/(LoW_ratio*rho_bergs*initial_thickness(:)))
+bergs%initial_length(:)=LoW_ratio*bergs%initial_width(:)
+grd%coastal_drift = coastal_drift
+grd%tidal_drift = tidal_drift
+
+if (read_old_restarts) call error_mesg('diamonds, ice_bergs_framework_init', 'Setting "read_old_restarts=.true." is obsolete and does nothing!', WARNING)
+
+! Diagnostics
+id_class = diag_axis_init('mass_class', initial_mass, 'kg','Z', 'iceberg mass')
+axes3d(1:2)=axes
+axes3d(3)=id_class
+grd%id_calving=register_diag_field('icebergs', 'calving', axes, Time, &
+   'Incoming Calving mass rate', 'kg/s')
+grd%id_calving_hflx_in=register_diag_field('icebergs', 'calving_hflx_in', axes, Time, &
+   'Incoming Calving heat flux', 'J/s')
+grd%id_accum=register_diag_field('icebergs', 'accum_calving', axes, Time, &
+   'Accumulated calving mass rate', 'kg/s')
+grd%id_unused=register_diag_field('icebergs', 'unused_calving', axes, Time, &
+   'Unused calving mass rate', 'kg/s')
+grd%id_floating_melt=register_diag_field('icebergs', 'melt', axes, Time, &
+   'Melt rate of icebergs + bits', 'kg/(m^2*s)')
+grd%id_melt_m_per_year=register_diag_field('icebergs', 'melt_m_per_year', axes, Time, &
+   'Melt rate of icebergs + bits (m/yr)', 'm/yr')
+grd%id_berg_melt=register_diag_field('icebergs', 'berg_melt', axes, Time, &
+   'Melt rate of icebergs', 'kg/(m^2*s)')
+grd%id_melt_buoy=register_diag_field('icebergs', 'melt_buoy', axes, Time, &
+   'Buoyancy component of iceberg melt rate', 'kg/(m^2*s)')
+grd%id_melt_eros=register_diag_field('icebergs', 'melt_eros', axes, Time, &
+   'Erosion component of iceberg melt rate', 'kg/(m^2*s)')
+grd%id_melt_conv=register_diag_field('icebergs', 'melt_conv', axes, Time, &
+   'Convective component of iceberg melt rate', 'kg/(m^2*s)')
+grd%id_bergy_src=register_diag_field('icebergs', 'bergy_src', axes, Time, &
+   'Mass source of bergy bits', 'kg/(m^2*s)')
+grd%id_bergy_melt=register_diag_field('icebergs', 'bergy_melt', axes, Time, &
+   'Melt rate of bergy bits', 'kg/(m^2*s)')
+grd%id_bergy_mass=register_diag_field('icebergs', 'bergy_mass', axes, Time, &
+   'Bergy bit density field', 'kg/(m^2)')
+grd%id_spread_mass=register_diag_field('icebergs', 'spread_mass', axes, Time, &
+   'Iceberg mass after spreading', 'kg/(m^2)')
+grd%id_spread_area=register_diag_field('icebergs', 'spread_area', axes, Time, &
+   'Iceberg area after spreading', 'm^2/(m^2)')
+grd%id_u_iceberg=register_diag_field('icebergs', 'u_iceberg', axes, Time, &
+   'Iceberg u velocity (m/s)')
+grd%id_v_iceberg=register_diag_field('icebergs', 'v_iceberg', axes, Time, &
+   'Iceberg v velocity (m/s)')
+grd%id_spread_uvel=register_diag_field('icebergs', 'spread_uvel', axes, Time, &
+   'Iceberg u velocity spread (m/s)')
+grd%id_spread_vvel=register_diag_field('icebergs', 'spread_vvel', axes, Time, &
+   'Iceberg v velocity spread (m/s)')
+grd%id_ustar_iceberg=register_diag_field('icebergs', 'ustar_iceberg', axes, Time, &
+   'Iceberg frictional velocity (m/s)')
+grd%id_virtual_area=register_diag_field('icebergs', 'virtual_area', axes, Time, &
+   'Virtual coverage by icebergs', 'm^2')
+grd%id_mass=register_diag_field('icebergs', 'mass', axes, Time, &
+   'Iceberg density field', 'kg/(m^2)')
+grd%id_stored_ice=register_diag_field('icebergs', 'stored_ice', axes3d, Time, &
+   'Accumulated ice mass by class', 'kg')
+grd%id_real_calving=register_diag_field('icebergs', 'real_calving', axes3d, Time, &
+   'Calving into iceberg class', 'kg/s')
+grd%id_rmean_calving=register_diag_field('icebergs', 'running_mean_calving', axes, Time, &
+   'Running mean of calving', 'kg/s')
+grd%id_rmean_calving_hflx=register_diag_field('icebergs', 'running_mean_calving_hflx', axes, Time, &
+   'Running mean of calving heat flux', 'J/s')
+grd%id_count=register_diag_field('icebergs', 'bergs_per_cell', axes, Time, &
+   'Number of bergs per cell', '#')
+grd%id_chksum=register_diag_field('icebergs', 'list_chksum', axes, Time, &
+   'mpp_chksum on bergs in each cell', '#')
+grd%id_uo=register_diag_field('icebergs', 'uo', axes, Time, &
+   'Ocean zonal component of velocity', 'm s^-1')
+grd%id_vo=register_diag_field('icebergs', 'vo', axes, Time, &
+   'Ocean meridional component of velocity', 'm s^-1')
+grd%id_ui=register_diag_field('icebergs', 'ui', axes, Time, &
+   'Ice zonal component of velocity', 'm s^-1')
+grd%id_vi=register_diag_field('icebergs', 'vi', axes, Time, &
+   'Ice meridional component of velocity', 'm s^-1')
+grd%id_ua=register_diag_field('icebergs', 'ua', axes, Time, &
+   'Atmos zonal component of velocity', 'm s^-1')
+grd%id_va=register_diag_field('icebergs', 'va', axes, Time, &
+   'Atmos meridional component of velocity', 'm s^-1')
+grd%id_sst=register_diag_field('icebergs', 'sst', axes, Time, &
+   'Sea surface temperature', 'degrees_C')
+grd%id_sss=register_diag_field('icebergs', 'sss', axes, Time, &
+   'Sea surface salinity', 'psu')
+grd%id_cn=register_diag_field('icebergs', 'cn', axes, Time, &
+   'Sea ice concentration', '(fraction)')
+grd%id_hi=register_diag_field('icebergs', 'hi', axes, Time, &
+   'Sea ice thickness', 'm')
+grd%id_ssh=register_diag_field('icebergs', 'ssh', axes, Time, &
+   'Sea surface hieght', 'm')
+grd%id_fax=register_diag_field('icebergs', 'taux', axes, Time, &
+   'X-stress on ice from atmosphere', 'N m^-2')
+grd%id_fay=register_diag_field('icebergs', 'tauy', axes, Time, &
+   'Y-stress on ice from atmosphere', 'N m^-2')
+grd%id_ocean_depth=register_diag_field('icebergs', 'Depth', axes, Time, &
+   'Ocean Depth', 'm')
+
+! Static fields
+id_class=register_static_field('icebergs', 'lon', axes, &
+   'longitude (corners)', 'degrees_E')
+if (id_class>0) lerr=send_data(id_class, grd%lon(grd%isc:grd%iec,grd%jsc:grd%jec))
+id_class=register_static_field('icebergs', 'lat', axes, &
+   'latitude (corners)', 'degrees_N')
+if (id_class>0) lerr=send_data(id_class, grd%lat(grd%isc:grd%iec,grd%jsc:grd%jec))
+id_class=register_static_field('icebergs', 'area', axes, &
+   'cell area', 'm^2')
+if (id_class>0) lerr=send_data(id_class, grd%area(grd%isc:grd%iec,grd%jsc:grd%jec))
+id_class=register_static_field('icebergs', 'mask', axes, &
+   'wet point mask', 'none')
+if (id_class>0) lerr=send_data(id_class, grd%msk(grd%isc:grd%iec,grd%jsc:grd%jec))
+id_class=register_static_field('icebergs', 'ocean_depth_static', axes, &
+   'ocean depth static', 'm')
+if (id_class>0) lerr=send_data(id_class, grd%ocean_depth(grd%isc:grd%iec,grd%jsc:grd%jec))
+
+if (debug) then
+ call grd_chksum2(grd, grd%lon, 'init lon')
+ call grd_chksum2(grd, grd%lat, 'init lat')
+ call grd_chksum2(grd, grd%lonc, 'init lonc')
+ call grd_chksum2(grd, grd%latc, 'init latc')
+ call grd_chksum2(grd, grd%area, 'init area')
+ call grd_chksum2(grd, grd%msk, 'init msk')
+ call grd_chksum2(grd, grd%cos, 'init cos')
+ call grd_chksum2(grd, grd%sin, 'init sin')
+ call grd_chksum2(grd, grd%ocean_depth, 'init ocean_depth')
+endif
 
-  if (do_unit_tests) then
-   if (unit_tests(bergs)) call error_mesg('diamonds, icebergs_init', 'Unit tests failed!', FATAL)
-  endif
+if (do_unit_tests) then
+ if (unit_tests(bergs)) call error_mesg('diamonds, icebergs_init', 'Unit tests failed!', FATAL)
+endif
 
- !write(stderrunit,*) 'diamonds: done'
-  call mpp_clock_end(bergs%clock_ini)
-  call mpp_clock_end(bergs%clock)
+!write(stderrunit,*) 'diamonds: done'
+call mpp_clock_end(bergs%clock_ini)
+call mpp_clock_end(bergs%clock)
 
 end subroutine ice_bergs_framework_init
 
@@ -2720,7 +2757,7 @@ subroutine print_berg(iochan, berg, label, il, jl)
 integer, optional, intent(in) :: jl !< j-index of cell berg should be in
 ! Local variables
 
-  write(iochan,'("diamonds, print_berg: ",2a,i5,a,i12,a,2f10.4,i5,f7.2,es12.4,f5.1)') &
+  write(iochan,'("diamonds, print_berg: ",2a,i5,a,i12,a,2f16.4,i5,f7.2,es12.4,f5.1)') &
     label, 'pe=(', mpp_pe(), ') #=', berg%id, ' start lon,lat,yr,day,mass,hb=', &
     berg%start_lon, berg%start_lat, berg%start_year, berg%start_day, berg%start_mass, berg%halo_berg
   if (present(il).and.present(jl)) then
@@ -2731,7 +2768,7 @@ subroutine print_berg(iochan, berg, label, il, jl)
     label, 'pe=(', mpp_pe(), ') #=', berg%id, &
     ' i,j=', berg%ine, berg%jne, &
     ' p,n=', associated(berg%prev), associated(berg%next)
-  write(iochan,'("diamonds, print_berg: ",2a,i5,a,i12,3(a,2f14.8))') &
+  write(iochan,'("diamonds, print_berg: ",2a,i5,a,i12,3(a,2f16.8))') &
     label, 'pe=(', mpp_pe(), ') #=', berg%id, &
     ' xi,yj=', berg%xi, berg%yj, &
     ' lon,lat=', berg%lon, berg%lat, &
@@ -4434,6 +4471,7 @@ subroutine bergs_chksum(bergs, txt, ignore_halo_violation)
       icnt(this%ine,this%jne)=icnt(this%ine,this%jne)+1
       fld2(i,:) = fld(i,:)*float( icnt(this%ine,this%jne) ) !*float( i )
       grd%tmp(this%ine,this%jne)=grd%tmp(this%ine,this%jne)+time_hash(this)*pos_hash(this)+log(this%mass)
+
       ichk5=ichk5+iberg
       this=>this%next
     enddo
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index 041a7a3..8df9e46 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -574,6 +574,8 @@ subroutine read_restart_bergs(bergs,Time)
        call read_int_vector(filename,'id_ij',id_ij,grd%domain)
      endif
      call read_real_vector(filename,'static_berg',static_berg,grd%domain,value_if_not_in_file=0.)
+  else
+     stop 'read_restart_bergs, RESTART NOT FOUND!'
   endif
 
   ! Find approx outer bounds for tile
@@ -774,8 +776,11 @@ subroutine generate_bergs(bergs,Time)
   call get_date(Time, iyr, imon, iday, ihr, imin, isec)
 
   do j=grd%jsc,grd%jec; do i=grd%isc,grd%iec
+     
     if (grd%msk(i,j)>0. .and. abs(grd%latc(i,j))>80.0) then
-      if (max(grd%lat(i,j),grd%lat(i-1,j),grd%lat(i,j-1),grd%lat(i-1,j-1))>89.999) cycle ! Cannot use this at Pole cells
+       if (max(grd%lat(i,j),grd%lat(i-1,j),grd%lat(i,j-1),grd%lat(i-1,j-1))>89.999) cycle ! Cannot use this at Pole cells
+       
+     
       localberg%xi=-999.
       localberg%yj=-999.
       localberg%ine=i
@@ -861,7 +866,7 @@ subroutine loc_set_berg_pos(grd, xi, yj, uvel, vvel, berg)
     write(0,*) 'bx=',berg%lon, 'gx=',grd%lon(i-1,j-1), grd%lon(i,j-1), grd%lon(i,j), grd%lon(i-1,j),'cx=', grd%lonc(i,j)
     write(0,*) 'by=',berg%lat, 'gy=',grd%lat(i-1,j-1), grd%lat(i,j-1), grd%lat(i,j), grd%lat(i-1,j),'cy=', grd%latc(i,j)
     stop 'generate_bergs, loc_set_berg_pos(): VERY FATAL!'
-  endif
+  Endif
 end subroutine loc_set_berg_pos
 
 !> Read bond restart file
diff --git a/test/Iceberg_repository b/test/Iceberg_repository
new file mode 160000
index 0000000..55ba490
--- /dev/null
+++ b/test/Iceberg_repository
@@ -0,0 +1 @@
+Subproject commit 55ba490bc7fb16a29937e9c7dff816a4b4e3a77f
diff --git a/test/README b/test/README
new file mode 100644
index 0000000..a4c4514
--- /dev/null
+++ b/test/README
@@ -0,0 +1,4 @@
+- Use the scripts in ./Iceberg_repository to create a tabular iceberg and restart (input) file for testing the solo driver
+- edit input.nml
+- run the model (e.g. ./RUN)
+- animate the results with animate_trajectories.py
\ No newline at end of file
diff --git a/test/RUN b/test/RUN
new file mode 100755
index 0000000..d125392
--- /dev/null
+++ b/test/RUN
@@ -0,0 +1,2 @@
+rm iceberg_trajectories.nc
+srun -n4 ./../build/bergs.x
diff --git a/test/animate_trajectories.py b/test/animate_trajectories.py
new file mode 100755
index 0000000..7367b6d
--- /dev/null
+++ b/test/animate_trajectories.py
@@ -0,0 +1,114 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+import matplotlib.pyplot as plt
+from matplotlib.animation import FuncAnimation
+
+
+print('reading file')
+
+filename = 'iceberg_trajectories.nc'
+field = 'lon'
+field2 = 'lat'
+
+with nc.Dataset(filename) as file:
+    x = file.variables['lon'][:]/1.e3
+    y = file.variables['lat'][:]/1.e3
+    day = file.variables['day'][:]
+
+ud = np.unique(day)
+t = ud[0]
+
+def animate(i):
+
+    x1 = x[day == ud[i]]
+    y1 = y[day == ud[i]]
+    data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
+    scat.set_offsets(data)
+    t = ud[i]
+    time_text.set_text('time = %.1f days' % t )        
+    return scat,time_text
+
+def init():
+    scat.set_offsets([])
+    return scat,
+
+def onClick(event):
+    global anim_running
+    if anim_running:
+        ani.event_source.stop()
+        anim_running = False
+    else:
+        ani.event_source.start()
+        anim_running = True
+
+# frame info
+num_frames = len(ud)
+movie_len = 5.0 #seconds
+frame_len = 1000.0*movie_len/num_frames
+
+smax = max(max(x),max(y),200)
+xmin = 0.0
+xmax = smax
+ymin = 0.0
+ymax = smax
+
+
+# Now we can do the plotting!
+f = plt.figure(figsize=(5,5))
+f.tight_layout()
+ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
+scat = ax1.scatter([],[],marker='H',facecolor='w',s=140,edgecolor='red')
+time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
+
+ax1.set_xlabel('x (km)')
+ax1.set_ylabel('y (km)')
+ax1.set_title('Iceberg trajectory')
+
+anim_running = True
+f.canvas.mpl_connect('button_press_event', onClick)
+ 
+ani = FuncAnimation(
+    f,animate,init_func=init,frames=num_frames,
+    interval=frame_len,blit=True)
+
+print('time',t)
+
+plt.show()
+
+#animation.save("iceberg_traj_animation.mp4")
+
+
+
+#old:
+#mid = int(np.ceil(len(ud)/2))
+#t1 = ud[0]
+#t2 = ud[mid]
+#t3 = ud[len(ud)-1]
+#print('plotting')
+#plt.figure()
+#figsize=(15,10))
+#plt.scatter(x[day == t1],y[day == t1],color = 'blue', marker='*')
+#plt.scatter(x[day == t2],y[day == t2],color = 'green',marker='o')
+#plt.scatter(x[day == t3],y[day == t3],color = 'red',marker='*')
+#plt.xlabel('x-extent (km)')
+#plt.ylabel('y-extent (km)')
+#plt.show()
+
+
+print('Script complete')
+
+
+
+
+
+
+
diff --git a/test/diag_table b/test/diag_table
new file mode 100644
index 0000000..c1c8819
--- /dev/null
+++ b/test/diag_table
@@ -0,0 +1,3 @@
+"icebergs test"
+1 1 1 0 0 0
+
diff --git a/test/input.nml b/test/input.nml
new file mode 100644
index 0000000..90a4d58
--- /dev/null
+++ b/test/input.nml
@@ -0,0 +1,49 @@
+&icebergs_driver_nml
+  ni=20,
+  nj=20,
+  ibdt=3600.0,
+  ibuo=0.3,
+  ibvo=0.0,
+  ibhrs=4000,
+  halo=4,
+  debug=.true.
+/
+
+&icebergs_nml
+    verbose=.false.,
+    verbose_hrs=5,
+    traj_sample_hrs=5,
+    debug=.false.,
+    really_debug=.false.,
+    use_slow_find=.true.,
+    add_weight_to_ocean=.false.,
+    passive_mode=.false.,
+    generate_test_icebergs=.false.,
+    use_roundoff_fix=.true.,
+    make_calving_reproduce=.true.,
+    grid_is_regular=.true.,
+    grid_is_latlon=.false.,
+    set_melt_rates_to_zero=.true.,
+    interactive_icebergs_on=.true.,
+    critical_interaction_damping_on=.true.,
+    use_new_predictive_corrective=.true.,
+    halo=4,
+    halo_debugging=.false.,
+    ignore_ij_restart=.true.,
+    parallel_reprod=.true.,
+    Lx=200000.0,
+    restart_input_dir='INPUT/',
+    hexagonal_icebergs=.true.,
+    iceberg_bonds_on=.false.,
+    use_old_spreading=.false., !for if bergs are rec
+    runge_not_verlet=.false.,
+    manually_initialize_bonds=.false.
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.,
+         threading_read='multi'
+ /

From aa62ce8c9e0b9d4a37c20a4369a449d7152ddb32 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Fri, 14 Aug 2020 14:51:18 -0400
Subject: [PATCH 248/361] add Iceberg_repository

---
 .gitignore                                    |    1 +
 build/.gitignore                              |    1 +
 test/.gitignore                               |    3 +
 test/Iceberg_repository                       |    1 -
 test/Iceberg_repository/.gitignore            |    3 +
 .../Bergs/Layer/Empty_run/MOM_input           |    1 +
 .../Bergs/Layer/Empty_run/MOM_override        |   73 +
 .../Bergs/Layer/Empty_run/SIS_input           |    1 +
 .../Bergs/Layer/Empty_run/SIS_override        |    8 +
 .../Bergs/Layer/Empty_run/clean_MOM.sh        |    1 +
 .../Bergs/Layer/Empty_run/data_table          |    1 +
 .../Bergs/Layer/Empty_run/diag_table          |    1 +
 .../Bergs/Layer/Empty_run/field_table         |    1 +
 .../Bergs/Layer/Empty_run/input.nml           |  140 ++
 .../Bergs/Layer/Empty_run/output              |   16 +
 .../Bergs/Layer/Empty_run/run_script.sh       |    1 +
 .../Bergs/Layer/Empty_run/submit_to_queue     |   25 +
 .../Bergs/Layer/Moving_berg_Bond/MOM_input    |    1 +
 .../Bergs/Layer/Moving_berg_Bond/MOM_override |   71 +
 .../Bergs/Layer/Moving_berg_Bond/README       |    4 +
 .../Bergs/Layer/Moving_berg_Bond/SIS_input    |    1 +
 .../Bergs/Layer/Moving_berg_Bond/SIS_override |    9 +
 .../Bergs/Layer/Moving_berg_Bond/clean_MOM.sh |    1 +
 .../Bergs/Layer/Moving_berg_Bond/data_table   |    1 +
 .../Bergs/Layer/Moving_berg_Bond/diag_table   |    1 +
 .../Bergs/Layer/Moving_berg_Bond/field_table  |    1 +
 .../Bergs/Layer/Moving_berg_Bond/input.nml    |  140 ++
 .../Layer/Moving_berg_Bond/run_script.sh      |    1 +
 .../Layer/Moving_berg_Bond/submit_to_queue    |   25 +
 .../Bergs/Layer/Moving_berg_Collapse/README   |    7 +
 .../Layer/Moving_berg_Collapse/input.nml      |  140 ++
 .../Bergs/Layer/Moving_berg_drift/MOM_input   |    1 +
 .../Layer/Moving_berg_drift/MOM_override      |   71 +
 .../Bergs/Layer/Moving_berg_drift/README      |    3 +
 .../Bergs/Layer/Moving_berg_drift/SIS_input   |    1 +
 .../Layer/Moving_berg_drift/SIS_override      |    9 +
 .../Layer/Moving_berg_drift/clean_MOM.sh      |    1 +
 .../Bergs/Layer/Moving_berg_drift/data_table  |    1 +
 .../Bergs/Layer/Moving_berg_drift/diag_table  |    1 +
 .../Bergs/Layer/Moving_berg_drift/field_table |    1 +
 .../Bergs/Layer/Moving_berg_drift/input.nml   |  140 ++
 .../Layer/Moving_berg_drift/run_script.sh     |    1 +
 .../Layer/Moving_berg_drift/submit_to_queue   |   25 +
 .../Bergs/Layer/Moving_berg_fixed/MOM_input   |    1 +
 .../Layer/Moving_berg_fixed/MOM_override      |   71 +
 .../Bergs/Layer/Moving_berg_fixed/README      |    5 +
 .../Bergs/Layer/Moving_berg_fixed/SIS_input   |    1 +
 .../Layer/Moving_berg_fixed/SIS_override      |    9 +
 .../Layer/Moving_berg_fixed/clean_MOM.sh      |    1 +
 .../Bergs/Layer/Moving_berg_fixed/data_table  |    1 +
 .../Bergs/Layer/Moving_berg_fixed/diag_table  |    1 +
 .../Bergs/Layer/Moving_berg_fixed/field_table |    1 +
 .../Bergs/Layer/Moving_berg_fixed/input.nml   |  140 ++
 .../Layer/Moving_berg_fixed/run_script.sh     |    1 +
 .../Layer/Moving_berg_fixed/submit_to_queue   |   25 +
 .../Bergs/Layer/Static_shelf/MOM_input        |    1 +
 .../Bergs/Layer/Static_shelf/MOM_override     |   73 +
 .../Bergs/Layer/Static_shelf/README           |    1 +
 .../Bergs/Layer/Static_shelf/SIS_input        |    1 +
 .../Bergs/Layer/Static_shelf/SIS_override     |    8 +
 .../Bergs/Layer/Static_shelf/clean_MOM.sh     |    1 +
 .../Bergs/Layer/Static_shelf/data_table       |    1 +
 .../Bergs/Layer/Static_shelf/diag_table       |    1 +
 .../Bergs/Layer/Static_shelf/field_table      |    1 +
 .../Bergs/Layer/Static_shelf/input.nml        |  140 ++
 .../Bergs/Layer/Static_shelf/run_script.sh    |    1 +
 .../Bergs/Layer/Static_shelf/submit_to_queue  |   25 +
 .../Sigma_Shelf_Star/Empty_run/MOM_input      |    1 +
 .../Sigma_Shelf_Star/Empty_run/MOM_override   |   91 +
 .../Sigma_Shelf_Star/Empty_run/SIS_input      |    1 +
 .../Sigma_Shelf_Star/Empty_run/SIS_override   |    8 +
 .../Sigma_Shelf_Star/Empty_run/clean_MOM.sh   |    1 +
 .../Sigma_Shelf_Star/Empty_run/data_table     |    1 +
 .../Sigma_Shelf_Star/Empty_run/diag_table     |    1 +
 .../Sigma_Shelf_Star/Empty_run/field_table    |    1 +
 .../Sigma_Shelf_Star/Empty_run/input.nml      |  140 ++
 .../Sigma_Shelf_Star/Empty_run/run_script.sh  |    1 +
 .../Empty_run/submit_to_queue                 |   25 +
 .../Moving_berg_Bond/MOM_input                |    1 +
 .../Moving_berg_Bond/MOM_override             |   91 +
 .../Sigma_Shelf_Star/Moving_berg_Bond/README  |    4 +
 .../Moving_berg_Bond/SIS_input                |    1 +
 .../Moving_berg_Bond/SIS_override             |    9 +
 .../Moving_berg_Bond/clean_MOM.sh             |    1 +
 .../Moving_berg_Bond/data_table               |    1 +
 .../Moving_berg_Bond/diag_table               |    1 +
 .../Moving_berg_Bond/field_table              |    1 +
 .../Moving_berg_Bond/input.nml                |  140 ++
 .../Moving_berg_Bond/run_script.sh            |    1 +
 .../Moving_berg_Bond/submit_to_queue          |   25 +
 .../Moving_berg_Collapse/README               |    7 +
 .../Moving_berg_Collapse/input.nml            |  140 ++
 .../Moving_berg_drift/MOM_input               |    1 +
 .../Moving_berg_drift/MOM_override            |   91 +
 .../Sigma_Shelf_Star/Moving_berg_drift/README |    3 +
 .../Moving_berg_drift/SIS_input               |    1 +
 .../Moving_berg_drift/SIS_override            |    9 +
 .../Moving_berg_drift/clean_MOM.sh            |    1 +
 .../Moving_berg_drift/data_table              |    1 +
 .../Moving_berg_drift/diag_table              |    1 +
 .../Moving_berg_drift/field_table             |    1 +
 .../Moving_berg_drift/input.nml               |  140 ++
 .../Moving_berg_drift/run_script.sh           |    1 +
 .../Moving_berg_drift/submit_to_queue         |   25 +
 .../Moving_berg_fixed/MOM_input               |    1 +
 .../Moving_berg_fixed/MOM_override            |   91 +
 .../Sigma_Shelf_Star/Moving_berg_fixed/README |    5 +
 .../Moving_berg_fixed/SIS_input               |    1 +
 .../Moving_berg_fixed/SIS_override            |    9 +
 .../Moving_berg_fixed/clean_MOM.sh            |    1 +
 .../Moving_berg_fixed/data_table              |    1 +
 .../Moving_berg_fixed/diag_table              |    1 +
 .../Moving_berg_fixed/field_table             |    1 +
 .../Moving_berg_fixed/input.nml               |  140 ++
 .../Moving_berg_fixed/run_script.sh           |    1 +
 .../Moving_berg_fixed/submit_to_queue         |   25 +
 .../Sigma_Shelf_Star/Static_shelf/MOM_input   |    1 +
 .../Static_shelf/MOM_override                 |   94 +
 .../Sigma_Shelf_Star/Static_shelf/README      |    1 +
 .../Sigma_Shelf_Star/Static_shelf/SIS_input   |    1 +
 .../Static_shelf/SIS_override                 |    8 +
 .../Static_shelf/clean_MOM.sh                 |    1 +
 .../Sigma_Shelf_Star/Static_shelf/data_table  |    1 +
 .../Sigma_Shelf_Star/Static_shelf/diag_table  |    1 +
 .../Sigma_Shelf_Star/Static_shelf/field_table |    1 +
 .../Sigma_Shelf_Star/Static_shelf/input.nml   |  140 ++
 .../Static_shelf/run_script.sh                |    1 +
 .../Static_shelf/submit_to_queue              |   25 +
 .../Shelf/Layer/Static_shelf/MOM_input        |    1 +
 .../Shelf/Layer/Static_shelf/MOM_override     |   64 +
 .../Shelf/Layer/Static_shelf/README           |    1 +
 .../Shelf/Layer/Static_shelf/SIS_input        |    1 +
 .../Shelf/Layer/Static_shelf/SIS_override     |    8 +
 .../Shelf/Layer/Static_shelf/clean_MOM.sh     |    1 +
 .../Shelf/Layer/Static_shelf/data_table       |    1 +
 .../Shelf/Layer/Static_shelf/diag_table       |    1 +
 .../Shelf/Layer/Static_shelf/field_table      |    1 +
 .../Shelf/Layer/Static_shelf/input.nml        |  140 ++
 .../Shelf/Layer/Static_shelf/run_script.sh    |    1 +
 .../Shelf/Layer/Static_shelf/submit_to_queue  |   25 +
 .../Sigma_Shelf_Star/Static_shelf/MOM_input   |    1 +
 .../Static_shelf/MOM_override                 |   91 +
 .../Sigma_Shelf_Star/Static_shelf/README      |    1 +
 .../Sigma_Shelf_Star/Static_shelf/SIS_input   |    1 +
 .../Static_shelf/SIS_override                 |    8 +
 .../Static_shelf/clean_MOM.sh                 |    1 +
 .../Sigma_Shelf_Star/Static_shelf/data_table  |    1 +
 .../Sigma_Shelf_Star/Static_shelf/diag_table  |    1 +
 .../Sigma_Shelf_Star/Static_shelf/field_table |    1 +
 .../Sigma_Shelf_Star/Static_shelf/input.nml   |  140 ++
 .../Static_shelf/run_script.sh                |    1 +
 .../Static_shelf/submit_to_queue              |   25 +
 .../ISOMIP_Calving/common/MOM_input           |  721 +++++++
 .../ISOMIP_Calving/common/SIS_input           |  125 ++
 .../ISOMIP_Calving/common/clean_MOM.sh        |   14 +
 .../ISOMIP_Calving/common/data_table          |   47 +
 .../ISOMIP_Calving/common/diag_table          |  453 ++++
 .../ISOMIP_Calving/common/field_table         |   71 +
 .../ISOMIP_Calving/common/input.nml           |  137 ++
 .../ISOMIP_Calving/common/run_script.sh       |    5 +
 .../ISOMIP_Calving/common/submit_to_queue     |   25 +
 .../python_scripts/Create_mosaic.py           |    1 +
 .../initialize_bergs_in_pattern.py            |    1 +
 test/Iceberg_repository/README                |   34 +
 test/Iceberg_repository/RUN                   |    9 +
 .../Create_a_cartesian_grid_and_mosaic.ipynb  |  649 ++++++
 .../Scripts_and_analysis/Create_mosaic.py     | 1387 +++++++++++++
 .../Idealized_cartesian_grid.py               |  395 ++++
 .../Weddell_Sea_initiation.sh                 |    1 +
 .../Weddell_sea_shelf_setup.py                | 1398 +++++++++++++
 .../Scripts_and_analysis/bergs_quickview.py   |  284 +++
 .../calving_and_extract.py                    |  126 ++
 .../Scripts_and_analysis/check_convergence.py |   77 +
 .../compare_Global_Quick_vs_Benchmark.py      |  121 ++
 .../copy_files_to_shelf_and_bergs.sh          |   42 +
 .../Scripts_and_analysis/create_C3_env.sh     |   14 +
 .../create_berg_restart.py                    |  172 ++
 .../Scripts_and_analysis/create_one_file.py   |   94 +
 .../create_thickness_file.py                  |  167 ++
 .../Scripts_and_analysis/filling_up_space.py  |  338 +++
 .../flat_isomip_create.py                     |   71 +
 .../grid_cartesian_create.py                  |  395 ++++
 .../Scripts_and_analysis/hexagon_area.py      | 1472 +++++++++++++
 .../Scripts_and_analysis/hexagon_area.pyc     |  Bin 0 -> 33327 bytes
 .../iceshelf_geometry_create.py               |  150 ++
 .../iceshelf_mass_file_create.py              |   83 +
 .../initialize_bergs_in_pattern.py            | 1838 +++++++++++++++++
 .../Scripts_and_analysis/movie_bergs_traj.py  |  283 +++
 .../old_bergs_quickview.py                    |  268 +++
 .../quick_benchmark_comparison.sh             |    5 +
 .../Scripts_and_analysis/quick_plot.py        |  205 ++
 .../Scripts_and_analysis/submit_to_queue.sh   |   23 +
 .../Scripts_and_analysis/topog_file_create.py |   89 +
 .../variables_comparison.sh                   |    5 +
 .../write_restart_iceberg.py                  |  424 ++++
 test/Iceberg_repository/hexagon_area.py       | 1472 +++++++++++++
 .../setup_ISOMIP_calving.sh                   |   54 +
 test/Iceberg_repository/testberg/testberg.py  |   72 +
 198 files changed, 17301 insertions(+), 1 deletion(-)
 create mode 100644 test/.gitignore
 delete mode 160000 test/Iceberg_repository
 create mode 100644 test/Iceberg_repository/.gitignore
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/MOM_input
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/MOM_override
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/SIS_input
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/SIS_override
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/clean_MOM.sh
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/data_table
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/diag_table
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/field_table
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/input.nml
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/output
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/run_script.sh
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/submit_to_queue
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/MOM_input
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/MOM_override
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/README
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/SIS_input
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/SIS_override
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/clean_MOM.sh
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/data_table
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/diag_table
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/field_table
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/input.nml
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/run_script.sh
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/submit_to_queue
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Collapse/README
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Collapse/input.nml
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/MOM_input
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/MOM_override
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/README
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/SIS_input
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/SIS_override
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/clean_MOM.sh
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/data_table
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/diag_table
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/field_table
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/input.nml
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/run_script.sh
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/submit_to_queue
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/MOM_input
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/MOM_override
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/README
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/SIS_input
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/SIS_override
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/clean_MOM.sh
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/data_table
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/diag_table
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/field_table
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/input.nml
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/run_script.sh
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/submit_to_queue
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/MOM_input
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/MOM_override
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/README
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/SIS_input
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/SIS_override
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/clean_MOM.sh
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/data_table
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/diag_table
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/field_table
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/input.nml
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/run_script.sh
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/submit_to_queue
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/MOM_input
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/MOM_override
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/SIS_input
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/SIS_override
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/clean_MOM.sh
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/data_table
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/diag_table
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/field_table
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/input.nml
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/run_script.sh
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/submit_to_queue
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/MOM_input
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/MOM_override
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/README
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/SIS_input
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/SIS_override
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/clean_MOM.sh
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/data_table
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/diag_table
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/field_table
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/input.nml
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/run_script.sh
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/submit_to_queue
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Collapse/README
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 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/MOM_input
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/MOM_override
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 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/SIS_override
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/clean_MOM.sh
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/data_table
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 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/input.nml
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/run_script.sh
 create mode 100644 test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/submit_to_queue
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 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/python_scripts/Create_mosaic.py
 create mode 120000 test/Iceberg_repository/ISOMIP_Calving/python_scripts/initialize_bergs_in_pattern.py
 create mode 100644 test/Iceberg_repository/README
 create mode 100755 test/Iceberg_repository/RUN
 create mode 100644 test/Iceberg_repository/Scripts_and_analysis/Create_a_cartesian_grid_and_mosaic.ipynb
 create mode 100755 test/Iceberg_repository/Scripts_and_analysis/Create_mosaic.py
 create mode 100644 test/Iceberg_repository/Scripts_and_analysis/Idealized_cartesian_grid.py
 create mode 100755 test/Iceberg_repository/Scripts_and_analysis/Weddell_Sea_initiation.sh
 create mode 100755 test/Iceberg_repository/Scripts_and_analysis/Weddell_sea_shelf_setup.py
 create mode 100755 test/Iceberg_repository/Scripts_and_analysis/bergs_quickview.py
 create mode 100644 test/Iceberg_repository/Scripts_and_analysis/calving_and_extract.py
 create mode 100755 test/Iceberg_repository/Scripts_and_analysis/check_convergence.py
 create mode 100644 test/Iceberg_repository/Scripts_and_analysis/compare_Global_Quick_vs_Benchmark.py
 create mode 100755 test/Iceberg_repository/Scripts_and_analysis/copy_files_to_shelf_and_bergs.sh
 create mode 100755 test/Iceberg_repository/Scripts_and_analysis/create_C3_env.sh
 create mode 100755 test/Iceberg_repository/Scripts_and_analysis/create_berg_restart.py
 create mode 100755 test/Iceberg_repository/Scripts_and_analysis/create_one_file.py
 create mode 100755 test/Iceberg_repository/Scripts_and_analysis/create_thickness_file.py
 create mode 100755 test/Iceberg_repository/Scripts_and_analysis/filling_up_space.py
 create mode 100755 test/Iceberg_repository/Scripts_and_analysis/flat_isomip_create.py
 create mode 100755 test/Iceberg_repository/Scripts_and_analysis/grid_cartesian_create.py
 create mode 100755 test/Iceberg_repository/Scripts_and_analysis/hexagon_area.py
 create mode 100644 test/Iceberg_repository/Scripts_and_analysis/hexagon_area.pyc
 create mode 100755 test/Iceberg_repository/Scripts_and_analysis/iceshelf_geometry_create.py
 create mode 100755 test/Iceberg_repository/Scripts_and_analysis/iceshelf_mass_file_create.py
 create mode 100755 test/Iceberg_repository/Scripts_and_analysis/initialize_bergs_in_pattern.py
 create mode 100755 test/Iceberg_repository/Scripts_and_analysis/movie_bergs_traj.py
 create mode 100755 test/Iceberg_repository/Scripts_and_analysis/old_bergs_quickview.py
 create mode 100755 test/Iceberg_repository/Scripts_and_analysis/quick_benchmark_comparison.sh
 create mode 100755 test/Iceberg_repository/Scripts_and_analysis/quick_plot.py
 create mode 100755 test/Iceberg_repository/Scripts_and_analysis/submit_to_queue.sh
 create mode 100755 test/Iceberg_repository/Scripts_and_analysis/topog_file_create.py
 create mode 100755 test/Iceberg_repository/Scripts_and_analysis/variables_comparison.sh
 create mode 100755 test/Iceberg_repository/Scripts_and_analysis/write_restart_iceberg.py
 create mode 100755 test/Iceberg_repository/hexagon_area.py
 create mode 100755 test/Iceberg_repository/setup_ISOMIP_calving.sh
 create mode 100755 test/Iceberg_repository/testberg/testberg.py

diff --git a/.gitignore b/.gitignore
index 5ebf562..cbab8f9 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,3 @@
 CVS
 *~
+*core
\ No newline at end of file
diff --git a/build/.gitignore b/build/.gitignore
index 512654e..19bf7ec 100644
--- a/build/.gitignore
+++ b/build/.gitignore
@@ -5,3 +5,4 @@ logfile.000000.out
 .bergs.x.cppdefs
 *.mod
 *.o
+core
diff --git a/test/.gitignore b/test/.gitignore
new file mode 100644
index 0000000..a9bd34f
--- /dev/null
+++ b/test/.gitignore
@@ -0,0 +1,3 @@
+*.out
+*~
+*.nc
\ No newline at end of file
diff --git a/test/Iceberg_repository b/test/Iceberg_repository
deleted file mode 160000
index 55ba490..0000000
--- a/test/Iceberg_repository
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 55ba490bc7fb16a29937e9c7dff816a4b4e3a77f
diff --git a/test/Iceberg_repository/.gitignore b/test/Iceberg_repository/.gitignore
new file mode 100644
index 0000000..3e14065
--- /dev/null
+++ b/test/Iceberg_repository/.gitignore
@@ -0,0 +1,3 @@
+*~
+*.out
+*.nc
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/MOM_input b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/MOM_input
new file mode 120000
index 0000000..a756962
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/MOM_input
@@ -0,0 +1 @@
+../../../common/MOM_input
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/MOM_override b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/MOM_override
new file mode 100644
index 0000000..45aaab7
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/MOM_override
@@ -0,0 +1,73 @@
+! Blank file in which we can put "overrides" for parameters
+
+!TPY params
+#override NK = 72
+#override NKML = 4
+
+! TIME STEP
+!#override DT = 720
+!#override DT_THERM = 720
+#override DT = 10
+#override DT_THERM = 10
+#override DT_FORCING = 10
+
+! MIXING
+#override SMAGORINSKY_KH = False
+#override BIHARMONIC = False
+#override KH = 6.0  ! back. horiz. visc.
+#override KHTR = 1.0    ! back. horiz. diff.
+#override KD = 5.0E-5     ! back. diapycnal diff.
+#override KV = 1.0E-3     ! back. diapycnal visc.
+
+!WARM IC
+#override ISOMIP_T_SUR = -1.9
+#override ISOMIP_S_SUR = 33.8
+#override ISOMIP_T_BOT = 1.0
+#override ISOMIP_S_BOT = 34.7
+
+! ice shelf
+#override ICE_SHELF = False                !   [Boolean] default = False
+#override SHELF_THERMO = True
+#override SHELF_THREE_EQN = True
+#override SHELF_3EQ_GAMMA = False
+#override UTIDE = 0.01
+!SHELF_S_ROOT = True
+!#override USE_HMIX_SFC_PROP = True
+!#override HMIX_SFC_PROP = 10.
+
+! FRAZIL  - making sure sea ice does not form
+#override FRAZIL = False
+#override PRESSURE_DEPENDENT_FRAZIL = False
+
+! MIXED LAYER
+#override BULKMIXEDLAYER = True
+#override BULK_RI_ML = 0.25
+#override MIXEDLAYER_RESTRAT = True
+#override HMIX_MIN = 2.0
+!#override KV_TBL_MIN = 1.0E-2
+#override HTBL_SHELF_MIN = 2.0
+#override BOUND_SALINITY = True
+ 
+! SHEAR MIXING
+#override USE_JACKSON_PARAM = True
+#override RINO_CRIT = 0.25
+!#override KD_KAPPA_SHEAR_0 = 1.0E-2
+
+! SPONGE
+#override SPONGE = True
+ISOMIP_SPONGE_FILE = "3D_LAYER_WARM_TPY_IC.nc"
+#override ISOMIP_TNUDG = 0.1
+!#override ISOMIP_SPONGE_TEMP_OFFSET=0.1
+
+
+! PASSIVE TRACERS
+USE_ISOMIP_TRACER = False
+
+! Simulation time
+#override DAYMAX = 730
+
+!#override FIT_SALINITY = False
+
+!Passing Iceberg field to ocean
+ICEBERGS_APPLY_RIGID_BOUNDARY=True !Different boundary condition is used under ice shelves
+ALLOW_ICEBERG_FLUX_DIAGNOSTICS=True
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/SIS_input b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/SIS_input
new file mode 120000
index 0000000..ad3cd99
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/SIS_input
@@ -0,0 +1 @@
+../../../common/SIS_input
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/SIS_override b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/SIS_override
new file mode 100644
index 0000000..fc641d7
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/SIS_override
@@ -0,0 +1,8 @@
+# Blank file in which we can put "overrides" for parameters
+DO_ICEBERGS =True              !   If true, use the icebergs module.
+
+!Time Stepping
+!#override DT_FORCING = 10.0              !   [s] default = 0.0
+!#override DT_RHEOLOGY = 10.0             ! The sub-cycling time step, in s, for iterating
+
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/clean_MOM.sh b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/clean_MOM.sh
new file mode 120000
index 0000000..c5370af
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/clean_MOM.sh
@@ -0,0 +1 @@
+../../../common/clean_MOM.sh
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/data_table b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/data_table
new file mode 120000
index 0000000..5b82b3c
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/data_table
@@ -0,0 +1 @@
+../../../common/data_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/diag_table b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/diag_table
new file mode 120000
index 0000000..cff65fe
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/diag_table
@@ -0,0 +1 @@
+../../../common/diag_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/field_table b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/field_table
new file mode 120000
index 0000000..b5ea991
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/field_table
@@ -0,0 +1 @@
+../../../common/field_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/input.nml b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/input.nml
new file mode 100644
index 0000000..7b69203
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/input.nml
@@ -0,0 +1,140 @@
+ &MOM_input_nml
+        output_directory = './',
+        input_filename = 'r'
+        restart_input_dir = 'INPUT/',
+        restart_output_dir = 'RESTART/',
+        parameter_filename = 'MOM_input',
+                             'MOM_override' /
+
+ &SIS_input_nml
+        output_directory = './',
+        input_filename = 'r'
+        restart_input_dir = 'INPUT/',
+        restart_output_dir = 'RESTART/',
+        parameter_filename = 'SIS_input',
+                             'SIS_override' /
+
+ &diag_manager_nml
+         max_output_fields=1000
+         max_input_fields=1000
+         max_num_axis_sets=1000
+	 flush_nc_files=.true.
+         max_files=1000
+         max_axes=2000
+ /
+
+ &coupler_nml
+            months = 0,
+            days   = 60,
+            current_date = 1,1,1,0,0,0,
+            hours = 0,
+            minutes =0, 
+            seconds = 0
+            calendar = 'NOLEAP',
+            dt_cpld  = 10.0,
+            dt_atmos = 10.0,
+            do_atmos = .false.,
+            do_land = .false.,
+            do_ice = .true.,
+            do_ocean = .true.,
+            atmos_npes = 0,
+            ocean_npes = 0,
+            concurrent = .false.
+            use_lag_fluxes=.false. /
+
+
+ &icebergs_nml
+    verbose=.false.,
+    verbose_hrs=240,
+    traj_sample_hrs=24000,
+    ignore_ij_restart=.true.
+    halo=2,
+    save_short_traj=.true.
+    debug=.false.,
+    really_debug=.false.,
+    use_slow_find=.true.,
+    add_weight_to_ocean=.true.,
+    passive_mode=.false.,
+    Static_icebergs=.False.,
+    ignore_missing_restart_bergs=.false.,
+    generate_test_icebergs=.false.,
+    speed_limit=0.,
+    use_roundoff_fix=.true.,
+    make_calving_reproduce=.false.,
+    Runge_not_Verlet=.false.,
+    iceberg_bonds_on=.true.,
+    critical_interaction_damping_on=.true.,
+    use_new_predictive_corrective=.true.,
+    interactive_icebergs_on=.true.
+    halo_debugging=.false.
+    spring_coef=0.00001
+    distribution=0.0, 0.99, 0.0, 0.00, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11,
+    hexagonal_icebergs=.true.
+    allow_bergs_to_roll=.true.
+    set_melt_rates_to_zero=.false.
+    use_roundoff_fix=.false.
+    grid_is_latlon=.false.
+    grid_is_regular=.true.
+    initial_orientation=-0.
+    rotate_icebergs_for_mass_spreading=.false.
+    lat_ref=-75.0
+    u_override=0.00
+    v_override=0.00
+    override_iceberg_velocities=.false.
+    add_iceberg_thickness_to_SSH=.false.
+    max_bonds=6
+    Iceberg_melt_without_decay=.true.
+    melt_icebergs_as_ice_shelf=.true.
+    Use_three_equation_model=.true.
+    find_melt_using_spread_mass=.true.
+    use_mixed_layer_salinity_for_thermo=.true.
+    pass_fields_to_ocean_model=.true.
+    rho_bergs=918.0
+    utide_icebergs=0.01
+    ustar_icebergs_bg=0.000
+    cdrag_icebergs =0.0025
+    const_gamma=.false.
+    Gamma_T_3EQ=0.22
+    ignore_traj=.False.
+    read_ocean_depth_from_file=.true.
+    apply_thickness_cutoff_to_bergs_melt=.true.
+    apply_thickness_cutoff_to_gridded_melt=.true.
+    melt_cutoff=10.
+    read_old_restarts=.false.
+    internal_bergs_for_drag=.true.
+    use_mixed_melting=.true.
+ &data_override_nml
+         /
+
+ &fms_io_nml
+         fms_netcdf_restart=.true.
+         threading_read='multi'
+ /
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC' /
+
+ &ice_albedo_nml
+      t_range = 10. /
+
+ &ice_model_nml
+           /
+
+ &monin_obukhov_nml
+            neutral = .true. /
+
+ &ocean_albedo_nml
+      ocean_albedo_option = 5 /
+
+ &sat_vapor_pres_nml
+      construct_table_wrt_liq = .true.,
+      construct_table_wrt_liq_and_ice = .true. /
+
+ &xgrid_nml
+            make_exchange_reproduce = .false.
+            interp_method = 'second_order' /
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/output b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/output
new file mode 100644
index 0000000..981abd1
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/output
@@ -0,0 +1,16 @@
+ 
+***NOTICE TO DDT USERS*** 
+With version 4.0 (and later) of DDT, the procedure for memory debugging has 
+changed.  You no longer need to compile with the ddtmem-cc, ddtmem-CC, 
+and ddtmem-ftn scripts.  Rather, just load the ddt-memdebug module (in 
+addition to this module) and compile as you normally would (with cc, 
+CC and/or ftn).  The appropriate memory debugging libraries will be 
+linked automatically. 
+ 
+Please direct questions to help@olcf.ornl.gov 
+ 
+python_scipy(3):ERROR:105: Unable to locate a modulefile for 'python_scipy/0.17.0'
+python_scipy(3):ERROR:105: Unable to locate a modulefile for 'python_scipy/0.17.0'
+python_scipy(3):ERROR:105: Unable to locate a modulefile for 'python_scipy/0.17.0'
+aprun: file ../../../../../build/intel/ice_ocean_SIS2/repro/old_executable/MOM6 not found
+aprun: Exiting due to errors. Application aborted
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/run_script.sh b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/run_script.sh
new file mode 120000
index 0000000..2a081b9
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/run_script.sh
@@ -0,0 +1 @@
+../../../common/run_script.sh
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/submit_to_queue b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/submit_to_queue
new file mode 100644
index 0000000..d35f1b8
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/submit_to_queue
@@ -0,0 +1,25 @@
+#!/bin/csh -f
+#PBS -r y                                                              #This job is restartable
+#PBS -j oe                                                             #STDOUT and STDERR are in the same file, specified below in the '-o' option
+#PBS -q batch                                                          #Do not change this - it tells your job where to run
+#PBS -S /bin/sh                                                        #Do not change this - it keeps your job from issuing a false alarm
+#PBS -E                                                                #Do not change this - it gives your job more and more useful Moab environment variables
+#PBS -N  Bergs_Empty_Run                                               #Job Name:             You may want to change this to reflect your job's purpose or relation to an experiment
+#PBS -l partition=c3
+#PBS -l size=4                                                        #You will need to change this to reflect your job's core requirements - 24 is the current core increment.
+#PBS -l walltime=16:00:00                                              #You MUST change this to reflect your job's expected run time, including copy time
+#PBS -m bea                                                            #Email options: You may want to change this to reduce your incoming email stream
+
+######################################################################################################################
+#
+#  Gaea c1ms batch skeleton version 0.9
+#  
+#  0.9 - Initial version - 20110906 - Daniel Gall - Daniel.Gall@noaa.gov
+#
+######################################################################################################################
+
+#Source the system initialization scripts (but not the user's so as to avoid interactive settings that can poison us)
+source /etc/csh.cshrc
+
+#Run the experiment
+aprun -n 128 ../../../../../build/intel/ice_ocean_SIS2/repro/MOM6
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/MOM_input b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/MOM_input
new file mode 120000
index 0000000..a756962
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/MOM_input
@@ -0,0 +1 @@
+../../../common/MOM_input
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/MOM_override b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/MOM_override
new file mode 100644
index 0000000..1fec204
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/MOM_override
@@ -0,0 +1,71 @@
+! Blank file in which we can put "overrides" for parameters
+
+!TPY params
+#override NK = 72
+#override NKML = 4
+
+! TIME STEP
+#override DT = 10
+#override DT_THERM = 10
+#override DT_FORCING = 10
+
+! MIXING
+#override SMAGORINSKY_KH = False
+#override BIHARMONIC = False
+#override KH = 6.0  ! back. horiz. visc.
+#override KHTR = 1.0    ! back. horiz. diff.
+#override KD = 5.0E-5     ! back. diapycnal diff.
+#override KV = 1.0E-3     ! back. diapycnal visc.
+
+!WARM IC
+#override ISOMIP_T_SUR = -1.9
+#override ISOMIP_S_SUR = 33.8
+#override ISOMIP_T_BOT = 1.0
+#override ISOMIP_S_BOT = 34.7
+
+! ice shelf
+#override ICE_SHELF = False                !   [Boolean] default = False
+#override SHELF_THERMO = True
+#override SHELF_THREE_EQN = True
+#override SHELF_3EQ_GAMMA = False
+#override UTIDE = 0.01
+!SHELF_S_ROOT = True
+!#override USE_HMIX_SFC_PROP = True
+!#override HMIX_SFC_PROP = 10.
+
+! FRAZIL  - making sure sea ice does not form
+#override FRAZIL = False
+#override PRESSURE_DEPENDENT_FRAZIL = False
+
+! MIXED LAYER
+#override BULKMIXEDLAYER = True
+#override BULK_RI_ML = 0.25
+#override MIXEDLAYER_RESTRAT = True
+#override HMIX_MIN = 2.0
+!#override KV_TBL_MIN = 1.0E-2
+#override HTBL_SHELF_MIN = 2.0
+#override BOUND_SALINITY = True
+ 
+! SHEAR MIXING
+#override USE_JACKSON_PARAM = True
+#override RINO_CRIT = 0.25
+!#override KD_KAPPA_SHEAR_0 = 1.0E-2
+
+! SPONGE
+#override SPONGE = True
+ISOMIP_SPONGE_FILE = "3D_LAYER_WARM_TPY_IC.nc"
+#override ISOMIP_TNUDG = 0.1
+!#override ISOMIP_SPONGE_TEMP_OFFSET=0.1
+
+
+! PASSIVE TRACERS
+USE_ISOMIP_TRACER = False
+
+! Simulation time
+#override DAYMAX = 730
+
+!#override FIT_SALINITY = False
+
+!Passing Iceberg field to ocean
+ICEBERGS_APPLY_RIGID_BOUNDARY=True !Different boundary condition is used under ice shelves
+ALLOW_ICEBERG_FLUX_DIAGNOSTICS=True
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/README b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/README
new file mode 100644
index 0000000..0972054
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/README
@@ -0,0 +1,4 @@
+A tabular icebergs breaks away from the ice shelf. The tabular icebergs is bonded together by numeric bonds. Icebergs are allowed to evolve freely
+
+Works best when started from restart file created by Static_berg simulation.
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/SIS_input b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/SIS_input
new file mode 120000
index 0000000..ad3cd99
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/SIS_input
@@ -0,0 +1 @@
+../../../common/SIS_input
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/SIS_override b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/SIS_override
new file mode 100644
index 0000000..605ca84
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/SIS_override
@@ -0,0 +1,9 @@
+# Blank file in which we can put "overrides" for parameters
+DO_ICEBERGS =True              !   If true, use the icebergs module.
+
+!Time Stepping
+#override DT_FORCING = 10.0              !   [s] default = 0.0
+#override DT_RHEOLOGY = 10.0             ! The sub-cycling time step, in s, for iterating
+#override DT_ICE_DYNAMICS = 10.0 
+
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/clean_MOM.sh b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/clean_MOM.sh
new file mode 120000
index 0000000..c5370af
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/clean_MOM.sh
@@ -0,0 +1 @@
+../../../common/clean_MOM.sh
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/data_table b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/data_table
new file mode 120000
index 0000000..5b82b3c
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/data_table
@@ -0,0 +1 @@
+../../../common/data_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/diag_table b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/diag_table
new file mode 120000
index 0000000..cff65fe
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/diag_table
@@ -0,0 +1 @@
+../../../common/diag_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/field_table b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/field_table
new file mode 120000
index 0000000..b5ea991
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/field_table
@@ -0,0 +1 @@
+../../../common/field_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/input.nml b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/input.nml
new file mode 100644
index 0000000..7b69203
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/input.nml
@@ -0,0 +1,140 @@
+ &MOM_input_nml
+        output_directory = './',
+        input_filename = 'r'
+        restart_input_dir = 'INPUT/',
+        restart_output_dir = 'RESTART/',
+        parameter_filename = 'MOM_input',
+                             'MOM_override' /
+
+ &SIS_input_nml
+        output_directory = './',
+        input_filename = 'r'
+        restart_input_dir = 'INPUT/',
+        restart_output_dir = 'RESTART/',
+        parameter_filename = 'SIS_input',
+                             'SIS_override' /
+
+ &diag_manager_nml
+         max_output_fields=1000
+         max_input_fields=1000
+         max_num_axis_sets=1000
+	 flush_nc_files=.true.
+         max_files=1000
+         max_axes=2000
+ /
+
+ &coupler_nml
+            months = 0,
+            days   = 60,
+            current_date = 1,1,1,0,0,0,
+            hours = 0,
+            minutes =0, 
+            seconds = 0
+            calendar = 'NOLEAP',
+            dt_cpld  = 10.0,
+            dt_atmos = 10.0,
+            do_atmos = .false.,
+            do_land = .false.,
+            do_ice = .true.,
+            do_ocean = .true.,
+            atmos_npes = 0,
+            ocean_npes = 0,
+            concurrent = .false.
+            use_lag_fluxes=.false. /
+
+
+ &icebergs_nml
+    verbose=.false.,
+    verbose_hrs=240,
+    traj_sample_hrs=24000,
+    ignore_ij_restart=.true.
+    halo=2,
+    save_short_traj=.true.
+    debug=.false.,
+    really_debug=.false.,
+    use_slow_find=.true.,
+    add_weight_to_ocean=.true.,
+    passive_mode=.false.,
+    Static_icebergs=.False.,
+    ignore_missing_restart_bergs=.false.,
+    generate_test_icebergs=.false.,
+    speed_limit=0.,
+    use_roundoff_fix=.true.,
+    make_calving_reproduce=.false.,
+    Runge_not_Verlet=.false.,
+    iceberg_bonds_on=.true.,
+    critical_interaction_damping_on=.true.,
+    use_new_predictive_corrective=.true.,
+    interactive_icebergs_on=.true.
+    halo_debugging=.false.
+    spring_coef=0.00001
+    distribution=0.0, 0.99, 0.0, 0.00, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11,
+    hexagonal_icebergs=.true.
+    allow_bergs_to_roll=.true.
+    set_melt_rates_to_zero=.false.
+    use_roundoff_fix=.false.
+    grid_is_latlon=.false.
+    grid_is_regular=.true.
+    initial_orientation=-0.
+    rotate_icebergs_for_mass_spreading=.false.
+    lat_ref=-75.0
+    u_override=0.00
+    v_override=0.00
+    override_iceberg_velocities=.false.
+    add_iceberg_thickness_to_SSH=.false.
+    max_bonds=6
+    Iceberg_melt_without_decay=.true.
+    melt_icebergs_as_ice_shelf=.true.
+    Use_three_equation_model=.true.
+    find_melt_using_spread_mass=.true.
+    use_mixed_layer_salinity_for_thermo=.true.
+    pass_fields_to_ocean_model=.true.
+    rho_bergs=918.0
+    utide_icebergs=0.01
+    ustar_icebergs_bg=0.000
+    cdrag_icebergs =0.0025
+    const_gamma=.false.
+    Gamma_T_3EQ=0.22
+    ignore_traj=.False.
+    read_ocean_depth_from_file=.true.
+    apply_thickness_cutoff_to_bergs_melt=.true.
+    apply_thickness_cutoff_to_gridded_melt=.true.
+    melt_cutoff=10.
+    read_old_restarts=.false.
+    internal_bergs_for_drag=.true.
+    use_mixed_melting=.true.
+ &data_override_nml
+         /
+
+ &fms_io_nml
+         fms_netcdf_restart=.true.
+         threading_read='multi'
+ /
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC' /
+
+ &ice_albedo_nml
+      t_range = 10. /
+
+ &ice_model_nml
+           /
+
+ &monin_obukhov_nml
+            neutral = .true. /
+
+ &ocean_albedo_nml
+      ocean_albedo_option = 5 /
+
+ &sat_vapor_pres_nml
+      construct_table_wrt_liq = .true.,
+      construct_table_wrt_liq_and_ice = .true. /
+
+ &xgrid_nml
+            make_exchange_reproduce = .false.
+            interp_method = 'second_order' /
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/run_script.sh b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/run_script.sh
new file mode 120000
index 0000000..2a081b9
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/run_script.sh
@@ -0,0 +1 @@
+../../../common/run_script.sh
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/submit_to_queue b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/submit_to_queue
new file mode 100644
index 0000000..cc5b649
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/submit_to_queue
@@ -0,0 +1,25 @@
+#!/bin/csh -f
+#PBS -r y                                                              #This job is restartable
+#PBS -j oe                                                             #STDOUT and STDERR are in the same file, specified below in the '-o' option
+#PBS -q batch                                                          #Do not change this - it tells your job where to run
+#PBS -S /bin/sh                                                        #Do not change this - it keeps your job from issuing a false alarm
+#PBS -E                                                                #Do not change this - it gives your job more and more useful Moab environment variables
+#PBS -N  Bergs_Bond_layer                                              #Job Name:             You may want to change this to reflect your job's purpose or relation to an experiment
+#PBS -l partition=c3
+#PBS -l size=4                                                        #You will need to change this to reflect your job's core requirements - 24 is the current core increment.
+#PBS -l walltime=16:00:00                                              #You MUST change this to reflect your job's expected run time, including copy time
+#PBS -m bea                                                            #Email options: You may want to change this to reduce your incoming email stream
+
+######################################################################################################################
+#
+#  Gaea c1ms batch skeleton version 0.9
+#  
+#  0.9 - Initial version - 20110906 - Daniel Gall - Daniel.Gall@noaa.gov
+#
+######################################################################################################################
+
+#Source the system initialization scripts (but not the user's so as to avoid interactive settings that can poison us)
+source /etc/csh.cshrc
+
+#Run the experiment
+aprun -n 128 ../../../../../build/intel/ice_ocean_SIS2/repro/MOM6
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Collapse/README b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Collapse/README
new file mode 100644
index 0000000..ac458b8
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Collapse/README
@@ -0,0 +1,7 @@
+A tabular icebergs breaks away from the ice shelf. Smaller pieces also break away, which allows the tabular iceberg to move more easily. The tabular icebergs is bonded together by numeric bonds. Icebergs are allowed to evolve freely
+
+Works best when started from restart file created by Static_berg simulation.
+
+Experimental setup is exactly the same as Moving_berg_Bond simulation, except that when icebergs.res is created, use the command line flag:
+./initialize_bergs_in_pattern.py -Make_icebergs_non_static_later=True
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Collapse/input.nml b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Collapse/input.nml
new file mode 100644
index 0000000..7b69203
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Collapse/input.nml
@@ -0,0 +1,140 @@
+ &MOM_input_nml
+        output_directory = './',
+        input_filename = 'r'
+        restart_input_dir = 'INPUT/',
+        restart_output_dir = 'RESTART/',
+        parameter_filename = 'MOM_input',
+                             'MOM_override' /
+
+ &SIS_input_nml
+        output_directory = './',
+        input_filename = 'r'
+        restart_input_dir = 'INPUT/',
+        restart_output_dir = 'RESTART/',
+        parameter_filename = 'SIS_input',
+                             'SIS_override' /
+
+ &diag_manager_nml
+         max_output_fields=1000
+         max_input_fields=1000
+         max_num_axis_sets=1000
+	 flush_nc_files=.true.
+         max_files=1000
+         max_axes=2000
+ /
+
+ &coupler_nml
+            months = 0,
+            days   = 60,
+            current_date = 1,1,1,0,0,0,
+            hours = 0,
+            minutes =0, 
+            seconds = 0
+            calendar = 'NOLEAP',
+            dt_cpld  = 10.0,
+            dt_atmos = 10.0,
+            do_atmos = .false.,
+            do_land = .false.,
+            do_ice = .true.,
+            do_ocean = .true.,
+            atmos_npes = 0,
+            ocean_npes = 0,
+            concurrent = .false.
+            use_lag_fluxes=.false. /
+
+
+ &icebergs_nml
+    verbose=.false.,
+    verbose_hrs=240,
+    traj_sample_hrs=24000,
+    ignore_ij_restart=.true.
+    halo=2,
+    save_short_traj=.true.
+    debug=.false.,
+    really_debug=.false.,
+    use_slow_find=.true.,
+    add_weight_to_ocean=.true.,
+    passive_mode=.false.,
+    Static_icebergs=.False.,
+    ignore_missing_restart_bergs=.false.,
+    generate_test_icebergs=.false.,
+    speed_limit=0.,
+    use_roundoff_fix=.true.,
+    make_calving_reproduce=.false.,
+    Runge_not_Verlet=.false.,
+    iceberg_bonds_on=.true.,
+    critical_interaction_damping_on=.true.,
+    use_new_predictive_corrective=.true.,
+    interactive_icebergs_on=.true.
+    halo_debugging=.false.
+    spring_coef=0.00001
+    distribution=0.0, 0.99, 0.0, 0.00, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11,
+    hexagonal_icebergs=.true.
+    allow_bergs_to_roll=.true.
+    set_melt_rates_to_zero=.false.
+    use_roundoff_fix=.false.
+    grid_is_latlon=.false.
+    grid_is_regular=.true.
+    initial_orientation=-0.
+    rotate_icebergs_for_mass_spreading=.false.
+    lat_ref=-75.0
+    u_override=0.00
+    v_override=0.00
+    override_iceberg_velocities=.false.
+    add_iceberg_thickness_to_SSH=.false.
+    max_bonds=6
+    Iceberg_melt_without_decay=.true.
+    melt_icebergs_as_ice_shelf=.true.
+    Use_three_equation_model=.true.
+    find_melt_using_spread_mass=.true.
+    use_mixed_layer_salinity_for_thermo=.true.
+    pass_fields_to_ocean_model=.true.
+    rho_bergs=918.0
+    utide_icebergs=0.01
+    ustar_icebergs_bg=0.000
+    cdrag_icebergs =0.0025
+    const_gamma=.false.
+    Gamma_T_3EQ=0.22
+    ignore_traj=.False.
+    read_ocean_depth_from_file=.true.
+    apply_thickness_cutoff_to_bergs_melt=.true.
+    apply_thickness_cutoff_to_gridded_melt=.true.
+    melt_cutoff=10.
+    read_old_restarts=.false.
+    internal_bergs_for_drag=.true.
+    use_mixed_melting=.true.
+ &data_override_nml
+         /
+
+ &fms_io_nml
+         fms_netcdf_restart=.true.
+         threading_read='multi'
+ /
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC' /
+
+ &ice_albedo_nml
+      t_range = 10. /
+
+ &ice_model_nml
+           /
+
+ &monin_obukhov_nml
+            neutral = .true. /
+
+ &ocean_albedo_nml
+      ocean_albedo_option = 5 /
+
+ &sat_vapor_pres_nml
+      construct_table_wrt_liq = .true.,
+      construct_table_wrt_liq_and_ice = .true. /
+
+ &xgrid_nml
+            make_exchange_reproduce = .false.
+            interp_method = 'second_order' /
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/MOM_input b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/MOM_input
new file mode 120000
index 0000000..a756962
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/MOM_input
@@ -0,0 +1 @@
+../../../common/MOM_input
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/MOM_override b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/MOM_override
new file mode 100644
index 0000000..1fec204
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/MOM_override
@@ -0,0 +1,71 @@
+! Blank file in which we can put "overrides" for parameters
+
+!TPY params
+#override NK = 72
+#override NKML = 4
+
+! TIME STEP
+#override DT = 10
+#override DT_THERM = 10
+#override DT_FORCING = 10
+
+! MIXING
+#override SMAGORINSKY_KH = False
+#override BIHARMONIC = False
+#override KH = 6.0  ! back. horiz. visc.
+#override KHTR = 1.0    ! back. horiz. diff.
+#override KD = 5.0E-5     ! back. diapycnal diff.
+#override KV = 1.0E-3     ! back. diapycnal visc.
+
+!WARM IC
+#override ISOMIP_T_SUR = -1.9
+#override ISOMIP_S_SUR = 33.8
+#override ISOMIP_T_BOT = 1.0
+#override ISOMIP_S_BOT = 34.7
+
+! ice shelf
+#override ICE_SHELF = False                !   [Boolean] default = False
+#override SHELF_THERMO = True
+#override SHELF_THREE_EQN = True
+#override SHELF_3EQ_GAMMA = False
+#override UTIDE = 0.01
+!SHELF_S_ROOT = True
+!#override USE_HMIX_SFC_PROP = True
+!#override HMIX_SFC_PROP = 10.
+
+! FRAZIL  - making sure sea ice does not form
+#override FRAZIL = False
+#override PRESSURE_DEPENDENT_FRAZIL = False
+
+! MIXED LAYER
+#override BULKMIXEDLAYER = True
+#override BULK_RI_ML = 0.25
+#override MIXEDLAYER_RESTRAT = True
+#override HMIX_MIN = 2.0
+!#override KV_TBL_MIN = 1.0E-2
+#override HTBL_SHELF_MIN = 2.0
+#override BOUND_SALINITY = True
+ 
+! SHEAR MIXING
+#override USE_JACKSON_PARAM = True
+#override RINO_CRIT = 0.25
+!#override KD_KAPPA_SHEAR_0 = 1.0E-2
+
+! SPONGE
+#override SPONGE = True
+ISOMIP_SPONGE_FILE = "3D_LAYER_WARM_TPY_IC.nc"
+#override ISOMIP_TNUDG = 0.1
+!#override ISOMIP_SPONGE_TEMP_OFFSET=0.1
+
+
+! PASSIVE TRACERS
+USE_ISOMIP_TRACER = False
+
+! Simulation time
+#override DAYMAX = 730
+
+!#override FIT_SALINITY = False
+
+!Passing Iceberg field to ocean
+ICEBERGS_APPLY_RIGID_BOUNDARY=True !Different boundary condition is used under ice shelves
+ALLOW_ICEBERG_FLUX_DIAGNOSTICS=True
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/README b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/README
new file mode 100644
index 0000000..b4eb12b
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/README
@@ -0,0 +1,3 @@
+A piece of the ice shelf breaks off. The elements are not bonded together, so they move freely away. However, they do interact with one another.
+
+Works best when started from restart file created by Static_berg simulation.
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/SIS_input b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/SIS_input
new file mode 120000
index 0000000..ad3cd99
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/SIS_input
@@ -0,0 +1 @@
+../../../common/SIS_input
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/SIS_override b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/SIS_override
new file mode 100644
index 0000000..605ca84
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/SIS_override
@@ -0,0 +1,9 @@
+# Blank file in which we can put "overrides" for parameters
+DO_ICEBERGS =True              !   If true, use the icebergs module.
+
+!Time Stepping
+#override DT_FORCING = 10.0              !   [s] default = 0.0
+#override DT_RHEOLOGY = 10.0             ! The sub-cycling time step, in s, for iterating
+#override DT_ICE_DYNAMICS = 10.0 
+
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/clean_MOM.sh b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/clean_MOM.sh
new file mode 120000
index 0000000..c5370af
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/clean_MOM.sh
@@ -0,0 +1 @@
+../../../common/clean_MOM.sh
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/data_table b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/data_table
new file mode 120000
index 0000000..5b82b3c
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/data_table
@@ -0,0 +1 @@
+../../../common/data_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/diag_table b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/diag_table
new file mode 120000
index 0000000..cff65fe
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/diag_table
@@ -0,0 +1 @@
+../../../common/diag_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/field_table b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/field_table
new file mode 120000
index 0000000..b5ea991
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/field_table
@@ -0,0 +1 @@
+../../../common/field_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/input.nml b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/input.nml
new file mode 100644
index 0000000..7424ccd
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/input.nml
@@ -0,0 +1,140 @@
+ &MOM_input_nml
+        output_directory = './',
+        input_filename = 'r'
+        restart_input_dir = 'INPUT/',
+        restart_output_dir = 'RESTART/',
+        parameter_filename = 'MOM_input',
+                             'MOM_override' /
+
+ &SIS_input_nml
+        output_directory = './',
+        input_filename = 'r'
+        restart_input_dir = 'INPUT/',
+        restart_output_dir = 'RESTART/',
+        parameter_filename = 'SIS_input',
+                             'SIS_override' /
+
+ &diag_manager_nml
+         max_output_fields=1000
+         max_input_fields=1000
+         max_num_axis_sets=1000
+	 flush_nc_files=.true.
+         max_files=1000
+         max_axes=2000
+ /
+
+ &coupler_nml
+            months = 0,
+            days   = 60,
+            current_date = 1,1,1,0,0,0,
+            hours = 0,
+            minutes =0, 
+            seconds = 0
+            calendar = 'NOLEAP',
+            dt_cpld  = 10.0,
+            dt_atmos = 10.0,
+            do_atmos = .false.,
+            do_land = .false.,
+            do_ice = .true.,
+            do_ocean = .true.,
+            atmos_npes = 0,
+            ocean_npes = 0,
+            concurrent = .false.
+            use_lag_fluxes=.false. /
+
+
+ &icebergs_nml
+    verbose=.false.,
+    verbose_hrs=240,
+    traj_sample_hrs=24000,
+    ignore_ij_restart=.true.
+    halo=2,
+    save_short_traj=.true.
+    debug=.false.,
+    really_debug=.false.,
+    use_slow_find=.true.,
+    add_weight_to_ocean=.true.,
+    passive_mode=.false.,
+    Static_icebergs=.False.,
+    ignore_missing_restart_bergs=.false.,
+    generate_test_icebergs=.false.,
+    speed_limit=0.,
+    use_roundoff_fix=.true.,
+    make_calving_reproduce=.false.,
+    Runge_not_Verlet=.false.,
+    iceberg_bonds_on=.false.,
+    critical_interaction_damping_on=.true.,
+    use_new_predictive_corrective=.true.,
+    interactive_icebergs_on=.true.
+    halo_debugging=.false.
+    spring_coef=0.00001
+    distribution=0.0, 0.99, 0.0, 0.00, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11,
+    hexagonal_icebergs=.true.
+    allow_bergs_to_roll=.true.
+    set_melt_rates_to_zero=.false.
+    use_roundoff_fix=.false.
+    grid_is_latlon=.false.
+    grid_is_regular=.true.
+    initial_orientation=-0.
+    rotate_icebergs_for_mass_spreading=.false.
+    lat_ref=-75.0
+    u_override=0.00
+    v_override=0.00
+    override_iceberg_velocities=.false.
+    add_iceberg_thickness_to_SSH=.false.
+    max_bonds=6
+    Iceberg_melt_without_decay=.true.
+    melt_icebergs_as_ice_shelf=.true.
+    Use_three_equation_model=.true.
+    find_melt_using_spread_mass=.true.
+    use_mixed_layer_salinity_for_thermo=.true.
+    pass_fields_to_ocean_model=.true.
+    rho_bergs=918.0
+    utide_icebergs=0.01
+    ustar_icebergs_bg=0.000
+    cdrag_icebergs =0.0025
+    const_gamma=.false.
+    Gamma_T_3EQ=0.22
+    ignore_traj=.False.
+    read_ocean_depth_from_file=.true.
+    apply_thickness_cutoff_to_bergs_melt=.true.
+    apply_thickness_cutoff_to_gridded_melt=.true.
+    melt_cutoff=10.
+    read_old_restarts=.false.
+    internal_bergs_for_drag=.true.
+    use_mixed_melting=.true.
+ &data_override_nml
+         /
+
+ &fms_io_nml
+         fms_netcdf_restart=.true.
+         threading_read='multi'
+ /
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC' /
+
+ &ice_albedo_nml
+      t_range = 10. /
+
+ &ice_model_nml
+           /
+
+ &monin_obukhov_nml
+            neutral = .true. /
+
+ &ocean_albedo_nml
+      ocean_albedo_option = 5 /
+
+ &sat_vapor_pres_nml
+      construct_table_wrt_liq = .true.,
+      construct_table_wrt_liq_and_ice = .true. /
+
+ &xgrid_nml
+            make_exchange_reproduce = .false.
+            interp_method = 'second_order' /
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/run_script.sh b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/run_script.sh
new file mode 120000
index 0000000..2a081b9
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/run_script.sh
@@ -0,0 +1 @@
+../../../common/run_script.sh
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/submit_to_queue b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/submit_to_queue
new file mode 100644
index 0000000..4895e94
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/submit_to_queue
@@ -0,0 +1,25 @@
+#!/bin/csh -f
+#PBS -r y                                                              #This job is restartable
+#PBS -j oe                                                             #STDOUT and STDERR are in the same file, specified below in the '-o' option
+#PBS -q batch                                                          #Do not change this - it tells your job where to run
+#PBS -S /bin/sh                                                        #Do not change this - it keeps your job from issuing a false alarm
+#PBS -E                                                                #Do not change this - it gives your job more and more useful Moab environment variables
+#PBS -N  Bergs_drift_layer                                               #Job Name:             You may want to change this to reflect your job's purpose or relation to an experiment
+#PBS -l partition=c3
+#PBS -l size=4                                                        #You will need to change this to reflect your job's core requirements - 24 is the current core increment.
+#PBS -l walltime=16:00:00                                              #You MUST change this to reflect your job's expected run time, including copy time
+#PBS -m bea                                                            #Email options: You may want to change this to reduce your incoming email stream
+
+######################################################################################################################
+#
+#  Gaea c1ms batch skeleton version 0.9
+#  
+#  0.9 - Initial version - 20110906 - Daniel Gall - Daniel.Gall@noaa.gov
+#
+######################################################################################################################
+
+#Source the system initialization scripts (but not the user's so as to avoid interactive settings that can poison us)
+source /etc/csh.cshrc
+
+#Run the experiment
+aprun -n 128 ../../../../../build/intel/ice_ocean_SIS2/repro/MOM6
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/MOM_input b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/MOM_input
new file mode 120000
index 0000000..a756962
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/MOM_input
@@ -0,0 +1 @@
+../../../common/MOM_input
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/MOM_override b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/MOM_override
new file mode 100644
index 0000000..1fec204
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/MOM_override
@@ -0,0 +1,71 @@
+! Blank file in which we can put "overrides" for parameters
+
+!TPY params
+#override NK = 72
+#override NKML = 4
+
+! TIME STEP
+#override DT = 10
+#override DT_THERM = 10
+#override DT_FORCING = 10
+
+! MIXING
+#override SMAGORINSKY_KH = False
+#override BIHARMONIC = False
+#override KH = 6.0  ! back. horiz. visc.
+#override KHTR = 1.0    ! back. horiz. diff.
+#override KD = 5.0E-5     ! back. diapycnal diff.
+#override KV = 1.0E-3     ! back. diapycnal visc.
+
+!WARM IC
+#override ISOMIP_T_SUR = -1.9
+#override ISOMIP_S_SUR = 33.8
+#override ISOMIP_T_BOT = 1.0
+#override ISOMIP_S_BOT = 34.7
+
+! ice shelf
+#override ICE_SHELF = False                !   [Boolean] default = False
+#override SHELF_THERMO = True
+#override SHELF_THREE_EQN = True
+#override SHELF_3EQ_GAMMA = False
+#override UTIDE = 0.01
+!SHELF_S_ROOT = True
+!#override USE_HMIX_SFC_PROP = True
+!#override HMIX_SFC_PROP = 10.
+
+! FRAZIL  - making sure sea ice does not form
+#override FRAZIL = False
+#override PRESSURE_DEPENDENT_FRAZIL = False
+
+! MIXED LAYER
+#override BULKMIXEDLAYER = True
+#override BULK_RI_ML = 0.25
+#override MIXEDLAYER_RESTRAT = True
+#override HMIX_MIN = 2.0
+!#override KV_TBL_MIN = 1.0E-2
+#override HTBL_SHELF_MIN = 2.0
+#override BOUND_SALINITY = True
+ 
+! SHEAR MIXING
+#override USE_JACKSON_PARAM = True
+#override RINO_CRIT = 0.25
+!#override KD_KAPPA_SHEAR_0 = 1.0E-2
+
+! SPONGE
+#override SPONGE = True
+ISOMIP_SPONGE_FILE = "3D_LAYER_WARM_TPY_IC.nc"
+#override ISOMIP_TNUDG = 0.1
+!#override ISOMIP_SPONGE_TEMP_OFFSET=0.1
+
+
+! PASSIVE TRACERS
+USE_ISOMIP_TRACER = False
+
+! Simulation time
+#override DAYMAX = 730
+
+!#override FIT_SALINITY = False
+
+!Passing Iceberg field to ocean
+ICEBERGS_APPLY_RIGID_BOUNDARY=True !Different boundary condition is used under ice shelves
+ALLOW_ICEBERG_FLUX_DIAGNOSTICS=True
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/README b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/README
new file mode 100644
index 0000000..fa2bc28
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/README
@@ -0,0 +1,5 @@
+A tabular iceberg breaks away from the ice shelf. The non-static icebergs move away from the ice shelf at a prescribed velocity. The time step is quite small (10s) in order to resolve ocean motions
+
+Works best when started from restart file created by Static_berg simulation.
+
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/SIS_input b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/SIS_input
new file mode 120000
index 0000000..ad3cd99
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/SIS_input
@@ -0,0 +1 @@
+../../../common/SIS_input
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/SIS_override b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/SIS_override
new file mode 100644
index 0000000..605ca84
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/SIS_override
@@ -0,0 +1,9 @@
+# Blank file in which we can put "overrides" for parameters
+DO_ICEBERGS =True              !   If true, use the icebergs module.
+
+!Time Stepping
+#override DT_FORCING = 10.0              !   [s] default = 0.0
+#override DT_RHEOLOGY = 10.0             ! The sub-cycling time step, in s, for iterating
+#override DT_ICE_DYNAMICS = 10.0 
+
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/clean_MOM.sh b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/clean_MOM.sh
new file mode 120000
index 0000000..c5370af
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/clean_MOM.sh
@@ -0,0 +1 @@
+../../../common/clean_MOM.sh
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/data_table b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/data_table
new file mode 120000
index 0000000..5b82b3c
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/data_table
@@ -0,0 +1 @@
+../../../common/data_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/diag_table b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/diag_table
new file mode 120000
index 0000000..cff65fe
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/diag_table
@@ -0,0 +1 @@
+../../../common/diag_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/field_table b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/field_table
new file mode 120000
index 0000000..b5ea991
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/field_table
@@ -0,0 +1 @@
+../../../common/field_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/input.nml b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/input.nml
new file mode 100644
index 0000000..97afa25
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/input.nml
@@ -0,0 +1,140 @@
+ &MOM_input_nml
+        output_directory = './',
+        input_filename = 'r'
+        restart_input_dir = 'INPUT/',
+        restart_output_dir = 'RESTART/',
+        parameter_filename = 'MOM_input',
+                             'MOM_override' /
+
+ &SIS_input_nml
+        output_directory = './',
+        input_filename = 'r'
+        restart_input_dir = 'INPUT/',
+        restart_output_dir = 'RESTART/',
+        parameter_filename = 'SIS_input',
+                             'SIS_override' /
+
+ &diag_manager_nml
+         max_output_fields=1000
+         max_input_fields=1000
+         max_num_axis_sets=1000
+	 flush_nc_files=.true.
+         max_files=1000
+         max_axes=2000
+ /
+
+ &coupler_nml
+            months = 0,
+            days   = 60,
+            current_date = 1,1,1,0,0,0,
+            hours = 0,
+            minutes =0, 
+            seconds = 0
+            calendar = 'NOLEAP',
+            dt_cpld  = 10.0,
+            dt_atmos = 10.0,
+            do_atmos = .false.,
+            do_land = .false.,
+            do_ice = .true.,
+            do_ocean = .true.,
+            atmos_npes = 0,
+            ocean_npes = 0,
+            concurrent = .false.
+            use_lag_fluxes=.false. /
+
+
+ &icebergs_nml
+    verbose=.false.,
+    verbose_hrs=240,
+    traj_sample_hrs=24000,
+    ignore_ij_restart=.true.
+    halo=2,
+    save_short_traj=.true.
+    debug=.false.,
+    really_debug=.false.,
+    use_slow_find=.true.,
+    add_weight_to_ocean=.true.,
+    passive_mode=.false.,
+    Static_icebergs=.False.,
+    ignore_missing_restart_bergs=.false.,
+    generate_test_icebergs=.false.,
+    speed_limit=0.,
+    use_roundoff_fix=.true.,
+    make_calving_reproduce=.false.,
+    Runge_not_Verlet=.false.,
+    iceberg_bonds_on=.false.,
+    critical_interaction_damping_on=.true.,
+    use_new_predictive_corrective=.true.,
+    interactive_icebergs_on=.false.
+    halo_debugging=.false.
+    spring_coef=0.00001
+    distribution=0.0, 0.99, 0.0, 0.00, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11,
+    hexagonal_icebergs=.true.
+    allow_bergs_to_roll=.true.
+    set_melt_rates_to_zero=.false.
+    use_roundoff_fix=.false.
+    grid_is_latlon=.false.
+    grid_is_regular=.true.
+    initial_orientation=-0.
+    rotate_icebergs_for_mass_spreading=.false.
+    lat_ref=-75.0
+    u_override=0.01
+    v_override=0.00
+    override_iceberg_velocities=.true.
+    add_iceberg_thickness_to_SSH=.false.
+    max_bonds=6
+    Iceberg_melt_without_decay=.true.
+    melt_icebergs_as_ice_shelf=.true.
+    Use_three_equation_model=.true.
+    find_melt_using_spread_mass=.true.
+    use_mixed_layer_salinity_for_thermo=.true.
+    pass_fields_to_ocean_model=.true.
+    rho_bergs=918.0
+    utide_icebergs=0.01
+    ustar_icebergs_bg=0.000
+    cdrag_icebergs =0.0025
+    const_gamma=.false.
+    Gamma_T_3EQ=0.22
+    ignore_traj=.False.
+    read_ocean_depth_from_file=.true.
+    apply_thickness_cutoff_to_bergs_melt=.true.
+    apply_thickness_cutoff_to_gridded_melt=.true.
+    melt_cutoff=10.
+    read_old_restarts=.false.
+    internal_bergs_for_drag=.true.
+    use_mixed_melting=.true.
+ &data_override_nml
+         /
+
+ &fms_io_nml
+         fms_netcdf_restart=.true.
+         threading_read='multi'
+ /
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC' /
+
+ &ice_albedo_nml
+      t_range = 10. /
+
+ &ice_model_nml
+           /
+
+ &monin_obukhov_nml
+            neutral = .true. /
+
+ &ocean_albedo_nml
+      ocean_albedo_option = 5 /
+
+ &sat_vapor_pres_nml
+      construct_table_wrt_liq = .true.,
+      construct_table_wrt_liq_and_ice = .true. /
+
+ &xgrid_nml
+            make_exchange_reproduce = .false.
+            interp_method = 'second_order' /
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/run_script.sh b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/run_script.sh
new file mode 120000
index 0000000..2a081b9
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/run_script.sh
@@ -0,0 +1 @@
+../../../common/run_script.sh
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/submit_to_queue b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/submit_to_queue
new file mode 100644
index 0000000..2e508c9
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/submit_to_queue
@@ -0,0 +1,25 @@
+#!/bin/csh -f
+#PBS -r y                                                              #This job is restartable
+#PBS -j oe                                                             #STDOUT and STDERR are in the same file, specified below in the '-o' option
+#PBS -q batch                                                          #Do not change this - it tells your job where to run
+#PBS -S /bin/sh                                                        #Do not change this - it keeps your job from issuing a false alarm
+#PBS -E                                                                #Do not change this - it gives your job more and more useful Moab environment variables
+#PBS -N  Bergs_fixed_layer                                               #Job Name:             You may want to change this to reflect your job's purpose or relation to an experiment
+#PBS -l partition=c3
+#PBS -l size=4                                                        #You will need to change this to reflect your job's core requirements - 24 is the current core increment.
+#PBS -l walltime=16:00:00                                              #You MUST change this to reflect your job's expected run time, including copy time
+#PBS -m bea                                                            #Email options: You may want to change this to reduce your incoming email stream
+
+######################################################################################################################
+#
+#  Gaea c1ms batch skeleton version 0.9
+#  
+#  0.9 - Initial version - 20110906 - Daniel Gall - Daniel.Gall@noaa.gov
+#
+######################################################################################################################
+
+#Source the system initialization scripts (but not the user's so as to avoid interactive settings that can poison us)
+source /etc/csh.cshrc
+
+#Run the experiment
+aprun -n 128 ../../../../../build/intel/ice_ocean_SIS2/repro/MOM6
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/MOM_input b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/MOM_input
new file mode 120000
index 0000000..a756962
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/MOM_input
@@ -0,0 +1 @@
+../../../common/MOM_input
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/MOM_override b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/MOM_override
new file mode 100644
index 0000000..5da8e97
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/MOM_override
@@ -0,0 +1,73 @@
+! Blank file in which we can put "overrides" for parameters
+
+!TPY params
+#override NK = 72
+#override NKML = 4
+
+! TIME STEP
+!#override DT = 720
+!#override DT_THERM = 720
+#override DT = 360
+#override DT_THERM = 360
+#override DT_FORCING = 360
+
+! MIXING
+#override SMAGORINSKY_KH = False
+#override BIHARMONIC = False
+#override KH = 6.0  ! back. horiz. visc.
+#override KHTR = 1.0    ! back. horiz. diff.
+#override KD = 5.0E-5     ! back. diapycnal diff.
+#override KV = 1.0E-3     ! back. diapycnal visc.
+
+!WARM IC
+#override ISOMIP_T_SUR = -1.9
+#override ISOMIP_S_SUR = 33.8
+#override ISOMIP_T_BOT = 1.0
+#override ISOMIP_S_BOT = 34.7
+
+! ice shelf
+#override ICE_SHELF = False                !   [Boolean] default = False
+#override SHELF_THERMO = True
+#override SHELF_THREE_EQN = True
+#override SHELF_3EQ_GAMMA = False
+#override UTIDE = 0.01
+!SHELF_S_ROOT = True
+!#override USE_HMIX_SFC_PROP = True
+!#override HMIX_SFC_PROP = 10.
+
+! FRAZIL  - making sure sea ice does not form
+#override FRAZIL = False
+#override PRESSURE_DEPENDENT_FRAZIL = False
+
+! MIXED LAYER
+#override BULKMIXEDLAYER = True
+#override BULK_RI_ML = 0.25
+#override MIXEDLAYER_RESTRAT = True
+#override HMIX_MIN = 2.0
+!#override KV_TBL_MIN = 1.0E-2
+#override HTBL_SHELF_MIN = 2.0
+#override BOUND_SALINITY = True
+ 
+! SHEAR MIXING
+#override USE_JACKSON_PARAM = True
+#override RINO_CRIT = 0.25
+!#override KD_KAPPA_SHEAR_0 = 1.0E-2
+
+! SPONGE
+#override SPONGE = True
+ISOMIP_SPONGE_FILE = "3D_LAYER_WARM_TPY_IC.nc"
+#override ISOMIP_TNUDG = 0.1
+!#override ISOMIP_SPONGE_TEMP_OFFSET=0.1
+
+
+! PASSIVE TRACERS
+USE_ISOMIP_TRACER = False
+
+! Simulation time
+#override DAYMAX = 730
+
+!#override FIT_SALINITY = False
+
+!Passing Iceberg field to ocean
+ICEBERGS_APPLY_RIGID_BOUNDARY=True !Different boundary condition is used under ice shelves
+ALLOW_ICEBERG_FLUX_DIAGNOSTICS=True
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/README b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/README
new file mode 100644
index 0000000..c042733
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/README
@@ -0,0 +1 @@
+Ice shelf does not move. Shelf melts using three equation model.
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/SIS_input b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/SIS_input
new file mode 120000
index 0000000..ad3cd99
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/SIS_input
@@ -0,0 +1 @@
+../../../common/SIS_input
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/SIS_override b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/SIS_override
new file mode 100644
index 0000000..fc641d7
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/SIS_override
@@ -0,0 +1,8 @@
+# Blank file in which we can put "overrides" for parameters
+DO_ICEBERGS =True              !   If true, use the icebergs module.
+
+!Time Stepping
+!#override DT_FORCING = 10.0              !   [s] default = 0.0
+!#override DT_RHEOLOGY = 10.0             ! The sub-cycling time step, in s, for iterating
+
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/clean_MOM.sh b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/clean_MOM.sh
new file mode 120000
index 0000000..c5370af
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/clean_MOM.sh
@@ -0,0 +1 @@
+../../../common/clean_MOM.sh
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/data_table b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/data_table
new file mode 120000
index 0000000..5b82b3c
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/data_table
@@ -0,0 +1 @@
+../../../common/data_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/diag_table b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/diag_table
new file mode 120000
index 0000000..cff65fe
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/diag_table
@@ -0,0 +1 @@
+../../../common/diag_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/field_table b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/field_table
new file mode 120000
index 0000000..b5ea991
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/field_table
@@ -0,0 +1 @@
+../../../common/field_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/input.nml b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/input.nml
new file mode 100644
index 0000000..3854fd4
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/input.nml
@@ -0,0 +1,140 @@
+ &MOM_input_nml
+        output_directory = './',
+        input_filename = 'r'
+        restart_input_dir = 'INPUT/',
+        restart_output_dir = 'RESTART/',
+        parameter_filename = 'MOM_input',
+                             'MOM_override' /
+
+ &SIS_input_nml
+        output_directory = './',
+        input_filename = 'r'
+        restart_input_dir = 'INPUT/',
+        restart_output_dir = 'RESTART/',
+        parameter_filename = 'SIS_input',
+                             'SIS_override' /
+
+ &diag_manager_nml
+         max_output_fields=1000
+         max_input_fields=1000
+         max_num_axis_sets=1000
+	 flush_nc_files=.true.
+         max_files=1000
+         max_axes=2000
+ /
+
+ &coupler_nml
+            months = 60,
+            days   = 0,
+            current_date = 1,1,1,0,0,0,
+            hours = 0,
+            minutes =0, 
+            seconds = 0
+            calendar = 'NOLEAP',
+            dt_cpld  = 360.0,
+            dt_atmos = 360.0,
+            do_atmos = .false.,
+            do_land = .false.,
+            do_ice = .true.,
+            do_ocean = .true.,
+            atmos_npes = 0,
+            ocean_npes = 0,
+            concurrent = .false.
+            use_lag_fluxes=.false. /
+
+
+ &icebergs_nml
+    verbose=.false.,
+    verbose_hrs=240,
+    traj_sample_hrs=24000,
+    ignore_ij_restart=.true.
+    halo=2,
+    save_short_traj=.true.
+    debug=.false.,
+    really_debug=.false.,
+    use_slow_find=.true.,
+    add_weight_to_ocean=.true.,
+    passive_mode=.false.,
+    Static_icebergs=.True.,
+    ignore_missing_restart_bergs=.false.,
+    generate_test_icebergs=.false.,
+    speed_limit=0.,
+    use_roundoff_fix=.true.,
+    make_calving_reproduce=.false.,
+    Runge_not_Verlet=.false.,
+    iceberg_bonds_on=.false.,
+    critical_interaction_damping_on=.true.,
+    use_new_predictive_corrective=.true.,
+    interactive_icebergs_on=.false.
+    halo_debugging=.false.
+    spring_coef=0.00001
+    distribution=0.0, 0.99, 0.0, 0.00, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11,
+    hexagonal_icebergs=.true.
+    allow_bergs_to_roll=.true.
+    set_melt_rates_to_zero=.false.
+    use_roundoff_fix=.false.
+    grid_is_latlon=.false.
+    grid_is_regular=.true.
+    initial_orientation=-0.
+    rotate_icebergs_for_mass_spreading=.false.
+    lat_ref=-75.0
+    u_override=0.00
+    v_override=0.00
+    override_iceberg_velocities=.false.
+    add_iceberg_thickness_to_SSH=.false.
+    max_bonds=6
+    Iceberg_melt_without_decay=.true.
+    melt_icebergs_as_ice_shelf=.true.
+    Use_three_equation_model=.true.
+    find_melt_using_spread_mass=.true.
+    use_mixed_layer_salinity_for_thermo=.true.
+    pass_fields_to_ocean_model=.true.
+    rho_bergs=918.0
+    utide_icebergs=0.01
+    ustar_icebergs_bg=0.000
+    cdrag_icebergs =0.0025
+    const_gamma=.false.
+    Gamma_T_3EQ=0.22
+    ignore_traj=.False.
+    read_ocean_depth_from_file=.true.
+    apply_thickness_cutoff_to_bergs_melt=.true.
+    apply_thickness_cutoff_to_gridded_melt=.true.
+    melt_cutoff=10.
+    read_old_restarts=.false.
+    internal_bergs_for_drag=.true.
+    use_mixed_melting=.true.
+ &data_override_nml
+         /
+
+ &fms_io_nml
+         fms_netcdf_restart=.true.
+         threading_read='multi'
+ /
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC' /
+
+ &ice_albedo_nml
+      t_range = 10. /
+
+ &ice_model_nml
+           /
+
+ &monin_obukhov_nml
+            neutral = .true. /
+
+ &ocean_albedo_nml
+      ocean_albedo_option = 5 /
+
+ &sat_vapor_pres_nml
+      construct_table_wrt_liq = .true.,
+      construct_table_wrt_liq_and_ice = .true. /
+
+ &xgrid_nml
+            make_exchange_reproduce = .false.
+            interp_method = 'second_order' /
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/run_script.sh b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/run_script.sh
new file mode 120000
index 0000000..2a081b9
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/run_script.sh
@@ -0,0 +1 @@
+../../../common/run_script.sh
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/submit_to_queue b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/submit_to_queue
new file mode 100644
index 0000000..d35f1b8
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/submit_to_queue
@@ -0,0 +1,25 @@
+#!/bin/csh -f
+#PBS -r y                                                              #This job is restartable
+#PBS -j oe                                                             #STDOUT and STDERR are in the same file, specified below in the '-o' option
+#PBS -q batch                                                          #Do not change this - it tells your job where to run
+#PBS -S /bin/sh                                                        #Do not change this - it keeps your job from issuing a false alarm
+#PBS -E                                                                #Do not change this - it gives your job more and more useful Moab environment variables
+#PBS -N  Bergs_Empty_Run                                               #Job Name:             You may want to change this to reflect your job's purpose or relation to an experiment
+#PBS -l partition=c3
+#PBS -l size=4                                                        #You will need to change this to reflect your job's core requirements - 24 is the current core increment.
+#PBS -l walltime=16:00:00                                              #You MUST change this to reflect your job's expected run time, including copy time
+#PBS -m bea                                                            #Email options: You may want to change this to reduce your incoming email stream
+
+######################################################################################################################
+#
+#  Gaea c1ms batch skeleton version 0.9
+#  
+#  0.9 - Initial version - 20110906 - Daniel Gall - Daniel.Gall@noaa.gov
+#
+######################################################################################################################
+
+#Source the system initialization scripts (but not the user's so as to avoid interactive settings that can poison us)
+source /etc/csh.cshrc
+
+#Run the experiment
+aprun -n 128 ../../../../../build/intel/ice_ocean_SIS2/repro/MOM6
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/MOM_input b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/MOM_input
new file mode 120000
index 0000000..a756962
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/MOM_input
@@ -0,0 +1 @@
+../../../common/MOM_input
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/MOM_override b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/MOM_override
new file mode 100644
index 0000000..cd50151
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/MOM_override
@@ -0,0 +1,91 @@
+! Blank file in which we can put "overrides" for parameters
+! z
+#override USE_REGRIDDING = True
+#override REGRIDDING_COORDINATE_MODE = "SIGMA_SHELF_ZSTAR" 
+#override INTERPOLATION_SCHEME = "PPM_H4"
+#override REMAPPING_SCHEME = "PPM_H4"
+
+
+!TPY params
+#override NK = 72
+#override NKML = 4
+
+! TIME STEP
+#override DT = 10
+#override DT_THERM = 10
+#override DT_FORCING = 10
+
+! MIXING
+#override SMAGORINSKY_KH = False
+#override BIHARMONIC = False
+#override KH = 6.0  ! back. horiz. visc.
+#override KHTR = 1.0    ! back. horiz. diff.
+#override KD = 5.0E-5     ! back. diapycnal diff.
+#override KV = 1.0E-3     ! back. diapycnal visc.
+
+!WARM IC
+#override ISOMIP_T_SUR = -1.9
+#override ISOMIP_S_SUR = 33.8
+#override ISOMIP_T_BOT = 1.0
+#override ISOMIP_S_BOT = 34.7
+
+! ice shelf
+#override ICE_SHELF = False                !   [Boolean] default = False
+#override SHELF_THERMO = TRUE
+#override SHELF_THREE_EQN = True
+#override SHELF_3EQ_GAMMA = False
+#override UTIDE = 0.01
+!SHELF_S_ROOT = True
+!#override USE_HMIX_SFC_PROP = True
+!#override HMIX_SFC_PROP = 10.
+
+! FRAZIL  - making sure sea ice does not form
+#override FRAZIL = False
+#override PRESSURE_DEPENDENT_FRAZIL = False
+
+! EPBL
+#override ENERGETICS_SFC_PBL = True       !   [Boolean] default = False
+                                ! If true, use an implied energetics planetary boundary
+                                ! layer scheme to determine the diffusivity and viscosity
+                                ! in the surface boundary layer.
+#override EPBL_IS_ADDITIVE = True         !   [Boolean] default = True
+                                ! If true, the diffusivity from ePBL is added to all
+                                ! other diffusivities. Otherwise, the larger of kappa-
+                                ! shear and ePBL diffusivities are used.
+#override USE_MLD_ITERATION = True        !   [Boolean] default = False
+                                ! A logical that determines whether or not to use the
+                                ! MLD to set the EPBL length scale.
+#override HTBL_SHELF_MIN = 10.0
+#override BOUND_SALINITY = True
+
+
+! SHEAR MIXING
+#override USE_JACKSON_PARAM = True
+#override RINO_CRIT = 0.25
+!#override KD_KAPPA_SHEAR_0 = 1.0E-2
+
+! SPONGE
+#override SPONGE = TRUE
+ISOMIP_SPONGE_FILE = "3D_LAYER_WARM_TPY_IC.nc"
+#override ISOMIP_TNUDG = 0.1
+#override ISOMIP_TNUDG = 0.1
+#override ISOMIP_S_SUR_SPONGE = 33.8      !   [not defined] default = 35.0
+                                ! Surface salinity in sponge layer.
+#override ISOMIP_S_BOT_SPONGE = 34.7      !   [not defined] default = 35.0
+                                ! Bottom salinity in sponge layer.
+#override ISOMIP_T_SUR_SPONGE = -1.9      !   [not defined] default = -1.9
+                                ! Surface temperature in sponge layer.
+#override ISOMIP_T_BOT_SPONGE = 1.0
+!#override ISOMIP_SPONGE_TEMP_OFFSET=0.1
+
+! PASSIVE TRACERS
+USE_ISOMIP_TRACER = False
+
+! Simulation time
+#override DAYMAX = 730
+
+!#override FIT_SALINITY = False
+
+!Passing Iceberg field to ocean
+ICEBERGS_APPLY_RIGID_BOUNDARY=True !Different boundary condition is used under ice shelves
+ALLOW_ICEBERG_FLUX_DIAGNOSTICS=True
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/SIS_input b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/SIS_input
new file mode 120000
index 0000000..ad3cd99
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/SIS_input
@@ -0,0 +1 @@
+../../../common/SIS_input
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/SIS_override b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/SIS_override
new file mode 100644
index 0000000..fc641d7
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/SIS_override
@@ -0,0 +1,8 @@
+# Blank file in which we can put "overrides" for parameters
+DO_ICEBERGS =True              !   If true, use the icebergs module.
+
+!Time Stepping
+!#override DT_FORCING = 10.0              !   [s] default = 0.0
+!#override DT_RHEOLOGY = 10.0             ! The sub-cycling time step, in s, for iterating
+
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/clean_MOM.sh b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/clean_MOM.sh
new file mode 120000
index 0000000..c5370af
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/clean_MOM.sh
@@ -0,0 +1 @@
+../../../common/clean_MOM.sh
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/data_table b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/data_table
new file mode 120000
index 0000000..5b82b3c
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/data_table
@@ -0,0 +1 @@
+../../../common/data_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/diag_table b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/diag_table
new file mode 120000
index 0000000..cff65fe
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/diag_table
@@ -0,0 +1 @@
+../../../common/diag_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/field_table b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/field_table
new file mode 120000
index 0000000..b5ea991
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/field_table
@@ -0,0 +1 @@
+../../../common/field_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/input.nml b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/input.nml
new file mode 100644
index 0000000..7b69203
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/input.nml
@@ -0,0 +1,140 @@
+ &MOM_input_nml
+        output_directory = './',
+        input_filename = 'r'
+        restart_input_dir = 'INPUT/',
+        restart_output_dir = 'RESTART/',
+        parameter_filename = 'MOM_input',
+                             'MOM_override' /
+
+ &SIS_input_nml
+        output_directory = './',
+        input_filename = 'r'
+        restart_input_dir = 'INPUT/',
+        restart_output_dir = 'RESTART/',
+        parameter_filename = 'SIS_input',
+                             'SIS_override' /
+
+ &diag_manager_nml
+         max_output_fields=1000
+         max_input_fields=1000
+         max_num_axis_sets=1000
+	 flush_nc_files=.true.
+         max_files=1000
+         max_axes=2000
+ /
+
+ &coupler_nml
+            months = 0,
+            days   = 60,
+            current_date = 1,1,1,0,0,0,
+            hours = 0,
+            minutes =0, 
+            seconds = 0
+            calendar = 'NOLEAP',
+            dt_cpld  = 10.0,
+            dt_atmos = 10.0,
+            do_atmos = .false.,
+            do_land = .false.,
+            do_ice = .true.,
+            do_ocean = .true.,
+            atmos_npes = 0,
+            ocean_npes = 0,
+            concurrent = .false.
+            use_lag_fluxes=.false. /
+
+
+ &icebergs_nml
+    verbose=.false.,
+    verbose_hrs=240,
+    traj_sample_hrs=24000,
+    ignore_ij_restart=.true.
+    halo=2,
+    save_short_traj=.true.
+    debug=.false.,
+    really_debug=.false.,
+    use_slow_find=.true.,
+    add_weight_to_ocean=.true.,
+    passive_mode=.false.,
+    Static_icebergs=.False.,
+    ignore_missing_restart_bergs=.false.,
+    generate_test_icebergs=.false.,
+    speed_limit=0.,
+    use_roundoff_fix=.true.,
+    make_calving_reproduce=.false.,
+    Runge_not_Verlet=.false.,
+    iceberg_bonds_on=.true.,
+    critical_interaction_damping_on=.true.,
+    use_new_predictive_corrective=.true.,
+    interactive_icebergs_on=.true.
+    halo_debugging=.false.
+    spring_coef=0.00001
+    distribution=0.0, 0.99, 0.0, 0.00, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11,
+    hexagonal_icebergs=.true.
+    allow_bergs_to_roll=.true.
+    set_melt_rates_to_zero=.false.
+    use_roundoff_fix=.false.
+    grid_is_latlon=.false.
+    grid_is_regular=.true.
+    initial_orientation=-0.
+    rotate_icebergs_for_mass_spreading=.false.
+    lat_ref=-75.0
+    u_override=0.00
+    v_override=0.00
+    override_iceberg_velocities=.false.
+    add_iceberg_thickness_to_SSH=.false.
+    max_bonds=6
+    Iceberg_melt_without_decay=.true.
+    melt_icebergs_as_ice_shelf=.true.
+    Use_three_equation_model=.true.
+    find_melt_using_spread_mass=.true.
+    use_mixed_layer_salinity_for_thermo=.true.
+    pass_fields_to_ocean_model=.true.
+    rho_bergs=918.0
+    utide_icebergs=0.01
+    ustar_icebergs_bg=0.000
+    cdrag_icebergs =0.0025
+    const_gamma=.false.
+    Gamma_T_3EQ=0.22
+    ignore_traj=.False.
+    read_ocean_depth_from_file=.true.
+    apply_thickness_cutoff_to_bergs_melt=.true.
+    apply_thickness_cutoff_to_gridded_melt=.true.
+    melt_cutoff=10.
+    read_old_restarts=.false.
+    internal_bergs_for_drag=.true.
+    use_mixed_melting=.true.
+ &data_override_nml
+         /
+
+ &fms_io_nml
+         fms_netcdf_restart=.true.
+         threading_read='multi'
+ /
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC' /
+
+ &ice_albedo_nml
+      t_range = 10. /
+
+ &ice_model_nml
+           /
+
+ &monin_obukhov_nml
+            neutral = .true. /
+
+ &ocean_albedo_nml
+      ocean_albedo_option = 5 /
+
+ &sat_vapor_pres_nml
+      construct_table_wrt_liq = .true.,
+      construct_table_wrt_liq_and_ice = .true. /
+
+ &xgrid_nml
+            make_exchange_reproduce = .false.
+            interp_method = 'second_order' /
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/run_script.sh b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/run_script.sh
new file mode 120000
index 0000000..2a081b9
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/run_script.sh
@@ -0,0 +1 @@
+../../../common/run_script.sh
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/submit_to_queue b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/submit_to_queue
new file mode 100644
index 0000000..d35f1b8
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/submit_to_queue
@@ -0,0 +1,25 @@
+#!/bin/csh -f
+#PBS -r y                                                              #This job is restartable
+#PBS -j oe                                                             #STDOUT and STDERR are in the same file, specified below in the '-o' option
+#PBS -q batch                                                          #Do not change this - it tells your job where to run
+#PBS -S /bin/sh                                                        #Do not change this - it keeps your job from issuing a false alarm
+#PBS -E                                                                #Do not change this - it gives your job more and more useful Moab environment variables
+#PBS -N  Bergs_Empty_Run                                               #Job Name:             You may want to change this to reflect your job's purpose or relation to an experiment
+#PBS -l partition=c3
+#PBS -l size=4                                                        #You will need to change this to reflect your job's core requirements - 24 is the current core increment.
+#PBS -l walltime=16:00:00                                              #You MUST change this to reflect your job's expected run time, including copy time
+#PBS -m bea                                                            #Email options: You may want to change this to reduce your incoming email stream
+
+######################################################################################################################
+#
+#  Gaea c1ms batch skeleton version 0.9
+#  
+#  0.9 - Initial version - 20110906 - Daniel Gall - Daniel.Gall@noaa.gov
+#
+######################################################################################################################
+
+#Source the system initialization scripts (but not the user's so as to avoid interactive settings that can poison us)
+source /etc/csh.cshrc
+
+#Run the experiment
+aprun -n 128 ../../../../../build/intel/ice_ocean_SIS2/repro/MOM6
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/MOM_input b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/MOM_input
new file mode 120000
index 0000000..a756962
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/MOM_input
@@ -0,0 +1 @@
+../../../common/MOM_input
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/MOM_override b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/MOM_override
new file mode 100644
index 0000000..cd50151
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/MOM_override
@@ -0,0 +1,91 @@
+! Blank file in which we can put "overrides" for parameters
+! z
+#override USE_REGRIDDING = True
+#override REGRIDDING_COORDINATE_MODE = "SIGMA_SHELF_ZSTAR" 
+#override INTERPOLATION_SCHEME = "PPM_H4"
+#override REMAPPING_SCHEME = "PPM_H4"
+
+
+!TPY params
+#override NK = 72
+#override NKML = 4
+
+! TIME STEP
+#override DT = 10
+#override DT_THERM = 10
+#override DT_FORCING = 10
+
+! MIXING
+#override SMAGORINSKY_KH = False
+#override BIHARMONIC = False
+#override KH = 6.0  ! back. horiz. visc.
+#override KHTR = 1.0    ! back. horiz. diff.
+#override KD = 5.0E-5     ! back. diapycnal diff.
+#override KV = 1.0E-3     ! back. diapycnal visc.
+
+!WARM IC
+#override ISOMIP_T_SUR = -1.9
+#override ISOMIP_S_SUR = 33.8
+#override ISOMIP_T_BOT = 1.0
+#override ISOMIP_S_BOT = 34.7
+
+! ice shelf
+#override ICE_SHELF = False                !   [Boolean] default = False
+#override SHELF_THERMO = TRUE
+#override SHELF_THREE_EQN = True
+#override SHELF_3EQ_GAMMA = False
+#override UTIDE = 0.01
+!SHELF_S_ROOT = True
+!#override USE_HMIX_SFC_PROP = True
+!#override HMIX_SFC_PROP = 10.
+
+! FRAZIL  - making sure sea ice does not form
+#override FRAZIL = False
+#override PRESSURE_DEPENDENT_FRAZIL = False
+
+! EPBL
+#override ENERGETICS_SFC_PBL = True       !   [Boolean] default = False
+                                ! If true, use an implied energetics planetary boundary
+                                ! layer scheme to determine the diffusivity and viscosity
+                                ! in the surface boundary layer.
+#override EPBL_IS_ADDITIVE = True         !   [Boolean] default = True
+                                ! If true, the diffusivity from ePBL is added to all
+                                ! other diffusivities. Otherwise, the larger of kappa-
+                                ! shear and ePBL diffusivities are used.
+#override USE_MLD_ITERATION = True        !   [Boolean] default = False
+                                ! A logical that determines whether or not to use the
+                                ! MLD to set the EPBL length scale.
+#override HTBL_SHELF_MIN = 10.0
+#override BOUND_SALINITY = True
+
+
+! SHEAR MIXING
+#override USE_JACKSON_PARAM = True
+#override RINO_CRIT = 0.25
+!#override KD_KAPPA_SHEAR_0 = 1.0E-2
+
+! SPONGE
+#override SPONGE = TRUE
+ISOMIP_SPONGE_FILE = "3D_LAYER_WARM_TPY_IC.nc"
+#override ISOMIP_TNUDG = 0.1
+#override ISOMIP_TNUDG = 0.1
+#override ISOMIP_S_SUR_SPONGE = 33.8      !   [not defined] default = 35.0
+                                ! Surface salinity in sponge layer.
+#override ISOMIP_S_BOT_SPONGE = 34.7      !   [not defined] default = 35.0
+                                ! Bottom salinity in sponge layer.
+#override ISOMIP_T_SUR_SPONGE = -1.9      !   [not defined] default = -1.9
+                                ! Surface temperature in sponge layer.
+#override ISOMIP_T_BOT_SPONGE = 1.0
+!#override ISOMIP_SPONGE_TEMP_OFFSET=0.1
+
+! PASSIVE TRACERS
+USE_ISOMIP_TRACER = False
+
+! Simulation time
+#override DAYMAX = 730
+
+!#override FIT_SALINITY = False
+
+!Passing Iceberg field to ocean
+ICEBERGS_APPLY_RIGID_BOUNDARY=True !Different boundary condition is used under ice shelves
+ALLOW_ICEBERG_FLUX_DIAGNOSTICS=True
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/README b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/README
new file mode 100644
index 0000000..0972054
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/README
@@ -0,0 +1,4 @@
+A tabular icebergs breaks away from the ice shelf. The tabular icebergs is bonded together by numeric bonds. Icebergs are allowed to evolve freely
+
+Works best when started from restart file created by Static_berg simulation.
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/SIS_input b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/SIS_input
new file mode 120000
index 0000000..ad3cd99
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/SIS_input
@@ -0,0 +1 @@
+../../../common/SIS_input
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/SIS_override b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/SIS_override
new file mode 100644
index 0000000..605ca84
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/SIS_override
@@ -0,0 +1,9 @@
+# Blank file in which we can put "overrides" for parameters
+DO_ICEBERGS =True              !   If true, use the icebergs module.
+
+!Time Stepping
+#override DT_FORCING = 10.0              !   [s] default = 0.0
+#override DT_RHEOLOGY = 10.0             ! The sub-cycling time step, in s, for iterating
+#override DT_ICE_DYNAMICS = 10.0 
+
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/clean_MOM.sh b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/clean_MOM.sh
new file mode 120000
index 0000000..c5370af
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/clean_MOM.sh
@@ -0,0 +1 @@
+../../../common/clean_MOM.sh
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/data_table b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/data_table
new file mode 120000
index 0000000..5b82b3c
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/data_table
@@ -0,0 +1 @@
+../../../common/data_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/diag_table b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/diag_table
new file mode 120000
index 0000000..cff65fe
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/diag_table
@@ -0,0 +1 @@
+../../../common/diag_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/field_table b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/field_table
new file mode 120000
index 0000000..b5ea991
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/field_table
@@ -0,0 +1 @@
+../../../common/field_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/input.nml b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/input.nml
new file mode 100644
index 0000000..7b69203
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/input.nml
@@ -0,0 +1,140 @@
+ &MOM_input_nml
+        output_directory = './',
+        input_filename = 'r'
+        restart_input_dir = 'INPUT/',
+        restart_output_dir = 'RESTART/',
+        parameter_filename = 'MOM_input',
+                             'MOM_override' /
+
+ &SIS_input_nml
+        output_directory = './',
+        input_filename = 'r'
+        restart_input_dir = 'INPUT/',
+        restart_output_dir = 'RESTART/',
+        parameter_filename = 'SIS_input',
+                             'SIS_override' /
+
+ &diag_manager_nml
+         max_output_fields=1000
+         max_input_fields=1000
+         max_num_axis_sets=1000
+	 flush_nc_files=.true.
+         max_files=1000
+         max_axes=2000
+ /
+
+ &coupler_nml
+            months = 0,
+            days   = 60,
+            current_date = 1,1,1,0,0,0,
+            hours = 0,
+            minutes =0, 
+            seconds = 0
+            calendar = 'NOLEAP',
+            dt_cpld  = 10.0,
+            dt_atmos = 10.0,
+            do_atmos = .false.,
+            do_land = .false.,
+            do_ice = .true.,
+            do_ocean = .true.,
+            atmos_npes = 0,
+            ocean_npes = 0,
+            concurrent = .false.
+            use_lag_fluxes=.false. /
+
+
+ &icebergs_nml
+    verbose=.false.,
+    verbose_hrs=240,
+    traj_sample_hrs=24000,
+    ignore_ij_restart=.true.
+    halo=2,
+    save_short_traj=.true.
+    debug=.false.,
+    really_debug=.false.,
+    use_slow_find=.true.,
+    add_weight_to_ocean=.true.,
+    passive_mode=.false.,
+    Static_icebergs=.False.,
+    ignore_missing_restart_bergs=.false.,
+    generate_test_icebergs=.false.,
+    speed_limit=0.,
+    use_roundoff_fix=.true.,
+    make_calving_reproduce=.false.,
+    Runge_not_Verlet=.false.,
+    iceberg_bonds_on=.true.,
+    critical_interaction_damping_on=.true.,
+    use_new_predictive_corrective=.true.,
+    interactive_icebergs_on=.true.
+    halo_debugging=.false.
+    spring_coef=0.00001
+    distribution=0.0, 0.99, 0.0, 0.00, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11,
+    hexagonal_icebergs=.true.
+    allow_bergs_to_roll=.true.
+    set_melt_rates_to_zero=.false.
+    use_roundoff_fix=.false.
+    grid_is_latlon=.false.
+    grid_is_regular=.true.
+    initial_orientation=-0.
+    rotate_icebergs_for_mass_spreading=.false.
+    lat_ref=-75.0
+    u_override=0.00
+    v_override=0.00
+    override_iceberg_velocities=.false.
+    add_iceberg_thickness_to_SSH=.false.
+    max_bonds=6
+    Iceberg_melt_without_decay=.true.
+    melt_icebergs_as_ice_shelf=.true.
+    Use_three_equation_model=.true.
+    find_melt_using_spread_mass=.true.
+    use_mixed_layer_salinity_for_thermo=.true.
+    pass_fields_to_ocean_model=.true.
+    rho_bergs=918.0
+    utide_icebergs=0.01
+    ustar_icebergs_bg=0.000
+    cdrag_icebergs =0.0025
+    const_gamma=.false.
+    Gamma_T_3EQ=0.22
+    ignore_traj=.False.
+    read_ocean_depth_from_file=.true.
+    apply_thickness_cutoff_to_bergs_melt=.true.
+    apply_thickness_cutoff_to_gridded_melt=.true.
+    melt_cutoff=10.
+    read_old_restarts=.false.
+    internal_bergs_for_drag=.true.
+    use_mixed_melting=.true.
+ &data_override_nml
+         /
+
+ &fms_io_nml
+         fms_netcdf_restart=.true.
+         threading_read='multi'
+ /
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC' /
+
+ &ice_albedo_nml
+      t_range = 10. /
+
+ &ice_model_nml
+           /
+
+ &monin_obukhov_nml
+            neutral = .true. /
+
+ &ocean_albedo_nml
+      ocean_albedo_option = 5 /
+
+ &sat_vapor_pres_nml
+      construct_table_wrt_liq = .true.,
+      construct_table_wrt_liq_and_ice = .true. /
+
+ &xgrid_nml
+            make_exchange_reproduce = .false.
+            interp_method = 'second_order' /
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/run_script.sh b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/run_script.sh
new file mode 120000
index 0000000..2a081b9
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/run_script.sh
@@ -0,0 +1 @@
+../../../common/run_script.sh
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/submit_to_queue b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/submit_to_queue
new file mode 100644
index 0000000..cc5b649
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/submit_to_queue
@@ -0,0 +1,25 @@
+#!/bin/csh -f
+#PBS -r y                                                              #This job is restartable
+#PBS -j oe                                                             #STDOUT and STDERR are in the same file, specified below in the '-o' option
+#PBS -q batch                                                          #Do not change this - it tells your job where to run
+#PBS -S /bin/sh                                                        #Do not change this - it keeps your job from issuing a false alarm
+#PBS -E                                                                #Do not change this - it gives your job more and more useful Moab environment variables
+#PBS -N  Bergs_Bond_layer                                              #Job Name:             You may want to change this to reflect your job's purpose or relation to an experiment
+#PBS -l partition=c3
+#PBS -l size=4                                                        #You will need to change this to reflect your job's core requirements - 24 is the current core increment.
+#PBS -l walltime=16:00:00                                              #You MUST change this to reflect your job's expected run time, including copy time
+#PBS -m bea                                                            #Email options: You may want to change this to reduce your incoming email stream
+
+######################################################################################################################
+#
+#  Gaea c1ms batch skeleton version 0.9
+#  
+#  0.9 - Initial version - 20110906 - Daniel Gall - Daniel.Gall@noaa.gov
+#
+######################################################################################################################
+
+#Source the system initialization scripts (but not the user's so as to avoid interactive settings that can poison us)
+source /etc/csh.cshrc
+
+#Run the experiment
+aprun -n 128 ../../../../../build/intel/ice_ocean_SIS2/repro/MOM6
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Collapse/README b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Collapse/README
new file mode 100644
index 0000000..ac458b8
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Collapse/README
@@ -0,0 +1,7 @@
+A tabular icebergs breaks away from the ice shelf. Smaller pieces also break away, which allows the tabular iceberg to move more easily. The tabular icebergs is bonded together by numeric bonds. Icebergs are allowed to evolve freely
+
+Works best when started from restart file created by Static_berg simulation.
+
+Experimental setup is exactly the same as Moving_berg_Bond simulation, except that when icebergs.res is created, use the command line flag:
+./initialize_bergs_in_pattern.py -Make_icebergs_non_static_later=True
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Collapse/input.nml b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Collapse/input.nml
new file mode 100644
index 0000000..7b69203
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Collapse/input.nml
@@ -0,0 +1,140 @@
+ &MOM_input_nml
+        output_directory = './',
+        input_filename = 'r'
+        restart_input_dir = 'INPUT/',
+        restart_output_dir = 'RESTART/',
+        parameter_filename = 'MOM_input',
+                             'MOM_override' /
+
+ &SIS_input_nml
+        output_directory = './',
+        input_filename = 'r'
+        restart_input_dir = 'INPUT/',
+        restart_output_dir = 'RESTART/',
+        parameter_filename = 'SIS_input',
+                             'SIS_override' /
+
+ &diag_manager_nml
+         max_output_fields=1000
+         max_input_fields=1000
+         max_num_axis_sets=1000
+	 flush_nc_files=.true.
+         max_files=1000
+         max_axes=2000
+ /
+
+ &coupler_nml
+            months = 0,
+            days   = 60,
+            current_date = 1,1,1,0,0,0,
+            hours = 0,
+            minutes =0, 
+            seconds = 0
+            calendar = 'NOLEAP',
+            dt_cpld  = 10.0,
+            dt_atmos = 10.0,
+            do_atmos = .false.,
+            do_land = .false.,
+            do_ice = .true.,
+            do_ocean = .true.,
+            atmos_npes = 0,
+            ocean_npes = 0,
+            concurrent = .false.
+            use_lag_fluxes=.false. /
+
+
+ &icebergs_nml
+    verbose=.false.,
+    verbose_hrs=240,
+    traj_sample_hrs=24000,
+    ignore_ij_restart=.true.
+    halo=2,
+    save_short_traj=.true.
+    debug=.false.,
+    really_debug=.false.,
+    use_slow_find=.true.,
+    add_weight_to_ocean=.true.,
+    passive_mode=.false.,
+    Static_icebergs=.False.,
+    ignore_missing_restart_bergs=.false.,
+    generate_test_icebergs=.false.,
+    speed_limit=0.,
+    use_roundoff_fix=.true.,
+    make_calving_reproduce=.false.,
+    Runge_not_Verlet=.false.,
+    iceberg_bonds_on=.true.,
+    critical_interaction_damping_on=.true.,
+    use_new_predictive_corrective=.true.,
+    interactive_icebergs_on=.true.
+    halo_debugging=.false.
+    spring_coef=0.00001
+    distribution=0.0, 0.99, 0.0, 0.00, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11,
+    hexagonal_icebergs=.true.
+    allow_bergs_to_roll=.true.
+    set_melt_rates_to_zero=.false.
+    use_roundoff_fix=.false.
+    grid_is_latlon=.false.
+    grid_is_regular=.true.
+    initial_orientation=-0.
+    rotate_icebergs_for_mass_spreading=.false.
+    lat_ref=-75.0
+    u_override=0.00
+    v_override=0.00
+    override_iceberg_velocities=.false.
+    add_iceberg_thickness_to_SSH=.false.
+    max_bonds=6
+    Iceberg_melt_without_decay=.true.
+    melt_icebergs_as_ice_shelf=.true.
+    Use_three_equation_model=.true.
+    find_melt_using_spread_mass=.true.
+    use_mixed_layer_salinity_for_thermo=.true.
+    pass_fields_to_ocean_model=.true.
+    rho_bergs=918.0
+    utide_icebergs=0.01
+    ustar_icebergs_bg=0.000
+    cdrag_icebergs =0.0025
+    const_gamma=.false.
+    Gamma_T_3EQ=0.22
+    ignore_traj=.False.
+    read_ocean_depth_from_file=.true.
+    apply_thickness_cutoff_to_bergs_melt=.true.
+    apply_thickness_cutoff_to_gridded_melt=.true.
+    melt_cutoff=10.
+    read_old_restarts=.false.
+    internal_bergs_for_drag=.true.
+    use_mixed_melting=.true.
+ &data_override_nml
+         /
+
+ &fms_io_nml
+         fms_netcdf_restart=.true.
+         threading_read='multi'
+ /
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC' /
+
+ &ice_albedo_nml
+      t_range = 10. /
+
+ &ice_model_nml
+           /
+
+ &monin_obukhov_nml
+            neutral = .true. /
+
+ &ocean_albedo_nml
+      ocean_albedo_option = 5 /
+
+ &sat_vapor_pres_nml
+      construct_table_wrt_liq = .true.,
+      construct_table_wrt_liq_and_ice = .true. /
+
+ &xgrid_nml
+            make_exchange_reproduce = .false.
+            interp_method = 'second_order' /
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/MOM_input b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/MOM_input
new file mode 120000
index 0000000..a756962
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/MOM_input
@@ -0,0 +1 @@
+../../../common/MOM_input
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/MOM_override b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/MOM_override
new file mode 100644
index 0000000..cd50151
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/MOM_override
@@ -0,0 +1,91 @@
+! Blank file in which we can put "overrides" for parameters
+! z
+#override USE_REGRIDDING = True
+#override REGRIDDING_COORDINATE_MODE = "SIGMA_SHELF_ZSTAR" 
+#override INTERPOLATION_SCHEME = "PPM_H4"
+#override REMAPPING_SCHEME = "PPM_H4"
+
+
+!TPY params
+#override NK = 72
+#override NKML = 4
+
+! TIME STEP
+#override DT = 10
+#override DT_THERM = 10
+#override DT_FORCING = 10
+
+! MIXING
+#override SMAGORINSKY_KH = False
+#override BIHARMONIC = False
+#override KH = 6.0  ! back. horiz. visc.
+#override KHTR = 1.0    ! back. horiz. diff.
+#override KD = 5.0E-5     ! back. diapycnal diff.
+#override KV = 1.0E-3     ! back. diapycnal visc.
+
+!WARM IC
+#override ISOMIP_T_SUR = -1.9
+#override ISOMIP_S_SUR = 33.8
+#override ISOMIP_T_BOT = 1.0
+#override ISOMIP_S_BOT = 34.7
+
+! ice shelf
+#override ICE_SHELF = False                !   [Boolean] default = False
+#override SHELF_THERMO = TRUE
+#override SHELF_THREE_EQN = True
+#override SHELF_3EQ_GAMMA = False
+#override UTIDE = 0.01
+!SHELF_S_ROOT = True
+!#override USE_HMIX_SFC_PROP = True
+!#override HMIX_SFC_PROP = 10.
+
+! FRAZIL  - making sure sea ice does not form
+#override FRAZIL = False
+#override PRESSURE_DEPENDENT_FRAZIL = False
+
+! EPBL
+#override ENERGETICS_SFC_PBL = True       !   [Boolean] default = False
+                                ! If true, use an implied energetics planetary boundary
+                                ! layer scheme to determine the diffusivity and viscosity
+                                ! in the surface boundary layer.
+#override EPBL_IS_ADDITIVE = True         !   [Boolean] default = True
+                                ! If true, the diffusivity from ePBL is added to all
+                                ! other diffusivities. Otherwise, the larger of kappa-
+                                ! shear and ePBL diffusivities are used.
+#override USE_MLD_ITERATION = True        !   [Boolean] default = False
+                                ! A logical that determines whether or not to use the
+                                ! MLD to set the EPBL length scale.
+#override HTBL_SHELF_MIN = 10.0
+#override BOUND_SALINITY = True
+
+
+! SHEAR MIXING
+#override USE_JACKSON_PARAM = True
+#override RINO_CRIT = 0.25
+!#override KD_KAPPA_SHEAR_0 = 1.0E-2
+
+! SPONGE
+#override SPONGE = TRUE
+ISOMIP_SPONGE_FILE = "3D_LAYER_WARM_TPY_IC.nc"
+#override ISOMIP_TNUDG = 0.1
+#override ISOMIP_TNUDG = 0.1
+#override ISOMIP_S_SUR_SPONGE = 33.8      !   [not defined] default = 35.0
+                                ! Surface salinity in sponge layer.
+#override ISOMIP_S_BOT_SPONGE = 34.7      !   [not defined] default = 35.0
+                                ! Bottom salinity in sponge layer.
+#override ISOMIP_T_SUR_SPONGE = -1.9      !   [not defined] default = -1.9
+                                ! Surface temperature in sponge layer.
+#override ISOMIP_T_BOT_SPONGE = 1.0
+!#override ISOMIP_SPONGE_TEMP_OFFSET=0.1
+
+! PASSIVE TRACERS
+USE_ISOMIP_TRACER = False
+
+! Simulation time
+#override DAYMAX = 730
+
+!#override FIT_SALINITY = False
+
+!Passing Iceberg field to ocean
+ICEBERGS_APPLY_RIGID_BOUNDARY=True !Different boundary condition is used under ice shelves
+ALLOW_ICEBERG_FLUX_DIAGNOSTICS=True
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/README b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/README
new file mode 100644
index 0000000..b4eb12b
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/README
@@ -0,0 +1,3 @@
+A piece of the ice shelf breaks off. The elements are not bonded together, so they move freely away. However, they do interact with one another.
+
+Works best when started from restart file created by Static_berg simulation.
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/SIS_input b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/SIS_input
new file mode 120000
index 0000000..ad3cd99
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/SIS_input
@@ -0,0 +1 @@
+../../../common/SIS_input
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/SIS_override b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/SIS_override
new file mode 100644
index 0000000..605ca84
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/SIS_override
@@ -0,0 +1,9 @@
+# Blank file in which we can put "overrides" for parameters
+DO_ICEBERGS =True              !   If true, use the icebergs module.
+
+!Time Stepping
+#override DT_FORCING = 10.0              !   [s] default = 0.0
+#override DT_RHEOLOGY = 10.0             ! The sub-cycling time step, in s, for iterating
+#override DT_ICE_DYNAMICS = 10.0 
+
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/clean_MOM.sh b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/clean_MOM.sh
new file mode 120000
index 0000000..c5370af
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/clean_MOM.sh
@@ -0,0 +1 @@
+../../../common/clean_MOM.sh
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/data_table b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/data_table
new file mode 120000
index 0000000..5b82b3c
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/data_table
@@ -0,0 +1 @@
+../../../common/data_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/diag_table b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/diag_table
new file mode 120000
index 0000000..cff65fe
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/diag_table
@@ -0,0 +1 @@
+../../../common/diag_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/field_table b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/field_table
new file mode 120000
index 0000000..b5ea991
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/field_table
@@ -0,0 +1 @@
+../../../common/field_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/input.nml b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/input.nml
new file mode 100644
index 0000000..7424ccd
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/input.nml
@@ -0,0 +1,140 @@
+ &MOM_input_nml
+        output_directory = './',
+        input_filename = 'r'
+        restart_input_dir = 'INPUT/',
+        restart_output_dir = 'RESTART/',
+        parameter_filename = 'MOM_input',
+                             'MOM_override' /
+
+ &SIS_input_nml
+        output_directory = './',
+        input_filename = 'r'
+        restart_input_dir = 'INPUT/',
+        restart_output_dir = 'RESTART/',
+        parameter_filename = 'SIS_input',
+                             'SIS_override' /
+
+ &diag_manager_nml
+         max_output_fields=1000
+         max_input_fields=1000
+         max_num_axis_sets=1000
+	 flush_nc_files=.true.
+         max_files=1000
+         max_axes=2000
+ /
+
+ &coupler_nml
+            months = 0,
+            days   = 60,
+            current_date = 1,1,1,0,0,0,
+            hours = 0,
+            minutes =0, 
+            seconds = 0
+            calendar = 'NOLEAP',
+            dt_cpld  = 10.0,
+            dt_atmos = 10.0,
+            do_atmos = .false.,
+            do_land = .false.,
+            do_ice = .true.,
+            do_ocean = .true.,
+            atmos_npes = 0,
+            ocean_npes = 0,
+            concurrent = .false.
+            use_lag_fluxes=.false. /
+
+
+ &icebergs_nml
+    verbose=.false.,
+    verbose_hrs=240,
+    traj_sample_hrs=24000,
+    ignore_ij_restart=.true.
+    halo=2,
+    save_short_traj=.true.
+    debug=.false.,
+    really_debug=.false.,
+    use_slow_find=.true.,
+    add_weight_to_ocean=.true.,
+    passive_mode=.false.,
+    Static_icebergs=.False.,
+    ignore_missing_restart_bergs=.false.,
+    generate_test_icebergs=.false.,
+    speed_limit=0.,
+    use_roundoff_fix=.true.,
+    make_calving_reproduce=.false.,
+    Runge_not_Verlet=.false.,
+    iceberg_bonds_on=.false.,
+    critical_interaction_damping_on=.true.,
+    use_new_predictive_corrective=.true.,
+    interactive_icebergs_on=.true.
+    halo_debugging=.false.
+    spring_coef=0.00001
+    distribution=0.0, 0.99, 0.0, 0.00, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11,
+    hexagonal_icebergs=.true.
+    allow_bergs_to_roll=.true.
+    set_melt_rates_to_zero=.false.
+    use_roundoff_fix=.false.
+    grid_is_latlon=.false.
+    grid_is_regular=.true.
+    initial_orientation=-0.
+    rotate_icebergs_for_mass_spreading=.false.
+    lat_ref=-75.0
+    u_override=0.00
+    v_override=0.00
+    override_iceberg_velocities=.false.
+    add_iceberg_thickness_to_SSH=.false.
+    max_bonds=6
+    Iceberg_melt_without_decay=.true.
+    melt_icebergs_as_ice_shelf=.true.
+    Use_three_equation_model=.true.
+    find_melt_using_spread_mass=.true.
+    use_mixed_layer_salinity_for_thermo=.true.
+    pass_fields_to_ocean_model=.true.
+    rho_bergs=918.0
+    utide_icebergs=0.01
+    ustar_icebergs_bg=0.000
+    cdrag_icebergs =0.0025
+    const_gamma=.false.
+    Gamma_T_3EQ=0.22
+    ignore_traj=.False.
+    read_ocean_depth_from_file=.true.
+    apply_thickness_cutoff_to_bergs_melt=.true.
+    apply_thickness_cutoff_to_gridded_melt=.true.
+    melt_cutoff=10.
+    read_old_restarts=.false.
+    internal_bergs_for_drag=.true.
+    use_mixed_melting=.true.
+ &data_override_nml
+         /
+
+ &fms_io_nml
+         fms_netcdf_restart=.true.
+         threading_read='multi'
+ /
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC' /
+
+ &ice_albedo_nml
+      t_range = 10. /
+
+ &ice_model_nml
+           /
+
+ &monin_obukhov_nml
+            neutral = .true. /
+
+ &ocean_albedo_nml
+      ocean_albedo_option = 5 /
+
+ &sat_vapor_pres_nml
+      construct_table_wrt_liq = .true.,
+      construct_table_wrt_liq_and_ice = .true. /
+
+ &xgrid_nml
+            make_exchange_reproduce = .false.
+            interp_method = 'second_order' /
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/run_script.sh b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/run_script.sh
new file mode 120000
index 0000000..2a081b9
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/run_script.sh
@@ -0,0 +1 @@
+../../../common/run_script.sh
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/submit_to_queue b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/submit_to_queue
new file mode 100644
index 0000000..4895e94
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/submit_to_queue
@@ -0,0 +1,25 @@
+#!/bin/csh -f
+#PBS -r y                                                              #This job is restartable
+#PBS -j oe                                                             #STDOUT and STDERR are in the same file, specified below in the '-o' option
+#PBS -q batch                                                          #Do not change this - it tells your job where to run
+#PBS -S /bin/sh                                                        #Do not change this - it keeps your job from issuing a false alarm
+#PBS -E                                                                #Do not change this - it gives your job more and more useful Moab environment variables
+#PBS -N  Bergs_drift_layer                                               #Job Name:             You may want to change this to reflect your job's purpose or relation to an experiment
+#PBS -l partition=c3
+#PBS -l size=4                                                        #You will need to change this to reflect your job's core requirements - 24 is the current core increment.
+#PBS -l walltime=16:00:00                                              #You MUST change this to reflect your job's expected run time, including copy time
+#PBS -m bea                                                            #Email options: You may want to change this to reduce your incoming email stream
+
+######################################################################################################################
+#
+#  Gaea c1ms batch skeleton version 0.9
+#  
+#  0.9 - Initial version - 20110906 - Daniel Gall - Daniel.Gall@noaa.gov
+#
+######################################################################################################################
+
+#Source the system initialization scripts (but not the user's so as to avoid interactive settings that can poison us)
+source /etc/csh.cshrc
+
+#Run the experiment
+aprun -n 128 ../../../../../build/intel/ice_ocean_SIS2/repro/MOM6
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/MOM_input b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/MOM_input
new file mode 120000
index 0000000..a756962
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/MOM_input
@@ -0,0 +1 @@
+../../../common/MOM_input
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/MOM_override b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/MOM_override
new file mode 100644
index 0000000..cd50151
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/MOM_override
@@ -0,0 +1,91 @@
+! Blank file in which we can put "overrides" for parameters
+! z
+#override USE_REGRIDDING = True
+#override REGRIDDING_COORDINATE_MODE = "SIGMA_SHELF_ZSTAR" 
+#override INTERPOLATION_SCHEME = "PPM_H4"
+#override REMAPPING_SCHEME = "PPM_H4"
+
+
+!TPY params
+#override NK = 72
+#override NKML = 4
+
+! TIME STEP
+#override DT = 10
+#override DT_THERM = 10
+#override DT_FORCING = 10
+
+! MIXING
+#override SMAGORINSKY_KH = False
+#override BIHARMONIC = False
+#override KH = 6.0  ! back. horiz. visc.
+#override KHTR = 1.0    ! back. horiz. diff.
+#override KD = 5.0E-5     ! back. diapycnal diff.
+#override KV = 1.0E-3     ! back. diapycnal visc.
+
+!WARM IC
+#override ISOMIP_T_SUR = -1.9
+#override ISOMIP_S_SUR = 33.8
+#override ISOMIP_T_BOT = 1.0
+#override ISOMIP_S_BOT = 34.7
+
+! ice shelf
+#override ICE_SHELF = False                !   [Boolean] default = False
+#override SHELF_THERMO = TRUE
+#override SHELF_THREE_EQN = True
+#override SHELF_3EQ_GAMMA = False
+#override UTIDE = 0.01
+!SHELF_S_ROOT = True
+!#override USE_HMIX_SFC_PROP = True
+!#override HMIX_SFC_PROP = 10.
+
+! FRAZIL  - making sure sea ice does not form
+#override FRAZIL = False
+#override PRESSURE_DEPENDENT_FRAZIL = False
+
+! EPBL
+#override ENERGETICS_SFC_PBL = True       !   [Boolean] default = False
+                                ! If true, use an implied energetics planetary boundary
+                                ! layer scheme to determine the diffusivity and viscosity
+                                ! in the surface boundary layer.
+#override EPBL_IS_ADDITIVE = True         !   [Boolean] default = True
+                                ! If true, the diffusivity from ePBL is added to all
+                                ! other diffusivities. Otherwise, the larger of kappa-
+                                ! shear and ePBL diffusivities are used.
+#override USE_MLD_ITERATION = True        !   [Boolean] default = False
+                                ! A logical that determines whether or not to use the
+                                ! MLD to set the EPBL length scale.
+#override HTBL_SHELF_MIN = 10.0
+#override BOUND_SALINITY = True
+
+
+! SHEAR MIXING
+#override USE_JACKSON_PARAM = True
+#override RINO_CRIT = 0.25
+!#override KD_KAPPA_SHEAR_0 = 1.0E-2
+
+! SPONGE
+#override SPONGE = TRUE
+ISOMIP_SPONGE_FILE = "3D_LAYER_WARM_TPY_IC.nc"
+#override ISOMIP_TNUDG = 0.1
+#override ISOMIP_TNUDG = 0.1
+#override ISOMIP_S_SUR_SPONGE = 33.8      !   [not defined] default = 35.0
+                                ! Surface salinity in sponge layer.
+#override ISOMIP_S_BOT_SPONGE = 34.7      !   [not defined] default = 35.0
+                                ! Bottom salinity in sponge layer.
+#override ISOMIP_T_SUR_SPONGE = -1.9      !   [not defined] default = -1.9
+                                ! Surface temperature in sponge layer.
+#override ISOMIP_T_BOT_SPONGE = 1.0
+!#override ISOMIP_SPONGE_TEMP_OFFSET=0.1
+
+! PASSIVE TRACERS
+USE_ISOMIP_TRACER = False
+
+! Simulation time
+#override DAYMAX = 730
+
+!#override FIT_SALINITY = False
+
+!Passing Iceberg field to ocean
+ICEBERGS_APPLY_RIGID_BOUNDARY=True !Different boundary condition is used under ice shelves
+ALLOW_ICEBERG_FLUX_DIAGNOSTICS=True
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/README b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/README
new file mode 100644
index 0000000..fa2bc28
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/README
@@ -0,0 +1,5 @@
+A tabular iceberg breaks away from the ice shelf. The non-static icebergs move away from the ice shelf at a prescribed velocity. The time step is quite small (10s) in order to resolve ocean motions
+
+Works best when started from restart file created by Static_berg simulation.
+
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/SIS_input b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/SIS_input
new file mode 120000
index 0000000..ad3cd99
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/SIS_input
@@ -0,0 +1 @@
+../../../common/SIS_input
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/SIS_override b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/SIS_override
new file mode 100644
index 0000000..605ca84
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/SIS_override
@@ -0,0 +1,9 @@
+# Blank file in which we can put "overrides" for parameters
+DO_ICEBERGS =True              !   If true, use the icebergs module.
+
+!Time Stepping
+#override DT_FORCING = 10.0              !   [s] default = 0.0
+#override DT_RHEOLOGY = 10.0             ! The sub-cycling time step, in s, for iterating
+#override DT_ICE_DYNAMICS = 10.0 
+
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/clean_MOM.sh b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/clean_MOM.sh
new file mode 120000
index 0000000..c5370af
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/clean_MOM.sh
@@ -0,0 +1 @@
+../../../common/clean_MOM.sh
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/data_table b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/data_table
new file mode 120000
index 0000000..5b82b3c
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/data_table
@@ -0,0 +1 @@
+../../../common/data_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/diag_table b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/diag_table
new file mode 120000
index 0000000..cff65fe
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/diag_table
@@ -0,0 +1 @@
+../../../common/diag_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/field_table b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/field_table
new file mode 120000
index 0000000..b5ea991
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/field_table
@@ -0,0 +1 @@
+../../../common/field_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/input.nml b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/input.nml
new file mode 100644
index 0000000..97afa25
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/input.nml
@@ -0,0 +1,140 @@
+ &MOM_input_nml
+        output_directory = './',
+        input_filename = 'r'
+        restart_input_dir = 'INPUT/',
+        restart_output_dir = 'RESTART/',
+        parameter_filename = 'MOM_input',
+                             'MOM_override' /
+
+ &SIS_input_nml
+        output_directory = './',
+        input_filename = 'r'
+        restart_input_dir = 'INPUT/',
+        restart_output_dir = 'RESTART/',
+        parameter_filename = 'SIS_input',
+                             'SIS_override' /
+
+ &diag_manager_nml
+         max_output_fields=1000
+         max_input_fields=1000
+         max_num_axis_sets=1000
+	 flush_nc_files=.true.
+         max_files=1000
+         max_axes=2000
+ /
+
+ &coupler_nml
+            months = 0,
+            days   = 60,
+            current_date = 1,1,1,0,0,0,
+            hours = 0,
+            minutes =0, 
+            seconds = 0
+            calendar = 'NOLEAP',
+            dt_cpld  = 10.0,
+            dt_atmos = 10.0,
+            do_atmos = .false.,
+            do_land = .false.,
+            do_ice = .true.,
+            do_ocean = .true.,
+            atmos_npes = 0,
+            ocean_npes = 0,
+            concurrent = .false.
+            use_lag_fluxes=.false. /
+
+
+ &icebergs_nml
+    verbose=.false.,
+    verbose_hrs=240,
+    traj_sample_hrs=24000,
+    ignore_ij_restart=.true.
+    halo=2,
+    save_short_traj=.true.
+    debug=.false.,
+    really_debug=.false.,
+    use_slow_find=.true.,
+    add_weight_to_ocean=.true.,
+    passive_mode=.false.,
+    Static_icebergs=.False.,
+    ignore_missing_restart_bergs=.false.,
+    generate_test_icebergs=.false.,
+    speed_limit=0.,
+    use_roundoff_fix=.true.,
+    make_calving_reproduce=.false.,
+    Runge_not_Verlet=.false.,
+    iceberg_bonds_on=.false.,
+    critical_interaction_damping_on=.true.,
+    use_new_predictive_corrective=.true.,
+    interactive_icebergs_on=.false.
+    halo_debugging=.false.
+    spring_coef=0.00001
+    distribution=0.0, 0.99, 0.0, 0.00, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11,
+    hexagonal_icebergs=.true.
+    allow_bergs_to_roll=.true.
+    set_melt_rates_to_zero=.false.
+    use_roundoff_fix=.false.
+    grid_is_latlon=.false.
+    grid_is_regular=.true.
+    initial_orientation=-0.
+    rotate_icebergs_for_mass_spreading=.false.
+    lat_ref=-75.0
+    u_override=0.01
+    v_override=0.00
+    override_iceberg_velocities=.true.
+    add_iceberg_thickness_to_SSH=.false.
+    max_bonds=6
+    Iceberg_melt_without_decay=.true.
+    melt_icebergs_as_ice_shelf=.true.
+    Use_three_equation_model=.true.
+    find_melt_using_spread_mass=.true.
+    use_mixed_layer_salinity_for_thermo=.true.
+    pass_fields_to_ocean_model=.true.
+    rho_bergs=918.0
+    utide_icebergs=0.01
+    ustar_icebergs_bg=0.000
+    cdrag_icebergs =0.0025
+    const_gamma=.false.
+    Gamma_T_3EQ=0.22
+    ignore_traj=.False.
+    read_ocean_depth_from_file=.true.
+    apply_thickness_cutoff_to_bergs_melt=.true.
+    apply_thickness_cutoff_to_gridded_melt=.true.
+    melt_cutoff=10.
+    read_old_restarts=.false.
+    internal_bergs_for_drag=.true.
+    use_mixed_melting=.true.
+ &data_override_nml
+         /
+
+ &fms_io_nml
+         fms_netcdf_restart=.true.
+         threading_read='multi'
+ /
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC' /
+
+ &ice_albedo_nml
+      t_range = 10. /
+
+ &ice_model_nml
+           /
+
+ &monin_obukhov_nml
+            neutral = .true. /
+
+ &ocean_albedo_nml
+      ocean_albedo_option = 5 /
+
+ &sat_vapor_pres_nml
+      construct_table_wrt_liq = .true.,
+      construct_table_wrt_liq_and_ice = .true. /
+
+ &xgrid_nml
+            make_exchange_reproduce = .false.
+            interp_method = 'second_order' /
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/run_script.sh b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/run_script.sh
new file mode 120000
index 0000000..2a081b9
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/run_script.sh
@@ -0,0 +1 @@
+../../../common/run_script.sh
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/submit_to_queue b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/submit_to_queue
new file mode 100644
index 0000000..2e508c9
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/submit_to_queue
@@ -0,0 +1,25 @@
+#!/bin/csh -f
+#PBS -r y                                                              #This job is restartable
+#PBS -j oe                                                             #STDOUT and STDERR are in the same file, specified below in the '-o' option
+#PBS -q batch                                                          #Do not change this - it tells your job where to run
+#PBS -S /bin/sh                                                        #Do not change this - it keeps your job from issuing a false alarm
+#PBS -E                                                                #Do not change this - it gives your job more and more useful Moab environment variables
+#PBS -N  Bergs_fixed_layer                                               #Job Name:             You may want to change this to reflect your job's purpose or relation to an experiment
+#PBS -l partition=c3
+#PBS -l size=4                                                        #You will need to change this to reflect your job's core requirements - 24 is the current core increment.
+#PBS -l walltime=16:00:00                                              #You MUST change this to reflect your job's expected run time, including copy time
+#PBS -m bea                                                            #Email options: You may want to change this to reduce your incoming email stream
+
+######################################################################################################################
+#
+#  Gaea c1ms batch skeleton version 0.9
+#  
+#  0.9 - Initial version - 20110906 - Daniel Gall - Daniel.Gall@noaa.gov
+#
+######################################################################################################################
+
+#Source the system initialization scripts (but not the user's so as to avoid interactive settings that can poison us)
+source /etc/csh.cshrc
+
+#Run the experiment
+aprun -n 128 ../../../../../build/intel/ice_ocean_SIS2/repro/MOM6
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/MOM_input b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/MOM_input
new file mode 120000
index 0000000..a756962
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/MOM_input
@@ -0,0 +1 @@
+../../../common/MOM_input
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/MOM_override b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/MOM_override
new file mode 100644
index 0000000..760b13d
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/MOM_override
@@ -0,0 +1,94 @@
+! Blank file in which we can put "overrides" for parameters
+! z
+#override USE_REGRIDDING = True
+#override REGRIDDING_COORDINATE_MODE = "SIGMA_SHELF_ZSTAR" 
+#override INTERPOLATION_SCHEME = "PPM_H4"
+#override REMAPPING_SCHEME = "PPM_H4"
+
+
+!TPY params
+#override NK = 72
+#override NKML = 4
+
+! TIME STEP
+!#override DT = 10
+!#override DT_THERM = 10
+!#override DT_FORCING = 10
+#override DT = 360
+#override DT_THERM = 360
+#override DT_FORCING = 360
+
+! MIXING
+#override SMAGORINSKY_KH = False
+#override BIHARMONIC = False
+#override KH = 6.0  ! back. horiz. visc.
+#override KHTR = 1.0    ! back. horiz. diff.
+#override KD = 5.0E-5     ! back. diapycnal diff.
+#override KV = 1.0E-3     ! back. diapycnal visc.
+
+!WARM IC
+#override ISOMIP_T_SUR = -1.9
+#override ISOMIP_S_SUR = 33.8
+#override ISOMIP_T_BOT = 1.0
+#override ISOMIP_S_BOT = 34.7
+
+! ice shelf
+#override ICE_SHELF = False                !   [Boolean] default = False
+#override SHELF_THERMO = TRUE
+#override SHELF_THREE_EQN = True
+#override SHELF_3EQ_GAMMA = False
+#override UTIDE = 0.01
+!SHELF_S_ROOT = True
+!#override USE_HMIX_SFC_PROP = True
+!#override HMIX_SFC_PROP = 10.
+
+! FRAZIL  - making sure sea ice does not form
+#override FRAZIL = False
+#override PRESSURE_DEPENDENT_FRAZIL = False
+
+! EPBL
+#override ENERGETICS_SFC_PBL = True       !   [Boolean] default = False
+                                ! If true, use an implied energetics planetary boundary
+                                ! layer scheme to determine the diffusivity and viscosity
+                                ! in the surface boundary layer.
+#override EPBL_IS_ADDITIVE = True         !   [Boolean] default = True
+                                ! If true, the diffusivity from ePBL is added to all
+                                ! other diffusivities. Otherwise, the larger of kappa-
+                                ! shear and ePBL diffusivities are used.
+#override USE_MLD_ITERATION = True        !   [Boolean] default = False
+                                ! A logical that determines whether or not to use the
+                                ! MLD to set the EPBL length scale.
+#override HTBL_SHELF_MIN = 10.0
+#override BOUND_SALINITY = True
+
+
+! SHEAR MIXING
+#override USE_JACKSON_PARAM = True
+#override RINO_CRIT = 0.25
+!#override KD_KAPPA_SHEAR_0 = 1.0E-2
+
+! SPONGE
+#override SPONGE = TRUE
+ISOMIP_SPONGE_FILE = "3D_LAYER_WARM_TPY_IC.nc"
+#override ISOMIP_TNUDG = 0.1
+#override ISOMIP_TNUDG = 0.1
+#override ISOMIP_S_SUR_SPONGE = 33.8      !   [not defined] default = 35.0
+                                ! Surface salinity in sponge layer.
+#override ISOMIP_S_BOT_SPONGE = 34.7      !   [not defined] default = 35.0
+                                ! Bottom salinity in sponge layer.
+#override ISOMIP_T_SUR_SPONGE = -1.9      !   [not defined] default = -1.9
+                                ! Surface temperature in sponge layer.
+#override ISOMIP_T_BOT_SPONGE = 1.0
+!#override ISOMIP_SPONGE_TEMP_OFFSET=0.1
+
+! PASSIVE TRACERS
+USE_ISOMIP_TRACER = False
+
+! Simulation time
+#override DAYMAX = 730
+
+!#override FIT_SALINITY = False
+
+!Passing Iceberg field to ocean
+ICEBERGS_APPLY_RIGID_BOUNDARY=True !Different boundary condition is used under ice shelves
+ALLOW_ICEBERG_FLUX_DIAGNOSTICS=True
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/README b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/README
new file mode 100644
index 0000000..c042733
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/README
@@ -0,0 +1 @@
+Ice shelf does not move. Shelf melts using three equation model.
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/SIS_input b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/SIS_input
new file mode 120000
index 0000000..ad3cd99
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/SIS_input
@@ -0,0 +1 @@
+../../../common/SIS_input
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/SIS_override b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/SIS_override
new file mode 100644
index 0000000..fc641d7
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/SIS_override
@@ -0,0 +1,8 @@
+# Blank file in which we can put "overrides" for parameters
+DO_ICEBERGS =True              !   If true, use the icebergs module.
+
+!Time Stepping
+!#override DT_FORCING = 10.0              !   [s] default = 0.0
+!#override DT_RHEOLOGY = 10.0             ! The sub-cycling time step, in s, for iterating
+
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/clean_MOM.sh b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/clean_MOM.sh
new file mode 120000
index 0000000..c5370af
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/clean_MOM.sh
@@ -0,0 +1 @@
+../../../common/clean_MOM.sh
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/data_table b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/data_table
new file mode 120000
index 0000000..5b82b3c
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/data_table
@@ -0,0 +1 @@
+../../../common/data_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/diag_table b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/diag_table
new file mode 120000
index 0000000..cff65fe
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/diag_table
@@ -0,0 +1 @@
+../../../common/diag_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/field_table b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/field_table
new file mode 120000
index 0000000..b5ea991
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/field_table
@@ -0,0 +1 @@
+../../../common/field_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/input.nml b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/input.nml
new file mode 100644
index 0000000..3854fd4
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/input.nml
@@ -0,0 +1,140 @@
+ &MOM_input_nml
+        output_directory = './',
+        input_filename = 'r'
+        restart_input_dir = 'INPUT/',
+        restart_output_dir = 'RESTART/',
+        parameter_filename = 'MOM_input',
+                             'MOM_override' /
+
+ &SIS_input_nml
+        output_directory = './',
+        input_filename = 'r'
+        restart_input_dir = 'INPUT/',
+        restart_output_dir = 'RESTART/',
+        parameter_filename = 'SIS_input',
+                             'SIS_override' /
+
+ &diag_manager_nml
+         max_output_fields=1000
+         max_input_fields=1000
+         max_num_axis_sets=1000
+	 flush_nc_files=.true.
+         max_files=1000
+         max_axes=2000
+ /
+
+ &coupler_nml
+            months = 60,
+            days   = 0,
+            current_date = 1,1,1,0,0,0,
+            hours = 0,
+            minutes =0, 
+            seconds = 0
+            calendar = 'NOLEAP',
+            dt_cpld  = 360.0,
+            dt_atmos = 360.0,
+            do_atmos = .false.,
+            do_land = .false.,
+            do_ice = .true.,
+            do_ocean = .true.,
+            atmos_npes = 0,
+            ocean_npes = 0,
+            concurrent = .false.
+            use_lag_fluxes=.false. /
+
+
+ &icebergs_nml
+    verbose=.false.,
+    verbose_hrs=240,
+    traj_sample_hrs=24000,
+    ignore_ij_restart=.true.
+    halo=2,
+    save_short_traj=.true.
+    debug=.false.,
+    really_debug=.false.,
+    use_slow_find=.true.,
+    add_weight_to_ocean=.true.,
+    passive_mode=.false.,
+    Static_icebergs=.True.,
+    ignore_missing_restart_bergs=.false.,
+    generate_test_icebergs=.false.,
+    speed_limit=0.,
+    use_roundoff_fix=.true.,
+    make_calving_reproduce=.false.,
+    Runge_not_Verlet=.false.,
+    iceberg_bonds_on=.false.,
+    critical_interaction_damping_on=.true.,
+    use_new_predictive_corrective=.true.,
+    interactive_icebergs_on=.false.
+    halo_debugging=.false.
+    spring_coef=0.00001
+    distribution=0.0, 0.99, 0.0, 0.00, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11,
+    hexagonal_icebergs=.true.
+    allow_bergs_to_roll=.true.
+    set_melt_rates_to_zero=.false.
+    use_roundoff_fix=.false.
+    grid_is_latlon=.false.
+    grid_is_regular=.true.
+    initial_orientation=-0.
+    rotate_icebergs_for_mass_spreading=.false.
+    lat_ref=-75.0
+    u_override=0.00
+    v_override=0.00
+    override_iceberg_velocities=.false.
+    add_iceberg_thickness_to_SSH=.false.
+    max_bonds=6
+    Iceberg_melt_without_decay=.true.
+    melt_icebergs_as_ice_shelf=.true.
+    Use_three_equation_model=.true.
+    find_melt_using_spread_mass=.true.
+    use_mixed_layer_salinity_for_thermo=.true.
+    pass_fields_to_ocean_model=.true.
+    rho_bergs=918.0
+    utide_icebergs=0.01
+    ustar_icebergs_bg=0.000
+    cdrag_icebergs =0.0025
+    const_gamma=.false.
+    Gamma_T_3EQ=0.22
+    ignore_traj=.False.
+    read_ocean_depth_from_file=.true.
+    apply_thickness_cutoff_to_bergs_melt=.true.
+    apply_thickness_cutoff_to_gridded_melt=.true.
+    melt_cutoff=10.
+    read_old_restarts=.false.
+    internal_bergs_for_drag=.true.
+    use_mixed_melting=.true.
+ &data_override_nml
+         /
+
+ &fms_io_nml
+         fms_netcdf_restart=.true.
+         threading_read='multi'
+ /
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC' /
+
+ &ice_albedo_nml
+      t_range = 10. /
+
+ &ice_model_nml
+           /
+
+ &monin_obukhov_nml
+            neutral = .true. /
+
+ &ocean_albedo_nml
+      ocean_albedo_option = 5 /
+
+ &sat_vapor_pres_nml
+      construct_table_wrt_liq = .true.,
+      construct_table_wrt_liq_and_ice = .true. /
+
+ &xgrid_nml
+            make_exchange_reproduce = .false.
+            interp_method = 'second_order' /
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/run_script.sh b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/run_script.sh
new file mode 120000
index 0000000..2a081b9
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/run_script.sh
@@ -0,0 +1 @@
+../../../common/run_script.sh
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/submit_to_queue b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/submit_to_queue
new file mode 100644
index 0000000..d35f1b8
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/submit_to_queue
@@ -0,0 +1,25 @@
+#!/bin/csh -f
+#PBS -r y                                                              #This job is restartable
+#PBS -j oe                                                             #STDOUT and STDERR are in the same file, specified below in the '-o' option
+#PBS -q batch                                                          #Do not change this - it tells your job where to run
+#PBS -S /bin/sh                                                        #Do not change this - it keeps your job from issuing a false alarm
+#PBS -E                                                                #Do not change this - it gives your job more and more useful Moab environment variables
+#PBS -N  Bergs_Empty_Run                                               #Job Name:             You may want to change this to reflect your job's purpose or relation to an experiment
+#PBS -l partition=c3
+#PBS -l size=4                                                        #You will need to change this to reflect your job's core requirements - 24 is the current core increment.
+#PBS -l walltime=16:00:00                                              #You MUST change this to reflect your job's expected run time, including copy time
+#PBS -m bea                                                            #Email options: You may want to change this to reduce your incoming email stream
+
+######################################################################################################################
+#
+#  Gaea c1ms batch skeleton version 0.9
+#  
+#  0.9 - Initial version - 20110906 - Daniel Gall - Daniel.Gall@noaa.gov
+#
+######################################################################################################################
+
+#Source the system initialization scripts (but not the user's so as to avoid interactive settings that can poison us)
+source /etc/csh.cshrc
+
+#Run the experiment
+aprun -n 128 ../../../../../build/intel/ice_ocean_SIS2/repro/MOM6
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/MOM_input b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/MOM_input
new file mode 120000
index 0000000..a756962
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/MOM_input
@@ -0,0 +1 @@
+../../../common/MOM_input
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/MOM_override b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/MOM_override
new file mode 100644
index 0000000..0e751df
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/MOM_override
@@ -0,0 +1,64 @@
+! Blank file in which we can put "overrides" for parameters
+
+!TPY params
+#override NK = 72
+#override NKML = 4
+
+! TIME STEP
+#override DT = 720
+#override DT_THERM = 720
+
+! MIXING
+#override SMAGORINSKY_KH = False
+#override BIHARMONIC = False
+#override KH = 6.0  ! back. horiz. visc.
+#override KHTR = 1.0    ! back. horiz. diff.
+#override KD = 5.0E-5     ! back. diapycnal diff.
+#override KV = 1.0E-3     ! back. diapycnal visc.
+
+!WARM IC
+#override ISOMIP_T_SUR = -1.9
+#override ISOMIP_S_SUR = 33.8
+#override ISOMIP_T_BOT = 1.0
+#override ISOMIP_S_BOT = 34.7
+
+! ice shelf
+#override SHELF_THERMO = TRUE
+#override SHELF_THREE_EQN = True
+#override SHELF_3EQ_GAMMA = False
+#override UTIDE = 0.01
+!SHELF_S_ROOT = True
+!#override USE_HMIX_SFC_PROP = True
+!#override HMIX_SFC_PROP = 10.
+
+! FRAZIL  - making sure sea ice does not form
+#override FRAZIL = False
+#override PRESSURE_DEPENDENT_FRAZIL = False
+
+! MIXED LAYER
+#override BULKMIXEDLAYER = True
+#override BULK_RI_ML = 0.25
+#override MIXEDLAYER_RESTRAT = True
+#override HMIX_MIN = 2.0
+!#override KV_TBL_MIN = 1.0E-2
+#override HTBL_SHELF_MIN = 2.0
+#override BOUND_SALINITY = True
+ 
+! SHEAR MIXING
+#override USE_JACKSON_PARAM = True
+#override RINO_CRIT = 0.25
+!#override KD_KAPPA_SHEAR_0 = 1.0E-2
+
+! SPONGE
+#override SPONGE = TRUE
+ISOMIP_SPONGE_FILE = "3D_LAYER_WARM_TPY_IC.nc"
+#override ISOMIP_TNUDG = 0.1
+!#override ISOMIP_SPONGE_TEMP_OFFSET=0.1
+
+! PASSIVE TRACERS
+USE_ISOMIP_TRACER = True
+
+! Simulation time
+#override DAYMAX = 730
+
+!#override FIT_SALINITY = False
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/README b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/README
new file mode 100644
index 0000000..c042733
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/README
@@ -0,0 +1 @@
+Ice shelf does not move. Shelf melts using three equation model.
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/SIS_input b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/SIS_input
new file mode 120000
index 0000000..ad3cd99
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/SIS_input
@@ -0,0 +1 @@
+../../../common/SIS_input
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/SIS_override b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/SIS_override
new file mode 100644
index 0000000..f591eb2
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/SIS_override
@@ -0,0 +1,8 @@
+# Blank file in which we can put "overrides" for parameters
+DO_ICEBERGS =False              !   If true, use the icebergs module.
+
+!Time Stepping
+!#override DT_FORCING = 10.0              !   [s] default = 0.0
+!#override DT_RHEOLOGY = 10.0             ! The sub-cycling time step, in s, for iterating
+
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/clean_MOM.sh b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/clean_MOM.sh
new file mode 120000
index 0000000..c5370af
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/clean_MOM.sh
@@ -0,0 +1 @@
+../../../common/clean_MOM.sh
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/data_table b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/data_table
new file mode 120000
index 0000000..5b82b3c
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/data_table
@@ -0,0 +1 @@
+../../../common/data_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/diag_table b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/diag_table
new file mode 120000
index 0000000..cff65fe
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/diag_table
@@ -0,0 +1 @@
+../../../common/diag_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/field_table b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/field_table
new file mode 120000
index 0000000..b5ea991
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/field_table
@@ -0,0 +1 @@
+../../../common/field_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/input.nml b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/input.nml
new file mode 100644
index 0000000..3854fd4
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/input.nml
@@ -0,0 +1,140 @@
+ &MOM_input_nml
+        output_directory = './',
+        input_filename = 'r'
+        restart_input_dir = 'INPUT/',
+        restart_output_dir = 'RESTART/',
+        parameter_filename = 'MOM_input',
+                             'MOM_override' /
+
+ &SIS_input_nml
+        output_directory = './',
+        input_filename = 'r'
+        restart_input_dir = 'INPUT/',
+        restart_output_dir = 'RESTART/',
+        parameter_filename = 'SIS_input',
+                             'SIS_override' /
+
+ &diag_manager_nml
+         max_output_fields=1000
+         max_input_fields=1000
+         max_num_axis_sets=1000
+	 flush_nc_files=.true.
+         max_files=1000
+         max_axes=2000
+ /
+
+ &coupler_nml
+            months = 60,
+            days   = 0,
+            current_date = 1,1,1,0,0,0,
+            hours = 0,
+            minutes =0, 
+            seconds = 0
+            calendar = 'NOLEAP',
+            dt_cpld  = 360.0,
+            dt_atmos = 360.0,
+            do_atmos = .false.,
+            do_land = .false.,
+            do_ice = .true.,
+            do_ocean = .true.,
+            atmos_npes = 0,
+            ocean_npes = 0,
+            concurrent = .false.
+            use_lag_fluxes=.false. /
+
+
+ &icebergs_nml
+    verbose=.false.,
+    verbose_hrs=240,
+    traj_sample_hrs=24000,
+    ignore_ij_restart=.true.
+    halo=2,
+    save_short_traj=.true.
+    debug=.false.,
+    really_debug=.false.,
+    use_slow_find=.true.,
+    add_weight_to_ocean=.true.,
+    passive_mode=.false.,
+    Static_icebergs=.True.,
+    ignore_missing_restart_bergs=.false.,
+    generate_test_icebergs=.false.,
+    speed_limit=0.,
+    use_roundoff_fix=.true.,
+    make_calving_reproduce=.false.,
+    Runge_not_Verlet=.false.,
+    iceberg_bonds_on=.false.,
+    critical_interaction_damping_on=.true.,
+    use_new_predictive_corrective=.true.,
+    interactive_icebergs_on=.false.
+    halo_debugging=.false.
+    spring_coef=0.00001
+    distribution=0.0, 0.99, 0.0, 0.00, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11,
+    hexagonal_icebergs=.true.
+    allow_bergs_to_roll=.true.
+    set_melt_rates_to_zero=.false.
+    use_roundoff_fix=.false.
+    grid_is_latlon=.false.
+    grid_is_regular=.true.
+    initial_orientation=-0.
+    rotate_icebergs_for_mass_spreading=.false.
+    lat_ref=-75.0
+    u_override=0.00
+    v_override=0.00
+    override_iceberg_velocities=.false.
+    add_iceberg_thickness_to_SSH=.false.
+    max_bonds=6
+    Iceberg_melt_without_decay=.true.
+    melt_icebergs_as_ice_shelf=.true.
+    Use_three_equation_model=.true.
+    find_melt_using_spread_mass=.true.
+    use_mixed_layer_salinity_for_thermo=.true.
+    pass_fields_to_ocean_model=.true.
+    rho_bergs=918.0
+    utide_icebergs=0.01
+    ustar_icebergs_bg=0.000
+    cdrag_icebergs =0.0025
+    const_gamma=.false.
+    Gamma_T_3EQ=0.22
+    ignore_traj=.False.
+    read_ocean_depth_from_file=.true.
+    apply_thickness_cutoff_to_bergs_melt=.true.
+    apply_thickness_cutoff_to_gridded_melt=.true.
+    melt_cutoff=10.
+    read_old_restarts=.false.
+    internal_bergs_for_drag=.true.
+    use_mixed_melting=.true.
+ &data_override_nml
+         /
+
+ &fms_io_nml
+         fms_netcdf_restart=.true.
+         threading_read='multi'
+ /
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC' /
+
+ &ice_albedo_nml
+      t_range = 10. /
+
+ &ice_model_nml
+           /
+
+ &monin_obukhov_nml
+            neutral = .true. /
+
+ &ocean_albedo_nml
+      ocean_albedo_option = 5 /
+
+ &sat_vapor_pres_nml
+      construct_table_wrt_liq = .true.,
+      construct_table_wrt_liq_and_ice = .true. /
+
+ &xgrid_nml
+            make_exchange_reproduce = .false.
+            interp_method = 'second_order' /
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/run_script.sh b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/run_script.sh
new file mode 120000
index 0000000..2a081b9
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/run_script.sh
@@ -0,0 +1 @@
+../../../common/run_script.sh
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/submit_to_queue b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/submit_to_queue
new file mode 100644
index 0000000..d35f1b8
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/submit_to_queue
@@ -0,0 +1,25 @@
+#!/bin/csh -f
+#PBS -r y                                                              #This job is restartable
+#PBS -j oe                                                             #STDOUT and STDERR are in the same file, specified below in the '-o' option
+#PBS -q batch                                                          #Do not change this - it tells your job where to run
+#PBS -S /bin/sh                                                        #Do not change this - it keeps your job from issuing a false alarm
+#PBS -E                                                                #Do not change this - it gives your job more and more useful Moab environment variables
+#PBS -N  Bergs_Empty_Run                                               #Job Name:             You may want to change this to reflect your job's purpose or relation to an experiment
+#PBS -l partition=c3
+#PBS -l size=4                                                        #You will need to change this to reflect your job's core requirements - 24 is the current core increment.
+#PBS -l walltime=16:00:00                                              #You MUST change this to reflect your job's expected run time, including copy time
+#PBS -m bea                                                            #Email options: You may want to change this to reduce your incoming email stream
+
+######################################################################################################################
+#
+#  Gaea c1ms batch skeleton version 0.9
+#  
+#  0.9 - Initial version - 20110906 - Daniel Gall - Daniel.Gall@noaa.gov
+#
+######################################################################################################################
+
+#Source the system initialization scripts (but not the user's so as to avoid interactive settings that can poison us)
+source /etc/csh.cshrc
+
+#Run the experiment
+aprun -n 128 ../../../../../build/intel/ice_ocean_SIS2/repro/MOM6
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/MOM_input b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/MOM_input
new file mode 120000
index 0000000..a756962
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/MOM_input
@@ -0,0 +1 @@
+../../../common/MOM_input
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/MOM_override b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/MOM_override
new file mode 100644
index 0000000..e2277a9
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/MOM_override
@@ -0,0 +1,91 @@
+! Blank file in which we can put "overrides" for parameters
+! z
+#override USE_REGRIDDING = True
+#override REGRIDDING_COORDINATE_MODE = "SIGMA_SHELF_ZSTAR" 
+#override INTERPOLATION_SCHEME = "PPM_H4"
+#override REMAPPING_SCHEME = "PPM_H4"
+
+
+!TPY params
+#override NK = 72
+#override NKML = 4
+
+! TIME STEP
+#override DT = 360
+#override DT_THERM = 360
+#override DT_FORCING = 360
+!#override DT = 10
+!#override DT_THERM = 10
+!#override DT_FORCING = 10
+
+! MIXING
+#override SMAGORINSKY_KH = False
+#override BIHARMONIC = False
+#override KH = 6.0  ! back. horiz. visc.
+#override KHTR = 1.0    ! back. horiz. diff.
+#override KD = 5.0E-5     ! back. diapycnal diff.
+#override KV = 1.0E-3     ! back. diapycnal visc.
+
+!WARM IC
+#override ISOMIP_T_SUR = -1.9
+#override ISOMIP_S_SUR = 33.8
+#override ISOMIP_T_BOT = 1.0
+#override ISOMIP_S_BOT = 34.7
+
+! ice shelf
+#override ICE_SHELF = True                !   [Boolean] default = False
+#override SHELF_THERMO = TRUE
+#override SHELF_THREE_EQN = True
+#override SHELF_3EQ_GAMMA = False
+#override UTIDE = 0.01
+!SHELF_S_ROOT = True
+!#override USE_HMIX_SFC_PROP = True
+!#override HMIX_SFC_PROP = 10.
+
+! FRAZIL  - making sure sea ice does not form
+#override FRAZIL = False
+#override PRESSURE_DEPENDENT_FRAZIL = False
+
+! EPBL
+#override ENERGETICS_SFC_PBL = True       !   [Boolean] default = False
+                                ! If true, use an implied energetics planetary boundary
+                                ! layer scheme to determine the diffusivity and viscosity
+                                ! in the surface boundary layer.
+#override EPBL_IS_ADDITIVE = True         !   [Boolean] default = True
+                                ! If true, the diffusivity from ePBL is added to all
+                                ! other diffusivities. Otherwise, the larger of kappa-
+                                ! shear and ePBL diffusivities are used.
+#override USE_MLD_ITERATION = True        !   [Boolean] default = False
+                                ! A logical that determines whether or not to use the
+                                ! MLD to set the EPBL length scale.
+#override HTBL_SHELF_MIN = 10.0
+#override BOUND_SALINITY = True
+
+
+! SHEAR MIXING
+#override USE_JACKSON_PARAM = True
+#override RINO_CRIT = 0.25
+!#override KD_KAPPA_SHEAR_0 = 1.0E-2
+
+! SPONGE
+#override SPONGE = TRUE
+ISOMIP_SPONGE_FILE = "3D_LAYER_WARM_TPY_IC.nc"
+#override ISOMIP_TNUDG = 0.1
+#override ISOMIP_TNUDG = 0.1
+#override ISOMIP_S_SUR_SPONGE = 33.8      !   [not defined] default = 35.0
+                                ! Surface salinity in sponge layer.
+#override ISOMIP_S_BOT_SPONGE = 34.7      !   [not defined] default = 35.0
+                                ! Bottom salinity in sponge layer.
+#override ISOMIP_T_SUR_SPONGE = -1.9      !   [not defined] default = -1.9
+                                ! Surface temperature in sponge layer.
+#override ISOMIP_T_BOT_SPONGE = 1.0
+!#override ISOMIP_SPONGE_TEMP_OFFSET=0.1
+
+! PASSIVE TRACERS
+USE_ISOMIP_TRACER = True
+
+! Simulation time
+#override DAYMAX = 730
+
+!#override FIT_SALINITY = False
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/README b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/README
new file mode 100644
index 0000000..c042733
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/README
@@ -0,0 +1 @@
+Ice shelf does not move. Shelf melts using three equation model.
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/SIS_input b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/SIS_input
new file mode 120000
index 0000000..ad3cd99
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/SIS_input
@@ -0,0 +1 @@
+../../../common/SIS_input
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/SIS_override b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/SIS_override
new file mode 100644
index 0000000..f591eb2
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/SIS_override
@@ -0,0 +1,8 @@
+# Blank file in which we can put "overrides" for parameters
+DO_ICEBERGS =False              !   If true, use the icebergs module.
+
+!Time Stepping
+!#override DT_FORCING = 10.0              !   [s] default = 0.0
+!#override DT_RHEOLOGY = 10.0             ! The sub-cycling time step, in s, for iterating
+
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/clean_MOM.sh b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/clean_MOM.sh
new file mode 120000
index 0000000..c5370af
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/clean_MOM.sh
@@ -0,0 +1 @@
+../../../common/clean_MOM.sh
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/data_table b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/data_table
new file mode 120000
index 0000000..5b82b3c
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/data_table
@@ -0,0 +1 @@
+../../../common/data_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/diag_table b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/diag_table
new file mode 120000
index 0000000..cff65fe
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/diag_table
@@ -0,0 +1 @@
+../../../common/diag_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/field_table b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/field_table
new file mode 120000
index 0000000..b5ea991
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/field_table
@@ -0,0 +1 @@
+../../../common/field_table
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/input.nml b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/input.nml
new file mode 100644
index 0000000..46b34b2
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/input.nml
@@ -0,0 +1,140 @@
+ &MOM_input_nml
+        output_directory = './',
+        input_filename = 'r'
+        restart_input_dir = 'INPUT/',
+        restart_output_dir = 'RESTART/',
+        parameter_filename = 'MOM_input',
+                             'MOM_override' /
+
+ &SIS_input_nml
+        output_directory = './',
+        input_filename = 'r'
+        restart_input_dir = 'INPUT/',
+        restart_output_dir = 'RESTART/',
+        parameter_filename = 'SIS_input',
+                             'SIS_override' /
+
+ &diag_manager_nml
+         max_output_fields=1000
+         max_input_fields=1000
+         max_num_axis_sets=1000
+	 flush_nc_files=.true.
+         max_files=1000
+         max_axes=2000
+ /
+
+ &coupler_nml
+            months = 60,
+            days   = 0,
+            current_date = 1,1,1,0,0,0,
+            hours = 0,
+            minutes =0, 
+            seconds = 0
+            calendar = 'NOLEAP',
+            dt_cpld  = 360.0,
+            dt_atmos = 3600.0,
+            do_atmos = .false.,
+            do_land = .false.,
+            do_ice = .true.,
+            do_ocean = .true.,
+            atmos_npes = 0,
+            ocean_npes = 0,
+            concurrent = .false.
+            use_lag_fluxes=.false. /
+
+
+ &icebergs_nml
+    verbose=.false.,
+    verbose_hrs=240,
+    traj_sample_hrs=24000,
+    ignore_ij_restart=.true.
+    halo=2,
+    save_short_traj=.true.
+    debug=.false.,
+    really_debug=.false.,
+    use_slow_find=.true.,
+    add_weight_to_ocean=.true.,
+    passive_mode=.false.,
+    Static_icebergs=.True.,
+    ignore_missing_restart_bergs=.false.,
+    generate_test_icebergs=.false.,
+    speed_limit=0.,
+    use_roundoff_fix=.true.,
+    make_calving_reproduce=.false.,
+    Runge_not_Verlet=.false.,
+    iceberg_bonds_on=.false.,
+    critical_interaction_damping_on=.true.,
+    use_new_predictive_corrective=.true.,
+    interactive_icebergs_on=.false.
+    halo_debugging=.false.
+    spring_coef=0.00001
+    distribution=0.0, 0.99, 0.0, 0.00, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11,
+    hexagonal_icebergs=.true.
+    allow_bergs_to_roll=.true.
+    set_melt_rates_to_zero=.false.
+    use_roundoff_fix=.false.
+    grid_is_latlon=.false.
+    grid_is_regular=.true.
+    initial_orientation=-0.
+    rotate_icebergs_for_mass_spreading=.false.
+    lat_ref=-75.0
+    u_override=0.00
+    v_override=0.00
+    override_iceberg_velocities=.false.
+    add_iceberg_thickness_to_SSH=.false.
+    max_bonds=6
+    Iceberg_melt_without_decay=.true.
+    melt_icebergs_as_ice_shelf=.true.
+    Use_three_equation_model=.true.
+    find_melt_using_spread_mass=.true.
+    use_mixed_layer_salinity_for_thermo=.true.
+    pass_fields_to_ocean_model=.true.
+    rho_bergs=918.0
+    utide_icebergs=0.01
+    ustar_icebergs_bg=0.000
+    cdrag_icebergs =0.0025
+    const_gamma=.false.
+    Gamma_T_3EQ=0.22
+    ignore_traj=.False.
+    read_ocean_depth_from_file=.true.
+    apply_thickness_cutoff_to_bergs_melt=.true.
+    apply_thickness_cutoff_to_gridded_melt=.true.
+    melt_cutoff=10.
+    read_old_restarts=.false.
+    internal_bergs_for_drag=.true.
+    use_mixed_melting=.true.
+ &data_override_nml
+         /
+
+ &fms_io_nml
+         fms_netcdf_restart=.true.
+         threading_read='multi'
+ /
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC' /
+
+ &ice_albedo_nml
+      t_range = 10. /
+
+ &ice_model_nml
+           /
+
+ &monin_obukhov_nml
+            neutral = .true. /
+
+ &ocean_albedo_nml
+      ocean_albedo_option = 5 /
+
+ &sat_vapor_pres_nml
+      construct_table_wrt_liq = .true.,
+      construct_table_wrt_liq_and_ice = .true. /
+
+ &xgrid_nml
+            make_exchange_reproduce = .false.
+            interp_method = 'second_order' /
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/run_script.sh b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/run_script.sh
new file mode 120000
index 0000000..2a081b9
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/run_script.sh
@@ -0,0 +1 @@
+../../../common/run_script.sh
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/submit_to_queue b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/submit_to_queue
new file mode 100644
index 0000000..d35f1b8
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/submit_to_queue
@@ -0,0 +1,25 @@
+#!/bin/csh -f
+#PBS -r y                                                              #This job is restartable
+#PBS -j oe                                                             #STDOUT and STDERR are in the same file, specified below in the '-o' option
+#PBS -q batch                                                          #Do not change this - it tells your job where to run
+#PBS -S /bin/sh                                                        #Do not change this - it keeps your job from issuing a false alarm
+#PBS -E                                                                #Do not change this - it gives your job more and more useful Moab environment variables
+#PBS -N  Bergs_Empty_Run                                               #Job Name:             You may want to change this to reflect your job's purpose or relation to an experiment
+#PBS -l partition=c3
+#PBS -l size=4                                                        #You will need to change this to reflect your job's core requirements - 24 is the current core increment.
+#PBS -l walltime=16:00:00                                              #You MUST change this to reflect your job's expected run time, including copy time
+#PBS -m bea                                                            #Email options: You may want to change this to reduce your incoming email stream
+
+######################################################################################################################
+#
+#  Gaea c1ms batch skeleton version 0.9
+#  
+#  0.9 - Initial version - 20110906 - Daniel Gall - Daniel.Gall@noaa.gov
+#
+######################################################################################################################
+
+#Source the system initialization scripts (but not the user's so as to avoid interactive settings that can poison us)
+source /etc/csh.cshrc
+
+#Run the experiment
+aprun -n 128 ../../../../../build/intel/ice_ocean_SIS2/repro/MOM6
diff --git a/test/Iceberg_repository/ISOMIP_Calving/common/MOM_input b/test/Iceberg_repository/ISOMIP_Calving/common/MOM_input
new file mode 100644
index 0000000..1b56f9f
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/common/MOM_input
@@ -0,0 +1,721 @@
+/* This input file provides the adjustable run-time parameters for version 6 of
+   the Modular Ocean Model (MOM6), a numerical ocean model developed at NOAA-GFDL.
+   Where appropriate, parameters use usually given in MKS units.
+
+   This particular file is for the "quiet" rho ISOMIP test case.
+
+   This MOM_input file typically contains only the non-default values that are
+   needed to reproduce this example.  A full list of parameters for this example
+   can be found in the corresponding MOM_parameter_doc.all file which is
+   generated by the model at run-time. */
+
+REENTRANT_X = False             !   [Boolean] default = True
+                                ! If true, the domain is zonally reentrant.
+NIHALO = 4                      ! default = 2
+                                ! The number of halo points on each side in the
+                                ! x-direction.  With STATIC_MEMORY_ this is set as NIHALO_
+                                ! in MOM_memory.h at compile time; without STATIC_MEMORY_
+                                ! the default is NIHALO_ in MOM_memory.h (if defined) or 2.
+NJHALO = 4                      ! default = 2
+                                ! The number of halo points on each side in the
+                                ! y-direction.  With STATIC_MEMORY_ this is set as NJHALO_
+                                ! in MOM_memory.h at compile time; without STATIC_MEMORY_
+                                ! the default is NJHALO_ in MOM_memory.h (if defined) or 2.
+NIGLOBAL = 240                  !
+                                ! The total number of thickness grid points in the
+                                ! x-direction in the physical domain. With STATIC_MEMORY_
+                                ! this is set in MOM_memory.h at compile time.
+NJGLOBAL = 40                   !
+                                ! The total number of thickness grid points in the
+                                ! y-direction in the physical domain. With STATIC_MEMORY_
+                                ! this is set in MOM_memory.h at compile time.
+IO_LAYOUT = 1, 1                ! default = 0
+                                ! The processor layout to be used, or 0,0 to automatically
+                                ! set the io_layout to be the same as the layout.
+
+! === module MOM_grid ===
+
+! === module MOM_verticalGrid ===
+Z_OUTPUT_GRID_FILE = "ISOMIP_zgrid.nc" ! default = ""
+                                ! The file that specifies the vertical grid for
+                                ! depth-space diagnostics, or blank to disable
+                                ! depth-space output.
+! Parameters providing information about the vertical grid.
+RHO_0 = 1028.0                  !   [kg m-3] default = 1035.0
+                                ! The mean ocean density used with BOUSSINESQ true to
+                                ! calculate accelerations and the mass for conservation
+                                ! properties, or with BOUSSINSEQ false to convert some
+                                ! parameters from vertical units of m to kg m-2.
+ANGSTROM = 1.0E-15              !   [m] default = 1.0E-10
+                                ! The minumum layer thickness, usually one-Angstrom.
+NK = 36                         !   [nondim]
+                                ! The number of model layers.
+
+! === module MOM ===
+BULKMIXEDLAYER = False          !   [Boolean] default = True
+                                ! If true, use a Kraus-Turner-like bulk mixed layer
+                                ! with transitional buffer layers.  Layers 1 through
+                                ! NKML+NKBL have variable densities. There must be at
+                                ! least NKML+NKBL+1 layers if BULKMIXEDLAYER is true.
+                                ! The default is the same setting as ENABLE_THERMODYNAMICS.
+REGRID_USE_OLD_DIRECTION = False ! [Boolean] default = True
+                                ! This is an undocumented parameter.
+DT = 1000.0                      !   [s]
+                                ! The (baroclinic) dynamics time step.  The time-step that
+                                ! is actually used will be an integer fraction of the
+                                ! forcing time-step (DT_FORCING in ocean-only mode or the
+                                ! coupling timestep in coupled mode.)
+DEBUG = False                   !   [Boolean] default = False
+                                ! If true, write out verbose debugging data.
+DT_THERM = 1000.0                !   [s] default = 300.0
+                                ! The thermodynamic and tracer advection time step.
+                                ! Ideally DT_THERM should be an integer multiple of DT
+                                ! and less than the forcing or coupling time-step, unless
+                                ! THERMO_SPANS_COUPLING is true, in which case DT_THERM
+                                ! can be an integer multiple of the coupling timestep.  By
+                                ! default DT_THERM is set to DT.
+DTBT_RESET_PERIOD = 0.0         !   [s] default = 300.0
+                                ! The period between recalculations of DTBT (if DTBT <= 0).
+                                ! If DTBT_RESET_PERIOD is negative, DTBT is set based
+                                ! only on information available at initialization.  If
+                                ! dynamic, DTBT will be set at least every forcing time
+                                ! step, and if 0, every dynamics time step.  The default is
+                                ! set by DT_THERM.  This is only used if SPLIT is true.
+C_P = 3974.0                    !   [J kg-1 K-1] default = 3991.86795711963
+                                ! The heat capacity of sea water, approximated as a
+                                ! constant. This is only used if ENABLE_THERMODYNAMICS is
+                                ! true. The default value is from the TEOS-10 definition
+                                ! of conservative temperature.
+SAVE_INITIAL_CONDS = True       !   [Boolean] default = False
+                                ! If true, write the initial conditions to a file given
+                                ! by IC_OUTPUT_FILE.
+IC_OUTPUT_FILE = "ISOMIP_IC"    ! default = "MOM_IC"
+                                ! The file into which to write the initial conditions.
+HMIX_SFC_PROP = 1.0             !   [m] default = 1.0
+                                ! If BULKMIXEDLAYER is false, HMIX_SFC_PROP is the depth
+                                ! over which to average to find surface properties like
+                                ! SST and SSS or density and surface velocities.
+
+! === module MOM_tracer_registry ===
+EQN_OF_STATE = "LINEAR"         ! default = "WRIGHT"
+                                ! EQN_OF_STATE determines which ocean equation of state
+                                ! should be used.  Currently, the valid choices are
+                                ! "LINEAR", "UNESCO", and "WRIGHT".
+                                ! This is only used if USE_EOS is true.
+RHO_T0_S0 = 999.910681          !   [kg m-3] default = 1000.0
+                                ! When EQN_OF_STATE=LINEAR,
+                                ! this is the density at T=0, S=0.
+DRHO_DT = -0.038357             !   [kg m-3 K-1] default = -0.2
+                                ! When EQN_OF_STATE=LINEAR,
+                                ! this is the partial derivative of density with
+                                ! temperature.
+DRHO_DS = 0.805876              !   [kg m-3 PSU-1] default = 0.8
+                                ! When EQN_OF_STATE=LINEAR,
+                                ! this is the partial derivative of density with
+                                ! salinity.
+TFREEZE_FORM = "LINEAR"         ! default = "LINEAR"
+                                ! TFREEZE_FORM determines which expression should be
+                                ! used for the freezing point.  Currently, the valid
+                                ! choices are "LINEAR", "MILLERO_78".
+TFREEZE_S0_P0 = 0.0832          !   [deg C] default = 0.0
+                                ! When TFREEZE_FORM=LINEAR,
+                                ! this is the freezing potential temperature at
+                                ! S=0, P=0.
+DTFREEZE_DS = -0.0573           !   [deg C PSU-1] default = -0.054
+                                ! When TFREEZE_FORM=LINEAR,
+                                ! this is the derivative of the freezing potential
+                                ! temperature with salinity.
+DTFREEZE_DP = -7.53E-08         !   [deg C Pa-1] default = 0.0
+                                ! When TFREEZE_FORM=LINEAR,
+                                ! this is the derivative of the freezing potential
+                                ! temperature with pressure.
+! === module MOM_tracer_flow_control ===
+INPUTDIR = "INPUT"              ! default = "."
+                                ! The directory in which input files are found.
+
+! === module MOM_grid_init ===
+GRID_CONFIG = "cartesian"       !
+                                ! A character string that determines the method for
+                                ! defining the horizontal grid.  Current options are:
+                                !     mosaic - read the grid from a mosaic (supergrid)
+                                !              file set by GRID_FILE.
+                                !     cartesian - use a (flat) Cartesian grid.
+                                !     spherical - use a simple spherical grid.
+                                !     mercator - use a Mercator spherical grid.
+AXIS_UNITS = "k"                ! default = "degrees"
+                                ! The units for the Cartesian axes. Valid entries are:
+                                !     degrees - degrees of latitude and longitude
+                                !     m - meters
+                                !     k - kilometers
+SOUTHLAT = 0.0                  !   [k]
+                                ! The southern latitude of the domain or the equivalent
+                                ! starting value for the y-axis.
+LENLAT = 80.0                   !   [k]
+                                ! The latitudinal or y-direction length of the domain.
+WESTLON = 320.0                 !   [k] default = 0.0
+                                ! The western longitude of the domain or the equivalent
+                                ! starting value for the x-axis.
+LENLON = 480.0                  !   [k]
+                                ! The longitudinal or x-direction length of the domain.
+TOPO_CONFIG = "ISOMIP"          !
+                                ! This specifies how bathymetry is specified:
+                                !     file - read bathymetric information from the file
+                                !       specified by (TOPO_FILE).
+                                !     flat - flat bottom set to MAXIMUM_DEPTH.
+                                !     bowl - an analytically specified bowl-shaped basin
+                                !       ranging between MAXIMUM_DEPTH and MINIMUM_DEPTH.
+                                !     spoon - a similar shape to 'bowl', but with an vertical
+                                !       wall at the southern face.
+                                !     halfpipe - a zonally uniform channel with a half-sine
+                                !       profile in the meridional direction.
+                                !     benchmark - use the benchmark test case topography.
+                                !     DOME - use a slope and channel configuration for the
+                                !       DOME sill-overflow test case.
+                                !     ISOMIP - use a slope and channel configuration for the
+                                !       ISOMIP test case.
+                                !     DOME2D - use a shelf and slope configuration for the
+                                !       DOME2D gravity current/overflow test case.
+                                !     seamount - Gaussian bump for spontaneous motion test case.
+                                !     Phillips - ACC-like idealized topography used in the Phillips config.
+                                !     USER - call a user modified routine.
+
+! === module ISOMIP_initialize_topography ===
+MINIMUM_DEPTH = 1.0             !   [m] default = 0.0
+                                ! The minimum depth of the ocean.
+MAXIMUM_DEPTH = 720.0           !   [m]
+                                ! The maximum depth of the ocean.
+ROTATION = "beta"               ! default = "2omegasinlat"
+                                ! This specifies how the Coriolis parameter is specified:
+                                !     2omegasinlat - Use twice the planetary rotation rate
+                                !       times the sine of latitude.
+                                !     betaplane - Use a beta-plane or f-plane.
+                                !     USER - call a user modified routine.
+F_0 = -1.40871E-04              !   [s-1] default = 0.0
+                                ! The reference value of the Coriolis parameter with the
+                                ! betaplane option.
+COORD_CONFIG = "linear"         !
+                                ! This specifies how layers are to be defined:
+                                !     file - read coordinate information from the file
+                                !       specified by (COORD_FILE).
+                                !     linear - linear based on interfaces not layers
+                                !     layer_ref - linear based on layer densities
+                                !     ts_ref - use reference temperature and salinity
+                                !     ts_range - use range of temperature and salinity
+                                !       (T_REF and S_REF) to determine surface density
+                                !       and GINT calculate internal densities.
+                                !     gprime - use reference density (RHO_0) for surface
+                                !       density and GINT calculate internal densities.
+                                !     ts_profile - use temperature and salinity profiles
+                                !       (read from COORD_FILE) to set layer densities.
+                                !     USER - call a user modified routine.
+LIGHTEST_DENSITY = 1027.1524    !   [kg m-3] default = 1027.0
+                                ! The reference potential density used for the surface
+                                ! interface.
+DENSITY_RANGE = 0.7438856       !   [kg m-3] default = 2.0
+                                ! The range of reference potential densities across
+                                ! all interfaces.
+BOUNDARY_EXTRAPOLATION_PRESSURE = True !   [Boolean] default = True
+                                ! When defined, the reconstruction is extrapolated
+                                ! within boundary cells rather than assume PCM for the.
+                                ! calculation of pressure. e.g. if PPM is used, a
+                                ! PPM reconstruction will also be used within
+                                ! boundary cells.
+RECONSTRUCT_FOR_PRESSURE = True !   [Boolean] default = True
+                                ! If True, use vertical reconstruction of T/S within
+                                ! the integrals of teh FV pressure gradient calculation.
+                                ! If False, use the constant-by-layer algorithm.
+                                ! By default, this is True when using ALE and False otherwise.
+PRESSURE_RECONSTRUCTION_SCHEME = 1 ! default = 1
+                                ! Type of vertical reconstruction of T/S to use in integrals
+                                ! within the FV pressure gradient calculation. 1: PLM reconstruction.
+                                !  2: PPM reconstruction.
+REMAP_UV_USING_OLD_ALG = False  !   [Boolean] default = True
+                                ! If true, uses the old remapping-via-a-delta-z method for
+                                ! remapping u and v. If false, uses the new method that remaps
+                                ! between grids described by an old and new thickness.
+MIN_THICKNESS = 1.0E-12         !   [m] default = 0.001
+                                ! When regridding, this is the minimum layer
+                                ! thickness allowed.
+BOUNDARY_EXTRAPOLATION = True   !   [Boolean] default = False
+                                ! When defined, a proper high-order reconstruction
+                                ! scheme is used within boundary cells rather
+                                ! than PCM. E.g., if PPM is used for remapping, a
+                                ! PPM reconstruction will also be used within
+                                ! boundary cells.
+REMAP_AFTER_INITIALIZATION = False !   [Boolean] default = True
+                                ! If true, applies regridding and remapping immediately after
+                                ! initialization so that the state is ALE consistent. This is a
+                                ! legacy step and should not be needed if the initialization is
+                                ! consistent with the coordinate mode.
+THICKNESS_CONFIG = "ISOMIP"     !
+                                ! A string that determines how the initial layer
+                                ! thicknesses are specified for a new run:
+                                !     file - read interface heights from the file specified
+                                !     thickness_file - read thicknesses from the file specified
+                                !       by (THICKNESS_FILE).
+                                !     coord - determined by ALE coordinate.
+                                !     uniform - uniform thickness layers evenly distributed
+                                !       between the surface and MAXIMUM_DEPTH.
+                                !     DOME - use a slope and channel configuration for the
+                                !       DOME sill-overflow test case.
+                                !     ISOMIP - use a configuration for the
+                                !       ISOMIP test case.
+                                !     benchmark - use the benchmark test case thicknesses.
+                                !     search - search a density profile for the interface
+                                !       densities. This is not yet implemented.
+                                !     circle_obcs - the circle_obcs test case is used.
+                                !     DOME2D - 2D version of DOME initialization.
+                                !     adjustment2d - TBD AJA.
+                                !     sloshing - TBD AJA.
+                                !     seamount - TBD AJA.
+                                !     rossby_front - a mixed layer front in thermal wind balance.
+                                !     USER - call a user modified routine.
+SPONGE_CONFIG = "ISOMIP"    ! default = "file"
+                                ! A string that sets how the sponges are configured:
+                                !     ISOMIP - use a configuration for the
+                                !       ISOMIP test case.
+                                !     USER - call a user modified routine.
+ISOMIP_TNUDG = 0.1                     !  default = 0.0 (days)
+                                ! Nudging time scale for sponge layers.
+TS_CONFIG = "ISOMIP"            !
+                                ! A string that determines how the initial tempertures
+                                ! and salinities are specified for a new run:
+                                !     file - read velocities from the file specified
+                                !       by (TS_FILE).
+                                !     fit - find the temperatures that are consistent with
+                                !       the layer densities and salinity S_REF.
+                                !     TS_profile - use temperature and salinity profiles
+                                !       (read from TS_FILE) to set layer densities.
+                                !     benchmark - use the benchmark test case T & S.
+                                !     linear - linear in logical layer space.
+                                !     DOME2D - 2D DOME initialization.
+                                !     ISOMIP - ISOMIP initialization.
+                                !     adjustment2d - TBD AJA.
+                                !     sloshing - TBD AJA.
+                                !     seamount - TBD AJA.
+                                !     rossby_front - a mixed layer front in thermal wind balance.
+                                !     SCM_ideal_hurr - used in the SCM idealized hurricane test.
+                                !     USER - call a user modified routine.
+T_REF = -1.9                    !   [degC]
+                                ! A reference temperature used in initialization.
+FIT_SALINITY = True             ! If true, accept the prescribed temperature and fit the
+                                ! salinity; otherwise take salinity and fit temperature.
+VELOCITY_CONFIG = "zero"        ! default = "zero"
+                                ! A string that determines how the initial velocities
+                                ! are specified for a new run:
+                                !     file - read velocities from the file specified
+                                !       by (VELOCITY_FILE).
+                                !     zero - the fluid is initially at rest.
+                                !     uniform - the flow is uniform (determined by
+                                !       parameters INITIAL_U_CONST and INITIAL_V_CONST).
+                                !     rossby_front - a mixed layer front in thermal wind balance.
+                                !     USER - call a user modified routine.
+TRIM_IC_FOR_P_SURF = True       !   [Boolean] default = False
+                                ! If true, cuts way the top of the column for initial conditions
+                                ! at the depth where the hydrostatic presure matches the imposed
+                                ! surface pressure which is read from file.
+SURFACE_PRESSURE_FILE = "isomip_ice_shelf1_clipped.nc" !
+                                ! The initial condition file for the surface height.
+SURFACE_PRESSURE_VAR = "p_surf"!   [kg m-2] default = ""
+!SURFACE_PRESSURE_VAR = "thick"  !   [kg m-2] default = ""
+                                ! The initial condition variable for the surface height.
+!SURFACE_PRESSURE_SCALE = 8996.4 ! [file dependent] default = 1.0
+SURFACE_PRESSURE_SCALE = 1.0   ! [file dependent] default = 1.0
+                                ! A scaling factor to convert SURFACE_PRESSURE_VAR from
+                                ! file SURFACE_PRESSURE_FILE into a surface pressure.
+SPONGE = False                  !   [Boolean] default = False
+                                ! If true, sponges may be applied anywhere in the domain.
+                                ! The exact location and properties of those sponges are
+                                ! specified via SPONGE_CONFIG.
+
+! === module MOM_MEKE ===
+! === module MOM_set_visc ===
+BOTTOMDRAGLAW = True            !   [Boolean] default = True
+                                ! If true, the bottom stress is calculated with a drag
+                                ! law of the form c_drag*|u|*u. The velocity magnitude
+                                ! may be an assumed value or it may be based on the
+                                ! actual velocity in the bottommost HBBL, depending on
+                                ! LINEAR_DRAG.
+CHANNEL_DRAG = False            !   [Boolean] default = False
+                                ! If true, the bottom drag is exerted directly on each
+                                ! layer proportional to the fraction of the bottom it
+                                ! overlies.
+CDRAG = 0.0025                   !   [nondim] default = 0.003
+                                ! CDRAG is the drag coefficient relating the magnitude of
+                                ! the velocity field to the bottom stress. CDRAG is only
+                                ! used if BOTTOMDRAGLAW is defined.
+BBL_USE_EOS = True              !   [Boolean] default = False
+                                ! If true, use the equation of state in determining the
+                                ! properties of the bottom boundary layer.  Otherwise use
+                                ! the layer target potential densities.
+BBL_THICK_MIN = 2.0             !   [m] default = 0.0
+                                ! The minimum bottom boundary layer thickness that can be
+                                ! used with BOTTOMDRAGLAW. This might be
+                                ! Kv / (cdrag * drag_bg_vel) to give Kv as the minimum
+                                ! near-bottom viscosity.
+HTBL_SHELF_MIN = 2.0            !   [m] default = 2.0
+                                ! The minimum top boundary layer thickness that can be
+                                ! used with BOTTOMDRAGLAW. This might be
+                                ! Kv / (cdrag * drag_bg_vel) to give Kv as the minimum
+                                ! near-top viscosity.
+HTBL_SHELF = 2.0               !   [m] default = 10.0
+                                ! The thickness over which near-surface velocities are
+                                ! averaged for the drag law under an ice shelf.  By
+                                ! default this is the same as HBBL
+KV = 1.0E-06                    !   [m2 s-1]
+                                ! The background kinematic viscosity in the interior.
+                                ! The molecular value, ~1e-6 m2 s-1, may be used.
+BE = 0.7                        !   [nondim] default = 0.6
+                                ! If SPLIT is true, BE determines the relative weighting
+                                ! of a  2nd-order Runga-Kutta baroclinic time stepping
+                                ! scheme (0.5) and a backward Euler scheme (1) that is
+                                ! used for the Coriolis and inertial terms.  BE may be
+                                ! from 0.5 to 1, but instability may occur near 0.5.
+                                ! BE is also applicable if SPLIT is false and USE_RK2
+                                ! is true.
+ETA_TOLERANCE = 1.0E-12         !   [m] default = 1.25E-14
+                                ! The tolerance for the differences between the
+                                ! barotropic and baroclinic estimates of the sea surface
+                                ! height due to the fluxes through each face.  The total
+                                ! tolerance for SSH is 4 times this value.  The default
+                                ! is 0.5*NK*ANGSTROM, and this should not be set less x
+                                ! than about 10^-15*MAXIMUM_DEPTH.
+CORIOLIS_EN_DIS = True          !   [Boolean] default = False
+                                ! If true, two estimates of the thickness fluxes are used
+                                ! to estimate the Coriolis term, and the one that
+                                ! dissipates energy relative to the other one is used.
+CORIOLIS_SCHEME = "SADOURNY75_ENERGY" ! default = "SADOURNY75_ENERGY"
+                                ! CORIOLIS_SCHEME selects the discretization for the
+                                ! Coriolis terms. Valid values are:
+                                !    SADOURNY75_ENERGY - Sadourny, 1975; energy cons.
+                                !    ARAKAWA_HSU90     - Arakawa & Hsu, 1990
+                                !    SADOURNY75_ENSTRO - Sadourny, 1975; enstrophy cons.
+                                !    ARAKAWA_LAMB81    - Arakawa & Lamb, 1981; En. + Enst.
+                                !    ARAKAWA_LAMB_BLEND - A blend of Arakawa & Lamb with
+                                !                         Arakawa & Hsu and Sadourny energy
+BOUND_CORIOLIS = True           !   [Boolean] default = False
+                                ! If true, the Coriolis terms at u-points are bounded by
+                                ! the four estimates of (f+rv)v from the four neighboring
+                                ! v-points, and similarly at v-points.  This option is
+                                ! always effectively false with CORIOLIS_EN_DIS defined and
+                                ! CORIOLIS_SCHEME set to SADOURNY75_ENERGY.
+ANALYTIC_FV_PGF = True          !   [Boolean] default = True
+                                ! If true the pressure gradient forces are calculated
+                                ! with a finite volume form that analytically integrates
+                                ! the equations of state in pressure to avoid any
+                                ! possibility of numerical thermobaric instability, as
+                                ! described in Adcroft et al., O. Mod. (2008).
+MASS_WEIGHT_IN_PRESSURE_GRADIENT = True !   [Boolean] default = False
+                                ! If true, use mass weighting when interpolation T/S for
+                                ! top/bottom integrals in AFV pressure gradient calculation.
+
+! === module MOM_hor_visc ===
+LAPLACIAN = True                !   [Boolean] default = False
+                                ! If true, use a Laplacian horizontal viscosity.
+KH = 0.0                        !   [m2 s-1] default = 0.0
+                                ! The background Laplacian horizontal viscosity.
+KH_VEL_SCALE = 0.0              !   [m s-1] default = 0.0
+                                ! The velocity scale which is multiplied by the grid
+                                ! spacing to calculate the Laplacian viscosity.
+                                ! The final viscosity is the largest of this scaled
+                                ! viscosity, the Smagorinsky viscosity and KH.
+SMAGORINSKY_KH = True           !   [Boolean] default = False
+                                ! If true, use a Smagorinsky nonlinear eddy viscosity.
+SMAG_LAP_CONST = 0.15           !   [nondim] default = 0.0
+                                ! The nondimensional Laplacian Smagorinsky constant,
+                                ! often 0.15.
+BIHARMONIC = True               !   [Boolean] default = True
+                                ! If true, use a biharmonic horizontal viscosity.
+                                ! BIHARMONIC may be used with LAPLACIAN.
+AH = 0.0                        !   [m4 s-1] default = 0.0
+                                ! The background biharmonic horizontal viscosity.
+AH_VEL_SCALE = 0.005            !   [m s-1] default = 0.0
+                                ! The velocity scale which is multiplied by the cube of
+                                ! the grid spacing to calculate the biharmonic viscosity.
+                                ! The final viscosity is the largest of this scaled
+                                ! viscosity, the Smagorinsky viscosity and AH.
+SMAGORINSKY_AH = True           !   [Boolean] default = False
+                                ! If true, use a biharmonic Smagorinsky nonlinear eddy
+                                ! viscosity.
+SMAG_BI_CONST = 0.06            !   [nondim] default = 0.0
+                                ! The nondimensional biharmonic Smagorinsky constant,
+                                ! typically 0.015 - 0.06.
+
+! === module MOM_vert_friction ===
+U_TRUNC_FILE = "U_velocity_truncations" ! default = ""
+                                ! The absolute path to a file into which the accelerations
+                                ! leading to zonal velocity truncations are written.
+                                ! Undefine this for efficiency if this diagnostic is not
+                                ! needed.
+V_TRUNC_FILE = "V_velocity_truncations" ! default = ""
+                                ! The absolute path to a file into which the accelerations
+                                ! leading to meridional velocity truncations are written.
+                                ! Undefine this for efficiency if this diagnostic is not
+                                ! needed.
+HARMONIC_BL_SCALE = 1.0         !   [nondim] default = 0.0
+                                ! A scale to determine when water is in the boundary
+                                ! layers based solely on harmonic mean thicknesses for
+                                ! the purpose of determining the extent to which the
+                                ! thicknesses used in the viscosities are upwinded.
+HMIX_FIXED = 20.0               !   [m]
+                                ! The prescribed depth over which the near-surface
+                                ! viscosity and diffusivity are elevated when the bulk
+                                ! mixed layer is not used.
+!KVML = 1.0E-06                  !   [m2 s-1] default = 1.0E-04
+                                ! The kinematic viscosity in the mixed layer.  A typical
+                                ! value is ~1e-2 m2 s-1. KVML is not used if
+                                ! BULKMIXEDLAYER is true.  The default is set by KV.
+HBBL = 5.0                     !   [m]
+                                ! The thickness of a bottom boundary layer with a
+                                ! viscosity of KVBBL if BOTTOMDRAGLAW is not defined, or
+                                ! the thickness over which near-bottom velocities are
+                                ! averaged for the drag law if BOTTOMDRAGLAW is defined
+                                ! but LINEAR_DRAG is not.
+!KV_BBL_MIN = 1.0E-06            !   [m2 s-1] default = 0.0
+                                ! The minimum viscosities in the bottom boundary layer.
+!KV_TBL_MIN = 1.0E-06            !   [m2 s-1] default = 0.0
+                                ! The minimum viscosities in the top boundary layer.
+MAXVEL = 10.0                   !   [m s-1] default = 3.0E+08
+                                ! The maximum velocity allowed before the velocity
+                                ! components are truncated.
+
+! === module MOM_PointAccel ===
+
+! === module MOM_barotropic ===
+BOUND_BT_CORRECTION = True      !   [Boolean] default = False
+                                ! If true, the corrective pseudo mass-fluxes into the
+                                ! barotropic solver are limited to values that require
+                                ! less than maxCFL_BT_cont to be accommodated.
+USE_BT_CONT_TYPE = True         !   [Boolean] default = True
+                                ! If true, use a structure with elements that describe
+                                ! effective face areas from the summed continuity solver
+                                ! as a function the barotropic flow in coupling between
+                                ! the barotropic and baroclinic flow.  This is only used
+                                ! if SPLIT is true.
+DYNAMIC_SURFACE_PRESSURE = True !   [Boolean] default = False
+                                ! If true, add a dynamic pressure due to a viscous ice
+                                ! shelf, for instance.
+BT_THICK_SCHEME = "FROM_BT_CONT" ! default = "FROM_BT_CONT"
+                                ! A string describing the scheme that is used to set the
+                                ! open face areas used for barotropic transport and the
+                                ! relative weights of the accelerations. Valid values are:
+                                !    ARITHMETIC - arithmetic mean layer thicknesses
+                                !    HARMONIC - harmonic mean layer thicknesses
+                                !    HYBRID (the default) - use arithmetic means for
+                                !       layers above the shallowest bottom, the harmonic
+                                !       mean for layers below, and a weighted average for
+                                !       layers that straddle that depth
+                                !    FROM_BT_CONT - use the average thicknesses kept
+                                !       in the h_u and h_v fields of the BT_cont_type
+BEBT = 0.2                      !   [nondim] default = 0.1
+                                ! BEBT determines whether the barotropic time stepping
+                                ! uses the forward-backward time-stepping scheme or a
+                                ! backward Euler scheme. BEBT is valid in the range from
+                                ! 0 (for a forward-backward treatment of nonrotating
+                                ! gravity waves) to 1 (for a backward Euler treatment).
+                                ! In practice, BEBT must be greater than about 0.05.
+DTBT = -0.9                     !   [s or nondim] default = -0.98
+                                ! The barotropic time step, in s. DTBT is only used with
+                                ! the split explicit time stepping. To set the time step
+                                ! automatically based the maximum stable value use 0, or
+                                ! a negative value gives the fraction of the stable value.
+                                ! Setting DTBT to 0 is the same as setting it to -0.98.
+                                ! The value of DTBT that will actually be used is an
+                                ! integer fraction of DT, rounding down.
+
+! === module MOM_thickness_diffuse ===
+KHTH = 0.0                      !   [m2 s-1] default = 0.0
+                                ! The background horizontal thickness diffusivity.
+! === module MOM_diabatic_driver ===
+! The following parameters are used for diabatic processes.
+ENERGETICS_SFC_PBL = False      !   [Boolean] default = False
+                                ! If true, use an implied energetics planetary boundary
+                                ! layer scheme to determine the diffusivity and viscosity
+                                ! in the surface boundary layer.
+
+! === module MOM_KPP ===
+! This is the MOM wrapper to CVmix:KPP
+! See http://code.google.com/p/cvmix/
+USE_KPP = False                 !   [Boolean] default = False
+                                ! If true, turns on the [CVmix] KPP scheme of Large et al., 1994,
+                                ! to calculate diffusivities and non-local transport in the OBL.
+
+! === module MOM_diffConvection ===
+! This module implements enhanced diffusivity as a
+! function of static stability, N^2.
+CONVECTION%
+%CONVECTION
+
+! === module MOM_entrain_diffusive ===
+CORRECT_DENSITY = False         !   [Boolean] default = True
+                                ! If true, and USE_EOS is true, the layer densities are
+                                ! restored toward their target values by the diapycnal
+                                ! mixing, as described in Hallberg (MWR, 2000).
+MAX_ENT_IT = 20                 ! default = 5
+                                ! The maximum number of iterations that may be used to
+                                ! calculate the interior diapycnal entrainment.
+TOLERANCE_ENT = 1.0E-08         !   [m] default = 1.0E-13
+                                ! The tolerance with which to solve for entrainment values.
+BBL_EFFIC = 0.2                 !   [nondim] default = 0.2
+                                ! The efficiency with which the energy extracted by
+                                ! bottom drag drives BBL diffusion.  This is only
+                                ! used if BOTTOMDRAGLAW is true.
+KD = 0.0                        !   [m2 s-1]
+                                ! The background diapycnal diffusivity of density in the
+                                ! interior. Zero or the molecular value, ~1e-7 m2 s-1,
+                                ! may be used.
+KD_MIN = 5.0E-05
+! === module MOM_kappa_shear ===
+! Parameterization of shear-driven turbulence following Jackson, Hallberg and Legg, JPO 2008
+USE_JACKSON_PARAM = False       !   [Boolean] default = False
+                                ! If true, use the Jackson-Hallberg-Legg (JPO 2008)
+                                ! shear mixing parameterization.
+
+! === module MOM_diabatic_aux ===
+! The following parameters are used for auxiliary diabatic processes.
+
+! === module MOM_regularize_layers ===
+
+! === module MOM_opacity ===
+PEN_SW_SCALE = 15.0             !   [m] default = 0.0
+                                ! The vertical absorption e-folding depth of the
+                                ! penetrating shortwave radiation.
+PEN_SW_FRAC = 0.42              !   [nondim] default = 0.0
+                                ! The fraction of the shortwave radiation that penetrates
+                                ! below the surface.
+
+! === module MOM_tracer_advect ===
+
+! === module MOM_tracer_hor_diff ===
+
+! === module MOM_neutral_diffusion ===
+! This module implements neutral diffusion of tracers
+
+! === module MOM_surface_forcing ===
+VARIABLE_WINDS = False          !   [Boolean] default = True
+                                ! If true, the winds vary in time after the initialization.
+VARIABLE_BUOYFORCE = False      !   [Boolean] default = True
+                                ! If true, the buoyancy forcing varies in time after the
+                                ! initialization of the model.
+BUOY_CONFIG = "NONE"            !
+                                ! The character string that indicates how buoyancy forcing
+                                ! is specified. Valid options include (file), (zero),
+                                ! (linear), (USER), and (NONE).
+WIND_CONFIG = "zero"            !
+                                ! The character string that indicates how wind forcing
+                                ! is specified. Valid options include (file), (2gyre),
+                                ! (1gyre), (gyres), (zero), and (USER).
+GUST_CONST = 0.0               !   [Pa] default = 0.02
+                                ! The background gustiness in the winds.
+ICE_SHELF = True                !   [Boolean] default = False
+                                ! If true, enables the ice shelf model.
+!ZSTAR_RIGID_SURFACE_THRESHOLD = 10 !
+
+! === module MOM_grid ===
+! Parameters providing information about the lateral grid.
+
+! === module MOM_hor_index ===
+! Sets the horizontal array index types.
+
+! === module MOM_grid_init ===
+
+! === module MOM_ice_shelf ===
+DYNAMIC_SHELF_MASS = False      !   [Boolean] default = False
+                                ! If true, the ice sheet mass can evolve with time.
+SHELF_THERMO = TRUE            !   [Boolean] default = False
+                                ! If true, use a thermodynamically interactive ice shelf.
+SHELF_THREE_EQN = False         !   [Boolean] default = True
+                                ! If true, use the three equation expression of
+                                ! consistency to calculate the fluxes at the ice-ocean
+                                ! interface.
+SHELF_INSULATOR = True          !   [Boolean] default = False
+                                ! If true, the ice shelf is a perfect insulatior
+                                ! (no conduction).
+SHELF_3EQ_GAMMA = True          !   [Boolean] default = False
+                                ! If true, user specifies a constant nondimensional heat-transfer coefficient
+                                ! (GAMMA_T_3EQ), from which the salt-transfer coefficient is then computed
+                                !  as GAMMA_T_3EQ/35. This is used with SHELF_THREE_EQN.
+SHELF_3EQ_GAMMA_T = 0.22       !   [nondim.] default = 0.022
+                                ! Nondimensional heat-transfer coefficient.
+SHELF_2EQ_GAMMA_T = 0.0         !   [m s-1]
+                                ! If SHELF_THREE_EQN is false, this the fixed turbulent
+                                ! exchange velocity at the ice-ocean interface.
+ICE_SHELF_FLUX_FACTOR = 1.0     !   [none] default = 1.0
+                                ! Non-dimensional factor applied to shelf thermodynamic
+                                ! fluxes.
+ICE_SHELF_TEMPERATURE = -20.0   !   [degC] default = -15.0
+                                ! The temperature at the center of the ice shelf.
+DT_FORCING = 300.0              !   [s] default = 0.0
+                                ! The time step for changing forcing, coupling with other
+                                ! components, or potentially writing certain diagnostics.
+                                ! The default value is given by DT.
+COL_THICK_MELT_THRESHOLD = 10.0  !   [m] default = 0.0
+                                ! The minimum ML thickness where melting is allowed.
+WRITE_OUTPUT_TO_FILE = True     !   [Boolean] default = False
+                                ! for debugging purposes
+USTAR_SHELF_BG = 0.0            !   [m s-1] default = 0.0
+                                ! The minimum value of ustar under ice sheves.
+CDRAG_SHELF = 0.0025            !   [nondim] default = 0.003
+                                ! CDRAG is the drag coefficient relating the magnitude of
+                                ! the velocity field to the surface stress.
+UTIDE = 0.01                   !   [m s-1] default = 0.0
+                                ! The constant tidal amplitude used with INT_TIDE_DISSIPATION.
+MELTING_CUTOFF_DEPTH = 0      ! default = 0.0
+                                ! Depth above which the melt is set to zero (it must be >= 0)
+                                ! Default value won't affect the solution.
+! === module ISOMIP_initialize_topography ===
+ICE_PROFILE_CONFIG = "FILE"     !
+                                ! This specifies how the initial ice profile is specified.
+                                ! Valid values are: CHANNEL, FILE, and USER.
+ICE_THICKNESS_FILE = "isomip_ice_shelf1_clipped.nc" ! default = "ice_shelf_h.nc"
+                                ! The file from which the bathymetry is read.
+ICE_THICKNESS_VARNAME = "thick" ! default = "h_shelf"
+                                ! The name of the thickness variable in ICE_THICKNESS_FILE.
+ICE_AREA_VARNAME = "area"       ! default = "area_shelf_h"
+                                ! The name of the area variable in ICE_THICKNESS_FILE.
+SHELF_IC_OUTPUT_FILE = "MOM_Shelf_IC" ! default = "MOM_Shelf_IC"
+                                ! The name-root of the output file for the ice shelf
+                                ! initial conditions.
+DENSITY_ICE = 918.0             !   [kg m-3] default = 900.0
+                                ! A typical density of ice.
+! === module MOM_sum_output ===
+CALCULATE_APE = False           !   [Boolean] default = True
+                                ! If true, calculate the available potential energy of
+                                ! the interfaces.  Setting this to false reduces the
+                                ! memory footprint of high-PE-count models dramatically.
+MAXTRUNC = 5000                 !   [truncations save_interval-1] default = 0
+                                ! The run will be stopped, and the day set to a very
+                                ! large value if the velocity is truncated more than
+                                ! MAXTRUNC times between energy saves.  Set MAXTRUNC to 0
+                                ! to stop if there is any truncation of velocities.
+DATE_STAMPED_STDOUT = False     !   [Boolean] default = True
+                                ! If true, use dates (not times) in messages to stdout
+MAXCPU = -1.0                   !   [wall-clock seconds] default = -1.0
+                                ! The maximum amount of cpu time per processor for which
+                                ! MOM should run before saving a restart file and
+                                ! quitting with a return value that indicates that a
+                                ! further run is required to complete the simulation.
+                                ! If automatic restarts are not desired, use a negative
+                                ! value for MAXCPU.  MAXCPU has units of wall-clock
+                                ! seconds, so the actual CPU time used is larger by a
+                                ! factor of the number of processors used.
+
+! === module MOM_main (MOM_driver) ===
+DAYMAX = 365.0                   !   [days]
+                                ! The final time of the whole simulation, in units of
+                                ! TIMEUNIT seconds.  This also sets the potential end
+                                ! time of the present run segment if the end time is
+                                ! not set via ocean_solo_nml in input.nml.
+RESTART_CONTROL = 1             ! default = 1
+                                ! An integer whose bits encode which restart files are
+                                ! written. Add 2 (bit 1) for a time-stamped file, and odd
+                                ! (bit 0) for a non-time-stamped file. A non-time-stamped
+                                ! restart file is saved at the end of the run segment
+                                ! for any non-negative value.
+RESTINT = 365.0                 !   [days] default = 0.0
+                                ! The interval between saves of the restart file in units
+                                ! of TIMEUNIT.  Use 0 (the default) to not save
+                                ! incremental restart files at all.
+ENERGYSAVEDAYS = 2.0            !   [days] default = 0.0034722222222222
+                                ! The interval in units of TIMEUNIT between saves of the
+CALC_RHO_FOR_SEA_LEVEL=True
diff --git a/test/Iceberg_repository/ISOMIP_Calving/common/SIS_input b/test/Iceberg_repository/ISOMIP_Calving/common/SIS_input
new file mode 100644
index 0000000..6c8a425
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/common/SIS_input
@@ -0,0 +1,125 @@
+!********+*********+*********+*********+*********+*********+*********+*
+!*   This file determines the adjustable run-time parameters for the  *
+!* Sea Ice Simulator (SIS), versions 2 and later.  Where              *
+!* appropriate, MKS units are used.                                   *
+!********+*********+*********+*********+*********+*********+*********+*
+! >>> Baltic sea coupled ice-ocean SIS2 5 layer ice, 63 layer ocean test case.
+
+!  Specify properties of the physical domain.
+GRID_CONFIG = "mosaic"          !    Method for defining horizontal grid
+                                !  = file|cartesian|spherical|mercator
+                                !  file - read grid from file "GRID_FILE"
+                                !  cartesian - a Cartesian grid
+                                !  spherical - a spherical grid
+                                !  mercator  - a Mercator grid
+GRID_FILE = "ocean_hgrid.nc"
+                                !    Name of file to read horizontal grid data
+INPUTDIR = "INPUT"
+                                !    INPUTDIR is a directory in which NetCDF
+                                !  input files might be found.
+
+CGRID_ICE_DYNAMICS = True       !   If true, use a C-grid discretization of the
+                                ! sea-ice dynamics; if false use a B-grid
+                                ! discretization.
+
+!  Specify the numerical domain.
+NIGLOBAL = 240                   !    NIGLOBAL and NJGLOBAL are the number of thickness
+NJGLOBAL = 40                   !  grid points in the zonal and meridional
+                                !  directions of the physical domain.
+NCAT_ICE = 1                    !    The number of sea ice thickness categories.
+NIHALO = 2                      !    NIHALO and NJHALO are the number of halo
+NJHALO = 2                      !  points on each side in the x- and y-directions.
+                                !  If static memory allocation is used, these
+                                !  must match the values of NIHALO_ and NJHALO_
+                                !  in MOM_memory.h.
+IO_LAYOUT = 1, 1                !    The processor layout to be used, or 0,0 to automatically
+                                !  set the io_layout to be the same as the layout.
+
+REENTRANT_X = False             !    If defined, the domain is zonally reentrant.
+REENTRANT_Y = False             !    If defined, the domain is meridionally
+                                !  reentrant.
+TRIPOLAR_N = False              !    Use tripolar connectivity at the northern
+                                !  edge of the domain.  With TRIPOLAR_N, NIGLOBAL
+                                !  must be even.
+
+DEBUG = False                   !    If true, write out verbose debugging data.
+SEND_LOG_TO_STDOUT = False      !    If true write out log information to stdout.
+TIMEUNIT = 8.64E+04             !   [s] default = 8.64E+04
+ICE_STATS_INTERVAL = 0.25       !    The interval in units of TIMEUNIT between
+                                ! writes of the globally summed ice statistics
+                                ! and conservation checks.
+
+!  Specify the time integration scheme for the ice dynamics.
+DT_ICE_DYNAMICS = 300.0        ! The time step used for the slow ice dynamics, 
+                                ! including stepping the continuity equation and
+                                ! interactions between the ice mass field and 
+                                ! velocities, in s.
+INTERSPERSED_ICE_THERMO = False ! If true, the sea ice thermodynamic updates are applied
+                                ! after the new velocities are determined, but before the
+                                ! transport occurs.  Otherwise, the ice thermodynamic
+                                ! updates occur at the start of the slow ice update and
+                                ! dynamics and continuity can occur together.
+                                ! The default should be changed to false.
+
+DT_RHEOLOGY = 300.0             ! The sub-cycling time step, in s, for iterating
+                                ! the rheology and ice momentum equations. If
+                                ! DT_RHEOLOGY is negative, the time step is set
+                                ! via NSTEPS_DYN.
+PROJECT_ICE_DRAG_VEL = True     ! If true, project forward the ice velocity used in the
+                                ! drag calculation to avoid an instability that can occur
+                                ! when an finite stress is applied to thin ice moving with
+                                ! the velocity of the ocean.
+ICE_TDAMP_ELASTIC = 0.0         !   The damping timescale associated with the
+                                ! elastic terms in the sea-ice dynamics.
+
+SIS_TRACER_ADVECTION_SCHEME = "PPM:H3" ! The horizontal transport scheme for
+                                ! tracers.  Valid options include:
+                                !   UPWIND_2D - Non-directionally split upwind
+                                !   PCM    - Directionally split peicewise constant
+                                !   PLM    - Piecewise Linear Method
+                                !   PPM:H3 - Piecewise Parabolic Method (Huyhn 3rd order)
+SIS_CONTINUITY_SCHEME = "UPWIND_2D" ! default = "UPWIND_2D"
+                                ! The horizontal transport scheme used in continuity:
+                                !   UPWIND_2D - Non-directionally split upwind
+                                !   PCM       - Directionally split peicewise constant
+                                !   PPM:C2PD  - Positive definite PPM with 2nd order edge values
+                                !   PPM:C2MO  - Monotonic PPM with 2nd order edge values
+
+!  Specify the ice properties.
+ICE_STRENGTH_PSTAR = 2.75e4     !    ICE_STRENGTH_PSTAR is a constant in the
+                                !  expression for the ice strength, P* in
+                                !  Hunke & Dukowics '97, in Pa.
+RHO_OCEAN = 1030.0              !    RHO_OCEAN is used in the Boussinesq
+                                !  approximation to calculations of pressure and
+                                !  pressure gradients, in units of kg m-3.
+RHO_ICE = 905.0                 !    RHO_ICE is the nominal density of sea ice
+                                !  used in SIS, in units of kg m-3.
+RHO_SNOW = 330.0                !    RHO_SNOW is the nominal density of snow
+                                !  used in SIS, in units of kg m-3.
+CP_ICE = 2100.0                 !    The heat capacity of fresh ice, approximated
+                                !  as a constant, in J kg-1 K-1.
+CP_SEAWATER = 4200.0            !   The heat capacity of sea water, approximated
+                                !  as a constant, in J kg-1 K-1.
+ICE_BULK_SALINITY = 5.0         !    The fixed bulk salinity of sea ice, in g/kg.
+ICE_RELATIVE_SALINITY = 0.0     !    The initial salinity of sea ice as a
+                                ! fraction of the salinity of the seawater from
+                                ! which it formed.
+SIS2_FILLING_FRAZIL = True      !   If true, apply frazil to fill as many categories as
+                                ! possible to fill in a uniform (minimum) amount of ice
+                                ! in all the thinnest categories. Otherwise the frazil is
+                                ! always assigned to a single category.
+FILLING_FRAZIL_TIMESCALE = 8.64e4 !  A timescale with which the filling frazil
+                                ! causes the thinest cells to attain similar
+                                ! thicknesses, or a negative number to apply
+                                ! the frazil flux uniformly, in s.
+
+!  Specify the properties of the surface forcing.
+ICE_OCEAN_STRESS_STAGGER = "C"  ! default = "B"
+                                ! A case-insensitive character string to indicate the
+                                ! staggering of the stress field on the ocean that is
+                                ! returned to the coupler.  Valid values include
+                                ! 'A', 'B', or 'C'.
+ADD_DIURNAL_SW = False           !    If true, add a synthetic diurnal cycle to
+                                !  the shortwave radiation.
+!OMEGA = 0.0                     !   [s-1] default = 7.2921E-05
+PASS_ICEBERG_AREA_TO_OCEAN = True !Iceberg area is passed to the ocean through the coupler.
diff --git a/test/Iceberg_repository/ISOMIP_Calving/common/clean_MOM.sh b/test/Iceberg_repository/ISOMIP_Calving/common/clean_MOM.sh
new file mode 100755
index 0000000..5ce2ea2
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/common/clean_MOM.sh
@@ -0,0 +1,14 @@
+rm *.nc*
+rm available_diags.000000
+rm logfile.000000.out
+rm MOM_parameter_doc.*
+rm ocean.stats
+rm time_stamp.out
+rm V_velocity_truncations
+rm U_velocity_truncations
+rm output
+rm SIS_parameter_doc.*
+rm seaice.stats
+rm SIS.available_diags
+rm SIS_fast.available_diags
+rm TPY_*
diff --git a/test/Iceberg_repository/ISOMIP_Calving/common/data_table b/test/Iceberg_repository/ISOMIP_Calving/common/data_table
new file mode 100644
index 0000000..e28f42c
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/common/data_table
@@ -0,0 +1,47 @@
+"ATM" , "p_surf"        , ""         , ""                             , .false. ,  100000000.0
+"ATM" , "p_bot"         , ""         , ""                             , .false. ,  100000000.0
+"ATM" , "t_bot"         , ""    , ""                             , .false. ,  273.0
+"ATM" , "sphum_bot"     , ""    , ""                             , .false. ,  1.e-3
+"ATM" , "u_bot"         , ""    , ""                             , .false. ,  0.0
+"ATM" , "v_bot"         , ""    , ""                             , .false. ,  0.0
+"ATM" , "z_bot"         , ""            , ""                             , .false. , 1.0
+"ATM" , "gust"          , ""            , ""                             , .false. ,  1.0
+"ICE" , "lprec"         , ""        , ""                            , .false. ,  0.0
+"ICE" , "fprec"         , ""        , ""                            , .false. ,  0.0
+"ICE" , "q_flux"         , ""        , ""                            , .false. ,  0.0
+"ICE" , "t_flux"         , ""        , ""                            , .false. ,  0.0
+"ICE" , "lw_flux"         , ""        , ""                            , .false. ,  0.0
+"ICE" , "u_flux"         , ""        , ""                            , .false. , -0.00000
+"ICE" , "v_flux"         , ""        , ""                            , .false. , -0.00000
+#"ICE" , "latent"         , ""        , ""                            , .false. ,  0.0
+#"ICE" , "runoff"        , ""            , ""                             , .false.  ,  0.0
+#"ICE" , "calving"       , ""     , ""                                     , .false.  ,  0.0
+#"ICE" , "calving_hflx"       , ""     , ""                                     , .false.  ,  0.0
+"ICE" , "dhdt"          , ""            , ""                             , .false.  ,  80.0
+"ICE" , "dedt"          , ""            , ""                             , .false.  ,  2.0e-6
+"ICE" , "drdt"          , ""            , ""                             , .false.  , 10.0
+#"ICE", "sic_obs"        , ""         , ""                             , .true. ,  0.00
+#"ICE", "sit_obs"        , ""         , ""                             , .true. ,  0.00
+#"ICE", "sst_obs"        , ""         , ""                             , .true. ,  -1.9
+"LND" , "t_surf"        , ""            , ""                             , .true.  ,  273.0
+"LND" , "t_ca"          , ""            , ""                             , .true.  ,  273.0
+"LND" , "q_ca"          , ""            , ""                             , .true.  ,  0.0
+"LND" , "rough_mom"     , ""            , ""                             , .true.  ,  0.01
+"LND" , "rough_heat"    , ""            , ""                             , .true.  ,  0.1
+"LND" , "albedo"        , ""            , ""                             , .true.  ,  0.1
+"LND" , "t_ca"          , ""            , ""                             , .true.  ,  273.0
+"LND" , "t_surf"        , ""            , ""                             , .true.  ,  273.0
+"LND" , "sphum_surf"    , ""            , ""                             , .true.  ,  0.0
+"LND" , "sphum_ca"      , ""            , ""                             , .true.  ,  0.0
+"LND" , "t_flux"        , ""            , ""                             , .true.  ,  0.0
+"LND" , "sphum_flux"    , ""            , ""                             , .true.  ,  0.0
+"LND" , "lw_flux"       , ""            , ""                             , .true.  ,  0.0
+"LND" , "sw_flux"       , ""            , ""                             , .true.  ,  0.0
+"LND" , "lprec"         , ""            , ""                             , .true.  ,  0.0
+"LND" , "fprec"         , ""            , ""                             , .true.  ,  0.0
+"LND" , "dhdt"          , ""            , ""                             , .true.  ,  5.0
+"LND" , "dedt"          , ""            , ""                             , .true.  ,  2e-6
+"LND" , "dedq"          , ""            , ""                             , .true.  ,  0.0
+"LND" , "drdt"          , ""            , ""                             , .true.  ,  0.0
+"LND" , "drag_q"        , ""            , ""                             , .true.  ,  0.0
+"LND" , "p_surf"        , ""            , ""                             , .true.  ,  1.e-5
diff --git a/test/Iceberg_repository/ISOMIP_Calving/common/diag_table b/test/Iceberg_repository/ISOMIP_Calving/common/diag_table
new file mode 100644
index 0000000..129f3c1
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/common/diag_table
@@ -0,0 +1,453 @@
+GOLD_SIS
+1 1 1 0 0 0 
+#output files
+#"prog",     1,"days",1,"days","time"
+#"ice_month",      1,  "months", 1, "days", "time",
+#"ocean_month",    1,  "months", 1, "days", "time",
+#"ocean_month_z",  1,  "months", 1, "days", "time",
+#"icebergs_month", 1, "months", 1, "days", "time",
+#"flux_month",     1,  "months", 1, "days", "time"
+#"ocean_sfc",    1,  "months", 1, "days", "time",
+
+"prog",           60,"minutes",1,"days","time"
+"ice_month",      60,  "minutes", 1, "days", "time",
+"icebergs_month", 60, "minutes", 1, "days", "time",
+"ocean_month",    60,  "minutes", 1, "days", "time",
+"ocean_month_z",  60,  "minutes", 1, "days", "time",
+"flux_month",     720,  "minutes", 1, "days", "time"
+"ocean_sfc",    720,  "minutes", 1, "days", "time",
+#
+#"prog",     720,"minutes",1,"days","time"
+#"ice_month",      720,  "minutes", 1, "days", "time",
+#"icebergs_month", 720, "minutes", 1, "days", "time",
+#"ocean_month",    720,  "minutes", 1, "days", "time",
+#"ocean_month_z",  720,  "minutes", 1, "days", "time",
+#"flux_month",     720,  "minutes", 1, "days", "time"
+#"ocean_sfc",    720,  "minutes", 1, "days", "time",
+#
+#"prog",     1,"days",1,"days","time"
+#"ice_month",      1,  "days", 1, "days", "time",
+#"icebergs_month", 1, "days", 1, "days", "time",
+#"ocean_month",    1,  "days", 1, "days", "time",
+#"ocean_sfc",    1,  "days", 1, "days", "time",
+#"ocean_month_z",  1,  "days", 1, "days", "time",
+#"flux_month",    1,  "days", 1, "days", "time"
+#
+"ocean_static",-1,  "days", 1, "days", "time",
+
+#"ocean_scalar", 1,  "months", 1, "days", "time"
+#
+#output variables
+#
+# OCEAN DIAGNOSTICS:
+#===================
+#===================
+#
+# Surface Ocean fields:
+#=========================
+"ocean_model","SSH","SSH","ocean_sfc","all",.true.,"none",2
+"ocean_model","SSU","SSU","ocean_sfc","all",.true.,"none",2
+"ocean_model","SSV","SSV","ocean_sfc","all",.true.,"none",2
+"ocean_model","SST","SST","ocean_sfc","all",.true.,"none",2
+"ocean_model","SSS","SSS","ocean_sfc","all",.true.,"none",2
+"ocean_model","speed","speed","ocean_sfc","all",.true.,"none",2
+
+# Prognostic Ocean fields:
+#=========================
+"ocean_model","u","u","ocean_month","all",.true.,"none",2
+"ocean_model","v","v","ocean_month","all",.true.,"none",2
+"ocean_model","h","h","ocean_month","all",.true.,"none",2
+"ocean_model","e","e","ocean_month","all",.true.,"none",2
+"ocean_model","temp","temp","ocean_month","all",.true.,"none",2
+"ocean_model","salt","salt","ocean_month","all",.true.,"none",2
+#"ocean_model","PRCmE","PRCmE","ocean_month","all",.true.,"none",2
+"ocean_model","melt","melt","ocean_month","all",.true.,"none",2
+#"ocean_model","mass_flux","mass_flux","ocean_month","all",.true.,"none",2
+#"ocean_model","frunoff","frunoff","ocean_month","all",.true.,"none",2
+#"ocean_model","heat_content_frunoff","heat_content_frunoff","ocean_month","all",.true.,"none",2
+#"ocean_model","net_heat_coupler","net_heat_coupler","ocean_month","all",.true.,"none",2
+#"ocean_model","tr_D1","tr1","ocean_month","all",.true.,"none",2
+#"ocean_model","tr_D2","tr2","ocean_month","all",.true.,"none",2
+"ocean_model","rhoinsitu","rhoinsitu","ocean_month","all",.true.,"none",2
+"ocean_model","ustar_shelf","ustar_shelf","ocean_month","all",.true.,"none",2
+#"ocean_model","exch_vel_s","exch_vel_s","ocean_month","all",.true.,"none",2
+#"ocean_model","exch_vel_t","exch_vel_t","ocean_month","all",.true.,"none",2
+"ocean_model","tfreeze","tfreeze","ocean_month","all",.true.,"none",2
+"ocean_model","u_ml","u_ml","ocean_month","all",.true.,"none",2
+"ocean_model","v_ml","v_ml","ocean_month","all",.true.,"none",2
+#"ocean_model","thermal_driving","thermal_driving","ocean_month","all",.true.,"none",2
+#"ocean_model","haline_driving","haline_driving","ocean_month","all",.true.,"none",2
+"ocean_model","h_ML","h_ML","ocean_month","all",.true.,"none",2
+#"ocean_model","ePBL_h_ML","ePBL_h_ML","ocean_month","all",.true.,"none",2
+"ocean_model","uhbt","uhbt","ocean_month","all",.true.,"none",2
+"ocean_model","vhbt","vhbt","ocean_month","all",.true.,"none",2
+#
+# Auxilary Tracers:
+#==================
+#"ocean_model","vintage","vintage","ocean_month","all",.true.,"none",2
+#"ocean_model","age","age","ocean_month","all",.true.,"none",2
+#
+# Z-space fields:
+#==================
+#"ocean_model_z_new","u","u","ocean_month_z","all",.true.,"none",2
+#"ocean_model_z_new","v","v","ocean_month_z","all",.true.,"none",2
+#"ocean_model_z_new","temp","temp","ocean_month_z","all",.true.,"none",2
+#"ocean_model_z_new","salt","salt","ocean_month_z","all",.true.,"none",2
+#"ocean_model_z_new","rhoinsitu","rhoinsitu","ocean_month_z","all",.true.,"none",2
+#"ocean_model_z","vintage","vintage","ocean_month_z","all",.true.,"none",2
+#"ocean_model_z","age","age","ocean_month_z","all",.true.,"none",2
+
+# Z-space fields:
+#==================
+ "ocean_model_z","temp","temp","ocean_month_z","all",.true.,"none",2
+ "ocean_model_z","salt","salt","ocean_month_z","all",.true.,"none",2
+ "ocean_model_z","u","u","ocean_month_z","all",.true.,"none",2
+ "ocean_model_z","uh","uh","ocean_month_z","all",.true.,"none",2
+ "ocean_model_z","v","v","ocean_month_z","all",.true.,"none",2
+ "ocean_model_z","vh","vh","ocean_month_z","all",.true.,"none",2 
+
+
+# Prognostic Ocean fields:
+#=========================
+"ocean_model","u","u","prog","all",.true.,"none",2
+"ocean_model","v","v","prog","all",.true.,"none",2
+"ocean_model","h","h","prog","all",.true.,"none",1
+"ocean_model","e","e","prog","all",.true.,"none",2
+"ocean_model","temp","temp","prog","all",.true.,"none",2
+"ocean_model","salt","salt","prog","all",.true.,"none",2
+"ocean_model","Rml","Rml","prog","all",.true.,"none",2
+#"ocean_model","tr_D1","tr1","prog","all",.true.,"none",2
+"ocean_model","tr_D2","tr2","prog","all",.true.,"none",2
+"ocean_model","rhoinsitu","rhoinsitu","prog","all",.true.,"none",2
+
+# Continuity Equation Terms:
+#===========================
+#"ocean_model","wd","wd","ocean_month","all",.true.,"none",2
+"ocean_model","uh","uh","ocean_month","all",.true.,"none",2
+"ocean_model","vh","vh","ocean_month","all",.true.,"none",2
+#"ocean_model","h_rho","h_rho","ocean_month","all",.true.,"none",2
+#"ocean_model","uh_rho","uh_rho","ocean_month","all",.true.,"none",2
+#"ocean_model","vh_rho","vh_rho","ocean_month","all",.true.,"none",2
+#"ocean_model","uhGM_rho","uhGM_rho","ocean_month","all",.true.,"none",2
+#"ocean_model","vhGM_rho","vhGM_rho","ocean_month","all",.true.,"none",2
+#"ocean_model","GMwork","GMwork","ocean_month","all",.true.,"none",2
+#
+# Mixed Layer TKE Budget Terms:
+#===========================
+"ocean_model","TKE_wind","TKE_wind","ocean_month","all",.true.,"none",2
+#"ocean_model","TKE_RiBulk","TKE_RiBulk","ocean_month","all",.true.,"none",2
+#"ocean_model","TKE_conv","TKE_conv","ocean_month","all",.true.,"none",2
+#"ocean_model","TKE_pen_SW","TKE_pen_SW","ocean_month","all",.true.,"none",2
+#"ocean_model","TKE_mixing","TKE_mixing","ocean_month","all",.true.,"none",2
+#"ocean_model","TKE_mech_decay","TKE_mech_decay","ocean_month","all",.true.,"none",2
+#"ocean_model","TKE_conv_decay","TKE_conv_decay","ocean_month","all",.true.,"none",2
+#"ocean_model","TKE_conv_s2","TKE_conv_s2","ocean_month","all",.true.,"none",2
+#"ocean_model","TKE_tidal","TKE_tidal","ocean_month","all",.true.,"none",2
+#"ocean_model","Kd_effective","Kd_effective","ocean_month","all",.true.,"none",2
+#
+# Tracer Fluxes:
+#==================
+#"ocean_model","T_adx",  "T_adx",  "ave_prog_%4yr_%3dy","all",.true.,"none",2
+#"ocean_model","T_ady",  "T_ady",  "ave_prog_%4yr_%3dy","all",.true.,"none",2
+#"ocean_model","T_diffx","T_diffx","ave_prog_%4yr_%3dy","all",.true.,"none",2
+#"ocean_model","T_diffy","T_diffy","ave_prog_%4yr_%3dy","all",.true.,"none",2
+#"ocean_model","S_adx",  "S_adx",  "ave_prog_%4yr_%3dy","all",.true.,"none",2
+#"ocean_model","S_ady",  "S_ady",  "ave_prog_%4yr_%3dy","all",.true.,"none",2
+#"ocean_model","S_diffx","S_diffx","ave_prog_%4yr_%3dy","all",.true.,"none",2
+#"ocean_model","S_diffy","S_diffy","ave_prog_%4yr_%3dy","all",.true.,"none",2
+
+
+# Momentum Balance Terms:
+#=======================
+#"ocean_model","dudt","dudt","ocean_month","all",.true.,"none",2
+#"ocean_model","dvdt","dvdt","ocean_month","all",.true.,"none",2
+#"ocean_model","CAu","CAu","ocean_month","all",.true.,"none",2
+#"ocean_model","CAv","CAv","ocean_month","all",.true.,"none",2
+#"ocean_model","PFu","PFu","ocean_month","all",.true.,"none",2
+#"ocean_model","PFv","PFv","ocean_month","all",.true.,"none",2
+#"ocean_model","du_dt_visc","du_dt_visc","ocean_month","all",.true.,"none",2
+#"ocean_model","dv_dt_visc","dv_dt_visc","ocean_month","all",.true.,"none",2
+#"ocean_model","diffu","diffu","ocean_month","all",.true.,"none",2
+#"ocean_model","diffv","diffv","ocean_month","all",.true.,"none",2
+#"ocean_model","dudt_dia","dudt_dia","ocean_month","all",.true.,"none",2
+#"ocean_model","dvdt_dia","dvdt_dia","ocean_month","all",.true.,"none",2
+# Subterms that should not be added to a closed budget.
+#"ocean_model","gKEu","gKEu","ocean_month","all",.true.,"none",2
+#"ocean_model","gKEv","gKEv","ocean_month","all",.true.,"none",2
+#"ocean_model","rvxu","rvxu","ocean_month","all",.true.,"none",2
+#"ocean_model","rvxv","rvxv","ocean_month","all",.true.,"none",2
+#"ocean_model","PFu_bc","PFu_bc","ocean_month","all",.true.,"none",2
+#"ocean_model","PFv_bc","PFv_bc","ocean_month","all",.true.,"none",2
+
+# Barotropic Momentum Balance Terms:
+# (only available with split time stepping.)
+#===========================================
+#"ocean_model","PFuBT","PFuBT","ocean_month","all",.true.,"none",2
+#"ocean_model","PFvBT","PFvBT","ocean_month","all",.true.,"none",2
+#"ocean_model","CoruBT","CoruBT","ocean_month","all",.true.,"none",2
+#"ocean_model","CorvBT","CorvBT","ocean_month","all",.true.,"none",2
+#"ocean_model","ubtforce","ubtforce","ocean_month","all",.true.,"none",2
+#"ocean_model","vbtforce","vbtforce","ocean_month","all",.true.,"none",2
+#"ocean_model","u_accel_bt","u_accel_bt","ocean_month","all",.true.,"none",2
+#"ocean_model","v_accel_bt","v_accel_bt","ocean_month","all",.true.,"none",2
+#
+# Viscosities and diffusivities:
+#===============================
+#"ocean_model","Kd","Kd","visc_%4yr_%3dy","all",.true.,"none",2
+#"ocean_model","Ahh","Ahh","visc_%4yr_%3dy","all",.true.,"none",2
+#"ocean_model","Ahq","Ahq","visc_%4yr_%3dy","all",.true.,"none",2
+#"ocean_model","Khh","Khh","visc_%4yr_%3dy","all",.true.,"none",2
+#"ocean_model","Khq","Khq","visc_%4yr_%3dy","all",.true.,"none",2
+#"ocean_model","bbl_thick_u","bbl_thick_u","visc_%4yr_%3dy","all",.true.,"none",2
+#"ocean_model","kv_bbl_u","kv_bbl_u","visc_%4yr_%3dy","all",.true.,"none",2
+#"ocean_model","bbl_thick_v","bbl_thick_v","visc_%4yr_%3dy","all",.true.,"none",2
+#"ocean_model","kv_bbl_v","kv_bbl_v","visc_%4yr_%3dy","all",.true.,"none",2
+#"ocean_model","av_visc","av_visc","visc_%4yr_%3dy","all",.true.,"none",2
+#"ocean_model","au_visc","au_visc","visc_%4yr_%3dy","all",.true.,"none",2
+#"ocean_model","FrictWork","FrictWork","ocean_month","all",.true.,"none",2
+#"ocean_model","SN_u","SN_u","ocean_month","all",.true.,"none",2
+#"ocean_model","SN_v","SN_v","ocean_month","all",.true.,"none",2
+#"ocean_model","NH","NH","ocean_month","all",.true.,"none",2
+#"ocean_model","Ld","Ld","ocean_month","all",.true.,"none",2
+#"ocean_model","Le","Le","ocean_month","all",.true.,"none",2
+#"ocean_model","L2u","L2u","ocean_month","all",.true.,"none",2
+#"ocean_model","L2v","L2v","ocean_month","all",.true.,"none",2
+#"ocean_model","S2u","S2u","ocean_month","all",.true.,"none",2
+#"ocean_model","S2v","S2v","ocean_month","all",.true.,"none",2
+#"ocean_model","eff_beta","eff_beta","ocean_month","all",.true.,"none",2
+#"ocean_model","KHTH_u","KHTH_u","ocean_month","all",.true.,"none",2
+#"ocean_model","KHTH_v","KHTH_v","ocean_month","all",.true.,"none",2
+#"ocean_model","KHTR_u","KHTR_u","ocean_month","all",.true.,"none",2
+#"ocean_model","KHTR_v","KHTR_v","ocean_month","all",.true.,"none",2
+
+# MEKE:
+#======
+# "ocean_model","MEKE","MEKE","ocean_month","all",.true.,"none",2
+# "ocean_model","MEKE_src","MEKE_src","ocean_month","all",.true.,"none",2
+# "ocean_model","MEKE_Kh","MEKE_Kh","ocean_month","all",.true.,"none",2
+#
+# Kinetic Energy Balance Terms:
+#=============================
+#"ocean_model","KE","KE","energy_%4yr_%3dy","all",.true.,"none",2
+#"ocean_model","dKE_dt","dKE_dt","energy_%4yr_%3dy","all",.true.,"none",2
+#"ocean_model","PE_to_KE","PE_to_KE","energy_%4yr_%3dy","all",.true.,"none",2
+#"ocean_model","KE_Coradv","KE_Coradv","energy_%4yr_%3dy","all",.true.,"none",2
+#"ocean_model","KE_adv","KE_adv","energy_%4yr_%3dy","all",.true.,"none",2
+#"ocean_model","KE_visc","KE_visc","energy_%4yr_%3dy","all",.true.,"none",2
+#"ocean_model","KE_horvisc","KE_horvisc","energy_%4yr_%3dy","all",.true.,"none",2
+#"ocean_model","KE_dia","KE_dia","energy_%4yr_%3dy","all",.true.,"none",2
+#
+# Surface Forcing:
+#=================
+"ocean_model","taux",     "taux",     "ocean_month","all",.true.,"none",2
+"ocean_model","tauy",     "tauy",     "ocean_month","all",.true.,"none",2
+"ocean_model","ustar",    "ustar",    "ocean_month","all",.true.,"none",2
+#"ocean_model","PRCmE",    "PRCmE",    "ocean_month","all",.true.,"none",2
+"ocean_model","SW",       "SW",       "ocean_month","all",.true.,"none",2
+"ocean_model","latent",   "latent",       "ocean_month","all",.true.,"none",2
+"ocean_model","latent_frunoff",   "latent_frunoff",       "ocean_month","all",.true.,"none",2
+"ocean_model","sensible",   "sensible",       "ocean_month","all",.true.,"none",2
+"ocean_model","LwLatSens","LwLatSens","ocean_month","all",.true.,"none",2
+"ocean_model","p_surf",   "p_surf",   "ocean_month","all",.true.,"none",2
+"ocean_model","salt_flux","salt_flux","ocean_month","all",.true.,"none",2
+"ocean_model","ustar_berg","ustar_berg","ocean_month","all",.true.,"none",2
+"ocean_model","area_berg","area_berg","ocean_month","all",.true.,"none",2
+"ocean_model","mass_berg","mass_berg","ocean_month","all",.true.,"none",2
+"ocean_model","ustar_ice_cover","ustar_ice_cover","ocean_month","all",.true.,"none",2
+"ocean_model","frac_ice_cover","frac_ice_cover","ocean_month","all",.true.,"none",2
+#"ocean_model","frunoff",   "frunoff",       "ocean_month","all",.true.,"none",2
+#"ocean_model","lrunoff",   "lrunoff",       "ocean_month","all",.true.,"none",2
+
+# Static ocean fields:
+#=====================
+"ocean_model", "geolon",      "geolon",      "ocean_static", "all", .true., "none", 2
+"ocean_model", "geolat",      "geolat",      "ocean_static", "all", .true., "none", 2
+"ocean_model", "geolon_c",    "geolon_c",    "ocean_static", "all", .true., "none", 2
+"ocean_model", "geolat_c",    "geolat_c",    "ocean_static", "all", .true., "none", 2
+"ocean_model", "geolon_u",    "geolon_u",    "ocean_static", "all", .true., "none", 2
+"ocean_model", "geolat_u",    "geolat_u",    "ocean_static", "all", .true., "none", 2
+"ocean_model", "geolon_v",    "geolon_v",    "ocean_static", "all", .true., "none", 2
+"ocean_model", "geolat_v",    "geolat_v",    "ocean_static", "all", .true., "none", 2
+"ocean_model", "area_t",      "area_t",      "ocean_static", "all", .true., "none", 2
+"ocean_model", "depth_ocean", "depth_ocean", "ocean_static", "all", .true., "none", 2
+"ocean_model", "wet",         "wet",         "ocean_static", "all", .true., "none", 2
+"ocean_model", "wet_c",       "wet_c",       "ocean_static", "all", .true., "none", 2
+"ocean_model", "wet_u",       "wet_u",       "ocean_static", "all", .true., "none", 2
+"ocean_model", "wet_v",       "wet_v",       "ocean_static", "all", .true., "none", 2
+"ocean_model", "Coriolis",    "Coriolis",    "ocean_static", "all", .true., "none", 2
+
+#
+# ICE DIAGNOSTICS:
+#=================
+#=================
+#"ice_model", "FRAZIL",     "FRAZIL",     "ice_month", "all", .true., "none", 2,
+"ice_model", "HI",         "HI",         "ice_month", "all", .true., "none", 2,
+#"ice_model", "HS",         "HS",         "ice_month", "all", .true., "none", 2,
+#"ice_model", "TS",         "TS",         "ice_month", "all", .true., "none", 2,
+#"ice_model", "T1",         "T1",         "ice_month", "all", .true., "none", 2,
+#"ice_model", "T2",         "T2",         "ice_month", "all", .true., "none", 2,
+"ice_model", "CN",         "CN",         "ice_month", "all", .true., "none", 2,
+#"ice_model", "EXT",        "EXT",        "ice_month", "all", .true., "none", 2,
+"ice_model", "MI",         "MI",         "ice_month", "all", .true., "none", 2,
+#"ice_model", "XPRT",       "XPRT",       "ice_month", "all", .true., "none", 2,
+#"ice_model", "LSRC",       "LSRC",       "ice_month", "all", .true., "none", 2,
+#"ice_model", "LSNK",       "LSNK",       "ice_month", "all", .true., "none", 2,
+#"ice_model", "BSNK",       "BSNK",       "ice_month", "all", .true., "none", 2,
+#"ice_model", "SN2IC",      "SN2IC",      "ice_month", "all", .true., "none", 2,
+#"ice_model", "ALB",        "ALB",        "ice_month", "all", .true., "none", 2,
+#"ice_model", "SW",         "SW",         "ice_month", "all", .true., "none", 2,
+"ice_model", "LW",         "LW",         "ice_month", "all", .true., "none", 2,
+"ice_model", "SH",         "SH",         "ice_month", "all", .true., "none", 2,
+#"ice_model", "LH",         "LH",         "ice_month", "all", .true., "none", 2,
+"ice_model", "TMELT",      "TMELT",      "ice_month", "all", .true., "none", 2,
+#"ice_model", "BMELT",      "BMELT",      "ice_month", "all", .true., "none", 2,
+#"ice_model", "BHEAT",      "BHEAT",      "ice_month", "all", .true., "none", 2,
+"ice_model", "UI",         "UI",         "ice_month", "all", .true., "none", 2,
+"ice_model", "VI",         "VI",         "ice_month", "all", .true., "none", 2,
+#"ice_model", "FA_X",       "FA_X",       "ice_month", "all", .true., "none", 2,
+#"ice_model", "FA_Y",       "FA_Y",       "ice_month", "all", .true., "none", 2,
+#"ice_model", "FI_X",       "FI_X",       "ice_month", "all", .true., "none", 2,
+#"ice_model", "FI_Y",       "FI_Y",       "ice_month", "all", .true., "none", 2,
+"ice_model", "SST",        "SST",        "ice_month", "all", .true., "none", 2,
+"ice_model", "SSS",        "SSS",        "ice_month", "all", .true., "none", 2,
+#"ice_model", "SSH",        "SSH",        "ice_month", "all", .true., "none", 2,
+"ice_model", "UO",         "UO",         "ice_month", "all", .true., "none", 2,
+"ice_model", "VO",         "VO",         "ice_month", "all", .true., "none", 2,
+"ice_model", "SNOWFL",     "SNOWFL",     "ice_month", "all", .true., "none", 2,
+#"ice_model", "RAIN",       "RAIN",       "ice_month", "all", .true., "none", 2,
+#"ice_model", "CALVING",    "CALVING",    "ice_month", "all", .true., "none", 2,
+#"ice_model", "RUNOFF",     "RUNOFF",     "ice_month", "all", .true., "none", 2,
+"ice_model", "CELL_AREA",  "CELL_AREA",  "ice_month", "all", .true., "none", 2,
+"ice_model", "GEOLON",     "GEOLON",     "ice_month", "all", .true., "none", 2,
+"ice_model", "GEOLAT",     "GEOLAT",     "ice_month", "all", .true., "none", 2,
+"ice_model", "SINROT",     "SINROT",     "ice_month", "all", .true., "none", 2,
+"ice_model", "COSROT",     "COSROT",     "ice_month", "all", .true., "none", 2,
+"ice_model", "SALTF",      "SALTF",      "ice_month", "all", .true., "none", 2,
+#"ice_model", "IX_TRANS",   "IX_TRANS",   "ice_month", "all", .true., "none", 2,
+#"ice_model", "IY_TRANS",   "IY_TRANS",   "ice_month", "all", .true., "none", 2,
+"ice_model", "MIB",   "MIB",   "ice_month", "all", .true., "none", 2,
+"ice_model", "USTAR_BERG",   "USTAR_BERG",   "ice_month", "all", .true., "none", 2,
+"ice_model", "AREA_BERG",   "AREA_BERG",   "ice_month", "all", .true., "none", 2,
+"ice_model", "MASS_BERG",   "MASS_BERG",   "ice_month", "all", .true., "none", 2,
+
+# ICEBERG DIAGNOSTICS:
+#=====================
+#=====================
+"icebergs", "calving",        "calving",        "icebergs_month", "all", .true., "none", 2,
+#"icebergs", "accum_calving",  "accum_calving",  "icebergs_month", "all", .true., "none", 2,
+#"icebergs", "unused_calving", "unused_calving", "icebergs_month", "all", .true., "none", 2,
+#"icebergs", "real_calving",   "real_calving",   "icebergs_month", "all", .true., "none", 2,
+#"icebergs", "stored_ice",     "stored_ice",     "icebergs_month", "all", .true., "none", 2,
+"icebergs", "hi",             "hi",             "icebergs_month", "all", .true., "none", 2,
+"icebergs", "cn",             "cn",             "icebergs_month", "all", .true., "none", 2,
+"icebergs", "ui",             "ui",             "icebergs_month", "all", .true., "none", 2,
+"icebergs", "vi",             "vi",             "icebergs_month", "all", .true., "none", 2,
+"icebergs", "ua",             "ua",             "icebergs_month", "all", .true., "none", 2,
+"icebergs", "va",             "va",             "icebergs_month", "all", .true., "none", 2,
+"icebergs", "uo",             "uo",             "icebergs_month", "all", .true., "none", 2,
+"icebergs", "vo",             "vo",             "icebergs_month", "all", .true., "none", 2,
+"icebergs", "sst",            "sst",            "icebergs_month", "all", .true., "none", 2,
+"icebergs", "sss",            "sss",            "icebergs_month", "all", .true., "none", 2,
+"icebergs", "ssh",            "ssh",            "icebergs_month", "all", .true., "none", 2,
+"icebergs", "mass",           "mass",           "icebergs_month", "all", .true., "none", 2,
+"icebergs", "virtual_area",   "virtual_area",   "icebergs_month", "all", .true., "none", 2,
+"icebergs", "melt",           "melt",           "icebergs_month", "all", .true., "none", 2,
+#"icebergs", "berg_melt",      "berg_melt",      "icebergs_month", "all", .true., "none", 2,
+"icebergs", "spread_mass",    "spread_mass",    "icebergs_month", "all", .true., "none", 2,
+"icebergs", "spread_area",    "spread_area",    "icebergs_month", "all", .true., "none", 2,
+#"icebergs", "melt_buoy",      "melt_buoy",      "icebergs_month", "all", .true., "none", 2,
+#"icebergs", "melt_eros",      "melt_eros",      "icebergs_month", "all", .true., "none", 2,
+#"icebergs", "melt_conv",      "melt_conv",      "icebergs_month", "all", .true., "none", 2,
+"icebergs", "melt_m_per_year","melt_m_per_year","icebergs_month", "all", .true., "none", 2,
+"icebergs", "mask",           "mask",           "icebergs_month", "all", .true., "none", 2,
+"icebergs", "area",           "area",           "icebergs_month", "all", .true., "none", 2,
+"icebergs", "lon",            "lon",            "icebergs_month", "all", .true., "none", 2,
+"icebergs", "lat",            "lat",            "icebergs_month", "all", .true., "none", 2,
+"icebergs", "u_iceberg",      "u_iceberg",      "icebergs_month", "all", .true., "none", 2,
+"icebergs", "v_iceberg",      "v_iceberg",      "icebergs_month", "all", .true., "none", 2,
+"icebergs", "spread_uvel",      "spread_uvel",      "icebergs_month", "all", .true., "none", 2,
+"icebergs", "spread_vvel",      "spread_vvel",      "icebergs_month", "all", .true., "none", 2,
+"icebergs", "ustar_iceberg",      "ustar_iceberg",      "icebergs_month", "all", .true., "none", 2,
+#"icebergs", "running_mean_calving",      "running_mean_calving",      "icebergs_month", "all", .true., "none", 2,
+#"icebergs", "running_mean_calving_hflx",      "running_mean_calving_hflx",      "icebergs_month", "all", .true., "none", 2,
+"icebergs", "ocean_depth", "ocean_depth", "icebergs_month", "all", .true., "none", 2,
+"icebergs", "Depth", "Depth", "icebergs_month", "all", .true., "none", 2,
+
+#
+#========================
+# ATMOSPHERE DIAGNOSTICS:
+#========================
+#========================
+# "flux",      "land_mask",   "land_mask",   "flux_month", "all", .true., "none", 2,
+# "flux",      "ice_mask",    "ice_mask",    "flux_month", "all", .true.,  "none", 2,
+# "flux",      "drag_moist",  "drag_moist",  "flux_month", "all", .true.,  "none", 2,
+# "flux",      "drag_heat",   "drag_heat",   "flux_month", "all", .true.,  "none", 2,
+# "flux",      "drag_mom",    "drag_mom",    "flux_month", "all", .true.,  "none", 2,
+# "flux",      "wind",        "wind",        "flux_month", "all", .true.,  "none", 2,
+# # "flux" forcing fields for land model: wind, q_ref atmos_8xdaily
+# #"flux",      "wind",        "wind",        "atmos_8xdaily", "all", .true., "none", 2,
+# #"flux",      "q_ref",       "q_ref",       "atmos_8xdaily", "all", .true., "none", 2,
+# "flux",      "tau_x",       "tau_x",       "flux_month", "all", .true.,  "none", 2,
+# "flux",      "tau_y",       "tau_y",       "flux_month", "all", .true.,  "none", 2,
+# "flux",      "shflx",       "shflx",       "flux_month", "all", .true.,  "none", 2,
+# "flux",      "evap",        "evap",        "flux_month", "all", .true.,  "none", 2,
+# "flux",      "lwflx",       "lwflx",       "flux_month", "all", .true.,  "none", 2,
+# "flux",      "rh_ref",      "rh_ref",      "flux_month", "all", .true.,  "none", 2,
+# "flux",      "u_ref",       "u_ref",       "flux_month", "all", .true.,  "none", 2,
+# "flux",      "v_ref",       "v_ref",       "flux_month", "all", .true.,  "none", 2,
+# "flux",      "u_atm",       "u_atm",       "flux_month", "all", .true.,"none", 2,
+# "flux",      "v_atm",       "v_atm",       "flux_month", "all", .true.,"none", 2,
+# "flux",      "t_atm",       "t_atm",       "flux_month", "all", .true.,"none", 2,
+# "flux",      "t_surf",      "t_surf",      "flux_month", "all", .true.,"none", 2,
+# "flux",      "q_atm",       "q_atm",       "flux_month", "all", .true.,"none", 2,
+#
+# For these "_col" fields, set do_cmip_diagnostics=.true. in &shortwave_driver_nml, and uncomment
+#"radiation", "organic_carbon_exopdep_col","org_crb_exdep_c", "atmos_month", "all", .true., "none", 2,
+#"radiation", "organic_carbon_abopdep_col","org_crb_abdep_c", "atmos_month", "all", .true., "none", 2,
+#"radiation", "black_carbon_exopdep_col",  "blk_crb_exdep_c", "atmos_month", "all", .true., "none", 2,
+#"radiation", "black_carbon_abopdep_col",  "blk_crb_abdep_c", "atmos_month", "all", .true., "none", 2,
+#"radiation", "sea_salt_exopdep_col",      "salt_exdep_c",    "atmos_month", "all", .true., "none", 2,
+#"radiation", "sea_salt_abopdep_col",      "salt_abdep_c",    "atmos_month", "all", .true., "none", 2,
+#"radiation", "so4_anthro_col",            "so4_ant_col",     "atmos_month", "all", .true., "none", 2,
+#"radiation", "so4_natural_col",           "so4_nat_col",     "atmos_month", "all", .true., "none", 2,
+#"radiation", "small_dust_exopdep_col",    "sm_dust_exdep_c", "atmos_month", "all", .true., "none", 2,
+#"radiation", "small_dust_abopdep_col",    "sm_dust_abdep_c", "atmos_month", "all", .true., "none", 2,
+#"radiation", "large_dust_exopdep_col",    "lg_dust_exdep_c", "atmos_month", "all", .true., "none", 2,
+#"radiation", "large_dust_abopdep_col",    "lg_dust_abdep_c", "atmos_month", "all", .true., "none", 2,
+#
+
+
+#=============================================================================================
+#
+#====> This file can be used with diag_manager/v2.0a (or higher) <====
+#
+#
+#  FORMATS FOR FILE ENTRIES (not all input values are used)
+#  ------------------------
+#
+#"file_name", output_freq, "output_units", format, "time_units", "long_name",
+#
+#
+#output_freq:  > 0  output frequency in "output_units"
+#              = 0  output frequency every time step
+#              =-1  output frequency at end of run
+#
+#output_units = units used for output frequency
+#               (years, months, days, minutes, hours, seconds)
+#
+#time_units   = units used to label the time axis
+#               (days, minutes, hours, seconds)
+#
+#
+#  FORMAT FOR FIELD ENTRIES (not all input values are used)
+#  ------------------------
+#
+#"module_name", "field_name", "output_name", "file_name" "time_sampling", time_avg, "other_opts", packing
+#
+#time_avg = .true. or .false.
+#
+#packing  = 1  double precision
+#         = 2  float
+#         = 4  packed 16-bit integers
+#         = 8  packed 1-byte (not tested?)
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/common/field_table b/test/Iceberg_repository/ISOMIP_Calving/common/field_table
new file mode 100644
index 0000000..a4e98a7
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/common/field_table
@@ -0,0 +1,71 @@
+"diag_tracers","ocean_mod","frazil"
+
+file_in  = INPUT/ocean_frazil.res.nc
+file_out = RESTART/ocean_frazil.res.nc
+/
+
+
+"prog_tracers","ocean_mod","temp"
+
+horizontal-advection-scheme = mdfl_sweby
+vertical-advection-scheme = mdfl_sweby
+file_in  = INPUT/ocean_temp_salt.res.nc
+file_out = RESTART/ocean_temp_salt.res.nc
+/
+
+"prog_tracers","ocean_mod","salt"
+
+rizontal-advection-scheme = mdfl_sweby
+vertical-advection-scheme = mdfl_sweby
+file_in  = INPUT/ocean_temp_salt.res.nc
+file_out = RESTART/ocean_temp_salt.res.nc
+/
+
+
+"tracer_packages","ocean_mod","ocean_age_tracer"
+
+names = global
+horizontal-advection-scheme = mdfl_sweby
+vertical-advection-scheme = mdfl_sweby
+file_in  = INPUT/ocean_age.res.nc
+file_out = RESTART/ocean_age.res.nc
+min_tracer_limit=0.0
+/
+
+"prog_tracers","ocean_mod","age_global"
+
+const_init_tracer = t
+const_init_value = 0.0
+/
+
+"namelists","ocean_mod","ocean_age_tracer/global"
+
+slat = -90.0
+nlat =  90.0
+wlon =   0.0
+elon = 360.0
+/
+
+ "TRACER", "atmos_mod", "sphum"
+           "longname",     "specific humidity"
+           "units",        "kg/kg" /
+
+# prognotic cloud scheme tracers
+  "TRACER", "atmos_mod", "liq_wat"
+            "longname",     "cloud liquid specific humidity"
+            "units",        "kg/kg" /
+  "TRACER", "atmos_mod", "ice_wat"
+            "longname",     "cloud ice water specific humidity"
+            "units",        "kg/kg" /
+  "TRACER", "atmos_mod", "cld_amt"
+            "longname",     "cloud fraction"
+            "units",        "none" /
+
+# test tracer for radon
+
+# "TRACER", "atmos_mod", "radon"
+#           "longname",     "radon test tracer"
+#           "units",        "kg/kg" /
+
+ "TRACER", "land_mod", "sphum"/
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/common/input.nml b/test/Iceberg_repository/ISOMIP_Calving/common/input.nml
new file mode 100644
index 0000000..fd79354
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/common/input.nml
@@ -0,0 +1,137 @@
+ &MOM_input_nml
+        output_directory = './',
+        input_filename = 'r'
+        restart_input_dir = 'INPUT/',
+        restart_output_dir = 'RESTART/',
+        parameter_filename = 'MOM_input',
+                             'MOM_override' /
+
+ &SIS_input_nml
+        output_directory = './',
+        input_filename = 'r'
+        restart_input_dir = 'INPUT/',
+        restart_output_dir = 'RESTART/',
+        parameter_filename = 'SIS_input',
+                             'SIS_override' /
+
+ &diag_manager_nml
+         max_output_fields=1000
+         max_input_fields=1000
+         max_num_axis_sets=1000
+         conserve_water=.false.,
+         max_files=1000
+         max_axes=2000
+ /
+
+ &coupler_nml
+            months = 60,
+            days   = 0,
+            current_date = 1,1,1,0,0,0,
+            hours = 0,
+            minutes =0, 
+            seconds = 0
+            calendar = 'NOLEAP',
+            dt_cpld  = 300.0,
+            dt_atmos = 300.0,
+            do_atmos = .false.,
+            do_land = .false.,
+            do_ice = .true.,
+            do_ocean = .true.,
+            atmos_npes = 0,
+            ocean_npes = 0,
+            concurrent = .false.
+            use_lag_fluxes=.false. /
+
+
+ &icebergs_nml
+    verbose=.false.,
+    verbose_hrs=24,
+    traj_sample_hrs=24000,
+    ignore_ij_restart=.true.
+    halo=2,
+    save_short_traj=.true.
+    debug=.false.,
+    really_debug=.false.,
+    use_slow_find=.true.,
+    add_weight_to_ocean=.true.,
+    passive_mode=.false.,
+    Static_icebergs=.True.,
+    ignore_missing_restart_bergs=.false.,
+    generate_test_icebergs=.false.,
+    speed_limit=0.,
+    use_roundoff_fix=.true.,
+    make_calving_reproduce=.false.,
+    Runge_not_Verlet=.false.,
+    iceberg_bonds_on=.false.,
+    critical_interaction_damping_on=.false.,
+    use_new_predictive_corrective=.true.,
+    interactive_icebergs_on=.false.
+    halo_debugging=.false.
+    spring_coef=0.000001
+    distribution=0.0, 0.99, 0.0, 0.00, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11,
+    hexagonal_icebergs=.true.
+    allow_bergs_to_roll=.false.
+    set_melt_rates_to_zero=.false.
+    use_roundoff_fix=.false.
+    grid_is_latlon=.false.
+    grid_is_regular=.true.
+    initial_orientation=-0.
+    rotate_icebergs_for_mass_spreading=.false.
+    lat_ref=-75.0
+    u_override=0.00
+    v_override=0.00
+    override_iceberg_velocities=.false.
+    add_iceberg_thickness_to_SSH=.true.
+    max_bonds=6
+    Iceberg_melt_without_decay=.true.
+    melt_icebergs_as_ice_shelf=.true.
+    Use_three_equation_model=.true.
+    find_melt_using_spread_mass=.true.
+    use_mixed_layer_salinity_for_thermo=.true.
+    pass_fields_to_ocean_model=.true.
+    rho_bergs=918.0
+    utide_icebergs=0.01
+    ustar_icebergs_bg=0.000
+    cdrag_icebergs =0.0025
+    const_gamma=.false.
+    Gamma_T_3EQ=0.22
+    ignore_traj=.False.
+    read_ocean_depth_from_file=.true.
+    apply_thickness_cutoff_to_bergs_melt=.true.
+    apply_thickness_cutoff_to_gridded_melt=.true.
+    melt_cutoff=10.
+ &data_override_nml
+         /
+
+ &fms_io_nml
+         fms_netcdf_restart=.true.
+         threading_read='multi'
+ /
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC' /
+
+ &ice_albedo_nml
+      t_range = 10. /
+
+ &ice_model_nml
+           /
+
+ &monin_obukhov_nml
+            neutral = .true. /
+
+ &ocean_albedo_nml
+      ocean_albedo_option = 5 /
+
+ &sat_vapor_pres_nml
+      construct_table_wrt_liq = .true.,
+      construct_table_wrt_liq_and_ice = .true. /
+
+ &xgrid_nml
+            make_exchange_reproduce = .false.
+            interp_method = 'second_order' /
+
diff --git a/test/Iceberg_repository/ISOMIP_Calving/common/run_script.sh b/test/Iceberg_repository/ISOMIP_Calving/common/run_script.sh
new file mode 100755
index 0000000..26e29af
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/common/run_script.sh
@@ -0,0 +1,5 @@
+#mv RESTART/* INPUT/
+#aprun -n 16 ../../build/intel/ice_ocean_SIS2/repro/MOM6
+aprun -n 128 ../../../../../build/intel/ice_ocean_SIS2/repro/old_executable/MOM6
+#aprun -n 32 MOM6
+#cp RESTART/* RESTART_BACKUP
diff --git a/test/Iceberg_repository/ISOMIP_Calving/common/submit_to_queue b/test/Iceberg_repository/ISOMIP_Calving/common/submit_to_queue
new file mode 100644
index 0000000..3cb9f5f
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/common/submit_to_queue
@@ -0,0 +1,25 @@
+#!/bin/csh -f
+#PBS -r y                                                              #This job is restartable
+#PBS -j oe                                                             #STDOUT and STDERR are in the same file, specified below in the '-o' option
+#PBS -q batch                                                          #Do not change this - it tells your job where to run
+#PBS -S /bin/sh                                                        #Do not change this - it keeps your job from issuing a false alarm
+#PBS -E                                                                #Do not change this - it gives your job more and more useful Moab environment variables
+#PBS -N  Melt_with_decay                                                  #Job Name:             You may want to change this to reflect your job's purpose or relation to an experiment
+#PBS -l partition=c3
+#PBS -l size=4                                                        #You will need to change this to reflect your job's core requirements - 24 is the current core increment.
+#PBS -l walltime=16:00:00                                              #You MUST change this to reflect your job's expected run time, including copy time
+#PBS -m bea                                                            #Email options: You may want to change this to reduce your incoming email stream
+
+######################################################################################################################
+#
+#  Gaea c1ms batch skeleton version 0.9
+#  
+#  0.9 - Initial version - 20110906 - Daniel Gall - Daniel.Gall@noaa.gov
+#
+######################################################################################################################
+
+#Source the system initialization scripts (but not the user's so as to avoid interactive settings that can poison us)
+source /etc/csh.cshrc
+
+#Run the experiment
+aprun -n 128 ../../../../build/intel/ice_ocean_SIS2/repro/old_executable/MOM6
diff --git a/test/Iceberg_repository/ISOMIP_Calving/python_scripts/Create_mosaic.py b/test/Iceberg_repository/ISOMIP_Calving/python_scripts/Create_mosaic.py
new file mode 120000
index 0000000..bab5810
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/python_scripts/Create_mosaic.py
@@ -0,0 +1 @@
+../../Scripts_and_analysis/Create_mosaic.py
\ No newline at end of file
diff --git a/test/Iceberg_repository/ISOMIP_Calving/python_scripts/initialize_bergs_in_pattern.py b/test/Iceberg_repository/ISOMIP_Calving/python_scripts/initialize_bergs_in_pattern.py
new file mode 120000
index 0000000..9824e45
--- /dev/null
+++ b/test/Iceberg_repository/ISOMIP_Calving/python_scripts/initialize_bergs_in_pattern.py
@@ -0,0 +1 @@
+../../Scripts_and_analysis/initialize_bergs_in_pattern.py
\ No newline at end of file
diff --git a/test/Iceberg_repository/README b/test/Iceberg_repository/README
new file mode 100644
index 0000000..09dc309
--- /dev/null
+++ b/test/Iceberg_repository/README
@@ -0,0 +1,34 @@
+- Alon's Iceberg Repository, edited for initializing a model setup for testing the iceberg driver.
+- Added the directory ./testberg, where file testberg.py can be edited and run to create a test iceberg.
+- This berg is then transformed into a restart (input) file via initialize_bergs_in_pattern.py,
+  as called by the RUN script.
+
+
+
+
+-----------------------------------------------------------
+
+
+
+
+Alon's readme:
+
+To set up the experiments, please run the setup_ISOMIP_calving.sh script. This will create all the netcdf files which are needed to run the simulations. To run the script, write the following at the command line:
+
+source setup_ISOMIP_calving.sh
+
+
+
+- Building an executable:
+
+You can create an executable using latest version of the code on dev/master, except for the coupler, which needs to be on the following branch
+
+Repository: git@github.com:sternalon/coupler.git
+Branch: passing_ustar_through_coupler
+
+These changes to the coupler have been added to Bob's branch
+Repository: git@github.com:NOAA-GFDL/coupler.git
+Branch: user/rwh/redesign_flux_exchange
+
+Note that there might be some incompatibility with the SIS code which require using a special branch. This is found on gitlab. 
+Branch: sis2_interface
diff --git a/test/Iceberg_repository/RUN b/test/Iceberg_repository/RUN
new file mode 100755
index 0000000..cabc714
--- /dev/null
+++ b/test/Iceberg_repository/RUN
@@ -0,0 +1,9 @@
+rm ./output_files/Generic*
+
+./Scripts_and_analysis/initialize_bergs_in_pattern.py -set_all_bergs_static_by_default=False -Run_plotting_subroutine=False \
+				 -break_some_bonds=False -Ice_geometry_source='Generic' \
+				 -Generic_ice_geometry_filename='./testberg/testtabularberg.nc' \
+				 -ISOMIP_reduced=False \
+
+cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
+cp ./output_files/Generic_bonds_iceberg.res.nc ./../INPUT/bonds_iceberg.res.nc
\ No newline at end of file
diff --git a/test/Iceberg_repository/Scripts_and_analysis/Create_a_cartesian_grid_and_mosaic.ipynb b/test/Iceberg_repository/Scripts_and_analysis/Create_a_cartesian_grid_and_mosaic.ipynb
new file mode 100644
index 0000000..13ebeb2
--- /dev/null
+++ b/test/Iceberg_repository/Scripts_and_analysis/Create_a_cartesian_grid_and_mosaic.ipynb
@@ -0,0 +1,649 @@
+{
+ "metadata": {
+  "name": "",
+  "signature": "sha256:d2ef6bae770b9c56ac62500a0a35fe92d46b49ffb6124a589b7173e88a66994f"
+ },
+ "nbformat": 3,
+ "nbformat_minor": 0,
+ "worksheets": [
+  {
+   "cells": [
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "import scipy.io.netcdf\n",
+      "import numpy\n",
+      "%pylab inline"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": [
+      {
+       "output_type": "stream",
+       "stream": "stdout",
+       "text": [
+        "Populating the interactive namespace from numpy and matplotlib\n"
+       ]
+      }
+     ],
+     "prompt_number": 1
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Model grid will have ni x nj h-point grid cells"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "nj,ni = 40,240"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": [],
+     "prompt_number": 2
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "A mosaic file has a supergrid of an integer refinement (e.g. 2*ni x 2*nj cells)"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "snj, sni = 2*nj, 2*ni"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": [],
+     "prompt_number": 3
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Uniform resolution of the ocean model grid will be dxo x dyo"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "dxo = 2.e3\n",
+      "dyo = 2.e3"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": [],
+     "prompt_number": 4
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Number of land points used nl"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "nl=0\n",
+      "Ocean_Depth=numpy.zeros((nj,ni))\n",
+      "Ocean_Depth[:,:]=1000.\n",
+      "#Define land points:\n",
+      "#Ocean_Depth[-1,:]=0  ;Ocean_Depth[0,:]=0  #Setting boundaries to zero\n",
+      "#Ocean_Depth[:,-1]=0  ;Ocean_Depth[:,0]=0  #Setting boundaries to zero\n",
+      "Ocean_Depth[0,0]=0.\n",
+      "for j in range(nj):\n",
+      "    for i in range(ni):\n",
+      "        if Ocean_Depth[j,i]==0:\n",
+      "            nl=nl+1"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": [],
+     "prompt_number": 5
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Using a supergrid refinement of 2, the grid lengths, area and coordinates are:"
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "dx = (0.5 * dxo) * numpy.ones((snj+1,sni))\n",
+      "dy = (0.5 * dyo) * numpy.ones((snj,sni+1))\n",
+      "area = (0.25 * (dxo * dyo)) * numpy.ones((snj,sni))\n",
+      "x = numpy.zeros((snj+1,sni+1))\n",
+      "x[:,1:] = numpy.cumsum( dx, axis=-1 )\n",
+      "y = numpy.zeros((snj+1,sni+1))\n",
+      "y[1:,:] = numpy.cumsum( dy, axis=-2 )"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": [],
+     "prompt_number": 6
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "# A helper function to use when writing strings in a netcdf file\n",
+      "def set_string(variable, value):\n",
+      "    \"\"\"Sets \"variable\" to \"value\" padded with blanks where\n",
+      "    \"variable\" is a netcdf variable object and \"value\" is a string.\"\"\"\n",
+      "    variable[:] = '\\000' * variable.shape[0]\n",
+      "    variable[:len(value)] = value"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": [],
+     "prompt_number": 7
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Create a netcdf3 horizontal ocean-grid file..."
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "rg = scipy.io.netcdf_file('ocean_hgrid.nc','w',version=2)"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": [],
+     "prompt_number": 8
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "rg.createDimension('nx',sni)\n",
+      "rg.createDimension('ny',snj)\n",
+      "rg.createDimension('nxp',sni+1)\n",
+      "rg.createDimension('nyp',snj+1)\n",
+      "rg.createDimension('string',255)"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": [],
+     "prompt_number": 9
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "dx_h = rg.createVariable('dx','f8',('nyp','nx',))\n",
+      "dx_h.units = 'm'\n",
+      "dy_h = rg.createVariable('dy','f8',('ny','nxp',))\n",
+      "dy_h.units = 'm'\n",
+      "area_h = rg.createVariable('area','f8',('ny','nx',))\n",
+      "area_h.units = 'm2'\n",
+      "x_h = rg.createVariable('x','f8',('nyp','nxp',))\n",
+      "x_h.units = 'm'\n",
+      "y_h = rg.createVariable('y','f8',('nyp','nxp',))\n",
+      "y_h.units = 'm'\n",
+      "tile = rg.createVariable('tile','c',('string',))"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": [],
+     "prompt_number": 10
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "dx_h[:,:] = dx[:,:]\n",
+      "dy_h[:,:] = dy[:,:]\n",
+      "area_h[:,:] = area[:,:]\n",
+      "x_h[:,:] = x[:,:]\n",
+      "y_h[:,:] = y[:,:]\n",
+      "tile[:] = '\\000' * 255\n",
+      "tile[:5] = 'tile1'\n",
+      "set_string(tile,'tile1')"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": [],
+     "prompt_number": 11
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "rg.close()"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": [],
+     "prompt_number": 12
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Create a netcdf3 ocean-mask file..."
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "rg = scipy.io.netcdf_file('ocean_mask.nc','w',version=2)\n",
+      "rg.createDimension('nx',ni)\n",
+      "rg.createDimension('ny',nj)\n",
+      "mask = rg.createVariable('mask','f4',('ny','nx',))\n",
+      "mask[:,:] = 1.\n",
+      "rg.close()"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": [],
+     "prompt_number": 13
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "Create a mosaic description for the above grid file..."
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "rg = scipy.io.netcdf_file('ocean_mosaic.nc','w',version=2)\n",
+      "rg.createDimension('ntiles',1)\n",
+      "rg.createDimension('string',255)\n",
+      "mosaic = rg.createVariable('mosaic','c',('string',))\n",
+      "mosaic.standard_name = 'grid_mosaic_spec'\n",
+      "mosaic.children = 'contacts'\n",
+      "mosaic.grid_descriptor = ''\n",
+      "gridlocation = rg.createVariable('gridlocation','c',('string',))\n",
+      "gridlocation.standard_name = 'grid_file_location'\n",
+      "gridfiles = rg.createVariable('gridfiles','c',('ntiles','string',))\n",
+      "gridtiles = rg.createVariable('gridtiles','c',('ntiles','string',))\n",
+      "rg.grid_version = '0.2'\n",
+      "# Fill in data\n",
+      "mosaic[:] = '\\000' * 255\n",
+      "mosaic[:12] = 'ocean_mosaic'\n",
+      "gridlocation[:] = '\\000' * 255\n",
+      "gridlocation[:2] = './'\n",
+      "gridfiles[:] = '\\000' * 255\n",
+      "gridfiles[0,:14] = 'ocean_hgrid.nc'\n",
+      "gridtiles[:] = '\\000' * 255\n",
+      "gridtiles[0,:5] = 'tile1'\n",
+      "rg.close()"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": [],
+     "prompt_number": 14
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "!pwd"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": [
+      {
+       "output_type": "stream",
+       "stream": "stdout",
+       "text": [
+        "/home/aas/Iceberg_Project/ISOMIP/Create_mosaics\r\n"
+       ]
+      }
+     ],
+     "prompt_number": 15
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "# Fake a ocean_topog.nc file\n",
+      "rg = scipy.io.netcdf_file('ocean_topog.nc','w',version=2)\n",
+      "rg.createDimension('nx',ni)\n",
+      "rg.createDimension('ny',nj)\n",
+      "rg.createDimension('ntiles',1)\n",
+      "depth = rg.createVariable('depth','f4',('ny','nx',))\n",
+      "depth[:,:] = 1000.\n",
+      "#depth[-1,-1] =0  #One point is being defined as a land point\n",
+      "rg.close()"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": [],
+     "prompt_number": 16
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "rg = scipy.io.netcdf_file('atmos_mosaic_tile1Xland_mosaic_tile1.nc','w',version=2) # atmos_mosaic_tile1Xland_mosaic_tile1.nc\n",
+      "rg.createDimension('string',255)\n",
+      "rg.createDimension('ncells',nl)  #It is unclear whether this works when nl=0. It does work for nl>0\n",
+      "rg.createDimension('two',2)\n",
+      "contact = rg.createVariable('contact','c',('string',))\n",
+      "contact.standard_name = 'grid_contact_spec'\n",
+      "contact.contact_type = 'exchange'\n",
+      "contact.parent1_cell = 'tile1_cell'\n",
+      "contact.parent2_cell = 'tile2_cell'\n",
+      "contact.xgrid_area_field = 'xgrid_area'\n",
+      "contact.distant_to_parent1_centroid = 'tile1_distance'\n",
+      "contact.distant_to_parent2_centroid = 'tile2_distance'\n",
+      "tile1_cell = rg.createVariable('tile1_cell','f8',('ncells','two',))\n",
+      "tile1_cell.standard_name = 'parent_cell_indices_in_mosaic1'\n",
+      "tile2_cell = rg.createVariable('tile2_cell','f8',('ncells','two',))\n",
+      "tile2_cell.standard_name = 'parent_cell_indices_in_mosaic2'\n",
+      "xgrid_area = rg.createVariable('xgrid_area','f8',('ncells',))\n",
+      "xgrid_area.standard_name = 'exchange_grid_area'\n",
+      "xgrid_area.units = 'm2'\n",
+      "tile1_distance = rg.createVariable('tile1_distance','f8',('ncells','two'))\n",
+      "tile1_distance.standard_name = 'distance_from_parent1_cell_centroid'\n",
+      "tile2_distance = rg.createVariable('tile2_distance','f8',('ncells','two'))\n",
+      "tile2_distance.standard_name = 'distance_from_parent2_cell_centroid'\n",
+      "rg.grid_version = '0.2'\n",
+      "# Fill in data\n",
+      "contact[:] = '\\000' * 255\n",
+      "contact[:37] = 'atmos_mosaic:tile1::land_mosaic:tile1'\n",
+      "tile1_cell[:] = [ni,nj]\n",
+      "tile2_cell[:] = [ni,nj]\n",
+      "xgrid_area[:] = dxo * dyo\n",
+      "tile1_distance[:] = 0.\n",
+      "tile2_distance[:] = 0.\n",
+      "rg.close()"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": [],
+     "prompt_number": 17
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "rg = scipy.io.netcdf_file('atmos_mosaic_tile1Xocean_mosaic_tile1.nc','w',version=2) # atmos_mosaic_tile1Xocean_mosaic_tile1.nc\n",
+      "rg.createDimension('string',255)\n",
+      "rg.createDimension('ncells',ni*nj-nl) # -1 is for a single land point\n",
+      "rg.createDimension('two',2)\n",
+      "contact = rg.createVariable('contact','c',('string',))\n",
+      "contact.standard_name = 'grid_contact_spec'\n",
+      "contact.contact_type = 'exchange'\n",
+      "contact.parent1_cell = 'tile1_cell'\n",
+      "contact.parent2_cell = 'tile2_cell'\n",
+      "contact.xgrid_area_field = 'xgrid_area'\n",
+      "contact.distant_to_parent1_centroid = 'tile1_distance'\n",
+      "contact.distant_to_parent2_centroid = 'tile2_distance'\n",
+      "tile1_cell = rg.createVariable('tile1_cell','f8',('ncells','two',))\n",
+      "tile1_cell.standard_name = 'parent_cell_indices_in_mosaic1'\n",
+      "tile2_cell = rg.createVariable('tile2_cell','f8',('ncells','two',))\n",
+      "tile2_cell.standard_name = 'parent_cell_indices_in_mosaic2'\n",
+      "xgrid_area = rg.createVariable('xgrid_area','f8',('ncells',))\n",
+      "xgrid_area.standard_name = 'exchange_grid_area'\n",
+      "xgrid_area.units = 'm2'\n",
+      "tile1_distance = rg.createVariable('tile1_distance','f8',('ncells','two'))\n",
+      "tile1_distance.standard_name = 'distance_from_parent1_cell_centroid'\n",
+      "tile2_distance = rg.createVariable('tile2_distance','f8',('ncells','two'))\n",
+      "tile2_distance.standard_name = 'distance_from_parent2_cell_centroid'\n",
+      "rg.grid_version = '0.2'\n",
+      "# Fill in data\n",
+      "contact[:] = '\\000' * 255\n",
+      "contact[:37] = 'atmos_mosaic:tile1::land_mosaic:tile1'\n",
+      "tile1_cell[:] = [ni,nj]\n",
+      "tile2_cell[:] = [ni,nj]\n",
+      "xgrid_area[:] = dxo * dyo\n",
+      "count=-1\n",
+      "for j in range(nj):\n",
+      "    for i in range(ni):\n",
+      "        if Ocean_Depth[j,i]!=0:\n",
+      "            count=count+1\n",
+      "            tile1_cell[count] = [i,j]\n",
+      "            tile2_cell[count] = [i,j]\n",
+      "            tile1_distance[count] = [0,0]\n",
+      "            tile2_distance[count] = [0,0]\n",
+      "            xgrid_area[count] = dxo * dyo\n",
+      "rg.close()"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": [],
+     "prompt_number": 18
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "rg = scipy.io.netcdf_file('land_mosaic_tile1Xocean_mosaic_tile1.nc','w',version=2) # land_mosaic_tile1Xocean_mosaic_tile1.nc\n",
+      "rg.createDimension('string',255)\n",
+      "rg.createDimension('ncells',ni*nj-nl) # -1 is for a single land point\n",
+      "rg.createDimension('two',2)\n",
+      "contact = rg.createVariable('contact','c',('string',))\n",
+      "contact.standard_name = 'grid_contact_spec'\n",
+      "contact.contact_type = 'exchange'\n",
+      "contact.parent1_cell = 'tile1_cell'\n",
+      "contact.parent2_cell = 'tile2_cell'\n",
+      "contact.xgrid_area_field = 'xgrid_area'\n",
+      "contact.distant_to_parent1_centroid = 'tile1_distance'\n",
+      "contact.distant_to_parent2_centroid = 'tile2_distance'\n",
+      "tile1_cell = rg.createVariable('tile1_cell','f8',('ncells','two',))\n",
+      "tile1_cell.standard_name = 'parent_cell_indices_in_mosaic1'\n",
+      "tile2_cell = rg.createVariable('tile2_cell','f8',('ncells','two',))\n",
+      "tile2_cell.standard_name = 'parent_cell_indices_in_mosaic2'\n",
+      "xgrid_area = rg.createVariable('xgrid_area','f8',('ncells',))\n",
+      "xgrid_area.standard_name = 'exchange_grid_area'\n",
+      "xgrid_area.units = 'm2'\n",
+      "tile1_distance = rg.createVariable('tile1_distance','f8',('ncells','two'))\n",
+      "tile1_distance.standard_name = 'distance_from_parent1_cell_centroid'\n",
+      "tile2_distance = rg.createVariable('tile2_distance','f8',('ncells','two'))\n",
+      "tile2_distance.standard_name = 'distance_from_parent2_cell_centroid'\n",
+      "rg.grid_version = '0.2'\n",
+      "# Fill in data\n",
+      "contact[:] = '\\000' * 255\n",
+      "contact[:37] = 'atmos_mosaic:tile1::land_mosaic:tile1'\n",
+      "tile1_cell[:] = [ni,nj]\n",
+      "tile2_cell[:] = [ni,nj]\n",
+      "xgrid_area[:] = dxo * dyo\n",
+      "count=-1\n",
+      "for j in range(nj):\n",
+      "    for i in range(ni):\n",
+      "        if Ocean_Depth[j,i]!=0:\n",
+      "            count=count+1\n",
+      "            tile1_cell[count] = [i,j]\n",
+      "            tile2_cell[count] = [i,j]\n",
+      "            tile1_distance[count] = [0,0]\n",
+      "            tile2_distance[count] = [0,0]\n",
+      "            xgrid_area[count] = dxo * dyo\n",
+      "rg.close()"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": [],
+     "prompt_number": 19
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "rg = scipy.io.netcdf_file('mosaic.nc','w',version=2) # land_mosaic_tile1Xocean_mosaic_tile1.nc\n",
+      "rg.createDimension('string',255)\n",
+      "rg.createDimension('nfile_aXo',1) # -1 is for a single land point\n",
+      "rg.createDimension('nfile_aXl',1) # -1 is for a single land point\n",
+      "rg.createDimension('nfile_lXo',1) # -1 is for a single land point\n",
+      "\n",
+      "atm_mosaic_dir = rg.createVariable('atm_mosaic_dir','c',('string',))\n",
+      "atm_mosaic_dir.standard_name = 'directory_storing_atmosphere_mosaic'\n",
+      "\n",
+      "atm_mosaic_file = rg.createVariable('atm_mosaic_file','c',('string',))\n",
+      "atm_mosaic_file.standard_name = 'atmosphere_mosaic_file_name'\n",
+      "\n",
+      "atm_mosaic = rg.createVariable('atm_mosaic','c',('string',))\n",
+      "atm_mosaic.standard_name = 'atmosphere_mosaic_name'\n",
+      "\n",
+      "lnd_mosaic_dir = rg.createVariable('lnd_mosaic_dir','c',('string',))\n",
+      "lnd_mosaic_dir.standard_name = 'directory_storing_land_mosaic'\n",
+      "\n",
+      "lnd_mosaic_file = rg.createVariable('lnd_mosaic_file','c',('string',))\n",
+      "lnd_mosaic_file.standard_name = 'land_mosaic_file_name'\n",
+      "\n",
+      "lnd_mosaic = rg.createVariable('lnd_mosaic','c',('string',))\n",
+      "lnd_mosaic.standard_name = 'land_mosaic_name'\n",
+      "\n",
+      "ocn_mosaic_dir = rg.createVariable('ocn_mosaic_dir','c',('string',))\n",
+      "ocn_mosaic_dir.standard_name = 'directory_storing_ocean_mosaic'\n",
+      "\n",
+      "ocn_mosaic_file = rg.createVariable('ocn_mosaic_file','c',('string',))\n",
+      "ocn_mosaic_file.standard_name = 'ocean_mosaic_file_name'\n",
+      "\n",
+      "ocn_mosaic = rg.createVariable('ocn_mosaic','c',('string',))\n",
+      "ocn_mosaic.standard_name = 'ocean_mosaic_name'\n",
+      "\n",
+      "\n",
+      "ocn_topog_dir = rg.createVariable('ocn_topog_dir','c',('string',))\n",
+      "ocn_mosaic_dir.standard_name = 'directory_storing_ocean_topog'\n",
+      "\n",
+      "ocn_topog_file = rg.createVariable('ocn_topog_file','c',('string',))\n",
+      "ocn_topog_file.standard_name = 'ocean_topog_file_name'\n",
+      "\n",
+      "aXo_file = rg.createVariable('aXo_file','c',('nfile_aXo','string',))\n",
+      "aXo_file.standard_name = 'atmXocn_exchange_grid_file'\n",
+      "\n",
+      "aXl_file = rg.createVariable('aXl_file','c',('nfile_aXl','string',))\n",
+      "aXl_file.standard_name = 'atmXlnd_exchange_grid_file'\n",
+      "\n",
+      "lXo_file = rg.createVariable('lXo_file','c',('nfile_lXo','string',))\n",
+      "lXo_file.standard_name = 'lndXocn_exchange_grid_file'\n",
+      "\n",
+      "#Global attributes\n",
+      "rg.grid_version = '0.2'\n",
+      "rg.code_version = \"$Name:  $\"\n",
+      "rg.history = \"/net2/aja/workspace/MOM6-examples/ice_ocean_SIS2/OM4_025/preprocessing/fre_nctools/tools/make_quick_mosaic/make_quick_mosaic --input_mosaic ocean_mosaic.nc --ocean_topog ocean_topog.nc\"\n",
+      "# Fill in data\n",
+      "atm_mosaic_dir[:] = '\\000' * 255\n",
+      "atm_mosaic_dir[:2] = './'\n",
+      "\n",
+      "atm_mosaic_file[:] = '\\000' * 255\n",
+      "atm_mosaic_file[:15] = 'ocean_mosaic.nc'\n",
+      "\n",
+      "atm_mosaic[:] = '\\000' * 255\n",
+      "atm_mosaic[:12] = 'atmos_mosaic'\n",
+      "\n",
+      "lnd_mosaic_dir[:] = '\\000' * 255\n",
+      "lnd_mosaic_dir[:2] = './'\n",
+      "\n",
+      "lnd_mosaic_file[:] = '\\000' * 255\n",
+      "lnd_mosaic_file[:15] = 'ocean_mosaic.nc'\n",
+      "\n",
+      "lnd_mosaic[:] = '\\000' * 255\n",
+      "lnd_mosaic[:11] = 'land_mosaic'\n",
+      "\n",
+      "ocn_mosaic_dir[:] = '\\000' * 255\n",
+      "ocn_mosaic_dir[:2] = './'\n",
+      "\n",
+      "ocn_mosaic_file[:] = '\\000' * 255\n",
+      "ocn_mosaic_file[:15] = 'ocean_mosaic.nc'\n",
+      "\n",
+      "ocn_mosaic[:] = '\\000' * 255\n",
+      "ocn_mosaic[:12] = 'ocean_mosaic'\n",
+      "\n",
+      "ocn_topog_dir[:] = '\\000' * 255\n",
+      "ocn_topog_dir[:2] = './'\n",
+      "\n",
+      "ocn_topog_file[:] = '\\000' * 255\n",
+      "ocn_topog_file[:14] = 'ocean_topog.nc'\n",
+      "\n",
+      "aXo_file[:,:] = '\\000' * 255\n",
+      "aXo_file[:,:40] = 'atmos_mosaic_tile1Xocean_mosaic_tile1.nc'\n",
+      "\n",
+      "aXl_file[:,:] = '\\000' * 255\n",
+      "aXl_file[:,:39] = 'atmos_mosaic_tile1Xland_mosaic_tile1.nc'\n",
+      "\n",
+      "lXo_file[:,:] = '\\000' * 255\n",
+      "lXo_file[:,:39] = 'land_mosaic_tile1Xocean_mosaic_tile1.nc'\n",
+      "\n",
+      "rg.close()\n",
+      "\n"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": [],
+     "prompt_number": 20
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [],
+     "language": "python",
+     "metadata": {},
+     "outputs": [],
+     "prompt_number": 20
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [],
+     "language": "python",
+     "metadata": {},
+     "outputs": [],
+     "prompt_number": 20
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [],
+     "language": "python",
+     "metadata": {},
+     "outputs": [],
+     "prompt_number": 20
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [],
+     "language": "python",
+     "metadata": {},
+     "outputs": [],
+     "prompt_number": 20
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [],
+     "language": "python",
+     "metadata": {},
+     "outputs": [],
+     "prompt_number": 20
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [],
+     "language": "python",
+     "metadata": {},
+     "outputs": [],
+     "prompt_number": 20
+    }
+   ],
+   "metadata": {}
+  }
+ ]
+}
\ No newline at end of file
diff --git a/test/Iceberg_repository/Scripts_and_analysis/Create_mosaic.py b/test/Iceberg_repository/Scripts_and_analysis/Create_mosaic.py
new file mode 100755
index 0000000..eab8050
--- /dev/null
+++ b/test/Iceberg_repository/Scripts_and_analysis/Create_mosaic.py
@@ -0,0 +1,1387 @@
+#!/usr/bin/env python
+
+# generate files for Idealized Ice Shelf problem.
+# Gustavo Marques
+
+#import matplotlib
+#matplotlib.use('Agg')
+import argparse
+from netCDF4 import MFDataset, Dataset
+from scipy.interpolate import interp1d
+from scipy.ndimage.filters import gaussian_filter
+from scipy.optimize import curve_fit
+import numpy as np
+import matplotlib.pyplot as plt
+#import wright_eos as eos
+#import gsw
+import warnings
+import os
+
+def parseCommandLine():
+  """
+  Parse the command line positional and optional arguments.
+  This is the highest level procedure invoked from the very end of the script.
+  """
+  parser = argparse.ArgumentParser(description=
+      '''
+      Generate files for ocean-ice simulations.
+      ''',
+  epilog='Written by Gustavo Marques and Alon Stern, Dec. 2016.')
+
+  parser.add_argument('-nx', type=int, default=300,
+      help='''The total number of grid points in the x direction (default = 1200).''')
+
+  parser.add_argument('-ny', type=int, default=200,
+      help='''The total number of grid points in the y direction (default = 2400).''')
+
+  parser.add_argument('-nz', type=int, default=36,
+      help='''Number of model layers (default = 63).''')
+  
+  parser.add_argument('-W', type=float, default=1500.,
+      help='''Domain width in the x direction (km). Default is 1500.''')
+  
+  parser.add_argument('-L', type=float, default=1000.,
+      help='''Domain lenght in the y direction (km). Default is 1.2E3''')
+
+  parser.add_argument('-cshelf_lenght', type=float, default=000.,
+      help='''Continental shelf lenght in the y direction (km). Default is 500.''')
+
+  parser.add_argument('-slope_lenght', type=float, default=50.,
+      help='''Continental shelf slope lenght in the y direction (km). Default is 50.''')
+
+  parser.add_argument('-u10_asf', type=float, default=-5.0,
+      help='''Max. wind speed at the ASF (m/2). Default is -5.0''')
+  
+  parser.add_argument('-ISL', type=float, default=0.,
+      help='''Ice shelf legnth (km). Default is 0.0E3''')
+
+  parser.add_argument('-max_depth', type=float, default=3.0e3,
+      help='''Maximum ocean depth (m). Default is 3E3.''')
+
+  parser.add_argument('-min_depth', type=float, default=1000.0,
+      help='''Minimum ocean depth (m). Default is 500.''')
+
+  parser.add_argument('-land_width', type=float, default=100.0,
+      help='''Widht of land region next to ice shelf (km)- this also controls the shape
+      of the ice shelf. Default is 100.''')
+
+  parser.add_argument('-coupled_run', help='''Generate all the files needed to run an ocean_SIS2 simulation.''', action="store_true")
+  
+  parser.add_argument('-create_wind_files', help='''Generate wind iles.''', action="store_true")
+  
+  parser.add_argument('-create_TS_files', help='''Generate initial T/S files.''', action="store_true")
+  
+  parser.add_argument('-create_forcing_files', help='''Generate forcing files.''', action="store_true")
+  
+  parser.add_argument('-debug', help='''Adds prints and plots to help debug.''', action="store_true")
+
+  parser.add_argument('-freeze_ic', help='''Sets the temp to the freezing point in the upper 50 m of the IC.''', action="store_true")
+
+  parser.add_argument('-trough', help='''Adds a trough cutting the continental shelf.''', action="store_true")
+  
+  parser.add_argument('-homogeneous_ts', help='''Make the initial T/S homogeneous in the horizontal.''', action="store_true")
+
+  optCmdLineArgs = parser.parse_args()
+  driver(optCmdLineArgs)
+
+def driver(args):
+   """
+   This is where all the action happends, i.e., calls to different functions that generate
+   files that are needed.
+   """
+   nx = args.nx ; ny = args.ny; nz = args.nz
+   L = args.L; W = args.W; D = args.max_depth
+
+   dy = L/ny; dx = W/nx
+   y = np.arange(dy/2.,L,dy)
+   x = np.arange(dx/2.,W,dx)
+
+   # create dir. to place figures
+   #os.system('mkdir PNG')
+
+   # create ice shelf
+   #make_ice_shelf(x,y,args)
+
+   # create topography
+   Ocean_Depth = make_topo(x,y,args)
+   
+   #Create wind forcing
+   if args.create_wind_files:
+	   make_wind(x,y,args) 
+
+   if args.coupled_run:
+   	make_mosaic(x,y,Ocean_Depth,args) 
+
+   # initial T/S
+   if args.create_TS_files:
+   	make_ts(x,y,args)
+
+   # create forcing
+   if args.create_forcing_files:
+   	make_forcing(x,y,args) 
+   
+
+   print 'Driver section complete'
+   
+   return
+
+def make_ice_shelf(x,y,args):
+   '''
+   Here is a slightly different version but with constants
+   H(x) = H0 *(Q0)^(1/4) / [Q0+4*H0^4*C^3*x]^(1/4)
+   where H0 is ice thickness at the grounding line Q0 = U0*H0 is ice flux at the grounding line, C = rho*g*(1-rho/rho_w)/4/Bbar, rho is the ice density, rho_w is the sea-water density, Bbar is ice stiffness parameter.
+   for the following parameters 
+   rho = 917 kg/m^3
+   rho_w = 1028 kg/m^3
+   Bbar = 1.68e8
+   C = 1.4440e-06
+   U0= 700 m/yr = 2.2182e-05 m/s
+   H0 = 1500 m
+   Q0 = 0.0333 m^2/s
+   rho = 917. #kg/m^3
+   rho_w = 1028. #kg/m^3
+   Bbar = 1.68e8
+   '''
+   x = x * 1.0e3 # im m
+   y = y * 1.0e3 # im m
+   C = 1.4440e-06
+   H0 = 2000.0 #m
+   Q0 = 0.03327 #m^2/s
+   gp = 20.e3 # grouding line position
+   dy = y[1]-y[0]
+   dx = x[1]-x[0]
+   Lice = 200.0e3
+   h =  H0 *(Q0)**(1./4.) / (Q0+100*H0**4*C**3*(y-gp))**(1./4.)
+   h[y<gp] = H0
+   h[y>Lice] = 0.0 
+   # smooth
+   h_smooth = gaussian_filter(h,2)
+   h_smooth[y<gp] = H0
+   h_smooth[h_smooth<50.0] = 0.0
+   # find meridional lenght of ice shelf
+   tmp = np.nonzero(h_smooth==0.0)[0][0]
+   args.ISL = x[tmp] / 1.0e3
+   print 'Ice shelf meridional lenght is (km):',x[tmp] / 1.0e3
+   
+   if args.debug:
+      plt.plot(y,h,'k',y,h_smooth,'r')
+      plt.savefig('PNG/ice_shelf_profile.png')
+
+   area_tmp = np.ones(args.ny) * dx * dy
+   area_tmp[h_smooth == 0.0] = 0.0
+
+   # Create a netcdf horizontal ocean-grid file
+   name = 'IC_IS'
+   ncfile = Dataset('output_files/'+name+'.nc','w')
+   ncfile.createDimension('nx',args.nx)
+   ncfile.createDimension('ny',args.ny)
+   thick = ncfile.createVariable('thick','double',('ny','nx',))
+   thick.units = 'm'
+   thick.standard_name =  'ice shelf thickness'
+   area = ncfile.createVariable('area','double',('ny','nx',))
+   area.units = 'm2'
+   area.standard_name =  'ice shelf area'  
+
+   # write into nc file
+   for i in range(args.nx):
+        thick[:,i] = h_smooth[:]
+        area[:,i] = area_tmp[:]
+
+   ncfile.sync()
+   ncfile.close()
+   print ('*** SUCCESS creating '+name+'.nc!') 
+
+def make_mosaic(x,y,Ocean_Depth,args):
+   '''
+   Create files used in coupled ice/ocean runs.
+   '''
+   ni = args.nx;   nj = args.ny
+   snj, sni = 2*nj, 2*ni
+   dxo = (x[1] - x[0]) * 1.0e3 # in m
+   dyo = (y[1] - y[0]) * 1.0e3 # in m
+
+   # Number of land points used nl GM: There has to be at least ONE land point
+   nl=0
+   #Define land points:
+   Ocean_Depth[0,0]=0.0
+   for j in range(nj):
+      for i in range(ni):
+          if Ocean_Depth[j,i]==0:
+              nl=nl+1
+
+   # Using a supergrid refinement of 2, the grid lengths, area and coordinates are:
+   dx = (0.5 * dxo) * np.ones((snj+1,sni))
+   dy = (0.5 * dyo) * np.ones((snj,sni+1))
+   area = (0.25 * (dxo * dyo)) * np.ones((snj,sni))
+   x = np.zeros((snj+1,sni+1))
+   x[:,1:] = np.cumsum( dx, axis=-1 )
+   y = np.zeros((snj+1,sni+1))
+   y[1:,:] = np.cumsum( dy, axis=-2 )
+
+   # Create a netcdf horizontal ocean-grid file
+   name = 'ocean_hgrid'
+   ncfile = Dataset('output_files/' +name+'.nc','w')
+   ncfile.createDimension('nx',sni)
+   ncfile.createDimension('ny',snj)
+   ncfile.createDimension('nxp',sni+1)
+   ncfile.createDimension('nyp',snj+1)
+   ncfile.createDimension('string',255)
+   dx_h = ncfile.createVariable('dx','f8',('nyp','nx',))
+   dx_h.units = 'm'
+   dy_h = ncfile.createVariable('dy','f8',('ny','nxp',))
+   dy_h.units = 'm'
+   area_h = ncfile.createVariable('area','f8',('ny','nx',))
+   area_h.units = 'm2'
+   x_h = ncfile.createVariable('x','f8',('nyp','nxp',))
+   x_h.units = 'm'
+   y_h = ncfile.createVariable('y','f8',('nyp','nxp',))
+   y_h.units = 'm'
+   tile = ncfile.createVariable('tile','c',('string',)) 
+   dx_h[:,:] = dx[:,:]
+   dy_h[:,:] = dy[:,:]
+   area_h[:,:] = area[:,:]
+   x_h[:,:] = x[:,:]
+   y_h[:,:] = y[:,:]
+   tile[:] = '\000' * 255
+   tile[:5] = 'tile1'
+   set_string(tile,'tile1')
+   ncfile.close()
+   print ('*** SUCCESS creating '+name+'.nc!')
+
+   # create ocean_mask file
+   name = 'ocean_mask'
+   rg = Dataset('output_files/' +name+'.nc','w')
+   rg.createDimension('nx',ni)
+   rg.createDimension('ny',nj)
+   mask = rg.createVariable('mask','f4',('ny','nx',))
+   mask[:,:] = 1.
+   rg.close()
+   print ('*** SUCCESS creating '+name+'.nc!')
+
+   # Create a mosaic description for the grid file
+   name = 'ocean_mosaic'
+   rg = Dataset('output_files/' +name+'.nc','w')
+   rg.createDimension('ntiles',1)
+   rg.createDimension('string',255)
+   mosaic = rg.createVariable('mosaic','c',('string',))
+   mosaic.standard_name = 'grid_mosaic_spec'
+   mosaic.children = 'contacts'
+   mosaic.grid_descriptor = ''
+   gridlocation = rg.createVariable('gridlocation','c',('string',))
+   gridlocation.standard_name = 'grid_file_location'
+   gridfiles = rg.createVariable('gridfiles','c',('ntiles','string',))
+   gridtiles = rg.createVariable('gridtiles','c',('ntiles','string',))
+   rg.grid_version = '0.2'
+   # Fill in data
+   mosaic[:] = '\000' * 255
+   mosaic[:12] = 'ocean_mosaic'
+   gridlocation[:] = '\000' * 255
+   gridlocation[:2] = './'
+   gridfiles[:] = '\000' * 255
+   gridfiles[0,:14] = 'ocean_hgrid.nc'
+   gridtiles[:] = '\000' * 255
+   gridtiles[0,:5] = 'tile1'
+   rg.close()
+   print ('*** SUCCESS creating '+name+'.nc!')
+
+   name = 'atmos_mosaic_tile1Xland_mosaic_tile1'
+   rg = Dataset('output_files/' + name+'.nc','w')
+   rg.createDimension('string',255)
+   rg.createDimension('ncells',nl)  #It is unclear whether this works when nl=0. It does work for nl>0
+   rg.createDimension('two',2)
+   contact = rg.createVariable('contact','c',('string',))
+   contact.standard_name = 'grid_contact_spec'
+   contact.contact_type = 'exchange'
+   contact.parent1_cell = 'tile1_cell'
+   contact.parent2_cell = 'tile2_cell'
+   contact.xgrid_area_field = 'xgrid_area'
+   contact.distant_to_parent1_centroid = 'tile1_distance'
+   contact.distant_to_parent2_centroid = 'tile2_distance'
+   tile1_cell = rg.createVariable('tile1_cell','f8',('ncells','two'))
+   tile1_cell.standard_name = 'parent_cell_indices_in_mosaic1'
+   tile2_cell = rg.createVariable('tile2_cell','f8',('ncells','two'))
+   tile2_cell.standard_name = 'parent_cell_indices_in_mosaic2'
+   xgrid_area = rg.createVariable('xgrid_area','f8',('ncells'))
+   xgrid_area.standard_name = 'exchange_grid_area'
+   xgrid_area.units = 'm2'
+   tile1_distance = rg.createVariable('tile1_distance','f8',('ncells','two'))
+   tile1_distance.standard_name = 'distance_from_parent1_cell_centroid'
+   tile2_distance = rg.createVariable('tile2_distance','f8',('ncells','two'))
+   tile2_distance.standard_name = 'distance_from_parent2_cell_centroid'
+   rg.grid_version = '0.2'
+   # Fill in data
+   contact[:] = '\000' * 255
+   contact[:37] = 'atmos_mosaic:tile1::land_mosaic:tile1'
+   for i in range(nl):
+      tile1_cell[i,:] = [ni,nj]
+      tile2_cell[i,:] = [ni,nj]
+
+   xgrid_area[:] = dxo * dyo
+   tile1_distance[:] = 0.
+   tile2_distance[:] = 0.
+   rg.close()
+   print ('*** SUCCESS creating '+name+'.nc!')
+
+   name = 'atmos_mosaic_tile1Xocean_mosaic_tile1'
+   rg = Dataset('output_files/' + name+'.nc','w')
+   rg.createDimension('string',255)
+   rg.createDimension('ncells',ni*nj-nl) # -1 is for a single land point
+   rg.createDimension('two',2)
+   contact = rg.createVariable('contact','c',('string',))
+   contact.standard_name = 'grid_contact_spec'
+   contact.contact_type = 'exchange'
+   contact.parent1_cell = 'tile1_cell'
+   contact.parent2_cell = 'tile2_cell'
+   contact.xgrid_area_field = 'xgrid_area'
+   contact.distant_to_parent1_centroid = 'tile1_distance'
+   contact.distant_to_parent2_centroid = 'tile2_distance'
+   tile1_cell = rg.createVariable('tile1_cell','f8',('ncells','two',))
+   tile1_cell.standard_name = 'parent_cell_indices_in_mosaic1'
+   tile2_cell = rg.createVariable('tile2_cell','f8',('ncells','two',))
+   tile2_cell.standard_name = 'parent_cell_indices_in_mosaic2'
+   xgrid_area = rg.createVariable('xgrid_area','f8',('ncells',))
+   xgrid_area.standard_name = 'exchange_grid_area'
+   xgrid_area.units = 'm2'
+   tile1_distance = rg.createVariable('tile1_distance','f8',('ncells','two'))
+   tile1_distance.standard_name = 'distance_from_parent1_cell_centroid'
+   tile2_distance = rg.createVariable('tile2_distance','f8',('ncells','two'))
+   tile2_distance.standard_name = 'distance_from_parent2_cell_centroid'
+   rg.grid_version = '0.2'
+   # Fill in data
+   contact[:] = '\000' * 255
+   contact[:37] = 'atmos_mosaic:tile1::land_mosaic:tile1'
+   for i in range(nl):
+      tile1_cell[i,:] = [ni,nj]
+      tile2_cell[i,:] = [ni,nj]
+   
+   xgrid_area[:] = dxo * dyo
+   count=-1
+   for j in range(nj):
+       for i in range(ni):
+          if Ocean_Depth[j,i]!=0:
+            count=count+1
+            tile1_cell[count] = [i,j]
+            tile2_cell[count] = [i,j]
+            tile1_distance[count] = [0,0]
+            tile2_distance[count] = [0,0]
+            xgrid_area[count] = dxo * dyo
+
+   rg.close()
+   print ('*** SUCCESS creating '+name+'.nc!') 
+
+   name = 'land_mosaic_tile1Xocean_mosaic_tile1'
+   rg = Dataset('output_files/' + name+'.nc','w')
+   rg.createDimension('string',255)
+   rg.createDimension('ncells',ni*nj-nl) # -1 is for a single land point
+   rg.createDimension('two',2)
+   contact = rg.createVariable('contact','c',('string',))
+   contact.standard_name = 'grid_contact_spec'
+   contact.contact_type = 'exchange'
+   contact.parent1_cell = 'tile1_cell'
+   contact.parent2_cell = 'tile2_cell'
+   contact.xgrid_area_field = 'xgrid_area'
+   contact.distant_to_parent1_centroid = 'tile1_distance'
+   contact.distant_to_parent2_centroid = 'tile2_distance'
+   tile1_cell = rg.createVariable('tile1_cell','f8',('ncells','two',))
+   tile1_cell.standard_name = 'parent_cell_indices_in_mosaic1'
+   tile2_cell = rg.createVariable('tile2_cell','f8',('ncells','two',))
+   tile2_cell.standard_name = 'parent_cell_indices_in_mosaic2'
+   xgrid_area = rg.createVariable('xgrid_area','f8',('ncells',))
+   xgrid_area.standard_name = 'exchange_grid_area'
+   xgrid_area.units = 'm2'
+   tile1_distance = rg.createVariable('tile1_distance','f8',('ncells','two'))
+   tile1_distance.standard_name = 'distance_from_parent1_cell_centroid'
+   tile2_distance = rg.createVariable('tile2_distance','f8',('ncells','two'))
+   tile2_distance.standard_name = 'distance_from_parent2_cell_centroid'
+   rg.grid_version = '0.2'
+   # Fill in data
+   contact[:] = '\000' * 255
+   contact[:37] = 'atmos_mosaic:tile1::land_mosaic:tile1'
+   for i in range(nl):
+      tile1_cell[i,:] = [ni,nj]
+      tile2_cell[i,:] = [ni,nj]
+   
+   xgrid_area[:] = dxo * dyo
+   count=-1
+   for j in range(nj):
+      for i in range(ni):
+        if Ocean_Depth[j,i]!=0:
+            count=count+1
+            tile1_cell[count] = [i,j]
+            tile2_cell[count] = [i,j]
+            tile1_distance[count] = [0,0]
+            tile2_distance[count] = [0,0]
+            xgrid_area[count] = dxo * dyo
+  
+   rg.close()
+   print ('*** SUCCESS creating '+name+'.nc!')
+
+
+   name = 'grid_spec' # sometimes grid_spec is called mosaic.nc
+   #name = 'mosaic' # sometimes grid_spec is called mosaic.nc
+   rg = Dataset('output_files/' + name+'.nc','w')
+   rg.createDimension('string',255)
+   rg.createDimension('nfile_aXo',1) # -1 is for a single land point
+   rg.createDimension('nfile_aXl',1) # -1 is for a single land point
+   rg.createDimension('nfile_lXo',1) # -1 is for a single land point
+   atm_mosaic_dir = rg.createVariable('atm_mosaic_dir','c',('string',))
+   atm_mosaic_dir.standard_name = 'directory_storing_atmosphere_mosaic'
+   atm_mosaic_file = rg.createVariable('atm_mosaic_file','c',('string',))
+   atm_mosaic_file.standard_name = 'atmosphere_mosaic_file_name'
+   atm_mosaic = rg.createVariable('atm_mosaic','c',('string',))
+   atm_mosaic.standard_name = 'atmosphere_mosaic_name'
+   lnd_mosaic_dir = rg.createVariable('lnd_mosaic_dir','c',('string',))
+   lnd_mosaic_dir.standard_name = 'directory_storing_land_mosaic'
+   lnd_mosaic_file = rg.createVariable('lnd_mosaic_file','c',('string',))
+   lnd_mosaic_file.standard_name = 'land_mosaic_file_name'
+   lnd_mosaic = rg.createVariable('lnd_mosaic','c',('string',))
+   lnd_mosaic.standard_name = 'land_mosaic_name'
+   ocn_mosaic_dir = rg.createVariable('ocn_mosaic_dir','c',('string',))
+   ocn_mosaic_dir.standard_name = 'directory_storing_ocean_mosaic'
+   ocn_mosaic_file = rg.createVariable('ocn_mosaic_file','c',('string',))
+   ocn_mosaic_file.standard_name = 'ocean_mosaic_file_name'
+   ocn_mosaic = rg.createVariable('ocn_mosaic','c',('string',))
+   ocn_mosaic.standard_name = 'ocean_mosaic_name'
+   ocn_topog_dir = rg.createVariable('ocn_topog_dir','c',('string',))
+   ocn_mosaic_dir.standard_name = 'directory_storing_ocean_topog'
+   ocn_topog_file = rg.createVariable('ocn_topog_file','c',('string',))
+   ocn_topog_file.standard_name = 'ocean_topog_file_name'
+   aXo_file = rg.createVariable('aXo_file','c',('nfile_aXo','string',))
+   aXo_file.standard_name = 'atmXocn_exchange_grid_file'
+   aXl_file = rg.createVariable('aXl_file','c',('nfile_aXl','string',))
+   aXl_file.standard_name = 'atmXlnd_exchange_grid_file'
+   lXo_file = rg.createVariable('lXo_file','c',('nfile_lXo','string',))
+   lXo_file.standard_name = 'lndXocn_exchange_grid_file'
+   #Global attributes
+   rg.grid_version = '0.2'
+   rg.code_version = "$Name:  $"
+   rg.history = "/net2/aja/workspace/MOM6-examples/ice_ocean_SIS2/OM4_025/preprocessing/fre_nctools/tools/make_quick_mosaic/make_quick_mosaic --input_mosaic ocean_mosaic.nc --ocean_topog ocean_topog.nc"
+   # Fill in data
+   atm_mosaic_dir[:] = '\000' * 255
+   atm_mosaic_dir[:2] = './'
+   atm_mosaic_file[:] = '\000' * 255
+   atm_mosaic_file[:15] = 'ocean_mosaic.nc'
+   atm_mosaic[:] = '\000' * 255
+   atm_mosaic[:12] = 'atmos_mosaic'
+   lnd_mosaic_dir[:] = '\000' * 255
+   lnd_mosaic_dir[:2] = './'
+   lnd_mosaic_file[:] = '\000' * 255
+   lnd_mosaic_file[:15] = 'ocean_mosaic.nc'
+   lnd_mosaic[:] = '\000' * 255
+   lnd_mosaic[:11] = 'land_mosaic'
+   ocn_mosaic_dir[:] = '\000' * 255
+   ocn_mosaic_dir[:2] = './'
+   ocn_mosaic_file[:] = '\000' * 255
+   ocn_mosaic_file[:15] = 'ocean_mosaic.nc'
+   ocn_mosaic[:] = '\000' * 255
+   ocn_mosaic[:12] = 'ocean_mosaic'
+   ocn_topog_dir[:] = '\000' * 255
+   ocn_topog_dir[:2] = './'
+   ocn_topog_file[:] = '\000' * 255
+   ocn_topog_file[:14] = 'ocean_topog.nc'
+   aXo_file[:,:] = '\000' * 255
+   aXo_file[:,:40] = 'atmos_mosaic_tile1Xocean_mosaic_tile1.nc'
+   aXl_file[:,:] = '\000' * 255
+   aXl_file[:,:39] = 'atmos_mosaic_tile1Xland_mosaic_tile1.nc'
+   lXo_file[:,:] = '\000' * 255
+   lXo_file[:,:39] = 'land_mosaic_tile1Xocean_mosaic_tile1.nc'
+   rg.close()
+   print ('*** SUCCESS creating '+name+'.nc!')
+
+def get_profile(t,i,j,var,depth,z,args,vname,take_mean = True):
+   '''
+   Get data (var), remove mask, smooth profile then interpolate to z grid.
+   '''
+   if take_mean:
+      data = np.mean(Dataset('WOA05_pottemp_salt.nc').variables[var][:,:,j,i], axis=0)
+      
+   else:
+      data = Dataset('WOA05_pottemp_salt.nc').variables[var][t,:,j,i]
+
+   # replace mask value with last good value
+   tmp = np.nonzero(data.mask==False)[0][-1]
+   data[tmp+1::] = data[tmp]
+   # smooth  
+   data = gaussian_filter(data,2) # filter std 2
+   # interpo
+   f1 = interp1d(depth, data)
+   if args.debug:
+      plt.figure()
+      plt.plot(data,-depth,'b',f1(z),-z,'rx')
+      plt.title(vname)
+      plt.savefig('PNG/'+vname+'.png')
+
+   return f1(z)
+
+def set_freezing_temp(T,S,z,y,args):
+    '''
+    Set the temp. in the upper 50 m to the surface freezing point, then smooth data
+    '''
+    d = np.nonzero(z<=50.)[0]
+    for k in range(len(d)):
+        for j in range(args.ny):
+           if y[j] <= (args.ISL + args.cshelf_lenght + args.slope_lenght):
+              T[0,k,j,:] = eos.tfreeze(S[0,k,j,:],1.0e5) 
+
+    for j in range(args.ny):
+      for i in range(args.nx):
+         T[0,d,j,i] = gaussian_filter(T[0,d,j,i],1) # filter std 1
+
+    # smooth T and S in the cross slope direction
+    #for k in range(args.nz):
+    #   for j in range(args.ny):
+    #       T[0,k,:,i] = gaussian_filter(T[0,k,:,i],2)
+    #       S[0,k,:,i] = gaussian_filter(T[0,k,:,i],2)
+
+    return T,S
+
+def make_ts(x,y,args):
+   '''
+   Extract T/S from WOA05 for a particulat lat. then interpolate results into ocean grid. 
+   '''
+   # climatology depth
+   depth = Dataset('WOA05_pottemp_salt.nc').variables['DEPTH'][:]
+   # model depth
+   z = np.linspace(0,args.max_depth,args.nz) # positive downward
+   # all values between -78 to - 60
+   # use sw.dist to find distance
+   # 176 lon (Ross Sea), July, southern wall conditions (-78)
+   i =  176; t = 6; j = 11
+   temp_south = get_profile(t,i,j,'PTEMP',depth,z,args,'TempSouth')
+   salt_south = get_profile(t,i,j,'SALT',depth,z,args,'SaltSouth')
+   # shelf break conditions (-72)
+   j = 17
+   temp_break = get_profile(t,i,j,'PTEMP',depth,z,args,'TempSlope')
+   salt_break = get_profile(t,i,j,'SALT',depth,z,args,'SaltSlope')
+   # northern wall conditions (-65)
+   j = 21
+   temp_north = get_profile(t,i,j,'PTEMP',depth,z,args,'TempNorth')
+   salt_north = get_profile(t,i,j,'SALT',depth,z,args,'SaltNorth')
+
+   # distace from southern wall to use in the interp.
+   #dist = [0,args.cshelf_lenght+args.slope_lenght*0.5,args.L,args.L]
+   dummy = args.ISL + args.cshelf_lenght
+   dist = [0, dummy, dummy+args.slope_lenght, args.L-50.,args.L]
+   # 3d fields
+   temp3D = np.zeros((1,args.nz,len(y),len(x)))
+   salt3D = np.zeros((1,args.nz,len(y),len(x)))
+
+   if args.homogeneous_ts:
+    dist = [0,args.max_depth]
+    f1 = interp1d(dist,[0, -2])
+    dummy_t = f1(z)
+    f1 = interp1d(dist,[34.,34.62])
+    dummy_s = f1(z)
+    sigma2 = eos.wright_eos(dummy_t,dummy_s,2.0e7)
+    # compute rho0/alpha/beta
+    alpha = eos.alpha_wright_eos(dummy_t,dummy_s,2.0e7)
+    beta = eos.beta_wright_eos(dummy_t,dummy_s,2.0e7)
+    Rho_T0_S0 = eos.wright_eos(0.,0.,2.0e7) + 0. # 0.017 is a correction factor
+    # compute linear eos
+    rho_lin = Rho_T0_S0 + alpha.mean()*dummy_t + beta.mean()*dummy_t
+    print 'sigma2 - rho_lin',sigma2 - rho_lin
+    plt.close('all')
+    plt.figure()
+    plt.plot(sigma2-1000.,-z,'k',rho_lin-1000,-z,'r')
+    plt.show()
+
+    for i in range(args.nx):
+       for j in range(args.ny):
+           temp3D[0,:,j,i] = dummy_t[:]
+           salt3D[0,:,j,i] = dummy_s[:]
+
+   else:
+     # distace from southern wall to use in the interp.
+     #dist = [0,args.cshelf_lenght+args.slope_lenght*0.5,args.L,args.L]
+     dummy = args.ISL + args.cshelf_lenght
+     dist = [0, dummy, dummy+args.slope_lenght, args.L-50.,args.L]
+     # horizontal interp
+     for k in range(args.nz):
+         #f1 = interp1d(dist, [temp_south[k],temp_break[k],temp_north[k], temp_north[k]])
+         f1 = interp1d(dist, [temp_south[k],temp_south[k],temp_north[k],temp_north[k], temp_north[k]])
+         dummy_t = f1(y)
+         #f1 = interp1d(dist, [salt_south[k],salt_break[k],salt_north[k], salt_north[k]])
+         f1 = interp1d(dist, [salt_south[k],salt_south[k],salt_north[k], salt_north[k], salt_north[k]])
+         dummy_s = f1(y)
+         for i in range(args.nx):
+            temp3D[0,k,:,i] = dummy_t[:]
+            salt3D[0,k,:,i] = dummy_s[:]
+
+   # set temp below 50 m to freezing point
+   if args.freeze_ic:
+      temp3D, salt3D = set_freezing_temp(temp3D,salt3D,z,y,args)
+
+   # compute sigma2
+   sigma2 = eos.wright_eos(temp3D,salt3D,2.0e7)
+   # compute rho0/alpha/beta
+   alpha = eos.alpha_wright_eos(temp3D,salt3D,2.0e7)
+   beta = eos.beta_wright_eos(temp3D,salt3D,2.0e7)
+   Rho_T0_S0 = eos.wright_eos(0.,0.,2.0e7) + 0.017 # 0.017 is a correction factor
+   
+   # compute linear eos
+   rho_lin = Rho_T0_S0 + alpha.mean()*temp3D + beta.mean()*salt3D
+
+   layers = Dataset('GOLD_IC.2010.11.15.nc').variables['Layer'][:] # used in the global run with sig2
+   if args.debug:
+      print 'alpha,beta,Rho_T0_S0',alpha.mean(),beta.mean(),Rho_T0_S0
+      print 'sigma2 - rho_lin',sigma2[0,:,0,0] - rho_lin[0,:,0,0]
+
+      plt.figure()
+      plt.contourf(y,-z,rho_lin[0,:,:,0])
+      plt.colorbar()
+      plt.contour(y,-z,rho_lin[0,:,:,0]-1000.,layers-1000,colors='k',linewidths=2)
+      plt.title('Density - 1000.')
+      plt.savefig('PNG/rho_section.png')
+  
+ 
+      plt.figure()
+      plt.plot(sigma2[0,:,0,0]-1000.,-z,'b',rho_lin[0,:,0,0]-1000.,-z,'bx')
+      plt.plot(sigma2[0,:,args.ny/2.,0]-1000.,-z,'r',rho_lin[0,:,args.ny/2.,0]-1000.,-z,'rx')
+      plt.plot(sigma2[0,:,args.ny-1,0]-1000.,-z,'k',rho_lin[0,:,args.ny-1,0]-1000.,-z,'kx')
+      plt.title('Linear (dashed) vs. nonlinear EoS at south, center and north (b,r,k)')
+      plt.savefig('PNG/rho_profiles.png')
+ 
+      # plot t - tfreeze at surface
+      tf = eos.tfreeze(salt3D[0,0,:,:],1.0e5) 
+      plt.figure()
+      plt.subplot(311)
+      plt.contourf(x,y,temp3D[0,0,:,:],np.linspace(temp3D[0,0,:,:].min(),temp3D[0,0,:,:].max(),50))
+      plt.colorbar()
+      plt.title('SST')
+      plt.subplot(312)
+      plt.contourf(x,y,tf,np.linspace(tf.min(),tf.max(),50))
+      plt.colorbar()
+      plt.title('Freezing temp. at surface')
+      plt.subplot(313)
+      plt.contourf(x,y,temp3D[0,0,:,:] - tf)
+      plt.colorbar()
+      plt.title('T - TFreeze')
+      plt.savefig('PNG/SST_and_Tfreeze.png')
+
+      #(S, T) = np.meshgrid(np.linspace(0.,40.,51), np.linspace(-2.5, 3.0, 51))
+      #r1 = eos.wright_eos(T,S,2.0e7)
+      #r2 = Rho_T0_S0 + alpha.mean()*T + beta.mean()*S
+
+      #plt.figure()
+      #CS1 = plt.contour(S,T,r1-1000,layers-1000,colors='b')
+      #plt.clabel(CS1, inline=1, fontsize=10)
+      #CS2 = plt.contour(S,T,r2-1000,layers-1000,colors='r')
+      #plt.clabel(CS2, inline=1, fontsize=10)
+      #plt.xlabel('Salt'); plt.ylabel('Temp')
+      #plt.grid()
+      #plt.show()
+
+   # create ncfiles
+
+   # vertical coord. (layers)
+   name = 'vertical_layers'
+   ncfile = Dataset('output_files/' + name+'.nc','w')
+   ncfile.createDimension('Layer',args.nz)
+   Layer = ncfile.createVariable('Layer',np.dtype('double').char,('Layer'))
+   Layer.units = 'kg/m^3'
+   Layer[:] = layers[:]
+
+   ncfile.close()
+   print ('*** SUCCESS creating '+name+'.nc!')
+   
+   # 1) The name of the z-space input file used to initialize
+   #  the layer thicknesses, temperatures and salinities.
+   name = 'ic_ts'
+   ncfile = Dataset('output_files/' + name+'.nc','w')
+   # create dimensions.
+   ncfile.createDimension('DEPTH',args.nz)
+   ncfile.createDimension('LAT',len(y))
+   ncfile.createDimension('LON',len(x))
+   ncfile.createDimension('TIME',1)
+
+   # create variables
+   LAT = ncfile.createVariable('LAT',np.dtype('double').char,('LAT'))
+   LAT.units = 'degrees_north'
+   LAT.long_name = 'h point nominal latitude'
+   LAT.cartesian_axis = 'Y'
+   LAT[:] = y[:]
+
+   LON = ncfile.createVariable('LON',np.dtype('double').char,('LON'))
+   LON.units = 'degrees_east'
+   LON.long_name = 'h point nominal longitude'
+   LON.cartesian_axis = 'X'
+   LON[:] = x[:]
+
+   TIME = ncfile.createVariable('TIME',np.dtype('double').char,('TIME'))
+   TIME.units = 'days since 0001-01-01 00:00:00'
+   TIME.calendar = 'noleap'
+   TIME.cartesian_axis = 'T'
+   TIME[0] = 0.0
+
+   DEPTH = ncfile.createVariable('DEPTH',np.dtype('double').char,('DEPTH'))
+   DEPTH.units = 'm'
+   DEPTH.direction = -1
+   DEPTH.cartesian_axis = 'Z'
+   DEPTH[:] = z[:]
+
+   PTEMP = ncfile.createVariable('PTEMP',np.dtype('float32').char,('TIME','DEPTH','LAT','LON'), fill_value = -1.e+34)
+   PTEMP.missing_value = -1.e+34
+   PTEMP[:] = temp3D[:] 
+
+   SALT = ncfile.createVariable('SALT',np.dtype('float32').char,('TIME','DEPTH','LAT','LON'), fill_value = -1.e+34)  
+   SALT.missing_value = -1.e+34
+   SALT[:] = salt3D[:]
+   ncfile.close()
+   print ('*** SUCCESS creating '+name+'.nc!')
+
+   # 2) The file from which the coordinate densities are read
+   #name = 'ts_ic_profile'
+   #ncfile = Dataset(name+'.nc','w')
+   # create dimensions.
+   #ncfile.createDimension('Layer',args.nz)
+
+   # create variables
+   #PTEMP = ncfile.createVariable('PTEMP',np.dtype('double').char,('Layer'))
+   #PTEMP.units = 'Celcius'
+   #PTEMP.long_name = 'Potential Temperature'
+   #PTEMP[:] = temp_int[:]
+
+   #SALT = ncfile.createVariable('SALT',np.dtype('double').char,('Layer'))
+   #SALT.units = 'PSU'
+   #SALT.long_name = 'Salinity'
+   #SALT[:] = salt_int[:]
+
+   #ncfile.close()
+   #print ('*** SUCCESS creating '+name+'.nc!')
+
+def make_wind(x,y,args):
+   # forcing parameters
+   nx = len(x); ny = len(y); nt =1 # time
+   Ly = args.L # domain size km
+   W = args.W # domain width km
+   u10_asf = args.u10_asf # def is -0.5  m/s
+   tau_asf = 0.05 # default is 0.075 # N/m^2
+   u10 = np.zeros((nt,ny,nx)) 
+   v10 = np.zeros((nt,ny,nx))
+   tau_x = np.zeros((nt,ny,nx)) # ice forcing
+   tau_y = np.zeros((nt,ny,nx))
+   
+   # Sin^2 wind profile
+   Lasf = 400.0 # km
+   for j in range(ny):
+         #tmp = np.pi*(y[j]-(Ly/2.0))/Lasf
+         tmp = np.pi*(y[j]/Ly)
+         u10[0,j,:] = u10_asf * np.sin(tmp)**2
+         tau_x[0,j,:] = tau_asf * np.sin(tmp)**2 
+   
+   
+   # create ncfile
+   # open a new netCDF file for writing.
+   # # used when forcing is applied in the atm
+   name = 'forcing_10'
+   ncfile = Dataset('output_files/' + name+'.nc','w')
+   # create dimensions.
+   ncfile.createDimension('LON',nx)
+   ncfile.createDimension('LAT',ny)
+   ncfile.createDimension('TIME',None)
+   # create variables
+   LON = ncfile.createVariable('LON',np.dtype('double').char,('LON'))
+   LON.units = 'km'
+   LON.long_name = 'h point nominal longitude'
+   LON.cartesian_axis = 'X'
+   LON[:] = x[:]
+
+   LAT = ncfile.createVariable('LAT',np.dtype('double').char,('LAT'))
+   LAT.units = 'km'
+   LAT.long_name = 'h point nominal latitude'
+   LAT.cartesian_axis = 'Y'
+   LAT[:] = y[:]
+
+   time = ncfile.createVariable('TIME',np.dtype('double').char,('TIME'))
+   time.long_name = 'time'
+   time.units = 'days since 0001-01-01 00:00:00'
+   time.cartesian_axis = 'T'
+   time.calendar_type = 'NOLEAP'
+   time.calendar = 'NOLEAP'
+   time.bounds = 'time_bounds'
+   time[0] = 0
+
+   u_10 = ncfile.createVariable('U_10',np.dtype('float32').char,('TIME','LAT','LON'))
+   u_10.long_name = 'U wind'
+   u_10.units = 'm/s'
+   u_10[:] = u10[:]
+
+   v_10 = ncfile.createVariable('V_10',np.dtype('float32').char,('TIME','LAT','LON'))
+   v_10.long_name = 'U wind'
+   v_10.units = 'm/s'
+   v_10[:] = v10[:]
+
+   ncfile.close()
+   print ('*** SUCCESS creating '+name+'.nc!')
+        
+   
+   
+   # used when forcing is applied in the sea ice
+   name = 'forcing'
+   ncfile = Dataset('output_files/' + name+'.nc','w')
+   # create dimensions.
+   ncfile.createDimension('xh',nx)
+   ncfile.createDimension('yh',ny)
+   ncfile.createDimension('xq',nx)
+   ncfile.createDimension('yq',ny)
+   ncfile.createDimension('time',None)
+   ncfile.createDimension('nv',2)
+
+   # create variables
+   xh = ncfile.createVariable('xh',np.dtype('double').char,('xh'))
+   xh.units = 'km'
+   xh.long_name = 'h point nominal longitude'
+   xh.cartesian_axis = 'X'
+   xh[:] = x[:]
+   
+   xq = ncfile.createVariable('xq',np.dtype('double').char,('xq'))
+   xq.units = 'km'
+   xq.long_name = 'q point nominal longitude'
+   xq.cartesian_axis = 'X'
+   xq[:] = x[:]
+
+   yh = ncfile.createVariable('yh',np.dtype('double').char,('yh'))
+   yh.units = 'km'
+   yh.long_name = 'h point nominal latitude'
+   yh.cartesian_axis = 'Y'
+   yh[:] = y[:]
+   
+   yq = ncfile.createVariable('yq',np.dtype('double').char,('yq'))
+   yq.units = 'km'
+   yq.long_name = 'q point nominal latitude'
+   yq.cartesian_axis = 'Y'
+   yq[:] = y[:]
+
+   time = ncfile.createVariable('time',np.dtype('double').char,('time'))
+   time.long_name = 'time'
+   time.units = 'days since 0001-01-01 00:00:00'
+   time.cartesian_axis = 'T'
+   time.calendar_type = 'NOLEAP'
+   time.calendar = 'NOLEAP'
+   time.bounds = 'time_bounds'
+   time[0] = 0
+
+   nv = ncfile.createVariable('nv',np.dtype('double').char,('nv'))   
+   nv.long_name = 'vertex number'
+   nv.units = 'none'
+   nv.cartesian_axis = 'N'
+   nv[:] = [1,2]
+
+   if args.coupled_run:
+     u_flux = ncfile.createVariable('u_flux',np.dtype('float32').char,('time', 'yh', 'xh'), fill_value = 1.e+20)
+     u_flux.units = 'Pa'
+     u_flux.missing_value = 1.e+20
+     u_flux.long_name = 'i-direction wind stress'
+     u_flux[:] = -tau_x[:] # change sign in ice
+
+     v_flux = ncfile.createVariable('v_flux',np.dtype('float32').char,('time', 'yh', 'xh'), fill_value = 1.e+20)
+     v_flux.units = 'Pa'
+     v_flux.missing_value = 1.e+20
+     v_flux.long_name = 'j-direction wind stress'
+     v_flux[:] = -tau_y[:] # change sign in ice
+
+   else:
+     taux = ncfile.createVariable('taux',np.dtype('float32').char,('time', 'yh', 'xq'), fill_value = 1.e+20)
+     taux.units = 'Pascal'
+     taux.missing_value = 1.e+20
+     taux.long_name = 'Zonal Wind Stress'
+     taux[:] = tau_x[:]   
+
+     tauy = ncfile.createVariable('tauy',np.dtype('float32').char,('time', 'yq', 'xh'), fill_value = 1.e+20)
+     tauy.units = 'Pascal'
+     tauy.missing_value = 1.e+20
+     tauy.long_name = 'Meridional Wind Stress'
+     tauy[:] = 0.0
+
+
+   ncfile.close()
+   print ('*** SUCCESS creating '+name+'.nc!')
+   
+   return
+
+def make_forcing(x,y,args):
+   # forcing parameters
+   Ly = args.L # domain size km
+   W = args.W # domain width km
+   CSL = args.cshelf_lenght  # km
+   Q0 = 10. # W/m^2
+   Qmax = 50.
+   Yt = 600.0  # km
+   Lasf = 400.0 # km
+   tau_acc = 0.2
+   tau_asf = -0.05 # default is -0.075 # N/m^2
+   katabatic_wind = 0.075 # def is 0.05 N/m2
+   sponge = 50.0 # km
+   # polynya salt and salt fluxes
+   major = 75.0
+   minor = 75.0
+   area = np.pi * major * minor * 0.5
+   print 'Polynya area is (km^2):', area
+   ISL = args.ISL
+   salt_flux = 0.0
+   heat_flux = 0.0
+   latent_flux = 0.0
+   #ice_form = ((np.abs(salt_flux)*3600*24) * area * 1.0e6* 1.0e3/34.) * 1.0e-3 / (area * 1.0e6) 
+   #print 'Sea ice formation (m/day)', ice_form
+   #ice_form = ice_form/area
+   nx = len(x); ny = len(y); nt =1 # time
+   tau_x = np.zeros((nt,ny,nx)) # ice forcing
+   tau_y = np.zeros((nt,ny,nx))
+   evaporation = np.zeros((nt,ny,nx))
+   salt = np.zeros((nt,ny,nx))
+   heat = np.zeros((nt,ny,nx))
+   latent = np.zeros((nt,ny,nx))
+   # core atm params and values
+   u10_asf = args.u10_asf # def is -0.5  m/s
+   v10_katabatic = 15.0 # m/s
+   t10_min = 250. # kelvin
+   t10_max = 270.
+   t10_polynya = 0.
+   u10 = np.zeros((nt,ny,nx)) 
+   v10 = np.zeros((nt,ny,nx))
+   t10 = np.ones((nt,ny,nx))* t10_min
+
+   # wind and heat
+   # x-dir
+   tmp1 = ISL + 100.
+   for j in range(ny):
+      if y[j] < tmp1:
+        tau_x[0,j,:] = 0.0
+        u10[0,j,:] = 0.0
+        heat[0,j,:] = -Q0
+      elif y[j] >= tmp1 and y[j] <= tmp1 + Lasf:
+         tmp = np.pi*(y[j]-tmp1)/Lasf
+         u10[0,j,:] = u10_asf * np.sin(tmp)**2
+         tau_x[0,j,:] = tau_asf * np.sin(tmp)**2 
+         heat[0,j,:] = -Q0 - (8 * Q0 * np.sin(tmp))
+      else:
+         tmp2 = (y[j] - tmp1 - Lasf)/(2.*(Ly-tmp1 - Lasf))
+         u10[0,j,:] = 0.0
+         tau_x[0,j,:] = tau_acc * np.sin(tmp2 * np.pi)**2
+         heat[0,j,:] = -Q0 
+        
+   # y-dir (decays linearly away from the ice shelf front)
+   # has a gaussian shape: tauy = tauy_max * np.exp(((x-W/2.)**2)/(2*W_v10))
+   W_v10 = 50000. # km
+   dummy = ISL + args.cshelf_lenght + args.slope_lenght
+   for i in range(nx):
+      for j in range(ny):
+         if y[j] < ISL:
+            tau_y[0,j,i] = katabatic_wind
+            v10[0,j,i] = v10_katabatic
+         elif y[j] <= dummy:
+            tmp =  np.exp((-(x[i]-W*0.5)**2)/(2*W_v10))
+            tau_y[0,j,i] = ((-katabatic_wind/(dummy)) * (y[j]) + katabatic_wind) * tmp
+            v10[0,j,i] = ((-v10_katabatic/(dummy)) * (y[j]) + v10_katabatic) * tmp
+
+   # read ocean's initial SST (in K)
+   T0 = Dataset('ic_ts.nc').variables['PTEMP'][0,1,:,0] + 273.
+   # T10 = T10 - 10 * np.exp(-(y[j]-ISL)/150.)
+   # e-folding scale is 150 km
+   efold = args.cshelf_lenght + args.slope_lenght
+   for j in range(ny):
+      if y[j]<=ISL:
+         t10[0,j,:] = 250. #T0[j] - 10. 
+         heat[0,j,:] = -100.
+      elif y[j]<=ISL + efold:
+         t10[0,j,:] = 270 - 20. * np.exp(-(y[j]-ISL)/100.)
+         heat[0,j,:] = -100. * np.exp(-(y[j]-ISL)/100.)
+      else:
+         t10[0,j,:] = 0.0
+         heat[0,j,:] = 0.0
+   
+   # evap, proxy for brine formation in polynyas
+   if t10_polynya > 0.:
+     for i in range(nx):
+       for j in range(ny):
+	 if (x[i] - W/2. >= -major and x[i] - W/2. <= major):
+	    if (y[j]-ISL >= 0.) and (y[j]-ISL <= (minor * np.abs((1-(x[i]-W/2.)**2/major**2)**(1/2.)))):
+	      evaporation[0,j,i] = salt_flux
+	      salt[0,j,i] = salt_flux
+	      heat[0,j,i] = heat_flux
+	      latent[0,j,i] = latent_flux
+	      t10[0,j,i] = t10_polynya
+
+   # set salt flux such that net buoynacy flux is zero
+   # B_heat = B_salt
+   cp = 3974.0 # J/(K kg)
+   rho0 = 1028.0; alpha = 0.11069/rho0; beta = 0.7906/rho0; g = 9.8
+   B_heat = heat[0,:,:] * g * alpha/ (rho0 * cp)
+   salt[0,:,:] = B_heat * rho0 / (beta * g)
+   print 'B_heat',B_heat.min(),B_heat.max()
+   print 'salt',salt.min(),salt.max()
+   # plots
+   if args.debug:
+
+      plt.figure()
+      u=u10[0,::5,::5]; v=v10[0,::5,::5]; mag = np.sqrt(u**2 + v**2)
+      plt.quiver(x[::5],y[::5],u, v, mag, cmap = plt.cm.seismic)
+      plt.colorbar()
+      plt.plot(x,np.ones(nx)*ISL,'k')
+      plt.plot(x,np.ones(nx)*(ISL+CSL),'k')
+      plt.title('Wind vel. at 10 m (m/s)')
+      plt.xlabel('x [km]'); plt.ylabel('y [km]')
+      plt.savefig('PNG/wind10m.png')
+
+      plt.figure()
+      plt.subplot(211)
+      plt.plot(y,u10[0,:,1])
+      plt.title('u10'); plt.xlabel('y [km]'); plt.ylabel('m/s')
+      plt.subplot(212)
+      plt.contourf(x,y,u10[0,:,:]); plt.colorbar()
+      plt.xlabel('x [km]'); plt.ylabel('y [km]')
+      plt.savefig('PNG/u10.png')
+
+      plt.figure()
+      plt.subplot(211)
+      plt.plot(y,v10[0,:,1])
+      plt.title('v10'); plt.xlabel('y [km]'); plt.ylabel('m/s')
+      plt.subplot(212)
+      plt.contourf(x,y,v10[0,:,:]); plt.colorbar()
+      plt.xlabel('x [km]'); plt.ylabel('y [km]')
+      plt.savefig('PNG/v10.png')
+
+      plt.figure()
+      plt.subplot(211)
+      plt.plot(y,tau_x[0,:,1])
+      plt.title('taux'); plt.xlabel('y [km]'); plt.ylabel('Pa')
+      plt.subplot(212)
+      plt.contourf(x,y,tau_x[0,:,:]); plt.colorbar()
+      plt.xlabel('x [km]'); plt.ylabel('y [km]')
+      plt.savefig('PNG/taux.png')
+
+      plt.figure()
+      plt.subplot(211)
+      plt.plot(y,tau_y[0,:,args.nx/2.])
+      plt.title('tauy'); plt.xlabel('y [km]'); plt.ylabel('Pa')
+      plt.subplot(212)
+      plt.contourf(x,y,tau_y[0,:,:]); plt.colorbar()
+      plt.xlabel('x [km]'); plt.ylabel('y [km]')
+      plt.savefig('PNG/tauy.png') 
+
+      plt.figure()
+      plt.subplot(211)
+      plt.plot(y,heat[0,:,1])
+      plt.title('Sensible Heat'); plt.xlabel('y [km]'); plt.ylabel('W/m^2')
+      plt.subplot(212)
+      plt.contourf(x,y,heat[0,:,:]); plt.colorbar()
+      plt.xlabel('x [km]'); plt.ylabel('y [km]')
+      plt.savefig('PNG/sensible_heat.png')
+
+      plt.figure()
+      plt.title('Salt flux kg/(m^2 s)')
+      plt.contourf(x,y,heat[0,:,:]); plt.colorbar()
+      plt.xlabel('x [km]'); plt.ylabel('y [km]')
+      plt.savefig('PNG/salt_flux.png')
+
+      plt.figure()
+      plt.subplot(211)
+      plt.plot(y,t10[0,:,1],'b',y,T0,'r')
+      plt.title('Atm temp at 10 m (b); Initial SST (r)'); plt.xlabel('y [km]'); plt.ylabel('K')
+      plt.subplot(212)
+      plt.contourf(x,y,t10[0,:,:]); plt.colorbar()
+      plt.xlabel('x [km]'); plt.ylabel('y [km]')
+      plt.savefig('PNG/t10.png')
+
+   # create ncfile
+   # open a new netCDF file for writing.
+   # # used when forcing is applied in the atm
+   name = 'forcing_10'
+   ncfile = Dataset('output_files/' + name+'.nc','w')
+   # create dimensions.
+   ncfile.createDimension('LON',nx)
+   ncfile.createDimension('LAT',ny)
+   ncfile.createDimension('TIME',None)
+   # create variables
+   LON = ncfile.createVariable('LON',np.dtype('double').char,('LON'))
+   LON.units = 'km'
+   LON.long_name = 'h point nominal longitude'
+   LON.cartesian_axis = 'X'
+   LON[:] = x[:]
+
+   LAT = ncfile.createVariable('LAT',np.dtype('double').char,('LAT'))
+   LAT.units = 'km'
+   LAT.long_name = 'h point nominal latitude'
+   LAT.cartesian_axis = 'Y'
+   LAT[:] = y[:]
+
+   time = ncfile.createVariable('TIME',np.dtype('double').char,('TIME'))
+   time.long_name = 'time'
+   time.units = 'days since 0001-01-01 00:00:00'
+   time.cartesian_axis = 'T'
+   time.calendar_type = 'NOLEAP'
+   time.calendar = 'NOLEAP'
+   time.bounds = 'time_bounds'
+   time[0] = 0
+
+   t_10 = ncfile.createVariable('T_10',np.dtype('float32').char,('TIME','LAT','LON')) 
+   t_10.long_name = 'Air Temperature'
+   t_10.units = 'Kelvin'
+   t_10[:] = t10[:]
+
+   u_10 = ncfile.createVariable('U_10',np.dtype('float32').char,('TIME','LAT','LON'))
+   u_10.long_name = 'U wind'
+   u_10.units = 'm/s'
+   u_10[:] = u10[:]
+
+   v_10 = ncfile.createVariable('V_10',np.dtype('float32').char,('TIME','LAT','LON'))
+   v_10.long_name = 'U wind'
+   v_10.units = 'm/s'
+   v_10[:] = v10[:]
+
+   ncfile.close()
+   print ('*** SUCCESS creating '+name+'.nc!')
+
+   # used when forcing is applied in the sea ice
+   name = 'forcing'
+   ncfile = Dataset('output_files/' + name+'.nc','w')
+   # create dimensions.
+   ncfile.createDimension('xh',nx)
+   ncfile.createDimension('yh',ny)
+   ncfile.createDimension('xq',nx)
+   ncfile.createDimension('yq',ny)
+   ncfile.createDimension('time',None)
+   ncfile.createDimension('nv',2)
+
+   # create variables
+   xh = ncfile.createVariable('xh',np.dtype('double').char,('xh'))
+   xh.units = 'km'
+   xh.long_name = 'h point nominal longitude'
+   xh.cartesian_axis = 'X'
+   xh[:] = x[:]
+   
+   xq = ncfile.createVariable('xq',np.dtype('double').char,('xq'))
+   xq.units = 'km'
+   xq.long_name = 'q point nominal longitude'
+   xq.cartesian_axis = 'X'
+   xq[:] = x[:]
+
+   yh = ncfile.createVariable('yh',np.dtype('double').char,('yh'))
+   yh.units = 'km'
+   yh.long_name = 'h point nominal latitude'
+   yh.cartesian_axis = 'Y'
+   yh[:] = y[:]
+   
+   yq = ncfile.createVariable('yq',np.dtype('double').char,('yq'))
+   yq.units = 'km'
+   yq.long_name = 'q point nominal latitude'
+   yq.cartesian_axis = 'Y'
+   yq[:] = y[:]
+
+   time = ncfile.createVariable('time',np.dtype('double').char,('time'))
+   time.long_name = 'time'
+   time.units = 'days since 0001-01-01 00:00:00'
+   time.cartesian_axis = 'T'
+   time.calendar_type = 'NOLEAP'
+   time.calendar = 'NOLEAP'
+   time.bounds = 'time_bounds'
+   time[0] = 0
+
+   nv = ncfile.createVariable('nv',np.dtype('double').char,('nv'))   
+   nv.long_name = 'vertex number'
+   nv.units = 'none'
+   nv.cartesian_axis = 'N'
+   nv[:] = [1,2]
+
+   if args.coupled_run:
+     u_flux = ncfile.createVariable('u_flux',np.dtype('float32').char,('time', 'yh', 'xh'), fill_value = 1.e+20)
+     u_flux.units = 'Pa'
+     u_flux.missing_value = 1.e+20
+     u_flux.long_name = 'i-direction wind stress'
+     u_flux[:] = -tau_x[:] # change sign in ice
+
+     v_flux = ncfile.createVariable('v_flux',np.dtype('float32').char,('time', 'yh', 'xh'), fill_value = 1.e+20)
+     v_flux.units = 'Pa'
+     v_flux.missing_value = 1.e+20
+     v_flux.long_name = 'j-direction wind stress'
+     v_flux[:] = -tau_y[:] # change sign in ice
+
+     t_flux = ncfile.createVariable('t_flux',np.dtype('float32').char,('time', 'yh', 'xh'), fill_value = 1.e+20)
+     t_flux.units = 'Watt meter-2'
+     t_flux.missing_value = 1.e+20
+     t_flux.long_name = 'Sensible heat flux'
+     t_flux[:] = -heat[:] # change sign in ice
+
+     # latent heat
+     lt = ncfile.createVariable('latent',np.dtype('float32').char,('time', 'yh', 'xh'), fill_value = 1.e+20)
+     lt.units = 'Watt meter-2'
+     lt.missing_value = 1.e+20
+     lt.long_name = 'Latent heat flux'
+     lt[:] = -latent # change sign in ice
+
+     salt_flux = ncfile.createVariable('salt_flux',np.dtype('float32').char,('time', 'yh', 'xh'), fill_value = 1.e+20)
+     salt_flux.units = 'kg/(m^2 s)'
+     salt_flux.missing_value = 1.e+20
+     salt_flux.long_name = 'salt flux'
+     salt_flux[:] = -salt[:] # + adds salt from ocean
+
+   else:
+     SW = ncfile.createVariable('SW',np.dtype('float32').char,('time', 'yh', 'xh'), fill_value = 1.e+20)
+     SW.units = 'Watt meter-2'
+     SW.missing_value = 1.e+20
+     SW.long_name = 'surface_net_downward_shortwave_flux'
+     SW[:] = 0.0
+
+     LW = ncfile.createVariable('LW',np.dtype('float32').char,('time', 'yh', 'xh'), fill_value = 1.e+20)
+     LW.units = 'Watt meter-2'
+     LW.missing_value = 1.e+20
+     LW.long_name = 'surface_net_downward_longwave_flux'
+     LW[:] = 0.0
+
+     latent = ncfile.createVariable('latent',np.dtype('float32').char,('time', 'yh', 'xh'), fill_value = 1.e+20)
+     latent.units = 'Watt meter-2'
+     latent.missing_value = 1.e+20
+     latent.long_name = 'Latent heat flux into ocean due to fusion and evaporation'
+     latent[:] = 0.0
+
+     sensible = ncfile.createVariable('sensible',np.dtype('float32').char,('time', 'yh', 'xh'), fill_value = 1.e+20)
+     sensible.units = 'Watt meter-2'
+     sensible.missing_value = 1.e+20
+     sensible.long_name = 'surface_downward_sensible_heat_flux'
+     sensible[:] = heat[:]
+
+     evap = ncfile.createVariable('evap',np.dtype('float32').char,('time', 'yh', 'xh'), fill_value = 1.e+20)
+     evap.units = 'kilogram meter-2 second-1'
+     evap.missing_value = 1.e+20
+     evap.long_name = 'Evaporation at ocean surface (usually negative)'
+     evap[:] = evaporation[:]
+
+     taux = ncfile.createVariable('taux',np.dtype('float32').char,('time', 'yh', 'xq'), fill_value = 1.e+20)
+     taux.units = 'Pascal'
+     taux.missing_value = 1.e+20
+     taux.long_name = 'Zonal Wind Stress'
+     taux[:] = tau_x[:]   
+
+     tauy = ncfile.createVariable('tauy',np.dtype('float32').char,('time', 'yq', 'xh'), fill_value = 1.e+20)
+     tauy.units = 'Pascal'
+     tauy.missing_value = 1.e+20
+     tauy.long_name = 'Meridional Wind Stress'
+     tauy[:] = 0.0
+
+     ustar = ncfile.createVariable('ustar',np.dtype('float32').char,('time', 'yh', 'xh'), fill_value = 1.e+20)
+     ustar.units = 'meter second-1'
+     ustar.missing_value = 1.e+20
+     ustar.long_name = 'Surface friction velocity'
+     ustar[:] = 0.0
+
+     SST = ncfile.createVariable('SST',np.dtype('float32').char,('time', 'yh', 'xh'), fill_value = -1.e+34)
+     SST.units = 'Celsius'
+     SST.missing_value = -1.e+34
+     SST.long_name = 'Sea Surface Temperature'
+     SST[:] = 0.0
+
+     SSS = ncfile.createVariable('SSS',np.dtype('float32').char,('time', 'yh', 'xh'), fill_value = -1.e+34)
+     SSS.units = 'PSU'
+     SSS.missing_value = -1.e+34
+     SSS.long_name = 'Sea Surface Salinity'
+     SSS[:] = 0.0
+
+   ncfile.close()
+   print ('*** SUCCESS creating '+name+'.nc!')
+   
+   return
+
+def make_topo(x,y,args):
+   # parameters
+   name = 'ocean_topog'
+   Hs = args.min_depth  # shelf's depth
+   x=x*1000  #Conversion to meters
+   y=y*1000  #Conversion to meters
+   nx = len(x); ny = len(y)
+   D = np.zeros((ny,nx))
+
+   #Adding a small Guassian bump/hill to bottom topography to break the symmetry
+   x0=(np.max(x)-np.min(x))/2.0
+   y0=(np.max(y)-np.min(y))/4.0
+   print x0
+   R=100*1000.0
+   H0=100.0
+   for j in range(ny):
+      for i in range(nx):
+	      #d=np.sqrt( ((x[i]-x0)**2)   + ((y[j]-y0)**2) ) #Gausian bump
+	      d=np.sqrt( ((x[i]-x0)**2) )  #Gausian hill
+              D[j,i] = Hs - (H0*np.exp(-(d/(R))**2))
+
+
+	
+   # to avoid sea ice formation under ice shelves,
+   # two topography files need to be constructed.
+   # The coupler topo is where the cavity is masked.
+
+   Dcoupler = D.copy()
+   #for j in range(ny):
+   #    if y[j]<= args.ISL:
+   #       Dcoupler[j,:] = 0.0
+
+   # 1) topography used in the coupler
+   # open a new netCDF file for writing.
+   name = 'ocean_topog'
+   ncfile = Dataset('output_files/' + name+'.nc','w')
+   # create dimensions.
+   ncfile.createDimension('nx',nx)
+   ncfile.createDimension('ny',ny)
+   ncfile.createDimension('ntiles',1)
+ 
+   # create variables
+   nxx = ncfile.createVariable('nx',np.dtype('double').char,('nx'))
+   nxx.units = 'km'
+   nxx.description = 'x location of cell centers'
+   nxx.long_name = 'x location of cell centers'
+   nxx[:] = x[:]
+
+   nyy = ncfile.createVariable('ny',np.dtype('double').char,('ny'))
+   nyy.units = 'km'
+   nyy.description = 'y location of cell centers'
+   nyy.long_name = 'y location of cell centers'
+   nyy[:] = y[:]
+
+   depth = ncfile.createVariable('depth',np.dtype('float32').char,('ny','nx'))
+   depth.units = 'm'
+   depth.description = 'depth at h points'
+   depth.long_name = 'depth at h points'
+   depth[:,:] = Dcoupler[:,:]
+   ncfile.close()
+   print ('*** SUCCESS creating '+name+'.nc!')
+
+   # 2) topography used ny the ocean
+   # open a new netCDF file for writing.
+   name = 'topog'
+   ncfile = Dataset('output_files/' + name+'.nc','w')
+   # create dimensions.
+   ncfile.createDimension('nx',nx)
+   ncfile.createDimension('ny',ny)
+   ncfile.createDimension('ntiles',1)
+
+   # create variables
+   nxx = ncfile.createVariable('nx',np.dtype('double').char,('nx'))
+   nxx.units = 'km'
+   nxx.description = 'x location of cell centers'
+   nxx.long_name = 'x location of cell centers'
+   nxx[:] = x[:]
+
+   nyy = ncfile.createVariable('ny',np.dtype('double').char,('ny'))
+   nyy.units = 'km'
+   nyy.description = 'y location of cell centers'
+   nyy.long_name = 'y location of cell centers'
+   nyy[:] = y[:]
+
+   depth = ncfile.createVariable('depth',np.dtype('float32').char,('ny','nx'))
+   depth.units = 'm'
+   depth.description = 'depth at h points'
+   depth.long_name = 'depth at h points'
+   depth[:,:] = D[:,:]
+   ncfile.close()
+   print ('*** SUCCESS creating '+name+'.nc!')
+ 
+   return Dcoupler
+
+# A helper function to use when writing strings in a netcdf file
+def set_string(variable, value):
+   """Sets "variable" to "value" padded with blanks where
+   "variable" is a netcdf variable object and "value" is a string."""
+   variable[:] = '\000' * variable.shape[0]
+   variable[:len(value)] = value
+   return
+
+# Invoke parseCommandLine(), the top-level prodedure
+if __name__ == '__main__': parseCommandLine()
diff --git a/test/Iceberg_repository/Scripts_and_analysis/Idealized_cartesian_grid.py b/test/Iceberg_repository/Scripts_and_analysis/Idealized_cartesian_grid.py
new file mode 100644
index 0000000..6aa3510
--- /dev/null
+++ b/test/Iceberg_repository/Scripts_and_analysis/Idealized_cartesian_grid.py
@@ -0,0 +1,395 @@
+
+# coding: utf-8
+
+# In[2]:
+
+import scipy.io.netcdf
+import numpy
+get_ipython().magic('pylab inline')
+
+
+# Model grid will have ni x nj h-point grid cells
+
+# In[3]:
+
+nj,ni = 40,240
+
+
+# A mosaic file has a supergrid of an integer refinement (e.g. 2*ni x 2*nj cells)
+
+# In[4]:
+
+snj, sni = 2*nj, 2*ni
+
+
+# Uniform resolution of the ocean model grid will be dxo x dyo
+
+# In[5]:
+
+dxo = 2.e3
+dyo = 2.e3
+
+
+# Using a supergrid refinement of 2, the grid lengths, area and coordinates are:
+
+# In[6]:
+
+dx = (0.5 * dxo) * numpy.ones((snj+1,sni))
+dy = (0.5 * dyo) * numpy.ones((snj,sni+1))
+area = (0.25 * (dxo * dyo)) * numpy.ones((snj,sni))
+x = numpy.zeros((snj+1,sni+1))
+x[:,1:] = numpy.cumsum( dx, axis=-1 )
+y = numpy.zeros((snj+1,sni+1))
+y[1:,:] = numpy.cumsum( dy, axis=-2 )
+
+
+# In[7]:
+
+# A helper function to use when writing strings in a netcdf file
+def set_string(variable, value):
+    """Sets "variable" to "value" padded with blanks where
+    "variable" is a netcdf variable object and "value" is a string."""
+    variable[:] = '\000' * variable.shape[0]
+    variable[:len(value)] = value
+
+
+# Create a netcdf3 horizontal ocean-grid file...
+
+# In[8]:
+
+rg = scipy.io.netcdf_file('ocean_hgrid.nc','w',version=2)
+
+
+# In[9]:
+
+rg.createDimension('nx',sni)
+rg.createDimension('ny',snj)
+rg.createDimension('nxp',sni+1)
+rg.createDimension('nyp',snj+1)
+rg.createDimension('string',255)
+
+
+# In[10]:
+
+dx_h = rg.createVariable('dx','f8',('nyp','nx',))
+dx_h.units = 'm'
+dy_h = rg.createVariable('dy','f8',('ny','nxp',))
+dy_h.units = 'm'
+area_h = rg.createVariable('area','f8',('ny','nx',))
+area_h.units = 'm2'
+x_h = rg.createVariable('x','f8',('nyp','nxp',))
+x_h.units = 'm'
+y_h = rg.createVariable('y','f8',('nyp','nxp',))
+y_h.units = 'm'
+tile = rg.createVariable('tile','c',('string',))
+
+
+# In[11]:
+
+dx_h[:,:] = dx[:,:]
+dy_h[:,:] = dy[:,:]
+area_h[:,:] = area[:,:]
+x_h[:,:] = x[:,:]
+y_h[:,:] = y[:,:]
+tile[:] = '\000' * 255
+tile[:5] = 'tile1'
+set_string(tile,'tile1')
+
+
+# In[12]:
+
+rg.close()
+
+
+# Create a netcdf3 ocean-mask file...
+
+# In[13]:
+
+rg = scipy.io.netcdf_file('ocean_mask.nc','w',version=2)
+rg.createDimension('nx',ni)
+rg.createDimension('ny',nj)
+mask = rg.createVariable('mask','f4',('ny','nx',))
+mask[:,:] = 1.
+rg.close()
+
+
+# Create a mosaic description for the above grid file...
+
+# In[14]:
+
+rg = scipy.io.netcdf_file('ocean_mosaic.nc','w',version=2)
+rg.createDimension('ntiles',1)
+rg.createDimension('string',255)
+mosaic = rg.createVariable('mosaic','c',('string',))
+mosaic.standard_name = 'grid_mosaic_spec'
+mosaic.children = 'contacts'
+mosaic.grid_descriptor = ''
+gridlocation = rg.createVariable('gridlocation','c',('string',))
+gridlocation.standard_name = 'grid_file_location'
+gridfiles = rg.createVariable('gridfiles','c',('ntiles','string',))
+gridtiles = rg.createVariable('gridtiles','c',('ntiles','string',))
+rg.grid_version = '0.2'
+# Fill in data
+mosaic[:] = '\000' * 255
+mosaic[:12] = 'ocean_mosaic'
+gridlocation[:] = '\000' * 255
+gridlocation[:2] = './'
+gridfiles[:] = '\000' * 255
+gridfiles[0,:14] = 'ocean_hgrid.nc'
+gridtiles[:] = '\000' * 255
+gridtiles[0,:5] = 'tile1'
+rg.close()
+
+
+# In[15]:
+
+get_ipython().system('pwd')
+
+
+# In[16]:
+
+# Fake a ocean_topog.nc file
+rg = scipy.io.netcdf_file('ocean_topog.nc','w',version=2)
+rg.createDimension('nx',ni)
+rg.createDimension('ny',nj)
+rg.createDimension('ntiles',1)
+depth = rg.createVariable('depth','f4',('ny','nx',))
+depth[:,:] = 1000.
+depth[-1,-1] =0
+rg.close()
+
+
+# In[17]:
+
+#fre_nctools/tools/make_quick_mosaic/make_quick_mosaic --input_mosaic ocean_mosaic.nc --ocean_topog ocean_topog.nc
+
+
+# In[18]:
+
+rg = scipy.io.netcdf_file('atmos_mosaic_tile1Xland_mosaic_tile1_BLAH.nc','w',version=2) # atmos_mosaic_tile1Xland_mosaic_tile1.nc
+rg.createDimension('string',255)
+rg.createDimension('ncells',1)
+rg.createDimension('two',2)
+contact = rg.createVariable('contact','c',('string',))
+contact.standard_name = 'grid_contact_spec'
+contact.contact_type = 'exchange'
+contact.parent1_cell = 'tile1_cell'
+contact.parent2_cell = 'tile2_cell'
+contact.xgrid_area_field = 'xgrid_area'
+contact.distant_to_parent1_centroid = 'tile1_distance'
+contact.distant_to_parent2_centroid = 'tile2_distance'
+tile1_cell = rg.createVariable('tile1_cell','f8',('ncells','two',))
+tile1_cell.standard_name = 'parent_cell_indices_in_mosaic1'
+tile2_cell = rg.createVariable('tile2_cell','f8',('ncells','two',))
+tile2_cell.standard_name = 'parent_cell_indices_in_mosaic2'
+xgrid_area = rg.createVariable('xgrid_area','f8',('ncells',))
+xgrid_area.standard_name = 'exchange_grid_area'
+xgrid_area.units = 'm2'
+tile1_distance = rg.createVariable('tile1_distance','f8',('ncells','two'))
+tile1_distance.standard_name = 'distance_from_parent1_cell_centroid'
+tile2_distance = rg.createVariable('tile2_distance','f8',('ncells','two'))
+tile2_distance.standard_name = 'distance_from_parent2_cell_centroid'
+rg.grid_version = '0.2'
+# Fill in data
+contact[:] = '\000' * 255
+contact[:37] = 'atmos_mosaic:tile1::land_mosaic:tile1'
+tile1_cell[:] = [ni,nj]
+tile2_cell[:] = [ni,nj]
+xgrid_area[:] = dxo * dyo
+tile1_distance[:] = 0.
+tile2_distance[:] = 0.
+rg.close()
+
+
+# In[19]:
+
+rg = scipy.io.netcdf_file('atmos_mosaic_tile1Xocean_mosaic_tile1_BLAH.nc','w',version=2) # atmos_mosaic_tile1Xocean_mosaic_tile1.nc
+rg.createDimension('string',255)
+rg.createDimension('ncells',ni*nj-1) # -1 is for a single land point
+rg.createDimension('two',2)
+contact = rg.createVariable('contact','c',('string',))
+contact.standard_name = 'grid_contact_spec'
+contact.contact_type = 'exchange'
+contact.parent1_cell = 'tile1_cell'
+contact.parent2_cell = 'tile2_cell'
+contact.xgrid_area_field = 'xgrid_area'
+contact.distant_to_parent1_centroid = 'tile1_distance'
+contact.distant_to_parent2_centroid = 'tile2_distance'
+tile1_cell = rg.createVariable('tile1_cell','f8',('ncells','two',))
+tile1_cell.standard_name = 'parent_cell_indices_in_mosaic1'
+tile2_cell = rg.createVariable('tile2_cell','f8',('ncells','two',))
+tile2_cell.standard_name = 'parent_cell_indices_in_mosaic2'
+xgrid_area = rg.createVariable('xgrid_area','f8',('ncells',))
+xgrid_area.standard_name = 'exchange_grid_area'
+xgrid_area.units = 'm2'
+tile1_distance = rg.createVariable('tile1_distance','f8',('ncells','two'))
+tile1_distance.standard_name = 'distance_from_parent1_cell_centroid'
+tile2_distance = rg.createVariable('tile2_distance','f8',('ncells','two'))
+tile2_distance.standard_name = 'distance_from_parent2_cell_centroid'
+rg.grid_version = '0.2'
+# Fill in data
+contact[:] = '\000' * 255
+contact[:37] = 'atmos_mosaic:tile1::land_mosaic:tile1'
+tile1_cell[:] = [ni,nj]
+tile2_cell[:] = [ni,nj]
+xgrid_area[:] = dxo * dyo
+for j in range(nj):
+    for i in range(ni):
+        if (i,j) != (ni-1,nj-1):
+            tile1_cell[i+ni*j] = [i,j]
+            tile2_cell[i+ni*j] = [i,j]
+            tile1_distance[i+ni*j] = [0,0]
+            tile2_distance[i+ni*j] = [0,0]
+            xgrid_area[i+ni*j] = dxo * dyo
+rg.close()
+
+
+# In[20]:
+
+rg = scipy.io.netcdf_file('land_mosaic_tile1Xocean_mosaic_tile1_BLAH.nc','w',version=2) # land_mosaic_tile1Xocean_mosaic_tile1.nc
+rg.createDimension('string',255)
+rg.createDimension('ncells',ni*nj-1) # -1 is for a single land point
+rg.createDimension('two',2)
+contact = rg.createVariable('contact','c',('string',))
+contact.standard_name = 'grid_contact_spec'
+contact.contact_type = 'exchange'
+contact.parent1_cell = 'tile1_cell'
+contact.parent2_cell = 'tile2_cell'
+contact.xgrid_area_field = 'xgrid_area'
+contact.distant_to_parent1_centroid = 'tile1_distance'
+contact.distant_to_parent2_centroid = 'tile2_distance'
+tile1_cell = rg.createVariable('tile1_cell','f8',('ncells','two',))
+tile1_cell.standard_name = 'parent_cell_indices_in_mosaic1'
+tile2_cell = rg.createVariable('tile2_cell','f8',('ncells','two',))
+tile2_cell.standard_name = 'parent_cell_indices_in_mosaic2'
+xgrid_area = rg.createVariable('xgrid_area','f8',('ncells',))
+xgrid_area.standard_name = 'exchange_grid_area'
+xgrid_area.units = 'm2'
+tile1_distance = rg.createVariable('tile1_distance','f8',('ncells','two'))
+tile1_distance.standard_name = 'distance_from_parent1_cell_centroid'
+tile2_distance = rg.createVariable('tile2_distance','f8',('ncells','two'))
+tile2_distance.standard_name = 'distance_from_parent2_cell_centroid'
+rg.grid_version = '0.2'
+# Fill in data
+contact[:] = '\000' * 255
+contact[:37] = 'atmos_mosaic:tile1::land_mosaic:tile1'
+tile1_cell[:] = [ni,nj]
+tile2_cell[:] = [ni,nj]
+xgrid_area[:] = dxo * dyo
+for j in range(nj):
+    for i in range(ni):
+        if (i,j) != (ni-1,nj-1):
+            tile1_cell[i+ni*j] = [i,j]
+            tile2_cell[i+ni*j] = [i,j]
+            tile1_distance[i+ni*j] = [0,0]
+            tile2_distance[i+ni*j] = [0,0]
+            xgrid_area[i+ni*j] = dxo * dyo
+rg.close()
+
+
+# In[24]:
+
+rg = scipy.io.netcdf_file('mosaic_BLAH.nc','w',version=2) # land_mosaic_tile1Xocean_mosaic_tile1.nc
+rg.createDimension('string',255)
+rg.createDimension('nfile_aXo',1) # -1 is for a single land point
+rg.createDimension('nfile_aXl',1) # -1 is for a single land point
+rg.createDimension('nfile_lXo',1) # -1 is for a single land point
+
+atm_mosaic_dir = rg.createVariable('atm_mosaic_dir','c',('string',))
+atm_mosaic_dir.standard_name = 'directory_storing_atmosphere_mosaic'
+
+atm_mosaic_file = rg.createVariable('atm_mosaic_file','c',('string',))
+atm_mosaic_file.standard_name = 'atmosphere_mosaic_file_name'
+
+atm_mosaic = rg.createVariable('atm_mosaic','c',('string',))
+atm_mosaic.standard_name = 'atmosphere_mosaic_name'
+
+lnd_mosaic_dir = rg.createVariable('lnd_mosaic_dir','c',('string',))
+lnd_mosaic_dir.standard_name = 'directory_storing_land_mosaic'
+
+lnd_mosaic_file = rg.createVariable('lnd_mosaic_file','c',('string',))
+lnd_mosaic_file.standard_name = 'land_mosaic_file_name'
+
+lnd_mosaic = rg.createVariable('lnd_mosaic','c',('string',))
+lnd_mosaic.standard_name = 'land_mosaic_name'
+
+ocn_mosaic_dir = rg.createVariable('ocn_mosaic_dir','c',('string',))
+ocn_mosaic_dir.standard_name = 'directory_storing_ocean_mosaic'
+
+ocn_mosaic_file = rg.createVariable('ocn_mosaic_file','c',('string',))
+ocn_mosaic_file.standard_name = 'ocean_mosaic_file_name'
+
+ocn_mosaic = rg.createVariable('ocn_mosaic','c',('string',))
+ocn_mosaic.standard_name = 'ocean_mosaic_name'
+
+
+ocn_topog_dir = rg.createVariable('ocn_topog_dir','c',('string',))
+ocn_mosaic_dir.standard_name = 'directory_storing_ocean_topog'
+
+ocn_topog_file = rg.createVariable('ocn_topog_file','c',('string',))
+ocn_topog_file.standard_name = 'ocean_topog_file_name'
+
+aXo_file = rg.createVariable('aXo_file','c',('string',))
+aXo_file.standard_name = 'atmXocn_exchange_grid_file'
+
+aXl_file = rg.createVariable('aXl_file','c',('string',))
+aXl_file.standard_name = 'atmXlnd_exchange_grid_file'
+
+lXo_file = rg.createVariable('lXo_file','c',('string',))
+lXo_file.standard_name = 'lndXocn_exchange_grid_file'
+
+#Global attributes
+rg.grid_version = '0.2'
+rg.code_version = "$Name:  $"
+rg.history = "/net2/aja/workspace/MOM6-examples/ice_ocean_SIS2/OM4_025/preprocessing/fre_nctools/tools/make_quick_mosaic/make_quick_mosaic --input_mosaic ocean_mosaic.nc --ocean_topog ocean_topog.nc"
+# Fill in data
+atm_mosaic_dir[:] = '\000' * 255
+atm_mosaic_dir[:2] = './'
+
+atm_mosaic_file[:] = '\000' * 255
+atm_mosaic_file[:15] = 'ocean_mosaic.nc'
+
+atm_mosaic[:] = '\000' * 255
+atm_mosaic[:12] = 'atmos_mosaic'
+
+lnd_mosaic_dir[:] = '\000' * 255
+lnd_mosaic_dir[:2] = './'
+
+lnd_mosaic_file[:] = '\000' * 255
+lnd_mosaic_file[:15] = 'ocean_mosaic.nc'
+
+lnd_mosaic[:] = '\000' * 255
+lnd_mosaic[:11] = 'land_mosaic'
+
+ocn_mosaic_dir[:] = '\000' * 255
+ocn_mosaic_dir[:2] = './'
+
+ocn_mosaic_file[:] = '\000' * 255
+ocn_mosaic_file[:15] = 'ocean_mosaic.nc'
+
+ocn_mosaic[:] = '\000' * 255
+ocn_mosaic[:12] = 'ocean_mosaic'
+
+ocn_topog_dir[:] = '\000' * 255
+ocn_topog_dir[:2] = './'
+
+ocn_topog_file[:] = '\000' * 255
+ocn_topog_file[:14] = 'ocean_topog.nc'
+
+aXo_file[:] = '\000' * 255
+aXo_file[:40] = 'atmos_mosaic_tile1Xocean_mosaic_tile1.nc'
+
+aXl_file[:] = '\000' * 255
+aXl_file[:39] = 'atmos_mosaic_tile1Xland_mosaic_tile1.nc'
+
+lXo_file[:] = '\000' * 255
+lXo_file[:39] = 'land_mosaic_tile1Xocean_mosaic_tile1.nc'
+
+rg.close()
+
+
+
+# In[ ]:
+
+
+
diff --git a/test/Iceberg_repository/Scripts_and_analysis/Weddell_Sea_initiation.sh b/test/Iceberg_repository/Scripts_and_analysis/Weddell_Sea_initiation.sh
new file mode 100755
index 0000000..5c92e87
--- /dev/null
+++ b/test/Iceberg_repository/Scripts_and_analysis/Weddell_Sea_initiation.sh
@@ -0,0 +1 @@
+./initialize_bergs_in_pattern.py -Make_icebergs_non_static_later=False -Ice_geometry_source=Weddell -Use_default_radius=True -Create_icebergs_bonds=False -break_some_bonds=False -plot_icebergs_positions=False
diff --git a/test/Iceberg_repository/Scripts_and_analysis/Weddell_sea_shelf_setup.py b/test/Iceberg_repository/Scripts_and_analysis/Weddell_sea_shelf_setup.py
new file mode 100755
index 0000000..ab2f704
--- /dev/null
+++ b/test/Iceberg_repository/Scripts_and_analysis/Weddell_sea_shelf_setup.py
@@ -0,0 +1,1398 @@
+#!/usr/bin/env python
+
+#First import the netcdf4 library
+from netCDF4 import Dataset  # http://code.google.com/p/netcdf4-python/
+import numpy as np  # http://code.google.com/p/netcdf4-python/
+import matplotlib
+import math
+import os
+matplotlib.use("GTKAgg")
+from pylab import *
+#import matplotlib.pyplot as plt
+import pdb
+import netCDF4 as nc
+from scipy import interpolate
+from hexagon_area import Divide_hexagon_into_4_quadrants_old
+from hexagon_area import Hexagon_into_quadrants_using_triangles
+
+
+def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg):
+	
+	print 'Writing iceberg restart files...'
+	# To copy the global attributes of the netCDF file  
+
+	#Input and output files	
+	f=Dataset('input_files/icebergs.res.nc','r') # r is for read only
+	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w') # w if for creating a file
+
+	for attname in f.ncattrs():
+		    setattr(g,attname,getattr(f,attname))
+
+
+	# To copy the dimension of the netCDF file
+	for dimname,dim in f.dimensions.iteritems():
+		# if you want to make changes in the dimensions of the new file
+		# you should add your own conditions here before the creation of the dimension.
+		#g.createDimension(dimname,len(dim))
+		g.createDimension(dimname,Number_of_bergs)
+
+	# To copy the variables of the netCDF file
+
+	for varname,ncvar in f.variables.iteritems():
+		# if you want to make changes in the variables of the new file
+		# you should add your own conditions here before the creation of the variable.
+		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
+		#Proceed to copy the variable attributes
+		for attname in ncvar.ncattrs():  
+			setattr(var,attname,getattr(ncvar,attname))
+		#Finally copy the variable data to the new created variable
+		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
+		
+		if varname=='i':
+			var[:]=Number_of_bergs
+		
+		if varname=='iceberg_num':
+			for j in range(Number_of_bergs):
+				#var[j]=j+1
+				var[j]=iceberg_num[j]
+
+		if varname=='uvel' or varname=='vvel' or varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
+		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
+		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
+		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
+			var[:]=0
+
+		if varname=='mass_scaling':
+			var[:]=mass_scaling
+
+		if varname=='thickness':
+			for j in range(Number_of_bergs):
+				var[j]=thickness[j]
+		
+		if varname=='mass':
+			for j in range(Number_of_bergs):
+				var[j]=mass[j]
+
+		if varname=='width'  or varname=='length':
+			for j in range(Number_of_bergs):
+				var[j]=width[j]
+
+		if varname=='lon':
+			for j in range(Number_of_bergs):
+				var[j]=lon[j]
+
+		if varname=='lat':
+			for j in range(Number_of_bergs):
+				var[j]=lat[j]
+
+		if varname=='static_berg':
+			for j in range(Number_of_bergs):
+				var[j]=static_berg[j]
+
+
+	f.close()
+	g.close()
+
+	
+def Create_bond_restart_file(Number_of_bonds,first_berg_num,first_berg_ine,first_berg_jne,other_berg_ine,other_berg_jne,iceberg_num,other_berg_num,Ice_geometry_source):
+	#Creating the bond restart file
+
+	print 'Writing bond restart files...'
+	# To copy the global attributes of the netCDF file  
+
+	#Input and output files	
+	h=Dataset('input_files/bonds_iceberg.res.nc','r') # r is for read only
+	q=Dataset('output_files/' + Ice_geometry_source + '_bonds_iceberg.res.nc','w') # w if for creating a file
+
+	for attname in h.ncattrs():
+		    setattr(q,attname,getattr(h,attname))
+
+
+	# To copy the dimension of the netCDF file
+	for dimname,dim in h.dimensions.iteritems():
+		# if you want to make changes in the dimensions of the new file
+		# you should add your own conditions here before the creation of the dimension.
+		#g.createDimension(dimname,len(dim))
+		q.createDimension(dimname,Number_of_bonds)
+
+	# To copy the variables of the netCDF file
+
+	for varname,ncvar in h.variables.iteritems():
+		# if you want to make changes in the variables of the new file
+		# you should add your own conditions here before the creation of the variable.
+		var = q.createVariable(varname,ncvar.dtype,ncvar.dimensions)
+		#Proceed to copy the variable attributes
+		for attname in ncvar.ncattrs():  
+			setattr(var,attname,getattr(ncvar,attname))
+		#Finally copy the variable data to the new created variable
+		#var[:] = ncvar[0]
+		var[:] = 0.
+
+		if varname=='i':
+			var[:]=Number_of_bonds
+
+		if varname=='first_berg_num':
+			for j in range(Number_of_bonds):
+				var[j]=first_berg_num[j]
+
+		if varname=='first_berg_ine':
+			for j in range(Number_of_bonds):
+				var[j]=first_berg_ine[j]
+
+		if varname=='first_berg_jne':
+			for j in range(Number_of_bonds):
+				var[j]=first_berg_jne[j]
+
+		if varname=='other_berg_num':
+			for j in range(Number_of_bonds):
+				var[j]=other_berg_num[j]
+
+		if varname=='other_berg_ine':
+			for j in range(Number_of_bonds):
+				var[j]=other_berg_ine[j]
+
+		if varname=='other_berg_jne':
+			for j in range(Number_of_bonds):
+				var[j]=other_berg_jne[j]
+
+	h.close()
+	q.close()
+
+
+
+def Define_iceberg_thickness_and_mass(Number_of_bergs,dx_berg,dy_berg,h_ice_vec,xi,yi,rho_ice,Radius,x_ind_vec,y_ind_vec,h_ice,x,y,\
+		width,Interpolate_from_four_corners,element_area,element_type,Find_thickness_using_vector,static_berg):
+	thickness=[]
+	mass=[]
+	ny,nx=h_ice.shape
+	dx=x[1]-x[0]
+	grid_area=dx*dx
+	for berg_count in range(Number_of_bergs):
+		x_val=dx_berg[berg_count] ; y_val=dy_berg[berg_count]
+		R_ind=(abs(xi-x_val)+(abs(yi-y_val))).argmin()
+		i_val=floor(x_val/dx)
+		j_val=floor(y_val/dx)
+
+		#Interpolate thickness from 4 corners - possibly do this later, but I worry about when you are between a shelf and non shelf piece.
+		if Interpolate_from_four_corners==True:
+
+			x_cell=(x_val-x[i_val])/sqrt(grid_area)+0.5
+			y_cell=(y_val-y[j_val])/sqrt(grid_area)+0.5
+
+			mass_on_ocean=np.zeros([nx,ny,10])   #Setting up matrix to spread mass to ocean.  Note that I have used 10 points  so that I can ignore 0 and match with python numbering
+			mass_val=1.
+			mass_on_ocean=spread_mass_to_ocean(nx,ny,i_val,j_val,mass_on_ocean,x_cell,y_cell,element_area,mass_val,element_type,grid_area,static_berg[berg_count])
+			Th=0.
+			h=np.array([0,0,0,0,0,0,0,0,0,0])
+			if i_val>0 and j_val>0:
+				h[1]=h_ice[j_val-1,i_val-1]
+			if j_val>0:
+				h[2]=h_ice[j_val-1,i_val]
+			if j_val>0 and i_val<(nx-1):
+				h[3]=h_ice[j_val-1,i_val+1]
+			if i_val>0:
+				h[4]=h_ice[j_val,i_val-1]
+			if True:
+				h[5]=h_ice[j_val,i_val]
+			if i_val<(nx-1):
+				h[6]=h_ice[j_val,i_val+1]
+			if i_val>0 and j_val<(ny-1):
+				h[7]=h_ice[j_val+1,i_val-1]
+			if j_val<(ny-1):
+				h[8]=h_ice[j_val+1,i_val]
+			if i_val<(nx-1) and j_val<(ny-1):
+				h[9]=h_ice[j_val+1,i_val+1]
+			for k in range(1,10):
+				Th=Th+(mass_on_ocean[i_val,j_val,k]*h[k])
+				#print i_val,j_val,k,mass_on_ocean[i_val,j_val,k]
+			#if abs(Th-1)>0.0000001:
+			#	print 'Thickness',Th-1,i_val,j_val
+			#	test=0.
+			#	for k in range(1,10):
+			#		print k,mass_on_ocean[i_val,j_val,k], h[k]
+			#		test=test+(mass_on_ocean[i_val,j_val,k])
+			#	print test
+			#	halt
+				
+
+		elif Find_thickness_using_vector==True:
+			Th=h_ice_vec[R_ind][0]
+		else:#MP3
+			Th=h_ice[j_val,i_val]
+		thickness.append(Th)
+		#Check that all thicknesses are positive
+		if Th<=0:
+			print 'Thickness is less than or equal to zero,0!',i_val, j_val,x_val,y_val
+			halt
+		#mass.append(Th*rho_ice*element_area) 
+		mass.append(Th*rho_ice*(width[berg_count])**2) 
+		#if element_type=='square': 
+		#	mass.append(Th*rho_ice*((2*Radius)**2)) # For square elements
+		#else:
+		#	mass.append(Th*rho_ice*np.pi*(Radius**2))  #For circular elements
+	return [thickness, mass]
+
+def Create_distance_and_ice_mask_vector(x,y,ice_mask,h_ice,input_is_cartesian,R_earth,lat_ref,adjust_lat_ref):
+	N=len(x)  ; M = len(y)
+	x_min=np.min(x)  ;y_min=np.min(y)
+	count=-1
+	#R=np.zeros([N*M,1])
+	xi=np.zeros([N*M,1])
+	yi=np.zeros([N*M,1])
+	ice_mask_vec=np.zeros([N*M,1])
+	h_ice_vec=np.zeros([N*M,1])
+	x_ind_vec=np.zeros([N*M,1])
+	y_ind_vec=np.zeros([N*M,1])
+
+	#print N,M
+	for i in range(N):
+		for j in range(M):
+			count=count+1
+			if input_is_cartesian==True:
+				#R[count]=sqrt(((x[i]-x_min)**2) + ((y[j]-y_min)**2))
+				xi[count]=x[i]-x_min
+				yi[count]=y[j]-y_min
+			else:
+				#x and y are given in lon and lat
+				dlon=x[i]-x_min
+				dlat=y[j]-y_min
+				dy_dlat=(np.pi/180)*(R_earth)			
+				if adjust_lat_ref==True:
+					lat_ref=y[j]
+
+				dx_dlon=(np.pi/180)*(R_earth)*(np.cos(lat_ref*np.pi/180))
+				dx=dlon*dx_dlon
+				dy=dlat*dy_dlat
+				#R[count]=sqrt((dx**2)+(dy**2))
+				xi[count]=dx
+				yi[count]=dy
+			ice_mask_vec[count,0]=ice_mask[j,i]
+			h_ice_vec[count,0]=h_ice[j,i]
+			x_ind_vec[count,0]=i
+			y_ind_vec[count,0]=j
+			
+
+	ice_mask_vec[np.where(np.isnan(ice_mask_vec))]=0
+	#cNorm = mpl.colors.Normalize(vmin=-1., vmax=5.)
+	#plt.pcolor(x,y,ice_mask,norm=cNorm,cmap='jet')
+	#plt.scatter(x_temp, y_temp,c=ice_mask_vec[:,0],cmap='jet',norm=cNorm)
+	plt.show()
+
+	return [xi,yi, ice_mask_vec,h_ice_vec,x_ind_vec,y_ind_vec]
+
+
+def check_if_it_is_in_domain(x_val,y_val,x_min,x_max,y_min,y_max,input_is_cartesian,R_earth,lat_init,adjust_lat_ref,dx,dy):
+	point_is_in_domain=True
+	if input_is_cartesian==False:
+		dlat_dy=(180/np.pi)*(1/R_earth)
+		if adjust_lat_ref==True:
+			lat_ref=lat_init+(dlat_dy*y_val)
+		else:
+			lat_ref=y_max 
+		dlon_dx=(180/np.pi)*(1/R_earth)*(1/np.cos(lat_ref*np.pi/180))
+		x_val=(x_val*dlon_dx)
+		y_val=(y_val*dlat_dy)
+	
+	if (x_val >= (x_max-x_min+(dx))) or (x_val<= 0) or  (y_val >= (y_max-y_min+(dy))) or (y_val <= 0):
+		point_is_in_domain=False
+	#print 'x', x_val,  x_max
+	#print 'y', y_val,  y_max, floor(y_val/dx), floor(y_max/dx)
+	
+	return point_is_in_domain
+
+def check_if_it_is_ice(x_val,y_val,xi,yi,ice_mask_vec,ice_mask,input_is_cartesian,Find_thickness_using_vector,dx):
+	#R_val=np.sqrt(((x_val)**2) +((y_val)**2))
+	#R_ind=(abs(R-R_val)).argmin()
+	if Find_thickness_using_vector==True:
+		R_ind= (abs(x_val-xi) + abs(yi-y_val)).argmin()
+		if ice_mask_vec[R_ind]==1:
+			it_is_ice=True
+		else:
+			it_is_ice=False
+
+	else:
+		i_val=floor(x_val/dx)
+		j_val=floor(y_val/dx)
+		#print i_val,j_val,x_val,y_val
+		if ice_mask[j_val,i_val]==1.:
+			it_is_ice=True
+		else:
+			it_is_ice=False
+
+	return it_is_ice
+
+def calculate_element_area(element_type,Radius):
+	if element_type=='square':
+		element_area=(2*Radius)**2
+	elif element_type=='hexagon':
+		element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*(Radius)**2) #Area of hexagon around circle (used for packing)  
+		#Another derivation uses innner hexagon with two more triangles added, which is a 1/6 of the hexagon area each (two since there are 6, shared by 3 each)
+		#element_area=(4./3.)*H_i, where H_i=(3.*np.sqrt(3.)/2.)*((Radius)**2)  is the area of the inner hexagon (with sides equal to the radius)
+
+	return element_area
+
+def add_and_extra_boundary_berg(i,j,New_thickness,y_shift,x_shift,Nbh_thickness_value,Nbh_mass_value,New_mass,berg_count,dx_berg,dy_berg,\
+		iceberg_num,thickness,width,mass,static_berg,grid_area,rho_ice):
+	tol=0.0000000000001
+	if New_thickness[j,i]>1.+tol:
+		print 'The new thickness is too big!!!', i,j,  New_thickness[j,i]
+		halt
+	if ((Nbh_thickness_value-New_thickness[j,i])>tol):
+		y_val=y_shift[j]
+		x_val=x_shift[i]
+		if Nbh_thickness_value>0. and (abs(Nbh_thickness_value-1)<tol) and (Nbh_mass_value>New_mass[j,i]):
+			berg_count=berg_count+1
+			dx_berg.append(x_val)
+			dy_berg.append(y_val)
+			iceberg_num.append(berg_count)
+			width_val=np.sqrt((Nbh_thickness_value-New_thickness[j,i])*grid_area)
+			if Nbh_thickness_value-New_thickness[j,i]<0:
+				print 'Stop', Nbh_thickness_value, New_thickness[j,i],i,j
+			mass_val=Nbh_mass_value-New_mass[j,i]
+			thickness_val=mass_val/(width_val*width_val*rho_ice)
+			thickness.append(thickness_val)
+			width.append(width_val)
+			mass.append(mass_val)
+			static_berg.append(1.)
+	return [berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg]
+
+
+def add_extra_bergs_on_boundary(dx,dy,x,y,Number_of_bergs,element_area,rho_ice,X_min,X_max,Y_min,Y_max,input_is_cartesian,R_earth,lat_init,adjust_lat_ref,xi,yi,ice_mask_vec,ice_mask,\
+		iceberg_num,width,dx_berg,dy_berg,h_ice,element_type,Find_thickness_using_vector,static_berg,thickness,mass):
+	eps=0.000001
+	grid_area=dx*dy
+	Nx=len(x)  ; Ny=len(y)
+	x_shift=(x-np.min(x))+(dx/2) ; y_shift=(y-np.min(y))+(dy/2)
+
+	thickness_temp= [1. for i in range(Number_of_bergs)] ;
+	mass_temp= [element_area*rho_ice*1. for i in range(Number_of_bergs)] ;
+	New_area=regrid_iceberg_thickness(dy_berg,dx_berg,Number_of_bergs,thickness_temp,mass_temp,h_ice,x_shift,y_shift,rho_ice,element_type,static_berg,plot_outcome=False)
+	New_thickness=(New_area)/(rho_ice*grid_area)  #Should be equal to one everywhere where there is ice shelf.
+	New_mass=regrid_iceberg_thickness(dy_berg,dx_berg,Number_of_bergs,thickness,mass,h_ice,x_shift,y_shift,rho_ice,element_type,static_berg,plot_outcome=False)
+	berg_count=Number_of_bergs
+	
+	
+	#Vertical boundary
+	for i in np.array([0,Nx-1]):
+		#for j in range(Ny):
+		for j in range(1,Ny-1):
+			Nbh_mass_value=h_ice[j,i]*rho_ice*grid_area  #Neighbouring shelf value
+			if i==0:
+				Nbh_thickness_value=New_thickness[j,1]  #Neighbouring shelf value
+				#x_val=0+(eps*dx)
+			if i==Nx-1:
+				Nbh_thickness_value=New_thickness[j,Nx-2]  #Neighbouring shelf value
+				#x_val=x_shift[i]+(dx/2)-eps
+			[berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg]=add_and_extra_boundary_berg(i,j,New_thickness,y_shift,x_shift,\
+					Nbh_thickness_value,Nbh_mass_value,New_mass,berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg,grid_area,rho_ice)
+
+	##Horizontal boundary
+	for j in np.array([0,Ny-1]):
+		#for i in range(1,Nx-1):
+		for i in range(1,Nx-1):
+			Nbh_mass_value=h_ice[j,i]*rho_ice*grid_area  #Neighbouring shelf value
+			if j==0:
+				Nbh_thickness_value=New_thickness[1,i]  #Neighbouring shelf value
+				#y_val=0+(eps*dy)
+			if j==Ny-1:
+				Nbh_thickness_value=New_thickness[Ny-2,i]  #Neighbouring shelf value
+				#y_val=y_shift[j]+(dy/2)-eps
+			#Nbh_thickness_value=np.mean(New_thickness[range(1,Ny-1),i])  #Neighbouring shelf value
+			[berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg]=add_and_extra_boundary_berg(i,j,New_thickness,y_shift,x_shift,\
+					Nbh_thickness_value,Nbh_mass_value,New_mass,berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg,grid_area,rho_ice)
+
+	#Doing the corners seperately
+	for j in np.array([0,Ny-1]):
+		#for i in range(1,Nx-1):
+		for i in np.array([0,Nx-1]):
+			Nbh_mass_value=h_ice[j,i]*rho_ice*grid_area  #Neighbouring shelf value
+			if j==0 and i==0:
+				Nbh_thickness_value=New_thickness[1,1]  #Neighbouring shelf value
+			if j==0 and i==Nx-1:
+				Nbh_thickness_value=New_thickness[1,Nx-2]  #Neighbouring shelf value
+			if j==Ny-1 and i==0:
+				Nbh_thickness_value=New_thickness[Ny-2,1]  #Neighbouring shelf value
+			if j==Ny-1 and i==Nx-1:
+				Nbh_thickness_value=New_thickness[Ny-2,Nx-2]  #Neighbouring shelf value
+			[berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg]=add_and_extra_boundary_berg(i,j,New_thickness,y_shift,x_shift,\
+					Nbh_thickness_value,Nbh_mass_value,New_mass,berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg,grid_area,rho_ice)
+
+
+	Number_of_bergs=berg_count
+	
+	return [dx_berg, dy_berg,iceberg_num, width,Number_of_bergs,static_berg,thickness,mass]
+
+
+def remove_stationary_bergs(dx_berg, dy_berg,iceberg_num,width,Number_of_bergs,static_berg):
+	dx_berg_new=[]
+	dy_berg_new=[]
+	iceberg_num_new=[]
+	width_new=[]
+	static_berg_new=[]
+	for i in range(Number_of_bergs):
+		if static_berg[i]<0.5:
+			dx_berg_new.append(dx_berg[i])
+			dy_berg_new.append(dy_berg[i])
+			iceberg_num_new.append(iceberg_num[i])
+			width_new.append(width[i])
+			static_berg_new.append(static_berg[i])
+
+	Number_of_bergs_new=len(iceberg_num_new)
+	return [dx_berg_new, dy_berg_new,iceberg_num_new, width_new,Number_of_bergs_new,static_berg_new]
+
+def Create_icebergs(lon_init,lat_init,Radius,R_earth, x, y,ice_mask,h_ice,Convert_to_lat_lon,rho_ice,input_is_cartesian,\
+		element_type,scale_the_grid_to_lat_lon,lat_ref,adjust_lat_ref,Interpolate_from_four_corners,\
+		Fill_in_the_boundaries,set_all_bergs_static_by_default,break_some_bonds,Find_thickness_using_vector,Remove_stationary_bergs):
+	print 'Starting to create icebergs...'
+	dx_berg=[]  #x distance in cartesian of berg from lon_init
+	dy_berg=[]  #y distance in cartesian of berg from lat_init
+	dlon_berg=[] #x distance in lon of berg from lon_init
+	#dlat_berg=[] #y distance in lat of berg from lat_init
+	lon=[] #Longitude of iceberg
+	lat=[] #Latitude of iceberg
+	iceberg_num=[] #ID of iceberg
+	
+	element_area=calculate_element_area(element_type,Radius)
+	#width=np.sqrt(element_area)
+	width=[]
+	
+	#Create a vector of distances from a minimum point.
+	(xi,yi,ice_mask_vec,h_ice_vec,x_ind_vec,y_ind_vec)=Create_distance_and_ice_mask_vector(x,y,ice_mask,h_ice,input_is_cartesian,R_earth,lat_ref,adjust_lat_ref)
+	
+	#dx=x[1]-x[0]  ;dy=y[1]-y[0]
+	#X_min=np.min(x)-dx; X_max=np.max(x)+dx  #In lat lon or cartesian
+	#Y_min=np.min(y)-dy; Y_max=np.max(y)+dy  #In lat lon or cartesian
+	X_min=np.min(x); X_max=np.max(x)  #In lat lon or cartesian
+	Y_min=np.min(y); Y_max=np.max(y)  #In lat lon or cartesian
+
+	#N=2*int(ceil((R_max)/(2*Radius))+2)
+	
+	if element_type=='square':
+		#N=int(ceil((np.max(xi))/(2*Radius))+2) +2
+		#M=int(ceil((np.max(yi))/(2*Radius))+2) +2
+		N=int(ceil((X_max-X_min)/(Radius)))
+		M=int(ceil((Y_max-Y_min)/(Radius)))
+	else:
+		#N=int(ceil((np.max(xi))/(Radius/2))+2) +2
+		#M=int(ceil((np.max(yi))/((1/sqrt(3))*Radius/2))+2) +2
+		N=2*int(ceil((X_max-X_min)/(Radius)))
+		M=2*int(ceil((Y_max-Y_min)/(Radius)))
+	#N=10
+	#M=6
+	#MP4
+
+ 	dx=x[1]-x[0]	
+ 	dy=y[1]-y[0]
+	Lx=X_max+dx
+	Ly=Y_max+dx
+
+	berg_count=0
+	#for j in range(N):
+	for i in range(N):
+		if element_type=='square':
+			x_start=Radius
+			y_start=(Radius)
+			x_val=x_start+(2*i*Radius)
+
+		#Hexagonal	
+		else:   
+			y_start=(Radius)+(((i%2)*Radius))
+			x_start=((2/sqrt(3))*Radius)
+			x_val=x_start + (np.sqrt(3)*Radius*i)
+
+		for j in range(M):
+		#for i in range(M):
+			#x_val=x_start+(2*i*Radius)  ; y_val=y_start
+			y_val=y_start+(2*j*Radius)  ;# x_val=x_start + (np.sqrt(3)*Radius*i)
+			if check_if_it_is_in_domain(x_val,y_val,X_min,X_max,Y_min,Y_max,input_is_cartesian,R_earth,lat_init,adjust_lat_ref,dx,dy):
+			#if True:
+				#R_val=np.sqrt(((x_val-x0)**2) +((y_val-y0)**2))
+				if check_if_it_is_ice(x_val,y_val,xi,yi,ice_mask_vec,ice_mask,input_is_cartesian,Find_thickness_using_vector,dx):
+					#Don't allow points closer than R from the boundary (these are sorted out later)
+					#if abs(y_val-Ly)<Radius or  ((abs(x_val-Lx)<((2/sqrt(3))*Radius)) and element_type=='hexagon') or ((abs(x_val-Lx)<Radius) and element_type=='square'):
+					berg_count=berg_count+1
+					iceberg_num.append(berg_count)
+					dx_berg.append(x_val)
+					dy_berg.append(y_val)
+					width.append(np.sqrt(element_area))
+
+	Number_of_bergs=berg_count
+	print 'Icebergs created. Number of bergs = ', Number_of_bergs
+	
+	#Deciding if icebergs are static or not
+	static_berg = [0. for i in dx_berg]
+	if set_all_bergs_static_by_default==True:
+		static_berg = [1. for i in static_berg]
+	if break_some_bonds==True:
+		#static_berg =Change_static_berg_after_calving(Number_of_bergs,lat,lon, static_berg)
+		static_berg =Change_static_berg_after_calving(Number_of_bergs,dy_berg,dx_berg, static_berg)
+		static_berg=static_berg[0]
+		
+	if Remove_stationary_bergs is True:
+		Fill_in_the_boundaries=False
+		[dx_berg, dy_berg,iceberg_num, width,Number_of_bergs,static_berg]=remove_stationary_bergs(dx_berg, dy_berg,iceberg_num,\
+				width,Number_of_bergs,static_berg)
+		print 'After purge  Number of bergs = ', Number_of_bergs
+
+
+	#Defining the thickness of the icebergs
+	(thickness, mass)=Define_iceberg_thickness_and_mass(Number_of_bergs,dx_berg,dy_berg,h_ice_vec,xi,yi,rho_ice,Radius,x_ind_vec,y_ind_vec, h_ice,x,y,\
+			width,Interpolate_from_four_corners,element_area,element_type,Find_thickness_using_vector,static_berg)	
+
+	N_bergs_before_bd=Number_of_bergs
+	if Fill_in_the_boundaries==True and element_type=='hexagon':
+	 	[dx_berg, dy_berg,iceberg_num, width,Number_of_bergs,static_berg,thickness,mass]= add_extra_bergs_on_boundary(dx,dy,x,y,Number_of_bergs,element_area,rho_ice,X_min,X_max,Y_min,\
+				Y_max,input_is_cartesian,R_earth,lat_init,adjust_lat_ref,xi,yi,ice_mask_vec,ice_mask,iceberg_num,width,dx_berg,dy_berg,\
+				h_ice,element_type,Find_thickness_using_vector,static_berg,thickness,mass)
+		print 'Number of icebergs after accounting for boundaries = ', Number_of_bergs
+	
+
+
+	if Convert_to_lat_lon==True:
+		#Defining lon lat positions:
+		#dlat_berg=(180/np.pi)*(1/R_earth)*dy_berg
+		#dlon_berg=(180/np.pi)*(1/R_earth)*(1/cos(lat_init*np.pi/180))*dx_berg
+		for i in range(Number_of_bergs):
+			#Finding latittude
+			dlat_dy=(180/np.pi)*(1/R_earth)
+
+			lat.append(lat_init+(dlat_dy*dy_berg[i]))
+
+			#Finding longitude
+			if adjust_lat_ref==True:
+				lat_ref=lat_init+(dlat_dy*dy_berg[i])
+			dlon_dx=(180/np.pi)*(1/R_earth)*(1/np.cos(lat_ref*np.pi/180)) #Note that this depends on the latitude of the iceberg. Could approx this with lat_init.
+			lon.append(lon_init+(dlon_dx*dx_berg[i] ))
+
+			#dlon_berg.append(dlon_dx*dx_berg[i])
+			#lon.append(lon_init+dlon_berg[i])
+	else:
+		if scale_the_grid_to_lat_lon==True:
+			Scale_up=1./2000.
+			Radius=Radius*Scale_up
+			dx_berg = [(i*Scale_up) for i in dx_berg] ; dy_berg = [i*Scale_up for i in dy_berg] 
+			x=x*Scale_up ; y=y*Scale_up
+			dx=dx*Scale_up ;dy=dy*Scale_up
+		x=(x-np.min(x))+(dx/2) ; y=(y-np.min(y))+(dy/2)
+		lon=dx_berg  ; lat=dy_berg
+	
+	#Note that static_berg calculations used to be here, after the conversion. I have moved them. I hope that this does not affect answers.
+
+	return (Number_of_bergs,lon,lat,iceberg_num,dx_berg,dy_berg,thickness, mass,width,x,y,Radius,static_berg,N_bergs_before_bd)
+
+
+
+def Create_calving_event(lat1,lon1,lat2,lon2):
+	[R_calve, Calve_lon, Calve_lat]=get_calving_parameters()
+	
+	R1=np.sqrt((lon1-Calve_lon)**2+ (lat1-Calve_lat)**2)
+	R2=np.sqrt((lon2-Calve_lon)**2+ (lat2-Calve_lat)**2)
+
+	bond_broken=False
+	if ((R1 < R_calve)*(R2>R_calve) )  > 0.5 :
+		bond_broken=True
+	if ((R2 < R_calve)*(R1>R_calve) )  > 0.5 :
+		bond_broken=True
+
+	return bond_broken
+
+def get_calving_parameters():
+	#Calve_lat =20  
+	#Calve_lon=160
+	#R_calve=15
+	Calve_lat =20.2*2000  
+	Calve_lon=160*2000
+	R_calve=15*2000
+	#R_calve=1.*2000.
+	
+	return [R_calve, Calve_lon, Calve_lat]
+
+def Change_static_berg_after_calving(Number_of_bergs,lat,lon, static_berg):
+	[R_calve, Calve_lon, Calve_lat]=get_calving_parameters()
+	count=0.
+	for i in range(Number_of_bergs):
+		R1=np.sqrt((lon[i]-Calve_lon)**2+ (lat[i]-Calve_lat)**2)
+		#Making calved icebergs not be static.
+		if R1<R_calve:
+			count=count+1.
+			#print 'An iceberg is now static!'
+			static_berg[i]=0.
+	print 'Amount of unstatic icebergs after calving = ', count
+
+	return [static_berg]
+
+def find_max_number_of_bonds(first_berg_num,Number_of_bonds):
+	count=1
+	best_count=1
+	sorted_bonds=np.sort(first_berg_num)
+	for k in range(1,Number_of_bonds):
+		previous_berg=sorted_bonds[k-1]
+		print k, sorted_bonds[k]
+		if sorted_bonds[k] == sorted_bonds[k-1]:
+			count=count+1
+			best_count=max(count,best_count)
+		else:
+			count=1
+	Max_number_of_bonds=best_count
+	return Max_number_of_bonds
+
+def Define_iceberg_bonds(Number_of_bergs,iceberg_num,lat,lon,dx_berg, dy_berg,Radius,break_some_bonds,static_berg, Allow_bonds_for_static_iceberg\
+		,N_bergs_before_bd,Allow_bonds_with_boundary_bergs):
+	print 'Starting to create bonds...'
+	#Defining Bonds:
+	Bond=np.zeros((Number_of_bergs, Number_of_bergs))
+	bond_broken=False
+	first_berg_num=[]  # Initializing bond list first berg
+	first_berg_ine=[]  # Initializing bond list first berg
+	first_berg_jne=[]  # Initializing bond list first berg
+	first_berg_lat=[]  # Initializing bond list first berg
+	first_berg_lon=[]  # Initializing bond list first berg
+	other_berg_num=[]  # Initializing bond list other berg
+	other_berg_ine=[]  # Initializing bond list other berg
+	other_berg_jne=[]  # Initializing bond list other berg
+	other_berg_lat=[]  # Initializing bond list other berg
+	other_berg_lon=[]  # Initializing bond list other berg
+	bond_count=0
+	for i in range(Number_of_bergs):
+		if (static_berg[i]<0.5) or (Allow_bonds_for_static_iceberg is True):
+			#for j in range(Number_of_bergs):
+			for j in range(i):
+				if (static_berg[j]<0.5) or (Allow_bonds_for_static_iceberg is True):
+					if i!=j:
+						if ((i <N_bergs_before_bd) and (j <N_bergs_before_bd))  or (Allow_bonds_with_boundary_bergs is True):
+							R_dist=np.sqrt(((dx_berg[i]-dx_berg[j])**2) + ((dy_berg[i]-dy_berg[j])**2))
+							if break_some_bonds==True:
+								bond_broken=Create_calving_event(lat[i],lon[i],lat[j],lon[j])
+							if R_dist < (2.01*Radius) and (bond_broken==False):
+								bond_count=bond_count+2
+								#Connect bond in the first direction
+								first_berg_num.append(iceberg_num[i]);	first_berg_ine.append(999); 
+								other_berg_num.append(iceberg_num[j]); 	other_berg_ine.append(999);
+								first_berg_jne.append(999);first_berg_lat.append(lat[i]); first_berg_lon.append(lon[i])
+								other_berg_jne.append(999);other_berg_lat.append(lat[j]); other_berg_lon.append(lon[j])
+								#Connect bond in the other direction
+								first_berg_num.append(iceberg_num[j]);	first_berg_ine.append(999);
+								other_berg_num.append(iceberg_num[i]); 	other_berg_ine.append(999);
+								first_berg_jne.append(999);first_berg_lat.append(lat[j]); first_berg_lon.append(lon[j])
+								other_berg_jne.append(999);other_berg_lat.append(lat[i]); other_berg_lon.append(lon[i])
+	Number_of_bonds=bond_count
+	Max_number_of_bonds=find_max_number_of_bonds(first_berg_num,Number_of_bonds)
+	print 'Number of bonds created = ' , Number_of_bonds
+	print 'Maximum number of bonds = ' ,  Max_number_of_bonds
+
+	return [ Number_of_bonds, first_berg_num,first_berg_ine,first_berg_jne,first_berg_lat,first_berg_lon, other_berg_num,other_berg_ine, other_berg_jne,other_berg_lat,other_berg_lon]
+
+def load_ISOMIP_ice_geometry(filename,buffer_number):
+	with nc.Dataset(filename) as file:
+		ocean_mask = file.variables['openOceanMask'][:,:]
+		upperSurface = file.variables['upperSurface'][:,:]
+		lowerSurface = file.variables['lowerSurface'][:,:]
+		x = file.variables['x'][:]
+		y = file.variables['y'][:]
+
+	ice_mask=1-ocean_mask #one if it ice, zero if it is ocean
+	h_ice=upperSurface-lowerSurface #The ice thickness
+	M=ice_mask.shape
+
+	#Setting the boundaries to non-ice
+	A=np.arange(0,buffer_number)
+	B=np.arange(M[0]-buffer_number,M[0])
+	C=np.arange(M[1]-buffer_number,M[1])
+	ice_mask[A,:]=0; ice_mask[B,:]=0
+	ice_mask[:,A]=0; ice_mask[:,C]=0
+	
+	return [x,y,ice_mask,h_ice]
+
+
+def create_clipped_icethickness_file(h_ice,area,mass,grid_area,gravity):
+	#Creating clipped file
+        [ny, nx]= h_ice.shape ; 
+	
+	New_ice_thickness_filename='output_files/isomip_ice_shelf1_clipped.nc'
+        g=Dataset(New_ice_thickness_filename,'w') # w if for creating a file
+
+        g.createDimension('nx',nx)
+        g.createDimension('ny',ny)
+
+        thick_h=g.createVariable('thick','f8',('ny','nx'))
+        area_h=g.createVariable('area','f8',('ny','nx'))
+        p_surf_h=g.createVariable('p_surf','f8',('ny','nx'))
+
+        thick_h.units = 'm'
+        thick_h.standard_name = 'ice shelf thickness (clipped)'
+        area_h.units = 'm2'
+        area_h.standard_name = 'ice shelf area'
+        p_surf_h.units = 'Pa'
+        p_surf_h.standard_name = 'surface pressure due to ice shelf'
+
+	p_surf=(gravity*mass)/grid_area
+        g.variables['thick'][:]=h_ice
+        g.variables['area'][:]=area
+        g.variables['p_surf'][:]=p_surf
+        print 'Creating clipped ice file: ' , New_ice_thickness_filename
+        
+        g.sync()
+        g.close()
+
+
+def load_ISOMIP_reduced_ice_geometry(ice_filename,buffer_number,topog_filename):
+	with nc.Dataset(ice_filename) as file:
+		h_ice = file.variables['thick'][:,:]
+		area =  file.variables['area'][:,:]
+		M=h_ice.shape
+
+	y=np.linspace(1000,79000,M[0],endpoint=True)
+	#x=np.linspace(321000,799000,M[1],endpoint=True)
+	x=np.linspace(1000,479000,M[1],endpoint=True)
+	ice_mask=h_ice>0.
+
+
+	count=0. #MP1
+	#Setting the boundaries to non-ice
+	A=np.arange(0,buffer_number)
+	B=np.arange(M[0]-buffer_number,M[0])
+	C=np.arange(M[1]-buffer_number,M[1])
+	#if buffer_number>0:
+	ice_mask[A,:]=0; ice_mask[B,:]=0
+	ice_mask[:,A]=0; ice_mask[:,C]=0
+	
+	return [x,y,ice_mask,h_ice]
+
+def load_Weddel_ice_geometry(filename):
+	with nc.Dataset(filename) as file:
+		h_ice = file.variables['thickness'][:,:]
+		ice_mask = file.variables['icemask_grounded_and_shelves'][:,:]
+		x = file.variables['lon'][:]
+		y = file.variables['lat'][:]
+		ice_mask[np.where(ice_mask<-1)]=0.
+		
+		h_ice[np.where(np.isnan(h_ice))]=0.
+		ice_mask[np.where(np.isnan(ice_mask))]=0.
+
+		#ice_mask=1-ocean_mask #one if it ice, zero if it is ocean
+	
+	return [x,y,ice_mask,h_ice]
+
+def Select_just_one_berg(lon,lat,thickness,width,mass,iceberg_num,chosen_berg_num,static_berg):
+	print 'You have chosen to choose just one icebergs!!!'
+	for k in range(len(lat)):
+		if iceberg_num[k]==chosen_berg_num:
+			berg_ind=k
+	lon_temp=lon[berg_ind]; lon=[] ; lon.append(lon_temp)
+	lat_temp=lat[berg_ind]; lat=[] ; lat.append(lat_temp)
+	thickness_temp=thickness[berg_ind]; thickness=[] ; thickness.append(thickness_temp)
+	mass_temp=mass[berg_ind]; mass=[] ; mass.append(mass_temp)
+	width_temp=width[berg_ind]; width=[] ; width.append(width_temp)
+	static_berg_temp=static_berg[berg_ind]; static_berg=[] ; static_berg.append(static_berg_temp)
+	iceberg_num_temp=iceberg_num[berg_ind]; iceberg_num=[] ; iceberg_num.append(iceberg_num_temp)
+	Number_of_bergs=1
+	return [Number_of_bergs,lon,lat,thickness,width,mass,iceberg_num]
+
+def plotting_iceberg_positions(lat,lon,Number_of_bergs,R_earth,Radius,IA_scaling,Convert_to_lat_lon, \
+		plot_circles,h_ice,ice_mask,x,y,plot_ice_mask,plot_ice_thickness,thickness,plot_icebergs_positions,static_berg):
+	print 'Starting to plot...'	
+	Radius=Radius*IA_scaling
+	circ_ind=np.linspace(0,2*pi,100);
+
+	if plot_ice_mask==True:
+		cNorm = mpl.colors.Normalize(vmin=0., vmax=1.)
+		plt.pcolormesh(x,y,ice_mask,norm=cNorm)
+	elif plot_ice_thickness==True:
+		cNorm = mpl.colors.Normalize(vmin=0., vmax=1000.)
+		plt.pcolor(x,y,h_ice,cmap='jet',norm=cNorm)
+
+
+	if plot_icebergs_positions==True:
+		#plt.scatter(lon, lat,color='yellow')
+		#cNorm = mpl.colors.Normalize(vmin=0., vmax=1000.)
+		plt.scatter(lon, lat,c=thickness,norm=cNorm,cmap='jet',s=150)
+		cNorm = mpl.colors.Normalize(vmin=-1, vmax=1.)
+		#plt.scatter(lon, lat,c=static_berg,norm=cNorm,cmap='jet',s=150)
+
+	#plt.plot(lon, lat,'bo-',linewidth=5)
+	if plot_circles==True:
+		for k in range(Number_of_bergs):
+			if Convert_to_lat_lon==True:
+				dR_lat=(Radius/R_earth)*(180/np.pi)
+				dR_lon=(Radius/R_earth)*(180/np.pi)*(1/np.cos(lat[k]*np.pi/180))
+				plt.plot(lon[k]+(dR_lon*cos(circ_ind)),lat[k]+(dR_lat*sin(circ_ind)),'b');
+			else:
+				plt.plot(lon[k]+(Radius*cos(circ_ind)),lat[k]+(Radius*sin(circ_ind)),'b');
+
+
+
+	#plt.plot(lon, lat,'bo-')
+	if Convert_to_lat_lon==True:
+		plt.xlabel('longitude (deg)')
+		plt.ylabel('latitude (deg)')
+	else:
+		plt.xlabel('longitude (m)')
+		plt.ylabel('latitude (m)')
+	plt.title('Iceberg initial positions')
+	plt.grid(True)
+ 	plt.colorbar()
+
+
+def plotting_iceberg_bonds(first_berg_lat,first_berg_lon,other_berg_lat,other_berg_lon,Number_of_bonds):
+
+	for k in range(Number_of_bonds):
+		x_bond=[]
+		y_bond=[]
+		x_bond.append(first_berg_lon[k])
+		x_bond.append(other_berg_lon[k])
+		y_bond.append(first_berg_lat[k])
+		y_bond.append(other_berg_lat[k])
+		plt.plot(x_bond, y_bond,'r',linewidth=5)
+
+
+def spread_mass_to_ocean(Nx,Ny,i,j,mass_on_ocean,x,y,Area,Mass,element_type,grid_area,static_berg):
+		#Note that the x,y coming into this routine are the position within a cell (from 0 to 1), with 0.5,0.5 being in the center of the cell.
+
+		#Initialize weights for each cell	
+		yDxL=0.  ; yDxC=0. ; yDxR=0. ; yCxL=0. ; yCxR=0. 
+		yUxL=0.  ; yUxC=0. ; yUxR=0. ; yCxC=1.
+
+		if element_type=='square':
+		#if True:
+			L = min(( (np.sqrt(Area)  / np.sqrt(grid_area))),1) ;  #Non dimensionalize element length by grid area. (This gives the non-dim length of the square)
+			xL=min(0.5, max(0., 0.5-(x/L)))
+			xR=min(0.5, max(0., (x/L)+(0.5-(1/L) )))
+			xC=max(0., 1.-(xL+xR))
+			yD=min(0.5, max(0., 0.5-(y/L)))
+			yU=min(0.5, max(0., (y/L)+(0.5-(1/L) )))
+			yC=max(0., 1.-(yD+yU))
+
+			yDxL=yD*xL#*grd%msk[i-1,j-1]
+			yDxC=yD*xC#*grd%msk[i  ,j-1]
+			yDxR=yD*xR#*grd%msk[i+1,j-1]
+			yCxL=yC*xL#*grd%msk[i-1,j  ]
+			yCxR=yC*xR#*grd%msk[i+1,j  ]
+			yUxL=yU*xL#*grd%msk[i-1,j+1]
+			yUxC=yU*xC#*grd%msk[i  ,j+1]
+			yUxR=yU*xR#*grd%msk(i+1,j+1]
+			yCxC=1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )
+
+		if element_type=='hexagon':
+		#if False:#element_type=='hexagon':
+			H = min(( (np.sqrt(Area/(2*sqrt(3)))  / np.sqrt(grid_area))),1) ;  #Non dimensionalize element length by grid area. (This gives the non-dim Apothen of the hexagon)
+			S=(2/np.sqrt(3))*H #Side of the hexagon
+			if S>0.5:
+				print 'Elements must be smaller than a whole gridcell', 'i.e.: S= ' , S , '>=0.5',i,j
+				halt
+
+			#Subtracting the position of the nearest corner from x,y
+			origin_x=1 ; origin_y=1
+			if x<0.5:
+				origin_x=0
+			if y<0.5:
+				origin_y=0
+
+			x0=(x-origin_x) #Position of the hexagon center, relative to origin at the nearest vertex
+			y0=(y-origin_y)
+			
+			#(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Divide_hexagon_into_4_quadrants_old(x0,y0,H)
+			(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Hexagon_into_quadrants_using_triangles(x0,y0,H,0.)
+			if min(min(Area_Q1,Area_Q2),min(Area_Q3, Area_Q4)) <0:
+				print 'Yolo'
+				print x0,y0,H
+				#print min(min(Area_Q1,Area_Q2),min(Area_Q3, Area_Q4))
+				print Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+
+			Area_Q1=Area_Q1/Area_hex
+			Area_Q2=Area_Q2/Area_hex
+			Area_Q3=Area_Q3/Area_hex
+			Area_Q4=Area_Q4/Area_hex
+
+
+			#Now, you decide which quadrant belongs to which mass on ocean cell.
+			#Top right vertex
+			if x>=0.5 and y>= 0.5:
+				yUxR=Area_Q1
+				yUxC=Area_Q2
+				yCxC=Area_Q3
+				yCxR=Area_Q4
+			
+			#Top left vertex
+			if x<0.5 and y>= 0.5:
+				yUxC=Area_Q1
+				yUxL=Area_Q2
+				yCxL=Area_Q3
+				yCxC=Area_Q4
+			
+			#Bottom left vertex
+			if x<0.5 and y< 0.5:
+				yCxC=Area_Q1
+				yCxL=Area_Q2
+				yDxL=Area_Q3
+				yDxC=Area_Q4
+
+			#Bottom right vertex
+			if x>=0.5 and y< 0.5:
+				yCxR=Area_Q1
+				yCxC=Area_Q2
+				yDxC=Area_Q3
+				yDxR=Area_Q4
+
+			#if Sector<4 and Sector>-1:
+			#	print Sector
+				
+					
+			#Check that this is true
+			if abs(yCxC-(1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )))>0.001:
+				print 'All the mass is not being used!!!'
+				#print W1 , W2 , W3 , W4 , W5 , W6
+				#print Area_Upper, Area_Lower, Area_right, Area_left
+				print 'Areas: ',Area_hex,Area_hex*Area_Q1, Area_hex*Area_Q2, Area_hex*Area_Q3, Area_hex*Area_Q4
+				print 'x0=',x0, 'y0=',y0, 'H=', H
+				print 'Total area= ',(Area_Q1+Area_Q2+Area_Q3+Area_Q4)#, Sector
+				
+
+		#Accounting for masked points 
+		a=1. ; b=1. ; c=1. ; d=1.
+		if i==0:
+			a=0.;
+		if j==0: 
+			b=0.;
+		if i==Nx-1:
+			c=0;
+		if j==Ny-1:
+			d=0;
+
+		fraction_used= ((yDxL*a*b) + (yDxC*b) + (yDxR*b*c) +(yCxL*a) + (yCxR*c) + (yUxL*a*d) + (yUxC*d) + (yUxR*c*d) + (yCxC))
+		if static_berg>0.5:
+			fraction_used=1.
+
+		mass_on_ocean[i,j,1]=mass_on_ocean[i,j,1]+(a*b*yDxL*Mass/fraction_used)
+		mass_on_ocean[i,j,2]=mass_on_ocean[i,j,2]+(b*yDxC*Mass/fraction_used)
+		mass_on_ocean[i,j,3]=mass_on_ocean[i,j,3]+(b*c*yDxR*Mass/fraction_used)
+		mass_on_ocean[i,j,4]=mass_on_ocean[i,j,4]+(a*yCxL*Mass/fraction_used)
+		mass_on_ocean[i,j,5]=mass_on_ocean[i,j,5]+(yCxC*Mass/fraction_used)
+		mass_on_ocean[i,j,6]=mass_on_ocean[i,j,6]+(c*yCxR*Mass/fraction_used)
+		mass_on_ocean[i,j,7]=mass_on_ocean[i,j,7]+(a*d*yUxL*Mass/fraction_used)
+		mass_on_ocean[i,j,8]=mass_on_ocean[i,j,8]+(d*yUxC*Mass/fraction_used)
+		mass_on_ocean[i,j,9]=mass_on_ocean[i,j,9]+(c*d*yUxR*Mass/fraction_used)
+
+
+		return mass_on_ocean
+
+
+def calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x, y, Lx):
+
+	Lx_2=Lx/2.
+  
+	alpha=x2-x1
+	delta=y2-y1
+	beta=x4-x1
+	epsilon=y4-y1
+	gamma=(x3-x1)-(alpha+beta)
+	kappa=(y3-y1)-(delta+epsilon)
+
+	a=(kappa*beta-gamma*epsilon)
+	dx=np.mod(x-(x1-Lx_2),Lx)+(x1-Lx_2)-x1
+	dy=y-y1
+	b=(delta*beta-alpha*epsilon)-(kappa*dx-gamma*dy)
+	c=(alpha*dy-delta*dx)
+	
+	#print 'alpha,beta,gamma',alpha,beta,gamma
+	#print 'delta,epsilon,kappa',delta,epsilon,kappa
+	#print 'dx,dy',dx,dy
+	#print 'A,B,C,',a,b,c
+
+	if (abs(a)>1.e-12):
+		d=0.25*(b**2)-a*c
+		if (d>=0.):
+			yy1=-(0.5*b+sqrt(d))/a
+			yy2=-(0.5*b-sqrt(d))/a
+			if (abs(yy1-0.5).lt.abs(yy2-0.5)):
+				yj=yy1;
+			else:
+				yj=yy2;
+    		else:
+			print 'ERROR', halt
+	else:
+		if (b!=0.):
+			yj=-c/b
+		else:
+			yj=0.
+
+	a=(alpha+gamma*yj)
+	b=(delta+kappa*yj)
+	if (a!=0.):
+		xi=(dx-beta*yj)/a
+	elif (b!=0.):
+		xi=(dy-epsilon*yj)/b
+	else:
+		c=(epsilon*alpha-beta*delta)+(epsilon*gamma-beta*kappa)*yj
+		if (c!=0.):
+			xi=(epsilon*dx-beta*dy)/c
+		else:
+			print 'ERROR', halt2
+
+	return xi,yj
+
+
+
+def regrid_iceberg_thickness(lat,lon,Number_of_bergs,thickness,mass,h_ice,x,y,rho_ice,element_type,static_berg,plot_outcome=True):
+	Nx=len(x)  ; Ny=len(y)
+	dx=x[1]-x[0]    ;dy=y[1]-y[0]
+	New_mass=h_ice*0 #Initializing regrided field to zero
+	Area = [(mass[i]/(rho_ice*thickness[i])) for i in range(Number_of_bergs)] ;
+	grid_area=dx*dy #Assuming a regular grid
+	Orig_mass=h_ice*rho_ice*grid_area
+	
+	mass_on_ocean=np.zeros([Nx,Ny,10])   #Setting up matrix to spread mass to ocean.  Note that I have used 10 points  so that I can ignore 0 and match with python numbering
+	#mass_on_ocean=np.zeros([Nx,Ny])   #Setting up matrix to spread mass to ocean.
+	#Note: You may want to import the grid that the ocean model actually sees.
+	for berg_count in range(Number_of_bergs):  
+		x_val=lon[berg_count]  
+		y_val=lat[berg_count]
+		Area_val=Area[berg_count]
+		mass_val=mass[berg_count]
+
+		j_val=floor(y_val/dy)
+		i_val=floor(x_val/dx)
+		x_cell=(x_val-x[i_val])/sqrt(grid_area)+0.5
+		y_cell=(y_val-y[j_val])/sqrt(grid_area)+0.5
+		mass_on_ocean=spread_mass_to_ocean(Nx,Ny,i_val,j_val,mass_on_ocean,x_cell,y_cell,Area_val,mass_val,element_type,grid_area,static_berg[berg_count])
+
+	#Adding mass_onto_ocean
+	for i in range(1,Nx-1):
+		for j in range(1,Ny-1):
+			New_mass[j,i]=mass_on_ocean[i,j,5]  \
+					+  ( ( (mass_on_ocean[i-1,j-1,9]+mass_on_ocean[i+1,j+1,1])   \
+					+  (mass_on_ocean[i+1,j-1,7]+mass_on_ocean[i-1,j+1,3]) ) \
+					+   ( (mass_on_ocean[i-1,j  ,6]+mass_on_ocean[i+1,j  ,4])   \
+					+  (mass_on_ocean[i  ,j-1,8]+mass_on_ocean[i  ,j+1,2]) ) )
+	
+	#Adding mass to boundary cells
+	for j in range(1,Ny-1):
+		i=0
+		New_mass[j,i]=mass_on_ocean[i,j,5] +  mass_on_ocean[i+1,j+1,1] +  mass_on_ocean[i+1,j-1,7] \
+			+  mass_on_ocean[i+1,j  ,4] 	+  mass_on_ocean[i  ,j-1,8] + mass_on_ocean[i  ,j+1,2] 
+		i=Nx-1	
+		New_mass[j,i]=mass_on_ocean[i,j,5] +  mass_on_ocean[i-1,j-1,9] + mass_on_ocean[i-1,j+1,3] \
+					+   mass_on_ocean[i-1,j ,6] + mass_on_ocean[i ,j-1,8]+mass_on_ocean[i ,j+1,2]
+	
+	for i in range(1,Nx-1):
+		j=0
+		New_mass[j,i]=mass_on_ocean[i,j,5] +   mass_on_ocean[i+1,j+1,1] +  mass_on_ocean[i-1,j+1,3]  \
+				+  mass_on_ocean[i-1,j  ,6] + mass_on_ocean[i+1,j  ,4] +  mass_on_ocean[i  ,j+1,2]
+
+		j=Ny-1	
+		New_mass[j,i]=mass_on_ocean[i,j,5] +  mass_on_ocean[i-1,j-1,9] 	+  mass_on_ocean[i+1,j-1,7] + \
+				mass_on_ocean[i-1,j  ,6]+mass_on_ocean[i+1,j  ,4] +  mass_on_ocean[i  ,j-1,8]
+
+	#Corners
+	i=0 ;j=0
+	New_mass[j,i]=mass_on_ocean[i,j,5] + mass_on_ocean[i+1,j+1,1] + mass_on_ocean[i+1,j  ,4] + mass_on_ocean[i  ,j+1,2]  
+	i=0 ;j=Ny-1
+	New_mass[j,i]=mass_on_ocean[i,j,5] + mass_on_ocean[i+1,j-1,7] + mass_on_ocean[i+1,j  ,4] + mass_on_ocean[i  ,j-1,8]  
+	i=Nx-1; j=0
+	New_mass[j,i]=mass_on_ocean[i,j,5] + mass_on_ocean[i-1,j+1,3] + mass_on_ocean[i-1,j  ,6] + mass_on_ocean[i  ,j+1,2]
+	i=Nx-1; j=Ny-1	
+	New_mass[j,i]=mass_on_ocean[i,j,5] + mass_on_ocean[i-1,j-1,9] + mass_on_ocean[i-1,j  ,6] + mass_on_ocean[i  ,j-1,8]
+
+
+	if plot_outcome==True: #MP2
+		#print 'Warning: the interpolation scheme is not the same as the one used in the model'	
+		
+		#plot_data=(Orig_mass-New_mass)/Orig_mass
+		#cNorm = mpl.colors.Normalize(vmin=-.1, vmax=.1)
+		#vmax=np.max(abs(plot_data))
+		#plt.pcolormesh(x,y,plot_data,cmap='bwr',norm=cNorm)
+		#plt.title('Error between bergs and shelf')
+
+		#plot_data=h_ice
+		plot_data=New_mass
+		vmax=np.max(abs(plot_data))
+		cNorm = mpl.colors.Normalize(vmin=-vmax, vmax=vmax)
+		plt.pcolormesh(x,y,plot_data,cmap='jet',norm=cNorm)
+		plt.title('h_ice')
+
+		#plot_data=(New_mass-Orig_mass)/(rho_ice*grid_area)
+		#cNorm = mpl.colors.Normalize(vmin=-0.00000000001, vmax=0.00000000001)
+		#vmax=np.max(abs(plot_data))
+		#plt.pcolormesh(x,y,plot_data,cmap='bwr',norm=cNorm)
+
+		plt.colorbar()
+		#plt.xlim([min(x)-,max(x)])
+		#plt.ylim([min(y),max(y)])
+		#plt.show()
+
+	return New_mass
+
+def Switch_x_and_y_directions(lat,lon, A, B, C):
+	print 'Switching x and y directions!!!'
+	lat_new=[]
+	lon_new=[]
+	for i in range(len(lat)):
+		lat_new.append(lon[i])
+		lon_new.append(lat[i])
+	M=A.shape
+	A_new=np.zeros([M[1],M[0]])
+	B_new=np.zeros([M[1],M[0]])
+	C_new=np.zeros([M[1],M[0]])
+	for i in range(M[0]):
+		for j in range(M[1]):
+			A_new[j,i]=A[i,j]
+			B_new[j,i]=B[i,j]
+			C_new[j,i]=C[i,j]
+
+	return	[lat_new,lon_new,A_new,B_new, C_new]
+
+def interpolate_field_onto_new_grid(x,y,x_new,y_new,field):
+	xx, yy = np.meshgrid(x, y)
+	#f = interpolate.interp2d(x, y, field, kind='cubic')
+	f = interpolate.interp2d(x, y, field, kind='linear')
+	field_new = f(x_new, y_new)
+	return field_new
+
+def convert_input_to_catesian_coordinates(lon,lat,ice_mask,h_ice,R_earth,dx):
+	#Parameters
+	thickness_threshhold=0.01
+
+	lon_max=np.max(lon) ; lon_min=np.min(lon)
+	lat_max=np.max(lat) ; lat_min=np.min(lat)
+	lat_ref=np.mean(lat)
+
+	#Converting to cartesian grid
+        x=(np.pi/180)*R_earth*np.cos(lat_ref*np.pi/180.)*lon
+	y=(np.pi/180)*R_earth*lat
+	x=x-np.min(x)
+	y=y-np.min(y)
+	
+	#Creating regular grid
+	x_new=np.linspace(np.min(x), np.max(x), num=len(x))
+	y_new=np.linspace(np.min(y),np.max(y), num=len(y))
+	x_new=np.arange(np.min(x), np.max(x), step=dx)
+	y_new=np.arange(np.min(y), np.max(y), step=dx)
+
+	h_ice_new=interpolate_field_onto_new_grid(x,y,x_new,y_new,h_ice)
+	h_ice_new[np.where(h_ice_new<thickness_threshhold)]=0.
+	ice_mask_new=interpolate_field_onto_new_grid(x,y,x_new,y_new,ice_mask)
+	#ice_mask_new=np.round(ice_mask_new)
+	#print ice_mask_new[50,:]
+	
+	return [x_new,y_new,ice_mask_new,h_ice_new]
+
+####################################################################################################################################################
+##########################################################  Main Program   #########################################################################
+####################################################################################################################################################
+
+def main():
+
+	#Flags
+	save_restart_files=False
+	save_new_h_ice_file=True
+	Convert_to_lat_lon=False
+	input_is_cartesian=True
+
+	#Iceberg setup flags
+	only_choose_one_berg=False  ; chosen_berg_num=4564
+	scale_the_grid_to_lat_lon=False  #Remember to change this back when providing fields for Isomip
+	adjust_lat_ref=True
+	set_all_thicknesses_to_one=False   ; Th_prescribed=1.
+	Interpolate_from_four_corners=False
+	set_all_bergs_static_by_default=True
+	Find_thickness_using_vector=False
+	Switch_x_and_y_to_rotate_90=False
+	set_all_domain_to_ice=False
+
+	#Mass spreadng flags
+	Switch_regridding_element_type=False
+	Fill_in_the_boundaries=False
+	regrid_icebergs_onto_grid=True
+
+	#Plotting flags
+	plotting_bergs_over_grid=True
+	plot_circles=False
+	plot_ice_mask=True
+	plot_ice_thickness=True
+	plot_icebergs_positions=True
+
+	#Bond related flags
+	Create_icebergs_bonds=False
+	plot_bonds=True
+	break_some_bonds=False
+	Remove_stationary_bergs=False 
+	Allow_bonds_for_static_iceberg=False
+	Allow_bonds_with_boundary_bergs=False
+
+	element_type='square' 
+	#element_type='hexagon'
+
+	#Which experiment
+	#Ice_geometry_source='ISOMIP'   ; Convert_to_lat_lon=False       ; input_is_cartesian=True ; 
+	Ice_geometry_source='Weddell'     ; Convert_to_lat_lon=False        ; input_is_cartesian=False
+
+	ISOMIP_reduced=True  #Reduced uses 2X2 grid, not reduced uses 1X1 grid
+
+	ISOMIP_ice_geometry_filename='input_files/Isomip_ice_geometry.nc'
+	ISOMIP_reduced_ice_geometry_filename='input_files/isomip_ice_shelf1.nc'
+	Weddell_ice_geometry_filename='input_files/Bedmap2_gridded_subset_Weddell_Sea_Region.nc'
+	ISOMIP_topography_filename='input_files/Isomip_topog.nc'
+
+
+	#Parameters
+	thickness=100.
+	#Radius=0.25*1000
+	#Radius=sqrt(3)/2.*1000
+	#Radius=1.*1000
+	Radius=0.5*10000.  #Hexagon only valid for S<half gridcell.  (about 0.85 using 2km)
+	print 'Radius = ', Radius
+	rho_ice=850.
+	gravity=9.8
+	mass_scaling=1.
+	R_earth=6360.*1000.
+	buffer_number=0   #Number of buffer points on the sides of the domain
+
+	#Let interactive radius be different from radius for testing the model:
+	IA_scaling=1.#(1./2.)
+	Radius=Radius/IA_scaling
+
+	#Here we create the lons and lats for a tabular iceberg
+	#N= 5  # Number of rows in iceberg
+	#M= 4   # Number of columns in iceberg
+
+	if element_type=='square' and Interpolate_from_four_corners==True:
+		print 'Square packing with R dividing dx, works best with interpolation off.'
+
+	print 'Element type= ', element_type, ';  Switched_regridding= ', Switch_regridding_element_type
+	if break_some_bonds==True:
+		print 'Some bonds are being broken'
+
+	#####################################################################################
+	#####################################################################################
+
+	if  Ice_geometry_source=='ISOMIP':
+		if ISOMIP_reduced==False:
+			lon_init=0  ; lat_init=-70.  #latitude  of bottom left corner of iceberg
+			(x,y,ice_mask,h_ice)=load_ISOMIP_ice_geometry(ISOMIP_ice_geometry_filename,buffer_number)
+			ice_filename=ISOMIP_ice_geometry_filename
+		else:
+			lon_init=0  ; lat_init=-70.  #latitude  of bottom left corner of iceberg
+			(x,y,ice_mask,h_ice)=load_ISOMIP_reduced_ice_geometry(ISOMIP_reduced_ice_geometry_filename,buffer_number,ISOMIP_topography_filename)
+			ice_filename=ISOMIP_reduced_ice_geometry_filename
+		topog_filename=ISOMIP_topography_filename
+
+
+	if  Ice_geometry_source=='Weddell':
+		lon_init=-32.9  ; lat_init=-70.  #latitude  of bottom left corner of iceberg
+		(x,y,ice_mask,h_ice)=load_Weddel_ice_geometry(Weddell_ice_geometry_filename)
+		ice_filename=Weddell_ice_geometry_filename
+	
+	if input_is_cartesian is False:
+		dx=10000.
+		lat_grid=y ; lon_grid=x
+		(x,y,ice_mask,h_ice)=convert_input_to_catesian_coordinates(x,y,ice_mask,h_ice,R_earth,dx)
+		input_is_cartesian=True
+
+
+	if set_all_thicknesses_to_one==True:
+		print 'All thicknesses being set equal to 1'
+		if set_all_domain_to_ice is True:
+			ice_mask[:,:]=1.
+		h_ice[np.where(ice_mask>0.5)]=Th_prescribed
+
+	
+	lat_ref=np.max(y)
+	if (Convert_to_lat_lon==True)  and (input_is_cartesian==True):
+		lat_ref=lat_init
+		x=x-np.min(x)
+		y=y-np.min(y)
+		x=lon_init+((x/R_earth)*(180./np.pi)*(1/np.cos(lat_ref*np.pi/180.)))
+		y=lat_init+((y/R_earth)*(180./np.pi))
+		input_is_cartesian=False
+
+	#Define the positions,thickness, mass,  of the icebergs
+	(Number_of_bergs,lon,lat,iceberg_num,dx_berg, dy_berg,thickness,mass,width,x,y,Radius,static_berg,N_bergs_before_bd)= Create_icebergs(lon_init,lat_init,\
+			Radius,R_earth, x, y,ice_mask,h_ice,Convert_to_lat_lon,rho_ice,input_is_cartesian,element_type,scale_the_grid_to_lat_lon,lat_ref,adjust_lat_ref,\
+			Interpolate_from_four_corners,Fill_in_the_boundaries, set_all_bergs_static_by_default,break_some_bonds,Find_thickness_using_vector,Remove_stationary_bergs)
+
+	print 'Maximum thickness:', np.max(thickness), np.min(thickness)
+	#Define the positions of the iceberg bonds
+	if Create_icebergs_bonds==True:
+		(Number_of_bonds, first_berg_num,first_berg_ine,first_berg_jne,first_berg_lat,first_berg_lon, other_berg_num,other_berg_ine, other_berg_jne,other_berg_lat,other_berg_lon)=\
+				Define_iceberg_bonds(Number_of_bergs,iceberg_num,lat,lon,dx_berg, dy_berg,Radius,break_some_bonds,static_berg,Allow_bonds_for_static_iceberg\
+				,N_bergs_before_bd,Allow_bonds_with_boundary_bergs)
+
+	temp_mass=[mass[i]/thickness[i] for i in range(len(thickness))]
+	if only_choose_one_berg==True:
+		(Number_of_bergs,lon,lat,thickness,width,mass,iceberg_num)= Select_just_one_berg(lon,lat,thickness,width,mass,iceberg_num,chosen_berg_num,static_berg)
+
+
+	if regrid_icebergs_onto_grid==True:
+		if scale_the_grid_to_lat_lon==True:
+			print 'Regridding should be run with scale_the_grid_to_lat_lon off'
+		else:
+			if Switch_regridding_element_type==True:
+				if element_type=='square':
+					element_type='hexagon'
+				else:
+					element_type='square'
+			temp_thickness=[1. for i in thickness]
+			temp_mass=[mass[i]/(thickness[i]*rho_ice) for i in range(len(thickness))]
+			temp_rho_ice=1.
+			New_area=regrid_iceberg_thickness(lat,lon,Number_of_bergs,temp_thickness,temp_mass,h_ice,x,y,temp_rho_ice,element_type,static_berg,plot_outcome=False)
+			New_mass=regrid_iceberg_thickness(lat,lon,Number_of_bergs,thickness,mass,h_ice,x,y,rho_ice,element_type,static_berg,plot_outcome=False)
+		if save_new_h_ice_file==True:
+			grid_area=(x[1]-x[0])*(x[1]-x[0])
+			h_ice_new=New_mass*0
+			M=h_ice.shape
+			for j in range(M[0]):
+				for i in range(M[1]):
+					if New_area[j,i]>0:
+						h_ice_new[j,i]=New_mass[j,i]/(rho_ice*New_area[j,i])  
+
+	if Switch_x_and_y_to_rotate_90 is True:
+		[lat,lon, h_ice_new,New_area,New_mass]=Switch_x_and_y_directions(lat,lon, h_ice_new,New_area,New_mass)
+			
+
+	if save_restart_files==True:	
+		#Creating iceberg restart file
+		Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg)
+		
+		#Creating bond restart file
+		if Create_icebergs_bonds==True:
+			Create_bond_restart_file(Number_of_bonds,first_berg_num,first_berg_ine,first_berg_jne,other_berg_ine,other_berg_jne,iceberg_num,other_berg_num,Ice_geometry_source)
+			
+		if save_new_h_ice_file==True:
+			create_clipped_icethickness_file(h_ice_new,New_area,New_mass,grid_area,gravity)
+
+	# Plotting the positions and bonds of the newly formed formation
+	if plotting_bergs_over_grid==True:
+		plotting_iceberg_positions(lat,lon,Number_of_bergs,R_earth,Radius,IA_scaling,Convert_to_lat_lon,\
+				plot_circles,h_ice,ice_mask,x,y,plot_ice_mask,plot_ice_thickness,thickness,plot_icebergs_positions,static_berg)
+		if (plot_bonds==True) and (Create_icebergs_bonds):
+			plotting_iceberg_bonds(first_berg_lat,first_berg_lon,other_berg_lat,other_berg_lon,Number_of_bonds)
+
+
+	#field=New_mass/(rho_ice*grid_area)
+	#field=New_area/grid_area -1. 
+	#M=field.shape	
+	#print 'field',(field[M[0]-1,:])
+	#print 'field',(field[M[0]-2,:])
+	#print 'h_ice',h_ice_new[:,:]
+	#print 'h_ice-1',h_ice_new[:,:]-1.
+	plt.show()
+	print 'Script complete'
+
+
+
+if __name__ == '__main__':
+	main()
+	#sys.exit(main())
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/test/Iceberg_repository/Scripts_and_analysis/bergs_quickview.py b/test/Iceberg_repository/Scripts_and_analysis/bergs_quickview.py
new file mode 100755
index 0000000..e4a1d68
--- /dev/null
+++ b/test/Iceberg_repository/Scripts_and_analysis/bergs_quickview.py
@@ -0,0 +1,284 @@
+#!/usr/bin/env python
+
+def bergs_yearday(bergs):
+	bergs=bergs_read(bergs,'year')
+	bergs=bergs_read(bergs,'day')
+	for b in xrange (0,len(bergs.berg)):
+		bergs.berg[b].yearday=bergs.berg[b].year+(bergs.berg[b].day/372)
+		#Note I have not included all the warnings about dimensions already existing.
+        return bergs
+
+
+def bergs_read(bergs,varname):
+	nc=bergs.nc
+	bergs_list=bergs.berg
+	var = nc.variables[varname][:]
+	for b in xrange (0,len(bergs.berg)):
+		k=[]
+		js=bergs.berg[b].js
+		je=bergs.berg[b].je
+		for l in xrange (0,len(js)):
+			temp=range(js[l],je[l]+1)
+			for i in xrange (0, len(temp)):
+				k.append(temp[i])
+			setattr(bergs.berg[b],varname,var[k])
+        return bergs
+
+
+def bergs_hash(year, day, x, y, m):
+	ilat=(90.+y)/180
+        ilon=(360 % x)/360;
+        iyear=np.floor(year);
+        iday=(day/372);
+        im=math.log(m,10)-7.9;
+        h=ilon+1e3*ilat+1e6*iday+1e9*iyear+1e12*im;
+        return h
+
+
+
+def bergs_open(filename):
+
+	#Creating a classes
+	class berg_handle:
+		def __init__(self,berg,nc):
+			self.berg=berg
+			self.nc=nc
+
+	class berg_type:
+		def __init__(self,hash):
+			self.hash=hash
+			self.year0=[]
+			self.day0=[]
+			self.lon0=[]
+			self.lat0=[]
+			self.mass0=[]
+			self.js=[]
+			self.je=[]
+			self.width=[]
+			self.lon=[]
+			self.lat=[]
+			self.year=[]
+			self.day=[]
+			self.uvel=[]
+			self.vvel=[]
+			self.uo=[]
+			self.vo=[]
+			self.ui=[]
+			self.ua=[]
+			self.vu=[]
+			self.mass_of_bits=[]
+			self.heat_density=[]
+			self.thickness=[]
+			self.length=[]
+			self.ssh_x=[]
+			self.ssh_y=[]
+			self.sst=[]
+			self.cn=[]
+			self.hi=[]
+			self.yearday=[]
+			self.iceberg_num=[]
+
+	#Importing the data
+	nc = Dataset(filename, mode='r')
+	lat = nc.variables['lat'][:]
+	N=len(lat)
+	js=np.where(lat>91)[0]
+	je=np.concatenate([js[1:]-1, np.array([N-1])])
+	lon = nc.variables['lon'][:]
+	year = nc.variables['year'][:]
+	day = nc.variables['day'][:]
+	#mass = nc.variables['mass'][:]
+	iceberg_num = nc.variables['iceberg_num'][:]
+
+	N=len(js)
+	h=np.zeros(N)
+	# Making a list of identifying hashes
+	k=0
+	for j in js+1:
+		#h[k]=bergs_hash(year[j], day[j],lon[j],lat[j],mass[j])
+		h[k]=iceberg_num[j]
+		k=k+1
+
+	#Creates a sorted array of unique elements of h
+	h=sorted(list(set(h)))
+
+	#Create a list of bergs, named by their hash values, h
+	berg=[]
+	for i in xrange (0,len(h)):
+		berg.append(berg_type(h[i]))
+
+	for i in xrange(0, len(js)):
+		j=js[i]+1
+		#l=np.where(h==bergs_hash(year[j], day[j],lon[j],lat[j],mass[j]))[0]
+		l=np.where(h==iceberg_num[j])[0]
+		berg[l].year0.append(year[j])
+		berg[l].day0.append(day[j])
+		berg[l].lon0.append(lon[j])
+		berg[l].lat0.append(lat[j])
+		#berg[l].mass0.append(mass[j])
+		berg[l].js.append(js[i]+2)
+		berg[l].je.append(je[i])
+
+	#Sort each segment
+	for i in xrange (0,len(h)):
+		yd=year[berg[i].js]+(day[berg[i].js]/373)
+		#Sort according to descending yd, and then pull out indicies for js, and je.
+		
+		berg[i].js=[berg[i].js[n] for n,_ in sorted(list(enumerate(yd)),reverse=True)]
+		berg[i].je=[berg[i].je[n] for n,_ in sorted(list(enumerate(yd)),reverse=True)]
+
+	bergs_handle=berg_handle(berg,nc)
+
+	return bergs_handle
+
+###############################################################################################
+#################################  Beginning of Script  #######################################
+###############################################################################################
+from netCDF4 import Dataset
+import numpy as np
+#from PIL import *
+import math
+import os
+import matplotlib
+matplotlib.use("GTKAgg")
+import matplotlib.pyplot as plt
+from pylab import *
+import pdb
+import argparse
+#This combination allows you to access the varibale imputted from the command line.
+import sys
+
+#Clear screen
+#os.system('clear')
+
+#This is a command which puts you into testing mode so that you can troubleshoot (like a breakpoint in matlab)
+#pdb.set_trace()
+
+#If no files are given at runtime, then use the files selected here:
+if len(sys.argv)==1:
+	Number_of_files=2  # How many files would you like to view?
+
+	#Choosing which files to use
+	#Weddel Sea Version
+	#fileroot='/home/aas/Iceberg_Project/Weddell_Sea/'
+	#dirname1='one_iceberg_testing_Verlet';
+	#dirname2='one_iceberg_testing_RK';
+	
+	#filename1=fileroot+dirname1+'/iceberg_trajectories.nc'
+	#filename2=fileroot+dirname2+'/iceberg_trajectories.nc'
+
+	#Other files
+	#filename1='/home/aas/Iceberg_Project/Test_data1/Quick_Global_RK15/iceberg_trajectories.nc';
+	#filename1= '/home/aas/Iceberg_Project/Weddell_Sea/one_iceberg_testing/iceberg_trajectories.nc'
+	filename1= '../Rolling/iceberg_trajectories.nc'
+
+else:
+	Number_of_files=len(sys.argv)-1
+	
+#Imput parameters
+berg_num=296190 #index of ic
+
+#Flags and on/off switches
+plot_timeseries=0
+plot_trajectory=1
+plot_bergsize=1
+fix_horizontal_scale=0
+plot_all_bergs=0  #plots all the icebergs and not just the one given by n
+plot_initial_size=0
+plot_size_at_start_and_finish_only=0
+short_form=1 #only looks up the lat / lon
+
+#Creating and filling up the bergs
+for loop in xrange(0,Number_of_files):
+	if len(sys.argv)==1:
+		if loop==0: filename=filename1
+		if loop==1: filename=filename2
+	else:
+		filename=sys.argv[loop+1]
+	print filename	
+
+	berg=[]; del berg
+	bergs=bergs_open(filename)
+	bergs=bergs_read(bergs,'width')
+	bergs=bergs_read(bergs,'length')
+	bergs=bergs_read(bergs,'lat')
+	bergs=bergs_read(bergs,'lon')
+	bergs=bergs_yearday(bergs)
+	
+	N=len(bergs.berg)
+	if plot_all_bergs==0:
+		N=1
+	for n in xrange (0, N):
+		if plot_all_bergs==0:
+			n=berg_num
+
+		#Loading variables
+		lon=bergs.berg[n].lon[:]
+		lat=bergs.berg[n].lat[:]
+		width=bergs.berg[n].width[:]
+		length=bergs.berg[n].length[:]
+		yearday=bergs.berg[n].yearday[:]
+
+		#Finding the index of the initial time
+		initial_time_ind=sorted(list(enumerate(yearday)),key=lambda x: x[0])[-1][0]
+		final_time_ind=sorted(list(enumerate(yearday)),key=lambda x: x[0])[0][0]
+
+###########################   Begining plotting  #################################
+
+		if plot_trajectory==1:
+			#plt.subplot(2,1,1)
+			if loop==0:
+				if n==1:
+					plt.plot(lon,lat,'ko-')
+				if n!=1:
+					plt.plot(lon,lat,'go-')
+			else:
+				plt.plot(lon,lat,'bo-')
+			plt.xlabel('longitude (deg)')
+			plt.ylabel('latitude (deg)')
+			plt.title('Iceberg trajectory')
+			plt.grid(True)
+			#savefig("test.png")
+
+			if plot_bergsize==1:
+				Radius_earth=6378.135*1000;
+				circ_ind=np.linspace(0,2*pi,100);
+				for k in xrange (0 ,len(lat)):
+    					L_eff=sqrt(((width[k]*length[k])/pi));
+					plt.plot(lon[k],lat[k],'bo',linewidth=5)
+				        #d_lat=(L_eff/Radius_earth)*(180/pi);
+					#d_lon=L_eff/(111.320*(10**(3))*cos(lat[k]*pi/180));
+				        d_lat=(L_eff/Radius_earth)*(180/pi);
+					d_lon=(L_eff/(Radius_earth*cos(lat[k]*pi/180)))*(180/pi);
+                                        if plot_size_at_start_and_finish_only==0:
+					        plt.plot(lon[k]+(d_lon*cos(circ_ind)),lat[k]+(d_lat*sin(circ_ind)),'b');
+					if k==initial_time_ind and plot_initial_size==1:
+						plt.plot(lon[k]+(d_lon*cos(circ_ind)),lat[k]+(d_lat*sin(circ_ind)),'r');
+					if k==final_time_ind:
+						plt.plot(lon[k]+(d_lon*cos(circ_ind)),lat[k]+(d_lat*sin(circ_ind)),'r');
+				
+			#Setting axes to have equal distance
+				if fix_horizontal_scale==1:
+					y_scale=(max(lat)-min(lat))*(Radius_earth*pi/180)
+					x_scale=(max(lon)-min(lon))*(111.320*(10**(3))*cos(np.mean(lat)/180*pi))
+					d=0.6*max(x_scale,y_scale)
+					d_lat=d*(180/(Radius_earth*pi))
+					d_lon=d/(111.320*(10**(3))*cos(np.mean(lat)*pi/180))
+					plt.xlim([((min(lon)+max(lon))/2)-d_lon,((min(lon)+max(lon))/2)+d_lon])
+					plt.ylim([((min(lat)+max(lat))/2)-d_lat,((min(lat)+max(lat))/2)+d_lat])
+	
+			plt.plot(lon[initial_time_ind],lat[initial_time_ind],'ro')
+plt.show()
+
+if plot_timeseries==1:
+	n=0
+	#plt.subplot(2,1,2)
+	plt.plot(yearday,lon,'ko-')
+	plt.xlabel('yearday')
+	plt.ylabel('lon (deg)')
+	plt.grid(True)
+	plt.savefig("test7.png")
+	plt.show()
+
+
+print 'Script complete'
diff --git a/test/Iceberg_repository/Scripts_and_analysis/calving_and_extract.py b/test/Iceberg_repository/Scripts_and_analysis/calving_and_extract.py
new file mode 100644
index 0000000..e4a9b62
--- /dev/null
+++ b/test/Iceberg_repository/Scripts_and_analysis/calving_and_extract.py
@@ -0,0 +1,126 @@
+#from midas.rectgrid import *
+#from PIL import *
+import netCDF4 as nc
+import numpy as np
+import os
+import matplotlib as ml
+import matplotlib.pyplot as plt
+
+#These lines could be used to help select a subset of another data set. Not used for now.
+#sgrid_path = '/archive/gold/datasets/OM4_025/mosaic.v20140610.unpacked/ocean_hgrid.nc'
+#topog_path = '/archive/gold/datasets/OM4_025/mosaic.v20140610.unpacked/ocean_topog.nc'
+#calving_path = '/home/Alon.Stern/Iceberg_Project/Weddell_Sea/subsampling_calving/example_calving.nc'
+#sgrid=supergrid(file=sgrid_path,cyclic_x=True,tripolar_n=True)
+#grid=quadmesh(supergrid=sgrid)
+#location='Weddell'
+#xextent={'Weddell':(-85.,20.2)}
+#yextent={'Weddell':(grid.lath[0],-60.)}
+#subreg=grid.geo_region(x=xextent[location],y=yextent[location])
+#depth=nc.Dataset(topog_path).variables['depth'][subreg['y'],subreg['x']]
+#ny,nx=depth.shape
+#calving=nc.Dataset(calving_path).variables['CALVING']
+#calving_time=nc.Dataset(calving_path).variables['time']
+
+
+
+#Size of the domain
+nx=420
+ny=200
+
+R=3.
+x_pos_ind_1=200
+y_pos_ind_1=180
+
+x_pos_ind_2=400
+y_pos_ind_2=180
+
+Max_C=0.0058 #Maximum comes from the other calving flux file.
+
+#Defining the amount of calving
+calving=np.zeros((1,nx,ny))
+C=np.zeros((nx,ny))
+for i in xrange(0,nx):
+    for j in xrange(1,ny):
+        r_sq= (i-x_pos_ind_1)**2+(j-y_pos_ind_1)**2
+        if r_sq  < 3*(R**2):
+            C[i,j]=Max_C*np.exp(-(r_sq/(R**2))) 
+        r_sq= (i-x_pos_ind_2)**2+(j-y_pos_ind_2)**2 
+        if r_sq  < 3*(R**2):
+            C[i,j]=Max_C*np.exp(-(r_sq/(R**2)))
+   # calving[0,i,j]=C[i,j]
+
+
+
+#Creating the calving file
+fnam='calving_new.nc'
+f=nc.Dataset(fnam,'w',format='NETCDF3_CLASSIC')
+time=f.createDimension('time', None)
+yt=f.createDimension('yt',ny)
+xt=f.createDimension('xt',nx)
+
+yt=f.createVariable('yt','f4',('yt'))
+xt=f.createVariable('xt','f4',('xt'))
+CALVING=f.createVariable('CALVING','f4',('time','yt','xt'))
+time=f.createVariable('time','f4',('time'))
+
+CALVING.long_name = "frozen runoff" ;
+CALVING.units = "kg/(m^2*s)" ;
+CALVING.missing_value =-10000;# -1.e+34f ;
+CALVING.FillValue = -10000;#-1.e+34f ;
+CALVING.cell_methods = "time: mean" ;
+CALVING.time_avg_info = "average_T1,average_T2,average_DT" ;
+
+time.long_name = "time" ;
+time.units = "days since 1900-01-01 00:00:00" ;
+time.cartesian_axis = "T" ;
+time.calendar_type = "NOLEAP" ;
+time.calendar = "NOLEAP" ;
+time.bounds = "time_bounds" ;
+time.modulo = " " ;
+
+xt.long_name = "longitude" ;
+xt.units = "degrees_E" ;
+xt.cartesian_axis = "X" ;
+xt.edges = "xb" ;
+
+yt.long_name = "latitude" ;
+yt.units = "degrees_N" ;
+yt.cartesian_axis = "Y" ;
+yt.edges = "yb" ;
+
+f.filename = "19090101.ice_month.nc" ;
+f.title = "CM2G_LM3_1990_DYNCODE_pi-control_C2_25sep2012_test" ;
+f.grid_type = "regular" ;
+f.grid_tile = "N/A" ;
+f.history = "Mon Apr 22 14:33:03 2013: ncks -v time,xt,yt,CALVING 19090101.ice_month.nc example_calving.nc" ;
+f.NCO = "4.0.3" ;
+
+
+f.variables['time'][:]=0.
+#f.variables['yt'][:]=yn
+#f.variables['xt'][:]=xy
+f.variables['CALVING'][:]=calving
+
+print f.dimensions
+for dimobj in f.dimensions.values():
+    print dimobj
+f.sync()
+f.close()
+
+
+
+H = np.array([[1,2,3,4],[5,6,7,8],[9,10,11,12],[13,14,15,16]])  # added some commas and array creation code
+#H=np.zeros((nx,ny))
+H=C
+fig = plt.figure(figsize=(10, 10))
+ax = fig.add_subplot(111)
+ax.set_title('colorMap')
+plt.imshow(H)
+ax.set_aspect('equal')
+cax = fig.add_axes([0.12, 0.1, 0.78, 0.8])
+cax.get_xaxis().set_visible(False)
+cax.get_yaxis().set_visible(False)
+cax.patch.set_alpha(0)
+cax.set_frame_on(False)
+plt.colorbar(orientation='vertical')
+plt.show()
diff --git a/test/Iceberg_repository/Scripts_and_analysis/check_convergence.py b/test/Iceberg_repository/Scripts_and_analysis/check_convergence.py
new file mode 100755
index 0000000..1f6fbd8
--- /dev/null
+++ b/test/Iceberg_repository/Scripts_and_analysis/check_convergence.py
@@ -0,0 +1,77 @@
+#!/usr/bin/env python
+
+###############################################################################################
+from netCDF4 import Dataset
+import sys
+import argparse
+import numpy as np
+import os
+import numpy
+import netCDF4 as nc
+import matplotlib
+import matplotlib.pyplot as plt
+from pylab import *
+#import pdb
+#import argparse
+#This combination allows you to access the varibale imputted from the command line.
+#import sys
+
+
+def load_timeseries_data_from_file(filename,field):
+	print 'Loading data from file: ', filename	
+	with nc.Dataset(filename) as file:
+			data = file.variables[field][:]
+			Time = file.variables['time'][:]
+			x = file.variables['xq'][:]
+			y = file.variables['yh'][:]
+	
+	print 'Data size:' ,data.shape
+	
+	if len(data.shape)==3:
+		data=np.squeeze(np.sum(data,axis=1))  #Mean over first variable
+		data=np.squeeze(np.mean(data,axis=1))  #Mean over first variable
+	if len(data.shape)==4:
+			#data=np.squeeze(np.mean(data,axis=0))  #Mean over first variable
+			data=np.squeeze(np.sum(data,axis=1))  #Mean over first variable
+			data=np.squeeze(np.mean(data,axis=1))  #Mean over first variable
+			data=np.squeeze(np.mean(data,axis=1))  #Mean over first variable
+
+	return [data, Time,x,y]
+
+def plot_time_series_data(data,Time,field): 
+	print 'Starting to plot...'	
+	
+	plt.plot(Time,data)
+	plt.title(field)
+
+
+
+#Clear screen
+def main():
+
+	#os.system('clear')
+	parser = argparse.ArgumentParser()
+	parser.add_argument('--file', default=None, help='The input data file in NetCDF format.')
+	parser.add_argument('--field', default='u', help='The field to be viewed')
+	args = parser.parse_args()
+
+	filename=args.file
+	field=args.field
+
+	(time_series, Time) =load_timeseries_data_from_file(filename,field,x,y)
+
+	plot_time_series_data(time_series,Time, field)
+
+
+
+
+	plt.show()
+
+
+	print 'Script complete'
+
+
+
+if __name__ == '__main__':
+        main()
+        #sys.exit(main())
diff --git a/test/Iceberg_repository/Scripts_and_analysis/compare_Global_Quick_vs_Benchmark.py b/test/Iceberg_repository/Scripts_and_analysis/compare_Global_Quick_vs_Benchmark.py
new file mode 100644
index 0000000..557e0dc
--- /dev/null
+++ b/test/Iceberg_repository/Scripts_and_analysis/compare_Global_Quick_vs_Benchmark.py
@@ -0,0 +1,121 @@
+!I still need to write this code comparing the files. 
+
+
+from midas.rectgrid import *
+from PIL import *
+import netCDF4 as nc
+import numpy as np
+import os
+
+
+sgrid_path = '/archive/gold/datasets/OM4_025/mosaic.v20140610.unpacked/ocean_hgrid.nc'
+topog_path = '/archive/gold/datasets/OM4_025/mosaic.v20140610.unpacked/ocean_topog.nc'
+tideamp_path = '/archive/gold/datasets/OM4_025/INPUT/tidal_amplitude.v20140616.nc'
+seawifs_path = '/archive/gold/datasets/OM4_025/INPUT/seawifs_1998-2006_smoothed_2X.v20140629.nc'
+
+sgrid=supergrid(file=sgrid_path,cyclic_x=True,tripolar_n=True)
+grid=quadmesh(supergrid=sgrid)
+
+location='Weddell'
+xextent={'Weddell':(-85.,20.2)}
+yextent={'Weddell':(grid.lath[0],-60.)}
+
+subreg=grid.geo_region(x=xextent[location],y=yextent[location])
+h2=nc.Dataset(topog_path).variables['h2'][subreg['y'],subreg['x']]
+depth=nc.Dataset(topog_path).variables['depth'][subreg['y'],subreg['x']]
+tideamp=nc.Dataset(tideamp_path).variables['tideamp'][subreg['y'],subreg['x']]
+
+
+fnam='topog.nc'
+f=nc.Dataset(fnam,'w',format='NETCDF3_CLASSIC')
+
+ny,nx=depth.shape
+
+f.createDimension('ny',ny)
+f.createDimension('nx',nx)
+f.createDimension('ntiles',1)
+f.createVariable('depth','f8',('ny','nx'))
+f.createVariable('h2','f8',('ny','nx'))
+f.variables['depth'][:]=depth
+f.variables['h2'][:]=h2
+f.sync()
+f.close()
+
+
+fnam='tideamp.nc'
+f=nc.Dataset(fnam,'w',format='NETCDF3_CLASSIC')
+ny,nx=tideamp.shape
+f.createDimension('ny',ny)
+f.createDimension('nx',nx)
+f.createVariable('tideamp','f4',('ny','nx'))
+f.variables['tideamp'][:]=tideamp
+f.sync()
+f.close()
+
+
+fnam='ocean_hgrid.nc'
+f=nc.Dataset(fnam,'w',format='NETCDF3_CLASSIC')
+f.createDimension('ny',ny*2)
+f.createDimension('nx',nx*2)
+f.createDimension('nyp',ny*2+1)
+f.createDimension('nxp',nx*2+1)
+f.createDimension('string',255)
+f.createVariable('y','f8',('nyp','nxp'))
+f.createVariable('x','f8',('nyp','nxp'))
+f.createVariable('dy','f8',('ny','nxp'))
+f.createVariable('dx','f8',('nyp','nx'))
+f.createVariable('area','f8',('ny','nx'))
+f.createVariable('angle_dx','f8',('nyp','nxp'))
+f.createVariable('tile','S1',('string'))
+
+x_read=subreg['x']
+y_read=subreg['y']
+
+
+if x_read[-1] < x_read[0]:
+    ib=np.where(np.roll(x_read,shift=-1)<x_read)[0][0]
+    tmp = np.arange(x_read[0]*2,x_read[ib]*2+2)
+    x_read=np.concatenate((tmp,np.arange(x_read[ib+1]*2,x_read[-1]*2+3)))
+    y_read = np.arange(y_read[0]*2,y_read[-1]*2+3)    
+else:
+    x_read = np.arange(x_read[0]*2,x_read[-1]*2+3)
+    y_read = np.arange(y_read[0]*2,y_read[-1]*2+3)
+
+
+f.variables['y'].units='degrees'
+f.variables['x'].units='degrees'
+f.variables['dy'].units='meters'
+f.variables['dx'].units='meters'
+f.variables['area'].units='m2'
+f.variables['angle_dx'].units='degrees'
+
+yn=sgrid.y[y_read,:]
+yn=yn[:,x_read]
+f.variables['y'][:]=yn
+xn=sgrid.x[y_read,:]
+xn=xn[:,x_read]
+f.variables['x'][:]=xn
+dyn=sgrid.dy[y_read[:-1],:]
+dyn=dyn[:,x_read]
+f.variables['dy'][:]=dyn
+dxn=sgrid.dx[y_read,:]
+dxn=dxn[:,x_read[:-1]]
+f.variables['dx'][:]=dxn
+arean=sgrid.area[y_read[:-1],:]
+arean=arean[:,x_read[:-1]]
+f.variables['area'][:]=arean
+ang=sgrid.angle_dx[y_read,:]
+ang=ang[:,x_read]
+f.variables['angle_dx'][:]=ang
+f.variables['tile'][0] = 't'  ## This is stupid
+f.variables['tile'][1] = 'i'
+f.variables['tile'][2] = 'l'
+f.variables['tile'][3] = 'e'
+f.variables['tile'][4] = '1'
+f.sync()
+f.close()
+
+
+
+
+
diff --git a/test/Iceberg_repository/Scripts_and_analysis/copy_files_to_shelf_and_bergs.sh b/test/Iceberg_repository/Scripts_and_analysis/copy_files_to_shelf_and_bergs.sh
new file mode 100755
index 0000000..bc41d80
--- /dev/null
+++ b/test/Iceberg_repository/Scripts_and_analysis/copy_files_to_shelf_and_bergs.sh
@@ -0,0 +1,42 @@
+#cp output_files/ISOMIP_icebergs.res.nc ../Bergs_cartesian_ISOMIP1_rho/INPUT/icebergs.res.nc
+#cp output_files/isomip_ice_shelf1_clipped.nc ../Shelf_cartesian_ISOMIP1_rho/INPUT/
+#cp output_files/isomip_ice_shelf1_clipped.nc ../Bergs_cartesian_ISOMIP1_rho/INPUT/
+
+#cp output_files/ISOMIP_icebergs.res.nc ../ISOMIP_ocean_ice/INPUT/icebergs.res.nc
+#cp output_files/ISOMIP_bonds_iceberg.res.nc ../ISOMIP_ocean_ice/INPUT/bonds_iceberg.res.nc
+#cp output_files/isomip_ice_shelf1_clipped.nc ../ISOMIP_ocean_ice/INPUT/isomip_ice_shelf1_clipped.nc
+
+#cp output_files/ISOMIP_icebergs.res.nc ../Tech_ISOMIP/INPUT/icebergs.res.nc
+#cp output_files/ISOMIP_bonds_iceberg.res.nc ../Tech_ISOMIP/INPUT/bonds_iceberg.res.nc
+#cp output_files/isomip_ice_shelf1_clipped.nc ../Tech_ISOMIP/INPUT/isomip_ice_shelf1_clipped.nc
+
+#cp output_files/ISOMIP_icebergs.res.nc ../Tech_ISOMIP//Bergs/Bond_drifting_Moving_berg_trimmed_shelf/INPUT/icebergs.res.nc
+#cp output_files/ISOMIP_bonds_iceberg.res.nc ../Tech_ISOMIP/Bergs/Bond_drifting_Moving_berg_trimmed_shelf/INPUT/bonds_iceberg.res.nc
+#cp output_files/isomip_ice_shelf1_clipped.nc ../Tech_ISOMIP/Bergs/Bond_drifting_Moving_berg_trimmed_shelf/INPUT/isomip_ice_shelf1_clipped.nc
+
+#cp output_files/ISOMIP_icebergs.res.nc ../Tech_ISOMIP//Bergs/Bond_drifting_Moving_berg_trimmed_shelf_larger_berg/INPUT/icebergs.res.nc
+#cp output_files/ISOMIP_bonds_iceberg.res.nc ../Tech_ISOMIP/Bergs/Bond_drifting_Moving_berg_trimmed_shelf_larger_berg/INPUT/bonds_iceberg.res.nc
+#cp output_files/isomip_ice_shelf1_clipped.nc ../Tech_ISOMIP/Bergs/Bond_drifting_Moving_berg_trimmed_shelf_larger_berg/INPUT/isomip_ice_shelf1_clipped.nc
+
+
+#cp output_files/ISOMIP_icebergs.res.nc ../Tech_ISOMIP/Bergs/Collapse_with_Bond_drifting_Moving_berg_trimmed_shelf_small_step_kd2/INPUT/icebergs.res.nc
+#cp output_files/ISOMIP_bonds_iceberg.res.nc ../Tech_ISOMIP/Bergs/Collapse_with_Bond_drifting_Moving_berg_trimmed_shelf_small_step_kd2/INPUT/bonds_iceberg.res.nc
+#cp output_files/isomip_ice_shelf1_clipped.nc ../Tech_ISOMIP/Bergs/Collapse_with_Bond_drifting_Moving_berg_trimmed_shelf_small_step_kd2/INPUT/isomip_ice_shelf1_clipped.nc
+
+
+#cp output_files/isomip_icebergs.res.nc ../tech_isomip/bergs/collapse_with_bond_drifting_moving_berg_trimmed_shelf_small_step_kd2_with_wind/input/icebergs.res.nc
+#cp output_files/isomip_bonds_iceberg.res.nc ../tech_isomip/bergs/collapse_with_bond_drifting_moving_berg_trimmed_shelf_small_step_kd2_with_wind/input/bonds_iceberg.res.nc
+#cp output_files/isomip_ice_shelf1_clipped.nc ../tech_isomip/bergs/collapse_with_bond_drifting_moving_berg_trimmed_shelf_small_step_kd2_with_wind/input/isomip_ice_shelf1_clipped.nc
+
+cp output_files/ISOMIP_icebergs.res.nc /lustre/f1/unswept/Alon.Stern/MOM6-examples_Alon/ice_ocean_SIS2/Tech_ISOMIP/Bergs/After_melt_bond_small_step/INPUT/icebergs.res.nc
+cp output_files/ISOMIP_bonds_iceberg.res.nc /lustre/f1/unswept/Alon.Stern/MOM6-examples_Alon/ice_ocean_SIS2/Tech_ISOMIP/Bergs/After_melt_bond_small_step/INPUT/bonds_iceberg.res.nc
+cp output_files/isomip_ice_shelf1_clipped.nc /lustre/f1/unswept/Alon.Stern/MOM6-examples_Alon/ice_ocean_SIS2/Tech_ISOMIP/Bergs/After_melt_bond_small_step/INPUT/isomip_ice_shelf1_clipped.nc
+
+#cp output_files/ISOMIP_icebergs.res.nc /lustre/f1/unswept/Alon.Stern/MOM6-examples_Alon/ice_ocean_SIS2/Tech_ISOMIP/Bergs/After_melt_Collapse_with_Bond_with_orientation/INPUT/icebergs.res.nc
+#cp output_files/ISOMIP_bonds_iceberg.res.nc /lustre/f1/unswept/Alon.Stern/MOM6-examples_Alon/ice_ocean_SIS2/Tech_ISOMIP/Bergs/After_melt_Collapse_with_Bond_with_orientation/INPUT/bonds_iceberg.res.nc
+#cp output_files/isomip_ice_shelf1_clipped.nc /lustre/f1/unswept/Alon.Stern/MOM6-examples_Alon/ice_ocean_SIS2/Tech_ISOMIP/Bergs/After_melt_Collapse_with_Bond_with_orientation/INPUT/isomip_ice_shelf1_clipped.nc
+
+#cp output_files/ISOMIP_icebergs.res.nc /lustre/f1/unswept/Alon.Stern/MOM6-examples_Alon/ice_ocean_SIS2/Tech_ISOMIP/Bergs/After_melt_Collapse_with_Bond_with_orientation/INPUT/icebergs.res.nc
+#cp output_files/ISOMIP_bonds_iceberg.res.nc /lustre/f1/unswept/Alon.Stern/MOM6-examples_Alon/ice_ocean_SIS2/Tech_ISOMIP/Bergs/After_melt_Collapse_with_Bond_with_orientation/INPUT/bonds_iceberg.res.nc
+#cp output_files/isomip_ice_shelf1_clipped.nc /lustre/f1/unswept/Alon.Stern/MOM6-examples_Alon/ice_ocean_SIS2/Tech_ISOMIP/Bergs/After_melt_Collapse_with_Bond_with_orientation/INPUT/isomip_ice_shelf1_clipped.nc
+
diff --git a/test/Iceberg_repository/Scripts_and_analysis/create_C3_env.sh b/test/Iceberg_repository/Scripts_and_analysis/create_C3_env.sh
new file mode 100755
index 0000000..e9aac87
--- /dev/null
+++ b/test/Iceberg_repository/Scripts_and_analysis/create_C3_env.sh
@@ -0,0 +1,14 @@
+#This script creates a C3 environment
+
+mkdir build/intel
+cat << EOFA > build/intel/env
+module unload PrgEnv-pgi
+module unload PrgEnv-pathscale
+module unload PrgEnv-intel
+module unload PrgEnv-gnu
+module unload PrgEnv-cray
+module load PrgEnv-intel
+module unload netcdf
+module load cray-netcdf
+EOFA
+
diff --git a/test/Iceberg_repository/Scripts_and_analysis/create_berg_restart.py b/test/Iceberg_repository/Scripts_and_analysis/create_berg_restart.py
new file mode 100755
index 0000000..27c4d5a
--- /dev/null
+++ b/test/Iceberg_repository/Scripts_and_analysis/create_berg_restart.py
@@ -0,0 +1,172 @@
+#!/usr/bin/env python
+
+###############################################################################################
+from netCDF4 import Dataset
+import numpy as np
+import os
+#import matplotlib
+#import matplotlib.pyplot as plt
+#from pylab import *
+#import pdb
+#import argparse
+#This combination allows you to access the varibale imputted from the command line.
+#import sys
+
+#Clear screen
+os.system('clear')
+
+new_filename = 'output_files/icebergs_test.res.nc'
+
+f = Dataset(new_filename,'w', format='NETCDF3_CLASSIC')
+
+
+#Creating the calving file
+#f=nc.Dataset(fnam,'w',format='NETCDF3_CLASSIC')
+
+if True:
+	if True:
+
+		i=f.createDimension('i', None)
+		
+		i=f.createVariable('i','i')
+		#i=f.createVariable('i','i',('i'))
+
+		lon=f.createVariable('lon','d',('i'))
+		lon.long_name = "longitude" ;
+		lon.units = "degrees_E" ;
+		lon.checksum = "               0" ;
+
+		lat=f.createVariable('lat','d',('i'))
+		lat.long_name = "latitude" ;
+		lat.units = "degrees_N" ;
+		lat.checksum = "               0" ;
+
+		uvel=f.createVariable('uvel','d',('i'))
+		uvel.long_name = "zonal velocity" ;
+		uvel.units = "m/s" ;
+		uvel.checksum = "               0" ;
+
+		vvel=f.createVariable('vvel','d',('i'))
+		vvel.long_name = "meridional velocity" ;
+		vvel.units = "m/s" ;
+		vvel.checksum = "               0" ;
+
+		mass=f.createVariable('mass','d',('i'))
+		mass.long_name = "mass" ;
+		mass.units = "kg" ;
+		mass.checksum = "               0" ;
+
+		axn=f.createVariable('axn','d',('i'))
+		axn.long_name = "explicit zonal acceleration" ;
+		axn.units = "m/s^2" ;
+		axn.checksum = "               0" ;
+
+		ayn=f.createVariable('ayn','d',('i'))
+		ayn.long_name = "explicit meridional acceleration" ;
+		ayn.units = "m/s^2" ;
+		ayn.checksum = "               0" ;
+
+		bxn=f.createVariable('bxn','d',('i'))
+		bxn.long_name = "inplicit zonal acceleration" ;
+		bxn.units = "m/s^2" ;
+		bxn.checksum = "               0" ;
+
+		byn=f.createVariable('byn','d',('i'))
+		byn.long_name = "implicit meridional acceleration" ;
+		byn.units = "m/s^2" ;
+		byn.checksum = "               0" ;
+
+		ine=f.createVariable('ine','i',('i'))
+		ine.long_name = "i index" ;
+		ine.units = "none" ;
+		ine.packing = 0 ;
+		ine.checksum = "               0" ;
+
+		jne=f.createVariable('jne','i',('i'))
+		jne.long_name = "j index" ;
+		jne.units = "none" ;
+		jne.packing = 0 ;
+
+		thickness=f.createVariable('thickness','d',('i'))
+		thickness.long_name = "thickness" ;
+		thickness.units = "m" ;
+		thickness.checksum = "               0" ;
+
+		width=f.createVariable('width','d',('i'))
+		width.long_name = "width" ;
+		width.units = "m" ;
+		width.checksum = "               0" ;
+
+		length=f.createVariable('length','d',('i'))
+		length.long_name = "length" ;
+		length.units = "m" ;
+		length.checksum = "               0" ;
+
+		start_lon=f.createVariable('start_lon','d',('i'))
+		start_lon.long_name = "longitude of calving location" ;
+		start_lon.units = "degrees_E" ;
+		start_lon.checksum = "               0" ;
+
+		start_lat=f.createVariable('start_lat','d',('i'))
+		start_lat.long_name = "latitude of calving location" ;
+		start_lat.units = "degrees_N" ;
+		start_lat.checksum = "               0" ;
+
+		start_year=f.createVariable('start_year','i',('i'))
+		start_year.long_name = "calendar year of calving event" ;
+		start_year.units = "years" ;
+		start_year.packing = 0 ;
+		start_year.checksum = "               0" ;
+
+		iceberg_num=f.createVariable('iceberg_num','i',('i'))
+		iceberg_num.long_name = "identification of the iceberg" ;
+		iceberg_num.units = "dimensionless" ;
+		iceberg_num.packing = 0 ;
+		iceberg_num.checksum = "               0" ;
+
+		start_day=f.createVariable('start_day','d',('i'))
+		start_day.long_name = "year day of calving event" ;
+		start_day.units = "days" ;
+		start_day.checksum = "               0" ;
+
+		start_mass=f.createVariable('start_mass','d',('i'))
+		start_mass.long_name = "initial mass of calving berg" ;
+		start_mass.units = "kg" ;
+		start_mass.checksum = "               0" ;
+
+		mass_scaling=f.createVariable('mass_scaling','d',('i'))
+		mass_scaling.long_name = "scaling factor for mass of calving berg" ;
+		mass_scaling.units = "none" ;
+		mass_scaling.checksum = "               0" ;
+
+		mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
+		mass_of_bits.long_name = "mass of bergy bits" ;
+		mass_of_bits.units = "kg" ;
+		mass_of_bits.checksum = "               0" ;
+
+		heat_density=f.createVariable('heat_density','d',('i'))
+		heat_density.long_name = "heat density" ;
+		heat_density.units = "J/kg" ;
+		heat_density.checksum = "               0" ;
+
+		halo_berg=f.createVariable('halo_berg','d',('i'))
+		halo_berg.long_name = "halo_berg" ;
+		halo_berg.units = "dimensionless" ;
+		halo_berg.checksum = "               0" ;
+
+		static_berg=f.createVariable('static_berg','d',('i'))
+		static_berg.long_name = "static_berg" ;
+		static_berg.units = "dimensionless" ;
+		static_berg.checksum = "               0" ;
+
+print 'Created restart file: ' ,new_filename
+print 'Script complete'
+
+f.sync()
+f.close()
+
+
+
+
+
+print 'Script complete'
diff --git a/test/Iceberg_repository/Scripts_and_analysis/create_one_file.py b/test/Iceberg_repository/Scripts_and_analysis/create_one_file.py
new file mode 100755
index 0000000..0c8bf5c
--- /dev/null
+++ b/test/Iceberg_repository/Scripts_and_analysis/create_one_file.py
@@ -0,0 +1,94 @@
+#!/usr/bin/env python
+
+###############################################################################################
+from netCDF4 import Dataset
+import numpy as np
+import os
+import numpy
+import netCDF4 as nc
+#import matplotlib
+#import matplotlib.pyplot as plt
+#from pylab import *
+#import pdb
+#import argparse
+#This combination allows you to access the varibale imputted from the command line.
+#import sys
+
+#Clear screen
+def main():
+
+	os.system('clear')
+	input_geometry_filename='input_files/Isomip_ocean_geometry.nc'
+
+	#Flags
+	new_filename='output_files/one_file.nc'
+
+	#f=Dataset(input_geometry_filename,'r')
+	#g=Dataset(new_filename,'w') # w if for creating a file
+
+
+	with nc.Dataset(input_geometry_filename) as file:
+		
+
+		Depth = file.variables['D'][:,:]
+
+	M= Depth.shape
+	ny=M[0]
+	nx=M[1]
+	print nx,ny
+	
+	#Creating the topog file
+	#g=Dataset(new_filename,'w') # w if for creating a file
+	g=nc.Dataset(new_filename,'w',format='NETCDF3_CLASSIC')
+	
+
+	lat=g.createDimension('lat',ny)
+	lon=g.createDimension('lon',nx)
+	time=g.createDimension('time', None)
+
+	lat=g.createVariable('lat','f4',('lat'))
+	lon=g.createVariable('lon','f4',('lon'))
+	time=g.createVariable('time','f4',('time'))
+	one_var=g.createVariable('one_var','f4',('lat','lon'))
+
+	time.long_name = "time" ;
+	time.units = "days since 1900-01-01 00:00:00" ;
+	time.cartesian_axis = "T" ;
+	time.calendar_type = "NOLEAP" ;
+	time.calendar = "NOLEAP" ;
+	time.bounds = "time_bounds" ;
+	time.modulo = " " ;
+
+	lon.units = "degrees_E" ;
+	lon.cartesian_axis = "X" ;
+	#lon.edges = "xb" ;
+
+	#lat.long_name = "latitude" ;
+	lat.units = "degrees_N" ;
+	lat.cartesian_axis = "Y" ;
+	#lat.edges = "yb" ;
+
+	one_var.long_name="unnamed_variable"
+	one_var.units="m/s"
+	
+
+	
+	g.variables['one_var'][:]=1.
+	g.variables['lon'][:]=np.linspace(0.5,239.5,nx,endpoint=True)
+	g.variables['lat'][:]=np.linspace(0.5,39.5,ny,endpoint=True)
+	g.variables['time'][0]=1.
+
+	g.sync()
+	g.close()
+
+
+
+
+
+	print 'Script complete'
+
+
+
+if __name__ == '__main__':
+        main()
+        #sys.exit(main())
diff --git a/test/Iceberg_repository/Scripts_and_analysis/create_thickness_file.py b/test/Iceberg_repository/Scripts_and_analysis/create_thickness_file.py
new file mode 100755
index 0000000..a01754d
--- /dev/null
+++ b/test/Iceberg_repository/Scripts_and_analysis/create_thickness_file.py
@@ -0,0 +1,167 @@
+#!/usr/bin/env python
+
+#First import the netcdf4 library
+from netCDF4 import Dataset  # http://code.google.com/p/netcdf4-python/
+import numpy as np  # http://code.google.com/p/netcdf4-python/
+import matplotlib
+import math
+import os
+matplotlib.use("GTKAgg")
+from pylab import *
+#import matplotlib.pyplot as plt
+import pdb
+import netCDF4 as nc
+from hexagon_area import Divide_hexagon_into_4_quadrants_old
+from hexagon_area import Hexagon_into_quadrants_using_triangles
+
+
+def load_ISOMIP_ice_geometry(filename):
+	with nc.Dataset(filename) as file:
+		ocean_mask = file.variables['openOceanMask'][:,:]
+		upperSurface = file.variables['upperSurface'][:,:]
+		lowerSurface = file.variables['lowerSurface'][:,:]
+		x = file.variables['x'][:]
+		y = file.variables['y'][:]
+
+	ice_mask=1-ocean_mask #one if it ice, zero if it is ocean
+	h_ice=upperSurface-lowerSurface #The ice thickness
+	M=ice_mask.shape
+
+	return [x,y,ice_mask,h_ice]
+
+def Switch_x_and_y_directions(lat,lon, A, B, C):
+        print 'Switching x and y directions!!!'
+        lat_new=[]
+        lon_new=[]
+        for i in range(len(lat)):
+                lat_new.append(lon[i])
+                lon_new.append(lat[i])
+        M=A.shape
+        A_new=np.zeros([M[1],M[0]])
+        B_new=np.zeros([M[1],M[0]])
+        C_new=np.zeros([M[1],M[0]])
+        for i in range(M[0]):
+                for j in range(M[1]):
+                        A_new[j,i]=A[i,j]
+                        B_new[j,i]=B[i,j]
+                        C_new[j,i]=C[i,j]
+
+        return  [lat_new,lon_new,A_new,B_new, C_new]
+
+
+def create_clipped_icethickness_file(h_ice,area,mass,grid_area,gravity,New_ice_thickness_filename):
+	#Creating clipped file
+        [ny, nx]= h_ice.shape ; 
+	
+        g=Dataset(New_ice_thickness_filename,'w') # w if for creating a file
+
+        g.createDimension('nx',nx)
+        g.createDimension('ny',ny)
+
+        thick_h=g.createVariable('thick','f8',('ny','nx'))
+        area_h=g.createVariable('area','f8',('ny','nx'))
+        p_surf_h=g.createVariable('p_surf','f8',('ny','nx'))
+
+        thick_h.units = 'm'
+        thick_h.standard_name = 'ice shelf thickness (clipped)'
+        area_h.units = 'm2'
+        area_h.standard_name = 'ice shelf area'
+        p_surf_h.units = 'Pa'
+        p_surf_h.standard_name = 'surface pressure due to ice shelf'
+
+	p_surf=(gravity*mass)/grid_area
+        g.variables['thick'][:]=h_ice
+        g.variables['area'][:]=area
+        g.variables['p_surf'][:]=p_surf
+        print 'Creating clipped ice file: ' , New_ice_thickness_filename
+        
+        g.sync()
+        g.close()
+
+
+def load_ISOMIP_reduced_ice_geometry(ice_filename,topog_filename):
+	with nc.Dataset(ice_filename) as file:
+		h_ice = file.variables['thick'][:,:]
+		area =  file.variables['area'][:,:]
+		M=h_ice.shape
+
+	y=np.linspace(1000,79000,M[0],endpoint=True)
+	#x=np.linspace(321000,799000,M[1],endpoint=True)
+	x=np.linspace(1000,479000,M[1],endpoint=True)
+	ice_mask=h_ice>0.
+	
+	return [x,y,ice_mask,h_ice]
+
+####################################################################################################################################################
+##########################################################  Main Program   #########################################################################
+####################################################################################################################################################
+
+def main():
+
+	#Flags
+	Switch_x_and_y_to_rotate_90=False
+
+
+	ISOMIP_ice_geometry_filename='input_files/Isomip_ice_geometry.nc'
+	ISOMIP_reduced_ice_geometry_filename='input_files/isomip_ice_shelf1.nc'
+	ISOMIP_reduced_ice_geometry_filename='output_files/isomip_ice_shelf1_clipped.nc'
+	Weddell_ice_geometry_filename='input_files/Bedmap2_gridded_subset_Weddell_Sea_Region.nc'
+	ISOMIP_topography_filename='input_files/Isomip_topog.nc'
+	Output_filename='output_files/isomip_ice_shelf1_new.nc'
+
+	(x,y,ice_mask,h_ice)=load_ISOMIP_reduced_ice_geometry(ISOMIP_reduced_ice_geometry_filename,ISOMIP_topography_filename)
+
+	#Parameters
+	rho_ice=850.
+	gravity=9.8
+
+
+	grid_area=(x[1]-x[0])*(x[1]-x[0])
+	New_area=h_ice*0.+grid_area
+	#New_area=ice_mask*grid_area
+	z_extra=0.00000000001
+	h_ice=h_ice+z_extra
+	#h_ice=(h_ice>0.)*0.00000000000001
+	New_mass=New_area*h_ice*rho_ice
+	h_ice=(0*h_ice)+z_extra
+	if Switch_x_and_y_to_rotate_90 is True:
+		lat=[];lon=[]
+		[lat,lon, h_ice,New_area,New_mass]=Switch_x_and_y_directions(lat,lon, h_ice,New_area,New_mass)
+		x_temp=x
+		x=y
+		y=x_temp
+	create_clipped_icethickness_file(h_ice,New_area,New_mass,grid_area,gravity,Output_filename)
+	
+
+
+	#Plotting the data
+	plot_data=(h_ice)
+        vmax=np.max(abs(plot_data))
+        cNorm = mpl.colors.Normalize(vmin=0., vmax=vmax)
+        plt.pcolormesh(x,y,plot_data,cmap='bwr',norm=cNorm)
+        plt.title('Ice geometry')
+	plt.colorbar()
+	
+
+	plt.show()
+	print 'Script complete'
+
+
+
+if __name__ == '__main__':
+	main()
+	#sys.exit(main())
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/test/Iceberg_repository/Scripts_and_analysis/filling_up_space.py b/test/Iceberg_repository/Scripts_and_analysis/filling_up_space.py
new file mode 100755
index 0000000..0334a5f
--- /dev/null
+++ b/test/Iceberg_repository/Scripts_and_analysis/filling_up_space.py
@@ -0,0 +1,338 @@
+#!/usr/bin/env python
+
+#First import the netcdf4 library
+from netCDF4 import Dataset  # http://code.google.com/p/netcdf4-python/
+import numpy as np  # http://code.google.com/p/netcdf4-python/
+import matplotlib
+import math
+import os
+matplotlib.use("GTKAgg")
+from pylab import *
+from scipy import interpolate
+#import matplotlib.pyplot as plt
+import argparse
+import pdb
+import netCDF4 as nc
+from hexagon_area import Divide_hexagon_into_4_quadrants_old
+from hexagon_area import Hexagon_into_quadrants_using_triangles
+
+
+
+def spread_mass_to_ocean(Nx,Ny,i,j,mass_on_ocean,x,y,Area,Mass,element_type,grid_area,static_berg,lat1, lat2, lat3, lat4, lon1, lon2, lon3, l):
+		#Using physical space
+
+		#Initialize weights for each cell	
+		yDxL=0.  ; yDxC=0. ; yDxR=0. ; yCxL=0. ; yCxR=0. 
+		yUxL=0.  ; yUxC=0. ; yUxR=0. ; yCxC=1.
+
+		if element_type=='square':
+		#if True:
+			L = min(( (np.sqrt(Area)  / np.sqrt(grid_area))),1) ;  #Non dimensionalize element length by grid area. (This gives the non-dim length of the square)
+			xL=min(0.5, max(0., 0.5-(x/L)))
+			xR=min(0.5, max(0., (x/L)+(0.5-(1/L) )))
+			xC=max(0., 1.-(xL+xR))
+			yD=min(0.5, max(0., 0.5-(y/L)))
+			yU=min(0.5, max(0., (y/L)+(0.5-(1/L) )))
+			yC=max(0., 1.-(yD+yU))
+
+			yDxL=yD*xL#*grd%msk[i-1,j-1]
+			yDxC=yD*xC#*grd%msk[i  ,j-1]
+			yDxR=yD*xR#*grd%msk[i+1,j-1]
+			yCxL=yC*xL#*grd%msk[i-1,j  ]
+			yCxR=yC*xR#*grd%msk[i+1,j  ]
+			yUxL=yU*xL#*grd%msk[i-1,j+1]
+			yUxC=yU*xC#*grd%msk[i  ,j+1]
+			yUxR=yU*xR#*grd%msk(i+1,j+1]
+			yCxC=1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )
+
+		if element_type=='hexagon':
+		#if False:#element_type=='hexagon':
+			H = min(( (np.sqrt(Area/(2*sqrt(3))) ;  #No longer no dimensionalizing, but rather using actual distances
+			S=(2/np.sqrt(3))*H #Side of the hexagon
+			grid_dist=1e15 #This should be changed to the minimum grid spacinge.
+			if S>0.5*(grid_dist):
+				print 'Elements must be smaller than a whole gridcell', 'i.e.: S= ' , S , '>=0.5',i,j
+				halt
+
+			#Subtracting the position of the nearest corner from x,y
+			#[origin_x, origin_y]=find_closest_corner(x,y,
+			origin_x=1 ; origin_y=1
+			if x<0.5:
+				origin_x=0
+			if y<0.5:
+				origin_y=0
+
+			x0=(x-origin_x) #Position of the hexagon center, relative to origin at the nearest vertex
+			y0=(y-origin_y)
+			
+			#(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Divide_hexagon_into_4_quadrants_old(x0,y0,H)
+			(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Hexagon_into_quadrants_using_triangles(x0,y0,H,0.)
+			if min(min(Area_Q1,Area_Q2),min(Area_Q3, Area_Q4)) <0:
+				print 'Yolo'
+				print x0,y0,H
+				#print min(min(Area_Q1,Area_Q2),min(Area_Q3, Area_Q4))
+				print Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+
+			Area_Q1=Area_Q1/Area_hex
+			Area_Q2=Area_Q2/Area_hex
+			Area_Q3=Area_Q3/Area_hex
+			Area_Q4=Area_Q4/Area_hex
+
+			#Now, you decide which quadrant belongs to which mass on ocean cell.
+			#Top right vertex
+			if x>=0.5 and y>= 0.5:
+				yUxR=Area_Q1
+				yUxC=Area_Q2
+				yCxC=Area_Q3
+				yCxR=Area_Q4
+			
+			#Top left vertex
+			if x<0.5 and y>= 0.5:
+				yUxC=Area_Q1
+				yUxL=Area_Q2
+				yCxL=Area_Q3
+				yCxC=Area_Q4
+			
+			#Bottom left vertex
+			if x<0.5 and y< 0.5:
+				yCxC=Area_Q1
+				yCxL=Area_Q2
+				yDxL=Area_Q3
+				yDxC=Area_Q4
+
+			#Bottom right vertex
+			if x>=0.5 and y< 0.5:
+				yCxR=Area_Q1
+				yCxC=Area_Q2
+				yDxC=Area_Q3
+				yDxR=Area_Q4
+
+			#if Sector<4 and Sector>-1:
+			#	print Sector
+				
+					
+			#Check that this is true
+			if abs(yCxC-(1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )))>0.001:
+				print 'All the mass is not being used!!!'
+				#print W1 , W2 , W3 , W4 , W5 , W6
+				#print Area_Upper, Area_Lower, Area_right, Area_left
+				print 'Areas: ',Area_hex,Area_hex*Area_Q1, Area_hex*Area_Q2, Area_hex*Area_Q3, Area_hex*Area_Q4
+				print 'x0=',x0, 'y0=',y0, 'H=', H
+				print 'Total area= ',(Area_Q1+Area_Q2+Area_Q3+Area_Q4)#, Sector
+				
+
+		#Accounting for masked points 
+		a=1. ; b=1. ; c=1. ; d=1.
+		if i==0:
+			a=0.;
+		if j==0: 
+			b=0.;
+		if i==Nx-1:
+			c=0;
+		if j==Ny-1:
+			d=0;
+
+		fraction_used= ((yDxL*a*b) + (yDxC*b) + (yDxR*b*c) +(yCxL*a) + (yCxR*c) + (yUxL*a*d) + (yUxC*d) + (yUxR*c*d) + (yCxC))
+		if static_berg>0.5:
+			fraction_used=1.
+
+		mass_on_ocean[i,j,1]=mass_on_ocean[i,j,1]+(a*b*yDxL*Mass/fraction_used)
+		mass_on_ocean[i,j,2]=mass_on_ocean[i,j,2]+(b*yDxC*Mass/fraction_used)
+		mass_on_ocean[i,j,3]=mass_on_ocean[i,j,3]+(b*c*yDxR*Mass/fraction_used)
+		mass_on_ocean[i,j,4]=mass_on_ocean[i,j,4]+(a*yCxL*Mass/fraction_used)
+		mass_on_ocean[i,j,5]=mass_on_ocean[i,j,5]+(yCxC*Mass/fraction_used)
+		mass_on_ocean[i,j,6]=mass_on_ocean[i,j,6]+(c*yCxR*Mass/fraction_used)
+		mass_on_ocean[i,j,7]=mass_on_ocean[i,j,7]+(a*d*yUxL*Mass/fraction_used)
+		mass_on_ocean[i,j,8]=mass_on_ocean[i,j,8]+(d*yUxC*Mass/fraction_used)
+		mass_on_ocean[i,j,9]=mass_on_ocean[i,j,9]+(c*d*yUxR*Mass/fraction_used)
+
+
+		return mass_on_ocean
+
+
+def Create_icebergs(Radius, R_earth):
+	dx_berg=[]
+	dy_berg=[]
+	lat=[]
+	lon=[]
+	berg_count=0
+	
+	#Flags
+	adjust_lat_ref=True
+
+
+	#Developing some elements in cartesian coordinates:
+	lat_init=20.0 ; lon_init=0.0 #Starting point
+
+
+	for i in range(40):
+		x_start=Radius
+		y_start=(Radius)
+		x_val=x_start+(2*i*Radius)
+		for j in range(40):
+			y_val=y_start+(2*j*Radius)  ;# x_val=x_start + (np.sqrt(3)*Radius*i)
+
+			berg_count=berg_count+1
+			dx_berg.append(x_val)
+			dy_berg.append(y_val)
+
+	Number_of_bergs=berg_count
+
+	#Convert_to_lat_lon==True:
+	dlat_dy=(180/np.pi)*(1/R_earth)
+	#dlat_berg=(180/np.pi)*(1/R_earth)*dy_berg
+	#dlon_berg=(180/np.pi)*(1/R_earth)*(1/cos(lat_init*np.pi/180))*dx_berg
+	for i in range(Number_of_bergs):
+		#Finding latittude
+		lat.append(lat_init+(dlat_dy*dy_berg[i]))
+		#Finding longitude
+		if adjust_lat_ref==True:
+			lat_ref=lat_init+(dlat_dy*dy_berg[i])
+			#print lat_ref
+		dlon_dx=(180/np.pi)*(1/R_earth)*(1/np.cos(lat_ref*np.pi/180)) #Note that this depends on the latitude of the iceberg. Could approx this with lat_init.
+		lon.append(lon_init+(dlon_dx*dx_berg[i] ))
+
+	return [Number_of_bergs, lat, lon] 
+	
+def Create_lat_lon_grid(lat_min,lat_max,lon_min,lon_max, N_lat, N_lon):
+	grd_lat=np.linspace(lat_min,lat_max,N_lat)
+	grd_lon=np.linspace(lon_min,lon_max,N_lon)
+	field=np.zeros((N_lat,N_lon))
+
+	return [grd_lat, grd_lon, field]
+	
+def Projecting_to_local_cartesian(lat0, lon0, lat_corner, lon_corner, R_earth):
+	#Creates a local tangent plan around an iceberg at lat0, lon0
+	d_lat=(lat_corner-lat0)
+	d_lon=(lon_corner-lon0)
+
+	dy=R_earth*(np.pi/180.0)*d_lat
+	dx=R_earth*(np.pi/180.0)*cos(lat0*(np.pi/180))*d_lon
+	#dx=R_earth*(np.pi/180.0)*cos(lat_corner*(np.pi/180))*d_lon
+
+	return dy,dx
+
+
+def find_corners_of_cell(lat_berg,lon_berg,grd_lat,grd_lon):
+	j=np.sum(grd_lat<lat_berg)
+	i=np.sum(grd_lon<lon_berg)
+	print lat_berg,lon_berg
+	print grd_lat[j-1],  grd_lat[j]
+	print grd_lon[i-1],  grd_lon[i]
+	i1=i-1 ; j1=j-1
+	i2=i ; j2=j-1
+	i3=i   ; j3=j
+	i4=i-1   ; j4=j
+
+	return [j1,j2,j3,j4,i1,i2,i3,i4]
+
+def plot_grid_cell_and_point(lat_berg, lon_berg, lat1, lat2, lat3, lat4, lon1, lon2, lon3, lon4):
+	plt.plot(lon_berg,lat_berg,'o')
+	#plt.plot(np.array([lon1, lon2]), np.array([lat1, lat2]))
+	#plt.plot(np.array([lon2, lon3]), np.array([lat2, lat3]))
+	plt.plot(np.array([lon1, lon2, lon3, lon4, lon1]), np.array([lat1, lat2, lat3, lat4, lat1]))
+	plt.plot(lon1,lat1,'*r')
+	plt.plot(lon2,lat2,'*c')
+	plt.plot(lon4,lat3,'*g')
+	plt.plot(lon4,lat4,'*b')
+	eps_lat=(lat3-lat2)/2.
+	eps_lon=(lon2-lon1)/2.
+	#print 'lon:',  lon1,lon2, lon3, lon4
+	#print 'lat:', lat1,lat2, lat3, lat4
+	print eps_lat, eps_lon
+	plt.ylim([lat2-eps_lat, lat3+eps_lat])
+	plt.xlim([lon1-eps_lon, lon2+eps_lon])
+
+
+####################################################################################################################################################
+##########################################################  Main Program   #########################################################################
+####################################################################################################################################################
+
+def main():
+
+	#Parameters
+	R_earth=6360000.0
+	Radius=5000.0 #In meters
+
+	#Lat Lon Parameters
+	lat_min=20.0 ;	lat_max=50.0 ;	N_lat=5
+	lon_min=0.0  ;	lon_max=40.0 ;	N_lon=5
+	
+	
+	
+
+
+
+	#Defining Lat Lon
+	(grd_lat, grd_lon, field)= Create_lat_lon_grid(lat_min,lat_max,lon_min,lon_max, N_lat, N_lon)
+
+	#Creating Icebergs
+	#(Number_of_bergs, lat_berg, lon_berg)=Create_icebergs(Radius, R_earth)
+
+
+
+	lat_berg=32.0
+	lon_berg=22.2
+
+	#Finding grid index of cell of berg:
+	j1,j2,j3,j4,i1,i2,i3,i4	=find_corners_of_cell(lat_berg,lon_berg,grd_lat,grd_lon)
+	lat1=grd_lat[j1] ; lat2=grd_lat[j2]; lat3=grd_lat[j3]; lat4=grd_lat[j4]
+	lon1=grd_lon[i1] ; lon2=grd_lon[i2]; lon3=grd_lon[i3]; lon4=grd_lon[i4]
+	i_berg=i1 ;j_berg=j1 #Lower left point
+
+
+	#Converting points to tangent plane
+	(y_berg,x_berg)= Projecting_to_local_cartesian(lat_berg, lon_berg, lat_berg, lon_berg, R_earth)
+	(y1,x1)= Projecting_to_local_cartesian(lat_berg, lon_berg, lat1, lon1, R_earth)
+	(y2,x2)= Projecting_to_local_cartesian(lat_berg, lon_berg, lat2, lon2, R_earth)
+	(y3,x3)= Projecting_to_local_cartesian(lat_berg, lon_berg, lat3, lon3, R_earth)
+	(y4,x4)= Projecting_to_local_cartesian(lat_berg, lon_berg, lat4, lon4, R_earth)
+
+	#Normalization of the shape in tangent plane
+	#x_cell=(x_berg-x[i_val])/sqrt(grid_area)+0.5
+
+
+
+	#Plotting everything
+	plt.figure(figsize=(16,8))
+	plt.subplot(1,2,1)
+	plot_grid_cell_and_point(lat_berg,lon_berg, lat1, lat2, lat3, lat4, lon1, lon2, lon3, lon4)
+	plt.xlabel('lon') ; plt.ylabel('lat') ; 
+	plt.subplot(1,2,2)
+	plot_grid_cell_and_point(y_berg,x_berg, y1, y2, y3, y4, x1, x2, x3, x4)
+	plt.xlabel('x') ; plt.ylabel('y') ; 
+	print x1,x2,x3,x4
+	print y1,y2,y3,y4
+		
+
+
+
+
+
+	#Plotting berg positions
+	#plt.pcolor(grd_lon,grd_lat,field)
+	#plt.colorbar
+	#plt.scatter(lon_berg, lat_berg,c='red')
+
+	plt.show()
+	print 'Script complete'
+
+
+
+if __name__ == '__main__':
+	main()
+	#sys.exit(main())
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/test/Iceberg_repository/Scripts_and_analysis/flat_isomip_create.py b/test/Iceberg_repository/Scripts_and_analysis/flat_isomip_create.py
new file mode 100755
index 0000000..9338dff
--- /dev/null
+++ b/test/Iceberg_repository/Scripts_and_analysis/flat_isomip_create.py
@@ -0,0 +1,71 @@
+#!/usr/bin/env python
+
+###############################################################################################
+from netCDF4 import Dataset
+import numpy as np
+import os
+import numpy
+import netCDF4 as nc
+#import matplotlib
+#import matplotlib.pyplot as plt
+#from pylab import *
+#import pdb
+#import argparse
+#This combination allows you to access the varibale imputted from the command line.
+#import sys
+
+#Clear screen
+def main():
+
+	os.system('clear')
+	input_filename='input_files/isomip_ice_shelf1.nc'
+	new_filename='output_files/flat_isomip_ice_shelf1.nc'
+
+	#f=Dataset(input_geometry_filename,'r')
+	#g=Dataset(new_filename,'w') # w if for creating a file
+
+	rho_ice=850.
+
+	with nc.Dataset(input_filename) as file:
+		thick = file.variables['thick'][:,:]
+		area = file.variables['area'][:,:]
+		height = file.variables['height'][:,:]
+
+	M= thick.shape
+	ny=M[0]
+	nx=M[1]
+	print nx,ny
+	print thick.shape
+
+	#Setting thickness to a prescribed value
+	prescribed_thickness=1.
+	thick[np.where(thick>0)]=prescribed_thickness
+
+	
+	#Creating the file
+	g=Dataset(new_filename,'w') # w if for creating a file
+
+	yt=g.createDimension('yt',ny)
+	xt=g.createDimension('xt',nx)
+
+	thick_h=g.createVariable('thick','f4',('yt','xt'))
+	g.variables['thick'][:]=thick>0
+	thick_h=g.createVariable('area','f4',('yt','xt'))
+	g.variables['area'][:]=area
+	height_h=g.createVariable('height','f4',('yt','xt'))
+	g.variables['height'][:]=height
+
+	g.sync()
+	g.close()
+
+
+
+
+
+	print 'Script complete'
+
+
+
+if __name__ == '__main__':
+        main()
+        #sys.exit(main())
diff --git a/test/Iceberg_repository/Scripts_and_analysis/grid_cartesian_create.py b/test/Iceberg_repository/Scripts_and_analysis/grid_cartesian_create.py
new file mode 100755
index 0000000..6aa3510
--- /dev/null
+++ b/test/Iceberg_repository/Scripts_and_analysis/grid_cartesian_create.py
@@ -0,0 +1,395 @@
+
+# coding: utf-8
+
+# In[2]:
+
+import scipy.io.netcdf
+import numpy
+get_ipython().magic('pylab inline')
+
+
+# Model grid will have ni x nj h-point grid cells
+
+# In[3]:
+
+nj,ni = 40,240
+
+
+# A mosaic file has a supergrid of an integer refinement (e.g. 2*ni x 2*nj cells)
+
+# In[4]:
+
+snj, sni = 2*nj, 2*ni
+
+
+# Uniform resolution of the ocean model grid will be dxo x dyo
+
+# In[5]:
+
+dxo = 2.e3
+dyo = 2.e3
+
+
+# Using a supergrid refinement of 2, the grid lengths, area and coordinates are:
+
+# In[6]:
+
+dx = (0.5 * dxo) * numpy.ones((snj+1,sni))
+dy = (0.5 * dyo) * numpy.ones((snj,sni+1))
+area = (0.25 * (dxo * dyo)) * numpy.ones((snj,sni))
+x = numpy.zeros((snj+1,sni+1))
+x[:,1:] = numpy.cumsum( dx, axis=-1 )
+y = numpy.zeros((snj+1,sni+1))
+y[1:,:] = numpy.cumsum( dy, axis=-2 )
+
+
+# In[7]:
+
+# A helper function to use when writing strings in a netcdf file
+def set_string(variable, value):
+    """Sets "variable" to "value" padded with blanks where
+    "variable" is a netcdf variable object and "value" is a string."""
+    variable[:] = '\000' * variable.shape[0]
+    variable[:len(value)] = value
+
+
+# Create a netcdf3 horizontal ocean-grid file...
+
+# In[8]:
+
+rg = scipy.io.netcdf_file('ocean_hgrid.nc','w',version=2)
+
+
+# In[9]:
+
+rg.createDimension('nx',sni)
+rg.createDimension('ny',snj)
+rg.createDimension('nxp',sni+1)
+rg.createDimension('nyp',snj+1)
+rg.createDimension('string',255)
+
+
+# In[10]:
+
+dx_h = rg.createVariable('dx','f8',('nyp','nx',))
+dx_h.units = 'm'
+dy_h = rg.createVariable('dy','f8',('ny','nxp',))
+dy_h.units = 'm'
+area_h = rg.createVariable('area','f8',('ny','nx',))
+area_h.units = 'm2'
+x_h = rg.createVariable('x','f8',('nyp','nxp',))
+x_h.units = 'm'
+y_h = rg.createVariable('y','f8',('nyp','nxp',))
+y_h.units = 'm'
+tile = rg.createVariable('tile','c',('string',))
+
+
+# In[11]:
+
+dx_h[:,:] = dx[:,:]
+dy_h[:,:] = dy[:,:]
+area_h[:,:] = area[:,:]
+x_h[:,:] = x[:,:]
+y_h[:,:] = y[:,:]
+tile[:] = '\000' * 255
+tile[:5] = 'tile1'
+set_string(tile,'tile1')
+
+
+# In[12]:
+
+rg.close()
+
+
+# Create a netcdf3 ocean-mask file...
+
+# In[13]:
+
+rg = scipy.io.netcdf_file('ocean_mask.nc','w',version=2)
+rg.createDimension('nx',ni)
+rg.createDimension('ny',nj)
+mask = rg.createVariable('mask','f4',('ny','nx',))
+mask[:,:] = 1.
+rg.close()
+
+
+# Create a mosaic description for the above grid file...
+
+# In[14]:
+
+rg = scipy.io.netcdf_file('ocean_mosaic.nc','w',version=2)
+rg.createDimension('ntiles',1)
+rg.createDimension('string',255)
+mosaic = rg.createVariable('mosaic','c',('string',))
+mosaic.standard_name = 'grid_mosaic_spec'
+mosaic.children = 'contacts'
+mosaic.grid_descriptor = ''
+gridlocation = rg.createVariable('gridlocation','c',('string',))
+gridlocation.standard_name = 'grid_file_location'
+gridfiles = rg.createVariable('gridfiles','c',('ntiles','string',))
+gridtiles = rg.createVariable('gridtiles','c',('ntiles','string',))
+rg.grid_version = '0.2'
+# Fill in data
+mosaic[:] = '\000' * 255
+mosaic[:12] = 'ocean_mosaic'
+gridlocation[:] = '\000' * 255
+gridlocation[:2] = './'
+gridfiles[:] = '\000' * 255
+gridfiles[0,:14] = 'ocean_hgrid.nc'
+gridtiles[:] = '\000' * 255
+gridtiles[0,:5] = 'tile1'
+rg.close()
+
+
+# In[15]:
+
+get_ipython().system('pwd')
+
+
+# In[16]:
+
+# Fake a ocean_topog.nc file
+rg = scipy.io.netcdf_file('ocean_topog.nc','w',version=2)
+rg.createDimension('nx',ni)
+rg.createDimension('ny',nj)
+rg.createDimension('ntiles',1)
+depth = rg.createVariable('depth','f4',('ny','nx',))
+depth[:,:] = 1000.
+depth[-1,-1] =0
+rg.close()
+
+
+# In[17]:
+
+#fre_nctools/tools/make_quick_mosaic/make_quick_mosaic --input_mosaic ocean_mosaic.nc --ocean_topog ocean_topog.nc
+
+
+# In[18]:
+
+rg = scipy.io.netcdf_file('atmos_mosaic_tile1Xland_mosaic_tile1_BLAH.nc','w',version=2) # atmos_mosaic_tile1Xland_mosaic_tile1.nc
+rg.createDimension('string',255)
+rg.createDimension('ncells',1)
+rg.createDimension('two',2)
+contact = rg.createVariable('contact','c',('string',))
+contact.standard_name = 'grid_contact_spec'
+contact.contact_type = 'exchange'
+contact.parent1_cell = 'tile1_cell'
+contact.parent2_cell = 'tile2_cell'
+contact.xgrid_area_field = 'xgrid_area'
+contact.distant_to_parent1_centroid = 'tile1_distance'
+contact.distant_to_parent2_centroid = 'tile2_distance'
+tile1_cell = rg.createVariable('tile1_cell','f8',('ncells','two',))
+tile1_cell.standard_name = 'parent_cell_indices_in_mosaic1'
+tile2_cell = rg.createVariable('tile2_cell','f8',('ncells','two',))
+tile2_cell.standard_name = 'parent_cell_indices_in_mosaic2'
+xgrid_area = rg.createVariable('xgrid_area','f8',('ncells',))
+xgrid_area.standard_name = 'exchange_grid_area'
+xgrid_area.units = 'm2'
+tile1_distance = rg.createVariable('tile1_distance','f8',('ncells','two'))
+tile1_distance.standard_name = 'distance_from_parent1_cell_centroid'
+tile2_distance = rg.createVariable('tile2_distance','f8',('ncells','two'))
+tile2_distance.standard_name = 'distance_from_parent2_cell_centroid'
+rg.grid_version = '0.2'
+# Fill in data
+contact[:] = '\000' * 255
+contact[:37] = 'atmos_mosaic:tile1::land_mosaic:tile1'
+tile1_cell[:] = [ni,nj]
+tile2_cell[:] = [ni,nj]
+xgrid_area[:] = dxo * dyo
+tile1_distance[:] = 0.
+tile2_distance[:] = 0.
+rg.close()
+
+
+# In[19]:
+
+rg = scipy.io.netcdf_file('atmos_mosaic_tile1Xocean_mosaic_tile1_BLAH.nc','w',version=2) # atmos_mosaic_tile1Xocean_mosaic_tile1.nc
+rg.createDimension('string',255)
+rg.createDimension('ncells',ni*nj-1) # -1 is for a single land point
+rg.createDimension('two',2)
+contact = rg.createVariable('contact','c',('string',))
+contact.standard_name = 'grid_contact_spec'
+contact.contact_type = 'exchange'
+contact.parent1_cell = 'tile1_cell'
+contact.parent2_cell = 'tile2_cell'
+contact.xgrid_area_field = 'xgrid_area'
+contact.distant_to_parent1_centroid = 'tile1_distance'
+contact.distant_to_parent2_centroid = 'tile2_distance'
+tile1_cell = rg.createVariable('tile1_cell','f8',('ncells','two',))
+tile1_cell.standard_name = 'parent_cell_indices_in_mosaic1'
+tile2_cell = rg.createVariable('tile2_cell','f8',('ncells','two',))
+tile2_cell.standard_name = 'parent_cell_indices_in_mosaic2'
+xgrid_area = rg.createVariable('xgrid_area','f8',('ncells',))
+xgrid_area.standard_name = 'exchange_grid_area'
+xgrid_area.units = 'm2'
+tile1_distance = rg.createVariable('tile1_distance','f8',('ncells','two'))
+tile1_distance.standard_name = 'distance_from_parent1_cell_centroid'
+tile2_distance = rg.createVariable('tile2_distance','f8',('ncells','two'))
+tile2_distance.standard_name = 'distance_from_parent2_cell_centroid'
+rg.grid_version = '0.2'
+# Fill in data
+contact[:] = '\000' * 255
+contact[:37] = 'atmos_mosaic:tile1::land_mosaic:tile1'
+tile1_cell[:] = [ni,nj]
+tile2_cell[:] = [ni,nj]
+xgrid_area[:] = dxo * dyo
+for j in range(nj):
+    for i in range(ni):
+        if (i,j) != (ni-1,nj-1):
+            tile1_cell[i+ni*j] = [i,j]
+            tile2_cell[i+ni*j] = [i,j]
+            tile1_distance[i+ni*j] = [0,0]
+            tile2_distance[i+ni*j] = [0,0]
+            xgrid_area[i+ni*j] = dxo * dyo
+rg.close()
+
+
+# In[20]:
+
+rg = scipy.io.netcdf_file('land_mosaic_tile1Xocean_mosaic_tile1_BLAH.nc','w',version=2) # land_mosaic_tile1Xocean_mosaic_tile1.nc
+rg.createDimension('string',255)
+rg.createDimension('ncells',ni*nj-1) # -1 is for a single land point
+rg.createDimension('two',2)
+contact = rg.createVariable('contact','c',('string',))
+contact.standard_name = 'grid_contact_spec'
+contact.contact_type = 'exchange'
+contact.parent1_cell = 'tile1_cell'
+contact.parent2_cell = 'tile2_cell'
+contact.xgrid_area_field = 'xgrid_area'
+contact.distant_to_parent1_centroid = 'tile1_distance'
+contact.distant_to_parent2_centroid = 'tile2_distance'
+tile1_cell = rg.createVariable('tile1_cell','f8',('ncells','two',))
+tile1_cell.standard_name = 'parent_cell_indices_in_mosaic1'
+tile2_cell = rg.createVariable('tile2_cell','f8',('ncells','two',))
+tile2_cell.standard_name = 'parent_cell_indices_in_mosaic2'
+xgrid_area = rg.createVariable('xgrid_area','f8',('ncells',))
+xgrid_area.standard_name = 'exchange_grid_area'
+xgrid_area.units = 'm2'
+tile1_distance = rg.createVariable('tile1_distance','f8',('ncells','two'))
+tile1_distance.standard_name = 'distance_from_parent1_cell_centroid'
+tile2_distance = rg.createVariable('tile2_distance','f8',('ncells','two'))
+tile2_distance.standard_name = 'distance_from_parent2_cell_centroid'
+rg.grid_version = '0.2'
+# Fill in data
+contact[:] = '\000' * 255
+contact[:37] = 'atmos_mosaic:tile1::land_mosaic:tile1'
+tile1_cell[:] = [ni,nj]
+tile2_cell[:] = [ni,nj]
+xgrid_area[:] = dxo * dyo
+for j in range(nj):
+    for i in range(ni):
+        if (i,j) != (ni-1,nj-1):
+            tile1_cell[i+ni*j] = [i,j]
+            tile2_cell[i+ni*j] = [i,j]
+            tile1_distance[i+ni*j] = [0,0]
+            tile2_distance[i+ni*j] = [0,0]
+            xgrid_area[i+ni*j] = dxo * dyo
+rg.close()
+
+
+# In[24]:
+
+rg = scipy.io.netcdf_file('mosaic_BLAH.nc','w',version=2) # land_mosaic_tile1Xocean_mosaic_tile1.nc
+rg.createDimension('string',255)
+rg.createDimension('nfile_aXo',1) # -1 is for a single land point
+rg.createDimension('nfile_aXl',1) # -1 is for a single land point
+rg.createDimension('nfile_lXo',1) # -1 is for a single land point
+
+atm_mosaic_dir = rg.createVariable('atm_mosaic_dir','c',('string',))
+atm_mosaic_dir.standard_name = 'directory_storing_atmosphere_mosaic'
+
+atm_mosaic_file = rg.createVariable('atm_mosaic_file','c',('string',))
+atm_mosaic_file.standard_name = 'atmosphere_mosaic_file_name'
+
+atm_mosaic = rg.createVariable('atm_mosaic','c',('string',))
+atm_mosaic.standard_name = 'atmosphere_mosaic_name'
+
+lnd_mosaic_dir = rg.createVariable('lnd_mosaic_dir','c',('string',))
+lnd_mosaic_dir.standard_name = 'directory_storing_land_mosaic'
+
+lnd_mosaic_file = rg.createVariable('lnd_mosaic_file','c',('string',))
+lnd_mosaic_file.standard_name = 'land_mosaic_file_name'
+
+lnd_mosaic = rg.createVariable('lnd_mosaic','c',('string',))
+lnd_mosaic.standard_name = 'land_mosaic_name'
+
+ocn_mosaic_dir = rg.createVariable('ocn_mosaic_dir','c',('string',))
+ocn_mosaic_dir.standard_name = 'directory_storing_ocean_mosaic'
+
+ocn_mosaic_file = rg.createVariable('ocn_mosaic_file','c',('string',))
+ocn_mosaic_file.standard_name = 'ocean_mosaic_file_name'
+
+ocn_mosaic = rg.createVariable('ocn_mosaic','c',('string',))
+ocn_mosaic.standard_name = 'ocean_mosaic_name'
+
+
+ocn_topog_dir = rg.createVariable('ocn_topog_dir','c',('string',))
+ocn_mosaic_dir.standard_name = 'directory_storing_ocean_topog'
+
+ocn_topog_file = rg.createVariable('ocn_topog_file','c',('string',))
+ocn_topog_file.standard_name = 'ocean_topog_file_name'
+
+aXo_file = rg.createVariable('aXo_file','c',('string',))
+aXo_file.standard_name = 'atmXocn_exchange_grid_file'
+
+aXl_file = rg.createVariable('aXl_file','c',('string',))
+aXl_file.standard_name = 'atmXlnd_exchange_grid_file'
+
+lXo_file = rg.createVariable('lXo_file','c',('string',))
+lXo_file.standard_name = 'lndXocn_exchange_grid_file'
+
+#Global attributes
+rg.grid_version = '0.2'
+rg.code_version = "$Name:  $"
+rg.history = "/net2/aja/workspace/MOM6-examples/ice_ocean_SIS2/OM4_025/preprocessing/fre_nctools/tools/make_quick_mosaic/make_quick_mosaic --input_mosaic ocean_mosaic.nc --ocean_topog ocean_topog.nc"
+# Fill in data
+atm_mosaic_dir[:] = '\000' * 255
+atm_mosaic_dir[:2] = './'
+
+atm_mosaic_file[:] = '\000' * 255
+atm_mosaic_file[:15] = 'ocean_mosaic.nc'
+
+atm_mosaic[:] = '\000' * 255
+atm_mosaic[:12] = 'atmos_mosaic'
+
+lnd_mosaic_dir[:] = '\000' * 255
+lnd_mosaic_dir[:2] = './'
+
+lnd_mosaic_file[:] = '\000' * 255
+lnd_mosaic_file[:15] = 'ocean_mosaic.nc'
+
+lnd_mosaic[:] = '\000' * 255
+lnd_mosaic[:11] = 'land_mosaic'
+
+ocn_mosaic_dir[:] = '\000' * 255
+ocn_mosaic_dir[:2] = './'
+
+ocn_mosaic_file[:] = '\000' * 255
+ocn_mosaic_file[:15] = 'ocean_mosaic.nc'
+
+ocn_mosaic[:] = '\000' * 255
+ocn_mosaic[:12] = 'ocean_mosaic'
+
+ocn_topog_dir[:] = '\000' * 255
+ocn_topog_dir[:2] = './'
+
+ocn_topog_file[:] = '\000' * 255
+ocn_topog_file[:14] = 'ocean_topog.nc'
+
+aXo_file[:] = '\000' * 255
+aXo_file[:40] = 'atmos_mosaic_tile1Xocean_mosaic_tile1.nc'
+
+aXl_file[:] = '\000' * 255
+aXl_file[:39] = 'atmos_mosaic_tile1Xland_mosaic_tile1.nc'
+
+lXo_file[:] = '\000' * 255
+lXo_file[:39] = 'land_mosaic_tile1Xocean_mosaic_tile1.nc'
+
+rg.close()
+
+
+
+# In[ ]:
+
+
+
diff --git a/test/Iceberg_repository/Scripts_and_analysis/hexagon_area.py b/test/Iceberg_repository/Scripts_and_analysis/hexagon_area.py
new file mode 100755
index 0000000..08ef572
--- /dev/null
+++ b/test/Iceberg_repository/Scripts_and_analysis/hexagon_area.py
@@ -0,0 +1,1472 @@
+#!/usr/bin/env python
+
+#First import the netcdf4 library
+from netCDF4 import Dataset  # http://code.google.com/p/netcdf4-python/
+import numpy as np  # http://code.google.com/p/netcdf4-python/
+import matplotlib
+import math
+import os
+matplotlib.use("GTKAgg")
+#from pylab import *
+#import matplotlib.pyplot as plt
+import pdb
+import netCDF4 as nc
+
+
+
+#######################
+
+def Divide_hexagon_into_4_quadrants_old(x0,y0,H):
+	S=(2/np.sqrt(3))*H
+	Area_hex=3*(np.sqrt(3)/2)*(S**2)  #Area of the hexagon (should be equal to Area/grid_area, since it is not dim)  - check this
+	#print 'y0,H',y0, H	
+	#Defining boundaries of hexagon, and if statements to see which side of the boundary you are on
+	W1= False ; W2=False ;W3=False ;W4=False ;W5=False ;W6=False ;H1=False ;V1=False ;V2=False
+	W1=(-y0<-np.sqrt(3)*(-x0) + ((np.sqrt(3)*(S))));#upper right
+	W2=(-y0<(H));#Top
+	W3=(-y0<np.sqrt(3)*(-x0) + ((np.sqrt(3)*(S))));#Upper left
+	W4=(-y0<np.sqrt(3)*(-x0) + (-(np.sqrt(3)*(S))));#Lower right
+	W5=(-y0>-H);#Bottom
+	W6=(-y0<-np.sqrt(3)*(-x0) + (-(np.sqrt(3)*(S))));#Lower left
+		
+
+	T1=(-x0<S) #Right
+	T2=(-y0<(H));#Top
+	T3= (-x0>-S) #Left
+	T4=(-y0>-H);#Bottom
+
+	H1=(y0<0);
+	V1=(x0<-(S/2));
+	V2=(x0<(S/2));
+	  
+	#Deciding if the origin is within the hexagon
+	#print W1 , W2 , W3 , W4 , W5 , W6
+	#if In_hex:
+	#	print In_hex
+		
+	#Calculating the area of the top and bottom half of the hexagon, 2 Cases for the majority above and below the y0=0 line
+	#(and two more for the hexagon totally above and below the y0=0 line)
+	if abs(y0)<H:
+		Trapesium=((np.sqrt(3)*H)-(abs(y0)/np.sqrt(3)))*(H-abs(y0));
+		if y0>=0:
+			Area_Lower=Trapesium;
+			Area_Upper=Area_hex-Trapesium;
+		else:
+			Area_Upper=Trapesium;
+			Area_Lower=Area_hex-Trapesium;
+	else:
+		if y0>=0:
+			Area_Lower=0.;
+			Area_Upper=Area_hex;
+		else: 
+			Area_Lower=Area_hex;
+			Area_Upper=0.;
+
+	#Calcularing Left and Right area of the hexagon, about the x0=0 line, 3 cases:
+	#(and two more for when the hexagon is totally to the left or right of the x0=0 line)
+	if abs(x0)<S:
+		if abs(x0)<S/2:
+			Rectangle=(abs(x0)*2*H);
+			Big_side =(Area_hex/2) +Rectangle;
+			Small_side=Area_hex-Big_side;
+		else:
+			Triangle=(np.sqrt(3))*((S-abs(x0))**2);
+			Small_side=Triangle;
+			Big_side=Area_hex-Small_side;
+		if x0>=0.:
+			Area_right=Big_side;
+			Area_left=Small_side;
+		else:
+			Area_right=Small_side;
+			Area_left=Big_side;
+	else:
+		if x0>=0.:
+			Area_right=Area_hex;
+			Area_left=0.;
+		else:
+			Area_right=0.;
+			Area_left=Area_hex;
+
+	In_hex= W1 & W2 & W3 & W4 & W5 & W6;
+	In_hex_box=T1 & T2 & T3 & T4
+	Area_Q1=0.; Area_Q2=0. ; Area_Q3=0.; Area_Q4=0.;
+	Sector=0
+	#if In_hex==False: #Then the hexagon is completely contained in the middle cell
+	if In_hex_box==False: #Then the hexagon is completely contained in the middle cell
+		Sector=-1
+		#mass_on_ocean[i,j,5]=mass_on_ocean[i,j,5]+Mass
+		if min(Area_Upper,Area_Lower)==0.:
+			Sector=-2
+			if Area_Upper==0.:
+				Area_Q3=Area_left;
+				Area_Q4=Area_right;
+			if Area_Lower==0.:
+				Area_Q1=Area_right;
+				Area_Q2=Area_left;
+
+		elif min(Area_right,Area_left)==0.:
+			Sector=-3
+			if Area_right==0.:
+				Area_Q2=Area_Upper;
+				Area_Q3=Area_Lower;
+		
+			if Area_left==0.:
+				Area_Q1=Area_Upper;
+				Area_Q4=Area_Lower;
+		
+
+		#yCxC=1.
+		#print 'out of hex'
+
+	else:
+		#Determine which sector within the hexagon you are in. (sectors 1 to 6 go counter clockwise starting with top right)
+		if (H1==True):  #Bottom half
+			if V1:
+				#if W1==False:
+				if ((y0+(np.sqrt(3)*(x0+S)))<=0.):
+					Sector=1;
+				else:
+					Sector=2;
+			elif (V1==False) & (V2==True):
+				Sector=3;
+			else:  
+				#if (W3==True):
+				if ((y0-(np.sqrt(3)*(x0-S)))>=0.):
+					Sector=4;
+				else:
+					Sector=5;
+		else:  #Bottom half
+			if V1:
+				#if W6==False:
+				if ((y0 -(np.sqrt(3)*(x0+S)))>=0.):
+					Sector=10;
+				else:
+					Sector=9;
+			elif (V1==False) & (V2==True):
+				Sector=8;
+			else:  
+				#if (W4==True):
+				if ((y0+(np.sqrt(3)*(x0-S)))<=0.):
+					Sector=7;
+				else:
+					Sector=6;
+
+		#print Sector
+
+		#If the hexagon is in Sector 1,3,4 or 6, then the intersetion of the hexagon and the corresponding sector forms a baby triangle
+		#If the hexagon is in Sector 2,5 then the intersetion of the hexagon and the corresponding sector forms a baby trapesoid
+		if Sector==2 or Sector==4  or Sector==7 or Sector==9:
+			Baby_triangle=(1/(2*np.sqrt(3)))*((-abs(y0)+(np.sqrt(3)*(S-abs(x0))))**2);
+		else:
+			#Baby_trap= (H-abs(y0)) * ((-H-abs(y0)+(2*np.sqrt(3)*(S-abs(x0))))/(2*np.sqrt(3)));  
+			Baby_trap=(H-abs(y0))*((S-abs(x0) - ((H+abs(y0))/(2*np.sqrt(3))))) ;
+
+		#Finally, we assign the correct areas in each quadrant (Q1,Q2,Q3,Q4), depending on which sector you are in.
+		C1=0.;C2=0.;C3=0.;C4=0.;
+
+		#Corner cases
+		if Sector==2:
+			Area_Q1=Baby_triangle;
+			Area_Q2=Area_Upper-Area_Q1
+			Area_Q3=Area_left-Area_Q2
+			Area_Q4=Area_right-Area_Q1
+
+		if Sector==4:
+			Area_Q2=Baby_triangle;
+			Area_Q1=Area_Upper-Area_Q2
+			Area_Q3=Area_left-Area_Q2
+			Area_Q4=Area_right-Area_Q1
+
+		if Sector==7:
+			Area_Q3=Baby_triangle;
+			Area_Q2=Area_left-Area_Q3
+			Area_Q1=Area_Upper-Area_Q2
+			Area_Q4=Area_right-Area_Q1
+
+		if Sector==9:
+			Area_Q4=Baby_triangle;
+			Area_Q1=Area_right-Area_Q4
+			Area_Q2=Area_Upper-Area_Q1
+			Area_Q3=Area_left-Area_Q2
+	
+		#Center cases
+		if Sector==3:
+			if x0<=0.:
+				Area_Q1=Baby_trap;
+				Area_Q2=Area_Upper-Area_Q1;
+				Area_Q3=Area_left-Area_Q2;
+				Area_Q4=Area_right-Area_Q1;
+			else:
+				Area_Q2=Baby_trap;
+				Area_Q1=Area_Upper-Area_Q2;
+				Area_Q3=Area_left-Area_Q2;
+				Area_Q4=Area_right-Area_Q1;
+			
+		if Sector==8:
+			if x0<=0.:
+				Area_Q4=Baby_trap;
+				Area_Q3=Area_Lower-Area_Q4;
+				Area_Q1=Area_right-Area_Q4;
+				Area_Q2=Area_Upper-Area_Q1;
+			else:
+				Area_Q3=Baby_trap;
+				Area_Q4=Area_Lower-Area_Q3;
+				Area_Q1=Area_right-Area_Q4;
+				Area_Q2=Area_Upper-Area_Q1;
+
+		#Outside triangle cases:
+		if Sector==1:
+			Area_Q1=0.;
+			Area_Q2=Area_Upper;
+			Area_Q4=Area_right;
+			Area_Q3=Area_left-Area_Q2;
+		
+		if Sector==5:
+			Area_Q2=0.;
+			Area_Q1=Area_Upper;
+			Area_Q3=Area_left;
+			Area_Q4=Area_Lower-Area_Q3;
+
+		if Sector==6:
+			Area_Q3=0.;
+			Area_Q2=Area_left;
+			Area_Q4=Area_Lower;
+			Area_Q1=Area_right-Area_Q4;
+		
+		if Sector==10:
+			Area_Q4=0.;
+			Area_Q3=Area_Lower;
+			Area_Q1=Area_right;
+			Area_Q2=Area_left-Area_Q3;
+
+		#print x0,y0,Sector
+	return [Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4]
+
+
+
+def Hexagon_into_quadrants_using_triangles_across_lines(x0,y0,H,theta,  Px, Py, Qx, Qy, Rx, Ry, Sx, Sy ):
+	#In this routine, the hexagon is divided across lines PQ, RS.	 
+	#Length of side of Hexagon
+	S=(2/np.sqrt(3))*H;  
+
+	#Finding positions of corners
+	C1x=S           ; C1y=0.  #Corner 1 (right)
+	C2x=H/np.sqrt(3.)  ; C2y=H;  #Corner 2 (top right)
+	C3x=-H/np.sqrt(3.) ; C3y=H;  #Corner 3 (top left)
+	C4x=-S          ; C4y=0.; #Corner 4 (left)
+	C5x=-H/np.sqrt(3.) ; C5y=-H; #Corner 5 (bottom right)
+	C6x=H/np.sqrt(3.)  ; C6y=-H; #Corner 6 (bottom right)
+
+	#Finding positions of corners
+	[C1x,C1y]=rotate_and_translate(C1x,C1y,theta,x0,y0)
+	[C2x,C2y]=rotate_and_translate(C2x,C2y,theta,x0,y0)
+	[C3x,C3y]=rotate_and_translate(C3x,C3y,theta,x0,y0)
+	[C4x,C4y]=rotate_and_translate(C4x,C4y,theta,x0,y0)
+	[C5x,C5y]=rotate_and_translate(C5x,C5y,theta,x0,y0)
+	[C6x,C6y]=rotate_and_translate(C6x,C6y,theta,x0,y0)
+	 
+	#Area of Hexagon is the sum of the triangles
+	[T12_Area,T12_Q1,T12_Q2,T12_Q3,T12_Q4]=Triangle_divided_into_four_parts(x0,y0,C1x,C1y,C2x,C2y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T012
+	[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]=Triangle_divided_into_four_parts(x0,y0,C2x,C2y,C3x,C3y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
+	[T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4]=Triangle_divided_into_four_parts(x0,y0,C3x,C3y,C4x,C4y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T034
+	[T45_Area,T45_Q1,T45_Q2,T45_Q3,T45_Q4]=Triangle_divided_into_four_parts(x0,y0,C4x,C4y,C5x,C5y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
+	[T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4]=Triangle_divided_into_four_parts(x0,y0,C5x,C5y,C6x,C6y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
+	[T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4]=Triangle_divided_into_four_parts(x0,y0,C6x,C6y,C1x,C1y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
+	
+	#Area of Hexagon is the sum of the triangles
+	#print '1:', Triangle_divided_into_four_parts(x0,y0,C1x,C1y,C2x,C2y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T012
+	#print '1b:', Triangle_divided_into_four_quadrants(x0,y0,C1x,C1y,C2x,C2y); #T012
+	#print '2', Triangle_divided_into_four_parts(x0,y0,C2x,C2y,C3x,C3y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
+	#print '2b',Triangle_divided_into_four_quadrants(x0,y0,C2x,C2y,C3x,C3y); #T023
+	#print '3:',Triangle_divided_into_four_parts(x0,y0,C3x,C3y,C4x,C4y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T034
+	#print '3b',Triangle_divided_into_four_quadrants(x0,y0,C3x,C3y,C4x,C4y); #T034
+	#print '4',Triangle_divided_into_four_parts(x0,y0,C4x,C4y,C5x,C5y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
+	#print '4b:',Triangle_divided_into_four_quadrants(x0,y0,C4x,C4y,C5x,C5y); #T023
+	#print '5', Triangle_divided_into_four_parts(x0,y0,C5x,C5y,C6x,C6y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
+	#print '5b',Triangle_divided_into_four_quadrants(x0,y0,C5x,C5y,C6x,C6y); #T023
+	#print '6:',Triangle_divided_into_four_parts(x0,y0,C6x,C6y,C1x,C1y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
+	#print '6b',Triangle_divided_into_four_quadrants(x0,y0,C6x,C6y,C1x,C1y); #T023
+
+	#Summing up
+	Area_hex=T12_Area+T23_Area+T34_Area+T45_Area+T56_Area+T61_Area;
+	Area_Q1=T12_Q1+T23_Q1+T34_Q1+T45_Q1+T56_Q1+T61_Q1;
+	Area_Q2=T12_Q2+T23_Q2+T34_Q2+T45_Q2+T56_Q2+T61_Q2;
+	Area_Q3=T12_Q3+T23_Q3+T34_Q3+T45_Q3+T56_Q3+T61_Q3;
+	Area_Q4=T12_Q4+T23_Q4+T34_Q4+T45_Q4+T56_Q4+T61_Q4;
+	#Area_Q4=Area_hex-(Area_Q1+Area_Q2+Area_Q3)
+
+
+
+
+	#if  (abs(x0-(-0.186672393129))<0.00001)  and (abs(y0-(-0.436171))<0.00001):
+	#	print 'Triangle 1,xo,y0',x0,y0 
+	#	print 'Triangle 1H,S',H,S 
+	#	print 'Triangle 1,Corners',C1x,C1y,C2x,C2y 
+	#	print 'Triangle 1, Area full', T12_Area
+	#	print 'Triangle 1, Area T1', T12_Q1
+	#	print 'Triangle 1, Area T2', T12_Q2
+	#	print 'Triangle 1, Area T3', T12_Q3
+	#	print 'Triangle 1, Area T4', T12_Q4 
+	#	#print 'Triangle 2',x0,y0,C2x,C2y,C3x,C3y,T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4
+	#	#print 'Triangle 3',x0,y0,C3x,C3y,C4x,C4y,T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4 
+	#	#print 'Triangle 4',x0,y0,C4x,C4y,C5x,C5y,T45_Area,T45_Q1,T45_Q2,T45_Q3,T45_Q4
+	#	#print 'Triangle 5',x0,y0,C5x,C5y,C6x,C6y,T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4 
+	#	#print 'Triangle 6',x0,y0,C6x,C6y,C1x,C1y,T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4
+
+	Area_Q1=max(Area_Q1,0.);
+	Area_Q2=max(Area_Q2,0.);
+	Area_Q3=max(Area_Q3,0.);
+	Area_Q4=max(Area_Q4,0.);
+
+
+	Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
+	if (abs(Error)>0.01):
+		print  'diamonds, hex error, H,x0,y0, Error', H, x0 , y0, Error
+        	print 'diamonds, hex error, Areas',Area_hex, (Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
+	      	print 'Hexagon error is large!!'
+
+
+
+	#Adjust Areas so that the error is zero by subtracting the error from the largest sector.
+	if  (((Area_Q1>=Area_Q2) and (Area_Q1>=Area_Q3)) and (Area_Q1>=Area_Q4)):
+		#print 'fix1',Error
+		Area_Q1=Area_Q1+Error
+	elif  (((Area_Q2>=Area_Q1) and (Area_Q2>=Area_Q3)) and (Area_Q2>=Area_Q4)):
+		#print 'fix2', Error
+		Area_Q2=Area_Q2+Error
+	elif  (((Area_Q3>=Area_Q1) and (Area_Q3>=Area_Q2)) and (Area_Q3>=Area_Q4)):
+		#print 'fix3',Error
+		Area_Q3=Area_Q3+Error
+   	elif  (((Area_Q4>=Area_Q1) and (Area_Q4>=Area_Q2)) and (Area_Q4>=Area_Q3)):
+		#print 'fix4',Error
+		Area_Q4=Area_Q4+Error
+	else:
+		print 'There is some thing wrong with this hexagon. Something very wrong'
+
+	#Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
+	Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
+	if ((abs(Error)>0.01)):
+		print 'The hexagon error is still too large!!!', Error
+
+
+
+	return [Area_hex ,Area_Q1, Area_Q2, Area_Q3, Area_Q4]
+
+def Hexagon_into_quadrants_using_triangles(x0,y0,H,theta):
+		 
+	#Length of side of Hexagon
+	S=(2/np.sqrt(3))*H;  
+
+	#Finding positions of corners
+	C1x=S           ; C1y=0.  #Corner 1 (right)
+	C2x=H/np.sqrt(3.)  ; C2y=H;  #Corner 2 (top right)
+	C3x=-H/np.sqrt(3.) ; C3y=H;  #Corner 3 (top left)
+	C4x=-S          ; C4y=0.; #Corner 4 (left)
+	C5x=-H/np.sqrt(3.) ; C5y=-H; #Corner 5 (bottom right)
+	C6x=H/np.sqrt(3.)  ; C6y=-H; #Corner 6 (bottom right)
+
+	#Finding positions of corners
+	[C1x,C1y]=rotate_and_translate(C1x,C1y,theta,x0,y0)
+	[C2x,C2y]=rotate_and_translate(C2x,C2y,theta,x0,y0)
+	[C3x,C3y]=rotate_and_translate(C3x,C3y,theta,x0,y0)
+	[C4x,C4y]=rotate_and_translate(C4x,C4y,theta,x0,y0)
+	[C5x,C5y]=rotate_and_translate(C5x,C5y,theta,x0,y0)
+	[C6x,C6y]=rotate_and_translate(C6x,C6y,theta,x0,y0)
+	 
+	#Area of Hexagon is the sum of the triangles
+	[T12_Area,T12_Q1,T12_Q2,T12_Q3,T12_Q4]=Triangle_divided_into_four_quadrants(x0,y0,C1x,C1y,C2x,C2y); #T012
+	[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]=Triangle_divided_into_four_quadrants(x0,y0,C2x,C2y,C3x,C3y); #T023
+	[T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4]=Triangle_divided_into_four_quadrants(x0,y0,C3x,C3y,C4x,C4y); #T034
+	[T45_Area,T45_Q1,T45_Q2,T45_Q3,T45_Q4]=Triangle_divided_into_four_quadrants(x0,y0,C4x,C4y,C5x,C5y); #T023
+	[T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4]=Triangle_divided_into_four_quadrants(x0,y0,C5x,C5y,C6x,C6y); #T023
+	[T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4]=Triangle_divided_into_four_quadrants(x0,y0,C6x,C6y,C1x,C1y); #T023
+
+	#Summing up
+	Area_hex=T12_Area+T23_Area+T34_Area+T45_Area+T56_Area+T61_Area;
+	Area_Q1=T12_Q1+T23_Q1+T34_Q1+T45_Q1+T56_Q1+T61_Q1;
+	Area_Q2=T12_Q2+T23_Q2+T34_Q2+T45_Q2+T56_Q2+T61_Q2;
+	Area_Q3=T12_Q3+T23_Q3+T34_Q3+T45_Q3+T56_Q3+T61_Q3;
+	Area_Q4=T12_Q4+T23_Q4+T34_Q4+T45_Q4+T56_Q4+T61_Q4;
+	#Area_Q4=Area_hex-(Area_Q1+Area_Q2+Area_Q3)
+
+
+
+
+	#if  (abs(x0-(-0.186672393129))<0.00001)  and (abs(y0-(-0.436171))<0.00001):
+	#	print 'Triangle 1,xo,y0',x0,y0 
+	#	print 'Triangle 1H,S',H,S 
+	#	print 'Triangle 1,Corners',C1x,C1y,C2x,C2y 
+	#	print 'Triangle 1, Area full', T12_Area
+	#	print 'Triangle 1, Area T1', T12_Q1
+	#	print 'Triangle 1, Area T2', T12_Q2
+	#	print 'Triangle 1, Area T3', T12_Q3
+	#	print 'Triangle 1, Area T4', T12_Q4 
+	#	#print 'Triangle 2',x0,y0,C2x,C2y,C3x,C3y,T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4
+	#	#print 'Triangle 3',x0,y0,C3x,C3y,C4x,C4y,T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4 
+	#	#print 'Triangle 4',x0,y0,C4x,C4y,C5x,C5y,T45_Area,T45_Q1,T45_Q2,T45_Q3,T45_Q4
+	#	#print 'Triangle 5',x0,y0,C5x,C5y,C6x,C6y,T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4 
+	#	#print 'Triangle 6',x0,y0,C6x,C6y,C1x,C1y,T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4
+
+	Area_Q1=max(Area_Q1,0.);
+	Area_Q2=max(Area_Q2,0.);
+	Area_Q3=max(Area_Q3,0.);
+	Area_Q4=max(Area_Q4,0.);
+
+
+	Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
+	if (abs(Error)>0.01):
+		print  'diamonds, hex error, H,x0,y0, Error', H, x0 , y0, Error
+        	print 'diamonds, hex error, Areas',Area_hex, (Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
+	      	print 'Hexagon error is large!!'
+
+
+
+	#Adjust Areas so that the error is zero by subtracting the error from the largest sector.
+	if  (((Area_Q1>=Area_Q2) and (Area_Q1>=Area_Q3)) and (Area_Q1>=Area_Q4)):
+		#print 'fix1',Error
+		Area_Q1=Area_Q1+Error
+	elif  (((Area_Q2>=Area_Q1) and (Area_Q2>=Area_Q3)) and (Area_Q2>=Area_Q4)):
+		#print 'fix2', Error
+		Area_Q2=Area_Q2+Error
+	elif  (((Area_Q3>=Area_Q1) and (Area_Q3>=Area_Q2)) and (Area_Q3>=Area_Q4)):
+		#print 'fix3',Error
+		Area_Q3=Area_Q3+Error
+   	elif  (((Area_Q4>=Area_Q1) and (Area_Q4>=Area_Q2)) and (Area_Q4>=Area_Q3)):
+		#print 'fix4',Error
+		Area_Q4=Area_Q4+Error
+	else:
+		print 'There is some thing wrong with this hexagon. Something very wrong'
+
+	#Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
+	Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
+	if ((abs(Error)>0.01)):
+		print 'The hexagon error is still too large!!!', Error
+
+
+
+	return [Area_hex ,Area_Q1, Area_Q2, Area_Q3, Area_Q4]
+
+
+def find_intersect_using_metric(Ax,Ay, Bx, By, Cx, Cy):
+	#Line AB
+	[AB_px, AB_py]=intercept_of_a_line(Ax,Ay,Bx,By,'x'); #x_intercept
+	[AB_qx, AB_qy]=intercept_of_a_line(Ax,Ay,Bx,By,'y'); #y_intercept
+	M_AB=point_in_interval_metric(Ax,Ay,Bx,By,AB_px,AB_py, AB_qx, AB_qy)
+	#Line AC
+	[AC_px, AC_py]=intercept_of_a_line(Ax,Ay,Cx,Cy,'x'); #x_intercept
+	[AC_qx, AC_qy]=intercept_of_a_line(Ax,Ay,Cx,Cy,'y'); #y_intercept
+	M_AC=point_in_interval_metric(Ax,Ay,Cx,Cy,AC_px, AC_py,AC_qx, AC_qy)
+	#Line AB
+	[BC_px, BC_py]=intercept_of_a_line(Bx,By,Cx,Cy,'x'); #x_intercept
+	[BC_qx, BC_qy]=intercept_of_a_line(Bx,By,Cx,Cy,'y'); #y_intercept
+	M_BC=point_in_interval_metric(Bx,By,Cx,Cy,BC_px,BC_py,BC_qx, BC_qy)
+
+	if M_AB<=min(M_BC, M_AC):
+		return AB_px, AB_py, AB_qx, AB_qy
+	elif M_AC<=min(M_BC, M_AB):
+		return AC_px, AC_py, AC_qx, AC_qy
+	elif M_BC<=min(M_AC, M_AB):
+		return BC_px, BC_py, BC_qx, BC_qy
+	else: 
+		print 'You should not get here'
+		halt
+
+def find_intersect_using_metric_and_lines(Ax,Ay, Bx, By, Cx, Cy,Px, Py, Qx, Qy, Rx, Ry, Sx, Sy):
+	#Line AB
+	[AB_px, AB_py]=intercept_of_two_lines(Ax,Ay,Bx,By,Px, Py, Qx, Qy); #PQ_intercept
+	[AB_qx, AB_qy]=intercept_of_two_lines(Ax,Ay,Bx,By,Rx, Ry, Sx, Sy); #RS_intercept
+	M_AB=point_in_interval_metric(Ax,Ay,Bx,By,AB_px,AB_py, AB_qx, AB_qy)
+	#Line AC
+	[AC_px, AC_py]=intercept_of_two_lines(Ax,Ay,Cx,Cy,Px, Py, Qx, Qy); #PQ_intercept
+	[AC_qx, AC_qy]=intercept_of_two_lines(Ax,Ay,Cx,Cy, Rx, Ry, Sx, Sy); #RS_intercept
+	M_AC=point_in_interval_metric(Ax,Ay,Cx,Cy,AC_px, AC_py,AC_qx, AC_qy)
+	#Line AB
+	[BC_px, BC_py]=intercept_of_two_lines(Bx,By,Cx,Cy,Px, Py, Qx, Qy); #PQ_intercept
+	[BC_qx, BC_qy]=intercept_of_two_lines(Bx,By,Cx,Cy, Rx, Ry, Sx, Sy); #RS_intercept
+	M_BC=point_in_interval_metric(Bx,By,Cx,Cy,BC_px,BC_py,BC_qx, BC_qy)
+
+	if M_AB<=min(M_BC, M_AC):
+		return AB_px, AB_py, AB_qx, AB_qy
+	elif M_AC<=min(M_BC, M_AB):
+		return AC_px, AC_py, AC_qx, AC_qy
+	elif M_BC<=min(M_AC, M_AB):
+		return BC_px, BC_py, BC_qx, BC_qy
+	else: 
+		print 'You should not get here'
+		halt
+
+
+def point_in_interval_metric(Ax,Ay,Bx,By,px,py,qx,qy):
+	metric=0.0
+	#print 'Ax,Ay,Bx,By',Ax,Ay,Bx,By,px,py,qx,qy
+	#print 'px,py,qx,qy',px,py,qx,qy
+
+	#Finds a metric for how close a point is to being inside an interval. If it is inside, then metric is equal to zero.
+	Mx1= max(px - max(Ax,Bx),0.)  #Zero is px <= max(Ax,Bx)
+	Mx2= max( min(Ax,Bx)-px ,0.)  #Zero is px <= max(Ax,Bx)
+	My1= max(py - max(Ay,By),0.)  #Zero is px <= max(Ax,Bx)
+	My2= max( min(Ay,By)-py ,0.)  #Zero is px <= max(Ax,Bx)
+	p_metric=abs(Mx1)+abs(Mx2)+abs(My1)+abs(My2)
+	#print 'Mx1, Mx2, My1, My2', Mx1, Mx2, My1, My2 
+
+	#Finds a metric for how close a point is to being inside an interval. If it is inside, then metric is equal to zero.
+	Mx1= max(qx - max(Ax,Bx),0.)  #Zero is qx <= max(Ax,Bx)
+	Mx2= max( min(Ax,Bx)-qx ,0.)  #Zero is qx <= max(Ax,Bx)
+	My1= max(qy - max(Ay,By),0.)  #Zero is qx <= max(Ax,Bx)
+	My2= max( min(Ay,By)-qy ,0.)  #Zero is qx <= max(Ax,Bx)
+	q_metric=abs(Mx1)+abs(Mx2)+abs(My1)+abs(My2)
+
+	metric=p_metric+q_metric
+	return metric
+
+
+def Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy):
+	Area_key_quadrant=0.0 #Initializing
+	Area_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
+	#if Area_triangle==0.0:
+	#	Area_triangle=0.0 ; Area_Q1=0.0 ; Area_Q2=0.0; Area_Q3=0.0; Area_Q4= 0.0
+	#	return [Area_triangle, Area_Q1, Area_Q2 ,Area_Q3 ,Area_Q4]
+
+
+	#Calculating area across axes
+	[Area_Upper ,Area_Lower]=divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,'x');
+	[Area_Right ,Area_Left]=divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,'y');
+	 
+	#Decide if the origin is in the triangle
+	if point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.):  #Then you have to divide area 4 ways.
+		#Find a line in the triangle that cuts both axes in/on the trianlge
+	    	[px, py]=intercept_of_a_line(Ax,Ay,Bx,By,'x'); #x_intercept
+	    	[qx, qy]=intercept_of_a_line(Ax,Ay,Bx,By,'y'); #y_intercept
+	    	if (point_in_interval(Ax,Ay,Bx,By,px,py) & point_in_interval(Ax,Ay,Bx,By,qx,qy))==False:
+			[px, py]=intercept_of_a_line(Ax,Ay,Cx,Cy,'x'); #x_intercept
+			[qx, qy]=intercept_of_a_line(Ax,Ay,Cx,Cy,'y'); #y_intercept
+			if (point_in_interval(Ax,Ay,Cx,Cy,px,py) & point_in_interval(Ax,Ay,Cx,Cy,qx,qy))==False:
+				[px, py]=intercept_of_a_line(Bx,By,Cx,Cy,'x'); #x_intercept
+				[qx, qy]=intercept_of_a_line(Bx,By,Cx,Cy,'y'); #y_intercept
+				if (point_in_interval(Bx,By,Cx,Cy,px,py) & point_in_interval(Bx,By,Cx,Cy,qx,qy))==False:
+					#point_in_interval_metric
+					[px, py, qx, qy]= find_intersect_using_metric(Ax,Ay, Bx, By, Cx, Cy)
+					#print 'Houston, we have a problem'
+					#plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy)
+					#halt
+
+		#Assigning quadrants. Key_quadrant is the quadrant with the baby triangle in it.
+		Area_key_quadrant=Area_of_triangle(px,py,qx,qy,0.,0.);
+		if Area_key_quadrant>0.0:
+			if px>=0. and qy>=0.: #First quadrant
+				Key_quadrant=1;
+			elif px<0. and qy>=0.:  #Second quadrant
+				Key_quadrant=2;
+			elif px<0. and qy<0.:
+				Key_quadrant=3;  #Third quadrant
+			else:
+				Key_quadrant=4;  #Forth quadrant
+	    
+	#if (point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.) is False) or (Area_key_quadrant==0):
+	if Area_key_quadrant==0:
+	#else:  #Then at least one quadrant is empty, and this can be used to find the areas in the other quadrant.  Assigning quadrants. Key_quadrant is the empty quadrant.
+		#print 'Mother...'
+		#print 'Ax, Ay',Ax,Ay
+		#print 'Bx, By',Bx,By
+		#print 'Cx, Cy',Cx,Cy
+		Area_key_quadrant=0;
+		if (((Ax>0. and Ay>0.) or (Bx>0. and By>0.) or (Cx>0. and Cy>0.))==False)  and (Area_Upper+Area_Right<=Area_triangle):
+		#if (((Ax>=0. and Ay>=0.) or (Bx>=0. and By>=0.) or (Cx>=0. and Cy>=0.))==False)  and (Area_Upper+Area_Right<=Area_triangle):
+			#No points land in this quadrant and triangle does not cross the quadrant
+			Key_quadrant=1;
+		elif  (((Ax<0. and Ay>0) or (Bx<0. and By>0.) or (Cx<0. and Cy>0.))==False)  and (Area_Upper+Area_Left<=Area_triangle):
+			#elif  (((Ax<0. and Ay>=0) or (Bx<0. and By>=0.) or (Cx<0. and Cy>=0.))==False)  and (Area_Upper+Area_Left<=Area_triangle):
+			Key_quadrant=2;
+		elif (((Ax<0. and Ay<0.) or (Bx<0. and By<0.) or (Cx<0. and Cy<0.))==False) & (Area_Lower+Area_Left<=Area_triangle):
+			#elif (((Ax<0. and Ay<0.) or (Bx<0. and By<0.) or (Cx<0. and Cy<0.))==False) & (Area_Lower+Area_Left<=Area_triangle):
+			Key_quadrant=3;
+		else:
+			Key_quadrant=4;
+	
+	#Assign values to quadrants
+	if Key_quadrant==1:
+		Area_Q1=Area_key_quadrant;
+		Area_Q2=Area_Upper-Area_Q1;
+		Area_Q4=Area_Right-Area_Q1;
+		#Area_Q3=Area_Left-Area_Q2;
+		Area_Q3=Area_triangle-Area_Q1-Area_Q2-Area_Q4;
+	elif Key_quadrant==2:
+		Area_Q2=Area_key_quadrant;
+		Area_Q1=Area_Upper-Area_Q2;
+		Area_Q4=Area_Right-Area_Q1;
+		#Area_Q3=Area_Left-Area_Q2;
+		Area_Q3=Area_triangle-Area_Q1-Area_Q2-Area_Q4;
+	elif Key_quadrant==3:
+		Area_Q3=Area_key_quadrant;
+		Area_Q2=Area_Left-Area_Q3;
+		Area_Q1=Area_Upper-Area_Q2;
+		#Area_Q4=Area_Right-Area_Q1;
+		Area_Q4=Area_triangle-Area_Q1-Area_Q2-Area_Q3;
+	elif Key_quadrant==4:
+		Area_Q4=Area_key_quadrant;
+		Area_Q1=Area_Right-Area_Q4;
+		Area_Q2=Area_Upper-Area_Q1;
+		#Area_Q3=Area_Left-Area_Q2;
+		Area_Q3=Area_triangle-Area_Q1-Area_Q2-Area_Q4;
+	else:
+	    print 'Help, I need somebody, help!'
+	    halt
+	
+	Area_Q1=max(Area_Q1,0.); 
+	Area_Q2=max(Area_Q2,0.);
+	Area_Q3=max(Area_Q3,0.);
+	Area_Q4=max(Area_Q4,0.); 
+
+	Error=abs(Area_Q1+Area_Q2+Area_Q3+Area_Q4-Area_triangle)
+	#Marker 1
+	if Error>1e-15:
+	#if True:
+		print 'The triangles are not accurate enough. This is a problem!'
+		print 'Triangle corners: ' ,Ax,Ay,Bx,By,Cx,Cy
+		print 'Error',Error
+		print 'Key_quadrant', Key_quadrant 
+		print 'Area Key_quadrant', Area_key_quadrant 
+		print 'Upper, Lower',Area_Upper ,Area_Lower
+		print 'Left, Right ', Area_Right ,Area_Left
+		print 'Point in triangle', point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.)
+		#plt.plot(np.array([Ax,Bx,Cx,Ax]),np.array([Ay, By, Cy,Ay]))
+		#plt.plot(np.array([-0.5,0.5]),np.array([0.,0.]),'k')
+		#plt.plot(np.array([0.,0.]),np.array([-0.5,0.5]),'k')
+		#plt.plot(0,0,'*')
+		#plt.show()
+		#halt
+		#return
+
+	return [Area_triangle, Area_Q1, Area_Q2 ,Area_Q3 ,Area_Q4]
+
+def find_quadrant_using_lines(x0 , y0 , Px, Py, Qx, Qy, Rx, Ry, Sx, Sy): #Finding "quadrant" of point using lines PQ, RS as axes.  (This assumes PQ is like the x axis and RS like the y axis)
+	#above_PQ=Point_above_line(x0,y0, Px, Py, Qx, Qy)
+	#above_RS=Point_above_line(x0,y0, Rx, Ry, Sx, Sy)
+	above_PQ=Above_on_below_line(x0,y0, Px, Py, Qx, Qy)
+	above_RS=Above_on_below_line(x0,y0, Rx, Ry, Sx, Sy)
+	if (above_PQ==1) and (above_RS==1):
+		quadrant=1
+	elif (above_PQ==1) and (above_RS==-1):
+		quadrant=2
+	elif (above_PQ==-1) and (above_RS==-1):
+		quadrant=3
+	elif (above_PQ==-1) and (above_RS==1):
+		quadrant=4
+	else:
+		#print 'Point not in a quadrant!'
+		quadrant=0
+		#halt
+
+	return quadrant
+
+def Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ):#Divides the triangle into 4 parts, across two intersecting lines. PQ, RS intersect at origin (for now)
+	Area_key_quadrant=0.0
+	Area_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
+	#if Area_triangle==0.0:
+	#	Area_triangle=0.0 ; Area_Q1=0.0 ; Area_Q2=0.0; Area_Q3=0.0; Area_Q4= 0.0
+	#	return [Area_triangle, Area_Q1, Area_Q2 ,Area_Q3 ,Area_Q4]
+
+
+	#Calculating area across axes
+	[Area_Upper ,Area_Lower]=divding_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy);
+	[Area_Right ,Area_Left] =divding_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Rx, Ry, Sx, Sy);
+	 
+	#Decide if the origin is in the triangle
+	if point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.):  #Then you have to divide area 4 ways.
+		#Find a line in the triangle that cuts both axes in/on the trianlge
+	    	[px, py]=intercept_of_two_lines(Ax,Ay,Bx,By,Px, Py, Qx, Qy); #PQ_intercept
+	    	[qx, qy]=intercept_of_two_lines(Ax,Ay,Bx,By,Rx, Ry, Sx, Sy); #RS_intercept
+	    	if (point_in_interval(Ax,Ay,Bx,By,px,py) & point_in_interval(Ax,Ay,Bx,By,qx,qy))==False:
+			[px, py]=intercept_of_two_lines(Ax,Ay,Cx,Cy,Px, Py, Qx, Qy); #PQ_intercept
+			[qx, qy]=intercept_of_two_lines(Ax,Ay,Cx,Cy,Rx, Ry, Sx, Sy); #RS_intercept
+			if (point_in_interval(Ax,Ay,Cx,Cy,px,py) & point_in_interval(Ax,Ay,Cx,Cy,qx,qy))==False:
+				[px, py]=intercept_of_two_lines(Bx,By,Cx,Cy,Px, Py, Qx, Qy); #PQ_intercept
+				[qx, qy]=intercept_of_two_lines(Bx,By,Cx,Cy,Rx, Ry, Sx, Sy); #RS_intercept
+				if (point_in_interval(Bx,By,Cx,Cy,px,py) & point_in_interval(Bx,By,Cx,Cy,qx,qy))==False:
+					#print 'Houston, we have a problem'
+					[px, py, qx, qy]= find_intersect_using_metric_and_lines(Ax,Ay, Bx, By, Cx, Cy,Px, Py, Qx, Qy, Rx, Ry, Sx, Sy)
+					#plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy)
+					#halt
+
+		#Assigning quadrants. Key_quadrant is the quadrant with the baby triangle in it.
+		Area_key_quadrant=Area_of_triangle(px,py,qx,qy,0.,0.);
+		if px>=0. and qy>=0.: #First quadrant  (I think the zeros here are because the PQ, RS intersect at zero)
+			Key_quadrant=1;
+		elif px<0. and qy>=0.:  #Second quadrant
+			Key_quadrant=2;
+		elif px<0. and qy<0.:
+			Key_quadrant=3;  #Third quadrant
+		else:
+			Key_quadrant=4;  #Forth quadrant
+	    
+	if Area_key_quadrant==0:
+		#else:  #Then at least one quadrant is empty, and this can be used to find the areas in the other quadrant.  Assigning quadrants. Key_quadrant is the empty quadrant.
+		#print 'Mother...'
+		#print 'Ax, Ay',Ax,Ay
+		#print 'Bx, By',Bx,By
+		#print 'Cx, Cy',Cx,Cy
+		Area_key_quadrant=0;
+		#Finding which quadrant the triangle points fall in.
+		A_quad = find_quadrant_using_lines(Ax,Ay,Px, Py, Qx, Qy, Rx, Ry, Sx, Sy)
+		B_quad = find_quadrant_using_lines(Bx,By,Px, Py, Qx, Qy, Rx, Ry, Sx, Sy)
+		C_quad = find_quadrant_using_lines(Cx,Cy,Px, Py, Qx, Qy, Rx, Ry, Sx, Sy)
+		#print 'A_quad, B_quad, C_quad',A_quad, B_quad, C_quad
+
+		if (((A_quad==1) or (B_quad==1) or (C_quad==1))==False)  and (Area_Upper+Area_Right<=Area_triangle):
+			#No points land in this quadrant and triangle does not cross the quadrant
+			Key_quadrant=1;
+		elif  (((A_quad==2) or (B_quad==2) or (C_quad==2))==False)  and (Area_Upper+Area_Left<=Area_triangle):
+			Key_quadrant=2;
+		elif (((A_quad==3) or (B_quad==3) or (C_quad==3))==False) & (Area_Lower+Area_Left<=Area_triangle):
+			Key_quadrant=3;
+		else:
+			Key_quadrant=4;
+	
+		#print Key_quadrant
+	#Assign values to quadrants
+	if Key_quadrant==1:
+		Area_Q1=Area_key_quadrant;
+		Area_Q2=Area_Upper-Area_Q1;
+		Area_Q4=Area_Right-Area_Q1;
+		#Area_Q3=Area_Left-Area_Q2;
+		Area_Q3=Area_triangle-Area_Q1-Area_Q2-Area_Q4;
+	elif Key_quadrant==2:
+		Area_Q2=Area_key_quadrant;
+		Area_Q1=Area_Upper-Area_Q2;
+		Area_Q4=Area_Right-Area_Q1;
+		#Area_Q3=Area_Left-Area_Q2;
+		Area_Q3=Area_triangle-Area_Q1-Area_Q2-Area_Q4;
+	elif Key_quadrant==3:
+		Area_Q3=Area_key_quadrant;
+		Area_Q2=Area_Left-Area_Q3;
+		Area_Q1=Area_Upper-Area_Q2;
+		#Area_Q4=Area_Right-Area_Q1;
+		Area_Q4=Area_triangle-Area_Q1-Area_Q2-Area_Q3;
+	elif Key_quadrant==4:
+		Area_Q4=Area_key_quadrant;
+		Area_Q1=Area_Right-Area_Q4;
+		Area_Q2=Area_Upper-Area_Q1;
+		#Area_Q3=Area_Left-Area_Q2;
+		Area_Q3=Area_triangle-Area_Q1-Area_Q2-Area_Q4;
+	else:
+	    print 'Help, I need somebody, help!'
+	    halt
+	
+	Area_Q1=max(Area_Q1,0.); 
+	Area_Q2=max(Area_Q2,0.);
+	Area_Q3=max(Area_Q3,0.);
+	Area_Q4=max(Area_Q4,0.); 
+
+	Error=abs(Area_Q1+Area_Q2+Area_Q3+Area_Q4-Area_triangle)
+	if Error>1e-15:
+	#if True:
+		print 'The triangles are not accurate enough. This is a problem!'
+		print 'Triangle corners: ' ,Ax,Ay,Bx,By,Cx,Cy
+		print 'Error',Error
+		print 'Key_quadrant', Key_quadrant 
+		print 'Area Key_quadrant', Area_key_quadrant 
+		print 'Upper, Lower',Area_Upper ,Area_Lower
+		print 'Left, Right ', Area_Right ,Area_Left
+		print 'Point in triangle', point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.)
+		#return
+
+	return [Area_triangle, Area_Q1, Area_Q2 ,Area_Q3 ,Area_Q4]
+
+def divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1):
+	if axes1=='x':  #Use the y-coordinates for if statements to see which side of the line you are on
+		A0=Ay; B0=By;  C0=Cy;
+	if axes1=='y':  #Use the y-coordinates for if statements to see which side of the line you are on
+		A0=Ax; B0=Bx;  C0=Cx;
+ 
+	#print 'A0,B0,C0', A0,B0,C0
+	A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
+	if B0*C0>0.: #then B and C are on the same side  (and non-zero)
+		#print 'HHHH1'	
+		if A0*B0>=0.: #then all three on the the same side (if it equals zero, then A0=0 and the otehrs are not)
+			if (A0>0.)  or  (A0==0. and  B0>0.):
+				Area_positive= A_triangle;
+				Area_negative= 0.;
+			else:
+				Area_positive= 0.;
+				Area_negative= A_triangle;
+		else:  #A is on the opposite side to B and C
+			[Area_positive, Area_negative]=Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1);
+
+	elif B0*C0<0.: #then B and C are on the opposite sides
+		#print 'HHHH2'	
+		if A0*B0>=0.:  #then C is all alone
+			[Area_positive, Area_negative]=Area_of_triangle_across_axes(Cx,Cy,Bx,By,Ax,Ay,axes1);
+		else: #then B is all alone
+			[Area_positive, Area_negative]=Area_of_triangle_across_axes(Bx,By,Cx,Cy,Ax,Ay,axes1);
+
+	else:  #This is the case when either B or C is equal to zero (or both), A0 could be zero too.
+		#print 'HHHH3'	
+		if (A0==0. and B0==0. and C0==0.):
+			Area_positive= 0.;
+			Area_negative= 0.;
+		elif (A0*B0<0.)  or  (A0*C0<0.):    #A, B are on opposite sides, and C is zero.  OR  A, C are on opposite sides, and B is zero.
+			[Area_positive, Area_negative]=Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1);
+			#print 'HHHH6'	
+		elif (A0*B0>0.) or (A0*C0>0.) or (abs(A0)>0. and (B0==0.) and (C0==0.)):
+			#print 'HHHH7'	
+		        if (A0>0.):
+		        	Area_positive= A_triangle;
+				Area_negative= 0.;
+        		else:
+				Area_positive= 0.;
+				Area_negative= A_triangle;
+    
+    		elif A0==0.:  #(Also, one of B,C is zero too)
+			#print 'HHHH8'	
+			if B0>0. or C0>0.:
+				Area_positive= A_triangle;
+				Area_negative= 0.;
+			elif B0<0. or C0<0.:
+				Area_positive= 0.;
+				Area_negative= A_triangle;
+		        else:
+				print 'You should not get here1'
+				halt
+    		else:
+			print 'You should not get here2'
+			print Ax,Ay,Bx,By,Cx,Cy
+			halt
+	
+	return [Area_positive, Area_negative]
+
+def divding_triangle_across_line2(Ax,Ay,Bx,By,Cx,Cy,  Px, Py, Qx, Qy ):
+	A0= Above_on_below_line(Ax,Ay, Px, Py, Qx, Qy)
+	B0= Above_on_below_line(Bx,By, Px, Py, Qx, Qy)
+	C0= Above_on_below_line(Cx,Cy, Px, Py, Qx, Qy) 
+	
+	#print 'A0,B0,C0', A0,B0,C0
+	#print Px, Py, Qx, Qy
+ 
+	A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
+	if B0*C0>0.: #then B and C are on the same side  (and non-zero)
+		#print 'GGG1'
+		if A0*B0>=0.: #then all three on the the same side (if it equals zero, then A0=0 and the otehrs are not)
+			if (A0>0.)  or  (A0==0. and  B0>0.):
+				Area_positive= A_triangle;
+				Area_negative= 0.;
+			else:
+				Area_positive= 0.;
+				Area_negative= A_triangle;
+		else:  #A is on the opposite side to B and C
+			[Area_positive, Area_negative]=Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy );
+
+	elif B0*C0<0.: #then B and C are on the opposite sides
+		#print 'GGG2'
+		if A0*B0>=0.:  #then C is all alone
+			[Area_positive, Area_negative]=Area_of_triangle_across_line(Cx,Cy,Bx,By,Ax,Ay, Px, Py, Qx, Qy );
+		else: #then B is all alone
+			[Area_positive, Area_negative]=Area_of_triangle_across_line(Bx,By,Cx,Cy,Ax,Ay, Px, Py, Qx, Qy );
+
+	else:  #This is the case when either B or C is equal to zero (or both), A0 could be zero too.
+		#print 'GGG3'
+		if (A0==0. and B0==0. and C0==0.):
+			Area_positive= 0.;
+			Area_negative= 0.;
+		elif (A0*B0<0.)  or  (A0*C0<0.):    #A, B are on opposite sides, and C is zero.  OR  A, C are on opposite sides, and B is zero.
+			[Area_positive, Area_negative]=Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy);
+			#print 'GGG5', Area_positive, Area_negative
+		elif (A0*B0>0.) or (A0*C0>0.) or (abs(A0)>0. and (B0==0.) and (C0==0.)):
+		        if (A0>0.):
+		        	Area_positive= A_triangle;
+				Area_negative= 0.;
+        		else:
+				Area_positive= 0.;
+				Area_negative= A_triangle;
+    
+    		elif A0==0.:  #(Also, one of B,C is zero too)
+			if B0>0. or C0>0.:
+				Area_positive= A_triangle;
+				Area_negative= 0.;
+			elif B0<0. or C0<0.:
+				Area_positive= 0.;
+				Area_negative= A_triangle;
+		        else:
+				print 'You should not get here1'
+				halt
+    		else:
+			print 'You should not get here2'
+			print Ax,Ay,Bx,By,Cx,Cy
+			halt
+	
+	return [Area_positive, Area_negative]
+
+
+def divding_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy,   Px, Py, Qx, Qy ):  #Triangle is ABC, line is PQ
+	A0= Above_on_below_line(Ax,Ay, Px, Py, Qx, Qy)
+	B0= Above_on_below_line(Bx,By, Px, Py, Qx, Qy)
+	C0= Above_on_below_line(Cx,Cy, Px, Py, Qx, Qy) 
+	#print 'BBB0', A0, B0, C0
+
+	A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
+	# B and C are on the same side of the line
+	#if (Point_above_line(Bx,By, Px, Py, Qx, Qy)==Point_above_line(Cx,Cy, Px, Py, Qx, Qy)) :
+	#if ((B0==C0) and (B0!=0))  or ((B0==0 or C0==0) and np.max(B0,C0)>0.5)   :
+	if ((B0==C0) and (B0!=0))  or ((B0==0 or C0==0))   : #B and C on the same side or B or C is zero
+		#print 'BBB1'
+		[Area_positive, Area_negative]=Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy);
+	else: #then B and C are on the opposite sides
+		#if Point_above_line(Ax,Ay, Px, Py, Qx, Qy)==Point_above_line(Bx,By, Px, Py, Qx, Qy):  #then C is all alone
+		if A0*B0>=0.:  #then C is all alone
+			#print 'BBB2'
+			[Area_positive, Area_negative]=Area_of_triangle_across_line(Cx,Cy,Bx,By,Ax,Ay, Px, Py, Qx, Qy);
+		else: #then B is all alone
+			#print 'BBB3'
+			[Area_positive, Area_negative]=Area_of_triangle_across_line(Bx,By,Cx,Cy,Ax,Ay, Px, Py, Qx, Qy);
+
+	return [Area_positive, Area_negative]
+
+
+def check_if_point_is_on_the_line(Ax,Ay,Bx,By,qx,qy,repeat_calculation=False):
+
+	tol=0.00000000000000;
+	dxc = qx - Ax;
+	dyc = qy - Ay;
+ 
+	dxl = Bx - Ax;
+	dyl = By - Ay;
+ 
+	cross = dxc * dyl - dyc * dxl;
+	
+	if abs(cross)<=tol:
+		point_is_on_line=True
+	else:
+		point_is_on_line=False
+
+	if repeat_calculation is False:
+		if point_is_on_line != check_if_point_is_on_the_line(Bx,By,Ax,Ay,qx,qy, True):
+			point_is_on_line=True
+
+	return point_is_on_line
+
+def intercept_of_a_line(Ax,Ay,Bx,By,axes1):
+	No_intercept_val=100000000000.; #Huge value used to make sure that the intercept is outside the triange in the parralel case. 
+	#No_intercept_val=np.NaN;
+	 
+	if axes1=='x': #x intercept
+		if (Ay==By)==False:
+			x0=Ax -(((Ax-Bx)/(Ay-By))*Ay);
+			y0=0.; 
+		else:
+			x0=No_intercept_val;
+			y0=No_intercept_val;
+	
+	if axes1=='y': #y intercept
+		if (Ax==Bx)==False:
+			x0=0.; 
+			y0=-(((Ay-By)/(Ax-Bx))*Ax)+Ay;  
+		else:
+			x0=No_intercept_val;
+			y0=No_intercept_val;
+	
+	return [x0, y0]
+
+def intercept_of_two_lines(Ax,Ay,Bx,By,Px,Py,Qx,Qy):
+	No_intercept_val=100000000000.; #Huge value used to make sure that the intercept is outside the triange in the parralel case. 
+	#No_intercept_val=np.NaN;
+
+	#One of the lines is actually a point:
+	if ((Ax==Bx) and (Ay==By)) or ((Px==Qx) and (Py==Qy)):
+		x0=No_intercept_val; y0=No_intercept_val;
+		halt6
+	else:
+		if (Ax==Bx):
+			(x0 , y0) =intercept_of_a_line(Px-Ax,Py,Qx-Ax,Qy,'y')
+			x0=Ax
+		#Here we check the other three directions to make code agree to machine precision with old version. The code could skip straight to the else.
+		elif (Px==Qx): 
+			(x0 , y0) =intercept_of_a_line(Ax-Px,Ay,Bx-Px,By,'y')
+			x0=Px
+		elif (Ay==By): 
+			(x0 , y0) =intercept_of_a_line(Px,Py-Ay,Qx,Qy-Ay,'x')
+			y0=Ay
+		elif (Py==Qy): 
+			(x0 , y0) =intercept_of_a_line(Ax,Ay-Py,Bx,By-Py,'x')
+			y0=Py
+		else:
+			m1=(Ay-By)/(Ax-Bx)
+			if (Px==Qx):
+				print 'Stop2'
+				(x0 , y0) =intercept_of_a_line(Ax-Px,Ay,Bx-Px,By,'y')
+				x0=Px
+			else:
+				m2=(Py-Qy)/(Px-Qx)
+				if m1==m2:
+					print 'Stop3'
+					x0=No_intercept_val;
+					y0=No_intercept_val;
+					halt2
+				else:
+					print 'Stop4'
+					x0=(1/(m1-m2))*( (m1*Ax -Ay) -(m2*Px - Py))
+					y0=m1*(x0-Ax)+Ay
+	
+	return [x0, y0]
+
+
+def Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axis1):#In this fuction, A is the point on one side of the axis, and B,C are on the opposite sides
+	#print 'Area_of_triangle_across_axes' ,Ax,Ay,Bx,By,Cx,Cy
+	A_triangle2=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
+	[pABx, pABy]=intercept_of_a_line(Ax,Ay,Bx,By,axis1);
+	[pACx, pACy]=intercept_of_a_line(Ax,Ay,Cx,Cy,axis1);
+	if axis1=='x':
+		A0=Ay; #Value used for if statements (deciding up/down vs left/right)
+	if axis1=='y':
+		A0=Ax; #Value used for if statements (deciding up/down vs left/right)
+	
+	#print 'QQQ', Ax,Ay,pABx,pABy,pACx,pACy
+	A_half_triangle=Area_of_triangle(Ax,Ay,pABx,pABy,pACx,pACy);
+	if (A0>=0.):
+		Area_positive= A_half_triangle;
+		Area_negative= A_triangle2-A_half_triangle;
+
+	else:
+		Area_positive= A_triangle2-A_half_triangle;
+		Area_negative= A_half_triangle;
+
+	return [Area_positive, Area_negative]
+
+def Above_on_below_line(x,y,Px, Py, Qx, Qy): #If the point is above the line, then returns True, otherwise false
+	if Px==Qx:
+		if x>Px:
+			Point_above_line=1.0
+		elif x<Px:
+			Point_above_line=-1.0
+		else:
+			Point_above_line=0.0
+	else:
+		m=(Py-Qy)/(Px-Qx)
+		if y > m*(x-Px) + Py:
+			Point_above_line=1.0
+		elif y < m*(x-Px) + Py:
+			Point_above_line=-1.0
+		else:
+			Point_above_line=0.0
+
+	return Point_above_line
+
+def Point_above_line(x,y,Px, Py, Qx, Qy): #If the point is above the line, then returns True, otherwise false
+	if Px==Qx:
+		if x>=Px:
+			Point_above_line=True
+		else:
+			Point_above_line=False
+	else:
+		m=(Py-Qy)/(Px-Qx)
+		if y >= m*(x-Px) + Py:
+			Point_above_line=True
+		else:
+			Point_above_line=False
+
+	return Point_above_line
+
+
+def Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px,Py, Qx, Qy, debug=False):
+	#In this fuction, B and C are the same side of the line. (I think this works even if B and/or C are on the line too)
+	#A is unknown. PQ is the line.
+	#print 'RRR Area_of_triangle_across_line' ,Ax,Ay,Bx,By,Cx,Cy
+	
+	if (Ax==Bx and Ay==By) or (Ax==Cx and Ay==Cy) or (Cx==Bx and Cy==By):
+		#print 'AAA1'
+		Area_positive=0.0
+		Area_negative=0.0
+	else:
+		#print 'AAA2'
+		A0= Above_on_below_line(Ax,Ay, Px, Py, Qx, Qy)
+		B0= Above_on_below_line(Bx,By, Px, Py, Qx, Qy)
+		C0= Above_on_below_line(Cx,Cy, Px, Py, Qx, Qy) 
+		A_triangle2=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
+
+		if check_if_point_is_on_the_line(Px,Py,Qx,Qy, Ax,Ay):  #Is point A on the line?
+			#print 'AAA3'
+			#if Point_above_line(Bx,By, Px,Py, Qx, Qy) or Point_above_line(Cx,Cy, Px,Py, Qx, Qy):
+			if B0==1 or C0==1:
+				Area_positive= A_triangle2;
+				Area_negative= 0.0;
+			else:
+				Area_positive= 0.0;
+				Area_negative= A_triangle2;
+		else: #If A is not on the line
+			#If A is on the same side of the line as B and C
+			#All on the same side of the line
+			if ((A0==B0 and A0==C0)  or (A0==B0 and C0==0) or (A0==C0 and B0==0)):  
+			#if Point_above_line(Ax,Ay, Px,Py, Qx, Qy) == Point_above_line( Bx,By, Px,Py, Qx, Qy)  and (Point_above_line(Ax,Ay,Px,Py,Qx,Qy)==Point_above_line(Cx,Cy,Px,Py,Qx,Qy)):  
+				#print 'AAA4'
+				#if Point_above_line(Bx,By, Px,Py, Qx, Qy) or Point_above_line(Cx,Cy, Px,Py, Qx, Qy):
+				if A0==1 or C0==1:
+					Area_positive= A_triangle2;
+					Area_negative= 0.0;
+				else:
+					Area_positive= 0.0;
+					Area_negative= A_triangle2;
+			elif (C0==0 and B0==0 and (abs(A0)>0)):  
+				if Point_above_line(Ax,Ay, Px,Py, Qx, Qy):
+					Area_positive= A_triangle2;
+					Area_negative= 0.0;
+				else:
+					Area_positive= 0.0;
+					Area_negative= A_triangle2;
+
+			else:  #If A is not on the same side of the line as B and C
+				#print 'AAA5'
+				[pABx, pABy]=intercept_of_two_lines(Ax,Ay,Bx,By, Px, Py, Qx, Qy);
+				[pACx, pACy]=intercept_of_two_lines(Ax,Ay,Cx,Cy, Px, Py, Qx, Qy);
+				#print 'Tri2', Ax,Ay,pABx,pABy,pACx,pACy
+				
+				A_half_triangle=Area_of_triangle(Ax,Ay,pABx,pABy,pACx,pACy);
+				if Point_above_line(Ax,Ay , Px,Py,Qx,Qy):
+					Area_positive= A_half_triangle;
+					Area_negative= A_triangle2-A_half_triangle;
+				else:
+					Area_positive= A_triangle2-A_half_triangle;
+					Area_negative= A_half_triangle;
+
+	return [Area_positive, Area_negative]
+
+def Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy):
+	Area    =   abs(    0.5*((Ax*(By-Cy))+(Bx*(Cy-Ay))+(Cx*(Ay-By))) );
+	return Area
+
+
+def point_in_interval(Ax,Ay,Bx,By,px,py):
+	point_is_in_interval=False
+	#print 'NNN1'
+	if ((px <= max(Ax,Bx)) and (px >= min(Ax,Bx))):
+		#print 'NNN2', 'py=', py,  'max=',max(Ay,By), 'XXX', (py - max(Ay,By))
+		if ((py <= max(Ay,By)) and (py >= min(Ay,By))):
+			##print 'NNN3'
+			point_is_in_interval=True
+	return point_is_in_interval
+
+def rotate_and_translate(px,py,theta,x0,y0):
+	#This function takes a point px,py, and rotates it clockwise around the origin by theta degrees, and then translates by (x0,y0)
+	 px_temp = (np.cos(theta*np.pi/180.)*px) + (np.sin(theta*np.pi/180.)*py)
+	 py_temp = (-np.sin(theta*np.pi/180.)*px) + (np.cos(theta*np.pi/180.)*py)
+	 px= px_temp +x0
+	 py= py_temp +y0
+	 return [px,py]
+
+
+def point_in_triangle_old(Ax,Ay,Bx,By,Cx,Cy,qx,qy):
+	#if False:
+	if (Ax==qx and Ay==qy) or (Bx==qx and By==qy) or (Cx==qx and Cy==qy):  #Exclude the pathelogical case
+	        	point_is_in_triangle = 0.;
+	else:
+		if (check_if_point_is_on_the_line(Ax,Ay,Bx,By,qx,qy) or (check_if_point_is_on_the_line(Ax,Ay,Cx,Cy,qx,qy)) or (check_if_point_is_on_the_line(Bx,By,Cx,Cy,qx,qy))):
+			point_is_in_triangle = 0;
+		else:
+			#Compute vectors
+			v0x=Cx-Ax;
+			v1x=Bx-Ax;
+			v2x=qx-Ax;
+			v0y=Cy-Ay;
+			v1y=By-Ay;
+			v2y=qy-Ay;
+
+			#%Compute dot products
+			dot00 = (v0x*v0x)+(v0y*v0y);
+			dot01 = (v0x*v1x)+(v0y*v1y);
+			dot02 = (v0x*v2x)+(v0y*v2y);
+			dot11 = (v1x*v1x)+(v1y*v1y);
+			dot12 = (v1x*v2x)+(v1y*v2y);
+
+			#Compute barycentric coordinates
+			invDenom= 1 / ((dot00 * dot11) - (dot01*dot01));
+			u=((dot11*dot02)-(dot01*dot12))*invDenom;
+			v=((dot00*dot12)-(dot01*dot02))*invDenom;
+
+			point_is_in_triangle = (((u)>=0) & ((v)>=0) & ((u+v)<(1)));
+	return point_is_in_triangle
+
+
+
+def point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,qx,qy):
+	point_is_in_triangle = 0;
+
+	if (Ax==qx and Ay==qy) or (Bx==qx and By==qy) or (Cx==qx and Cy==qy):  #Exclude the pathelogical case
+	        	point_is_in_triangle = 0.;
+	else:
+		if (check_if_point_is_on_the_line(Ax,Ay,Bx,By,qx,qy) or (check_if_point_is_on_the_line(Ax,Ay,Cx,Cy,qx,qy)) or (check_if_point_is_on_the_line(Bx,By,Cx,Cy,qx,qy))):
+			point_is_in_triangle = 0;
+		else:
+			l0=(qx-Ax)*(By-Ay)-(qy-Ay)*(Bx-Ax)
+			l1=(qx-Bx)*(Cy-By)-(qy-By)*(Cx-Bx)
+			l2=(qx-Cx)*(Ay-Cy)-(qy-Cy)*(Ax-Cx)
+
+			p0=np.sign( l0);
+			p1=np.sign( l1);
+			p2=np.sign( l2);
+			if (l0 == 0.):
+				p0=0.
+			if (l1==0.):
+				p1=0.
+			if (l2==0.):
+				p2=0.
+			
+			if ( (abs(p0)+abs(p2))+(abs(p1)) == abs((p0+p2)+(p1)) ):
+				point_is_in_triangle = 1;
+	return point_is_in_triangle
+
+
+def roundoff(x,sig_fig):
+	x_roundoff=round(x*(10**(sig_fig)))/(10**(sig_fig))
+	#x_roundoff=(FLOAT (INT(x * (10.**sig_fig) + 0.5)) / (10.**sig_fig))
+	return x_roundoff
+
+
+
+def square_spreading_calculation(x,y,L):
+	xL=min(0.5, max(0., 0.5-(x/L)))
+        xR=min(0.5, max(0., (x/L)+(0.5-(1/L) )))
+        xC=max(0., 1.-(xL+xR))
+        yD=min(0.5, max(0., 0.5-(y/L)))
+        yU=min(0.5, max(0., (y/L)+(0.5-(1/L) )))
+        yC=max(0., 1.-(yD+yU))
+
+def plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy, Px=None, Py=None, Qx=None, Qy=None, Rx=None, Ry=None, Sx=None, Sy=None):
+	if Px is None:
+		Px=-1. ; Py=0. ; Qx=1. ; Qy=0. #x-axis 
+                Rx=0. ; Ry=-1. ; Sx=0. ; Sy=1. #y-axis 
+	plt.plot(np.array([Px, Qx]), np.array([Py, Qy]))
+	plt.plot(np.array([Rx, Sx]), np.array([Ry, Sy]))
+	plt.plot(np.array([Ax, Bx, Cx, Ax]), np.array([Ay, By, Cy, Ay]))
+	plt.plot(np.array([Ax, Bx, Cx, Ax]), np.array([Ay, By, Cy, Ay]),'8')
+	text(Ax,Ay,'A',fontsize=20)
+	text(Bx,By,'B',fontsize=20)
+	text(Cx,Cy,'C',fontsize=20)
+	plt.show()
+
+####################################################################################################################################################
+##########################################################  Main Program   #########################################################################
+####################################################################################################################################################
+
+def main():
+
+	#test_case='hexagon'
+	#test_case='triangle'
+	#test_case='square'
+	#test_case='point_in_triangle'
+	#test_case='line_intercept'
+	#test_case='Point_above_line'
+	#test_case='Triangle_across_line'
+	#test_case='Triangle_into_fours'
+	test_case='many_hexagons'
+
+	if test_case=='line_intercept':
+		Ax=1. ; Ay=1.5 ; Bx=1. ; By=-3.4 
+		Px=0.2; Py=-1.0; Qx=0.2; Qy=2.2
+		(x0,y0)=intercept_of_two_lines(Ax,Ay,Bx,By,Px,Py,Qx,Qy)
+		plt.plot( np.array([Ax, Bx])  , np.array([Ay, By]))
+		plt.plot(np.array([Px, Qx]), np.array([Py, Qy]))
+		plt.plot(x0,y0,'*')
+		#plt.plot(Ax,Ay,'*')
+		#plt.plot(Bx,By,'*')
+		#plt.plot(Px,Py,'*')
+		#plt.plot(Qx,Qy,'*')
+
+		print 'x0, y0' , x0 , y0
+		plt.show()
+
+
+	if test_case=='Triangle_across_line':
+		#y-axis
+		Px=0.0 ; Py=-1.0 ;Qx=0.0 ;Qy=1.0
+		axes1='y'
+
+		#x-axis
+		#Px=-1.0 ; Py=0.0 ;Qx=1.0 ;Qy=0.0
+		#axes1='x'
+
+		N=11 #Choose an odd number
+		count=0
+		for Ax in np.linspace(-0.5 , 0.5 , N):
+			for Ay in np.linspace(-0.5 , 0.5 , N):
+				for Bx in np.linspace(-0.5 , 0.5 , N):
+					for By in np.linspace(-0.5 , 0.5 , N):
+						for Cx in np.linspace(-0.5 , 0.5 , N):
+							for Cy in np.linspace(-0.5 , 0.5 , N):
+								count=count+1
+								if count>0:
+									x=divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1)
+									y=divding_triangle_across_line2(Ax,Ay,Bx,By,Cx,Cy, Px,Py, Qx, Qy)
+									#y=divding_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px,Py, Qx, Qy)
+									#if abs(x[0]-y[0])>0 or  abs(x[1]-y[1])>0 or  abs(x[0]-z[0])>0 or  abs(x[1]-z[1])>0:
+									if abs(x[0]-y[0])>0 or  abs(x[1]-y[1])>0:
+										print 'Broken!!!: ', 'Ax, Ay =', Ax, Ay, 'Bx, By =' , Bx, By, 'Cx, Cy =' ,Cx, Cy
+										print 'count', count
+										print x
+										print y
+										plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy)
+										halt
+
+		print 'Test Successful'
+
+
+
+	if test_case=='Triangle_into_fours':
+		Px=1. ; Py=0. ; Qx=2. ; Qy=0. #x-axis 
+		Rx=0. ; Ry=1. ; Sx=0. ; Sy=2. #y-axis 
+		
+		count=0
+		N=11 #Use an odd number
+		for Ax in np.linspace(-0.5 , 0.5 , N):
+			for Ay in np.linspace(-0.5 , 0.5 , N):
+				for Bx in np.linspace(-0.5 , 0.5 , N):
+					for By in np.linspace(-0.5 , 0.5 , N):
+						for Cx in np.linspace(-0.5 , 0.5 , N):
+							for Cy in np.linspace(-0.5 , 0.5 , N):
+								count=count+1
+								#print count
+								if count>0:
+									x=Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy)
+									y=Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy )
+									Error=abs(x[1]+x[2]+x[3]+x[4]-x[0])
+									#if Error>1e-15:
+									if abs(x[0]-y[0])>0 or  abs(x[1]-y[1])>0 or abs(x[2]-y[2])>0 or  abs(x[3]-y[3])>0 or  abs(x[4]-y[4])>0 :
+										print 'Broken!!!: ', 'Ax, Ay =', Ax, Ay, 'Bx, By =' , Bx, By, 'Cx, Cy =' ,Cx, Cy
+										print 'count=', count
+										#print 'Error = ', Error
+										print x
+										#print y
+										plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy)
+										halt
+
+		print 'Triangle_into_fours Test Successful'
+
+		#[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]=Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy); 
+		#[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]= Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  )
+
+	if test_case=='Point_above_line':
+		x0=0.1 ;y0=0.3 ; Px=0.4; Py=-1.0; Qx=0.2; Qy=2.2
+		plt.plot(np.array([Px, Qx]), np.array([Py, Qy]))
+                plt.plot(x0,y0,'*')
+		print Point_above_line(x0,y0,Px, Py, Qx, Qy)
+		plt.show()
+
+
+
+
+	if test_case=='many_hexagons':
+		Px=-1. ; Py=0. ; Qx=1. ; Qy=0. #x-axis 
+		Rx=0. ; Ry=-1. ; Sx=0. ; Sy=1. #y-axis 
+		N=101
+		theta=0.0
+		count=0
+		for x0 in np.linspace(-0.5 , 0.5 , N):
+			for y0 in np.linspace(-0.5 , 0.5 , N):
+				for H in np.linspace(0.0 , 0.5 , N):
+					count=count+1
+					#print count
+					if count>0:
+						C5x=-H/np.sqrt(3.) ; C5y=-H; #Corner 5 (bottom right)
+						C6x=H/np.sqrt(3.)  ; C6y=-H; #Corner 6 (bottom right)
+						[C5x,C5y]=rotate_and_translate(C5x,C5y,theta,x0,y0)
+						[C6x,C6y]=rotate_and_translate(C6x,C6y,theta,x0,y0)
+						#x = Triangle_divided_into_four_parts(x0,y0,C5x,C5y,C6x,C6y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
+						#y = Triangle_divided_into_four_quadrants(x0,y0,C5x,C5y,C6x,C6y); #T023
+						#print x
+						#print y
+						#Ax=x0 ;  Ay=y0
+						#Bx=C5x ; By=C5y ;
+						#Cx=C6x ; Cy=C6y ;
+						#plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy)
+						#(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)=Hexagon_into_quadrants_using_triangles_across_lines(x0,y0,H,theta,  Px, Py, Qx, Qy, Rx, Ry, Sx, Sy )
+						#(Area_hexb, Area_Q1b, Area_Q2b, Area_Q3b, Area_Q4b)= Hexagon_into_quadrants_using_triangles(x0,y0,H,theta=0)
+						x=Hexagon_into_quadrants_using_triangles_across_lines(x0,y0,H,theta,  Px, Py, Qx, Qy, Rx, Ry, Sx, Sy )
+						y= Hexagon_into_quadrants_using_triangles(x0,y0,H,theta=0)
+						eps=1e-15
+						#eps=0.0
+						#if abs(Area_hex-Area_hexb)>eps or  abs(Area_Q1-Area_Q1b)>eps or abs(Area_Q2-Area_Q2b)>eps \
+						#		or  abs(Area_Q3-Area_Q3b)>eps or  abs(Area_Q4-Area_Q4b)>eps :
+						if abs(x[0]-y[0])>0 or  abs(x[1]-y[1])>0 or abs(x[2]-y[2])>0 or  abs(x[3]-y[3])>0 or  abs(x[4]-y[4])>0 :
+							print 'Broken!!!: ', x0, y0, H
+							print Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4 
+							print Area_hexb, Area_Q1b, Area_Q2b, Area_Q3b, Area_Q4b
+							print 'count=', count
+							halt
+		
+		print 'Many_Hexagons Test Successful'
+
+
+	if test_case=='hexagon':
+		H=1.
+		S=2.*H/np.sqrt(3.)
+		x0=0.
+		y0=0.
+		#(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Divide_hexagon_into_4_quadrants_old(x0,y0,H)
+		#print x0,y0,H
+		#print 'First version', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+		(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Hexagon_into_quadrants_using_triangles(x0,y0,H,theta=0)
+		print 'Triangle version1',Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+		(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Hexagon_into_quadrants_using_triangles(x0,y0,H,theta=90.)
+		print 'Triangle version2',Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+		
+		#print 'Analysis'	
+		#print 'sum of quadrants: ', (Area_Q1+Area_Q2+Area_Q3+Area_Q4)
+		print 'Scaled areas: '
+		print (Area_Q1+Area_Q2+Area_Q3+Area_Q4)/Area_hex, Area_Q1/Area_hex, Area_Q2/Area_hex, Area_Q3/Area_hex, Area_Q4/Area_hex
+		
+
+	elif test_case=='square':
+	 
+		x0=0.6999999999999
+		y0=0.3
+		L=0.6
+		square_spreading_calculation(x0,y0,L)
+
+	elif test_case=='triangle':
+		Ax=-0.5
+		Ay=-0.3 -((8./9.)/10.)
+		Bx=-0.277777777778
+		By= -0.5
+
+		Cx=0.5
+		Cy=0.3 +((8./9.)/10.)
+
+		[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]=Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy); #T023
+
+		#Px=1. ; Py=0. ; Qx=2. ; Qy=0.  
+		#Rx=0. ; Ry=1. ; Sx=0. ; Sy=2.  
+		#[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]= Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  )
+
+		print 'Triangle 2: ',Ax,Ay,Bx,By,Cx,Cy
+		print 'Full',T23_Q1+T23_Q2+T23_Q3+T23_Q4
+		print 'Q1, Q2,Q3,Q4',T23_Q1,T23_Q2,T23_Q3,T23_Q4
+		print 'Full triangle area',T23_Area
+		print 'Error',(T23_Q1+T23_Q2+T23_Q3+T23_Q4-T23_Area)
+		
+		
+
+	elif test_case=='point_in_triangle':
+		Ax= -2.695732526092343E-012
+		Ay=0.204344508198090
+		Bx=-2.695750202346321E-012 
+		By= -8.433062639672301E-002
+		Cx=0.249999999997304
+		Cy=6.000694090068343E-002
+		print 'Point in triangle', point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.)
+
+
+	print 'Script complete'
+
+if __name__ == '__main__':
+	main()
+	#sys.exit(main())
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/test/Iceberg_repository/Scripts_and_analysis/hexagon_area.pyc b/test/Iceberg_repository/Scripts_and_analysis/hexagon_area.pyc
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diff --git a/test/Iceberg_repository/Scripts_and_analysis/iceshelf_geometry_create.py b/test/Iceberg_repository/Scripts_and_analysis/iceshelf_geometry_create.py
new file mode 100755
index 0000000..a819716
--- /dev/null
+++ b/test/Iceberg_repository/Scripts_and_analysis/iceshelf_geometry_create.py
@@ -0,0 +1,150 @@
+#!/usr/bin/env python
+
+###############################################################################################
+from netCDF4 import Dataset
+import numpy as np
+import os
+import numpy
+import netCDF4 as nc
+import matplotlib
+import matplotlib.pyplot as plt
+from pylab import *
+#import pdb
+#import argparse
+#This combination allows you to access the varibale imputted from the command line.
+#import sys
+
+#Clear screen
+def main():
+
+	os.system('clear')
+	input_geometry_filename='input_files/Isomip_ocean_geometry.nc'
+	input_iceshelf_filename='input_files/Ocean1_3D_no_calving.nc'
+
+	new_filename='output_files/Ocean1_3D_no_calving_trimmed.nc'
+
+
+	#Parameters
+	rho_water=1028
+	rho_ice=918
+
+	#f=Dataset(input_geometry_filename,'r')
+	#g=Dataset(new_filename,'w') # w if for creating a file
+
+
+	with nc.Dataset(input_geometry_filename) as file:
+		Depth = file.variables['D'][:,:]
+	with nc.Dataset(input_iceshelf_filename) as file:
+		thick = file.variables['thick'][:,:]
+	with nc.Dataset(input_iceshelf_filename) as file:
+		area= file.variables['area'][:,:]
+
+
+
+	M=thick.shape
+	thick_orig=np.zeros((M[0],M[1]))
+	for i in range(M[0]):
+		for j in range(M[01]):
+			thick_orig[i,j]=thick[i,j]
+	
+	#Making ice shelf symetric
+	M=thick.shape
+	thick_tmp=thick
+	print M
+	for i in range(M[0]/2):
+		for j in range(M[1]):
+			i_sym=(M[0]-1-i)
+			if j==0:
+				print i, i_sym
+			thick_tmp[i,j]=((thick[i,j]+thick[i_sym,j])/2.)
+			thick_tmp[i_sym,j]=((thick[i,j]+thick[i_sym,j])/2.)
+	thick=thick_tmp
+
+	#Making draft increase going inwards
+	M=thick.shape
+	thick_tmp=thick
+	print M
+	for k in range(5):
+		#for i in range(M[0]/2):
+		#for i in range(M[0]/8):
+		for i in range(5):
+			#for j in range(M[1]):
+			for j in range(118):
+				i_sym=(M[0]-1-i)
+				if (thick_tmp[i,j]<thick_tmp[i+1,j]):
+					thick_tmp[i,j]=thick_tmp[i+1,j]
+					#thick_tmp[i,j]=((thick_tmp[i+1,j] +thick_tmp[i+2,j])/2)
+				thick_tmp[i_sym,j]=thick_tmp[i,j]
+
+		thick=thick_tmp
+	
+
+
+
+	draft=thick*(rho_water/rho_ice)
+
+	ocean_thick=Depth-draft
+	ocean_thick[np.where(ocean_thick<0)]=0.
+
+	#ocean_thick=draft
+	
+	subplot(4,1,1)
+	cNorm = mpl.colors.Normalize(vmin=0, vmax=10)
+	cmap='jet'
+	plt.pcolormesh(ocean_thick,norm=cNorm,cmap=cmap)
+	plt.colorbar()
+	
+	subplot(4,1,2)
+	cNorm = mpl.colors.Normalize(vmin=0, vmax=1000)
+	cmap='jet'
+	plt.pcolormesh(thick_orig,norm=cNorm,cmap=cmap)
+	plt.colorbar()
+
+
+	subplot(4,1,3)
+	cNorm = mpl.colors.Normalize(vmin=0, vmax=1000)
+	cmap='jet'
+	plt.pcolormesh(thick,norm=cNorm,cmap=cmap)
+	plt.colorbar()
+
+	subplot(4,1,4)
+	cNorm = mpl.colors.Normalize(vmin=0, vmax=10)
+	cmap='jet'
+	plt.pcolormesh(thick-thick_orig,norm=cNorm,cmap=cmap)
+	plt.colorbar()
+
+
+
+	ny=M[0]
+	nx=M[1]
+	print nx,ny
+
+
+	#Creating the topog file
+	g=Dataset(new_filename,'w') # w if for creating a file
+
+	yt=g.createDimension('yt',ny)
+	xt=g.createDimension('xt',nx)
+
+	thick_h=g.createVariable('thick','f4',('yt','xt'))
+	g.variables['thick'][:]=thick
+	area_h=g.createVariable('area','f4',('yt','xt'))
+	g.variables['area'][:]=area
+
+	print 'Writing file: ' , new_filename
+	
+	g.sync()
+	g.close()
+
+
+
+	plt.show()
+
+
+	print 'Script complete'
+
+
+
+if __name__ == '__main__':
+        main()
+        #sys.exit(main())
diff --git a/test/Iceberg_repository/Scripts_and_analysis/iceshelf_mass_file_create.py b/test/Iceberg_repository/Scripts_and_analysis/iceshelf_mass_file_create.py
new file mode 100755
index 0000000..b98e66d
--- /dev/null
+++ b/test/Iceberg_repository/Scripts_and_analysis/iceshelf_mass_file_create.py
@@ -0,0 +1,83 @@
+#!/usr/bin/env python
+
+###############################################################################################
+from netCDF4 import Dataset
+import numpy as np
+import os
+import numpy
+import netCDF4 as nc
+#import matplotlib
+#import matplotlib.pyplot as plt
+#from pylab import *
+#import pdb
+#import argparse
+#This combination allows you to access the varibale imputted from the command line.
+#import sys
+
+#Clear screen
+def main():
+
+	os.system('clear')
+	input_filename='input_files/Isomip_ice_geometry.nc'
+	new_filename='output_files/ISOMIP_MIB.nc'
+
+	#f=Dataset(input_geometry_filename,'r')
+	#g=Dataset(new_filename,'w') # w if for creating a file
+
+	rho_ice=850.
+
+	with nc.Dataset(input_filename) as file:
+		ocean_mask = file.variables['openOceanMask'][:,:]
+		upperSurface = file.variables['upperSurface'][:,:]
+		lowerSurface = file.variables['lowerSurface'][:,:]
+		h_ice=upperSurface-lowerSurface
+		mass=h_ice*rho_ice
+		x = file.variables['x'][:]
+		y = file.variables['y'][:]
+
+
+	M= mass.shape
+	ny=M[0]
+	nx=M[1]
+	print nx,ny
+	print mass.shape
+
+	#subsampling data onto a grid half the size
+	MIB=np.zeros((ny/2,nx/2))
+	print MIB.shape
+	for i in range(0,nx,2):
+		for j in range(0,ny,2):
+			MIB[j/2,i/2]=mass[j,i]
+
+	
+	#Creating the topog file
+	g=Dataset(new_filename,'w') # w if for creating a file
+
+	time=g.createDimension('time',1)
+	yt=g.createDimension('yt',ny)
+	xt=g.createDimension('xt',nx)
+
+	mass_h=g.createVariable('mass','f4',('time','yt','xt'))
+	g.variables['mass'][:]=mass
+
+	#Creating subsampled version
+	yh=g.createDimension('yh',ny/2)
+	xh=g.createDimension('xh',nx/2)
+	MIB_h=g.createVariable('MIB','f4',('time','yh','xh'))
+	g.variables['MIB'][:]=MIB
+
+
+	g.sync()
+	g.close()
+
+
+
+
+
+	print 'Script complete'
+
+
+
+if __name__ == '__main__':
+        main()
+        #sys.exit(main())
diff --git a/test/Iceberg_repository/Scripts_and_analysis/initialize_bergs_in_pattern.py b/test/Iceberg_repository/Scripts_and_analysis/initialize_bergs_in_pattern.py
new file mode 100755
index 0000000..436f27c
--- /dev/null
+++ b/test/Iceberg_repository/Scripts_and_analysis/initialize_bergs_in_pattern.py
@@ -0,0 +1,1838 @@
+#!/usr/bin/env python
+
+#First import the netcdf4 library
+from netCDF4 import Dataset  # http://code.google.com/p/netcdf4-python/
+import numpy as np  # http://code.google.com/p/netcdf4-python/
+import matplotlib
+import matplotlib as mpl
+import math
+import os
+#matplotlib.use("GTKAgg")
+#from pylab import *
+from scipy import interpolate
+import matplotlib.pyplot as plt
+import argparse
+import pdb
+import netCDF4 as nc
+from hexagon_area import Divide_hexagon_into_4_quadrants_old
+from hexagon_area import Hexagon_into_quadrants_using_triangles
+
+
+def parseCommandLine():
+	"""
+	Parse the command line positional and optional arguments.
+	This is the highest level procedure invoked from the very end of the script.
+	"""
+
+	parser = argparse.ArgumentParser(description=
+	'''
+	Generate files for iceberg and bond restart files, matching given ice thickness fields.
+	''',
+	epilog='Written by Alon Stern, Dec. 2016.')
+
+	#Adding an extra boolian type argument
+	#p = argparse.ArgumentParser()
+	parser.register('type','bool',str2bool) # add type keyword to registries
+	#p.add_argument('-b',type='bool')  # do not use 'type=bool'
+
+	#Flags
+	parser.add_argument('-save_restart_files', type='bool', default=True,
+		          help=''' Writes an iceberg restart file,  icebergs.res ''')
+
+	parser.add_argument('-save_new_h_ice_file', type='bool', default=True,
+		          help=''' Writes a new gridded ice thickness file, which is what the ice thickness after the berg mass is interpolated back onto the grid''')
+
+	parser.add_argument('-Convert_to_lat_lon', type='bool', default=False,
+		          help=''' Converts the iceberg positions to lat / lon coordinates  ''')
+
+	parser.add_argument('-input_is_cartesian', type='bool', default=True,
+		          help=''' The positions in the ice thickness input file is given in cartesian coordiantes''')
+
+	#Iceberg setup flags
+	parser.add_argument('-only_choose_one_berg', type='bool', default=False,
+		          help=''' When true, only one iceberg (with number chosen_berg_num) is written to icebergs.res. This is for debugging  ''')
+
+	parser.add_argument('-chosen_berg_num', type=int, default=1,
+		          help='''When only_choose_one_berg=True, then only the iceberg with this number is written to the icebergs.res file  ''')
+
+	parser.add_argument('-scale_the_grid_to_lat_lon', type='bool', default=False,
+		          help=''' This option scales dimensions by a fixed amount. Option should be removed   ''')
+
+	parser.add_argument('-adjust_lat_ref', type='bool', default=True,
+		          help=''' This option is only used when Convert_to_lat_lon is true. If true, then the reference latitudes depends on iceberg position.\
+					  This still needs to be tested using lat lon test cases.''')
+
+	parser.add_argument('-set_all_thicknesses_to_one', type='bool', default=False,
+		          help=''' Sets all non-zero ice thickness to Th_prescibed (default 1), useful for debugging.  ''')
+
+	parser.add_argument('-Th_prescribed', type=float, default=1.0,
+		          help='''Prescibed ice thickness used when the flag set_all_thicknesses_to_one=True   ''')
+
+	parser.add_argument('-Interpolate_from_four_corners', type='bool', default=True,
+		          help=''' The thickness of an iceberg is calcaulated from the 4 corners of the gridded thickness. When flag is false, the near thickness is used  ''')
+
+	parser.add_argument('-Switch_x_and_y_to_rotate_90', type='bool', default=False,
+		          help=''' Rotates the whole domain by 90 degrees by switching lat and lon of icebergs.  ''')
+
+	parser.add_argument('-set_all_domain_to_ice', type='bool', default=False,
+		          help=''' Sets the ice thickness = Th_prescibed (default 1) throughout the entire domain. Applied only when flag set_all_thicknesses_to_one=True   ''')
+
+	parser.add_argument('-Use_default_radius', type='bool', default=False,
+		          help=''' Calculates an appropriate ice element radius based on the ocean grid spacing.   ''')
+
+	parser.add_argument('-Remove_stationary_bergs', type='bool', default=False,
+		          help=''' All stationary icebergs are removed.  ''')
+
+	#Static vs non-static flags (These are needed for calving away from Static shelf)
+	parser.add_argument('-set_all_bergs_static_by_default', type='bool', default=True,
+			help='''Bergs are static unless instructed otherwise (e.g.: after applying calving)   ''')
+
+	parser.add_argument('-set_some_bergs_static_by_default', type='bool', default=False,
+		          help=''' Bergs in part of the domain are set to static by default (see subroutine for details)  ''')
+
+	parser.add_argument('-Make_icebergs_non_static_later', type='bool', default=True,
+			help=''' Run subroutine which makes some icebergs non-static later (eg: icebergs around calved tabular icebergs).  Note that bonds are \
+					only created for non_static, so by making bergs non_static later, it means they can move, but are not bonded.  ''')
+
+	#Mass spreadng flags
+	parser.add_argument('-Switch_regridding_element_type', type='bool', default=False,
+		          help=''' When true, element shape is switched from hexagon to square (and visa versa) before regridding. Used in debugging to see if having \
+			  the wrond elemnt type makes a bid difference. Maybe this option should be removed(?)''')
+
+	parser.add_argument('-Fill_in_the_boundaries', type='bool', default=True,
+		          help=''' Adds extra (static)  ice elements at the edges of the domain when the ice shelf extends right up until the boundaries of the domain.\
+					  Only used with hexagonal ice elements (for now).''')
+
+	parser.add_argument('-regrid_icebergs_onto_grid', type='bool', default=True,
+		          help=''' After icebergs have been defined, the iceberg mass is interpolated back onto the ocean grid  ''')
+
+	parser.add_argument('-element_type', type=str, default='hexagon',
+			help='''Shape of element used in mass spreading. Options are: 'hexagon' or 'square'   ''')
+
+
+	#Plotting flags - Only affect how the ice elements are plotted and does not affect files created by this script
+	parser.add_argument('-Run_plotting_subroutine', type='bool', default=True,
+		          help=''' Subrouting is run plots icebergs and ice thickness. All other plotting flags require this to be true.  ''')
+
+	parser.add_argument('-plot_circles', type='bool', default=False,
+		          help=''' Circles are plotted to scale which show how large each ice element is. (Useful when converting to lat lon)  ''')
+
+	parser.add_argument('-plot_ice_mask', type='bool', default=False,
+		          help=''' The ice mask (showing where ice shelf is present) is plotted under iceberg positions. Option may be removed.  ''')
+
+	parser.add_argument('-plot_ice_thickness', type='bool', default=True,
+		          help=''' The ice thickness is plotted under iceberg positions   ''')
+
+	parser.add_argument('-plot_icebergs_positions', type='bool', default=True,
+		          help='''  Positions of ice elements are plotted  ''')
+
+	parser.add_argument('-plot_h_ice_new', type='bool', default=True,
+		          help='''  The newly interpolated ice thickness is plotted under iceberg positions ''')
+	
+	parser.add_argument('-plot_bonds', type='bool', default=False,
+		          help=''' Bonds are plotted between the ice elements   ''')
+
+	#Bond related flags
+	parser.add_argument('-Create_icebergs_bonds', type='bool', default=True,
+		          help=''' Bonds are created between icebergs  ''')
+
+	parser.add_argument('-break_some_bonds', type='bool', default=True,
+		          help=''' After the bonds have been set up, some are broken. This simulates a iceberg / ice shelf calving.\
+					  Note that this flag is also used to make a calving event even if bonds are not used since \
+					  the "calving" process also sets some icebergs to static and others to non-static''')
+
+	parser.add_argument('-Allow_bonds_for_static_iceberg', type='bool', default=False,
+		          help=''' If True then bonds are allowed for ice elements which are static.   ''')
+
+	parser.add_argument('-Allow_bonds_with_boundary_bergs', type='bool', default=False,
+		          help=''' When true, bonds are allowed to form with elements close to the boundary. \
+					  When false, bonds are allowed for bergs closer with i,j < N_bergs_before_bd.\
+					  This option is a little confusing and might need to be removed (>)''')
+
+	#Experimental setup flags
+	parser.add_argument('-Ice_geometry_source', type=str, default='ISOMIP',
+			help=''' Name of experiment which is being run. Options are 'ISOMIP', 'Generic' and 'Weddell'\
+					These experiments override some of the flags above and have standary input files  (see below).\
+					This will be made more general later so that ice thickness files are passed into the script with standarized formate through driver.\
+					''')
+
+	parser.add_argument('-ISOMIP_ice_geometry_filename', type=str, default='input_files/Isomip_ice_geometry.nc',
+			help=''' Ice thickness from the ISOMIP experiment, given on ice grid, rather than ocean grid.  ''')
+
+	parser.add_argument('-ISOMIP_reduced_ice_geometry_filename', type=str, default='input_files/Ocean1_3D_no_calving_trimmed.nc',
+			help=''' Ice thickness from ISOMIP experiment, given on ocean grid. Later all input files will be made to have this format\
+					(or to specify if they are on the ice grid, what format the ocean should have)''')
+
+	parser.add_argument('-Weddell_ice_geometry_filename', type=str, default='input_files/Bedmap2_gridded_subset_Weddell_Sea_Region.nc',
+			help='''  Ice thickness from the ice shelves in the Weddell Sea, given on ice grid, rather than ocean grid.  ''')
+
+	parser.add_argument('-Generic_ice_geometry_filename', type=str, \
+			default='/lustre/f1/unswept/Alon.Stern/MOM6-examples_Alon/ice_ocean_SIS2/Drifting_tabular/python_scripts/output_files/Ice_shelf_file.nc',
+			help=''' Ice thickness used in a generic setup.   ''')
+
+
+	parser.add_argument('-ISOMIP_reduced', type='bool', default=True,
+			help=''' Flag which specifies that we are using the reduced ISOMIP file (on the ocean grid), rather than geomety on the ice grid. \
+					Reduced uses 2X2 grid, not reduced uses 1X1 grid \
+					This should be made more general later.''')
+
+	#Parameters
+	parser.add_argument('-Radius', type=float, default='850.0',
+			help='''Radius of ice element (m). This is overriden if Use_default_radius=True\
+					Note that Hexagon only valid if the Radius, S< half gridcell  (about 0.85 using 2km grid)''')
+
+	parser.add_argument('-rho_ice', type=float, default=918.0,
+			help=''' Density of icebergs (kg/m^3)  ''')
+
+	parser.add_argument('-gravity', type=float, default=9.8,
+			help=''' Gravitational acceleration  (m/s^2)''')
+
+	parser.add_argument('-mass_scaling', type=float, default=1.0,
+			help=''' Number of icebergs represented by one ice element  ''')
+
+	parser.add_argument('-R_earth', type=float, default=6360000.,
+			help=''' Radius of the earch (m) - used in Lat/Lon conversions.   ''')
+
+	parser.add_argument('-buffer_number', type=int, default=0,
+			help=''' Amount of points from the boundaries where ice thickness is set to zero for debugging. This should be removed.  ''')
+
+	parser.add_argument('-IA_scaling', type=float, default=1.,
+			help='''  A scaling parameter which allows the interactive radius be different from radius for testing the bonds.\
+					(This has not been used in a long while, and perhaps should be removed)''')
+
+	optCmdLineArgs = parser.parse_args()
+	return optCmdLineArgs
+
+def str2bool(string):
+	if string.lower() in  ("yes", "true", "t", "1"):
+		Value=True
+	elif string.lower() in ("no", "false", "f", "0"):
+		Value=False
+	else:
+		print '**********************************************************************'
+		print 'The input variable ' ,str(string) ,  ' is not suitable for boolean conversion, using default'
+		print '**********************************************************************'
+
+		Value=None
+		return
+	
+	return Value
+
+	
+
+def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg):
+	
+	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
+	# To copy the global attributes of the netCDF file  
+
+	#Input and output files	
+	#Create Empty restart file. This is later read so that the attributes can be used.
+	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
+	create_empty_iceberg_restart_file(Empty_restart_filename)
+	#Empty_restart_filename='input_files/icebergs.res.nc'
+
+	#Read empty restart file
+	f=Dataset(Empty_restart_filename,'r') # r is for read only
+	#Write a new restart file
+	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
+
+	for attname in f.ncattrs():
+		    setattr(g,attname,getattr(f,attname))
+
+
+	# To copy the dimension of the netCDF file
+	for dimname,dim in f.dimensions.iteritems():
+		# if you want to make changes in the dimensions of the new file
+		# you should add your own conditions here before the creation of the dimension.
+		#g.createDimension(dimname,len(dim))
+		g.createDimension(dimname,Number_of_bergs)
+
+	# To copy the variables of the netCDF file
+
+	for varname,ncvar in f.variables.iteritems():
+		# if you want to make changes in the variables of the new file
+		# you should add your own conditions here before the creation of the variable.
+		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
+		#Proceed to copy the variable attributes
+		for attname in ncvar.ncattrs():  
+			setattr(var,attname,getattr(ncvar,attname))
+		#Finally copy the variable data to the new created variable
+		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
+		
+		if varname=='i':
+			var[:]=Number_of_bergs
+		
+		if varname=='iceberg_num':
+			for j in range(Number_of_bergs):
+				#var[j]=j+1
+				var[j]=iceberg_num[j]
+
+		if varname=='uvel' or varname=='vvel' or varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
+		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
+		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
+		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
+			var[:]=0
+
+		if varname=='mass_scaling':
+			var[:]=mass_scaling
+
+		if varname=='thickness':
+			for j in range(Number_of_bergs):
+				var[j]=thickness[j]
+		
+		if varname=='mass':
+			for j in range(Number_of_bergs):
+				var[j]=mass[j]
+
+		if varname=='width'  or varname=='length':
+			for j in range(Number_of_bergs):
+				var[j]=width[j]
+
+		if varname=='lon':
+			for j in range(Number_of_bergs):
+				var[j]=lon[j]
+
+		if varname=='lat':
+			for j in range(Number_of_bergs):
+				var[j]=lat[j]
+
+		if varname=='static_berg':
+			for j in range(Number_of_bergs):
+				var[j]=static_berg[j]
+
+
+	f.close()
+	g.close()
+
+
+	
+def Create_bond_restart_file(Number_of_bonds,first_berg_num,first_berg_ine,first_berg_jne,other_berg_ine,other_berg_jne,iceberg_num,other_berg_num,Ice_geometry_source):
+	#Creating the bond restart file
+
+	print 'Writing bond restart files with  ', Number_of_bonds, ' Bonds'
+	# To copy the global attributes of the netCDF file  
+
+	#Input and output files	
+	#Create Empty restart file. This is later read so that the attributes can be used.
+	Empty_bond_restart_filename='output_files/Empty_bonds_icebergs.res.nc'
+	create_empty_bond_restart_file(Empty_bond_restart_filename)
+	#Empty_bond_restart_filename='input_files/bonds_iceberg.res.nc'
+      
+	h=Dataset(Empty_bond_restart_filename,'r',format='NETCDF3_CLASSIC') # r is for read only
+	q=Dataset('output_files/' + Ice_geometry_source + '_bonds_iceberg.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
+
+	for attname in h.ncattrs():
+		    setattr(q,attname,getattr(h,attname))
+
+
+	# To copy the dimension of the netCDF file
+	for dimname,dim in h.dimensions.iteritems():
+		# if you want to make changes in the dimensions of the new file
+		# you should add your own conditions here before the creation of the dimension.
+		#g.createDimension(dimname,len(dim))
+		q.createDimension(dimname,Number_of_bonds)
+
+	# To copy the variables of the netCDF file
+
+	for varname,ncvar in h.variables.iteritems():
+		# if you want to make changes in the variables of the new file
+		# you should add your own conditions here before the creation of the variable.
+		var = q.createVariable(varname,ncvar.dtype,ncvar.dimensions)
+		#Proceed to copy the variable attributes
+		for attname in ncvar.ncattrs():  
+			setattr(var,attname,getattr(ncvar,attname))
+		#Finally copy the variable data to the new created variable
+		#var[:] = ncvar[0]
+		var[:] = 0.
+
+		if varname=='i':
+			var[:]=Number_of_bonds
+
+		if varname=='first_berg_num':
+			for j in range(Number_of_bonds):
+				var[j]=first_berg_num[j]
+
+		if varname=='first_berg_ine':
+			for j in range(Number_of_bonds):
+				var[j]=first_berg_ine[j]
+
+		if varname=='first_berg_jne':
+			for j in range(Number_of_bonds):
+				var[j]=first_berg_jne[j]
+
+		if varname=='other_berg_num':
+			for j in range(Number_of_bonds):
+				var[j]=other_berg_num[j]
+
+		if varname=='other_berg_ine':
+			for j in range(Number_of_bonds):
+				var[j]=other_berg_ine[j]
+
+		if varname=='other_berg_jne':
+			for j in range(Number_of_bonds):
+				var[j]=other_berg_jne[j]
+
+	h.close()
+	q.close()
+
+
+def create_empty_iceberg_restart_file(Empty_restart_filename):
+
+	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
+
+	i=f.createDimension('i', None)
+	lon=f.createVariable('i','i')
+
+	lon=f.createVariable('lon','d',('i'))
+	lon.long_name = "longitude" ;
+	lon.units = "degrees_E" ;
+	lon.checksum = "               0" ;
+
+	lat=f.createVariable('lat','d',('i'))
+	lat.long_name = "latitude" ;
+	lat.units = "degrees_N" ;
+	lat.checksum = "               0" ;
+
+	uvel=f.createVariable('uvel','d',('i'))
+	uvel.long_name = "zonal velocity" ;
+	uvel.units = "m/s" ;
+	uvel.checksum = "               0" ;
+
+	vvel=f.createVariable('vvel','d',('i'))
+	vvel.long_name = "meridional velocity" ;
+	vvel.units = "m/s" ;
+	vvel.checksum = "               0" ;
+
+	mass=f.createVariable('mass','d',('i'))
+	mass.long_name = "mass" ;
+	mass.units = "kg" ;
+	mass.checksum = "               0" ;
+
+	axn=f.createVariable('axn','d',('i'))
+	axn.long_name = "explicit zonal acceleration" ;
+	axn.units = "m/s^2" ;
+	axn.checksum = "               0" ;
+
+	ayn=f.createVariable('ayn','d',('i'))
+	ayn.long_name = "explicit meridional acceleration" ;
+	ayn.units = "m/s^2" ;
+	ayn.checksum = "               0" ;
+
+	bxn=f.createVariable('bxn','d',('i'))
+	bxn.long_name = "inplicit zonal acceleration" ;
+	bxn.units = "m/s^2" ;
+	bxn.checksum = "               0" ;
+
+	byn=f.createVariable('byn','d',('i'))
+	byn.long_name = "implicit meridional acceleration" ;
+	byn.units = "m/s^2" ;
+	byn.checksum = "               0" ;
+
+	ine=f.createVariable('ine','i',('i'))
+	ine.long_name = "i index" ;
+	ine.units = "none" ;
+	ine.packing = 0 ;
+	ine.checksum = "               0" ;
+
+	jne=f.createVariable('jne','i',('i'))
+	jne.long_name = "j index" ;
+	jne.units = "none" ;
+	jne.packing = 0 ;
+	jne.checksum = "               0" ;
+
+	thickness=f.createVariable('thickness','d',('i'))
+	thickness.long_name = "thickness" ;
+	thickness.units = "m" ;
+	thickness.checksum = "               0" ;
+
+	width=f.createVariable('width','d',('i'))
+	width.long_name = "width" ;
+	width.units = "m" ;
+	width.checksum = "               0" ;
+
+	length=f.createVariable('length','d',('i'))
+	length.long_name = "length" ;
+	length.units = "m" ;
+	length.checksum = "               0" ;
+
+	start_lon=f.createVariable('start_lon','d',('i'))
+	start_lon.long_name = "longitude of calving location" ;
+	start_lon.units = "degrees_E" ;
+	start_lon.checksum = "               0" ;
+
+	start_lat=f.createVariable('start_lat','d',('i'))
+	start_lat.long_name = "latitude of calving location" ;
+	start_lat.units = "degrees_N" ;
+	start_lat.checksum = "               0" ;
+
+	start_year=f.createVariable('start_year','i',('i'))
+	start_year.long_name = "calendar year of calving event" ;
+	start_year.units = "years" ;
+	start_year.packing = 0 ;
+	start_year.checksum = "               0" ;
+
+	iceberg_num=f.createVariable('iceberg_num','i',('i'))
+	iceberg_num.long_name = "identification of the iceberg" ;
+	iceberg_num.units = "dimensionless" ;
+	iceberg_num.packing = 0 ;
+	iceberg_num.checksum = "               0" ;
+
+	start_day=f.createVariable('start_day','d',('i'))
+	start_day.long_name = "year day of calving event" ;
+	start_day.units = "days" ;
+	start_day.checksum = "               0" ;
+
+	start_mass=f.createVariable('start_mass','d',('i'))
+	start_mass.long_name = "initial mass of calving berg" ;
+	start_mass.units = "kg" ;
+	start_mass.checksum = "               0" ;
+
+	mass_scaling=f.createVariable('mass_scaling','d',('i'))
+	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
+	mass_scaling.units = "none" ;
+	mass_scaling.checksum = "               0" ;
+
+	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
+	mass_of_bits.long_name = "mass of bergy bits" ;
+	mass_of_bits.units = "kg" ;
+	mass_of_bits.checksum = "               0" ;
+
+	heat_density=f.createVariable('heat_density','d',('i'))
+	heat_density.long_name = "heat density" ;
+	heat_density.units = "J/kg" ;
+	heat_density.checksum = "               0" ;
+		
+	halo_berg=f.createVariable('halo_berg','d',('i'))
+	halo_berg.long_name = "halo_berg" ;
+	halo_berg.units = "dimensionless" ;
+	halo_berg.checksum = "               0" ;
+
+	static_berg=f.createVariable('static_berg','d',('i'))
+	static_berg.long_name = "static_berg" ;
+	static_berg.units = "dimensionless" ;
+	static_berg.checksum = "               0" ;
+
+	f.sync()
+	f.close()
+
+def create_empty_bond_restart_file(Empty_bond_restart_filename):
+
+	f = Dataset(Empty_bond_restart_filename,'w', format='NETCDF3_CLASSIC')
+
+	i=f.createDimension('i', None)
+	i=f.createVariable('i','i')
+
+	first_berg_ine=f.createVariable('first_berg_ine','i',('i'))
+	first_berg_ine.long_name = "iceberg ine of first berg in bond" ;
+	first_berg_ine.units = "dimensionless" ;
+	first_berg_ine.packing = 0 ;
+	first_berg_ine.checksum = "               0" ;
+
+	first_berg_jne=f.createVariable('first_berg_jne','i',('i'))
+	first_berg_jne.long_name = "iceberg jne of first berg in bond" ;
+	first_berg_jne.units = "dimensionless" ;
+	first_berg_jne.packing = 0 ;
+	first_berg_jne.checksum = "               0" ;
+
+	first_berg_num=f.createVariable('first_berg_num','i',('i'))
+	first_berg_num.long_name = "iceberg id first berg in bond" ;
+	first_berg_num.units = "dimensionless" ;
+	first_berg_num.packing = 0 ;
+	first_berg_num.checksum = "               0" ;
+
+	other_berg_ine=f.createVariable('other_berg_ine','i',('i'))
+	other_berg_ine.long_name = "iceberg ine of second berg in bond" ;
+	other_berg_ine.units = "dimensionless" ;
+	other_berg_ine.packing = 0 ;
+	other_berg_ine.checksum = "               0" ;
+
+	other_berg_jne=f.createVariable('other_berg_jne','i',('i'))
+	other_berg_jne.long_name = "iceberg jne of second berg in bond" ;
+	other_berg_jne.units = "dimensionless" ;
+	other_berg_jne.packing = 0 ;
+	other_berg_jne.checksum = "                0" ;
+
+	other_berg_num=f.createVariable('other_berg_num','i',('i'))
+	other_berg_num.long_name = "iceberg id second berg in bond" ;
+	other_berg_num.units = "dimensionless" ;
+	other_berg_num.packing = 0 ;
+	other_berg_num.checksum = "               0" ;
+
+	f.sync()
+	f.close()
+
+def Define_iceberg_thickness_and_mass(Number_of_bergs,dx_berg,dy_berg,rho_ice,Radius,h_ice,x,y,\
+		width,Interpolate_from_four_corners,element_area,element_type,static_berg):
+	thickness=[]
+	mass=[]
+	ny,nx=h_ice.shape
+	dx=x[1]-x[0]
+	grid_area=dx*dx
+	for berg_count in range(Number_of_bergs):
+		x_val=dx_berg[berg_count] ; y_val=dy_berg[berg_count]
+		i_val=int(math.floor(x_val/dx))
+		j_val=int(math.floor(y_val/dx))
+
+		#Interpolate thickness from 4 corners - possibly do this later, but I worry about when you are between a shelf and non shelf piece.
+		if Interpolate_from_four_corners==True:
+
+			x_cell=(x_val-x[i_val])/np.sqrt(grid_area)+0.5
+			y_cell=(y_val-y[j_val])/np.sqrt(grid_area)+0.5
+
+			mass_on_ocean=np.zeros([nx,ny,10])   #Setting up matrix to spread mass to ocean.  Note that I have used 10 points  so that I can ignore 0 and match with python numbering
+			mass_val=1.
+			mass_on_ocean=spread_mass_to_ocean(nx,ny,i_val,j_val,mass_on_ocean,x_cell,y_cell,element_area,mass_val,element_type,grid_area,static_berg[berg_count])
+			Th=0.
+			h=np.array([0,0,0,0,0,0,0,0,0,0])
+			if i_val>0 and j_val>0:
+				h[1]=h_ice[j_val-1,i_val-1]
+			if j_val>0:
+				h[2]=h_ice[j_val-1,i_val]
+			if j_val>0 and i_val<(nx-1):
+				h[3]=h_ice[j_val-1,i_val+1]
+			if i_val>0:
+				h[4]=h_ice[j_val,i_val-1]
+			if True:
+				h[5]=h_ice[j_val,i_val]
+			if i_val<(nx-1):
+				h[6]=h_ice[j_val,i_val+1]
+			if i_val>0 and j_val<(ny-1):
+				h[7]=h_ice[j_val+1,i_val-1]
+			if j_val<(ny-1):
+				h[8]=h_ice[j_val+1,i_val]
+			if i_val<(nx-1) and j_val<(ny-1):
+				h[9]=h_ice[j_val+1,i_val+1]
+			for k in range(1,10):
+				Th=Th+(mass_on_ocean[i_val,j_val,k]*h[k])
+				#print i_val,j_val,k,mass_on_ocean[i_val,j_val,k]
+			#if abs(Th-1)>0.0000001:
+			#	print 'Thickness',Th-1,i_val,j_val
+			#	test=0.
+			#	for k in range(1,10):
+			#		print k,mass_on_ocean[i_val,j_val,k], h[k]
+			#		test=test+(mass_on_ocean[i_val,j_val,k])
+			#	print test
+			#	halt
+				
+
+	
+		Th=h_ice[j_val,i_val]
+		thickness.append(Th)
+		#Check that all thicknesses are positive
+		if Th<=0:
+			print 'Thickness is less than or equal to zero,0!',i_val, j_val,x_val,y_val
+			halt
+		#mass.append(Th*rho_ice*element_area) 
+		mass.append(Th*rho_ice*(width[berg_count])**2) 
+		#if element_type=='square': 
+		#	mass.append(Th*rho_ice*((2*Radius)**2)) # For square elements
+		#else:
+		#	mass.append(Th*rho_ice*np.pi*(Radius**2))  #For circular elements
+	return [thickness, mass]
+
+
+def check_if_it_is_in_domain(x_val,y_val,x_min,x_max,y_min,y_max,R_earth,lat_init,adjust_lat_ref,dx,dy):
+	point_is_in_domain=True
+	
+	if (x_val >= (x_max-x_min+(dx))) or (x_val<= 0) or  (y_val >= (y_max-y_min+(dy))) or (y_val <= 0):
+		point_is_in_domain=False
+	
+	return point_is_in_domain
+
+def check_if_it_is_ice(x_val,y_val,ice_mask,dx):
+	i_val=int(math.floor(x_val/dx))
+	j_val=int(math.floor(y_val/dx))
+	if ice_mask[j_val,i_val]==1.:
+		it_is_ice=True
+	else:
+		it_is_ice=False
+	return it_is_ice
+
+def calculate_element_area(element_type,Radius):
+	if element_type=='square':
+		element_area=(2*Radius)**2
+	elif element_type=='hexagon':
+		element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*(Radius)**2) #Area of hexagon around circle (used for packing)  
+		#Another derivation uses innner hexagon with two more triangles added, which is a 1/6 of the hexagon area each (two since there are 6, shared by 3 each)
+		#element_area=(4./3.)*H_i, where H_i=(3.*np.sqrt(3.)/2.)*((Radius)**2)  is the area of the inner hexagon (with sides equal to the radius)
+
+	return element_area
+
+def add_and_extra_boundary_berg(i,j,New_thickness,y_shift,x_shift,Nbh_thickness_value,Nbh_mass_value,New_mass,berg_count,dx_berg,dy_berg,\
+		iceberg_num,thickness,width,mass,static_berg,grid_area,rho_ice):
+	tol=0.0000000000001
+	if New_thickness[j,i]>1.+tol:
+		print 'The new thickness is too big!!!', i,j,  New_thickness[j,i]
+		halt
+	if ((Nbh_thickness_value-New_thickness[j,i])>tol):
+		y_val=y_shift[j]
+		x_val=x_shift[i]
+		if Nbh_thickness_value>0. and (abs(Nbh_thickness_value-1)<tol) and (Nbh_mass_value>New_mass[j,i]):
+			berg_count=berg_count+1
+			dx_berg.append(x_val)
+			dy_berg.append(y_val)
+			iceberg_num.append(berg_count)
+			width_val=np.sqrt((Nbh_thickness_value-New_thickness[j,i])*grid_area)
+			if Nbh_thickness_value-New_thickness[j,i]<0:
+				print 'Stop', Nbh_thickness_value, New_thickness[j,i],i,j
+			mass_val=Nbh_mass_value-New_mass[j,i]
+			thickness_val=mass_val/(width_val*width_val*rho_ice)
+			thickness.append(thickness_val)
+			width.append(width_val)
+			mass.append(mass_val)
+			static_berg.append(1.)
+	return [berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg]
+
+
+def add_extra_bergs_on_boundary(dx,dy,x,y,Number_of_bergs,element_area,rho_ice,X_min,X_max,Y_min,Y_max,R_earth,lat_init,adjust_lat_ref,ice_mask,\
+		iceberg_num,width,dx_berg,dy_berg,h_ice,element_type,static_berg,thickness,mass):
+	eps=0.000001
+	grid_area=dx*dy
+	Nx=len(x)  ; Ny=len(y)
+	x_shift=(x-np.min(x))+(dx/2) ; y_shift=(y-np.min(y))+(dy/2)
+
+	thickness_temp= [1. for i in range(Number_of_bergs)] ;
+	mass_temp= [element_area*rho_ice*1. for i in range(Number_of_bergs)] ;
+	New_area=regrid_iceberg_thickness(dy_berg,dx_berg,Number_of_bergs,thickness_temp,mass_temp,h_ice,x_shift,y_shift,rho_ice,element_type,static_berg,plot_outcome=False)
+	New_thickness=(New_area)/(rho_ice*grid_area)  #Should be equal to one everywhere where there is ice shelf.
+	New_mass=regrid_iceberg_thickness(dy_berg,dx_berg,Number_of_bergs,thickness,mass,h_ice,x_shift,y_shift,rho_ice,element_type,static_berg,plot_outcome=False)
+	berg_count=Number_of_bergs
+	
+	
+	#Vertical boundary
+	for i in np.array([0,Nx-1]):
+		#for j in range(Ny):
+		for j in range(1,Ny-1):
+			Nbh_mass_value=h_ice[j,i]*rho_ice*grid_area  #Neighbouring shelf value
+			if i==0:
+				Nbh_thickness_value=New_thickness[j,1]  #Neighbouring shelf value
+				#x_val=0+(eps*dx)
+			if i==Nx-1:
+				Nbh_thickness_value=New_thickness[j,Nx-2]  #Neighbouring shelf value
+				#x_val=x_shift[i]+(dx/2)-eps
+			[berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg]=add_and_extra_boundary_berg(i,j,New_thickness,y_shift,x_shift,\
+					Nbh_thickness_value,Nbh_mass_value,New_mass,berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg,grid_area,rho_ice)
+
+	##Horizontal boundary
+	for j in np.array([0,Ny-1]):
+		#for i in range(1,Nx-1):
+		for i in range(1,Nx-1):
+			Nbh_mass_value=h_ice[j,i]*rho_ice*grid_area  #Neighbouring shelf value
+			if j==0:
+				Nbh_thickness_value=New_thickness[1,i]  #Neighbouring shelf value
+				#y_val=0+(eps*dy)
+			if j==Ny-1:
+				Nbh_thickness_value=New_thickness[Ny-2,i]  #Neighbouring shelf value
+				#y_val=y_shift[j]+(dy/2)-eps
+			#Nbh_thickness_value=np.mean(New_thickness[range(1,Ny-1),i])  #Neighbouring shelf value
+			[berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg]=add_and_extra_boundary_berg(i,j,New_thickness,y_shift,x_shift,\
+					Nbh_thickness_value,Nbh_mass_value,New_mass,berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg,grid_area,rho_ice)
+
+	#Doing the corners seperately
+	for j in np.array([0,Ny-1]):
+		#for i in range(1,Nx-1):
+		for i in np.array([0,Nx-1]):
+			Nbh_mass_value=h_ice[j,i]*rho_ice*grid_area  #Neighbouring shelf value
+			if j==0 and i==0:
+				Nbh_thickness_value=New_thickness[1,1]  #Neighbouring shelf value
+			if j==0 and i==Nx-1:
+				Nbh_thickness_value=New_thickness[1,Nx-2]  #Neighbouring shelf value
+			if j==Ny-1 and i==0:
+				Nbh_thickness_value=New_thickness[Ny-2,1]  #Neighbouring shelf value
+			if j==Ny-1 and i==Nx-1:
+				Nbh_thickness_value=New_thickness[Ny-2,Nx-2]  #Neighbouring shelf value
+			[berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg]=add_and_extra_boundary_berg(i,j,New_thickness,y_shift,x_shift,\
+					Nbh_thickness_value,Nbh_mass_value,New_mass,berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg,grid_area,rho_ice)
+
+
+	Number_of_bergs=berg_count
+	
+	return [dx_berg, dy_berg,iceberg_num, width,Number_of_bergs,static_berg,thickness,mass]
+
+
+def remove_stationary_bergs(dx_berg, dy_berg,iceberg_num,width,Number_of_bergs,static_berg):
+	dx_berg_new=[]
+	dy_berg_new=[]
+	iceberg_num_new=[]
+	width_new=[]
+	static_berg_new=[]
+	for i in range(Number_of_bergs):
+		if static_berg[i]>0.5:
+		#if static_berg[i]<0.5:
+			dx_berg_new.append(dx_berg[i])
+			dy_berg_new.append(dy_berg[i])
+			iceberg_num_new.append(iceberg_num[i])
+			width_new.append(width[i])
+			static_berg_new.append(static_berg[i])
+
+	Number_of_bergs_new=len(iceberg_num_new)
+	return [dx_berg_new, dy_berg_new,iceberg_num_new, width_new,Number_of_bergs_new,static_berg_new]
+
+def Create_icebergs(lon_init,lat_init,Radius,R_earth, x, y,ice_mask,h_ice,Convert_to_lat_lon,rho_ice,\
+		element_type,scale_the_grid_to_lat_lon,lat_ref,adjust_lat_ref,Interpolate_from_four_corners,\
+		Fill_in_the_boundaries,set_all_bergs_static_by_default,break_some_bonds,Remove_stationary_bergs,set_some_bergs_static_by_default):
+	print 'Starting to create icebergs...'
+	dx_berg=[]  #x distance in cartesian of berg from lon_init
+	dy_berg=[]  #y distance in cartesian of berg from lat_init
+	dlon_berg=[] #x distance in lon of berg from lon_init
+	#dlat_berg=[] #y distance in lat of berg from lat_init
+	lon=[] #Longitude of iceberg
+	lat=[] #Latitude of iceberg
+	iceberg_num=[] #ID of iceberg
+	
+	element_area=calculate_element_area(element_type,Radius)
+	#width=np.sqrt(element_area)
+	width=[]
+	
+	#dx=x[1]-x[0]  ;dy=y[1]-y[0]
+	#X_min=np.min(x)-dx; X_max=np.max(x)+dx  #In lat lon or cartesian
+	#Y_min=np.min(y)-dy; Y_max=np.max(y)+dy  #In lat lon or cartesian
+	X_min=np.min(x); X_max=np.max(x)  #In lat lon or cartesian
+	Y_min=np.min(y); Y_max=np.max(y)  #In lat lon or cartesian
+
+	#N=2*int(ceil((R_max)/(2*Radius))+2)
+	
+	if element_type=='square':
+		N=int(math.ceil((X_max-X_min)/(Radius)))
+		M=int(math.ceil((Y_max-Y_min)/(Radius)))
+	else:
+
+                print 'X_max',X_max
+                print 'X_min',X_min
+                print 'Radius',Radius
+		N=2*int(math.ceil((X_max-X_min)/(Radius)))
+		M=2*int(math.ceil((Y_max-Y_min)/(Radius)))
+	#N=10
+	#M=6
+	#MP4
+
+ 	dx=x[1]-x[0]	
+ 	dy=y[1]-y[0]
+	Lx=X_max+dx
+	Ly=Y_max+dx
+
+	berg_count=0
+	#for j in range(N):
+	for i in range(N):
+		if element_type=='square':
+			x_start=Radius
+			y_start=(Radius)
+			x_val=x_start+(2*i*Radius)
+
+		#Hexagonal	
+		else:   
+			y_start=(Radius)+(((i%2)*Radius))
+			x_start=((2/np.sqrt(3))*Radius)
+			x_val=x_start + (np.sqrt(3)*Radius*i)
+
+		for j in range(M):
+		#for i in range(M):
+			#x_val=x_start+(2*i*Radius)  ; y_val=y_start
+			y_val=y_start+(2*j*Radius)  ;# x_val=x_start + (np.sqrt(3)*Radius*i)
+			if check_if_it_is_in_domain(x_val,y_val,X_min,X_max,Y_min,Y_max,R_earth,lat_init,adjust_lat_ref,dx,dy):
+			#if True:
+				#R_val=np.sqrt(((x_val-x0)**2) +((y_val-y0)**2))
+				if check_if_it_is_ice(x_val,y_val,ice_mask,dx):
+					#Don't allow points closer than R from the boundary (these are sorted out later)
+					#if abs(y_val-Ly)<Radius or  ((abs(x_val-Lx)<((2/np.sqrt(3))*Radius)) and element_type=='hexagon') or ((abs(x_val-Lx)<Radius) and element_type=='square'):
+					berg_count=berg_count+1
+					iceberg_num.append(berg_count)
+					dx_berg.append(x_val)
+					dy_berg.append(y_val)
+					width.append(np.sqrt(element_area))
+	#print 'dx_berg',dx_berg
+	#print 'dy_berg',dy_berg
+
+
+
+	Number_of_bergs=berg_count
+	print 'Icebergs created. Number of bergs = ', Number_of_bergs
+	
+	#Deciding if icebergs are static or not
+	static_berg = [0. for i in dx_berg]
+	if set_all_bergs_static_by_default==True:
+		static_berg = [1. for i in static_berg]
+	if set_some_bergs_static_by_default is True:
+		for i in range(len(dx_berg)):
+			if dx_berg[i]>Lx/2:
+				static_berg[i]=1.
+	if break_some_bonds==True:
+		#static_berg =Change_static_berg_after_calving(Number_of_bergs,lat,lon, static_berg)
+		static_berg =Change_static_berg_after_calving(Number_of_bergs,dy_berg,dx_berg, static_berg)
+		static_berg=static_berg[0]
+		
+	if Remove_stationary_bergs is True:
+		Fill_in_the_boundaries=False
+		[dx_berg, dy_berg,iceberg_num, width,Number_of_bergs,static_berg]=remove_stationary_bergs(dx_berg, dy_berg,iceberg_num,\
+				width,Number_of_bergs,static_berg)
+		print 'After purge  Number of bergs = ', Number_of_bergs
+
+
+	#Defining the thickness of the icebergs
+	(thickness, mass)=Define_iceberg_thickness_and_mass(Number_of_bergs,dx_berg,dy_berg,rho_ice,Radius, h_ice,x,y,\
+			width,Interpolate_from_four_corners,element_area,element_type,static_berg)	
+
+	N_bergs_before_bd=Number_of_bergs
+	if Fill_in_the_boundaries==True and element_type=='hexagon':
+	 	[dx_berg, dy_berg,iceberg_num, width,Number_of_bergs,static_berg,thickness,mass]= add_extra_bergs_on_boundary(dx,dy,x,y,Number_of_bergs,element_area,rho_ice,X_min,X_max,Y_min,\
+				Y_max,R_earth,lat_init,adjust_lat_ref,ice_mask,iceberg_num,width,dx_berg,dy_berg,\
+				h_ice,element_type,static_berg,thickness,mass)
+		print 'Number of icebergs after accounting for boundaries = ', Number_of_bergs
+	
+
+
+	if Convert_to_lat_lon==True:
+		#Defining lon lat positions:
+		#dlat_berg=(180/np.pi)*(1/R_earth)*dy_berg
+		#dlon_berg=(180/np.pi)*(1/R_earth)*(1/np.cos(lat_init*np.pi/180))*dx_berg
+		for i in range(Number_of_bergs):
+			#Finding latittude
+			dlat_dy=(180/np.pi)*(1/R_earth)
+
+			lat.append(lat_init+(dlat_dy*dy_berg[i]))
+
+			#Finding longitude
+			if adjust_lat_ref==True:
+				lat_ref=lat_init+(dlat_dy*dy_berg[i])
+				#print lat_ref
+			dlon_dx=(180/np.pi)*(1/R_earth)*(1/np.cos(lat_ref*np.pi/180)) #Note that this depends on the latitude of the iceberg. Could approx this with lat_init.
+			lon.append(lon_init+(dlon_dx*dx_berg[i] ))
+
+			#dlon_berg.append(dlon_dx*dx_berg[i])
+			#lon.append(lon_init+dlon_berg[i])
+	else:
+		if scale_the_grid_to_lat_lon==True:
+			Scale_up=1./2000.
+			Radius=Radius*Scale_up
+			dx_berg = [(i*Scale_up) for i in dx_berg] ; dy_berg = [i*Scale_up for i in dy_berg] 
+			x=x*Scale_up ; y=y*Scale_up
+			dx=dx*Scale_up ;dy=dy*Scale_up
+		x=(x-np.min(x))+(dx/2) ; y=(y-np.min(y))+(dy/2)
+		lon=dx_berg  ; lat=dy_berg
+	
+	#Note that static_berg calculations used to be here, after the conversion. I have moved them. I hope that this does not affect answers.
+
+	return (Number_of_bergs,lon,lat,iceberg_num,dx_berg,dy_berg,thickness, mass,width,x,y,Radius,static_berg,N_bergs_before_bd)
+
+
+
+def Create_calving_event(lat1,lon1,lat2,lon2):
+	[R_calve, R_long, R_short, Calve_lon, Calve_lat]=get_calving_parameters()
+
+	#Circular calving from ice front
+	R1=np.sqrt((lon1-Calve_lon)**2+ (lat1-Calve_lat)**2)
+	R2=np.sqrt((lon2-Calve_lon)**2+ (lat2-Calve_lat)**2)
+
+	#Iceberg splitting down the midde (length wise)
+	#R1=lat1
+	#R2=lat2
+	#R_calve=500*1000
+	#Iceberg splitting down the midde (width wise)
+	#R1=lon1
+	#R2=lon2
+	#R_calve=250*1000
+
+	#Circular Calving
+	bond_broken=False
+	if ((R1 < R_calve)*(R2>R_calve) )  > 0.5 :
+		bond_broken=True
+	if ((R2 < R_calve)*(R1>R_calve) )  > 0.5 :
+		bond_broken=True
+
+
+
+	#Rectabgular Calving
+	#R1_x=np.sqrt((lon1-Calve_lon)**2)
+	#R1_y=np.sqrt((lat1-Calve_lat)**2)
+	#R2_x=np.sqrt((lon2-Calve_lon)**2)
+	#R2_y=np.sqrt((lat2-Calve_lat)**2)
+	#bond_broken=False
+	#if ((R1_x<R_short)*(R1_y<R_long))*(1-((R2_x<R_short)*(R2_y<R_long)))  > 0.5 :
+	#	bond_broken=True
+	#if ((R2_x<R_short)*(R2_y<R_long))*(1-((R1_x<R_short)*(R1_y<R_long)))  > 0.5 :
+	#	bond_broken=True
+
+
+	return bond_broken
+
+def get_calving_parameters():
+	#Calve_lat =20  
+	#Calve_lon=160
+	#R_calve=15
+	Calve_lat =20.2*2000  
+	Calve_lon=165*2000
+	R_calve=15*2000
+	R_long =18*2000
+	R_short =12*2000
+	
+	return [R_calve,  R_long, R_short, Calve_lon, Calve_lat]
+
+def Change_static_berg_after_calving(Number_of_bergs,lat,lon, static_berg):
+	[R_calve, R_long, R_short, Calve_lon, Calve_lat]=get_calving_parameters()
+	count=0.
+	for i in range(Number_of_bergs):
+		#R1=np.sqrt((lon[i]-Calve_lon)**2)
+		#R2=np.sqrt((lat[i]-Calve_lat)**2)
+		R1=np.sqrt((lon[i]-Calve_lon)**2+ (lat[i]-Calve_lat)**2)
+		#Making calved icebergs not be static.
+		#if R1<R_calve and (R2<1.6*R_calve):
+		#if R1<R_short and (R2<R_long):
+		if R1<R_calve:
+			count=count+1.
+			#print 'An iceberg is now static!'
+			static_berg[i]=0.
+	print 'Amount of unstatic icebergs after calving = ', count
+
+	return [static_berg]
+
+def Change_static_berg_after_bonding(Number_of_bergs,lat,lon, static_berg):
+	#For now, it just uses a bigger circle.
+	multiplier=1.2
+	[R_calve, R_long, R_short, Calve_lon, Calve_lat]=get_calving_parameters()
+	count=0.
+	for i in range(Number_of_bergs):
+		R1=np.sqrt((lon[i]-Calve_lon)**2+ (lat[i]-Calve_lat)**2)
+		#Making calved icebergs not be static.
+		#R1=np.sqrt((lon[i]-Calve_lon)**2)
+		#R2=np.sqrt((lat[i]-Calve_lat)**2)
+		#if R1<(multiplier*R_short) and (R2<(multiplier*R_long)):
+		if R1<(R_calve*multiplier):
+			count=count+1.
+			#print 'An iceberg is now static!'
+			static_berg[i]=0.
+	print 'Amount of unstatic icebergs after bonding and restatic= ', count
+
+	return [static_berg]
+
+def find_max_number_of_bonds(first_berg_num,Number_of_bonds):
+	count=1
+	best_count=1
+	sorted_bonds=np.sort(first_berg_num)
+	for k in range(1,Number_of_bonds):
+		previous_berg=sorted_bonds[k-1]
+		#print k, sorted_bonds[k]
+		if sorted_bonds[k] == sorted_bonds[k-1]:
+			count=count+1
+			best_count=max(count,best_count)
+		else:
+			count=1
+	Max_number_of_bonds=best_count
+	return Max_number_of_bonds
+
+def Define_iceberg_bonds(Number_of_bergs,iceberg_num,lat,lon,dx_berg, dy_berg,Radius,break_some_bonds,static_berg, Allow_bonds_for_static_iceberg\
+		,N_bergs_before_bd,Allow_bonds_with_boundary_bergs):
+	print 'Starting to create bonds...'
+	#Defining Bonds:
+	Bond=np.zeros((Number_of_bergs, Number_of_bergs))
+	bond_broken=False
+	first_berg_num=[]  # Initializing bond list first berg
+	first_berg_ine=[]  # Initializing bond list first berg
+	first_berg_jne=[]  # Initializing bond list first berg
+	first_berg_lat=[]  # Initializing bond list first berg
+	first_berg_lon=[]  # Initializing bond list first berg
+	other_berg_num=[]  # Initializing bond list other berg
+	other_berg_ine=[]  # Initializing bond list other berg
+	other_berg_jne=[]  # Initializing bond list other berg
+	other_berg_lat=[]  # Initializing bond list other berg
+	other_berg_lon=[]  # Initializing bond list other berg
+	bond_count=0
+	for i in range(Number_of_bergs):
+		if (static_berg[i]<0.5) or (Allow_bonds_for_static_iceberg is True):
+			#for j in range(Number_of_bergs):
+			for j in range(i):
+				if (static_berg[j]<0.5) or (Allow_bonds_for_static_iceberg is True):
+					if i!=j:
+						if ((i <N_bergs_before_bd) and (j <N_bergs_before_bd))  or (Allow_bonds_with_boundary_bergs is True):
+							R_dist=np.sqrt(((dx_berg[i]-dx_berg[j])**2) + ((dy_berg[i]-dy_berg[j])**2))
+							if break_some_bonds==True:
+								bond_broken=Create_calving_event(lat[i],lon[i],lat[j],lon[j])
+							if R_dist < (2.01*Radius) and (bond_broken==False):
+								bond_count=bond_count+2
+								#Connect bond in the first direction
+								first_berg_num.append(iceberg_num[i]);	first_berg_ine.append(999); 
+								other_berg_num.append(iceberg_num[j]); 	other_berg_ine.append(999);
+								first_berg_jne.append(999);first_berg_lat.append(lat[i]); first_berg_lon.append(lon[i])
+								other_berg_jne.append(999);other_berg_lat.append(lat[j]); other_berg_lon.append(lon[j])
+								#Connect bond in the other direction
+								first_berg_num.append(iceberg_num[j]);	first_berg_ine.append(999);
+								other_berg_num.append(iceberg_num[i]); 	other_berg_ine.append(999);
+								first_berg_jne.append(999);first_berg_lat.append(lat[j]); first_berg_lon.append(lon[j])
+								other_berg_jne.append(999);other_berg_lat.append(lat[i]); other_berg_lon.append(lon[i])
+	Number_of_bonds=bond_count
+	Max_number_of_bonds=find_max_number_of_bonds(first_berg_num,Number_of_bonds)
+	print 'Number of bonds created = ' , Number_of_bonds
+	print 'Maximum number of bonds = ' ,  Max_number_of_bonds
+
+	return [ Number_of_bonds, first_berg_num,first_berg_ine,first_berg_jne,first_berg_lat,first_berg_lon, other_berg_num,other_berg_ine, other_berg_jne,other_berg_lat,other_berg_lon]
+
+def load_ISOMIP_ice_geometry(filename,buffer_number):
+	with nc.Dataset(filename) as file:
+		ocean_mask = file.variables['openOceanMask'][:,:]
+		upperSurface = file.variables['upperSurface'][:,:]
+		lowerSurface = file.variables['lowerSurface'][:,:]
+		x = file.variables['x'][:]
+		y = file.variables['y'][:]
+
+	ice_mask=1-ocean_mask #one if it ice, zero if it is ocean
+	h_ice=upperSurface-lowerSurface #The ice thickness
+	M=ice_mask.shape
+
+	#Setting the boundaries to non-ice
+	A=np.arange(0,buffer_number)
+	B=np.arange(M[0]-buffer_number,M[0])
+	C=np.arange(M[1]-buffer_number,M[1])
+	ice_mask[A,:]=0; ice_mask[B,:]=0
+	ice_mask[:,A]=0; ice_mask[:,C]=0
+	
+	return [x,y,ice_mask,h_ice]
+
+
+def create_clipped_icethickness_file(h_ice,area,mass,grid_area,gravity,Ice_geometry_source):
+	#Creating clipped file
+        [ny, nx]= h_ice.shape ; 
+	
+	New_ice_thickness_filename='output_files/'+ Ice_geometry_source +'_Ice_Shelf_clipped.nc'
+        g=Dataset(New_ice_thickness_filename,'w') # w if for creating a file
+
+        g.createDimension('nx',nx)
+        g.createDimension('ny',ny)
+
+        thick_h=g.createVariable('thick','f8',('ny','nx'))
+        area_h=g.createVariable('area','f8',('ny','nx'))
+        p_surf_h=g.createVariable('p_surf','f8',('ny','nx'))
+
+        thick_h.units = 'm'
+        thick_h.standard_name = 'ice shelf thickness (clipped)'
+        area_h.units = 'm2'
+        area_h.standard_name = 'ice shelf area'
+        p_surf_h.units = 'Pa'
+        p_surf_h.standard_name = 'surface pressure due to ice shelf'
+
+	p_surf=(gravity*mass)/grid_area
+        g.variables['thick'][:]=h_ice
+        g.variables['area'][:]=area
+        g.variables['p_surf'][:]=p_surf
+        print 'Creating clipped ice file: ' , New_ice_thickness_filename
+        
+        g.sync()
+        g.close()
+
+
+def load_ISOMIP_reduced_ice_geometry(ice_filename,buffer_number):
+	with nc.Dataset(ice_filename) as file:
+		h_ice = file.variables['thick'][:,:]
+		area =  file.variables['area'][:,:]
+		M=h_ice.shape
+
+	y=np.linspace(1000,79000,M[0],endpoint=True)
+	#x=np.linspace(321000,799000,M[1],endpoint=True)
+	x=np.linspace(1000,479000,M[1],endpoint=True)
+	ice_mask=h_ice>0.
+
+
+	count=0. #MP1
+	#Setting the boundaries to non-ice
+	A=np.arange(0,buffer_number)
+	B=np.arange(M[0]-buffer_number,M[0])
+	C=np.arange(M[1]-buffer_number,M[1])
+	#if buffer_number>0:
+	ice_mask[A,:]=0; ice_mask[B,:]=0
+	ice_mask[:,A]=0; ice_mask[:,C]=0
+	
+	return [x,y,ice_mask,h_ice]
+
+def load_generic_ice_geometry(filename):
+	print 'Loading from ' , filename
+	with nc.Dataset(filename) as file:
+		h_ice = file.variables['thick'][:]
+		area = file.variables['area'][:,:]
+		x = file.variables['lon'][:]
+		y = file.variables['lat'][:]
+
+               # x = x.flatten('F')
+               # y = y.flatten('F')
+                #h_ice = h_ice.flatten('F')
+
+		ice_mask=h_ice>0.
+		ice_mask[np.where(ice_mask<-1)]=0.
+		#ice_mask=1-ocean_mask #one if it ice, zero if it is ocean
+		h_ice[np.where(np.isnan(h_ice))]=0.
+                ice_mask[np.where(np.isnan(ice_mask))]=0.
+		dx=x[1]-x[0]
+		lon_init=x[0]-(dx/2.)
+		lat_init=y[0]-(dx/2.)
+		print 'Bottom corner = [ ', lon_init,' , ' , lat_init, ' dx = ' , dx
+	
+	return [x,y,ice_mask,h_ice,lon_init, lat_init]
+
+def load_Weddel_ice_geometry(filename):
+	with nc.Dataset(filename) as file:
+		h_ice = file.variables['thickness'][:,:]
+		ice_mask = file.variables['icemask_grounded_and_shelves'][:,:]
+		x = file.variables['lon'][:]
+		y = file.variables['lat'][:]
+
+		ice_mask[np.where(ice_mask<-1)]=0.
+		#ice_mask=1-ocean_mask #one if it ice, zero if it is ocean
+		h_ice[np.where(np.isnan(h_ice))]=0.
+                ice_mask[np.where(np.isnan(ice_mask))]=0.
+	
+	return [x,y,ice_mask,h_ice]
+
+def Select_just_one_berg(lon,lat,thickness,width,mass,iceberg_num,chosen_berg_num,static_berg):
+	print 'You have chosen to choose just one icebergs!!!'
+	for k in range(len(lat)):
+		if iceberg_num[k]==chosen_berg_num:
+			berg_ind=k
+	lon_temp=lon[berg_ind]; lon=[] ; lon.append(lon_temp)
+	lat_temp=lat[berg_ind]; lat=[] ; lat.append(lat_temp)
+	thickness_temp=thickness[berg_ind]; thickness=[] ; thickness.append(thickness_temp)
+	mass_temp=mass[berg_ind]; mass=[] ; mass.append(mass_temp)
+	width_temp=width[berg_ind]; width=[] ; width.append(width_temp)
+	static_berg_temp=static_berg[berg_ind]; static_berg=[] ; static_berg.append(static_berg_temp)
+	iceberg_num_temp=iceberg_num[berg_ind]; iceberg_num=[] ; iceberg_num.append(iceberg_num_temp)
+	Number_of_bergs=1
+	return [Number_of_bergs,lon,lat,thickness,width,mass,iceberg_num]
+
+def plotting_iceberg_positions(lat,lon,Number_of_bergs,R_earth,Radius,IA_scaling,Convert_to_lat_lon, \
+		plot_circles,h_ice,ice_mask,x,y,plot_ice_mask,plot_ice_thickness,thickness,plot_icebergs_positions,static_berg,h_ice_new,plot_h_ice_new):
+	print 'Starting to plot...'	
+	Radius=Radius*IA_scaling
+	circ_ind=np.linspace(0,2*np.pi,100);
+
+
+
+	if plot_ice_mask==True:
+		cNorm = mpl.colors.Normalize(vmin=0., vmax=1.)
+		plt.pcolor(x,y,ice_mask,norm=cNorm)
+		plt.title('Ice mask')
+
+	elif plot_h_ice_new is True: # Ice thickness after interpolation
+		cNorm = mpl.colors.Normalize(vmin=np.min(h_ice_new), vmax=np.max(h_ice_new))
+		plt.pcolor(x,y,h_ice_new , norm=cNorm)
+		plt.title('New thickness')
+
+	elif plot_ice_thickness==True:
+		cNorm = mpl.colors.Normalize(vmin=0., vmax=1000.)
+		plt.pcolor(x,y,h_ice,cmap='jet',norm=cNorm)
+		plt.title('Old thickness')
+
+	if plot_icebergs_positions==True:
+		#variable=thickness
+		variable=static_berg
+		plt.scatter(lon, lat,color='yellow')
+		cNorm = mpl.colors.Normalize(vmin=0., vmax=np.max(variable))
+		plt.scatter(lon, lat,c=variable,norm=cNorm,cmap='jet',s=150)
+		#cNorm = mpl.colors.Normalize(vmin=-1, vmax=1.)
+		#plt.scatter(lon, lat,c=static_berg,norm=cNorm,cmap='jet',s=150)
+		#plt.title('Iceberg positions')
+
+	#plt.plot(lon, lat,'bo-',linewidth=5)
+	if plot_circles==True:
+		for k in range(Number_of_bergs):
+			if Convert_to_lat_lon==True:
+				dR_lat=(Radius/R_earth)*(180/np.pi)
+				dR_lon=(Radius/R_earth)*(180/np.pi)*(1/np.cos(lat[k]*np.pi/180))
+				plt.plot(lon[k]+(dR_lon*np.cos(circ_ind)),lat[k]+(dR_lat*np.sin(circ_ind)),'b');
+			else:
+				plt.plot(lon[k]+(Radius*np.cos(circ_ind)),lat[k]+(Radius*np.sin(circ_ind)),'b');
+
+
+
+	#plt.plot(lon, lat,'bo-')
+	if Convert_to_lat_lon==True:
+		plt.xlabel('longitude (deg)')
+		plt.ylabel('latitude (deg)')
+	else:
+		plt.xlabel('longitude (m)')
+		plt.ylabel('latitude (m)')
+	plt.colorbar()
+	plt.grid(True)
+
+
+def plotting_iceberg_bonds(first_berg_lat,first_berg_lon,other_berg_lat,other_berg_lon,Number_of_bonds):
+
+	for k in range(Number_of_bonds):
+		x_bond=[]
+		y_bond=[]
+		x_bond.append(first_berg_lon[k])
+		x_bond.append(other_berg_lon[k])
+		y_bond.append(first_berg_lat[k])
+		y_bond.append(other_berg_lat[k])
+		plt.plot(x_bond, y_bond,'r',linewidth=5)
+
+
+def spread_mass_to_ocean(Nx,Ny,i,j,mass_on_ocean,x,y,Area,Mass,element_type,grid_area,static_berg):
+		#Note that the x,y coming into this routine are the position within a cell (from 0 to 1), with 0.5,0.5 being in the center of the cell.
+
+		#Initialize weights for each cell	
+		yDxL=0.  ; yDxC=0. ; yDxR=0. ; yCxL=0. ; yCxR=0. 
+		yUxL=0.  ; yUxC=0. ; yUxR=0. ; yCxC=1.
+
+		if element_type=='square':
+		#if True:
+			L = min(( (np.sqrt(Area)  / np.sqrt(grid_area))),1) ;  #Non dimensionalize element length by grid area. (This gives the non-dim length of the square)
+			xL=min(0.5, max(0., 0.5-(x/L)))
+			xR=min(0.5, max(0., (x/L)+(0.5-(1/L) )))
+			xC=max(0., 1.-(xL+xR))
+			yD=min(0.5, max(0., 0.5-(y/L)))
+			yU=min(0.5, max(0., (y/L)+(0.5-(1/L) )))
+			yC=max(0., 1.-(yD+yU))
+
+			yDxL=yD*xL#*grd%msk[i-1,j-1]
+			yDxC=yD*xC#*grd%msk[i  ,j-1]
+			yDxR=yD*xR#*grd%msk[i+1,j-1]
+			yCxL=yC*xL#*grd%msk[i-1,j  ]
+			yCxR=yC*xR#*grd%msk[i+1,j  ]
+			yUxL=yU*xL#*grd%msk[i-1,j+1]
+			yUxC=yU*xC#*grd%msk[i  ,j+1]
+			yUxR=yU*xR#*grd%msk(i+1,j+1]
+			yCxC=1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )
+
+		if element_type=='hexagon':
+		#if False:#element_type=='hexagon':
+			H = min(( (np.sqrt(Area/(2*np.sqrt(3)))  / np.sqrt(grid_area))),1) ;  #Non dimensionalize element length by grid area. (This gives the non-dim Apothen of the hexagon)
+			S=(2/np.sqrt(3))*H #Side of the hexagon
+			if S>0.5:
+				print 'Elements must be smaller than a whole gridcell', 'i.e.: S= ' , S , '>=0.5',i,j
+				halt
+
+			#Subtracting the position of the nearest corner from x,y
+			origin_x=1 ; origin_y=1
+			if x<0.5:
+				origin_x=0
+			if y<0.5:
+				origin_y=0
+
+			x0=(x-origin_x) #Position of the hexagon center, relative to origin at the nearest vertex
+			y0=(y-origin_y)
+			
+			#(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Divide_hexagon_into_4_quadrants_old(x0,y0,H)
+			(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Hexagon_into_quadrants_using_triangles(x0,y0,H,0.)
+			if min(min(Area_Q1,Area_Q2),min(Area_Q3, Area_Q4)) <0:
+				print 'Yolo'
+				print x0,y0,H
+				#print min(min(Area_Q1,Area_Q2),min(Area_Q3, Area_Q4))
+				print Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+
+			Area_Q1=Area_Q1/Area_hex
+			Area_Q2=Area_Q2/Area_hex
+			Area_Q3=Area_Q3/Area_hex
+			Area_Q4=Area_Q4/Area_hex
+
+
+			#Now, you decide which quadrant belongs to which mass on ocean cell.
+			#Top right vertex
+			if x>=0.5 and y>= 0.5:
+				yUxR=Area_Q1
+				yUxC=Area_Q2
+				yCxC=Area_Q3
+				yCxR=Area_Q4
+			
+			#Top left vertex
+			if x<0.5 and y>= 0.5:
+				yUxC=Area_Q1
+				yUxL=Area_Q2
+				yCxL=Area_Q3
+				yCxC=Area_Q4
+			
+			#Bottom left vertex
+			if x<0.5 and y< 0.5:
+				yCxC=Area_Q1
+				yCxL=Area_Q2
+				yDxL=Area_Q3
+				yDxC=Area_Q4
+
+			#Bottom right vertex
+			if x>=0.5 and y< 0.5:
+				yCxR=Area_Q1
+				yCxC=Area_Q2
+				yDxC=Area_Q3
+				yDxR=Area_Q4
+
+			#if Sector<4 and Sector>-1:
+			#	print Sector
+				
+					
+			#Check that this is true
+			if abs(yCxC-(1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )))>0.001:
+				print 'All the mass is not being used!!!'
+				#print W1 , W2 , W3 , W4 , W5 , W6
+				#print Area_Upper, Area_Lower, Area_right, Area_left
+				print 'Areas: ',Area_hex,Area_hex*Area_Q1, Area_hex*Area_Q2, Area_hex*Area_Q3, Area_hex*Area_Q4
+				print 'x0=',x0, 'y0=',y0, 'H=', H
+				print 'Total area= ',(Area_Q1+Area_Q2+Area_Q3+Area_Q4)#, Sector
+				
+
+		#Accounting for masked points 
+		a=1. ; b=1. ; c=1. ; d=1.
+		if i==0:
+			a=0.;
+		if j==0: 
+			b=0.;
+		if i==Nx-1:
+			c=0;
+		if j==Ny-1:
+			d=0;
+
+		fraction_used= ((yDxL*a*b) + (yDxC*b) + (yDxR*b*c) +(yCxL*a) + (yCxR*c) + (yUxL*a*d) + (yUxC*d) + (yUxR*c*d) + (yCxC))
+		if static_berg>0.5:
+			fraction_used=1.
+
+		mass_on_ocean[i,j,1]=mass_on_ocean[i,j,1]+(a*b*yDxL*Mass/fraction_used)
+		mass_on_ocean[i,j,2]=mass_on_ocean[i,j,2]+(b*yDxC*Mass/fraction_used)
+		mass_on_ocean[i,j,3]=mass_on_ocean[i,j,3]+(b*c*yDxR*Mass/fraction_used)
+		mass_on_ocean[i,j,4]=mass_on_ocean[i,j,4]+(a*yCxL*Mass/fraction_used)
+		mass_on_ocean[i,j,5]=mass_on_ocean[i,j,5]+(yCxC*Mass/fraction_used)
+		mass_on_ocean[i,j,6]=mass_on_ocean[i,j,6]+(c*yCxR*Mass/fraction_used)
+		mass_on_ocean[i,j,7]=mass_on_ocean[i,j,7]+(a*d*yUxL*Mass/fraction_used)
+		mass_on_ocean[i,j,8]=mass_on_ocean[i,j,8]+(d*yUxC*Mass/fraction_used)
+		mass_on_ocean[i,j,9]=mass_on_ocean[i,j,9]+(c*d*yUxR*Mass/fraction_used)
+
+
+		return mass_on_ocean
+
+
+def calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x, y, Lx):
+
+	Lx_2=Lx/2.
+  
+	alpha=x2-x1
+	delta=y2-y1
+	beta=x4-x1
+	epsilon=y4-y1
+	gamma=(x3-x1)-(alpha+beta)
+	kappa=(y3-y1)-(delta+epsilon)
+
+	a=(kappa*beta-gamma*epsilon)
+	dx=np.mod(x-(x1-Lx_2),Lx)+(x1-Lx_2)-x1
+	dy=y-y1
+	b=(delta*beta-alpha*epsilon)-(kappa*dx-gamma*dy)
+	c=(alpha*dy-delta*dx)
+	
+	#print 'alpha,beta,gamma',alpha,beta,gamma
+	#print 'delta,epsilon,kappa',delta,epsilon,kappa
+	#print 'dx,dy',dx,dy
+	#print 'A,B,C,',a,b,c
+
+	if (abs(a)>1.e-12):
+		d=0.25*(b**2)-a*c
+		if (d>=0.):
+			yy1=-(0.5*b+np.sqrt(d))/a
+			yy2=-(0.5*b-np.sqrt(d))/a
+			if (abs(yy1-0.5).lt.abs(yy2-0.5)):
+				yj=yy1;
+			else:
+				yj=yy2;
+    		else:
+			print 'ERROR', halt
+	else:
+		if (b!=0.):
+			yj=-c/b
+		else:
+			yj=0.
+
+	a=(alpha+gamma*yj)
+	b=(delta+kappa*yj)
+	if (a!=0.):
+		xi=(dx-beta*yj)/a
+	elif (b!=0.):
+		xi=(dy-epsilon*yj)/b
+	else:
+		c=(epsilon*alpha-beta*delta)+(epsilon*gamma-beta*kappa)*yj
+		if (c!=0.):
+			xi=(epsilon*dx-beta*dy)/c
+		else:
+			print 'ERROR', halt2
+
+	return xi,yj
+
+
+
+def regrid_iceberg_thickness(lat,lon,Number_of_bergs,thickness,mass,h_ice,x,y,rho_ice,element_type,static_berg,plot_outcome=True):
+	Nx=len(x)  ; Ny=len(y)
+	dx=x[1]-x[0]    ;dy=y[1]-y[0]
+	New_mass=h_ice*0 #Initializing regrided field to zero
+	Area = [(mass[i]/(rho_ice*thickness[i])) for i in range(Number_of_bergs)] ;
+	grid_area=dx*dy #Assuming a regular grid
+	Orig_mass=h_ice*rho_ice*grid_area
+	
+	mass_on_ocean=np.zeros([Nx,Ny,10])   #Setting up matrix to spread mass to ocean.  Note that I have used 10 points  so that I can ignore 0 and match with python numbering
+	#mass_on_ocean=np.zeros([Nx,Ny])   #Setting up matrix to spread mass to ocean.
+	#Note: You may want to import the grid that the ocean model actually sees.
+	for berg_count in range(Number_of_bergs):  
+		x_val=lon[berg_count]  
+		y_val=lat[berg_count]
+		Area_val=Area[berg_count]
+		mass_val=mass[berg_count]
+
+		j_val=int(math.floor(y_val/dy))
+		i_val=int(math.floor(x_val/dx))
+		x_cell=(x_val-x[i_val])/np.sqrt(grid_area)+0.5
+		y_cell=(y_val-y[j_val])/np.sqrt(grid_area)+0.5
+
+		#if plot_outcome==True:
+		#	print 'YOLO0', x_val-123626.65521,y_val
+		#	print 'YOLO1', x[i_val],y[j_val]
+		#	print 'YOLO2', x_cell,y_cell
+
+		#Using the same interpolation as in the model
+		#x1=x[i_val]-(dx/2.)   ; y1=y[j_val]-(dx/2.)
+		#x2=x[i_val]+(dx/2.) ; y2=y[j_val]-(dx/2.)
+		#x3=x[i_val]+(dx/2.) ; y3=y[j_val]+(dx/2.)
+		#x4=x[i_val]-(dx/2.) ; y4=y[j_val]+(dx/2.)
+		#[xi,yj]=calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x_val, y_val, Lx=100000000000000.)
+		#[x_cell,y_cell]=calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x_val, y_val, Lx=100000000000000.)
+		#print 'YOLO:x1,x2,x3,x4',x1,x2,x3,x4
+		#print 'YOLO:y1,y2,y3,y4',y1,y2,y3,y4
+		#print 'YOLO:xi,yj,x_cell,y_cell', xi,yj, x_cell,y_cell
+
+		mass_on_ocean=spread_mass_to_ocean(Nx,Ny,i_val,j_val,mass_on_ocean,x_cell,y_cell,Area_val,mass_val,element_type,grid_area,static_berg[berg_count])
+
+	#Adding mass_onto_ocean
+	for i in range(1,Nx-1):
+		for j in range(1,Ny-1):
+			New_mass[j,i]=mass_on_ocean[i,j,5]  \
+					+  ( ( (mass_on_ocean[i-1,j-1,9]+mass_on_ocean[i+1,j+1,1])   \
+					+  (mass_on_ocean[i+1,j-1,7]+mass_on_ocean[i-1,j+1,3]) ) \
+					+   ( (mass_on_ocean[i-1,j  ,6]+mass_on_ocean[i+1,j  ,4])   \
+					+  (mass_on_ocean[i  ,j-1,8]+mass_on_ocean[i  ,j+1,2]) ) )
+	
+	#Adding mass to boundary cells
+	for j in range(1,Ny-1):
+		i=0
+		New_mass[j,i]=mass_on_ocean[i,j,5] +  mass_on_ocean[i+1,j+1,1] +  mass_on_ocean[i+1,j-1,7] \
+			+  mass_on_ocean[i+1,j  ,4] 	+  mass_on_ocean[i  ,j-1,8] + mass_on_ocean[i  ,j+1,2] 
+		i=Nx-1	
+		New_mass[j,i]=mass_on_ocean[i,j,5] +  mass_on_ocean[i-1,j-1,9] + mass_on_ocean[i-1,j+1,3] \
+					+   mass_on_ocean[i-1,j ,6] + mass_on_ocean[i ,j-1,8]+mass_on_ocean[i ,j+1,2]
+	
+	for i in range(1,Nx-1):
+		j=0
+		New_mass[j,i]=mass_on_ocean[i,j,5] +   mass_on_ocean[i+1,j+1,1] +  mass_on_ocean[i-1,j+1,3]  \
+				+  mass_on_ocean[i-1,j  ,6] + mass_on_ocean[i+1,j  ,4] +  mass_on_ocean[i  ,j+1,2]
+
+		j=Ny-1	
+		New_mass[j,i]=mass_on_ocean[i,j,5] +  mass_on_ocean[i-1,j-1,9] 	+  mass_on_ocean[i+1,j-1,7] + \
+				mass_on_ocean[i-1,j  ,6]+mass_on_ocean[i+1,j  ,4] +  mass_on_ocean[i  ,j-1,8]
+
+	#Corners
+	i=0 ;j=0
+	New_mass[j,i]=mass_on_ocean[i,j,5] + mass_on_ocean[i+1,j+1,1] + mass_on_ocean[i+1,j  ,4] + mass_on_ocean[i  ,j+1,2]  
+	i=0 ;j=Ny-1
+	New_mass[j,i]=mass_on_ocean[i,j,5] + mass_on_ocean[i+1,j-1,7] + mass_on_ocean[i+1,j  ,4] + mass_on_ocean[i  ,j-1,8]  
+	i=Nx-1; j=0
+	New_mass[j,i]=mass_on_ocean[i,j,5] + mass_on_ocean[i-1,j+1,3] + mass_on_ocean[i-1,j  ,6] + mass_on_ocean[i  ,j+1,2]
+	i=Nx-1; j=Ny-1	
+	New_mass[j,i]=mass_on_ocean[i,j,5] + mass_on_ocean[i-1,j-1,9] + mass_on_ocean[i-1,j  ,6] + mass_on_ocean[i  ,j-1,8]
+
+
+	if plot_outcome==True: #MP2
+		#print 'Warning: the interpolation scheme is not the same as the one used in the model'	
+		
+		plot_data=(Orig_mass-New_mass)/Orig_mass
+		cNorm = mpl.colors.Normalize(vmin=-.1, vmax=.1)
+		vmax=np.max(abs(plot_data))
+		plt.pcolormesh(x,y,plot_data,cmap='bwr',norm=cNorm)
+		plt.title('Error between bergs and shelf')
+
+		#plot_data=(New_mass/New_thickness/rho_ice)
+		#vmax=np.max(abs(plot_data))
+		#cNorm = mpl.colors.Normalize(vmin=-vmax, vmax=vmax)
+		#plt.pcolormesh(x,y,plot_data,cmap='jet',norm=cNorm)
+		#plt.title('h_ice')
+
+		#plot_data=(New_mass-Orig_mass)/(rho_ice*grid_area)
+		#cNorm = mpl.colors.Normalize(vmin=-0.00000000001, vmax=0.00000000001)
+		#vmax=np.max(abs(plot_data))
+		#plt.pcolormesh(x,y,plot_data,cmap='bwr',norm=cNorm)
+
+		plt.colorbar()
+		#plt.xlim([min(x)-,max(x)])
+		#plt.ylim([min(y),max(y)])
+		#plt.show()
+
+	return New_mass
+
+def Switch_x_and_y_directions(lat,lon, A, B, C):
+	print 'Switching x and y directions!!!'
+	lat_new=[]
+	lon_new=[]
+	for i in range(len(lat)):
+		lat_new.append(lon[i])
+		lon_new.append(lat[i])
+	M=A.shape
+	A_new=np.zeros([M[1],M[0]])
+	B_new=np.zeros([M[1],M[0]])
+	C_new=np.zeros([M[1],M[0]])
+	for i in range(M[0]):
+		for j in range(M[1]):
+			A_new[j,i]=A[i,j]
+			B_new[j,i]=B[i,j]
+			C_new[j,i]=C[i,j]
+
+	return	[lat_new,lon_new,A_new,B_new, C_new]
+
+def interpolate_field_onto_new_grid(x,y,x_new,y_new,field):
+        xx, yy = np.meshgrid(x, y)
+        #f = interpolate.interp2d(x, y, field, kind='cubic')
+	f = interpolate.interp2d(x, y, field, kind='linear')
+        field_new = f(x_new, y_new)
+        return field_new
+
+def convert_input_to_catesian_coordinates(lon,lat,ice_mask,h_ice,R_earth,dx):
+	#Parameters
+        thickness_threshhold=0.01
+
+        lon_max=np.max(lon) ; lon_min=np.min(lon)
+        lat_max=np.max(lat) ; lat_min=np.min(lat)
+        lat_ref=np.mean(lat)
+
+        #Converting to cartesian grid
+        x=(np.pi/180)*R_earth*np.cos(lat_ref*np.pi/180.)*lon
+        y=(np.pi/180)*R_earth*lat
+        x=x-np.min(x)
+        y=y-np.min(y)
+        
+        #Creating regular grid
+        x_new=np.linspace(np.min(x), np.max(x), num=len(x))
+        y_new=np.linspace(np.min(y),np.max(y), num=len(y))
+        x_new=np.arange(np.min(x), np.max(x), step=dx)
+        y_new=np.arange(np.min(y), np.max(y), step=dx)
+
+        h_ice_new=interpolate_field_onto_new_grid(x,y,x_new,y_new,h_ice)
+        h_ice_new[np.where(h_ice_new<thickness_threshhold)]=0.
+        ice_mask_new=interpolate_field_onto_new_grid(x,y,x_new,y_new,ice_mask)
+        #ice_mask_new=np.round(ice_mask_new)
+        #print ice_mask_new[50,:]
+        
+        return [x_new,y_new,ice_mask_new,h_ice_new]
+
+
+####################################################################################################################################################
+##########################################################  Main Program   #########################################################################
+####################################################################################################################################################
+
+def main(args):
+
+	#Flags
+	save_restart_files=args.save_restart_files
+	save_new_h_ice_file=args.save_new_h_ice_file
+	Convert_to_lat_lon=args.Convert_to_lat_lon
+	input_is_cartesian=args.input_is_cartesian
+
+	#Iceberg setup flags
+	only_choose_one_berg=args.only_choose_one_berg  ; chosen_berg_num=args.chosen_berg_num
+	scale_the_grid_to_lat_lon=args.scale_the_grid_to_lat_lon
+	adjust_lat_ref=args.adjust_lat_ref
+	set_all_thicknesses_to_one=args.set_all_thicknesses_to_one   ; Th_prescribed=args.Th_prescribed
+	Interpolate_from_four_corners=args.Interpolate_from_four_corners
+	Switch_x_and_y_to_rotate_90=args.Switch_x_and_y_to_rotate_90
+	set_all_domain_to_ice=args.set_all_domain_to_ice
+	Use_default_radius=args.Use_default_radius
+
+	#Static vs non-static flags
+	set_all_bergs_static_by_default=args.set_all_bergs_static_by_default 
+	set_some_bergs_static_by_default=args.set_some_bergs_static_by_default 
+	Make_icebergs_non_static_later=args.Make_icebergs_non_static_later 
+
+	#Mass spreadng flags
+	element_type=args.element_type
+	Switch_regridding_element_type=args.Switch_regridding_element_type
+	Fill_in_the_boundaries=args.Fill_in_the_boundaries
+	regrid_icebergs_onto_grid=args.regrid_icebergs_onto_grid
+
+	#Plotting flags
+	Run_plotting_subroutine=args.Run_plotting_subroutine
+	plot_circles=args.plot_circles
+	plot_ice_mask=args.plot_ice_mask
+	plot_ice_thickness=args.plot_ice_thickness
+	plot_icebergs_positions=args.plot_icebergs_positions
+	plot_h_ice_new=args.plot_h_ice_new
+	plot_bonds=args.plot_bonds
+
+	#Bond related flags
+	Create_icebergs_bonds=args.Create_icebergs_bonds
+	break_some_bonds=args.break_some_bonds
+	Remove_stationary_bergs=args.Remove_stationary_bergs
+	Allow_bonds_for_static_iceberg=args.Allow_bonds_for_static_iceberg
+	Allow_bonds_with_boundary_bergs=args.Allow_bonds_with_boundary_bergs
+
+
+	#Which experiment
+	Ice_geometry_source=args.Ice_geometry_source
+	ISOMIP_reduced=args.ISOMIP_reduced
+	ISOMIP_ice_geometry_filename=args.ISOMIP_ice_geometry_filename
+	ISOMIP_reduced_ice_geometry_filename=args.ISOMIP_reduced_ice_geometry_filename
+	Weddell_ice_geometry_filename=args.Weddell_ice_geometry_filename
+	Generic_ice_geometry_filename=args.Generic_ice_geometry_filename
+
+
+	#Parameters
+	Radius=args.Radius
+	rho_ice=args.rho_ice
+	gravity=args.gravity
+	mass_scaling=args.mass_scaling
+	R_earth=args.R_earth
+	buffer_number=args.buffer_number
+
+	#Let interactive radius be different from radius for testing the model:
+	IA_scaling=args.IA_scaling
+
+	#Applying some special case flags
+	if Ice_geometry_source=='ISOMIP':
+		Convert_to_lat_lon=False       ; input_is_cartesian=True ; 
+	if Ice_geometry_source=='Generic':
+		Convert_to_lat_lon=False       ; input_is_cartesian=True ; set_all_bergs_static_by_default=False ; Fill_in_the_boundaries=False ; Use_default_radius=True 
+	if Ice_geometry_source=='Weddell':
+		Convert_to_lat_lon=False        ; input_is_cartesian=False
+
+	#Applying Warnings
+	if element_type=='square' and Interpolate_from_four_corners==True:
+		print 'Square packing with R dividing dx, works best with interpolation off.'
+
+	print 'Element type= ', element_type, ';  Switched_regridding= ', Switch_regridding_element_type
+	if break_some_bonds==True:
+		print 'Some bonds are being broken'
+
+	#####################################################################################
+	#####################################################################################
+	Radius=Radius/IA_scaling
+
+	if  Ice_geometry_source=='ISOMIP':
+		if ISOMIP_reduced==False:
+			lon_init=0  ; lat_init=-70.  #latitude  of bottom left corner of iceberg
+			(x,y,ice_mask,h_ice)=load_ISOMIP_ice_geometry(ISOMIP_ice_geometry_filename,buffer_number)
+			ice_filename=ISOMIP_ice_geometry_filename
+		else:
+			lon_init=0  ; lat_init=-70.  #latitude  of bottom left corner of iceberg
+			(x,y,ice_mask,h_ice)=load_ISOMIP_reduced_ice_geometry(ISOMIP_reduced_ice_geometry_filename,buffer_number)
+			ice_filename=ISOMIP_reduced_ice_geometry_filename
+
+	if  Ice_geometry_source=='Weddell':
+		lon_init=-32.9  ; lat_init=-70.  #latitude  of bottom left corner of iceberg
+		(x,y,ice_mask,h_ice)=load_Weddel_ice_geometry(Weddell_ice_geometry_filename)
+		ice_filename=Weddell_ice_geometry_filename
+		Radius=0.5*10000. 
+
+	if  Ice_geometry_source=='Generic':
+		(x,y,ice_mask,h_ice, lon_init, lat_init)=load_generic_ice_geometry(Generic_ice_geometry_filename)
+
+        if input_is_cartesian is False:
+                dx=10000.
+                lat_grid=y ; lon_grid=x
+                (x,y,ice_mask,h_ice)=convert_input_to_catesian_coordinates(x,y,ice_mask,h_ice,R_earth,dx)
+
+	if set_all_thicknesses_to_one==True:
+		print 'All thicknesses being set equal to 1'
+		if set_all_domain_to_ice is True:
+			ice_mask[:,:]=1.
+		h_ice[np.where(ice_mask>0.5)]=Th_prescribed
+
+	if Use_default_radius is True:
+		dx=x[1]-x[0]  #This is used as the ocean grid size
+		R_frac=0.45
+		if element_type=='square':
+			Radius=R_frac*dx  #(less than half the grid size)
+		if element_type=='hexagon':
+			Radius= (np.sqrt(3)/2.) *(R_frac*dx)   #(S is < half the grid size)
+	print 'Radius set to R= ' , Radius
+	
+	lat_ref=np.max(y)
+	#Define the positions,thickness, mass,  of the icebergs
+	(Number_of_bergs,lon,lat,iceberg_num,dx_berg, dy_berg,thickness,mass,width,x,y,Radius,static_berg,N_bergs_before_bd)= Create_icebergs(lon_init,lat_init,\
+			Radius,R_earth, x, y,ice_mask,h_ice,Convert_to_lat_lon,rho_ice,element_type,scale_the_grid_to_lat_lon,lat_ref,adjust_lat_ref,\
+			Interpolate_from_four_corners,Fill_in_the_boundaries, set_all_bergs_static_by_default,break_some_bonds,Remove_stationary_bergs,set_some_bergs_static_by_default)
+
+	print 'Maximum thickness:', np.max(thickness), np.min(thickness)
+	#Define the positions of the iceberg bonds
+	if Create_icebergs_bonds==True:
+		(Number_of_bonds, first_berg_num,first_berg_ine,first_berg_jne,first_berg_lat,first_berg_lon, other_berg_num,other_berg_ine, other_berg_jne,other_berg_lat,other_berg_lon)=\
+				Define_iceberg_bonds(Number_of_bergs,iceberg_num,lat,lon,dx_berg, dy_berg,Radius,break_some_bonds,static_berg,Allow_bonds_for_static_iceberg\
+				,N_bergs_before_bd,Allow_bonds_with_boundary_bergs)
+
+	if Make_icebergs_non_static_later is True:
+		Change_static_berg_after_bonding(Number_of_bergs,lat,lon, static_berg)
+
+
+	temp_mass=[mass[i]/thickness[i] for i in range(len(thickness))]
+	if only_choose_one_berg==True:
+		(Number_of_bergs,lon,lat,thickness,width,mass,iceberg_num)= Select_just_one_berg(lon,lat,thickness,width,mass,iceberg_num,chosen_berg_num,static_berg)
+
+
+	if regrid_icebergs_onto_grid==True:
+		if scale_the_grid_to_lat_lon==True:
+			print 'Regridding should be run with scale_the_grid_to_lat_lon off'
+		else:
+			if Switch_regridding_element_type==True:
+				if element_type=='square':
+					element_type='hexagon'
+				else:
+					element_type='square'
+			temp_thickness=[1. for i in thickness]
+			temp_mass=[mass[i]/(thickness[i]*rho_ice) for i in range(len(thickness))]
+			temp_rho_ice=1.
+			New_area=regrid_iceberg_thickness(lat,lon,Number_of_bergs,temp_thickness,temp_mass,h_ice,x,y,temp_rho_ice,element_type,static_berg,plot_outcome=False)
+			New_mass=regrid_iceberg_thickness(lat,lon,Number_of_bergs,thickness,mass,h_ice,x,y,rho_ice,element_type,static_berg,plot_outcome=False)
+		if save_new_h_ice_file==True:
+			grid_area=(x[1]-x[0])*(x[1]-x[0])
+			h_ice_new=New_mass*0
+			M=h_ice.shape
+			for j in range(M[0]):
+				for i in range(M[1]):
+					if New_area[j,i]>0:
+						h_ice_new[j,i]=New_mass[j,i]/(rho_ice*New_area[j,i])  
+
+	if Switch_x_and_y_to_rotate_90 is True:
+		[lat,lon, h_ice_new,New_area,New_mass]=Switch_x_and_y_directions(lat,lon, h_ice_new,New_area,New_mass)
+			
+
+	if save_restart_files==True:	
+		#Creating iceberg restart file
+		Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg)
+		
+		#Creating bond restart file
+		if Create_icebergs_bonds==True:
+			Create_bond_restart_file(Number_of_bonds,first_berg_num,first_berg_ine,first_berg_jne,other_berg_ine,other_berg_jne,iceberg_num,other_berg_num,Ice_geometry_source)
+			
+		if save_new_h_ice_file==True:
+			create_clipped_icethickness_file(h_ice_new,New_area,New_mass,grid_area,gravity,Ice_geometry_source)
+
+	# Plotting the positions and bonds of the newly formed formation
+	if Run_plotting_subroutine==True:
+		plotting_iceberg_positions(lat,lon,Number_of_bergs,R_earth,Radius,IA_scaling,Convert_to_lat_lon,\
+				plot_circles,h_ice,ice_mask,x,y,plot_ice_mask,plot_ice_thickness,thickness,plot_icebergs_positions,static_berg,h_ice_new,plot_h_ice_new)
+		if (plot_bonds==True) and (Create_icebergs_bonds):
+			plotting_iceberg_bonds(first_berg_lat,first_berg_lon,other_berg_lat,other_berg_lon,Number_of_bonds)
+
+	#field=New_mass/(rho_ice*grid_area)
+	field=New_area/grid_area -1. 
+	M=field.shape	
+	#print 'field',(field[M[0]-1,:])
+	#print 'field',(field[M[0]-2,:])
+	#print 'h_ice',h_ice_new[:,:]
+	#print 'h_ice-1',h_ice_new[:,:]-1.
+	if Run_plotting_subroutine:
+		plt.show()
+	print 'Script complete'
+
+
+
+if __name__ == '__main__':
+	optCmdLineArgs=	parseCommandLine()
+	main(optCmdLineArgs)
+	#sys.exit(main())
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/test/Iceberg_repository/Scripts_and_analysis/movie_bergs_traj.py b/test/Iceberg_repository/Scripts_and_analysis/movie_bergs_traj.py
new file mode 100755
index 0000000..ec99778
--- /dev/null
+++ b/test/Iceberg_repository/Scripts_and_analysis/movie_bergs_traj.py
@@ -0,0 +1,283 @@
+#!/usr/bin/env python
+
+def bergs_yearday(bergs):
+	bergs=bergs_read(bergs,'year')
+	bergs=bergs_read(bergs,'day')
+	for b in xrange (0,len(bergs.berg)):
+		bergs.berg[b].yearday=bergs.berg[b].year+(bergs.berg[b].day/372)
+		#Note I have not included all the warnings about dimensions already existing.
+        return bergs
+
+
+def bergs_read(bergs,varname):
+	nc=bergs.nc
+	bergs_list=bergs.berg
+	var = nc.variables[varname][:]
+	for b in xrange (0,len(bergs.berg)):
+		k=[]
+		js=bergs.berg[b].js
+		je=bergs.berg[b].je
+		for l in xrange (0,len(js)):
+			temp=range(js[l],je[l]+1)
+			for i in xrange (0, len(temp)):
+				k.append(temp[i])
+			setattr(bergs.berg[b],varname,var[k])
+        return bergs
+
+
+def bergs_hash(year, day, x, y, m):
+	ilat=(90.+y)/180
+        ilon=(360 % x)/360;
+        iyear=np.floor(year);
+        iday=(day/372);
+        im=math.log(m,10)-7.9;
+        h=ilon+1e3*ilat+1e6*iday+1e9*iyear+1e12*im;
+        return h
+
+
+
+def bergs_open(filename):
+
+	#Creating a classes
+	class berg_handle:
+		def __init__(self,berg,nc):
+			self.berg=berg
+			self.nc=nc
+
+	class berg_type:
+		def __init__(self,hash):
+			self.hash=hash
+			self.year0=[]
+			self.day0=[]
+			self.lon0=[]
+			self.lat0=[]
+			self.mass0=[]
+			self.js=[]
+			self.je=[]
+			self.width=[]
+			self.lon=[]
+			self.lat=[]
+			self.year=[]
+			self.day=[]
+			self.uvel=[]
+			self.vvel=[]
+			self.uo=[]
+			self.vo=[]
+			self.ui=[]
+			self.ua=[]
+			self.vu=[]
+			self.mass_of_bits=[]
+			self.heat_density=[]
+			self.thickness=[]
+			self.length=[]
+			self.ssh_x=[]
+			self.ssh_y=[]
+			self.sst=[]
+			self.cn=[]
+			self.hi=[]
+			self.yearday=[]
+			self.iceberg_num=[]
+
+	#Importing the data
+	nc = Dataset(filename, mode='r')
+	lat = nc.variables['lat'][:]
+	N=len(lat)
+	js=np.where(lat>91)[0]
+	je=np.concatenate([js[1:]-1, np.array([N-1])])
+	lon = nc.variables['lon'][:]
+	year = nc.variables['year'][:]
+	day = nc.variables['day'][:]
+	#mass = nc.variables['mass'][:]
+	iceberg_num = nc.variables['iceberg_num'][:]
+
+	N=len(js)
+	h=np.zeros(N)
+	# Making a list of identifying hashes
+	k=0
+	for j in js+1:
+		#h[k]=bergs_hash(year[j], day[j],lon[j],lat[j],mass[j])
+		h[k]=iceberg_num[j]
+		k=k+1
+
+	#Creates a sorted array of unique elements of h
+	h=sorted(list(set(h)))
+
+	#Create a list of bergs, named by their hash values, h
+	berg=[]
+	for i in xrange (0,len(h)):
+		berg.append(berg_type(h[i]))
+
+	for i in xrange(0, len(js)):
+		j=js[i]+1
+		#l=np.where(h==bergs_hash(year[j], day[j],lon[j],lat[j],mass[j]))[0]
+		l=np.where(h==iceberg_num[j])[0]
+		berg[l].year0.append(year[j])
+		berg[l].day0.append(day[j])
+		berg[l].lon0.append(lon[j])
+		berg[l].lat0.append(lat[j])
+		#berg[l].mass0.append(mass[j])
+		berg[l].js.append(js[i]+2)
+		berg[l].je.append(je[i])
+
+	#Sort each segment
+	for i in xrange (0,len(h)):
+		yd=year[berg[i].js]+(day[berg[i].js]/373)
+		#Sort according to descending yd, and then pull out indicies for js, and je.
+		
+		berg[i].js=[berg[i].js[n] for n,_ in sorted(list(enumerate(yd)),reverse=True)]
+		berg[i].je=[berg[i].je[n] for n,_ in sorted(list(enumerate(yd)),reverse=True)]
+
+	bergs_handle=berg_handle(berg,nc)
+
+	return bergs_handle
+
+###############################################################################################
+#################################  Beginning of Script  #######################################
+###############################################################################################
+from netCDF4 import Dataset
+import numpy as np
+#from PIL import *
+import math
+import os
+import matplotlib
+matplotlib.use("GTKAgg")
+import matplotlib.pyplot as plt
+from pylab import *
+import pdb
+import argparse
+#This combination allows you to access the varibale imputted from the command line.
+import sys
+
+#Clear screen
+#os.system('clear')
+
+#This is a command which puts you into testing mode so that you can troubleshoot (like a breakpoint in matlab)
+#pdb.set_trace()
+
+#If no files are given at runtime, then use the files selected here:
+if len(sys.argv)==1:
+	Number_of_files=2  # How many files would you like to view?
+
+	#Choosing which files to use
+	#Weddel Sea Version
+	fileroot='/home/aas/Iceberg_Project/Weddell_Sea/'
+	dirname1='one_iceberg_testing_Verlet';
+	dirname2='one_iceberg_testing_RK';
+	
+	filename1=fileroot+dirname1+'/iceberg_trajectories.nc'
+	filename2=fileroot+dirname2+'/iceberg_trajectories.nc'
+
+	#Other files
+	#filename1='/home/aas/Iceberg_Project/Test_data1/Quick_Global_RK15/iceberg_trajectories.nc';
+	#filename1= '/home/aas/Iceberg_Project/Weddell_Sea/one_iceberg_testing/iceberg_trajectories.nc'
+
+else:
+	Number_of_files=len(sys.argv)-1
+	
+#Imput parameters
+berg_num=0 #index of ic
+
+#Flags and on/off switches
+plot_timeseries=0
+plot_trajectory=1
+plot_bergsize=1
+fix_horizontal_scale=0
+plot_all_bergs=1  #plots all the icebergs and not just the one given by n
+plot_initial_size=0
+plot_size_at_start_and_finish_only=1
+short_form=1 #only looks up the lat / lon
+
+#Creating and filling up the bergs
+for loop in xrange(0,Number_of_files):
+	if len(sys.argv)==1:
+		if loop==0: filename=filename1
+		if loop==1: filename=filename2
+	else:
+		filename=sys.argv[loop+1]
+	print filename	
+
+	berg=[]; del berg
+	bergs=bergs_open(filename)
+	bergs=bergs_read(bergs,'width')
+	bergs=bergs_read(bergs,'length')
+	bergs=bergs_read(bergs,'lat')
+	bergs=bergs_read(bergs,'lon')
+	bergs=bergs_yearday(bergs)
+	
+	N=len(bergs.berg)
+	if plot_all_bergs==0:
+		N=1
+	for n in xrange (0, N):
+		if plot_all_bergs==0:
+			n=berg_num
+
+		#Loading variables
+		lon=bergs.berg[n].lon[:]
+		lat=bergs.berg[n].lat[:]
+		width=bergs.berg[n].width[:]
+		length=bergs.berg[n].length[:]
+		yearday=bergs.berg[n].yearday[:]
+
+		#Finding the index of the initial time
+		initial_time_ind=sorted(list(enumerate(yearday)),key=lambda x: x[0])[-1][0]
+		final_time_ind=sorted(list(enumerate(yearday)),key=lambda x: x[0])[0][0]
+
+###########################   Begining plotting  #################################
+
+		if plot_trajectory==1:
+			#plt.subplot(2,1,1)
+			if loop==0:
+				if n==1:
+					plt.plot(lon,lat,'ko-')
+				if n!=1:
+					plt.plot(lon,lat,'go-')
+			else:
+				plt.plot(lon,lat,'bo-')
+			plt.xlabel('longitude (deg)')
+			plt.ylabel('latitude (deg)')
+			plt.title('Iceberg trajectory')
+			plt.grid(True)
+			#savefig("test.png")
+
+			if plot_bergsize==1:
+				Radius_earth=6378.135*1000;
+				circ_ind=np.linspace(0,2*pi,100);
+				for k in xrange (0 ,len(lat)):
+    					L_eff=sqrt(((width[k]*length[k])/pi));
+					plt.plot(lon[k],lat[k],'bo',linewidth=5)
+				        #d_lat=(L_eff/Radius_earth)*(180/pi);
+					#d_lon=L_eff/(111.320*(10**(3))*cos(lat[k]*pi/180));
+				        d_lat=(L_eff/Radius_earth)*(180/pi);
+					d_lon=(L_eff/(Radius_earth*cos(lat[k]*pi/180)))*(180/pi);
+                                        if plot_size_at_start_and_finish_only==0:
+					        plt.plot(lon[k]+(d_lon*cos(circ_ind)),lat[k]+(d_lat*sin(circ_ind)),'b');
+					if k==initial_time_ind and plot_initial_size==1:
+						plt.plot(lon[k]+(d_lon*cos(circ_ind)),lat[k]+(d_lat*sin(circ_ind)),'r');
+					if k==final_time_ind:
+						plt.plot(lon[k]+(d_lon*cos(circ_ind)),lat[k]+(d_lat*sin(circ_ind)),'r');
+				
+			#Setting axes to have equal distance
+				if fix_horizontal_scale==1:
+					y_scale=(max(lat)-min(lat))*(Radius_earth*pi/180)
+					x_scale=(max(lon)-min(lon))*(111.320*(10**(3))*cos(np.mean(lat)/180*pi))
+					d=0.6*max(x_scale,y_scale)
+					d_lat=d*(180/(Radius_earth*pi))
+					d_lon=d/(111.320*(10**(3))*cos(np.mean(lat)*pi/180))
+					plt.xlim([((min(lon)+max(lon))/2)-d_lon,((min(lon)+max(lon))/2)+d_lon])
+					plt.ylim([((min(lat)+max(lat))/2)-d_lat,((min(lat)+max(lat))/2)+d_lat])
+	
+			plt.plot(lon[initial_time_ind],lat[initial_time_ind],'ro')
+plt.show()
+
+if plot_timeseries==1:
+	n=0
+	#plt.subplot(2,1,2)
+	plt.plot(yearday,lon,'ko-')
+	plt.xlabel('yearday')
+	plt.ylabel('lon (deg)')
+	plt.grid(True)
+	plt.savefig("test7.png")
+	plt.show()
+
+
+print 'Script complete'
diff --git a/test/Iceberg_repository/Scripts_and_analysis/old_bergs_quickview.py b/test/Iceberg_repository/Scripts_and_analysis/old_bergs_quickview.py
new file mode 100755
index 0000000..c67c638
--- /dev/null
+++ b/test/Iceberg_repository/Scripts_and_analysis/old_bergs_quickview.py
@@ -0,0 +1,268 @@
+#!/usr/bin/env python
+
+def bergs_yearday(bergs):
+	bergs=bergs_read(bergs,'year')
+	bergs=bergs_read(bergs,'day')
+	for b in xrange (0,len(bergs.berg)):
+		bergs.berg[b].yearday=bergs.berg[b].year+(bergs.berg[b].day/372)
+		#Note I have not included all the warnings about dimensions already existing.
+        return bergs
+
+
+def bergs_read(bergs,varname):
+	nc=bergs.nc
+	bergs_list=bergs.berg
+	var = nc.variables[varname][:]
+	for b in xrange (0,len(bergs.berg)):
+		k=[]
+		js=bergs.berg[b].js
+		je=bergs.berg[b].je
+		for l in xrange (0,len(js)):
+			temp=range(js[l],je[l]+1)
+			for i in xrange (0, len(temp)):
+				k.append(temp[i])
+			setattr(bergs.berg[b],varname,var[k])
+        return bergs
+
+
+def bergs_hash(year, day, x, y, m):
+	ilat=(90.+y)/180
+        ilon=(360 % x)/360;
+        iyear=np.floor(year);
+        iday=(day/372);
+        im=math.log(m,10)-7.9;
+        h=ilon+1e3*ilat+1e6*iday+1e9*iyear+1e12*im;
+        return h
+
+
+
+def bergs_open(filename):
+
+	#Creating a classes
+	class berg_handle:
+		def __init__(self,berg,nc):
+			self.berg=berg
+			self.nc=nc
+
+	class berg_type:
+		def __init__(self,hash):
+			self.hash=hash
+			self.year0=[]
+			self.day0=[]
+			self.lon0=[]
+			self.lat0=[]
+			self.mass0=[]
+			self.js=[]
+			self.je=[]
+			self.width=[]
+			self.lon=[]
+			self.lat=[]
+			self.year=[]
+			self.day=[]
+			self.uvel=[]
+			self.vvel=[]
+			self.uo=[]
+			self.vo=[]
+			self.ui=[]
+			self.ua=[]
+			self.vu=[]
+			self.mass_of_bits=[]
+			self.heat_density=[]
+			self.thickness=[]
+			self.length=[]
+			self.ssh_x=[]
+			self.ssh_y=[]
+			self.sst=[]
+			self.cn=[]
+			self.hi=[]
+			self.yearday=[]
+
+	#Importing the data
+	nc = Dataset(filename, mode='r')
+	lat = nc.variables['lat'][:]
+	N=len(lat)
+	js=np.where(lat>91)[0]
+	je=np.concatenate([js[1:]-1, np.array([N-1])])
+	lon = nc.variables['lon'][:]
+	year = nc.variables['year'][:]
+	day = nc.variables['day'][:]
+	mass = nc.variables['mass'][:]
+
+	N=len(js)
+	h=np.zeros(N)
+	# Making a list of identifying hashes
+	k=0
+	for j in js+1:
+		h[k]=bergs_hash(year[j], day[j],lon[j],lat[j],mass[j])
+		k=k+1
+
+	#Creates a sorted array of unique elements of h
+	h=sorted(list(set(h)))
+
+	#Create a list of bergs, named by their hash values, h
+	berg=[]
+	for i in xrange (0,len(h)):
+		berg.append(berg_type(h[i]))
+
+	for i in xrange(0, len(js)):
+		j=js[i]+1
+		l=np.where(h==bergs_hash(year[j], day[j],lon[j],lat[j],mass[j]))[0]
+		berg[l].year0.append(year[j])
+		berg[l].day0.append(day[j])
+		berg[l].lon0.append(lon[j])
+		berg[l].lat0.append(lat[j])
+		berg[l].mass0.append(mass[j])
+		berg[l].js.append(js[i]+2)
+		berg[l].je.append(je[i])
+
+	#Sort each segment
+	for i in xrange (0,len(h)):
+		yd=year[berg[i].js]+(day[berg[i].js]/373)
+		#Sort according to descending yd, and then pull out indicies for js, and je.
+		
+		berg[i].js=[berg[i].js[n] for n,_ in sorted(list(enumerate(yd)),reverse=True)]
+		berg[i].je=[berg[i].je[n] for n,_ in sorted(list(enumerate(yd)),reverse=True)]
+
+	bergs_handle=berg_handle(berg,nc)
+
+	return bergs_handle
+
+###############################################################################################
+#################################  Beginning of Script  #######################################
+###############################################################################################
+from netCDF4 import Dataset
+import numpy as np
+#from PIL import *
+import math
+import os
+import matplotlib
+matplotlib.use("GTKAgg")
+import matplotlib.pyplot as plt
+from pylab import *
+import pdb
+import argparse
+#This combination allows you to access the varibale imputted from the command line.
+import sys
+
+#Clear screen
+#os.system('clear')
+
+#This is a command which puts you into testing mode so that you can troubleshoot (like a breakpoint in matlab)
+#pdb.set_trace()
+
+#If no files are given at runtime, then use the files selected here:
+if len(sys.argv)==1:
+	Number_of_files=2  # How many files would you like to view?
+
+	#Choosing which files to use
+	#Weddel Sea Version
+	fileroot='/home/aas/Iceberg_Project/Weddell_Sea/'
+	dirname1='one_iceberg_testing_Verlet';
+	dirname2='one_iceberg_testing_RK';
+	
+	filename1=fileroot+dirname1+'/iceberg_trajectories.nc'
+	filename2=fileroot+dirname2+'/iceberg_trajectories.nc'
+
+	#Other files
+	#filename1='/home/aas/Iceberg_Project/Test_data1/Quick_Global_RK15/iceberg_trajectories.nc';
+	#filename1= '/home/aas/Iceberg_Project/Weddell_Sea/one_iceberg_testing/iceberg_trajectories.nc'
+
+else:
+	Number_of_files=len(sys.argv)-1
+	
+#Imput parameters
+berg_num=0 #index of ic
+
+#Flags and on/off switches
+plot_timeseries=0
+plot_trajectory=1
+plot_bergsize=0
+fix_horizontal_scale=0
+plot_all_bergs=1  #plots all the icebergs and not just the one given by n
+
+
+#Creating and filling up the bergs
+for loop in xrange(0,Number_of_files):
+	if len(sys.argv)==1:
+		if loop==0: filename=filename1
+		if loop==1: filename=filename2
+	else:
+		filename=sys.argv[loop+1]
+	print filename	
+
+	berg=[]; del berg
+	bergs=bergs_open(filename)
+	bergs=bergs_read(bergs,'width')
+	bergs=bergs_read(bergs,'length')
+	bergs=bergs_read(bergs,'lat')
+	bergs=bergs_read(bergs,'lon')
+	bergs=bergs_yearday(bergs)
+	
+	N=len(bergs.berg)
+	if plot_all_bergs==0:
+		N=1
+	for n in xrange (0, N):
+		if plot_all_bergs==0:
+			n=berg_num
+
+		#Loading variables
+		lon=bergs.berg[n].lon[:]
+		lat=bergs.berg[n].lat[:]
+		width=bergs.berg[n].width[:]
+		length=bergs.berg[n].length[:]
+		yearday=bergs.berg[n].yearday[:]
+
+		#Finding the index of the initial time
+		initial_time_ind=sorted(list(enumerate(yearday)),key=lambda x: x[1])[0][0]
+
+###########################   Begining plotting  #################################
+
+		if plot_trajectory==1:
+			#plt.subplot(2,1,1)
+			if loop==0:
+				plt.plot(lon,lat,'ko-')
+			else:
+				plt.plot(lon,lat,'bo-')
+			plt.xlabel('longitude (deg)')
+			plt.ylabel('latitude (deg)')
+			plt.title('Iceberg trajectory')
+			plt.grid(True)
+			#savefig("test.png")
+
+			if plot_bergsize==1:
+				Radius_earth=6378.135*(10^(3));
+				circ_ind=np.linspace(0,2*pi,100);
+				for k in xrange (0 ,len(lat)):
+    					L_eff=sqrt(((width[k]*length[k])/pi));
+					plt.plot(lon[k],lat[k],'bo',linewidth=5)
+				        d_lat=(L_eff/Radius_earth)*(180/pi);
+					d_lon=L_eff/(111.320*(10**(3))*cos(lat[k]/180*pi));
+				        plt.plot(lon[k]+(d_lon*cos(circ_ind)),lat[k]+(d_lat*sin(circ_ind)),'b');
+					if k==initial_time_ind:
+						plt.plot(lon[k]+(d_lon*cos(circ_ind)),lat[k]+(d_lat*sin(circ_ind)),'r');
+				
+			#Setting axes to have equal distance
+				if fix_horizontal_scale==1:
+					y_scale=(max(lat)-min(lat))*(Radius_earth*pi/180)
+					x_scale=(max(lon)-min(lon))*(111.320*(10**(3))*cos(np.mean(lat)/180*pi))
+					d=0.6*max(x_scale,y_scale)
+					d_lat=d*(180/(Radius_earth*pi))
+					d_lon=d/(111.320*(10**(3))*cos(np.mean(lat)/180*pi))
+					plt.xlim([((min(lon)+max(lon))/2)-d_lon,((min(lon)+max(lon))/2)+d_lon])
+					plt.ylim([((min(lat)+max(lat))/2)-d_lat,((min(lat)+max(lat))/2)+d_lat])
+	
+			plt.plot(lon[initial_time_ind],lat[initial_time_ind],'ro')
+plt.show()
+
+if plot_timeseries==1:
+	n=0
+	#plt.subplot(2,1,2)
+	plt.plot(yearday,lon,'ko-')
+	plt.xlabel('yearday')
+	plt.ylabel('lon (deg)')
+	plt.grid(True)
+	plt.savefig("test7.png")
+	plt.show()
+
+
+print 'Script complete'
diff --git a/test/Iceberg_repository/Scripts_and_analysis/quick_benchmark_comparison.sh b/test/Iceberg_repository/Scripts_and_analysis/quick_benchmark_comparison.sh
new file mode 100755
index 0000000..6f179c2
--- /dev/null
+++ b/test/Iceberg_repository/Scripts_and_analysis/quick_benchmark_comparison.sh
@@ -0,0 +1,5 @@
+echo "Difference between benchmark and quick test are:"
+cd ../
+diff Benchmark_Quick_Global_test/iceberg_trajectories.nc Quick_Global_test/iceberg_trajectories.nc
+
+echo "End of differences"
diff --git a/test/Iceberg_repository/Scripts_and_analysis/quick_plot.py b/test/Iceberg_repository/Scripts_and_analysis/quick_plot.py
new file mode 100755
index 0000000..3d1f39b
--- /dev/null
+++ b/test/Iceberg_repository/Scripts_and_analysis/quick_plot.py
@@ -0,0 +1,205 @@
+#!/usr/bin/env python
+
+#First import the netcdf4 library
+from netCDF4 import Dataset  # http://code.google.com/p/netcdf4-python/
+import numpy as np  # http://code.google.com/p/netcdf4-python/
+import matplotlib
+import math
+import os
+matplotlib.use("GTKAgg")
+from pylab import *
+#import matplotlib.pyplot as plt
+import pdb
+import netCDF4 as nc
+import sys
+import argparse
+
+
+def transpose_matrix(data):
+	M=data.shape
+	data_new=np.zeros([M[1],M[0]])
+	for i in range(M[0]):
+		for j in range(M[1]):
+			data_new[j,i]=data[i,j]
+	print 'After rotation' ,data.shape
+	return data_new
+
+def load_data_from_file(filename,field,dim_num,layer_number,rotated=None):
+	with nc.Dataset(filename) as file:
+		if dim_num==2:
+			data = file.variables[field][:]
+		if dim_num==3:
+			data = file.variables[field][:]
+		if dim_num==4:
+			data = file.variables[field][:]
+	
+	print 'Data size:' ,data.shape
+	
+	if len(data.shape)==3:
+		#data=np.squeeze(np.mean(data,axis=0))  #Mean over first variable
+		data=np.squeeze(data[-1,:,:])  #Final time
+	if len(data.shape)==4:
+			#data=np.squeeze(np.mean(data,axis=0))  #Mean over first variable
+			data=np.squeeze((data[-1,:,:,:]))  #Mean over first variable
+			data=np.squeeze(data[layer_number,:,:])#Layer choice over second 
+
+
+	if rotated=='rotated':
+		data=transpose_matrix(data)
+	return data
+
+def plot_data_field(data,field,vmin=None,vmax=None): 
+	print 'Starting to plot...'	
+	if vmin==None:
+		vmin=np.min(data)
+	else:
+		vmin=float(vmin)
+
+	if vmax==None:
+		vmax=np.max(data)
+	else:
+		vmax=float(vmax)
+	cmap='jet'
+	print vmin	
+	print vmax	
+
+	cNorm = mpl.colors.Normalize(vmin=vmin, vmax=vmax)
+	#cNorm = mpl.colors.Normalize(vmin=600, vmax=850)
+	plt.pcolormesh(data,norm=cNorm,cmap=cmap)
+	plt.colorbar()
+	plt.grid(True)
+	plt.title(field)
+
+def plot_operated_fields(data1,data2,field,operation,vmax_lim=None): 
+	print 'Starting to plot...'	
+
+	#Temp lines to subtract maximum
+	#temp_val=np.max(data1)
+	#data1=data1-temp_val ;	data2=data2-temp_val
+	
+	vmin=min(np.min(data1),np.min(data2))
+	vmax=max(np.max(data1),np.max(data2))
+	#vmin=-vmax
+
+	cmap='jet'
+	cNorm = mpl.colors.Normalize(vmin=vmin, vmax=vmax)
+
+	#Data from file 1:
+	plt.subplot(1,3,1)
+	plt.pcolormesh(data1,norm=cNorm,cmap=cmap)
+	plt.colorbar()
+	plt.title('File 1: ' + field)
+	#Data from file 2:
+	plt.subplot(1,3,2)
+	plt.pcolormesh(data2,norm=cNorm,cmap=cmap)
+	plt.colorbar()
+	plt.title('File 2: ' + field)
+
+
+	#Data from difference:
+	data3=data1-data2 #subtraction is the default
+	if operation=='divide':
+		data3=data1/data2
+	if operation=='relative':
+		data3=(data1-data2)/data1
+	if vmax_lim==None:
+		vmax=np.max(abs(data3))
+	else:
+		vmax=float(vmax_lim)
+	vmin=-vmax
+	cmap='bwr'
+	cNorm = mpl.colors.Normalize(vmin=vmin, vmax=vmax)
+	if operation=='divide':
+		cNorm = mpl.colors.Normalize(vmin=0, vmax=2)
+	if operation=='relative':
+		cNorm = mpl.colors.Normalize(vmin=-1, vmax=1)
+	plt.subplot(1,3,3)
+	plt.pcolormesh(data3,norm=cNorm,cmap=cmap)
+	plt.colorbar()
+	plt.title('Difference')
+	print 'Max/Min data3=', np.max(data3), np.min(data3)
+
+####################################################################################################################################################
+##########################################################  Main Program   #########################################################################
+####################################################################################################################################################
+
+def main():
+	parser = argparse.ArgumentParser()
+        parser.add_argument('--file1', default=None, help='The input data file1 in NetCDF format.')
+        parser.add_argument('--file2', default=None, help='The input data file2 in NetCDF format.')
+        parser.add_argument('--field', default=None, help='Feild to plot')
+        parser.add_argument('--field2', default=None, help='Feild to plot')
+        parser.add_argument('--operation',default=None, help='Operation betweeen fields')
+        parser.add_argument('--layer_number', default=0, help='Operation betweeen fields')
+        parser.add_argument('--dim_num', default=2, help='Number of dimensions of data')
+        parser.add_argument('--vmax', default=None, help='Maximum for plotting')
+        parser.add_argument('--vmin', default=None, help='Minimum for plotting')
+        parser.add_argument('--rotated', default=None, help='Minimum for plotting')
+	args = parser.parse_args()
+
+	#Converting input
+	field=args.field
+	field2=args.field
+	if args.field2 is not None:
+		field2=args.field2
+	layer_number=int(args.layer_number)
+	dim_num=int(args.dim_num)
+	operation=args.operation
+	filename1=args.file1
+	rotated=args.rotated
+	print 'File 1 = ' , filename1
+
+	#filename3='../../ocean_only/Alistair_ISOMIP/rho/ISOMIP_IC.nc'
+	#filename1='/lustre/f1/unswept/Alon.Stern/MOM6-examples_Alon/ocean_only/Alistair_ISOMIP/rho/ISOMIP.nc'
+
+	#if filename1==filename3:
+	#	print 'BOOM'
+	#else:
+	#	print 'NO'
+	plt.figure(figsize=(15,10))
+	#fig = plt.figure(1)
+
+	#Loading data from file1
+	data1=load_data_from_file(filename1,field,dim_num,layer_number,rotated)
+
+	if args.file2!=None:
+		filename2=args.file2
+		print 'File 2 = ' ,filename2
+		#Loading data from file1
+		data2=load_data_from_file(filename2,field2,dim_num,layer_number,rotated)
+
+		if operation=='subtract':
+			print 'Subtracting fields'
+			#data=data-data2
+			#operation='subtract'
+
+	if args.file2==None:
+		plot_data_field(data1,field,args.vmin,args.vmax)	
+	else:
+		plot_operated_fields(data1,data2,field,operation,args.vmax)	
+
+
+	#Plotting flags
+	#fig.set_size_inches(9,4.5)
+	plt.show()
+	print 'Script complete'
+
+
+
+if __name__ == '__main__':
+	main()
+	#sys.exit(main())
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/test/Iceberg_repository/Scripts_and_analysis/submit_to_queue.sh b/test/Iceberg_repository/Scripts_and_analysis/submit_to_queue.sh
new file mode 100755
index 0000000..bc0f32f
--- /dev/null
+++ b/test/Iceberg_repository/Scripts_and_analysis/submit_to_queue.sh
@@ -0,0 +1,23 @@
+#!/bin/csh -fx
+#PBS -N Tech_Bergs
+#PBS -l walltime=16:00:00
+#PBS -l size=128
+#PBS -S /bin/tcsh
+#PBS -r n
+#PBS -m ae
+#PBS -j oe
+#PBS -E
+#PBS -A gfdl_o
+
+#set compiler = intel
+
+
+module load totalview
+env
+pwd
+time aprun -n 128 ../../build/intel/ice_ocean_SIS2/repro/MOM6
+#date
+
+#time aprun ...
+
+#date
diff --git a/test/Iceberg_repository/Scripts_and_analysis/topog_file_create.py b/test/Iceberg_repository/Scripts_and_analysis/topog_file_create.py
new file mode 100755
index 0000000..59ba3ad
--- /dev/null
+++ b/test/Iceberg_repository/Scripts_and_analysis/topog_file_create.py
@@ -0,0 +1,89 @@
+#!/usr/bin/env python
+
+###############################################################################################
+from netCDF4 import Dataset
+import numpy as np
+import os
+import numpy
+import netCDF4 as nc
+#import matplotlib
+#import matplotlib.pyplot as plt
+#from pylab import *
+#import pdb
+#import argparse
+#This combination allows you to access the varibale imputted from the command line.
+#import sys
+
+#Clear screen
+def main():
+
+	os.system('clear')
+	input_geometry_filename='input_files/Isomip_ocean_geometry.nc'
+
+	#Flags
+	use_flat_bottom=True
+	use_side_walls=True
+
+	#Parameters
+	constant_depth=750.
+
+	if use_flat_bottom==True:
+		new_filename='output_files/topog_flat'
+	else:
+		new_filename='output_files/topog'
+	if use_side_walls==True:
+		new_filename=new_filename+'_boundaries'
+	new_filename=new_filename+'.nc'
+
+
+	#f=Dataset(input_geometry_filename,'r')
+	#g=Dataset(new_filename,'w') # w if for creating a file
+
+
+	with nc.Dataset(input_geometry_filename) as file:
+		Depth = file.variables['D'][:,:]
+
+	M= Depth.shape
+	ny=M[0]
+	nx=M[1]
+	print nx,ny
+
+	if use_flat_bottom==True:
+		Depth[:,:]=(Depth[:,:]*0.0)+constant_depth
+	if use_side_walls==True:
+		Depth[0,:]=0.0
+		Depth[ny-1,:]=0.0
+		Depth[:,0]=0.0
+		Depth[:,nx-1]=0.0
+	
+		Depth[ny-2,:]=0.0
+		Depth[ny-3,:]=0.0
+		Depth[ny-4,:]=0.0
+		Depth[ny-5,:]=0.0
+		Depth[ny-6,:]=0.0
+
+	#Creating the topog file
+	g=Dataset(new_filename,'w') # w if for creating a file
+
+	yt=g.createDimension('yt',ny)
+	xt=g.createDimension('xt',nx)
+
+	depth_h=g.createVariable('depth','f4',('yt','xt'))
+	g.variables['depth'][:]=Depth
+
+	print 'Writing file: ' , new_filename
+	
+	g.sync()
+	g.close()
+
+
+
+
+
+	print 'Script complete'
+
+
+
+if __name__ == '__main__':
+        main()
+        #sys.exit(main())
diff --git a/test/Iceberg_repository/Scripts_and_analysis/variables_comparison.sh b/test/Iceberg_repository/Scripts_and_analysis/variables_comparison.sh
new file mode 100755
index 0000000..8e8619c
--- /dev/null
+++ b/test/Iceberg_repository/Scripts_and_analysis/variables_comparison.sh
@@ -0,0 +1,5 @@
+ncdump -v  VI ../ISOMIP_ocean_ice/Shelf/rho/00010101.ice_day.nc > a 
+ncdump -v  VI ../ISOMIP_ocean_ice/Bergs/rho/00010101.ice_day.nc > b
+diff a b > c
+more c
+
diff --git a/test/Iceberg_repository/Scripts_and_analysis/write_restart_iceberg.py b/test/Iceberg_repository/Scripts_and_analysis/write_restart_iceberg.py
new file mode 100755
index 0000000..c170f52
--- /dev/null
+++ b/test/Iceberg_repository/Scripts_and_analysis/write_restart_iceberg.py
@@ -0,0 +1,424 @@
+#!/usr/bin/env python
+
+#First import the netcdf4 library
+from netCDF4 import Dataset  # http://code.google.com/p/netcdf4-python/
+import numpy as np  # http://code.google.com/p/netcdf4-python/
+import matplotlib
+#import matplotlib.pyplot as plt
+import math
+import os
+matplotlib.use("GTKAgg")
+import matplotlib.pyplot as plt
+from pylab import *
+import pdb
+
+
+
+def Create_iceberg_restart_file(f,g,Number_of_bergs, Number_of_bonds,lon,lat,thickness,width,mass,mass_scaling,iceberg_num,make_icebergs_static):
+	
+	# To copy the global attributes of the netCDF file  
+
+	for attname in f.ncattrs():
+		    setattr(g,attname,getattr(f,attname))
+
+
+	# To copy the dimension of the netCDF file
+	for dimname,dim in f.dimensions.iteritems():
+		# if you want to make changes in the dimensions of the new file
+		# you should add your own conditions here before the creation of the dimension.
+		#g.createDimension(dimname,len(dim))
+		g.createDimension(dimname,Number_of_bergs)
+
+	# To copy the variables of the netCDF file
+
+	for varname,ncvar in f.variables.iteritems():
+		# if you want to make changes in the variables of the new file
+		# you should add your own conditions here before the creation of the variable.
+		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
+		#Proceed to copy the variable attributes
+		for attname in ncvar.ncattrs():  
+			setattr(var,attname,getattr(ncvar,attname))
+		#Finally copy the variable data to the new created variable
+		#var[:] = ncvar[0]  Remove this. Not sure what it does.
+		
+		if varname=='i':
+			var[:]=Number_of_bergs
+		
+		if varname=='iceberg_num':
+			for j in range(Number_of_bergs):
+				#var[j]=j+1
+				var[j]=iceberg_num[j]
+
+		if varname=='uvel' or varname=='vvel' or varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
+		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
+		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
+		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old' \
+		or varname=='static_berg':
+			var[:]=0
+
+		if varname=='mass_scaling':
+			var[:]=mass_scaling
+
+		if varname=='thickness':
+			var[:]=thickness
+		
+		if varname=='mass':
+			var[:]=mass
+
+		if varname=='width'  or varname=='length':
+			var[:]=width
+
+		if varname=='lon':
+			for j in range(Number_of_bergs):
+				var[j]=lon[j]
+
+		if varname=='lat':
+			for j in range(Number_of_bergs):
+				var[j]=lat[j]
+
+		if varname=='static_berg' and  make_icebergs_static==True:
+			for j in range(Number_of_bergs):
+				var[j]=1.
+
+	f.close()
+	g.close()
+
+
+def Create_bond_restart_file(q,h, Number_of_bonds,first_berg_num,first_berg_ine,first_berg_jne,other_berg_ine,other_berg_jne,iceberg_num,other_berg_num):
+	#Creating the bond restart file
+
+
+	# To copy the global attributes of the netCDF file  
+
+	for attname in h.ncattrs():
+		    setattr(q,attname,getattr(h,attname))
+
+
+	# To copy the dimension of the netCDF file
+	for dimname,dim in h.dimensions.iteritems():
+		# if you want to make changes in the dimensions of the new file
+		# you should add your own conditions here before the creation of the dimension.
+		#g.createDimension(dimname,len(dim))
+		q.createDimension(dimname,Number_of_bonds)
+
+	# To copy the variables of the netCDF file
+
+	for varname,ncvar in h.variables.iteritems():
+		# if you want to make changes in the variables of the new file
+		# you should add your own conditions here before the creation of the variable.
+		var = q.createVariable(varname,ncvar.dtype,ncvar.dimensions)
+		#Proceed to copy the variable attributes
+		for attname in ncvar.ncattrs():  
+			setattr(var,attname,getattr(ncvar,attname))
+		#Finally copy the variable data to the new created variable
+		#var[:] = ncvar[0]
+		var[:] = 0
+
+		if varname=='i':
+			var[:]=Number_of_bonds
+
+		if varname=='first_berg_num':
+			for j in range(Number_of_bonds):
+				var[j]=first_berg_num[j]
+
+		if varname=='first_berg_ine':
+			for j in range(Number_of_bonds):
+				var[j]=first_berg_ine[j]
+
+		if varname=='first_berg_jne':
+			for j in range(Number_of_bonds):
+				var[j]=first_berg_jne[j]
+
+		if varname=='other_berg_num':
+			for j in range(Number_of_bonds):
+				var[j]=other_berg_num[j]
+
+		if varname=='other_berg_ine':
+			for j in range(Number_of_bonds):
+				var[j]=other_berg_ine[j]
+
+		if varname=='other_berg_jne':
+			for j in range(Number_of_bonds):
+				var[j]=other_berg_jne[j]
+
+	h.close()
+	q.close()
+	
+	if Number_of_bonds==0:
+		print 'Warning: Iceberg bond files do not work for single icebergs (no bonds). Turn iceberg bonds off'
+
+def plotting_iceberg_positions_and_bonds(lat,lon,first_berg_lat,first_berg_lon,other_berg_lat,other_berg_lon,Number_of_bergs,Number_of_bonds,R_earth,Radius,IA_scaling,convert_to_lat_lon):
+
+	Radius=Radius*IA_scaling
+	circ_ind=np.linspace(0,2*pi,100);
+	for k in range(Number_of_bergs):
+		if convert_to_lat_lon==True:
+			dR_lat=(1/R_earth)*(180/np.pi)
+			dR_lon=(1/R_earth)*(180/np.pi)*(1/np.cos(lat[k]*np.pi/180))
+		else:
+			dR_lat=1 ; dR_lon=1
+
+		plt.plot(lon[k], lat[k],'bo-',linewidth=5)
+		plt.plot(lon[k]+(Radius*dR_lon*cos(circ_ind)),lat[k]+(Radius*dR_lat*sin(circ_ind)),'b');
+
+	for k in range(Number_of_bonds):
+		x_bond=[]
+		y_bond=[]
+		x_bond.append(first_berg_lon[k])
+		x_bond.append(other_berg_lon[k])
+		y_bond.append(first_berg_lat[k])
+		y_bond.append(other_berg_lat[k])
+		plt.plot(x_bond, y_bond,'r',linewidth=5)
+
+
+	#plt.plot(lon, lat,'bo-')
+	if convert_to_lat_lon==True:
+		plt.xlabel('longitude (deg)')
+		plt.ylabel('latitude (deg)')
+	else:
+		plt.xlabel('x (m)')
+		plt.ylabel('y (m)')
+	plt.title('Iceberg initial positions')
+	plt.grid(True)
+	plt.show()
+
+
+def calculate_element_area(element_type,Radius):
+        if element_type=='square':
+                element_area=(2*Radius)**2
+        elif element_type=='hexagon':
+                element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*(Radius)**2) #Area of hexagon around circle (used for packing)  
+                #Another derivation uses innner hexagon with two more triangles added, which is a 1/6 of the hexagon area each (two since there are 6, shared by 3 each)
+                #element_area=(4./3.)*H_i, where H_i=(3.*np.sqrt(3.)/2.)*((Radius)**2)  is the area of the inner hexagon (with sides equal to the radius)
+
+        return element_area
+
+
+def Define_iceberg_positions(N,M ,lon_init,lat_init,Radius,R_earth,convert_to_lat_lon,scale_the_grid_to_lat_lon,element_type, thickness,rho_ice):
+	dx_berg=[]  #x distance in cartesian of berg from lon_init
+	dy_berg=[]  #y distance in cartesian of berg from lat_init
+	dlon_berg=[] #x distance in lon of berg from lon_init
+	dlat_berg=[] #y distance in lat of berg from lat_init
+	lon=[] #Longitude of iceberg
+	lat=[] #Latitude of iceberg
+	iceberg_num=[] #ID of iceberg
+
+
+
+
+	berg_count=0
+	#for j in range(N):
+        for i in range(M):
+		if element_type=='square':
+			x_start=Radius+(2*Radius*i)
+                        y_start=(Radius)
+                        #y_start=(Radius)+(2*Radius*j)
+                else:
+                        #x_start=(Radius)+(((j%2)*Radius))
+                        #y_start=(Radius)+(np.sqrt(3)*Radius*j)
+                        y_start=(Radius)+(((i%2)*Radius))
+                        x_start=(Radius)+(np.sqrt(3)*Radius*i)
+
+		#for i in range(M):
+        	for j in range(N):
+                        #x_val=x_start+(2*i*Radius)  ; y_val=y_start
+                        y_val=y_start+(2*j*Radius)  ; x_val=x_start
+			berg_count=berg_count+1
+			iceberg_num.append(berg_count)
+			dx_berg.append(x_val)
+			dy_berg.append(y_val)
+
+	#Old version
+	#berg_count=0
+	#for j in range(M):
+	#	x_start=(j%2)*Radius
+	#	y_start=np.sqrt(3)*Radius*j
+	#	for i in range(N):
+	#		berg_count=berg_count+1
+	#		iceberg_num.append(berg_count)
+	#		dx_berg.append(x_start+(2*i*Radius))
+	#		dy_berg.append(y_start)
+
+	Number_of_bergs=berg_count
+
+	#Calculating iceberg properties (assuming constant thickness and area)
+	element_area=calculate_element_area(element_type,Radius)
+        width=np.sqrt(element_area)
+	thickness=thickness
+	mass=thickness*rho_ice*element_area
+
+	#Defining lon lat positions:
+	#dlat_berg=(180/np.pi)*(1/R_earth)*dy_berg
+	#dlon_berg=(180/np.pi)*(1/R_earth)*(1/cos(lat_init*np.pi/180))*dx_berg
+	if convert_to_lat_lon==True:
+		for i in range(Number_of_bergs):
+			#Finding latittude
+			dlat_dy=(180/np.pi)*(1/R_earth)
+			dlat_berg.append(dlat_dy*dy_berg[i])
+			lat.append(lat_init+dlat_berg[i])
+
+			#Finding longitude
+			dlon_dx=(180/np.pi)*(1/R_earth)*(1/np.cos(lat[i]*np.pi/180)) #Note that this depends on the latitude of the iceberg. Could approx this with lat_init.
+			dlon_berg.append(dlon_dx*dx_berg[i])
+			lon.append(lon_init+dlon_berg[i])
+	else:
+		if scale_the_grid_to_lat_lon==True:
+			Scale_up=1./2000.
+			Radius=Radius*Scale_up
+			dx_berg = [(i*Scale_up) for i in dx_berg] ; dy_berg = [i*Scale_up for i in dy_berg]
+			#x=x*Scale_up ; y=y*Scale_up
+			#dx=dx*Scale_up ;dy=dy*Scale_up
+		#x=(x-np.min(x))+(dx/2) ; y=(y-np.min(y))+(dy/2)
+
+		for i in range(Number_of_bergs):
+			lon.append(lon_init+dx_berg[i])
+			lat.append(lat_init+dy_berg[i])
+
+	return (Number_of_bergs,lon,lat,iceberg_num,dx_berg,dy_berg,Radius, width,mass)
+
+def Define_iceberg_bonds(Number_of_bergs,iceberg_num,lat,lon,dx_berg, dy_berg,Radius):
+	
+	#Defining Bonds:
+	Bond=np.zeros((Number_of_bergs, Number_of_bergs))
+	first_berg_num=[]  # Initializing bond list first berg
+	first_berg_ine=[]  # Initializing bond list first berg
+	first_berg_jne=[]  # Initializing bond list first berg
+	first_berg_lat=[]  # Initializing bond list first berg
+	first_berg_lon=[]  # Initializing bond list first berg
+	other_berg_num=[]  # Initializing bond list other berg
+	other_berg_ine=[]  # Initializing bond list other berg
+	other_berg_jne=[]  # Initializing bond list other berg
+	other_berg_lat=[]  # Initializing bond list other berg
+	other_berg_lon=[]  # Initializing bond list other berg
+	bond_count=0
+	for i in range(Number_of_bergs):
+		for j in range(Number_of_bergs):
+			if i!=j:
+				R_dist=np.sqrt(((dx_berg[i]-dx_berg[j])**2) + ((dy_berg[i]-dy_berg[j])**2))
+				if R_dist < (2.01*Radius):
+					bond_count=bond_count+1
+					Bond[i,j]=1 # This is not really used.
+					first_berg_num.append(iceberg_num[i])
+					first_berg_ine.append(999)
+					first_berg_jne.append(999)
+					other_berg_num.append(iceberg_num[j])
+					other_berg_ine.append(999)
+					other_berg_jne.append(999)
+					#Also get the lat lon of each for plotting
+					first_berg_lat.append(lat[i])
+					first_berg_lon.append(lon[i])
+					other_berg_lat.append(lat[j])
+					other_berg_lon.append(lon[j])
+	Number_of_bonds=bond_count
+
+	return [ Number_of_bonds, first_berg_num,first_berg_ine,first_berg_jne,first_berg_lat,first_berg_lon, other_berg_num,other_berg_ine, other_berg_jne,other_berg_lat,other_berg_lon]
+
+####################################################################################################################################################
+##########################################################  Main Program   #########################################################################
+####################################################################################################################################################
+
+
+def main():
+	# Read en existing NetCDF file and create a new one
+	# f is going to be the existing NetCDF file from where we want to import data
+	# and g is going to be the new file.
+
+	f=Dataset('input_files/icebergs.res.nc','r') # r is for read only
+	g=Dataset('output_files/New_icebergs.res.nc','w') # w if for creating a file
+					      # if the file exists it the file will be deleted to write on it
+
+	h=Dataset('input_files/bonds_iceberg.res.nc','r') # r is for read only
+	q=Dataset('output_files/New_bonds_iceberg.res.nc','w') # w if for creating a file
+
+	#Flags
+	save_restart_files=True
+	make_icebergs_static=False
+
+	#Parameters
+	thickness=1.
+	Radius=0.8*1000
+	rho_ice=850.
+	mass_scaling=1.
+	R_earth=6360.*1000.
+
+	#Derived quanities
+	#width=np.sqrt(np.pi*(Radius**2))
+	#mass=thickness*rho_ice*np.pi*(Radius**2)  
+	#width=2*Radius
+	#mass=thickness*rho_ice*((2*Radius)**2)  
+
+	#Let interactive radius be different from radius for testing the model:
+	IA_scaling=1.#(1./2.)
+	Radius=Radius/IA_scaling
+
+	#Here we create the lons and lats for a tabular iceberg
+	N=20  # Number of rows in iceberg
+	M=20   # Number of columns in iceberg
+	lon_init=-32.9  #longitude of bottom left corner of iceberg
+	lat_init=-70.  #latitude  of bottom left corner of iceberg
+	#x_init=100  #For ISOMIP Case
+	#y_init=3  #For ISOMIP Case
+	x_init=100*2000  #For ISOMIP Case
+	y_init=11*2000  #For ISOMIP Case
+	#x_init=354000.003288060  #
+	#y_init=33600.0000000000  #
+	#Experiment_name='Weddell'  ;  Convert_to_lat_lon=True     ; scale_the_grid_to_lat_lon=False
+	Experiment_name='ISOMIP'  ;  convert_to_lat_lon=False      ; scale_the_grid_to_lat_lon=False
+
+
+	#element_type='square' #'hexagonal'
+        element_type='hexagon'
+
+
+	#Defining lon_init, lat_init
+	if Experiment_name=='ISOMIP':
+		if convert_to_lat_lon==True:
+			lon_init=5  ; lat_init=-69.8  
+		else:
+			lon_init=x_init  ; lat_init=y_init
+
+	#Define the positions of the icebergs
+	(Number_of_bergs,lon,lat,iceberg_num,dx_berg, dy_berg,Radius,width,mass)\
+			= Define_iceberg_positions(N,M ,lon_init,lat_init,Radius,R_earth,convert_to_lat_lon,scale_the_grid_to_lat_lon,element_type, thickness,rho_ice)
+
+	#Define the positions of the iceberg bonds
+	(Number_of_bonds, first_berg_num,first_berg_ine,first_berg_jne,first_berg_lat,first_berg_lon, other_berg_num,other_berg_ine, other_berg_jne,other_berg_lat,other_berg_lon)=\
+			Define_iceberg_bonds(Number_of_bergs,iceberg_num,lat,lon,dx_berg, dy_berg,Radius)
+
+
+
+	#####################################################################################
+	#Creating iceberg restart file
+	Create_iceberg_restart_file(f,g,Number_of_bergs, Number_of_bonds,lon,lat,thickness,width,mass,mass_scaling,iceberg_num,make_icebergs_static)
+	
+	#Creating bond restart file
+	Create_bond_restart_file(q,h, Number_of_bonds,first_berg_num,first_berg_ine,first_berg_jne,other_berg_ine,other_berg_jne,iceberg_num,other_berg_num)
+
+	##################################################################################
+	
+	print 'Number of bergs created= ' , Number_of_bergs
+	print 'Number of Bonds created= ' , Number_of_bonds
+	plotting_iceberg_positions_and_bonds(lat,lon,first_berg_lat,first_berg_lon,other_berg_lat,other_berg_lon,Number_of_bergs,Number_of_bonds,R_earth,Radius,IA_scaling,convert_to_lat_lon)
+	# Plotting the positions and bonds of the newly formed formation
+
+	print 'Script complete'
+
+
+
+if __name__ == '__main__':
+	main()
+	#sys.exit(main())
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/test/Iceberg_repository/hexagon_area.py b/test/Iceberg_repository/hexagon_area.py
new file mode 100755
index 0000000..08020cc
--- /dev/null
+++ b/test/Iceberg_repository/hexagon_area.py
@@ -0,0 +1,1472 @@
+#!/usr/bin/env python
+
+#First import the netcdf4 library
+from netCDF4 import Dataset  # http://code.google.com/p/netcdf4-python/
+import numpy as np  # http://code.google.com/p/netcdf4-python/
+import matplotlib
+import math
+import os
+matplotlib.use("GTKAgg")
+from pylab import *
+#import matplotlib.pyplot as plt
+import pdb
+import netCDF4 as nc
+
+
+
+#######################
+
+def Divide_hexagon_into_4_quadrants_old(x0,y0,H):
+	S=(2/sqrt(3))*H
+	Area_hex=3*(np.sqrt(3)/2)*(S**2)  #Area of the hexagon (should be equal to Area/grid_area, since it is not dim)  - check this
+	#print 'y0,H',y0, H	
+	#Defining boundaries of hexagon, and if statements to see which side of the boundary you are on
+	W1= False ; W2=False ;W3=False ;W4=False ;W5=False ;W6=False ;H1=False ;V1=False ;V2=False
+	W1=(-y0<-sqrt(3)*(-x0) + ((sqrt(3)*(S))));#upper right
+	W2=(-y0<(H));#Top
+	W3=(-y0<sqrt(3)*(-x0) + ((sqrt(3)*(S))));#Upper left
+	W4=(-y0<sqrt(3)*(-x0) + (-(sqrt(3)*(S))));#Lower right
+	W5=(-y0>-H);#Bottom
+	W6=(-y0<-sqrt(3)*(-x0) + (-(sqrt(3)*(S))));#Lower left
+		
+
+	T1=(-x0<S) #Right
+	T2=(-y0<(H));#Top
+	T3= (-x0>-S) #Left
+	T4=(-y0>-H);#Bottom
+
+	H1=(y0<0);
+	V1=(x0<-(S/2));
+	V2=(x0<(S/2));
+	  
+	#Deciding if the origin is within the hexagon
+	#print W1 , W2 , W3 , W4 , W5 , W6
+	#if In_hex:
+	#	print In_hex
+		
+	#Calculating the area of the top and bottom half of the hexagon, 2 Cases for the majority above and below the y0=0 line
+	#(and two more for the hexagon totally above and below the y0=0 line)
+	if abs(y0)<H:
+		Trapesium=((sqrt(3)*H)-(abs(y0)/sqrt(3)))*(H-abs(y0));
+		if y0>=0:
+			Area_Lower=Trapesium;
+			Area_Upper=Area_hex-Trapesium;
+		else:
+			Area_Upper=Trapesium;
+			Area_Lower=Area_hex-Trapesium;
+	else:
+		if y0>=0:
+			Area_Lower=0.;
+			Area_Upper=Area_hex;
+		else: 
+			Area_Lower=Area_hex;
+			Area_Upper=0.;
+
+	#Calcularing Left and Right area of the hexagon, about the x0=0 line, 3 cases:
+	#(and two more for when the hexagon is totally to the left or right of the x0=0 line)
+	if abs(x0)<S:
+		if abs(x0)<S/2:
+			Rectangle=(abs(x0)*2*H);
+			Big_side =(Area_hex/2) +Rectangle;
+			Small_side=Area_hex-Big_side;
+		else:
+			Triangle=(sqrt(3))*((S-abs(x0))**2);
+			Small_side=Triangle;
+			Big_side=Area_hex-Small_side;
+		if x0>=0.:
+			Area_right=Big_side;
+			Area_left=Small_side;
+		else:
+			Area_right=Small_side;
+			Area_left=Big_side;
+	else:
+		if x0>=0.:
+			Area_right=Area_hex;
+			Area_left=0.;
+		else:
+			Area_right=0.;
+			Area_left=Area_hex;
+
+	In_hex= W1 & W2 & W3 & W4 & W5 & W6;
+	In_hex_box=T1 & T2 & T3 & T4
+	Area_Q1=0.; Area_Q2=0. ; Area_Q3=0.; Area_Q4=0.;
+	Sector=0
+	#if In_hex==False: #Then the hexagon is completely contained in the middle cell
+	if In_hex_box==False: #Then the hexagon is completely contained in the middle cell
+		Sector=-1
+		#mass_on_ocean[i,j,5]=mass_on_ocean[i,j,5]+Mass
+		if min(Area_Upper,Area_Lower)==0.:
+			Sector=-2
+			if Area_Upper==0.:
+				Area_Q3=Area_left;
+				Area_Q4=Area_right;
+			if Area_Lower==0.:
+				Area_Q1=Area_right;
+				Area_Q2=Area_left;
+
+		elif min(Area_right,Area_left)==0.:
+			Sector=-3
+			if Area_right==0.:
+				Area_Q2=Area_Upper;
+				Area_Q3=Area_Lower;
+		
+			if Area_left==0.:
+				Area_Q1=Area_Upper;
+				Area_Q4=Area_Lower;
+		
+
+		#yCxC=1.
+		#print 'out of hex'
+
+	else:
+		#Determine which sector within the hexagon you are in. (sectors 1 to 6 go counter clockwise starting with top right)
+		if (H1==True):  #Bottom half
+			if V1:
+				#if W1==False:
+				if ((y0+(sqrt(3)*(x0+S)))<=0.):
+					Sector=1;
+				else:
+					Sector=2;
+			elif (V1==False) & (V2==True):
+				Sector=3;
+			else:  
+				#if (W3==True):
+				if ((y0-(sqrt(3)*(x0-S)))>=0.):
+					Sector=4;
+				else:
+					Sector=5;
+		else:  #Bottom half
+			if V1:
+				#if W6==False:
+				if ((y0 -(sqrt(3)*(x0+S)))>=0.):
+					Sector=10;
+				else:
+					Sector=9;
+			elif (V1==False) & (V2==True):
+				Sector=8;
+			else:  
+				#if (W4==True):
+				if ((y0+(sqrt(3)*(x0-S)))<=0.):
+					Sector=7;
+				else:
+					Sector=6;
+
+		#print Sector
+
+		#If the hexagon is in Sector 1,3,4 or 6, then the intersetion of the hexagon and the corresponding sector forms a baby triangle
+		#If the hexagon is in Sector 2,5 then the intersetion of the hexagon and the corresponding sector forms a baby trapesoid
+		if Sector==2 or Sector==4  or Sector==7 or Sector==9:
+			Baby_triangle=(1/(2*sqrt(3)))*((-abs(y0)+(sqrt(3)*(S-abs(x0))))**2);
+		else:
+			#Baby_trap= (H-abs(y0)) * ((-H-abs(y0)+(2*sqrt(3)*(S-abs(x0))))/(2*sqrt(3)));  
+			Baby_trap=(H-abs(y0))*((S-abs(x0) - ((H+abs(y0))/(2*sqrt(3))))) ;
+
+		#Finally, we assign the correct areas in each quadrant (Q1,Q2,Q3,Q4), depending on which sector you are in.
+		C1=0.;C2=0.;C3=0.;C4=0.;
+
+		#Corner cases
+		if Sector==2:
+			Area_Q1=Baby_triangle;
+			Area_Q2=Area_Upper-Area_Q1
+			Area_Q3=Area_left-Area_Q2
+			Area_Q4=Area_right-Area_Q1
+
+		if Sector==4:
+			Area_Q2=Baby_triangle;
+			Area_Q1=Area_Upper-Area_Q2
+			Area_Q3=Area_left-Area_Q2
+			Area_Q4=Area_right-Area_Q1
+
+		if Sector==7:
+			Area_Q3=Baby_triangle;
+			Area_Q2=Area_left-Area_Q3
+			Area_Q1=Area_Upper-Area_Q2
+			Area_Q4=Area_right-Area_Q1
+
+		if Sector==9:
+			Area_Q4=Baby_triangle;
+			Area_Q1=Area_right-Area_Q4
+			Area_Q2=Area_Upper-Area_Q1
+			Area_Q3=Area_left-Area_Q2
+	
+		#Center cases
+		if Sector==3:
+			if x0<=0.:
+				Area_Q1=Baby_trap;
+				Area_Q2=Area_Upper-Area_Q1;
+				Area_Q3=Area_left-Area_Q2;
+				Area_Q4=Area_right-Area_Q1;
+			else:
+				Area_Q2=Baby_trap;
+				Area_Q1=Area_Upper-Area_Q2;
+				Area_Q3=Area_left-Area_Q2;
+				Area_Q4=Area_right-Area_Q1;
+			
+		if Sector==8:
+			if x0<=0.:
+				Area_Q4=Baby_trap;
+				Area_Q3=Area_Lower-Area_Q4;
+				Area_Q1=Area_right-Area_Q4;
+				Area_Q2=Area_Upper-Area_Q1;
+			else:
+				Area_Q3=Baby_trap;
+				Area_Q4=Area_Lower-Area_Q3;
+				Area_Q1=Area_right-Area_Q4;
+				Area_Q2=Area_Upper-Area_Q1;
+
+		#Outside triangle cases:
+		if Sector==1:
+			Area_Q1=0.;
+			Area_Q2=Area_Upper;
+			Area_Q4=Area_right;
+			Area_Q3=Area_left-Area_Q2;
+		
+		if Sector==5:
+			Area_Q2=0.;
+			Area_Q1=Area_Upper;
+			Area_Q3=Area_left;
+			Area_Q4=Area_Lower-Area_Q3;
+
+		if Sector==6:
+			Area_Q3=0.;
+			Area_Q2=Area_left;
+			Area_Q4=Area_Lower;
+			Area_Q1=Area_right-Area_Q4;
+		
+		if Sector==10:
+			Area_Q4=0.;
+			Area_Q3=Area_Lower;
+			Area_Q1=Area_right;
+			Area_Q2=Area_left-Area_Q3;
+
+		#print x0,y0,Sector
+	return [Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4]
+
+
+
+def Hexagon_into_quadrants_using_triangles_across_lines(x0,y0,H,theta,  Px, Py, Qx, Qy, Rx, Ry, Sx, Sy ):
+	#In this routine, the hexagon is divided across lines PQ, RS.	 
+	#Length of side of Hexagon
+	S=(2/sqrt(3))*H;  
+
+	#Finding positions of corners
+	C1x=S           ; C1y=0.  #Corner 1 (right)
+	C2x=H/sqrt(3.)  ; C2y=H;  #Corner 2 (top right)
+	C3x=-H/sqrt(3.) ; C3y=H;  #Corner 3 (top left)
+	C4x=-S          ; C4y=0.; #Corner 4 (left)
+	C5x=-H/sqrt(3.) ; C5y=-H; #Corner 5 (bottom right)
+	C6x=H/sqrt(3.)  ; C6y=-H; #Corner 6 (bottom right)
+
+	#Finding positions of corners
+	[C1x,C1y]=rotate_and_translate(C1x,C1y,theta,x0,y0)
+	[C2x,C2y]=rotate_and_translate(C2x,C2y,theta,x0,y0)
+	[C3x,C3y]=rotate_and_translate(C3x,C3y,theta,x0,y0)
+	[C4x,C4y]=rotate_and_translate(C4x,C4y,theta,x0,y0)
+	[C5x,C5y]=rotate_and_translate(C5x,C5y,theta,x0,y0)
+	[C6x,C6y]=rotate_and_translate(C6x,C6y,theta,x0,y0)
+	 
+	#Area of Hexagon is the sum of the triangles
+	[T12_Area,T12_Q1,T12_Q2,T12_Q3,T12_Q4]=Triangle_divided_into_four_parts(x0,y0,C1x,C1y,C2x,C2y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T012
+	[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]=Triangle_divided_into_four_parts(x0,y0,C2x,C2y,C3x,C3y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
+	[T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4]=Triangle_divided_into_four_parts(x0,y0,C3x,C3y,C4x,C4y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T034
+	[T45_Area,T45_Q1,T45_Q2,T45_Q3,T45_Q4]=Triangle_divided_into_four_parts(x0,y0,C4x,C4y,C5x,C5y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
+	[T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4]=Triangle_divided_into_four_parts(x0,y0,C5x,C5y,C6x,C6y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
+	[T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4]=Triangle_divided_into_four_parts(x0,y0,C6x,C6y,C1x,C1y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
+	
+	#Area of Hexagon is the sum of the triangles
+	#print '1:', Triangle_divided_into_four_parts(x0,y0,C1x,C1y,C2x,C2y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T012
+	#print '1b:', Triangle_divided_into_four_quadrants(x0,y0,C1x,C1y,C2x,C2y); #T012
+	#print '2', Triangle_divided_into_four_parts(x0,y0,C2x,C2y,C3x,C3y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
+	#print '2b',Triangle_divided_into_four_quadrants(x0,y0,C2x,C2y,C3x,C3y); #T023
+	#print '3:',Triangle_divided_into_four_parts(x0,y0,C3x,C3y,C4x,C4y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T034
+	#print '3b',Triangle_divided_into_four_quadrants(x0,y0,C3x,C3y,C4x,C4y); #T034
+	#print '4',Triangle_divided_into_four_parts(x0,y0,C4x,C4y,C5x,C5y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
+	#print '4b:',Triangle_divided_into_four_quadrants(x0,y0,C4x,C4y,C5x,C5y); #T023
+	#print '5', Triangle_divided_into_four_parts(x0,y0,C5x,C5y,C6x,C6y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
+	#print '5b',Triangle_divided_into_four_quadrants(x0,y0,C5x,C5y,C6x,C6y); #T023
+	#print '6:',Triangle_divided_into_four_parts(x0,y0,C6x,C6y,C1x,C1y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
+	#print '6b',Triangle_divided_into_four_quadrants(x0,y0,C6x,C6y,C1x,C1y); #T023
+
+	#Summing up
+	Area_hex=T12_Area+T23_Area+T34_Area+T45_Area+T56_Area+T61_Area;
+	Area_Q1=T12_Q1+T23_Q1+T34_Q1+T45_Q1+T56_Q1+T61_Q1;
+	Area_Q2=T12_Q2+T23_Q2+T34_Q2+T45_Q2+T56_Q2+T61_Q2;
+	Area_Q3=T12_Q3+T23_Q3+T34_Q3+T45_Q3+T56_Q3+T61_Q3;
+	Area_Q4=T12_Q4+T23_Q4+T34_Q4+T45_Q4+T56_Q4+T61_Q4;
+	#Area_Q4=Area_hex-(Area_Q1+Area_Q2+Area_Q3)
+
+
+
+
+	#if  (abs(x0-(-0.186672393129))<0.00001)  and (abs(y0-(-0.436171))<0.00001):
+	#	print 'Triangle 1,xo,y0',x0,y0 
+	#	print 'Triangle 1H,S',H,S 
+	#	print 'Triangle 1,Corners',C1x,C1y,C2x,C2y 
+	#	print 'Triangle 1, Area full', T12_Area
+	#	print 'Triangle 1, Area T1', T12_Q1
+	#	print 'Triangle 1, Area T2', T12_Q2
+	#	print 'Triangle 1, Area T3', T12_Q3
+	#	print 'Triangle 1, Area T4', T12_Q4 
+	#	#print 'Triangle 2',x0,y0,C2x,C2y,C3x,C3y,T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4
+	#	#print 'Triangle 3',x0,y0,C3x,C3y,C4x,C4y,T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4 
+	#	#print 'Triangle 4',x0,y0,C4x,C4y,C5x,C5y,T45_Area,T45_Q1,T45_Q2,T45_Q3,T45_Q4
+	#	#print 'Triangle 5',x0,y0,C5x,C5y,C6x,C6y,T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4 
+	#	#print 'Triangle 6',x0,y0,C6x,C6y,C1x,C1y,T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4
+
+	Area_Q1=max(Area_Q1,0.);
+	Area_Q2=max(Area_Q2,0.);
+	Area_Q3=max(Area_Q3,0.);
+	Area_Q4=max(Area_Q4,0.);
+
+
+	Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
+	if (abs(Error)>0.01):
+		print  'diamonds, hex error, H,x0,y0, Error', H, x0 , y0, Error
+        	print 'diamonds, hex error, Areas',Area_hex, (Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
+	      	print 'Hexagon error is large!!'
+
+
+
+	#Adjust Areas so that the error is zero by subtracting the error from the largest sector.
+	if  (((Area_Q1>=Area_Q2) and (Area_Q1>=Area_Q3)) and (Area_Q1>=Area_Q4)):
+		#print 'fix1',Error
+		Area_Q1=Area_Q1+Error
+	elif  (((Area_Q2>=Area_Q1) and (Area_Q2>=Area_Q3)) and (Area_Q2>=Area_Q4)):
+		#print 'fix2', Error
+		Area_Q2=Area_Q2+Error
+	elif  (((Area_Q3>=Area_Q1) and (Area_Q3>=Area_Q2)) and (Area_Q3>=Area_Q4)):
+		#print 'fix3',Error
+		Area_Q3=Area_Q3+Error
+   	elif  (((Area_Q4>=Area_Q1) and (Area_Q4>=Area_Q2)) and (Area_Q4>=Area_Q3)):
+		#print 'fix4',Error
+		Area_Q4=Area_Q4+Error
+	else:
+		print 'There is some thing wrong with this hexagon. Something very wrong'
+
+	#Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
+	Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
+	if ((abs(Error)>0.01)):
+		print 'The hexagon error is still too large!!!', Error
+
+
+
+	return [Area_hex ,Area_Q1, Area_Q2, Area_Q3, Area_Q4]
+
+def Hexagon_into_quadrants_using_triangles(x0,y0,H,theta):
+		 
+	#Length of side of Hexagon
+	S=(2/sqrt(3))*H;  
+
+	#Finding positions of corners
+	C1x=S           ; C1y=0.  #Corner 1 (right)
+	C2x=H/sqrt(3.)  ; C2y=H;  #Corner 2 (top right)
+	C3x=-H/sqrt(3.) ; C3y=H;  #Corner 3 (top left)
+	C4x=-S          ; C4y=0.; #Corner 4 (left)
+	C5x=-H/sqrt(3.) ; C5y=-H; #Corner 5 (bottom right)
+	C6x=H/sqrt(3.)  ; C6y=-H; #Corner 6 (bottom right)
+
+	#Finding positions of corners
+	[C1x,C1y]=rotate_and_translate(C1x,C1y,theta,x0,y0)
+	[C2x,C2y]=rotate_and_translate(C2x,C2y,theta,x0,y0)
+	[C3x,C3y]=rotate_and_translate(C3x,C3y,theta,x0,y0)
+	[C4x,C4y]=rotate_and_translate(C4x,C4y,theta,x0,y0)
+	[C5x,C5y]=rotate_and_translate(C5x,C5y,theta,x0,y0)
+	[C6x,C6y]=rotate_and_translate(C6x,C6y,theta,x0,y0)
+	 
+	#Area of Hexagon is the sum of the triangles
+	[T12_Area,T12_Q1,T12_Q2,T12_Q3,T12_Q4]=Triangle_divided_into_four_quadrants(x0,y0,C1x,C1y,C2x,C2y); #T012
+	[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]=Triangle_divided_into_four_quadrants(x0,y0,C2x,C2y,C3x,C3y); #T023
+	[T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4]=Triangle_divided_into_four_quadrants(x0,y0,C3x,C3y,C4x,C4y); #T034
+	[T45_Area,T45_Q1,T45_Q2,T45_Q3,T45_Q4]=Triangle_divided_into_four_quadrants(x0,y0,C4x,C4y,C5x,C5y); #T023
+	[T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4]=Triangle_divided_into_four_quadrants(x0,y0,C5x,C5y,C6x,C6y); #T023
+	[T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4]=Triangle_divided_into_four_quadrants(x0,y0,C6x,C6y,C1x,C1y); #T023
+
+	#Summing up
+	Area_hex=T12_Area+T23_Area+T34_Area+T45_Area+T56_Area+T61_Area;
+	Area_Q1=T12_Q1+T23_Q1+T34_Q1+T45_Q1+T56_Q1+T61_Q1;
+	Area_Q2=T12_Q2+T23_Q2+T34_Q2+T45_Q2+T56_Q2+T61_Q2;
+	Area_Q3=T12_Q3+T23_Q3+T34_Q3+T45_Q3+T56_Q3+T61_Q3;
+	Area_Q4=T12_Q4+T23_Q4+T34_Q4+T45_Q4+T56_Q4+T61_Q4;
+	#Area_Q4=Area_hex-(Area_Q1+Area_Q2+Area_Q3)
+
+
+
+
+	#if  (abs(x0-(-0.186672393129))<0.00001)  and (abs(y0-(-0.436171))<0.00001):
+	#	print 'Triangle 1,xo,y0',x0,y0 
+	#	print 'Triangle 1H,S',H,S 
+	#	print 'Triangle 1,Corners',C1x,C1y,C2x,C2y 
+	#	print 'Triangle 1, Area full', T12_Area
+	#	print 'Triangle 1, Area T1', T12_Q1
+	#	print 'Triangle 1, Area T2', T12_Q2
+	#	print 'Triangle 1, Area T3', T12_Q3
+	#	print 'Triangle 1, Area T4', T12_Q4 
+	#	#print 'Triangle 2',x0,y0,C2x,C2y,C3x,C3y,T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4
+	#	#print 'Triangle 3',x0,y0,C3x,C3y,C4x,C4y,T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4 
+	#	#print 'Triangle 4',x0,y0,C4x,C4y,C5x,C5y,T45_Area,T45_Q1,T45_Q2,T45_Q3,T45_Q4
+	#	#print 'Triangle 5',x0,y0,C5x,C5y,C6x,C6y,T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4 
+	#	#print 'Triangle 6',x0,y0,C6x,C6y,C1x,C1y,T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4
+
+	Area_Q1=max(Area_Q1,0.);
+	Area_Q2=max(Area_Q2,0.);
+	Area_Q3=max(Area_Q3,0.);
+	Area_Q4=max(Area_Q4,0.);
+
+
+	Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
+	if (abs(Error)>0.01):
+		print  'diamonds, hex error, H,x0,y0, Error', H, x0 , y0, Error
+        	print 'diamonds, hex error, Areas',Area_hex, (Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
+	      	print 'Hexagon error is large!!'
+
+
+
+	#Adjust Areas so that the error is zero by subtracting the error from the largest sector.
+	if  (((Area_Q1>=Area_Q2) and (Area_Q1>=Area_Q3)) and (Area_Q1>=Area_Q4)):
+		#print 'fix1',Error
+		Area_Q1=Area_Q1+Error
+	elif  (((Area_Q2>=Area_Q1) and (Area_Q2>=Area_Q3)) and (Area_Q2>=Area_Q4)):
+		#print 'fix2', Error
+		Area_Q2=Area_Q2+Error
+	elif  (((Area_Q3>=Area_Q1) and (Area_Q3>=Area_Q2)) and (Area_Q3>=Area_Q4)):
+		#print 'fix3',Error
+		Area_Q3=Area_Q3+Error
+   	elif  (((Area_Q4>=Area_Q1) and (Area_Q4>=Area_Q2)) and (Area_Q4>=Area_Q3)):
+		#print 'fix4',Error
+		Area_Q4=Area_Q4+Error
+	else:
+		print 'There is some thing wrong with this hexagon. Something very wrong'
+
+	#Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
+	Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
+	if ((abs(Error)>0.01)):
+		print 'The hexagon error is still too large!!!', Error
+
+
+
+	return [Area_hex ,Area_Q1, Area_Q2, Area_Q3, Area_Q4]
+
+
+def find_intersect_using_metric(Ax,Ay, Bx, By, Cx, Cy):
+	#Line AB
+	[AB_px, AB_py]=intercept_of_a_line(Ax,Ay,Bx,By,'x'); #x_intercept
+	[AB_qx, AB_qy]=intercept_of_a_line(Ax,Ay,Bx,By,'y'); #y_intercept
+	M_AB=point_in_interval_metric(Ax,Ay,Bx,By,AB_px,AB_py, AB_qx, AB_qy)
+	#Line AC
+	[AC_px, AC_py]=intercept_of_a_line(Ax,Ay,Cx,Cy,'x'); #x_intercept
+	[AC_qx, AC_qy]=intercept_of_a_line(Ax,Ay,Cx,Cy,'y'); #y_intercept
+	M_AC=point_in_interval_metric(Ax,Ay,Cx,Cy,AC_px, AC_py,AC_qx, AC_qy)
+	#Line AB
+	[BC_px, BC_py]=intercept_of_a_line(Bx,By,Cx,Cy,'x'); #x_intercept
+	[BC_qx, BC_qy]=intercept_of_a_line(Bx,By,Cx,Cy,'y'); #y_intercept
+	M_BC=point_in_interval_metric(Bx,By,Cx,Cy,BC_px,BC_py,BC_qx, BC_qy)
+
+	if M_AB<=min(M_BC, M_AC):
+		return AB_px, AB_py, AB_qx, AB_qy
+	elif M_AC<=min(M_BC, M_AB):
+		return AC_px, AC_py, AC_qx, AC_qy
+	elif M_BC<=min(M_AC, M_AB):
+		return BC_px, BC_py, BC_qx, BC_qy
+	else: 
+		print 'You should not get here'
+		halt
+
+def find_intersect_using_metric_and_lines(Ax,Ay, Bx, By, Cx, Cy,Px, Py, Qx, Qy, Rx, Ry, Sx, Sy):
+	#Line AB
+	[AB_px, AB_py]=intercept_of_two_lines(Ax,Ay,Bx,By,Px, Py, Qx, Qy); #PQ_intercept
+	[AB_qx, AB_qy]=intercept_of_two_lines(Ax,Ay,Bx,By,Rx, Ry, Sx, Sy); #RS_intercept
+	M_AB=point_in_interval_metric(Ax,Ay,Bx,By,AB_px,AB_py, AB_qx, AB_qy)
+	#Line AC
+	[AC_px, AC_py]=intercept_of_two_lines(Ax,Ay,Cx,Cy,Px, Py, Qx, Qy); #PQ_intercept
+	[AC_qx, AC_qy]=intercept_of_two_lines(Ax,Ay,Cx,Cy, Rx, Ry, Sx, Sy); #RS_intercept
+	M_AC=point_in_interval_metric(Ax,Ay,Cx,Cy,AC_px, AC_py,AC_qx, AC_qy)
+	#Line AB
+	[BC_px, BC_py]=intercept_of_two_lines(Bx,By,Cx,Cy,Px, Py, Qx, Qy); #PQ_intercept
+	[BC_qx, BC_qy]=intercept_of_two_lines(Bx,By,Cx,Cy, Rx, Ry, Sx, Sy); #RS_intercept
+	M_BC=point_in_interval_metric(Bx,By,Cx,Cy,BC_px,BC_py,BC_qx, BC_qy)
+
+	if M_AB<=min(M_BC, M_AC):
+		return AB_px, AB_py, AB_qx, AB_qy
+	elif M_AC<=min(M_BC, M_AB):
+		return AC_px, AC_py, AC_qx, AC_qy
+	elif M_BC<=min(M_AC, M_AB):
+		return BC_px, BC_py, BC_qx, BC_qy
+	else: 
+		print 'You should not get here'
+		halt
+
+
+def point_in_interval_metric(Ax,Ay,Bx,By,px,py,qx,qy):
+	metric=0.0
+	#print 'Ax,Ay,Bx,By',Ax,Ay,Bx,By,px,py,qx,qy
+	#print 'px,py,qx,qy',px,py,qx,qy
+
+	#Finds a metric for how close a point is to being inside an interval. If it is inside, then metric is equal to zero.
+	Mx1= max(px - max(Ax,Bx),0.)  #Zero is px <= max(Ax,Bx)
+	Mx2= max( min(Ax,Bx)-px ,0.)  #Zero is px <= max(Ax,Bx)
+	My1= max(py - max(Ay,By),0.)  #Zero is px <= max(Ax,Bx)
+	My2= max( min(Ay,By)-py ,0.)  #Zero is px <= max(Ax,Bx)
+	p_metric=abs(Mx1)+abs(Mx2)+abs(My1)+abs(My2)
+	#print 'Mx1, Mx2, My1, My2', Mx1, Mx2, My1, My2 
+
+	#Finds a metric for how close a point is to being inside an interval. If it is inside, then metric is equal to zero.
+	Mx1= max(qx - max(Ax,Bx),0.)  #Zero is qx <= max(Ax,Bx)
+	Mx2= max( min(Ax,Bx)-qx ,0.)  #Zero is qx <= max(Ax,Bx)
+	My1= max(qy - max(Ay,By),0.)  #Zero is qx <= max(Ax,Bx)
+	My2= max( min(Ay,By)-qy ,0.)  #Zero is qx <= max(Ax,Bx)
+	q_metric=abs(Mx1)+abs(Mx2)+abs(My1)+abs(My2)
+
+	metric=p_metric+q_metric
+	return metric
+
+
+def Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy):
+	Area_key_quadrant=0.0 #Initializing
+	Area_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
+	#if Area_triangle==0.0:
+	#	Area_triangle=0.0 ; Area_Q1=0.0 ; Area_Q2=0.0; Area_Q3=0.0; Area_Q4= 0.0
+	#	return [Area_triangle, Area_Q1, Area_Q2 ,Area_Q3 ,Area_Q4]
+
+
+	#Calculating area across axes
+	[Area_Upper ,Area_Lower]=divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,'x');
+	[Area_Right ,Area_Left]=divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,'y');
+	 
+	#Decide if the origin is in the triangle
+	if point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.):  #Then you have to divide area 4 ways.
+		#Find a line in the triangle that cuts both axes in/on the trianlge
+	    	[px, py]=intercept_of_a_line(Ax,Ay,Bx,By,'x'); #x_intercept
+	    	[qx, qy]=intercept_of_a_line(Ax,Ay,Bx,By,'y'); #y_intercept
+	    	if (point_in_interval(Ax,Ay,Bx,By,px,py) & point_in_interval(Ax,Ay,Bx,By,qx,qy))==False:
+			[px, py]=intercept_of_a_line(Ax,Ay,Cx,Cy,'x'); #x_intercept
+			[qx, qy]=intercept_of_a_line(Ax,Ay,Cx,Cy,'y'); #y_intercept
+			if (point_in_interval(Ax,Ay,Cx,Cy,px,py) & point_in_interval(Ax,Ay,Cx,Cy,qx,qy))==False:
+				[px, py]=intercept_of_a_line(Bx,By,Cx,Cy,'x'); #x_intercept
+				[qx, qy]=intercept_of_a_line(Bx,By,Cx,Cy,'y'); #y_intercept
+				if (point_in_interval(Bx,By,Cx,Cy,px,py) & point_in_interval(Bx,By,Cx,Cy,qx,qy))==False:
+					#point_in_interval_metric
+					[px, py, qx, qy]= find_intersect_using_metric(Ax,Ay, Bx, By, Cx, Cy)
+					#print 'Houston, we have a problem'
+					#plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy)
+					#halt
+
+		#Assigning quadrants. Key_quadrant is the quadrant with the baby triangle in it.
+		Area_key_quadrant=Area_of_triangle(px,py,qx,qy,0.,0.);
+		if Area_key_quadrant>0.0:
+			if px>=0. and qy>=0.: #First quadrant
+				Key_quadrant=1;
+			elif px<0. and qy>=0.:  #Second quadrant
+				Key_quadrant=2;
+			elif px<0. and qy<0.:
+				Key_quadrant=3;  #Third quadrant
+			else:
+				Key_quadrant=4;  #Forth quadrant
+	    
+	#if (point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.) is False) or (Area_key_quadrant==0):
+	if Area_key_quadrant==0:
+	#else:  #Then at least one quadrant is empty, and this can be used to find the areas in the other quadrant.  Assigning quadrants. Key_quadrant is the empty quadrant.
+		#print 'Mother...'
+		#print 'Ax, Ay',Ax,Ay
+		#print 'Bx, By',Bx,By
+		#print 'Cx, Cy',Cx,Cy
+		Area_key_quadrant=0;
+		if (((Ax>0. and Ay>0.) or (Bx>0. and By>0.) or (Cx>0. and Cy>0.))==False)  and (Area_Upper+Area_Right<=Area_triangle):
+		#if (((Ax>=0. and Ay>=0.) or (Bx>=0. and By>=0.) or (Cx>=0. and Cy>=0.))==False)  and (Area_Upper+Area_Right<=Area_triangle):
+			#No points land in this quadrant and triangle does not cross the quadrant
+			Key_quadrant=1;
+		elif  (((Ax<0. and Ay>0) or (Bx<0. and By>0.) or (Cx<0. and Cy>0.))==False)  and (Area_Upper+Area_Left<=Area_triangle):
+			#elif  (((Ax<0. and Ay>=0) or (Bx<0. and By>=0.) or (Cx<0. and Cy>=0.))==False)  and (Area_Upper+Area_Left<=Area_triangle):
+			Key_quadrant=2;
+		elif (((Ax<0. and Ay<0.) or (Bx<0. and By<0.) or (Cx<0. and Cy<0.))==False) & (Area_Lower+Area_Left<=Area_triangle):
+			#elif (((Ax<0. and Ay<0.) or (Bx<0. and By<0.) or (Cx<0. and Cy<0.))==False) & (Area_Lower+Area_Left<=Area_triangle):
+			Key_quadrant=3;
+		else:
+			Key_quadrant=4;
+	
+	#Assign values to quadrants
+	if Key_quadrant==1:
+		Area_Q1=Area_key_quadrant;
+		Area_Q2=Area_Upper-Area_Q1;
+		Area_Q4=Area_Right-Area_Q1;
+		#Area_Q3=Area_Left-Area_Q2;
+		Area_Q3=Area_triangle-Area_Q1-Area_Q2-Area_Q4;
+	elif Key_quadrant==2:
+		Area_Q2=Area_key_quadrant;
+		Area_Q1=Area_Upper-Area_Q2;
+		Area_Q4=Area_Right-Area_Q1;
+		#Area_Q3=Area_Left-Area_Q2;
+		Area_Q3=Area_triangle-Area_Q1-Area_Q2-Area_Q4;
+	elif Key_quadrant==3:
+		Area_Q3=Area_key_quadrant;
+		Area_Q2=Area_Left-Area_Q3;
+		Area_Q1=Area_Upper-Area_Q2;
+		#Area_Q4=Area_Right-Area_Q1;
+		Area_Q4=Area_triangle-Area_Q1-Area_Q2-Area_Q3;
+	elif Key_quadrant==4:
+		Area_Q4=Area_key_quadrant;
+		Area_Q1=Area_Right-Area_Q4;
+		Area_Q2=Area_Upper-Area_Q1;
+		#Area_Q3=Area_Left-Area_Q2;
+		Area_Q3=Area_triangle-Area_Q1-Area_Q2-Area_Q4;
+	else:
+	    print 'Help, I need somebody, help!'
+	    halt
+	
+	Area_Q1=max(Area_Q1,0.); 
+	Area_Q2=max(Area_Q2,0.);
+	Area_Q3=max(Area_Q3,0.);
+	Area_Q4=max(Area_Q4,0.); 
+
+	Error=abs(Area_Q1+Area_Q2+Area_Q3+Area_Q4-Area_triangle)
+	#Marker 1
+	if Error>1e-15:
+	#if True:
+		print 'The triangles are not accurate enough. This is a problem!'
+		print 'Triangle corners: ' ,Ax,Ay,Bx,By,Cx,Cy
+		print 'Error',Error
+		print 'Key_quadrant', Key_quadrant 
+		print 'Area Key_quadrant', Area_key_quadrant 
+		print 'Upper, Lower',Area_Upper ,Area_Lower
+		print 'Left, Right ', Area_Right ,Area_Left
+		print 'Point in triangle', point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.)
+		#plt.plot(np.array([Ax,Bx,Cx,Ax]),np.array([Ay, By, Cy,Ay]))
+		#plt.plot(np.array([-0.5,0.5]),np.array([0.,0.]),'k')
+		#plt.plot(np.array([0.,0.]),np.array([-0.5,0.5]),'k')
+		#plt.plot(0,0,'*')
+		#plt.show()
+		#halt
+		#return
+
+	return [Area_triangle, Area_Q1, Area_Q2 ,Area_Q3 ,Area_Q4]
+
+def find_quadrant_using_lines(x0 , y0 , Px, Py, Qx, Qy, Rx, Ry, Sx, Sy): #Finding "quadrant" of point using lines PQ, RS as axes.  (This assumes PQ is like the x axis and RS like the y axis)
+	#above_PQ=Point_above_line(x0,y0, Px, Py, Qx, Qy)
+	#above_RS=Point_above_line(x0,y0, Rx, Ry, Sx, Sy)
+	above_PQ=Above_on_below_line(x0,y0, Px, Py, Qx, Qy)
+	above_RS=Above_on_below_line(x0,y0, Rx, Ry, Sx, Sy)
+	if (above_PQ==1) and (above_RS==1):
+		quadrant=1
+	elif (above_PQ==1) and (above_RS==-1):
+		quadrant=2
+	elif (above_PQ==-1) and (above_RS==-1):
+		quadrant=3
+	elif (above_PQ==-1) and (above_RS==1):
+		quadrant=4
+	else:
+		#print 'Point not in a quadrant!'
+		quadrant=0
+		#halt
+
+	return quadrant
+
+def Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ):#Divides the triangle into 4 parts, across two intersecting lines. PQ, RS intersect at origin (for now)
+	Area_key_quadrant=0.0
+	Area_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
+	#if Area_triangle==0.0:
+	#	Area_triangle=0.0 ; Area_Q1=0.0 ; Area_Q2=0.0; Area_Q3=0.0; Area_Q4= 0.0
+	#	return [Area_triangle, Area_Q1, Area_Q2 ,Area_Q3 ,Area_Q4]
+
+
+	#Calculating area across axes
+	[Area_Upper ,Area_Lower]=divding_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy);
+	[Area_Right ,Area_Left] =divding_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Rx, Ry, Sx, Sy);
+	 
+	#Decide if the origin is in the triangle
+	if point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.):  #Then you have to divide area 4 ways.
+		#Find a line in the triangle that cuts both axes in/on the trianlge
+	    	[px, py]=intercept_of_two_lines(Ax,Ay,Bx,By,Px, Py, Qx, Qy); #PQ_intercept
+	    	[qx, qy]=intercept_of_two_lines(Ax,Ay,Bx,By,Rx, Ry, Sx, Sy); #RS_intercept
+	    	if (point_in_interval(Ax,Ay,Bx,By,px,py) & point_in_interval(Ax,Ay,Bx,By,qx,qy))==False:
+			[px, py]=intercept_of_two_lines(Ax,Ay,Cx,Cy,Px, Py, Qx, Qy); #PQ_intercept
+			[qx, qy]=intercept_of_two_lines(Ax,Ay,Cx,Cy,Rx, Ry, Sx, Sy); #RS_intercept
+			if (point_in_interval(Ax,Ay,Cx,Cy,px,py) & point_in_interval(Ax,Ay,Cx,Cy,qx,qy))==False:
+				[px, py]=intercept_of_two_lines(Bx,By,Cx,Cy,Px, Py, Qx, Qy); #PQ_intercept
+				[qx, qy]=intercept_of_two_lines(Bx,By,Cx,Cy,Rx, Ry, Sx, Sy); #RS_intercept
+				if (point_in_interval(Bx,By,Cx,Cy,px,py) & point_in_interval(Bx,By,Cx,Cy,qx,qy))==False:
+					#print 'Houston, we have a problem'
+					[px, py, qx, qy]= find_intersect_using_metric_and_lines(Ax,Ay, Bx, By, Cx, Cy,Px, Py, Qx, Qy, Rx, Ry, Sx, Sy)
+					#plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy)
+					#halt
+
+		#Assigning quadrants. Key_quadrant is the quadrant with the baby triangle in it.
+		Area_key_quadrant=Area_of_triangle(px,py,qx,qy,0.,0.);
+		if px>=0. and qy>=0.: #First quadrant  (I think the zeros here are because the PQ, RS intersect at zero)
+			Key_quadrant=1;
+		elif px<0. and qy>=0.:  #Second quadrant
+			Key_quadrant=2;
+		elif px<0. and qy<0.:
+			Key_quadrant=3;  #Third quadrant
+		else:
+			Key_quadrant=4;  #Forth quadrant
+	    
+	if Area_key_quadrant==0:
+		#else:  #Then at least one quadrant is empty, and this can be used to find the areas in the other quadrant.  Assigning quadrants. Key_quadrant is the empty quadrant.
+		#print 'Mother...'
+		#print 'Ax, Ay',Ax,Ay
+		#print 'Bx, By',Bx,By
+		#print 'Cx, Cy',Cx,Cy
+		Area_key_quadrant=0;
+		#Finding which quadrant the triangle points fall in.
+		A_quad = find_quadrant_using_lines(Ax,Ay,Px, Py, Qx, Qy, Rx, Ry, Sx, Sy)
+		B_quad = find_quadrant_using_lines(Bx,By,Px, Py, Qx, Qy, Rx, Ry, Sx, Sy)
+		C_quad = find_quadrant_using_lines(Cx,Cy,Px, Py, Qx, Qy, Rx, Ry, Sx, Sy)
+		#print 'A_quad, B_quad, C_quad',A_quad, B_quad, C_quad
+
+		if (((A_quad==1) or (B_quad==1) or (C_quad==1))==False)  and (Area_Upper+Area_Right<=Area_triangle):
+			#No points land in this quadrant and triangle does not cross the quadrant
+			Key_quadrant=1;
+		elif  (((A_quad==2) or (B_quad==2) or (C_quad==2))==False)  and (Area_Upper+Area_Left<=Area_triangle):
+			Key_quadrant=2;
+		elif (((A_quad==3) or (B_quad==3) or (C_quad==3))==False) & (Area_Lower+Area_Left<=Area_triangle):
+			Key_quadrant=3;
+		else:
+			Key_quadrant=4;
+	
+		#print Key_quadrant
+	#Assign values to quadrants
+	if Key_quadrant==1:
+		Area_Q1=Area_key_quadrant;
+		Area_Q2=Area_Upper-Area_Q1;
+		Area_Q4=Area_Right-Area_Q1;
+		#Area_Q3=Area_Left-Area_Q2;
+		Area_Q3=Area_triangle-Area_Q1-Area_Q2-Area_Q4;
+	elif Key_quadrant==2:
+		Area_Q2=Area_key_quadrant;
+		Area_Q1=Area_Upper-Area_Q2;
+		Area_Q4=Area_Right-Area_Q1;
+		#Area_Q3=Area_Left-Area_Q2;
+		Area_Q3=Area_triangle-Area_Q1-Area_Q2-Area_Q4;
+	elif Key_quadrant==3:
+		Area_Q3=Area_key_quadrant;
+		Area_Q2=Area_Left-Area_Q3;
+		Area_Q1=Area_Upper-Area_Q2;
+		#Area_Q4=Area_Right-Area_Q1;
+		Area_Q4=Area_triangle-Area_Q1-Area_Q2-Area_Q3;
+	elif Key_quadrant==4:
+		Area_Q4=Area_key_quadrant;
+		Area_Q1=Area_Right-Area_Q4;
+		Area_Q2=Area_Upper-Area_Q1;
+		#Area_Q3=Area_Left-Area_Q2;
+		Area_Q3=Area_triangle-Area_Q1-Area_Q2-Area_Q4;
+	else:
+	    print 'Help, I need somebody, help!'
+	    halt
+	
+	Area_Q1=max(Area_Q1,0.); 
+	Area_Q2=max(Area_Q2,0.);
+	Area_Q3=max(Area_Q3,0.);
+	Area_Q4=max(Area_Q4,0.); 
+
+	Error=abs(Area_Q1+Area_Q2+Area_Q3+Area_Q4-Area_triangle)
+	if Error>1e-15:
+	#if True:
+		print 'The triangles are not accurate enough. This is a problem!'
+		print 'Triangle corners: ' ,Ax,Ay,Bx,By,Cx,Cy
+		print 'Error',Error
+		print 'Key_quadrant', Key_quadrant 
+		print 'Area Key_quadrant', Area_key_quadrant 
+		print 'Upper, Lower',Area_Upper ,Area_Lower
+		print 'Left, Right ', Area_Right ,Area_Left
+		print 'Point in triangle', point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.)
+		#return
+
+	return [Area_triangle, Area_Q1, Area_Q2 ,Area_Q3 ,Area_Q4]
+
+def divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1):
+	if axes1=='x':  #Use the y-coordinates for if statements to see which side of the line you are on
+		A0=Ay; B0=By;  C0=Cy;
+	if axes1=='y':  #Use the y-coordinates for if statements to see which side of the line you are on
+		A0=Ax; B0=Bx;  C0=Cx;
+ 
+	#print 'A0,B0,C0', A0,B0,C0
+	A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
+	if B0*C0>0.: #then B and C are on the same side  (and non-zero)
+		#print 'HHHH1'	
+		if A0*B0>=0.: #then all three on the the same side (if it equals zero, then A0=0 and the otehrs are not)
+			if (A0>0.)  or  (A0==0. and  B0>0.):
+				Area_positive= A_triangle;
+				Area_negative= 0.;
+			else:
+				Area_positive= 0.;
+				Area_negative= A_triangle;
+		else:  #A is on the opposite side to B and C
+			[Area_positive, Area_negative]=Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1);
+
+	elif B0*C0<0.: #then B and C are on the opposite sides
+		#print 'HHHH2'	
+		if A0*B0>=0.:  #then C is all alone
+			[Area_positive, Area_negative]=Area_of_triangle_across_axes(Cx,Cy,Bx,By,Ax,Ay,axes1);
+		else: #then B is all alone
+			[Area_positive, Area_negative]=Area_of_triangle_across_axes(Bx,By,Cx,Cy,Ax,Ay,axes1);
+
+	else:  #This is the case when either B or C is equal to zero (or both), A0 could be zero too.
+		#print 'HHHH3'	
+		if (A0==0. and B0==0. and C0==0.):
+			Area_positive= 0.;
+			Area_negative= 0.;
+		elif (A0*B0<0.)  or  (A0*C0<0.):    #A, B are on opposite sides, and C is zero.  OR  A, C are on opposite sides, and B is zero.
+			[Area_positive, Area_negative]=Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1);
+			#print 'HHHH6'	
+		elif (A0*B0>0.) or (A0*C0>0.) or (abs(A0)>0. and (B0==0.) and (C0==0.)):
+			#print 'HHHH7'	
+		        if (A0>0.):
+		        	Area_positive= A_triangle;
+				Area_negative= 0.;
+        		else:
+				Area_positive= 0.;
+				Area_negative= A_triangle;
+    
+    		elif A0==0.:  #(Also, one of B,C is zero too)
+			#print 'HHHH8'	
+			if B0>0. or C0>0.:
+				Area_positive= A_triangle;
+				Area_negative= 0.;
+			elif B0<0. or C0<0.:
+				Area_positive= 0.;
+				Area_negative= A_triangle;
+		        else:
+				print 'You should not get here1'
+				halt
+    		else:
+			print 'You should not get here2'
+			print Ax,Ay,Bx,By,Cx,Cy
+			halt
+	
+	return [Area_positive, Area_negative]
+
+def divding_triangle_across_line2(Ax,Ay,Bx,By,Cx,Cy,  Px, Py, Qx, Qy ):
+	A0= Above_on_below_line(Ax,Ay, Px, Py, Qx, Qy)
+	B0= Above_on_below_line(Bx,By, Px, Py, Qx, Qy)
+	C0= Above_on_below_line(Cx,Cy, Px, Py, Qx, Qy) 
+	
+	#print 'A0,B0,C0', A0,B0,C0
+	#print Px, Py, Qx, Qy
+ 
+	A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
+	if B0*C0>0.: #then B and C are on the same side  (and non-zero)
+		#print 'GGG1'
+		if A0*B0>=0.: #then all three on the the same side (if it equals zero, then A0=0 and the otehrs are not)
+			if (A0>0.)  or  (A0==0. and  B0>0.):
+				Area_positive= A_triangle;
+				Area_negative= 0.;
+			else:
+				Area_positive= 0.;
+				Area_negative= A_triangle;
+		else:  #A is on the opposite side to B and C
+			[Area_positive, Area_negative]=Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy );
+
+	elif B0*C0<0.: #then B and C are on the opposite sides
+		#print 'GGG2'
+		if A0*B0>=0.:  #then C is all alone
+			[Area_positive, Area_negative]=Area_of_triangle_across_line(Cx,Cy,Bx,By,Ax,Ay, Px, Py, Qx, Qy );
+		else: #then B is all alone
+			[Area_positive, Area_negative]=Area_of_triangle_across_line(Bx,By,Cx,Cy,Ax,Ay, Px, Py, Qx, Qy );
+
+	else:  #This is the case when either B or C is equal to zero (or both), A0 could be zero too.
+		#print 'GGG3'
+		if (A0==0. and B0==0. and C0==0.):
+			Area_positive= 0.;
+			Area_negative= 0.;
+		elif (A0*B0<0.)  or  (A0*C0<0.):    #A, B are on opposite sides, and C is zero.  OR  A, C are on opposite sides, and B is zero.
+			[Area_positive, Area_negative]=Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy);
+			#print 'GGG5', Area_positive, Area_negative
+		elif (A0*B0>0.) or (A0*C0>0.) or (abs(A0)>0. and (B0==0.) and (C0==0.)):
+		        if (A0>0.):
+		        	Area_positive= A_triangle;
+				Area_negative= 0.;
+        		else:
+				Area_positive= 0.;
+				Area_negative= A_triangle;
+    
+    		elif A0==0.:  #(Also, one of B,C is zero too)
+			if B0>0. or C0>0.:
+				Area_positive= A_triangle;
+				Area_negative= 0.;
+			elif B0<0. or C0<0.:
+				Area_positive= 0.;
+				Area_negative= A_triangle;
+		        else:
+				print 'You should not get here1'
+				halt
+    		else:
+			print 'You should not get here2'
+			print Ax,Ay,Bx,By,Cx,Cy
+			halt
+	
+	return [Area_positive, Area_negative]
+
+
+def divding_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy,   Px, Py, Qx, Qy ):  #Triangle is ABC, line is PQ
+	A0= Above_on_below_line(Ax,Ay, Px, Py, Qx, Qy)
+	B0= Above_on_below_line(Bx,By, Px, Py, Qx, Qy)
+	C0= Above_on_below_line(Cx,Cy, Px, Py, Qx, Qy) 
+	#print 'BBB0', A0, B0, C0
+
+	A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
+	# B and C are on the same side of the line
+	#if (Point_above_line(Bx,By, Px, Py, Qx, Qy)==Point_above_line(Cx,Cy, Px, Py, Qx, Qy)) :
+	#if ((B0==C0) and (B0!=0))  or ((B0==0 or C0==0) and np.max(B0,C0)>0.5)   :
+	if ((B0==C0) and (B0!=0))  or ((B0==0 or C0==0))   : #B and C on the same side or B or C is zero
+		#print 'BBB1'
+		[Area_positive, Area_negative]=Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy);
+	else: #then B and C are on the opposite sides
+		#if Point_above_line(Ax,Ay, Px, Py, Qx, Qy)==Point_above_line(Bx,By, Px, Py, Qx, Qy):  #then C is all alone
+		if A0*B0>=0.:  #then C is all alone
+			#print 'BBB2'
+			[Area_positive, Area_negative]=Area_of_triangle_across_line(Cx,Cy,Bx,By,Ax,Ay, Px, Py, Qx, Qy);
+		else: #then B is all alone
+			#print 'BBB3'
+			[Area_positive, Area_negative]=Area_of_triangle_across_line(Bx,By,Cx,Cy,Ax,Ay, Px, Py, Qx, Qy);
+
+	return [Area_positive, Area_negative]
+
+
+def check_if_point_is_on_the_line(Ax,Ay,Bx,By,qx,qy,repeat_calculation=False):
+
+	tol=0.00000000000000;
+	dxc = qx - Ax;
+	dyc = qy - Ay;
+ 
+	dxl = Bx - Ax;
+	dyl = By - Ay;
+ 
+	cross = dxc * dyl - dyc * dxl;
+	
+	if abs(cross)<=tol:
+		point_is_on_line=True
+	else:
+		point_is_on_line=False
+
+	if repeat_calculation is False:
+		if point_is_on_line != check_if_point_is_on_the_line(Bx,By,Ax,Ay,qx,qy, True):
+			point_is_on_line=True
+
+	return point_is_on_line
+
+def intercept_of_a_line(Ax,Ay,Bx,By,axes1):
+	No_intercept_val=100000000000.; #Huge value used to make sure that the intercept is outside the triange in the parralel case. 
+	#No_intercept_val=np.NaN;
+	 
+	if axes1=='x': #x intercept
+		if (Ay==By)==False:
+			x0=Ax -(((Ax-Bx)/(Ay-By))*Ay);
+			y0=0.; 
+		else:
+			x0=No_intercept_val;
+			y0=No_intercept_val;
+	
+	if axes1=='y': #y intercept
+		if (Ax==Bx)==False:
+			x0=0.; 
+			y0=-(((Ay-By)/(Ax-Bx))*Ax)+Ay;  
+		else:
+			x0=No_intercept_val;
+			y0=No_intercept_val;
+	
+	return [x0, y0]
+
+def intercept_of_two_lines(Ax,Ay,Bx,By,Px,Py,Qx,Qy):
+	No_intercept_val=100000000000.; #Huge value used to make sure that the intercept is outside the triange in the parralel case. 
+	#No_intercept_val=np.NaN;
+
+	#One of the lines is actually a point:
+	if ((Ax==Bx) and (Ay==By)) or ((Px==Qx) and (Py==Qy)):
+		x0=No_intercept_val; y0=No_intercept_val;
+		halt6
+	else:
+		if (Ax==Bx):
+			(x0 , y0) =intercept_of_a_line(Px-Ax,Py,Qx-Ax,Qy,'y')
+			x0=Ax
+		#Here we check the other three directions to make code agree to machine precision with old version. The code could skip straight to the else.
+		elif (Px==Qx): 
+			(x0 , y0) =intercept_of_a_line(Ax-Px,Ay,Bx-Px,By,'y')
+			x0=Px
+		elif (Ay==By): 
+			(x0 , y0) =intercept_of_a_line(Px,Py-Ay,Qx,Qy-Ay,'x')
+			y0=Ay
+		elif (Py==Qy): 
+			(x0 , y0) =intercept_of_a_line(Ax,Ay-Py,Bx,By-Py,'x')
+			y0=Py
+		else:
+			m1=(Ay-By)/(Ax-Bx)
+			if (Px==Qx):
+				print 'Stop2'
+				(x0 , y0) =intercept_of_a_line(Ax-Px,Ay,Bx-Px,By,'y')
+				x0=Px
+			else:
+				m2=(Py-Qy)/(Px-Qx)
+				if m1==m2:
+					print 'Stop3'
+					x0=No_intercept_val;
+					y0=No_intercept_val;
+					halt2
+				else:
+					print 'Stop4'
+					x0=(1/(m1-m2))*( (m1*Ax -Ay) -(m2*Px - Py))
+					y0=m1*(x0-Ax)+Ay
+	
+	return [x0, y0]
+
+
+def Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axis1):#In this fuction, A is the point on one side of the axis, and B,C are on the opposite sides
+	#print 'Area_of_triangle_across_axes' ,Ax,Ay,Bx,By,Cx,Cy
+	A_triangle2=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
+	[pABx, pABy]=intercept_of_a_line(Ax,Ay,Bx,By,axis1);
+	[pACx, pACy]=intercept_of_a_line(Ax,Ay,Cx,Cy,axis1);
+	if axis1=='x':
+		A0=Ay; #Value used for if statements (deciding up/down vs left/right)
+	if axis1=='y':
+		A0=Ax; #Value used for if statements (deciding up/down vs left/right)
+	
+	#print 'QQQ', Ax,Ay,pABx,pABy,pACx,pACy
+	A_half_triangle=Area_of_triangle(Ax,Ay,pABx,pABy,pACx,pACy);
+	if (A0>=0.):
+		Area_positive= A_half_triangle;
+		Area_negative= A_triangle2-A_half_triangle;
+
+	else:
+		Area_positive= A_triangle2-A_half_triangle;
+		Area_negative= A_half_triangle;
+
+	return [Area_positive, Area_negative]
+
+def Above_on_below_line(x,y,Px, Py, Qx, Qy): #If the point is above the line, then returns True, otherwise false
+	if Px==Qx:
+		if x>Px:
+			Point_above_line=1.0
+		elif x<Px:
+			Point_above_line=-1.0
+		else:
+			Point_above_line=0.0
+	else:
+		m=(Py-Qy)/(Px-Qx)
+		if y > m*(x-Px) + Py:
+			Point_above_line=1.0
+		elif y < m*(x-Px) + Py:
+			Point_above_line=-1.0
+		else:
+			Point_above_line=0.0
+
+	return Point_above_line
+
+def Point_above_line(x,y,Px, Py, Qx, Qy): #If the point is above the line, then returns True, otherwise false
+	if Px==Qx:
+		if x>=Px:
+			Point_above_line=True
+		else:
+			Point_above_line=False
+	else:
+		m=(Py-Qy)/(Px-Qx)
+		if y >= m*(x-Px) + Py:
+			Point_above_line=True
+		else:
+			Point_above_line=False
+
+	return Point_above_line
+
+
+def Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px,Py, Qx, Qy, debug=False):
+	#In this fuction, B and C are the same side of the line. (I think this works even if B and/or C are on the line too)
+	#A is unknown. PQ is the line.
+	#print 'RRR Area_of_triangle_across_line' ,Ax,Ay,Bx,By,Cx,Cy
+	
+	if (Ax==Bx and Ay==By) or (Ax==Cx and Ay==Cy) or (Cx==Bx and Cy==By):
+		#print 'AAA1'
+		Area_positive=0.0
+		Area_negative=0.0
+	else:
+		#print 'AAA2'
+		A0= Above_on_below_line(Ax,Ay, Px, Py, Qx, Qy)
+		B0= Above_on_below_line(Bx,By, Px, Py, Qx, Qy)
+		C0= Above_on_below_line(Cx,Cy, Px, Py, Qx, Qy) 
+		A_triangle2=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
+
+		if check_if_point_is_on_the_line(Px,Py,Qx,Qy, Ax,Ay):  #Is point A on the line?
+			#print 'AAA3'
+			#if Point_above_line(Bx,By, Px,Py, Qx, Qy) or Point_above_line(Cx,Cy, Px,Py, Qx, Qy):
+			if B0==1 or C0==1:
+				Area_positive= A_triangle2;
+				Area_negative= 0.0;
+			else:
+				Area_positive= 0.0;
+				Area_negative= A_triangle2;
+		else: #If A is not on the line
+			#If A is on the same side of the line as B and C
+			#All on the same side of the line
+			if ((A0==B0 and A0==C0)  or (A0==B0 and C0==0) or (A0==C0 and B0==0)):  
+			#if Point_above_line(Ax,Ay, Px,Py, Qx, Qy) == Point_above_line( Bx,By, Px,Py, Qx, Qy)  and (Point_above_line(Ax,Ay,Px,Py,Qx,Qy)==Point_above_line(Cx,Cy,Px,Py,Qx,Qy)):  
+				#print 'AAA4'
+				#if Point_above_line(Bx,By, Px,Py, Qx, Qy) or Point_above_line(Cx,Cy, Px,Py, Qx, Qy):
+				if A0==1 or C0==1:
+					Area_positive= A_triangle2;
+					Area_negative= 0.0;
+				else:
+					Area_positive= 0.0;
+					Area_negative= A_triangle2;
+			elif (C0==0 and B0==0 and (abs(A0)>0)):  
+				if Point_above_line(Ax,Ay, Px,Py, Qx, Qy):
+					Area_positive= A_triangle2;
+					Area_negative= 0.0;
+				else:
+					Area_positive= 0.0;
+					Area_negative= A_triangle2;
+
+			else:  #If A is not on the same side of the line as B and C
+				#print 'AAA5'
+				[pABx, pABy]=intercept_of_two_lines(Ax,Ay,Bx,By, Px, Py, Qx, Qy);
+				[pACx, pACy]=intercept_of_two_lines(Ax,Ay,Cx,Cy, Px, Py, Qx, Qy);
+				#print 'Tri2', Ax,Ay,pABx,pABy,pACx,pACy
+				
+				A_half_triangle=Area_of_triangle(Ax,Ay,pABx,pABy,pACx,pACy);
+				if Point_above_line(Ax,Ay , Px,Py,Qx,Qy):
+					Area_positive= A_half_triangle;
+					Area_negative= A_triangle2-A_half_triangle;
+				else:
+					Area_positive= A_triangle2-A_half_triangle;
+					Area_negative= A_half_triangle;
+
+	return [Area_positive, Area_negative]
+
+def Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy):
+	Area    =   abs(    0.5*((Ax*(By-Cy))+(Bx*(Cy-Ay))+(Cx*(Ay-By))) );
+	return Area
+
+
+def point_in_interval(Ax,Ay,Bx,By,px,py):
+	point_is_in_interval=False
+	#print 'NNN1'
+	if ((px <= max(Ax,Bx)) and (px >= min(Ax,Bx))):
+		#print 'NNN2', 'py=', py,  'max=',max(Ay,By), 'XXX', (py - max(Ay,By))
+		if ((py <= max(Ay,By)) and (py >= min(Ay,By))):
+			##print 'NNN3'
+			point_is_in_interval=True
+	return point_is_in_interval
+
+def rotate_and_translate(px,py,theta,x0,y0):
+	#This function takes a point px,py, and rotates it clockwise around the origin by theta degrees, and then translates by (x0,y0)
+	 px_temp = (cos(theta*pi/180.)*px) + (sin(theta*pi/180.)*py)
+	 py_temp = (-sin(theta*pi/180.)*px) + (cos(theta*pi/180.)*py)
+	 px= px_temp +x0
+	 py= py_temp +y0
+	 return [px,py]
+
+
+def point_in_triangle_old(Ax,Ay,Bx,By,Cx,Cy,qx,qy):
+	#if False:
+	if (Ax==qx and Ay==qy) or (Bx==qx and By==qy) or (Cx==qx and Cy==qy):  #Exclude the pathelogical case
+	        	point_is_in_triangle = 0.;
+	else:
+		if (check_if_point_is_on_the_line(Ax,Ay,Bx,By,qx,qy) or (check_if_point_is_on_the_line(Ax,Ay,Cx,Cy,qx,qy)) or (check_if_point_is_on_the_line(Bx,By,Cx,Cy,qx,qy))):
+			point_is_in_triangle = 0;
+		else:
+			#Compute vectors
+			v0x=Cx-Ax;
+			v1x=Bx-Ax;
+			v2x=qx-Ax;
+			v0y=Cy-Ay;
+			v1y=By-Ay;
+			v2y=qy-Ay;
+
+			#%Compute dot products
+			dot00 = (v0x*v0x)+(v0y*v0y);
+			dot01 = (v0x*v1x)+(v0y*v1y);
+			dot02 = (v0x*v2x)+(v0y*v2y);
+			dot11 = (v1x*v1x)+(v1y*v1y);
+			dot12 = (v1x*v2x)+(v1y*v2y);
+
+			#Compute barycentric coordinates
+			invDenom= 1 / ((dot00 * dot11) - (dot01*dot01));
+			u=((dot11*dot02)-(dot01*dot12))*invDenom;
+			v=((dot00*dot12)-(dot01*dot02))*invDenom;
+
+			point_is_in_triangle = (((u)>=0) & ((v)>=0) & ((u+v)<(1)));
+	return point_is_in_triangle
+
+
+
+def point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,qx,qy):
+	point_is_in_triangle = 0;
+
+	if (Ax==qx and Ay==qy) or (Bx==qx and By==qy) or (Cx==qx and Cy==qy):  #Exclude the pathelogical case
+	        	point_is_in_triangle = 0.;
+	else:
+		if (check_if_point_is_on_the_line(Ax,Ay,Bx,By,qx,qy) or (check_if_point_is_on_the_line(Ax,Ay,Cx,Cy,qx,qy)) or (check_if_point_is_on_the_line(Bx,By,Cx,Cy,qx,qy))):
+			point_is_in_triangle = 0;
+		else:
+			l0=(qx-Ax)*(By-Ay)-(qy-Ay)*(Bx-Ax)
+			l1=(qx-Bx)*(Cy-By)-(qy-By)*(Cx-Bx)
+			l2=(qx-Cx)*(Ay-Cy)-(qy-Cy)*(Ax-Cx)
+
+			p0=np.sign( l0);
+			p1=np.sign( l1);
+			p2=np.sign( l2);
+			if (l0 == 0.):
+				p0=0.
+			if (l1==0.):
+				p1=0.
+			if (l2==0.):
+				p2=0.
+			
+			if ( (abs(p0)+abs(p2))+(abs(p1)) == abs((p0+p2)+(p1)) ):
+				point_is_in_triangle = 1;
+	return point_is_in_triangle
+
+
+def roundoff(x,sig_fig):
+	x_roundoff=round(x*(10**(sig_fig)))/(10**(sig_fig))
+	#x_roundoff=(FLOAT (INT(x * (10.**sig_fig) + 0.5)) / (10.**sig_fig))
+	return x_roundoff
+
+
+
+def square_spreading_calculation(x,y,L):
+	xL=min(0.5, max(0., 0.5-(x/L)))
+        xR=min(0.5, max(0., (x/L)+(0.5-(1/L) )))
+        xC=max(0., 1.-(xL+xR))
+        yD=min(0.5, max(0., 0.5-(y/L)))
+        yU=min(0.5, max(0., (y/L)+(0.5-(1/L) )))
+        yC=max(0., 1.-(yD+yU))
+
+def plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy, Px=None, Py=None, Qx=None, Qy=None, Rx=None, Ry=None, Sx=None, Sy=None):
+	if Px is None:
+		Px=-1. ; Py=0. ; Qx=1. ; Qy=0. #x-axis 
+                Rx=0. ; Ry=-1. ; Sx=0. ; Sy=1. #y-axis 
+	plt.plot(np.array([Px, Qx]), np.array([Py, Qy]))
+	plt.plot(np.array([Rx, Sx]), np.array([Ry, Sy]))
+	plt.plot(np.array([Ax, Bx, Cx, Ax]), np.array([Ay, By, Cy, Ay]))
+	plt.plot(np.array([Ax, Bx, Cx, Ax]), np.array([Ay, By, Cy, Ay]),'8')
+	text(Ax,Ay,'A',fontsize=20)
+	text(Bx,By,'B',fontsize=20)
+	text(Cx,Cy,'C',fontsize=20)
+	plt.show()
+
+####################################################################################################################################################
+##########################################################  Main Program   #########################################################################
+####################################################################################################################################################
+
+def main():
+
+	#test_case='hexagon'
+	#test_case='triangle'
+	#test_case='square'
+	#test_case='point_in_triangle'
+	#test_case='line_intercept'
+	#test_case='Point_above_line'
+	#test_case='Triangle_across_line'
+	#test_case='Triangle_into_fours'
+	test_case='many_hexagons'
+
+	if test_case=='line_intercept':
+		Ax=1. ; Ay=1.5 ; Bx=1. ; By=-3.4 
+		Px=0.2; Py=-1.0; Qx=0.2; Qy=2.2
+		(x0,y0)=intercept_of_two_lines(Ax,Ay,Bx,By,Px,Py,Qx,Qy)
+		plt.plot( np.array([Ax, Bx])  , np.array([Ay, By]))
+		plt.plot(np.array([Px, Qx]), np.array([Py, Qy]))
+		plt.plot(x0,y0,'*')
+		#plt.plot(Ax,Ay,'*')
+		#plt.plot(Bx,By,'*')
+		#plt.plot(Px,Py,'*')
+		#plt.plot(Qx,Qy,'*')
+
+		print 'x0, y0' , x0 , y0
+		plt.show()
+
+
+	if test_case=='Triangle_across_line':
+		#y-axis
+		Px=0.0 ; Py=-1.0 ;Qx=0.0 ;Qy=1.0
+		axes1='y'
+
+		#x-axis
+		#Px=-1.0 ; Py=0.0 ;Qx=1.0 ;Qy=0.0
+		#axes1='x'
+
+		N=11 #Choose an odd number
+		count=0
+		for Ax in np.linspace(-0.5 , 0.5 , N):
+			for Ay in np.linspace(-0.5 , 0.5 , N):
+				for Bx in np.linspace(-0.5 , 0.5 , N):
+					for By in np.linspace(-0.5 , 0.5 , N):
+						for Cx in np.linspace(-0.5 , 0.5 , N):
+							for Cy in np.linspace(-0.5 , 0.5 , N):
+								count=count+1
+								if count>0:
+									x=divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1)
+									y=divding_triangle_across_line2(Ax,Ay,Bx,By,Cx,Cy, Px,Py, Qx, Qy)
+									#y=divding_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px,Py, Qx, Qy)
+									#if abs(x[0]-y[0])>0 or  abs(x[1]-y[1])>0 or  abs(x[0]-z[0])>0 or  abs(x[1]-z[1])>0:
+									if abs(x[0]-y[0])>0 or  abs(x[1]-y[1])>0:
+										print 'Broken!!!: ', 'Ax, Ay =', Ax, Ay, 'Bx, By =' , Bx, By, 'Cx, Cy =' ,Cx, Cy
+										print 'count', count
+										print x
+										print y
+										plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy)
+										halt
+
+		print 'Test Successful'
+
+
+
+	if test_case=='Triangle_into_fours':
+		Px=1. ; Py=0. ; Qx=2. ; Qy=0. #x-axis 
+		Rx=0. ; Ry=1. ; Sx=0. ; Sy=2. #y-axis 
+		
+		count=0
+		N=11 #Use an odd number
+		for Ax in np.linspace(-0.5 , 0.5 , N):
+			for Ay in np.linspace(-0.5 , 0.5 , N):
+				for Bx in np.linspace(-0.5 , 0.5 , N):
+					for By in np.linspace(-0.5 , 0.5 , N):
+						for Cx in np.linspace(-0.5 , 0.5 , N):
+							for Cy in np.linspace(-0.5 , 0.5 , N):
+								count=count+1
+								#print count
+								if count>0:
+									x=Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy)
+									y=Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy )
+									Error=abs(x[1]+x[2]+x[3]+x[4]-x[0])
+									#if Error>1e-15:
+									if abs(x[0]-y[0])>0 or  abs(x[1]-y[1])>0 or abs(x[2]-y[2])>0 or  abs(x[3]-y[3])>0 or  abs(x[4]-y[4])>0 :
+										print 'Broken!!!: ', 'Ax, Ay =', Ax, Ay, 'Bx, By =' , Bx, By, 'Cx, Cy =' ,Cx, Cy
+										print 'count=', count
+										#print 'Error = ', Error
+										print x
+										#print y
+										plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy)
+										halt
+
+		print 'Triangle_into_fours Test Successful'
+
+		#[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]=Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy); 
+		#[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]= Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  )
+
+	if test_case=='Point_above_line':
+		x0=0.1 ;y0=0.3 ; Px=0.4; Py=-1.0; Qx=0.2; Qy=2.2
+		plt.plot(np.array([Px, Qx]), np.array([Py, Qy]))
+                plt.plot(x0,y0,'*')
+		print Point_above_line(x0,y0,Px, Py, Qx, Qy)
+		plt.show()
+
+
+
+
+	if test_case=='many_hexagons':
+		Px=-1. ; Py=0. ; Qx=1. ; Qy=0. #x-axis 
+		Rx=0. ; Ry=-1. ; Sx=0. ; Sy=1. #y-axis 
+		N=101
+		theta=0.0
+		count=0
+		for x0 in np.linspace(-0.5 , 0.5 , N):
+			for y0 in np.linspace(-0.5 , 0.5 , N):
+				for H in np.linspace(0.0 , 0.5 , N):
+					count=count+1
+					#print count
+					if count>0:
+						C5x=-H/sqrt(3.) ; C5y=-H; #Corner 5 (bottom right)
+						C6x=H/sqrt(3.)  ; C6y=-H; #Corner 6 (bottom right)
+						[C5x,C5y]=rotate_and_translate(C5x,C5y,theta,x0,y0)
+						[C6x,C6y]=rotate_and_translate(C6x,C6y,theta,x0,y0)
+						#x = Triangle_divided_into_four_parts(x0,y0,C5x,C5y,C6x,C6y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
+						#y = Triangle_divided_into_four_quadrants(x0,y0,C5x,C5y,C6x,C6y); #T023
+						#print x
+						#print y
+						#Ax=x0 ;  Ay=y0
+						#Bx=C5x ; By=C5y ;
+						#Cx=C6x ; Cy=C6y ;
+						#plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy)
+						#(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)=Hexagon_into_quadrants_using_triangles_across_lines(x0,y0,H,theta,  Px, Py, Qx, Qy, Rx, Ry, Sx, Sy )
+						#(Area_hexb, Area_Q1b, Area_Q2b, Area_Q3b, Area_Q4b)= Hexagon_into_quadrants_using_triangles(x0,y0,H,theta=0)
+						x=Hexagon_into_quadrants_using_triangles_across_lines(x0,y0,H,theta,  Px, Py, Qx, Qy, Rx, Ry, Sx, Sy )
+						y= Hexagon_into_quadrants_using_triangles(x0,y0,H,theta=0)
+						eps=1e-15
+						#eps=0.0
+						#if abs(Area_hex-Area_hexb)>eps or  abs(Area_Q1-Area_Q1b)>eps or abs(Area_Q2-Area_Q2b)>eps \
+						#		or  abs(Area_Q3-Area_Q3b)>eps or  abs(Area_Q4-Area_Q4b)>eps :
+						if abs(x[0]-y[0])>0 or  abs(x[1]-y[1])>0 or abs(x[2]-y[2])>0 or  abs(x[3]-y[3])>0 or  abs(x[4]-y[4])>0 :
+							print 'Broken!!!: ', x0, y0, H
+							print Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4 
+							print Area_hexb, Area_Q1b, Area_Q2b, Area_Q3b, Area_Q4b
+							print 'count=', count
+							halt
+		
+		print 'Many_Hexagons Test Successful'
+
+
+	if test_case=='hexagon':
+		H=1.
+		S=2.*H/sqrt(3.)
+		x0=0.
+		y0=0.
+		#(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Divide_hexagon_into_4_quadrants_old(x0,y0,H)
+		#print x0,y0,H
+		#print 'First version', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+		(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Hexagon_into_quadrants_using_triangles(x0,y0,H,theta=0)
+		print 'Triangle version1',Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+		(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Hexagon_into_quadrants_using_triangles(x0,y0,H,theta=90.)
+		print 'Triangle version2',Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+		
+		#print 'Analysis'	
+		#print 'sum of quadrants: ', (Area_Q1+Area_Q2+Area_Q3+Area_Q4)
+		print 'Scaled areas: '
+		print (Area_Q1+Area_Q2+Area_Q3+Area_Q4)/Area_hex, Area_Q1/Area_hex, Area_Q2/Area_hex, Area_Q3/Area_hex, Area_Q4/Area_hex
+		
+
+	elif test_case=='square':
+	 
+		x0=0.6999999999999
+		y0=0.3
+		L=0.6
+		square_spreading_calculation(x0,y0,L)
+
+	elif test_case=='triangle':
+		Ax=-0.5
+		Ay=-0.3 -((8./9.)/10.)
+		Bx=-0.277777777778
+		By= -0.5
+
+		Cx=0.5
+		Cy=0.3 +((8./9.)/10.)
+
+		[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]=Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy); #T023
+
+		#Px=1. ; Py=0. ; Qx=2. ; Qy=0.  
+		#Rx=0. ; Ry=1. ; Sx=0. ; Sy=2.  
+		#[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]= Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  )
+
+		print 'Triangle 2: ',Ax,Ay,Bx,By,Cx,Cy
+		print 'Full',T23_Q1+T23_Q2+T23_Q3+T23_Q4
+		print 'Q1, Q2,Q3,Q4',T23_Q1,T23_Q2,T23_Q3,T23_Q4
+		print 'Full triangle area',T23_Area
+		print 'Error',(T23_Q1+T23_Q2+T23_Q3+T23_Q4-T23_Area)
+		
+		
+
+	elif test_case=='point_in_triangle':
+		Ax= -2.695732526092343E-012
+		Ay=0.204344508198090
+		Bx=-2.695750202346321E-012 
+		By= -8.433062639672301E-002
+		Cx=0.249999999997304
+		Cy=6.000694090068343E-002
+		print 'Point in triangle', point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.)
+
+
+	print 'Script complete'
+
+if __name__ == '__main__':
+	main()
+	#sys.exit(main())
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/test/Iceberg_repository/setup_ISOMIP_calving.sh b/test/Iceberg_repository/setup_ISOMIP_calving.sh
new file mode 100755
index 0000000..725891d
--- /dev/null
+++ b/test/Iceberg_repository/setup_ISOMIP_calving.sh
@@ -0,0 +1,54 @@
+echo 'Beginning setup...'
+
+
+
+#Loading python libraries (its possible that not all of these are needed)
+module unload PrgEnv-intel/5.2.8
+module load PrgEnv-gnu/5.2.82
+module load python_scipy/0.17.0
+
+module load python
+module load python_netcdf4
+module load python_numpy
+module load python_pygtk
+module load python_matplotlib
+module load python_scipy/0.17.0
+
+
+
+git submodule init
+git submodule update
+
+cd ISOMIP_Calving/python_scripts
+mkdir -p output_files
+
+#Creating mosaic files using script
+echo 'Creating mosaic files...'
+./Create_mosaic.py -coupled_run -nx=240 -ny=40 -nz=36  -L=80.0 -W=480.0 
+echo 'Creating mosaic files complete'
+
+#Copying mosaic files to INPUT directory  (Files created by python script Create_mosaic)
+cp output_files/atmos_mosaic_tile1Xland_mosaic_tile1.nc ../INPUT/
+cp output_files/atmos_mosaic_tile1Xocean_mosaic_tile1.nc ../INPUT/
+cp output_files/land_mosaic_tile1Xocean_mosaic_tile1.nc ../INPUT/
+cp output_files/grid_spec.nc ../INPUT/
+cp output_files/ocean_hgrid.nc ../INPUT/
+cp output_files/ocean_mask.nc ../INPUT/
+cp output_files/ocean_mosaic.nc ../INPUT/
+cp output_files/ocean_topog.nc ../INPUT/
+cp output_files/topog.nc ../INPUT/
+
+#Creating iceberg and bond restart files, and ice shelf file
+echo 'Creating iceberg restart files...'
+./initialize_bergs_in_pattern.py -Make_icebergs_non_static_later=False -Run_plotting_subroutine=False
+echo 'Creating iceberg restart files complete'
+
+#Copying iceberg restarts and iceshelf file to INPUT directory  (Files created by python script initialize_bergs_in_pattern_Tech.py)
+cp output_files/ISOMIP_icebergs.res.nc ../INPUT/icebergs.res.nc
+cp output_files/ISOMIP_bonds_iceberg.res.nc ../INPUT/bonds_iceberg.res.nc
+cp output_files/ISOMIP_Ice_Shelf_clipped.nc ../INPUT/isomip_ice_shelf1_clipped.nc
+
+#Copying 3D_LAYER_WARM_TPY_IC.nc to INPUT
+cp input_files/3D_LAYER_WARM_TPY_IC.nc ../INPUT/
+cd ..
+echo 'Setup complete!'
diff --git a/test/Iceberg_repository/testberg/testberg.py b/test/Iceberg_repository/testberg/testberg.py
new file mode 100755
index 0000000..10d6a92
--- /dev/null
+++ b/test/Iceberg_repository/testberg/testberg.py
@@ -0,0 +1,72 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset  
+import numpy as np 
+import math
+#import os
+from pylab import *
+#import pdb
+import netCDF4 as nc
+
+nx = 20
+ny = 20
+New_ice_thickness_filename='testberg.nc'
+grid_area = 10.e3*10.e3 #10 km grid res
+h_ice = 300.0
+
+New_ice_thickness_filename='testtabularberg.nc'
+g=Dataset(New_ice_thickness_filename,'w') # w if for creating a file
+
+g.createDimension('nx',nx)
+g.createDimension('ny',ny)
+thick_h=g.createVariable('thick','f8',('ny','nx'))
+area_h=g.createVariable('area','f8',('ny','nx'))
+lat_h=g.createVariable('lat','f8','ny')
+lon_h=g.createVariable('lon','f8','nx')
+#lat_h=g.createVariable('lat','f8',('ny','nx'))
+#lon_h=g.createVariable('lon','f8',('ny','nx'))
+
+thick_h.units = 'm'
+thick_h.standard_name = 'ice shelf thickness'
+area_h.units = 'm2'
+area_h.standard_name = 'ice shelf area'
+lon_h.unit = 'm'
+lon_h.standard_name = 'longitude'
+lat_h.unit = 'm'
+lat_h.standard_name = 'latitude'
+
+
+
+#g.variables['thick'][:]=h_ice
+g.variables['area'][:,:]=grid_area
+
+#create a circular tabular berg centered on the following coords (km)
+cx = 60.e3
+cy = 60.e3
+
+for i in range(nx):
+
+        tx = float(i) * 10.e3
+        g.variables['lon'][i] = tx
+        
+        for j in range(ny):
+               
+                ty = float(j) * 10.e3
+                dist = sqrt((tx-cx)*(tx-cx) + (ty-cy)*(ty-cy))
+                #g.variables['lon'][i,j] = tx
+                #g.variables['lat'][i,j] = ty
+        
+                if (dist < 50.e3):
+                        g.variables['thick'][i,j]=h_ice
+                else:
+                        g.variables['thick'][i,j]=0.0
+
+for j in range(ny):
+        g.variables['lat'][j] = float(j) * 10.e3
+
+print('Creating file: ' , New_ice_thickness_filename)
+
+g.sync()
+g.close()
+
+        

From f59cc7d54d89730811cc5f2adf1a995ac43c0ad5 Mon Sep 17 00:00:00 2001
From: Niki Zadeh <niki.zadeh@noaa.gov>
Date: Mon, 24 Aug 2020 17:17:12 -0400
Subject: [PATCH 249/361] Fixes CM4highres model crash with insufficient
 virtual memory

- Closes issue #61
- The mpp_sent variable ntrajs_sent_io goes out of scope before it is mpp_recv'ed
  causing invalid/junk numbers to be received which cause the model to
crash.
---
 icebergs_io.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 041a7a3..7128951 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -58,6 +58,7 @@ module ice_bergs_io
 integer, save :: io_tile_id(1), io_tile_root_pe, io_npes
 integer, allocatable,save :: io_tile_pelist(:)
 logical :: is_io_tile_root_pe = .true.
+integer :: ntrajs_sent_io,ntrajs_rcvd_io
 
 integer :: clock_trw,clock_trp
 
@@ -1255,7 +1256,6 @@ subroutine write_trajectory(trajectory, save_short_traj)
 integer :: stderrunit, cnt, ij
 !I/O vars
 type(xyt), pointer :: traj4io=>null()
-integer :: ntrajs_sent_io,ntrajs_rcvd_io
 integer :: from_pe,np
 type(buffer), pointer :: obuffer_io=>null(), ibuffer_io=>null()
 logical :: io_is_in_append_mode

From 13655b4979070d45eb444484a335da4bfdadb1bd Mon Sep 17 00:00:00 2001
From: Niki Zadeh <niki.zadeh@noaa.gov>
Date: Mon, 24 Aug 2020 17:17:12 -0400
Subject: [PATCH 250/361] Fixes CM4highres model crash with insufficient
 virtual memory

- Closes issue #61
- The mpp_sent variable ntrajs_sent_io goes out of scope before it is mpp_recv'ed
  causing invalid/junk numbers to be received which cause the model to
crash.
---
 icebergs_io.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 041a7a3..7128951 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -58,6 +58,7 @@ module ice_bergs_io
 integer, save :: io_tile_id(1), io_tile_root_pe, io_npes
 integer, allocatable,save :: io_tile_pelist(:)
 logical :: is_io_tile_root_pe = .true.
+integer :: ntrajs_sent_io,ntrajs_rcvd_io
 
 integer :: clock_trw,clock_trp
 
@@ -1255,7 +1256,6 @@ subroutine write_trajectory(trajectory, save_short_traj)
 integer :: stderrunit, cnt, ij
 !I/O vars
 type(xyt), pointer :: traj4io=>null()
-integer :: ntrajs_sent_io,ntrajs_rcvd_io
 integer :: from_pe,np
 type(buffer), pointer :: obuffer_io=>null(), ibuffer_io=>null()
 logical :: io_is_in_append_mode

From 744216ff298373a587f0bfefdae28fa7b30875f3 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Tue, 25 Aug 2020 16:10:57 -0400
Subject: [PATCH 251/361] reorg, collision test, fixed bond issues related to
 initialization and periodic boundaries, renamed diamonds to kid

---
 build/mkmkf                                   |   2 +-
 driver/icebergs_driver.F90                    | 104 ++-
 src/icebergs.F90                              | 760 +++++++++---------
 src/icebergs_framework.F90                    | 484 +++++------
 src/icebergs_io.F90                           | 602 +++++++-------
 test/Iceberg_repository/RUN                   |   9 -
 test/README                                   |   4 -
 test/RUN                                      |   2 -
 test/input.nml                                |  49 --
 {test => tests}/.gitignore                    |   3 +-
 {test => tests}/Iceberg_repository/.gitignore |   0
 .../Bergs/Layer/Empty_run/MOM_input           |   0
 .../Bergs/Layer/Empty_run/MOM_override        |   0
 .../Bergs/Layer/Empty_run/SIS_input           |   0
 .../Bergs/Layer/Empty_run/SIS_override        |   0
 .../Bergs/Layer/Empty_run/clean_MOM.sh        |   0
 .../Bergs/Layer/Empty_run/data_table          |   0
 .../Bergs/Layer/Empty_run/diag_table          |   0
 .../Bergs/Layer/Empty_run/field_table         |   0
 .../Bergs/Layer/Empty_run/input.nml           |   0
 .../Bergs/Layer/Empty_run/output              |   0
 .../Bergs/Layer/Empty_run/run_script.sh       |   0
 .../Bergs/Layer/Empty_run/submit_to_queue     |   0
 .../Bergs/Layer/Moving_berg_Bond/MOM_input    |   0
 .../Bergs/Layer/Moving_berg_Bond/MOM_override |   0
 .../Bergs/Layer/Moving_berg_Bond/README       |   0
 .../Bergs/Layer/Moving_berg_Bond/SIS_input    |   0
 .../Bergs/Layer/Moving_berg_Bond/SIS_override |   0
 .../Bergs/Layer/Moving_berg_Bond/clean_MOM.sh |   0
 .../Bergs/Layer/Moving_berg_Bond/data_table   |   0
 .../Bergs/Layer/Moving_berg_Bond/diag_table   |   0
 .../Bergs/Layer/Moving_berg_Bond/field_table  |   0
 .../Bergs/Layer/Moving_berg_Bond/input.nml    |   0
 .../Layer/Moving_berg_Bond/run_script.sh      |   0
 .../Layer/Moving_berg_Bond/submit_to_queue    |   0
 .../Bergs/Layer/Moving_berg_Collapse/README   |   0
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 .../Layer/Moving_berg_drift/clean_MOM.sh      |   0
 .../Bergs/Layer/Moving_berg_drift/data_table  |   0
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 .../Bergs/Layer/Moving_berg_drift/input.nml   |   0
 .../Layer/Moving_berg_drift/run_script.sh     |   0
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 .../Bergs/Layer/Moving_berg_fixed/MOM_input   |   0
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 .../Layer/Moving_berg_fixed/clean_MOM.sh      |   0
 .../Bergs/Layer/Moving_berg_fixed/data_table  |   0
 .../Bergs/Layer/Moving_berg_fixed/diag_table  |   0
 .../Bergs/Layer/Moving_berg_fixed/field_table |   0
 .../Bergs/Layer/Moving_berg_fixed/input.nml   |   0
 .../Layer/Moving_berg_fixed/run_script.sh     |   0
 .../Layer/Moving_berg_fixed/submit_to_queue   |   0
 .../Bergs/Layer/Static_shelf/MOM_input        |   0
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 .../Bergs/Layer/Static_shelf/README           |   0
 .../Bergs/Layer/Static_shelf/SIS_input        |   0
 .../Bergs/Layer/Static_shelf/SIS_override     |   0
 .../Bergs/Layer/Static_shelf/clean_MOM.sh     |   0
 .../Bergs/Layer/Static_shelf/data_table       |   0
 .../Bergs/Layer/Static_shelf/diag_table       |   0
 .../Bergs/Layer/Static_shelf/field_table      |   0
 .../Bergs/Layer/Static_shelf/input.nml        |   0
 .../Bergs/Layer/Static_shelf/run_script.sh    |   0
 .../Bergs/Layer/Static_shelf/submit_to_queue  |   0
 .../Sigma_Shelf_Star/Empty_run/MOM_input      |   0
 .../Sigma_Shelf_Star/Empty_run/MOM_override   |   0
 .../Sigma_Shelf_Star/Empty_run/SIS_input      |   0
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 .../Sigma_Shelf_Star/Empty_run/clean_MOM.sh   |   0
 .../Sigma_Shelf_Star/Empty_run/data_table     |   0
 .../Sigma_Shelf_Star/Empty_run/diag_table     |   0
 .../Sigma_Shelf_Star/Empty_run/field_table    |   0
 .../Sigma_Shelf_Star/Empty_run/input.nml      |   0
 .../Sigma_Shelf_Star/Empty_run/run_script.sh  |   0
 .../Empty_run/submit_to_queue                 |   0
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 .../Sigma_Shelf_Star/Moving_berg_Bond/README  |   0
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 .../Moving_berg_Bond/input.nml                |   0
 .../Moving_berg_Bond/run_script.sh            |   0
 .../Moving_berg_Bond/submit_to_queue          |   0
 .../Moving_berg_Collapse/README               |   0
 .../Moving_berg_Collapse/input.nml            |   0
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 .../Sigma_Shelf_Star/Moving_berg_drift/README |   0
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 .../Moving_berg_drift/input.nml               |   0
 .../Moving_berg_drift/run_script.sh           |   0
 .../Moving_berg_drift/submit_to_queue         |   0
 .../Moving_berg_fixed/MOM_input               |   0
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 .../Sigma_Shelf_Star/Moving_berg_fixed/README |   0
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 .../Moving_berg_fixed/data_table              |   0
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 .../Moving_berg_fixed/input.nml               |   0
 .../Moving_berg_fixed/run_script.sh           |   0
 .../Moving_berg_fixed/submit_to_queue         |   0
 .../Sigma_Shelf_Star/Static_shelf/MOM_input   |   0
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 .../Sigma_Shelf_Star/Static_shelf/README      |   0
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 .../Static_shelf/clean_MOM.sh                 |   0
 .../Sigma_Shelf_Star/Static_shelf/data_table  |   0
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 .../Sigma_Shelf_Star/Static_shelf/input.nml   |   0
 .../Static_shelf/run_script.sh                |   0
 .../Static_shelf/submit_to_queue              |   0
 .../Shelf/Layer/Static_shelf/MOM_input        |   0
 .../Shelf/Layer/Static_shelf/MOM_override     |   0
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 rename {test => tests}/Iceberg_repository/Scripts_and_analysis/bergs_quickview.py (100%)
 rename {test => tests}/Iceberg_repository/Scripts_and_analysis/calving_and_extract.py (100%)
 rename {test => tests}/Iceberg_repository/Scripts_and_analysis/check_convergence.py (100%)
 rename {test => tests}/Iceberg_repository/Scripts_and_analysis/compare_Global_Quick_vs_Benchmark.py (100%)
 rename {test => tests}/Iceberg_repository/Scripts_and_analysis/copy_files_to_shelf_and_bergs.sh (100%)
 rename {test => tests}/Iceberg_repository/Scripts_and_analysis/create_C3_env.sh (100%)
 rename {test => tests}/Iceberg_repository/Scripts_and_analysis/create_berg_restart.py (100%)
 rename {test => tests}/Iceberg_repository/Scripts_and_analysis/create_one_file.py (100%)
 rename {test => tests}/Iceberg_repository/Scripts_and_analysis/create_thickness_file.py (100%)
 rename {test => tests}/Iceberg_repository/Scripts_and_analysis/filling_up_space.py (100%)
 rename {test => tests}/Iceberg_repository/Scripts_and_analysis/flat_isomip_create.py (100%)
 rename {test => tests}/Iceberg_repository/Scripts_and_analysis/grid_cartesian_create.py (100%)
 rename {test => tests}/Iceberg_repository/Scripts_and_analysis/hexagon_area.py (100%)
 rename {test => tests}/Iceberg_repository/Scripts_and_analysis/hexagon_area.pyc (100%)
 rename {test => tests}/Iceberg_repository/Scripts_and_analysis/iceshelf_geometry_create.py (100%)
 rename {test => tests}/Iceberg_repository/Scripts_and_analysis/iceshelf_mass_file_create.py (100%)
 rename {test => tests}/Iceberg_repository/Scripts_and_analysis/initialize_bergs_in_pattern.py (100%)
 rename {test => tests}/Iceberg_repository/Scripts_and_analysis/movie_bergs_traj.py (100%)
 rename {test => tests}/Iceberg_repository/Scripts_and_analysis/old_bergs_quickview.py (100%)
 rename {test => tests}/Iceberg_repository/Scripts_and_analysis/quick_benchmark_comparison.sh (100%)
 rename {test => tests}/Iceberg_repository/Scripts_and_analysis/quick_plot.py (100%)
 rename {test => tests}/Iceberg_repository/Scripts_and_analysis/submit_to_queue.sh (100%)
 rename {test => tests}/Iceberg_repository/Scripts_and_analysis/topog_file_create.py (100%)
 rename {test => tests}/Iceberg_repository/Scripts_and_analysis/variables_comparison.sh (100%)
 rename {test => tests}/Iceberg_repository/Scripts_and_analysis/write_restart_iceberg.py (100%)
 rename {test => tests}/Iceberg_repository/hexagon_area.py (100%)
 rename {test => tests}/Iceberg_repository/setup_ISOMIP_calving.sh (100%)
 create mode 100644 tests/collision_test/README
 create mode 100755 tests/collision_test/RUN
 rename {test => tests/collision_test}/animate_trajectories.py (92%)
 rename {test => tests/collision_test}/diag_table (100%)
 create mode 100644 tests/collision_test/input.nml
 create mode 100755 tests/collision_test/makeberg/RUN
 rename test/Iceberg_repository/testberg/testberg.py => tests/collision_test/makeberg/makeberg.py (81%)

diff --git a/build/mkmkf b/build/mkmkf
index 7a8943e..bb29be6 100644
--- a/build/mkmkf
+++ b/build/mkmkf
@@ -1,3 +1,3 @@
 rm -f path_names
-../../mkmf/bin/list_paths ../../FMS/{mpp,diag_manager,time_manager,include,memutils,constants,platform,fms,random_numbers,mosaic,exchange} ../src/ ../driver/ ../test/
+../../mkmf/bin/list_paths ../../FMS/{mpp,diag_manager,time_manager,include,memutils,constants,platform,fms,random_numbers,mosaic,exchange} ../src/ ../driver/ ../tests/collision_test/
 ../../mkmf/bin/mkmf -t ../../mkmf/templates/ncrc-intel.mk -c "-Duse_libMPI -Duse_netCDF" -p bergs.x path_names
\ No newline at end of file
diff --git a/driver/icebergs_driver.F90 b/driver/icebergs_driver.F90
index e39ea46..ff24237 100644
--- a/driver/icebergs_driver.F90
+++ b/driver/icebergs_driver.F90
@@ -25,6 +25,7 @@ program icebergs_driver
   use time_manager_mod, only : operator(+), operator(-), operator(*), operator(/)
   use time_manager_mod, only : operator(>), operator(<), operator(>=)  
   use diag_manager_mod, only : diag_manager_init
+  use time_manager_mod, only: get_date 
   use diag_axis_mod, only : diag_axis_init
   use ice_bergs, only : icebergs
   use ice_bergs, only : icebergs_init
@@ -38,7 +39,7 @@ program icebergs_driver
   integer :: layout(2) !< Layout of MPI processes
   integer :: io_layout(2) !< Layout of I/O processes
 
-  integer :: iflags= 2  !< For i-direction flags ( cyclic_global_domain)
+  integer :: iflags= CYCLIC_GLOBAL_DOMAIN !< For i-direction flags
   integer :: jflags= 0  !< For j-direction flags
   type(domain2D) :: mpp_domain !< Parallel decomposition
   ! For declarations
@@ -53,12 +54,19 @@ program icebergs_driver
   integer :: ni=0 !< Global number of grid cells in i-direction (mandatory input)
   integer :: nj=0 !< Global number of grid cells in j-direction (mandatory input)
   logical :: debug=.true. !< If true, do some debugging
+  logical :: saverestart=.false. !< If true, save a berg restart file at the end
+  logical :: collision_test=.false.
   integer :: halo=1 !< Width of halo in parallel decomposition
   real :: ibdt=3600.0
   real :: ibuo=0.1
   real :: ibvo=0.0
+  real :: ibui=0.0
+  real :: ibvi=0.0
+  real :: gridres
   integer :: ibhrs=2
-  namelist /icebergs_driver_nml/ debug, ni, nj, halo, ibhrs, ibdt, ibuo, ibvo
+  integer :: nmax = 2000000000 !<max number of iterations    
+  namelist /icebergs_driver_nml/ debug, ni, nj, halo, ibhrs, ibdt, ibuo, ibvo, nmax, &
+       saverestart,ibui,ibvi,collision_test
   ! For loops
   integer :: isc !< Start of i-index for computational domain (used for loops)
   integer :: iec !< End of i-index for computational domain (used for loops)
@@ -67,9 +75,9 @@ program icebergs_driver
   ! Time
   type(time_type) :: Time !< Model time
   type(time_type) :: Time_end  !<end time for the experiment (s)
-  real :: nmax = 2000000000 !<max number of iterations  
   real :: dt !<time increment
   integer :: ns !<timestep counter
+  integer :: iyr, imon, iday, ihr, imin, isec
   ! For icebergs
   type(icebergs), pointer :: bergs !< Container for icebergs
   real, allocatable :: lon(:,:) !< Longitude or position in x
@@ -101,14 +109,11 @@ program icebergs_driver
   real, dimension(:,:), pointer  :: ustar_berg !< Friction velocity on base of bergs (m/s)
   real, dimension(:,:), pointer :: area_berg !< Area of bergs (m2)
 
-
-
-  
   ! Boot FMS
   call fms_init()
 
   ! Read run-time parameters
-  nmunit = open_namelist_file(file='./../test/input.nml')
+  nmunit = open_namelist_file(file='input.nml')
   read(nmunit, nml=icebergs_driver_nml)
   call close_file(nmunit)
   if (min(ni,nj)<1) call error_mesg('icebergs_driver:', &
@@ -120,10 +125,10 @@ program icebergs_driver
   nprocs = mpp_npes() ! How many processes are we using?
   call mpp_define_layout((/1, ni, 1, nj/), nprocs, layout)
   if (debug .and. mpp_root_pe()==0) print *,'layout=',layout,'nprocs=',nprocs,'PE=',mpp_pe()
-  
+
   ! Create a decomposed domain with the given layout from above
   call mpp_define_domains((/1,ni,1,nj/), layout, mpp_domain, &
-       xflags=cyclic_global_domain, yflags=jflags, &
+       xflags=iflags, yflags=jflags, &
        xhalo=halo, yhalo=halo, &
        symmetry=.false., name='iceberg_driver')
 
@@ -155,6 +160,7 @@ program icebergs_driver
   call mpp_get_compute_domain(mpp_domain, isc, iec, jsc, jec)
   if (debug .and. mpp_root_pe()==0) print *,'isd,isc,iec,ied=',isd,isc,iec,ied
   if (debug .and. mpp_root_pe()==0) print *,'jsd,jsc,jec,jed=',jsd,jsc,jec,jed
+  if (debug .and. mpp_root_pe()==0) print *,''
 
   allocate( lon(isd:ied,jsd:jed) )
   allocate( lat(isd:ied,jsd:jed) )
@@ -166,15 +172,21 @@ program icebergs_driver
   allocate( sin_rot(isd:ied,jsd:jed) )
   allocate( depth(isd:ied,jsd:jed) )
 
-   
+  gridres = 1.e3
+
+
   do j = jsd, jed
      do i = isd, ied
-        lon(i,j) = 10.e3*real(i)
-        lat(i,j) = 10.e3*real(j)
-        dx(i,j) = 10.e3
-        dy(i,j) = 10.e3
-        area(i,j) = 1.e8
+        lon(i,j) = gridres*real(i)
+        lat(i,j) = gridres*real(j)
+        dx(i,j) = gridres
+        dy(i,j) = gridres
+        area(i,j) = gridres*gridres
+        ! if (j>18.0 .or. j < 2.0) then
+        !    wet(i,j)=0.0
+        ! else
         wet(i,j) = 1.0
+        ! end if
         cos_rot(i,j) = 1.0 
         sin_rot(i,j) = 0.0
         depth(i,j) = 1000.
@@ -188,9 +200,10 @@ program icebergs_driver
 
   call icebergs_init(bergs, &
        ni, nj, layout, io_layout, axes, iflags, jflags, dt, time, &
-       lon(isc:iec,jsc:jec), lat(isc:iec,jsc:jec), wet, dx, dy, area(isc:iec,jsc:jec), &
-       cos_rot, sin_rot, depth(isc:iec,jsc:jec), fractional_area=.false.)
-
+       lon(isc:iec,jsc:jec), lat(isc:iec,jsc:jec), wet(isc-1:iec+1,jsc-1:jec+1), &
+       dx(isc-1:iec+1,jsc-1:jec+1), dy(isc-1:iec+1,jsc-1:jec+1), area(isc:iec,jsc:jec), &
+       cos_rot(isc-1:iec+1,jsc-1:jec+1), sin_rot(isc-1:iec+1,jsc-1:jec+1), &
+       depth(isc:iec,jsc:jec), fractional_area=.false.)
 
   ! for icebergs_run: 
   allocate( calving(isd:ied,jsd:jed) )
@@ -207,10 +220,10 @@ program icebergs_driver
   allocate( calving_hflx(isd:ied,jsd:jed) )
 
   calving = 0.0 !"calving" flux (kg/s) due to "melt" of bergs
-  uo = ibuo !0.1 !zonal ocean velocities (m/s)
+  uo = ibuo !zonal ocean velocities (m/s)
   vo = ibvo !meridonal ocean velocities (m/s)
-  ui = 0.0 !zonal ice velocities (m/s)
-  vi = 0.0 !meridonal ice velocities (m/s)
+  ui = ibui !zonal ice velocities (m/s)
+  vi = ibvi !meridonal ice velocities (m/s)
   tauxa = 0.0 !zonal wind stress (Pa)
   tauya = 0.0 !meridonal wind stress (Pa)
   ssh = 0.0 !eff sea-surf height
@@ -219,14 +232,14 @@ program icebergs_driver
   hi = 0.0 !sea-ice thickness (m)
   calving_hflx = 0.0 !calving heat flux (W/m2)
 
- 
-  ! do j = jsc, jec
-  !    do i = isc, iec
-  !       if (i == j) then
-  !          calving(i,j) = 2.0
-  !       end if
-  !    enddo
-  ! enddo
+  if (collision_test) then
+    do j = jsc,jec
+       if (j>10) vo = -ibvo
+    enddo
+    do i = isc,iec
+       if (i>10) vo = 0.0
+    enddo
+  end if
 
   ! optional:
   ! allocate( sss(isd:ied,jsd:jed) )
@@ -241,24 +254,31 @@ program icebergs_driver
   ! area_berg = !Area of bergs (m2)
 
   ns = 1 !timestep counter
-  ! Time_end = increment_date(Time, years, months, days, hours, minutes, seconds)
 
+  ! Time_end = increment_date(Time, years, months, days, hours, minutes, seconds)
   Time_end = increment_date(Time,0,0,0,ibhrs,0,0) 
 
   do while ((ns < nmax) .and. (Time < Time_end))
 
-     print *,''
-     print *,'----------------------------'
-     print *,''
-     print *,'ns',ns
-     print *,'time',time_type_to_real(Time)
-     print *,''
-     print *,'----------------------------'
-     print *,''
+     if (mpp_pe()==0 .and. debug) then
+        call get_date(Time, iyr, imon, iday, ihr, imin, isec)
+        write(*,*),''
+        write(*,'(a)'),'-------------------------------------------'
+        write(*,'(a,i5)')' Timestep   ',ns
+        write(*,'(a,i5,a,i5,a,i5)')' year',iyr,'  month ',imon,'  day   ',iday
+        write(*,'(a,i5,a,i5,a,i5)')' hour',ihr,'  minute',imin,'  second',isec       
+        write(*,'(a)'),'-------------------------------------------'
+        write(*,*),''
+     end if
 
      ! The main driver the steps updates icebergs
-     call icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh, sst, &
-          calving_hflx, cn, hi)
+     call icebergs_run(bergs, time, calving(isc:iec,jsc:jec), &
+          uo(isc-1:iec+1,jsc-1:jec+1), vo(isc-1:iec+1,jsc-1:jec+1), &
+          ui(isc-1:iec+1,jsc-1:jec+1), vi(isc-1:iec+1,jsc-1:jec+1), &
+          tauxa(isc:iec,jsc:jec), tauya(isc:iec,jsc:jec), &
+          ssh(isc-1:iec+1,jsc-1:jec+1), sst(isc:iec,jsc:jec), &
+          calving_hflx(isc:iec,jsc:jec), &
+          cn(isc-1:iec+1,jsc-1:jec+1), hi(isc-1:iec+1,jsc-1:jec+1))
 
      ! full form, with optional vars:
      ! call icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh, sst, &
@@ -273,8 +293,8 @@ program icebergs_driver
      ns = ns+1
   enddo
 
-!  call icebergs_save_restart(bergs)
- 
+  if (saverestart) call icebergs_save_restart(bergs)
+
   !Deallocate all memory and disassociated pointer
   call icebergs_end(bergs)
 
diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 38bf357..4328479 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -127,7 +127,7 @@ subroutine icebergs_init(bergs, &
   call ice_bergs_io_init(bergs,io_layout)
   call read_restart_calving(bergs)
   if (orig_read) then
-    call error_mesg('diamonds, icebergs_init: ', 'Parameter "orig_read" is no longer supported!', FATAL)
+    call error_mesg('KID, icebergs_init: ', 'Parameter "orig_read" is no longer supported!', FATAL)
   else
     call read_restart_bergs(bergs,Time)
   endif
@@ -149,6 +149,7 @@ subroutine icebergs_init(bergs, &
     endif
     call update_halo_icebergs(bergs)
     call connect_all_bonds(bergs)
+    
     nbonds=0
     check_bond_quality=.True.
     call count_bonds(bergs, nbonds,check_bond_quality)
@@ -206,7 +207,7 @@ subroutine point_in_triangle_test()
   Cy=6.000694090068343E-002
 
   fail_unit_test=(.not. point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.))
-  if (fail_unit_test) call error_mesg('diamonds, hexagon unit testing:', 'Point in triangle test does not pass!', FATAL)
+  if (fail_unit_test) call error_mesg('KID, hexagon unit testing:', 'Point in triangle test does not pass!', FATAL)
 
 end subroutine point_in_triangle_test
 
@@ -234,13 +235,13 @@ subroutine hexagon_test()
   x0=0.  ;  y0=0.
   call Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
   if (abs(Area_hex - ((3.*sqrt(3.)/2.)*(S*S)))>tol) then
-    call error_mesg('diamonds, hexagon unit testing:', 'Hexagon at origin has the wrong area!', WARNING)
-    if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'diamonds, hexagon areas =', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+    call error_mesg('KID, hexagon unit testing:', 'Hexagon at origin has the wrong area!', WARNING)
+    if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'KID, hexagon areas =', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
     fail_unit_test=.True.
   endif
   if (((abs((Area_hex/4)-Area_Q1 )>tol) .or.  (abs((Area_hex/4)-Area_Q2 )>tol)) .or. ((abs((Area_hex/4)-Area_Q3 )>tol) .or. (abs((Area_hex/4)-Area_Q4 )>tol))) then
-  if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'diamonds, hexagon areas =', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
-    call error_mesg('diamonds, hexagon unit testing:', 'Hexagon at origin divides into unqual parts!', WARNING)
+  if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'KID, hexagon areas =', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+    call error_mesg('KID, hexagon unit testing:', 'Hexagon at origin divides into unqual parts!', WARNING)
     fail_unit_test=.True.
   endif
 
@@ -249,32 +250,32 @@ subroutine hexagon_test()
   x0=S  ;  y0=0.
   call Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
   if (((abs((Area_hex/2)-Area_Q1 )>tol) .or.  (abs(0-Area_Q2 )>tol)) .or. ((abs(0-Area_Q3 )>tol) .or. (abs((Area_hex/2)-Area_Q4 )>tol))) then
-  if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'diamonds, hexagon areas =', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
-    call error_mesg('diamonds, hexagon unit testing:', 'Hexagon split btw 1 and 4!', WARNING)
+  if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'KID, hexagon areas =', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+    call error_mesg('KID, hexagon unit testing:', 'Hexagon split btw 1 and 4!', WARNING)
     fail_unit_test=.True.
   endif
   !Test 2b: center on x<0 axis
   x0=-S  ;  y0=0.
   call Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
   if (((abs((Area_hex/2)-Area_Q2 )>tol) .or.  (abs(0-Area_Q1 )>tol)) .or. ((abs(0-Area_Q4 )>tol) .or. (abs((Area_hex/2)-Area_Q3 )>tol))) then
-  if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'diamonds, hexagon areas =', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
-    call error_mesg('diamonds, hexagon unit testing:', 'Hexagon split btw 2 and 3!', WARNING)
+  if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'KID, hexagon areas =', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+    call error_mesg('KID, hexagon unit testing:', 'Hexagon split btw 2 and 3!', WARNING)
     fail_unit_test=.True.
   endif
   !Test 2c: center on y>0 axis
   x0=0.  ;  y0=H
   call Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
   if (((abs((Area_hex/2)-Area_Q1 )>tol) .or.  (abs(0-Area_Q3 )>tol)) .or. ((abs(0-Area_Q4 )>tol) .or. (abs((Area_hex/2)-Area_Q2 )>tol))) then
-  if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'diamonds, hexagon areas =', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
-    call error_mesg('diamonds, hexagon unit testing:', 'Hexagon split btw 1 and 2!', WARNING)
+  if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'KID, hexagon areas =', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+    call error_mesg('KID, hexagon unit testing:', 'Hexagon split btw 1 and 2!', WARNING)
     fail_unit_test=.True.
   endif
   !Test 3d: center on y<0 axis
   x0=0.  ;  y0=-H
   call Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
   if (((abs((Area_hex/2)-Area_Q3 )>tol) .or.  (abs(0-Area_Q1 )>tol)) .or. ((abs(0-Area_Q2 )>tol) .or. (abs((Area_hex/2)-Area_Q4 )>tol))) then
-  if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'diamonds, hexagon areas =', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
-    call error_mesg('diamonds, hexagon unit testing:', 'Hexagon split btw 3 and 4!', WARNING)
+  if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'KID, hexagon areas =', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+    call error_mesg('KID, hexagon unit testing:', 'Hexagon split btw 3 and 4!', WARNING)
     fail_unit_test=.True.
   endif
 
@@ -283,39 +284,39 @@ subroutine hexagon_test()
   x0=S/2.  ;  y0=0.
   call Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
   if (((abs((2.5*Area_hex/6.)-Area_Q1 )>tol) .or.  (abs((0.5*Area_hex/6.)-Area_Q2 )>tol)) .or. ((abs((0.5*Area_hex/6.)-Area_Q3 )>tol) .or. (abs((2.5*Area_hex/6.)-Area_Q4 )>tol))) then
-  if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'diamonds, hexagon areas =', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
-    call error_mesg('diamonds, hexagon unit testing:', 'Hexagon split two coners of hex (x>0)!', WARNING)
+  if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'KID, hexagon areas =', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+    call error_mesg('KID, hexagon unit testing:', 'Hexagon split two coners of hex (x>0)!', WARNING)
     fail_unit_test=.True.
   endif
   !Test 3b: center on x<0 axis
   x0=-S/2.  ;  y0=0.
   call Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
   if (((abs((2.5*Area_hex/6.)-Area_Q2 )>tol) .or.  (abs((0.5*Area_hex/6.)-Area_Q1 )>tol)) .or. ((abs((0.5*Area_hex/6.)-Area_Q4 )>tol) .or. (abs((2.5*Area_hex/6.)-Area_Q3 )>tol))) then
-  if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'diamonds, hexagon areas =', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
-    call error_mesg('diamonds, hexagon unit testing:', 'Hexagon split two coners of hex (x<0)!', WARNING)
+  if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'KID, hexagon areas =', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+    call error_mesg('KID, hexagon unit testing:', 'Hexagon split two coners of hex (x<0)!', WARNING)
     fail_unit_test=.True.
   endif
   !Test 3c: center on y>0 axis
   !x0=0.  ;  y0=H/2.
   !call Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
   !if (((abs((2.5*Area_hex/6.)-Area_Q1 )>tol) .or.  (abs((0.5*Area_hex/6.)-Area_Q3 )>tol)) .or. ((abs((0.5*Area_hex/6.)-Area_Q4 )>tol) .or. (abs((2.5*Area_hex/6.)-Area_Q2 )>tol))) then
-  !if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'diamonds, hexagon areas =', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
-  !if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'diamonds, hexagon errors =', (abs((2.5*Area_hex/6.)-Area_Q1 )), (abs((0.5*Area_hex/6.)-Area_Q3 )),&
-  !  call error_mesg('diamonds, hexagon unit testing:', 'Hexagon split two coners of hex (y>0)!', WARNING)
+  !if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'KID, hexagon areas =', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+  !if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'KID, hexagon errors =', (abs((2.5*Area_hex/6.)-Area_Q1 )), (abs((0.5*Area_hex/6.)-Area_Q3 )),&
+  !  call error_mesg('KID, hexagon unit testing:', 'Hexagon split two coners of hex (y>0)!', WARNING)
   !  fail_unit_test=.True.
   !endif
   !!Test 3d: center on y<0 axis
   !x0=0.  ;  y0=-H/2.
   !call Hexagon_into_quadrants_using_triangles(x0,y0,H,theta,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
   !if (((abs((2.5*Area_hex/6.)-Area_Q3 )>tol) .or.  (abs((0.5*Area_hex/6.)-Area_Q2 )>tol)) .or. ((abs((0.5*Area_hex/6.)-Area_Q1 )>tol) .or. (abs((2.5*Area_hex/6.)-Area_Q4 )>tol))) then
-  !if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'diamonds, hexagon areas =', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
-  !if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'diamonds, hexagon errots =', (abs((2.5*Area_hex/6.)-Area_Q3 )), (abs((0.5*Area_hex/6.)-Area_Q2 )),&
-  !  call error_mesg('diamonds, hexagon unit testing:', 'Hexagon split two coners of hex (y<0)!', WARNING)
+  !if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'KID, hexagon areas =', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+  !if (mpp_pe() .eq. mpp_root_pe()) write(stderrunit,*) 'KID, hexagon errots =', (abs((2.5*Area_hex/6.)-Area_Q3 )), (abs((0.5*Area_hex/6.)-Area_Q2 )),&
+  !  call error_mesg('KID, hexagon unit testing:', 'Hexagon split two coners of hex (y<0)!', WARNING)
   !  fail_unit_test=.True.
   !endif
 
 
-  if (fail_unit_test) call error_mesg('diamonds, hexagon unit testing:', 'Hexagon unit testing does not pass!', FATAL)
+  if (fail_unit_test) call error_mesg('KID, hexagon unit testing:', 'Hexagon unit testing does not pass!', FATAL)
 
 end subroutine hexagon_test
 
@@ -338,14 +339,16 @@ subroutine initialize_iceberg_bonds(bergs)
   ! For convenience
   grd=>bergs%grd
   !Should update halos before doing this
-  do grdj_outer = grd%jsc,grd%jec ; do grdi_outer = grd%isc,grd%iec  !Should you be on the data domain??
+  ! do grdj_outer = grd%jsc,grd%jec ; do grdi_outer = grd%isc,grd%iec  !Should you be on the data domain??
+  do grdj_outer = grd%jsd,grd%jed ; do grdi_outer = grd%isd,grd%ied  !using data domain -Alex     
     berg=>bergs%list(grdi_outer,grdj_outer)%first
     do while (associated(berg)) ! loop over all bergs
 
       lon1=berg%lon; lat1=berg%lat
       !call rotpos_to_tang(lon1,lat1,x1,y1)  !Is this correct? Shouldn't it only be on tangent plane?
 
-      do grdj_inner = grd%jsc,grd%jec ; do grdi_inner = grd%isc,grd%iec  !This line uses n^2 steps
+      ! do grdj_inner = grd%jsc,grd%jec ; do grdi_inner = grd%isc,grd%iec  !This line uses n^2 steps
+      do grdj_inner = grd%jsd,grd%jed ; do grdi_inner = grd%isd,grd%ied !Uses n^2 steps. Change to data domain-Alex         
 !     do grdj_inner = berg%jne-1,berg%jne+1 ; do grdi_inner = berg%ine-1,berg%ine+1   !Only looping through adjacent cells.
         other_berg=>bergs%list(grdi_inner,grdj_inner)%first
         do while (associated(other_berg)) ! loop over all other bergs
@@ -364,9 +367,10 @@ subroutine initialize_iceberg_bonds(bergs)
             r_dist_y=dlat*dy_dlat
             r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) )
 
-            !if (r_dist.gt.1000.) then  ! If the bergs are close together, then form a bond
+            ! If the bergs are closer than bergs%length_for_manually_initialize_bonds, then form a bond -Alex
+            if (r_dist.lt.bergs%length_for_manually_initialize_bonds) then  
               call form_a_bond(berg, other_berg%id, other_berg%ine, other_berg%jne, other_berg)
-            !endif
+            endif
           endif
           other_berg=>other_berg%next
         enddo  ! End of looping through all other bergs in the inner list
@@ -463,7 +467,7 @@ subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
     do while (associated(current_bond)) ! loop over all bonds
       other_berg=>current_bond%other_berg
       if (.not. associated(other_berg)) then
-        call error_mesg('diamonds,bond interactions', 'Trying to do Bond interactions with unassosiated berg!' ,FATAL)
+        call error_mesg('KID,bond interactions', 'Trying to do Bond interactions with unassosiated berg!' ,FATAL)
       else
         call calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,  &
                              P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded)
@@ -985,10 +989,10 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
           vveln=vveln*(new_speed/speed) ! without changing the direction
           bergs%nspeeding_tickets=bergs%nspeeding_tickets+1
         else
-          call error_mesg('diamonds, Speeding icebergs', 'Faster than the CFL!', WARNING)
-          write(stderrunit,*) 'diamonds, Speeding berg1! =',mpp_pe(), berg%id
-          write(stderrunit,*) 'diamonds, Speeding berg2, speed =',speed, loc_dx/dt
-          write(stderrunit,*) 'diamonds, Speeding berg3, lat, lon =',lat,xi,yj
+          call error_mesg('KID, Speeding icebergs', 'Faster than the CFL!', WARNING)
+          write(stderrunit,*) 'KID, Speeding berg1! =',mpp_pe(), berg%id
+          write(stderrunit,*) 'KID, Speeding berg2, speed =',speed, loc_dx/dt
+          write(stderrunit,*) 'KID, Speeding berg3, lat, lon =',lat,xi,yj
         endif
       endif
     endif
@@ -1093,7 +1097,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
     call dump_locfld(grd,i,j,grd%cn,'CN')
     call dump_locvel(grd,i,j,grd%lon,'Lon')
     call dump_locvel(grd,i,j,grd%lat,'Lat')
-    call print_berg(stderrunit,berg,'diamonds, accel, large accel')
+    call print_berg(stderrunit,berg,'KID, accel, large accel')
   endif
 
   !Used for testing the ocean response to fixed iceberg motion.
@@ -1347,12 +1351,12 @@ subroutine thermodynamics(bergs)
         endif
       else
         stderrunit = stderr()
-        write(stderrunit,*) 'diamonds, thermodynamics: berg appears to have grounded!!!! PE=',mpp_pe(),i,j
+        write(stderrunit,*) 'KID, thermodynamics: berg appears to have grounded!!!! PE=',mpp_pe(),i,j
         call print_berg(stderrunit,this,'thermodynamics, grounded')
         if (associated(this%trajectory)) &
           write(stderrunit,*) 'traj=',this%trajectory%lon,this%trajectory%lat
         write(stderrunit,*) 'msk=',grd%msk(i,j),grd%area(i,j)
-        call error_mesg('diamonds, thermodynamics', 'berg appears to have grounded!', FATAL)
+        call error_mesg('KID, thermodynamics', 'berg appears to have grounded!', FATAL)
       endif
 
       ! Rolling
@@ -1790,7 +1794,7 @@ subroutine find_basal_melt(bergs, dvo, lat, salt, temp, Use_three_equation_model
       if (dS_it < 0.0) then ! Sbdry is now the upper bound.
         if (Sb_max_set .and. (Sbdry > Sb_max)) then
           if (debug) then
-            call error_mesg('diamonds,Find basal melt', 'shelf_calc_flux: Irregular iteration for Sbdry (max).' ,WARNING)
+            call error_mesg('KID,Find basal melt', 'shelf_calc_flux: Irregular iteration for Sbdry (max).' ,WARNING)
             print *, 'Sbdry error: id,dvo,temp,salt,lat,thickness :',id,dvo,temp,salt,lat,thickness
           endif
           out_of_bounds=.true.
@@ -1800,7 +1804,7 @@ subroutine find_basal_melt(bergs, dvo, lat, salt, temp, Use_three_equation_model
       else ! Sbdry is now the lower bound.
         if (Sb_min_set .and. (Sbdry < Sb_min)) then
           if (debug) then
-            call error_mesg('diamonds,Find basal melt', 'shelf_calc_flux: Irregular iteration for Sbdry (min).' ,WARNING)
+            call error_mesg('KID,Find basal melt', 'shelf_calc_flux: Irregular iteration for Sbdry (min).' ,WARNING)
             print *, 'Sbdry error: id,dvo,temp,salt,lat,thickness :',id,dvo,temp,salt,lat,thickness
           endif
           out_of_bounds=.true.
@@ -1900,7 +1904,7 @@ subroutine find_orientation_using_iceberg_bonds(grd, berg, orientation)
   real :: r_dist_x, r_dist_y
   real :: lat_ref, dx_dlon, dy_dlat
   real :: theta, bond_count, Average_angle
-
+  
   bond_count=0.
   Average_angle=0.
   !Don't check orientation of the edges of halo,  since they can contain unassosiated bonds  (this is why halo width must be larger >= 2 to use bonds)
@@ -1916,7 +1920,7 @@ subroutine find_orientation_using_iceberg_bonds(grd, berg, orientation)
         !print *, 'Iceberg bond details2:',berg%ine, berg%jne, current_bond%other_berg_ine, current_bond%other_berg_jne
         !print *, 'Iceberg isd,ied,jsd,jed:',grd%isd, grd%ied, grd%jsd, grd%jed
         !print *, 'Iceberg isc,iec,jsc,jec:',grd%isc, grd%iec, grd%jsc, grd%jec
-        !call error_mesg('diamonds,calculating orientation', 'Looking at bond interactions of unassosiated berg!' ,FATAL)
+        !call error_mesg('KID,calculating orientation', 'Looking at bond interactions of unassosiated berg!' ,FATAL)
         !endif
       else
         lat2=other_berg%lat
@@ -2058,7 +2062,7 @@ subroutine spread_mass_across_ocean_cells(bergs, berg, i, j, x, y, Mberg, Mbits,
     if (S>0.5) then
       ! The width of an iceberg should not be greater than half the grid cell, or else it can spread over 3 cells  (i.e. S must be less than 0.5 non-dimensionally)
       !print 'Elements must be smaller than a whole grid cell', 'i.e.: S= ' , S , '>=0.5'
-      call error_mesg('diamonds, hexagonal spreading', 'Diameter of the iceberg is larger than a grid cell. Use smaller icebergs', WARNING)
+      call error_mesg('KID, hexagonal spreading', 'Diameter of the iceberg is larger than a grid cell. Use smaller icebergs', WARNING)
     endif
 
     !Subtracting the position of the nearest corner from x,y  (The mass will then be spread over the 4 cells connected to that corner)
@@ -2073,8 +2077,8 @@ subroutine spread_mass_across_ocean_cells(bergs, berg, i, j, x, y, Mberg, Mbits,
     call Hexagon_into_quadrants_using_triangles(x0,y0,H,orientation,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
 
     if (min(min(Area_Q1,Area_Q2),min(Area_Q3, Area_Q4)) <-tol) then
-      call error_mesg('diamonds, hexagonal spreading', 'Intersection with hexagons should not be negative!!!', WARNING)
-      write(stderrunit,*) 'diamonds, yU,yC,yD', Area_Q1, Area_Q2, Area_Q3, Area_Q4
+      call error_mesg('KID, hexagonal spreading', 'Intersection with hexagons should not be negative!!!', WARNING)
+      write(stderrunit,*) 'KID, yU,yC,yD', Area_Q1, Area_Q2, Area_Q3, Area_Q4
     endif
 
     Area_Q1=Area_Q1/Area_hex
@@ -2107,17 +2111,17 @@ subroutine spread_mass_across_ocean_cells(bergs, berg, i, j, x, y, Mberg, Mbits,
 
     !Temporary for debugging reasons.
     if (mpp_pe()==mpp_root_pe()) then
-      !write(stderrunit,*) 'diamonds, You are in the hexagonal domain now!!!'
+      !write(stderrunit,*) 'KID, You are in the hexagonal domain now!!!'
     endif
 
     !Double check that all the mass is being used.
     if ((abs(yCxC-(1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )))>tol) .and. (mpp_pe().eq. mpp_root_pe())) then
-      !call error_mesg('diamonds, hexagonal spreading', 'All the mass is not being used!!!', WARNING)
-      write(stderrunit,*) 'diamonds, hexagonal, H,x0,y0', H, x0 , y0
-      write(stderrunit,*) 'diamonds, hexagonal, Areas',(Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
+      !call error_mesg('KID, hexagonal spreading', 'All the mass is not being used!!!', WARNING)
+      write(stderrunit,*) 'KID, hexagonal, H,x0,y0', H, x0 , y0
+      write(stderrunit,*) 'KID, hexagonal, Areas',(Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
       debug=.True.
       !call Hexagon_into_quadrants_using_triangles(x0,y0,H,orientation,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4, debug)
-      call error_mesg('diamonds, hexagonal spreading', 'All the mass is not being used!!!', FATAL)
+      call error_mesg('KID, hexagonal spreading', 'All the mass is not being used!!!', FATAL)
     endif
 
     !Scale each cell by (1/fraction_used) in order to redisribute ice mass which landed up on the land, back into the ocean
@@ -2430,10 +2434,10 @@ subroutine divding_triangle_across_axes(Ax, Ay, Bx, By, Cx, Cy, axes1, Area_posi
         Area_positive= 0.
         Area_negative= A_triangle
       else
-        call error_mesg('diamonds, iceberg_run', 'Logical error inside triangle dividing routine', FATAL)
+        call error_mesg('KID, iceberg_run', 'Logical error inside triangle dividing routine', FATAL)
       endif
     else
-      call error_mesg('diamonds, iceberg_run', 'Another logical error inside triangle dividing routine', FATAL)
+      call error_mesg('KID, iceberg_run', 'Another logical error inside triangle dividing routine', FATAL)
     endif
   endif
 end subroutine divding_triangle_across_axes
@@ -2490,9 +2494,9 @@ subroutine Triangle_divided_into_four_quadrants(Ax, Ay, Bx, By, Cx, Cy, Area_tri
         if (.not.((point_in_interval(Bx,By,Cx,Cy,px,py)) .and. (point_in_interval(Bx,By,Cx,Cy,qx,qy)))) then
           ! You should not get here, but there might be some bugs in the code to do with points exactly falling on axes.
           !if (mpp_pe().eq.12) then
-            write(stderrunit,*) 'diamonds,corners', Ax,Ay,Bx,By,Cx,Cy
+            write(stderrunit,*) 'KID,corners', Ax,Ay,Bx,By,Cx,Cy
           !endif
-          call error_mesg('diamonds, iceberg_run', 'Something went wrong with Triangle_divide_into_four_quadrants', FATAL)
+          call error_mesg('KID, iceberg_run', 'Something went wrong with Triangle_divide_into_four_quadrants', FATAL)
         endif
       endif
     endif
@@ -2508,8 +2512,8 @@ subroutine Triangle_divided_into_four_quadrants(Ax, Ay, Bx, By, Cx, Cy, Area_tri
     elseif ((px.ge. 0.) .and. (qy.lt. 0.)) then !Forth quadrant
       Key_quadrant=4
     else  !
-      call error_mesg('diamonds, iceberg_run', 'None of the quadrants are Key', WARNING)
-      write(stderrunit,*) 'diamonds, Triangle, px,qy', px,qy
+      call error_mesg('KID, iceberg_run', 'None of the quadrants are Key', WARNING)
+      write(stderrunit,*) 'KID, Triangle, px,qy', px,qy
     endif
 
   else ! At least one quadrant is empty, and this can be used to find the areas in the other quadrant.  Assigning quadrants. Key_quadrant is the empty quadrant.
@@ -2552,7 +2556,7 @@ subroutine Triangle_divided_into_four_quadrants(Ax, Ay, Bx, By, Cx, Cy, Area_tri
     !Area_Q3=Area_Left-Area_Q2
     Area_Q3=Area_triangle-(Area_Q1+Area_Q2+Area_Q4)
   else
-    call error_mesg('diamonds, iceberg_run', 'Logical error inside triangle into four quadrants. Should not get here.', FATAL)
+    call error_mesg('KID, iceberg_run', 'Logical error inside triangle into four quadrants. Should not get here.', FATAL)
   endif
 
   Area_Q1=max(Area_Q1,0.)
@@ -2563,16 +2567,16 @@ subroutine Triangle_divided_into_four_quadrants(Ax, Ay, Bx, By, Cx, Cy, Area_tri
 
   Error=abs(Area_Q1+Area_Q2+Area_Q3+Area_Q4-Area_triangle)
   if (Error>tol) then
-    call error_mesg('diamonds, triangle spreading', 'Triangle not evaluated accurately!!', WARNING)
+    call error_mesg('KID, triangle spreading', 'Triangle not evaluated accurately!!', WARNING)
     !if (mpp_pe().eq.mpp_root_pe()) then
     if (mpp_pe().eq. 20) then
-      write(stderrunit,*) 'diamonds, Triangle corners:',Ax,Ay,Bx,By,Cx,Cy
-      write(stderrunit,*) 'diamonds, Triangle, Full Area', Area_Q1+ Area_Q2+ Area_Q3+ Area_Q4
-      write(stderrunit,*) 'diamonds, Triangle, Areas', Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
-      write(stderrunit,*) 'diamonds, Triangle, Areas', Error
-      write(stderrunit,*) 'diamonds, Key quadrant',Key_quadrant,Area_key_quadrant
-      write(stderrunit,*) 'diamonds, point in triangle',(point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.))
-      write(stderrunit,*) 'diamonds, halves',Area_Upper,Area_Lower,Area_Right,Area_Left
+      write(stderrunit,*) 'KID, Triangle corners:',Ax,Ay,Bx,By,Cx,Cy
+      write(stderrunit,*) 'KID, Triangle, Full Area', Area_Q1+ Area_Q2+ Area_Q3+ Area_Q4
+      write(stderrunit,*) 'KID, Triangle, Areas', Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
+      write(stderrunit,*) 'KID, Triangle, Areas', Error
+      write(stderrunit,*) 'KID, Key quadrant',Key_quadrant,Area_key_quadrant
+      write(stderrunit,*) 'KID, point in triangle',(point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.))
+      write(stderrunit,*) 'KID, halves',Area_Upper,Area_Lower,Area_Right,Area_Left
     endif
   endif
 
@@ -2674,24 +2678,24 @@ subroutine Hexagon_into_quadrants_using_triangles(x0, y0, H, theta, Area_hex ,Ar
   Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
   if ((abs(Error)>tol))then
     if (mpp_pe().eq.mpp_root_pe()) then
-      call error_mesg('diamonds, hexagonal spreading', 'Hexagon error is large!!', WARNING)
-      write(stderrunit,*) 'diamonds, hex error, H,x0,y0, Error', H, x0 , y0, Error
-      write(stderrunit,*) 'diamonds, hex error, Areas',Area_hex, (Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
-      write(stderrunit,*) 'diamonds, Triangle1',C1x,C1y,C2x,C2y,T12_Area,T12_Q1,T12_Q2,T12_Q3,T12_Q4,(T12_Q1+T12_Q2+T12_Q3+T12_Q4-T12_Area)
-      write(stderrunit,*) 'diamonds, Triangle2',C2x,C2y,C3x,C3y,T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4,(T23_Q1+T23_Q2+T23_Q3+T23_Q4-T23_Area)
-      write(stderrunit,*) 'diamonds, Triangle3',C3x,C3y,C4x,C4y,T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4,(T34_Q1+T34_Q2+T34_Q3+T34_Q4-T34_Area)
-      write(stderrunit,*) 'diamonds, Triangle4',C4x,C4y,C5x,C5y,T45_Area,T45_Q1,T45_Q2,T45_Q3,T45_Q4,(T45_Q1+T45_Q2+T45_Q3+T45_Q4-T45_Area)
-      write(stderrunit,*) 'diamonds, Triangle5',C5x,C5y,C6x,C6y,T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4,(T56_Q1+T56_Q2+T56_Q3+T56_Q4-T56_Area)
-      write(stderrunit,*) 'diamonds, Triangle6',C6x,C6y,C1x,C1y,T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4,(T61_Q1+T61_Q2+T61_Q3+T61_Q4-T61_Area)
+      call error_mesg('KID, hexagonal spreading', 'Hexagon error is large!!', WARNING)
+      write(stderrunit,*) 'KID, hex error, H,x0,y0, Error', H, x0 , y0, Error
+      write(stderrunit,*) 'KID, hex error, Areas',Area_hex, (Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
+      write(stderrunit,*) 'KID, Triangle1',C1x,C1y,C2x,C2y,T12_Area,T12_Q1,T12_Q2,T12_Q3,T12_Q4,(T12_Q1+T12_Q2+T12_Q3+T12_Q4-T12_Area)
+      write(stderrunit,*) 'KID, Triangle2',C2x,C2y,C3x,C3y,T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4,(T23_Q1+T23_Q2+T23_Q3+T23_Q4-T23_Area)
+      write(stderrunit,*) 'KID, Triangle3',C3x,C3y,C4x,C4y,T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4,(T34_Q1+T34_Q2+T34_Q3+T34_Q4-T34_Area)
+      write(stderrunit,*) 'KID, Triangle4',C4x,C4y,C5x,C5y,T45_Area,T45_Q1,T45_Q2,T45_Q3,T45_Q4,(T45_Q1+T45_Q2+T45_Q3+T45_Q4-T45_Area)
+      write(stderrunit,*) 'KID, Triangle5',C5x,C5y,C6x,C6y,T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4,(T56_Q1+T56_Q2+T56_Q3+T56_Q4-T56_Area)
+      write(stderrunit,*) 'KID, Triangle6',C6x,C6y,C1x,C1y,T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4,(T61_Q1+T61_Q2+T61_Q3+T61_Q4-T61_Area)
     endif
   endif
 
   exact_hex_area=((3.*sqrt(3.)/2)*(S*S))
   if (abs(Area_hex-exact_hex_area)>tol) then
-    call error_mesg('diamonds, hexagonal spreading', 'Hexagon not evaluated accurately!!', WARNING)
+    call error_mesg('KID, hexagonal spreading', 'Hexagon not evaluated accurately!!', WARNING)
     if (mpp_pe().eq.mpp_root_pe()) then
-      write(stderrunit,*) 'diamonds, hex calculations, H,x0,y0', H, x0 , y0
-      write(stderrunit,*) 'diamonds, hex calculations, Areas',Area_hex, (Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
+      write(stderrunit,*) 'KID, hex calculations, H,x0,y0', H, x0 , y0
+      write(stderrunit,*) 'KID, hex calculations, Areas',Area_hex, (Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
     endif
   endif
 
@@ -2705,10 +2709,10 @@ subroutine Hexagon_into_quadrants_using_triangles(x0, y0, H, theta, Area_hex ,Ar
    elseif  (((Area_Q4>=Area_Q1) .and. (Area_Q4>=Area_Q2)) .and. (Area_Q4>=Area_Q3)) then
      Area_Q4=Area_Q4+Error
    else
-     call error_mesg('diamonds, hexagonal spreading', 'Error in hexagon is larger than any quadrant!!', WARNING)
+     call error_mesg('KID, hexagonal spreading', 'Error in hexagon is larger than any quadrant!!', WARNING)
      if (mpp_pe().eq.mpp_root_pe()) then
-      write(stderrunit,*) 'diamonds, hex quadrants, H,x0,y0', H, x0 , y0, Error
-      write(stderrunit,*) 'diamonds, hex quadrants, Areas',Area_hex, (Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
+      write(stderrunit,*) 'KID, hex quadrants, H,x0,y0', H, x0 , y0, Error
+      write(stderrunit,*) 'KID, hex quadrants, Areas',Area_hex, (Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
      endif
    endif
 
@@ -2800,7 +2804,7 @@ subroutine interp_flds(grd, i, j, xi, yj, rx, ry, uo, vo, ui, vi, ua, va, ssh_x,
   !     write(stderrunit,'(i3,32f7.1)') j,(grd%msk(i,j),i=grd%isd,grd%ied)
   !   enddo
   ! endif
-      call error_mesg('diamonds, interp fields', 'ua is NaNs', FATAL)
+      call error_mesg('KID, interp fields', 'ua is NaNs', FATAL)
     endif
   endif
 
@@ -2866,10 +2870,10 @@ subroutine interp_flds(grd, i, j, xi, yj, rx, ry, uo, vo, ui, vi, ua, va, ssh_x,
   if (((((uo.ne.uo) .or. (vo.ne.vo)) .or. ((ui.ne.ui) .or. (vi.ne.vi))) .or. &
        (((ua.ne.ua) .or. (va.ne.va)) .or. ((ssh_x.ne.ssh_x) .or. (ssh_y.ne.ssh_y)))) .or. &
        (((sst.ne. sst) .or. (sss.ne. sss) .or. (cn.ne.cn)) .or. (hi.ne. hi))) then
-    write(stderrunit,*) 'diamonds, Error in interpolate: uo,vo,ui,vi',uo, vo, ui, vi
-    write(stderrunit,*) 'diamonds, Error in interpolate: ua,va,ssh_x,ssh_y', ua, va, ssh_x, ssh_y
-    write(stderrunit,*) 'diamonds, Error in interpolate: sst,cn,hi', sst, sss, cn, hi, mpp_pe()
-    call error_mesg('diamonds, interp fields', 'field interpaolations has NaNs', FATAL)
+    write(stderrunit,*) 'KID, Error in interpolate: uo,vo,ui,vi',uo, vo, ui, vi
+    write(stderrunit,*) 'KID, Error in interpolate: ua,va,ssh_x,ssh_y', ua, va, ssh_x, ssh_y
+    write(stderrunit,*) 'KID, Error in interpolate: sst,cn,hi', sst, sss, cn, hi, mpp_pe()
+    call error_mesg('KID, interp fields', 'field interpaolations has NaNs', FATAL)
 
   endif
 
@@ -3104,7 +3108,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
      if (mod(24*iday+ihr+(imin/60.),float(bergs%verbose_hrs)).eq.0) lbudget=budget  !Added minutes, so that it does not repeat when smaller time steps are used.
   endif
   if (mpp_pe()==mpp_root_pe().and.lverbose) write(*,'(a,3i5,a,3i5,a,i5,f8.3)') &
-       'diamonds: y,m,d=',iyr, imon, iday,' h,m,s=', ihr, imin, isec, &
+       'KID: y,m,d=',iyr, imon, iday,' h,m,s=', ihr, imin, isec, &
        ' yr,yrdy=', bergs%current_year, bergs%current_yearday
 
 
@@ -3167,7 +3171,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
       grd%vi(I,J) = mask * 0.5*(vi(iv,Jv)+vi(iv+1,Jv))
     enddo ; enddo
   else
-    call error_mesg('diamonds, iceberg_run', 'Unrecognized value of stagger!', FATAL)
+    call error_mesg('KID, iceberg_run', 'Unrecognized value of stagger!', FATAL)
   endif
 
   if (str_stagger == BGRID_NE) then
@@ -3221,7 +3225,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 
     deallocate(uA_tmp, vA_tmp)
   else
-    call error_mesg('diamonds, iceberg_run', 'Unrecognized value of stress_stagger!', FATAL)
+    call error_mesg('KID, iceberg_run', 'Unrecognized value of stress_stagger!', FATAL)
   endif
 
   call mpp_update_domains(grd%uo, grd%vo, grd%domain, gridtype=BGRID_NE)
@@ -3263,11 +3267,11 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   else
     grd%sss(grd%isc:grd%iec,grd%jsc:grd%jec)=-1.0
     if ((bergs%use_mixed_layer_salinity_for_thermo) .and. (bergs%melt_icebergs_as_ice_shelf))  then
-      call error_mesg('diamonds, icebergs_run', 'Can not use salinity for thermo. Ocean ML salinity not present!', FATAL)
+      call error_mesg('KID, icebergs_run', 'Can not use salinity for thermo. Ocean ML salinity not present!', FATAL)
     endif
   endif
 
-  ! Make sure that gridded values agree with mask  (to get ride of NaN values)
+  ! Make sure that gridded values agree with mask  (to get rid of NaN values)
   do i=grd%isd,grd%ied ; do j=grd%jsd,grd%jed
     ! Initializing all gridded values to zero
     if (grd%msk(i,j).lt. 0.5) then
@@ -3318,6 +3322,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   call mpp_clock_begin(bergs%clock_mom)
 
   if (.not.bergs%Static_icebergs) then
+    call update_latlon(bergs) !guarantees correct coords for halo bergs. Needed if interacting bergs & domain is periodic - Alex 
     call evolve_icebergs(bergs)
     if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after evolve()     ')
   endif
@@ -3330,7 +3335,6 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   ! Send bergs to other PEs
   call mpp_clock_begin(bergs%clock_com)
   if (bergs%iceberg_bonds_on)  call  bond_address_update(bergs)
-
   call send_bergs_to_other_pes(bergs)
   if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after send_bergs() ')
   if ((bergs%interactive_icebergs_on) .or. (bergs%iceberg_bonds_on)) then
@@ -3589,8 +3593,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     grdd_spread_area=sum( grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
     call mpp_sum(grdd_spread_area)
     if (mpp_pe().eq.mpp_root_pe()) then
- 100 format("diamonds: ",a19,3(a18,"=",es14.7,x,a2,:,","),a12,i8)
- 200 format("diamonds: ",a19,10(a18,"=",es14.7,x,a2,:,","))
+ 100 format("KID: ",a19,3(a18,"=",es14.7,x,a2,:,","),a12,i8)
+ 200 format("KID: ",a19,10(a18,"=",es14.7,x,a2,:,","))
       call report_state('stored ice','kg','',bergs%stored_start,'',bergs%stored_end,'')
       call report_state('floating','kg','',bergs%floating_mass_start,'',bergs%floating_mass_end,'',bergs%nbergs_end)
       call report_state('icebergs','kg','',bergs%icebergs_mass_start,'',bergs%icebergs_mass_end,'')
@@ -3637,12 +3641,12 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
                                            'melt',bergs%net_heat_to_ocean, &
                                            'net heat',bergs%floating_heat_start,bergs%floating_heat_end)
       if (debug) then
-        call report_consistant('top interface','kg','from SIS',bergs%net_incoming_calving,'seen by diamonds',&
+        call report_consistant('top interface','kg','from SIS',bergs%net_incoming_calving,'seen by KID',&
              & bergs%net_calving_received)
         call report_consistant('bot interface','kg','sent',bergs%net_outgoing_calving,'seen by SIS',bergs%net_calving_returned)
       endif
-      write(*,'("diamonds: calved by class = ",i4,20(",",i4))') (bergs%nbergs_calved_by_class(k),k=1,nclasses)
-      if (bergs%nspeeding_tickets>0) write(*,'("diamonds: speeding tickets issued = ",i4)') bergs%nspeeding_tickets
+      write(*,'("KID: calved by class = ",i4,20(",",i4))') (bergs%nbergs_calved_by_class(k),k=1,nclasses)
+      if (bergs%nspeeding_tickets>0) write(*,'("KID: speeding tickets issued = ",i4)') bergs%nspeeding_tickets
     endif
     bergs%nbergs_start=bergs%nbergs_end
     bergs%stored_start=bergs%stored_end
@@ -3712,7 +3716,7 @@ subroutine report_state(budgetstr, budgetunits, startstr, startval, endstr, endv
                         endstr//' end',endval,budgetunits, &
                         delstr//'Delta',endval-startval,budgetunits
   endif
-  100 format("diamonds: ",a19,3(a18,"=",es14.7,x,a2,:,","),a12,i8)
+  100 format("KID: ",a19,3(a18,"=",es14.7,x,a2,:,","),a12,i8)
 end subroutine report_state
 
 !> Prints consistency summary of start and end states
@@ -3729,7 +3733,7 @@ subroutine report_consistant(budgetstr, budgetunits, startstr, startval, endstr,
                       startstr,startval,budgetunits, &
                       endstr,endval,budgetunits, &
                       'error',(endval-startval)/((endval+startval)+1e-30),'nd'
-  200 format("diamonds: ",a19,10(a18,"=",es14.7,x,a2,:,","))
+  200 format("KID: ",a19,10(a18,"=",es14.7,x,a2,:,","))
 end subroutine report_consistant
 
 !> Prints a budget
@@ -3750,7 +3754,7 @@ subroutine report_budget(budgetstr, budgetunits, instr, inval, outstr, outval, d
                       outstr//' out',outval,budgetunits, &
                       'Delta '//delstr,inval-outval,budgetunits, &
                       'error',((endval-startval)-(inval-outval))/max(1.e-30,max(abs(endval-startval),abs(inval-outval))),'nd'
-  200 format("diamonds: ",a19,3(a18,"=",es14.7,x,a2,:,","),a8,"=",es10.3,x,a2)
+  200 format("KID: ",a19,3(a18,"=",es14.7,x,a2,:,","),a8,"=",es10.3,x,a2)
 end subroutine report_budget
 
 !> Prints summary of start and end states
@@ -3767,7 +3771,7 @@ subroutine report_istate(budgetstr, startstr, startval, endstr, endval, delstr)
                         startstr//' start',startval, &
                         endstr//' end',endval, &
                         delstr//'Delta',endval-startval
-  100 format("diamonds: ",a19,3(a18,"=",i14,x,:,","))
+  100 format("KID: ",a19,3(a18,"=",i14,x,:,","))
 end subroutine report_istate
 
 !> Prints a budget
@@ -3787,7 +3791,7 @@ subroutine report_ibudget(budgetstr,instr,inval,outstr,outval,delstr,startval,en
                       outstr//' out',outval, &
                       'Delta '//delstr,inval-outval, &
                       'error',((endval-startval)-(inval-outval))
-  200 format("diamonds: ",a19,10(a18,"=",i14,x,:,","))
+  200 format("KID: ",a19,10(a18,"=",i14,x,:,","))
 end subroutine report_ibudget
 
 !> Time-filter calving and calving_hflx with a running mean.
@@ -3974,7 +3978,7 @@ subroutine accumulate_calving(bergs)
     bergs%stored_start=sum( grd%stored_ice(grd%isc:grd%iec,grd%jsc:grd%jec,:) )
     call mpp_sum( bergs%stored_start )
     if (mpp_pe().eq.mpp_root_pe()) write(*,'(a,es13.6,a)') &
-        'diamonds, accumulate_calving: initial stored mass=',bergs%stored_start,' kg'
+        'KID, accumulate_calving: initial stored mass=',bergs%stored_start,' kg'
     do j=grd%jsc,grd%jec; do i=grd%isc,grd%iec
       if (grd%calving(i,j).ne.0.) grd%stored_heat(i,j)= & ! Need units of J
             sum(grd%stored_ice(i,j,:)) & ! initial stored ice in kg
@@ -3984,7 +3988,7 @@ subroutine accumulate_calving(bergs)
     bergs%stored_heat_start=sum( grd%stored_heat(grd%isc:grd%iec,grd%jsc:grd%jec) )
     call mpp_sum( bergs%stored_heat_start )
     if (mpp_pe().eq.mpp_root_pe()) write(*,'(a,es13.6,a)') &
-        'diamonds, accumulate_calving: initial stored heat=',bergs%stored_heat_start,' J'
+        'KID, accumulate_calving: initial stored heat=',bergs%stored_heat_start,' J'
    endif
 
   remaining_dist=1.
@@ -3993,8 +3997,8 @@ subroutine accumulate_calving(bergs)
     remaining_dist=remaining_dist-bergs%distribution(k)
   enddo
   if (remaining_dist.lt.0.) then
-    write(stderrunit,*) 'diamonds, accumulate_calving: sum(distribution)>1!!!',remaining_dist
-    call error_mesg('diamonds, accumulate_calving', 'calving is OVER distributed!', WARNING)
+    write(stderrunit,*) 'KID, accumulate_calving: sum(distribution)>1!!!',remaining_dist
+    call error_mesg('KID, accumulate_calving', 'calving is OVER distributed!', WARNING)
   endif
   net_calving_used=sum( grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec) )*(1.-remaining_dist)
   bergs%net_calving_used=bergs%net_calving_used+net_calving_used*bergs%dt
@@ -4043,19 +4047,19 @@ subroutine calve_icebergs(bergs)
         do while (grd%stored_ice(i,j,k).ge.bergs%initial_mass(k)*bergs%mass_scaling(k))
           newberg%lon=0.25*((grd%lon(i,j)+grd%lon(i-1,j-1))+(grd%lon(i-1,j)+grd%lon(i,j-1)))
           newberg%lat=0.25*((grd%lat(i,j)+grd%lat(i-1,j-1))+(grd%lat(i-1,j)+grd%lat(i,j-1)))
-         !write(stderr(),*) 'diamonds, calve_icebergs: creating new iceberg at ',newberg%lon,newberg%lat
+         !write(stderr(),*) 'KID, calve_icebergs: creating new iceberg at ',newberg%lon,newberg%lat
           lret=pos_within_cell(grd, newberg%lon, newberg%lat, i, j, xi, yj)
           if (.not.lret) then
-            write(stderrunit,*) 'diamonds, calve_icebergs: something went very wrong!',i,j,xi,yj
-            call error_mesg('diamonds, calve_icebergs', 'berg is not in the correct cell!', FATAL)
+            write(stderrunit,*) 'KID, calve_icebergs: something went very wrong!',i,j,xi,yj
+            call error_mesg('KID, calve_icebergs', 'berg is not in the correct cell!', FATAL)
           endif
           if (debug.and.(xi<0..or.xi>1..or.yj<0..or.yj>1.)) then
-            write(stderrunit,*) 'diamonds, calve_icebergs: something went very wrong!',i,j,xi,yj
-            call error_mesg('diamonds, calve_icebergs', 'berg xi,yj is not correct!', FATAL)
+            write(stderrunit,*) 'KID, calve_icebergs: something went very wrong!',i,j,xi,yj
+            call error_mesg('KID, calve_icebergs', 'berg xi,yj is not correct!', FATAL)
           endif
           if (grd%msk(i,j)<0.5) then
-            write(stderrunit,*) 'diamonds, calve_icebergs: WARNING!!! Iceberg born in land cell',i,j,newberg%lon,newberg%lat
-            if (debug) call error_mesg('diamonds, calve_icebergs', 'Iceberg born in Land Cell!', FATAL)
+            write(stderrunit,*) 'KID, calve_icebergs: WARNING!!! Iceberg born in land cell',i,j,newberg%lon,newberg%lat
+            if (debug) call error_mesg('KID, calve_icebergs', 'Iceberg born in Land Cell!', FATAL)
           endif
           newberg%ine=i
           newberg%jne=j
@@ -4109,6 +4113,37 @@ subroutine calve_icebergs(bergs)
 
 end subroutine calve_icebergs
 
+!> Update berg lat & lon from local position in cell - Alex
+subroutine update_latlon(bergs)
+  !Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  ! Local variables
+  type(icebergs_gridded), pointer :: grd
+  type(iceberg), pointer :: berg
+  real :: dlon, dlat,xi,yj
+  integer :: grdi,grdj
+  logical :: lret
+
+  ! For convenience
+  grd=>bergs%grd
+
+  do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+    berg=>bergs%list(grdi,grdj)%first
+    do while (associated(berg))
+      dlon = berg%lon - berg%lon_old
+      dlat = berg%lat - berg%lat_old
+      berg%lon=bilin(grd, grd%lon, berg%ine, berg%jne, berg%xi, berg%yj)
+      berg%lat=bilin(grd, grd%lat, berg%ine, berg%jne, berg%xi, berg%yj)
+      berg%lon_old = berg%lon-dlon
+      berg%lat_old = berg%lat-dlat
+      !need to update local positon in cell from updated global coords, due to roundoff
+      lret=pos_within_cell(grd, berg%lon, berg%lat, berg%ine, berg%jne, berg%xi, berg%yj)      
+      berg=>berg%next
+    enddo !loop over all bergs
+  enddo; enddo
+end subroutine update_latlon
+
+
 !> Evolves icebergs forward by updating velocity and position with a time-stepping scheme
 subroutine evolve_icebergs(bergs)
   ! Arguments
@@ -4159,7 +4194,7 @@ subroutine evolve_icebergs(bergs)
           write(stderrunit,'(a,i3,2(i4,3f8.2))') 'evolve_iceberg: pe,lon/lat(i,j)=', mpp_pe(), &
                    berg%ine,berg%lon,grd%lon(berg%ine-1,berg%jne-1),grd%lon(berg%ine,berg%jne), &
                    berg%jne,berg%lat,grd%lat(berg%ine-1,berg%jne-1),grd%lat(berg%ine,berg%jne)
-          if (debug) call error_mesg('diamonds, evolve_iceberg','berg is in wrong starting cell!',FATAL)
+          if (debug) call error_mesg('KID, evolve_iceberg','berg is in wrong starting cell!',FATAL)
         endif
         if (debug) call check_position(grd, berg, 'evolve_iceberg (top)')
 
@@ -4281,7 +4316,7 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln, rx, ry)
   axn  = berg%axn ;   ayn  = berg%ayn
   bxn=   berg%bxn ;   byn  = berg%byn
   uvel1=berg%uvel ;   vvel1=berg%vvel
-  i=berg%ine     ;   j=berg%jne
+  i=berg%ine      ;   j=berg%jne
   xi=berg%xi      ;   yj=berg%yj
 
   ! Turn the velocities into u_star, v_star.(uvel3 is v_star) - Alon (not sure how this works with tangent plane)
@@ -4322,18 +4357,18 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln, rx, ry)
     call print_fld(grd, grd%sst, 'sst')
     call print_fld(grd, grd%sss, 'sss')
     call print_fld(grd, grd%hi, 'hi')
-    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
-    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lonn=',lonn,berg%lon
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: latn=',latn,berg%lat
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u3,un,u0=',uvel3,uveln,berg%uvel
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v3,vn,v0=',vvel3,vveln,berg%vvel
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: id=',berg%id
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1=',&
+    write(stderrunit,'(a,6i5)') 'KID, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
+    write(stderrunit,'(a,6i5)') 'KID, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: lonn=',lonn,berg%lon
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: latn=',latn,berg%lat
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: u3,un,u0=',uvel3,uveln,berg%uvel
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: v3,vn,v0=',vvel3,vveln,berg%vvel
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: id=',berg%id
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: dt* ax1=',&
          & dt*ax1
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ay1=',&
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: dt* ay1=',&
          & dt*ay1
-    write(stderrunit,*) 'diamonds, evolve_iceberg: on_tangential_plane=',on_tangential_plane
+    write(stderrunit,*) 'KID, evolve_iceberg: on_tangential_plane=',on_tangential_plane
     write(stderrunit,*) 'Acceleration terms for position 1'
     error_flag=pos_within_cell(grd, lonn, latn, i, j, xi,  yj)
     call accel(bergs, berg, i, j, xi, yj, latn, uvel3, vvel3, uvel1, vvel1, dt_2, rx, ry, ax1, ay1, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn, bxn, byn - Added by Alon
@@ -4342,7 +4377,7 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln, rx, ry)
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'posn box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
     call print_berg(stderrunit, berg, 'evolve_iceberg, out of cell at end!')
     bounced=is_point_in_cell(bergs%grd, lonn, latn, i, j,explain=.true.)
-    if (debug) call error_mesg('diamonds, evolve_iceberg','berg is out of posn at end!',FATAL)
+    if (debug) call error_mesg('KID, evolve_iceberg','berg is out of posn at end!',FATAL)
     write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lon',(i,i=grd%isd,grd%ied)
     do j=grd%jed,grd%jsd,-1
       write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lon(i,j),i=grd%isd,grd%ied)
@@ -4445,7 +4480,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
   if (on_tangential_plane) call rotvec_to_tang(lon1,axn1,ayn1,xddot1n,yddot1n) !Alon
 
   !  X2 = X1+dt/2*V1 ; V2 = V1+dt/2*A1; A2=A(X2)
-  !if (debug) write(stderr(),*) 'diamonds, evolve: x2=...'
+  !if (debug) write(stderr(),*) 'KID, evolve: x2=...'
   if (on_tangential_plane) then
     x2=x1+dt_2*xdot1; y2=y1+dt_2*ydot1
     xdot2=xdot1+dt_2*xddot1; ydot2=ydot1+dt_2*yddot1
@@ -4470,20 +4505,20 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
     call print_fld(grd, grd%sst, 'sst')
     call print_fld(grd, grd%sss, 'sss')
     call print_fld(grd, grd%hi, 'hi')
-    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
-    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
-    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: i1,i2,i=',i1,i2,i
-    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: j1,j2,j=',j1,j2,j
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lon1,lon2=',lon1,lon2,berg%lon
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lat1,lat2=',lat1,lat2,berg%lat
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u1,u2,u0=',uvel1,uvel2,berg%uvel
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v1,v2,v0=',vvel1,vvel2,berg%vvel
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1,ax2=',dt*ax1,dt*ax2
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ay1,ay2=',dt*ay1,dt*ay2
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u0=',dt*uvel1,dt*uvel2,dt*berg%uvel
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v0=',dt*vvel1,dt*vvel2,dt*berg%vvel
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2 (deg)=',dt*u1,dt*u2
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2 (deg)=',dt*v1,dt*v2
+    write(stderrunit,'(a,6i5)') 'KID, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
+    write(stderrunit,'(a,6i5)') 'KID, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
+    write(stderrunit,'(a,6i5)') 'KID, evolve_iceberg: i1,i2,i=',i1,i2,i
+    write(stderrunit,'(a,6i5)') 'KID, evolve_iceberg: j1,j2,j=',j1,j2,j
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: lon1,lon2=',lon1,lon2,berg%lon
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: lat1,lat2=',lat1,lat2,berg%lat
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: u1,u2,u0=',uvel1,uvel2,berg%uvel
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: v1,v2,v0=',vvel1,vvel2,berg%vvel
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: dt* ax1,ax2=',dt*ax1,dt*ax2
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: dt* ay1,ay2=',dt*ay1,dt*ay2
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: dt* u1,u2,u0=',dt*uvel1,dt*uvel2,dt*berg%uvel
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: dt* v1,v2,v0=',dt*vvel1,dt*vvel2,dt*berg%vvel
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: dt* u1,u2 (deg)=',dt*u1,dt*u2
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: dt* v1,v2 (deg)=',dt*v1,dt*v2
     write(stderrunit,*) 'Acceleration terms for position 1'
     error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
     call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, rx, ry, ax1, ay1, axn1, ayn1, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn,- Added by Alon
@@ -4491,7 +4526,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos2 i,j,lon,lat,xi,yj=',i,j,lon2,lat2,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos2 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
     bounced=is_point_in_cell(bergs%grd, lon2, lat2, i, j,explain=.true.)
-    call error_mesg('diamonds, evolve_iceberg','berg is out of posn at 2!',FATAL)
+    call error_mesg('KID, evolve_iceberg','berg is out of posn at 2!',FATAL)
   endif
   call  convert_from_meters_to_grid(lat2,bergs%grd%grid_is_latlon ,dxdl2,dydl)
   !dxdl2=r180_pi/(Rearth*cos(lat2*pi_180))
@@ -4502,7 +4537,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
   if (on_tangential_plane) call rotvec_to_tang(lon2,axn2,ayn2,xddot2n,yddot2n) !Alon
 
   !  X3 = X1+dt/2*V2 ; V3 = V1+dt/2*A2; A3=A(X3)
-  !if (debug) write(stderr(),*) 'diamonds, evolve: x3=...'
+  !if (debug) write(stderr(),*) 'KID, evolve: x3=...'
   if (on_tangential_plane) then
     x3=x1+dt_2*xdot2; y3=y1+dt_2*ydot2
     xdot3=xdot1+dt_2*xddot2; ydot3=ydot1+dt_2*yddot2
@@ -4527,20 +4562,20 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
     call print_fld(grd, grd%sst, 'sst')
     call print_fld(grd, grd%sss, 'sss')
     call print_fld(grd, grd%hi, 'hi')
-    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
-    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
-    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: i1,i2,i3,i=',i1,i2,i3,i
-    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: j1,j2,j3,j=',j1,j2,j3,j
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lon1,lon2,lon3=',lon1,lon2,lon3,berg%lon
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lat1,lat2,lat3=',lat1,lat2,lat3,berg%lat
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u1,u2,u3,u0=',uvel1,uvel2,uvel3,berg%uvel
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v1,v2,v3,v0=',vvel1,vvel2,vvel3,berg%vvel
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1,ax2,ax3=',dt*ax1,dt*ax2,dt*ax3
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ay1,ay2,ay3=',dt*ay1,dt*ay2,dt*ay3
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3,u0=',dt*uvel1,dt*uvel2,dt*uvel3,dt*berg%uvel
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v0=',dt*vvel1,dt*vvel2,dt*vvel3,dt*berg%vvel
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3 (deg)=',dt*u1,dt*u2,dt*u3
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3 (deg)=',dt*v1,dt*v2,dt*v3
+    write(stderrunit,'(a,6i5)') 'KID, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
+    write(stderrunit,'(a,6i5)') 'KID, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
+    write(stderrunit,'(a,6i5)') 'KID, evolve_iceberg: i1,i2,i3,i=',i1,i2,i3,i
+    write(stderrunit,'(a,6i5)') 'KID, evolve_iceberg: j1,j2,j3,j=',j1,j2,j3,j
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: lon1,lon2,lon3=',lon1,lon2,lon3,berg%lon
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: lat1,lat2,lat3=',lat1,lat2,lat3,berg%lat
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: u1,u2,u3,u0=',uvel1,uvel2,uvel3,berg%uvel
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: v1,v2,v3,v0=',vvel1,vvel2,vvel3,berg%vvel
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: dt* ax1,ax2,ax3=',dt*ax1,dt*ax2,dt*ax3
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: dt* ay1,ay2,ay3=',dt*ay1,dt*ay2,dt*ay3
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: dt* u1,u2,u3,u0=',dt*uvel1,dt*uvel2,dt*uvel3,dt*berg%uvel
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: dt* v1,v2,v3,v0=',dt*vvel1,dt*vvel2,dt*vvel3,dt*berg%vvel
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: dt* u1,u2,u3 (deg)=',dt*u1,dt*u2,dt*u3
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: dt* v1,v2,v3 (deg)=',dt*v1,dt*v2,dt*v3
     write(stderrunit,*) 'Acceleration terms for position 1'
     error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
     call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, rx, ry, ax1, ay1, axn1, ayn1, bxn, byn, debug_flag=.true.) !axn, ayn - Added by Alon
@@ -4551,7 +4586,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos3 i,j,lon,lat,xi,yj=',i,j,lon3,lat3,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos3 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
     bounced=is_point_in_cell(bergs%grd, lon2, lat2, i, j,explain=.true.)
-    call error_mesg('diamonds, evolve_iceberg','berg is out of posn at 3!',FATAL)
+    call error_mesg('KID, evolve_iceberg','berg is out of posn at 3!',FATAL)
   endif
   call  convert_from_meters_to_grid(lat3,bergs%grd%grid_is_latlon ,dxdl3,dydl)
   !dxdl3=r180_pi/(Rearth*cos(lat3*pi_180))
@@ -4561,7 +4596,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
   if (on_tangential_plane) call rotvec_to_tang(lon3,axn3,ayn3,xddot3n,yddot3n) !Alon
 
   !  X4 = X1+dt*V3 ; V4 = V1+dt*A3; A4=A(X4)
-  !if (debug) write(stderr(),*) 'diamonds, evolve: x4=...'
+  !if (debug) write(stderr(),*) 'KID, evolve: x4=...'
   if (on_tangential_plane) then
     x4=x1+dt*xdot3; y4=y1+dt*ydot3
     xdot4=xdot1+dt*xddot3; ydot4=ydot1+dt*yddot3
@@ -4584,20 +4619,20 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
     call print_fld(grd, grd%sst, 'sst')
     call print_fld(grd, grd%sss, 'sss')
     call print_fld(grd, grd%hi, 'hi')
-    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
-    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
-    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: i1,i2,i3,i4,i=',i1,i2,i3,i4,i
-    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: j1,j2,j3,j4,j=',j1,j2,j3,j4,j
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lon1,lon2,lon3,lon4=',lon1,lon2,lon3,lon4,berg%lon
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lat1,lat2,lat3,lat4=',lat1,lat2,lat3,lat4,berg%lat
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u1,u2,u3,u4,u0=',uvel1,uvel2,uvel3,uvel4,berg%uvel
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v1,v2,v3,v4,v0=',vvel1,vvel2,vvel3,vvel4,berg%vvel
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1,ax2,ax3,ax4=',dt*ax1,dt*ax2,dt*ax3,dt*ax4
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ay1,ay2,ay3,ay4=',dt*ay1,dt*ay2,dt*ay3,dt*ay4
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3,u4,u0=',dt*uvel1,dt*uvel2,dt*uvel3,dt*uvel4,dt*berg%uvel
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v4,v0=',dt*vvel1,dt*vvel2,dt*vvel3,dt*vvel4,dt*berg%vvel
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3,u4 (deg)=',dt*u1,dt*u2,dt*u3,dt*u4
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v4 (deg)=',dt*v1,dt*v2,dt*v3,dt*v4
+    write(stderrunit,'(a,6i5)') 'KID, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
+    write(stderrunit,'(a,6i5)') 'KID, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
+    write(stderrunit,'(a,6i5)') 'KID, evolve_iceberg: i1,i2,i3,i4,i=',i1,i2,i3,i4,i
+    write(stderrunit,'(a,6i5)') 'KID, evolve_iceberg: j1,j2,j3,j4,j=',j1,j2,j3,j4,j
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: lon1,lon2,lon3,lon4=',lon1,lon2,lon3,lon4,berg%lon
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: lat1,lat2,lat3,lat4=',lat1,lat2,lat3,lat4,berg%lat
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: u1,u2,u3,u4,u0=',uvel1,uvel2,uvel3,uvel4,berg%uvel
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: v1,v2,v3,v4,v0=',vvel1,vvel2,vvel3,vvel4,berg%vvel
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: dt* ax1,ax2,ax3,ax4=',dt*ax1,dt*ax2,dt*ax3,dt*ax4
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: dt* ay1,ay2,ay3,ay4=',dt*ay1,dt*ay2,dt*ay3,dt*ay4
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: dt* u1,u2,u3,u4,u0=',dt*uvel1,dt*uvel2,dt*uvel3,dt*uvel4,dt*berg%uvel
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: dt* v1,v2,v3,v4,v0=',dt*vvel1,dt*vvel2,dt*vvel3,dt*vvel4,dt*berg%vvel
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: dt* u1,u2,u3,u4 (deg)=',dt*u1,dt*u2,dt*u3,dt*u4
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: dt* v1,v2,v3,v4 (deg)=',dt*v1,dt*v2,dt*v3,dt*v4
     write(stderrunit,*) 'Acceleration terms for position 1'
     error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
     call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, rx, ry, ax1, ay1, axn1, ayn1, bxn, byn, debug_flag=.true.) !axn, ayn, bxn, byn - Added by Alon
@@ -4611,7 +4646,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
     write(stderrunit,'(a,i3,a,2i4,4f8.3)') 'pe=',mpp_pe(),'pos4 i,j,lon,lat,xi,yj=',i,j,lon4,lat4,xi,yj
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'pos4 box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
     bounced=is_point_in_cell(bergs%grd, lon2, lat2, i, j, explain=.true.)
-    call error_mesg('diamonds, evolve_iceberg','berg is out of posn at 4!',FATAL)
+    call error_mesg('KID, evolve_iceberg','berg is out of posn at 4!',FATAL)
   endif
   call  convert_from_meters_to_grid(lat4,bergs%grd%grid_is_latlon ,dxdl4,dydl)
   !dxdl4=r180_pi/(Rearth*cos(lat4*pi_180))
@@ -4657,27 +4692,27 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
     call print_fld(grd, grd%sst, 'sst')
     call print_fld(grd, grd%sss, 'sss')
     call print_fld(grd, grd%hi, 'hi')
-    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
-    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
-    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: i1,i2,i3,i4,i=',i1,i2,i3,i4,i
-    write(stderrunit,'(a,6i5)') 'diamonds, evolve_iceberg: j1,j2,j3,j4,j=',j1,j2,j3,j4,j
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lon1,lon2,lon3,lon4,lonn=',lon1,lon2,lon3,lon4,lonn,berg%lon
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: lat1,lat2,lat3,lat4,latn=',lat1,lat2,lat3,lat4,latn,berg%lat
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: u1,u2,u3,u4,un,u0=',uvel1,uvel2,uvel3,uvel4,uveln,berg%uvel
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: v1,v2,v3,v4,vn,v0=',vvel1,vvel2,vvel3,vvel4,vveln,berg%vvel
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ax1,ax2,ax3,ax4,axn=',&
+    write(stderrunit,'(a,6i5)') 'KID, evolve_iceberg: isd,isc,iec,ied=',grd%isd,grd%isc,grd%iec,grd%ied
+    write(stderrunit,'(a,6i5)') 'KID, evolve_iceberg: jsd,jsc,jec,jed=',grd%jsd,grd%jsc,grd%jec,grd%jed
+    write(stderrunit,'(a,6i5)') 'KID, evolve_iceberg: i1,i2,i3,i4,i=',i1,i2,i3,i4,i
+    write(stderrunit,'(a,6i5)') 'KID, evolve_iceberg: j1,j2,j3,j4,j=',j1,j2,j3,j4,j
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: lon1,lon2,lon3,lon4,lonn=',lon1,lon2,lon3,lon4,lonn,berg%lon
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: lat1,lat2,lat3,lat4,latn=',lat1,lat2,lat3,lat4,latn,berg%lat
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: u1,u2,u3,u4,un,u0=',uvel1,uvel2,uvel3,uvel4,uveln,berg%uvel
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: v1,v2,v3,v4,vn,v0=',vvel1,vvel2,vvel3,vvel4,vveln,berg%vvel
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: dt* ax1,ax2,ax3,ax4,axn=',&
          & dt*ax1,dt*ax2,dt*ax3,dt*ax4,dt_6*( (ax1+ax4)+2.*(ax2+ax3) )
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* ay1,ay2,ay3,ay4,ayn=',&
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: dt* ay1,ay2,ay3,ay4,ayn=',&
          & dt*ay1,dt*ay2,dt*ay3,dt*ay4,dt_6*( (ay1+ay4)+2.*(ay2+ay3) )
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3,u4,un,u0=',&
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: dt* u1,u2,u3,u4,un,u0=',&
          & dt*uvel1,dt*uvel2,dt*uvel3,dt*uvel4,dt*uveln,dt*berg%uvel
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v4,vn,v0=',&
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: dt* v1,v2,v3,v4,vn,v0=',&
          & dt*vvel1,dt*vvel2,dt*vvel3,dt*vvel4,dt*vveln,dt*berg%vvel
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* u1,u2,u3,u4,u_rk (deg)=',&
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: dt* u1,u2,u3,u4,u_rk (deg)=',&
          & dt*u1,dt*u2,dt*u3,dt*u4,dt_6*( (u1+u4)+2.*(u2+u3) )
-    write(stderrunit,'(a,6es9.3)') 'diamonds, evolve_iceberg: dt* v1,v2,v3,v4,v_rk (deg)=',&
+    write(stderrunit,'(a,6es9.3)') 'KID, evolve_iceberg: dt* v1,v2,v3,v4,v_rk (deg)=',&
          & dt*v1,dt*v2,dt*v3,dt*v4,dt_6*( (v1+v4)+2.*(v2+v3) )
-    write(stderrunit,*) 'diamonds, evolve_iceberg: on_tangential_plane=',on_tangential_plane
+    write(stderrunit,*) 'KID, evolve_iceberg: on_tangential_plane=',on_tangential_plane
     write(stderrunit,*) 'Acceleration terms for position 1'
     error_flag=pos_within_cell(grd, lon1, lat1, i1, j1, xi, yj)
     call accel(bergs, berg, i1, j1, xi, yj, lat1, uvel1, vvel1, uvel1, vvel1, dt_2, rx, ry, ax1, ay1, axn, ayn, bxn, byn, debug_flag=.true.)  !axn, ayn - Added by Alon
@@ -4694,7 +4729,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
     write(stderrunit,'(a,i3,a,4f8.3)') 'pe=',mpp_pe(),'posn box=',grd%lon(i-1,j-1),grd%lon(i,j),grd%lat(i-1,j-1),grd%lat(i,j)
     call print_berg(stderrunit, berg, 'evolve_iceberg, out of cell at end!')
     bounced=is_point_in_cell(bergs%grd, lonn, latn, i, j, explain=.true.)
-    if (debug) call error_mesg('diamonds, evolve_iceberg','berg is out of posn at end!',FATAL)
+    if (debug) call error_mesg('KID, evolve_iceberg','berg is out of posn at end!',FATAL)
     write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lon',(i,i=grd%isd,grd%ied)
     do j=grd%jed,grd%jsd,-1
       write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lon(i,j),i=grd%isd,grd%ied)
@@ -4874,52 +4909,51 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
   lon0=lon; lat0=lat ! original position
   i0=i; j0=j ! original i,j
   lret=pos_within_cell(grd, lon, lat, i, j, xi, yj)
-!  print *, 'Alon:', lon, lat, i, j, xi, yj, lret
+  !  print *, 'Alon:', lon, lat, i, j, xi, yj, lret
   xi0=xi; yj0=yj ! original xi,yj
 
-
   !Removing this while debuggin
   if (debug) then
-    !Sanity check lret, xi and yj
-    lret=is_point_in_cell(grd, lon, lat, i, j)
-    point_in_cell_using_xi_yj=is_point_within_xi_yj_bounds(xi,yj)
-    if (.not. point_in_cell_using_xi_yj) then
-
-      if (lret) then
-        write(stderrunit,*) 'diamonds, adjust: WARNING!!! lret=T but |xi,yj|>1',mpp_pe()
-        write(stderrunit,*) 'diamonds, adjust: xi=',xi,' lon=',lon
-        write(stderrunit,*) 'diamonds, adjust: x3 x2=',grd%lon(i-1,j),grd%lon(i,j)
-        write(stderrunit,*) 'diamonds, adjust: x0 x1=',grd%lon(i-1,j-1),grd%lon(i,j-1)
-        write(stderrunit,*) 'diamonds, adjust: yi=',yj,' lat=',lat
-        write(stderrunit,*) 'diamonds, adjust: y3 y2=',grd%lat(i-1,j),grd%lat(i,j)
-        write(stderrunit,*) 'diamonds, adjust: y0 y1=',grd%lat(i-1,j-1),grd%lat(i,j-1)
-        lret=is_point_in_cell(grd, lon, lat, i, j,explain=.true.)
-        write(stderrunit,*) 'diamonds, adjust: fn is_point_in_cell=',lret
-        lret=pos_within_cell(grd, lon, lat, i, j, xi, yj,explain=.true.)
-        write(stderrunit,*) 'diamonds, adjust: fn pos_within_cell=',lret
-        write(0,*) 'This should never happen!'
-        call error_mesg('adjust index, ','Iceberg is_point_in_cell=True but xi, yi are out of cell',FATAL)
-        error=.true.; return
+     !Sanity check lret, xi and yj
+     lret=is_point_in_cell(grd, lon, lat, i, j)
+     point_in_cell_using_xi_yj=is_point_within_xi_yj_bounds(xi,yj)
+     if (.not. point_in_cell_using_xi_yj) then
+
+        if (lret) then
+           write(stderrunit,*) 'KID, adjust: WARNING!!! lret=T but |xi,yj|>1',mpp_pe()
+           write(stderrunit,*) 'KID, adjust: xi=',xi,' lon=',lon
+           write(stderrunit,*) 'KID, adjust: x3 x2=',grd%lon(i-1,j),grd%lon(i,j)
+           write(stderrunit,*) 'KID, adjust: x0 x1=',grd%lon(i-1,j-1),grd%lon(i,j-1)
+           write(stderrunit,*) 'KID, adjust: yi=',yj,' lat=',lat
+           write(stderrunit,*) 'KID, adjust: y3 y2=',grd%lat(i-1,j),grd%lat(i,j)
+           write(stderrunit,*) 'KID, adjust: y0 y1=',grd%lat(i-1,j-1),grd%lat(i,j-1)
+           lret=is_point_in_cell(grd, lon, lat, i, j,explain=.true.)
+           write(stderrunit,*) 'KID, adjust: fn is_point_in_cell=',lret
+           lret=pos_within_cell(grd, lon, lat, i, j, xi, yj,explain=.true.)
+           write(stderrunit,*) 'KID, adjust: fn pos_within_cell=',lret
+           write(0,*) 'This should never happen!'
+           call error_mesg('adjust index, ','Iceberg is_point_in_cell=True but xi, yi are out of cell',FATAL)
+           error=.true.; return
+        endif
+     else
+        if (.not.lret) then
+           write(stderrunit,*) 'KID, adjust: WARNING!!! lret=F but |xi,yj|<1',mpp_pe()
+           write(stderrunit,*) 'KID, adjust: xi=',xi,' lon=',lon
+           write(stderrunit,*) 'KID, adjust: x3 x2=',grd%lon(i-1,j),grd%lon(i,j)
+           write(stderrunit,*) 'KID, adjust: x0 x1=',grd%lon(i-1,j-1),grd%lon(i,j-1)
+           write(stderrunit,*) 'KID, adjust: yi=',yj,' lat=',lat
+           write(stderrunit,*) 'KID, adjust: y3 y2=',grd%lat(i-1,j),grd%lat(i,j)
+           write(stderrunit,*) 'KID, adjust: y0 y1=',grd%lat(i-1,j-1),grd%lat(i,j-1)
+           lret=is_point_in_cell(grd, lon, lat, i, j,  explain=.true.)
+           write(stderrunit,*) 'KID, adjust: fn is_point_in_cell=',lret
+           lret=pos_within_cell(grd, lon, lat, i, j, xi, yj, explain=.true.)
+           write(stderrunit,*) 'KID, adjust: fn pos_within_cell=',lret
+           write(0,*) 'This should never happen!'
+           call error_mesg('adjust index, ','Iceberg is_point_in_cell=False but xi, yi are out of cell',FATAL)
+           error=.true.; return
+        endif
      endif
-    else
-      if (.not.lret) then
-        write(stderrunit,*) 'diamonds, adjust: WARNING!!! lret=F but |xi,yj|<1',mpp_pe()
-        write(stderrunit,*) 'diamonds, adjust: xi=',xi,' lon=',lon
-        write(stderrunit,*) 'diamonds, adjust: x3 x2=',grd%lon(i-1,j),grd%lon(i,j)
-        write(stderrunit,*) 'diamonds, adjust: x0 x1=',grd%lon(i-1,j-1),grd%lon(i,j-1)
-        write(stderrunit,*) 'diamonds, adjust: yi=',yj,' lat=',lat
-        write(stderrunit,*) 'diamonds, adjust: y3 y2=',grd%lat(i-1,j),grd%lat(i,j)
-        write(stderrunit,*) 'diamonds, adjust: y0 y1=',grd%lat(i-1,j-1),grd%lat(i,j-1)
-        lret=is_point_in_cell(grd, lon, lat, i, j,  explain=.true.)
-        write(stderrunit,*) 'diamonds, adjust: fn is_point_in_cell=',lret
-        lret=pos_within_cell(grd, lon, lat, i, j, xi, yj, explain=.true.)
-        write(stderrunit,*) 'diamonds, adjust: fn pos_within_cell=',lret
-        write(0,*) 'This should never happen!'
-        call error_mesg('adjust index, ','Iceberg is_point_in_cell=False but xi, yi are out of cell',FATAL)
-        error=.true.; return
-      endif
-    endif
-    lret=pos_within_cell(grd, lon, lat, i, j, xi, yj)
+     lret=pos_within_cell(grd, lon, lat, i, j, xi, yj)
   endif ! debug
 
   if (lret) return ! Berg was already in cell
@@ -4931,164 +4965,168 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
   icount=0
   inm=i0; jnm=j0 ! original i,j
   do while (debug .and. .not.lret .and. icount<4)
-    icount=icount+1
-    if (xi.lt.0.) then
-      if (inm>grd%isd) then
-        inm=inm-1
-      endif
-    elseif (xi.gt.1.) then
-!    elseif (xi.ge.1.) then   !Alon: maybe it should be .ge.
-      if (inm<grd%ied) then
-        inm=inm+1
-      endif
-    endif
-    if (yj.lt.0.) then
-      if (jnm>grd%jsd) then
-        jnm=jnm-1
-      endif
-    elseif (yj.gt.1.) then
-!    elseif (yj.ge.1.) then   !Alon:maybe it should be .ge.
-      if (jnm<grd%jed) then
-        jnm=jnm+1
-      endif
-    endif
-    lret=pos_within_cell(grd, lon, lat, inm, jnm, xi, yj) ! Update xi and yj
+     icount=icount+1
+     if (xi.lt.0.) then
+        if (inm>grd%isd) then
+           inm=inm-1
+        endif
+     elseif (xi.gt.1.) then
+        !    elseif (xi.ge.1.) then   !Alon: maybe it should be .ge.
+        if (inm<grd%ied) then
+           inm=inm+1
+        endif
+     endif
+     if (yj.lt.0.) then
+        if (jnm>grd%jsd) then
+           jnm=jnm-1
+        endif
+     elseif (yj.gt.1.) then
+        !    elseif (yj.ge.1.) then   !Alon:maybe it should be .ge.
+        if (jnm<grd%jed) then
+           jnm=jnm+1
+        endif
+     endif
+     lret=pos_within_cell(grd, lon, lat, inm, jnm, xi, yj) ! Update xi and yj
   enddo
   if (abs(inm-i0)>1) then
-    write(stderrunit,*) 'pe=',mpp_pe(),'diamonds, adjust: inm,i0,inm-i0=',inm,i0,inm-i0
-   !stop 'Moved too far in i without mask!'
+     write(stderrunit,*) 'pe=',mpp_pe(),'KID, adjust: inm,i0,inm-i0=',inm,i0,inm-i0
+     !stop 'Moved too far in i without mask!'
   endif
   if (abs(jnm-j0)>1) then
-    write(stderrunit,*) 'pe=',mpp_pe(),'diamonds, adjust: jnm,i0,jnm-j0=',jnm,j0,inm-j0
-   !stop 'Moved too far in j without mask!'
+     write(stderrunit,*) 'pe=',mpp_pe(),'KID, adjust: jnm,i0,jnm-j0=',jnm,j0,inm-j0
+     !stop 'Moved too far in j without mask!'
   endif
 
   ! Adjust i,j based on xi,yj while bouncing off of masked land cells
   icount=0
   lret=pos_within_cell(grd, lon, lat, i0, j0, xi, yj)
   do while ( .not.lret.and. icount<4 )
-    icount=icount+1
-    if (xi.lt.0.) then
-      if (i>grd%isd) then
-        if (grd%msk(i-1,j)>0.) then
-          if (i>grd%isd+1) i=i-1
-        else
-         !write(stderr(),'(a,6f8.3,i)') 'diamonds, adjust: bouncing berg from west',lon,lat,xi,yj,uvel,vvel,mpp_pe()
-          bounced=.true.
+     icount=icount+1
+     if (xi.lt.0.) then
+        if (i>grd%isd) then
+           if (grd%msk(i-1,j)>0.) then
+              if (i>grd%isd+1) i=i-1
+           else
+              !write(stderr(),'(a,6f8.3,i)') 'KID, adjust: bouncing berg from west',lon,lat,xi,yj,uvel,vvel,mpp_pe()
+              bounced=.true.
+           endif
         endif
-      endif
-    elseif (xi.ge.1.) then    !Alon!!!!
-!    elseif (xi.gt.1.) then
-      if (i<grd%ied) then
-        if (grd%msk(i+1,j)>0.) then
-          if (i<grd%ied) i=i+1
-        else
-         !write(stderr(),'(a,6f8.3,i)') 'diamonds, adjust: bouncing berg from east',lon,lat,xi,yj,uvel,vvel,mpp_pe()
-          bounced=.true.
+     elseif (xi.ge.1.) then    !Alon!!!!
+        !    elseif (xi.gt.1.) then
+        if (i<grd%ied) then
+           if (grd%msk(i+1,j)>0.) then
+              if (i<grd%ied) i=i+1
+           else
+              !write(stderr(),'(a,6f8.3,i)') 'KID, adjust: bouncing berg from east',lon,lat,xi,yj,uvel,vvel,mpp_pe()
+              bounced=.true.
+           endif
         endif
-      endif
-    endif
-    if (yj.lt.0.) then
-      if (j>grd%jsd) then
-        if (grd%msk(i,j-1)>0.) then
-          if (j>grd%jsd+1) j=j-1
-        else
-         !write(stderr(),'(a,6f8.3,i)') 'diamonds, adjust: bouncing berg from south',lon,lat,xi,yj,uvel,vvel,mpp_pe()
-          bounced=.true.
+     endif
+     if (yj.lt.0.) then
+        if (j>grd%jsd) then
+           if (grd%msk(i,j-1)>0.) then
+              if (j>grd%jsd+1) j=j-1
+           else
+              !write(stderr(),'(a,6f8.3,i)') 'KID, adjust: bouncing berg from south',lon,lat,xi,yj,uvel,vvel,mpp_pe()
+              bounced=.true.
+           endif
         endif
-      endif
-    elseif (yj.ge.1.) then     !Alon.
-!    elseif (yj.gt.1.) then
-      if (j<grd%jed) then
-        if (grd%msk(i,j+1)>0.) then
-          if (j<grd%jed) j=j+1
-        else
-         !write(stderr(),'(a,6f8.3,i)') 'diamonds, adjust: bouncing berg from north',lon,lat,xi,yj,uvel,vvel,mpp_pe()
-          bounced=.true.
+     elseif (yj.ge.1.) then     !Alon.
+        !    elseif (yj.gt.1.) then
+        if (j<grd%jed) then
+           if (grd%msk(i,j+1)>0.) then
+              if (j<grd%jed) j=j+1
+           else
+              !write(stderr(),'(a,6f8.3,i)') 'KID, adjust: bouncing berg from north',lon,lat,xi,yj,uvel,vvel,mpp_pe()
+              bounced=.true.
+           endif
         endif
-      endif
-    endif
-    if (bounced) then
-      if (xi>=1.) xi=1.-posn_eps   !Alon.
-!      if (xi>1.) xi=1.-posn_eps   !
-      if (xi<0.) xi=posn_eps
-      if (yj>=1.) yj=1.-posn_eps  !Alon.
-!      if (yj>1.) yj=1.-posn_eps
-      if (yj<0.) yj=posn_eps
-      lon=bilin(grd, grd%lon, i, j, xi, yj)
-      lat=bilin(grd, grd%lat, i, j, xi, yj)
-    endif
-    if (debug) then
-      if (grd%msk(i,j)==0.) stop 'diamonds, adjust: Berg is in land! This should not happen...'
-    endif
-    lret=pos_within_cell(grd, lon, lat, i, j, xi, yj) ! Update xi and yj
+     endif
+     if (bounced) then
+        if (xi>=1.) xi=1.-posn_eps   !Alon.
+        !      if (xi>1.) xi=1.-posn_eps   !
+        if (xi<0.) xi=posn_eps
+        if (yj>=1.) yj=1.-posn_eps  !Alon.
+        !      if (yj>1.) yj=1.-posn_eps
+        if (yj<0.) yj=posn_eps
+        lon=bilin(grd, grd%lon, i, j, xi, yj)
+        lat=bilin(grd, grd%lat, i, j, xi, yj)
+     endif
+     if (debug) then
+        if (grd%msk(i,j)==0.) stop 'KID, adjust: Berg is in land! This should not happen...'
+     endif
+     lret=pos_within_cell(grd, lon, lat, i, j, xi, yj) ! Update xi and yj
 
   enddo
- !if (debug) then
- !  if (abs(i-i0)>2) then
- !    stop 'diamonds, adjust: Moved too far in i!'
- !  endif
- !  if (abs(j-j0)>2) then
- !    stop 'diamonds, adjust: Moved too far in j!'
- !  endif
- !endif
+  !if (debug) then
+  !  if (abs(i-i0)>2) then
+  !    stop 'KID, adjust: Moved too far in i!'
+  !  endif
+  !  if (abs(j-j0)>2) then
+  !    stop 'KID, adjust: Moved too far in j!'
+  !  endif
+  !endif
+
+
+  if (.not.bounced.and.lret.and.grd%msk(i,j)>0.) then ! Landed in ocean without bouncing so all is wel
+      return
+  endif
 
-  if (.not.bounced.and.lret.and.grd%msk(i,j)>0.) return ! Landed in ocean without bouncing so all is well
 
   if (.not.bounced.and..not.lret) then ! This implies the berg traveled many cells without getting far enough
-    if (debug) then
-      write(stderrunit,*) 'diamonds, adjust: lon0, lat0=',lon0,lat0
-      write(stderrunit,*) 'diamonds, adjust: xi0, yj0=',xi0,yj0
-      write(stderrunit,*) 'diamonds, adjust: i0,j0=',i0,j0
-      write(stderrunit,*) 'diamonds, adjust: lon, lat=',lon,lat
-      write(stderrunit,*) 'diamonds, adjust: xi,yj=',xi,yj
-      write(stderrunit,*) 'diamonds, adjust: i,j=',i,j
-      write(stderrunit,*) 'diamonds, adjust: inm,jnm=',inm,jnm
-      write(stderrunit,*) 'diamonds, adjust: icount=',icount
-      lret=pos_within_cell(grd, lon, lat, i, j, xi, yj,explain=.true.)
-      write(stderrunit,*) 'diamonds, adjust: lret=',lret
-    endif
+     if (debug) then
+        write(stderrunit,*) 'KID, adjust: lon0, lat0=',lon0,lat0
+        write(stderrunit,*) 'KID, adjust: xi0, yj0=',xi0,yj0
+        write(stderrunit,*) 'KID, adjust: i0,j0=',i0,j0
+        write(stderrunit,*) 'KID, adjust: lon, lat=',lon,lat
+        write(stderrunit,*) 'KID, adjust: xi,yj=',xi,yj
+        write(stderrunit,*) 'KID, adjust: i,j=',i,j
+        write(stderrunit,*) 'KID, adjust: inm,jnm=',inm,jnm
+        write(stderrunit,*) 'KID, adjust: icount=',icount
+        lret=pos_within_cell(grd, lon, lat, i, j, xi, yj,explain=.true.)
+        write(stderrunit,*) 'KID, adjust: lret=',lret
+     endif
 
-    if (abs(i-i0)+abs(j-j0)==0) then
-      if (use_roundoff_fix) then
-        ! This is a special case due to round off where is_point_in_cell()
-        ! returns false but xi and yj are between 0 and 1.
-        ! It occurs very rarely but often enough to have brought down
-        ! ESM2G four times since the spin-up began. (as of 8/10/2010)
-        ! This temporary fix arbitrarily moves the berg toward the
-        ! center of the current cell.
-        xi=(xi-0.5)*(1.-posn_eps)+0.5
-        yj=(yj-0.5)*(1.-posn_eps)+0.5
-      endif
-      call error_mesg('diamonds, adjust', 'Berg did not move or bounce during iterations AND was not in cell. Adjusting!', WARNING)
-      write(stderrunit,*) 'diamonds, adjust: The adjusting iceberg is: ', id,  mpp_pe()
-      write(stderrunit,*) 'diamonds, adjust: The adjusting lon,lat,u,v: ', lon, lat, uvel, vvel
-      write(stderrunit,*) 'diamonds, adjust: The adjusting xi,ji: ', xi, yj
-      lret=pos_within_cell(grd, lon, lat, inm, jnm, xi, yj,explain=.true.)
-    else
-      call error_mesg('diamonds, adjust', 'Berg iterated many times without bouncing!', WARNING)
-    endif
+     if (abs(i-i0)+abs(j-j0)==0) then
+        if (use_roundoff_fix) then
+           ! This is a special case due to round off where is_point_in_cell()
+           ! returns false but xi and yj are between 0 and 1.
+           ! It occurs very rarely but often enough to have brought down
+           ! ESM2G four times since the spin-up began. (as of 8/10/2010)
+           ! This temporary fix arbitrarily moves the berg toward the
+           ! center of the current cell.
+           xi=(xi-0.5)*(1.-posn_eps)+0.5
+           yj=(yj-0.5)*(1.-posn_eps)+0.5
+        endif
+        call error_mesg('KID, adjust', 'Berg did not move or bounce during iterations AND was not in cell. Adjusting!', WARNING)
+        write(stderrunit,*) 'KID, adjust: The adjusting iceberg is: ', id,  mpp_pe()
+        write(stderrunit,*) 'KID, adjust: The adjusting lon,lat,u,v: ', lon, lat, uvel, vvel
+        write(stderrunit,*) 'KID, adjust: The adjusting xi,ji: ', xi, yj
+        lret=pos_within_cell(grd, lon, lat, inm, jnm, xi, yj,explain=.true.)
+     else
+        call error_mesg('KID, adjust', 'Berg iterated many times without bouncing!', WARNING)
+     endif
   endif
-!  if (xi>1.) xi=1.-posn_eps    !Alon
+  !  if (xi>1.) xi=1.-posn_eps    !Alon
   if (xi>=1.) xi=1.-posn_eps
   if (xi<0.) xi=posn_eps
   if (yj>1.) yj=1.-posn_eps
-!  if (yj>1.) yj=1.-posn_eps
+  !  if (yj>1.) yj=1.-posn_eps
   if (yj<=0.) yj=posn_eps        !Alon
   lon=bilin(grd, grd%lon, i, j, xi, yj)
   lat=bilin(grd, grd%lat, i, j, xi, yj)
   lret=pos_within_cell(grd, lon, lat, i, j, xi, yj) ! Update xi and yj
 
   if (.not. lret) then
-    write(0,*) 'i0, j0,=', i0,j0
-    write(0,*) 'xi0, yj0,=', xi0,yj0
-    write(0,*) 'grd%msk(i0, j0)=', grd%msk(i0,j0)
-    write(0,*) 'lon0, lat0,=', lon0,lat0
-    write(0,*) 'i,j,lon, lat,grd%msk(i,j)=', i,j,lon,lat,grd%msk(i,j)
-    write(stderrunit,*) 'diamonds, adjust: Should not get here! Berg is not in cell after adjustment', id, mpp_pe()
-    if (debug) error=.true.
+     write(0,*) 'i0, j0,=', i0,j0
+     write(0,*) 'xi0, yj0,=', xi0,yj0
+     write(0,*) 'grd%msk(i0, j0)=', grd%msk(i0,j0)
+     write(0,*) 'lon0, lat0,=', lon0,lat0
+     write(0,*) 'i,j,lon, lat,grd%msk(i,j)=', i,j,lon,lat,grd%msk(i,j)
+     write(stderrunit,*) 'KID, adjust: Should not get here! Berg is not in cell after adjustment', id, mpp_pe()
+     if (debug) error=.true.
   endif
- end subroutine adjust_index_and_ground
+end subroutine adjust_index_and_ground
 
 !> Calculate longitude-latitude from tangent plane coordinates
 subroutine rotpos_to_tang(lon, lat, x, y, id_in)
@@ -5109,12 +5147,12 @@ subroutine rotpos_to_tang(lon, lat, x, y, id_in)
   endif
 
   if (lat>90.) then
-      write(stderrunit,*) 'diamonds, rotpos_to_tang: lat>90 already!',lat, lon, id
-      call error_mesg('diamonds, rotpos_to_tang','Something went very wrong!',FATAL)
+      write(stderrunit,*) 'KID, rotpos_to_tang: lat>90 already!',lat, lon, id
+      call error_mesg('KID, rotpos_to_tang','Something went very wrong!',FATAL)
   endif
   if (lat==90.) then
-    write(stderrunit,*) 'diamonds, rotpos_to_tang: lat==90 already!',lat, lon
-    call error_mesg('diamonds, rotpos_to_tang','Something went wrong!',FATAL)
+    write(stderrunit,*) 'KID, rotpos_to_tang: lat==90 already!',lat, lon
+    call error_mesg('KID, rotpos_to_tang','Something went wrong!',FATAL)
   endif
 
   colat=90.-lat
@@ -5264,7 +5302,7 @@ subroutine icebergs_end(bergs)
   call mpp_clock_end(bergs%clock_ini)
   deallocate(bergs)
 
-  if (mpp_pe()==mpp_root_pe()) write(*,'(a,i8)') 'diamonds: icebergs_end complete',mpp_pe()
+  if (mpp_pe()==mpp_root_pe()) write(*,'(a,i8)') 'KID: icebergs_end complete',mpp_pe()
 
 end subroutine icebergs_end
 
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 79884da..eb47867 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -24,7 +24,7 @@ module ice_bergs_framework
 
 !Local Vars
 ! Global data (minimal for debugging)
-logical :: folded_north_on_pe = .false. !< If true, indicates the presence of the tri-polar grid
+Logical :: folded_north_on_pe = .false. !< If true, indicates the presence of the tri-polar grid
 logical :: verbose=.false. !< Be verbose to stderr
 logical :: budget=.true. !< Calculate budgets
 logical :: debug=.false. !< Turn on debugging
@@ -372,6 +372,7 @@ module ice_bergs_framework
   logical :: read_ocean_depth_from_file=.false. !< If true, ocean depth is read from a file.
   integer(kind=8) :: debug_iceberg_with_id = -1 !< If positive, monitors a berg with this id
 
+  real :: length_for_manually_initialize_bonds=1000.0 !<if manually init bonds, only  bond if dist between particles is .lt. this length -Added by Alex
   real :: speed_limit=0. !< CFL speed limit for a berg [m/s]
   real :: tau_calving=0. !< Time scale for smoothing out calving field (years)
   real :: tip_parameter=0. !< parameter to override iceberg rolling critical ratio (use zero to get parameter directly from ice and seawater densities)
@@ -513,6 +514,7 @@ subroutine ice_bergs_framework_init(bergs, &
     logical :: add_weight_to_ocean=.true. ! Add weight of icebergs + bits to ocean
     logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
     logical :: time_average_weight=.false. ! Time average the weight on the ocean
+    real :: length_for_manually_initialize_bonds=1000.0 !<if manually init bonds, only  bond if dist between particles is .lt. this length - Alex
     real :: speed_limit=0. ! CFL speed limit for a berg
     real :: tau_calving=0. ! Time scale for smoothing out calving field (years)
     real :: tip_parameter=0. ! Parameter to override iceberg rolling critical ratio (use zero to get parameter directly from ice and seawater densities
@@ -561,11 +563,12 @@ subroutine ice_bergs_framework_init(bergs, &
     real, dimension(nclasses) :: initial_thickness=(/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) ! Total thickness of newly calved bergs (m)
     integer(kind=8) :: debug_iceberg_with_id = -1 ! If positive, monitors a berg with this id
 
-    namelist /icebergs_nml/ verbose, budget, halo,  traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,Static_icebergs,  &
+    Namelist /icebergs_nml/ Verbose, budget, halo,  traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,Static_icebergs,  &
          distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,bond_coef, radial_damping_coef, tangental_damping_coef, only_interactive_forces, &
          rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, iceberg_bonds_on, manually_initialize_bonds, ignore_missing_restart_bergs, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, halo_debugging, hexagonal_icebergs, &
-         time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, interactive_icebergs_on, critical_interaction_damping_on, &
+         time_average_weight, generate_test_icebergs, length_for_manually_initialize_bonds, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, &
+         interactive_icebergs_on, critical_interaction_damping_on, &
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution, force_all_pes_traj, &
          allow_bergs_to_roll,set_melt_rates_to_zero,lat_ref,initial_orientation,rotate_icebergs_for_mass_spreading,grid_is_latlon,Lx,use_f_plane,use_old_spreading, &
          grid_is_regular,override_iceberg_velocities,u_override,v_override,add_iceberg_thickness_to_SSH,Iceberg_melt_without_decay,melt_icebergs_as_ice_shelf, &
@@ -587,7 +590,7 @@ subroutine ice_bergs_framework_init(bergs, &
     write(stdlogunit,*) "ice_bergs_framework: "//trim(version)
 
     ! Read namelist parameters
-    !write(stderrunit,*) 'diamonds: reading namelist'
+    !write(stderrunit,*) 'KID: reading namelist'
 #ifdef INTERNAL_FILE_NML
     read (input_nml_file, nml=icebergs_nml, iostat=ierr)
 #else
@@ -603,11 +606,11 @@ subroutine ice_bergs_framework_init(bergs, &
 
 
     ! Allocate overall structure
-    !write(stderrunit,*) 'diamonds: allocating bergs'
+    !write(stderrunit,*) 'KID: allocating bergs'
     allocate(bergs)
     allocate(bergs%grd)
     grd=>bergs%grd ! For convenience to avoid bergs%grd%X
-    !write(stderrunit,*) 'diamonds: allocating domain'
+    !write(stderrunit,*) 'KID: allocating domain'
     allocate(grd%domain)
 
     ! Clocks
@@ -626,15 +629,15 @@ subroutine ice_bergs_framework_init(bergs, &
     call mpp_clock_begin(bergs%clock_ini)
 
     ! Set up iceberg domain
-    !write(stderrunit,*) 'diamonds: defining domain'
+    !write(stderrunit,*) 'KID: defining domain'
     call mpp_define_domains( (/1,gni,1,gnj/), layout, grd%domain, &
          maskmap=maskmap, &
          xflags=dom_x_flags, xhalo=halo,  &
-         yflags=dom_y_flags, yhalo=halo, name='diamond')
+         yflags=dom_y_flags, yhalo=halo, name='KID')
 
     call mpp_define_io_domain(grd%domain, io_layout)
 
-    !write(stderrunit,*) 'diamond: get compute domain'
+    !write(stderrunit,*) 'KID: get compute domain'
     call mpp_get_compute_domain( grd%domain, grd%isc, grd%iec, grd%jsc, grd%jec )
     call mpp_get_data_domain( grd%domain, grd%isd, grd%ied, grd%jsd, grd%jed )
     call mpp_get_global_domain( grd%domain, grd%isg, grd%ieg, grd%jsg, grd%jeg )
@@ -646,13 +649,13 @@ subroutine ice_bergs_framework_init(bergs, &
 
 
     folded_north_on_pe = ((dom_y_flags == FOLD_NORTH_EDGE) .and. (grd%jec == gnj))
-    !write(stderrunit,'(a,6i4)') 'diamonds, icebergs_init: pe,n,s,e,w =',mpp_pe(),grd%pe_N,grd%pe_S,grd%pe_E,grd%pe_W, NULL_PE
+    !write(stderrunit,'(a,6i4)') 'KID, icebergs_init: pe,n,s,e,w =',mpp_pe(),grd%pe_N,grd%pe_S,grd%pe_E,grd%pe_W, NULL_PE
 
     !if (verbose) &
-    !write(stderrunit,'(a,i3,a,4i4,a,4f8.2)') 'diamonds, icebergs_init: (',mpp_pe(),') [ij][se]c=', &
+    !write(stderrunit,'(a,i3,a,4i4,a,4f8.2)') 'KID, icebergs_init: (',mpp_pe(),') [ij][se]c=', &
     !     grd%isc,grd%iec,grd%jsc,grd%jec, &
     !     ' [lon|lat][min|max]=', minval(ice_lon),maxval(ice_lon),minval(ice_lat),maxval(ice_lat)
-    !write(stderrunit,*) 'diamonds, int args = ', mpp_pe(),gni, gnj, layout, axes
+    !write(stderrunit,*) 'KID, int args = ', mpp_pe(),gni, gnj, layout, axes
 
     ! Allocate grid of pointers
     allocate( bergs%list(grd%isd:grd%ied, grd%jsd:grd%jed) )
@@ -661,7 +664,7 @@ subroutine ice_bergs_framework_init(bergs, &
     enddo; enddo
 
     big_number=1.0E15
-    !write(stderrunit,*) 'diamonds: allocating grid'
+    !write(stderrunit,*) 'KID: allocating grid'
     allocate( grd%lon(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%lon(:,:)=big_number
     allocate( grd%lat(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%lat(:,:)=big_number
     allocate( grd%lonc(grd%isd:grd%ied, grd%jsd:grd%jed) );grd%lon(:,:)=big_number
@@ -720,7 +723,7 @@ subroutine ice_bergs_framework_init(bergs, &
     allocate( grd%parity_y(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%parity_y(:,:)=1.
     allocate( grd%iceberg_counter_grd(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%iceberg_counter_grd(:,:)=0
 
-    !write(stderrunit,*) 'diamonds: copying grid'
+    !write(stderrunit,*) 'KID: copying grid'
     ! Copy data declared on ice model computational domain
     is=grd%isc; ie=grd%iec; js=grd%jsc; je=grd%jec
     grd%lon(is:ie,js:je)=ice_lon(:,:)
@@ -797,16 +800,10 @@ subroutine ice_bergs_framework_init(bergs, &
     enddo; enddo
 
 
-    if (mpp_pe() == 0) then
-       print *,'before'
-       print *,'grd%lon(:,1)',grd%lon(:,grd%jsd)
-       ! print *,''
-       ! print *,'grd%lat(:,1)',grd%lat(:,grd%jsd)
-       ! print *,''
-       ! print *,'grd%lon(1,:)',grd%lon(grd%isd,:)
-       ! print *,''
-       ! print *,'grd%lat(1,:)',grd%lat(grd%isd,:)
-       ! print *,''
+    if ( (mpp_pe() == 0) .and. (Lx .ne. 360.) .and. .not. (grid_is_latlon) ) then
+       print *,''
+       print *,'pe0 x-domain before periodicity fix'
+       write(*,'(f12.2)') (grd%lon(i,grd%jsd), i=grd%isd,grd%ied)
     end if
 
 
@@ -818,11 +815,11 @@ subroutine ice_bergs_framework_init(bergs, &
     endif
 
     if ((Lx.gt.1E15 ) .and. (mpp_pe().eq.mpp_root_pe())) then
-       call error_mesg('diamonds, framework', 'Model does not enjoy the domain being larger than 1E15. Not sure why. Probably to do with floating point precision.', WARNING)
+       call error_mesg('KID, framework', 'Model does not enjoy the domain being larger than 1E15. Not sure why. Probably to do with floating point precision.', WARNING)
     endif
     if ((.not. grid_is_latlon) .and. (Lx.eq.360.)) then
        if (mpp_pe().eq.mpp_root_pe())  then
-          call error_mesg('diamonds, framework', 'Since the lat/lon grid is off, the x-direction is being set as non-periodic. Set Lx not equal to 360 override.', WARNING)
+          call error_mesg('KID, framework', 'Since the lat/lon grid is off, the x-direction is being set as non-periodic. Set Lx not equal to 360 override.', WARNING)
        endif
        Lx=-1.
     endif
@@ -862,12 +859,12 @@ subroutine ice_bergs_framework_init(bergs, &
 enddo; enddo
 
 if (debug) then
-   ! Write(stderrunit,'(a,i3,a,4i4,a,4f8.2)') 'diamonds, icebergs_init: (',mpp_pe(),') [ij][se]c=', &
+   ! Write(stderrunit,'(a,i3,a,4i4,a,4f8.2)') 'KID, icebergs_init: (',mpp_pe(),') [ij][se]c=', &
    !      grd%isc,grd%iec,grd%jsc,grd%jec, &
    !      ' [Lon|lat][min|max]=', minval(grd%lon),maxval(grd%lon),minval(grd%lat),maxval(grd%lat)
 
 
- Write(stderrunit,'(a,i3,a,4i4)') 'diamonds, icebergs_init: (',mpp_pe(),') [ij][se]c=', &
+ Write(stderrunit,'(a,i3,a,4i4)') 'KID, icebergs_init: (',mpp_pe(),') [ij][se]c=', &
       grd%isc,grd%iec,grd%jsc,grd%jec   
 
  print *,'minval(grd%lon)',minval(grd%lon)
@@ -879,17 +876,11 @@ subroutine ice_bergs_framework_init(bergs, &
       minval(grd%lon),maxval(grd%lon),minval(grd%lat),maxval(grd%lat)
 endif
 
- if (mpp_pe() == 1) then
-    print *,'after'
-    print *,'grd%lon(:,1)',grd%lon(:,grd%jsd)
-    ! print *,''
-    ! print *,'grd%lat(:,1)',grd%lat(:,grd%jsd)
-    ! print *,''
-    ! print *,'grd%lon(1,:)',grd%lon(grd%isd,:)
-    ! print *,''
-    ! print *,'grd%lat(1,:)',grd%lat(grd%isd,:)
-    ! print *,''
- end if
+if ( (mpp_pe() == 0) .and. (Lx .ne. -1.) .and. .not. (grid_is_latlon) ) then
+ print *,''
+ print *,'pe 0 x-domain after periodicity fix'
+ write(*,'(f12.2)') (grd%lon(i,grd%jsd), i=grd%isd,grd%ied)
+end if
 
 !if (mpp_pe().eq.5) then
 !  write(stderrunit,'(a3,32i7)') 'Lon',(i,i=grd%isd,grd%ied)
@@ -910,11 +901,11 @@ subroutine ice_bergs_framework_init(bergs, &
 do j=grd%jsd+1,grd%jed; do i=grd%isd+1,grd%ied
  if (grd%lat(i,j) .ne. grd%lat(i,j)) then
     write(stderrunit,*) 'Lat not defined properly', mpp_pe(),i,j,grd%lat(i,j)
-    call error_mesg('diamonds,grid defining', 'Latitude contains NaNs', FATAL)
+    call error_mesg('KID,grid defining', 'Latitude contains NaNs', FATAL)
  endif
  if (grd%lon(i,j) .ne. grd%lon(i,j)) then
     write(stderrunit,*) 'Lon not defined properly', mpp_pe(),i,j,grd%lon(i,j)
-    call error_mesg('diamonds, grid defining', 'Longatudes contains NaNs', FATAL)
+    call error_mesg('KID, grid defining', 'Longatudes contains NaNs', FATAL)
  endif
 enddo; enddo
 
@@ -932,22 +923,22 @@ subroutine ice_bergs_framework_init(bergs, &
 
 if ((halo .lt. 3) .and. (rotate_icebergs_for_mass_spreading .and. iceberg_bonds_on) )   then
  halo=3
- call error_mesg('diamonds, framework', 'Setting iceberg halos =3, since halos must be >= 3 for rotating icebergs for mass spreading', WARNING)
+ call error_mesg('KID, framework', 'Setting iceberg halos =3, since halos must be >= 3 for rotating icebergs for mass spreading', WARNING)
 elseif  ((halo .lt. 2) .and. (interactive_icebergs_on .or. iceberg_bonds_on) )   then
  halo=2
- call error_mesg('diamonds, framework', 'Setting iceberg halos =2, since halos must be >= 2 for interactions', WARNING)
+ call error_mesg('KID, framework', 'Setting iceberg halos =2, since halos must be >= 2 for interactions', WARNING)
 endif
 
 if (interactive_icebergs_on) then
  if (Runge_not_Verlet) then
     !Runge_not_Verlet=.false.  ! Iceberg interactions only with Verlet
-    call error_mesg('diamonds, framework', 'It is unlcear whther interactive icebergs work with Runge Kutta stepping.', WARNING)
+    call error_mesg('KID, framework', 'It is unlcear whther interactive icebergs work with Runge Kutta stepping.', WARNING)
  endif
 endif
 if (.not.interactive_icebergs_on) then
  if (iceberg_bonds_on) then
     !iceberg_bonds_on=.false.
-    call error_mesg('diamonds, framework', 'Interactive icebergs off requires iceberg bonds off (turning bonds off).', WARNING)
+    call error_mesg('KID, framework', 'Interactive icebergs off requires iceberg bonds off (turning bonds off).', WARNING)
  endif
 endif
 if (.not. iceberg_bonds_on) then
@@ -1020,6 +1011,7 @@ subroutine ice_bergs_framework_init(bergs, &
 bergs%halo_debugging=halo_debugging
 bergs%iceberg_bonds_on=iceberg_bonds_on   !Alon
 bergs%manually_initialize_bonds=manually_initialize_bonds   !Alon
+bergs%length_for_manually_initialize_bonds=length_for_manually_initialize_bonds !Alex
 bergs%critical_interaction_damping_on=critical_interaction_damping_on   !Alon
 bergs%interactive_icebergs_on=interactive_icebergs_on   !Alon
 bergs%use_new_predictive_corrective=use_new_predictive_corrective  !Alon
@@ -1038,7 +1030,7 @@ subroutine ice_bergs_framework_init(bergs, &
 grd%coastal_drift = coastal_drift
 grd%tidal_drift = tidal_drift
 
-if (read_old_restarts) call error_mesg('diamonds, ice_bergs_framework_init', 'Setting "read_old_restarts=.true." is obsolete and does nothing!', WARNING)
+if (read_old_restarts) call error_mesg('KID, ice_bergs_framework_init', 'Setting "read_old_restarts=.true." is obsolete and does nothing!', WARNING)
 
 ! Diagnostics
 id_class = diag_axis_init('mass_class', initial_mass, 'kg','Z', 'iceberg mass')
@@ -1159,10 +1151,10 @@ subroutine ice_bergs_framework_init(bergs, &
 endif
 
 if (do_unit_tests) then
- if (unit_tests(bergs)) call error_mesg('diamonds, icebergs_init', 'Unit tests failed!', FATAL)
+ if (unit_tests(bergs)) call error_mesg('KID, icebergs_init', 'Unit tests failed!', FATAL)
 endif
 
-!write(stderrunit,*) 'diamonds: done'
+!write(stderrunit,*) 'KID: done'
 call mpp_clock_end(bergs%clock_ini)
 call mpp_clock_end(bergs%clock)
 
@@ -1198,7 +1190,7 @@ subroutine offset_berg_dates(bergs,Time)
 
   yr_offset=int(latest_start_year+1.)-iyr
   if (mpp_pe().eq.mpp_root_pe()) write(*,'(a,i8,a)') &
-    'diamonds: Bergs found with creation dates after model date! Adjusting berg dates by ',yr_offset,' years'
+    'KID: Bergs found with creation dates after model date! Adjusting berg dates by ',yr_offset,' years'
   call bergs_chksum(bergs, 'before adjusting start dates')
   do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
     this=>bergs%list(grdi,grdj)%first
@@ -1219,7 +1211,7 @@ subroutine move_berg_between_cells(bergs)
 type(icebergs_gridded), pointer :: grd => null()
 type(iceberg), pointer :: moving_berg => null(), this => null()
 integer :: grdi, grdj
-logical :: quick
+
 ! For convenience
 grd=>bergs%grd
 
@@ -1286,7 +1278,7 @@ subroutine update_halo_icebergs(bergs)
     do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
       this=>bergs%list(grdi,grdj)%first
       do while (associated(this))
-          write(stderrunit,*) 'A', this%id, mpp_pe(), this%halo_berg, grdi, grdj
+          write(stderrunit,'(a,5i)') 'A', this%id, mpp_pe(), int(this%halo_berg), grdi, grdj
         this=>this%next
       enddo
     enddo; enddo
@@ -1319,7 +1311,7 @@ subroutine update_halo_icebergs(bergs)
     do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
       this=>bergs%list(grdi,grdj)%first
         do while (associated(this))
-        write(stderrunit,*) 'B', this%id, mpp_pe(), this%halo_berg, grdi, grdj
+        write(stderrunit,'(a,5i)') 'B', this%id, mpp_pe(), int(this%halo_berg), grdi, grdj
       this=>this%next
       enddo
     enddo; enddo
@@ -1522,7 +1514,7 @@ subroutine update_halo_icebergs(bergs)
     do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
       this=>bergs%list(grdi,grdj)%first
       do while (associated(this))
-        write(stderrunit,*)  'C', this%id, mpp_pe(), this%halo_berg,  grdi, grdj
+        write(stderrunit,'(a,5i)')  'C', this%id, mpp_pe(), int(this%halo_berg),  grdi, grdj
         this=>this%next
       enddo
     enddo; enddo
@@ -1535,19 +1527,19 @@ subroutine update_halo_icebergs(bergs)
     i=nbergs_rcvd_from_n+nbergs_rcvd_from_s+nbergs_rcvd_from_e+nbergs_rcvd_from_w &
      -nbergs_to_send_n-nbergs_to_send_s-nbergs_to_send_e-nbergs_to_send_w
     if (nbergs_end-(nbergs_start+i).ne.0) then
-      write(stderrunit,'(a,i4,a,i4)') 'diamonds, update_halos: nbergs_end=',nbergs_end,' on PE',mpp_pe()
-      write(stderrunit,'(a,i4,a,i4)') 'diamonds, update_halos: nbergs_start=',nbergs_start,' on PE',mpp_pe()
-      write(stderrunit,'(a,i4,a,i4)') 'diamonds, update_halos: delta=',i,' on PE',mpp_pe()
-      write(stderrunit,'(a,i4,a,i4)') 'diamonds, update_halos: error=',nbergs_end-(nbergs_start+i),' on PE',mpp_pe()
-      write(stderrunit,'(a,i4,a,i4)') 'diamonds, update_halos: nbergs_to_send_n=',nbergs_to_send_n,' on PE',mpp_pe()
-      write(stderrunit,'(a,i4,a,i4)') 'diamonds, update_halos: nbergs_to_send_s=',nbergs_to_send_s,' on PE',mpp_pe()
-      write(stderrunit,'(a,i4,a,i4)') 'diamonds, update_halos: nbergs_to_send_e=',nbergs_to_send_e,' on PE',mpp_pe()
-      write(stderrunit,'(a,i4,a,i4)') 'diamonds, update_halos: nbergs_to_send_w=',nbergs_to_send_w,' on PE',mpp_pe()
-      write(stderrunit,'(a,i4,a,i4)') 'diamonds, update_halos: nbergs_rcvd_from_n=',nbergs_rcvd_from_n,' on PE',mpp_pe()
-      write(stderrunit,'(a,i4,a,i4)') 'diamonds, update_halos: nbergs_rcvd_from_s=',nbergs_rcvd_from_s,' on PE',mpp_pe()
-      write(stderrunit,'(a,i4,a,i4)') 'diamonds, update_halos: nbergs_rcvd_from_e=',nbergs_rcvd_from_e,' on PE',mpp_pe()
-      write(stderrunit,'(a,i4,a,i4)') 'diamonds, update_halos: nbergs_rcvd_from_w=',nbergs_rcvd_from_w,' on PE',mpp_pe()
-      !call error_mesg('diamonds, update_halos:', 'We lost some bergs!', FATAL)
+      write(stderrunit,'(a,i4,a,i4)') 'KID, update_halos: nbergs_end=',nbergs_end,' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'KID, update_halos: nbergs_start=',nbergs_start,' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'KID, update_halos: delta=',i,' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'KID, update_halos: error=',nbergs_end-(nbergs_start+i),' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'KID, update_halos: nbergs_to_send_n=',nbergs_to_send_n,' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'KID, update_halos: nbergs_to_send_s=',nbergs_to_send_s,' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'KID, update_halos: nbergs_to_send_e=',nbergs_to_send_e,' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'KID, update_halos: nbergs_to_send_w=',nbergs_to_send_w,' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'KID, update_halos: nbergs_rcvd_from_n=',nbergs_rcvd_from_n,' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'KID, update_halos: nbergs_rcvd_from_s=',nbergs_rcvd_from_s,' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'KID, update_halos: nbergs_rcvd_from_e=',nbergs_rcvd_from_e,' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'KID, update_halos: nbergs_rcvd_from_w=',nbergs_rcvd_from_w,' on PE',mpp_pe()
+      !call error_mesg('KID, update_halos:', 'We lost some bergs!', FATAL)
     endif
   endif
   if (debug) then
@@ -1565,8 +1557,8 @@ subroutine update_halo_icebergs(bergs)
     enddo ; enddo
     call mpp_sum(i)
     if (i>0 .and. mpp_pe()==mpp_root_pe()) then
-      write(stderrunit,'(a,i4)') 'diamonds, update_halos: # of bergs outside computational domain = ',i
-      call error_mesg('diamonds, update_halos:', 'there are bergs still in halos!', FATAL)
+      write(stderrunit,'(a,i4)') 'KID, update_halos: # of bergs outside computational domain = ',i
+      call error_mesg('KID, update_halos:', 'there are bergs still in halos!', FATAL)
     endif ! root_pe
   endif ! debug
   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!Debugging!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!111
@@ -1804,19 +1796,19 @@ subroutine send_bergs_to_other_pes(bergs)
     i=nbergs_rcvd_from_n+nbergs_rcvd_from_s+nbergs_rcvd_from_e+nbergs_rcvd_from_w &
      -nbergs_to_send_n-nbergs_to_send_s-nbergs_to_send_e-nbergs_to_send_w
     if (nbergs_end-(nbergs_start+i).ne.0) then
-      write(stderrunit,'(a,i4,a,i4)') 'diamonds, send_bergs_to_other_pes: nbergs_end=',nbergs_end,' on PE',mpp_pe()
-      write(stderrunit,'(a,i4,a,i4)') 'diamonds, send_bergs_to_other_pes: nbergs_start=',nbergs_start,' on PE',mpp_pe()
-      write(stderrunit,'(a,i4,a,i4)') 'diamonds, send_bergs_to_other_pes: delta=',i,' on PE',mpp_pe()
-      write(stderrunit,'(a,i4,a,i4)') 'diamonds, send_bergs_to_other_pes: error=',nbergs_end-(nbergs_start+i),' on PE',mpp_pe()
-      write(stderrunit,'(a,i4,a,i4)') 'diamonds, send_bergs_to_other_pes: nbergs_to_send_n=',nbergs_to_send_n,' on PE',mpp_pe()
-      write(stderrunit,'(a,i4,a,i4)') 'diamonds, send_bergs_to_other_pes: nbergs_to_send_s=',nbergs_to_send_s,' on PE',mpp_pe()
-      write(stderrunit,'(a,i4,a,i4)') 'diamonds, send_bergs_to_other_pes: nbergs_to_send_e=',nbergs_to_send_e,' on PE',mpp_pe()
-      write(stderrunit,'(a,i4,a,i4)') 'diamonds, send_bergs_to_other_pes: nbergs_to_send_w=',nbergs_to_send_w,' on PE',mpp_pe()
-      write(stderrunit,'(a,i4,a,i4)') 'diamonds, send_bergs_to_other_pes: nbergs_rcvd_from_n=',nbergs_rcvd_from_n,' on PE',mpp_pe()
-      write(stderrunit,'(a,i4,a,i4)') 'diamonds, send_bergs_to_other_pes: nbergs_rcvd_from_s=',nbergs_rcvd_from_s,' on PE',mpp_pe()
-      write(stderrunit,'(a,i4,a,i4)') 'diamonds, send_bergs_to_other_pes: nbergs_rcvd_from_e=',nbergs_rcvd_from_e,' on PE',mpp_pe()
-      write(stderrunit,'(a,i4,a,i4)') 'diamonds, send_bergs_to_other_pes: nbergs_rcvd_from_w=',nbergs_rcvd_from_w,' on PE',mpp_pe()
-      call error_mesg('diamonds, send_bergs_to_other_pes:', 'We lost some bergs!', FATAL)
+      write(stderrunit,'(a,i4,a,i4)') 'KID, send_bergs_to_other_pes: nbergs_end=',nbergs_end,' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'KID, send_bergs_to_other_pes: nbergs_start=',nbergs_start,' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'KID, send_bergs_to_other_pes: delta=',i,' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'KID, send_bergs_to_other_pes: error=',nbergs_end-(nbergs_start+i),' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'KID, send_bergs_to_other_pes: nbergs_to_send_n=',nbergs_to_send_n,' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'KID, send_bergs_to_other_pes: nbergs_to_send_s=',nbergs_to_send_s,' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'KID, send_bergs_to_other_pes: nbergs_to_send_e=',nbergs_to_send_e,' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'KID, send_bergs_to_other_pes: nbergs_to_send_w=',nbergs_to_send_w,' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'KID, send_bergs_to_other_pes: nbergs_rcvd_from_n=',nbergs_rcvd_from_n,' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'KID, send_bergs_to_other_pes: nbergs_rcvd_from_s=',nbergs_rcvd_from_s,' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'KID, send_bergs_to_other_pes: nbergs_rcvd_from_e=',nbergs_rcvd_from_e,' on PE',mpp_pe()
+      write(stderrunit,'(a,i4,a,i4)') 'KID, send_bergs_to_other_pes: nbergs_rcvd_from_w=',nbergs_rcvd_from_w,' on PE',mpp_pe()
+      call error_mesg('KID, send_bergs_to_other_pes:', 'We lost some bergs!', FATAL)
     endif
   endif
 
@@ -1835,8 +1827,8 @@ subroutine send_bergs_to_other_pes(bergs)
     enddo ; enddo
     call mpp_sum(i)
     if (i>0 .and. mpp_pe()==mpp_root_pe()) then
-      write(stderrunit,'(a,i4)') 'diamonds, send_bergs_to_other_pes: # of bergs outside computational domain = ',i
-      call error_mesg('diamonds, send_bergs_to_other_pes:', 'there are bergs still in halos!', FATAL)
+      write(stderrunit,'(a,i4)') 'KID, send_bergs_to_other_pes: # of bergs outside computational domain = ',i
+      call error_mesg('KID, send_bergs_to_other_pes:', 'there are bergs still in halos!', FATAL)
     endif ! root_pe
   endif ! debug
 
@@ -1994,7 +1986,7 @@ subroutine clear_berg_from_partners_bonds(berg)
       enddo
     else
      ! Note: This is meant to be unmatched after you have cleared the first berg
-     ! call error_mesg('diamonds, clear berg from partners', 'The bond you are trying to clear is unmatched!', WARNING)
+     ! call error_mesg('KID, clear berg from partners', 'The bond you are trying to clear is unmatched!', WARNING)
     endif
     current_bond=>current_bond%next_bond
   enddo !End loop over bonds
@@ -2022,12 +2014,10 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
 integer(kind=8) :: id
 integer :: stderrunit
 logical :: force_app
-logical :: quick
 
   ! Get the stderr unit number
   stderrunit = stderr()
 
-  quick=.false.
   max_bonds=0
   if (present(max_bonds_in)) max_bonds=max_bonds_in
 
@@ -2073,19 +2063,19 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
 
   ! force_app=.true.
   if(force_app) then !force append with origin ine,jne (for I/O)
-    call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg, quick, this)
+    call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg, this)
   else
     lres=find_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
     if (lres) then
       lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
-      call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg,quick,this)
+      call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg,this)
     else
       lres=find_cell_wide(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
       if (lres) then
         lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
-        call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg,quick,this)
+        call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg,this)
       else
-        write(stderrunit,'("diamonds, unpack_berg_from_buffer pe=(",i3,a,2i4,a,2f8.2)')&
+        write(stderrunit,'("KID, unpack_berg_from_buffer pe=(",i3,a,2i4,a,2f8.2)')&
          & mpp_pe(),') Failed to find i,j=',localberg%ine,localberg%jne,' for lon,lat=',localberg%lon,localberg%lat
         write(stderrunit,*) localberg%lon,localberg%lat
         write(stderrunit,*) localberg%uvel,localberg%vvel
@@ -2100,7 +2090,7 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
         write(stderrunit,*) grd%lon(grd%isd,grd%jsd),grd%lon(grd%ied,grd%jsd)
         write(stderrunit,*) grd%lat(grd%isd,grd%jsd),grd%lat(grd%ied,grd%jed)
         write(stderrunit,*) lres
-        call error_mesg('diamonds, unpack_berg_from_buffer', 'can not find a cell to place berg in!', FATAL)
+        call error_mesg('KID, unpack_berg_from_buffer', 'can not find a cell to place berg in!', FATAL)
       endif
     endif
   endif
@@ -2160,7 +2150,7 @@ subroutine increase_ibuffer(old, num_bergs, width)
       deallocate(old)
     endif
     old=>new
-   !write(stderr(),*) 'diamonds, increase_ibuffer',mpp_pe(),' increased to',new_size
+   !write(stderr(),*) 'KID, increase_ibuffer',mpp_pe(),' increased to',new_size
   endif
 
 end subroutine increase_ibuffer
@@ -2276,12 +2266,11 @@ end subroutine unpack_traj_from_buffer2
 !! temporary. This routine allocates memory for a new berg and copies the
 !! the input values into it. The memory for the new berg is pointed to
 !! by newberg_return (if present).
-subroutine add_new_berg_to_list(first, bergvals, quick, newberg_return)
+subroutine add_new_berg_to_list(first, bergvals, newberg_return)
 ! Arguments
 type(iceberg), pointer :: first !< List of icebergs
 type(iceberg), intent(in) :: bergvals !< Berg values to copy
 type(iceberg), intent(out), pointer, optional :: newberg_return !< New berg
-logical, intent(in), optional :: quick !< If true, use the quick insertion algorithm
 ! Local variables
 type(iceberg), pointer :: new=>null()
 
@@ -2293,15 +2282,7 @@ subroutine add_new_berg_to_list(first, bergvals, quick, newberg_return)
     !newberg_return=>null()
   endif
 
-  if (present(quick)) then
-    if(quick) then
-      call insert_berg_into_list(first, new, quick=.true.)
-    else
-      call insert_berg_into_list(first, new)
-    endif
-  else
-    call insert_berg_into_list(first, new)
-  endif
+  call insert_berg_into_list(first, new)
 
   !Clear new
   new=>null()
@@ -2347,14 +2328,14 @@ subroutine count_out_of_order(bergs,label)
           this%jne>bergs%grd%jec) icnt2=icnt2+1
       this=>this%next
       if (i>1.and..not.associated(this%prev)) then
-        call error_mesg('diamonds, count_out_of_order', 'Pointer %prev is unassociated. This should not happen!', FATAL)
+        call error_mesg('KID, count_out_of_order', 'Pointer %prev is unassociated. This should not happen!', FATAL)
       endif
     enddo
   enddo; enddo
   call mpp_sum(icnt2)
 
   if ((debug.or.icnt1.ne.0).and.mpp_pe().eq.mpp_root_pe()) then
-    write(*,'(a,3(x,a,i6),x,a)') 'diamonds, count_out_of_order:', &
+    write(*,'(a,3(x,a,i6),x,a)') 'KID, count_out_of_order:', &
       '# out of order=', icnt1,'# in halo=',icnt2,'# identicals=',icnt3,label
   endif
 
@@ -2399,7 +2380,7 @@ subroutine check_for_duplicates(bergs,label)
   call mpp_sum(icnt_same)
 
   if ((debug.or.icnt_id>0.or.icnt_same>0).and.mpp_pe().eq.mpp_root_pe()) then
-    write(*,'(a,2(x,a,i9),x,a)') 'diamonds, check_for_duplicates:', &
+    write(*,'(a,2(x,a,i9),x,a)') 'KID, check_for_duplicates:', &
       '# with same id=', icnt_id,'# identical bergs=',icnt_same,label
   endif
 
@@ -2515,20 +2496,15 @@ subroutine monitor_a_berg(bergs, label)
 end subroutine monitor_a_berg
 
 !> Inserts a berg into a list
-subroutine insert_berg_into_list(first, newberg, quick)
+subroutine insert_berg_into_list(first, newberg)
 ! Arguments
 type(iceberg), pointer :: first !< List of bergs
 type(iceberg), pointer :: newberg !< New berg to insert
-logical, intent(in), optional :: quick !< If true, use the quick insertion algorithm
-                                       !! \todo Delete arguments since the code does not appear to use it.
 ! Local variables
 type(iceberg), pointer :: this, prev
-logical :: quickly
-
-  quickly = .false.
 
   if (associated(first)) then
-    if (.not. parallel_reprod .or. quickly) then
+    if (.not. parallel_reprod) then
       newberg%next=>first
       newberg%prev=>null()
       first%prev=>newberg
@@ -2698,8 +2674,8 @@ subroutine create_iceberg(berg, bergvals)
   stderrunit=stderr()
 
   if (associated(berg)) then
-    write(stderrunit,*) 'diamonds, create_iceberg: berg already associated!!!!',mpp_pe()
-    call error_mesg('diamonds, create_iceberg', 'berg already associated. This should not happen!', FATAL)
+    write(stderrunit,*) 'KID, create_iceberg: berg already associated!!!!',mpp_pe()
+    call error_mesg('KID, create_iceberg', 'berg already associated. This should not happen!', FATAL)
   endif
   allocate(berg)
   berg=bergvals
@@ -2757,31 +2733,31 @@ subroutine print_berg(iochan, berg, label, il, jl)
 integer, optional, intent(in) :: jl !< j-index of cell berg should be in
 ! Local variables
 
-  write(iochan,'("diamonds, print_berg: ",2a,i5,a,i12,a,2f16.4,i5,f7.2,es12.4,f5.1)') &
+  write(iochan,'("KID, print_berg: ",2a,i5,a,i12,a,2f16.4,i5,f7.2,es12.4,f5.1)') &
     label, 'pe=(', mpp_pe(), ') #=', berg%id, ' start lon,lat,yr,day,mass,hb=', &
     berg%start_lon, berg%start_lat, berg%start_year, berg%start_day, berg%start_mass, berg%halo_berg
   if (present(il).and.present(jl)) then
-    write(iochan,'("diamonds, print_berg: ",2a,i5,a,i12,a,2i5)') &
+    write(iochan,'("KID, print_berg: ",2a,i5,a,i12,a,2i5)') &
       label, 'pe=(', mpp_pe(), ') #=', berg%id, ' List i,j=',il,jl
   endif
-  write(iochan,'("diamonds, print_berg: ",2a,i5,a,i12,a,2i5,a,2l2)') &
+  write(iochan,'("KID, print_berg: ",2a,i5,a,i12,a,2i5,a,2l2)') &
     label, 'pe=(', mpp_pe(), ') #=', berg%id, &
     ' i,j=', berg%ine, berg%jne, &
     ' p,n=', associated(berg%prev), associated(berg%next)
-  write(iochan,'("diamonds, print_berg: ",2a,i5,a,i12,3(a,2f16.8))') &
+  write(iochan,'("KID, print_berg: ",2a,i5,a,i12,3(a,2f16.8))') &
     label, 'pe=(', mpp_pe(), ') #=', berg%id, &
     ' xi,yj=', berg%xi, berg%yj, &
     ' lon,lat=', berg%lon, berg%lat, &
     ' lon_old,lat_old=', berg%lon_old, berg%lat_old
-  write(iochan,'("diamonds, print_berg: ",2a,i5,a,i12,2(a,2f14.8))') &
+  write(iochan,'("KID, print_berg: ",2a,i5,a,i12,2(a,2f14.8))') &
     label, 'pe=(', mpp_pe(), ') #=', berg%id, &
     ' u,v=', berg%uvel, berg%vvel, &
     ' uvel_old,vvel_old=', berg%uvel_old, berg%vvel_old
-  write(iochan,'("diamonds, print_berg: ",2a,i5,a,i12,2(a,2f14.8))') &
+  write(iochan,'("KID, print_berg: ",2a,i5,a,i12,2(a,2f14.8))') &
     label, 'pe=(', mpp_pe(), ') #=', berg%id, &
     ' axn,ayn=', berg%axn, berg%ayn, &
     ' bxn,byn=', berg%bxn, berg%byn
-  write(iochan,'("diamonds, print_berg: ",2a,i5,a,i12,3(a,2f14.8))') &
+  write(iochan,'("KID, print_berg: ",2a,i5,a,i12,3(a,2f14.8))') &
     label, 'pe=(', mpp_pe(), ') #=', berg%id, &
     ' uo,vo=', berg%uo, berg%vo, &
     ' ua,va=', berg%ua, berg%va, &
@@ -2809,7 +2785,7 @@ subroutine print_bergs(iochan, bergs, label)
   nbergs=count_bergs(bergs)
   nnbergs=nbergs
   call mpp_sum(nnbergs)
-  if (nbergs.gt.0) write(iochan,'("diamonds, ",a," there are",i5," bergs out of",i6," on PE ",i4)') label, nbergs, nnbergs, mpp_pe()
+  if (nbergs.gt.0) write(iochan,'("KID, ",a," there are",i5," bergs out of",i6," on PE ",i4)') label, nbergs, nnbergs, mpp_pe()
 
 end subroutine print_bergs
 
@@ -2857,7 +2833,7 @@ subroutine form_a_bond(berg, other_id, other_berg_ine, other_berg_jne, other_ber
    endif
    new_bond=>null()
  else
-   call error_mesg('diamonds, bonds', 'An iceberg is trying to bond with itself!!!', FATAL)
+   call error_mesg('KID, bonds', 'An iceberg is trying to bond with itself!!!', FATAL)
  endif
 
 end subroutine form_a_bond
@@ -2886,7 +2862,7 @@ subroutine bond_address_update(bergs)
           current_bond%other_berg_jne=current_bond%other_berg%jne
         else
           if (berg%halo_berg .lt. 0.5) then
-            call error_mesg('diamonds, bond address update', 'other berg in bond not assosiated!', FATAL)
+            call error_mesg('KID, bond address update', 'other berg in bond not assosiated!', FATAL)
           endif
         endif
         current_bond=>current_bond%next_bond
@@ -2914,17 +2890,22 @@ subroutine show_all_bonds(bergs)
     do while (associated(berg)) ! loop over all bergs
       current_bond=>berg%first_bond
       do while (associated(current_bond)) ! loop over all bonds
-        print *, 'Show Bond1 :', berg%id, current_bond%other_id, current_bond%other_berg_ine, current_bond%other_berg_jne,  mpp_pe()
+         !print *, 'Show Bond1 :', berg%id, current_bond%other_id, current_bond%other_berg_ine, current_bond%other_berg_jne,  mpp_pe()
+        !write(*,'(a,5i)')'Show Bond1 :',berg%id, current_bond%other_id, current_bond%other_berg_ine, current_bond%other_berg_jne, mpp_pe()
         !print *, 'Current:', berg%id, berg%ine, berg%jne,berg%halo_berg, mpp_pe()
         if  (associated(current_bond%other_berg)) then
           if (current_bond%other_berg%id .ne. current_bond%other_id) then
-            print *, 'Bond matching', berg%id,current_bond%other_berg%id, current_bond%other_id,&
-            berg%halo_berg,current_bond%other_berg%halo_berg ,mpp_pe()
-            call error_mesg('diamonds, show all bonds:', 'The bonds are not matching properly!', FATAL)
+            !print *, 'Bond matching', berg%id,current_bond%other_berg%id, current_bond%other_id,&
+            !     berg%halo_berg,current_bond%other_berg%halo_berg ,mpp_pe()
+            write(*,'(a,3i,2i3,i4)')'Bond matching :',berg%id,current_bond%other_berg%id, current_bond%other_id,&
+                 int(berg%halo_berg),current_bond%other_berg%halo_berg ,mpp_pe()
+            call error_mesg('KID, show all bonds:', 'The bonds are not matching properly!', FATAL)
           endif
         else
-            print *, 'This bond has an non-assosiated other berg :', berg%id, current_bond%other_id,&
-            current_bond%other_berg_ine, current_bond%other_berg_jne, berg%halo_berg,  mpp_pe()
+            !print *, 'This bond has an non-assosiated other berg :', berg%id, current_bond%other_id,&
+            !     current_bond%other_berg_ine, current_bond%other_berg_jne, berg%halo_berg,  mpp_pe()
+         !   write(*,'(a,4i,i3,i4)')'This bond has an non-assosiated other berg :', berg%id, current_bond%other_id,&
+         !        current_bond%other_berg_ine, current_bond%other_berg_jne, int(berg%halo_berg),  mpp_pe()
         endif
         current_bond=>current_bond%next_bond
       enddo
@@ -2935,89 +2916,114 @@ subroutine show_all_bonds(bergs)
 end subroutine show_all_bonds
 
 subroutine connect_all_bonds(bergs)
-type(icebergs), pointer :: bergs !< Container for all types and memory
-type(iceberg), pointer :: other_berg, berg
-type(icebergs_gridded), pointer :: grd
-integer :: i, j
-integer :: grdi, grdj
-integer :: grdi_inner, grdj_inner
-type(bond) , pointer :: current_bond, other_berg_bond
-logical :: bond_matched, missing_bond, check_bond_quality
-integer nbonds
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  type(iceberg), pointer :: other_berg, berg
+  type(icebergs_gridded), pointer :: grd
+  integer :: i, j
+  integer :: grdi, grdj
+  integer :: grdi_inner, grdj_inner
+  type(bond) , pointer :: current_bond, other_berg_bond
+  logical :: bond_matched, missing_bond, check_bond_quality
+  integer nbonds
 
-missing_bond=.false.
-bond_matched=.false.
+  missing_bond=.false.
+  bond_matched=.false.
 
-! For convenience
+  ! For convenience
   grd=>bergs%grd
 
   do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
-! do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec  ! Don't connect halo bergs
-    berg=>bergs%list(grdi,grdj)%first
-    do while (associated(berg)) ! loop over all bergs
-      current_bond=>berg%first_bond
-      do while (associated(current_bond)) ! loop over all bonds
-        !code to find parter bond goes here
-        if (.not.associated(current_bond%other_berg)) then
-          bond_matched=.false.
-          i = current_bond%other_berg_ine ; j = current_bond%other_berg_jne
-          if ( (i.gt. grd%isd-1) .and. (i .lt. grd%ied+1) .and. (j .gt. grd%jsd-1) .and. (j .lt. grd%jed+1)) then
-            other_berg=>bergs%list(i,j)%first
-            do while (associated(other_berg)) ! loop over all other bergs
-              if (other_berg%id .eq. current_bond%other_id) then
-                current_bond%other_berg=>other_berg
-                other_berg=>null()
-                bond_matched=.true.
-              else
-                other_berg=>other_berg%next
-              endif
-            enddo
-          endif
-          if (.not.bond_matched) then
-            ! If you are stil not matched, then search adjacent cells
-            do grdj_inner = j-1,j+1 ; do grdi_inner = i-1,i+1
-              if (.not. bond_matched) then
-                if    ((grdj_inner .gt. grd%jsd-1) .and. (grdj_inner .lt. grd%jed+1)        &
-                .and.  (grdi_inner .gt. grd%isd-1) .and. (grdi_inner .lt. grd%ied+1)      &
-                .and. ((grdi_inner .ne. i) .or. (grdj_inner .ne. j)) ) then
-                  other_berg=>bergs%list(grdi_inner,grdj_inner)%first
-                  do while (associated(other_berg)) ! loop over all other bergs
+     ! do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec  ! Don't connect halo bergs
+     berg=>bergs%list(grdi,grdj)%first
+     do while (associated(berg)) ! loop over all bergs
+        current_bond=>berg%first_bond
+        do while (associated(current_bond)) ! loop over all bonds
+           !code to find parter bond goes here
+           if (.not.associated(current_bond%other_berg)) then
+              bond_matched=.false.
+              i = current_bond%other_berg_ine ; j = current_bond%other_berg_jne
+              if ( (i.gt. grd%isd-1) .and. (i .lt. grd%ied+1) .and. (j .gt. grd%jsd-1) .and. (j .lt. grd%jed+1)) then
+                 other_berg=>bergs%list(i,j)%first
+                 do while (associated(other_berg)) ! loop over all other bergs
                     if (other_berg%id .eq. current_bond%other_id) then
-                      current_bond%other_berg=>other_berg
-                      other_berg=>null()
-                      bond_matched=.true.
+                       current_bond%other_berg=>other_berg
+                       other_berg=>null()
+                       bond_matched=.true.
                     else
-                      other_berg=>other_berg%next
+                       other_berg=>other_berg%next
                     endif
-                  enddo
-                endif
+                 enddo
               endif
-            enddo;enddo
-          endif
-          if (.not.bond_matched) then
-            if (berg%halo_berg .lt. 0.5) then
-              missing_bond=.true.
-              print * ,'non-halo berg unmatched: ', berg%id, mpp_pe(), current_bond%other_id, current_bond%other_berg_ine
-              call error_mesg('diamonds, connect_all_bonds', 'A non-halo bond is missing!!!', FATAL)
-            else  ! This is not a problem if the partner berg is not yet in the halo
-              !if (  (current_bond%other_berg_ine .gt.grd%isd-1) .and. (current_bond%other_berg_ine .lt.grd%ied+1) &
-                !.and.  (current_bond%other_berg_jne .gt.grd%jsd-1) .and. (current_bond%other_berg_jne .lt.grd%jed+1) ) then
-                !print * ,'halo berg unmatched: ',mpp_pe(),  berg%id, current_bond%other_id, current_bond%other_berg_ine,current_bond%other_berg_jne
-                !call error_mesg('diamonds, connect_all_bonds', 'A halo bond is missing!!!', WARNING)
-              !endif
-            endif
-          endif
-        endif
-        current_bond=>current_bond%next_bond
-      enddo
-      berg=>berg%next
-    enddo
+              if (.not.bond_matched) then
+                 ! If you are still not matched, then search adjacent cells (to other berg)
+                 do grdj_inner = j-1,j+1 ; do grdi_inner = i-1,i+1
+                    if (.not. bond_matched) then
+                       if    ((grdj_inner .gt. grd%jsd-1) .and. (grdj_inner .lt. grd%jed+1)        &
+                            .and.  (grdi_inner .gt. grd%isd-1) .and. (grdi_inner .lt. grd%ied+1)      &
+                            .and. ((grdi_inner .ne. i) .or. (grdj_inner .ne. j)) ) then
+                          other_berg=>bergs%list(grdi_inner,grdj_inner)%first
+                          do while (associated(other_berg)) ! loop over all other bergs
+                             if (other_berg%id .eq. current_bond%other_id) then
+                                current_bond%other_berg=>other_berg
+                                other_berg=>null()
+                                bond_matched=.true.
+                             else
+                                other_berg=>other_berg%next
+                             endif
+                          enddo
+                       endif
+                    endif
+                 enddo;enddo
+              endif
+              if (.not.bond_matched) then
+                 ! Finally, if still not matched, search adjacent cells to current berg -Alex (periodicity fix)
+                 i = berg%ine; j = berg%jne            
+                 do grdj_inner = j-2,j+2 ; do grdi_inner = i-2,i+2 !probably wider search than necessary...
+                    if (.not. bond_matched) then                    
+                       if    ((grdj_inner .gt. grd%jsd-1) .and. (grdj_inner .lt. grd%jed+1)        &
+                            .and.  (grdi_inner .gt. grd%isd-1) .and. (grdi_inner .lt. grd%ied+1) ) then
+                          other_berg=>bergs%list(grdi_inner,grdj_inner)%first
+                          do while (associated(other_berg)) ! loop over all other bergs
+                             if (other_berg%id .eq. current_bond%other_id) then
+                                current_bond%other_berg=>other_berg
+                                current_bond%other_berg_ine = grdi_inner
+                                current_bond%other_berg_jne = grdj_inner
+                                other_berg=>null()
+                                bond_matched=.true.
+                             else
+                                other_berg=>other_berg%next
+                             endif
+                          enddo
+                       endif
+                    endif
+                 enddo;enddo
+              endif
+
+              if (.not.bond_matched) then
+                 if (berg%halo_berg .lt. 0.5) then
+                    missing_bond=.true.
+                    print * ,'non-halo berg unmatched: ', berg%id, berg%ine, berg%jne, mpp_pe(), &
+                         current_bond%other_id, current_bond%other_berg_ine, current_bond%other_berg_jne
+                    call error_mesg('KID, connect_all_bonds', 'A non-halo bond is missing!!!', FATAL)
+                 else  ! This is not a problem if the partner berg is not yet in the halo
+                    !if (  (current_bond%other_berg_ine .gt.grd%isd-1) .and. (current_bond%other_berg_ine .lt.grd%ied+1) &
+                    !.and.  (current_bond%other_berg_jne .gt.grd%jsd-1) .and. (current_bond%other_berg_jne .lt.grd%jed+1) ) then
+                    !print * ,'halo berg unmatched: ',mpp_pe(),  berg%id, current_bond%other_id, current_bond%other_berg_ine,current_bond%other_berg_jne
+                    !call error_mesg('KID, connect_all_bonds', 'A halo bond is missing!!!', WARNING)
+                    !endif
+                 endif
+              endif
+           endif
+           current_bond=>current_bond%next_bond
+        enddo
+        berg=>berg%next
+     enddo
   enddo;enddo
 
   if (debug) then
-    check_bond_quality=.true.
-    nbonds=0
-    call count_bonds(bergs, nbonds,check_bond_quality)
+     check_bond_quality=.true.
+     nbonds=0
+     call count_bonds(bergs, nbonds,check_bond_quality)
   endif
 end subroutine connect_all_bonds
 
@@ -3115,12 +3121,12 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
       call mpp_sum(num_unassosiated_bond_pairs_all_pe)
 
       if (num_unmatched_bonds_all_pe .gt. 0) then
-        call error_mesg('diamonds, bonds', 'Bonds are not matching!', FATAL)
+        call error_mesg('KID, bonds', 'Bonds are not matching!', FATAL)
       endif
       if (num_unassosiated_bond_pairs_all_pe .ne. 0) then
-        call error_mesg('diamonds, bonds', 'Bonds partners not located!', Warning)
+        call error_mesg('KID, bonds', 'Bonds partners not located!', Warning)
         if (num_unassosiated_bond_pairs .ne. 0) then
-          write(*,'(2a)') 'diamonds, Bonds parnters not located!!!! PE=', mpp_pe()
+          write(*,'(2a)') 'KID, Bonds parnters not located!!!! PE=', mpp_pe()
         endif
       endif
       if ((num_unmatched_bonds_all_pe .eq. 0)  .and. (num_unassosiated_bond_pairs_all_pe .eq. 0)) then
@@ -3129,7 +3135,7 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
         endif
         check_bond_quality=.true.
       else
-        if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') 'diamonds: Warning, Broken Bonds! '
+        if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') 'KID: Warning, Broken Bonds! '
       endif
     endif
 
@@ -3358,7 +3364,7 @@ logical function find_cell_by_search(grd, x, y, i, j)
   elseif (d3==dmin) then; i=ie-1; j=je-1
   elseif (d4==dmin) then; i=is+1; j=je-1
   else
-    call error_mesg('diamonds, find_cell_by_search:', 'This should never EVER happen! (1)', FATAL)
+    call error_mesg('KID, find_cell_by_search:', 'This should never EVER happen! (1)', FATAL)
   endif
 
   if (explain) then
@@ -3397,7 +3403,7 @@ logical function find_cell_by_search(grd, x, y, i, j)
     elseif (d5==dmin) then; di=0; dj=-1
     elseif (d7==dmin) then; di=1; dj=0
     else
-      call error_mesg('diamonds, find_cell_by_search:', 'This should never EVER happen!', FATAL)
+      call error_mesg('KID, find_cell_by_search:', 'This should never EVER happen!', FATAL)
     endif
 
     i=min(ie, max(is, io+di))
@@ -3437,7 +3443,7 @@ logical function find_cell_by_search(grd, x, y, i, j)
   !         call print_fld(grd, grd%tmp, 'Cost')
   !         stop 'Avoid recursing'
   !       endif
-  !       write(0,'(i3,a,2i5,a,2i3,a,2f8.3)') mpp_pe(),'diamonds, find_cell_by_search: false negative io,jo=',io,jo,' di,dj=',di,dj,' targ=',x,y
+  !       write(0,'(i3,a,2i5,a,2i3,a,2f8.3)') mpp_pe(),'KID, find_cell_by_search: false negative io,jo=',io,jo,' di,dj=',di,dj,' targ=',x,y
   !       explain=.true.; goto 911
   !     endif
       endif
@@ -3453,9 +3459,9 @@ logical function find_cell_by_search(grd, x, y, i, j)
     write(0,'(i3,a,3f9.5)') mpp_pe(),'cost ',d4,d5,d6
     write(0,'(i3,a,2f9.5)') mpp_pe(),'x,y ',x,y
     write(0,'(i3,a,4i5)') mpp_pe(),'io,jo ',io,jo,di,dj
-    write(0,'(i3,a,2i5,a,2i3)') mpp_pe(),'diamonds, find_cell_by_search: false negative 2 i,j=',i-is,j-js,' di,dj=',di,dj
-    write(0,'(i3,a,2i5,a,2f8.3)') mpp_pe(),'diamonds, find_cell_by_search: false negative 2 io,jo=',io,jo
-    write(0,'(i3,a,2i5,a,2f8.3)') mpp_pe(),'diamonds, find_cell_by_search: false negative 2 i,j=',i,j,' targ=',x,y
+    write(0,'(i3,a,2i5,a,2i3)') mpp_pe(),'KID, find_cell_by_search: false negative 2 i,j=',i-is,j-js,' di,dj=',di,dj
+    write(0,'(i3,a,2i5,a,2f8.3)') mpp_pe(),'KID, find_cell_by_search: false negative 2 io,jo=',io,jo
+    write(0,'(i3,a,2i5,a,2f8.3)') mpp_pe(),'KID, find_cell_by_search: false negative 2 i,j=',i,j,' targ=',x,y
     return
   endif
   find_cell_by_search=.false.
@@ -3639,9 +3645,9 @@ logical function is_point_in_cell(grd, x, y, i, j, explain)
   ! Safety check index bounds
   if (i-1.lt.grd%isd.or.i.gt.grd%ied.or.j-1.lt.grd%jsd.or.j.gt.grd%jed) then
     write(stderrunit,'(a,i3,(a,3i4))') &
-                     'diamonds, is_point_in_cell: pe=(',mpp_pe(),') i,s,e=', &
+                     'KID, is_point_in_cell: pe=(',mpp_pe(),') i,s,e=', &
                      i,grd%isd,grd%ied,' j,s,e=', j,grd%jsd,grd%jed
-    call error_mesg('diamonds, is_point_in_cell', 'test is off the PE!', FATAL)
+    call error_mesg('KID, is_point_in_cell', 'test is off the PE!', FATAL)
   endif
 
   is_point_in_cell=.false.
@@ -3937,14 +3943,14 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
         fac=2.1*max( abs(xi-0.5), abs(yj-0.5) ); fac=max(1., fac)
         xi=0.5+(xi-0.5)/fac
         yj=0.5+(yj-0.5)/fac
-        if (debug) call error_mesg('diamonds, pos_within_cell', 'in cell but scaling internal coordinates!', WARNING)
+        if (debug) call error_mesg('KID, pos_within_cell', 'in cell but scaling internal coordinates!', WARNING)
       endif
     else
       ! The point is not inside the spherical quad
       if (abs(xi-0.5)<0.5.and.abs(yj-0.5)<0.5) then
         ! The projection of the spherical quad onto the tangent plane should be larger than
         ! quad in the tangent plane so we should never be able to get here.
-        call error_mesg('diamonds, pos_within_cell', 'not in cell but coordinates <0.5!', FATAL)
+        call error_mesg('KID, pos_within_cell', 'not in cell but coordinates <0.5!', FATAL)
       endif
     endif
   endif
@@ -3963,7 +3969,7 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
       if (debug) then
         write(stderrunit,'(a,1p6e12.4)') 'values of xi, yj ',xi, yj
         pos_within_cell=is_point_in_cell(grd, x, y, i, j,explain=.True.)
-        call error_mesg('diamonds, pos_within_cell', 'pos_within_cell is False BUT is_point_in_cell disagrees!', FATAL)
+        call error_mesg('KID, pos_within_cell', 'pos_within_cell is False BUT is_point_in_cell disagrees!', FATAL)
       endif
     endif
   else
@@ -3973,7 +3979,7 @@ logical function pos_within_cell(grd, x, y, i, j, xi, yj, explain)
       if (debug) then
         write(stderrunit,'(a,1p6e12.4)') 'values of xi, yj ',xi, yj
         pos_within_cell=is_point_in_cell(grd, x, y, i, j,explain=.True.)
-        call error_mesg('diamonds, pos_within_cell', 'pos_within_cell is True BUT is_point_in_cell disagrees!', FATAL)
+        call error_mesg('KID, pos_within_cell', 'pos_within_cell is True BUT is_point_in_cell disagrees!', FATAL)
       endif
     endif
   endif
@@ -4044,7 +4050,7 @@ subroutine calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x, y, xi, yj, Lx, explain)
     write(stderrunit,'(a,i3,1p6e12.4)') 'calc_xiyj: coeffs alpha..kappa',mpp_pe(),alpha,beta,gamma,delta,epsilon,kappa
     write(stderrunit,'(a,i3)') 'calc_xiyj: b<0 in quadratic root solver!!!!',mpp_pe()
     write(stderrunit,'(a,i3,1p6e12.4)') 'calc_xiyj: coeffs a,b,c,d,dx,dy',mpp_pe(),a,b,c,d,dx,dy
-    call error_mesg('diamonds, calc_xiyj', 'We have complex roots. The grid must be very distorted!', FATAL)
+    call error_mesg('KID, calc_xiyj', 'We have complex roots. The grid must be very distorted!', FATAL)
   endif
 else
   if (b.ne.0.) then
@@ -4071,7 +4077,7 @@ subroutine calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x, y, xi, yj, Lx, explain)
     write(stderrunit,'(a,i3,3f8.2)') 'calc_xiyj: y2..y4 - x1',mpp_pe(),y2-y1,y3-y1,y4-y1
     write(stderrunit,'(a,i3,1p6e12.4)') 'calc_xiyj: coeffs alpha..kappa',mpp_pe(),alpha,beta,gamma,delta,epsilon,kappa
     write(stderrunit,'(a,i3,1p2e12.4)') 'calc_xiyj: coeffs a,b',mpp_pe(),a,b
-    call error_mesg('diamonds, calc_xiyj', 'Can not invert either linear equaton for xi! This should not happen!', FATAL)
+    call error_mesg('KID, calc_xiyj', 'Can not invert either linear equaton for xi! This should not happen!', FATAL)
   endif
 endif
 if (expl) write(stderrunit,'(a,2e12.4)') 'calc_xiyj: xi,yj=',xi,yj
@@ -4135,14 +4141,14 @@ subroutine check_position(grd, berg, label, il, jl)
 
   lret=pos_within_cell(grd, berg%lon, berg%lat, berg%ine, berg%jne, xi, yj)
   if (xi.ne.berg%xi.or.yj.ne.berg%yj) then
-    write(stderrunit,'("diamonds: check_position (",i4,") b%x,x,-=",3(es12.4,x),a)') mpp_pe(),berg%xi,xi,berg%xi-xi,label
-    write(stderrunit,'("diamonds: check_position (",i4,") b%y,y,-=",3(es12.4,x),a)') mpp_pe(),berg%yj,yj,berg%yj-yj,label
+    write(stderrunit,'("KID: check_position (",i4,") b%x,x,-=",3(es12.4,x),a)') mpp_pe(),berg%xi,xi,berg%xi-xi,label
+    write(stderrunit,'("KID: check_position (",i4,") b%y,y,-=",3(es12.4,x),a)') mpp_pe(),berg%yj,yj,berg%yj-yj,label
     call print_berg(stderrunit, berg, 'check_position', il, jl)
-    call error_mesg('diamonds, check_position, '//trim(label),'berg has inconsistent xi,yj!',FATAL)
+    call error_mesg('KID, check_position, '//trim(label),'berg has inconsistent xi,yj!',FATAL)
   endif
   if (grd%msk(berg%ine, berg%jne)==0.) then
     call print_berg(stderrunit, berg, 'check_position, '//trim(label), il, jl)
-    call error_mesg('diamonds, check_position, '//trim(label),'berg is in a land cell!',FATAL)
+    call error_mesg('KID, check_position, '//trim(label),'berg is in a land cell!',FATAL)
   endif
 
 end subroutine check_position
@@ -4227,7 +4233,7 @@ subroutine checksum_gridded(grd, label)
 character(len=*) :: label !< Label to use in messages
 ! Local variables
 
-  if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') 'diamonds: checksumming gridded data @ ',trim(label)
+  if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') 'KID: checksumming gridded data @ ',trim(label)
 
   ! external forcing
   call grd_chksum2(grd, grd%uo, 'uo')
@@ -4343,7 +4349,7 @@ subroutine grd_chksum3(grd, fld, txt)
   j=mpp_chksum( tmp(lbound(fld,1)+halo:ubound(fld,1)-halo, &
                     lbound(fld,2)+halo:ubound(fld,2)-halo,:) )
   if (mpp_pe().eq.mpp_root_pe()) &
-    write(*,'("diamonds, grd_chksum3: ",a18,2(x,a,"=",i22),5(x,a,"=",es16.9))') &
+    write(*,'("KID, grd_chksum3: ",a18,2(x,a,"=",i22),5(x,a,"=",es16.9))') &
      txt, 'chksum', i, 'chksum2', j, 'min', minv, 'max', maxv, 'mean',  mean, 'rms', rms, 'sd', sd
 #ifdef CHECKSUM_HALOS
   i=mpp_chksum( fld(lbound(fld,1):ubound(fld,1), &
@@ -4351,7 +4357,7 @@ subroutine grd_chksum3(grd, fld, txt)
   j=mpp_chksum( tmp(lbound(fld,1):ubound(fld,1), &
                     lbound(fld,2):ubound(fld,2),:) )
   if (mpp_pe().eq.mpp_root_pe()) &
-    write(*,'("diamonds, grd_chksum3* ",a18,2(x,a,"=",i22),5(x,a,"=",es16.9))') &
+    write(*,'("KID, grd_chksum3* ",a18,2(x,a,"=",i22),5(x,a,"=",es16.9))') &
      txt, 'chksum', i, 'chksum2', j, 'min', minv, 'max', maxv, 'mean',  mean, 'rms', rms, 'sd', sd
 #endif
 
@@ -4402,13 +4408,13 @@ subroutine grd_chksum2(grd, fld, txt)
   i=mpp_chksum( fld(grd%isc:grd%iec,grd%jsc:grd%jec) )
   j=mpp_chksum( grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec) )
   if (mpp_pe().eq.mpp_root_pe()) &
-    write(*,'("diamonds, grd_chksum2: ",a18,2(x,a,"=",i22),5(x,a,"=",es16.9),x,a,"=",i8)') &
+    write(*,'("KID, grd_chksum2: ",a18,2(x,a,"=",i22),5(x,a,"=",es16.9),x,a,"=",i8)') &
      txt, 'chksum', i, 'chksum2', j, 'min', minv, 'max', maxv, 'mean',  mean, 'rms', rms, 'sd', sd!, '#', icount
 #ifdef CHECKSUM_HALOS
   i=mpp_chksum( fld(grd%isd:grd%ied,grd%jsd:grd%jed) )
   j=mpp_chksum( grd%tmp(grd%isd:grd%ied,grd%jsd:grd%jed) )
   if (mpp_pe().eq.mpp_root_pe()) &
-    write(*,'("diamonds, grd_chksum2* ",a18,2(x,a,"=",i22),5(x,a,"=",es16.9),x,a,"=",i)') &
+    write(*,'("KID, grd_chksum2* ",a18,2(x,a,"=",i22),5(x,a,"=",es16.9),x,a,"=",i)') &
      txt, 'chksum', i, 'chksum2', j, 'min', minv, 'max', maxv, 'mean',  mean, 'rms', rms, 'sd', sd!, '#', icount
 #endif
 
@@ -4485,9 +4491,9 @@ subroutine bergs_chksum(bergs, txt, ignore_halo_violation)
   nbergs=count_bergs(bergs)
 
   if (nbergs.ne.sum(icnt(:,:))) then
-    write(*,'("diamonds, bergs_chksum: ",2(a,i8))') &
+    write(*,'("KID, bergs_chksum: ",2(a,i8))') &
       '# bergs =', nbergs, ' sum(icnt) =',sum(icnt(:,:))
-    call error_mesg('diamonds, bergs_chksum:', 'mismatch in berg count!', FATAL)
+    call error_mesg('KID, bergs_chksum:', 'mismatch in berg count!', FATAL)
   endif
 
   check_halo=.true.
@@ -4495,14 +4501,14 @@ subroutine bergs_chksum(bergs, txt, ignore_halo_violation)
     if (ignore_halo_violation) check_halo=.false.
   endif
   if (check_halo.and.nbergs.ne.sum(icnt(grd%isc:grd%iec, grd%jsc:grd%jec))) then
-    write(*,'("diamonds, bergs_chksum: ",2(a,i8))') &
+    write(*,'("KID, bergs_chksum: ",2(a,i8))') &
       '# bergs =', nbergs, ' sum(icnt(comp_dom)) =',sum(icnt(:,:))
-    call error_mesg('diamonds, bergs_chksum:', 'mismatch in berg count on computational domain!', FATAL)
+    call error_mesg('KID, bergs_chksum:', 'mismatch in berg count on computational domain!', FATAL)
   endif
 
   call mpp_sum(nbergs)
   if (mpp_pe().eq.mpp_root_pe()) &
-    write(*,'("diamonds, bergs_chksum: ",a18,6(x,a,"=",i22))') &
+    write(*,'("KID, bergs_chksum: ",a18,6(x,a,"=",i22))') &
       txt, 'chksum', ichk1, 'chksum2', ichk2, 'chksum3', ichk3, 'chksum4', ichk4, 'chksum5', ichk5, '#', nbergs
 
   grd%tmp(:,:)=real(icnt(:,:))
@@ -4736,10 +4742,10 @@ subroutine check_for_duplicates_in_parallel(bergs)
   endif
   if (k /= nbergs) then
     write(stderrunit,*) 'counted bergs=',k,'count_bergs()=',nbergs
-    call error_mesg('diamonds, check_for_duplicates:', 'Mismatch between concatenation of lists and count_bergs()!', FATAL)
+    call error_mesg('KID, check_for_duplicates:', 'Mismatch between concatenation of lists and count_bergs()!', FATAL)
   endif
   k = check_for_duplicate_ids_in_list(nbergs, ids, verbose=.true.)
-  if (k /= 0) call error_mesg('diamonds, check_for_duplicates:', 'Duplicate berg detected across PEs!', FATAL)
+  if (k /= 0) call error_mesg('KID, check_for_duplicates:', 'Duplicate berg detected across PEs!', FATAL)
   if (nbergs>0) deallocate(ids)
 end subroutine check_for_duplicates_in_parallel
 
@@ -4831,21 +4837,21 @@ subroutine test_check_for_duplicate_ids_in_list()
   call mpp_sum(error_count)
   if (error_count /= 0) then
     error_count = check_for_duplicate_ids_in_list(5, ids, verbose=.true.)
-    call error_mesg('diamonds, test_check_for_duplicate_ids_in_list:', 'Unit test for clean list failed!', FATAL)
+    call error_mesg('KID, test_check_for_duplicate_ids_in_list:', 'Unit test for clean list failed!', FATAL)
   endif
   if (mpp_pe() == mpp_root_pe()) ids(5) = ids(4)
   error_count = check_for_duplicate_ids_in_list(5, ids, verbose=.false.)
   call mpp_sum(error_count)
   if (error_count == 0) then
     error_count = check_for_duplicate_ids_in_list(5, ids, verbose=.true.)
-    call error_mesg('diamonds, test_check_for_duplicate_ids_in_list:', 'Unit test for dirty list failed!', FATAL)
+    call error_mesg('KID, test_check_for_duplicate_ids_in_list:', 'Unit test for dirty list failed!', FATAL)
   endif
   if (mpp_pe() == mpp_root_pe()) ids(5) = 7 + 5*mpp_pe()
   error_count = check_for_duplicate_ids_in_list(5, ids, verbose=.false.)
   call mpp_sum(error_count)
   if (error_count == 0 .and. mpp_npes()>1) then
     error_count = check_for_duplicate_ids_in_list(5, ids, verbose=.true.)
-    call error_mesg('diamonds, test_check_for_duplicate_ids_in_list:', 'Unit test for a really dirty list failed!', FATAL)
+    call error_mesg('KID, test_check_for_duplicate_ids_in_list:', 'Unit test for a really dirty list failed!', FATAL)
   endif
   deallocate(ids)
 end subroutine test_check_for_duplicate_ids_in_list
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index 8df9e46..cb8af5b 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -401,7 +401,7 @@ subroutine write_restart(bergs, time_stamp)
 
   ! Write stored ice
   filename='calving.res.nc'
-  if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(stderrunit,'(2a)') 'diamonds, write_restart: writing ',filename
+  if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(stderrunit,'(2a)') 'KID, write_restart: writing ',filename
   call grd_chksum3(bergs%grd, bergs%grd%stored_ice, 'write stored_ice')
   call grd_chksum2(bergs%grd, bergs%grd%stored_heat, 'write stored_heat')
   if (bergs%tau_calving>0.) then
@@ -604,9 +604,9 @@ subroutine read_restart_bergs(bergs,Time)
       endif
     endif
     if (really_debug) then
-      write(stderrunit,'(a,i8,a,2f9.4,a,i8)') 'diamonds, read_restart_bergs: berg ',k,' is at ',localberg%lon,localberg%lat,&
+      write(stderrunit,'(a,i8,a,2f9.4,a,i8)') 'KID, read_restart_bergs: berg ',k,' is at ',localberg%lon,localberg%lat,&
            & ' on PE ',mpp_pe()
-      write(stderrunit,*) 'diamonds, read_restart_bergs: lres = ',lres
+      write(stderrunit,*) 'KID, read_restart_bergs: lres = ',lres
     endif
     if (lres) then ! true if we reside on this PE grid
       localberg%uvel=uvel(k)
@@ -642,20 +642,20 @@ subroutine read_restart_bergs(bergs,Time)
 
       if (really_debug) lres=is_point_in_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, explain=.true.)
       lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
-      !call add_new_berg_to_list(bergs%first, localberg, quick=.true.)
+      !call add_new_berg_to_list(bergs%first, localberg)
 
       if (bergs%grd%area(localberg%ine,localberg%jne) .ne. 0)  then
         call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg)
       else
         if (mpp_pe().eq.mpp_root_pe()) then
           print * , 'Grounded iceberg: ', lat(k),lon(k), localberg%id
-          call error_mesg('diamonds, read_restart_bergs', 'Iceberg not added because it is grounded', WARNING)
+          call error_mesg('KID, read_restart_bergs', 'Iceberg not added because it is grounded', WARNING)
         endif
        endif
 
       if (really_debug) call print_berg(stderrunit, bergs%list(localberg%ine,localberg%jne)%first, 'read_restart_bergs, add_new_berg_to_list')
     elseif (multiPErestart .and. io_tile_id(1) .lt. 0) then
-      call error_mesg('diamonds, read_restart_bergs', 'berg in PE file was not on PE!', FATAL)
+      call error_mesg('KID, read_restart_bergs', 'berg in PE file was not on PE!', FATAL)
     endif
   enddo
 
@@ -698,17 +698,17 @@ subroutine read_restart_bergs(bergs,Time)
     !nbergs_read=count_bergs(bergs)
     !call mpp_sum(nbergs_read)
     !if (mpp_pe().eq.mpp_root_pe()) then
-    !  write(*,'(a,i8,a,i8,a)') 'diamonds, read_restart_bergs: Number of Icebergs in restart file=',nbergs_in_file,' Number of Icebergs read=', nbergs_read
+    !  write(*,'(a,i8,a,i8,a)') 'KID, read_restart_bergs: Number of Icebergs in restart file=',nbergs_in_file,' Number of Icebergs read=', nbergs_read
     !  if (nbergs_read .gt. nbergs_in_file) then
-    !    call error_mesg('diamonds, read_restart_bergs', 'More icebergs read than exist in restart file.', FATAL)
+    !    call error_mesg('KID, read_restart_bergs', 'More icebergs read than exist in restart file.', FATAL)
     !  elseif (nbergs_read .lt. nbergs_in_file) then
     !    if (bergs%ignore_missing_restart_bergs) then
-    !      call error_mesg('diamonds, read_restart_bergs', 'Some Icebergs from restart file were not found (ignore_missing flag is on)', WARNING)
+    !      call error_mesg('KID, read_restart_bergs', 'Some Icebergs from restart file were not found (ignore_missing flag is on)', WARNING)
     !    else
-    !      call error_mesg('diamonds, read_restart_bergs', 'Some Icebergs from restart file were not found', FATAL)
+    !      call error_mesg('KID, read_restart_bergs', 'Some Icebergs from restart file were not found', FATAL)
     !    endif
     !  elseif (nbergs_read .eq. nbergs_in_file) then
-    !    write(*,'(a,i8,a,i8,a)') 'diamonds, read_restart_bergs: Number of icebergs read (#',nbergs_read,') matches the number of icebergs in the file'
+    !    write(*,'(a,i8,a,i8,a)') 'KID, read_restart_bergs: Number of icebergs read (#',nbergs_read,') matches the number of icebergs in the file'
     !  endif
     !endif
 
@@ -724,7 +724,7 @@ subroutine read_restart_bergs(bergs,Time)
   call mpp_sum( bergs%icebergs_mass_start )
   bergs%bergy_mass_start=sum_mass(bergs,justbits=.true.)
   call mpp_sum( bergs%bergy_mass_start )
-  if (mpp_pe().eq.mpp_root_pe().and.verbose) write(*,'(a)') 'diamonds, read_restart_bergs: completed'
+  if (mpp_pe().eq.mpp_root_pe().and.verbose) write(*,'(a)') 'KID, read_restart_bergs: completed'
 
 end subroutine read_restart_bergs
 
@@ -832,7 +832,7 @@ subroutine generate_bergs(bergs,Time)
   bergs%nbergs_start=count_bergs(bergs)
   call mpp_sum(bergs%nbergs_start)
   if (mpp_pe().eq.mpp_root_pe()) &
-    write(*,'(a,i8,a)') 'diamonds, generate_bergs: ',bergs%nbergs_start,' were generated'
+    write(*,'(a,i8,a)') 'KID, generate_bergs: ',bergs%nbergs_start,' were generated'
 
 end subroutine generate_bergs
 
@@ -926,7 +926,7 @@ subroutine read_restart_bonds(bergs,Time)
   nbonds_in_file = siz(1)
 
     if (mpp_pe() .eq. mpp_root_pe()) then
-      write(stderrunit,*)  'diamonds, bond read restart : ','Number of bonds in file',  nbonds_in_file
+      write(stderrunit,*)  'KID, bond read restart : ','Number of bonds in file',  nbonds_in_file
     endif
 
   if (nbonds_in_file .gt. 0) then
@@ -1061,7 +1061,7 @@ subroutine read_restart_bonds(bergs,Time)
             !call form_a_bond(first_berg, other_id(k), other_berg_ine(k),other_berg_jne(k))
           endif
         else
-          write(stderrunit,*) 'diamonds, bond read restart : ','Not enough partial bonds formed', k, mpp_pe(), nbonds_in_file
+          write(stderrunit,*) 'KID, bond read restart : ','Not enough partial bonds formed', k, mpp_pe(), nbonds_in_file
           call error_mesg('read_restart_bonds_bergs_new', 'Failure with reading bonds: First bond not found on pe', FATAL)
         endif
       endif
@@ -1078,23 +1078,23 @@ subroutine read_restart_bonds(bergs,Time)
     call mpp_sum(all_pe_number_perfect_bonds_with_first_on_pe)
 
     if (all_pe_number_partial_bonds .lt. nbonds_in_file) then
-      write(stderrunit,*) 'diamonds, bond read restart : ','Not enough partial bonds formed', all_pe_number_partial_bonds , nbonds_in_file
+      write(stderrunit,*) 'KID, bond read restart : ','Not enough partial bonds formed', all_pe_number_partial_bonds , nbonds_in_file
       call error_mesg('read_restart_bonds_bergs_new', 'Not enough partial bonds formed', FATAL)
     endif
 
     if (all_pe_number_perfect_bonds .lt. nbonds_in_file) then
       call mpp_sum(all_pe_number_first_bonds_matched)
       call mpp_sum(all_pe_number_second_bonds_matched)
-      write(stderrunit,*)  'diamonds, bond read restart : ','Warning, some bonds are not fully formed',  all_pe_number_first_bonds_matched , nbonds_in_file
-      write(stderrunit,*)  'diamonds, bond read restart : ','Number of first and second bonds matched:', all_pe_number_second_bonds_matched , nbonds_in_file
+      write(stderrunit,*)  'KID, bond read restart : ','Warning, some bonds are not fully formed',  all_pe_number_first_bonds_matched , nbonds_in_file
+      write(stderrunit,*)  'KID, bond read restart : ','Number of first and second bonds matched:', all_pe_number_second_bonds_matched , nbonds_in_file
       call error_mesg('read_restart_bonds_bergs_new', 'Not enough perfect bonds formed', NOTE)
     endif
 
     if (all_pe_number_perfect_bonds_with_first_on_pe .ne. nbonds_in_file) then
       call mpp_sum(all_pe_number_first_bonds_matched)
       call mpp_sum(all_pe_number_second_bonds_matched)
-      write(stderrunit,*)  'diamonds, bond read restart : ','Warning, # bonds with first bond on computational domain, does not match file',  all_pe_number_first_bonds_matched , nbonds_in_file
-      write(stderrunit,*)  'diamonds, bond read restart : ','Computational bond, first second:', all_pe_number_second_bonds_matched , nbonds_in_file
+      write(stderrunit,*)  'KID, bond read restart : ','Warning, # bonds with first bond on computational domain, does not match file',  all_pe_number_first_bonds_matched , nbonds_in_file
+      write(stderrunit,*)  'KID, bond read restart : ','Computational bond, first second:', all_pe_number_second_bonds_matched , nbonds_in_file
       call error_mesg('read_restart_bonds_bergs_new', 'Computational perfect bonds do not match those in file', NOTE)
     endif
 
@@ -1106,8 +1106,8 @@ subroutine read_restart_bonds(bergs,Time)
   endif
 
   if (mpp_pe() .eq. mpp_root_pe()) then
-    write(stderrunit,*)  'diamonds, bond read restart : ','Number of bonds (including halos)',  all_pe_number_perfect_bonds
-    write(stderrunit,*)  'diamonds, bond read restart : ','Number of true bonds created',  all_pe_number_perfect_bonds_with_first_on_pe
+    write(stderrunit,*)  'KID, bond read restart : ','Number of bonds (including halos)',  all_pe_number_perfect_bonds
+    write(stderrunit,*)  'KID, bond read restart : ','Number of true bonds created',  all_pe_number_perfect_bonds_with_first_on_pe
   endif
 
 end subroutine read_restart_bonds
@@ -1131,48 +1131,48 @@ subroutine read_restart_calving(bergs)
   filename=trim(restart_input_dir)//'calving.res.nc'
   if (file_exist(filename)) then
     if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') &
-     'diamonds, read_restart_calving: reading ',filename
+     'KID, read_restart_calving: reading ',filename
     call read_data(filename, 'stored_ice', grd%stored_ice, grd%domain)
     if (field_exist(filename, 'stored_heat')) then
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
-       'diamonds, read_restart_calving: reading stored_heat from restart file.'
+       'KID, read_restart_calving: reading stored_heat from restart file.'
       call read_data(filename, 'stored_heat', grd%stored_heat, grd%domain)
     else
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
-     'diamonds, read_restart_calving: stored_heat WAS NOT FOUND in the file. Setting to 0.'
+     'KID, read_restart_calving: stored_heat WAS NOT FOUND in the file. Setting to 0.'
       grd%stored_heat(:,:)=0.
     endif
     if (field_exist(filename, 'rmean_calving')) then
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
-       'diamonds, read_restart_calving: reading rmean_calving from restart file.'
+       'KID, read_restart_calving: reading rmean_calving from restart file.'
       call read_data(filename, 'rmean_calving', grd%rmean_calving, grd%domain)
       grd%rmean_calving_initialized=.true.
     else
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
-     'diamonds, read_restart_calving: rmean_calving WAS NOT FOUND in the file. Setting to 0.'
+     'KID, read_restart_calving: rmean_calving WAS NOT FOUND in the file. Setting to 0.'
     endif
     if (field_exist(filename, 'rmean_calving_hflx')) then
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
-       'diamonds, read_restart_calving: reading rmean_calving_hflx from restart file.'
+       'KID, read_restart_calving: reading rmean_calving_hflx from restart file.'
       call read_data(filename, 'rmean_calving_hflx', grd%rmean_calving_hflx, grd%domain)
       grd%rmean_calving_hflx_initialized=.true.
     else
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
-     'diamonds, read_restart_calving: rmean_calving_hflx WAS NOT FOUND in the file. Setting to 0.'
+     'KID, read_restart_calving: rmean_calving_hflx WAS NOT FOUND in the file. Setting to 0.'
     endif
     if (field_exist(filename, 'iceberg_counter_grd')) then
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
-       'diamonds, read_restart_calving: reading iceberg_counter_grd from restart file.'
+       'KID, read_restart_calving: reading iceberg_counter_grd from restart file.'
       call read_data(filename, 'iceberg_counter_grd', grd%iceberg_counter_grd, grd%domain)
     else
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
-     'diamonds, read_restart_calving: iceberg_counter_grd WAS NOT FOUND in the file. Setting to 0.'
+     'KID, read_restart_calving: iceberg_counter_grd WAS NOT FOUND in the file. Setting to 0.'
       grd%iceberg_counter_grd(:,:) = 0
     endif
     bergs%restarted=.true.
   else
     if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
-     'diamonds, read_restart_calving: initializing stored ice to random numbers'
+     'KID, read_restart_calving: initializing stored ice to random numbers'
     if ( make_calving_reproduce ) then
        allocate(randnum(1,nclasses))
        do j=grd%jsc, grd%jec
@@ -1225,19 +1225,19 @@ subroutine read_ocean_depth(grd)
   filename=trim(restart_input_dir)//'topog.nc'
   if (file_exist(filename)) then
     if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') &
-     'diamonds, read_ocean_depth: reading ',filename
+     'KID, read_ocean_depth: reading ',filename
     if (field_exist(filename, 'depth')) then
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
-       'diamonds, read_ocean_depth: reading depth from topog file.'
+       'KID, read_ocean_depth: reading depth from topog file.'
       call read_data(filename, 'depth', grd%ocean_depth, grd%domain)
     else
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
-     'diamonds, read_ocean_depth: depth WAS NOT FOUND in the file. Setting to 0.'
+     'KID, read_ocean_depth: depth WAS NOT FOUND in the file. Setting to 0.'
       !grd%ocean_depth(:,:)=0.
     endif
   else
     if (mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
-     'diamonds, read_ocean_depth: Ocean depth file (topog.nc) not present)'
+     'KID, read_ocean_depth: Ocean depth file (topog.nc) not present)'
   endif
 
   !call grd_chksum2(bergs%grd, bergs%grd%ocean_depth, 'read_ocean_depth, ocean_depth')
@@ -1245,25 +1245,25 @@ end subroutine read_ocean_depth
 
 !> Write a trajectory-based diagnostics file
 subroutine write_trajectory(trajectory, save_short_traj)
-! Arguments
-type(xyt), pointer :: trajectory !< An iceberg trajectory
-logical, intent(in) :: save_short_traj !< If true, record less data
-! Local variables
-integer :: iret, ncid, i_dim, i
-integer :: lonid, latid, yearid, dayid, uvelid, vvelid, idcntid, idijid
-integer :: uoid, void, uiid, viid, uaid, vaid, sshxid, sshyid, sstid, sssid
-integer :: cnid, hiid
-integer :: mid, did, wid, lid, mbid, hdid
-character(len=37) :: filename
-character(len=7) :: pe_name
-type(xyt), pointer :: this, next
-integer :: stderrunit, cnt, ij
-!I/O vars
-type(xyt), pointer :: traj4io=>null()
-integer :: ntrajs_sent_io,ntrajs_rcvd_io
-integer :: from_pe,np
-type(buffer), pointer :: obuffer_io=>null(), ibuffer_io=>null()
-logical :: io_is_in_append_mode
+  ! Arguments
+  type(xyt), pointer :: trajectory !< An iceberg trajectory
+  logical, intent(in) :: save_short_traj !< If true, record less data
+  ! Local variables
+  integer :: iret, ncid, i_dim, i
+  integer :: lonid, latid, yearid, dayid, uvelid, vvelid, idcntid, idijid
+  integer :: uoid, void, uiid, viid, uaid, vaid, sshxid, sshyid, sstid, sssid
+  integer :: cnid, hiid
+  integer :: mid, did, wid, lid, mbid, hdid
+  character(len=37) :: filename
+  character(len=7) :: pe_name
+  type(xyt), pointer :: this, next
+  integer :: stderrunit, cnt, ij
+  !I/O vars
+  type(xyt), pointer :: traj4io=>null()
+  integer :: ntrajs_sent_io,ntrajs_rcvd_io
+  integer :: from_pe,np
+  type(buffer), pointer :: obuffer_io=>null(), ibuffer_io=>null()
+  logical :: io_is_in_append_mode
 
   ! Get the stderr unit number
   stderrunit=stderr()
@@ -1288,38 +1288,38 @@ subroutine write_trajectory(trajectory, save_short_traj)
 
   if(.NOT. force_all_pes_traj ) then
 
-  !Now gather and append the bergs from all pes in the io_tile to the list on corresponding io_tile_root_pe
-  ntrajs_sent_io =0
-  ntrajs_rcvd_io =0
-
-  if(is_io_tile_root_pe) then
-     !Receive trajs from all pes in this I/O tile !FRAGILE!SCARY!
-     do np=2,size(io_tile_pelist) ! Note: np starts from 2 to exclude self
-        from_pe=io_tile_pelist(np)
-        call mpp_recv(ntrajs_rcvd_io, glen=1, from_pe=from_pe, tag=COMM_TAG_11)
-        if (ntrajs_rcvd_io .gt. 0) then
-           call increase_ibuffer(ibuffer_io, ntrajs_rcvd_io,buffer_width_traj)
-           call mpp_recv(ibuffer_io%data, ntrajs_rcvd_io*buffer_width_traj,from_pe=from_pe, tag=COMM_TAG_12)
-           do i=1, ntrajs_rcvd_io
-              call unpack_traj_from_buffer2(traj4io, ibuffer_io, i, save_short_traj)
-           enddo
-       endif
-     enddo
-  else
-     ! Pack and send trajectories to the root PE for this I/O tile
-     do while (associated(trajectory))
-       ntrajs_sent_io = ntrajs_sent_io +1
-       call pack_traj_into_buffer2(trajectory, obuffer_io, ntrajs_sent_io, save_short_traj)
-       this => trajectory ! Need to keep pointer in order to free up the links memory
-       trajectory => trajectory%next ! This will eventually result in trajectory => null()
-       deallocate(this) ! Delete the link from memory
-     enddo
+     !Now gather and append the bergs from all pes in the io_tile to the list on corresponding io_tile_root_pe
+     ntrajs_sent_io =0
+     ntrajs_rcvd_io =0
+
+     if(is_io_tile_root_pe) then
+        !Receive trajs from all pes in this I/O tile !FRAGILE!SCARY!
+        do np=2,size(io_tile_pelist) ! Note: np starts from 2 to exclude self
+           from_pe=io_tile_pelist(np)
+           call mpp_recv(ntrajs_rcvd_io, glen=1, from_pe=from_pe, tag=COMM_TAG_11)
+           if (ntrajs_rcvd_io .gt. 0) then
+              call increase_ibuffer(ibuffer_io, ntrajs_rcvd_io,buffer_width_traj)
+              call mpp_recv(ibuffer_io%data, ntrajs_rcvd_io*buffer_width_traj,from_pe=from_pe, tag=COMM_TAG_12)
+              do i=1, ntrajs_rcvd_io
+                 call unpack_traj_from_buffer2(traj4io, ibuffer_io, i, save_short_traj)
+              enddo
+           endif
+        enddo
+     else
+        ! Pack and send trajectories to the root PE for this I/O tile
+        do while (associated(trajectory))
+           ntrajs_sent_io = ntrajs_sent_io +1
+           call pack_traj_into_buffer2(trajectory, obuffer_io, ntrajs_sent_io, save_short_traj)
+           this => trajectory ! Need to keep pointer in order to free up the links memory
+           trajectory => trajectory%next ! This will eventually result in trajectory => null()
+           deallocate(this) ! Delete the link from memory
+        enddo
 
-     call mpp_send(ntrajs_sent_io, plen=1, to_pe=io_tile_root_pe, tag=COMM_TAG_11)
-     if (ntrajs_sent_io .gt. 0) then
-        call mpp_send(obuffer_io%data, ntrajs_sent_io*buffer_width_traj, to_pe=io_tile_root_pe, tag=COMM_TAG_12)
+        call mpp_send(ntrajs_sent_io, plen=1, to_pe=io_tile_root_pe, tag=COMM_TAG_11)
+        if (ntrajs_sent_io .gt. 0) then
+           call mpp_send(obuffer_io%data, ntrajs_sent_io*buffer_width_traj, to_pe=io_tile_root_pe, tag=COMM_TAG_12)
+        endif
      endif
-  endif
 
   endif !.NOT. force_all_pes_traj
 
@@ -1330,213 +1330,213 @@ subroutine write_trajectory(trajectory, save_short_traj)
 
   if((force_all_pes_traj .OR. is_io_tile_root_pe) .AND. associated(traj4io)) then
 
-    call get_instance_filename("iceberg_trajectories.nc", filename)
-    if(io_tile_id(1) .ge. 0 .AND. .NOT. force_all_pes_traj) then !io_tile_root_pes write
-       if(io_npes .gt. 1) then !attach tile_id  to filename only if there is more than one I/O pe
-          if (io_tile_id(1)<10000) then
-             write(filename,'(A,".",I4.4)') trim(filename), io_tile_id(1)
-          else
-             write(filename,'(A,".",I6.6)') trim(filename), io_tile_id(1)
-          endif
-       endif
-    else !All pes write, attach pe# to filename
-       if (mpp_npes()<10000) then
-          write(filename,'(A,".",I4.4)') trim(filename), mpp_pe()
-       else
-          write(filename,'(A,".",I6.6)') trim(filename), mpp_pe()
-       endif
-    endif
+     call get_instance_filename("iceberg_trajectories.nc", filename)
+     if(io_tile_id(1) .ge. 0 .AND. .NOT. force_all_pes_traj) then !io_tile_root_pes write
+        if(io_npes .gt. 1) then !attach tile_id  to filename only if there is more than one I/O pe
+           if (io_tile_id(1)<10000) then
+              write(filename,'(A,".",I4.4)') trim(filename), io_tile_id(1)
+           else
+              write(filename,'(A,".",I6.6)') trim(filename), io_tile_id(1)
+           endif
+        endif
+     else !All pes write, attach pe# to filename
+        if (mpp_npes()<10000) then
+           write(filename,'(A,".",I4.4)') trim(filename), mpp_pe()
+        else
+           write(filename,'(A,".",I6.6)') trim(filename), mpp_pe()
+        endif
+     endif
 
-    io_is_in_append_mode = .false.
-    iret = nf_create(filename, NF_NOCLOBBER, ncid)
-    if (iret .ne. NF_NOERR) then
-      iret = nf_open(filename, NF_WRITE, ncid)
-      io_is_in_append_mode = .true.
-      if (iret .ne. NF_NOERR) write(stderrunit,*) 'diamonds, write_trajectory: nf_open failed'
-    endif
-    if (verbose) then
-      if (io_is_in_append_mode) then
-        write(*,'(2a)') 'diamonds, write_trajectory: appending to ',filename
-      else
-        write(*,'(2a)') 'diamonds, write_trajectory: creating ',filename
-      endif
-    endif
+     io_is_in_append_mode = .false.
+     iret = nf_create(filename, NF_NOCLOBBER, ncid)
+     if (iret .ne. NF_NOERR) then
+        iret = nf_open(filename, NF_WRITE, ncid)
+        io_is_in_append_mode = .true.
+        if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_trajectory: nf_open failed'
+     endif
+     if (verbose) then
+        if (io_is_in_append_mode) then
+           write(*,'(2a)') 'KID, write_trajectory: appending to ',filename
+        else
+           write(*,'(2a)') 'KID, write_trajectory: creating ',filename
+        endif
+     endif
 
-    if (io_is_in_append_mode) then
-      iret = nf_inq_dimid(ncid, 'i', i_dim)
-      if (iret .ne. NF_NOERR) write(stderrunit,*) 'diamonds, write_trajectory: nf_inq_dimid i failed'
-      lonid = inq_varid(ncid, 'lon')
-      latid = inq_varid(ncid, 'lat')
-      yearid = inq_varid(ncid, 'year')
-      dayid = inq_varid(ncid, 'day')
-      idcntid = inq_varid(ncid, 'id_cnt')
-      idijid = inq_varid(ncid, 'id_ij')
-      if (.not.save_short_traj) then
-        uvelid = inq_varid(ncid, 'uvel')
-        vvelid = inq_varid(ncid, 'vvel')
-        uoid = inq_varid(ncid, 'uo')
-        void = inq_varid(ncid, 'vo')
-        uiid = inq_varid(ncid, 'ui')
-        viid = inq_varid(ncid, 'vi')
-        uaid = inq_varid(ncid, 'ua')
-        vaid = inq_varid(ncid, 'va')
-        mid = inq_varid(ncid, 'mass')
-        mbid = inq_varid(ncid, 'mass_of_bits')
-        hdid = inq_varid(ncid, 'heat_density')
-        did = inq_varid(ncid, 'thickness')
-        wid = inq_varid(ncid, 'width')
-        lid = inq_varid(ncid, 'length')
-        sshxid = inq_varid(ncid, 'ssh_x')
-        sshyid = inq_varid(ncid, 'ssh_y')
-        sstid = inq_varid(ncid, 'sst')
-        sssid = inq_varid(ncid, 'sss')
-        cnid = inq_varid(ncid, 'cn')
-        hiid = inq_varid(ncid, 'hi')
-      endif
-    else
-      ! Dimensions
-      iret = nf_def_dim(ncid, 'i', NF_UNLIMITED, i_dim)
-      if (iret .ne. NF_NOERR) write(stderrunit,*) 'diamonds, write_trajectory: nf_def_dim i failed'
-
-      ! Variables
-      lonid = def_var(ncid, 'lon', NF_DOUBLE, i_dim)
-      latid = def_var(ncid, 'lat', NF_DOUBLE, i_dim)
-      yearid = def_var(ncid, 'year', NF_INT, i_dim)
-      dayid = def_var(ncid, 'day', NF_DOUBLE, i_dim)
-      idcntid = def_var(ncid, 'id_cnt', NF_INT, i_dim)
-      idijid = def_var(ncid, 'id_ij', NF_INT, i_dim)
-      if (.not. save_short_traj) then
-        uvelid = def_var(ncid, 'uvel', NF_DOUBLE, i_dim)
-        vvelid = def_var(ncid, 'vvel', NF_DOUBLE, i_dim)
-        uoid = def_var(ncid, 'uo', NF_DOUBLE, i_dim)
-        void = def_var(ncid, 'vo', NF_DOUBLE, i_dim)
-        uiid = def_var(ncid, 'ui', NF_DOUBLE, i_dim)
-        viid = def_var(ncid, 'vi', NF_DOUBLE, i_dim)
-        uaid = def_var(ncid, 'ua', NF_DOUBLE, i_dim)
-        vaid = def_var(ncid, 'va', NF_DOUBLE, i_dim)
-        mid = def_var(ncid, 'mass', NF_DOUBLE, i_dim)
-        mbid = def_var(ncid, 'mass_of_bits', NF_DOUBLE, i_dim)
-        hdid = def_var(ncid, 'heat_density', NF_DOUBLE, i_dim)
-        did = def_var(ncid, 'thickness', NF_DOUBLE, i_dim)
-        wid = def_var(ncid, 'width', NF_DOUBLE, i_dim)
-        lid = def_var(ncid, 'length', NF_DOUBLE, i_dim)
-        sshxid = def_var(ncid, 'ssh_x', NF_DOUBLE, i_dim)
-        sshyid = def_var(ncid, 'ssh_y', NF_DOUBLE, i_dim)
-        sstid = def_var(ncid, 'sst', NF_DOUBLE, i_dim)
-        sssid = def_var(ncid, 'sss', NF_DOUBLE, i_dim)
-        cnid = def_var(ncid, 'cn', NF_DOUBLE, i_dim)
-        hiid = def_var(ncid, 'hi', NF_DOUBLE, i_dim)
-      endif
+     if (io_is_in_append_mode) then
+        iret = nf_inq_dimid(ncid, 'i', i_dim)
+        if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_trajectory: nf_inq_dimid i failed'
+        lonid = inq_varid(ncid, 'lon')
+        latid = inq_varid(ncid, 'lat')
+        yearid = inq_varid(ncid, 'year')
+        dayid = inq_varid(ncid, 'day')
+        idcntid = inq_varid(ncid, 'id_cnt')
+        idijid = inq_varid(ncid, 'id_ij')
+        if (.not.save_short_traj) then
+           uvelid = inq_varid(ncid, 'uvel')
+           vvelid = inq_varid(ncid, 'vvel')
+           uoid = inq_varid(ncid, 'uo')
+           void = inq_varid(ncid, 'vo')
+           uiid = inq_varid(ncid, 'ui')
+           viid = inq_varid(ncid, 'vi')
+           uaid = inq_varid(ncid, 'ua')
+           vaid = inq_varid(ncid, 'va')
+           mid = inq_varid(ncid, 'mass')
+           mbid = inq_varid(ncid, 'mass_of_bits')
+           hdid = inq_varid(ncid, 'heat_density')
+           did = inq_varid(ncid, 'thickness')
+           wid = inq_varid(ncid, 'width')
+           lid = inq_varid(ncid, 'length')
+           sshxid = inq_varid(ncid, 'ssh_x')
+           sshyid = inq_varid(ncid, 'ssh_y')
+           sstid = inq_varid(ncid, 'sst')
+           sssid = inq_varid(ncid, 'sss')
+           cnid = inq_varid(ncid, 'cn')
+           hiid = inq_varid(ncid, 'hi')
+        endif
+     else
+        ! Dimensions
+        iret = nf_def_dim(ncid, 'i', NF_UNLIMITED, i_dim)
+        if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_trajectory: nf_def_dim i failed'
+
+        ! Variables
+        lonid = def_var(ncid, 'lon', NF_DOUBLE, i_dim)
+        latid = def_var(ncid, 'lat', NF_DOUBLE, i_dim)
+        yearid = def_var(ncid, 'year', NF_INT, i_dim)
+        dayid = def_var(ncid, 'day', NF_DOUBLE, i_dim)
+        idcntid = def_var(ncid, 'id_cnt', NF_INT, i_dim)
+        idijid = def_var(ncid, 'id_ij', NF_INT, i_dim)
+        if (.not. save_short_traj) then
+           uvelid = def_var(ncid, 'uvel', NF_DOUBLE, i_dim)
+           vvelid = def_var(ncid, 'vvel', NF_DOUBLE, i_dim)
+           uoid = def_var(ncid, 'uo', NF_DOUBLE, i_dim)
+           void = def_var(ncid, 'vo', NF_DOUBLE, i_dim)
+           uiid = def_var(ncid, 'ui', NF_DOUBLE, i_dim)
+           viid = def_var(ncid, 'vi', NF_DOUBLE, i_dim)
+           uaid = def_var(ncid, 'ua', NF_DOUBLE, i_dim)
+           vaid = def_var(ncid, 'va', NF_DOUBLE, i_dim)
+           mid = def_var(ncid, 'mass', NF_DOUBLE, i_dim)
+           mbid = def_var(ncid, 'mass_of_bits', NF_DOUBLE, i_dim)
+           hdid = def_var(ncid, 'heat_density', NF_DOUBLE, i_dim)
+           did = def_var(ncid, 'thickness', NF_DOUBLE, i_dim)
+           wid = def_var(ncid, 'width', NF_DOUBLE, i_dim)
+           lid = def_var(ncid, 'length', NF_DOUBLE, i_dim)
+           sshxid = def_var(ncid, 'ssh_x', NF_DOUBLE, i_dim)
+           sshyid = def_var(ncid, 'ssh_y', NF_DOUBLE, i_dim)
+           sstid = def_var(ncid, 'sst', NF_DOUBLE, i_dim)
+           sssid = def_var(ncid, 'sss', NF_DOUBLE, i_dim)
+           cnid = def_var(ncid, 'cn', NF_DOUBLE, i_dim)
+           hiid = def_var(ncid, 'hi', NF_DOUBLE, i_dim)
+        endif
 
-      ! Attributes
-      iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_major_version', NF_INT, 1, 0)
-      iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_minor_version', NF_INT, 1, 1)
-      call put_att(ncid, lonid, 'long_name', 'longitude')
-      call put_att(ncid, lonid, 'units', 'degrees_E')
-      call put_att(ncid, latid, 'long_name', 'latitude')
-      call put_att(ncid, latid, 'units', 'degrees_N')
-      call put_att(ncid, yearid, 'long_name', 'year')
-      call put_att(ncid, yearid, 'units', 'years')
-      call put_att(ncid, dayid, 'long_name', 'year day')
-      call put_att(ncid, dayid, 'units', 'days')
-      call put_att(ncid, idcntid, 'long_name', 'counter component of iceberg id')
-      call put_att(ncid, idcntid, 'units', 'dimensionless')
-      call put_att(ncid, idijid, 'long_name', 'position component of iceberg id')
-      call put_att(ncid, idijid, 'units', 'dimensionless')
-
-      if (.not. save_short_traj) then
-        call put_att(ncid, uvelid, 'long_name', 'zonal spped')
-        call put_att(ncid, uvelid, 'units', 'm/s')
-        call put_att(ncid, vvelid, 'long_name', 'meridional spped')
-        call put_att(ncid, vvelid, 'units', 'm/s')
-        call put_att(ncid, uoid, 'long_name', 'ocean zonal spped')
-        call put_att(ncid, uoid, 'units', 'm/s')
-        call put_att(ncid, void, 'long_name', 'ocean meridional spped')
-        call put_att(ncid, void, 'units', 'm/s')
-        call put_att(ncid, uiid, 'long_name', 'ice zonal spped')
-        call put_att(ncid, uiid, 'units', 'm/s')
-        call put_att(ncid, viid, 'long_name', 'ice meridional spped')
-        call put_att(ncid, viid, 'units', 'm/s')
-        call put_att(ncid, uaid, 'long_name', 'atmos zonal spped')
-        call put_att(ncid, uaid, 'units', 'm/s')
-        call put_att(ncid, vaid, 'long_name', 'atmos meridional spped')
-        call put_att(ncid, vaid, 'units', 'm/s')
-        call put_att(ncid, mid, 'long_name', 'mass')
-        call put_att(ncid, mid, 'units', 'kg')
-        call put_att(ncid, mbid, 'long_name', 'mass_of_bits')
-        call put_att(ncid, mbid, 'units', 'kg')
-        call put_att(ncid, hdid, 'long_name', 'heat_density')
-        call put_att(ncid, hdid, 'units', 'J/kg')
-        call put_att(ncid, did, 'long_name', 'thickness')
-        call put_att(ncid, did, 'units', 'm')
-        call put_att(ncid, wid, 'long_name', 'width')
-        call put_att(ncid, wid, 'units', 'm')
-        call put_att(ncid, lid, 'long_name', 'length')
-        call put_att(ncid, lid, 'units', 'm')
-        call put_att(ncid, sshxid, 'long_name', 'sea surface height gradient_x')
-        call put_att(ncid, sshxid, 'units', 'non-dim')
-        call put_att(ncid, sshyid, 'long_name', 'sea surface height gradient_y')
-        call put_att(ncid, sshyid, 'units', 'non-dim')
-        call put_att(ncid, sstid, 'long_name', 'sea surface temperature')
-        call put_att(ncid, sstid, 'units', 'degrees_C')
-        call put_att(ncid, sssid, 'long_name', 'sea surface salinity')
-        call put_att(ncid, sssid, 'units', 'psu')
-        call put_att(ncid, cnid, 'long_name', 'sea ice concentration')
-        call put_att(ncid, cnid, 'units', 'none')
-        call put_att(ncid, hiid, 'long_name', 'sea ice thickness')
-        call put_att(ncid, hiid, 'units', 'm')
-      endif
-    endif
+        ! Attributes
+        iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_major_version', NF_INT, 1, 0)
+        iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_minor_version', NF_INT, 1, 1)
+        call put_att(ncid, lonid, 'long_name', 'longitude')
+        call put_att(ncid, lonid, 'units', 'degrees_E')
+        call put_att(ncid, latid, 'long_name', 'latitude')
+        call put_att(ncid, latid, 'units', 'degrees_N')
+        call put_att(ncid, yearid, 'long_name', 'year')
+        call put_att(ncid, yearid, 'units', 'years')
+        call put_att(ncid, dayid, 'long_name', 'year day')
+        call put_att(ncid, dayid, 'units', 'days')
+        call put_att(ncid, idcntid, 'long_name', 'counter component of iceberg id')
+        call put_att(ncid, idcntid, 'units', 'dimensionless')
+        call put_att(ncid, idijid, 'long_name', 'position component of iceberg id')
+        call put_att(ncid, idijid, 'units', 'dimensionless')
+
+        if (.not. save_short_traj) then
+           call put_att(ncid, uvelid, 'long_name', 'zonal spped')
+           call put_att(ncid, uvelid, 'units', 'm/s')
+           call put_att(ncid, vvelid, 'long_name', 'meridional spped')
+           call put_att(ncid, vvelid, 'units', 'm/s')
+           call put_att(ncid, uoid, 'long_name', 'ocean zonal spped')
+           call put_att(ncid, uoid, 'units', 'm/s')
+           call put_att(ncid, void, 'long_name', 'ocean meridional spped')
+           call put_att(ncid, void, 'units', 'm/s')
+           call put_att(ncid, uiid, 'long_name', 'ice zonal spped')
+           call put_att(ncid, uiid, 'units', 'm/s')
+           call put_att(ncid, viid, 'long_name', 'ice meridional spped')
+           call put_att(ncid, viid, 'units', 'm/s')
+           call put_att(ncid, uaid, 'long_name', 'atmos zonal spped')
+           call put_att(ncid, uaid, 'units', 'm/s')
+           call put_att(ncid, vaid, 'long_name', 'atmos meridional spped')
+           call put_att(ncid, vaid, 'units', 'm/s')
+           call put_att(ncid, mid, 'long_name', 'mass')
+           call put_att(ncid, mid, 'units', 'kg')
+           call put_att(ncid, mbid, 'long_name', 'mass_of_bits')
+           call put_att(ncid, mbid, 'units', 'kg')
+           call put_att(ncid, hdid, 'long_name', 'heat_density')
+           call put_att(ncid, hdid, 'units', 'J/kg')
+           call put_att(ncid, did, 'long_name', 'thickness')
+           call put_att(ncid, did, 'units', 'm')
+           call put_att(ncid, wid, 'long_name', 'width')
+           call put_att(ncid, wid, 'units', 'm')
+           call put_att(ncid, lid, 'long_name', 'length')
+           call put_att(ncid, lid, 'units', 'm')
+           call put_att(ncid, sshxid, 'long_name', 'sea surface height gradient_x')
+           call put_att(ncid, sshxid, 'units', 'non-dim')
+           call put_att(ncid, sshyid, 'long_name', 'sea surface height gradient_y')
+           call put_att(ncid, sshyid, 'units', 'non-dim')
+           call put_att(ncid, sstid, 'long_name', 'sea surface temperature')
+           call put_att(ncid, sstid, 'units', 'degrees_C')
+           call put_att(ncid, sssid, 'long_name', 'sea surface salinity')
+           call put_att(ncid, sssid, 'units', 'psu')
+           call put_att(ncid, cnid, 'long_name', 'sea ice concentration')
+           call put_att(ncid, cnid, 'units', 'none')
+           call put_att(ncid, hiid, 'long_name', 'sea ice thickness')
+           call put_att(ncid, hiid, 'units', 'm')
+        endif
+     endif
 
-    ! End define mode
-    iret = nf_enddef(ncid)
+     ! End define mode
+     iret = nf_enddef(ncid)
 
-    ! Write variables
-    this=>traj4io
-    if (io_is_in_append_mode) then
-      iret = nf_inq_dimlen(ncid, i_dim, i)
-      if (iret .ne. NF_NOERR) write(stderrunit,*) 'diamonds, write_trajectory: nf_inq_dimlen i failed'
-    else
-      i = 0
-    endif
-    do while (associated(this))
-      i=i+1
-      call put_double(ncid, lonid, i, this%lon)
-      call put_double(ncid, latid, i, this%lat)
-      call put_int(ncid, yearid, i, this%year)
-      call put_double(ncid, dayid, i, this%day)
-      call split_id(this%id, cnt, ij)
-      call put_int(ncid, idcntid, i, cnt)
-      call put_int(ncid, idijid, i, ij)
-      if (.not. save_short_traj) then
-        call put_double(ncid, uvelid, i, this%uvel)
-        call put_double(ncid, vvelid, i, this%vvel)
-        call put_double(ncid, uoid, i, this%uo)
-        call put_double(ncid, void, i, this%vo)
-        call put_double(ncid, uiid, i, this%ui)
-        call put_double(ncid, viid, i, this%vi)
-        call put_double(ncid, uaid, i, this%ua)
-        call put_double(ncid, vaid, i, this%va)
-        call put_double(ncid, mid, i, this%mass)
-        call put_double(ncid, hdid, i, this%heat_density)
-        call put_double(ncid, did, i, this%thickness)
-        call put_double(ncid, wid, i, this%width)
-        call put_double(ncid, lid, i, this%length)
-        call put_double(ncid, sshxid, i, this%ssh_x)
-        call put_double(ncid, sshyid, i, this%ssh_y)
-        call put_double(ncid, sstid, i, this%sst)
-        call put_double(ncid, sssid, i, this%sss)
-        call put_double(ncid, cnid, i, this%cn)
-        call put_double(ncid, hiid, i, this%hi)
-      endif
-      next=>this%next
-      deallocate(this)
-      this=>next
-    enddo
+     ! Write variables
+     this=>traj4io
+     if (io_is_in_append_mode) then
+        iret = nf_inq_dimlen(ncid, i_dim, i)
+        if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_trajectory: nf_inq_dimlen i failed'
+     else
+        i = 0
+     endif
+     do while (associated(this))
+        i=i+1
+        call put_double(ncid, lonid, i, this%lon)
+        call put_double(ncid, latid, i, this%lat)
+        call put_int(ncid, yearid, i, this%year)
+        call put_double(ncid, dayid, i, this%day)
+        call split_id(this%id, cnt, ij)
+        call put_int(ncid, idcntid, i, cnt)
+        call put_int(ncid, idijid, i, ij)
+        if (.not. save_short_traj) then
+           call put_double(ncid, uvelid, i, this%uvel)
+           call put_double(ncid, vvelid, i, this%vvel)
+           call put_double(ncid, uoid, i, this%uo)
+           call put_double(ncid, void, i, this%vo)
+           call put_double(ncid, uiid, i, this%ui)
+           call put_double(ncid, viid, i, this%vi)
+           call put_double(ncid, uaid, i, this%ua)
+           call put_double(ncid, vaid, i, this%va)
+           call put_double(ncid, mid, i, this%mass)
+           call put_double(ncid, hdid, i, this%heat_density)
+           call put_double(ncid, did, i, this%thickness)
+           call put_double(ncid, wid, i, this%width)
+           call put_double(ncid, lid, i, this%length)
+           call put_double(ncid, sshxid, i, this%ssh_x)
+           call put_double(ncid, sshyid, i, this%ssh_y)
+           call put_double(ncid, sstid, i, this%sst)
+           call put_double(ncid, sssid, i, this%sss)
+           call put_double(ncid, cnid, i, this%cn)
+           call put_double(ncid, hiid, i, this%hi)
+        endif
+        next=>this%next
+        deallocate(this)
+        this=>next
+     enddo
 
-    ! Finish up
-    iret = nf_close(ncid)
-    if (iret .ne. NF_NOERR) write(stderrunit,*) 'diamonds, write_trajectory: nf_close failed',mpp_pe(),filename
+     ! Finish up
+     iret = nf_close(ncid)
+     if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_trajectory: nf_close failed',mpp_pe(),filename
 
   endif !(is_io_tile_root_pe .AND. associated(traj4io))
   call mpp_clock_end(clock_trw)
@@ -1561,8 +1561,8 @@ integer function inq_var(ncid, var, unsafe)
   iret=nf_inq_varid(ncid, var, inq_var)
   if (iret .ne. NF_NOERR) then
     if (.not. unsafely) then
-      write(stderrunit,*) 'diamonds, inq_var: nf_inq_varid ',var,' failed'
-      call error_mesg('diamonds, inq_var', 'netcdf function returned a failure!', FATAL)
+      write(stderrunit,*) 'KID, inq_var: nf_inq_varid ',var,' failed'
+      call error_mesg('KID, inq_var', 'netcdf function returned a failure!', FATAL)
     else
       inq_var=-1
     endif
@@ -1586,7 +1586,7 @@ integer function def_var(ncid, var, ntype, idim)
 
   iret = nf_def_var(ncid, var, ntype, 1, idim, def_var)
   if (iret .ne. NF_NOERR) then
-    call error_mesg('diamonds, def_var', nf_strerror(iret), FATAL)
+    call error_mesg('KID, def_var', nf_strerror(iret), FATAL)
   endif
 
 end function def_var
@@ -1605,8 +1605,8 @@ integer function inq_varid(ncid, var)
 
   iret = nf_inq_varid(ncid, var, inq_varid)
   if (iret .ne. NF_NOERR) then
-    write(stderrunit,*) 'diamonds, inq_varid: nf_inq_varid failed for ',trim(var)
-    call error_mesg('diamonds, inq_varid', 'netcdf function returned a failure!', FATAL)
+    write(stderrunit,*) 'KID, inq_varid: nf_inq_varid failed for ',trim(var)
+    call error_mesg('KID, inq_varid', 'netcdf function returned a failure!', FATAL)
   endif
 
 end function inq_varid
@@ -1628,9 +1628,9 @@ subroutine put_att(ncid, id, att, attval)
   vallen=len_trim(attval)
   iret = nf_put_att_text(ncid, id, att, vallen, attval)
   if (iret .ne. NF_NOERR) then
-    write(stderrunit,*) 'diamonds, put_att: nf_put_att_text failed adding', &
+    write(stderrunit,*) 'KID, put_att: nf_put_att_text failed adding', &
       trim(att),' = ',trim(attval)
-    call error_mesg('diamonds, put_att', 'netcdf function returned a failure!', FATAL)
+    call error_mesg('KID, put_att', 'netcdf function returned a failure!', FATAL)
   endif
 
 end subroutine put_att
@@ -1650,8 +1650,8 @@ real function get_double(ncid, id, i)
 
   iret=nf_get_var1_double(ncid, id, i, get_double)
   if (iret .ne. NF_NOERR) then
-    write(stderrunit,*) 'diamonds, get_double: nf_get_var1_double failed reading'
-    call error_mesg('diamonds, get_double', 'netcdf function returned a failure!', FATAL)
+    write(stderrunit,*) 'KID, get_double: nf_get_var1_double failed reading'
+    call error_mesg('KID, get_double', 'netcdf function returned a failure!', FATAL)
   endif
 
 end function get_double
@@ -1671,8 +1671,8 @@ integer function get_int(ncid, id, i)
 
   iret=nf_get_var1_int(ncid, id, i, get_int)
   if (iret .ne. NF_NOERR) then
-    write(stderrunit,*) 'diamonds, get_int: nf_get_var1_int failed reading'
-    call error_mesg('diamonds, get_int', 'netcdf function returned a failure!', FATAL)
+    write(stderrunit,*) 'KID, get_int: nf_get_var1_int failed reading'
+    call error_mesg('KID, get_int', 'netcdf function returned a failure!', FATAL)
   endif
 
 end function get_int
@@ -1693,8 +1693,8 @@ subroutine put_double(ncid, id, i, val)
 
   iret = nf_put_vara_double(ncid, id, i, 1, val)
   if (iret .ne. NF_NOERR) then
-    write(stderrunit,*) 'diamonds, put_double: nf_put_vara_double failed writing'
-    call error_mesg('diamonds, put_double', 'netcdf function returned a failure!', FATAL)
+    write(stderrunit,*) 'KID, put_double: nf_put_vara_double failed writing'
+    call error_mesg('KID, put_double', 'netcdf function returned a failure!', FATAL)
   endif
 
 end subroutine put_double
@@ -1715,8 +1715,8 @@ subroutine put_int(ncid, id, i, val)
 
   iret = nf_put_vara_int(ncid, id, i, 1, val)
   if (iret .ne. NF_NOERR) then
-    write(stderrunit,*) 'diamonds, put_int: nf_put_vara_int failed writing'
-    call error_mesg('diamonds, put_int', 'netcdf function returned a failure!', FATAL)
+    write(stderrunit,*) 'KID, put_int: nf_put_vara_int failed writing'
+    call error_mesg('KID, put_int', 'netcdf function returned a failure!', FATAL)
   endif
 
 end subroutine put_int
diff --git a/test/Iceberg_repository/RUN b/test/Iceberg_repository/RUN
deleted file mode 100755
index cabc714..0000000
--- a/test/Iceberg_repository/RUN
+++ /dev/null
@@ -1,9 +0,0 @@
-rm ./output_files/Generic*
-
-./Scripts_and_analysis/initialize_bergs_in_pattern.py -set_all_bergs_static_by_default=False -Run_plotting_subroutine=False \
-				 -break_some_bonds=False -Ice_geometry_source='Generic' \
-				 -Generic_ice_geometry_filename='./testberg/testtabularberg.nc' \
-				 -ISOMIP_reduced=False \
-
-cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
-cp ./output_files/Generic_bonds_iceberg.res.nc ./../INPUT/bonds_iceberg.res.nc
\ No newline at end of file
diff --git a/test/README b/test/README
deleted file mode 100644
index a4c4514..0000000
--- a/test/README
+++ /dev/null
@@ -1,4 +0,0 @@
-- Use the scripts in ./Iceberg_repository to create a tabular iceberg and restart (input) file for testing the solo driver
-- edit input.nml
-- run the model (e.g. ./RUN)
-- animate the results with animate_trajectories.py
\ No newline at end of file
diff --git a/test/RUN b/test/RUN
deleted file mode 100755
index d125392..0000000
--- a/test/RUN
+++ /dev/null
@@ -1,2 +0,0 @@
-rm iceberg_trajectories.nc
-srun -n4 ./../build/bergs.x
diff --git a/test/input.nml b/test/input.nml
deleted file mode 100644
index 90a4d58..0000000
--- a/test/input.nml
+++ /dev/null
@@ -1,49 +0,0 @@
-&icebergs_driver_nml
-  ni=20,
-  nj=20,
-  ibdt=3600.0,
-  ibuo=0.3,
-  ibvo=0.0,
-  ibhrs=4000,
-  halo=4,
-  debug=.true.
-/
-
-&icebergs_nml
-    verbose=.false.,
-    verbose_hrs=5,
-    traj_sample_hrs=5,
-    debug=.false.,
-    really_debug=.false.,
-    use_slow_find=.true.,
-    add_weight_to_ocean=.false.,
-    passive_mode=.false.,
-    generate_test_icebergs=.false.,
-    use_roundoff_fix=.true.,
-    make_calving_reproduce=.true.,
-    grid_is_regular=.true.,
-    grid_is_latlon=.false.,
-    set_melt_rates_to_zero=.true.,
-    interactive_icebergs_on=.true.,
-    critical_interaction_damping_on=.true.,
-    use_new_predictive_corrective=.true.,
-    halo=4,
-    halo_debugging=.false.,
-    ignore_ij_restart=.true.,
-    parallel_reprod=.true.,
-    Lx=200000.0,
-    restart_input_dir='INPUT/',
-    hexagonal_icebergs=.true.,
-    iceberg_bonds_on=.false.,
-    use_old_spreading=.false., !for if bergs are rec
-    runge_not_verlet=.false.,
-    manually_initialize_bonds=.false.
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.,
-         threading_read='multi'
- /
diff --git a/test/.gitignore b/tests/.gitignore
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index a9bd34f..35c3337 100644
--- a/test/.gitignore
+++ b/tests/.gitignore
@@ -1,3 +1,4 @@
 *.out
 *~
-*.nc
\ No newline at end of file
+*.nc
+core
\ No newline at end of file
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index 09dc309..922b12f 100644
--- a/test/Iceberg_repository/README
+++ b/tests/Iceberg_repository/README
@@ -1,8 +1,8 @@
-- Alon's Iceberg Repository, edited for initializing a model setup for testing the iceberg driver.
-- Added the directory ./testberg, where file testberg.py can be edited and run to create a test iceberg.
-- This berg is then transformed into a restart (input) file via initialize_bergs_in_pattern.py,
-  as called by the RUN script.
 
+- Alon's Iceberg Repository, edited for initializing a model setup for testing the iceberg driver.
+- 1. Initialize a berg using the scripts in one of the test directories
+- 2. Use ./Scripts_and_analysis/initialize_bergs_in_pattern.py to convert the berg into a restart (input)
+     file
 
 
 
diff --git a/tests/Iceberg_repository/RUN b/tests/Iceberg_repository/RUN
new file mode 100755
index 0000000..12706a3
--- /dev/null
+++ b/tests/Iceberg_repository/RUN
@@ -0,0 +1,12 @@
+#sample runfile:
+
+#rm ./output_files/Generic*
+
+#./Scripts_and_analysis/initialize_bergs_in_pattern.py -set_all_bergs_static_by_default=False -Run_plotting_subroutine=False \
+#				 -break_some_bonds=False -Ice_geometry_source='Generic' \
+#				 -Generic_ice_geometry_filename='./testberg/testtabularberg.nc' \
+#				 -ISOMIP_reduced=False \
+
+#copy iceberg and bond restart files to input directories
+#cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
+#cp ./output_files/Generic_bonds_iceberg.res.nc ./../INPUT/bonds_iceberg.res.nc
\ No newline at end of file
diff --git a/test/Iceberg_repository/Scripts_and_analysis/Create_a_cartesian_grid_and_mosaic.ipynb b/tests/Iceberg_repository/Scripts_and_analysis/Create_a_cartesian_grid_and_mosaic.ipynb
similarity index 100%
rename from test/Iceberg_repository/Scripts_and_analysis/Create_a_cartesian_grid_and_mosaic.ipynb
rename to tests/Iceberg_repository/Scripts_and_analysis/Create_a_cartesian_grid_and_mosaic.ipynb
diff --git a/test/Iceberg_repository/Scripts_and_analysis/Create_mosaic.py b/tests/Iceberg_repository/Scripts_and_analysis/Create_mosaic.py
similarity index 100%
rename from test/Iceberg_repository/Scripts_and_analysis/Create_mosaic.py
rename to tests/Iceberg_repository/Scripts_and_analysis/Create_mosaic.py
diff --git a/test/Iceberg_repository/Scripts_and_analysis/Idealized_cartesian_grid.py b/tests/Iceberg_repository/Scripts_and_analysis/Idealized_cartesian_grid.py
similarity index 100%
rename from test/Iceberg_repository/Scripts_and_analysis/Idealized_cartesian_grid.py
rename to tests/Iceberg_repository/Scripts_and_analysis/Idealized_cartesian_grid.py
diff --git a/test/Iceberg_repository/Scripts_and_analysis/Weddell_Sea_initiation.sh b/tests/Iceberg_repository/Scripts_and_analysis/Weddell_Sea_initiation.sh
similarity index 100%
rename from test/Iceberg_repository/Scripts_and_analysis/Weddell_Sea_initiation.sh
rename to tests/Iceberg_repository/Scripts_and_analysis/Weddell_Sea_initiation.sh
diff --git a/test/Iceberg_repository/Scripts_and_analysis/Weddell_sea_shelf_setup.py b/tests/Iceberg_repository/Scripts_and_analysis/Weddell_sea_shelf_setup.py
similarity index 100%
rename from test/Iceberg_repository/Scripts_and_analysis/Weddell_sea_shelf_setup.py
rename to tests/Iceberg_repository/Scripts_and_analysis/Weddell_sea_shelf_setup.py
diff --git a/test/Iceberg_repository/Scripts_and_analysis/bergs_quickview.py b/tests/Iceberg_repository/Scripts_and_analysis/bergs_quickview.py
similarity index 100%
rename from test/Iceberg_repository/Scripts_and_analysis/bergs_quickview.py
rename to tests/Iceberg_repository/Scripts_and_analysis/bergs_quickview.py
diff --git a/test/Iceberg_repository/Scripts_and_analysis/calving_and_extract.py b/tests/Iceberg_repository/Scripts_and_analysis/calving_and_extract.py
similarity index 100%
rename from test/Iceberg_repository/Scripts_and_analysis/calving_and_extract.py
rename to tests/Iceberg_repository/Scripts_and_analysis/calving_and_extract.py
diff --git a/test/Iceberg_repository/Scripts_and_analysis/check_convergence.py b/tests/Iceberg_repository/Scripts_and_analysis/check_convergence.py
similarity index 100%
rename from test/Iceberg_repository/Scripts_and_analysis/check_convergence.py
rename to tests/Iceberg_repository/Scripts_and_analysis/check_convergence.py
diff --git a/test/Iceberg_repository/Scripts_and_analysis/compare_Global_Quick_vs_Benchmark.py b/tests/Iceberg_repository/Scripts_and_analysis/compare_Global_Quick_vs_Benchmark.py
similarity index 100%
rename from test/Iceberg_repository/Scripts_and_analysis/compare_Global_Quick_vs_Benchmark.py
rename to tests/Iceberg_repository/Scripts_and_analysis/compare_Global_Quick_vs_Benchmark.py
diff --git a/test/Iceberg_repository/Scripts_and_analysis/copy_files_to_shelf_and_bergs.sh b/tests/Iceberg_repository/Scripts_and_analysis/copy_files_to_shelf_and_bergs.sh
similarity index 100%
rename from test/Iceberg_repository/Scripts_and_analysis/copy_files_to_shelf_and_bergs.sh
rename to tests/Iceberg_repository/Scripts_and_analysis/copy_files_to_shelf_and_bergs.sh
diff --git a/test/Iceberg_repository/Scripts_and_analysis/create_C3_env.sh b/tests/Iceberg_repository/Scripts_and_analysis/create_C3_env.sh
similarity index 100%
rename from test/Iceberg_repository/Scripts_and_analysis/create_C3_env.sh
rename to tests/Iceberg_repository/Scripts_and_analysis/create_C3_env.sh
diff --git a/test/Iceberg_repository/Scripts_and_analysis/create_berg_restart.py b/tests/Iceberg_repository/Scripts_and_analysis/create_berg_restart.py
similarity index 100%
rename from test/Iceberg_repository/Scripts_and_analysis/create_berg_restart.py
rename to tests/Iceberg_repository/Scripts_and_analysis/create_berg_restart.py
diff --git a/test/Iceberg_repository/Scripts_and_analysis/create_one_file.py b/tests/Iceberg_repository/Scripts_and_analysis/create_one_file.py
similarity index 100%
rename from test/Iceberg_repository/Scripts_and_analysis/create_one_file.py
rename to tests/Iceberg_repository/Scripts_and_analysis/create_one_file.py
diff --git a/test/Iceberg_repository/Scripts_and_analysis/create_thickness_file.py b/tests/Iceberg_repository/Scripts_and_analysis/create_thickness_file.py
similarity index 100%
rename from test/Iceberg_repository/Scripts_and_analysis/create_thickness_file.py
rename to tests/Iceberg_repository/Scripts_and_analysis/create_thickness_file.py
diff --git a/test/Iceberg_repository/Scripts_and_analysis/filling_up_space.py b/tests/Iceberg_repository/Scripts_and_analysis/filling_up_space.py
similarity index 100%
rename from test/Iceberg_repository/Scripts_and_analysis/filling_up_space.py
rename to tests/Iceberg_repository/Scripts_and_analysis/filling_up_space.py
diff --git a/test/Iceberg_repository/Scripts_and_analysis/flat_isomip_create.py b/tests/Iceberg_repository/Scripts_and_analysis/flat_isomip_create.py
similarity index 100%
rename from test/Iceberg_repository/Scripts_and_analysis/flat_isomip_create.py
rename to tests/Iceberg_repository/Scripts_and_analysis/flat_isomip_create.py
diff --git a/test/Iceberg_repository/Scripts_and_analysis/grid_cartesian_create.py b/tests/Iceberg_repository/Scripts_and_analysis/grid_cartesian_create.py
similarity index 100%
rename from test/Iceberg_repository/Scripts_and_analysis/grid_cartesian_create.py
rename to tests/Iceberg_repository/Scripts_and_analysis/grid_cartesian_create.py
diff --git a/test/Iceberg_repository/Scripts_and_analysis/hexagon_area.py b/tests/Iceberg_repository/Scripts_and_analysis/hexagon_area.py
similarity index 100%
rename from test/Iceberg_repository/Scripts_and_analysis/hexagon_area.py
rename to tests/Iceberg_repository/Scripts_and_analysis/hexagon_area.py
diff --git a/test/Iceberg_repository/Scripts_and_analysis/hexagon_area.pyc b/tests/Iceberg_repository/Scripts_and_analysis/hexagon_area.pyc
similarity index 100%
rename from test/Iceberg_repository/Scripts_and_analysis/hexagon_area.pyc
rename to tests/Iceberg_repository/Scripts_and_analysis/hexagon_area.pyc
diff --git a/test/Iceberg_repository/Scripts_and_analysis/iceshelf_geometry_create.py b/tests/Iceberg_repository/Scripts_and_analysis/iceshelf_geometry_create.py
similarity index 100%
rename from test/Iceberg_repository/Scripts_and_analysis/iceshelf_geometry_create.py
rename to tests/Iceberg_repository/Scripts_and_analysis/iceshelf_geometry_create.py
diff --git a/test/Iceberg_repository/Scripts_and_analysis/iceshelf_mass_file_create.py b/tests/Iceberg_repository/Scripts_and_analysis/iceshelf_mass_file_create.py
similarity index 100%
rename from test/Iceberg_repository/Scripts_and_analysis/iceshelf_mass_file_create.py
rename to tests/Iceberg_repository/Scripts_and_analysis/iceshelf_mass_file_create.py
diff --git a/test/Iceberg_repository/Scripts_and_analysis/initialize_bergs_in_pattern.py b/tests/Iceberg_repository/Scripts_and_analysis/initialize_bergs_in_pattern.py
similarity index 100%
rename from test/Iceberg_repository/Scripts_and_analysis/initialize_bergs_in_pattern.py
rename to tests/Iceberg_repository/Scripts_and_analysis/initialize_bergs_in_pattern.py
diff --git a/test/Iceberg_repository/Scripts_and_analysis/movie_bergs_traj.py b/tests/Iceberg_repository/Scripts_and_analysis/movie_bergs_traj.py
similarity index 100%
rename from test/Iceberg_repository/Scripts_and_analysis/movie_bergs_traj.py
rename to tests/Iceberg_repository/Scripts_and_analysis/movie_bergs_traj.py
diff --git a/test/Iceberg_repository/Scripts_and_analysis/old_bergs_quickview.py b/tests/Iceberg_repository/Scripts_and_analysis/old_bergs_quickview.py
similarity index 100%
rename from test/Iceberg_repository/Scripts_and_analysis/old_bergs_quickview.py
rename to tests/Iceberg_repository/Scripts_and_analysis/old_bergs_quickview.py
diff --git a/test/Iceberg_repository/Scripts_and_analysis/quick_benchmark_comparison.sh b/tests/Iceberg_repository/Scripts_and_analysis/quick_benchmark_comparison.sh
similarity index 100%
rename from test/Iceberg_repository/Scripts_and_analysis/quick_benchmark_comparison.sh
rename to tests/Iceberg_repository/Scripts_and_analysis/quick_benchmark_comparison.sh
diff --git a/test/Iceberg_repository/Scripts_and_analysis/quick_plot.py b/tests/Iceberg_repository/Scripts_and_analysis/quick_plot.py
similarity index 100%
rename from test/Iceberg_repository/Scripts_and_analysis/quick_plot.py
rename to tests/Iceberg_repository/Scripts_and_analysis/quick_plot.py
diff --git a/test/Iceberg_repository/Scripts_and_analysis/submit_to_queue.sh b/tests/Iceberg_repository/Scripts_and_analysis/submit_to_queue.sh
similarity index 100%
rename from test/Iceberg_repository/Scripts_and_analysis/submit_to_queue.sh
rename to tests/Iceberg_repository/Scripts_and_analysis/submit_to_queue.sh
diff --git a/test/Iceberg_repository/Scripts_and_analysis/topog_file_create.py b/tests/Iceberg_repository/Scripts_and_analysis/topog_file_create.py
similarity index 100%
rename from test/Iceberg_repository/Scripts_and_analysis/topog_file_create.py
rename to tests/Iceberg_repository/Scripts_and_analysis/topog_file_create.py
diff --git a/test/Iceberg_repository/Scripts_and_analysis/variables_comparison.sh b/tests/Iceberg_repository/Scripts_and_analysis/variables_comparison.sh
similarity index 100%
rename from test/Iceberg_repository/Scripts_and_analysis/variables_comparison.sh
rename to tests/Iceberg_repository/Scripts_and_analysis/variables_comparison.sh
diff --git a/test/Iceberg_repository/Scripts_and_analysis/write_restart_iceberg.py b/tests/Iceberg_repository/Scripts_and_analysis/write_restart_iceberg.py
similarity index 100%
rename from test/Iceberg_repository/Scripts_and_analysis/write_restart_iceberg.py
rename to tests/Iceberg_repository/Scripts_and_analysis/write_restart_iceberg.py
diff --git a/test/Iceberg_repository/hexagon_area.py b/tests/Iceberg_repository/hexagon_area.py
similarity index 100%
rename from test/Iceberg_repository/hexagon_area.py
rename to tests/Iceberg_repository/hexagon_area.py
diff --git a/test/Iceberg_repository/setup_ISOMIP_calving.sh b/tests/Iceberg_repository/setup_ISOMIP_calving.sh
similarity index 100%
rename from test/Iceberg_repository/setup_ISOMIP_calving.sh
rename to tests/Iceberg_repository/setup_ISOMIP_calving.sh
diff --git a/tests/collision_test/README b/tests/collision_test/README
new file mode 100644
index 0000000..83093c2
--- /dev/null
+++ b/tests/collision_test/README
@@ -0,0 +1,5 @@
+1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
+2.(optional) edit input.nml
+3. run the model: ./RUN
+4, animate the results: animate_trajectories.py
+
diff --git a/tests/collision_test/RUN b/tests/collision_test/RUN
new file mode 100755
index 0000000..6330154
--- /dev/null
+++ b/tests/collision_test/RUN
@@ -0,0 +1,4 @@
+rm iceberg_trajectories.nc
+srun -n4 ./../../build/bergs.x
+
+
diff --git a/test/animate_trajectories.py b/tests/collision_test/animate_trajectories.py
similarity index 92%
rename from test/animate_trajectories.py
rename to tests/collision_test/animate_trajectories.py
index 7367b6d..3cb36be 100755
--- a/test/animate_trajectories.py
+++ b/tests/collision_test/animate_trajectories.py
@@ -55,7 +55,7 @@ def onClick(event):
 movie_len = 5.0 #seconds
 frame_len = 1000.0*movie_len/num_frames
 
-smax = max(max(x),max(y),200)
+smax = max(max(x),max(y),20)
 xmin = 0.0
 xmax = smax
 ymin = 0.0
@@ -66,9 +66,11 @@ def onClick(event):
 f = plt.figure(figsize=(5,5))
 f.tight_layout()
 ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
-scat = ax1.scatter([],[],marker='H',facecolor='w',s=140,edgecolor='red')
+scat = ax1.scatter([],[],marker='o',facecolor='w',s=110,edgecolor='red')
 time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
 
+ax1.set_xticks(np.arange(0, xmax+1, 1)) 
+ax1.set_yticks(np.arange(0, ymax+1, 1)) 
 ax1.set_xlabel('x (km)')
 ax1.set_ylabel('y (km)')
 ax1.set_title('Iceberg trajectory')
@@ -82,6 +84,7 @@ def onClick(event):
 
 print('time',t)
 
+plt.grid()
 plt.show()
 
 #animation.save("iceberg_traj_animation.mp4")
diff --git a/test/diag_table b/tests/collision_test/diag_table
similarity index 100%
rename from test/diag_table
rename to tests/collision_test/diag_table
diff --git a/tests/collision_test/input.nml b/tests/collision_test/input.nml
new file mode 100644
index 0000000..539b16d
--- /dev/null
+++ b/tests/collision_test/input.nml
@@ -0,0 +1,156 @@
+!TARGET CHKSUM:
+!Total number of bonds is:           52 
+!KID, bergs_chksum: write_restart berg chksum = 892128108  chksum2= -515180265  chksum3= 1707263945  chksum4= 1707263945  chksum5 = 0           #= 16
+!KID, grd_chksum2 : # of bergs/cell chksum    = 0          chksum2= 0           min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
+!KID, grd_chksum3 : write stored_ice chksum   = -540079793 chksum2= -1237287029 min= 6.393358811E+05 max= 7.380127765E+11 mean= 8.033602570E+10 rms= 1.613270384E+11 sd= 1.399018810E+11
+!KID, grd_chksum2 : write stored_heat chksum  = 0          chksum2= 0           min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
+
+
+&icebergs_driver_nml
+  ni=20 !number of elements, x direction
+  nj=20 !number of elements, y direction
+  ibdt=10.0 !seconds
+  ibuo=0.2 !ocean x velocity
+  ibvo=0.2 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=48 !total simulation hours
+  nmax=99999999 !max number of timesteps
+  saverestart=.true. 
+  halo=4
+  debug=.false.  
+  collision_test=.true. !specific to the current test, must be true here
+/
+
+
+&icebergs_nml
+
+    !defaults given in parentheses:
+
+    halo=4 !(4) halo width
+    Lx=20000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.True. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move    
+    
+    rho_bergs=850. ! (850) iceberg density
+    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs= 0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs =  1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0.4 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #) 
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. ! (T) Allows bergs toroll over when rolling conditions are met    
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.False. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)    
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread			
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.False. !(F)Bergs only feel interactive forces, not ocean, wind...    
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val    
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors    
+
+    verbose=.true. !(F) Be verbose to stderr
+    verbose_hrs=1 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !(24) sampling period for trajectory storage
+    traj_write_hrs=480 ! (480) Period for writing sampled trajectories to disk    
+    budget=.true. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1 !12884902036 ! If positive, monitors a berg with this id    
+    
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.True. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.False. ! (F) If true, then model does not traj trajectory data at all    
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart 
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually    
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir = 'INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.    
+    do_unit_tests=.true. ! (F) Conduct some unit tests    
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+    
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+    
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+    
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+    
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+ 
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/collision_test/makeberg/RUN b/tests/collision_test/makeberg/RUN
new file mode 100755
index 0000000..0863960
--- /dev/null
+++ b/tests/collision_test/makeberg/RUN
@@ -0,0 +1,12 @@
+./makeberg.py
+
+rm ./output_files/Generic*
+
+./../../Iceberg_repository/Scripts_and_analysis/initialize_bergs_in_pattern.py \
+	-set_all_bergs_static_by_default=False -Run_plotting_subroutine=False \
+	-break_some_bonds=False -Ice_geometry_source='Generic' \
+	-Generic_ice_geometry_filename='./testtabularberg.nc' \
+	-ISOMIP_reduced=False \
+
+cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
+cp ./output_files/Generic_bonds_iceberg.res.nc ./../INPUT/bonds_iceberg.res.nc
\ No newline at end of file
diff --git a/test/Iceberg_repository/testberg/testberg.py b/tests/collision_test/makeberg/makeberg.py
similarity index 81%
rename from test/Iceberg_repository/testberg/testberg.py
rename to tests/collision_test/makeberg/makeberg.py
index 10d6a92..ff4c853 100755
--- a/test/Iceberg_repository/testberg/testberg.py
+++ b/tests/collision_test/makeberg/makeberg.py
@@ -11,7 +11,8 @@
 nx = 20
 ny = 20
 New_ice_thickness_filename='testberg.nc'
-grid_area = 10.e3*10.e3 #10 km grid res
+grid_res = 1.e3 #1 km 
+grid_area = grid_res * grid_res
 h_ice = 300.0
 
 New_ice_thickness_filename='testtabularberg.nc'
@@ -41,28 +42,32 @@
 g.variables['area'][:,:]=grid_area
 
 #create a circular tabular berg centered on the following coords (km)
-cx = 60.e3
-cy = 60.e3
+cy = 4.5e3
+cx = 4.5e3
+cx2 = 15.5e3
 
 for i in range(nx):
 
-        tx = float(i) * 10.e3
+        tx = float(i) * grid_res
         g.variables['lon'][i] = tx
         
         for j in range(ny):
                
-                ty = float(j) * 10.e3
+                ty = float(j) * grid_res
                 dist = sqrt((tx-cx)*(tx-cx) + (ty-cy)*(ty-cy))
+                dist2 =  sqrt((tx-cx2)*(tx-cx2) + (ty-cy)*(ty-cy))
                 #g.variables['lon'][i,j] = tx
                 #g.variables['lat'][i,j] = ty
         
-                if (dist < 50.e3):
+                if (dist <1.e3 or dist2<1.e3):
                         g.variables['thick'][i,j]=h_ice
                 else:
                         g.variables['thick'][i,j]=0.0
 
+                        
+
 for j in range(ny):
-        g.variables['lat'][j] = float(j) * 10.e3
+        g.variables['lat'][j] = float(j) * grid_res
 
 print('Creating file: ' , New_ice_thickness_filename)
 

From 2891feba7af50e0e9c1660c136df98c8ab759e90 Mon Sep 17 00:00:00 2001
From: Niki Zadeh <niki.zadeh@noaa.gov>
Date: Wed, 26 Aug 2020 11:16:58 -0400
Subject: [PATCH 252/361] Fix with mpp_sync_self rather than global vars

- This still fixes issue #62
- This fix uses mpp_sync_self to wait for all processes before exiting
the subroutine.
- The fix was originally suggested by Rusty Benson.
- If this issue ever surfaces again I recommend going back to the
  global vars solution.
- Also note that the mpp tags used in this module are not unique across
  the components. In particular land model uses the same tags!
---
 icebergs_io.F90 | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 7128951..e92c4a2 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -8,7 +8,7 @@ module ice_bergs_io
 use mpp_domains_mod, only: mpp_get_tile_pelist,mpp_get_tile_npes,mpp_get_io_domain,mpp_get_tile_id
 
 use mpp_mod, only: mpp_npes, mpp_pe, mpp_root_pe, mpp_sum, mpp_min, mpp_max, NULL_PE
-use mpp_mod, only: mpp_send, mpp_recv, mpp_gather, mpp_chksum
+use mpp_mod, only: mpp_send, mpp_recv, mpp_gather, mpp_chksum, mpp_sync_self
 use mpp_mod, only: COMM_TAG_11, COMM_TAG_12, COMM_TAG_13, COMM_TAG_14
 
 use fms_mod, only: stdlog, stderr, error_mesg, FATAL, WARNING, NOTE
@@ -58,7 +58,6 @@ module ice_bergs_io
 integer, save :: io_tile_id(1), io_tile_root_pe, io_npes
 integer, allocatable,save :: io_tile_pelist(:)
 logical :: is_io_tile_root_pe = .true.
-integer :: ntrajs_sent_io,ntrajs_rcvd_io
 
 integer :: clock_trw,clock_trp
 
@@ -1259,6 +1258,7 @@ subroutine write_trajectory(trajectory, save_short_traj)
 integer :: from_pe,np
 type(buffer), pointer :: obuffer_io=>null(), ibuffer_io=>null()
 logical :: io_is_in_append_mode
+integer :: ntrajs_sent_io,ntrajs_rcvd_io
 
   ! Get the stderr unit number
   stderrunit=stderr()
@@ -1315,7 +1315,7 @@ subroutine write_trajectory(trajectory, save_short_traj)
         call mpp_send(obuffer_io%data, ntrajs_sent_io*buffer_width_traj, to_pe=io_tile_root_pe, tag=COMM_TAG_12)
      endif
   endif
-
+  call mpp_sync_self()
   endif !.NOT. force_all_pes_traj
 
   call mpp_clock_end(clock_trp)

From 73694cdba62324dad6c7ee625dd908f0a844f9aa Mon Sep 17 00:00:00 2001
From: Niki Zadeh <niki.zadeh@noaa.gov>
Date: Wed, 26 Aug 2020 11:16:58 -0400
Subject: [PATCH 253/361] Fix with mpp_sync_self rather than global vars

- This still fixes issue #62
- This fix uses mpp_sync_self to wait for all processes before exiting
the subroutine.
- The fix was originally suggested by Rusty Benson.
- If this issue ever surfaces again I recommend going back to the
  global vars solution.
- Also note that the mpp tags used in this module are not unique across
  the components. In particular land model uses the same tags!
---
 icebergs_io.F90 | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/icebergs_io.F90 b/icebergs_io.F90
index 7128951..e92c4a2 100644
--- a/icebergs_io.F90
+++ b/icebergs_io.F90
@@ -8,7 +8,7 @@ module ice_bergs_io
 use mpp_domains_mod, only: mpp_get_tile_pelist,mpp_get_tile_npes,mpp_get_io_domain,mpp_get_tile_id
 
 use mpp_mod, only: mpp_npes, mpp_pe, mpp_root_pe, mpp_sum, mpp_min, mpp_max, NULL_PE
-use mpp_mod, only: mpp_send, mpp_recv, mpp_gather, mpp_chksum
+use mpp_mod, only: mpp_send, mpp_recv, mpp_gather, mpp_chksum, mpp_sync_self
 use mpp_mod, only: COMM_TAG_11, COMM_TAG_12, COMM_TAG_13, COMM_TAG_14
 
 use fms_mod, only: stdlog, stderr, error_mesg, FATAL, WARNING, NOTE
@@ -58,7 +58,6 @@ module ice_bergs_io
 integer, save :: io_tile_id(1), io_tile_root_pe, io_npes
 integer, allocatable,save :: io_tile_pelist(:)
 logical :: is_io_tile_root_pe = .true.
-integer :: ntrajs_sent_io,ntrajs_rcvd_io
 
 integer :: clock_trw,clock_trp
 
@@ -1259,6 +1258,7 @@ subroutine write_trajectory(trajectory, save_short_traj)
 integer :: from_pe,np
 type(buffer), pointer :: obuffer_io=>null(), ibuffer_io=>null()
 logical :: io_is_in_append_mode
+integer :: ntrajs_sent_io,ntrajs_rcvd_io
 
   ! Get the stderr unit number
   stderrunit=stderr()
@@ -1315,7 +1315,7 @@ subroutine write_trajectory(trajectory, save_short_traj)
         call mpp_send(obuffer_io%data, ntrajs_sent_io*buffer_width_traj, to_pe=io_tile_root_pe, tag=COMM_TAG_12)
      endif
   endif
-
+  call mpp_sync_self()
   endif !.NOT. force_all_pes_traj
 
   call mpp_clock_end(clock_trp)

From ecaf44e6539ade7a7ce08fe24e699838f381c621 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Thu, 24 Sep 2020 18:49:46 -0400
Subject: [PATCH 254/361] added mts velocity verlet scheme to increase time
 step size, which includes a routine to pass whole conglomerate bergs between
 processors. Added separate spring constant for collisions and an option to
 vary the distance at which contact between bergs occurs. New test cases.

---
 driver/icebergs_driver.F90                    |   58 +-
 src/icebergs.F90                              |  690 +++++++--
 src/icebergs_framework.F90                    | 1239 ++++++++++++++++-
 src/icebergs_io.F90                           |   31 +-
 tests/.gitignore                              |    5 +-
 tests/2p_collision_test/README                |    5 +
 tests/2p_collision_test/RUN                   |    5 +
 tests/2p_collision_test/RUN1p                 |    5 +
 .../2p_collision_test/animate_trajectories.py |  158 +++
 .../animate_trajectories_1pe.py               |  175 +++
 tests/2p_collision_test/diag_table            |    3 +
 tests/2p_collision_test/input.nml             |  165 +++
 tests/2p_collision_test/makeberg/RUN          |   13 +
 tests/2p_collision_test/makeberg/makeberg.py  |   77 +
 .../initialize_bergs_in_pattern.py            |   63 +-
 tests/collision_test/RUN                      |    1 +
 tests/collision_test/RUN1p                    |    5 +
 tests/collision_test/RUN_tstest.sh            |   33 +
 tests/collision_test/animate_trajectories.py  |  190 +--
 .../animate_trajectories_1pe.py               |  175 +++
 tests/collision_test/input.nml                |   45 +-
 tests/collision_test/input_tstest.nml         |  151 ++
 tests/collision_test/makeberg/RUN             |    2 +-
 tests/collision_test/makeberg/makeberg.py     |   12 +-
 tests/collision_test_mts/README               |    5 +
 tests/collision_test_mts/RUN                  |    5 +
 tests/collision_test_mts/RUN1p                |    5 +
 tests/collision_test_mts/RUN_tstest.sh        |   33 +
 .../animate_trajectories.py                   |  129 ++
 .../animate_trajectories_1pe.py               |  175 +++
 tests/collision_test_mts/diag_table           |    3 +
 tests/collision_test_mts/input.nml            |  158 +++
 tests/collision_test_mts/input_tstest.nml     |  159 +++
 tests/collision_test_mts/makeberg/RUN         |   12 +
 tests/collision_test_mts/makeberg/makeberg.py |   77 +
 35 files changed, 3728 insertions(+), 339 deletions(-)
 create mode 100644 tests/2p_collision_test/README
 create mode 100755 tests/2p_collision_test/RUN
 create mode 100755 tests/2p_collision_test/RUN1p
 create mode 100755 tests/2p_collision_test/animate_trajectories.py
 create mode 100755 tests/2p_collision_test/animate_trajectories_1pe.py
 create mode 100644 tests/2p_collision_test/diag_table
 create mode 100644 tests/2p_collision_test/input.nml
 create mode 100755 tests/2p_collision_test/makeberg/RUN
 create mode 100755 tests/2p_collision_test/makeberg/makeberg.py
 create mode 100755 tests/collision_test/RUN1p
 create mode 100755 tests/collision_test/RUN_tstest.sh
 create mode 100755 tests/collision_test/animate_trajectories_1pe.py
 create mode 100644 tests/collision_test/input_tstest.nml
 create mode 100644 tests/collision_test_mts/README
 create mode 100755 tests/collision_test_mts/RUN
 create mode 100755 tests/collision_test_mts/RUN1p
 create mode 100755 tests/collision_test_mts/RUN_tstest.sh
 create mode 100755 tests/collision_test_mts/animate_trajectories.py
 create mode 100755 tests/collision_test_mts/animate_trajectories_1pe.py
 create mode 100644 tests/collision_test_mts/diag_table
 create mode 100644 tests/collision_test_mts/input.nml
 create mode 100644 tests/collision_test_mts/input_tstest.nml
 create mode 100755 tests/collision_test_mts/makeberg/RUN
 create mode 100755 tests/collision_test_mts/makeberg/makeberg.py

diff --git a/driver/icebergs_driver.F90 b/driver/icebergs_driver.F90
index ff24237..5c88fcf 100644
--- a/driver/icebergs_driver.F90
+++ b/driver/icebergs_driver.F90
@@ -62,11 +62,12 @@ program icebergs_driver
   real :: ibvo=0.0
   real :: ibui=0.0
   real :: ibvi=0.0
-  real :: gridres
+  real :: gridres=1.e3
   integer :: ibhrs=2
   integer :: nmax = 2000000000 !<max number of iterations    
   namelist /icebergs_driver_nml/ debug, ni, nj, halo, ibhrs, ibdt, ibuo, ibvo, nmax, &
-       saverestart,ibui,ibvi,collision_test
+       saverestart,ibui,ibvi,collision_test,gridres
+  real :: time_begin, time_finish
   ! For loops
   integer :: isc !< Start of i-index for computational domain (used for loops)
   integer :: iec !< End of i-index for computational domain (used for loops)
@@ -109,6 +110,8 @@ program icebergs_driver
   real, dimension(:,:), pointer  :: ustar_berg !< Friction velocity on base of bergs (m/s)
   real, dimension(:,:), pointer :: area_berg !< Area of bergs (m2)
 
+  call cpu_time(time_begin)
+  
   ! Boot FMS
   call fms_init()
 
@@ -172,7 +175,6 @@ program icebergs_driver
   allocate( sin_rot(isd:ied,jsd:jed) )
   allocate( depth(isd:ied,jsd:jed) )
 
-  gridres = 1.e3
 
 
   do j = jsd, jed
@@ -182,11 +184,7 @@ program icebergs_driver
         dx(i,j) = gridres
         dy(i,j) = gridres
         area(i,j) = gridres*gridres
-        ! if (j>18.0 .or. j < 2.0) then
-        !    wet(i,j)=0.0
-        ! else
         wet(i,j) = 1.0
-        ! end if
         cos_rot(i,j) = 1.0 
         sin_rot(i,j) = 0.0
         depth(i,j) = 1000.
@@ -232,14 +230,35 @@ program icebergs_driver
   hi = 0.0 !sea-ice thickness (m)
   calving_hflx = 0.0 !calving heat flux (W/m2)
 
+  ! if (collision_test) then
+  !   do j = jsd,jed
+  !     if (j>10) then
+  !       vo(:,j) = -ibvo
+  !     elseif (j==10) then
+  !       vo(:,j) = 0.
+  !     else
+  !       vo(:,j) = ibvo
+  !     endif
+  !   enddo
+  !   do i = isd,ied
+  !      if (i>10) vo(i,:) = 0.0
+  !   enddo
+  ! end if
+
   if (collision_test) then
-    do j = jsc,jec
-       if (j>10) vo = -ibvo
-    enddo
-    do i = isc,iec
-       if (i>10) vo = 0.0
-    enddo
-  end if
+    do j=jsd,jed; do i=isd,ied
+      if (lon(i,j)>10.e3 .or. lon(i,j)<=0.0 .or. lat(i,j)==10.e3) then
+        vo(i,j)=0.0
+      else
+        if (lat(i,j)>10.e3) then
+          vo(i,j)=-ibvo
+        else
+          vo(i,j)=ibvo
+        endif
+      endif
+    enddo;enddo
+  endif
+  
 
   ! optional:
   ! allocate( sss(isd:ied,jsd:jed) )
@@ -284,11 +303,6 @@ program icebergs_driver
      ! call icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh, sst, &
      ! calving_hflx, cn, hi,stagger, stress_stagger, sss, mass_berg, ustar_berg, area_berg)       
 
-     ! if (ns == 1) then
-     !    calving = 0.0
-     ! endif
-
-
      Time = Time + real_to_time_type(dt)
      ns = ns+1
   enddo
@@ -298,4 +312,10 @@ program icebergs_driver
   !Deallocate all memory and disassociated pointer
   call icebergs_end(bergs)
 
+  call cpu_time(time_finish)
+
+  if (mpp_pe()==0) then
+     write(*,*) 'Simulation finished in ', (time_finish - time_begin)/60., 'minutes'
+  end if
+
 end program icebergs_driver
diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 4328479..8d38623 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -44,6 +44,7 @@ module ice_bergs
 use ice_bergs_framework, only: is_point_within_xi_yj_bounds
 use ice_bergs_framework, only: test_check_for_duplicate_ids_in_list
 use ice_bergs_framework, only: generate_id
+use ice_bergs_framework, only: update_latlon
 
 use ice_bergs_io,        only: ice_bergs_io_init, write_restart, write_trajectory
 use ice_bergs_io,        only: read_restart_bergs, read_restart_calving
@@ -368,7 +369,7 @@ subroutine initialize_iceberg_bonds(bergs)
             r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) )
 
             ! If the bergs are closer than bergs%length_for_manually_initialize_bonds, then form a bond -Alex
-            if (r_dist.lt.bergs%length_for_manually_initialize_bonds) then  
+            if (r_dist.lt.bergs%length_for_manually_initialize_bonds) then
               call form_a_bond(berg, other_berg%id, other_berg%ine, other_berg%jne, other_berg)
             endif
           endif
@@ -417,9 +418,10 @@ subroutine  convert_from_meters_to_grid(lat_ref,grid_is_latlon ,dlon_dx,dlat_dy)
 
 end subroutine convert_from_meters_to_grid
 
+
 !> Calculates interactions between a berg and all bergs in range
 subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
-                             P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y)
+  P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
   type(iceberg), pointer :: berg !< Primary iceberg
@@ -443,7 +445,9 @@ subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
   integer :: grdi, grdj
   logical :: iceberg_bonds_on
   logical :: bonded
+  integer :: nc
 
+  nc=bergs%num_contact_cells
   iceberg_bonds_on=bergs%iceberg_bonds_on
 
   IA_x=0.
@@ -451,36 +455,111 @@ subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
   P_ia_11=0. ; P_ia_12=0. ;  P_ia_21=0.;  P_ia_22=0.
   P_ia_times_u_x=0. ; P_ia_times_u_y=0.
 
-  bonded=.false. ! Unbonded iceberg interactions
-  do grdj = berg%jne-1,berg%jne+1 ; do grdi = berg%ine-1,berg%ine+1 ! Note: need to make sure this is wide enough, but less than the halo width
-    other_berg=>bergs%list(grdi,grdj)%first
-    do while (associated(other_berg)) ! loop over all other bergs
-      call calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1, &
-                           P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y, bonded)
-      other_berg=>other_berg%next
-    enddo ! loop over all bergs
-  enddo ; enddo
+  if (bergs%mts .or. (bergs%contact_distance>0.) .or. (bergs%contact_spring_coef .ne. bergs%spring_coef) ) then
+
+    ! Interactions for bonded berg elements only. For the mts scheme, this is only called if mts_part==3
+    if ( (.not. bergs%mts) .or. (bergs%mts .and. bergs%mts_part .eq. 3)) then
+      bonded=.true. 
+      if (iceberg_bonds_on) then 
+        current_bond=>berg%first_bond
+        do while (associated(current_bond)) ! loop over all bonds
+          other_berg=>current_bond%other_berg
+          if (.not. associated(other_berg)) then
+            call error_mesg('KID,bond interactions', 'Trying to do Bond interactions with unassosiated berg!' ,FATAL)
+          else
+            call calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,  &
+              P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded)
+          endif
+          current_bond=>current_bond%next_bond
+        enddo
+      endif
+    endif
+
+    ! Interactions for non-bonded berg elements only. For the mts scheme, this is only called if mts_part==1
+    if (.not. (bergs%mts .and. bergs%mts_part .eq. 3)) then
+      bonded=.false. ! Interactions for non-bonded berg elements
+      call mark_conglomerate_bergs(berg,1)
+      berg%id=abs(berg%id)
+      do grdj = max(berg%jne-nc,bergs%grd%jsd+1),min(berg%jne+nc,bergs%grd%jed);&
+        do grdi = max(berg%ine-nc,bergs%grd%isd+1),min(berg%ine+nc,bergs%grd%ied)
+
+        other_berg=>bergs%list(grdi,grdj)%first
+        do while (associated(other_berg)) ! loop over all other bergs
+          if (other_berg%id>0) then !no bond with other_berg
+            call calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,  &
+              P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded)
+          endif
+          other_berg=>other_berg%next
+        enddo
+      enddo; enddo
+      call mark_conglomerate_bergs(berg,2)
+    endif
+
+  else
+    !Alon's original code, only usuable for simulations WITHOUT MTS Verlet, a specified contact_distance,
+    !or a separate spring constant for collision. 
+    bonded=.false. ! 'Unbonded' iceberg interactions (here, not to be taken literally)
+    do grdj = berg%jne-1,berg%jne+1 ; do grdi = berg%ine-1,berg%ine+1
+      other_berg=>bergs%list(grdi,grdj)%first
+      do while (associated(other_berg)) ! loop over all other bergs
+        call calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1, &
+          P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y, bonded)
+        other_berg=>other_berg%next
+      enddo ! loop over all bergs
+    enddo; enddo
+
+    bonded=.true. ! Interactions due to iceberg bonds
+    if (iceberg_bonds_on) then ! MP1
+      current_bond=>berg%first_bond
+      do while (associated(current_bond)) ! loop over all bonds
+        other_berg=>current_bond%other_berg
+        if (.not. associated(other_berg)) then
+          call error_mesg('KID,bond interactions', 'Trying to do Bond interactions with unassosiated berg!' ,FATAL)
+        else
+          call calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,  &
+            P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded)
+        endif
+        current_bond=>current_bond%next_bond
+      enddo
+    endif
+  endif
+end subroutine interactive_force
 
-  bonded=.true. ! Interactions due to iceberg bonds
-  if (iceberg_bonds_on) then ! MP1
+!> Marks conglomerate icebergs with negative their id
+recursive subroutine mark_conglomerate_bergs(berg,mark_or_unmark)
+  type(iceberg), pointer :: berg
+  type(iceberg), pointer :: other_berg
+  type(bond) , pointer :: current_bond
+  integer :: mark_or_unmark
+
+  if (mark_or_unmark==1) then
+    if (berg%id>0) berg%id=-berg%id
     current_bond=>berg%first_bond
-    do while (associated(current_bond)) ! loop over all bonds
-      other_berg=>current_bond%other_berg
-      if (.not. associated(other_berg)) then
-        call error_mesg('KID,bond interactions', 'Trying to do Bond interactions with unassosiated berg!' ,FATAL)
-      else
-        call calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,  &
-                             P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded)
-      endif
+    do while (associated(current_bond))
+      if  (associated(current_bond%other_berg)) then
+        other_berg=>current_bond%other_berg
+        if (other_berg%id>0) then
+          call mark_conglomerate_bergs(other_berg,1)
+        end if
+      end if
+      current_bond=>current_bond%next_bond
+    enddo
+  else
+    if (berg%id<0) berg%id=-berg%id
+    current_bond=>berg%first_bond
+    do while (associated(current_bond))
+      if  (associated(current_bond%other_berg)) then
+        other_berg=>current_bond%other_berg
+        if (other_berg%id<0) then
+          call mark_conglomerate_bergs(other_berg,2)
+        end if
+      end if
       current_bond=>current_bond%next_bond
     enddo
   endif
+  
+end subroutine mark_conglomerate_bergs
 
-  !print *,'IA_x=',IA_x,'IA_y',IA_y, berg%id
-  !print *,'P_ia_11',P_ia_11,'P_ia_12',P_ia_12, 'P_ia_21',P_ia_21,'P_ia_22', P_ia_22
-  !print *, 'P_ia_times_u_x', P_ia_times_u_x, 'P_ia_times_u_y', P_ia_times_u_y
-
-end subroutine interactive_force
 
 !> Calculate interactive forces between two bergs
 subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1, &
@@ -493,8 +572,10 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
   real, intent(inout) :: IA_y !< Net meridional acceleration of berg due to interactions (m/s2)
   real, intent(in) :: u0 !< Zonal velocity of primary berg (m/s)
   real, intent(in) :: v0 !< Meridional velocity of primary berg (m/s)
-  real, intent(in) :: u1 !< Zonal velocity of other berg (m/s)
-  real, intent(in) :: v1 !< Meridional velocity of other berg (m/s)
+  
+  !u1 and v1: actually, also vel for primary berg, but might be updated vel if runge-kutta? -Alex
+  real, intent(in) :: u1 !< Zonal velocity of other berg (m/s) 
+  real, intent(in) :: v1 !< Meridional velocity of other berg (m/s) 
   real, intent(inout) :: P_ia_11
   real, intent(inout) :: P_ia_12
   real, intent(inout) :: P_ia_22
@@ -511,20 +592,9 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
   real :: M1, M2, M_min
   real :: u2, v2
   real :: lat_ref, dx_dlon, dy_dlat
-  logical :: critical_interaction_damping_on
+  logical :: critical_interaction_damping_on,tbonded
   real :: spring_coef, accel_spring, radial_damping_coef, p_ia_coef, tangental_damping_coef, bond_coef
-
-  spring_coef=bergs%spring_coef
-  !bond_coef=bergs%bond_coef
-  radial_damping_coef=bergs%radial_damping_coef
-  tangental_damping_coef=bergs%tangental_damping_coef
-  critical_interaction_damping_on=bergs%critical_interaction_damping_on
-
-  ! Using critical values for damping rather than manually setting the damping.
-  if (critical_interaction_damping_on) then
-    radial_damping_coef=2.*sqrt(spring_coef) ! Critical damping
-    tangental_damping_coef=(2.*sqrt(spring_coef))/4 ! Critical damping (just a guess)
-  endif
+  real :: crit_dist
 
   if (berg%id .ne. other_berg%id) then
     ! From Berg 1
@@ -548,7 +618,7 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
 
     !call rotpos_to_tang(lon2,lat2,x2,y2)
 
-    dlon=lon1-lon2
+    dlon=lon1-lon2 
     dlat=lat1-lat2
 
     ! Note that this is not the exact distance along a great circle.
@@ -560,12 +630,13 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
 
     r_dist_x=dlon*dx_dlon
     r_dist_y=dlat*dy_dlat
-    r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) )
+    r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) ) !(Stern et al 2017, Eqn 3)
 
+    !Stern et al 2017, Eqn 4: radius of circle inscribed within hexagon or square with area A1 or A2 
     if (bergs%hexagonal_icebergs) then
-      R1=sqrt(A1/(2.*sqrt(3.)))
+      R1=sqrt(A1/(2.*sqrt(3.)))  
       R2=sqrt(A2/(2.*sqrt(3.)))
-    else !square packing
+    else !square packing 
       R1=sqrt(A1/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
       R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
     endif
@@ -579,32 +650,51 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
     ! print *, 'outside the loop',R1, R2,r_dist, bonded
     !!!!!!!!!!!!!!!!!!!!!!!!!!!debugging!!!!!!!!!!!!!!!!!!!!!!!!!!
 
-
     !call overlap_area(R1,R2,r_dist,A_o,trapped)
     !T_min=min(T1,T2)
     !A_min = min((pi*R1**R1),(pi*R2*R2))
     M_min=min(M1,M2)
-    !Calculating spring force  (later this should only be done on the first time around)
-    if ((r_dist>0.) .AND. ((r_dist< (R1+R2).AND. (.not. bonded)) .OR. ( (r_dist> (R1+R2)) .AND. (bonded) ) )) then
-      ! Spring force
+    
+    !Calculating spring force (Stern et al 2017, Eqn 6):
+    if (bonded) then
+      crit_dist=R1+R2 !Stern et al 2017, Eqn 5
+      spring_coef=bergs%spring_coef
+    else
+      crit_dist=max(R1+R2,bergs%contact_distance)
+      spring_coef=bergs%contact_spring_coef
+    end if
+  
+    radial_damping_coef=bergs%radial_damping_coef
+    tangental_damping_coef=bergs%tangental_damping_coef
+    critical_interaction_damping_on=bergs%critical_interaction_damping_on
+
+    ! Using critical values for damping rather than manually setting the damping.
+    if (critical_interaction_damping_on) then
+      radial_damping_coef=2.*sqrt(spring_coef) ! Critical damping
+      tangental_damping_coef=(2.*sqrt(spring_coef))/4 ! Critical damping (just a guess)
+    endif
+
+    tbonded=bonded
+    if (bonded .and. .not. (bergs%mts .or. (bergs%contact_distance>0.) .or. &
+      (bergs%contact_spring_coef .ne. bergs%spring_coef) )) then
+      if (.not. (r_dist>crit_dist)) tbonded=.false.
+    endif
+
+
+    if  ((r_dist>0.) .and. ( tbonded .or. (r_dist<crit_dist .and. .not. bonded) )) then
+      
+      !Spring force (Stern et al 2017, Eqn 7):
       !accel_spring=spring_coef*(T_min/T1)*(A_o/A1) ! Old version dependent on area
-      accel_spring=spring_coef*(M_min/M1)*(R1+R2-r_dist)
+      accel_spring=spring_coef*(M_min/M1)*(crit_dist-r_dist)
       IA_x=IA_x+(accel_spring*(r_dist_x/r_dist))
       IA_y=IA_y+(accel_spring*(r_dist_y/r_dist))
 
-
       if (r_dist < 5*(R1+R2)) then
 
-        !MP1
-        !if (berg%id .eq. 1) then
-        !  !print *,  '************************************************************'
-        !  print *, 'INSIDE, r_dist', berg%id, other_berg%id, r_dist, bonded
-        !endif
-        !print *, 'in the loop1', spring_coef, (M_min/M1), accel_spring,(R1+R2-r_dist)
-        !print *, 'in the loop2', IA_x, IA_y, R1, R2,r_dist, berg%id,other_berg%id
-        ! Damping force:
+        ! Damping force (Stern et al 2017, Eqn 8):
         ! Paralel velocity
-        P_11=(r_dist_x*r_dist_x)/(r_dist**2)
+        !projection matrix in Stern et al 2017, Eqn 8:
+        P_11=(r_dist_x*r_dist_x)/(r_dist**2) 
         P_12=(r_dist_x*r_dist_y)/(r_dist**2)
         P_21=(r_dist_x*r_dist_y)/(r_dist**2)
         P_22=(r_dist_y*r_dist_y)/(r_dist**2)
@@ -740,18 +830,27 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
     use_new_predictive_corrective=.True.
   endif
 
-  !print *, 'axn=',axn,'ayn=',ayn
+  
   u_star=uvel0+(axn*(dt/2.))  !Alon
   v_star=vvel0+(ayn*(dt/2.))  !Alon
 
+
   ! Get the stderr unit number.
   stderrunit = stderr()
 
   ! For convenience
   grd=>bergs%grd
 
-  ! Interpolate gridded fields to berg     - Note: It should be possible to move this to evolve, so that it only needs to be called once. !!!!
-  call interp_flds(grd, i, j, xi, yj, rx, ry, uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, sss, cn, hi)
+  ! Interpolate gridded fields to berg 
+  if (bergs%mts) then
+    !dummy values for MTS scheme halo bergs (this should only occur during berg%mts_part==3,
+    !when bergs%only_interactive_forces=.true., and therefore should have no effect)
+    uo=berg%uo; vo=berg%vo; ua=berg%ua; va=berg%va; ui=berg%ui; vi=berg%vi;
+    ssh_x=berg%ssh_x; ssh_y=berg%ssh_y; sst=berg%sst; sss=berg%sss;  cn=berg%cn; hi=berg%hi
+  else
+    call interp_flds(grd, i, j, xi, yj, rx, ry, uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, sss, cn, hi)
+  end if
+  
 
   if ((grd%grid_is_latlon) .and. (.not. bergs%use_f_plane)) then
      f_cori=(2.*omega)*sin(pi_180*lat)
@@ -776,7 +875,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
   hi=min(hi,D)
   D_hi=max(0.,D-hi)
 
-  ! Wave radiation
+  ! Wave radiation (Stern et al 2017, Eqs A4-A5)
   uwave=ua-uo; vwave=va-vo  ! Use wind speed rel. to ocean for wave model (aja)?
   wmod=uwave*uwave+vwave*vwave ! The wave amplitude and length depend on the wind speed relative to the ocean current
                                ! actually wmod is wmod**2 here.
@@ -796,7 +895,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
     uwave=0.; vwave=0.; wave_rad=0. ! ... and only when wind is present.
   endif
 
-  ! Weighted drag coefficients
+  ! Weighted drag coefficients (Stern et al 2017, Eqs A1-A3)
   c_ocn=rho_seawater/M*(0.5*Cd_wv*W*(D_hi)+Cd_wh*W*L)
   c_atm=rho_air     /M*(0.5*Cd_av*W*F     +Cd_ah*W*L)
   if (abs(hi).eq.0.) then
@@ -811,6 +910,10 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
 !c_atm=0.
 !c_ice=0.
 
+  ! Stern et al 2017, explicit accel due to
+  ! sea surface slope and wave radiation force
+  ! (forces F_R and F_SS, respectively, in Eq. 1.
+  ! Also see Eqn (A4+A6)) :
     ! Half half accelerations  - axn, ayn
     if (.not.Runge_not_Verlet) then
       axn=-gravity*ssh_x +wave_rad*uwave
@@ -822,16 +925,17 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
     endif
 
   ! Interactive spring acceleration - (Does the spring part need to be called twice?)
-  if (interactive_icebergs_on) then
-    call interactive_force(bergs, berg, IA_x, IA_y, uvel0, vvel0, uvel0, vvel0, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y) ! Spring forces, Made by Alon.
-    if (.not.Runge_not_Verlet) then
-      axn=axn + IA_x
-      ayn=ayn + IA_y
-    else
-      bxn=bxn + IA_x
-      byn=byn + IA_y
+    if (interactive_icebergs_on) then
+      !
+      call interactive_force(bergs, berg, IA_x, IA_y, uvel0, vvel0, uvel0, vvel0, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y) ! Spring forces, Made by Alon.
+      if (.not.Runge_not_Verlet) then
+        axn=axn + IA_x
+        ayn=ayn + IA_y
+      else
+        bxn=bxn + IA_x
+        byn=byn + IA_y
+      endif
     endif
-  endif
 
   if (alpha>0.) then ! If implicit Coriolis, use u_star rather than RK4 latest  !Alon
     if (C_N>0.) then !  C_N=1 for Crank Nicolson Coriolis, C_N=0 for full implicit Coriolis !Alon
@@ -857,6 +961,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
     if (itloop .eq. 2) then
       us=uveln ; vs=vveln
     endif
+   !Stern et al 2017, Eqn A1-A3
   if (use_new_predictive_corrective) then
     !Alon's proposed change - using Bob's improved scheme.
     drag_ocn=c_ocn*0.5*(sqrt( (uveln-uo)**2+(vveln-vo)**2 )+sqrt( (uvel0-uo)**2+(vvel0-vo)**2 ))
@@ -870,7 +975,8 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
     drag_ice=c_ice*sqrt( (us-ui)**2+(vs-vi)**2 )
   endif
 
-  RHS_x=(axn/2) + bxn
+  !RHS ~ similar to accel terms in Stern et al 2017, Eqn B5
+  RHS_x=(axn/2) + bxn 
   RHS_y=(ayn/2) + byn
 
   if (beta>0.) then ! If implicit, use u_star, v_star rather than RK4 latest
@@ -898,6 +1004,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
   ! Solve for implicit accelerations
   if (alpha+beta.gt.0.) then
     lambda=drag_ocn+drag_atm+drag_ice
+    !Matrix A = [A11 A12; A21 A22] is the denominator on the rhs of Stern et al 2017, Eqn B7
     A11=1.+beta*dt*lambda
     A22=1.+beta*dt*lambda
     A12=-alpha*dt*f_cori
@@ -926,6 +1033,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
        A22=1+(dt*P_ia_22)
     endif
 
+    ! note damping finally satisfies Stern et al 2017, Eqn 8
     detA=1./((A11*A22)-(A12*A21))
     ax=detA*(A22*RHS_x-A12*RHS_y)
     ay=detA*(A11*RHS_y-A21*RHS_x)
@@ -938,6 +1046,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
       ax=RHS_x; ay=RHS_y
     endif
 
+    ! Stern et al 2017, Eqn B5 and B6. Here, ax accounts for both acceleration terms (separated below)
     uveln=u_star+dt*ax        ! Alon
     vveln=v_star+dt*ay        ! Alon
 !MP4
@@ -951,6 +1060,8 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
   !    endif
   enddo ! itloop
 
+  !Below: axn and ayn are the new explicit acceleration terms in Stern et al 2017, Eqn B5
+  !       bxn and byn are the new implicit accerelation terms
   !Saving the totally explicit part of the acceleration to use in finding the next position and u_star -Alon
   axn=0.
   ayn=0.
@@ -2716,7 +2827,48 @@ subroutine Hexagon_into_quadrants_using_triangles(x0, y0, H, theta, Area_hex ,Ar
      endif
    endif
 
-end subroutine Hexagon_into_quadrants_using_triangles
+ end subroutine Hexagon_into_quadrants_using_triangles
+
+subroutine interp_gridded_fields_to_bergs(bergs)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  ! Local variables
+  type(icebergs_gridded), pointer :: grd
+  type(iceberg), pointer :: berg
+  integer :: grdj,grdi
+  type(randomNumberStream) :: rns ! Random numbers for stochastic tidal parameterization
+  real :: rx,ry
+
+  ! For convenience
+  grd=>bergs%grd
+  rx=0.0; ry=0.0;
+
+  do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec ! just for computational domain
+    berg=>bergs%list(grdi,grdj)%first
+    if (associated(berg) .and. grd%tidal_drift>0.) then
+      ! Seed random numbers based on space and "time"
+      rns = initializeRandomNumberStream( grdi + 10000*grdj + &
+                                          int( 16384.*abs( sin(262144.*grd%ssh(grdi,grdj)) ) ) )
+    endif    
+    do while (associated(berg)) ! loop over all bergs
+      if (berg%halo_berg.lt.0.5) then
+        
+        if (grd%tidal_drift>0.) then
+          call getRandomNumbers(rns, rx)
+          rx = 2.*rx - 1.
+          call getRandomNumbers(rns, ry)
+          ry = 2.*ry - 1.
+        endif
+        
+        call interp_flds(grd, berg%ine, berg%jne, berg%xi, berg%yj, rx, ry, berg%uo, berg%vo, &
+          berg%ui, berg%vi, berg%ua, berg%va, berg%ssh_x, berg%ssh_y, berg%sst, berg%sss, berg%cn, berg%hi)
+      endif
+      berg=>berg%next
+    enddo
+  enddo;enddo
+
+end subroutine interp_gridded_fields_to_bergs
+ 
 
 subroutine interp_flds(grd, i, j, xi, yj, rx, ry, uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, sss, cn, hi)
   ! Arguments
@@ -2945,22 +3097,24 @@ subroutine calculate_mass_on_ocean(bergs, with_diagnostics)
   do grdj = grd%jsc-1,grd%jec+1 ; do grdi = grd%isc-1,grd%iec+1
     berg=>bergs%list(grdi,grdj)%first
     do while(associated(berg))
-      i=berg%ine  ;     j=berg%jne
-      if (grd%area(i,j) > 0.) then
-
-        !Increasing Mass on ocean
-        if ((bergs%add_weight_to_ocean .and. .not. bergs%time_average_weight) .or.(bergs%find_melt_using_spread_mass)) then
-          call spread_mass_across_ocean_cells(bergs, berg, berg%ine, berg%jne, berg%xi, berg%yj, berg%mass,berg%mass_of_bits, berg%mass_scaling, &
-                berg%length*berg%width, berg%thickness)
-        endif
+      if (berg%halo_berg<1 .or. .not. bergs%mts) then
+        i=berg%ine  ;     j=berg%jne
+        if (grd%area(i,j) > 0.) then
+
+          !Increasing Mass on ocean
+          if ((bergs%add_weight_to_ocean .and. .not. bergs%time_average_weight) .or.(bergs%find_melt_using_spread_mass)) then
+            call spread_mass_across_ocean_cells(bergs, berg, berg%ine, berg%jne, berg%xi, berg%yj, berg%mass,berg%mass_of_bits, berg%mass_scaling, &
+              berg%length*berg%width, berg%thickness)
+          endif
 
-        !Calculated some iceberg diagnositcs
-        if (with_diagnostics) call calculate_sum_over_bergs_diagnositcs(bergs,grd,berg,i,j)
+          !Calculated some iceberg diagnositcs
+          if (with_diagnostics) call calculate_sum_over_bergs_diagnositcs(bergs,grd,berg,i,j)
 
+        endif
       endif
       berg=>berg%next
     enddo
-  enddo ;enddo
+  enddo;enddo
 
 end subroutine calculate_mass_on_ocean
 
@@ -3038,6 +3192,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   real, dimension(:,:), allocatable :: iCount
   integer :: nbonds
   integer :: stderrunit
+  logical :: Visited
+  save :: Visited
 
   ! Get the stderr unit number
   stderrunit = stderr()
@@ -3091,21 +3247,27 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   ! Turn on sampling of trajectories, verbosity, budgets
   sample_traj=.false.
   if ( (bergs%traj_sample_hrs>0)  .and. (.not. bergs%ignore_traj) ) then
-    if (mod(60*60*24*iday+ 60*60*ihr + 60*imin + isec ,60*60*bergs%traj_sample_hrs).eq.0) &
-        sample_traj=.true.
+    if (mod(60*60*24*iday+ 60*60*ihr + 60.*imin + isec ,60*60*bergs%traj_sample_hrs).eq.0) &
+      sample_traj=.true.
+  elseif (bergs%traj_sample_hrs==0) then
+    sample_traj=.true.
   endif
   write_traj=.false.
   if ((bergs%traj_write_hrs>0) .and. (.not. bergs%ignore_traj))  then
-     if (mod(60*60*24*iday+ 60*60*ihr + 60*imin + isec ,60*60*bergs%traj_write_hrs).eq.0) &
-         write_traj=.true.
+     if (mod(60*60*24*iday+ 60*60*ihr + 60.*imin + isec ,60*60*bergs%traj_write_hrs).eq.0) &
+       write_traj=.true.
+   elseif (bergs%traj_write_hrs==0) then
+     write_traj=.true.
   endif
   lverbose=.false.
   if (bergs%verbose_hrs>0) then
-     if (mod(24*iday+ihr+(imin/60.),float(bergs%verbose_hrs)).eq.0) lverbose=verbose
+    !if (mod(24*iday+ihr+(imin/60.),float(bergs%verbose_hrs)).eq.0) lverbose=verbose
+    if (mod(24*iday+ihr+(imin/60.),bergs%verbose_hrs).eq.0) lverbose=verbose
   endif
   lbudget=.false.
   if (bergs%verbose_hrs>0) then
-     if (mod(24*iday+ihr+(imin/60.),float(bergs%verbose_hrs)).eq.0) lbudget=budget  !Added minutes, so that it does not repeat when smaller time steps are used.
+     !if (mod(24*iday+ihr+(imin/60.),float(bergs%verbose_hrs)).eq.0) lbudget=budget
+     if (mod(24*iday+ihr+(imin/60.),bergs%verbose_hrs).eq.0) lbudget=budget  !Added minutes, so that it does not repeat when smaller time steps are used.
   endif
   if (mpp_pe()==mpp_root_pe().and.lverbose) write(*,'(a,3i5,a,3i5,a,i5,f8.3)') &
        'KID: y,m,d=',iyr, imon, iday,' h,m,s=', ihr, imin, isec, &
@@ -3296,7 +3458,22 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   if (debug) call bergs_chksum(bergs, 'run bergs (top)')
   if (debug) call checksum_gridded(bergs%grd, 'top of s/r run')
 
-
+  !If MTS VV and first visit, perform initial interp of gridded fields to bergs
+  if (.not. Visited) then
+    Visited=.true.
+    if (bergs%mts) then
+      call interp_gridded_fields_to_bergs(bergs)   
+      if ((bergs%interactive_icebergs_on) .or. (bergs%iceberg_bonds_on)) then      
+        call update_halo_icebergs(bergs)
+        if (bergs%iceberg_bonds_on)  then
+          call connect_all_bonds(bergs)
+        else
+          if (grd%Lx>0.) call update_latlon(bergs)
+        endif
+      endif
+    endif
+  endif
+  
   ! Accumulate ice from calving
   call accumulate_calving(bergs)
   if (grd%id_accum>0) then
@@ -3322,33 +3499,45 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   call mpp_clock_begin(bergs%clock_mom)
 
   if (.not.bergs%Static_icebergs) then
-    call update_latlon(bergs) !guarantees correct coords for halo bergs. Needed if interacting bergs & domain is periodic - Alex 
-    call evolve_icebergs(bergs)
+    if (bergs%mts) then
+      call evolve_icebergs_mts(bergs)
+    else
+      call evolve_icebergs(bergs)
+    end if
     if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after evolve()     ')
-  endif
+  end if
   call move_berg_between_cells(bergs)  !Markpoint6
   if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after move_lists() ')
   if (debug) call bergs_chksum(bergs, 'run bergs (evolved)',ignore_halo_violation=.true.)
   if (debug) call checksum_gridded(bergs%grd, 's/r run after evolve')
   call mpp_clock_end(bergs%clock_mom)
 
+
   ! Send bergs to other PEs
   call mpp_clock_begin(bergs%clock_com)
   if (bergs%iceberg_bonds_on)  call  bond_address_update(bergs)
   call send_bergs_to_other_pes(bergs)
-  if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after send_bergs() ')
-  if ((bergs%interactive_icebergs_on) .or. (bergs%iceberg_bonds_on)) then
-    call update_halo_icebergs(bergs)
+  if (bergs%mts) call interp_gridded_fields_to_bergs(bergs)  
+  if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after send_bergs() ')  
+  if ((bergs%interactive_icebergs_on) .or. (bergs%iceberg_bonds_on)) then      
+  call update_halo_icebergs(bergs)
     if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after update_halo()')
-    if (bergs%iceberg_bonds_on)  call connect_all_bonds(bergs)
+    if (bergs%iceberg_bonds_on)  then
+      call connect_all_bonds(bergs)
+    else
+      if (grd%Lx>0.) call update_latlon(bergs)
+    endif
   endif
   if (debug) call bergs_chksum(bergs, 'run bergs (exchanged)')
   if (debug) call checksum_gridded(bergs%grd, 's/r run after exchange')
   call mpp_clock_end(bergs%clock_com)
 
+  if (bergs%find_melt_using_spread_mass .or. bergs%mts) then
+    call calculate_mass_on_ocean(bergs, with_diagnostics=.false.)
+  end if
+  
   ! Calculate mass on ocean before thermodynamics, to use in melt rate calculation
   if (bergs%find_melt_using_spread_mass) then
-    call calculate_mass_on_ocean(bergs, with_diagnostics=.false.)
     grd%spread_mass_old(:,:)=0.
     call sum_up_spread_fields(bergs,grd%spread_mass_old(grd%isc:grd%iec,grd%jsc:grd%jec), 'mass')
     !Reset fields
@@ -3689,7 +3878,9 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   call mpp_clock_end(bergs%clock_dia)
 
   call mpp_clock_end(bergs%clock)
-
+!  call cpu_time(tend0)
+ ! tott0 = tott0+(tend0-tstart0)
+ ! if (mpp_pe()==mpp_root_pe().and.lverbose) print *,'tott0',tott0
 end subroutine icebergs_run
 
 !> Prints summary of start and end states
@@ -4067,10 +4258,16 @@ subroutine calve_icebergs(bergs)
           newberg%yj=yj
           newberg%uvel=0.
           newberg%vvel=0.
+          newberg%uvel_prev=0.
+          newberg%vvel_prev=0.
           newberg%axn=0. !Added by Alon
           newberg%ayn=0. !Added by Alon
           newberg%bxn=0. !Added by Alon
           newberg%byn=0. !Added by Alon
+          newberg%axn_fast=0. !Added by Alex
+          newberg%ayn_fast=0. !Added by Alex
+          newberg%bxn_fast=0. !Added by Alex
+          newberg%byn_fast=0. !Added by Alex         
           newberg%mass=bergs%initial_mass(k)
           newberg%thickness=bergs%initial_thickness(k)
           newberg%width=bergs%initial_width(k)
@@ -4113,36 +4310,270 @@ subroutine calve_icebergs(bergs)
 
 end subroutine calve_icebergs
 
-!> Update berg lat & lon from local position in cell - Alex
-subroutine update_latlon(bergs)
-  !Arguments
+!> Evolves icebergs forward by updating velocity and position with a multiple-time-step
+!! Velocity Verlet scheme.
+subroutine evolve_icebergs_mts(bergs)
+  ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
   ! Local variables
   type(icebergs_gridded), pointer :: grd
   type(iceberg), pointer :: berg
-  real :: dlon, dlat,xi,yj
-  integer :: grdi,grdj
-  logical :: lret
+  real :: uveln, vveln, lonn, latn
+  real :: axn, ayn, bxn, byn          
+  real :: xi, yj, rx, ry
+  integer :: i, j, k
+  integer :: grdi, grdj
+  integer :: stderrunit
+  logical :: only_interactive_forces
+  real :: lon1, lat1, dxdl1, dydl
+  real :: uvel1, vvel1, uvel2, vvel2, uvel3, vvel3
+  real :: xddot1, yddot1, xdot2, ydot2, xdot3, ydot3, xdotn, ydotn
+  real :: u2, v2, x1, y1, xn, yn
+  real :: ax1,ay1
+  real :: dx, dt, dt_2
+  logical :: on_tangential_plane, error_flag, bounced
+
+  ! Multiple Time Step Velocity Verlet:
+  ! NOTE: To avoid the need for computationally expensive transfers between processors
+  ! at the end of each MTS sub-step, each PE updates a complete copy of any
+  ! conglomerate of bonded iceberg elements that spans over the computational domain of
+  ! several processors (see subroutine transfer_mts_bergs). Berg elements that lie within
+  ! the contact distance of the conglomerate are also included, as to account for collision
+  ! forces. The conglomerate iceberg elements with coords that lie outside of a PE's domain
+  ! are assigned to the nearest halo cell, but the coords are not changed.
+  
+  ! Get the stderr unit number
+  stderrunit = stderr()
+  only_interactive_forces=bergs%only_interactive_forces
 
   ! For convenience
   grd=>bergs%grd
 
+  !Checking if everything is ok:
+  do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec ! just for computational domain
+    berg=>bergs%list(grdi,grdj)%first
+    do while (associated(berg)) ! loop over all bergs
+      if (berg%static_berg .lt. 0.5 .and. berg%halo_berg .lt. 0.5) then
+        if (.not. is_point_in_cell(bergs%grd, berg%lon, berg%lat, berg%ine, berg%jne) ) then
+          write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lon',(i,i=grd%isd,grd%ied)
+          do j=grd%jed,grd%jsd,-1
+            write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lon(i,j),i=grd%isd,grd%ied)
+          enddo
+          write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lat',(i,i=grd%isd,grd%ied)
+          do j=grd%jed,grd%jsd,-1
+            write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lat(i,j),i=grd%isd,grd%ied)
+          enddo
+          call print_berg(stderrunit, berg, 'evolve_iceberg_mts, berg is not in proper starting cell')
+          write(stderrunit,'(a,i3,2(i4,3f8.2))') 'evolve_icebergs_mts: pe,lon/lat(i,j)=', mpp_pe(), &
+            berg%ine,berg%lon,grd%lon(berg%ine-1,berg%jne-1),grd%lon(berg%ine,berg%jne), &
+            berg%jne,berg%lat,grd%lat(berg%ine-1,berg%jne-1),grd%lat(berg%ine,berg%jne)
+          if (debug) call error_mesg('KID, evolve_icebergs_mts','berg is in wrong starting cell!',FATAL)
+        endif
+        if (debug) call check_position(grd, berg, 'evolve_icebergs_mts (top)')
+      end if
+      berg=>berg%next
+    enddo
+  enddo; enddo
+
+  ! PART 1: solve for V_n+1
+  bergs%mts_part=1
+  dt = bergs%dt
+  dt_2=0.5*dt
+  rx = 0.0; ry = 0.0 !not needed, because interp_gridded_fields_to_bergs was already called
+
   do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
     berg=>bergs%list(grdi,grdj)%first
-    do while (associated(berg))
-      dlon = berg%lon - berg%lon_old
-      dlat = berg%lat - berg%lat_old
-      berg%lon=bilin(grd, grd%lon, berg%ine, berg%jne, berg%xi, berg%yj)
-      berg%lat=bilin(grd, grd%lat, berg%ine, berg%jne, berg%xi, berg%yj)
-      berg%lon_old = berg%lon-dlon
-      berg%lat_old = berg%lat-dlat
-      !need to update local positon in cell from updated global coords, due to roundoff
-      lret=pos_within_cell(grd, berg%lon, berg%lat, berg%ine, berg%jne, berg%xi, berg%yj)      
+    do while (associated(berg)) ! loop over all bergs
+      if (berg%static_berg .lt. 0.5 .and. berg%halo_berg<10) then
+        latn = berg%lat ;   lonn = berg%lon
+        uvel1=berg%uvel_prev ;   vvel1=berg%vvel_prev !V_n (previous cycle)
+        !subroutine accel expects uvel1=berg%uvel_prev, and calculates ustar=uvel1+axn*dt_2. 
+        !However, for the MTS case, ustar should equal berg%uvel from after the final fast force
+        !iteration k from the previous cycle. To enforce this, fake in input accelerations
+        !axn and ayn as:
+        axn  = (berg%uvel-berg%uvel_prev)/dt_2
+        ayn  = (berg%vvel-berg%vvel_prev)/dt_2
+        bxn  = 0.0      ;   byn  = 0.0
+        i=berg%ine      ;   j=berg%jne
+        xi=berg%xi      ;   yj=berg%yj                               
+        ! if (berg%id==4294967382 .and. berg%halo_berg==0) then
+        !   print *,'berg check 1',mpp_pe(),berg%id, berg%uvel, berg%vvel, berg%lat, berg%lon
+        ! endif
+        call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, &
+          ax1, ay1, axn, ayn, bxn, byn)
+        ! Saving all the iceberg variables.        
+        berg%axn=axn                ; berg%ayn=ayn
+        berg%bxn=bxn                ; berg%byn=byn
+        berg%uvel=berg%uvel+(dt*ax1); berg%vvel=berg%vvel+(dt*ay1)
+
+        !save this velocity for next time, and output 
+        berg%uvel_prev=berg%uvel    ; berg%vvel_prev=berg%vvel
+      endif
       berg=>berg%next
-    enddo !loop over all bergs
+    enddo ! loop over all bergs
   enddo; enddo
-end subroutine update_latlon
 
+  !PART 2: X_0 and V_0, before fast sub-steps
+  !X_0=X_n (no change)
+  !update V_0 on uvel_old and vvel_old
+  !update lat and lon with implicit slow force component  
+  do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+    berg=>bergs%list(grdi,grdj)%first
+    do while (associated(berg)) ! loop over all bergs
+      if (berg%static_berg .lt. 0.5 .and. berg%halo_berg<10) then
+        ! if (berg%id==4294967382 .and. berg%halo_berg==0) then
+        !   print *,'berg check 2',mpp_pe(),berg%id, berg%uvel, berg%vvel, &
+        !     berg%lat, berg%lon, berg%axn, berg%ayn, berg%bxn, berg%byn
+        ! endif
+        berg%uvel = berg%uvel + dt_2*berg%axn
+        berg%vvel = berg%vvel + dt_2*berg%ayn
+        berg%lat = berg%lat + 0.5*(dt**2)*berg%byn
+        berg%lon = berg%lon + 0.5*(dt**2)*berg%bxn
+        berg%lat_old = berg%lat; berg%lon_old = berg%lon 
+        berg%uvel_old=berg%uvel; berg%vvel_old=berg%vvel
+         ! if (berg%id==4294967382 .and. berg%halo_berg==0) then
+         !   print *,'berg check 3',mpp_pe(),berg%id, berg%uvel, berg%vvel, &
+         !     berg%lat, berg%lon, berg%axn, berg%ayn, berg%bxn, berg%byn
+         ! endif            
+      endif
+      berg=>berg%next
+    enddo
+  enddo; enddo
+
+
+  ! PART 3: MTS fast sub-steps (bonded interactions only):
+  ! Position and velocity are updated by:
+  ! X2 = X1+dt*V1+((dt^2)/2)*a_k +((dt^2)/2)*b_k
+  ! V2 = V1+dt/2*a_k +dt/2*a_kp1 +dt*b_k+1
+
+  bergs%only_interactive_forces=.true. !so that external forcings are ignored in subroutine accel
+  bergs%mts_part=3 !so that only bonded interactions are considered in subroutine interactive_force
+  dt = bergs%mts_fast_dt
+  dt_2=0.5*dt
+  
+  do k = 1,bergs%mts_sub_steps ! loop over sub-steps
+
+    do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied ! update positions 
+      berg=>bergs%list(grdi,grdj)%first
+      do while (associated(berg)) ! loop over all bergs
+        if (berg%static_berg .lt. 0.5 .and. berg%halo_berg<10) then
+
+          on_tangential_plane=.false.
+          if ((berg%lat>89.) .and. (grd%grid_is_latlon)) on_tangential_plane=.true.
+
+          lon1=berg%lon; lat1=berg%lat
+          if (on_tangential_plane) call rotpos_to_tang(lon1,lat1,x1,y1,berg%id)
+          !dxdl1=r180_pi/(Rearth*cos(lat1*pi_180))
+          !dydl=r180_pi/Rearth
+          call convert_from_meters_to_grid(lat1,grd%grid_is_latlon ,dxdl1,dydl)
+          uvel1=berg%uvel; vvel1=berg%vvel
+
+          ! Loading past accelerations
+          axn=berg%axn_fast; ayn=berg%ayn_fast
+          bxn=berg%bxn_fast; byn=berg%byn_fast
+
+          ! Velocities used to update the position
+          uvel2=uvel1+(dt_2*axn)+(dt_2*bxn)
+          vvel2=vvel1+(dt_2*ayn)+(dt_2*byn)
+
+          if (on_tangential_plane) call rotvec_to_tang(lon1,uvel2,vvel2,xdot2,ydot2)
+          u2=uvel2*dxdl1; v2=vvel2*dydl
+
+          ! Solving for new position
+          if (on_tangential_plane) then
+            xn=x1+(dt*xdot2) ; yn=y1+(dt*ydot2)
+            call rotpos_from_tang(xn,yn,lonn,latn)
+          else
+            lonn=lon1+(dt*u2) ; latn=lat1+(dt*v2)
+          endif
+
+          berg%lon=lonn      ;  berg%lat=latn
+          berg%lon_old=lonn  ;  berg%lat_old=latn
+        end if
+        berg=>berg%next
+      enddo !loop over all bergs
+    enddo;enddo !update positions 
+    
+    ! update velocities
+    do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+      berg=>bergs%list(grdi,grdj)%first
+      do while (associated(berg)) ! loop over all bergs
+        if (berg%static_berg .lt. 0.5 .and. berg%halo_berg<10) then 
+
+          latn = berg%lat ;   lonn = berg%lon
+          axn  = berg%axn_fast ;   ayn  = berg%ayn_fast
+          bxn  = berg%bxn_fast ;   byn  = berg%byn_fast       
+          uvel1=berg%uvel ;   vvel1=berg%vvel
+          i=berg%ine      ;   j=berg%jne
+          xi=berg%xi      ;   yj=berg%yj
+
+          ! Turn the velocities into u_star, v_star.(uvel3 is v_star) - (possible issues with tangent plane?)
+          uvel3=uvel1+(dt_2*axn)                  !(Stern et al 2017, Eq B4)
+          vvel3=vvel1+(dt_2*ayn)                          
+
+          call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, &
+            ax1, ay1, axn, ayn, bxn, byn)
+
+          ! Solving for the new velocity (Stern et al 2017, Eqn B5)
+          on_tangential_plane=.false.
+          if ((berg%lat>89.) .and. (bergs%grd%grid_is_latlon)) on_tangential_plane=.true.
+          if (on_tangential_plane) then
+            call rotvec_to_tang(lonn,uvel3,vvel3,xdot3,ydot3)
+            call rotvec_to_tang(lonn,ax1,ay1,xddot1,yddot1)
+            xdotn=xdot3+(dt*xddot1); ydotn=ydot3+(dt*yddot1)                                   
+            call rotvec_from_tang(lonn,xdotn,ydotn,uveln,vveln)
+          else
+            !uvel3, vvel3 become uveln and vveln after they are put into lat/lon co-ordinates         
+            uveln=uvel3+(dt*ax1); vveln=vvel3+(dt*ay1)    
+          endif
+
+          ! Saving all the iceberg variables.
+          berg%axn_fast=axn; berg%ayn_fast=ayn
+          berg%bxn_fast=bxn; berg%byn_fast=byn        
+          berg%uvel=uveln  ; berg%vvel=vveln
+        endif
+        berg=>berg%next
+      enddo ! loop over all bergs
+    enddo; enddo ! update velocities
+
+    !update 'old' velocities used for interactions
+    do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+      berg=>bergs%list(grdi,grdj)%first
+      do while (associated(berg)) ! loop over all bergs
+        if (berg%static_berg .lt. 0.5 .and. berg%halo_berg<10) then  
+          berg%uvel_old=berg%uvel; berg%vvel_old=berg%vvel
+        endif
+        berg=>berg%next
+      enddo ! loop over all bergs
+    enddo; enddo ! update 'old' velocities
+  enddo ! loop over sub-steps
+
+  !reset interactive_forces
+  bergs%only_interactive_forces=only_interactive_forces
+  
+  !update indices
+  do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
+    !no reason to worry about halo/conglomerate bergs here
+    berg=>bergs%list(grdi,grdj)%first
+    do while (associated(berg)) ! loop over all bergs
+      if (berg%static_berg .lt. 0.5 .and. berg%halo_berg<1) then  
+        berg%uvel_old=berg%uvel; berg%vvel_old=berg%vvel
+        uveln=berg%uvel; vveln=berg%vvel
+        lonn=berg%lon  ; latn=berg%lat
+        i=berg%ine     ; j=berg%jne
+        xi=berg%xi     ; yj=berg%yj
+        ! finalize new iceberg positions and index
+        call adjust_index_and_ground(grd, lonn, latn, uveln, vveln, i, j, xi, yj, bounced, error_flag, berg%id)
+        berg%lon=lonn      ;  berg%lat=latn
+        berg%lon_old=lonn  ;  berg%lat_old=latn
+        berg%ine=i    ;  berg%jne=j
+        berg%xi=xi    ;  berg%yj=yj        
+      endif
+      berg=>berg%next
+    enddo ! loop over all bergs
+  enddo; enddo ! update 'old' velocities
+
+end subroutine evolve_icebergs_mts
 
 !> Evolves icebergs forward by updating velocity and position with a time-stepping scheme
 subroutine evolve_icebergs(bergs)
@@ -4169,7 +4600,7 @@ subroutine evolve_icebergs(bergs)
 
   interactive_icebergs_on=bergs%interactive_icebergs_on
   Runge_not_Verlet=bergs%Runge_not_Verlet
-
+  
   do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
     berg=>bergs%list(grdi,grdj)%first
     if (associated(berg) .and. grd%tidal_drift>0.) then
@@ -4210,7 +4641,7 @@ subroutine evolve_icebergs(bergs)
             call Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, &
                                       lonn, latn, i, j, xi, yj, rx, ry)
           endif
-          if (.not.Runge_not_Verlet) then
+          if (.not.Runge_not_Verlet) then           
             call verlet_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, rx, ry)
           endif
 
@@ -4227,6 +4658,9 @@ subroutine evolve_icebergs(bergs)
         berg%byn=byn
         berg%uvel=uveln
         berg%vvel=vveln
+        ! if (berg%id==4294967382 .and. berg%halo_berg==0) then
+        !   print *,'berg check 2',mpp_pe(),berg%id, berg%uvel, berg%vvel, berg%lat, berg%lon
+        ! endif        
 
         if (Runge_not_Verlet) then
           berg%lon=lonn  ;   berg%lat=latn
@@ -4320,18 +4754,20 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln, rx, ry)
   xi=berg%xi      ;   yj=berg%yj
 
   ! Turn the velocities into u_star, v_star.(uvel3 is v_star) - Alon (not sure how this works with tangent plane)
-  uvel3=uvel1+(dt_2*axn)                  !Alon
+  uvel3=uvel1+(dt_2*axn)                  !Alon (Stern et al 2017, Eq B4)
   vvel3=vvel1+(dt_2*ayn)                  !Alon
-
+  ! if (berg%id==4294967382 .and. berg%halo_berg==0) then
+  !   print *,'berg check 1',mpp_pe(),berg%id, uvel3, vvel3, berg%lat, berg%lon
+  ! endif
   ! Note, the mass scaling is equal to 1 (rather than 0.25 as in RK), since
   ! this is only called once in Verlet stepping.
   if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
     call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 1.0*berg%mass_scaling,berg%length*berg%width, berg%thickness)
-
   ! Calling the acceleration   (note that the velocity is converted to u_star inside the accel script)
-  call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, ax1, ay1, axn, ayn, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
+    call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, ax1, ay1, axn, ayn, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
+              
 
-  ! Solving for the new velocity
+  ! Solving for the new velocity (Stern et al 2017, Eqn B5)
   on_tangential_plane=.false.
   if ((berg%lat>89.) .and. (bergs%grd%grid_is_latlon)) on_tangential_plane=.true.
   if (on_tangential_plane) then
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index eb47867..9eea156 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -43,12 +43,14 @@ module ice_bergs_framework
 logical :: fix_restart_dates=.true. !< After a restart, check that bergs were created before the current model date
 logical :: do_unit_tests=.false. !< Conduct some unit tests
 logical :: force_all_pes_traj=.false. !< Force all pes write trajectory files regardless of io_layout
+logical :: mts=.false.
 
 !Public params !Niki: write a subroutine to expose these
 public nclasses,buffer_width,buffer_width_traj
 public verbose, really_debug, debug, restart_input_dir,make_calving_reproduce,old_bug_bilin,use_roundoff_fix
 public ignore_ij_restart, use_slow_find,generate_test_icebergs,old_bug_rotated_weights,budget
 public orig_read, force_all_pes_traj
+public mts !Alex
 
 !Public types
 public icebergs_gridded, xyt, iceberg, icebergs, buffer, bond
@@ -76,6 +78,7 @@ module ice_bergs_framework
 public test_check_for_duplicate_ids_in_list
 public check_for_duplicates_in_parallel
 public split_id, id_from_2_ints, generate_id, cij_from_old_id, convert_old_id
+public update_latlon
 
 !> Container for gridded fields
 type :: icebergs_gridded
@@ -101,6 +104,8 @@ module ice_bergs_framework
   logical :: grid_is_latlon !< Flag to say whether the coordinate is in lat-lon degrees, or meters
   logical :: grid_is_regular !< Flag to say whether point in cell can be found assuming regular Cartesian grid
   real :: Lx !< Length of the domain in x direction
+  real :: maxlon_c !< maximum x coord of computational domain
+  real :: minlon_c !< minimum x coord of computational domain
   real, dimension(:,:), pointer :: lon=>null() !< Longitude of cell corners (degree E)
   real, dimension(:,:), pointer :: lat=>null() !< Latitude of cell corners (degree N)
   real, dimension(:,:), pointer :: lonc=>null() !< Longitude of cell centers (degree E)
@@ -197,6 +202,12 @@ module ice_bergs_framework
   real :: ayn
   real :: bxn
   real :: byn
+  real :: axn_fast
+  real :: ayn_fast
+  real :: bxn_fast
+  real :: byn_fast  
+  real :: uvel_prev
+  real :: vvel_prev  
   real :: uvel_old
   real :: vvel_old
   real :: lat_old
@@ -239,6 +250,12 @@ module ice_bergs_framework
   real :: ayn
   real :: bxn
   real :: byn
+  real :: axn_fast
+  real :: ayn_fast
+  real :: bxn_fast
+  real :: byn_fast
+  real :: uvel_prev
+  real :: vvel_prev 
   real :: uvel_old
   real :: vvel_old
   real :: lon_old
@@ -300,14 +317,14 @@ module ice_bergs_framework
 type :: icebergs !; private !Niki: Ask Alistair why this is private. ice_bergs_io cannot compile if this is private!
   type(icebergs_gridded), pointer :: grd !< Container with all gridded data
   type(linked_list), dimension(:,:), allocatable :: list !< Linked list of icebergs
-  type(xyt), pointer :: trajectories=>null() !< A linked list for detached segments of trajectories
+  type(xyt), pointer :: trajectories=>null() !< A linked list for detached segments of trajectories  
   real :: dt !< Time-step between iceberg calls
              !! \todo Should make dt adaptive?
   integer :: current_year !< Current year (years)
   real :: current_yearday !< Current year-day, 1.00-365.99, (days)
-  integer :: traj_sample_hrs !< Period between sampling for trajectories (hours)
-  integer :: traj_write_hrs !< Period between writing of trajectories (hours)
-  integer :: verbose_hrs !< Period between terminal status reports (hours)
+  real :: traj_sample_hrs !< Period between sampling for trajectories (hours)
+  real :: traj_write_hrs !< Period between writing of trajectories (hours)
+  real :: verbose_hrs !< Period between terminal status reports (hours)
   integer :: max_bonds
   !>@{
   !! Handles for clocks
@@ -315,7 +332,8 @@ module ice_bergs_framework
   integer :: clock_trw, clock_trp
   !>@}
   real :: rho_bergs !< Density of icebergs [kg/m^3]
-  real :: spring_coef !< Spring constant for iceberg interactions
+  real :: spring_coef !< Spring constant for bonded iceberg interactions
+  real :: contact_spring_coef !<Spring coefficient for berg collisions -Alex
   real :: bond_coef !< Spring constant for iceberg bonds
   real :: radial_damping_coef !< Coefficient for relative iceberg motion damping (radial component) -Alon
   real :: tangental_damping_coef !< Coefficient for relative iceberg motion damping (tangential component) -Alon
@@ -415,6 +433,13 @@ module ice_bergs_framework
   integer :: nspeeding_tickets=0
   integer :: nbonds=0
   integer, dimension(:), pointer :: nbergs_calved_by_class=>null()
+  ! mts parameters - added by Alex
+  logical :: mts=.false. !use multiple timestepping scheme (substep size is automatically determined)
+  integer :: mts_sub_steps
+  real :: mts_fast_dt
+  integer :: mts_part !for turning on/off berg interactions/collisions during different mts scheme
+  real :: contact_distance
+  integer :: num_contact_cells !for how many cells to search to find contact pairs
 end type icebergs
 
 !> Read original restarts. Needs to be module global so can be public to icebergs_mod.
@@ -487,12 +512,13 @@ subroutine ice_bergs_framework_init(bergs, &
 
     ! Namelist parameters (and defaults)
     integer :: halo=4 ! Width of halo region
-    integer :: traj_sample_hrs=24 ! Period between sampling of position for trajectory storage
-    integer :: traj_write_hrs=480 ! Period between writing sampled trajectories to disk
-    integer :: verbose_hrs=24 ! Period between verbose messages
+    real :: traj_sample_hrs=24. ! Period between sampling of position for trajectory storage
+    real :: traj_write_hrs=480. ! Period between writing sampled trajectories to disk
+    real :: verbose_hrs=24. ! Period between verbose messages
     integer :: max_bonds=6 ! Maximum number of iceberg bond passed between processors
     real :: rho_bergs=850. ! Density of icebergs
     real :: spring_coef=1.e-8 ! Spring constant for iceberg interactions (this seems to be the highest stable value)
+    real :: contact_spring_coef=0. !Spring coef for berg collisions (is set to spring_coef if not specified)
     real :: bond_coef=1.e-8 ! Spring constant for iceberg bonds - not being used right now
     real :: radial_damping_coef=1.e-4 ! Coefficient for relative iceberg motion damping (radial component) -Alon
     real :: tangental_damping_coef=2.e-5 ! Coefficient for relative iceberg motion damping (tangential component) -Alon
@@ -557,6 +583,9 @@ subroutine ice_bergs_framework_init(bergs, &
     logical :: read_old_restarts=.false. ! Legacy option that does nothing
     logical :: use_old_spreading=.true. ! If true, spreads iceberg mass as if the berg is one grid cell wide
     logical :: read_ocean_depth_from_file=.false. ! If true, ocean depth is read from a file.
+    !logical :: mts=.false. !use multiple timestepping scheme (substep size is automatically determined)
+    integer :: mts_sub_steps=-1 !if -1, the number of mts sub-steps will be automatically determined
+    real :: contact_distance=0.0 !for unbonded berg interactions, collision is assumed at max(contact_distance,sum of the 2 bergs radii)
     real, dimension(nclasses) :: initial_mass=(/8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11/) ! Mass thresholds between iceberg classes (kg)
     real, dimension(nclasses) :: distribution=(/0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02/) ! Fraction of calving to apply to this class (non-dim) ,
     real, dimension(nclasses) :: mass_scaling=(/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) ! Ratio between effective and real iceberg mass (non-dim)
@@ -564,7 +593,7 @@ subroutine ice_bergs_framework_init(bergs, &
     integer(kind=8) :: debug_iceberg_with_id = -1 ! If positive, monitors a berg with this id
 
     Namelist /icebergs_nml/ Verbose, budget, halo,  traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,Static_icebergs,  &
-         distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,bond_coef, radial_damping_coef, tangental_damping_coef, only_interactive_forces, &
+         distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,contact_spring_coef,bond_coef, radial_damping_coef, tangental_damping_coef, only_interactive_forces, &
          rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, iceberg_bonds_on, manually_initialize_bonds, ignore_missing_restart_bergs, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, halo_debugging, hexagonal_icebergs, &
          time_average_weight, generate_test_icebergs, length_for_manually_initialize_bonds, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, &
@@ -574,15 +603,16 @@ subroutine ice_bergs_framework_init(bergs, &
          grid_is_regular,override_iceberg_velocities,u_override,v_override,add_iceberg_thickness_to_SSH,Iceberg_melt_without_decay,melt_icebergs_as_ice_shelf, &
          Use_three_equation_model,find_melt_using_spread_mass,use_mixed_layer_salinity_for_thermo,utide_icebergs,ustar_icebergs_bg,cdrag_icebergs, pass_fields_to_ocean_model, &
          const_gamma, Gamma_T_3EQ, ignore_traj, debug_iceberg_with_id,use_updated_rolling_scheme, tip_parameter, read_old_restarts, tau_calving, read_ocean_depth_from_file, melt_cutoff,&
-         apply_thickness_cutoff_to_gridded_melt, apply_thickness_cutoff_to_bergs_melt, use_mixed_melting, coastal_drift, tidal_drift
+         apply_thickness_cutoff_to_gridded_melt, apply_thickness_cutoff_to_bergs_melt, use_mixed_melting, coastal_drift, tidal_drift,mts,mts_sub_steps,contact_distance
 
     ! Local variables
     integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
     type(icebergs_gridded), pointer :: grd
-    real :: lon_mod, big_number
+    real :: lon_mod, big_number,mts_fast_dt=0.0
     logical :: lerr
     integer :: stdlogunit, stderrunit
     real :: Total_mass  !Added by Alon
+    real :: maxlon_c,minlon_c !Alex, for mts verlet periodicity
 
     ! Get the stderr and stdlog unit numbers
     stderrunit=stderr()
@@ -949,6 +979,32 @@ subroutine ice_bergs_framework_init(bergs, &
 if (save_short_traj) buffer_width_traj=6 ! This is the length of the short buffer used for abrevated traj
 if (ignore_traj) buffer_width_traj=0 ! If this is true, then all traj files should be ignored
 
+!must use verlet with mts - Alex
+if (mts) then
+
+  buffer_width_traj=buffer_width_traj+6 !to accomodate fast acceration and vel_prev terms
+  buffer_width=buffer_width+18 !to accomodate external forcing (uo,vo,ua,va,ui,vi,ssh_x,ssh_y,sst,sss,cn,hi)
+  
+  !if mts_sub_steps is not given in the nml already,
+  !then detemine according to the max dt according to the spring coef
+  if (mts_sub_steps .eq. -1) then
+    mts_fast_dt = 2./sqrt(bergs%spring_coef)   !the (theoretical) maximum "fast" dt for mts scheme      
+    mts_sub_steps = ceiling(dt/mts_fast_dt)    !the number of substeps
+  end if
+
+  mts_fast_dt = dt/mts_sub_steps !adjust mts_fast_dt so that dt is an integer multiple of mts_fast_dt
+
+  if (Runge_not_Verlet) then
+    call error_mesg('KID, framework', &
+      'Multiple time stepping does not work with Runge Kutta stepping, switching to Verlet.', WARNING)
+    Runge_not_Verlet=.false.
+  end if
+end if
+
+!by default, set contact_spring_coef equal to the spring_coef for bonded interactions, unless
+!contact_spring_coef is specified as > 0.
+if (contact_spring_coef.le.0.) contact_spring_coef=spring_coef
+
 
 ! Parameters
 bergs%dt=dt
@@ -964,6 +1020,7 @@ subroutine ice_bergs_framework_init(bergs, &
 bergs%max_bonds=max_bonds
 bergs%rho_bergs=rho_bergs
 bergs%spring_coef=spring_coef
+bergs%contact_spring_coef=contact_spring_coef !Alex
 bergs%bond_coef=bond_coef
 bergs%radial_damping_coef=radial_damping_coef
 bergs%tangental_damping_coef=tangental_damping_coef
@@ -1019,6 +1076,21 @@ subroutine ice_bergs_framework_init(bergs, &
 bergs%add_weight_to_ocean=add_weight_to_ocean
 bergs%use_old_spreading=use_old_spreading
 bergs%debug_iceberg_with_id=debug_iceberg_with_id
+bergs%mts=mts
+bergs%mts_fast_dt = mts_fast_dt
+bergs%mts_sub_steps = mts_sub_steps
+bergs%mts_part = 1
+bergs%contact_distance=contact_distance
+bergs%num_contact_cells = max(int(ceiling(contact_distance/(grd%lon(grd%isc+1,grd%jsc)-grd%lon(grd%isc,grd%jsc)))),1)
+if (halo<bergs%num_contact_cells) then
+  if (mpp_pe()==0) then  
+    write(stderrunit,'(a,i3)') 'KID, icebergs_init: halo width ',halo
+    write(stderrunit,'(a,f8.2,a,i3)') 'KID, icebergs_init: contact distance ',bergs%contact_distance,&
+      ' num contact cells',bergs%num_contact_cells
+    call error_mesg('KID, ice_bergs_framework_init', &
+      'halo width must be increased to accomodate specified contact distance!!!', FATAL)
+  endif
+endif
 allocate( bergs%initial_mass(nclasses) ); bergs%initial_mass(:)=initial_mass(:)
 allocate( bergs%distribution(nclasses) ); bergs%distribution(:)=distribution(:)
 allocate( bergs%mass_scaling(nclasses) ); bergs%mass_scaling(:)=mass_scaling(:)
@@ -1030,6 +1102,12 @@ subroutine ice_bergs_framework_init(bergs, &
 grd%coastal_drift = coastal_drift
 grd%tidal_drift = tidal_drift
 
+!needed for periodicity
+maxlon_c = grd%lon(grd%iec,grd%jec); minlon_c = grd%lon(grd%isc-1,grd%jsc-1)
+call mpp_max(maxlon_c); call mpp_min(minlon_c)
+grd%maxlon_c=maxlon_c; grd%minlon_c=minlon_c
+
+
 if (read_old_restarts) call error_mesg('KID, ice_bergs_framework_init', 'Setting "read_old_restarts=.true." is obsolete and does nothing!', WARNING)
 
 ! Diagnostics
@@ -1302,7 +1380,21 @@ subroutine update_halo_icebergs(bergs)
 
   do grdj = grd%jsd,grd%jed ;    do grdi = grd%iec+1,grd%ied
     call delete_all_bergs_in_list(bergs,grdj,grdi)
-  enddo ; enddo
+  enddo; enddo
+
+  if (bergs%mts) then
+    !remove conglomerate bergs outside halo
+    do grdj = grd%jsc,grd%jec ;    do grdi = grd%isc,grd%iec
+      this=>bergs%list(grdi,grdj)%first
+      do while (associated(this))
+        kick_the_bucket=>this
+        this=>this%next
+        if (kick_the_bucket%halo_berg .ne. 0) then
+          call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
+        end if
+      enddo
+    enddo;enddo
+  end if  
 
   call mpp_sync_self()
 
@@ -1521,6 +1613,11 @@ subroutine update_halo_icebergs(bergs)
     call show_all_bonds(bergs)
   endif
 
+  if (bergs%mts) then
+    call mpp_sync_self()    
+    call transfer_mts_bergs(bergs)
+  end if  
+
   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!Debugging!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
   if (debug) then
     nbergs_end=count_bergs(bergs)
@@ -1565,6 +1662,742 @@ subroutine update_halo_icebergs(bergs)
 
 end subroutine update_halo_icebergs
 
+!> For the MTS Verlet scheme: entire conglomerates of iceberg elements are passed between all
+!! PEs that they overlap, skipping the elements that were already transferred. Berg elements
+!! within contact distance of the conglomerates must also be transferred.
+subroutine transfer_mts_bergs(bergs)
+! Arguments
+type(icebergs), pointer :: bergs !< Container for all types and memory
+! Local variables
+type(iceberg), pointer :: kick_the_bucket, this
+integer :: nbergs_to_send_e, nbergs_to_send_w
+integer :: nbergs_to_send_n, nbergs_to_send_s
+integer :: nbergs_rcvd_from_e, nbergs_rcvd_from_w
+integer :: nbergs_rcvd_from_n, nbergs_rcvd_from_s
+type(icebergs_gridded), pointer :: grd
+integer :: i
+integer :: stderrunit
+integer :: grdi, grdj, grdi2, grdj2
+integer :: halo_width
+real :: current_halo_status,current_lat,current_lon
+logical :: halo_debugging,leavedo
+integer :: conglom_count,nc,contact_distance,last_berg,last_cell
+real :: Lx,dist,dx,dy
+logical :: periodicityfix
+
+  halo_width=bergs%grd%halo
+  halo_debugging=bergs%halo_debugging
+  nc=bergs%num_contact_cells
+  contact_distance=bergs%contact_distance
+
+  ! Get the stderr unit number
+  stderrunit = stderr()
+
+  ! For convenience
+  grd=>bergs%grd
+  
+  Lx = grd%Lx
+  periodicityfix=.false.
+  
+  nbergs_to_send_e=0
+  nbergs_to_send_w=0
+
+  !connect bonds currently residing on each PE.
+  !Needed to determine which conglomerate elements to send.
+  call connect_all_bonds(bergs,ignore_unmatched=.true.)
+
+  !---Step A. summary of current halo_berg statuses on current PE---
+  !halo_berg=0: bergs on computational domain
+  !halo_berg=1: bergs on halo domain
+  
+  ! Send all berg elements (east/west) in conglomerate:
+  ! conglomerate berg elements to send EAST:
+  last_berg=-1
+  if (Lx>0.0 .and. grd%lon(grd%iec,grd%jec).eq. grd%maxlon_c) periodicityfix=.true.
+  grdi = grd%iec-halo_width+2
+  do grdj = grd%jsd+1,grd%jed   !mark the additional elements to send
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this))
+      !mark conglomerate elements west of the eastern halo as
+      !halo_berg = halo_berg+2 (so their new halo_berg will equal 2 or 3)      
+      call mts_mark_conglomerate_bergs(this,grdi,1) 
+      this=>this%next
+    enddo
+  enddo
+  !add them to the buffer:
+  conglom_count = 1
+  do while(conglom_count>0)
+    grdi=grdi-1
+    if (grdi<grd%isd+1) exit
+    conglom_count = 0
+    do grdj = grd%jsd+1,grd%jed
+      this=>bergs%list(grdi,grdj)%first
+      do while (associated(this))
+        if (this%halo_berg>1) then
+          conglom_count=conglom_count+1
+          kick_the_bucket=>this
+          current_halo_status=kick_the_bucket%halo_berg
+          this=>this%next
+          kick_the_bucket%halo_berg=2.
+          nbergs_to_send_e=nbergs_to_send_e+1
+          if (periodicityfix) kick_the_bucket%lon=kick_the_bucket%lon-Lx
+          call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_e, nbergs_to_send_e, bergs%max_bonds)        
+          !kick_the_bucket%halo_berg=current_halo_status-2 !unmark
+          kick_the_bucket%halo_berg=current_halo_status
+          last_berg=kick_the_bucket%id
+          if (periodicityfix) kick_the_bucket%lon=kick_the_bucket%lon+Lx
+        else
+          this=>this%next
+        end if
+      enddo
+    enddo
+  enddo
+
+  !---Step B: updated summary of current halo_berg statuses on current PE---
+  !halo_berg=0: bergs on computational domain
+  !halo_berg=1: bergs on halo domain
+  !halo_berg=2: conglomerate bergs, packed to send east, from computational domain
+  !halo_berg=3: conglomerate bergs, packed to send east, from halo domain
+
+  !now mark non-conglomerate bergs within the contact distance of the conglomerate
+  !to send EAST as halo_berg=halo_berg+4,that also need to sent EAST:
+  last_cell=grd%iec-halo_width+1
+  leavedo=.false.
+
+  do grdi=grd%iec-halo_width+2,grd%isd+1,-1 !outer cell i-loop
+    do grdj = grd%jsd+1,grd%jed !outer cell j-loop
+      this=>bergs%list(grdi,grdj)%first
+      do while (associated(this)) !outer berg loop
+        if (this%halo_berg>1) then
+          !conglomerate berg found. search surroundings for non_conglomerate bergs within the
+          !contact distance, and add to buffer
+          if (grdi<last_cell) last_cell=grdi
+          do grdj2=max(grdj-nc,grd%jsd+1),min(grdj+nc,grd%jed); &
+            do grdi2=max(grdi-nc,grd%isd+1),min(grdi+nc,grd%iec-halo_width+1) !inner cell loop
+            !if (grdi2>grd%iec-halo_width+1) cycle !don't process east halo cells 
+            kick_the_bucket=>bergs%list(grdi2,grdj2)%first
+            do while (associated(kick_the_bucket)) ! inner berg loop
+              if (kick_the_bucket%halo_berg < 2) then
+                dx=kick_the_bucket%lon-this%lon
+                dy=kick_the_bucket%lat-this%lat
+                dist=dx*dx+dy*dy
+                if (dist<contact_distance*contact_distance) then
+                  current_halo_status=kick_the_bucket%halo_berg+4
+                  kick_the_bucket%halo_berg=10
+                  nbergs_to_send_e=nbergs_to_send_e+1
+                  if (periodicityfix) kick_the_bucket%lon=kick_the_bucket%lon-Lx
+                  call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_e, nbergs_to_send_e, bergs%max_bonds)
+                  kick_the_bucket%halo_berg=current_halo_status
+                  if (periodicityfix) kick_the_bucket%lon=kick_the_bucket%lon+Lx
+                  if (kick_the_bucket%ine<last_cell) last_cell=kick_the_bucket%ine
+                endif
+              endif
+              kick_the_bucket=>kick_the_bucket%next
+            enddo !inner berg loop
+          enddo; enddo !inner cell loop
+        endif
+        if (this%id==last_berg) then
+          leavedo=.true.
+          this=>null()
+          exit
+        else
+          this=>this%next
+        endif
+      enddo !outer berg loop
+      if (leavedo) exit
+    enddo !outer cell j-loop
+    if (leavedo) exit
+  enddo !outer cell i-loop
+
+  periodicityfix=.false.
+  leavedo=.false.
+
+  !---Step C: updated summary of current halo_berg statuses on current PE---
+  !adding to Step B, we now also have:
+  !halo_berg=4: non-conglomerate bergs on computational domain, within contact distance of conglom to send E
+  !halo_berg=5: non-conglomerate bergs on a halo domain, within contact distance of conglom to send E
+
+  !now go back and reset berg halo statuses that are being sent EAST to the way it was in Step A above
+  do grdi=grd%iec-halo_width+1,last_cell,-1
+    do grdj = grd%jsd+1,grd%jed
+      this=>bergs%list(grdi,grdj)%first
+      do while (associated(this))
+        if (this%halo_berg>1) then 
+          if (this%halo_berg<4) then
+            this%halo_berg=this%halo_berg-2
+          else
+            this%halo_berg=this%halo_berg-4
+          endif
+        endif
+        this=>this%next
+      enddo
+    enddo
+  enddo
+
+  !---Step D: updated summary of current halo_berg statuses on current PE---
+  ! Same as Step A summary
+  
+
+  !----now do Steps A-D for the bergs to send west:----
+  ! conglomerate berg elements to send WEST:  
+  last_berg=-1  
+  if (Lx>0.0 .and. grd%lon(grd%isc-1,grd%jsc-1).eq. grd%minlon_c) periodicityfix=.true.  
+  grdi = grd%isc+halo_width-1
+  do grdj = grd%jsd+1,grd%jed
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this))
+      call mts_mark_conglomerate_bergs(this,grdi,-1)
+      this=>this%next
+    enddo
+  enddo
+  !add them to the buffer:
+  conglom_count = 1
+  do while(conglom_count>0)
+    grdi=grdi+1
+    if (grdi>grd%ied) exit
+    conglom_count = 0
+    do grdj = grd%jsd+1,grd%jed
+      this=>bergs%list(grdi,grdj)%first
+      do while (associated(this))
+        if (this%halo_berg>1) then
+          conglom_count=conglom_count+1
+          kick_the_bucket=>this
+          current_halo_status=kick_the_bucket%halo_berg
+          this=>this%next
+          kick_the_bucket%halo_berg=2.
+          nbergs_to_send_w=nbergs_to_send_w+1
+          if (periodicityfix) kick_the_bucket%lon=kick_the_bucket%lon+Lx
+          call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_w, nbergs_to_send_w, bergs%max_bonds)
+          !kick_the_bucket%halo_berg=current_halo_status-2 !unmark
+          kick_the_bucket%halo_berg=current_halo_status
+          last_berg=kick_the_bucket%id          
+          if (periodicityfix) kick_the_bucket%lon=kick_the_bucket%lon-Lx
+        else
+          this=>this%next
+        end if
+      enddo
+    enddo
+  enddo
+
+  !now mark non-conglomerate bergs within the contact distance of the conglomerate
+  !to send WEST as halo_berg=halo_berg+4,that also need to be sent WEST:
+  last_cell=grd%isc+halo_width
+
+  do grdi=grd%isc+halo_width-1,grd%ied !outer cell i-loop
+    do grdj = grd%jsd+1,grd%jed !outer cell j-loop
+      this=>bergs%list(grdi,grdj)%first
+      do while (associated(this)) !outer berg loop
+        if (this%halo_berg>1) then
+          !conglomerate berg found. search surroundings for non_conglomerate bergs within the
+          !contact distance, and add to buffer
+          if (grdi>last_cell) last_cell=grdi
+          do grdj2=max(grdj-nc,grd%jsd+1),min(grdj+nc,grd%jed); &
+            do grdi2=max(grdi-nc,grd%isc+halo_width),min(grdi+nc,grd%ied) !inner cell loop
+            !if (grdi2<grd%isc+halo_width) cycle
+            kick_the_bucket=>bergs%list(grdi2,grdj2)%first
+            do while (associated(kick_the_bucket)) ! inner berg loop
+              if (kick_the_bucket%halo_berg < 2) then
+                dx=kick_the_bucket%lon-this%lon
+                dy=kick_the_bucket%lat-this%lat
+                dist=dx*dx+dy*dy
+                if (dist<contact_distance*contact_distance) then                
+                  current_halo_status=kick_the_bucket%halo_berg+4
+                  kick_the_bucket%halo_berg=10
+                  nbergs_to_send_w=nbergs_to_send_w+1
+                  if (periodicityfix) kick_the_bucket%lon=kick_the_bucket%lon+Lx
+                  call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_w, nbergs_to_send_w, bergs%max_bonds)
+                  kick_the_bucket%halo_berg=current_halo_status
+                  if (periodicityfix) kick_the_bucket%lon=kick_the_bucket%lon-Lx
+                  if (kick_the_bucket%ine>last_cell) last_cell=kick_the_bucket%ine
+                endif
+              endif
+              kick_the_bucket=>kick_the_bucket%next
+            enddo !inner berg loop
+          enddo; enddo !inner cell loop
+        endif
+        if (this%id==last_berg) then
+          leavedo=.true.
+          this=>null()
+          exit
+        else
+          this=>this%next
+        endif
+      enddo !outer berg loop
+      if (leavedo) exit
+    enddo !outer cell j-loop
+    if (leavedo) exit
+  enddo !outer cell i-loop
+  
+  periodicityfix=.false.
+  leavedo=.false.
+
+  !now go back and reset berg halo statuses that are being sent WEST to the way it was in Step A above
+  do grdi=grd%isc+halo_width,last_cell
+    do grdj = grd%jsd+1,grd%jed
+      this=>bergs%list(grdi,grdj)%first
+      do while (associated(this))
+        if (this%halo_berg>1) then 
+          if (this%halo_berg<4) then
+            this%halo_berg=this%halo_berg-2
+          else
+            this%halo_berg=this%halo_berg-4
+          endif
+        endif
+        this=>this%next
+      enddo
+    enddo
+  enddo
+
+  !----finished E/W packing----
+
+  ! Send bergs east
+  if (grd%pe_E.ne.NULL_PE) then
+    call mpp_send(nbergs_to_send_e, plen=1, to_pe=grd%pe_E, tag=COMM_TAG_1)
+    if (nbergs_to_send_e.gt.0) then
+      call mpp_send(bergs%obuffer_e%data, nbergs_to_send_e*buffer_width, grd%pe_E, tag=COMM_TAG_2)
+    endif
+  endif
+
+  ! Send bergs west
+  if (grd%pe_W.ne.NULL_PE) then
+    call mpp_send(nbergs_to_send_w, plen=1, to_pe=grd%pe_W, tag=COMM_TAG_3)
+    if (nbergs_to_send_w.gt.0) then
+      call mpp_send(bergs%obuffer_w%data, nbergs_to_send_w*buffer_width, grd%pe_W, tag=COMM_TAG_4)
+    endif
+  endif
+
+  ! Receive bergs from west
+  if (grd%pe_W.ne.NULL_PE) then
+    nbergs_rcvd_from_w=-999
+    call mpp_recv(nbergs_rcvd_from_w, glen=1, from_pe=grd%pe_W, tag=COMM_TAG_1)
+    if (nbergs_rcvd_from_w.lt.0) then
+      write(stderrunit,*) 'pe=',mpp_pe(),' received a bad number',nbergs_rcvd_from_w,' from',grd%pe_W,' (W) !!!!!!!!!!!!!!!!!!!!!!'
+    endif
+    if (nbergs_rcvd_from_w.gt.0) then
+      call increase_ibuffer(bergs%ibuffer_w, nbergs_rcvd_from_w,buffer_width)
+      call mpp_recv(bergs%ibuffer_w%data, nbergs_rcvd_from_w*buffer_width, grd%pe_W, tag=COMM_TAG_2)
+      do i=1, nbergs_rcvd_from_w
+        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_w, i, grd, max_bonds_in=bergs%max_bonds )
+      enddo
+    endif
+  else
+    nbergs_rcvd_from_w=0
+  endif
+
+  ! Receive bergs from east
+  if (grd%pe_E.ne.NULL_PE) then
+    nbergs_rcvd_from_e=-999
+    call mpp_recv(nbergs_rcvd_from_e, glen=1, from_pe=grd%pe_E, tag=COMM_TAG_3)
+    if (nbergs_rcvd_from_e.lt.0) then
+      write(stderrunit,*) 'pe=',mpp_pe(),' received a bad number',nbergs_rcvd_from_e,' from',grd%pe_E,' (E) !!!!!!!!!!!!!!!!!!!!!!'
+    endif
+    if (nbergs_rcvd_from_e.gt.0) then
+      call increase_ibuffer(bergs%ibuffer_e, nbergs_rcvd_from_e,buffer_width)
+      call mpp_recv(bergs%ibuffer_e%data, nbergs_rcvd_from_e*buffer_width, grd%pe_E, tag=COMM_TAG_4)
+      do i=1, nbergs_rcvd_from_e
+        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_e, i, grd, max_bonds_in=bergs%max_bonds )
+      enddo
+    endif
+  else
+    nbergs_rcvd_from_e=0
+  endif
+
+  !---Step E. updated summary of current halo_berg statuses on current PE---
+  !halo_berg=0: bergs on computational domain
+  !halo_berg=1: bergs on halo domain
+  !halo_berg=2: conglomerate bergs received from the computational domain of the PE to the East or West
+  !halo_berg=10: bergs received from the computational domain of the PE to the East or West that are
+  !             within contact distance to any of the current PE bergs with halo_berg==1 or 2
+
+  !reconnect bonds in preparation for sending north/south
+  call mpp_sync_self() 
+  call connect_all_bonds(bergs,ignore_unmatched=.true.)
+  do grdj = grd%jsd+1,grd%jed ;  do grdi = grd%isd+1,grd%ied
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this))
+      !conglomerate elements from the E/W transfers now have berg%halo_berg==2 or 3, and
+      !
+      !The conglomerate elements for the N/S transfers will also be given halo_berg>1 below.
+      !Before the N/S transfer procedure, temporarily change the sign of the conglomerate
+      !halo_berg statuses from the E/W transfers to differentiate between the E/W vs N/S procedures.
+      if (this%halo_berg>1) this%halo_berg=-this%halo_berg      
+      this=>this%next
+    enddo
+  enddo; enddo
+
+  nbergs_to_send_n=0
+  nbergs_to_send_s=0
+
+  ! ---Send all berg elements (north/south) in conglomerate---:
+  ! conglomerate berg elements to send NORTH:  
+  last_berg=-1  
+  do grdj = grd%jec-halo_width+2,grd%jed; do grdi = grd%isd+1,grd%ied
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this))
+      call mts_mark_conglomerate_bergs(this,grdj,2)
+      this=>this%next
+    enddo
+  enddo; enddo
+  !add them to the buffer:
+  grdj = grd%jed+1
+  conglom_count = 1
+  do while(conglom_count>0 .or. grdj .ge. grd%jec-halo_width+2)
+    grdj=grdj-1
+    if (grdj<grd%jsd+1) exit
+    conglom_count = 0
+    do grdi = grd%isd,grd%ied
+      this=>bergs%list(grdi,grdj)%first
+      do while (associated(this))
+        if (this%halo_berg>1) then
+          conglom_count=conglom_count+1
+          kick_the_bucket=>this
+          current_halo_status=kick_the_bucket%halo_berg
+          this=>this%next
+          kick_the_bucket%halo_berg=2.
+          nbergs_to_send_n=nbergs_to_send_n+1
+          call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_n, nbergs_to_send_n, bergs%max_bonds)
+          !kick_the_bucket%halo_berg=-(current_halo_status-2) !unmark
+          kick_the_bucket%halo_berg=current_halo_status
+          last_berg=kick_the_bucket%id   
+        else
+          this=>this%next
+        end if
+      enddo
+    enddo
+  enddo
+
+    !---Step F. updated summary of current halo_berg statuses on current PE---
+  !halo_berg=0: bergs on computational domain
+  !halo_berg=1: bergs on halo domain
+  !halo_berg=-2: conglomerate bergs received from the computational domain of the PE to the East or West
+  !halo_berg=-10: bergs received from the computational domain of the PE to the East or West that are
+  !             within contact distance to any of the current PE bergs with halo_berg==1 or 2
+  !halo_berg=2:  same as halo_berg=0,   but marked as conglom to send North
+  !halo_berg=3:  same as halo_berg=1,   but marked as conglom to send North
+  !halo_berg=4:  same as halo_berg=-2,  but marked as conglom to send North
+  !halo_berg=12: same as halo_berg=-10, but marked as conglom to send North
+
+  !now mark non-conglomerate bergs within the contact distance of the conglomerate
+  !to send NORTH as halo_berg=halo_berg+111,that also need to sent NORTH:
+  last_cell=grd%jec-halo_width+1
+
+  do grdj=grd%jec-halo_width+2,grd%jsd+1,-1 !outer cell j-loop
+    do grdi = grd%isd+1,grd%ied !outer cell i-loop
+      this=>bergs%list(grdi,grdj)%first
+      do while (associated(this)) !outer berg loop
+        if (this%halo_berg>1) then
+          !conglomerate berg found. search surroundings for non_conglomerate bergs within the
+          !contact distance, and add to buffer
+          if (grdj<last_cell) last_cell=grdj
+          do grdj2=max(grdj-nc,grd%jsd+1),min(grdj+nc,grd%jec-halo_width+1) !inner cell j-loop
+            !if (grdj2>grd%jec-halo_width+1) cycle !don't process east halo cells 
+            do grdi2=max(grdi-nc,grd%isd+1),min(grdi+nc,grd%ied) !inner cell i-loop
+              kick_the_bucket=>bergs%list(grdi2,grdj2)%first
+              do while (associated(kick_the_bucket)) ! inner berg loop
+                if (kick_the_bucket%halo_berg < 2) then
+                  dx=kick_the_bucket%lon-this%lon
+                  dy=kick_the_bucket%lat-this%lat
+                  dist=dx*dx+dy*dy
+                  if (dist<contact_distance*contact_distance) then                  
+                    current_halo_status=kick_the_bucket%halo_berg+111 !guaranteed to be above 100
+                    kick_the_bucket%halo_berg=10 
+                    nbergs_to_send_e=nbergs_to_send_n+1
+                    call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_n, nbergs_to_send_n, bergs%max_bonds)
+                    kick_the_bucket%halo_berg=current_halo_status
+                    if (kick_the_bucket%jne<last_cell) last_cell=kick_the_bucket%jne
+                  endif
+                endif
+                kick_the_bucket=>kick_the_bucket%next
+              enddo !inner berg loop
+            enddo !inner cell i-loop
+          enddo !inner cell j-loop
+        endif
+        if (this%id==last_berg) then
+          leavedo=.true.
+          this=>null()
+          exit
+        else
+          this=>this%next
+        endif
+      enddo !outer berg loop
+      if (leavedo) exit
+    enddo !outer cell i-loop
+    if (leavedo) exit
+  enddo !outer cell j-loop
+
+  leavedo=.false.
+
+  !now go back and reset berg halo statuses that are being sent NORTH to the way it was in Step F above
+  do grdj=grd%jec-halo_width+1,last_cell,-1
+    do grdi = grd%isd+1,grd%ied
+      this=>bergs%list(grdi,grdj)%first
+      do while (associated(this))
+        if (this%halo_berg>1) then 
+          if (this%halo_berg<4) then
+            this%halo_berg=this%halo_berg-2
+          elseif (this%halo_berg>100) then
+            this%halo_berg=this%halo_berg-111
+          else
+            this%halo_berg=-(this%halo_berg-2)
+          endif
+        endif
+        this=>this%next
+      enddo
+    enddo
+  enddo  
+
+  !--do the same for transfers to SOUTH--
+
+  ! conglomerate berg elements to send SOUTH:  
+  last_berg=-1  
+  do grdj = grd%jsd+1,grd%jsc+halo_width-1; do grdi = grd%isd,grd%ied
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this))
+      call mts_mark_conglomerate_bergs(this,grdj,-2)
+      this=>this%next
+    enddo
+  enddo; enddo
+  grdj = grd%jsd
+  !add them to the buffer:
+  conglom_count = 1
+  do while(conglom_count>0 .or. grdj .le. grd%jsc+halo_width-1)
+    grdj=grdj+1
+    if (grdj>grd%jed) exit
+    conglom_count = 0
+    do grdi = grd%isd,grd%ied
+      this=>bergs%list(grdi,grdj)%first
+      do while (associated(this))
+        if (this%halo_berg>1) then
+          conglom_count=conglom_count+1
+          kick_the_bucket=>this
+          current_halo_status=kick_the_bucket%halo_berg
+          this=>this%next
+          kick_the_bucket%halo_berg=2.
+          nbergs_to_send_s=nbergs_to_send_s+1
+          call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_s, nbergs_to_send_s, bergs%max_bonds)
+          !kick_the_bucket%halo_berg=-(current_halo_status-2) !unmark
+          kick_the_bucket%halo_berg=current_halo_status
+          last_berg=kick_the_bucket%id    
+        else
+          this=>this%next
+        end if
+      enddo
+    enddo
+  enddo
+
+  !now mark non-conglomerate bergs within the contact distance of the conglomerate
+  !to send SOUTH as halo_berg=halo_berg+111,that also need to be sent SOUTH:
+  last_cell=grd%jsc+halo_width
+
+  do grdj=grd%jsc+halo_width-1,grd%jed !outer cell i-loop
+    do grdi = grd%isd+1,grd%ied !outer cell j-loop
+      this=>bergs%list(grdi,grdj)%first
+      do while (associated(this)) !outer berg loop
+        if (this%halo_berg>1) then
+          !conglomerate berg found. search surroundings for non_conglomerate bergs within the
+          !contact distance, and add to buffer
+          if (grdj>last_cell) last_cell=grdj
+          do grdj2=max(grdj-nc,grd%jsc+halo_width),min(grdj+nc,grd%jed) !inner cell j-loop
+            !if (grdj2<grd%jsc+halo_width) cycle
+            do grdi2=max(grdi-nc,grd%isd+1),min(grdi+nc,grd%ied) !inner cell i-loop
+              kick_the_bucket=>bergs%list(grdi2,grdj2)%first
+              do while (associated(kick_the_bucket)) ! inner berg loop
+                if (kick_the_bucket%halo_berg < 2) then
+                  dx=kick_the_bucket%lon-this%lon
+                  dy=kick_the_bucket%lat-this%lat
+                  dist=dx*dx+dy*dy
+                  if (dist<contact_distance*contact_distance) then                  
+                    current_halo_status=kick_the_bucket%halo_berg+111
+                    kick_the_bucket%halo_berg=10
+                    nbergs_to_send_n=nbergs_to_send_n+1
+                    call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_n, nbergs_to_send_n, bergs%max_bonds)
+                    kick_the_bucket%halo_berg=current_halo_status
+                    if (kick_the_bucket%jne>last_cell) last_cell=kick_the_bucket%jne
+                  endif
+                endif
+                kick_the_bucket=>kick_the_bucket%next
+              enddo !inner berg loop
+            enddo !inner cell i-loop
+          enddo !inner cell j-loop
+        endif
+        if (this%id==last_berg) then
+          leavedo=.true.
+          this=>null()
+          exit
+        else
+          this=>this%next
+        endif
+      enddo !outer berg loop
+      if (leavedo) exit
+    enddo !outer cell i-loop
+    if (leavedo) exit
+  enddo !outer cell j-loop
+  
+  leavedo=.false.
+
+  !now go back and reset berg halo statuses that are being sent SOUTH to the way it was in Step E above
+  do grdj=grd%jsd+1,grd%jed
+    do grdi = grd%isd+1,grd%ied
+      this=>bergs%list(grdi,grdj)%first
+      do while (associated(this))
+        if (this%halo_berg>1) then 
+          if (this%halo_berg<4) then
+            this%halo_berg=this%halo_berg-2
+          elseif (this%halo_berg>100) then
+            this%halo_berg=abs(this%halo_berg-111)
+          else
+            this%halo_berg=this%halo_berg-2
+          endif
+        elseif (this%halo_berg<0) then
+          this%halo_berg=abs(this%halo_berg)
+        endif
+        this=>this%next        
+      enddo
+    enddo
+  enddo
+
+  !---Step G. updated summary of current halo_berg statuses on current PE---
+  ! Same as Step E
+
+
+ ! Send bergs north
+  if (grd%pe_N.ne.NULL_PE) then
+    if(folded_north_on_pe) then
+      call mpp_send(nbergs_to_send_n, plen=1, to_pe=grd%pe_N, tag=COMM_TAG_9)
+    else
+      call mpp_send(nbergs_to_send_n, plen=1, to_pe=grd%pe_N, tag=COMM_TAG_5)
+    endif
+    if (nbergs_to_send_n.gt.0) then
+      if(folded_north_on_pe) then
+        call mpp_send(bergs%obuffer_n%data, nbergs_to_send_n*buffer_width, grd%pe_N, tag=COMM_TAG_10)
+      else
+        call mpp_send(bergs%obuffer_n%data, nbergs_to_send_n*buffer_width, grd%pe_N, tag=COMM_TAG_6)
+      endif
+    endif
+  endif
+
+  ! Send bergs south
+  if (grd%pe_S.ne.NULL_PE) then
+    call mpp_send(nbergs_to_send_s, plen=1, to_pe=grd%pe_S, tag=COMM_TAG_7)
+    if (nbergs_to_send_s.gt.0) then
+      call mpp_send(bergs%obuffer_s%data, nbergs_to_send_s*buffer_width, grd%pe_S, tag=COMM_TAG_8)
+    endif
+  endif
+
+  ! Receive bergs from south
+  if (grd%pe_S.ne.NULL_PE) then
+    nbergs_rcvd_from_s=-999
+    call mpp_recv(nbergs_rcvd_from_s, glen=1, from_pe=grd%pe_S, tag=COMM_TAG_5)
+    if (nbergs_rcvd_from_s.lt.0) then
+      write(stderrunit,*) 'pe=',mpp_pe(),' received a bad number',nbergs_rcvd_from_s,' from',grd%pe_S,' (S) !!!!!!!!!!!!!!!!!!!!!!'
+    endif
+    if (nbergs_rcvd_from_s.gt.0) then
+      call increase_ibuffer(bergs%ibuffer_s, nbergs_rcvd_from_s,buffer_width)
+      call mpp_recv(bergs%ibuffer_s%data, nbergs_rcvd_from_s*buffer_width, grd%pe_S, tag=COMM_TAG_6)
+      do i=1, nbergs_rcvd_from_s
+        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_s, i, grd, max_bonds_in=bergs%max_bonds  )
+      enddo
+    endif
+  else
+    nbergs_rcvd_from_s=0
+  endif
+
+  ! Receive bergs from north
+  if (grd%pe_N.ne.NULL_PE) then
+    nbergs_rcvd_from_n=-999
+    if(folded_north_on_pe) then
+      call mpp_recv(nbergs_rcvd_from_n, glen=1, from_pe=grd%pe_N, tag=COMM_TAG_9)
+    else
+      call mpp_recv(nbergs_rcvd_from_n, glen=1, from_pe=grd%pe_N, tag=COMM_TAG_7)
+    endif
+    if (nbergs_rcvd_from_n.lt.0) then
+      write(stderrunit,*) 'pe=',mpp_pe(),' received a bad number',nbergs_rcvd_from_n,' from',grd%pe_N,' (N) !!!!!!!!!!!!!!!!!!!!!!'
+    endif
+    if (nbergs_rcvd_from_n.gt.0) then
+      call increase_ibuffer(bergs%ibuffer_n, nbergs_rcvd_from_n,buffer_width)
+      if(folded_north_on_pe) then
+        call mpp_recv(bergs%ibuffer_n%data, nbergs_rcvd_from_n*buffer_width, grd%pe_N, tag=COMM_TAG_10)
+      else
+        call mpp_recv(bergs%ibuffer_n%data, nbergs_rcvd_from_n*buffer_width, grd%pe_N, tag=COMM_TAG_8)
+      endif
+      do i=1, nbergs_rcvd_from_n
+        call unpack_berg_from_buffer2(bergs, bergs%ibuffer_n, i, grd, max_bonds_in=bergs%max_bonds )
+      enddo
+    endif
+  else
+    nbergs_rcvd_from_n=0
+  endif
+
+  call mpp_sync_self()
+  
+  ! For debugging
+  if (halo_debugging) then
+    call mpp_sync_self()
+    do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
+      this=>bergs%list(grdi,grdj)%first
+      do while (associated(this))
+        write(stderrunit,'(a,5i)')  'MTS_C', this%id, mpp_pe(), int(this%halo_berg),  grdi, grdj
+        this=>this%next
+      enddo
+    enddo; enddo
+    call show_all_bonds(bergs)
+  endif
+
+end subroutine transfer_mts_bergs
+
+
+!> For the MTS scheme, marks the conglomerate icebergs elements that overlap
+!! multiple processors as berg%halo_berg>1.
+recursive subroutine mts_mark_conglomerate_bergs(berg,completedcell,dir)
+  type(iceberg), pointer :: berg
+  integer,intent(in) :: completedcell !<column of halo cells that has already sent bergs
+  integer, intent(in) :: dir !<direction bergs will be sent. East/West=1, North/South=2
+  integer :: k
+  type(iceberg), pointer :: other_berg
+  type(bond) , pointer :: current_bond
+  
+  current_bond=>berg%first_bond
+  do while (associated(current_bond))
+    if  (associated(current_bond%other_berg)) then
+      other_berg=>current_bond%other_berg
+      if (abs(dir) == 1) then         !for an east/west transfer
+        !to east
+        if (dir==1) then
+          !mark other berg if not already marked, and not in halo cell (which has already been processed)
+          if (other_berg%halo_berg<2 .and. other_berg%ine .lt. completedcell) then
+            other_berg%halo_berg=other_berg%halo_berg+2 
+            call mts_mark_conglomerate_bergs(other_berg,completedcell,dir)
+          end if
+        else
+          !to west
+          if (other_berg%halo_berg<2 .and. other_berg%ine .gt. completedcell) then
+            other_berg%halo_berg=other_berg%halo_berg+2
+            call mts_mark_conglomerate_bergs(other_berg,completedcell,dir)
+          end if
+        end if
+      elseif (abs(dir) == 2) then     !for a north/south transfer
+        if (dir == 2) then
+          !to north
+          !mark other berg if not already marked. The other berg can be located in a halo cell, but only
+          !if it has ended up there from being passed between PEs during the earlier E/W conglomerate transfer
+          if ((other_berg%halo_berg<2 .and. other_berg%jne .lt. completedcell) .or. other_berg%halo_berg<1) then
+            other_berg%halo_berg=abs(other_berg%halo_berg)+2
+            call mts_mark_conglomerate_bergs(other_berg,completedcell,dir)
+          end if
+        else
+          !to south
+          if ((other_berg%halo_berg<2 .and. other_berg%jne .gt. completedcell) .or. other_berg%halo_berg<1) then          
+            other_berg%halo_berg=abs(other_berg%halo_berg)+2
+            call mts_mark_conglomerate_bergs(other_berg,completedcell,dir)
+          end if
+        end if
+      end if
+    end if
+    current_bond=>current_bond%next_bond
+  enddo
+end subroutine mts_mark_conglomerate_bergs
+
+
 !> Destroys all bergs in a list
 subroutine delete_all_bergs_in_list(bergs, grdj, grdi)
   type(icebergs), pointer :: bergs !< Container for all types and memory
@@ -1884,7 +2717,28 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
   call split_id(berg%id, id_cnt, id_ij)
   call push_buffer_value(buff%data(:,n), counter, id_cnt)
   call push_buffer_value(buff%data(:,n), counter, id_ij)
-
+  
+  if (mts) then
+    call push_buffer_value(buff%data(:,n), counter, berg%uvel_prev)
+    call push_buffer_value(buff%data(:,n), counter, berg%vvel_prev)
+    call push_buffer_value(buff%data(:,n), counter, berg%axn_fast)
+    call push_buffer_value(buff%data(:,n), counter, berg%ayn_fast)
+    call push_buffer_value(buff%data(:,n), counter, berg%bxn_fast)
+    call push_buffer_value(buff%data(:,n), counter, berg%byn_fast)  
+    call push_buffer_value(buff%data(:,n), counter, berg%uo)
+    call push_buffer_value(buff%data(:,n), counter, berg%vo)
+    call push_buffer_value(buff%data(:,n), counter, berg%ua)
+    call push_buffer_value(buff%data(:,n), counter, berg%va)
+    call push_buffer_value(buff%data(:,n), counter, berg%ui)
+    call push_buffer_value(buff%data(:,n), counter, berg%vi)
+    call push_buffer_value(buff%data(:,n), counter, berg%ssh_x)
+    call push_buffer_value(buff%data(:,n), counter, berg%ssh_y)
+    call push_buffer_value(buff%data(:,n), counter, berg%sst)
+    call push_buffer_value(buff%data(:,n), counter, berg%sss)
+    call push_buffer_value(buff%data(:,n), counter, berg%cn)
+    call push_buffer_value(buff%data(:,n), counter, berg%hi)
+  endif
+  
   if (max_bonds .gt. 0) then
     current_bond=>berg%first_bond
     do k = 1,max_bonds
@@ -1995,25 +2849,26 @@ end subroutine clear_berg_from_partners_bonds
 
 !> Unpacks a berg entry from a buffer to a new berg
 subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds_in)
-! Arguments
-type(icebergs), pointer :: bergs !< Container for all types and memory
-type(buffer), pointer :: buff !< Buffer from which to unpack berg
-integer, intent(in) :: n !< Position in buffer to unpack
-type(icebergs_gridded), pointer :: grd !< Container for gridded fields
-logical, optional :: force_append !< <undocumented>
-integer, optional :: max_bonds_in !< <undocumented>
-! Local variables
-!real :: lon, lat, uvel, vvel, xi, yj
-!real :: start_lon, start_lat, start_day, start_mass
-!integer :: ine, jne, start_year
-logical :: lres
-type(iceberg) :: localberg
-type(iceberg), pointer :: this
-integer :: other_berg_ine, other_berg_jne
-integer :: counter, k, max_bonds, id_cnt, id_ij
-integer(kind=8) :: id
-integer :: stderrunit
-logical :: force_app
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  type(buffer), pointer :: buff !< Buffer from which to unpack berg
+  integer, intent(in) :: n !< Position in buffer to unpack
+  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+  logical, optional :: force_append !< <undocumented>
+  integer, optional :: max_bonds_in !< <undocumented>
+  ! Local variables
+  !real :: lon, lat, uvel, vvel, xi, yj
+  !real :: start_lon, start_lat, start_day, start_mass
+  !integer :: ine, jne, start_year
+  logical :: lres
+  type(iceberg) :: localberg
+  type(iceberg), pointer :: this,kick_the_bucket
+  integer :: other_berg_ine, other_berg_jne
+  integer :: counter, k, max_bonds, id_cnt, id_ij
+  integer(kind=8) :: id
+  integer :: stderrunit
+  logical :: force_app,duplicate
+  real :: temp_lon,temp_lat
 
   ! Get the stderr unit number
   stderrunit = stderr()
@@ -2055,42 +2910,142 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
   call pull_buffer_value(buff%data(:,n), counter, id_ij)
   localberg%id = id_from_2_ints(id_cnt, id_ij)
 
+  if (bergs%mts) then
+    call pull_buffer_value(buff%data(:,n), counter, localberg%uvel_prev)
+    call pull_buffer_value(buff%data(:,n), counter, localberg%vvel_prev)    
+    call pull_buffer_value(buff%data(:,n), counter, localberg%axn_fast)
+    call pull_buffer_value(buff%data(:,n), counter, localberg%ayn_fast)
+    call pull_buffer_value(buff%data(:,n), counter, localberg%bxn_fast)
+    call pull_buffer_value(buff%data(:,n), counter, localberg%byn_fast)  
+    call pull_buffer_value(buff%data(:,n), counter, localberg%uo)
+    call pull_buffer_value(buff%data(:,n), counter, localberg%vo)
+    call pull_buffer_value(buff%data(:,n), counter, localberg%ua)
+    call pull_buffer_value(buff%data(:,n), counter, localberg%va)
+    call pull_buffer_value(buff%data(:,n), counter, localberg%ui)
+    call pull_buffer_value(buff%data(:,n), counter, localberg%vi)
+    call pull_buffer_value(buff%data(:,n), counter, localberg%ssh_x)
+    call pull_buffer_value(buff%data(:,n), counter, localberg%ssh_y)
+    call pull_buffer_value(buff%data(:,n), counter, localberg%sst)
+    call pull_buffer_value(buff%data(:,n), counter, localberg%sss)
+    call pull_buffer_value(buff%data(:,n), counter, localberg%cn)
+    call pull_buffer_value(buff%data(:,n), counter, localberg%hi)
+  endif
+
   !These quantities no longer need to be passed between processors
   localberg%uvel_old=localberg%uvel
   localberg%vvel_old=localberg%vvel
   localberg%lon_old=localberg%lon
   localberg%lat_old=localberg%lat
 
-  ! force_app=.true.
-  if(force_app) then !force append with origin ine,jne (for I/O)
-    call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg, this)
-  else
-    lres=find_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
+
+  !when using MTS Verlet, iceberg elements that are part of a conglomerate may lie outside
+  !of the PE's grid. They are assigned to the berg list of the nearest halo cell.
+  !The global (lon/lat) and local (xi,yi) coords of these elements are not adjusted.
+  if (bergs%mts .and. abs(localberg%halo_berg)>1) then
+    temp_lon = localberg%lon
+    temp_lat = localberg%lat
+
+    if (temp_lon > grd%lon(grd%ied,grd%jed)) then
+      temp_lon = grd%lonc(grd%ied,grd%jed)
+    endif
+    if (temp_lon < grd%lon(grd%isd,grd%jsd)) then
+      temp_lon = grd%lonc(grd%isd+1,grd%jsd+1)
+    endif
+    if (temp_lat > grd%lat(grd%ied,grd%jed)) then
+      temp_lat = grd%latc(grd%ied,grd%jed)
+    endif
+    if (temp_lat < grd%lat(grd%isd,grd%jsd)) then
+      temp_lat = grd%latc(grd%isd+1,grd%jsd+1)
+    endif
+
+    lres=find_cell_wide(grd, temp_lon, temp_lat, localberg%ine, localberg%jne)
     if (lres) then
-      lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
-      call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg,this)
+      duplicate=.false.
+      this=>bergs%list(localberg%ine,localberg%jne)%first
+      do while (associated(this) .and. .not. duplicate)
+        if (this%id.eq.localberg%id) then
+          if (this%halo_berg==10) then
+            kick_the_bucket=>this
+            this=>this%next
+            print *,'deleting an iceberg from the list',mpp_pe()
+            call delete_iceberg_from_list(bergs%list(localberg%ine,localberg%jne)%first,kick_the_bucket)
+            print *,'deleted an iceberg from the list',mpp_pe()
+          else
+            duplicate=.true.
+            this=>this%next
+          endif
+        else
+          this=>this%next
+        endif
+      end do
+      if (.not. duplicate) then
+        call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg,this)
+      else
+        return
+      end if
+    else
+      write(stderrunit,'("KID, unpack_berg_from_buffer pe=(",i3,a,2i4,a,2f8.2)')&
+        & mpp_pe(),') Failed to find i,j=',localberg%ine,localberg%jne,&
+        ' for mts conglom berg lon,lat=',localberg%lon,localberg%lat
+      write(stderrunit,*) localberg%lon,localberg%lat
+      write(stderrunit,*) localberg%uvel,localberg%vvel
+      write(stderrunit,*) localberg%axn,localberg%ayn !Alon
+      write(stderrunit,*) localberg%bxn,localberg%byn !Alon
+      if (bergs%mts) then
+        write(stderrunit,*) localberg%axn_fast,localberg%ayn_fast !Alex
+        write(stderrunit,*) localberg%bxn_fast,localberg%byn_fast !Alex
+      endif
+      write(stderrunit,*) localberg%uvel_old,localberg%vvel_old
+      write(stderrunit,*) localberg%lon_old,localberg%lat_old
+      write(stderrunit,*) grd%isc,grd%iec,grd%jsc,grd%jec
+      write(stderrunit,*) grd%isd,grd%ied,grd%jsd,grd%jed
+      write(stderrunit,*) grd%lon(grd%isc-1,grd%jsc-1),grd%lon(grd%iec,grd%jsc)
+      write(stderrunit,*) grd%lat(grd%isc-1,grd%jsc-1),grd%lat(grd%iec,grd%jec)
+      write(stderrunit,*) grd%lon(grd%isd,grd%jsd),grd%lon(grd%ied,grd%jsd)
+      write(stderrunit,*) grd%lat(grd%isd,grd%jsd),grd%lat(grd%ied,grd%jed)
+      write(stderrunit,*) temp_lat,temp_lon
+      write(stderrunit,*) lres
+      call error_mesg('KID, unpack_berg_from_buffer', 'can not find a cell to place berg in!', FATAL)
+    endif
+  else
+    ! force_app=.true.
+    if(force_app) then !force append with origin ine,jne (for I/O)
+      call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg, this)
     else
-      lres=find_cell_wide(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
+      ! lres=find_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
+      !this version is faster, by checking if current ine and jne are appropriate before searching rest of cells.
+      lres=check_and_find_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
       if (lres) then
         lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
         call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg,this)
       else
-        write(stderrunit,'("KID, unpack_berg_from_buffer pe=(",i3,a,2i4,a,2f8.2)')&
-         & mpp_pe(),') Failed to find i,j=',localberg%ine,localberg%jne,' for lon,lat=',localberg%lon,localberg%lat
-        write(stderrunit,*) localberg%lon,localberg%lat
-        write(stderrunit,*) localberg%uvel,localberg%vvel
-        write(stderrunit,*) localberg%axn,localberg%ayn !Alon
-        write(stderrunit,*) localberg%bxn,localberg%byn !Alon
-        write(stderrunit,*) localberg%uvel_old,localberg%vvel_old
-        write(stderrunit,*) localberg%lon_old,localberg%lat_old
-        write(stderrunit,*) grd%isc,grd%iec,grd%jsc,grd%jec
-        write(stderrunit,*) grd%isd,grd%ied,grd%jsd,grd%jed
-        write(stderrunit,*) grd%lon(grd%isc-1,grd%jsc-1),grd%lon(grd%iec,grd%jsc)
-        write(stderrunit,*) grd%lat(grd%isc-1,grd%jsc-1),grd%lat(grd%iec,grd%jec)
-        write(stderrunit,*) grd%lon(grd%isd,grd%jsd),grd%lon(grd%ied,grd%jsd)
-        write(stderrunit,*) grd%lat(grd%isd,grd%jsd),grd%lat(grd%ied,grd%jed)
-        write(stderrunit,*) lres
-        call error_mesg('KID, unpack_berg_from_buffer', 'can not find a cell to place berg in!', FATAL)
+        lres=find_cell_wide(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
+        if (lres) then
+          lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
+          call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg,this)
+        else
+          write(stderrunit,'("KID, unpack_berg_from_buffer pe=(",i3,a,2i4,a,2f8.2)')&
+            & mpp_pe(),') Failed to find i,j=',localberg%ine,localberg%jne,' for lon,lat=',localberg%lon,localberg%lat
+          write(stderrunit,*) localberg%halo_berg
+          write(stderrunit,*) localberg%lon,localberg%lat
+          write(stderrunit,*) localberg%uvel,localberg%vvel
+          write(stderrunit,*) localberg%axn,localberg%ayn !Alon
+          write(stderrunit,*) localberg%bxn,localberg%byn !Alon
+          if (bergs%mts) then
+            write(stderrunit,*) localberg%axn_fast,localberg%ayn_fast !Alex
+            write(stderrunit,*) localberg%bxn_fast,localberg%byn_fast !Alex
+          endif
+          write(stderrunit,*) localberg%uvel_old,localberg%vvel_old
+          write(stderrunit,*) localberg%lon_old,localberg%lat_old
+          write(stderrunit,*) grd%isc,grd%iec,grd%jsc,grd%jec
+          write(stderrunit,*) grd%isd,grd%ied,grd%jsd,grd%jed
+          write(stderrunit,*) grd%lon(grd%isc-1,grd%jsc-1),grd%lon(grd%iec,grd%jsc)
+          write(stderrunit,*) grd%lat(grd%isc-1,grd%jsc-1),grd%lat(grd%iec,grd%jec)
+          write(stderrunit,*) grd%lon(grd%isd,grd%jsd),grd%lon(grd%ied,grd%jsd)
+          write(stderrunit,*) grd%lat(grd%isd,grd%jsd),grd%lat(grd%ied,grd%jed)
+          write(stderrunit,*) lres
+          call error_mesg('KID, unpack_berg_from_buffer', 'can not find a cell to place berg in!', FATAL)
+        endif
       endif
     endif
   endif
@@ -2177,6 +3132,7 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj)
   call split_id(traj%id, cnt, ij)
   call push_buffer_value(buff%data(:,n),counter,cnt)
   call push_buffer_value(buff%data(:,n),counter,ij)
+  
   if (.not. save_short_traj) then
     call push_buffer_value(buff%data(:,n),counter,traj%uvel)
     call push_buffer_value(buff%data(:,n),counter,traj%vvel)
@@ -2200,10 +3156,19 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj)
     call push_buffer_value(buff%data(:,n),counter,traj%axn)
     call push_buffer_value(buff%data(:,n),counter,traj%ayn)
     call push_buffer_value(buff%data(:,n),counter,traj%bxn)
-    call push_buffer_value(buff%data(:,n),counter,traj%byn)
+    call push_buffer_value(buff%data(:,n),counter,traj%byn)  
     call push_buffer_value(buff%data(:,n),counter,traj%halo_berg)
     call push_buffer_value(buff%data(:,n),counter,traj%static_berg)
     call push_buffer_value(buff%data(:,n),counter,traj%sss)
+
+    if (mts) then
+      call push_buffer_value(buff%data(:,n),counter,traj%uvel_prev)
+      call push_buffer_value(buff%data(:,n),counter,traj%vvel_prev)
+      call push_buffer_value(buff%data(:,n),counter,traj%axn_fast)
+      call push_buffer_value(buff%data(:,n),counter,traj%ayn_fast)
+      call push_buffer_value(buff%data(:,n),counter,traj%bxn_fast)
+      call push_buffer_value(buff%data(:,n),counter,traj%byn_fast)
+    endif
   endif
 
 end subroutine pack_traj_into_buffer2
@@ -2251,10 +3216,19 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj)
     call pull_buffer_value(buff%data(:,n),counter,traj%axn)
     call pull_buffer_value(buff%data(:,n),counter,traj%ayn)
     call pull_buffer_value(buff%data(:,n),counter,traj%bxn)
-    call pull_buffer_value(buff%data(:,n),counter,traj%byn)
+    call pull_buffer_value(buff%data(:,n),counter,traj%byn)  
     call pull_buffer_value(buff%data(:,n),counter,traj%halo_berg)
     call pull_buffer_value(buff%data(:,n),counter,traj%static_berg)
     call pull_buffer_value(buff%data(:,n),counter,traj%sss)
+
+    if (mts) then
+      call pull_buffer_value(buff%data(:,n),counter,traj%uvel_prev)
+      call pull_buffer_value(buff%data(:,n),counter,traj%vvel_prev)      
+      call pull_buffer_value(buff%data(:,n),counter,traj%axn_fast)
+      call pull_buffer_value(buff%data(:,n),counter,traj%ayn_fast)
+      call pull_buffer_value(buff%data(:,n),counter,traj%bxn_fast)
+      call pull_buffer_value(buff%data(:,n),counter,traj%byn_fast)
+    endif
   endif
   call append_posn(first, traj)
 
@@ -2646,6 +3620,13 @@ logical function sameberg(berg1, berg2)
   if (berg1%vvel_old.ne.berg2%vvel_old) return  !Alon
   if (berg1%lon_old .ne.berg2%lon_old) return  !Alon
   if (berg1%lat_old.ne.berg2%lat_old) return  !Alon
+
+  if (mts) then
+    if (berg1%axn_fast.ne.berg2%axn_fast) return  !Alex
+    if (berg1%ayn_fast.ne.berg2%ayn_fast) return  !Alex
+    if (berg1%bxn_fast.ne.berg2%bxn_fast) return  !Alex
+    if (berg1%byn_fast.ne.berg2%byn_fast) return  !Alex
+  endif
   sameberg=.true. ! passing the above tests mean that bergs 1 and 2 are identical
 end function sameberg
 
@@ -2757,6 +3738,12 @@ subroutine print_berg(iochan, berg, label, il, jl)
     label, 'pe=(', mpp_pe(), ') #=', berg%id, &
     ' axn,ayn=', berg%axn, berg%ayn, &
     ' bxn,byn=', berg%bxn, berg%byn
+  if (mts) then
+    write(iochan,'("KID, print_berg: ",2a,i5,a,i12,2(a,2f14.8))') &
+      label, 'pe=(', mpp_pe(), ') #=', berg%id, &
+      ' axn_fast,ayn_fast=', berg%axn_fast, berg%ayn_fast, &
+      ' bxn_fast,byn_fast=', berg%bxn_fast, berg%byn_fast
+  endif
   write(iochan,'("KID, print_berg: ",2a,i5,a,i12,3(a,2f14.8))') &
     label, 'pe=(', mpp_pe(), ') #=', berg%id, &
     ' uo,vo=', berg%uo, berg%vo, &
@@ -2915,27 +3902,44 @@ subroutine show_all_bonds(bergs)
 
 end subroutine show_all_bonds
 
-subroutine connect_all_bonds(bergs)
+subroutine connect_all_bonds(bergs,ignore_unmatched)
   type(icebergs), pointer :: bergs !< Container for all types and memory
   type(iceberg), pointer :: other_berg, berg
   type(icebergs_gridded), pointer :: grd
+  logical,optional :: ignore_unmatched
   integer :: i, j
   integer :: grdi, grdj
   integer :: grdi_inner, grdj_inner
   type(bond) , pointer :: current_bond, other_berg_bond
-  logical :: bond_matched, missing_bond, check_bond_quality
+  logical :: bond_matched, missing_bond, check_bond_quality,check_match
   integer nbonds
 
+  check_match = .true.
+  if (present(ignore_unmatched)) then
+    if (ignore_unmatched) check_match = .false.
+  end if
+
   missing_bond=.false.
   bond_matched=.false.
 
   ! For convenience
   grd=>bergs%grd
 
+  !If interacting bergs & domain is periodic, then correct lat & lon for halo bergs - Alex   
+  call update_latlon(bergs)   
+
   do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
      ! do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec  ! Don't connect halo bergs
      berg=>bergs%list(grdi,grdj)%first
      do while (associated(berg)) ! loop over all bergs
+
+       if (berg%halo_berg==10) then
+         !these bergs only serve the purpose of exerting a contact force on a conglomerate berg
+         !when bergs%contact_distance>0, and bonds are not needed
+         berg=>berg%next
+         cycle
+       endif
+       
         current_bond=>berg%first_bond
         do while (associated(current_bond)) ! loop over all bonds
            !code to find parter bond goes here
@@ -2999,7 +4003,7 @@ subroutine connect_all_bonds(bergs)
                  enddo;enddo
               endif
 
-              if (.not.bond_matched) then
+              if (check_match .and. .not.bond_matched) then
                  if (berg%halo_berg .lt. 0.5) then
                     missing_bond=.true.
                     print * ,'non-halo berg unmatched: ', berg%id, berg%ine, berg%jne, mpp_pe(), &
@@ -3008,8 +4012,20 @@ subroutine connect_all_bonds(bergs)
                  else  ! This is not a problem if the partner berg is not yet in the halo
                     !if (  (current_bond%other_berg_ine .gt.grd%isd-1) .and. (current_bond%other_berg_ine .lt.grd%ied+1) &
                     !.and.  (current_bond%other_berg_jne .gt.grd%jsd-1) .and. (current_bond%other_berg_jne .lt.grd%jed+1) ) then
-                    !print * ,'halo berg unmatched: ',mpp_pe(),  berg%id, current_bond%other_id, current_bond%other_berg_ine,current_bond%other_berg_jne
-                    !call error_mesg('KID, connect_all_bonds', 'A halo bond is missing!!!', WARNING)
+                   !print * ,'halo berg unmatched: ',mpp_pe(),  berg%id, current_bond%other_id, current_bond%other_berg_ine,current_bond%other_berg_jne
+                   if (bergs%mts) call error_mesg('KID, connect_all_bonds', 'A halo bond is missing!!!', WARNING)
+                   if (bergs%mts) print *,'berg,target,x,y,halo_stat',berg%id,current_bond%other_id,i,j,berg%halo_berg
+                   ! do grdj_inner = j-2,j+2 ; do grdi_inner = i-2,i+2
+                   !   if    ((grdj_inner .gt. grd%jsd-1) .and. (grdj_inner .lt. grd%jed+1)        &
+                   !     .and.  (grdi_inner .gt. grd%isd-1) .and. (grdi_inner .lt. grd%ied+1) ) then
+                   !     other_berg=>bergs%list(grdi_inner,grdj_inner)%first
+                   !     do while (associated(other_berg))
+                   !       print *,'berg,other_berg,ob_halo_stat',berg%id,other_berg%id,other_berg%halo_berg
+                   !       other_berg=>other_berg%next
+                   !     enddo
+                   !   endif
+                   ! enddo;enddo
+                   
                     !endif
                  endif
               endif
@@ -3027,6 +4043,49 @@ subroutine connect_all_bonds(bergs)
   endif
 end subroutine connect_all_bonds
 
+!> If periodic domain, update lat & lon for bergs located beyond Lx - Alex
+subroutine update_latlon(bergs)
+  !Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  ! Local variables
+  type(icebergs_gridded), pointer :: grd
+  type(iceberg), pointer :: berg
+  real :: dlon, dlat,xi,yj,Lx
+  integer :: grdi,grdj
+  logical :: lret
+
+  ! For convenience
+  grd=>bergs%grd
+  Lx=grd%Lx
+
+  if (Lx > 0.) then
+    if ((grd%lon(grd%isc-1,grd%jsc-1) == grd%minlon_c) .or.  (grd%lon(grd%iec,grd%jec) == grd%maxlon_c)) then
+      do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+        berg=>bergs%list(grdi,grdj)%first
+        do while (associated(berg))
+          if ((.not. bergs%mts) .or. (abs(berg%halo_berg .le. 1))) then
+            !for bergs%mts skip halo elements that only exist due to their
+            !inclusion in a conglomerate (berg%halo_berg > 1). Their coords have
+            !already been corrected (if needed), as the scheme below would fail.             
+            dlon = berg%lon - berg%lon_old
+            dlat = berg%lat - berg%lat_old
+
+            berg%lon=bilin(grd, grd%lon, berg%ine, berg%jne, berg%xi, berg%yj)
+            berg%lat=bilin(grd, grd%lat, berg%ine, berg%jne, berg%xi, berg%yj)
+
+            berg%lon_old = berg%lon-dlon
+            berg%lat_old = berg%lat-dlat
+            !need to update local positon in cell from updated global coords, due to roundoff
+            lret=pos_within_cell(grd, berg%lon, berg%lat, berg%ine, berg%jne, berg%xi, berg%yj)
+          end if          
+          berg=>berg%next
+        enddo !loop over all bergs
+      enddo; enddo
+    end if
+  end if
+
+end subroutine update_latlon
+
 subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
 
 type(icebergs), pointer :: bergs !< Container for all types and memory
@@ -3189,8 +4248,15 @@ subroutine record_posn(bergs)
 type(xyt) :: posn
 type(iceberg), pointer :: this
 integer :: grdi, grdj
+integer :: js,je,is,ie
 
-  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
+if (force_all_pes_traj) then
+  js=bergs%grd%jsd+1; je=bergs%grd%jed; is=bergs%grd%isd+1; ie=bergs%grd%ied
+else
+  js=bergs%grd%jsc; je=bergs%grd%jec; is=bergs%grd%isc; ie=bergs%grd%iec
+endif
+
+    do grdj = js,je ; do grdi = is,ie
     this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
       posn%lon=this%lon
@@ -3222,13 +4288,22 @@ subroutine record_posn(bergs)
         posn%axn=this%axn
         posn%ayn=this%ayn
         posn%bxn=this%bxn
-        posn%byn=this%byn
+        posn%byn=this%byn       
         posn%uvel_old=this%uvel_old
         posn%vvel_old=this%vvel_old
         posn%lon_old=this%lon_old
         posn%lat_old=this%lat_old
         posn%halo_berg=this%halo_berg
         posn%static_berg=this%static_berg
+
+        if (bergs%mts) then
+          posn%uvel_prev=this%uvel_prev
+          posn%vvel_prev=this%vvel_prev        
+          posn%axn_fast=this%axn_fast
+          posn%ayn_fast=this%ayn_fast
+          posn%bxn_fast=this%bxn_fast
+          posn%byn_fast=this%byn_fast
+        endif
       endif
 
       call push_posn(this%trajectory, posn)
@@ -3321,7 +4396,8 @@ subroutine move_all_trajectories(bergs, delete_bergs)
 
   delete_bergs_after_moving_traj = .false.
   if (present(delete_bergs)) delete_bergs_after_moving_traj = delete_bergs
-  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
+  !do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
+    do grdj = bergs%grd%jsd+1,bergs%grd%jed ; do grdi = bergs%grd%isd+1,bergs%grd%ied
     this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
       next=>this%next
@@ -3577,7 +4653,36 @@ subroutine find_individual_iceberg(bergs, id, ine, jne, berg_found, search_data_
         this=>this%next
       enddo
     enddo ; enddo
-end subroutine  find_individual_iceberg
+  end subroutine  find_individual_iceberg
+
+!> Scans each computational grid cell until is_point_in_cell() is true
+logical function check_and_find_cell(grd, x, y, oi, oj)
+! Arguments
+type(icebergs_gridded), intent(in) :: grd !< Container for gridded fields
+real, intent(in) :: x !< Longitude of position
+real, intent(in) :: y !< Latitude of position
+integer, intent(out) :: oi !< i-index of cell containing position or -999
+integer, intent(out) :: oj !< j-index of cell containing position or -999
+! Local variables
+integer :: i,j
+
+check_and_find_cell=.false.
+
+if (.not. (oi-1.lt.grd%isd.or.oi.gt.grd%ied.or.oj-1.lt.grd%jsd.or.oj.gt.grd%jed)) then
+  if (is_point_in_cell(grd, x, y, oi, oj)) then
+    check_and_find_cell=.true.
+        return
+      endif  
+endif
+
+  oi=-999; oj=-999
+  do j=grd%jsc,grd%jec; do i=grd%isc,grd%iec
+      if (is_point_in_cell(grd, x, y, i, j)) then
+        oi=i; oj=j; check_and_find_cell=.true.
+        return
+      endif
+    enddo; enddo
+end function check_and_find_cell  
 
 !> Scans each computational grid cell until is_point_in_cell() is true
 logical function find_cell(grd, x, y, oi, oj)
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index cb8af5b..adc92b4 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -40,6 +40,7 @@ module ice_bergs_io
 use ice_bergs_framework, only: force_all_pes_traj
 use ice_bergs_framework, only: check_for_duplicates_in_parallel
 use ice_bergs_framework, only: split_id, id_from_2_ints, generate_id
+use ice_bergs_framework, only: mts !-alex
 
 implicit none ; private
 
@@ -809,6 +810,12 @@ subroutine generate_bergs(bergs,Time)
       localberg%vvel_old=0. !Alon
       localberg%bxn=0. !Alon
       localberg%byn=0. !Alon
+      localberg%uvel_prev=0. !Alon
+      localberg%vvel_prev=0. !Alon
+      localberg%axn_fast=0. !Alex
+      localberg%ayn_fast=0. !Alex
+      localberg%bxn_fast=0. !Alex
+      localberg%byn_fast=0. !Alex      
 
       !Berg A
       call loc_set_berg_pos(grd, 0.9, 0.5, 1., 0., localberg)
@@ -1251,8 +1258,9 @@ subroutine write_trajectory(trajectory, save_short_traj)
   ! Local variables
   integer :: iret, ncid, i_dim, i
   integer :: lonid, latid, yearid, dayid, uvelid, vvelid, idcntid, idijid
+  integer :: uvelpid,vvelpid
   integer :: uoid, void, uiid, viid, uaid, vaid, sshxid, sshyid, sstid, sssid
-  integer :: cnid, hiid
+  integer :: cnid, hiid, hsid
   integer :: mid, did, wid, lid, mbid, hdid
   character(len=37) :: filename
   character(len=7) :: pe_name
@@ -1392,6 +1400,11 @@ subroutine write_trajectory(trajectory, save_short_traj)
            sssid = inq_varid(ncid, 'sss')
            cnid = inq_varid(ncid, 'cn')
            hiid = inq_varid(ncid, 'hi')
+           hsid = inq_varid(ncid, 'halo_berg')
+           if (mts) then
+             uvelpid = inq_varid(ncid, 'uvel_prev')
+             vvelpid = inq_varid(ncid, 'vvel_prev')             
+           endif
         endif
      else
         ! Dimensions
@@ -1426,6 +1439,11 @@ subroutine write_trajectory(trajectory, save_short_traj)
            sssid = def_var(ncid, 'sss', NF_DOUBLE, i_dim)
            cnid = def_var(ncid, 'cn', NF_DOUBLE, i_dim)
            hiid = def_var(ncid, 'hi', NF_DOUBLE, i_dim)
+           hsid = def_var(ncid, 'halo_berg', NF_DOUBLE, i_dim)
+           if (mts) then
+             uvelpid = def_var(ncid, 'uvel_prev', NF_DOUBLE, i_dim)
+             vvelpid = def_var(ncid, 'vvel_prev', NF_DOUBLE, i_dim)                         
+           endif           
         endif
 
         ! Attributes
@@ -1485,6 +1503,14 @@ subroutine write_trajectory(trajectory, save_short_traj)
            call put_att(ncid, cnid, 'units', 'none')
            call put_att(ncid, hiid, 'long_name', 'sea ice thickness')
            call put_att(ncid, hiid, 'units', 'm')
+           call put_att(ncid, hsid, 'long_name', 'halo status')
+           call put_att(ncid, hsid, 'units', 'non-dim')
+           if (mts) then
+             call put_att(ncid, uvelpid, 'long_name', 'zonal speed mts')
+             call put_att(ncid, uvelpid, 'units', 'm/s')
+             call put_att(ncid, vvelpid, 'long_name', 'meridional speed mts')
+             call put_att(ncid, vvelpid, 'units', 'm/s')                        
+           endif             
         endif
      endif
 
@@ -1528,6 +1554,9 @@ subroutine write_trajectory(trajectory, save_short_traj)
            call put_double(ncid, sssid, i, this%sss)
            call put_double(ncid, cnid, i, this%cn)
            call put_double(ncid, hiid, i, this%hi)
+           call put_double(ncid, hsid, i, this%halo_berg)
+           call put_double(ncid, uvelpid, i, this%uvel_prev)
+           call put_double(ncid, vvelpid, i, this%vvel_prev)           
         endif
         next=>this%next
         deallocate(this)
diff --git a/tests/.gitignore b/tests/.gitignore
index 35c3337..f127ba8 100644
--- a/tests/.gitignore
+++ b/tests/.gitignore
@@ -1,4 +1,7 @@
 *.out
 *~
 *.nc
-core
\ No newline at end of file
+core
+single_test/
+size_test_tab/
+steady_test/
diff --git a/tests/2p_collision_test/README b/tests/2p_collision_test/README
new file mode 100644
index 0000000..83093c2
--- /dev/null
+++ b/tests/2p_collision_test/README
@@ -0,0 +1,5 @@
+1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
+2.(optional) edit input.nml
+3. run the model: ./RUN
+4, animate the results: animate_trajectories.py
+
diff --git a/tests/2p_collision_test/RUN b/tests/2p_collision_test/RUN
new file mode 100755
index 0000000..090c034
--- /dev/null
+++ b/tests/2p_collision_test/RUN
@@ -0,0 +1,5 @@
+rm iceberg_trajectories.nc
+rm iceberg_trajectories.nc.*
+srun -n4 ./../../build/bergs.x
+
+
diff --git a/tests/2p_collision_test/RUN1p b/tests/2p_collision_test/RUN1p
new file mode 100755
index 0000000..c3bf53e
--- /dev/null
+++ b/tests/2p_collision_test/RUN1p
@@ -0,0 +1,5 @@
+rm iceberg_trajectories.nc
+rm iceberg_trajectories.nc.*
+srun -n1 ./../../build/bergs.x
+
+
diff --git a/tests/2p_collision_test/animate_trajectories.py b/tests/2p_collision_test/animate_trajectories.py
new file mode 100755
index 0000000..b41d801
--- /dev/null
+++ b/tests/2p_collision_test/animate_trajectories.py
@@ -0,0 +1,158 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+import matplotlib.pyplot as plt
+from matplotlib.animation import FuncAnimation
+from mpl_toolkits.axes_grid1 import make_axes_locatable
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
+                    help=''' provide filename to plot''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+
+
+def main(args):
+    
+    print('reading file')
+
+    filename=args.fname
+    #filename = 'iceberg_trajectories.nc'
+    field = 'lon'
+    field2 = 'lat'
+
+    with nc.Dataset(filename) as file:
+        x = file.variables['lon'][:]/1.e3
+        y = file.variables['lat'][:]/1.e3
+        day = file.variables['day'][:]
+        bid = file.variables['id_ij'][:]
+        #vo = file.variables['vvel'][:]
+        #vo = file.variables['vvel_prev'][:]
+        vo = file.variables['id_ij'][:]
+
+    ud = np.unique(day)
+    ub = np.unique(bid)
+    t = ud[0]
+
+
+    # frame info
+    num_frames = len(ud)
+    movie_len = 20.0 #seconds
+    frame_len = 1000.0*movie_len/num_frames
+    
+    xmin = 0 #np.floor(min(min(x),min(y),0))
+    xmax = 20 #np.ceil(max(max(x),max(y),20))
+    ymin = xmin
+    ymax = xmax
+
+    anim_running = True
+
+    def animate(i):
+
+        x1 = x[day == ud[i]]
+        y1 = y[day == ud[i]]
+        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
+
+        scat.set_offsets(data)
+        
+        # bid1 = bid[day == ud[i]]        
+        # cstring=[]
+        # for j in range(len(bid1)):
+        #     if (bid1[j]==ub[1]):
+        #         cstring.append("b")
+        #     else:                 
+        #         cstring.append("r")
+        # scat.set_color(cstring)
+
+        vo1 = vo[day == ud[i]]
+        scat.set_edgecolor('k')
+        scat.set_color(cmap(norm(vo1)))
+
+        t = ud[i]
+        time_text.set_text('time = %.1f days' % t )        
+        return scat,time_text
+
+    def init():
+        scat.set_offsets([])
+        return scat,
+
+    def onClick(event):
+        global anim_running
+        if anim_running:
+            ani.event_source.stop()
+            anim_running = False
+        else:
+            ani.event_source.start()
+            anim_running = True       
+    
+    # Now we can do the plotting!    
+    f = plt.figure(figsize=(5,5))
+    f.tight_layout()
+    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
+    div = make_axes_locatable(ax1)
+    cax = div.append_axes('right', '5%', '5%') 
+    scat = ax1.scatter([],[],c=[],marker='o',s=100) #,edgecolor='k')
+    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
+
+    cmap = plt.cm.get_cmap('RdYlBu')
+    norm = plt.Normalize(vo.min(), vo.max())
+    cb1 = matplotlib.colorbar.ColorbarBase(cax, cmap=cmap,
+                                           norm=norm,
+                                           orientation='vertical')      
+
+   
+    # Change major ticks to show every 20.
+    ax1.xaxis.set_major_locator(MultipleLocator(5))
+    ax1.yaxis.set_major_locator(MultipleLocator(5))
+
+    ax1.xaxis.set_minor_locator(MultipleLocator(1))
+    ax1.yaxis.set_minor_locator(MultipleLocator(1))
+
+    # Turn grid on for both major and minor ticks and style minor slightly
+    # differently.
+    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
+    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
+
+    ax1.set_xlabel('x (km)')
+    ax1.set_ylabel('y (km)')
+    ax1.set_title('Iceberg trajectory')
+ 
+    f.canvas.mpl_connect('button_press_event', onClick)
+
+    ani = FuncAnimation(
+        f,animate,init_func=init,frames=num_frames,
+        interval=frame_len,blit=True,repeat=True)
+
+    print('time',t)
+
+    plt.show()
+    #animation.save("iceberg_traj_animation.mp4")
+
+
+print('Script complete')
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
+
+
+
+
+
+
+
+
diff --git a/tests/2p_collision_test/animate_trajectories_1pe.py b/tests/2p_collision_test/animate_trajectories_1pe.py
new file mode 100755
index 0000000..19db84d
--- /dev/null
+++ b/tests/2p_collision_test/animate_trajectories_1pe.py
@@ -0,0 +1,175 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+import matplotlib.pyplot as plt
+from matplotlib.animation import FuncAnimation
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc.0000',
+                    help=''' provide filename to plot''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+
+
+def main(args):
+    
+    print('reading file')
+
+    filename=args.fname
+    #filename = 'iceberg_trajectories.nc'
+    field = 'lon'
+    field2 = 'lat'
+
+    with nc.Dataset(filename) as file:
+        x = file.variables['lon'][:]/1.e3
+        y = file.variables['lat'][:]/1.e3
+        day = file.variables['day'][:]
+        hs = file.variables['halo_berg'][:]
+
+    #hs = hs+1
+    ud = np.unique(day)
+    t = ud[0]
+
+    print('unique hs',np.unique(hs))
+
+    # frame info
+    num_frames = len(ud)
+    movie_len = 5.0 #seconds
+    frame_len = 1000.0*movie_len/num_frames
+    
+    xmin = np.floor(min(min(x),min(y),-5))
+    xmax = np.ceil(max(max(x),max(y),25))
+    ymin = xmin
+    ymax = xmax
+
+    anim_running = True
+
+    def animate(i):
+
+        x1 = x[day == ud[i]]
+        y1 = y[day == ud[i]]
+        hstat = hs[day == ud[i]]
+        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
+
+        cstring=[]
+        for j in range(len(hstat)):
+            if (hstat[j]<0):
+                cstring.append("y")
+            elif (hstat[j]==0):                 
+                cstring.append("b")
+            elif (hstat[j]==1):
+                cstring.append("r")
+            elif (hstat[j]==2):
+                cstring.append("g")
+            elif (hstat[j]==3):
+                cstring.append("k")
+            elif (hstat[j]==4):
+                cstring.append("m")
+            else:
+                cstring.append("c")
+                                                           
+        scat.set_offsets(data)
+        scat.set_color(cstring)
+        scat.set_edgecolor('k')
+        
+        t = ud[i]
+        time_text.set_text('time = %.1f days' % t )        
+        return scat,time_text
+
+    def init():
+        scat.set_offsets([])
+        return scat,
+
+    def onClick(event):
+        global anim_running
+        if anim_running:
+            ani.event_source.stop()
+            anim_running = False
+        else:
+            ani.event_source.start()
+            anim_running = True       
+    
+    # Now we can do the plotting!
+    f = plt.figure(figsize=(5,5))
+    f.tight_layout()
+    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
+    scat = ax1.scatter([],[],marker='o',s=60) 
+    #scat = ax1.scatter([],[],marker='o',facecolor='w',s=60,edgecolor='red')
+    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
+
+    # Change major ticks to show every 20.
+    ax1.xaxis.set_major_locator(MultipleLocator(5))
+    ax1.yaxis.set_major_locator(MultipleLocator(5))
+
+    ax1.xaxis.set_minor_locator(MultipleLocator(1))
+    ax1.yaxis.set_minor_locator(MultipleLocator(1))
+
+    # Turn grid on for both major and minor ticks and style minor slightly
+    # differently.
+    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
+    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
+
+    ax1.set_xlabel('x (km)')
+    ax1.set_ylabel('y (km)')
+    ax1.set_title('Iceberg trajectory')
+ 
+    f.canvas.mpl_connect('button_press_event', onClick)
+
+    ani = FuncAnimation(
+        f,animate,init_func=init,frames=num_frames,
+        interval=frame_len,blit=True,repeat=True)
+
+    print('time',t)
+
+    plt.plot([0,0],[0,20],'k-',lw=1)
+    plt.plot([10,10],[0,20],'k-',lw=1)
+    plt.plot([20,20],[0,20],'k-',lw=1)
+    plt.plot([0,0],[0,20],'k-',lw=1)
+    plt.plot([20,20],[0,20],'k-',lw=1)
+    plt.plot([0,0],[0,20],'k-',lw=1)
+    plt.plot([0,20],[10,10],'k-',lw=1)
+    plt.plot([0,20],[20,20],'k-',lw=1)
+    plt.plot([0,20],[0,0],'k-',lw=1)
+    plt.plot([0,20],[20,20],'k-',lw=1)
+
+    plt.plot([-2,-2],[-2,23],'b:',lw=1)
+    plt.plot([8,8],[-2,23],'b:',lw=1)
+    plt.plot([13,13],[-2,23],'b:',lw=1)
+    plt.plot([23,23],[-2,23],'b:',lw=1)
+    plt.plot([-2,23],[-2,-2],'b:',lw=1)
+    plt.plot([-2,23],[8,8],'b:',lw=1)
+    plt.plot([-2,23],[13,13],'b:',lw=1)
+    plt.plot([-2,23],[23,23],'b:',lw=1)      
+ 
+    
+    plt.show()
+    #animation.save("iceberg_traj_animation.mp4")
+
+
+print('Script complete')
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
+
+
+
+
+
+
+
+
diff --git a/tests/2p_collision_test/diag_table b/tests/2p_collision_test/diag_table
new file mode 100644
index 0000000..c1c8819
--- /dev/null
+++ b/tests/2p_collision_test/diag_table
@@ -0,0 +1,3 @@
+"icebergs test"
+1 1 1 0 0 0
+
diff --git a/tests/2p_collision_test/input.nml b/tests/2p_collision_test/input.nml
new file mode 100644
index 0000000..26a988f
--- /dev/null
+++ b/tests/2p_collision_test/input.nml
@@ -0,0 +1,165 @@
+!test that the mts and sts velocity verlet schemes agree, when mts is run with a single inner loop
+! note that chksums will not agree. TODO: modify chksums to be invariant to mts vs sts
+
+! for mts=.false.:
+! KID, bergs_chksum: write_restart berg chksum= -982041486 chksum2=  -982041486 chksum3=           -1680028706 chksum4=           -1680028706 chksum5=                     0 #=2
+
+!for mts=.true.:
+! KID, bergs_chksum: write_restart berg chksum=  160896535 chksum2=   160896535 chksum3=           -1680028706 chksum4=           -1680028706 chksum5=                     0 #=2
+
+! for both
+! KID, grd_chksum2:    # of bergs/cell chksum=           0 chksum2=           0 min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
+! KID, grd_chksum3:   write stored_ice chksum=  -540079793 chksum2= -1237287029 min= 6.393358811E+05 max= 7.380127765E+11 mean= 8.033602570E+10 rms= 1.613270384E+11 sd= 1.399018810E+11
+! KID, grd_chksum2:  write stored_heat chksum=           0 chksum2=           0 min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
+
+&icebergs_driver_nml
+  ni=20 !number of elements, x direction
+  nj=20 !number of elements, y direction
+  ibdt=600.0 !seconds
+  ibuo=0.2 !ocean x velocity
+  ibvo=0.2 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=48 !total simulation hours
+  nmax=99999999 !max number of timesteps
+  saverestart=.true. 
+  halo=3
+  debug=.false.   
+  collision_test=.true. !specific to the current test, must be true here
+/
+
+
+&icebergs_nml
+
+    !defaults given in parentheses:
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=1 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
+    contact_distance=0 !3.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-5!(default=spring_coeff) Berg spring coeff for collisions
+
+    halo=3 !(4) halo width
+    Lx=20000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.True. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move    
+    
+    rho_bergs=850. ! (850) iceberg density
+    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val 
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0.4 !4 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #) 
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met    
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)    
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread			
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.false. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...       
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors    
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=24 ! (24) Period between verbose messages
+    traj_sample_hrs=0.5 !1 !(24) sampling period for trajectory storage
+    traj_write_hrs=0.5 ! (480) Period for writing sampled trajectories to disk    
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id    
+    
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.true. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all    
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart 
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.false. ! (F) True= Bonds are initialize manually.
+    length_for_manually_initialize_bonds=0.0 !(1e3)Dist b/w bergs to init bonds manually    
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.      
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+    
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+    
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+    
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+    
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+ 
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/2p_collision_test/makeberg/RUN b/tests/2p_collision_test/makeberg/RUN
new file mode 100755
index 0000000..d998794
--- /dev/null
+++ b/tests/2p_collision_test/makeberg/RUN
@@ -0,0 +1,13 @@
+./makeberg.py
+
+rm ./output_files/Generic*
+
+./../../Iceberg_repository/Scripts_and_analysis/initialize_bergs_in_pattern.py \
+	-set_all_bergs_static_by_default=False -Run_plotting_subroutine=False \
+	-break_some_bonds=False -Ice_geometry_source='Generic' \
+	-Generic_ice_geometry_filename='./testtabularberg.nc' \
+	-ISOMIP_reduced=False -collision_test=True \
+	-select_just_min_and_max_lat_berg=True
+
+cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
+cp ./output_files/Generic_bonds_iceberg.res.nc ./../INPUT/bonds_iceberg.res.nc
\ No newline at end of file
diff --git a/tests/2p_collision_test/makeberg/makeberg.py b/tests/2p_collision_test/makeberg/makeberg.py
new file mode 100755
index 0000000..423b6a5
--- /dev/null
+++ b/tests/2p_collision_test/makeberg/makeberg.py
@@ -0,0 +1,77 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset  
+import numpy as np 
+import math
+#import os
+from pylab import *
+#import pdb
+import netCDF4 as nc
+
+nx = 20
+ny = 20
+New_ice_thickness_filename='testberg.nc'
+grid_res = 1.e3 #1 km 
+grid_area = grid_res * grid_res
+h_ice = 300.0
+
+New_ice_thickness_filename='testtabularberg.nc'
+g=Dataset(New_ice_thickness_filename,'w') # w if for creating a file
+
+g.createDimension('nx',nx)
+g.createDimension('ny',ny)
+thick_h=g.createVariable('thick','f8',('ny','nx'))
+area_h=g.createVariable('area','f8',('ny','nx'))
+lat_h=g.createVariable('lat','f8','ny')
+lon_h=g.createVariable('lon','f8','nx')
+#lat_h=g.createVariable('lat','f8',('ny','nx'))
+#lon_h=g.createVariable('lon','f8',('ny','nx'))
+
+thick_h.units = 'm'
+thick_h.standard_name = 'ice shelf thickness'
+area_h.units = 'm2'
+area_h.standard_name = 'ice shelf area'
+lon_h.unit = 'm'
+lon_h.standard_name = 'longitude'
+lat_h.unit = 'm'
+lat_h.standard_name = 'latitude'
+
+
+
+#g.variables['thick'][:]=h_ice
+g.variables['area'][:,:]=grid_area
+
+#create a circular tabular berg centered on the following coords (km)
+cy = 4.5e3
+cx = 4.5e3
+#cx2 = 15.5e3
+
+for i in range(nx):
+
+        tx = float(i) * grid_res 
+        g.variables['lon'][i] = tx
+        
+        for j in range(ny):
+               
+                ty = float(j) * grid_res 
+                dist = sqrt((tx-cx)*(tx-cx) + (ty-cy)*(ty-cy))
+                #dist2 =  sqrt((tx-cx2)*(tx-cx2) + (ty-cy)*(ty-cy))
+                #g.variables['lon'][i,j] = tx
+                #g.variables['lat'][i,j] = ty
+        
+                if (dist <1.e3): #or dist2<1.e3):
+                        g.variables['thick'][i,j]=h_ice
+                else:
+                        g.variables['thick'][i,j]=0.0
+
+                        
+
+for j in range(ny):
+        g.variables['lat'][j] = float(j) * grid_res 
+
+print('Creating file: ' , New_ice_thickness_filename)
+
+g.sync()
+g.close()
+
+        
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/initialize_bergs_in_pattern.py b/tests/Iceberg_repository/Scripts_and_analysis/initialize_bergs_in_pattern.py
index 436f27c..f9665a5 100755
--- a/tests/Iceberg_repository/Scripts_and_analysis/initialize_bergs_in_pattern.py
+++ b/tests/Iceberg_repository/Scripts_and_analysis/initialize_bergs_in_pattern.py
@@ -36,6 +36,9 @@ def parseCommandLine():
 	#p.add_argument('-b',type='bool')  # do not use 'type=bool'
 
 	#Flags
+	parser.add_argument('-collision_test', type='bool', default=False,
+		          help=''' symmetry for berg around y=10 km ''')
+        
 	parser.add_argument('-save_restart_files', type='bool', default=True,
 		          help=''' Writes an iceberg restart file,  icebergs.res ''')
 
@@ -52,6 +55,9 @@ def parseCommandLine():
 	parser.add_argument('-only_choose_one_berg', type='bool', default=False,
 		          help=''' When true, only one iceberg (with number chosen_berg_num) is written to icebergs.res. This is for debugging  ''')
 
+	parser.add_argument('-select_just_min_and_max_lat_berg', type='bool', default=False,
+		          help=''' When true, only the bergs with max and min lat are written to icebergs.res. This is for debugging  ''')        
+
 	parser.add_argument('-chosen_berg_num', type=int, default=1,
 		          help='''When only_choose_one_berg=True, then only the iceberg with this number is written to the icebergs.res file  ''')
 
@@ -770,7 +776,8 @@ def remove_stationary_bergs(dx_berg, dy_berg,iceberg_num,width,Number_of_bergs,s
 
 def Create_icebergs(lon_init,lat_init,Radius,R_earth, x, y,ice_mask,h_ice,Convert_to_lat_lon,rho_ice,\
 		element_type,scale_the_grid_to_lat_lon,lat_ref,adjust_lat_ref,Interpolate_from_four_corners,\
-		Fill_in_the_boundaries,set_all_bergs_static_by_default,break_some_bonds,Remove_stationary_bergs,set_some_bergs_static_by_default):
+		Fill_in_the_boundaries,set_all_bergs_static_by_default,break_some_bonds,Remove_stationary_bergs,\
+                set_some_bergs_static_by_default,collision_test):
 	print 'Starting to create icebergs...'
 	dx_berg=[]  #x distance in cartesian of berg from lon_init
 	dy_berg=[]  #y distance in cartesian of berg from lat_init
@@ -840,13 +847,14 @@ def Create_icebergs(lon_init,lat_init,Radius,R_earth, x, y,ice_mask,h_ice,Conver
 					dx_berg.append(x_val)
 					dy_berg.append(y_val)
 					width.append(np.sqrt(element_area))
+
+                                               
 	#print 'dx_berg',dx_berg
 	#print 'dy_berg',dy_berg
 
 
-
 	Number_of_bergs=berg_count
-	print 'Icebergs created. Number of bergs = ', Number_of_bergs
+	
 	
 	#Deciding if icebergs are static or not
 	static_berg = [0. for i in dx_berg]
@@ -879,7 +887,17 @@ def Create_icebergs(lon_init,lat_init,Radius,R_earth, x, y,ice_mask,h_ice,Conver
 				h_ice,element_type,static_berg,thickness,mass)
 		print 'Number of icebergs after accounting for boundaries = ', Number_of_bergs
 	
-
+        if collision_test:
+                for i in range(berg_count):
+                        berg_count=berg_count+1
+			iceberg_num.append(berg_count)
+			dx_berg.append(dx_berg[i])
+			dy_berg.append(20000.0-dy_berg[i])
+			width.append(width[i])
+                        thickness.append(thickness[i])
+                        mass.append(mass[i])
+                        static_berg.append(static_berg[i])
+                Number_of_bergs=berg_count
 
 	if Convert_to_lat_lon==True:
 		#Defining lon lat positions:
@@ -911,7 +929,8 @@ def Create_icebergs(lon_init,lat_init,Radius,R_earth, x, y,ice_mask,h_ice,Conver
 		lon=dx_berg  ; lat=dy_berg
 	
 	#Note that static_berg calculations used to be here, after the conversion. I have moved them. I hope that this does not affect answers.
-
+                        
+        print 'Icebergs created. Number of bergs = ', Number_of_bergs
 	return (Number_of_bergs,lon,lat,iceberg_num,dx_berg,dy_berg,thickness, mass,width,x,y,Radius,static_berg,N_bergs_before_bd)
 
 
@@ -1194,6 +1213,29 @@ def Select_just_one_berg(lon,lat,thickness,width,mass,iceberg_num,chosen_berg_nu
 	Number_of_bergs=1
 	return [Number_of_bergs,lon,lat,thickness,width,mass,iceberg_num]
 
+def Select_just_min_and_max_lat_bergs(lon,lat,thickness,width,mass,iceberg_num,static_berg):
+	print 'You have chosen to choose just two icebergs!!!'
+        minlat = lat[1]
+        maxlat = lat[1]
+        minnum = iceberg_num[1]
+        maxnum = iceberg_num[1]
+        for k in range(len(lat)):
+                if lat[k]<minlat:
+                        minlat=lat[k]
+                        minnum=k
+                if lat[k]>maxlat:
+                        maxlat=lat[k]
+                        maxnum=k
+        lon=[lon[minnum],lon[maxnum]]
+        lat=[lat[minnum],lat[maxnum]]
+        thickness=[thickness[minnum],thickness[maxnum]]
+        mass=[mass[minnum],mass[maxnum]]
+        width=[width[minnum],width[maxnum]]
+        static_berg=[static_berg[minnum],static_berg[maxnum]]
+        iceberg_num=[iceberg_num[minnum],iceberg_num[maxnum]]
+        Number_of_bergs=2
+	return [Number_of_bergs,lon,lat,thickness,width,mass,iceberg_num,static_berg]        
+
 def plotting_iceberg_positions(lat,lon,Number_of_bergs,R_earth,Radius,IA_scaling,Convert_to_lat_lon, \
 		plot_circles,h_ice,ice_mask,x,y,plot_ice_mask,plot_ice_thickness,thickness,plot_icebergs_positions,static_berg,h_ice_new,plot_h_ice_new):
 	print 'Starting to plot...'	
@@ -1623,6 +1665,7 @@ def main(args):
 
 	#Iceberg setup flags
 	only_choose_one_berg=args.only_choose_one_berg  ; chosen_berg_num=args.chosen_berg_num
+        select_just_min_and_max_lat_berg=args.select_just_min_and_max_lat_berg
 	scale_the_grid_to_lat_lon=args.scale_the_grid_to_lat_lon
 	adjust_lat_ref=args.adjust_lat_ref
 	set_all_thicknesses_to_one=args.set_all_thicknesses_to_one   ; Th_prescribed=args.Th_prescribed
@@ -1666,7 +1709,7 @@ def main(args):
 	ISOMIP_reduced_ice_geometry_filename=args.ISOMIP_reduced_ice_geometry_filename
 	Weddell_ice_geometry_filename=args.Weddell_ice_geometry_filename
 	Generic_ice_geometry_filename=args.Generic_ice_geometry_filename
-
+        collision_test=args.collision_test
 
 	#Parameters
 	Radius=args.Radius
@@ -1742,7 +1785,8 @@ def main(args):
 	#Define the positions,thickness, mass,  of the icebergs
 	(Number_of_bergs,lon,lat,iceberg_num,dx_berg, dy_berg,thickness,mass,width,x,y,Radius,static_berg,N_bergs_before_bd)= Create_icebergs(lon_init,lat_init,\
 			Radius,R_earth, x, y,ice_mask,h_ice,Convert_to_lat_lon,rho_ice,element_type,scale_the_grid_to_lat_lon,lat_ref,adjust_lat_ref,\
-			Interpolate_from_four_corners,Fill_in_the_boundaries, set_all_bergs_static_by_default,break_some_bonds,Remove_stationary_bergs,set_some_bergs_static_by_default)
+			Interpolate_from_four_corners,Fill_in_the_boundaries, set_all_bergs_static_by_default,break_some_bonds,Remove_stationary_bergs,\
+                        set_some_bergs_static_by_default,collision_test)
 
 	print 'Maximum thickness:', np.max(thickness), np.min(thickness)
 	#Define the positions of the iceberg bonds
@@ -1759,6 +1803,11 @@ def main(args):
 	if only_choose_one_berg==True:
 		(Number_of_bergs,lon,lat,thickness,width,mass,iceberg_num)= Select_just_one_berg(lon,lat,thickness,width,mass,iceberg_num,chosen_berg_num,static_berg)
 
+        if select_just_min_and_max_lat_berg==True:
+                (Number_of_bergs,lon,lat,thickness,width,mass,iceberg_num,static_berg)=\
+                        Select_just_min_and_max_lat_bergs(lon,lat,thickness,width,mass,iceberg_num,static_berg)
+                print 'Selected just min and max lat bergs. New number of bergs = ', Number_of_bergs
+
 
 	if regrid_icebergs_onto_grid==True:
 		if scale_the_grid_to_lat_lon==True:
diff --git a/tests/collision_test/RUN b/tests/collision_test/RUN
index 6330154..090c034 100755
--- a/tests/collision_test/RUN
+++ b/tests/collision_test/RUN
@@ -1,4 +1,5 @@
 rm iceberg_trajectories.nc
+rm iceberg_trajectories.nc.*
 srun -n4 ./../../build/bergs.x
 
 
diff --git a/tests/collision_test/RUN1p b/tests/collision_test/RUN1p
new file mode 100755
index 0000000..c3bf53e
--- /dev/null
+++ b/tests/collision_test/RUN1p
@@ -0,0 +1,5 @@
+rm iceberg_trajectories.nc
+rm iceberg_trajectories.nc.*
+srun -n1 ./../../build/bergs.x
+
+
diff --git a/tests/collision_test/RUN_tstest.sh b/tests/collision_test/RUN_tstest.sh
new file mode 100755
index 0000000..fe5f81c
--- /dev/null
+++ b/tests/collision_test/RUN_tstest.sh
@@ -0,0 +1,33 @@
+#!/bin/bash
+
+rm iceberg_trajectories.nc
+
+space="s_"
+nc="c_.nc"
+r="./results/iceberg_trajectories_"
+
+s1='10' # 960' #'10 30 60 90'
+c1='1.e-5' # 1.e-4'
+
+for i in $s1
+do
+	for j in $c1
+	do
+	    	result="$r$i$space$j$nc"
+		echo $i
+		echo $j
+		echo $result
+
+		sed "s/<sec>/$i/; s/<coef>/$j/g" \
+		    input_tstest.nml > input.nml
+
+		srun -n4 ./../../build/bergs.x
+
+		mv iceberg_trajectories.nc $result
+	done
+done
+
+
+
+
+
diff --git a/tests/collision_test/animate_trajectories.py b/tests/collision_test/animate_trajectories.py
index 3cb36be..7deaa77 100755
--- a/tests/collision_test/animate_trajectories.py
+++ b/tests/collision_test/animate_trajectories.py
@@ -11,103 +11,115 @@
 from pylab import *
 import matplotlib.pyplot as plt
 from matplotlib.animation import FuncAnimation
-
-
-print('reading file')
-
-filename = 'iceberg_trajectories.nc'
-field = 'lon'
-field2 = 'lat'
-
-with nc.Dataset(filename) as file:
-    x = file.variables['lon'][:]/1.e3
-    y = file.variables['lat'][:]/1.e3
-    day = file.variables['day'][:]
-
-ud = np.unique(day)
-t = ud[0]
-
-def animate(i):
-
-    x1 = x[day == ud[i]]
-    y1 = y[day == ud[i]]
-    data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
-    scat.set_offsets(data)
-    t = ud[i]
-    time_text.set_text('time = %.1f days' % t )        
-    return scat,time_text
-
-def init():
-    scat.set_offsets([])
-    return scat,
-
-def onClick(event):
-    global anim_running
-    if anim_running:
-        ani.event_source.stop()
-        anim_running = False
-    else:
-        ani.event_source.start()
-        anim_running = True
-
-# frame info
-num_frames = len(ud)
-movie_len = 5.0 #seconds
-frame_len = 1000.0*movie_len/num_frames
-
-smax = max(max(x),max(y),20)
-xmin = 0.0
-xmax = smax
-ymin = 0.0
-ymax = smax
-
-
-# Now we can do the plotting!
-f = plt.figure(figsize=(5,5))
-f.tight_layout()
-ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
-scat = ax1.scatter([],[],marker='o',facecolor='w',s=110,edgecolor='red')
-time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
-
-ax1.set_xticks(np.arange(0, xmax+1, 1)) 
-ax1.set_yticks(np.arange(0, ymax+1, 1)) 
-ax1.set_xlabel('x (km)')
-ax1.set_ylabel('y (km)')
-ax1.set_title('Iceberg trajectory')
-
-anim_running = True
-f.canvas.mpl_connect('button_press_event', onClick)
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
+                    help=''' provide filename to plot''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+
+
+def main(args):
+    
+    print('reading file')
+
+    filename=args.fname
+    #filename = 'iceberg_trajectories.nc'
+    field = 'lon'
+    field2 = 'lat'
+
+    with nc.Dataset(filename) as file:
+        x = file.variables['lon'][:]/1.e3
+        y = file.variables['lat'][:]/1.e3
+        day = file.variables['day'][:]
+
+    ud = np.unique(day)
+    t = ud[0]
+
+    # frame info
+    num_frames = len(ud)
+    movie_len = 5.0 #seconds
+    frame_len = 1000.0*movie_len/num_frames
+    
+    xmin = 0 #np.floor(min(min(x),min(y),0))
+    xmax = 20 #np.ceil(max(max(x),max(y),20))
+    ymin = xmin
+    ymax = xmax
+
+    anim_running = True
+
+    def animate(i):
+
+        x1 = x[day == ud[i]]
+        y1 = y[day == ud[i]]
+        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
+           
+        scat.set_offsets(data)
+        
+        t = ud[i]
+        time_text.set_text('time = %.1f days' % t )        
+        return scat,time_text
+
+    def init():
+        scat.set_offsets([])
+        return scat,
+
+    def onClick(event):
+        global anim_running
+        if anim_running:
+            ani.event_source.stop()
+            anim_running = False
+        else:
+            ani.event_source.start()
+            anim_running = True       
+    
+    # Now we can do the plotting!
+    f = plt.figure(figsize=(5,5))
+    f.tight_layout()
+    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
+    scat = ax1.scatter([],[],marker='o',facecolor='w',s=100,edgecolor='red')
+    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
+
+    # Change major ticks to show every 20.
+    ax1.xaxis.set_major_locator(MultipleLocator(5))
+    ax1.yaxis.set_major_locator(MultipleLocator(5))
+
+    ax1.xaxis.set_minor_locator(MultipleLocator(1))
+    ax1.yaxis.set_minor_locator(MultipleLocator(1))
+
+    # Turn grid on for both major and minor ticks and style minor slightly
+    # differently.
+    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
+    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
+
+    ax1.set_xlabel('x (km)')
+    ax1.set_ylabel('y (km)')
+    ax1.set_title('Iceberg trajectory')
  
-ani = FuncAnimation(
-    f,animate,init_func=init,frames=num_frames,
-    interval=frame_len,blit=True)
-
-print('time',t)
+    f.canvas.mpl_connect('button_press_event', onClick)
 
-plt.grid()
-plt.show()
+    ani = FuncAnimation(
+        f,animate,init_func=init,frames=num_frames,
+        interval=frame_len,blit=True,repeat=True)
 
-#animation.save("iceberg_traj_animation.mp4")
+    print('time',t)
 
+    plt.show()
+    #animation.save("iceberg_traj_animation.mp4")
 
 
-#old:
-#mid = int(np.ceil(len(ud)/2))
-#t1 = ud[0]
-#t2 = ud[mid]
-#t3 = ud[len(ud)-1]
-#print('plotting')
-#plt.figure()
-#figsize=(15,10))
-#plt.scatter(x[day == t1],y[day == t1],color = 'blue', marker='*')
-#plt.scatter(x[day == t2],y[day == t2],color = 'green',marker='o')
-#plt.scatter(x[day == t3],y[day == t3],color = 'red',marker='*')
-#plt.xlabel('x-extent (km)')
-#plt.ylabel('y-extent (km)')
-#plt.show()
+print('Script complete')
 
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
 
-print('Script complete')
 
 
 
diff --git a/tests/collision_test/animate_trajectories_1pe.py b/tests/collision_test/animate_trajectories_1pe.py
new file mode 100755
index 0000000..19db84d
--- /dev/null
+++ b/tests/collision_test/animate_trajectories_1pe.py
@@ -0,0 +1,175 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+import matplotlib.pyplot as plt
+from matplotlib.animation import FuncAnimation
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc.0000',
+                    help=''' provide filename to plot''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+
+
+def main(args):
+    
+    print('reading file')
+
+    filename=args.fname
+    #filename = 'iceberg_trajectories.nc'
+    field = 'lon'
+    field2 = 'lat'
+
+    with nc.Dataset(filename) as file:
+        x = file.variables['lon'][:]/1.e3
+        y = file.variables['lat'][:]/1.e3
+        day = file.variables['day'][:]
+        hs = file.variables['halo_berg'][:]
+
+    #hs = hs+1
+    ud = np.unique(day)
+    t = ud[0]
+
+    print('unique hs',np.unique(hs))
+
+    # frame info
+    num_frames = len(ud)
+    movie_len = 5.0 #seconds
+    frame_len = 1000.0*movie_len/num_frames
+    
+    xmin = np.floor(min(min(x),min(y),-5))
+    xmax = np.ceil(max(max(x),max(y),25))
+    ymin = xmin
+    ymax = xmax
+
+    anim_running = True
+
+    def animate(i):
+
+        x1 = x[day == ud[i]]
+        y1 = y[day == ud[i]]
+        hstat = hs[day == ud[i]]
+        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
+
+        cstring=[]
+        for j in range(len(hstat)):
+            if (hstat[j]<0):
+                cstring.append("y")
+            elif (hstat[j]==0):                 
+                cstring.append("b")
+            elif (hstat[j]==1):
+                cstring.append("r")
+            elif (hstat[j]==2):
+                cstring.append("g")
+            elif (hstat[j]==3):
+                cstring.append("k")
+            elif (hstat[j]==4):
+                cstring.append("m")
+            else:
+                cstring.append("c")
+                                                           
+        scat.set_offsets(data)
+        scat.set_color(cstring)
+        scat.set_edgecolor('k')
+        
+        t = ud[i]
+        time_text.set_text('time = %.1f days' % t )        
+        return scat,time_text
+
+    def init():
+        scat.set_offsets([])
+        return scat,
+
+    def onClick(event):
+        global anim_running
+        if anim_running:
+            ani.event_source.stop()
+            anim_running = False
+        else:
+            ani.event_source.start()
+            anim_running = True       
+    
+    # Now we can do the plotting!
+    f = plt.figure(figsize=(5,5))
+    f.tight_layout()
+    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
+    scat = ax1.scatter([],[],marker='o',s=60) 
+    #scat = ax1.scatter([],[],marker='o',facecolor='w',s=60,edgecolor='red')
+    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
+
+    # Change major ticks to show every 20.
+    ax1.xaxis.set_major_locator(MultipleLocator(5))
+    ax1.yaxis.set_major_locator(MultipleLocator(5))
+
+    ax1.xaxis.set_minor_locator(MultipleLocator(1))
+    ax1.yaxis.set_minor_locator(MultipleLocator(1))
+
+    # Turn grid on for both major and minor ticks and style minor slightly
+    # differently.
+    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
+    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
+
+    ax1.set_xlabel('x (km)')
+    ax1.set_ylabel('y (km)')
+    ax1.set_title('Iceberg trajectory')
+ 
+    f.canvas.mpl_connect('button_press_event', onClick)
+
+    ani = FuncAnimation(
+        f,animate,init_func=init,frames=num_frames,
+        interval=frame_len,blit=True,repeat=True)
+
+    print('time',t)
+
+    plt.plot([0,0],[0,20],'k-',lw=1)
+    plt.plot([10,10],[0,20],'k-',lw=1)
+    plt.plot([20,20],[0,20],'k-',lw=1)
+    plt.plot([0,0],[0,20],'k-',lw=1)
+    plt.plot([20,20],[0,20],'k-',lw=1)
+    plt.plot([0,0],[0,20],'k-',lw=1)
+    plt.plot([0,20],[10,10],'k-',lw=1)
+    plt.plot([0,20],[20,20],'k-',lw=1)
+    plt.plot([0,20],[0,0],'k-',lw=1)
+    plt.plot([0,20],[20,20],'k-',lw=1)
+
+    plt.plot([-2,-2],[-2,23],'b:',lw=1)
+    plt.plot([8,8],[-2,23],'b:',lw=1)
+    plt.plot([13,13],[-2,23],'b:',lw=1)
+    plt.plot([23,23],[-2,23],'b:',lw=1)
+    plt.plot([-2,23],[-2,-2],'b:',lw=1)
+    plt.plot([-2,23],[8,8],'b:',lw=1)
+    plt.plot([-2,23],[13,13],'b:',lw=1)
+    plt.plot([-2,23],[23,23],'b:',lw=1)      
+ 
+    
+    plt.show()
+    #animation.save("iceberg_traj_animation.mp4")
+
+
+print('Script complete')
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
+
+
+
+
+
+
+
+
diff --git a/tests/collision_test/input.nml b/tests/collision_test/input.nml
index 539b16d..e62d354 100644
--- a/tests/collision_test/input.nml
+++ b/tests/collision_test/input.nml
@@ -1,15 +1,15 @@
-!TARGET CHKSUM:
+!TARGET CHKSUM (60 s time increments, non-MTS):
 !Total number of bonds is:           52 
-!KID, bergs_chksum: write_restart berg chksum = 892128108  chksum2= -515180265  chksum3= 1707263945  chksum4= 1707263945  chksum5 = 0           #= 16
-!KID, grd_chksum2 : # of bergs/cell chksum    = 0          chksum2= 0           min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
-!KID, grd_chksum3 : write stored_ice chksum   = -540079793 chksum2= -1237287029 min= 6.393358811E+05 max= 7.380127765E+11 mean= 8.033602570E+10 rms= 1.613270384E+11 sd= 1.399018810E+11
-!KID, grd_chksum2 : write stored_heat chksum  = 0          chksum2= 0           min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
+!KID, bergs_chksum: write_restart berg chksum = -1211104969 chksum2= -1211104969 chksum3= 1964715299  chksum4= 1964715299  chksum5= 0            #= 16
+!KID, grd_chksum2 : # of bergs/cell chksum    = 0           chksum2= 0           min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
+!KID, grd_chksum3 : write stored_ice chksum   = -540079793  chksum2= -1237287029 min= 6.393358811E+05 max= 7.380127765E+11 mean= 8.033602570E+10 rms= 1.613270384E+11 sd= 1.399018810E+11
+!KID, grd_chksum2 : write stored_heat chksum  = 0           chksum2= 0           min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
 
 
 &icebergs_driver_nml
   ni=20 !number of elements, x direction
   nj=20 !number of elements, y direction
-  ibdt=10.0 !seconds
+  ibdt=60.0 !seconds
   ibuo=0.2 !ocean x velocity
   ibvo=0.2 !ocean y velocity
   ibui=0.0 !ice x velocity
@@ -17,8 +17,8 @@
   ibhrs=48 !total simulation hours
   nmax=99999999 !max number of timesteps
   saverestart=.true. 
-  halo=4
-  debug=.false.  
+  halo=3
+  debug=.false.   
   collision_test=.true. !specific to the current test, must be true here
 /
 
@@ -26,8 +26,12 @@
 &icebergs_nml
 
     !defaults given in parentheses:
+    !mts=.false. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    !mts_sub_steps=0 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
+    !contact_distance=0 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    !contact_spring_coef=1.e-5!(default=spring_coeff) Berg spring coeff for collisions    
 
-    halo=4 !(4) halo width
+    halo=3 !(4) halo width
     Lx=20000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
     grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
     grid_is_regular=.True. !(T) Point in cell can be found assuming regular Cartesian grid
@@ -39,15 +43,16 @@
     bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
     radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
     tangental_damping_coef=2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val 
     LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
     bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
     sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
     u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
     v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
     initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs= 0. ! (0.) Tidal speeds, set to zero for now.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
     ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs =  1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
     Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
     const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
     use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
@@ -82,8 +87,7 @@
 
     iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
     interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.False. !(F)Bergs only feel interactive forces, not ocean, wind...    
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val    
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...       
     use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
     input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
     use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
@@ -91,17 +95,17 @@
 
     verbose=.true. !(F) Be verbose to stderr
     verbose_hrs=1 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !(24) sampling period for trajectory storage
-    traj_write_hrs=480 ! (480) Period for writing sampled trajectories to disk    
+    traj_sample_hrs=1 !1 !(24) sampling period for trajectory storage
+    traj_write_hrs=6 ! (480) Period for writing sampled trajectories to disk    
     budget=.true. !(T) Calculate budgets
     debug=.false. !(F) Turn on debugging
     really_debug=.false. !(F) Turn on debugging
     halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1 !12884902036 ! If positive, monitors a berg with this id    
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id    
     
     parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.True. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.False. ! (F) If true, then model does not traj trajectory data at all    
+    save_short_traj=.true. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.False. ! (F) If true, then model does not track trajectory data at all    
 
     ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart 
     use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
@@ -110,9 +114,8 @@
     ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
     generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
     fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir = 'INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.    
-    do_unit_tests=.true. ! (F) Conduct some unit tests    
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.      
     orig_read=.false. !(F) Legacy option that does nothing
     read_old_restarts=.false. ! (F) Legacy option that does nothing
     
diff --git a/tests/collision_test/input_tstest.nml b/tests/collision_test/input_tstest.nml
new file mode 100644
index 0000000..792b4f2
--- /dev/null
+++ b/tests/collision_test/input_tstest.nml
@@ -0,0 +1,151 @@
+&icebergs_driver_nml
+  ni=20 !number of elements, x direction
+  nj=20 !number of elements, y direction
+  ibdt=<sec>.0 !10.0 !seconds
+  ibuo=0.2 !ocean x velocity
+  ibvo=0.2 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=48 !total simulation hours
+  nmax=99999999 !max number of timesteps
+  saverestart=.false. 
+  halo=3
+  debug=.false.  
+  collision_test=.true. !specific to the current test, must be true here
+/
+
+
+&icebergs_nml
+
+    !defaults given in parentheses:
+    
+    !vectorized=.true. !(F) use vectorized version of the code
+    !mts=.false. !(F) use multiple timestepping scheme (substep size is automatically determined)
+
+    halo=3 !(4) halo width
+    Lx=20000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.True. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move    
+    
+    rho_bergs=850. ! (850) iceberg density
+    spring_coef=<coef> !1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs= 0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs =  1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0.4 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #) 
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. ! (T) Allows bergs toroll over when rolling conditions are met    
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.False. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)    
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread			
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.False. !(F)Bergs only feel interactive forces, not ocean, wind...    
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val    
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors    
+
+    verbose=.true. !(F) Be verbose to stderr
+    verbose_hrs=1 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !(24) sampling period for trajectory storage
+    traj_write_hrs=1 ! (480) Period for writing sampled trajectories to disk    
+    budget=.true. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1 !12884902036 ! If positive, monitors a berg with this id    
+    
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.True. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.False. ! (F) If true, then model does not traj trajectory data at all    
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart 
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually    
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir = 'INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.    
+    do_unit_tests=.true. ! (F) Conduct some unit tests    
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+    
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+    
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+    
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+    
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+ 
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/collision_test/makeberg/RUN b/tests/collision_test/makeberg/RUN
index 0863960..ae7808f 100755
--- a/tests/collision_test/makeberg/RUN
+++ b/tests/collision_test/makeberg/RUN
@@ -6,7 +6,7 @@ rm ./output_files/Generic*
 	-set_all_bergs_static_by_default=False -Run_plotting_subroutine=False \
 	-break_some_bonds=False -Ice_geometry_source='Generic' \
 	-Generic_ice_geometry_filename='./testtabularberg.nc' \
-	-ISOMIP_reduced=False \
+	-ISOMIP_reduced=False -collision_test=True
 
 cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
 cp ./output_files/Generic_bonds_iceberg.res.nc ./../INPUT/bonds_iceberg.res.nc
\ No newline at end of file
diff --git a/tests/collision_test/makeberg/makeberg.py b/tests/collision_test/makeberg/makeberg.py
index ff4c853..423b6a5 100755
--- a/tests/collision_test/makeberg/makeberg.py
+++ b/tests/collision_test/makeberg/makeberg.py
@@ -44,22 +44,22 @@
 #create a circular tabular berg centered on the following coords (km)
 cy = 4.5e3
 cx = 4.5e3
-cx2 = 15.5e3
+#cx2 = 15.5e3
 
 for i in range(nx):
 
-        tx = float(i) * grid_res
+        tx = float(i) * grid_res 
         g.variables['lon'][i] = tx
         
         for j in range(ny):
                
-                ty = float(j) * grid_res
+                ty = float(j) * grid_res 
                 dist = sqrt((tx-cx)*(tx-cx) + (ty-cy)*(ty-cy))
-                dist2 =  sqrt((tx-cx2)*(tx-cx2) + (ty-cy)*(ty-cy))
+                #dist2 =  sqrt((tx-cx2)*(tx-cx2) + (ty-cy)*(ty-cy))
                 #g.variables['lon'][i,j] = tx
                 #g.variables['lat'][i,j] = ty
         
-                if (dist <1.e3 or dist2<1.e3):
+                if (dist <1.e3): #or dist2<1.e3):
                         g.variables['thick'][i,j]=h_ice
                 else:
                         g.variables['thick'][i,j]=0.0
@@ -67,7 +67,7 @@
                         
 
 for j in range(ny):
-        g.variables['lat'][j] = float(j) * grid_res
+        g.variables['lat'][j] = float(j) * grid_res 
 
 print('Creating file: ' , New_ice_thickness_filename)
 
diff --git a/tests/collision_test_mts/README b/tests/collision_test_mts/README
new file mode 100644
index 0000000..83093c2
--- /dev/null
+++ b/tests/collision_test_mts/README
@@ -0,0 +1,5 @@
+1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
+2.(optional) edit input.nml
+3. run the model: ./RUN
+4, animate the results: animate_trajectories.py
+
diff --git a/tests/collision_test_mts/RUN b/tests/collision_test_mts/RUN
new file mode 100755
index 0000000..090c034
--- /dev/null
+++ b/tests/collision_test_mts/RUN
@@ -0,0 +1,5 @@
+rm iceberg_trajectories.nc
+rm iceberg_trajectories.nc.*
+srun -n4 ./../../build/bergs.x
+
+
diff --git a/tests/collision_test_mts/RUN1p b/tests/collision_test_mts/RUN1p
new file mode 100755
index 0000000..c3bf53e
--- /dev/null
+++ b/tests/collision_test_mts/RUN1p
@@ -0,0 +1,5 @@
+rm iceberg_trajectories.nc
+rm iceberg_trajectories.nc.*
+srun -n1 ./../../build/bergs.x
+
+
diff --git a/tests/collision_test_mts/RUN_tstest.sh b/tests/collision_test_mts/RUN_tstest.sh
new file mode 100755
index 0000000..fe5f81c
--- /dev/null
+++ b/tests/collision_test_mts/RUN_tstest.sh
@@ -0,0 +1,33 @@
+#!/bin/bash
+
+rm iceberg_trajectories.nc
+
+space="s_"
+nc="c_.nc"
+r="./results/iceberg_trajectories_"
+
+s1='10' # 960' #'10 30 60 90'
+c1='1.e-5' # 1.e-4'
+
+for i in $s1
+do
+	for j in $c1
+	do
+	    	result="$r$i$space$j$nc"
+		echo $i
+		echo $j
+		echo $result
+
+		sed "s/<sec>/$i/; s/<coef>/$j/g" \
+		    input_tstest.nml > input.nml
+
+		srun -n4 ./../../build/bergs.x
+
+		mv iceberg_trajectories.nc $result
+	done
+done
+
+
+
+
+
diff --git a/tests/collision_test_mts/animate_trajectories.py b/tests/collision_test_mts/animate_trajectories.py
new file mode 100755
index 0000000..7deaa77
--- /dev/null
+++ b/tests/collision_test_mts/animate_trajectories.py
@@ -0,0 +1,129 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+import matplotlib.pyplot as plt
+from matplotlib.animation import FuncAnimation
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
+                    help=''' provide filename to plot''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+
+
+def main(args):
+    
+    print('reading file')
+
+    filename=args.fname
+    #filename = 'iceberg_trajectories.nc'
+    field = 'lon'
+    field2 = 'lat'
+
+    with nc.Dataset(filename) as file:
+        x = file.variables['lon'][:]/1.e3
+        y = file.variables['lat'][:]/1.e3
+        day = file.variables['day'][:]
+
+    ud = np.unique(day)
+    t = ud[0]
+
+    # frame info
+    num_frames = len(ud)
+    movie_len = 5.0 #seconds
+    frame_len = 1000.0*movie_len/num_frames
+    
+    xmin = 0 #np.floor(min(min(x),min(y),0))
+    xmax = 20 #np.ceil(max(max(x),max(y),20))
+    ymin = xmin
+    ymax = xmax
+
+    anim_running = True
+
+    def animate(i):
+
+        x1 = x[day == ud[i]]
+        y1 = y[day == ud[i]]
+        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
+           
+        scat.set_offsets(data)
+        
+        t = ud[i]
+        time_text.set_text('time = %.1f days' % t )        
+        return scat,time_text
+
+    def init():
+        scat.set_offsets([])
+        return scat,
+
+    def onClick(event):
+        global anim_running
+        if anim_running:
+            ani.event_source.stop()
+            anim_running = False
+        else:
+            ani.event_source.start()
+            anim_running = True       
+    
+    # Now we can do the plotting!
+    f = plt.figure(figsize=(5,5))
+    f.tight_layout()
+    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
+    scat = ax1.scatter([],[],marker='o',facecolor='w',s=100,edgecolor='red')
+    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
+
+    # Change major ticks to show every 20.
+    ax1.xaxis.set_major_locator(MultipleLocator(5))
+    ax1.yaxis.set_major_locator(MultipleLocator(5))
+
+    ax1.xaxis.set_minor_locator(MultipleLocator(1))
+    ax1.yaxis.set_minor_locator(MultipleLocator(1))
+
+    # Turn grid on for both major and minor ticks and style minor slightly
+    # differently.
+    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
+    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
+
+    ax1.set_xlabel('x (km)')
+    ax1.set_ylabel('y (km)')
+    ax1.set_title('Iceberg trajectory')
+ 
+    f.canvas.mpl_connect('button_press_event', onClick)
+
+    ani = FuncAnimation(
+        f,animate,init_func=init,frames=num_frames,
+        interval=frame_len,blit=True,repeat=True)
+
+    print('time',t)
+
+    plt.show()
+    #animation.save("iceberg_traj_animation.mp4")
+
+
+print('Script complete')
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
+
+
+
+
+
+
+
+
diff --git a/tests/collision_test_mts/animate_trajectories_1pe.py b/tests/collision_test_mts/animate_trajectories_1pe.py
new file mode 100755
index 0000000..19db84d
--- /dev/null
+++ b/tests/collision_test_mts/animate_trajectories_1pe.py
@@ -0,0 +1,175 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+import matplotlib.pyplot as plt
+from matplotlib.animation import FuncAnimation
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc.0000',
+                    help=''' provide filename to plot''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+
+
+def main(args):
+    
+    print('reading file')
+
+    filename=args.fname
+    #filename = 'iceberg_trajectories.nc'
+    field = 'lon'
+    field2 = 'lat'
+
+    with nc.Dataset(filename) as file:
+        x = file.variables['lon'][:]/1.e3
+        y = file.variables['lat'][:]/1.e3
+        day = file.variables['day'][:]
+        hs = file.variables['halo_berg'][:]
+
+    #hs = hs+1
+    ud = np.unique(day)
+    t = ud[0]
+
+    print('unique hs',np.unique(hs))
+
+    # frame info
+    num_frames = len(ud)
+    movie_len = 5.0 #seconds
+    frame_len = 1000.0*movie_len/num_frames
+    
+    xmin = np.floor(min(min(x),min(y),-5))
+    xmax = np.ceil(max(max(x),max(y),25))
+    ymin = xmin
+    ymax = xmax
+
+    anim_running = True
+
+    def animate(i):
+
+        x1 = x[day == ud[i]]
+        y1 = y[day == ud[i]]
+        hstat = hs[day == ud[i]]
+        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
+
+        cstring=[]
+        for j in range(len(hstat)):
+            if (hstat[j]<0):
+                cstring.append("y")
+            elif (hstat[j]==0):                 
+                cstring.append("b")
+            elif (hstat[j]==1):
+                cstring.append("r")
+            elif (hstat[j]==2):
+                cstring.append("g")
+            elif (hstat[j]==3):
+                cstring.append("k")
+            elif (hstat[j]==4):
+                cstring.append("m")
+            else:
+                cstring.append("c")
+                                                           
+        scat.set_offsets(data)
+        scat.set_color(cstring)
+        scat.set_edgecolor('k')
+        
+        t = ud[i]
+        time_text.set_text('time = %.1f days' % t )        
+        return scat,time_text
+
+    def init():
+        scat.set_offsets([])
+        return scat,
+
+    def onClick(event):
+        global anim_running
+        if anim_running:
+            ani.event_source.stop()
+            anim_running = False
+        else:
+            ani.event_source.start()
+            anim_running = True       
+    
+    # Now we can do the plotting!
+    f = plt.figure(figsize=(5,5))
+    f.tight_layout()
+    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
+    scat = ax1.scatter([],[],marker='o',s=60) 
+    #scat = ax1.scatter([],[],marker='o',facecolor='w',s=60,edgecolor='red')
+    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
+
+    # Change major ticks to show every 20.
+    ax1.xaxis.set_major_locator(MultipleLocator(5))
+    ax1.yaxis.set_major_locator(MultipleLocator(5))
+
+    ax1.xaxis.set_minor_locator(MultipleLocator(1))
+    ax1.yaxis.set_minor_locator(MultipleLocator(1))
+
+    # Turn grid on for both major and minor ticks and style minor slightly
+    # differently.
+    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
+    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
+
+    ax1.set_xlabel('x (km)')
+    ax1.set_ylabel('y (km)')
+    ax1.set_title('Iceberg trajectory')
+ 
+    f.canvas.mpl_connect('button_press_event', onClick)
+
+    ani = FuncAnimation(
+        f,animate,init_func=init,frames=num_frames,
+        interval=frame_len,blit=True,repeat=True)
+
+    print('time',t)
+
+    plt.plot([0,0],[0,20],'k-',lw=1)
+    plt.plot([10,10],[0,20],'k-',lw=1)
+    plt.plot([20,20],[0,20],'k-',lw=1)
+    plt.plot([0,0],[0,20],'k-',lw=1)
+    plt.plot([20,20],[0,20],'k-',lw=1)
+    plt.plot([0,0],[0,20],'k-',lw=1)
+    plt.plot([0,20],[10,10],'k-',lw=1)
+    plt.plot([0,20],[20,20],'k-',lw=1)
+    plt.plot([0,20],[0,0],'k-',lw=1)
+    plt.plot([0,20],[20,20],'k-',lw=1)
+
+    plt.plot([-2,-2],[-2,23],'b:',lw=1)
+    plt.plot([8,8],[-2,23],'b:',lw=1)
+    plt.plot([13,13],[-2,23],'b:',lw=1)
+    plt.plot([23,23],[-2,23],'b:',lw=1)
+    plt.plot([-2,23],[-2,-2],'b:',lw=1)
+    plt.plot([-2,23],[8,8],'b:',lw=1)
+    plt.plot([-2,23],[13,13],'b:',lw=1)
+    plt.plot([-2,23],[23,23],'b:',lw=1)      
+ 
+    
+    plt.show()
+    #animation.save("iceberg_traj_animation.mp4")
+
+
+print('Script complete')
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
+
+
+
+
+
+
+
+
diff --git a/tests/collision_test_mts/diag_table b/tests/collision_test_mts/diag_table
new file mode 100644
index 0000000..c1c8819
--- /dev/null
+++ b/tests/collision_test_mts/diag_table
@@ -0,0 +1,3 @@
+"icebergs test"
+1 1 1 0 0 0
+
diff --git a/tests/collision_test_mts/input.nml b/tests/collision_test_mts/input.nml
new file mode 100644
index 0000000..2e78b46
--- /dev/null
+++ b/tests/collision_test_mts/input.nml
@@ -0,0 +1,158 @@
+!TARGET CHKSUM (1 hr time increments, MTS w/ 20 sub-steps, contact at 1.5e3 m, contact spring 1.e-7, spring_coef 1.0e-5):
+!Total number of bonds is:           52 
+!KID, bergs_chksum: write_restart berg chksum = 44984808 chksum2= 1088077442 chksum3= 609798238  chksum4= 609798238  chksum5= 0            #= 16
+!KID, grd_chksum2 : # of bergs/cell chksum    = 0           chksum2= 0           min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
+!KID, grd_chksum3 : write stored_ice chksum   = -540079793  chksum2= -1237287029 min= 6.393358811E+05 max= 7.380127765E+11 mean= 8.033602570E+10 rms= 1.613270384E+11 sd= 1.399018810E+11
+!KID, grd_chksum2 : write stored_heat chksum  = 0           chksum2= 0           min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
+
+
+&icebergs_driver_nml
+  ni=20 !number of elements, x direction
+  nj=20 !number of elements, y direction
+  ibdt=3600.0 !seconds
+  ibuo=0.2 !ocean x velocity
+  ibvo=0.2 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=48 !total simulation hours
+  nmax=99999999 !max number of timesteps
+  saverestart=.true. 
+  halo=3
+  debug=.false.   
+  collision_test=.true. !specific to the current test, must be true here
+/
+
+&icebergs_nml  
+
+    !defaults given in parentheses:
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=20 !1 !30 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
+    contact_distance=1.5e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+
+    halo=3 !(4) halo width
+    Lx=20000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.True. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move    
+    
+    rho_bergs=850. ! (850) iceberg density
+    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val 
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0.4 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #) 
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met    
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)    
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread			
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...       
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors    
+
+    verbose=.true. !(F) Be verbose to stderr
+    verbose_hrs=24 ! (24) Period between verbose messages
+    traj_sample_hrs=0.5 !1 !(24) sampling period for trajectory storage
+    traj_write_hrs=0 ! (480) Period for writing sampled trajectories to disk    
+    budget=.true. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id    
+    
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.False. ! (F) If true, then model does not track trajectory data at all    
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart 
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually    
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.      
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+    
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.true. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+    
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+    
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+    
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+ 
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/collision_test_mts/input_tstest.nml b/tests/collision_test_mts/input_tstest.nml
new file mode 100644
index 0000000..bd13bd4
--- /dev/null
+++ b/tests/collision_test_mts/input_tstest.nml
@@ -0,0 +1,159 @@
+!TARGET CHKSUM:
+!Total number of bonds is:           52 
+!KID, bergs_chksum: write_restart berg chksum = 892128108  chksum2= -515180265  chksum3= 1707263945  chksum4= 1707263945  chksum5 = 0           #= 16
+!KID, grd_chksum2 : # of bergs/cell chksum    = 0          chksum2= 0           min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
+!KID, grd_chksum3 : write stored_ice chksum   = -540079793 chksum2= -1237287029 min= 6.393358811E+05 max= 7.380127765E+11 mean= 8.033602570E+10 rms= 1.613270384E+11 sd= 1.399018810E+11
+!KID, grd_chksum2 : write stored_heat chksum  = 0          chksum2= 0           min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
+
+
+&icebergs_driver_nml
+  ni=20 !number of elements, x direction
+  nj=20 !number of elements, y direction
+  ibdt=<sec>.0 !10.0 !seconds
+  ibuo=0.2 !ocean x velocity
+  ibvo=0.2 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=48 !total simulation hours
+  nmax=99999999 !max number of timesteps
+  saverestart=.false. 
+  halo=3
+  debug=.false.  
+  collision_test=.true. !specific to the current test, must be true here
+/
+
+
+&icebergs_nml
+
+    !defaults given in parentheses:
+    
+    !vectorized=.true. !(F) use vectorized version of the code
+    !mts=.false. !(F) use multiple timestepping scheme (substep size is automatically determined)
+
+    halo=3 !(4) halo width
+    Lx=20000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.True. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move    
+    
+    rho_bergs=850. ! (850) iceberg density
+    spring_coef=<coef> !1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs= 0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs =  1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0.4 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #) 
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. ! (T) Allows bergs toroll over when rolling conditions are met    
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.False. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)    
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread			
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.False. !(F)Bergs only feel interactive forces, not ocean, wind...    
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val    
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors    
+
+    verbose=.true. !(F) Be verbose to stderr
+    verbose_hrs=1 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !(24) sampling period for trajectory storage
+    traj_write_hrs=1 ! (480) Period for writing sampled trajectories to disk    
+    budget=.true. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1 !12884902036 ! If positive, monitors a berg with this id    
+    
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.True. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.False. ! (F) If true, then model does not traj trajectory data at all    
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart 
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually    
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir = 'INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.    
+    do_unit_tests=.true. ! (F) Conduct some unit tests    
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+    
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+    
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+    
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+    
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+ 
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/collision_test_mts/makeberg/RUN b/tests/collision_test_mts/makeberg/RUN
new file mode 100755
index 0000000..ae7808f
--- /dev/null
+++ b/tests/collision_test_mts/makeberg/RUN
@@ -0,0 +1,12 @@
+./makeberg.py
+
+rm ./output_files/Generic*
+
+./../../Iceberg_repository/Scripts_and_analysis/initialize_bergs_in_pattern.py \
+	-set_all_bergs_static_by_default=False -Run_plotting_subroutine=False \
+	-break_some_bonds=False -Ice_geometry_source='Generic' \
+	-Generic_ice_geometry_filename='./testtabularberg.nc' \
+	-ISOMIP_reduced=False -collision_test=True
+
+cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
+cp ./output_files/Generic_bonds_iceberg.res.nc ./../INPUT/bonds_iceberg.res.nc
\ No newline at end of file
diff --git a/tests/collision_test_mts/makeberg/makeberg.py b/tests/collision_test_mts/makeberg/makeberg.py
new file mode 100755
index 0000000..423b6a5
--- /dev/null
+++ b/tests/collision_test_mts/makeberg/makeberg.py
@@ -0,0 +1,77 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset  
+import numpy as np 
+import math
+#import os
+from pylab import *
+#import pdb
+import netCDF4 as nc
+
+nx = 20
+ny = 20
+New_ice_thickness_filename='testberg.nc'
+grid_res = 1.e3 #1 km 
+grid_area = grid_res * grid_res
+h_ice = 300.0
+
+New_ice_thickness_filename='testtabularberg.nc'
+g=Dataset(New_ice_thickness_filename,'w') # w if for creating a file
+
+g.createDimension('nx',nx)
+g.createDimension('ny',ny)
+thick_h=g.createVariable('thick','f8',('ny','nx'))
+area_h=g.createVariable('area','f8',('ny','nx'))
+lat_h=g.createVariable('lat','f8','ny')
+lon_h=g.createVariable('lon','f8','nx')
+#lat_h=g.createVariable('lat','f8',('ny','nx'))
+#lon_h=g.createVariable('lon','f8',('ny','nx'))
+
+thick_h.units = 'm'
+thick_h.standard_name = 'ice shelf thickness'
+area_h.units = 'm2'
+area_h.standard_name = 'ice shelf area'
+lon_h.unit = 'm'
+lon_h.standard_name = 'longitude'
+lat_h.unit = 'm'
+lat_h.standard_name = 'latitude'
+
+
+
+#g.variables['thick'][:]=h_ice
+g.variables['area'][:,:]=grid_area
+
+#create a circular tabular berg centered on the following coords (km)
+cy = 4.5e3
+cx = 4.5e3
+#cx2 = 15.5e3
+
+for i in range(nx):
+
+        tx = float(i) * grid_res 
+        g.variables['lon'][i] = tx
+        
+        for j in range(ny):
+               
+                ty = float(j) * grid_res 
+                dist = sqrt((tx-cx)*(tx-cx) + (ty-cy)*(ty-cy))
+                #dist2 =  sqrt((tx-cx2)*(tx-cx2) + (ty-cy)*(ty-cy))
+                #g.variables['lon'][i,j] = tx
+                #g.variables['lat'][i,j] = ty
+        
+                if (dist <1.e3): #or dist2<1.e3):
+                        g.variables['thick'][i,j]=h_ice
+                else:
+                        g.variables['thick'][i,j]=0.0
+
+                        
+
+for j in range(ny):
+        g.variables['lat'][j] = float(j) * grid_res 
+
+print('Creating file: ' , New_ice_thickness_filename)
+
+g.sync()
+g.close()
+
+        

From c4355d3e0fccdb5cb3e57abd99c31ab7a79b32c0 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Fri, 25 Sep 2020 17:33:26 -0400
Subject: [PATCH 255/361] formatting

---
 build/README.md                     |    4 +-
 driver/icebergs_driver.F90          |  588 +++++----
 src/icebergs.F90                    |  516 ++++----
 src/icebergs_framework.F90          | 1778 +++++++++++++--------------
 src/icebergs_io.F90                 |  549 ++++-----
 tests/collision_test/.gitignore     |    1 +
 tests/collision_test_mts/.gitignore |    1 +
 7 files changed, 1686 insertions(+), 1751 deletions(-)
 create mode 100644 tests/collision_test/.gitignore
 create mode 100644 tests/collision_test_mts/.gitignore

diff --git a/build/README.md b/build/README.md
index 6b5b28d..5b43574 100644
--- a/build/README.md
+++ b/build/README.md
@@ -11,10 +11,10 @@ To create a `Makefile`:
 ../../mkmf/bin/mkmf -t ../../mkmf/templates/ncrc-gnu.mk -c "-Duse_libMPI -Duse_netCDF" -p bergs.x path_names
 
 
-##../../mkmf/bin/mkmf -t ../../mkmf/templates/ncrc-intel.mk -c "-Duse_libMPI -Duse_netCDF" -p bergs.x path_names 
+##../../mkmf/bin/mkmf -t ../../mkmf/templates/ncrc-intel.mk -c "-Duse_libMPI -Duse_netCDF" -p bergs.x path_names
 ```
 To compile a "debug" executable:
 ```
 make DEBUG=1 -j
 ##make NETCDF=3 DEBUG=1 bergs.x -j
-```
+```
\ No newline at end of file
diff --git a/driver/icebergs_driver.F90 b/driver/icebergs_driver.F90
index 5c88fcf..dc6df52 100644
--- a/driver/icebergs_driver.F90
+++ b/driver/icebergs_driver.F90
@@ -1,321 +1,297 @@
 program icebergs_driver
 
-  use fms_mod, only : fms_init
-  use fms_mod, only : fms_end
-  use fms_mod, only : open_namelist_file
-  use fms_mod, only : close_file
-  use fms_mod, only : error_mesg
-  use fms_mod, only : FATAL
-  use mpp_domains_mod, only : mpp_define_layout
-  use mpp_domains_mod, only : mpp_define_domains
-  use mpp_domains_mod, only : mpp_define_io_domain
-  use mpp_domains_mod, only : mpp_get_compute_domain
-  use mpp_domains_mod, only : mpp_get_data_domain
-  use mpp_domains_mod, only : domain2D
-  use mpp_domains_mod, only : CYCLIC_GLOBAL_DOMAIN,GLOBAL_DATA_DOMAIN
-  use mpp_mod, only : mpp_npes
-  use mpp_mod, only : mpp_pe
-  use mpp_mod, only : mpp_root_pe
-  use time_manager_mod, only : time_type
-  use time_manager_mod, only : set_date
-  use time_manager_mod, only : set_calendar_type
-  use time_manager_mod, only : THIRTY_DAY_MONTHS
-  use time_manager_mod, only : increment_date
-  use time_manager_mod, only : real_to_time_type,time_type_to_real
-  use time_manager_mod, only : operator(+), operator(-), operator(*), operator(/)
-  use time_manager_mod, only : operator(>), operator(<), operator(>=)  
-  use diag_manager_mod, only : diag_manager_init
-  use time_manager_mod, only: get_date 
-  use diag_axis_mod, only : diag_axis_init
-  use ice_bergs, only : icebergs
-  use ice_bergs, only : icebergs_init
-  use ice_bergs, only : icebergs_run
-  use ice_bergs, only : icebergs_end
-  use ice_bergs, only : icebergs_save_restart
-
-
-  ! For parallelism
-  integer :: nprocs !< Number of processes
-  integer :: layout(2) !< Layout of MPI processes
-  integer :: io_layout(2) !< Layout of I/O processes
-
-  integer :: iflags= CYCLIC_GLOBAL_DOMAIN !< For i-direction flags
-  integer :: jflags= 0  !< For j-direction flags
-  type(domain2D) :: mpp_domain !< Parallel decomposition
-  ! For declarations
-  integer :: isd !< Start of i-index for data domain (used in declarations)
-  integer :: ied !< End of i-index for data domain (used in declarations)
-  integer :: jsd !< Start of j-index for data domain (used in declarations)
-  integer :: jed !< End of j-index for data domain (used in declarations)
-  ! I/O
-  integer :: nmunit !< Namelist file unit 
-  integer :: axes(2) !< Diagnostic axes
-  ! Run-time parameters for this driver
-  integer :: ni=0 !< Global number of grid cells in i-direction (mandatory input)
-  integer :: nj=0 !< Global number of grid cells in j-direction (mandatory input)
-  logical :: debug=.true. !< If true, do some debugging
-  logical :: saverestart=.false. !< If true, save a berg restart file at the end
-  logical :: collision_test=.false.
-  integer :: halo=1 !< Width of halo in parallel decomposition
-  real :: ibdt=3600.0
-  real :: ibuo=0.1
-  real :: ibvo=0.0
-  real :: ibui=0.0
-  real :: ibvi=0.0
-  real :: gridres=1.e3
-  integer :: ibhrs=2
-  integer :: nmax = 2000000000 !<max number of iterations    
-  namelist /icebergs_driver_nml/ debug, ni, nj, halo, ibhrs, ibdt, ibuo, ibvo, nmax, &
+use fms_mod, only : fms_init
+use fms_mod, only : fms_end
+use fms_mod, only : open_namelist_file
+use fms_mod, only : close_file
+use fms_mod, only : error_mesg
+use fms_mod, only : FATAL
+use mpp_domains_mod, only : mpp_define_layout
+use mpp_domains_mod, only : mpp_define_domains
+use mpp_domains_mod, only : mpp_define_io_domain
+use mpp_domains_mod, only : mpp_get_compute_domain
+use mpp_domains_mod, only : mpp_get_data_domain
+use mpp_domains_mod, only : domain2D
+use mpp_domains_mod, only : CYCLIC_GLOBAL_DOMAIN,GLOBAL_DATA_DOMAIN
+use mpp_mod, only : mpp_npes
+use mpp_mod, only : mpp_pe
+use mpp_mod, only : mpp_root_pe
+use time_manager_mod, only : time_type
+use time_manager_mod, only : set_date
+use time_manager_mod, only : set_calendar_type
+use time_manager_mod, only : THIRTY_DAY_MONTHS
+use time_manager_mod, only : increment_date
+use time_manager_mod, only : real_to_time_type,time_type_to_real
+use time_manager_mod, only : operator(+), operator(-), operator(*), operator(/)
+use time_manager_mod, only : operator(>), operator(<), operator(>=)
+use diag_manager_mod, only : diag_manager_init
+use time_manager_mod, only: get_date
+use diag_axis_mod, only : diag_axis_init
+use ice_bergs, only : icebergs
+use ice_bergs, only : icebergs_init
+use ice_bergs, only : icebergs_run
+use ice_bergs, only : icebergs_end
+use ice_bergs, only : icebergs_save_restart
+
+! For parallelism
+integer :: nprocs !< Number of processes
+integer :: layout(2) !< Layout of MPI processes
+integer :: io_layout(2) !< Layout of I/O processes
+integer :: iflags=CYCLIC_GLOBAL_DOMAIN !< For i-direction flags
+integer :: jflags=0 !< For j-direction flags
+type(domain2D) :: mpp_domain !< Parallel decomposition
+! For declarations
+integer :: isd !< Start of i-index for data domain (used in declarations)
+integer :: ied !< End of i-index for data domain (used in declarations)
+integer :: jsd !< Start of j-index for data domain (used in declarations)
+integer :: jed !< End of j-index for data domain (used in declarations)
+! I/O
+integer :: nmunit !< Namelist file unit
+integer :: axes(2) !< Diagnostic axes
+! Run-time parameters for this driver
+integer :: ni=0 !< Global number of grid cells in i-direction (mandatory input)
+integer :: nj=0 !< Global number of grid cells in j-direction (mandatory input)
+logical :: debug=.true. !< If true, do some debugging
+logical :: saverestart=.false. !< If true, save a berg restart file at the end
+logical :: collision_test=.false.
+integer :: halo=1 !< Width of halo in parallel decomposition
+real :: ibdt=3600.0
+real :: ibuo=0.1
+real :: ibvo=0.0
+real :: ibui=0.0
+real :: ibvi=0.0
+real :: gridres=1.e3
+integer :: ibhrs=2
+integer :: nmax = 2000000000 !<max number of iteration
+namelist /icebergs_driver_nml/ debug, ni, nj, halo, ibhrs, ibdt, ibuo, ibvo, nmax, &
        saverestart,ibui,ibvi,collision_test,gridres
-  real :: time_begin, time_finish
-  ! For loops
-  integer :: isc !< Start of i-index for computational domain (used for loops)
-  integer :: iec !< End of i-index for computational domain (used for loops)
-  integer :: jsc !< Start of j-index for computational domain (used for loops)
-  integer :: jec !< End of j-index for computational domain (used for loops)
-  ! Time
-  type(time_type) :: Time !< Model time
-  type(time_type) :: Time_end  !<end time for the experiment (s)
-  real :: dt !<time increment
-  integer :: ns !<timestep counter
-  integer :: iyr, imon, iday, ihr, imin, isec
-  ! For icebergs
-  type(icebergs), pointer :: bergs !< Container for icebergs
-  real, allocatable :: lon(:,:) !< Longitude or position in x
-  real, allocatable :: lat(:,:) !< Latitude or position in y
-  real, allocatable :: wet(:,:) !< Wet-dry mask to indicate ocean/land
-  real, allocatable :: dx(:,:) !< Length of northern edge of cell (m)
-  real, allocatable :: dy(:,:) !< Length of eatern edge of cell (m)
-  real, allocatable :: area(:,:) !< Area of cell (m2)
-  real, allocatable :: cos_rot(:,:) !< Cosine of angle of grid orientation
-  real, allocatable :: sin_rot(:,:) !< Sine of angle of grid orientation
-  real, allocatable :: depth(:,:) !< Depth of ocean (m)
-  ! Work variables
-  integer :: i,j
-  real, allocatable :: coord(:) !< One dimensional coordinate for initializing diagnostics
-
-  ! For icebergs_run
-  real, dimension(:,:), allocatable :: calving !<Calving (kg/s)
-  real, dimension(:,:), allocatable :: uo,vo !<zonal and meridonal ocean velocities (m/s)
-  real, dimension(:,:), allocatable :: ui,vi !<zonal and meridonal ice velocities (m/s)
-  real, dimension(:,:), allocatable :: tauxa,tauya !< Zonal and meridonal wind stress (Pa)
-  real, dimension(:,:), allocatable :: ssh !< Effective sea-surface height (m)
-  real, dimension(:,:), allocatable :: sst !< Sea-surface temperature (C or K)
-  real, dimension(:,:), allocatable :: cn !< Sea-ice concentration (nondim)
-  real, dimension(:,:), allocatable :: hi !< Sea-ice thickness (m)
-  real, dimension(:,:), allocatable :: calving_hflx !< Calving heat flux (W/m2)
-  integer :: stagger, stress_stagger
-  real, dimension(:,:), allocatable :: sss !< Sea-surface salinity (1e-3)
-  real, dimension(:,:), pointer :: mass_berg !< Mass of bergs (kg)
-  real, dimension(:,:), pointer  :: ustar_berg !< Friction velocity on base of bergs (m/s)
-  real, dimension(:,:), pointer :: area_berg !< Area of bergs (m2)
-
-  call cpu_time(time_begin)
-  
-  ! Boot FMS
-  call fms_init()
-
-  ! Read run-time parameters
-  nmunit = open_namelist_file(file='input.nml')
-  read(nmunit, nml=icebergs_driver_nml)
-  call close_file(nmunit)
-  if (min(ni,nj)<1) call error_mesg('icebergs_driver:', &
-       'Both ni,nj must be positive in icebergs_driver_nml namelist', FATAL)
-
-
-  ! Ask FMS to figure our how to decompose the global ni x nj grid
-  layout = (/0,0/) ! 0,0 lets FMS find an optimal layout
-  nprocs = mpp_npes() ! How many processes are we using?
-  call mpp_define_layout((/1, ni, 1, nj/), nprocs, layout)
-  if (debug .and. mpp_root_pe()==0) print *,'layout=',layout,'nprocs=',nprocs,'PE=',mpp_pe()
-
-  ! Create a decomposed domain with the given layout from above
-  call mpp_define_domains((/1,ni,1,nj/), layout, mpp_domain, &
-       xflags=iflags, yflags=jflags, &
-       xhalo=halo, yhalo=halo, &
-       symmetry=.false., name='iceberg_driver')
-
-  ! Set up I/O
-  io_layout = (/1,1/) ! 1,1 tells FMS to use just one processor for I/O
-  call mpp_define_io_domain(mpp_domain, io_layout)
-
-  ! Diagnostics manager
-  call diag_manager_init()
-  ! Axes for diagnostics
-  allocate( coord(ni) )
-  do i = 1, ni
-     coord(i) =  real(i)
-  enddo
-  axes(1) = diag_axis_init('i', coord, 'index', 'X', 'cell index i', Domain2=mpp_domain)
-  deallocate( coord )
-  allocate( coord(nj) )
-  do j = 1, nj
-     coord(j) = real(j)
-  enddo
-  axes(2) = diag_axis_init('j', coord, 'index', 'Y', 'cell index j', Domain2=mpp_domain)
-  deallocate( coord )
-
-  ! Query for declaration ranges
-  call mpp_get_data_domain(mpp_domain, isd, ied, jsd, jed)
-  if (debug .and. mpp_root_pe()==0) print *,'isd,ied,jsd,jed=',isd,ied,jsd,jed
-
-  ! Query for loop ranges
-  call mpp_get_compute_domain(mpp_domain, isc, iec, jsc, jec)
-  if (debug .and. mpp_root_pe()==0) print *,'isd,isc,iec,ied=',isd,isc,iec,ied
-  if (debug .and. mpp_root_pe()==0) print *,'jsd,jsc,jec,jed=',jsd,jsc,jec,jed
-  if (debug .and. mpp_root_pe()==0) print *,''
-
-  allocate( lon(isd:ied,jsd:jed) )
-  allocate( lat(isd:ied,jsd:jed) )
-  allocate( wet(isd:ied,jsd:jed) )
-  allocate( dx(isd:ied,jsd:jed) )
-  allocate( dy(isd:ied,jsd:jed) )
-  allocate( area(isd:ied,jsd:jed) )
-  allocate( cos_rot(isd:ied,jsd:jed) )
-  allocate( sin_rot(isd:ied,jsd:jed) )
-  allocate( depth(isd:ied,jsd:jed) )
-
-
-
-  do j = jsd, jed
-     do i = isd, ied
-        lon(i,j) = gridres*real(i)
-        lat(i,j) = gridres*real(j)
-        dx(i,j) = gridres
-        dy(i,j) = gridres
-        area(i,j) = gridres*gridres
-        wet(i,j) = 1.0
-        cos_rot(i,j) = 1.0 
-        sin_rot(i,j) = 0.0
-        depth(i,j) = 1000.
-     enddo
+! For loops
+integer :: isc !< Start of i-index for computational domain (used for loops)
+integer :: iec !< End of i-index for computational domain (used for loops)
+integer :: jsc !< Start of j-index for computational domain (used for loops)
+integer :: jec !< End of j-index for computational domain (used for loops)
+! Time
+type(time_type) :: Time !< Model time
+type(time_type) :: Time_end  !<end time for the experiment (s)
+real :: dt !<time increment
+integer :: ns !<timestep counter
+integer :: iyr, imon, iday, ihr, imin, isec
+real :: time_begin, time_finish
+! For icebergs
+type(icebergs), pointer :: bergs !< Container for icebergs
+real, allocatable :: lon(:,:) !< Longitude or position in x
+real, allocatable :: lat(:,:) !< Latitude or position in y
+real, allocatable :: wet(:,:) !< Wet-dry mask to indicate ocean/land
+real, allocatable :: dx(:,:) !< Length of northern edge of cell (m)
+real, allocatable :: dy(:,:) !< Length of eatern edge of cell (m)
+real, allocatable :: area(:,:) !< Area of cell (m2)
+real, allocatable :: cos_rot(:,:) !< Cosine of angle of grid orientation
+real, allocatable :: sin_rot(:,:) !< Sine of angle of grid orientation
+real, allocatable :: depth(:,:) !< Depth of ocean (m)
+! Work variables
+integer :: i,j
+real, allocatable :: coord(:) !< One dimensional coordinate for initializing diagnostics
+
+! For icebergs_run
+real, dimension(:,:), allocatable :: calving !<Calving (kg/s)
+real, dimension(:,:), allocatable :: uo,vo !<zonal and meridonal ocean velocities (m/s)
+real, dimension(:,:), allocatable :: ui,vi !<zonal and meridonal ice velocities (m/s)
+real, dimension(:,:), allocatable :: tauxa,tauya !< Zonal and meridonal wind stress (Pa)
+real, dimension(:,:), allocatable :: ssh !< Effective sea-surface height (m)
+real, dimension(:,:), allocatable :: sst !< Sea-surface temperature (C or K)
+real, dimension(:,:), allocatable :: cn !< Sea-ice concentration (nondim)
+real, dimension(:,:), allocatable :: hi !< Sea-ice thickness (m)
+real, dimension(:,:), allocatable :: calving_hflx !< Calving heat flux (W/m2)
+integer :: stagger, stress_stagger
+real, dimension(:,:), allocatable :: sss !< Sea-surface salinity (1e-3)
+real, dimension(:,:), pointer :: mass_berg !< Mass of bergs (kg)
+real, dimension(:,:), pointer  :: ustar_berg !< Friction velocity on base of bergs (m/s)
+real, dimension(:,:), pointer :: area_berg !< Area of bergs (m2)
+
+call cpu_time(time_begin)
+
+! Boot FMS
+call fms_init()
+
+! Read run-time parameters
+nmunit = open_namelist_file(file='input.nml')
+read(nmunit, nml=icebergs_driver_nml)
+call close_file(nmunit)
+if (min(ni,nj)<1) call error_mesg('icebergs_driver:', &
+  'Both ni,nj must be positive in icebergs_driver_nml namelist', FATAL)
+
+! Ask FMS to figure our how to decompose the global ni x nj grid
+layout = (/0,0/) ! 0,0 lets FMS find an optimal layout
+nprocs = mpp_npes() ! How many processes are we using?
+call mpp_define_layout((/1, ni, 1, nj/), nprocs, layout)
+if (debug .and. mpp_root_pe()==0) print *,'layout=',layout,'nprocs=',nprocs,'PE=',mpp_pe()
+
+! Create a decomposed domain with the given layout from above
+call mpp_define_domains((/1,ni,1,nj/), layout, mpp_domain, &
+         xflags=iflags, yflags=jflags, &
+         xhalo=halo, yhalo=halo, &
+         symmetry=.false., name='iceberg_driver')
+
+! Set up I/O
+io_layout = (/1,1/) ! 1,1 tells FMS to use just one processor for I/O
+call mpp_define_io_domain(mpp_domain, io_layout)
+
+! Diagnostics manager
+call diag_manager_init()
+! Axes for diagnostics
+allocate( coord(ni) )
+do i = 1, ni
+  coord(i) = real(i)
+enddo
+axes(1) = diag_axis_init('i', coord, 'index', 'X', 'cell index i', Domain2=mpp_domain)
+deallocate( coord )
+allocate( coord(nj) )
+do j = 1, nj
+  coord(j) = real(j)
+enddo
+axes(2) = diag_axis_init('j', coord, 'index', 'Y', 'cell index j', Domain2=mpp_domain)
+deallocate( coord )
+
+! Query for declaration ranges
+call mpp_get_data_domain(mpp_domain, isd, ied, jsd, jed)
+if (debug .and. mpp_root_pe()==0) print *,'isd,ied,jsd,jed=',isd,ied,jsd,jed
+
+! Query for loop ranges
+call mpp_get_compute_domain(mpp_domain, isc, iec, jsc, jec)
+if (debug .and. mpp_root_pe()==0) print *,'isd,isc,iec,ied=',isd,isc,iec,ied
+if (debug .and. mpp_root_pe()==0) print *,'jsd,jsc,jec,jed=',jsd,jsc,jec,jed
+
+allocate( lon(isd:ied,jsd:jed) )
+allocate( lat(isd:ied,jsd:jed) )
+allocate( wet(isd:ied,jsd:jed) )
+allocate( dx(isd:ied,jsd:jed) )
+allocate( dy(isd:ied,jsd:jed) )
+allocate( area(isd:ied,jsd:jed) )
+allocate( cos_rot(isd:ied,jsd:jed) )
+allocate( sin_rot(isd:ied,jsd:jed) )
+allocate( depth(isd:ied,jsd:jed) )
+
+do j = jsd, jed
+  do i = isd, ied
+    lon(i,j) = gridres*real(i)
+    lat(i,j) = gridres*real(j)
+    dx(i,j) = gridres
+    dy(i,j) = gridres
+    area(i,j) = gridres*gridres
+    wet(i,j) = 1.0
+    cos_rot(i,j) = 1.0
+    sin_rot(i,j) = 0.0
+    depth(i,j) = 1000.
   enddo
-
-
-  call set_calendar_type(THIRTY_DAY_MONTHS)
-  time = set_date(1,1,1,0,0,0)
-  dt = ibdt !3600.0
-
-  call icebergs_init(bergs, &
-       ni, nj, layout, io_layout, axes, iflags, jflags, dt, time, &
-       lon(isc:iec,jsc:jec), lat(isc:iec,jsc:jec), wet(isc-1:iec+1,jsc-1:jec+1), &
-       dx(isc-1:iec+1,jsc-1:jec+1), dy(isc-1:iec+1,jsc-1:jec+1), area(isc:iec,jsc:jec), &
-       cos_rot(isc-1:iec+1,jsc-1:jec+1), sin_rot(isc-1:iec+1,jsc-1:jec+1), &
-       depth(isc:iec,jsc:jec), fractional_area=.false.)
-
-  ! for icebergs_run: 
-  allocate( calving(isd:ied,jsd:jed) )
-  allocate( uo(isd:ied,jsd:jed) )
-  allocate( vo(isd:ied,jsd:jed) )
-  allocate( ui(isd:ied,jsd:jed) )
-  allocate( vi(isd:ied,jsd:jed) )
-  allocate( tauxa(isd:ied,jsd:jed) )
-  allocate( tauya(isd:ied,jsd:jed) )
-  allocate( ssh(isd:ied,jsd:jed) )
-  allocate( sst(isd:ied,jsd:jed) ) 
-  allocate( cn(isd:ied,jsd:jed) )
-  allocate( hi(isd:ied,jsd:jed) )
-  allocate( calving_hflx(isd:ied,jsd:jed) )
-
-  calving = 0.0 !"calving" flux (kg/s) due to "melt" of bergs
-  uo = ibuo !zonal ocean velocities (m/s)
-  vo = ibvo !meridonal ocean velocities (m/s)
-  ui = ibui !zonal ice velocities (m/s)
-  vi = ibvi !meridonal ice velocities (m/s)
-  tauxa = 0.0 !zonal wind stress (Pa)
-  tauya = 0.0 !meridonal wind stress (Pa)
-  ssh = 0.0 !eff sea-surf height
-  sst = -2.0 !sea surface temperature (C or K; if K, will automatically adjust to C)
-  cn = 0.0 !sea-ice concentration (nondim)
-  hi = 0.0 !sea-ice thickness (m)
-  calving_hflx = 0.0 !calving heat flux (W/m2)
-
-  ! if (collision_test) then
-  !   do j = jsd,jed
-  !     if (j>10) then
-  !       vo(:,j) = -ibvo
-  !     elseif (j==10) then
-  !       vo(:,j) = 0.
-  !     else
-  !       vo(:,j) = ibvo
-  !     endif
-  !   enddo
-  !   do i = isd,ied
-  !      if (i>10) vo(i,:) = 0.0
-  !   enddo
-  ! end if
-
-  if (collision_test) then
-    do j=jsd,jed; do i=isd,ied
-      if (lon(i,j)>10.e3 .or. lon(i,j)<=0.0 .or. lat(i,j)==10.e3) then
-        vo(i,j)=0.0
+enddo
+
+call set_calendar_type(THIRTY_DAY_MONTHS)
+time = set_date(1,1,1,0,0,0)
+dt = ibdt
+
+call icebergs_init(bergs, &
+                   ni, nj, layout, io_layout, axes, iflags, jflags, dt, time, &
+                   lon(isc:iec,jsc:jec), lat(isc:iec,jsc:jec), wet(isc-1:iec+1,jsc-1:jec+1), &
+                   dx(isc-1:iec+1,jsc-1:jec+1), dy(isc-1:iec+1,jsc-1:jec+1), area(isc:iec,jsc:jec), &
+                   cos_rot(isc-1:iec+1,jsc-1:jec+1), sin_rot(isc-1:iec+1,jsc-1:jec+1), &
+                   depth(isc:iec,jsc:jec), fractional_area=.false.)
+
+! for icebergs_run:
+allocate( calving(isd:ied,jsd:jed) )
+allocate( uo(isd:ied,jsd:jed) )
+allocate( vo(isd:ied,jsd:jed) )
+allocate( ui(isd:ied,jsd:jed) )
+allocate( vi(isd:ied,jsd:jed) )
+allocate( tauxa(isd:ied,jsd:jed) )
+allocate( tauya(isd:ied,jsd:jed) )
+allocate( ssh(isd:ied,jsd:jed) )
+allocate( sst(isd:ied,jsd:jed) )
+allocate( cn(isd:ied,jsd:jed) )
+allocate( hi(isd:ied,jsd:jed) )
+allocate( calving_hflx(isd:ied,jsd:jed) )
+
+calving = 0.0 !"calving" flux (kg/s) due to "melt" of bergs
+uo = ibuo !zonal ocean velocities (m/s)
+vo = ibvo !meridonal ocean velocities (m/s)
+ui = ibui !zonal ice velocities (m/s)
+vi = ibvi !meridonal ice velocities (m/s)
+tauxa = 0.0 !zonal wind stress (Pa)
+tauya = 0.0 !meridonal wind stress (Pa)
+ssh = 0.0 !eff sea-surf height
+sst = -2.0 !sea surface temperature (C or K; if K, will automatically adjust to C)
+cn = 0.0 !sea-ice concentration (nondim)
+hi = 0.0 !sea-ice thickness (m)
+calving_hflx = 0.0 !calving heat flux (W/m2)
+
+if (collision_test) then
+  do j=jsd,jed; do i=isd,ied
+    if (lon(i,j)>10.e3 .or. lon(i,j)<=0.0 .or. lat(i,j)==10.e3) then
+      vo(i,j)=0.0
+    else
+      if (lat(i,j)>10.e3) then
+        vo(i,j)=-ibvo
       else
-        if (lat(i,j)>10.e3) then
-          vo(i,j)=-ibvo
-        else
-          vo(i,j)=ibvo
-        endif
+        vo(i,j)=ibvo
       endif
-    enddo;enddo
-  endif
-  
-
-  ! optional:
-  ! allocate( sss(isd:ied,jsd:jed) )
-  ! allocate( mass_berg(isd:ied,jsd:jed) )
-  ! allocate( ustar_berg(isd:ied,jsd:jed) )
-  ! allocate( area_berg(isd:ied,jsd:jed) )  
-  ! stagger =  !scalar integer
-  ! stress_stagger = !scalar integer
-  ! sss = !sea surface salinity (1e-3)
-  ! mass_berg = !mass of bergs (kg)
-  ! ustar_berg = !Friction velocity on base of bergs (m/s)
-  ! area_berg = !Area of bergs (m2)
-
-  ns = 1 !timestep counter
-
-  ! Time_end = increment_date(Time, years, months, days, hours, minutes, seconds)
-  Time_end = increment_date(Time,0,0,0,ibhrs,0,0) 
-
-  do while ((ns < nmax) .and. (Time < Time_end))
-
-     if (mpp_pe()==0 .and. debug) then
-        call get_date(Time, iyr, imon, iday, ihr, imin, isec)
-        write(*,*),''
-        write(*,'(a)'),'-------------------------------------------'
-        write(*,'(a,i5)')' Timestep   ',ns
-        write(*,'(a,i5,a,i5,a,i5)')' year',iyr,'  month ',imon,'  day   ',iday
-        write(*,'(a,i5,a,i5,a,i5)')' hour',ihr,'  minute',imin,'  second',isec       
-        write(*,'(a)'),'-------------------------------------------'
-        write(*,*),''
-     end if
+    endif
+  enddo;enddo
+endif
+
+! optional:
+! allocate( sss(isd:ied,jsd:jed) )
+! allocate( mass_berg(isd:ied,jsd:jed) )
+! allocate( ustar_berg(isd:ied,jsd:jed) )
+! allocate( area_berg(isd:ied,jsd:jed) )
+! stagger =  !scalar integer
+! stress_stagger = !scalar integer
+! sss = !sea surface salinity (1e-3)
+! mass_berg = !mass of bergs (kg)
+! ustar_berg = !Friction velocity on base of bergs (m/s)
+! area_berg = !Area of bergs (m2)
+
+ns = 1 !timestep counter
+
+! Time_end = increment_date(Time, years, months, days, hours, minutes, seconds)
+Time_end = increment_date(Time,0,0,0,ibhrs,0,0)
+
+do while ((ns < nmax) .and. (Time < Time_end))
+  if (mpp_pe()==0 .and. debug) then
+    call get_date(Time, iyr, imon, iday, ihr, imin, isec)
+    write(*,*),''
+    write(*,'(a)'),'-------------------------------------------'
+    write(*,'(a,i5)')' Timestep   ',ns
+    write(*,'(a,i5,a,i5,a,i5)')' year',iyr,'  month ',imon,'  day   ',iday
+    write(*,'(a,i5,a,i5,a,i5)')' hour',ihr,'  minute',imin,'  second',isec
+    write(*,'(a)'),'-------------------------------------------'
+    write(*,*),''
+  end if
 
-     ! The main driver the steps updates icebergs
-     call icebergs_run(bergs, time, calving(isc:iec,jsc:jec), &
-          uo(isc-1:iec+1,jsc-1:jec+1), vo(isc-1:iec+1,jsc-1:jec+1), &
-          ui(isc-1:iec+1,jsc-1:jec+1), vi(isc-1:iec+1,jsc-1:jec+1), &
-          tauxa(isc:iec,jsc:jec), tauya(isc:iec,jsc:jec), &
-          ssh(isc-1:iec+1,jsc-1:jec+1), sst(isc:iec,jsc:jec), &
-          calving_hflx(isc:iec,jsc:jec), &
-          cn(isc-1:iec+1,jsc-1:jec+1), hi(isc-1:iec+1,jsc-1:jec+1))
+  ! The main driver the steps updates icebergs
+  call icebergs_run(bergs, time, calving(isc:iec,jsc:jec), &
+                    uo(isc-1:iec+1,jsc-1:jec+1), vo(isc-1:iec+1,jsc-1:jec+1), &
+                    ui(isc-1:iec+1,jsc-1:jec+1), vi(isc-1:iec+1,jsc-1:jec+1), &
+                    tauxa(isc:iec,jsc:jec), tauya(isc:iec,jsc:jec), &
+                    ssh(isc-1:iec+1,jsc-1:jec+1), sst(isc:iec,jsc:jec), &
+                    calving_hflx(isc:iec,jsc:jec), &
+                    cn(isc-1:iec+1,jsc-1:jec+1), hi(isc-1:iec+1,jsc-1:jec+1))
 
-     ! full form, with optional vars:
-     ! call icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh, sst, &
-     ! calving_hflx, cn, hi,stagger, stress_stagger, sss, mass_berg, ustar_berg, area_berg)       
+  ! full form, with optional vars:
+  ! call icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh, sst, &
+  ! calving_hflx, cn, hi,stagger, stress_stagger, sss, mass_berg, ustar_berg, area_berg)
 
-     Time = Time + real_to_time_type(dt)
-     ns = ns+1
-  enddo
+  Time = Time + real_to_time_type(dt)
+  ns = ns+1
+enddo
 
-  if (saverestart) call icebergs_save_restart(bergs)
+if (saverestart) call icebergs_save_restart(bergs)
 
-  !Deallocate all memory and disassociated pointer
-  call icebergs_end(bergs)
+!Deallocate all memory and disassociated pointer
+call icebergs_end(bergs)
 
-  call cpu_time(time_finish)
+call cpu_time(time_finish)
 
-  if (mpp_pe()==0) then
-     write(*,*) 'Simulation finished in ', (time_finish - time_begin)/60., 'minutes'
-  end if
+if (mpp_pe()==0) then
+  write(*,*) 'Simulation finished in ', (time_finish - time_begin)/60., 'minutes'
+end if
 
 end program icebergs_driver
diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 8d38623..d4460c0 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -150,7 +150,6 @@ subroutine icebergs_init(bergs, &
     endif
     call update_halo_icebergs(bergs)
     call connect_all_bonds(bergs)
-    
     nbonds=0
     check_bond_quality=.True.
     call count_bonds(bergs, nbonds,check_bond_quality)
@@ -341,7 +340,7 @@ subroutine initialize_iceberg_bonds(bergs)
   grd=>bergs%grd
   !Should update halos before doing this
   ! do grdj_outer = grd%jsc,grd%jec ; do grdi_outer = grd%isc,grd%iec  !Should you be on the data domain??
-  do grdj_outer = grd%jsd,grd%jed ; do grdi_outer = grd%isd,grd%ied  !using data domain -Alex     
+  do grdj_outer = grd%jsd,grd%jed ; do grdi_outer = grd%isd,grd%ied  !using data domain -Alex
     berg=>bergs%list(grdi_outer,grdj_outer)%first
     do while (associated(berg)) ! loop over all bergs
 
@@ -349,7 +348,7 @@ subroutine initialize_iceberg_bonds(bergs)
       !call rotpos_to_tang(lon1,lat1,x1,y1)  !Is this correct? Shouldn't it only be on tangent plane?
 
       ! do grdj_inner = grd%jsc,grd%jec ; do grdi_inner = grd%isc,grd%iec  !This line uses n^2 steps
-      do grdj_inner = grd%jsd,grd%jed ; do grdi_inner = grd%isd,grd%ied !Uses n^2 steps. Change to data domain-Alex         
+      do grdj_inner = grd%jsd,grd%jed ; do grdi_inner = grd%isd,grd%ied !Uses n^2 steps. Change to data domain-Alex
 !     do grdj_inner = berg%jne-1,berg%jne+1 ; do grdi_inner = berg%ine-1,berg%ine+1   !Only looping through adjacent cells.
         other_berg=>bergs%list(grdi_inner,grdj_inner)%first
         do while (associated(other_berg)) ! loop over all other bergs
@@ -418,10 +417,9 @@ subroutine  convert_from_meters_to_grid(lat_ref,grid_is_latlon ,dlon_dx,dlat_dy)
 
 end subroutine convert_from_meters_to_grid
 
-
 !> Calculates interactions between a berg and all bergs in range
 subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
-  P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y)
+                             P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
   type(iceberg), pointer :: berg !< Primary iceberg
@@ -459,8 +457,8 @@ subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
 
     ! Interactions for bonded berg elements only. For the mts scheme, this is only called if mts_part==3
     if ( (.not. bergs%mts) .or. (bergs%mts .and. bergs%mts_part .eq. 3)) then
-      bonded=.true. 
-      if (iceberg_bonds_on) then 
+      bonded=.true.
+      if (iceberg_bonds_on) then
         current_bond=>berg%first_bond
         do while (associated(current_bond)) ! loop over all bonds
           other_berg=>current_bond%other_berg
@@ -497,7 +495,7 @@ subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
 
   else
     !Alon's original code, only usuable for simulations WITHOUT MTS Verlet, a specified contact_distance,
-    !or a separate spring constant for collision. 
+    !or a separate spring constant for collision.
     bonded=.false. ! 'Unbonded' iceberg interactions (here, not to be taken literally)
     do grdj = berg%jne-1,berg%jne+1 ; do grdi = berg%ine-1,berg%ine+1
       other_berg=>bergs%list(grdi,grdj)%first
@@ -557,7 +555,7 @@ recursive subroutine mark_conglomerate_bergs(berg,mark_or_unmark)
       current_bond=>current_bond%next_bond
     enddo
   endif
-  
+
 end subroutine mark_conglomerate_bergs
 
 
@@ -572,10 +570,8 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
   real, intent(inout) :: IA_y !< Net meridional acceleration of berg due to interactions (m/s2)
   real, intent(in) :: u0 !< Zonal velocity of primary berg (m/s)
   real, intent(in) :: v0 !< Meridional velocity of primary berg (m/s)
-  
-  !u1 and v1: actually, also vel for primary berg, but might be updated vel if runge-kutta? -Alex
-  real, intent(in) :: u1 !< Zonal velocity of other berg (m/s) 
-  real, intent(in) :: v1 !< Meridional velocity of other berg (m/s) 
+  real, intent(in) :: u1 !< Zonal velocity of other berg (m/s)
+  real, intent(in) :: v1 !< Meridional velocity of other berg (m/s)
   real, intent(inout) :: P_ia_11
   real, intent(inout) :: P_ia_12
   real, intent(inout) :: P_ia_22
@@ -618,7 +614,7 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
 
     !call rotpos_to_tang(lon2,lat2,x2,y2)
 
-    dlon=lon1-lon2 
+    dlon=lon1-lon2
     dlat=lat1-lat2
 
     ! Note that this is not the exact distance along a great circle.
@@ -632,11 +628,11 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
     r_dist_y=dlat*dy_dlat
     r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) ) !(Stern et al 2017, Eqn 3)
 
-    !Stern et al 2017, Eqn 4: radius of circle inscribed within hexagon or square with area A1 or A2 
+    !Stern et al 2017, Eqn 4: radius of circle inscribed within hexagon or square with area A1 or A2
     if (bergs%hexagonal_icebergs) then
-      R1=sqrt(A1/(2.*sqrt(3.)))  
+      R1=sqrt(A1/(2.*sqrt(3.)))
       R2=sqrt(A2/(2.*sqrt(3.)))
-    else !square packing 
+    else !square packing
       R1=sqrt(A1/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
       R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
     endif
@@ -650,11 +646,11 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
     ! print *, 'outside the loop',R1, R2,r_dist, bonded
     !!!!!!!!!!!!!!!!!!!!!!!!!!!debugging!!!!!!!!!!!!!!!!!!!!!!!!!!
 
+
     !call overlap_area(R1,R2,r_dist,A_o,trapped)
     !T_min=min(T1,T2)
     !A_min = min((pi*R1**R1),(pi*R2*R2))
     M_min=min(M1,M2)
-    
     !Calculating spring force (Stern et al 2017, Eqn 6):
     if (bonded) then
       crit_dist=R1+R2 !Stern et al 2017, Eqn 5
@@ -663,7 +659,7 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
       crit_dist=max(R1+R2,bergs%contact_distance)
       spring_coef=bergs%contact_spring_coef
     end if
-  
+
     radial_damping_coef=bergs%radial_damping_coef
     tangental_damping_coef=bergs%tangental_damping_coef
     critical_interaction_damping_on=bergs%critical_interaction_damping_on
@@ -682,19 +678,20 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
 
 
     if  ((r_dist>0.) .and. ( tbonded .or. (r_dist<crit_dist .and. .not. bonded) )) then
-      
+
       !Spring force (Stern et al 2017, Eqn 7):
       !accel_spring=spring_coef*(T_min/T1)*(A_o/A1) ! Old version dependent on area
       accel_spring=spring_coef*(M_min/M1)*(crit_dist-r_dist)
       IA_x=IA_x+(accel_spring*(r_dist_x/r_dist))
       IA_y=IA_y+(accel_spring*(r_dist_y/r_dist))
 
+
       if (r_dist < 5*(R1+R2)) then
 
         ! Damping force (Stern et al 2017, Eqn 8):
         ! Paralel velocity
         !projection matrix in Stern et al 2017, Eqn 8:
-        P_11=(r_dist_x*r_dist_x)/(r_dist**2) 
+        P_11=(r_dist_x*r_dist_x)/(r_dist**2)
         P_12=(r_dist_x*r_dist_y)/(r_dist**2)
         P_21=(r_dist_x*r_dist_y)/(r_dist**2)
         P_22=(r_dist_y*r_dist_y)/(r_dist**2)
@@ -830,18 +827,17 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
     use_new_predictive_corrective=.True.
   endif
 
-  
+
   u_star=uvel0+(axn*(dt/2.))  !Alon
   v_star=vvel0+(ayn*(dt/2.))  !Alon
 
-
   ! Get the stderr unit number.
   stderrunit = stderr()
 
   ! For convenience
   grd=>bergs%grd
 
-  ! Interpolate gridded fields to berg 
+  ! Interpolate gridded fields to berg
   if (bergs%mts) then
     !dummy values for MTS scheme halo bergs (this should only occur during berg%mts_part==3,
     !when bergs%only_interactive_forces=.true., and therefore should have no effect)
@@ -850,7 +846,6 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
   else
     call interp_flds(grd, i, j, xi, yj, rx, ry, uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, sss, cn, hi)
   end if
-  
 
   if ((grd%grid_is_latlon) .and. (.not. bergs%use_f_plane)) then
      f_cori=(2.*omega)*sin(pi_180*lat)
@@ -925,17 +920,16 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
     endif
 
   ! Interactive spring acceleration - (Does the spring part need to be called twice?)
-    if (interactive_icebergs_on) then
-      !
-      call interactive_force(bergs, berg, IA_x, IA_y, uvel0, vvel0, uvel0, vvel0, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y) ! Spring forces, Made by Alon.
-      if (.not.Runge_not_Verlet) then
-        axn=axn + IA_x
-        ayn=ayn + IA_y
-      else
-        bxn=bxn + IA_x
-        byn=byn + IA_y
-      endif
+  if (interactive_icebergs_on) then
+    call interactive_force(bergs, berg, IA_x, IA_y, uvel0, vvel0, uvel0, vvel0, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y) ! Spring forces, Made by Alon.
+    if (.not.Runge_not_Verlet) then
+      axn=axn + IA_x
+      ayn=ayn + IA_y
+    else
+      bxn=bxn + IA_x
+      byn=byn + IA_y
     endif
+  endif
 
   if (alpha>0.) then ! If implicit Coriolis, use u_star rather than RK4 latest  !Alon
     if (C_N>0.) then !  C_N=1 for Crank Nicolson Coriolis, C_N=0 for full implicit Coriolis !Alon
@@ -976,7 +970,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
   endif
 
   !RHS ~ similar to accel terms in Stern et al 2017, Eqn B5
-  RHS_x=(axn/2) + bxn 
+  RHS_x=(axn/2) + bxn
   RHS_y=(ayn/2) + byn
 
   if (beta>0.) then ! If implicit, use u_star, v_star rather than RK4 latest
@@ -2015,7 +2009,7 @@ subroutine find_orientation_using_iceberg_bonds(grd, berg, orientation)
   real :: r_dist_x, r_dist_y
   real :: lat_ref, dx_dlon, dy_dlat
   real :: theta, bond_count, Average_angle
-  
+
   bond_count=0.
   Average_angle=0.
   !Don't check orientation of the edges of halo,  since they can contain unassosiated bonds  (this is why halo width must be larger >= 2 to use bonds)
@@ -2849,17 +2843,15 @@ subroutine interp_gridded_fields_to_bergs(bergs)
       ! Seed random numbers based on space and "time"
       rns = initializeRandomNumberStream( grdi + 10000*grdj + &
                                           int( 16384.*abs( sin(262144.*grd%ssh(grdi,grdj)) ) ) )
-    endif    
+    endif
     do while (associated(berg)) ! loop over all bergs
       if (berg%halo_berg.lt.0.5) then
-        
         if (grd%tidal_drift>0.) then
           call getRandomNumbers(rns, rx)
           rx = 2.*rx - 1.
           call getRandomNumbers(rns, ry)
           ry = 2.*ry - 1.
         endif
-        
         call interp_flds(grd, berg%ine, berg%jne, berg%xi, berg%yj, rx, ry, berg%uo, berg%vo, &
           berg%ui, berg%vi, berg%ua, berg%va, berg%ssh_x, berg%ssh_y, berg%sst, berg%sss, berg%cn, berg%hi)
       endif
@@ -2868,7 +2860,7 @@ subroutine interp_gridded_fields_to_bergs(bergs)
   enddo;enddo
 
 end subroutine interp_gridded_fields_to_bergs
- 
+
 
 subroutine interp_flds(grd, i, j, xi, yj, rx, ry, uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, sss, cn, hi)
   ! Arguments
@@ -3114,7 +3106,7 @@ subroutine calculate_mass_on_ocean(bergs, with_diagnostics)
       endif
       berg=>berg%next
     enddo
-  enddo;enddo
+  enddo ;enddo
 
 end subroutine calculate_mass_on_ocean
 
@@ -3266,8 +3258,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   endif
   lbudget=.false.
   if (bergs%verbose_hrs>0) then
-     !if (mod(24*iday+ihr+(imin/60.),float(bergs%verbose_hrs)).eq.0) lbudget=budget
-     if (mod(24*iday+ihr+(imin/60.),bergs%verbose_hrs).eq.0) lbudget=budget  !Added minutes, so that it does not repeat when smaller time steps are used.
+     !if (mod(24*iday+ihr+(imin/60.),float(bergs%verbose_hrs)).eq.0) lbudget=budget  !Added minutes, so that it does not repeat when smaller time steps are used.
+     if (mod(24*iday+ihr+(imin/60.),bergs%verbose_hrs).eq.0) lbudget=budget
   endif
   if (mpp_pe()==mpp_root_pe().and.lverbose) write(*,'(a,3i5,a,3i5,a,i5,f8.3)') &
        'KID: y,m,d=',iyr, imon, iday,' h,m,s=', ihr, imin, isec, &
@@ -3462,10 +3454,10 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   if (.not. Visited) then
     Visited=.true.
     if (bergs%mts) then
-      call interp_gridded_fields_to_bergs(bergs)   
-      if ((bergs%interactive_icebergs_on) .or. (bergs%iceberg_bonds_on)) then      
+      call interp_gridded_fields_to_bergs(bergs)
+      if ((bergs%interactive_icebergs_on) .or. (bergs%iceberg_bonds_on)) then
         call update_halo_icebergs(bergs)
-        if (bergs%iceberg_bonds_on)  then
+        if (bergs%iceberg_bonds_on) then
           call connect_all_bonds(bergs)
         else
           if (grd%Lx>0.) call update_latlon(bergs)
@@ -3473,7 +3465,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
       endif
     endif
   endif
-  
+
   ! Accumulate ice from calving
   call accumulate_calving(bergs)
   if (grd%id_accum>0) then
@@ -3505,24 +3497,24 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
       call evolve_icebergs(bergs)
     end if
     if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after evolve()     ')
-  end if
+  endif
   call move_berg_between_cells(bergs)  !Markpoint6
   if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after move_lists() ')
   if (debug) call bergs_chksum(bergs, 'run bergs (evolved)',ignore_halo_violation=.true.)
   if (debug) call checksum_gridded(bergs%grd, 's/r run after evolve')
   call mpp_clock_end(bergs%clock_mom)
 
-
   ! Send bergs to other PEs
   call mpp_clock_begin(bergs%clock_com)
   if (bergs%iceberg_bonds_on)  call  bond_address_update(bergs)
+
   call send_bergs_to_other_pes(bergs)
-  if (bergs%mts) call interp_gridded_fields_to_bergs(bergs)  
-  if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after send_bergs() ')  
-  if ((bergs%interactive_icebergs_on) .or. (bergs%iceberg_bonds_on)) then      
-  call update_halo_icebergs(bergs)
+  if (bergs%mts) call interp_gridded_fields_to_bergs(bergs)
+  if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after send_bergs() ')
+  if ((bergs%interactive_icebergs_on) .or. (bergs%iceberg_bonds_on)) then
+    call update_halo_icebergs(bergs)
     if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after update_halo()')
-    if (bergs%iceberg_bonds_on)  then
+    if (bergs%iceberg_bonds_on) then
       call connect_all_bonds(bergs)
     else
       if (grd%Lx>0.) call update_latlon(bergs)
@@ -3535,7 +3527,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   if (bergs%find_melt_using_spread_mass .or. bergs%mts) then
     call calculate_mass_on_ocean(bergs, with_diagnostics=.false.)
   end if
-  
+
   ! Calculate mass on ocean before thermodynamics, to use in melt rate calculation
   if (bergs%find_melt_using_spread_mass) then
     grd%spread_mass_old(:,:)=0.
@@ -3878,9 +3870,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   call mpp_clock_end(bergs%clock_dia)
 
   call mpp_clock_end(bergs%clock)
-!  call cpu_time(tend0)
- ! tott0 = tott0+(tend0-tstart0)
- ! if (mpp_pe()==mpp_root_pe().and.lverbose) print *,'tott0',tott0
+
 end subroutine icebergs_run
 
 !> Prints summary of start and end states
@@ -4258,8 +4248,8 @@ subroutine calve_icebergs(bergs)
           newberg%yj=yj
           newberg%uvel=0.
           newberg%vvel=0.
-          newberg%uvel_prev=0.
-          newberg%vvel_prev=0.
+          newberg%uvel_prev=0.  !Added by Alex
+          newberg%vvel_prev=0.  !Added by Alex
           newberg%axn=0. !Added by Alon
           newberg%ayn=0. !Added by Alon
           newberg%bxn=0. !Added by Alon
@@ -4267,7 +4257,7 @@ subroutine calve_icebergs(bergs)
           newberg%axn_fast=0. !Added by Alex
           newberg%ayn_fast=0. !Added by Alex
           newberg%bxn_fast=0. !Added by Alex
-          newberg%byn_fast=0. !Added by Alex         
+          newberg%byn_fast=0. !Added by Alex
           newberg%mass=bergs%initial_mass(k)
           newberg%thickness=bergs%initial_thickness(k)
           newberg%width=bergs%initial_width(k)
@@ -4319,7 +4309,7 @@ subroutine evolve_icebergs_mts(bergs)
   type(icebergs_gridded), pointer :: grd
   type(iceberg), pointer :: berg
   real :: uveln, vveln, lonn, latn
-  real :: axn, ayn, bxn, byn          
+  real :: axn, ayn, bxn, byn
   real :: xi, yj, rx, ry
   integer :: i, j, k
   integer :: grdi, grdj
@@ -4341,7 +4331,7 @@ subroutine evolve_icebergs_mts(bergs)
   ! the contact distance of the conglomerate are also included, as to account for collision
   ! forces. The conglomerate iceberg elements with coords that lie outside of a PE's domain
   ! are assigned to the nearest halo cell, but the coords are not changed.
-  
+
   ! Get the stderr unit number
   stderrunit = stderr()
   only_interactive_forces=bergs%only_interactive_forces
@@ -4387,7 +4377,7 @@ subroutine evolve_icebergs_mts(bergs)
       if (berg%static_berg .lt. 0.5 .and. berg%halo_berg<10) then
         latn = berg%lat ;   lonn = berg%lon
         uvel1=berg%uvel_prev ;   vvel1=berg%vvel_prev !V_n (previous cycle)
-        !subroutine accel expects uvel1=berg%uvel_prev, and calculates ustar=uvel1+axn*dt_2. 
+        !subroutine accel expects uvel1=berg%uvel_prev, and calculates ustar=uvel1+axn*dt_2.
         !However, for the MTS case, ustar should equal berg%uvel from after the final fast force
         !iteration k from the previous cycle. To enforce this, fake in input accelerations
         !axn and ayn as:
@@ -4395,18 +4385,18 @@ subroutine evolve_icebergs_mts(bergs)
         ayn  = (berg%vvel-berg%vvel_prev)/dt_2
         bxn  = 0.0      ;   byn  = 0.0
         i=berg%ine      ;   j=berg%jne
-        xi=berg%xi      ;   yj=berg%yj                               
+        xi=berg%xi      ;   yj=berg%yj
         ! if (berg%id==4294967382 .and. berg%halo_berg==0) then
         !   print *,'berg check 1',mpp_pe(),berg%id, berg%uvel, berg%vvel, berg%lat, berg%lon
         ! endif
         call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, &
           ax1, ay1, axn, ayn, bxn, byn)
-        ! Saving all the iceberg variables.        
+        ! Saving all the iceberg variables
         berg%axn=axn                ; berg%ayn=ayn
         berg%bxn=bxn                ; berg%byn=byn
         berg%uvel=berg%uvel+(dt*ax1); berg%vvel=berg%vvel+(dt*ay1)
 
-        !save this velocity for next time, and output 
+        !save this velocity for next time, and output
         berg%uvel_prev=berg%uvel    ; berg%vvel_prev=berg%vvel
       endif
       berg=>berg%next
@@ -4416,7 +4406,7 @@ subroutine evolve_icebergs_mts(bergs)
   !PART 2: X_0 and V_0, before fast sub-steps
   !X_0=X_n (no change)
   !update V_0 on uvel_old and vvel_old
-  !update lat and lon with implicit slow force component  
+  !update lat and lon with implicit slow force component
   do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
     berg=>bergs%list(grdi,grdj)%first
     do while (associated(berg)) ! loop over all bergs
@@ -4429,12 +4419,12 @@ subroutine evolve_icebergs_mts(bergs)
         berg%vvel = berg%vvel + dt_2*berg%ayn
         berg%lat = berg%lat + 0.5*(dt**2)*berg%byn
         berg%lon = berg%lon + 0.5*(dt**2)*berg%bxn
-        berg%lat_old = berg%lat; berg%lon_old = berg%lon 
+        berg%lat_old = berg%lat; berg%lon_old = berg%lon
         berg%uvel_old=berg%uvel; berg%vvel_old=berg%vvel
          ! if (berg%id==4294967382 .and. berg%halo_berg==0) then
          !   print *,'berg check 3',mpp_pe(),berg%id, berg%uvel, berg%vvel, &
          !     berg%lat, berg%lon, berg%axn, berg%ayn, berg%bxn, berg%byn
-         ! endif            
+         ! endif
       endif
       berg=>berg%next
     enddo
@@ -4450,10 +4440,10 @@ subroutine evolve_icebergs_mts(bergs)
   bergs%mts_part=3 !so that only bonded interactions are considered in subroutine interactive_force
   dt = bergs%mts_fast_dt
   dt_2=0.5*dt
-  
+
   do k = 1,bergs%mts_sub_steps ! loop over sub-steps
 
-    do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied ! update positions 
+    do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied ! update positions
       berg=>bergs%list(grdi,grdj)%first
       do while (associated(berg)) ! loop over all bergs
         if (berg%static_berg .lt. 0.5 .and. berg%halo_berg<10) then
@@ -4492,24 +4482,24 @@ subroutine evolve_icebergs_mts(bergs)
         end if
         berg=>berg%next
       enddo !loop over all bergs
-    enddo;enddo !update positions 
-    
+    enddo;enddo !update positions
+
     ! update velocities
     do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
       berg=>bergs%list(grdi,grdj)%first
       do while (associated(berg)) ! loop over all bergs
-        if (berg%static_berg .lt. 0.5 .and. berg%halo_berg<10) then 
+        if (berg%static_berg .lt. 0.5 .and. berg%halo_berg<10) then
 
           latn = berg%lat ;   lonn = berg%lon
           axn  = berg%axn_fast ;   ayn  = berg%ayn_fast
-          bxn  = berg%bxn_fast ;   byn  = berg%byn_fast       
+          bxn  = berg%bxn_fast ;   byn  = berg%byn_fast
           uvel1=berg%uvel ;   vvel1=berg%vvel
           i=berg%ine      ;   j=berg%jne
           xi=berg%xi      ;   yj=berg%yj
 
           ! Turn the velocities into u_star, v_star.(uvel3 is v_star) - (possible issues with tangent plane?)
           uvel3=uvel1+(dt_2*axn)                  !(Stern et al 2017, Eq B4)
-          vvel3=vvel1+(dt_2*ayn)                          
+          vvel3=vvel1+(dt_2*ayn)
 
           call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, &
             ax1, ay1, axn, ayn, bxn, byn)
@@ -4520,16 +4510,16 @@ subroutine evolve_icebergs_mts(bergs)
           if (on_tangential_plane) then
             call rotvec_to_tang(lonn,uvel3,vvel3,xdot3,ydot3)
             call rotvec_to_tang(lonn,ax1,ay1,xddot1,yddot1)
-            xdotn=xdot3+(dt*xddot1); ydotn=ydot3+(dt*yddot1)                                   
+            xdotn=xdot3+(dt*xddot1); ydotn=ydot3+(dt*yddot1)
             call rotvec_from_tang(lonn,xdotn,ydotn,uveln,vveln)
           else
-            !uvel3, vvel3 become uveln and vveln after they are put into lat/lon co-ordinates         
-            uveln=uvel3+(dt*ax1); vveln=vvel3+(dt*ay1)    
+            !uvel3, vvel3 become uveln and vveln after they are put into lat/lon co-ordinates
+            uveln=uvel3+(dt*ax1); vveln=vvel3+(dt*ay1)
           endif
 
           ! Saving all the iceberg variables.
           berg%axn_fast=axn; berg%ayn_fast=ayn
-          berg%bxn_fast=bxn; berg%byn_fast=byn        
+          berg%bxn_fast=bxn; berg%byn_fast=byn
           berg%uvel=uveln  ; berg%vvel=vveln
         endif
         berg=>berg%next
@@ -4540,7 +4530,7 @@ subroutine evolve_icebergs_mts(bergs)
     do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
       berg=>bergs%list(grdi,grdj)%first
       do while (associated(berg)) ! loop over all bergs
-        if (berg%static_berg .lt. 0.5 .and. berg%halo_berg<10) then  
+        if (berg%static_berg .lt. 0.5 .and. berg%halo_berg<10) then
           berg%uvel_old=berg%uvel; berg%vvel_old=berg%vvel
         endif
         berg=>berg%next
@@ -4550,13 +4540,13 @@ subroutine evolve_icebergs_mts(bergs)
 
   !reset interactive_forces
   bergs%only_interactive_forces=only_interactive_forces
-  
+
   !update indices
   do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
     !no reason to worry about halo/conglomerate bergs here
     berg=>bergs%list(grdi,grdj)%first
     do while (associated(berg)) ! loop over all bergs
-      if (berg%static_berg .lt. 0.5 .and. berg%halo_berg<1) then  
+      if (berg%static_berg .lt. 0.5 .and. berg%halo_berg<1) then
         berg%uvel_old=berg%uvel; berg%vvel_old=berg%vvel
         uveln=berg%uvel; vveln=berg%vvel
         lonn=berg%lon  ; latn=berg%lat
@@ -4567,7 +4557,7 @@ subroutine evolve_icebergs_mts(bergs)
         berg%lon=lonn      ;  berg%lat=latn
         berg%lon_old=lonn  ;  berg%lat_old=latn
         berg%ine=i    ;  berg%jne=j
-        berg%xi=xi    ;  berg%yj=yj        
+        berg%xi=xi    ;  berg%yj=yj
       endif
       berg=>berg%next
     enddo ! loop over all bergs
@@ -4600,7 +4590,7 @@ subroutine evolve_icebergs(bergs)
 
   interactive_icebergs_on=bergs%interactive_icebergs_on
   Runge_not_Verlet=bergs%Runge_not_Verlet
-  
+
   do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
     berg=>bergs%list(grdi,grdj)%first
     if (associated(berg) .and. grd%tidal_drift>0.) then
@@ -4641,7 +4631,7 @@ subroutine evolve_icebergs(bergs)
             call Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, &
                                       lonn, latn, i, j, xi, yj, rx, ry)
           endif
-          if (.not.Runge_not_Verlet) then           
+          if (.not.Runge_not_Verlet) then
             call verlet_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, rx, ry)
           endif
 
@@ -4658,9 +4648,6 @@ subroutine evolve_icebergs(bergs)
         berg%byn=byn
         berg%uvel=uveln
         berg%vvel=vveln
-        ! if (berg%id==4294967382 .and. berg%halo_berg==0) then
-        !   print *,'berg check 2',mpp_pe(),berg%id, berg%uvel, berg%vvel, berg%lat, berg%lon
-        ! endif        
 
         if (Runge_not_Verlet) then
           berg%lon=lonn  ;   berg%lat=latn
@@ -4756,16 +4743,14 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln, rx, ry)
   ! Turn the velocities into u_star, v_star.(uvel3 is v_star) - Alon (not sure how this works with tangent plane)
   uvel3=uvel1+(dt_2*axn)                  !Alon (Stern et al 2017, Eq B4)
   vvel3=vvel1+(dt_2*ayn)                  !Alon
-  ! if (berg%id==4294967382 .and. berg%halo_berg==0) then
-  !   print *,'berg check 1',mpp_pe(),berg%id, uvel3, vvel3, berg%lat, berg%lon
-  ! endif
+
   ! Note, the mass scaling is equal to 1 (rather than 0.25 as in RK), since
   ! this is only called once in Verlet stepping.
   if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
     call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 1.0*berg%mass_scaling,berg%length*berg%width, berg%thickness)
+
   ! Calling the acceleration   (note that the velocity is converted to u_star inside the accel script)
-    call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, ax1, ay1, axn, ayn, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
-              
+  call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, ax1, ay1, axn, ayn, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
 
   ! Solving for the new velocity (Stern et al 2017, Eqn B5)
   on_tangential_plane=.false.
@@ -5345,51 +5330,52 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
   lon0=lon; lat0=lat ! original position
   i0=i; j0=j ! original i,j
   lret=pos_within_cell(grd, lon, lat, i, j, xi, yj)
-  !  print *, 'Alon:', lon, lat, i, j, xi, yj, lret
+!  print *, 'Alon:', lon, lat, i, j, xi, yj, lret
   xi0=xi; yj0=yj ! original xi,yj
 
+
   !Removing this while debuggin
   if (debug) then
-     !Sanity check lret, xi and yj
-     lret=is_point_in_cell(grd, lon, lat, i, j)
-     point_in_cell_using_xi_yj=is_point_within_xi_yj_bounds(xi,yj)
-     if (.not. point_in_cell_using_xi_yj) then
-
-        if (lret) then
-           write(stderrunit,*) 'KID, adjust: WARNING!!! lret=T but |xi,yj|>1',mpp_pe()
-           write(stderrunit,*) 'KID, adjust: xi=',xi,' lon=',lon
-           write(stderrunit,*) 'KID, adjust: x3 x2=',grd%lon(i-1,j),grd%lon(i,j)
-           write(stderrunit,*) 'KID, adjust: x0 x1=',grd%lon(i-1,j-1),grd%lon(i,j-1)
-           write(stderrunit,*) 'KID, adjust: yi=',yj,' lat=',lat
-           write(stderrunit,*) 'KID, adjust: y3 y2=',grd%lat(i-1,j),grd%lat(i,j)
-           write(stderrunit,*) 'KID, adjust: y0 y1=',grd%lat(i-1,j-1),grd%lat(i,j-1)
-           lret=is_point_in_cell(grd, lon, lat, i, j,explain=.true.)
-           write(stderrunit,*) 'KID, adjust: fn is_point_in_cell=',lret
-           lret=pos_within_cell(grd, lon, lat, i, j, xi, yj,explain=.true.)
-           write(stderrunit,*) 'KID, adjust: fn pos_within_cell=',lret
-           write(0,*) 'This should never happen!'
-           call error_mesg('adjust index, ','Iceberg is_point_in_cell=True but xi, yi are out of cell',FATAL)
-           error=.true.; return
-        endif
-     else
-        if (.not.lret) then
-           write(stderrunit,*) 'KID, adjust: WARNING!!! lret=F but |xi,yj|<1',mpp_pe()
-           write(stderrunit,*) 'KID, adjust: xi=',xi,' lon=',lon
-           write(stderrunit,*) 'KID, adjust: x3 x2=',grd%lon(i-1,j),grd%lon(i,j)
-           write(stderrunit,*) 'KID, adjust: x0 x1=',grd%lon(i-1,j-1),grd%lon(i,j-1)
-           write(stderrunit,*) 'KID, adjust: yi=',yj,' lat=',lat
-           write(stderrunit,*) 'KID, adjust: y3 y2=',grd%lat(i-1,j),grd%lat(i,j)
-           write(stderrunit,*) 'KID, adjust: y0 y1=',grd%lat(i-1,j-1),grd%lat(i,j-1)
-           lret=is_point_in_cell(grd, lon, lat, i, j,  explain=.true.)
-           write(stderrunit,*) 'KID, adjust: fn is_point_in_cell=',lret
-           lret=pos_within_cell(grd, lon, lat, i, j, xi, yj, explain=.true.)
-           write(stderrunit,*) 'KID, adjust: fn pos_within_cell=',lret
-           write(0,*) 'This should never happen!'
-           call error_mesg('adjust index, ','Iceberg is_point_in_cell=False but xi, yi are out of cell',FATAL)
-           error=.true.; return
-        endif
+    !Sanity check lret, xi and yj
+    lret=is_point_in_cell(grd, lon, lat, i, j)
+    point_in_cell_using_xi_yj=is_point_within_xi_yj_bounds(xi,yj)
+    if (.not. point_in_cell_using_xi_yj) then
+
+      if (lret) then
+        write(stderrunit,*) 'KID, adjust: WARNING!!! lret=T but |xi,yj|>1',mpp_pe()
+        write(stderrunit,*) 'KID, adjust: xi=',xi,' lon=',lon
+        write(stderrunit,*) 'KID, adjust: x3 x2=',grd%lon(i-1,j),grd%lon(i,j)
+        write(stderrunit,*) 'KID, adjust: x0 x1=',grd%lon(i-1,j-1),grd%lon(i,j-1)
+        write(stderrunit,*) 'KID, adjust: yi=',yj,' lat=',lat
+        write(stderrunit,*) 'KID, adjust: y3 y2=',grd%lat(i-1,j),grd%lat(i,j)
+        write(stderrunit,*) 'KID, adjust: y0 y1=',grd%lat(i-1,j-1),grd%lat(i,j-1)
+        lret=is_point_in_cell(grd, lon, lat, i, j,explain=.true.)
+        write(stderrunit,*) 'KID, adjust: fn is_point_in_cell=',lret
+        lret=pos_within_cell(grd, lon, lat, i, j, xi, yj,explain=.true.)
+        write(stderrunit,*) 'KID, adjust: fn pos_within_cell=',lret
+        write(0,*) 'This should never happen!'
+        call error_mesg('adjust index, ','Iceberg is_point_in_cell=True but xi, yi are out of cell',FATAL)
+        error=.true.; return
      endif
-     lret=pos_within_cell(grd, lon, lat, i, j, xi, yj)
+    else
+      if (.not.lret) then
+        write(stderrunit,*) 'KID, adjust: WARNING!!! lret=F but |xi,yj|<1',mpp_pe()
+        write(stderrunit,*) 'KID, adjust: xi=',xi,' lon=',lon
+        write(stderrunit,*) 'KID, adjust: x3 x2=',grd%lon(i-1,j),grd%lon(i,j)
+        write(stderrunit,*) 'KID, adjust: x0 x1=',grd%lon(i-1,j-1),grd%lon(i,j-1)
+        write(stderrunit,*) 'KID, adjust: yi=',yj,' lat=',lat
+        write(stderrunit,*) 'KID, adjust: y3 y2=',grd%lat(i-1,j),grd%lat(i,j)
+        write(stderrunit,*) 'KID, adjust: y0 y1=',grd%lat(i-1,j-1),grd%lat(i,j-1)
+        lret=is_point_in_cell(grd, lon, lat, i, j,  explain=.true.)
+        write(stderrunit,*) 'KID, adjust: fn is_point_in_cell=',lret
+        lret=pos_within_cell(grd, lon, lat, i, j, xi, yj, explain=.true.)
+        write(stderrunit,*) 'KID, adjust: fn pos_within_cell=',lret
+        write(0,*) 'This should never happen!'
+        call error_mesg('adjust index, ','Iceberg is_point_in_cell=False but xi, yi are out of cell',FATAL)
+        error=.true.; return
+      endif
+    endif
+    lret=pos_within_cell(grd, lon, lat, i, j, xi, yj)
   endif ! debug
 
   if (lret) return ! Berg was already in cell
@@ -5401,168 +5387,164 @@ subroutine adjust_index_and_ground(grd, lon, lat, uvel, vvel, i, j, xi, yj, boun
   icount=0
   inm=i0; jnm=j0 ! original i,j
   do while (debug .and. .not.lret .and. icount<4)
-     icount=icount+1
-     if (xi.lt.0.) then
-        if (inm>grd%isd) then
-           inm=inm-1
-        endif
-     elseif (xi.gt.1.) then
-        !    elseif (xi.ge.1.) then   !Alon: maybe it should be .ge.
-        if (inm<grd%ied) then
-           inm=inm+1
-        endif
-     endif
-     if (yj.lt.0.) then
-        if (jnm>grd%jsd) then
-           jnm=jnm-1
-        endif
-     elseif (yj.gt.1.) then
-        !    elseif (yj.ge.1.) then   !Alon:maybe it should be .ge.
-        if (jnm<grd%jed) then
-           jnm=jnm+1
-        endif
-     endif
-     lret=pos_within_cell(grd, lon, lat, inm, jnm, xi, yj) ! Update xi and yj
+    icount=icount+1
+    if (xi.lt.0.) then
+      if (inm>grd%isd) then
+        inm=inm-1
+      endif
+    elseif (xi.gt.1.) then
+!    elseif (xi.ge.1.) then   !Alon: maybe it should be .ge.
+      if (inm<grd%ied) then
+        inm=inm+1
+      endif
+    endif
+    if (yj.lt.0.) then
+      if (jnm>grd%jsd) then
+        jnm=jnm-1
+      endif
+    elseif (yj.gt.1.) then
+!    elseif (yj.ge.1.) then   !Alon:maybe it should be .ge.
+      if (jnm<grd%jed) then
+        jnm=jnm+1
+      endif
+    endif
+    lret=pos_within_cell(grd, lon, lat, inm, jnm, xi, yj) ! Update xi and yj
   enddo
   if (abs(inm-i0)>1) then
-     write(stderrunit,*) 'pe=',mpp_pe(),'KID, adjust: inm,i0,inm-i0=',inm,i0,inm-i0
-     !stop 'Moved too far in i without mask!'
+    write(stderrunit,*) 'pe=',mpp_pe(),'KID, adjust: inm,i0,inm-i0=',inm,i0,inm-i0
+   !stop 'Moved too far in i without mask!'
   endif
   if (abs(jnm-j0)>1) then
-     write(stderrunit,*) 'pe=',mpp_pe(),'KID, adjust: jnm,i0,jnm-j0=',jnm,j0,inm-j0
-     !stop 'Moved too far in j without mask!'
+    write(stderrunit,*) 'pe=',mpp_pe(),'KID, adjust: jnm,i0,jnm-j0=',jnm,j0,inm-j0
+   !stop 'Moved too far in j without mask!'
   endif
 
   ! Adjust i,j based on xi,yj while bouncing off of masked land cells
   icount=0
   lret=pos_within_cell(grd, lon, lat, i0, j0, xi, yj)
   do while ( .not.lret.and. icount<4 )
-     icount=icount+1
-     if (xi.lt.0.) then
-        if (i>grd%isd) then
-           if (grd%msk(i-1,j)>0.) then
-              if (i>grd%isd+1) i=i-1
-           else
-              !write(stderr(),'(a,6f8.3,i)') 'KID, adjust: bouncing berg from west',lon,lat,xi,yj,uvel,vvel,mpp_pe()
-              bounced=.true.
-           endif
+    icount=icount+1
+    if (xi.lt.0.) then
+      if (i>grd%isd) then
+        if (grd%msk(i-1,j)>0.) then
+          if (i>grd%isd+1) i=i-1
+        else
+         !write(stderr(),'(a,6f8.3,i)') 'KID, adjust: bouncing berg from west',lon,lat,xi,yj,uvel,vvel,mpp_pe()
+          bounced=.true.
         endif
-     elseif (xi.ge.1.) then    !Alon!!!!
-        !    elseif (xi.gt.1.) then
-        if (i<grd%ied) then
-           if (grd%msk(i+1,j)>0.) then
-              if (i<grd%ied) i=i+1
-           else
-              !write(stderr(),'(a,6f8.3,i)') 'KID, adjust: bouncing berg from east',lon,lat,xi,yj,uvel,vvel,mpp_pe()
-              bounced=.true.
-           endif
+      endif
+    elseif (xi.ge.1.) then    !Alon!!!!
+!    elseif (xi.gt.1.) then
+      if (i<grd%ied) then
+        if (grd%msk(i+1,j)>0.) then
+          if (i<grd%ied) i=i+1
+        else
+         !write(stderr(),'(a,6f8.3,i)') 'KID, adjust: bouncing berg from east',lon,lat,xi,yj,uvel,vvel,mpp_pe()
+          bounced=.true.
         endif
-     endif
-     if (yj.lt.0.) then
-        if (j>grd%jsd) then
-           if (grd%msk(i,j-1)>0.) then
-              if (j>grd%jsd+1) j=j-1
-           else
-              !write(stderr(),'(a,6f8.3,i)') 'KID, adjust: bouncing berg from south',lon,lat,xi,yj,uvel,vvel,mpp_pe()
-              bounced=.true.
-           endif
+      endif
+    endif
+    if (yj.lt.0.) then
+      if (j>grd%jsd) then
+        if (grd%msk(i,j-1)>0.) then
+          if (j>grd%jsd+1) j=j-1
+        else
+         !write(stderr(),'(a,6f8.3,i)') 'KID, adjust: bouncing berg from south',lon,lat,xi,yj,uvel,vvel,mpp_pe()
+          bounced=.true.
         endif
-     elseif (yj.ge.1.) then     !Alon.
-        !    elseif (yj.gt.1.) then
-        if (j<grd%jed) then
-           if (grd%msk(i,j+1)>0.) then
-              if (j<grd%jed) j=j+1
-           else
-              !write(stderr(),'(a,6f8.3,i)') 'KID, adjust: bouncing berg from north',lon,lat,xi,yj,uvel,vvel,mpp_pe()
-              bounced=.true.
-           endif
+      endif
+    elseif (yj.ge.1.) then     !Alon.
+!    elseif (yj.gt.1.) then
+      if (j<grd%jed) then
+        if (grd%msk(i,j+1)>0.) then
+          if (j<grd%jed) j=j+1
+        else
+         !write(stderr(),'(a,6f8.3,i)') 'KID, adjust: bouncing berg from north',lon,lat,xi,yj,uvel,vvel,mpp_pe()
+          bounced=.true.
         endif
-     endif
-     if (bounced) then
-        if (xi>=1.) xi=1.-posn_eps   !Alon.
-        !      if (xi>1.) xi=1.-posn_eps   !
-        if (xi<0.) xi=posn_eps
-        if (yj>=1.) yj=1.-posn_eps  !Alon.
-        !      if (yj>1.) yj=1.-posn_eps
-        if (yj<0.) yj=posn_eps
-        lon=bilin(grd, grd%lon, i, j, xi, yj)
-        lat=bilin(grd, grd%lat, i, j, xi, yj)
-     endif
-     if (debug) then
-        if (grd%msk(i,j)==0.) stop 'KID, adjust: Berg is in land! This should not happen...'
-     endif
-     lret=pos_within_cell(grd, lon, lat, i, j, xi, yj) ! Update xi and yj
+      endif
+    endif
+    if (bounced) then
+      if (xi>=1.) xi=1.-posn_eps   !Alon.
+!      if (xi>1.) xi=1.-posn_eps   !
+      if (xi<0.) xi=posn_eps
+      if (yj>=1.) yj=1.-posn_eps  !Alon.
+!      if (yj>1.) yj=1.-posn_eps
+      if (yj<0.) yj=posn_eps
+      lon=bilin(grd, grd%lon, i, j, xi, yj)
+      lat=bilin(grd, grd%lat, i, j, xi, yj)
+    endif
+    if (debug) then
+      if (grd%msk(i,j)==0.) stop 'KID, adjust: Berg is in land! This should not happen...'
+    endif
+    lret=pos_within_cell(grd, lon, lat, i, j, xi, yj) ! Update xi and yj
 
   enddo
-  !if (debug) then
-  !  if (abs(i-i0)>2) then
-  !    stop 'KID, adjust: Moved too far in i!'
-  !  endif
-  !  if (abs(j-j0)>2) then
-  !    stop 'KID, adjust: Moved too far in j!'
-  !  endif
-  !endif
-
-
-  if (.not.bounced.and.lret.and.grd%msk(i,j)>0.) then ! Landed in ocean without bouncing so all is wel
-      return
-  endif
+ !if (debug) then
+ !  if (abs(i-i0)>2) then
+ !    stop 'KID, adjust: Moved too far in i!'
+ !  endif
+ !  if (abs(j-j0)>2) then
+ !    stop 'KID, adjust: Moved too far in j!'
+ !  endif
+ !endif
 
+  if (.not.bounced.and.lret.and.grd%msk(i,j)>0.) return ! Landed in ocean without bouncing so all is well
 
   if (.not.bounced.and..not.lret) then ! This implies the berg traveled many cells without getting far enough
-     if (debug) then
-        write(stderrunit,*) 'KID, adjust: lon0, lat0=',lon0,lat0
-        write(stderrunit,*) 'KID, adjust: xi0, yj0=',xi0,yj0
-        write(stderrunit,*) 'KID, adjust: i0,j0=',i0,j0
-        write(stderrunit,*) 'KID, adjust: lon, lat=',lon,lat
-        write(stderrunit,*) 'KID, adjust: xi,yj=',xi,yj
-        write(stderrunit,*) 'KID, adjust: i,j=',i,j
-        write(stderrunit,*) 'KID, adjust: inm,jnm=',inm,jnm
-        write(stderrunit,*) 'KID, adjust: icount=',icount
-        lret=pos_within_cell(grd, lon, lat, i, j, xi, yj,explain=.true.)
-        write(stderrunit,*) 'KID, adjust: lret=',lret
-     endif
+    if (debug) then
+      write(stderrunit,*) 'KID, adjust: lon0, lat0=',lon0,lat0
+      write(stderrunit,*) 'KID, adjust: xi0, yj0=',xi0,yj0
+      write(stderrunit,*) 'KID, adjust: i0,j0=',i0,j0
+      write(stderrunit,*) 'KID, adjust: lon, lat=',lon,lat
+      write(stderrunit,*) 'KID, adjust: xi,yj=',xi,yj
+      write(stderrunit,*) 'KID, adjust: i,j=',i,j
+      write(stderrunit,*) 'KID, adjust: inm,jnm=',inm,jnm
+      write(stderrunit,*) 'KID, adjust: icount=',icount
+      lret=pos_within_cell(grd, lon, lat, i, j, xi, yj,explain=.true.)
+      write(stderrunit,*) 'KID, adjust: lret=',lret
+    endif
 
-     if (abs(i-i0)+abs(j-j0)==0) then
-        if (use_roundoff_fix) then
-           ! This is a special case due to round off where is_point_in_cell()
-           ! returns false but xi and yj are between 0 and 1.
-           ! It occurs very rarely but often enough to have brought down
-           ! ESM2G four times since the spin-up began. (as of 8/10/2010)
-           ! This temporary fix arbitrarily moves the berg toward the
-           ! center of the current cell.
-           xi=(xi-0.5)*(1.-posn_eps)+0.5
-           yj=(yj-0.5)*(1.-posn_eps)+0.5
-        endif
-        call error_mesg('KID, adjust', 'Berg did not move or bounce during iterations AND was not in cell. Adjusting!', WARNING)
-        write(stderrunit,*) 'KID, adjust: The adjusting iceberg is: ', id,  mpp_pe()
-        write(stderrunit,*) 'KID, adjust: The adjusting lon,lat,u,v: ', lon, lat, uvel, vvel
-        write(stderrunit,*) 'KID, adjust: The adjusting xi,ji: ', xi, yj
-        lret=pos_within_cell(grd, lon, lat, inm, jnm, xi, yj,explain=.true.)
-     else
-        call error_mesg('KID, adjust', 'Berg iterated many times without bouncing!', WARNING)
-     endif
+    if (abs(i-i0)+abs(j-j0)==0) then
+      if (use_roundoff_fix) then
+        ! This is a special case due to round off where is_point_in_cell()
+        ! returns false but xi and yj are between 0 and 1.
+        ! It occurs very rarely but often enough to have brought down
+        ! ESM2G four times since the spin-up began. (as of 8/10/2010)
+        ! This temporary fix arbitrarily moves the berg toward the
+        ! center of the current cell.
+        xi=(xi-0.5)*(1.-posn_eps)+0.5
+        yj=(yj-0.5)*(1.-posn_eps)+0.5
+      endif
+      call error_mesg('KID, adjust', 'Berg did not move or bounce during iterations AND was not in cell. Adjusting!', WARNING)
+      write(stderrunit,*) 'KID, adjust: The adjusting iceberg is: ', id,  mpp_pe()
+      write(stderrunit,*) 'KID, adjust: The adjusting lon,lat,u,v: ', lon, lat, uvel, vvel
+      write(stderrunit,*) 'KID, adjust: The adjusting xi,ji: ', xi, yj
+      lret=pos_within_cell(grd, lon, lat, inm, jnm, xi, yj,explain=.true.)
+    else
+      call error_mesg('KID, adjust', 'Berg iterated many times without bouncing!', WARNING)
+    endif
   endif
-  !  if (xi>1.) xi=1.-posn_eps    !Alon
+!  if (xi>1.) xi=1.-posn_eps    !Alon
   if (xi>=1.) xi=1.-posn_eps
   if (xi<0.) xi=posn_eps
   if (yj>1.) yj=1.-posn_eps
-  !  if (yj>1.) yj=1.-posn_eps
+!  if (yj>1.) yj=1.-posn_eps
   if (yj<=0.) yj=posn_eps        !Alon
   lon=bilin(grd, grd%lon, i, j, xi, yj)
   lat=bilin(grd, grd%lat, i, j, xi, yj)
   lret=pos_within_cell(grd, lon, lat, i, j, xi, yj) ! Update xi and yj
 
   if (.not. lret) then
-     write(0,*) 'i0, j0,=', i0,j0
-     write(0,*) 'xi0, yj0,=', xi0,yj0
-     write(0,*) 'grd%msk(i0, j0)=', grd%msk(i0,j0)
-     write(0,*) 'lon0, lat0,=', lon0,lat0
-     write(0,*) 'i,j,lon, lat,grd%msk(i,j)=', i,j,lon,lat,grd%msk(i,j)
-     write(stderrunit,*) 'KID, adjust: Should not get here! Berg is not in cell after adjustment', id, mpp_pe()
-     if (debug) error=.true.
+    write(0,*) 'i0, j0,=', i0,j0
+    write(0,*) 'xi0, yj0,=', xi0,yj0
+    write(0,*) 'grd%msk(i0, j0)=', grd%msk(i0,j0)
+    write(0,*) 'lon0, lat0,=', lon0,lat0
+    write(0,*) 'i,j,lon, lat,grd%msk(i,j)=', i,j,lon,lat,grd%msk(i,j)
+    write(stderrunit,*) 'KID, adjust: Should not get here! Berg is not in cell after adjustment', id, mpp_pe()
+    if (debug) error=.true.
   endif
-end subroutine adjust_index_and_ground
+ end subroutine adjust_index_and_ground
 
 !> Calculate longitude-latitude from tangent plane coordinates
 subroutine rotpos_to_tang(lon, lat, x, y, id_in)
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 9eea156..d6d80a9 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -24,7 +24,7 @@ module ice_bergs_framework
 
 !Local Vars
 ! Global data (minimal for debugging)
-Logical :: folded_north_on_pe = .false. !< If true, indicates the presence of the tri-polar grid
+logical :: folded_north_on_pe = .false. !< If true, indicates the presence of the tri-polar grid
 logical :: verbose=.false. !< Be verbose to stderr
 logical :: budget=.true. !< Calculate budgets
 logical :: debug=.false. !< Turn on debugging
@@ -205,9 +205,9 @@ module ice_bergs_framework
   real :: axn_fast
   real :: ayn_fast
   real :: bxn_fast
-  real :: byn_fast  
+  real :: byn_fast
   real :: uvel_prev
-  real :: vvel_prev  
+  real :: vvel_prev
   real :: uvel_old
   real :: vvel_old
   real :: lat_old
@@ -255,7 +255,7 @@ module ice_bergs_framework
   real :: bxn_fast
   real :: byn_fast
   real :: uvel_prev
-  real :: vvel_prev 
+  real :: vvel_prev
   real :: uvel_old
   real :: vvel_old
   real :: lon_old
@@ -317,7 +317,7 @@ module ice_bergs_framework
 type :: icebergs !; private !Niki: Ask Alistair why this is private. ice_bergs_io cannot compile if this is private!
   type(icebergs_gridded), pointer :: grd !< Container with all gridded data
   type(linked_list), dimension(:,:), allocatable :: list !< Linked list of icebergs
-  type(xyt), pointer :: trajectories=>null() !< A linked list for detached segments of trajectories  
+  type(xyt), pointer :: trajectories=>null() !< A linked list for detached segments of trajectories
   real :: dt !< Time-step between iceberg calls
              !! \todo Should make dt adaptive?
   integer :: current_year !< Current year (years)
@@ -466,529 +466,529 @@ module ice_bergs_framework
 contains
 
 !> Initializes parallel framework
-  subroutine ice_bergs_framework_init(bergs, &
-       gni, gnj, layout, io_layout, axes, dom_x_flags, dom_y_flags, &
-       dt, Time, ice_lon, ice_lat, ice_wet, ice_dx, ice_dy, ice_area, &
-       cos_rot, sin_rot, ocean_depth, maskmap, fractional_area)
-
-    use mpp_parameter_mod, only: SCALAR_PAIR, CGRID_NE, BGRID_NE, CORNER, AGRID
-    use mpp_domains_mod, only: mpp_update_domains, mpp_define_domains
-    use mpp_domains_mod, only: mpp_get_compute_domain, mpp_get_data_domain, mpp_get_global_domain
-    use mpp_domains_mod, only: CYCLIC_GLOBAL_DOMAIN, FOLD_NORTH_EDGE
-    use mpp_domains_mod, only: mpp_get_neighbor_pe, NORTH, SOUTH, EAST, WEST
-    use mpp_domains_mod, only: mpp_define_io_domain
-
-    use mpp_mod, only: mpp_clock_begin, mpp_clock_end, mpp_clock_id, input_nml_file
-    use mpp_mod, only: CLOCK_COMPONENT, CLOCK_SUBCOMPONENT, CLOCK_LOOP
-
-    use fms_mod, only: open_namelist_file, check_nml_error, close_file
-    use fms_mod, only: clock_flag_default
-
-    use diag_manager_mod, only: register_diag_field, register_static_field, send_data
-    use diag_manager_mod, only: diag_axis_init
-
-    ! Arguments
-    type(icebergs), pointer :: bergs !< Container for all types and memory
-    integer, intent(in) :: gni !< Number grid cells in i-direction
-    integer, intent(in) :: gnj !< Number grid cells in j-direction
-    integer, intent(in) :: layout(2) !< Number of processing cores in i,j direction
-    integer, intent(in) :: io_layout(2) !< Number of i/o cores in i,j direction
-    integer, intent(in) :: axes(2) !< Diagnostic axes
-    integer, intent(in) :: dom_x_flags !< Domain flags in i-direction
-    integer, intent(in) :: dom_y_flags !< Domain flags in j-direction
-    real, intent(in) :: dt !< Time-step (s)
-    type (time_type), intent(in) :: Time !< Current model time
-    real, dimension(:,:), intent(in) :: ice_lon !< Longitude of cell corners using NE convention (degree E)
-    real, dimension(:,:), intent(in) :: ice_lat !< Latitude of cell corners using NE convention (degree N)
-    real, dimension(:,:), intent(in) :: ice_wet !< Wet/dry mask (1 is wet, 0 is dry) of cell centers
-    real, dimension(:,:), intent(in) :: ice_dx !< Zonal length of cell on northern side (m)
-    real, dimension(:,:), intent(in) :: ice_dy !< Meridional length of cell on eastern side (m)
-    real, dimension(:,:), intent(in) :: ice_area !< Area of cells (m^2, or non-dim is fractional_area=True)
-    real, dimension(:,:), intent(in) :: cos_rot !< Cosine from rotation matrix to lat-lon coords
-    real, dimension(:,:), intent(in) :: sin_rot !< Sine from rotation matrix to lat-lon coords
-    real, dimension(:,:), intent(in),optional :: ocean_depth !< Depth of ocean bottom (m)
-    logical, intent(in), optional :: maskmap(:,:) !< Masks out parallel cores
-    logical, intent(in), optional :: fractional_area !< If true, ice_area contains cell area as fraction of entire spherical surface
-
-    ! Namelist parameters (and defaults)
-    integer :: halo=4 ! Width of halo region
-    real :: traj_sample_hrs=24. ! Period between sampling of position for trajectory storage
-    real :: traj_write_hrs=480. ! Period between writing sampled trajectories to disk
-    real :: verbose_hrs=24. ! Period between verbose messages
-    integer :: max_bonds=6 ! Maximum number of iceberg bond passed between processors
-    real :: rho_bergs=850. ! Density of icebergs
-    real :: spring_coef=1.e-8 ! Spring constant for iceberg interactions (this seems to be the highest stable value)
-    real :: contact_spring_coef=0. !Spring coef for berg collisions (is set to spring_coef if not specified)
-    real :: bond_coef=1.e-8 ! Spring constant for iceberg bonds - not being used right now
-    real :: radial_damping_coef=1.e-4 ! Coefficient for relative iceberg motion damping (radial component) -Alon
-    real :: tangental_damping_coef=2.e-5 ! Coefficient for relative iceberg motion damping (tangential component) -Alon
-    real :: LoW_ratio=1.5 ! Initial ratio L/W for newly calved icebergs
-    real :: bergy_bit_erosion_fraction=0. ! Fraction of erosion melt flux to divert to bergy bits
-    real :: sicn_shift=0. ! Shift of sea-ice concentration in erosion flux modulation (0<sicn_shift<1)
-    real :: lat_ref=0. ! Reference latitude for f-plane (when this option is on)
-    real :: u_override=0.0 ! Overrides the u velocity of icebergs (for ocean testing)
-    real :: v_override=0.0 ! Overrides the v velocity of icebergs (for ocean testing)
-    real :: Lx=360. ! Length of domain in x direction, used for periodicity (use a huge number for non-periodic)
-    real :: initial_orientation=0. ! Iceberg orientation relative to this angle (in degrees). Used for hexagonal mass spreading.
-    real :: utide_icebergs= 0. ! Tidal speeds, set to zero for now.
-    real :: ustar_icebergs_bg=0.001 ! Background u_star under icebergs. This should be linked to a value felt by the ocean boundary layer
-    real :: cdrag_icebergs =  1.5e-3 ! Momentum Drag coef, taken from HJ99  (Holland and Jenkins 1999)
-    real :: Gamma_T_3EQ=0.022 ! Non-dimensional heat-transfer coefficient
-    real :: melt_cutoff=-1.0 ! Minimum ocean thickness for melting to occur (is not applied for values < 0)
-    logical :: const_gamma=.True. ! If true uses a constant heat transfer coefficient, from which the salt transfer is calculated
-    logical :: use_operator_splitting=.true. ! Use first order operator splitting for thermodynamics
-    logical :: add_weight_to_ocean=.true. ! Add weight of icebergs + bits to ocean
-    logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
-    logical :: time_average_weight=.false. ! Time average the weight on the ocean
-    real :: length_for_manually_initialize_bonds=1000.0 !<if manually init bonds, only  bond if dist between particles is .lt. this length - Alex
-    real :: speed_limit=0. ! CFL speed limit for a berg
-    real :: tau_calving=0. ! Time scale for smoothing out calving field (years)
-    real :: tip_parameter=0. ! Parameter to override iceberg rolling critical ratio (use zero to get parameter directly from ice and seawater densities
-    real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
-    real :: coastal_drift=0. ! A velocity added to ocean currents to cause bergs to drift away from land cells
-    real :: tidal_drift=0. ! Amplitude of a stochastic tidal velocity added to ocean currents to cause bergs to drift randomly
-    logical :: Runge_not_Verlet=.True. ! True=Runge Kutta, False=Verlet.
-    logical :: use_mixed_melting=.False. ! If true, then the melt is determined partly using 3 eq model partly using iceberg parameterizations (according to iceberg bond number)
-    logical :: apply_thickness_cutoff_to_gridded_melt=.False. ! Prevents melt for ocean thickness below melt_cuttoff (applied to gridded melt fields)
-    logical :: apply_thickness_cutoff_to_bergs_melt=.False. ! Prevents melt for ocean thickness below melt_cuttoff (applied to bergs)
-    logical :: use_updated_rolling_scheme=.false. ! Use the corrected Rolling Scheme rather than the erroneous one
-    logical :: pass_fields_to_ocean_model=.False. ! Iceberg area, mass and ustar fields are prepared to pass to ocean model
-    logical :: use_mixed_layer_salinity_for_thermo=.False. ! If true, then model uses ocean salinity for 3 and 2 equation melt model.
-    logical :: find_melt_using_spread_mass=.False. ! If true, then the model calculates ice loss by looping at the spread_mass before and after.
-    logical :: Use_three_equation_model=.True. ! Uses 3 equation model for melt when ice shelf type thermodynamics are used.
-    logical :: melt_icebergs_as_ice_shelf=.False. ! Uses iceshelf type thermodynamics
-    logical :: Iceberg_melt_without_decay=.False. ! Allows icebergs meltwater fluxes to enter the ocean, without the iceberg decaying or changing shape.
-    logical :: add_iceberg_thickness_to_SSH=.False. ! Adds the iceberg contribution to SSH.
-    logical :: override_iceberg_velocities=.False. ! Allows you to set a fixed iceberg velocity for all non-static icebergs.
-    logical :: use_f_plane=.False. ! Flag to use a f-plane for the rotation
-    logical :: grid_is_latlon=.True. ! True means that the grid is specified in lat lon, and uses to radius of the earth to convert to distance
-    logical :: grid_is_regular=.True. ! Flag to say whether point in cell can be found assuming regular Cartesian grid
-    logical :: rotate_icebergs_for_mass_spreading=.True. ! Flag allows icebergs to rotate for spreading their mass (in hexagonal spreading mode)
-    logical :: set_melt_rates_to_zero=.False. ! Sets all melt rates to zero, for testing purposes (thermodynamics routine is still run)
-    logical :: allow_bergs_to_roll=.True. ! Allows icebergs to roll over when rolling conditions are met
-    logical :: hexagonal_icebergs=.False. ! True treats icebergs as rectangles, False as hexagonal elements (for the purpose of mass spreading)
-    logical :: ignore_missing_restart_bergs=.False. ! True Allows the model to ignore icebergs missing in the restart.
-    logical :: Static_icebergs=.False. ! True= icebergs do no move
-    logical :: only_interactive_forces=.False. ! Icebergs only feel interactive forces, and not ocean, wind...
-    logical :: halo_debugging=.False. ! Use for debugging halos (remove when its working)
-    logical :: save_short_traj=.True. ! True saves only lon,lat,time,id in iceberg_trajectory.nc
-    logical :: ignore_traj=.False. ! If true, then model does not traj trajectory data at all
-    logical :: iceberg_bonds_on=.False. ! True=Allow icebergs to have bonds, False=don't allow.
-    logical :: manually_initialize_bonds=.False. ! True= Bonds are initialize manually.
-    logical :: use_new_predictive_corrective =.False. ! Flag to use Bob's predictive corrective iceberg scheme- Added by Alon
-    logical :: interactive_icebergs_on=.false. ! Turn on/off interactions between icebergs  - Added by Alon
-    logical :: critical_interaction_damping_on=.true. ! Sets the damping on relative iceberg velocity to critical value - Added by Alon
-    logical :: do_unit_tests=.false. ! Conduct some unit tests
-    logical :: input_freq_distribution=.false. ! Flag to show if input distribution is freq or mass dist (=1 if input is a freq dist, =0 to use an input mass dist)
-    logical :: read_old_restarts=.false. ! Legacy option that does nothing
-    logical :: use_old_spreading=.true. ! If true, spreads iceberg mass as if the berg is one grid cell wide
-    logical :: read_ocean_depth_from_file=.false. ! If true, ocean depth is read from a file.
-    !logical :: mts=.false. !use multiple timestepping scheme (substep size is automatically determined)
-    integer :: mts_sub_steps=-1 !if -1, the number of mts sub-steps will be automatically determined
-    real :: contact_distance=0.0 !for unbonded berg interactions, collision is assumed at max(contact_distance,sum of the 2 bergs radii)
-    real, dimension(nclasses) :: initial_mass=(/8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11/) ! Mass thresholds between iceberg classes (kg)
-    real, dimension(nclasses) :: distribution=(/0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02/) ! Fraction of calving to apply to this class (non-dim) ,
-    real, dimension(nclasses) :: mass_scaling=(/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) ! Ratio between effective and real iceberg mass (non-dim)
-    real, dimension(nclasses) :: initial_thickness=(/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) ! Total thickness of newly calved bergs (m)
-    integer(kind=8) :: debug_iceberg_with_id = -1 ! If positive, monitors a berg with this id
-
-    Namelist /icebergs_nml/ Verbose, budget, halo,  traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,Static_icebergs,  &
-         distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,contact_spring_coef,bond_coef, radial_damping_coef, tangental_damping_coef, only_interactive_forces, &
+subroutine ice_bergs_framework_init(bergs, &
+             gni, gnj, layout, io_layout, axes, dom_x_flags, dom_y_flags, &
+             dt, Time, ice_lon, ice_lat, ice_wet, ice_dx, ice_dy, ice_area, &
+             cos_rot, sin_rot, ocean_depth, maskmap, fractional_area)
+
+use mpp_parameter_mod, only: SCALAR_PAIR, CGRID_NE, BGRID_NE, CORNER, AGRID
+use mpp_domains_mod, only: mpp_update_domains, mpp_define_domains
+use mpp_domains_mod, only: mpp_get_compute_domain, mpp_get_data_domain, mpp_get_global_domain
+use mpp_domains_mod, only: CYCLIC_GLOBAL_DOMAIN, FOLD_NORTH_EDGE
+use mpp_domains_mod, only: mpp_get_neighbor_pe, NORTH, SOUTH, EAST, WEST
+use mpp_domains_mod, only: mpp_define_io_domain
+
+use mpp_mod, only: mpp_clock_begin, mpp_clock_end, mpp_clock_id, input_nml_file
+use mpp_mod, only: CLOCK_COMPONENT, CLOCK_SUBCOMPONENT, CLOCK_LOOP
+
+use fms_mod, only: open_namelist_file, check_nml_error, close_file
+use fms_mod, only: clock_flag_default
+
+use diag_manager_mod, only: register_diag_field, register_static_field, send_data
+use diag_manager_mod, only: diag_axis_init
+
+! Arguments
+type(icebergs), pointer :: bergs !< Container for all types and memory
+integer, intent(in) :: gni !< Number grid cells in i-direction
+integer, intent(in) :: gnj !< Number grid cells in j-direction
+integer, intent(in) :: layout(2) !< Number of processing cores in i,j direction
+integer, intent(in) :: io_layout(2) !< Number of i/o cores in i,j direction
+integer, intent(in) :: axes(2) !< Diagnostic axes
+integer, intent(in) :: dom_x_flags !< Domain flags in i-direction
+integer, intent(in) :: dom_y_flags !< Domain flags in j-direction
+real, intent(in) :: dt !< Time-step (s)
+type (time_type), intent(in) :: Time !< Current model time
+real, dimension(:,:), intent(in) :: ice_lon !< Longitude of cell corners using NE convention (degree E)
+real, dimension(:,:), intent(in) :: ice_lat !< Latitude of cell corners using NE convention (degree N)
+real, dimension(:,:), intent(in) :: ice_wet !< Wet/dry mask (1 is wet, 0 is dry) of cell centers
+real, dimension(:,:), intent(in) :: ice_dx !< Zonal length of cell on northern side (m)
+real, dimension(:,:), intent(in) :: ice_dy !< Meridional length of cell on eastern side (m)
+real, dimension(:,:), intent(in) :: ice_area !< Area of cells (m^2, or non-dim is fractional_area=True)
+real, dimension(:,:), intent(in) :: cos_rot !< Cosine from rotation matrix to lat-lon coords
+real, dimension(:,:), intent(in) :: sin_rot !< Sine from rotation matrix to lat-lon coords
+real, dimension(:,:), intent(in),optional :: ocean_depth !< Depth of ocean bottom (m)
+logical, intent(in), optional :: maskmap(:,:) !< Masks out parallel cores
+logical, intent(in), optional :: fractional_area !< If true, ice_area contains cell area as fraction of entire spherical surface
+
+! Namelist parameters (and defaults)
+integer :: halo=4 ! Width of halo region
+real :: traj_sample_hrs=24. ! Period between sampling of position for trajectory storage
+real :: traj_write_hrs=480. ! Period between writing sampled trajectories to disk
+real :: verbose_hrs=24. ! Period between verbose messages
+integer :: max_bonds=6 ! Maximum number of iceberg bond passed between processors
+real :: rho_bergs=850. ! Density of icebergs
+real :: spring_coef=1.e-8 ! Spring constant for iceberg interactions (this seems to be the highest stable value)
+real :: contact_spring_coef=0. !Spring coef for berg collisions (is set to spring_coef if not specified)
+real :: bond_coef=1.e-8 ! Spring constant for iceberg bonds - not being used right now
+real :: radial_damping_coef=1.e-4 ! Coefficient for relative iceberg motion damping (radial component) -Alon
+real :: tangental_damping_coef=2.e-5 ! Coefficient for relative iceberg motion damping (tangential component) -Alon
+real :: LoW_ratio=1.5 ! Initial ratio L/W for newly calved icebergs
+real :: bergy_bit_erosion_fraction=0. ! Fraction of erosion melt flux to divert to bergy bits
+real :: sicn_shift=0. ! Shift of sea-ice concentration in erosion flux modulation (0<sicn_shift<1)
+real :: lat_ref=0. ! Reference latitude for f-plane (when this option is on)
+real :: u_override=0.0 ! Overrides the u velocity of icebergs (for ocean testing)
+real :: v_override=0.0 ! Overrides the v velocity of icebergs (for ocean testing)
+real :: Lx=360. ! Length of domain in x direction, used for periodicity (use a huge number for non-periodic)
+real :: initial_orientation=0. ! Iceberg orientation relative to this angle (in degrees). Used for hexagonal mass spreading.
+real :: utide_icebergs= 0. ! Tidal speeds, set to zero for now.
+real :: ustar_icebergs_bg=0.001 ! Background u_star under icebergs. This should be linked to a value felt by the ocean boundary layer
+real :: cdrag_icebergs =  1.5e-3 ! Momentum Drag coef, taken from HJ99  (Holland and Jenkins 1999)
+real :: Gamma_T_3EQ=0.022 ! Non-dimensional heat-transfer coefficient
+real :: melt_cutoff=-1.0 ! Minimum ocean thickness for melting to occur (is not applied for values < 0)
+logical :: const_gamma=.True. ! If true uses a constant heat transfer coefficient, from which the salt transfer is calculated
+logical :: use_operator_splitting=.true. ! Use first order operator splitting for thermodynamics
+logical :: add_weight_to_ocean=.true. ! Add weight of icebergs + bits to ocean
+logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
+logical :: time_average_weight=.false. ! Time average the weight on the ocean
+real :: length_for_manually_initialize_bonds=1000.0 !<if manually init bonds, only  bond if dist between particles is .lt. this length - Alex
+real :: speed_limit=0. ! CFL speed limit for a berg
+real :: tau_calving=0. ! Time scale for smoothing out calving field (years)
+real :: tip_parameter=0. ! Parameter to override iceberg rolling critical ratio (use zero to get parameter directly from ice and seawater densities
+real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
+real :: coastal_drift=0. ! A velocity added to ocean currents to cause bergs to drift away from land cells
+real :: tidal_drift=0. ! Amplitude of a stochastic tidal velocity added to ocean currents to cause bergs to drift randomly
+logical :: Runge_not_Verlet=.True. ! True=Runge Kutta, False=Verlet.
+logical :: use_mixed_melting=.False. ! If true, then the melt is determined partly using 3 eq model partly using iceberg parameterizations (according to iceberg bond number)
+logical :: apply_thickness_cutoff_to_gridded_melt=.False. ! Prevents melt for ocean thickness below melt_cuttoff (applied to gridded melt fields)
+logical :: apply_thickness_cutoff_to_bergs_melt=.False. ! Prevents melt for ocean thickness below melt_cuttoff (applied to bergs)
+logical :: use_updated_rolling_scheme=.false. ! Use the corrected Rolling Scheme rather than the erroneous one
+logical :: pass_fields_to_ocean_model=.False. ! Iceberg area, mass and ustar fields are prepared to pass to ocean model
+logical :: use_mixed_layer_salinity_for_thermo=.False. ! If true, then model uses ocean salinity for 3 and 2 equation melt model.
+logical :: find_melt_using_spread_mass=.False. ! If true, then the model calculates ice loss by looping at the spread_mass before and after.
+logical :: Use_three_equation_model=.True. ! Uses 3 equation model for melt when ice shelf type thermodynamics are used.
+logical :: melt_icebergs_as_ice_shelf=.False. ! Uses iceshelf type thermodynamics
+logical :: Iceberg_melt_without_decay=.False. ! Allows icebergs meltwater fluxes to enter the ocean, without the iceberg decaying or changing shape.
+logical :: add_iceberg_thickness_to_SSH=.False. ! Adds the iceberg contribution to SSH.
+logical :: override_iceberg_velocities=.False. ! Allows you to set a fixed iceberg velocity for all non-static icebergs.
+logical :: use_f_plane=.False. ! Flag to use a f-plane for the rotation
+logical :: grid_is_latlon=.True. ! True means that the grid is specified in lat lon, and uses to radius of the earth to convert to distance
+logical :: grid_is_regular=.True. ! Flag to say whether point in cell can be found assuming regular Cartesian grid
+logical :: rotate_icebergs_for_mass_spreading=.True. ! Flag allows icebergs to rotate for spreading their mass (in hexagonal spreading mode)
+logical :: set_melt_rates_to_zero=.False. ! Sets all melt rates to zero, for testing purposes (thermodynamics routine is still run)
+logical :: allow_bergs_to_roll=.True. ! Allows icebergs to roll over when rolling conditions are met
+logical :: hexagonal_icebergs=.False. ! True treats icebergs as rectangles, False as hexagonal elements (for the purpose of mass spreading)
+logical :: ignore_missing_restart_bergs=.False. ! True Allows the model to ignore icebergs missing in the restart.
+logical :: Static_icebergs=.False. ! True= icebergs do no move
+logical :: only_interactive_forces=.False. ! Icebergs only feel interactive forces, and not ocean, wind...
+logical :: halo_debugging=.False. ! Use for debugging halos (remove when its working)
+logical :: save_short_traj=.True. ! True saves only lon,lat,time,id in iceberg_trajectory.nc
+logical :: ignore_traj=.False. ! If true, then model does not traj trajectory data at all
+logical :: iceberg_bonds_on=.False. ! True=Allow icebergs to have bonds, False=don't allow.
+logical :: manually_initialize_bonds=.False. ! True= Bonds are initialize manually.
+logical :: use_new_predictive_corrective =.False. ! Flag to use Bob's predictive corrective iceberg scheme- Added by Alon
+logical :: interactive_icebergs_on=.false. ! Turn on/off interactions between icebergs  - Added by Alon
+logical :: critical_interaction_damping_on=.true. ! Sets the damping on relative iceberg velocity to critical value - Added by Alon
+logical :: do_unit_tests=.false. ! Conduct some unit tests
+logical :: input_freq_distribution=.false. ! Flag to show if input distribution is freq or mass dist (=1 if input is a freq dist, =0 to use an input mass dist)
+logical :: read_old_restarts=.false. ! Legacy option that does nothing
+logical :: use_old_spreading=.true. ! If true, spreads iceberg mass as if the berg is one grid cell wide
+logical :: read_ocean_depth_from_file=.false. ! If true, ocean depth is read from a file.
+!logical :: mts=.false. !use multiple timestepping scheme (substep size is automatically determined) !(commented because mts was changed to global parameter for now)
+integer :: mts_sub_steps=-1 !if -1, the number of mts sub-steps will be automatically determined
+real :: contact_distance=0.0 !for unbonded berg interactions, collision is assumed at max(contact_distance,sum of the 2 bergs radii)
+real, dimension(nclasses) :: initial_mass=(/8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11/) ! Mass thresholds between iceberg classes (kg)
+real, dimension(nclasses) :: distribution=(/0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02/) ! Fraction of calving to apply to this class (non-dim) ,
+real, dimension(nclasses) :: mass_scaling=(/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) ! Ratio between effective and real iceberg mass (non-dim)
+real, dimension(nclasses) :: initial_thickness=(/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) ! Total thickness of newly calved bergs (m)
+integer(kind=8) :: debug_iceberg_with_id = -1 ! If positive, monitors a berg with this id
+
+namelist /icebergs_nml/ verbose, budget, halo,  traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,Static_icebergs,  &
+         distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,bond_coef, radial_damping_coef, tangental_damping_coef, only_interactive_forces, &
          rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, iceberg_bonds_on, manually_initialize_bonds, ignore_missing_restart_bergs, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, halo_debugging, hexagonal_icebergs, &
-         time_average_weight, generate_test_icebergs, length_for_manually_initialize_bonds, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, &
-         interactive_icebergs_on, critical_interaction_damping_on, &
+         time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, interactive_icebergs_on, critical_interaction_damping_on, &
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution, force_all_pes_traj, &
          allow_bergs_to_roll,set_melt_rates_to_zero,lat_ref,initial_orientation,rotate_icebergs_for_mass_spreading,grid_is_latlon,Lx,use_f_plane,use_old_spreading, &
          grid_is_regular,override_iceberg_velocities,u_override,v_override,add_iceberg_thickness_to_SSH,Iceberg_melt_without_decay,melt_icebergs_as_ice_shelf, &
          Use_three_equation_model,find_melt_using_spread_mass,use_mixed_layer_salinity_for_thermo,utide_icebergs,ustar_icebergs_bg,cdrag_icebergs, pass_fields_to_ocean_model, &
          const_gamma, Gamma_T_3EQ, ignore_traj, debug_iceberg_with_id,use_updated_rolling_scheme, tip_parameter, read_old_restarts, tau_calving, read_ocean_depth_from_file, melt_cutoff,&
-         apply_thickness_cutoff_to_gridded_melt, apply_thickness_cutoff_to_bergs_melt, use_mixed_melting, coastal_drift, tidal_drift,mts,mts_sub_steps,contact_distance
-
-    ! Local variables
-    integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
-    type(icebergs_gridded), pointer :: grd
-    real :: lon_mod, big_number,mts_fast_dt=0.0
-    logical :: lerr
-    integer :: stdlogunit, stderrunit
-    real :: Total_mass  !Added by Alon
-    real :: maxlon_c,minlon_c !Alex, for mts verlet periodicity
-
-    ! Get the stderr and stdlog unit numbers
-    stderrunit=stderr()
-    stdlogunit=stdlog()
-    write(stdlogunit,*) "ice_bergs_framework: "//trim(version)
-
-    ! Read namelist parameters
-    !write(stderrunit,*) 'KID: reading namelist'
+         apply_thickness_cutoff_to_gridded_melt, apply_thickness_cutoff_to_bergs_melt, use_mixed_melting, coastal_drift, tidal_drift,&
+				 mts,mts_sub_steps,contact_distance,length_for_manually_initialize_bonds,contact_spring_coef
+
+! Local variables
+integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
+type(icebergs_gridded), pointer :: grd
+real :: lon_mod, big_number
+logical :: lerr
+integer :: stdlogunit, stderrunit
+real :: Total_mass  !Added by Alon
+real :: mts_fast_dt=0.0 !Added by Alex
+real :: maxlon_c,minlon_c !Added by Alex, for mts verlet periodicity
+
+  ! Get the stderr and stdlog unit numbers
+  stderrunit=stderr()
+  stdlogunit=stdlog()
+  write(stdlogunit,*) "ice_bergs_framework: "//trim(version)
+
+! Read namelist parameters
+ !write(stderrunit,*) 'KID: reading namelist'
 #ifdef INTERNAL_FILE_NML
-    read (input_nml_file, nml=icebergs_nml, iostat=ierr)
+  read (input_nml_file, nml=icebergs_nml, iostat=ierr)
 #else
-    iunit = open_namelist_file()
-    read  (iunit, icebergs_nml,iostat=ierr)
-    call close_file (iunit)
+  iunit = open_namelist_file()
+  read  (iunit, icebergs_nml,iostat=ierr)
+  call close_file (iunit)
 #endif
-    ierr = check_nml_error(ierr,'icebergs_nml')
-
-    if (really_debug) debug=.true. ! One implies the other...
-
-    write (stdlogunit, icebergs_nml)
-
-
-    ! Allocate overall structure
-    !write(stderrunit,*) 'KID: allocating bergs'
-    allocate(bergs)
-    allocate(bergs%grd)
-    grd=>bergs%grd ! For convenience to avoid bergs%grd%X
-    !write(stderrunit,*) 'KID: allocating domain'
-    allocate(grd%domain)
-
-    ! Clocks
-    bergs%clock=mpp_clock_id( 'Icebergs', flags=clock_flag_default, grain=CLOCK_COMPONENT )
-    bergs%clock_mom=mpp_clock_id( 'Icebergs-momentum', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
-    bergs%clock_the=mpp_clock_id( 'Icebergs-thermodyn', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
-    bergs%clock_int=mpp_clock_id( 'Icebergs-interface', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
-    bergs%clock_cal=mpp_clock_id( 'Icebergs-calving', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
-    bergs%clock_com=mpp_clock_id( 'Icebergs-communication', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
-    bergs%clock_ini=mpp_clock_id( 'Icebergs-initialization', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
-    bergs%clock_ior=mpp_clock_id( 'Icebergs-I/O read', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
-    bergs%clock_iow=mpp_clock_id( 'Icebergs-I/O write', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
-    bergs%clock_dia=mpp_clock_id( 'Icebergs-diagnostics', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
-
-    call mpp_clock_begin(bergs%clock)
-    call mpp_clock_begin(bergs%clock_ini)
-
-    ! Set up iceberg domain
-    !write(stderrunit,*) 'KID: defining domain'
-    call mpp_define_domains( (/1,gni,1,gnj/), layout, grd%domain, &
-         maskmap=maskmap, &
-         xflags=dom_x_flags, xhalo=halo,  &
-         yflags=dom_y_flags, yhalo=halo, name='KID')
-
-    call mpp_define_io_domain(grd%domain, io_layout)
-
-    !write(stderrunit,*) 'KID: get compute domain'
-    call mpp_get_compute_domain( grd%domain, grd%isc, grd%iec, grd%jsc, grd%jec )
-    call mpp_get_data_domain( grd%domain, grd%isd, grd%ied, grd%jsd, grd%jed )
-    call mpp_get_global_domain( grd%domain, grd%isg, grd%ieg, grd%jsg, grd%jeg )
-
-    call mpp_get_neighbor_pe(grd%domain, NORTH, grd%pe_N)
-    call mpp_get_neighbor_pe(grd%domain, SOUTH, grd%pe_S)
-    call mpp_get_neighbor_pe(grd%domain, EAST, grd%pe_E)
-    call mpp_get_neighbor_pe(grd%domain, WEST, grd%pe_W)
-
-
-    folded_north_on_pe = ((dom_y_flags == FOLD_NORTH_EDGE) .and. (grd%jec == gnj))
-    !write(stderrunit,'(a,6i4)') 'KID, icebergs_init: pe,n,s,e,w =',mpp_pe(),grd%pe_N,grd%pe_S,grd%pe_E,grd%pe_W, NULL_PE
-
-    !if (verbose) &
-    !write(stderrunit,'(a,i3,a,4i4,a,4f8.2)') 'KID, icebergs_init: (',mpp_pe(),') [ij][se]c=', &
-    !     grd%isc,grd%iec,grd%jsc,grd%jec, &
-    !     ' [lon|lat][min|max]=', minval(ice_lon),maxval(ice_lon),minval(ice_lat),maxval(ice_lat)
-    !write(stderrunit,*) 'KID, int args = ', mpp_pe(),gni, gnj, layout, axes
-
-    ! Allocate grid of pointers
-    allocate( bergs%list(grd%isd:grd%ied, grd%jsd:grd%jed) )
-    do j = grd%jsd,grd%jed ; do i = grd%isd,grd%ied
-       bergs%list(i,j)%first => null()
-    enddo; enddo
+  ierr = check_nml_error(ierr,'icebergs_nml')
+
+  if (really_debug) debug=.true. ! One implies the other...
+
+  write (stdlogunit, icebergs_nml)
+
+
+! Allocate overall structure
+ !write(stderrunit,*) 'KID: allocating bergs'
+  allocate(bergs)
+  allocate(bergs%grd)
+  grd=>bergs%grd ! For convenience to avoid bergs%grd%X
+ !write(stderrunit,*) 'KID: allocating domain'
+  allocate(grd%domain)
+
+! Clocks
+  bergs%clock=mpp_clock_id( 'Icebergs', flags=clock_flag_default, grain=CLOCK_COMPONENT )
+  bergs%clock_mom=mpp_clock_id( 'Icebergs-momentum', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+  bergs%clock_the=mpp_clock_id( 'Icebergs-thermodyn', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+  bergs%clock_int=mpp_clock_id( 'Icebergs-interface', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+  bergs%clock_cal=mpp_clock_id( 'Icebergs-calving', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+  bergs%clock_com=mpp_clock_id( 'Icebergs-communication', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+  bergs%clock_ini=mpp_clock_id( 'Icebergs-initialization', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+  bergs%clock_ior=mpp_clock_id( 'Icebergs-I/O read', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+  bergs%clock_iow=mpp_clock_id( 'Icebergs-I/O write', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+  bergs%clock_dia=mpp_clock_id( 'Icebergs-diagnostics', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+
+  call mpp_clock_begin(bergs%clock)
+  call mpp_clock_begin(bergs%clock_ini)
+
+! Set up iceberg domain
+ !write(stderrunit,*) 'KID: defining domain'
+  call mpp_define_domains( (/1,gni,1,gnj/), layout, grd%domain, &
+                           maskmap=maskmap, &
+                           xflags=dom_x_flags, xhalo=halo,  &
+                           yflags=dom_y_flags, yhalo=halo, name='KID')
+
+  call mpp_define_io_domain(grd%domain, io_layout)
+
+ !write(stderrunit,*) 'KID: get compute domain'
+  call mpp_get_compute_domain( grd%domain, grd%isc, grd%iec, grd%jsc, grd%jec )
+  call mpp_get_data_domain( grd%domain, grd%isd, grd%ied, grd%jsd, grd%jed )
+  call mpp_get_global_domain( grd%domain, grd%isg, grd%ieg, grd%jsg, grd%jeg )
+
+  call mpp_get_neighbor_pe(grd%domain, NORTH, grd%pe_N)
+  call mpp_get_neighbor_pe(grd%domain, SOUTH, grd%pe_S)
+  call mpp_get_neighbor_pe(grd%domain, EAST, grd%pe_E)
+  call mpp_get_neighbor_pe(grd%domain, WEST, grd%pe_W)
+
+
+  folded_north_on_pe = ((dom_y_flags == FOLD_NORTH_EDGE) .and. (grd%jec == gnj))
+ !write(stderrunit,'(a,6i4)') 'KID, icebergs_init: pe,n,s,e,w =',mpp_pe(),grd%pe_N,grd%pe_S,grd%pe_E,grd%pe_W, NULL_PE
+
+ !if (verbose) &
+ !write(stderrunit,'(a,i3,a,4i4,a,4f8.2)') 'KID, icebergs_init: (',mpp_pe(),') [ij][se]c=', &
+ !     grd%isc,grd%iec,grd%jsc,grd%jec, &
+ !     ' [lon|lat][min|max]=', minval(ice_lon),maxval(ice_lon),minval(ice_lat),maxval(ice_lat)
+ !write(stderrunit,*) 'KID, int args = ', mpp_pe(),gni, gnj, layout, axes
+
+ ! Allocate grid of pointers
+  allocate( bergs%list(grd%isd:grd%ied, grd%jsd:grd%jed) )
+  do j = grd%jsd,grd%jed ; do i = grd%isd,grd%ied
+    bergs%list(i,j)%first => null()
+  enddo ; enddo
 
-    big_number=1.0E15
-    !write(stderrunit,*) 'KID: allocating grid'
-    allocate( grd%lon(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%lon(:,:)=big_number
-    allocate( grd%lat(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%lat(:,:)=big_number
-    allocate( grd%lonc(grd%isd:grd%ied, grd%jsd:grd%jed) );grd%lon(:,:)=big_number
-    allocate( grd%latc(grd%isd:grd%ied, grd%jsd:grd%jed) );grd%lat(:,:)=big_number
-    allocate( grd%dx(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%dx(:,:)=0.
-    allocate( grd%dy(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%dy(:,:)=0.
-    allocate( grd%area(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%area(:,:)=0.
-    allocate( grd%msk(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%msk(:,:)=0.
-    allocate( grd%cos(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%cos(:,:)=1.
-    allocate( grd%sin(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%sin(:,:)=0.
-    allocate( grd%ocean_depth(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%ocean_depth(:,:)=0.
-    allocate( grd%calving(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%calving(:,:)=0.
-    allocate( grd%calving_hflx(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%calving_hflx(:,:)=0.
-    allocate( grd%stored_heat(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%stored_heat(:,:)=0.
-    allocate( grd%floating_melt(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%floating_melt(:,:)=0.
-    allocate( grd%berg_melt(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%berg_melt(:,:)=0.
-    allocate( grd%melt_buoy(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%melt_buoy(:,:)=0.
-    allocate( grd%melt_eros(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%melt_eros(:,:)=0.
-    allocate( grd%melt_conv(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%melt_conv(:,:)=0.
-    allocate( grd%bergy_src(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%bergy_src(:,:)=0.
-    allocate( grd%bergy_melt(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%bergy_melt(:,:)=0.
-    allocate( grd%bergy_mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%bergy_mass(:,:)=0.
-    allocate( grd%spread_mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_mass(:,:)=0.
-    allocate( grd%spread_mass_old(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_mass_old(:,:)=0.
-    allocate( grd%spread_area(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_area(:,:)=0.
-    allocate( grd%u_iceberg(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%u_iceberg(:,:)=0.
-    allocate( grd%v_iceberg(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%v_iceberg(:,:)=0.
-    allocate( grd%spread_uvel(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_uvel(:,:)=0.
-    allocate( grd%spread_vvel(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_vvel(:,:)=0.
-    allocate( grd%ustar_iceberg(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%ustar_iceberg(:,:)=0.
-    allocate( grd%virtual_area(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%virtual_area(:,:)=0.
-    allocate( grd%mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%mass(:,:)=0.
-    allocate( grd%mass_on_ocean(grd%isd:grd%ied, grd%jsd:grd%jed, 9) ); grd%mass_on_ocean(:,:,:)=0.
-    allocate( grd%area_on_ocean(grd%isd:grd%ied, grd%jsd:grd%jed, 9) ); grd%area_on_ocean(:,:,:)=0.
-    allocate( grd%Uvel_on_ocean(grd%isd:grd%ied, grd%jsd:grd%jed, 9) ); grd%Uvel_on_ocean(:,:,:)=0.
-    allocate( grd%Vvel_on_ocean(grd%isd:grd%ied, grd%jsd:grd%jed, 9) ); grd%Vvel_on_ocean(:,:,:)=0.
-    allocate( grd%stored_ice(grd%isd:grd%ied, grd%jsd:grd%jed, nclasses) ); grd%stored_ice(:,:,:)=0.
-    allocate( grd%rmean_calving(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%rmean_calving(:,:)=0.
-    allocate( grd%rmean_calving_hflx(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%rmean_calving_hflx(:,:)=0.
-    allocate( grd%real_calving(grd%isd:grd%ied, grd%jsd:grd%jed, nclasses) ); grd%real_calving(:,:,:)=0.
-    allocate( grd%uo(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%uo(:,:)=0.
-    allocate( grd%vo(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%vo(:,:)=0.
-    allocate( grd%ui(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%ui(:,:)=0.
-    allocate( grd%vi(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%vi(:,:)=0.
-    allocate( grd%ua(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%ua(:,:)=0.
-    allocate( grd%va(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%va(:,:)=0.
-    allocate( grd%ssh(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%ssh(:,:)=0.
-    allocate( grd%sst(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%sst(:,:)=0.
-    allocate( grd%sss(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%sss(:,:)=0.
-    allocate( grd%cn(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%cn(:,:)=0.
-    allocate( grd%hi(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%hi(:,:)=0.
-    allocate( grd%tmp(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%tmp(:,:)=0.
-    allocate( grd%tmpc(grd%isc:grd%iec, grd%jsc:grd%jec) ); grd%tmpc(:,:)=0.
-    allocate( bergs%nbergs_calved_by_class(nclasses) ); bergs%nbergs_calved_by_class(:)=0
-    allocate( grd%parity_x(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%parity_x(:,:)=1.
-    allocate( grd%parity_y(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%parity_y(:,:)=1.
-    allocate( grd%iceberg_counter_grd(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%iceberg_counter_grd(:,:)=0
-
-    !write(stderrunit,*) 'KID: copying grid'
-    ! Copy data declared on ice model computational domain
-    is=grd%isc; ie=grd%iec; js=grd%jsc; je=grd%jec
-    grd%lon(is:ie,js:je)=ice_lon(:,:)
-    grd%lat(is:ie,js:je)=ice_lat(:,:)
-    grd%area(is:ie,js:je)=ice_area(:,:) !sis2 has *(4.*pi*radius*radius)
-
-!!!!!!!!!!!!!!!debugging!!!!!!!!!!!!!!!!!!
-    !if (mpp_pe().eq.5) then
-    ! write(stderrunit,'(a3,32i7)') 'LB',(i,i=grd%isd,grd%ied)
-    ! do j=grd%jed,grd%jsd,-1
-    !   write(stderrunit,'(i3,32f7.1)') j,(grd%lon(i,j),i=grd%isd,grd%ied)
-    ! enddo
-    ! write(stderrunit,'(a3,32i7)') 'Ice lon',(i,i=grd%isd,grd%ied)
-    ! do j=grd%jed,grd%jsd,-1
-    !   write(stderrunit,'(i3,32f7.1)') j,(ice_lon(i,j),i=grd%isd,grd%ied)
-    ! enddo
-    ! write(stderrunit,'(a3,32i7)') 'LA',(i,i=grd%isd,grd%ied)
-    ! do j=grd%jed,grd%jsd,-1
-    !   write(stderrunit,'(i3,32f7.1)') j,(grd%lon(i,j),i=grd%isd,grd%ied)
-    ! enddo
-    !endif
-!!!!!!!!!!!!!!!debugging!!!!!!!!!!!!!!!!!!
-
-    !For SIS not to change answers
-    if(present(fractional_area)) then
-       if(fractional_area) grd%area(is:ie,js:je)=ice_area(:,:) *(4.*pi*radius*radius)
-    endif
-    if(present(ocean_depth)) grd%ocean_depth(is:ie,js:je)=ocean_depth(:,:)
-
-    ! Copy data declared on ice model data domain
-    is=grd%isc-1; ie=grd%iec+1; js=grd%jsc-1; je=grd%jec+1
-    grd%dx(is:ie,js:je)=ice_dx(:,:)
-    grd%dy(is:ie,js:je)=ice_dy(:,:)
-    grd%msk(is:ie,js:je)=ice_wet(:,:)
-    grd%cos(is:ie,js:je)=cos_rot(:,:)
-    grd%sin(is:ie,js:je)=sin_rot(:,:)
-
-    call mpp_update_domains(grd%lon, grd%domain, position=CORNER)
-    call mpp_update_domains(grd%lat, grd%domain, position=CORNER)
-    call mpp_update_domains(grd%dy, grd%dx, grd%domain, gridtype=CGRID_NE, flags=SCALAR_PAIR)
-    call mpp_update_domains(grd%area, grd%domain)
-    call mpp_update_domains(grd%msk, grd%domain)
-    call mpp_update_domains(grd%cos, grd%domain, position=CORNER)
-    call mpp_update_domains(grd%sin, grd%domain, position=CORNER)
-    call mpp_update_domains(grd%ocean_depth, grd%domain)
-    call mpp_update_domains(grd%parity_x, grd%parity_y, grd%domain, gridtype=AGRID) ! If either parity_x/y is -ve, we need rotation of vectors
-
-    ! Sanitize lon and lat in the southern halo
-    do j=grd%jsc-1,grd%jsd,-1; do i=grd%isd,grd%ied
-       if (grd%lon(i,j).ge.big_number) grd%lon(i,j)=grd%lon(i,j+1)
-       if (grd%lat(i,j).ge.big_number) grd%lat(i,j)=2.*grd%lat(i,j+1)-grd%lat(i,j+2)
-    enddo; enddo
+  big_number=1.0E15
+ !write(stderrunit,*) 'KID: allocating grid'
+  allocate( grd%lon(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%lon(:,:)=big_number
+  allocate( grd%lat(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%lat(:,:)=big_number
+  allocate( grd%lonc(grd%isd:grd%ied, grd%jsd:grd%jed) );grd%lon(:,:)=big_number
+  allocate( grd%latc(grd%isd:grd%ied, grd%jsd:grd%jed) );grd%lat(:,:)=big_number
+  allocate( grd%dx(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%dx(:,:)=0.
+  allocate( grd%dy(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%dy(:,:)=0.
+  allocate( grd%area(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%area(:,:)=0.
+  allocate( grd%msk(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%msk(:,:)=0.
+  allocate( grd%cos(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%cos(:,:)=1.
+  allocate( grd%sin(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%sin(:,:)=0.
+  allocate( grd%ocean_depth(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%ocean_depth(:,:)=0.
+  allocate( grd%calving(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%calving(:,:)=0.
+  allocate( grd%calving_hflx(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%calving_hflx(:,:)=0.
+  allocate( grd%stored_heat(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%stored_heat(:,:)=0.
+  allocate( grd%floating_melt(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%floating_melt(:,:)=0.
+  allocate( grd%berg_melt(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%berg_melt(:,:)=0.
+  allocate( grd%melt_buoy(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%melt_buoy(:,:)=0.
+  allocate( grd%melt_eros(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%melt_eros(:,:)=0.
+  allocate( grd%melt_conv(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%melt_conv(:,:)=0.
+  allocate( grd%bergy_src(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%bergy_src(:,:)=0.
+  allocate( grd%bergy_melt(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%bergy_melt(:,:)=0.
+  allocate( grd%bergy_mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%bergy_mass(:,:)=0.
+  allocate( grd%spread_mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_mass(:,:)=0.
+  allocate( grd%spread_mass_old(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_mass_old(:,:)=0.
+  allocate( grd%spread_area(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_area(:,:)=0.
+  allocate( grd%u_iceberg(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%u_iceberg(:,:)=0.
+  allocate( grd%v_iceberg(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%v_iceberg(:,:)=0.
+  allocate( grd%spread_uvel(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_uvel(:,:)=0.
+  allocate( grd%spread_vvel(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_vvel(:,:)=0.
+  allocate( grd%ustar_iceberg(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%ustar_iceberg(:,:)=0.
+  allocate( grd%virtual_area(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%virtual_area(:,:)=0.
+  allocate( grd%mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%mass(:,:)=0.
+  allocate( grd%mass_on_ocean(grd%isd:grd%ied, grd%jsd:grd%jed, 9) ); grd%mass_on_ocean(:,:,:)=0.
+  allocate( grd%area_on_ocean(grd%isd:grd%ied, grd%jsd:grd%jed, 9) ); grd%area_on_ocean(:,:,:)=0.
+  allocate( grd%Uvel_on_ocean(grd%isd:grd%ied, grd%jsd:grd%jed, 9) ); grd%Uvel_on_ocean(:,:,:)=0.
+  allocate( grd%Vvel_on_ocean(grd%isd:grd%ied, grd%jsd:grd%jed, 9) ); grd%Vvel_on_ocean(:,:,:)=0.
+  allocate( grd%stored_ice(grd%isd:grd%ied, grd%jsd:grd%jed, nclasses) ); grd%stored_ice(:,:,:)=0.
+  allocate( grd%rmean_calving(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%rmean_calving(:,:)=0.
+  allocate( grd%rmean_calving_hflx(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%rmean_calving_hflx(:,:)=0.
+  allocate( grd%real_calving(grd%isd:grd%ied, grd%jsd:grd%jed, nclasses) ); grd%real_calving(:,:,:)=0.
+  allocate( grd%uo(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%uo(:,:)=0.
+  allocate( grd%vo(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%vo(:,:)=0.
+  allocate( grd%ui(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%ui(:,:)=0.
+  allocate( grd%vi(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%vi(:,:)=0.
+  allocate( grd%ua(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%ua(:,:)=0.
+  allocate( grd%va(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%va(:,:)=0.
+  allocate( grd%ssh(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%ssh(:,:)=0.
+  allocate( grd%sst(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%sst(:,:)=0.
+  allocate( grd%sss(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%sss(:,:)=0.
+  allocate( grd%cn(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%cn(:,:)=0.
+  allocate( grd%hi(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%hi(:,:)=0.
+  allocate( grd%tmp(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%tmp(:,:)=0.
+  allocate( grd%tmpc(grd%isc:grd%iec, grd%jsc:grd%jec) ); grd%tmpc(:,:)=0.
+  allocate( bergs%nbergs_calved_by_class(nclasses) ); bergs%nbergs_calved_by_class(:)=0
+  allocate( grd%parity_x(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%parity_x(:,:)=1.
+  allocate( grd%parity_y(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%parity_y(:,:)=1.
+  allocate( grd%iceberg_counter_grd(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%iceberg_counter_grd(:,:)=0
+
+ !write(stderrunit,*) 'KID: copying grid'
+  ! Copy data declared on ice model computational domain
+  is=grd%isc; ie=grd%iec; js=grd%jsc; je=grd%jec
+  grd%lon(is:ie,js:je)=ice_lon(:,:)
+  grd%lat(is:ie,js:je)=ice_lat(:,:)
+  grd%area(is:ie,js:je)=ice_area(:,:) !sis2 has *(4.*pi*radius*radius)
+
+  !!!!!!!!!!!!!!!debugging!!!!!!!!!!!!!!!!!!
+  !if (mpp_pe().eq.5) then
+  ! write(stderrunit,'(a3,32i7)') 'LB',(i,i=grd%isd,grd%ied)
+  ! do j=grd%jed,grd%jsd,-1
+  !   write(stderrunit,'(i3,32f7.1)') j,(grd%lon(i,j),i=grd%isd,grd%ied)
+  ! enddo
+  ! write(stderrunit,'(a3,32i7)') 'Ice lon',(i,i=grd%isd,grd%ied)
+  ! do j=grd%jed,grd%jsd,-1
+  !   write(stderrunit,'(i3,32f7.1)') j,(ice_lon(i,j),i=grd%isd,grd%ied)
+  ! enddo
+  ! write(stderrunit,'(a3,32i7)') 'LA',(i,i=grd%isd,grd%ied)
+  ! do j=grd%jed,grd%jsd,-1
+  !   write(stderrunit,'(i3,32f7.1)') j,(grd%lon(i,j),i=grd%isd,grd%ied)
+  ! enddo
+  !endif
+  !!!!!!!!!!!!!!!debugging!!!!!!!!!!!!!!!!!!
 
-    ! fix halos on edge of the domain
-    !1) South
-    do j=grd%jsc-1,grd%jsd,-1; do i=grd%isd,grd%ied
-       if (grd%lon(i,j).ge.big_number) grd%lon(i,j)=2.*grd%lon(i,j+1)-grd%lon(i,j+2)
-       if (grd%lat(i,j).ge.big_number) grd%lat(i,j)=2.*grd%lat(i,j+1)-grd%lat(i,j+2)
-    enddo; enddo
-    !2) North
-    do j=grd%jec+1,grd%jed; do i=grd%isd,grd%ied
-       if (grd%lon(i,j).ge.big_number) grd%lon(i,j)=2.*grd%lon(i,j-1)-grd%lon(i,j-2)
-       if (grd%lat(i,j).ge.big_number) grd%lat(i,j)=2.*grd%lat(i,j-1)-grd%lat(i,j-2)
-    enddo; enddo
-    !3) West
-    do i=grd%isc-1,grd%isd,-1; do j=grd%jsd,grd%jed
-       if (grd%lon(i,j).ge.big_number) grd%lon(i,j)=2.*grd%lon(i+1,j)-grd%lon(i+2,j)
-       if (grd%lat(i,j).ge.big_number) grd%lat(i,j)=2.*grd%lat(i+1,j)-grd%lat(i+2,j)
-    enddo; enddo
-    !4) East
-    do i=grd%iec+1,grd%ied; do j=grd%jsd,grd%jed
-       if (grd%lon(i,j).ge.big_number) grd%lon(i,j)=2.*grd%lon(i-1,j)-grd%lon(i-2,j)
-       if (grd%lat(i,j).ge.big_number) grd%lat(i,j)=2.*grd%lat(i-1,j)-grd%lat(i-2,j)
-    enddo; enddo
+  !For SIS not to change answers
+  if(present(fractional_area)) then
+    if(fractional_area) grd%area(is:ie,js:je)=ice_area(:,:) *(4.*pi*radius*radius)
+  endif
+  if(present(ocean_depth)) grd%ocean_depth(is:ie,js:je)=ocean_depth(:,:)
+
+  ! Copy data declared on ice model data domain
+  is=grd%isc-1; ie=grd%iec+1; js=grd%jsc-1; je=grd%jec+1
+  grd%dx(is:ie,js:je)=ice_dx(:,:)
+  grd%dy(is:ie,js:je)=ice_dy(:,:)
+  grd%msk(is:ie,js:je)=ice_wet(:,:)
+  grd%cos(is:ie,js:je)=cos_rot(:,:)
+  grd%sin(is:ie,js:je)=sin_rot(:,:)
+
+  call mpp_update_domains(grd%lon, grd%domain, position=CORNER)
+  call mpp_update_domains(grd%lat, grd%domain, position=CORNER)
+  call mpp_update_domains(grd%dy, grd%dx, grd%domain, gridtype=CGRID_NE, flags=SCALAR_PAIR)
+  call mpp_update_domains(grd%area, grd%domain)
+  call mpp_update_domains(grd%msk, grd%domain)
+  call mpp_update_domains(grd%cos, grd%domain, position=CORNER)
+  call mpp_update_domains(grd%sin, grd%domain, position=CORNER)
+  call mpp_update_domains(grd%ocean_depth, grd%domain)
+  call mpp_update_domains(grd%parity_x, grd%parity_y, grd%domain, gridtype=AGRID) ! If either parity_x/y is -ve, we need rotation of vectors
+
+  ! Sanitize lon and lat in the southern halo
+  do j=grd%jsc-1,grd%jsd,-1; do i=grd%isd,grd%ied
+      if (grd%lon(i,j).ge.big_number) grd%lon(i,j)=grd%lon(i,j+1)
+      if (grd%lat(i,j).ge.big_number) grd%lat(i,j)=2.*grd%lat(i,j+1)-grd%lat(i,j+2)
+  enddo; enddo
 
+  ! fix halos on edge of the domain
+  !1) South
+  do j=grd%jsc-1,grd%jsd,-1; do i=grd%isd,grd%ied
+      if (grd%lon(i,j).ge.big_number) grd%lon(i,j)=2.*grd%lon(i,j+1)-grd%lon(i,j+2)
+      if (grd%lat(i,j).ge.big_number) grd%lat(i,j)=2.*grd%lat(i,j+1)-grd%lat(i,j+2)
+  enddo; enddo
+  !2) North
+  do j=grd%jec+1,grd%jed; do i=grd%isd,grd%ied
+      if (grd%lon(i,j).ge.big_number) grd%lon(i,j)=2.*grd%lon(i,j-1)-grd%lon(i,j-2)
+      if (grd%lat(i,j).ge.big_number) grd%lat(i,j)=2.*grd%lat(i,j-1)-grd%lat(i,j-2)
+  enddo; enddo
+  !3) West
+  do i=grd%isc-1,grd%isd,-1; do j=grd%jsd,grd%jed
+      if (grd%lon(i,j).ge.big_number) grd%lon(i,j)=2.*grd%lon(i+1,j)-grd%lon(i+2,j)
+      if (grd%lat(i,j).ge.big_number) grd%lat(i,j)=2.*grd%lat(i+1,j)-grd%lat(i+2,j)
+  enddo; enddo
+  !4) East
+  do i=grd%iec+1,grd%ied; do j=grd%jsd,grd%jed
+      if (grd%lon(i,j).ge.big_number) grd%lon(i,j)=2.*grd%lon(i-1,j)-grd%lon(i-2,j)
+      if (grd%lat(i,j).ge.big_number) grd%lat(i,j)=2.*grd%lat(i-1,j)-grd%lat(i-2,j)
+  enddo; enddo
 
-    if ( (mpp_pe() == 0) .and. (Lx .ne. 360.) .and. .not. (grid_is_latlon) ) then
-       print *,''
-       print *,'pe0 x-domain before periodicity fix'
-       write(*,'(f12.2)') (grd%lon(i,grd%jsd), i=grd%isd,grd%ied)
-    end if
 
+  if ( (mpp_pe() == 0) .and. (Lx .ne. 360.) .and. .not. (grid_is_latlon) ) then
+    print *,''
+    print *,'pe0 x-domain before periodicity fix'
+    write(*,'(f12.2)') (grd%lon(i,grd%jsd), i=grd%isd,grd%ied)
+  endif
 
-    if (.not. present(maskmap)) then ! Using a maskmap causes tickles this sanity check
-       do j=grd%jsd,grd%jed; do i=grd%isd,grd%ied
-          !if (grd%lon(i,j).ge.big_number) write(stderrunit,*) 'bad lon: ',mpp_pe(),i-grd%isc+1,j-grd%jsc+1,grd%lon(i,j)
-          !if (grd%lat(i,j).ge.big_number) write(stderrunit,*) 'bad lat: ',mpp_pe(),i-grd%isc+1,j-grd%jsc+1,grd%lat(i,j)
-       enddo; enddo
-    endif
 
-    if ((Lx.gt.1E15 ) .and. (mpp_pe().eq.mpp_root_pe())) then
-       call error_mesg('KID, framework', 'Model does not enjoy the domain being larger than 1E15. Not sure why. Probably to do with floating point precision.', WARNING)
-    endif
-    if ((.not. grid_is_latlon) .and. (Lx.eq.360.)) then
-       if (mpp_pe().eq.mpp_root_pe())  then
-          call error_mesg('KID, framework', 'Since the lat/lon grid is off, the x-direction is being set as non-periodic. Set Lx not equal to 360 override.', WARNING)
-       endif
-       Lx=-1.
+  if (.not. present(maskmap)) then ! Using a maskmap causes tickles this sanity check
+    do j=grd%jsd,grd%jed; do i=grd%isd,grd%ied
+      !if (grd%lon(i,j).ge.big_number) write(stderrunit,*) 'bad lon: ',mpp_pe(),i-grd%isc+1,j-grd%jsc+1,grd%lon(i,j)
+      !if (grd%lat(i,j).ge.big_number) write(stderrunit,*) 'bad lat: ',mpp_pe(),i-grd%isc+1,j-grd%jsc+1,grd%lat(i,j)
+    enddo; enddo
+  endif
+
+  if ((Lx.gt.1E15 ) .and. (mpp_pe().eq.mpp_root_pe())) then
+          call error_mesg('KID, framework', 'Model does not enjoy the domain being larger than 1E15. Not sure why. Probably to do with floating point precision.', WARNING)
+  endif
+  if ((.not. grid_is_latlon) .and. (Lx.eq.360.)) then
+    if (mpp_pe().eq.mpp_root_pe())  then
+            call error_mesg('KID, framework', 'Since the lat/lon grid is off, the x-direction is being set as non-periodic. Set Lx not equal to 360 override.', WARNING)
     endif
+    Lx=-1.
+  endif
 
 
-    !The fix to reproduce across PE layout change, from AJA
-    if (Lx>0.) then
-       j=grd%jsc; do i=grd%isc+1,grd%ied
-       lon_mod = apply_modulo_around_point(grd%lon(i,j),grd%lon(i-1,j),Lx)
-       if (abs(grd%lon(i,j)-lon_mod)>(Lx/2.)) &
-            grd%lon(i,j)= lon_mod
+ !The fix to reproduce across PE layout change, from AJA
+  if (Lx>0.) then
+    j=grd%jsc; do i=grd%isc+1,grd%ied
+      lon_mod = apply_modulo_around_point(grd%lon(i,j),grd%lon(i-1,j),Lx)
+      if (abs(grd%lon(i,j)-lon_mod)>(Lx/2.)) &
+        grd%lon(i,j)= lon_mod
     enddo
     j=grd%jsc; do i=grd%isc-1,grd%isd,-1
-    lon_mod = apply_modulo_around_point(grd%lon(i,j),grd%lon(i+1,j) ,Lx)
-    if (abs(grd%lon(i,j)-  lon_mod )>(Lx/2.)) &
-         grd%lon(i,j)= lon_mod
- enddo
- do j=grd%jsc+1,grd%jed; do i=grd%isd,grd%ied
-    lon_mod = apply_modulo_around_point(grd%lon(i,j),grd%lon(i,j-1) ,Lx)
-    if (abs(grd%lon(i,j)-(lon_mod ))>(Lx/2.)) &
-         grd%lon(i,j)= lon_mod
- enddo; enddo
- do j=grd%jsc-1,grd%jsd,-1; do i=grd%isd,grd%ied
-    lon_mod = apply_modulo_around_point(grd%lon(i,j),grd%lon(i,j+1) ,Lx)
-    if (abs(grd%lon(i,j)- lon_mod )>(Lx/2.)) &
-         grd%lon(i,j)=  lon_mod
- enddo; enddo
-endif
+      lon_mod = apply_modulo_around_point(grd%lon(i,j),grd%lon(i+1,j) ,Lx)
+      if (abs(grd%lon(i,j)-  lon_mod )>(Lx/2.)) &
+        grd%lon(i,j)= lon_mod
+    enddo
+    do j=grd%jsc+1,grd%jed; do i=grd%isd,grd%ied
+      lon_mod = apply_modulo_around_point(grd%lon(i,j),grd%lon(i,j-1) ,Lx)
+      if (abs(grd%lon(i,j)-(lon_mod ))>(Lx/2.)) &
+        grd%lon(i,j)= lon_mod
+    enddo; enddo
+    do j=grd%jsc-1,grd%jsd,-1; do i=grd%isd,grd%ied
+      lon_mod = apply_modulo_around_point(grd%lon(i,j),grd%lon(i,j+1) ,Lx)
+      if (abs(grd%lon(i,j)- lon_mod )>(Lx/2.)) &
+        grd%lon(i,j)=  lon_mod
+    enddo; enddo
+  endif
 
 
-! lonc, latc used for searches
-do j=grd%jsd+1,grd%jed; do i=grd%isd+1,grd%ied
- grd%lonc(i,j)=0.25*( (grd%lon(i,j)+grd%lon(i-1,j-1)) &
-      +(grd%lon(i-1,j)+grd%lon(i,j-1)) )
- grd%latc(i,j)=0.25*( (grd%lat(i,j)+grd%lat(i-1,j-1)) &
-      +(grd%lat(i-1,j)+grd%lat(i,j-1)) )
-enddo; enddo
 
-if (debug) then
-   ! Write(stderrunit,'(a,i3,a,4i4,a,4f8.2)') 'KID, icebergs_init: (',mpp_pe(),') [ij][se]c=', &
-   !      grd%isc,grd%iec,grd%jsc,grd%jec, &
-   !      ' [Lon|lat][min|max]=', minval(grd%lon),maxval(grd%lon),minval(grd%lat),maxval(grd%lat)
+  ! lonc, latc used for searches
+  do j=grd%jsd+1,grd%jed; do i=grd%isd+1,grd%ied
+    grd%lonc(i,j)=0.25*( (grd%lon(i,j)+grd%lon(i-1,j-1)) &
+                        +(grd%lon(i-1,j)+grd%lon(i,j-1)) )
+    grd%latc(i,j)=0.25*( (grd%lat(i,j)+grd%lat(i-1,j-1)) &
+                        +(grd%lat(i-1,j)+grd%lat(i,j-1)) )
+  enddo; enddo
 
+  if (debug) then
+   ! write(stderrunit,'(a,i3,a,4i4,a,4f8.2)') 'KID, icebergs_init: (',mpp_pe(),') [ij][se]c=', &
+   !      grd%isc,grd%iec,grd%jsc,grd%jec, &
+   !      ' [lon|lat][min|max]=', minval(grd%lon),maxval(grd%lon),minval(grd%lat),maxval(grd%lat)
 
- Write(stderrunit,'(a,i3,a,4i4)') 'KID, icebergs_init: (',mpp_pe(),') [ij][se]c=', &
-      grd%isc,grd%iec,grd%jsc,grd%jec   
+    write(stderrunit,'(a,i3,a,4i4)') 'KID, icebergs_init: (',mpp_pe(),') [ij][se]c=', &
+          grd%isc,grd%iec,grd%jsc,grd%jec
 
- print *,'minval(grd%lon)',minval(grd%lon)
- print *,'maxval(grd%lon)',maxval(grd%lon)
- print *,'minval(grd%lat)',minval(grd%lat)
- print *,'maxval(grd%lat)',maxval(grd%lat)    
+    print *,'minval(grd%lon)',minval(grd%lon)
+    print *,'maxval(grd%lon)',maxval(grd%lon)
+    print *,'minval(grd%lat)',minval(grd%lat)
+    print *,'maxval(grd%lat)',maxval(grd%lat)
 
- write(stderrunit,'(a,4f10.2)') '[Lon|lat][min|max]=', &
-      minval(grd%lon),maxval(grd%lon),minval(grd%lat),maxval(grd%lat)
-endif
+    write(stderrunit,'(a,4f10.2)') '[Lon|lat][min|max]=', &
+          minval(grd%lon),maxval(grd%lon),minval(grd%lat),maxval(grd%lat)
+  endif
 
-if ( (mpp_pe() == 0) .and. (Lx .ne. -1.) .and. .not. (grid_is_latlon) ) then
- print *,''
- print *,'pe 0 x-domain after periodicity fix'
- write(*,'(f12.2)') (grd%lon(i,grd%jsd), i=grd%isd,grd%ied)
-end if
+  if ( (mpp_pe() == 0) .and. (Lx .ne. -1.) .and. .not. (grid_is_latlon) ) then
+    print *,''
+    print *,'pe 0 x-domain after periodicity fix'
+    write(*,'(f12.2)') (grd%lon(i,grd%jsd), i=grd%isd,grd%ied)
+  end if
 
-!if (mpp_pe().eq.5) then
-!  write(stderrunit,'(a3,32i7)') 'Lon',(i,i=grd%isd,grd%ied)
-!  do j=grd%jed,grd%jsd,-1
-!    write(stderrunit,'(i3,32f7.1)') j,(grd%lon(i,j),i=grd%isd,grd%ied)
-!  enddo
-!  write(stderrunit,'(a3,32i7)') 'Lat',(i,i=grd%isd,grd%ied)
-!  do j=grd%jed,grd%jsd,-1
-!    write(stderrunit,'(i3,32f7.1)') j,(grd%lat(i,j),i=grd%isd,grd%ied)
-!  enddo
-!  write(stderrunit,'(a3,32i7)') 'Msk',(i,i=grd%isd,grd%ied)
-!  do j=grd%jed,grd%jsd,-1
-!    write(stderrunit,'(i3,32f7.1)') j,(grd%msk(i,j),i=grd%isd,grd%ied)
-!  enddo
-!endif
+ !if (mpp_pe().eq.5) then
+ !  write(stderrunit,'(a3,32i7)') 'Lon',(i,i=grd%isd,grd%ied)
+ !  do j=grd%jed,grd%jsd,-1
+ !    write(stderrunit,'(i3,32f7.1)') j,(grd%lon(i,j),i=grd%isd,grd%ied)
+ !  enddo
+ !  write(stderrunit,'(a3,32i7)') 'Lat',(i,i=grd%isd,grd%ied)
+ !  do j=grd%jed,grd%jsd,-1
+ !    write(stderrunit,'(i3,32f7.1)') j,(grd%lat(i,j),i=grd%isd,grd%ied)
+ !  enddo
+ !  write(stderrunit,'(a3,32i7)') 'Msk',(i,i=grd%isd,grd%ied)
+ !  do j=grd%jed,grd%jsd,-1
+ !    write(stderrunit,'(i3,32f7.1)') j,(grd%msk(i,j),i=grd%isd,grd%ied)
+ !  enddo
+ !endif
 
 ! Final check for NaN's in the latlon grid:
-do j=grd%jsd+1,grd%jed; do i=grd%isd+1,grd%ied
- if (grd%lat(i,j) .ne. grd%lat(i,j)) then
-    write(stderrunit,*) 'Lat not defined properly', mpp_pe(),i,j,grd%lat(i,j)
-    call error_mesg('KID,grid defining', 'Latitude contains NaNs', FATAL)
- endif
- if (grd%lon(i,j) .ne. grd%lon(i,j)) then
-    write(stderrunit,*) 'Lon not defined properly', mpp_pe(),i,j,grd%lon(i,j)
-    call error_mesg('KID, grid defining', 'Longatudes contains NaNs', FATAL)
- endif
-enddo; enddo
+  do j=grd%jsd+1,grd%jed; do i=grd%isd+1,grd%ied
+    if (grd%lat(i,j) .ne. grd%lat(i,j)) then
+      write(stderrunit,*) 'Lat not defined properly', mpp_pe(),i,j,grd%lat(i,j)
+      call error_mesg('KID,grid defining', 'Latitude contains NaNs', FATAL)
+    endif
+    if (grd%lon(i,j) .ne. grd%lon(i,j)) then
+      write(stderrunit,*) 'Lon not defined properly', mpp_pe(),i,j,grd%lon(i,j)
+      call error_mesg('KID, grid defining', 'Longatudes contains NaNs', FATAL)
+    endif
+  enddo; enddo
 
 
 !Added by Alon  - If a freq distribution is input, we have to convert the freq distribution to a mass flux distribution)
 if (input_freq_distribution) then
- Total_mass=0.
- do j=1,nclasses
-    Total_mass=Total_mass+(distribution(j)*initial_mass(j))
- enddo
- do j=1,nclasses
-    distribution(j)=(distribution(j)*initial_mass(j))/Total_mass
- enddo
+     Total_mass=0.
+     do j=1,nclasses
+          Total_mass=Total_mass+(distribution(j)*initial_mass(j))
+     enddo
+     do j=1,nclasses
+           distribution(j)=(distribution(j)*initial_mass(j))/Total_mass
+     enddo
 endif
 
 if ((halo .lt. 3) .and. (rotate_icebergs_for_mass_spreading .and. iceberg_bonds_on) )   then
- halo=3
- call error_mesg('KID, framework', 'Setting iceberg halos =3, since halos must be >= 3 for rotating icebergs for mass spreading', WARNING)
+    halo=3
+    call error_mesg('KID, framework', 'Setting iceberg halos =3, since halos must be >= 3 for rotating icebergs for mass spreading', WARNING)
 elseif  ((halo .lt. 2) .and. (interactive_icebergs_on .or. iceberg_bonds_on) )   then
- halo=2
- call error_mesg('KID, framework', 'Setting iceberg halos =2, since halos must be >= 2 for interactions', WARNING)
+    halo=2
+    call error_mesg('KID, framework', 'Setting iceberg halos =2, since halos must be >= 2 for interactions', WARNING)
 endif
 
 if (interactive_icebergs_on) then
- if (Runge_not_Verlet) then
+  if (Runge_not_Verlet) then
     !Runge_not_Verlet=.false.  ! Iceberg interactions only with Verlet
     call error_mesg('KID, framework', 'It is unlcear whther interactive icebergs work with Runge Kutta stepping.', WARNING)
- endif
+  endif
 endif
 if (.not.interactive_icebergs_on) then
- if (iceberg_bonds_on) then
+  if (iceberg_bonds_on) then
     !iceberg_bonds_on=.false.
     call error_mesg('KID, framework', 'Interactive icebergs off requires iceberg bonds off (turning bonds off).', WARNING)
- endif
+  endif
 endif
 if (.not. iceberg_bonds_on) then
- max_bonds=0
+   max_bonds=0
 else
- buffer_width=buffer_width+(max_bonds*4) ! Increase buffer width to include bonds being passed between processors
+  buffer_width=buffer_width+(max_bonds*4) ! Increase buffer width to include bonds being passed between processors
 endif
 if (save_short_traj) buffer_width_traj=6 ! This is the length of the short buffer used for abrevated traj
 if (ignore_traj) buffer_width_traj=0 ! If this is true, then all traj files should be ignored
 
 !must use verlet with mts - Alex
 if (mts) then
-
   buffer_width_traj=buffer_width_traj+6 !to accomodate fast acceration and vel_prev terms
   buffer_width=buffer_width+18 !to accomodate external forcing (uo,vo,ua,va,ui,vi,ssh_x,ssh_y,sst,sss,cn,hi)
-  
+
   !if mts_sub_steps is not given in the nml already,
   !then detemine according to the max dt according to the spring coef
   if (mts_sub_steps .eq. -1) then
-    mts_fast_dt = 2./sqrt(bergs%spring_coef)   !the (theoretical) maximum "fast" dt for mts scheme      
+    mts_fast_dt = 2./sqrt(bergs%spring_coef)   !the (theoretical) maximum "fast" dt for mts scheme
     mts_sub_steps = ceiling(dt/mts_fast_dt)    !the number of substeps
   end if
 
@@ -1006,235 +1006,234 @@ subroutine ice_bergs_framework_init(bergs, &
 if (contact_spring_coef.le.0.) contact_spring_coef=spring_coef
 
 
-! Parameters
-bergs%dt=dt
-bergs%traj_sample_hrs=traj_sample_hrs
-bergs%traj_write_hrs=traj_write_hrs
-bergs%save_short_traj=save_short_traj
-bergs%ignore_traj=ignore_traj
-bergs%verbose_hrs=verbose_hrs
-bergs%grd%halo=halo
-bergs%grd%Lx=Lx
-bergs%grd%grid_is_latlon=grid_is_latlon
-bergs%grd%grid_is_regular=grid_is_regular
-bergs%max_bonds=max_bonds
-bergs%rho_bergs=rho_bergs
-bergs%spring_coef=spring_coef
-bergs%contact_spring_coef=contact_spring_coef !Alex
-bergs%bond_coef=bond_coef
-bergs%radial_damping_coef=radial_damping_coef
-bergs%tangental_damping_coef=tangental_damping_coef
-bergs%LoW_ratio=LoW_ratio
-bergs%use_operator_splitting=use_operator_splitting
-bergs%bergy_bit_erosion_fraction=bergy_bit_erosion_fraction
-bergs%sicn_shift=sicn_shift
-bergs%passive_mode=passive_mode
-bergs%time_average_weight=time_average_weight
-bergs%speed_limit=speed_limit
-bergs%tau_calving=tau_calving
-bergs%tip_parameter=tip_parameter
-bergs%use_updated_rolling_scheme=use_updated_rolling_scheme  !Alon
-bergs%Runge_not_Verlet=Runge_not_Verlet
-bergs%use_mixed_melting=use_mixed_melting
-bergs%apply_thickness_cutoff_to_bergs_melt=apply_thickness_cutoff_to_bergs_melt
-bergs%apply_thickness_cutoff_to_gridded_melt=apply_thickness_cutoff_to_gridded_melt
-bergs%melt_cutoff=melt_cutoff
-bergs%read_ocean_depth_from_file=read_ocean_depth_from_file
-bergs%const_gamma=const_gamma
-bergs%Gamma_T_3EQ=Gamma_T_3EQ
-bergs%pass_fields_to_ocean_model=pass_fields_to_ocean_model
-bergs%ustar_icebergs_bg=ustar_icebergs_bg
-bergs%utide_icebergs=utide_icebergs
-bergs%cdrag_icebergs=cdrag_icebergs
-bergs%use_mixed_layer_salinity_for_thermo=use_mixed_layer_salinity_for_thermo
-bergs%find_melt_using_spread_mass=find_melt_using_spread_mass
-bergs%Use_three_equation_model=Use_three_equation_model
-bergs%melt_icebergs_as_ice_shelf=melt_icebergs_as_ice_shelf
-bergs%Iceberg_melt_without_decay=Iceberg_melt_without_decay
-bergs%add_iceberg_thickness_to_SSH=add_iceberg_thickness_to_SSH
-bergs%override_iceberg_velocities=override_iceberg_velocities
-bergs%use_f_plane=use_f_plane
-bergs%rotate_icebergs_for_mass_spreading=rotate_icebergs_for_mass_spreading
-bergs%lat_ref=lat_ref
-bergs%u_override=u_override
-bergs%v_override=v_override
-bergs%initial_orientation=initial_orientation
-bergs%set_melt_rates_to_zero=set_melt_rates_to_zero
-bergs%allow_bergs_to_roll=allow_bergs_to_roll
-bergs%hexagonal_icebergs=hexagonal_icebergs
-bergs%ignore_missing_restart_bergs=ignore_missing_restart_bergs
-bergs%Static_icebergs=Static_icebergs
-bergs%only_interactive_forces=only_interactive_forces
-bergs%halo_debugging=halo_debugging
-bergs%iceberg_bonds_on=iceberg_bonds_on   !Alon
-bergs%manually_initialize_bonds=manually_initialize_bonds   !Alon
-bergs%length_for_manually_initialize_bonds=length_for_manually_initialize_bonds !Alex
-bergs%critical_interaction_damping_on=critical_interaction_damping_on   !Alon
-bergs%interactive_icebergs_on=interactive_icebergs_on   !Alon
-bergs%use_new_predictive_corrective=use_new_predictive_corrective  !Alon
-bergs%grounding_fraction=grounding_fraction
-bergs%add_weight_to_ocean=add_weight_to_ocean
-bergs%use_old_spreading=use_old_spreading
-bergs%debug_iceberg_with_id=debug_iceberg_with_id
-bergs%mts=mts
-bergs%mts_fast_dt = mts_fast_dt
-bergs%mts_sub_steps = mts_sub_steps
-bergs%mts_part = 1
-bergs%contact_distance=contact_distance
-bergs%num_contact_cells = max(int(ceiling(contact_distance/(grd%lon(grd%isc+1,grd%jsc)-grd%lon(grd%isc,grd%jsc)))),1)
-if (halo<bergs%num_contact_cells) then
-  if (mpp_pe()==0) then  
-    write(stderrunit,'(a,i3)') 'KID, icebergs_init: halo width ',halo
-    write(stderrunit,'(a,f8.2,a,i3)') 'KID, icebergs_init: contact distance ',bergs%contact_distance,&
-      ' num contact cells',bergs%num_contact_cells
-    call error_mesg('KID, ice_bergs_framework_init', &
-      'halo width must be increased to accomodate specified contact distance!!!', FATAL)
+ ! Parameters
+  bergs%dt=dt
+  bergs%traj_sample_hrs=traj_sample_hrs
+  bergs%traj_write_hrs=traj_write_hrs
+  bergs%save_short_traj=save_short_traj
+  bergs%ignore_traj=ignore_traj
+  bergs%verbose_hrs=verbose_hrs
+  bergs%grd%halo=halo
+  bergs%grd%Lx=Lx
+  bergs%grd%grid_is_latlon=grid_is_latlon
+  bergs%grd%grid_is_regular=grid_is_regular
+  bergs%max_bonds=max_bonds
+  bergs%rho_bergs=rho_bergs
+  bergs%spring_coef=spring_coef
+	bergs%contact_spring_coef=contact_spring_coef !Alex
+  bergs%bond_coef=bond_coef
+  bergs%radial_damping_coef=radial_damping_coef
+  bergs%tangental_damping_coef=tangental_damping_coef
+  bergs%LoW_ratio=LoW_ratio
+  bergs%use_operator_splitting=use_operator_splitting
+  bergs%bergy_bit_erosion_fraction=bergy_bit_erosion_fraction
+  bergs%sicn_shift=sicn_shift
+  bergs%passive_mode=passive_mode
+  bergs%time_average_weight=time_average_weight
+  bergs%speed_limit=speed_limit
+  bergs%tau_calving=tau_calving
+  bergs%tip_parameter=tip_parameter
+  bergs%use_updated_rolling_scheme=use_updated_rolling_scheme  !Alon
+  bergs%Runge_not_Verlet=Runge_not_Verlet
+  bergs%use_mixed_melting=use_mixed_melting
+  bergs%apply_thickness_cutoff_to_bergs_melt=apply_thickness_cutoff_to_bergs_melt
+  bergs%apply_thickness_cutoff_to_gridded_melt=apply_thickness_cutoff_to_gridded_melt
+  bergs%melt_cutoff=melt_cutoff
+  bergs%read_ocean_depth_from_file=read_ocean_depth_from_file
+  bergs%const_gamma=const_gamma
+  bergs%Gamma_T_3EQ=Gamma_T_3EQ
+  bergs%pass_fields_to_ocean_model=pass_fields_to_ocean_model
+  bergs%ustar_icebergs_bg=ustar_icebergs_bg
+  bergs%utide_icebergs=utide_icebergs
+  bergs%cdrag_icebergs=cdrag_icebergs
+  bergs%use_mixed_layer_salinity_for_thermo=use_mixed_layer_salinity_for_thermo
+  bergs%find_melt_using_spread_mass=find_melt_using_spread_mass
+  bergs%Use_three_equation_model=Use_three_equation_model
+  bergs%melt_icebergs_as_ice_shelf=melt_icebergs_as_ice_shelf
+  bergs%Iceberg_melt_without_decay=Iceberg_melt_without_decay
+  bergs%add_iceberg_thickness_to_SSH=add_iceberg_thickness_to_SSH
+  bergs%override_iceberg_velocities=override_iceberg_velocities
+  bergs%use_f_plane=use_f_plane
+  bergs%rotate_icebergs_for_mass_spreading=rotate_icebergs_for_mass_spreading
+  bergs%lat_ref=lat_ref
+  bergs%u_override=u_override
+  bergs%v_override=v_override
+  bergs%initial_orientation=initial_orientation
+  bergs%set_melt_rates_to_zero=set_melt_rates_to_zero
+  bergs%allow_bergs_to_roll=allow_bergs_to_roll
+  bergs%hexagonal_icebergs=hexagonal_icebergs
+  bergs%ignore_missing_restart_bergs=ignore_missing_restart_bergs
+  bergs%Static_icebergs=Static_icebergs
+  bergs%only_interactive_forces=only_interactive_forces
+  bergs%halo_debugging=halo_debugging
+  bergs%iceberg_bonds_on=iceberg_bonds_on   !Alon
+  bergs%manually_initialize_bonds=manually_initialize_bonds   !Alon
+  bergs%length_for_manually_initialize_bonds=length_for_manually_initialize_bonds !Alex
+  bergs%critical_interaction_damping_on=critical_interaction_damping_on   !Alon
+  bergs%interactive_icebergs_on=interactive_icebergs_on   !Alon
+  bergs%use_new_predictive_corrective=use_new_predictive_corrective  !Alon
+  bergs%grounding_fraction=grounding_fraction
+  bergs%add_weight_to_ocean=add_weight_to_ocean
+  bergs%use_old_spreading=use_old_spreading
+  bergs%debug_iceberg_with_id=debug_iceberg_with_id
+  bergs%mts=mts
+  bergs%mts_fast_dt = mts_fast_dt
+  bergs%mts_sub_steps = mts_sub_steps
+  bergs%mts_part = 1
+  bergs%contact_distance=contact_distance
+  bergs%num_contact_cells = max(int(ceiling(contact_distance/(grd%lon(grd%isc+1,grd%jsc)-grd%lon(grd%isc,grd%jsc)))),1)
+  if (halo<bergs%num_contact_cells) then
+	  if (mpp_pe()==0) then
+		  write(stderrunit,'(a,i3)') 'KID, icebergs_init: halo width ',halo
+		  write(stderrunit,'(a,f8.2,a,i3)') 'KID, icebergs_init: contact distance ',bergs%contact_distance,&
+		    ' num contact cells',bergs%num_contact_cells
+		  call error_mesg('KID, ice_bergs_framework_init', &
+		    'halo width must be increased to accomodate specified contact distance!!!', FATAL)
+    endif
   endif
-endif
-allocate( bergs%initial_mass(nclasses) ); bergs%initial_mass(:)=initial_mass(:)
-allocate( bergs%distribution(nclasses) ); bergs%distribution(:)=distribution(:)
-allocate( bergs%mass_scaling(nclasses) ); bergs%mass_scaling(:)=mass_scaling(:)
-allocate( bergs%initial_thickness(nclasses) ); bergs%initial_thickness(:)=initial_thickness(:)
-allocate( bergs%initial_width(nclasses) )
-allocate( bergs%initial_length(nclasses) )
-bergs%initial_width(:)=sqrt(initial_mass(:)/(LoW_ratio*rho_bergs*initial_thickness(:)))
-bergs%initial_length(:)=LoW_ratio*bergs%initial_width(:)
-grd%coastal_drift = coastal_drift
-grd%tidal_drift = tidal_drift
-
-!needed for periodicity
-maxlon_c = grd%lon(grd%iec,grd%jec); minlon_c = grd%lon(grd%isc-1,grd%jsc-1)
-call mpp_max(maxlon_c); call mpp_min(minlon_c)
-grd%maxlon_c=maxlon_c; grd%minlon_c=minlon_c
-
-
-if (read_old_restarts) call error_mesg('KID, ice_bergs_framework_init', 'Setting "read_old_restarts=.true." is obsolete and does nothing!', WARNING)
-
-! Diagnostics
-id_class = diag_axis_init('mass_class', initial_mass, 'kg','Z', 'iceberg mass')
-axes3d(1:2)=axes
-axes3d(3)=id_class
-grd%id_calving=register_diag_field('icebergs', 'calving', axes, Time, &
-   'Incoming Calving mass rate', 'kg/s')
-grd%id_calving_hflx_in=register_diag_field('icebergs', 'calving_hflx_in', axes, Time, &
-   'Incoming Calving heat flux', 'J/s')
-grd%id_accum=register_diag_field('icebergs', 'accum_calving', axes, Time, &
-   'Accumulated calving mass rate', 'kg/s')
-grd%id_unused=register_diag_field('icebergs', 'unused_calving', axes, Time, &
-   'Unused calving mass rate', 'kg/s')
-grd%id_floating_melt=register_diag_field('icebergs', 'melt', axes, Time, &
-   'Melt rate of icebergs + bits', 'kg/(m^2*s)')
-grd%id_melt_m_per_year=register_diag_field('icebergs', 'melt_m_per_year', axes, Time, &
-   'Melt rate of icebergs + bits (m/yr)', 'm/yr')
-grd%id_berg_melt=register_diag_field('icebergs', 'berg_melt', axes, Time, &
-   'Melt rate of icebergs', 'kg/(m^2*s)')
-grd%id_melt_buoy=register_diag_field('icebergs', 'melt_buoy', axes, Time, &
-   'Buoyancy component of iceberg melt rate', 'kg/(m^2*s)')
-grd%id_melt_eros=register_diag_field('icebergs', 'melt_eros', axes, Time, &
-   'Erosion component of iceberg melt rate', 'kg/(m^2*s)')
-grd%id_melt_conv=register_diag_field('icebergs', 'melt_conv', axes, Time, &
-   'Convective component of iceberg melt rate', 'kg/(m^2*s)')
-grd%id_bergy_src=register_diag_field('icebergs', 'bergy_src', axes, Time, &
-   'Mass source of bergy bits', 'kg/(m^2*s)')
-grd%id_bergy_melt=register_diag_field('icebergs', 'bergy_melt', axes, Time, &
-   'Melt rate of bergy bits', 'kg/(m^2*s)')
-grd%id_bergy_mass=register_diag_field('icebergs', 'bergy_mass', axes, Time, &
-   'Bergy bit density field', 'kg/(m^2)')
-grd%id_spread_mass=register_diag_field('icebergs', 'spread_mass', axes, Time, &
-   'Iceberg mass after spreading', 'kg/(m^2)')
-grd%id_spread_area=register_diag_field('icebergs', 'spread_area', axes, Time, &
-   'Iceberg area after spreading', 'm^2/(m^2)')
-grd%id_u_iceberg=register_diag_field('icebergs', 'u_iceberg', axes, Time, &
-   'Iceberg u velocity (m/s)')
-grd%id_v_iceberg=register_diag_field('icebergs', 'v_iceberg', axes, Time, &
-   'Iceberg v velocity (m/s)')
-grd%id_spread_uvel=register_diag_field('icebergs', 'spread_uvel', axes, Time, &
-   'Iceberg u velocity spread (m/s)')
-grd%id_spread_vvel=register_diag_field('icebergs', 'spread_vvel', axes, Time, &
-   'Iceberg v velocity spread (m/s)')
-grd%id_ustar_iceberg=register_diag_field('icebergs', 'ustar_iceberg', axes, Time, &
-   'Iceberg frictional velocity (m/s)')
-grd%id_virtual_area=register_diag_field('icebergs', 'virtual_area', axes, Time, &
-   'Virtual coverage by icebergs', 'm^2')
-grd%id_mass=register_diag_field('icebergs', 'mass', axes, Time, &
-   'Iceberg density field', 'kg/(m^2)')
-grd%id_stored_ice=register_diag_field('icebergs', 'stored_ice', axes3d, Time, &
-   'Accumulated ice mass by class', 'kg')
-grd%id_real_calving=register_diag_field('icebergs', 'real_calving', axes3d, Time, &
-   'Calving into iceberg class', 'kg/s')
-grd%id_rmean_calving=register_diag_field('icebergs', 'running_mean_calving', axes, Time, &
-   'Running mean of calving', 'kg/s')
-grd%id_rmean_calving_hflx=register_diag_field('icebergs', 'running_mean_calving_hflx', axes, Time, &
-   'Running mean of calving heat flux', 'J/s')
-grd%id_count=register_diag_field('icebergs', 'bergs_per_cell', axes, Time, &
-   'Number of bergs per cell', '#')
-grd%id_chksum=register_diag_field('icebergs', 'list_chksum', axes, Time, &
-   'mpp_chksum on bergs in each cell', '#')
-grd%id_uo=register_diag_field('icebergs', 'uo', axes, Time, &
-   'Ocean zonal component of velocity', 'm s^-1')
-grd%id_vo=register_diag_field('icebergs', 'vo', axes, Time, &
-   'Ocean meridional component of velocity', 'm s^-1')
-grd%id_ui=register_diag_field('icebergs', 'ui', axes, Time, &
-   'Ice zonal component of velocity', 'm s^-1')
-grd%id_vi=register_diag_field('icebergs', 'vi', axes, Time, &
-   'Ice meridional component of velocity', 'm s^-1')
-grd%id_ua=register_diag_field('icebergs', 'ua', axes, Time, &
-   'Atmos zonal component of velocity', 'm s^-1')
-grd%id_va=register_diag_field('icebergs', 'va', axes, Time, &
-   'Atmos meridional component of velocity', 'm s^-1')
-grd%id_sst=register_diag_field('icebergs', 'sst', axes, Time, &
-   'Sea surface temperature', 'degrees_C')
-grd%id_sss=register_diag_field('icebergs', 'sss', axes, Time, &
-   'Sea surface salinity', 'psu')
-grd%id_cn=register_diag_field('icebergs', 'cn', axes, Time, &
-   'Sea ice concentration', '(fraction)')
-grd%id_hi=register_diag_field('icebergs', 'hi', axes, Time, &
-   'Sea ice thickness', 'm')
-grd%id_ssh=register_diag_field('icebergs', 'ssh', axes, Time, &
-   'Sea surface hieght', 'm')
-grd%id_fax=register_diag_field('icebergs', 'taux', axes, Time, &
-   'X-stress on ice from atmosphere', 'N m^-2')
-grd%id_fay=register_diag_field('icebergs', 'tauy', axes, Time, &
-   'Y-stress on ice from atmosphere', 'N m^-2')
-grd%id_ocean_depth=register_diag_field('icebergs', 'Depth', axes, Time, &
-   'Ocean Depth', 'm')
-
-! Static fields
-id_class=register_static_field('icebergs', 'lon', axes, &
-   'longitude (corners)', 'degrees_E')
-if (id_class>0) lerr=send_data(id_class, grd%lon(grd%isc:grd%iec,grd%jsc:grd%jec))
-id_class=register_static_field('icebergs', 'lat', axes, &
-   'latitude (corners)', 'degrees_N')
-if (id_class>0) lerr=send_data(id_class, grd%lat(grd%isc:grd%iec,grd%jsc:grd%jec))
-id_class=register_static_field('icebergs', 'area', axes, &
-   'cell area', 'm^2')
-if (id_class>0) lerr=send_data(id_class, grd%area(grd%isc:grd%iec,grd%jsc:grd%jec))
-id_class=register_static_field('icebergs', 'mask', axes, &
-   'wet point mask', 'none')
-if (id_class>0) lerr=send_data(id_class, grd%msk(grd%isc:grd%iec,grd%jsc:grd%jec))
-id_class=register_static_field('icebergs', 'ocean_depth_static', axes, &
-   'ocean depth static', 'm')
-if (id_class>0) lerr=send_data(id_class, grd%ocean_depth(grd%isc:grd%iec,grd%jsc:grd%jec))
-
-if (debug) then
- call grd_chksum2(grd, grd%lon, 'init lon')
- call grd_chksum2(grd, grd%lat, 'init lat')
- call grd_chksum2(grd, grd%lonc, 'init lonc')
- call grd_chksum2(grd, grd%latc, 'init latc')
- call grd_chksum2(grd, grd%area, 'init area')
- call grd_chksum2(grd, grd%msk, 'init msk')
- call grd_chksum2(grd, grd%cos, 'init cos')
- call grd_chksum2(grd, grd%sin, 'init sin')
- call grd_chksum2(grd, grd%ocean_depth, 'init ocean_depth')
-endif
+  allocate( bergs%initial_mass(nclasses) ); bergs%initial_mass(:)=initial_mass(:)
+  allocate( bergs%distribution(nclasses) ); bergs%distribution(:)=distribution(:)
+  allocate( bergs%mass_scaling(nclasses) ); bergs%mass_scaling(:)=mass_scaling(:)
+  allocate( bergs%initial_thickness(nclasses) ); bergs%initial_thickness(:)=initial_thickness(:)
+  allocate( bergs%initial_width(nclasses) )
+  allocate( bergs%initial_length(nclasses) )
+  bergs%initial_width(:)=sqrt(initial_mass(:)/(LoW_ratio*rho_bergs*initial_thickness(:)))
+  bergs%initial_length(:)=LoW_ratio*bergs%initial_width(:)
+  grd%coastal_drift = coastal_drift
+  grd%tidal_drift = tidal_drift
+
+  !needed for periodicity
+  maxlon_c = grd%lon(grd%iec,grd%jec); minlon_c = grd%lon(grd%isc-1,grd%jsc-1)
+  call mpp_max(maxlon_c); call mpp_min(minlon_c)
+  grd%maxlon_c=maxlon_c; grd%minlon_c=minlon_c
+
+  if (read_old_restarts) call error_mesg('KID, ice_bergs_framework_init', 'Setting "read_old_restarts=.true." is obsolete and does nothing!', WARNING)
+
+  ! Diagnostics
+  id_class = diag_axis_init('mass_class', initial_mass, 'kg','Z', 'iceberg mass')
+  axes3d(1:2)=axes
+  axes3d(3)=id_class
+  grd%id_calving=register_diag_field('icebergs', 'calving', axes, Time, &
+     'Incoming Calving mass rate', 'kg/s')
+  grd%id_calving_hflx_in=register_diag_field('icebergs', 'calving_hflx_in', axes, Time, &
+     'Incoming Calving heat flux', 'J/s')
+  grd%id_accum=register_diag_field('icebergs', 'accum_calving', axes, Time, &
+     'Accumulated calving mass rate', 'kg/s')
+  grd%id_unused=register_diag_field('icebergs', 'unused_calving', axes, Time, &
+     'Unused calving mass rate', 'kg/s')
+  grd%id_floating_melt=register_diag_field('icebergs', 'melt', axes, Time, &
+     'Melt rate of icebergs + bits', 'kg/(m^2*s)')
+  grd%id_melt_m_per_year=register_diag_field('icebergs', 'melt_m_per_year', axes, Time, &
+     'Melt rate of icebergs + bits (m/yr)', 'm/yr')
+  grd%id_berg_melt=register_diag_field('icebergs', 'berg_melt', axes, Time, &
+     'Melt rate of icebergs', 'kg/(m^2*s)')
+  grd%id_melt_buoy=register_diag_field('icebergs', 'melt_buoy', axes, Time, &
+     'Buoyancy component of iceberg melt rate', 'kg/(m^2*s)')
+  grd%id_melt_eros=register_diag_field('icebergs', 'melt_eros', axes, Time, &
+     'Erosion component of iceberg melt rate', 'kg/(m^2*s)')
+  grd%id_melt_conv=register_diag_field('icebergs', 'melt_conv', axes, Time, &
+     'Convective component of iceberg melt rate', 'kg/(m^2*s)')
+  grd%id_bergy_src=register_diag_field('icebergs', 'bergy_src', axes, Time, &
+     'Mass source of bergy bits', 'kg/(m^2*s)')
+  grd%id_bergy_melt=register_diag_field('icebergs', 'bergy_melt', axes, Time, &
+     'Melt rate of bergy bits', 'kg/(m^2*s)')
+  grd%id_bergy_mass=register_diag_field('icebergs', 'bergy_mass', axes, Time, &
+     'Bergy bit density field', 'kg/(m^2)')
+  grd%id_spread_mass=register_diag_field('icebergs', 'spread_mass', axes, Time, &
+     'Iceberg mass after spreading', 'kg/(m^2)')
+  grd%id_spread_area=register_diag_field('icebergs', 'spread_area', axes, Time, &
+     'Iceberg area after spreading', 'm^2/(m^2)')
+  grd%id_u_iceberg=register_diag_field('icebergs', 'u_iceberg', axes, Time, &
+     'Iceberg u velocity (m/s)')
+  grd%id_v_iceberg=register_diag_field('icebergs', 'v_iceberg', axes, Time, &
+     'Iceberg v velocity (m/s)')
+  grd%id_spread_uvel=register_diag_field('icebergs', 'spread_uvel', axes, Time, &
+     'Iceberg u velocity spread (m/s)')
+  grd%id_spread_vvel=register_diag_field('icebergs', 'spread_vvel', axes, Time, &
+     'Iceberg v velocity spread (m/s)')
+  grd%id_ustar_iceberg=register_diag_field('icebergs', 'ustar_iceberg', axes, Time, &
+     'Iceberg frictional velocity (m/s)')
+  grd%id_virtual_area=register_diag_field('icebergs', 'virtual_area', axes, Time, &
+     'Virtual coverage by icebergs', 'm^2')
+  grd%id_mass=register_diag_field('icebergs', 'mass', axes, Time, &
+     'Iceberg density field', 'kg/(m^2)')
+  grd%id_stored_ice=register_diag_field('icebergs', 'stored_ice', axes3d, Time, &
+     'Accumulated ice mass by class', 'kg')
+  grd%id_real_calving=register_diag_field('icebergs', 'real_calving', axes3d, Time, &
+     'Calving into iceberg class', 'kg/s')
+  grd%id_rmean_calving=register_diag_field('icebergs', 'running_mean_calving', axes, Time, &
+     'Running mean of calving', 'kg/s')
+  grd%id_rmean_calving_hflx=register_diag_field('icebergs', 'running_mean_calving_hflx', axes, Time, &
+     'Running mean of calving heat flux', 'J/s')
+  grd%id_count=register_diag_field('icebergs', 'bergs_per_cell', axes, Time, &
+     'Number of bergs per cell', '#')
+  grd%id_chksum=register_diag_field('icebergs', 'list_chksum', axes, Time, &
+     'mpp_chksum on bergs in each cell', '#')
+  grd%id_uo=register_diag_field('icebergs', 'uo', axes, Time, &
+     'Ocean zonal component of velocity', 'm s^-1')
+  grd%id_vo=register_diag_field('icebergs', 'vo', axes, Time, &
+     'Ocean meridional component of velocity', 'm s^-1')
+  grd%id_ui=register_diag_field('icebergs', 'ui', axes, Time, &
+     'Ice zonal component of velocity', 'm s^-1')
+  grd%id_vi=register_diag_field('icebergs', 'vi', axes, Time, &
+     'Ice meridional component of velocity', 'm s^-1')
+  grd%id_ua=register_diag_field('icebergs', 'ua', axes, Time, &
+     'Atmos zonal component of velocity', 'm s^-1')
+  grd%id_va=register_diag_field('icebergs', 'va', axes, Time, &
+     'Atmos meridional component of velocity', 'm s^-1')
+  grd%id_sst=register_diag_field('icebergs', 'sst', axes, Time, &
+     'Sea surface temperature', 'degrees_C')
+  grd%id_sss=register_diag_field('icebergs', 'sss', axes, Time, &
+     'Sea surface salinity', 'psu')
+  grd%id_cn=register_diag_field('icebergs', 'cn', axes, Time, &
+     'Sea ice concentration', '(fraction)')
+  grd%id_hi=register_diag_field('icebergs', 'hi', axes, Time, &
+     'Sea ice thickness', 'm')
+  grd%id_ssh=register_diag_field('icebergs', 'ssh', axes, Time, &
+     'Sea surface hieght', 'm')
+  grd%id_fax=register_diag_field('icebergs', 'taux', axes, Time, &
+     'X-stress on ice from atmosphere', 'N m^-2')
+  grd%id_fay=register_diag_field('icebergs', 'tauy', axes, Time, &
+     'Y-stress on ice from atmosphere', 'N m^-2')
+  grd%id_ocean_depth=register_diag_field('icebergs', 'Depth', axes, Time, &
+     'Ocean Depth', 'm')
+
+  ! Static fields
+  id_class=register_static_field('icebergs', 'lon', axes, &
+               'longitude (corners)', 'degrees_E')
+  if (id_class>0) lerr=send_data(id_class, grd%lon(grd%isc:grd%iec,grd%jsc:grd%jec))
+  id_class=register_static_field('icebergs', 'lat', axes, &
+               'latitude (corners)', 'degrees_N')
+  if (id_class>0) lerr=send_data(id_class, grd%lat(grd%isc:grd%iec,grd%jsc:grd%jec))
+  id_class=register_static_field('icebergs', 'area', axes, &
+               'cell area', 'm^2')
+  if (id_class>0) lerr=send_data(id_class, grd%area(grd%isc:grd%iec,grd%jsc:grd%jec))
+  id_class=register_static_field('icebergs', 'mask', axes, &
+               'wet point mask', 'none')
+  if (id_class>0) lerr=send_data(id_class, grd%msk(grd%isc:grd%iec,grd%jsc:grd%jec))
+  id_class=register_static_field('icebergs', 'ocean_depth_static', axes, &
+               'ocean depth static', 'm')
+  if (id_class>0) lerr=send_data(id_class, grd%ocean_depth(grd%isc:grd%iec,grd%jsc:grd%jec))
 
-if (do_unit_tests) then
- if (unit_tests(bergs)) call error_mesg('KID, icebergs_init', 'Unit tests failed!', FATAL)
-endif
+  if (debug) then
+    call grd_chksum2(grd, grd%lon, 'init lon')
+    call grd_chksum2(grd, grd%lat, 'init lat')
+    call grd_chksum2(grd, grd%lonc, 'init lonc')
+    call grd_chksum2(grd, grd%latc, 'init latc')
+    call grd_chksum2(grd, grd%area, 'init area')
+    call grd_chksum2(grd, grd%msk, 'init msk')
+    call grd_chksum2(grd, grd%cos, 'init cos')
+    call grd_chksum2(grd, grd%sin, 'init sin')
+    call grd_chksum2(grd, grd%ocean_depth, 'init ocean_depth')
+  endif
+
+  if (do_unit_tests) then
+   if (unit_tests(bergs)) call error_mesg('KID, icebergs_init', 'Unit tests failed!', FATAL)
+  endif
 
-!write(stderrunit,*) 'KID: done'
-call mpp_clock_end(bergs%clock_ini)
-call mpp_clock_end(bergs%clock)
+ !write(stderrunit,*) 'KID: done'
+  call mpp_clock_end(bergs%clock_ini)
+  call mpp_clock_end(bergs%clock)
 
 end subroutine ice_bergs_framework_init
 
@@ -1380,7 +1379,7 @@ subroutine update_halo_icebergs(bergs)
 
   do grdj = grd%jsd,grd%jed ;    do grdi = grd%iec+1,grd%ied
     call delete_all_bergs_in_list(bergs,grdj,grdi)
-  enddo; enddo
+  enddo ; enddo
 
   if (bergs%mts) then
     !remove conglomerate bergs outside halo
@@ -1394,7 +1393,7 @@ subroutine update_halo_icebergs(bergs)
         end if
       enddo
     enddo;enddo
-  end if  
+  endif
 
   call mpp_sync_self()
 
@@ -1614,9 +1613,9 @@ subroutine update_halo_icebergs(bergs)
   endif
 
   if (bergs%mts) then
-    call mpp_sync_self()    
+    call mpp_sync_self()
     call transfer_mts_bergs(bergs)
-  end if  
+  end if
 
   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!Debugging!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
   if (debug) then
@@ -1695,10 +1694,10 @@ subroutine transfer_mts_bergs(bergs)
 
   ! For convenience
   grd=>bergs%grd
-  
+
   Lx = grd%Lx
   periodicityfix=.false.
-  
+
   nbergs_to_send_e=0
   nbergs_to_send_w=0
 
@@ -1709,7 +1708,7 @@ subroutine transfer_mts_bergs(bergs)
   !---Step A. summary of current halo_berg statuses on current PE---
   !halo_berg=0: bergs on computational domain
   !halo_berg=1: bergs on halo domain
-  
+
   ! Send all berg elements (east/west) in conglomerate:
   ! conglomerate berg elements to send EAST:
   last_berg=-1
@@ -1719,8 +1718,8 @@ subroutine transfer_mts_bergs(bergs)
     this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
       !mark conglomerate elements west of the eastern halo as
-      !halo_berg = halo_berg+2 (so their new halo_berg will equal 2 or 3)      
-      call mts_mark_conglomerate_bergs(this,grdi,1) 
+      !halo_berg = halo_berg+2 (so their new halo_berg will equal 2 or 3)
+      call mts_mark_conglomerate_bergs(this,grdi,1)
       this=>this%next
     enddo
   enddo
@@ -1741,14 +1740,14 @@ subroutine transfer_mts_bergs(bergs)
           kick_the_bucket%halo_berg=2.
           nbergs_to_send_e=nbergs_to_send_e+1
           if (periodicityfix) kick_the_bucket%lon=kick_the_bucket%lon-Lx
-          call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_e, nbergs_to_send_e, bergs%max_bonds)        
+          call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_e, nbergs_to_send_e, bergs%max_bonds)
           !kick_the_bucket%halo_berg=current_halo_status-2 !unmark
           kick_the_bucket%halo_berg=current_halo_status
           last_berg=kick_the_bucket%id
           if (periodicityfix) kick_the_bucket%lon=kick_the_bucket%lon+Lx
         else
           this=>this%next
-        end if
+        endif
       enddo
     enddo
   enddo
@@ -1774,7 +1773,7 @@ subroutine transfer_mts_bergs(bergs)
           if (grdi<last_cell) last_cell=grdi
           do grdj2=max(grdj-nc,grd%jsd+1),min(grdj+nc,grd%jed); &
             do grdi2=max(grdi-nc,grd%isd+1),min(grdi+nc,grd%iec-halo_width+1) !inner cell loop
-            !if (grdi2>grd%iec-halo_width+1) cycle !don't process east halo cells 
+            !if (grdi2>grd%iec-halo_width+1) cycle !don't process east halo cells
             kick_the_bucket=>bergs%list(grdi2,grdj2)%first
             do while (associated(kick_the_bucket)) ! inner berg loop
               if (kick_the_bucket%halo_berg < 2) then
@@ -1822,7 +1821,7 @@ subroutine transfer_mts_bergs(bergs)
     do grdj = grd%jsd+1,grd%jed
       this=>bergs%list(grdi,grdj)%first
       do while (associated(this))
-        if (this%halo_berg>1) then 
+        if (this%halo_berg>1) then
           if (this%halo_berg<4) then
             this%halo_berg=this%halo_berg-2
           else
@@ -1836,12 +1835,12 @@ subroutine transfer_mts_bergs(bergs)
 
   !---Step D: updated summary of current halo_berg statuses on current PE---
   ! Same as Step A summary
-  
+
 
   !----now do Steps A-D for the bergs to send west:----
-  ! conglomerate berg elements to send WEST:  
-  last_berg=-1  
-  if (Lx>0.0 .and. grd%lon(grd%isc-1,grd%jsc-1).eq. grd%minlon_c) periodicityfix=.true.  
+  ! conglomerate berg elements to send WEST:
+  last_berg=-1
+  if (Lx>0.0 .and. grd%lon(grd%isc-1,grd%jsc-1).eq. grd%minlon_c) periodicityfix=.true.
   grdi = grd%isc+halo_width-1
   do grdj = grd%jsd+1,grd%jed
     this=>bergs%list(grdi,grdj)%first
@@ -1870,11 +1869,11 @@ subroutine transfer_mts_bergs(bergs)
           call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_w, nbergs_to_send_w, bergs%max_bonds)
           !kick_the_bucket%halo_berg=current_halo_status-2 !unmark
           kick_the_bucket%halo_berg=current_halo_status
-          last_berg=kick_the_bucket%id          
+          last_berg=kick_the_bucket%id
           if (periodicityfix) kick_the_bucket%lon=kick_the_bucket%lon-Lx
         else
           this=>this%next
-        end if
+        endif
       enddo
     enddo
   enddo
@@ -1900,7 +1899,7 @@ subroutine transfer_mts_bergs(bergs)
                 dx=kick_the_bucket%lon-this%lon
                 dy=kick_the_bucket%lat-this%lat
                 dist=dx*dx+dy*dy
-                if (dist<contact_distance*contact_distance) then                
+                if (dist<contact_distance*contact_distance) then
                   current_halo_status=kick_the_bucket%halo_berg+4
                   kick_the_bucket%halo_berg=10
                   nbergs_to_send_w=nbergs_to_send_w+1
@@ -1927,7 +1926,7 @@ subroutine transfer_mts_bergs(bergs)
     enddo !outer cell j-loop
     if (leavedo) exit
   enddo !outer cell i-loop
-  
+
   periodicityfix=.false.
   leavedo=.false.
 
@@ -1936,7 +1935,7 @@ subroutine transfer_mts_bergs(bergs)
     do grdj = grd%jsd+1,grd%jed
       this=>bergs%list(grdi,grdj)%first
       do while (associated(this))
-        if (this%halo_berg>1) then 
+        if (this%halo_berg>1) then
           if (this%halo_berg<4) then
             this%halo_berg=this%halo_berg-2
           else
@@ -2010,17 +2009,15 @@ subroutine transfer_mts_bergs(bergs)
   !             within contact distance to any of the current PE bergs with halo_berg==1 or 2
 
   !reconnect bonds in preparation for sending north/south
-  call mpp_sync_self() 
+  call mpp_sync_self()
   call connect_all_bonds(bergs,ignore_unmatched=.true.)
   do grdj = grd%jsd+1,grd%jed ;  do grdi = grd%isd+1,grd%ied
     this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
-      !conglomerate elements from the E/W transfers now have berg%halo_berg==2 or 3, and
-      !
       !The conglomerate elements for the N/S transfers will also be given halo_berg>1 below.
       !Before the N/S transfer procedure, temporarily change the sign of the conglomerate
       !halo_berg statuses from the E/W transfers to differentiate between the E/W vs N/S procedures.
-      if (this%halo_berg>1) this%halo_berg=-this%halo_berg      
+      if (this%halo_berg>1) this%halo_berg=-this%halo_berg
       this=>this%next
     enddo
   enddo; enddo
@@ -2029,8 +2026,8 @@ subroutine transfer_mts_bergs(bergs)
   nbergs_to_send_s=0
 
   ! ---Send all berg elements (north/south) in conglomerate---:
-  ! conglomerate berg elements to send NORTH:  
-  last_berg=-1  
+  ! conglomerate berg elements to send NORTH:
+  last_berg=-1
   do grdj = grd%jec-halo_width+2,grd%jed; do grdi = grd%isd+1,grd%ied
     this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
@@ -2058,10 +2055,10 @@ subroutine transfer_mts_bergs(bergs)
           call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_n, nbergs_to_send_n, bergs%max_bonds)
           !kick_the_bucket%halo_berg=-(current_halo_status-2) !unmark
           kick_the_bucket%halo_berg=current_halo_status
-          last_berg=kick_the_bucket%id   
+          last_berg=kick_the_bucket%id
         else
           this=>this%next
-        end if
+        endif
       enddo
     enddo
   enddo
@@ -2090,7 +2087,7 @@ subroutine transfer_mts_bergs(bergs)
           !contact distance, and add to buffer
           if (grdj<last_cell) last_cell=grdj
           do grdj2=max(grdj-nc,grd%jsd+1),min(grdj+nc,grd%jec-halo_width+1) !inner cell j-loop
-            !if (grdj2>grd%jec-halo_width+1) cycle !don't process east halo cells 
+            !if (grdj2>grd%jec-halo_width+1) cycle !don't process east halo cells
             do grdi2=max(grdi-nc,grd%isd+1),min(grdi+nc,grd%ied) !inner cell i-loop
               kick_the_bucket=>bergs%list(grdi2,grdj2)%first
               do while (associated(kick_the_bucket)) ! inner berg loop
@@ -2098,9 +2095,9 @@ subroutine transfer_mts_bergs(bergs)
                   dx=kick_the_bucket%lon-this%lon
                   dy=kick_the_bucket%lat-this%lat
                   dist=dx*dx+dy*dy
-                  if (dist<contact_distance*contact_distance) then                  
+                  if (dist<contact_distance*contact_distance) then
                     current_halo_status=kick_the_bucket%halo_berg+111 !guaranteed to be above 100
-                    kick_the_bucket%halo_berg=10 
+                    kick_the_bucket%halo_berg=10
                     nbergs_to_send_e=nbergs_to_send_n+1
                     call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_n, nbergs_to_send_n, bergs%max_bonds)
                     kick_the_bucket%halo_berg=current_halo_status
@@ -2132,7 +2129,7 @@ subroutine transfer_mts_bergs(bergs)
     do grdi = grd%isd+1,grd%ied
       this=>bergs%list(grdi,grdj)%first
       do while (associated(this))
-        if (this%halo_berg>1) then 
+        if (this%halo_berg>1) then
           if (this%halo_berg<4) then
             this%halo_berg=this%halo_berg-2
           elseif (this%halo_berg>100) then
@@ -2144,12 +2141,12 @@ subroutine transfer_mts_bergs(bergs)
         this=>this%next
       enddo
     enddo
-  enddo  
+  enddo
 
   !--do the same for transfers to SOUTH--
 
-  ! conglomerate berg elements to send SOUTH:  
-  last_berg=-1  
+  ! conglomerate berg elements to send SOUTH:
+  last_berg=-1
   do grdj = grd%jsd+1,grd%jsc+halo_width-1; do grdi = grd%isd,grd%ied
     this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
@@ -2177,7 +2174,7 @@ subroutine transfer_mts_bergs(bergs)
           call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_s, nbergs_to_send_s, bergs%max_bonds)
           !kick_the_bucket%halo_berg=-(current_halo_status-2) !unmark
           kick_the_bucket%halo_berg=current_halo_status
-          last_berg=kick_the_bucket%id    
+          last_berg=kick_the_bucket%id
         else
           this=>this%next
         end if
@@ -2206,7 +2203,7 @@ subroutine transfer_mts_bergs(bergs)
                   dx=kick_the_bucket%lon-this%lon
                   dy=kick_the_bucket%lat-this%lat
                   dist=dx*dx+dy*dy
-                  if (dist<contact_distance*contact_distance) then                  
+                  if (dist<contact_distance*contact_distance) then
                     current_halo_status=kick_the_bucket%halo_berg+111
                     kick_the_bucket%halo_berg=10
                     nbergs_to_send_n=nbergs_to_send_n+1
@@ -2232,7 +2229,7 @@ subroutine transfer_mts_bergs(bergs)
     enddo !outer cell i-loop
     if (leavedo) exit
   enddo !outer cell j-loop
-  
+
   leavedo=.false.
 
   !now go back and reset berg halo statuses that are being sent SOUTH to the way it was in Step E above
@@ -2240,7 +2237,7 @@ subroutine transfer_mts_bergs(bergs)
     do grdi = grd%isd+1,grd%ied
       this=>bergs%list(grdi,grdj)%first
       do while (associated(this))
-        if (this%halo_berg>1) then 
+        if (this%halo_berg>1) then
           if (this%halo_berg<4) then
             this%halo_berg=this%halo_berg-2
           elseif (this%halo_berg>100) then
@@ -2251,7 +2248,7 @@ subroutine transfer_mts_bergs(bergs)
         elseif (this%halo_berg<0) then
           this%halo_berg=abs(this%halo_berg)
         endif
-        this=>this%next        
+        this=>this%next
       enddo
     enddo
   enddo
@@ -2329,7 +2326,7 @@ subroutine transfer_mts_bergs(bergs)
   endif
 
   call mpp_sync_self()
-  
+
   ! For debugging
   if (halo_debugging) then
     call mpp_sync_self()
@@ -2355,7 +2352,7 @@ recursive subroutine mts_mark_conglomerate_bergs(berg,completedcell,dir)
   integer :: k
   type(iceberg), pointer :: other_berg
   type(bond) , pointer :: current_bond
-  
+
   current_bond=>berg%first_bond
   do while (associated(current_bond))
     if  (associated(current_bond%other_berg)) then
@@ -2365,7 +2362,7 @@ recursive subroutine mts_mark_conglomerate_bergs(berg,completedcell,dir)
         if (dir==1) then
           !mark other berg if not already marked, and not in halo cell (which has already been processed)
           if (other_berg%halo_berg<2 .and. other_berg%ine .lt. completedcell) then
-            other_berg%halo_berg=other_berg%halo_berg+2 
+            other_berg%halo_berg=other_berg%halo_berg+2
             call mts_mark_conglomerate_bergs(other_berg,completedcell,dir)
           end if
         else
@@ -2386,7 +2383,7 @@ recursive subroutine mts_mark_conglomerate_bergs(berg,completedcell,dir)
           end if
         else
           !to south
-          if ((other_berg%halo_berg<2 .and. other_berg%jne .gt. completedcell) .or. other_berg%halo_berg<1) then          
+          if ((other_berg%halo_berg<2 .and. other_berg%jne .gt. completedcell) .or. other_berg%halo_berg<1) then
             other_berg%halo_berg=abs(other_berg%halo_berg)+2
             call mts_mark_conglomerate_bergs(other_berg,completedcell,dir)
           end if
@@ -2717,14 +2714,14 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
   call split_id(berg%id, id_cnt, id_ij)
   call push_buffer_value(buff%data(:,n), counter, id_cnt)
   call push_buffer_value(buff%data(:,n), counter, id_ij)
-  
+
   if (mts) then
     call push_buffer_value(buff%data(:,n), counter, berg%uvel_prev)
     call push_buffer_value(buff%data(:,n), counter, berg%vvel_prev)
     call push_buffer_value(buff%data(:,n), counter, berg%axn_fast)
     call push_buffer_value(buff%data(:,n), counter, berg%ayn_fast)
     call push_buffer_value(buff%data(:,n), counter, berg%bxn_fast)
-    call push_buffer_value(buff%data(:,n), counter, berg%byn_fast)  
+    call push_buffer_value(buff%data(:,n), counter, berg%byn_fast)
     call push_buffer_value(buff%data(:,n), counter, berg%uo)
     call push_buffer_value(buff%data(:,n), counter, berg%vo)
     call push_buffer_value(buff%data(:,n), counter, berg%ua)
@@ -2738,7 +2735,7 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
     call push_buffer_value(buff%data(:,n), counter, berg%cn)
     call push_buffer_value(buff%data(:,n), counter, berg%hi)
   endif
-  
+
   if (max_bonds .gt. 0) then
     current_bond=>berg%first_bond
     do k = 1,max_bonds
@@ -2849,26 +2846,26 @@ end subroutine clear_berg_from_partners_bonds
 
 !> Unpacks a berg entry from a buffer to a new berg
 subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds_in)
-  ! Arguments
-  type(icebergs), pointer :: bergs !< Container for all types and memory
-  type(buffer), pointer :: buff !< Buffer from which to unpack berg
-  integer, intent(in) :: n !< Position in buffer to unpack
-  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
-  logical, optional :: force_append !< <undocumented>
-  integer, optional :: max_bonds_in !< <undocumented>
-  ! Local variables
-  !real :: lon, lat, uvel, vvel, xi, yj
-  !real :: start_lon, start_lat, start_day, start_mass
-  !integer :: ine, jne, start_year
-  logical :: lres
-  type(iceberg) :: localberg
-  type(iceberg), pointer :: this,kick_the_bucket
-  integer :: other_berg_ine, other_berg_jne
-  integer :: counter, k, max_bonds, id_cnt, id_ij
-  integer(kind=8) :: id
-  integer :: stderrunit
-  logical :: force_app,duplicate
-  real :: temp_lon,temp_lat
+! Arguments
+type(icebergs), pointer :: bergs !< Container for all types and memory
+type(buffer), pointer :: buff !< Buffer from which to unpack berg
+integer, intent(in) :: n !< Position in buffer to unpack
+type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+logical, optional :: force_append !< <undocumented>
+integer, optional :: max_bonds_in !< <undocumented>
+! Local variables
+!real :: lon, lat, uvel, vvel, xi, yj
+!real :: start_lon, start_lat, start_day, start_mass
+!integer :: ine, jne, start_year
+logical :: lres
+type(iceberg) :: localberg
+type(iceberg), pointer :: this,kick_the_bucket
+integer :: other_berg_ine, other_berg_jne
+integer :: counter, k, max_bonds, id_cnt, id_ij
+integer(kind=8) :: id
+integer :: stderrunit
+logical :: force_app,duplicate
+real :: temp_lon,temp_lat
 
   ! Get the stderr unit number
   stderrunit = stderr()
@@ -2912,11 +2909,11 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
 
   if (bergs%mts) then
     call pull_buffer_value(buff%data(:,n), counter, localberg%uvel_prev)
-    call pull_buffer_value(buff%data(:,n), counter, localberg%vvel_prev)    
+    call pull_buffer_value(buff%data(:,n), counter, localberg%vvel_prev)
     call pull_buffer_value(buff%data(:,n), counter, localberg%axn_fast)
     call pull_buffer_value(buff%data(:,n), counter, localberg%ayn_fast)
     call pull_buffer_value(buff%data(:,n), counter, localberg%bxn_fast)
-    call pull_buffer_value(buff%data(:,n), counter, localberg%byn_fast)  
+    call pull_buffer_value(buff%data(:,n), counter, localberg%byn_fast)
     call pull_buffer_value(buff%data(:,n), counter, localberg%uo)
     call pull_buffer_value(buff%data(:,n), counter, localberg%vo)
     call pull_buffer_value(buff%data(:,n), counter, localberg%ua)
@@ -3132,7 +3129,6 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj)
   call split_id(traj%id, cnt, ij)
   call push_buffer_value(buff%data(:,n),counter,cnt)
   call push_buffer_value(buff%data(:,n),counter,ij)
-  
   if (.not. save_short_traj) then
     call push_buffer_value(buff%data(:,n),counter,traj%uvel)
     call push_buffer_value(buff%data(:,n),counter,traj%vvel)
@@ -3156,7 +3152,7 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj)
     call push_buffer_value(buff%data(:,n),counter,traj%axn)
     call push_buffer_value(buff%data(:,n),counter,traj%ayn)
     call push_buffer_value(buff%data(:,n),counter,traj%bxn)
-    call push_buffer_value(buff%data(:,n),counter,traj%byn)  
+    call push_buffer_value(buff%data(:,n),counter,traj%byn)
     call push_buffer_value(buff%data(:,n),counter,traj%halo_berg)
     call push_buffer_value(buff%data(:,n),counter,traj%static_berg)
     call push_buffer_value(buff%data(:,n),counter,traj%sss)
@@ -3216,14 +3212,14 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj)
     call pull_buffer_value(buff%data(:,n),counter,traj%axn)
     call pull_buffer_value(buff%data(:,n),counter,traj%ayn)
     call pull_buffer_value(buff%data(:,n),counter,traj%bxn)
-    call pull_buffer_value(buff%data(:,n),counter,traj%byn)  
+    call pull_buffer_value(buff%data(:,n),counter,traj%byn)
     call pull_buffer_value(buff%data(:,n),counter,traj%halo_berg)
     call pull_buffer_value(buff%data(:,n),counter,traj%static_berg)
     call pull_buffer_value(buff%data(:,n),counter,traj%sss)
 
     if (mts) then
       call pull_buffer_value(buff%data(:,n),counter,traj%uvel_prev)
-      call pull_buffer_value(buff%data(:,n),counter,traj%vvel_prev)      
+      call pull_buffer_value(buff%data(:,n),counter,traj%vvel_prev)
       call pull_buffer_value(buff%data(:,n),counter,traj%axn_fast)
       call pull_buffer_value(buff%data(:,n),counter,traj%ayn_fast)
       call pull_buffer_value(buff%data(:,n),counter,traj%bxn_fast)
@@ -3877,22 +3873,22 @@ subroutine show_all_bonds(bergs)
     do while (associated(berg)) ! loop over all bergs
       current_bond=>berg%first_bond
       do while (associated(current_bond)) ! loop over all bonds
-         !print *, 'Show Bond1 :', berg%id, current_bond%other_id, current_bond%other_berg_ine, current_bond%other_berg_jne,  mpp_pe()
+        !print *, 'Show Bond1 :', berg%id, current_bond%other_id, current_bond%other_berg_ine, current_bond%other_berg_jne,  mpp_pe()
         !write(*,'(a,5i)')'Show Bond1 :',berg%id, current_bond%other_id, current_bond%other_berg_ine, current_bond%other_berg_jne, mpp_pe()
         !print *, 'Current:', berg%id, berg%ine, berg%jne,berg%halo_berg, mpp_pe()
         if  (associated(current_bond%other_berg)) then
           if (current_bond%other_berg%id .ne. current_bond%other_id) then
             !print *, 'Bond matching', berg%id,current_bond%other_berg%id, current_bond%other_id,&
-            !     berg%halo_berg,current_bond%other_berg%halo_berg ,mpp_pe()
+            !  berg%halo_berg,current_bond%other_berg%halo_berg ,mpp_pe()
             write(*,'(a,3i,2i3,i4)')'Bond matching :',berg%id,current_bond%other_berg%id, current_bond%other_id,&
-                 int(berg%halo_berg),current_bond%other_berg%halo_berg ,mpp_pe()
+              int(berg%halo_berg),current_bond%other_berg%halo_berg ,mpp_pe()
             call error_mesg('KID, show all bonds:', 'The bonds are not matching properly!', FATAL)
           endif
         else
             !print *, 'This bond has an non-assosiated other berg :', berg%id, current_bond%other_id,&
-            !     current_bond%other_berg_ine, current_bond%other_berg_jne, berg%halo_berg,  mpp_pe()
+            !  current_bond%other_berg_ine, current_bond%other_berg_jne, berg%halo_berg,  mpp_pe()
          !   write(*,'(a,4i,i3,i4)')'This bond has an non-assosiated other berg :', berg%id, current_bond%other_id,&
-         !        current_bond%other_berg_ine, current_bond%other_berg_jne, int(berg%halo_berg),  mpp_pe()
+         !     current_bond%other_berg_ine, current_bond%other_berg_jne, int(berg%halo_berg),  mpp_pe()
         endif
         current_bond=>current_bond%next_bond
       enddo
@@ -3903,143 +3899,126 @@ subroutine show_all_bonds(bergs)
 end subroutine show_all_bonds
 
 subroutine connect_all_bonds(bergs,ignore_unmatched)
-  type(icebergs), pointer :: bergs !< Container for all types and memory
-  type(iceberg), pointer :: other_berg, berg
-  type(icebergs_gridded), pointer :: grd
-  logical,optional :: ignore_unmatched
-  integer :: i, j
-  integer :: grdi, grdj
-  integer :: grdi_inner, grdj_inner
-  type(bond) , pointer :: current_bond, other_berg_bond
-  logical :: bond_matched, missing_bond, check_bond_quality,check_match
-  integer nbonds
+type(icebergs), pointer :: bergs !< Container for all types and memory
+type(iceberg), pointer :: other_berg, berg
+type(icebergs_gridded), pointer :: grd
+logical,optional :: ignore_unmatched
+integer :: i, j
+integer :: grdi, grdj
+integer :: grdi_inner, grdj_inner
+type(bond) , pointer :: current_bond, other_berg_bond
+logical :: bond_matched, missing_bond, check_bond_quality,check_match
+integer nbonds
 
   check_match = .true.
   if (present(ignore_unmatched)) then
     if (ignore_unmatched) check_match = .false.
   end if
 
-  missing_bond=.false.
-  bond_matched=.false.
+missing_bond=.false.
+bond_matched=.false.
 
-  ! For convenience
+! For convenience
   grd=>bergs%grd
 
-  !If interacting bergs & domain is periodic, then correct lat & lon for halo bergs - Alex   
-  call update_latlon(bergs)   
+  !If interacting bergs & domain is periodic, then correct lat & lon for halo bergs - Alex
+  call update_latlon(bergs)
 
   do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
-     ! do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec  ! Don't connect halo bergs
-     berg=>bergs%list(grdi,grdj)%first
-     do while (associated(berg)) ! loop over all bergs
-
-       if (berg%halo_berg==10) then
-         !these bergs only serve the purpose of exerting a contact force on a conglomerate berg
-         !when bergs%contact_distance>0, and bonds are not needed
-         berg=>berg%next
-         cycle
-       endif
-       
-        current_bond=>berg%first_bond
-        do while (associated(current_bond)) ! loop over all bonds
-           !code to find parter bond goes here
-           if (.not.associated(current_bond%other_berg)) then
-              bond_matched=.false.
-              i = current_bond%other_berg_ine ; j = current_bond%other_berg_jne
-              if ( (i.gt. grd%isd-1) .and. (i .lt. grd%ied+1) .and. (j .gt. grd%jsd-1) .and. (j .lt. grd%jed+1)) then
-                 other_berg=>bergs%list(i,j)%first
-                 do while (associated(other_berg)) ! loop over all other bergs
+! do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec  ! Don't connect halo bergs
+    berg=>bergs%list(grdi,grdj)%first
+    do while (associated(berg)) ! loop over all bergs
+      if (berg%halo_berg==10) then
+        !these bergs only serve the purpose of exerting a contact force on a conglomerate berg
+        !when bergs%contact_distance>0, and bonds are not needed
+        berg=>berg%next
+        cycle
+      endif
+      current_bond=>berg%first_bond
+      do while (associated(current_bond)) ! loop over all bonds
+        !code to find parter bond goes here
+        if (.not.associated(current_bond%other_berg)) then
+          bond_matched=.false.
+          i = current_bond%other_berg_ine ; j = current_bond%other_berg_jne
+          if ( (i.gt. grd%isd-1) .and. (i .lt. grd%ied+1) .and. (j .gt. grd%jsd-1) .and. (j .lt. grd%jed+1)) then
+            other_berg=>bergs%list(i,j)%first
+            do while (associated(other_berg)) ! loop over all other bergs
+              if (other_berg%id .eq. current_bond%other_id) then
+                current_bond%other_berg=>other_berg
+                other_berg=>null()
+                bond_matched=.true.
+              else
+                other_berg=>other_berg%next
+              endif
+            enddo
+          endif
+          if (.not.bond_matched) then
+            ! If you are stil not matched, then search adjacent cells
+            do grdj_inner = j-1,j+1 ; do grdi_inner = i-1,i+1
+              if (.not. bond_matched) then
+                if    ((grdj_inner .gt. grd%jsd-1) .and. (grdj_inner .lt. grd%jed+1)        &
+                .and.  (grdi_inner .gt. grd%isd-1) .and. (grdi_inner .lt. grd%ied+1)      &
+                .and. ((grdi_inner .ne. i) .or. (grdj_inner .ne. j)) ) then
+                  other_berg=>bergs%list(grdi_inner,grdj_inner)%first
+                  do while (associated(other_berg)) ! loop over all other bergs
                     if (other_berg%id .eq. current_bond%other_id) then
-                       current_bond%other_berg=>other_berg
-                       other_berg=>null()
-                       bond_matched=.true.
+                      current_bond%other_berg=>other_berg
+                      other_berg=>null()
+                      bond_matched=.true.
                     else
-                       other_berg=>other_berg%next
-                    endif
-                 enddo
-              endif
-              if (.not.bond_matched) then
-                 ! If you are still not matched, then search adjacent cells (to other berg)
-                 do grdj_inner = j-1,j+1 ; do grdi_inner = i-1,i+1
-                    if (.not. bond_matched) then
-                       if    ((grdj_inner .gt. grd%jsd-1) .and. (grdj_inner .lt. grd%jed+1)        &
-                            .and.  (grdi_inner .gt. grd%isd-1) .and. (grdi_inner .lt. grd%ied+1)      &
-                            .and. ((grdi_inner .ne. i) .or. (grdj_inner .ne. j)) ) then
-                          other_berg=>bergs%list(grdi_inner,grdj_inner)%first
-                          do while (associated(other_berg)) ! loop over all other bergs
-                             if (other_berg%id .eq. current_bond%other_id) then
-                                current_bond%other_berg=>other_berg
-                                other_berg=>null()
-                                bond_matched=.true.
-                             else
-                                other_berg=>other_berg%next
-                             endif
-                          enddo
-                       endif
+                      other_berg=>other_berg%next
                     endif
-                 enddo;enddo
+                  enddo
+                endif
               endif
-              if (.not.bond_matched) then
-                 ! Finally, if still not matched, search adjacent cells to current berg -Alex (periodicity fix)
-                 i = berg%ine; j = berg%jne            
-                 do grdj_inner = j-2,j+2 ; do grdi_inner = i-2,i+2 !probably wider search than necessary...
-                    if (.not. bond_matched) then                    
-                       if    ((grdj_inner .gt. grd%jsd-1) .and. (grdj_inner .lt. grd%jed+1)        &
-                            .and.  (grdi_inner .gt. grd%isd-1) .and. (grdi_inner .lt. grd%ied+1) ) then
-                          other_berg=>bergs%list(grdi_inner,grdj_inner)%first
-                          do while (associated(other_berg)) ! loop over all other bergs
-                             if (other_berg%id .eq. current_bond%other_id) then
-                                current_bond%other_berg=>other_berg
-                                current_bond%other_berg_ine = grdi_inner
-                                current_bond%other_berg_jne = grdj_inner
-                                other_berg=>null()
-                                bond_matched=.true.
-                             else
-                                other_berg=>other_berg%next
-                             endif
-                          enddo
-                       endif
+            enddo;enddo
+          endif
+          if (.not.bond_matched) then
+            ! Finally, if still not matched, search adjacent cells to current berg -Alex (periodicity fix)
+            i = berg%ine; j = berg%jne
+            do grdj_inner = j-2,j+2 ; do grdi_inner = i-2,i+2 !probably wider search than necessary...
+              if (.not. bond_matched) then
+                if ((grdj_inner .gt. grd%jsd-1) .and. (grdj_inner .lt. grd%jed+1) &
+                    .and.  (grdi_inner .gt. grd%isd-1) .and. (grdi_inner .lt. grd%ied+1) ) then
+                  other_berg=>bergs%list(grdi_inner,grdj_inner)%first
+                  do while (associated(other_berg)) ! loop over all other bergs
+                    if (other_berg%id .eq. current_bond%other_id) then
+                      current_bond%other_berg=>other_berg
+                      current_bond%other_berg_ine = grdi_inner
+                      current_bond%other_berg_jne = grdj_inner
+                      other_berg=>null()
+                      bond_matched=.true.
+                    else
+                      other_berg=>other_berg%next
                     endif
-                 enddo;enddo
+                  enddo
+                endif
               endif
+            enddo;enddo
+          endif
 
-              if (check_match .and. .not.bond_matched) then
-                 if (berg%halo_berg .lt. 0.5) then
-                    missing_bond=.true.
-                    print * ,'non-halo berg unmatched: ', berg%id, berg%ine, berg%jne, mpp_pe(), &
-                         current_bond%other_id, current_bond%other_berg_ine, current_bond%other_berg_jne
-                    call error_mesg('KID, connect_all_bonds', 'A non-halo bond is missing!!!', FATAL)
-                 else  ! This is not a problem if the partner berg is not yet in the halo
-                    !if (  (current_bond%other_berg_ine .gt.grd%isd-1) .and. (current_bond%other_berg_ine .lt.grd%ied+1) &
-                    !.and.  (current_bond%other_berg_jne .gt.grd%jsd-1) .and. (current_bond%other_berg_jne .lt.grd%jed+1) ) then
-                   !print * ,'halo berg unmatched: ',mpp_pe(),  berg%id, current_bond%other_id, current_bond%other_berg_ine,current_bond%other_berg_jne
-                   if (bergs%mts) call error_mesg('KID, connect_all_bonds', 'A halo bond is missing!!!', WARNING)
-                   if (bergs%mts) print *,'berg,target,x,y,halo_stat',berg%id,current_bond%other_id,i,j,berg%halo_berg
-                   ! do grdj_inner = j-2,j+2 ; do grdi_inner = i-2,i+2
-                   !   if    ((grdj_inner .gt. grd%jsd-1) .and. (grdj_inner .lt. grd%jed+1)        &
-                   !     .and.  (grdi_inner .gt. grd%isd-1) .and. (grdi_inner .lt. grd%ied+1) ) then
-                   !     other_berg=>bergs%list(grdi_inner,grdj_inner)%first
-                   !     do while (associated(other_berg))
-                   !       print *,'berg,other_berg,ob_halo_stat',berg%id,other_berg%id,other_berg%halo_berg
-                   !       other_berg=>other_berg%next
-                   !     enddo
-                   !   endif
-                   ! enddo;enddo
-                   
-                    !endif
-                 endif
-              endif
-           endif
-           current_bond=>current_bond%next_bond
-        enddo
-        berg=>berg%next
-     enddo
+          if (check_match .and. .not.bond_matched) then
+            if (berg%halo_berg .lt. 0.5) then
+              missing_bond=.true.
+              print * ,'non-halo berg unmatched: ', berg%id, berg%ine, berg%jne, mpp_pe(), &
+                current_bond%other_id, current_bond%other_berg_ine, current_bond%other_berg_jne
+              call error_mesg('KID, connect_all_bonds', 'A non-halo bond is missing!!!', FATAL)
+            else  ! This is not a problem if the partner berg is not yet in the halo
+              if (bergs%mts) call error_mesg('KID, connect_all_bonds', 'A halo bond is missing!!!', WARNING)
+              if (bergs%mts) print *,'berg,target,x,y,halo_stat',berg%id,current_bond%other_id,i,j,berg%halo_berg
+            endif
+          endif
+        endif
+        current_bond=>current_bond%next_bond
+      enddo
+      berg=>berg%next
+    enddo
   enddo;enddo
 
   if (debug) then
-     check_bond_quality=.true.
-     nbonds=0
-     call count_bonds(bergs, nbonds,check_bond_quality)
+    check_bond_quality=.true.
+    nbonds=0
+    call count_bonds(bergs, nbonds,check_bond_quality)
   endif
 end subroutine connect_all_bonds
 
@@ -4066,7 +4045,7 @@ subroutine update_latlon(bergs)
           if ((.not. bergs%mts) .or. (abs(berg%halo_berg .le. 1))) then
             !for bergs%mts skip halo elements that only exist due to their
             !inclusion in a conglomerate (berg%halo_berg > 1). Their coords have
-            !already been corrected (if needed), as the scheme below would fail.             
+            !already been corrected (if needed), as the scheme below would fail.
             dlon = berg%lon - berg%lon_old
             dlat = berg%lat - berg%lat_old
 
@@ -4077,12 +4056,12 @@ subroutine update_latlon(bergs)
             berg%lat_old = berg%lat-dlat
             !need to update local positon in cell from updated global coords, due to roundoff
             lret=pos_within_cell(grd, berg%lon, berg%lat, berg%ine, berg%jne, berg%xi, berg%yj)
-          end if          
+          endif
           berg=>berg%next
         enddo !loop over all bergs
       enddo; enddo
-    end if
-  end if
+    endif
+  endif
 
 end subroutine update_latlon
 
@@ -4256,7 +4235,7 @@ subroutine record_posn(bergs)
   js=bergs%grd%jsc; je=bergs%grd%jec; is=bergs%grd%isc; ie=bergs%grd%iec
 endif
 
-    do grdj = js,je ; do grdi = is,ie
+  do grdj = js,je ; do grdi = is,ie
     this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
       posn%lon=this%lon
@@ -4288,17 +4267,16 @@ subroutine record_posn(bergs)
         posn%axn=this%axn
         posn%ayn=this%ayn
         posn%bxn=this%bxn
-        posn%byn=this%byn       
+        posn%byn=this%byn
         posn%uvel_old=this%uvel_old
         posn%vvel_old=this%vvel_old
         posn%lon_old=this%lon_old
         posn%lat_old=this%lat_old
         posn%halo_berg=this%halo_berg
         posn%static_berg=this%static_berg
-
         if (bergs%mts) then
           posn%uvel_prev=this%uvel_prev
-          posn%vvel_prev=this%vvel_prev        
+          posn%vvel_prev=this%vvel_prev
           posn%axn_fast=this%axn_fast
           posn%ayn_fast=this%ayn_fast
           posn%bxn_fast=this%bxn_fast
@@ -4397,7 +4375,7 @@ subroutine move_all_trajectories(bergs, delete_bergs)
   delete_bergs_after_moving_traj = .false.
   if (present(delete_bergs)) delete_bergs_after_moving_traj = delete_bergs
   !do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
-    do grdj = bergs%grd%jsd+1,bergs%grd%jed ; do grdi = bergs%grd%isd+1,bergs%grd%ied
+  do grdj = bergs%grd%jsd+1,bergs%grd%jed ; do grdi = bergs%grd%isd+1,bergs%grd%ied
     this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
       next=>this%next
@@ -4653,9 +4631,10 @@ subroutine find_individual_iceberg(bergs, id, ine, jne, berg_found, search_data_
         this=>this%next
       enddo
     enddo ; enddo
-  end subroutine  find_individual_iceberg
+end subroutine  find_individual_iceberg
 
-!> Scans each computational grid cell until is_point_in_cell() is true
+!> Scans each computational grid cell until is_point_in_cell() is true,
+!! checking the current cell first.
 logical function check_and_find_cell(grd, x, y, oi, oj)
 ! Arguments
 type(icebergs_gridded), intent(in) :: grd !< Container for gridded fields
@@ -4672,7 +4651,7 @@ logical function check_and_find_cell(grd, x, y, oi, oj)
   if (is_point_in_cell(grd, x, y, oi, oj)) then
     check_and_find_cell=.true.
         return
-      endif  
+      endif
 endif
 
   oi=-999; oj=-999
@@ -4682,7 +4661,7 @@ logical function check_and_find_cell(grd, x, y, oi, oj)
         return
       endif
     enddo; enddo
-end function check_and_find_cell  
+end function check_and_find_cell
 
 !> Scans each computational grid cell until is_point_in_cell() is true
 logical function find_cell(grd, x, y, oi, oj)
@@ -5582,7 +5561,6 @@ subroutine bergs_chksum(bergs, txt, ignore_halo_violation)
       icnt(this%ine,this%jne)=icnt(this%ine,this%jne)+1
       fld2(i,:) = fld(i,:)*float( icnt(this%ine,this%jne) ) !*float( i )
       grd%tmp(this%ine,this%jne)=grd%tmp(this%ine,this%jne)+time_hash(this)*pos_hash(this)+log(this%mass)
-
       ichk5=ichk5+iberg
       this=>this%next
     enddo
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index adc92b4..8d17383 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -40,7 +40,7 @@ module ice_bergs_io
 use ice_bergs_framework, only: force_all_pes_traj
 use ice_bergs_framework, only: check_for_duplicates_in_parallel
 use ice_bergs_framework, only: split_id, id_from_2_ints, generate_id
-use ice_bergs_framework, only: mts !-alex
+use ice_bergs_framework, only: mts !-Alex
 
 implicit none ; private
 
@@ -777,11 +777,8 @@ subroutine generate_bergs(bergs,Time)
   call get_date(Time, iyr, imon, iday, ihr, imin, isec)
 
   do j=grd%jsc,grd%jec; do i=grd%isc,grd%iec
-     
     if (grd%msk(i,j)>0. .and. abs(grd%latc(i,j))>80.0) then
-       if (max(grd%lat(i,j),grd%lat(i-1,j),grd%lat(i,j-1),grd%lat(i-1,j-1))>89.999) cycle ! Cannot use this at Pole cells
-       
-     
+      if (max(grd%lat(i,j),grd%lat(i-1,j),grd%lat(i,j-1),grd%lat(i-1,j-1))>89.999) cycle ! Cannot use this at Pole cells
       localberg%xi=-999.
       localberg%yj=-999.
       localberg%ine=i
@@ -815,7 +812,7 @@ subroutine generate_bergs(bergs,Time)
       localberg%axn_fast=0. !Alex
       localberg%ayn_fast=0. !Alex
       localberg%bxn_fast=0. !Alex
-      localberg%byn_fast=0. !Alex      
+      localberg%byn_fast=0. !Alex
 
       !Berg A
       call loc_set_berg_pos(grd, 0.9, 0.5, 1., 0., localberg)
@@ -873,7 +870,7 @@ subroutine loc_set_berg_pos(grd, xi, yj, uvel, vvel, berg)
     write(0,*) 'bx=',berg%lon, 'gx=',grd%lon(i-1,j-1), grd%lon(i,j-1), grd%lon(i,j), grd%lon(i-1,j),'cx=', grd%lonc(i,j)
     write(0,*) 'by=',berg%lat, 'gy=',grd%lat(i-1,j-1), grd%lat(i,j-1), grd%lat(i,j), grd%lat(i-1,j),'cy=', grd%latc(i,j)
     stop 'generate_bergs, loc_set_berg_pos(): VERY FATAL!'
-  Endif
+  endif
 end subroutine loc_set_berg_pos
 
 !> Read bond restart file
@@ -1252,26 +1249,26 @@ end subroutine read_ocean_depth
 
 !> Write a trajectory-based diagnostics file
 subroutine write_trajectory(trajectory, save_short_traj)
-  ! Arguments
-  type(xyt), pointer :: trajectory !< An iceberg trajectory
-  logical, intent(in) :: save_short_traj !< If true, record less data
-  ! Local variables
-  integer :: iret, ncid, i_dim, i
-  integer :: lonid, latid, yearid, dayid, uvelid, vvelid, idcntid, idijid
-  integer :: uvelpid,vvelpid
-  integer :: uoid, void, uiid, viid, uaid, vaid, sshxid, sshyid, sstid, sssid
-  integer :: cnid, hiid, hsid
-  integer :: mid, did, wid, lid, mbid, hdid
-  character(len=37) :: filename
-  character(len=7) :: pe_name
-  type(xyt), pointer :: this, next
-  integer :: stderrunit, cnt, ij
-  !I/O vars
-  type(xyt), pointer :: traj4io=>null()
-  integer :: ntrajs_sent_io,ntrajs_rcvd_io
-  integer :: from_pe,np
-  type(buffer), pointer :: obuffer_io=>null(), ibuffer_io=>null()
-  logical :: io_is_in_append_mode
+! Arguments
+type(xyt), pointer :: trajectory !< An iceberg trajectory
+logical, intent(in) :: save_short_traj !< If true, record less data
+! Local variables
+integer :: iret, ncid, i_dim, i
+integer :: lonid, latid, yearid, dayid, uvelid, vvelid, idcntid, idijid
+integer :: uvelpid,vvelpid
+integer :: uoid, void, uiid, viid, uaid, vaid, sshxid, sshyid, sstid, sssid
+integer :: cnid, hiid, hsid
+integer :: mid, did, wid, lid, mbid, hdid
+character(len=37) :: filename
+character(len=7) :: pe_name
+type(xyt), pointer :: this, next
+integer :: stderrunit, cnt, ij
+!I/O vars
+type(xyt), pointer :: traj4io=>null()
+integer :: ntrajs_sent_io,ntrajs_rcvd_io
+integer :: from_pe,np
+type(buffer), pointer :: obuffer_io=>null(), ibuffer_io=>null()
+logical :: io_is_in_append_mode
 
   ! Get the stderr unit number
   stderrunit=stderr()
@@ -1296,38 +1293,38 @@ subroutine write_trajectory(trajectory, save_short_traj)
 
   if(.NOT. force_all_pes_traj ) then
 
-     !Now gather and append the bergs from all pes in the io_tile to the list on corresponding io_tile_root_pe
-     ntrajs_sent_io =0
-     ntrajs_rcvd_io =0
-
-     if(is_io_tile_root_pe) then
-        !Receive trajs from all pes in this I/O tile !FRAGILE!SCARY!
-        do np=2,size(io_tile_pelist) ! Note: np starts from 2 to exclude self
-           from_pe=io_tile_pelist(np)
-           call mpp_recv(ntrajs_rcvd_io, glen=1, from_pe=from_pe, tag=COMM_TAG_11)
-           if (ntrajs_rcvd_io .gt. 0) then
-              call increase_ibuffer(ibuffer_io, ntrajs_rcvd_io,buffer_width_traj)
-              call mpp_recv(ibuffer_io%data, ntrajs_rcvd_io*buffer_width_traj,from_pe=from_pe, tag=COMM_TAG_12)
-              do i=1, ntrajs_rcvd_io
-                 call unpack_traj_from_buffer2(traj4io, ibuffer_io, i, save_short_traj)
-              enddo
-           endif
-        enddo
-     else
-        ! Pack and send trajectories to the root PE for this I/O tile
-        do while (associated(trajectory))
-           ntrajs_sent_io = ntrajs_sent_io +1
-           call pack_traj_into_buffer2(trajectory, obuffer_io, ntrajs_sent_io, save_short_traj)
-           this => trajectory ! Need to keep pointer in order to free up the links memory
-           trajectory => trajectory%next ! This will eventually result in trajectory => null()
-           deallocate(this) ! Delete the link from memory
-        enddo
+  !Now gather and append the bergs from all pes in the io_tile to the list on corresponding io_tile_root_pe
+  ntrajs_sent_io =0
+  ntrajs_rcvd_io =0
+
+  if(is_io_tile_root_pe) then
+     !Receive trajs from all pes in this I/O tile !FRAGILE!SCARY!
+     do np=2,size(io_tile_pelist) ! Note: np starts from 2 to exclude self
+        from_pe=io_tile_pelist(np)
+        call mpp_recv(ntrajs_rcvd_io, glen=1, from_pe=from_pe, tag=COMM_TAG_11)
+        if (ntrajs_rcvd_io .gt. 0) then
+           call increase_ibuffer(ibuffer_io, ntrajs_rcvd_io,buffer_width_traj)
+           call mpp_recv(ibuffer_io%data, ntrajs_rcvd_io*buffer_width_traj,from_pe=from_pe, tag=COMM_TAG_12)
+           do i=1, ntrajs_rcvd_io
+              call unpack_traj_from_buffer2(traj4io, ibuffer_io, i, save_short_traj)
+           enddo
+       endif
+     enddo
+  else
+     ! Pack and send trajectories to the root PE for this I/O tile
+     do while (associated(trajectory))
+       ntrajs_sent_io = ntrajs_sent_io +1
+       call pack_traj_into_buffer2(trajectory, obuffer_io, ntrajs_sent_io, save_short_traj)
+       this => trajectory ! Need to keep pointer in order to free up the links memory
+       trajectory => trajectory%next ! This will eventually result in trajectory => null()
+       deallocate(this) ! Delete the link from memory
+     enddo
 
-        call mpp_send(ntrajs_sent_io, plen=1, to_pe=io_tile_root_pe, tag=COMM_TAG_11)
-        if (ntrajs_sent_io .gt. 0) then
-           call mpp_send(obuffer_io%data, ntrajs_sent_io*buffer_width_traj, to_pe=io_tile_root_pe, tag=COMM_TAG_12)
-        endif
+     call mpp_send(ntrajs_sent_io, plen=1, to_pe=io_tile_root_pe, tag=COMM_TAG_11)
+     if (ntrajs_sent_io .gt. 0) then
+        call mpp_send(obuffer_io%data, ntrajs_sent_io*buffer_width_traj, to_pe=io_tile_root_pe, tag=COMM_TAG_12)
      endif
+  endif
 
   endif !.NOT. force_all_pes_traj
 
@@ -1338,234 +1335,234 @@ subroutine write_trajectory(trajectory, save_short_traj)
 
   if((force_all_pes_traj .OR. is_io_tile_root_pe) .AND. associated(traj4io)) then
 
-     call get_instance_filename("iceberg_trajectories.nc", filename)
-     if(io_tile_id(1) .ge. 0 .AND. .NOT. force_all_pes_traj) then !io_tile_root_pes write
-        if(io_npes .gt. 1) then !attach tile_id  to filename only if there is more than one I/O pe
-           if (io_tile_id(1)<10000) then
-              write(filename,'(A,".",I4.4)') trim(filename), io_tile_id(1)
-           else
-              write(filename,'(A,".",I6.6)') trim(filename), io_tile_id(1)
-           endif
-        endif
-     else !All pes write, attach pe# to filename
-        if (mpp_npes()<10000) then
-           write(filename,'(A,".",I4.4)') trim(filename), mpp_pe()
-        else
-           write(filename,'(A,".",I6.6)') trim(filename), mpp_pe()
-        endif
-     endif
+    call get_instance_filename("iceberg_trajectories.nc", filename)
+    if(io_tile_id(1) .ge. 0 .AND. .NOT. force_all_pes_traj) then !io_tile_root_pes write
+       if(io_npes .gt. 1) then !attach tile_id  to filename only if there is more than one I/O pe
+          if (io_tile_id(1)<10000) then
+             write(filename,'(A,".",I4.4)') trim(filename), io_tile_id(1)
+          else
+             write(filename,'(A,".",I6.6)') trim(filename), io_tile_id(1)
+          endif
+       endif
+    else !All pes write, attach pe# to filename
+       if (mpp_npes()<10000) then
+          write(filename,'(A,".",I4.4)') trim(filename), mpp_pe()
+       else
+          write(filename,'(A,".",I6.6)') trim(filename), mpp_pe()
+       endif
+    endif
 
-     io_is_in_append_mode = .false.
-     iret = nf_create(filename, NF_NOCLOBBER, ncid)
-     if (iret .ne. NF_NOERR) then
-        iret = nf_open(filename, NF_WRITE, ncid)
-        io_is_in_append_mode = .true.
-        if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_trajectory: nf_open failed'
-     endif
-     if (verbose) then
-        if (io_is_in_append_mode) then
-           write(*,'(2a)') 'KID, write_trajectory: appending to ',filename
-        else
-           write(*,'(2a)') 'KID, write_trajectory: creating ',filename
-        endif
-     endif
+    io_is_in_append_mode = .false.
+    iret = nf_create(filename, NF_NOCLOBBER, ncid)
+    if (iret .ne. NF_NOERR) then
+      iret = nf_open(filename, NF_WRITE, ncid)
+      io_is_in_append_mode = .true.
+      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_trajectory: nf_open failed'
+    endif
+    if (verbose) then
+      if (io_is_in_append_mode) then
+        write(*,'(2a)') 'KID, write_trajectory: appending to ',filename
+      else
+        write(*,'(2a)') 'KID, write_trajectory: creating ',filename
+      endif
+    endif
 
-     if (io_is_in_append_mode) then
-        iret = nf_inq_dimid(ncid, 'i', i_dim)
-        if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_trajectory: nf_inq_dimid i failed'
-        lonid = inq_varid(ncid, 'lon')
-        latid = inq_varid(ncid, 'lat')
-        yearid = inq_varid(ncid, 'year')
-        dayid = inq_varid(ncid, 'day')
-        idcntid = inq_varid(ncid, 'id_cnt')
-        idijid = inq_varid(ncid, 'id_ij')
-        if (.not.save_short_traj) then
-           uvelid = inq_varid(ncid, 'uvel')
-           vvelid = inq_varid(ncid, 'vvel')
-           uoid = inq_varid(ncid, 'uo')
-           void = inq_varid(ncid, 'vo')
-           uiid = inq_varid(ncid, 'ui')
-           viid = inq_varid(ncid, 'vi')
-           uaid = inq_varid(ncid, 'ua')
-           vaid = inq_varid(ncid, 'va')
-           mid = inq_varid(ncid, 'mass')
-           mbid = inq_varid(ncid, 'mass_of_bits')
-           hdid = inq_varid(ncid, 'heat_density')
-           did = inq_varid(ncid, 'thickness')
-           wid = inq_varid(ncid, 'width')
-           lid = inq_varid(ncid, 'length')
-           sshxid = inq_varid(ncid, 'ssh_x')
-           sshyid = inq_varid(ncid, 'ssh_y')
-           sstid = inq_varid(ncid, 'sst')
-           sssid = inq_varid(ncid, 'sss')
-           cnid = inq_varid(ncid, 'cn')
-           hiid = inq_varid(ncid, 'hi')
-           hsid = inq_varid(ncid, 'halo_berg')
-           if (mts) then
-             uvelpid = inq_varid(ncid, 'uvel_prev')
-             vvelpid = inq_varid(ncid, 'vvel_prev')             
-           endif
+    if (io_is_in_append_mode) then
+      iret = nf_inq_dimid(ncid, 'i', i_dim)
+      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_trajectory: nf_inq_dimid i failed'
+      lonid = inq_varid(ncid, 'lon')
+      latid = inq_varid(ncid, 'lat')
+      yearid = inq_varid(ncid, 'year')
+      dayid = inq_varid(ncid, 'day')
+      idcntid = inq_varid(ncid, 'id_cnt')
+      idijid = inq_varid(ncid, 'id_ij')
+      if (.not.save_short_traj) then
+        uvelid = inq_varid(ncid, 'uvel')
+        vvelid = inq_varid(ncid, 'vvel')
+        uoid = inq_varid(ncid, 'uo')
+        void = inq_varid(ncid, 'vo')
+        uiid = inq_varid(ncid, 'ui')
+        viid = inq_varid(ncid, 'vi')
+        uaid = inq_varid(ncid, 'ua')
+        vaid = inq_varid(ncid, 'va')
+        mid = inq_varid(ncid, 'mass')
+        mbid = inq_varid(ncid, 'mass_of_bits')
+        hdid = inq_varid(ncid, 'heat_density')
+        did = inq_varid(ncid, 'thickness')
+        wid = inq_varid(ncid, 'width')
+        lid = inq_varid(ncid, 'length')
+        sshxid = inq_varid(ncid, 'ssh_x')
+        sshyid = inq_varid(ncid, 'ssh_y')
+        sstid = inq_varid(ncid, 'sst')
+        sssid = inq_varid(ncid, 'sss')
+        cnid = inq_varid(ncid, 'cn')
+        hiid = inq_varid(ncid, 'hi')
+        hsid = inq_varid(ncid, 'halo_berg')
+        if (mts) then
+          uvelpid = inq_varid(ncid, 'uvel_prev')
+          vvelpid = inq_varid(ncid, 'vvel_prev')
         endif
-     else
-        ! Dimensions
-        iret = nf_def_dim(ncid, 'i', NF_UNLIMITED, i_dim)
-        if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_trajectory: nf_def_dim i failed'
-
-        ! Variables
-        lonid = def_var(ncid, 'lon', NF_DOUBLE, i_dim)
-        latid = def_var(ncid, 'lat', NF_DOUBLE, i_dim)
-        yearid = def_var(ncid, 'year', NF_INT, i_dim)
-        dayid = def_var(ncid, 'day', NF_DOUBLE, i_dim)
-        idcntid = def_var(ncid, 'id_cnt', NF_INT, i_dim)
-        idijid = def_var(ncid, 'id_ij', NF_INT, i_dim)
-        if (.not. save_short_traj) then
-           uvelid = def_var(ncid, 'uvel', NF_DOUBLE, i_dim)
-           vvelid = def_var(ncid, 'vvel', NF_DOUBLE, i_dim)
-           uoid = def_var(ncid, 'uo', NF_DOUBLE, i_dim)
-           void = def_var(ncid, 'vo', NF_DOUBLE, i_dim)
-           uiid = def_var(ncid, 'ui', NF_DOUBLE, i_dim)
-           viid = def_var(ncid, 'vi', NF_DOUBLE, i_dim)
-           uaid = def_var(ncid, 'ua', NF_DOUBLE, i_dim)
-           vaid = def_var(ncid, 'va', NF_DOUBLE, i_dim)
-           mid = def_var(ncid, 'mass', NF_DOUBLE, i_dim)
-           mbid = def_var(ncid, 'mass_of_bits', NF_DOUBLE, i_dim)
-           hdid = def_var(ncid, 'heat_density', NF_DOUBLE, i_dim)
-           did = def_var(ncid, 'thickness', NF_DOUBLE, i_dim)
-           wid = def_var(ncid, 'width', NF_DOUBLE, i_dim)
-           lid = def_var(ncid, 'length', NF_DOUBLE, i_dim)
-           sshxid = def_var(ncid, 'ssh_x', NF_DOUBLE, i_dim)
-           sshyid = def_var(ncid, 'ssh_y', NF_DOUBLE, i_dim)
-           sstid = def_var(ncid, 'sst', NF_DOUBLE, i_dim)
-           sssid = def_var(ncid, 'sss', NF_DOUBLE, i_dim)
-           cnid = def_var(ncid, 'cn', NF_DOUBLE, i_dim)
-           hiid = def_var(ncid, 'hi', NF_DOUBLE, i_dim)
-           hsid = def_var(ncid, 'halo_berg', NF_DOUBLE, i_dim)
-           if (mts) then
-             uvelpid = def_var(ncid, 'uvel_prev', NF_DOUBLE, i_dim)
-             vvelpid = def_var(ncid, 'vvel_prev', NF_DOUBLE, i_dim)                         
-           endif           
+      endif
+    else
+      ! Dimensions
+      iret = nf_def_dim(ncid, 'i', NF_UNLIMITED, i_dim)
+      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_trajectory: nf_def_dim i failed'
+
+      ! Variables
+      lonid = def_var(ncid, 'lon', NF_DOUBLE, i_dim)
+      latid = def_var(ncid, 'lat', NF_DOUBLE, i_dim)
+      yearid = def_var(ncid, 'year', NF_INT, i_dim)
+      dayid = def_var(ncid, 'day', NF_DOUBLE, i_dim)
+      idcntid = def_var(ncid, 'id_cnt', NF_INT, i_dim)
+      idijid = def_var(ncid, 'id_ij', NF_INT, i_dim)
+      if (.not. save_short_traj) then
+        uvelid = def_var(ncid, 'uvel', NF_DOUBLE, i_dim)
+        vvelid = def_var(ncid, 'vvel', NF_DOUBLE, i_dim)
+        uoid = def_var(ncid, 'uo', NF_DOUBLE, i_dim)
+        void = def_var(ncid, 'vo', NF_DOUBLE, i_dim)
+        uiid = def_var(ncid, 'ui', NF_DOUBLE, i_dim)
+        viid = def_var(ncid, 'vi', NF_DOUBLE, i_dim)
+        uaid = def_var(ncid, 'ua', NF_DOUBLE, i_dim)
+        vaid = def_var(ncid, 'va', NF_DOUBLE, i_dim)
+        mid = def_var(ncid, 'mass', NF_DOUBLE, i_dim)
+        mbid = def_var(ncid, 'mass_of_bits', NF_DOUBLE, i_dim)
+        hdid = def_var(ncid, 'heat_density', NF_DOUBLE, i_dim)
+        did = def_var(ncid, 'thickness', NF_DOUBLE, i_dim)
+        wid = def_var(ncid, 'width', NF_DOUBLE, i_dim)
+        lid = def_var(ncid, 'length', NF_DOUBLE, i_dim)
+        sshxid = def_var(ncid, 'ssh_x', NF_DOUBLE, i_dim)
+        sshyid = def_var(ncid, 'ssh_y', NF_DOUBLE, i_dim)
+        sstid = def_var(ncid, 'sst', NF_DOUBLE, i_dim)
+        sssid = def_var(ncid, 'sss', NF_DOUBLE, i_dim)
+        cnid = def_var(ncid, 'cn', NF_DOUBLE, i_dim)
+        hiid = def_var(ncid, 'hi', NF_DOUBLE, i_dim)
+        hsid = def_var(ncid, 'halo_berg', NF_DOUBLE, i_dim)
+        if (mts) then
+          uvelpid = def_var(ncid, 'uvel_prev', NF_DOUBLE, i_dim)
+          vvelpid = def_var(ncid, 'vvel_prev', NF_DOUBLE, i_dim)
         endif
+      endif
 
-        ! Attributes
-        iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_major_version', NF_INT, 1, 0)
-        iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_minor_version', NF_INT, 1, 1)
-        call put_att(ncid, lonid, 'long_name', 'longitude')
-        call put_att(ncid, lonid, 'units', 'degrees_E')
-        call put_att(ncid, latid, 'long_name', 'latitude')
-        call put_att(ncid, latid, 'units', 'degrees_N')
-        call put_att(ncid, yearid, 'long_name', 'year')
-        call put_att(ncid, yearid, 'units', 'years')
-        call put_att(ncid, dayid, 'long_name', 'year day')
-        call put_att(ncid, dayid, 'units', 'days')
-        call put_att(ncid, idcntid, 'long_name', 'counter component of iceberg id')
-        call put_att(ncid, idcntid, 'units', 'dimensionless')
-        call put_att(ncid, idijid, 'long_name', 'position component of iceberg id')
-        call put_att(ncid, idijid, 'units', 'dimensionless')
-
-        if (.not. save_short_traj) then
-           call put_att(ncid, uvelid, 'long_name', 'zonal spped')
-           call put_att(ncid, uvelid, 'units', 'm/s')
-           call put_att(ncid, vvelid, 'long_name', 'meridional spped')
-           call put_att(ncid, vvelid, 'units', 'm/s')
-           call put_att(ncid, uoid, 'long_name', 'ocean zonal spped')
-           call put_att(ncid, uoid, 'units', 'm/s')
-           call put_att(ncid, void, 'long_name', 'ocean meridional spped')
-           call put_att(ncid, void, 'units', 'm/s')
-           call put_att(ncid, uiid, 'long_name', 'ice zonal spped')
-           call put_att(ncid, uiid, 'units', 'm/s')
-           call put_att(ncid, viid, 'long_name', 'ice meridional spped')
-           call put_att(ncid, viid, 'units', 'm/s')
-           call put_att(ncid, uaid, 'long_name', 'atmos zonal spped')
-           call put_att(ncid, uaid, 'units', 'm/s')
-           call put_att(ncid, vaid, 'long_name', 'atmos meridional spped')
-           call put_att(ncid, vaid, 'units', 'm/s')
-           call put_att(ncid, mid, 'long_name', 'mass')
-           call put_att(ncid, mid, 'units', 'kg')
-           call put_att(ncid, mbid, 'long_name', 'mass_of_bits')
-           call put_att(ncid, mbid, 'units', 'kg')
-           call put_att(ncid, hdid, 'long_name', 'heat_density')
-           call put_att(ncid, hdid, 'units', 'J/kg')
-           call put_att(ncid, did, 'long_name', 'thickness')
-           call put_att(ncid, did, 'units', 'm')
-           call put_att(ncid, wid, 'long_name', 'width')
-           call put_att(ncid, wid, 'units', 'm')
-           call put_att(ncid, lid, 'long_name', 'length')
-           call put_att(ncid, lid, 'units', 'm')
-           call put_att(ncid, sshxid, 'long_name', 'sea surface height gradient_x')
-           call put_att(ncid, sshxid, 'units', 'non-dim')
-           call put_att(ncid, sshyid, 'long_name', 'sea surface height gradient_y')
-           call put_att(ncid, sshyid, 'units', 'non-dim')
-           call put_att(ncid, sstid, 'long_name', 'sea surface temperature')
-           call put_att(ncid, sstid, 'units', 'degrees_C')
-           call put_att(ncid, sssid, 'long_name', 'sea surface salinity')
-           call put_att(ncid, sssid, 'units', 'psu')
-           call put_att(ncid, cnid, 'long_name', 'sea ice concentration')
-           call put_att(ncid, cnid, 'units', 'none')
-           call put_att(ncid, hiid, 'long_name', 'sea ice thickness')
-           call put_att(ncid, hiid, 'units', 'm')
-           call put_att(ncid, hsid, 'long_name', 'halo status')
-           call put_att(ncid, hsid, 'units', 'non-dim')
-           if (mts) then
-             call put_att(ncid, uvelpid, 'long_name', 'zonal speed mts')
-             call put_att(ncid, uvelpid, 'units', 'm/s')
-             call put_att(ncid, vvelpid, 'long_name', 'meridional speed mts')
-             call put_att(ncid, vvelpid, 'units', 'm/s')                        
-           endif             
+      ! Attributes
+      iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_major_version', NF_INT, 1, 0)
+      iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_minor_version', NF_INT, 1, 1)
+      call put_att(ncid, lonid, 'long_name', 'longitude')
+      call put_att(ncid, lonid, 'units', 'degrees_E')
+      call put_att(ncid, latid, 'long_name', 'latitude')
+      call put_att(ncid, latid, 'units', 'degrees_N')
+      call put_att(ncid, yearid, 'long_name', 'year')
+      call put_att(ncid, yearid, 'units', 'years')
+      call put_att(ncid, dayid, 'long_name', 'year day')
+      call put_att(ncid, dayid, 'units', 'days')
+      call put_att(ncid, idcntid, 'long_name', 'counter component of iceberg id')
+      call put_att(ncid, idcntid, 'units', 'dimensionless')
+      call put_att(ncid, idijid, 'long_name', 'position component of iceberg id')
+      call put_att(ncid, idijid, 'units', 'dimensionless')
+
+      if (.not. save_short_traj) then
+        call put_att(ncid, uvelid, 'long_name', 'zonal spped')
+        call put_att(ncid, uvelid, 'units', 'm/s')
+        call put_att(ncid, vvelid, 'long_name', 'meridional spped')
+        call put_att(ncid, vvelid, 'units', 'm/s')
+        call put_att(ncid, uoid, 'long_name', 'ocean zonal spped')
+        call put_att(ncid, uoid, 'units', 'm/s')
+        call put_att(ncid, void, 'long_name', 'ocean meridional spped')
+        call put_att(ncid, void, 'units', 'm/s')
+        call put_att(ncid, uiid, 'long_name', 'ice zonal spped')
+        call put_att(ncid, uiid, 'units', 'm/s')
+        call put_att(ncid, viid, 'long_name', 'ice meridional spped')
+        call put_att(ncid, viid, 'units', 'm/s')
+        call put_att(ncid, uaid, 'long_name', 'atmos zonal spped')
+        call put_att(ncid, uaid, 'units', 'm/s')
+        call put_att(ncid, vaid, 'long_name', 'atmos meridional spped')
+        call put_att(ncid, vaid, 'units', 'm/s')
+        call put_att(ncid, mid, 'long_name', 'mass')
+        call put_att(ncid, mid, 'units', 'kg')
+        call put_att(ncid, mbid, 'long_name', 'mass_of_bits')
+        call put_att(ncid, mbid, 'units', 'kg')
+        call put_att(ncid, hdid, 'long_name', 'heat_density')
+        call put_att(ncid, hdid, 'units', 'J/kg')
+        call put_att(ncid, did, 'long_name', 'thickness')
+        call put_att(ncid, did, 'units', 'm')
+        call put_att(ncid, wid, 'long_name', 'width')
+        call put_att(ncid, wid, 'units', 'm')
+        call put_att(ncid, lid, 'long_name', 'length')
+        call put_att(ncid, lid, 'units', 'm')
+        call put_att(ncid, sshxid, 'long_name', 'sea surface height gradient_x')
+        call put_att(ncid, sshxid, 'units', 'non-dim')
+        call put_att(ncid, sshyid, 'long_name', 'sea surface height gradient_y')
+        call put_att(ncid, sshyid, 'units', 'non-dim')
+        call put_att(ncid, sstid, 'long_name', 'sea surface temperature')
+        call put_att(ncid, sstid, 'units', 'degrees_C')
+        call put_att(ncid, sssid, 'long_name', 'sea surface salinity')
+        call put_att(ncid, sssid, 'units', 'psu')
+        call put_att(ncid, cnid, 'long_name', 'sea ice concentration')
+        call put_att(ncid, cnid, 'units', 'none')
+        call put_att(ncid, hiid, 'long_name', 'sea ice thickness')
+        call put_att(ncid, hiid, 'units', 'm')
+        call put_att(ncid, hsid, 'long_name', 'halo status')
+        call put_att(ncid, hsid, 'units', 'non-dim')
+        if (mts) then
+          call put_att(ncid, uvelpid, 'long_name', 'zonal speed mts')
+          call put_att(ncid, uvelpid, 'units', 'm/s')
+          call put_att(ncid, vvelpid, 'long_name', 'meridional speed mts')
+          call put_att(ncid, vvelpid, 'units', 'm/s')
         endif
-     endif
+      endif
+    endif
 
-     ! End define mode
-     iret = nf_enddef(ncid)
+    ! End define mode
+    iret = nf_enddef(ncid)
 
-     ! Write variables
-     this=>traj4io
-     if (io_is_in_append_mode) then
-        iret = nf_inq_dimlen(ncid, i_dim, i)
-        if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_trajectory: nf_inq_dimlen i failed'
-     else
-        i = 0
-     endif
-     do while (associated(this))
-        i=i+1
-        call put_double(ncid, lonid, i, this%lon)
-        call put_double(ncid, latid, i, this%lat)
-        call put_int(ncid, yearid, i, this%year)
-        call put_double(ncid, dayid, i, this%day)
-        call split_id(this%id, cnt, ij)
-        call put_int(ncid, idcntid, i, cnt)
-        call put_int(ncid, idijid, i, ij)
-        if (.not. save_short_traj) then
-           call put_double(ncid, uvelid, i, this%uvel)
-           call put_double(ncid, vvelid, i, this%vvel)
-           call put_double(ncid, uoid, i, this%uo)
-           call put_double(ncid, void, i, this%vo)
-           call put_double(ncid, uiid, i, this%ui)
-           call put_double(ncid, viid, i, this%vi)
-           call put_double(ncid, uaid, i, this%ua)
-           call put_double(ncid, vaid, i, this%va)
-           call put_double(ncid, mid, i, this%mass)
-           call put_double(ncid, hdid, i, this%heat_density)
-           call put_double(ncid, did, i, this%thickness)
-           call put_double(ncid, wid, i, this%width)
-           call put_double(ncid, lid, i, this%length)
-           call put_double(ncid, sshxid, i, this%ssh_x)
-           call put_double(ncid, sshyid, i, this%ssh_y)
-           call put_double(ncid, sstid, i, this%sst)
-           call put_double(ncid, sssid, i, this%sss)
-           call put_double(ncid, cnid, i, this%cn)
-           call put_double(ncid, hiid, i, this%hi)
-           call put_double(ncid, hsid, i, this%halo_berg)
-           call put_double(ncid, uvelpid, i, this%uvel_prev)
-           call put_double(ncid, vvelpid, i, this%vvel_prev)           
-        endif
-        next=>this%next
-        deallocate(this)
-        this=>next
-     enddo
+    ! Write variables
+    this=>traj4io
+    if (io_is_in_append_mode) then
+      iret = nf_inq_dimlen(ncid, i_dim, i)
+      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_trajectory: nf_inq_dimlen i failed'
+    else
+      i = 0
+    endif
+    do while (associated(this))
+      i=i+1
+      call put_double(ncid, lonid, i, this%lon)
+      call put_double(ncid, latid, i, this%lat)
+      call put_int(ncid, yearid, i, this%year)
+      call put_double(ncid, dayid, i, this%day)
+      call split_id(this%id, cnt, ij)
+      call put_int(ncid, idcntid, i, cnt)
+      call put_int(ncid, idijid, i, ij)
+      if (.not. save_short_traj) then
+        call put_double(ncid, uvelid, i, this%uvel)
+        call put_double(ncid, vvelid, i, this%vvel)
+        call put_double(ncid, uoid, i, this%uo)
+        call put_double(ncid, void, i, this%vo)
+        call put_double(ncid, uiid, i, this%ui)
+        call put_double(ncid, viid, i, this%vi)
+        call put_double(ncid, uaid, i, this%ua)
+        call put_double(ncid, vaid, i, this%va)
+        call put_double(ncid, mid, i, this%mass)
+        call put_double(ncid, hdid, i, this%heat_density)
+        call put_double(ncid, did, i, this%thickness)
+        call put_double(ncid, wid, i, this%width)
+        call put_double(ncid, lid, i, this%length)
+        call put_double(ncid, sshxid, i, this%ssh_x)
+        call put_double(ncid, sshyid, i, this%ssh_y)
+        call put_double(ncid, sstid, i, this%sst)
+        call put_double(ncid, sssid, i, this%sss)
+        call put_double(ncid, cnid, i, this%cn)
+        call put_double(ncid, hiid, i, this%hi)
+        call put_double(ncid, hsid, i, this%halo_berg)
+        call put_double(ncid, uvelpid, i, this%uvel_prev)
+        call put_double(ncid, vvelpid, i, this%vvel_prev)
+      endif
+      next=>this%next
+      deallocate(this)
+      this=>next
+    enddo
 
-     ! Finish up
-     iret = nf_close(ncid)
-     if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_trajectory: nf_close failed',mpp_pe(),filename
+    ! Finish up
+    iret = nf_close(ncid)
+    if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_trajectory: nf_close failed',mpp_pe(),filename
 
   endif !(is_io_tile_root_pe .AND. associated(traj4io))
   call mpp_clock_end(clock_trw)
diff --git a/tests/collision_test/.gitignore b/tests/collision_test/.gitignore
new file mode 100644
index 0000000..68bcbc9
--- /dev/null
+++ b/tests/collision_test/.gitignore
@@ -0,0 +1 @@
+results/
\ No newline at end of file
diff --git a/tests/collision_test_mts/.gitignore b/tests/collision_test_mts/.gitignore
new file mode 100644
index 0000000..68bcbc9
--- /dev/null
+++ b/tests/collision_test_mts/.gitignore
@@ -0,0 +1 @@
+results/
\ No newline at end of file

From 5b590998572ae37f88efc59fd5d61f88bd7b7216 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Fri, 16 Oct 2020 19:00:00 -0400
Subject: [PATCH 256/361] New MTS-Verlet parallelization scheme. New 'chaotic'
 test case for a large number of bergs with pseudo-randomly generated
 sizes,thicknesses,radii,etc, which serves the purpose of testing the
 robustness of the MTS scheme with high-parallelization,long
 timescales,diverse icebergs, and essentially random collision scenarios.
 Includes a python script w/ slightly different approach for initializing test
 bergs. Also some fixes regarding MTS+spherical coords.

---
 driver/icebergs_driver.F90                    |   31 +-
 src/icebergs.F90                              |  158 +-
 src/icebergs_framework.F90                    | 1404 +++++++++--------
 src/icebergs_io.F90                           |   13 +-
 tests/chaotic_test/.gitignore                 |    1 +
 tests/chaotic_test/README                     |    5 +
 tests/chaotic_test/RUN                        |    5 +
 tests/chaotic_test/animate_trajectories.py    |  121 ++
 .../chaotic_test/animate_trajectories_1pe.py  |  158 ++
 tests/chaotic_test/diag_table                 |    3 +
 tests/chaotic_test/input.nml                  |  160 ++
 tests/chaotic_test/makeberg/RUN               |    3 +
 tests/chaotic_test/makeberg/makeberg.py       |  406 +++++
 tests/collision_test/animate_trajectories.py  |   24 +-
 tests/collision_test/input.nml                |    2 +-
 .../animate_trajectories.py                   |   24 +-
 .../animate_trajectories_1pe.py               |    8 +-
 tests/collision_test_mts/input.nml            |   57 +-
 18 files changed, 1770 insertions(+), 813 deletions(-)
 create mode 100644 tests/chaotic_test/.gitignore
 create mode 100644 tests/chaotic_test/README
 create mode 100755 tests/chaotic_test/RUN
 create mode 100755 tests/chaotic_test/animate_trajectories.py
 create mode 100755 tests/chaotic_test/animate_trajectories_1pe.py
 create mode 100644 tests/chaotic_test/diag_table
 create mode 100644 tests/chaotic_test/input.nml
 create mode 100755 tests/chaotic_test/makeberg/RUN
 create mode 100755 tests/chaotic_test/makeberg/makeberg.py

diff --git a/driver/icebergs_driver.F90 b/driver/icebergs_driver.F90
index dc6df52..aea2b61 100644
--- a/driver/icebergs_driver.F90
+++ b/driver/icebergs_driver.F90
@@ -54,6 +54,7 @@ program icebergs_driver
 logical :: debug=.true. !< If true, do some debugging
 logical :: saverestart=.false. !< If true, save a berg restart file at the end
 logical :: collision_test=.false.
+logical :: chaotic_test=.false.
 integer :: halo=1 !< Width of halo in parallel decomposition
 real :: ibdt=3600.0
 real :: ibuo=0.1
@@ -64,7 +65,7 @@ program icebergs_driver
 integer :: ibhrs=2
 integer :: nmax = 2000000000 !<max number of iteration
 namelist /icebergs_driver_nml/ debug, ni, nj, halo, ibhrs, ibdt, ibuo, ibvo, nmax, &
-       saverestart,ibui,ibvi,collision_test,gridres
+       saverestart,ibui,ibvi,collision_test,chaotic_test,gridres
 ! For loops
 integer :: isc !< Start of i-index for computational domain (used for loops)
 integer :: iec !< End of i-index for computational domain (used for loops)
@@ -185,6 +186,14 @@ program icebergs_driver
   enddo
 enddo
 
+if (chaotic_test) then
+  !assign land cells at the N and S portions of the domain.
+  !input.nml: set coastal drift parameter to prevent grounding
+  do j=jsd,jed; do i=isd,ied
+    if (lat(i,j)<=0.0+2*gridres .or. lat(i,j)>=1000.e3-2*gridres) wet(i,j)=0.0
+  enddo;enddo
+endif
+
 call set_calendar_type(THIRTY_DAY_MONTHS)
 time = set_date(1,1,1,0,0,0)
 dt = ibdt
@@ -237,6 +246,26 @@ program icebergs_driver
   enddo;enddo
 endif
 
+if (chaotic_test) then
+  do j=jsd,jed; do i=isd,ied
+    if (lat(i,j)==500.e3 .or. lon(i,j)==500.e3) then
+      vo(i,j)=0.0
+    elseif (lon(i,j)>500.e3) then
+      if (lat(i,j)>500.e3) then
+        vo(i,j)=0.5*ibvo
+      else
+        vo(i,j)=-0.5*ibvo
+      endif
+    else
+      if (lat(i,j)>500.e3) then
+        vo(i,j)=-ibvo
+      else
+        vo(i,j)=ibvo
+      endif
+    endif
+  enddo;enddo
+endif
+
 ! optional:
 ! allocate( sss(isd:ied,jsd:jed) )
 ! allocate( mass_berg(isd:ied,jsd:jed) )
diff --git a/src/icebergs.F90 b/src/icebergs.F90
index d4460c0..e007a96 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -10,7 +10,7 @@ module ice_bergs
 use fms_mod, only: write_version_number, read_data, write_data, file_exist
 use mosaic_mod, only: get_mosaic_ntiles, get_mosaic_ncontacts
 use mpp_mod, only: mpp_npes, mpp_pe, mpp_root_pe, mpp_sum, mpp_min, mpp_max, NULL_PE
-use mpp_mod, only: mpp_send, mpp_recv, mpp_sync_self, mpp_chksum
+use mpp_mod, only: mpp_send, mpp_recv, mpp_sync_self, mpp_chksum, mpp_sync
 use mpp_mod, only: mpp_clock_begin, mpp_clock_end, mpp_clock_id
 use mpp_mod, only: CLOCK_COMPONENT, CLOCK_SUBCOMPONENT, CLOCK_LOOP
 use random_numbers_mod, only: initializeRandomNumberStream, getRandomNumbers, randomNumberStream
@@ -45,6 +45,8 @@ module ice_bergs
 use ice_bergs_framework, only: test_check_for_duplicate_ids_in_list
 use ice_bergs_framework, only: generate_id
 use ice_bergs_framework, only: update_latlon
+use ice_bergs_framework, only: set_conglom_ids
+use ice_bergs_framework, only: transfer_mts_bergs
 
 use ice_bergs_io,        only: ice_bergs_io_init, write_restart, write_trajectory
 use ice_bergs_io,        only: read_restart_bergs, read_restart_calving
@@ -148,8 +150,12 @@ subroutine icebergs_init(bergs, &
     else
       call read_restart_bonds(bergs,Time)
     endif
-    call update_halo_icebergs(bergs)
-    call connect_all_bonds(bergs)
+    if (bergs%mts) then
+      call transfer_mts_bergs(bergs)
+    else
+      call update_halo_icebergs(bergs)
+      call connect_all_bonds(bergs)
+    endif
     nbonds=0
     check_bond_quality=.True.
     call count_bonds(bergs, nbonds,check_bond_quality)
@@ -333,6 +339,7 @@ subroutine initialize_iceberg_bonds(bergs)
   real :: dlon,dlat
   real :: dx_dlon,dy_dlat, lat_ref
   real :: r_dist_x, r_dist_y, r_dist
+  real :: radius
   integer :: grdi_outer, grdj_outer
   integer :: grdi_inner, grdj_inner
 
@@ -367,8 +374,11 @@ subroutine initialize_iceberg_bonds(bergs)
             r_dist_y=dlat*dy_dlat
             r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) )
 
-            ! If the bergs are closer than bergs%length_for_manually_initialize_bonds, then form a bond -Alex
-            if (r_dist.lt.bergs%length_for_manually_initialize_bonds) then
+            if (bergs%manually_initialize_bonds_from_radii) then
+              radius=sqrt(min(berg%length*berg%width,other_berg%length*other_berg%width))
+              if (r_dist.lt.1.25*radius) call form_a_bond(berg, other_berg%id, other_berg%ine, other_berg%jne, other_berg)
+            elseif (r_dist.lt.bergs%length_for_manually_initialize_bonds) then
+              ! If the bergs are closer than bergs%length_for_manually_initialize_bonds, then form a bond -Alex
               call form_a_bond(berg, other_berg%id, other_berg%ine, other_berg%jne, other_berg)
             endif
           endif
@@ -443,9 +453,9 @@ subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
   integer :: grdi, grdj
   logical :: iceberg_bonds_on
   logical :: bonded
-  integer :: nc
+  integer :: nc_x,nc_y
 
-  nc=bergs%num_contact_cells
+  nc_x=bergs%contact_cells_lon; nc_y=bergs%contact_cells_lat
   iceberg_bonds_on=bergs%iceberg_bonds_on
 
   IA_x=0.
@@ -476,21 +486,18 @@ subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
     ! Interactions for non-bonded berg elements only. For the mts scheme, this is only called if mts_part==1
     if (.not. (bergs%mts .and. bergs%mts_part .eq. 3)) then
       bonded=.false. ! Interactions for non-bonded berg elements
-      call mark_conglomerate_bergs(berg,1)
-      berg%id=abs(berg%id)
-      do grdj = max(berg%jne-nc,bergs%grd%jsd+1),min(berg%jne+nc,bergs%grd%jed);&
-        do grdi = max(berg%ine-nc,bergs%grd%isd+1),min(berg%ine+nc,bergs%grd%ied)
+      do grdj = max(berg%jne-nc_y,bergs%grd%jsd+1),min(berg%jne+nc_y,bergs%grd%jed);&
+        do grdi = max(berg%ine-nc_x,bergs%grd%isd+1),min(berg%ine+nc_x,bergs%grd%ied)
 
         other_berg=>bergs%list(grdi,grdj)%first
         do while (associated(other_berg)) ! loop over all other bergs
-          if (other_berg%id>0) then !no bond with other_berg
+          if (other_berg%conglom_id.ne.berg%conglom_id) then
             call calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,  &
               P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded)
           endif
           other_berg=>other_berg%next
         enddo
       enddo; enddo
-      call mark_conglomerate_bergs(berg,2)
     endif
 
   else
@@ -523,42 +530,6 @@ subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
   endif
 end subroutine interactive_force
 
-!> Marks conglomerate icebergs with negative their id
-recursive subroutine mark_conglomerate_bergs(berg,mark_or_unmark)
-  type(iceberg), pointer :: berg
-  type(iceberg), pointer :: other_berg
-  type(bond) , pointer :: current_bond
-  integer :: mark_or_unmark
-
-  if (mark_or_unmark==1) then
-    if (berg%id>0) berg%id=-berg%id
-    current_bond=>berg%first_bond
-    do while (associated(current_bond))
-      if  (associated(current_bond%other_berg)) then
-        other_berg=>current_bond%other_berg
-        if (other_berg%id>0) then
-          call mark_conglomerate_bergs(other_berg,1)
-        end if
-      end if
-      current_bond=>current_bond%next_bond
-    enddo
-  else
-    if (berg%id<0) berg%id=-berg%id
-    current_bond=>berg%first_bond
-    do while (associated(current_bond))
-      if  (associated(current_bond%other_berg)) then
-        other_berg=>current_bond%other_berg
-        if (other_berg%id<0) then
-          call mark_conglomerate_bergs(other_berg,2)
-        end if
-      end if
-      current_bond=>current_bond%next_bond
-    enddo
-  endif
-
-end subroutine mark_conglomerate_bergs
-
-
 !> Calculate interactive forces between two bergs
 subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1, &
                            P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y, bonded)
@@ -1105,24 +1076,32 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
 
   dumpit=.false.
   if (abs(uveln)>vel_lim.or.abs(vveln)>vel_lim) then
-    dumpit=.true.
-    write(stderrunit,'("pe=",i3,x,a)') mpp_pe(),'Dump triggered by excessive velocity'
+    if (debug) then
+      dumpit=.true.
+      write(stderrunit,'("pe=",i3,x,a)') mpp_pe(),'Dump triggered by excessive velocity'
+    else
+      write(stderrunit,'("pe=",i3,x,a)') mpp_pe(),'Excessive velocity detected'
+    endif
   endif
   if (abs(ax)>accel_lim.or.abs(ay)>accel_lim) then
-    dumpit=.true.
-    write(stderrunit,'("pe=",i3,x,a)') mpp_pe(),'Dump triggered by excessive acceleration'
+    if (debug) then
+      dumpit=.true.
+      write(stderrunit,'("pe=",i3,x,a)') mpp_pe(),'Dump triggered by excessive acceleration'
+    else
+      write(stderrunit,'("pe=",i3,x,a)') mpp_pe(),'Excessive acceleration detected'
+    endif
   endif
   if (present(debug_flag)) then
     if (debug_flag) dumpit=.true.
     write(stderrunit,'("pe=",i3,x,a)') mpp_pe(),'Debug dump flagged by arguments'
   endif
   if (dumpit) then
- 100 format('pe=',i3,a15,9(x,a8,es12.3))
- 200 format('pe=',i3,a15,(x,a8,i12),9(x,a8,es12.3))
-    write(stderrunit,200) mpp_pe(),'Starting pars:', &
+100 format('pe=',i3,a15,9(x,a8,es12.3))
+200 format('pe=',i3,a5,i14,(a8,i5),(a7,es12.3))
+    write(stderrunit,200) mpp_pe(),'id0=',berg%id, &
       'yr0=',berg%start_year, 'day0=',berg%start_day, &
       'lon0=',berg%start_lon, 'lat0=',berg%start_lat, 'mass0=',berg%start_mass, &
-      'sclng=',berg%mass_scaling, 'id0=',berg%id
+      'sclng=',berg%mass_scaling
     write(stderrunit,100) mpp_pe(),'Geometry:', &
       'M=',M, 'T=',T, 'D=',D, 'F=',F, 'W=',W, 'L=',L
     write(stderrunit,100) mpp_pe(),'delta U:', &
@@ -1537,7 +1516,7 @@ subroutine thermodynamics(bergs)
 
       ! Did berg completely melt?
       if (Mnew<=0.) then ! Delete the berg
-        call move_trajectory(bergs, this)
+        if (.not. bergs%debug_write) call move_trajectory(bergs, this)
         call delete_iceberg_from_list(bergs%list(grdi,grdj)%first, this)
         bergs%nbergs_melted=bergs%nbergs_melted+1
       endif
@@ -3089,7 +3068,7 @@ subroutine calculate_mass_on_ocean(bergs, with_diagnostics)
   do grdj = grd%jsc-1,grd%jec+1 ; do grdi = grd%isc-1,grd%iec+1
     berg=>bergs%list(grdi,grdj)%first
     do while(associated(berg))
-      if (berg%halo_berg<1 .or. .not. bergs%mts) then
+      if (berg%halo_berg<2 .or. .not. bergs%mts) then
         i=berg%ine  ;     j=berg%jne
         if (grd%area(i,j) > 0.) then
 
@@ -3455,14 +3434,9 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     Visited=.true.
     if (bergs%mts) then
       call interp_gridded_fields_to_bergs(bergs)
-      if ((bergs%interactive_icebergs_on) .or. (bergs%iceberg_bonds_on)) then
-        call update_halo_icebergs(bergs)
-        if (bergs%iceberg_bonds_on) then
-          call connect_all_bonds(bergs)
-        else
-          if (grd%Lx>0.) call update_latlon(bergs)
-        endif
-      endif
+      call transfer_mts_bergs(bergs)
+    elseif ((bergs%contact_distance>0.) .or. (bergs%contact_spring_coef .ne. bergs%spring_coef)) then
+        call set_conglom_ids(bergs)
     endif
   endif
 
@@ -3509,15 +3483,22 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   if (bergs%iceberg_bonds_on)  call  bond_address_update(bergs)
 
   call send_bergs_to_other_pes(bergs)
-  if (bergs%mts) call interp_gridded_fields_to_bergs(bergs)
   if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after send_bergs() ')
-  if ((bergs%interactive_icebergs_on) .or. (bergs%iceberg_bonds_on)) then
-    call update_halo_icebergs(bergs)
-    if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after update_halo()')
-    if (bergs%iceberg_bonds_on) then
-      call connect_all_bonds(bergs)
-    else
-      if (grd%Lx>0.) call update_latlon(bergs)
+  if (bergs%mts) then
+    call interp_gridded_fields_to_bergs(bergs)
+    call transfer_mts_bergs(bergs)
+  else
+    if ((bergs%interactive_icebergs_on) .or. (bergs%iceberg_bonds_on)) then
+      call update_halo_icebergs(bergs)
+      if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after update_halo()')
+      if (bergs%iceberg_bonds_on) then
+        call connect_all_bonds(bergs)
+      else
+        if (grd%Lx>0.) call update_latlon(bergs)
+      endif
+      if ((bergs%contact_distance>0.) .or. (bergs%contact_spring_coef .ne. bergs%spring_coef)) then
+        call set_conglom_ids(bergs)
+      endif
     endif
   endif
   if (debug) call bergs_chksum(bergs, 'run bergs (exchanged)')
@@ -3550,12 +3531,18 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 
   ! For each berg, record
   call mpp_clock_begin(bergs%clock_dia)
-  if (sample_traj) call record_posn(bergs)
-  if (write_traj) then
+  if (sample_traj .or. bergs%writeandstop) call record_posn(bergs)
+  if (write_traj .or. bergs%writeandstop) then
     call move_all_trajectories(bergs)
     call write_trajectory(bergs%trajectories, bergs%save_short_traj)
   endif
 
+  if (bergs%writeandstop) then
+    call mpp_sync()
+    call error_mesg('KID', 'WRITE AND STOP!!!', FATAL)
+  endif
+
+
   ! Gridded diagnostics
   if (grd%id_uo>0) &
     lerr=send_data(grd%id_uo, grd%uo(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
@@ -4266,6 +4253,7 @@ subroutine calve_icebergs(bergs)
           newberg%start_lat=newberg%lat
           newberg%start_year=bergs%current_year
           newberg%id = generate_id(grd, i, j)
+          newberg%conglom_id=0
           newberg%start_day=bergs%current_yearday+ddt/86400.
           newberg%start_mass=bergs%initial_mass(k)
           newberg%mass_scaling=bergs%mass_scaling(k)
@@ -4374,7 +4362,9 @@ subroutine evolve_icebergs_mts(bergs)
   do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
     berg=>bergs%list(grdi,grdj)%first
     do while (associated(berg)) ! loop over all bergs
-      if (berg%static_berg .lt. 0.5 .and. berg%halo_berg<10) then
+      !if (berg%static_berg .lt. 0.5 .and. berg%halo_berg<10) then
+      !only evolve non-static bergs that overlap, or are part of a conglom that overlaps, the computational domain:
+      if (berg%static_berg .lt. 0.5 .and. berg%conglom_id.ne.0) then
         latn = berg%lat ;   lonn = berg%lon
         uvel1=berg%uvel_prev ;   vvel1=berg%vvel_prev !V_n (previous cycle)
         !subroutine accel expects uvel1=berg%uvel_prev, and calculates ustar=uvel1+axn*dt_2.
@@ -4410,7 +4400,8 @@ subroutine evolve_icebergs_mts(bergs)
   do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
     berg=>bergs%list(grdi,grdj)%first
     do while (associated(berg)) ! loop over all bergs
-      if (berg%static_berg .lt. 0.5 .and. berg%halo_berg<10) then
+      !if (berg%static_berg .lt. 0.5 .and. berg%halo_berg<10) then
+      if (berg%static_berg .lt. 0.5 .and. berg%conglom_id.ne.0) then
         ! if (berg%id==4294967382 .and. berg%halo_berg==0) then
         !   print *,'berg check 2',mpp_pe(),berg%id, berg%uvel, berg%vvel, &
         !     berg%lat, berg%lon, berg%axn, berg%ayn, berg%bxn, berg%byn
@@ -4446,7 +4437,8 @@ subroutine evolve_icebergs_mts(bergs)
     do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied ! update positions
       berg=>bergs%list(grdi,grdj)%first
       do while (associated(berg)) ! loop over all bergs
-        if (berg%static_berg .lt. 0.5 .and. berg%halo_berg<10) then
+        !if (berg%static_berg .lt. 0.5 .and. berg%halo_berg<10) then
+        if (berg%static_berg .lt. 0.5 .and. berg%conglom_id.ne.0) then
 
           on_tangential_plane=.false.
           if ((berg%lat>89.) .and. (grd%grid_is_latlon)) on_tangential_plane=.true.
@@ -4488,7 +4480,8 @@ subroutine evolve_icebergs_mts(bergs)
     do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
       berg=>bergs%list(grdi,grdj)%first
       do while (associated(berg)) ! loop over all bergs
-        if (berg%static_berg .lt. 0.5 .and. berg%halo_berg<10) then
+        !if (berg%static_berg .lt. 0.5 .and. berg%halo_berg<10) then
+        if (berg%static_berg .lt. 0.5 .and. berg%conglom_id.ne.0) then
 
           latn = berg%lat ;   lonn = berg%lon
           axn  = berg%axn_fast ;   ayn  = berg%ayn_fast
@@ -4530,7 +4523,8 @@ subroutine evolve_icebergs_mts(bergs)
     do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
       berg=>bergs%list(grdi,grdj)%first
       do while (associated(berg)) ! loop over all bergs
-        if (berg%static_berg .lt. 0.5 .and. berg%halo_berg<10) then
+        !if (berg%static_berg .lt. 0.5 .and. berg%halo_berg<10) then
+        if (berg%static_berg .lt. 0.5 .and. berg%conglom_id.ne.0) then
           berg%uvel_old=berg%uvel; berg%vvel_old=berg%vvel
         endif
         berg=>berg%next
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index d6d80a9..de08aca 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -40,6 +40,7 @@ module ice_bergs_framework
 character(len=10) :: restart_input_dir = 'INPUT/' !< Directory to look for restart files
 integer, parameter :: delta_buf=25 !< Size by which to increment buffers
 real, parameter :: pi_180=pi/180. !< Converts degrees to radians
+real, parameter :: Rearth=6360000. !< Radius of earth (m)
 logical :: fix_restart_dates=.true. !< After a restart, check that bergs were created before the current model date
 logical :: do_unit_tests=.false. !< Conduct some unit tests
 logical :: force_all_pes_traj=.false. !< Force all pes write trajectory files regardless of io_layout
@@ -79,6 +80,8 @@ module ice_bergs_framework
 public check_for_duplicates_in_parallel
 public split_id, id_from_2_ints, generate_id, cij_from_old_id, convert_old_id
 public update_latlon
+public set_conglom_ids
+public transfer_mts_bergs
 
 !> Container for gridded fields
 type :: icebergs_gridded
@@ -202,16 +205,8 @@ module ice_bergs_framework
   real :: ayn
   real :: bxn
   real :: byn
-  real :: axn_fast
-  real :: ayn_fast
-  real :: bxn_fast
-  real :: byn_fast
   real :: uvel_prev
   real :: vvel_prev
-  real :: uvel_old
-  real :: vvel_old
-  real :: lat_old
-  real :: lon_old
   real :: uo !< Zonal velocity of ocean (m/s)
   real :: vo !< Meridional velocity of ocean (m/s)
   real :: ui !< Zonal velocity of ice (m/s)
@@ -228,6 +223,7 @@ module ice_bergs_framework
   real :: static_berg
   real :: mass_of_bits !< Mass of bergy bits (kg)
   real :: heat_density !< Heat density of berg (???)
+  integer :: conglom_id
   integer :: year !< Year of this record (years)
   integer(kind=8) :: id = -1 !< Iceberg identifier
   type(xyt), pointer :: next=>null() !< Next link in list
@@ -271,6 +267,7 @@ module ice_bergs_framework
   real :: static_berg  ! Equal to 1 for icebergs which are static (not allowed to move). Might be extended to grounding later.
   integer :: start_year !< Year that berg was created (years)
   integer(kind=8) :: id !< Iceberg identifier
+  integer :: conglom_id !<ID for a conglomerate
   integer :: ine !< Nearest i-index in NE direction (for convenience)
   integer :: jne !< Nearest j-index in NE direction (for convenience)
   real :: xi !< Non-dimensional x-coordinate within current cell (0..1)
@@ -334,6 +331,7 @@ module ice_bergs_framework
   real :: rho_bergs !< Density of icebergs [kg/m^3]
   real :: spring_coef !< Spring constant for bonded iceberg interactions
   real :: contact_spring_coef !<Spring coefficient for berg collisions -Alex
+  logical :: debug_write !<Sets traj_sample_hours=traj_write_hours & includes halo bergs in write
   real :: bond_coef !< Spring constant for iceberg bonds
   real :: radial_damping_coef !< Coefficient for relative iceberg motion damping (radial component) -Alon
   real :: tangental_damping_coef !< Coefficient for relative iceberg motion damping (tangential component) -Alon
@@ -391,6 +389,7 @@ module ice_bergs_framework
   integer(kind=8) :: debug_iceberg_with_id = -1 !< If positive, monitors a berg with this id
 
   real :: length_for_manually_initialize_bonds=1000.0 !<if manually init bonds, only  bond if dist between particles is .lt. this length -Added by Alex
+  logical :: manually_initialize_bonds_from_radii=.false. !<if manually init bonds, form bonds if dist between particles is < 1.25x the smaller radii-Alex
   real :: speed_limit=0. !< CFL speed limit for a berg [m/s]
   real :: tau_calving=0. !< Time scale for smoothing out calving field (years)
   real :: tip_parameter=0. !< parameter to override iceberg rolling critical ratio (use zero to get parameter directly from ice and seawater densities)
@@ -439,7 +438,8 @@ module ice_bergs_framework
   real :: mts_fast_dt
   integer :: mts_part !for turning on/off berg interactions/collisions during different mts scheme
   real :: contact_distance
-  integer :: num_contact_cells !for how many cells to search to find contact pairs
+  integer :: contact_cells_lon=1,contact_cells_lat=1 !how many cells to search to find contact pairs
+  logical :: writeandstop=.false. !for debugging
 end type icebergs
 
 !> Read original restarts. Needs to be module global so can be public to icebergs_mod.
@@ -519,6 +519,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: rho_bergs=850. ! Density of icebergs
 real :: spring_coef=1.e-8 ! Spring constant for iceberg interactions (this seems to be the highest stable value)
 real :: contact_spring_coef=0. !Spring coef for berg collisions (is set to spring_coef if not specified)
+logical :: debug_write=.false. !Sets traj_sample_hours=traj_write_hours & includes halo bergs in write
 real :: bond_coef=1.e-8 ! Spring constant for iceberg bonds - not being used right now
 real :: radial_damping_coef=1.e-4 ! Coefficient for relative iceberg motion damping (radial component) -Alon
 real :: tangental_damping_coef=2.e-5 ! Coefficient for relative iceberg motion damping (tangential component) -Alon
@@ -541,6 +542,7 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
 logical :: time_average_weight=.false. ! Time average the weight on the ocean
 real :: length_for_manually_initialize_bonds=1000.0 !<if manually init bonds, only  bond if dist between particles is .lt. this length - Alex
+logical :: manually_initialize_bonds_from_radii=.false. !<if manually init bonds, form bonds if dist between particles is < 1.25x the smaller radii - Alex
 real :: speed_limit=0. ! CFL speed limit for a berg
 real :: tau_calving=0. ! Time scale for smoothing out calving field (years)
 real :: tip_parameter=0. ! Parameter to override iceberg rolling critical ratio (use zero to get parameter directly from ice and seawater densities
@@ -603,7 +605,7 @@ subroutine ice_bergs_framework_init(bergs, &
          Use_three_equation_model,find_melt_using_spread_mass,use_mixed_layer_salinity_for_thermo,utide_icebergs,ustar_icebergs_bg,cdrag_icebergs, pass_fields_to_ocean_model, &
          const_gamma, Gamma_T_3EQ, ignore_traj, debug_iceberg_with_id,use_updated_rolling_scheme, tip_parameter, read_old_restarts, tau_calving, read_ocean_depth_from_file, melt_cutoff,&
          apply_thickness_cutoff_to_gridded_melt, apply_thickness_cutoff_to_bergs_melt, use_mixed_melting, coastal_drift, tidal_drift,&
-				 mts,mts_sub_steps,contact_distance,length_for_manually_initialize_bonds,contact_spring_coef
+				 mts,mts_sub_steps,contact_distance,length_for_manually_initialize_bonds,manually_initialize_bonds_from_radii,contact_spring_coef,debug_write
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -614,6 +616,8 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: Total_mass  !Added by Alon
 real :: mts_fast_dt=0.0 !Added by Alex
 real :: maxlon_c,minlon_c !Added by Alex, for mts verlet periodicity
+integer :: k,maxk
+real :: dx,dy,dx_dlon,dy_dlat,lat_ref2,lon_ref
 
   ! Get the stderr and stdlog unit numbers
   stderrunit=stderr()
@@ -982,8 +986,8 @@ subroutine ice_bergs_framework_init(bergs, &
 
 !must use verlet with mts - Alex
 if (mts) then
-  buffer_width_traj=buffer_width_traj+6 !to accomodate fast acceration and vel_prev terms
-  buffer_width=buffer_width+18 !to accomodate external forcing (uo,vo,ua,va,ui,vi,ssh_x,ssh_y,sst,sss,cn,hi)
+  buffer_width_traj=buffer_width_traj+3 !to accomodate uvel_prev, vvel_prev, conglom_id
+  buffer_width=buffer_width+19 !to accomodate external forcing (conglom_id,uo,vo,ua,va,ui,vi,ssh_x,ssh_y,sst,sss,cn,hi)
 
   !if mts_sub_steps is not given in the nml already,
   !then detemine according to the max dt according to the spring coef
@@ -1004,6 +1008,18 @@ subroutine ice_bergs_framework_init(bergs, &
 !by default, set contact_spring_coef equal to the spring_coef for bonded interactions, unless
 !contact_spring_coef is specified as > 0.
 if (contact_spring_coef.le.0.) contact_spring_coef=spring_coef
+if (debug_write) then
+  if (traj_sample_hrs.ne.traj_write_hrs) then
+    call error_mesg('KID, framework', &
+      'Debug_write activated: setting traj_sample_hrs=traj_write_hrs', WARNING)
+    traj_sample_hrs=traj_write_hrs
+  endif
+  if (.not. force_all_pes_traj) then
+    call error_mesg('KID, framework', &
+      'Debug_write activated: setting force_all_pes_traj=.true.', WARNING)
+    force_all_pes_traj=.true.
+  endif
+endif
 
 
  ! Parameters
@@ -1020,7 +1036,8 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%max_bonds=max_bonds
   bergs%rho_bergs=rho_bergs
   bergs%spring_coef=spring_coef
-	bergs%contact_spring_coef=contact_spring_coef !Alex
+  bergs%contact_spring_coef=contact_spring_coef !Alex
+  bergs%debug_write=debug_write
   bergs%bond_coef=bond_coef
   bergs%radial_damping_coef=radial_damping_coef
   bergs%tangental_damping_coef=tangental_damping_coef
@@ -1069,6 +1086,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%iceberg_bonds_on=iceberg_bonds_on   !Alon
   bergs%manually_initialize_bonds=manually_initialize_bonds   !Alon
   bergs%length_for_manually_initialize_bonds=length_for_manually_initialize_bonds !Alex
+  bergs%manually_initialize_bonds_from_radii=manually_initialize_bonds_from_radii !Alex
   bergs%critical_interaction_damping_on=critical_interaction_damping_on   !Alon
   bergs%interactive_icebergs_on=interactive_icebergs_on   !Alon
   bergs%use_new_predictive_corrective=use_new_predictive_corrective  !Alon
@@ -1081,12 +1099,42 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%mts_sub_steps = mts_sub_steps
   bergs%mts_part = 1
   bergs%contact_distance=contact_distance
-  bergs%num_contact_cells = max(int(ceiling(contact_distance/(grd%lon(grd%isc+1,grd%jsc)-grd%lon(grd%isc,grd%jsc)))),1)
-  if (halo<bergs%num_contact_cells) then
+
+  if (bergs%contact_distance>0) then
+    dx_dlon=1; dy_dlat=1
+    maxk=0
+    do j=grd%jsd,grd%jed; do i=grd%isd,grd%ied
+      if (grd%grid_is_latlon) then
+        lat_ref2=grd%lat(i,j)
+        dx_dlon=pi_180*Rearth*cos(lat_ref2*pi_180)
+      endif
+      lon_ref=grd%lon(i,j)
+      k=0
+      do while(k+i<grd%ied)
+        k=k+1
+        dx=(grd%lon(k+i,j)-lon_ref)*dx_dlon
+        if (k>maxk) maxk=k
+        if (dx>contact_distance) exit
+      enddo
+    enddo;enddo
+
+    if (grd%grid_is_latlon) dy_dlat=pi_180*Rearth
+    dy=(grd%lat(grd%isc,grd%jsc+1)-grd%lat(grd%isc,grd%jsc))*dy_dlat
+
+    bergs%contact_cells_lon = max(maxk,1)
+    bergs%contact_cells_lat = max(int(ceiling(contact_distance/dy)),1)
+  else
+    bergs%contact_cells_lon = 1
+    bergs%contact_cells_lat = 1
+  endif
+
+  !necessary?
+  if (halo<bergs%contact_cells_lon .or. halo<bergs%contact_cells_lat) then
 	  if (mpp_pe()==0) then
 		  write(stderrunit,'(a,i3)') 'KID, icebergs_init: halo width ',halo
-		  write(stderrunit,'(a,f8.2,a,i3)') 'KID, icebergs_init: contact distance ',bergs%contact_distance,&
-		    ' num contact cells',bergs%num_contact_cells
+		  write(stderrunit,'(a,f8.2,a,2i3)') 'KID, icebergs_init:  contact distance ',bergs%contact_distance,&
+      ' num contact cells lon and lat',bergs%contact_cells_lon,bergs%contact_cells_lat
+
 		  call error_mesg('KID, ice_bergs_framework_init', &
 		    'halo width must be increased to accomodate specified contact distance!!!', FATAL)
     endif
@@ -1099,6 +1147,7 @@ subroutine ice_bergs_framework_init(bergs, &
   allocate( bergs%initial_length(nclasses) )
   bergs%initial_width(:)=sqrt(initial_mass(:)/(LoW_ratio*rho_bergs*initial_thickness(:)))
   bergs%initial_length(:)=LoW_ratio*bergs%initial_width(:)
+  bergs%writeandstop=.false.
   grd%coastal_drift = coastal_drift
   grd%tidal_drift = tidal_drift
 
@@ -1612,11 +1661,6 @@ subroutine update_halo_icebergs(bergs)
     call show_all_bonds(bergs)
   endif
 
-  if (bergs%mts) then
-    call mpp_sync_self()
-    call transfer_mts_bergs(bergs)
-  end if
-
   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!Debugging!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
   if (debug) then
     nbergs_end=count_bergs(bergs)
@@ -1661,293 +1705,636 @@ subroutine update_halo_icebergs(bergs)
 
 end subroutine update_halo_icebergs
 
-!> For the MTS Verlet scheme: entire conglomerates of iceberg elements are passed between all
-!! PEs that they overlap, skipping the elements that were already transferred. Berg elements
-!! within contact distance of the conglomerates must also be transferred.
-subroutine transfer_mts_bergs(bergs)
+!> For the multiple-timestepping velocity verlet scheme, populates the current PE with the following
+!! bergs from neighboring PEs: halo bergs, bergs that comprise any conglomerate that overlaps both
+!! PEs, and bergs within the contact distance of these halo and conglomerate bergs.
+Subroutine transfer_mts_bergs(bergs)
 ! Arguments
 type(icebergs), pointer :: bergs !< Container for all types and memory
 ! Local variables
-type(iceberg), pointer :: kick_the_bucket, this
-integer :: nbergs_to_send_e, nbergs_to_send_w
-integer :: nbergs_to_send_n, nbergs_to_send_s
-integer :: nbergs_rcvd_from_e, nbergs_rcvd_from_w
-integer :: nbergs_rcvd_from_n, nbergs_rcvd_from_s
 type(icebergs_gridded), pointer :: grd
-integer :: i
 integer :: stderrunit
-integer :: grdi, grdj, grdi2, grdj2
-integer :: halo_width
-real :: current_halo_status,current_lat,current_lon
-logical :: halo_debugging,leavedo
-integer :: conglom_count,nc,contact_distance,last_berg,last_cell
-real :: Lx,dist,dx,dy
-logical :: periodicityfix
-
-  halo_width=bergs%grd%halo
-  halo_debugging=bergs%halo_debugging
-  nc=bergs%num_contact_cells
-  contact_distance=bergs%contact_distance
-
-  ! Get the stderr unit number
-  stderrunit = stderr()
+integer :: grdi, grdj,i
+type(iceberg), pointer :: this,kick_the_bucket
+integer :: nbergs_to_send_e, nbergs_to_send_w
+integer :: nbergs_to_send_n, nbergs_to_send_s
 
-  ! For convenience
-  grd=>bergs%grd
+  grd=>bergs%grd ! for convenience
+  stderrunit = stderr() ! Get the stderr unit number
 
-  Lx = grd%Lx
-  periodicityfix=.false.
+  ! Step 1: Clear the current halos
+  do grdj = grd%jsd,grd%jsc-1 ;  do grdi = grd%isd,grd%ied
+    call delete_all_bergs_in_list(bergs, grdj, grdi)
+  enddo ; enddo
 
-  nbergs_to_send_e=0
-  nbergs_to_send_w=0
+  do grdj = grd%jec+1,grd%jed ;  do grdi = grd%isd,grd%ied
+    call delete_all_bergs_in_list(bergs,grdj,grdi)
+  enddo ; enddo
 
-  !connect bonds currently residing on each PE.
-  !Needed to determine which conglomerate elements to send.
-  call connect_all_bonds(bergs,ignore_unmatched=.true.)
+  do grdj = grd%jsd,grd%jed ;    do grdi = grd%isd,grd%isc-1
+    call delete_all_bergs_in_list(bergs,grdj,grdi)
+  enddo ; enddo
 
-  !---Step A. summary of current halo_berg statuses on current PE---
-  !halo_berg=0: bergs on computational domain
-  !halo_berg=1: bergs on halo domain
+  do grdj = grd%jsd,grd%jed ;    do grdi = grd%iec+1,grd%ied
+    call delete_all_bergs_in_list(bergs,grdj,grdi)
+  enddo ; enddo
 
-  ! Send all berg elements (east/west) in conglomerate:
-  ! conglomerate berg elements to send EAST:
-  last_berg=-1
-  if (Lx>0.0 .and. grd%lon(grd%iec,grd%jec).eq. grd%maxlon_c) periodicityfix=.true.
-  grdi = grd%iec-halo_width+2
-  do grdj = grd%jsd+1,grd%jed   !mark the additional elements to send
+  !Remove contact-only/conglom bergs outside halo. Reset conglom IDs to zero for all other bergs
+  do grdj = grd%jsc,grd%jec ;    do grdi = grd%isc,grd%iec
     this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
-      !mark conglomerate elements west of the eastern halo as
-      !halo_berg = halo_berg+2 (so their new halo_berg will equal 2 or 3)
-      call mts_mark_conglomerate_bergs(this,grdi,1)
-      this=>this%next
+      if (this%halo_berg .ne. 0) then
+        kick_the_bucket=>this
+        this=>this%next
+        call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
+      else
+        this%conglom_id=0
+        this=>this%next
+      end if
     enddo
+  enddo;enddo
+
+  !Copy bergs between PEs
+  do i = 1,2 !run twice to account for diagonal transfers and guarantee robust transfers of conglomerates
+    call connect_all_bonds(bergs,ignore_unmatched=.true.)
+    nbergs_to_send_e=0; nbergs_to_send_w=0; nbergs_to_send_n=0; nbergs_to_send_s=0
+
+    call mts_pack_in_dir(bergs,nbergs_to_send_e,"e")
+    call mts_pack_in_dir(bergs,nbergs_to_send_w,"w")
+    call mts_pack_in_dir(bergs,nbergs_to_send_n,"n")
+    call mts_pack_in_dir(bergs,nbergs_to_send_s,"s")
+
+    call mts_send_and_receive(bergs,nbergs_to_send_e,nbergs_to_send_w,nbergs_to_send_n,nbergs_to_send_s)
   enddo
-  !add them to the buffer:
-  conglom_count = 1
-  do while(conglom_count>0)
-    grdi=grdi-1
-    if (grdi<grd%isd+1) exit
-    conglom_count = 0
-    do grdj = grd%jsd+1,grd%jed
+
+  if (debug) then
+    call connect_all_bonds(bergs,ignore_unmatched=.false.)
+  else
+    call connect_all_bonds(bergs,ignore_unmatched=.true.)
+  endif
+
+  call set_conglom_ids(bergs)
+  call mts_remove_unused_bergs(bergs)
+
+  ! For debugging
+  if (bergs%halo_debugging) then
+    do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
       this=>bergs%list(grdi,grdj)%first
       do while (associated(this))
-        if (this%halo_berg>1) then
-          conglom_count=conglom_count+1
-          kick_the_bucket=>this
-          current_halo_status=kick_the_bucket%halo_berg
-          this=>this%next
-          kick_the_bucket%halo_berg=2.
-          nbergs_to_send_e=nbergs_to_send_e+1
-          if (periodicityfix) kick_the_bucket%lon=kick_the_bucket%lon-Lx
-          call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_e, nbergs_to_send_e, bergs%max_bonds)
-          !kick_the_bucket%halo_berg=current_halo_status-2 !unmark
-          kick_the_bucket%halo_berg=current_halo_status
-          last_berg=kick_the_bucket%id
-          if (periodicityfix) kick_the_bucket%lon=kick_the_bucket%lon+Lx
-        else
-          this=>this%next
-        endif
+        write(stderrunit,'(a,5i)')  'transfer_mts_bergs', this%id, mpp_pe(), int(this%halo_berg),  grdi, grdj
+        this=>this%next
       enddo
-    enddo
-  enddo
+    enddo; enddo
+    call show_all_bonds(bergs)
+  endif
 
-  !---Step B: updated summary of current halo_berg statuses on current PE---
-  !halo_berg=0: bergs on computational domain
-  !halo_berg=1: bergs on halo domain
-  !halo_berg=2: conglomerate bergs, packed to send east, from computational domain
-  !halo_berg=3: conglomerate bergs, packed to send east, from halo domain
+end subroutine transfer_mts_bergs
 
-  !now mark non-conglomerate bergs within the contact distance of the conglomerate
-  !to send EAST as halo_berg=halo_berg+4,that also need to sent EAST:
-  last_cell=grd%iec-halo_width+1
-  leavedo=.false.
+!>For the MTS scheme, packs bergs for transfers between PEs to the N,S,E, and W
+subroutine mts_pack_in_dir(bergs,nbergs_to_send,dir)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  integer :: nbergs_to_send !<counter for number of bergs to send
+  character(len=1) :: dir !<indicates PE to the north,south,east,or west
+  ! Local variables
+  type(icebergs_gridded), pointer :: grd
+  type(iceberg), pointer :: berg
+  integer :: halo_width,nc_x,nc_y
+  real :: cds !<contact distance squared
+  logical :: edgecontact
+  integer :: is,ie,js,je,grdi,grdj
+  integer :: ics,ice,jcs,jce
+  integer :: inhs,inhe,jnhs,jnhe
+  real :: pfix !<used to adjust for periodicity
+  real :: hexdenom,rhc(4)
+  real :: clat,clon,dlat,dlon,r_dist
+  integer :: current_conglom_id
+  real :: current_halo_id
+
+  !---INITIALIZATION---!
+  grd=>bergs%grd
+  halo_width=bergs%grd%halo
+  nc_x=bergs%contact_cells_lon; nc_y=bergs%contact_cells_lat
+  cds=bergs%contact_distance**2
+  edgecontact=.false.
+  pfix=0.0
+  hexdenom=2.*sqrt(3.)
+
+  select case (dir)
+  case ("e")
+    !congloms overlapping this range of cells are always sent:
+    is=grd%iec-halo_width+2; ie=grd%ied; js=grd%jsd; je=grd%jed
+    if (grd%Lx>0.0 .and. grd%lon(grd%iec,grd%jec).eq.grd%maxlon_c) pfix=grd%Lx
+    !lat/lon range of halo cells
+    rhc(1)=grd%lon(is-1,js);    rhc(2)=grd%lat(is-1,js)    !min corner
+    rhc(3)=grd%lon(grd%iec,je); rhc(4)=grd%lat(grd%iec,je) !max corner
+    !range for non-halo cells (for contact with conglom)
+    inhs=grd%isd; inhe=is-1; jnhs=js; jnhe=je
+    !range for cells w/in contact dist of edge of comp domain:
+    ics=max(grd%iec-nc_x,grd%isd+1)
+    if (ics<is) then
+      edgecontact=.true.; ice=grd%iec; jcs=js; jce=je
+      clon=grd%lon(grd%iec,grd%jec) !closest lon from the east PE computational domain
+    endif
+  case ("w")
+    is=grd%isd; ie=grd%isc+halo_width-1; js=grd%jsd; je=grd%jed
+    if (grd%Lx>0.0 .and. grd%lon(grd%isc-1,grd%jsc-1).eq.grd%minlon_c) pfix=-grd%Lx
+    rhc(1)=grd%lon(grd%isc-1,js); rhc(2)=grd%lat(grd%isc-1,js)
+    rhc(3)=grd%lon(ie,je);        rhc(4)=grd%lat(ie,je)
+    inhs=ie+1; inhe=grd%ied; jnhs=js; jnhe=je
+    ice=min(grd%isc+nc_x,grd%ied)
+    if (ice>ie) then
+      edgecontact=.true.; ics=grd%isc; jcs=js; jce=je
+      clon=grd%lon(grd%isc-1,grd%jsc-1)
+    endif
+  case ("n")
+    is=grd%isd; ie=grd%ied; js=grd%jec-halo_width+2; je=grd%jed
+    rhc(1)=grd%lon(is,js-1);    rhc(2)=grd%lat(is,js-1)
+    rhc(3)=grd%lon(ie,grd%jec); rhc(4)=grd%lat(ie,grd%jec)
+    inhs=is; inhe=ie; jnhs=grd%jsd; jnhe=js-1
+    jcs=max(grd%jec-nc_y,grd%jsd+1)
+    if (jcs<js) then
+      edgecontact=.true.; ics=is; ice=ie; jce=grd%jec
+      clat=grd%lat(grd%iec,grd%jec)
+    endif
+  case ("s")
+    is=grd%isd; ie=grd%ied; js=grd%jsd; je=grd%jsc+halo_width-1
+    rhc(1)=grd%lon(is,grd%jsc-1); rhc(2)=grd%lat(is,grd%jsc-1)
+    rhc(3)=grd%lon(ie,je);        rhc(4)=grd%lat(ie,je)
+    inhs=is; inhe=ie; jnhs=je+1; jnhe=grd%jed
+    jce=min(grd%jsc+nc_y,grd%jed)
+    if (jce>je) then
+      edgecontact=.true.; ics=is; ice=ie; jcs=grd%jsc
+      clat=grd%lat(grd%isc-1,grd%jsc-1)
+    endif
+  case default
+    call error_mesg('mts_pack_in_dir', 'dir not specified correctly!', FATAL)
+  end select
+
+  !---MAIN ALGORITHM---:
+  !
+  !The packing procedure is split into the three routines below. A note on bookkeeping:
+  !
+  !-In routines 1 & 2, the sign of berg%id is used to mark if a berg has already been processed
+  !
+  !-The packing routines rely on knowing which neighboring PEs already contain (or will contain,
+  ! after sending) copies of a berg. The locations of copies are tracked using bergs%conglom_id, which
+  ! initially equals zero at the start of subroutine transfer_mts_bergs. Whenever a copy of a berg is
+  ! packed to send to a neighboring PE, the original berg’s conglom_id=conglom_id+a, where a is an integer
+  ! associated with the direction of the PE that the copy will reside (East=4, West=8, North=2, South=1).
+  ! The copy’s conglom_id=conglom_id+b, where b is the integer for the direction of the original
+  ! berg’s PE relative to the PE to which the copy will be sent. From a berg’s growing conglom_id, it is
+  ! possible to backtrack which neighboring PEs contain (or will contain after sending) a copy of the
+  ! berg by using the function mts_berg_sent, which is called in all routines below. Note: during the MTS
+  ! scheme, conglom_id is reset and repurposed for marking bergs that belong to the same conglomerate.
+
+  !1. Pack bergs to send to the neighboring PE in the given dir if they are in the
+  !   corresponding halo cells, or connected to bergs in the halo cells as a conglomerate.
+  do grdj=js,je; do grdi=is,ie
+    berg=>bergs%list(grdi,grdj)%first
+    do while (associated(berg))
+      if (berg%id>0) then !bergs that have already been processed are marked with negative berg%id
+        call mts_mark_and_pack_halo_and_congloms(bergs,berg,dir,nbergs_to_send,pfix,rhc)
+      endif
+      berg=>berg%next
+    enddo
+  enddo;enddo
 
-  do grdi=grd%iec-halo_width+2,grd%isd+1,-1 !outer cell i-loop
-    do grdj = grd%jsd+1,grd%jed !outer cell j-loop
-      this=>bergs%list(grdi,grdj)%first
-      do while (associated(this)) !outer berg loop
-        if (this%halo_berg>1) then
-          !conglomerate berg found. search surroundings for non_conglomerate bergs within the
-          !contact distance, and add to buffer
-          if (grdi<last_cell) last_cell=grdi
-          do grdj2=max(grdj-nc,grd%jsd+1),min(grdj+nc,grd%jed); &
-            do grdi2=max(grdi-nc,grd%isd+1),min(grdi+nc,grd%iec-halo_width+1) !inner cell loop
-            !if (grdi2>grd%iec-halo_width+1) cycle !don't process east halo cells
-            kick_the_bucket=>bergs%list(grdi2,grdj2)%first
-            do while (associated(kick_the_bucket)) ! inner berg loop
-              if (kick_the_bucket%halo_berg < 2) then
-                dx=kick_the_bucket%lon-this%lon
-                dy=kick_the_bucket%lat-this%lat
-                dist=dx*dx+dy*dy
-                if (dist<contact_distance*contact_distance) then
-                  current_halo_status=kick_the_bucket%halo_berg+4
-                  kick_the_bucket%halo_berg=10
-                  nbergs_to_send_e=nbergs_to_send_e+1
-                  if (periodicityfix) kick_the_bucket%lon=kick_the_bucket%lon-Lx
-                  call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_e, nbergs_to_send_e, bergs%max_bonds)
-                  kick_the_bucket%halo_berg=current_halo_status
-                  if (periodicityfix) kick_the_bucket%lon=kick_the_bucket%lon+Lx
-                  if (kick_the_bucket%ine<last_cell) last_cell=kick_the_bucket%ine
-                endif
-              endif
-              kick_the_bucket=>kick_the_bucket%next
-            enddo !inner berg loop
-          enddo; enddo !inner cell loop
-        endif
-        if (this%id==last_berg) then
-          leavedo=.true.
-          this=>null()
-          exit
-        else
-          this=>this%next
-        endif
-      enddo !outer berg loop
-      if (leavedo) exit
-    enddo !outer cell j-loop
-    if (leavedo) exit
-  enddo !outer cell i-loop
-
-  periodicityfix=.false.
-  leavedo=.false.
-
-  !---Step C: updated summary of current halo_berg statuses on current PE---
-  !adding to Step B, we now also have:
-  !halo_berg=4: non-conglomerate bergs on computational domain, within contact distance of conglom to send E
-  !halo_berg=5: non-conglomerate bergs on a halo domain, within contact distance of conglom to send E
-
-  !now go back and reset berg halo statuses that are being sent EAST to the way it was in Step A above
-  do grdi=grd%iec-halo_width+1,last_cell,-1
-    do grdj = grd%jsd+1,grd%jed
-      this=>bergs%list(grdi,grdj)%first
-      do while (associated(this))
-        if (this%halo_berg>1) then
-          if (this%halo_berg<4) then
-            this%halo_berg=this%halo_berg-2
+  !2. Find and pack bergs within contact distance of the bergs on the edge of the conglom
+  do grdj=js,je; do grdi=is,ie
+    berg=>bergs%list(grdi,grdj)%first
+    do while (associated(berg))
+      if (berg%id<0) then !berg was processed in 1. Will be reset to positive berg%id here.
+        call mts_pack_contact_bergs(bergs,berg,dir,pfix,nbergs_to_send,inhs,inhe,jnhs,jnhe)
+      endif
+      berg=>berg%next
+    enddo
+  enddo;enddo
+
+  !3. Find and pack bergs within contact distance to the closest possible coords on the neighbor
+  !   PE, to account for the possibility of a berg being located there.
+  if (edgecontact) then
+    do grdj=jcs,jce; do grdi=ics,ice
+      berg=>bergs%list(grdi,grdj)%first
+      do while (associated(berg))
+        !has the berg already been sent/packed in this dir?
+        if (.not. mts_berg_sent(berg%conglom_id,dir)) then
+          if (dir.eq."e" .or. dir.eq."w") then
+            dlon=berg%lon-clon; dlat=0.0 !lat_ref=berg%lat
+            if (grd%grid_is_latlon) dlon=dlon*pi_180*Rearth*cos(berg%lat*pi_180)
           else
-            this%halo_berg=this%halo_berg-4
+            dlat=berg%lat-clat; dlon=0.0
+            if (grd%grid_is_latlon) dlat=dlat*pi_180*Rearth
+          endif
+          r_dist=dlat**2+dlon**2
+          if (r_dist<cds) then
+            current_conglom_id=berg%conglom_id; current_halo_id=berg%halo_berg
+            berg%halo_berg=10
+            nbergs_to_send=nbergs_to_send+1
+            select case (dir)
+            case ("s")
+              berg%conglom_id=2
+              call pack_berg_into_buffer2(berg, bergs%obuffer_s, nbergs_to_send, bergs%max_bonds)
+              berg%conglom_id=current_conglom_id+1
+            case ("n")
+              berg%conglom_id=1
+              call pack_berg_into_buffer2(berg, bergs%obuffer_n, nbergs_to_send, bergs%max_bonds)
+              berg%conglom_id=current_conglom_id+2
+            case ("w")
+              berg%lon=berg%lon-pfix; berg%conglom_id=4
+              call pack_berg_into_buffer2(berg, bergs%obuffer_w, nbergs_to_send, bergs%max_bonds)
+              berg%lon=berg%lon+pfix; berg%conglom_id=current_conglom_id+8
+            case ("e")
+              berg%lon=berg%lon-pfix; berg%conglom_id=8
+              call pack_berg_into_buffer2(berg, bergs%obuffer_e, nbergs_to_send, bergs%max_bonds)
+              berg%lon=berg%lon+pfix; berg%conglom_id=current_conglom_id+4
+            end select
+            berg%halo_berg=current_halo_id
           endif
         endif
-        this=>this%next
+        berg=>berg%next
       enddo
-    enddo
+    enddo;enddo
+  endif
+end subroutine mts_pack_in_dir
+
+!>find, mark, and pack the halo and conglomerate bergs
+recursive subroutine mts_mark_and_pack_halo_and_congloms(bergs,berg,dir,nbergs_to_send,pfix,rhc)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  type(iceberg), pointer :: berg
+  character(len=1) :: dir
+  integer :: nbergs_to_send
+  real :: pfix !<for periodicity
+  real :: rhc(4) !<lat/lon bounds of halo region for receiving cell
+  ! Local variables
+  type(iceberg), pointer :: other_berg
+  type(bond) , pointer :: current_bond
+  integer :: k !<bond counter
+  integer :: current_conglom_id
+  real :: current_halo_id
+
+  !pack the berg for transfer if it has not been packed already
+  if (.not. mts_berg_sent(berg%conglom_id,dir)) then
+    current_halo_id=berg%halo_berg; current_conglom_id=berg%conglom_id
+    nbergs_to_send=nbergs_to_send+1
+
+    if (berg%lon<rhc(1).or.berg%lat<rhc(2).or.berg%lon>rhc(3).or.berg%lat>rhc(4)) then
+      berg%halo_berg=max(2.,current_halo_id) !outside neighboring PE halo
+    else
+      berg%halo_berg=1 !inside neighboring PE halo
+    endif
+
+    select case (dir)
+    case ("e")
+      berg%conglom_id=8;                    berg%lon=berg%lon-pfix
+      call pack_berg_into_buffer2(berg,bergs%obuffer_e, nbergs_to_send, bergs%max_bonds)
+      berg%conglom_id=current_conglom_id+4; berg%lon=berg%lon+pfix
+    case ("w")
+      berg%conglom_id=4;                    berg%lon=berg%lon-pfix
+      call pack_berg_into_buffer2(berg,bergs%obuffer_w, nbergs_to_send, bergs%max_bonds)
+      berg%conglom_id=current_conglom_id+8; berg%lon=berg%lon+pfix
+    case ("n")
+      berg%conglom_id=1
+      call pack_berg_into_buffer2(berg,bergs%obuffer_n, nbergs_to_send, bergs%max_bonds)
+      berg%conglom_id=current_conglom_id+2
+    case ("s")
+      berg%conglom_id=2
+      call pack_berg_into_buffer2(berg,bergs%obuffer_s, nbergs_to_send, bergs%max_bonds)
+      berg%conglom_id=current_conglom_id+1
+    end select
+
+    berg%halo_berg=current_halo_id
+  endif
+
+  berg%id=-berg%id !marks that the berg has been processed
+
+  !process connected bergs:
+  k=0 !bond counter
+  current_bond=>berg%first_bond
+  do while (associated(current_bond))
+    k=k+1
+    if  (associated(current_bond%other_berg)) then
+      other_berg=>current_bond%other_berg
+      if (other_berg%id>0) then
+        call mts_mark_and_pack_halo_and_congloms(bergs,other_berg,dir,nbergs_to_send,pfix,rhc)
+      endif
+    endif
+    current_bond=>current_bond%next_bond
   enddo
 
-  !---Step D: updated summary of current halo_berg statuses on current PE---
-  ! Same as Step A summary
+  if (k.ne.bergs%max_bonds) then !mark the berg element as belonging to the outer layer of a conglomerate
+    berg%conglom_id=-berg%conglom_id
+  endif
+
+end subroutine mts_mark_and_pack_halo_and_congloms
+
+!>pack the bergs within contact distance of conglom/halo bergs
+recursive subroutine mts_pack_contact_bergs(bergs,berg,dir,pfix,nbergs_to_send,inhs,inhe,jnhs,jnhe)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  type(iceberg), pointer :: berg !< Berg to find contact with
+  character(len=1) :: dir !< north,south,east,or west
+  real :: pfix !< for periodicity
+  integer :: nbergs_to_send
+  integer :: inhs,inhe,jnhs,jnhe !<bounds of non-halo domain, i.e. where contact bergs may exist
+  ! Local variables
+  type(bond) , pointer :: current_bond
+  type(icebergs_gridded), pointer :: grd
+  type(iceberg), pointer :: other_berg
+  integer :: nc_x,nc_y,grdj,grdi,js,je,is,ie
+  integer :: current_conglom_id,radial_contact
+  real :: R1,R2,dlon,dlat,lat_ref,dx_dlon,dy_dlat,r_dist,crit_dist,current_halo_id
+  real :: hexdenom
+  logical :: pack_contacts
+
+  pack_contacts=.false.
+  radial_contact=.false.
+  berg%id=-berg%id !unmark
+
+  if (berg%conglom_id<0) then
+    berg%conglom_id=-berg%conglom_id !unmark
+    grd=>bergs%grd
+    nc_x=bergs%contact_cells_lon; nc_y=bergs%contact_cells_lat
+    grdj=berg%jne; grdi=berg%ine
+    js=max(grdj-nc_y,jnhs); je=min(grdj+nc_y,jnhe)
+    is=max(grdi-nc_x,inhs); ie=min(grdi+nc_x,inhe)
+    !only pack contacs on computational domain (bergs on data domain already sent)
+    if (.not. (je<js .or. ie<is)) pack_contacts=.true.
+  endif
+
+  if (pack_contacts) then
+    if (nc_x.eq.1 .and. nc_y.eq.1) then
+      radial_contact=.true. !contact based on berg radii can occur
+      !radius of current berg:
+      if (bergs%hexagonal_icebergs) then
+        hexdenom=2.*sqrt(3.)
+        R1=sqrt(berg%length*berg%width/hexdenom)
+      else !square packing
+        R1=sqrt(berg%length*berg%width/pi)
+      endif
+    else
+      crit_dist=bergs%contact_distance**2
+    endif
+
+    do grdj=js,je; do grdi=is,ie
+      other_berg=>bergs%list(grdi,grdj)%first
+      do while (associated(other_berg)) ! inner berg loop
+        if (other_berg%id>0) then
+          !has the berg already been sent/packed in this dir?
+          if (.not. mts_berg_sent(other_berg%conglom_id,dir)) then
+            if (radial_contact) then
+              if (bergs%hexagonal_icebergs) then
+                R2=sqrt(other_berg%length*other_berg%width/hexdenom)
+              else
+                R2=sqrt(other_berg%length*other_berg%width/pi)
+              endif
+              crit_dist=max(R1+R2,bergs%contact_distance)**2
+            endif
 
+            if (grd%grid_is_latlon) then
+              lat_ref=0.5*(berg%lat+other_berg%lat)
+              dx_dlon=pi_180*Rearth*cos(lat_ref*pi_180); dy_dlat=pi_180*Rearth
+              dlon=berg%lon-other_berg%lon; dlat=berg%lat-other_berg%lat
+              r_dist=(dlon*dx_dlon)**2 + (dlat*dy_dlat)**2
+            else
+              r_dist=(berg%lon-other_berg%lon)**2 + (berg%lat-other_berg%lat)**2
+            endif
 
-  !----now do Steps A-D for the bergs to send west:----
-  ! conglomerate berg elements to send WEST:
-  last_berg=-1
-  if (Lx>0.0 .and. grd%lon(grd%isc-1,grd%jsc-1).eq. grd%minlon_c) periodicityfix=.true.
-  grdi = grd%isc+halo_width-1
-  do grdj = grd%jsd+1,grd%jed
+            if (r_dist<crit_dist) then       !other_berg is within the contact distance
+              current_halo_id=other_berg%halo_berg; current_conglom_id=other_berg%conglom_id
+              other_berg%halo_berg=10
+              nbergs_to_send=nbergs_to_send+1
+              select case (dir)
+              case ("s")
+                other_berg%conglom_id=2
+                call pack_berg_into_buffer2(other_berg,bergs%obuffer_s, nbergs_to_send, bergs%max_bonds)
+                other_berg%conglom_id=current_conglom_id+1
+              case ("n")
+                other_berg%conglom_id=1
+                call pack_berg_into_buffer2(other_berg,bergs%obuffer_n, nbergs_to_send, bergs%max_bonds)
+                other_berg%conglom_id=current_conglom_id+2
+              case ("w")
+                other_berg%lon=other_berg%lon-pfix; other_berg%conglom_id=4
+                call pack_berg_into_buffer2(other_berg,bergs%obuffer_w, nbergs_to_send, bergs%max_bonds)
+                other_berg%lon=other_berg%lon+pfix; other_berg%conglom_id=current_conglom_id+8
+              case ("e")
+                other_berg%lon=other_berg%lon-pfix; other_berg%conglom_id=8
+                call pack_berg_into_buffer2(other_berg,bergs%obuffer_e, nbergs_to_send, bergs%max_bonds)
+                other_berg%lon=other_berg%lon+pfix; other_berg%conglom_id=current_conglom_id+4
+              end select
+              other_berg%halo_berg=current_halo_id
+            endif
+          endif
+        endif
+        other_berg=>other_berg%next
+      enddo !inner berg loop
+    enddo;enddo
+  endif
+
+  !process connected bergs:
+  current_bond=>berg%first_bond
+  do while (associated(current_bond))
+    if  (associated(current_bond%other_berg)) then
+      other_berg=>current_bond%other_berg
+      if (other_berg%id<0) then
+        call mts_pack_contact_bergs(bergs,other_berg,dir,pfix,nbergs_to_send,inhs,inhe,jnhs,jnhe)
+      endif
+    endif
+    current_bond=>current_bond%next_bond
+  enddo
+end subroutine mts_pack_contact_bergs
+
+!>For MTS scheme, determines if a berg has been packed to send to the neighboring PE in a given direction
+!!based on its evolving conglom_id from subroutines transfer_mts_bergs and mts_pack_in_dir
+logical function mts_berg_sent(conglom_id,dir)
+  integer :: conglom_id
+  character(len=1) :: dir
+
+  mts_berg_sent=.false.
+  select case (dir)
+  case ("e")
+    if (mod(conglom_id,8)>3) mts_berg_sent=.true.
+  case ("w")
+    if (conglom_id>7) mts_berg_sent=.true.
+  case ("n")
+    if (mod(conglom_id,4)>1) mts_berg_sent=.true.
+  case ("s")
+    if (mod(conglom_id,2).eq.1) mts_berg_sent=.true.
+  end select
+end function mts_berg_sent
+
+!>Clear and reassign conglom ids
+subroutine set_conglom_ids(bergs)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  ! Local variables
+  type(icebergs_gridded), pointer :: grd
+  type(iceberg), pointer :: this
+  integer :: grdi,grdj,new_conglom_id
+
+  grd=>bergs%grd
+
+  !Reset all conglom ids to zero
+  do grdj = grd%jsd,grd%jed; do grdi = grd%isd,grd%ied
     this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
-      call mts_mark_conglomerate_bergs(this,grdi,-1)
+      this%conglom_id=0
       this=>this%next
     enddo
-  enddo
-  !add them to the buffer:
-  conglom_count = 1
-  do while(conglom_count>0)
-    grdi=grdi+1
-    if (grdi>grd%ied) exit
-    conglom_count = 0
-    do grdj = grd%jsd+1,grd%jed
-      this=>bergs%list(grdi,grdj)%first
-      do while (associated(this))
-        if (this%halo_berg>1) then
-          conglom_count=conglom_count+1
-          kick_the_bucket=>this
-          current_halo_status=kick_the_bucket%halo_berg
-          this=>this%next
-          kick_the_bucket%halo_berg=2.
-          nbergs_to_send_w=nbergs_to_send_w+1
-          if (periodicityfix) kick_the_bucket%lon=kick_the_bucket%lon+Lx
-          call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_w, nbergs_to_send_w, bergs%max_bonds)
-          !kick_the_bucket%halo_berg=current_halo_status-2 !unmark
-          kick_the_bucket%halo_berg=current_halo_status
-          last_berg=kick_the_bucket%id
-          if (periodicityfix) kick_the_bucket%lon=kick_the_bucket%lon-Lx
-        else
-          this=>this%next
-        endif
-      enddo
+  enddo;enddo
+
+  !Set the conglom_id for conglomerate bergs that overlap the computational domain
+  new_conglom_id=0
+  do grdj = grd%jsc,grd%jec; do grdi=grd%isc,grd%iec
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this))
+      if (this%conglom_id.eq.0) then
+        new_conglom_id=new_conglom_id+1
+        this%conglom_id=new_conglom_id
+        call label_conglomerates(this,new_conglom_id)
+      endif
+      this=>this%next
     enddo
+  enddo;enddo
+end subroutine set_conglom_ids
+
+!>Identify all bergs in the same conglomerate as the given berg, and assign them the given conglom_id
+recursive subroutine label_conglomerates(berg,new_conglom_id)
+  type(iceberg), pointer :: berg,other_berg
+  type(bond) , pointer :: current_bond
+  integer :: new_conglom_id
+
+  current_bond=>berg%first_bond
+  do while (associated(current_bond))
+    if  (associated(current_bond%other_berg)) then
+      other_berg=>current_bond%other_berg
+      if (other_berg%conglom_id.ne.new_conglom_id) then
+        other_berg%conglom_id=new_conglom_id
+        if (other_berg%halo_berg==10) other_berg%halo_berg=2
+        call label_conglomerates(other_berg,new_conglom_id)
+      endif
+    endif
+    current_bond=>current_bond%next_bond
   enddo
+end subroutine label_conglomerates
 
-  !now mark non-conglomerate bergs within the contact distance of the conglomerate
-  !to send WEST as halo_berg=halo_berg+4,that also need to be sent WEST:
-  last_cell=grd%isc+halo_width
+!>Keep only the bergs which are part of, or within contact distance of, a conglomerate that overlaps
+!!the computational domain, or which are halo_berg=1
+subroutine mts_remove_unused_bergs(bergs)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  ! Local variables
+  type(icebergs_gridded), pointer :: grd
+  type(iceberg), pointer :: this,other_berg,kick_the_bucket
+  integer :: i,nc_x,nc_y,is,ie,js,je
+  integer :: grdi, grdj, grdi2, grdj2
+  logical :: contact,radial_contact
+  real :: lat1,lat2,lon1,lon2,dlon,dlat,dx_dlon,dy_dlat,lat_ref
+  real :: r_dist,crit_dist,R1,R2,hexdenom
 
-  do grdi=grd%isc+halo_width-1,grd%ied !outer cell i-loop
-    do grdj = grd%jsd+1,grd%jed !outer cell j-loop
-      this=>bergs%list(grdi,grdj)%first
-      do while (associated(this)) !outer berg loop
-        if (this%halo_berg>1) then
-          !conglomerate berg found. search surroundings for non_conglomerate bergs within the
-          !contact distance, and add to buffer
-          if (grdi>last_cell) last_cell=grdi
-          do grdj2=max(grdj-nc,grd%jsd+1),min(grdj+nc,grd%jed); &
-            do grdi2=max(grdi-nc,grd%isc+halo_width),min(grdi+nc,grd%ied) !inner cell loop
-            !if (grdi2<grd%isc+halo_width) cycle
-            kick_the_bucket=>bergs%list(grdi2,grdj2)%first
-            do while (associated(kick_the_bucket)) ! inner berg loop
-              if (kick_the_bucket%halo_berg < 2) then
-                dx=kick_the_bucket%lon-this%lon
-                dy=kick_the_bucket%lat-this%lat
-                dist=dx*dx+dy*dy
-                if (dist<contact_distance*contact_distance) then
-                  current_halo_status=kick_the_bucket%halo_berg+4
-                  kick_the_bucket%halo_berg=10
-                  nbergs_to_send_w=nbergs_to_send_w+1
-                  if (periodicityfix) kick_the_bucket%lon=kick_the_bucket%lon+Lx
-                  call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_w, nbergs_to_send_w, bergs%max_bonds)
-                  kick_the_bucket%halo_berg=current_halo_status
-                  if (periodicityfix) kick_the_bucket%lon=kick_the_bucket%lon-Lx
-                  if (kick_the_bucket%ine>last_cell) last_cell=kick_the_bucket%ine
-                endif
-              endif
-              kick_the_bucket=>kick_the_bucket%next
-            enddo !inner berg loop
-          enddo; enddo !inner cell loop
-        endif
-        if (this%id==last_berg) then
-          leavedo=.true.
-          this=>null()
-          exit
-        else
-          this=>this%next
-        endif
-      enddo !outer berg loop
-      if (leavedo) exit
-    enddo !outer cell j-loop
-    if (leavedo) exit
-  enddo !outer cell i-loop
-
-  periodicityfix=.false.
-  leavedo=.false.
-
-  !now go back and reset berg halo statuses that are being sent WEST to the way it was in Step A above
-  do grdi=grd%isc+halo_width,last_cell
-    do grdj = grd%jsd+1,grd%jed
+  grd=>bergs%grd
+  nc_x=bergs%contact_cells_lon; nc_y=bergs%contact_cells_lat
+  if (nc_x.eq.1 .and. nc_y.eq.1) then
+    radial_contact=.true. !contact based on berg radii can occur
+    hexdenom=2.*sqrt(3.)
+  else
+    radial_contact=.false.
+    crit_dist=bergs%contact_distance**2
+  endif
+
+  do i =1,4
+    select case (i) !halo cells on each side of the current PE
+    case (1)
+      is=grd%isd+1; ie=grd%isc-1; js=grd%jsd+1; je=grd%jed
+    case (2)
+      is=grd%iec+1; ie=grd%ied;   js=grd%jsd+1; je=grd%jed
+    case (3)
+      is=grd%isc;   ie=grd%iec;   js=grd%jsd+1; je=grd%jsc-1
+    case (4)
+      is=grd%isc;   ie=grd%iec;   js=grd%jec+1; je=grd%jed
+    end select
+
+    ! Loop over the current PE's halo cells
+    do grdj = js,je ;  do grdi = is,ie
       this=>bergs%list(grdi,grdj)%first
       do while (associated(this))
-        if (this%halo_berg>1) then
-          if (this%halo_berg<4) then
-            this%halo_berg=this%halo_berg-2
+        if (this%halo_berg<2 .or. this%conglom_id>0) then !keep true halo and congloms bergs
+          this=>this%next
+        else !if not a halo/conglom berg, then test if w/in contact dist to a conglom/halo berg
+          contact=.false.
+          lat1=this%lat; lon1=this%lon
+          if (radial_contact) then
+            !radius of current berg
+            if (bergs%hexagonal_icebergs) then
+              R1=sqrt(this%length*this%width/hexdenom)
+            else !square packing
+              R1=sqrt(this%length*this%width/pi)
+            endif
+          endif
+          do grdj2=max(grdj-nc_y,grd%jsd+1),min(grdj+nc_y,grd%jed)
+            do grdi2=max(grdi-nc_x,grd%isd+1),min(grdi+nc_x,grd%ied)
+              other_berg=>bergs%list(grdi2,grdj2)%first
+              do while (associated(other_berg))
+                if (other_berg%conglom_id>0) then !test contact w/ conglom berg
+                  lat2=other_berg%lat; lon2=other_berg%lon
+                  dlon=lon2-lon1; dlat=lat2-lat1
+                  if (radial_contact) then
+                    if (bergs%hexagonal_icebergs) then
+                      R2=sqrt(other_berg%length*other_berg%width/hexdenom)
+                    else
+                      R2=sqrt(other_berg%length*other_berg%width/pi)
+                    endif
+                    crit_dist=max(R1+R2,bergs%contact_distance)**2
+                  endif
+                  if (bergs%grd%grid_is_latlon) then
+                    lat_ref=0.5*(lat1+lat2)
+                    dx_dlon=pi_180*Rearth*cos(lat_ref*pi_180); dy_dlat=pi_180*Rearth
+                    r_dist=(dlon*dx_dlon)**2 + (dlat*dy_dlat)**2
+                  else
+                    r_dist=dlon**2 + dlat**2
+                  endif
+                  if (r_dist<crit_dist) then
+                    contact=.true.
+                    exit
+                  endif
+                endif
+                other_berg=>other_berg%next
+              enddo
+              if (contact) exit
+            enddo
+            if (contact) exit
+          enddo
+
+          if (.not. contact) then  !remove if not w/in contact dist to a true halo/conglom berg
+            kick_the_bucket=>this
+            this=>this%next
+            call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
           else
-            this%halo_berg=this%halo_berg-4
+            this%halo_berg=10 !contact berg
+            this=>this%next
           endif
         endif
-        this=>this%next
       enddo
-    enddo
+    enddo; enddo
   enddo
+end subroutine mts_remove_unused_bergs
 
-  !----finished E/W packing----
+!>for MTS velocity verlet, the send and receive call for for transfer_mts_bergs
+subroutine mts_send_and_receive(bergs,nbergs_to_send_e,nbergs_to_send_w,nbergs_to_send_n,nbergs_to_send_s)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  integer :: nbergs_to_send_e, nbergs_to_send_w, nbergs_to_send_n, nbergs_to_send_s
+  ! Local vars
+  type(icebergs_gridded), pointer :: grd
+  integer :: nbergs_rcvd_from_e, nbergs_rcvd_from_w, nbergs_rcvd_from_n, nbergs_rcvd_from_s
+  integer :: i,stderrunit
+
+  ! Get the stderr unit number
+  stderrunit = stderr()
+
+  ! For convenience
+  grd=>bergs%grd
 
   ! Send bergs east
   if (grd%pe_E.ne.NULL_PE) then
@@ -1970,7 +2357,7 @@ subroutine transfer_mts_bergs(bergs)
     nbergs_rcvd_from_w=-999
     call mpp_recv(nbergs_rcvd_from_w, glen=1, from_pe=grd%pe_W, tag=COMM_TAG_1)
     if (nbergs_rcvd_from_w.lt.0) then
-      write(stderrunit,*) 'pe=',mpp_pe(),' received a bad number',nbergs_rcvd_from_w,' from',grd%pe_W,' (W) !!!!!!!!!!!!!!!!!!!!!!'
+      write(stderrunit,*) 'pe=',mpp_pe(),' received a bad number',nbergs_rcvd_from_w,' from',grd%pe_W,' (W) !!!!!'
     endif
     if (nbergs_rcvd_from_w.gt.0) then
       call increase_ibuffer(bergs%ibuffer_w, nbergs_rcvd_from_w,buffer_width)
@@ -1988,7 +2375,7 @@ subroutine transfer_mts_bergs(bergs)
     nbergs_rcvd_from_e=-999
     call mpp_recv(nbergs_rcvd_from_e, glen=1, from_pe=grd%pe_E, tag=COMM_TAG_3)
     if (nbergs_rcvd_from_e.lt.0) then
-      write(stderrunit,*) 'pe=',mpp_pe(),' received a bad number',nbergs_rcvd_from_e,' from',grd%pe_E,' (E) !!!!!!!!!!!!!!!!!!!!!!'
+      write(stderrunit,*) 'pe=',mpp_pe(),' received a bad number',nbergs_rcvd_from_e,' from',grd%pe_E,' (E) !!!!!'
     endif
     if (nbergs_rcvd_from_e.gt.0) then
       call increase_ibuffer(bergs%ibuffer_e, nbergs_rcvd_from_e,buffer_width)
@@ -2001,263 +2388,9 @@ subroutine transfer_mts_bergs(bergs)
     nbergs_rcvd_from_e=0
   endif
 
-  !---Step E. updated summary of current halo_berg statuses on current PE---
-  !halo_berg=0: bergs on computational domain
-  !halo_berg=1: bergs on halo domain
-  !halo_berg=2: conglomerate bergs received from the computational domain of the PE to the East or West
-  !halo_berg=10: bergs received from the computational domain of the PE to the East or West that are
-  !             within contact distance to any of the current PE bergs with halo_berg==1 or 2
-
-  !reconnect bonds in preparation for sending north/south
   call mpp_sync_self()
-  call connect_all_bonds(bergs,ignore_unmatched=.true.)
-  do grdj = grd%jsd+1,grd%jed ;  do grdi = grd%isd+1,grd%ied
-    this=>bergs%list(grdi,grdj)%first
-    do while (associated(this))
-      !The conglomerate elements for the N/S transfers will also be given halo_berg>1 below.
-      !Before the N/S transfer procedure, temporarily change the sign of the conglomerate
-      !halo_berg statuses from the E/W transfers to differentiate between the E/W vs N/S procedures.
-      if (this%halo_berg>1) this%halo_berg=-this%halo_berg
-      this=>this%next
-    enddo
-  enddo; enddo
-
-  nbergs_to_send_n=0
-  nbergs_to_send_s=0
 
-  ! ---Send all berg elements (north/south) in conglomerate---:
-  ! conglomerate berg elements to send NORTH:
-  last_berg=-1
-  do grdj = grd%jec-halo_width+2,grd%jed; do grdi = grd%isd+1,grd%ied
-    this=>bergs%list(grdi,grdj)%first
-    do while (associated(this))
-      call mts_mark_conglomerate_bergs(this,grdj,2)
-      this=>this%next
-    enddo
-  enddo; enddo
-  !add them to the buffer:
-  grdj = grd%jed+1
-  conglom_count = 1
-  do while(conglom_count>0 .or. grdj .ge. grd%jec-halo_width+2)
-    grdj=grdj-1
-    if (grdj<grd%jsd+1) exit
-    conglom_count = 0
-    do grdi = grd%isd,grd%ied
-      this=>bergs%list(grdi,grdj)%first
-      do while (associated(this))
-        if (this%halo_berg>1) then
-          conglom_count=conglom_count+1
-          kick_the_bucket=>this
-          current_halo_status=kick_the_bucket%halo_berg
-          this=>this%next
-          kick_the_bucket%halo_berg=2.
-          nbergs_to_send_n=nbergs_to_send_n+1
-          call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_n, nbergs_to_send_n, bergs%max_bonds)
-          !kick_the_bucket%halo_berg=-(current_halo_status-2) !unmark
-          kick_the_bucket%halo_berg=current_halo_status
-          last_berg=kick_the_bucket%id
-        else
-          this=>this%next
-        endif
-      enddo
-    enddo
-  enddo
-
-    !---Step F. updated summary of current halo_berg statuses on current PE---
-  !halo_berg=0: bergs on computational domain
-  !halo_berg=1: bergs on halo domain
-  !halo_berg=-2: conglomerate bergs received from the computational domain of the PE to the East or West
-  !halo_berg=-10: bergs received from the computational domain of the PE to the East or West that are
-  !             within contact distance to any of the current PE bergs with halo_berg==1 or 2
-  !halo_berg=2:  same as halo_berg=0,   but marked as conglom to send North
-  !halo_berg=3:  same as halo_berg=1,   but marked as conglom to send North
-  !halo_berg=4:  same as halo_berg=-2,  but marked as conglom to send North
-  !halo_berg=12: same as halo_berg=-10, but marked as conglom to send North
-
-  !now mark non-conglomerate bergs within the contact distance of the conglomerate
-  !to send NORTH as halo_berg=halo_berg+111,that also need to sent NORTH:
-  last_cell=grd%jec-halo_width+1
-
-  do grdj=grd%jec-halo_width+2,grd%jsd+1,-1 !outer cell j-loop
-    do grdi = grd%isd+1,grd%ied !outer cell i-loop
-      this=>bergs%list(grdi,grdj)%first
-      do while (associated(this)) !outer berg loop
-        if (this%halo_berg>1) then
-          !conglomerate berg found. search surroundings for non_conglomerate bergs within the
-          !contact distance, and add to buffer
-          if (grdj<last_cell) last_cell=grdj
-          do grdj2=max(grdj-nc,grd%jsd+1),min(grdj+nc,grd%jec-halo_width+1) !inner cell j-loop
-            !if (grdj2>grd%jec-halo_width+1) cycle !don't process east halo cells
-            do grdi2=max(grdi-nc,grd%isd+1),min(grdi+nc,grd%ied) !inner cell i-loop
-              kick_the_bucket=>bergs%list(grdi2,grdj2)%first
-              do while (associated(kick_the_bucket)) ! inner berg loop
-                if (kick_the_bucket%halo_berg < 2) then
-                  dx=kick_the_bucket%lon-this%lon
-                  dy=kick_the_bucket%lat-this%lat
-                  dist=dx*dx+dy*dy
-                  if (dist<contact_distance*contact_distance) then
-                    current_halo_status=kick_the_bucket%halo_berg+111 !guaranteed to be above 100
-                    kick_the_bucket%halo_berg=10
-                    nbergs_to_send_e=nbergs_to_send_n+1
-                    call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_n, nbergs_to_send_n, bergs%max_bonds)
-                    kick_the_bucket%halo_berg=current_halo_status
-                    if (kick_the_bucket%jne<last_cell) last_cell=kick_the_bucket%jne
-                  endif
-                endif
-                kick_the_bucket=>kick_the_bucket%next
-              enddo !inner berg loop
-            enddo !inner cell i-loop
-          enddo !inner cell j-loop
-        endif
-        if (this%id==last_berg) then
-          leavedo=.true.
-          this=>null()
-          exit
-        else
-          this=>this%next
-        endif
-      enddo !outer berg loop
-      if (leavedo) exit
-    enddo !outer cell i-loop
-    if (leavedo) exit
-  enddo !outer cell j-loop
-
-  leavedo=.false.
-
-  !now go back and reset berg halo statuses that are being sent NORTH to the way it was in Step F above
-  do grdj=grd%jec-halo_width+1,last_cell,-1
-    do grdi = grd%isd+1,grd%ied
-      this=>bergs%list(grdi,grdj)%first
-      do while (associated(this))
-        if (this%halo_berg>1) then
-          if (this%halo_berg<4) then
-            this%halo_berg=this%halo_berg-2
-          elseif (this%halo_berg>100) then
-            this%halo_berg=this%halo_berg-111
-          else
-            this%halo_berg=-(this%halo_berg-2)
-          endif
-        endif
-        this=>this%next
-      enddo
-    enddo
-  enddo
-
-  !--do the same for transfers to SOUTH--
-
-  ! conglomerate berg elements to send SOUTH:
-  last_berg=-1
-  do grdj = grd%jsd+1,grd%jsc+halo_width-1; do grdi = grd%isd,grd%ied
-    this=>bergs%list(grdi,grdj)%first
-    do while (associated(this))
-      call mts_mark_conglomerate_bergs(this,grdj,-2)
-      this=>this%next
-    enddo
-  enddo; enddo
-  grdj = grd%jsd
-  !add them to the buffer:
-  conglom_count = 1
-  do while(conglom_count>0 .or. grdj .le. grd%jsc+halo_width-1)
-    grdj=grdj+1
-    if (grdj>grd%jed) exit
-    conglom_count = 0
-    do grdi = grd%isd,grd%ied
-      this=>bergs%list(grdi,grdj)%first
-      do while (associated(this))
-        if (this%halo_berg>1) then
-          conglom_count=conglom_count+1
-          kick_the_bucket=>this
-          current_halo_status=kick_the_bucket%halo_berg
-          this=>this%next
-          kick_the_bucket%halo_berg=2.
-          nbergs_to_send_s=nbergs_to_send_s+1
-          call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_s, nbergs_to_send_s, bergs%max_bonds)
-          !kick_the_bucket%halo_berg=-(current_halo_status-2) !unmark
-          kick_the_bucket%halo_berg=current_halo_status
-          last_berg=kick_the_bucket%id
-        else
-          this=>this%next
-        end if
-      enddo
-    enddo
-  enddo
-
-  !now mark non-conglomerate bergs within the contact distance of the conglomerate
-  !to send SOUTH as halo_berg=halo_berg+111,that also need to be sent SOUTH:
-  last_cell=grd%jsc+halo_width
-
-  do grdj=grd%jsc+halo_width-1,grd%jed !outer cell i-loop
-    do grdi = grd%isd+1,grd%ied !outer cell j-loop
-      this=>bergs%list(grdi,grdj)%first
-      do while (associated(this)) !outer berg loop
-        if (this%halo_berg>1) then
-          !conglomerate berg found. search surroundings for non_conglomerate bergs within the
-          !contact distance, and add to buffer
-          if (grdj>last_cell) last_cell=grdj
-          do grdj2=max(grdj-nc,grd%jsc+halo_width),min(grdj+nc,grd%jed) !inner cell j-loop
-            !if (grdj2<grd%jsc+halo_width) cycle
-            do grdi2=max(grdi-nc,grd%isd+1),min(grdi+nc,grd%ied) !inner cell i-loop
-              kick_the_bucket=>bergs%list(grdi2,grdj2)%first
-              do while (associated(kick_the_bucket)) ! inner berg loop
-                if (kick_the_bucket%halo_berg < 2) then
-                  dx=kick_the_bucket%lon-this%lon
-                  dy=kick_the_bucket%lat-this%lat
-                  dist=dx*dx+dy*dy
-                  if (dist<contact_distance*contact_distance) then
-                    current_halo_status=kick_the_bucket%halo_berg+111
-                    kick_the_bucket%halo_berg=10
-                    nbergs_to_send_n=nbergs_to_send_n+1
-                    call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_n, nbergs_to_send_n, bergs%max_bonds)
-                    kick_the_bucket%halo_berg=current_halo_status
-                    if (kick_the_bucket%jne>last_cell) last_cell=kick_the_bucket%jne
-                  endif
-                endif
-                kick_the_bucket=>kick_the_bucket%next
-              enddo !inner berg loop
-            enddo !inner cell i-loop
-          enddo !inner cell j-loop
-        endif
-        if (this%id==last_berg) then
-          leavedo=.true.
-          this=>null()
-          exit
-        else
-          this=>this%next
-        endif
-      enddo !outer berg loop
-      if (leavedo) exit
-    enddo !outer cell i-loop
-    if (leavedo) exit
-  enddo !outer cell j-loop
-
-  leavedo=.false.
-
-  !now go back and reset berg halo statuses that are being sent SOUTH to the way it was in Step E above
-  do grdj=grd%jsd+1,grd%jed
-    do grdi = grd%isd+1,grd%ied
-      this=>bergs%list(grdi,grdj)%first
-      do while (associated(this))
-        if (this%halo_berg>1) then
-          if (this%halo_berg<4) then
-            this%halo_berg=this%halo_berg-2
-          elseif (this%halo_berg>100) then
-            this%halo_berg=abs(this%halo_berg-111)
-          else
-            this%halo_berg=this%halo_berg-2
-          endif
-        elseif (this%halo_berg<0) then
-          this%halo_berg=abs(this%halo_berg)
-        endif
-        this=>this%next
-      enddo
-    enddo
-  enddo
-
-  !---Step G. updated summary of current halo_berg statuses on current PE---
-  ! Same as Step E
-
-
- ! Send bergs north
+  ! Send bergs north
   if (grd%pe_N.ne.NULL_PE) then
     if(folded_north_on_pe) then
       call mpp_send(nbergs_to_send_n, plen=1, to_pe=grd%pe_N, tag=COMM_TAG_9)
@@ -2286,7 +2419,7 @@ subroutine transfer_mts_bergs(bergs)
     nbergs_rcvd_from_s=-999
     call mpp_recv(nbergs_rcvd_from_s, glen=1, from_pe=grd%pe_S, tag=COMM_TAG_5)
     if (nbergs_rcvd_from_s.lt.0) then
-      write(stderrunit,*) 'pe=',mpp_pe(),' received a bad number',nbergs_rcvd_from_s,' from',grd%pe_S,' (S) !!!!!!!!!!!!!!!!!!!!!!'
+      write(stderrunit,*) 'pe=',mpp_pe(),' received a bad number',nbergs_rcvd_from_s,' from',grd%pe_S,' (S) !!!!!'
     endif
     if (nbergs_rcvd_from_s.gt.0) then
       call increase_ibuffer(bergs%ibuffer_s, nbergs_rcvd_from_s,buffer_width)
@@ -2308,7 +2441,7 @@ subroutine transfer_mts_bergs(bergs)
       call mpp_recv(nbergs_rcvd_from_n, glen=1, from_pe=grd%pe_N, tag=COMM_TAG_7)
     endif
     if (nbergs_rcvd_from_n.lt.0) then
-      write(stderrunit,*) 'pe=',mpp_pe(),' received a bad number',nbergs_rcvd_from_n,' from',grd%pe_N,' (N) !!!!!!!!!!!!!!!!!!!!!!'
+      write(stderrunit,*) 'pe=',mpp_pe(),' received a bad number',nbergs_rcvd_from_n,' from',grd%pe_N,' (N) !!!!!'
     endif
     if (nbergs_rcvd_from_n.gt.0) then
       call increase_ibuffer(bergs%ibuffer_n, nbergs_rcvd_from_n,buffer_width)
@@ -2326,73 +2459,7 @@ subroutine transfer_mts_bergs(bergs)
   endif
 
   call mpp_sync_self()
-
-  ! For debugging
-  if (halo_debugging) then
-    call mpp_sync_self()
-    do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
-      this=>bergs%list(grdi,grdj)%first
-      do while (associated(this))
-        write(stderrunit,'(a,5i)')  'MTS_C', this%id, mpp_pe(), int(this%halo_berg),  grdi, grdj
-        this=>this%next
-      enddo
-    enddo; enddo
-    call show_all_bonds(bergs)
-  endif
-
-end subroutine transfer_mts_bergs
-
-
-!> For the MTS scheme, marks the conglomerate icebergs elements that overlap
-!! multiple processors as berg%halo_berg>1.
-recursive subroutine mts_mark_conglomerate_bergs(berg,completedcell,dir)
-  type(iceberg), pointer :: berg
-  integer,intent(in) :: completedcell !<column of halo cells that has already sent bergs
-  integer, intent(in) :: dir !<direction bergs will be sent. East/West=1, North/South=2
-  integer :: k
-  type(iceberg), pointer :: other_berg
-  type(bond) , pointer :: current_bond
-
-  current_bond=>berg%first_bond
-  do while (associated(current_bond))
-    if  (associated(current_bond%other_berg)) then
-      other_berg=>current_bond%other_berg
-      if (abs(dir) == 1) then         !for an east/west transfer
-        !to east
-        if (dir==1) then
-          !mark other berg if not already marked, and not in halo cell (which has already been processed)
-          if (other_berg%halo_berg<2 .and. other_berg%ine .lt. completedcell) then
-            other_berg%halo_berg=other_berg%halo_berg+2
-            call mts_mark_conglomerate_bergs(other_berg,completedcell,dir)
-          end if
-        else
-          !to west
-          if (other_berg%halo_berg<2 .and. other_berg%ine .gt. completedcell) then
-            other_berg%halo_berg=other_berg%halo_berg+2
-            call mts_mark_conglomerate_bergs(other_berg,completedcell,dir)
-          end if
-        end if
-      elseif (abs(dir) == 2) then     !for a north/south transfer
-        if (dir == 2) then
-          !to north
-          !mark other berg if not already marked. The other berg can be located in a halo cell, but only
-          !if it has ended up there from being passed between PEs during the earlier E/W conglomerate transfer
-          if ((other_berg%halo_berg<2 .and. other_berg%jne .lt. completedcell) .or. other_berg%halo_berg<1) then
-            other_berg%halo_berg=abs(other_berg%halo_berg)+2
-            call mts_mark_conglomerate_bergs(other_berg,completedcell,dir)
-          end if
-        else
-          !to south
-          if ((other_berg%halo_berg<2 .and. other_berg%jne .gt. completedcell) .or. other_berg%halo_berg<1) then
-            other_berg%halo_berg=abs(other_berg%halo_berg)+2
-            call mts_mark_conglomerate_bergs(other_berg,completedcell,dir)
-          end if
-        end if
-      end if
-    end if
-    current_bond=>current_bond%next_bond
-  enddo
-end subroutine mts_mark_conglomerate_bergs
+end subroutine mts_send_and_receive
 
 
 !> Destroys all bergs in a list
@@ -2450,14 +2517,14 @@ subroutine send_bergs_to_other_pes(bergs)
           this=>this%next
           nbergs_to_send_e=nbergs_to_send_e+1
           call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_e, nbergs_to_send_e, bergs%max_bonds  )
-          call move_trajectory(bergs, kick_the_bucket)
+          if (.not. bergs%debug_write) call move_trajectory(bergs, kick_the_bucket)
           call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
         elseif (this%ine.lt.bergs%grd%isc) then
           kick_the_bucket=>this
           this=>this%next
           nbergs_to_send_w=nbergs_to_send_w+1
           call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_w, nbergs_to_send_w, bergs%max_bonds  )
-          call move_trajectory(bergs, kick_the_bucket)
+          if (.not. bergs%debug_write) call move_trajectory(bergs, kick_the_bucket)
           call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
         else
           this=>this%next
@@ -2535,14 +2602,14 @@ subroutine send_bergs_to_other_pes(bergs)
           this=>this%next
           nbergs_to_send_n=nbergs_to_send_n+1
           call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_n, nbergs_to_send_n,bergs%max_bonds)
-          call move_trajectory(bergs, kick_the_bucket)
+          if (.not. bergs%debug_write) call move_trajectory(bergs, kick_the_bucket)
           call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
         elseif (this%jne.lt.bergs%grd%jsc) then
           kick_the_bucket=>this
           this=>this%next
           nbergs_to_send_s=nbergs_to_send_s+1
           call pack_berg_into_buffer2(kick_the_bucket, bergs%obuffer_s, nbergs_to_send_s,bergs%max_bonds)
-          call move_trajectory(bergs, kick_the_bucket)
+          if (.not. bergs%debug_write) call move_trajectory(bergs, kick_the_bucket)
           call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
         else
           this=>this%next
@@ -2716,6 +2783,7 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
   call push_buffer_value(buff%data(:,n), counter, id_ij)
 
   if (mts) then
+    call push_buffer_value(buff%data(:,n), counter, berg%conglom_id)
     call push_buffer_value(buff%data(:,n), counter, berg%uvel_prev)
     call push_buffer_value(buff%data(:,n), counter, berg%vvel_prev)
     call push_buffer_value(buff%data(:,n), counter, berg%axn_fast)
@@ -2740,6 +2808,9 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
     current_bond=>berg%first_bond
     do k = 1,max_bonds
       if (associated(current_bond)) then
+        if (current_bond%other_id==0) then
+          print *,'zero other id',berg%id,mpp_pe()
+        endif
         call split_id(current_bond%other_id, id_cnt, id_ij)
         call push_buffer_value(buff%data(:,n), counter, id_cnt)
         call push_buffer_value(buff%data(:,n), counter, id_ij)
@@ -2908,6 +2979,7 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
   localberg%id = id_from_2_ints(id_cnt, id_ij)
 
   if (bergs%mts) then
+    call pull_buffer_value(buff%data(:,n), counter, localberg%conglom_id)
     call pull_buffer_value(buff%data(:,n), counter, localberg%uvel_prev)
     call pull_buffer_value(buff%data(:,n), counter, localberg%vvel_prev)
     call pull_buffer_value(buff%data(:,n), counter, localberg%axn_fast)
@@ -2934,52 +3006,28 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
   localberg%lon_old=localberg%lon
   localberg%lat_old=localberg%lat
 
-
   !when using MTS Verlet, iceberg elements that are part of a conglomerate may lie outside
   !of the PE's grid. They are assigned to the berg list of the nearest halo cell.
   !The global (lon/lat) and local (xi,yi) coords of these elements are not adjusted.
   if (bergs%mts .and. abs(localberg%halo_berg)>1) then
-    temp_lon = localberg%lon
-    temp_lat = localberg%lat
+    temp_lon = localberg%lon; temp_lat = localberg%lat
 
     if (temp_lon > grd%lon(grd%ied,grd%jed)) then
       temp_lon = grd%lonc(grd%ied,grd%jed)
-    endif
-    if (temp_lon < grd%lon(grd%isd,grd%jsd)) then
+    elseif (temp_lon < grd%lon(grd%isd,grd%jsd)) then
       temp_lon = grd%lonc(grd%isd+1,grd%jsd+1)
     endif
     if (temp_lat > grd%lat(grd%ied,grd%jed)) then
       temp_lat = grd%latc(grd%ied,grd%jed)
-    endif
-    if (temp_lat < grd%lat(grd%isd,grd%jsd)) then
+    elseif (temp_lat < grd%lat(grd%isd,grd%jsd)) then
       temp_lat = grd%latc(grd%isd+1,grd%jsd+1)
     endif
 
     lres=find_cell_wide(grd, temp_lon, temp_lat, localberg%ine, localberg%jne)
     if (lres) then
-      duplicate=.false.
-      this=>bergs%list(localberg%ine,localberg%jne)%first
-      do while (associated(this) .and. .not. duplicate)
-        if (this%id.eq.localberg%id) then
-          if (this%halo_berg==10) then
-            kick_the_bucket=>this
-            this=>this%next
-            print *,'deleting an iceberg from the list',mpp_pe()
-            call delete_iceberg_from_list(bergs%list(localberg%ine,localberg%jne)%first,kick_the_bucket)
-            print *,'deleted an iceberg from the list',mpp_pe()
-          else
-            duplicate=.true.
-            this=>this%next
-          endif
-        else
-          this=>this%next
-        endif
-      end do
-      if (.not. duplicate) then
-        call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg,this)
-      else
-        return
-      end if
+      call unpack_duplicate_check(bergs,localberg,duplicate)
+      if (duplicate) return
+      call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg,this)
     else
       write(stderrunit,'("KID, unpack_berg_from_buffer pe=(",i3,a,2i4,a,2f8.2)')&
         & mpp_pe(),') Failed to find i,j=',localberg%ine,localberg%jne,&
@@ -3007,17 +3055,23 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
   else
     ! force_app=.true.
     if(force_app) then !force append with origin ine,jne (for I/O)
+      call unpack_duplicate_check(bergs,localberg,duplicate)
+      if (duplicate) return
       call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg, this)
     else
       ! lres=find_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
       !this version is faster, by checking if current ine and jne are appropriate before searching rest of cells.
       lres=check_and_find_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
       if (lres) then
+        call unpack_duplicate_check(bergs,localberg,duplicate)
+        if (duplicate) return
         lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
         call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg,this)
       else
         lres=find_cell_wide(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
         if (lres) then
+          call unpack_duplicate_check(bergs,localberg,duplicate)
+          if (duplicate) return
           lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
           call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg,this)
         else
@@ -3147,6 +3201,7 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj)
     call push_buffer_value(buff%data(:,n),counter,traj%ssh_x)
     call push_buffer_value(buff%data(:,n),counter,traj%ssh_y)
     call push_buffer_value(buff%data(:,n),counter,traj%sst)
+    call push_buffer_value(buff%data(:,n),counter,traj%sss)
     call push_buffer_value(buff%data(:,n),counter,traj%cn)
     call push_buffer_value(buff%data(:,n),counter,traj%hi)
     call push_buffer_value(buff%data(:,n),counter,traj%axn)
@@ -3155,15 +3210,11 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj)
     call push_buffer_value(buff%data(:,n),counter,traj%byn)
     call push_buffer_value(buff%data(:,n),counter,traj%halo_berg)
     call push_buffer_value(buff%data(:,n),counter,traj%static_berg)
-    call push_buffer_value(buff%data(:,n),counter,traj%sss)
 
     if (mts) then
+      call push_buffer_value(buff%data(:,n),counter,traj%conglom_id)
       call push_buffer_value(buff%data(:,n),counter,traj%uvel_prev)
       call push_buffer_value(buff%data(:,n),counter,traj%vvel_prev)
-      call push_buffer_value(buff%data(:,n),counter,traj%axn_fast)
-      call push_buffer_value(buff%data(:,n),counter,traj%ayn_fast)
-      call push_buffer_value(buff%data(:,n),counter,traj%bxn_fast)
-      call push_buffer_value(buff%data(:,n),counter,traj%byn_fast)
     endif
   endif
 
@@ -3207,6 +3258,7 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj)
     call pull_buffer_value(buff%data(:,n),counter,traj%ssh_x)
     call pull_buffer_value(buff%data(:,n),counter,traj%ssh_y)
     call pull_buffer_value(buff%data(:,n),counter,traj%sst)
+    call pull_buffer_value(buff%data(:,n),counter,traj%sss)
     call pull_buffer_value(buff%data(:,n),counter,traj%cn)
     call pull_buffer_value(buff%data(:,n),counter,traj%hi)
     call pull_buffer_value(buff%data(:,n),counter,traj%axn)
@@ -3215,15 +3267,11 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj)
     call pull_buffer_value(buff%data(:,n),counter,traj%byn)
     call pull_buffer_value(buff%data(:,n),counter,traj%halo_berg)
     call pull_buffer_value(buff%data(:,n),counter,traj%static_berg)
-    call pull_buffer_value(buff%data(:,n),counter,traj%sss)
 
     if (mts) then
+      call pull_buffer_value(buff%data(:,n),counter,traj%conglom_id)
       call pull_buffer_value(buff%data(:,n),counter,traj%uvel_prev)
       call pull_buffer_value(buff%data(:,n),counter,traj%vvel_prev)
-      call pull_buffer_value(buff%data(:,n),counter,traj%axn_fast)
-      call pull_buffer_value(buff%data(:,n),counter,traj%ayn_fast)
-      call pull_buffer_value(buff%data(:,n),counter,traj%bxn_fast)
-      call pull_buffer_value(buff%data(:,n),counter,traj%byn_fast)
     endif
   endif
   call append_posn(first, traj)
@@ -3313,6 +3361,32 @@ subroutine count_out_of_order(bergs,label)
 
 end subroutine count_out_of_order
 
+!>scans a single cell for duplicate bergs
+subroutine unpack_duplicate_check(bergs,localberg,duplicate)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  type(iceberg) :: localberg !<input iceberg
+  logical :: duplicate
+  ! Local variables
+  type(iceberg), pointer :: this !<bergs for comparison
+
+  duplicate=.false.
+  if (.not. bergs%mts) return
+  this=>bergs%list(localberg%ine,localberg%jne)%first
+  do while (associated(this) .and. .not. duplicate)
+    if (this%id.eq.localberg%id) then
+      if (localberg%halo_berg==10) then
+        this%halo_berg=10
+      elseif (localberg%halo_berg<this%halo_berg) then
+        this%halo_berg=localberg%halo_berg
+      endif
+      duplicate=.true.
+    endif
+    this=>this%next
+  end do
+  this=>null()
+end subroutine unpack_duplicate_check
+
 !> Scans all lists and checks for duplicate identifiers between lists
 subroutine check_for_duplicates(bergs,label)
 ! Arguments
@@ -3429,7 +3503,7 @@ integer function ij_component_of_id(grd, i, j)
   integer :: iNg ! Zonal size of the global grid
 
   ! Using the current grid shape maximizes the numbers of IDs that can be represented
-  ! allowing up to 30-minute uniform global resolution, or potentially finer if non-uniform. 
+  ! allowing up to 30-minute uniform global resolution, or potentially finer if non-uniform.
   iNg = grd%ieg - grd%isg + 1
 
   ! ij_component_of_id is unique number for each grid cell (32-bit integers allow for ~1/100th degree global resolution)
@@ -3885,10 +3959,10 @@ subroutine show_all_bonds(bergs)
             call error_mesg('KID, show all bonds:', 'The bonds are not matching properly!', FATAL)
           endif
         else
-            !print *, 'This bond has an non-assosiated other berg :', berg%id, current_bond%other_id,&
-            !  current_bond%other_berg_ine, current_bond%other_berg_jne, berg%halo_berg,  mpp_pe()
-         !   write(*,'(a,4i,i3,i4)')'This bond has an non-assosiated other berg :', berg%id, current_bond%other_id,&
-         !     current_bond%other_berg_ine, current_bond%other_berg_jne, int(berg%halo_berg),  mpp_pe()
+          ! print *, 'This bond has an non-assosiated other berg :', berg%id, current_bond%other_id,&
+          !   current_bond%other_berg_ine, current_bond%other_berg_jne, berg%halo_berg,  mpp_pe()
+          ! write(*,'(a,4i,i3,i4)')'This bond has an non-assosiated other berg :', berg%id, current_bond%other_id,&
+          !   current_bond%other_berg_ine, current_bond%other_berg_jne, int(berg%halo_berg),  mpp_pe()
         endif
         current_bond=>current_bond%next_bond
       enddo
@@ -3924,16 +3998,10 @@ subroutine connect_all_bonds(bergs,ignore_unmatched)
   !If interacting bergs & domain is periodic, then correct lat & lon for halo bergs - Alex
   call update_latlon(bergs)
 
-  do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+  do grdj = grd%jsd+1,grd%jed ; do grdi = grd%isd+1,grd%ied
 ! do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec  ! Don't connect halo bergs
     berg=>bergs%list(grdi,grdj)%first
     do while (associated(berg)) ! loop over all bergs
-      if (berg%halo_berg==10) then
-        !these bergs only serve the purpose of exerting a contact force on a conglomerate berg
-        !when bergs%contact_distance>0, and bonds are not needed
-        berg=>berg%next
-        cycle
-      endif
       current_bond=>berg%first_bond
       do while (associated(current_bond)) ! loop over all bonds
         !code to find parter bond goes here
@@ -3997,15 +4065,23 @@ subroutine connect_all_bonds(bergs,ignore_unmatched)
             enddo;enddo
           endif
 
-          if (check_match .and. .not.bond_matched) then
+          if (check_match .and. .not.bond_matched .and. berg%halo_berg.ne.10) then
             if (berg%halo_berg .lt. 0.5) then
               missing_bond=.true.
               print * ,'non-halo berg unmatched: ', berg%id, berg%ine, berg%jne, mpp_pe(), &
                 current_bond%other_id, current_bond%other_berg_ine, current_bond%other_berg_jne
               call error_mesg('KID, connect_all_bonds', 'A non-halo bond is missing!!!', FATAL)
             else  ! This is not a problem if the partner berg is not yet in the halo
-              if (bergs%mts) call error_mesg('KID, connect_all_bonds', 'A halo bond is missing!!!', WARNING)
-              if (bergs%mts) print *,'berg,target,x,y,halo_stat',berg%id,current_bond%other_id,i,j,berg%halo_berg
+              if (bergs%mts) then
+                call error_mesg('KID, connect_all_bonds', 'A halo bond is missing!!!', WARNING)
+                print *,'mpp_pe(),berg,target,ine,jne,halo_stat,lon,lat',&
+                  mpp_pe(),berg%id,current_bond%other_id,i,j,berg%halo_berg,berg%lon,berg%lat
+                print *,'mpp_pe(),latbounds:',mpp_pe(),grd%lat(grd%isd,grd%jsd),grd%lat(grd%isc-1,grd%jsc-1),&
+                  grd%lat(grd%iec,grd%jec),grd%lat(grd%ied,grd%jed)
+                print *,'mpp_pe(),lonbounds:',mpp_pe(),grd%lon(grd%isd,grd%jsd),grd%lon(grd%isc-1,grd%jsc-1),&
+                  grd%lon(grd%iec,grd%jec),grd%lon(grd%ied,grd%jed)
+                !bergs%writeandstop=.true.
+              endif
             endif
           endif
         endif
@@ -4125,7 +4201,7 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
             enddo  ! End of loop over the other berg's bonds.
 
             if (bond_is_good) then
-              if (debug) write(stderrunit,*) 'Perfect quality Bond:', berg%id, current_bond%other_id
+              !if (debug) write(stderrunit,*) 'Perfect quality Bond:', berg%id, current_bond%other_id
             else
               if (debug) write(stderrunit,*) 'Non-matching bond...:', berg%id, current_bond%other_id
               num_unmatched_bonds=num_unmatched_bonds+1
@@ -4229,10 +4305,10 @@ subroutine record_posn(bergs)
 integer :: grdi, grdj
 integer :: js,je,is,ie
 
-if (force_all_pes_traj) then
+if (bergs%debug_write) then
   js=bergs%grd%jsd+1; je=bergs%grd%jed; is=bergs%grd%isd+1; ie=bergs%grd%ied
 else
-  js=bergs%grd%jsc; je=bergs%grd%jec; is=bergs%grd%isc; ie=bergs%grd%iec
+  js=bergs%grd%jsc;   je=bergs%grd%jec; is=bergs%grd%isc;   ie=bergs%grd%iec
 endif
 
   do grdj = js,je ; do grdi = is,ie
@@ -4268,19 +4344,16 @@ subroutine record_posn(bergs)
         posn%ayn=this%ayn
         posn%bxn=this%bxn
         posn%byn=this%byn
-        posn%uvel_old=this%uvel_old
-        posn%vvel_old=this%vvel_old
-        posn%lon_old=this%lon_old
-        posn%lat_old=this%lat_old
+        ! posn%uvel_old=this%uvel_old
+        ! posn%vvel_old=this%vvel_old
+        ! posn%lon_old=this%lon_old
+        ! posn%lat_old=this%lat_old
         posn%halo_berg=this%halo_berg
         posn%static_berg=this%static_berg
         if (bergs%mts) then
+          posn%conglom_id=this%conglom_id
           posn%uvel_prev=this%uvel_prev
           posn%vvel_prev=this%vvel_prev
-          posn%axn_fast=this%axn_fast
-          posn%ayn_fast=this%ayn_fast
-          posn%bxn_fast=this%bxn_fast
-          posn%byn_fast=this%byn_fast
         endif
       endif
 
@@ -4368,14 +4441,21 @@ subroutine move_all_trajectories(bergs, delete_bergs)
 ! Local variables
 type(iceberg), pointer :: this, next
 logical :: delete_bergs_after_moving_traj
-integer :: grdi, grdj
+integer :: grdi, grdj, is, ie, js, je
 
   if (bergs%ignore_traj) return
 
   delete_bergs_after_moving_traj = .false.
   if (present(delete_bergs)) delete_bergs_after_moving_traj = delete_bergs
+
+  if (bergs%debug_write) then
+    js=bergs%grd%jsd+1; je=bergs%grd%jed; is=bergs%grd%isd+1; ie=bergs%grd%ied
+  else
+    js=bergs%grd%jsc;   je=bergs%grd%jec; is=bergs%grd%isc;   ie=bergs%grd%iec
+  endif
+
   !do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
-  do grdj = bergs%grd%jsd+1,bergs%grd%jed ; do grdi = bergs%grd%isd+1,bergs%grd%ied
+  do grdj = js,je ; do grdi = is,ie
     this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
       next=>this%next
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index 8d17383..4169c47 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -1258,7 +1258,7 @@ subroutine write_trajectory(trajectory, save_short_traj)
 integer :: uvelpid,vvelpid
 integer :: uoid, void, uiid, viid, uaid, vaid, sshxid, sshyid, sstid, sssid
 integer :: cnid, hiid, hsid
-integer :: mid, did, wid, lid, mbid, hdid
+integer :: mid, did, wid, lid, mbid, hdid, cid
 character(len=37) :: filename
 character(len=7) :: pe_name
 type(xyt), pointer :: this, next
@@ -1399,6 +1399,7 @@ subroutine write_trajectory(trajectory, save_short_traj)
         hiid = inq_varid(ncid, 'hi')
         hsid = inq_varid(ncid, 'halo_berg')
         if (mts) then
+          cid = inq_varid(ncid, 'conglom_id')
           uvelpid = inq_varid(ncid, 'uvel_prev')
           vvelpid = inq_varid(ncid, 'vvel_prev')
         endif
@@ -1438,6 +1439,7 @@ subroutine write_trajectory(trajectory, save_short_traj)
         hiid = def_var(ncid, 'hi', NF_DOUBLE, i_dim)
         hsid = def_var(ncid, 'halo_berg', NF_DOUBLE, i_dim)
         if (mts) then
+          cid = def_var(ncid, 'conglom_id', NF_INT, i_dim)
           uvelpid = def_var(ncid, 'uvel_prev', NF_DOUBLE, i_dim)
           vvelpid = def_var(ncid, 'vvel_prev', NF_DOUBLE, i_dim)
         endif
@@ -1503,6 +1505,8 @@ subroutine write_trajectory(trajectory, save_short_traj)
         call put_att(ncid, hsid, 'long_name', 'halo status')
         call put_att(ncid, hsid, 'units', 'non-dim')
         if (mts) then
+          call put_att(ncid, cid, 'long_name', 'conglomerate id')
+          call put_att(ncid, cid, 'units', 'dimensionless')
           call put_att(ncid, uvelpid, 'long_name', 'zonal speed mts')
           call put_att(ncid, uvelpid, 'units', 'm/s')
           call put_att(ncid, vvelpid, 'long_name', 'meridional speed mts')
@@ -1552,8 +1556,11 @@ subroutine write_trajectory(trajectory, save_short_traj)
         call put_double(ncid, cnid, i, this%cn)
         call put_double(ncid, hiid, i, this%hi)
         call put_double(ncid, hsid, i, this%halo_berg)
-        call put_double(ncid, uvelpid, i, this%uvel_prev)
-        call put_double(ncid, vvelpid, i, this%vvel_prev)
+        if (mts) then
+          call put_int(ncid, cid, i, this%conglom_id)
+          call put_double(ncid, uvelpid, i, this%uvel_prev)
+          call put_double(ncid, vvelpid, i, this%vvel_prev)
+        endif
       endif
       next=>this%next
       deallocate(this)
diff --git a/tests/chaotic_test/.gitignore b/tests/chaotic_test/.gitignore
new file mode 100644
index 0000000..68bcbc9
--- /dev/null
+++ b/tests/chaotic_test/.gitignore
@@ -0,0 +1 @@
+results/
\ No newline at end of file
diff --git a/tests/chaotic_test/README b/tests/chaotic_test/README
new file mode 100644
index 0000000..83093c2
--- /dev/null
+++ b/tests/chaotic_test/README
@@ -0,0 +1,5 @@
+1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
+2.(optional) edit input.nml
+3. run the model: ./RUN
+4, animate the results: animate_trajectories.py
+
diff --git a/tests/chaotic_test/RUN b/tests/chaotic_test/RUN
new file mode 100755
index 0000000..208e8a7
--- /dev/null
+++ b/tests/chaotic_test/RUN
@@ -0,0 +1,5 @@
+rm iceberg_trajectories.nc
+rm iceberg_trajectories.nc.*
+srun -n100 ./../../build/bergs.x
+
+
diff --git a/tests/chaotic_test/animate_trajectories.py b/tests/chaotic_test/animate_trajectories.py
new file mode 100755
index 0000000..28ab658
--- /dev/null
+++ b/tests/chaotic_test/animate_trajectories.py
@@ -0,0 +1,121 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+import matplotlib.pyplot as plt
+from matplotlib.animation import FuncAnimation
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
+                    help=''' provide filename to plot''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+
+
+def main(args ):
+
+    print('reading file')
+
+    filename=args.fname
+    #filename = 'iceberg_trajectories.nc'
+    field = 'lon'
+    field2 = 'lat'
+
+    with nc.Dataset(filename) as file:
+        x = file.variables['lon'][:]/1.e4
+        y = file.variables['lat'][:]/1.e4 #10km
+        day = file.variables['day'][:]
+
+    ud = np.unique(day)
+    t = ud[0]
+
+    # frame info
+    num_frames = len(ud)
+    movie_len = 5.0 #seconds
+    frame_len = 1000.0*movie_len/num_frames
+
+    xmin = 0 #np.floor(min(min(x),min(y),0))
+    xmax = 100 #20 #np.ceil(max(max(x),max(y),20))
+    ymin = xmin
+    ymax = xmax
+
+    anim_running = True
+
+    def animate(i):
+
+        x1 = x[day == ud[i]]
+        y1 = y[day == ud[i]]
+        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
+
+        scat.set_offsets(data)
+
+        t = ud[i]
+        time_text.set_text('time = %.1f days' % t )
+        return scat,time_text
+
+    def init():
+        scat.set_offsets([])
+        return scat,
+
+    def onClick(event):
+        global anim_running
+        if anim_running:
+            ani.event_source.stop()
+            anim_running = False
+        else:
+            ani.event_source.start()
+            anim_running = True
+
+    # Now we can do the plotting!
+    f = plt.figure(figsize=(5,5))
+    f.tight_layout()
+    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
+    scat = ax1.scatter([],[],marker='o',facecolor='w',s=10,edgecolor='red')
+    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
+
+    # Change major ticks 
+    ax1.xaxis.set_major_locator(MultipleLocator(10))
+    ax1.yaxis.set_major_locator(MultipleLocator(10))
+
+    ax1.xaxis.set_minor_locator(MultipleLocator(5))
+    ax1.yaxis.set_minor_locator(MultipleLocator(5))
+
+    # Turn grid on for both major and minor ticks and style minor slightly
+    # differently.
+    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
+    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
+
+    ax1.set_xlabel('x (10 km)')
+    ax1.set_ylabel('y (10 km)')
+    ax1.set_title('Iceberg trajectory')
+
+    f.canvas.mpl_connect('button_press_event', onClick)
+
+    ani = FuncAnimation(
+        f,animate,init_func=init,frames=num_frames,
+        interval=frame_len,blit=True,repeat=True)
+
+    print('time',t)
+
+    plt.show()
+    #animation.save("iceberg_traj_animation.mp4")
+
+
+print('Script complete')
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
diff --git a/tests/chaotic_test/animate_trajectories_1pe.py b/tests/chaotic_test/animate_trajectories_1pe.py
new file mode 100755
index 0000000..e115e29
--- /dev/null
+++ b/tests/chaotic_test/animate_trajectories_1pe.py
@@ -0,0 +1,158 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+import matplotlib.pyplot as plt
+from matplotlib.animation import FuncAnimation
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc.0000',
+                    help=''' provide filename to plot''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+
+
+def main(args):
+
+    print('reading file')
+
+    filename=args.fname
+    field = 'lon'
+    field2 = 'lat'
+
+    with nc.Dataset(filename) as file:
+        x = file.variables['lon'][:]/1.e4
+        y = file.variables['lat'][:]/1.e4
+        day = file.variables['day'][:]
+        hs = file.variables['halo_berg'][:]
+        idij = file.variables['id_ij'][:]
+        idcnt = file.variables['id_cnt'][:]
+
+    ud = np.unique(day)
+    t = ud[0]
+
+    print('unique hs',np.unique(hs))
+
+    # frame info
+    num_frames = len(ud)
+    movie_len = 5.0 #seconds
+    frame_len = 1000.0*movie_len/num_frames
+
+    xmin = 25
+    xmax = 65
+    ymin = 40
+    ymax = 70
+
+    anim_running = True
+
+    def animate(i):
+
+        x1 = x[day == ud[i]]
+        y1 = y[day == ud[i]]
+        hstat = hs[day == ud[i]]
+        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
+        idd = idij[day == ud[i]]
+        idc = idcnt[day == ud[i]]
+
+        cstring=[]
+        for j in range(len(hstat)):
+
+            if (hstat[j]<0):
+                cstring.append("y")
+            elif (hstat[j]==0):
+                cstring.append("b")
+            elif (hstat[j]==1):
+                cstring.append("r")
+            elif (hstat[j]==2):
+                cstring.append("g")
+            elif (hstat[j]==10):
+                cstring.append("c")
+            else:
+                cstring.append("k")
+
+        scat.set_offsets(data)
+        scat.set_color(cstring)
+        scat.set_edgecolor('none')
+
+        t = ud[i]
+        time_text.set_text('time = %.1f days' % t )
+        return scat,time_text
+
+    def init():
+        scat.set_offsets([])
+        return scat,
+
+    def onClick(event):
+        global anim_running
+        if anim_running:
+            ani.event_source.stop()
+            anim_running = False
+        else:
+            ani.event_source.start()
+            anim_running = True
+
+    # Now we can do the plotting!
+    f = plt.figure(figsize=(5,5))
+    f.tight_layout()
+    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
+    scat = ax1.scatter([],[],marker='o',s=6)
+    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
+
+    # Turn grid on for both major and minor ticks and style minor slightly
+    # differently.
+    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
+    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
+
+    ax1.set_xlabel('x (km)')
+    ax1.set_ylabel('y (km)')
+    ax1.set_title('Iceberg trajectory')
+
+    f.canvas.mpl_connect('button_press_event', onClick)
+
+    ani = FuncAnimation(
+        f,animate,init_func=init,frames=num_frames,
+        interval=frame_len,blit=True,repeat=False)
+
+    print('time',t)
+
+    jsd=49
+    jsc=50
+    jec=60
+    jed=61.5
+    isd=39
+    isc=40
+    iec=50
+    ied=51.5
+
+    plt.plot([isc,isc],[jsc,jec],'k-',lw=1)
+    plt.plot([iec,iec],[jsc,jec],'k-',lw=1)
+    plt.plot([isc,iec],[jsc,jsc],'k-',lw=1)
+    plt.plot([isc,iec],[jec,jec],'k-',lw=1)
+
+    plt.plot([isd,isd],[jsd,jed],'b:',lw=1)
+    plt.plot([ied,ied],[jsd,jed],'b:',lw=1)
+    plt.plot([isd,ied],[jsd,jsd],'b:',lw=1)
+    plt.plot([isd,ied],[jed,jed],'b:',lw=1)
+
+    plt.show()
+    #animation.save("iceberg_traj_animation.mp4")
+
+
+print('Script complete')
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
diff --git a/tests/chaotic_test/diag_table b/tests/chaotic_test/diag_table
new file mode 100644
index 0000000..c1c8819
--- /dev/null
+++ b/tests/chaotic_test/diag_table
@@ -0,0 +1,3 @@
+"icebergs test"
+1 1 1 0 0 0
+
diff --git a/tests/chaotic_test/input.nml b/tests/chaotic_test/input.nml
new file mode 100644
index 0000000..8c8d433
--- /dev/null
+++ b/tests/chaotic_test/input.nml
@@ -0,0 +1,160 @@
+!KID, bergs_chksum: write_restart berg chksum=            1999445081 chksum2=           -1410727016 chksum3=             622127949 chksum4=             622127949 chksum5=            2101409293 #=                 11795
+!KID, grd_chksum2:    # of bergs/cell chksum=                     0 chksum2=                     0 min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
+! All iceberg bonds are connected and working well
+!KID, write_restart: writing calving.res.nc                     
+!KID, grd_chksum3:   write stored_ice chksum=             879111700 chksum2=           -1289231459 min= 0.000000000E+00 max= 7.399978449E+11 mean= 7.819993372E+10 rms= 1.579219025E+11 sd= 1.372009390E+11
+
+&icebergs_driver_nml
+  ni=200 !number of elements, x direction
+  nj=200 !number of elements, y direction
+  ibdt=1800.0 !seconds
+  ibuo=0.2 !ocean x velocity
+  ibvo=0.2 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=1460 !~2 months !8760!1 year !total simulation hours
+  nmax=99999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.true.
+  collision_test=.false.
+  chaotic_test=.true.
+  gridres=5.e3
+/
+
+&icebergs_nml
+
+    !defaults given in parentheses:
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=40 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
+    contact_distance=8.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7 !(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+
+    halo=3 !(4) halo width
+    Lx=1000.e3 ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    rho_bergs=850. ! (850) iceberg density
+    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=2.0 !0.4 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+
+    verbose=.true. !(F) Be verbose to stderr
+    verbose_hrs=24 ! (24) Period between verbose messages
+    traj_sample_hrs=24 !.5 !1 !(24) sampling period for trajectory storage
+    traj_write_hrs=24 !(480) Period for writing sampled trajectories to disk
+    budget=.true. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.!(F) Init bond b/w bergs if dist<1.25*radius
+    length_for_manually_initialize_bonds=0.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+       fms_netcdf_restart=.false.
+       threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE' !'ROUTINE'
+       domains_stack_size = 200000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/chaotic_test/makeberg/RUN b/tests/chaotic_test/makeberg/RUN
new file mode 100755
index 0000000..d985f3f
--- /dev/null
+++ b/tests/chaotic_test/makeberg/RUN
@@ -0,0 +1,3 @@
+rm ./output_files/Generic*
+./makeberg.py
+cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
\ No newline at end of file
diff --git a/tests/chaotic_test/makeberg/makeberg.py b/tests/chaotic_test/makeberg/makeberg.py
new file mode 100755
index 0000000..90efab7
--- /dev/null
+++ b/tests/chaotic_test/makeberg/makeberg.py
@@ -0,0 +1,406 @@
+#!/usr/bin/env python
+import numpy as np
+import math
+from netCDF4 import Dataset
+from pylab import *
+#import pdb
+import netCDF4 as nc
+
+#based on a simple Lehmer "random" number generator
+#where the final result is scaled from 0 to 1
+def lrng(count,m,a,initval):
+
+        r = m % a
+        q = m // a
+
+        z=np.zeros(count+1)
+        z[0]=initval
+
+        for i in range(0,count):
+                t = a * (z[i] % q) - r * (z[i] // q)
+                if (t > 0):
+                        z[i+1]=t
+                else:
+                        z[i+1]=t+m
+        #z = z/m
+
+        #normalize within [0,1]
+        z=z-np.min(z)
+        z=z/(np.max(z))
+
+        return z
+
+def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg):
+
+	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
+	# To copy the global attributes of the netCDF file
+
+	#Input and output files
+	#Create Empty restart file. This is later read so that the attributes can be used.
+	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
+	create_empty_iceberg_restart_file(Empty_restart_filename)
+	#Empty_restart_filename='input_files/icebergs.res.nc'
+
+	#Read empty restart file
+	f=Dataset(Empty_restart_filename,'r') # r is for read only
+	#Write a new restart file
+	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
+
+	for attname in f.ncattrs():
+		    setattr(g,attname,getattr(f,attname))
+
+
+	# To copy the dimension of the netCDF file
+	for dimname,dim in f.dimensions.iteritems():
+		# if you want to make changes in the dimensions of the new file
+		# you should add your own conditions here before the creation of the dimension.
+		#g.createDimension(dimname,len(dim))
+		g.createDimension(dimname,Number_of_bergs)
+
+	# To copy the variables of the netCDF file
+
+	for varname,ncvar in f.variables.iteritems():
+		# if you want to make changes in the variables of the new file
+		# you should add your own conditions here before the creation of the variable.
+		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
+		#Proceed to copy the variable attributes
+		for attname in ncvar.ncattrs():
+			setattr(var,attname,getattr(ncvar,attname))
+		#Finally copy the variable data to the new created variable
+		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
+
+		if varname=='i':
+			var[:]=Number_of_bergs
+
+		if varname=='iceberg_num':
+			for j in range(Number_of_bergs):
+				#var[j]=j+1
+				var[j]=iceberg_num[j]
+
+		if varname=='uvel' or varname=='vvel' or varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
+		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
+		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
+		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
+			var[:]=0
+
+		if varname=='mass_scaling':
+			var[:]=mass_scaling
+
+		if varname=='thickness':
+			for j in range(Number_of_bergs):
+				var[j]=thickness[j]
+
+		if varname=='mass':
+			for j in range(Number_of_bergs):
+				var[j]=mass[j]
+
+		if varname=='width'  or varname=='length':
+			for j in range(Number_of_bergs):
+				var[j]=width[j]
+
+		if varname=='lon':
+			for j in range(Number_of_bergs):
+				var[j]=lon[j]
+
+		if varname=='lat':
+			for j in range(Number_of_bergs):
+				var[j]=lat[j]
+
+		if varname=='static_berg':
+			for j in range(Number_of_bergs):
+				var[j]=static_berg[j]
+
+
+	f.close()
+	g.close()
+
+
+def create_empty_iceberg_restart_file(Empty_restart_filename):
+
+	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
+
+	i=f.createDimension('i', None)
+	lon=f.createVariable('i','i')
+
+	lon=f.createVariable('lon','d',('i'))
+	lon.long_name = "longitude" ;
+	lon.units = "degrees_E" ;
+	lon.checksum = "               0" ;
+
+	lat=f.createVariable('lat','d',('i'))
+	lat.long_name = "latitude" ;
+	lat.units = "degrees_N" ;
+	lat.checksum = "               0" ;
+
+	uvel=f.createVariable('uvel','d',('i'))
+	uvel.long_name = "zonal velocity" ;
+	uvel.units = "m/s" ;
+	uvel.checksum = "               0" ;
+
+	vvel=f.createVariable('vvel','d',('i'))
+	vvel.long_name = "meridional velocity" ;
+	vvel.units = "m/s" ;
+	vvel.checksum = "               0" ;
+
+	mass=f.createVariable('mass','d',('i'))
+	mass.long_name = "mass" ;
+	mass.units = "kg" ;
+	mass.checksum = "               0" ;
+
+	axn=f.createVariable('axn','d',('i'))
+	axn.long_name = "explicit zonal acceleration" ;
+	axn.units = "m/s^2" ;
+	axn.checksum = "               0" ;
+
+	ayn=f.createVariable('ayn','d',('i'))
+	ayn.long_name = "explicit meridional acceleration" ;
+	ayn.units = "m/s^2" ;
+	ayn.checksum = "               0" ;
+
+	bxn=f.createVariable('bxn','d',('i'))
+	bxn.long_name = "inplicit zonal acceleration" ;
+	bxn.units = "m/s^2" ;
+	bxn.checksum = "               0" ;
+
+	byn=f.createVariable('byn','d',('i'))
+	byn.long_name = "implicit meridional acceleration" ;
+	byn.units = "m/s^2" ;
+	byn.checksum = "               0" ;
+
+	ine=f.createVariable('ine','i',('i'))
+	ine.long_name = "i index" ;
+	ine.units = "none" ;
+	ine.packing = 0 ;
+	ine.checksum = "               0" ;
+
+	jne=f.createVariable('jne','i',('i'))
+	jne.long_name = "j index" ;
+	jne.units = "none" ;
+	jne.packing = 0 ;
+	jne.checksum = "               0" ;
+
+	thickness=f.createVariable('thickness','d',('i'))
+	thickness.long_name = "thickness" ;
+	thickness.units = "m" ;
+	thickness.checksum = "               0" ;
+
+	width=f.createVariable('width','d',('i'))
+	width.long_name = "width" ;
+	width.units = "m" ;
+	width.checksum = "               0" ;
+
+	length=f.createVariable('length','d',('i'))
+	length.long_name = "length" ;
+	length.units = "m" ;
+	length.checksum = "               0" ;
+
+	start_lon=f.createVariable('start_lon','d',('i'))
+	start_lon.long_name = "longitude of calving location" ;
+	start_lon.units = "degrees_E" ;
+	start_lon.checksum = "               0" ;
+
+	start_lat=f.createVariable('start_lat','d',('i'))
+	start_lat.long_name = "latitude of calving location" ;
+	start_lat.units = "degrees_N" ;
+	start_lat.checksum = "               0" ;
+
+	start_year=f.createVariable('start_year','i',('i'))
+	start_year.long_name = "calendar year of calving event" ;
+	start_year.units = "years" ;
+	start_year.packing = 0 ;
+	start_year.checksum = "               0" ;
+
+	iceberg_num=f.createVariable('iceberg_num','i',('i'))
+	iceberg_num.long_name = "identification of the iceberg" ;
+	iceberg_num.units = "dimensionless" ;
+	iceberg_num.packing = 0 ;
+	iceberg_num.checksum = "               0" ;
+
+	start_day=f.createVariable('start_day','d',('i'))
+	start_day.long_name = "year day of calving event" ;
+	start_day.units = "days" ;
+	start_day.checksum = "               0" ;
+
+	start_mass=f.createVariable('start_mass','d',('i'))
+	start_mass.long_name = "initial mass of calving berg" ;
+	start_mass.units = "kg" ;
+	start_mass.checksum = "               0" ;
+
+	mass_scaling=f.createVariable('mass_scaling','d',('i'))
+	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
+	mass_scaling.units = "none" ;
+	mass_scaling.checksum = "               0" ;
+
+	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
+	mass_of_bits.long_name = "mass of bergy bits" ;
+	mass_of_bits.units = "kg" ;
+	mass_of_bits.checksum = "               0" ;
+
+	heat_density=f.createVariable('heat_density','d',('i'))
+	heat_density.long_name = "heat density" ;
+	heat_density.units = "J/kg" ;
+	heat_density.checksum = "               0" ;
+
+	halo_berg=f.createVariable('halo_berg','d',('i'))
+	halo_berg.long_name = "halo_berg" ;
+	halo_berg.units = "dimensionless" ;
+	halo_berg.checksum = "               0" ;
+
+	static_berg=f.createVariable('static_berg','d',('i'))
+	static_berg.long_name = "static_berg" ;
+	static_berg.units = "dimensionless" ;
+	static_berg.checksum = "               0" ;
+
+	f.sync()
+	f.close()
+
+
+
+#-----------------------------------#
+#               Main                #
+#-----------------------------------#
+
+#ice params
+rho_ice=850
+
+#grid parameters (m)
+grdres=5000
+grdxmin=0; grdxmax=1000e3
+grdymin=0; grdymax=1000e3
+
+#--- berg locs: ---
+nbergs_x=10 #num of conglomerate bergs in x-dir
+nbergs_y=10 #num of conglomerate bergs in y-dir
+nbergs=nbergs_x*nbergs_y
+start=50e3; end=950e3; #m
+#center coords of each (rectangular) conglomerate berg (CB=conglomerate berg)
+CBxc=np.linspace(start,end,num=nbergs_x); CByc=np.linspace(start,end,num=nbergs_y)
+#CBxc=np.tile(CBxc,nbergs_y); CByc=np.tile(CByc,nbergs_x)
+CBxc,CByc=np.meshgrid(CBxc,CByc)
+CBxc=CBxc.flatten()
+CByc=CByc.flatten()
+
+#reduced version
+# mask = abs(500e3-CByc)
+# CBxc=CBxc[mask<100e3]
+# CByc=CByc[mask<100e3]
+# mask = abs(500e3-CBxc)
+# CBxc=CBxc[mask<300e3]
+# CByc=CByc[mask<300e3]
+# nbergs=len(CBxc)
+
+#reduced version 2
+#CBxc=CBxc[CByc<100e3]
+#CByc=CByc[CByc<100e3]
+#nbergs=len(CBxc)
+
+#--- Lehmer pseudo-random number generator params ---
+m=2147483647; a=16807l
+iv=a #first value
+
+#--- side lengths for the rectangular bergs ---
+m=2147483647; a=16807 #Lehmer pseudo-random number generator params
+rn=lrng(nbergs+1,m,a,iv) #the pseudo-random numbers
+minn=5e3; maxn=60e3 #bounds of side lengths, in m (diag should be < length of a processor)
+start=0; end=nbergs #slice of random number array with which to work
+CBxl=(maxn-minn)*rn[start:end]+minn #array of berg lengths in the x-dir, adjusted for bounds
+CByl=rn[start+1:end+1] #array of berg lengths in the y-dir
+CByl[CByl<0.33]=0.33 #keep the aspect ratio somewhat realistic
+CBxl=np.around(CBxl)
+CByl=CByl*CBxl
+CByl=np.around(CByl)
+CByl[CByl<minn]=minn
+CByl=CByl.astype(int); CBxl=CBxl.astype(int)
+#flip CBxl and CByl for half of them, so that CBxl is not always > CByl
+yl2=CByl.copy(); xl2=CBxl.copy()
+CByl[start:end:2]=xl2[start:end:2]; CBxl[start:end:2]=yl2[start:end:2]
+
+#--- xmax, xmin, ymax, ymin for each CB --
+CBxmin=CBxc-(0.5*CBxl); CBxmax=CBxc+(0.5*CBxl)
+CBymin=CByc-(0.5*CByl); CBymax=CByc+(0.5*CByl)
+#this shouldn't happen:
+CBxmin[CBxmin<grdxmin]=grdxmin; CBxmax[CBxmax>grdxmax]=grdxmax
+CBymin[CBxmin<grdymin]=grdymin; CBymax[CBymax>grdymax]=grdymax
+CBxc=0.5*(CBxmin+CBxmax); CByc=0.5*(CBymin+CBymax)
+
+#--- min and max thicknesses for each CB ---
+minn=50; maxn=350
+#minn=250; maxn=250
+iv=rn[-1]; rn=lrng(nbergs+1,m,a,iv)
+h1=(maxn-minn)*rn[start:end]+minn
+h2=(maxn-minn)*rn[start+1:end+1]+minn
+CBhmax=np.maximum(h1,h2); CBhmin=np.minimum(h1,h2)
+
+#--- berg element radii ---
+R_frac=0.45
+maxn=(np.sqrt(3)/2.)*(R_frac*grdres) #S is < 0.5 grid res
+minn=maxn/2 # smaller radii are allowed
+iv=rn[-1]; rn=lrng(nbergs+1,m,a,iv)
+CBrad=(maxn-minn)*rn[start:end]+minn
+
+print('maxn,minn',maxn,minn)
+
+#-- create berg elements for each conglomerate berg --
+# CBxc,CByc=center coords for each conglom berg
+# CByl,CBxl=side lengths for each conglom berg
+# CBhmax,CBhmin=max and min thicknesses on each berg
+# CBrad=radius of each berg element
+# CBnx,CBny=number of bergs in each dir
+# CBxmin,CBxmax,CBymin,CBymax
+
+berg_x=[]; berg_y=[]
+berg_id=[]; berg_static=[]
+berg_width=[]; berg_bonds=[]
+berg_h=[]; berg_mass_scaling=[]
+berg_mass=[]
+
+#berg_CBid=[];
+berg_count=0
+
+for i in range(nbergs):
+        x_start=CBxmin[i]+(CBrad[i]*2./np.sqrt(3))
+
+        #pdb.set_trace()
+        if x_start>CBxmax[i]:
+                x_start=CBxmax[i]
+        y_start0=CBymin[i]+CBrad[i]
+        if y_start0>CBymax[i]:
+                y_start0=CBymax[i]
+        element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*(CBrad[i])**2)
+        #H (thickness) is a linear function of a berg element's position from the
+        #center of the CB. H=Hmax at the center of the CB and H=Hmin at a corner of the
+        #CB, where the dist of a corner from the center is:
+        cdistb=np.sqrt((CBxmin[i]-CBxc[i])**2+(CBymin[i]-CByc[i])**2)
+        j=0
+        x_val=x_start
+        #berg_count_start=berg_count
+        while x_val<=CBxmax[i]:
+                y_start=y_start0+((j%2)*CBrad[i])
+                k=0
+                y_val=y_start
+                while y_val<CBymax[i]:
+                        berg_count=berg_count+1
+                        berg_id.append(berg_count)
+                        berg_x.append(x_val)
+                        berg_y.append(y_val)
+                        berg_width.append(sqrt(element_area))
+                        #dist of berg elem from center of CB
+                        bdistc=np.sqrt((x_val-CBxc[i])**2+(y_val-CByc[i])**2)
+                        bh=CBhmin[i]*bdistc/cdistb + CBhmax[i]*(1-bdistc/cdistb)
+                        berg_h.append(bh) #thickness
+                        berg_mass_scaling.append(1)
+                        berg_mass.append(bh*rho_ice*element_area)
+                        berg_static.append(0)
+                        #berg_CBid.append(i)
+                        k=k+1
+                        y_val=y_start+(2*k*CBrad[i])
+                j=j+1
+                x_val=x_start+(np.sqrt(3)*CBrad[i]*j)
+
+print('Number of bergs',berg_count)
+
+#pdb.set_trace()
+
+#Create iceberg restart file
+Ice_geometry_source='Generic'
+Create_iceberg_restart_file(berg_count,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static)
diff --git a/tests/collision_test/animate_trajectories.py b/tests/collision_test/animate_trajectories.py
index 7deaa77..50831d8 100755
--- a/tests/collision_test/animate_trajectories.py
+++ b/tests/collision_test/animate_trajectories.py
@@ -25,7 +25,7 @@ def parseCommandLine():
 
 
 def main(args):
-    
+
     print('reading file')
 
     filename=args.fname
@@ -45,7 +45,7 @@ def main(args):
     num_frames = len(ud)
     movie_len = 5.0 #seconds
     frame_len = 1000.0*movie_len/num_frames
-    
+
     xmin = 0 #np.floor(min(min(x),min(y),0))
     xmax = 20 #np.ceil(max(max(x),max(y),20))
     ymin = xmin
@@ -58,11 +58,11 @@ def animate(i):
         x1 = x[day == ud[i]]
         y1 = y[day == ud[i]]
         data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
-           
+
         scat.set_offsets(data)
-        
+
         t = ud[i]
-        time_text.set_text('time = %.1f days' % t )        
+        time_text.set_text('time = %.1f days' % t )
         return scat,time_text
 
     def init():
@@ -76,8 +76,8 @@ def onClick(event):
             anim_running = False
         else:
             ani.event_source.start()
-            anim_running = True       
-    
+            anim_running = True
+
     # Now we can do the plotting!
     f = plt.figure(figsize=(5,5))
     f.tight_layout()
@@ -100,7 +100,7 @@ def onClick(event):
     ax1.set_xlabel('x (km)')
     ax1.set_ylabel('y (km)')
     ax1.set_title('Iceberg trajectory')
- 
+
     f.canvas.mpl_connect('button_press_event', onClick)
 
     ani = FuncAnimation(
@@ -119,11 +119,3 @@ def onClick(event):
     optCmdLineArgs=	parseCommandLine()
     anim_running = True
     main(optCmdLineArgs)
-
-
-
-
-
-
-
-
diff --git a/tests/collision_test/input.nml b/tests/collision_test/input.nml
index e62d354..802b94f 100644
--- a/tests/collision_test/input.nml
+++ b/tests/collision_test/input.nml
@@ -156,4 +156,4 @@
        clock_grain='MODULE'
        domains_stack_size = 2000000
        clock_flags='SYNC'
-/
\ No newline at end of file
+/
diff --git a/tests/collision_test_mts/animate_trajectories.py b/tests/collision_test_mts/animate_trajectories.py
index 7deaa77..50831d8 100755
--- a/tests/collision_test_mts/animate_trajectories.py
+++ b/tests/collision_test_mts/animate_trajectories.py
@@ -25,7 +25,7 @@ def parseCommandLine():
 
 
 def main(args):
-    
+
     print('reading file')
 
     filename=args.fname
@@ -45,7 +45,7 @@ def main(args):
     num_frames = len(ud)
     movie_len = 5.0 #seconds
     frame_len = 1000.0*movie_len/num_frames
-    
+
     xmin = 0 #np.floor(min(min(x),min(y),0))
     xmax = 20 #np.ceil(max(max(x),max(y),20))
     ymin = xmin
@@ -58,11 +58,11 @@ def animate(i):
         x1 = x[day == ud[i]]
         y1 = y[day == ud[i]]
         data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
-           
+
         scat.set_offsets(data)
-        
+
         t = ud[i]
-        time_text.set_text('time = %.1f days' % t )        
+        time_text.set_text('time = %.1f days' % t )
         return scat,time_text
 
     def init():
@@ -76,8 +76,8 @@ def onClick(event):
             anim_running = False
         else:
             ani.event_source.start()
-            anim_running = True       
-    
+            anim_running = True
+
     # Now we can do the plotting!
     f = plt.figure(figsize=(5,5))
     f.tight_layout()
@@ -100,7 +100,7 @@ def onClick(event):
     ax1.set_xlabel('x (km)')
     ax1.set_ylabel('y (km)')
     ax1.set_title('Iceberg trajectory')
- 
+
     f.canvas.mpl_connect('button_press_event', onClick)
 
     ani = FuncAnimation(
@@ -119,11 +119,3 @@ def onClick(event):
     optCmdLineArgs=	parseCommandLine()
     anim_running = True
     main(optCmdLineArgs)
-
-
-
-
-
-
-
-
diff --git a/tests/collision_test_mts/animate_trajectories_1pe.py b/tests/collision_test_mts/animate_trajectories_1pe.py
index 19db84d..c3839d0 100755
--- a/tests/collision_test_mts/animate_trajectories_1pe.py
+++ b/tests/collision_test_mts/animate_trajectories_1pe.py
@@ -67,7 +67,7 @@ def animate(i):
         cstring=[]
         for j in range(len(hstat)):
             if (hstat[j]<0):
-                cstring.append("y")
+                cstring.append("m")
             elif (hstat[j]==0):                 
                 cstring.append("b")
             elif (hstat[j]==1):
@@ -76,10 +76,10 @@ def animate(i):
                 cstring.append("g")
             elif (hstat[j]==3):
                 cstring.append("k")
-            elif (hstat[j]==4):
-                cstring.append("m")
-            else:
+            elif (hstat[j]==10):
                 cstring.append("c")
+            else:
+                cstring.append("y")
                                                            
         scat.set_offsets(data)
         scat.set_color(cstring)
diff --git a/tests/collision_test_mts/input.nml b/tests/collision_test_mts/input.nml
index 2e78b46..bef4ec7 100644
--- a/tests/collision_test_mts/input.nml
+++ b/tests/collision_test_mts/input.nml
@@ -1,6 +1,6 @@
 !TARGET CHKSUM (1 hr time increments, MTS w/ 20 sub-steps, contact at 1.5e3 m, contact spring 1.e-7, spring_coef 1.0e-5):
-!Total number of bonds is:           52 
-!KID, bergs_chksum: write_restart berg chksum = 44984808 chksum2= 1088077442 chksum3= 609798238  chksum4= 609798238  chksum5= 0            #= 16
+!Total number of bonds is:           52
+!KID, bergs_chksum: write_restart berg chksum = -1984749888 chksum2= 2128479089 chksum3= 609798238  chksum4= 609798238  chksum5= 0            #= 16
 !KID, grd_chksum2 : # of bergs/cell chksum    = 0           chksum2= 0           min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
 !KID, grd_chksum3 : write stored_ice chksum   = -540079793  chksum2= -1237287029 min= 6.393358811E+05 max= 7.380127765E+11 mean= 8.033602570E+10 rms= 1.613270384E+11 sd= 1.399018810E+11
 !KID, grd_chksum2 : write stored_heat chksum  = 0           chksum2= 0           min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
@@ -16,33 +16,34 @@
   ibvi=0.0 !ice y velocity
   ibhrs=48 !total simulation hours
   nmax=99999999 !max number of timesteps
-  saverestart=.true. 
+  saverestart=.true.
   halo=3
-  debug=.false.   
+  debug=.false.
   collision_test=.true. !specific to the current test, must be true here
 /
 
-&icebergs_nml  
+&icebergs_nml
 
     !defaults given in parentheses:
     mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
     mts_sub_steps=20 !1 !30 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
     contact_distance=1.5e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
     contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
 
     halo=3 !(4) halo width
     Lx=20000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
     grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
     grid_is_regular=.True. !(T) Point in cell can be found assuming regular Cartesian grid
     hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move    
-    
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
     rho_bergs=850. ! (850) iceberg density
     spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
     bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
     radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
     tangental_damping_coef=2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val 
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
     LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
     bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
     sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
@@ -65,11 +66,11 @@
     coastal_drift=0.4 !(0.)Vel added to currents to cause bergs to drift away from land cells
     tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
     Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #) 
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
     apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
     apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
     melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met    
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
     use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
     pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
     use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
@@ -80,63 +81,63 @@
     add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
     override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
     use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)    
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread			
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
     set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
 
     iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
     interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...       
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
     use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
     input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
     use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors    
+    max_bonds=6 ! (6) Max # of bonds passed between processors
 
     verbose=.true. !(F) Be verbose to stderr
     verbose_hrs=24 ! (24) Period between verbose messages
     traj_sample_hrs=0.5 !1 !(24) sampling period for trajectory storage
-    traj_write_hrs=0 ! (480) Period for writing sampled trajectories to disk    
+    traj_write_hrs=0 ! (480) Period for writing sampled trajectories to disk
     budget=.true. !(T) Calculate budgets
     debug=.false. !(F) Turn on debugging
     really_debug=.false. !(F) Turn on debugging
     halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id    
-    
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
     parallel_reprod=.true. !(T) Reproduce across different PE decompositions
     save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.False. ! (F) If true, then model does not track trajectory data at all    
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
 
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart 
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
     use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
     manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually    
+    length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
     ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
     generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
     fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
     restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.      
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
     orig_read=.false. !(F) Legacy option that does nothing
     read_old_restarts=.false. ! (F) Legacy option that does nothing
-    
+
     use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
     old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
     make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
     old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
     do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.true. !(F) Force all pes write traj files regardless of io_layout
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
 
     ! Mass thresholds between iceberg classes (kg):
     !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
     initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-    
+
     ! Fraction of calving to apply to this class (non-dim):
     !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
     distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-    
+
     ! Ratio between effective and real iceberg mass (non-dim):
     !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
     mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-    
+
     ! Total thickness of newly calved bergs (m):
     !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
     initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
@@ -150,9 +151,9 @@
          fms_netcdf_restart=.false.
          threading_read='multi'
 /
- 
+
  &fms_nml
        clock_grain='MODULE'
        domains_stack_size = 2000000
        clock_flags='SYNC'
-/
\ No newline at end of file
+/

From 4a15fbe4ce93bde33b77aafaf4eee07b19d61428 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Wed, 6 Jan 2021 11:12:55 -0500
Subject: [PATCH 257/361] 1.  Grounding friction w/ quadratic interpolation of
 ocean floor topography to iceberg elements 2.  Large-scale
 fracture/bond-breaking scheme based on bond normal & angular strain or
 strain-rate 3.  Energy & momentum tracking and plotting (plot_energy.py) 4. 
 Four new test cases to test above 3 changes: tests/ground_frac_test and
 tests/energy_test(1-3) 5.  The new test cases each have new berg
 initialization python scripts (e.g. makeberg.py) 6.  Subroutines to save bond
 trajectories 7.  Fixed error in damping scheme, concerning the projection 8. 
 Identification of elements at conglomerate edges, w/ separate melting/force
 treatment for these edge elements 9.  Separated MTS and STS accel subroutines
 for clarity 10. Some minor changes to MTS scheme, e.g. which velocities used
 at half-steps (ustar) and damping 11. Experimental MTS iterative schemes that
 force convergence of damping velocities. For better conserve momentum/for
 testing the impact on fracture of violating conservation of momentum 12.
 Conversion of .nc to .csv for elements (nc2csv.py) and bonds (nc2csv.py) to
 enable correct visualization in programs such as paraview

g#	new file:   tests/energy_test3/RUN
---
 driver/icebergs_driver.F90                    |   56 +-
 src/icebergs.F90                              | 7222 ++++++++++-------
 src/icebergs_framework.F90                    | 1167 ++-
 src/icebergs_io.F90                           |  371 +-
 tests/.gitignore                              |    1 +
 .../initialize_bergs_in_pattern.py            |   54 +-
 tests/chaotic_test/input.nml                  |    4 +-
 tests/collision_test_mts/input.nml            |    5 +
 tests/energy_test/.gitignore                  |    1 +
 tests/energy_test/README                      |    7 +
 tests/energy_test/RUN                         |    7 +
 tests/energy_test/animate_trajectories.py     |  121 +
 tests/energy_test/animate_trajectories_1pe.py |  180 +
 tests/energy_test/diag_table                  |    3 +
 tests/energy_test/input.nml                   |  177 +
 tests/energy_test/makeberg/README             |    4 +
 tests/energy_test/makeberg/RUN                |    3 +
 tests/energy_test/makeberg/RUN2               |    3 +
 tests/energy_test/makeberg/makeberg.py        |  374 +
 tests/energy_test/makeberg/makeberg2.py       |  276 +
 tests/energy_test2/.gitignore                 |    1 +
 tests/energy_test2/README                     |   20 +
 tests/energy_test2/RUN                        |    7 +
 tests/energy_test2/animate_trajectories.py    |  121 +
 .../energy_test2/animate_trajectories_1pe.py  |  180 +
 tests/energy_test2/diag_table                 |    3 +
 tests/energy_test2/input.nml                  |  176 +
 tests/energy_test2/makeberg/RUN               |    3 +
 tests/energy_test2/makeberg/makeberg.py       |  367 +
 tests/energy_test3/.gitignore                 |    1 +
 tests/energy_test3/README                     |   13 +
 tests/energy_test3/RUN                        |    7 +
 tests/energy_test3/RUN1p                      |    7 +
 tests/energy_test3/animate_trajectories.py    |  128 +
 .../energy_test3/animate_trajectories_1pe.py  |  189 +
 tests/energy_test3/diag_table                 |    3 +
 tests/energy_test3/input.nml                  |  180 +
 tests/energy_test3/makeberg/RUN               |    3 +
 tests/energy_test3/makeberg/makeberg.py       |  374 +
 tests/ground_frac_test/.gitignore             |    1 +
 tests/ground_frac_test/README                 |    5 +
 tests/ground_frac_test/RUN                    |    7 +
 .../ground_frac_test/animate_trajectories.py  |  121 +
 .../animate_trajectories_1pe.py               |  180 +
 tests/ground_frac_test/diag_table             |    3 +
 tests/ground_frac_test/input.nml              |  180 +
 tests/ground_frac_test/makeberg/RUN           |   12 +
 tests/ground_frac_test/makeberg/makeberg.py   |   89 +
 tests/ground_frac_test/reference_input.nml    |  183 +
 tests/nc2csv.py                               |  164 +
 tests/nc2csv_bonds.py                         |  130 +
 tests/plot_energy.py                          |  218 +
 52 files changed, 10023 insertions(+), 3089 deletions(-)
 create mode 100644 tests/energy_test/.gitignore
 create mode 100644 tests/energy_test/README
 create mode 100755 tests/energy_test/RUN
 create mode 100755 tests/energy_test/animate_trajectories.py
 create mode 100755 tests/energy_test/animate_trajectories_1pe.py
 create mode 100644 tests/energy_test/diag_table
 create mode 100644 tests/energy_test/input.nml
 create mode 100644 tests/energy_test/makeberg/README
 create mode 100755 tests/energy_test/makeberg/RUN
 create mode 100755 tests/energy_test/makeberg/RUN2
 create mode 100755 tests/energy_test/makeberg/makeberg.py
 create mode 100755 tests/energy_test/makeberg/makeberg2.py
 create mode 100644 tests/energy_test2/.gitignore
 create mode 100644 tests/energy_test2/README
 create mode 100755 tests/energy_test2/RUN
 create mode 100755 tests/energy_test2/animate_trajectories.py
 create mode 100755 tests/energy_test2/animate_trajectories_1pe.py
 create mode 100644 tests/energy_test2/diag_table
 create mode 100644 tests/energy_test2/input.nml
 create mode 100755 tests/energy_test2/makeberg/RUN
 create mode 100755 tests/energy_test2/makeberg/makeberg.py
 create mode 100644 tests/energy_test3/.gitignore
 create mode 100644 tests/energy_test3/README
 create mode 100755 tests/energy_test3/RUN
 create mode 100755 tests/energy_test3/RUN1p
 create mode 100755 tests/energy_test3/animate_trajectories.py
 create mode 100755 tests/energy_test3/animate_trajectories_1pe.py
 create mode 100644 tests/energy_test3/diag_table
 create mode 100644 tests/energy_test3/input.nml
 create mode 100755 tests/energy_test3/makeberg/RUN
 create mode 100755 tests/energy_test3/makeberg/makeberg.py
 create mode 100644 tests/ground_frac_test/.gitignore
 create mode 100644 tests/ground_frac_test/README
 create mode 100755 tests/ground_frac_test/RUN
 create mode 100755 tests/ground_frac_test/animate_trajectories.py
 create mode 100755 tests/ground_frac_test/animate_trajectories_1pe.py
 create mode 100644 tests/ground_frac_test/diag_table
 create mode 100644 tests/ground_frac_test/input.nml
 create mode 100755 tests/ground_frac_test/makeberg/RUN
 create mode 100755 tests/ground_frac_test/makeberg/makeberg.py
 create mode 100644 tests/ground_frac_test/reference_input.nml
 create mode 100755 tests/nc2csv.py
 create mode 100755 tests/nc2csv_bonds.py
 create mode 100755 tests/plot_energy.py

diff --git a/driver/icebergs_driver.F90 b/driver/icebergs_driver.F90
index aea2b61..fee0e35 100644
--- a/driver/icebergs_driver.F90
+++ b/driver/icebergs_driver.F90
@@ -1,5 +1,6 @@
 program icebergs_driver
 
+use constants_mod, only: pi
 use fms_mod, only : fms_init
 use fms_mod, only : fms_end
 use fms_mod, only : open_namelist_file
@@ -55,6 +56,7 @@ program icebergs_driver
 logical :: saverestart=.false. !< If true, save a berg restart file at the end
 logical :: collision_test=.false.
 logical :: chaotic_test=.false.
+logical :: grounding_test=.false.
 integer :: halo=1 !< Width of halo in parallel decomposition
 real :: ibdt=3600.0
 real :: ibuo=0.1
@@ -62,10 +64,13 @@ program icebergs_driver
 real :: ibui=0.0
 real :: ibvi=0.0
 real :: gridres=1.e3
+real :: bump_deptht=0
 integer :: ibhrs=2
 integer :: nmax = 2000000000 !<max number of iteration
+integer :: write_time_inc=1
 namelist /icebergs_driver_nml/ debug, ni, nj, halo, ibhrs, ibdt, ibuo, ibvo, nmax, &
-       saverestart,ibui,ibvi,collision_test,chaotic_test,gridres
+  saverestart,ibui,ibvi,collision_test,chaotic_test,grounding_test,&
+  gridres,write_time_inc,bump_depth
 ! For loops
 integer :: isc !< Start of i-index for computational domain (used for loops)
 integer :: iec !< End of i-index for computational domain (used for loops)
@@ -108,6 +113,10 @@ program icebergs_driver
 real, dimension(:,:), pointer :: mass_berg !< Mass of bergs (kg)
 real, dimension(:,:), pointer  :: ustar_berg !< Friction velocity on base of bergs (m/s)
 real, dimension(:,:), pointer :: area_berg !< Area of bergs (m2)
+!grounding_test
+real :: a,bx,by,c,xc,yc !gaussian params
+!grounding/collision tests
+real :: mid
 
 call cpu_time(time_begin)
 
@@ -194,6 +203,27 @@ program icebergs_driver
   enddo;enddo
 endif
 
+if (grounding_test) then
+  lat(:,:)=lat(:,:)-15000.0
+  !assign land cells at the N and S portions of the domain.
+  !input.nml: set coastal drift parameter to prevent grounding
+  do j=jsd,jed; do i=isd,ied
+    if (lat(i,j)<=0.0+2*gridres .or. lat(i,j)>=30.e3-2*gridres) wet(i,j)=0.0
+  enddo;enddo
+
+  !introduce gaussian bump to bathymetry
+  a = 1000.0-bump_depth !max height(m)
+  c = 2.5e3; !controls width
+  bx = 15.e3; by = 15.e3
+  do j=jsd,jed; do i=isd,ied
+    xc=lon(i,j)-(gridres/2.); yc=lat(i,j)-(gridres/2.) !define at cell centers
+    depth(i,j)=a*exp(-((xc-bx)*(xc-bx)/(2.*c*c)+(yc-by)*(yc-by)/(2.*c*c)))
+  enddo; enddo
+  print *,'min, max depth',minval(depth(:,:)),maxval(depth(:,:))
+  depth = 1000.0-depth
+endif
+
+
 call set_calendar_type(THIRTY_DAY_MONTHS)
 time = set_date(1,1,1,0,0,0)
 dt = ibdt
@@ -232,12 +262,26 @@ program icebergs_driver
 hi = 0.0 !sea-ice thickness (m)
 calving_hflx = 0.0 !calving heat flux (W/m2)
 
-if (collision_test) then
+if (collision_test .or. grounding_test) then
+  if (grounding_test) then
+    mid=15.e3
+  else
+    mid=10.e3
+  endif
+
   do j=jsd,jed; do i=isd,ied
-    if (lon(i,j)>10.e3 .or. lon(i,j)<=0.0 .or. lat(i,j)==10.e3) then
+    if (lon(i,j)>mid .or. lon(i,j)<=0.0 .or. lat(i,j)==mid) then
       vo(i,j)=0.0
-    else
-      if (lat(i,j)>10.e3) then
+      ! if (grounding_test .and. lon(i,j)>mid+5.e3) then
+      !   if (lat(i,j)>mid) then
+      !     vo(i,j)=+ibvo
+      !   else
+      !     vo(i,j)=-ibvo
+      !   endif
+      ! endif
+
+     else
+      if (lat(i,j)>mid) then
         vo(i,j)=-ibvo
       else
         vo(i,j)=ibvo
@@ -284,7 +328,7 @@ program icebergs_driver
 Time_end = increment_date(Time,0,0,0,ibhrs,0,0)
 
 do while ((ns < nmax) .and. (Time < Time_end))
-  if (mpp_pe()==0 .and. debug) then
+  if (mpp_pe()==0 .and. debug .and. mod(ns-1,write_time_inc)==0) then
     call get_date(Time, iyr, imon, iday, ihr, imin, isec)
     write(*,*),''
     write(*,'(a)'),'-------------------------------------------'
diff --git a/src/icebergs.F90 b/src/icebergs.F90
index e007a96..436cf36 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -44,11 +44,15 @@ module ice_bergs
 use ice_bergs_framework, only: is_point_within_xi_yj_bounds
 use ice_bergs_framework, only: test_check_for_duplicate_ids_in_list
 use ice_bergs_framework, only: generate_id
-use ice_bergs_framework, only: update_latlon
-use ice_bergs_framework, only: set_conglom_ids
-use ice_bergs_framework, only: transfer_mts_bergs
-
-use ice_bergs_io,        only: ice_bergs_io_init, write_restart, write_trajectory
+use ice_bergs_framework, only: update_latlon,set_conglom_ids,transfer_mts_bergs,quad_interp_from_agrid
+use ice_bergs_framework, only: save_bond_traj
+use ice_bergs_framework, only: fracture_testing_initialization, orig_bond_length
+use ice_bergs_framework, only: update_and_break_bonds,assign_n_bonds,reset_bond_rotation
+use ice_bergs_framework, only: update_bond_angles
+use ice_bergs_framework, only: monitor_energy, energy_tests_init, new_mts
+use ice_bergs_framework, only: imp_loop_iters_short,imp_loop_iters_long
+
+use ice_bergs_io,        only: ice_bergs_io_init, write_restart, write_trajectory, write_bond_trajectory
 use ice_bergs_io,        only: read_restart_bergs, read_restart_calving
 use ice_bergs_io,        only: read_restart_bonds
 use ice_bergs_io,        only: read_ocean_depth
@@ -143,7 +147,14 @@ subroutine icebergs_init(bergs, &
   !Reading ocean depth from a file
   if (bergs%read_ocean_depth_from_file) call read_ocean_depth(bergs%grd)
 
+  if (monitor_energy) call energy_tests_init(bergs)
+
   if (bergs%iceberg_bonds_on) then
+    if (bergs%manually_initialize_bonds) then
+      call initialize_iceberg_bonds(bergs)
+    else
+      call read_restart_bonds(bergs,Time)
+    endif
     call update_halo_icebergs(bergs)
     if (bergs%manually_initialize_bonds) then
       call initialize_iceberg_bonds(bergs)
@@ -159,10 +170,24 @@ subroutine icebergs_init(bergs, &
     nbonds=0
     check_bond_quality=.True.
     call count_bonds(bergs, nbonds,check_bond_quality)
+    call assign_n_bonds(bergs)
+    call fracture_testing_initialization(bergs)
   endif
 
 end subroutine icebergs_init
 
+subroutine debugwriteandstop(bergs)
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  bergs%debug_write=.true.
+  call record_posn(bergs)
+  call move_all_trajectories(bergs)
+  call write_trajectory(bergs%trajectories, bergs%save_short_traj)
+  if (save_bond_traj) call write_bond_trajectory(bergs%bond_trajectories)
+  call mpp_sync()
+  call error_mesg('KID', 'WRITE AND STOP!!!', FATAL)
+end subroutine debugwriteandstop
+
+
 !> Invoke some unit testing
 subroutine unit_testing(bergs)
   ! Arguments
@@ -334,15 +359,25 @@ subroutine initialize_iceberg_bonds(bergs)
   type(iceberg), pointer :: berg
   type(iceberg), pointer :: other_berg
   type(icebergs_gridded), pointer :: grd
+  type(bond) , pointer :: current_bond
+  logical :: already_bonded
   real :: T1, L1, W1, lon1, lat1, x1, y1, R1, A1   !Current iceberg
   real :: T2, L2, W2, lon2, lat2, x2, y2, R2, A2   !Other iceberg
   real :: dlon,dlat
   real :: dx_dlon,dy_dlat, lat_ref
   real :: r_dist_x, r_dist_y, r_dist
-  real :: radius
+  real :: radius1,radius2,rdenom
   integer :: grdi_outer, grdj_outer
   integer :: grdi_inner, grdj_inner
 
+  if (bergs%manually_initialize_bonds_from_radii) then
+    if (bergs%hexagonal_icebergs) then
+      rdenom=1./(2.*sqrt(3.))
+    else
+      rdenom=1./pi
+    endif
+  endif
+
   ! For convenience
   grd=>bergs%grd
   !Should update halos before doing this
@@ -361,25 +396,37 @@ subroutine initialize_iceberg_bonds(bergs)
         do while (associated(other_berg)) ! loop over all other bergs
 
           if (berg%id .ne. other_berg%id) then
-            lon2=other_berg%lon; lat2=other_berg%lat
-            !call rotpos_to_tang(lon2,lat2,x2,y2) !Is this correct? Shouldn't it only be on tangent plane?
-            !r_dist_x=x1-x2 ; r_dist_y=y1-y2
-            !r_dist=sqrt( ((x1-x2)**2) + ((y1-y2)**2) )
-
-            dlon=lon1-lon2
-            dlat=lat1-lat2
-            lat_ref=0.5*(lat1+lat2)
-            call convert_from_grid_to_meters(lat_ref,grd%grid_is_latlon,dx_dlon,dy_dlat)
-            r_dist_x=dlon*dx_dlon
-            r_dist_y=dlat*dy_dlat
-            r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) )
-
-            if (bergs%manually_initialize_bonds_from_radii) then
-              radius=sqrt(min(berg%length*berg%width,other_berg%length*other_berg%width))
-              if (r_dist.lt.1.25*radius) call form_a_bond(berg, other_berg%id, other_berg%ine, other_berg%jne, other_berg)
-            elseif (r_dist.lt.bergs%length_for_manually_initialize_bonds) then
-              ! If the bergs are closer than bergs%length_for_manually_initialize_bonds, then form a bond -Alex
-              call form_a_bond(berg, other_berg%id, other_berg%ine, other_berg%jne, other_berg)
+            !first, make sure the bergs are not bonded already
+            already_bonded=.false.
+            current_bond=>berg%first_bond
+            do while (associated(current_bond))
+              if (current_bond%other_id .ne. other_berg%id) then
+                current_bond=>current_bond%next_bond
+              else
+                current_bond=>null()
+                already_bonded=.true.
+              endif
+            enddo
+
+            if (.not. already_bonded) then
+              lon2=other_berg%lon; lat2=other_berg%lat
+              dlon=lon1-lon2;      dlat=lat1-lat2
+              lat_ref=0.5*(lat1+lat2)
+              call convert_from_grid_to_meters(lat_ref,grd%grid_is_latlon,dx_dlon,dy_dlat)
+              r_dist_x=dlon*dx_dlon
+              r_dist_y=dlat*dy_dlat
+              r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) )
+
+              if (bergs%manually_initialize_bonds_from_radii) then
+                radius1=sqrt(berg%length*berg%width*rdenom)
+                radius2=sqrt(other_berg%length*other_berg%width*rdenom)
+                !radius=sqrt(min(berg%length*berg%width,other_berg%length*other_berg%width))
+                if (r_dist.lt.1.1*(radius1+radius2)) &
+                  call form_a_bond(berg, other_berg%id, other_berg%ine, other_berg%jne, other_berg)
+              elseif (r_dist.lt.bergs%length_for_manually_initialize_bonds) then
+                ! If the bergs are closer than bergs%length_for_manually_initialize_bonds, then form a bond -Alex
+                call form_a_bond(berg, other_berg%id, other_berg%ine, other_berg%jne, other_berg)
+              endif
             endif
           endif
           other_berg=>other_berg%next
@@ -452,7 +499,7 @@ subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
   logical :: critical_interaction_damping_on
   integer :: grdi, grdj
   logical :: iceberg_bonds_on
-  logical :: bonded
+  logical :: bonded !,contact_eligible,c_crit_dist
   integer :: nc_x,nc_y
 
   nc_x=bergs%contact_cells_lon; nc_y=bergs%contact_cells_lat
@@ -476,21 +523,45 @@ subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
             call error_mesg('KID,bond interactions', 'Trying to do Bond interactions with unassosiated berg!' ,FATAL)
           else
             call calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,  &
-              P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded)
+              P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded,current_bond=current_bond)
+            other_berg%id=-other_berg%id !mark, as to not repeat in contact search below
           endif
           current_bond=>current_bond%next_bond
         enddo
+        !contact search: find any surrounding non-bonded bergs in the same conglom, and processes
+        !them for contact using the regular (non-contact) spring constant and crit_dist based on radii
+        bonded=.false.
+        do grdj = max(berg%jne-2,bergs%grd%jsd+1),min(berg%jne+2,bergs%grd%jed);&
+          do grdi = max(berg%ine-2,bergs%grd%isd+1),min(berg%ine+2,bergs%grd%ied)
+          other_berg=>bergs%list(grdi,grdj)%first
+          do while (associated(other_berg))
+            if (other_berg%id>0 .and. other_berg%conglom_id.eq.berg%conglom_id) then
+              call calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,  &
+                P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded,c_crit_dist=.true.)
+            endif
+            other_berg=>other_berg%next
+          enddo
+        enddo;enddo
+        !unmark the bonded bergs
+        current_bond=>berg%first_bond
+        do while (associated(current_bond))
+          other_berg=>current_bond%other_berg
+          other_berg%id=abs(other_berg%id)
+          current_bond=>current_bond%next_bond
+        enddo
       endif
     endif
 
     ! Interactions for non-bonded berg elements only. For the mts scheme, this is only called if mts_part==1
     if (.not. (bergs%mts .and. bergs%mts_part .eq. 3)) then
       bonded=.false. ! Interactions for non-bonded berg elements
-      do grdj = max(berg%jne-nc_y,bergs%grd%jsd+1),min(berg%jne+nc_y,bergs%grd%jed);&
-        do grdi = max(berg%ine-nc_x,bergs%grd%isd+1),min(berg%ine+nc_x,bergs%grd%ied)
+      do grdj = max(berg%jne-nc_y,bergs%grd%jsd),min(berg%jne+nc_y,bergs%grd%jed);&
+        do grdi = max(berg%ine-nc_x,bergs%grd%isd),min(berg%ine+nc_x,bergs%grd%ied)
 
         other_berg=>bergs%list(grdi,grdj)%first
         do while (associated(other_berg)) ! loop over all other bergs
+          !call contact_eligibility(berg,other_berg,contact_eligible,c_crit_dist)
+          !if (contact_eligible) then
           if (other_berg%conglom_id.ne.berg%conglom_id) then
             call calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,  &
               P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded)
@@ -530,9 +601,47 @@ subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
   endif
 end subroutine interactive_force
 
+!>Determines whether two bergs interact via contact. If they are w/in the same conglomerate,
+!!returns a flag to set the crit dist for contact to the sum of their radii
+subroutine contact_eligibility(berg,other_berg,contact_eligible,c_crit_dist)
+  ! Arguments
+  type(iceberg), pointer :: berg !< Primary berg
+  type(iceberg), pointer :: other_berg !< Berg that primary is interacting with
+  logical, intent(out) :: contact_eligible !< Are the berg eligible for interaction via contact?
+  logical, intent(out) :: c_crit_dist !<Flag to use crit_dist=R1+R2 for contact bergs w/in the same conglom
+  ! Local variables
+  type(iceberg), pointer :: this
+  type(bond), pointer :: current_bond
+
+  if (other_berg%conglom_id.ne.berg%conglom_id) then
+    contact_eligible=.true. !Bergs are in different congloms. Contact eligible.
+    c_crit_dist=.false.
+  else
+    !Bergs in same conglom. Determine whether they are bonded:
+    current_bond=>berg%first_bond
+    do while (associated(current_bond))
+      this=>current_bond%other_berg
+      if (associated(this)) then
+        if (this%id .eq. other_berg%id) then !bergs are bonded and not eligible for contact
+          contact_eligible=.false.
+          c_crit_dist=.false.
+          return
+        endif
+      endif
+      current_bond=>current_bond%next_bond
+    enddo
+
+    !Bergs are not bonded are are contact eligible. The c_crit_dist flag sets the crit_dist to
+    !the sum of the two bergs' radii within calculate_force.
+    contact_eligible=.true.
+    c_crit_dist=.true.
+  endif
+end subroutine contact_eligibility
+
+
 !> Calculate interactive forces between two bergs
 subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1, &
-                           P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y, bonded)
+  P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y, bonded, c_crit_dist, current_bond)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
   type(iceberg), pointer :: berg !< Primary berg
@@ -550,6 +659,8 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
   real, intent(inout) :: P_ia_times_u_x
   real, intent(inout) :: P_ia_times_u_y
   logical ,intent(in) :: bonded
+  logical ,intent(in), optional :: c_crit_dist
+  type(bond), intent(in), optional :: current_bond
   ! Local variables
   real :: T1, L1, W1, lon1, lat1, x1, y1, R1, A1 ! Current iceberg
   real :: T2, L2, W2, lon2, lat2, x2, y2, R2, A2 ! Other iceberg
@@ -559,9 +670,9 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
   real :: M1, M2, M_min
   real :: u2, v2
   real :: lat_ref, dx_dlon, dy_dlat
-  logical :: critical_interaction_damping_on,tbonded
+  logical :: critical_interaction_damping_on,tbonded,crit_dist_from_radius_only
   real :: spring_coef, accel_spring, radial_damping_coef, p_ia_coef, tangental_damping_coef, bond_coef
-  real :: crit_dist
+  real :: crit_dist, vr1,vr2,vn,vn1,vn2,vt1,vt2
 
   if (berg%id .ne. other_berg%id) then
     ! From Berg 1
@@ -627,8 +738,17 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
       crit_dist=R1+R2 !Stern et al 2017, Eqn 5
       spring_coef=bergs%spring_coef
     else
-      crit_dist=max(R1+R2,bergs%contact_distance)
       spring_coef=bergs%contact_spring_coef
+      if (present(c_crit_dist)) then
+        if (c_crit_dist) then
+          crit_dist=R1+R2
+          spring_coef=bergs%spring_coef
+        else
+          crit_dist=max(R1+R2,bergs%contact_distance)
+        endif
+      else
+        crit_dist=max(R1+R2,bergs%contact_distance)
+      endif
     end if
 
     radial_damping_coef=bergs%radial_damping_coef
@@ -638,10 +758,13 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
     ! Using critical values for damping rather than manually setting the damping.
     if (critical_interaction_damping_on) then
       radial_damping_coef=2.*sqrt(spring_coef) ! Critical damping
-      tangental_damping_coef=(2.*sqrt(spring_coef))/4 ! Critical damping (just a guess)
+      if (bergs%tang_crit_int_damp_on) then
+        tangental_damping_coef=(2.*sqrt(spring_coef))/4 ! Critical damping (just a guess)
+      endif
     endif
 
     tbonded=bonded
+    !if bonded and  STS,contact_dist=0, and  contact_spring coeff==spring coeff
     if (bonded .and. .not. (bergs%mts .or. (bergs%contact_distance>0.) .or. &
       (bergs%contact_spring_coef .ne. bergs%spring_coef) )) then
       if (.not. (r_dist>crit_dist)) tbonded=.false.
@@ -656,9 +779,7 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
       IA_x=IA_x+(accel_spring*(r_dist_x/r_dist))
       IA_y=IA_y+(accel_spring*(r_dist_y/r_dist))
 
-
-      if (r_dist < 5*(R1+R2)) then
-
+      ! if (r_dist < 5*(R1+R2)) then
         ! Damping force (Stern et al 2017, Eqn 8):
         ! Paralel velocity
         !projection matrix in Stern et al 2017, Eqn 8:
@@ -668,8 +789,11 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
         P_22=(r_dist_y*r_dist_y)/(r_dist**2)
         !p_ia_coef=radial_damping_coef*(T_min/T1)*(A_min/A1)
         p_ia_coef=radial_damping_coef*(M_min/M1)
-        p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2)) &
-        + sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
+        !the following was done originally, but it is wrong:
+        if (bergs%scale_damping_by_pmag) then
+          p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2)) &
+            + sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
+        endif
 
         P_ia_11=P_ia_11+p_ia_coef*P_11
         P_ia_12=P_ia_12+p_ia_coef*P_12
@@ -683,8 +807,11 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
         P_11=1-P_11  ;  P_12=-P_12 ; P_21= -P_21 ;    P_22=1-P_22
         !p_ia_coef=tangental_damping_coef*(T_min/T1)*(A_min/A1)
         p_ia_coef=tangental_damping_coef*(M_min/M1)
-        p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2))  &
-        + sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
+        !the following was done originally, but it is wrong:
+        if (bergs%scale_damping_by_pmag) then
+          p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2))  &
+            + sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
+        endif
         P_ia_11=P_ia_11+p_ia_coef*P_11
         P_ia_12=P_ia_12+p_ia_coef*P_12
         P_ia_21=P_ia_21+p_ia_coef*P_21
@@ -696,7 +823,7 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
         !print *, 'P_21',P_21
         !print *, 'P_12',P_12
         !print *, 'P_22',P_22
-      endif
+      !endif
     endif
   endif
 
@@ -735,8 +862,8 @@ subroutine overlap_area(R1, R2, d, A, trapped)
 
 end subroutine overlap_area
 
-!> Calculates the instantaneous acceleration of an iceberg
-subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, rx, ry, ax, ay, axn, ayn, bxn, byn, debug_flag)
+subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, rx, ry, &
+  ax, ay, axn, ayn, bxn, byn, save_bond_energy, Fec_x, Fec_y, Fdc_x, Fdc_y, debug_flag)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
   type(iceberg), pointer :: berg !< An iceberg
@@ -745,10 +872,10 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
   real, intent(in) :: xi !< Non-dimensional x-position within cell of berg
   real, intent(in) :: yj !< Non-dimensional y-position within cell of berg
   real, intent(in) :: lat !< Latitude of berg (degree N)
-  real, intent(in) :: uvel !< Zonal velocity of berg (m/s)
-  real, intent(in) :: vvel !< Meridional velocity of berg (m/s)
-  real, intent(in) :: uvel0 !< Zonal velocity of berg at beginning of time-step (m/s)
-  real, intent(in) :: vvel0 !< Meridional velocity of berg at beginning of time-step (m/s)
+  real, intent(inout) :: uvel !< Zonal velocity of berg (m/s)
+  real, intent(inout) :: vvel !< Meridional velocity of berg (m/s)
+  real, intent(inout) :: uvel0 !< Zonal velocity of berg at beginning of time-step (m/s)
+  real, intent(inout) :: vvel0 !< Meridional velocity of berg at beginning of time-step (m/s)
   real, intent(in) :: dt !< Time step (s)
   real, intent(in) :: rx !< Random number between -1 and 1 for use in x-component of stochastic tidal parameterization
   real, intent(in) :: ry !< Random number between -1 and 1 for use in y-component of stochastic tidal parameterization
@@ -758,16 +885,17 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
   real, intent(inout) :: ayn !< Explicit estimate of meridional acceleration (m/s2)
   real, intent(inout) :: bxn !< Implicit component of zonal acceleration (m/s2)
   real, intent(inout) :: byn !< Implicit component of meridional acceleration (m/s2)
+  logical, intent(in) :: save_bond_energy
+  real, optional, intent(out) :: Fec_x,Fec_y,Fdc_x,Fdc_y !< Collisional elastic and damping forces (if bergs%mts_part==1)
   logical, optional :: debug_flag !< If true, print debugging
   ! Local variables
   type(icebergs_gridded), pointer :: grd
-  real :: uo, vo, ui, vi, ua, va, uwave, vwave, ssh_x, ssh_y, sst, sss, cn, hi
+  real :: uo, vo, ui, vi, ua, va, uwave, vwave, ssh_x, ssh_y, sst, sss, cn, hi, od
   real :: f_cori, T, D, W, L, M, F
   real :: drag_ocn, drag_atm, drag_ice, wave_rad
   real :: c_ocn, c_atm, c_ice
   real :: ampl, wmod, Cr, Lwavelength, Lcutoff, Ltop
   real, parameter :: accel_lim=1.e-2, Cr0=0.06, vel_lim=15.
-  real :: alpha, beta, C_N
   real :: lambda, detA, A11, A12, A21, A22, RHS_x, RHS_y, D_hi
   real :: uveln, vveln, us, vs, speed, loc_dx, new_speed
   real :: u_star, v_star    !Added by Alon
@@ -779,278 +907,306 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
   logical :: use_new_predictive_corrective !Flad to use Bob's predictive corrective scheme. (default off)
   integer :: itloop
   integer :: stderrunit
+  real :: dragfrac, N_bonds, N_max, groundfrac, c_gnd, drag_gnd, scaling
+  real :: minfricvel=3.17e-12 !m/s (~0.0001 m/a)
+  type(bond), pointer :: current_bond
+  real :: IAd_x, IAd_y, sum_bond_Ee, sum_bond_Ed
+  type(iceberg), pointer :: other_berg
 
   Runge_not_Verlet=bergs%Runge_not_Verlet  ! Loading directly from namelist/default , Alon
   interactive_icebergs_on=bergs%interactive_icebergs_on  ! Loading directly from namelist/default , Alon
   use_new_predictive_corrective=bergs%use_new_predictive_corrective  ! Loading directly from namelist/default , Alon
 
-  !These values are no longer set as parameters, but rather can be changed as variables.
-  alpha=0.0
-  beta=1.0
-  C_N=0.0
-
-  !Alon: Verlet requires implicit Coriolis and implicit drag.
-  !Alon: Also, I think that the implicit Coriolis with RK gives icebergs which do not complete inertial circles.
-  if (.not.Runge_not_Verlet) then
-    alpha=1.0
-    C_N=1.0
-    beta=1.0
-    use_new_predictive_corrective=.True.
+  u_star=uvel0+(axn*(dt/2.)); v_star=vvel0+(ayn*(dt/2.))  !Alon
+  stderrunit = stderr()   ! Get the stderr unit number.
+  grd=>bergs%grd   ! For convenience
+
+  if (bergs%mts_part == 1) then
+    !in this case, u_star and v_star equal u_k and v_k, respectively, the
+    !the velocity components from the previous cycle final MTS 'fast' force iteration, k.
+    u_star=berg%uvel; v_star=berg%vvel
+    !might as well set it for the berg velocity, too.
+    uvel0=berg%uvel;  vvel0=berg%vvel
+    uvel=berg%uvel;   vvel=berg%vvel
   endif
 
-
-  u_star=uvel0+(axn*(dt/2.))  !Alon
-  v_star=vvel0+(ayn*(dt/2.))  !Alon
-
-  ! Get the stderr unit number.
-  stderrunit = stderr()
-
-  ! For convenience
-  grd=>bergs%grd
-
-  ! Interpolate gridded fields to berg
-  if (bergs%mts) then
-    !dummy values for MTS scheme halo bergs (this should only occur during berg%mts_part==3,
-    !when bergs%only_interactive_forces=.true., and therefore should have no effect)
-    uo=berg%uo; vo=berg%vo; ua=berg%ua; va=berg%va; ui=berg%ui; vi=berg%vi;
-    ssh_x=berg%ssh_x; ssh_y=berg%ssh_y; sst=berg%sst; sss=berg%sss;  cn=berg%cn; hi=berg%hi
-  else
-    call interp_flds(grd, i, j, xi, yj, rx, ry, uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, sss, cn, hi)
-  end if
-
-  if ((grd%grid_is_latlon) .and. (.not. bergs%use_f_plane)) then
-     f_cori=(2.*omega)*sin(pi_180*lat)
+  if (new_mts) then
+    scaling=0.5
   else
-     f_cori=(2.*omega)*sin(pi_180*bergs%lat_ref)
+    scaling=1.0
   endif
-  !f_cori=0.
 
-  M=berg%mass
-  T=berg%thickness ! total thickness
-  D=(bergs%rho_bergs/rho_seawater)*T ! draught (keel depth)
-  F=T-D ! freeboard
-  W=berg%width
-  L=berg%length
 
-  ! Initializing accelerations - Alon. (I am not 100% sure this is needed). I'm not sure what is output if variable is not defined in the subroutine.
-  axn=0.
-  ayn=0.
-  bxn=0.
-  byn=0.
+  ! Initializing accelerations
+  axn=0.; ayn=0.; bxn=0.; byn=0.
 
-  hi=min(hi,D)
-  D_hi=max(0.,D-hi)
+  if (.not. bergs%only_interactive_forces) then
+    !for mts, gridded fields already saved on berg
+    uo=berg%uo; vo=berg%vo; ua=berg%ua; va=berg%va; ui=berg%ui; vi=berg%vi;
+    ssh_x=berg%ssh_x; ssh_y=berg%ssh_y; sst=berg%sst; sss=berg%sss;  cn=berg%cn; hi=berg%hi; od=berg%od
 
-  ! Wave radiation (Stern et al 2017, Eqs A4-A5)
-  uwave=ua-uo; vwave=va-vo  ! Use wind speed rel. to ocean for wave model (aja)?
-  wmod=uwave*uwave+vwave*vwave ! The wave amplitude and length depend on the wind speed relative to the ocean current
-                               ! actually wmod is wmod**2 here.
-  ampl=0.5*0.02025*wmod ! This is "a", the wave amplitude
-  Lwavelength=0.32*wmod ! Surface wave length fitted to data in table at
-                        ! http://www4.ncsu.edu/eos/users/c/ceknowle/public/chapter10/part2.html
-  Lcutoff=0.125*Lwavelength
-  Ltop=0.25*Lwavelength
-  Cr=Cr0*min(max(0.,(L-Lcutoff)/((Ltop-Lcutoff)+1.e-30)),1.) ! Wave radiation coefficient fitted to
-                                                             ! graph from Carrieres et al.,  POAC Drift Model.
-  wave_rad=0.5*rho_seawater/M*Cr*gravity*ampl*min(ampl,F)*(2.*W*L)/(W+L)
-  wmod = sqrt(ua*ua+va*va) ! Wind speed
-  if (wmod.ne.0.) then
-    uwave=ua/wmod ! Wave radiation force acts in wind direction ...
-    vwave=va/wmod
-  else
-    uwave=0.; vwave=0.; wave_rad=0. ! ... and only when wind is present.
-  endif
+    if ((grd%grid_is_latlon) .and. (.not. bergs%use_f_plane)) then
+      f_cori=(2.*omega)*sin(pi_180*lat)
+    else
+      f_cori=(2.*omega)*sin(pi_180*bergs%lat_ref)
+    endif
+    !f_cori=0.
 
-  ! Weighted drag coefficients (Stern et al 2017, Eqs A1-A3)
-  c_ocn=rho_seawater/M*(0.5*Cd_wv*W*(D_hi)+Cd_wh*W*L)
-  c_atm=rho_air     /M*(0.5*Cd_av*W*F     +Cd_ah*W*L)
-  if (abs(hi).eq.0.) then
-    c_ice=0.
-  else
-    c_ice=rho_ice     /M*(0.5*Cd_iv*W*hi              )
-  endif
-  if (abs(ui)+abs(vi).eq.0.) c_ice=0.
+    M=berg%mass
+    T=berg%thickness ! total thickness
+    D=(bergs%rho_bergs/rho_seawater)*T ! draught (keel depth)
+    F=T-D ! freeboard
+    W=berg%width; L=berg%length
 
-!Turning drag off for testing - Alon
-!c_ocn=0.
-!c_atm=0.
-!c_ice=0.
+    hi=min(hi,D)
+    D_hi=max(0.,D-hi)
 
-  ! Stern et al 2017, explicit accel due to
-  ! sea surface slope and wave radiation force
-  ! (forces F_R and F_SS, respectively, in Eq. 1.
-  ! Also see Eqn (A4+A6)) :
-    ! Half half accelerations  - axn, ayn
-    if (.not.Runge_not_Verlet) then
-      axn=-gravity*ssh_x +wave_rad*uwave
-      ayn=-gravity*ssh_y +wave_rad*vwave
+
+    !start to feel grounded with draught of bergs%h_to_init_grounding meters of the sea floor topography
+    !at groundfrac=0, apply no grounding force. at groundfrac=1, apply max grounding force
+    if (bergs%h_to_init_grounding>0.0) then
+      groundfrac=1.0-(od-D)/bergs%h_to_init_grounding
+      groundfrac=max(groundfrac,0.0); groundfrac=min(groundfrac,1.0)
     else
-      ! Not half half accelerations  - for RK
-      bxn=-gravity*ssh_x +wave_rad*uwave
-      byn=-gravity*ssh_y +wave_rad*vwave
+      if (D>od) then
+        groundfrac=1.0
+      else
+        groundfrac=0.0
+      endif
+    endif
+    if (groundfrac>0.0) then
+      c_gnd=(bergs%cdrag_grounding*W*L*groundfrac)/M
+    else
+      c_gnd=0.0
     endif
 
-  ! Interactive spring acceleration - (Does the spring part need to be called twice?)
-  if (interactive_icebergs_on) then
-    call interactive_force(bergs, berg, IA_x, IA_y, uvel0, vvel0, uvel0, vvel0, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y) ! Spring forces, Made by Alon.
-    if (.not.Runge_not_Verlet) then
-      axn=axn + IA_x
-      ayn=ayn + IA_y
+    ! Wave radiation (Stern et al 2017, Eqs A4-A5)
+    uwave=ua-uo; vwave=va-vo  ! Use wind speed rel. to ocean for wave model (aja)?
+    wmod=uwave*uwave+vwave*vwave ! The wave amplitude and length depend on the wind speed relative to the ocean current
+    ! actually wmod is wmod**2 here.
+    ampl=0.5*0.02025*wmod ! This is "a", the wave amplitude
+    Lwavelength=0.32*wmod ! Surface wave length fitted to data in table at
+    ! http://www4.ncsu.edu/eos/users/c/ceknowle/public/chapter10/part2.html
+    Lcutoff=0.125*Lwavelength
+    Ltop=0.25*Lwavelength
+    Cr=Cr0*min(max(0.,(L-Lcutoff)/((Ltop-Lcutoff)+1.e-30)),1.) ! Wave radiation coefficient fitted to
+    ! graph from Carrieres et al.,  POAC Drift Model.
+    wave_rad=0.5*rho_seawater/M*Cr*gravity*ampl*min(ampl,F)*(2.*W*L)/(W+L)
+    wmod = sqrt(ua*ua+va*va) ! Wind speed
+    if (wmod.ne.0.) then
+      uwave=ua/wmod ! Wave radiation force acts in wind direction ...
+      vwave=va/wmod
     else
-      bxn=bxn + IA_x
-      byn=byn + IA_y
+      uwave=0.; vwave=0.; wave_rad=0. ! ... and only when wind is present.
     endif
-  endif
 
-  if (alpha>0.) then ! If implicit Coriolis, use u_star rather than RK4 latest  !Alon
-    if (C_N>0.) then !  C_N=1 for Crank Nicolson Coriolis, C_N=0 for full implicit Coriolis !Alon
-      axn=axn+f_cori*v_star
-      ayn=ayn-f_cori*u_star
+    dragfrac = 1.0
+    if ((bergs%iceberg_bonds_on) .and. (bergs%internal_bergs_for_drag)) then
+      N_bonds=0.
+      N_max=4.0  !Maximum number of bonds that element can form based on shape
+      if (bergs%hexagonal_icebergs) N_max=6.0
+      ! Determining number of bonds
+      current_bond=>berg%first_bond
+      do while (associated(current_bond)) ! loop over all bonds
+        N_bonds=N_bonds+1.0
+        current_bond=>current_bond%next_bond
+      enddo
+      dragfrac = ((N_max-N_bonds)/N_max)
+    endif
+
+    ! Weighted drag coefficients (Stern et al 2017, Eqs A1-A3)
+    c_ocn=rho_seawater/M*(0.5*Cd_wv*dragfrac*W*(D_hi)+Cd_wh*W*L)
+    c_atm=rho_air     /M*(0.5*Cd_av*dragfrac*W*F     +Cd_ah*W*L)
+    if (abs(hi).eq.0.) then
+      c_ice=0.
     else
-      bxn=bxn+f_cori*v_star
-      byn=byn-f_cori*u_star
+      c_ice=rho_ice   /M*(0.5*Cd_iv*dragfrac*W*hi              )
     endif
-  else
-    bxn=bxn+f_cori*vvel
-    byn=byn-f_cori*uvel
-  endif
+    if (abs(ui)+abs(vi).eq.0.) c_ice=0.
+
+    !Turning drag off for testing - Alon
+    !c_ocn=0.; c_atm=0.; c_ice=0.
+    ! Stern et al 2017, explicit accel due to sea surface slope and wave radiation force
+    ! (forces F_R and F_SS, respectively, in Eq. 1. Also see Eqn (A4+A6)) :
+    ! Half half accelerations  - axn, ayn
+    axn=-gravity*ssh_x +wave_rad*uwave; ayn=-gravity*ssh_y +wave_rad*vwave
+
+    ! Interactive spring acceleration - (Does the spring part need to be called twice?)
+    if (interactive_icebergs_on) then
+      call interactive_force(bergs, berg, IA_x, IA_y, uvel0, vvel0, uvel0, vvel0, &
+        P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y) ! Spring forces, Made by Alon.
+      axn=axn + IA_x; ayn=ayn + IA_y
+    endif
+    axn=axn+f_cori*v_star; ayn=ayn-f_cori*u_star
 
-  if (use_new_predictive_corrective) then
-    uveln=uvel0; vveln=vvel0 ! Discuss this change with Alistair. Alon thinks that it is needed.
   else
-    uveln=uvel; vveln=vvel
-  endif
+    !only_interactive_forces
+    if (interactive_icebergs_on) then
+      call interactive_force(bergs, berg, IA_x, IA_y, uvel0, vvel0, uvel0, vvel0, &
+        P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y) ! Spring forces
+       !axn=axn + IA_x; ayn=ayn + IA_y
+    endif
+  endif !if (.not. bergs%only_interactive_forces)
 
-  us=uvel0   ; vs=vvel0
+  uveln=uvel0;           vveln=vvel0
+  us=uvel0   ;           vs=vvel0
   do itloop=1,2 ! Iterate on drag coefficients
     if (itloop .eq. 2) then
       us=uveln ; vs=vveln
     endif
-   !Stern et al 2017, Eqn A1-A3
-  if (use_new_predictive_corrective) then
-    !Alon's proposed change - using Bob's improved scheme.
-    drag_ocn=c_ocn*0.5*(sqrt( (uveln-uo)**2+(vveln-vo)**2 )+sqrt( (uvel0-uo)**2+(vvel0-vo)**2 ))
-    drag_atm=c_atm*0.5*(sqrt( (uveln-ua)**2+(vveln-va)**2 )+sqrt( (uvel0-ua)**2+(vvel0-va)**2 ))
-    drag_ice=c_ice*0.5*(sqrt( (uveln-ui)**2+(vveln-vi)**2 )+sqrt( (uvel0-ui)**2+(vvel0-vi)**2 ))
-  else
-    !Original Scheme
-    us=0.5*(uveln+uvel); vs=0.5*(vveln+vvel)
-    drag_ocn=c_ocn*sqrt( (us-uo)**2+(vs-vo)**2 )
-    drag_atm=c_atm*sqrt( (us-ua)**2+(vs-va)**2 )
-    drag_ice=c_ice*sqrt( (us-ui)**2+(vs-vi)**2 )
-  endif
 
-  !RHS ~ similar to accel terms in Stern et al 2017, Eqn B5
-  RHS_x=(axn/2) + bxn
-  RHS_y=(ayn/2) + byn
+    if (bergs%only_interactive_forces) then
+      if (interactive_icebergs_on) then
+        if (itloop>1) then
+          call interactive_force(bergs, berg, IA_x, IA_y, uvel0, vvel0, us,vs, &
+            P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y) ! Spring forces, Made by Alon.
+        endif
 
-  if (beta>0.) then ! If implicit, use u_star, v_star rather than RK4 latest
-    RHS_x=RHS_x - drag_ocn*(u_star-uo) -drag_atm*(u_star-ua) -drag_ice*(u_star-ui)
-    RHS_y=RHS_y - drag_ocn*(v_star-vo) -drag_atm*(v_star-va) -drag_ice*(v_star-vi)
-  else
-    RHS_x=RHS_x - drag_ocn*(uvel-uo) -drag_atm*(uvel-ua) -drag_ice*(uvel-ui)
-    RHS_y=RHS_y - drag_ocn*(vvel-vo) -drag_atm*(vvel-va) -drag_ice*(vvel-vi)
-  endif
+        ! Solve for implicit accelerations
+        RHS_x=(IA_x/2) -scaling*(((P_ia_11*u_star)+(P_ia_12*v_star))-P_ia_times_u_x)
+        RHS_y=(IA_y/2) -scaling*(((P_ia_21*u_star)+(P_ia_22*v_star))-P_ia_times_u_y)
+
+        A11=1+(scaling*dt*P_ia_11); A22=1+(scaling*dt*P_ia_22)
+        A12=(scaling*dt*P_ia_12);   A21=(scaling*dt*P_ia_21)
+      endif
 
-  if (interactive_icebergs_on) then
-    if (itloop>1) then
-      call interactive_force(bergs, berg, IA_x, IA_y, uvel0, vvel0, us,vs, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y) ! Spring forces, Made by Alon.
-    endif
-    if (beta>0.) then ! If implicit, use u_star, v_star rather than RK4 latest
-      RHS_x=RHS_x -(((P_ia_11*u_star)+(P_ia_12*v_star))-P_ia_times_u_x)
-      RHS_y=RHS_y -(((P_ia_21*u_star)+(P_ia_22*v_star))-P_ia_times_u_y)
     else
-      RHS_x=RHS_x - (((P_ia_11*uvel)+(P_ia_12*vvel))-P_ia_times_u_x)
-      RHS_y=RHS_y - (((P_ia_21*uvel)+(P_ia_22*vvel))-P_ia_times_u_y)
-    endif
-    !print *,'Before calculation:', berg%id, IA_x, IA_y, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y
-  endif
+      !Stern et al 2017, Eqn A1-A3 !Alon's proposed change - using Bob's improved scheme.
+      drag_ocn=c_ocn*0.5*(sqrt( (uveln-uo)**2+(vveln-vo)**2 )+sqrt( (uvel0-uo)**2+(vvel0-vo)**2 ))
+      drag_atm=c_atm*0.5*(sqrt( (uveln-ua)**2+(vveln-va)**2 )+sqrt( (uvel0-ua)**2+(vvel0-va)**2 ))
+      drag_ice=c_ice*0.5*(sqrt( (uveln-ui)**2+(vveln-vi)**2 )+sqrt( (uvel0-ui)**2+(vvel0-vi)**2 ))
+      drag_gnd=c_gnd*max(0.5*(sqrt(uveln**2+vveln**2)+sqrt(uvel0**2+vvel0**2)),minfricvel)**(1.0/3.0 - 1.0)
+      !RHS ~ similar to accel terms in Stern et al 2017, Eqn B5
+      RHS_x=(axn/2) + scaling*(-drag_ocn*(u_star-uo) -drag_atm*(u_star-ua) -drag_ice*(u_star-ui) -drag_gnd*u_star)
+      RHS_y=(ayn/2) + scaling*(-drag_ocn*(v_star-vo) -drag_atm*(v_star-va) -drag_ice*(v_star-vi) -drag_gnd*v_star)
+
+      if (interactive_icebergs_on) then
+        if (itloop>1) then
+          call interactive_force(bergs, berg, IA_x, IA_y, uvel0, vvel0, us,vs, &
+            P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y) ! Spring forces, Made by Alon.
+        endif
+        RHS_x=RHS_x -scaling*(((P_ia_11*u_star)+(P_ia_12*v_star))-P_ia_times_u_x)
+        RHS_y=RHS_y -scaling*(((P_ia_21*u_star)+(P_ia_22*v_star))-P_ia_times_u_y)
+      endif
 
-  ! Solve for implicit accelerations
-  if (alpha+beta.gt.0.) then
-    lambda=drag_ocn+drag_atm+drag_ice
-    !Matrix A = [A11 A12; A21 A22] is the denominator on the rhs of Stern et al 2017, Eqn B7
-    A11=1.+beta*dt*lambda
-    A22=1.+beta*dt*lambda
-    A12=-alpha*dt*f_cori
-    A21=alpha*dt*f_cori
-    !A12=dt*f_cori  !Removed by ALon (in order to have the entire matrix. I hope the sign is correct)
-
-    if (C_N>0.) then ! For Crank-Nicolson Coriolis term.
-        A12=A12/2.
-        A21=A21/2.
-    endif
+      ! Solve for implicit accelerations
+      lambda=drag_ocn+drag_atm+drag_ice+drag_gnd
+      !Matrix A = [A11 A12; A21 A22] is the denominator on the rhs of Stern et al 2017, Eqn B7
+      A11=1.+scaling*dt*lambda; A22=1.+scaling*dt*lambda
+      A12=-scaling*dt*f_cori; A21=scaling*dt*f_cori
+      !A12=dt*f_cori  !Removed by ALon (in order to have the entire matrix. I hope the sign is correct)
 
-    if (interactive_icebergs_on) then
-          A11=A11+(dt*P_ia_11)
-          A12=A12+(dt*P_ia_12)
-          A21=A21+(dt*P_ia_21)
-          A22=A22+(dt*P_ia_22)
-    endif
+      ! For Crank-Nicolson Coriolis term.
+      A12=A12/2.; A21=A21/2.
 
-    ! This is for testing the code using only interactive forces
-    if (bergs%only_interactive_forces) then
-       RHS_x=(IA_x/2) -(((P_ia_11*u_star)+(P_ia_12*v_star))-P_ia_times_u_x)
-       RHS_y=(IA_y/2) -(((P_ia_21*u_star)+(P_ia_22*v_star))-P_ia_times_u_y)
-       A11=1+(dt*P_ia_11)
-       A12=(dt*P_ia_12)
-       A21=(dt*P_ia_21)
-       A22=1+(dt*P_ia_22)
-    endif
+      if (interactive_icebergs_on) then
+        A11=A11+(scaling*dt*P_ia_11); A22=A22+(scaling*dt*P_ia_22)
+        A12=A12+(scaling*dt*P_ia_12); A21=A21+(scaling*dt*P_ia_21)
+      endif
+    endif !if (bergs%only_interactive_forces)
 
-    ! note damping finally satisfies Stern et al 2017, Eqn 8
+    !inverse of matrix A * RHS
     detA=1./((A11*A22)-(A12*A21))
-    ax=detA*(A22*RHS_x-A12*RHS_y)
-    ay=detA*(A11*RHS_y-A21*RHS_x)
-
-!Alistair's version removed by Alon
-!      detA=1./(A11**2+A12**2)
-!      ax=detA*(A11*RHS_x+A12*RHS_y)
-!      ay=detA*(A11*RHS_y-A12*RHS_x)
-    else
-      ax=RHS_x; ay=RHS_y
-    endif
+    ax=detA*(A22*RHS_x-A12*RHS_y); ay=detA*(A11*RHS_y-A21*RHS_x)
 
     ! Stern et al 2017, Eqn B5 and B6. Here, ax accounts for both acceleration terms (separated below)
-    uveln=u_star+dt*ax        ! Alon
-    vveln=v_star+dt*ay        ! Alon
-!MP4
-  !    if (berg%id .eq. 1) then
-  !      print *, '***************************************************'
-  !      print *,'id, itloop', berg%id, itloop
-  !      print *, 'P matrix:', P_ia_11, P_ia_12,P_ia_21,P_ia_22,P_ia_times_u_x, P_ia_times_u_x
-  !      print *,'A_matrix', A11, A12, A21, A22
-  !      print *,'IA_x IA_y', IA_x, IA_y
-  !      print *, 'RHS, ustar, uvel,ax: ', RHS_x, u_star,uveln, ax
-  !    endif
+    uveln=u_star+dt*ax; vveln=v_star+dt*ay        ! Alon
   enddo ! itloop
 
-  !Below: axn and ayn are the new explicit acceleration terms in Stern et al 2017, Eqn B5
-  !       bxn and byn are the new implicit accerelation terms
+  !(axn & ayn) / (bxn & byn) are the new (explicit) / (implicit) acceleration terms in Stern et al 2017, Eqn B5
   !Saving the totally explicit part of the acceleration to use in finding the next position and u_star -Alon
-  axn=0.
-  ayn=0.
-  if (.not.Runge_not_Verlet) then
-    axn=-gravity*ssh_x +wave_rad*uwave
-    ayn=-gravity*ssh_y +wave_rad*vwave
+  if (bergs%only_interactive_forces) then
+    axn=IA_x; ayn=IA_y
+  else
+    axn=-gravity*ssh_x +wave_rad*uwave; ayn=-gravity*ssh_y +wave_rad*vwave
     if (interactive_icebergs_on) then
-      axn=axn + IA_x
-      ayn=ayn + IA_y
+      axn=axn + IA_x; ayn=ayn + IA_y
     endif
-  endif
-  if (C_N>0.) then !  C_N=1 for Crank Nicolson Coriolis, C_N=0 for full implicit Coriolis !Alon
-    axn=axn+f_cori*vveln
-    ayn=ayn-f_cori*uveln
+    axn=axn+f_cori*vveln; ayn=ayn-f_cori*uveln    !for Crank Nicolson Coriolis
   endif
 
-  !This is for testing the code using only interactive forces
-  if (bergs%only_interactive_forces) then
-    axn=IA_x
-    ayn=IA_y
+  if (new_mts) then
+    !ax = 0.5*(axn + bxn)
+    !where uvel_new = uvel_old + dt*ax
+    bxn = 2*ax-axn; byn = 2*ay-ayn
+  else
+    !ax = axn/2 + bxn
+    !where uvel_new = uvel_old + dt*ax
+    bxn= ax-(axn/2); byn= ay-(ayn/2) !Alon
   endif
 
-  bxn= ax-(axn/2) !Alon
-  byn= ay-(ayn/2) !Alon
+  if (bergs%mts_part==1) then
+    !collisional elastic forces
+    if (present(Fec_x) .and. present(Fec_y)) then
+      Fec_x=berg%mass*IA_x
+      Fec_y=berg%mass*IA_y
+    endif
+    !collisional damping forces
+    if (present(Fdc_x) .and. present(Fdc_y)) then
+      Fdc_x=berg%mass*( P_ia_times_u_x - (P_ia_11*uveln+P_ia_12*vveln))
+      Fdc_y=berg%mass*( P_ia_times_u_y - (P_ia_21*uveln+P_ia_22*vveln))
+    endif
+  elseif (save_bond_energy) then
+    !save bond energies
+    if (monitor_energy) then
+      sum_bond_Ee=0.0
+      sum_bond_Ed=0.0
+      M=berg%mass
+      current_bond=>berg%first_bond
+      do while (associated(current_bond)) ! loop over all bonds
+        other_berg=>current_bond%other_berg
+
+        !first, the half-step:
+        current_bond%Ee=current_bond%Ee - 0.25*dt*(&
+          (uvel0 + u_star)*M*current_bond%axn_fast +&
+          (vvel0 + v_star)*M*current_bond%ayn_fast)
+
+        if (new_mts) then
+          current_bond%Ed=current_bond%Ed - 0.25*dt*(&
+            (uvel0 + u_star)*M*current_bond%bxn_fast +&
+            (vvel0 + v_star)*M*current_bond%byn_fast)
+        endif
+
+        !the rest:
+        IA_x=0.0; IA_y=0.0 !explicit elastic force
+        P_ia_11=0.0; P_ia_12=0.0; P_ia_21=0.0; P_ia_22=0.0
+        call calculate_force(bergs, berg, other_berg, IA_x, IA_y, uveln, vveln, uveln, vveln,  &
+          P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded=.true.)
+        !implicit damping force
+        IAd_x=P_ia_11*(other_berg%uvel_old-uveln)+P_ia_12*(other_berg%vvel_old-vveln)
+        IAd_y=P_ia_12*(other_berg%uvel_old-uveln)+P_ia_22*(other_berg%vvel_old-vveln)
+
+        current_bond%Ee=berg%Ee - 0.25*dt*(&
+          (u_star + uveln)*M*IA_x + &
+          (v_star + vveln)*M*IA_y)
+
+        if (new_mts) then
+          !V{i+0.5} to V{i+1}
+          current_bond%Ed=current_bond%Ed- 0.25*dt*(&
+            (u_star + uveln)*M*IAd_x + &
+            (v_star + vveln)*M*IAd_y)
+        else
+          !old way: V{i} to V{i+1}
+          ! current_bond%Ed=current_bond%Ed - 0.5*dt*(&
+          !   (berg%uvel + uveln)*M*IAd_x + &
+          !   (berg%vvel + vveln)*M*IAd_y)
+
+          !new, better way
+          current_bond%Ed=current_bond%Ed - 0.5*dt*(&
+            (u_star + uveln)*M*IAd_x + &
+            (v_star + vveln)*M*IAd_y)
+        endif
+
+        sum_bond_Ee = sum_bond_Ee + current_bond%Ee
+        sum_bond_Ed = sum_bond_Ed + current_bond%Ed
+
+        current_bond%axn_fast=IA_x;  current_bond%ayn_fast=IA_y
+        current_bond%bxn_fast=IAd_x; current_bond%byn_fast=IAd_y
+
+        current_bond=>current_bond%next_bond
+      enddo
+    endif
+  endif
 
   ! Limit speed of bergs based on a CFL criteria
   if ((bergs%speed_limit>0.) .or. (bergs%speed_limit .eq.-1.)) then
@@ -1088,14 +1244,14 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
       dumpit=.true.
       write(stderrunit,'("pe=",i3,x,a)') mpp_pe(),'Dump triggered by excessive acceleration'
     else
-      write(stderrunit,'("pe=",i3,x,a)') mpp_pe(),'Excessive acceleration detected'
+      !write(stderrunit,'("pe=",i3,x,a)') mpp_pe(),'Excessive acceleration detected'
     endif
   endif
   if (present(debug_flag)) then
     if (debug_flag) dumpit=.true.
     write(stderrunit,'("pe=",i3,x,a)') mpp_pe(),'Debug dump flagged by arguments'
   endif
-  if (dumpit) then
+  if (dumpit .and. (.not. bergs%only_interactive_forces)) then
 100 format('pe=',i3,a15,9(x,a8,es12.3))
 200 format('pe=',i3,a5,i14,(a8,i5),(a7,es12.3))
     write(stderrunit,200) mpp_pe(),'id0=',berg%id, &
@@ -1191,1345 +1347,1575 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
     bxn = 0.0;  byn = 0.0
   endif
 
-end subroutine accel
+end subroutine accel_mts
 
-!> Print 3x3 cells from 2d array A
-subroutine dump_locfld(grd, i0, j0, A, lbl)
+!> Calculates the instantaneous acceleration of an iceberg
+subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, rx, ry, ax, ay, axn, ayn, bxn, byn, debug_flag)
   ! Arguments
-  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
-  integer, intent(in) :: i0 !< i-index of center of 3x3 patch to print
-  integer, intent(in) :: j0 !< j-index of center of 3x3 patch to print
-  real, dimension(grd%isd:grd%ied,grd%jsd:grd%jed), intent(in) :: A !< Field to print
-  character(len=*) :: lbl !< Label to add to messages
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  type(iceberg), pointer :: berg !< An iceberg
+  integer, intent(in) :: i !< i-index of cell berg is in
+  integer, intent(in) :: j !< j-index of cell berg is in
+  real, intent(in) :: xi !< Non-dimensional x-position within cell of berg
+  real, intent(in) :: yj !< Non-dimensional y-position within cell of berg
+  real, intent(in) :: lat !< Latitude of berg (degree N)
+  real, intent(in) :: uvel !< Zonal velocity of berg (m/s)
+  real, intent(in) :: vvel !< Meridional velocity of berg (m/s)
+  real, intent(in) :: uvel0 !< Zonal velocity of berg at beginning of time-step (m/s)
+  real, intent(in) :: vvel0 !< Meridional velocity of berg at beginning of time-step (m/s)
+  real, intent(in) :: dt !< Time step (s)
+  real, intent(in) :: rx !< Random number between -1 and 1 for use in x-component of stochastic tidal parameterization
+  real, intent(in) :: ry !< Random number between -1 and 1 for use in y-component of stochastic tidal parameterization
+  real, intent(out) :: ax !< Zonal acceleration (m/s2)
+  real, intent(out) :: ay !< Meridional acceleration (m/s2)
+  real, intent(inout) :: axn !< Explicit estimate of zonal acceleration (m/s2)
+  real, intent(inout) :: ayn !< Explicit estimate of meridional acceleration (m/s2)
+  real, intent(inout) :: bxn !< Implicit component of zonal acceleration (m/s2)
+  real, intent(inout) :: byn !< Implicit component of meridional acceleration (m/s2)
+  logical, optional :: debug_flag !< If true, print debugging
   ! Local variables
-  integer :: i, j, ii, jj
-  real :: B(-1:1,-1:1), fac
+  type(icebergs_gridded), pointer :: grd
+  real :: uo, vo, ui, vi, ua, va, uwave, vwave, ssh_x, ssh_y, sst, sss, cn, hi, od
+  real :: f_cori, T, D, W, L, M, F
+  real :: drag_ocn, drag_atm, drag_ice, wave_rad
+  real :: c_ocn, c_atm, c_ice
+  real :: ampl, wmod, Cr, Lwavelength, Lcutoff, Ltop
+  real, parameter :: accel_lim=1.e-2, Cr0=0.06, vel_lim=15.
+  real :: alpha, beta, C_N
+  real :: lambda, detA, A11, A12, A21, A22, RHS_x, RHS_y, D_hi
+  real :: uveln, vveln, us, vs, speed, loc_dx, new_speed
+  real :: u_star, v_star    !Added by Alon
+  real :: IA_x, IA_y    !Added by Alon
+  real :: P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y    !Added by Alon
+  logical :: dumpit
+  logical :: interactive_icebergs_on  ! Flag to decide whether to use forces between icebergs.
+  logical :: Runge_not_Verlet  ! Flag to specify whether it is Runge-Kutta or Verlet
+  logical :: use_new_predictive_corrective !Flad to use Bob's predictive corrective scheme. (default off)
+  integer :: itloop
   integer :: stderrunit
-  stderrunit = stderr()
+  real :: dragfrac, N_bonds, N_max, groundfrac, c_gnd, drag_gnd
+  real :: minfricvel=3.17e-12 !m/s (~0.0001 m/a)
+  type(bond), pointer :: current_bond
 
-  do jj=-1,1
-    j=max(grd%jsd,min(grd%jed,jj+j0))
-    do ii=-1,1
-      i=max(grd%isd,min(grd%ied,ii+i0))
-      B(ii,jj)=A(i,j)
-      if ((i.ne.ii+i0).or.(j.ne.jj+j0)) B(ii,jj)=-9.999999e-99
-    enddo
-  enddo
-  write(stderrunit,'("pe=",i3,x,a8,3i12)') mpp_pe(),lbl,(i0+ii,ii=-1,1)
-  do jj=1,-1,-1
-    write(stderrunit,'("pe=",i3,x,i8,3es12.4)') mpp_pe(),j0+jj,(B(ii,jj),ii=-1,1)
-  enddo
-end subroutine dump_locfld
+  Runge_not_Verlet=bergs%Runge_not_Verlet  ! Loading directly from namelist/default , Alon
+  interactive_icebergs_on=bergs%interactive_icebergs_on  ! Loading directly from namelist/default , Alon
+  use_new_predictive_corrective=bergs%use_new_predictive_corrective  ! Loading directly from namelist/default , Alon
 
-!> Print 2x2 cells from 2d array A
-subroutine dump_locvel(grd, i0, j0, A, lbl)
-  ! Arguments
-  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
-  integer, intent(in) :: i0 !< i-index of NE-cell of 2x2 patch to print
-  integer, intent(in) :: j0 !< j-index of NE-cell of 2x2 patch to print
-  real, dimension(grd%isd:grd%ied,grd%jsd:grd%jed), intent(in) :: A !< Field to print
-  character(len=*) :: lbl !< Label to add to messages
-  ! Local variables
-  integer :: i, j, ii, jj
-  real :: B(-1:0,-1:0), fac
-  integer :: stderrunit
-  stderrunit = stderr()
+  !These values are no longer set as parameters, but rather can be changed as variables.
+  alpha=0.0
+  beta=1.0
+  C_N=0.0
 
-  do jj=-1,0
-    j=max(grd%jsd,min(grd%jed,jj+j0))
-    do ii=-1,0
-      i=max(grd%isd,min(grd%ied,ii+i0))
-      B(ii,jj)=A(i,j)
-      if ((i.ne.ii+i0).or.(j.ne.jj+j0)) B(ii,jj)=-9.999999e-99
-    enddo
-  enddo
-  write(stderrunit,'("pe=",i3,x,a8,3i12)') mpp_pe(),lbl,(i0+ii,ii=-1,0)
-  do jj=0,-1,-1
-    write(stderrunit,'("pe=",i3,x,i8,3es12.4)') mpp_pe(),j0+jj,(B(ii,jj),ii=-1,0)
-  enddo
-end subroutine dump_locvel
+  !Alon: Verlet requires implicit Coriolis and implicit drag.
+  !Alon: Also, I think that the implicit Coriolis with RK gives icebergs which do not complete inertial circles.
+  if (.not.Runge_not_Verlet) then
+    alpha=1.0
+    C_N=1.0
+    beta=1.0
+    use_new_predictive_corrective=.True.
+  endif
 
-!> Steps forward thermodynamic state of all bergs
-subroutine thermodynamics(bergs)
-  ! Arguments
-  type(icebergs), pointer :: bergs !< Container for all types and memory
-  ! Local variables
-  type(icebergs_gridded), pointer :: grd
-  type(bond), pointer :: current_bond
-  real :: M, T, W, L, SST, Vol, Ln, Wn, Tn, nVol, IC, Dn
-  real :: Mv, Me, Mb, melt, dvo, dva, dM, Ss, dMe, dMb, dMv
-  real :: Mnew, Mnew1, Mnew2, Hocean
-  real :: Mbits, nMbits, dMbitsE, dMbitsM, Lbits, Abits, Mbb
-  real :: tip_parameter
-  real :: Ms, N_bonds, N_max !Ice shelf melt, Number of bonds, Max_number of bonds
-  real :: Delta, q
-  integer :: i,j, stderrunit
-  type(iceberg), pointer :: this, next
-  real, parameter :: perday=1./86400.
-  integer :: grdi, grdj
-  real :: SSS !Temporarily here
+
+  u_star=uvel0+(axn*(dt/2.))  !Alon
+  v_star=vvel0+(ayn*(dt/2.))  !Alon
+
+  ! Get the stderr unit number.
+  stderrunit = stderr()
 
   ! For convenience
   grd=>bergs%grd
 
-  !Initializing
-  grd%Uvel_on_ocean(:,:,:)=0.
-  grd%Vvel_on_ocean(:,:,:)=0.
+  ! Interpolate gridded fields to berg
+  if (bergs%mts) then
+    !gridded fields already saved on berg
+    uo=berg%uo; vo=berg%vo; ua=berg%ua; va=berg%va; ui=berg%ui; vi=berg%vi;
+    ssh_x=berg%ssh_x; ssh_y=berg%ssh_y; sst=berg%sst; sss=berg%sss;  cn=berg%cn; hi=berg%hi; od=berg%od
+  else
+    call interp_flds(grd, berg%lon, berg%lat, i, j, xi, yj, rx, ry, uo, vo, ui, vi, ua, va, ssh_x, &
+      ssh_y, sst, sss, cn, hi, od)
+  end if
 
-  ! Thermodynamics of first halo row is calculated, so that spread mass to ocean works correctly
-  do grdj = grd%jsc-1,grd%jec+1 ; do grdi = grd%isc-1,grd%iec+1
-    this=>bergs%list(grdi,grdj)%first
-    do while(associated(this))
-      if (debug) call check_position(grd, this, 'thermodynamics (top)')
-      call interp_flds(grd, this%ine, this%jne, this%xi, this%yj, 0., 0., this%uo, this%vo, &
-              this%ui, this%vi, this%ua, this%va, this%ssh_x, this%ssh_y, this%sst, &
-              this%sss,this%cn, this%hi)
-      SST=this%sst
-      SSS=this%sss
-      IC=min(1.,this%cn+bergs%sicn_shift) ! Shift sea-ice concentration
-      M=this%mass
-      T=this%thickness ! total thickness
-      !D=(bergs%rho_bergs/rho_seawater)*T ! draught (keel depth)
-      !F=T-D ! freeboard
-      W=this%width
-      L=this%length
-      i=this%ine
-      j=this%jne
-      Vol=T*W*L
+  if ((grd%grid_is_latlon) .and. (.not. bergs%use_f_plane)) then
+     f_cori=(2.*omega)*sin(pi_180*lat)
+  else
+     f_cori=(2.*omega)*sin(pi_180*bergs%lat_ref)
+  endif
+  !f_cori=0.
 
-      ! Environment
-      dvo=sqrt((this%uvel-this%uo)**2+(this%vvel-this%vo)**2)
-      dva=sqrt((this%ua-this%uo)**2+(this%va-this%vo)**2)
-      Ss=1.5*(dva**0.5)+0.1*dva ! Sea state
+  M=berg%mass
+  T=berg%thickness ! total thickness
+  D=(bergs%rho_bergs/rho_seawater)*T ! draught (keel depth)
+  F=T-D ! freeboard
+  W=berg%width
+  L=berg%length
 
-      ! Melt rates in m/s
-      Mv=max( 7.62e-3*SST+1.29e-3*(SST**2), 0.) &! Buoyant convection at sides
-          *perday ! convert to m/s
-      Mb=max( 0.58*(dvo**0.8)*(SST+4.0)/(L**0.2), 0.) &! Basal turbulent melting
-          *perday ! convert to m/s
-      Me=max( 1./12.*(SST+2.)*Ss*(1+cos(pi*(IC**3))) ,0.) &! Wave erosion
-          *perday ! convert to m/s
+  ! Initializing accelerations - Alon. (I am not 100% sure this is needed). I'm not sure what is output if variable is not defined in the subroutine.
+  axn=0.
+  ayn=0.
+  bxn=0.
+  byn=0.
 
-      !For icebergs acting as ice shelves
-      if ((bergs%melt_icebergs_as_ice_shelf) .or.(bergs%use_mixed_melting))  then
-        if (.not. bergs%use_mixed_layer_salinity_for_thermo)  SSS=35.0
-        call find_basal_melt(bergs,dvo,this%lat,SSS,SST,bergs%Use_three_equation_model,T,Ms,this%id)
-        Ms=max(Ms,0.) !No refreezing allowed for now
-        !Set melt to zero if ocean is too thin.
-        if ((bergs%melt_cutoff >=0.) .and. (bergs%apply_thickness_cutoff_to_bergs_melt)) then
-          Dn=(bergs%rho_bergs/rho_seawater)*this%thickness ! draught (keel depth)
-          if ((grd%ocean_depth(i,j)-Dn) < bergs%melt_cutoff) then
-            Ms=0.
-          endif
-        endif
+  hi=min(hi,D)
+  D_hi=max(0.,D-hi)
 
-        if (bergs%use_mixed_melting) then
-          N_bonds=0.
-          N_max=4.0  !Maximum number of bonds that element can form based on shape
-          if (bergs%hexagonal_icebergs) N_max=6.0
-          if (bergs%iceberg_bonds_on) then
-            ! Determining number of bonds
-            current_bond=>this%first_bond
-            do while (associated(current_bond)) ! loop over all bonds
-              N_bonds=N_bonds+1.0
-              current_bond=>current_bond%next_bond
-            enddo
-          endif
-          if  (this%static_berg .eq. 1)  N_bonds=N_max  !Static icebergs melt  like ice shelves
-          Me=((N_max-N_bonds)/N_max)*(Mv+Me)
-          Mv=0.0
-          Mb=(((N_max-N_bonds)/N_max)*(Mb)) + (N_bonds/N_max)*Ms
-        else  !Using Three equation model only.
-          Mv=0.0
-          Me=0.0
-          Mb=Ms
-        endif
-      endif
+  !start to feel grounded with draught of bergs%h_to_init_grounding meters of the sea floor topography
+  !at groundfrac=0, apply no grounding force. at groundfrac=1, apply max grounding force
+  if (bergs%h_to_init_grounding>0.0) then
+    groundfrac=1.0-(od-D)/bergs%h_to_init_grounding
+    groundfrac=max(groundfrac,0.0); groundfrac=min(groundfrac,1.0)
+  else
+    if (D>od) then
+      groundfrac=1.0
+    else
+      groundfrac=0.0
+    endif
+  endif
+  if (groundfrac>0.0) then
+    c_gnd=(bergs%cdrag_grounding*W*L*groundfrac)/M
+  else
+    c_gnd=0.0
+  endif
 
-      if (bergs%set_melt_rates_to_zero) then
-        Mv=0.0
-        Mb=0.0
-        Me=0.0
-      endif
+  ! Wave radiation (Stern et al 2017, Eqs A4-A5)
+  uwave=ua-uo; vwave=va-vo  ! Use wind speed rel. to ocean for wave model (aja)?
+  wmod=uwave*uwave+vwave*vwave ! The wave amplitude and length depend on the wind speed relative to the ocean current
+                               ! actually wmod is wmod**2 here.
+  ampl=0.5*0.02025*wmod ! This is "a", the wave amplitude
+  Lwavelength=0.32*wmod ! Surface wave length fitted to data in table at
+                        ! http://www4.ncsu.edu/eos/users/c/ceknowle/public/chapter10/part2.html
+  Lcutoff=0.125*Lwavelength
+  Ltop=0.25*Lwavelength
+  Cr=Cr0*min(max(0.,(L-Lcutoff)/((Ltop-Lcutoff)+1.e-30)),1.) ! Wave radiation coefficient fitted to
+                                                             ! graph from Carrieres et al.,  POAC Drift Model.
+  wave_rad=0.5*rho_seawater/M*Cr*gravity*ampl*min(ampl,F)*(2.*W*L)/(W+L)
+  wmod = sqrt(ua*ua+va*va) ! Wind speed
+  if (wmod.ne.0.) then
+    uwave=ua/wmod ! Wave radiation force acts in wind direction ...
+    vwave=va/wmod
+  else
+    uwave=0.; vwave=0.; wave_rad=0. ! ... and only when wind is present.
+  endif
 
-      if (bergs%use_operator_splitting) then
-        ! Operator split update of volume/mass
-        Tn=max(T-Mb*bergs%dt,0.) ! new total thickness (m)
-        nVol=Tn*W*L ! new volume (m^3)
-        Mnew1=(nVol/Vol)*M ! new mass (kg)
-        dMb=M-Mnew1 ! mass lost to basal melting (>0) (kg)
+  dragfrac = 1.0
+  if ((bergs%iceberg_bonds_on) .and. (bergs%internal_bergs_for_drag)) then
+    N_bonds=0.
+    N_max=4.0  !Maximum number of bonds that element can form based on shape
+    if (bergs%hexagonal_icebergs) N_max=6.0
+    ! Determining number of bonds
+    current_bond=>berg%first_bond
+    do while (associated(current_bond)) ! loop over all bonds
+      N_bonds=N_bonds+1.0
+      current_bond=>current_bond%next_bond
+    enddo
+    dragfrac = ((N_max-N_bonds)/N_max)
+  endif
 
-        Ln=max(L-Mv*bergs%dt,0.) ! new length (m)
-        Wn=max(W-Mv*bergs%dt,0.) ! new width (m)
-        nVol=Tn*Wn*Ln ! new volume (m^3)
-        Mnew2=(nVol/Vol)*M ! new mass (kg)
-        dMv=Mnew1-Mnew2 ! mass lost to buoyant convection (>0) (kg)
+  ! Weighted drag coefficients (Stern et al 2017, Eqs A1-A3)
+  c_ocn=rho_seawater/M*(0.5*Cd_wv*dragfrac*W*(D_hi)+Cd_wh*W*L)
+  c_atm=rho_air     /M*(0.5*Cd_av*dragfrac*W*F     +Cd_ah*W*L)
+  if (abs(hi).eq.0.) then
+    c_ice=0.
+  else
+    c_ice=rho_ice     /M*(0.5*Cd_iv*dragfrac*W*hi              )
+  endif
+  if (abs(ui)+abs(vi).eq.0.) c_ice=0.
 
-        Ln=max(Ln-Me*bergs%dt,0.) ! new length (m)
-        Wn=max(Wn-Me*bergs%dt,0.) ! new width (m)
-        nVol=Tn*Wn*Ln ! new volume (m^3)
-        Mnew=(nVol/Vol)*M ! new mass (kg)
-        dMe=Mnew2-Mnew ! mass lost to erosion (>0) (kg)
-        dM=M-Mnew ! mass lost to all erosion and melting (>0) (kg)
-      else
-        ! Update dimensions of berg
-        Ln=max(L-(Mv+Me)*(bergs%dt),0.) ! (m)
-        Wn=max(W-(Mv+Me)*(bergs%dt),0.) ! (m)
-        Tn=max(T-Mb*(bergs%dt),0.) ! (m)
-        ! Update volume and mass of berg
-        nVol=Tn*Wn*Ln ! (m^3)
-        Mnew=(nVol/Vol)*M ! (kg)
-        dM=M-Mnew ! (kg)
-        dMb=(M/Vol)*(W*L)*Mb*bergs%dt ! approx. mass loss to basal melting (kg)
-        dMe=(M/Vol)*(T*(W+L))*Me*bergs%dt ! approx. mass lost to erosion (kg)
-        dMv=(M/Vol)*(T*(W+L))*Mv*bergs%dt ! approx. mass loss to buoyant convection (kg)
-      endif
+!Turning drag off for testing - Alon
+!c_ocn=0.
+!c_atm=0.
+!c_ice=0.
 
-      ! Bergy bits
-      if (bergs%bergy_bit_erosion_fraction>0.) then
-        Mbits=this%mass_of_bits ! mass of bergy bits (kg)
-        dMbitsE=bergs%bergy_bit_erosion_fraction*dMe ! change in mass of bits (kg)
-        nMbits=Mbits+dMbitsE ! add new bergy bits to mass (kg)
-        Lbits=min(L,W,T,40.) ! assume bergy bits are smallest dimension or 40 meters
-        Abits=(Mbits/bergs%rho_bergs)/Lbits ! Effective bottom area (assuming T=Lbits)
-        Mbb=max( 0.58*(dvo**0.8)*(SST+2.0)/(Lbits**0.2), 0.) &! Basal turbulent melting (for bits)
-             *perday ! convert to m/s
-        Mbb=bergs%rho_bergs*Abits*Mbb ! in kg/s
-        dMbitsM=min(Mbb*bergs%dt,nMbits) ! bergy bits mass lost to melting (kg)
-        nMbits=nMbits-dMbitsM ! remove mass lost to bergy bits melt
-        if (Mnew==0.) then ! if parent berg has completely melted then
-          dMbitsM=dMbitsM+nMbits ! instantly melt all the bergy bits
-          nMbits=0.
-        endif
-      else
-        Abits=0.
-        dMbitsE=0.
-        dMbitsM=0.
-        nMbits=this%mass_of_bits ! retain previous value incase non-zero
-      endif
+  ! Stern et al 2017, explicit accel due to
+  ! sea surface slope and wave radiation force
+  ! (forces F_R and F_SS, respectively, in Eq. 1.
+  ! Also see Eqn (A4+A6)) :
+    ! Half half accelerations  - axn, ayn
+    if (.not.Runge_not_Verlet) then
+      axn=-gravity*ssh_x +wave_rad*uwave
+      ayn=-gravity*ssh_y +wave_rad*vwave
+    else
+      ! Not half half accelerations  - for RK
+      bxn=-gravity*ssh_x +wave_rad*uwave
+      byn=-gravity*ssh_y +wave_rad*vwave
+    endif
 
-      ! Add melting to the grid and field diagnostics
-      if (grd%area(i,j).ne.0.) then
-        melt=(dM-(dMbitsE-dMbitsM))/bergs%dt ! kg/s
-        grd%floating_melt(i,j)=grd%floating_melt(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
-        melt=melt*this%heat_density ! kg/s x J/kg = J/s
-        grd%calving_hflx(i,j)=grd%calving_hflx(i,j)+melt/grd%area(i,j)*this%mass_scaling ! W/m2
-        bergs%net_heat_to_ocean=bergs%net_heat_to_ocean+melt*this%mass_scaling*bergs%dt ! J
-        melt=dM/bergs%dt ! kg/s
-        grd%berg_melt(i,j)=grd%berg_melt(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
-        melt=dMbitsE/bergs%dt ! mass flux into bergy bits in kg/s
-        grd%bergy_src(i,j)=grd%bergy_src(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
-        melt=dMbitsM/bergs%dt ! melt rate of bergy bits in kg/s
-        grd%bergy_melt(i,j)=grd%bergy_melt(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
-        if(grd%id_melt_buoy>0) then
-          melt=dMb/bergs%dt ! melt rate due to buoyancy term in kg/s
-          grd%melt_buoy(i,j)=grd%melt_buoy(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
-        endif
-        if(grd%id_melt_eros>0) then
-          melt=dMe/bergs%dt ! erosion rate in kg/s
-          grd%melt_eros(i,j)=grd%melt_eros(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
-        endif
-        if(grd%id_melt_conv>0) then
-          melt=dMv/bergs%dt ! melt rate due to convection term in kg/s
-          grd%melt_conv(i,j)=grd%melt_conv(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
-        endif
-      else
-        stderrunit = stderr()
-        write(stderrunit,*) 'KID, thermodynamics: berg appears to have grounded!!!! PE=',mpp_pe(),i,j
-        call print_berg(stderrunit,this,'thermodynamics, grounded')
-        if (associated(this%trajectory)) &
-          write(stderrunit,*) 'traj=',this%trajectory%lon,this%trajectory%lat
-        write(stderrunit,*) 'msk=',grd%msk(i,j),grd%area(i,j)
-        call error_mesg('KID, thermodynamics', 'berg appears to have grounded!', FATAL)
-      endif
+  ! Interactive spring acceleration - (Does the spring part need to be called twice?)
+  if (interactive_icebergs_on) then
+    call interactive_force(bergs, berg, IA_x, IA_y, uvel0, vvel0, uvel0, vvel0, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y) ! Spring forces, Made by Alon.
+    if (.not.Runge_not_Verlet) then
+      axn=axn + IA_x
+      ayn=ayn + IA_y
+    else
+      bxn=bxn + IA_x
+      byn=byn + IA_y
+    endif
+  endif
 
-      ! Rolling
-      !There are now 3 iceberg rolling schemes:
-      !1) Rolling based on aspect ratio threshold (iceberg of constant density)
-      !2) Rolling based on corrected Weeks and Mellor scheme
-      !3) Rolling based on incorrect Weeks and Mellor scheme - kept for legacy reasons
-      if (bergs%allow_bergs_to_roll) then
-        Dn=(bergs%rho_bergs/rho_seawater)*Tn ! draught (keel depth)
-        if ( Dn>0. ) then
-          if ( (.not.bergs%use_updated_rolling_scheme) .and. (bergs%tip_parameter<999.) ) then    !Use Rolling Scheme 3
-              if ( max(Wn,Ln)<sqrt(0.92*(Dn**2)+58.32*Dn) ) then
-                call swap_variables(Tn,Wn)
-              endif
-          else
-            if (Wn>Ln) call swap_variables(Ln,Wn)  !Make sure that Wn is the smaller dimension
+  if (alpha>0.) then ! If implicit Coriolis, use u_star rather than RK4 latest  !Alon
+    if (C_N>0.) then !  C_N=1 for Crank Nicolson Coriolis, C_N=0 for full implicit Coriolis !Alon
+      axn=axn+f_cori*v_star
+      ayn=ayn-f_cori*u_star
+    else
+      bxn=bxn+f_cori*v_star
+      byn=byn-f_cori*u_star
+    endif
+  else
+    bxn=bxn+f_cori*vvel
+    byn=byn-f_cori*uvel
+  endif
 
-            if ( (.not.bergs%use_updated_rolling_scheme) .and. (bergs%tip_parameter>=999.) ) then    !Use Rolling Scheme 2
-              q=bergs%rho_bergs/rho_seawater
-              Delta=6.0
-              if (Wn<sqrt((6.0*q*(1-q)*(Tn**2))-(12*Delta*q*Tn))) then
-                  call swap_variables(Tn,Wn)
-              endif
-            endif
+  if (use_new_predictive_corrective) then
+    uveln=uvel0; vveln=vvel0 ! Discuss this change with Alistair. Alon thinks that it is needed.
+  else
+    uveln=uvel; vveln=vvel
+  endif
 
-            if (bergs%use_updated_rolling_scheme) then    !Use Rolling Scheme 1
-              if (bergs%tip_parameter>0.) then
-                tip_parameter=bergs%tip_parameter
-              else
-                ! Equation 27 from Burton et al 2012, or equivolently, Weeks and Mellor 1979 with constant density
-                tip_parameter=sqrt(6*(bergs%rho_bergs/rho_seawater)*(1-(bergs%rho_bergs/rho_seawater)))   !using default values gives 0.92
-              endif
-              if ((tip_parameter*Tn)>Wn)  then     !note that we use the Thickness instead of the Draft
-                  call swap_variables(Tn,Wn)
-              endif
-            endif
-          endif
-          Dn=(bergs%rho_bergs/rho_seawater)*Tn ! re-calculate draught (keel depth) for grounding
-        endif
-      endif
+  us=uvel0   ; vs=vvel0
+  do itloop=1,2 ! Iterate on drag coefficients
+    if (itloop .eq. 2) then
+      us=uveln ; vs=vveln
+    endif
+   !Stern et al 2017, Eqn A1-A3
+  if (use_new_predictive_corrective) then
+    !Alon's proposed change - using Bob's improved scheme.
+    drag_ocn=c_ocn*0.5*(sqrt( (uveln-uo)**2+(vveln-vo)**2 )+sqrt( (uvel0-uo)**2+(vvel0-vo)**2 ))
+    drag_atm=c_atm*0.5*(sqrt( (uveln-ua)**2+(vveln-va)**2 )+sqrt( (uvel0-ua)**2+(vvel0-va)**2 ))
+    drag_ice=c_ice*0.5*(sqrt( (uveln-ui)**2+(vveln-vi)**2 )+sqrt( (uvel0-ui)**2+(vvel0-vi)**2 ))
+    drag_gnd=c_gnd*max(0.5*(sqrt(uveln**2+vveln**2)+sqrt(uvel0**2+vvel0**2)),minfricvel)**(1.0/3.0 - 1.0)
+  else
+    !Original Scheme
+    us=0.5*(uveln+uvel); vs=0.5*(vveln+vvel)
+    drag_ocn=c_ocn*sqrt( (us-uo)**2+(vs-vo)**2 )
+    drag_atm=c_atm*sqrt( (us-ua)**2+(vs-va)**2 )
+    drag_ice=c_ice*sqrt( (us-ui)**2+(vs-vi)**2 )
+    drag_gnd=c_gnd*max(sqrt(us**2+vs**2),minfricvel)**(1.0/3.0 - 1.0)
+  endif
 
-      !This option allows iceberg melt fluxes to enter the ocean without the icebergs changing shape
-      if (bergs%Iceberg_melt_without_decay) then
-        !In this case, the iceberg dimension are reset to their values before
-        !the thermodynamics are applied.
-        !If the spread_mass is being used to calculate melt, we calculate this
-        !before reseting
-        if (bergs%find_melt_using_spread_mass) then
-          if (Mnew>0.) then !If the berg still exists
-            call spread_mass_across_ocean_cells(bergs,this, i, j, this%xi, this%yj,Mnew , nMbits, this%mass_scaling, Ln*Wn,  Tn)
-          endif
-        endif
-        !Reset all the values
-        Mnew=this%mass
-        nMbits=this%mass_of_bits
-        Tn=this%thickness
-        Wn=this%width
-        Ln=this%length
-        if (bergs%bergy_bit_erosion_fraction>0.) then
-          Mbits=this%mass_of_bits ! mass of bergy bits (kg)
-          Lbits=min(L,W,T,40.) ! assume bergy bits are smallest dimension or 40 meters
-          Abits=(Mbits/bergs%rho_bergs)/Lbits ! Effective bottom area (assuming T=Lbits)
-        endif
-      else
-        ! Store the new state of iceberg (with L>W)
-        this%mass=Mnew
-        this%mass_of_bits=nMbits
-        this%thickness=Tn
-        this%width=min(Wn,Ln)
-        this%length=max(Wn,Ln)
-      endif
-      next=>this%next
+  !RHS ~ similar to accel terms in Stern et al 2017, Eqn B5
+  RHS_x=(axn/2) + bxn
+  RHS_y=(ayn/2) + byn
 
-      ! Did berg completely melt?
-      if (Mnew<=0.) then ! Delete the berg
-        if (.not. bergs%debug_write) call move_trajectory(bergs, this)
-        call delete_iceberg_from_list(bergs%list(grdi,grdj)%first, this)
-        bergs%nbergs_melted=bergs%nbergs_melted+1
-      endif
-      this=>next
-    enddo
-  enddo ; enddo
+  if (beta>0.) then ! If implicit, use u_star, v_star rather than RK4 latest
+    RHS_x=RHS_x - drag_ocn*(u_star-uo) -drag_atm*(u_star-ua) -drag_ice*(u_star-ui) -drag_gnd*u_star
+    RHS_y=RHS_y - drag_ocn*(v_star-vo) -drag_atm*(v_star-va) -drag_ice*(v_star-vi) -drag_gnd*v_star
+  else
+    RHS_x=RHS_x - drag_ocn*(uvel-uo) -drag_atm*(uvel-ua) -drag_ice*(uvel-ui) -drag_gnd*uvel
+    RHS_y=RHS_y - drag_ocn*(vvel-vo) -drag_atm*(vvel-va) -drag_ice*(vvel-vi) -drag_gnd*vvel
+  endif
 
-  contains
+  if (interactive_icebergs_on) then
+    if (itloop>1) then
+      call interactive_force(bergs, berg, IA_x, IA_y, uvel0, vvel0, us,vs, &
+        P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y) ! Spring forces, Made by Alon.
+    endif
+    if (beta>0.) then ! If implicit, use u_star, v_star rather than RK4 latest
+      RHS_x=RHS_x -(((P_ia_11*u_star)+(P_ia_12*v_star))-P_ia_times_u_x)
+      RHS_y=RHS_y -(((P_ia_21*u_star)+(P_ia_22*v_star))-P_ia_times_u_y)
+    else
+      RHS_x=RHS_x - (((P_ia_11*uvel)+(P_ia_12*vvel))-P_ia_times_u_x)
+      RHS_y=RHS_y - (((P_ia_21*uvel)+(P_ia_22*vvel))-P_ia_times_u_y)
+    endif
+    !print *,'Before calculation:', berg%id, IA_x, IA_y, P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y
+  endif
 
-  subroutine swap_variables(x,y)
-    ! Arguments
-    real, intent(inout) :: x, y
-    real :: temp
-    temp=x
-    x=y
-    y=temp
-  end subroutine swap_variables
+  ! Solve for implicit accelerations
+  if (alpha+beta.gt.0.) then
+    if (bergs%only_interactive_forces) then
+      RHS_x=(IA_x/2) -(((P_ia_11*u_star)+(P_ia_12*v_star))-P_ia_times_u_x)
+      RHS_y=(IA_y/2) -(((P_ia_21*u_star)+(P_ia_22*v_star))-P_ia_times_u_y)
+      A11=1+(dt*P_ia_11)
+      A12=(dt*P_ia_12)
+      A21=(dt*P_ia_21)
+      A22=1+(dt*P_ia_22)
+    else
+      lambda=drag_ocn+drag_atm+drag_ice+drag_gnd
+      !Matrix A = [A11 A12; A21 A22] is the denominator on the rhs of Stern et al 2017, Eqn B7
+      A11=1.+beta*dt*lambda
+      A22=1.+beta*dt*lambda
+      A12=-alpha*dt*f_cori
+      A21=alpha*dt*f_cori
+      !A12=dt*f_cori  !Removed by ALon (in order to have the entire matrix. I hope the sign is correct)
+
+      if (C_N>0.) then ! For Crank-Nicolson Coriolis term.
+        A12=A12/2.
+        A21=A21/2.
+      endif
 
-end subroutine thermodynamics
+      if (interactive_icebergs_on) then
+        A11=A11+(dt*P_ia_11)
+        A12=A12+(dt*P_ia_12)
+        A21=A21+(dt*P_ia_21)
+        A22=A22+(dt*P_ia_22)
+      endif
+    endif
 
-subroutine create_gridded_icebergs_fields(bergs)
-! Arguments
-type(icebergs), pointer :: bergs !< Container for all types and memory
-! Local variables
-type(icebergs_gridded), pointer :: grd
-type(iceberg), pointer :: this
-integer i,j
-integer :: grdi, grdj
-real :: Hocean, Dn,Tn,dvo, mass_tmp
-real :: ustar_h, ustar
-real :: orientation
-real :: ave_thickness, ave_draft
-real, dimension(bergs%grd%isd:bergs%grd%ied,bergs%grd%jsd:bergs%grd%jed)  :: spread_mass_tmp
-real :: tmp
+    !inverse of matrix A * RHS
+    detA=1./((A11*A22)-(A12*A21))
+    ax=detA*(A22*RHS_x-A12*RHS_y)
+    ay=detA*(A11*RHS_y-A21*RHS_x)
 
-  ! For convenience
-  grd=>bergs%grd
+!Alistair's version removed by Alon
+!      detA=1./(A11**2+A12**2)
+!      ax=detA*(A11*RHS_x+A12*RHS_y)
+!      ay=detA*(A11*RHS_y-A12*RHS_x)
+    else
+      ax=RHS_x; ay=RHS_y
+    endif
 
-  spread_mass_tmp(:,:)=0. !Initializing temporary variable to use in iceberg melt calculation
+    ! Stern et al 2017, Eqn B5 and B6. Here, ax accounts for both acceleration terms (separated below)
+    uveln=u_star+dt*ax        ! Alon
+    vveln=v_star+dt*ay        ! Alon
+  enddo ! itloop
 
-  !Special case for icebergs not decaying, but mass diffence being used for melt rates
-  if ((bergs%find_melt_using_spread_mass) .and.  (bergs%Iceberg_melt_without_decay)) then
-    call sum_up_spread_fields(bergs, spread_mass_tmp(grd%isc:grd%iec,grd%jsc:grd%jec),'mass')
+  !Below: axn and ayn are the new explicit acceleration terms in Stern et al 2017, Eqn B5
+  !       bxn and byn are the new implicit accerelation terms
+  !Saving the totally explicit part of the acceleration to use in finding the next position and u_star -Alon
+  if (bergs%only_interactive_forces) then
+    axn=IA_x
+    ayn=IA_y
+  else
+    axn=0.; ayn=0.
+    if (.not.Runge_not_Verlet) then
+      axn=-gravity*ssh_x +wave_rad*uwave
+      ayn=-gravity*ssh_y +wave_rad*vwave
+      if (interactive_icebergs_on) then
+        axn=axn + IA_x
+        ayn=ayn + IA_y
+      endif
+    endif
+    if (C_N>0.) then !  C_N=1 for Crank Nicolson Coriolis, C_N=0 for full implicit Coriolis !Alon
+      axn=axn+f_cori*vveln
+      ayn=ayn-f_cori*uveln
+    endif
   endif
 
-  !Loop through icebergs and spread mass on ocean
-  call calculate_mass_on_ocean(bergs, with_diagnostics=.true.)
+  bxn= ax-(axn/2); byn= ay-(ayn/2) !Alon
 
-  !Finding the spread fields
-  if ((grd%id_spread_uvel>0)  .or. (bergs%pass_fields_to_ocean_model)) then
-    grd%spread_uvel(:,:)=0.
-    call sum_up_spread_fields(bergs, grd%spread_uvel(grd%isc:grd%iec,grd%jsc:grd%jec), 'Uvel')
+  ! Limit speed of bergs based on a CFL criteria
+  if ((bergs%speed_limit>0.) .or. (bergs%speed_limit .eq.-1.)) then
+    speed=sqrt(uveln*uveln+vveln*vveln) ! Speed of berg
+    if (speed>0.) then
+      loc_dx=min(0.5*(grd%dx(i,j)+grd%dx(i,j-1)),0.5*(grd%dy(i,j)+grd%dy(i-1,j))) ! min(dx,dy)
+      !new_speed=min(loc_dx/dt*bergs%speed_limit,speed) ! Restrict speed to dx/dt x factor
+      new_speed=loc_dx/dt*bergs%speed_limit ! Speed limit as a factor of dx / dt
+      if (new_speed<speed) then
+        if (bergs%speed_limit>0.) then
+          uveln=uveln*(new_speed/speed) ! Scale velocity to reduce speed
+          vveln=vveln*(new_speed/speed) ! without changing the direction
+          bergs%nspeeding_tickets=bergs%nspeeding_tickets+1
+        else
+          call error_mesg('KID, Speeding icebergs', 'Faster than the CFL!', WARNING)
+          write(stderrunit,*) 'KID, Speeding berg1! =',mpp_pe(), berg%id
+          write(stderrunit,*) 'KID, Speeding berg2, speed =',speed, loc_dx/dt
+          write(stderrunit,*) 'KID, Speeding berg3, lat, lon =',lat,xi,yj
+        endif
+      endif
+    endif
   endif
-  if ( (grd%id_spread_vvel>0)  .or. (bergs%pass_fields_to_ocean_model)) then
-    grd%spread_vvel(:,:)=0.
-    call sum_up_spread_fields(bergs, grd%spread_vvel(grd%isc:grd%iec,grd%jsc:grd%jec), 'Vvel')
+
+  dumpit=.false.
+  if (abs(uveln)>vel_lim.or.abs(vveln)>vel_lim) then
+    if (debug) then
+      dumpit=.true.
+      write(stderrunit,'("pe=",i3,x,a)') mpp_pe(),'Dump triggered by excessive velocity'
+    else
+      write(stderrunit,'("pe=",i3,x,a)') mpp_pe(),'Excessive velocity detected'
+    endif
   endif
-  if ( (grd%id_spread_area>0)  .or. (bergs%pass_fields_to_ocean_model)) then
-    grd%spread_area(:,:)=0.
-    call sum_up_spread_fields(bergs, grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec), 'area')
+  if (abs(ax)>accel_lim.or.abs(ay)>accel_lim) then
+    if (debug) then
+      dumpit=.true.
+      write(stderrunit,'("pe=",i3,x,a)') mpp_pe(),'Dump triggered by excessive acceleration'
+    else
+      !write(stderrunit,'("pe=",i3,x,a)') mpp_pe(),'Excessive acceleration detected'
+    endif
   endif
-  !Always find spread_mass since it is used for so many things.
-  grd%spread_mass(:,:)=0.
-    call sum_up_spread_fields(bergs, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec),'mass')
-
-  !Using spread_mass_to_ocean to calculate melt rates (if this option is chosen)
-  if (bergs%find_melt_using_spread_mass) then
-    if (.not. bergs%Iceberg_melt_without_decay) &
-         spread_mass_tmp(grd%isc:grd%iec,grd%jsc:grd%jec)= grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec)
-    do i=grd%isd,grd%ied ; do j=grd%jsd,grd%jed
-      if (grd%area(i,j)>0.0) then
-        grd%floating_melt(i,j)=max((grd%spread_mass_old(i,j) - spread_mass_tmp(i,j))/(bergs%dt),0.0)
-      else
-        grd%floating_melt(i,j)=0.0
-      endif
-    enddo ;enddo
-    grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)=grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec)*HLF !Not 100% sure this is correct.
+  if (present(debug_flag)) then
+    if (debug_flag) dumpit=.true.
+    write(stderrunit,'("pe=",i3,x,a)') mpp_pe(),'Debug dump flagged by arguments'
+  endif
+  if (dumpit) then
+100 format('pe=',i3,a15,9(x,a8,es12.3))
+200 format('pe=',i3,a5,i14,(a8,i5),(a7,es12.3))
+    write(stderrunit,200) mpp_pe(),'id0=',berg%id, &
+      'yr0=',berg%start_year, 'day0=',berg%start_day, &
+      'lon0=',berg%start_lon, 'lat0=',berg%start_lat, 'mass0=',berg%start_mass, &
+      'sclng=',berg%mass_scaling
+    write(stderrunit,100) mpp_pe(),'Geometry:', &
+      'M=',M, 'T=',T, 'D=',D, 'F=',F, 'W=',W, 'L=',L
+    write(stderrunit,100) mpp_pe(),'delta U:', &
+      'u(n)=',uvel0, 'u(*)=', uvel, 'u(n+1)=',uvel+dt*ax, 'del u=',dt*ax
+    write(stderrunit,100) mpp_pe(),'U terms', &
+      'f*v=',f_cori*vvel, &
+      'g*H_x=',-gravity*ssh_x, &
+      'wave*ua=',wave_rad*uwave, &
+      'd*(u-uo)=',-drag_ocn*(uvel-uo), &
+      'd*(u-ua)=',-drag_atm*(uvel-ua), &
+      'd*(u-ui)=',-drag_ice*(uvel-ui)
+    write(stderrunit,100) mpp_pe(),'U accel.', &
+      'RHS_x=',RHS_x, &
+      'ax=',ax, &
+      'ax(cori)=',detA*(A11*(f_cori*vvel)+A12*(-f_cori*uvel)), &
+      'ax(grav)=',detA*(A11*(-gravity*ssh_x)+A12*(-gravity*ssh_y)), &
+      'ax(wave)=',detA*(A11*(wave_rad*uwave)+A12*(wave_rad*vwave)), &
+      'ax(ocn)=',detA*(A11*(-drag_ocn*(uvel-uo))+A12*(-drag_ocn*(vvel-vo))), &
+      'ax(atm)=',detA*(A11*(-drag_atm*(uvel-ua))+A12*(-drag_atm*(vvel-va))), &
+      'ax(ice)=',detA*(A11*(-drag_ice*(uvel-ui))+A12*(-drag_ice*(vvel-vi)))
+    write(stderrunit,100) mpp_pe(),'delta V:', &
+      'v(n)=',vvel0, 'v(*)=', vvel, 'v(n+1)=',vvel+dt*ay, 'del v=',dt*ay
+    write(stderrunit,100) mpp_pe(),'V terms', &
+      'f*u=',-f_cori*uvel, &
+      'g*H_y=',-gravity*ssh_y, &
+      'wave*va=',wave_rad*vwave, &
+      'd*(v-vo)=',-drag_ocn*(vvel-vo), &
+      'd*(v-va)=',-drag_atm*(vvel-va), &
+      'd*(v-vi)=',-drag_ice*(vvel-vi)
+    write(stderrunit,100) mpp_pe(),'V accel. pe=', &
+      'RHS_y=',RHS_y, &
+      'ay=',ay, &
+      'ay(cori)=',detA*(-A12*(f_cori*vvel)+A11*(-f_cori*uvel)), &
+      'ay(grav)=',detA*(-A12*(-gravity*ssh_x)+A11*(-gravity*ssh_y)), &
+      'ay(wave)=',detA*(-A12*(wave_rad*uwave)+A11*(wave_rad*vwave)), &
+      'ay(ocn)=',detA*(-A12*(-drag_ocn*(uvel-uo))+A11*(-drag_ocn*(vvel-vo))), &
+      'ay(atm)=',detA*(-A12*(-drag_atm*(uvel-ua))+A11*(-drag_atm*(vvel-va))), &
+      'ay(ice)=',detA*(-A12*(-drag_ice*(uvel-ui))+A11*(-drag_ice*(vvel-vi)))
+    write(stderrunit,100) mpp_pe(),'Vel scales', &
+      '|va-vo|=',sqrt((ua-uo)**2+(va-vo)**2), &
+      '|vo-vb|=',sqrt((uvel-uo)**2+(vvel-vo)**2), &
+      '|va-vb|=',sqrt((uvel-ua)**2+(vvel-va)**2), &
+      '|vi-vb|=',sqrt((uvel-ui)**2+(vvel-vi)**2), &
+      '|vb|=',sqrt((uvel)**2+(vvel)**2), &
+      '|va|=',sqrt((ua)**2+(va)**2), &
+      '|vo|=',sqrt((uo)**2+(vo)**2), &
+      '|vi|=',sqrt((ui)**2+(vi)**2)
+    write(stderrunit,100) mpp_pe(),'Time scales', &
+      'f=',f_cori, 'wave_rad=',wave_rad, 'do=',drag_ocn, 'da=',drag_atm, 'di=',drag_ice
+    write(stderrunit,100) mpp_pe(),'u*', &
+      'd*=',lambda, &
+      'u*=',(drag_ocn*uo+drag_atm*ua+drag_ice*ui)/lambda, &
+      'uo*=',(drag_ocn*uo)/lambda, &
+      'ua*=',(drag_atm*ua)/lambda, &
+      'ui*=',(drag_ice*ui)/lambda
+    write(stderrunit,100) mpp_pe(),'v*', &
+      'd*=',lambda, &
+      'v*=',(drag_ocn*vo+drag_atm*va+drag_ice*vi)/lambda, &
+      'vo*=',(drag_ocn*vo)/lambda, &
+      'va*=',(drag_atm*va)/lambda, &
+      'vi*=',(drag_ice*vi)/lambda
+    write(stderrunit,100) mpp_pe(),'params', &
+      'a=',ampl, 'Lwl=',Lwavelength, 'Lcut=',Lcutoff, 'Ltop=',Ltop, 'hi=',hi, 'Cr=',Cr
+    write(stderrunit,100) mpp_pe(),'Position', &
+      'xi=',xi, 'yj=',yj, 'lat=',lat
+    call dump_locfld(grd,i,j,grd%msk,'MSK')
+    call dump_locfld(grd,i,j,grd%ssh,'SSH')
+    call dump_locfld(grd,i,j,grd%sst,'SST')
+    call dump_locfld(grd,i,j,grd%sss,'SSS')
+    call dump_locvel(grd,i,j,grd%uo,'Uo')
+    call dump_locvel(grd,i,j,grd%vo,'Vo')
+    call dump_locvel(grd,i,j,grd%ua,'Ua')
+    call dump_locvel(grd,i,j,grd%va,'Va')
+    call dump_locvel(grd,i,j,grd%ui,'Ui')
+    call dump_locvel(grd,i,j,grd%vi,'Vi')
+    call dump_locfld(grd,i,j,grd%hi,'HI')
+    call dump_locfld(grd,i,j,grd%cn,'CN')
+    call dump_locvel(grd,i,j,grd%lon,'Lon')
+    call dump_locvel(grd,i,j,grd%lat,'Lat')
+    call print_berg(stderrunit,berg,'KID, accel, large accel')
   endif
 
-  ! Dividing the gridded iceberg momentum diagnostic by the iceberg mass to get velocities
-  if ((grd%id_u_iceberg>0) .or. (grd%id_v_iceberg>0)) then
-    do j = grd%jsc,grd%jec ; do i = grd%isc,grd%iec
-      if (grd%mass(i,j)>0.) then
-        if (grd%id_u_iceberg>0) &
-          grd%u_iceberg(i,j)=grd%u_iceberg(i,j)/grd%mass(i,j)
-        if (grd%id_v_iceberg>0) &
-          grd%v_iceberg(i,j)=grd%v_iceberg(i,j)/grd%mass(i,j)
-      else
-        if (grd%id_u_iceberg>0)  grd%u_iceberg(i,j)=0.
-        if (grd%id_v_iceberg>0)  grd%v_iceberg(i,j)=0.
-      endif
-    enddo; enddo
+  !Used for testing the ocean response to fixed iceberg motion.
+  if (bergs%override_iceberg_velocities) then
+    ax  = 0.0;  ay  = 0.0
+    axn = 0.0;  ayn = 0.0
+    bxn = 0.0;  byn = 0.0
   endif
 
-  !Calculating ustar_iceberg (gridded)
-  grd%ustar_iceberg(:,:)=0.
-  if  ((grd%id_ustar_iceberg>0) .or. (bergs%pass_fields_to_ocean_model)) then   !Update diagnostic of iceberg mass spread on ocean
-    do j = grd%jsc,grd%jec ; do i = grd%isc,grd%iec
-      dvo=sqrt((grd%spread_uvel(i,j)-grd%uo(i,j))**2+(grd%spread_vvel(i,j)-grd%vo(i,j))**2)
-      ustar = sqrt(bergs%cdrag_icebergs*(dvo**2  + bergs%utide_icebergs**2))
-      ustar_h = max(bergs%ustar_icebergs_bg, ustar)
-      if (grd%spread_area(i,j) ==0.0) ustar_h=0.
-        grd%ustar_iceberg(i,j)=ustar_h
-    enddo; enddo
-  endif
-
-  !Only allowing melt in ocean above a minimum cutoff thickness
-  if (bergs%apply_thickness_cutoff_to_gridded_melt) then
-    do i=grd%isd,grd%ied ; do j=grd%jsd,grd%jed
-      if ((bergs%melt_cutoff >=0.) .and. (grd%spread_area(i,j)>0.)) then
-        ave_thickness=grd%spread_mass(i,j)/(grd%spread_area(i,j)*bergs%rho_bergs)
-        ave_draft=ave_thickness*(bergs%rho_bergs/rho_seawater)
-        if ((grd%ocean_depth(i,j)-ave_draft) < bergs%melt_cutoff) then
-          grd%floating_melt(i,j)=0.0
-          grd%calving_hflx(i,j)=0.0
-        endif
-      endif
-    enddo ;enddo
-  endif
-end subroutine create_gridded_icebergs_fields
+end subroutine accel
 
-!> Calculates basal melt for given thermodynamic properties
-subroutine find_basal_melt(bergs, dvo, lat, salt, temp, Use_three_equation_model, thickness, basal_melt, id)
+!> Print 3x3 cells from 2d array A
+subroutine dump_locfld(grd, i0, j0, A, lbl)
   ! Arguments
-  type(icebergs), pointer :: bergs !< Container for all types and memory
-  real, intent(in) :: dvo !< Speed of iceberg relative to ocean mixed layer
-  real, intent(in) :: lat !< Latitude (for boundary layer calculation)
-  real, intent(in) :: salt !< Salinity of mixed layer
-  real, intent(in) :: temp !< Temperature of mixed layer
-  logical, intent(in) :: Use_three_equation_model !< True uses the 3 equation model, False uses the 2 equation model.
-  real, intent(in) :: thickness !< Ice thickness - needed to work out the pressure below the ice
-  real, intent(out) :: basal_melt !< Melt rate underneath the icebergs
-  integer(kind=8), intent(in) :: id !< Iceberg id, used for debugging (error messages)
+  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+  integer, intent(in) :: i0 !< i-index of center of 3x3 patch to print
+  integer, intent(in) :: j0 !< j-index of center of 3x3 patch to print
+  real, dimension(grd%isd:grd%ied,grd%jsd:grd%jed), intent(in) :: A !< Field to print
+  character(len=*) :: lbl !< Label to add to messages
   ! Local variables
-  real :: ustar, f_cori, absf,tfreeze
-  real :: Hml !Mixed layer depth
-
-  !These could also be useful output variables if needed.
-  real :: t_flux, exch_vel_t, exch_vel_s,tflux_shelf,lprec
-
-  real ::  Rhoml   ! Ocean mixed layer density in kg m-3.
-  real ::  p_int   ! The pressure at the ice-ocean interface, in Pa.
+  integer :: i, j, ii, jj
+  real :: B(-1:1,-1:1), fac
+  integer :: stderrunit
+  stderrunit = stderr()
 
-  real, parameter :: VK    = 0.40     ! Von Karman's constant - dimensionless
-  real :: ZETA_N = 0.052   ! The fraction of the boundary layer over which the
-                           ! viscosity is linearly increasing. (Was 1/8. Why?)
-  real, parameter :: RC    = 0.20     ! critical flux Richardson number.
-  real :: I_ZETA_N  ! The inverse of ZETA_N.
-  real :: I_LF  ! Inverse of Latent Heat of fusion (J kg-1)
-  real :: I_VK      ! The inverse of VK.
-  real :: PR, SC    ! The Prandtl number and Schmidt number, nondim.
+  do jj=-1,1
+    j=max(grd%jsd,min(grd%jed,jj+j0))
+    do ii=-1,1
+      i=max(grd%isd,min(grd%ied,ii+i0))
+      B(ii,jj)=A(i,j)
+      if ((i.ne.ii+i0).or.(j.ne.jj+j0)) B(ii,jj)=-9.999999e-99
+    enddo
+  enddo
+  write(stderrunit,'("pe=",i3,x,a8,3i12)') mpp_pe(),lbl,(i0+ii,ii=-1,1)
+  do jj=1,-1,-1
+    write(stderrunit,'("pe=",i3,x,i8,3es12.4)') mpp_pe(),j0+jj,(B(ii,jj),ii=-1,1)
+  enddo
+end subroutine dump_locfld
 
-  ! 3 equation formulation variables
-  real :: Sbdry     !   Salinities in the ocean at the interface with the
-  real :: Sbdry_it  ! the ice shelf, in PSU.
-  real :: dS_it     ! The interface salinity change during an iteration, in PSU.
-  real :: hBL_neut  ! The neutral boundary layer thickness, in m.
-  real :: hBL_neut_h_molec ! The ratio of the neutral boundary layer thickness
-                           ! to the molecular boundary layer thickness, ND.
-  real :: wT_flux ! The vertical fluxes of heat and buoyancy just inside the
-  real :: wB_flux ! ocean, in C m s-1 and m2 s-3, ###CURRENTLY POSITIVE UPWARD.
-  real :: dB_dS  ! The derivative of buoyancy with salinity, in m s-2 PSU-1.
-  real :: dB_dT  ! The derivative of buoyancy with temperature, in m s-2 C-1.
-  real :: I_n_star, n_star_term
-  real :: dIns_dwB  ! The partial derivative of I_n_star with wB_flux, in ???.
-  real :: dT_ustar, dS_ustar
-  real :: ustar_h
-  real :: Gam_turb
-  real :: Gam_mol_t, Gam_mol_s
-  real :: RhoCp
-  real :: I_RhoLF
-  real :: Rho0
-  real :: ln_neut
-  real :: mass_exch
-  real :: Sb_min, Sb_max
-  real :: dS_min, dS_max
-  real :: density_ice
+!> Print 2x2 cells from 2d array A
+subroutine dump_locvel(grd, i0, j0, A, lbl)
+  ! Arguments
+  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+  integer, intent(in) :: i0 !< i-index of NE-cell of 2x2 patch to print
+  integer, intent(in) :: j0 !< j-index of NE-cell of 2x2 patch to print
+  real, dimension(grd%isd:grd%ied,grd%jsd:grd%jed), intent(in) :: A !< Field to print
+  character(len=*) :: lbl !< Label to add to messages
+  ! Local variables
+  integer :: i, j, ii, jj
+  real :: B(-1:0,-1:0), fac
+  integer :: stderrunit
+  stderrunit = stderr()
 
-  ! Variables used in iterating for wB_flux.
-  real :: wB_flux_new, DwB, dDwB_dwB_in
-  real :: I_Gam_T, I_Gam_S
-  real :: dG_dwB, iDens
-  logical :: Sb_min_set, Sb_max_set
-  logical :: out_of_bounds
+  do jj=-1,0
+    j=max(grd%jsd,min(grd%jed,jj+j0))
+    do ii=-1,0
+      i=max(grd%isd,min(grd%ied,ii+i0))
+      B(ii,jj)=A(i,j)
+      if ((i.ne.ii+i0).or.(j.ne.jj+j0)) B(ii,jj)=-9.999999e-99
+    enddo
+  enddo
+  write(stderrunit,'("pe=",i3,x,a8,3i12)') mpp_pe(),lbl,(i0+ii,ii=-1,0)
+  do jj=0,-1,-1
+    write(stderrunit,'("pe=",i3,x,i8,3es12.4)') mpp_pe(),j0+jj,(B(ii,jj),ii=-1,0)
+  enddo
+end subroutine dump_locvel
 
-  real, parameter :: c2_3 = 2.0/3.0
-  integer ::  it1, it3
+!> Steps forward thermodynamic state of all bergs
+subroutine thermodynamics(bergs)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  ! Local variables
+  type(icebergs_gridded), pointer :: grd
+  type(bond), pointer :: current_bond
+  real :: M, T, W, L, SST, Vol, Ln, Wn, Tn, nVol, IC, Dn
+  real :: Mv, Me, Mb, melt, dvo, dva, dM, Ss, dMe, dMb, dMv
+  real :: Mnew, Mnew1, Mnew2, Hocean
+  real :: Mbits, nMbits, dMbitsE, dMbitsM, Lbits, Abits, Mbb
+  real :: tip_parameter
+  real :: Ms, N_bonds, N_max !Ice shelf melt, Number of bonds, Max_number of bonds
+  real :: Delta, q
+  integer :: i,j, stderrunit
+  type(iceberg), pointer :: this, next
+  real, parameter :: perday=1./86400.
+  integer :: grdi, grdj
+  real :: SSS !Temporarily here
 
-  !Parameters copied ice shelf module defaults (could be entered in the namelist later)
-  real, parameter :: dR0_dT = -0.038357 ! Partial derivative of the mixed layer density with temperature, in units of kg m-3 K-1.
-  real, parameter :: dR0_dS = 0.805876 ! Partial derivative of the mixed layer density with salinity, in units of kg m-3 psu-1.
-  real, parameter :: RHO_T0_S0 = 999.910681 ! Density of water with T=0, S=0 for linear EOS
-  real, parameter :: Salin_Ice =0.0 !Salinity of ice
-  real, parameter :: Temp_Ice = -15.0 !Salinity of ice
-  real, parameter :: kd_molec_salt=  8.02e-10 !The molecular diffusivity of salt in sea water at the freezing point
-  real, parameter :: kd_molec_temp=  1.41e-7 !The molecular diffusivity of heat in sea water at the freezing point
-  real, parameter :: kv_molec=  1.95e-6 !The molecular molecular kinematic viscosity of sea water at the freezing point
-  real, parameter :: Cp_Ice =  2009.0 !Specific heat capacity of ice, taking from HJ99 (Holland and Jenkins 1999)
-  real, parameter :: Cp_ml =  3974.0 !Specific heat capacity of mixed layer, taking from HJ99 (Holland and Jenkins 1999)
-  real, parameter :: LF =  3.335e5 !Latent heat of fusion, taken from HJ99 (Holland and Jenkins 1999)
-  real, parameter :: gamma_t =  0.0 ! Exchange velocity used in 2 equation model. Whn gamma_t is >0, the exchange velocity is independent of u_star.
-                                  ! When gamma_t=0.0, then gamma_t is not used, and the exchange velocity is found using u_star.
-  real, parameter :: p_atm =  101325 ! Average atmospheric pressure (Pa) - from Google.
+  ! For convenience
+  grd=>bergs%grd
 
-  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-  density_ice = bergs%rho_bergs
-  Rho0=rho_seawater  !Note that the ice shelf code has a default of Rho0=1035
-  Hml =10.      !Mixed layer depth. This is an approximate value. It looks like the code is not sensitive to it (since it enters in log(Hml)
-  p_int= p_atm+(gravity*thickness*density_ice)    ! The pressure at the ice-ocean interface, in Pa.
+  !Initializing
+  grd%Uvel_on_ocean(:,:,:)=0.
+  grd%Vvel_on_ocean(:,:,:)=0.
 
-  ! Find the ocean mixed layer density in kg m-3.
-  call calculate_density(temp, salt, p_int, Rhoml, Rho_T0_S0, dR0_dT, dR0_dS)
+  if (bergs%use_mixed_melting .or. bergs%allow_bergs_to_roll) then
+    !Maximum number of bonds that element can form based on shape
+    if (bergs%hexagonal_icebergs) then
+      N_max=6.0
+    else
+      N_max=4.0
+    endif
+  endif
 
-  ! This routine finds the melt at the base of the icebergs using the 2 equation
-  ! model or 3 equation model. This code is adapted from the ice shelf code. Once
-  ! the iceberg model is inside the ocean model, we should use the same code.
+  ! Thermodynamics of first halo row is calculated, so that spread mass to ocean works correctly
+  do grdj = grd%jsc-1,grd%jec+1 ; do grdi = grd%isc-1,grd%iec+1
+    this=>bergs%list(grdi,grdj)%first
+    do while(associated(this))
+      if (debug) call check_position(grd, this, 'thermodynamics (top)')
+      call interp_flds(grd, this%lon, this%lat, this%ine, this%jne, this%xi, this%yj, 0., 0., &
+                       this%uo, this%vo, this%ui, this%vi, this%ua, this%va, this%ssh_x, &
+                       this%ssh_y, this%sst, this%sss,this%cn, this%hi)
+      SST=this%sst
+      SSS=this%sss
+      IC=min(1.,this%cn+bergs%sicn_shift) ! Shift sea-ice concentration
+      M=this%mass
+      T=this%thickness ! total thickness
+      !D=(bergs%rho_bergs/rho_seawater)*T ! draught (keel depth)
+      !F=T-D ! freeboard
+      W=this%width
+      L=this%length
+      i=this%ine
+      j=this%jne
+      Vol=T*W*L
 
-  I_ZETA_N = 1.0 / ZETA_N
-  I_RhoLF = 1.0/(Rho0*LF)
-  I_LF = 1.0 / LF
-  SC = kv_molec/kd_molec_salt
-  PR = kv_molec/kd_molec_temp
-  I_VK = 1.0/VK
-  RhoCp = Rho0 * Cp_ml
+      ! Environment
+      dvo=sqrt((this%uvel-this%uo)**2+(this%vvel-this%vo)**2)
+      dva=sqrt((this%ua-this%uo)**2+(this%va-this%vo)**2)
+      Ss=1.5*(dva**0.5)+0.1*dva ! Sea state
 
-  !first calculate molecular component
-  Gam_mol_t = 12.5 * (PR**c2_3) - 6
-  Gam_mol_s = 12.5 * (SC**c2_3) - 6
+      ! Melt rates in m/s
+      Mv=max( 7.62e-3*SST+1.29e-3*(SST**2), 0.) &! Buoyant convection at sides
+          *perday ! convert to m/s
+      Mb=max( 0.58*(dvo**0.8)*(SST+4.0)/(L**0.2), 0.) &! Basal turbulent melting
+          *perday ! convert to m/s
+      Me=max( 1./12.*(SST+2.)*Ss*(1+cos(pi*(IC**3))) ,0.) &! Wave erosion
+          *perday ! convert to m/s
 
-  iDens = 1.0/Rho0
+        if (bergs%use_mixed_melting .or. bergs%allow_bergs_to_roll) then
+          N_bonds=0.
+          if (bergs%iceberg_bonds_on) then
+            ! Determining number of bonds
+            current_bond=>this%first_bond
+            do while (associated(current_bond)) ! loop over all bonds
+              N_bonds=N_bonds+1.0
+              current_bond=>current_bond%next_bond
+            enddo
+          endif
+          if  (this%static_berg .eq. 1)  N_bonds=N_max  !Static icebergs melt like ice shelves
+        endif
 
-  !Preparing the mixed layer properties for use in both 2 and 3 equation version
-  ustar = sqrt(bergs%cdrag_icebergs*(dvo**2  + bergs%utide_icebergs**2))
-  ustar_h = max(bergs%ustar_icebergs_bg, ustar)
+      !For icebergs acting as ice shelves
+      if ((bergs%melt_icebergs_as_ice_shelf) .or.(bergs%use_mixed_melting))  then
+        if (.not. bergs%use_mixed_layer_salinity_for_thermo)  SSS=35.0
+        call find_basal_melt(bergs,dvo,this%lat,SSS,SST,bergs%Use_three_equation_model,T,Ms,this%id)
+        Ms=max(Ms,0.) !No refreezing allowed for now
+        !Set melt to zero if ocean is too thin.
+        if ((bergs%melt_cutoff >=0.) .and. (bergs%apply_thickness_cutoff_to_bergs_melt)) then
+          Dn=(bergs%rho_bergs/rho_seawater)*this%thickness ! draught (keel depth)
+          if ((grd%ocean_depth(i,j)-Dn) < bergs%melt_cutoff) then
+            Ms=0.
+          endif
+        endif
 
-  ! Estimate the neutral ocean boundary layer thickness as the minimum of the
-  ! reported ocean mixed layer thickness and the neutral Ekman depth.
-  !(Note that in Dan's code, f is spread over adjacent grid cells)
-  if ((bergs%grd%grid_is_latlon) .and. (.not. bergs%use_f_plane)) then
-     f_cori=(2.*omega)*sin(pi_180*lat)
-  else
-     f_cori=(2.*omega)*sin(pi_180*bergs%lat_ref)
-  endif
-  absf = abs(f_cori)  !Absolute value of the Coriolis parameter
-  if ((absf*Hml <= VK*ustar_h) .or. (absf.eq.0.))  then
-    hBL_neut = Hml
-  else
-    hBL_neut = (VK*ustar_h) / absf
-  endif
-  hBL_neut_h_molec = ZETA_N * ((hBL_neut * ustar_h) / (5.0 * Kv_molec))
-  ln_neut = 0.0 ; if (hBL_neut_h_molec > 1.0) ln_neut = log(hBL_neut_h_molec)
-
-  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-  if (Use_three_equation_model) then   ! Use 3 equation model
-    ! 3 equation model solves for the melt rates iteratively. This is not working right now, because we don't have access to the mixed layer
-    ! temperature and salinity gradients
+        if (bergs%use_mixed_melting) then
+          Me=((N_max-N_bonds)/N_max)*(Mv+Me)
+          Mv=0.0
+          Mb=(((N_max-N_bonds)/N_max)*(Mb)) + (N_bonds/N_max)*Ms
+        else  !Using Three equation model only.
+          Mv=0.0
+          Me=0.0
+          Mb=Ms
+        endif
+      endif
 
-    ! Guess sss as the iteration starting point for the boundary salinity.
-    Sbdry = salt ; Sb_max_set = .false. ; Sb_min_set = .false.
-    out_of_bounds=.false.
+      if (bergs%set_melt_rates_to_zero) then
+        Mv=0.0
+        Mb=0.0
+        Me=0.0
+      endif
 
-    ! Determine the mixed layer buoyancy flux, wB_flux.
-    dB_dS = (gravity / Rhoml) * dR0_dS
-    dB_dT = (gravity / Rhoml) * dR0_dT
+      if (bergs%use_operator_splitting) then
+        ! Operator split update of volume/mass
+        Tn=max(T-Mb*bergs%dt,0.) ! new total thickness (m)
+        nVol=Tn*W*L ! new volume (m^3)
+        Mnew1=(nVol/Vol)*M ! new mass (kg)
+        dMb=M-Mnew1 ! mass lost to basal melting (>0) (kg)
 
-    do it1 = 1,20
-      ! Determine the potential temperature at the ice-ocean interface.
-      call calculate_TFreeze(Sbdry, p_int, tfreeze)
+        Ln=max(L-Mv*bergs%dt,0.) ! new length (m)
+        Wn=max(W-Mv*bergs%dt,0.) ! new width (m)
+        nVol=Tn*Wn*Ln ! new volume (m^3)
+        Mnew2=(nVol/Vol)*M ! new mass (kg)
+        dMv=Mnew1-Mnew2 ! mass lost to buoyant convection (>0) (kg)
 
-      dT_ustar = (temp - tfreeze) * ustar_h
-      dS_ustar = (salt - Sbdry) * ustar_h
+        Ln=max(Ln-Me*bergs%dt,0.) ! new length (m)
+        Wn=max(Wn-Me*bergs%dt,0.) ! new width (m)
+        nVol=Tn*Wn*Ln ! new volume (m^3)
+        Mnew=(nVol/Vol)*M ! new mass (kg)
+        dMe=Mnew2-Mnew ! mass lost to erosion (>0) (kg)
+        dM=M-Mnew ! mass lost to all erosion and melting (>0) (kg)
+      else
+        ! Update dimensions of berg
+        Ln=max(L-(Mv+Me)*(bergs%dt),0.) ! (m)
+        Wn=max(W-(Mv+Me)*(bergs%dt),0.) ! (m)
+        Tn=max(T-Mb*(bergs%dt),0.) ! (m)
+        ! Update volume and mass of berg
+        nVol=Tn*Wn*Ln ! (m^3)
+        Mnew=(nVol/Vol)*M ! (kg)
+        dM=M-Mnew ! (kg)
+        dMb=(M/Vol)*(W*L)*Mb*bergs%dt ! approx. mass loss to basal melting (kg)
+        dMe=(M/Vol)*(T*(W+L))*Me*bergs%dt ! approx. mass lost to erosion (kg)
+        dMv=(M/Vol)*(T*(W+L))*Mv*bergs%dt ! approx. mass loss to buoyant convection (kg)
+      endif
 
-      ! First, determine the buoyancy flux assuming no effects of stability
-      ! on the turbulence.  Following H & J '99, this limit also applies
-      ! when the buoyancy flux is destabilizing.
+      ! Bergy bits
+      if (bergs%bergy_bit_erosion_fraction>0.) then
+        Mbits=this%mass_of_bits ! mass of bergy bits (kg)
+        dMbitsE=bergs%bergy_bit_erosion_fraction*dMe ! change in mass of bits (kg)
+        nMbits=Mbits+dMbitsE ! add new bergy bits to mass (kg)
+        Lbits=min(L,W,T,40.) ! assume bergy bits are smallest dimension or 40 meters
+        Abits=(Mbits/bergs%rho_bergs)/Lbits ! Effective bottom area (assuming T=Lbits)
+        Mbb=max( 0.58*(dvo**0.8)*(SST+2.0)/(Lbits**0.2), 0.) &! Basal turbulent melting (for bits)
+             *perday ! convert to m/s
+        Mbb=bergs%rho_bergs*Abits*Mbb ! in kg/s
+        dMbitsM=min(Mbb*bergs%dt,nMbits) ! bergy bits mass lost to melting (kg)
+        nMbits=nMbits-dMbitsM ! remove mass lost to bergy bits melt
+        if (Mnew==0.) then ! if parent berg has completely melted then
+          dMbitsM=dMbitsM+nMbits ! instantly melt all the bergy bits
+          nMbits=0.
+        endif
+      else
+        Abits=0.
+        dMbitsE=0.
+        dMbitsM=0.
+        nMbits=this%mass_of_bits ! retain previous value incase non-zero
+      endif
 
-      if (bergs%const_gamma) then ! if using a constant gamma_T
-        I_Gam_T = bergs%Gamma_T_3EQ
-        I_Gam_S = bergs%Gamma_T_3EQ/35.
+      ! Add melting to the grid and field diagnostics
+      if (grd%area(i,j).ne.0.) then
+        melt=(dM-(dMbitsE-dMbitsM))/bergs%dt ! kg/s
+        grd%floating_melt(i,j)=grd%floating_melt(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+        melt=melt*this%heat_density ! kg/s x J/kg = J/s
+        grd%calving_hflx(i,j)=grd%calving_hflx(i,j)+melt/grd%area(i,j)*this%mass_scaling ! W/m2
+        bergs%net_heat_to_ocean=bergs%net_heat_to_ocean+melt*this%mass_scaling*bergs%dt ! J
+        melt=dM/bergs%dt ! kg/s
+        grd%berg_melt(i,j)=grd%berg_melt(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+        melt=dMbitsE/bergs%dt ! mass flux into bergy bits in kg/s
+        grd%bergy_src(i,j)=grd%bergy_src(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+        melt=dMbitsM/bergs%dt ! melt rate of bergy bits in kg/s
+        grd%bergy_melt(i,j)=grd%bergy_melt(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+        if(grd%id_melt_buoy>0) then
+          melt=dMb/bergs%dt ! melt rate due to buoyancy term in kg/s
+          grd%melt_buoy(i,j)=grd%melt_buoy(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+        endif
+        if(grd%id_melt_eros>0) then
+          melt=dMe/bergs%dt ! erosion rate in kg/s
+          grd%melt_eros(i,j)=grd%melt_eros(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+        endif
+        if(grd%id_melt_conv>0) then
+          melt=dMv/bergs%dt ! melt rate due to convection term in kg/s
+          grd%melt_conv(i,j)=grd%melt_conv(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+        endif
       else
-        Gam_turb = I_VK * (ln_neut + (0.5 * I_ZETA_N - 1.0))
-        I_Gam_T = 1.0 / (Gam_mol_t + Gam_turb)
-        I_Gam_S = 1.0 / (Gam_mol_s + Gam_turb)
+        stderrunit = stderr()
+        write(stderrunit,*) 'KID, thermodynamics: berg appears to have grounded!!!! PE=',mpp_pe(),i,j
+        call print_berg(stderrunit,this,'thermodynamics, grounded')
+        if (associated(this%trajectory)) &
+          write(stderrunit,*) 'traj=',this%trajectory%lon,this%trajectory%lat
+        write(stderrunit,*) 'msk=',grd%msk(i,j),grd%area(i,j)
+        call error_mesg('KID, thermodynamics', 'berg appears to have grounded!', FATAL)
       endif
-      wT_flux = dT_ustar * I_Gam_T
-      wB_flux = dB_dS * (dS_ustar * I_Gam_S) + dB_dT * wT_flux
 
-      if (wB_flux > 0.0) then
-        ! The buoyancy flux is stabilizing and will reduce the tubulent
-        ! fluxes, and iteration is required.
-        n_star_term = (ZETA_N/RC) * (hBL_neut * VK) / ustar_h**3
-        do it3 = 1,30
-          ! n_star <= 1.0 is the ratio of working boundary layer thickness
-          ! to the neutral thickness.
-          ! hBL = n_star*hBL_neut ; hSub = 1/8*n_star*hBL
-          I_n_star = sqrt(1.0 + n_star_term * wB_flux)
-          dIns_dwB = 0.5 * n_star_term / I_n_star
-          if (hBL_neut_h_molec > I_n_star**2) then
-            Gam_turb = I_VK * ((ln_neut - 2.0*log(I_n_star)) + &
-                       (0.5*I_ZETA_N*I_n_star - 1.0))
-            dG_dwB =  I_VK * ( -2.0 / I_n_star + (0.5 * I_ZETA_N)) * dIns_dwB
+      ! Rolling
+      !There are now 3 iceberg rolling schemes:
+      !1) Rolling based on aspect ratio threshold (iceberg of constant density)
+      !2) Rolling based on corrected Weeks and Mellor scheme
+      !3) Rolling based on incorrect Weeks and Mellor scheme - kept for legacy reasons
+      if (bergs%allow_bergs_to_roll .and. N_bonds.eq.0.) then !only allow non-bonded,non-static bergs to roll
+        Dn=(bergs%rho_bergs/rho_seawater)*Tn ! draught (keel depth)
+        if ( Dn>0. ) then
+          if ( (.not.bergs%use_updated_rolling_scheme) .and. (bergs%tip_parameter<999.) ) then    !Use Rolling Scheme 3
+              if ( max(Wn,Ln)<sqrt(0.92*(Dn**2)+58.32*Dn) ) then
+                call swap_variables(Tn,Wn)
+              endif
           else
-            !   The layer dominated by molecular viscosity is smaller than
-            ! the assumed boundary layer.  This should be rare!
-            Gam_turb = I_VK * (0.5 * I_ZETA_N*I_n_star - 1.0)
-            dG_dwB = I_VK * (0.5 * I_ZETA_N) * dIns_dwB
-          endif
+            if (Wn>Ln) call swap_variables(Ln,Wn)  !Make sure that Wn is the smaller dimension
 
-          if (bergs%const_gamma) then ! if using a constant gamma_T
-            I_Gam_T = bergs%Gamma_T_3EQ
-            I_Gam_S = bergs%Gamma_T_3EQ/35.
-          else
-            I_Gam_T = 1.0 / (Gam_mol_t + Gam_turb)
-            I_Gam_S = 1.0 / (Gam_mol_s + Gam_turb)
-          endif
+            if ( (.not.bergs%use_updated_rolling_scheme) .and. (bergs%tip_parameter>=999.) ) then    !Use Rolling Scheme 2
+              q=bergs%rho_bergs/rho_seawater
+              Delta=6.0
+              if (Wn<sqrt((6.0*q*(1-q)*(Tn**2))-(12*Delta*q*Tn))) then
+                  call swap_variables(Tn,Wn)
+              endif
+            endif
 
-          wT_flux = dT_ustar * I_Gam_T
-          wB_flux_new = dB_dS * (dS_ustar * I_Gam_S) + dB_dT * wT_flux
+            if (bergs%use_updated_rolling_scheme) then    !Use Rolling Scheme 1
+              if (bergs%tip_parameter>0.) then
+                tip_parameter=bergs%tip_parameter
+              else
+                ! Equation 27 from Burton et al 2012, or equivolently, Weeks and Mellor 1979 with constant density
+                tip_parameter=sqrt(6*(bergs%rho_bergs/rho_seawater)*(1-(bergs%rho_bergs/rho_seawater)))   !using default values gives 0.92
+              endif
+              if ((tip_parameter*Tn)>Wn)  then     !note that we use the Thickness instead of the Draft
+                  call swap_variables(Tn,Wn)
+              endif
+            endif
+          endif
+          Dn=(bergs%rho_bergs/rho_seawater)*Tn ! re-calculate draught (keel depth) for grounding
+        endif
+      endif
 
-          ! Find the root where dwB = 0.0
-          DwB = wB_flux_new - wB_flux
-          if (abs(wB_flux_new - wB_flux) < &
-            1e-4*(abs(wB_flux_new) + abs(wB_flux))) exit
+      !This option allows iceberg melt fluxes to enter the ocean without the icebergs changing shape
+      if (bergs%Iceberg_melt_without_decay) then
+        !In this case, the iceberg dimension are reset to their values before
+        !the thermodynamics are applied.
+        !If the spread_mass is being used to calculate melt, we calculate this
+        !before reseting
+        if (bergs%find_melt_using_spread_mass) then
+          if (Mnew>0.) then !If the berg still exists
+            call spread_mass_across_ocean_cells(bergs,this, i, j, this%xi, this%yj,Mnew , nMbits, this%mass_scaling, Ln*Wn,  Tn)
+          endif
+        endif
+        !Reset all the values
+        Mnew=this%mass
+        nMbits=this%mass_of_bits
+        Tn=this%thickness
+        Wn=this%width
+        Ln=this%length
+        if (bergs%bergy_bit_erosion_fraction>0.) then
+          Mbits=this%mass_of_bits ! mass of bergy bits (kg)
+          Lbits=min(L,W,T,40.) ! assume bergy bits are smallest dimension or 40 meters
+          Abits=(Mbits/bergs%rho_bergs)/Lbits ! Effective bottom area (assuming T=Lbits)
+        endif
+      else
+        ! Store the new state of iceberg (with L>W)
+        this%mass=Mnew
+        this%mass_of_bits=nMbits
+        this%thickness=Tn
+        this%width=min(Wn,Ln)
+        this%length=max(Wn,Ln)
+      endif
+      next=>this%next
 
-          dDwB_dwB_in = -dG_dwB * (dB_dS * (dS_ustar * I_Gam_S**2) + &
-                                         dB_dT * (dT_ustar * I_Gam_T**2)) - 1.0
-          ! This is Newton's method without any bounds. ( ### SHOULD BOUNDS BE NEEDED?)
-          wB_flux_new = wB_flux - DwB / dDwB_dwB_in
-        enddo !it3
+      ! Did berg completely melt?
+      if (Mnew<=0.) then ! Delete the berg
+        if (.not. bergs%debug_write) call move_trajectory(bergs, this)
+        call delete_iceberg_from_list(bergs%list(grdi,grdj)%first, this)
+        bergs%nbergs_melted=bergs%nbergs_melted+1
       endif
+      this=>next
+    enddo
+  enddo ; enddo
 
-      t_flux  = RhoCp * wT_flux
-      exch_vel_t = ustar_h * I_Gam_T
-      exch_vel_s = ustar_h * I_Gam_S
+  contains
 
-      if (t_flux <= 0.0) then  ! Freezing occurs, so zero ice heat flux.
-        lprec = I_LF * t_flux
-        tflux_shelf = 0.0
-      else
-      !no conduction/perfect insulator
-      tflux_shelf = 0.0
-      lprec = I_LF * t_flux
-      ! With melting, from H&J 1999, eqs (31) & (26)...
-      !   Q_ice ~= cp_ice * (Temp_Ice-T_freeze) * lprec
-      !   RhoLF*lprec = Q_ice + t_flux
-      !   lprec = (t_flux) / (LF + cp_ice * (T_freeze-Temp_Ice))
-      !   lprec = t_flux /  (LF + Cp_ice * (tfreeze - Temp_Ice))
-      !   tflux_shelf = t_flux - LF*lprec
-      !other options: dTi/dz linear through shelf
-      !            dTi_dz = (Temp_Ice - tfreeze)/draft
-      !            tflux_shelf = - Rho_Ice * Cp_ice * KTI * dTi_dz
-      endif
+  subroutine swap_variables(x,y)
+    ! Arguments
+    real, intent(inout) :: x, y
+    real :: temp
+    temp=x
+    x=y
+    y=temp
+  end subroutine swap_variables
 
-      mass_exch = exch_vel_s * Rho0
-      Sbdry_it = (salt * mass_exch + Salin_Ice * lprec) / (mass_exch + lprec)
-      dS_it = Sbdry_it - Sbdry
-      if (abs(dS_it) < 1e-4*(0.5*(salt + Sbdry + 1.e-10))) exit
+end subroutine thermodynamics
 
-      if (dS_it < 0.0) then ! Sbdry is now the upper bound.
-        if (Sb_max_set .and. (Sbdry > Sb_max)) then
-          if (debug) then
-            call error_mesg('KID,Find basal melt', 'shelf_calc_flux: Irregular iteration for Sbdry (max).' ,WARNING)
-            print *, 'Sbdry error: id,dvo,temp,salt,lat,thickness :',id,dvo,temp,salt,lat,thickness
-          endif
-          out_of_bounds=.true.
-          exit
-        endif
-        Sb_max = Sbdry ; dS_max = dS_it ; Sb_max_set = .true.
-      else ! Sbdry is now the lower bound.
-        if (Sb_min_set .and. (Sbdry < Sb_min)) then
-          if (debug) then
-            call error_mesg('KID,Find basal melt', 'shelf_calc_flux: Irregular iteration for Sbdry (min).' ,WARNING)
-            print *, 'Sbdry error: id,dvo,temp,salt,lat,thickness :',id,dvo,temp,salt,lat,thickness
-          endif
-          out_of_bounds=.true.
-          exit
-        endif
-        Sb_min = Sbdry ; dS_min = dS_it ; Sb_min_set = .true.
-      endif
-      if (Sb_min_set .and. Sb_max_set) then
-        ! Use the false position method for the next iteration.
-        Sbdry = Sb_min + (Sb_max-Sb_min) * (dS_min / (dS_min - dS_max))
-      else
-        Sbdry = Sbdry_it
-      endif
-      Sbdry = Sbdry_it
-    enddo !it1
-  endif
+subroutine create_gridded_icebergs_fields(bergs)
+! Arguments
+type(icebergs), pointer :: bergs !< Container for all types and memory
+! Local variables
+type(icebergs_gridded), pointer :: grd
+type(iceberg), pointer :: this
+integer i,j
+integer :: grdi, grdj
+real :: Hocean, Dn,Tn,dvo, mass_tmp
+real :: ustar_h, ustar
+real :: orientation
+real :: ave_thickness, ave_draft
+real, dimension(bergs%grd%isd:bergs%grd%ied,bergs%grd%jsd:bergs%grd%jed)  :: spread_mass_tmp
+real :: tmp
 
-  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-  if ((.not. Use_three_equation_model) .or. (out_of_bounds)) then
-    ! In the 2-equation form, the mixed layer turbulent exchange velocity
-    ! is specified and large enough that the ocean salinity at the interface
-    ! is about the same as the boundary layer salinity.
-    ! Alon: I have adapted the code so that the turbulent exchange velocoty is not constant, but rather proportional to the frictional velocity.
-    ! This should give you the same answers as the 3 equation model when salinity gradients in the mixed layer are zero (I think/hope)
-    ! Use 2-equation model when 3 equation version fails.
+  ! For convenience
+  grd=>bergs%grd
 
-    call calculate_TFreeze(salt, p_int, tfreeze)
+  spread_mass_tmp(:,:)=0. !Initializing temporary variable to use in iceberg melt calculation
 
-    Gam_turb = I_VK * (ln_neut + (0.5 * I_ZETA_N - 1.0))
-    I_Gam_T = 1.0 / (Gam_mol_t + Gam_turb)
+  !Special case for icebergs not decaying, but mass diffence being used for melt rates
+  if ((bergs%find_melt_using_spread_mass) .and.  (bergs%Iceberg_melt_without_decay)) then
+    call sum_up_spread_fields(bergs, spread_mass_tmp(grd%isc:grd%iec,grd%jsc:grd%jec),'mass')
+  endif
 
-    exch_vel_t= ustar_h * I_Gam_T
-    if (gamma_t>0.0) exch_vel_t = gamma_t  !Option to set the exchange to a constant, independent of the frictional velocity (as was previously coded)
-    wT_flux = exch_vel_t *(temp - tfreeze)
+  !Loop through icebergs and spread mass on ocean
+  call calculate_mass_on_ocean(bergs, with_diagnostics=.true.)
 
-    t_flux  = RhoCp * wT_flux
-    tflux_shelf = 0.0
-    lprec = I_LF * t_flux
+  !Finding the spread fields
+  if ((grd%id_spread_uvel>0)  .or. (bergs%pass_fields_to_ocean_model)) then
+    grd%spread_uvel(:,:)=0.
+    call sum_up_spread_fields(bergs, grd%spread_uvel(grd%isc:grd%iec,grd%jsc:grd%jec), 'Uvel')
   endif
-    !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-  ! melt in m/s (melts of ice melted per second)
-  basal_melt = lprec /density_ice
+  if ( (grd%id_spread_vvel>0)  .or. (bergs%pass_fields_to_ocean_model)) then
+    grd%spread_vvel(:,:)=0.
+    call sum_up_spread_fields(bergs, grd%spread_vvel(grd%isc:grd%iec,grd%jsc:grd%jec), 'Vvel')
+  endif
+  if ( (grd%id_spread_area>0)  .or. (bergs%pass_fields_to_ocean_model)) then
+    grd%spread_area(:,:)=0.
+    call sum_up_spread_fields(bergs, grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec), 'area')
+  endif
+  !Always find spread_mass since it is used for so many things.
+  grd%spread_mass(:,:)=0.
+    call sum_up_spread_fields(bergs, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec),'mass')
 
-end subroutine find_basal_melt
+  !Using spread_mass_to_ocean to calculate melt rates (if this option is chosen)
+  if (bergs%find_melt_using_spread_mass) then
+    if (.not. bergs%Iceberg_melt_without_decay) &
+         spread_mass_tmp(grd%isc:grd%iec,grd%jsc:grd%jec)= grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec)
+    do i=grd%isd,grd%ied ; do j=grd%jsd,grd%jed
+      if (grd%area(i,j)>0.0) then
+        grd%floating_melt(i,j)=max((grd%spread_mass_old(i,j) - spread_mass_tmp(i,j))/(bergs%dt),0.0)
+      else
+        grd%floating_melt(i,j)=0.0
+      endif
+    enddo ;enddo
+    grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)=grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec)*HLF !Not 100% sure this is correct.
+  endif
 
-!> Calculates freezing point potential temperature of seawater using a linear relation
-!!
-!! This subroutine computes the freezing point potential temperature
-!! (in deg C) from salinity (in psu), and pressure (in Pa) using a simple
-!! linear expression, with coefficients passed in as arguments.
-!!
-!! Copied from subroutine calculate_TFreeze_linear_scalar (in MOM/equation_of_state)
-subroutine calculate_TFreeze(S, pres, T_Fr)
-  ! Arguments
-  real, intent(in) :: S !< Salinity (1e-3)
-  real, intent(in) :: pres !< Presure (Pa)
-  real, intent(out) :: T_Fr !< Freezing point (C)
-  ! Local variables
-  real, parameter :: dTFr_dp    = -7.53E-08    !DTFREEZE_DP in MOM_input
-  real, parameter :: dTFr_dS    = -0.0573      !DTFREEZE_DS in MOM_input
-  real, parameter :: TFr_S0_P0  =0.0832        !TFREEZE_S0_P0 in MOM_input
-  ! TFr_S0_P0 - The freezing point at S=0, p=0, in deg C.
-  ! dTFr_dS - The derivatives of freezing point with salinity, in deg C PSU-1.
-  ! dTFr_dp - The derivatives of freezing point with pressure, in deg C Pa-1.
-  T_Fr = (TFr_S0_P0 + dTFr_dS*S) + dTFr_dp*pres
-end subroutine calculate_TFreeze
+  ! Dividing the gridded iceberg momentum diagnostic by the iceberg mass to get velocities
+  if ((grd%id_u_iceberg>0) .or. (grd%id_v_iceberg>0)) then
+    do j = grd%jsc,grd%jec ; do i = grd%isc,grd%iec
+      if (grd%mass(i,j)>0.) then
+        if (grd%id_u_iceberg>0) &
+          grd%u_iceberg(i,j)=grd%u_iceberg(i,j)/grd%mass(i,j)
+        if (grd%id_v_iceberg>0) &
+          grd%v_iceberg(i,j)=grd%v_iceberg(i,j)/grd%mass(i,j)
+      else
+        if (grd%id_u_iceberg>0)  grd%u_iceberg(i,j)=0.
+        if (grd%id_v_iceberg>0)  grd%v_iceberg(i,j)=0.
+      endif
+    enddo; enddo
+  endif
 
-!> Calculates density of seawater using a linear equation of state
-!!
-!! This subroutine computes the density of sea water with a trivial
-!! linear equation of state (in kg/m^3) from salinity (sal in psu),
-!! potential temperature (T in deg C), and pressure in Pa.
-!!
-!! Copied from subroutine calculate_density_scalar_linear (in MOM/equation_of_state)
-subroutine calculate_density(T, S, pressure, rho, Rho_T0_S0, dRho_dT, dRho_dS)
-  !Arguments
-  real, intent(in)  :: T !< Potential temperature (C)
-  real, intent(in)  :: S !< Salinity (1e-3)
-  real, intent(in)  :: pressure !< Pressure (Pa)
-  real, intent(out) :: rho !< In situ density (kg/3)
-  real, intent(in)  :: Rho_T0_S0 !< Density at T=0, S=0 (kg/m3)
-  real, intent(in)  :: dRho_dT !< Derivative of density w.r.t. potential temperature (kg/m3/C)
-  real, intent(in)  :: dRho_dS !< Derivative of density w.r.t. salinity (1e3 kg/m3)
-  rho = Rho_T0_S0 + dRho_dT*T + dRho_dS*S
-end subroutine calculate_density
+  !Calculating ustar_iceberg (gridded)
+  grd%ustar_iceberg(:,:)=0.
+  if  ((grd%id_ustar_iceberg>0) .or. (bergs%pass_fields_to_ocean_model)) then   !Update diagnostic of iceberg mass spread on ocean
+    do j = grd%jsc,grd%jec ; do i = grd%isc,grd%iec
+      dvo=sqrt((grd%spread_uvel(i,j)-grd%uo(i,j))**2+(grd%spread_vvel(i,j)-grd%vo(i,j))**2)
+      ustar = sqrt(bergs%cdrag_icebergs*(dvo**2  + bergs%utide_icebergs**2))
+      ustar_h = max(bergs%ustar_icebergs_bg, ustar)
+      if (grd%spread_area(i,j) ==0.0) ustar_h=0.
+        grd%ustar_iceberg(i,j)=ustar_h
+    enddo; enddo
+  endif
 
-!> Returns orientation of a berg determined by its bonds
-subroutine find_orientation_using_iceberg_bonds(grd, berg, orientation)
+  !Only allowing melt in ocean above a minimum cutoff thickness
+  if (bergs%apply_thickness_cutoff_to_gridded_melt) then
+    do i=grd%isd,grd%ied ; do j=grd%jsd,grd%jed
+      if ((bergs%melt_cutoff >=0.) .and. (grd%spread_area(i,j)>0.)) then
+        ave_thickness=grd%spread_mass(i,j)/(grd%spread_area(i,j)*bergs%rho_bergs)
+        ave_draft=ave_thickness*(bergs%rho_bergs/rho_seawater)
+        if ((grd%ocean_depth(i,j)-ave_draft) < bergs%melt_cutoff) then
+          grd%floating_melt(i,j)=0.0
+          grd%calving_hflx(i,j)=0.0
+        endif
+      endif
+    enddo ;enddo
+  endif
+end subroutine create_gridded_icebergs_fields
+
+!> Calculates basal melt for given thermodynamic properties
+subroutine find_basal_melt(bergs, dvo, lat, salt, temp, Use_three_equation_model, thickness, basal_melt, id)
   ! Arguments
-  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
-  type(iceberg), pointer :: berg !< Berg for which orientation is needed
-  real, intent(inout) :: orientation !< Angle of orientation (radians)
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  real, intent(in) :: dvo !< Speed of iceberg relative to ocean mixed layer
+  real, intent(in) :: lat !< Latitude (for boundary layer calculation)
+  real, intent(in) :: salt !< Salinity of mixed layer
+  real, intent(in) :: temp !< Temperature of mixed layer
+  logical, intent(in) :: Use_three_equation_model !< True uses the 3 equation model, False uses the 2 equation model.
+  real, intent(in) :: thickness !< Ice thickness - needed to work out the pressure below the ice
+  real, intent(out) :: basal_melt !< Melt rate underneath the icebergs
+  integer(kind=8), intent(in) :: id !< Iceberg id, used for debugging (error messages)
   ! Local variables
-  type(iceberg), pointer :: other_berg
-  type(bond), pointer :: current_bond
-  real :: angle, lat1,lat2,lon1,lon2,dlat,dlon
-  real :: r_dist_x, r_dist_y
-  real :: lat_ref, dx_dlon, dy_dlat
-  real :: theta, bond_count, Average_angle
+  real :: ustar, f_cori, absf,tfreeze
+  real :: Hml !Mixed layer depth
 
-  bond_count=0.
-  Average_angle=0.
-  !Don't check orientation of the edges of halo,  since they can contain unassosiated bonds  (this is why halo width must be larger >= 2 to use bonds)
-  if  (  ((berg%ine .gt.  grd%isd) .and. (berg%ine .lt. grd%ied)) .and. ((berg%jne .ge.  grd%jsd) .and. (berg%jne .le. grd%jed) ) ) then
-    current_bond=>berg%first_bond
-    lat1=berg%lat
-    lon1=berg%lon
-    do while (associated(current_bond)) ! loop over all bonds
-      other_berg=>current_bond%other_berg
-      if (.not. associated(other_berg)) then !good place for debugging
-        !One valid option: current iceberg is on the edge of halo, with other berg on the next pe (not influencing mass spreading)
-        !print *, 'Iceberg bond details:',berg%id, current_bond%other_id,berg%halo_berg, mpp_pe()
-        !print *, 'Iceberg bond details2:',berg%ine, berg%jne, current_bond%other_berg_ine, current_bond%other_berg_jne
-        !print *, 'Iceberg isd,ied,jsd,jed:',grd%isd, grd%ied, grd%jsd, grd%jed
-        !print *, 'Iceberg isc,iec,jsc,jec:',grd%isc, grd%iec, grd%jsc, grd%jec
-        !call error_mesg('KID,calculating orientation', 'Looking at bond interactions of unassosiated berg!' ,FATAL)
-        !endif
-      else
-        lat2=other_berg%lat
-        lon2=other_berg%lon
+  !These could also be useful output variables if needed.
+  real :: t_flux, exch_vel_t, exch_vel_s,tflux_shelf,lprec
 
-        dlat=lat2-lat1
-        dlon=lon2-lon1
-
-        lat_ref=0.5*(lat1+lat2)
-        call convert_from_grid_to_meters(lat_ref,grd%grid_is_latlon,dx_dlon,dy_dlat)
-        r_dist_x=dlon*dx_dlon
-        r_dist_y=dlat*dy_dlat
+  real ::  Rhoml   ! Ocean mixed layer density in kg m-3.
+  real ::  p_int   ! The pressure at the ice-ocean interface, in Pa.
 
-        if (r_dist_x .eq. 0.) then
-          angle=pi/2.
-        else
-          angle=atan(r_dist_y/r_dist_x)
-          angle= ((pi/2.)  - (orientation*(pi/180.)))  - angle
-          !print *, 'angle: ', angle*(180/pi), initial_orientation
-          angle=modulo(angle ,pi/3.)
-        endif
-        bond_count=bond_count+1.
-        Average_angle=Average_angle+angle
-      endif
-      current_bond=>current_bond%next_bond
-    enddo  !End loop over bonds
-    if (bond_count.gt.0) then
-      Average_angle =Average_angle/bond_count
-    else
-      Average_angle =0.
-    endif
-    orientation=modulo(Average_angle ,pi/3.)
-  endif
+  real, parameter :: VK    = 0.40     ! Von Karman's constant - dimensionless
+  real :: ZETA_N = 0.052   ! The fraction of the boundary layer over which the
+                           ! viscosity is linearly increasing. (Was 1/8. Why?)
+  real, parameter :: RC    = 0.20     ! critical flux Richardson number.
+  real :: I_ZETA_N  ! The inverse of ZETA_N.
+  real :: I_LF  ! Inverse of Latent Heat of fusion (J kg-1)
+  real :: I_VK      ! The inverse of VK.
+  real :: PR, SC    ! The Prandtl number and Schmidt number, nondim.
 
-end subroutine find_orientation_using_iceberg_bonds
+  ! 3 equation formulation variables
+  real :: Sbdry     !   Salinities in the ocean at the interface with the
+  real :: Sbdry_it  ! the ice shelf, in PSU.
+  real :: dS_it     ! The interface salinity change during an iteration, in PSU.
+  real :: hBL_neut  ! The neutral boundary layer thickness, in m.
+  real :: hBL_neut_h_molec ! The ratio of the neutral boundary layer thickness
+                           ! to the molecular boundary layer thickness, ND.
+  real :: wT_flux ! The vertical fluxes of heat and buoyancy just inside the
+  real :: wB_flux ! ocean, in C m s-1 and m2 s-3, ###CURRENTLY POSITIVE UPWARD.
+  real :: dB_dS  ! The derivative of buoyancy with salinity, in m s-2 PSU-1.
+  real :: dB_dT  ! The derivative of buoyancy with temperature, in m s-2 C-1.
+  real :: I_n_star, n_star_term
+  real :: dIns_dwB  ! The partial derivative of I_n_star with wB_flux, in ???.
+  real :: dT_ustar, dS_ustar
+  real :: ustar_h
+  real :: Gam_turb
+  real :: Gam_mol_t, Gam_mol_s
+  real :: RhoCp
+  real :: I_RhoLF
+  real :: Rho0
+  real :: ln_neut
+  real :: mass_exch
+  real :: Sb_min, Sb_max
+  real :: dS_min, dS_max
+  real :: density_ice
 
-!> Spread mass of a berg around cells centered on i,j
-subroutine spread_mass_across_ocean_cells(bergs, berg, i, j, x, y, Mberg, Mbits, scaling, Area, Tn)
-  ! Arguments
-  type(icebergs), pointer :: bergs !< Container for all types and memory
-  type(iceberg), pointer :: berg !< Berg whose mass is being considered
-  integer, intent(in) :: i !< i-index of cell contained center of berg
-  integer, intent(in) :: j !< j-index of cell contained center of berg
-  real, intent(in) :: x !< Longitude of berg (degree E)
-  real, intent(in) :: y !< Latitude of berg (degree N)
-  real, intent(in) :: Mberg !< Mass of berg (kg)
-  real, intent(in) :: Mbits !< Mass of bergy bits (kg)
-  real, intent(in) :: scaling !< Multiplier to scale mass (nondim)
-  real, intent(in) :: Area !< Area of berg (m2)
-  real, intent(in) :: Tn !< Thickness of berg (m)
-  ! Local variables
-  type(icebergs_gridded), pointer :: grd
-  real :: xL, xC, xR, yD, yC, yU, Mass, L
-  real :: yDxL, yDxC, yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR
-  real :: S, H, origin_x, origin_y, x0, y0
-  real :: Area_Q1,Area_Q2 , Area_Q3,Area_Q4, Area_hex
-  real :: fraction_used !fraction of iceberg mass included (part of the mass near the boundary is discarded sometimes)
-  real :: I_fraction_used !Inverse of fraction used
-  real :: tol
-  real :: Dn, Hocean
-  real, parameter :: rho_seawater=1035.
-  integer :: stderrunit
-  logical :: debug
-  real :: orientation, Mass_berg
+  ! Variables used in iterating for wB_flux.
+  real :: wB_flux_new, DwB, dDwB_dwB_in
+  real :: I_Gam_T, I_Gam_S
+  real :: dG_dwB, iDens
+  logical :: Sb_min_set, Sb_max_set
+  logical :: out_of_bounds
 
-  ! Get the stderr unit number
-  stderrunit = stderr()
+  real, parameter :: c2_3 = 2.0/3.0
+  integer ::  it1, it3
 
-  tol=1.e-10
-  grd=>bergs%grd
-  Mass_berg=Mberg
+  !Parameters copied ice shelf module defaults (could be entered in the namelist later)
+  real, parameter :: dR0_dT = -0.038357 ! Partial derivative of the mixed layer density with temperature, in units of kg m-3 K-1.
+  real, parameter :: dR0_dS = 0.805876 ! Partial derivative of the mixed layer density with salinity, in units of kg m-3 psu-1.
+  real, parameter :: RHO_T0_S0 = 999.910681 ! Density of water with T=0, S=0 for linear EOS
+  real, parameter :: Salin_Ice =0.0 !Salinity of ice
+  real, parameter :: Temp_Ice = -15.0 !Salinity of ice
+  real, parameter :: kd_molec_salt=  8.02e-10 !The molecular diffusivity of salt in sea water at the freezing point
+  real, parameter :: kd_molec_temp=  1.41e-7 !The molecular diffusivity of heat in sea water at the freezing point
+  real, parameter :: kv_molec=  1.95e-6 !The molecular molecular kinematic viscosity of sea water at the freezing point
+  real, parameter :: Cp_Ice =  2009.0 !Specific heat capacity of ice, taking from HJ99 (Holland and Jenkins 1999)
+  real, parameter :: Cp_ml =  3974.0 !Specific heat capacity of mixed layer, taking from HJ99 (Holland and Jenkins 1999)
+  real, parameter :: LF =  3.335e5 !Latent heat of fusion, taken from HJ99 (Holland and Jenkins 1999)
+  real, parameter :: gamma_t =  0.0 ! Exchange velocity used in 2 equation model. Whn gamma_t is >0, the exchange velocity is independent of u_star.
+                                  ! When gamma_t=0.0, then gamma_t is not used, and the exchange velocity is found using u_star.
+  real, parameter :: p_atm =  101325 ! Average atmospheric pressure (Pa) - from Google.
 
-  ! Trimming icebergs to account for grounded fraction.
-  if (bergs%grounding_fraction>0.) then
-    Hocean=bergs%grounding_fraction*(grd%ocean_depth(i,j)+grd%ssh(i,j))
-    Dn=(bergs%rho_bergs/rho_seawater)*Tn ! re-calculate draught (keel depth)
-    if (Dn>Hocean) Mass_berg=Mberg*min(1.,Hocean/Dn)
-  endif
+  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+  density_ice = bergs%rho_bergs
+  Rho0=rho_seawater  !Note that the ice shelf code has a default of Rho0=1035
+  Hml =10.      !Mixed layer depth. This is an approximate value. It looks like the code is not sensitive to it (since it enters in log(Hml)
+  p_int= p_atm+(gravity*thickness*density_ice)    ! The pressure at the ice-ocean interface, in Pa.
 
-  Mass=(Mass_berg+Mbits)*scaling
-  ! This line attempts to "clip" the weight felt by the ocean. The concept of
-  ! clipping is non-physical and this step should be replaced by grounding.
-  if (grd%clipping_depth>0.) Mass=min(Mass,grd%clipping_depth*grd%area(i,j)*rho_seawater)
+  ! Find the ocean mixed layer density in kg m-3.
+  call calculate_density(temp, salt, p_int, Rhoml, Rho_T0_S0, dR0_dT, dR0_dS)
 
-  !Initialize weights for each cell
-  yDxL=0.  ; yDxC=0. ; yDxR=0. ; yCxL=0. ; yCxR=0.
-  yUxL=0.  ; yUxC=0. ; yUxR=0. ; yCxC=1.
+  ! This routine finds the melt at the base of the icebergs using the 2 equation
+  ! model or 3 equation model. This code is adapted from the ice shelf code. Once
+  ! the iceberg model is inside the ocean model, we should use the same code.
 
-  if (.not. bergs%hexagonal_icebergs) then ! Treat icebergs as rectangles of size L: (this is the default)
+  I_ZETA_N = 1.0 / ZETA_N
+  I_RhoLF = 1.0/(Rho0*LF)
+  I_LF = 1.0 / LF
+  SC = kv_molec/kd_molec_salt
+  PR = kv_molec/kd_molec_temp
+  I_VK = 1.0/VK
+  RhoCp = Rho0 * Cp_ml
 
-    ! L is the non dimensional length of the iceberg [ L=(Area of berg/ Area of grid cell)^0.5 ] or something like that.
-    if (grd%area(i,j)>0) then
-      L=min( sqrt(Area / grd%area(i,j)),1.0)
-    else
-      L=1.
-    endif
+  !first calculate molecular component
+  Gam_mol_t = 12.5 * (PR**c2_3) - 6
+  Gam_mol_s = 12.5 * (SC**c2_3) - 6
 
-    if (bergs%use_old_spreading) then
-      ! Old version before icebergs were given size L
-      xL=min(0.5, max(0., 0.5-x))
-      xR=min(0.5, max(0., x-0.5))
-      xC=max(0., 1.-(xL+xR))
-      yD=min(0.5, max(0., 0.5-y))
-      yU=min(0.5, max(0., y-0.5))
-      yC=max(0., 1.-(yD+yU))
-    else
-      xL=min(0.5, max(0., 0.5-(x/L)))
-      xR=min(0.5, max(0., (x/L)+(0.5-(1/L) )))
-      xC=max(0., 1.-(xL+xR))
-      yD=min(0.5, max(0., 0.5-(y/L)))
-      yU=min(0.5, max(0., (y/L)+(0.5-(1/L) )))
-      yC=max(0., 1.-(yD+yU))
-    endif
+  iDens = 1.0/Rho0
 
-    yDxL=yD*xL*grd%msk(i-1,j-1)
-    yDxC=yD*xC*grd%msk(i  ,j-1)
-    yDxR=yD*xR*grd%msk(i+1,j-1)
-    yCxL=yC*xL*grd%msk(i-1,j  )
-    yCxR=yC*xR*grd%msk(i+1,j  )
-    yUxL=yU*xL*grd%msk(i-1,j+1)
-    yUxC=yU*xC*grd%msk(i  ,j+1)
-    yUxR=yU*xR*grd%msk(i+1,j+1)
-    yCxC=1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )
+  !Preparing the mixed layer properties for use in both 2 and 3 equation version
+  ustar = sqrt(bergs%cdrag_icebergs*(dvo**2  + bergs%utide_icebergs**2))
+  ustar_h = max(bergs%ustar_icebergs_bg, ustar)
 
-    fraction_used=1. ! rectangular bergs do share mass with boundaries (all mass is included in cells)
+  ! Estimate the neutral ocean boundary layer thickness as the minimum of the
+  ! reported ocean mixed layer thickness and the neutral Ekman depth.
+  !(Note that in Dan's code, f is spread over adjacent grid cells)
+  if ((bergs%grd%grid_is_latlon) .and. (.not. bergs%use_f_plane)) then
+     f_cori=(2.*omega)*sin(pi_180*lat)
+  else
+     f_cori=(2.*omega)*sin(pi_180*bergs%lat_ref)
+  endif
+  absf = abs(f_cori)  !Absolute value of the Coriolis parameter
+  if ((absf*Hml <= VK*ustar_h) .or. (absf.eq.0.))  then
+    hBL_neut = Hml
+  else
+    hBL_neut = (VK*ustar_h) / absf
+  endif
+  hBL_neut_h_molec = ZETA_N * ((hBL_neut * ustar_h) / (5.0 * Kv_molec))
+  ln_neut = 0.0 ; if (hBL_neut_h_molec > 1.0) ln_neut = log(hBL_neut_h_molec)
 
-  else ! Spread mass as if elements area hexagonal
+  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+  if (Use_three_equation_model) then   ! Use 3 equation model
+    ! 3 equation model solves for the melt rates iteratively. This is not working right now, because we don't have access to the mixed layer
+    ! temperature and salinity gradients
 
-    orientation=bergs%initial_orientation
-    if ((bergs%iceberg_bonds_on) .and. (bergs%rotate_icebergs_for_mass_spreading)) call find_orientation_using_iceberg_bonds(grd,berg,orientation)
+    ! Guess sss as the iteration starting point for the boundary salinity.
+    Sbdry = salt ; Sb_max_set = .false. ; Sb_min_set = .false.
+    out_of_bounds=.false.
 
-    if (grd%area(i,j)>0) then
-      H=min(( (sqrt(Area/(2.*sqrt(3.))) / sqrt(grd%area(i,j)))),1.) ! Non-dimensionalize element length by grid area. (This gives the non-dim Apothem of the hexagon)
-    else
-      H=(sqrt(3.)/2)*(0.49) ! Largest allowable H, since this makes S=0.49, and S has to be less than 0.5 (Not sure what the implications of this are)
-    endif
-    S=(2/sqrt(3.))*H !Side of the hexagon
+    ! Determine the mixed layer buoyancy flux, wB_flux.
+    dB_dS = (gravity / Rhoml) * dR0_dS
+    dB_dT = (gravity / Rhoml) * dR0_dT
 
-    if (S>0.5) then
-      ! The width of an iceberg should not be greater than half the grid cell, or else it can spread over 3 cells  (i.e. S must be less than 0.5 non-dimensionally)
-      !print 'Elements must be smaller than a whole grid cell', 'i.e.: S= ' , S , '>=0.5'
-      call error_mesg('KID, hexagonal spreading', 'Diameter of the iceberg is larger than a grid cell. Use smaller icebergs', WARNING)
-    endif
+    do it1 = 1,20
+      ! Determine the potential temperature at the ice-ocean interface.
+      call calculate_TFreeze(Sbdry, p_int, tfreeze)
 
-    !Subtracting the position of the nearest corner from x,y  (The mass will then be spread over the 4 cells connected to that corner)
-    origin_x=1. ; origin_y=1.
-    if (x<0.5) origin_x=0.
-    if (y<0.5) origin_y=0.
+      dT_ustar = (temp - tfreeze) * ustar_h
+      dS_ustar = (salt - Sbdry) * ustar_h
 
-    !Position of the hexagon center, relative to origin at the nearest vertex
-    x0=(x-origin_x)
-    y0=(y-origin_y)
+      ! First, determine the buoyancy flux assuming no effects of stability
+      ! on the turbulence.  Following H & J '99, this limit also applies
+      ! when the buoyancy flux is destabilizing.
 
-    call Hexagon_into_quadrants_using_triangles(x0,y0,H,orientation,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
+      if (bergs%const_gamma) then ! if using a constant gamma_T
+        I_Gam_T = bergs%Gamma_T_3EQ
+        I_Gam_S = bergs%Gamma_T_3EQ/35.
+      else
+        Gam_turb = I_VK * (ln_neut + (0.5 * I_ZETA_N - 1.0))
+        I_Gam_T = 1.0 / (Gam_mol_t + Gam_turb)
+        I_Gam_S = 1.0 / (Gam_mol_s + Gam_turb)
+      endif
+      wT_flux = dT_ustar * I_Gam_T
+      wB_flux = dB_dS * (dS_ustar * I_Gam_S) + dB_dT * wT_flux
 
-    if (min(min(Area_Q1,Area_Q2),min(Area_Q3, Area_Q4)) <-tol) then
-      call error_mesg('KID, hexagonal spreading', 'Intersection with hexagons should not be negative!!!', WARNING)
-      write(stderrunit,*) 'KID, yU,yC,yD', Area_Q1, Area_Q2, Area_Q3, Area_Q4
-    endif
+      if (wB_flux > 0.0) then
+        ! The buoyancy flux is stabilizing and will reduce the tubulent
+        ! fluxes, and iteration is required.
+        n_star_term = (ZETA_N/RC) * (hBL_neut * VK) / ustar_h**3
+        do it3 = 1,30
+          ! n_star <= 1.0 is the ratio of working boundary layer thickness
+          ! to the neutral thickness.
+          ! hBL = n_star*hBL_neut ; hSub = 1/8*n_star*hBL
+          I_n_star = sqrt(1.0 + n_star_term * wB_flux)
+          dIns_dwB = 0.5 * n_star_term / I_n_star
+          if (hBL_neut_h_molec > I_n_star**2) then
+            Gam_turb = I_VK * ((ln_neut - 2.0*log(I_n_star)) + &
+                       (0.5*I_ZETA_N*I_n_star - 1.0))
+            dG_dwB =  I_VK * ( -2.0 / I_n_star + (0.5 * I_ZETA_N)) * dIns_dwB
+          else
+            !   The layer dominated by molecular viscosity is smaller than
+            ! the assumed boundary layer.  This should be rare!
+            Gam_turb = I_VK * (0.5 * I_ZETA_N*I_n_star - 1.0)
+            dG_dwB = I_VK * (0.5 * I_ZETA_N) * dIns_dwB
+          endif
 
-    Area_Q1=Area_Q1/Area_hex
-    Area_Q2=Area_Q2/Area_hex
-    Area_Q3=Area_Q3/Area_hex
-    Area_Q4=Area_Q4/Area_hex
+          if (bergs%const_gamma) then ! if using a constant gamma_T
+            I_Gam_T = bergs%Gamma_T_3EQ
+            I_Gam_S = bergs%Gamma_T_3EQ/35.
+          else
+            I_Gam_T = 1.0 / (Gam_mol_t + Gam_turb)
+            I_Gam_S = 1.0 / (Gam_mol_s + Gam_turb)
+          endif
 
-    !Now, you decide which quadrant belongs to which mass on ocean cell.
-    if ((x.ge. 0.5) .and. (y.ge. 0.5)) then !Top right vertex
-      yUxR=Area_Q1
-      yUxC=Area_Q2
-      yCxC=Area_Q3
-      yCxR=Area_Q4
-    elseif ((x .lt. 0.5) .and. (y.ge. 0.5)) then  !Top left vertex
-      yUxC=Area_Q1
-      yUxL=Area_Q2
-      yCxL=Area_Q3
-      yCxC=Area_Q4
-    elseif ((x.lt.0.5) .and. (y.lt. 0.5)) then !Bottom left vertex
-      yCxC=Area_Q1
-      yCxL=Area_Q2
-      yDxL=Area_Q3
-      yDxC=Area_Q4
-    elseif ((x.ge.0.5) .and. (y.lt. 0.5)) then!Bottom right vertex
-      yCxR=Area_Q1
-      yCxC=Area_Q2
-      yDxC=Area_Q3
-      yDxR=Area_Q4
-    endif
+          wT_flux = dT_ustar * I_Gam_T
+          wB_flux_new = dB_dS * (dS_ustar * I_Gam_S) + dB_dT * wT_flux
 
-    !Temporary for debugging reasons.
-    if (mpp_pe()==mpp_root_pe()) then
-      !write(stderrunit,*) 'KID, You are in the hexagonal domain now!!!'
-    endif
+          ! Find the root where dwB = 0.0
+          DwB = wB_flux_new - wB_flux
+          if (abs(wB_flux_new - wB_flux) < &
+            1e-4*(abs(wB_flux_new) + abs(wB_flux))) exit
 
-    !Double check that all the mass is being used.
-    if ((abs(yCxC-(1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )))>tol) .and. (mpp_pe().eq. mpp_root_pe())) then
-      !call error_mesg('KID, hexagonal spreading', 'All the mass is not being used!!!', WARNING)
-      write(stderrunit,*) 'KID, hexagonal, H,x0,y0', H, x0 , y0
-      write(stderrunit,*) 'KID, hexagonal, Areas',(Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
-      debug=.True.
-      !call Hexagon_into_quadrants_using_triangles(x0,y0,H,orientation,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4, debug)
-      call error_mesg('KID, hexagonal spreading', 'All the mass is not being used!!!', FATAL)
-    endif
+          dDwB_dwB_in = -dG_dwB * (dB_dS * (dS_ustar * I_Gam_S**2) + &
+                                         dB_dT * (dT_ustar * I_Gam_T**2)) - 1.0
+          ! This is Newton's method without any bounds. ( ### SHOULD BOUNDS BE NEEDED?)
+          wB_flux_new = wB_flux - DwB / dDwB_dwB_in
+        enddo !it3
+      endif
 
-    !Scale each cell by (1/fraction_used) in order to redisribute ice mass which landed up on the land, back into the ocean
-    !Note that for the square elements, the mass has already been reassigned, so fraction_used shoule be equal to 1 aready
-    fraction_used= ((yDxL*grd%msk(i-1,j-1)) + (yDxC*grd%msk(i  ,j-1))  +(yDxR*grd%msk(i+1,j-1)) +(yCxL*grd%msk(i-1,j  )) +  (yCxR*grd%msk(i+1,j  ))&
-                   +(yUxL*grd%msk(i-1,j+1)) +(yUxC*grd%msk(i  ,j+1))   +(yUxR*grd%msk(i+1,j+1)) + (yCxC**grd%msk(i,j)))
-    if  (berg%static_berg .eq. 1)  fraction_used=1.  !Static icebergs do not share their mass with the boundary
-                                                ! (this allows us to easily  initialize hexagonal icebergs in regular arrangements against boundaries)
-  endif
-  I_fraction_used=1./fraction_used !Invert this so that the arithmatec reprocudes
+      t_flux  = RhoCp * wT_flux
+      exch_vel_t = ustar_h * I_Gam_T
+      exch_vel_s = ustar_h * I_Gam_S
 
-  !Spreading the iceberg mass onto the ocean
-  call spread_variable_across_cells(grd, grd%mass_on_ocean, Mass, i ,j, &
-             yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR, I_fraction_used)
-  !Spreading the iceberg area onto the ocean
-  call spread_variable_across_cells(grd, grd%area_on_ocean, Area*scaling , i ,j, &
-             yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR,I_fraction_used)
-  !Spreading the iceberg x momentum onto the ocean
-  call spread_variable_across_cells(grd,grd%Uvel_on_ocean, berg%uvel*Area*scaling , i ,j, &
-             yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR, I_fraction_used)
-  !Spreading the iceberg y momentum onto the ocean
-  call spread_variable_across_cells(grd,grd%Vvel_on_ocean, berg%vvel*Area*scaling , i ,j, &
-             yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR, I_fraction_used)
+      if (t_flux <= 0.0) then  ! Freezing occurs, so zero ice heat flux.
+        lprec = I_LF * t_flux
+        tflux_shelf = 0.0
+      else
+      !no conduction/perfect insulator
+      tflux_shelf = 0.0
+      lprec = I_LF * t_flux
+      ! With melting, from H&J 1999, eqs (31) & (26)...
+      !   Q_ice ~= cp_ice * (Temp_Ice-T_freeze) * lprec
+      !   RhoLF*lprec = Q_ice + t_flux
+      !   lprec = (t_flux) / (LF + cp_ice * (T_freeze-Temp_Ice))
+      !   lprec = t_flux /  (LF + Cp_ice * (tfreeze - Temp_Ice))
+      !   tflux_shelf = t_flux - LF*lprec
+      !other options: dTi/dz linear through shelf
+      !            dTi_dz = (Temp_Ice - tfreeze)/draft
+      !            tflux_shelf = - Rho_Ice * Cp_ice * KTI * dTi_dz
+      endif
 
-end subroutine spread_mass_across_ocean_cells
+      mass_exch = exch_vel_s * Rho0
+      Sbdry_it = (salt * mass_exch + Salin_Ice * lprec) / (mass_exch + lprec)
+      dS_it = Sbdry_it - Sbdry
+      if (abs(dS_it) < 1e-4*(0.5*(salt + Sbdry + 1.e-10))) exit
 
-!> Distribute a quantity among nine cells on a grid centered at cell i,j
-subroutine spread_variable_across_cells(grd, variable_on_ocean, Var, i, j, &
-           yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR, I_fraction_used)
-  ! Arguments
-  type(icebergs_gridded), pointer, intent(in) :: grd !< Container for gridded fields
-  real, dimension(grd%isd:grd%ied, grd%jsd:grd%jed, 9), intent(inout) :: variable_on_ocean !< Gridded field to augment
-  real, intent(in) :: Var !< Variable to be spread accross cell
-  real, intent(in) :: yDxL !< Weight for the cell at i-1,j-1
-  real, intent(in) :: yDxC !< Weight for the cell at i-1,j
-  real, intent(in) :: yDxR !< Weight for the cell at i-1,j+1
-  real, intent(in) :: yCxL !< Weight for the cell at i,j-1
-  real, intent(in) :: yCxC !< Weight for the cell at i,j
-  real, intent(in) :: yCxR !< Weight for the cell at i,j-1
-  real, intent(in) :: yUxL !< Weight for the cell at i+1,j-1
-  real, intent(in) :: yUxC !< Weight for the cell at i+1,j
-  real, intent(in) :: yUxR !< Weight for the cell at i+1,j+1
-  real, intent(in) :: I_fraction_used !< Amount of iceberg used (inverse)
-  integer, intent(in) :: i !< i-index of cell containing center of berg
-  integer, intent(in) :: j !< j-index of cell containing center of berg
+      if (dS_it < 0.0) then ! Sbdry is now the upper bound.
+        if (Sb_max_set .and. (Sbdry > Sb_max)) then
+          if (debug) then
+            call error_mesg('KID,Find basal melt', 'shelf_calc_flux: Irregular iteration for Sbdry (max).' ,WARNING)
+            print *, 'Sbdry error: id,dvo,temp,salt,lat,thickness :',id,dvo,temp,salt,lat,thickness
+          endif
+          out_of_bounds=.true.
+          exit
+        endif
+        Sb_max = Sbdry ; dS_max = dS_it ; Sb_max_set = .true.
+      else ! Sbdry is now the lower bound.
+        if (Sb_min_set .and. (Sbdry < Sb_min)) then
+          if (debug) then
+            call error_mesg('KID,Find basal melt', 'shelf_calc_flux: Irregular iteration for Sbdry (min).' ,WARNING)
+            print *, 'Sbdry error: id,dvo,temp,salt,lat,thickness :',id,dvo,temp,salt,lat,thickness
+          endif
+          out_of_bounds=.true.
+          exit
+        endif
+        Sb_min = Sbdry ; dS_min = dS_it ; Sb_min_set = .true.
+      endif
+      if (Sb_min_set .and. Sb_max_set) then
+        ! Use the false position method for the next iteration.
+        Sbdry = Sb_min + (Sb_max-Sb_min) * (dS_min / (dS_min - dS_max))
+      else
+        Sbdry = Sbdry_it
+      endif
+      Sbdry = Sbdry_it
+    enddo !it1
+  endif
 
-  !Spreading the iceberg mass onto the ocean
-  variable_on_ocean(i,j,1)=variable_on_ocean(i,j,1)+(yDxL*Var*I_fraction_used)
-  variable_on_ocean(i,j,2)=variable_on_ocean(i,j,2)+(yDxC*Var*I_fraction_used)
-  variable_on_ocean(i,j,3)=variable_on_ocean(i,j,3)+(yDxR*Var*I_fraction_used)
-  variable_on_ocean(i,j,4)=variable_on_ocean(i,j,4)+(yCxL*Var*I_fraction_used)
-  variable_on_ocean(i,j,5)=variable_on_ocean(i,j,5)+(yCxC*Var*I_fraction_used)
-  variable_on_ocean(i,j,6)=variable_on_ocean(i,j,6)+(yCxR*Var*I_fraction_used)
-  variable_on_ocean(i,j,7)=variable_on_ocean(i,j,7)+(yUxL*Var*I_fraction_used)
-  variable_on_ocean(i,j,8)=variable_on_ocean(i,j,8)+(yUxC*Var*I_fraction_used)
-  variable_on_ocean(i,j,9)=variable_on_ocean(i,j,9)+(yUxR*Var*I_fraction_used)
+  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+  if ((.not. Use_three_equation_model) .or. (out_of_bounds)) then
+    ! In the 2-equation form, the mixed layer turbulent exchange velocity
+    ! is specified and large enough that the ocean salinity at the interface
+    ! is about the same as the boundary layer salinity.
+    ! Alon: I have adapted the code so that the turbulent exchange velocoty is not constant, but rather proportional to the frictional velocity.
+    ! This should give you the same answers as the 3 equation model when salinity gradients in the mixed layer are zero (I think/hope)
+    ! Use 2-equation model when 3 equation version fails.
 
-end subroutine spread_variable_across_cells
+    call calculate_TFreeze(salt, p_int, tfreeze)
 
-!> Returns area of a triangle
-real function Area_of_triangle(Ax, Ay, Bx, By, Cx, Cy)
-  ! Arguments
-  real, intent(in) :: Ax !< x-position of corner A
-  real, intent(in) :: Ay !< y-position of corner A
-  real, intent(in) :: Bx !< x-position of corner B
-  real, intent(in) :: By !< y-position of corner B
-  real, intent(in) :: Cx !< x-position of corner C
-  real, intent(in) :: Cy !< y-position of corner C
-  Area_of_triangle    =   abs(    0.5*((Ax*(By-Cy))+(Bx*(Cy-Ay))+(Cx*(Ay-By))) )
-end function Area_of_triangle
+    Gam_turb = I_VK * (ln_neut + (0.5 * I_ZETA_N - 1.0))
+    I_Gam_T = 1.0 / (Gam_mol_t + Gam_turb)
 
-!> Returns x rounded of to sig_fig
-!! \todo What the heck is this for? -AJA
-real function roundoff(x,sig_fig)
-  ! Arguments
-  real, intent(in) :: x !< A quantity with 15 significant figures of useful information
-  integer, intent(in) :: sig_fig !< Number of significant figures to keep
-  !roundoff=round(x*(10**(sig_fig))
-  roundoff=(FLOAT(INT(x * (10.**sig_fig) + 0.5)) / (10.**sig_fig))
-end function roundoff
+    exch_vel_t= ustar_h * I_Gam_T
+    if (gamma_t>0.0) exch_vel_t = gamma_t  !Option to set the exchange to a constant, independent of the frictional velocity (as was previously coded)
+    wT_flux = exch_vel_t *(temp - tfreeze)
 
-!> Returns true of a point is in or on the rectangle with opposite corners A and B
-logical function point_in_interval(Ax, Ay, Bx, By, px, py)
-  ! Arguments
-  real, intent(in) :: Ax !< x-position of corner A
-  real, intent(in) :: Ay !< y-position of corner A
-  real, intent(in) :: Bx !< x-position of corner B
-  real, intent(in) :: By !< y-position of corner B
-  real, intent(in) :: px !< x-position of point
-  real, intent(in) :: py !< y-position of point
-  point_in_interval=.False.
-  if ((px <= max(Ax,Bx)) .and. (px >= min(Ax,Bx))) then
-    if ((py <= max(Ay,By)) .and. (py >= min(Ay,By))) then
-      point_in_interval=.True.
-    endif
+    t_flux  = RhoCp * wT_flux
+    tflux_shelf = 0.0
+    lprec = I_LF * t_flux
   endif
-end function point_in_interval
+    !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+  ! melt in m/s (melts of ice melted per second)
+  basal_melt = lprec /density_ice
 
-!> Returns true if point q is on a line through points A and B
-logical function point_is_on_the_line(Ax, Ay, Bx, By, qx, qy)
+end subroutine find_basal_melt
+
+!> Calculates freezing point potential temperature of seawater using a linear relation
+!!
+!! This subroutine computes the freezing point potential temperature
+!! (in deg C) from salinity (in psu), and pressure (in Pa) using a simple
+!! linear expression, with coefficients passed in as arguments.
+!!
+!! Copied from subroutine calculate_TFreeze_linear_scalar (in MOM/equation_of_state)
+subroutine calculate_TFreeze(S, pres, T_Fr)
   ! Arguments
-  real, intent(in) :: Ax !< x-position of point A
-  real, intent(in) :: Ay !< y-position of point A
-  real, intent(in) :: Bx !< x-position of point B
-  real, intent(in) :: By !< y-position of point B
-  real, intent(in) :: qx !< x-position of point q
-  real, intent(in) :: qy !< y-position of point q
+  real, intent(in) :: S !< Salinity (1e-3)
+  real, intent(in) :: pres !< Presure (Pa)
+  real, intent(out) :: T_Fr !< Freezing point (C)
   ! Local variables
-  real :: tol, dxc,dyc,dxl,dyl,cross
-  !tol=1.e-12
-  tol=0.0
-  dxc = qx - Ax
-  dyc = qy - Ay
-  dxl = Bx - Ax
-  dyl = By - Ay
-  cross = dxc * dyl - dyc * dxl
-  if (abs(cross)<=tol) then
-    point_is_on_the_line=.True.
-  else
-   point_is_on_the_line=.False.
-  endif
-end function point_is_on_the_line
+  real, parameter :: dTFr_dp    = -7.53E-08    !DTFREEZE_DP in MOM_input
+  real, parameter :: dTFr_dS    = -0.0573      !DTFREEZE_DS in MOM_input
+  real, parameter :: TFr_S0_P0  =0.0832        !TFREEZE_S0_P0 in MOM_input
+  ! TFr_S0_P0 - The freezing point at S=0, p=0, in deg C.
+  ! dTFr_dS - The derivatives of freezing point with salinity, in deg C PSU-1.
+  ! dTFr_dp - The derivatives of freezing point with pressure, in deg C Pa-1.
+  T_Fr = (TFr_S0_P0 + dTFr_dS*S) + dTFr_dp*pres
+end subroutine calculate_TFreeze
 
-!> Returns True if a point q is inside a triangle ABC
+!> Calculates density of seawater using a linear equation of state
 !!
-!! This function decides whether a point (qx,qy) is inside the triangle ABC.
-!! There is also the option to include the boundary of the triangle.
-logical function point_in_triangle(Ax, Ay, Bx, By, Cx, Cy, qx, qy)
+!! This subroutine computes the density of sea water with a trivial
+!! linear equation of state (in kg/m^3) from salinity (sal in psu),
+!! potential temperature (T in deg C), and pressure in Pa.
+!!
+!! Copied from subroutine calculate_density_scalar_linear (in MOM/equation_of_state)
+subroutine calculate_density(T, S, pressure, rho, Rho_T0_S0, dRho_dT, dRho_dS)
+  !Arguments
+  real, intent(in)  :: T !< Potential temperature (C)
+  real, intent(in)  :: S !< Salinity (1e-3)
+  real, intent(in)  :: pressure !< Pressure (Pa)
+  real, intent(out) :: rho !< In situ density (kg/3)
+  real, intent(in)  :: Rho_T0_S0 !< Density at T=0, S=0 (kg/m3)
+  real, intent(in)  :: dRho_dT !< Derivative of density w.r.t. potential temperature (kg/m3/C)
+  real, intent(in)  :: dRho_dS !< Derivative of density w.r.t. salinity (1e3 kg/m3)
+  rho = Rho_T0_S0 + dRho_dT*T + dRho_dS*S
+end subroutine calculate_density
+
+!> Returns orientation of a berg determined by its bonds
+subroutine find_orientation_using_iceberg_bonds(grd, berg, orientation)
   ! Arguments
-  real, intent(in) :: Ax !< x-position of corner A
-  real, intent(in) :: Ay !< y-position of corner A
-  real, intent(in) :: Bx !< x-position of corner B
-  real, intent(in) :: By !< y-position of corner B
-  real, intent(in) :: Cx !< x-position of corner C
-  real, intent(in) :: Cy !< y-position of corner C
-  real, intent(in) :: qx !< x-position of point q
-  real, intent(in) :: qy !< y-position of point q
+  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+  type(iceberg), pointer :: berg !< Berg for which orientation is needed
+  real, intent(inout) :: orientation !< Angle of orientation (radians)
   ! Local variables
-  real :: l0,l1,l2,p0,p1,p2
-  real :: v0x,v1x,v2x,v0y,v1y,v2y,dot00,dot01,dot02,dot11,dot12
+  type(iceberg), pointer :: other_berg
+  type(bond), pointer :: current_bond
+  real :: angle, lat1,lat2,lon1,lon2,dlat,dlon
+  real :: r_dist_x, r_dist_y
+  real :: lat_ref, dx_dlon, dy_dlat
+  real :: theta, bond_count, Average_angle
 
-  point_in_triangle = .False.
-  if ((Ax==qx .and. Ay==qy) .or. (Bx==qx .and. By==qy) .or. (Cx==qx .and. Cy==qy)) then ! Exclude the pathelogical case
-      point_in_triangle = .False.
-  else
-    if (((point_is_on_the_line(Ax,Ay,Bx,By,qx,qy) .or. (point_is_on_the_line(Ax,Ay,Cx,Cy,qx,qy))) .or. (point_is_on_the_line(Bx,By,Cx,Cy,qx,qy)))) then
-      point_in_triangle = .False.
-    else
-      ! Compute point in triangle using Barycentric coordinates (the same as sum_sign_dot_prod routines)
-      l0=(qx-Ax)*(By-Ay)-(qy-Ay)*(Bx-Ax)
-      l1=(qx-Bx)*(Cy-By)-(qy-By)*(Cx-Bx)
-      l2=(qx-Cx)*(Ay-Cy)-(qy-Cy)*(Ax-Cx)
+  bond_count=0.
+  Average_angle=0.
+  !Don't check orientation of the edges of halo,  since they can contain unassosiated bonds  (this is why halo width must be larger >= 2 to use bonds)
+  if  (  ((berg%ine .gt.  grd%isd) .and. (berg%ine .lt. grd%ied)) .and. ((berg%jne .ge.  grd%jsd) .and. (berg%jne .le. grd%jed) ) ) then
+    current_bond=>berg%first_bond
+    lat1=berg%lat
+    lon1=berg%lon
+    do while (associated(current_bond)) ! loop over all bonds
+      other_berg=>current_bond%other_berg
+      if (.not. associated(other_berg)) then !good place for debugging
+        !One valid option: current iceberg is on the edge of halo, with other berg on the next pe (not influencing mass spreading)
+        !print *, 'Iceberg bond details:',berg%id, current_bond%other_id,berg%halo_berg, mpp_pe()
+        !print *, 'Iceberg bond details2:',berg%ine, berg%jne, current_bond%other_berg_ine, current_bond%other_berg_jne
+        !print *, 'Iceberg isd,ied,jsd,jed:',grd%isd, grd%ied, grd%jsd, grd%jed
+        !print *, 'Iceberg isc,iec,jsc,jec:',grd%isc, grd%iec, grd%jsc, grd%jec
+        !call error_mesg('KID,calculating orientation', 'Looking at bond interactions of unassosiated berg!' ,FATAL)
+        !endif
+      else
+        lat2=other_berg%lat
+        lon2=other_berg%lon
 
-      p0=sign(1., l0); if (l0==0.)  p0=0.
-      p1=sign(1., l1); if (l1==0.)  p1=0.
-      p2=sign(1., l2); if (l2==0.)  p2=0.
+        dlat=lat2-lat1
+        dlon=lon2-lon1
 
-      if ( (abs(p0)+abs(p2))+(abs(p1)) == abs((p0+p2)+(p1)) )  point_in_triangle = .True.
+        lat_ref=0.5*(lat1+lat2)
+        call convert_from_grid_to_meters(lat_ref,grd%grid_is_latlon,dx_dlon,dy_dlat)
+        r_dist_x=dlon*dx_dlon
+        r_dist_y=dlat*dy_dlat
+
+        if (r_dist_x .eq. 0.) then
+          angle=pi/2.
+        else
+          angle=atan(r_dist_y/r_dist_x)
+          angle= ((pi/2.)  - (orientation*(pi/180.)))  - angle
+          !print *, 'angle: ', angle*(180/pi), initial_orientation
+          angle=modulo(angle ,pi/3.)
+        endif
+        bond_count=bond_count+1.
+        Average_angle=Average_angle+angle
+      endif
+      current_bond=>current_bond%next_bond
+    enddo  !End loop over bonds
+    if (bond_count.gt.0) then
+      Average_angle =Average_angle/bond_count
+    else
+      Average_angle =0.
     endif
+    orientation=modulo(Average_angle ,pi/3.)
   endif
-end function point_in_triangle
 
-!> Calculates the two areas of a triangle divided by an axis line
-!!
-!! This function calculates the area of a triangle on opposite sides of an axis when the
-!! triangle is split with two points on one side, and one point on the other.
-!! In this function, A is the point on one side of the axis, and B,C are on the opposite sides.
-!! \todo You should change this name a little, so that it not similar the other routine.
-subroutine Area_of_triangle_across_axes(Ax, Ay, Bx, By, Cx, Cy, axis1, Area_positive, Area_negative)
+end subroutine find_orientation_using_iceberg_bonds
+
+!> Spread mass of a berg around cells centered on i,j
+subroutine spread_mass_across_ocean_cells(bergs, berg, i, j, x, y, Mberg, Mbits, scaling, Area, Tn)
   ! Arguments
-  real, intent(in) :: Ax !< x-position of corner A
-  real, intent(in) :: Ay !< y-position of corner A
-  real, intent(in) :: Bx !< x-position of corner B
-  real, intent(in) :: By !< y-position of corner B
-  real, intent(in) :: Cx !< x-position of corner C
-  real, intent(in) :: Cy !< y-position of corner C
-  character, intent(in) :: axis1 !< Either 'x' or 'y'
-  real, intent(out) :: Area_positive !< Area on negative side of axis line
-  real, intent(out) :: Area_negative !< Area on positive side of axis line
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  type(iceberg), pointer :: berg !< Berg whose mass is being considered
+  integer, intent(in) :: i !< i-index of cell contained center of berg
+  integer, intent(in) :: j !< j-index of cell contained center of berg
+  real, intent(in) :: x !< Longitude of berg (degree E)
+  real, intent(in) :: y !< Latitude of berg (degree N)
+  real, intent(in) :: Mberg !< Mass of berg (kg)
+  real, intent(in) :: Mbits !< Mass of bergy bits (kg)
+  real, intent(in) :: scaling !< Multiplier to scale mass (nondim)
+  real, intent(in) :: Area !< Area of berg (m2)
+  real, intent(in) :: Tn !< Thickness of berg (m)
   ! Local variables
-  real :: pABx, pABy, pACx, pACy, A0
-  real :: A_half_triangle, A_triangle
-
-  A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy)
+  type(icebergs_gridded), pointer :: grd
+  real :: xL, xC, xR, yD, yC, yU, Mass, L
+  real :: yDxL, yDxC, yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR
+  real :: S, H, origin_x, origin_y, x0, y0
+  real :: Area_Q1,Area_Q2 , Area_Q3,Area_Q4, Area_hex
+  real :: fraction_used !fraction of iceberg mass included (part of the mass near the boundary is discarded sometimes)
+  real :: I_fraction_used !Inverse of fraction used
+  real :: tol
+  real :: Dn, Hocean
+  real, parameter :: rho_seawater=1035.
+  integer :: stderrunit
+  logical :: debug
+  real :: orientation, Mass_berg
 
-  call intercept_of_a_line(Ax,Ay,Bx,By,axis1,pABx, pABy)
-  call intercept_of_a_line(Ax,Ay,Cx,Cy,axis1,pACx, pACy)
+  ! Get the stderr unit number
+  stderrunit = stderr()
 
-  if (axis1=='x')  A0=Ay; !Value used for if statements (deciding up/down vs left/right)
-  if (axis1=='y')  A0=Ax; !Value used for if statements (deciding up/down vs left/right)
+  tol=1.e-10
+  grd=>bergs%grd
+  Mass_berg=Mberg
 
-  A_half_triangle=Area_of_triangle(Ax,Ay,pABx,pABy,pACx,pACy)
-  if (A0>=0.) then
-    Area_positive= A_half_triangle
-    Area_negative= A_triangle-A_half_triangle
-  else
-    Area_positive= A_triangle-A_half_triangle
-    Area_negative= A_half_triangle
+  ! Trimming icebergs to account for grounded fraction.
+  if (bergs%grounding_fraction>0.) then
+    Hocean=bergs%grounding_fraction*(grd%ocean_depth(i,j)+grd%ssh(i,j))
+    Dn=(bergs%rho_bergs/rho_seawater)*Tn ! re-calculate draught (keel depth)
+    if (Dn>Hocean) Mass_berg=Mberg*min(1.,Hocean/Dn)
   endif
 
-end subroutine Area_of_triangle_across_axes
+  Mass=(Mass_berg+Mbits)*scaling
+  ! This line attempts to "clip" the weight felt by the ocean. The concept of
+  ! clipping is non-physical and this step should be replaced by grounding.
+  if (grd%clipping_depth>0.) Mass=min(Mass,grd%clipping_depth*grd%area(i,j)*rho_seawater)
 
-!> Returns the axis intercept of a line AB
-!!
-!! This routine returns the position (x0,y0) at which a line AB intercepts the x or y axis.
-!! The value No_intercept_val is returned when the line does not intercept the axis.
-subroutine intercept_of_a_line(Ax, Ay, Bx, By, axes1, x0, y0)
-  ! Arguments
-  real, intent(in) :: Ax !< x-position of corner A
-  real, intent(in) :: Ay !< y-position of corner A
-  real, intent(in) :: Bx !< x-position of corner B
-  real, intent(in) :: By !< y-position of corner B
-  character, intent(in) :: axes1 !< Either 'x' or 'y'
-  real, intent(out) :: x0 !< x-position of intercept
-  real, intent(out) :: y0 !< y-position of intercept
-  ! Local variables
-  real :: No_intercept_val ! Huge value used to make sure that the intercept is outside the triangle in the parallel case.
+  !Initialize weights for each cell
+  yDxL=0.  ; yDxC=0. ; yDxR=0. ; yCxL=0. ; yCxR=0.
+  yUxL=0.  ; yUxC=0. ; yUxR=0. ; yCxC=1.
 
-  No_intercept_val=100000000000. ! Huge value used to make sure that the intercept is outside the triangle in the parallel case.
-  x0=No_intercept_val
-  y0=No_intercept_val
+  if (.not. bergs%hexagonal_icebergs) then ! Treat icebergs as rectangles of size L: (this is the default)
 
-  if (axes1=='x') then ! x intercept
-    if (Ay.ne.By) then
-      x0=Ax -(((Ax-Bx)/(Ay-By))*Ay)
-      y0=0.
+    ! L is the non dimensional length of the iceberg [ L=(Area of berg/ Area of grid cell)^0.5 ] or something like that.
+    if (grd%area(i,j)>0) then
+      L=min( sqrt(Area / grd%area(i,j)),1.0)
+    else
+      L=1.
     endif
-  endif
 
-  if (axes1=='y') then ! y intercept
-    if (Ax.ne.Bx) then
-      x0=0.
-      y0=-(((Ay-By)/(Ax-Bx))*Ax)+Ay
+    if (bergs%use_old_spreading) then
+      ! Old version before icebergs were given size L
+      xL=min(0.5, max(0., 0.5-x))
+      xR=min(0.5, max(0., x-0.5))
+      xC=max(0., 1.-(xL+xR))
+      yD=min(0.5, max(0., 0.5-y))
+      yU=min(0.5, max(0., y-0.5))
+      yC=max(0., 1.-(yD+yU))
+    else
+      xL=min(0.5, max(0., 0.5-(x/L)))
+      xR=min(0.5, max(0., (x/L)+(0.5-(1/L) )))
+      xC=max(0., 1.-(xL+xR))
+      yD=min(0.5, max(0., 0.5-(y/L)))
+      yU=min(0.5, max(0., (y/L)+(0.5-(1/L) )))
+      yC=max(0., 1.-(yD+yU))
     endif
-  endif
-end subroutine intercept_of_a_line
 
-!> Calculates the area of a triangle on either side of an axis, if any.
-!!
-!! This routine gives you the area of a triangle on opposite sides of the axis specified.
-!! It also takes care of the special case where the triangle is totally on one side.
-!! This routine calls Area_of_triangle_across_axes to calculate the areas when the triangles are split.
-subroutine divding_triangle_across_axes(Ax, Ay, Bx, By, Cx, Cy, axes1, Area_positive, Area_negative)
-  ! Arguments
-  real, intent(in) :: Ax !< x-position of corner A
-  real, intent(in) :: Ay !< y-position of corner A
-  real, intent(in) :: Bx !< x-position of corner B
-  real, intent(in) :: By !< y-position of corner B
-  real, intent(in) :: Cx !< x-position of corner C
-  real, intent(in) :: Cy !< y-position of corner C
-  character, intent(in) :: axes1 !< Either 'x' or 'y'
-  real, intent(out) :: Area_positive !< Area on negative side of axis line
-  real, intent(out) :: Area_negative !< Area on positive side of axis line
-  ! Local variables
-  real :: A0,B0,C0
-  real A_triangle
+    yDxL=yD*xL*grd%msk(i-1,j-1)
+    yDxC=yD*xC*grd%msk(i  ,j-1)
+    yDxR=yD*xR*grd%msk(i+1,j-1)
+    yCxL=yC*xL*grd%msk(i-1,j  )
+    yCxR=yC*xR*grd%msk(i+1,j  )
+    yUxL=yU*xL*grd%msk(i-1,j+1)
+    yUxC=yU*xC*grd%msk(i  ,j+1)
+    yUxR=yU*xR*grd%msk(i+1,j+1)
+    yCxC=1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )
 
-  if (axes1=='x') then ! Use the y-coordinates for if statements to see which side of the line you are on
-    A0=Ay
-    B0=By
-    C0=Cy
-  endif
-  if (axes1=='y') then ! Use the y-coordinates for if statements to see which side of the line you are on
-    A0=Ax
-    B0=Bx
-    C0=Cx
-  endif
+    fraction_used=1. ! rectangular bergs do share mass with boundaries (all mass is included in cells)
 
-  A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy)
-  if ((B0*C0)>0.) then ! B and C are on the same side  (and non-zero)
-    if ((A0*B0).ge.0.) then ! all three on the same side (if it equals zero, then A0=0 and the others are not)
-      if ((A0>0.)  .or.  ((A0==0.) .and.  (B0>0.))) then
-        Area_positive= A_triangle
-        Area_negative= 0.
-      else
-        Area_positive= 0.
-        Area_negative= A_triangle
-      endif
-    else  !A is on the opposite side to B and C
-      call Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1,Area_positive, Area_negative)
+  else ! Spread mass as if elements area hexagonal
+
+    orientation=bergs%initial_orientation
+    if ((bergs%iceberg_bonds_on) .and. (bergs%rotate_icebergs_for_mass_spreading)) call find_orientation_using_iceberg_bonds(grd,berg,orientation)
+
+    if (grd%area(i,j)>0) then
+      H=min(( (sqrt(Area/(2.*sqrt(3.))) / sqrt(grd%area(i,j)))),1.) ! Non-dimensionalize element length by grid area. (This gives the non-dim Apothem of the hexagon)
+    else
+      H=(sqrt(3.)/2)*(0.49) ! Largest allowable H, since this makes S=0.49, and S has to be less than 0.5 (Not sure what the implications of this are)
     endif
+    S=(2/sqrt(3.))*H !Side of the hexagon
 
-  elseif ((B0*C0)<0.) then !B and C are on the opposite sides
-    if ((A0*B0).ge. 0.) then !C is all alone
-      call Area_of_triangle_across_axes(Cx,Cy,Bx,By,Ax,Ay,axes1,Area_positive, Area_negative)
-    else !B is all alone
-      call Area_of_triangle_across_axes(Bx,By,Cx,Cy,Ax,Ay,axes1,Area_positive, Area_negative)
+    if (S>0.5) then
+      ! The width of an iceberg should not be greater than half the grid cell, or else it can spread over 3 cells  (i.e. S must be less than 0.5 non-dimensionally)
+      !print 'Elements must be smaller than a whole grid cell', 'i.e.: S= ' , S , '>=0.5'
+      call error_mesg('KID, hexagonal spreading', 'Diameter of the iceberg is larger than a grid cell. Use smaller icebergs', WARNING)
     endif
 
-  else  !This is the case when either B or C is equal to zero (or both), A0 could be zero too.
-    if (((A0.eq.0.) .and. (B0.eq.0.)) .and. (C0.eq.0.)) then
-      Area_positive= 0.
-      Area_negative= 0.
-    elseif ((A0*B0<0.)  .or.  (A0*C0<0.)) then    !A, B are on opposite sides, and C is zero.  OR  A, C are on opposite sides, and B is zero.
-      call Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1,Area_positive, Area_negative)
-    elseif (((A0*B0>0.) .or. (A0*C0>0.)) .or. (((abs(A0)>0.) .and. (B0==0.)) .and. (C0==0.))) then
-      if (A0>0.) then
-        Area_positive= A_triangle
-        Area_negative= 0.
-      else
-        Area_positive= 0.
-        Area_negative= A_triangle
-      endif
+    !Subtracting the position of the nearest corner from x,y  (The mass will then be spread over the 4 cells connected to that corner)
+    origin_x=1. ; origin_y=1.
+    if (x<0.5) origin_x=0.
+    if (y<0.5) origin_y=0.
 
-    elseif (A0.eq. 0.) then   !(one of B,C is zero too)
-      if ((B0>0.) .or. (C0>0.)) then
-        Area_positive= A_triangle
-        Area_negative= 0.
-      elseif ((B0<0.) .or. (C0<0.)) then
-        Area_positive= 0.
-        Area_negative= A_triangle
-      else
-        call error_mesg('KID, iceberg_run', 'Logical error inside triangle dividing routine', FATAL)
-      endif
-    else
-      call error_mesg('KID, iceberg_run', 'Another logical error inside triangle dividing routine', FATAL)
+    !Position of the hexagon center, relative to origin at the nearest vertex
+    x0=(x-origin_x)
+    y0=(y-origin_y)
+
+    call Hexagon_into_quadrants_using_triangles(x0,y0,H,orientation,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
+
+    if (min(min(Area_Q1,Area_Q2),min(Area_Q3, Area_Q4)) <-tol) then
+      call error_mesg('KID, hexagonal spreading', 'Intersection with hexagons should not be negative!!!', WARNING)
+      write(stderrunit,*) 'KID, yU,yC,yD', Area_Q1, Area_Q2, Area_Q3, Area_Q4
+    endif
+
+    Area_Q1=Area_Q1/Area_hex
+    Area_Q2=Area_Q2/Area_hex
+    Area_Q3=Area_Q3/Area_hex
+    Area_Q4=Area_Q4/Area_hex
+
+    !Now, you decide which quadrant belongs to which mass on ocean cell.
+    if ((x.ge. 0.5) .and. (y.ge. 0.5)) then !Top right vertex
+      yUxR=Area_Q1
+      yUxC=Area_Q2
+      yCxC=Area_Q3
+      yCxR=Area_Q4
+    elseif ((x .lt. 0.5) .and. (y.ge. 0.5)) then  !Top left vertex
+      yUxC=Area_Q1
+      yUxL=Area_Q2
+      yCxL=Area_Q3
+      yCxC=Area_Q4
+    elseif ((x.lt.0.5) .and. (y.lt. 0.5)) then !Bottom left vertex
+      yCxC=Area_Q1
+      yCxL=Area_Q2
+      yDxL=Area_Q3
+      yDxC=Area_Q4
+    elseif ((x.ge.0.5) .and. (y.lt. 0.5)) then!Bottom right vertex
+      yCxR=Area_Q1
+      yCxC=Area_Q2
+      yDxC=Area_Q3
+      yDxR=Area_Q4
+    endif
+
+    !Temporary for debugging reasons.
+    if (mpp_pe()==mpp_root_pe()) then
+      !write(stderrunit,*) 'KID, You are in the hexagonal domain now!!!'
+    endif
+
+    !Double check that all the mass is being used.
+    if ((abs(yCxC-(1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )))>tol) .and. (mpp_pe().eq. mpp_root_pe())) then
+      !call error_mesg('KID, hexagonal spreading', 'All the mass is not being used!!!', WARNING)
+      write(stderrunit,*) 'KID, hexagonal, H,x0,y0', H, x0 , y0
+      write(stderrunit,*) 'KID, hexagonal, Areas',(Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
+      debug=.True.
+      !call Hexagon_into_quadrants_using_triangles(x0,y0,H,orientation,Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4, debug)
+      call error_mesg('KID, hexagonal spreading', 'All the mass is not being used!!!', FATAL)
     endif
+
+    !Scale each cell by (1/fraction_used) in order to redisribute ice mass which landed up on the land, back into the ocean
+    !Note that for the square elements, the mass has already been reassigned, so fraction_used shoule be equal to 1 aready
+    fraction_used= ((yDxL*grd%msk(i-1,j-1)) + (yDxC*grd%msk(i  ,j-1))  +(yDxR*grd%msk(i+1,j-1)) +(yCxL*grd%msk(i-1,j  )) +  (yCxR*grd%msk(i+1,j  ))&
+                   +(yUxL*grd%msk(i-1,j+1)) +(yUxC*grd%msk(i  ,j+1))   +(yUxR*grd%msk(i+1,j+1)) + (yCxC**grd%msk(i,j)))
+    if  (berg%static_berg .eq. 1)  fraction_used=1.  !Static icebergs do not share their mass with the boundary
+                                                ! (this allows us to easily  initialize hexagonal icebergs in regular arrangements against boundaries)
   endif
-end subroutine divding_triangle_across_axes
+  I_fraction_used=1./fraction_used !Invert this so that the arithmatec reprocudes
 
-!> Areas of a triangle divided into quadrants
-!!
-!! This routine takes a triangle, and finds the intersection with the four quadrants.
-subroutine Triangle_divided_into_four_quadrants(Ax, Ay, Bx, By, Cx, Cy, Area_triangle, Area_Q1, Area_Q2 ,Area_Q3 ,Area_Q4)
+  !Spreading the iceberg mass onto the ocean
+  call spread_variable_across_cells(grd, grd%mass_on_ocean, Mass, i ,j, &
+             yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR, I_fraction_used)
+  !Spreading the iceberg area onto the ocean
+  call spread_variable_across_cells(grd, grd%area_on_ocean, Area*scaling , i ,j, &
+             yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR,I_fraction_used)
+  !Spreading the iceberg x momentum onto the ocean
+  call spread_variable_across_cells(grd,grd%Uvel_on_ocean, berg%uvel*Area*scaling , i ,j, &
+             yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR, I_fraction_used)
+  !Spreading the iceberg y momentum onto the ocean
+  call spread_variable_across_cells(grd,grd%Vvel_on_ocean, berg%vvel*Area*scaling , i ,j, &
+             yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR, I_fraction_used)
+
+end subroutine spread_mass_across_ocean_cells
+
+!> Distribute a quantity among nine cells on a grid centered at cell i,j
+subroutine spread_variable_across_cells(grd, variable_on_ocean, Var, i, j, &
+           yDxL, yDxC,yDxR, yCxL, yCxC, yCxR, yUxL, yUxC, yUxR, I_fraction_used)
+  ! Arguments
+  type(icebergs_gridded), pointer, intent(in) :: grd !< Container for gridded fields
+  real, dimension(grd%isd:grd%ied, grd%jsd:grd%jed, 9), intent(inout) :: variable_on_ocean !< Gridded field to augment
+  real, intent(in) :: Var !< Variable to be spread accross cell
+  real, intent(in) :: yDxL !< Weight for the cell at i-1,j-1
+  real, intent(in) :: yDxC !< Weight for the cell at i-1,j
+  real, intent(in) :: yDxR !< Weight for the cell at i-1,j+1
+  real, intent(in) :: yCxL !< Weight for the cell at i,j-1
+  real, intent(in) :: yCxC !< Weight for the cell at i,j
+  real, intent(in) :: yCxR !< Weight for the cell at i,j-1
+  real, intent(in) :: yUxL !< Weight for the cell at i+1,j-1
+  real, intent(in) :: yUxC !< Weight for the cell at i+1,j
+  real, intent(in) :: yUxR !< Weight for the cell at i+1,j+1
+  real, intent(in) :: I_fraction_used !< Amount of iceberg used (inverse)
+  integer, intent(in) :: i !< i-index of cell containing center of berg
+  integer, intent(in) :: j !< j-index of cell containing center of berg
+
+  !Spreading the iceberg mass onto the ocean
+  variable_on_ocean(i,j,1)=variable_on_ocean(i,j,1)+(yDxL*Var*I_fraction_used)
+  variable_on_ocean(i,j,2)=variable_on_ocean(i,j,2)+(yDxC*Var*I_fraction_used)
+  variable_on_ocean(i,j,3)=variable_on_ocean(i,j,3)+(yDxR*Var*I_fraction_used)
+  variable_on_ocean(i,j,4)=variable_on_ocean(i,j,4)+(yCxL*Var*I_fraction_used)
+  variable_on_ocean(i,j,5)=variable_on_ocean(i,j,5)+(yCxC*Var*I_fraction_used)
+  variable_on_ocean(i,j,6)=variable_on_ocean(i,j,6)+(yCxR*Var*I_fraction_used)
+  variable_on_ocean(i,j,7)=variable_on_ocean(i,j,7)+(yUxL*Var*I_fraction_used)
+  variable_on_ocean(i,j,8)=variable_on_ocean(i,j,8)+(yUxC*Var*I_fraction_used)
+  variable_on_ocean(i,j,9)=variable_on_ocean(i,j,9)+(yUxR*Var*I_fraction_used)
+
+end subroutine spread_variable_across_cells
+
+!> Returns area of a triangle
+real function Area_of_triangle(Ax, Ay, Bx, By, Cx, Cy)
   ! Arguments
   real, intent(in) :: Ax !< x-position of corner A
   real, intent(in) :: Ay !< y-position of corner A
@@ -2537,1160 +2923,1450 @@ subroutine Triangle_divided_into_four_quadrants(Ax, Ay, Bx, By, Cx, Cy, Area_tri
   real, intent(in) :: By !< y-position of corner B
   real, intent(in) :: Cx !< x-position of corner C
   real, intent(in) :: Cy !< y-position of corner C
-  real, intent(out) :: Area_triangle !< Are of triangle
-  real, intent(out) :: Area_Q1 !< Are in quadrant 1
-  real, intent(out) :: Area_Q2 !< Are in quadrant 2
-  real, intent(out) :: Area_Q3 !< Are in quadrant 2
-  real, intent(out) :: Area_Q4 !< Are in quadrant 4
-  ! Local variables
-  real :: Area_Upper, Area_Lower, Area_Right, Area_Left
-  real :: px, py , qx , qy
-  real :: Area_key_quadrant,Error
-  real :: tol
-  integer :: Key_quadrant
-  integer ::sig_fig
-  integer :: stderrunit
-
-  ! Get the stderr unit number
-  stderrunit = stderr()
-  tol=1.e-10
-
-  Area_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy)
+  Area_of_triangle    =   abs(    0.5*((Ax*(By-Cy))+(Bx*(Cy-Ay))+(Cx*(Ay-By))) )
+end function Area_of_triangle
 
-  ! Calculating area across axes
-  call divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,'x',Area_Upper ,Area_Lower)
-  call divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,'y',Area_Right ,Area_Left)
+!> Returns x rounded of to sig_fig
+!! \todo What the heck is this for? -AJA
+real function roundoff(x,sig_fig)
+  ! Arguments
+  real, intent(in) :: x !< A quantity with 15 significant figures of useful information
+  integer, intent(in) :: sig_fig !< Number of significant figures to keep
+  !roundoff=round(x*(10**(sig_fig))
+  roundoff=(FLOAT(INT(x * (10.**sig_fig) + 0.5)) / (10.**sig_fig))
+end function roundoff
 
-  ! Decide if the origin is in the triangle. If so, then you have to divide the area 4 ways
-  ! This is done by finding a quadrant where the intersection between the triangle and quadrant forms a new triangle
-  ! (This occurs when on of the sides of the triangle  intersects both the x and y axis)
-  if (point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.)) then
-    ! Find a line in the triangle that cuts both axes in/on the triangle
-    call intercept_of_a_line(Ax,Ay,Bx,By,'x',px,py); !x_intercept
-    call intercept_of_a_line(Ax,Ay,Bx,By,'y',qx,qy); !y_intercept
-    ! Note that the 1. here means that we include points on the boundary of the triangle.
-    if (.not.((point_in_interval(Ax,Ay,Bx,By,px,py)) .and. (point_in_interval(Ax,Ay,Bx,By,qx,qy)))) then
-      call intercept_of_a_line(Ax,Ay,Cx,Cy,'x',px,py); !x_intercept
-      call intercept_of_a_line(Ax,Ay,Cx,Cy,'y',qx,qy); !y_intercept
-      if (.not.((point_in_interval(Ax,Ay,Cx,Cy,px,py)) .and. (point_in_interval(Ax,Ay,Cx,Cy,qx,qy)))) then
-        call intercept_of_a_line(Bx,By,Cx,Cy,'x',px,py); !x_intercept
-        call intercept_of_a_line(Bx,By,Cx,Cy,'y',qx,qy); !y_intercept
-        if (.not.((point_in_interval(Bx,By,Cx,Cy,px,py)) .and. (point_in_interval(Bx,By,Cx,Cy,qx,qy)))) then
-          ! You should not get here, but there might be some bugs in the code to do with points exactly falling on axes.
-          !if (mpp_pe().eq.12) then
-            write(stderrunit,*) 'KID,corners', Ax,Ay,Bx,By,Cx,Cy
-          !endif
-          call error_mesg('KID, iceberg_run', 'Something went wrong with Triangle_divide_into_four_quadrants', FATAL)
-        endif
-      endif
-    endif
-
-    ! Assigning quadrants. Key_quadrant is the quadrant with the baby triangle in it.
-    Area_key_quadrant=Area_of_triangle(px,py,qx,qy,0.,0.)
-    if ((px.ge. 0.) .and. (qy.ge. 0.)) then  !First quadrant
-      Key_quadrant=1
-    elseif ((px.lt.0.) .and. (qy.ge. 0.)) then  !Second quadrant
-      Key_quadrant=2
-    elseif ((px.lt. 0.) .and. (qy.lt. 0.)) then !Third quadrant
-      Key_quadrant=3
-    elseif ((px.ge. 0.) .and. (qy.lt. 0.)) then !Forth quadrant
-      Key_quadrant=4
-    else  !
-      call error_mesg('KID, iceberg_run', 'None of the quadrants are Key', WARNING)
-      write(stderrunit,*) 'KID, Triangle, px,qy', px,qy
-    endif
-
-  else ! At least one quadrant is empty, and this can be used to find the areas in the other quadrant.  Assigning quadrants. Key_quadrant is the empty quadrant.
-    Area_key_quadrant=0
-    if      ( (.not. ((((Ax>0.) .and. (Ay>0.)) .or. ((Bx>0.) .and. (By> 0.))) .or. ((Cx>0.) .and. (Cy> 0.)))) .and. ((Area_Upper+Area_Right).le.Area_triangle) ) then
-      ! No points land in this quadrant and triangle does not cross the quadrant
-      Key_quadrant=1
-    elseif  ( (.not. ((((Ax<0.) .and. (Ay>0)) .or. ((Bx<0.) .and. (By>0.))) .or. ((Cx<0.) .and. (Cy>0.)))) .and. ((Area_Upper+Area_Left).le. Area_triangle) ) then
-      Key_quadrant=2
-    elseif  ( (.not. ((((Ax<0.) .and. (Ay<0.)) .or. ((Bx<0.) .and. (By< 0.))) .or. ((Cx<0.) .and. (Cy< 0.)))) .and. ((Area_Lower+Area_Left) .le.Area_triangle) ) then
-      Key_quadrant=3
-    else
-      Key_quadrant=4
+!> Returns true of a point is in or on the rectangle with opposite corners A and B
+logical function point_in_interval(Ax, Ay, Bx, By, px, py)
+  ! Arguments
+  real, intent(in) :: Ax !< x-position of corner A
+  real, intent(in) :: Ay !< y-position of corner A
+  real, intent(in) :: Bx !< x-position of corner B
+  real, intent(in) :: By !< y-position of corner B
+  real, intent(in) :: px !< x-position of point
+  real, intent(in) :: py !< y-position of point
+  point_in_interval=.False.
+  if ((px <= max(Ax,Bx)) .and. (px >= min(Ax,Bx))) then
+    if ((py <= max(Ay,By)) .and. (py >= min(Ay,By))) then
+      point_in_interval=.True.
     endif
   endif
+end function point_in_interval
 
-  ! Assign values to quadrants
-  if (Key_quadrant .eq. 1) then
-    Area_Q1=Area_key_quadrant
-    Area_Q2=Area_Upper-Area_Q1
-    Area_Q4=Area_Right-Area_Q1
-    !Area_Q3=Area_Left-Area_Q2 ! These lines have been changes so that the sum of the 4 quadrants exactly matches the triangle area.
-    Area_Q3=Area_triangle-(Area_Q1+Area_Q2+Area_Q4)
-  elseif (Key_quadrant .eq. 2) then
-    Area_Q2=Area_key_quadrant
-    Area_Q1=Area_Upper-Area_Q2
-    Area_Q4=Area_Right-Area_Q1
-    !Area_Q3=Area_Left-Area_Q2
-    Area_Q3=Area_triangle-(Area_Q1+Area_Q2+Area_Q4)
-  elseif (Key_quadrant==3) then
-    Area_Q3=Area_key_quadrant
-    Area_Q2=Area_Left-Area_Q3
-    Area_Q1=Area_Upper-Area_Q2
-    !Area_Q4=Area_Right-Area_Q1
-    Area_Q4=Area_triangle-(Area_Q1+Area_Q2+Area_Q3)
-  elseif (Key_quadrant==4) then
-    Area_Q4=Area_key_quadrant
-    Area_Q1=Area_Right-Area_Q4
-    Area_Q2=Area_Upper-Area_Q1
-    !Area_Q3=Area_Left-Area_Q2
-    Area_Q3=Area_triangle-(Area_Q1+Area_Q2+Area_Q4)
+!> Returns true if point q is on a line through points A and B
+logical function point_is_on_the_line(Ax, Ay, Bx, By, qx, qy)
+  ! Arguments
+  real, intent(in) :: Ax !< x-position of point A
+  real, intent(in) :: Ay !< y-position of point A
+  real, intent(in) :: Bx !< x-position of point B
+  real, intent(in) :: By !< y-position of point B
+  real, intent(in) :: qx !< x-position of point q
+  real, intent(in) :: qy !< y-position of point q
+  ! Local variables
+  real :: tol, dxc,dyc,dxl,dyl,cross
+  !tol=1.e-12
+  tol=0.0
+  dxc = qx - Ax
+  dyc = qy - Ay
+  dxl = Bx - Ax
+  dyl = By - Ay
+  cross = dxc * dyl - dyc * dxl
+  if (abs(cross)<=tol) then
+    point_is_on_the_line=.True.
   else
-    call error_mesg('KID, iceberg_run', 'Logical error inside triangle into four quadrants. Should not get here.', FATAL)
+   point_is_on_the_line=.False.
   endif
+end function point_is_on_the_line
 
-  Area_Q1=max(Area_Q1,0.)
-  Area_Q2=max(Area_Q2,0.)
-  Area_Q3=max(Area_Q3,0.)
-  Area_Q4=max(Area_Q4,0.)
+!> Returns True if a point q is inside a triangle ABC
+!!
+!! This function decides whether a point (qx,qy) is inside the triangle ABC.
+!! There is also the option to include the boundary of the triangle.
+logical function point_in_triangle(Ax, Ay, Bx, By, Cx, Cy, qx, qy)
+  ! Arguments
+  real, intent(in) :: Ax !< x-position of corner A
+  real, intent(in) :: Ay !< y-position of corner A
+  real, intent(in) :: Bx !< x-position of corner B
+  real, intent(in) :: By !< y-position of corner B
+  real, intent(in) :: Cx !< x-position of corner C
+  real, intent(in) :: Cy !< y-position of corner C
+  real, intent(in) :: qx !< x-position of point q
+  real, intent(in) :: qy !< y-position of point q
+  ! Local variables
+  real :: l0,l1,l2,p0,p1,p2
+  real :: v0x,v1x,v2x,v0y,v1y,v2y,dot00,dot01,dot02,dot11,dot12
+
+  point_in_triangle = .False.
+  if ((Ax==qx .and. Ay==qy) .or. (Bx==qx .and. By==qy) .or. (Cx==qx .and. Cy==qy)) then ! Exclude the pathelogical case
+      point_in_triangle = .False.
+  else
+    if (((point_is_on_the_line(Ax,Ay,Bx,By,qx,qy) .or. (point_is_on_the_line(Ax,Ay,Cx,Cy,qx,qy))) .or. (point_is_on_the_line(Bx,By,Cx,Cy,qx,qy)))) then
+      point_in_triangle = .False.
+    else
+      ! Compute point in triangle using Barycentric coordinates (the same as sum_sign_dot_prod routines)
+      l0=(qx-Ax)*(By-Ay)-(qy-Ay)*(Bx-Ax)
+      l1=(qx-Bx)*(Cy-By)-(qy-By)*(Cx-Bx)
+      l2=(qx-Cx)*(Ay-Cy)-(qy-Cy)*(Ax-Cx)
 
+      p0=sign(1., l0); if (l0==0.)  p0=0.
+      p1=sign(1., l1); if (l1==0.)  p1=0.
+      p2=sign(1., l2); if (l2==0.)  p2=0.
 
-  Error=abs(Area_Q1+Area_Q2+Area_Q3+Area_Q4-Area_triangle)
-  if (Error>tol) then
-    call error_mesg('KID, triangle spreading', 'Triangle not evaluated accurately!!', WARNING)
-    !if (mpp_pe().eq.mpp_root_pe()) then
-    if (mpp_pe().eq. 20) then
-      write(stderrunit,*) 'KID, Triangle corners:',Ax,Ay,Bx,By,Cx,Cy
-      write(stderrunit,*) 'KID, Triangle, Full Area', Area_Q1+ Area_Q2+ Area_Q3+ Area_Q4
-      write(stderrunit,*) 'KID, Triangle, Areas', Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
-      write(stderrunit,*) 'KID, Triangle, Areas', Error
-      write(stderrunit,*) 'KID, Key quadrant',Key_quadrant,Area_key_quadrant
-      write(stderrunit,*) 'KID, point in triangle',(point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.))
-      write(stderrunit,*) 'KID, halves',Area_Upper,Area_Lower,Area_Right,Area_Left
+      if ( (abs(p0)+abs(p2))+(abs(p1)) == abs((p0+p2)+(p1)) )  point_in_triangle = .True.
     endif
   endif
+end function point_in_triangle
 
-end subroutine Triangle_divided_into_four_quadrants
-
-!> Rotates a point clockwise about origin and then translates by x0,y0
-subroutine rotate_and_translate(px, py, theta, x0, y0)
+!> Calculates the two areas of a triangle divided by an axis line
+!!
+!! This function calculates the area of a triangle on opposite sides of an axis when the
+!! triangle is split with two points on one side, and one point on the other.
+!! In this function, A is the point on one side of the axis, and B,C are on the opposite sides.
+!! \todo You should change this name a little, so that it not similar the other routine.
+subroutine Area_of_triangle_across_axes(Ax, Ay, Bx, By, Cx, Cy, axis1, Area_positive, Area_negative)
   ! Arguments
-  real, intent(in) :: x0 !< x-direction shift
-  real, intent(in) :: y0 !< y-direction shift
-  real, intent(in) :: theta !< Angle to rotate (degrees)
-  real, intent(inout) :: px !< x-coordinate of point
-  real, intent(inout) :: py !< y-coordinate of point
+  real, intent(in) :: Ax !< x-position of corner A
+  real, intent(in) :: Ay !< y-position of corner A
+  real, intent(in) :: Bx !< x-position of corner B
+  real, intent(in) :: By !< y-position of corner B
+  real, intent(in) :: Cx !< x-position of corner C
+  real, intent(in) :: Cy !< y-position of corner C
+  character, intent(in) :: axis1 !< Either 'x' or 'y'
+  real, intent(out) :: Area_positive !< Area on negative side of axis line
+  real, intent(out) :: Area_negative !< Area on positive side of axis line
   ! Local variables
-  real :: px_temp,py_temp
+  real :: pABx, pABy, pACx, pACy, A0
+  real :: A_half_triangle, A_triangle
 
-  ! Rotation
-  px_temp = ( cos(theta*pi/180)*px) + (sin(theta*pi/180)*py)
-  py_temp = (-sin(theta*pi/180)*px) + (cos(theta*pi/180)*py)
+  A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy)
 
-  ! Translation
-  px= px_temp + x0
-  py= py_temp + y0
-end subroutine rotate_and_translate
+  call intercept_of_a_line(Ax,Ay,Bx,By,axis1,pABx, pABy)
+  call intercept_of_a_line(Ax,Ay,Cx,Cy,axis1,pACx, pACy)
 
-!> Areas of a hexagon divided into quadrants
+  if (axis1=='x')  A0=Ay; !Value used for if statements (deciding up/down vs left/right)
+  if (axis1=='y')  A0=Ax; !Value used for if statements (deciding up/down vs left/right)
+
+  A_half_triangle=Area_of_triangle(Ax,Ay,pABx,pABy,pACx,pACy)
+  if (A0>=0.) then
+    Area_positive= A_half_triangle
+    Area_negative= A_triangle-A_half_triangle
+  else
+    Area_positive= A_triangle-A_half_triangle
+    Area_negative= A_half_triangle
+  endif
+
+end subroutine Area_of_triangle_across_axes
+
+!> Returns the axis intercept of a line AB
 !!
-!! This subroutine divides a regular hexagon centered at x0,y0 with apothem H, and orientation theta into its intersection with the 4 quadrants.
-!! Theta=0 assumes that the apothem points upwards.
-!! Routine works by finding the corners of the 6 triangles, and then finding the intersection of each of these with each quadrant.
-!! \todo (also the rotation is not working yet)
-subroutine Hexagon_into_quadrants_using_triangles(x0, y0, H, theta, Area_hex ,Area_Q1, Area_Q2, Area_Q3, Area_Q4)
+!! This routine returns the position (x0,y0) at which a line AB intercepts the x or y axis.
+!! The value No_intercept_val is returned when the line does not intercept the axis.
+subroutine intercept_of_a_line(Ax, Ay, Bx, By, axes1, x0, y0)
   ! Arguments
-  real, intent(in) :: x0 !< x-coordinate of center of hexagon
-  real, intent(in) :: y0 !< y-coordinate of center of hexagon
-  real, intent(in) :: H !< Apothem (inner radius of hexagon)
-  real, intent(in) :: theta !< Orientation angle of hexagon
-  real, intent(out) :: Area_hex !< Area of hexagon
-  real, intent(out) :: Area_Q1 !< Are in quadrant 1
-  real, intent(out) :: Area_Q2 !< Are in quadrant 2
-  real, intent(out) :: Area_Q3 !< Are in quadrant 2
-  real, intent(out) :: Area_Q4 !< Are in quadrant 4
+  real, intent(in) :: Ax !< x-position of corner A
+  real, intent(in) :: Ay !< y-position of corner A
+  real, intent(in) :: Bx !< x-position of corner B
+  real, intent(in) :: By !< y-position of corner B
+  character, intent(in) :: axes1 !< Either 'x' or 'y'
+  real, intent(out) :: x0 !< x-position of intercept
+  real, intent(out) :: y0 !< y-position of intercept
   ! Local variables
-  real :: C1x, C2x, C3x, C4x, C5x, C6x
-  real :: C1y, C2y, C3y, C4y, C5y, C6y
-  real :: T12_Area, T12_Q1, T12_Q2, T12_Q3, T12_Q4
-  real :: T23_Area, T23_Q1, T23_Q2, T23_Q3, T23_Q4
-  real :: T34_Area, T34_Q1, T34_Q2, T34_Q3, T34_Q4
-  real :: T45_Area, T45_Q1, T45_Q2, T45_Q3, T45_Q4
-  real :: T56_Area, T56_Q1, T56_Q2, T56_Q3, T56_Q4
-  real :: T61_Area, T61_Q1, T61_Q2, T61_Q3, T61_Q4
-  real :: S, exact_hex_area, Error
-  real :: tol
-  integer :: stderrunit
-
-  ! Get the stderr unit number
-  stderrunit = stderr()
-  tol=1.e-10
+  real :: No_intercept_val ! Huge value used to make sure that the intercept is outside the triangle in the parallel case.
 
-  ! Length of side of Hexagon
-  S=(2/sqrt(3.))*H
+  No_intercept_val=100000000000. ! Huge value used to make sure that the intercept is outside the triangle in the parallel case.
+  x0=No_intercept_val
+  y0=No_intercept_val
 
-  ! Finding positions of corners
-  C1x=S           ; C1y=0.  !Corner 1 (right)
-  C2x=H/sqrt(3.)  ; C2y=H;  !Corner 2 (top right)
-  C3x=-H/sqrt(3.) ; C3y=H;  !Corner 3 (top left)
-  C4x=-S          ; C4y=0.; !Corner 4 (left)
-  C5x=-H/sqrt(3.) ; C5y=-H; !Corner 5 (bottom left)
-  C6x=H/sqrt(3.)  ; C6y=-H; !Corner 6 (bottom right)
-
-  ! Finding positions of corners
-  call rotate_and_translate(C1x,C1y,theta,x0,y0)
-  call rotate_and_translate(C2x,C2y,theta,x0,y0)
-  call rotate_and_translate(C3x,C3y,theta,x0,y0)
-  call rotate_and_translate(C4x,C4y,theta,x0,y0)
-  call rotate_and_translate(C5x,C5y,theta,x0,y0)
-  call rotate_and_translate(C6x,C6y,theta,x0,y0)
-
-  ! Area of Hexagon is the sum of the triangles
-  call Triangle_divided_into_four_quadrants(x0,y0,C1x,C1y,C2x,C2y,T12_Area,T12_Q1,T12_Q2,T12_Q3,T12_Q4); !Triangle 012
-  call Triangle_divided_into_four_quadrants(x0,y0,C2x,C2y,C3x,C3y,T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4); !Triangle 023
-  call Triangle_divided_into_four_quadrants(x0,y0,C3x,C3y,C4x,C4y,T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4); !Triangle 034
-  call Triangle_divided_into_four_quadrants(x0,y0,C4x,C4y,C5x,C5y,T45_Area,T45_Q1,T45_Q2,T45_Q3,T45_Q4); !Triangle 045
-  call Triangle_divided_into_four_quadrants(x0,y0,C5x,C5y,C6x,C6y,T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4); !Triangle 056
-  call Triangle_divided_into_four_quadrants(x0,y0,C6x,C6y,C1x,C1y,T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4); !Triangle 061
-
-  ! Summing up the triangles
-  Area_hex=T12_Area+T23_Area+T34_Area+T45_Area+T56_Area+T61_Area
-  Area_Q1=T12_Q1+T23_Q1+T34_Q1+T45_Q1+T56_Q1+T61_Q1
-  Area_Q2=T12_Q2+T23_Q2+T34_Q2+T45_Q2+T56_Q2+T61_Q2
-  Area_Q3=T12_Q3+T23_Q3+T34_Q3+T45_Q3+T56_Q3+T61_Q3
-  Area_Q4=T12_Q4+T23_Q4+T34_Q4+T45_Q4+T56_Q4+T61_Q4
-
-  Area_Q1=max(Area_Q1,0.)
-  Area_Q2=max(Area_Q2,0.)
-  Area_Q3=max(Area_Q3,0.)
-  Area_Q4=max(Area_Q4,0.)
-
-  Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
-  if ((abs(Error)>tol))then
-    if (mpp_pe().eq.mpp_root_pe()) then
-      call error_mesg('KID, hexagonal spreading', 'Hexagon error is large!!', WARNING)
-      write(stderrunit,*) 'KID, hex error, H,x0,y0, Error', H, x0 , y0, Error
-      write(stderrunit,*) 'KID, hex error, Areas',Area_hex, (Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
-      write(stderrunit,*) 'KID, Triangle1',C1x,C1y,C2x,C2y,T12_Area,T12_Q1,T12_Q2,T12_Q3,T12_Q4,(T12_Q1+T12_Q2+T12_Q3+T12_Q4-T12_Area)
-      write(stderrunit,*) 'KID, Triangle2',C2x,C2y,C3x,C3y,T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4,(T23_Q1+T23_Q2+T23_Q3+T23_Q4-T23_Area)
-      write(stderrunit,*) 'KID, Triangle3',C3x,C3y,C4x,C4y,T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4,(T34_Q1+T34_Q2+T34_Q3+T34_Q4-T34_Area)
-      write(stderrunit,*) 'KID, Triangle4',C4x,C4y,C5x,C5y,T45_Area,T45_Q1,T45_Q2,T45_Q3,T45_Q4,(T45_Q1+T45_Q2+T45_Q3+T45_Q4-T45_Area)
-      write(stderrunit,*) 'KID, Triangle5',C5x,C5y,C6x,C6y,T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4,(T56_Q1+T56_Q2+T56_Q3+T56_Q4-T56_Area)
-      write(stderrunit,*) 'KID, Triangle6',C6x,C6y,C1x,C1y,T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4,(T61_Q1+T61_Q2+T61_Q3+T61_Q4-T61_Area)
+  if (axes1=='x') then ! x intercept
+    if (Ay.ne.By) then
+      x0=Ax -(((Ax-Bx)/(Ay-By))*Ay)
+      y0=0.
     endif
   endif
 
-  exact_hex_area=((3.*sqrt(3.)/2)*(S*S))
-  if (abs(Area_hex-exact_hex_area)>tol) then
-    call error_mesg('KID, hexagonal spreading', 'Hexagon not evaluated accurately!!', WARNING)
-    if (mpp_pe().eq.mpp_root_pe()) then
-      write(stderrunit,*) 'KID, hex calculations, H,x0,y0', H, x0 , y0
-      write(stderrunit,*) 'KID, hex calculations, Areas',Area_hex, (Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
+  if (axes1=='y') then ! y intercept
+    if (Ax.ne.Bx) then
+      x0=0.
+      y0=-(((Ay-By)/(Ax-Bx))*Ax)+Ay
     endif
   endif
+end subroutine intercept_of_a_line
 
-  ! Adjust Areas so that the error is zero by subtracting the error from the largest sector.
-   if  (((Area_Q1>=Area_Q2) .and. (Area_Q1>=Area_Q3)) .and. (Area_Q1>=Area_Q4)) then
-     Area_Q1=Area_Q1+Error
-   elseif  (((Area_Q2>=Area_Q1) .and. (Area_Q2>=Area_Q3)) .and. (Area_Q2>=Area_Q4)) then
-     Area_Q2=Area_Q2+Error
-   elseif  (((Area_Q3>=Area_Q1) .and. (Area_Q3>=Area_Q2)) .and. (Area_Q3>=Area_Q4)) then
-     Area_Q3=Area_Q3+Error
-   elseif  (((Area_Q4>=Area_Q1) .and. (Area_Q4>=Area_Q2)) .and. (Area_Q4>=Area_Q3)) then
-     Area_Q4=Area_Q4+Error
-   else
-     call error_mesg('KID, hexagonal spreading', 'Error in hexagon is larger than any quadrant!!', WARNING)
-     if (mpp_pe().eq.mpp_root_pe()) then
-      write(stderrunit,*) 'KID, hex quadrants, H,x0,y0', H, x0 , y0, Error
-      write(stderrunit,*) 'KID, hex quadrants, Areas',Area_hex, (Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
-     endif
-   endif
-
- end subroutine Hexagon_into_quadrants_using_triangles
-
-subroutine interp_gridded_fields_to_bergs(bergs)
+!> Calculates the area of a triangle on either side of an axis, if any.
+!!
+!! This routine gives you the area of a triangle on opposite sides of the axis specified.
+!! It also takes care of the special case where the triangle is totally on one side.
+!! This routine calls Area_of_triangle_across_axes to calculate the areas when the triangles are split.
+subroutine divding_triangle_across_axes(Ax, Ay, Bx, By, Cx, Cy, axes1, Area_positive, Area_negative)
   ! Arguments
-  type(icebergs), pointer :: bergs !< Container for all types and memory
+  real, intent(in) :: Ax !< x-position of corner A
+  real, intent(in) :: Ay !< y-position of corner A
+  real, intent(in) :: Bx !< x-position of corner B
+  real, intent(in) :: By !< y-position of corner B
+  real, intent(in) :: Cx !< x-position of corner C
+  real, intent(in) :: Cy !< y-position of corner C
+  character, intent(in) :: axes1 !< Either 'x' or 'y'
+  real, intent(out) :: Area_positive !< Area on negative side of axis line
+  real, intent(out) :: Area_negative !< Area on positive side of axis line
   ! Local variables
-  type(icebergs_gridded), pointer :: grd
-  type(iceberg), pointer :: berg
-  integer :: grdj,grdi
-  type(randomNumberStream) :: rns ! Random numbers for stochastic tidal parameterization
-  real :: rx,ry
+  real :: A0,B0,C0
+  real A_triangle
 
-  ! For convenience
-  grd=>bergs%grd
-  rx=0.0; ry=0.0;
+  if (axes1=='x') then ! Use the y-coordinates for if statements to see which side of the line you are on
+    A0=Ay
+    B0=By
+    C0=Cy
+  endif
+  if (axes1=='y') then ! Use the y-coordinates for if statements to see which side of the line you are on
+    A0=Ax
+    B0=Bx
+    C0=Cx
+  endif
 
-  do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec ! just for computational domain
-    berg=>bergs%list(grdi,grdj)%first
-    if (associated(berg) .and. grd%tidal_drift>0.) then
-      ! Seed random numbers based on space and "time"
-      rns = initializeRandomNumberStream( grdi + 10000*grdj + &
-                                          int( 16384.*abs( sin(262144.*grd%ssh(grdi,grdj)) ) ) )
-    endif
-    do while (associated(berg)) ! loop over all bergs
-      if (berg%halo_berg.lt.0.5) then
-        if (grd%tidal_drift>0.) then
-          call getRandomNumbers(rns, rx)
-          rx = 2.*rx - 1.
-          call getRandomNumbers(rns, ry)
-          ry = 2.*ry - 1.
-        endif
-        call interp_flds(grd, berg%ine, berg%jne, berg%xi, berg%yj, rx, ry, berg%uo, berg%vo, &
-          berg%ui, berg%vi, berg%ua, berg%va, berg%ssh_x, berg%ssh_y, berg%sst, berg%sss, berg%cn, berg%hi)
+  A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy)
+  if ((B0*C0)>0.) then ! B and C are on the same side  (and non-zero)
+    if ((A0*B0).ge.0.) then ! all three on the same side (if it equals zero, then A0=0 and the others are not)
+      if ((A0>0.)  .or.  ((A0==0.) .and.  (B0>0.))) then
+        Area_positive= A_triangle
+        Area_negative= 0.
+      else
+        Area_positive= 0.
+        Area_negative= A_triangle
       endif
-      berg=>berg%next
-    enddo
-  enddo;enddo
+    else  !A is on the opposite side to B and C
+      call Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1,Area_positive, Area_negative)
+    endif
 
-end subroutine interp_gridded_fields_to_bergs
+  elseif ((B0*C0)<0.) then !B and C are on the opposite sides
+    if ((A0*B0).ge. 0.) then !C is all alone
+      call Area_of_triangle_across_axes(Cx,Cy,Bx,By,Ax,Ay,axes1,Area_positive, Area_negative)
+    else !B is all alone
+      call Area_of_triangle_across_axes(Bx,By,Cx,Cy,Ax,Ay,axes1,Area_positive, Area_negative)
+    endif
+
+  else  !This is the case when either B or C is equal to zero (or both), A0 could be zero too.
+    if (((A0.eq.0.) .and. (B0.eq.0.)) .and. (C0.eq.0.)) then
+      Area_positive= 0.
+      Area_negative= 0.
+    elseif ((A0*B0<0.)  .or.  (A0*C0<0.)) then    !A, B are on opposite sides, and C is zero.  OR  A, C are on opposite sides, and B is zero.
+      call Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1,Area_positive, Area_negative)
+    elseif (((A0*B0>0.) .or. (A0*C0>0.)) .or. (((abs(A0)>0.) .and. (B0==0.)) .and. (C0==0.))) then
+      if (A0>0.) then
+        Area_positive= A_triangle
+        Area_negative= 0.
+      else
+        Area_positive= 0.
+        Area_negative= A_triangle
+      endif
 
+    elseif (A0.eq. 0.) then   !(one of B,C is zero too)
+      if ((B0>0.) .or. (C0>0.)) then
+        Area_positive= A_triangle
+        Area_negative= 0.
+      elseif ((B0<0.) .or. (C0<0.)) then
+        Area_positive= 0.
+        Area_negative= A_triangle
+      else
+        call error_mesg('KID, iceberg_run', 'Logical error inside triangle dividing routine', FATAL)
+      endif
+    else
+      call error_mesg('KID, iceberg_run', 'Another logical error inside triangle dividing routine', FATAL)
+    endif
+  endif
+end subroutine divding_triangle_across_axes
 
-subroutine interp_flds(grd, i, j, xi, yj, rx, ry, uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, sss, cn, hi)
+!> Areas of a triangle divided into quadrants
+!!
+!! This routine takes a triangle, and finds the intersection with the four quadrants.
+subroutine Triangle_divided_into_four_quadrants(Ax, Ay, Bx, By, Cx, Cy, Area_triangle, Area_Q1, Area_Q2 ,Area_Q3 ,Area_Q4)
   ! Arguments
-  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
-  integer, intent(in) :: i !< i-index of cell in which to interpolate
-  integer, intent(in) :: j !< j-index of cell in which to interpolate
-  real, intent(in) :: xi !< Non-dimensional x-position within cell to interpolate to
-  real, intent(in) :: yj !< Non-dimensional y-position within cell to interpolate to
-  real, intent(in) :: rx !< Random number between -1 and 1 for use in x-component of stochastic tidal parameterization
-  real, intent(in) :: ry !< Random number between -1 and 1 for use in y-component of stochastic tidal parameterization
-  real, intent(out) :: uo !< Ocean zonal velocity at point xi,yj (m/s)
-  real, intent(out) :: vo !< Ocean meridional velocity at point xi,yj (m/s)
-  real, intent(out) :: ui !< Ice zonal velocity at point xi,yj (m/s)
-  real, intent(out) :: vi !< Ice meridional velocity at point xi,yj (m/s)
-  real, intent(out) :: ua !< Atmospheric zonal velocity at point xi,yj (m/s)
-  real, intent(out) :: va !< Atmospheric meridional velocity at point xi,yj (m/s)
-  real, intent(out) :: ssh_x !< Zonal slope of sea-surface height (nondim)
-  real, intent(out) :: ssh_y !< Meridional slope of sea-surface height (nondim)
-  real, intent(out) :: sst !< Sea-surface temperature (C)
-  real, intent(out) :: sss !< Sea-surface salinity (1e-3)
-  real, intent(out) :: cn !< Sea-ice concentration (nondim)
-  real, intent(out) :: hi !< Sea-ice thickness (m)
+  real, intent(in) :: Ax !< x-position of corner A
+  real, intent(in) :: Ay !< y-position of corner A
+  real, intent(in) :: Bx !< x-position of corner B
+  real, intent(in) :: By !< y-position of corner B
+  real, intent(in) :: Cx !< x-position of corner C
+  real, intent(in) :: Cy !< y-position of corner C
+  real, intent(out) :: Area_triangle !< Are of triangle
+  real, intent(out) :: Area_Q1 !< Are in quadrant 1
+  real, intent(out) :: Area_Q2 !< Are in quadrant 2
+  real, intent(out) :: Area_Q3 !< Are in quadrant 2
+  real, intent(out) :: Area_Q4 !< Are in quadrant 4
   ! Local variables
-  real :: cos_rot, sin_rot, du, dv
-#ifdef USE_OLD_SSH_GRADIENT
-  real :: dxm, dx0, dxp
-  real, parameter :: ssh_coast=0.00
-#endif
-  real :: hxm, hxp
+  real :: Area_Upper, Area_Lower, Area_Right, Area_Left
+  real :: px, py , qx , qy
+  real :: Area_key_quadrant,Error
+  real :: tol
+  integer :: Key_quadrant
+  integer ::sig_fig
   integer :: stderrunit
-  integer :: ii, jj
 
   ! Get the stderr unit number
   stderrunit = stderr()
+  tol=1.e-10
 
-  cos_rot=bilin(grd, grd%cos, i, j, xi, yj) ! If true, uses the inverted bilin function
-  sin_rot=bilin(grd, grd%sin, i, j, xi, yj)
-
-  uo=bilin(grd, grd%uo, i, j, xi, yj)
-  vo=bilin(grd, grd%vo, i, j, xi, yj)
-  ui=bilin(grd, grd%ui, i, j, xi, yj)
-  vi=bilin(grd, grd%vi, i, j, xi, yj)
-  ua=bilin(grd, grd%ua, i, j, xi, yj)
-  va=bilin(grd, grd%va, i, j, xi, yj)
+  Area_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy)
 
-  ! The following block accelerates a berg away from coastlines towards open water
-  ! which is a bias needed to avoid piling up in coarse resolution models
-  if (grd%coastal_drift > 0.) then
-    ! If a cell to the west is land (msk=0), accelerate to the east, and vice versa.
-    uo = uo + grd%coastal_drift * ( grd%msk(i+1,j) - grd%msk(i-1,j) ) * grd%msk(i,j)
-    ui = ui + grd%coastal_drift * ( grd%msk(i+1,j) - grd%msk(i-1,j) ) * grd%msk(i,j)
-    ! If a cell to the south is land (msk=0), accelerate to the north, and vice versa.
-    vo = vo + grd%coastal_drift * ( grd%msk(i,j+1) - grd%msk(i,j-1) ) * grd%msk(i,j)
-    vi = vi + grd%coastal_drift * ( grd%msk(i,j+1) - grd%msk(i,j-1) ) * grd%msk(i,j)
-  endif
+  ! Calculating area across axes
+  call divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,'x',Area_Upper ,Area_Lower)
+  call divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,'y',Area_Right ,Area_Left)
 
-  ! Stochastic acceleration to represent unresolved tidal and wave motions.
-  ! Note: this scheme should account for the time-step and have memory!
-  if (grd%tidal_drift > 0.) then
-    ! The acceleration is modulated to not move particles towards land cells.
-    du = ( min(0., rx) * grd%msk(i-1,j) + max(0., rx) * grd%msk(i+1,j) ) &
-         * ( 1. - grd%msk(i,j-1) * grd%msk(i,j+1) ) ! Do not apply in open ocean
-    dv = ( min(0., ry) * grd%msk(i,j-1) + max(0., ry) * grd%msk(i,j+1) ) &
-         * ( 1. - grd%msk(i-1,j) * grd%msk(i+1,j) ) ! Do not apply in open ocean
-    du = du * grd%tidal_drift * grd%msk(i,j)
-    dv = dv * grd%tidal_drift * grd%msk(i,j)
-    uo = uo + du
-    ui = ui + du
-    vo = vo + dv
-    vi = vi + dv
-  endif
-
-  if (ua.ne.ua) then
-    if (mpp_pe().eq.9) then
-      write(stderrunit,'(a3,32i7)') 'ua',(ii,ii=grd%isd,grd%ied)
-      do jj=grd%jed,grd%jsd,-1
-        write(stderrunit,'(i3,32f7.1)') jj,(grd%ua(ii,jj),ii=grd%isd,grd%ied)
-      enddo
-  !   write(stderrunit,'(a3,32i7)') 'Lat',(i,i=grd%isd,grd%ied)
-  !   do j=grd%jed,grd%jsd,-1
-  !     write(stderrunit,'(i3,32f7.1)') j,(grd%lat(i,j),i=grd%isd,grd%ied)
-  !   enddo
-  !   write(stderrunit,'(a3,32i7)') 'Msk',(i,i=grd%isd,grd%ied)
-  !   do j=grd%jed,grd%jsd,-1
-  !     write(stderrunit,'(i3,32f7.1)') j,(grd%msk(i,j),i=grd%isd,grd%ied)
-  !   enddo
-  ! endif
-      call error_mesg('KID, interp fields', 'ua is NaNs', FATAL)
+  ! Decide if the origin is in the triangle. If so, then you have to divide the area 4 ways
+  ! This is done by finding a quadrant where the intersection between the triangle and quadrant forms a new triangle
+  ! (This occurs when on of the sides of the triangle  intersects both the x and y axis)
+  if (point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.)) then
+    ! Find a line in the triangle that cuts both axes in/on the triangle
+    call intercept_of_a_line(Ax,Ay,Bx,By,'x',px,py); !x_intercept
+    call intercept_of_a_line(Ax,Ay,Bx,By,'y',qx,qy); !y_intercept
+    ! Note that the 1. here means that we include points on the boundary of the triangle.
+    if (.not.((point_in_interval(Ax,Ay,Bx,By,px,py)) .and. (point_in_interval(Ax,Ay,Bx,By,qx,qy)))) then
+      call intercept_of_a_line(Ax,Ay,Cx,Cy,'x',px,py); !x_intercept
+      call intercept_of_a_line(Ax,Ay,Cx,Cy,'y',qx,qy); !y_intercept
+      if (.not.((point_in_interval(Ax,Ay,Cx,Cy,px,py)) .and. (point_in_interval(Ax,Ay,Cx,Cy,qx,qy)))) then
+        call intercept_of_a_line(Bx,By,Cx,Cy,'x',px,py); !x_intercept
+        call intercept_of_a_line(Bx,By,Cx,Cy,'y',qx,qy); !y_intercept
+        if (.not.((point_in_interval(Bx,By,Cx,Cy,px,py)) .and. (point_in_interval(Bx,By,Cx,Cy,qx,qy)))) then
+          ! You should not get here, but there might be some bugs in the code to do with points exactly falling on axes.
+          !if (mpp_pe().eq.12) then
+            write(stderrunit,*) 'KID,corners', Ax,Ay,Bx,By,Cx,Cy
+          !endif
+          call error_mesg('KID, iceberg_run', 'Something went wrong with Triangle_divide_into_four_quadrants', FATAL)
+        endif
+      endif
     endif
-  endif
 
-  ! These fields are cell centered (A-grid) and would
-  ! best be interpolated using PLM. For now we use PCM!
-  sst=grd%sst(i,j) ! A-grid
-  sss=grd%sss(i,j) ! A-grid
-  cn=grd%cn(i,j) ! A-grid
-  hi=grd%hi(i,j) ! A-grid
+    ! Assigning quadrants. Key_quadrant is the quadrant with the baby triangle in it.
+    Area_key_quadrant=Area_of_triangle(px,py,qx,qy,0.,0.)
+    if ((px.ge. 0.) .and. (qy.ge. 0.)) then  !First quadrant
+      Key_quadrant=1
+    elseif ((px.lt.0.) .and. (qy.ge. 0.)) then  !Second quadrant
+      Key_quadrant=2
+    elseif ((px.lt. 0.) .and. (qy.lt. 0.)) then !Third quadrant
+      Key_quadrant=3
+    elseif ((px.ge. 0.) .and. (qy.lt. 0.)) then !Forth quadrant
+      Key_quadrant=4
+    else  !
+      call error_mesg('KID, iceberg_run', 'None of the quadrants are Key', WARNING)
+      write(stderrunit,*) 'KID, Triangle, px,qy', px,qy
+    endif
 
-  ! Estimate SSH gradient in X direction
-#ifdef USE_OLD_SSH_GRADIENT
-  dxp=0.5*(grd%dx(i+1,j)+grd%dx(i+1,j-1))
-  dx0=0.5*(grd%dx(i,j)+grd%dx(i,j-1))
-  dxm=0.5*(grd%dx(i-1,j)+grd%dx(i-1,j-1))
-  hxm=2.*(grd%ssh(i,j)-grd%ssh(i-1,j))/(dx0+dxm)*grd%msk(i-1,j) &
-        +(-ssh_coast)/(dx0+dxm)*(1.-grd%msk(i-1,j)) ! force to drive bergs away from coasts
-  hxp=2.*(grd%ssh(i+1,j)-grd%ssh(i,j))/(dx0+dxp)*grd%msk(i+1,j) &
-        +(+ssh_coast)/(dx0+dxp)*(1.-grd%msk(i+1,j)) ! force to drive bergs away from coasts
-#else
-  if (yj>=0.5) then
-    hxp=(yj-0.5)*ddx_ssh(grd,i  ,j+1)+(1.5-yj)*ddx_ssh(grd,i  ,j  )
-    hxm=(yj-0.5)*ddx_ssh(grd,i-1,j+1)+(1.5-yj)*ddx_ssh(grd,i-1,j  )
-  else
-    hxp=(yj+0.5)*ddx_ssh(grd,i  ,j  )+(0.5-yj)*ddx_ssh(grd,i  ,j-1)
-    hxm=(yj+0.5)*ddx_ssh(grd,i-1,j  )+(0.5-yj)*ddx_ssh(grd,i-1,j-1)
+  else ! At least one quadrant is empty, and this can be used to find the areas in the other quadrant.  Assigning quadrants. Key_quadrant is the empty quadrant.
+    Area_key_quadrant=0
+    if      ( (.not. ((((Ax>0.) .and. (Ay>0.)) .or. ((Bx>0.) .and. (By> 0.))) .or. ((Cx>0.) .and. (Cy> 0.)))) .and. ((Area_Upper+Area_Right).le.Area_triangle) ) then
+      ! No points land in this quadrant and triangle does not cross the quadrant
+      Key_quadrant=1
+    elseif  ( (.not. ((((Ax<0.) .and. (Ay>0)) .or. ((Bx<0.) .and. (By>0.))) .or. ((Cx<0.) .and. (Cy>0.)))) .and. ((Area_Upper+Area_Left).le. Area_triangle) ) then
+      Key_quadrant=2
+    elseif  ( (.not. ((((Ax<0.) .and. (Ay<0.)) .or. ((Bx<0.) .and. (By< 0.))) .or. ((Cx<0.) .and. (Cy< 0.)))) .and. ((Area_Lower+Area_Left) .le.Area_triangle) ) then
+      Key_quadrant=3
+    else
+      Key_quadrant=4
+    endif
   endif
-#endif
-  ! ssh_x is at the u-point on a C-grid
-  ssh_x=xi*hxp+(1.-xi)*hxm
 
-  ! Estimate SSH gradient in Y direction
-#ifdef USE_OLD_SSH_GRADIENT
-  dxp=0.5*(grd%dy(i,j+1)+grd%dy(i-1,j+1))
-  dx0=0.5*(grd%dy(i,j)+grd%dy(i-1,j))
-  dxm=0.5*(grd%dy(i,j-1)+grd%dy(i-1,j-1))
-  hxm=2.*(grd%ssh(i,j)-grd%ssh(i,j-1))/(dx0+dxm)*grd%msk(i,j-1) &
-        +(-ssh_coast)/(dx0+dxm)*(1.-grd%msk(i,j-1)) ! force to drive bergs away from coasts
-  hxp=2.*(grd%ssh(i,j+1)-grd%ssh(i,j))/(dx0+dxp)*grd%msk(i,j+1) &
-        +(+ssh_coast)/(dx0+dxp)*(1.-grd%msk(i,j+1)) ! force to drive bergs away from coasts
-#else
-  if (xi>=0.5) then
-    hxp=(xi-0.5)*ddy_ssh(grd,i+1,j  )+(1.5-xi)*ddy_ssh(grd,i  ,j  )
-    hxm=(xi-0.5)*ddy_ssh(grd,i+1,j-1)+(1.5-xi)*ddy_ssh(grd,i  ,j-1)
+  ! Assign values to quadrants
+  if (Key_quadrant .eq. 1) then
+    Area_Q1=Area_key_quadrant
+    Area_Q2=Area_Upper-Area_Q1
+    Area_Q4=Area_Right-Area_Q1
+    !Area_Q3=Area_Left-Area_Q2 ! These lines have been changes so that the sum of the 4 quadrants exactly matches the triangle area.
+    Area_Q3=Area_triangle-(Area_Q1+Area_Q2+Area_Q4)
+  elseif (Key_quadrant .eq. 2) then
+    Area_Q2=Area_key_quadrant
+    Area_Q1=Area_Upper-Area_Q2
+    Area_Q4=Area_Right-Area_Q1
+    !Area_Q3=Area_Left-Area_Q2
+    Area_Q3=Area_triangle-(Area_Q1+Area_Q2+Area_Q4)
+  elseif (Key_quadrant==3) then
+    Area_Q3=Area_key_quadrant
+    Area_Q2=Area_Left-Area_Q3
+    Area_Q1=Area_Upper-Area_Q2
+    !Area_Q4=Area_Right-Area_Q1
+    Area_Q4=Area_triangle-(Area_Q1+Area_Q2+Area_Q3)
+  elseif (Key_quadrant==4) then
+    Area_Q4=Area_key_quadrant
+    Area_Q1=Area_Right-Area_Q4
+    Area_Q2=Area_Upper-Area_Q1
+    !Area_Q3=Area_Left-Area_Q2
+    Area_Q3=Area_triangle-(Area_Q1+Area_Q2+Area_Q4)
   else
-    hxp=(xi+0.5)*ddy_ssh(grd,i  ,j  )+(0.5-xi)*ddy_ssh(grd,i-1,j  )
-    hxm=(xi+0.5)*ddy_ssh(grd,i  ,j-1)+(0.5-xi)*ddy_ssh(grd,i-1,j-1)
+    call error_mesg('KID, iceberg_run', 'Logical error inside triangle into four quadrants. Should not get here.', FATAL)
   endif
-#endif
-  ! ssh_y is at the v-point on a C-grid
-  ssh_y=yj*hxp+(1.-yj)*hxm
-
-  ! Rotate vectors from local grid to lat/lon coordinates
-  call rotate(uo, vo, cos_rot, sin_rot)
-  call rotate(ui, vi, cos_rot, sin_rot)
-  call rotate(ua, va, cos_rot, sin_rot)
-  call rotate(ssh_x, ssh_y, cos_rot, sin_rot)
 
-  !There are some issues with the boundaries ssh gradient calculation in a finite domain. This is a temporary fix
-  if (ssh_x.ne.ssh_x) ssh_x=0.
-  if (ssh_y.ne.ssh_y) ssh_y=0.
+  Area_Q1=max(Area_Q1,0.)
+  Area_Q2=max(Area_Q2,0.)
+  Area_Q3=max(Area_Q3,0.)
+  Area_Q4=max(Area_Q4,0.)
 
-  if (((((uo.ne.uo) .or. (vo.ne.vo)) .or. ((ui.ne.ui) .or. (vi.ne.vi))) .or. &
-       (((ua.ne.ua) .or. (va.ne.va)) .or. ((ssh_x.ne.ssh_x) .or. (ssh_y.ne.ssh_y)))) .or. &
-       (((sst.ne. sst) .or. (sss.ne. sss) .or. (cn.ne.cn)) .or. (hi.ne. hi))) then
-    write(stderrunit,*) 'KID, Error in interpolate: uo,vo,ui,vi',uo, vo, ui, vi
-    write(stderrunit,*) 'KID, Error in interpolate: ua,va,ssh_x,ssh_y', ua, va, ssh_x, ssh_y
-    write(stderrunit,*) 'KID, Error in interpolate: sst,cn,hi', sst, sss, cn, hi, mpp_pe()
-    call error_mesg('KID, interp fields', 'field interpaolations has NaNs', FATAL)
 
+  Error=abs(Area_Q1+Area_Q2+Area_Q3+Area_Q4-Area_triangle)
+  if (Error>tol) then
+    call error_mesg('KID, triangle spreading', 'Triangle not evaluated accurately!!', WARNING)
+    !if (mpp_pe().eq.mpp_root_pe()) then
+    if (mpp_pe().eq. 20) then
+      write(stderrunit,*) 'KID, Triangle corners:',Ax,Ay,Bx,By,Cx,Cy
+      write(stderrunit,*) 'KID, Triangle, Full Area', Area_Q1+ Area_Q2+ Area_Q3+ Area_Q4
+      write(stderrunit,*) 'KID, Triangle, Areas', Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
+      write(stderrunit,*) 'KID, Triangle, Areas', Error
+      write(stderrunit,*) 'KID, Key quadrant',Key_quadrant,Area_key_quadrant
+      write(stderrunit,*) 'KID, point in triangle',(point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.))
+      write(stderrunit,*) 'KID, halves',Area_Upper,Area_Lower,Area_Right,Area_Left
+    endif
   endif
 
-end subroutine interp_flds
-
-!> Returns zonal slope of sea-surface height across the east face of cell i,j
-real function ddx_ssh(grd,i,j)
-  ! Arguments
-  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
-  integer, intent(in) :: i !< i-index of cell
-  integer, intent(in) :: j !< j-index of cell
-  ! Local variables
-  real :: dxp,dx0
-  dxp=0.5*(grd%dx(i+1,j)+grd%dx(i+1,j-1))
-  dx0=0.5*(grd%dx(i,j)+grd%dx(i,j-1))
-  ddx_ssh=2.*(grd%ssh(i+1,j)-grd%ssh(i,j))/(dx0+dxp)*grd%msk(i+1,j)*grd%msk(i,j)
-end function ddx_ssh
-
-!> Returns meridional slope of sea-surface height across the northern face of cell i,j
-real function ddy_ssh(grd,i,j)
-  ! Arguments
-  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
-  integer, intent(in) :: i !< i-index of cell
-  integer, intent(in) :: j !< j-index of cell
-  ! Local variables
-  real :: dyp,dy0
-  dyp=0.5*(grd%dy(i,j+1)+grd%dy(i-1,j+1))
-  dy0=0.5*(grd%dy(i,j)+grd%dy(i-1,j))
-  ddy_ssh=2.*(grd%ssh(i,j+1)-grd%ssh(i,j))/(dy0+dyp)*grd%msk(i,j+1)*grd%msk(i,j)
-end function ddy_ssh
+end subroutine Triangle_divided_into_four_quadrants
 
-! Rotates vector (u,v) using rotation matrix with elements cos_rot and sin_rot
-subroutine rotate(u, v, cos_rot, sin_rot)
+!> Rotates a point clockwise about origin and then translates by x0,y0
+subroutine rotate_and_translate(px, py, theta, x0, y0)
   ! Arguments
-  real, intent(inout) :: u !< x-component of vector
-  real, intent(inout) :: v !< y-component of vector
-  real, intent(in) :: cos_rot !< Cosine of rotation angle
-  real, intent(in) :: sin_rot !< Sine of rotation angle
+  real, intent(in) :: x0 !< x-direction shift
+  real, intent(in) :: y0 !< y-direction shift
+  real, intent(in) :: theta !< Angle to rotate (degrees)
+  real, intent(inout) :: px !< x-coordinate of point
+  real, intent(inout) :: py !< y-coordinate of point
   ! Local variables
-  real :: u_old, v_old
+  real :: px_temp,py_temp
 
-  u_old=u
-  v_old=v
-  u=cos_rot*u_old+sin_rot*v_old
-  v=cos_rot*v_old-sin_rot*u_old
+  ! Rotation
+  px_temp = ( cos(theta*pi/180)*px) + (sin(theta*pi/180)*py)
+  py_temp = (-sin(theta*pi/180)*px) + (cos(theta*pi/180)*py)
 
-end subroutine rotate
+  ! Translation
+  px= px_temp + x0
+  py= py_temp + y0
+end subroutine rotate_and_translate
 
-!> Calculates bergs%grd%mass_on_ocean
-subroutine calculate_mass_on_ocean(bergs, with_diagnostics)
+!> Areas of a hexagon divided into quadrants
+!!
+!! This subroutine divides a regular hexagon centered at x0,y0 with apothem H, and orientation theta into its intersection with the 4 quadrants.
+!! Theta=0 assumes that the apothem points upwards.
+!! Routine works by finding the corners of the 6 triangles, and then finding the intersection of each of these with each quadrant.
+!! \todo (also the rotation is not working yet)
+subroutine Hexagon_into_quadrants_using_triangles(x0, y0, H, theta, Area_hex ,Area_Q1, Area_Q2, Area_Q3, Area_Q4)
   ! Arguments
-  type(icebergs), pointer :: bergs !< Container for all types and memory
-  logical, intent(in) :: with_diagnostics
+  real, intent(in) :: x0 !< x-coordinate of center of hexagon
+  real, intent(in) :: y0 !< y-coordinate of center of hexagon
+  real, intent(in) :: H !< Apothem (inner radius of hexagon)
+  real, intent(in) :: theta !< Orientation angle of hexagon
+  real, intent(out) :: Area_hex !< Area of hexagon
+  real, intent(out) :: Area_Q1 !< Are in quadrant 1
+  real, intent(out) :: Area_Q2 !< Are in quadrant 2
+  real, intent(out) :: Area_Q3 !< Are in quadrant 2
+  real, intent(out) :: Area_Q4 !< Are in quadrant 4
   ! Local variables
-  type(iceberg), pointer :: berg
-  type(icebergs_gridded), pointer :: grd
-  integer :: grdj, grdi
-  integer :: j, i
-
-  ! For convenience
-  grd=>bergs%grd
+  real :: C1x, C2x, C3x, C4x, C5x, C6x
+  real :: C1y, C2y, C3y, C4y, C5y, C6y
+  real :: T12_Area, T12_Q1, T12_Q2, T12_Q3, T12_Q4
+  real :: T23_Area, T23_Q1, T23_Q2, T23_Q3, T23_Q4
+  real :: T34_Area, T34_Q1, T34_Q2, T34_Q3, T34_Q4
+  real :: T45_Area, T45_Q1, T45_Q2, T45_Q3, T45_Q4
+  real :: T56_Area, T56_Q1, T56_Q2, T56_Q3, T56_Q4
+  real :: T61_Area, T61_Q1, T61_Q2, T61_Q3, T61_Q4
+  real :: S, exact_hex_area, Error
+  real :: tol
+  integer :: stderrunit
 
-  !Initialize fields
-  grd%mass_on_ocean(:,:,:)=0.
-  grd%area_on_ocean(:,:,:)=0.
-  grd%Uvel_on_ocean(:,:,:)=0.
-  grd%Vvel_on_ocean(:,:,:)=0.
+  ! Get the stderr unit number
+  stderrunit = stderr()
+  tol=1.e-10
 
-  do grdj = grd%jsc-1,grd%jec+1 ; do grdi = grd%isc-1,grd%iec+1
-    berg=>bergs%list(grdi,grdj)%first
-    do while(associated(berg))
-      if (berg%halo_berg<2 .or. .not. bergs%mts) then
-        i=berg%ine  ;     j=berg%jne
-        if (grd%area(i,j) > 0.) then
+  ! Length of side of Hexagon
+  S=(2/sqrt(3.))*H
 
-          !Increasing Mass on ocean
-          if ((bergs%add_weight_to_ocean .and. .not. bergs%time_average_weight) .or.(bergs%find_melt_using_spread_mass)) then
-            call spread_mass_across_ocean_cells(bergs, berg, berg%ine, berg%jne, berg%xi, berg%yj, berg%mass,berg%mass_of_bits, berg%mass_scaling, &
-              berg%length*berg%width, berg%thickness)
-          endif
+  ! Finding positions of corners
+  C1x=S           ; C1y=0.  !Corner 1 (right)
+  C2x=H/sqrt(3.)  ; C2y=H;  !Corner 2 (top right)
+  C3x=-H/sqrt(3.) ; C3y=H;  !Corner 3 (top left)
+  C4x=-S          ; C4y=0.; !Corner 4 (left)
+  C5x=-H/sqrt(3.) ; C5y=-H; !Corner 5 (bottom left)
+  C6x=H/sqrt(3.)  ; C6y=-H; !Corner 6 (bottom right)
 
-          !Calculated some iceberg diagnositcs
-          if (with_diagnostics) call calculate_sum_over_bergs_diagnositcs(bergs,grd,berg,i,j)
+  ! Finding positions of corners
+  call rotate_and_translate(C1x,C1y,theta,x0,y0)
+  call rotate_and_translate(C2x,C2y,theta,x0,y0)
+  call rotate_and_translate(C3x,C3y,theta,x0,y0)
+  call rotate_and_translate(C4x,C4y,theta,x0,y0)
+  call rotate_and_translate(C5x,C5y,theta,x0,y0)
+  call rotate_and_translate(C6x,C6y,theta,x0,y0)
 
-        endif
-      endif
-      berg=>berg%next
-    enddo
-  enddo ;enddo
+  ! Area of Hexagon is the sum of the triangles
+  call Triangle_divided_into_four_quadrants(x0,y0,C1x,C1y,C2x,C2y,T12_Area,T12_Q1,T12_Q2,T12_Q3,T12_Q4); !Triangle 012
+  call Triangle_divided_into_four_quadrants(x0,y0,C2x,C2y,C3x,C3y,T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4); !Triangle 023
+  call Triangle_divided_into_four_quadrants(x0,y0,C3x,C3y,C4x,C4y,T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4); !Triangle 034
+  call Triangle_divided_into_four_quadrants(x0,y0,C4x,C4y,C5x,C5y,T45_Area,T45_Q1,T45_Q2,T45_Q3,T45_Q4); !Triangle 045
+  call Triangle_divided_into_four_quadrants(x0,y0,C5x,C5y,C6x,C6y,T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4); !Triangle 056
+  call Triangle_divided_into_four_quadrants(x0,y0,C6x,C6y,C1x,C1y,T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4); !Triangle 061
 
-end subroutine calculate_mass_on_ocean
+  ! Summing up the triangles
+  Area_hex=T12_Area+T23_Area+T34_Area+T45_Area+T56_Area+T61_Area
+  Area_Q1=T12_Q1+T23_Q1+T34_Q1+T45_Q1+T56_Q1+T61_Q1
+  Area_Q2=T12_Q2+T23_Q2+T34_Q2+T45_Q2+T56_Q2+T61_Q2
+  Area_Q3=T12_Q3+T23_Q3+T34_Q3+T45_Q3+T56_Q3+T61_Q3
+  Area_Q4=T12_Q4+T23_Q4+T34_Q4+T45_Q4+T56_Q4+T61_Q4
 
-!> Projects additional diagnostics of bergs on to the grid
-subroutine calculate_sum_over_bergs_diagnositcs(bergs, grd, berg, i, j)
-  ! Arguments
-  type(icebergs), pointer :: bergs !< Container for all types and memory
-  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
-  type(iceberg), pointer :: berg !< An iceberg
-  integer, intent(in) :: i !< i-index of cell containing berg
-  integer, intent(in) :: j !< j-index of cell containing berg
-  ! Local variables
-  real ::  Abits, Lbits, Mbits
+  Area_Q1=max(Area_Q1,0.)
+  Area_Q2=max(Area_Q2,0.)
+  Area_Q3=max(Area_Q3,0.)
+  Area_Q4=max(Area_Q4,0.)
 
-  !Virtual area diagnostic
-  if (grd%id_virtual_area>0) then
-    if (bergs%bergy_bit_erosion_fraction>0.) then
-      Lbits=min(berg%length,berg%width,berg%thickness,40.) ! assume bergy bits are smallest dimension or 40 meters
-      Abits=(berg%mass_of_bits/bergs%rho_bergs)/Lbits ! Effective bottom area (assuming T=Lbits)
-    else
-      Abits=0.0
+  Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
+  if ((abs(Error)>tol))then
+    if (mpp_pe().eq.mpp_root_pe()) then
+      call error_mesg('KID, hexagonal spreading', 'Hexagon error is large!!', WARNING)
+      write(stderrunit,*) 'KID, hex error, H,x0,y0, Error', H, x0 , y0, Error
+      write(stderrunit,*) 'KID, hex error, Areas',Area_hex, (Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
+      write(stderrunit,*) 'KID, Triangle1',C1x,C1y,C2x,C2y,T12_Area,T12_Q1,T12_Q2,T12_Q3,T12_Q4,(T12_Q1+T12_Q2+T12_Q3+T12_Q4-T12_Area)
+      write(stderrunit,*) 'KID, Triangle2',C2x,C2y,C3x,C3y,T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4,(T23_Q1+T23_Q2+T23_Q3+T23_Q4-T23_Area)
+      write(stderrunit,*) 'KID, Triangle3',C3x,C3y,C4x,C4y,T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4,(T34_Q1+T34_Q2+T34_Q3+T34_Q4-T34_Area)
+      write(stderrunit,*) 'KID, Triangle4',C4x,C4y,C5x,C5y,T45_Area,T45_Q1,T45_Q2,T45_Q3,T45_Q4,(T45_Q1+T45_Q2+T45_Q3+T45_Q4-T45_Area)
+      write(stderrunit,*) 'KID, Triangle5',C5x,C5y,C6x,C6y,T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4,(T56_Q1+T56_Q2+T56_Q3+T56_Q4-T56_Area)
+      write(stderrunit,*) 'KID, Triangle6',C6x,C6y,C1x,C1y,T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4,(T61_Q1+T61_Q2+T61_Q3+T61_Q4-T61_Area)
     endif
-    grd%virtual_area(i,j)=grd%virtual_area(i,j)+(berg%width*berg%length+Abits)*berg%mass_scaling ! m^2
   endif
 
-  !Mass diagnostic (also used in u_iceberg, v_iceberg
-  if ((grd%id_mass>0 ) .or. ((grd%id_u_iceberg>0) .or. (grd%id_v_iceberg>0)))   &
-       & grd%mass(i,j)=grd%mass(i,j)+berg%mass/grd%area(i,j)*berg%mass_scaling ! kg/m2
+  exact_hex_area=((3.*sqrt(3.)/2)*(S*S))
+  if (abs(Area_hex-exact_hex_area)>tol) then
+    call error_mesg('KID, hexagonal spreading', 'Hexagon not evaluated accurately!!', WARNING)
+    if (mpp_pe().eq.mpp_root_pe()) then
+      write(stderrunit,*) 'KID, hex calculations, H,x0,y0', H, x0 , y0
+      write(stderrunit,*) 'KID, hex calculations, Areas',Area_hex, (Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
+    endif
+  endif
 
-  !Finding the average iceberg velocity in a grid cell (mass weighted)
-  if (grd%id_u_iceberg>0) &
-  grd%u_iceberg(i,j)=grd%u_iceberg(i,j)+((berg%mass/grd%area(i,j)*berg%mass_scaling)*berg%uvel) ! kg/m2
-  if (grd%id_v_iceberg>0) &
-  grd%v_iceberg(i,j)=grd%v_iceberg(i,j)+((berg%mass/grd%area(i,j)*berg%mass_scaling)*berg%vvel) ! kg/m2
+  ! Adjust Areas so that the error is zero by subtracting the error from the largest sector.
+   if  (((Area_Q1>=Area_Q2) .and. (Area_Q1>=Area_Q3)) .and. (Area_Q1>=Area_Q4)) then
+     Area_Q1=Area_Q1+Error
+   elseif  (((Area_Q2>=Area_Q1) .and. (Area_Q2>=Area_Q3)) .and. (Area_Q2>=Area_Q4)) then
+     Area_Q2=Area_Q2+Error
+   elseif  (((Area_Q3>=Area_Q1) .and. (Area_Q3>=Area_Q2)) .and. (Area_Q3>=Area_Q4)) then
+     Area_Q3=Area_Q3+Error
+   elseif  (((Area_Q4>=Area_Q1) .and. (Area_Q4>=Area_Q2)) .and. (Area_Q4>=Area_Q3)) then
+     Area_Q4=Area_Q4+Error
+   else
+     call error_mesg('KID, hexagonal spreading', 'Error in hexagon is larger than any quadrant!!', WARNING)
+     if (mpp_pe().eq.mpp_root_pe()) then
+      write(stderrunit,*) 'KID, hex quadrants, H,x0,y0', H, x0 , y0, Error
+      write(stderrunit,*) 'KID, hex quadrants, Areas',Area_hex, (Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
+     endif
+   endif
 
-  !Mass of bergy bits
-  if (grd%id_bergy_mass>0 .or. bergs%add_weight_to_ocean)&
-       & grd%bergy_mass(i,j)=grd%bergy_mass(i,j)+berg%mass_of_bits/grd%area(i,j)*berg%mass_scaling ! kg/m2
-end subroutine calculate_sum_over_bergs_diagnositcs
+ end subroutine Hexagon_into_quadrants_using_triangles
 
-!> The main driver the steps updates icebergs
-subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh, sst, calving_hflx, cn, hi, &
-                        stagger, stress_stagger, sss, mass_berg, ustar_berg, area_berg)
+subroutine interp_gridded_fields_to_bergs(bergs)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
-  type(time_type), intent(in) :: time !< Model time
-  real, dimension(:,:), intent(inout) :: calving !< Calving (kg/s). This field is updated with melt by bergs.
-  real, dimension(:,:), intent(inout) :: calving_hflx !< Calving heat flux (W/m2)
-  real, dimension(:,:), intent(in) :: uo !< Ocean zonal velocity (m/s)
-  real, dimension(:,:), intent(in) :: vo !< Ocean meridional velocity (m/s)
-  real, dimension(:,:), intent(in) :: ui !< Ice zonal velocity (m/s)
-  real, dimension(:,:), intent(in) :: vi !< Ice meridional velocity (m/s)
-  real, dimension(:,:), intent(in) :: tauxa !< Zonal wind stress (Pa)
-  real, dimension(:,:), intent(in) :: tauya !< Meridional wind stress (Pa)
-  real, dimension(:,:), intent(in) :: ssh !< Effective sea-surface height (m)
-  real, dimension(:,:), intent(in) :: sst !< Sea-surface temperature (C or K)
-  real, dimension(:,:), intent(in) :: cn !< Sea-ice concentration (nondim)
-  real, dimension(:,:), intent(in) :: hi !< Sea-ice thickness (m)
-  integer, optional, intent(in) :: stagger
-  integer, optional, intent(in) :: stress_stagger
-  real, dimension(:,:), optional, intent(in) :: sss !< Sea-surface salinity (1e-3)
-  real, dimension(:,:), optional, pointer :: mass_berg !< Mass of bergs (kg)
-  real, dimension(:,:), optional, pointer :: ustar_berg !< Friction velocity on base of bergs (m/s)
-  real, dimension(:,:), optional, pointer :: area_berg !< Area of bergs (m2)
   ! Local variables
-  integer :: iyr, imon, iday, ihr, imin, isec, k
   type(icebergs_gridded), pointer :: grd
-  logical :: lerr, sample_traj, write_traj, lbudget, lverbose, check_bond_quality
-  real :: unused_calving, tmpsum, grdd_berg_mass, grdd_bergy_mass,grdd_spread_mass, grdd_spread_area
-  real :: grdd_u_iceberg, grdd_v_iceberg, grdd_ustar_iceberg, grdd_spread_uvel, grdd_spread_vvel
-  integer :: i, j, Iu, ju, iv, Jv, Iu_off, ju_off, iv_off, Jv_off
-  real :: mask, max_SST
-  real, dimension(:,:), allocatable :: uC_tmp, vC_tmp, uA_tmp, vA_tmp
-  integer :: vel_stagger, str_stagger
-  real, dimension(:,:), allocatable :: iCount
-  integer :: nbonds
-  integer :: stderrunit
-  logical :: Visited
-  save :: Visited
-
-  ! Get the stderr unit number
-  stderrunit = stderr()
-
-  call mpp_clock_begin(bergs%clock)
-  call mpp_clock_begin(bergs%clock_int)
-
-  vel_stagger = BGRID_NE ; if (present(stagger)) vel_stagger = stagger
-  str_stagger = vel_stagger ; if (present(stress_stagger)) str_stagger = stress_stagger
+  type(iceberg), pointer :: berg
+  integer :: grdj,grdi,i
+  type(randomNumberStream) :: rns ! Random numbers for stochastic tidal parameterization
+  real :: rx,ry
 
   ! For convenience
   grd=>bergs%grd
+  rx=0.0; ry=0.0;
 
-  grd%floating_melt(:,:)=0.
-  grd%berg_melt(:,:)=0.
-  grd%melt_buoy(:,:)=0.
-  grd%melt_eros(:,:)=0.
-  grd%melt_conv(:,:)=0.
-  grd%bergy_src(:,:)=0.
-  grd%bergy_melt(:,:)=0.
-  grd%bergy_mass(:,:)=0.
-  grd%spread_mass_old(:,:)=0.
-  !grd%spread_mass(:,:)=0.  !Don't zero this out yet, because we can first use this an add it onto the SSH
-  grd%spread_area(:,:)=0.
-  grd%u_iceberg(:,:)=0.
-  grd%v_iceberg(:,:)=0.
-  grd%spread_uvel(:,:)=0.
-  grd%spread_vvel(:,:)=0.
-  grd%ustar_iceberg(:,:)=0.
-  grd%mass(:,:)=0.
-  grd%virtual_area(:,:)=0.
+  do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec ! just for computational domain
+    berg=>bergs%list(grdi,grdj)%first
+    if (associated(berg) .and. grd%tidal_drift>0.) then
+      ! Seed random numbers based on space and "time"
+      rns = initializeRandomNumberStream( grdi + 10000*grdj + &
+                                          int( 16384.*abs( sin(262144.*grd%ssh(grdi,grdj)) ) ) )
+    endif
+    do while (associated(berg)) ! loop over all bergs
+      if (berg%halo_berg.lt.0.5) then
+        if (grd%tidal_drift>0.) then
+          call getRandomNumbers(rns, rx)
+          rx = 2.*rx - 1.
+          call getRandomNumbers(rns, ry)
+          ry = 2.*ry - 1.
+        endif
+        call interp_flds(grd, berg%lon, berg%lat, berg%ine, berg%jne, berg%xi, berg%yj, rx, ry, berg%uo, berg%vo, &
+          berg%ui, berg%vi, berg%ua, berg%va, berg%ssh_x, berg%ssh_y, berg%sst, berg%sss, berg%cn, berg%hi, berg%od)
+      endif
+      berg=>berg%next
+    enddo
+  enddo;enddo
 
-  !Initializing _on_ocean_fields
-  grd%mass_on_ocean(:,:,:)=0. ;   grd%area_on_ocean(:,:,:)=0.
-  grd%Uvel_on_ocean(:,:,:)=0. ;   grd%Vvel_on_ocean(:,:,:)=0.
+end subroutine interp_gridded_fields_to_bergs
 
-  if (present(mass_berg)) then ;  if (associated(mass_berg)) then
-    mass_berg(:,:)=0.0
-  endif ;  endif
-  if (present(ustar_berg)) then ; if (associated(ustar_berg)) then
-    ustar_berg(:,:)=0.0
-  endif ;  endif
-  if (present(area_berg)) then ;  if (associated(area_berg)) then
-    area_berg(:,:)=0.0
-  endif ;  endif
-
-  ! Manage time
-  call get_date(time, iyr, imon, iday, ihr, imin, isec)
-  bergs%current_year=iyr
-  bergs%current_yearday=yearday(imon, iday, ihr, imin, isec)
-  ! Turn on sampling of trajectories, verbosity, budgets
-  sample_traj=.false.
-  if ( (bergs%traj_sample_hrs>0)  .and. (.not. bergs%ignore_traj) ) then
-    if (mod(60*60*24*iday+ 60*60*ihr + 60.*imin + isec ,60*60*bergs%traj_sample_hrs).eq.0) &
-      sample_traj=.true.
-  elseif (bergs%traj_sample_hrs==0) then
-    sample_traj=.true.
-  endif
-  write_traj=.false.
-  if ((bergs%traj_write_hrs>0) .and. (.not. bergs%ignore_traj))  then
-     if (mod(60*60*24*iday+ 60*60*ihr + 60.*imin + isec ,60*60*bergs%traj_write_hrs).eq.0) &
-       write_traj=.true.
-   elseif (bergs%traj_write_hrs==0) then
-     write_traj=.true.
-  endif
-  lverbose=.false.
-  if (bergs%verbose_hrs>0) then
-    !if (mod(24*iday+ihr+(imin/60.),float(bergs%verbose_hrs)).eq.0) lverbose=verbose
-    if (mod(24*iday+ihr+(imin/60.),bergs%verbose_hrs).eq.0) lverbose=verbose
-  endif
-  lbudget=.false.
-  if (bergs%verbose_hrs>0) then
-     !if (mod(24*iday+ihr+(imin/60.),float(bergs%verbose_hrs)).eq.0) lbudget=budget  !Added minutes, so that it does not repeat when smaller time steps are used.
-     if (mod(24*iday+ihr+(imin/60.),bergs%verbose_hrs).eq.0) lbudget=budget
-  endif
-  if (mpp_pe()==mpp_root_pe().and.lverbose) write(*,'(a,3i5,a,3i5,a,i5,f8.3)') &
-       'KID: y,m,d=',iyr, imon, iday,' h,m,s=', ihr, imin, isec, &
-       ' yr,yrdy=', bergs%current_year, bergs%current_yearday
 
+subroutine interp_flds(grd, x, y, i, j, xi, yj, rx, ry, uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, sss, cn, hi, od)
+  ! Arguments
+  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+  integer, intent(in) :: i !< i-index of cell in which to interpolate
+  integer, intent(in) :: j !< j-index of cell in which to interpolate
+  real, intent(in) :: x !<Longitude of position
+  real, intent(in) :: y !<Latitude of position
+  real, intent(in) :: xi !< Non-dimensional x-position within cell to interpolate to
+  real, intent(in) :: yj !< Non-dimensional y-position within cell to interpolate to
+  real, intent(in) :: rx !< Random number between -1 and 1 for use in x-component of stochastic tidal parameterization
+  real, intent(in) :: ry !< Random number between -1 and 1 for use in y-component of stochastic tidal parameterization
+  real, intent(out) :: uo !< Ocean zonal velocity at point xi,yj (m/s)
+  real, intent(out) :: vo !< Ocean meridional velocity at point xi,yj (m/s)
+  real, intent(out) :: ui !< Ice zonal velocity at point xi,yj (m/s)
+  real, intent(out) :: vi !< Ice meridional velocity at point xi,yj (m/s)
+  real, intent(out) :: ua !< Atmospheric zonal velocity at point xi,yj (m/s)
+  real, intent(out) :: va !< Atmospheric meridional velocity at point xi,yj (m/s)
+  real, intent(out) :: ssh_x !< Zonal slope of sea-surface height (nondim)
+  real, intent(out) :: ssh_y !< Meridional slope of sea-surface height (nondim)
+  real, intent(out) :: sst !< Sea-surface temperature (C)
+  real, intent(out) :: sss !< Sea-surface salinity (1e-3)
+  real, intent(out) :: cn !< Sea-ice concentration (nondim)
+  real, intent(out) :: hi !< Sea-ice thickness (m)
+  real, optional, intent(out) :: od !< Ocean depth (m)
+  ! Local variables
+  real :: cos_rot, sin_rot, du, dv
+#ifdef USE_OLD_SSH_GRADIENT
+  real :: dxm, dx0, dxp
+  real, parameter :: ssh_coast=0.00
+#endif
+  real :: hxm, hxp, ssh
+  integer :: stderrunit
+  integer :: ii, jj
 
- !call sanitize_field(grd%calving,1.e20)
-  tmpsum=sum( calving(:,:)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
-  bergs%net_calving_received=bergs%net_calving_received+tmpsum*bergs%dt
+  ! Get the stderr unit number
+  stderrunit = stderr()
 
-  ! Adapt calving heat flux from coupler
-  grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)=calving_hflx(:,:) & ! Units of W/m2
-       *grd%msk(grd%isc:grd%iec,grd%jsc:grd%jec)
+  cos_rot=bilin(grd, grd%cos, i, j, xi, yj) ! If true, uses the inverted bilin function
+  sin_rot=bilin(grd, grd%sin, i, j, xi, yj)
 
-  ! Adapt calving flux from coupler for use here
-  grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec)=calving(:,:) & ! Units of kg/m2/s
-       *grd%msk(grd%isc:grd%iec,grd%jsc:grd%jec)
+  uo=bilin(grd, grd%uo, i, j, xi, yj)
+  vo=bilin(grd, grd%vo, i, j, xi, yj)
+  ui=bilin(grd, grd%ui, i, j, xi, yj)
+  vi=bilin(grd, grd%vi, i, j, xi, yj)
+  ua=bilin(grd, grd%ua, i, j, xi, yj)
+  va=bilin(grd, grd%va, i, j, xi, yj)
 
-  ! Running means of calving and calving_hflx
-  if (bergs%tau_calving>0.) then
-    call get_running_mean_calving(bergs, grd%calving, grd%calving_hflx)
-    calving(:,:)=grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec) ! Copy back from grd%calving if using running-mean
-    calving_hflx(:,:)=grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)
+  ! The following block accelerates a berg away from coastlines towards open water
+  ! which is a bias needed to avoid piling up in coarse resolution models
+  if (grd%coastal_drift > 0.) then
+    ! If a cell to the west is land (msk=0), accelerate to the east, and vice versa.
+    uo = uo + grd%coastal_drift * ( grd%msk(i+1,j) - grd%msk(i-1,j) ) * grd%msk(i,j)
+    ui = ui + grd%coastal_drift * ( grd%msk(i+1,j) - grd%msk(i-1,j) ) * grd%msk(i,j)
+    ! If a cell to the south is land (msk=0), accelerate to the north, and vice versa.
+    vo = vo + grd%coastal_drift * ( grd%msk(i,j+1) - grd%msk(i,j-1) ) * grd%msk(i,j)
+    vi = vi + grd%coastal_drift * ( grd%msk(i,j+1) - grd%msk(i,j-1) ) * grd%msk(i,j)
   endif
 
-  grd%calving(:,:)=grd%calving(:,:)*grd%msk(:,:)*grd%area(:,:) ! Convert to kg/s
-  tmpsum=sum( grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec) )
-  bergs%net_incoming_calving=bergs%net_incoming_calving+tmpsum*bergs%dt
-  if (grd%id_calving>0) &
-    lerr=send_data(grd%id_calving, grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  ! Stochastic acceleration to represent unresolved tidal and wave motions.
+  ! Note: this scheme should account for the time-step and have memory!
+  if (grd%tidal_drift > 0.) then
+    ! The acceleration is modulated to not move particles towards land cells.
+    du = ( min(0., rx) * grd%msk(i-1,j) + max(0., rx) * grd%msk(i+1,j) ) &
+         * ( 1. - grd%msk(i,j-1) * grd%msk(i,j+1) ) ! Do not apply in open ocean
+    dv = ( min(0., ry) * grd%msk(i,j-1) + max(0., ry) * grd%msk(i,j+1) ) &
+         * ( 1. - grd%msk(i-1,j) * grd%msk(i+1,j) ) ! Do not apply in open ocean
+    du = du * grd%tidal_drift * grd%msk(i,j)
+    dv = dv * grd%tidal_drift * grd%msk(i,j)
+    uo = uo + du
+    ui = ui + du
+    vo = vo + dv
+    vi = vi + dv
+  endif
 
-  grd%calving_hflx(:,:)=grd%calving_hflx(:,:)*grd%msk(:,:) ! Mask (just in case)
-  if (grd%id_calving_hflx_in>0) &
-    lerr=send_data(grd%id_calving_hflx_in, grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  tmpsum=sum( grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
-  bergs%net_incoming_calving_heat=bergs%net_incoming_calving_heat+tmpsum*bergs%dt ! Units of J
+  if (ua.ne.ua) then
+    if (mpp_pe().eq.9) then
+      write(stderrunit,'(a3,32i7)') 'ua',(ii,ii=grd%isd,grd%ied)
+      do jj=grd%jed,grd%jsd,-1
+        write(stderrunit,'(i3,32f7.1)') jj,(grd%ua(ii,jj),ii=grd%isd,grd%ied)
+      enddo
+  !   write(stderrunit,'(a3,32i7)') 'Lat',(i,i=grd%isd,grd%ied)
+  !   do j=grd%jed,grd%jsd,-1
+  !     write(stderrunit,'(i3,32f7.1)') j,(grd%lat(i,j),i=grd%isd,grd%ied)
+  !   enddo
+  !   write(stderrunit,'(a3,32i7)') 'Msk',(i,i=grd%isd,grd%ied)
+  !   do j=grd%jed,grd%jsd,-1
+  !     write(stderrunit,'(i3,32f7.1)') j,(grd%msk(i,j),i=grd%isd,grd%ied)
+  !   enddo
+  ! endif
+      call error_mesg('KID, interp fields', 'ua is NaNs', FATAL)
+    endif
+  endif
 
-  if (grd%id_ocean_depth>0) &
-    lerr=send_data(grd%id_ocean_depth, grd%ocean_depth(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  ! These fields are cell centered (A-grid) and would
+  ! best be interpolated using PLM. For now we use PCM!
+  sst=grd%sst(i,j) ! A-grid
+  sss=grd%sss(i,j) ! A-grid
+  cn=grd%cn(i,j) ! A-grid
+  hi=grd%hi(i,j) ! A-grid
 
-  if (vel_stagger == BGRID_NE) then
-    ! Copy ocean and ice velocities. They are already on B-grid u-points.
-    grd%uo(grd%isc-1:grd%iec+1,grd%jsc-1:grd%jec+1) = uo(:,:)
-    grd%vo(grd%isc-1:grd%iec+1,grd%jsc-1:grd%jec+1) = vo(:,:)
-    call mpp_update_domains(grd%uo, grd%vo, grd%domain, gridtype=BGRID_NE)
-    grd%ui(grd%isc-1:grd%iec+1,grd%jsc-1:grd%jec+1) = ui(:,:)
-    grd%vi(grd%isc-1:grd%iec+1,grd%jsc-1:grd%jec+1) = vi(:,:)
-    call mpp_update_domains(grd%ui, grd%vi, grd%domain, gridtype=BGRID_NE)
-  elseif (vel_stagger == CGRID_NE) then
-    ! The u- and v- points will have different offsets with symmetric memory.
-    Iu_off = (size(uo,1) - (grd%iec - grd%isc))/2 - grd%isc + 1
-    ju_off = (size(uo,2) - (grd%jec - grd%jsc))/2 - grd%jsc + 1
-    iv_off = (size(vo,1) - (grd%iec - grd%isc))/2 - grd%isc + 1
-    Jv_off = (size(vo,2) - (grd%jec - grd%jsc))/2 - grd%jsc + 1
-    do I=grd%isc-1,grd%iec ; do J=grd%jsc-1,grd%jec
-      ! Interpolate ocean and ice velocities from C-grid velocity points.
-      Iu = i + Iu_off ; ju = j + ju_off ; iv = i + iv_off ; Jv = j + Jv_off
-      ! This masking is needed for now to prevent icebergs from running up on to land.
-      mask = min(grd%msk(i,j), grd%msk(i+1,j), grd%msk(i,j+1), grd%msk(i+1,j+1))
-      grd%uo(I,J) = mask * 0.5*(uo(Iu,ju)+uo(Iu,ju+1))
-      grd%ui(I,J) = mask * 0.5*(ui(Iu,ju)+ui(Iu,ju+1))
-      grd%vo(I,J) = mask * 0.5*(vo(iv,Jv)+vo(iv+1,Jv))
-      grd%vi(I,J) = mask * 0.5*(vi(iv,Jv)+vi(iv+1,Jv))
-    enddo ; enddo
+  ! Estimate SSH gradient in X direction
+#ifdef USE_OLD_SSH_GRADIENT
+  dxp=0.5*(grd%dx(i+1,j)+grd%dx(i+1,j-1))
+  dx0=0.5*(grd%dx(i,j)+grd%dx(i,j-1))
+  dxm=0.5*(grd%dx(i-1,j)+grd%dx(i-1,j-1))
+  hxm=2.*(grd%ssh(i,j)-grd%ssh(i-1,j))/(dx0+dxm)*grd%msk(i-1,j) &
+        +(-ssh_coast)/(dx0+dxm)*(1.-grd%msk(i-1,j)) ! force to drive bergs away from coasts
+  hxp=2.*(grd%ssh(i+1,j)-grd%ssh(i,j))/(dx0+dxp)*grd%msk(i+1,j) &
+        +(+ssh_coast)/(dx0+dxp)*(1.-grd%msk(i+1,j)) ! force to drive bergs away from coasts
+#else
+  if (yj>=0.5) then
+    hxp=(yj-0.5)*ddx_ssh(grd,i  ,j+1)+(1.5-yj)*ddx_ssh(grd,i  ,j  )
+    hxm=(yj-0.5)*ddx_ssh(grd,i-1,j+1)+(1.5-yj)*ddx_ssh(grd,i-1,j  )
   else
-    call error_mesg('KID, iceberg_run', 'Unrecognized value of stagger!', FATAL)
+    hxp=(yj+0.5)*ddx_ssh(grd,i  ,j  )+(0.5-yj)*ddx_ssh(grd,i  ,j-1)
+    hxm=(yj+0.5)*ddx_ssh(grd,i-1,j  )+(0.5-yj)*ddx_ssh(grd,i-1,j-1)
   endif
+#endif
+  ! ssh_x is at the u-point on a C-grid
+  ssh_x=xi*hxp+(1.-xi)*hxm
 
-  if (str_stagger == BGRID_NE) then
-    ! Copy wind stress components on B-grid u-points.
-    grd%ua(grd%isc:grd%iec,grd%jsc:grd%jec) = tauxa(:,:)
-    grd%va(grd%isc:grd%iec,grd%jsc:grd%jec) = tauya(:,:)
-  elseif (str_stagger == CGRID_NE) then
-    ! The u- and v- points will have different offsets with symmetric memory.
-    Iu_off = (size(tauxa,1) - (grd%iec - grd%isc))/2 - grd%isc + 1
-    ju_off = (size(tauxa,2) - (grd%jec - grd%jsc))/2 - grd%jsc + 1
-    iv_off = (size(tauya,1) - (grd%iec - grd%isc))/2 - grd%isc + 1
-    Jv_off = (size(tauya,2) - (grd%jec - grd%jsc))/2 - grd%jsc + 1
-    allocate(uC_tmp(grd%isd:grd%ied,grd%jsd:grd%jed), &
-             vC_tmp(grd%isd:grd%ied,grd%jsd:grd%jed))
-    uC_tmp(:,:) = 0. ! This avoids uninitialized values that might remain in halo
-    vC_tmp(:,:) = 0. ! regions after the call to mpp_update_domains() below.
-    !   If the iceberg model used symmetric memory, the starting value of these
-    ! copies would need to be decremented by 1.
-    do i=grd%isc,grd%iec ; do j=grd%jsc,grd%jec
-      uC_tmp(i,j) = tauxa(i+Iu_off, j+ju_off)
-      vC_tmp(i,J) = tauya(i+iv_off, J+Jv_off)
-    enddo ; enddo
-
-    call mpp_update_domains(uC_tmp, vC_tmp, grd%domain, gridtype=CGRID_NE)
-    do I=grd%isc-1,grd%iec ; do J=grd%jsc-1,grd%jec
-      ! Interpolate wind stresses from C-grid velocity-points.
-      ! This masking is needed for now to prevent icebergs from running up on to land.
-      mask = min(grd%msk(i,j), grd%msk(i+1,j), grd%msk(i,j+1), grd%msk(i+1,j+1))
-       grd%ua(I,J) = mask * 0.5*(uC_tmp(I,j)+uC_tmp(I,j+1))
-       grd%va(I,J) = mask * 0.5*(vC_tmp(i,J)+vC_tmp(i+1,J))
-    enddo ; enddo
-    deallocate(uC_tmp, vC_tmp)
-  elseif (str_stagger == AGRID) then
-    ! Copy into arrays with local index conventions and halos.
-    allocate(uA_tmp(grd%isd:grd%ied,grd%jsd:grd%jed), &
-             vA_tmp(grd%isd:grd%ied,grd%jsd:grd%jed))
-    uA_tmp(:,:) = 0.0 ! This avoids uninitialized values that might remain in halo
-    vA_tmp(:,:) = 0.0 ! regions after the call to mpp_update_domains() below.
-    uA_tmp(grd%isc:grd%iec,grd%jsc:grd%jec) = tauxa(:,:)
-    vA_tmp(grd%isc:grd%iec,grd%jsc:grd%jec) = tauya(:,:)
-    call mpp_update_domains(uA_tmp, vA_tmp, grd%domain, gridtype=AGRID)
-    do I=grd%isc-1,grd%iec ; do J=grd%jsc-1,grd%jec
-      ! Interpolate wind stresses from A-grid tracer points to the corner B-grid points.
-      ! This masking is needed for now to prevent icebergs from running up on to land.
-      mask = min(grd%msk(i,j), grd%msk(i+1,j), grd%msk(i,j+1), grd%msk(i+1,j+1))
-      grd%ua(I,J) = mask * 0.25*((uA_tmp(i,j) + uA_tmp(i+1,j+1)) + &
-                                 (uA_tmp(i+1,j) + uA_tmp(i,j+1)))
-      grd%va(I,J) = mask * 0.25*((vA_tmp(i,j) + vA_tmp(i+1,j+1)) + &
-                                 (vA_tmp(i+1,j) + vA_tmp(i,j+1)))
-    enddo ; enddo
-
-    deallocate(uA_tmp, vA_tmp)
+  ! Estimate SSH gradient in Y direction
+#ifdef USE_OLD_SSH_GRADIENT
+  dxp=0.5*(grd%dy(i,j+1)+grd%dy(i-1,j+1))
+  dx0=0.5*(grd%dy(i,j)+grd%dy(i-1,j))
+  dxm=0.5*(grd%dy(i,j-1)+grd%dy(i-1,j-1))
+  hxm=2.*(grd%ssh(i,j)-grd%ssh(i,j-1))/(dx0+dxm)*grd%msk(i,j-1) &
+        +(-ssh_coast)/(dx0+dxm)*(1.-grd%msk(i,j-1)) ! force to drive bergs away from coasts
+  hxp=2.*(grd%ssh(i,j+1)-grd%ssh(i,j))/(dx0+dxp)*grd%msk(i,j+1) &
+        +(+ssh_coast)/(dx0+dxp)*(1.-grd%msk(i,j+1)) ! force to drive bergs away from coasts
+#else
+  if (xi>=0.5) then
+    hxp=(xi-0.5)*ddy_ssh(grd,i+1,j  )+(1.5-xi)*ddy_ssh(grd,i  ,j  )
+    hxm=(xi-0.5)*ddy_ssh(grd,i+1,j-1)+(1.5-xi)*ddy_ssh(grd,i  ,j-1)
   else
-    call error_mesg('KID, iceberg_run', 'Unrecognized value of stress_stagger!', FATAL)
+    hxp=(xi+0.5)*ddy_ssh(grd,i  ,j  )+(0.5-xi)*ddy_ssh(grd,i-1,j  )
+    hxm=(xi+0.5)*ddy_ssh(grd,i  ,j-1)+(0.5-xi)*ddy_ssh(grd,i-1,j-1)
   endif
+#endif
+  ! ssh_y is at the v-point on a C-grid
+  ssh_y=yj*hxp+(1.-yj)*hxm
 
-  call mpp_update_domains(grd%uo, grd%vo, grd%domain, gridtype=BGRID_NE)
-  call mpp_update_domains(grd%ui, grd%vi, grd%domain, gridtype=BGRID_NE)
-
-  call invert_tau_for_du(grd%ua, grd%va) ! Note rough conversion from stress to speed
- !grd%ua(grd%isc:grd%iec,grd%jsc:grd%jec)=sign(sqrt(abs(tauxa(:,:))/0.01),tauxa(:,:))  ! Note rough conversion from stress to speed
- !grd%va(grd%isc:grd%iec,grd%jsc:grd%jec)=sign(sqrt(abs(tauya(:,:))/0.01),tauya(:,:))  ! Note rough conversion from stress to speed
-  call mpp_update_domains(grd%ua, grd%va, grd%domain, gridtype=BGRID_NE)
+  ! Rotate vectors from local grid to lat/lon coordinates
+  call rotate(uo, vo, cos_rot, sin_rot)
+  call rotate(ui, vi, cos_rot, sin_rot)
+  call rotate(ua, va, cos_rot, sin_rot)
+  call rotate(ssh_x, ssh_y, cos_rot, sin_rot)
 
-  ! Copy sea surface height and temperature(resides on A grid)
-  grd%ssh(grd%isc-1:grd%iec+1,grd%jsc-1:grd%jec+1)=ssh(:,:)
-  if (bergs%add_iceberg_thickness_to_SSH) then
-    !We might need to make sure spread_mass is defined on halos (or this might be done automatically. I need to look into this)
-    do i=grd%isd,grd%ied ; do j=grd%jsd,grd%jed
-      if (grd%area(i,j)>0) then
-        grd%ssh(i,j) =   ((grd%spread_mass(i,j)/grd%area(i,j))*(bergs%rho_bergs/rho_seawater))  !Is this an appropriate sea water density to use? Should be freezing point.
-      endif
-    enddo ;enddo
-  endif
+  !There are some issues with the boundaries ssh gradient calculation in a finite domain. This is a temporary fix
+  if (ssh_x.ne.ssh_x) ssh_x=0.
+  if (ssh_y.ne.ssh_y) ssh_y=0.
+
+  if (((((uo.ne.uo) .or. (vo.ne.vo)) .or. ((ui.ne.ui) .or. (vi.ne.vi))) .or. &
+       (((ua.ne.ua) .or. (va.ne.va)) .or. ((ssh_x.ne.ssh_x) .or. (ssh_y.ne.ssh_y)))) .or. &
+       (((sst.ne. sst) .or. (sss.ne. sss) .or. (cn.ne.cn)) .or. (hi.ne. hi))) then
+    write(stderrunit,*) 'KID, Error in interpolate: uo,vo,ui,vi',uo, vo, ui, vi
+    write(stderrunit,*) 'KID, Error in interpolate: ua,va,ssh_x,ssh_y', ua, va, ssh_x, ssh_y
+    write(stderrunit,*) 'KID, Error in interpolate: sst,cn,hi', sst, sss, cn, hi, mpp_pe()
+    call error_mesg('KID, interp fields', 'field interpaolations has NaNs', FATAL)
 
-  call mpp_update_domains(grd%ssh, grd%domain)
-  max_SST = maxval(sst(:,:))
-  if (max_SST > 120.0) then ! The input sst is in degrees Kelvin, otherwise the water would be boiling.
-    grd%sst(grd%isc:grd%iec,grd%jsc:grd%jec) = sst(:,:)-273.15 ! Note convert from Kelvin to Celsius
-  else  ! The input sst is already in degrees Celsius.
-    grd%sst(grd%isc:grd%iec,grd%jsc:grd%jec) = sst(:,:) ! Note no conversion necessary.
   endif
-  call mpp_update_domains(grd%sst, grd%domain)
-  ! Copy sea-ice concentration and thickness (resides on A grid)
-  grd%cn(grd%isc-1:grd%iec+1,grd%jsc-1:grd%jec+1)=cn(:,:)
-  call mpp_update_domains(grd%cn, grd%domain)
-  grd%hi(grd%isc-1:grd%iec+1,grd%jsc-1:grd%jec+1)=hi(:,:)
-  call mpp_update_domains(grd%hi, grd%domain)
 
-  ! Adding gridded salinity.
-  if (present(sss)) then
-    grd%sss(grd%isc:grd%iec,grd%jsc:grd%jec)=sss(:,:)
-  else
-    grd%sss(grd%isc:grd%iec,grd%jsc:grd%jec)=-1.0
-    if ((bergs%use_mixed_layer_salinity_for_thermo) .and. (bergs%melt_icebergs_as_ice_shelf))  then
-      call error_mesg('KID, icebergs_run', 'Can not use salinity for thermo. Ocean ML salinity not present!', FATAL)
-    endif
+  ! Quadratic interpolation of ocean depth+sea surface height (A-grid)
+  if (present(od)) then
+    od=quad_interp_from_agrid(grd,grd%ocean_depth,x,y,i,j,xi,yj)+quad_interp_from_agrid(grd,grd%ssh,x,y,i,j,xi,yj)
   endif
+end subroutine interp_flds
 
-  ! Make sure that gridded values agree with mask  (to get rid of NaN values)
-  do i=grd%isd,grd%ied ; do j=grd%jsd,grd%jed
-    ! Initializing all gridded values to zero
-    if (grd%msk(i,j).lt. 0.5) then
-      grd%ua(i,j) = 0.0 ;  grd%va(i,j) = 0.0
-      grd%uo(i,j) = 0.0 ;  grd%vo(i,j) = 0.0
-      grd%ui(i,j) = 0.0 ;  grd%vi(i,j) = 0.0
-      grd%sst(i,j)= 0.0;  grd%sss(i,j)= 0.0
-      grd%cn(i,j) = 0.0 ;  grd%hi(i,j) = 0.0
-    endif
-    if (grd%ua(i,j) .ne. grd%ua(i,j)) grd%ua(i,j)=0.
-    if (grd%va(i,j) .ne. grd%va(i,j)) grd%va(i,j)=0.
-    if (grd%uo(i,j) .ne. grd%uo(i,j)) grd%uo(i,j)=0.
-    if (grd%vo(i,j) .ne. grd%vo(i,j)) grd%vo(i,j)=0.
-    if (grd%ui(i,j) .ne. grd%ui(i,j)) grd%ui(i,j)=0.
-    if (grd%vi(i,j) .ne. grd%vi(i,j)) grd%vi(i,j)=0.
-    if (grd%sst(i,j) .ne. grd%sst(i,j)) grd%sst(i,j)=0.
-    if (grd%sss(i,j) .ne. grd%sss(i,j)) grd%sss(i,j)=0.
-    if (grd%cn(i,j) .ne. grd%cn(i,j)) grd%cn(i,j)=0.
-    if (grd%hi(i,j) .ne. grd%hi(i,j)) grd%hi(i,j)=0.
-  enddo; enddo
+!> Returns zonal slope of sea-surface height across the east face of cell i,j
+real function ddx_ssh(grd,i,j)
+  ! Arguments
+  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+  integer, intent(in) :: i !< i-index of cell
+  integer, intent(in) :: j !< j-index of cell
+  ! Local variables
+  real :: dxp,dx0
+  dxp=0.5*(grd%dx(i+1,j)+grd%dx(i+1,j-1))
+  dx0=0.5*(grd%dx(i,j)+grd%dx(i,j-1))
+  ddx_ssh=2.*(grd%ssh(i+1,j)-grd%ssh(i,j))/(dx0+dxp)*grd%msk(i+1,j)*grd%msk(i,j)
+end function ddx_ssh
 
-  if (debug) call bergs_chksum(bergs, 'run bergs (top)')
-  if (debug) call checksum_gridded(bergs%grd, 'top of s/r run')
+!> Returns meridional slope of sea-surface height across the northern face of cell i,j
+real function ddy_ssh(grd,i,j)
+  ! Arguments
+  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+  integer, intent(in) :: i !< i-index of cell
+  integer, intent(in) :: j !< j-index of cell
+  ! Local variables
+  real :: dyp,dy0
+  dyp=0.5*(grd%dy(i,j+1)+grd%dy(i-1,j+1))
+  dy0=0.5*(grd%dy(i,j)+grd%dy(i-1,j))
+  ddy_ssh=2.*(grd%ssh(i,j+1)-grd%ssh(i,j))/(dy0+dyp)*grd%msk(i,j+1)*grd%msk(i,j)
+end function ddy_ssh
 
-  !If MTS VV and first visit, perform initial interp of gridded fields to bergs
-  if (.not. Visited) then
-    Visited=.true.
-    if (bergs%mts) then
-      call interp_gridded_fields_to_bergs(bergs)
-      call transfer_mts_bergs(bergs)
-    elseif ((bergs%contact_distance>0.) .or. (bergs%contact_spring_coef .ne. bergs%spring_coef)) then
-        call set_conglom_ids(bergs)
-    endif
-  endif
+! Rotates vector (u,v) using rotation matrix with elements cos_rot and sin_rot
+subroutine rotate(u, v, cos_rot, sin_rot)
+  ! Arguments
+  real, intent(inout) :: u !< x-component of vector
+  real, intent(inout) :: v !< y-component of vector
+  real, intent(in) :: cos_rot !< Cosine of rotation angle
+  real, intent(in) :: sin_rot !< Sine of rotation angle
+  ! Local variables
+  real :: u_old, v_old
 
-  ! Accumulate ice from calving
-  call accumulate_calving(bergs)
-  if (grd%id_accum>0) then
-    grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec)=calving(:,:)
-    grd%tmp(:,:)=grd%tmp(:,:)*grd%msk(:,:)*grd%area(:,:)-grd%calving(:,:)
-    lerr=send_data(grd%id_accum, grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  endif
-  if (grd%id_unused>0) &
-    lerr=send_data(grd%id_unused, grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  unused_calving=sum( grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec) )
-  call mpp_clock_end(bergs%clock_int)
+  u_old=u
+  v_old=v
+  u=cos_rot*u_old+sin_rot*v_old
+  v=cos_rot*v_old-sin_rot*u_old
 
-  call mpp_clock_begin(bergs%clock_cal)
-  ! Calve excess stored ice into icebergs
-  if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, before calving()   ')
-  call calve_icebergs(bergs)
-  if (debug) call bergs_chksum(bergs, 'run bergs (calved)')
-  if (debug) call checksum_gridded(bergs%grd, 's/r run after calving')
-  if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after calving()    ')
-  call mpp_clock_end(bergs%clock_cal)
+end subroutine rotate
 
-  ! For each berg, evolve
-  call mpp_clock_begin(bergs%clock_mom)
+!> Calculates bergs%grd%mass_on_ocean
+subroutine calculate_mass_on_ocean(bergs, with_diagnostics)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  logical, intent(in) :: with_diagnostics
+  ! Local variables
+  type(iceberg), pointer :: berg
+  type(icebergs_gridded), pointer :: grd
+  integer :: grdj, grdi
+  integer :: j, i
 
-  if (.not.bergs%Static_icebergs) then
-    if (bergs%mts) then
-      call evolve_icebergs_mts(bergs)
-    else
-      call evolve_icebergs(bergs)
-    end if
-    if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after evolve()     ')
-  endif
-  call move_berg_between_cells(bergs)  !Markpoint6
-  if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after move_lists() ')
-  if (debug) call bergs_chksum(bergs, 'run bergs (evolved)',ignore_halo_violation=.true.)
-  if (debug) call checksum_gridded(bergs%grd, 's/r run after evolve')
-  call mpp_clock_end(bergs%clock_mom)
+  ! For convenience
+  grd=>bergs%grd
 
-  ! Send bergs to other PEs
-  call mpp_clock_begin(bergs%clock_com)
-  if (bergs%iceberg_bonds_on)  call  bond_address_update(bergs)
+  !Initialize fields
+  grd%mass_on_ocean(:,:,:)=0.
+  grd%area_on_ocean(:,:,:)=0.
+  grd%Uvel_on_ocean(:,:,:)=0.
+  grd%Vvel_on_ocean(:,:,:)=0.
 
-  call send_bergs_to_other_pes(bergs)
-  if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after send_bergs() ')
-  if (bergs%mts) then
-    call interp_gridded_fields_to_bergs(bergs)
-    call transfer_mts_bergs(bergs)
-  else
-    if ((bergs%interactive_icebergs_on) .or. (bergs%iceberg_bonds_on)) then
-      call update_halo_icebergs(bergs)
-      if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after update_halo()')
-      if (bergs%iceberg_bonds_on) then
-        call connect_all_bonds(bergs)
-      else
-        if (grd%Lx>0.) call update_latlon(bergs)
-      endif
-      if ((bergs%contact_distance>0.) .or. (bergs%contact_spring_coef .ne. bergs%spring_coef)) then
-        call set_conglom_ids(bergs)
-      endif
-    endif
-  endif
-  if (debug) call bergs_chksum(bergs, 'run bergs (exchanged)')
-  if (debug) call checksum_gridded(bergs%grd, 's/r run after exchange')
-  call mpp_clock_end(bergs%clock_com)
+  do grdj = grd%jsc-1,grd%jec+1 ; do grdi = grd%isc-1,grd%iec+1
+    berg=>bergs%list(grdi,grdj)%first
+    do while(associated(berg))
+      if (berg%halo_berg<2 .or. .not. bergs%mts) then
+        i=berg%ine  ;     j=berg%jne
+        if (grd%area(i,j) > 0.) then
 
-  if (bergs%find_melt_using_spread_mass .or. bergs%mts) then
-    call calculate_mass_on_ocean(bergs, with_diagnostics=.false.)
-  end if
+          !Increasing Mass on ocean
+          if ((bergs%add_weight_to_ocean .and. .not. bergs%time_average_weight) .or.(bergs%find_melt_using_spread_mass)) then
+            call spread_mass_across_ocean_cells(bergs, berg, berg%ine, berg%jne, berg%xi, berg%yj, berg%mass,berg%mass_of_bits, berg%mass_scaling, &
+              berg%length*berg%width, berg%thickness)
+          endif
 
-  ! Calculate mass on ocean before thermodynamics, to use in melt rate calculation
-  if (bergs%find_melt_using_spread_mass) then
-    grd%spread_mass_old(:,:)=0.
-    call sum_up_spread_fields(bergs,grd%spread_mass_old(grd%isc:grd%iec,grd%jsc:grd%jec), 'mass')
-    !Reset fields
-    grd%mass_on_ocean(:,:,:)=0.  ;  grd%area_on_ocean(:,:,:)=0.
-    grd%Uvel_on_ocean(:,:,:)=0.  ;  grd%Vvel_on_ocean(:,:,:)=0.
-  endif
+          !Calculated some iceberg diagnositcs
+          if (with_diagnostics) call calculate_sum_over_bergs_diagnositcs(bergs,grd,berg,i,j)
 
-  ! Iceberg thermodynamics (melting) + rolling
-  call mpp_clock_begin(bergs%clock_the)
-  call thermodynamics(bergs)
-  if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after thermodyn()  ')
-  if (debug) call bergs_chksum(bergs, 'run bergs (thermo)')
-  if (debug) call checksum_gridded(bergs%grd, 's/r run after thermodynamics')
-  call mpp_clock_end(bergs%clock_the)
+        endif
+      endif
+      berg=>berg%next
+    enddo
+  enddo ;enddo
 
-  !Creating gridded fields from new icebergs
-  call create_gridded_icebergs_fields(bergs)
+end subroutine calculate_mass_on_ocean
 
-  ! For each berg, record
-  call mpp_clock_begin(bergs%clock_dia)
-  if (sample_traj .or. bergs%writeandstop) call record_posn(bergs)
-  if (write_traj .or. bergs%writeandstop) then
-    call move_all_trajectories(bergs)
-    call write_trajectory(bergs%trajectories, bergs%save_short_traj)
-  endif
+!> Projects additional diagnostics of bergs on to the grid
+subroutine calculate_sum_over_bergs_diagnositcs(bergs, grd, berg, i, j)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+  type(iceberg), pointer :: berg !< An iceberg
+  integer, intent(in) :: i !< i-index of cell containing berg
+  integer, intent(in) :: j !< j-index of cell containing berg
+  ! Local variables
+  real ::  Abits, Lbits, Mbits
 
-  if (bergs%writeandstop) then
-    call mpp_sync()
-    call error_mesg('KID', 'WRITE AND STOP!!!', FATAL)
+  !Virtual area diagnostic
+  if (grd%id_virtual_area>0) then
+    if (bergs%bergy_bit_erosion_fraction>0.) then
+      Lbits=min(berg%length,berg%width,berg%thickness,40.) ! assume bergy bits are smallest dimension or 40 meters
+      Abits=(berg%mass_of_bits/bergs%rho_bergs)/Lbits ! Effective bottom area (assuming T=Lbits)
+    else
+      Abits=0.0
+    endif
+    grd%virtual_area(i,j)=grd%virtual_area(i,j)+(berg%width*berg%length+Abits)*berg%mass_scaling ! m^2
   endif
 
-
-  ! Gridded diagnostics
-  if (grd%id_uo>0) &
-    lerr=send_data(grd%id_uo, grd%uo(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  if (grd%id_vo>0) &
-    lerr=send_data(grd%id_vo, grd%vo(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  if (grd%id_ui>0) &
-    lerr=send_data(grd%id_ui, grd%ui(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  if (grd%id_vi>0) &
-    lerr=send_data(grd%id_vi, grd%vi(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  if (grd%id_ua>0) &
-    lerr=send_data(grd%id_ua, grd%ua(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  if (grd%id_va>0) &
-    lerr=send_data(grd%id_va, grd%va(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  if (grd%id_sst>0) &
-    lerr=send_data(grd%id_sst, grd%sst(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  if (grd%id_sss>0) &
-    lerr=send_data(grd%id_sss, grd%sss(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  if (grd%id_cn>0) &
-    lerr=send_data(grd%id_cn, grd%cn(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  if (grd%id_hi>0) &
-    lerr=send_data(grd%id_hi, grd%hi(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  if (grd%id_floating_melt>0) &
-    lerr=send_data(grd%id_floating_melt, grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  if (grd%id_melt_m_per_year>0) &
-    lerr=send_data(grd%id_melt_m_per_year, grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec)* (86400.0*365.0/bergs%rho_bergs), Time)
-  if (grd%id_berg_melt>0) &
-    lerr=send_data(grd%id_berg_melt, grd%berg_melt(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  if (grd%id_melt_buoy>0) &
-    lerr=send_data(grd%id_melt_buoy, grd%melt_buoy(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  if (grd%id_melt_eros>0) &
-    lerr=send_data(grd%id_melt_eros, grd%melt_eros(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  if (grd%id_melt_conv>0) &
-    lerr=send_data(grd%id_melt_conv, grd%melt_conv(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  if (grd%id_virtual_area>0) &
-    lerr=send_data(grd%id_virtual_area, grd%virtual_area(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  if (grd%id_bergy_src>0) &
-    lerr=send_data(grd%id_bergy_src, grd%bergy_src(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  if (grd%id_bergy_melt>0) &
-    lerr=send_data(grd%id_bergy_melt, grd%bergy_melt(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  if (grd%id_bergy_mass>0) &
-    lerr=send_data(grd%id_bergy_mass, grd%bergy_mass(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  if (grd%id_spread_mass>0) &
-    lerr=send_data(grd%id_spread_mass, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  if (grd%id_spread_area>0) &
-    lerr=send_data(grd%id_spread_area, grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  !Mass diagnostic (also used in u_iceberg, v_iceberg
+  if ((grd%id_mass>0 ) .or. ((grd%id_u_iceberg>0) .or. (grd%id_v_iceberg>0)))   &
+       & grd%mass(i,j)=grd%mass(i,j)+berg%mass/grd%area(i,j)*berg%mass_scaling ! kg/m2
+
+  !Finding the average iceberg velocity in a grid cell (mass weighted)
   if (grd%id_u_iceberg>0) &
-    lerr=send_data(grd%id_u_iceberg, grd%u_iceberg(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  grd%u_iceberg(i,j)=grd%u_iceberg(i,j)+((berg%mass/grd%area(i,j)*berg%mass_scaling)*berg%uvel) ! kg/m2
   if (grd%id_v_iceberg>0) &
-    lerr=send_data(grd%id_v_iceberg, grd%v_iceberg(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  if (grd%id_spread_uvel>0) &
-    lerr=send_data(grd%id_spread_uvel, grd%spread_uvel(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  if (grd%id_spread_vvel>0) &
-    lerr=send_data(grd%id_spread_vvel, grd%spread_vvel(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  if (grd%id_ustar_iceberg>0) &
-    lerr=send_data(grd%id_ustar_iceberg, grd%ustar_iceberg(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  if (grd%id_mass>0) &
-    lerr=send_data(grd%id_mass, grd%mass(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  if (grd%id_stored_ice>0) &
-    lerr=send_data(grd%id_stored_ice, grd%stored_ice(grd%isc:grd%iec,grd%jsc:grd%jec,:), Time)
-  if (grd%id_rmean_calving>0) &
-    lerr=send_data(grd%id_rmean_calving, grd%rmean_calving(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  if (grd%id_rmean_calving_hflx>0) &
-    lerr=send_data(grd%id_rmean_calving_hflx, grd%rmean_calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  if (grd%id_real_calving>0) &
-    lerr=send_data(grd%id_real_calving, grd%real_calving(grd%isc:grd%iec,grd%jsc:grd%jec,:), Time)
-  if (grd%id_ssh>0) &
-    lerr=send_data(grd%id_ssh, grd%ssh(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
-  if (grd%id_fax>0) &
-    lerr=send_data(grd%id_fax, tauxa(:,:), Time)
-  if (grd%id_fay>0) &
-    lerr=send_data(grd%id_fay, tauya(:,:), Time)
-  if (grd%id_count>0) then
-    allocate( iCount(grd%isc:grd%iec,grd%jsc:grd%jec) ); iCount(:,:)=0
-    do j = grd%jsc, grd%jec ; do i = grd%isc, grd%iec
-      iCount(i,j) = count_bergs_in_list(bergs%list(i,j)%first)
-    enddo ; enddo
-    lerr=send_data(grd%id_count, iCount(:,:), Time)
-    deallocate( iCount )
-  endif
-  if (grd%id_chksum>0) then
-    allocate( iCount(grd%isc:grd%iec,grd%jsc:grd%jec) ); iCount(:,:)=0
-    do j = grd%jsc, grd%jec ; do i = grd%isc, grd%iec
-      iCount(i,j) = list_chksum(bergs%list(i,j)%first)
-    enddo ; enddo
-    lerr=send_data(grd%id_chksum, iCount(:,:), Time)
-    deallocate( iCount )
-  endif
+  grd%v_iceberg(i,j)=grd%v_iceberg(i,j)+((berg%mass/grd%area(i,j)*berg%mass_scaling)*berg%vvel) ! kg/m2
 
-  ! Dump icebergs to screen
-  if (really_debug) call print_bergs(stderrunit,bergs,'icebergs_run, status')
+  !Mass of bergy bits
+  if (grd%id_bergy_mass>0 .or. bergs%add_weight_to_ocean)&
+       & grd%bergy_mass(i,j)=grd%bergy_mass(i,j)+berg%mass_of_bits/grd%area(i,j)*berg%mass_scaling ! kg/m2
+end subroutine calculate_sum_over_bergs_diagnositcs
 
-  ! Dump icebergs bonds to screen
-  if (really_debug)  call show_all_bonds(bergs)
+!> The main driver the steps updates icebergs
+subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh, sst, calving_hflx, cn, hi, &
+                        stagger, stress_stagger, sss, mass_berg, ustar_berg, area_berg)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  type(time_type), intent(in) :: time !< Model time
+  real, dimension(:,:), intent(inout) :: calving !< Calving (kg/s). This field is updated with melt by bergs.
+  real, dimension(:,:), intent(inout) :: calving_hflx !< Calving heat flux (W/m2)
+  real, dimension(:,:), intent(in) :: uo !< Ocean zonal velocity (m/s)
+  real, dimension(:,:), intent(in) :: vo !< Ocean meridional velocity (m/s)
+  real, dimension(:,:), intent(in) :: ui !< Ice zonal velocity (m/s)
+  real, dimension(:,:), intent(in) :: vi !< Ice meridional velocity (m/s)
+  real, dimension(:,:), intent(in) :: tauxa !< Zonal wind stress (Pa)
+  real, dimension(:,:), intent(in) :: tauya !< Meridional wind stress (Pa)
+  real, dimension(:,:), intent(in) :: ssh !< Effective sea-surface height (m)
+  real, dimension(:,:), intent(in) :: sst !< Sea-surface temperature (C or K)
+  real, dimension(:,:), intent(in) :: cn !< Sea-ice concentration (nondim)
+  real, dimension(:,:), intent(in) :: hi !< Sea-ice thickness (m)
+  integer, optional, intent(in) :: stagger
+  integer, optional, intent(in) :: stress_stagger
+  real, dimension(:,:), optional, intent(in) :: sss !< Sea-surface salinity (1e-3)
+  real, dimension(:,:), optional, pointer :: mass_berg !< Mass of bergs (kg)
+  real, dimension(:,:), optional, pointer :: ustar_berg !< Friction velocity on base of bergs (m/s)
+  real, dimension(:,:), optional, pointer :: area_berg !< Area of bergs (m2)
+  ! Local variables
+  integer :: iyr, imon, iday, ihr, imin, isec, k
+  type(icebergs_gridded), pointer :: grd
+  logical :: lerr, sample_traj, write_traj, lbudget, lverbose, check_bond_quality
+  real :: unused_calving, tmpsum, grdd_berg_mass, grdd_bergy_mass,grdd_spread_mass, grdd_spread_area
+  real :: grdd_u_iceberg, grdd_v_iceberg, grdd_ustar_iceberg, grdd_spread_uvel, grdd_spread_vvel
+  integer :: i, j, Iu, ju, iv, Jv, Iu_off, ju_off, iv_off, Jv_off
+  real :: mask, max_SST
+  real, dimension(:,:), allocatable :: uC_tmp, vC_tmp, uA_tmp, vA_tmp
+  integer :: vel_stagger, str_stagger
+  real, dimension(:,:), allocatable :: iCount
+  integer :: nbonds
+  integer :: stderrunit
+  logical :: Visited=.false.
+  save :: Visited
 
-  call mpp_clock_end(bergs%clock_dia)
+  ! Get the stderr unit number
+  stderrunit = stderr()
 
-  ! This is the point in the algorithm which determines which fields get passed to the ice model
-  ! Return what ever calving we did not use and additional icebergs melt
+  call mpp_clock_begin(bergs%clock)
+  call mpp_clock_begin(bergs%clock_int)
 
-  ! Making sure that spread_mass has the correct mass
-  !grd%spread_mass(:,:)=0.0
-  !call icebergs_incr_mass(bergs, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec), within_iceberg_model=.True.)
+  vel_stagger = BGRID_NE ; if (present(stagger)) vel_stagger = stagger
+  str_stagger = vel_stagger ; if (present(stress_stagger)) str_stagger = stress_stagger
 
+  ! For convenience
+  grd=>bergs%grd
 
-  ! Return what ever calving we did not use and additional icebergs melt
-  call mpp_clock_begin(bergs%clock_int)
-  if (.not. bergs%passive_mode) then
-    where (grd%area(grd%isc:grd%iec,grd%jsc:grd%jec)>0.)
-      calving(:,:)=grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec)/grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) &
-                  +grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec)
-    elsewhere
-      calving(:,:)=0.
-    end where
-    calving_hflx(:,:)=grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)
-    !Return iceberg mass, area and ustar to pass on to ocean model
-    if (present(mass_berg)) then
-      if (associated(mass_berg)) then
-        if (bergs%add_weight_to_ocean) &
-          mass_berg(:,:)=grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec)
-      endif
-    endif
-    if (present(ustar_berg)) then
-      if (associated(ustar_berg)) then
-        ustar_berg(:,:)=grd%ustar_iceberg(grd%isc:grd%iec,grd%jsc:grd%jec)
-      endif
-    endif
-    if (present(area_berg)) then
-      if (associated(area_berg)) then
-        area_berg(:,:)=grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec)
-      endif
-    endif
+  grd%floating_melt(:,:)=0.
+  grd%berg_melt(:,:)=0.
+  grd%melt_buoy(:,:)=0.
+  grd%melt_eros(:,:)=0.
+  grd%melt_conv(:,:)=0.
+  grd%bergy_src(:,:)=0.
+  grd%bergy_melt(:,:)=0.
+  grd%bergy_mass(:,:)=0.
+  grd%spread_mass_old(:,:)=0.
+  !grd%spread_mass(:,:)=0.  !Don't zero this out yet, because we can first use this an add it onto the SSH
+  grd%spread_area(:,:)=0.
+  grd%u_iceberg(:,:)=0.
+  grd%v_iceberg(:,:)=0.
+  grd%spread_uvel(:,:)=0.
+  grd%spread_vvel(:,:)=0.
+  grd%ustar_iceberg(:,:)=0.
+  grd%mass(:,:)=0.
+  grd%virtual_area(:,:)=0.
+
+  !Initializing _on_ocean_fields
+  grd%mass_on_ocean(:,:,:)=0. ;   grd%area_on_ocean(:,:,:)=0.
+  grd%Uvel_on_ocean(:,:,:)=0. ;   grd%Vvel_on_ocean(:,:,:)=0.
+
+  if (present(mass_berg)) then ;  if (associated(mass_berg)) then
+    mass_berg(:,:)=0.0
+  endif ;  endif
+  if (present(ustar_berg)) then ; if (associated(ustar_berg)) then
+    ustar_berg(:,:)=0.0
+  endif ;  endif
+  if (present(area_berg)) then ;  if (associated(area_berg)) then
+    area_berg(:,:)=0.0
+  endif ;  endif
+
+  ! Manage time
+  call get_date(time, iyr, imon, iday, ihr, imin, isec)
+  bergs%current_year=iyr
+  bergs%current_yearday=yearday(imon, iday, ihr, imin, isec)
+  ! Turn on sampling of trajectories, verbosity, budgets
+  sample_traj=.false.
+  if ( (bergs%traj_sample_hrs>0)  .and. (.not. bergs%ignore_traj) ) then
+    if (mod(60*60*24*iday+ 60*60*ihr + 60.*imin + isec ,60*60*bergs%traj_sample_hrs).eq.0) &
+      sample_traj=.true.
+  elseif (bergs%traj_sample_hrs==0) then
+    sample_traj=.true.
+  endif
+  write_traj=.false.
+  if ((bergs%traj_write_hrs>0) .and. (.not. bergs%ignore_traj))  then
+     if (mod(60*60*24*iday+ 60*60*ihr + 60.*imin + isec ,60*60*bergs%traj_write_hrs).eq.0) &
+       write_traj=.true.
+   elseif (bergs%traj_write_hrs==0) then
+     write_traj=.true.
+  endif
+  lverbose=.false.
+  if (bergs%verbose_hrs>0) then
+    !if (mod(24*iday+ihr+(imin/60.),float(bergs%verbose_hrs)).eq.0) lverbose=verbose
+    if (mod(24*iday+ihr+(imin/60.),bergs%verbose_hrs).eq.0) lverbose=verbose
+  endif
+  lbudget=.false.
+  if (bergs%verbose_hrs>0) then
+     !if (mod(24*iday+ihr+(imin/60.),float(bergs%verbose_hrs)).eq.0) lbudget=budget  !Added minutes, so that it does not repeat when smaller time steps are used.
+     if (mod(24*iday+ihr+(imin/60.),bergs%verbose_hrs).eq.0) lbudget=budget
   endif
+  if (mpp_pe()==mpp_root_pe().and.lverbose) write(*,'(a,3i5,a,3i5,a,i5,f8.3)') &
+       'KID: y,m,d=',iyr, imon, iday,' h,m,s=', ihr, imin, isec, &
+       ' yr,yrdy=', bergs%current_year, bergs%current_yearday
 
-  call mpp_clock_end(bergs%clock_int)
 
-  ! Diagnose budgets
-  call mpp_clock_begin(bergs%clock_dia)
-  tmpsum=sum( grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
-  bergs%net_melt=bergs%net_melt+tmpsum*bergs%dt
-  bergs%net_outgoing_calving=bergs%net_outgoing_calving+(unused_calving+tmpsum)*bergs%dt
-  tmpsum=sum( grd%berg_melt(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
-  bergs%berg_melt=bergs%berg_melt+tmpsum*bergs%dt
-  tmpsum=sum( grd%bergy_src(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
-  bergs%bergy_src=bergs%bergy_src+tmpsum*bergs%dt
-  tmpsum=sum( grd%bergy_melt(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
-  bergs%bergy_melt=bergs%bergy_melt+tmpsum*bergs%dt
+ !call sanitize_field(grd%calving,1.e20)
   tmpsum=sum( calving(:,:)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
-  bergs%net_calving_returned=bergs%net_calving_returned+tmpsum*bergs%dt
+  bergs%net_calving_received=bergs%net_calving_received+tmpsum*bergs%dt
+
+  ! Adapt calving heat flux from coupler
+  grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)=calving_hflx(:,:) & ! Units of W/m2
+       *grd%msk(grd%isc:grd%iec,grd%jsc:grd%jec)
+
+  ! Adapt calving flux from coupler for use here
+  grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec)=calving(:,:) & ! Units of kg/m2/s
+       *grd%msk(grd%isc:grd%iec,grd%jsc:grd%jec)
+
+  ! Running means of calving and calving_hflx
+  if (bergs%tau_calving>0.) then
+    call get_running_mean_calving(bergs, grd%calving, grd%calving_hflx)
+    calving(:,:)=grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec) ! Copy back from grd%calving if using running-mean
+    calving_hflx(:,:)=grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)
+  endif
+
+  grd%calving(:,:)=grd%calving(:,:)*grd%msk(:,:)*grd%area(:,:) ! Convert to kg/s
+  tmpsum=sum( grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec) )
+  bergs%net_incoming_calving=bergs%net_incoming_calving+tmpsum*bergs%dt
+  if (grd%id_calving>0) &
+    lerr=send_data(grd%id_calving, grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+
+  grd%calving_hflx(:,:)=grd%calving_hflx(:,:)*grd%msk(:,:) ! Mask (just in case)
+  if (grd%id_calving_hflx_in>0) &
+    lerr=send_data(grd%id_calving_hflx_in, grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  tmpsum=sum( grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
+  bergs%net_incoming_calving_heat=bergs%net_incoming_calving_heat+tmpsum*bergs%dt ! Units of J
+
+  if (grd%id_ocean_depth>0) &
+    lerr=send_data(grd%id_ocean_depth, grd%ocean_depth(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+
+  if (vel_stagger == BGRID_NE) then
+    ! Copy ocean and ice velocities. They are already on B-grid u-points.
+    grd%uo(grd%isc-1:grd%iec+1,grd%jsc-1:grd%jec+1) = uo(:,:)
+    grd%vo(grd%isc-1:grd%iec+1,grd%jsc-1:grd%jec+1) = vo(:,:)
+    call mpp_update_domains(grd%uo, grd%vo, grd%domain, gridtype=BGRID_NE)
+    grd%ui(grd%isc-1:grd%iec+1,grd%jsc-1:grd%jec+1) = ui(:,:)
+    grd%vi(grd%isc-1:grd%iec+1,grd%jsc-1:grd%jec+1) = vi(:,:)
+    call mpp_update_domains(grd%ui, grd%vi, grd%domain, gridtype=BGRID_NE)
+  elseif (vel_stagger == CGRID_NE) then
+    ! The u- and v- points will have different offsets with symmetric memory.
+    Iu_off = (size(uo,1) - (grd%iec - grd%isc))/2 - grd%isc + 1
+    ju_off = (size(uo,2) - (grd%jec - grd%jsc))/2 - grd%jsc + 1
+    iv_off = (size(vo,1) - (grd%iec - grd%isc))/2 - grd%isc + 1
+    Jv_off = (size(vo,2) - (grd%jec - grd%jsc))/2 - grd%jsc + 1
+    do I=grd%isc-1,grd%iec ; do J=grd%jsc-1,grd%jec
+      ! Interpolate ocean and ice velocities from C-grid velocity points.
+      Iu = i + Iu_off ; ju = j + ju_off ; iv = i + iv_off ; Jv = j + Jv_off
+      ! This masking is needed for now to prevent icebergs from running up on to land.
+      mask = min(grd%msk(i,j), grd%msk(i+1,j), grd%msk(i,j+1), grd%msk(i+1,j+1))
+      grd%uo(I,J) = mask * 0.5*(uo(Iu,ju)+uo(Iu,ju+1))
+      grd%ui(I,J) = mask * 0.5*(ui(Iu,ju)+ui(Iu,ju+1))
+      grd%vo(I,J) = mask * 0.5*(vo(iv,Jv)+vo(iv+1,Jv))
+      grd%vi(I,J) = mask * 0.5*(vi(iv,Jv)+vi(iv+1,Jv))
+    enddo ; enddo
+  else
+    call error_mesg('KID, iceberg_run', 'Unrecognized value of stagger!', FATAL)
+  endif
+
+  if (str_stagger == BGRID_NE) then
+    ! Copy wind stress components on B-grid u-points.
+    grd%ua(grd%isc:grd%iec,grd%jsc:grd%jec) = tauxa(:,:)
+    grd%va(grd%isc:grd%iec,grd%jsc:grd%jec) = tauya(:,:)
+  elseif (str_stagger == CGRID_NE) then
+    ! The u- and v- points will have different offsets with symmetric memory.
+    Iu_off = (size(tauxa,1) - (grd%iec - grd%isc))/2 - grd%isc + 1
+    ju_off = (size(tauxa,2) - (grd%jec - grd%jsc))/2 - grd%jsc + 1
+    iv_off = (size(tauya,1) - (grd%iec - grd%isc))/2 - grd%isc + 1
+    Jv_off = (size(tauya,2) - (grd%jec - grd%jsc))/2 - grd%jsc + 1
+    allocate(uC_tmp(grd%isd:grd%ied,grd%jsd:grd%jed), &
+             vC_tmp(grd%isd:grd%ied,grd%jsd:grd%jed))
+    uC_tmp(:,:) = 0. ! This avoids uninitialized values that might remain in halo
+    vC_tmp(:,:) = 0. ! regions after the call to mpp_update_domains() below.
+    !   If the iceberg model used symmetric memory, the starting value of these
+    ! copies would need to be decremented by 1.
+    do i=grd%isc,grd%iec ; do j=grd%jsc,grd%jec
+      uC_tmp(i,j) = tauxa(i+Iu_off, j+ju_off)
+      vC_tmp(i,J) = tauya(i+iv_off, J+Jv_off)
+    enddo ; enddo
+
+    call mpp_update_domains(uC_tmp, vC_tmp, grd%domain, gridtype=CGRID_NE)
+    do I=grd%isc-1,grd%iec ; do J=grd%jsc-1,grd%jec
+      ! Interpolate wind stresses from C-grid velocity-points.
+      ! This masking is needed for now to prevent icebergs from running up on to land.
+      mask = min(grd%msk(i,j), grd%msk(i+1,j), grd%msk(i,j+1), grd%msk(i+1,j+1))
+       grd%ua(I,J) = mask * 0.5*(uC_tmp(I,j)+uC_tmp(I,j+1))
+       grd%va(I,J) = mask * 0.5*(vC_tmp(i,J)+vC_tmp(i+1,J))
+    enddo ; enddo
+    deallocate(uC_tmp, vC_tmp)
+  elseif (str_stagger == AGRID) then
+    ! Copy into arrays with local index conventions and halos.
+    allocate(uA_tmp(grd%isd:grd%ied,grd%jsd:grd%jed), &
+             vA_tmp(grd%isd:grd%ied,grd%jsd:grd%jed))
+    uA_tmp(:,:) = 0.0 ! This avoids uninitialized values that might remain in halo
+    vA_tmp(:,:) = 0.0 ! regions after the call to mpp_update_domains() below.
+    uA_tmp(grd%isc:grd%iec,grd%jsc:grd%jec) = tauxa(:,:)
+    vA_tmp(grd%isc:grd%iec,grd%jsc:grd%jec) = tauya(:,:)
+    call mpp_update_domains(uA_tmp, vA_tmp, grd%domain, gridtype=AGRID)
+    do I=grd%isc-1,grd%iec ; do J=grd%jsc-1,grd%jec
+      ! Interpolate wind stresses from A-grid tracer points to the corner B-grid points.
+      ! This masking is needed for now to prevent icebergs from running up on to land.
+      mask = min(grd%msk(i,j), grd%msk(i+1,j), grd%msk(i,j+1), grd%msk(i+1,j+1))
+      grd%ua(I,J) = mask * 0.25*((uA_tmp(i,j) + uA_tmp(i+1,j+1)) + &
+                                 (uA_tmp(i+1,j) + uA_tmp(i,j+1)))
+      grd%va(I,J) = mask * 0.25*((vA_tmp(i,j) + vA_tmp(i+1,j+1)) + &
+                                 (vA_tmp(i+1,j) + vA_tmp(i,j+1)))
+    enddo ; enddo
+
+    deallocate(uA_tmp, vA_tmp)
+  else
+    call error_mesg('KID, iceberg_run', 'Unrecognized value of stress_stagger!', FATAL)
+  endif
+
+  call mpp_update_domains(grd%uo, grd%vo, grd%domain, gridtype=BGRID_NE)
+  call mpp_update_domains(grd%ui, grd%vi, grd%domain, gridtype=BGRID_NE)
+
+  call invert_tau_for_du(grd%ua, grd%va) ! Note rough conversion from stress to speed
+ !grd%ua(grd%isc:grd%iec,grd%jsc:grd%jec)=sign(sqrt(abs(tauxa(:,:))/0.01),tauxa(:,:))  ! Note rough conversion from stress to speed
+ !grd%va(grd%isc:grd%iec,grd%jsc:grd%jec)=sign(sqrt(abs(tauya(:,:))/0.01),tauya(:,:))  ! Note rough conversion from stress to speed
+  call mpp_update_domains(grd%ua, grd%va, grd%domain, gridtype=BGRID_NE)
+
+  ! Copy sea surface height and temperature(resides on A grid)
+  grd%ssh(grd%isc-1:grd%iec+1,grd%jsc-1:grd%jec+1)=ssh(:,:)
+  if (bergs%add_iceberg_thickness_to_SSH) then
+    !We might need to make sure spread_mass is defined on halos (or this might be done automatically. I need to look into this)
+    do i=grd%isd,grd%ied ; do j=grd%jsd,grd%jed
+      if (grd%area(i,j)>0) then
+        grd%ssh(i,j) =   ((grd%spread_mass(i,j)/grd%area(i,j))*(bergs%rho_bergs/rho_seawater))  !Is this an appropriate sea water density to use? Should be freezing point.
+      endif
+    enddo ;enddo
+  endif
+
+  call mpp_update_domains(grd%ssh, grd%domain)
+  max_SST = maxval(sst(:,:))
+  if (max_SST > 120.0) then ! The input sst is in degrees Kelvin, otherwise the water would be boiling.
+    grd%sst(grd%isc:grd%iec,grd%jsc:grd%jec) = sst(:,:)-273.15 ! Note convert from Kelvin to Celsius
+  else  ! The input sst is already in degrees Celsius.
+    grd%sst(grd%isc:grd%iec,grd%jsc:grd%jec) = sst(:,:) ! Note no conversion necessary.
+  endif
+  call mpp_update_domains(grd%sst, grd%domain)
+  ! Copy sea-ice concentration and thickness (resides on A grid)
+  grd%cn(grd%isc-1:grd%iec+1,grd%jsc-1:grd%jec+1)=cn(:,:)
+  call mpp_update_domains(grd%cn, grd%domain)
+  grd%hi(grd%isc-1:grd%iec+1,grd%jsc-1:grd%jec+1)=hi(:,:)
+  call mpp_update_domains(grd%hi, grd%domain)
+
+  ! Adding gridded salinity.
+  if (present(sss)) then
+    grd%sss(grd%isc:grd%iec,grd%jsc:grd%jec)=sss(:,:)
+  else
+    grd%sss(grd%isc:grd%iec,grd%jsc:grd%jec)=-1.0
+    if ((bergs%use_mixed_layer_salinity_for_thermo) .and. (bergs%melt_icebergs_as_ice_shelf))  then
+      call error_mesg('KID, icebergs_run', 'Can not use salinity for thermo. Ocean ML salinity not present!', FATAL)
+    endif
+  endif
+
+  ! Make sure that gridded values agree with mask  (to get rid of NaN values)
+  do i=grd%isd,grd%ied ; do j=grd%jsd,grd%jed
+    ! Initializing all gridded values to zero
+    if (grd%msk(i,j).lt. 0.5) then
+      grd%ua(i,j) = 0.0 ;  grd%va(i,j) = 0.0
+      grd%uo(i,j) = 0.0 ;  grd%vo(i,j) = 0.0
+      grd%ui(i,j) = 0.0 ;  grd%vi(i,j) = 0.0
+      grd%sst(i,j)= 0.0;  grd%sss(i,j)= 0.0
+      grd%cn(i,j) = 0.0 ;  grd%hi(i,j) = 0.0
+    endif
+    if (grd%ua(i,j) .ne. grd%ua(i,j)) grd%ua(i,j)=0.
+    if (grd%va(i,j) .ne. grd%va(i,j)) grd%va(i,j)=0.
+    if (grd%uo(i,j) .ne. grd%uo(i,j)) grd%uo(i,j)=0.
+    if (grd%vo(i,j) .ne. grd%vo(i,j)) grd%vo(i,j)=0.
+    if (grd%ui(i,j) .ne. grd%ui(i,j)) grd%ui(i,j)=0.
+    if (grd%vi(i,j) .ne. grd%vi(i,j)) grd%vi(i,j)=0.
+    if (grd%sst(i,j) .ne. grd%sst(i,j)) grd%sst(i,j)=0.
+    if (grd%sss(i,j) .ne. grd%sss(i,j)) grd%sss(i,j)=0.
+    if (grd%cn(i,j) .ne. grd%cn(i,j)) grd%cn(i,j)=0.
+    if (grd%hi(i,j) .ne. grd%hi(i,j)) grd%hi(i,j)=0.
+  enddo; enddo
+
+  if (debug) call bergs_chksum(bergs, 'run bergs (top)')
+  if (debug) call checksum_gridded(bergs%grd, 'top of s/r run')
+
+  !If MTS VV and first visit, perform initial interp of gridded fields to bergs
+  if (.not. Visited) then
+    Visited=.true.
+    if (bergs%mts) then
+      call interp_gridded_fields_to_bergs(bergs)
+      call transfer_mts_bergs(bergs)
+    elseif ((bergs%contact_distance>0.) .or. (bergs%contact_spring_coef .ne. bergs%spring_coef)) then
+      call set_conglom_ids(bergs)
+    endif
+    call orig_bond_length(bergs)
+
+    if (monitor_energy) then
+      call energy_tests_init(bergs)
+    endif
+  endif
+
+  ! Accumulate ice from calving
+  call accumulate_calving(bergs)
+  if (grd%id_accum>0) then
+    grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec)=calving(:,:)
+    grd%tmp(:,:)=grd%tmp(:,:)*grd%msk(:,:)*grd%area(:,:)-grd%calving(:,:)
+    lerr=send_data(grd%id_accum, grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  endif
+  if (grd%id_unused>0) &
+    lerr=send_data(grd%id_unused, grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  unused_calving=sum( grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec) )
+  call mpp_clock_end(bergs%clock_int)
+
+  call mpp_clock_begin(bergs%clock_cal)
+  ! Calve excess stored ice into icebergs
+  if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, before calving()   ')
+  call calve_icebergs(bergs)
+  if (debug) call bergs_chksum(bergs, 'run bergs (calved)')
+  if (debug) call checksum_gridded(bergs%grd, 's/r run after calving')
+  if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after calving()    ')
+  call mpp_clock_end(bergs%clock_cal)
+
+  ! For each berg, evolve
+  call mpp_clock_begin(bergs%clock_mom)
+
+  if (.not.bergs%Static_icebergs) then
+    call reset_bond_rotation(bergs)
+    if (bergs%mts) then
+
+      !Call the MTS subroutine for iceberg evolution:
+      !There are two versions of the MTS subroutine: evolve_icebergs_mts and evolve_icebergs_mts2. Each version
+      !has an experimental option to iterate each short/long step many times to better conserve momentum during
+      !collisions, which may or may not be needed to get consistent fracture behavior. Evolve_icebergs_mts allows
+      !these iterations to be specified with parameters imp_loop_iters_short and imp_loop_iters_long.
+      !Evolve_icebergs_mts2 iterates to a given convergence tolerance (bergs%convergence_tolerance)
+      !if bergs%force_convergence==.true.
+
+      if ((imp_loop_iters_long > 1 .or. imp_loop_iters_short > 1) .and. (.not. bergs%force_convergence)) then
+        call evolve_icebergs_mts(bergs)
+      else
+        call evolve_icebergs_mts2(bergs)
+      endif
+    else
+      call evolve_icebergs(bergs) !The single time step (STS) scheme
+    end if
+    if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after evolve()     ')
+  endif
+  call move_berg_between_cells(bergs)  !Markpoint6
+  if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after move_lists() ')
+  if (debug) call bergs_chksum(bergs, 'run bergs (evolved)',ignore_halo_violation=.true.)
+  if (debug) call checksum_gridded(bergs%grd, 's/r run after evolve')
+  call mpp_clock_end(bergs%clock_mom)
+
+  ! Send bergs to other PEs
+  call mpp_clock_begin(bergs%clock_com)
+  if (bergs%iceberg_bonds_on)  call  bond_address_update(bergs)
+
+  call send_bergs_to_other_pes(bergs)
+  if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after send_bergs() ')
+  if (bergs%mts) then
+    call interp_gridded_fields_to_bergs(bergs)
+    call transfer_mts_bergs(bergs)
+  else
+    if ((bergs%interactive_icebergs_on) .or. (bergs%iceberg_bonds_on)) then
+      call update_halo_icebergs(bergs)
+      if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after update_halo()')
+      if (bergs%iceberg_bonds_on) then
+        call connect_all_bonds(bergs)
+      else
+        if (grd%Lx>0.) call update_latlon(bergs)
+      endif
+      if ((bergs%contact_distance>0.) .or. (bergs%contact_spring_coef .ne. bergs%spring_coef)) then
+        call set_conglom_ids(bergs)
+      endif
+    endif
+  endif
+  if (debug) call bergs_chksum(bergs, 'run bergs (exchanged)')
+  if (debug) call checksum_gridded(bergs%grd, 's/r run after exchange')
+  call mpp_clock_end(bergs%clock_com)
+
+  if (bergs%find_melt_using_spread_mass .or. bergs%mts) then
+    call calculate_mass_on_ocean(bergs, with_diagnostics=.false.)
+  end if
+
+  ! Calculate mass on ocean before thermodynamics, to use in melt rate calculation
+  if (bergs%find_melt_using_spread_mass) then
+    grd%spread_mass_old(:,:)=0.
+    call sum_up_spread_fields(bergs,grd%spread_mass_old(grd%isc:grd%iec,grd%jsc:grd%jec), 'mass')
+    !Reset fields
+    grd%mass_on_ocean(:,:,:)=0.  ;  grd%area_on_ocean(:,:,:)=0.
+    grd%Uvel_on_ocean(:,:,:)=0.  ;  grd%Vvel_on_ocean(:,:,:)=0.
+  endif
+
+  ! Iceberg thermodynamics (melting) + rolling
+  call mpp_clock_begin(bergs%clock_the)
+  call thermodynamics(bergs)
+  if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after thermodyn()  ')
+  if (debug) call bergs_chksum(bergs, 'run bergs (thermo)')
+  if (debug) call checksum_gridded(bergs%grd, 's/r run after thermodynamics')
+  call mpp_clock_end(bergs%clock_the)
+
+  !Creating gridded fields from new icebergs
+  call create_gridded_icebergs_fields(bergs)
+
+  ! For each berg, record
+  call mpp_clock_begin(bergs%clock_dia)
+  if (sample_traj .or. bergs%writeandstop) call record_posn(bergs)
+  if (write_traj .or. bergs%writeandstop) then
+    call move_all_trajectories(bergs)
+    call write_trajectory(bergs%trajectories, bergs%save_short_traj)
+    if (save_bond_traj) call write_bond_trajectory(bergs%bond_trajectories)
+  endif
+
+  if (bergs%writeandstop) then
+    call mpp_sync()
+    call error_mesg('KID', 'WRITE AND STOP!!!', FATAL)
+  endif
+
+
+  ! Gridded diagnostics
+  if (grd%id_uo>0) &
+    lerr=send_data(grd%id_uo, grd%uo(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_vo>0) &
+    lerr=send_data(grd%id_vo, grd%vo(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_ui>0) &
+    lerr=send_data(grd%id_ui, grd%ui(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_vi>0) &
+    lerr=send_data(grd%id_vi, grd%vi(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_ua>0) &
+    lerr=send_data(grd%id_ua, grd%ua(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_va>0) &
+    lerr=send_data(grd%id_va, grd%va(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_sst>0) &
+    lerr=send_data(grd%id_sst, grd%sst(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_sss>0) &
+    lerr=send_data(grd%id_sss, grd%sss(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_cn>0) &
+    lerr=send_data(grd%id_cn, grd%cn(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_hi>0) &
+    lerr=send_data(grd%id_hi, grd%hi(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_floating_melt>0) &
+    lerr=send_data(grd%id_floating_melt, grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_melt_m_per_year>0) &
+    lerr=send_data(grd%id_melt_m_per_year, grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec)* (86400.0*365.0/bergs%rho_bergs), Time)
+  if (grd%id_berg_melt>0) &
+    lerr=send_data(grd%id_berg_melt, grd%berg_melt(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_melt_buoy>0) &
+    lerr=send_data(grd%id_melt_buoy, grd%melt_buoy(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_melt_eros>0) &
+    lerr=send_data(grd%id_melt_eros, grd%melt_eros(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_melt_conv>0) &
+    lerr=send_data(grd%id_melt_conv, grd%melt_conv(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_virtual_area>0) &
+    lerr=send_data(grd%id_virtual_area, grd%virtual_area(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_bergy_src>0) &
+    lerr=send_data(grd%id_bergy_src, grd%bergy_src(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_bergy_melt>0) &
+    lerr=send_data(grd%id_bergy_melt, grd%bergy_melt(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_bergy_mass>0) &
+    lerr=send_data(grd%id_bergy_mass, grd%bergy_mass(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_spread_mass>0) &
+    lerr=send_data(grd%id_spread_mass, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_spread_area>0) &
+    lerr=send_data(grd%id_spread_area, grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_u_iceberg>0) &
+    lerr=send_data(grd%id_u_iceberg, grd%u_iceberg(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_v_iceberg>0) &
+    lerr=send_data(grd%id_v_iceberg, grd%v_iceberg(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_spread_uvel>0) &
+    lerr=send_data(grd%id_spread_uvel, grd%spread_uvel(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_spread_vvel>0) &
+    lerr=send_data(grd%id_spread_vvel, grd%spread_vvel(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_ustar_iceberg>0) &
+    lerr=send_data(grd%id_ustar_iceberg, grd%ustar_iceberg(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_mass>0) &
+    lerr=send_data(grd%id_mass, grd%mass(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_stored_ice>0) &
+    lerr=send_data(grd%id_stored_ice, grd%stored_ice(grd%isc:grd%iec,grd%jsc:grd%jec,:), Time)
+  if (grd%id_rmean_calving>0) &
+    lerr=send_data(grd%id_rmean_calving, grd%rmean_calving(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_rmean_calving_hflx>0) &
+    lerr=send_data(grd%id_rmean_calving_hflx, grd%rmean_calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_real_calving>0) &
+    lerr=send_data(grd%id_real_calving, grd%real_calving(grd%isc:grd%iec,grd%jsc:grd%jec,:), Time)
+  if (grd%id_ssh>0) &
+    lerr=send_data(grd%id_ssh, grd%ssh(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_fax>0) &
+    lerr=send_data(grd%id_fax, tauxa(:,:), Time)
+  if (grd%id_fay>0) &
+    lerr=send_data(grd%id_fay, tauya(:,:), Time)
+  if (grd%id_count>0) then
+    allocate( iCount(grd%isc:grd%iec,grd%jsc:grd%jec) ); iCount(:,:)=0
+    do j = grd%jsc, grd%jec ; do i = grd%isc, grd%iec
+      iCount(i,j) = count_bergs_in_list(bergs%list(i,j)%first)
+    enddo ; enddo
+    lerr=send_data(grd%id_count, iCount(:,:), Time)
+    deallocate( iCount )
+  endif
+  if (grd%id_chksum>0) then
+    allocate( iCount(grd%isc:grd%iec,grd%jsc:grd%jec) ); iCount(:,:)=0
+    do j = grd%jsc, grd%jec ; do i = grd%isc, grd%iec
+      iCount(i,j) = list_chksum(bergs%list(i,j)%first)
+    enddo ; enddo
+    lerr=send_data(grd%id_chksum, iCount(:,:), Time)
+    deallocate( iCount )
+  endif
+
+  ! Dump icebergs to screen
+  if (really_debug) call print_bergs(stderrunit,bergs,'icebergs_run, status')
+
+  ! Dump icebergs bonds to screen
+  if (really_debug)  call show_all_bonds(bergs)
+
+  call mpp_clock_end(bergs%clock_dia)
+
+  ! This is the point in the algorithm which determines which fields get passed to the ice model
+  ! Return what ever calving we did not use and additional icebergs melt
+
+  ! Making sure that spread_mass has the correct mass
+  !grd%spread_mass(:,:)=0.0
+  !call icebergs_incr_mass(bergs, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec), within_iceberg_model=.True.)
+
+
+  ! Return what ever calving we did not use and additional icebergs melt
+  call mpp_clock_begin(bergs%clock_int)
+  if (.not. bergs%passive_mode) then
+    where (grd%area(grd%isc:grd%iec,grd%jsc:grd%jec)>0.)
+      calving(:,:)=grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec)/grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) &
+                  +grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec)
+    elsewhere
+      calving(:,:)=0.
+    end where
+    calving_hflx(:,:)=grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)
+    !Return iceberg mass, area and ustar to pass on to ocean model
+    if (present(mass_berg)) then
+      if (associated(mass_berg)) then
+        if (bergs%add_weight_to_ocean) &
+          mass_berg(:,:)=grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec)
+      endif
+    endif
+    if (present(ustar_berg)) then
+      if (associated(ustar_berg)) then
+        ustar_berg(:,:)=grd%ustar_iceberg(grd%isc:grd%iec,grd%jsc:grd%jec)
+      endif
+    endif
+    if (present(area_berg)) then
+      if (associated(area_berg)) then
+        area_berg(:,:)=grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec)
+      endif
+    endif
+  endif
+
+  call mpp_clock_end(bergs%clock_int)
+
+  ! Diagnose budgets
+  call mpp_clock_begin(bergs%clock_dia)
+  tmpsum=sum( grd%floating_melt(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
+  bergs%net_melt=bergs%net_melt+tmpsum*bergs%dt
+  bergs%net_outgoing_calving=bergs%net_outgoing_calving+(unused_calving+tmpsum)*bergs%dt
+  tmpsum=sum( grd%berg_melt(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
+  bergs%berg_melt=bergs%berg_melt+tmpsum*bergs%dt
+  tmpsum=sum( grd%bergy_src(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
+  bergs%bergy_src=bergs%bergy_src+tmpsum*bergs%dt
+  tmpsum=sum( grd%bergy_melt(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
+  bergs%bergy_melt=bergs%bergy_melt+tmpsum*bergs%dt
+  tmpsum=sum( calving(:,:)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
+  bergs%net_calving_returned=bergs%net_calving_returned+tmpsum*bergs%dt
   tmpsum=sum( grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
   bergs%net_outgoing_calving_heat=bergs%net_outgoing_calving_heat+tmpsum*bergs%dt ! Units of J
   if (lbudget) then
@@ -3813,484 +4489,848 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
              & bergs%net_calving_received)
         call report_consistant('bot interface','kg','sent',bergs%net_outgoing_calving,'seen by SIS',bergs%net_calving_returned)
       endif
-      write(*,'("KID: calved by class = ",i4,20(",",i4))') (bergs%nbergs_calved_by_class(k),k=1,nclasses)
-      if (bergs%nspeeding_tickets>0) write(*,'("KID: speeding tickets issued = ",i4)') bergs%nspeeding_tickets
-    endif
-    bergs%nbergs_start=bergs%nbergs_end
-    bergs%stored_start=bergs%stored_end
-    bergs%nbergs_melted=0
-    bergs%nbergs_calved=0
-    bergs%nbergs_calved_by_class(:)=0
-    bergs%nspeeding_tickets=0
-    bergs%stored_heat_start=bergs%stored_heat_end
-    bergs%floating_heat_start=bergs%floating_heat_end
-    bergs%floating_mass_start=bergs%floating_mass_end
-    bergs%icebergs_mass_start=bergs%icebergs_mass_end
-    bergs%bergy_mass_start=bergs%bergy_mass_end
-    bergs%spread_mass_start=bergs%spread_mass_end
-    bergs%spread_area_start=bergs%spread_area_end
-    bergs%net_calving_used=0.
-    bergs%net_calving_to_bergs=0.
-    bergs%net_heat_to_bergs=0.
-    bergs%net_heat_to_ocean=0.
-    bergs%net_calving_received=0.
-    bergs%net_calving_returned=0.
-    bergs%net_incoming_calving=0.
-    bergs%net_outgoing_calving=0.
-    bergs%net_incoming_calving_heat=0.
-    bergs%net_incoming_calving_heat_used=0.
-    bergs%net_outgoing_calving_heat=0.
-    bergs%net_melt=0.
-    bergs%berg_melt=0.
-    bergs%bergy_melt=0.
-    bergs%bergy_src=0.
+      write(*,'("KID: calved by class = ",i4,20(",",i4))') (bergs%nbergs_calved_by_class(k),k=1,nclasses)
+      if (bergs%nspeeding_tickets>0) write(*,'("KID: speeding tickets issued = ",i4)') bergs%nspeeding_tickets
+    endif
+    bergs%nbergs_start=bergs%nbergs_end
+    bergs%stored_start=bergs%stored_end
+    bergs%nbergs_melted=0
+    bergs%nbergs_calved=0
+    bergs%nbergs_calved_by_class(:)=0
+    bergs%nspeeding_tickets=0
+    bergs%stored_heat_start=bergs%stored_heat_end
+    bergs%floating_heat_start=bergs%floating_heat_end
+    bergs%floating_mass_start=bergs%floating_mass_end
+    bergs%icebergs_mass_start=bergs%icebergs_mass_end
+    bergs%bergy_mass_start=bergs%bergy_mass_end
+    bergs%spread_mass_start=bergs%spread_mass_end
+    bergs%spread_area_start=bergs%spread_area_end
+    bergs%net_calving_used=0.
+    bergs%net_calving_to_bergs=0.
+    bergs%net_heat_to_bergs=0.
+    bergs%net_heat_to_ocean=0.
+    bergs%net_calving_received=0.
+    bergs%net_calving_returned=0.
+    bergs%net_incoming_calving=0.
+    bergs%net_outgoing_calving=0.
+    bergs%net_incoming_calving_heat=0.
+    bergs%net_incoming_calving_heat_used=0.
+    bergs%net_outgoing_calving_heat=0.
+    bergs%net_melt=0.
+    bergs%berg_melt=0.
+    bergs%bergy_melt=0.
+    bergs%bergy_src=0.
+
+    if (bergs%iceberg_bonds_on) then
+      check_bond_quality=.true.
+      nbonds=0
+      call count_bonds(bergs, nbonds,check_bond_quality)
+    endif
+  endif
+
+  if (debug) call bergs_chksum(bergs, 'run bergs (bot)')
+  if (debug) call checksum_gridded(bergs%grd, 'end of s/r run')
+  call mpp_clock_end(bergs%clock_dia)
+
+  call mpp_clock_end(bergs%clock)
+
+end subroutine icebergs_run
+
+!> Prints summary of start and end states
+subroutine report_state(budgetstr, budgetunits, startstr, startval, endstr, endval, delstr, nbergs)
+  ! Arguments
+  character*(*), intent(in) :: budgetstr !< Budget title
+  character*(*), intent(in) :: budgetunits !< Units of budgeted quantity
+  character*(*), intent(in) :: startstr !< Start label
+  real, intent(in) :: startval !< Start value for budget
+  character*(*), intent(in) :: endstr !< End label
+  real, intent(in) :: endval !< End value for budget
+  character*(*), intent(in) :: delstr !< Delta label
+  integer, intent(in), optional :: nbergs !< Number of bergs
+  ! Local variables
+  if (present(nbergs)) then
+    write(*,100) budgetstr//' state:', &
+                        startstr//' start',startval,budgetunits, &
+                        endstr//' end',endval,budgetunits, &
+                        'Delta '//delstr,endval-startval,budgetunits, &
+                        '# of bergs',nbergs
+  else
+    write(*,100) budgetstr//' state:', &
+                        startstr//' start',startval,budgetunits, &
+                        endstr//' end',endval,budgetunits, &
+                        delstr//'Delta',endval-startval,budgetunits
+  endif
+  100 format("KID: ",a19,3(a18,"=",es14.7,x,a2,:,","),a12,i8)
+end subroutine report_state
+
+!> Prints consistency summary of start and end states
+subroutine report_consistant(budgetstr, budgetunits, startstr, startval, endstr, endval)
+  ! Arguments
+  character*(*), intent(in) :: budgetstr !< Budget title
+  character*(*), intent(in) :: budgetunits !< Units of budgeted quantity
+  character*(*), intent(in) :: startstr !< Start label
+  real, intent(in) :: startval !< Start value for budget
+  character*(*), intent(in) :: endstr !< End label
+  real, intent(in) :: endval !< End value for budget
+  ! Local variables
+  write(*,200) budgetstr//' check:', &
+                      startstr,startval,budgetunits, &
+                      endstr,endval,budgetunits, &
+                      'error',(endval-startval)/((endval+startval)+1e-30),'nd'
+  200 format("KID: ",a19,10(a18,"=",es14.7,x,a2,:,","))
+end subroutine report_consistant
+
+!> Prints a budget
+subroutine report_budget(budgetstr, budgetunits, instr, inval, outstr, outval, delstr, startval, endval)
+  ! Arguments
+  character*(*), intent(in) :: budgetstr !< Budget title
+  character*(*), intent(in) :: budgetunits !< Units of budgeted quantity
+  character*(*), intent(in) :: instr !< Incoming label
+  real, intent(in) :: inval !< Incoming value
+  character*(*), intent(in) :: outstr !< Outgoing label
+  real, intent(in) :: outval !< Outgoing value
+  character*(*), intent(in) :: delstr !< Delta label
+  real, intent(in) :: startval !< Start value for budget
+  real, intent(in) :: endval !< End value for budget
+  ! Local variables
+  write(*,200) budgetstr//' budget:', &
+                      instr//' in',inval,budgetunits, &
+                      outstr//' out',outval,budgetunits, &
+                      'Delta '//delstr,inval-outval,budgetunits, &
+                      'error',((endval-startval)-(inval-outval))/max(1.e-30,max(abs(endval-startval),abs(inval-outval))),'nd'
+  200 format("KID: ",a19,3(a18,"=",es14.7,x,a2,:,","),a8,"=",es10.3,x,a2)
+end subroutine report_budget
+
+!> Prints summary of start and end states
+subroutine report_istate(budgetstr, startstr, startval, endstr, endval, delstr)
+  ! Arguments
+  character*(*), intent(in) :: budgetstr !< Budget title
+  character*(*), intent(in) :: startstr !< Start label
+  integer, intent(in) :: startval !< Start value for budget
+  character*(*), intent(in) :: endstr !< End label
+  integer, intent(in) :: endval !< End value for budget
+  character*(*), intent(in) :: delstr !< Delta label
+  ! Local variables
+  write(*,100) budgetstr//' state:', &
+                        startstr//' start',startval, &
+                        endstr//' end',endval, &
+                        delstr//'Delta',endval-startval
+  100 format("KID: ",a19,3(a18,"=",i14,x,:,","))
+end subroutine report_istate
+
+!> Prints a budget
+subroutine report_ibudget(budgetstr,instr,inval,outstr,outval,delstr,startval,endval)
+  ! Arguments
+  character*(*), intent(in) :: budgetstr !< Budget title
+  character*(*), intent(in) :: instr !< Incoming label
+  integer, intent(in) :: inval !< Incoming value
+  character*(*), intent(in) :: outstr !< Outgoing label
+  integer, intent(in) :: outval !< Outgoing value
+  character*(*), intent(in) :: delstr !< Delta label
+  integer, intent(in) :: startval !< Start value for budget
+  integer, intent(in) :: endval !< End value for budget
+  ! Local variables
+  write(*,200) budgetstr//' budget:', &
+                      instr//' in',inval, &
+                      outstr//' out',outval, &
+                      'Delta '//delstr,inval-outval, &
+                      'error',((endval-startval)-(inval-outval))
+  200 format("KID: ",a19,10(a18,"=",i14,x,:,","))
+end subroutine report_ibudget
+
+!> Time-filter calving and calving_hflx with a running mean.
+!!
+!! This subroutine takes in the new calving and calving_hflx, and uses them to time step a running-mean_calving value.
+!! The time stepping uses a time scale tau. When tau is equal to zero, the
+!! running mean is exactly equal to the new calving value.
+subroutine get_running_mean_calving(bergs, calving, calving_hflx)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  real, dimension(:,:), intent(inout) :: calving !< Calving (kg/s)
+  real, dimension(:,:), intent(inout) :: calving_hflx !< Calving heat flux (W/m2)
+  ! Local variables
+  real :: alpha  !Parameter used for calving relaxation time stepping.  (0<=alpha<1)
+  real :: tau  !Relaxation timescale in seconds
+  real :: beta  ! = 1-alpha (0<=beta<1)
+
+  ! For the first time-step, initialize the running mean with the current data
+  if (.not. bergs%grd%rmean_calving_initialized) then
+    bergs%grd%rmean_calving(:,:)=calving(:,:)
+    bergs%grd%rmean_calving_initialized=.true.
+  endif
+  if (.not. bergs%grd%rmean_calving_hflx_initialized) then
+    bergs%grd%rmean_calving_hflx(:,:)=calving_hflx(:,:)
+    bergs%grd%rmean_calving_hflx_initialized=.true.
+  endif
+
+  !Applying "Newton cooling" with timescale tau, to smooth out the calving field.
+  tau=bergs%tau_calving/(365.*24*60*60) !Converting time scale from years to seconds
+  alpha=tau/(tau+bergs%dt)
+  if (alpha==0.) return ! Avoids unnecessary copying of arrays
+  if (alpha>0.5) then ! beta is small
+    beta=bergs%dt/(tau+bergs%dt)
+    alpha=1.-beta
+  else ! alpha is small
+    beta=1.-alpha
+  endif
+
+  ! For non-negative alpha and beta, these expressions for the running means are sign preserving
+  bergs%grd%rmean_calving(:,:)=beta*calving(:,:) + alpha*bergs%grd%rmean_calving(:,:)
+  bergs%grd%rmean_calving_hflx(:,:)=beta*calving_hflx(:,:) + alpha*bergs%grd%rmean_calving_hflx(:,:)
+
+  !Setting calving used by the iceberg model equal to the running mean
+  calving(:,:)=bergs%grd%rmean_calving(:,:)
+  calving_hflx(:,:)=bergs%grd%rmean_calving_hflx(:,:)
+
+end subroutine get_running_mean_calving
+
+!> Increments a gridded mass field with the mass of bergs (called from outside icebergs_run)
+!!
+!! This routine is called from SIS, (and older versions of SIS2), but not within
+!! the iceberg model. The routine adds the spread iceberg mass to mass provided
+!! the add weight to ocean flag is on, and passive mode is off. It also appears to
+!! play some role in diagnostics
+subroutine icebergs_incr_mass(bergs, mass, Time)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  real, dimension(bergs%grd%isc:bergs%grd%iec,bergs%grd%jsc:bergs%grd%jec), intent(inout) :: mass !< Mass field to increment
+  type(time_type), intent(in), optional :: Time !< Model time
+  ! Local variables
+  type(icebergs_gridded), pointer :: grd
+  integer :: i, j
+  logical :: lerr
+
+  if (.not. associated(bergs)) return
+  if (.not. bergs%add_weight_to_ocean) return
+
+  ! For convenience
+  grd=>bergs%grd
+
+  !Start the clocks
+  call mpp_clock_begin(bergs%clock)
+  call mpp_clock_begin(bergs%clock_int)
+
+  do j=grd%jsc, grd%jec; do i=grd%isc, grd%iec
+    if (.not. bergs%passive_mode)   mass(i,j)=mass(i,j) + grd%spread_mass(i,j)
+  enddo  ;enddo
+
+  !Stop the clocks
+  call mpp_clock_end(bergs%clock_int)
+  call mpp_clock_end(bergs%clock)
+
+end subroutine icebergs_incr_mass
+
+!> Sums up a berg property into a gridded field
+subroutine sum_up_spread_fields(bergs, field, field_name)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  real, dimension(bergs%grd%isc:bergs%grd%iec,bergs%grd%jsc:bergs%grd%jec), intent(out) :: field !< Gridded field
+  character(len=4), intent(in) :: field_name !< Name of field to grid
+  ! Local variables
+  integer :: i, j
+  type(icebergs_gridded), pointer :: grd
+  real :: dmda
+  logical :: lerr
+  real, dimension(bergs%grd%isd:bergs%grd%ied, bergs%grd%jsd:bergs%grd%jed,9) :: var_on_ocean   !Variable being spread onto the ocean  (mass, area, Uvel, Vvel)
+  integer :: stderrunit
+
+  ! Get the stderr unit number
+  stderrunit = stderr()
+  ! For convenience
+  grd=>bergs%grd
+
+  field(:,:)=0.
+
+  !Deciding which varibale to spread across cells across grid cells
+  if (field_name=='mass') var_on_ocean(:,:,:)=grd%mass_on_ocean(:,:,:)
+  if (field_name=='area') var_on_ocean(:,:,:)=grd%area_on_ocean(:,:,:)
+  if (field_name=='Uvel') var_on_ocean(:,:,:)=grd%Uvel_on_ocean(:,:,:)
+  if (field_name=='Vvel') var_on_ocean(:,:,:)=grd%Vvel_on_ocean(:,:,:)
+
+  !This line has been removed, for that routine can be used for other fields
+  !if (.not. bergs%add_weight_to_ocean) return
+
+  !Update the halos of the var_on_ocean
+  call mpp_update_domains(var_on_ocean, grd%domain)
+
+  !Rotatine when old_bug_rotated_weights is on  - we should remove this.
+  if (.not. old_bug_rotated_weights) then
+    do j=grd%jsd, grd%jed; do i=grd%isd, grd%ied
+      if (grd%parity_x(i,j)<0.) then
+        ! This block assumes both parity_x and parity_y are negative
+        ! (i.e. a 180 degree rotation). In general, we should handle
+        ! +/- 90 degree rotations as well but in CM2*-class models
+        ! this is not necessary. -aja
+        dmda=var_on_ocean(i,j,9); var_on_ocean(i,j,9)=var_on_ocean(i,j,1); var_on_ocean(i,j,1)=dmda
+        dmda=var_on_ocean(i,j,8); var_on_ocean(i,j,8)=var_on_ocean(i,j,2); var_on_ocean(i,j,2)=dmda
+        dmda=var_on_ocean(i,j,7); var_on_ocean(i,j,7)=var_on_ocean(i,j,3); var_on_ocean(i,j,3)=dmda
+        dmda=var_on_ocean(i,j,6); var_on_ocean(i,j,6)=var_on_ocean(i,j,4); var_on_ocean(i,j,4)=dmda
+      endif
+    enddo; enddo
+  endif
 
-    if (bergs%iceberg_bonds_on) then
-      check_bond_quality=.true.
-      nbonds=0
-      call count_bonds(bergs, nbonds,check_bond_quality)
+  !Here we add the contribution of the 9 cells. This is the heart of the routine.
+  do j=grd%jsc, grd%jec; do i=grd%isc, grd%iec
+    dmda=var_on_ocean(i,j,5) &
+         + ( ( (var_on_ocean(i-1,j-1,9)+var_on_ocean(i+1,j+1,1))   &
+         +     (var_on_ocean(i+1,j-1,7)+var_on_ocean(i-1,j+1,3)) ) &
+         +   ( (var_on_ocean(i-1,j  ,6)+var_on_ocean(i+1,j  ,4))   &
+         +     (var_on_ocean(i  ,j-1,8)+var_on_ocean(i  ,j+1,2)) ) )
+    if (grd%area(i,j)>0) dmda=dmda/grd%area(i,j)*grd%msk(i,j)
+
+    !Make sure that area <=1.0
+    if (field_name=='area') dmda=min(dmda,1.0)
+
+    field(i,j)=dmda
+  enddo; enddo
+
+  if (debug) then
+    grd%tmp(:,:)=0.; grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec)=field
+    if (field_name=='mass') then
+      call grd_chksum3(grd, grd%mass_on_ocean, 'mass bergs (incr)')
+      call grd_chksum2(grd, grd%tmp, 'mass out (incr)')
+    elseif (field_name=='area') then
+      call grd_chksum3(grd, grd%area_on_ocean, 'area bergs (incr)')
+      call grd_chksum2(grd, grd%tmp, 'area out (incr)')
     endif
+ endif
+end subroutine sum_up_spread_fields
+
+!> Adds calving (from driver) to the coastal "buckets"
+subroutine accumulate_calving(bergs)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  ! Local variables
+  type(icebergs_gridded), pointer :: grd
+  real :: remaining_dist, net_calving_used
+  integer :: k, i, j
+  logical, save :: first_call=.true.
+  integer :: stderrunit
+
+  ! Get the stderr unit number
+  stderrunit = stderr()
+
+  ! For convenience
+  grd=>bergs%grd
+
+  ! This is a hack to simplify initialization
+  if (first_call.and..not.bergs%restarted) then
+    first_call=.false.
+   !do k=1, nclasses
+   !  where (grd%calving==0.) grd%stored_ice(:,:,k)=0.
+   !enddo
+    bergs%stored_start=sum( grd%stored_ice(grd%isc:grd%iec,grd%jsc:grd%jec,:) )
+    call mpp_sum( bergs%stored_start )
+    if (mpp_pe().eq.mpp_root_pe()) write(*,'(a,es13.6,a)') &
+        'KID, accumulate_calving: initial stored mass=',bergs%stored_start,' kg'
+    do j=grd%jsc,grd%jec; do i=grd%isc,grd%iec
+      if (grd%calving(i,j).ne.0.) grd%stored_heat(i,j)= & ! Need units of J
+            sum(grd%stored_ice(i,j,:)) & ! initial stored ice in kg
+           *grd%calving_hflx(i,j)*grd%area(i,j) & ! J/s/m2 x m^2 = J/s
+           /grd%calving(i,j) ! /calving in kg/s
+    enddo; enddo
+    bergs%stored_heat_start=sum( grd%stored_heat(grd%isc:grd%iec,grd%jsc:grd%jec) )
+    call mpp_sum( bergs%stored_heat_start )
+    if (mpp_pe().eq.mpp_root_pe()) write(*,'(a,es13.6,a)') &
+        'KID, accumulate_calving: initial stored heat=',bergs%stored_heat_start,' J'
+   endif
+
+  remaining_dist=1.
+  do k=1, nclasses
+    grd%stored_ice(:,:,k)=grd%stored_ice(:,:,k)+bergs%dt*grd%calving(:,:)*bergs%distribution(k)
+    remaining_dist=remaining_dist-bergs%distribution(k)
+  enddo
+  if (remaining_dist.lt.0.) then
+    write(stderrunit,*) 'KID, accumulate_calving: sum(distribution)>1!!!',remaining_dist
+    call error_mesg('KID, accumulate_calving', 'calving is OVER distributed!', WARNING)
   endif
+  net_calving_used=sum( grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec) )*(1.-remaining_dist)
+  bergs%net_calving_used=bergs%net_calving_used+net_calving_used*bergs%dt
+  ! Remove the calving accounted for by accumulation
+  grd%calving(:,:)=grd%calving(:,:)*remaining_dist
+
+  ! Do the same for heat (no separate classes needed)
+  grd%tmp(:,:)=bergs%dt*grd%calving_hflx(:,:)*grd%area(:,:)*(1.-remaining_dist)
+  bergs%net_incoming_calving_heat_used=bergs%net_incoming_calving_heat_used+sum( grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec) )
+  grd%stored_heat(:,:)=grd%stored_heat(:,:)+grd%tmp(:,:) ! +=bergs%dt*grd%calving_hflx(:,:)*grd%area(:,:)*(1.-remaining_dist)
+  grd%calving_hflx(:,:)=grd%calving_hflx(:,:)*remaining_dist
+
+end subroutine accumulate_calving
+
+!> Generate icebergs from overflowing "buckets"
+subroutine calve_icebergs(bergs)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  ! Local variables
+  type(icebergs_gridded), pointer :: grd
+  integer :: i,j,k,icnt,icntmax
+  integer :: iNg, jNg ! Total number of points globally in i and j direction
+  type(iceberg) :: newberg
+  logical :: lret
+  real :: xi, yj, ddt, calving_to_bergs, calved_to_berg, heat_to_bergs, heat_to_berg
+  integer :: stderrunit
+
+  ! Get the stderr unit number
+  stderrunit = stderr()
+
+  ! For convenience
+  grd=>bergs%grd
+
+  iNg=(grd%ieg-grd%isg+1) ! Total number of points globally in i direction
+  jNg=(grd%jeg-grd%jsg+1) ! Total number of points globally in j direction
+
+  grd%real_calving(:,:,:)=0.
+  calving_to_bergs=0.
+  heat_to_bergs=0.
+  icntmax=0
+
+  do k=1, nclasses
+    do j=grd%jsc, grd%jec
+      do i=grd%isc, grd%iec
+        ddt=0.; icnt=0
+        do while (grd%stored_ice(i,j,k).ge.bergs%initial_mass(k)*bergs%mass_scaling(k))
+          newberg%lon=0.25*((grd%lon(i,j)+grd%lon(i-1,j-1))+(grd%lon(i-1,j)+grd%lon(i,j-1)))
+          newberg%lat=0.25*((grd%lat(i,j)+grd%lat(i-1,j-1))+(grd%lat(i-1,j)+grd%lat(i,j-1)))
+         !write(stderr(),*) 'KID, calve_icebergs: creating new iceberg at ',newberg%lon,newberg%lat
+          lret=pos_within_cell(grd, newberg%lon, newberg%lat, i, j, xi, yj)
+          if (.not.lret) then
+            write(stderrunit,*) 'KID, calve_icebergs: something went very wrong!',i,j,xi,yj
+            call error_mesg('KID, calve_icebergs', 'berg is not in the correct cell!', FATAL)
+          endif
+          if (debug.and.(xi<0..or.xi>1..or.yj<0..or.yj>1.)) then
+            write(stderrunit,*) 'KID, calve_icebergs: something went very wrong!',i,j,xi,yj
+            call error_mesg('KID, calve_icebergs', 'berg xi,yj is not correct!', FATAL)
+          endif
+          if (grd%msk(i,j)<0.5) then
+            write(stderrunit,*) 'KID, calve_icebergs: WARNING!!! Iceberg born in land cell',i,j,newberg%lon,newberg%lat
+            if (debug) call error_mesg('KID, calve_icebergs', 'Iceberg born in Land Cell!', FATAL)
+          endif
+          newberg%ine=i
+          newberg%jne=j
+          newberg%xi=xi
+          newberg%yj=yj
+          newberg%uvel=0.
+          newberg%vvel=0.
+          newberg%uvel_prev=0.  !Added by Alex
+          newberg%vvel_prev=0.  !Added by Alex
+          newberg%axn=0. !Added by Alon
+          newberg%ayn=0. !Added by Alon
+          newberg%bxn=0. !Added by Alon
+          newberg%byn=0. !Added by Alon
+          newberg%axn_fast=0. !Added by Alex
+          newberg%ayn_fast=0. !Added by Alex
+          newberg%bxn_fast=0. !Added by Alex
+          newberg%byn_fast=0. !Added by Alex
+          newberg%mass=bergs%initial_mass(k)
+          newberg%thickness=bergs%initial_thickness(k)
+          newberg%width=bergs%initial_width(k)
+          newberg%length=bergs%initial_length(k)
+          newberg%start_lon=newberg%lon
+          newberg%start_lat=newberg%lat
+          newberg%start_year=bergs%current_year
+          newberg%id = generate_id(grd, i, j)
+          newberg%conglom_id=0
+          newberg%start_day=bergs%current_yearday+ddt/86400.
+          newberg%start_mass=bergs%initial_mass(k)
+          newberg%mass_scaling=bergs%mass_scaling(k)
+          newberg%mass_of_bits=0.
+          newberg%halo_berg=0.
+          newberg%static_berg=0.
+          newberg%heat_density=grd%stored_heat(i,j)/grd%stored_ice(i,j,k) ! This is in J/kg
+          call add_new_berg_to_list(bergs%list(i,j)%first, newberg)
+          calved_to_berg=bergs%initial_mass(k)*bergs%mass_scaling(k) ! Units of kg
+          ! Heat content
+          heat_to_berg=calved_to_berg*newberg%heat_density ! Units of J
+          grd%stored_heat(i,j)=grd%stored_heat(i,j)-heat_to_berg
+          heat_to_bergs=heat_to_bergs+heat_to_berg
+          ! Stored mass
+          grd%stored_ice(i,j,k)=grd%stored_ice(i,j,k)-calved_to_berg
+          calving_to_bergs=calving_to_bergs+calved_to_berg
+          grd%real_calving(i,j,k)=grd%real_calving(i,j,k)+calved_to_berg/bergs%dt
+          ddt=ddt-bergs%dt*2./17. ! Minor offset to start day (negative offsets)
+          icnt=icnt+1
+          bergs%nbergs_calved=bergs%nbergs_calved+1
+          bergs%nbergs_calved_by_class(k)=bergs%nbergs_calved_by_class(k)+1
+        enddo
+        icntmax=max(icntmax,icnt)
+      enddo
+    enddo
+  enddo
 
-  if (debug) call bergs_chksum(bergs, 'run bergs (bot)')
-  if (debug) call checksum_gridded(bergs%grd, 'end of s/r run')
-  call mpp_clock_end(bergs%clock_dia)
+  if (debug.and.icntmax>1) write(stderrunit,*) 'calve_icebergs: icnt=',icnt,' on',mpp_pe()
 
-  call mpp_clock_end(bergs%clock)
+  bergs%net_calving_to_bergs=bergs%net_calving_to_bergs+calving_to_bergs
+  bergs%net_heat_to_bergs=bergs%net_heat_to_bergs+heat_to_bergs
 
-end subroutine icebergs_run
+end subroutine calve_icebergs
 
-!> Prints summary of start and end states
-subroutine report_state(budgetstr, budgetunits, startstr, startval, endstr, endval, delstr, nbergs)
+!> Evolves icebergs forward by updating velocity and position with a multiple-time-step Velocity Verlet
+!! scheme. Experimental option: each short/long step can be iterated the number of times specified by
+!! imp_loop_iters_short and imp_loop_iters_long, respectively, which better enforces momentum
+!! conservation during collision...this iterative scheme may or may not be needed to yield consistent
+!! fracture behavior. Alternatively, use evolve_icebergs_mts2 to iterate to a given convergence tolerance.
+subroutine evolve_icebergs_mts(bergs)
   ! Arguments
-  character*(*), intent(in) :: budgetstr !< Budget title
-  character*(*), intent(in) :: budgetunits !< Units of budgeted quantity
-  character*(*), intent(in) :: startstr !< Start label
-  real, intent(in) :: startval !< Start value for budget
-  character*(*), intent(in) :: endstr !< End label
-  real, intent(in) :: endval !< End value for budget
-  character*(*), intent(in) :: delstr !< Delta label
-  integer, intent(in), optional :: nbergs !< Number of bergs
+  type(icebergs), pointer :: bergs !< Container for all types and memory
   ! Local variables
-  if (present(nbergs)) then
-    write(*,100) budgetstr//' state:', &
-                        startstr//' start',startval,budgetunits, &
-                        endstr//' end',endval,budgetunits, &
-                        'Delta '//delstr,endval-startval,budgetunits, &
-                        '# of bergs',nbergs
-  else
-    write(*,100) budgetstr//' state:', &
-                        startstr//' start',startval,budgetunits, &
-                        endstr//' end',endval,budgetunits, &
-                        delstr//'Delta',endval-startval,budgetunits
-  endif
-  100 format("KID: ",a19,3(a18,"=",es14.7,x,a2,:,","),a12,i8)
-end subroutine report_state
+  type(icebergs_gridded), pointer :: grd
+  type(iceberg), pointer :: berg
+  real :: uveln, vveln, lonn, latn
+  real :: axn, ayn, bxn, byn
+  real :: xi, yj, rx, ry
+  integer :: i, j, k
+  integer :: grdi, grdj
+  integer :: stderrunit
+  logical :: only_interactive_forces
+  real :: lon1, lat1, dxdl1, dydl
+  real :: uvel1, vvel1, uvel2, vvel2, uvel3, vvel3
+  real :: xddot1, yddot1, xdot2, ydot2, xdot3, ydot3, xdotn, ydotn
+  real :: u2, v2, x1, y1, xn, yn
+  real :: ax1,ay1
+  real :: dt, dt_2
+  logical :: on_tangential_plane, error_flag, bounced
+  !energy stuff
+  real :: dx,dy,M,Fex,Fey,Fex_prev,Fey_prev,Fdx_prev,Fdy_prev,Fdx,Fdy,Fx_tot,Fy_tot,Fx_tot_prev,Fy_tot_prev
+  logical :: save_bond_energy
+  real :: Fex_i, Fey_i, Fec_x, Fec_y, Fdc_x, Fdc_y, ustar, vstar, uveln_star, vveln_star
+  integer :: imp_loop
 
-!> Prints consistency summary of start and end states
-subroutine report_consistant(budgetstr, budgetunits, startstr, startval, endstr, endval)
-  ! Arguments
-  character*(*), intent(in) :: budgetstr !< Budget title
-  character*(*), intent(in) :: budgetunits !< Units of budgeted quantity
-  character*(*), intent(in) :: startstr !< Start label
-  real, intent(in) :: startval !< Start value for budget
-  character*(*), intent(in) :: endstr !< End label
-  real, intent(in) :: endval !< End value for budget
-  ! Local variables
-  write(*,200) budgetstr//' check:', &
-                      startstr,startval,budgetunits, &
-                      endstr,endval,budgetunits, &
-                      'error',(endval-startval)/((endval+startval)+1e-30),'nd'
-  200 format("KID: ",a19,10(a18,"=",es14.7,x,a2,:,","))
-end subroutine report_consistant
+  ! Multiple Time Step Velocity Verlet:
+  ! NOTE: To avoid the need for computationally expensive transfers between processors
+  ! at the end of each MTS sub-step, each PE updates a complete copy of any
+  ! conglomerate of bonded iceberg elements that spans over the computational domain of
+  ! several processors (see subroutine transfer_mts_bergs). Berg elements that lie within
+  ! the contact distance of the conglomerate are also included, as to account for collision
+  ! forces. The conglomerate iceberg elements with coords that lie outside of a PE's domain
+  ! are assigned to the nearest halo cell, but the coords are not changed.
 
-!> Prints a budget
-subroutine report_budget(budgetstr, budgetunits, instr, inval, outstr, outval, delstr, startval, endval)
-  ! Arguments
-  character*(*), intent(in) :: budgetstr !< Budget title
-  character*(*), intent(in) :: budgetunits !< Units of budgeted quantity
-  character*(*), intent(in) :: instr !< Incoming label
-  real, intent(in) :: inval !< Incoming value
-  character*(*), intent(in) :: outstr !< Outgoing label
-  real, intent(in) :: outval !< Outgoing value
-  character*(*), intent(in) :: delstr !< Delta label
-  real, intent(in) :: startval !< Start value for budget
-  real, intent(in) :: endval !< End value for budget
-  ! Local variables
-  write(*,200) budgetstr//' budget:', &
-                      instr//' in',inval,budgetunits, &
-                      outstr//' out',outval,budgetunits, &
-                      'Delta '//delstr,inval-outval,budgetunits, &
-                      'error',((endval-startval)-(inval-outval))/max(1.e-30,max(abs(endval-startval),abs(inval-outval))),'nd'
-  200 format("KID: ",a19,3(a18,"=",es14.7,x,a2,:,","),a8,"=",es10.3,x,a2)
-end subroutine report_budget
+  ! Get the stderr unit number
+  stderrunit = stderr()
+  only_interactive_forces=bergs%only_interactive_forces
 
-!> Prints summary of start and end states
-subroutine report_istate(budgetstr, startstr, startval, endstr, endval, delstr)
-  ! Arguments
-  character*(*), intent(in) :: budgetstr !< Budget title
-  character*(*), intent(in) :: startstr !< Start label
-  integer, intent(in) :: startval !< Start value for budget
-  character*(*), intent(in) :: endstr !< End label
-  integer, intent(in) :: endval !< End value for budget
-  character*(*), intent(in) :: delstr !< Delta label
-  ! Local variables
-  write(*,100) budgetstr//' state:', &
-                        startstr//' start',startval, &
-                        endstr//' end',endval, &
-                        delstr//'Delta',endval-startval
-  100 format("KID: ",a19,3(a18,"=",i14,x,:,","))
-end subroutine report_istate
+  ! For convenience
+  grd=>bergs%grd
 
-!> Prints a budget
-subroutine report_ibudget(budgetstr,instr,inval,outstr,outval,delstr,startval,endval)
-  ! Arguments
-  character*(*), intent(in) :: budgetstr !< Budget title
-  character*(*), intent(in) :: instr !< Incoming label
-  integer, intent(in) :: inval !< Incoming value
-  character*(*), intent(in) :: outstr !< Outgoing label
-  integer, intent(in) :: outval !< Outgoing value
-  character*(*), intent(in) :: delstr !< Delta label
-  integer, intent(in) :: startval !< Start value for budget
-  integer, intent(in) :: endval !< End value for budget
-  ! Local variables
-  write(*,200) budgetstr//' budget:', &
-                      instr//' in',inval, &
-                      outstr//' out',outval, &
-                      'Delta '//delstr,inval-outval, &
-                      'error',((endval-startval)-(inval-outval))
-  200 format("KID: ",a19,10(a18,"=",i14,x,:,","))
-end subroutine report_ibudget
+  !Checking if everything is ok:
+  do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec ! just for computational domain
+    berg=>bergs%list(grdi,grdj)%first
+    do while (associated(berg)) ! loop over all bergs
+      if (berg%static_berg .lt. 0.5 .and. berg%halo_berg .lt. 0.5) then
+        if (.not. is_point_in_cell(bergs%grd, berg%lon, berg%lat, berg%ine, berg%jne) ) then
+          write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lon',(i,i=grd%isd,grd%ied)
+          do j=grd%jed,grd%jsd,-1
+            write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lon(i,j),i=grd%isd,grd%ied)
+          enddo
+          write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lat',(i,i=grd%isd,grd%ied)
+          do j=grd%jed,grd%jsd,-1
+            write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lat(i,j),i=grd%isd,grd%ied)
+          enddo
+          call print_berg(stderrunit, berg, 'evolve_iceberg_mts, berg is not in proper starting cell')
+          write(stderrunit,'(a,i3,2(i4,3f8.2))') 'evolve_icebergs_mts: pe,lon/lat(i,j)=', mpp_pe(), &
+            berg%ine,berg%lon,grd%lon(berg%ine-1,berg%jne-1),grd%lon(berg%ine,berg%jne), &
+            berg%jne,berg%lat,grd%lat(berg%ine-1,berg%jne-1),grd%lat(berg%ine,berg%jne)
+          if (debug) call error_mesg('KID, evolve_icebergs_mts','berg is in wrong starting cell!',FATAL)
+        endif
+        if (debug) call check_position(grd, berg, 'evolve_icebergs_mts (top)')
+      end if
+      berg=>berg%next
+    enddo
+  enddo; enddo
 
-!> Time-filter calving and calving_hflx with a running mean.
-!!
-!! This subroutine takes in the new calving and calving_hflx, and uses them to time step a running-mean_calving value.
-!! The time stepping uses a time scale tau. When tau is equal to zero, the
-!! running mean is exactly equal to the new calving value.
-subroutine get_running_mean_calving(bergs, calving, calving_hflx)
-  ! Arguments
-  type(icebergs), pointer :: bergs !< Container for all types and memory
-  real, dimension(:,:), intent(inout) :: calving !< Calving (kg/s)
-  real, dimension(:,:), intent(inout) :: calving_hflx !< Calving heat flux (W/m2)
-  ! Local variables
-  real :: alpha  !Parameter used for calving relaxation time stepping.  (0<=alpha<1)
-  real :: tau  !Relaxation timescale in seconds
-  real :: beta  ! = 1-alpha (0<=beta<1)
+  ! PART 1: solve for V_n+1 (from the previous timestep)
+  bergs%mts_part=1
+  dt = bergs%dt
+  dt_2=0.5*dt
+  rx = 0.0; ry = 0.0 !not needed, because interp_gridded_fields_to_bergs was already called
+  save_bond_energy=.false.
 
-  ! For the first time-step, initialize the running mean with the current data
-  if (.not. bergs%grd%rmean_calving_initialized) then
-    bergs%grd%rmean_calving(:,:)=calving(:,:)
-    bergs%grd%rmean_calving_initialized=.true.
-  endif
-  if (.not. bergs%grd%rmean_calving_hflx_initialized) then
-    bergs%grd%rmean_calving_hflx(:,:)=calving_hflx(:,:)
-    bergs%grd%rmean_calving_hflx_initialized=.true.
-  endif
+  !imp_loop_iters is a global variable specified in the nml that specifies how many iterations the implicit
+  !loop is run, where uvel_old and vvel_old continuously update each iteration so that the damping force is
+  !more accurate for each bond pair
 
-  !Applying "Newton cooling" with timescale tau, to smooth out the calving field.
-  tau=bergs%tau_calving/(365.*24*60*60) !Converting time scale from years to seconds
-  alpha=tau/(tau+bergs%dt)
-  if (alpha==0.) return ! Avoids unnecessary copying of arrays
-  if (alpha>0.5) then ! beta is small
-    beta=bergs%dt/(tau+bergs%dt)
-    alpha=1.-beta
-  else ! alpha is small
-    beta=1.-alpha
-  endif
+  do imp_loop = 1,imp_loop_iters_long
+    do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+      berg=>bergs%list(grdi,grdj)%first
+      do while (associated(berg)) ! loop over all bergs
+        !only evolve non-static bergs that overlap, or are part of a conglom that overlaps, the computational domain:
+        if (berg%static_berg .lt. 0.5 .and. (berg%conglom_id.ne.0 .or. imp_loop_iters_long>1)) then
+          latn = berg%lat ;   lonn = berg%lon
+          uvel1=berg%uvel ;   vvel1=berg%vvel !V_n (previous cycle)
+          axn  = 0.0      ;   ayn  = 0.0 !note these are redefined at the start of subroutine accel_mts
+          bxn  = 0.0      ;   byn  = 0.0
+          i=berg%ine      ;   j=berg%jne
+          xi=berg%xi      ;   yj=berg%yj
 
-  ! For non-negative alpha and beta, these expressions for the running means are sign preserving
-  bergs%grd%rmean_calving(:,:)=beta*calving(:,:) + alpha*bergs%grd%rmean_calving(:,:)
-  bergs%grd%rmean_calving_hflx(:,:)=beta*calving_hflx(:,:) + alpha*bergs%grd%rmean_calving_hflx(:,:)
+          call accel_mts(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, &
+            ax1, ay1, axn, ayn, bxn, byn, save_bond_energy,Fec_x, Fec_y, Fdc_x, Fdc_y)
 
-  !Setting calving used by the iceberg model equal to the running mean
-  calving(:,:)=bergs%grd%rmean_calving(:,:)
-  calving_hflx(:,:)=bergs%grd%rmean_calving_hflx(:,:)
+          if (monitor_energy .and. imp_loop==imp_loop_iters_long) &
+            call mts_energy_part_1(bergs,berg,ax1,ay1,axn,ayn,bxn,byn,Fec_x,Fec_y,Fdc_x,Fdc_y)
 
-end subroutine get_running_mean_calving
+          ! Saving all the iceberg variables
+          berg%axn=axn                ; berg%ayn=ayn
+          berg%bxn=bxn                ; berg%byn=byn
 
-!> Increments a gridded mass field with the mass of bergs (called from outside icebergs_run)
-!!
-!! This routine is called from SIS, (and older versions of SIS2), but not within
-!! the iceberg model. The routine adds the spread iceberg mass to mass provided
-!! the add weight to ocean flag is on, and passive mode is off. It also appears to
-!! play some role in diagnostics
-subroutine icebergs_incr_mass(bergs, mass, Time)
-  ! Arguments
-  type(icebergs), pointer :: bergs !< Container for all types and memory
-  real, dimension(bergs%grd%isc:bergs%grd%iec,bergs%grd%jsc:bergs%grd%jec), intent(inout) :: mass !< Mass field to increment
-  type(time_type), intent(in), optional :: Time !< Model time
-  ! Local variables
-  type(icebergs_gridded), pointer :: grd
-  integer :: i, j
-  logical :: lerr
+          if (imp_loop_iters_long>1) then
+            berg%uvel_prev=berg%uvel+(dt*ax1); berg%vvel_prev=berg%vvel+(dt*ay1)
+          else
+            berg%uvel=berg%uvel+(dt*ax1); berg%vvel=berg%vvel+(dt*ay1)
+
+            !The final velocity from the previous cycle, which can be used
+            !during post-processing to calculate kinetic energy and momentum
+            berg%uvel_prev=berg%uvel    ; berg%vvel_prev=berg%vvel
+          endif
+        endif
+        berg=>berg%next
+      enddo ! loop over all bergs
+    enddo; enddo
+
+    if (imp_loop_iters_long>1) then
+      do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+        berg=>bergs%list(grdi,grdj)%first
+        do while (associated(berg)) ! loop over all bergs
+          berg%uvel_old=berg%uvel_prev; berg%vvel_old=berg%vvel_prev
+          if (imp_loop==imp_loop_iters_long) then
+            berg%uvel=berg%uvel_prev; berg%vvel=berg%vvel_prev
+          endif
+          berg=>berg%next
+        enddo
+      enddo; enddo
+    endif
+  enddo
 
-  if (.not. associated(bergs)) return
-  if (.not. bergs%add_weight_to_ocean) return
+  call update_bond_angles(bergs)
+  call update_and_break_bonds(bergs)
 
-  ! For convenience
-  grd=>bergs%grd
+  !PART 2: X_0 and V_0, before fast sub-steps
+  !X_0=X_n (no change)
+  !update V_0 on uvel_old and vvel_old
+  !update lat and lon with implicit slow force component
+  do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+    berg=>bergs%list(grdi,grdj)%first
+    do while (associated(berg)) ! loop over all bergs
+      if (berg%static_berg .lt. 0.5 .and. berg%conglom_id.ne.0) then
+        berg%lat_prev = berg%lat; berg%lon_prev = berg%lon
 
-  !Start the clocks
-  call mpp_clock_begin(bergs%clock)
-  call mpp_clock_begin(bergs%clock_int)
+        if (new_mts) then
+          berg%uvel = berg%uvel + dt_2*(berg%axn+berg%bxn)
+          berg%vvel = berg%vvel + dt_2*(berg%ayn+berg%byn)
+        else
+          berg%uvel = berg%uvel + dt_2*berg%axn
+          berg%vvel = berg%vvel + dt_2*berg%ayn
+          berg%lat = berg%lat + 0.5*(dt**2)*berg%byn
+          berg%lon = berg%lon + 0.5*(dt**2)*berg%bxn
+        endif
 
-  do j=grd%jsc, grd%jec; do i=grd%isc, grd%iec
-    if (.not. bergs%passive_mode)   mass(i,j)=mass(i,j) + grd%spread_mass(i,j)
-  enddo  ;enddo
+        berg%uvel_old=berg%uvel; berg%vvel_old=berg%vvel
 
-  !Stop the clocks
-  call mpp_clock_end(bergs%clock_int)
-  call mpp_clock_end(bergs%clock)
+        if (imp_loop_iters_short>1) then
+          berg%axn=berg%axn_fast; berg%ayn=berg%ayn_fast
+          berg%bxn=berg%bxn_fast; berg%byn=berg%byn_fast
+        endif
 
-end subroutine icebergs_incr_mass
+        !if (monitor energy): already did energy update in part I
+      endif
 
-!> Sums up a berg property into a gridded field
-subroutine sum_up_spread_fields(bergs, field, field_name)
-  ! Arguments
-  type(icebergs), pointer :: bergs !< Container for all types and memory
-  real, dimension(bergs%grd%isc:bergs%grd%iec,bergs%grd%jsc:bergs%grd%jec), intent(out) :: field !< Gridded field
-  character(len=4), intent(in) :: field_name !< Name of field to grid
-  ! Local variables
-  integer :: i, j
-  type(icebergs_gridded), pointer :: grd
-  real :: dmda
-  logical :: lerr
-  real, dimension(bergs%grd%isd:bergs%grd%ied, bergs%grd%jsd:bergs%grd%jed,9) :: var_on_ocean   !Variable being spread onto the ocean  (mass, area, Uvel, Vvel)
-  integer :: stderrunit
+      berg=>berg%next
+    enddo
+  enddo; enddo
 
-  ! Get the stderr unit number
-  stderrunit = stderr()
-  ! For convenience
-  grd=>bergs%grd
 
-  field(:,:)=0.
+  ! PART 3: MTS fast sub-steps (bonded interactions only):
+  ! Position and velocity are updated by:
+  ! X2 = X1+dt*V1+((dt^2)/2)*a_k +((dt^2)/2)*b_k
+  ! V2 = V1+dt/2*a_k +dt/2*a_kp1 +dt*b_k+1
 
-  !Deciding which varibale to spread across cells across grid cells
-  if (field_name=='mass') var_on_ocean(:,:,:)=grd%mass_on_ocean(:,:,:)
-  if (field_name=='area') var_on_ocean(:,:,:)=grd%area_on_ocean(:,:,:)
-  if (field_name=='Uvel') var_on_ocean(:,:,:)=grd%Uvel_on_ocean(:,:,:)
-  if (field_name=='Vvel') var_on_ocean(:,:,:)=grd%Vvel_on_ocean(:,:,:)
+  bergs%only_interactive_forces=.true. !so that external forcings are ignored in subroutine accel
+  bergs%mts_part=3 !so that only bonded interactions are considered in subroutine interactive_force
+  dt = bergs%mts_fast_dt
+  dt_2=0.5*dt
 
-  !This line has been removed, for that routine can be used for other fields
-  !if (.not. bergs%add_weight_to_ocean) return
+  do k = 1,bergs%mts_sub_steps ! loop over sub-steps
 
-  !Update the halos of the var_on_ocean
-  call mpp_update_domains(var_on_ocean, grd%domain)
+    do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied ! update positions
+      berg=>bergs%list(grdi,grdj)%first
+      do while (associated(berg)) ! loop over all bergs
+        if (berg%static_berg .lt. 0.5 .and. berg%conglom_id.ne.0) then
 
-  !Rotatine when old_bug_rotated_weights is on  - we should remove this.
-  if (.not. old_bug_rotated_weights) then
-    do j=grd%jsd, grd%jed; do i=grd%isd, grd%ied
-      if (grd%parity_x(i,j)<0.) then
-        ! This block assumes both parity_x and parity_y are negative
-        ! (i.e. a 180 degree rotation). In general, we should handle
-        ! +/- 90 degree rotations as well but in CM2*-class models
-        ! this is not necessary. -aja
-        dmda=var_on_ocean(i,j,9); var_on_ocean(i,j,9)=var_on_ocean(i,j,1); var_on_ocean(i,j,1)=dmda
-        dmda=var_on_ocean(i,j,8); var_on_ocean(i,j,8)=var_on_ocean(i,j,2); var_on_ocean(i,j,2)=dmda
-        dmda=var_on_ocean(i,j,7); var_on_ocean(i,j,7)=var_on_ocean(i,j,3); var_on_ocean(i,j,3)=dmda
-        dmda=var_on_ocean(i,j,6); var_on_ocean(i,j,6)=var_on_ocean(i,j,4); var_on_ocean(i,j,4)=dmda
-      endif
-    enddo; enddo
-  endif
+          on_tangential_plane=.false.
+          if ((berg%lat>89.) .and. (grd%grid_is_latlon)) on_tangential_plane=.true.
 
-  !Here we add the contribution of the 9 cells. This is the heart of the routine.
-  do j=grd%jsc, grd%jec; do i=grd%isc, grd%iec
-    dmda=var_on_ocean(i,j,5) &
-         + ( ( (var_on_ocean(i-1,j-1,9)+var_on_ocean(i+1,j+1,1))   &
-         +     (var_on_ocean(i+1,j-1,7)+var_on_ocean(i-1,j+1,3)) ) &
-         +   ( (var_on_ocean(i-1,j  ,6)+var_on_ocean(i+1,j  ,4))   &
-         +     (var_on_ocean(i  ,j-1,8)+var_on_ocean(i  ,j+1,2)) ) )
-    if (grd%area(i,j)>0) dmda=dmda/grd%area(i,j)*grd%msk(i,j)
+          lon1=berg%lon; lat1=berg%lat
+          if (on_tangential_plane) call rotpos_to_tang(lon1,lat1,x1,y1,berg%id)
+          !dxdl1=r180_pi/(Rearth*cos(lat1*pi_180))
+          !dydl=r180_pi/Rearth
+          call convert_from_meters_to_grid(lat1,grd%grid_is_latlon ,dxdl1,dydl)
+          uvel1=berg%uvel; vvel1=berg%vvel
 
-    !Make sure that area <=1.0
-    if (field_name=='area') dmda=min(dmda,1.0)
+          ! Loading past accelerations
+          axn=berg%axn_fast; ayn=berg%ayn_fast
+          bxn=berg%bxn_fast; byn=berg%byn_fast
 
-    field(i,j)=dmda
-  enddo; enddo
+          ! Velocities used to update the position
+          uvel2=uvel1+(dt_2*axn)+(dt_2*bxn)
+          vvel2=vvel1+(dt_2*ayn)+(dt_2*byn)
 
-  if (debug) then
-    grd%tmp(:,:)=0.; grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec)=field
-    if (field_name=='mass') then
-      call grd_chksum3(grd, grd%mass_on_ocean, 'mass bergs (incr)')
-      call grd_chksum2(grd, grd%tmp, 'mass out (incr)')
-    elseif (field_name=='area') then
-      call grd_chksum3(grd, grd%area_on_ocean, 'area bergs (incr)')
-      call grd_chksum2(grd, grd%tmp, 'area out (incr)')
-    endif
- endif
-end subroutine sum_up_spread_fields
+          if (on_tangential_plane) call rotvec_to_tang(lon1,uvel2,vvel2,xdot2,ydot2)
+          u2=uvel2*dxdl1; v2=vvel2*dydl
 
-!> Adds calving (from driver) to the coastal "buckets"
-subroutine accumulate_calving(bergs)
-  ! Arguments
-  type(icebergs), pointer :: bergs !< Container for all types and memory
-  ! Local variables
-  type(icebergs_gridded), pointer :: grd
-  real :: remaining_dist, net_calving_used
-  integer :: k, i, j
-  logical, save :: first_call=.true.
-  integer :: stderrunit
+          ! Solving for new position
+          if (on_tangential_plane) then
+            xn=x1+(dt*xdot2) ; yn=y1+(dt*ydot2)
+            call rotpos_from_tang(xn,yn,lonn,latn)
+          else
+            lonn=lon1+(dt*u2) ; latn=lat1+(dt*v2)
+          endif
 
-  ! Get the stderr unit number
-  stderrunit = stderr()
+          berg%lon=lonn      ;  berg%lat=latn
+          berg%lon_old=lonn  ;  berg%lat_old=latn
+        end if
 
-  ! For convenience
-  grd=>bergs%grd
+        berg=>berg%next
+      enddo !loop over all bergs
+    enddo;enddo !update positions
 
-  ! This is a hack to simplify initialization
-  if (first_call.and..not.bergs%restarted) then
-    first_call=.false.
-   !do k=1, nclasses
-   !  where (grd%calving==0.) grd%stored_ice(:,:,k)=0.
-   !enddo
-    bergs%stored_start=sum( grd%stored_ice(grd%isc:grd%iec,grd%jsc:grd%jec,:) )
-    call mpp_sum( bergs%stored_start )
-    if (mpp_pe().eq.mpp_root_pe()) write(*,'(a,es13.6,a)') &
-        'KID, accumulate_calving: initial stored mass=',bergs%stored_start,' kg'
-    do j=grd%jsc,grd%jec; do i=grd%isc,grd%iec
-      if (grd%calving(i,j).ne.0.) grd%stored_heat(i,j)= & ! Need units of J
-            sum(grd%stored_ice(i,j,:)) & ! initial stored ice in kg
-           *grd%calving_hflx(i,j)*grd%area(i,j) & ! J/s/m2 x m^2 = J/s
-           /grd%calving(i,j) ! /calving in kg/s
-    enddo; enddo
-    bergs%stored_heat_start=sum( grd%stored_heat(grd%isc:grd%iec,grd%jsc:grd%jec) )
-    call mpp_sum( bergs%stored_heat_start )
-    if (mpp_pe().eq.mpp_root_pe()) write(*,'(a,es13.6,a)') &
-        'KID, accumulate_calving: initial stored heat=',bergs%stored_heat_start,' J'
-   endif
+    do imp_loop = 1,imp_loop_iters_short
 
-  remaining_dist=1.
-  do k=1, nclasses
-    grd%stored_ice(:,:,k)=grd%stored_ice(:,:,k)+bergs%dt*grd%calving(:,:)*bergs%distribution(k)
-    remaining_dist=remaining_dist-bergs%distribution(k)
-  enddo
-  if (remaining_dist.lt.0.) then
-    write(stderrunit,*) 'KID, accumulate_calving: sum(distribution)>1!!!',remaining_dist
-    call error_mesg('KID, accumulate_calving', 'calving is OVER distributed!', WARNING)
-  endif
-  net_calving_used=sum( grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec) )*(1.-remaining_dist)
-  bergs%net_calving_used=bergs%net_calving_used+net_calving_used*bergs%dt
-  ! Remove the calving accounted for by accumulation
-  grd%calving(:,:)=grd%calving(:,:)*remaining_dist
+      if (monitor_energy .and. imp_loop==imp_loop_iters_short) then
+        save_bond_energy=.true.
+      else
+        save_bond_energy=.false.
+      endif
+    ! update velocities
+    do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+      berg=>bergs%list(grdi,grdj)%first
+      do while (associated(berg)) ! loop over all bergs
 
-  ! Do the same for heat (no separate classes needed)
-  grd%tmp(:,:)=bergs%dt*grd%calving_hflx(:,:)*grd%area(:,:)*(1.-remaining_dist)
-  bergs%net_incoming_calving_heat_used=bergs%net_incoming_calving_heat_used+sum( grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec) )
-  grd%stored_heat(:,:)=grd%stored_heat(:,:)+grd%tmp(:,:) ! +=bergs%dt*grd%calving_hflx(:,:)*grd%area(:,:)*(1.-remaining_dist)
-  grd%calving_hflx(:,:)=grd%calving_hflx(:,:)*remaining_dist
+        if (berg%static_berg .lt. 0.5 .and. berg%conglom_id.ne.0) then
 
-end subroutine accumulate_calving
+          latn = berg%lat ;   lonn = berg%lon
+          axn  = berg%axn_fast ;   ayn  = berg%ayn_fast
+          bxn  = berg%bxn_fast ;   byn  = berg%byn_fast
+          uvel1=berg%uvel ;   vvel1=berg%vvel
+          i=berg%ine      ;   j=berg%jne
+          xi=berg%xi      ;   yj=berg%yj
 
-!> Generate icebergs from overflowing "buckets"
-subroutine calve_icebergs(bergs)
-  ! Arguments
-  type(icebergs), pointer :: bergs !< Container for all types and memory
-  ! Local variables
-  type(icebergs_gridded), pointer :: grd
-  integer :: i,j,k,icnt,icntmax
-  integer :: iNg, jNg ! Total number of points globally in i and j direction
-  type(iceberg) :: newberg
-  logical :: lret
-  real :: xi, yj, ddt, calving_to_bergs, calved_to_berg, heat_to_bergs, heat_to_berg
-  integer :: stderrunit
+          if (new_mts) then
+            axn = axn+bxn; ayn=ayn+byn
+          endif
 
-  ! Get the stderr unit number
-  stderrunit = stderr()
+          ! Turn the velocities into u_star, v_star.(uvel3 is v_star) - (possible issues with tangent plane?)
+          uvel3=uvel1+(dt_2*axn)                  !(Stern et al 2017, Eq B4)
+          vvel3=vvel1+(dt_2*ayn)
 
-  ! For convenience
-  grd=>bergs%grd
+          if (monitor_energy .and. imp_loop==imp_loop_iters_short) &
+            call mts_energy_part_3(bergs,berg,uvel3,vvel3,whichtime=1)
 
-  iNg=(grd%ieg-grd%isg+1) ! Total number of points globally in i direction
-  jNg=(grd%jeg-grd%jsg+1) ! Total number of points globally in j direction
+          call accel_mts(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, &
+            ax1, ay1, axn, ayn, bxn, byn, save_bond_energy)
 
-  grd%real_calving(:,:,:)=0.
-  calving_to_bergs=0.
-  heat_to_bergs=0.
-  icntmax=0
 
-  do k=1, nclasses
-    do j=grd%jsc, grd%jec
-      do i=grd%isc, grd%iec
-        ddt=0.; icnt=0
-        do while (grd%stored_ice(i,j,k).ge.bergs%initial_mass(k)*bergs%mass_scaling(k))
-          newberg%lon=0.25*((grd%lon(i,j)+grd%lon(i-1,j-1))+(grd%lon(i-1,j)+grd%lon(i,j-1)))
-          newberg%lat=0.25*((grd%lat(i,j)+grd%lat(i-1,j-1))+(grd%lat(i-1,j)+grd%lat(i,j-1)))
-         !write(stderr(),*) 'KID, calve_icebergs: creating new iceberg at ',newberg%lon,newberg%lat
-          lret=pos_within_cell(grd, newberg%lon, newberg%lat, i, j, xi, yj)
-          if (.not.lret) then
-            write(stderrunit,*) 'KID, calve_icebergs: something went very wrong!',i,j,xi,yj
-            call error_mesg('KID, calve_icebergs', 'berg is not in the correct cell!', FATAL)
-          endif
-          if (debug.and.(xi<0..or.xi>1..or.yj<0..or.yj>1.)) then
-            write(stderrunit,*) 'KID, calve_icebergs: something went very wrong!',i,j,xi,yj
-            call error_mesg('KID, calve_icebergs', 'berg xi,yj is not correct!', FATAL)
+          ! Solving for the new velocity (Stern et al 2017, Eqn B5)
+          on_tangential_plane=.false.
+          if ((berg%lat>89.) .and. (bergs%grd%grid_is_latlon)) on_tangential_plane=.true.
+          if (on_tangential_plane) then
+            call rotvec_to_tang(lonn,uvel3,vvel3,xdot3,ydot3)
+            call rotvec_to_tang(lonn,ax1,ay1,xddot1,yddot1)
+            xdotn=xdot3+(dt*xddot1); ydotn=ydot3+(dt*yddot1)
+            call rotvec_from_tang(lonn,xdotn,ydotn,uveln,vveln)
+          else
+            !uvel3, vvel3 become uveln and vveln after they are put into lat/lon co-ordinates
+            uveln=uvel3+(dt*ax1); vveln=vvel3+(dt*ay1)
           endif
-          if (grd%msk(i,j)<0.5) then
-            write(stderrunit,*) 'KID, calve_icebergs: WARNING!!! Iceberg born in land cell',i,j,newberg%lon,newberg%lat
-            if (debug) call error_mesg('KID, calve_icebergs', 'Iceberg born in Land Cell!', FATAL)
+
+          ! Saving all the iceberg variables.
+          berg%axn_fast=axn; berg%ayn_fast=ayn
+          berg%bxn_fast=bxn; berg%byn_fast=byn
+          berg%uvel=uveln  ; berg%vvel=vveln
+
+          if (monitor_energy .and. imp_loop==imp_loop_iters_short) &
+            call mts_energy_part_3(bergs,berg,uvel3,vvel3,whichtime=2)
+        endif
+        berg=>berg%next
+      enddo ! loop over all bergs
+    enddo; enddo ! update velocities
+
+
+    if (imp_loop_iters_short>1 .and. imp_loop.ne.imp_loop_iters_short) then
+      do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+        berg=>bergs%list(grdi,grdj)%first
+        do while (associated(berg)) ! loop over all bergs
+          if (berg%static_berg .lt. 0.5 .and. berg%conglom_id.ne.0) then
+
+            berg%uvel_old=berg%uvel; berg%vvel_old=berg%vvel
+            if (new_mts) then
+              berg%uvel=berg%uvel-dt_2*(berg%axn_fast+berg%bxn_fast)-dt_2*(berg%axn+berg%bxn)
+              berg%vvel=berg%vvel-dt_2*(berg%ayn_fast+berg%byn_fast)-dt_2*(berg%ayn+berg%byn)
+            else
+              berg%uvel=berg%uvel-dt_2*(berg%axn_fast+2.0*berg%bxn_fast)-dt_2*berg%axn
+              berg%vvel=berg%vvel-dt_2*(berg%ayn_fast+2.0*berg%byn_fast)-dt_2*berg%ayn
+            endif
+            berg%axn_fast=berg%axn; berg%ayn_fast=berg%ayn
+            berg%bxn_fast=berg%bxn; berg%byn_fast=berg%byn
           endif
-          newberg%ine=i
-          newberg%jne=j
-          newberg%xi=xi
-          newberg%yj=yj
-          newberg%uvel=0.
-          newberg%vvel=0.
-          newberg%uvel_prev=0.  !Added by Alex
-          newberg%vvel_prev=0.  !Added by Alex
-          newberg%axn=0. !Added by Alon
-          newberg%ayn=0. !Added by Alon
-          newberg%bxn=0. !Added by Alon
-          newberg%byn=0. !Added by Alon
-          newberg%axn_fast=0. !Added by Alex
-          newberg%ayn_fast=0. !Added by Alex
-          newberg%bxn_fast=0. !Added by Alex
-          newberg%byn_fast=0. !Added by Alex
-          newberg%mass=bergs%initial_mass(k)
-          newberg%thickness=bergs%initial_thickness(k)
-          newberg%width=bergs%initial_width(k)
-          newberg%length=bergs%initial_length(k)
-          newberg%start_lon=newberg%lon
-          newberg%start_lat=newberg%lat
-          newberg%start_year=bergs%current_year
-          newberg%id = generate_id(grd, i, j)
-          newberg%conglom_id=0
-          newberg%start_day=bergs%current_yearday+ddt/86400.
-          newberg%start_mass=bergs%initial_mass(k)
-          newberg%mass_scaling=bergs%mass_scaling(k)
-          newberg%mass_of_bits=0.
-          newberg%halo_berg=0.
-          newberg%static_berg=0.
-          newberg%heat_density=grd%stored_heat(i,j)/grd%stored_ice(i,j,k) ! This is in J/kg
-          call add_new_berg_to_list(bergs%list(i,j)%first, newberg)
-          calved_to_berg=bergs%initial_mass(k)*bergs%mass_scaling(k) ! Units of kg
-          ! Heat content
-          heat_to_berg=calved_to_berg*newberg%heat_density ! Units of J
-          grd%stored_heat(i,j)=grd%stored_heat(i,j)-heat_to_berg
-          heat_to_bergs=heat_to_bergs+heat_to_berg
-          ! Stored mass
-          grd%stored_ice(i,j,k)=grd%stored_ice(i,j,k)-calved_to_berg
-          calving_to_bergs=calving_to_bergs+calved_to_berg
-          grd%real_calving(i,j,k)=grd%real_calving(i,j,k)+calved_to_berg/bergs%dt
-          ddt=ddt-bergs%dt*2./17. ! Minor offset to start day (negative offsets)
-          icnt=icnt+1
-          bergs%nbergs_calved=bergs%nbergs_calved+1
-          bergs%nbergs_calved_by_class(k)=bergs%nbergs_calved_by_class(k)+1
+          berg=>berg%next
         enddo
-        icntmax=max(icntmax,icnt)
-      enddo
-    enddo
+      enddo; enddo
+    endif
+
   enddo
 
-  if (debug.and.icntmax>1) write(stderrunit,*) 'calve_icebergs: icnt=',icnt,' on',mpp_pe()
+    !update 'old' velocities used for interactions
+    do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+      berg=>bergs%list(grdi,grdj)%first
+      do while (associated(berg)) ! loop over all bergs
+        if (berg%static_berg .lt. 0.5 .and. berg%conglom_id.ne.0) then
+          berg%uvel_old=berg%uvel; berg%vvel_old=berg%vvel
 
-  bergs%net_calving_to_bergs=bergs%net_calving_to_bergs+calving_to_bergs
-  bergs%net_heat_to_bergs=bergs%net_heat_to_bergs+heat_to_bergs
+          if (imp_loop_iters_short>1) then
+            berg%axn=berg%axn_fast; berg%ayn=berg%ayn_fast
+            berg%bxn=berg%bxn_fast; berg%byn=berg%byn_fast
+          endif
+        endif
+        berg=>berg%next
+      enddo ! loop over all bergs
+    enddo; enddo ! update 'old' velocities
+  enddo ! loop over sub-steps
 
-end subroutine calve_icebergs
+  !reset interactive_forces
+  bergs%only_interactive_forces=only_interactive_forces
 
-!> Evolves icebergs forward by updating velocity and position with a multiple-time-step
-!! Velocity Verlet scheme.
-subroutine evolve_icebergs_mts(bergs)
+  !call update_and_break_bonds(bergs)
+
+  !update indices
+  do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
+    !no reason to worry about halo/conglomerate bergs here
+    berg=>bergs%list(grdi,grdj)%first
+    do while (associated(berg)) ! loop over all bergs
+      if (berg%static_berg .lt. 0.5 .and. berg%halo_berg<1) then
+        berg%uvel_old=berg%uvel; berg%vvel_old=berg%vvel
+        uveln=berg%uvel; vveln=berg%vvel
+        lonn=berg%lon  ; latn=berg%lat
+        i=berg%ine     ; j=berg%jne
+        xi=berg%xi     ; yj=berg%yj
+        ! finalize new iceberg positions and index
+        call adjust_index_and_ground(grd, lonn, latn, uveln, vveln, i, j, xi, yj, bounced, error_flag, berg%id)
+        berg%lon=lonn      ;  berg%lat=latn
+        berg%lon_old=lonn  ;  berg%lat_old=latn
+        berg%ine=i    ;  berg%jne=j
+        berg%xi=xi    ;  berg%yj=yj
+
+      endif
+      berg=>berg%next
+    enddo ! loop over all bergs
+  enddo; enddo ! update 'old' velocities
+
+end subroutine evolve_icebergs_mts
+
+
+!> Evolves icebergs forward by updating velocity and position with a multiple-time-step Velocity Verlet
+!! scheme. Experimental option: each short/long step can be iterated until a given convergence tolerance
+!! is met, which better enforces momentum conservation during collision...this iterative scheme may or may
+!! not be needed to yield consistent fracture behavior. Alternatively, use evolve_icebergs_mts to specify
+!! the number of iterations directly.
+subroutine evolve_icebergs_mts2(bergs)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
   ! Local variables
@@ -4308,8 +5348,15 @@ subroutine evolve_icebergs_mts(bergs)
   real :: xddot1, yddot1, xdot2, ydot2, xdot3, ydot3, xdotn, ydotn
   real :: u2, v2, x1, y1, xn, yn
   real :: ax1,ay1
-  real :: dx, dt, dt_2
+  real :: dt, dt_2
   logical :: on_tangential_plane, error_flag, bounced
+  !energy stuff
+  real :: dx,dy,M,Fex,Fey,Fex_prev,Fey_prev,Fdx_prev,Fdy_prev,Fdx,Fdy,Fx_tot,Fy_tot,Fx_tot_prev,Fy_tot_prev
+  logical :: save_bond_energy
+  real :: Fex_i, Fey_i, Fec_x, Fec_y, Fdc_x, Fdc_y, ustar, vstar, uveln_star, vveln_star
+  integer :: ii,jj,maxii,minii,maxjj,minjj
+  real :: usum,usum1,usum2,normchange,denom
+  logical :: finished,last_iter
 
   ! Multiple Time Step Velocity Verlet:
   ! NOTE: To avoid the need for computationally expensive transfers between processors
@@ -4341,7 +5388,7 @@ subroutine evolve_icebergs_mts(bergs)
           do j=grd%jed,grd%jsd,-1
             write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lat(i,j),i=grd%isd,grd%ied)
           enddo
-          call print_berg(stderrunit, berg, 'evolve_iceberg_mts, berg is not in proper starting cell')
+          call print_berg(stderrunit, berg, 'evolve_icebergs_mts, berg is not in proper starting cell')
           write(stderrunit,'(a,i3,2(i4,3f8.2))') 'evolve_icebergs_mts: pe,lon/lat(i,j)=', mpp_pe(), &
             berg%ine,berg%lon,grd%lon(berg%ine-1,berg%jne-1),grd%lon(berg%ine,berg%jne), &
             berg%jne,berg%lat,grd%lat(berg%ine-1,berg%jne-1),grd%lat(berg%ine,berg%jne)
@@ -4353,45 +5400,102 @@ subroutine evolve_icebergs_mts(bergs)
     enddo
   enddo; enddo
 
-  ! PART 1: solve for V_n+1
+  ! PART 1: solve for V_n+1 (from the previous timestep)
   bergs%mts_part=1
   dt = bergs%dt
   dt_2=0.5*dt
   rx = 0.0; ry = 0.0 !not needed, because interp_gridded_fields_to_bergs was already called
+  ii = 0
+  save_bond_energy=.false.
+  usum=0.0; usum1=0.0; usum2=0.0
+  finished=.false.
 
-  do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
-    berg=>bergs%list(grdi,grdj)%first
-    do while (associated(berg)) ! loop over all bergs
-      !if (berg%static_berg .lt. 0.5 .and. berg%halo_berg<10) then
-      !only evolve non-static bergs that overlap, or are part of a conglom that overlaps, the computational domain:
-      if (berg%static_berg .lt. 0.5 .and. berg%conglom_id.ne.0) then
-        latn = berg%lat ;   lonn = berg%lon
-        uvel1=berg%uvel_prev ;   vvel1=berg%vvel_prev !V_n (previous cycle)
-        !subroutine accel expects uvel1=berg%uvel_prev, and calculates ustar=uvel1+axn*dt_2.
-        !However, for the MTS case, ustar should equal berg%uvel from after the final fast force
-        !iteration k from the previous cycle. To enforce this, fake in input accelerations
-        !axn and ayn as:
-        axn  = (berg%uvel-berg%uvel_prev)/dt_2
-        ayn  = (berg%vvel-berg%vvel_prev)/dt_2
-        bxn  = 0.0      ;   byn  = 0.0
-        i=berg%ine      ;   j=berg%jne
-        xi=berg%xi      ;   yj=berg%yj
-        ! if (berg%id==4294967382 .and. berg%halo_berg==0) then
-        !   print *,'berg check 1',mpp_pe(),berg%id, berg%uvel, berg%vvel, berg%lat, berg%lon
-        ! endif
-        call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, &
-          ax1, ay1, axn, ayn, bxn, byn)
-        ! Saving all the iceberg variables
-        berg%axn=axn                ; berg%ayn=ayn
-        berg%bxn=bxn                ; berg%byn=byn
-        berg%uvel=berg%uvel+(dt*ax1); berg%vvel=berg%vvel+(dt*ay1)
-
-        !save this velocity for next time, and output
-        berg%uvel_prev=berg%uvel    ; berg%vvel_prev=berg%vvel
+  if (bergs%force_convergence) then
+    last_iter=.false.
+  else
+    last_iter=.true.
+  endif
+
+  do while (.not. finished)
+
+    ii=ii+1
+
+    do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+      berg=>bergs%list(grdi,grdj)%first
+      do while (associated(berg)) ! loop over all bergs
+        !only evolve non-static bergs that overlap, or are part of a conglom that overlaps, the computational domain:
+        if (berg%static_berg .lt. 0.5 .and. (berg%conglom_id.ne.0 .or. bergs%force_convergence)) then
+          latn = berg%lat ;   lonn = berg%lon
+          uvel1=berg%uvel ;   vvel1=berg%vvel !V_n (previous cycle)
+          axn  = 0.0      ;   ayn  = 0.0 !note these are redefined at the start of subroutine accel_mts
+          bxn  = 0.0      ;   byn  = 0.0
+          i=berg%ine      ;   j=berg%jne
+          xi=berg%xi      ;   yj=berg%yj
+
+          call accel_mts(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, &
+            ax1, ay1, axn, ayn, bxn, byn, save_bond_energy,Fec_x, Fec_y, Fdc_x, Fdc_y)
+
+          if (monitor_energy .and. last_iter) &
+            call mts_energy_part_1(bergs,berg,ax1,ay1,axn,ayn,bxn,byn,Fec_x,Fec_y,Fdc_x,Fdc_y)
+
+          ! Saving all the iceberg variables
+          berg%axn=axn; berg%ayn=ayn
+          berg%bxn=bxn; berg%byn=byn
+
+          if (bergs%force_convergence) then
+            berg%uvel_prev=berg%uvel+(dt*ax1); berg%vvel_prev=berg%vvel+(dt*ay1) !the new velocity
+            if (ii==1) usum=usum+berg%uvel_old**2 + berg%vvel_old**2
+            usum1=usum1+berg%uvel_prev**2+berg%vvel_prev**2
+            usum2=usum2+(berg%uvel_prev-berg%uvel_old)**2+(berg%vvel_prev-berg%vvel_old)**2
+          else
+            berg%uvel=berg%uvel+(dt*ax1); berg%vvel=berg%vvel+(dt*ay1)
+
+            !The final velocity from the previous cycle, which can be used
+            !during post-processing to calculate kinetic energy and momentum
+            berg%uvel_prev=berg%uvel    ; berg%vvel_prev=berg%vvel
+          endif
+        endif
+        berg=>berg%next
+      enddo ! loop over all bergs
+    enddo; enddo
+
+    !update uvel_old and vvel_old for damping interaction with other elements
+    if (bergs%force_convergence) then
+      do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+        berg=>bergs%list(grdi,grdj)%first
+        do while (associated(berg)) ! loop over all bergs
+          if (berg%static_berg .lt. 0.5) then
+            berg%uvel_old=berg%uvel_prev; berg%vvel_old=berg%vvel_prev
+          endif
+          berg=>berg%next
+        enddo
+      enddo; enddo
+    endif
+
+    if (bergs%force_convergence .and. .not. last_iter) then
+      if (ii>1) then
+        denom=sqrt(usum)+sqrt(usum1)
+        if (denom>0) then
+          normchange=2.0*sqrt(usum2)/denom
+        else
+          normchange=0.0
+        endif
+        if (normchange<bergs%convergence_tolerance) last_iter=.true.
       endif
-      berg=>berg%next
-    enddo ! loop over all bergs
-  enddo; enddo
+      usum=usum1 !previous norm (squared)
+    else
+      finished=.true.
+    endif
+
+    if (last_iter .and. .not. monitor_energy) finished=.true.
+
+    usum1=0.0; usum2=0.0
+
+  enddo
+
+
+  call update_bond_angles(bergs)
+  call update_and_break_bonds(bergs)
 
   !PART 2: X_0 and V_0, before fast sub-steps
   !X_0=X_n (no change)
@@ -4400,22 +5504,28 @@ subroutine evolve_icebergs_mts(bergs)
   do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
     berg=>bergs%list(grdi,grdj)%first
     do while (associated(berg)) ! loop over all bergs
-      !if (berg%static_berg .lt. 0.5 .and. berg%halo_berg<10) then
       if (berg%static_berg .lt. 0.5 .and. berg%conglom_id.ne.0) then
-        ! if (berg%id==4294967382 .and. berg%halo_berg==0) then
-        !   print *,'berg check 2',mpp_pe(),berg%id, berg%uvel, berg%vvel, &
-        !     berg%lat, berg%lon, berg%axn, berg%ayn, berg%bxn, berg%byn
-        ! endif
-        berg%uvel = berg%uvel + dt_2*berg%axn
-        berg%vvel = berg%vvel + dt_2*berg%ayn
-        berg%lat = berg%lat + 0.5*(dt**2)*berg%byn
-        berg%lon = berg%lon + 0.5*(dt**2)*berg%bxn
-        berg%lat_old = berg%lat; berg%lon_old = berg%lon
+        berg%lat_prev = berg%lat; berg%lon_prev = berg%lon
+        berg%uvel=berg%uvel_prev; berg%vvel=berg%vvel_prev
+
+        if (new_mts) then
+          berg%uvel = berg%uvel + dt_2*(berg%axn+berg%bxn)
+          berg%vvel = berg%vvel + dt_2*(berg%ayn+berg%byn)
+        else
+          berg%uvel = berg%uvel + dt_2*berg%axn
+          berg%vvel = berg%vvel + dt_2*berg%ayn
+          berg%lat = berg%lat + 0.5*(dt**2)*berg%byn
+          berg%lon = berg%lon + 0.5*(dt**2)*berg%bxn
+        endif
+
         berg%uvel_old=berg%uvel; berg%vvel_old=berg%vvel
-         ! if (berg%id==4294967382 .and. berg%halo_berg==0) then
-         !   print *,'berg check 3',mpp_pe(),berg%id, berg%uvel, berg%vvel, &
-         !     berg%lat, berg%lon, berg%axn, berg%ayn, berg%bxn, berg%byn
-         ! endif
+
+        if (bergs%force_convergence) then
+          berg%axn=berg%axn_fast; berg%ayn=berg%ayn_fast
+          berg%bxn=berg%bxn_fast; berg%byn=berg%byn_fast
+        endif
+
+        !if (monitor energy): already did energy update in part I
       endif
       berg=>berg%next
     enddo
@@ -4431,13 +5541,13 @@ subroutine evolve_icebergs_mts(bergs)
   bergs%mts_part=3 !so that only bonded interactions are considered in subroutine interactive_force
   dt = bergs%mts_fast_dt
   dt_2=0.5*dt
+  maxjj=0; minjj=huge(1)
 
   do k = 1,bergs%mts_sub_steps ! loop over sub-steps
 
     do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied ! update positions
       berg=>bergs%list(grdi,grdj)%first
       do while (associated(berg)) ! loop over all bergs
-        !if (berg%static_berg .lt. 0.5 .and. berg%halo_berg<10) then
         if (berg%static_berg .lt. 0.5 .and. berg%conglom_id.ne.0) then
 
           on_tangential_plane=.false.
@@ -4451,12 +5561,10 @@ subroutine evolve_icebergs_mts(bergs)
           uvel1=berg%uvel; vvel1=berg%vvel
 
           ! Loading past accelerations
-          axn=berg%axn_fast; ayn=berg%ayn_fast
-          bxn=berg%bxn_fast; byn=berg%byn_fast
+          axn=berg%axn_fast; ayn=berg%ayn_fast; bxn=berg%bxn_fast; byn=berg%byn_fast
 
           ! Velocities used to update the position
-          uvel2=uvel1+(dt_2*axn)+(dt_2*bxn)
-          vvel2=vvel1+(dt_2*ayn)+(dt_2*byn)
+          uvel2=uvel1+(dt_2*axn)+(dt_2*bxn); vvel2=vvel1+(dt_2*ayn)+(dt_2*byn)
 
           if (on_tangential_plane) call rotvec_to_tang(lon1,uvel2,vvel2,xdot2,ydot2)
           u2=uvel2*dxdl1; v2=vvel2*dydl
@@ -4476,11 +5584,26 @@ subroutine evolve_icebergs_mts(bergs)
       enddo !loop over all bergs
     enddo;enddo !update positions
 
+    jj=0
+    usum=0.0; usum1=0.0; usum2=0.0
+    finished=.false.
+    save_bond_energy=.false.
+    if (bergs%force_convergence) then
+      last_iter=.false.
+    else
+      last_iter=.true.
+    endif
+
+    do while (.not. finished)
+
+      jj=jj+1
+
+      if (monitor_energy .and. last_iter) save_bond_energy=.true.
+
     ! update velocities
     do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
       berg=>bergs%list(grdi,grdj)%first
       do while (associated(berg)) ! loop over all bergs
-        !if (berg%static_berg .lt. 0.5 .and. berg%halo_berg<10) then
         if (berg%static_berg .lt. 0.5 .and. berg%conglom_id.ne.0) then
 
           latn = berg%lat ;   lonn = berg%lon
@@ -4490,12 +5613,19 @@ subroutine evolve_icebergs_mts(bergs)
           i=berg%ine      ;   j=berg%jne
           xi=berg%xi      ;   yj=berg%yj
 
+          if (new_mts) then
+            axn = axn+bxn; ayn=ayn+byn
+          endif
+
           ! Turn the velocities into u_star, v_star.(uvel3 is v_star) - (possible issues with tangent plane?)
           uvel3=uvel1+(dt_2*axn)                  !(Stern et al 2017, Eq B4)
           vvel3=vvel1+(dt_2*ayn)
 
-          call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, &
-            ax1, ay1, axn, ayn, bxn, byn)
+          if (monitor_energy .and. last_iter) call mts_energy_part_3(bergs,berg,uvel3,vvel3,whichtime=1)
+
+          call accel_mts(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, &
+            ax1, ay1, axn, ayn, bxn, byn, save_bond_energy)
+
 
           ! Solving for the new velocity (Stern et al 2017, Eqn B5)
           on_tangential_plane=.false.
@@ -4510,22 +5640,82 @@ subroutine evolve_icebergs_mts(bergs)
             uveln=uvel3+(dt*ax1); vveln=vvel3+(dt*ay1)
           endif
 
+          if (bergs%force_convergence) then
+            if (jj==1) usum=usum+berg%uvel_old**2 + berg%vvel_old**2
+            usum1=usum1 + uveln**2 + vveln**2
+            usum2=usum2+(uveln-berg%uvel_old)**2+(vveln-berg%vvel_old)**2
+          endif
+
           ! Saving all the iceberg variables.
           berg%axn_fast=axn; berg%ayn_fast=ayn
           berg%bxn_fast=bxn; berg%byn_fast=byn
           berg%uvel=uveln  ; berg%vvel=vveln
+
+          if (monitor_energy .and. last_iter) call mts_energy_part_3(bergs,berg,uvel3,vvel3,whichtime=2)
+
         endif
         berg=>berg%next
       enddo ! loop over all bergs
     enddo; enddo ! update velocities
 
+    if (bergs%force_convergence .and. .not. last_iter) then
+      if (jj>1) then
+        denom=sqrt(usum)+sqrt(usum1)
+        if (denom>0) then
+          normchange=2.0*sqrt(usum2)/denom
+        else
+          normchange=0.0
+        endif
+        if (normchange<bergs%convergence_tolerance) last_iter=.true.
+      endif
+      usum=usum1 !previous norm (squared)
+    else
+      finished=.true.
+    endif
+
+    if (last_iter .and. .not. monitor_energy) finished=.true.
+
+    if (bergs%force_convergence .and. (.not. finished)) then
+      do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+        berg=>bergs%list(grdi,grdj)%first
+        do while (associated(berg)) ! loop over all bergs
+          if (berg%static_berg .lt. 0.5 .and. berg%conglom_id.ne.0) then
+
+            !update old velocities for interactions
+            berg%uvel_old=berg%uvel; berg%vvel_old=berg%vvel
+
+            if (new_mts) then
+              berg%uvel=berg%uvel-dt_2*(berg%axn_fast+berg%bxn_fast)-dt_2*(berg%axn+berg%bxn)
+              berg%vvel=berg%vvel-dt_2*(berg%ayn_fast+berg%byn_fast)-dt_2*(berg%ayn+berg%byn)
+            else
+              berg%uvel=berg%uvel-dt_2*(berg%axn_fast+2.0*berg%bxn_fast)-dt_2*berg%axn
+              berg%vvel=berg%vvel-dt_2*(berg%ayn_fast+2.0*berg%byn_fast)-dt_2*berg%ayn
+            endif
+            berg%axn_fast=berg%axn; berg%ayn_fast=berg%ayn
+            berg%bxn_fast=berg%bxn; berg%byn_fast=berg%byn
+          endif
+          berg=>berg%next
+        enddo
+      enddo; enddo
+    endif
+
+    usum1=0.0; usum2=0.0
+
+    if (jj<minjj .and. finished) minjj=jj
+    if (jj>maxjj .and. finished) maxjj=jj
+  enddo
+
     !update 'old' velocities used for interactions
     do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
       berg=>bergs%list(grdi,grdj)%first
       do while (associated(berg)) ! loop over all bergs
-        !if (berg%static_berg .lt. 0.5 .and. berg%halo_berg<10) then
         if (berg%static_berg .lt. 0.5 .and. berg%conglom_id.ne.0) then
           berg%uvel_old=berg%uvel; berg%vvel_old=berg%vvel
+
+          if (bergs%force_convergence) then
+            berg%axn=berg%axn_fast; berg%ayn=berg%ayn_fast
+            berg%bxn=berg%bxn_fast; berg%byn=berg%byn_fast
+          endif
         endif
         berg=>berg%next
       enddo ! loop over all bergs
@@ -4535,6 +5725,8 @@ subroutine evolve_icebergs_mts(bergs)
   !reset interactive_forces
   bergs%only_interactive_forces=only_interactive_forces
 
+  !call update_and_break_bonds(bergs)
+
   !update indices
   do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
     !no reason to worry about halo/conglomerate bergs here
@@ -4557,7 +5749,150 @@ subroutine evolve_icebergs_mts(bergs)
     enddo ! loop over all bergs
   enddo; enddo ! update 'old' velocities
 
-end subroutine evolve_icebergs_mts
+
+  ! for testing:
+  ! maxii=ii; minii=ii
+  ! call mpp_max(maxii); call mpp_min(minii); call mpp_max(maxjj); call mpp_min(minjj)
+  !if (maxii>2 .or. maxjj>2) print *,'outer max iters, inner max iters',maxii,maxjj
+
+end subroutine evolve_icebergs_mts2
+
+!> Energy calculations for MTS_part==1
+subroutine mts_energy_part_1(bergs,berg,ax1,ay1,axn,ayn,bxn,byn,Fec_x,Fec_y,Fdc_x,Fdc_y)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  type(iceberg), pointer :: berg
+  real, intent(in) :: ax1,ay1,axn,ayn,bxn,byn,Fec_x,Fec_y,Fdc_x,Fdc_y
+  ! Local
+  real :: dt, M, Fex, Fey, Fex_i, Fey_i
+  real :: uveln, vveln, uveln_star, vveln_star, ustar, vstar
+
+  dt=bergs%dt
+
+  !Again, MTS part 1 solves for V_n+1 from the previous timestep
+  !"Temp" energy variables are from the previous cycle
+  !At the end of MTS part 1, the non-"temp" energy variables are saved for post-processing/analysis
+  !see plot_energy.py
+
+  !derived from Mayrhofer,Hager, and Kloss 2017 (MHK17) and Asmar et al 2003
+  M = berg%mass
+  if (new_mts) then
+    Fex = M * 2*ax1; Fey = M * 2*ay1 !external forces
+    Fex = Fex - Fec_x - Fdc_x; Fey = Fey - Fec_y - Fdc_y !external forces minus collisional
+
+    uveln=berg%uvel+(dt*ax1); vveln=berg%vvel+(dt*ay1)
+    ustar=berg%uvel; vstar=berg%vvel
+
+    !dEext=0.5*(V_{i+1} + V_{i+0.5})*F_{ext,i+1}*dt/2
+    berg%Eext=berg%Eext_temp - 0.25*dt*(&
+      (uveln + ustar)*Fex + (vveln + vstar)*Fey)
+
+    berg%Ee_contact=berg%Ee_contact_temp - 0.25*dt*(&
+      (uveln + ustar)*Fec_x + (vveln + vstar)*Fec_y)
+
+    berg%Ed_contact=berg%Ed_contact_temp - 0.25*dt*(&
+      (uveln + ustar)*Fdc_x + (vveln + vstar)*Fdc_y)
+
+    !The following is for part II
+    !V{i+1.5}
+    uveln_star = uveln + dt*ax1; vveln_star = vveln + dt*ay1
+
+    berg%Eext_temp=berg%Eext - 0.25*dt*(&
+      (uveln + uveln_star)*Fex + (vveln + vveln_star)*Fey)
+
+    berg%Ee_contact_temp=berg%Ee_contact - 0.25*dt*(&
+      (uveln + uveln_star)*Fec_x + (vveln + vveln_star)*Fec_y)
+
+    berg%Ed_contact_temp=berg%Ed_contact - 0.25*dt*(&
+      (uveln + uveln_star)*Fdc_x + (vveln + vveln_star)*Fdc_y)
+
+  else
+    Fex = M * axn; Fey = M * ayn !explicit forces
+    Fex = Fex - Fec_x; Fey = Fey - Fec_y !explicit forces minus collisional elastic
+    Fex_i = M * bxn;     Fey_i= M * byn !implicit forces
+    Fex_i = Fex_i - Fdc_x; Fey_i = Fey_i - Fdc_y !implicit forces minus collisional damping
+
+    uveln=berg%uvel+(dt*ax1); vveln=berg%vvel+(dt*ay1)
+    ustar=berg%uvel; vstar=berg%vvel
+
+    !explicit:
+    !dEext=0.5*(V_{i+1} + V_{i+0.5})*F_{ext,i+1}*dt/2
+    berg%Eext=berg%Eext_temp - 0.25*dt*(&
+      (uveln + ustar)*Fex + (vveln + vstar)*Fey)
+
+    berg%Ee_contact=berg%Ee_contact_temp - 0.25*dt*(&
+      (uveln + ustar)*Fec_x + (vveln + vstar)*Fec_y)
+
+    !old way:
+    !implicit:
+    !dEext=0.5*(V_{i+1} + V_{i})*F_{ext,i+1}*dt/2
+    ! berg%Eext=berg%Eext - 0.5*dt*(&
+    !   (uveln + berg%uvel_prev)*Fex_i + &
+    !   (vveln + berg%vvel_prev)*Fey_i)
+
+    ! berg%Ed_contact=berg%Ed_contact - 0.5*dt*(&
+    !   (uveln + berg%uvel_prev)*Fdc_x + &
+    !   (vveln + berg%vvel_prev)*Fdc_y)
+
+    berg%Eext=berg%Eext - 0.5*dt*(&
+      (uveln + ustar)*Fex_i + (vveln + vstar)*Fey_i)
+
+    berg%Ed_contact=berg%Ed_contact - 0.5*dt*(&
+      (uveln + ustar)*Fdc_x + (vveln + vstar)*Fdc_y)
+
+    !The following is for part II
+    !V{i+1.5}
+    uveln_star = uveln + 0.5*dt*axn; vveln_star = vveln + 0.5*dt*ayn
+
+    berg%Eext_temp=berg%Eext - 0.25*dt*(&
+      (uveln + uveln_star)*Fex + (vveln + vveln_star)*Fey)
+
+    berg%Ee_contact_temp=berg%Ee_contact - 0.25*dt*(&
+      (uveln + uveln_star)*Fec_x + (vveln + vveln_star)*Fec_y)
+  endif
+
+  berg%Ee=berg%Ee_temp; berg%Ed=berg%Ed_temp
+end subroutine mts_energy_part_1
+
+!> Energy calculations for MTS_part==3
+subroutine mts_energy_part_3(bergs,berg,uvel3,vvel3,whichtime)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  type(iceberg), pointer :: berg
+  real,intent(in) :: uvel3,vvel3
+  integer,intent(in) :: whichtime
+  ! Local
+  real :: dt, M, Fex, Fey, Fdx, Fdy
+
+
+  !MTS sub-step forces
+  dt = bergs%mts_fast_dt
+  M = berg%mass
+  Fex = M * berg%axn_fast; Fey = M * berg%ayn_fast !elastic forces
+
+  !for i to i+1/2 or i+1/2 to i+1
+  berg%Ee_temp=berg%Ee_temp - 0.25*dt*(&
+    (uvel3 + berg%uvel)*Fex + &
+    (vvel3 + berg%vvel)*Fey)
+
+  if (new_mts) then   !for i to i+1/2 or i+1/2 to i+1
+    Fdx = M * berg%bxn_fast; Fdy = M * berg%byn_fast !damping forces
+    berg%Ed_temp=berg%Ed_temp - 0.25*dt*(&
+      (uvel3 + berg%uvel)*Fdx + &
+      (vvel3 + berg%vvel)*Fdy)
+  elseif (whichtime==2) then !for i+1/2 to i+1
+    Fdx = M * berg%bxn_fast; Fdy = M * berg%byn_fast !damping forces
+    berg%Ed_temp=berg%Ed_temp - 0.5*dt*(&
+      (uvel3 + berg%uvel)*Fdx + &
+      (vvel3 + berg%vvel)*Fdy)
+
+    !old way
+    !V{i} to V{i+1}
+    ! berg%Ed_temp=berg%Ed_temp - 0.5*dt*(&
+    ! (berg%uvel + uveln)*Fdx + &
+    ! (berg%vvel + vveln)*Fdy)
+  endif
+end subroutine mts_energy_part_3
 
 !> Evolves icebergs forward by updating velocity and position with a time-stepping scheme
 subroutine evolve_icebergs(bergs)
@@ -4651,7 +5986,8 @@ subroutine evolve_icebergs(bergs)
           if (.not. interactive_icebergs_on) call update_verlet_position(bergs,berg)
         endif
 
-        !call interp_flds(grd, i, j, xi, yj, berg%uo, berg%vo, berg%ui, berg%vi, berg%ua, berg%va, berg%ssh_x, berg%ssh_y, berg%sst)
+        !call interp_flds(grd, berg%lon, berg%lat, i, j, xi, yj, berg%uo, berg%vo, berg%ui, &
+        !berg%vi, berg%ua, berg%va, berg%ssh_x, berg%ssh_y, berg%sst,berg%od)
         !if (debug) call print_berg(stderr(), berg, 'evolve_iceberg, final posn.')
         if (debug) call check_position(grd, berg, 'evolve_iceberg (bot)')
       endif
@@ -4734,6 +6070,8 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln, rx, ry)
   i=berg%ine      ;   j=berg%jne
   xi=berg%xi      ;   yj=berg%yj
 
+  berg%uvel_prev=berg%uvel-dt_2*berg%bxn; berg%vvel_prev=berg%vvel-dt_2*berg%byn
+
   ! Turn the velocities into u_star, v_star.(uvel3 is v_star) - Alon (not sure how this works with tangent plane)
   uvel3=uvel1+(dt_2*axn)                  !Alon (Stern et al 2017, Eq B4)
   vvel3=vvel1+(dt_2*ayn)                  !Alon
@@ -5645,8 +6983,10 @@ subroutine icebergs_end(bergs)
   ! Delete bergs and structures
   call move_all_trajectories(bergs, delete_bergs=.true.)
 
-  if (.not. bergs%ignore_traj) &
-  call write_trajectory(bergs%trajectories, bergs%save_short_traj)
+  if (.not. bergs%ignore_traj) then
+    call write_trajectory(bergs%trajectories, bergs%save_short_traj)
+    if (save_bond_traj) call write_bond_trajectory(bergs%bond_trajectories)
+  endif
 
   deallocate(bergs%grd%lon)
   deallocate(bergs%grd%lat)
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index de08aca..cadec85 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -18,8 +18,9 @@ module ice_bergs_framework
 
 implicit none ; private
 
-integer :: buffer_width=28 ! This should be a parameter
-integer :: buffer_width_traj=32 ! This should be a parameter
+integer :: buffer_width=35 ! This should be a parameter
+integer :: buffer_width_traj=37 ! This should be a parameter
+integer :: buffer_width_bond_traj=15 !This should be a parameter
 integer, parameter :: nclasses=10 ! Number of ice bergs classes
 
 !Local Vars
@@ -45,16 +46,23 @@ module ice_bergs_framework
 logical :: do_unit_tests=.false. !< Conduct some unit tests
 logical :: force_all_pes_traj=.false. !< Force all pes write trajectory files regardless of io_layout
 logical :: mts=.false.
+logical :: new_mts=.false. !If T, implicit accel is added 50% at the current time step and 50% at the next time step
+logical :: save_bond_traj=.false. !<Save trajectory files for bonds
+logical :: ewsame=.false. !<(F) set T if periodic and 2 PEs along the x direction (zonal) (i.e. E/W PEs are the same)
+logical :: monitor_energy=.false. !<monitors energies: elastic (spring+collision), external, dissipated, fracture
+integer :: imp_loop_iters_long=1 !if >1, the # of times the each long MTS step will iterate (alt to force_convergence)
+integer :: imp_loop_iters_short=1!if >1, the # of times the each short MTS step will iterate (alt to force_convergence)
 
 !Public params !Niki: write a subroutine to expose these
-public nclasses,buffer_width,buffer_width_traj
+public nclasses,buffer_width,buffer_width_traj,buffer_width_bond_traj
 public verbose, really_debug, debug, restart_input_dir,make_calving_reproduce,old_bug_bilin,use_roundoff_fix
 public ignore_ij_restart, use_slow_find,generate_test_icebergs,old_bug_rotated_weights,budget
 public orig_read, force_all_pes_traj
-public mts !Alex
+public mts,new_mts,save_bond_traj,ewsame,monitor_energy
+public imp_loop_iters_long, imp_loop_iters_short
 
 !Public types
-public icebergs_gridded, xyt, iceberg, icebergs, buffer, bond
+public icebergs_gridded, xyt, iceberg, icebergs, buffer, bond, bond_xyt
 
 !Public subs
 public ice_bergs_framework_init
@@ -79,9 +87,11 @@ module ice_bergs_framework
 public test_check_for_duplicate_ids_in_list
 public check_for_duplicates_in_parallel
 public split_id, id_from_2_ints, generate_id, cij_from_old_id, convert_old_id
-public update_latlon
-public set_conglom_ids
-public transfer_mts_bergs
+public update_latlon,set_conglom_ids,transfer_mts_bergs,quad_interp_from_agrid
+public pack_bond_traj_into_buffer2, unpack_bond_traj_from_buffer2, push_bond_posn, append_bond_posn
+public update_and_break_bonds,assign_n_bonds,reset_bond_rotation,update_bond_angles
+public fracture_testing_initialization, orig_bond_length
+public energy_tests_init
 
 !> Container for gridded fields
 type :: icebergs_gridded
@@ -205,6 +215,12 @@ module ice_bergs_framework
   real :: ayn
   real :: bxn
   real :: byn
+  real :: axn_fast
+  real :: ayn_fast
+  real :: bxn_fast
+  real :: byn_fast
+  integer :: n_bonds
+  real :: accum_bond_rotation
   real :: uvel_prev
   real :: vvel_prev
   real :: uo !< Zonal velocity of ocean (m/s)
@@ -223,12 +239,32 @@ module ice_bergs_framework
   real :: static_berg
   real :: mass_of_bits !< Mass of bergy bits (kg)
   real :: heat_density !< Heat density of berg (???)
-  integer :: conglom_id
+  real :: od !< Ocean depth
   integer :: year !< Year of this record (years)
   integer(kind=8) :: id = -1 !< Iceberg identifier
   type(xyt), pointer :: next=>null() !< Next link in list
+  real, allocatable :: Ee, Ed, Eext, Ee_contact, Ed_contact, Efrac !<energy stuff
 end type xyt
 
+!> A link in the trajectory record (diagnostic)
+type :: bond_xyt
+  real :: lon !< Longitude of bond (degree E or unit of grid coordinate)
+  real :: lat !< Latitude of bond (degree N or unit of grid coordinate)
+  integer :: year !< Year of this record (years)
+  real :: day !< Day of this record (days)
+  real :: length !<Length of bond
+  real :: n1 !<Unit vector, x-component
+  real :: n2 !<Unit vector, y-component
+  integer(kind=8) :: id1 !<ID of first berg
+  integer(kind=8) :: id2 !<ID of second berg
+  real :: rotation
+  real :: rel_rotation
+  real :: n_strain
+  real :: n_strain_rate
+  type(bond_xyt), pointer :: next=>null() !< Next link in list
+  real, allocatable :: Ee, Ed
+end type bond_xyt
+
 !> An iceberg object, used as a link in a linked list
 type :: iceberg
   type(iceberg), pointer :: prev=>null() !< Previous link in list
@@ -236,6 +272,8 @@ module ice_bergs_framework
   ! State variables (specific to the iceberg, needed for restarts)
   real :: lon !< Longitude of berg (degree N or unit of grid coordinate)
   real :: lat !< Latitude of berg (degree E or unit of grid coordinate)
+  real :: lon_prev !< Previous timestep longitude of berg
+  real :: lat_prev !< Previous timestep latitude of berg
   real :: uvel !< Zonal velocity of berg (m/s)
   real :: vvel !< Meridional velocity of berg (m/s)
   real :: mass !< Mass of berg (kg)
@@ -250,6 +288,8 @@ module ice_bergs_framework
   real :: ayn_fast
   real :: bxn_fast
   real :: byn_fast
+  integer :: n_bonds
+  real :: accum_bond_rotation
   real :: uvel_prev
   real :: vvel_prev
   real :: uvel_old
@@ -285,8 +325,11 @@ module ice_bergs_framework
   real :: sss !< Sea-surface salinity (1e-3)
   real :: cn !< Sea-ice concentration (nondim)
   real :: hi !< Sea-ice thickness (m)
+  real :: od !< Ocean depth
   type(xyt), pointer :: trajectory=>null() !< Trajectory for this berg
   type(bond), pointer :: first_bond=>null() !< First element of bond list.
+  real, allocatable :: Ee, Ed, Eext, Ee_contact, Ed_contact, Efrac !<energy stuff
+  real, allocatable :: Ee_temp, Ed_temp, Eext_temp, Ee_contact_temp, Ed_contact_temp !<energy stuff
 end type iceberg
 
 !> A bond object connecting two bergs, used as a link in a linked list
@@ -297,6 +340,16 @@ module ice_bergs_framework
   integer(kind=8) :: other_id !< ID of other berg
   integer :: other_berg_ine
   integer :: other_berg_jne
+  real :: length
+  !if bergs%fracture_criterion=='strain', the following are accumulated over all timesteps, but if
+  !bergs%fracture_criterion=='strain_rate', the following correspond to only the most recent timestep and
+  !units are per second
+  real :: rotation !radians
+  real :: rel_rotation !<rotation relative to the mean of all bonds for a berg
+  real :: n_strain !<normal strain (lengthwise stretching of the bond)
+  real :: n_strain_rate !<for bergs%fracture_criterion=='strain_rate' only
+  type(bond_xyt), pointer :: bond_trajectory=>null()
+  real, allocatable :: Ee, Ed, axn_fast, ayn_fast, bxn_fast, byn_fast !<energy stuff
 end type bond
 
 ! A dynamic buffer, used for communication, that packs types into rectangular memory
@@ -315,6 +368,7 @@ module ice_bergs_framework
   type(icebergs_gridded), pointer :: grd !< Container with all gridded data
   type(linked_list), dimension(:,:), allocatable :: list !< Linked list of icebergs
   type(xyt), pointer :: trajectories=>null() !< A linked list for detached segments of trajectories
+  type(bond_xyt), pointer :: bond_trajectories=>null() !< A linked list for detached segments of bond trajectories
   real :: dt !< Time-step between iceberg calls
              !! \todo Should make dt adaptive?
   integer :: current_year !< Current year (years)
@@ -327,10 +381,16 @@ module ice_bergs_framework
   !! Handles for clocks
   integer :: clock, clock_mom, clock_the, clock_int, clock_cal, clock_com, clock_ini, clock_ior, clock_iow, clock_dia
   integer :: clock_trw, clock_trp
+  integer :: clock_btrw, clock_btrp
   !>@}
   real :: rho_bergs !< Density of icebergs [kg/m^3]
   real :: spring_coef !< Spring constant for bonded iceberg interactions
   real :: contact_spring_coef !<Spring coefficient for berg collisions -Alex
+  character(len=11) :: fracture_criterion !<'strain_rate','strain',or 'none'
+  real :: cdrag_grounding
+  real :: h_to_init_grounding
+  real :: frac_thres_n !normal fracture strain threshold
+  real :: frac_thres_t !tangential fracture strain threshold
   logical :: debug_write !<Sets traj_sample_hours=traj_write_hours & includes halo bergs in write
   real :: bond_coef !< Spring constant for iceberg bonds
   real :: radial_damping_coef !< Coefficient for relative iceberg motion damping (radial component) -Alon
@@ -357,6 +417,7 @@ module ice_bergs_framework
   logical :: time_average_weight=.false. !< Time average the weight on the ocean
   logical :: Runge_not_Verlet=.True. !< True=Runge-Kutta, False=Verlet.
   logical :: use_mixed_melting=.False. !< If true, then the melt is determined partly using 3 eq model partly using iceberg parameterizations (according to iceberg bond number)
+  logical :: internal_bergs_for_drag=.False. !< True=reduces side drag for bonded elements in momentum equation.
   logical :: apply_thickness_cutoff_to_gridded_melt=.False. !< Prevents melt for ocean thickness below melt_cuttoff (applied to gridded melt fields)
   logical :: apply_thickness_cutoff_to_bergs_melt=.False. !< Prevents melt for ocean thickness below melt_cuttoff (applied to bergs)
   logical :: use_updated_rolling_scheme=.false. !< True to use the aspect ratio based rolling scheme rather than incorrect version of WM scheme (set tip_parameter=1000. for correct WM scheme)
@@ -383,7 +444,9 @@ module ice_bergs_framework
   logical :: manually_initialize_bonds=.False. !< True= Bonds are initialize manually.
   logical :: use_new_predictive_corrective =.False. !< Flag to use Bob's predictive corrective iceberg scheme- Added by Alon
   logical :: interactive_icebergs_on=.false. !< Turn on/off interactions between icebergs  - Added by Alon
+  logical :: scale_damping_by_pmag=.true. !<scales damping by magnitude of (projection matrix \cdot relative velocity)
   logical :: critical_interaction_damping_on=.true. !< Sets the damping on relative iceberg velocity to critical value - Added by Alon
+  logical :: tang_crit_int_damp_on=.true. !<crit interaction damping for tangential component?
   logical :: use_old_spreading=.true. !< If true, spreads iceberg mass as if the berg is one grid cell wide
   logical :: read_ocean_depth_from_file=.false. !< If true, ocean depth is read from a file.
   integer(kind=8) :: debug_iceberg_with_id = -1 !< If positive, monitors a berg with this id
@@ -437,9 +500,12 @@ module ice_bergs_framework
   integer :: mts_sub_steps
   real :: mts_fast_dt
   integer :: mts_part !for turning on/off berg interactions/collisions during different mts scheme
+  logical :: remove_unused_bergs=.true. !remove unneeded bergs after PEs transfers
   real :: contact_distance
   integer :: contact_cells_lon=1,contact_cells_lat=1 !how many cells to search to find contact pairs
   logical :: writeandstop=.false. !for debugging
+  logical :: force_convergence !experimental MTS convergence scheme to better conserve momentum during collisions
+  real :: convergence_tolerance !tolerance for the MTS convergence scheme
 end type icebergs
 
 !> Read original restarts. Needs to be module global so can be public to icebergs_mod.
@@ -519,6 +585,12 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: rho_bergs=850. ! Density of icebergs
 real :: spring_coef=1.e-8 ! Spring constant for iceberg interactions (this seems to be the highest stable value)
 real :: contact_spring_coef=0. !Spring coef for berg collisions (is set to spring_coef if not specified)
+character(len=11) :: fracture_criterion='none' !<'strain_rate','strain',or 'none'
+real :: cdrag_grounding=20.0
+real :: h_to_init_grounding=100.0
+real :: frac_thres_n=0.0 !normal fracture strain threshold
+real :: frac_thres_t=0.0 !tangential fracture strain threshold
+real :: frac_thres_scaling=1.0 !scaling factor for frac_thres_n and frac_thres_t, useful for tuning
 logical :: debug_write=.false. !Sets traj_sample_hours=traj_write_hours & includes halo bergs in write
 real :: bond_coef=1.e-8 ! Spring constant for iceberg bonds - not being used right now
 real :: radial_damping_coef=1.e-4 ! Coefficient for relative iceberg motion damping (radial component) -Alon
@@ -551,6 +623,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: tidal_drift=0. ! Amplitude of a stochastic tidal velocity added to ocean currents to cause bergs to drift randomly
 logical :: Runge_not_Verlet=.True. ! True=Runge Kutta, False=Verlet.
 logical :: use_mixed_melting=.False. ! If true, then the melt is determined partly using 3 eq model partly using iceberg parameterizations (according to iceberg bond number)
+logical :: internal_bergs_for_drag=.False. !< True=reduces side drag for bonded elements in momentum equation.
 logical :: apply_thickness_cutoff_to_gridded_melt=.False. ! Prevents melt for ocean thickness below melt_cuttoff (applied to gridded melt fields)
 logical :: apply_thickness_cutoff_to_bergs_melt=.False. ! Prevents melt for ocean thickness below melt_cuttoff (applied to bergs)
 logical :: use_updated_rolling_scheme=.false. ! Use the corrected Rolling Scheme rather than the erroneous one
@@ -579,15 +652,19 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: manually_initialize_bonds=.False. ! True= Bonds are initialize manually.
 logical :: use_new_predictive_corrective =.False. ! Flag to use Bob's predictive corrective iceberg scheme- Added by Alon
 logical :: interactive_icebergs_on=.false. ! Turn on/off interactions between icebergs  - Added by Alon
+logical :: scale_damping_by_pmag=.true. !<scales damping by magnitude of (projection matrix \cdot relative velocity)
 logical :: critical_interaction_damping_on=.true. ! Sets the damping on relative iceberg velocity to critical value - Added by Alon
+logical :: tang_crit_int_damp_on=.true. !crit interaction damping for tangential component?
 logical :: do_unit_tests=.false. ! Conduct some unit tests
 logical :: input_freq_distribution=.false. ! Flag to show if input distribution is freq or mass dist (=1 if input is a freq dist, =0 to use an input mass dist)
 logical :: read_old_restarts=.false. ! Legacy option that does nothing
 logical :: use_old_spreading=.true. ! If true, spreads iceberg mass as if the berg is one grid cell wide
 logical :: read_ocean_depth_from_file=.false. ! If true, ocean depth is read from a file.
-!logical :: mts=.false. !use multiple timestepping scheme (substep size is automatically determined) !(commented because mts was changed to global parameter for now)
 integer :: mts_sub_steps=-1 !if -1, the number of mts sub-steps will be automatically determined
+logical :: remove_unused_bergs=.true. !remove unneeded bergs after PEs transfers
 real :: contact_distance=0.0 !for unbonded berg interactions, collision is assumed at max(contact_distance,sum of the 2 bergs radii)
+logical :: force_convergence=.false. !experimental MTS convergence scheme that better preserves momentum during collisions
+real :: convergence_tolerance=1.e-8 !tolerance for the MTS force_convergence scheme
 real, dimension(nclasses) :: initial_mass=(/8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11/) ! Mass thresholds between iceberg classes (kg)
 real, dimension(nclasses) :: distribution=(/0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02/) ! Fraction of calving to apply to this class (non-dim) ,
 real, dimension(nclasses) :: mass_scaling=(/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) ! Ratio between effective and real iceberg mass (non-dim)
@@ -598,14 +675,17 @@ subroutine ice_bergs_framework_init(bergs, &
          distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,bond_coef, radial_damping_coef, tangental_damping_coef, only_interactive_forces, &
          rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, iceberg_bonds_on, manually_initialize_bonds, ignore_missing_restart_bergs, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, halo_debugging, hexagonal_icebergs, &
-         time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, interactive_icebergs_on, critical_interaction_damping_on, &
+         time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, interactive_icebergs_on, scale_damping_by_pmag,&
+         critical_interaction_damping_on, tang_crit_int_damp_on, &
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution, force_all_pes_traj, &
          allow_bergs_to_roll,set_melt_rates_to_zero,lat_ref,initial_orientation,rotate_icebergs_for_mass_spreading,grid_is_latlon,Lx,use_f_plane,use_old_spreading, &
          grid_is_regular,override_iceberg_velocities,u_override,v_override,add_iceberg_thickness_to_SSH,Iceberg_melt_without_decay,melt_icebergs_as_ice_shelf, &
          Use_three_equation_model,find_melt_using_spread_mass,use_mixed_layer_salinity_for_thermo,utide_icebergs,ustar_icebergs_bg,cdrag_icebergs, pass_fields_to_ocean_model, &
          const_gamma, Gamma_T_3EQ, ignore_traj, debug_iceberg_with_id,use_updated_rolling_scheme, tip_parameter, read_old_restarts, tau_calving, read_ocean_depth_from_file, melt_cutoff,&
-         apply_thickness_cutoff_to_gridded_melt, apply_thickness_cutoff_to_bergs_melt, use_mixed_melting, coastal_drift, tidal_drift,&
-				 mts,mts_sub_steps,contact_distance,length_for_manually_initialize_bonds,manually_initialize_bonds_from_radii,contact_spring_coef,debug_write
+         apply_thickness_cutoff_to_gridded_melt, apply_thickness_cutoff_to_bergs_melt, use_mixed_melting, internal_bergs_for_drag, coastal_drift, tidal_drift,&
+         mts,new_mts,ewsame,monitor_energy,mts_sub_steps,contact_distance,length_for_manually_initialize_bonds,manually_initialize_bonds_from_radii,contact_spring_coef,&
+         fracture_criterion, debug_write,cdrag_grounding,h_to_init_grounding,frac_thres_scaling,frac_thres_n,frac_thres_t,save_bond_traj,remove_unused_bergs,&
+         imp_loop_iters_short,imp_loop_iters_long,force_convergence,convergence_tolerance
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -787,6 +867,7 @@ subroutine ice_bergs_framework_init(bergs, &
     if(fractional_area) grd%area(is:ie,js:je)=ice_area(:,:) *(4.*pi*radius*radius)
   endif
   if(present(ocean_depth)) grd%ocean_depth(is:ie,js:je)=ocean_depth(:,:)
+  !if(present(ocean_depth)) grd%ocean_depth(grd%isd:grd%ied,grd%jsd:grd%jed)=ocean_depth(:,:)
 
   ! Copy data declared on ice model data domain
   is=grd%isc-1; ie=grd%iec+1; js=grd%jsc-1; je=grd%jec+1
@@ -979,20 +1060,26 @@ subroutine ice_bergs_framework_init(bergs, &
 if (.not. iceberg_bonds_on) then
    max_bonds=0
 else
-  buffer_width=buffer_width+(max_bonds*4) ! Increase buffer width to include bonds being passed between processors
+  buffer_width=buffer_width+(max_bonds*9) ! Increase buffer width to include bonds being passed between processors
 endif
 if (save_short_traj) buffer_width_traj=6 ! This is the length of the short buffer used for abrevated traj
 if (ignore_traj) buffer_width_traj=0 ! If this is true, then all traj files should be ignored
 
+if (monitor_energy) then
+  buffer_width=buffer_width+11+(max_bonds*6)
+  buffer_width_traj=buffer_width_traj+6
+  buffer_width_bond_traj=buffer_width_bond_traj+2
+endif
+
 !must use verlet with mts - Alex
 if (mts) then
-  buffer_width_traj=buffer_width_traj+3 !to accomodate uvel_prev, vvel_prev, conglom_id
-  buffer_width=buffer_width+19 !to accomodate external forcing (conglom_id,uo,vo,ua,va,ui,vi,ssh_x,ssh_y,sst,sss,cn,hi)
+  buffer_width_traj=buffer_width_traj+4 !to accomodate n_bonds,fast-step accel terms, overall accel terms
+  buffer_width=buffer_width+17 !to accomodate external forcing (conglom_id,uo,vo,ua,va,ui,vi,ssh_x,ssh_y,sst,sss,cn,hi,accel)
 
   !if mts_sub_steps is not given in the nml already,
   !then detemine according to the max dt according to the spring coef
   if (mts_sub_steps .eq. -1) then
-    mts_fast_dt = 2./sqrt(bergs%spring_coef)   !the (theoretical) maximum "fast" dt for mts scheme
+    mts_fast_dt = 2./sqrt(spring_coef)   !the (theoretical) maximum "fast" dt for mts scheme
     mts_sub_steps = ceiling(dt/mts_fast_dt)    !the number of substeps
   end if
 
@@ -1037,6 +1124,12 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%rho_bergs=rho_bergs
   bergs%spring_coef=spring_coef
   bergs%contact_spring_coef=contact_spring_coef !Alex
+  bergs%fracture_criterion=fracture_criterion
+  bergs%cdrag_grounding=cdrag_grounding
+  bergs%h_to_init_grounding=h_to_init_grounding
+  bergs%frac_thres_n=frac_thres_n*frac_thres_scaling
+  bergs%frac_thres_t=frac_thres_t*frac_thres_scaling
+  if (mpp_pe()==0) print *,'FRAC_THRES: N,T:', bergs%frac_thres_n,bergs%frac_thres_t
   bergs%debug_write=debug_write
   bergs%bond_coef=bond_coef
   bergs%radial_damping_coef=radial_damping_coef
@@ -1052,6 +1145,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%tip_parameter=tip_parameter
   bergs%use_updated_rolling_scheme=use_updated_rolling_scheme  !Alon
   bergs%Runge_not_Verlet=Runge_not_Verlet
+  bergs%internal_bergs_for_drag=internal_bergs_for_drag
   bergs%use_mixed_melting=use_mixed_melting
   bergs%apply_thickness_cutoff_to_bergs_melt=apply_thickness_cutoff_to_bergs_melt
   bergs%apply_thickness_cutoff_to_gridded_melt=apply_thickness_cutoff_to_gridded_melt
@@ -1087,7 +1181,9 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%manually_initialize_bonds=manually_initialize_bonds   !Alon
   bergs%length_for_manually_initialize_bonds=length_for_manually_initialize_bonds !Alex
   bergs%manually_initialize_bonds_from_radii=manually_initialize_bonds_from_radii !Alex
+  bergs%scale_damping_by_pmag=scale_damping_by_pmag
   bergs%critical_interaction_damping_on=critical_interaction_damping_on   !Alon
+  bergs%tang_crit_int_damp_on=tang_crit_int_damp_on
   bergs%interactive_icebergs_on=interactive_icebergs_on   !Alon
   bergs%use_new_predictive_corrective=use_new_predictive_corrective  !Alon
   bergs%grounding_fraction=grounding_fraction
@@ -1098,10 +1194,14 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%mts_fast_dt = mts_fast_dt
   bergs%mts_sub_steps = mts_sub_steps
   bergs%mts_part = 1
+  bergs%remove_unused_bergs = remove_unused_bergs
   bergs%contact_distance=contact_distance
+  bergs%force_convergence=force_convergence
+  bergs%convergence_tolerance=convergence_tolerance
 
   if (bergs%contact_distance>0) then
     dx_dlon=1; dy_dlat=1
+    if (grd%grid_is_latlon) dy_dlat=pi_180*Rearth
     maxk=0
     do j=grd%jsd,grd%jed; do i=grd%isd,grd%ied
       if (grd%grid_is_latlon) then
@@ -1110,11 +1210,11 @@ subroutine ice_bergs_framework_init(bergs, &
       endif
       lon_ref=grd%lon(i,j)
       k=0
-      do while(k+i<grd%ied)
+      do while((k+i)<grd%ied)
         k=k+1
         dx=(grd%lon(k+i,j)-lon_ref)*dx_dlon
         if (k>maxk) maxk=k
-        if (dx>contact_distance) exit
+        if (dx>=contact_distance) exit
       enddo
     enddo;enddo
 
@@ -1128,15 +1228,19 @@ subroutine ice_bergs_framework_init(bergs, &
     bergs%contact_cells_lat = 1
   endif
 
+  print *,'# contact cells lon/lat',bergs%contact_cells_lon,bergs%contact_cells_lat
+
   !necessary?
-  if (halo<bergs%contact_cells_lon .or. halo<bergs%contact_cells_lat) then
-	  if (mpp_pe()==0) then
-		  write(stderrunit,'(a,i3)') 'KID, icebergs_init: halo width ',halo
-		  write(stderrunit,'(a,f8.2,a,2i3)') 'KID, icebergs_init:  contact distance ',bergs%contact_distance,&
-      ' num contact cells lon and lat',bergs%contact_cells_lon,bergs%contact_cells_lat
-
-		  call error_mesg('KID, ice_bergs_framework_init', &
-		    'halo width must be increased to accomodate specified contact distance!!!', FATAL)
+  if (.not. mts) then
+    if ((halo-1)<bergs%contact_cells_lon .or. (halo-1)<bergs%contact_cells_lat) then
+      if (mpp_pe()==0) then
+        write(stderrunit,'(a,i3)') 'KID, icebergs_init: halo width minus 1 ',halo - 1
+        write(stderrunit,'(a,f8.2,a,2i3)') 'KID, icebergs_init:  contact distance ',bergs%contact_distance,&
+          ' num contact cells lon and lat',bergs%contact_cells_lon,bergs%contact_cells_lat
+
+        call error_mesg('KID, ice_bergs_framework_init', &
+          'halo width must be increased to accomodate specified contact distance!!!', FATAL)
+      endif
     endif
   endif
   allocate( bergs%initial_mass(nclasses) ); bergs%initial_mass(:)=initial_mass(:)
@@ -1430,19 +1534,19 @@ subroutine update_halo_icebergs(bergs)
     call delete_all_bergs_in_list(bergs,grdj,grdi)
   enddo ; enddo
 
-  if (bergs%mts) then
-    !remove conglomerate bergs outside halo
-    do grdj = grd%jsc,grd%jec ;    do grdi = grd%isc,grd%iec
-      this=>bergs%list(grdi,grdj)%first
-      do while (associated(this))
-        kick_the_bucket=>this
-        this=>this%next
-        if (kick_the_bucket%halo_berg .ne. 0) then
-          call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
-        end if
-      enddo
-    enddo;enddo
-  endif
+  ! if (bergs%mts) then
+  !   !remove conglomerate bergs outside halo
+  !   do grdj = grd%jsc,grd%jec ;    do grdi = grd%isc,grd%iec
+  !     this=>bergs%list(grdi,grdj)%first
+  !     do while (associated(this))
+  !       kick_the_bucket=>this
+  !       this=>this%next
+  !       if (kick_the_bucket%halo_berg .ne. 0) then
+  !         call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
+  !       end if
+  !     enddo
+  !   enddo;enddo
+  ! endif
 
   call mpp_sync_self()
 
@@ -1457,7 +1561,7 @@ subroutine update_halo_icebergs(bergs)
     enddo; enddo
   endif
   if (debug) then
-    nbergs_start=count_bergs(bergs)
+    nbergs_start=count_bergs(bergs, with_halos=.true.)
   endif
 
   call mpp_sync_self()
@@ -1663,7 +1767,7 @@ subroutine update_halo_icebergs(bergs)
 
   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!Debugging!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
   if (debug) then
-    nbergs_end=count_bergs(bergs)
+    nbergs_end=count_bergs(bergs, with_halos=.true.)
     i=nbergs_rcvd_from_n+nbergs_rcvd_from_s+nbergs_rcvd_from_e+nbergs_rcvd_from_w &
      -nbergs_to_send_n-nbergs_to_send_s-nbergs_to_send_e-nbergs_to_send_w
     if (nbergs_end-(nbergs_start+i).ne.0) then
@@ -1774,7 +1878,7 @@ Subroutine transfer_mts_bergs(bergs)
   endif
 
   call set_conglom_ids(bergs)
-  call mts_remove_unused_bergs(bergs)
+  if (bergs%remove_unused_bergs) call mts_remove_unused_bergs(bergs)
 
   ! For debugging
   if (bergs%halo_debugging) then
@@ -1806,7 +1910,7 @@ subroutine mts_pack_in_dir(bergs,nbergs_to_send,dir)
   integer :: ics,ice,jcs,jce
   integer :: inhs,inhe,jnhs,jnhe
   real :: pfix !<used to adjust for periodicity
-  real :: hexdenom,rhc(4)
+  real :: rhc(4)
   real :: clat,clon,dlat,dlon,r_dist
   integer :: current_conglom_id
   real :: current_halo_id
@@ -1818,7 +1922,6 @@ subroutine mts_pack_in_dir(bergs,nbergs_to_send,dir)
   cds=bergs%contact_distance**2
   edgecontact=.false.
   pfix=0.0
-  hexdenom=2.*sqrt(3.)
 
   select case (dir)
   case ("e")
@@ -1942,12 +2045,16 @@ subroutine mts_pack_in_dir(bergs,nbergs_to_send,dir)
               berg%conglom_id=current_conglom_id+2
             case ("w")
               berg%lon=berg%lon-pfix; berg%conglom_id=4
+              berg%lon_prev=berg%lon_prev-pfix
               call pack_berg_into_buffer2(berg, bergs%obuffer_w, nbergs_to_send, bergs%max_bonds)
               berg%lon=berg%lon+pfix; berg%conglom_id=current_conglom_id+8
+              berg%lon_prev=berg%lon_prev+pfix
             case ("e")
               berg%lon=berg%lon-pfix; berg%conglom_id=8
+              berg%lon_prev=berg%lon_prev-pfix
               call pack_berg_into_buffer2(berg, bergs%obuffer_e, nbergs_to_send, bergs%max_bonds)
               berg%lon=berg%lon+pfix; berg%conglom_id=current_conglom_id+4
+              berg%lon_prev=berg%lon_prev+pfix
             end select
             berg%halo_berg=current_halo_id
           endif
@@ -1987,13 +2094,13 @@ recursive subroutine mts_mark_and_pack_halo_and_congloms(bergs,berg,dir,nbergs_t
 
     select case (dir)
     case ("e")
-      berg%conglom_id=8;                    berg%lon=berg%lon-pfix
+      berg%conglom_id=8;                    berg%lon=berg%lon-pfix; berg%lon_prev=berg%lon_prev-pfix
       call pack_berg_into_buffer2(berg,bergs%obuffer_e, nbergs_to_send, bergs%max_bonds)
-      berg%conglom_id=current_conglom_id+4; berg%lon=berg%lon+pfix
+      berg%conglom_id=current_conglom_id+4; berg%lon=berg%lon+pfix; berg%lon_prev=berg%lon_prev+pfix
     case ("w")
-      berg%conglom_id=4;                    berg%lon=berg%lon-pfix
+      berg%conglom_id=4;                    berg%lon=berg%lon-pfix; berg%lon_prev=berg%lon_prev-pfix
       call pack_berg_into_buffer2(berg,bergs%obuffer_w, nbergs_to_send, bergs%max_bonds)
-      berg%conglom_id=current_conglom_id+8; berg%lon=berg%lon+pfix
+      berg%conglom_id=current_conglom_id+8; berg%lon=berg%lon+pfix; berg%lon_prev=berg%lon_prev+pfix
     case ("n")
       berg%conglom_id=1
       call pack_berg_into_buffer2(berg,bergs%obuffer_n, nbergs_to_send, bergs%max_bonds)
@@ -2045,7 +2152,7 @@ recursive subroutine mts_pack_contact_bergs(bergs,berg,dir,pfix,nbergs_to_send,i
   integer :: nc_x,nc_y,grdj,grdi,js,je,is,ie
   integer :: current_conglom_id,radial_contact
   real :: R1,R2,dlon,dlat,lat_ref,dx_dlon,dy_dlat,r_dist,crit_dist,current_halo_id
-  real :: hexdenom
+  real :: rdenom
   logical :: pack_contacts
 
   pack_contacts=.false.
@@ -2064,15 +2171,14 @@ recursive subroutine mts_pack_contact_bergs(bergs,berg,dir,pfix,nbergs_to_send,i
   endif
 
   if (pack_contacts) then
+    if (bergs%hexagonal_icebergs) then
+      rdenom=1./(2.*sqrt(3.))
+    else
+      rdenom=1./pi
+    endif
     if (nc_x.eq.1 .and. nc_y.eq.1) then
       radial_contact=.true. !contact based on berg radii can occur
-      !radius of current berg:
-      if (bergs%hexagonal_icebergs) then
-        hexdenom=2.*sqrt(3.)
-        R1=sqrt(berg%length*berg%width/hexdenom)
-      else !square packing
-        R1=sqrt(berg%length*berg%width/pi)
-      endif
+      R1=sqrt(berg%length*berg%width*rdenom) !radius of current berg
     else
       crit_dist=bergs%contact_distance**2
     endif
@@ -2084,11 +2190,7 @@ recursive subroutine mts_pack_contact_bergs(bergs,berg,dir,pfix,nbergs_to_send,i
           !has the berg already been sent/packed in this dir?
           if (.not. mts_berg_sent(other_berg%conglom_id,dir)) then
             if (radial_contact) then
-              if (bergs%hexagonal_icebergs) then
-                R2=sqrt(other_berg%length*other_berg%width/hexdenom)
-              else
-                R2=sqrt(other_berg%length*other_berg%width/pi)
-              endif
+              R2=sqrt(other_berg%length*other_berg%width*rdenom)
               crit_dist=max(R1+R2,bergs%contact_distance)**2
             endif
 
@@ -2116,12 +2218,16 @@ recursive subroutine mts_pack_contact_bergs(bergs,berg,dir,pfix,nbergs_to_send,i
                 other_berg%conglom_id=current_conglom_id+2
               case ("w")
                 other_berg%lon=other_berg%lon-pfix; other_berg%conglom_id=4
+                other_berg%lon_prev=other_berg%lon_prev-pfix
                 call pack_berg_into_buffer2(other_berg,bergs%obuffer_w, nbergs_to_send, bergs%max_bonds)
                 other_berg%lon=other_berg%lon+pfix; other_berg%conglom_id=current_conglom_id+8
+                other_berg%lon_prev=other_berg%lon_prev+pfix
               case ("e")
                 other_berg%lon=other_berg%lon-pfix; other_berg%conglom_id=8
+                other_berg%lon_prev=other_berg%lon_prev-pfix
                 call pack_berg_into_buffer2(other_berg,bergs%obuffer_e, nbergs_to_send, bergs%max_bonds)
                 other_berg%lon=other_berg%lon+pfix; other_berg%conglom_id=current_conglom_id+4
+                other_berg%lon_prev=other_berg%lon_prev+pfix
               end select
               other_berg%halo_berg=current_halo_id
             endif
@@ -2155,8 +2261,14 @@ logical function mts_berg_sent(conglom_id,dir)
   select case (dir)
   case ("e")
     if (mod(conglom_id,8)>3) mts_berg_sent=.true.
+    if (ewsame) then
+      if (conglom_id>7) mts_berg_sent=.true.
+    endif
   case ("w")
     if (conglom_id>7) mts_berg_sent=.true.
+    if (ewsame) then
+      if (mod(conglom_id,8)>3) mts_berg_sent=.true.
+    endif
   case ("n")
     if (mod(conglom_id,4)>1) mts_berg_sent=.true.
   case ("s")
@@ -2197,8 +2309,54 @@ subroutine set_conglom_ids(bergs)
       this=>this%next
     enddo
   enddo;enddo
+
 end subroutine set_conglom_ids
 
+
+!>Assign initial velocities and energies for energy tracking tests
+subroutine energy_tests_init(bergs)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  ! Local variables
+  type(icebergs_gridded), pointer :: grd
+  type(iceberg), pointer :: this
+  integer :: grdi,grdj
+  real :: vol
+  type(bond), pointer :: current_bond
+
+  grd=>bergs%grd
+
+  !Reset all conglom ids to zero
+  do grdj = grd%jsd,grd%jed; do grdi = grd%isd,grd%ied
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this))
+
+      !test changing the radius
+      ! Vol=this%length*this%width*this%thickness
+      ! this%length=this%length*0.9
+      ! this%width=this%width*0.9
+      ! this%mass=(this%length*this%width*this%thickness/Vol)*this%mass
+
+
+      this%uvel_old=this%uvel; this%uvel_prev=this%uvel
+      this%vvel_old=this%vvel; this%vvel_prev=this%vvel
+
+      this%Ee=0.0; this%Ed=0.0; this%Eext=0.0; this%Ee_contact=0.0; this%Ed_contact=0.0; this%Efrac=0.0
+      this%Ee_temp=0.0; this%Ed_temp=0.0; this%Eext_temp=0.0; this%Ee_contact_temp=0.0; this%Ed_contact_temp=0.0
+
+      current_bond=>this%first_bond
+      do while (associated(current_bond)) ! loop over all bonds
+        current_bond%Ee=0.0; current_bond%Ed=0.0
+        current_bond%axn_fast=0.0; current_bond%ayn_fast=0.0
+        current_bond%bxn_fast=0.0; current_bond%byn_fast=0.0
+        current_bond=>current_bond%next_bond
+      enddo
+
+      this=>this%next
+    enddo
+  enddo;enddo
+end subroutine energy_tests_init
+
 !>Identify all bergs in the same conglomerate as the given berg, and assign them the given conglom_id
 recursive subroutine label_conglomerates(berg,new_conglom_id)
   type(iceberg), pointer :: berg,other_berg
@@ -2231,13 +2389,17 @@ subroutine mts_remove_unused_bergs(bergs)
   integer :: grdi, grdj, grdi2, grdj2
   logical :: contact,radial_contact
   real :: lat1,lat2,lon1,lon2,dlon,dlat,dx_dlon,dy_dlat,lat_ref
-  real :: r_dist,crit_dist,R1,R2,hexdenom
+  real :: r_dist,crit_dist,R1,R2,rdenom
 
   grd=>bergs%grd
   nc_x=bergs%contact_cells_lon; nc_y=bergs%contact_cells_lat
   if (nc_x.eq.1 .and. nc_y.eq.1) then
     radial_contact=.true. !contact based on berg radii can occur
-    hexdenom=2.*sqrt(3.)
+    if (bergs%hexagonal_icebergs) then
+      rdenom=1./(2.*sqrt(3.))
+    else
+      rdenom=1./pi
+    endif
   else
     radial_contact=.false.
     crit_dist=bergs%contact_distance**2
@@ -2264,14 +2426,7 @@ subroutine mts_remove_unused_bergs(bergs)
         else !if not a halo/conglom berg, then test if w/in contact dist to a conglom/halo berg
           contact=.false.
           lat1=this%lat; lon1=this%lon
-          if (radial_contact) then
-            !radius of current berg
-            if (bergs%hexagonal_icebergs) then
-              R1=sqrt(this%length*this%width/hexdenom)
-            else !square packing
-              R1=sqrt(this%length*this%width/pi)
-            endif
-          endif
+          if (radial_contact) R1=sqrt(this%length*this%width*rdenom) !radius of current berg
           do grdj2=max(grdj-nc_y,grd%jsd+1),min(grdj+nc_y,grd%jed)
             do grdi2=max(grdi-nc_x,grd%isd+1),min(grdi+nc_x,grd%ied)
               other_berg=>bergs%list(grdi2,grdj2)%first
@@ -2280,11 +2435,7 @@ subroutine mts_remove_unused_bergs(bergs)
                   lat2=other_berg%lat; lon2=other_berg%lon
                   dlon=lon2-lon1; dlat=lat2-lat1
                   if (radial_contact) then
-                    if (bergs%hexagonal_icebergs) then
-                      R2=sqrt(other_berg%length*other_berg%width/hexdenom)
-                    else
-                      R2=sqrt(other_berg%length*other_berg%width/pi)
-                    endif
+                    R2=sqrt(other_berg%length*other_berg%width*rdenom)
                     crit_dist=max(R1+R2,bergs%contact_distance)**2
                   endif
                   if (bergs%grd%grid_is_latlon) then
@@ -2754,8 +2905,12 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
   counter = 0
   call push_buffer_value(buff%data(:,n), counter, berg%lon)
   call push_buffer_value(buff%data(:,n), counter, berg%lat)
+  call push_buffer_value(buff%data(:,n), counter, berg%lon_prev)
+  call push_buffer_value(buff%data(:,n), counter, berg%lat_prev)
   call push_buffer_value(buff%data(:,n), counter, berg%uvel)
   call push_buffer_value(buff%data(:,n), counter, berg%vvel)
+  call push_buffer_value(buff%data(:,n), counter, berg%uvel_prev)
+  call push_buffer_value(buff%data(:,n), counter, berg%vvel_prev)
   call push_buffer_value(buff%data(:,n), counter, berg%xi)
   call push_buffer_value(buff%data(:,n), counter, berg%yj)
   call push_buffer_value(buff%data(:,n), counter, berg%start_lon)
@@ -2781,11 +2936,13 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
   call split_id(berg%id, id_cnt, id_ij)
   call push_buffer_value(buff%data(:,n), counter, id_cnt)
   call push_buffer_value(buff%data(:,n), counter, id_ij)
+  call push_buffer_value(buff%data(:,n), counter, berg%od)
+  call push_buffer_value(buff%data(:,n), counter, berg%n_bonds)
+  call push_buffer_value(buff%data(:,n), counter, berg%accum_bond_rotation)
+
 
   if (mts) then
     call push_buffer_value(buff%data(:,n), counter, berg%conglom_id)
-    call push_buffer_value(buff%data(:,n), counter, berg%uvel_prev)
-    call push_buffer_value(buff%data(:,n), counter, berg%vvel_prev)
     call push_buffer_value(buff%data(:,n), counter, berg%axn_fast)
     call push_buffer_value(buff%data(:,n), counter, berg%ayn_fast)
     call push_buffer_value(buff%data(:,n), counter, berg%bxn_fast)
@@ -2804,24 +2961,66 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
     call push_buffer_value(buff%data(:,n), counter, berg%hi)
   endif
 
+  if (monitor_energy) then
+    call push_buffer_value(buff%data(:,n), counter, berg%Ee)
+    call push_buffer_value(buff%data(:,n), counter, berg%Ed)
+    call push_buffer_value(buff%data(:,n), counter, berg%Eext)
+    call push_buffer_value(buff%data(:,n), counter, berg%Ee_contact)
+    call push_buffer_value(buff%data(:,n), counter, berg%Ed_contact)
+    call push_buffer_value(buff%data(:,n), counter, berg%Efrac)
+    call push_buffer_value(buff%data(:,n), counter, berg%Ee_contact_temp)
+    call push_buffer_value(buff%data(:,n), counter, berg%Ed_contact_temp)
+    call push_buffer_value(buff%data(:,n), counter, berg%Ee_temp)
+    call push_buffer_value(buff%data(:,n), counter, berg%Ed_temp)
+    call push_buffer_value(buff%data(:,n), counter, berg%Eext_temp)
+  endif
+
+
   if (max_bonds .gt. 0) then
     current_bond=>berg%first_bond
     do k = 1,max_bonds
       if (associated(current_bond)) then
-        if (current_bond%other_id==0) then
-          print *,'zero other id',berg%id,mpp_pe()
-        endif
         call split_id(current_bond%other_id, id_cnt, id_ij)
         call push_buffer_value(buff%data(:,n), counter, id_cnt)
         call push_buffer_value(buff%data(:,n), counter, id_ij)
         call push_buffer_value(buff%data(:,n), counter, current_bond%other_berg_ine)
         call push_buffer_value(buff%data(:,n), counter, current_bond%other_berg_jne)
+        call push_buffer_value(buff%data(:,n), counter, current_bond%length)
+        call push_buffer_value(buff%data(:,n), counter, current_bond%rotation)
+        call push_buffer_value(buff%data(:,n), counter, current_bond%rel_rotation)
+        call push_buffer_value(buff%data(:,n), counter, current_bond%n_strain)
+        call push_buffer_value(buff%data(:,n), counter, current_bond%n_strain_rate)
+
+        if (monitor_energy) then
+          call push_buffer_value(buff%data(:,n), counter, current_bond%Ee)
+          call push_buffer_value(buff%data(:,n), counter, current_bond%Ed)
+          call push_buffer_value(buff%data(:,n), counter, current_bond%axn_fast)
+          call push_buffer_value(buff%data(:,n), counter, current_bond%ayn_fast)
+          call push_buffer_value(buff%data(:,n), counter, current_bond%bxn_fast)
+          call push_buffer_value(buff%data(:,n), counter, current_bond%byn_fast)
+        endif
+
         current_bond=>current_bond%next_bond
       else
         call push_buffer_value(buff%data(:,n), counter, 0)
         call push_buffer_value(buff%data(:,n), counter, 0)
         call push_buffer_value(buff%data(:,n), counter, 0)
         call push_buffer_value(buff%data(:,n), counter, 0)
+        call push_buffer_value(buff%data(:,n), counter, 0)
+        call push_buffer_value(buff%data(:,n), counter, 0)
+        call push_buffer_value(buff%data(:,n), counter, 0)
+        call push_buffer_value(buff%data(:,n), counter, 0)
+        call push_buffer_value(buff%data(:,n), counter, 0)
+
+        if (monitor_energy) then
+          call push_buffer_value(buff%data(:,n), counter, 0)
+          call push_buffer_value(buff%data(:,n), counter, 0)
+          call push_buffer_value(buff%data(:,n), counter, 0)
+          call push_buffer_value(buff%data(:,n), counter, 0)
+          call push_buffer_value(buff%data(:,n), counter, 0)
+          call push_buffer_value(buff%data(:,n), counter, 0)
+        endif
+
       endif
     enddo
   endif
@@ -2931,12 +3130,14 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
 logical :: lres
 type(iceberg) :: localberg
 type(iceberg), pointer :: this,kick_the_bucket
+type(bond) , pointer :: current_bond
 integer :: other_berg_ine, other_berg_jne
 integer :: counter, k, max_bonds, id_cnt, id_ij
 integer(kind=8) :: id
 integer :: stderrunit
 logical :: force_app,duplicate
-real :: temp_lon,temp_lat
+real :: temp_lon,temp_lat,length
+real :: rotation,rel_rotation,n_strain,n_strain_rate
 
   ! Get the stderr unit number
   stderrunit = stderr()
@@ -2947,11 +3148,20 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
   force_app = .false.
   if(present(force_append)) force_app = force_append
 
+  if (monitor_energy) then
+    allocate(localberg%Ee,localberg%Ed,localberg%Eext,localberg%Ee_contact,localberg%Ed_contact,localberg%Efrac,&
+      localberg%Ee_temp,localberg%Ed_temp,localberg%Eext_temp,localberg%Ee_contact_temp,localberg%Ed_contact_temp)
+  endif
+
   counter = 0
   call pull_buffer_value(buff%data(:,n), counter, localberg%lon)
   call pull_buffer_value(buff%data(:,n), counter, localberg%lat)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%lon_prev)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%lat_prev)
   call pull_buffer_value(buff%data(:,n), counter, localberg%uvel)
   call pull_buffer_value(buff%data(:,n), counter, localberg%vvel)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%uvel_prev)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%vvel_prev)
   call pull_buffer_value(buff%data(:,n), counter, localberg%xi)
   call pull_buffer_value(buff%data(:,n), counter, localberg%yj)
   call pull_buffer_value(buff%data(:,n), counter, localberg%start_lon)
@@ -2977,11 +3187,12 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
   call pull_buffer_value(buff%data(:,n), counter, id_cnt)
   call pull_buffer_value(buff%data(:,n), counter, id_ij)
   localberg%id = id_from_2_ints(id_cnt, id_ij)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%od)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%n_bonds)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%accum_bond_rotation)
 
   if (bergs%mts) then
     call pull_buffer_value(buff%data(:,n), counter, localberg%conglom_id)
-    call pull_buffer_value(buff%data(:,n), counter, localberg%uvel_prev)
-    call pull_buffer_value(buff%data(:,n), counter, localberg%vvel_prev)
     call pull_buffer_value(buff%data(:,n), counter, localberg%axn_fast)
     call pull_buffer_value(buff%data(:,n), counter, localberg%ayn_fast)
     call pull_buffer_value(buff%data(:,n), counter, localberg%bxn_fast)
@@ -3000,6 +3211,20 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
     call pull_buffer_value(buff%data(:,n), counter, localberg%hi)
   endif
 
+  if (monitor_energy) then
+    call pull_buffer_value(buff%data(:,n), counter, localberg%Ee)
+    call pull_buffer_value(buff%data(:,n), counter, localberg%Ed)
+    call pull_buffer_value(buff%data(:,n), counter, localberg%Eext)
+    call pull_buffer_value(buff%data(:,n), counter, localberg%Ee_contact)
+    call pull_buffer_value(buff%data(:,n), counter, localberg%Ed_contact)
+    call pull_buffer_value(buff%data(:,n), counter, localberg%Efrac)
+    call pull_buffer_value(buff%data(:,n), counter, localberg%Ee_contact_temp)
+    call pull_buffer_value(buff%data(:,n), counter, localberg%Ed_contact_temp)
+    call pull_buffer_value(buff%data(:,n), counter, localberg%Ee_temp)
+    call pull_buffer_value(buff%data(:,n), counter, localberg%Ed_temp)
+    call pull_buffer_value(buff%data(:,n), counter, localberg%Eext_temp)
+  endif
+
   !These quantities no longer need to be passed between processors
   localberg%uvel_old=localberg%uvel
   localberg%vvel_old=localberg%vvel
@@ -3031,8 +3256,8 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
     else
       write(stderrunit,'("KID, unpack_berg_from_buffer pe=(",i3,a,2i4,a,2f8.2)')&
         & mpp_pe(),') Failed to find i,j=',localberg%ine,localberg%jne,&
-        ' for mts conglom berg lon,lat=',localberg%lon,localberg%lat
-      write(stderrunit,*) localberg%lon,localberg%lat
+        ' for mts conglom berg lon,lat=',temp_lon, temp_lat
+      write(stderrunit,*) temp_lon, temp_lat
       write(stderrunit,*) localberg%uvel,localberg%vvel
       write(stderrunit,*) localberg%axn,localberg%ayn !Alon
       write(stderrunit,*) localberg%bxn,localberg%byn !Alon
@@ -3110,8 +3335,29 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
       id = id_from_2_ints(id_cnt, id_ij)
       call pull_buffer_value(buff%data(:,n), counter, other_berg_ine)
       call pull_buffer_value(buff%data(:,n), counter, other_berg_jne)
+      call pull_buffer_value(buff%data(:,n), counter, length)
+      call pull_buffer_value(buff%data(:,n), counter, rotation)
+      call pull_buffer_value(buff%data(:,n), counter, rel_rotation)
+      call pull_buffer_value(buff%data(:,n), counter, n_strain)
+      call pull_buffer_value(buff%data(:,n), counter, n_strain_rate)
+
       if (id_ij > 0) then
         call form_a_bond(this, id, other_berg_ine, other_berg_jne)
+        current_bond=>this%first_bond
+        current_bond%length=length
+        current_bond%rotation=rotation
+        current_bond%rel_rotation=rel_rotation
+        current_bond%n_strain=n_strain
+        current_bond%n_strain_rate=n_strain_rate
+
+        if (monitor_energy) then
+          call pull_buffer_value(buff%data(:,n), counter, current_bond%Ee)
+          call pull_buffer_value(buff%data(:,n), counter, current_bond%Ed)
+          call pull_buffer_value(buff%data(:,n), counter, current_bond%axn_fast)
+          call pull_buffer_value(buff%data(:,n), counter, current_bond%ayn_fast)
+          call pull_buffer_value(buff%data(:,n), counter, current_bond%bxn_fast)
+          call pull_buffer_value(buff%data(:,n), counter, current_bond%byn_fast)
+        endif
       endif
     enddo
   endif
@@ -3186,6 +3432,8 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj)
   if (.not. save_short_traj) then
     call push_buffer_value(buff%data(:,n),counter,traj%uvel)
     call push_buffer_value(buff%data(:,n),counter,traj%vvel)
+    call push_buffer_value(buff%data(:,n),counter,traj%uvel_prev)
+    call push_buffer_value(buff%data(:,n),counter,traj%vvel_prev)
     call push_buffer_value(buff%data(:,n),counter,traj%mass)
     call push_buffer_value(buff%data(:,n),counter,traj%mass_of_bits)
     call push_buffer_value(buff%data(:,n),counter,traj%heat_density)
@@ -3210,12 +3458,26 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj)
     call push_buffer_value(buff%data(:,n),counter,traj%byn)
     call push_buffer_value(buff%data(:,n),counter,traj%halo_berg)
     call push_buffer_value(buff%data(:,n),counter,traj%static_berg)
+    call push_buffer_value(buff%data(:,n),counter,traj%od)
+    call push_buffer_value(buff%data(:,n),counter,traj%n_bonds)
+    call push_buffer_value(buff%data(:,n),counter,traj%accum_bond_rotation)
 
     if (mts) then
-      call push_buffer_value(buff%data(:,n),counter,traj%conglom_id)
-      call push_buffer_value(buff%data(:,n),counter,traj%uvel_prev)
-      call push_buffer_value(buff%data(:,n),counter,traj%vvel_prev)
+      call push_buffer_value(buff%data(:,n),counter,traj%axn_fast)
+      call push_buffer_value(buff%data(:,n),counter,traj%ayn_fast)
+      call push_buffer_value(buff%data(:,n),counter,traj%bxn_fast)
+      call push_buffer_value(buff%data(:,n),counter,traj%byn_fast)
     endif
+
+    if (monitor_energy) then
+      call push_buffer_value(buff%data(:,n), counter, traj%Ee)
+      call push_buffer_value(buff%data(:,n), counter, traj%Ed)
+      call push_buffer_value(buff%data(:,n), counter, traj%Eext)
+      call push_buffer_value(buff%data(:,n), counter, traj%Ee_contact)
+      call push_buffer_value(buff%data(:,n), counter, traj%Ed_contact)
+      call push_buffer_value(buff%data(:,n), counter, traj%Efrac)
+    endif
+
   endif
 
 end subroutine pack_traj_into_buffer2
@@ -3232,6 +3494,10 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj)
   integer :: counter ! Position in stack
   integer :: cnt, ij
 
+  if (monitor_energy) then
+    allocate(traj%Ee,traj%Ed,traj%Eext,traj%Ee_contact,traj%Ed_contact,traj%Efrac)
+  endif
+
   counter = 0
   call pull_buffer_value(buff%data(:,n),counter,traj%lon)
   call pull_buffer_value(buff%data(:,n),counter,traj%lat)
@@ -3243,6 +3509,8 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj)
   if (.not. save_short_traj) then
     call pull_buffer_value(buff%data(:,n),counter,traj%uvel)
     call pull_buffer_value(buff%data(:,n),counter,traj%vvel)
+    call pull_buffer_value(buff%data(:,n),counter,traj%uvel_prev)
+    call pull_buffer_value(buff%data(:,n),counter,traj%vvel_prev)
     call pull_buffer_value(buff%data(:,n),counter,traj%mass)
     call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_bits)
     call pull_buffer_value(buff%data(:,n),counter,traj%heat_density)
@@ -3267,17 +3535,112 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj)
     call pull_buffer_value(buff%data(:,n),counter,traj%byn)
     call pull_buffer_value(buff%data(:,n),counter,traj%halo_berg)
     call pull_buffer_value(buff%data(:,n),counter,traj%static_berg)
+    call pull_buffer_value(buff%data(:,n),counter,traj%od)
+    call pull_buffer_value(buff%data(:,n),counter,traj%n_bonds)
+    call pull_buffer_value(buff%data(:,n),counter,traj%accum_bond_rotation)
 
     if (mts) then
-      call pull_buffer_value(buff%data(:,n),counter,traj%conglom_id)
-      call pull_buffer_value(buff%data(:,n),counter,traj%uvel_prev)
-      call pull_buffer_value(buff%data(:,n),counter,traj%vvel_prev)
+      call pull_buffer_value(buff%data(:,n),counter,traj%axn_fast)
+      call pull_buffer_value(buff%data(:,n),counter,traj%ayn_fast)
+      call pull_buffer_value(buff%data(:,n),counter,traj%bxn_fast)
+      call pull_buffer_value(buff%data(:,n),counter,traj%byn_fast)
+    endif
+
+    if (monitor_energy) then
+      call pull_buffer_value(buff%data(:,n), counter, traj%Ee)
+      call pull_buffer_value(buff%data(:,n), counter, traj%Ed)
+      call pull_buffer_value(buff%data(:,n), counter, traj%Eext)
+      call pull_buffer_value(buff%data(:,n), counter, traj%Ee_contact)
+      call pull_buffer_value(buff%data(:,n), counter, traj%Ed_contact)
+      call pull_buffer_value(buff%data(:,n), counter, traj%Efrac)
     endif
   endif
   call append_posn(first, traj)
 
 end subroutine unpack_traj_from_buffer2
 
+!> Packs a trajectory entry into a buffer
+subroutine pack_bond_traj_into_buffer2(bond_traj, buff, n)
+  ! Arguments
+  type(bond_xyt), pointer :: bond_traj !< Trajectory entry to pack
+  type(buffer), pointer :: buff !< Buffer to pack entry into
+  integer, intent(in) :: n !< Position in buffer to place entry
+  ! Local variables
+  integer :: counter ! Position in stack
+  integer :: cnt1, ij1, cnt2, ij2
+
+  if (.not.associated(buff)) call increase_ibuffer(buff,n,buffer_width_bond_traj)
+  if (n>buff%size) call increase_ibuffer(buff,n,buffer_width_bond_traj)
+
+  counter = 0
+  call push_buffer_value(buff%data(:,n),counter,bond_traj%lon)
+  call push_buffer_value(buff%data(:,n),counter,bond_traj%lat)
+  call push_buffer_value(buff%data(:,n),counter,bond_traj%year)
+  call push_buffer_value(buff%data(:,n),counter,bond_traj%day)
+  call push_buffer_value(buff%data(:,n),counter,bond_traj%length)
+  call push_buffer_value(buff%data(:,n),counter,bond_traj%n1)
+  call push_buffer_value(buff%data(:,n),counter,bond_traj%n2)
+  call push_buffer_value(buff%data(:,n),counter,bond_traj%rotation)
+  call push_buffer_value(buff%data(:,n),counter,bond_traj%rel_rotation)
+  call push_buffer_value(buff%data(:,n),counter,bond_traj%n_strain)
+  call push_buffer_value(buff%data(:,n),counter,bond_traj%n_strain_rate)
+
+  call split_id(bond_traj%id1, cnt1, ij1)
+  call push_buffer_value(buff%data(:,n),counter,cnt1)
+  call push_buffer_value(buff%data(:,n),counter,ij1)
+  call split_id(bond_traj%id2, cnt2, ij2)
+  call push_buffer_value(buff%data(:,n),counter,cnt2)
+  call push_buffer_value(buff%data(:,n),counter,ij2)
+
+  if (monitor_energy) then
+    call push_buffer_value(buff%data(:,n),counter,bond_traj%Ee)
+    call push_buffer_value(buff%data(:,n),counter,bond_traj%Ed)
+  endif
+
+end subroutine pack_bond_traj_into_buffer2
+
+!> Unpacks a trajectory entry from a buffer
+subroutine unpack_bond_traj_from_buffer2(first, buff, n)
+  ! Arguments
+  type(bond_xyt), pointer :: first !< Bond trajectory list
+  type(buffer), pointer :: buff !< Buffer from which to unpack
+  integer, intent(in) :: n !< Position in buffer to unpack
+  ! Local variables
+  type(bond_xyt) :: bond_traj
+  integer :: counter ! Position in stack
+  integer :: cnt1, ij1, cnt2, ij2
+
+if (monitor_energy) allocate(bond_traj%Ee,bond_traj%Ed)
+
+  counter = 0
+  call pull_buffer_value(buff%data(:,n),counter,bond_traj%lon)
+  call pull_buffer_value(buff%data(:,n),counter,bond_traj%lat)
+  call pull_buffer_value(buff%data(:,n),counter,bond_traj%year)
+  call pull_buffer_value(buff%data(:,n),counter,bond_traj%day)
+  call pull_buffer_value(buff%data(:,n),counter,bond_traj%length)
+  call pull_buffer_value(buff%data(:,n),counter,bond_traj%n1)
+  call pull_buffer_value(buff%data(:,n),counter,bond_traj%n2)
+  call pull_buffer_value(buff%data(:,n),counter,bond_traj%rotation)
+  call pull_buffer_value(buff%data(:,n),counter,bond_traj%rel_rotation)
+  call pull_buffer_value(buff%data(:,n),counter,bond_traj%n_strain)
+  call pull_buffer_value(buff%data(:,n),counter,bond_traj%n_strain_rate)
+
+  call pull_buffer_value(buff%data(:,n),counter,cnt1)
+  call pull_buffer_value(buff%data(:,n),counter,ij1)
+  bond_traj%id1 = id_from_2_ints(cnt1, ij1)
+  call pull_buffer_value(buff%data(:,n),counter,cnt2)
+  call pull_buffer_value(buff%data(:,n),counter,ij2)
+  bond_traj%id2 = id_from_2_ints(cnt2, ij2)
+
+  if (monitor_energy) then
+    call pull_buffer_value(buff%data(:,n),counter,bond_traj%Ee)
+    call pull_buffer_value(buff%data(:,n),counter,bond_traj%Ed)
+  endif
+
+  call append_bond_posn(first, bond_traj)
+
+end subroutine unpack_bond_traj_from_buffer2
+
 !> Add a new berg to a list by copying values
 !!
 !! The input berg are a berg with set values whose memory is assumed to be
@@ -3729,6 +4092,10 @@ subroutine create_iceberg(berg, bergvals)
     call error_mesg('KID, create_iceberg', 'berg already associated. This should not happen!', FATAL)
   endif
   allocate(berg)
+  if (monitor_energy) then
+    allocate(berg%Ee,berg%Ed,berg%Eext,berg%Ee_contact,berg%Ed_contact,berg%Efrac,&
+      berg%Ee_temp,berg%Ed_temp,berg%Eext_temp,berg%Ee_contact_temp,berg%Ed_contact_temp)
+  endif
   berg=bergvals
   berg%prev=>null()
   berg%next=>null()
@@ -3846,6 +4213,331 @@ subroutine print_bergs(iochan, bergs, label)
 
 end subroutine print_bergs
 
+
+subroutine orig_bond_length(bergs)
+type(icebergs), pointer :: bergs !< Container for all types and memory
+type(iceberg), pointer :: other_berg, berg
+type(icebergs_gridded), pointer :: grd
+integer :: grdi, grdj
+type(bond) , pointer :: current_bond,prev,next
+real :: dist
+
+  grd=>bergs%grd
+
+  do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+    berg=>bergs%list(grdi,grdj)%first
+    do while (associated(berg)) ! loop over all bergs
+      current_bond=>berg%first_bond
+      do while (associated(current_bond)) ! loop over all bonds
+        other_berg=>current_bond%other_berg
+        if (associated(current_bond%other_berg)) then
+          dist=(berg%lon-other_berg%lon)**2+(berg%lat-other_berg%lat)**2
+          current_bond%length=sqrt(dist)
+        endif
+        current_bond=>current_bond%next_bond
+      enddo
+      berg=>berg%next
+    enddo
+  enddo; enddo
+end subroutine orig_bond_length
+
+subroutine assign_n_bonds(bergs)
+type(icebergs), pointer :: bergs !< Container for all types and memory
+type(iceberg), pointer :: this, other_berg
+type(bond) , pointer :: current_bond
+type(icebergs_gridded), pointer :: grd
+integer :: grdi, grdj
+
+  grd=>bergs%grd
+  do grdj=grd%jsd,grd%jed ; do grdi=grd%isd,grd%ied !loop over all cells
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this)) ! loop over all bergs in cell
+      this%accum_bond_rotation=0.0
+      current_bond=>this%first_bond
+      do while (associated(current_bond)) ! loop over all bonds
+        current_bond%rotation=0.0
+        current_bond%rel_rotation=0.0
+        current_bond%n_strain=0.0
+        current_bond%n_strain_rate=0.0
+        current_bond=>current_bond%next_bond
+      enddo
+      this=>this%next
+    enddo
+  enddo;enddo
+end subroutine assign_n_bonds
+
+subroutine fracture_testing_initialization(bergs)
+type(icebergs), pointer :: bergs !< Container for all types and memory
+type(iceberg), pointer :: this, other_berg
+type(bond) , pointer :: current_bond
+type(icebergs_gridded), pointer :: grd
+integer :: grdi, grdj
+
+  grd=>bergs%grd
+  do grdj=grd%jsd,grd%jed ; do grdi=grd%isd,grd%ied !loop over all cells
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this)) ! loop over all bergs in cell
+      this%n_bonds=0
+      current_bond=>this%first_bond
+      do while (associated(current_bond)) ! loop over all bonds
+        this%n_bonds=this%n_bonds+1
+        current_bond=>current_bond%next_bond
+      enddo
+      this=>this%next
+    enddo
+  enddo;enddo
+end subroutine fracture_testing_initialization
+
+subroutine reset_bond_rotation(bergs)
+type(icebergs), pointer :: bergs !< Container for all types and memory
+type(iceberg), pointer :: this, other_berg
+type(bond) , pointer :: current_bond
+type(icebergs_gridded), pointer :: grd
+integer :: grdi, grdj
+
+if (.not. bergs%fracture_criterion=='strain_rate') return
+
+  grd=>bergs%grd
+  do grdj=grd%jsd,grd%jed ; do grdi=grd%isd,grd%ied !loop over all cells
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this)) ! loop over all bergs in cell
+      this%accum_bond_rotation=0.0
+      current_bond=>this%first_bond
+      do while (associated(current_bond)) ! loop over all bonds
+        current_bond%rotation=0.0
+        current_bond=>current_bond%next_bond
+      enddo
+      this=>this%next
+    enddo
+  enddo;enddo
+end subroutine reset_bond_rotation
+
+!>Saves rotation of bond on each bond, and accumulates the rotation of all bonds connected to a particle
+!!onto the particle.
+subroutine update_bond_angles(bergs)
+type(icebergs), pointer :: bergs !< Container for all types and memory
+type(iceberg), pointer :: this, other_berg
+type(icebergs_gridded), pointer :: grd
+integer :: grdi, grdj
+type(bond) , pointer :: current_bond
+real :: dx_dlon1,dx_dlon2,dx_dlon,dy_dlat,lat_ref,b1_u,b1_v,b2_u,b2_v
+real :: dxa,dya,dxb,dyb,vr1,vr2
+real :: angular_momentum,moment_of_inertia,tangent_velocity
+real :: cross_b1b2,dot_b1b2,angle
+
+  if (bergs%fracture_criterion=='none') return
+
+  grd=>bergs%grd
+
+  if (.not. bergs%grd%grid_is_latlon) then
+    dx_dlon=1.0; dy_dlat=1.0; !dx_dlon1=1.0; dx_dlon2=1.0;
+  else
+    dy_dlat=pi_180*Rearth
+  endif
+
+  do grdj=grd%jsd,grd%jed ; do grdi=grd%isd,grd%ied !loop over all cells
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this)) ! loop over all bergs in cell
+      if (this%conglom_id>0) then
+        current_bond=>this%first_bond
+        if (associated(current_bond)) then
+
+          do while (associated(current_bond)) ! loop over all bonds
+            other_berg=>current_bond%other_berg
+            if (associated(other_berg)) then
+
+              !relative coords from previous cycle
+              if (bergs%grd%grid_is_latlon) then
+                lat_ref=0.5*(this%lat_prev+other_berg%lat_prev); dx_dlon=pi_180*Rearth*cos(lat_ref*pi_180)
+              endif
+              dxa=(other_berg%lon_prev-this%lon_prev)*dx_dlon;   dya=(other_berg%lat_prev-this%lat_prev)*dy_dlat
+
+              !relative coords from current cycle
+              if (bergs%grd%grid_is_latlon) then
+                lat_ref=0.5*(this%lat+other_berg%lat);         dx_dlon=pi_180*Rearth*cos(lat_ref*pi_180)
+              endif
+              dxb=(other_berg%lon-this%lon)*dx_dlon;           dyb=(other_berg%lat-this%lat)*dy_dlat
+
+              current_bond%length=sqrt(dxb*dxb+dyb*dyb) !update bond length
+
+              !The angle of rotation over the previous cycle (may need to be corrected by +/- 2*pi, see below)
+              cross_b1b2=dxa*dyb-dya*dxb !([dxa dya 0] x [dxb dyb 0]) . [0 0 1]
+              dot_b1b2 = dxa*dxb+dya*dyb ![dxa dya] . [dxa dxb]
+              angle = atan2(cross_b1b2,dot_b1b2)
+
+              current_bond%rotation=current_bond%rotation+angle
+            endif
+            current_bond=>current_bond%next_bond
+          enddo !loop over all bonds
+        endif
+      endif
+      this=>this%next
+    enddo ! loop over all bergs in cell
+  enddo; enddo !loop over all cells
+end subroutine update_bond_angles
+
+
+!> For each berg element, calculates the average rotation rate of all bonds connected to a particle. Bonds are
+!! then broken based on their individual rotation rate compared to the average rotation rates accumulated on
+!! the berg elements that the bonds connect, and based on the rate of bond stretching (normal strain-rate).
+!! Alternatively, bonds can be broken based on the total accumulated relative rotation and normal strain (not rates).
+subroutine update_and_break_bonds(bergs)
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  type(iceberg), pointer :: other_berg, this
+  type(icebergs_gridded), pointer :: grd
+  integer :: grdi, grdj
+  type(bond) , pointer :: current_bond,other_bond,kick_the_bucket
+  real :: frac_thres_n,frac_thres_t
+  real :: inv_dt, rdenom, mean_denom, R1, R2, n_strain
+
+  frac_thres_n=bergs%frac_thres_n; frac_thres_t=bergs%frac_thres_t
+  if (frac_thres_n<=0.0 .and. frac_thres_t<=0.0) return !all fracture ignored
+  if (frac_thres_n<=0.0) frac_thres_n=huge(1.0) !no fracture from normal strain
+  if (frac_thres_t<=0.0) frac_thres_t=huge(1.0) !no fracture from bond rotation
+
+  if (bergs%fracture_criterion=='strain_rate') then
+    inv_dt=1.0/bergs%dt
+  elseif (bergs%fracture_criterion=='strain') then
+    inv_dt=1.0
+  else
+    return
+  endif
+
+  if (bergs%hexagonal_icebergs) then
+    rdenom=1./(2.*sqrt(3.))
+  else
+    rdenom=1./pi
+  endif
+
+  grd=>bergs%grd
+
+  !1. accumulate bond rotation/rotation-rate to the berg element
+  do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this)) ! loop over all bergs
+      this%accum_bond_rotation=0.0
+      current_bond=>this%first_bond
+      do while (associated(current_bond)) ! loop over all bonds
+        current_bond%rotation=current_bond%rotation*inv_dt
+        this%accum_bond_rotation=this%accum_bond_rotation+current_bond%rotation
+        current_bond=>current_bond%next_bond
+      enddo
+      this=>this%next
+    enddo
+  enddo;enddo
+
+  !2. Compare rotation/rotation-rate of each bond to the berg-based mean w/o the bond it in
+  do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied !loop over cells
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this)) ! loop over all bergs
+      if (this%conglom_id>0 .and. this%n_bonds>1) then
+        R1=sqrt(this%length*this%width*rdenom)
+        mean_denom=1.0/(this%n_bonds-1)
+
+        !2. Bond updates: normal strain/strain-rate, and relative rotation/rotation-rate
+        current_bond=>this%first_bond
+        do while (associated(current_bond)) ! loop over all bonds
+          other_berg=>current_bond%other_berg
+          if (.not. associated(other_berg)) &
+            call error_mesg('KID,update_and_break_bonds','other_berg not associated!' ,FATAL)
+          R2=sqrt(other_berg%length*other_berg%width*rdenom)
+
+          !normal strain or strain-rate: note original length is taken as the sum of the
+          !radii (calculated according to area) of the two bergs the bond connects.
+          n_strain=current_bond%length/(R1+R2) - 1.0
+          if (bergs%fracture_criterion=='strain_rate') then
+            current_bond%n_strain_rate=(n_strain-current_bond%n_strain)*inv_dt
+            current_bond%n_strain=n_strain
+            n_strain=current_bond%n_strain_rate
+          else
+            current_bond%n_strain=n_strain
+          endif
+
+          !the relative rotation (or rotation-rate) of the current bond relative to the mean
+          !rotation (or rotation-rate) of bonds on the parent berg, where the current bond is
+          !excluded from the mean.
+          current_bond%rel_rotation = current_bond%rotation-&
+            (this%accum_bond_rotation-current_bond%rotation)*mean_denom
+
+          !mark bond and matching bond on other_berg as fractured
+          if (abs(current_bond%rel_rotation)>frac_thres_t.or.n_strain>frac_thres_n) then
+            current_bond%other_id=-1
+
+            !mark matching bond on other_berg
+            other_bond=>other_berg%first_bond
+            do while (associated(other_bond)) ! loop over all bonds
+              if (other_bond%other_id.eq.this%id) other_bond%other_id=-1
+              other_bond=>other_bond%next_bond
+            enddo
+          endif
+          current_bond=>current_bond%next_bond
+        enddo
+      endif
+      this=>this%next
+    enddo
+  enddo; enddo
+
+  !4. final cleanup
+  do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this)) ! loop over all bergs
+      current_bond=>this%first_bond
+      do while (associated(current_bond)) ! loop over all bonds
+        if (current_bond%other_id==-1) then
+          if (grdj>=grd%jsc .and. grdj<=grd%jec .and. grdi>=grd%isc .and. grdi<=grd%iec) then
+            if (bergs%fracture_criterion=='strain_rate') then
+              n_strain=current_bond%n_strain_rate
+            else
+              n_strain=current_bond%n_strain
+            endif
+            if (abs(current_bond%rel_rotation)>frac_thres_t.and.n_strain>frac_thres_n) then
+              print *,'angle and n_strain break',current_bond%rel_rotation,n_strain,this%id
+            elseif (abs(current_bond%rel_rotation)>frac_thres_t) then
+              print *,'angle break',current_bond%rel_rotation,n_strain,this%id
+            elseif (n_strain>frac_thres_n) then
+              print *,'n_strain break',current_bond%rel_rotation,n_strain,this%id
+            else
+              print *,'break due to bond match',current_bond%rel_rotation,n_strain,this%id
+            endif
+          endif
+          this%accum_bond_rotation=this%accum_bond_rotation-current_bond%rotation
+          this%n_bonds=this%n_bonds-1
+          if (monitor_energy) then
+            !convert the elastic spring energy associated with the bond to dissipated energy
+            !on the parent element.
+            this%Ee=this%Ee-current_bond%Ee
+            this%Ee_temp=this%Ee_temp-current_bond%Ee
+            this%Efrac=this%Efrac+current_bond%Ee
+          endif
+          kick_the_bucket=>current_bond
+          current_bond=>current_bond%next_bond
+          call delete_bond_from_list(this,kick_the_bucket)
+        else
+          current_bond=>current_bond%next_bond
+        endif
+      enddo
+      this=>this%next
+    enddo
+  enddo;enddo
+
+end subroutine update_and_break_bonds
+
+!> Delete current_bond from the list of its parent berg
+subroutine delete_bond_from_list(berg,bond_to_delete)
+type(iceberg), intent(in), pointer :: berg !<parent berg to bond_to_delete
+type(bond), pointer :: bond_to_delete !<deleting this bond
+type(bond), pointer :: prev,next,current_bond
+  prev=>bond_to_delete%prev_bond
+  next=>bond_to_delete%next_bond
+  if (associated(prev)) then
+    prev%next_bond=>next
+  else
+    berg%first_bond=>next
+  endif
+  if (associated(next)) next%prev_bond=>prev
+  deallocate(bond_to_delete)
+end subroutine delete_bond_from_list
+
 subroutine form_a_bond(berg, other_id, other_berg_ine, other_berg_jne, other_berg)
 ! Arguments
 type(iceberg), pointer :: berg
@@ -3863,6 +4555,10 @@ subroutine form_a_bond(berg, other_id, other_berg_ine, other_berg_jne, other_ber
 
   ! Step 1: Create a new bond
   allocate(new_bond)
+  if (monitor_energy) then
+    allocate(new_bond%Ee,new_bond%Ed,new_bond%axn_fast,new_bond%ayn_fast,new_bond%bxn_fast,new_bond%byn_fast)
+    new_bond%Ee=0.; new_bond%Ed=0.; new_bond%axn_fast=0.; new_bond%ayn_fast=0.; new_bond%bxn_fast=0.; new_bond%byn_fast=0.
+  endif
   new_bond%other_id=other_id
   if(present(other_berg)) then
     new_bond%other_berg=>other_berg
@@ -4181,8 +4877,8 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
         ! ##### Beginning Quality Check on Bonds ######
         !      print *, 'Quality check', mpp_pe(), berg%id
         if (quality_check) then
-          num_unmatched_bonds=0
-          num_unassosiated_bond_pairs=0
+          !num_unmatched_bonds=0
+          !num_unassosiated_bond_pairs=0
           bond_is_good=.False.
           other_berg=>current_bond%other_berg
           if (associated(other_berg)) then
@@ -4207,8 +4903,9 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
               num_unmatched_bonds=num_unmatched_bonds+1
             endif
           else
-            if (debug) write(stderrunit,*) 'Opposite berg is not assosiated:', berg%id, current_bond%other_berg%id
-            num_unassosiated_bond_pairs=0
+            if (debug) write(stderrunit,*) 'Opposite berg is not assosiated:', berg%id, current_bond%other_id, mpp_pe()
+            !num_unassosiated_bond_pairs=0
+            num_unassosiated_bond_pairs=num_unassosiated_bond_pairs+1
           endif
         endif
         ! ##### Ending Quality Check on Bonds ######
@@ -4301,9 +4998,13 @@ subroutine record_posn(bergs)
 type(icebergs), pointer :: bergs !< Container for all types and memory
 ! Local variables
 type(xyt) :: posn
-type(iceberg), pointer :: this
+type(iceberg), pointer :: this, other_berg
 integer :: grdi, grdj
 integer :: js,je,is,ie
+type(bond) , pointer :: current_bond
+! Local bond variables
+type(bond_xyt) :: bond_posn
+real :: dx_dlon,dy_dlat,lat_ref,dx,dy,n1,n2,id1,id2
 
 if (bergs%debug_write) then
   js=bergs%grd%jsd+1; je=bergs%grd%jed; is=bergs%grd%isd+1; ie=bergs%grd%ied
@@ -4311,6 +5012,11 @@ subroutine record_posn(bergs)
   js=bergs%grd%jsc;   je=bergs%grd%jec; is=bergs%grd%isc;   ie=bergs%grd%iec
 endif
 
+if (monitor_energy) then
+  allocate(posn%Ee,posn%Ed,posn%Eext,posn%Ee_contact,posn%Ed_contact,posn%Efrac)
+  if (save_bond_traj) allocate(bond_posn%Ee,bond_posn%Ed)
+endif
+
   do grdj = js,je ; do grdi = is,ie
     this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
@@ -4322,6 +5028,8 @@ subroutine record_posn(bergs)
       if (.not. bergs%save_short_traj) then !Not totally sure that this is correct
         posn%uvel=this%uvel
         posn%vvel=this%vvel
+        posn%uvel_prev=this%uvel_prev
+        posn%vvel_prev=this%vvel_prev
         posn%mass=this%mass
         posn%mass_of_bits=this%mass_of_bits
         posn%heat_density=this%heat_density
@@ -4344,21 +5052,67 @@ subroutine record_posn(bergs)
         posn%ayn=this%ayn
         posn%bxn=this%bxn
         posn%byn=this%byn
-        ! posn%uvel_old=this%uvel_old
-        ! posn%vvel_old=this%vvel_old
-        ! posn%lon_old=this%lon_old
-        ! posn%lat_old=this%lat_old
         posn%halo_berg=this%halo_berg
         posn%static_berg=this%static_berg
+        posn%od=this%od
+        posn%n_bonds=this%n_bonds
+        posn%accum_bond_rotation=this%accum_bond_rotation
         if (bergs%mts) then
-          posn%conglom_id=this%conglom_id
-          posn%uvel_prev=this%uvel_prev
-          posn%vvel_prev=this%vvel_prev
+          posn%axn_fast=this%axn_fast
+          posn%ayn_fast=this%ayn_fast
+          posn%bxn_fast=this%bxn_fast
+          posn%byn_fast=this%byn_fast
+        endif
+
+        if (monitor_energy) then
+          posn%Ee=this%Ee
+          posn%Ed=this%Ed
+          posn%Eext=this%Eext
+          posn%Ee_contact=this%Ee_contact
+          posn%Ed_contact=this%Ed_contact
+          posn%Efrac=this%Efrac
         endif
       endif
 
       call push_posn(this%trajectory, posn)
 
+      if (save_bond_traj) then
+        current_bond=>this%first_bond
+        do while (associated(current_bond)) ! loop over all bonds
+          if  (associated(current_bond%other_berg)) then
+            other_berg=>current_bond%other_berg
+
+            ! From icebergs.F90 --> subroutine convert_from_grid_to_meters
+            if (bergs%grd%grid_is_latlon) then
+              lat_ref=0.5*(this%lat+other_berg%lat)
+              dx_dlon=pi_180*Rearth*cos(lat_ref*pi_180);  dy_dlat=pi_180*Rearth
+            else
+              dx_dlon=1.0;                                dy_dlat=1.0
+            endif
+
+            dx=(this%lon-other_berg%lon)*dx_dlon; dy=(this%lat-other_berg%lat)*dy_dlat
+            n1=dx/this%length; n2=dy/this%length !unit vector
+            bond_posn%lon=this%lon-dx/2;          bond_posn%lat=this%lat-dy/2
+            bond_posn%year=bergs%current_year;    bond_posn%day=bergs%current_yearday
+            bond_posn%length=current_bond%length;
+            bond_posn%n1=n1;                      bond_posn%n2=n2
+            bond_posn%rotation=current_bond%rotation
+            bond_posn%rel_rotation=current_bond%rel_rotation
+            bond_posn%n_strain=current_bond%n_strain
+            bond_posn%n_strain_rate=current_bond%n_strain_rate
+            bond_posn%id1=this%id;                bond_posn%id2=other_berg%id
+
+            if (monitor_energy) then
+              bond_posn%Ee=current_bond%Ee
+              bond_posn%Ed=current_bond%Ed
+            endif
+
+            call push_bond_posn(current_bond%bond_trajectory, bond_posn)
+          endif
+          current_bond=>current_bond%next_bond
+        enddo
+      endif
+
       this=>this%next
     enddo
   enddo ; enddo
@@ -4374,12 +5128,31 @@ subroutine push_posn(trajectory, posn_vals)
 type(xyt), pointer :: new_posn
 
   allocate(new_posn)
+  if (monitor_energy) then
+    allocate(new_posn%Ee,new_posn%Ed,new_posn%Eext,new_posn%Ee_contact,new_posn%Ed_contact,new_posn%Efrac)
+  endif
   new_posn=posn_vals
   new_posn%next=>trajectory
   trajectory=>new_posn
 
 end subroutine push_posn
 
+!> Add bond trajectory values as a new record in a bond trajectory
+subroutine push_bond_posn(bond_trajectory, bond_posn_vals)
+! Arguments
+type(bond_xyt), pointer :: bond_trajectory !< Trajectory list
+type(bond_xyt) :: bond_posn_vals !< Values to add
+! Local variables
+type(bond_xyt), pointer :: new_bond_posn
+
+  allocate(new_bond_posn)
+  if (monitor_energy) allocate(new_bond_posn%Ee,new_bond_posn%Ed)
+  new_bond_posn=bond_posn_vals
+  new_bond_posn%next=>bond_trajectory
+  bond_trajectory=>new_bond_posn
+
+end subroutine push_bond_posn
+
 !> Appends trajectory values to the end of the trajectory list (slow)
 !! \todo append_posn() is very slow and should be removed a.s.a.p.
 subroutine append_posn(trajectory, posn_vals)
@@ -4390,6 +5163,9 @@ subroutine append_posn(trajectory, posn_vals)
 type(xyt), pointer :: new_posn,next,last
 
   allocate(new_posn)
+  if (monitor_energy) then
+    allocate(new_posn%Ee,new_posn%Ed,new_posn%Eext,new_posn%Ee_contact,new_posn%Ed_contact,new_posn%Efrac)
+  endif
   new_posn=posn_vals
   new_posn%next=>null()
   if(.NOT. associated(trajectory)) then
@@ -4405,6 +5181,32 @@ subroutine append_posn(trajectory, posn_vals)
   endif
 end subroutine append_posn
 
+!> Appends bond trajectory values to the end of the bond trajectory list (slow)
+!! \todo append_bond_posn() is very slow and should be removed a.s.a.p.
+subroutine append_bond_posn(bond_trajectory, bond_posn_vals)
+! Arguments
+type(bond_xyt), pointer :: bond_trajectory !< Trajectory list
+type(bond_xyt) :: bond_posn_vals !< Values to add
+! Local variables
+type(bond_xyt), pointer :: new_bond_posn,next,last
+
+  allocate(new_bond_posn)
+  if (monitor_energy) allocate(new_bond_posn%Ee,new_bond_posn%Ed)
+  new_bond_posn=bond_posn_vals
+  new_bond_posn%next=>null()
+  if(.NOT. associated(bond_trajectory)) then
+     bond_trajectory=>new_bond_posn
+  else
+     ! Find end of the trajectory and point it to the  new leaf
+     next=>bond_trajectory
+     do while (associated(next))
+        last=>next
+        next=>next%next
+     enddo
+     last%next=>new_bond_posn
+  endif
+end subroutine append_bond_posn
+
 !> Disconnect a trajectory from a berg and add it to a list of trajectory segments
 subroutine move_trajectory(bergs, berg)
 ! Arguments
@@ -4413,6 +5215,7 @@ subroutine move_trajectory(bergs, berg)
 ! Local variables
 type(xyt), pointer :: next, last
 type(xyt) :: vals
+type(bond) , pointer :: current_bond
 
   if (bergs%ignore_traj) return
 
@@ -4428,10 +5231,46 @@ subroutine move_trajectory(bergs, berg)
   last%next=>bergs%trajectories
 
   bergs%trajectories=>berg%trajectory
+
+  if (save_bond_traj) then
+    current_bond=>berg%first_bond
+    do while (associated(current_bond)) ! loop over all bonds
+      call move_bond_trajectory(bergs, current_bond)
+      current_bond=>current_bond%next_bond
+    enddo
+  endif
+
   berg%trajectory=>null()
 
 end subroutine move_trajectory
 
+!> Disconnect a trajectory from a berg and add it to a list of trajectory segments
+subroutine move_bond_trajectory(bergs, current_bond)
+! Arguments
+type(icebergs), pointer :: bergs !< Container for all types and memory
+type(bond) , pointer :: current_bond
+! Local variables
+type(bond_xyt), pointer :: next, last
+type(bond_xyt) :: vals
+
+  if (bergs%ignore_traj) return
+
+  ! If the trajectory is empty, ignore it
+  if (.not.associated(current_bond%bond_trajectory)) return
+
+  ! Find end of berg trajectory and point it to start of existing trajectories
+  next=>current_bond%bond_trajectory
+  do while (associated(next))
+    last=>next
+    next=>next%next
+  enddo
+  last%next=>bergs%bond_trajectories
+
+  bergs%bond_trajectories=>current_bond%bond_trajectory
+  current_bond%bond_trajectory=>null()
+
+end subroutine move_bond_trajectory
+
 !> Scan all bergs in a list and disconnect trajectories and more to the list of trajectory segments
 !! \todo The argument delete_bergs should be removed.
 subroutine move_all_trajectories(bergs, delete_bergs)
@@ -4734,8 +5573,17 @@ logical function check_and_find_cell(grd, x, y, oi, oj)
       endif
 endif
 
+!find cell for structured grid without looping:
+oi=floor((x-grd%lon(grd%isd,grd%jsd))/(grd%lon(grd%isd+1,grd%jsd+1)-grd%lon(grd%isd,grd%jsd)))+grd%isd+1
+oj=floor((y-grd%lat(grd%isd,grd%jsd))/(grd%lat(grd%isd+1,grd%jsd+1)-grd%lat(grd%isd,grd%jsd)))+grd%jsd+1
+if (.not. (oi-1.lt.grd%isd.or.oi.gt.grd%ied.or.oj-1.lt.grd%jsd.or.oj.gt.grd%jed)) then
+  if (is_point_in_cell(grd, x, y, oi, oj)) then
+    check_and_find_cell=.true.; return
+  endif
+endif
+
   oi=-999; oj=-999
-  do j=grd%jsc,grd%jec; do i=grd%isc,grd%iec
+  do j=grd%jsd+1,grd%jed; do i=grd%isd+1,grd%ied
       if (is_point_in_cell(grd, x, y, i, j)) then
         oi=i; oj=j; check_and_find_cell=.true.
         return
@@ -4754,8 +5602,19 @@ logical function find_cell(grd, x, y, oi, oj)
 ! Local variables
 integer :: i,j
 
-  find_cell=.false.; oi=-999; oj=-999
+find_cell=.false.
 
+
+!find cell for structured grid without looping:
+oi=floor((x-grd%lon(grd%isd,grd%jsd))/(grd%lon(grd%isd+1,grd%jsd+1)-grd%lon(grd%isd,grd%jsd)))+grd%isd+1
+oj=floor((y-grd%lat(grd%isd,grd%jsd))/(grd%lat(grd%isd+1,grd%jsd+1)-grd%lat(grd%isd,grd%jsd)))+grd%jsd+1
+if (oi>grd%isc-1 .and. oi<grd%iec+1 .and. oj>grd%jsc-1 .and. oj<grd%jec+1) then
+  if (is_point_in_cell(grd, x, y, oi, oj)) then
+    find_cell=.true.; return
+  endif
+endif
+
+  oi=-999; oj=-999
   do j=grd%jsc,grd%jec; do i=grd%isc,grd%iec
       if (is_point_in_cell(grd, x, y, i, j)) then
         oi=i; oj=j; find_cell=.true.
@@ -4776,7 +5635,17 @@ logical function find_cell_wide(grd, x, y, oi, oj)
 ! Local variables
 integer :: i,j
 
-  find_cell_wide=.false.; oi=-999; oj=-999
+find_cell_wide=.false.
+!find cell for structured grid without looping:
+oi=floor((x-grd%lon(grd%isd,grd%jsd))/(grd%lon(grd%isd+1,grd%jsd+1)-grd%lon(grd%isd,grd%jsd)))+grd%isd+1
+oj=floor((y-grd%lat(grd%isd,grd%jsd))/(grd%lat(grd%isd+1,grd%jsd+1)-grd%lat(grd%isd,grd%jsd)))+grd%jsd+1
+if (.not. (oi-1.lt.grd%isd.or.oi.gt.grd%ied.or.oj-1.lt.grd%jsd.or.oj.gt.grd%jed)) then
+  if (is_point_in_cell(grd, x, y, oi, oj)) then
+    find_cell_wide=.true.; return
+  endif
+endif
+
+oi=-999; oj=-999
 
   do j=grd%jsd+1,grd%jed; do i=grd%isd+1,grd%ied
       if (is_point_in_cell(grd, x, y, i, j)) then
@@ -5786,6 +6655,88 @@ real function bilin(grd, fld, i, j, xi, yj)
   endif
 end function bilin
 
+!> Quadratic interpolation of an A-grid field to a location within a cell
+real function quad_interp_from_agrid(grd, fld, x, y, i, j, xi, yj)
+! Arguments
+type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+real, intent(in) :: fld(grd%isd:grd%ied,grd%jsd:grd%jed) !< Field to interpolate
+real, intent(in) :: x !<Longitude of position
+real, intent(in) :: y !<Latitude of position
+real, intent(in) :: xi !< Non-dimensional x-position within cell
+real, intent(in) :: yj !< Non-dimensional y-position within cell
+integer, intent(in) :: i !< i-index of cell
+integer, intent(in) :: j !< j-index of cell
+! Local variables
+integer :: is,ie,js,je
+real :: x1,x2,x3,x4,y1,y2,y3,y4
+real :: dx,dy,Delta_x,xx,yy
+real :: xloc,yloc !local coords
+real :: xb(3,3), yb(3,3) !basis functions
+
+!Uses bi-quadratic lagrange quadrilateral basis functions (like in FEM), where the 9
+!nodes of an "element" are defined by a 3x3 array of neigboring cell-centers
+
+!bounds of "node" array (is:ie,js:je).
+if (mod(i,2)==1) then
+  if (xi>=0.5) then
+    is=i; ie=i+2
+  else
+    is=i-2; ie=i
+  endif
+else
+  is=i-1; ie=i+1
+endif
+if (mod(j,2)==1) then
+  if (yj>=0.5) then
+    js=j; je=j+2
+  else
+    js=j-2; je=j
+  endif
+else
+  js=j-1; je=j+1
+endif
+
+!four corners
+x1=grd%lonc(is,js); y1=grd%latc(is,js)
+x2=grd%lonc(ie,js); y2=grd%latc(ie,js)
+x3=grd%lonc(ie,je); y3=grd%latc(ie,je)
+x4=grd%lonc(is,je); y4=grd%latc(is,je)
+
+!get non-dimensional, local (natural) coords xloc and yloc:
+!largely copied from to pos_within_cell
+if ((.not. grd%grid_is_latlon) .and. (grd%grid_is_regular))  then
+  dx=abs(x3-x4); dy=abs(y3-y2)
+  x1=x3-(dx/2); y1=y3-(dy/2)
+  Delta_x= apply_modulo_around_point(x,x1,grd%Lx)-x1
+  xloc=((Delta_x)/dx)+0.5; yloc=((y-y1)/dy)+0.5
+elseif ((max(y1,y2,y3,y4)<89.999) .or.(.not. grd%grid_is_latlon)) then
+  ! This returns non-dimensional position xi,yj for quad cells (not at a pole)
+  call calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x, y, xloc, yloc, grd%Lx)
+else
+  ! One of the cell corners is at the north pole so we switch to a tangent plane with
+  ! co-latitude as a radial coordinate.
+  xx=(90.-y)*cos(x*pi_180); yy=(90.-y)*sin(x*pi_180)
+  x1=(90.-y1)*cos(grd%lon(is,js)*pi_180); y1=(90.-y1)*sin(grd%lon(is,js)*pi_180)
+  x2=(90.-y2)*cos(grd%lon(ie,je)*pi_180); y2=(90.-y2)*sin(grd%lon(ie,je)*pi_180)
+  x3=(90.-y3)*cos(grd%lon(ie,je)*pi_180); y3=(90.-y3)*sin(grd%lon(ie,je)*pi_180)
+  x4=(90.-y4)*cos(grd%lon(is,je)*pi_180); y4=(90.-y4)*sin(grd%lon(is,je)*pi_180)
+  call calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, xx, yy, xloc, yloc, grd%Lx)
+endif
+
+!convert local coords to lie within the range [-1,1] rather than [0,1]
+xloc=xloc*2-1; yloc=yloc*2-1
+
+!basis functions:
+xb(1,:)=0.5*xloc*(xloc-1); yb(:,1)=0.5*yloc*(yloc-1)
+xb(2,:)=(1+xloc)*(1-xloc); yb(:,2)=(1+yloc)*(1-yloc)
+xb(3,:)=0.5*xloc*(xloc+1); yb(:,3)=0.5*yloc*(yloc+1)
+
+!interpolate:
+quad_interp_from_agrid=sum(xb*yb*fld(is:ie,js:je))
+
+end function quad_interp_from_agrid
+
+
 !> Prints a field
 subroutine print_fld(grd, fld, label)
 ! Arguments
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index 4169c47..f60bdf3 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -25,7 +25,7 @@ module ice_bergs_io
 
 use time_manager_mod, only: time_type, get_date, get_time, set_date, operator(-)
 
-use ice_bergs_framework, only: icebergs_gridded, xyt, iceberg, icebergs, buffer, bond
+use ice_bergs_framework, only: icebergs_gridded, xyt, bond_xyt, iceberg, icebergs, buffer, bond
 use ice_bergs_framework, only: pack_traj_into_buffer2,unpack_traj_from_buffer2
 use ice_bergs_framework, only: find_cell,find_cell_by_search,count_bergs,is_point_in_cell,pos_within_cell,append_posn
 use ice_bergs_framework, only: count_bonds, form_a_bond, find_individual_iceberg
@@ -34,20 +34,23 @@ module ice_bergs_io
 use ice_bergs_framework, only: increase_ibuffer,grd_chksum2,grd_chksum3
 use ice_bergs_framework, only: sum_mass,sum_heat,bilin
 !params !Niki: write a subroutine to get these
-use ice_bergs_framework, only: nclasses, buffer_width, buffer_width_traj
+use ice_bergs_framework, only: nclasses, buffer_width, buffer_width_traj, buffer_width_bond_traj
 use ice_bergs_framework, only: verbose, really_debug, debug, restart_input_dir,make_calving_reproduce
 use ice_bergs_framework, only: ignore_ij_restart, use_slow_find,generate_test_icebergs,print_berg
 use ice_bergs_framework, only: force_all_pes_traj
 use ice_bergs_framework, only: check_for_duplicates_in_parallel
 use ice_bergs_framework, only: split_id, id_from_2_ints, generate_id
-use ice_bergs_framework, only: mts !-Alex
+use ice_bergs_framework, only: mts,save_bond_traj !-Alex
+use ice_bergs_framework, only: push_bond_posn, append_bond_posn !-Alex
+use ice_bergs_framework, only: pack_bond_traj_into_buffer2,unpack_bond_traj_from_buffer2 !-Alex
+use ice_bergs_framework, only: monitor_energy
 
 implicit none ; private
 
 include 'netcdf.inc'
 
 public ice_bergs_io_init
-public read_restart_bergs, write_restart, write_trajectory
+public read_restart_bergs, write_restart, write_trajectory, write_bond_trajectory
 public read_restart_calving, read_restart_bonds
 public read_ocean_depth
 
@@ -61,6 +64,7 @@ module ice_bergs_io
 logical :: is_io_tile_root_pe = .true.
 
 integer :: clock_trw,clock_trp
+integer :: clock_btrw,clock_btrp !bond trajectories
 
 #ifdef _FILE_VERSION
   character(len=128) :: version = _FILE_VERSION
@@ -98,6 +102,8 @@ subroutine ice_bergs_io_init(bergs, io_layout)
 
   clock_trw=mpp_clock_id( 'Icebergs-traj write', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
   clock_trp=mpp_clock_id( 'Icebergs-traj prepare', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+  clock_btrw=mpp_clock_id( 'Iceberg-bonds-traj write', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+  clock_btrp=mpp_clock_id( 'Iceberg-bonds-traj prepare', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
 
 end subroutine ice_bergs_io_init
 
@@ -619,6 +625,8 @@ subroutine read_restart_bergs(bergs,Time)
       localberg%vvel_old=vvel(k) !Alon
       localberg%lon_old=lon(k) !Alon
       localberg%lat_old=lat(k) !Alon
+      localberg%lon_prev=lon(k)
+      localberg%lat_prev=lat(k)
       localberg%bxn=bxn(k) !Alon
       localberg%byn=byn(k) !Alon
       localberg%thickness=thickness(k)
@@ -787,6 +795,8 @@ subroutine generate_bergs(bergs,Time)
       localberg%lat=grd%latc(i,j)
       localberg%lon_old=localberg%lon
       localberg%lat_old=localberg%lat
+      localberg%lon_prev=localberg%lon
+      localberg%lat_prev=localberg%lat
       localberg%mass=bergs%initial_mass(1)
       localberg%thickness=bergs%initial_thickness(1)
       localberg%width=bergs%initial_width(1)
@@ -1258,7 +1268,9 @@ subroutine write_trajectory(trajectory, save_short_traj)
 integer :: uvelpid,vvelpid
 integer :: uoid, void, uiid, viid, uaid, vaid, sshxid, sshyid, sstid, sssid
 integer :: cnid, hiid, hsid
-integer :: mid, did, wid, lid, mbid, hdid, cid
+integer :: mid, did, wid, lid, mbid, hdid, nbid, odid, abrid
+integer :: axnid,aynid,bxnid,bynid,axnfid,aynfid,bxnfid,bynfid
+integer :: eecid,edcid,eeid,edid,aeid,efid !energy vars
 character(len=37) :: filename
 character(len=7) :: pe_name
 type(xyt), pointer :: this, next
@@ -1379,6 +1391,8 @@ subroutine write_trajectory(trajectory, save_short_traj)
       if (.not.save_short_traj) then
         uvelid = inq_varid(ncid, 'uvel')
         vvelid = inq_varid(ncid, 'vvel')
+        uvelpid = inq_varid(ncid, 'uvel_prev')
+        vvelpid = inq_varid(ncid, 'vvel_prev')
         uoid = inq_varid(ncid, 'uo')
         void = inq_varid(ncid, 'vo')
         uiid = inq_varid(ncid, 'ui')
@@ -1397,11 +1411,29 @@ subroutine write_trajectory(trajectory, save_short_traj)
         sssid = inq_varid(ncid, 'sss')
         cnid = inq_varid(ncid, 'cn')
         hiid = inq_varid(ncid, 'hi')
+        axnid = inq_varid(ncid, 'axn')
+        aynid = inq_varid(ncid, 'ayn')
+        bxnid = inq_varid(ncid, 'bxn')
+        bynid = inq_varid(ncid, 'byn')
         hsid = inq_varid(ncid, 'halo_berg')
+        odid = inq_varid(ncid, 'od')
+        nbid = inq_varid(ncid, 'n_bonds')
+        abrid = inq_varid(ncid, 'accum_bond_rotation')
+
         if (mts) then
-          cid = inq_varid(ncid, 'conglom_id')
-          uvelpid = inq_varid(ncid, 'uvel_prev')
-          vvelpid = inq_varid(ncid, 'vvel_prev')
+          axnfid = inq_varid(ncid, 'axn_fast')
+          aynfid = inq_varid(ncid, 'ayn_fast')
+          bxnfid = inq_varid(ncid, 'bxn_fast')
+          bynfid = inq_varid(ncid, 'byn_fast')
+        endif
+
+        if (monitor_energy) then
+          eeid = inq_varid(ncid, 'Ee')
+          edid = inq_varid(ncid, 'Ed')
+          aeid = inq_varid(ncid, 'Eext')
+          eecid = inq_varid(ncid, 'Ee_contact')
+          edcid = inq_varid(ncid, 'Ed_contact')
+          efid =  inq_varid(ncid, 'Efrac')
         endif
       endif
     else
@@ -1419,6 +1451,8 @@ subroutine write_trajectory(trajectory, save_short_traj)
       if (.not. save_short_traj) then
         uvelid = def_var(ncid, 'uvel', NF_DOUBLE, i_dim)
         vvelid = def_var(ncid, 'vvel', NF_DOUBLE, i_dim)
+        uvelpid = def_var(ncid, 'uvel_prev', NF_DOUBLE, i_dim)
+        vvelpid = def_var(ncid, 'vvel_prev', NF_DOUBLE, i_dim)
         uoid = def_var(ncid, 'uo', NF_DOUBLE, i_dim)
         void = def_var(ncid, 'vo', NF_DOUBLE, i_dim)
         uiid = def_var(ncid, 'ui', NF_DOUBLE, i_dim)
@@ -1437,11 +1471,29 @@ subroutine write_trajectory(trajectory, save_short_traj)
         sssid = def_var(ncid, 'sss', NF_DOUBLE, i_dim)
         cnid = def_var(ncid, 'cn', NF_DOUBLE, i_dim)
         hiid = def_var(ncid, 'hi', NF_DOUBLE, i_dim)
+        axnid = def_var(ncid, 'axn', NF_DOUBLE, i_dim)
+        aynid = def_var(ncid, 'ayn', NF_DOUBLE, i_dim)
+        bxnid = def_var(ncid, 'bxn', NF_DOUBLE, i_dim)
+        bynid = def_var(ncid, 'byn', NF_DOUBLE, i_dim)
         hsid = def_var(ncid, 'halo_berg', NF_DOUBLE, i_dim)
+        odid = def_var(ncid, 'od', NF_DOUBLE, i_dim)
+        nbid = def_var(ncid, 'n_bonds', NF_INT, i_dim)
+        abrid = def_var(ncid, 'accum_bond_rotation', NF_DOUBLE, i_dim)
+
         if (mts) then
-          cid = def_var(ncid, 'conglom_id', NF_INT, i_dim)
-          uvelpid = def_var(ncid, 'uvel_prev', NF_DOUBLE, i_dim)
-          vvelpid = def_var(ncid, 'vvel_prev', NF_DOUBLE, i_dim)
+          axnfid = def_var(ncid, 'axn_fast', NF_DOUBLE, i_dim)
+          aynfid = def_var(ncid, 'ayn_fast', NF_DOUBLE, i_dim)
+          bxnfid = def_var(ncid, 'bxn_fast', NF_DOUBLE, i_dim)
+          bynfid = def_var(ncid, 'byn_fast', NF_DOUBLE, i_dim)
+        endif
+
+        if (monitor_energy) then
+          eeid = def_var(ncid, 'Ee', NF_DOUBLE, i_dim)
+          edid = def_var(ncid, 'Ed', NF_DOUBLE, i_dim)
+          aeid = def_var(ncid, 'Eext', NF_DOUBLE, i_dim)
+          eecid = def_var(ncid, 'Ee_contact', NF_DOUBLE, i_dim)
+          edcid = def_var(ncid, 'Ed_contact', NF_DOUBLE, i_dim)
+          efid = def_var(ncid, 'Efrac', NF_DOUBLE, i_dim)
         endif
       endif
 
@@ -1502,15 +1554,49 @@ subroutine write_trajectory(trajectory, save_short_traj)
         call put_att(ncid, cnid, 'units', 'none')
         call put_att(ncid, hiid, 'long_name', 'sea ice thickness')
         call put_att(ncid, hiid, 'units', 'm')
+        call put_att(ncid, axnid, 'long_name', 'explicit zonal acceleration')
+        call put_att(ncid, axnid, 'units', 'm')
+        call put_att(ncid, aynid, 'long_name', 'explicit meridional acceleration')
+        call put_att(ncid, aynid, 'units', 'm')
+        call put_att(ncid, bxnid, 'long_name', 'implicit zonal acceleration')
+        call put_att(ncid, bxnid, 'units', 'm')
+        call put_att(ncid, bynid, 'long_name', 'implicit meridional acceleration')
+        call put_att(ncid, bynid, 'units', 'm')
         call put_att(ncid, hsid, 'long_name', 'halo status')
         call put_att(ncid, hsid, 'units', 'non-dim')
+        call put_att(ncid, odid, 'long_name', 'ocean_depth')
+        call put_att(ncid, odid, 'units', 'm')
+        call put_att(ncid, nbid, 'long_name', 'number of bonds')
+        call put_att(ncid, nbid, 'units', 'dimensionless')
+        call put_att(ncid, abrid, 'long_name', 'accumulated bond rotation')
+        call put_att(ncid, abrid, 'units', 'radians')
         if (mts) then
-          call put_att(ncid, cid, 'long_name', 'conglomerate id')
-          call put_att(ncid, cid, 'units', 'dimensionless')
           call put_att(ncid, uvelpid, 'long_name', 'zonal speed mts')
           call put_att(ncid, uvelpid, 'units', 'm/s')
           call put_att(ncid, vvelpid, 'long_name', 'meridional speed mts')
           call put_att(ncid, vvelpid, 'units', 'm/s')
+          call put_att(ncid, axnfid, 'long_name', 'explicit fast step zonal acceleration')
+          call put_att(ncid, axnfid, 'units', 'm')
+          call put_att(ncid, aynfid, 'long_name', 'explicit fast step meridional acceleration')
+          call put_att(ncid, aynfid, 'units', 'm')
+          call put_att(ncid, bxnfid, 'long_name', 'implicit fast step zonal acceleration')
+          call put_att(ncid, bxnfid, 'units', 'm')
+          call put_att(ncid, bynfid, 'long_name', 'implicit fast step meridional acceleration')
+          call put_att(ncid, bynfid, 'units', 'm')
+        endif
+        if (monitor_energy) then
+          call put_att(ncid, eeid, 'long_name', 'bonded elastic energy')
+          call put_att(ncid, eeid, 'units', 'J')
+          call put_att(ncid, edid, 'long_name', 'bonded damping energy')
+          call put_att(ncid, edid, 'units', 'J')
+          call put_att(ncid, aeid, 'long_name', 'external energy')
+          call put_att(ncid, aeid, 'units', 'J')
+          call put_att(ncid, eecid, 'long_name', 'contact elastic energy')
+          call put_att(ncid, eecid, 'units', 'J')
+          call put_att(ncid, edcid, 'long_name', 'contact damping energy')
+          call put_att(ncid, edcid, 'units', 'J')
+          call put_att(ncid, efid, 'long_name', 'dissipated fracture energy')
+          call put_att(ncid, efid, 'units', 'J')
         endif
       endif
     endif
@@ -1538,6 +1624,8 @@ subroutine write_trajectory(trajectory, save_short_traj)
       if (.not. save_short_traj) then
         call put_double(ncid, uvelid, i, this%uvel)
         call put_double(ncid, vvelid, i, this%vvel)
+        call put_double(ncid, uvelpid, i, this%uvel_prev)
+        call put_double(ncid, vvelpid, i, this%vvel_prev)
         call put_double(ncid, uoid, i, this%uo)
         call put_double(ncid, void, i, this%vo)
         call put_double(ncid, uiid, i, this%ui)
@@ -1555,12 +1643,31 @@ subroutine write_trajectory(trajectory, save_short_traj)
         call put_double(ncid, sssid, i, this%sss)
         call put_double(ncid, cnid, i, this%cn)
         call put_double(ncid, hiid, i, this%hi)
+        call put_double(ncid, axnid, i, this%axn)
+        call put_double(ncid, aynid, i, this%ayn)
+        call put_double(ncid, bxnid, i, this%bxn)
+        call put_double(ncid, bynid, i, this%byn)
         call put_double(ncid, hsid, i, this%halo_berg)
+        call put_double(ncid, odid, i, this%od)
+        call put_int(ncid, nbid, i, this%n_bonds)
+        call put_double(ncid, abrid, i, this%accum_bond_rotation)
+
         if (mts) then
-          call put_int(ncid, cid, i, this%conglom_id)
-          call put_double(ncid, uvelpid, i, this%uvel_prev)
-          call put_double(ncid, vvelpid, i, this%vvel_prev)
+          call put_double(ncid, axnfid, i, this%axn_fast)
+          call put_double(ncid, aynfid, i, this%ayn_fast)
+          call put_double(ncid, bxnfid, i, this%bxn_fast)
+          call put_double(ncid, bynfid, i, this%byn_fast)
         endif
+
+        if (monitor_energy) then
+          call put_double(ncid, eeid, i, this%Ee)
+          call put_double(ncid, edid, i, this%Ed)
+          call put_double(ncid, aeid, i, this%Eext)
+          call put_double(ncid, eecid, i, this%Ee_contact)
+          call put_double(ncid, edcid, i, this%Ed_contact)
+          call put_double(ncid, efid, i, this%Efrac)
+        endif
+
       endif
       next=>this%next
       deallocate(this)
@@ -1576,6 +1683,238 @@ subroutine write_trajectory(trajectory, save_short_traj)
 
 end subroutine write_trajectory
 
+!> Write a trajectory-based diagnostics file for bonds
+subroutine write_bond_trajectory(trajectory)
+! Arguments
+type(bond_xyt), pointer :: trajectory !< An iceberg bond trajectory
+! Local variables
+integer :: iret, ncid, i_dim, i
+integer :: lonid, latid, yearid, dayid, lenid,n1id, n2id
+integer :: rotid,rrotid,nsid,nsrid
+integer :: idcnt1_id, idcnt2_id, idij1_id, idij2_id, eeid, edid
+character(len=34) :: filename
+character(len=7) :: pe_name
+type(bond_xyt), pointer :: this, next
+integer :: stderrunit, cnt, ij
+!I/O vars
+type(bond_xyt), pointer :: traj4io=>null()
+integer :: ntrajs_sent_io,ntrajs_rcvd_io
+integer :: from_pe,np
+type(buffer), pointer :: obuffer_io=>null(), ibuffer_io=>null()
+logical :: io_is_in_append_mode
+
+  stderrunit=stderr()  ! Get the stderr unit number
+  traj4io=>null()
+  ibuffer_io=>null(); obuffer_io=>null()
+
+  !Assemble the list of trajectories from all pes in this I/O tile
+  call mpp_clock_begin(clock_btrp)
+
+  !First add the trajs on the io_tile_root_pe (if any) to the I/O list
+  if(is_io_tile_root_pe .OR. force_all_pes_traj ) then
+    if(associated(trajectory)) then
+      this=>trajectory
+      do while (associated(this))
+        call append_bond_posn(traj4io, this)
+        this=>this%next
+      enddo
+      trajectory => null()
+    endif
+  endif
+
+  if(.NOT. force_all_pes_traj ) then
+    !Now gather and append the bergs from all pes in the io_tile to the list on corresponding io_tile_root_pe
+    ntrajs_sent_io =0; ntrajs_rcvd_io =0
+
+    if(is_io_tile_root_pe) then
+      !Receive trajs from all pes in this I/O tile !FRAGILE!SCARY!
+      do np=2,size(io_tile_pelist) ! Note: np starts from 2 to exclude self
+        from_pe=io_tile_pelist(np)
+        call mpp_recv(ntrajs_rcvd_io, glen=1, from_pe=from_pe, tag=COMM_TAG_11)
+        if (ntrajs_rcvd_io .gt. 0) then
+          call increase_ibuffer(ibuffer_io, ntrajs_rcvd_io,buffer_width_bond_traj)
+          call mpp_recv(ibuffer_io%data, ntrajs_rcvd_io*buffer_width_bond_traj,from_pe=from_pe, tag=COMM_TAG_12)
+          do i=1, ntrajs_rcvd_io
+            call unpack_bond_traj_from_buffer2(traj4io, ibuffer_io, i)
+          enddo
+        endif
+      enddo
+    else
+      ! Pack and send trajectories to the root PE for this I/O tile
+      do while (associated(trajectory))
+        ntrajs_sent_io = ntrajs_sent_io +1
+        call pack_bond_traj_into_buffer2(trajectory, obuffer_io, ntrajs_sent_io)
+        this => trajectory ! Need to keep pointer in order to free up the links memory
+        trajectory => trajectory%next ! This will eventually result in trajectory => null()
+        deallocate(this) ! Delete the link from memory
+      enddo
+
+      call mpp_send(ntrajs_sent_io, plen=1, to_pe=io_tile_root_pe, tag=COMM_TAG_11)
+      if (ntrajs_sent_io .gt. 0) then
+        call mpp_send(obuffer_io%data, ntrajs_sent_io*buffer_width_bond_traj, to_pe=io_tile_root_pe, tag=COMM_TAG_12)
+      endif
+    endif
+  endif !.NOT. force_all_pes_traj
+
+  call mpp_clock_end(clock_btrp)
+
+  !Now start writing in the io_tile_root_pe if there are any bergs in the I/O list
+  call mpp_clock_begin(clock_btrw)
+
+  if((force_all_pes_traj .OR. is_io_tile_root_pe) .AND. associated(traj4io)) then
+
+    call get_instance_filename("bond_trajectories.nc", filename)
+    if(io_tile_id(1) .ge. 0 .AND. .NOT. force_all_pes_traj) then !io_tile_root_pes write
+      if(io_npes .gt. 1) then !attach tile_id  to filename only if there is more than one I/O pe
+        if (io_tile_id(1)<10000) then
+          write(filename,'(A,".",I4.4)') trim(filename), io_tile_id(1)
+        else
+          write(filename,'(A,".",I6.6)') trim(filename), io_tile_id(1)
+        endif
+      endif
+    else !All pes write, attach pe# to filename
+      if (mpp_npes()<10000) then
+        write(filename,'(A,".",I4.4)') trim(filename), mpp_pe()
+      else
+        write(filename,'(A,".",I6.6)') trim(filename), mpp_pe()
+      endif
+    endif
+
+    io_is_in_append_mode = .false.
+    iret = nf_create(filename, NF_NOCLOBBER, ncid)
+    if (iret .ne. NF_NOERR) then
+      iret = nf_open(filename, NF_WRITE, ncid)
+      io_is_in_append_mode = .true.
+      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_bond_trajectory: nf_open failed'
+    endif
+    if (verbose) then
+      if (io_is_in_append_mode) then
+        write(*,'(2a)') 'KID, write_bond_trajectory: appending to ',filename
+      else
+        write(*,'(2a)') 'KID, write_bond_trajectory: creating ',filename
+      endif
+    endif
+
+    if (io_is_in_append_mode) then
+      iret = nf_inq_dimid(ncid, 'i', i_dim)
+      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_bond_trajectory: nf_inq_dimid i failed'
+      lonid = inq_varid(ncid, 'lon');         latid = inq_varid(ncid, 'lat')
+      yearid = inq_varid(ncid, 'year');       dayid = inq_varid(ncid, 'day')
+      lenid = inq_varid(ncid, 'length');
+      n1id = inq_varid(ncid, 'n1');           n2id = inq_varid(ncid, 'n2')
+
+      !fracture params
+      rotid = inq_varid(ncid, 'rotation');    rrotid = inq_varid(ncid, 'rel_rotation')
+      nsid = inq_varid(ncid, 'n_strain');     nsrid = inq_varid(ncid, 'n_strain_rate')
+
+      idcnt1_id = inq_varid(ncid, 'id_cnt1'); idij1_id = inq_varid(ncid, 'id_ij1')
+      idcnt2_id = inq_varid(ncid, 'id_cnt2'); idij2_id = inq_varid(ncid, 'id_ij2')
+
+      if (monitor_energy) then
+        eeid = inq_varid(ncid, 'Ee'); edid = inq_varid(ncid, 'Ed')
+      endif
+
+    else
+      ! Dimensions
+      iret = nf_def_dim(ncid, 'i', NF_UNLIMITED, i_dim)
+      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_bond_trajectory: nf_def_dim i failed'
+
+      ! Variables
+      lonid = def_var(ncid, 'lon', NF_DOUBLE, i_dim);      latid = def_var(ncid, 'lat', NF_DOUBLE, i_dim)
+      yearid = def_var(ncid, 'year', NF_INT, i_dim);       dayid = def_var(ncid, 'day', NF_DOUBLE, i_dim)
+      lenid = def_var(ncid, 'length', NF_DOUBLE, i_dim);
+      n1id = def_var(ncid, 'n1', NF_DOUBLE, i_dim);        n2id = def_var(ncid, 'n2', NF_DOUBLE, i_dim)
+
+      !fracture params
+      rotid = def_var(ncid, 'rotation', NF_DOUBLE, i_dim); rrotid = def_var(ncid, 'rel_rotation', NF_DOUBLE, i_dim)
+      nsid = def_var(ncid, 'n_strain', NF_DOUBLE, i_dim);  nsrid = def_var(ncid, 'n_strain_rate', NF_DOUBLE, i_dim)
+
+      idcnt1_id = def_var(ncid, 'id_cnt1', NF_INT, i_dim); idij1_id = def_var(ncid, 'id_ij1', NF_INT, i_dim)
+      idcnt2_id = def_var(ncid, 'id_cnt2', NF_INT, i_dim); idij2_id = def_var(ncid, 'id_ij2', NF_INT, i_dim)
+
+      if (monitor_energy) then
+        eeid = def_var(ncid, 'Ee', NF_DOUBLE, i_dim); edid = def_var(ncid, 'Ed', NF_DOUBLE, i_dim)
+      endif
+
+      ! Attributes
+      iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_major_version', NF_INT, 1, 0)
+      iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_minor_version', NF_INT, 1, 1)
+      call put_att(ncid, lonid, 'long_name', 'longitude');    call put_att(ncid, lonid, 'units', 'degrees_E')
+      call put_att(ncid, latid, 'long_name', 'latitude');     call put_att(ncid, latid, 'units', 'degrees_N')
+      call put_att(ncid, yearid, 'long_name', 'year');        call put_att(ncid, yearid, 'units', 'years')
+      call put_att(ncid, dayid, 'long_name', 'year day');     call put_att(ncid, dayid, 'units', 'days')
+      call put_att(ncid, lenid, 'long_name', 'length');       call put_att(ncid, lenid, 'units', 'm')
+      call put_att(ncid, n1id, 'long_name', 'unit vector 1'); call put_att(ncid, n1id, 'units', 'non-dim')
+      call put_att(ncid, n2id, 'long_name', 'unit vector 2'); call put_att(ncid, n2id, 'units', 'non-dim')
+
+      !fracture params
+      call put_att(ncid, rotid, 'long_name', 'rotation');           call put_att(ncid, rotid, 'units', 'rad')
+      call put_att(ncid, rrotid, 'long_name', 'relative rotation'); call put_att(ncid, rrotid, 'units', 'rad')
+      call put_att(ncid, nsid, 'long_name', 'normal strain');       call put_att(ncid, nsid, 'units', 'non-dim')
+      call put_att(ncid, nsrid, 'long_name', 'normal strain-rate'); call put_att(ncid, nsrid, 'units', '1/seconds')
+
+      call put_att(ncid, idcnt1_id, 'long_name', 'counter component of first connected iceberg id')
+      call put_att(ncid, idcnt1_id, 'units', 'dimensionless')
+      call put_att(ncid, idij1_id, 'long_name', 'position component of first connected iceberg id')
+      call put_att(ncid, idij1_id, 'units', 'dimensionless')
+      call put_att(ncid, idcnt2_id, 'long_name', 'counter component of second connected iceberg id')
+      call put_att(ncid, idcnt2_id, 'units', 'dimensionless')
+      call put_att(ncid, idij2_id, 'long_name', 'position component of second connected iceberg id')
+      call put_att(ncid, idij2_id, 'units', 'dimensionless')
+
+      if (monitor_energy) then
+        call put_att(ncid, eeid, 'long_name', 'elastic energy')
+        call put_att(ncid, eeid, 'units', 'J')
+        call put_att(ncid, edid, 'long_name', 'damping energy')
+        call put_att(ncid, edid, 'units', 'J')
+      endif
+    endif
+
+    ! End define mode
+    iret = nf_enddef(ncid)
+
+    ! Write variables
+    this=>traj4io
+    if (io_is_in_append_mode) then
+      iret = nf_inq_dimlen(ncid, i_dim, i)
+      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_bond_trajectory: nf_inq_dimlen i failed'
+    else
+      i = 0
+    endif
+    do while (associated(this))
+      i=i+1
+      call put_double(ncid, lonid, i, this%lon);    call put_double(ncid, latid, i, this%lat)
+      call put_int(ncid, yearid, i, this%year);     call put_double(ncid, dayid, i, this%day)
+      call put_double(ncid, lenid, i, this%length);
+      call put_double(ncid, n1id, i, this%n1);      call put_double(ncid, n2id, i, this%n2)
+
+      !fracture params
+      call put_double(ncid,rotid,i,this%rotation);  call put_double(ncid,rrotid,i,this%rel_rotation)
+      call put_double(ncid,nsid,i,this%n_strain);   call put_double(ncid,nsrid,i,this%n_strain_rate)
+
+      call split_id(this%id1, cnt, ij)
+      call put_int(ncid, idcnt1_id, i, cnt);        call put_int(ncid, idij1_id, i, ij)
+      call split_id(this%id2, cnt, ij)
+      call put_int(ncid, idcnt2_id, i, cnt);        call put_int(ncid, idij2_id, i, ij)
+
+      if (monitor_energy) then
+        call put_double(ncid,eeid,i,this%Ee);   call put_double(ncid,edid,i,this%Ed)
+      endif
+
+      next=>this%next
+      deallocate(this)
+      this=>next
+    enddo
+
+    ! Finish up
+    iret = nf_close(ncid)
+    if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_bond_trajectory: nf_close failed',mpp_pe(),filename
+
+  endif !(is_io_tile_root_pe .AND. associated(traj4io))
+  call mpp_clock_end(clock_btrw)
+
+end subroutine write_bond_trajectory
+
 !> Returns netcdf id of variable
 integer function inq_var(ncid, var, unsafe)
 ! Arguments
diff --git a/tests/.gitignore b/tests/.gitignore
index f127ba8..e40f6b9 100644
--- a/tests/.gitignore
+++ b/tests/.gitignore
@@ -1,6 +1,7 @@
 *.out
 *~
 *.nc
+*.csv
 core
 single_test/
 size_test_tab/
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/initialize_bergs_in_pattern.py b/tests/Iceberg_repository/Scripts_and_analysis/initialize_bergs_in_pattern.py
index f9665a5..0008179 100755
--- a/tests/Iceberg_repository/Scripts_and_analysis/initialize_bergs_in_pattern.py
+++ b/tests/Iceberg_repository/Scripts_and_analysis/initialize_bergs_in_pattern.py
@@ -36,6 +36,9 @@ def parseCommandLine():
 	#p.add_argument('-b',type='bool')  # do not use 'type=bool'
 
 	#Flags
+	parser.add_argument('-grounding_test', type='bool', default=False,
+		          help=''' old: displace 500 m S. new: get rid of SE element ''')
+        
 	parser.add_argument('-collision_test', type='bool', default=False,
 		          help=''' symmetry for berg around y=10 km ''')
         
@@ -777,7 +780,7 @@ def remove_stationary_bergs(dx_berg, dy_berg,iceberg_num,width,Number_of_bergs,s
 def Create_icebergs(lon_init,lat_init,Radius,R_earth, x, y,ice_mask,h_ice,Convert_to_lat_lon,rho_ice,\
 		element_type,scale_the_grid_to_lat_lon,lat_ref,adjust_lat_ref,Interpolate_from_four_corners,\
 		Fill_in_the_boundaries,set_all_bergs_static_by_default,break_some_bonds,Remove_stationary_bergs,\
-                set_some_bergs_static_by_default,collision_test):
+                set_some_bergs_static_by_default,collision_test,grounding_test):
 	print 'Starting to create icebergs...'
 	dx_berg=[]  #x distance in cartesian of berg from lon_init
 	dy_berg=[]  #y distance in cartesian of berg from lat_init
@@ -832,21 +835,33 @@ def Create_icebergs(lon_init,lat_init,Radius,R_earth, x, y,ice_mask,h_ice,Conver
 			x_start=((2/np.sqrt(3))*Radius)
 			x_val=x_start + (np.sqrt(3)*Radius*i)
 
-		for j in range(M):
-		#for i in range(M):
-			#x_val=x_start+(2*i*Radius)  ; y_val=y_start
-			y_val=y_start+(2*j*Radius)  ;# x_val=x_start + (np.sqrt(3)*Radius*i)
-			if check_if_it_is_in_domain(x_val,y_val,X_min,X_max,Y_min,Y_max,R_earth,lat_init,adjust_lat_ref,dx,dy):
-			#if True:
-				#R_val=np.sqrt(((x_val-x0)**2) +((y_val-y0)**2))
-				if check_if_it_is_ice(x_val,y_val,ice_mask,dx):
-					#Don't allow points closer than R from the boundary (these are sorted out later)
-					#if abs(y_val-Ly)<Radius or  ((abs(x_val-Lx)<((2/np.sqrt(3))*Radius)) and element_type=='hexagon') or ((abs(x_val-Lx)<Radius) and element_type=='square'):
-					berg_count=berg_count+1
-					iceberg_num.append(berg_count)
-					dx_berg.append(x_val)
-					dy_berg.append(y_val)
-					width.append(np.sqrt(element_area))
+                if grounding_test:
+                        for j in range(M):
+                                y_val=y_start+(2*j*Radius)  ;
+                                if check_if_it_is_in_domain(x_val,y_val,X_min,X_max,Y_min,Y_max,R_earth,lat_init,adjust_lat_ref,dx,dy):
+                                        if check_if_it_is_ice(x_val,y_val,ice_mask,dx):
+                                                if not (x_val>5.5e3 and (y_val<12.0e3 or y_val>19.5e3)):
+                                                        berg_count=berg_count+1
+                                                        iceberg_num.append(berg_count)
+                                                        dx_berg.append(x_val)
+                                                        dy_berg.append(y_val)
+                                                        width.append(np.sqrt(element_area))
+                else:
+                        for j in range(M):
+                                #for i in range(M):
+                                #x_val=x_start+(2*i*Radius)  ; y_val=y_start
+                                y_val=y_start+(2*j*Radius)  ;# x_val=x_start + (np.sqrt(3)*Radius*i)
+                                if check_if_it_is_in_domain(x_val,y_val,X_min,X_max,Y_min,Y_max,R_earth,lat_init,adjust_lat_ref,dx,dy):
+                                        #if True:
+                                        #R_val=np.sqrt(((x_val-x0)**2) +((y_val-y0)**2))
+                                        if check_if_it_is_ice(x_val,y_val,ice_mask,dx):
+                                                #Don't allow points closer than R from the boundary (these are sorted out later)
+                                                #if abs(y_val-Ly)<Radius or  ((abs(x_val-Lx)<((2/np.sqrt(3))*Radius)) and element_type=='hexagon') or ((abs(x_val-Lx)<Radius) and element_type=='square'):
+                                                berg_count=berg_count+1
+                                                iceberg_num.append(berg_count)
+                                                dx_berg.append(x_val)
+                                                dy_berg.append(y_val)
+                                                width.append(np.sqrt(element_area))
 
                                                
 	#print 'dx_berg',dx_berg
@@ -927,6 +942,10 @@ def Create_icebergs(lon_init,lat_init,Radius,R_earth, x, y,ice_mask,h_ice,Conver
 			dx=dx*Scale_up ;dy=dy*Scale_up
 		x=(x-np.min(x))+(dx/2) ; y=(y-np.min(y))+(dy/2)
 		lon=dx_berg  ; lat=dy_berg
+
+        if grounding_test:
+                for i in range(Number_of_bergs):
+                        lat[i]=lat[i]-0.0 #500.0
 	
 	#Note that static_berg calculations used to be here, after the conversion. I have moved them. I hope that this does not affect answers.
                         
@@ -1710,6 +1729,7 @@ def main(args):
 	Weddell_ice_geometry_filename=args.Weddell_ice_geometry_filename
 	Generic_ice_geometry_filename=args.Generic_ice_geometry_filename
         collision_test=args.collision_test
+        grounding_test=args.grounding_test
 
 	#Parameters
 	Radius=args.Radius
@@ -1786,7 +1806,7 @@ def main(args):
 	(Number_of_bergs,lon,lat,iceberg_num,dx_berg, dy_berg,thickness,mass,width,x,y,Radius,static_berg,N_bergs_before_bd)= Create_icebergs(lon_init,lat_init,\
 			Radius,R_earth, x, y,ice_mask,h_ice,Convert_to_lat_lon,rho_ice,element_type,scale_the_grid_to_lat_lon,lat_ref,adjust_lat_ref,\
 			Interpolate_from_four_corners,Fill_in_the_boundaries, set_all_bergs_static_by_default,break_some_bonds,Remove_stationary_bergs,\
-                        set_some_bergs_static_by_default,collision_test)
+                        set_some_bergs_static_by_default,collision_test,grounding_test)
 
 	print 'Maximum thickness:', np.max(thickness), np.min(thickness)
 	#Define the positions of the iceberg bonds
diff --git a/tests/chaotic_test/input.nml b/tests/chaotic_test/input.nml
index 8c8d433..d01278d 100644
--- a/tests/chaotic_test/input.nml
+++ b/tests/chaotic_test/input.nml
@@ -92,11 +92,13 @@
     input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
     use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
     max_bonds=6 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.false. !(F) True reduces side drag for bonded bergs in momentum eqn.    
 
     verbose=.true. !(F) Be verbose to stderr
     verbose_hrs=24 ! (24) Period between verbose messages
     traj_sample_hrs=24 !.5 !1 !(24) sampling period for trajectory storage
     traj_write_hrs=24 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.true.
     budget=.true. !(T) Calculate budgets
     debug=.false. !(F) Turn on debugging
     really_debug=.false. !(F) Turn on debugging
@@ -157,4 +159,4 @@
        clock_grain='MODULE' !'ROUTINE'
        domains_stack_size = 200000
        clock_flags='SYNC'
-/
\ No newline at end of file
+/
diff --git a/tests/collision_test_mts/input.nml b/tests/collision_test_mts/input.nml
index bef4ec7..299ab50 100644
--- a/tests/collision_test_mts/input.nml
+++ b/tests/collision_test_mts/input.nml
@@ -1,3 +1,5 @@
+!chksum different than below after setting uvel0=u_star at start of accel_mts for bergs%MTS_part==1
+
 !TARGET CHKSUM (1 hr time increments, MTS w/ 20 sub-steps, contact at 1.5e3 m, contact spring 1.e-7, spring_coef 1.0e-5):
 !Total number of bonds is:           52
 !KID, bergs_chksum: write_restart berg chksum = -1984749888 chksum2= 2128479089 chksum3= 609798238  chksum4= 609798238  chksum5= 0            #= 16
@@ -25,11 +27,13 @@
 &icebergs_nml
 
     !defaults given in parentheses:
+    new_mts=.false.
     mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
     mts_sub_steps=20 !1 !30 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
     contact_distance=1.5e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
     contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
     debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    remove_unused_bergs=.false. !(T) remove unneeded bergs after PEs transfers
 
     halo=3 !(4) halo width
     Lx=20000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
@@ -92,6 +96,7 @@
     input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
     use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
     max_bonds=6 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.false. !(F) True reduces side drag for bonded bergs in momentum eqn.
 
     verbose=.true. !(F) Be verbose to stderr
     verbose_hrs=24 ! (24) Period between verbose messages
diff --git a/tests/energy_test/.gitignore b/tests/energy_test/.gitignore
new file mode 100644
index 0000000..68bcbc9
--- /dev/null
+++ b/tests/energy_test/.gitignore
@@ -0,0 +1 @@
+results/
\ No newline at end of file
diff --git a/tests/energy_test/README b/tests/energy_test/README
new file mode 100644
index 0000000..b95ec8e
--- /dev/null
+++ b/tests/energy_test/README
@@ -0,0 +1,7 @@
+A simple test for momentum and energy conservation. In ./makeberg, a conglomerate berg with 60 (./makeberg/RUN) or 2 (./makeberg/RUN2) elements can be initialized. The right half of each conglomerate of elements has an initial x-velocity of 0.2, while all other element velocities are zero.
+
+1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
+2.(optional) edit input.nml
+3. run the model: ./RUN
+4, animate the results: animate_trajectories.py
+
diff --git a/tests/energy_test/RUN b/tests/energy_test/RUN
new file mode 100755
index 0000000..f881323
--- /dev/null
+++ b/tests/energy_test/RUN
@@ -0,0 +1,7 @@
+rm iceberg_trajectories.nc
+rm iceberg_trajectories.nc.*
+rm bond_trajectories.nc
+rm bond_trajectories.nc.*
+srun -n9 ./../../build/bergs.x
+
+
diff --git a/tests/energy_test/animate_trajectories.py b/tests/energy_test/animate_trajectories.py
new file mode 100755
index 0000000..8b9aa7d
--- /dev/null
+++ b/tests/energy_test/animate_trajectories.py
@@ -0,0 +1,121 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+import matplotlib.pyplot as plt
+from matplotlib.animation import FuncAnimation
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
+                    help=''' provide filename to plot''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+
+
+def main(args):
+
+    print('reading file')
+
+    filename=args.fname
+    #filename = 'iceberg_trajectories.nc'
+    field = 'lon'
+    field2 = 'lat'
+
+    with nc.Dataset(filename) as file:
+        x = file.variables['lon'][:]/1.e3
+        y = file.variables['lat'][:]/1.e3
+        day = file.variables['day'][:]
+
+    ud = np.unique(day)
+    t = ud[0]
+
+    # frame info
+    num_frames = len(ud)
+    movie_len = 10.0 #seconds
+    frame_len = 1000.0*movie_len/num_frames
+
+    xmin = 0
+    xmax = 30
+    ymin = xmin
+    ymax = xmax
+
+    anim_running = True
+
+    def animate(i):
+
+        x1 = x[day == ud[i]]
+        y1 = y[day == ud[i]]
+        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
+
+        scat.set_offsets(data)
+
+        t = ud[i]
+        time_text.set_text('time = %.1f days' % t )
+        return scat,time_text
+
+    def init():
+        scat.set_offsets([])
+        return scat,
+
+    def onClick(event):
+        global anim_running
+        if anim_running:
+            ani.event_source.stop()
+            anim_running = False
+        else:
+            ani.event_source.start()
+            anim_running = True
+
+    # Now we can do the plotting!
+    f = plt.figure(figsize=(5,5))
+    f.tight_layout()
+    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
+    scat = ax1.scatter([],[],marker='o',facecolor='w',s=50,edgecolor='red')
+    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
+
+    # Change major ticks to show every 20.
+    ax1.xaxis.set_major_locator(MultipleLocator(5))
+    ax1.yaxis.set_major_locator(MultipleLocator(5))
+
+    ax1.xaxis.set_minor_locator(MultipleLocator(1))
+    ax1.yaxis.set_minor_locator(MultipleLocator(1))
+
+    # Turn grid on for both major and minor ticks and style minor slightly
+    # differently.
+    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
+    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
+
+    ax1.set_xlabel('x (km)')
+    ax1.set_ylabel('y (km)')
+    ax1.set_title('Iceberg trajectory')
+
+    f.canvas.mpl_connect('button_press_event', onClick)
+
+    ani = FuncAnimation(
+        f,animate,init_func=init,frames=num_frames,
+        interval=frame_len,blit=True,repeat=True)
+
+    print('time',t)
+
+    plt.show()
+    #animation.save("iceberg_traj_animation.mp4")
+
+
+print('Script complete')
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
diff --git a/tests/energy_test/animate_trajectories_1pe.py b/tests/energy_test/animate_trajectories_1pe.py
new file mode 100755
index 0000000..beee932
--- /dev/null
+++ b/tests/energy_test/animate_trajectories_1pe.py
@@ -0,0 +1,180 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+import matplotlib.pyplot as plt
+from matplotlib.animation import FuncAnimation
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc.0000',
+                    help=''' provide filename to plot''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+
+
+def main(args):
+
+    print('reading file')
+
+    filename=args.fname
+    #filename = 'iceberg_trajectories.nc'
+    field = 'lon'
+    field2 = 'lat'
+
+    with nc.Dataset(filename) as file:
+        x = file.variables['lon'][:]/1.e3
+        y = file.variables['lat'][:]/1.e3
+        day = file.variables['day'][:]
+        hs = file.variables['halo_berg'][:]
+        #hs = file.variables['n_bonds'][:]        
+
+    #hs = hs+1
+    ud = np.unique(day)
+    t = ud[0]
+
+    print('unique hs',np.unique(hs))
+
+    # frame info
+    num_frames = len(ud)
+    movie_len = 10.0 #seconds
+    frame_len = 1000.0*movie_len/num_frames
+
+    xmin = np.floor(min(min(x),min(y),-5))
+    xmax = np.ceil(max(max(x),max(y),35))
+    ymin = xmin
+    ymax = xmax
+
+    anim_running = True
+
+    def animate(i):
+
+        x1 = x[day == ud[i]]
+        y1 = y[day == ud[i]]
+        hstat = hs[day == ud[i]]
+        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
+
+        cstring=[]
+        for j in range(len(hstat)):
+            if (hstat[j]<0):
+                cstring.append("m")
+            elif (hstat[j]==0):
+                cstring.append("b")
+            elif (hstat[j]==1):
+                cstring.append("r")
+            elif (hstat[j]==2):
+                cstring.append("g")
+            elif (hstat[j]==3):
+                cstring.append("k")
+            elif (hstat[j]==4):
+                cstring.append("c")
+            elif (hstat[j]==5):
+                cstring.append("y")
+            elif (hstat[j]==6):
+                cstring.append("w")
+            elif (hstat[j]==10):                
+                cstring.append("c")
+            # else:
+            #     cstring.append("y")
+
+        scat.set_offsets(data)
+        scat.set_color(cstring)
+        scat.set_edgecolor('k')
+
+        t = ud[i]
+        time_text.set_text('time = %.1f days' % t )
+        return scat,time_text
+
+    def init():
+        scat.set_offsets([])
+        return scat,
+
+    def onClick(event):
+        global anim_running
+        if anim_running:
+            ani.event_source.stop()
+            anim_running = False
+        else:
+            ani.event_source.start()
+            anim_running = True
+
+    # Now we can do the plotting!
+    f = plt.figure(figsize=(5,5))
+    f.tight_layout()
+    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
+    scat = ax1.scatter([],[],marker='o',s=60)
+    #scat = ax1.scatter([],[],marker='o',facecolor='w',s=60,edgecolor='red')
+    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
+
+    # Change major ticks to show every 20.
+    ax1.xaxis.set_major_locator(MultipleLocator(5))
+    ax1.yaxis.set_major_locator(MultipleLocator(5))
+
+    ax1.xaxis.set_minor_locator(MultipleLocator(1))
+    ax1.yaxis.set_minor_locator(MultipleLocator(1))
+
+    # Turn grid on for both major and minor ticks and style minor slightly
+    # differently.
+    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
+    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
+
+    ax1.set_xlabel('x (km)')
+    ax1.set_ylabel('y (km)')
+    ax1.set_title('Iceberg trajectory')
+
+    f.canvas.mpl_connect('button_press_event', onClick)
+
+    ani = FuncAnimation(
+        f,animate,init_func=init,frames=num_frames,
+        interval=frame_len,blit=True,repeat=True)
+
+    print('time',t)
+
+    plt.plot([0,0],[0,30],'k-',lw=1)
+    plt.plot([10,10],[0,30],'k-',lw=1)
+    plt.plot([20,20],[0,30],'k-',lw=1)
+    plt.plot([30,30],[0,30],'k-',lw=1)
+    plt.plot([0,30],[0,0],'k-',lw=1)
+    plt.plot([0,30],[10,10],'k-',lw=1)
+    plt.plot([0,30],[20,20],'k-',lw=1)
+    plt.plot([0,30],[30,30],'k-',lw=1)
+
+    plt.plot([-2,-2],[-2,33],'b:',lw=1)
+    plt.plot([3,3],[-2,33],'b:',lw=1)
+    plt.plot([8,8],[-2,33],'b:',lw=1)
+    plt.plot([13,13],[-2,33],'b:',lw=1)
+    plt.plot([18,18],[-2,33],'b:',lw=1)
+    plt.plot([23,23],[-2,33],'b:',lw=1)
+    plt.plot([28,28],[-2,33],'b:',lw=1)
+    plt.plot([33,33],[-2,33],'b:',lw=1)    
+
+    plt.plot([-2,33],[-2,-2],'b:',lw=1)
+    plt.plot([-2,33],[3,3],'b:',lw=1)
+    plt.plot([-2,33],[8,8],'b:',lw=1)
+    plt.plot([-2,33],[13,13],'b:',lw=1)
+    plt.plot([-2,33],[18,18],'b:',lw=1)
+    plt.plot([-2,33],[23,23],'b:',lw=1)
+    plt.plot([-2,33],[28,28],'b:',lw=1)
+    plt.plot([-2,33],[33,33],'b:',lw=1)
+
+    plt.show()
+    #animation.save("iceberg_traj_animation.mp4")
+
+
+print('Script complete')
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
diff --git a/tests/energy_test/diag_table b/tests/energy_test/diag_table
new file mode 100644
index 0000000..c1c8819
--- /dev/null
+++ b/tests/energy_test/diag_table
@@ -0,0 +1,3 @@
+"icebergs test"
+1 1 1 0 0 0
+
diff --git a/tests/energy_test/input.nml b/tests/energy_test/input.nml
new file mode 100644
index 0000000..0b04c03
--- /dev/null
+++ b/tests/energy_test/input.nml
@@ -0,0 +1,177 @@
+!For the 60 element test:
+!KID, bergs_chksum: write_restart berg chksum=            1143158595 chksum2=           -1591676389 chksum3=            1858541605 chksum4=            1858541605 chksum5=                     0 #=                    60
+!KID, grd_chksum2:    # of bergs/cell chksum=                     0 chksum2=                     0 min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
+!Total number of bonds is:          298 
+
+
+
+&icebergs_driver_nml
+  ni=45 !30 !number of elements, x direction
+  nj=45 !30 !number of elements, y direction
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=999999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.true.
+  collision_test=.false.
+  grounding_test=.false.
+  bump_depth=9999.0 !(m) depth of top of gaussian bump below sea level 
+/
+
+&icebergs_nml
+
+    !defaults given in parentheses:
+    monitor_energy=.true. !(F)
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=10 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
+
+    contact_distance=1.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7 !!5.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=3.16e6 !friction drag param
+    h_to_init_grounding=200.0
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='strain' !('none') 'strain_rate','strain',or 'none'
+    !frac_thres_n = 0.018
+    !frac_thres_t = 0.05076
+
+    halo=3 !(4) halo width
+    Lx=45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    rho_bergs=850. ! (850) iceberg density
+    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.0!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=1.0 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true.!.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.true. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=24000 ! (24) Period between verbose messages
+    traj_sample_hrs=0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false.!.true. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.!(F) Init bond b/w bergs if dist<1.25*radius
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/energy_test/makeberg/README b/tests/energy_test/makeberg/README
new file mode 100644
index 0000000..4d7f3fe
--- /dev/null
+++ b/tests/energy_test/makeberg/README
@@ -0,0 +1,4 @@
+RUN makes a conglomerate berg with 60 elements
+RUN2 makes a conglomerate berg with 2 elements
+
+For both conglomerate, the right half of the particles are initialized with an x-velocity>0, which the left half has x-velocity=0. All y-velocity is zero.
\ No newline at end of file
diff --git a/tests/energy_test/makeberg/RUN b/tests/energy_test/makeberg/RUN
new file mode 100755
index 0000000..520d671
--- /dev/null
+++ b/tests/energy_test/makeberg/RUN
@@ -0,0 +1,3 @@
+rm ./output_files/Generic*
+./makeberg.py
+cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
diff --git a/tests/energy_test/makeberg/RUN2 b/tests/energy_test/makeberg/RUN2
new file mode 100755
index 0000000..0a6834e
--- /dev/null
+++ b/tests/energy_test/makeberg/RUN2
@@ -0,0 +1,3 @@
+rm ./output_files/Generic*
+./makeberg2.py
+cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
diff --git a/tests/energy_test/makeberg/makeberg.py b/tests/energy_test/makeberg/makeberg.py
new file mode 100755
index 0000000..4ef99eb
--- /dev/null
+++ b/tests/energy_test/makeberg/makeberg.py
@@ -0,0 +1,374 @@
+#!/usr/bin/env python
+import numpy as np
+import math
+from netCDF4 import Dataset
+from pylab import *
+#import pdb
+import netCDF4 as nc
+
+#
+# Initialize 2 iceberg elements, which can later be bonded in the fortran code if needed
+#
+
+def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
+
+	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
+	# To copy the global attributes of the netCDF file
+
+	#Input and output files
+	#Create Empty restart file. This is later read so that the attributes can be used.
+	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
+	create_empty_iceberg_restart_file(Empty_restart_filename)
+	#Empty_restart_filename='input_files/icebergs.res.nc'
+
+	#Read empty restart file
+	f=Dataset(Empty_restart_filename,'r') # r is for read only
+	#Write a new restart file
+	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
+
+	for attname in f.ncattrs():
+		    setattr(g,attname,getattr(f,attname))
+
+
+	# To copy the dimension of the netCDF file
+	for dimname,dim in f.dimensions.iteritems():
+		# if you want to make changes in the dimensions of the new file
+		# you should add your own conditions here before the creation of the dimension.
+		#g.createDimension(dimname,len(dim))
+		g.createDimension(dimname,Number_of_bergs)
+
+	# To copy the variables of the netCDF file
+
+	for varname,ncvar in f.variables.iteritems():
+		# if you want to make changes in the variables of the new file
+		# you should add your own conditions here before the creation of the variable.
+		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
+		#Proceed to copy the variable attributes
+		for attname in ncvar.ncattrs():
+			setattr(var,attname,getattr(ncvar,attname))
+		#Finally copy the variable data to the new created variable
+		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
+
+		if varname=='i':
+			var[:]=Number_of_bergs
+
+		if varname=='iceberg_num':
+			for j in range(Number_of_bergs):
+				#var[j]=j+1
+				var[j]=iceberg_num[j]
+
+		if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
+		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
+		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
+		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
+			var[:]=0
+
+                if varname=='uvel':
+                        var[:]=uvel
+
+                if varname=='vvel':
+                        var[:]=vvel
+
+		if varname=='mass_scaling':
+			var[:]=mass_scaling
+
+		if varname=='thickness':
+			for j in range(Number_of_bergs):
+				var[j]=thickness[j]
+
+		if varname=='mass':
+			for j in range(Number_of_bergs):
+				var[j]=mass[j]
+
+		if varname=='width'  or varname=='length':
+			for j in range(Number_of_bergs):
+				var[j]=width[j]
+
+		if varname=='lon':
+			for j in range(Number_of_bergs):
+				var[j]=lon[j]
+
+		if varname=='lat':
+			for j in range(Number_of_bergs):
+				var[j]=lat[j]
+
+		if varname=='static_berg':
+			for j in range(Number_of_bergs):
+				var[j]=static_berg[j]
+
+
+	f.close()
+	g.close()
+
+
+def create_empty_iceberg_restart_file(Empty_restart_filename):
+
+	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
+
+	i=f.createDimension('i', None)
+	lon=f.createVariable('i','i')
+
+	lon=f.createVariable('lon','d',('i'))
+	lon.long_name = "longitude" ;
+	lon.units = "degrees_E" ;
+	lon.checksum = "               0" ;
+
+	lat=f.createVariable('lat','d',('i'))
+	lat.long_name = "latitude" ;
+	lat.units = "degrees_N" ;
+	lat.checksum = "               0" ;
+
+	uvel=f.createVariable('uvel','d',('i'))
+	uvel.long_name = "zonal velocity" ;
+	uvel.units = "m/s" ;
+	uvel.checksum = "               0" ;
+
+	vvel=f.createVariable('vvel','d',('i'))
+	vvel.long_name = "meridional velocity" ;
+	vvel.units = "m/s" ;
+	vvel.checksum = "               0" ;
+
+	mass=f.createVariable('mass','d',('i'))
+	mass.long_name = "mass" ;
+	mass.units = "kg" ;
+	mass.checksum = "               0" ;
+
+	axn=f.createVariable('axn','d',('i'))
+	axn.long_name = "explicit zonal acceleration" ;
+	axn.units = "m/s^2" ;
+	axn.checksum = "               0" ;
+
+	ayn=f.createVariable('ayn','d',('i'))
+	ayn.long_name = "explicit meridional acceleration" ;
+	ayn.units = "m/s^2" ;
+	ayn.checksum = "               0" ;
+
+	bxn=f.createVariable('bxn','d',('i'))
+	bxn.long_name = "inplicit zonal acceleration" ;
+	bxn.units = "m/s^2" ;
+	bxn.checksum = "               0" ;
+
+	byn=f.createVariable('byn','d',('i'))
+	byn.long_name = "implicit meridional acceleration" ;
+	byn.units = "m/s^2" ;
+	byn.checksum = "               0" ;
+
+	ine=f.createVariable('ine','i',('i'))
+	ine.long_name = "i index" ;
+	ine.units = "none" ;
+	ine.packing = 0 ;
+	ine.checksum = "               0" ;
+
+	jne=f.createVariable('jne','i',('i'))
+	jne.long_name = "j index" ;
+	jne.units = "none" ;
+	jne.packing = 0 ;
+	jne.checksum = "               0" ;
+
+	thickness=f.createVariable('thickness','d',('i'))
+	thickness.long_name = "thickness" ;
+	thickness.units = "m" ;
+	thickness.checksum = "               0" ;
+
+	width=f.createVariable('width','d',('i'))
+	width.long_name = "width" ;
+	width.units = "m" ;
+	width.checksum = "               0" ;
+
+	length=f.createVariable('length','d',('i'))
+	length.long_name = "length" ;
+	length.units = "m" ;
+	length.checksum = "               0" ;
+
+	start_lon=f.createVariable('start_lon','d',('i'))
+	start_lon.long_name = "longitude of calving location" ;
+	start_lon.units = "degrees_E" ;
+	start_lon.checksum = "               0" ;
+
+	start_lat=f.createVariable('start_lat','d',('i'))
+	start_lat.long_name = "latitude of calving location" ;
+	start_lat.units = "degrees_N" ;
+	start_lat.checksum = "               0" ;
+
+	start_year=f.createVariable('start_year','i',('i'))
+	start_year.long_name = "calendar year of calving event" ;
+	start_year.units = "years" ;
+	start_year.packing = 0 ;
+	start_year.checksum = "               0" ;
+
+	iceberg_num=f.createVariable('iceberg_num','i',('i'))
+	iceberg_num.long_name = "identification of the iceberg" ;
+	iceberg_num.units = "dimensionless" ;
+	iceberg_num.packing = 0 ;
+	iceberg_num.checksum = "               0" ;
+
+	start_day=f.createVariable('start_day','d',('i'))
+	start_day.long_name = "year day of calving event" ;
+	start_day.units = "days" ;
+	start_day.checksum = "               0" ;
+
+	start_mass=f.createVariable('start_mass','d',('i'))
+	start_mass.long_name = "initial mass of calving berg" ;
+	start_mass.units = "kg" ;
+	start_mass.checksum = "               0" ;
+
+	mass_scaling=f.createVariable('mass_scaling','d',('i'))
+	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
+	mass_scaling.units = "none" ;
+	mass_scaling.checksum = "               0" ;
+
+	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
+	mass_of_bits.long_name = "mass of bergy bits" ;
+	mass_of_bits.units = "kg" ;
+	mass_of_bits.checksum = "               0" ;
+
+	heat_density=f.createVariable('heat_density','d',('i'))
+	heat_density.long_name = "heat density" ;
+	heat_density.units = "J/kg" ;
+	heat_density.checksum = "               0" ;
+
+	halo_berg=f.createVariable('halo_berg','d',('i'))
+	halo_berg.long_name = "halo_berg" ;
+	halo_berg.units = "dimensionless" ;
+	halo_berg.checksum = "               0" ;
+
+	static_berg=f.createVariable('static_berg','d',('i'))
+	static_berg.long_name = "static_berg" ;
+	static_berg.units = "dimensionless" ;
+	static_berg.checksum = "               0" ;
+
+	f.sync()
+	f.close()
+
+
+
+#-----------------------------------#
+#               Main                #
+#-----------------------------------#
+
+just2particles=False
+flip2ndconglom=False
+offset2ndconglom=False
+
+grdxmin=0; grdxmax=45000e3
+grdymin=0; grdymax=45000e3
+grdres=1000.0
+R_frac=0.45
+radius=(np.sqrt(3)/2.)*(R_frac*grdres) #S is < 0.5 grid res
+element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*radius**2)
+width=np.sqrt(element_area)
+thickness1=300.0
+thickness2=300.0
+rho_ice=850.0
+
+
+nbergs=1 #number of conglomerates
+
+#center coords of each (rectangular) conglomerate berg (CB=conglomerate berg)
+CBxc=np.array([8000]); CByc=np.array([15000])
+
+
+#side lengths
+CBxl=np.array([4000]); CByl=np.array([8000])
+
+CByl=CByl.astype(int); CBxl=CBxl.astype(int)
+
+#--- xmax, xmin, ymax, ymin for each CB --
+CBxmin=CBxc-(0.5*CBxl); CBxmax=CBxc+(0.5*CBxl)
+CBymin=CByc-(0.5*CByl); CBymax=CByc+(0.5*CByl)
+#this shouldn't happen:
+CBxmin[CBxmin<grdxmin]=grdxmin; CBxmax[CBxmax>grdxmax]=grdxmax
+CBymin[CBxmin<grdymin]=grdymin; CBymax[CBymax>grdymax]=grdymax
+CBxc=0.5*(CBxmin+CBxmax); CByc=0.5*(CBymin+CBymax)
+
+#if just want one particle per CB
+if just2particles:
+        CBxmin=CBxc; CBxmax=CBxc
+        CBymin=CByc; CBymax=CByc
+
+#--- min and max thicknesses for each CB ---
+h1=thickness1; h2=thickness2
+CBhmax=np.array([h1]); CBhmin=np.array([h2])
+
+#radii
+CBrad=np.array([radius])
+
+berg_x=[]; berg_y=[]
+berg_id=[]; berg_static=[]
+berg_width=[]; berg_bonds=[]
+berg_h=[]; berg_mass_scaling=[]
+berg_mass=[]
+berg_uvel=[]; berg_vvel=[]
+
+berg_count=0
+
+for i in range(nbergs):
+
+        x_start=CBxmin[i]+(CBrad[i]*2./np.sqrt(3))
+
+        if flip2ndconglom and i>0:
+                x_start=CBxmax[i]-(CBrad[i]*2./np.sqrt(3))
+
+        #pdb.set_trace()
+        if x_start>CBxmax[i]:
+                x_start=CBxmax[i]
+        y_start0=CBymin[i]+CBrad[i]
+        if y_start0>CBymax[i]:
+                y_start0=CBymax[i]
+        element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*(CBrad[i])**2)
+        #H (thickness) is a linear function of a berg element's position from the
+        #center of the CB. H=Hmax at the center of the CB and H=Hmin at a corner of the
+        #CB, where the dist of a corner from the center is:
+        cdistb=np.sqrt((CBxmin[i]-CBxc[i])**2+(CBymin[i]-CByc[i])**2)
+        j=0
+        x_val=x_start
+        offset=0.0
+        if (i==0):
+                uvel=0.
+        else:
+                uvel=0.
+                if (offset2ndconglom):
+                        offset=250.0
+        vvel=0
+        #berg_count_start=berg_count
+        while x_val<=CBxmax[i] and x_val>=CBxmin[i]:
+                y_start=y_start0+((j%2)*CBrad[i])+offset
+                k=0
+                y_val=y_start
+                while y_val<=(CBymax[i]+offset):
+                        berg_count=berg_count+1
+                        berg_id.append(berg_count)
+                        berg_x.append(x_val)
+                        berg_y.append(y_val)
+                        berg_width.append(sqrt(element_area))
+                        #dist of berg elem from center of CB
+                        bdistc=np.sqrt((x_val-CBxc[i])**2+(y_val-CByc[i])**2)
+                        bh=CBhmin[i]*bdistc/cdistb + CBhmax[i]*(1-bdistc/cdistb)
+                        if (just2particles):
+                                bh=h1
+                        berg_h.append(bh) #thickness
+                        berg_mass_scaling.append(1)
+                        berg_mass.append(bh*rho_ice*element_area)
+                        berg_static.append(0)
+                        #berg_uvel.append(uvel)
+                        berg_vvel.append(vvel)
+                        if (x_val>8000):
+                                berg_uvel.append(0.2)
+                        else:
+                                berg_uvel.append(uvel)
+
+                        k=k+1
+                        y_val=y_start+(2*k*CBrad[i])
+                j=j+1
+                if flip2ndconglom and i>0:
+                        x_val=x_start-(np.sqrt(3)*CBrad[i]*j)
+                else:
+                        x_val=x_start+(np.sqrt(3)*CBrad[i]*j)
+
+print('Number of bergs',berg_count)
+
+#pdb.set_trace()
+
+#Create iceberg restart file
+Ice_geometry_source='Generic'
+Create_iceberg_restart_file(berg_count,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)
diff --git a/tests/energy_test/makeberg/makeberg2.py b/tests/energy_test/makeberg/makeberg2.py
new file mode 100755
index 0000000..635a5b7
--- /dev/null
+++ b/tests/energy_test/makeberg/makeberg2.py
@@ -0,0 +1,276 @@
+#!/usr/bin/env python
+import numpy as np
+import math
+from netCDF4 import Dataset
+from pylab import *
+#import pdb
+import netCDF4 as nc
+
+#
+# Initialize 2 iceberg elements, which can later be bonded in the fortran code if needed
+#
+
+def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
+
+	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
+	# To copy the global attributes of the netCDF file
+
+	#Input and output files
+	#Create Empty restart file. This is later read so that the attributes can be used.
+	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
+	create_empty_iceberg_restart_file(Empty_restart_filename)
+	#Empty_restart_filename='input_files/icebergs.res.nc'
+
+	#Read empty restart file
+	f=Dataset(Empty_restart_filename,'r') # r is for read only
+	#Write a new restart file
+	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
+
+	for attname in f.ncattrs():
+		    setattr(g,attname,getattr(f,attname))
+
+
+	# To copy the dimension of the netCDF file
+	for dimname,dim in f.dimensions.iteritems():
+		# if you want to make changes in the dimensions of the new file
+		# you should add your own conditions here before the creation of the dimension.
+		#g.createDimension(dimname,len(dim))
+		g.createDimension(dimname,Number_of_bergs)
+
+	# To copy the variables of the netCDF file
+
+	for varname,ncvar in f.variables.iteritems():
+		# if you want to make changes in the variables of the new file
+		# you should add your own conditions here before the creation of the variable.
+		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
+		#Proceed to copy the variable attributes
+		for attname in ncvar.ncattrs():
+			setattr(var,attname,getattr(ncvar,attname))
+		#Finally copy the variable data to the new created variable
+		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
+
+		if varname=='i':
+			var[:]=Number_of_bergs
+
+		if varname=='iceberg_num':
+			for j in range(Number_of_bergs):
+				#var[j]=j+1
+				var[j]=iceberg_num[j]
+
+		if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
+		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
+		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
+		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
+			var[:]=0
+
+                if varname=='uvel':
+                        var[:]=uvel
+
+                if varname=='vvel':
+                        var[:]=vvel
+
+		if varname=='mass_scaling':
+			var[:]=mass_scaling
+
+		if varname=='thickness':
+			for j in range(Number_of_bergs):
+				var[j]=thickness[j]
+
+		if varname=='mass':
+			for j in range(Number_of_bergs):
+				var[j]=mass[j]
+
+		if varname=='width'  or varname=='length':
+			for j in range(Number_of_bergs):
+				var[j]=width[j]
+
+		if varname=='lon':
+			for j in range(Number_of_bergs):
+				var[j]=lon[j]
+
+		if varname=='lat':
+			for j in range(Number_of_bergs):
+				var[j]=lat[j]
+
+		if varname=='static_berg':
+			for j in range(Number_of_bergs):
+				var[j]=static_berg[j]
+
+
+	f.close()
+	g.close()
+
+
+def create_empty_iceberg_restart_file(Empty_restart_filename):
+
+	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
+
+	i=f.createDimension('i', None)
+	lon=f.createVariable('i','i')
+
+	lon=f.createVariable('lon','d',('i'))
+	lon.long_name = "longitude" ;
+	lon.units = "degrees_E" ;
+	lon.checksum = "               0" ;
+
+	lat=f.createVariable('lat','d',('i'))
+	lat.long_name = "latitude" ;
+	lat.units = "degrees_N" ;
+	lat.checksum = "               0" ;
+
+	uvel=f.createVariable('uvel','d',('i'))
+	uvel.long_name = "zonal velocity" ;
+	uvel.units = "m/s" ;
+	uvel.checksum = "               0" ;
+
+	vvel=f.createVariable('vvel','d',('i'))
+	vvel.long_name = "meridional velocity" ;
+	vvel.units = "m/s" ;
+	vvel.checksum = "               0" ;
+
+	mass=f.createVariable('mass','d',('i'))
+	mass.long_name = "mass" ;
+	mass.units = "kg" ;
+	mass.checksum = "               0" ;
+
+	axn=f.createVariable('axn','d',('i'))
+	axn.long_name = "explicit zonal acceleration" ;
+	axn.units = "m/s^2" ;
+	axn.checksum = "               0" ;
+
+	ayn=f.createVariable('ayn','d',('i'))
+	ayn.long_name = "explicit meridional acceleration" ;
+	ayn.units = "m/s^2" ;
+	ayn.checksum = "               0" ;
+
+	bxn=f.createVariable('bxn','d',('i'))
+	bxn.long_name = "inplicit zonal acceleration" ;
+	bxn.units = "m/s^2" ;
+	bxn.checksum = "               0" ;
+
+	byn=f.createVariable('byn','d',('i'))
+	byn.long_name = "implicit meridional acceleration" ;
+	byn.units = "m/s^2" ;
+	byn.checksum = "               0" ;
+
+	ine=f.createVariable('ine','i',('i'))
+	ine.long_name = "i index" ;
+	ine.units = "none" ;
+	ine.packing = 0 ;
+	ine.checksum = "               0" ;
+
+	jne=f.createVariable('jne','i',('i'))
+	jne.long_name = "j index" ;
+	jne.units = "none" ;
+	jne.packing = 0 ;
+	jne.checksum = "               0" ;
+
+	thickness=f.createVariable('thickness','d',('i'))
+	thickness.long_name = "thickness" ;
+	thickness.units = "m" ;
+	thickness.checksum = "               0" ;
+
+	width=f.createVariable('width','d',('i'))
+	width.long_name = "width" ;
+	width.units = "m" ;
+	width.checksum = "               0" ;
+
+	length=f.createVariable('length','d',('i'))
+	length.long_name = "length" ;
+	length.units = "m" ;
+	length.checksum = "               0" ;
+
+	start_lon=f.createVariable('start_lon','d',('i'))
+	start_lon.long_name = "longitude of calving location" ;
+	start_lon.units = "degrees_E" ;
+	start_lon.checksum = "               0" ;
+
+	start_lat=f.createVariable('start_lat','d',('i'))
+	start_lat.long_name = "latitude of calving location" ;
+	start_lat.units = "degrees_N" ;
+	start_lat.checksum = "               0" ;
+
+	start_year=f.createVariable('start_year','i',('i'))
+	start_year.long_name = "calendar year of calving event" ;
+	start_year.units = "years" ;
+	start_year.packing = 0 ;
+	start_year.checksum = "               0" ;
+
+	iceberg_num=f.createVariable('iceberg_num','i',('i'))
+	iceberg_num.long_name = "identification of the iceberg" ;
+	iceberg_num.units = "dimensionless" ;
+	iceberg_num.packing = 0 ;
+	iceberg_num.checksum = "               0" ;
+
+	start_day=f.createVariable('start_day','d',('i'))
+	start_day.long_name = "year day of calving event" ;
+	start_day.units = "days" ;
+	start_day.checksum = "               0" ;
+
+	start_mass=f.createVariable('start_mass','d',('i'))
+	start_mass.long_name = "initial mass of calving berg" ;
+	start_mass.units = "kg" ;
+	start_mass.checksum = "               0" ;
+
+	mass_scaling=f.createVariable('mass_scaling','d',('i'))
+	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
+	mass_scaling.units = "none" ;
+	mass_scaling.checksum = "               0" ;
+
+	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
+	mass_of_bits.long_name = "mass of bergy bits" ;
+	mass_of_bits.units = "kg" ;
+	mass_of_bits.checksum = "               0" ;
+
+	heat_density=f.createVariable('heat_density','d',('i'))
+	heat_density.long_name = "heat density" ;
+	heat_density.units = "J/kg" ;
+	heat_density.checksum = "               0" ;
+
+	halo_berg=f.createVariable('halo_berg','d',('i'))
+	halo_berg.long_name = "halo_berg" ;
+	halo_berg.units = "dimensionless" ;
+	halo_berg.checksum = "               0" ;
+
+	static_berg=f.createVariable('static_berg','d',('i'))
+	static_berg.long_name = "static_berg" ;
+	static_berg.units = "dimensionless" ;
+	static_berg.checksum = "               0" ;
+
+	f.sync()
+	f.close()
+
+
+
+#-----------------------------------#
+#               Main                #
+#-----------------------------------#
+
+grdres=1000.0
+xc=4500.0
+yc=15001.0
+R_frac=0.45
+radius=(np.sqrt(3)/2.)*(R_frac*grdres) #S is < 0.5 grid res
+element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*radius**2)
+width=np.sqrt(element_area)
+thickness=300.0
+rhoi=850.0
+mass=thickness*rhoi*element_area
+
+berg_count=2
+berg_x=[xc-radius,xc+radius]
+berg_y=[yc,yc]
+berg_h=[thickness,thickness]
+berg_width=[width,width]
+berg_mass=[mass,mass]
+berg_mass_scaling=[1,1]
+berg_id=[1,2]
+berg_static=[0,0]
+berg_uvel=[0,0.2]
+berg_vvel=[0,0]
+
+print('Number of bergs',berg_count)
+
+#Create iceberg restart file
+Ice_geometry_source='Generic'
+Create_iceberg_restart_file(berg_count,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)
diff --git a/tests/energy_test2/.gitignore b/tests/energy_test2/.gitignore
new file mode 100644
index 0000000..68bcbc9
--- /dev/null
+++ b/tests/energy_test2/.gitignore
@@ -0,0 +1 @@
+results/
\ No newline at end of file
diff --git a/tests/energy_test2/README b/tests/energy_test2/README
new file mode 100644
index 0000000..147e393
--- /dev/null
+++ b/tests/energy_test2/README
@@ -0,0 +1,20 @@
+Collision and (subsequent fracture?) of two conglomerate bergs. For testing a scheme where the MTS solution is iterated a given number of times in order to help conserve momentum conservation when collisions occur. Also for testing fracture scheme (e.g. effects of particle size, fracture thresholds, sensitivity to violation of momentum conservation).
+
+Iterative scheme options:
+Option 1: Set the number of iterations (>1) for each long/short step using imp_loop_iters_long and imp_loop_iters_short, respectively. Force_convergence must be set false. (this option uses subroutine evolve_icebergs_mts)
+Option 2: Set force_convergence to true and specify a convergence tolerance. Iterations will stop once convergence tolerance is reached. (this option, or if both imp_loop_iters==1, uses subroutine evolve_icebergs_mts2)
+
+Unlike in energy_test3, this test conserves momentum during collision even without the iterative scheme.
+
+1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
+2.(optional) edit input.nml
+3. run the model: ./RUN
+4, animate the results: animate_trajectories.py
+
+
+
+1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
+2.(optional) edit input.nml
+3. run the model: ./RUN
+4, animate the results: animate_trajectories.py
+
diff --git a/tests/energy_test2/RUN b/tests/energy_test2/RUN
new file mode 100755
index 0000000..f881323
--- /dev/null
+++ b/tests/energy_test2/RUN
@@ -0,0 +1,7 @@
+rm iceberg_trajectories.nc
+rm iceberg_trajectories.nc.*
+rm bond_trajectories.nc
+rm bond_trajectories.nc.*
+srun -n9 ./../../build/bergs.x
+
+
diff --git a/tests/energy_test2/animate_trajectories.py b/tests/energy_test2/animate_trajectories.py
new file mode 100755
index 0000000..dacd0ca
--- /dev/null
+++ b/tests/energy_test2/animate_trajectories.py
@@ -0,0 +1,121 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+import matplotlib.pyplot as plt
+from matplotlib.animation import FuncAnimation
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
+                    help=''' provide filename to plot''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+
+
+def main(args):
+
+    print('reading file')
+
+    filename=args.fname
+    #filename = 'iceberg_trajectories.nc'
+    field = 'lon'
+    field2 = 'lat'
+
+    with nc.Dataset(filename) as file:
+        x = file.variables['lon'][:]/1.e3
+        y = file.variables['lat'][:]/1.e3
+        day = file.variables['day'][:]
+
+    ud = np.unique(day)
+    t = ud[0]
+
+    # frame info
+    num_frames = len(ud)
+    movie_len = 10.0 #seconds
+    frame_len = 1000.0*movie_len/num_frames
+
+    xmin = 0
+    xmax = 30
+    ymin = 7.5
+    ymax = 37.5
+
+    anim_running = True
+
+    def animate(i):
+
+        x1 = x[day == ud[i]]
+        y1 = y[day == ud[i]]
+        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
+
+        scat.set_offsets(data)
+
+        t = ud[i]
+        time_text.set_text('time = %.1f days' % t )
+        return scat,time_text
+
+    def init():
+        scat.set_offsets([])
+        return scat,
+
+    def onClick(event):
+        global anim_running
+        if anim_running:
+            ani.event_source.stop()
+            anim_running = False
+        else:
+            ani.event_source.start()
+            anim_running = True
+
+    # Now we can do the plotting!
+    f = plt.figure(figsize=(5,5))
+    f.tight_layout()
+    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
+    scat = ax1.scatter([],[],marker='o',facecolor='w',s=50,edgecolor='red')
+    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
+
+    # Change major ticks to show every 20.
+    ax1.xaxis.set_major_locator(MultipleLocator(5))
+    ax1.yaxis.set_major_locator(MultipleLocator(5))
+
+    ax1.xaxis.set_minor_locator(MultipleLocator(1))
+    ax1.yaxis.set_minor_locator(MultipleLocator(1))
+
+    # Turn grid on for both major and minor ticks and style minor slightly
+    # differently.
+    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
+    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
+
+    ax1.set_xlabel('x (km)')
+    ax1.set_ylabel('y (km)')
+    ax1.set_title('Iceberg trajectory')
+
+    f.canvas.mpl_connect('button_press_event', onClick)
+
+    ani = FuncAnimation(
+        f,animate,init_func=init,frames=num_frames,
+        interval=frame_len,blit=True,repeat=True)
+
+    print('time',t)
+
+    plt.show()
+    #animation.save("iceberg_traj_animation.mp4")
+
+
+print('Script complete')
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
diff --git a/tests/energy_test2/animate_trajectories_1pe.py b/tests/energy_test2/animate_trajectories_1pe.py
new file mode 100755
index 0000000..93480db
--- /dev/null
+++ b/tests/energy_test2/animate_trajectories_1pe.py
@@ -0,0 +1,180 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+import matplotlib.pyplot as plt
+from matplotlib.animation import FuncAnimation
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc.0000',
+                    help=''' provide filename to plot''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+
+
+def main(args):
+
+    print('reading file')
+
+    filename=args.fname
+    #filename = 'iceberg_trajectories.nc'
+    field = 'lon'
+    field2 = 'lat'
+
+    with nc.Dataset(filename) as file:
+        x = file.variables['lon'][:]/1.e3
+        y = file.variables['lat'][:]/1.e3
+        day = file.variables['day'][:]
+        hs = file.variables['halo_berg'][:]
+        #hs = file.variables['conglom_id'][:]        
+
+    #hs = hs+1
+    ud = np.unique(day)
+    t = ud[0]
+
+    print('unique hs',np.unique(hs))
+
+    # frame info
+    num_frames = len(ud)
+    movie_len = 10.0 #seconds
+    frame_len = 1000.0*movie_len/num_frames
+
+    xmin = np.floor(min(min(x),min(y),-5))
+    xmax = np.ceil(max(max(x),max(y),35))
+    ymin = xmin
+    ymax = xmax
+
+    anim_running = True
+
+    def animate(i):
+
+        x1 = x[day == ud[i]]
+        y1 = y[day == ud[i]]
+        hstat = hs[day == ud[i]]
+        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
+
+        cstring=[]
+        for j in range(len(hstat)):
+            if (hstat[j]<0):
+                cstring.append("m")
+            elif (hstat[j]==0):
+                cstring.append("b")
+            elif (hstat[j]==1):
+                cstring.append("r")
+            elif (hstat[j]==2):
+                cstring.append("g")
+            elif (hstat[j]==3):
+                cstring.append("k")
+            elif (hstat[j]==4):
+                cstring.append("c")
+            elif (hstat[j]==5):
+                cstring.append("y")
+            elif (hstat[j]==6):
+                cstring.append("w")
+            elif (hstat[j]==10):                
+                cstring.append("c")
+            # else:
+            #     cstring.append("y")
+
+        scat.set_offsets(data)
+        scat.set_color(cstring)
+        scat.set_edgecolor('k')
+
+        t = ud[i]
+        time_text.set_text('time = %.1f days' % t )
+        return scat,time_text
+
+    def init():
+        scat.set_offsets([])
+        return scat,
+
+    def onClick(event):
+        global anim_running
+        if anim_running:
+            ani.event_source.stop()
+            anim_running = False
+        else:
+            ani.event_source.start()
+            anim_running = True
+
+    # Now we can do the plotting!
+    f = plt.figure(figsize=(5,5))
+    f.tight_layout()
+    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
+    scat = ax1.scatter([],[],marker='o',s=30)
+    #scat = ax1.scatter([],[],marker='o',facecolor='w',s=60,edgecolor='red')
+    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
+
+    # Change major ticks to show every 20.
+    ax1.xaxis.set_major_locator(MultipleLocator(5))
+    ax1.yaxis.set_major_locator(MultipleLocator(5))
+
+    ax1.xaxis.set_minor_locator(MultipleLocator(1))
+    ax1.yaxis.set_minor_locator(MultipleLocator(1))
+
+    # Turn grid on for both major and minor ticks and style minor slightly
+    # differently.
+    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
+    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
+
+    ax1.set_xlabel('x (km)')
+    ax1.set_ylabel('y (km)')
+    ax1.set_title('Iceberg trajectory')
+
+    f.canvas.mpl_connect('button_press_event', onClick)
+
+    ani = FuncAnimation(
+        f,animate,init_func=init,frames=num_frames,
+        interval=frame_len,blit=True,repeat=True)
+
+    print('time',t)
+
+    plt.plot([0,0],[0,30],'k-',lw=1)
+    plt.plot([10,10],[0,30],'k-',lw=1)
+    plt.plot([20,20],[0,30],'k-',lw=1)
+    plt.plot([30,30],[0,30],'k-',lw=1)
+    plt.plot([0,30],[0,0],'k-',lw=1)
+    plt.plot([0,30],[10,10],'k-',lw=1)
+    plt.plot([0,30],[20,20],'k-',lw=1)
+    plt.plot([0,30],[30,30],'k-',lw=1)
+
+    plt.plot([-2,-2],[-2,33],'b:',lw=1)
+    plt.plot([3,3],[-2,33],'b:',lw=1)
+    plt.plot([8,8],[-2,33],'b:',lw=1)
+    plt.plot([13,13],[-2,33],'b:',lw=1)
+    plt.plot([18,18],[-2,33],'b:',lw=1)
+    plt.plot([23,23],[-2,33],'b:',lw=1)
+    plt.plot([28,28],[-2,33],'b:',lw=1)
+    plt.plot([33,33],[-2,33],'b:',lw=1)    
+
+    plt.plot([-2,33],[-2,-2],'b:',lw=1)
+    plt.plot([-2,33],[3,3],'b:',lw=1)
+    plt.plot([-2,33],[8,8],'b:',lw=1)
+    plt.plot([-2,33],[13,13],'b:',lw=1)
+    plt.plot([-2,33],[18,18],'b:',lw=1)
+    plt.plot([-2,33],[23,23],'b:',lw=1)
+    plt.plot([-2,33],[28,28],'b:',lw=1)
+    plt.plot([-2,33],[33,33],'b:',lw=1)
+
+    plt.show()
+    #animation.save("iceberg_traj_animation.mp4")
+
+
+print('Script complete')
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
diff --git a/tests/energy_test2/diag_table b/tests/energy_test2/diag_table
new file mode 100644
index 0000000..c1c8819
--- /dev/null
+++ b/tests/energy_test2/diag_table
@@ -0,0 +1,3 @@
+"icebergs test"
+1 1 1 0 0 0
+
diff --git a/tests/energy_test2/input.nml b/tests/energy_test2/input.nml
new file mode 100644
index 0000000..fb224e7
--- /dev/null
+++ b/tests/energy_test2/input.nml
@@ -0,0 +1,176 @@
+
+&icebergs_driver_nml
+  ni=45 !number of elements, x direction
+  nj=45 !number of elements, y direction
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=46 !total simulation hours
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=999999999 !max number of timesteps
+  saverestart=.true.
+  halo=4
+  debug=.true.
+  collision_test=.false.
+  grounding_test=.false.
+  bump_depth=9999.0 !(m) depth of top of gaussian bump below sea level 
+/
+
+&icebergs_nml
+
+    !defaults given in parentheses:
+    monitor_energy=.true. !(F)save total elastic (spring+collision),external,dissipated,&fracture energy
+    new_mts=.true. !(F) If T, implicit accel is added 50% at the current time step and 50% at the next time step
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=20  !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
+    imp_loop_iters_long=1 !(1) if >1, # of iterations for each long MTS step (alt to force_convergence)
+    imp_loop_iters_short=1!(1)if >1, # of iterations for each short MTS step (alt to force_convergence)
+    force_convergence=.false. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=3e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-8!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=3.16e6 !friction drag param
+    h_to_init_grounding=200.0
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='strain' !('none') 'strain_rate','strain',or 'none'
+    !frac_thres_scaling = 1.0 !(1) scales frac_thres_n and frac_thres_t
+    !frac_thres_n = 0.018  !normal fracture strain threshold
+    !frac_thres_t = 0.05076 !tangential fracture strain threshold    
+
+    halo=4 !(4) halo width
+    Lx=45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    rho_bergs=850. ! (850) iceberg density
+    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.0!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.true. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0.0 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.false. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.false. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true.!.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.true. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.false. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=24000 ! (24) Period between verbose messages
+    traj_sample_hrs=0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false.!.true. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.!(F) Init bond b/w bergs if dist<1.25*radius
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/energy_test2/makeberg/RUN b/tests/energy_test2/makeberg/RUN
new file mode 100755
index 0000000..d985f3f
--- /dev/null
+++ b/tests/energy_test2/makeberg/RUN
@@ -0,0 +1,3 @@
+rm ./output_files/Generic*
+./makeberg.py
+cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
\ No newline at end of file
diff --git a/tests/energy_test2/makeberg/makeberg.py b/tests/energy_test2/makeberg/makeberg.py
new file mode 100755
index 0000000..61605f9
--- /dev/null
+++ b/tests/energy_test2/makeberg/makeberg.py
@@ -0,0 +1,367 @@
+#!/usr/bin/env python
+import numpy as np
+import math
+from netCDF4 import Dataset
+from pylab import *
+#import pdb
+import netCDF4 as nc
+
+#
+# Initialize 2 iceberg elements, which can later be bonded in the fortran code if needed
+#
+
+def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
+
+	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
+	# To copy the global attributes of the netCDF file
+
+	#Input and output files
+	#Create Empty restart file. This is later read so that the attributes can be used.
+	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
+	create_empty_iceberg_restart_file(Empty_restart_filename)
+	#Empty_restart_filename='input_files/icebergs.res.nc'
+
+	#Read empty restart file
+	f=Dataset(Empty_restart_filename,'r') # r is for read only
+	#Write a new restart file
+	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
+
+	for attname in f.ncattrs():
+		    setattr(g,attname,getattr(f,attname))
+
+
+	# To copy the dimension of the netCDF file
+	for dimname,dim in f.dimensions.iteritems():
+		# if you want to make changes in the dimensions of the new file
+		# you should add your own conditions here before the creation of the dimension.
+		#g.createDimension(dimname,len(dim))
+		g.createDimension(dimname,Number_of_bergs)
+
+	# To copy the variables of the netCDF file
+
+	for varname,ncvar in f.variables.iteritems():
+		# if you want to make changes in the variables of the new file
+		# you should add your own conditions here before the creation of the variable.
+		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
+		#Proceed to copy the variable attributes
+		for attname in ncvar.ncattrs():
+			setattr(var,attname,getattr(ncvar,attname))
+		#Finally copy the variable data to the new created variable
+		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
+
+		if varname=='i':
+			var[:]=Number_of_bergs
+
+		if varname=='iceberg_num':
+			for j in range(Number_of_bergs):
+				#var[j]=j+1
+				var[j]=iceberg_num[j]
+
+		if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
+		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
+		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
+		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
+			var[:]=0
+
+                if varname=='uvel':
+                        var[:]=uvel
+
+                if varname=='vvel':
+                        var[:]=vvel
+
+		if varname=='mass_scaling':
+			var[:]=mass_scaling
+
+		if varname=='thickness':
+			for j in range(Number_of_bergs):
+				var[j]=thickness[j]
+
+		if varname=='mass':
+			for j in range(Number_of_bergs):
+				var[j]=mass[j]
+
+		if varname=='width'  or varname=='length':
+			for j in range(Number_of_bergs):
+				var[j]=width[j]
+
+		if varname=='lon':
+			for j in range(Number_of_bergs):
+				var[j]=lon[j]
+
+		if varname=='lat':
+			for j in range(Number_of_bergs):
+				var[j]=lat[j]
+
+		if varname=='static_berg':
+			for j in range(Number_of_bergs):
+				var[j]=static_berg[j]
+
+
+	f.close()
+	g.close()
+
+
+def create_empty_iceberg_restart_file(Empty_restart_filename):
+
+	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
+
+	i=f.createDimension('i', None)
+	lon=f.createVariable('i','i')
+
+	lon=f.createVariable('lon','d',('i'))
+	lon.long_name = "longitude" ;
+	lon.units = "degrees_E" ;
+	lon.checksum = "               0" ;
+
+	lat=f.createVariable('lat','d',('i'))
+	lat.long_name = "latitude" ;
+	lat.units = "degrees_N" ;
+	lat.checksum = "               0" ;
+
+	uvel=f.createVariable('uvel','d',('i'))
+	uvel.long_name = "zonal velocity" ;
+	uvel.units = "m/s" ;
+	uvel.checksum = "               0" ;
+
+	vvel=f.createVariable('vvel','d',('i'))
+	vvel.long_name = "meridional velocity" ;
+	vvel.units = "m/s" ;
+	vvel.checksum = "               0" ;
+
+	mass=f.createVariable('mass','d',('i'))
+	mass.long_name = "mass" ;
+	mass.units = "kg" ;
+	mass.checksum = "               0" ;
+
+	axn=f.createVariable('axn','d',('i'))
+	axn.long_name = "explicit zonal acceleration" ;
+	axn.units = "m/s^2" ;
+	axn.checksum = "               0" ;
+
+	ayn=f.createVariable('ayn','d',('i'))
+	ayn.long_name = "explicit meridional acceleration" ;
+	ayn.units = "m/s^2" ;
+	ayn.checksum = "               0" ;
+
+	bxn=f.createVariable('bxn','d',('i'))
+	bxn.long_name = "inplicit zonal acceleration" ;
+	bxn.units = "m/s^2" ;
+	bxn.checksum = "               0" ;
+
+	byn=f.createVariable('byn','d',('i'))
+	byn.long_name = "implicit meridional acceleration" ;
+	byn.units = "m/s^2" ;
+	byn.checksum = "               0" ;
+
+	ine=f.createVariable('ine','i',('i'))
+	ine.long_name = "i index" ;
+	ine.units = "none" ;
+	ine.packing = 0 ;
+	ine.checksum = "               0" ;
+
+	jne=f.createVariable('jne','i',('i'))
+	jne.long_name = "j index" ;
+	jne.units = "none" ;
+	jne.packing = 0 ;
+	jne.checksum = "               0" ;
+
+	thickness=f.createVariable('thickness','d',('i'))
+	thickness.long_name = "thickness" ;
+	thickness.units = "m" ;
+	thickness.checksum = "               0" ;
+
+	width=f.createVariable('width','d',('i'))
+	width.long_name = "width" ;
+	width.units = "m" ;
+	width.checksum = "               0" ;
+
+	length=f.createVariable('length','d',('i'))
+	length.long_name = "length" ;
+	length.units = "m" ;
+	length.checksum = "               0" ;
+
+	start_lon=f.createVariable('start_lon','d',('i'))
+	start_lon.long_name = "longitude of calving location" ;
+	start_lon.units = "degrees_E" ;
+	start_lon.checksum = "               0" ;
+
+	start_lat=f.createVariable('start_lat','d',('i'))
+	start_lat.long_name = "latitude of calving location" ;
+	start_lat.units = "degrees_N" ;
+	start_lat.checksum = "               0" ;
+
+	start_year=f.createVariable('start_year','i',('i'))
+	start_year.long_name = "calendar year of calving event" ;
+	start_year.units = "years" ;
+	start_year.packing = 0 ;
+	start_year.checksum = "               0" ;
+
+	iceberg_num=f.createVariable('iceberg_num','i',('i'))
+	iceberg_num.long_name = "identification of the iceberg" ;
+	iceberg_num.units = "dimensionless" ;
+	iceberg_num.packing = 0 ;
+	iceberg_num.checksum = "               0" ;
+
+	start_day=f.createVariable('start_day','d',('i'))
+	start_day.long_name = "year day of calving event" ;
+	start_day.units = "days" ;
+	start_day.checksum = "               0" ;
+
+	start_mass=f.createVariable('start_mass','d',('i'))
+	start_mass.long_name = "initial mass of calving berg" ;
+	start_mass.units = "kg" ;
+	start_mass.checksum = "               0" ;
+
+	mass_scaling=f.createVariable('mass_scaling','d',('i'))
+	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
+	mass_scaling.units = "none" ;
+	mass_scaling.checksum = "               0" ;
+
+	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
+	mass_of_bits.long_name = "mass of bergy bits" ;
+	mass_of_bits.units = "kg" ;
+	mass_of_bits.checksum = "               0" ;
+
+	heat_density=f.createVariable('heat_density','d',('i'))
+	heat_density.long_name = "heat density" ;
+	heat_density.units = "J/kg" ;
+	heat_density.checksum = "               0" ;
+
+	halo_berg=f.createVariable('halo_berg','d',('i'))
+	halo_berg.long_name = "halo_berg" ;
+	halo_berg.units = "dimensionless" ;
+	halo_berg.checksum = "               0" ;
+
+	static_berg=f.createVariable('static_berg','d',('i'))
+	static_berg.long_name = "static_berg" ;
+	static_berg.units = "dimensionless" ;
+	static_berg.checksum = "               0" ;
+
+	f.sync()
+	f.close()
+
+
+
+#-----------------------------------#
+#               Main                #
+#-----------------------------------#
+
+just2particles=False
+flip2ndconglom=True
+offset2ndconglom=True
+
+grdxmin=0; grdxmax=45000e3
+grdymin=0; grdymax=45000e3
+grdres=1000.0
+R_frac=0.45
+radius=(np.sqrt(3)/2.)*(R_frac*grdres) #S is < 0.5 grid res
+element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*radius**2)
+width=np.sqrt(element_area)
+thickness1=300.0
+thickness2=300.0
+rho_ice=850.0
+
+
+nbergs=2 #number of conglomerates
+
+#center coords of each (rectangular) conglomerate berg (CB=conglomerate berg)
+CBxc=np.array([9500, 17500]); CByc=np.array([22500, 22500])
+
+#side lengths
+#CBxl=np.array([2500, 10000]); CByl=np.array([10000, 2500])
+CBxl=np.array([3000, 3000]); CByl=np.array([3000, 3000])
+CByl=CByl.astype(int); CBxl=CBxl.astype(int)
+
+#--- xmax, xmin, ymax, ymin for each CB --
+CBxmin=CBxc-(0.5*CBxl); CBxmax=CBxc+(0.5*CBxl)
+CBymin=CByc-(0.5*CByl); CBymax=CByc+(0.5*CByl)
+#this shouldn't happen:
+CBxmin[CBxmin<grdxmin]=grdxmin; CBxmax[CBxmax>grdxmax]=grdxmax
+CBymin[CBxmin<grdymin]=grdymin; CBymax[CBymax>grdymax]=grdymax
+CBxc=0.5*(CBxmin+CBxmax); CByc=0.5*(CBymin+CBymax)
+
+#if just want one particle per CB
+if just2particles:
+        CBxmin=CBxc; CBxmax=CBxc
+        CBymin=CByc; CBymax=CByc
+
+#--- min and max thicknesses for each CB ---
+h1=thickness1; h2=thickness2
+CBhmax=np.array([h1,h1]); CBhmin=np.array([h2,h2])
+
+#radii
+CBrad=np.array([radius,radius])
+
+berg_x=[]; berg_y=[]
+berg_id=[]; berg_static=[]
+berg_width=[]; berg_bonds=[]
+berg_h=[]; berg_mass_scaling=[]
+berg_mass=[]; berg_uvel=[]; berg_vvel=[]
+
+berg_count=0
+
+for i in range(nbergs):
+        x_start=CBxmin[i]+(CBrad[i]*2./np.sqrt(3))
+
+        if flip2ndconglom and i>0:
+                x_start=CBxmax[i]-(CBrad[i]*2./np.sqrt(3))
+
+        #pdb.set_trace()
+        if x_start>CBxmax[i]:
+                x_start=CBxmax[i]
+        y_start0=CBymin[i]+CBrad[i]
+        if y_start0>CBymax[i]:
+                y_start0=CBymax[i]
+        element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*(CBrad[i])**2)
+        #H (thickness) is a linear function of a berg element's position from the
+        #center of the CB. H=Hmax at the center of the CB and H=Hmin at a corner of the
+        #CB, where the dist of a corner from the center is:
+        cdistb=np.sqrt((CBxmin[i]-CBxc[i])**2+(CBymin[i]-CByc[i])**2)
+        j=0
+        x_val=x_start
+        offset=0.0
+        vvel=0.025
+        if (i==0):
+                uvel=0.05
+        else:
+                uvel=-0.15
+                if (offset2ndconglom):
+                        offset=2000.0 #250.0
+        #berg_count_start=berg_count
+        while x_val<=CBxmax[i] and x_val>=CBxmin[i]:
+                y_start=y_start0+((j%2)*CBrad[i])+offset
+                k=0
+                y_val=y_start
+                while y_val<=(CBymax[i]+offset):
+                        berg_count=berg_count+1
+                        berg_id.append(berg_count)
+                        berg_x.append(x_val)
+                        berg_y.append(y_val)
+                        berg_width.append(sqrt(element_area))
+                        #dist of berg elem from center of CB
+                        bdistc=np.sqrt((x_val-CBxc[i])**2+(y_val-CByc[i])**2)
+                        bh=CBhmin[i]*bdistc/cdistb + CBhmax[i]*(1-bdistc/cdistb)
+                        if (just2particles):
+                                bh=h1
+                        berg_h.append(bh) #thickness
+                        berg_mass_scaling.append(1)
+                        berg_mass.append(bh*rho_ice*element_area)
+                        berg_static.append(0)
+                        berg_uvel.append(uvel)
+                        berg_vvel.append(vvel)
+                        #berg_CBid.append(i)
+                        k=k+1
+                        y_val=y_start+(2*k*CBrad[i])
+                j=j+1
+                if flip2ndconglom and i>0:
+                        x_val=x_start-(np.sqrt(3)*CBrad[i]*j)
+                else:
+                        x_val=x_start+(np.sqrt(3)*CBrad[i]*j)
+
+print('Number of bergs',berg_count)
+
+#pdb.set_trace()
+
+#Create iceberg restart file
+Ice_geometry_source='Generic'
+Create_iceberg_restart_file(berg_count,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)
diff --git a/tests/energy_test3/.gitignore b/tests/energy_test3/.gitignore
new file mode 100644
index 0000000..68bcbc9
--- /dev/null
+++ b/tests/energy_test3/.gitignore
@@ -0,0 +1 @@
+results/
\ No newline at end of file
diff --git a/tests/energy_test3/README b/tests/energy_test3/README
new file mode 100644
index 0000000..e882f41
--- /dev/null
+++ b/tests/energy_test3/README
@@ -0,0 +1,13 @@
+Collision and subsequent fracture of two conglomerate bergs. For testing a scheme where the MTS solution is iterated to convergence in order to help conserve momentum conservation when collisions occur. Also for testing fracture scheme (e.g. effects of particle size, fracture thresholds, sensitivity to violation of momentum conservation).
+
+Iterative scheme options:
+Option 1: Set the number of iterations (>1) for each long/short step using imp_loop_iters_long and imp_loop_iters_short, respectively. Force_convergence must be set false. (this option uses subroutine evolve_icebergs_mts)
+Option 2: Set force_convergence to true and specify a convergence tolerance. Iterations will stop once convergence tolerance is reached. (this option, or if both imp_loop_iters==1, uses subroutine evolve_icebergs_mts2)
+
+Unlike in energy_test2, this test will not conserve momentum sufficiently during collision unless the iterative scheme is used.
+
+1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
+2.(optional) edit input.nml
+3. run the model: ./RUN
+4, animate the results: animate_trajectories.py
+
diff --git a/tests/energy_test3/RUN b/tests/energy_test3/RUN
new file mode 100755
index 0000000..f881323
--- /dev/null
+++ b/tests/energy_test3/RUN
@@ -0,0 +1,7 @@
+rm iceberg_trajectories.nc
+rm iceberg_trajectories.nc.*
+rm bond_trajectories.nc
+rm bond_trajectories.nc.*
+srun -n9 ./../../build/bergs.x
+
+
diff --git a/tests/energy_test3/RUN1p b/tests/energy_test3/RUN1p
new file mode 100755
index 0000000..3dfc97d
--- /dev/null
+++ b/tests/energy_test3/RUN1p
@@ -0,0 +1,7 @@
+rm iceberg_trajectories.nc
+rm iceberg_trajectories.nc.*
+rm bond_trajectories.nc
+rm bond_trajectories.nc.*
+srun -n1 ./../../build/bergs.x
+
+
diff --git a/tests/energy_test3/animate_trajectories.py b/tests/energy_test3/animate_trajectories.py
new file mode 100755
index 0000000..cd325e1
--- /dev/null
+++ b/tests/energy_test3/animate_trajectories.py
@@ -0,0 +1,128 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+import matplotlib.pyplot as plt
+from matplotlib.animation import FuncAnimation
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
+                    help=''' provide filename to plot''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+
+
+def main(args):
+
+    print('reading file')
+
+    filename=args.fname
+    #filename = 'iceberg_trajectories.nc'
+    field = 'lon'
+    field2 = 'lat'
+
+    with nc.Dataset(filename) as file:
+        x = file.variables['lon'][:]/1.e3
+        y = file.variables['lat'][:]/1.e3
+        day = file.variables['day'][:]
+
+    crop=False
+    tc=1.25
+    if crop:
+        x=x[day<=tc]
+        y=y[day<=tc]
+        day=day[day<=tc]
+
+    ud = np.unique(day)
+    t = ud[0]
+
+    # frame info
+    num_frames = len(ud)
+    movie_len = 10.0 #seconds
+    frame_len = 1000.0*movie_len/num_frames
+
+    xmin = 0
+    xmax = 30 #45 #30
+    ymin = 7.5 #0 #7.5
+    ymax = 37.5 #45 #37.5
+
+    anim_running = True
+
+    def animate(i):
+
+        x1 = x[day == ud[i]]
+        y1 = y[day == ud[i]]
+        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
+
+        scat.set_offsets(data)
+
+        t = ud[i]
+        time_text.set_text('time = %.1f days' % t )
+        return scat,time_text
+
+    def init():
+        scat.set_offsets([])
+        return scat,
+
+    def onClick(event):
+        global anim_running
+        if anim_running:
+            ani.event_source.stop()
+            anim_running = False
+        else:
+            ani.event_source.start()
+            anim_running = True
+
+    # Now we can do the plotting!
+    f = plt.figure(figsize=(5,5))
+    f.tight_layout()
+    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
+    scat = ax1.scatter([],[],marker='o',facecolor='w',s=40,edgecolor='red')
+    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
+
+    # Change major ticks to show every 20.
+    ax1.xaxis.set_major_locator(MultipleLocator(5))
+    ax1.yaxis.set_major_locator(MultipleLocator(5))
+
+    ax1.xaxis.set_minor_locator(MultipleLocator(1))
+    ax1.yaxis.set_minor_locator(MultipleLocator(1))
+
+    # Turn grid on for both major and minor ticks and style minor slightly
+    # differently.
+    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
+    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
+
+    ax1.set_xlabel('x (km)')
+    ax1.set_ylabel('y (km)')
+    ax1.set_title('Iceberg trajectory')
+
+    f.canvas.mpl_connect('button_press_event', onClick)
+
+    ani = FuncAnimation(
+        f,animate,init_func=init,frames=num_frames,
+        interval=frame_len,blit=True,repeat=True)
+
+    print('time',t)
+
+    plt.show()
+    #animation.save("iceberg_traj_animation.mp4")
+
+
+print('Script complete')
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
diff --git a/tests/energy_test3/animate_trajectories_1pe.py b/tests/energy_test3/animate_trajectories_1pe.py
new file mode 100755
index 0000000..931c727
--- /dev/null
+++ b/tests/energy_test3/animate_trajectories_1pe.py
@@ -0,0 +1,189 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+import matplotlib.pyplot as plt
+from matplotlib.animation import FuncAnimation
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc.0000',
+                    help=''' provide filename to plot''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+
+
+def main(args):
+
+    print('reading file')
+
+    filename=args.fname
+    #filename = 'iceberg_trajectories.nc'
+    field = 'lon'
+    field2 = 'lat'
+
+    with nc.Dataset(filename) as file:
+        x = file.variables['lon'][:]/1.e3
+        y = file.variables['lat'][:]/1.e3
+        day = file.variables['day'][:]
+        hs = file.variables['halo_berg'][:]
+        #hs = file.variables['conglom_id'][:]        
+
+    #hs = hs+1
+    ud = np.unique(day)
+    t = ud[0]
+
+    print('unique hs',np.unique(hs))
+
+    # frame info
+    num_frames = len(ud)
+    movie_len = 10.0 #seconds
+    frame_len = 1000.0*movie_len/num_frames
+
+    xmin = np.floor(min(min(x),min(y),-5))
+    xmax = np.ceil(max(max(x),max(y),35))
+    ymin = xmin
+    ymax = xmax
+
+    anim_running = True
+
+    def animate(i):
+
+        x1 = x[day == ud[i]]
+        y1 = y[day == ud[i]]
+        hstat = hs[day == ud[i]]
+        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
+
+        cstring=[]
+        for j in range(len(hstat)):
+            if (hstat[j]<0):
+                cstring.append("m")
+            elif (hstat[j]==0):
+                cstring.append("b")
+            elif (hstat[j]==1):
+                cstring.append("r")
+            elif (hstat[j]==2):
+                cstring.append("g")
+            elif (hstat[j]==3):
+                cstring.append("k")
+            elif (hstat[j]==4):
+                cstring.append("c")
+            elif (hstat[j]==5):
+                cstring.append("y")
+            elif (hstat[j]==6):
+                cstring.append("w")
+            elif (hstat[j]==10):                
+                cstring.append("c")
+            # else:
+            #     cstring.append("y")
+
+        scat.set_offsets(data)
+        scat.set_color(cstring)
+        scat.set_edgecolor('k')
+
+        t = ud[i]
+        time_text.set_text('time = %.1f days' % t )
+        return scat,time_text
+
+    def init():
+        scat.set_offsets([])
+        return scat,
+
+    def onClick(event):
+        global anim_running
+        if anim_running:
+            ani.event_source.stop()
+            anim_running = False
+        else:
+            ani.event_source.start()
+            anim_running = True
+
+    # Now we can do the plotting!
+    f = plt.figure(figsize=(5,5))
+    f.tight_layout()
+    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
+    scat = ax1.scatter([],[],marker='o',s=30)
+    #scat = ax1.scatter([],[],marker='o',facecolor='w',s=60,edgecolor='red')
+    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
+
+    # Change major ticks to show every 20.
+    ax1.xaxis.set_major_locator(MultipleLocator(5))
+    ax1.yaxis.set_major_locator(MultipleLocator(5))
+
+    ax1.xaxis.set_minor_locator(MultipleLocator(1))
+    ax1.yaxis.set_minor_locator(MultipleLocator(1))
+
+    # Turn grid on for both major and minor ticks and style minor slightly
+    # differently.
+    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
+    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
+
+    ax1.set_xlabel('x (km)')
+    ax1.set_ylabel('y (km)')
+    ax1.set_title('Iceberg trajectory')
+
+    f.canvas.mpl_connect('button_press_event', onClick)
+
+    ani = FuncAnimation(
+        f,animate,init_func=init,frames=num_frames,
+        interval=frame_len,blit=True,repeat=True)
+
+    print('time',t)
+
+    plt.plot([0,0],[0,30],'k-',lw=1)
+    plt.plot([10,10],[0,30],'k-',lw=1)
+    plt.plot([20,20],[0,30],'k-',lw=1)
+    plt.plot([30,30],[0,30],'k-',lw=1)
+    plt.plot([0,30],[0,0],'k-',lw=1)
+    plt.plot([0,30],[10,10],'k-',lw=1)
+    plt.plot([0,30],[20,20],'k-',lw=1)
+    plt.plot([0,30],[30,30],'k-',lw=1)
+
+
+    h=3 #halo width
+    w=h-1
+
+    x1=0; x2=10; x3=20; x4=30
+    y1=0; y2=10; y3=20; y4=30    
+    
+
+    plt.plot([x1-w,x1-w],[y1-w,y4+h],'b:',lw=1)
+    plt.plot([x1+h,x1+h],[y1-w,y4+h],'b:',lw=1)
+    plt.plot([x2-w,x2-w],[y1-w,y4+h],'b:',lw=1)
+    plt.plot([x2+h,x2+h],[y1-w,y4+h],'b:',lw=1)
+    plt.plot([x3-w,x3-w],[y1-w,y4+h],'b:',lw=1)
+    plt.plot([x3+h,x3+h],[y1-w,y4+h],'b:',lw=1)
+    plt.plot([x4-w,x4-w],[y1-w,y4+h],'b:',lw=1)
+    plt.plot([x4+h,x4+h],[y1-w,y4+h],'b:',lw=1) 
+       
+
+    plt.plot([x1-w,x4+h],[y1-w,y1-w],'b:',lw=1)
+    plt.plot([x1-w,x4+h],[y1+h,y1+h],'b:',lw=1)
+    plt.plot([x1-w,x4+h],[y2-w,y2-w],'b:',lw=1)
+    plt.plot([x1-w,x4+h],[y2+h,y2+h],'b:',lw=1)
+    plt.plot([x1-w,x4+h],[y3-w,y3-w],'b:',lw=1)
+    plt.plot([x1-w,x4+h],[y3+h,y3+h],'b:',lw=1)
+    plt.plot([x1-w,x4+h],[y4-w,y4-w],'b:',lw=1)
+    plt.plot([x1-w,x4+h],[y4+h,y4+h],'b:',lw=1)
+
+    plt.show()
+    #animation.save("iceberg_traj_animation.mp4")
+
+
+print('Script complete')
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
diff --git a/tests/energy_test3/diag_table b/tests/energy_test3/diag_table
new file mode 100644
index 0000000..c1c8819
--- /dev/null
+++ b/tests/energy_test3/diag_table
@@ -0,0 +1,3 @@
+"icebergs test"
+1 1 1 0 0 0
+
diff --git a/tests/energy_test3/input.nml b/tests/energy_test3/input.nml
new file mode 100644
index 0000000..6f97e4d
--- /dev/null
+++ b/tests/energy_test3/input.nml
@@ -0,0 +1,180 @@
+!KID, bergs_chksum: write_restart berg chksum=           -1918812055 chksum2=             743944572 chksum3=             -78785014 chksum4=             -78785014 chksum5=                     0 #=                    71
+!KID, grd_chksum2:    # of bergs/cell chksum=                     0 chksum2=                     0 min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
+! Total number of bonds is:          276 
+
+&icebergs_driver_nml
+  ni=45 !number of elements, x direction
+  nj=45 !number of elements, y direction
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=24 !total simulation hours
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=999999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.true.
+  collision_test=.false.
+  grounding_test=.false.
+  bump_depth=9999.0 !(m) depth of top of gaussian bump below sea level
+/
+
+&icebergs_nml
+
+    !defaults given in parentheses:
+
+    monitor_energy=.true. !(F)save total elastic (spring+collision),external,dissipated,&fracture energy
+    new_mts=.true. !(F) If T, implicit accel is added 50% at the current time step and 50% at the next time step
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=20  !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
+    imp_loop_iters_long=1 !(1) if >1, # of iterations for each long MTS step (alt to force_convergence)
+    imp_loop_iters_short=1!(1)if >1, # of iterations for each short MTS step (alt to force_convergence)
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=2000 !2500 !2500 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-8 !(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=3.16e6 !friction drag param
+    h_to_init_grounding=200.0 !300.0 !150.0 !300.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.false. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='strain' !('none') 'strain_rate','strain',or 'none'
+    !here, try setting scaling 1.0 if force_convergence=.false., 0.5 if force_convergence=.true.
+    frac_thres_scaling = 0.5 !(1) scales frac_thres_n and frac_thres_t
+    frac_thres_n = 0.018  !normal fracture strain threshold
+    frac_thres_t = 0.05076 !tangential fracture strain threshold
+
+    halo=3 !(4) halo width
+    Lx=45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    rho_bergs=850. ! (850) iceberg density
+    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    radial_damping_coef=0.0 !(1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0.0 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.false. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.false. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.true. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=24000 ! (24) Period between verbose messages
+    traj_sample_hrs=0 !(24) sampling period for trajectory storage
+    traj_write_hrs=0 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.true. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.!(F) Init bond b/w bergs if dist<1.25*radius
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/energy_test3/makeberg/RUN b/tests/energy_test3/makeberg/RUN
new file mode 100755
index 0000000..d985f3f
--- /dev/null
+++ b/tests/energy_test3/makeberg/RUN
@@ -0,0 +1,3 @@
+rm ./output_files/Generic*
+./makeberg.py
+cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
\ No newline at end of file
diff --git a/tests/energy_test3/makeberg/makeberg.py b/tests/energy_test3/makeberg/makeberg.py
new file mode 100755
index 0000000..2dd9eca
--- /dev/null
+++ b/tests/energy_test3/makeberg/makeberg.py
@@ -0,0 +1,374 @@
+#!/usr/bin/env python
+import numpy as np
+import math
+from netCDF4 import Dataset
+from pylab import *
+#import pdb
+import netCDF4 as nc
+
+#
+# Initialize 2 iceberg elements, which can later be bonded in the fortran code if needed
+#
+
+def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
+
+	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
+	# To copy the global attributes of the netCDF file
+
+	#Input and output files
+	#Create Empty restart file. This is later read so that the attributes can be used.
+	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
+	create_empty_iceberg_restart_file(Empty_restart_filename)
+	#Empty_restart_filename='input_files/icebergs.res.nc'
+
+	#Read empty restart file
+	f=Dataset(Empty_restart_filename,'r') # r is for read only
+	#Write a new restart file
+	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
+
+	for attname in f.ncattrs():
+		    setattr(g,attname,getattr(f,attname))
+
+
+	# To copy the dimension of the netCDF file
+	for dimname,dim in f.dimensions.iteritems():
+		# if you want to make changes in the dimensions of the new file
+		# you should add your own conditions here before the creation of the dimension.
+		#g.createDimension(dimname,len(dim))
+		g.createDimension(dimname,Number_of_bergs)
+
+	# To copy the variables of the netCDF file
+
+	for varname,ncvar in f.variables.iteritems():
+		# if you want to make changes in the variables of the new file
+		# you should add your own conditions here before the creation of the variable.
+		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
+		#Proceed to copy the variable attributes
+		for attname in ncvar.ncattrs():
+			setattr(var,attname,getattr(ncvar,attname))
+		#Finally copy the variable data to the new created variable
+		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
+
+		if varname=='i':
+			var[:]=Number_of_bergs
+
+		if varname=='iceberg_num':
+			for j in range(Number_of_bergs):
+				#var[j]=j+1
+				var[j]=iceberg_num[j]
+
+		if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
+		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
+		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
+		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
+			var[:]=0
+
+                if varname=='uvel':
+                        var[:]=uvel
+
+                if varname=='vvel':
+                        var[:]=vvel
+
+		if varname=='mass_scaling':
+			var[:]=mass_scaling
+
+		if varname=='thickness':
+			for j in range(Number_of_bergs):
+				var[j]=thickness[j]
+
+		if varname=='mass':
+			for j in range(Number_of_bergs):
+				var[j]=mass[j]
+
+		if varname=='width'  or varname=='length':
+			for j in range(Number_of_bergs):
+				var[j]=width[j]
+
+		if varname=='lon':
+			for j in range(Number_of_bergs):
+				var[j]=lon[j]
+
+		if varname=='lat':
+			for j in range(Number_of_bergs):
+				var[j]=lat[j]
+
+		if varname=='static_berg':
+			for j in range(Number_of_bergs):
+				var[j]=static_berg[j]
+
+
+	f.close()
+	g.close()
+
+
+def create_empty_iceberg_restart_file(Empty_restart_filename):
+
+	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
+
+	i=f.createDimension('i', None)
+	lon=f.createVariable('i','i')
+
+	lon=f.createVariable('lon','d',('i'))
+	lon.long_name = "longitude" ;
+	lon.units = "degrees_E" ;
+	lon.checksum = "               0" ;
+
+	lat=f.createVariable('lat','d',('i'))
+	lat.long_name = "latitude" ;
+	lat.units = "degrees_N" ;
+	lat.checksum = "               0" ;
+
+	uvel=f.createVariable('uvel','d',('i'))
+	uvel.long_name = "zonal velocity" ;
+	uvel.units = "m/s" ;
+	uvel.checksum = "               0" ;
+
+	vvel=f.createVariable('vvel','d',('i'))
+	vvel.long_name = "meridional velocity" ;
+	vvel.units = "m/s" ;
+	vvel.checksum = "               0" ;
+
+	mass=f.createVariable('mass','d',('i'))
+	mass.long_name = "mass" ;
+	mass.units = "kg" ;
+	mass.checksum = "               0" ;
+
+	axn=f.createVariable('axn','d',('i'))
+	axn.long_name = "explicit zonal acceleration" ;
+	axn.units = "m/s^2" ;
+	axn.checksum = "               0" ;
+
+	ayn=f.createVariable('ayn','d',('i'))
+	ayn.long_name = "explicit meridional acceleration" ;
+	ayn.units = "m/s^2" ;
+	ayn.checksum = "               0" ;
+
+	bxn=f.createVariable('bxn','d',('i'))
+	bxn.long_name = "inplicit zonal acceleration" ;
+	bxn.units = "m/s^2" ;
+	bxn.checksum = "               0" ;
+
+	byn=f.createVariable('byn','d',('i'))
+	byn.long_name = "implicit meridional acceleration" ;
+	byn.units = "m/s^2" ;
+	byn.checksum = "               0" ;
+
+	ine=f.createVariable('ine','i',('i'))
+	ine.long_name = "i index" ;
+	ine.units = "none" ;
+	ine.packing = 0 ;
+	ine.checksum = "               0" ;
+
+	jne=f.createVariable('jne','i',('i'))
+	jne.long_name = "j index" ;
+	jne.units = "none" ;
+	jne.packing = 0 ;
+	jne.checksum = "               0" ;
+
+	thickness=f.createVariable('thickness','d',('i'))
+	thickness.long_name = "thickness" ;
+	thickness.units = "m" ;
+	thickness.checksum = "               0" ;
+
+	width=f.createVariable('width','d',('i'))
+	width.long_name = "width" ;
+	width.units = "m" ;
+	width.checksum = "               0" ;
+
+	length=f.createVariable('length','d',('i'))
+	length.long_name = "length" ;
+	length.units = "m" ;
+	length.checksum = "               0" ;
+
+	start_lon=f.createVariable('start_lon','d',('i'))
+	start_lon.long_name = "longitude of calving location" ;
+	start_lon.units = "degrees_E" ;
+	start_lon.checksum = "               0" ;
+
+	start_lat=f.createVariable('start_lat','d',('i'))
+	start_lat.long_name = "latitude of calving location" ;
+	start_lat.units = "degrees_N" ;
+	start_lat.checksum = "               0" ;
+
+	start_year=f.createVariable('start_year','i',('i'))
+	start_year.long_name = "calendar year of calving event" ;
+	start_year.units = "years" ;
+	start_year.packing = 0 ;
+	start_year.checksum = "               0" ;
+
+	iceberg_num=f.createVariable('iceberg_num','i',('i'))
+	iceberg_num.long_name = "identification of the iceberg" ;
+	iceberg_num.units = "dimensionless" ;
+	iceberg_num.packing = 0 ;
+	iceberg_num.checksum = "               0" ;
+
+	start_day=f.createVariable('start_day','d',('i'))
+	start_day.long_name = "year day of calving event" ;
+	start_day.units = "days" ;
+	start_day.checksum = "               0" ;
+
+	start_mass=f.createVariable('start_mass','d',('i'))
+	start_mass.long_name = "initial mass of calving berg" ;
+	start_mass.units = "kg" ;
+	start_mass.checksum = "               0" ;
+
+	mass_scaling=f.createVariable('mass_scaling','d',('i'))
+	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
+	mass_scaling.units = "none" ;
+	mass_scaling.checksum = "               0" ;
+
+	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
+	mass_of_bits.long_name = "mass of bergy bits" ;
+	mass_of_bits.units = "kg" ;
+	mass_of_bits.checksum = "               0" ;
+
+	heat_density=f.createVariable('heat_density','d',('i'))
+	heat_density.long_name = "heat density" ;
+	heat_density.units = "J/kg" ;
+	heat_density.checksum = "               0" ;
+
+	halo_berg=f.createVariable('halo_berg','d',('i'))
+	halo_berg.long_name = "halo_berg" ;
+	halo_berg.units = "dimensionless" ;
+	halo_berg.checksum = "               0" ;
+
+	static_berg=f.createVariable('static_berg','d',('i'))
+	static_berg.long_name = "static_berg" ;
+	static_berg.units = "dimensionless" ;
+	static_berg.checksum = "               0" ;
+
+	f.sync()
+	f.close()
+
+
+
+#-----------------------------------#
+#               Main                #
+#-----------------------------------#
+
+just2particles=False
+flip2ndconglom=True#False
+offset2ndconglom=True#False
+
+grdxmin=0; grdxmax=45000e3
+grdymin=0; grdymax=45000e3
+grdres=1000.0
+R_frac=0.45
+radius=(np.sqrt(3)/2.)*(R_frac*grdres) #S is < 0.5 grid res
+element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*radius**2)
+width=np.sqrt(element_area)
+thickness1=300.0
+thickness2=300.0
+rho_ice=850.0
+
+
+nbergs=2 #number of conglomerates
+
+#center coords of each (rectangular) conglomerate berg (CB=conglomerate berg)
+CBxc=np.array([10500, 22500]); CByc=np.array([22500, 22500])
+#CBxc=np.array([9500, 17500]); CByc=np.array([22500, 22500])
+
+#side lengths
+CBxl=np.array([2500, 7500]); CByl=np.array([7500, 2500])
+#CBxl=np.array([2500, 2500]); CByl=np.array([7500, 7500])
+#CBxl=np.array([3000, 3000]); CByl=np.array([3000, 3000])
+CByl=CByl.astype(int); CBxl=CBxl.astype(int)
+
+#--- xmax, xmin, ymax, ymin for each CB --
+CBxmin=CBxc-(0.5*CBxl); CBxmax=CBxc+(0.5*CBxl)
+CBymin=CByc-(0.5*CByl); CBymax=CByc+(0.5*CByl)
+#this shouldn't happen:
+CBxmin[CBxmin<grdxmin]=grdxmin; CBxmax[CBxmax>grdxmax]=grdxmax
+CBymin[CBxmin<grdymin]=grdymin; CBymax[CBymax>grdymax]=grdymax
+CBxc=0.5*(CBxmin+CBxmax); CByc=0.5*(CBymin+CBymax)
+
+#if just want one particle per CB
+if just2particles:
+        CBxmin=CBxc; CBxmax=CBxc
+        CBymin=CByc; CBymax=CByc
+
+#--- min and max thicknesses for each CB ---
+h1=thickness1; h2=thickness2
+CBhmax=np.array([h1,h1]); CBhmin=np.array([h2,h2])
+
+#radii
+CBrad=np.array([radius,radius])
+
+berg_x=[]; berg_y=[]
+berg_id=[]; berg_static=[]
+berg_width=[]; berg_bonds=[]
+berg_h=[]; berg_mass_scaling=[]
+berg_mass=[]
+berg_uvel=[]; berg_vvel=[]
+
+berg_count=0
+
+for i in range(nbergs):
+        x_start=CBxmin[i]+(CBrad[i]*2./np.sqrt(3))
+
+        if flip2ndconglom and i>0:
+                x_start=CBxmax[i]-(CBrad[i]*2./np.sqrt(3))
+
+        #pdb.set_trace()
+        if x_start>CBxmax[i]:
+                x_start=CBxmax[i]
+        y_start0=CBymin[i]+CBrad[i]
+        if y_start0>CBymax[i]:
+                y_start0=CBymax[i]
+        element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*(CBrad[i])**2)
+        #H (thickness) is a linear function of a berg element's position from the
+        #center of the CB. H=Hmax at the center of the CB and H=Hmin at a corner of the
+        #CB, where the dist of a corner from the center is:
+        cdistb=np.sqrt((CBxmin[i]-CBxc[i])**2+(CBymin[i]-CByc[i])**2)
+        j=0
+        x_val=x_start
+        offset=0.0
+        if (i==0):
+                uvel=0.05#0.075
+        else:
+                uvel=-0.15#-0.05
+                if (offset2ndconglom):
+                        offset=250.0
+        vvel=0.025#0.01
+        #berg_count_start=berg_count
+        while x_val<=CBxmax[i] and x_val>=CBxmin[i]:
+                y_start=y_start0+((j%2)*CBrad[i])+offset
+                k=0
+                y_val=y_start
+                while y_val<=(CBymax[i]+offset):
+                        berg_count=berg_count+1
+                        berg_id.append(berg_count)
+                        berg_x.append(x_val)
+                        berg_y.append(y_val)
+                        berg_width.append(sqrt(element_area))
+                        #dist of berg elem from center of CB
+                        bdistc=np.sqrt((x_val-CBxc[i])**2+(y_val-CByc[i])**2)
+                        bh=CBhmin[i]*bdistc/cdistb + CBhmax[i]*(1-bdistc/cdistb)
+                        if (just2particles):
+                                bh=h1
+                        berg_h.append(bh) #thickness
+                        berg_mass_scaling.append(1)
+                        berg_mass.append(bh*rho_ice*element_area)
+                        berg_static.append(0)
+                        berg_uvel.append(uvel)
+                        berg_vvel.append(vvel)
+                        # if (x_val<22000):
+                        #         berg_vvel.append(vvel)
+                        # else:
+                        #         berg_vvel.append(0.4)
+                        #berg_CBid.append(i)
+                        k=k+1
+                        y_val=y_start+(2*k*CBrad[i])
+                j=j+1
+                if flip2ndconglom and i>0:
+                        x_val=x_start-(np.sqrt(3)*CBrad[i]*j)
+                else:
+                        x_val=x_start+(np.sqrt(3)*CBrad[i]*j)
+
+print('Number of bergs',berg_count)
+
+#pdb.set_trace()
+
+#Create iceberg restart file
+Ice_geometry_source='Generic'
+Create_iceberg_restart_file(berg_count,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)
diff --git a/tests/ground_frac_test/.gitignore b/tests/ground_frac_test/.gitignore
new file mode 100644
index 0000000..68bcbc9
--- /dev/null
+++ b/tests/ground_frac_test/.gitignore
@@ -0,0 +1 @@
+results/
\ No newline at end of file
diff --git a/tests/ground_frac_test/README b/tests/ground_frac_test/README
new file mode 100644
index 0000000..83093c2
--- /dev/null
+++ b/tests/ground_frac_test/README
@@ -0,0 +1,5 @@
+1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
+2.(optional) edit input.nml
+3. run the model: ./RUN
+4, animate the results: animate_trajectories.py
+
diff --git a/tests/ground_frac_test/RUN b/tests/ground_frac_test/RUN
new file mode 100755
index 0000000..f881323
--- /dev/null
+++ b/tests/ground_frac_test/RUN
@@ -0,0 +1,7 @@
+rm iceberg_trajectories.nc
+rm iceberg_trajectories.nc.*
+rm bond_trajectories.nc
+rm bond_trajectories.nc.*
+srun -n9 ./../../build/bergs.x
+
+
diff --git a/tests/ground_frac_test/animate_trajectories.py b/tests/ground_frac_test/animate_trajectories.py
new file mode 100755
index 0000000..8b9aa7d
--- /dev/null
+++ b/tests/ground_frac_test/animate_trajectories.py
@@ -0,0 +1,121 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+import matplotlib.pyplot as plt
+from matplotlib.animation import FuncAnimation
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
+                    help=''' provide filename to plot''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+
+
+def main(args):
+
+    print('reading file')
+
+    filename=args.fname
+    #filename = 'iceberg_trajectories.nc'
+    field = 'lon'
+    field2 = 'lat'
+
+    with nc.Dataset(filename) as file:
+        x = file.variables['lon'][:]/1.e3
+        y = file.variables['lat'][:]/1.e3
+        day = file.variables['day'][:]
+
+    ud = np.unique(day)
+    t = ud[0]
+
+    # frame info
+    num_frames = len(ud)
+    movie_len = 10.0 #seconds
+    frame_len = 1000.0*movie_len/num_frames
+
+    xmin = 0
+    xmax = 30
+    ymin = xmin
+    ymax = xmax
+
+    anim_running = True
+
+    def animate(i):
+
+        x1 = x[day == ud[i]]
+        y1 = y[day == ud[i]]
+        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
+
+        scat.set_offsets(data)
+
+        t = ud[i]
+        time_text.set_text('time = %.1f days' % t )
+        return scat,time_text
+
+    def init():
+        scat.set_offsets([])
+        return scat,
+
+    def onClick(event):
+        global anim_running
+        if anim_running:
+            ani.event_source.stop()
+            anim_running = False
+        else:
+            ani.event_source.start()
+            anim_running = True
+
+    # Now we can do the plotting!
+    f = plt.figure(figsize=(5,5))
+    f.tight_layout()
+    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
+    scat = ax1.scatter([],[],marker='o',facecolor='w',s=50,edgecolor='red')
+    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
+
+    # Change major ticks to show every 20.
+    ax1.xaxis.set_major_locator(MultipleLocator(5))
+    ax1.yaxis.set_major_locator(MultipleLocator(5))
+
+    ax1.xaxis.set_minor_locator(MultipleLocator(1))
+    ax1.yaxis.set_minor_locator(MultipleLocator(1))
+
+    # Turn grid on for both major and minor ticks and style minor slightly
+    # differently.
+    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
+    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
+
+    ax1.set_xlabel('x (km)')
+    ax1.set_ylabel('y (km)')
+    ax1.set_title('Iceberg trajectory')
+
+    f.canvas.mpl_connect('button_press_event', onClick)
+
+    ani = FuncAnimation(
+        f,animate,init_func=init,frames=num_frames,
+        interval=frame_len,blit=True,repeat=True)
+
+    print('time',t)
+
+    plt.show()
+    #animation.save("iceberg_traj_animation.mp4")
+
+
+print('Script complete')
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
diff --git a/tests/ground_frac_test/animate_trajectories_1pe.py b/tests/ground_frac_test/animate_trajectories_1pe.py
new file mode 100755
index 0000000..beee932
--- /dev/null
+++ b/tests/ground_frac_test/animate_trajectories_1pe.py
@@ -0,0 +1,180 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+import matplotlib.pyplot as plt
+from matplotlib.animation import FuncAnimation
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc.0000',
+                    help=''' provide filename to plot''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+
+
+def main(args):
+
+    print('reading file')
+
+    filename=args.fname
+    #filename = 'iceberg_trajectories.nc'
+    field = 'lon'
+    field2 = 'lat'
+
+    with nc.Dataset(filename) as file:
+        x = file.variables['lon'][:]/1.e3
+        y = file.variables['lat'][:]/1.e3
+        day = file.variables['day'][:]
+        hs = file.variables['halo_berg'][:]
+        #hs = file.variables['n_bonds'][:]        
+
+    #hs = hs+1
+    ud = np.unique(day)
+    t = ud[0]
+
+    print('unique hs',np.unique(hs))
+
+    # frame info
+    num_frames = len(ud)
+    movie_len = 10.0 #seconds
+    frame_len = 1000.0*movie_len/num_frames
+
+    xmin = np.floor(min(min(x),min(y),-5))
+    xmax = np.ceil(max(max(x),max(y),35))
+    ymin = xmin
+    ymax = xmax
+
+    anim_running = True
+
+    def animate(i):
+
+        x1 = x[day == ud[i]]
+        y1 = y[day == ud[i]]
+        hstat = hs[day == ud[i]]
+        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
+
+        cstring=[]
+        for j in range(len(hstat)):
+            if (hstat[j]<0):
+                cstring.append("m")
+            elif (hstat[j]==0):
+                cstring.append("b")
+            elif (hstat[j]==1):
+                cstring.append("r")
+            elif (hstat[j]==2):
+                cstring.append("g")
+            elif (hstat[j]==3):
+                cstring.append("k")
+            elif (hstat[j]==4):
+                cstring.append("c")
+            elif (hstat[j]==5):
+                cstring.append("y")
+            elif (hstat[j]==6):
+                cstring.append("w")
+            elif (hstat[j]==10):                
+                cstring.append("c")
+            # else:
+            #     cstring.append("y")
+
+        scat.set_offsets(data)
+        scat.set_color(cstring)
+        scat.set_edgecolor('k')
+
+        t = ud[i]
+        time_text.set_text('time = %.1f days' % t )
+        return scat,time_text
+
+    def init():
+        scat.set_offsets([])
+        return scat,
+
+    def onClick(event):
+        global anim_running
+        if anim_running:
+            ani.event_source.stop()
+            anim_running = False
+        else:
+            ani.event_source.start()
+            anim_running = True
+
+    # Now we can do the plotting!
+    f = plt.figure(figsize=(5,5))
+    f.tight_layout()
+    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
+    scat = ax1.scatter([],[],marker='o',s=60)
+    #scat = ax1.scatter([],[],marker='o',facecolor='w',s=60,edgecolor='red')
+    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
+
+    # Change major ticks to show every 20.
+    ax1.xaxis.set_major_locator(MultipleLocator(5))
+    ax1.yaxis.set_major_locator(MultipleLocator(5))
+
+    ax1.xaxis.set_minor_locator(MultipleLocator(1))
+    ax1.yaxis.set_minor_locator(MultipleLocator(1))
+
+    # Turn grid on for both major and minor ticks and style minor slightly
+    # differently.
+    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
+    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
+
+    ax1.set_xlabel('x (km)')
+    ax1.set_ylabel('y (km)')
+    ax1.set_title('Iceberg trajectory')
+
+    f.canvas.mpl_connect('button_press_event', onClick)
+
+    ani = FuncAnimation(
+        f,animate,init_func=init,frames=num_frames,
+        interval=frame_len,blit=True,repeat=True)
+
+    print('time',t)
+
+    plt.plot([0,0],[0,30],'k-',lw=1)
+    plt.plot([10,10],[0,30],'k-',lw=1)
+    plt.plot([20,20],[0,30],'k-',lw=1)
+    plt.plot([30,30],[0,30],'k-',lw=1)
+    plt.plot([0,30],[0,0],'k-',lw=1)
+    plt.plot([0,30],[10,10],'k-',lw=1)
+    plt.plot([0,30],[20,20],'k-',lw=1)
+    plt.plot([0,30],[30,30],'k-',lw=1)
+
+    plt.plot([-2,-2],[-2,33],'b:',lw=1)
+    plt.plot([3,3],[-2,33],'b:',lw=1)
+    plt.plot([8,8],[-2,33],'b:',lw=1)
+    plt.plot([13,13],[-2,33],'b:',lw=1)
+    plt.plot([18,18],[-2,33],'b:',lw=1)
+    plt.plot([23,23],[-2,33],'b:',lw=1)
+    plt.plot([28,28],[-2,33],'b:',lw=1)
+    plt.plot([33,33],[-2,33],'b:',lw=1)    
+
+    plt.plot([-2,33],[-2,-2],'b:',lw=1)
+    plt.plot([-2,33],[3,3],'b:',lw=1)
+    plt.plot([-2,33],[8,8],'b:',lw=1)
+    plt.plot([-2,33],[13,13],'b:',lw=1)
+    plt.plot([-2,33],[18,18],'b:',lw=1)
+    plt.plot([-2,33],[23,23],'b:',lw=1)
+    plt.plot([-2,33],[28,28],'b:',lw=1)
+    plt.plot([-2,33],[33,33],'b:',lw=1)
+
+    plt.show()
+    #animation.save("iceberg_traj_animation.mp4")
+
+
+print('Script complete')
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
diff --git a/tests/ground_frac_test/diag_table b/tests/ground_frac_test/diag_table
new file mode 100644
index 0000000..c1c8819
--- /dev/null
+++ b/tests/ground_frac_test/diag_table
@@ -0,0 +1,3 @@
+"icebergs test"
+1 1 1 0 0 0
+
diff --git a/tests/ground_frac_test/input.nml b/tests/ground_frac_test/input.nml
new file mode 100644
index 0000000..7168d82
--- /dev/null
+++ b/tests/ground_frac_test/input.nml
@@ -0,0 +1,180 @@
+!KID, bergs_chksum: write_restart berg chksum=              32083975 chksum2=            2055392101 chksum3=           -2018330166 chksum4=           -2018330166 chksum5=           -1470408987 #=                    67
+!KID, grd_chksum2:    # of bergs/cell chksum=                     0 chksum2=                     0 min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
+! Total number of bonds is:          286 
+
+&icebergs_driver_nml
+  ni=45 !30 !number of elements, x direction
+  nj=45 !30 !number of elements, y direction
+  ibdt=1800.0 !seconds
+  ibuo=0.1 !ocean x velocity
+  ibvo=0.0 !1 !2 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=999999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.true.
+  collision_test=.false.
+  grounding_test=.true.
+  bump_depth=200.0 !(m) depth of top of gaussian bump below sea level 
+/
+
+&icebergs_nml
+!200 n:0.0278 vo=.1
+!200 n:0.0325 or 0.03 vo=0
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=10 !20 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
+    contact_distance=1.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7 !!5.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=3.16e6 !200.0 !for power-law-type friction
+    h_to_init_grounding=200.0 !300.0 !150.0 !300.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='strain' !('none') 'strain_rate','strain',or 'none'
+
+    !for scale_damping_by_pmag=.false., old_mts
+    !frac_thres_n = 0.018 !0.02
+    !frac_thres_t = 0.05076 !0.0564
+
+    !scale_damping_by_pmag=.false., new_mts
+    frac_thres_n = 0.0162
+    frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    rho_bergs=850. ! (850) iceberg density
+    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    !tangent_spring_coef=3.85e-6 !10 !6
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=1.0 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=24000 ! (24) Period between verbose messages
+    traj_sample_hrs=0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.true. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/ground_frac_test/makeberg/RUN b/tests/ground_frac_test/makeberg/RUN
new file mode 100755
index 0000000..24c0f15
--- /dev/null
+++ b/tests/ground_frac_test/makeberg/RUN
@@ -0,0 +1,12 @@
+./makeberg.py
+
+rm ./output_files/Generic*
+
+./../../Iceberg_repository/Scripts_and_analysis/initialize_bergs_in_pattern.py \
+	-set_all_bergs_static_by_default=False -Run_plotting_subroutine=False \
+	-break_some_bonds=False -Ice_geometry_source='Generic' \
+	-Generic_ice_geometry_filename='./testtabularberg.nc' \
+	-ISOMIP_reduced=False -collision_test=False -grounding_test=true
+
+cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
+cp ./output_files/Generic_bonds_iceberg.res.nc ./../INPUT/bonds_iceberg.res.nc
diff --git a/tests/ground_frac_test/makeberg/makeberg.py b/tests/ground_frac_test/makeberg/makeberg.py
new file mode 100755
index 0000000..b38e604
--- /dev/null
+++ b/tests/ground_frac_test/makeberg/makeberg.py
@@ -0,0 +1,89 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset  
+import numpy as np 
+import math
+#import os
+from pylab import *
+#import pdb
+import netCDF4 as nc
+
+nx = 30
+ny = 30
+New_ice_thickness_filename='testberg.nc'
+grid_res = 1.e3 #1 km 
+grid_area = grid_res * grid_res
+h_ice = 300.0
+
+New_ice_thickness_filename='testtabularberg.nc'
+g=Dataset(New_ice_thickness_filename,'w') # w if for creating a file
+
+g.createDimension('nx',nx)
+g.createDimension('ny',ny)
+thick_h=g.createVariable('thick','f8',('ny','nx'))
+area_h=g.createVariable('area','f8',('ny','nx'))
+lat_h=g.createVariable('lat','f8','ny')
+lon_h=g.createVariable('lon','f8','nx')
+#lat_h=g.createVariable('lat','f8',('ny','nx'))
+#lon_h=g.createVariable('lon','f8',('ny','nx'))
+
+thick_h.units = 'm'
+thick_h.standard_name = 'ice shelf thickness'
+area_h.units = 'm2'
+area_h.standard_name = 'ice shelf area'
+lon_h.unit = 'm'
+lon_h.standard_name = 'longitude'
+lat_h.unit = 'm'
+lat_h.standard_name = 'latitude'
+
+
+
+#g.variables['thick'][:]=h_ice
+g.variables['area'][:,:]=grid_area
+
+#create a circular tabular berg centered on the following coords (km)
+cy = 3.5e3
+cx = 15.0e3
+xl = 8.e3 #7.0e3 #5.0e3
+yl = 4.e3 #5.0e3
+xmin=cx-xl/2
+xmax=cx+xl/2
+ymin=cy-yl/2
+ymax=cy+yl/2
+maxh=h_ice
+minh=300 #100
+slopedist=sqrt((xl/2)**2 + (yl/2)**2)
+slope=(minh-h_ice)/slopedist
+
+#cx2 = 15.5e3
+
+for i in range(nx):
+
+        tx = float(i) * grid_res 
+        g.variables['lon'][i] = tx
+        
+        for j in range(ny):
+               
+                ty = float(j) * grid_res
+
+                # dist = sqrt((tx-cx)*(tx-cx) + (ty-cy)*(ty-cy))
+                # if (dist <1.e3): #or dist2<1.e3):
+                #         g.variables['thick'][i,j]=h_ice
+                if (tx>=xmin and tx<=xmax and ty>=ymin and ty<=ymax):
+                        dist = sqrt((tx-cx)*(tx-cx) + (ty-cy)*(ty-cy))                         
+                        g.variables['thick'][i,j]=slope*dist+h_ice
+                                               
+                else:
+                        g.variables['thick'][i,j]=0.0
+
+                        
+
+for j in range(ny):
+        g.variables['lat'][j] = float(j) * grid_res 
+
+print('Creating file: ' , New_ice_thickness_filename)
+
+g.sync()
+g.close()
+
+        
diff --git a/tests/ground_frac_test/reference_input.nml b/tests/ground_frac_test/reference_input.nml
new file mode 100644
index 0000000..3921603
--- /dev/null
+++ b/tests/ground_frac_test/reference_input.nml
@@ -0,0 +1,183 @@
+!KID, bergs_chksum: write_restart berg chksum=            -195625967 chksum2=            1455880446 chksum3=            -243405929 chksum4=            -243405929 chksum5=            -495829423 #=                    67
+!KID, grd_chksum2:    # of bergs/cell chksum=                     0 chksum2=                     0 min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
+! Total number of bonds is:          240 
+! All iceberg bonds are connected and working well
+!KID, grd_chksum3:   write stored_ice chksum=             859876028 chksum2=            -702294156 min= 0.000000000E+00 max= 7.389503907E+11 mean= 4.320307812E+10 rms= 1.148723635E+11 sd= 1.064384984E+11
+
+
+&icebergs_driver_nml
+  ni=45 !30 !number of elements, x direction
+  nj=45 !30 !number of elements, y direction
+  ibdt=1800.0 !seconds
+  ibuo=0.1 !ocean x velocity
+  ibvo=0.0 !1 !2 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=999999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.true.
+  collision_test=.false.
+  grounding_test=.true.
+  bump_depth=200.0 !(m) depth of top of gaussian bump below sea level 
+/
+
+&icebergs_nml
+!200 n:0.0278 vo=.1
+!200 n:0.0325 or 0.03 vo=0
+    !defaults given in parentheses:
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=10 !20 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
+    contact_distance=1.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7 !!5.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=3.16e6 !200.0 !for power-law-type friction
+    h_to_init_grounding=200.0 !300.0 !150.0 !300.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='strain' !('none') 'strain_rate','strain',or 'none'
+    !old !frac_thres_n strain, 200 m bd  0.045, 0.04, 
+    !old !frac_trhes_t strain, 200 m bd: 0.08 , 0.1 .
+    !old !frac_thres_n sr, 200 m bd: 2.5e-5 
+    !old !frac_thres_t sr, 200 m bd: 5.e-5
+    frac_thres_n= 0.025 !0.04 !0.0415 !0.045 !0.05
+    frac_thres_t= 0.0705 !0.095 !0.0925 !0.1 !0.09
+
+    !for scale_damping_by_pmag=.false.
+    !frac_thres_n = 0.018 !0.02
+    !frac_thres_t = 0.05076 !0.0564
+
+    halo=3 !(4) halo width
+    Lx=45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    rho_bergs=850. ! (850) iceberg density
+    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    !tangent_spring_coef=3.85e-6 !10 !6
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.true. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.true. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=1.0 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=24000 ! (24) Period between verbose messages
+    traj_sample_hrs=6 !(24) sampling period for trajectory storage
+    traj_write_hrs=6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.true. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/nc2csv.py b/tests/nc2csv.py
new file mode 100755
index 0000000..be5f7bc
--- /dev/null
+++ b/tests/nc2csv.py
@@ -0,0 +1,164 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import csv
+import math
+import os
+import argparse
+
+#CONVERT BERG TRAJECTORIES FROM NETCDF TO CSV FILE FOR VISUALIZATION IN PARAVIEW
+#returns a series of csv files (one for each time step)
+#To view csv in paraview:
+#1. load all csv files in the series
+#2. Filters --> Table To Points
+#3. In the TableToPoints filter, assign x for X Column, and y for Y Column. Check 2D Points.
+
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+                                     '''Convert iceberg trajectories netcdf file to csv file.''',
+                                     epilog='Written by Alex Huth, 2020')
+    parser.register('type','bool',str2bool) # add type keyword to registries
+    parser.add_argument('-fin', type=str, default='iceberg_trajectories.nc',
+                        help=''' provide netcdf filename''')
+    parser.add_argument('-fout', type=str, default='./csvresults/iceberg_trajectories',
+                        help=''' provide filename prefix for csv''')
+    parser.add_argument('-short_traj', type='bool', default=False,
+		        help=''' indicate whether save_short_traj was used ''')
+    parser.add_argument('-mts', type='bool', default=True,
+       	                help=''' indicate whether mts was used ''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+
+
+def main(args ):
+
+    print('reading file')
+
+    fin=args.fin
+    fout=args.fout
+    short_traj=args.short_traj
+    mts=args.mts
+    if short_traj==True:
+        mts=False
+
+    with nc.Dataset(fin) as file:
+        lon = file.variables['lon'][:]
+        lat = file.variables['lat'][:]
+        year = file.variables['year'][:]
+        day = file.variables['day'][:]
+        id_cnt = file.variables['id_cnt'][:]
+        id_ij = file.variables['id_ij'][:]
+        if short_traj==True:
+            fields = ['x','y','time','id']
+        else:
+            uvel = file.variables['uvel'][:]
+            vvel = file.variables['vvel'][:]
+            # uo = file.variables['uo'][:]
+            # vo = file.variables['vo'][:]
+            # ui = file.variables['ui'][:]
+            # vi = file.variables['vi'][:]
+            # ua = file.variables['ua'][:]
+            # va = file.variables['va'][:]
+            pmass = file.variables['mass'][:]
+            # mass_of_bits= file.variables['mass_of_bits'][:]
+            # heat_density= file.variables['heat_density'][:]
+            thickness = file.variables['thickness'][:]
+            width = file.variables['width'][:]
+            length = file.variables['length'][:]
+            # ssh_x = file.variables['ssh_x'][:]
+            # ssh_y = file.variables['ssh_y'][:]
+            # sst = file.variables['sst'][:]
+            # sss = file.variables['sss'][:]
+            # cn = file.variables['cn'][:]
+            # hi = file.variables['hi'][:]
+            axn = file.variables['axn'][:]
+            ayn = file.variables['ayn'][:]
+            bxn = file.variables['bxn'][:]
+            byn = file.variables['byn'][:]
+            #halo_berg = file.variables['halo_berg'][:]
+            ocean_depth  = file.variables['od'][:]
+            if mts==True:
+                nbonds_id = file.variables['n_bonds'][:]
+                #uvprev = file.variables['uvel_prev'][:]
+                #vvprev = file.variables['vvel_prev'][:]
+                axnf = file.variables['axn_fast'][:]
+                aynf = file.variables['ayn_fast'][:]
+                bxnf = file.variables['bxn_fast'][:]
+                bynf = file.variables['byn_fast'][:]
+                tot_axn = file.variables['tot_accel_x'][:]
+                tot_ayn = file.variables['tot_accel_y'][:]
+                fields = ['x','y','time','id','uv','vv','mass','H','W','L','axn','ayn','bxn','byn','ocean_depth','axnf','aynf','bxnf','bynf','nbonds_id','accelx','accely']
+            else:
+                fields = ['x','y','time','id','uv','vv','mass','H','W','L','axn','ayn','bxn','byn','ocean_depth']
+
+    idmid=int('2',8)**32
+    ptime=year+day/365.15
+    pidin=id_cnt*idmid+id_ij
+    utime=np.unique(ptime)
+
+    for i in range(len(utime)):
+        x = lon[ptime == utime[i]]
+        y = lat[ptime == utime[i]]
+        time = ptime[ptime == utime[i]]
+        pid = pidin[ptime == utime[i]]
+        if short_traj==False:
+            uv = uvel[ptime == utime[i]]
+            vv = vvel[ptime == utime[i]]
+            mass = pmass[ptime == utime[i]]
+            H = thickness[ptime == utime[i]]
+            W = width[ptime == utime[i]]
+            L = length[ptime == utime[i]]
+            ax = axn[ptime == utime[i]]
+            ay = ayn[ptime == utime[i]]
+            bx = bxn[ptime == utime[i]]
+            by = byn[ptime == utime[i]]
+            od = ocean_depth[ptime == utime[i]]
+            if mts==True:
+                nb = nbonds_id[ptime == utime[i]]
+                axf = axnf[ptime == utime[i]]
+                ayf = aynf[ptime == utime[i]]
+                bxf = bxnf[ptime == utime[i]]
+                byf = bynf[ptime == utime[i]]
+                tot_ax = tot_axn[ptime == utime[i]]
+                tot_ay = tot_ayn[ptime == utime[i]]
+        filename = fout+str(i)+".csv"
+        with open(filename, 'w') as file:
+            writer = csv.writer(file)
+            writer.writerow(fields)
+            if short_traj==True:
+                for j in range(len(x)):
+                    writer.writerow([x[j],y[j],time[j],pid[j]])
+            else:
+                if mts==True:
+                    for j in range(len(x)):
+                        writer.writerow([x[j],y[j],time[j],pid[j],uv[j],vv[j],mass[j],H[j],W[j],L[j],ax[j],ay[j],bx[j],by[j],od[j],axf[j],ayf[j],bxf[j],byf[j],nb[j],tot_ax[j],tot_ay[j]])
+                else:
+                    for j in range(len(x)):
+                        writer.writerow([x[j],y[j],time[j],pid[j],uv[j],vv[j],mass[j],H[j],W[j],L[j],ax[j],ay[j],bx[j],by[j],od[j]])
+
+print('Script complete')
+
+def str2bool(string):
+	if string.lower() in  ("yes", "true", "t", "1"):
+		Value=True
+	elif string.lower() in ("no", "false", "f", "0"):
+		Value=False
+	else:
+		print '**********************************************************************'
+		print 'The input variable ' ,str(string) ,  ' is not suitable for boolean conversion, using default'
+		print '**********************************************************************'
+
+		Value=None
+		return
+
+	return Value
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
diff --git a/tests/nc2csv_bonds.py b/tests/nc2csv_bonds.py
new file mode 100755
index 0000000..b8caa0e
--- /dev/null
+++ b/tests/nc2csv_bonds.py
@@ -0,0 +1,130 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import csv
+import math
+import os
+import argparse
+
+#CONVERT BOND TRAJECTORIES FROM NETCDF TO CSV FILE FOR VISUALIZATION IN PARAVIEW
+#returns a series of csv files (one for each time step)
+#To view csv in paraview:
+#1. load all csv files in the series
+#2. Filters --> Table To Points
+#3. In the TableToPoints filter, assign x for X Column, and y for Y Column. Check 2D Points.
+#4. Use calculator to define a vector field for visualizing the bond:
+#   bond_vect = n1*iHat+n2*iHat
+#5. Make a line glyph w/ orientation given by bond_vect components and magnitude by length
+
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+                                     '''Convert iceberg bond trajectories netcdf file to csv file.''',
+                                     epilog='Written by Alex Huth, 2020')
+    parser.register('type','bool',str2bool) # add type keyword to registries
+    parser.add_argument('-fin', type=str, default='bond_trajectories.nc',
+                        help=''' provide netcdf filename''')
+    parser.add_argument('-fout', type=str, default='./csvresults/bond_trajectories',
+                        help=''' provide filename prefix for csv''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+def main(args ):
+
+    print('reading file')
+
+    fin=args.fin
+    fout=args.fout
+
+    with nc.Dataset(fin) as file:
+        lon = file.variables['lon'][:]
+        lat = file.variables['lat'][:]
+        year = file.variables['year'][:]
+        day = file.variables['day'][:]
+        length = file.variables['length'][:]
+        n1 = file.variables['n1'][:]
+        n2 = file.variables['n2'][:]
+        rot = file.variables['rotation'][:]
+        rrot = file.variables['rel_rotation'][:]
+        ns = file.variables['n_strain'][:]
+        nsr = file.variables['n_strain_rate'][:]
+        id_cnt1 = file.variables['id_cnt1'][:]
+        id_ij1 = file.variables['id_ij1'][:]
+        id_cnt2 = file.variables['id_cnt2'][:]
+        id_ij2 = file.variables['id_ij2'][:]
+        fields = ['x','y','time','len','n1','n2','rot','rrot','ns','nsr','berg_id1','berg_id2']
+
+    idmid=int('2',8)**32
+    btime=year+day/365.15
+    bidin1=id_cnt1*idmid+id_ij1
+    bidin2=id_cnt2*idmid+id_ij2
+
+    # uid=np.unique(bidin1)
+    # uid2=np.unique(bidin2)
+    # print('uid',uid)
+    # print('uid2',uid2)
+
+    #there are originally 2 copies of each bond (one copy for each particle in the bond)
+    #Remove the duplicates:
+    biddiff=bidin2-bidin1
+
+    lon = lon[biddiff>0]
+    lat = lat[biddiff>0]
+    btime = btime[biddiff>0]
+    length = length[biddiff>0]
+    n1 = n1[biddiff>0]
+    n2 = n2[biddiff>0]
+    rot=rot[biddiff>0]
+    rrot=rrot[biddiff>0]
+    ns=ns[biddiff>0]
+    nsr=nsr[biddiff>0]
+    bidin1 = bidin1[biddiff>0]
+    bidin2 = bidin2[biddiff>0]
+
+    utime=np.unique(btime)
+
+    for i in range(len(utime)):
+        x = lon[btime == utime[i]]
+        y = lat[btime == utime[i]]
+        time = btime[btime == utime[i]]
+        blen = length[btime == utime[i]]
+        bn1 = n1[btime == utime[i]]
+        bn2 = n2[btime == utime[i]]
+        brot = rot[btime == utime[i]]
+        brrot = rrot[btime == utime[i]]
+        bns = ns[btime == utime[i]]
+        bnsr = nsr[btime == utime[i]]
+        bid1 = bidin1[btime == utime[i]]
+        bid2 = bidin2[btime == utime[i]]
+
+        filename = fout+str(i)+".csv"
+        with open(filename, 'w') as file:
+            writer = csv.writer(file)
+            writer.writerow(fields)
+            for j in range(len(x)):
+                writer.writerow([x[j],y[j],time[j],blen[j],bn1[j],bn2[j],brot[j],brrot[j],bns[j],bnsr[j],bid1[j],bid2[j]])
+
+print('Script complete')
+
+def str2bool(string):
+	if string.lower() in  ("yes", "true", "t", "1"):
+		Value=True
+	elif string.lower() in ("no", "false", "f", "0"):
+		Value=False
+	else:
+		print '**********************************************************************'
+		print 'The input variable ' ,str(string) ,  ' is not suitable for boolean conversion, using default'
+		print '**********************************************************************'
+
+		Value=None
+		return
+
+	return Value
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
diff --git a/tests/plot_energy.py b/tests/plot_energy.py
new file mode 100755
index 0000000..f22f89b
--- /dev/null
+++ b/tests/plot_energy.py
@@ -0,0 +1,218 @@
+#!/usr/bin/env python3
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+import matplotlib.pyplot as plt
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Plot energy from iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
+                    help=''' provide filename to plot''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+
+
+def main(args):
+
+    print('reading file')
+
+    filename=args.fname
+
+    with nc.Dataset(filename) as file:
+        Ee    = file.variables['Ee'][:]
+        Ed    = file.variables['Ed'][:]
+        Eext  = file.variables['Eext'][:]
+        Eec   = file.variables['Ee_contact'][:]
+        Edc   = file.variables['Ed_contact'][:]
+        Efrac = file.variables['Efrac'][:]
+        day   = file.variables['day'][:]
+        vx    = file.variables['uvel_prev'][:]
+        vy    = file.variables['vvel_prev'][:]
+        mass  = file.variables['mass'][:]
+        x    = file.variables['lon'][:]
+        y    = file.variables['lat'][:]
+        vx2    = file.variables['uvel'][:]
+        vy2    = file.variables['vvel'][:]
+
+    crop=False
+    tc=1.0
+    if crop:
+        Ee = Ee[day<=tc]
+        Ed = Ed[day<=tc]
+        Eext=Eext[day<=tc]
+        Eec=Eec[day<=tc]
+        Edc=Edc[day<=tc]
+        Efrac=Efrac[day<=tc]
+        vx=vx[day<=tc]
+        vy=vy[day<=tc]
+        mass=mass[day<=tc]
+        x=x[day<=tc]
+        y=y[day<=tc]
+        day=day[day<=tc]
+        vx2=vx2[day<=tc]
+        vy2=vy2[day<=tc]
+
+
+    # vx=np.copy(vx2); vy=np.copy(vy2)
+
+    ud = np.unique(day)
+    step0 = 0
+    dt = ud[1]-ud[0]
+
+    print('dt',dt)
+
+    tot_Ee = np.zeros(len(ud)-step0)
+    tot_Ed = np.zeros(len(ud)-step0)
+    tot_Eext = np.zeros(len(ud)-step0)
+    tot_Eec = np.zeros(len(ud)-step0)
+    tot_Edc = np.zeros(len(ud)-step0)
+    tot_Efrac = np.zeros(len(ud)-step0)
+    tot_Ek = np.zeros(len(ud)-step0)
+    tot_E  = np.zeros(len(ud)-step0)
+    tot_momentum_x = np.zeros(len(ud)-step0)
+    tot_momentum_y = np.zeros(len(ud)-step0)
+    tot_momentum = np.zeros(len(ud)-step0)
+    tot_momentum_x2 = np.zeros(len(ud)-step0)
+    tot_momentum_y2 = np.zeros(len(ud)-step0)
+    tot_momentum2 = np.zeros(len(ud)-step0)
+
+    # tot_vel_diff = np.zeros(len(ud)-step0)
+
+
+    #regular version
+    mom_x0 = mass[day == ud[step0]]*vx[day == ud[step0]]
+    mom_y0 = mass[day == ud[step0]]*vy[day == ud[step0]]
+    mom_x0_tot = np.sum(mom_x0); mom_y0_tot = np.sum(mom_y0)
+
+    #'uncorrected' version
+    mom_x02 = mom_x0; mom_y02=mom_y0
+    mom_x0_tot2=mom_x0_tot; mom_y0_tot2=mom_y0_tot
+
+    #if needed, 'correct' the regular version by changing the reference frame
+    #so that mom_x0_tot>0 and mom_y0_tot>0
+    dvx=0.0; dvy=0.0
+    if (mom_x0_tot==0):
+        print('changing x reference frame!')
+        dvx=0.01#e-8
+        mom_x0 = mass[day == ud[step0]]*(vx[day == ud[step0]]+dvx)
+        mom_x0_tot = np.sum(mom_x0)
+    if (mom_y0_tot==0):
+        print('changing y reference frame!')
+        dvy=0.01#e-8
+        mom_y0 = mass[day == ud[step0]]*(vy[day == ud[step0]]+dvy)
+        mom_y0_tot = np.sum(mom_y0)
+
+
+    for i in range(len(ud)-step0):
+
+        j=i+step0
+
+        #ENERGY STUFF
+        Ee1 = Ee[day == ud[j]]
+        Ed1 = Ed[day == ud[j]]
+        Eec1 = Eec[day == ud[j]]
+        Edc1 = Edc[day == ud[j]]
+        Efrac1 = Efrac[day == ud[j]]
+        Eext1 = Eext[day == ud[j]]
+        Ek1 = 0.5*mass[day == ud[j]]*(vx[day == ud[j]]**2+vy[day == ud[j]]**2)
+
+        tot_Ee[i] = np.sum(Ee1)
+        tot_Ed[i] = np.sum(Ed1)
+        tot_Eec[i] = np.sum(Eec1)
+        tot_Edc[i] = np.sum(Edc1)
+
+        tot_Efrac[i] = np.sum(Efrac1)
+        tot_Eext[i] = np.sum(Eext1)
+        tot_Ek[i] = np.sum(Ek1)
+
+        tot_E[i] = tot_Ee[i]+tot_Ed[i]+tot_Eec[i]+tot_Edc[i]+tot_Efrac[i]+tot_Eext[i]+tot_Ek[i]
+
+        #MOMENTUM STUFF
+
+        #--reg version, corrected--
+        mom_x = mass[day == ud[j]] * (vx[day == ud[j]]+dvx)
+        mom_y = mass[day == ud[j]] * (vy[day == ud[j]]+dvy)
+        tot_momentum_x[i] = (np.sum(mom_x)-mom_x0_tot)/mom_x0_tot
+        tot_momentum_y[i] = (np.sum(mom_y)-mom_y0_tot)/mom_y0_tot
+
+        #--reg version, uncorrected--
+        mom_x2 = mass[day == ud[j]] * (vx[day == ud[j]])
+        mom_y2 = mass[day == ud[j]] * (vy[day == ud[j]])
+        tot_momentum_x2[i] = (np.sum(mom_x2)-mom_x0_tot2)/mom_x0_tot2
+        tot_momentum_y2[i] = (np.sum(mom_y2)-mom_y0_tot2)/mom_y0_tot2
+
+        # ua =  vx[day == ud[j]]; va =  vy[day == ud[j]]
+        # ub = vx2[day == ud[j]]; vb = vy2[day == ud[j]]
+        # tot_vel_diff[i] = np.sum(sqrt((ua-ub)**2 + (va-vb)**2))
+
+
+    ud=ud[0:len(ud)-step0]
+
+    fig = plt.figure(1)
+    ax = plt.subplot(111)
+    ax.plot(ud, tot_E,  color='k', label='total')
+    ax.plot(ud, tot_Eext, color='c', label='external', linestyle='dashed')
+    ax.plot(ud, tot_Ee, color='b', label='elastic (bonded)', linestyle='dashed')
+    ax.plot(ud, tot_Ed, color='g', label='damping (bonded)', linestyle='dashed')
+    ax.plot(ud, tot_Eec, color='b', label='elastic (collision)', linestyle='dotted')
+    ax.plot(ud, tot_Edc, color='g', label='damping (collision)', linestyle='dotted')
+    ax.plot(ud, tot_Ek, color='r', label='kinetic', linestyle='dotted')
+    ax.plot(ud, tot_Efrac, color='m', label='dissipated fracture', linestyle='dotted')
+
+    print('min/max tot_E',np.min(tot_E),np.max(tot_E))
+
+    #ax.legend(loc="upper right")
+    chartBox = ax.get_position()
+    ax.set_position([chartBox.x0, chartBox.y0, chartBox.width*0.6, chartBox.height])
+    ax.legend(loc='upper center', bbox_to_anchor=(1.45, 0.8), shadow=True, ncol=1)
+    plt.xlabel('time (days)')
+    plt.ylabel('energy (J)')
+    #axes=plt.gca()
+    #axes.set_ylim([-1.e-14,1.e-14])
+
+    fig2 = plt.figure(2)
+    ax = plt.subplot(111)
+    ax.plot(ud[step0:], tot_momentum_x[step0:],  color='k', label='x momentum')
+    #ax.plot(ud[step0:], tot_momentum_x2[step0:],  color='y', label='x momentum 2', linestyle='dashed')
+    chartBox = ax.get_position()
+    ax.set_position([chartBox.x0, chartBox.y0, chartBox.width*0.6, chartBox.height])
+    ax.legend(loc='upper center', bbox_to_anchor=(1.45, 0.8), shadow=True, ncol=1)
+
+
+    fig3 = plt.figure(3)
+    ax = plt.subplot(111)
+    ax.plot(ud[step0:], tot_momentum_y[step0:],  color='k', label='y momentum')
+    #if (abs(mom_y0_tot2)>0):
+    #    ax.plot(ud[step0:], tot_momentum_y2[step0:],  color='y', label='y momentum 2', linestyle='dashed')
+    chartBox = ax.get_position()
+    ax.set_position([chartBox.x0, chartBox.y0, chartBox.width*0.6, chartBox.height])
+    ax.legend(loc='upper center', bbox_to_anchor=(1.45, 0.8), shadow=True, ncol=1)
+
+
+    # fig4 = plt.figure(4)
+    # ax = plt.subplot(111)
+    # ax.plot(ud[step0:], tot_vel_diff[step0:],  color='k', label='vel diff')
+    # chartBox = ax.get_position()
+    # ax.set_position([chartBox.x0, chartBox.y0, chartBox.width*0.6, chartBox.height])
+    # ax.legend(loc='upper center', bbox_to_anchor=(1.45, 0.8), shadow=True, ncol=1)
+
+
+    plt.show()
+
+print('Script complete')
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)

From d6d1c9d04cc93aefa8400d8e2244a5af7932f577 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Thu, 7 Jan 2021 16:44:47 -0500
Subject: [PATCH 258/361] Fix integer i/o formatting for gnu compiler

While intel seems happy to make up a width, gnu is more pedantic and errors when we do not
specify the formatting width. These errors are fixed in this commit:
```
 ../../../../MOM6-examples/src/icebergs/src/icebergs_framework.F90:1511:33:

            write(stderrunit,'(a,5i)') 'A', this%id, mpp_pe(), int(this%halo_berg), grdi, grdj
                                  1
 Error: Nonnegative width required in format string at (1)
 ../../../../MOM6-examples/src/icebergs/src/icebergs_framework.F90:1558:31:

          write(stderrunit,'(a,5i)') 'B', this%id, mpp_pe(), int(this%halo_berg), grdi, grdj
                                1
 Error: Nonnegative width required in format string at (1)
 ../../../../MOM6-examples/src/icebergs/src/icebergs_framework.F90:1761:31:

          write(stderrunit,'(a,5i)')  'C', this%id, mpp_pe(), int(this%halo_berg),  grdi, grdj
                                1
 Error: Nonnegative width required in format string at (1)
 ../../../../MOM6-examples/src/icebergs/src/icebergs_framework.F90:1888:31:

          write(stderrunit,'(a,5i)')  'transfer_mts_bergs', this%id, mpp_pe(), int(this%halo_berg),  grdi, grdj
                                1
 Error: Nonnegative width required in format string at (1)
 ../../../../MOM6-examples/src/icebergs/src/icebergs_framework.F90:4653:26:

              write(*,'(a,3i,2i3,i4)')'Bond matching :',berg%id,current_bond%other_berg%id, current_bond%other_id,&
                           1
 Error: Nonnegative width required in format string at (1)
```
---
 src/icebergs_framework.F90 | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index cadec85..90dcd1f 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -1508,7 +1508,7 @@ subroutine update_halo_icebergs(bergs)
     do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
       this=>bergs%list(grdi,grdj)%first
       do while (associated(this))
-          write(stderrunit,'(a,5i)') 'A', this%id, mpp_pe(), int(this%halo_berg), grdi, grdj
+        write(stderrunit,'(a,5i8)') 'A', this%id, mpp_pe(), int(this%halo_berg), grdi, grdj
         this=>this%next
       enddo
     enddo; enddo
@@ -1554,9 +1554,9 @@ subroutine update_halo_icebergs(bergs)
   if (halo_debugging) then
     do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
       this=>bergs%list(grdi,grdj)%first
-        do while (associated(this))
-        write(stderrunit,'(a,5i)') 'B', this%id, mpp_pe(), int(this%halo_berg), grdi, grdj
-      this=>this%next
+      do while (associated(this))
+        write(stderrunit,'(a,5i8)') 'B', this%id, mpp_pe(), int(this%halo_berg), grdi, grdj
+        this=>this%next
       enddo
     enddo; enddo
   endif
@@ -1758,7 +1758,7 @@ subroutine update_halo_icebergs(bergs)
     do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
       this=>bergs%list(grdi,grdj)%first
       do while (associated(this))
-        write(stderrunit,'(a,5i)')  'C', this%id, mpp_pe(), int(this%halo_berg),  grdi, grdj
+        write(stderrunit,'(a,5i8)') 'C', this%id, mpp_pe(), int(this%halo_berg),  grdi, grdj
         this=>this%next
       enddo
     enddo; enddo
@@ -1885,7 +1885,7 @@ Subroutine transfer_mts_bergs(bergs)
     do grdj = grd%jsd,grd%jed ;  do grdi = grd%isd,grd%ied
       this=>bergs%list(grdi,grdj)%first
       do while (associated(this))
-        write(stderrunit,'(a,5i)')  'transfer_mts_bergs', this%id, mpp_pe(), int(this%halo_berg),  grdi, grdj
+        write(stderrunit,'(a,5i8)') 'transfer_mts_bergs', this%id, mpp_pe(), int(this%halo_berg),  grdi, grdj
         this=>this%next
       enddo
     enddo; enddo
@@ -4650,7 +4650,7 @@ subroutine show_all_bonds(bergs)
           if (current_bond%other_berg%id .ne. current_bond%other_id) then
             !print *, 'Bond matching', berg%id,current_bond%other_berg%id, current_bond%other_id,&
             !  berg%halo_berg,current_bond%other_berg%halo_berg ,mpp_pe()
-            write(*,'(a,3i,2i3,i4)')'Bond matching :',berg%id,current_bond%other_berg%id, current_bond%other_id,&
+            write(*,'(a,3i8,2i3,i4)')'Bond matching :',berg%id,current_bond%other_berg%id, current_bond%other_id,&
               int(berg%halo_berg),current_bond%other_berg%halo_berg ,mpp_pe()
             call error_mesg('KID, show all bonds:', 'The bonds are not matching properly!', FATAL)
           endif

From 141267fb53b7cacf4e83db6cba15fb92c3c41f1f Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Thu, 7 Jan 2021 17:03:00 -0500
Subject: [PATCH 259/361] Fixed expression using abs() of logical

I'm not sure how Intel was dealing with this but gnu was very correctly calling the
abs() of a logical expression an error:

```
 ../../../../MOM6-examples/src/icebergs/src/icebergs_framework.F90:4817:42:

            if ((.not. bergs%mts) .or. (abs(berg%halo_berg .le. 1))) then
                                           1
 Error: 'a' argument of 'abs' intrinsic at (1) must have a numeric type

```
---
 src/icebergs_framework.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 90dcd1f..6070ef8 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -4814,7 +4814,7 @@ subroutine update_latlon(bergs)
       do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
         berg=>bergs%list(grdi,grdj)%first
         do while (associated(berg))
-          if ((.not. bergs%mts) .or. (abs(berg%halo_berg .le. 1))) then
+          if ((.not. bergs%mts) .or. (berg%halo_berg .le. 1)) then
             !for bergs%mts skip halo elements that only exist due to their
             !inclusion in a conglomerate (berg%halo_berg > 1). Their coords have
             !already been corrected (if needed), as the scheme below would fail.

From 2a8a337ec502db21db774327cc33c3880a2c9726 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Thu, 7 Jan 2021 17:08:00 -0500
Subject: [PATCH 260/361] Corrected declaration of radial_contact

`radial_contact` was declared as an integer but is being used as a logical.
While intel was happy to interpret .false. and 0 and .true. as 1, gnu is
not so generous. Errors were:

```
 ../../../../MOM6-examples/src/icebergs/src/icebergs_framework.F90:2159:17:

    radial_contact=.false.
                  1
 Warning: Extension: Conversion from LOGICAL(4) to INTEGER(4) at (1)
 ../../../../MOM6-examples/src/icebergs/src/icebergs_framework.F90:2180:21:

        radial_contact=.true. !contact based on berg radii can occur
                      1
 Warning: Extension: Conversion from LOGICAL(4) to INTEGER(4) at (1)
 ../../../../MOM6-examples/src/icebergs/src/icebergs_framework.F90:2192:16:

              if (radial_contact) then
                 1
 Error: IF clause at (1) requires a scalar LOGICAL expression
```
---
 src/icebergs_framework.F90 | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 6070ef8..c6693be 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -2150,7 +2150,8 @@ recursive subroutine mts_pack_contact_bergs(bergs,berg,dir,pfix,nbergs_to_send,i
   type(icebergs_gridded), pointer :: grd
   type(iceberg), pointer :: other_berg
   integer :: nc_x,nc_y,grdj,grdi,js,je,is,ie
-  integer :: current_conglom_id,radial_contact
+  integer :: current_conglom_id
+  logical :: radial_contact
   real :: R1,R2,dlon,dlat,lat_ref,dx_dlon,dy_dlat,r_dist,crit_dist,current_halo_id
   real :: rdenom
   logical :: pack_contacts

From 30274327487c60ee57f3de495ed7e7061cad8e5d Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Thu, 7 Jan 2021 17:11:39 -0500
Subject: [PATCH 261/361] Fix legacy syntax issue with write()

gnu compiler was issuing legacy warnings about an extra comma. Messages:
```
 ../../../../MOM6-examples/src/icebergs/driver/icebergs_driver.F90:333:14:

      write(*,*),''
               1
 Warning: Legacy Extension: Comma before i/o item list at (1)
 ../../../../MOM6-examples/src/icebergs/driver/icebergs_driver.F90:334:18:

      write(*,'(a)'),'-------------------------------------------'
                   1
 Warning: Legacy Extension: Comma before i/o item list at (1)
 ../../../../MOM6-examples/src/icebergs/driver/icebergs_driver.F90:338:18:

      write(*,'(a)'),'-------------------------------------------'
                   1
 Warning: Legacy Extension: Comma before i/o item list at (1)
 ../../../../MOM6-examples/src/icebergs/driver/icebergs_driver.F90:339:14:

      write(*,*),''
               1
 Warning: Legacy Extension: Comma before i/o item list at (1)
```
---
 driver/icebergs_driver.F90 | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/driver/icebergs_driver.F90 b/driver/icebergs_driver.F90
index fee0e35..a026efd 100644
--- a/driver/icebergs_driver.F90
+++ b/driver/icebergs_driver.F90
@@ -330,13 +330,13 @@ program icebergs_driver
 do while ((ns < nmax) .and. (Time < Time_end))
   if (mpp_pe()==0 .and. debug .and. mod(ns-1,write_time_inc)==0) then
     call get_date(Time, iyr, imon, iday, ihr, imin, isec)
-    write(*,*),''
-    write(*,'(a)'),'-------------------------------------------'
+    write(*,*) ''
+    write(*,'(a)') '-------------------------------------------'
     write(*,'(a,i5)')' Timestep   ',ns
     write(*,'(a,i5,a,i5,a,i5)')' year',iyr,'  month ',imon,'  day   ',iday
     write(*,'(a,i5,a,i5,a,i5)')' hour',ihr,'  minute',imin,'  second',isec
-    write(*,'(a)'),'-------------------------------------------'
-    write(*,*),''
+    write(*,'(a)') '-------------------------------------------'
+    write(*,*) ''
   end if
 
   ! The main driver the steps updates icebergs

From 5eae63470c996119af2669c1fb05cd10c0fb7903 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Thu, 7 Jan 2021 18:07:48 -0500
Subject: [PATCH 262/361] Add flag to bypass requirement for restart file

- The FMS policy is to read a restart file if it is present but
  otherwise do a cold start. For safety reason a "stop" had been
  added to make sure the model wasn't running "dry" but this
  broke compatibility with the climate model.
- I've added the namelist parameter `require_restart` which
  defaults to false to be compatibility with FMS and added it as
  true in all the test input.nml files
---
 src/icebergs_framework.F90         | 5 ++++-
 src/icebergs_io.F90                | 2 +-
 tests/2p_collision_test/input.nml  | 3 ++-
 tests/chaotic_test/input.nml       | 1 +
 tests/collision_test/input.nml     | 1 +
 tests/collision_test_mts/input.nml | 1 +
 tests/energy_test/input.nml        | 1 +
 tests/energy_test2/input.nml       | 1 +
 tests/energy_test3/input.nml       | 1 +
 tests/ground_frac_test/input.nml   | 1 +
 10 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index c6693be..bc31e78 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -435,6 +435,7 @@ module ice_bergs_framework
   logical :: hexagonal_icebergs=.False. !< True treats icebergs as rectangles, False as hexagonal elements (for the purpose of mass spreading)
   logical :: allow_bergs_to_roll=.True. !< Allows icebergs to roll over when rolling conditions are met
   logical :: ignore_missing_restart_bergs=.False. !< True Allows the model to ignore icebergs missing in the restart.
+  logical :: require_restart=.false. !< If true, requires a restart file to be present when starting the model.
   logical :: Static_icebergs=.False. !< True= icebergs do no move
   logical :: only_interactive_forces=.False. !< Icebergs only feel interactive forces, and not ocean, wind...
   logical :: halo_debugging=.False. !< Use for debugging halos (remove when its working)
@@ -643,6 +644,7 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: allow_bergs_to_roll=.True. ! Allows icebergs to roll over when rolling conditions are met
 logical :: hexagonal_icebergs=.False. ! True treats icebergs as rectangles, False as hexagonal elements (for the purpose of mass spreading)
 logical :: ignore_missing_restart_bergs=.False. ! True Allows the model to ignore icebergs missing in the restart.
+logical :: require_restart=.false. ! If true, requires a restart file to be present when starting the model.
 logical :: Static_icebergs=.False. ! True= icebergs do no move
 logical :: only_interactive_forces=.False. ! Icebergs only feel interactive forces, and not ocean, wind...
 logical :: halo_debugging=.False. ! Use for debugging halos (remove when its working)
@@ -676,7 +678,7 @@ subroutine ice_bergs_framework_init(bergs, &
          rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, iceberg_bonds_on, manually_initialize_bonds, ignore_missing_restart_bergs, &
          parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, halo_debugging, hexagonal_icebergs, &
          time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, interactive_icebergs_on, scale_damping_by_pmag,&
-         critical_interaction_damping_on, tang_crit_int_damp_on, &
+         critical_interaction_damping_on, tang_crit_int_damp_on, require_restart, &
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution, force_all_pes_traj, &
          allow_bergs_to_roll,set_melt_rates_to_zero,lat_ref,initial_orientation,rotate_icebergs_for_mass_spreading,grid_is_latlon,Lx,use_f_plane,use_old_spreading, &
          grid_is_regular,override_iceberg_velocities,u_override,v_override,add_iceberg_thickness_to_SSH,Iceberg_melt_without_decay,melt_icebergs_as_ice_shelf, &
@@ -1174,6 +1176,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%allow_bergs_to_roll=allow_bergs_to_roll
   bergs%hexagonal_icebergs=hexagonal_icebergs
   bergs%ignore_missing_restart_bergs=ignore_missing_restart_bergs
+  bergs%require_restart=require_restart
   bergs%Static_icebergs=Static_icebergs
   bergs%only_interactive_forces=only_interactive_forces
   bergs%halo_debugging=halo_debugging
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index f60bdf3..bb5df40 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -581,7 +581,7 @@ subroutine read_restart_bergs(bergs,Time)
        call read_int_vector(filename,'id_ij',id_ij,grd%domain)
      endif
      call read_real_vector(filename,'static_berg',static_berg,grd%domain,value_if_not_in_file=0.)
-  else
+  elseif (bergs%require_restart) then
      stop 'read_restart_bergs, RESTART NOT FOUND!'
   endif
 
diff --git a/tests/2p_collision_test/input.nml b/tests/2p_collision_test/input.nml
index 26a988f..2d4ab32 100644
--- a/tests/2p_collision_test/input.nml
+++ b/tests/2p_collision_test/input.nml
@@ -114,6 +114,7 @@
     ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all    
 
     ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart 
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
     use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
     manually_initialize_bonds=.false. ! (F) True= Bonds are initialize manually.
     length_for_manually_initialize_bonds=0.0 !(1e3)Dist b/w bergs to init bonds manually    
@@ -162,4 +163,4 @@
        clock_grain='MODULE'
        domains_stack_size = 2000000
        clock_flags='SYNC'
-/
\ No newline at end of file
+/
diff --git a/tests/chaotic_test/input.nml b/tests/chaotic_test/input.nml
index d01278d..bcde5cb 100644
--- a/tests/chaotic_test/input.nml
+++ b/tests/chaotic_test/input.nml
@@ -111,6 +111,7 @@
     force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
 
     ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
     use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
     manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
     manually_initialize_bonds_from_radii=.true.!(F) Init bond b/w bergs if dist<1.25*radius
diff --git a/tests/collision_test/input.nml b/tests/collision_test/input.nml
index 802b94f..98b0b11 100644
--- a/tests/collision_test/input.nml
+++ b/tests/collision_test/input.nml
@@ -108,6 +108,7 @@
     ignore_traj=.False. ! (F) If true, then model does not track trajectory data at all    
 
     ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart 
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
     use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
     manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
     length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually    
diff --git a/tests/collision_test_mts/input.nml b/tests/collision_test_mts/input.nml
index 299ab50..2421207 100644
--- a/tests/collision_test_mts/input.nml
+++ b/tests/collision_test_mts/input.nml
@@ -113,6 +113,7 @@
     ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
 
     ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
     use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
     manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
     length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
diff --git a/tests/energy_test/input.nml b/tests/energy_test/input.nml
index 0b04c03..22d6fd9 100644
--- a/tests/energy_test/input.nml
+++ b/tests/energy_test/input.nml
@@ -125,6 +125,7 @@
     ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
 
     ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
     use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
     manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
     manually_initialize_bonds_from_radii=.true.!(F) Init bond b/w bergs if dist<1.25*radius
diff --git a/tests/energy_test2/input.nml b/tests/energy_test2/input.nml
index fb224e7..e4ffd31 100644
--- a/tests/energy_test2/input.nml
+++ b/tests/energy_test2/input.nml
@@ -124,6 +124,7 @@
     ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
 
     ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
     use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
     manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
     manually_initialize_bonds_from_radii=.true.!(F) Init bond b/w bergs if dist<1.25*radius
diff --git a/tests/energy_test3/input.nml b/tests/energy_test3/input.nml
index 6f97e4d..9e20b83 100644
--- a/tests/energy_test3/input.nml
+++ b/tests/energy_test3/input.nml
@@ -128,6 +128,7 @@
     ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
 
     ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
     use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
     manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
     manually_initialize_bonds_from_radii=.true.!(F) Init bond b/w bergs if dist<1.25*radius
diff --git a/tests/ground_frac_test/input.nml b/tests/ground_frac_test/input.nml
index 7168d82..1c15148 100644
--- a/tests/ground_frac_test/input.nml
+++ b/tests/ground_frac_test/input.nml
@@ -129,6 +129,7 @@
     ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
 
     ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
     use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
     manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
     length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually

From fd14a22d3077afd07952d4f22a21f97e2440999d Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Fri, 8 Jan 2021 17:09:52 -0500
Subject: [PATCH 263/361] Changes default value of cdrag_grounding

- A non-zero default value turns on grounding which changes exisiting
  configurations making it hard to upgrade the code in those configs.
  This sets the default to 0. The grounding tests already has a non-zero
  value in the input.nml and so still tests the grounding code.
---
 src/icebergs_framework.F90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index bc31e78..87cc878 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -387,7 +387,7 @@ module ice_bergs_framework
   real :: spring_coef !< Spring constant for bonded iceberg interactions
   real :: contact_spring_coef !<Spring coefficient for berg collisions -Alex
   character(len=11) :: fracture_criterion !<'strain_rate','strain',or 'none'
-  real :: cdrag_grounding
+  real :: cdrag_grounding=0.0 !< Drag coefficient against ocean bottom
   real :: h_to_init_grounding
   real :: frac_thres_n !normal fracture strain threshold
   real :: frac_thres_t !tangential fracture strain threshold
@@ -587,7 +587,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: spring_coef=1.e-8 ! Spring constant for iceberg interactions (this seems to be the highest stable value)
 real :: contact_spring_coef=0. !Spring coef for berg collisions (is set to spring_coef if not specified)
 character(len=11) :: fracture_criterion='none' !<'strain_rate','strain',or 'none'
-real :: cdrag_grounding=20.0
+real :: cdrag_grounding=0.0 ! Drag coefficient against ocean bottom
 real :: h_to_init_grounding=100.0
 real :: frac_thres_n=0.0 !normal fracture strain threshold
 real :: frac_thres_t=0.0 !tangential fracture strain threshold

From fe5e9c1907af57108082e33cbe5a2857e69874a7 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Tue, 12 Jan 2021 14:41:33 -0500
Subject: [PATCH 264/361] Corrected source path

---
 docs/Doxyfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/Doxyfile b/docs/Doxyfile
index 40cc078..72c10ff 100644
--- a/docs/Doxyfile
+++ b/docs/Doxyfile
@@ -780,7 +780,7 @@ WARN_LOGFILE           = doxygen.log
 # spaces.
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = ../
+INPUT                  = ../src
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses

From ca2ed5d0df302174e9e6a574eef355357656ede6 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Tue, 12 Jan 2021 15:21:18 -0500
Subject: [PATCH 265/361] First draft for RTD/sphinx

---
 docs/.gitignore |  1 +
 docs/Doxyfile   |  4 ++--
 docs/Makefile   | 20 ++++++++++++++++
 docs/README.md  | 13 ++++++++++
 docs/conf.py    | 63 +++++++++++++++++++++++++++++++++++++++++++++++++
 docs/index.rst  | 20 ++++++++++++++++
 src/README.md   | 13 ++++++++++
 7 files changed, 132 insertions(+), 2 deletions(-)
 create mode 100644 docs/Makefile
 create mode 100644 docs/README.md
 create mode 100644 docs/conf.py
 create mode 100644 docs/index.rst
 create mode 100644 src/README.md

diff --git a/docs/.gitignore b/docs/.gitignore
index 8bbe7ac..6d8610b 100644
--- a/docs/.gitignore
+++ b/docs/.gitignore
@@ -1,2 +1,3 @@
+_build
 html 
 doxygen.log
diff --git a/docs/Doxyfile b/docs/Doxyfile
index 72c10ff..774c699 100644
--- a/docs/Doxyfile
+++ b/docs/Doxyfile
@@ -32,7 +32,7 @@ DOXYFILE_ENCODING      = UTF-8
 # title of most generated pages and in a few other places.
 # The default value is: My Project.
 
-PROJECT_NAME           = "icebergs"
+PROJECT_NAME           = "KID (icebergs)"
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number. This
 # could be handy for archiving the generated documentation or if some version
@@ -948,7 +948,7 @@ FILTER_SOURCE_PATTERNS =
 # (index.html). This can be useful if you have a project on for instance GitHub
 # and want to reuse the introduction page also for the doxygen output.
 
-USE_MDFILE_AS_MAINPAGE = ../README.md
+USE_MDFILE_AS_MAINPAGE = ../src/README.md
 
 #---------------------------------------------------------------------------
 # Configuration options related to source browsing
diff --git a/docs/Makefile b/docs/Makefile
new file mode 100644
index 0000000..d4bb2cb
--- /dev/null
+++ b/docs/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/README.md b/docs/README.md
new file mode 100644
index 0000000..e629f1a
--- /dev/null
+++ b/docs/README.md
@@ -0,0 +1,13 @@
+Building the documentation
+==========================
+
+Using just doxygen
+```
+doxygen
+```
+will create HTML in the directory `html/`. Error messages will appear in `doxygen.log`.
+
+The readthedocs site, https://kid.readthedocs.io/, is generated using sphinx (see https://sphinx-doc.org/, install with `conda install sphinx`) with
+```
+make html
+```
diff --git a/docs/conf.py b/docs/conf.py
new file mode 100644
index 0000000..b7678ef
--- /dev/null
+++ b/docs/conf.py
@@ -0,0 +1,63 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+import subprocess
+subprocess.call('doxygen', shell=True)
+
+# -- Project information -----------------------------------------------------
+
+project = 'KID (icebergs)'
+copyright = '2021, Adcroft, Huth, Martin, Stern'
+author = 'Adcroft, Huth, Martin, Stern'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+]
+
+# Add any paths that contain templates here, relative to this directory.
+#templates_path = ['_templates']
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = 'ls'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+#html_static_path = ['_static']
+
+html_extra_path = ['html']
diff --git a/docs/index.rst b/docs/index.rst
new file mode 100644
index 0000000..eddcbd2
--- /dev/null
+++ b/docs/index.rst
@@ -0,0 +1,20 @@
+.. KID documentation master file, created by
+   sphinx-quickstart on Tue Jan 12 14:38:30 2021.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to KID's documentation!
+===============================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/src/README.md b/src/README.md
new file mode 100644
index 0000000..8b6439f
--- /dev/null
+++ b/src/README.md
@@ -0,0 +1,13 @@
+# Krazy Icebergs Dude (KID)
+
+KID is a Lagrangian element model of icebergs. Initially, the icebergs were represented as infinitesimal points (Martin & Adcroft, 2010), and then given finite extent and element-element interactions so that can now represent giant tabular icebergs by joining elements togeter (Stern et al., 2017).
+
+It should be noted that the K and D in KID can be anything you like, e.g. Kinematic and Dynamics. Suggestions are welcome, since we haven't thought of anything that makes sense.
+
+
+## Publications about KID
+
+- Stern, A. A., A. Adcroft, and O. Sergienko, 2019: Modeling Ice Shelf Cavities and Tabular Icebergs Using Lagrangian Elements. Journal Geophysical Research: Oceans, 124, 3378–3392, https://doi.org/10.1029/2018JC014876.
+- Stern, A. A., A. Adcroft, O. Sergienko, and G. Marques, 2017: Modeling tabular icebergs submerged in the ocean. Journal for Advances in Modeling Earth Systems, 9, 1948–1972, https://doi.org/10.1002/2017MS001002.
+- Stern, A. A., A. Adcroft, and O. Sergienko, 2016: The effects of Antarctic iceberg calving-size distribution in a global climate model. Journal of Geophysical Research: Oceans, 121, 5773–5788, https://doi.org/10.1002/2016JC011835.
+- Martin, T., and A. Adcroft, 2010: Parameterizing the fresh-water flux from land ice to ocean with interactive icebergs in a coupled climate model. Ocean Modelling, 34, 111–124, https://doi.org/10.1016/j.ocemod.2010.05.001.

From ffda5921fc26ffe6defcea9f000f34e5f10b0b6a Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Tue, 12 Jan 2021 15:36:42 -0500
Subject: [PATCH 266/361] Try to avoid reading contents.rst on RTS

---
 docs/index.rst | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/docs/index.rst b/docs/index.rst
index eddcbd2..1085caf 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -6,11 +6,6 @@
 Welcome to KID's documentation!
 ===============================
 
-.. toctree::
-   :maxdepth: 2
-   :caption: Contents:
-
-
 
 Indices and tables
 ==================

From 5e75f436aa8edba571c84c9abc4552f16286c55c Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Tue, 12 Jan 2021 15:40:18 -0500
Subject: [PATCH 267/361] Another try to avoid reading contents.rst on RTS

---
 docs/contents.rst | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 docs/contents.rst

diff --git a/docs/contents.rst b/docs/contents.rst
new file mode 100644
index 0000000..e69de29

From 54969d21a3fca724e614bdddfb03e26763929efc Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Tue, 12 Jan 2021 15:51:43 -0500
Subject: [PATCH 268/361] Added badge and folder descriptions

---
 README.md | 33 +++++++++++++++++----------------
 1 file changed, 17 insertions(+), 16 deletions(-)

diff --git a/README.md b/README.md
index fd73b8a..e30b70e 100644
--- a/README.md
+++ b/README.md
@@ -1,18 +1,19 @@
-Disclaimer
-==========
+# KID (icebergs)
 
-The United States Department of Commerce (DOC) GitHub project code is provided
-on an "as is" basis and the user assumes responsibility for its use. DOC has
-relinquished control of the information and no longer has responsibility to
-protect the integrity, confidentiality, or availability of the information. Any
-claims against the Department of Commerce stemming from the use of its GitHub
-project will be governed by all applicable Federal law. Any reference to
-specific commercial products, processes, or services by service mark,
-trademark, manufacturer, or otherwise, does not constitute or imply their
-endorsement, recommendation or favoring by the Department of Commerce. The
-Department of Commerce seal and logo, or the seal and logo of a DOC bureau,
-shall not be used in any manner to imply endorsement of any commercial product
-or activity by DOC or the United States Government.
+[![Documentation Status](https://readthedocs.org/projects/kid/badge/?version=latest)](https://kid.readthedocs.io/en/latest/?badge=latest)
 
-This project code is made available through GitHub but is managed by NOAA-GFDL
-at https://gitlab.gfdl.noaa.gov.
+# What files are what
+
+| File/directory    | Purpose |
+| --------------    | ------- |
+| src/              | Source code for icebergs |
+| driver/           | A driver for creating a stand-alone (uncoupled to ocean/atmosphere) model |
+| build/            | A workspace for building a stand alone executable using src/ and driver/ |
+| tests/            | Test cases |
+| docs/             | A workspace for generating documentation with doxygen and sphinx |
+
+# Disclaimer
+
+The United States Department of Commerce (DOC) GitHub project code is provided on an "as is" basis and the user assumes responsibility for its use. DOC has relinquished control of the information and no longer has responsibility to protect the integrity, confidentiality, or availability of the information. Any claims against the Department of Commerce stemming from the use of its GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.
+
+This project code is made available through GitHub but is managed by NOAA-GFDL at https://gitlab.gfdl.noaa.gov.

From dbcbf139e032485373dbab86466e6a44453a5126 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Tue, 12 Jan 2021 17:16:36 -0500
Subject: [PATCH 269/361] Fixed doxygen errors in icebergs_framework.F90

---
 src/icebergs_framework.F90 | 173 +++++++++++++++++++++----------------
 1 file changed, 100 insertions(+), 73 deletions(-)

diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index bc31e78..53603f5 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -445,18 +445,18 @@ module ice_bergs_framework
   logical :: manually_initialize_bonds=.False. !< True= Bonds are initialize manually.
   logical :: use_new_predictive_corrective =.False. !< Flag to use Bob's predictive corrective iceberg scheme- Added by Alon
   logical :: interactive_icebergs_on=.false. !< Turn on/off interactions between icebergs  - Added by Alon
-  logical :: scale_damping_by_pmag=.true. !<scales damping by magnitude of (projection matrix \cdot relative velocity)
+  logical :: scale_damping_by_pmag=.true. !< Scales damping by magnitude of (projection matrix dot relative velocity)
   logical :: critical_interaction_damping_on=.true. !< Sets the damping on relative iceberg velocity to critical value - Added by Alon
   logical :: tang_crit_int_damp_on=.true. !<crit interaction damping for tangential component?
   logical :: use_old_spreading=.true. !< If true, spreads iceberg mass as if the berg is one grid cell wide
   logical :: read_ocean_depth_from_file=.false. !< If true, ocean depth is read from a file.
   integer(kind=8) :: debug_iceberg_with_id = -1 !< If positive, monitors a berg with this id
 
-  real :: length_for_manually_initialize_bonds=1000.0 !<if manually init bonds, only  bond if dist between particles is .lt. this length -Added by Alex
-  logical :: manually_initialize_bonds_from_radii=.false. !<if manually init bonds, form bonds if dist between particles is < 1.25x the smaller radii-Alex
+  real :: length_for_manually_initialize_bonds=1000.0 !< If manually initialing bonds, only  bond if dist between particles is < this length -Added by Alex
+  logical :: manually_initialize_bonds_from_radii=.false. !< If manually initialing bonds, form bonds if dist between particles is < 1.25x the smaller radii-Alex
   real :: speed_limit=0. !< CFL speed limit for a berg [m/s]
   real :: tau_calving=0. !< Time scale for smoothing out calving field (years)
-  real :: tip_parameter=0. !< parameter to override iceberg rolling critical ratio (use zero to get parameter directly from ice and seawater densities)
+  real :: tip_parameter=0. !< If non-zero, overrides iceberg rolling critical ratio (use zero to get parameter directly from ice and seawater densities)
   real :: grounding_fraction=0. !< Fraction of water column depth at which grounding occurs
   type(buffer), pointer :: obuffer_n=>null() !< Buffer for outgoing bergs to the north
   type(buffer), pointer :: ibuffer_n=>null() !< Buffer for incoming bergs from the north
@@ -497,7 +497,7 @@ module ice_bergs_framework
   integer :: nbonds=0
   integer, dimension(:), pointer :: nbergs_calved_by_class=>null()
   ! mts parameters - added by Alex
-  logical :: mts=.false. !use multiple timestepping scheme (substep size is automatically determined)
+  logical :: mts=.false. !< Use multiple timestepping scheme (substep size is automatically determined)
   integer :: mts_sub_steps
   real :: mts_fast_dt
   integer :: mts_part !for turning on/off berg interactions/collisions during different mts scheme
@@ -654,19 +654,19 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: manually_initialize_bonds=.False. ! True= Bonds are initialize manually.
 logical :: use_new_predictive_corrective =.False. ! Flag to use Bob's predictive corrective iceberg scheme- Added by Alon
 logical :: interactive_icebergs_on=.false. ! Turn on/off interactions between icebergs  - Added by Alon
-logical :: scale_damping_by_pmag=.true. !<scales damping by magnitude of (projection matrix \cdot relative velocity)
+logical :: scale_damping_by_pmag=.true. ! Scales damping by magnitude of (projection matrix dot relative velocity)
 logical :: critical_interaction_damping_on=.true. ! Sets the damping on relative iceberg velocity to critical value - Added by Alon
-logical :: tang_crit_int_damp_on=.true. !crit interaction damping for tangential component?
+logical :: tang_crit_int_damp_on=.true. ! Critical interaction damping for tangential component?
 logical :: do_unit_tests=.false. ! Conduct some unit tests
 logical :: input_freq_distribution=.false. ! Flag to show if input distribution is freq or mass dist (=1 if input is a freq dist, =0 to use an input mass dist)
 logical :: read_old_restarts=.false. ! Legacy option that does nothing
 logical :: use_old_spreading=.true. ! If true, spreads iceberg mass as if the berg is one grid cell wide
 logical :: read_ocean_depth_from_file=.false. ! If true, ocean depth is read from a file.
-integer :: mts_sub_steps=-1 !if -1, the number of mts sub-steps will be automatically determined
-logical :: remove_unused_bergs=.true. !remove unneeded bergs after PEs transfers
-real :: contact_distance=0.0 !for unbonded berg interactions, collision is assumed at max(contact_distance,sum of the 2 bergs radii)
-logical :: force_convergence=.false. !experimental MTS convergence scheme that better preserves momentum during collisions
-real :: convergence_tolerance=1.e-8 !tolerance for the MTS force_convergence scheme
+integer :: mts_sub_steps=-1 ! If -1, the number of mts sub-steps will be automatically determined
+logical :: remove_unused_bergs=.true. ! Remove unneeded bergs after PEs transfers
+real :: contact_distance=0.0 ! For unbonded berg interactions, collision is assumed at max(contact_distance,sum of the 2 bergs radii)
+logical :: force_convergence=.false. ! Experimental MTS convergence scheme that better preserves momentum during collisions
+real :: convergence_tolerance=1.e-8 ! Tolerance for the MTS force_convergence scheme
 real, dimension(nclasses) :: initial_mass=(/8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11/) ! Mass thresholds between iceberg classes (kg)
 real, dimension(nclasses) :: distribution=(/0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02/) ! Fraction of calving to apply to this class (non-dim) ,
 real, dimension(nclasses) :: mass_scaling=(/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) ! Ratio between effective and real iceberg mass (non-dim)
@@ -1897,12 +1897,12 @@ Subroutine transfer_mts_bergs(bergs)
 
 end subroutine transfer_mts_bergs
 
-!>For the MTS scheme, packs bergs for transfers between PEs to the N,S,E, and W
-subroutine mts_pack_in_dir(bergs,nbergs_to_send,dir)
+!> For the MTS scheme, packs bergs for transfers between PEs to the N,S,E, and W
+subroutine mts_pack_in_dir(bergs, nbergs_to_send, dir)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
-  integer :: nbergs_to_send !<counter for number of bergs to send
-  character(len=1) :: dir !<indicates PE to the north,south,east,or west
+  integer :: nbergs_to_send !< Counter for number of bergs to send
+  character(len=1) :: dir !< Indicates PE to the north,south,east,or west
   ! Local variables
   type(icebergs_gridded), pointer :: grd
   type(iceberg), pointer :: berg
@@ -2068,13 +2068,13 @@ subroutine mts_pack_in_dir(bergs,nbergs_to_send,dir)
   endif
 end subroutine mts_pack_in_dir
 
-!>find, mark, and pack the halo and conglomerate bergs
-recursive subroutine mts_mark_and_pack_halo_and_congloms(bergs,berg,dir,nbergs_to_send,pfix,rhc)
+!> Find, mark, and pack the halo and conglomerate bergs
+recursive subroutine mts_mark_and_pack_halo_and_congloms(bergs, berg, dir, nbergs_to_send,pfix, rhc)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
-  type(iceberg), pointer :: berg
-  character(len=1) :: dir
-  integer :: nbergs_to_send
+  type(iceberg), pointer :: berg !< Berg to pack ???
+  character(len=1) :: dir !< north,south,east,or west
+  integer :: nbergs_to_send !< Number of bergs to send
   real :: pfix !<for periodicity
   real :: rhc(4) !<lat/lon bounds of halo region for receiving cell
   ! Local variables
@@ -2139,15 +2139,18 @@ recursive subroutine mts_mark_and_pack_halo_and_congloms(bergs,berg,dir,nbergs_t
 
 end subroutine mts_mark_and_pack_halo_and_congloms
 
-!>pack the bergs within contact distance of conglom/halo bergs
-recursive subroutine mts_pack_contact_bergs(bergs,berg,dir,pfix,nbergs_to_send,inhs,inhe,jnhs,jnhe)
+!> Pack the bergs within contact distance of conglom/halo bergs
+recursive subroutine mts_pack_contact_bergs(bergs, berg, dir, pfix, nbergs_to_send, inhs, inhe, jnhs, jnhe)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
   type(iceberg), pointer :: berg !< Berg to find contact with
   character(len=1) :: dir !< north,south,east,or west
   real :: pfix !< for periodicity
-  integer :: nbergs_to_send
-  integer :: inhs,inhe,jnhs,jnhe !<bounds of non-halo domain, i.e. where contact bergs may exist
+  integer :: nbergs_to_send !< Number of bergs to send
+  integer :: inhs !< Start i bounds of non-halo domain, i.e. where contact bergs may exist
+  integer :: inhe !< End i bounds of non-halo domain, i.e. where contact bergs may exist
+  integer :: jnhs !< Start j bounds of non-halo domain, i.e. where contact bergs may exist
+  integer :: jnhe !< End j bounds of non-halo domain, i.e. where contact bergs may exist
   ! Local variables
   type(bond) , pointer :: current_bond
   type(icebergs_gridded), pointer :: grd
@@ -2255,11 +2258,11 @@ recursive subroutine mts_pack_contact_bergs(bergs,berg,dir,pfix,nbergs_to_send,i
   enddo
 end subroutine mts_pack_contact_bergs
 
-!>For MTS scheme, determines if a berg has been packed to send to the neighboring PE in a given direction
-!!based on its evolving conglom_id from subroutines transfer_mts_bergs and mts_pack_in_dir
-logical function mts_berg_sent(conglom_id,dir)
-  integer :: conglom_id
-  character(len=1) :: dir
+!> For MTS scheme, determines if a berg has been packed to send to the neighboring PE in a given direction
+!! based on its evolving conglom_id from subroutines transfer_mts_bergs and mts_pack_in_dir
+logical function mts_berg_sent(conglom_id, dir)
+  integer :: conglom_id !< Id of conglomerate
+  character(len=1) :: dir !< Direction for sending
 
   mts_berg_sent=.false.
   select case (dir)
@@ -2280,7 +2283,7 @@ logical function mts_berg_sent(conglom_id,dir)
   end select
 end function mts_berg_sent
 
-!>Clear and reassign conglom ids
+!> Clear and reassign conglom ids
 subroutine set_conglom_ids(bergs)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
@@ -2316,8 +2319,7 @@ subroutine set_conglom_ids(bergs)
 
 end subroutine set_conglom_ids
 
-
-!>Assign initial velocities and energies for energy tracking tests
+!> Assign initial velocities and energies for energy tracking tests
 subroutine energy_tests_init(bergs)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
@@ -2361,11 +2363,13 @@ subroutine energy_tests_init(bergs)
   enddo;enddo
 end subroutine energy_tests_init
 
-!>Identify all bergs in the same conglomerate as the given berg, and assign them the given conglom_id
-recursive subroutine label_conglomerates(berg,new_conglom_id)
-  type(iceberg), pointer :: berg,other_berg
+!> Identify all bergs in the same conglomerate as the given berg, and assign them the given conglom_id
+recursive subroutine label_conglomerates(berg, new_conglom_id)
+  type(iceberg), pointer :: berg !< Berg to start search from
+  integer :: new_conglom_id !< Conglomerate id to assign
+  ! Local variables
+  type(iceberg), pointer :: other_berg
   type(bond) , pointer :: current_bond
-  integer :: new_conglom_id
 
   current_bond=>berg%first_bond
   do while (associated(current_bond))
@@ -2381,8 +2385,8 @@ recursive subroutine label_conglomerates(berg,new_conglom_id)
   enddo
 end subroutine label_conglomerates
 
-!>Keep only the bergs which are part of, or within contact distance of, a conglomerate that overlaps
-!!the computational domain, or which are halo_berg=1
+!> Keep only the bergs which are part of, or within contact distance of, a conglomerate that overlaps
+!! the computational domain, or which are halo_berg=1
 subroutine mts_remove_unused_bergs(bergs)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
@@ -2475,11 +2479,14 @@ subroutine mts_remove_unused_bergs(bergs)
   enddo
 end subroutine mts_remove_unused_bergs
 
-!>for MTS velocity verlet, the send and receive call for for transfer_mts_bergs
-subroutine mts_send_and_receive(bergs,nbergs_to_send_e,nbergs_to_send_w,nbergs_to_send_n,nbergs_to_send_s)
+!> For MTS velocity verlet, the send and receive call for for transfer_mts_bergs
+subroutine mts_send_and_receive(bergs, nbergs_to_send_e, nbergs_to_send_w, nbergs_to_send_n, nbergs_to_send_s)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
-  integer :: nbergs_to_send_e, nbergs_to_send_w, nbergs_to_send_n, nbergs_to_send_s
+  integer :: nbergs_to_send_e !< Number of bergs to send to the east
+  integer :: nbergs_to_send_w !< Number of bergs to send to the west
+  integer :: nbergs_to_send_n !< Number of bergs to send to the north
+  integer :: nbergs_to_send_s !< Number of bergs to send to the south
   ! Local vars
   type(icebergs_gridded), pointer :: grd
   integer :: nbergs_rcvd_from_e, nbergs_rcvd_from_w, nbergs_rcvd_from_n, nbergs_rcvd_from_s
@@ -2894,7 +2901,7 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
 type(iceberg), pointer :: berg !< Iceberg to pack into buffer
 type(buffer), pointer :: buff !< Buffer to pack berg into
 integer, intent(in) :: n !< Position in buffer to place berg
-integer, optional :: max_bonds_in !< <undocumented>
+integer, optional :: max_bonds_in !< undocumented
 !integer, intent(in) :: max_bonds  ! Change this later
 ! Local variables
 integer :: counter, k, max_bonds, id_cnt, id_ij
@@ -3125,8 +3132,8 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
 type(buffer), pointer :: buff !< Buffer from which to unpack berg
 integer, intent(in) :: n !< Position in buffer to unpack
 type(icebergs_gridded), pointer :: grd !< Container for gridded fields
-logical, optional :: force_append !< <undocumented>
-integer, optional :: max_bonds_in !< <undocumented>
+logical, optional :: force_append !< undocumented
+integer, optional :: max_bonds_in !< undocumented
 ! Local variables
 !real :: lon, lat, uvel, vvel, xi, yj
 !real :: start_lon, start_lat, start_day, start_mass
@@ -3728,12 +3735,12 @@ subroutine count_out_of_order(bergs,label)
 
 end subroutine count_out_of_order
 
-!>scans a single cell for duplicate bergs
+!> Scans a single cell for duplicate bergs
 subroutine unpack_duplicate_check(bergs,localberg,duplicate)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
-  type(iceberg) :: localberg !<input iceberg
-  logical :: duplicate
+  type(iceberg) :: localberg !< Input iceberg
+  logical :: duplicate !< True if a duplicate is detected
   ! Local variables
   type(iceberg), pointer :: this !<bergs for comparison
 
@@ -4672,11 +4679,13 @@ subroutine show_all_bonds(bergs)
 
 end subroutine show_all_bonds
 
-subroutine connect_all_bonds(bergs,ignore_unmatched)
+!> Sweep across all bergs filling in bond data ???
+subroutine connect_all_bonds(bergs, ignore_unmatched)
 type(icebergs), pointer :: bergs !< Container for all types and memory
+logical,optional :: ignore_unmatched !< If true, skip error checking ???
+! Local variables
 type(iceberg), pointer :: other_berg, berg
 type(icebergs_gridded), pointer :: grd
-logical,optional :: ignore_unmatched
 integer :: i, j
 integer :: grdi, grdj
 integer :: grdi_inner, grdj_inner
@@ -4841,14 +4850,16 @@ subroutine update_latlon(bergs)
 
 end subroutine update_latlon
 
+!> Counts (and error checks) bonds
 subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
-
 type(icebergs), pointer :: bergs !< Container for all types and memory
+integer, intent(out) :: number_of_bonds !< Number of bonds
+logical, intent(inout), optional :: check_bond_quality !< If true, check bond quality
+! Local variables
 type(iceberg), pointer :: berg
 type(iceberg), pointer :: other_berg
 type(icebergs_gridded), pointer :: grd
 type(bond) , pointer :: current_bond, other_berg_bond
-integer, intent(out) :: number_of_bonds
 integer :: number_of_bonds_all_pe
 integer :: grdi, grdj
 logical :: bond_is_good
@@ -5252,7 +5263,7 @@ end subroutine move_trajectory
 subroutine move_bond_trajectory(bergs, current_bond)
 ! Arguments
 type(icebergs), pointer :: bergs !< Container for all types and memory
-type(bond) , pointer :: current_bond
+type(bond) , pointer :: current_bond !< Bond to break ???
 ! Local variables
 type(bond_xyt), pointer :: next, last
 type(bond_xyt) :: vals
@@ -5445,9 +5456,14 @@ logical function find_cell_by_search(grd, x, y, i, j)
 
 end function find_cell_by_search
 
-real function dcost(x1, y1, x2, y2,Lx)
+!< A cost function with minimum when x2==x1 and y2==y1
+real function dcost(x1, y1, x2, y2, Lx)
   ! Arguments
-  real, intent(in) :: x1, x2, y1, y2,Lx
+  real, intent(in) :: x1 !< x-coordinate or point 1
+  real, intent(in) :: x2 !< x-coordinate or point 2
+  real, intent(in) :: y1 !< y-coordinate or point 1
+  real, intent(in) :: y2 !< y-coordinate or point 2
+  real, intent(in) :: Lx !< Periodicity of x-coordinate
   ! Local variables
   real :: x1m
 
@@ -5456,12 +5472,16 @@ real function dcost(x1, y1, x2, y2,Lx)
     dcost=(x2-x1m)**2+(y2-y1)**2
 end function dcost
 
+!> A better way to find the indices (oi,oj) or the cell containing position (x,y).
+!! Returns True if a cell is found and updates oi,oj.
 logical function find_better_min(grd, x, y, w, oi, oj)
   ! Arguments
   type(icebergs_gridded), intent(in) :: grd !< Container for gridded fields
-  real, intent(in) :: x, y
-  integer, intent(in) :: w
-  integer, intent(inout) :: oi, oj
+  real, intent(in) :: x !< x-coordinate being searched for
+  real, intent(in) :: y !< y-coordinate being searched for
+  integer, intent(in) :: w !< Width into halo to search ???
+  integer, intent(inout) :: oi !< i-index of cell containing x,y
+  integer, intent(inout) :: oj !< j-index of cell containing x,y
   ! Local variables
   integer :: i,j,xs,xe,ys,ye
   real :: dmin, dcst
@@ -5487,27 +5507,34 @@ logical function find_better_min(grd, x, y, w, oi, oj)
 
 end function find_better_min
 
+! Returns true and updates oi and oj, if a cell containing x,y is found within w cells of the input oi, oj
 logical function find_cell_loc(grd, x, y, is, ie, js, je, w, oi, oj)
   ! Arguments
   type(icebergs_gridded), intent(in) :: grd !< Container for gridded fields
-  real, intent(in) :: x, y
-  integer, intent(in) :: is, ie, js, je, w
-  integer, intent(inout) :: oi, oj
+  real, intent(in) :: x !< Longitude
+  real, intent(in) :: y !< Latitude
+  integer, intent(in) :: is !< Start i-index of computational grid
+  integer, intent(in) :: ie !< End i-index of computational grid
+  integer, intent(in) :: js !< Start j-index of computational grid
+  integer, intent(in) :: je !< End j-index of computational grid
+  integer, intent(in) :: w !< Width to search around
+  integer, intent(inout) :: oi !< Starting and updated i-index
+  integer, intent(inout) :: oj !< Starting and updated j-index
   ! Local variables
   integer :: i,j,xs,xe,ys,ye
 
-    xs=max(is, oi-w)
-    xe=min(ie, oi+w)
-    ys=max(js, oj-w)
-    ye=min(je, oj+w)
+  xs=max(is, oi-w)
+  xe=min(ie, oi+w)
+  ys=max(js, oj-w)
+  ye=min(je, oj+w)
 
-    find_cell_loc=.false.
-    do j=ys,ye; do i=xs,xe
-        if (is_point_in_cell(grd, x, y, i, j)) then
-          oi=i; oj=j; find_cell_loc=.true.
-          return
-        endif
-    enddo; enddo
+  find_cell_loc=.false.
+  do j=ys,ye; do i=xs,xe
+      if (is_point_in_cell(grd, x, y, i, j)) then
+        oi=i; oj=j; find_cell_loc=.true.
+        return
+      endif
+  enddo; enddo
 
 end function find_cell_loc
 
@@ -6462,7 +6489,7 @@ subroutine bergs_chksum(bergs, txt, ignore_halo_violation)
 ! Arguments
 type(icebergs), pointer :: bergs !< Container for all types and memory
 character(len=*), intent(in) :: txt !< Label to use in messages
-logical, optional :: ignore_halo_violation
+logical, optional :: ignore_halo_violation !< If true, skip error checking ???
 ! Local variables
 integer :: i, nbergs, ichk1, ichk2, ichk3, ichk4, ichk5, iberg
 real, allocatable :: fld(:,:), fld2(:,:)

From a21d3d3b4d3a92db39e51301963be73fb77d939a Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Tue, 12 Jan 2021 17:29:13 -0500
Subject: [PATCH 270/361] Added missing doxygen comments for most of
 icebergs.F90

---
 src/icebergs.F90 | 28 +++++++++++++++++++---------
 1 file changed, 19 insertions(+), 9 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 436cf36..e5e941f 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -3705,7 +3705,7 @@ end subroutine rotate
 subroutine calculate_mass_on_ocean(bergs, with_diagnostics)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
-  logical, intent(in) :: with_diagnostics
+  logical, intent(in) :: with_diagnostics !< If true, calculate diagnostics
   ! Local variables
   type(iceberg), pointer :: berg
   type(icebergs_gridded), pointer :: grd
@@ -3800,8 +3800,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   real, dimension(:,:), intent(in) :: sst !< Sea-surface temperature (C or K)
   real, dimension(:,:), intent(in) :: cn !< Sea-ice concentration (nondim)
   real, dimension(:,:), intent(in) :: hi !< Sea-ice thickness (m)
-  integer, optional, intent(in) :: stagger
-  integer, optional, intent(in) :: stress_stagger
+  integer, optional, intent(in) :: stagger !< Enumerated value indicating staggering of ocean/ice u,v variables
+  integer, optional, intent(in) :: stress_stagger !< Enumerated value indicating staggering of stress variables
   real, dimension(:,:), optional, intent(in) :: sss !< Sea-surface salinity (1e-3)
   real, dimension(:,:), optional, pointer :: mass_berg !< Mass of bergs (kg)
   real, dimension(:,:), optional, pointer :: ustar_berg !< Friction velocity on base of bergs (m/s)
@@ -5758,11 +5758,20 @@ subroutine evolve_icebergs_mts2(bergs)
 end subroutine evolve_icebergs_mts2
 
 !> Energy calculations for MTS_part==1
-subroutine mts_energy_part_1(bergs,berg,ax1,ay1,axn,ayn,bxn,byn,Fec_x,Fec_y,Fdc_x,Fdc_y)
+subroutine mts_energy_part_1(bergs, berg, ax1, ay1, axn, ayn, bxn, byn, Fec_x, Fec_y, Fdc_x, Fdc_y)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
-  type(iceberg), pointer :: berg
-  real, intent(in) :: ax1,ay1,axn,ayn,bxn,byn,Fec_x,Fec_y,Fdc_x,Fdc_y
+  type(iceberg), pointer :: berg !< Berg for which to do calculations
+  real, intent(in) :: ax1 !< x acceleration at beginning of step [m s-2] ???
+  real, intent(in) :: ay1 !< y acceleration at beginning of step [m s-2] ???
+  real, intent(in) :: axn !< x acceleration at end of step [m s-2] ???
+  real, intent(in) :: ayn !< y acceleration at end of step [m s-2] ???
+  real, intent(in) :: bxn !< x implicit acceleration [m s-2] ???
+  real, intent(in) :: byn !< y implicit acceleration [m s-2] ???
+  real, intent(in) :: Fec_x !< x component of some force [units ?] ???
+  real, intent(in) :: Fec_y !< y component of some force [units ?] ???
+  real, intent(in) :: Fdc_x !< x component of some other force [units ?] ???
+  real, intent(in) :: Fdc_y !< y component of some other force [units ?] ???
   ! Local
   real :: dt, M, Fex, Fey, Fex_i, Fey_i
   real :: uveln, vveln, uveln_star, vveln_star, ustar, vstar
@@ -5858,9 +5867,10 @@ end subroutine mts_energy_part_1
 subroutine mts_energy_part_3(bergs,berg,uvel3,vvel3,whichtime)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
-  type(iceberg), pointer :: berg
-  real,intent(in) :: uvel3,vvel3
-  integer,intent(in) :: whichtime
+  type(iceberg), pointer :: berg !< Berg to do calculations for
+  real,intent(in) :: uvel3 !< u-component of velocity [m s-1]  but why 3???
+  real,intent(in) :: vvel3 !< v-component of velocity [m s-1]  but why 3???
+  integer,intent(in) :: whichtime !< Time level ???
   ! Local
   real :: dt, M, Fex, Fey, Fdx, Fdy
 

From 61f6cbec5f911e15d2caec483d99c6682e6c6052 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Tue, 12 Jan 2021 17:42:59 -0500
Subject: [PATCH 271/361] Add GH action to verify documentation

---
 .github/workflows/documentation-and-style.yml | 21 +++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 .github/workflows/documentation-and-style.yml

diff --git a/.github/workflows/documentation-and-style.yml b/.github/workflows/documentation-and-style.yml
new file mode 100644
index 0000000..10a6250
--- /dev/null
+++ b/.github/workflows/documentation-and-style.yml
@@ -0,0 +1,21 @@
+name: Doxygen completeness
+
+on: [push, pull_request]
+
+jobs:
+  doxygen:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Build doxygen HTML
+      run: |
+        cd docs
+        doxygen
+
+    - name: Report doxygen errors
+      run: |
+        cat docs/doxygen.log
+        test ! -s docs/doxygen.log

From 0aaccd909064364dad5db83a880065610738c5bf Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Tue, 12 Jan 2021 17:50:20 -0500
Subject: [PATCH 272/361] Add doxygen to package list

---
 .github/workflows/documentation-and-style.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/documentation-and-style.yml b/.github/workflows/documentation-and-style.yml
index 10a6250..989871b 100644
--- a/.github/workflows/documentation-and-style.yml
+++ b/.github/workflows/documentation-and-style.yml
@@ -10,6 +10,11 @@ jobs:
     steps:
     - uses: actions/checkout@v2
 
+    - name: Install packages used when generating documentation
+      run: |
+        sudo apt-get update
+        sudo apt-get install doxygen
+
     - name: Build doxygen HTML
       run: |
         cd docs

From 38ee4419fa5cdfdbcff32a4b10c54eb85797dc7f Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Tue, 12 Jan 2021 17:52:32 -0500
Subject: [PATCH 273/361] Add graphviz (dot) to package list

---
 .github/workflows/documentation-and-style.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/documentation-and-style.yml b/.github/workflows/documentation-and-style.yml
index 989871b..cfefd7a 100644
--- a/.github/workflows/documentation-and-style.yml
+++ b/.github/workflows/documentation-and-style.yml
@@ -13,7 +13,7 @@ jobs:
     - name: Install packages used when generating documentation
       run: |
         sudo apt-get update
-        sudo apt-get install doxygen
+        sudo apt-get install doxygen dot
 
     - name: Build doxygen HTML
       run: |

From 68611e9727ed64d7b5649f887a6759975e4f1bd7 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Tue, 12 Jan 2021 18:03:45 -0500
Subject: [PATCH 274/361] Trying Ubuntu-20.04

---
 .github/workflows/documentation-and-style.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/documentation-and-style.yml b/.github/workflows/documentation-and-style.yml
index cfefd7a..64ed0b3 100644
--- a/.github/workflows/documentation-and-style.yml
+++ b/.github/workflows/documentation-and-style.yml
@@ -5,7 +5,7 @@ on: [push, pull_request]
 jobs:
   doxygen:
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
 
     steps:
     - uses: actions/checkout@v2
@@ -13,7 +13,7 @@ jobs:
     - name: Install packages used when generating documentation
       run: |
         sudo apt-get update
-        sudo apt-get install doxygen dot
+        sudo apt-get install doxygen graphviz
 
     - name: Build doxygen HTML
       run: |

From ac688c30256102e863c2102b2257a2012238fc52 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Thu, 14 Jan 2021 17:30:54 -0500
Subject: [PATCH 275/361] removed redundant parameter

---
 src/icebergs_framework.F90 | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 954e80e..8462ea5 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -4863,7 +4863,6 @@ subroutine count_bonds(bergs, number_of_bonds, check_bond_quality)
 integer :: number_of_bonds_all_pe
 integer :: grdi, grdj
 logical :: bond_is_good
-logical, intent(inout), optional :: check_bond_quality
 logical :: quality_check
 integer :: num_unmatched_bonds,num_unmatched_bonds_all_pe
 integer :: num_unassosiated_bond_pairs, num_unassosiated_bond_pairs_all_pe

From 813c4a3334df56871807d13b91ba30ff0144d6e1 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Tue, 9 Feb 2021 17:41:54 -0500
Subject: [PATCH 276/361] -Added a scale-invariant DEM-mode, complete with
 tangential forces, torque, and stress-based fracture criterion (can currently
 be used during inner MTS sub-steps only) -Added several 'beam' tests for
 DEM-mode that make sure it can match analytical solutions -Added a
 fracture-upon-grounding test for DEM-mode -Added an energy-based fracture
 criterion -New option to use explicit velocity Verlet during MTS inner
 iterations. This explicit option requires ~2x smaller MTS sub-time steps than
 the previous partially-implicit scheme, but actually may run faster.
 Furthermore, the explicit option ensures momentum conservation without
 needing to iterate to convergence like with the partially-implicit scheme.
 Currently, DEM-mode always uses this explicit approach. -Fixed radius
 definition for square packing -Consolidated MTS code to a single
 evolve_icebergs_mts subroutine -Finished up some documentation

---
 src/icebergs.F90                              | 1166 +++++++++--------
 src/icebergs_framework.F90                    |  399 +++++-
 src/icebergs_io.F90                           |    6 +-
 tests/.gitignore                              |    1 +
 .../Scripts_and_analysis/hexagon_area.pyc     |  Bin 33327 -> 33356 bytes
 tests/dem_cbeam_test/.gitignore               |    1 +
 tests/dem_cbeam_test/README                   |    2 +
 tests/dem_cbeam_test/RUN                      |    5 +
 tests/dem_cbeam_test/animate_trajectories.py  |  179 +++
 .../dem_cbeam_test/animate_trajectories_1l.py |  187 +++
 tests/dem_cbeam_test/diag_table               |    3 +
 tests/dem_cbeam_test/input.nml                |  181 +++
 tests/dem_cbeam_test/makeberg/README          |    2 +
 tests/dem_cbeam_test/makeberg/RUN             |    3 +
 tests/dem_cbeam_test/makeberg/RUN_1l          |    3 +
 tests/dem_cbeam_test/makeberg/RUN_2p          |    3 +
 tests/dem_cbeam_test/makeberg/makeberg.py     |  321 +++++
 tests/dem_cbeam_test/makeberg/makeberg_1l.py  |  321 +++++
 tests/dem_cbeam_test/makeberg/makeberg_2p.py  |  300 +++++
 tests/dem_ground_frac_test/.gitignore         |    1 +
 tests/dem_ground_frac_test/README             |    7 +
 tests/dem_ground_frac_test/RUN                |    7 +
 .../animate_trajectories.py                   |  158 +++
 tests/dem_ground_frac_test/diag_table         |    3 +
 tests/dem_ground_frac_test/input.nml          |  185 +++
 tests/dem_ground_frac_test/input_dem.nml      |  186 +++
 tests/dem_ground_frac_test/input_reg.nml      |  192 +++
 .../dem_ground_frac_test/input_reg_stress.nml |  192 +++
 tests/dem_ground_frac_test/makeberg/RUN       |    3 +
 .../dem_ground_frac_test/makeberg/makeberg.py |  375 ++++++
 tests/dem_rbeam_test/.gitignore               |    1 +
 tests/dem_rbeam_test/README                   |    8 +
 tests/dem_rbeam_test/RUN                      |    5 +
 tests/dem_rbeam_test/animate_trajectories.py  |  164 +++
 tests/dem_rbeam_test/diag_table               |    3 +
 tests/dem_rbeam_test/input.nml                |  184 +++
 tests/dem_rbeam_test/makeberg/RUN             |    3 +
 tests/dem_rbeam_test/makeberg/makeberg.py     |  321 +++++
 tests/dem_ssbeam_test/.gitignore              |    1 +
 tests/dem_ssbeam_test/README                  |    1 +
 tests/dem_ssbeam_test/RUN                     |    5 +
 tests/dem_ssbeam_test/animate_trajectories.py |  178 +++
 tests/dem_ssbeam_test/diag_table              |    3 +
 tests/dem_ssbeam_test/input.nml               |  182 +++
 tests/dem_ssbeam_test/makeberg/RUN            |    3 +
 tests/dem_ssbeam_test/makeberg/makeberg.py    |  321 +++++
 tests/energy_test/input.nml                   |    3 +
 tests/energy_test2/README                     |   15 +-
 tests/energy_test2/input.nml                  |    3 +-
 tests/energy_test3/README                     |    6 +-
 tests/energy_test3/animate_trajectories.py    |   17 +-
 tests/energy_test3/input.nml                  |   24 +-
 tests/energy_test3/makeberg/makeberg.py       |    3 +
 tests/frac_test/.gitignore                    |    1 +
 tests/frac_test/README                        |    9 +
 tests/frac_test/RUN                           |    7 +
 tests/frac_test/RUN1p                         |    7 +
 tests/frac_test/animate_trajectories.py       |  140 ++
 tests/frac_test/animate_trajectories_1pe.py   |  189 +++
 tests/frac_test/diag_table                    |    3 +
 tests/frac_test/input.nml                     |  186 +++
 tests/frac_test/makeberg/RUN                  |    3 +
 tests/frac_test/makeberg/makeberg.py          |  376 ++++++
 tests/plot_bond_strain.py                     |   79 ++
 tests/plot_energy.py                          |    5 +-
 65 files changed, 6235 insertions(+), 616 deletions(-)
 create mode 100644 tests/dem_cbeam_test/.gitignore
 create mode 100644 tests/dem_cbeam_test/README
 create mode 100755 tests/dem_cbeam_test/RUN
 create mode 100755 tests/dem_cbeam_test/animate_trajectories.py
 create mode 100755 tests/dem_cbeam_test/animate_trajectories_1l.py
 create mode 100644 tests/dem_cbeam_test/diag_table
 create mode 100644 tests/dem_cbeam_test/input.nml
 create mode 100644 tests/dem_cbeam_test/makeberg/README
 create mode 100755 tests/dem_cbeam_test/makeberg/RUN
 create mode 100755 tests/dem_cbeam_test/makeberg/RUN_1l
 create mode 100755 tests/dem_cbeam_test/makeberg/RUN_2p
 create mode 100755 tests/dem_cbeam_test/makeberg/makeberg.py
 create mode 100755 tests/dem_cbeam_test/makeberg/makeberg_1l.py
 create mode 100755 tests/dem_cbeam_test/makeberg/makeberg_2p.py
 create mode 100644 tests/dem_ground_frac_test/.gitignore
 create mode 100644 tests/dem_ground_frac_test/README
 create mode 100755 tests/dem_ground_frac_test/RUN
 create mode 100755 tests/dem_ground_frac_test/animate_trajectories.py
 create mode 100644 tests/dem_ground_frac_test/diag_table
 create mode 100644 tests/dem_ground_frac_test/input.nml
 create mode 100644 tests/dem_ground_frac_test/input_dem.nml
 create mode 100644 tests/dem_ground_frac_test/input_reg.nml
 create mode 100644 tests/dem_ground_frac_test/input_reg_stress.nml
 create mode 100755 tests/dem_ground_frac_test/makeberg/RUN
 create mode 100755 tests/dem_ground_frac_test/makeberg/makeberg.py
 create mode 100644 tests/dem_rbeam_test/.gitignore
 create mode 100644 tests/dem_rbeam_test/README
 create mode 100755 tests/dem_rbeam_test/RUN
 create mode 100755 tests/dem_rbeam_test/animate_trajectories.py
 create mode 100644 tests/dem_rbeam_test/diag_table
 create mode 100644 tests/dem_rbeam_test/input.nml
 create mode 100755 tests/dem_rbeam_test/makeberg/RUN
 create mode 100755 tests/dem_rbeam_test/makeberg/makeberg.py
 create mode 100644 tests/dem_ssbeam_test/.gitignore
 create mode 100644 tests/dem_ssbeam_test/README
 create mode 100755 tests/dem_ssbeam_test/RUN
 create mode 100755 tests/dem_ssbeam_test/animate_trajectories.py
 create mode 100644 tests/dem_ssbeam_test/diag_table
 create mode 100644 tests/dem_ssbeam_test/input.nml
 create mode 100755 tests/dem_ssbeam_test/makeberg/RUN
 create mode 100755 tests/dem_ssbeam_test/makeberg/makeberg.py
 create mode 100644 tests/frac_test/.gitignore
 create mode 100644 tests/frac_test/README
 create mode 100755 tests/frac_test/RUN
 create mode 100755 tests/frac_test/RUN1p
 create mode 100755 tests/frac_test/animate_trajectories.py
 create mode 100755 tests/frac_test/animate_trajectories_1pe.py
 create mode 100644 tests/frac_test/diag_table
 create mode 100644 tests/frac_test/input.nml
 create mode 100755 tests/frac_test/makeberg/RUN
 create mode 100755 tests/frac_test/makeberg/makeberg.py
 create mode 100755 tests/plot_bond_strain.py

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index e5e941f..15f0178 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -47,10 +47,11 @@ module ice_bergs
 use ice_bergs_framework, only: update_latlon,set_conglom_ids,transfer_mts_bergs,quad_interp_from_agrid
 use ice_bergs_framework, only: save_bond_traj
 use ice_bergs_framework, only: fracture_testing_initialization, orig_bond_length
-use ice_bergs_framework, only: update_and_break_bonds,assign_n_bonds,reset_bond_rotation
+use ice_bergs_framework, only: update_and_break_bonds,break_bonds_dem,assign_n_bonds,reset_bond_rotation
 use ice_bergs_framework, only: update_bond_angles
 use ice_bergs_framework, only: monitor_energy, energy_tests_init, new_mts
-use ice_bergs_framework, only: imp_loop_iters_short,imp_loop_iters_long
+use ice_bergs_framework, only: dem_tests_init
+use ice_bergs_framework, only: dem, init_dem_params
 
 use ice_bergs_io,        only: ice_bergs_io_init, write_restart, write_trajectory, write_bond_trajectory
 use ice_bergs_io,        only: read_restart_bergs, read_restart_calving
@@ -67,15 +68,15 @@ module ice_bergs
 real, parameter :: Rearth=6360000. !< Radius of earth (m)
 real, parameter :: rho_ice=916.7 !< Density of fresh ice @ 0oC (kg/m^3)
 real, parameter :: rho_water=999.8 !< Density of fresh water @ 0oC (kg/m^3)
-real, parameter :: rho_air=1.1 !< Density of air @ 0oC (kg/m^3) ???
+real, parameter :: rho_air=1.1 !< Density of air @ 0oC (kg/m^3)
 real, parameter :: rho_seawater=1025. !< Approx. density of surface sea water @ 0oC (kg/m^3)
 real, parameter :: gravity=9.8 !< Gravitational acceleratio (m/s^2)
-real, parameter :: Cd_av=1.3 !< (Vertical) Drag coefficient between bergs and atmos (?)
-real, parameter :: Cd_ah=0.0055 !< (Horizontal) Drag coefficient between bergs and atmos (?)
-real, parameter :: Cd_wv=0.9 !< (Vertical) Drag coefficient between bergs and ocean (?)
-real, parameter :: Cd_wh=0.0012 !< (Horizontal) Drag coefficient between bergs and ocean (?)
-real, parameter :: Cd_iv=0.9 !< (Vertical) Drag coefficient between bergs and sea-ice (?)
-!TOM> no horizontal drag for sea ice! real, parameter :: Cd_ih=0.0012 !< (Horizontal) Drag coefficient between bergs and sea-ice (?)
+real, parameter :: Cd_av=1.3 !< (Vertical) Drag coefficient between bergs and atmos
+real, parameter :: Cd_ah=0.0055 !< (Horizontal) Drag coefficient between bergs and atmos
+real, parameter :: Cd_wv=0.9 !< (Vertical) Drag coefficient between bergs and ocean
+real, parameter :: Cd_wh=0.0012 !< (Horizontal) Drag coefficient between bergs and ocean
+real, parameter :: Cd_iv=0.9 !< (Vertical) Drag coefficient between bergs and sea-ice
+!TOM> no horizontal drag for sea ice! real, parameter :: Cd_ih=0.0012 !< (Horizontal) Drag coefficient between bergs and sea-ice
 
 #ifdef _FILE_VERSION
 character(len=128) :: version = _FILE_VERSION !< Version of file
@@ -148,6 +149,7 @@ subroutine icebergs_init(bergs, &
   if (bergs%read_ocean_depth_from_file) call read_ocean_depth(bergs%grd)
 
   if (monitor_energy) call energy_tests_init(bergs)
+  if (bergs%dem) call init_dem_params(bergs)
 
   if (bergs%iceberg_bonds_on) then
     if (bergs%manually_initialize_bonds) then
@@ -174,6 +176,8 @@ subroutine icebergs_init(bergs, &
     call fracture_testing_initialization(bergs)
   endif
 
+  if (bergs%uniaxial_test .or. bergs%dem_beam_test>0) call dem_tests_init(bergs)
+
 end subroutine icebergs_init
 
 subroutine debugwriteandstop(bergs)
@@ -374,7 +378,8 @@ subroutine initialize_iceberg_bonds(bergs)
     if (bergs%hexagonal_icebergs) then
       rdenom=1./(2.*sqrt(3.))
     else
-      rdenom=1./pi
+      !rdenom=1./pi
+      rdenom=1./4.
     endif
   endif
 
@@ -487,12 +492,12 @@ subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
   real, intent(in) :: v1 !< Meridional velocity of other berg (m/s)
   real, intent(out) :: IA_x !< Net zonal acceleration of berg due to interactions (m/s2)
   real, intent(out) :: IA_y !< Net meridional acceleration of berg due to interactions (m/s2)
-  real, intent(out) :: P_ia_11
-  real, intent(out) :: P_ia_12
-  real, intent(out) :: P_ia_22
-  real, intent(out) :: P_ia_21
-  real, intent(out) :: P_ia_times_u_x
-  real, intent(out) :: P_ia_times_u_y
+  real, intent(out) :: P_ia_11 !< Damping projection matrix, xx component (kg/s)
+  real, intent(out) :: P_ia_12 !< Damping projection matrix, xy component (kg/s)
+  real, intent(out) :: P_ia_22 !< Damping projection matrix, yy component (kg/s)
+  real, intent(out) :: P_ia_21 !< Damping projection matrix, yx component (kg/s)
+  real, intent(out) :: P_ia_times_u_x !< Zonal damping projection (without new berg velocity) (kg m/s)
+  real, intent(out) :: P_ia_times_u_y !< Meridional damping projection (without new berg velocity) (kg m/s)
   ! Local variables
   type(bond), pointer :: current_bond
   real :: u2, v2
@@ -523,7 +528,7 @@ subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
             call error_mesg('KID,bond interactions', 'Trying to do Bond interactions with unassosiated berg!' ,FATAL)
           else
             call calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,  &
-              P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded,current_bond=current_bond)
+              P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded)
             other_berg%id=-other_berg%id !mark, as to not repeat in contact search below
           endif
           current_bond=>current_bond%next_bond
@@ -641,7 +646,7 @@ end subroutine contact_eligibility
 
 !> Calculate interactive forces between two bergs
 subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1, &
-  P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y, bonded, c_crit_dist, current_bond)
+  P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y, bonded, c_crit_dist)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
   type(iceberg), pointer :: berg !< Primary berg
@@ -652,15 +657,14 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
   real, intent(in) :: v0 !< Meridional velocity of primary berg (m/s)
   real, intent(in) :: u1 !< Zonal velocity of other berg (m/s)
   real, intent(in) :: v1 !< Meridional velocity of other berg (m/s)
-  real, intent(inout) :: P_ia_11
-  real, intent(inout) :: P_ia_12
-  real, intent(inout) :: P_ia_22
-  real, intent(inout) :: P_ia_21
-  real, intent(inout) :: P_ia_times_u_x
-  real, intent(inout) :: P_ia_times_u_y
-  logical ,intent(in) :: bonded
-  logical ,intent(in), optional :: c_crit_dist
-  type(bond), intent(in), optional :: current_bond
+  real, intent(inout) :: P_ia_11 !< Damping projection matrix, xx component (kg/s)
+  real, intent(inout) :: P_ia_12 !< Damping projection matrix, xy component (kg/s)
+  real, intent(inout) :: P_ia_22 !< Damping projection matrix, yy component (kg/s)
+  real, intent(inout) :: P_ia_21 !< Damping projection matrix, yx component (kg/s)
+  real, intent(inout) :: P_ia_times_u_x !< Zonal damping projection (without new berg velocity) (kg m/s)
+  real, intent(inout) :: P_ia_times_u_y !< Meridional damping projection (without new berg velocity) (kg m/s)
+  logical ,intent(in) :: bonded !< If T, berg and other_berg are bonded
+  logical ,intent(in), optional :: c_crit_dist !< Modified critical interaction distance for contact (m)
   ! Local variables
   real :: T1, L1, W1, lon1, lat1, x1, y1, R1, A1 ! Current iceberg
   real :: T2, L2, W2, lon2, lat2, x2, y2, R2, A2 ! Other iceberg
@@ -684,7 +688,7 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
     lon1=berg%lon_old; lat1=berg%lat_old
     !call rotpos_to_tang(lon1,lat1,x1,y1)
 
-    ! From Berg 1
+    ! From Berg 2
     L2=other_berg%length
     W2=other_berg%width
     T2=other_berg%thickness
@@ -715,8 +719,10 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
       R1=sqrt(A1/(2.*sqrt(3.)))
       R2=sqrt(A2/(2.*sqrt(3.)))
     else !square packing
-      R1=sqrt(A1/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
-      R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
+      !R1=sqrt(A1/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
+      !R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
+      R1=0.5*sqrt(A1)
+      R2=0.5*sqrt(A2)
     endif
     !!!!!!!!!!!!!!!!!!!!!!!!!!!debugging!!!!!!!!!!!!!!!!!!!!!!!!!!MP1
     ! if (berg%id .eq. 1) then
@@ -770,6 +776,10 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
       if (.not. (r_dist>crit_dist)) tbonded=.false.
     endif
 
+    if (bergs%uniaxial_test) then
+      if (berg%start_lon==bergs%dem_tests_start_lon) IA_x=IA_x-1.e-5
+      if (berg%start_lon==bergs%dem_tests_end_lon)   IA_x=IA_x+1.e-5
+    endif
 
     if  ((r_dist>0.) .and. ( tbonded .or. (r_dist<crit_dist .and. .not. bonded) )) then
 
@@ -829,6 +839,169 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
 
 end subroutine calculate_force
 
+!> Calculate interactive forces between two bergs using a discrete element method (DEM)
+!> that includes additional terms for tangential forces and torque.
+subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
+  dt, F_x, F_y, T, Fd_x, Fd_y, T_d, savestress)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  type(iceberg), pointer :: berg !< Primary berg
+  type(iceberg), pointer :: other_berg !< Berg that primary is interacting with
+  type(bond), pointer :: current_bond !< Bond being processed
+  real, intent(in) :: dt !< Time step size
+  real, intent(inout) :: F_x !< Net x-force without damping (N)
+  real, intent(inout) :: F_y !< Net y-force without damping (N)
+  real, intent(inout) :: T !< Net torque without damping (Nm)
+  real, intent(inout) :: Fd_x !< Net x-force from damping (N)
+  real, intent(inout) :: Fd_y !< Net y-force from damping (N)
+  real, intent(inout) :: T_d !< Net torque from damping (Nm)
+  logical, intent(in) :: savestress !< Save stress/tangential displacement on bond or not
+  ! Local variables
+  real :: T1,M1,u1,v1,lon1,lat1,R1 ! Current iceberg
+  real :: T2,M2,u2,v2,lon2,lat2,R2 ! Other iceberg
+  real :: dlon, dlat, lat_ref, dx_dlon, dy_dlat
+  real :: r_dist_x, r_dist_y, r_dist
+  real :: Rmin, delta, L, l0, youngs, Thick, T_Rmin, n1, n2
+  real :: ur, vr, up, vp, rotu, rotv, rtu, rtv, RR1, RR2
+  real :: ur2, vr2
+  real :: ss_factor, ss1, ss2
+  real :: K_damp, Meff, damping_coef
+  real :: Fn_x, Fn_y, Fs_x, Fs_y, Ts, Tr
+  real :: tangdotnt,tangd1p,tangd2p, tmag, tmagp
+  real :: RR1x,RR1y,RR2x,RR2y
+
+  !This DEM formulation follows Wang 2020 "A scale-invariant bonded particle model for
+  !simulating large deformation and failure of continua", which differs from "classic"
+  !DEM (e.g. Potyondy & Cundall, 2004) in its definition of bond width and torque from
+  !relative particle rotation. Forces and torques were further modified here to depend
+  !on ice thickness.
+
+  if (berg%id .ne. other_berg%id) then
+
+    ! From Berg 1
+    T1=berg%thickness
+    M1=berg%mass
+    lon1=berg%lon_old; lat1=berg%lat_old
+
+    ! From Berg 2
+    T2=other_berg%thickness
+    M2=other_berg%mass
+    lon2=other_berg%lon_old; lat2=other_berg%lat_old !Old values are used to make it order invariant
+
+    dlon=lon1-lon2; dlat=lat1-lat2
+
+    ! Note that this is not the exact distance along a great circle.
+    ! Approximation for small distances. Should be fine.
+    lat_ref=0.5*(lat1+lat2)
+    call convert_from_grid_to_meters(lat_ref,bergs%grd%grid_is_latlon,dx_dlon,dy_dlat)
+
+    r_dist_x=dlon*dx_dlon
+    r_dist_y=dlat*dy_dlat
+    r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) ) !(Stern et al 2017, Eqn 3)
+
+    !unit vec
+    n1=r_dist_x/r_dist; n2=r_dist_y/r_dist
+
+    !Stern et al 2017, Eqn 4: radius of circle inscribed within hexagon or square with area A1 or A2
+    if (bergs%hexagonal_icebergs) then
+      R1=sqrt(berg%length*berg%width/(2.*sqrt(3.)))
+      R2=sqrt(other_berg%length*other_berg%width/(2.*sqrt(3.)))
+    else !square packing
+      !R1=sqrt(A1/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
+      !R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
+      R1=0.5*sqrt(berg%length*berg%width)
+      R2=0.5*sqrt(other_berg%length*other_berg%width)
+    endif
+
+    !Rmin=min(R1,R2) !old
+    if (R1<R2) then
+      Rmin=R1
+      !T_Rmin=T1 !thickness of element w/ minimum radius
+    else
+      Rmin=R2
+      !T_Rmin=T2
+    endif
+    l0=R1+R2
+    delta=l0-r_dist
+
+    !element distances to contact point
+    RR1=R1-0.5*delta; RR2=R2-0.5*delta !magnitude
+    RR1x=RR1*n1;  RR1y=RR1*n2 !element 1 components
+    RR2x=RR2*n1;  RR2y=RR2*n2 !element 2 components
+
+    !bond width (determined at contact point)
+    L=2.0*(Rmin+(Rmin-0.5*delta)*abs(R1-R2)/r_dist)
+
+    !Thick=T_Rmin+(Rmin-0.5*delta)*abs(T1-T2)/r_dist !the thickness (determined at contact point)
+    Thick=min(T1,T2) !minimum thickness makes more sense?
+
+    youngs=bergs%dem_spring_coef
+
+    !normal force:
+    !Fn_x=youngs*Thick*delta*n1*L/l0 !Fn_y=youngs*Thick*delta*n2*L/l0
+    if (savestress) current_bond%nstress=-youngs*delta/l0 !normal stress
+    Fn_x=youngs*Thick*delta*L/l0; Fn_y=Fn_x*n2; Fn_x=Fn_x*n1
+
+    !relative translational velocity
+    ur=berg%uvel_old-other_berg%uvel_old; vr=berg%vvel_old-other_berg%vvel_old
+
+    if (savestress) then
+      !Rotation of contact plane:
+      tmag=sqrt(current_bond%tangd1**2+current_bond%tangd2**2) !old magnitude
+      !project old tangential displacement to current tangent plane
+      tangdotnt=current_bond%tangd1*n1+current_bond%tangd2*n2
+      tangd1p=current_bond%tangd1-tangdotnt*n1; tangd2p=current_bond%tangd2-tangdotnt*n2
+      !rescale to the old magnitude
+      tmagp=sqrt(tangd1p**2+tangd2p**2)
+      if (tmagp>0.) then
+        tangd1p=(tmag/tmagp)*tangd1p; tangd2p=(tmag/tmagp)*tangd2p
+      else
+        tangd1p=0.; tangd2p=0.
+      endif
+      current_bond%tangd1=tangd1p; current_bond%tangd2=tangd2p
+
+      !relative tangential velocities from rotation
+      rotu=RR1y*berg%ang_vel + RR2y*other_berg%ang_vel
+      rotv=-(RR1x*berg%ang_vel + RR2x*other_berg%ang_vel)
+      ur2=ur+rotu; vr2=vr+rotv
+
+      !'parallel' velocity = dot(relative velocity,unit vec)*unit vec
+      up=ur2*n1+vr2*n2; vp=up*n2; up=up*n1
+      rtu=ur2-up; rtv=vr2-vp !the relative tangential velocities
+
+      !add the new tangential displacement
+      current_bond%tangd1=current_bond%tangd1+rtu*dt; current_bond%tangd2=current_bond%tangd2+rtv*dt
+      current_bond%length=r_dist
+    endif
+
+    !shear terms
+    ss_factor=-L*Thick*youngs/(l0*2.0*(1.0+bergs%poisson))
+    Fs_x=ss_factor*current_bond%tangd1; Fs_y=ss_factor*current_bond%tangd2 !shear forces
+    if (savestress) current_bond%sstress=sqrt(Fs_x**2+Fs_y**2)/(L*Thick) !shear stress
+
+    !Torque from shearing force: Ts = R .cross. Fs
+    Ts = -(RR1x*Fs_y-RR1y*Fs_x)
+
+    !Torque from relative particle rotation
+    Tr = -youngs*Thick*(L*L*L)*sin(berg%rot-other_berg%rot)/(12.*l0)
+
+    !damping
+    K_damp = 2.*youngs/(3.*(1.-bergs%poisson**2)) !damping factor
+    Meff = M1*M2/(M1+M2) !effective mass
+
+    damping_coef = bergs%dem_damping_coef*sqrt(K_damp*Meff)
+
+    Fd_x = Fd_x-damping_coef*ur; Fd_y = Fd_y-damping_coef*vr  !linear damping force
+    T_d  = T_d-damping_coef*(berg%ang_vel-other_berg%ang_vel) !damping torque
+
+    !final forces
+    T = T + (Ts + Tr) !torque
+    F_x = F_x + Fn_x + Fs_x; F_y = F_y + Fn_y + Fs_y !linear forces
+  endif
+
+end subroutine calculate_force_dem
+
+
 !> Calculates area of overlap between two circular bergs
 subroutine overlap_area(R1, R2, d, A, trapped)
   ! Arguments
@@ -862,6 +1035,7 @@ subroutine overlap_area(R1, R2, d, A, trapped)
 
 end subroutine overlap_area
 
+!> For the MTS scheme, calculates the instantaneous acceleration of an iceberg
 subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, rx, ry, &
   ax, ay, axn, ayn, bxn, byn, save_bond_energy, Fec_x, Fec_y, Fdc_x, Fdc_y, debug_flag)
   ! Arguments
@@ -885,8 +1059,11 @@ subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, d
   real, intent(inout) :: ayn !< Explicit estimate of meridional acceleration (m/s2)
   real, intent(inout) :: bxn !< Implicit component of zonal acceleration (m/s2)
   real, intent(inout) :: byn !< Implicit component of meridional acceleration (m/s2)
-  logical, intent(in) :: save_bond_energy
-  real, optional, intent(out) :: Fec_x,Fec_y,Fdc_x,Fdc_y !< Collisional elastic and damping forces (if bergs%mts_part==1)
+  logical, intent(in) :: save_bond_energy !< Track energy terms for bonds (when monitor_energy==T)
+  real, optional, intent(out) :: Fec_x !< If bergs%mts_part==1: Zonal collisional elastic force (N)
+  real, optional, intent(out) :: Fec_y !< If bergs%mts_part==1: Meridional collisional elastic force (N)
+  real, optional, intent(out) :: Fdc_x !< If bergs%mts_part==1: Zonal collisional damping force (N)
+  real, optional, intent(out) :: Fdc_y !< If bergs%mts_part==1: Meridional collisional damping force (N)
   logical, optional :: debug_flag !< If true, print debugging
   ! Local variables
   type(icebergs_gridded), pointer :: grd
@@ -910,7 +1087,7 @@ subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, d
   real :: dragfrac, N_bonds, N_max, groundfrac, c_gnd, drag_gnd, scaling
   real :: minfricvel=3.17e-12 !m/s (~0.0001 m/a)
   type(bond), pointer :: current_bond
-  real :: IAd_x, IAd_y, sum_bond_Ee, sum_bond_Ed
+  real :: IAd_x, IAd_y, sum_bond_Ee, sum_bond_Ed, oneoverkn
   type(iceberg), pointer :: other_berg
 
   Runge_not_Verlet=bergs%Runge_not_Verlet  ! Loading directly from namelist/default , Alon
@@ -981,7 +1158,7 @@ subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, d
     endif
 
     ! Wave radiation (Stern et al 2017, Eqs A4-A5)
-    uwave=ua-uo; vwave=va-vo  ! Use wind speed rel. to ocean for wave model (aja)?
+    uwave=ua-uo; vwave=va-vo  ! Use wind speed rel. to ocean for wave model (aja)
     wmod=uwave*uwave+vwave*vwave ! The wave amplitude and length depend on the wind speed relative to the ocean current
     ! actually wmod is wmod**2 here.
     ampl=0.5*0.02025*wmod ! This is "a", the wave amplitude
@@ -1148,7 +1325,7 @@ subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, d
     endif
   elseif (save_bond_energy) then
     !save bond energies
-    if (monitor_energy) then
+    if (monitor_energy .or. bergs%fracture_criterion=='energy') then
       sum_bond_Ee=0.0
       sum_bond_Ed=0.0
       M=berg%mass
@@ -1156,15 +1333,17 @@ subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, d
       do while (associated(current_bond)) ! loop over all bonds
         other_berg=>current_bond%other_berg
 
-        !first, the half-step:
-        current_bond%Ee=current_bond%Ee - 0.25*dt*(&
-          (uvel0 + u_star)*M*current_bond%axn_fast +&
-          (vvel0 + v_star)*M*current_bond%ayn_fast)
+        if (monitor_energy) then
+          !first, the half-step:
+          current_bond%Ee=current_bond%Ee - 0.25*dt*(&
+            (uvel0 + u_star)*M*current_bond%axn_fast +&
+            (vvel0 + v_star)*M*current_bond%ayn_fast)
 
-        if (new_mts) then
-          current_bond%Ed=current_bond%Ed - 0.25*dt*(&
-            (uvel0 + u_star)*M*current_bond%bxn_fast +&
-            (vvel0 + v_star)*M*current_bond%byn_fast)
+          if (new_mts) then
+            current_bond%Ed=current_bond%Ed - 0.25*dt*(&
+              (uvel0 + u_star)*M*current_bond%bxn_fast +&
+              (vvel0 + v_star)*M*current_bond%byn_fast)
+          endif
         endif
 
         !the rest:
@@ -1176,32 +1355,36 @@ subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, d
         IAd_x=P_ia_11*(other_berg%uvel_old-uveln)+P_ia_12*(other_berg%vvel_old-vveln)
         IAd_y=P_ia_12*(other_berg%uvel_old-uveln)+P_ia_22*(other_berg%vvel_old-vveln)
 
-        current_bond%Ee=berg%Ee - 0.25*dt*(&
-          (u_star + uveln)*M*IA_x + &
-          (v_star + vveln)*M*IA_y)
-
-        if (new_mts) then
-          !V{i+0.5} to V{i+1}
-          current_bond%Ed=current_bond%Ed- 0.25*dt*(&
-            (u_star + uveln)*M*IAd_x + &
-            (v_star + vveln)*M*IAd_y)
-        else
-          !old way: V{i} to V{i+1}
-          ! current_bond%Ed=current_bond%Ed - 0.5*dt*(&
-          !   (berg%uvel + uveln)*M*IAd_x + &
-          !   (berg%vvel + vveln)*M*IAd_y)
-
-          !new, better way
-          current_bond%Ed=current_bond%Ed - 0.5*dt*(&
-            (u_star + uveln)*M*IAd_x + &
-            (v_star + vveln)*M*IAd_y)
+        if (bergs%fracture_criterion=='energy') then
+          oneoverkn = 1./bergs%spring_coef
+          oneoverkn=oneoverkn*(M/min(M,other_berg%mass))
+          current_bond%spring_pe = 0.5*((M*IA_x)**2+(M*IA_y)**2)*oneoverkn
         endif
 
-        sum_bond_Ee = sum_bond_Ee + current_bond%Ee
-        sum_bond_Ed = sum_bond_Ed + current_bond%Ed
+        if (monitor_energy) then
+          !work
+          current_bond%Ee=current_bond%Ee - 0.25*dt*(&
+            (u_star + uveln)*M*IA_x + &
+            (v_star + vveln)*M*IA_y)
 
-        current_bond%axn_fast=IA_x;  current_bond%ayn_fast=IA_y
-        current_bond%bxn_fast=IAd_x; current_bond%byn_fast=IAd_y
+
+          if (new_mts) then
+            !V{i+0.5} to V{i+1}
+            current_bond%Ed=current_bond%Ed- 0.25*dt*(&
+              (u_star + uveln)*M*IAd_x + &
+              (v_star + vveln)*M*IAd_y)
+          else
+            current_bond%Ed=current_bond%Ed - 0.5*dt*(&
+              (u_star + uveln)*M*IAd_x + &
+              (v_star + vveln)*M*IAd_y)
+          endif
+
+          sum_bond_Ee = sum_bond_Ee + current_bond%Ee
+          sum_bond_Ed = sum_bond_Ed + current_bond%Ed
+
+          current_bond%axn_fast=IA_x;  current_bond%ayn_fast=IA_y
+          current_bond%bxn_fast=IAd_x; current_bond%byn_fast=IAd_y
+        endif
 
         current_bond=>current_bond%next_bond
       enddo
@@ -1236,7 +1419,7 @@ subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, d
       dumpit=.true.
       write(stderrunit,'("pe=",i3,x,a)') mpp_pe(),'Dump triggered by excessive velocity'
     else
-      write(stderrunit,'("pe=",i3,x,a)') mpp_pe(),'Excessive velocity detected'
+      !write(stderrunit,'("pe=",i3,x,a)') mpp_pe(),'Excessive velocity detected'
     endif
   endif
   if (abs(ax)>accel_lim.or.abs(ay)>accel_lim) then
@@ -1349,6 +1532,298 @@ subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, d
 
 end subroutine accel_mts
 
+!> Calculates the instantaneous acceleration of an iceberg due to berg interactions
+!> For the inner steps of the mts scheme only. Explicit velocity verlet (no implicit terms)
+subroutine accel_explicit_inner_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt,  &
+  ax, ay, axn, ayn, save_bond_energy, debug_flag)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  type(iceberg), pointer :: berg !< An iceberg
+  integer, intent(in) :: i !< i-index of cell berg is in
+  integer, intent(in) :: j !< j-index of cell berg is in
+  real, intent(in) :: xi !< Non-dimensional x-position within cell of berg
+  real, intent(in) :: yj !< Non-dimensional y-position within cell of berg
+  real, intent(in) :: lat !< Latitude of berg (degree N)
+  real, intent(inout) :: uvel !< Zonal velocity of berg (m/s)
+  real, intent(inout) :: vvel !< Meridional velocity of berg (m/s)
+  real, intent(inout) :: uvel0 !< Zonal velocity of berg at beginning of time-step (m/s)
+  real, intent(inout) :: vvel0 !< Meridional velocity of berg at beginning of time-step (m/s)
+  real, intent(in) :: dt !< Time step (s)
+  real, intent(out) :: ax !< Zonal acceleration (m/s2)
+  real, intent(out) :: ay !< Meridional acceleration (m/s2)
+  real, intent(inout) :: axn !< Explicit estimate of zonal acceleration (m/s2)
+  real, intent(inout) :: ayn !< Explicit estimate of meridional acceleration (m/s2)
+  logical, intent(in) :: save_bond_energy !< Track energy terms for bonds (when monitor_energy==T)
+  logical, optional :: debug_flag !< If true, print debugging
+  ! Local variables
+  type(icebergs_gridded), pointer :: grd
+  real :: bxn, byn
+  real :: M
+  real :: uveln, vveln, speed, loc_dx, new_speed
+  real :: u_star, v_star
+  real :: IA_x, IA_y
+  real :: P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y    !Added by Alon
+  integer :: stderrunit
+  type(bond), pointer :: current_bond
+  real :: IAd_x, IAd_y, sum_bond_Ee, sum_bond_Ed, oneoverkn
+  type(iceberg), pointer :: other_berg
+  integer :: grdi,grdj
+  logical :: bonded
+  ! DEM-mode local variables
+  real :: F_x, F_y, T, Fd_x, Fd_y, T_d, R1, at
+
+  u_star=uvel0+(axn*(dt/2.)); v_star=vvel0+(ayn*(dt/2.))  !Alon
+  stderrunit = stderr()   ! Get the stderr unit number.
+  grd=>bergs%grd   ! For convenience
+
+  ! Initializing accelerations
+  axn=0.; ayn=0.; bxn=0.; byn=0.
+  IA_x=0.; IA_y=0.; IAd_x=0.; IAd_y=0.
+
+  if (bergs%dem) then
+    F_x=0.; F_y=0.; T=0.; Fd_x=0.; Fd_y=0.; T_d=0.
+  endif
+
+  bonded=.true.
+  if (bergs%iceberg_bonds_on) then
+    current_bond=>berg%first_bond
+    do while (associated(current_bond)) ! loop over all bonds
+      other_berg=>current_bond%other_berg
+      if (.not. associated(other_berg)) then
+        call error_mesg('KID,bond interactions', 'Trying to do Bond interactions with unassosiated berg!' ,FATAL)
+      else
+        if (bergs%dem) then
+          call calculate_force_dem(bergs,berg,other_berg,current_bond,&
+            dt,F_x,F_y,T,Fd_x,Fd_y,T_d,savestress=.true.)
+          other_berg%id=-other_berg%id !mark, as to not repeat in contact search below
+        else
+          P_ia_11=0. ; P_ia_12=0. ;  P_ia_21=0.;  P_ia_22=0.
+          P_ia_times_u_x=0. ; P_ia_times_u_y=0.
+          call calculate_force(bergs, berg, other_berg, IA_x, IA_y, uvel0, vvel0, uvel0, vvel0,  &
+            P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded)
+          other_berg%id=-other_berg%id !mark, as to not repeat in contact search below
+          IAd_x=IAd_x+P_ia_11*(other_berg%uvel_old-berg%uvel_old)+P_ia_12*(other_berg%vvel_old-berg%vvel_old)
+          IAd_y=IAd_y+P_ia_12*(other_berg%uvel_old-berg%uvel_old)+P_ia_22*(other_berg%vvel_old-berg%vvel_old)
+        endif
+      endif
+      current_bond=>current_bond%next_bond
+    enddo
+    !contact search: find any surrounding non-bonded bergs in the same conglom, and processes
+    !them for contact using the regular (non-contact) spring constant and crit_dist based on radii
+    bonded=.false.
+    do grdj = max(berg%jne-2,bergs%grd%jsd+1),min(berg%jne+2,bergs%grd%jed);&
+      do grdi = max(berg%ine-2,bergs%grd%isd+1),min(berg%ine+2,bergs%grd%ied)
+      other_berg=>bergs%list(grdi,grdj)%first
+      do while (associated(other_berg))
+        if (other_berg%id>0 .and. other_berg%conglom_id.eq.berg%conglom_id) then
+          P_ia_11=0. ; P_ia_12=0. ;  P_ia_21=0.;  P_ia_22=0.
+          P_ia_times_u_x=0. ; P_ia_times_u_y=0.
+          call calculate_force(bergs, berg, other_berg, IA_x, IA_y, uvel0, vvel0, uvel0, vvel0,  &
+            P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded,c_crit_dist=.true.)
+          IAd_x=IAd_x+P_ia_11*(other_berg%uvel_old-berg%uvel_old)+P_ia_12*(other_berg%vvel_old-berg%vvel_old)
+          IAd_y=IAd_y+P_ia_12*(other_berg%uvel_old-berg%uvel_old)+P_ia_22*(other_berg%vvel_old-berg%vvel_old)
+        endif
+        other_berg=>other_berg%next
+      enddo
+    enddo;enddo
+
+    !unmark the bonded bergs
+    current_bond=>berg%first_bond
+    do while (associated(current_bond))
+      other_berg=>current_bond%other_berg
+      other_berg%id=abs(other_berg%id)
+      current_bond=>current_bond%next_bond
+    enddo
+  endif
+
+  if (bergs%dem) then
+
+    if (bergs%hexagonal_icebergs) then
+      R1=sqrt(berg%length*berg%width/(2.*sqrt(3.)))
+    else !square packing
+      !R1=sqrt(berg%length*berg%width/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
+      R1=0.5*sqrt(berg%length*berg%width)
+    endif
+
+    if (bergs%dem_beam_test>0) then
+      if (bergs%dem_beam_test==1) then
+        !3.1 (Wang,2020): Simply supported beam test
+        !no vertical load on ends of beam, add vertical load to center of beam
+        if (berg%start_lon==bergs%dem_tests_start_lon .or. berg%start_lon==bergs%dem_tests_end_lon) then
+          F_y=0.0; Fd_y=0.0
+        elseif (berg%start_lon==0.5*(bergs%dem_tests_start_lon+bergs%dem_tests_end_lon)) then
+          F_y = F_y - 1.5e5
+        endif
+      elseif (bergs%dem_beam_test==2) then
+        !3.2 (Wang,2020): Cantilever beam test
+        !add vertical load to end of the cantilever beam
+        if (berg%start_lon==bergs%dem_tests_end_lon) then
+          F_y = F_y - 1.5e10/3.
+        endif
+      elseif (bergs%dem_beam_test==3) then
+        !Angular velocity test (starting element has constant rot=-pi/2)
+        if (berg%start_lon==bergs%dem_tests_start_lon) then
+          T=0.0; T_d=0.0
+        endif
+      elseif (bergs%dem_beam_test==4) then
+        if (berg%start_lon==bergs%dem_tests_start_lon) then
+          F_y=0.0; Fd_y=0.0
+        endif
+      endif
+    endif
+
+    !M=berg%thickness*(pi*R1**2)*bergs%rho_bergs
+    M=berg%mass
+    IA_x=IA_x+F_x/M; IA_y=IA_y+F_y/M
+    IAd_x=IAd_x+Fd_x/M; IAd_y=IAd_y+Fd_y/M
+
+    at=(T+T_d)/(0.5*M*R1**2) !torque acceleration
+    berg%ang_accel = at
+  endif
+
+  axn=IA_x+IAd_x; ayn=IA_y+IAd_y
+  bxn=0.0; byn=0.0
+
+  if (new_mts) then
+    ax=0.5*(axn+bxn); ay=0.5*(ayn+byn)
+  else
+    ax=0.5*axn+bxn; ay=0.5*ayn+byn
+  endif
+
+  uveln=u_star+dt*ax; vveln=v_star+dt*ay
+
+  if (save_bond_energy) then
+
+    !save bond energies
+    if (monitor_energy .or. bergs%fracture_criterion=='energy') then
+      M=berg%mass
+      current_bond=>berg%first_bond
+      do while (associated(current_bond)) ! loop over all bonds
+        other_berg=>current_bond%other_berg
+
+        if (monitor_energy) then
+          !first, the half-step:
+          current_bond%Ee=current_bond%Ee - 0.25*dt*(&
+            (uvel0 + u_star)*M*current_bond%axn_fast +&
+            (vvel0 + v_star)*M*current_bond%ayn_fast)
+
+          if (new_mts) then
+            !here, bxn_fast and byn_fast are explicit damping accel (not implicit!)
+            current_bond%Ed=current_bond%Ed - 0.25*dt*(&
+              (uvel0 + u_star)*M*current_bond%bxn_fast +&
+              (vvel0 + v_star)*M*current_bond%byn_fast)
+          endif
+        endif
+
+        !the rest:
+
+        if (bergs%dem) then
+          F_x=0.; F_y=0.; T=0.; Fd_x=0.; Fd_y=0.; T_d=0.
+          call calculate_force_dem(bergs,berg,other_berg,current_bond,dt,&
+            F_x,F_y,T,Fd_x,Fd_y,T_d,savestress=.false.)
+          if (bergs%dem_beam_test>0) then
+            if (bergs%dem_beam_test==1) then
+              !3.1 (Wang,2020): Simply supported beam test
+              !no vertical load on ends of beam, add vertical load to center of beam
+              if (berg%start_lon==bergs%dem_tests_start_lon .or. berg%start_lon==bergs%dem_tests_end_lon) then
+                F_y=0.0; Fd_y=0.0
+              elseif (berg%start_lon==0.5*(bergs%dem_tests_start_lon+bergs%dem_tests_end_lon)) then
+                F_y = F_y - 1.5e5
+              endif
+            elseif (bergs%dem_beam_test==2) then
+              !3.2 (Wang,2020): Cantilever beam test
+              !add vertical load to end of the cantilever beam
+              if (berg%start_lon==bergs%dem_tests_end_lon) then
+                F_y = F_y - 1.5e10/3.
+              endif
+            elseif (bergs%dem_beam_test==3) then
+              !Angular velocity test (starting element has constant rot=-pi/2)
+              if (berg%start_lon==bergs%dem_tests_start_lon) then
+                T=0.0; T_d=0.0
+              endif
+            elseif (bergs%dem_beam_test==4) then
+              if (berg%start_lon==bergs%dem_tests_start_lon) then
+                F_y=0.0; Fd_y=0.0
+              endif
+            endif
+          endif
+          IA_x=F_x/M; IA_y=F_y/M; IAd_x=Fd_x/M; IAd_y=Fd_y/M
+        else
+          IA_x=0.0; IA_y=0.0 !explicit elastic force
+          P_ia_11=0.0; P_ia_12=0.0; P_ia_21=0.0; P_ia_22=0.0
+          call calculate_force(bergs, berg, other_berg, IA_x, IA_y, uvel0, vvel0, uvel0, vvel0,  &
+            P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded=.true.)
+          !damping force
+          IAd_x=P_ia_11*(other_berg%uvel_old-berg%uvel_old)+P_ia_12*(other_berg%vvel_old-berg%vvel_old)
+          IAd_y=P_ia_12*(other_berg%uvel_old-berg%uvel_old)+P_ia_22*(other_berg%vvel_old-berg%vvel_old)
+        endif
+
+        if (bergs%fracture_criterion=='energy') then
+          oneoverkn = 1./bergs%spring_coef
+          oneoverkn=oneoverkn*(M/min(M,other_berg%mass))
+          current_bond%spring_pe = 0.5*((M*IA_x)**2+(M*IA_y)**2)*oneoverkn
+        endif
+
+        if (monitor_energy) then
+          !work
+          current_bond%Ee=current_bond%Ee - 0.25*dt*(&
+            (u_star + uveln)*M*IA_x + &
+            (v_star + vveln)*M*IA_y)
+
+
+          if (new_mts) then
+            !V{i+0.5} to V{i+1}
+            current_bond%Ed=current_bond%Ed- 0.25*dt*(&
+              (u_star + uveln)*M*IAd_x + &
+              (v_star + vveln)*M*IAd_y)
+          else
+            current_bond%Ed=current_bond%Ed - 0.5*dt*(&
+              (u_star + uveln)*M*IAd_x + &
+              (v_star + vveln)*M*IAd_y)
+          endif
+
+          current_bond%axn_fast=IA_x;  current_bond%ayn_fast=IA_y
+
+          !here, bxn_fast and byn_fast are explicit damping accel (not implicit!)
+          current_bond%bxn_fast=IAd_x; current_bond%byn_fast=IAd_y
+        endif
+
+        current_bond=>current_bond%next_bond
+      enddo
+    endif
+  endif
+
+  ! Limit speed of bergs based on a CFL criteria
+  if ((bergs%speed_limit>0.) .or. (bergs%speed_limit .eq.-1.)) then
+    speed=sqrt(uveln*uveln+vveln*vveln) ! Speed of berg
+    if (speed>0.) then
+      loc_dx=min(0.5*(grd%dx(i,j)+grd%dx(i,j-1)),0.5*(grd%dy(i,j)+grd%dy(i-1,j))) ! min(dx,dy)
+      !new_speed=min(loc_dx/dt*bergs%speed_limit,speed) ! Restrict speed to dx/dt x factor
+      new_speed=loc_dx/dt*bergs%speed_limit ! Speed limit as a factor of dx / dt
+      if (new_speed<speed) then
+        if (bergs%speed_limit>0.) then
+          uveln=uveln*(new_speed/speed) ! Scale velocity to reduce speed
+          vveln=vveln*(new_speed/speed) ! without changing the direction
+          bergs%nspeeding_tickets=bergs%nspeeding_tickets+1
+        else
+          call error_mesg('KID, Speeding icebergs', 'Faster than the CFL!', WARNING)
+          write(stderrunit,*) 'KID, Speeding berg1! =',mpp_pe(), berg%id
+          write(stderrunit,*) 'KID, Speeding berg2, speed =',speed, loc_dx/dt
+          write(stderrunit,*) 'KID, Speeding berg3, lat, lon =',lat,xi,yj
+        endif
+      endif
+    endif
+  endif
+
+  !Used for testing the ocean response to fixed iceberg motion.
+  if (bergs%override_iceberg_velocities) then
+    ax  = 0.0;  ay  = 0.0
+    axn = 0.0;  ayn = 0.0
+    bxn = 0.0;  byn = 0.0
+  endif
+
+end subroutine accel_explicit_inner_mts
+
 !> Calculates the instantaneous acceleration of an iceberg
 subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, rx, ry, ax, ay, axn, ayn, bxn, byn, debug_flag)
   ! Arguments
@@ -1477,7 +1952,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
   endif
 
   ! Wave radiation (Stern et al 2017, Eqs A4-A5)
-  uwave=ua-uo; vwave=va-vo  ! Use wind speed rel. to ocean for wave model (aja)?
+  uwave=ua-uo; vwave=va-vo  ! Use wind speed rel. to ocean for wave model (aja)
   wmod=uwave*uwave+vwave*vwave ! The wave amplitude and length depend on the wind speed relative to the ocean current
                                ! actually wmod is wmod**2 here.
   ampl=0.5*0.02025*wmod ! This is "a", the wave amplitude
@@ -1719,7 +2194,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
       dumpit=.true.
       write(stderrunit,'("pe=",i3,x,a)') mpp_pe(),'Dump triggered by excessive velocity'
     else
-      write(stderrunit,'("pe=",i3,x,a)') mpp_pe(),'Excessive velocity detected'
+      !write(stderrunit,'("pe=",i3,x,a)') mpp_pe(),'Excessive velocity detected'
     endif
   endif
   if (abs(ax)>accel_lim.or.abs(ay)>accel_lim) then
@@ -4126,22 +4601,10 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   call mpp_clock_begin(bergs%clock_mom)
 
   if (.not.bergs%Static_icebergs) then
-    call reset_bond_rotation(bergs)
-    if (bergs%mts) then
+    if (.not. bergs%dem) call reset_bond_rotation(bergs)
 
-      !Call the MTS subroutine for iceberg evolution:
-      !There are two versions of the MTS subroutine: evolve_icebergs_mts and evolve_icebergs_mts2. Each version
-      !has an experimental option to iterate each short/long step many times to better conserve momentum during
-      !collisions, which may or may not be needed to get consistent fracture behavior. Evolve_icebergs_mts allows
-      !these iterations to be specified with parameters imp_loop_iters_short and imp_loop_iters_long.
-      !Evolve_icebergs_mts2 iterates to a given convergence tolerance (bergs%convergence_tolerance)
-      !if bergs%force_convergence==.true.
-
-      if ((imp_loop_iters_long > 1 .or. imp_loop_iters_short > 1) .and. (.not. bergs%force_convergence)) then
-        call evolve_icebergs_mts(bergs)
-      else
-        call evolve_icebergs_mts2(bergs)
-      endif
+    if (bergs%mts) then
+      call evolve_icebergs_mts(bergs)
     else
       call evolve_icebergs(bergs) !The single time step (STS) scheme
     end if
@@ -4964,11 +5427,12 @@ subroutine calve_icebergs(bergs)
 
 end subroutine calve_icebergs
 
+
 !> Evolves icebergs forward by updating velocity and position with a multiple-time-step Velocity Verlet
-!! scheme. Experimental option: each short/long step can be iterated the number of times specified by
-!! imp_loop_iters_short and imp_loop_iters_long, respectively, which better enforces momentum
-!! conservation during collision...this iterative scheme may or may not be needed to yield consistent
-!! fracture behavior. Alternatively, use evolve_icebergs_mts2 to iterate to a given convergence tolerance.
+!! scheme. Experimental option: each short/long step can be iterated until a given convergence tolerance
+!! is met, which better enforces momentum conservation during collision...this iterative scheme may or may
+!! not be needed to yield consistent fracture behavior. The short steps can also be evaluated explicitly,
+!! which is the default for dem mode.
 subroutine evolve_icebergs_mts(bergs)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
@@ -4993,7 +5457,9 @@ subroutine evolve_icebergs_mts(bergs)
   real :: dx,dy,M,Fex,Fey,Fex_prev,Fey_prev,Fdx_prev,Fdy_prev,Fdx,Fdy,Fx_tot,Fy_tot,Fx_tot_prev,Fy_tot_prev
   logical :: save_bond_energy
   real :: Fex_i, Fey_i, Fec_x, Fec_y, Fdc_x, Fdc_y, ustar, vstar, uveln_star, vveln_star
-  integer :: imp_loop
+  integer :: ii,jj,maxii,minii,maxjj,minjj
+  real :: usum,usum1,usum2,normchange,denom
+  logical :: finished,last_iter
 
   ! Multiple Time Step Velocity Verlet:
   ! NOTE: To avoid the need for computationally expensive transfers between processors
@@ -5025,7 +5491,7 @@ subroutine evolve_icebergs_mts(bergs)
           do j=grd%jed,grd%jsd,-1
             write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lat(i,j),i=grd%isd,grd%ied)
           enddo
-          call print_berg(stderrunit, berg, 'evolve_iceberg_mts, berg is not in proper starting cell')
+          call print_berg(stderrunit, berg, 'evolve_icebergs_mts, berg is not in proper starting cell')
           write(stderrunit,'(a,i3,2(i4,3f8.2))') 'evolve_icebergs_mts: pe,lon/lat(i,j)=', mpp_pe(), &
             berg%ine,berg%lon,grd%lon(berg%ine-1,berg%jne-1),grd%lon(berg%ine,berg%jne), &
             berg%jne,berg%lat,grd%lat(berg%ine-1,berg%jne-1),grd%lat(berg%ine,berg%jne)
@@ -5042,18 +5508,26 @@ subroutine evolve_icebergs_mts(bergs)
   dt = bergs%dt
   dt_2=0.5*dt
   rx = 0.0; ry = 0.0 !not needed, because interp_gridded_fields_to_bergs was already called
+  ii = 0
   save_bond_energy=.false.
+  usum=0.0; usum1=0.0; usum2=0.0
+  finished=.false.
+
+  if (bergs%force_convergence) then
+    last_iter=.false.
+  else
+    last_iter=.true.
+  endif
 
-  !imp_loop_iters is a global variable specified in the nml that specifies how many iterations the implicit
-  !loop is run, where uvel_old and vvel_old continuously update each iteration so that the damping force is
-  !more accurate for each bond pair
+  do while (.not. finished)
+
+    ii=ii+1
 
-  do imp_loop = 1,imp_loop_iters_long
     do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
       berg=>bergs%list(grdi,grdj)%first
       do while (associated(berg)) ! loop over all bergs
         !only evolve non-static bergs that overlap, or are part of a conglom that overlaps, the computational domain:
-        if (berg%static_berg .lt. 0.5 .and. (berg%conglom_id.ne.0 .or. imp_loop_iters_long>1)) then
+        if (berg%static_berg .lt. 0.5 .and. (berg%conglom_id.ne.0 .or. bergs%force_convergence)) then
           latn = berg%lat ;   lonn = berg%lon
           uvel1=berg%uvel ;   vvel1=berg%vvel !V_n (previous cycle)
           axn  = 0.0      ;   ayn  = 0.0 !note these are redefined at the start of subroutine accel_mts
@@ -5064,15 +5538,18 @@ subroutine evolve_icebergs_mts(bergs)
           call accel_mts(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, &
             ax1, ay1, axn, ayn, bxn, byn, save_bond_energy,Fec_x, Fec_y, Fdc_x, Fdc_y)
 
-          if (monitor_energy .and. imp_loop==imp_loop_iters_long) &
+          if (monitor_energy .and. last_iter) &
             call mts_energy_part_1(bergs,berg,ax1,ay1,axn,ayn,bxn,byn,Fec_x,Fec_y,Fdc_x,Fdc_y)
 
           ! Saving all the iceberg variables
-          berg%axn=axn                ; berg%ayn=ayn
-          berg%bxn=bxn                ; berg%byn=byn
+          berg%axn=axn; berg%ayn=ayn
+          berg%bxn=bxn; berg%byn=byn
 
-          if (imp_loop_iters_long>1) then
-            berg%uvel_prev=berg%uvel+(dt*ax1); berg%vvel_prev=berg%vvel+(dt*ay1)
+          if (bergs%force_convergence) then
+            berg%uvel_prev=berg%uvel+(dt*ax1); berg%vvel_prev=berg%vvel+(dt*ay1) !the new velocity
+            if (ii==1) usum=usum+berg%uvel_old**2 + berg%vvel_old**2
+            usum1=usum1+berg%uvel_prev**2+berg%vvel_prev**2
+            usum2=usum2+(berg%uvel_prev-berg%uvel_old)**2+(berg%vvel_prev-berg%vvel_old)**2
           else
             berg%uvel=berg%uvel+(dt*ax1); berg%vvel=berg%vvel+(dt*ay1)
 
@@ -5085,387 +5562,13 @@ subroutine evolve_icebergs_mts(bergs)
       enddo ! loop over all bergs
     enddo; enddo
 
-    if (imp_loop_iters_long>1) then
+    !update uvel_old and vvel_old for damping interaction with other elements
+    if (bergs%force_convergence) then
       do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
         berg=>bergs%list(grdi,grdj)%first
         do while (associated(berg)) ! loop over all bergs
-          berg%uvel_old=berg%uvel_prev; berg%vvel_old=berg%vvel_prev
-          if (imp_loop==imp_loop_iters_long) then
-            berg%uvel=berg%uvel_prev; berg%vvel=berg%vvel_prev
-          endif
-          berg=>berg%next
-        enddo
-      enddo; enddo
-    endif
-  enddo
-
-  call update_bond_angles(bergs)
-  call update_and_break_bonds(bergs)
-
-  !PART 2: X_0 and V_0, before fast sub-steps
-  !X_0=X_n (no change)
-  !update V_0 on uvel_old and vvel_old
-  !update lat and lon with implicit slow force component
-  do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
-    berg=>bergs%list(grdi,grdj)%first
-    do while (associated(berg)) ! loop over all bergs
-      if (berg%static_berg .lt. 0.5 .and. berg%conglom_id.ne.0) then
-        berg%lat_prev = berg%lat; berg%lon_prev = berg%lon
-
-        if (new_mts) then
-          berg%uvel = berg%uvel + dt_2*(berg%axn+berg%bxn)
-          berg%vvel = berg%vvel + dt_2*(berg%ayn+berg%byn)
-        else
-          berg%uvel = berg%uvel + dt_2*berg%axn
-          berg%vvel = berg%vvel + dt_2*berg%ayn
-          berg%lat = berg%lat + 0.5*(dt**2)*berg%byn
-          berg%lon = berg%lon + 0.5*(dt**2)*berg%bxn
-        endif
-
-        berg%uvel_old=berg%uvel; berg%vvel_old=berg%vvel
-
-        if (imp_loop_iters_short>1) then
-          berg%axn=berg%axn_fast; berg%ayn=berg%ayn_fast
-          berg%bxn=berg%bxn_fast; berg%byn=berg%byn_fast
-        endif
-
-        !if (monitor energy): already did energy update in part I
-      endif
-
-      berg=>berg%next
-    enddo
-  enddo; enddo
-
-
-  ! PART 3: MTS fast sub-steps (bonded interactions only):
-  ! Position and velocity are updated by:
-  ! X2 = X1+dt*V1+((dt^2)/2)*a_k +((dt^2)/2)*b_k
-  ! V2 = V1+dt/2*a_k +dt/2*a_kp1 +dt*b_k+1
-
-  bergs%only_interactive_forces=.true. !so that external forcings are ignored in subroutine accel
-  bergs%mts_part=3 !so that only bonded interactions are considered in subroutine interactive_force
-  dt = bergs%mts_fast_dt
-  dt_2=0.5*dt
-
-  do k = 1,bergs%mts_sub_steps ! loop over sub-steps
-
-    do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied ! update positions
-      berg=>bergs%list(grdi,grdj)%first
-      do while (associated(berg)) ! loop over all bergs
-        if (berg%static_berg .lt. 0.5 .and. berg%conglom_id.ne.0) then
-
-          on_tangential_plane=.false.
-          if ((berg%lat>89.) .and. (grd%grid_is_latlon)) on_tangential_plane=.true.
-
-          lon1=berg%lon; lat1=berg%lat
-          if (on_tangential_plane) call rotpos_to_tang(lon1,lat1,x1,y1,berg%id)
-          !dxdl1=r180_pi/(Rearth*cos(lat1*pi_180))
-          !dydl=r180_pi/Rearth
-          call convert_from_meters_to_grid(lat1,grd%grid_is_latlon ,dxdl1,dydl)
-          uvel1=berg%uvel; vvel1=berg%vvel
-
-          ! Loading past accelerations
-          axn=berg%axn_fast; ayn=berg%ayn_fast
-          bxn=berg%bxn_fast; byn=berg%byn_fast
-
-          ! Velocities used to update the position
-          uvel2=uvel1+(dt_2*axn)+(dt_2*bxn)
-          vvel2=vvel1+(dt_2*ayn)+(dt_2*byn)
-
-          if (on_tangential_plane) call rotvec_to_tang(lon1,uvel2,vvel2,xdot2,ydot2)
-          u2=uvel2*dxdl1; v2=vvel2*dydl
-
-          ! Solving for new position
-          if (on_tangential_plane) then
-            xn=x1+(dt*xdot2) ; yn=y1+(dt*ydot2)
-            call rotpos_from_tang(xn,yn,lonn,latn)
-          else
-            lonn=lon1+(dt*u2) ; latn=lat1+(dt*v2)
-          endif
-
-          berg%lon=lonn      ;  berg%lat=latn
-          berg%lon_old=lonn  ;  berg%lat_old=latn
-        end if
-
-        berg=>berg%next
-      enddo !loop over all bergs
-    enddo;enddo !update positions
-
-    do imp_loop = 1,imp_loop_iters_short
-
-      if (monitor_energy .and. imp_loop==imp_loop_iters_short) then
-        save_bond_energy=.true.
-      else
-        save_bond_energy=.false.
-      endif
-    ! update velocities
-    do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
-      berg=>bergs%list(grdi,grdj)%first
-      do while (associated(berg)) ! loop over all bergs
-
-        if (berg%static_berg .lt. 0.5 .and. berg%conglom_id.ne.0) then
-
-          latn = berg%lat ;   lonn = berg%lon
-          axn  = berg%axn_fast ;   ayn  = berg%ayn_fast
-          bxn  = berg%bxn_fast ;   byn  = berg%byn_fast
-          uvel1=berg%uvel ;   vvel1=berg%vvel
-          i=berg%ine      ;   j=berg%jne
-          xi=berg%xi      ;   yj=berg%yj
-
-          if (new_mts) then
-            axn = axn+bxn; ayn=ayn+byn
-          endif
-
-          ! Turn the velocities into u_star, v_star.(uvel3 is v_star) - (possible issues with tangent plane?)
-          uvel3=uvel1+(dt_2*axn)                  !(Stern et al 2017, Eq B4)
-          vvel3=vvel1+(dt_2*ayn)
-
-          if (monitor_energy .and. imp_loop==imp_loop_iters_short) &
-            call mts_energy_part_3(bergs,berg,uvel3,vvel3,whichtime=1)
-
-          call accel_mts(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, &
-            ax1, ay1, axn, ayn, bxn, byn, save_bond_energy)
-
-
-          ! Solving for the new velocity (Stern et al 2017, Eqn B5)
-          on_tangential_plane=.false.
-          if ((berg%lat>89.) .and. (bergs%grd%grid_is_latlon)) on_tangential_plane=.true.
-          if (on_tangential_plane) then
-            call rotvec_to_tang(lonn,uvel3,vvel3,xdot3,ydot3)
-            call rotvec_to_tang(lonn,ax1,ay1,xddot1,yddot1)
-            xdotn=xdot3+(dt*xddot1); ydotn=ydot3+(dt*yddot1)
-            call rotvec_from_tang(lonn,xdotn,ydotn,uveln,vveln)
-          else
-            !uvel3, vvel3 become uveln and vveln after they are put into lat/lon co-ordinates
-            uveln=uvel3+(dt*ax1); vveln=vvel3+(dt*ay1)
-          endif
-
-          ! Saving all the iceberg variables.
-          berg%axn_fast=axn; berg%ayn_fast=ayn
-          berg%bxn_fast=bxn; berg%byn_fast=byn
-          berg%uvel=uveln  ; berg%vvel=vveln
-
-          if (monitor_energy .and. imp_loop==imp_loop_iters_short) &
-            call mts_energy_part_3(bergs,berg,uvel3,vvel3,whichtime=2)
-        endif
-        berg=>berg%next
-      enddo ! loop over all bergs
-    enddo; enddo ! update velocities
-
-
-    if (imp_loop_iters_short>1 .and. imp_loop.ne.imp_loop_iters_short) then
-      do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
-        berg=>bergs%list(grdi,grdj)%first
-        do while (associated(berg)) ! loop over all bergs
-          if (berg%static_berg .lt. 0.5 .and. berg%conglom_id.ne.0) then
-
-            berg%uvel_old=berg%uvel; berg%vvel_old=berg%vvel
-            if (new_mts) then
-              berg%uvel=berg%uvel-dt_2*(berg%axn_fast+berg%bxn_fast)-dt_2*(berg%axn+berg%bxn)
-              berg%vvel=berg%vvel-dt_2*(berg%ayn_fast+berg%byn_fast)-dt_2*(berg%ayn+berg%byn)
-            else
-              berg%uvel=berg%uvel-dt_2*(berg%axn_fast+2.0*berg%bxn_fast)-dt_2*berg%axn
-              berg%vvel=berg%vvel-dt_2*(berg%ayn_fast+2.0*berg%byn_fast)-dt_2*berg%ayn
-            endif
-            berg%axn_fast=berg%axn; berg%ayn_fast=berg%ayn
-            berg%bxn_fast=berg%bxn; berg%byn_fast=berg%byn
-          endif
-          berg=>berg%next
-        enddo
-      enddo; enddo
-    endif
-
-  enddo
-
-    !update 'old' velocities used for interactions
-    do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
-      berg=>bergs%list(grdi,grdj)%first
-      do while (associated(berg)) ! loop over all bergs
-        if (berg%static_berg .lt. 0.5 .and. berg%conglom_id.ne.0) then
-          berg%uvel_old=berg%uvel; berg%vvel_old=berg%vvel
-
-          if (imp_loop_iters_short>1) then
-            berg%axn=berg%axn_fast; berg%ayn=berg%ayn_fast
-            berg%bxn=berg%bxn_fast; berg%byn=berg%byn_fast
-          endif
-        endif
-        berg=>berg%next
-      enddo ! loop over all bergs
-    enddo; enddo ! update 'old' velocities
-  enddo ! loop over sub-steps
-
-  !reset interactive_forces
-  bergs%only_interactive_forces=only_interactive_forces
-
-  !call update_and_break_bonds(bergs)
-
-  !update indices
-  do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
-    !no reason to worry about halo/conglomerate bergs here
-    berg=>bergs%list(grdi,grdj)%first
-    do while (associated(berg)) ! loop over all bergs
-      if (berg%static_berg .lt. 0.5 .and. berg%halo_berg<1) then
-        berg%uvel_old=berg%uvel; berg%vvel_old=berg%vvel
-        uveln=berg%uvel; vveln=berg%vvel
-        lonn=berg%lon  ; latn=berg%lat
-        i=berg%ine     ; j=berg%jne
-        xi=berg%xi     ; yj=berg%yj
-        ! finalize new iceberg positions and index
-        call adjust_index_and_ground(grd, lonn, latn, uveln, vveln, i, j, xi, yj, bounced, error_flag, berg%id)
-        berg%lon=lonn      ;  berg%lat=latn
-        berg%lon_old=lonn  ;  berg%lat_old=latn
-        berg%ine=i    ;  berg%jne=j
-        berg%xi=xi    ;  berg%yj=yj
-
-      endif
-      berg=>berg%next
-    enddo ! loop over all bergs
-  enddo; enddo ! update 'old' velocities
-
-end subroutine evolve_icebergs_mts
-
-
-!> Evolves icebergs forward by updating velocity and position with a multiple-time-step Velocity Verlet
-!! scheme. Experimental option: each short/long step can be iterated until a given convergence tolerance
-!! is met, which better enforces momentum conservation during collision...this iterative scheme may or may
-!! not be needed to yield consistent fracture behavior. Alternatively, use evolve_icebergs_mts to specify
-!! the number of iterations directly.
-subroutine evolve_icebergs_mts2(bergs)
-  ! Arguments
-  type(icebergs), pointer :: bergs !< Container for all types and memory
-  ! Local variables
-  type(icebergs_gridded), pointer :: grd
-  type(iceberg), pointer :: berg
-  real :: uveln, vveln, lonn, latn
-  real :: axn, ayn, bxn, byn
-  real :: xi, yj, rx, ry
-  integer :: i, j, k
-  integer :: grdi, grdj
-  integer :: stderrunit
-  logical :: only_interactive_forces
-  real :: lon1, lat1, dxdl1, dydl
-  real :: uvel1, vvel1, uvel2, vvel2, uvel3, vvel3
-  real :: xddot1, yddot1, xdot2, ydot2, xdot3, ydot3, xdotn, ydotn
-  real :: u2, v2, x1, y1, xn, yn
-  real :: ax1,ay1
-  real :: dt, dt_2
-  logical :: on_tangential_plane, error_flag, bounced
-  !energy stuff
-  real :: dx,dy,M,Fex,Fey,Fex_prev,Fey_prev,Fdx_prev,Fdy_prev,Fdx,Fdy,Fx_tot,Fy_tot,Fx_tot_prev,Fy_tot_prev
-  logical :: save_bond_energy
-  real :: Fex_i, Fey_i, Fec_x, Fec_y, Fdc_x, Fdc_y, ustar, vstar, uveln_star, vveln_star
-  integer :: ii,jj,maxii,minii,maxjj,minjj
-  real :: usum,usum1,usum2,normchange,denom
-  logical :: finished,last_iter
-
-  ! Multiple Time Step Velocity Verlet:
-  ! NOTE: To avoid the need for computationally expensive transfers between processors
-  ! at the end of each MTS sub-step, each PE updates a complete copy of any
-  ! conglomerate of bonded iceberg elements that spans over the computational domain of
-  ! several processors (see subroutine transfer_mts_bergs). Berg elements that lie within
-  ! the contact distance of the conglomerate are also included, as to account for collision
-  ! forces. The conglomerate iceberg elements with coords that lie outside of a PE's domain
-  ! are assigned to the nearest halo cell, but the coords are not changed.
-
-  ! Get the stderr unit number
-  stderrunit = stderr()
-  only_interactive_forces=bergs%only_interactive_forces
-
-  ! For convenience
-  grd=>bergs%grd
-
-  !Checking if everything is ok:
-  do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec ! just for computational domain
-    berg=>bergs%list(grdi,grdj)%first
-    do while (associated(berg)) ! loop over all bergs
-      if (berg%static_berg .lt. 0.5 .and. berg%halo_berg .lt. 0.5) then
-        if (.not. is_point_in_cell(bergs%grd, berg%lon, berg%lat, berg%ine, berg%jne) ) then
-          write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lon',(i,i=grd%isd,grd%ied)
-          do j=grd%jed,grd%jsd,-1
-            write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lon(i,j),i=grd%isd,grd%ied)
-          enddo
-          write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lat',(i,i=grd%isd,grd%ied)
-          do j=grd%jed,grd%jsd,-1
-            write(stderrunit,'(2i4,32f7.1)') mpp_pe(),j,(grd%lat(i,j),i=grd%isd,grd%ied)
-          enddo
-          call print_berg(stderrunit, berg, 'evolve_icebergs_mts, berg is not in proper starting cell')
-          write(stderrunit,'(a,i3,2(i4,3f8.2))') 'evolve_icebergs_mts: pe,lon/lat(i,j)=', mpp_pe(), &
-            berg%ine,berg%lon,grd%lon(berg%ine-1,berg%jne-1),grd%lon(berg%ine,berg%jne), &
-            berg%jne,berg%lat,grd%lat(berg%ine-1,berg%jne-1),grd%lat(berg%ine,berg%jne)
-          if (debug) call error_mesg('KID, evolve_icebergs_mts','berg is in wrong starting cell!',FATAL)
-        endif
-        if (debug) call check_position(grd, berg, 'evolve_icebergs_mts (top)')
-      end if
-      berg=>berg%next
-    enddo
-  enddo; enddo
-
-  ! PART 1: solve for V_n+1 (from the previous timestep)
-  bergs%mts_part=1
-  dt = bergs%dt
-  dt_2=0.5*dt
-  rx = 0.0; ry = 0.0 !not needed, because interp_gridded_fields_to_bergs was already called
-  ii = 0
-  save_bond_energy=.false.
-  usum=0.0; usum1=0.0; usum2=0.0
-  finished=.false.
-
-  if (bergs%force_convergence) then
-    last_iter=.false.
-  else
-    last_iter=.true.
-  endif
-
-  do while (.not. finished)
-
-    ii=ii+1
-
-    do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
-      berg=>bergs%list(grdi,grdj)%first
-      do while (associated(berg)) ! loop over all bergs
-        !only evolve non-static bergs that overlap, or are part of a conglom that overlaps, the computational domain:
-        if (berg%static_berg .lt. 0.5 .and. (berg%conglom_id.ne.0 .or. bergs%force_convergence)) then
-          latn = berg%lat ;   lonn = berg%lon
-          uvel1=berg%uvel ;   vvel1=berg%vvel !V_n (previous cycle)
-          axn  = 0.0      ;   ayn  = 0.0 !note these are redefined at the start of subroutine accel_mts
-          bxn  = 0.0      ;   byn  = 0.0
-          i=berg%ine      ;   j=berg%jne
-          xi=berg%xi      ;   yj=berg%yj
-
-          call accel_mts(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, &
-            ax1, ay1, axn, ayn, bxn, byn, save_bond_energy,Fec_x, Fec_y, Fdc_x, Fdc_y)
-
-          if (monitor_energy .and. last_iter) &
-            call mts_energy_part_1(bergs,berg,ax1,ay1,axn,ayn,bxn,byn,Fec_x,Fec_y,Fdc_x,Fdc_y)
-
-          ! Saving all the iceberg variables
-          berg%axn=axn; berg%ayn=ayn
-          berg%bxn=bxn; berg%byn=byn
-
-          if (bergs%force_convergence) then
-            berg%uvel_prev=berg%uvel+(dt*ax1); berg%vvel_prev=berg%vvel+(dt*ay1) !the new velocity
-            if (ii==1) usum=usum+berg%uvel_old**2 + berg%vvel_old**2
-            usum1=usum1+berg%uvel_prev**2+berg%vvel_prev**2
-            usum2=usum2+(berg%uvel_prev-berg%uvel_old)**2+(berg%vvel_prev-berg%vvel_old)**2
-          else
-            berg%uvel=berg%uvel+(dt*ax1); berg%vvel=berg%vvel+(dt*ay1)
-
-            !The final velocity from the previous cycle, which can be used
-            !during post-processing to calculate kinetic energy and momentum
-            berg%uvel_prev=berg%uvel    ; berg%vvel_prev=berg%vvel
-          endif
-        endif
-        berg=>berg%next
-      enddo ! loop over all bergs
-    enddo; enddo
-
-    !update uvel_old and vvel_old for damping interaction with other elements
-    if (bergs%force_convergence) then
-      do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
-        berg=>bergs%list(grdi,grdj)%first
-        do while (associated(berg)) ! loop over all bergs
-          if (berg%static_berg .lt. 0.5) then
-            berg%uvel_old=berg%uvel_prev; berg%vvel_old=berg%vvel_prev
+          if (berg%static_berg .lt. 0.5) then
+            berg%uvel_old=berg%uvel_prev; berg%vvel_old=berg%vvel_prev
           endif
           berg=>berg%next
         enddo
@@ -5494,8 +5597,12 @@ subroutine evolve_icebergs_mts2(bergs)
   enddo
 
 
-  call update_bond_angles(bergs)
-  call update_and_break_bonds(bergs)
+  if (.not. bergs%dem) then
+    call update_bond_angles(bergs)
+    call update_and_break_bonds(bergs)
+  else
+    call break_bonds_dem(bergs)
+  endif
 
   !PART 2: X_0 and V_0, before fast sub-steps
   !X_0=X_n (no change)
@@ -5579,6 +5686,20 @@ subroutine evolve_icebergs_mts2(bergs)
 
           berg%lon=lonn      ;  berg%lat=latn
           berg%lon_old=lonn  ;  berg%lat_old=latn
+
+          ! Set uvel_old to ustar for berg interactions?
+          ! if (new_mts) then
+          !   berg%uvel_old=berg%uvel+dt_2*(berg%axn_fast+berg%bxn_fast)
+          !   berg%vvel_old=berg%vvel+dt_2*(berg%ayn_fast+berg%bxn_fast)
+          ! else
+          !   berg%uvel_old=berg%uvel+dt_2*(berg%axn_fast)
+          !   berg%vvel_old=berg%vvel+dt_2*(berg%ayn_fast)
+          ! endif
+
+          if (bergs%dem) then
+            berg%ang_vel=berg%ang_vel+dt_2*berg%ang_accel
+            berg%rot=berg%rot+dt_2*berg%ang_vel
+          endif
         end if
         berg=>berg%next
       enddo !loop over all bergs
@@ -5588,7 +5709,7 @@ subroutine evolve_icebergs_mts2(bergs)
     usum=0.0; usum1=0.0; usum2=0.0
     finished=.false.
     save_bond_energy=.false.
-    if (bergs%force_convergence) then
+    if (bergs%force_convergence .and. (.not. bergs%explicit_inner_mts)) then
       last_iter=.false.
     else
       last_iter=.true.
@@ -5621,10 +5742,16 @@ subroutine evolve_icebergs_mts2(bergs)
           uvel3=uvel1+(dt_2*axn)                  !(Stern et al 2017, Eq B4)
           vvel3=vvel1+(dt_2*ayn)
 
-          if (monitor_energy .and. last_iter) call mts_energy_part_3(bergs,berg,uvel3,vvel3,whichtime=1)
+          if (monitor_energy .and. last_iter) call mts_energy_part_3(bergs,berg,uvel3,vvel3,wt=1)
 
-          call accel_mts(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, &
-            ax1, ay1, axn, ayn, bxn, byn, save_bond_energy)
+          if (bergs%explicit_inner_mts) then
+            call accel_explicit_inner_mts(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, &
+              ax1, ay1, axn, ayn, save_bond_energy)
+              bxn=0.; byn=0.
+          else
+            call accel_mts(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, &
+              ax1, ay1, axn, ayn, bxn, byn, save_bond_energy)
+          endif
 
 
           ! Solving for the new velocity (Stern et al 2017, Eqn B5)
@@ -5640,7 +5767,7 @@ subroutine evolve_icebergs_mts2(bergs)
             uveln=uvel3+(dt*ax1); vveln=vvel3+(dt*ay1)
           endif
 
-          if (bergs%force_convergence) then
+          if (bergs%force_convergence .and. (.not. bergs%explicit_inner_mts)) then
             if (jj==1) usum=usum+berg%uvel_old**2 + berg%vvel_old**2
             usum1=usum1 + uveln**2 + vveln**2
             usum2=usum2+(uveln-berg%uvel_old)**2+(vveln-berg%vvel_old)**2
@@ -5651,7 +5778,7 @@ subroutine evolve_icebergs_mts2(bergs)
           berg%bxn_fast=bxn; berg%byn_fast=byn
           berg%uvel=uveln  ; berg%vvel=vveln
 
-          if (monitor_energy .and. last_iter) call mts_energy_part_3(bergs,berg,uvel3,vvel3,whichtime=2)
+          if (monitor_energy .and. last_iter) call mts_energy_part_3(bergs,berg,uvel3,vvel3,wt=2)
 
         endif
         berg=>berg%next
@@ -5712,6 +5839,11 @@ subroutine evolve_icebergs_mts2(bergs)
         if (berg%static_berg .lt. 0.5 .and. berg%conglom_id.ne.0) then
           berg%uvel_old=berg%uvel; berg%vvel_old=berg%vvel
 
+          if (bergs%dem) then
+            berg%ang_vel=berg%ang_vel+dt_2*berg%ang_accel
+            berg%rot=berg%rot+dt_2*berg%ang_vel
+          endif
+
           if (bergs%force_convergence) then
             berg%axn=berg%axn_fast; berg%ayn=berg%ayn_fast
             berg%bxn=berg%bxn_fast; berg%byn=berg%byn_fast
@@ -5755,23 +5887,24 @@ subroutine evolve_icebergs_mts2(bergs)
   ! call mpp_max(maxii); call mpp_min(minii); call mpp_max(maxjj); call mpp_min(minjj)
   !if (maxii>2 .or. maxjj>2) print *,'outer max iters, inner max iters',maxii,maxjj
 
-end subroutine evolve_icebergs_mts2
+end subroutine evolve_icebergs_mts
+
 
 !> Energy calculations for MTS_part==1
 subroutine mts_energy_part_1(bergs, berg, ax1, ay1, axn, ayn, bxn, byn, Fec_x, Fec_y, Fdc_x, Fdc_y)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
   type(iceberg), pointer :: berg !< Berg for which to do calculations
-  real, intent(in) :: ax1 !< x acceleration at beginning of step [m s-2] ???
-  real, intent(in) :: ay1 !< y acceleration at beginning of step [m s-2] ???
-  real, intent(in) :: axn !< x acceleration at end of step [m s-2] ???
-  real, intent(in) :: ayn !< y acceleration at end of step [m s-2] ???
-  real, intent(in) :: bxn !< x implicit acceleration [m s-2] ???
-  real, intent(in) :: byn !< y implicit acceleration [m s-2] ???
-  real, intent(in) :: Fec_x !< x component of some force [units ?] ???
-  real, intent(in) :: Fec_y !< y component of some force [units ?] ???
-  real, intent(in) :: Fdc_x !< x component of some other force [units ?] ???
-  real, intent(in) :: Fdc_y !< y component of some other force [units ?] ???
+  real, intent(in) :: ax1 !< Zonal acceleration [m s-2]
+  real, intent(in) :: ay1 !< Meridional acceleration [m s-2]
+  real, intent(in) :: axn !< Explicit estimate of zonal acceleration [m s-2]
+  real, intent(in) :: ayn !< Explicit estimate of meridional acceleration [m s-2]
+  real, intent(in) :: bxn !< Implicit estimate of zonal acceleration [m s-2]
+  real, intent(in) :: byn !< Implicit estimate of meridional acceleration [m s-2]
+  real, intent(in) :: Fec_x !< Zonal elastic force from collision with other conglomerate [N]
+  real, intent(in) :: Fec_y !< Meridional elastic force from collision with other conglomerate [N]
+  real, intent(in) :: Fdc_x !< !< Zonal damping force from collision with other conglomerate [N]
+  real, intent(in) :: Fdc_y !< !< Meridional damping force from collision with other conglomerate [N]
   ! Local
   real :: dt, M, Fex, Fey, Fex_i, Fey_i
   real :: uveln, vveln, uveln_star, vveln_star, ustar, vstar
@@ -5832,17 +5965,6 @@ subroutine mts_energy_part_1(bergs, berg, ax1, ay1, axn, ayn, bxn, byn, Fec_x, F
     berg%Ee_contact=berg%Ee_contact_temp - 0.25*dt*(&
       (uveln + ustar)*Fec_x + (vveln + vstar)*Fec_y)
 
-    !old way:
-    !implicit:
-    !dEext=0.5*(V_{i+1} + V_{i})*F_{ext,i+1}*dt/2
-    ! berg%Eext=berg%Eext - 0.5*dt*(&
-    !   (uveln + berg%uvel_prev)*Fex_i + &
-    !   (vveln + berg%vvel_prev)*Fey_i)
-
-    ! berg%Ed_contact=berg%Ed_contact - 0.5*dt*(&
-    !   (uveln + berg%uvel_prev)*Fdc_x + &
-    !   (vveln + berg%vvel_prev)*Fdc_y)
-
     berg%Eext=berg%Eext - 0.5*dt*(&
       (uveln + ustar)*Fex_i + (vveln + vstar)*Fey_i)
 
@@ -5864,13 +5986,13 @@ subroutine mts_energy_part_1(bergs, berg, ax1, ay1, axn, ayn, bxn, byn, Fec_x, F
 end subroutine mts_energy_part_1
 
 !> Energy calculations for MTS_part==3
-subroutine mts_energy_part_3(bergs,berg,uvel3,vvel3,whichtime)
+subroutine mts_energy_part_3(bergs,berg,ustar,vstar,wt)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
   type(iceberg), pointer :: berg !< Berg to do calculations for
-  real,intent(in) :: uvel3 !< u-component of velocity [m s-1]  but why 3???
-  real,intent(in) :: vvel3 !< v-component of velocity [m s-1]  but why 3???
-  integer,intent(in) :: whichtime !< Time level ???
+  real,intent(in) :: ustar !< u-component of half-step velocity [m s-1]
+  real,intent(in) :: vstar !< v-component of half-step velocity [m s-1]
+  integer,intent(in) :: wt !< integrate from time i to i+1/2 (wt==1) or i+1/2 to i+1 (wt==2)
   ! Local
   real :: dt, M, Fex, Fey, Fdx, Fdy
 
@@ -5882,25 +6004,19 @@ subroutine mts_energy_part_3(bergs,berg,uvel3,vvel3,whichtime)
 
   !for i to i+1/2 or i+1/2 to i+1
   berg%Ee_temp=berg%Ee_temp - 0.25*dt*(&
-    (uvel3 + berg%uvel)*Fex + &
-    (vvel3 + berg%vvel)*Fey)
+    (ustar + berg%uvel)*Fex + &
+    (vstar + berg%vvel)*Fey)
 
   if (new_mts) then   !for i to i+1/2 or i+1/2 to i+1
     Fdx = M * berg%bxn_fast; Fdy = M * berg%byn_fast !damping forces
     berg%Ed_temp=berg%Ed_temp - 0.25*dt*(&
-      (uvel3 + berg%uvel)*Fdx + &
-      (vvel3 + berg%vvel)*Fdy)
-  elseif (whichtime==2) then !for i+1/2 to i+1
+      (ustar + berg%uvel)*Fdx + &
+      (vstar + berg%vvel)*Fdy)
+  elseif (wt==2) then !for i+1/2 to i+1
     Fdx = M * berg%bxn_fast; Fdy = M * berg%byn_fast !damping forces
     berg%Ed_temp=berg%Ed_temp - 0.5*dt*(&
-      (uvel3 + berg%uvel)*Fdx + &
-      (vvel3 + berg%vvel)*Fdy)
-
-    !old way
-    !V{i} to V{i+1}
-    ! berg%Ed_temp=berg%Ed_temp - 0.5*dt*(&
-    ! (berg%uvel + uveln)*Fdx + &
-    ! (berg%vvel + vveln)*Fdy)
+      (ustar + berg%uvel)*Fdx + &
+      (vstar + berg%vvel)*Fdy)
   endif
 end subroutine mts_energy_part_3
 
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 8462ea5..8efb7aa 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -20,7 +20,7 @@ module ice_bergs_framework
 
 integer :: buffer_width=35 ! This should be a parameter
 integer :: buffer_width_traj=37 ! This should be a parameter
-integer :: buffer_width_bond_traj=15 !This should be a parameter
+integer :: buffer_width_bond_traj=16 !This should be a parameter
 integer, parameter :: nclasses=10 ! Number of ice bergs classes
 
 !Local Vars
@@ -50,8 +50,7 @@ module ice_bergs_framework
 logical :: save_bond_traj=.false. !<Save trajectory files for bonds
 logical :: ewsame=.false. !<(F) set T if periodic and 2 PEs along the x direction (zonal) (i.e. E/W PEs are the same)
 logical :: monitor_energy=.false. !<monitors energies: elastic (spring+collision), external, dissipated, fracture
-integer :: imp_loop_iters_long=1 !if >1, the # of times the each long MTS step will iterate (alt to force_convergence)
-integer :: imp_loop_iters_short=1!if >1, the # of times the each short MTS step will iterate (alt to force_convergence)
+logical :: dem=.false. !< If T, run in DEM-mode with angular terms, variable stiffness, etc
 
 !Public params !Niki: write a subroutine to expose these
 public nclasses,buffer_width,buffer_width_traj,buffer_width_bond_traj
@@ -59,7 +58,7 @@ module ice_bergs_framework
 public ignore_ij_restart, use_slow_find,generate_test_icebergs,old_bug_rotated_weights,budget
 public orig_read, force_all_pes_traj
 public mts,new_mts,save_bond_traj,ewsame,monitor_energy
-public imp_loop_iters_long, imp_loop_iters_short
+public dem
 
 !Public types
 public icebergs_gridded, xyt, iceberg, icebergs, buffer, bond, bond_xyt
@@ -89,9 +88,10 @@ module ice_bergs_framework
 public split_id, id_from_2_ints, generate_id, cij_from_old_id, convert_old_id
 public update_latlon,set_conglom_ids,transfer_mts_bergs,quad_interp_from_agrid
 public pack_bond_traj_into_buffer2, unpack_bond_traj_from_buffer2, push_bond_posn, append_bond_posn
-public update_and_break_bonds,assign_n_bonds,reset_bond_rotation,update_bond_angles
+public update_and_break_bonds,break_bonds_dem,assign_n_bonds,reset_bond_rotation,update_bond_angles
 public fracture_testing_initialization, orig_bond_length
-public energy_tests_init
+public energy_tests_init,dem_tests_init
+public init_dem_params
 
 !> Container for gridded fields
 type :: icebergs_gridded
@@ -238,7 +238,7 @@ module ice_bergs_framework
   real :: halo_berg
   real :: static_berg
   real :: mass_of_bits !< Mass of bergy bits (kg)
-  real :: heat_density !< Heat density of berg (???)
+  real :: heat_density !< Heat density of berg (J/kg)
   real :: od !< Ocean depth
   integer :: year !< Year of this record (years)
   integer(kind=8) :: id = -1 !< Iceberg identifier
@@ -261,6 +261,7 @@ module ice_bergs_framework
   real :: rel_rotation
   real :: n_strain
   real :: n_strain_rate
+  real :: spring_pe
   type(bond_xyt), pointer :: next=>null() !< Next link in list
   real, allocatable :: Ee, Ed
 end type bond_xyt
@@ -302,7 +303,7 @@ module ice_bergs_framework
   real :: start_mass !< Mass berg had when created (kg)
   real :: mass_scaling !< Multiplier to scale mass when interpreting berg as a cloud of bergs (nondim)
   real :: mass_of_bits !< Mass of bergy bits following berg (kg)
-  real :: heat_density !< Heat density of berg (???)
+  real :: heat_density !< Heat density of berg (J/kg)
   real :: halo_berg  ! Equal to zero for bergs on computational domain, and =1 for bergs on the halo
   real :: static_berg  ! Equal to 1 for icebergs which are static (not allowed to move). Might be extended to grounding later.
   integer :: start_year !< Year that berg was created (years)
@@ -328,8 +329,22 @@ module ice_bergs_framework
   real :: od !< Ocean depth
   type(xyt), pointer :: trajectory=>null() !< Trajectory for this berg
   type(bond), pointer :: first_bond=>null() !< First element of bond list.
-  real, allocatable :: Ee, Ed, Eext, Ee_contact, Ed_contact, Efrac !<energy stuff
-  real, allocatable :: Ee_temp, Ed_temp, Eext_temp, Ee_contact_temp, Ed_contact_temp !<energy stuff
+  ! For optional energy monitoring
+  real, allocatable :: Ee !< Energy from bonds, elastic (J)
+  real, allocatable :: Ed !< Energy from bonds, damping (J)
+  real, allocatable :: Eext !< Energy from external forces (J)
+  real, allocatable :: Ee_contact !< Energy from contact, elastic (J)
+  real, allocatable :: Ed_contact !< Energy from contanct, damping (J)
+  real, allocatable :: Efrac !< Energy from breaking bonds (J)
+  real, allocatable :: Ee_temp !< Temporary storage: Energy from bonds, elastic (J)
+  real, allocatable :: Ed_temp !< Temporary storage: Energy from bonds, damping (J)
+  real, allocatable :: Eext_temp !< Temporary storage: Energy from external forces (J)
+  real, allocatable :: Ee_contact_temp !< Temporary storage: Energy from contact, elastic (J)
+  real, allocatable :: Ed_contact_temp !< Temporary storage: Energy from damping, elastic (J)
+  ! For DEM-mode
+  real, allocatable :: ang_vel !< Angular velocity
+  real, allocatable :: ang_accel !< Angular acceleration
+  real, allocatable :: rot !< Accumulated rotation
 end type iceberg
 
 !> A bond object connecting two bergs, used as a link in a linked list
@@ -348,8 +363,20 @@ module ice_bergs_framework
   real :: rel_rotation !<rotation relative to the mean of all bonds for a berg
   real :: n_strain !<normal strain (lengthwise stretching of the bond)
   real :: n_strain_rate !<for bergs%fracture_criterion=='strain_rate' only
+  real :: spring_pe
   type(bond_xyt), pointer :: bond_trajectory=>null()
-  real, allocatable :: Ee, Ed, axn_fast, ayn_fast, bxn_fast, byn_fast !<energy stuff
+  ! For optional energy monitoring
+  real, allocatable :: Ee !< Bond energy, elastic (J)
+  real, allocatable :: Ed !< Bond energy, damping (J)
+  real, allocatable :: axn_fast !< Zonal acceleration contribution to parent berg, explicit (m s^-2)
+  real, allocatable :: ayn_fast !< Meridional  acceleration contribution to parent berg, explicit (m s^-2)
+  real, allocatable :: bxn_fast !< Zonal acceleration contribution to parent berg, implicit (m s^-2)
+  real, allocatable :: byn_fast !< Meridional acceleration contribution to parent berg, implicit (m s^-2)
+  ! For DEM-mode
+  real, allocatable :: tangd1 !< Accumulated tangential displacement, x-component (m)
+  real, allocatable :: tangd2 !< Accumulated tangential displacement, y-component (m)
+  real, allocatable :: nstress !< Normal stress (Pa)
+  real, allocatable :: sstress !< Shear stress (Pa)
 end type bond
 
 ! A dynamic buffer, used for communication, that packs types into rectangular memory
@@ -386,7 +413,10 @@ module ice_bergs_framework
   real :: rho_bergs !< Density of icebergs [kg/m^3]
   real :: spring_coef !< Spring constant for bonded iceberg interactions
   real :: contact_spring_coef !<Spring coefficient for berg collisions -Alex
-  character(len=11) :: fracture_criterion !<'strain_rate','strain',or 'none'
+  character(len=11) :: fracture_criterion !<'energy','stress','strain_rate','strain',or 'none'logical ::
+  logical :: uniaxial_test=.false. !adds a tensile stress to the east-most berg element
+  real :: dem_tests_start_lon !starting lon of west-most berg element for uniaxial/dem tests
+  real :: dem_tests_end_lon !starting lon of east-most berg element for uniaxial/dem tests
   real :: cdrag_grounding=0.0 !< Drag coefficient against ocean bottom
   real :: h_to_init_grounding
   real :: frac_thres_n !normal fracture strain threshold
@@ -506,7 +536,14 @@ module ice_bergs_framework
   integer :: contact_cells_lon=1,contact_cells_lat=1 !how many cells to search to find contact pairs
   logical :: writeandstop=.false. !for debugging
   logical :: force_convergence !experimental MTS convergence scheme to better conserve momentum during collisions
-  real :: convergence_tolerance !tolerance for the MTS convergence scheme
+  logical :: explicit_inner_mts=.false. !If T, inner MTS iterations are treated explicitly
+  real :: convergence_tolerance=1.e-8 !tolerance for the MTS convergence scheme
+  ! DEM-mode parameters
+  logical :: dem=.false. !if T, run in DEM-mode with angular terms, variable stiffness, etc
+  real :: poisson=0.3 ! Poisson's ratio
+  real :: dem_spring_coef=0.
+  real :: dem_damping_coef=0.1
+  integer :: dem_beam_test=0 !1=Simply supported beam,2=cantilever beam,3=angular vel test
 end type icebergs
 
 !> Read original restarts. Needs to be module global so can be public to icebergs_mod.
@@ -586,7 +623,8 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: rho_bergs=850. ! Density of icebergs
 real :: spring_coef=1.e-8 ! Spring constant for iceberg interactions (this seems to be the highest stable value)
 real :: contact_spring_coef=0. !Spring coef for berg collisions (is set to spring_coef if not specified)
-character(len=11) :: fracture_criterion='none' !<'strain_rate','strain',or 'none'
+character(len=11) :: fracture_criterion='none' !<'energy','stress','strain_rate','strain',or 'none'
+logical :: uniaxial_test=.false. !adds a tensile stress to the east-most berg element
 real :: cdrag_grounding=0.0 ! Drag coefficient against ocean bottom
 real :: h_to_init_grounding=100.0
 real :: frac_thres_n=0.0 !normal fracture strain threshold
@@ -666,12 +704,19 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: remove_unused_bergs=.true. ! Remove unneeded bergs after PEs transfers
 real :: contact_distance=0.0 ! For unbonded berg interactions, collision is assumed at max(contact_distance,sum of the 2 bergs radii)
 logical :: force_convergence=.false. ! Experimental MTS convergence scheme that better preserves momentum during collisions
+logical :: explicit_inner_mts=.false. !If T, inner MTS iterations are treated explicitly
 real :: convergence_tolerance=1.e-8 ! Tolerance for the MTS force_convergence scheme
 real, dimension(nclasses) :: initial_mass=(/8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11/) ! Mass thresholds between iceberg classes (kg)
 real, dimension(nclasses) :: distribution=(/0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02/) ! Fraction of calving to apply to this class (non-dim) ,
 real, dimension(nclasses) :: mass_scaling=(/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) ! Ratio between effective and real iceberg mass (non-dim)
 real, dimension(nclasses) :: initial_thickness=(/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) ! Total thickness of newly calved bergs (m)
 integer(kind=8) :: debug_iceberg_with_id = -1 ! If positive, monitors a berg with this id
+! DEM-mode parameters
+!logical :: dem=.false. !if T, run in DEM-mode with angular terms, variable stiffness, etc
+real :: poisson=0.3 ! Poisson's ratio
+real :: dem_spring_coef=0.
+real :: dem_damping_coef=0.1
+integer :: dem_beam_test=0 !1=Simply supported beam,2=cantilever beam,3=angular vel test
 
 namelist /icebergs_nml/ verbose, budget, halo,  traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,Static_icebergs,  &
          distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,bond_coef, radial_damping_coef, tangental_damping_coef, only_interactive_forces, &
@@ -686,8 +731,9 @@ subroutine ice_bergs_framework_init(bergs, &
          const_gamma, Gamma_T_3EQ, ignore_traj, debug_iceberg_with_id,use_updated_rolling_scheme, tip_parameter, read_old_restarts, tau_calving, read_ocean_depth_from_file, melt_cutoff,&
          apply_thickness_cutoff_to_gridded_melt, apply_thickness_cutoff_to_bergs_melt, use_mixed_melting, internal_bergs_for_drag, coastal_drift, tidal_drift,&
          mts,new_mts,ewsame,monitor_energy,mts_sub_steps,contact_distance,length_for_manually_initialize_bonds,manually_initialize_bonds_from_radii,contact_spring_coef,&
-         fracture_criterion, debug_write,cdrag_grounding,h_to_init_grounding,frac_thres_scaling,frac_thres_n,frac_thres_t,save_bond_traj,remove_unused_bergs,&
-         imp_loop_iters_short,imp_loop_iters_long,force_convergence,convergence_tolerance
+         fracture_criterion, uniaxial_test, debug_write,cdrag_grounding,h_to_init_grounding,frac_thres_scaling,frac_thres_n,frac_thres_t,save_bond_traj,remove_unused_bergs,&
+         force_convergence,explicit_inner_mts,convergence_tolerance,&
+         dem,poisson,dem_spring_coef,dem_damping_coef,dem_beam_test
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -1062,7 +1108,7 @@ subroutine ice_bergs_framework_init(bergs, &
 if (.not. iceberg_bonds_on) then
    max_bonds=0
 else
-  buffer_width=buffer_width+(max_bonds*9) ! Increase buffer width to include bonds being passed between processors
+  buffer_width=buffer_width+(max_bonds*10) ! Increase buffer width to include bonds being passed between processors
 endif
 if (save_short_traj) buffer_width_traj=6 ! This is the length of the short buffer used for abrevated traj
 if (ignore_traj) buffer_width_traj=0 ! If this is true, then all traj files should be ignored
@@ -1073,6 +1119,10 @@ subroutine ice_bergs_framework_init(bergs, &
   buffer_width_bond_traj=buffer_width_bond_traj+2
 endif
 
+if (dem) then
+  buffer_width=buffer_width+3+(max_bonds*4)
+endif
+
 !must use verlet with mts - Alex
 if (mts) then
   buffer_width_traj=buffer_width_traj+4 !to accomodate n_bonds,fast-step accel terms, overall accel terms
@@ -1127,6 +1177,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%spring_coef=spring_coef
   bergs%contact_spring_coef=contact_spring_coef !Alex
   bergs%fracture_criterion=fracture_criterion
+  bergs%uniaxial_test=uniaxial_test
   bergs%cdrag_grounding=cdrag_grounding
   bergs%h_to_init_grounding=h_to_init_grounding
   bergs%frac_thres_n=frac_thres_n*frac_thres_scaling
@@ -1200,7 +1251,15 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%remove_unused_bergs = remove_unused_bergs
   bergs%contact_distance=contact_distance
   bergs%force_convergence=force_convergence
+  bergs%explicit_inner_mts=explicit_inner_mts
   bergs%convergence_tolerance=convergence_tolerance
+  ! DEM-mode parameters
+  bergs%dem=dem
+  if (bergs%dem) bergs%explicit_inner_mts=.true.
+  bergs%poisson=poisson
+  bergs%dem_spring_coef=dem_spring_coef
+  bergs%dem_damping_coef=dem_damping_coef
+  bergs%dem_beam_test=dem_beam_test
 
   if (bergs%contact_distance>0) then
     dx_dlon=1; dy_dlat=1
@@ -2072,7 +2131,7 @@ end subroutine mts_pack_in_dir
 recursive subroutine mts_mark_and_pack_halo_and_congloms(bergs, berg, dir, nbergs_to_send,pfix, rhc)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
-  type(iceberg), pointer :: berg !< Berg to pack ???
+  type(iceberg), pointer :: berg !< Berg to pack
   character(len=1) :: dir !< north,south,east,or west
   integer :: nbergs_to_send !< Number of bergs to send
   real :: pfix !<for periodicity
@@ -2181,7 +2240,8 @@ recursive subroutine mts_pack_contact_bergs(bergs, berg, dir, pfix, nbergs_to_se
     if (bergs%hexagonal_icebergs) then
       rdenom=1./(2.*sqrt(3.))
     else
-      rdenom=1./pi
+      !rdenom=1./pi
+      rdenom=1./4.
     endif
     if (nc_x.eq.1 .and. nc_y.eq.1) then
       radial_contact=.true. !contact based on berg radii can occur
@@ -2406,7 +2466,8 @@ subroutine mts_remove_unused_bergs(bergs)
     if (bergs%hexagonal_icebergs) then
       rdenom=1./(2.*sqrt(3.))
     else
-      rdenom=1./pi
+      !rdenom=1./pi
+      rdenom=1./4.
     endif
   else
     radial_contact=.false.
@@ -2986,6 +3047,11 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
     call push_buffer_value(buff%data(:,n), counter, berg%Eext_temp)
   endif
 
+  if (dem) then
+    call push_buffer_value(buff%data(:,n), counter, berg%ang_vel)
+    call push_buffer_value(buff%data(:,n), counter, berg%ang_accel)
+    call push_buffer_value(buff%data(:,n), counter, berg%rot)
+  endif
 
   if (max_bonds .gt. 0) then
     current_bond=>berg%first_bond
@@ -3001,6 +3067,7 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
         call push_buffer_value(buff%data(:,n), counter, current_bond%rel_rotation)
         call push_buffer_value(buff%data(:,n), counter, current_bond%n_strain)
         call push_buffer_value(buff%data(:,n), counter, current_bond%n_strain_rate)
+        call push_buffer_value(buff%data(:,n), counter, current_bond%spring_pe)
 
         if (monitor_energy) then
           call push_buffer_value(buff%data(:,n), counter, current_bond%Ee)
@@ -3011,6 +3078,13 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
           call push_buffer_value(buff%data(:,n), counter, current_bond%byn_fast)
         endif
 
+        if (dem) then
+          call push_buffer_value(buff%data(:,n), counter, current_bond%tangd1)
+          call push_buffer_value(buff%data(:,n), counter, current_bond%tangd2)
+          call push_buffer_value(buff%data(:,n), counter, current_bond%nstress)
+          call push_buffer_value(buff%data(:,n), counter, current_bond%sstress)
+        endif
+
         current_bond=>current_bond%next_bond
       else
         call push_buffer_value(buff%data(:,n), counter, 0)
@@ -3022,6 +3096,7 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
         call push_buffer_value(buff%data(:,n), counter, 0)
         call push_buffer_value(buff%data(:,n), counter, 0)
         call push_buffer_value(buff%data(:,n), counter, 0)
+        call push_buffer_value(buff%data(:,n), counter, 0)
 
         if (monitor_energy) then
           call push_buffer_value(buff%data(:,n), counter, 0)
@@ -3032,6 +3107,13 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
           call push_buffer_value(buff%data(:,n), counter, 0)
         endif
 
+        if (dem) then
+          call push_buffer_value(buff%data(:,n), counter, 0)
+          call push_buffer_value(buff%data(:,n), counter, 0)
+          call push_buffer_value(buff%data(:,n), counter, 0)
+          call push_buffer_value(buff%data(:,n), counter, 0)
+        endif
+
       endif
     enddo
   endif
@@ -3148,7 +3230,7 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
 integer :: stderrunit
 logical :: force_app,duplicate
 real :: temp_lon,temp_lat,length
-real :: rotation,rel_rotation,n_strain,n_strain_rate
+real :: rotation,rel_rotation,n_strain,n_strain_rate,spring_pe
 
   ! Get the stderr unit number
   stderrunit = stderr()
@@ -3164,6 +3246,10 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
       localberg%Ee_temp,localberg%Ed_temp,localberg%Eext_temp,localberg%Ee_contact_temp,localberg%Ed_contact_temp)
   endif
 
+  if (dem) then
+    allocate(localberg%ang_vel,localberg%ang_accel,localberg%rot)
+  endif
+
   counter = 0
   call pull_buffer_value(buff%data(:,n), counter, localberg%lon)
   call pull_buffer_value(buff%data(:,n), counter, localberg%lat)
@@ -3236,6 +3322,12 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
     call pull_buffer_value(buff%data(:,n), counter, localberg%Eext_temp)
   endif
 
+  if (dem) then
+    call pull_buffer_value(buff%data(:,n), counter, localberg%ang_vel)
+    call pull_buffer_value(buff%data(:,n), counter, localberg%ang_accel)
+    call pull_buffer_value(buff%data(:,n), counter, localberg%rot)
+  endif
+
   !These quantities no longer need to be passed between processors
   localberg%uvel_old=localberg%uvel
   localberg%vvel_old=localberg%vvel
@@ -3351,6 +3443,7 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
       call pull_buffer_value(buff%data(:,n), counter, rel_rotation)
       call pull_buffer_value(buff%data(:,n), counter, n_strain)
       call pull_buffer_value(buff%data(:,n), counter, n_strain_rate)
+      call pull_buffer_value(buff%data(:,n), counter, spring_pe)
 
       if (id_ij > 0) then
         call form_a_bond(this, id, other_berg_ine, other_berg_jne)
@@ -3360,6 +3453,7 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
         current_bond%rel_rotation=rel_rotation
         current_bond%n_strain=n_strain
         current_bond%n_strain_rate=n_strain_rate
+        current_bond%spring_pe=spring_pe
 
         if (monitor_energy) then
           call pull_buffer_value(buff%data(:,n), counter, current_bond%Ee)
@@ -3369,6 +3463,13 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
           call pull_buffer_value(buff%data(:,n), counter, current_bond%bxn_fast)
           call pull_buffer_value(buff%data(:,n), counter, current_bond%byn_fast)
         endif
+
+        if (dem) then
+          call pull_buffer_value(buff%data(:,n), counter, current_bond%tangd1)
+          call pull_buffer_value(buff%data(:,n), counter, current_bond%tangd2)
+          call pull_buffer_value(buff%data(:,n), counter, current_bond%sstress)
+          call pull_buffer_value(buff%data(:,n), counter, current_bond%nstress)
+        endif
       endif
     enddo
   endif
@@ -3595,6 +3696,7 @@ subroutine pack_bond_traj_into_buffer2(bond_traj, buff, n)
   call push_buffer_value(buff%data(:,n),counter,bond_traj%rel_rotation)
   call push_buffer_value(buff%data(:,n),counter,bond_traj%n_strain)
   call push_buffer_value(buff%data(:,n),counter,bond_traj%n_strain_rate)
+  call push_buffer_value(buff%data(:,n),counter,bond_traj%spring_pe)
 
   call split_id(bond_traj%id1, cnt1, ij1)
   call push_buffer_value(buff%data(:,n),counter,cnt1)
@@ -4107,6 +4209,9 @@ subroutine create_iceberg(berg, bergvals)
     allocate(berg%Ee,berg%Ed,berg%Eext,berg%Ee_contact,berg%Ed_contact,berg%Efrac,&
       berg%Ee_temp,berg%Ed_temp,berg%Eext_temp,berg%Ee_contact_temp,berg%Ed_contact_temp)
   endif
+  if (dem) then
+    allocate(berg%ang_vel,berg%ang_accel,berg%rot)
+  endif
   berg=bergvals
   berg%prev=>null()
   berg%next=>null()
@@ -4252,7 +4357,8 @@ subroutine orig_bond_length(bergs)
   enddo; enddo
 end subroutine orig_bond_length
 
-subroutine assign_n_bonds(bergs)
+!> Initialize fracture parameters for non-DEM style fracture
+subroutine fracture_testing_initialization(bergs)
 type(icebergs), pointer :: bergs !< Container for all types and memory
 type(iceberg), pointer :: this, other_berg
 type(bond) , pointer :: current_bond
@@ -4275,9 +4381,10 @@ subroutine assign_n_bonds(bergs)
       this=>this%next
     enddo
   enddo;enddo
-end subroutine assign_n_bonds
+end subroutine fracture_testing_initialization
 
-subroutine fracture_testing_initialization(bergs)
+!> Save number of bonds on element
+subroutine assign_n_bonds(bergs)
 type(icebergs), pointer :: bergs !< Container for all types and memory
 type(iceberg), pointer :: this, other_berg
 type(bond) , pointer :: current_bond
@@ -4297,7 +4404,73 @@ subroutine fracture_testing_initialization(bergs)
       this=>this%next
     enddo
   enddo;enddo
-end subroutine fracture_testing_initialization
+end subroutine assign_n_bonds
+
+!> Initialization for the DEM beam tests
+subroutine dem_tests_init(bergs)
+type(icebergs), pointer :: bergs !< Container for all types and memory
+type(iceberg), pointer :: this
+type(icebergs_gridded), pointer :: grd
+integer :: grdi, grdj
+real :: minlon,maxlon
+
+  maxlon=-huge(1.0); minlon=huge(1.0)
+  grd=>bergs%grd
+  do grdj=grd%jsd,grd%jed ; do grdi=grd%isd,grd%ied !loop over all cells
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this)) ! loop over all bergs in cell
+      this%start_lon=this%lon; this%start_lat=this%lat
+      if (this%lon>maxlon) maxlon=this%lon
+      if (this%lon<minlon) minlon=this%lon
+      this=>this%next
+    enddo
+  enddo;enddo
+
+  call mpp_max(maxlon); call mpp_min(minlon)
+  bergs%dem_tests_start_lon=minlon; bergs%dem_tests_end_lon=maxlon
+
+  print *,'pe,dem tests start lon,dem tests end lon',mpp_pe(),minlon,maxlon
+
+  if (bergs%dem_beam_test>=3) then
+    do grdj=grd%jsd,grd%jed ; do grdi=grd%isd,grd%ied !loop over all cells
+      this=>bergs%list(grdi,grdj)%first
+      do while (associated(this)) ! loop over all bergs in cell
+        if (bergs%dem_beam_test==3) then
+          if (this%start_lon==minlon) this%rot=-pi/2.
+        elseif (bergs%dem_beam_test==4) then
+          if (this%start_lon==maxlon) then
+            this%vvel=-40.0
+            this%vvel_old=-40.0
+            this%vvel_prev=-40.0
+          endif
+        endif
+        this=>this%next
+      enddo
+    enddo;enddo
+  endif
+
+end subroutine dem_tests_init
+
+!> Initialize berg element parameters for DEM-style simulations
+subroutine init_dem_params(bergs)
+type(icebergs), pointer :: bergs !< Container for all types and memory
+type(iceberg), pointer :: this
+type(icebergs_gridded), pointer :: grd
+integer :: grdi, grdj
+real :: maxlon
+
+  grd=>bergs%grd
+  do grdj=grd%jsd,grd%jed ; do grdi=grd%isd,grd%ied !loop over all cells
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this)) ! loop over all bergs in cell
+      this%ang_vel=0.
+      this%ang_accel=0.
+      this%rot=0.
+      this=>this%next
+    enddo
+  enddo;enddo
+end subroutine init_dem_params
+
 
 subroutine reset_bond_rotation(bergs)
 type(icebergs), pointer :: bergs !< Container for all types and memory
@@ -4371,7 +4544,6 @@ subroutine update_bond_angles(bergs)
 
               current_bond%length=sqrt(dxb*dxb+dyb*dyb) !update bond length
 
-              !The angle of rotation over the previous cycle (may need to be corrected by +/- 2*pi, see below)
               cross_b1b2=dxa*dyb-dya*dxb !([dxa dya 0] x [dxb dyb 0]) . [0 0 1]
               dot_b1b2 = dxa*dxb+dya*dyb ![dxa dya] . [dxa dxb]
               angle = atan2(cross_b1b2,dot_b1b2)
@@ -4398,8 +4570,8 @@ subroutine update_and_break_bonds(bergs)
   type(icebergs_gridded), pointer :: grd
   integer :: grdi, grdj
   type(bond) , pointer :: current_bond,other_bond,kick_the_bucket
-  real :: frac_thres_n,frac_thres_t
-  real :: inv_dt, rdenom, mean_denom, R1, R2, n_strain
+  real :: frac_thres_n,frac_thres_t,spring_coef
+  real :: inv_dt, rdenom, mean_denom, R1, R2, n_strain, BondEetot
 
   frac_thres_n=bergs%frac_thres_n; frac_thres_t=bergs%frac_thres_t
   if (frac_thres_n<=0.0 .and. frac_thres_t<=0.0) return !all fracture ignored
@@ -4408,7 +4580,7 @@ subroutine update_and_break_bonds(bergs)
 
   if (bergs%fracture_criterion=='strain_rate') then
     inv_dt=1.0/bergs%dt
-  elseif (bergs%fracture_criterion=='strain') then
+  elseif (bergs%fracture_criterion=='strain' .or. bergs%fracture_criterion=='stress') then
     inv_dt=1.0
   else
     return
@@ -4417,7 +4589,8 @@ subroutine update_and_break_bonds(bergs)
   if (bergs%hexagonal_icebergs) then
     rdenom=1./(2.*sqrt(3.))
   else
-    rdenom=1./pi
+    !rdenom=1./pi
+    rdenom=1./4.
   endif
 
   grd=>bergs%grd
@@ -4443,7 +4616,7 @@ subroutine update_and_break_bonds(bergs)
     do while (associated(this)) ! loop over all bergs
       if (this%conglom_id>0 .and. this%n_bonds>1) then
         R1=sqrt(this%length*this%width*rdenom)
-        mean_denom=1.0/(this%n_bonds-1)
+        if (this%n_bonds>1) mean_denom=1.0/(this%n_bonds-1)
 
         !2. Bond updates: normal strain/strain-rate, and relative rotation/rotation-rate
         current_bond=>this%first_bond
@@ -4453,40 +4626,53 @@ subroutine update_and_break_bonds(bergs)
             call error_mesg('KID,update_and_break_bonds','other_berg not associated!' ,FATAL)
           R2=sqrt(other_berg%length*other_berg%width*rdenom)
 
+          !the relative rotation (or rotation-rate) of the current bond relative to the mean
+          !rotation (or rotation-rate) of bonds on the parent berg, where the current bond is
+          !excluded from the mean.
+          if (this%n_bonds>1) then
+            current_bond%rel_rotation = current_bond%rotation-&
+              (this%accum_bond_rotation-current_bond%rotation)*mean_denom
+          else
+            current_bond%rel_rotation = 0.0
+          endif
+
           !normal strain or strain-rate: note original length is taken as the sum of the
           !radii (calculated according to area) of the two bergs the bond connects.
-          n_strain=current_bond%length/(R1+R2) - 1.0
           if (bergs%fracture_criterion=='strain_rate') then
+            n_strain=current_bond%length/(R1+R2) - 1.0
             current_bond%n_strain_rate=(n_strain-current_bond%n_strain)*inv_dt
             current_bond%n_strain=n_strain
             n_strain=current_bond%n_strain_rate
-          else
+          elseif (bergs%fracture_criterion=='strain') then
+            n_strain=current_bond%length/(R1+R2) - 1.0
             current_bond%n_strain=n_strain
+          elseif (bergs%fracture_criterion=='stress') then
+            n_strain=(current_bond%length-(R1+R2))*min(this%mass,other_berg%mass)*&
+              (bergs%spring_coef)/(R1+R2)
+            current_bond%rel_rotation = current_bond%rel_rotation*R1*min(this%mass,other_berg%mass)*&
+              bergs%spring_coef/(R1+R2)
+            current_bond%n_strain=n_strain
+          elseif (bergs%fracture_criterion=='energy') then
+            current_bond%n_strain=current_bond%spring_pe
           endif
 
-          !the relative rotation (or rotation-rate) of the current bond relative to the mean
-          !rotation (or rotation-rate) of bonds on the parent berg, where the current bond is
-          !excluded from the mean.
-          current_bond%rel_rotation = current_bond%rotation-&
-            (this%accum_bond_rotation-current_bond%rotation)*mean_denom
-
-          !mark bond and matching bond on other_berg as fractured
-          if (abs(current_bond%rel_rotation)>frac_thres_t.or.n_strain>frac_thres_n) then
-            current_bond%other_id=-1
+        !mark bond and matching bond on other_berg as fractured
+        if (abs(current_bond%rel_rotation)>frac_thres_t.or.n_strain>frac_thres_n) then
+          current_bond%other_id=-1
 
-            !mark matching bond on other_berg
-            other_bond=>other_berg%first_bond
-            do while (associated(other_bond)) ! loop over all bonds
-              if (other_bond%other_id.eq.this%id) other_bond%other_id=-1
-              other_bond=>other_bond%next_bond
-            enddo
-          endif
-          current_bond=>current_bond%next_bond
-        enddo
-      endif
-      this=>this%next
-    enddo
-  enddo; enddo
+          !mark matching bond on other_berg
+          other_bond=>other_berg%first_bond
+          do while (associated(other_bond)) ! loop over all bonds
+            if (other_bond%other_id.eq.this%id) other_bond%other_id=-1
+            other_bond=>other_bond%next_bond
+          enddo
+        endif
+        current_bond=>current_bond%next_bond
+      enddo
+    endif
+    this=>this%next
+  enddo
+enddo; enddo
 
   !4. final cleanup
   do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
@@ -4533,6 +4719,82 @@ subroutine update_and_break_bonds(bergs)
 
 end subroutine update_and_break_bonds
 
+!> DEM-style fracture
+subroutine break_bonds_dem(bergs)
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  type(iceberg), pointer :: other_berg, this
+  type(icebergs_gridded), pointer :: grd
+  integer :: grdi, grdj
+  type(bond) , pointer :: current_bond,other_bond,kick_the_bucket
+  real :: frac_thres_n,frac_thres_t
+
+  frac_thres_n=bergs%frac_thres_n; frac_thres_t=bergs%frac_thres_t
+
+  if (frac_thres_n<=0.0 .and. frac_thres_t<=0.0) return !all fracture ignored
+  if (frac_thres_n<=0.0) frac_thres_n=huge(1.0) !no fracture from normal strain
+  if (frac_thres_t<=0.0) frac_thres_t=huge(1.0) !no fracture from bond rotation
+  grd=>bergs%grd
+  do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this)) ! loop over all bergs
+      current_bond=>this%first_bond
+      do while (associated(current_bond)) ! loop over all bonds
+
+        if ((current_bond%other_id .ne. -1) .and. &
+          (current_bond%nstress>frac_thres_n .or. current_bond%sstress>frac_thres_t)) then
+          if (current_bond%nstress>frac_thres_n .and. current_bond%sstress>frac_thres_t) then
+            print *,'normal and shear stress break',this%id,current_bond%nstress,current_bond%sstress
+          elseif (current_bond%nstress>frac_thres_n) then
+            print *,'normal stress break',this%id,current_bond%nstress,current_bond%sstress
+          else
+            print *,'shear stress break',this%id,current_bond%nstress,current_bond%sstress
+          endif
+
+          current_bond%other_id=-1
+          other_berg=>current_bond%other_berg
+          if (associated(other_berg)) then
+            !mark matching bond on other_berg
+            other_bond=>other_berg%first_bond
+            do while (associated(other_bond)) ! loop over all bonds
+              if (other_bond%other_id.eq.this%id) other_bond%other_id=-1
+              other_bond=>other_bond%next_bond
+            enddo
+          endif
+        else
+          current_bond=>current_bond%next_bond
+        endif
+      enddo
+      this=>this%next
+    enddo
+  enddo;enddo
+
+
+  do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this)) ! loop over all bergs
+      current_bond=>this%first_bond
+      do while (associated(current_bond)) ! loop over all bonds
+        if (current_bond%other_id.eq.-1) then
+          this%n_bonds=this%n_bonds-1
+          if (monitor_energy) then
+            !convert the elastic spring energy associated with the bond to dissipated energy
+            !on the parent element.
+            this%Ee=this%Ee-current_bond%Ee
+            this%Ee_temp=this%Ee_temp-current_bond%Ee
+            this%Efrac=this%Efrac+current_bond%Ee
+          endif
+          kick_the_bucket=>current_bond
+          current_bond=>current_bond%next_bond
+          call delete_bond_from_list(this,kick_the_bucket)
+        else
+          current_bond=>current_bond%next_bond
+        endif
+      enddo
+      this=>this%next
+    enddo
+  enddo;enddo
+end subroutine break_bonds_dem
+
 !> Delete current_bond from the list of its parent berg
 subroutine delete_bond_from_list(berg,bond_to_delete)
 type(iceberg), intent(in), pointer :: berg !<parent berg to bond_to_delete
@@ -4570,6 +4832,14 @@ subroutine form_a_bond(berg, other_id, other_berg_ine, other_berg_jne, other_ber
     allocate(new_bond%Ee,new_bond%Ed,new_bond%axn_fast,new_bond%ayn_fast,new_bond%bxn_fast,new_bond%byn_fast)
     new_bond%Ee=0.; new_bond%Ed=0.; new_bond%axn_fast=0.; new_bond%ayn_fast=0.; new_bond%bxn_fast=0.; new_bond%byn_fast=0.
   endif
+
+  if (dem) then
+    allocate(new_bond%tangd1,new_bond%tangd2)
+    new_bond%tangd1=0.; new_bond%tangd2=0.
+    allocate(new_bond%nstress,new_bond%sstress)
+    new_bond%nstress=0.; new_bond%sstress=0.
+  endif
+
   new_bond%other_id=other_id
   if(present(other_berg)) then
     new_bond%other_berg=>other_berg
@@ -4679,10 +4949,10 @@ subroutine show_all_bonds(bergs)
 
 end subroutine show_all_bonds
 
-!> Sweep across all bergs filling in bond data ???
+!> Sweep across all bergs filling in bond data
 subroutine connect_all_bonds(bergs, ignore_unmatched)
 type(icebergs), pointer :: bergs !< Container for all types and memory
-logical,optional :: ignore_unmatched !< If true, skip error checking ???
+logical,optional :: ignore_unmatched !< If true, do not call error if the other berg in a bond is not found
 ! Local variables
 type(iceberg), pointer :: other_berg, berg
 type(icebergs_gridded), pointer :: grd
@@ -4814,7 +5084,7 @@ subroutine update_latlon(bergs)
   ! Local variables
   type(icebergs_gridded), pointer :: grd
   type(iceberg), pointer :: berg
-  real :: dlon, dlat,xi,yj,Lx
+  real :: dlon, dlat,dlon2,dlat2,xi,yj,Lx
   integer :: grdi,grdj
   logical :: lret
 
@@ -4833,12 +5103,17 @@ subroutine update_latlon(bergs)
             !already been corrected (if needed), as the scheme below would fail.
             dlon = berg%lon - berg%lon_old
             dlat = berg%lat - berg%lat_old
+            dlon2 = berg%lon - berg%lon_prev
+            dlat2 = berg%lat - berg%lat_prev
 
             berg%lon=bilin(grd, grd%lon, berg%ine, berg%jne, berg%xi, berg%yj)
             berg%lat=bilin(grd, grd%lat, berg%ine, berg%jne, berg%xi, berg%yj)
 
             berg%lon_old = berg%lon-dlon
             berg%lat_old = berg%lat-dlat
+            berg%lon_prev = berg%lon-dlon2
+            berg%lat_prev = berg%lat-dlat2
+
             !need to update local positon in cell from updated global coords, due to roundoff
             lret=pos_within_cell(grd, berg%lon, berg%lat, berg%ine, berg%jne, berg%xi, berg%yj)
           endif
@@ -5258,11 +5533,11 @@ subroutine move_trajectory(bergs, berg)
 
 end subroutine move_trajectory
 
-!> Disconnect a trajectory from a berg and add it to a list of trajectory segments
+!> Disconnect a trajectory from a bond and add it to a list of trajectory segments
 subroutine move_bond_trajectory(bergs, current_bond)
 ! Arguments
 type(icebergs), pointer :: bergs !< Container for all types and memory
-type(bond) , pointer :: current_bond !< Bond to break ???
+type(bond) , pointer :: current_bond !< Bond containing trajectory
 ! Local variables
 type(bond_xyt), pointer :: next, last
 type(bond_xyt) :: vals
@@ -5478,7 +5753,7 @@ logical function find_better_min(grd, x, y, w, oi, oj)
   type(icebergs_gridded), intent(in) :: grd !< Container for gridded fields
   real, intent(in) :: x !< x-coordinate being searched for
   real, intent(in) :: y !< y-coordinate being searched for
-  integer, intent(in) :: w !< Width into halo to search ???
+  integer, intent(in) :: w !< Number of surrounding cells to the N,S,E, and W to search
   integer, intent(inout) :: oi !< i-index of cell containing x,y
   integer, intent(inout) :: oj !< j-index of cell containing x,y
   ! Local variables
@@ -6488,7 +6763,7 @@ subroutine bergs_chksum(bergs, txt, ignore_halo_violation)
 ! Arguments
 type(icebergs), pointer :: bergs !< Container for all types and memory
 character(len=*), intent(in) :: txt !< Label to use in messages
-logical, optional :: ignore_halo_violation !< If true, skip error checking ???
+logical, optional :: ignore_halo_violation !< If true, skip error checking
 ! Local variables
 integer :: i, nbergs, ichk1, ichk2, ichk3, ichk4, ichk5, iberg
 real, allocatable :: fld(:,:), fld2(:,:)
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index bb5df40..c65d8f6 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -1689,7 +1689,7 @@ subroutine write_bond_trajectory(trajectory)
 type(bond_xyt), pointer :: trajectory !< An iceberg bond trajectory
 ! Local variables
 integer :: iret, ncid, i_dim, i
-integer :: lonid, latid, yearid, dayid, lenid,n1id, n2id
+integer :: lonid, latid, yearid, dayid, lenid,n1id, n2id, peid
 integer :: rotid,rrotid,nsid,nsrid
 integer :: idcnt1_id, idcnt2_id, idij1_id, idij2_id, eeid, edid
 character(len=34) :: filename
@@ -1806,6 +1806,7 @@ subroutine write_bond_trajectory(trajectory)
       !fracture params
       rotid = inq_varid(ncid, 'rotation');    rrotid = inq_varid(ncid, 'rel_rotation')
       nsid = inq_varid(ncid, 'n_strain');     nsrid = inq_varid(ncid, 'n_strain_rate')
+      peid = inq_varid(ncid, 'spring_pe');
 
       idcnt1_id = inq_varid(ncid, 'id_cnt1'); idij1_id = inq_varid(ncid, 'id_ij1')
       idcnt2_id = inq_varid(ncid, 'id_cnt2'); idij2_id = inq_varid(ncid, 'id_ij2')
@@ -1828,6 +1829,7 @@ subroutine write_bond_trajectory(trajectory)
       !fracture params
       rotid = def_var(ncid, 'rotation', NF_DOUBLE, i_dim); rrotid = def_var(ncid, 'rel_rotation', NF_DOUBLE, i_dim)
       nsid = def_var(ncid, 'n_strain', NF_DOUBLE, i_dim);  nsrid = def_var(ncid, 'n_strain_rate', NF_DOUBLE, i_dim)
+      peid = def_var(ncid, 'spring_pe', NF_DOUBLE, i_dim);
 
       idcnt1_id = def_var(ncid, 'id_cnt1', NF_INT, i_dim); idij1_id = def_var(ncid, 'id_ij1', NF_INT, i_dim)
       idcnt2_id = def_var(ncid, 'id_cnt2', NF_INT, i_dim); idij2_id = def_var(ncid, 'id_ij2', NF_INT, i_dim)
@@ -1852,6 +1854,7 @@ subroutine write_bond_trajectory(trajectory)
       call put_att(ncid, rrotid, 'long_name', 'relative rotation'); call put_att(ncid, rrotid, 'units', 'rad')
       call put_att(ncid, nsid, 'long_name', 'normal strain');       call put_att(ncid, nsid, 'units', 'non-dim')
       call put_att(ncid, nsrid, 'long_name', 'normal strain-rate'); call put_att(ncid, nsrid, 'units', '1/seconds')
+      call put_att(ncid, peid, 'long_name', 'spring potential energy'); call put_att(ncid, peid, 'units', 'J')
 
       call put_att(ncid, idcnt1_id, 'long_name', 'counter component of first connected iceberg id')
       call put_att(ncid, idcnt1_id, 'units', 'dimensionless')
@@ -1891,6 +1894,7 @@ subroutine write_bond_trajectory(trajectory)
       !fracture params
       call put_double(ncid,rotid,i,this%rotation);  call put_double(ncid,rrotid,i,this%rel_rotation)
       call put_double(ncid,nsid,i,this%n_strain);   call put_double(ncid,nsrid,i,this%n_strain_rate)
+      call put_double(ncid,peid,i,this%spring_pe)
 
       call split_id(this%id1, cnt, ij)
       call put_int(ncid, idcnt1_id, i, cnt);        call put_int(ncid, idij1_id, i, ij)
diff --git a/tests/.gitignore b/tests/.gitignore
index e40f6b9..b733a1e 100644
--- a/tests/.gitignore
+++ b/tests/.gitignore
@@ -6,3 +6,4 @@ core
 single_test/
 size_test_tab/
 steady_test/
+uniaxial_test/
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/hexagon_area.pyc b/tests/Iceberg_repository/Scripts_and_analysis/hexagon_area.pyc
index 1acba0d6d324254ce731ae420bb6ccd5abcc8df8..97776014762ca5b310f73cbd13d88dce6ef061a2 100644
GIT binary patch
delta 503
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delta 418
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diff --git a/tests/dem_cbeam_test/.gitignore b/tests/dem_cbeam_test/.gitignore
new file mode 100644
index 0000000..68bcbc9
--- /dev/null
+++ b/tests/dem_cbeam_test/.gitignore
@@ -0,0 +1 @@
+results/
\ No newline at end of file
diff --git a/tests/dem_cbeam_test/README b/tests/dem_cbeam_test/README
new file mode 100644
index 0000000..be1f91d
--- /dev/null
+++ b/tests/dem_cbeam_test/README
@@ -0,0 +1,2 @@
+This is the cantilever beam test from Section 3.2 of Wang 2020 "A scale-invariant bonded particle model for simulating large deformation and failure of continua"
+
diff --git a/tests/dem_cbeam_test/RUN b/tests/dem_cbeam_test/RUN
new file mode 100755
index 0000000..0ffc895
--- /dev/null
+++ b/tests/dem_cbeam_test/RUN
@@ -0,0 +1,5 @@
+rm iceberg_trajectories.nc
+rm iceberg_trajectories.nc.*
+rm bond_trajectories.nc
+rm bond_trajectories.nc.*
+srun -n1 ./../../build/bergs.x
diff --git a/tests/dem_cbeam_test/animate_trajectories.py b/tests/dem_cbeam_test/animate_trajectories.py
new file mode 100755
index 0000000..343e418
--- /dev/null
+++ b/tests/dem_cbeam_test/animate_trajectories.py
@@ -0,0 +1,179 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+import matplotlib.pyplot as plt
+from matplotlib.animation import FuncAnimation
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
+                    help=''' provide filename to plot''')
+    parser.add_argument('-s', type=int, default='100000',
+                    help='''plotted particle size''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+
+def main(args):
+
+    print('reading file')
+
+    filename=args.fname
+    psize=args.s
+    #filename = 'iceberg_trajectories.nc'
+    field = 'lon'
+    field2 = 'lat'
+
+    with nc.Dataset(filename) as file:
+        x = file.variables['lon'][:]/1.e3
+        y = file.variables['lat'][:]/1.e3
+        day = file.variables['day'][:]
+        length = file.variables['length'][:]
+        width = file.variables['width'][:]
+        hs = file.variables['thickness'][:]
+
+
+    radius = length*width*(1./(2*np.sqrt(3)))
+
+    #print('day',day)
+    crop=False
+    tc=1.25
+    if crop:
+        x=x[day<=tc]
+        y=y[day<=tc]
+        day=day[day<=tc]
+
+    ud = np.unique(day)
+    #print('ud',ud)
+    t = ud[0]
+
+    # frame info
+    num_frames = len(ud)
+    movie_len = 4.0 #seconds
+    frame_len = 1000.0*movie_len/num_frames
+
+    xshift=101
+    yshift=(151.e3+5000.0)/1.e3
+
+    xmin = 90-xshift
+    xmax = 260-xshift
+    ymin = 0-yshift
+    ymax = 170-yshift
+
+    x=x-xshift
+    y=y-yshift
+
+    anim_running = True
+
+    def animate(i):
+
+        x1 = x[day == ud[i]]
+        y1 = y[day == ud[i]]
+        # hstat = hs[day == ud[i]]
+        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
+        hstat= day[day == ud[i]]
+
+        ud_max=np.max(ud)
+
+        cstring=[]
+
+        for j in range(len(hstat)):
+            if (hstat[j]<ud_max):
+                cstring.append("r")
+            else:
+                cstring.append("b")
+
+        scat.set_offsets(data)
+        scat.set_color(cstring)
+        scat.set_edgecolor('k')
+        #scat2.set_offsets(data)
+
+        t = ud[i]
+        time_text.set_text('time = %.1f days' % t )
+
+        r1 = radius[day == ud[i]]
+
+        scat.set_sizes(r1/psize)
+        return scat,time_text #,scat2
+
+    def init():
+        scat.set_offsets([])
+        return scat,
+
+    def onClick(event):
+        global anim_running
+        if anim_running:
+            ani.event_source.stop()
+            anim_running = False
+        else:
+            ani.event_source.start()
+            anim_running = True
+
+    # Now we can do the plotting!
+    f = plt.figure(figsize=(5,5))
+    f.tight_layout()
+    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
+    #scat = ax1.scatter([],[],marker='o',facecolor='w',s=psize,edgecolor='red')
+    scat = ax1.scatter([],[],marker='o')#,facecolor='w',edgecolor='red')
+    #scat2 = ax1.scatter([],[],marker='.',color='k',s=5)
+    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
+
+    # Change major ticks to show every 20.
+    ax1.xaxis.set_major_locator(MultipleLocator(50))
+    ax1.yaxis.set_major_locator(MultipleLocator(50))
+
+    ax1.xaxis.set_minor_locator(MultipleLocator(10))
+    ax1.yaxis.set_minor_locator(MultipleLocator(10))
+
+    # Turn grid on for both major and minor ticks and style minor slightly
+    # differently.
+    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
+    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
+
+    ax1.set_xlabel('x (km)')
+    ax1.set_ylabel('displacement (km)')
+    ax1.set_title('Iceberg trajectory')
+
+
+    #analytical solution
+    thick=1
+    xa=np.linspace(0,150000,100)
+    P=-(1.5e10)#/3. #Newtons
+    l=29*5000 #total beam length (m) between center of start and end particles (x-dir)
+    h=3.*5000 #total beam height (m) between center of start and end particles (y-dir)
+    AI= thick*(h**3)/12. #second  moment of area
+    YM=1.e9 #young's modulus (Pa)
+    w= P*(xa**2.)*(3.*l-xa)/(6.*YM*AI) #deflection
+
+    xa=(xa)/1.e3
+    w=w/1.e3
+    ax1.plot(xa,w)
+
+    f.canvas.mpl_connect('button_press_event', onClick)
+    ani = FuncAnimation(
+        f,animate,init_func=init,frames=num_frames,
+        interval=frame_len,blit=True,repeat=False)
+
+    print('time',t)
+
+    plt.show()
+    #animation.save("iceberg_traj_animation.mp4")
+
+
+print('Script complete')
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
diff --git a/tests/dem_cbeam_test/animate_trajectories_1l.py b/tests/dem_cbeam_test/animate_trajectories_1l.py
new file mode 100755
index 0000000..501a507
--- /dev/null
+++ b/tests/dem_cbeam_test/animate_trajectories_1l.py
@@ -0,0 +1,187 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+import matplotlib.pyplot as plt
+from matplotlib.animation import FuncAnimation
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
+                    help=''' provide filename to plot''')
+    parser.add_argument('-s', type=int, default='100000',
+                    help='''plotted particle size''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+
+def main(args):
+
+    print('reading file')
+
+    filename=args.fname
+    psize=args.s
+    #filename = 'iceberg_trajectories.nc'
+    field = 'lon'
+    field2 = 'lat'
+
+    with nc.Dataset(filename) as file:
+        x = file.variables['lon'][:]/1.e3
+        y = file.variables['lat'][:]/1.e3
+        day = file.variables['day'][:]
+        length = file.variables['length'][:]
+        width = file.variables['width'][:]
+        hs = file.variables['thickness'][:]
+
+
+    radius = length*width*(1./(2*np.sqrt(3)))
+
+    #print('day',day)
+    crop=False
+    tc=1.25
+    if crop:
+        x=x[day<=tc]
+        y=y[day<=tc]
+        day=day[day<=tc]
+
+    ud = np.unique(day)
+    #print('ud',ud)
+    t = ud[0]
+
+    # frame info
+    num_frames = len(ud)
+    movie_len = 4.0 #seconds
+    frame_len = 1000.0*movie_len/num_frames
+
+    d=5000.0
+    r=d/2.
+    xshift=101
+    yshift=(151.e3+2*r)/1.e3
+
+    xmin = 90-xshift
+    xmax = 260-xshift
+    ymin = 0-yshift
+    ymax = 170-yshift
+
+    x=x-xshift
+    y=y-yshift
+
+    anim_running = True
+
+    def animate(i):
+
+        x1 = x[day == ud[i]]
+        y1 = y[day == ud[i]]
+        # hstat = hs[day == ud[i]]
+        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
+        hstat= day[day == ud[i]]
+
+        ud_max=np.max(ud)
+
+        cstring=[]
+        # for j in range(len(hstat)):
+        #     if (hstat[j]<=200):
+        #         cstring.append("r")
+        #     else:
+        #         cstring.append("b")
+
+        for j in range(len(hstat)):
+            if (hstat[j]<ud_max):
+                cstring.append("r")
+            else:
+                cstring.append("b")
+
+        scat.set_offsets(data)
+        scat.set_color(cstring)
+        scat.set_edgecolor('k')
+        #scat2.set_offsets(data)
+
+        t = ud[i]
+        time_text.set_text('time = %.1f days' % t )
+
+        r1 = radius[day == ud[i]]
+
+        scat.set_sizes(r1/psize)
+        return scat,time_text #,scat2
+
+    def init():
+        scat.set_offsets([])
+        return scat,
+
+    def onClick(event):
+        global anim_running
+        if anim_running:
+            ani.event_source.stop()
+            anim_running = False
+        else:
+            ani.event_source.start()
+            anim_running = True
+
+    # Now we can do the plotting!
+    f = plt.figure(figsize=(5,5))
+    f.tight_layout()
+    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
+    #scat = ax1.scatter([],[],marker='o',facecolor='w',s=psize,edgecolor='red')
+    scat = ax1.scatter([],[],marker='o')#,facecolor='w',edgecolor='red')
+    #scat2 = ax1.scatter([],[],marker='.',color='k',s=5)
+    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
+
+    # Change major ticks to show every 20.
+    ax1.xaxis.set_major_locator(MultipleLocator(50))
+    ax1.yaxis.set_major_locator(MultipleLocator(50))
+
+    ax1.xaxis.set_minor_locator(MultipleLocator(10))
+    ax1.yaxis.set_minor_locator(MultipleLocator(10))
+
+    # Turn grid on for both major and minor ticks and style minor slightly
+    # differently.
+    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
+    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
+
+    ax1.set_xlabel('x (km)')
+    ax1.set_ylabel('displacement (km)')
+    ax1.set_title('Iceberg trajectory')
+
+
+    #analytical solution
+    thick=4
+    xa=np.linspace(0,150000,100)
+    P=-(1.5e10)/3. #Newtons
+    l=29*d #total beam length (m) between center of start and end particles (x-dir)
+    h=d  #total beam height (m) between center of start and end particles (y-dir)
+    AI= thick*(h**3)/12. #second  moment of area
+    YM=1.e9 #young's modulus (Pa)
+    w= P*(xa**2.)*(3.*l-xa)/(6.*YM*AI) #deflection
+
+    xa=(xa)/1.e3
+    w=w/1.e3
+    ax1.plot(xa,w)
+
+    f.canvas.mpl_connect('button_press_event', onClick)
+    ani = FuncAnimation(
+        f,animate,init_func=init,frames=num_frames,
+        interval=frame_len,blit=True,repeat=False)
+
+
+    print('time',t)
+
+    plt.show()
+    #animation.save("iceberg_traj_animation.mp4")
+
+
+print('Script complete')
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
diff --git a/tests/dem_cbeam_test/diag_table b/tests/dem_cbeam_test/diag_table
new file mode 100644
index 0000000..c1c8819
--- /dev/null
+++ b/tests/dem_cbeam_test/diag_table
@@ -0,0 +1,3 @@
+"icebergs test"
+1 1 1 0 0 0
+
diff --git a/tests/dem_cbeam_test/input.nml b/tests/dem_cbeam_test/input.nml
new file mode 100644
index 0000000..50d2e0f
--- /dev/null
+++ b/tests/dem_cbeam_test/input.nml
@@ -0,0 +1,181 @@
+&icebergs_driver_nml
+  ni=20 !number of elements, x direction
+  nj=20 !number of elements, y direction
+  ibdt=100. !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=200 !total simulation hours
+  write_time_inc = 600 !increment at which time is written to screen
+  nmax=1200  !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.true.
+  collision_test=.false.
+  grounding_test=.false.
+  bump_depth=9999.0 !(m) depth of top of gaussian bump below sea level
+  gridres=15000
+/
+
+&icebergs_nml
+
+    !defaults given in parentheses:
+    dem_beam_test=2
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=0.7!1
+    rho_bergs=900. ! (850) iceberg density
+    dem_spring_coef=1.e9 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+
+    monitor_energy=.false. !(F)save total elastic (spring+collision),external,dissipated,&fracture energy
+    new_mts=.true. !(F) If T, implicit accel is added 50% at the current time step and 50% at the next time step
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=2000  !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=2000.0 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-8 !(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=3.16e6 !friction drag param
+    h_to_init_grounding=200.0 !300.0 !150.0 !300.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.false. !(T) remove unneeded bergs after PEs transfers
+
+
+    fracture_criterion='none' !('none') 'strain_rate','strain','stress',or 'none'
+    !here, try setting scaling 1.0 if force_convergence=.false., 0.5 if force_convergence=.true.
+    frac_thres_scaling = 1.0 !(1) scales frac_thres_n and frac_thres_t
+    frac_thres_n = 0. !1.e7  !normal fracture strain threshold
+    frac_thres_t = 0. !5.e7 !tangential fracture strain threshold
+
+    halo=3 !(4) halo width
+    Lx=300.e3 ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.false. ! (T) True=icebergs do no move
+
+    spring_coef=1.e-5
+    radial_damping_coef=0.0 !(1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.false. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0.0 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.false. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.false. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.true. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=24000 ! (24) Period between verbose messages
+    traj_sample_hrs=0.05 !(24) sampling period for trajectory storage
+    traj_write_hrs=0.05 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.!(F) Init bond b/w bergs if dist<1.1*radius
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/dem_cbeam_test/makeberg/README b/tests/dem_cbeam_test/makeberg/README
new file mode 100644
index 0000000..9a03aec
--- /dev/null
+++ b/tests/dem_cbeam_test/makeberg/README
@@ -0,0 +1,2 @@
+RUN makes a 30x3 element conglomerate berg. The leftmost column of elements are static. The rightmost column will be assigned an additional shear force during the model run. This is the cantilever beam test from Section 3.2 of Wang 2020 "A scale-invariant bonded particle model for simulating large deformation and failure of continua"
+
diff --git a/tests/dem_cbeam_test/makeberg/RUN b/tests/dem_cbeam_test/makeberg/RUN
new file mode 100755
index 0000000..9456794
--- /dev/null
+++ b/tests/dem_cbeam_test/makeberg/RUN
@@ -0,0 +1,3 @@
+rm ./output_files/Generic*
+./makeberg.py -t=1
+cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
diff --git a/tests/dem_cbeam_test/makeberg/RUN_1l b/tests/dem_cbeam_test/makeberg/RUN_1l
new file mode 100755
index 0000000..7a790b4
--- /dev/null
+++ b/tests/dem_cbeam_test/makeberg/RUN_1l
@@ -0,0 +1,3 @@
+rm ./output_files/Generic*
+./makeberg_1l.py -t=1
+cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
diff --git a/tests/dem_cbeam_test/makeberg/RUN_2p b/tests/dem_cbeam_test/makeberg/RUN_2p
new file mode 100755
index 0000000..72b7d99
--- /dev/null
+++ b/tests/dem_cbeam_test/makeberg/RUN_2p
@@ -0,0 +1,3 @@
+rm ./output_files/Generic*
+./makeberg_2p.py -t=1
+cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
diff --git a/tests/dem_cbeam_test/makeberg/makeberg.py b/tests/dem_cbeam_test/makeberg/makeberg.py
new file mode 100755
index 0000000..11ff0dc
--- /dev/null
+++ b/tests/dem_cbeam_test/makeberg/makeberg.py
@@ -0,0 +1,321 @@
+#!/usr/bin/env python
+import numpy as np
+import math
+from netCDF4 import Dataset
+from pylab import *
+#import pdb
+import netCDF4 as nc
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-t', type=int, default='1',
+                    help='''which test case''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
+
+	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
+	# To copy the global attributes of the netCDF file
+
+	#Input and output files
+	#Create Empty restart file. This is later read so that the attributes can be used.
+	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
+	create_empty_iceberg_restart_file(Empty_restart_filename)
+	#Empty_restart_filename='input_files/icebergs.res.nc'
+
+	#Read empty restart file
+	f=Dataset(Empty_restart_filename,'r') # r is for read only
+	#Write a new restart file
+	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
+
+	for attname in f.ncattrs():
+		    setattr(g,attname,getattr(f,attname))
+
+
+	# To copy the dimension of the netCDF file
+	for dimname,dim in f.dimensions.iteritems():
+		# if you want to make changes in the dimensions of the new file
+		# you should add your own conditions here before the creation of the dimension.
+		#g.createDimension(dimname,len(dim))
+		g.createDimension(dimname,Number_of_bergs)
+
+	# To copy the variables of the netCDF file
+
+	for varname,ncvar in f.variables.iteritems():
+		# if you want to make changes in the variables of the new file
+		# you should add your own conditions here before the creation of the variable.
+		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
+		#Proceed to copy the variable attributes
+		for attname in ncvar.ncattrs():
+			setattr(var,attname,getattr(ncvar,attname))
+		#Finally copy the variable data to the new created variable
+		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
+
+		if varname=='i':
+			var[:]=Number_of_bergs
+
+		if varname=='iceberg_num':
+			for j in range(Number_of_bergs):
+				#var[j]=j+1
+				var[j]=iceberg_num[j]
+
+		if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
+		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
+		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
+		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
+			var[:]=0
+
+                if varname=='uvel':
+			for j in range(Number_of_bergs):
+				var[j]=uvel[j]
+
+                if varname=='vvel':
+			for j in range(Number_of_bergs):
+				var[j]=vvel[j]
+
+		if varname=='mass_scaling':
+			for j in range(Number_of_bergs):
+				var[j]=mass_scaling[j]
+
+		if varname=='thickness':
+			for j in range(Number_of_bergs):
+				var[j]=thickness[j]
+
+		if varname=='mass':
+			for j in range(Number_of_bergs):
+				var[j]=mass[j]
+
+		if varname=='width'  or varname=='length':
+			for j in range(Number_of_bergs):
+				var[j]=width[j]
+
+		if varname=='lon':
+			for j in range(Number_of_bergs):
+				var[j]=lon[j]
+
+		if varname=='lat':
+			for j in range(Number_of_bergs):
+				var[j]=lat[j]
+
+		if varname=='static_berg':
+			for j in range(Number_of_bergs):
+				var[j]=static_berg[j]
+
+
+	f.close()
+	g.close()
+
+
+def create_empty_iceberg_restart_file(Empty_restart_filename):
+
+	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
+
+	i=f.createDimension('i', None)
+	lon=f.createVariable('i','i')
+
+	lon=f.createVariable('lon','d',('i'))
+	lon.long_name = "longitude" ;
+	lon.units = "degrees_E" ;
+	lon.checksum = "               0" ;
+
+	lat=f.createVariable('lat','d',('i'))
+	lat.long_name = "latitude" ;
+	lat.units = "degrees_N" ;
+	lat.checksum = "               0" ;
+
+	uvel=f.createVariable('uvel','d',('i'))
+	uvel.long_name = "zonal velocity" ;
+	uvel.units = "m/s" ;
+	uvel.checksum = "               0" ;
+
+	vvel=f.createVariable('vvel','d',('i'))
+	vvel.long_name = "meridional velocity" ;
+	vvel.units = "m/s" ;
+	vvel.checksum = "               0" ;
+
+	mass=f.createVariable('mass','d',('i'))
+	mass.long_name = "mass" ;
+	mass.units = "kg" ;
+	mass.checksum = "               0" ;
+
+	axn=f.createVariable('axn','d',('i'))
+	axn.long_name = "explicit zonal acceleration" ;
+	axn.units = "m/s^2" ;
+	axn.checksum = "               0" ;
+
+	ayn=f.createVariable('ayn','d',('i'))
+	ayn.long_name = "explicit meridional acceleration" ;
+	ayn.units = "m/s^2" ;
+	ayn.checksum = "               0" ;
+
+	bxn=f.createVariable('bxn','d',('i'))
+	bxn.long_name = "inplicit zonal acceleration" ;
+	bxn.units = "m/s^2" ;
+	bxn.checksum = "               0" ;
+
+	byn=f.createVariable('byn','d',('i'))
+	byn.long_name = "implicit meridional acceleration" ;
+	byn.units = "m/s^2" ;
+	byn.checksum = "               0" ;
+
+	ine=f.createVariable('ine','i',('i'))
+	ine.long_name = "i index" ;
+	ine.units = "none" ;
+	ine.packing = 0 ;
+	ine.checksum = "               0" ;
+
+	jne=f.createVariable('jne','i',('i'))
+	jne.long_name = "j index" ;
+	jne.units = "none" ;
+	jne.packing = 0 ;
+	jne.checksum = "               0" ;
+
+	thickness=f.createVariable('thickness','d',('i'))
+	thickness.long_name = "thickness" ;
+	thickness.units = "m" ;
+	thickness.checksum = "               0" ;
+
+	width=f.createVariable('width','d',('i'))
+	width.long_name = "width" ;
+	width.units = "m" ;
+	width.checksum = "               0" ;
+
+	length=f.createVariable('length','d',('i'))
+	length.long_name = "length" ;
+	length.units = "m" ;
+	length.checksum = "               0" ;
+
+	start_lon=f.createVariable('start_lon','d',('i'))
+	start_lon.long_name = "longitude of calving location" ;
+	start_lon.units = "degrees_E" ;
+	start_lon.checksum = "               0" ;
+
+	start_lat=f.createVariable('start_lat','d',('i'))
+	start_lat.long_name = "latitude of calving location" ;
+	start_lat.units = "degrees_N" ;
+	start_lat.checksum = "               0" ;
+
+	start_year=f.createVariable('start_year','i',('i'))
+	start_year.long_name = "calendar year of calving event" ;
+	start_year.units = "years" ;
+	start_year.packing = 0 ;
+	start_year.checksum = "               0" ;
+
+	iceberg_num=f.createVariable('iceberg_num','i',('i'))
+	iceberg_num.long_name = "identification of the iceberg" ;
+	iceberg_num.units = "dimensionless" ;
+	iceberg_num.packing = 0 ;
+	iceberg_num.checksum = "               0" ;
+
+	start_day=f.createVariable('start_day','d',('i'))
+	start_day.long_name = "year day of calving event" ;
+	start_day.units = "days" ;
+	start_day.checksum = "               0" ;
+
+	start_mass=f.createVariable('start_mass','d',('i'))
+	start_mass.long_name = "initial mass of calving berg" ;
+	start_mass.units = "kg" ;
+	start_mass.checksum = "               0" ;
+
+	mass_scaling=f.createVariable('mass_scaling','d',('i'))
+	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
+	mass_scaling.units = "none" ;
+	mass_scaling.checksum = "               0" ;
+
+	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
+	mass_of_bits.long_name = "mass of bergy bits" ;
+	mass_of_bits.units = "kg" ;
+	mass_of_bits.checksum = "               0" ;
+
+	heat_density=f.createVariable('heat_density','d',('i'))
+	heat_density.long_name = "heat density" ;
+	heat_density.units = "J/kg" ;
+	heat_density.checksum = "               0" ;
+
+	halo_berg=f.createVariable('halo_berg','d',('i'))
+	halo_berg.long_name = "halo_berg" ;
+	halo_berg.units = "dimensionless" ;
+	halo_berg.checksum = "               0" ;
+
+	static_berg=f.createVariable('static_berg','d',('i'))
+	static_berg.long_name = "static_berg" ;
+	static_berg.units = "dimensionless" ;
+	static_berg.checksum = "               0" ;
+
+	f.sync()
+	f.close()
+
+
+def main(args):
+
+    #SQUARE PACKING
+
+        test=args.t
+        grdres=20.e3
+        r=2500.0
+
+        #start coords
+        xs=101.e3
+        ys=151.e3
+
+        h=1. #thickness
+        rho_ice=900.0
+
+
+        if test==1:
+            #5 particles w/ large radius
+            nbergs=90
+            width=5000.0
+            length=5000.0
+
+        #radii for evenly distrib cases
+        #element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*r**2)
+        element_area=(2.*r)**2
+
+        berg_x=[]; berg_y=[]
+        berg_id=[]; berg_static=[]
+        berg_width=[]; berg_bonds=[]
+        berg_h=[]; berg_mass_scaling=[]
+        berg_mass=[]
+        berg_uvel=[]; berg_vvel=[]
+
+        x=xs
+        y=ys-2*r
+
+        berg_count=0.
+        while berg_count<nbergs:
+                berg_count=berg_count+1
+                if berg_count%30==1:
+                    x=xs
+                    y=y+2*r
+                    static=1
+                else:
+                    static=0
+                    x=x+2*r
+
+                berg_x.append(x)
+                berg_y.append(y)
+                berg_width.append(sqrt(element_area))
+                berg_h.append(h)
+                berg_mass_scaling.append(1)
+                berg_mass.append(h*rho_ice*element_area)
+                berg_static.append(static)
+                berg_uvel.append(0)
+                berg_vvel.append(0)
+                berg_id.append(berg_count)
+
+        print('Number of bergs',berg_count)
+
+        #Create iceberg restart file
+        Ice_geometry_source='Generic'
+        Create_iceberg_restart_file(nbergs,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)
+
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
diff --git a/tests/dem_cbeam_test/makeberg/makeberg_1l.py b/tests/dem_cbeam_test/makeberg/makeberg_1l.py
new file mode 100755
index 0000000..79a39f2
--- /dev/null
+++ b/tests/dem_cbeam_test/makeberg/makeberg_1l.py
@@ -0,0 +1,321 @@
+#!/usr/bin/env python
+import numpy as np
+import math
+from netCDF4 import Dataset
+from pylab import *
+#import pdb
+import netCDF4 as nc
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-t', type=int, default='1',
+                    help='''which test case''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
+
+	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
+	# To copy the global attributes of the netCDF file
+
+	#Input and output files
+	#Create Empty restart file. This is later read so that the attributes can be used.
+	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
+	create_empty_iceberg_restart_file(Empty_restart_filename)
+	#Empty_restart_filename='input_files/icebergs.res.nc'
+
+	#Read empty restart file
+	f=Dataset(Empty_restart_filename,'r') # r is for read only
+	#Write a new restart file
+	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
+
+	for attname in f.ncattrs():
+		    setattr(g,attname,getattr(f,attname))
+
+
+	# To copy the dimension of the netCDF file
+	for dimname,dim in f.dimensions.iteritems():
+		# if you want to make changes in the dimensions of the new file
+		# you should add your own conditions here before the creation of the dimension.
+		#g.createDimension(dimname,len(dim))
+		g.createDimension(dimname,Number_of_bergs)
+
+	# To copy the variables of the netCDF file
+
+	for varname,ncvar in f.variables.iteritems():
+		# if you want to make changes in the variables of the new file
+		# you should add your own conditions here before the creation of the variable.
+		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
+		#Proceed to copy the variable attributes
+		for attname in ncvar.ncattrs():
+			setattr(var,attname,getattr(ncvar,attname))
+		#Finally copy the variable data to the new created variable
+		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
+
+		if varname=='i':
+			var[:]=Number_of_bergs
+
+		if varname=='iceberg_num':
+			for j in range(Number_of_bergs):
+				#var[j]=j+1
+				var[j]=iceberg_num[j]
+
+		if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
+		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
+		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
+		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
+			var[:]=0
+
+                if varname=='uvel':
+			for j in range(Number_of_bergs):
+				var[j]=uvel[j]
+
+                if varname=='vvel':
+			for j in range(Number_of_bergs):
+				var[j]=vvel[j]
+
+		if varname=='mass_scaling':
+			for j in range(Number_of_bergs):
+				var[j]=mass_scaling[j]
+
+		if varname=='thickness':
+			for j in range(Number_of_bergs):
+				var[j]=thickness[j]
+
+		if varname=='mass':
+			for j in range(Number_of_bergs):
+				var[j]=mass[j]
+
+		if varname=='width'  or varname=='length':
+			for j in range(Number_of_bergs):
+				var[j]=width[j]
+
+		if varname=='lon':
+			for j in range(Number_of_bergs):
+				var[j]=lon[j]
+
+		if varname=='lat':
+			for j in range(Number_of_bergs):
+				var[j]=lat[j]
+
+		if varname=='static_berg':
+			for j in range(Number_of_bergs):
+				var[j]=static_berg[j]
+
+
+	f.close()
+	g.close()
+
+
+def create_empty_iceberg_restart_file(Empty_restart_filename):
+
+	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
+
+	i=f.createDimension('i', None)
+	lon=f.createVariable('i','i')
+
+	lon=f.createVariable('lon','d',('i'))
+	lon.long_name = "longitude" ;
+	lon.units = "degrees_E" ;
+	lon.checksum = "               0" ;
+
+	lat=f.createVariable('lat','d',('i'))
+	lat.long_name = "latitude" ;
+	lat.units = "degrees_N" ;
+	lat.checksum = "               0" ;
+
+	uvel=f.createVariable('uvel','d',('i'))
+	uvel.long_name = "zonal velocity" ;
+	uvel.units = "m/s" ;
+	uvel.checksum = "               0" ;
+
+	vvel=f.createVariable('vvel','d',('i'))
+	vvel.long_name = "meridional velocity" ;
+	vvel.units = "m/s" ;
+	vvel.checksum = "               0" ;
+
+	mass=f.createVariable('mass','d',('i'))
+	mass.long_name = "mass" ;
+	mass.units = "kg" ;
+	mass.checksum = "               0" ;
+
+	axn=f.createVariable('axn','d',('i'))
+	axn.long_name = "explicit zonal acceleration" ;
+	axn.units = "m/s^2" ;
+	axn.checksum = "               0" ;
+
+	ayn=f.createVariable('ayn','d',('i'))
+	ayn.long_name = "explicit meridional acceleration" ;
+	ayn.units = "m/s^2" ;
+	ayn.checksum = "               0" ;
+
+	bxn=f.createVariable('bxn','d',('i'))
+	bxn.long_name = "inplicit zonal acceleration" ;
+	bxn.units = "m/s^2" ;
+	bxn.checksum = "               0" ;
+
+	byn=f.createVariable('byn','d',('i'))
+	byn.long_name = "implicit meridional acceleration" ;
+	byn.units = "m/s^2" ;
+	byn.checksum = "               0" ;
+
+	ine=f.createVariable('ine','i',('i'))
+	ine.long_name = "i index" ;
+	ine.units = "none" ;
+	ine.packing = 0 ;
+	ine.checksum = "               0" ;
+
+	jne=f.createVariable('jne','i',('i'))
+	jne.long_name = "j index" ;
+	jne.units = "none" ;
+	jne.packing = 0 ;
+	jne.checksum = "               0" ;
+
+	thickness=f.createVariable('thickness','d',('i'))
+	thickness.long_name = "thickness" ;
+	thickness.units = "m" ;
+	thickness.checksum = "               0" ;
+
+	width=f.createVariable('width','d',('i'))
+	width.long_name = "width" ;
+	width.units = "m" ;
+	width.checksum = "               0" ;
+
+	length=f.createVariable('length','d',('i'))
+	length.long_name = "length" ;
+	length.units = "m" ;
+	length.checksum = "               0" ;
+
+	start_lon=f.createVariable('start_lon','d',('i'))
+	start_lon.long_name = "longitude of calving location" ;
+	start_lon.units = "degrees_E" ;
+	start_lon.checksum = "               0" ;
+
+	start_lat=f.createVariable('start_lat','d',('i'))
+	start_lat.long_name = "latitude of calving location" ;
+	start_lat.units = "degrees_N" ;
+	start_lat.checksum = "               0" ;
+
+	start_year=f.createVariable('start_year','i',('i'))
+	start_year.long_name = "calendar year of calving event" ;
+	start_year.units = "years" ;
+	start_year.packing = 0 ;
+	start_year.checksum = "               0" ;
+
+	iceberg_num=f.createVariable('iceberg_num','i',('i'))
+	iceberg_num.long_name = "identification of the iceberg" ;
+	iceberg_num.units = "dimensionless" ;
+	iceberg_num.packing = 0 ;
+	iceberg_num.checksum = "               0" ;
+
+	start_day=f.createVariable('start_day','d',('i'))
+	start_day.long_name = "year day of calving event" ;
+	start_day.units = "days" ;
+	start_day.checksum = "               0" ;
+
+	start_mass=f.createVariable('start_mass','d',('i'))
+	start_mass.long_name = "initial mass of calving berg" ;
+	start_mass.units = "kg" ;
+	start_mass.checksum = "               0" ;
+
+	mass_scaling=f.createVariable('mass_scaling','d',('i'))
+	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
+	mass_scaling.units = "none" ;
+	mass_scaling.checksum = "               0" ;
+
+	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
+	mass_of_bits.long_name = "mass of bergy bits" ;
+	mass_of_bits.units = "kg" ;
+	mass_of_bits.checksum = "               0" ;
+
+	heat_density=f.createVariable('heat_density','d',('i'))
+	heat_density.long_name = "heat density" ;
+	heat_density.units = "J/kg" ;
+	heat_density.checksum = "               0" ;
+
+	halo_berg=f.createVariable('halo_berg','d',('i'))
+	halo_berg.long_name = "halo_berg" ;
+	halo_berg.units = "dimensionless" ;
+	halo_berg.checksum = "               0" ;
+
+	static_berg=f.createVariable('static_berg','d',('i'))
+	static_berg.long_name = "static_berg" ;
+	static_berg.units = "dimensionless" ;
+	static_berg.checksum = "               0" ;
+
+	f.sync()
+	f.close()
+
+
+def main(args):
+
+    #SQUARE PACKING
+
+        test=args.t
+        grdres=20.e3
+        r=2500.0#/3.
+
+        #start coords
+        xs=101.e3
+        ys=151.e3
+
+        h=1. #thickness
+        rho_ice=900.0
+
+
+        if test==1:
+            #5 particles w/ large radius
+            nbergs=30#90
+            width=r*2.
+            length=r*2.
+
+        #radii for evenly distrib cases
+        #element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*r**2)
+        element_area=(2.*r)**2
+
+        berg_x=[]; berg_y=[]
+        berg_id=[]; berg_static=[]
+        berg_width=[]; berg_bonds=[]
+        berg_h=[]; berg_mass_scaling=[]
+        berg_mass=[]
+        berg_uvel=[]; berg_vvel=[]
+
+        x=xs
+        y=ys#-2*r
+
+        berg_count=0.
+        while berg_count<nbergs:
+                berg_count=berg_count+1
+                if berg_count==1:
+                    #x=xs
+                    y=y+2*r
+                    static=1
+                else:
+                    static=0
+                    x=x+2*r
+
+                berg_x.append(x)
+                berg_y.append(y)
+                berg_width.append(sqrt(element_area))
+                berg_h.append(h)
+                berg_mass_scaling.append(1)
+                berg_mass.append(h*rho_ice*element_area)
+                berg_static.append(static)
+                berg_uvel.append(0)
+                berg_vvel.append(0)
+                berg_id.append(berg_count)
+
+        print('Number of bergs',berg_count)
+
+        #Create iceberg restart file
+        Ice_geometry_source='Generic'
+        Create_iceberg_restart_file(nbergs,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)
+
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
diff --git a/tests/dem_cbeam_test/makeberg/makeberg_2p.py b/tests/dem_cbeam_test/makeberg/makeberg_2p.py
new file mode 100755
index 0000000..0947559
--- /dev/null
+++ b/tests/dem_cbeam_test/makeberg/makeberg_2p.py
@@ -0,0 +1,300 @@
+#!/usr/bin/env python
+import numpy as np
+import math
+from netCDF4 import Dataset
+from pylab import *
+#import pdb
+import netCDF4 as nc
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-t', type=int, default='1',
+                    help='''which test case''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
+
+	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
+	# To copy the global attributes of the netCDF file
+
+	#Input and output files
+	#Create Empty restart file. This is later read so that the attributes can be used.
+	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
+	create_empty_iceberg_restart_file(Empty_restart_filename)
+	#Empty_restart_filename='input_files/icebergs.res.nc'
+
+	#Read empty restart file
+	f=Dataset(Empty_restart_filename,'r') # r is for read only
+	#Write a new restart file
+	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
+
+	for attname in f.ncattrs():
+		    setattr(g,attname,getattr(f,attname))
+
+
+	# To copy the dimension of the netCDF file
+	for dimname,dim in f.dimensions.iteritems():
+		# if you want to make changes in the dimensions of the new file
+		# you should add your own conditions here before the creation of the dimension.
+		#g.createDimension(dimname,len(dim))
+		g.createDimension(dimname,Number_of_bergs)
+
+	# To copy the variables of the netCDF file
+
+	for varname,ncvar in f.variables.iteritems():
+		# if you want to make changes in the variables of the new file
+		# you should add your own conditions here before the creation of the variable.
+		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
+		#Proceed to copy the variable attributes
+		for attname in ncvar.ncattrs():
+			setattr(var,attname,getattr(ncvar,attname))
+		#Finally copy the variable data to the new created variable
+		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
+
+		if varname=='i':
+			var[:]=Number_of_bergs
+
+		if varname=='iceberg_num':
+			for j in range(Number_of_bergs):
+				#var[j]=j+1
+				var[j]=iceberg_num[j]
+
+		if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
+		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
+		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
+		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
+			var[:]=0
+
+                if varname=='uvel':
+			for j in range(Number_of_bergs):
+				var[j]=uvel[j]
+
+                if varname=='vvel':
+			for j in range(Number_of_bergs):
+				var[j]=vvel[j]
+
+		if varname=='mass_scaling':
+			for j in range(Number_of_bergs):
+				var[j]=mass_scaling[j]
+
+		if varname=='thickness':
+			for j in range(Number_of_bergs):
+				var[j]=thickness[j]
+
+		if varname=='mass':
+			for j in range(Number_of_bergs):
+				var[j]=mass[j]
+
+		if varname=='width'  or varname=='length':
+			for j in range(Number_of_bergs):
+				var[j]=width[j]
+
+		if varname=='lon':
+			for j in range(Number_of_bergs):
+				var[j]=lon[j]
+
+		if varname=='lat':
+			for j in range(Number_of_bergs):
+				var[j]=lat[j]
+
+		if varname=='static_berg':
+			for j in range(Number_of_bergs):
+				var[j]=static_berg[j]
+
+
+	f.close()
+	g.close()
+
+
+def create_empty_iceberg_restart_file(Empty_restart_filename):
+
+	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
+
+	i=f.createDimension('i', None)
+	lon=f.createVariable('i','i')
+
+	lon=f.createVariable('lon','d',('i'))
+	lon.long_name = "longitude" ;
+	lon.units = "degrees_E" ;
+	lon.checksum = "               0" ;
+
+	lat=f.createVariable('lat','d',('i'))
+	lat.long_name = "latitude" ;
+	lat.units = "degrees_N" ;
+	lat.checksum = "               0" ;
+
+	uvel=f.createVariable('uvel','d',('i'))
+	uvel.long_name = "zonal velocity" ;
+	uvel.units = "m/s" ;
+	uvel.checksum = "               0" ;
+
+	vvel=f.createVariable('vvel','d',('i'))
+	vvel.long_name = "meridional velocity" ;
+	vvel.units = "m/s" ;
+	vvel.checksum = "               0" ;
+
+	mass=f.createVariable('mass','d',('i'))
+	mass.long_name = "mass" ;
+	mass.units = "kg" ;
+	mass.checksum = "               0" ;
+
+	axn=f.createVariable('axn','d',('i'))
+	axn.long_name = "explicit zonal acceleration" ;
+	axn.units = "m/s^2" ;
+	axn.checksum = "               0" ;
+
+	ayn=f.createVariable('ayn','d',('i'))
+	ayn.long_name = "explicit meridional acceleration" ;
+	ayn.units = "m/s^2" ;
+	ayn.checksum = "               0" ;
+
+	bxn=f.createVariable('bxn','d',('i'))
+	bxn.long_name = "inplicit zonal acceleration" ;
+	bxn.units = "m/s^2" ;
+	bxn.checksum = "               0" ;
+
+	byn=f.createVariable('byn','d',('i'))
+	byn.long_name = "implicit meridional acceleration" ;
+	byn.units = "m/s^2" ;
+	byn.checksum = "               0" ;
+
+	ine=f.createVariable('ine','i',('i'))
+	ine.long_name = "i index" ;
+	ine.units = "none" ;
+	ine.packing = 0 ;
+	ine.checksum = "               0" ;
+
+	jne=f.createVariable('jne','i',('i'))
+	jne.long_name = "j index" ;
+	jne.units = "none" ;
+	jne.packing = 0 ;
+	jne.checksum = "               0" ;
+
+	thickness=f.createVariable('thickness','d',('i'))
+	thickness.long_name = "thickness" ;
+	thickness.units = "m" ;
+	thickness.checksum = "               0" ;
+
+	width=f.createVariable('width','d',('i'))
+	width.long_name = "width" ;
+	width.units = "m" ;
+	width.checksum = "               0" ;
+
+	length=f.createVariable('length','d',('i'))
+	length.long_name = "length" ;
+	length.units = "m" ;
+	length.checksum = "               0" ;
+
+	start_lon=f.createVariable('start_lon','d',('i'))
+	start_lon.long_name = "longitude of calving location" ;
+	start_lon.units = "degrees_E" ;
+	start_lon.checksum = "               0" ;
+
+	start_lat=f.createVariable('start_lat','d',('i'))
+	start_lat.long_name = "latitude of calving location" ;
+	start_lat.units = "degrees_N" ;
+	start_lat.checksum = "               0" ;
+
+	start_year=f.createVariable('start_year','i',('i'))
+	start_year.long_name = "calendar year of calving event" ;
+	start_year.units = "years" ;
+	start_year.packing = 0 ;
+	start_year.checksum = "               0" ;
+
+	iceberg_num=f.createVariable('iceberg_num','i',('i'))
+	iceberg_num.long_name = "identification of the iceberg" ;
+	iceberg_num.units = "dimensionless" ;
+	iceberg_num.packing = 0 ;
+	iceberg_num.checksum = "               0" ;
+
+	start_day=f.createVariable('start_day','d',('i'))
+	start_day.long_name = "year day of calving event" ;
+	start_day.units = "days" ;
+	start_day.checksum = "               0" ;
+
+	start_mass=f.createVariable('start_mass','d',('i'))
+	start_mass.long_name = "initial mass of calving berg" ;
+	start_mass.units = "kg" ;
+	start_mass.checksum = "               0" ;
+
+	mass_scaling=f.createVariable('mass_scaling','d',('i'))
+	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
+	mass_scaling.units = "none" ;
+	mass_scaling.checksum = "               0" ;
+
+	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
+	mass_of_bits.long_name = "mass of bergy bits" ;
+	mass_of_bits.units = "kg" ;
+	mass_of_bits.checksum = "               0" ;
+
+	heat_density=f.createVariable('heat_density','d',('i'))
+	heat_density.long_name = "heat density" ;
+	heat_density.units = "J/kg" ;
+	heat_density.checksum = "               0" ;
+
+	halo_berg=f.createVariable('halo_berg','d',('i'))
+	halo_berg.long_name = "halo_berg" ;
+	halo_berg.units = "dimensionless" ;
+	halo_berg.checksum = "               0" ;
+
+	static_berg=f.createVariable('static_berg','d',('i'))
+	static_berg.long_name = "static_berg" ;
+	static_berg.units = "dimensionless" ;
+	static_berg.checksum = "               0" ;
+
+	f.sync()
+	f.close()
+
+
+def main(args):
+
+    #SQUARE PACKING
+
+        test=args.t
+        grdres=20.e3
+        r=2500.0
+
+        #start coords
+        xs=101.e3
+        ys=101.e3
+
+        h=1 #thickness
+        rho_ice=900.0
+
+
+        if test==1:
+            #5 particles w/ large radius
+            nbergs=2
+            width=5000.0
+            length=5000.0
+
+        #radii for evenly distrib cases
+        #element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*r**2)
+        element_area=(2.*r)**2
+
+        berg_x=[xs,xs+2.*r]
+        berg_y=[ys,ys]
+        berg_width=[sqrt(element_area),sqrt(element_area)]
+        berg_h=[h,h]
+        berg_mass_scaling=[1,1]
+        berg_mass=[h*rho_ice*element_area,h*rho_ice*element_area]
+        berg_static=[0,0]
+        berg_uvel=[0,0]
+        berg_vvel=[0,0]
+        berg_id=[1,2]
+
+        nbergs=2
+
+        #Create iceberg restart file
+        Ice_geometry_source='Generic'
+        Create_iceberg_restart_file(nbergs,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)
+
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
diff --git a/tests/dem_ground_frac_test/.gitignore b/tests/dem_ground_frac_test/.gitignore
new file mode 100644
index 0000000..68bcbc9
--- /dev/null
+++ b/tests/dem_ground_frac_test/.gitignore
@@ -0,0 +1 @@
+results/
\ No newline at end of file
diff --git a/tests/dem_ground_frac_test/README b/tests/dem_ground_frac_test/README
new file mode 100644
index 0000000..ec575a8
--- /dev/null
+++ b/tests/dem_ground_frac_test/README
@@ -0,0 +1,7 @@
+1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
+2.(optional) edit input.nml
+3. run the model: ./RUN
+4, animate the results: animate_trajectories.py
+
+This is a good test for visualizing fracture dependence on particle size. Try running makeberg.py with the full radius and then half the radius, and with regular vs dem nmls. Make sure to edit the nmls so that contact distance is halved when radius is halved
+
diff --git a/tests/dem_ground_frac_test/RUN b/tests/dem_ground_frac_test/RUN
new file mode 100755
index 0000000..f881323
--- /dev/null
+++ b/tests/dem_ground_frac_test/RUN
@@ -0,0 +1,7 @@
+rm iceberg_trajectories.nc
+rm iceberg_trajectories.nc.*
+rm bond_trajectories.nc
+rm bond_trajectories.nc.*
+srun -n9 ./../../build/bergs.x
+
+
diff --git a/tests/dem_ground_frac_test/animate_trajectories.py b/tests/dem_ground_frac_test/animate_trajectories.py
new file mode 100755
index 0000000..815b6d6
--- /dev/null
+++ b/tests/dem_ground_frac_test/animate_trajectories.py
@@ -0,0 +1,158 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+import matplotlib.pyplot as plt
+from matplotlib.animation import FuncAnimation
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
+                    help=''' provide filename to plot''')
+    parser.add_argument('-s', type=int, default='3500',
+                        help='''plotted particle size''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+
+
+def main(args):
+
+    print('reading file')
+
+    filename=args.fname
+    psize=args.s
+    #filename = 'iceberg_trajectories.nc'
+    field = 'lon'
+    field2 = 'lat'
+
+    with nc.Dataset(filename) as file:
+        x = file.variables['lon'][:]/1.e3
+        y = file.variables['lat'][:]/1.e3
+        day = file.variables['day'][:]
+        length = file.variables['length'][:]
+        width = file.variables['width'][:]
+        thick = file.variables['thickness'][:]
+        od = file.variables['od'][:]
+
+    ud = np.unique(day)
+    t = ud[0]
+
+    radius = length*width*(1./(2*np.sqrt(3)))
+
+    #for determining if grounded:
+    rho_bergs=850.
+    rho_seawater=1025.
+    h_to_ground=200.
+    draught=(rho_bergs/rho_seawater)*thick
+    groundfrac=1.-(od-draught)/h_to_ground
+    groundfrac[groundfrac<0.]=0.
+    groundfrac[groundfrac>1.]=1.
+
+    #groundfrac[thick<200.]=0.
+    #groundfrac[thick>=200.]=1.
+
+
+    # frame info
+    num_frames = len(ud)
+    movie_len = 5 #seconds
+    #frame_len = 1000.0*movie_len/num_frames/10000000
+    frame_len = movie_len/num_frames/1000
+
+    xmin = 0
+    xmax = 30
+    ymin = xmin
+    ymax = xmax
+
+    anim_running = True
+
+    def animate(i):
+
+        x1 = x[day == ud[i]]
+        y1 = y[day == ud[i]]
+        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
+
+        scat.set_offsets(data)
+
+        t = ud[i]
+        time_text.set_text('time = %.1f days' % t )
+
+        r1 = radius[day == ud[i]]
+        scat.set_sizes(r1/psize)
+
+        hstat = groundfrac[day == ud[i]]
+        cstring=[]
+        for j in range(len(hstat)):
+            if (hstat[j]==0):
+                cstring.append("none")
+            else:
+                cstring.append("b")
+        scat.set_color(cstring)
+        scat.set_edgecolor('r')
+
+        return scat,time_text
+
+    def init():
+        scat.set_offsets([])
+        return scat,
+
+    def onClick(event):
+        global anim_running
+        if anim_running:
+            ani.event_source.stop()
+            anim_running = False
+        else:
+            ani.event_source.start()
+            anim_running = True
+
+    # Now we can do the plotting!
+    f = plt.figure(figsize=(5,5))
+    f.tight_layout()
+    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
+    scat = ax1.scatter([],[],marker='o')#,edgecolor='red')
+    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
+
+    # Change major ticks to show every 20.
+    ax1.xaxis.set_major_locator(MultipleLocator(5))
+    ax1.yaxis.set_major_locator(MultipleLocator(5))
+
+    ax1.xaxis.set_minor_locator(MultipleLocator(1))
+    ax1.yaxis.set_minor_locator(MultipleLocator(1))
+
+    # Turn grid on for both major and minor ticks and style minor slightly
+    # differently.
+    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
+    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
+
+    ax1.set_xlabel('x (km)')
+    ax1.set_ylabel('y (km)')
+    ax1.set_title('Iceberg trajectory')
+
+    f.canvas.mpl_connect('button_press_event', onClick)
+
+    ani = FuncAnimation(
+        f,animate,init_func=init,frames=num_frames,
+        interval=frame_len,blit=True,repeat=True)
+
+    print('time',t)
+
+    plt.show()
+    #animation.save("iceberg_traj_animation.mp4")
+
+
+print('Script complete')
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
diff --git a/tests/dem_ground_frac_test/diag_table b/tests/dem_ground_frac_test/diag_table
new file mode 100644
index 0000000..c1c8819
--- /dev/null
+++ b/tests/dem_ground_frac_test/diag_table
@@ -0,0 +1,3 @@
+"icebergs test"
+1 1 1 0 0 0
+
diff --git a/tests/dem_ground_frac_test/input.nml b/tests/dem_ground_frac_test/input.nml
new file mode 100644
index 0000000..e94afc9
--- /dev/null
+++ b/tests/dem_ground_frac_test/input.nml
@@ -0,0 +1,185 @@
+
+&icebergs_driver_nml
+  ni=45 !30 !number of elements, x direction
+  nj=45 !30 !number of elements, y direction
+  ibdt=1800.0 !seconds
+  ibuo=0.1 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=999999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.true.
+  collision_test=.false.
+  grounding_test=.true.
+  bump_depth=200.0 !(m) depth of top of gaussian bump below sea level
+/
+
+&icebergs_nml
+
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=0.99
+    rho_bergs=850. ! (850) iceberg density
+    dem_spring_coef=1000.0
+    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=500 !300 !1000 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=1.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=3.16e6 !for power-law-type friction
+    h_to_init_grounding=200.0
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_n = 12.
+    frac_thres_t = 12.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=1.0 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=24000 ! (24) Period between verbose messages
+    traj_sample_hrs=0!0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=0!0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/dem_ground_frac_test/input_dem.nml b/tests/dem_ground_frac_test/input_dem.nml
new file mode 100644
index 0000000..8c267fd
--- /dev/null
+++ b/tests/dem_ground_frac_test/input_dem.nml
@@ -0,0 +1,186 @@
+
+&icebergs_driver_nml
+  ni=45 !30 !number of elements, x direction
+  nj=45 !30 !number of elements, y direction
+  ibdt=1800.0 !seconds
+  ibuo=0.1 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=999999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.true.
+  collision_test=.false.
+  grounding_test=.true.
+  bump_depth=200.0 !(m) depth of top of gaussian bump below sea level 
+/
+
+&icebergs_nml
+
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=0.99
+    rho_bergs=850. ! (850) iceberg density
+    dem_spring_coef=1000.0
+    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=500 !300 !1000 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
+    
+    contact_distance=1.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=3.16e6 !for power-law-type friction
+    h_to_init_grounding=200.0
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_n = 12.
+    frac_thres_t = 12.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=1.0 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=24000 ! (24) Period between verbose messages
+    traj_sample_hrs=0!0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=0!0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/dem_ground_frac_test/input_reg.nml b/tests/dem_ground_frac_test/input_reg.nml
new file mode 100644
index 0000000..332d03e
--- /dev/null
+++ b/tests/dem_ground_frac_test/input_reg.nml
@@ -0,0 +1,192 @@
+
+&icebergs_driver_nml
+  ni=45 !30 !number of elements, x direction
+  nj=45 !30 !number of elements, y direction
+  ibdt=1800.0 !seconds
+  ibuo=0.1 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=999999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.true.
+  collision_test=.false.
+  grounding_test=.true.
+  bump_depth=200.0 !(m) depth of top of gaussian bump below sea level 
+/
+
+&icebergs_nml
+
+
+    !dem=.true.
+    !poisson=0.3
+    !dem_damping_coef=0.99
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=1000.0
+    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    !mts_sub_steps=1000 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
+    mts_sub_steps=300
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
+    
+    contact_distance=500.!1.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=3.16e6 !for power-law-type friction
+    h_to_init_grounding=200.0
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    !frac_thres_n = 12.
+    !frac_thres_t = 12.
+
+    frac_thres_scaling=0.8 !h=300
+    fracture_criterion='strain' !('none') 'strain_rate','strain',or 'none'    
+    frac_thres_n = 0.0162
+    frac_thres_t = 0.0!457
+
+    !fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    !frac_thres_scaling=1.0 !h=300 to 200, stress
+    !frac_thres_n = 2.5e3
+    !frac_thres_t = 0.0
+
+    halo=3 !(4) halo width
+    Lx=45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=1.0 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=24000 ! (24) Period between verbose messages
+    traj_sample_hrs=0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/dem_ground_frac_test/input_reg_stress.nml b/tests/dem_ground_frac_test/input_reg_stress.nml
new file mode 100644
index 0000000..0b71d12
--- /dev/null
+++ b/tests/dem_ground_frac_test/input_reg_stress.nml
@@ -0,0 +1,192 @@
+
+&icebergs_driver_nml
+  ni=45 !30 !number of elements, x direction
+  nj=45 !30 !number of elements, y direction
+  ibdt=1800.0 !seconds
+  ibuo=0.1 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=999999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.true.
+  collision_test=.false.
+  grounding_test=.true.
+  bump_depth=200.0 !(m) depth of top of gaussian bump below sea level 
+/
+
+&icebergs_nml
+
+
+    !dem=.true.
+    !poisson=0.3
+    !dem_damping_coef=0.99
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=1000.0
+    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    !mts_sub_steps=1000 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
+    mts_sub_steps=10 !300
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
+    
+    contact_distance=1.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=3.16e6 !for power-law-type friction
+    h_to_init_grounding=200.0
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    !frac_thres_n = 12.
+    !frac_thres_t = 12.
+
+    !frac_thres_scaling=0.25 !h=300
+    !fracture_criterion='strain' !('none') 'strain_rate','strain',or 'none'    
+    !frac_thres_n = 0.0162
+    !frac_thres_t = 0.0!457
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling=1.0 !h=300 to 200, stress
+    frac_thres_n = 3.5e3 !2.5e3
+    frac_thres_t = 50.e3!0.0
+
+    halo=3 !(4) halo width
+    Lx=45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=1.0 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=24000 ! (24) Period between verbose messages
+    traj_sample_hrs=0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/dem_ground_frac_test/makeberg/RUN b/tests/dem_ground_frac_test/makeberg/RUN
new file mode 100755
index 0000000..520d671
--- /dev/null
+++ b/tests/dem_ground_frac_test/makeberg/RUN
@@ -0,0 +1,3 @@
+rm ./output_files/Generic*
+./makeberg.py
+cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
diff --git a/tests/dem_ground_frac_test/makeberg/makeberg.py b/tests/dem_ground_frac_test/makeberg/makeberg.py
new file mode 100755
index 0000000..de25628
--- /dev/null
+++ b/tests/dem_ground_frac_test/makeberg/makeberg.py
@@ -0,0 +1,375 @@
+#!/usr/bin/env python
+import numpy as np
+import math
+from netCDF4 import Dataset
+from pylab import *
+#import pdb
+import netCDF4 as nc
+
+#
+# Initialize 2 iceberg elements, which can later be bonded in the fortran code if needed
+#
+
+def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
+
+	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
+	# To copy the global attributes of the netCDF file
+
+	#Input and output files
+	#Create Empty restart file. This is later read so that the attributes can be used.
+	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
+	create_empty_iceberg_restart_file(Empty_restart_filename)
+	#Empty_restart_filename='input_files/icebergs.res.nc'
+
+	#Read empty restart file
+	f=Dataset(Empty_restart_filename,'r') # r is for read only
+	#Write a new restart file
+	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
+
+	for attname in f.ncattrs():
+		    setattr(g,attname,getattr(f,attname))
+
+
+	# To copy the dimension of the netCDF file
+	for dimname,dim in f.dimensions.iteritems():
+		# if you want to make changes in the dimensions of the new file
+		# you should add your own conditions here before the creation of the dimension.
+		#g.createDimension(dimname,len(dim))
+		g.createDimension(dimname,Number_of_bergs)
+
+	# To copy the variables of the netCDF file
+
+	for varname,ncvar in f.variables.iteritems():
+		# if you want to make changes in the variables of the new file
+		# you should add your own conditions here before the creation of the variable.
+		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
+		#Proceed to copy the variable attributes
+		for attname in ncvar.ncattrs():
+			setattr(var,attname,getattr(ncvar,attname))
+		#Finally copy the variable data to the new created variable
+		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
+
+		if varname=='i':
+			var[:]=Number_of_bergs
+
+		if varname=='iceberg_num':
+			for j in range(Number_of_bergs):
+				#var[j]=j+1
+				var[j]=iceberg_num[j]
+
+		if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
+		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
+		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
+		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
+			var[:]=0
+
+                if varname=='uvel':
+                        var[:]=uvel
+
+                if varname=='vvel':
+                        var[:]=vvel
+
+		if varname=='mass_scaling':
+			var[:]=mass_scaling
+
+		if varname=='thickness':
+			for j in range(Number_of_bergs):
+				var[j]=thickness[j]
+
+		if varname=='mass':
+			for j in range(Number_of_bergs):
+				var[j]=mass[j]
+
+		if varname=='width'  or varname=='length':
+			for j in range(Number_of_bergs):
+				var[j]=width[j]
+
+		if varname=='lon':
+			for j in range(Number_of_bergs):
+				var[j]=lon[j]
+
+		if varname=='lat':
+			for j in range(Number_of_bergs):
+				var[j]=lat[j]
+
+		if varname=='static_berg':
+			for j in range(Number_of_bergs):
+				var[j]=static_berg[j]
+
+
+	f.close()
+	g.close()
+
+
+def create_empty_iceberg_restart_file(Empty_restart_filename):
+
+	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
+
+	i=f.createDimension('i', None)
+	lon=f.createVariable('i','i')
+
+	lon=f.createVariable('lon','d',('i'))
+	lon.long_name = "longitude" ;
+	lon.units = "degrees_E" ;
+	lon.checksum = "               0" ;
+
+	lat=f.createVariable('lat','d',('i'))
+	lat.long_name = "latitude" ;
+	lat.units = "degrees_N" ;
+	lat.checksum = "               0" ;
+
+	uvel=f.createVariable('uvel','d',('i'))
+	uvel.long_name = "zonal velocity" ;
+	uvel.units = "m/s" ;
+	uvel.checksum = "               0" ;
+
+	vvel=f.createVariable('vvel','d',('i'))
+	vvel.long_name = "meridional velocity" ;
+	vvel.units = "m/s" ;
+	vvel.checksum = "               0" ;
+
+	mass=f.createVariable('mass','d',('i'))
+	mass.long_name = "mass" ;
+	mass.units = "kg" ;
+	mass.checksum = "               0" ;
+
+	axn=f.createVariable('axn','d',('i'))
+	axn.long_name = "explicit zonal acceleration" ;
+	axn.units = "m/s^2" ;
+	axn.checksum = "               0" ;
+
+	ayn=f.createVariable('ayn','d',('i'))
+	ayn.long_name = "explicit meridional acceleration" ;
+	ayn.units = "m/s^2" ;
+	ayn.checksum = "               0" ;
+
+	bxn=f.createVariable('bxn','d',('i'))
+	bxn.long_name = "inplicit zonal acceleration" ;
+	bxn.units = "m/s^2" ;
+	bxn.checksum = "               0" ;
+
+	byn=f.createVariable('byn','d',('i'))
+	byn.long_name = "implicit meridional acceleration" ;
+	byn.units = "m/s^2" ;
+	byn.checksum = "               0" ;
+
+	ine=f.createVariable('ine','i',('i'))
+	ine.long_name = "i index" ;
+	ine.units = "none" ;
+	ine.packing = 0 ;
+	ine.checksum = "               0" ;
+
+	jne=f.createVariable('jne','i',('i'))
+	jne.long_name = "j index" ;
+	jne.units = "none" ;
+	jne.packing = 0 ;
+	jne.checksum = "               0" ;
+
+	thickness=f.createVariable('thickness','d',('i'))
+	thickness.long_name = "thickness" ;
+	thickness.units = "m" ;
+	thickness.checksum = "               0" ;
+
+	width=f.createVariable('width','d',('i'))
+	width.long_name = "width" ;
+	width.units = "m" ;
+	width.checksum = "               0" ;
+
+	length=f.createVariable('length','d',('i'))
+	length.long_name = "length" ;
+	length.units = "m" ;
+	length.checksum = "               0" ;
+
+	start_lon=f.createVariable('start_lon','d',('i'))
+	start_lon.long_name = "longitude of calving location" ;
+	start_lon.units = "degrees_E" ;
+	start_lon.checksum = "               0" ;
+
+	start_lat=f.createVariable('start_lat','d',('i'))
+	start_lat.long_name = "latitude of calving location" ;
+	start_lat.units = "degrees_N" ;
+	start_lat.checksum = "               0" ;
+
+	start_year=f.createVariable('start_year','i',('i'))
+	start_year.long_name = "calendar year of calving event" ;
+	start_year.units = "years" ;
+	start_year.packing = 0 ;
+	start_year.checksum = "               0" ;
+
+	iceberg_num=f.createVariable('iceberg_num','i',('i'))
+	iceberg_num.long_name = "identification of the iceberg" ;
+	iceberg_num.units = "dimensionless" ;
+	iceberg_num.packing = 0 ;
+	iceberg_num.checksum = "               0" ;
+
+	start_day=f.createVariable('start_day','d',('i'))
+	start_day.long_name = "year day of calving event" ;
+	start_day.units = "days" ;
+	start_day.checksum = "               0" ;
+
+	start_mass=f.createVariable('start_mass','d',('i'))
+	start_mass.long_name = "initial mass of calving berg" ;
+	start_mass.units = "kg" ;
+	start_mass.checksum = "               0" ;
+
+	mass_scaling=f.createVariable('mass_scaling','d',('i'))
+	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
+	mass_scaling.units = "none" ;
+	mass_scaling.checksum = "               0" ;
+
+	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
+	mass_of_bits.long_name = "mass of bergy bits" ;
+	mass_of_bits.units = "kg" ;
+	mass_of_bits.checksum = "               0" ;
+
+	heat_density=f.createVariable('heat_density','d',('i'))
+	heat_density.long_name = "heat density" ;
+	heat_density.units = "J/kg" ;
+	heat_density.checksum = "               0" ;
+
+	halo_berg=f.createVariable('halo_berg','d',('i'))
+	halo_berg.long_name = "halo_berg" ;
+	halo_berg.units = "dimensionless" ;
+	halo_berg.checksum = "               0" ;
+
+	static_berg=f.createVariable('static_berg','d',('i'))
+	static_berg.long_name = "static_berg" ;
+	static_berg.units = "dimensionless" ;
+	static_berg.checksum = "               0" ;
+
+	f.sync()
+	f.close()
+
+
+
+#-----------------------------------#
+#               Main                #
+#-----------------------------------#
+
+# just2particles=False
+# flip2ndconglom=True#False
+# offset2ndconglom=True#False
+
+grdxmin=0; grdxmax=45000e3
+grdymin=0; grdymax=45000e3
+grdres=1000.0
+R_frac=0.45 #1st option
+#R_frac=0.5*0.45 #2nd option
+radius=(np.sqrt(3)/2.)*(R_frac*grdres) #S is < 0.5 grid res
+#radius2=(np.sqrt(3)/2.)*(R_frac2*grdres) #S is < 0.5 grid res
+thickness1=300.0
+thickness2=300.0
+rho_ice=850.0
+
+
+nbergs=1 #number of conglomerates
+
+#center coords of each (rectangular) conglomerate berg (CB=conglomerate berg)
+CBxc=np.array([3500]); CByc=np.array([15000])
+#side lengths
+CBxl=np.array([4000]); CByl=np.array([8000])
+
+
+CByl=CByl.astype(int); CBxl=CBxl.astype(int)
+
+#--- xmax, xmin, ymax, ymin for each CB --
+CBxmin=CBxc-(0.5*CBxl); CBxmax=CBxc+(0.5*CBxl)
+CBymin=CByc-(0.5*CByl); CBymax=CByc+(0.5*CByl)
+#this shouldn't happen:
+CBxmin[CBxmin<grdxmin]=grdxmin; CBxmax[CBxmax>grdxmax]=grdxmax
+CBymin[CBxmin<grdymin]=grdymin; CBymax[CBymax>grdymax]=grdymax
+CBxc=0.5*(CBxmin+CBxmax); CByc=0.5*(CBymin+CBymax)
+
+# #if just want one particle per CB
+# if just2particles:
+#         CBxmin=CBxc; CBxmax=CBxc
+#         CBymin=CByc; CBymax=CByc
+
+#--- min and max thicknesses for each CB ---
+h1=thickness1
+h2=thickness2
+CBhmax=np.array([h1]); CBhmin=np.array([h2])
+
+#radii
+CBrad=np.array([radius])
+print('radii',CBrad)
+
+berg_x=[]; berg_y=[]
+berg_id=[]; berg_static=[]
+berg_width=[]; berg_bonds=[]
+berg_h=[]; berg_mass_scaling=[]
+berg_mass=[]
+berg_uvel=[]; berg_vvel=[]
+
+berg_count=0
+
+for i in range(nbergs):
+        x_start=CBxmin[i]+(CBrad[i]*2./np.sqrt(3))
+
+        # if flip2ndconglom and i>0:
+        #         x_start=CBxmax[i]-(CBrad[i]*2./np.sqrt(3))
+
+        #pdb.set_trace()
+        if x_start>CBxmax[i]:
+                x_start=CBxmax[i]
+        y_start0=CBymin[i]+CBrad[i]
+        if y_start0>CBymax[i]:
+                y_start0=CBymax[i]
+        element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*(CBrad[i])**2)
+        #H (thickness) is a linear function of a berg element's position from the
+        #center of the CB. H=Hmax at the center of the CB and H=Hmin at a corner of the
+        #CB, where the dist of a corner from the center is:
+        cdistb=np.sqrt((CBxmin[i]-CBxc[i])**2+(CBymin[i]-CByc[i])**2)
+        j=0
+        x_val=x_start
+        offset=0.0
+        # if (i==0):
+        uvel=0.#1
+        # else:
+        #         uvel=-0.15#-0.05
+        #         if (offset2ndconglom):
+        #                 offset=250.0
+        vvel=0.0#25
+        #uvel=0;vvel=0
+        #berg_count_start=berg_count
+        while x_val<=CBxmax[i] and x_val>=CBxmin[i]:
+                y_start=y_start0+((j%2)*CBrad[i])+offset
+                k=0
+                y_val=y_start
+                while y_val<=(CBymax[i]+offset):
+                        berg_count=berg_count+1
+                        berg_id.append(berg_count)
+                        berg_x.append(x_val)
+                        berg_y.append(y_val)
+                        berg_width.append(sqrt(element_area))
+                        #dist of berg elem from center of CB
+                        bdistc=np.sqrt((x_val-CBxc[i])**2+(y_val-CByc[i])**2)
+                        bh=CBhmin[i]*bdistc/cdistb + CBhmax[i]*(1-bdistc/cdistb)
+                        # if (just2particles):
+                        #         bh=h1
+                        berg_h.append(bh) #thickness
+                        berg_mass_scaling.append(1)
+                        berg_mass.append(bh*rho_ice*element_area)
+                        berg_static.append(0)
+                        berg_uvel.append(uvel)
+                        berg_vvel.append(vvel)
+                        # if (x_val<22000):
+                        #         berg_vvel.append(vvel)
+                        # else:
+                        #         berg_vvel.append(0.4)
+                        #berg_CBid.append(i)
+                        k=k+1
+                        y_val=y_start+(2*k*CBrad[i])
+                j=j+1
+                # if flip2ndconglom and i>0:
+                #         x_val=x_start-(np.sqrt(3)*CBrad[i]*j)
+                # else:
+                x_val=x_start+(np.sqrt(3)*CBrad[i]*j)
+
+print('Number of bergs',berg_count)
+
+#pdb.set_trace()
+
+#Create iceberg restart file
+Ice_geometry_source='Generic'
+Create_iceberg_restart_file(berg_count,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)
diff --git a/tests/dem_rbeam_test/.gitignore b/tests/dem_rbeam_test/.gitignore
new file mode 100644
index 0000000..68bcbc9
--- /dev/null
+++ b/tests/dem_rbeam_test/.gitignore
@@ -0,0 +1 @@
+results/
\ No newline at end of file
diff --git a/tests/dem_rbeam_test/README b/tests/dem_rbeam_test/README
new file mode 100644
index 0000000..c59aa7d
--- /dev/null
+++ b/tests/dem_rbeam_test/README
@@ -0,0 +1,8 @@
+Testing of angular/rotational terms in DEM mode. In ./makeberg, a "1-D" conglomerate with 30 elements is initialized.
+There are two tests using this configuration, where the test is specified by setting dem_beam_test to either 3 or 4 in the nml. See nml for details.
+
+1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
+2.(optional) edit input.nml
+3. run the model: ./RUN
+4, animate the results: animate_trajectories.py
+
diff --git a/tests/dem_rbeam_test/RUN b/tests/dem_rbeam_test/RUN
new file mode 100755
index 0000000..0ffc895
--- /dev/null
+++ b/tests/dem_rbeam_test/RUN
@@ -0,0 +1,5 @@
+rm iceberg_trajectories.nc
+rm iceberg_trajectories.nc.*
+rm bond_trajectories.nc
+rm bond_trajectories.nc.*
+srun -n1 ./../../build/bergs.x
diff --git a/tests/dem_rbeam_test/animate_trajectories.py b/tests/dem_rbeam_test/animate_trajectories.py
new file mode 100755
index 0000000..5cae233
--- /dev/null
+++ b/tests/dem_rbeam_test/animate_trajectories.py
@@ -0,0 +1,164 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+import matplotlib.pyplot as plt
+from matplotlib.animation import FuncAnimation
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
+                    help=''' provide filename to plot''')
+    parser.add_argument('-s', type=int, default='100000',
+                    help='''plotted particle size''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+
+def main(args):
+
+    print('reading file')
+
+    filename=args.fname
+    psize=args.s
+    #filename = 'iceberg_trajectories.nc'
+    field = 'lon'
+    field2 = 'lat'
+
+    with nc.Dataset(filename) as file:
+        x = file.variables['lon'][:]/1.e3
+        y = file.variables['lat'][:]/1.e3
+        day = file.variables['day'][:]
+        length = file.variables['length'][:]
+        width = file.variables['width'][:]
+        hs = file.variables['thickness'][:]
+
+
+    radius = length*width*(1./(2*np.sqrt(3)))
+
+    #print('day',day)
+    crop=False
+    tc=1.25
+    if crop:
+        x=x[day<=tc]
+        y=y[day<=tc]
+        day=day[day<=tc]
+
+    ud = np.unique(day)
+    #print('ud',ud)
+    t = ud[0]
+
+    # frame info
+    num_frames = len(ud)
+    movie_len = 4.0 #seconds
+    frame_len = 1000.0*movie_len/num_frames
+
+    d=5000.0
+    r=d/2.
+    xshift=101
+    yshift=(151.e3+2*r)/1.e3
+
+    xmin = 90-xshift
+    xmax = 260-xshift
+    ymin = 0-yshift
+    ymax = 170-yshift
+
+    x=x-xshift
+    y=y-yshift
+
+    anim_running = True
+
+    def animate(i):
+
+        x1 = x[day == ud[i]]
+        y1 = y[day == ud[i]]
+        # hstat = hs[day == ud[i]]
+        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
+        hstat= day[day == ud[i]]
+
+        ud_max=np.max(ud)
+
+        cstring=[]
+
+        for j in range(len(hstat)):
+            if (hstat[j]<ud_max):
+                cstring.append("r")
+            else:
+                cstring.append("b")
+
+        scat.set_offsets(data)
+        scat.set_color(cstring)
+        scat.set_edgecolor('k')
+
+        t = ud[i]
+        time_text.set_text('time = %.1f days' % t )
+
+        r1 = radius[day == ud[i]]
+
+        scat.set_sizes(r1/psize)
+        return scat,time_text
+
+    def init():
+        scat.set_offsets([])
+        return scat,
+
+    def onClick(event):
+        global anim_running
+        if anim_running:
+            ani.event_source.stop()
+            anim_running = False
+        else:
+            ani.event_source.start()
+            anim_running = True
+
+    # Now we can do the plotting!
+    f = plt.figure(figsize=(5,5))
+    f.tight_layout()
+    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
+    scat = ax1.scatter([],[],marker='o')
+    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
+
+    # Change major ticks to show every 20.
+    ax1.xaxis.set_major_locator(MultipleLocator(50))
+    ax1.yaxis.set_major_locator(MultipleLocator(50))
+
+    ax1.xaxis.set_minor_locator(MultipleLocator(10))
+    ax1.yaxis.set_minor_locator(MultipleLocator(10))
+
+    # Turn grid on for both major and minor ticks and style minor slightly
+    # differently.
+    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
+    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
+
+    ax1.set_xlabel('x (km)')
+    ax1.set_ylabel('displacement (km)')
+    ax1.set_title('Iceberg trajectory')
+
+    f.canvas.mpl_connect('button_press_event', onClick)
+    ani = FuncAnimation(
+        f,animate,init_func=init,frames=num_frames,
+        interval=frame_len,blit=True,repeat=False)
+
+
+    print('time',t)
+
+    plt.show()
+    #animation.save("iceberg_traj_animation.mp4")
+
+
+print('Script complete')
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
diff --git a/tests/dem_rbeam_test/diag_table b/tests/dem_rbeam_test/diag_table
new file mode 100644
index 0000000..c1c8819
--- /dev/null
+++ b/tests/dem_rbeam_test/diag_table
@@ -0,0 +1,3 @@
+"icebergs test"
+1 1 1 0 0 0
+
diff --git a/tests/dem_rbeam_test/input.nml b/tests/dem_rbeam_test/input.nml
new file mode 100644
index 0000000..b1d2542
--- /dev/null
+++ b/tests/dem_rbeam_test/input.nml
@@ -0,0 +1,184 @@
+&icebergs_driver_nml
+  ni=20 !number of elements, x direction
+  nj=20 !number of elements, y direction
+  ibdt=10. !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=200 !total simulation hours
+  write_time_inc = 600 !increment at which time is written to screen
+  nmax=12000  !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.true.
+  collision_test=.false.
+  grounding_test=.false.
+  bump_depth=9999.0 !(m) depth of top of gaussian bump below sea level
+  gridres=15000
+/
+
+&icebergs_nml
+
+    !defaults given in parentheses:
+    !For this test, two options for dem_beam_test:
+    !3=1st element has rotation=-pi/2. Other elements adjust accordingly.
+    !4=vvel is always zero for 1st element. Last element initialized with vvel=-40 m/s
+    dem_beam_test=3
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=0.7
+    rho_bergs=900. ! (850) iceberg density
+    dem_spring_coef=1.e9 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+
+    monitor_energy=.false. !(F)save total elastic (spring+collision),external,dissipated,&fracture energy
+    new_mts=.true. !(F) If T, implicit accel is added 50% at the current time step and 50% at the next time step
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=200  !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=2000.0 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-8 !(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=3.16e6 !friction drag param
+    h_to_init_grounding=200.0 !300.0 !150.0 !300.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.false. !(T) remove unneeded bergs after PEs transfers
+
+
+    fracture_criterion='none' !('none') 'strain_rate','strain','stress',or 'none'
+    !here, try setting scaling 1.0 if force_convergence=.false., 0.5 if force_convergence=.true.
+    frac_thres_scaling = 1.0 !(1) scales frac_thres_n and frac_thres_t
+    frac_thres_n = 0. !1.e7  !normal fracture strain threshold
+    frac_thres_t = 0. !5.e7 !tangential fracture strain threshold
+
+    halo=3 !(4) halo width
+    Lx=300.e3 ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.false. ! (T) True=icebergs do no move
+
+    spring_coef=1.e-5
+    radial_damping_coef=0.0 !(1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.false. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0.0 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.false. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.false. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.true. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=24000 ! (24) Period between verbose messages
+    traj_sample_hrs=0.05 !(24) sampling period for trajectory storage
+    traj_write_hrs=0.05 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.!(F) Init bond b/w bergs if dist<1.1*radius
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/dem_rbeam_test/makeberg/RUN b/tests/dem_rbeam_test/makeberg/RUN
new file mode 100755
index 0000000..9456794
--- /dev/null
+++ b/tests/dem_rbeam_test/makeberg/RUN
@@ -0,0 +1,3 @@
+rm ./output_files/Generic*
+./makeberg.py -t=1
+cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
diff --git a/tests/dem_rbeam_test/makeberg/makeberg.py b/tests/dem_rbeam_test/makeberg/makeberg.py
new file mode 100755
index 0000000..1f68b34
--- /dev/null
+++ b/tests/dem_rbeam_test/makeberg/makeberg.py
@@ -0,0 +1,321 @@
+#!/usr/bin/env python
+import numpy as np
+import math
+from netCDF4 import Dataset
+from pylab import *
+#import pdb
+import netCDF4 as nc
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-t', type=int, default='1',
+                    help='''which test case''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
+
+	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
+	# To copy the global attributes of the netCDF file
+
+	#Input and output files
+	#Create Empty restart file. This is later read so that the attributes can be used.
+	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
+	create_empty_iceberg_restart_file(Empty_restart_filename)
+	#Empty_restart_filename='input_files/icebergs.res.nc'
+
+	#Read empty restart file
+	f=Dataset(Empty_restart_filename,'r') # r is for read only
+	#Write a new restart file
+	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
+
+	for attname in f.ncattrs():
+		    setattr(g,attname,getattr(f,attname))
+
+
+	# To copy the dimension of the netCDF file
+	for dimname,dim in f.dimensions.iteritems():
+		# if you want to make changes in the dimensions of the new file
+		# you should add your own conditions here before the creation of the dimension.
+		#g.createDimension(dimname,len(dim))
+		g.createDimension(dimname,Number_of_bergs)
+
+	# To copy the variables of the netCDF file
+
+	for varname,ncvar in f.variables.iteritems():
+		# if you want to make changes in the variables of the new file
+		# you should add your own conditions here before the creation of the variable.
+		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
+		#Proceed to copy the variable attributes
+		for attname in ncvar.ncattrs():
+			setattr(var,attname,getattr(ncvar,attname))
+		#Finally copy the variable data to the new created variable
+		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
+
+		if varname=='i':
+			var[:]=Number_of_bergs
+
+		if varname=='iceberg_num':
+			for j in range(Number_of_bergs):
+				#var[j]=j+1
+				var[j]=iceberg_num[j]
+
+		if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
+		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
+		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
+		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
+			var[:]=0
+
+                if varname=='uvel':
+			for j in range(Number_of_bergs):
+				var[j]=uvel[j]
+
+                if varname=='vvel':
+			for j in range(Number_of_bergs):
+				var[j]=vvel[j]
+
+		if varname=='mass_scaling':
+			for j in range(Number_of_bergs):
+				var[j]=mass_scaling[j]
+
+		if varname=='thickness':
+			for j in range(Number_of_bergs):
+				var[j]=thickness[j]
+
+		if varname=='mass':
+			for j in range(Number_of_bergs):
+				var[j]=mass[j]
+
+		if varname=='width'  or varname=='length':
+			for j in range(Number_of_bergs):
+				var[j]=width[j]
+
+		if varname=='lon':
+			for j in range(Number_of_bergs):
+				var[j]=lon[j]
+
+		if varname=='lat':
+			for j in range(Number_of_bergs):
+				var[j]=lat[j]
+
+		if varname=='static_berg':
+			for j in range(Number_of_bergs):
+				var[j]=static_berg[j]
+
+
+	f.close()
+	g.close()
+
+
+def create_empty_iceberg_restart_file(Empty_restart_filename):
+
+	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
+
+	i=f.createDimension('i', None)
+	lon=f.createVariable('i','i')
+
+	lon=f.createVariable('lon','d',('i'))
+	lon.long_name = "longitude" ;
+	lon.units = "degrees_E" ;
+	lon.checksum = "               0" ;
+
+	lat=f.createVariable('lat','d',('i'))
+	lat.long_name = "latitude" ;
+	lat.units = "degrees_N" ;
+	lat.checksum = "               0" ;
+
+	uvel=f.createVariable('uvel','d',('i'))
+	uvel.long_name = "zonal velocity" ;
+	uvel.units = "m/s" ;
+	uvel.checksum = "               0" ;
+
+	vvel=f.createVariable('vvel','d',('i'))
+	vvel.long_name = "meridional velocity" ;
+	vvel.units = "m/s" ;
+	vvel.checksum = "               0" ;
+
+	mass=f.createVariable('mass','d',('i'))
+	mass.long_name = "mass" ;
+	mass.units = "kg" ;
+	mass.checksum = "               0" ;
+
+	axn=f.createVariable('axn','d',('i'))
+	axn.long_name = "explicit zonal acceleration" ;
+	axn.units = "m/s^2" ;
+	axn.checksum = "               0" ;
+
+	ayn=f.createVariable('ayn','d',('i'))
+	ayn.long_name = "explicit meridional acceleration" ;
+	ayn.units = "m/s^2" ;
+	ayn.checksum = "               0" ;
+
+	bxn=f.createVariable('bxn','d',('i'))
+	bxn.long_name = "inplicit zonal acceleration" ;
+	bxn.units = "m/s^2" ;
+	bxn.checksum = "               0" ;
+
+	byn=f.createVariable('byn','d',('i'))
+	byn.long_name = "implicit meridional acceleration" ;
+	byn.units = "m/s^2" ;
+	byn.checksum = "               0" ;
+
+	ine=f.createVariable('ine','i',('i'))
+	ine.long_name = "i index" ;
+	ine.units = "none" ;
+	ine.packing = 0 ;
+	ine.checksum = "               0" ;
+
+	jne=f.createVariable('jne','i',('i'))
+	jne.long_name = "j index" ;
+	jne.units = "none" ;
+	jne.packing = 0 ;
+	jne.checksum = "               0" ;
+
+	thickness=f.createVariable('thickness','d',('i'))
+	thickness.long_name = "thickness" ;
+	thickness.units = "m" ;
+	thickness.checksum = "               0" ;
+
+	width=f.createVariable('width','d',('i'))
+	width.long_name = "width" ;
+	width.units = "m" ;
+	width.checksum = "               0" ;
+
+	length=f.createVariable('length','d',('i'))
+	length.long_name = "length" ;
+	length.units = "m" ;
+	length.checksum = "               0" ;
+
+	start_lon=f.createVariable('start_lon','d',('i'))
+	start_lon.long_name = "longitude of calving location" ;
+	start_lon.units = "degrees_E" ;
+	start_lon.checksum = "               0" ;
+
+	start_lat=f.createVariable('start_lat','d',('i'))
+	start_lat.long_name = "latitude of calving location" ;
+	start_lat.units = "degrees_N" ;
+	start_lat.checksum = "               0" ;
+
+	start_year=f.createVariable('start_year','i',('i'))
+	start_year.long_name = "calendar year of calving event" ;
+	start_year.units = "years" ;
+	start_year.packing = 0 ;
+	start_year.checksum = "               0" ;
+
+	iceberg_num=f.createVariable('iceberg_num','i',('i'))
+	iceberg_num.long_name = "identification of the iceberg" ;
+	iceberg_num.units = "dimensionless" ;
+	iceberg_num.packing = 0 ;
+	iceberg_num.checksum = "               0" ;
+
+	start_day=f.createVariable('start_day','d',('i'))
+	start_day.long_name = "year day of calving event" ;
+	start_day.units = "days" ;
+	start_day.checksum = "               0" ;
+
+	start_mass=f.createVariable('start_mass','d',('i'))
+	start_mass.long_name = "initial mass of calving berg" ;
+	start_mass.units = "kg" ;
+	start_mass.checksum = "               0" ;
+
+	mass_scaling=f.createVariable('mass_scaling','d',('i'))
+	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
+	mass_scaling.units = "none" ;
+	mass_scaling.checksum = "               0" ;
+
+	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
+	mass_of_bits.long_name = "mass of bergy bits" ;
+	mass_of_bits.units = "kg" ;
+	mass_of_bits.checksum = "               0" ;
+
+	heat_density=f.createVariable('heat_density','d',('i'))
+	heat_density.long_name = "heat density" ;
+	heat_density.units = "J/kg" ;
+	heat_density.checksum = "               0" ;
+
+	halo_berg=f.createVariable('halo_berg','d',('i'))
+	halo_berg.long_name = "halo_berg" ;
+	halo_berg.units = "dimensionless" ;
+	halo_berg.checksum = "               0" ;
+
+	static_berg=f.createVariable('static_berg','d',('i'))
+	static_berg.long_name = "static_berg" ;
+	static_berg.units = "dimensionless" ;
+	static_berg.checksum = "               0" ;
+
+	f.sync()
+	f.close()
+
+
+def main(args):
+
+    #SQUARE PACKING
+
+        test=args.t
+        grdres=20.e3
+        r=2500.0#/3.
+
+        #start coords
+        xs=101.e3
+        ys=151.e3
+
+        h=4. #thickness
+        rho_ice=900.0
+
+
+        if test==1:
+            #5 particles w/ large radius
+            nbergs=30#90
+            width=r*2.
+            length=r*2.
+
+        #radii for evenly distrib cases
+        #element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*r**2)
+        element_area=(2.*r)**2
+
+        berg_x=[]; berg_y=[]
+        berg_id=[]; berg_static=[]
+        berg_width=[]; berg_bonds=[]
+        berg_h=[]; berg_mass_scaling=[]
+        berg_mass=[]
+        berg_uvel=[]; berg_vvel=[]
+
+        x=xs
+        y=ys#-2*r
+
+        berg_count=0.
+        while berg_count<nbergs:
+                berg_count=berg_count+1
+                if berg_count==1:
+                    #x=xs
+                    y=y+2*r
+                    static=1
+                else:
+                    static=0
+                    x=x+2*r
+
+                berg_x.append(x)
+                berg_y.append(y)
+                berg_width.append(sqrt(element_area))
+                berg_h.append(h)
+                berg_mass_scaling.append(1)
+                berg_mass.append(h*rho_ice*element_area)
+                berg_static.append(static)
+                berg_uvel.append(0)
+                berg_vvel.append(0)
+                berg_id.append(berg_count)
+
+        print('Number of bergs',berg_count)
+
+        #Create iceberg restart file
+        Ice_geometry_source='Generic'
+        Create_iceberg_restart_file(nbergs,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)
+
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
diff --git a/tests/dem_ssbeam_test/.gitignore b/tests/dem_ssbeam_test/.gitignore
new file mode 100644
index 0000000..68bcbc9
--- /dev/null
+++ b/tests/dem_ssbeam_test/.gitignore
@@ -0,0 +1 @@
+results/
\ No newline at end of file
diff --git a/tests/dem_ssbeam_test/README b/tests/dem_ssbeam_test/README
new file mode 100644
index 0000000..38ed5d7
--- /dev/null
+++ b/tests/dem_ssbeam_test/README
@@ -0,0 +1 @@
+This is the simply supported beam test from Section 3.1 of Wang 2020 "A scale-invariant bonded particle model for simulating large deformation and failure of continua"
\ No newline at end of file
diff --git a/tests/dem_ssbeam_test/RUN b/tests/dem_ssbeam_test/RUN
new file mode 100755
index 0000000..0ffc895
--- /dev/null
+++ b/tests/dem_ssbeam_test/RUN
@@ -0,0 +1,5 @@
+rm iceberg_trajectories.nc
+rm iceberg_trajectories.nc.*
+rm bond_trajectories.nc
+rm bond_trajectories.nc.*
+srun -n1 ./../../build/bergs.x
diff --git a/tests/dem_ssbeam_test/animate_trajectories.py b/tests/dem_ssbeam_test/animate_trajectories.py
new file mode 100755
index 0000000..9b8cf0d
--- /dev/null
+++ b/tests/dem_ssbeam_test/animate_trajectories.py
@@ -0,0 +1,178 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+import matplotlib.pyplot as plt
+from matplotlib.animation import FuncAnimation
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
+                    help=''' provide filename to plot''')
+    parser.add_argument('-s', type=float, default='0.0025',
+                    help='''plotted particle size''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+
+def main(args):
+
+    print('reading file')
+
+    filename=args.fname
+    psize=args.s
+    #filename = 'iceberg_trajectories.nc'
+    field = 'lon'
+    field2 = 'lat'
+
+    with nc.Dataset(filename) as file:
+        x = file.variables['lon'][:] #/1.e3
+        y = file.variables['lat'][:] #/1.e3
+        day = file.variables['day'][:]
+        length = file.variables['length'][:]
+        width = file.variables['width'][:]
+        hs = file.variables['thickness'][:]
+
+
+    radius = 0.5*sqrt(length*width) #*(1./(2*np.sqrt(3)))
+
+    #print('day',day)
+    crop=False
+    tc=1.25
+    if crop:
+        x=x[day<=tc]
+        y=y[day<=tc]
+        day=day[day<=tc]
+
+    ud = np.unique(day)
+    print('ud',ud)
+    t = ud[0]
+
+    # frame info
+    num_frames = len(ud)
+    movie_len = 4.0 #seconds
+    frame_len = 1000.0*movie_len/num_frames
+
+    d=0.5 #5000.0
+    r=d/2.
+    xshift=101.e3
+    yshift=(151.e3+2*r) #/1.e3
+    x=x-xshift
+    y=y-yshift
+
+    xmin=np.min(x)-1
+    xmax=np.max(x)+1
+    ymin=np.min(y)-1
+    ymax=np.max(y)+1
+
+
+    anim_running = True
+
+    def animate(i):
+
+        x1 = x[day == ud[i]]
+        y1 = y[day == ud[i]]
+        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
+        hstat= day[day == ud[i]]
+
+        ud_max=np.max(ud)
+
+        cstring=[]
+
+        for j in range(len(hstat)):
+            cstring.append("none")
+
+        scat.set_offsets(data)
+        scat.set_color(cstring)
+        scat.set_edgecolor('k')
+
+        t = ud[i]
+        time_text.set_text('time = %.1f days' % t )
+
+        r1 = radius[day == ud[i]]
+        scat.set_sizes(r1/psize)
+        return scat,time_text #,scat2
+
+    def init():
+        scat.set_offsets([])
+        return scat,
+
+    def onClick(event):
+        global anim_running
+        if anim_running:
+            ani.event_source.stop()
+            anim_running = False
+        else:
+            ani.event_source.start()
+            anim_running = True
+
+    # Now we can do the plotting!
+    f = plt.figure(figsize=(5,5))
+    f.tight_layout()
+    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
+    scat = ax1.scatter([],[],marker='o')
+    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
+
+    # Change major ticks to show every 20.
+    ax1.xaxis.set_major_locator(MultipleLocator(50))
+    ax1.yaxis.set_major_locator(MultipleLocator(50))
+
+    ax1.xaxis.set_minor_locator(MultipleLocator(10))
+    ax1.yaxis.set_minor_locator(MultipleLocator(10))
+
+    # Turn grid on for both major and minor ticks and style minor slightly
+    # differently.
+    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
+    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
+
+    ax1.set_xlabel('x (m)')
+    ax1.set_ylabel('displacement (m)')
+    ax1.set_title('Iceberg trajectory')
+
+    #analytical solution
+    xa=np.arange(0,29)
+    xa=xa*0.5
+    print('xa',xa)
+    l=np.max(xa)
+    print('l',l)
+    P=-(1.5e5) #Newtons
+    YM=1.e9 #young's
+    thick=1
+    h=0.5
+    AI= thick*(h**3)/12. #second  moment of area
+    w1=-P*xa*(4.*xa*xa-3.*l*l)/(48.*YM*AI)
+    w2=P*(xa-l)*(l*l-8.*l*xa+4*xa*xa)/(48.*YM*AI)
+    w=w1
+    w[xa>0.5*l]=w2[xa>0.5*l] #deflection
+    print('w',w)
+
+    ax1.plot(xa,w)
+
+    f.canvas.mpl_connect('button_press_event', onClick)
+    ani = FuncAnimation(
+        f,animate,init_func=init,frames=num_frames,
+        interval=frame_len,blit=True,repeat=False)
+
+
+    print('time',t)
+
+    plt.show()
+    #animation.save("iceberg_traj_animation.mp4")
+
+
+print('Script complete')
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
diff --git a/tests/dem_ssbeam_test/diag_table b/tests/dem_ssbeam_test/diag_table
new file mode 100644
index 0000000..c1c8819
--- /dev/null
+++ b/tests/dem_ssbeam_test/diag_table
@@ -0,0 +1,3 @@
+"icebergs test"
+1 1 1 0 0 0
+
diff --git a/tests/dem_ssbeam_test/input.nml b/tests/dem_ssbeam_test/input.nml
new file mode 100644
index 0000000..a6c18cd
--- /dev/null
+++ b/tests/dem_ssbeam_test/input.nml
@@ -0,0 +1,182 @@
+&icebergs_driver_nml
+  ni=20 !number of elements, x direction
+  nj=20 !number of elements, y direction
+  ibdt=1 !00. !0.05 !120.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=200 !total simulation hours
+  write_time_inc = 1 !600 !increment at which time is written to screen
+  nmax=30 !1200  !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.true.
+  collision_test=.false.
+  grounding_test=.false.
+  bump_depth=9999.0 !(m) depth of top of gaussian bump below sea level
+  gridres=15000
+/
+
+&icebergs_nml
+
+    !defaults given in parentheses:
+    dem_beam_test=1
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=0.1
+    rho_bergs=800. ! (850) iceberg density
+    dem_spring_coef=1.e9 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+
+    monitor_energy=.false. !(F)save total elastic (spring+collision),external,dissipated,&fracture energy
+    new_mts=.true. !(F) If T, implicit accel is added 50% at the current time step and 50% at the next time step
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=1e5 !20 !00  !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
+
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=2000.0 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-8 !(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=3.16e6 !friction drag param
+    h_to_init_grounding=200.0 !300.0 !150.0 !300.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.false. !(T) remove unneeded bergs after PEs transfers
+
+
+    fracture_criterion='none' !('none') 'strain_rate','strain','stress',or 'none'
+    !here, try setting scaling 1.0 if force_convergence=.false., 0.5 if force_convergence=.true.
+    frac_thres_scaling = 1.0 !(1) scales frac_thres_n and frac_thres_t
+    frac_thres_n = 0. !1.e7  !normal fracture strain threshold
+    frac_thres_t = 0. !5.e7 !tangential fracture strain threshold
+
+    halo=3 !(4) halo width
+    Lx=300.e3 ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.false. ! (T) True=icebergs do no move
+
+    spring_coef=1.e-5
+    radial_damping_coef=0.0 !(1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.false. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0.0 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.false. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.false. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.true. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=24000 ! (24) Period between verbose messages
+    traj_sample_hrs=0.0!5 !(24) sampling period for trajectory storage
+    traj_write_hrs=0.0!5 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.!(F) Init bond b/w bergs if dist<1.1*radius
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/dem_ssbeam_test/makeberg/RUN b/tests/dem_ssbeam_test/makeberg/RUN
new file mode 100755
index 0000000..9456794
--- /dev/null
+++ b/tests/dem_ssbeam_test/makeberg/RUN
@@ -0,0 +1,3 @@
+rm ./output_files/Generic*
+./makeberg.py -t=1
+cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
diff --git a/tests/dem_ssbeam_test/makeberg/makeberg.py b/tests/dem_ssbeam_test/makeberg/makeberg.py
new file mode 100755
index 0000000..9b14fb3
--- /dev/null
+++ b/tests/dem_ssbeam_test/makeberg/makeberg.py
@@ -0,0 +1,321 @@
+#!/usr/bin/env python
+import numpy as np
+import math
+from netCDF4 import Dataset
+from pylab import *
+#import pdb
+import netCDF4 as nc
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-t', type=int, default='1',
+                    help='''which test case''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
+
+	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
+	# To copy the global attributes of the netCDF file
+
+	#Input and output files
+	#Create Empty restart file. This is later read so that the attributes can be used.
+	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
+	create_empty_iceberg_restart_file(Empty_restart_filename)
+	#Empty_restart_filename='input_files/icebergs.res.nc'
+
+	#Read empty restart file
+	f=Dataset(Empty_restart_filename,'r') # r is for read only
+	#Write a new restart file
+	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
+
+	for attname in f.ncattrs():
+		    setattr(g,attname,getattr(f,attname))
+
+
+	# To copy the dimension of the netCDF file
+	for dimname,dim in f.dimensions.iteritems():
+		# if you want to make changes in the dimensions of the new file
+		# you should add your own conditions here before the creation of the dimension.
+		#g.createDimension(dimname,len(dim))
+		g.createDimension(dimname,Number_of_bergs)
+
+	# To copy the variables of the netCDF file
+
+	for varname,ncvar in f.variables.iteritems():
+		# if you want to make changes in the variables of the new file
+		# you should add your own conditions here before the creation of the variable.
+		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
+		#Proceed to copy the variable attributes
+		for attname in ncvar.ncattrs():
+			setattr(var,attname,getattr(ncvar,attname))
+		#Finally copy the variable data to the new created variable
+		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
+
+		if varname=='i':
+			var[:]=Number_of_bergs
+
+		if varname=='iceberg_num':
+			for j in range(Number_of_bergs):
+				#var[j]=j+1
+				var[j]=iceberg_num[j]
+
+		if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
+		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
+		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
+		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
+			var[:]=0
+
+                if varname=='uvel':
+			for j in range(Number_of_bergs):
+				var[j]=uvel[j]
+
+                if varname=='vvel':
+			for j in range(Number_of_bergs):
+				var[j]=vvel[j]
+
+		if varname=='mass_scaling':
+			for j in range(Number_of_bergs):
+				var[j]=mass_scaling[j]
+
+		if varname=='thickness':
+			for j in range(Number_of_bergs):
+				var[j]=thickness[j]
+
+		if varname=='mass':
+			for j in range(Number_of_bergs):
+				var[j]=mass[j]
+
+		if varname=='width'  or varname=='length':
+			for j in range(Number_of_bergs):
+				var[j]=width[j]
+
+		if varname=='lon':
+			for j in range(Number_of_bergs):
+				var[j]=lon[j]
+
+		if varname=='lat':
+			for j in range(Number_of_bergs):
+				var[j]=lat[j]
+
+		if varname=='static_berg':
+			for j in range(Number_of_bergs):
+				var[j]=static_berg[j]
+
+
+	f.close()
+	g.close()
+
+
+def create_empty_iceberg_restart_file(Empty_restart_filename):
+
+	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
+
+	i=f.createDimension('i', None)
+	lon=f.createVariable('i','i')
+
+	lon=f.createVariable('lon','d',('i'))
+	lon.long_name = "longitude" ;
+	lon.units = "degrees_E" ;
+	lon.checksum = "               0" ;
+
+	lat=f.createVariable('lat','d',('i'))
+	lat.long_name = "latitude" ;
+	lat.units = "degrees_N" ;
+	lat.checksum = "               0" ;
+
+	uvel=f.createVariable('uvel','d',('i'))
+	uvel.long_name = "zonal velocity" ;
+	uvel.units = "m/s" ;
+	uvel.checksum = "               0" ;
+
+	vvel=f.createVariable('vvel','d',('i'))
+	vvel.long_name = "meridional velocity" ;
+	vvel.units = "m/s" ;
+	vvel.checksum = "               0" ;
+
+	mass=f.createVariable('mass','d',('i'))
+	mass.long_name = "mass" ;
+	mass.units = "kg" ;
+	mass.checksum = "               0" ;
+
+	axn=f.createVariable('axn','d',('i'))
+	axn.long_name = "explicit zonal acceleration" ;
+	axn.units = "m/s^2" ;
+	axn.checksum = "               0" ;
+
+	ayn=f.createVariable('ayn','d',('i'))
+	ayn.long_name = "explicit meridional acceleration" ;
+	ayn.units = "m/s^2" ;
+	ayn.checksum = "               0" ;
+
+	bxn=f.createVariable('bxn','d',('i'))
+	bxn.long_name = "inplicit zonal acceleration" ;
+	bxn.units = "m/s^2" ;
+	bxn.checksum = "               0" ;
+
+	byn=f.createVariable('byn','d',('i'))
+	byn.long_name = "implicit meridional acceleration" ;
+	byn.units = "m/s^2" ;
+	byn.checksum = "               0" ;
+
+	ine=f.createVariable('ine','i',('i'))
+	ine.long_name = "i index" ;
+	ine.units = "none" ;
+	ine.packing = 0 ;
+	ine.checksum = "               0" ;
+
+	jne=f.createVariable('jne','i',('i'))
+	jne.long_name = "j index" ;
+	jne.units = "none" ;
+	jne.packing = 0 ;
+	jne.checksum = "               0" ;
+
+	thickness=f.createVariable('thickness','d',('i'))
+	thickness.long_name = "thickness" ;
+	thickness.units = "m" ;
+	thickness.checksum = "               0" ;
+
+	width=f.createVariable('width','d',('i'))
+	width.long_name = "width" ;
+	width.units = "m" ;
+	width.checksum = "               0" ;
+
+	length=f.createVariable('length','d',('i'))
+	length.long_name = "length" ;
+	length.units = "m" ;
+	length.checksum = "               0" ;
+
+	start_lon=f.createVariable('start_lon','d',('i'))
+	start_lon.long_name = "longitude of calving location" ;
+	start_lon.units = "degrees_E" ;
+	start_lon.checksum = "               0" ;
+
+	start_lat=f.createVariable('start_lat','d',('i'))
+	start_lat.long_name = "latitude of calving location" ;
+	start_lat.units = "degrees_N" ;
+	start_lat.checksum = "               0" ;
+
+	start_year=f.createVariable('start_year','i',('i'))
+	start_year.long_name = "calendar year of calving event" ;
+	start_year.units = "years" ;
+	start_year.packing = 0 ;
+	start_year.checksum = "               0" ;
+
+	iceberg_num=f.createVariable('iceberg_num','i',('i'))
+	iceberg_num.long_name = "identification of the iceberg" ;
+	iceberg_num.units = "dimensionless" ;
+	iceberg_num.packing = 0 ;
+	iceberg_num.checksum = "               0" ;
+
+	start_day=f.createVariable('start_day','d',('i'))
+	start_day.long_name = "year day of calving event" ;
+	start_day.units = "days" ;
+	start_day.checksum = "               0" ;
+
+	start_mass=f.createVariable('start_mass','d',('i'))
+	start_mass.long_name = "initial mass of calving berg" ;
+	start_mass.units = "kg" ;
+	start_mass.checksum = "               0" ;
+
+	mass_scaling=f.createVariable('mass_scaling','d',('i'))
+	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
+	mass_scaling.units = "none" ;
+	mass_scaling.checksum = "               0" ;
+
+	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
+	mass_of_bits.long_name = "mass of bergy bits" ;
+	mass_of_bits.units = "kg" ;
+	mass_of_bits.checksum = "               0" ;
+
+	heat_density=f.createVariable('heat_density','d',('i'))
+	heat_density.long_name = "heat density" ;
+	heat_density.units = "J/kg" ;
+	heat_density.checksum = "               0" ;
+
+	halo_berg=f.createVariable('halo_berg','d',('i'))
+	halo_berg.long_name = "halo_berg" ;
+	halo_berg.units = "dimensionless" ;
+	halo_berg.checksum = "               0" ;
+
+	static_berg=f.createVariable('static_berg','d',('i'))
+	static_berg.long_name = "static_berg" ;
+	static_berg.units = "dimensionless" ;
+	static_berg.checksum = "               0" ;
+
+	f.sync()
+	f.close()
+
+
+def main(args):
+
+    #SQUARE PACKING
+
+        test=args.t
+        grdres=20.e3
+        r=0.25
+
+        #start coords
+        xs=101.e3
+        ys=151.e3
+
+        h=1. #thickness
+        rho_ice=800.0
+
+
+        if test==1:
+            #5 particles w/ large radius
+            nbergs=29
+            width=r*2.
+            length=r*2.
+
+        #radii for evenly distrib cases
+        #element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*r**2)
+        element_area=(2.*r)**2
+
+        berg_x=[]; berg_y=[]
+        berg_id=[]; berg_static=[]
+        berg_width=[]; berg_bonds=[]
+        berg_h=[]; berg_mass_scaling=[]
+        berg_mass=[]
+        berg_uvel=[]; berg_vvel=[]
+
+        x=xs
+        y=ys#-2*r
+
+        berg_count=0.
+        while berg_count<nbergs:
+                berg_count=berg_count+1
+                if berg_count==1:
+                    #x=xs
+                    y=y+2*r
+                    static=0
+                else:
+                    static=0
+                    x=x+2*r
+
+                berg_x.append(x)
+                berg_y.append(y)
+                berg_width.append(sqrt(element_area))
+                berg_h.append(h)
+                berg_mass_scaling.append(1)
+                berg_mass.append(h*rho_ice*element_area)
+                berg_static.append(static)
+                berg_uvel.append(0)
+                berg_vvel.append(0)
+                berg_id.append(berg_count)
+
+        print('Number of bergs',berg_count)
+
+        #Create iceberg restart file
+        Ice_geometry_source='Generic'
+        Create_iceberg_restart_file(nbergs,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)
+
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
diff --git a/tests/energy_test/input.nml b/tests/energy_test/input.nml
index 22d6fd9..070b0f9 100644
--- a/tests/energy_test/input.nml
+++ b/tests/energy_test/input.nml
@@ -32,6 +32,9 @@
     mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
     mts_sub_steps=10 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
 
+    !force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    !convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
     contact_distance=1.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
     contact_spring_coef=1.e-7 !!5.e-7!(default=spring_coeff) Berg spring coeff for collisions
     debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
diff --git a/tests/energy_test2/README b/tests/energy_test2/README
index 147e393..d555978 100644
--- a/tests/energy_test2/README
+++ b/tests/energy_test2/README
@@ -1,20 +1,9 @@
-Collision and (subsequent fracture?) of two conglomerate bergs. For testing a scheme where the MTS solution is iterated a given number of times in order to help conserve momentum conservation when collisions occur. Also for testing fracture scheme (e.g. effects of particle size, fracture thresholds, sensitivity to violation of momentum conservation).
-
-Iterative scheme options:
-Option 1: Set the number of iterations (>1) for each long/short step using imp_loop_iters_long and imp_loop_iters_short, respectively. Force_convergence must be set false. (this option uses subroutine evolve_icebergs_mts)
-Option 2: Set force_convergence to true and specify a convergence tolerance. Iterations will stop once convergence tolerance is reached. (this option, or if both imp_loop_iters==1, uses subroutine evolve_icebergs_mts2)
+Collision and (subsequent fracture?) of two conglomerate bergs. For testing a scheme where the implicit part of the MTS solution is iterated to convergence to help conserve momentum conservation when collisions occur. Also for testing fracture scheme (e.g. effects of particle size, fracture thresholds, sensitivity to violation of momentum conservation). Set force_convergence to true and specify a convergence tolerance.
 
 Unlike in energy_test3, this test conserves momentum during collision even without the iterative scheme.
 
 1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
 2.(optional) edit input.nml
 3. run the model: ./RUN
-4, animate the results: animate_trajectories.py
-
-
-
-1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
-2.(optional) edit input.nml
-3. run the model: ./RUN
-4, animate the results: animate_trajectories.py
+4. animate the results: animate_trajectories.py
 
diff --git a/tests/energy_test2/input.nml b/tests/energy_test2/input.nml
index e4ffd31..6bd133d 100644
--- a/tests/energy_test2/input.nml
+++ b/tests/energy_test2/input.nml
@@ -25,8 +25,7 @@
     new_mts=.true. !(F) If T, implicit accel is added 50% at the current time step and 50% at the next time step
     mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
     mts_sub_steps=20  !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
-    imp_loop_iters_long=1 !(1) if >1, # of iterations for each long MTS step (alt to force_convergence)
-    imp_loop_iters_short=1!(1)if >1, # of iterations for each short MTS step (alt to force_convergence)
+
     force_convergence=.false. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
     convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
 
diff --git a/tests/energy_test3/README b/tests/energy_test3/README
index e882f41..7482b12 100644
--- a/tests/energy_test3/README
+++ b/tests/energy_test3/README
@@ -1,8 +1,4 @@
-Collision and subsequent fracture of two conglomerate bergs. For testing a scheme where the MTS solution is iterated to convergence in order to help conserve momentum conservation when collisions occur. Also for testing fracture scheme (e.g. effects of particle size, fracture thresholds, sensitivity to violation of momentum conservation).
-
-Iterative scheme options:
-Option 1: Set the number of iterations (>1) for each long/short step using imp_loop_iters_long and imp_loop_iters_short, respectively. Force_convergence must be set false. (this option uses subroutine evolve_icebergs_mts)
-Option 2: Set force_convergence to true and specify a convergence tolerance. Iterations will stop once convergence tolerance is reached. (this option, or if both imp_loop_iters==1, uses subroutine evolve_icebergs_mts2)
+Collision and subsequent fracture of two conglomerate bergs. For testing a scheme where the MTS solution is iterated to convergence in order to help conserve momentum conservation when collisions occur. Also for testing fracture scheme (e.g. effects of particle size, fracture thresholds, sensitivity to violation of momentum conservation). Set force_convergence to true and specify a convergence tolerance. Iterations will stop once convergence tolerance is reached.
 
 Unlike in energy_test2, this test will not conserve momentum sufficiently during collision unless the iterative scheme is used.
 
diff --git a/tests/energy_test3/animate_trajectories.py b/tests/energy_test3/animate_trajectories.py
index cd325e1..3bcce56 100755
--- a/tests/energy_test3/animate_trajectories.py
+++ b/tests/energy_test3/animate_trajectories.py
@@ -19,16 +19,19 @@ def parseCommandLine():
     epilog='Written by Alex Huth, 2020')
     parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
                     help=''' provide filename to plot''')
+    parser.add_argument('-s', type=int, default='4000',
+                    help='''plotted particle size''')
+    optCmdLineArgs = parser.parse_args()    
     optCmdLineArgs = parser.parse_args()
     return optCmdLineArgs
 
 
-
 def main(args):
 
     print('reading file')
 
     filename=args.fname
+    psize=args.s
     #filename = 'iceberg_trajectories.nc'
     field = 'lon'
     field2 = 'lat'
@@ -37,6 +40,11 @@ def main(args):
         x = file.variables['lon'][:]/1.e3
         y = file.variables['lat'][:]/1.e3
         day = file.variables['day'][:]
+        length = file.variables['length'][:]
+        width = file.variables['width'][:]
+
+        
+    radius = length*width*(1/(2*np.sqrt(3)))
 
     crop=False
     tc=1.25
@@ -70,6 +78,10 @@ def animate(i):
 
         t = ud[i]
         time_text.set_text('time = %.1f days' % t )
+
+        r1 = radius[day == ud[i]]
+        
+        scat.set_sizes(r1/psize)
         return scat,time_text
 
     def init():
@@ -89,7 +101,8 @@ def onClick(event):
     f = plt.figure(figsize=(5,5))
     f.tight_layout()
     ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
-    scat = ax1.scatter([],[],marker='o',facecolor='w',s=40,edgecolor='red')
+    #scat = ax1.scatter([],[],marker='o',facecolor='w',s=psize,edgecolor='red')
+    scat = ax1.scatter([],[],marker='o',facecolor='w',edgecolor='red')    
     time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
 
     # Change major ticks to show every 20.
diff --git a/tests/energy_test3/input.nml b/tests/energy_test3/input.nml
index 9e20b83..4edbd32 100644
--- a/tests/energy_test3/input.nml
+++ b/tests/energy_test3/input.nml
@@ -1,7 +1,13 @@
 !KID, bergs_chksum: write_restart berg chksum=           -1918812055 chksum2=             743944572 chksum3=             -78785014 chksum4=             -78785014 chksum5=                     0 #=                    71
 !KID, grd_chksum2:    # of bergs/cell chksum=                     0 chksum2=                     0 min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
+! Total number of bonds is:          276
+
+!test: replace uvel_old and vvel_old during damping with ustar and vstar
+!KID, bergs_chksum: write_restart berg chksum=           -1514198739 chksum2=            -764201033 chksum3=             -78785014 chksum4=             -78785014 chksum5=                     0 #=                    71
+!KID, grd_chksum2:    # of bergs/cell chksum=                     0 chksum2=                     0 min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
 ! Total number of bonds is:          276 
 
+
 &icebergs_driver_nml
   ni=45 !number of elements, x direction
   nj=45 !number of elements, y direction
@@ -24,15 +30,14 @@
 &icebergs_nml
 
     !defaults given in parentheses:
+    explicit_inner_mts=.false. !(F) If T, inner MTS iterations are treated explicitly
 
     monitor_energy=.true. !(F)save total elastic (spring+collision),external,dissipated,&fracture energy
     new_mts=.true. !(F) If T, implicit accel is added 50% at the current time step and 50% at the next time step
     mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
     mts_sub_steps=20  !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
-    imp_loop_iters_long=1 !(1) if >1, # of iterations for each long MTS step (alt to force_convergence)
-    imp_loop_iters_short=1!(1)if >1, # of iterations for each short MTS step (alt to force_convergence)
     force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
+    convergence_tolerance=1.e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
 
     contact_distance=2000 !2500 !2500 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
     contact_spring_coef=1.e-8 !(default=spring_coeff) Berg spring coeff for collisions
@@ -42,12 +47,23 @@
     ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
     remove_unused_bergs=.false. !(T) remove unneeded bergs after PEs transfers
 
-    fracture_criterion='strain' !('none') 'strain_rate','strain',or 'none'
+    fracture_criterion='strain' !('none') 'strain_rate','strain','stress',or 'none'
     !here, try setting scaling 1.0 if force_convergence=.false., 0.5 if force_convergence=.true.
     frac_thres_scaling = 0.5 !(1) scales frac_thres_n and frac_thres_t
     frac_thres_n = 0.018  !normal fracture strain threshold
     frac_thres_t = 0.05076 !tangential fracture strain threshold
 
+    !fracture_criterion='strain_rate' !('none') 'strain_rate','strain','stress',or 'none'
+    !frac_thres_scaling = 1 !(1) scales frac_thres_n and frac_thres_t
+    !frac_thres_n = 2.e-6  !normal fracture strain threshold
+    !frac_thres_t = 0!1.e-5 !tangential fracture strain threshold
+
+    !fracture_criterion='stress' !('none') 'strain_rate','strain','stress',or 'none'
+    !here, try setting scaling 1.0 if force_convergence=.false., 0.5 if force_convergence=.true.
+    !frac_thres_scaling = 1.0 !(1) scales frac_thres_n and frac_thres_t
+    !frac_thres_n = 8000.0  !normal fracture strain threshold
+    !frac_thres_t = 0.!12000.0 !0.05076 !tangential fracture strain threshold
+
     halo=3 !(4) halo width
     Lx=45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
     grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
diff --git a/tests/energy_test3/makeberg/makeberg.py b/tests/energy_test3/makeberg/makeberg.py
index 2dd9eca..829fe4c 100755
--- a/tests/energy_test3/makeberg/makeberg.py
+++ b/tests/energy_test3/makeberg/makeberg.py
@@ -261,6 +261,9 @@ def create_empty_iceberg_restart_file(Empty_restart_filename):
 thickness2=300.0
 rho_ice=850.0
 
+#mass
+mass=thickness1*element_area*rho_ice
+print('mass',mass)
 
 nbergs=2 #number of conglomerates
 
diff --git a/tests/frac_test/.gitignore b/tests/frac_test/.gitignore
new file mode 100644
index 0000000..68bcbc9
--- /dev/null
+++ b/tests/frac_test/.gitignore
@@ -0,0 +1 @@
+results/
\ No newline at end of file
diff --git a/tests/frac_test/README b/tests/frac_test/README
new file mode 100644
index 0000000..7482b12
--- /dev/null
+++ b/tests/frac_test/README
@@ -0,0 +1,9 @@
+Collision and subsequent fracture of two conglomerate bergs. For testing a scheme where the MTS solution is iterated to convergence in order to help conserve momentum conservation when collisions occur. Also for testing fracture scheme (e.g. effects of particle size, fracture thresholds, sensitivity to violation of momentum conservation). Set force_convergence to true and specify a convergence tolerance. Iterations will stop once convergence tolerance is reached.
+
+Unlike in energy_test2, this test will not conserve momentum sufficiently during collision unless the iterative scheme is used.
+
+1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
+2.(optional) edit input.nml
+3. run the model: ./RUN
+4, animate the results: animate_trajectories.py
+
diff --git a/tests/frac_test/RUN b/tests/frac_test/RUN
new file mode 100755
index 0000000..f881323
--- /dev/null
+++ b/tests/frac_test/RUN
@@ -0,0 +1,7 @@
+rm iceberg_trajectories.nc
+rm iceberg_trajectories.nc.*
+rm bond_trajectories.nc
+rm bond_trajectories.nc.*
+srun -n9 ./../../build/bergs.x
+
+
diff --git a/tests/frac_test/RUN1p b/tests/frac_test/RUN1p
new file mode 100755
index 0000000..3dfc97d
--- /dev/null
+++ b/tests/frac_test/RUN1p
@@ -0,0 +1,7 @@
+rm iceberg_trajectories.nc
+rm iceberg_trajectories.nc.*
+rm bond_trajectories.nc
+rm bond_trajectories.nc.*
+srun -n1 ./../../build/bergs.x
+
+
diff --git a/tests/frac_test/animate_trajectories.py b/tests/frac_test/animate_trajectories.py
new file mode 100755
index 0000000..ca7d5cd
--- /dev/null
+++ b/tests/frac_test/animate_trajectories.py
@@ -0,0 +1,140 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+import matplotlib.pyplot as plt
+from matplotlib.animation import FuncAnimation
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
+                    help=''' provide filename to plot''')
+    parser.add_argument('-s', type=int, default='4000',
+                    help='''plotted particle size''')  
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+
+def main(args):
+
+    print('reading file')
+
+    filename=args.fname
+    psize=args.s
+    #filename = 'iceberg_trajectories.nc'
+    field = 'lon'
+    field2 = 'lat'
+
+    with nc.Dataset(filename) as file:
+        x = file.variables['lon'][:]/1.e3
+        y = file.variables['lat'][:]/1.e3
+        day = file.variables['day'][:]
+        length = file.variables['length'][:]
+        width = file.variables['width'][:]
+
+        
+    radius = length*width*(1/(2*np.sqrt(3)))
+
+    crop=False
+    tc=1.25
+    if crop:
+        x=x[day<=tc]
+        y=y[day<=tc]
+        day=day[day<=tc]
+
+    ud = np.unique(day)
+    t = ud[0]
+
+    # frame info
+    num_frames = len(ud)
+    movie_len = 10.0 #seconds
+    frame_len = 1000.0*movie_len/num_frames
+
+    xmin = 0
+    xmax = 30 #45 #30
+    ymin = 7.5 #0 #7.5
+    ymax = 37.5 #45 #37.5
+
+    anim_running = True
+
+    def animate(i):
+
+        x1 = x[day == ud[i]]
+        y1 = y[day == ud[i]]
+        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
+
+        scat.set_offsets(data)
+
+        t = ud[i]
+        time_text.set_text('time = %.1f days' % t )
+
+        r1 = radius[day == ud[i]]
+        
+        scat.set_sizes(r1/psize)
+        return scat,time_text
+
+    def init():
+        scat.set_offsets([])
+        return scat,
+
+    def onClick(event):
+        global anim_running
+        if anim_running:
+            ani.event_source.stop()
+            anim_running = False
+        else:
+            ani.event_source.start()
+            anim_running = True
+
+    # Now we can do the plotting!
+    f = plt.figure(figsize=(5,5))
+    f.tight_layout()
+    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
+    #scat = ax1.scatter([],[],marker='o',facecolor='w',s=psize,edgecolor='red')
+    scat = ax1.scatter([],[],marker='o',facecolor='w',edgecolor='red')    
+    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
+
+    # Change major ticks to show every 20.
+    ax1.xaxis.set_major_locator(MultipleLocator(5))
+    ax1.yaxis.set_major_locator(MultipleLocator(5))
+
+    ax1.xaxis.set_minor_locator(MultipleLocator(1))
+    ax1.yaxis.set_minor_locator(MultipleLocator(1))
+
+    # Turn grid on for both major and minor ticks and style minor slightly
+    # differently.
+    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
+    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
+
+    ax1.set_xlabel('x (km)')
+    ax1.set_ylabel('y (km)')
+    ax1.set_title('Iceberg trajectory')
+
+    f.canvas.mpl_connect('button_press_event', onClick)
+
+    ani = FuncAnimation(
+        f,animate,init_func=init,frames=num_frames,
+        interval=frame_len,blit=True,repeat=True)
+
+    print('time',t)
+
+    plt.show()
+    #animation.save("iceberg_traj_animation.mp4")
+
+
+print('Script complete')
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
diff --git a/tests/frac_test/animate_trajectories_1pe.py b/tests/frac_test/animate_trajectories_1pe.py
new file mode 100755
index 0000000..931c727
--- /dev/null
+++ b/tests/frac_test/animate_trajectories_1pe.py
@@ -0,0 +1,189 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+import matplotlib.pyplot as plt
+from matplotlib.animation import FuncAnimation
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc.0000',
+                    help=''' provide filename to plot''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+
+
+def main(args):
+
+    print('reading file')
+
+    filename=args.fname
+    #filename = 'iceberg_trajectories.nc'
+    field = 'lon'
+    field2 = 'lat'
+
+    with nc.Dataset(filename) as file:
+        x = file.variables['lon'][:]/1.e3
+        y = file.variables['lat'][:]/1.e3
+        day = file.variables['day'][:]
+        hs = file.variables['halo_berg'][:]
+        #hs = file.variables['conglom_id'][:]        
+
+    #hs = hs+1
+    ud = np.unique(day)
+    t = ud[0]
+
+    print('unique hs',np.unique(hs))
+
+    # frame info
+    num_frames = len(ud)
+    movie_len = 10.0 #seconds
+    frame_len = 1000.0*movie_len/num_frames
+
+    xmin = np.floor(min(min(x),min(y),-5))
+    xmax = np.ceil(max(max(x),max(y),35))
+    ymin = xmin
+    ymax = xmax
+
+    anim_running = True
+
+    def animate(i):
+
+        x1 = x[day == ud[i]]
+        y1 = y[day == ud[i]]
+        hstat = hs[day == ud[i]]
+        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
+
+        cstring=[]
+        for j in range(len(hstat)):
+            if (hstat[j]<0):
+                cstring.append("m")
+            elif (hstat[j]==0):
+                cstring.append("b")
+            elif (hstat[j]==1):
+                cstring.append("r")
+            elif (hstat[j]==2):
+                cstring.append("g")
+            elif (hstat[j]==3):
+                cstring.append("k")
+            elif (hstat[j]==4):
+                cstring.append("c")
+            elif (hstat[j]==5):
+                cstring.append("y")
+            elif (hstat[j]==6):
+                cstring.append("w")
+            elif (hstat[j]==10):                
+                cstring.append("c")
+            # else:
+            #     cstring.append("y")
+
+        scat.set_offsets(data)
+        scat.set_color(cstring)
+        scat.set_edgecolor('k')
+
+        t = ud[i]
+        time_text.set_text('time = %.1f days' % t )
+        return scat,time_text
+
+    def init():
+        scat.set_offsets([])
+        return scat,
+
+    def onClick(event):
+        global anim_running
+        if anim_running:
+            ani.event_source.stop()
+            anim_running = False
+        else:
+            ani.event_source.start()
+            anim_running = True
+
+    # Now we can do the plotting!
+    f = plt.figure(figsize=(5,5))
+    f.tight_layout()
+    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
+    scat = ax1.scatter([],[],marker='o',s=30)
+    #scat = ax1.scatter([],[],marker='o',facecolor='w',s=60,edgecolor='red')
+    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
+
+    # Change major ticks to show every 20.
+    ax1.xaxis.set_major_locator(MultipleLocator(5))
+    ax1.yaxis.set_major_locator(MultipleLocator(5))
+
+    ax1.xaxis.set_minor_locator(MultipleLocator(1))
+    ax1.yaxis.set_minor_locator(MultipleLocator(1))
+
+    # Turn grid on for both major and minor ticks and style minor slightly
+    # differently.
+    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
+    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
+
+    ax1.set_xlabel('x (km)')
+    ax1.set_ylabel('y (km)')
+    ax1.set_title('Iceberg trajectory')
+
+    f.canvas.mpl_connect('button_press_event', onClick)
+
+    ani = FuncAnimation(
+        f,animate,init_func=init,frames=num_frames,
+        interval=frame_len,blit=True,repeat=True)
+
+    print('time',t)
+
+    plt.plot([0,0],[0,30],'k-',lw=1)
+    plt.plot([10,10],[0,30],'k-',lw=1)
+    plt.plot([20,20],[0,30],'k-',lw=1)
+    plt.plot([30,30],[0,30],'k-',lw=1)
+    plt.plot([0,30],[0,0],'k-',lw=1)
+    plt.plot([0,30],[10,10],'k-',lw=1)
+    plt.plot([0,30],[20,20],'k-',lw=1)
+    plt.plot([0,30],[30,30],'k-',lw=1)
+
+
+    h=3 #halo width
+    w=h-1
+
+    x1=0; x2=10; x3=20; x4=30
+    y1=0; y2=10; y3=20; y4=30    
+    
+
+    plt.plot([x1-w,x1-w],[y1-w,y4+h],'b:',lw=1)
+    plt.plot([x1+h,x1+h],[y1-w,y4+h],'b:',lw=1)
+    plt.plot([x2-w,x2-w],[y1-w,y4+h],'b:',lw=1)
+    plt.plot([x2+h,x2+h],[y1-w,y4+h],'b:',lw=1)
+    plt.plot([x3-w,x3-w],[y1-w,y4+h],'b:',lw=1)
+    plt.plot([x3+h,x3+h],[y1-w,y4+h],'b:',lw=1)
+    plt.plot([x4-w,x4-w],[y1-w,y4+h],'b:',lw=1)
+    plt.plot([x4+h,x4+h],[y1-w,y4+h],'b:',lw=1) 
+       
+
+    plt.plot([x1-w,x4+h],[y1-w,y1-w],'b:',lw=1)
+    plt.plot([x1-w,x4+h],[y1+h,y1+h],'b:',lw=1)
+    plt.plot([x1-w,x4+h],[y2-w,y2-w],'b:',lw=1)
+    plt.plot([x1-w,x4+h],[y2+h,y2+h],'b:',lw=1)
+    plt.plot([x1-w,x4+h],[y3-w,y3-w],'b:',lw=1)
+    plt.plot([x1-w,x4+h],[y3+h,y3+h],'b:',lw=1)
+    plt.plot([x1-w,x4+h],[y4-w,y4-w],'b:',lw=1)
+    plt.plot([x1-w,x4+h],[y4+h,y4+h],'b:',lw=1)
+
+    plt.show()
+    #animation.save("iceberg_traj_animation.mp4")
+
+
+print('Script complete')
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
diff --git a/tests/frac_test/diag_table b/tests/frac_test/diag_table
new file mode 100644
index 0000000..c1c8819
--- /dev/null
+++ b/tests/frac_test/diag_table
@@ -0,0 +1,3 @@
+"icebergs test"
+1 1 1 0 0 0
+
diff --git a/tests/frac_test/input.nml b/tests/frac_test/input.nml
new file mode 100644
index 0000000..0ea5017
--- /dev/null
+++ b/tests/frac_test/input.nml
@@ -0,0 +1,186 @@
+
+&icebergs_driver_nml
+  ni=45 !number of elements, x direction
+  nj=45 !number of elements, y direction
+  ibdt=900!1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=24 !total simulation hours
+  write_time_inc = 1!48 !increment at which time is written to screen
+  nmax=999999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.true.
+  collision_test=.false.
+  grounding_test=.false.
+  bump_depth=9999.0 !(m) depth of top of gaussian bump below sea level
+/
+
+&icebergs_nml
+
+    !defaults given in parentheses:
+    monitor_energy=.true. !(F)save total elastic (spring+collision),external,dissipated,&fracture energy
+    new_mts=.true. !(F) If T, implicit accel is added 50% at the current time step and 50% at the next time step
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=20  !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=2000 !2500 !2500 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=0.5e-8!4.471938678723104 !0.5e-8 !1.e-8 !(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=3.16e6 !friction drag param
+    h_to_init_grounding=200.0 !300.0 !150.0 !300.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.false. !(T) remove unneeded bergs after PEs transfers
+
+    !fracture_criterion='strain' !('none') 'strain_rate','strain','stress',or 'none'
+    !!here, try setting scaling 1.0 if force_convergence=.false., 0.5 if force_convergence=.true.
+    !frac_thres_scaling = 0.5 !(1) scales frac_thres_n and frac_thres_t
+    !frac_thres_n = 0.018  !normal fracture strain threshold
+    !frac_thres_t = 0.!0.05076 !tangential fracture strain threshold
+
+    !fracture_criterion='strain_rate' !('none') 'strain_rate','strain','stress',or 'none'
+    !frac_thres_scaling = 1 !(1) scales frac_thres_n and frac_thres_t
+    !frac_thres_n = 2.e-6  !normal fracture strain threshold
+    !frac_thres_t = 0!1.e-5 !tangential fracture strain threshold
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain','stress',or 'none'
+    !here, try setting scaling 1.0 if force_convergence=.false., 0.5 if force_convergence=.true.
+    frac_thres_scaling = 1.0 !(1) scales frac_thres_n and frac_thres_t
+    frac_thres_n = 0.!8000.0  !normal fracture strain threshold
+    frac_thres_t = 0.!12000.0 !0.05076 !tangential fracture strain threshold
+
+    halo=3 !(4) halo width
+    Lx=45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    rho_bergs=850. ! (850) iceberg density
+    spring_coef=1.e-5!4471.938678723104 !7.8e-3(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    radial_damping_coef=0.0 !(1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.false. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0.0 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.false. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.false. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.true. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=24000 ! (24) Period between verbose messages
+    traj_sample_hrs=0 !(24) sampling period for trajectory storage
+    traj_write_hrs=0 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    !require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.!(F) Init bond b/w bergs if dist<1.25*radius
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/frac_test/makeberg/RUN b/tests/frac_test/makeberg/RUN
new file mode 100755
index 0000000..d985f3f
--- /dev/null
+++ b/tests/frac_test/makeberg/RUN
@@ -0,0 +1,3 @@
+rm ./output_files/Generic*
+./makeberg.py
+cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
\ No newline at end of file
diff --git a/tests/frac_test/makeberg/makeberg.py b/tests/frac_test/makeberg/makeberg.py
new file mode 100755
index 0000000..be410b2
--- /dev/null
+++ b/tests/frac_test/makeberg/makeberg.py
@@ -0,0 +1,376 @@
+#!/usr/bin/env python
+import numpy as np
+import math
+from netCDF4 import Dataset
+from pylab import *
+#import pdb
+import netCDF4 as nc
+
+#
+# Initialize 2 iceberg elements, which can later be bonded in the fortran code if needed
+#
+
+def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
+
+	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
+	# To copy the global attributes of the netCDF file
+
+	#Input and output files
+	#Create Empty restart file. This is later read so that the attributes can be used.
+	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
+	create_empty_iceberg_restart_file(Empty_restart_filename)
+	#Empty_restart_filename='input_files/icebergs.res.nc'
+
+	#Read empty restart file
+	f=Dataset(Empty_restart_filename,'r') # r is for read only
+	#Write a new restart file
+	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
+
+	for attname in f.ncattrs():
+		    setattr(g,attname,getattr(f,attname))
+
+
+	# To copy the dimension of the netCDF file
+	for dimname,dim in f.dimensions.iteritems():
+		# if you want to make changes in the dimensions of the new file
+		# you should add your own conditions here before the creation of the dimension.
+		#g.createDimension(dimname,len(dim))
+		g.createDimension(dimname,Number_of_bergs)
+
+	# To copy the variables of the netCDF file
+
+	for varname,ncvar in f.variables.iteritems():
+		# if you want to make changes in the variables of the new file
+		# you should add your own conditions here before the creation of the variable.
+		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
+		#Proceed to copy the variable attributes
+		for attname in ncvar.ncattrs():
+			setattr(var,attname,getattr(ncvar,attname))
+		#Finally copy the variable data to the new created variable
+		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
+
+		if varname=='i':
+			var[:]=Number_of_bergs
+
+		if varname=='iceberg_num':
+			for j in range(Number_of_bergs):
+				#var[j]=j+1
+				var[j]=iceberg_num[j]
+
+		if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
+		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
+		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
+		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
+			var[:]=0
+
+                if varname=='uvel':
+                        var[:]=uvel
+
+                if varname=='vvel':
+                        var[:]=vvel
+
+		if varname=='mass_scaling':
+			var[:]=mass_scaling
+
+		if varname=='thickness':
+			for j in range(Number_of_bergs):
+				var[j]=thickness[j]
+
+		if varname=='mass':
+			for j in range(Number_of_bergs):
+				var[j]=mass[j]
+
+		if varname=='width'  or varname=='length':
+			for j in range(Number_of_bergs):
+				var[j]=width[j]
+
+		if varname=='lon':
+			for j in range(Number_of_bergs):
+				var[j]=lon[j]
+
+		if varname=='lat':
+			for j in range(Number_of_bergs):
+				var[j]=lat[j]
+
+		if varname=='static_berg':
+			for j in range(Number_of_bergs):
+				var[j]=static_berg[j]
+
+
+	f.close()
+	g.close()
+
+
+def create_empty_iceberg_restart_file(Empty_restart_filename):
+
+	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
+
+	i=f.createDimension('i', None)
+	lon=f.createVariable('i','i')
+
+	lon=f.createVariable('lon','d',('i'))
+	lon.long_name = "longitude" ;
+	lon.units = "degrees_E" ;
+	lon.checksum = "               0" ;
+
+	lat=f.createVariable('lat','d',('i'))
+	lat.long_name = "latitude" ;
+	lat.units = "degrees_N" ;
+	lat.checksum = "               0" ;
+
+	uvel=f.createVariable('uvel','d',('i'))
+	uvel.long_name = "zonal velocity" ;
+	uvel.units = "m/s" ;
+	uvel.checksum = "               0" ;
+
+	vvel=f.createVariable('vvel','d',('i'))
+	vvel.long_name = "meridional velocity" ;
+	vvel.units = "m/s" ;
+	vvel.checksum = "               0" ;
+
+	mass=f.createVariable('mass','d',('i'))
+	mass.long_name = "mass" ;
+	mass.units = "kg" ;
+	mass.checksum = "               0" ;
+
+	axn=f.createVariable('axn','d',('i'))
+	axn.long_name = "explicit zonal acceleration" ;
+	axn.units = "m/s^2" ;
+	axn.checksum = "               0" ;
+
+	ayn=f.createVariable('ayn','d',('i'))
+	ayn.long_name = "explicit meridional acceleration" ;
+	ayn.units = "m/s^2" ;
+	ayn.checksum = "               0" ;
+
+	bxn=f.createVariable('bxn','d',('i'))
+	bxn.long_name = "inplicit zonal acceleration" ;
+	bxn.units = "m/s^2" ;
+	bxn.checksum = "               0" ;
+
+	byn=f.createVariable('byn','d',('i'))
+	byn.long_name = "implicit meridional acceleration" ;
+	byn.units = "m/s^2" ;
+	byn.checksum = "               0" ;
+
+	ine=f.createVariable('ine','i',('i'))
+	ine.long_name = "i index" ;
+	ine.units = "none" ;
+	ine.packing = 0 ;
+	ine.checksum = "               0" ;
+
+	jne=f.createVariable('jne','i',('i'))
+	jne.long_name = "j index" ;
+	jne.units = "none" ;
+	jne.packing = 0 ;
+	jne.checksum = "               0" ;
+
+	thickness=f.createVariable('thickness','d',('i'))
+	thickness.long_name = "thickness" ;
+	thickness.units = "m" ;
+	thickness.checksum = "               0" ;
+
+	width=f.createVariable('width','d',('i'))
+	width.long_name = "width" ;
+	width.units = "m" ;
+	width.checksum = "               0" ;
+
+	length=f.createVariable('length','d',('i'))
+	length.long_name = "length" ;
+	length.units = "m" ;
+	length.checksum = "               0" ;
+
+	start_lon=f.createVariable('start_lon','d',('i'))
+	start_lon.long_name = "longitude of calving location" ;
+	start_lon.units = "degrees_E" ;
+	start_lon.checksum = "               0" ;
+
+	start_lat=f.createVariable('start_lat','d',('i'))
+	start_lat.long_name = "latitude of calving location" ;
+	start_lat.units = "degrees_N" ;
+	start_lat.checksum = "               0" ;
+
+	start_year=f.createVariable('start_year','i',('i'))
+	start_year.long_name = "calendar year of calving event" ;
+	start_year.units = "years" ;
+	start_year.packing = 0 ;
+	start_year.checksum = "               0" ;
+
+	iceberg_num=f.createVariable('iceberg_num','i',('i'))
+	iceberg_num.long_name = "identification of the iceberg" ;
+	iceberg_num.units = "dimensionless" ;
+	iceberg_num.packing = 0 ;
+	iceberg_num.checksum = "               0" ;
+
+	start_day=f.createVariable('start_day','d',('i'))
+	start_day.long_name = "year day of calving event" ;
+	start_day.units = "days" ;
+	start_day.checksum = "               0" ;
+
+	start_mass=f.createVariable('start_mass','d',('i'))
+	start_mass.long_name = "initial mass of calving berg" ;
+	start_mass.units = "kg" ;
+	start_mass.checksum = "               0" ;
+
+	mass_scaling=f.createVariable('mass_scaling','d',('i'))
+	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
+	mass_scaling.units = "none" ;
+	mass_scaling.checksum = "               0" ;
+
+	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
+	mass_of_bits.long_name = "mass of bergy bits" ;
+	mass_of_bits.units = "kg" ;
+	mass_of_bits.checksum = "               0" ;
+
+	heat_density=f.createVariable('heat_density','d',('i'))
+	heat_density.long_name = "heat density" ;
+	heat_density.units = "J/kg" ;
+	heat_density.checksum = "               0" ;
+
+	halo_berg=f.createVariable('halo_berg','d',('i'))
+	halo_berg.long_name = "halo_berg" ;
+	halo_berg.units = "dimensionless" ;
+	halo_berg.checksum = "               0" ;
+
+	static_berg=f.createVariable('static_berg','d',('i'))
+	static_berg.long_name = "static_berg" ;
+	static_berg.units = "dimensionless" ;
+	static_berg.checksum = "               0" ;
+
+	f.sync()
+	f.close()
+
+
+
+#-----------------------------------#
+#               Main                #
+#-----------------------------------#
+
+just2particles=False
+flip2ndconglom=True#False
+offset2ndconglom=True#False
+
+grdxmin=0; grdxmax=45000e3
+grdymin=0; grdymax=45000e3
+grdres=1000.0
+R_frac=0.3375 #225
+R_frac2=0.3375 #45
+radius=(np.sqrt(3)/2.)*(R_frac*grdres) #S is < 0.5 grid res
+radius2=(np.sqrt(3)/2.)*(R_frac2*grdres) #S is < 0.5 grid res
+thickness1=300.0
+thickness2=200.0
+rho_ice=850.0
+
+
+nbergs=2 #number of conglomerates
+
+#center coords of each (rectangular) conglomerate berg (CB=conglomerate berg)
+CBxc=np.array([10500, 22500]); CByc=np.array([22500, 22500])
+#CBxc=np.array([9500, 17500]); CByc=np.array([22500, 22500])
+
+#side lengths
+CBxl=np.array([2500, 7500]); CByl=np.array([7500, 2500])
+#CBxl=np.array([2500, 2500]); CByl=np.array([7500, 7500])
+#CBxl=np.array([3000, 3000]); CByl=np.array([3000, 3000])
+CByl=CByl.astype(int); CBxl=CBxl.astype(int)
+
+#--- xmax, xmin, ymax, ymin for each CB --
+CBxmin=CBxc-(0.5*CBxl); CBxmax=CBxc+(0.5*CBxl)
+CBymin=CByc-(0.5*CByl); CBymax=CByc+(0.5*CByl)
+#this shouldn't happen:
+CBxmin[CBxmin<grdxmin]=grdxmin; CBxmax[CBxmax>grdxmax]=grdxmax
+CBymin[CBxmin<grdymin]=grdymin; CBymax[CBymax>grdymax]=grdymax
+CBxc=0.5*(CBxmin+CBxmax); CByc=0.5*(CBymin+CBymax)
+
+#if just want one particle per CB
+if just2particles:
+        CBxmin=CBxc; CBxmax=CBxc
+        CBymin=CByc; CBymax=CByc
+
+#--- min and max thicknesses for each CB ---
+h1=thickness1; h2=thickness2
+CBhmax=np.array([h1,h2]); CBhmin=np.array([h1,h2])
+
+#radii
+CBrad=np.array([radius,radius2])
+print('radii',CBrad)
+
+berg_x=[]; berg_y=[]
+berg_id=[]; berg_static=[]
+berg_width=[]; berg_bonds=[]
+berg_h=[]; berg_mass_scaling=[]
+berg_mass=[]
+berg_uvel=[]; berg_vvel=[]
+
+berg_count=0
+
+for i in range(nbergs):
+        x_start=CBxmin[i]+(CBrad[i]*2./np.sqrt(3))
+
+        if flip2ndconglom and i>0:
+                x_start=CBxmax[i]-(CBrad[i]*2./np.sqrt(3))
+
+        #pdb.set_trace()
+        if x_start>CBxmax[i]:
+                x_start=CBxmax[i]
+        y_start0=CBymin[i]+CBrad[i]
+        if y_start0>CBymax[i]:
+                y_start0=CBymax[i]
+        element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*(CBrad[i])**2)
+        #H (thickness) is a linear function of a berg element's position from the
+        #center of the CB. H=Hmax at the center of the CB and H=Hmin at a corner of the
+        #CB, where the dist of a corner from the center is:
+        cdistb=np.sqrt((CBxmin[i]-CBxc[i])**2+(CBymin[i]-CByc[i])**2)
+        j=0
+        x_val=x_start
+        offset=0.0
+        if (i==0):
+                uvel=0.05#0.075
+        else:
+                uvel=-0.15#-0.05
+                if (offset2ndconglom):
+                        offset=250.0
+        vvel=0.025#0.01
+        #uvel=0;vvel=0
+        #berg_count_start=berg_count
+        while x_val<=CBxmax[i] and x_val>=CBxmin[i]:
+                y_start=y_start0+((j%2)*CBrad[i])+offset
+                k=0
+                y_val=y_start
+                while y_val<=(CBymax[i]+offset):
+                        berg_count=berg_count+1
+                        berg_id.append(berg_count)
+                        berg_x.append(x_val)
+                        berg_y.append(y_val)
+                        berg_width.append(sqrt(element_area))
+                        #dist of berg elem from center of CB
+                        bdistc=np.sqrt((x_val-CBxc[i])**2+(y_val-CByc[i])**2)
+                        bh=CBhmin[i]*bdistc/cdistb + CBhmax[i]*(1-bdistc/cdistb)
+                        if (just2particles):
+                                bh=h1
+                        berg_h.append(bh) #thickness
+                        berg_mass_scaling.append(1)
+                        berg_mass.append(bh*rho_ice*element_area)
+                        berg_static.append(0)
+                        berg_uvel.append(uvel)
+                        berg_vvel.append(vvel)
+                        # if (x_val<22000):
+                        #         berg_vvel.append(vvel)
+                        # else:
+                        #         berg_vvel.append(0.4)
+                        #berg_CBid.append(i)
+                        k=k+1
+                        y_val=y_start+(2*k*CBrad[i])
+                j=j+1
+                if flip2ndconglom and i>0:
+                        x_val=x_start-(np.sqrt(3)*CBrad[i]*j)
+                else:
+                        x_val=x_start+(np.sqrt(3)*CBrad[i]*j)
+
+print('Number of bergs',berg_count)
+
+#pdb.set_trace()
+
+#Create iceberg restart file
+Ice_geometry_source='Generic'
+Create_iceberg_restart_file(berg_count,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)
diff --git a/tests/plot_bond_strain.py b/tests/plot_bond_strain.py
new file mode 100755
index 0000000..49b2fe6
--- /dev/null
+++ b/tests/plot_bond_strain.py
@@ -0,0 +1,79 @@
+#!/usr/bin/env python3
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+import matplotlib.pyplot as plt
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Plot energy from bond trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-fname', type=str, default='bond_trajectories.nc',
+                    help=''' provide filename to plot''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+
+
+def main(args):
+
+    print('reading file')
+
+    filename=args.fname
+
+    with nc.Dataset(filename) as file:
+        rot    = file.variables['rotation'][:]
+        rrot    = file.variables['rel_rotation'][:]
+        ns  = file.variables['n_strain'][:]
+        nsr   = file.variables['n_strain_rate'][:]
+        day   = file.variables['day'][:]
+
+    print('rrotmin','rrotmax',np.min(nsr),np.max(nsr))
+
+    ud = np.unique(day)
+    dt = ud[1]-ud[0]
+
+    print('dt',dt)
+
+    fig = plt.figure(1)
+    ax = plt.subplot(111)
+    
+    for j in range(len(ud)):
+
+        #ENERGY STUFF
+        rot1 = rot[day == ud[j]]
+        rrot1 = rrot[day == ud[j]]
+        ns1 = ns[day == ud[j]]
+        nsr1 = nsr[day == ud[j]]
+        ud1 = day[day == ud[j]]
+
+
+        ax.plot(ud1, rot1,  color='k', label='rotation')
+        ax.plot(ud1, rrot1, color='c', label='relative rot', linestyle='dashed')
+        #ax.plot(ud1, ns1, color='b', label='normal strain', linestyle='dashed')
+        ax.plot(ud1, nsr1, color='g', label='normal strain rate', linestyle='dashed')
+
+
+    #ax.legend(loc="upper right")
+    chartBox = ax.get_position()
+    ax.set_position([chartBox.x0, chartBox.y0, chartBox.width*0.6, chartBox.height])
+    ax.legend(loc='upper center', bbox_to_anchor=(1.45, 0.8), shadow=True, ncol=1)
+    plt.xlabel('time (days)')
+    plt.ylabel('strains')
+
+    plt.show()
+
+print('Script complete')
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
diff --git a/tests/plot_energy.py b/tests/plot_energy.py
index f22f89b..358e1f5 100755
--- a/tests/plot_energy.py
+++ b/tests/plot_energy.py
@@ -59,9 +59,10 @@ def main(args):
         mass=mass[day<=tc]
         x=x[day<=tc]
         y=y[day<=tc]
-        day=day[day<=tc]
         vx2=vx2[day<=tc]
-        vy2=vy2[day<=tc]
+        vy2=vy2[day<=tc]       
+        day=day[day<=tc]
+
 
 
     # vx=np.copy(vx2); vy=np.copy(vy2)

From decca5cc2b41afc1a738a698f5a40070d535335a Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Thu, 18 Feb 2021 19:27:32 -0500
Subject: [PATCH 277/361] Many changes regarding reading/writing restart files,
 saving trajectories, and allocating the iceberg/bond variables in preparation
 for full coupling of this version of the iceberg code with MOM6. Changed the
 value for traj_sample_hrs and traj_write_hrs that would always force output
 every timestep from 0 to -1, which fixes a conflict when running with MOM6.
 Added a 'damage' variable that weakens the stress threshold in areas of
 pre-existing rifts, crevasses, etc that were inherited from when iceberg was
 still attached to the ice shelf. Added some experimental options for DEM-mode
 that (1) track the shear force for fracture purposes but ignore its influence
 during berg interactions or (2) set the shear force to zero entirely.

---
 src/icebergs.F90                              | 153 ++--
 src/icebergs_framework.F90                    | 809 ++++++++++++++----
 src/icebergs_io.F90                           | 649 ++++++++++++--
 tests/collision_test_mts/input.nml            |   2 +-
 tests/dem_ground_frac_test/input.nml          |  29 +-
 tests/dem_ground_frac_test/input_dem.nml      |  26 +-
 tests/dem_ground_frac_test/input_dem_comp.nml | 192 +++++
 tests/dem_ground_frac_test/input_dem_orig.nml | 191 +++++
 tests/dem_ground_frac_test/input_reg.nml      |  29 +-
 tests/dem_ground_frac_test/input_reg_comp.nml | 192 +++++
 .../dem_ground_frac_test/input_reg_stress.nml |  10 +-
 .../dem_ground_frac_test/makeberg/makeberg.py |   4 +-
 tests/dem_ssbeam_test/input.nml               |   4 +-
 tests/energy_test/input.nml                   |   4 +-
 tests/energy_test2/input.nml                  |   4 +-
 tests/energy_test3/input.nml                  |   4 +-
 tests/frac_test/input.nml                     |   4 +-
 tests/ground_frac_test/input.nml              |   4 +-
 18 files changed, 1934 insertions(+), 376 deletions(-)
 create mode 100644 tests/dem_ground_frac_test/input_dem_comp.nml
 create mode 100644 tests/dem_ground_frac_test/input_dem_orig.nml
 create mode 100644 tests/dem_ground_frac_test/input_reg_comp.nml

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 15f0178..797fd85 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -52,6 +52,8 @@ module ice_bergs
 use ice_bergs_framework, only: monitor_energy, energy_tests_init, new_mts
 use ice_bergs_framework, only: dem_tests_init
 use ice_bergs_framework, only: dem, init_dem_params
+use ice_bergs_framework, only: set_constant_interaction_length_and_width
+use ice_bergs_framework, only: use_damage, damage_test_1_init
 
 use ice_bergs_io,        only: ice_bergs_io_init, write_restart, write_trajectory, write_bond_trajectory
 use ice_bergs_io,        only: read_restart_bergs, read_restart_calving
@@ -173,11 +175,15 @@ subroutine icebergs_init(bergs, &
     check_bond_quality=.True.
     call count_bonds(bergs, nbonds,check_bond_quality)
     call assign_n_bonds(bergs)
-    call fracture_testing_initialization(bergs)
+    !call fracture_testing_initialization(bergs)
   endif
 
   if (bergs%uniaxial_test .or. bergs%dem_beam_test>0) call dem_tests_init(bergs)
+  if (bergs%damage_test_1) call damage_test_1_init(bergs)
 
+  if (bergs%constant_interaction_LW .and. (bergs%constant_length==0. .or. bergs%constant_width==0.)) then
+    call set_constant_interaction_length_and_width(bergs)
+  endif
 end subroutine icebergs_init
 
 subroutine debugwriteandstop(bergs)
@@ -565,8 +571,6 @@ subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
 
         other_berg=>bergs%list(grdi,grdj)%first
         do while (associated(other_berg)) ! loop over all other bergs
-          !call contact_eligibility(berg,other_berg,contact_eligible,c_crit_dist)
-          !if (contact_eligible) then
           if (other_berg%conglom_id.ne.berg%conglom_id) then
             call calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,  &
               P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded)
@@ -606,43 +610,6 @@ subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
   endif
 end subroutine interactive_force
 
-!>Determines whether two bergs interact via contact. If they are w/in the same conglomerate,
-!!returns a flag to set the crit dist for contact to the sum of their radii
-subroutine contact_eligibility(berg,other_berg,contact_eligible,c_crit_dist)
-  ! Arguments
-  type(iceberg), pointer :: berg !< Primary berg
-  type(iceberg), pointer :: other_berg !< Berg that primary is interacting with
-  logical, intent(out) :: contact_eligible !< Are the berg eligible for interaction via contact?
-  logical, intent(out) :: c_crit_dist !<Flag to use crit_dist=R1+R2 for contact bergs w/in the same conglom
-  ! Local variables
-  type(iceberg), pointer :: this
-  type(bond), pointer :: current_bond
-
-  if (other_berg%conglom_id.ne.berg%conglom_id) then
-    contact_eligible=.true. !Bergs are in different congloms. Contact eligible.
-    c_crit_dist=.false.
-  else
-    !Bergs in same conglom. Determine whether they are bonded:
-    current_bond=>berg%first_bond
-    do while (associated(current_bond))
-      this=>current_bond%other_berg
-      if (associated(this)) then
-        if (this%id .eq. other_berg%id) then !bergs are bonded and not eligible for contact
-          contact_eligible=.false.
-          c_crit_dist=.false.
-          return
-        endif
-      endif
-      current_bond=>current_bond%next_bond
-    enddo
-
-    !Bergs are not bonded are are contact eligible. The c_crit_dist flag sets the crit_dist to
-    !the sum of the two bergs' radii within calculate_force.
-    contact_eligible=.true.
-    c_crit_dist=.true.
-  endif
-end subroutine contact_eligibility
-
 
 !> Calculate interactive forces between two bergs
 subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1, &
@@ -680,25 +647,28 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
 
   if (berg%id .ne. other_berg%id) then
     ! From Berg 1
-    L1=berg%length
-    W1=berg%width
     T1=berg%thickness
-    M1=berg%mass
-    A1=L1*W1
     lon1=berg%lon_old; lat1=berg%lat_old
     !call rotpos_to_tang(lon1,lat1,x1,y1)
 
     ! From Berg 2
-    L2=other_berg%length
-    W2=other_berg%width
     T2=other_berg%thickness
-    M2=other_berg%mass
-    u2=other_berg%uvel_old !Old values are used to make it order invariant
-    v2=other_berg%vvel_old !Old values are used to make it order invariant
-    A2=L2*W2
     lon2=other_berg%lon_old; lat2=other_berg%lat_old !Old values are used to make it order invariant
 
     !call rotpos_to_tang(lon2,lat2,x2,y2)
+    u2=other_berg%uvel_old;  v2=other_berg%vvel_old !Old values are used to make it order invariant
+
+    if (bergs%constant_interaction_LW) then
+      ! use constant length and width here, just for interactions
+      A1=bergs%constant_length*bergs%constant_width !Berg 1 area
+      M1=A1*T1*bergs%rho_bergs                      !Berg 1 mass
+      A2=A1                                         !Berg 2 area
+      M2=A2*T2*bergs%rho_bergs                      !Berg 2 mass
+    else
+      ! use actual length and width of bergs
+      L1=berg%length; W1=berg%width; M1=berg%mass; A1=L1*W1                   !From Berg 1
+      L2=other_berg%length; W2=other_berg%width; M2=other_berg%mass; A2=L2*W2 !From Berg 2
+    endif
 
     dlon=lon1-lon2
     dlat=lat1-lat2
@@ -857,8 +827,8 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
   real, intent(inout) :: T_d !< Net torque from damping (Nm)
   logical, intent(in) :: savestress !< Save stress/tangential displacement on bond or not
   ! Local variables
-  real :: T1,M1,u1,v1,lon1,lat1,R1 ! Current iceberg
-  real :: T2,M2,u2,v2,lon2,lat2,R2 ! Other iceberg
+  real :: A1,T1,M1,u1,v1,lon1,lat1,R1 ! Current iceberg
+  real :: A2,T2,M2,u2,v2,lon2,lat2,R2 ! Other iceberg
   real :: dlon, dlat, lat_ref, dx_dlon, dy_dlat
   real :: r_dist_x, r_dist_y, r_dist
   real :: Rmin, delta, L, l0, youngs, Thick, T_Rmin, n1, n2
@@ -880,13 +850,23 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
 
     ! From Berg 1
     T1=berg%thickness
-    M1=berg%mass
     lon1=berg%lon_old; lat1=berg%lat_old
 
     ! From Berg 2
     T2=other_berg%thickness
-    M2=other_berg%mass
-    lon2=other_berg%lon_old; lat2=other_berg%lat_old !Old values are used to make it order invariant
+    lon2=other_berg%lon_old; lat2=other_berg%lat_old
+
+    if (bergs%constant_interaction_LW) then
+      ! use constant length and width here, just for interactions
+      A1=bergs%constant_length*bergs%constant_width !Berg 1 area
+      M1=A1*T1*bergs%rho_bergs                      !Berg 1 mass
+      A2=A1                                         !Berg 2 area
+      M2=A2*T2*bergs%rho_bergs                      !Berg 2 mass
+    else
+      ! use actual length and width of bergs
+      M1=berg%mass; A1=berg%length*berg%width                   !From Berg 1
+      M2=other_berg%mass; A2=other_berg%length*other_berg%width !From Berg 2
+    endif
 
     dlon=lon1-lon2; dlat=lat1-lat2
 
@@ -898,19 +878,20 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
     r_dist_x=dlon*dx_dlon
     r_dist_y=dlat*dy_dlat
     r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) ) !(Stern et al 2017, Eqn 3)
+    current_bond%length=r_dist
 
     !unit vec
     n1=r_dist_x/r_dist; n2=r_dist_y/r_dist
 
     !Stern et al 2017, Eqn 4: radius of circle inscribed within hexagon or square with area A1 or A2
     if (bergs%hexagonal_icebergs) then
-      R1=sqrt(berg%length*berg%width/(2.*sqrt(3.)))
-      R2=sqrt(other_berg%length*other_berg%width/(2.*sqrt(3.)))
+      R1=sqrt(A1/(2.*sqrt(3.)))
+      R2=sqrt(A2/(2.*sqrt(3.)))
     else !square packing
       !R1=sqrt(A1/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
       !R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
-      R1=0.5*sqrt(berg%length*berg%width)
-      R2=0.5*sqrt(other_berg%length*other_berg%width)
+      R1=0.5*sqrt(A1)
+      R2=0.5*sqrt(A2)
     endif
 
     !Rmin=min(R1,R2) !old
@@ -971,11 +952,11 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
 
       !add the new tangential displacement
       current_bond%tangd1=current_bond%tangd1+rtu*dt; current_bond%tangd2=current_bond%tangd2+rtv*dt
-      current_bond%length=r_dist
     endif
 
     !shear terms
     ss_factor=-L*Thick*youngs/(l0*2.0*(1.0+bergs%poisson))
+    if (bergs%ignore_tangential_force) ss_factor=0.
     Fs_x=ss_factor*current_bond%tangd1; Fs_y=ss_factor*current_bond%tangd2 !shear forces
     if (savestress) current_bond%sstress=sqrt(Fs_x**2+Fs_y**2)/(L*Thick) !shear stress
 
@@ -994,6 +975,10 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
     Fd_x = Fd_x-damping_coef*ur; Fd_y = Fd_y-damping_coef*vr  !linear damping force
     T_d  = T_d-damping_coef*(berg%ang_vel-other_berg%ang_vel) !damping torque
 
+    if (bergs%dem_shear_for_frac_only) then
+      Fs_x=0.; Fs_y=0.
+    endif
+
     !final forces
     T = T + (Ts + Tr) !torque
     F_x = F_x + Fn_x + Fs_x; F_y = F_y + Fn_y + Fs_y !linear forces
@@ -4351,14 +4336,14 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   if ( (bergs%traj_sample_hrs>0)  .and. (.not. bergs%ignore_traj) ) then
     if (mod(60*60*24*iday+ 60*60*ihr + 60.*imin + isec ,60*60*bergs%traj_sample_hrs).eq.0) &
       sample_traj=.true.
-  elseif (bergs%traj_sample_hrs==0) then
+  elseif (bergs%traj_sample_hrs==-1) then
     sample_traj=.true.
   endif
   write_traj=.false.
   if ((bergs%traj_write_hrs>0) .and. (.not. bergs%ignore_traj))  then
      if (mod(60*60*24*iday+ 60*60*ihr + 60.*imin + isec ,60*60*bergs%traj_write_hrs).eq.0) &
        write_traj=.true.
-   elseif (bergs%traj_write_hrs==0) then
+   elseif (bergs%traj_write_hrs==-1) then
      write_traj=.true.
   endif
   lverbose=.false.
@@ -4569,7 +4554,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     elseif ((bergs%contact_distance>0.) .or. (bergs%contact_spring_coef .ne. bergs%spring_coef)) then
       call set_conglom_ids(bergs)
     endif
-    call orig_bond_length(bergs)
+    if (bergs%iceberg_bonds_on) call orig_bond_length(bergs)
 
     if (monitor_energy) then
       call energy_tests_init(bergs)
@@ -4601,7 +4586,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   call mpp_clock_begin(bergs%clock_mom)
 
   if (.not.bergs%Static_icebergs) then
-    if (.not. bergs%dem) call reset_bond_rotation(bergs)
+    if (bergs%iceberg_bonds_on .and. (.not. bergs%dem)) call reset_bond_rotation(bergs)
 
     if (bergs%mts) then
       call evolve_icebergs_mts(bergs)
@@ -5376,14 +5361,16 @@ subroutine calve_icebergs(bergs)
           newberg%vvel=0.
           newberg%uvel_prev=0.  !Added by Alex
           newberg%vvel_prev=0.  !Added by Alex
+          newberg%uvel_old=0.  !Added by Alex
+          newberg%vvel_old=0.  !Added by Alex
+          newberg%lon_prev=newberg%lon  !Added by Alex
+          newberg%lat_prev=newberg%lat  !Added by Alex
+          newberg%lon_old=newberg%lon  !Added by Alex
+          newberg%lat_old=newberg%lat  !Added by Alex
           newberg%axn=0. !Added by Alon
           newberg%ayn=0. !Added by Alon
           newberg%bxn=0. !Added by Alon
           newberg%byn=0. !Added by Alon
-          newberg%axn_fast=0. !Added by Alex
-          newberg%ayn_fast=0. !Added by Alex
-          newberg%bxn_fast=0. !Added by Alex
-          newberg%byn_fast=0. !Added by Alex
           newberg%mass=bergs%initial_mass(k)
           newberg%thickness=bergs%initial_thickness(k)
           newberg%width=bergs%initial_width(k)
@@ -5392,7 +5379,6 @@ subroutine calve_icebergs(bergs)
           newberg%start_lat=newberg%lat
           newberg%start_year=bergs%current_year
           newberg%id = generate_id(grd, i, j)
-          newberg%conglom_id=0
           newberg%start_day=bergs%current_yearday+ddt/86400.
           newberg%start_mass=bergs%initial_mass(k)
           newberg%mass_scaling=bergs%mass_scaling(k)
@@ -5400,6 +5386,35 @@ subroutine calve_icebergs(bergs)
           newberg%halo_berg=0.
           newberg%static_berg=0.
           newberg%heat_density=grd%stored_heat(i,j)/grd%stored_ice(i,j,k) ! This is in J/kg
+
+          if (bergs%mts) then
+            allocate(newberg%axn_fast,newberg%ayn_fast,newberg%bxn_fast,newberg%byn_fast,newberg%conglom_id)
+            newberg%axn_fast=0.; newberg%ayn_fast=0.; newberg%bxn_fast=0.; newberg%byn_fast=0.; newberg%conglom_id=0
+          endif
+
+          if (bergs%iceberg_bonds_on) then
+            allocate(newberg%n_bonds)
+            newberg%n_bonds=0
+          endif
+
+          if (bergs%dem) then
+            allocate(newberg%ang_vel,newberg%ang_accel,newberg%rot)
+            newberg%ang_vel=0.; newberg%ang_accel=0.; newberg%rot=0.
+          endif
+
+          if (monitor_energy) then
+            allocate(newberg%Ee,newberg%Ed,newberg%Eext,newberg%Ee_contact,newberg%Ed_contact,newberg%Efrac,&
+              newberg%Ee_temp,newberg%Ed_temp,newberg%Eext_temp,newberg%Ee_contact_temp,newberg%Ed_contact_temp)
+            newberg%Ee=0.; newberg%Ed=0.; newberg%Eext=0.; newberg%Ee_contact=0.; newberg%Ed_contact=0.
+            newberg%Efrac=0.; newberg%Ee_temp=0.; newberg%Ed_temp=0.;newberg%Eext_temp=0.;
+            newberg%Ee_contact_temp=0.; newberg%Ed_contact_temp =0.
+          endif
+
+          if (bergs%fracture_criterion .ne. 'none' .and. (.not. bergs%dem)) then
+            allocate(newberg%accum_bond_rotation)
+            newberg%accum_bond_rotation=0.
+          endif
+
           call add_new_berg_to_list(bergs%list(i,j)%first, newberg)
           calved_to_berg=bergs%initial_mass(k)*bergs%mass_scaling(k) ! Units of kg
           ! Heat content
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 8efb7aa..27384ae 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -18,9 +18,9 @@ module ice_bergs_framework
 
 implicit none ; private
 
-integer :: buffer_width=35 ! This should be a parameter
-integer :: buffer_width_traj=37 ! This should be a parameter
-integer :: buffer_width_bond_traj=16 !This should be a parameter
+integer :: buffer_width=33 ! This should be a parameter
+integer :: buffer_width_traj=35 ! This should be a parameter
+integer :: buffer_width_bond_traj=11 !This should be a parameter
 integer, parameter :: nclasses=10 ! Number of ice bergs classes
 
 !Local Vars
@@ -45,20 +45,23 @@ module ice_bergs_framework
 logical :: fix_restart_dates=.true. !< After a restart, check that bergs were created before the current model date
 logical :: do_unit_tests=.false. !< Conduct some unit tests
 logical :: force_all_pes_traj=.false. !< Force all pes write trajectory files regardless of io_layout
-logical :: mts=.false.
+logical :: mts=.false. !< Use multiple time stepping scheme
 logical :: new_mts=.false. !If T, implicit accel is added 50% at the current time step and 50% at the next time step
 logical :: save_bond_traj=.false. !<Save trajectory files for bonds
 logical :: ewsame=.false. !<(F) set T if periodic and 2 PEs along the x direction (zonal) (i.e. E/W PEs are the same)
 logical :: monitor_energy=.false. !<monitors energies: elastic (spring+collision), external, dissipated, fracture
+logical :: iceberg_bonds_on=.False. ! True=Allow icebergs to have bonds, False=don't allow.
 logical :: dem=.false. !< If T, run in DEM-mode with angular terms, variable stiffness, etc
+character(len=11) :: fracture_criterion !<'energy','stress','strain_rate','strain',or 'none'
+logical :: use_damage=.false. !< Damage on bonds. Can evolve and serve as fracture criterion, or just to represent weaker bond
 
 !Public params !Niki: write a subroutine to expose these
 public nclasses,buffer_width,buffer_width_traj,buffer_width_bond_traj
 public verbose, really_debug, debug, restart_input_dir,make_calving_reproduce,old_bug_bilin,use_roundoff_fix
 public ignore_ij_restart, use_slow_find,generate_test_icebergs,old_bug_rotated_weights,budget
 public orig_read, force_all_pes_traj
-public mts,new_mts,save_bond_traj,ewsame,monitor_energy
-public dem
+public mts,new_mts,save_bond_traj,ewsame,monitor_energy,iceberg_bonds_on
+public dem, fracture_criterion
 
 !Public types
 public icebergs_gridded, xyt, iceberg, icebergs, buffer, bond, bond_xyt
@@ -92,6 +95,7 @@ module ice_bergs_framework
 public fracture_testing_initialization, orig_bond_length
 public energy_tests_init,dem_tests_init
 public init_dem_params
+public set_constant_interaction_length_and_width,use_damage,damage_test_1_init
 
 !> Container for gridded fields
 type :: icebergs_gridded
@@ -215,12 +219,6 @@ module ice_bergs_framework
   real :: ayn
   real :: bxn
   real :: byn
-  real :: axn_fast
-  real :: ayn_fast
-  real :: bxn_fast
-  real :: byn_fast
-  integer :: n_bonds
-  real :: accum_bond_rotation
   real :: uvel_prev
   real :: vvel_prev
   real :: uo !< Zonal velocity of ocean (m/s)
@@ -243,28 +241,33 @@ module ice_bergs_framework
   integer :: year !< Year of this record (years)
   integer(kind=8) :: id = -1 !< Iceberg identifier
   type(xyt), pointer :: next=>null() !< Next link in list
-  real, allocatable :: Ee, Ed, Eext, Ee_contact, Ed_contact, Efrac !<energy stuff
-end type xyt
 
-!> A link in the trajectory record (diagnostic)
-type :: bond_xyt
-  real :: lon !< Longitude of bond (degree E or unit of grid coordinate)
-  real :: lat !< Latitude of bond (degree N or unit of grid coordinate)
-  integer :: year !< Year of this record (years)
-  real :: day !< Day of this record (days)
-  real :: length !<Length of bond
-  real :: n1 !<Unit vector, x-component
-  real :: n2 !<Unit vector, y-component
-  integer(kind=8) :: id1 !<ID of first berg
-  integer(kind=8) :: id2 !<ID of second berg
-  real :: rotation
-  real :: rel_rotation
-  real :: n_strain
-  real :: n_strain_rate
-  real :: spring_pe
-  type(bond_xyt), pointer :: next=>null() !< Next link in list
-  real, allocatable :: Ee, Ed
-end type bond_xyt
+    ! For MTS
+  real, allocatable :: axn_fast
+  real, allocatable :: ayn_fast
+  real, allocatable :: bxn_fast
+  real, allocatable :: byn_fast
+  ! If iceberg_bonds_on
+  integer, allocatable :: n_bonds
+  ! If frac
+  real, allocatable :: accum_bond_rotation
+  ! For optional energy monitoring
+  real, allocatable :: Ee !< Energy from bonds, elastic (J)
+  real, allocatable :: Ed !< Energy from bonds, damping (J)
+  real, allocatable :: Eext !< Energy from external forces (J)
+  real, allocatable :: Ee_contact !< Energy from contact, elastic (J)
+  real, allocatable :: Ed_contact !< Energy from contanct, damping (J)
+  real, allocatable :: Efrac !< Energy from breaking bonds (J)
+  real, allocatable :: Ee_temp !< Temporary storage: Energy from bonds, elastic (J)
+  real, allocatable :: Ed_temp !< Temporary storage: Energy from bonds, damping (J)
+  real, allocatable :: Eext_temp !< Temporary storage: Energy from external forces (J)
+  real, allocatable :: Ee_contact_temp !< Temporary storage: Energy from contact, elastic (J)
+  real, allocatable :: Ed_contact_temp !< Temporary storage: Energy from damping, elastic (J)
+  ! For DEM-mode
+  real, allocatable :: ang_vel !< Angular velocity
+  real, allocatable :: ang_accel !< Angular acceleration
+  real, allocatable :: rot !< Accumulated rotation
+end type xyt
 
 !> An iceberg object, used as a link in a linked list
 type :: iceberg
@@ -285,12 +288,6 @@ module ice_bergs_framework
   real :: ayn
   real :: bxn
   real :: byn
-  real :: axn_fast
-  real :: ayn_fast
-  real :: bxn_fast
-  real :: byn_fast
-  integer :: n_bonds
-  real :: accum_bond_rotation
   real :: uvel_prev
   real :: vvel_prev
   real :: uvel_old
@@ -308,7 +305,6 @@ module ice_bergs_framework
   real :: static_berg  ! Equal to 1 for icebergs which are static (not allowed to move). Might be extended to grounding later.
   integer :: start_year !< Year that berg was created (years)
   integer(kind=8) :: id !< Iceberg identifier
-  integer :: conglom_id !<ID for a conglomerate
   integer :: ine !< Nearest i-index in NE direction (for convenience)
   integer :: jne !< Nearest j-index in NE direction (for convenience)
   real :: xi !< Non-dimensional x-coordinate within current cell (0..1)
@@ -329,6 +325,17 @@ module ice_bergs_framework
   real :: od !< Ocean depth
   type(xyt), pointer :: trajectory=>null() !< Trajectory for this berg
   type(bond), pointer :: first_bond=>null() !< First element of bond list.
+
+  ! For MTS
+  real, allocatable :: axn_fast
+  real, allocatable :: ayn_fast
+  real, allocatable :: bxn_fast
+  real, allocatable :: byn_fast
+  integer, allocatable :: conglom_id !<ID for a conglomerate
+  ! If iceberg_bonds_on
+  integer, allocatable :: n_bonds
+  ! If frac
+  real, allocatable :: accum_bond_rotation
   ! For optional energy monitoring
   real, allocatable :: Ee !< Energy from bonds, elastic (J)
   real, allocatable :: Ed !< Energy from bonds, damping (J)
@@ -356,15 +363,16 @@ module ice_bergs_framework
   integer :: other_berg_ine
   integer :: other_berg_jne
   real :: length
-  !if bergs%fracture_criterion=='strain', the following are accumulated over all timesteps, but if
-  !bergs%fracture_criterion=='strain_rate', the following correspond to only the most recent timestep and
-  !units are per second
-  real :: rotation !radians
-  real :: rel_rotation !<rotation relative to the mean of all bonds for a berg
-  real :: n_strain !<normal strain (lengthwise stretching of the bond)
-  real :: n_strain_rate !<for bergs%fracture_criterion=='strain_rate' only
-  real :: spring_pe
   type(bond_xyt), pointer :: bond_trajectory=>null()
+  ! Fracture parameters:
+  !The following are accumulated over all timesteps, unless fracture_criterion=='strain_rate',
+  !in which case the following correspond to only the most recent timestep and units are s^(-1)
+  real, allocatable :: damage
+  real, allocatable :: rotation !radians
+  real, allocatable :: rel_rotation !<rotation relative to the mean of all bonds for a berg
+  real, allocatable :: n_frac_var !<normal strain, stress, or spring energy
+  real, allocatable :: n_strain_rate !<for fracture_criterion=='strain_rate' only
+  real, allocatable :: spring_pe
   ! For optional energy monitoring
   real, allocatable :: Ee !< Bond energy, elastic (J)
   real, allocatable :: Ed !< Bond energy, damping (J)
@@ -379,6 +387,39 @@ module ice_bergs_framework
   real, allocatable :: sstress !< Shear stress (Pa)
 end type bond
 
+!> A link in the bond trajectory record (diagnostic)
+type :: bond_xyt
+  real :: lon !< Longitude of bond (degree E or unit of grid coordinate)
+  real :: lat !< Latitude of bond (degree N or unit of grid coordinate)
+  integer :: year !< Year of this record (years)
+  real :: day !< Day of this record (days)
+  real :: length !<Length of bond
+  real :: n1 !<Unit vector, x-component
+  real :: n2 !<Unit vector, y-component
+  integer(kind=8) :: id1 !<ID of first berg
+  integer(kind=8) :: id2 !<ID of second berg
+  type(bond_xyt), pointer :: next=>null() !< Next link in list
+  ! Fracture parameters:
+  real, allocatable :: damage
+  real, allocatable :: rotation !radians
+  real, allocatable :: rel_rotation !<rotation relative to the mean of all bonds for a berg
+  real, allocatable :: n_frac_var !<normal strain, stress, or spring energy
+  real, allocatable :: n_strain_rate !<for fracture_criterion=='strain_rate' only
+  real, allocatable :: spring_pe
+  ! For optional energy monitoring
+  real, allocatable :: Ee !< Bond energy (elastic)
+  real, allocatable :: Ed !< Bond energy (damping)
+  real, allocatable :: axn_fast !< Zonal acceleration contribution to parent berg, explicit (m s^-2)
+  real, allocatable :: ayn_fast !< Meridional  acceleration contribution to parent berg, explicit (m s^-2)
+  real, allocatable :: bxn_fast !< Zonal acceleration contribution to parent berg, implicit (m s^-2)
+  real, allocatable :: byn_fast !< Meridional acceleration contribution to parent berg, implicit (m s^-2)
+  ! For DEM-mode
+  real, allocatable :: tangd1 !< Accumulated tangential displacement, x-component (m)
+  real, allocatable :: tangd2 !< Accumulated tangential displacement, y-component (m)
+  real, allocatable :: nstress
+  real, allocatable :: sstress
+end type bond_xyt
+
 ! A dynamic buffer, used for communication, that packs types into rectangular memory
 type :: buffer
   integer :: size=0 !< Size of buffer
@@ -413,15 +454,13 @@ module ice_bergs_framework
   real :: rho_bergs !< Density of icebergs [kg/m^3]
   real :: spring_coef !< Spring constant for bonded iceberg interactions
   real :: contact_spring_coef !<Spring coefficient for berg collisions -Alex
-  character(len=11) :: fracture_criterion !<'energy','stress','strain_rate','strain',or 'none'logical ::
-  logical :: uniaxial_test=.false. !adds a tensile stress to the east-most berg element
-  real :: dem_tests_start_lon !starting lon of west-most berg element for uniaxial/dem tests
-  real :: dem_tests_end_lon !starting lon of east-most berg element for uniaxial/dem tests
   real :: cdrag_grounding=0.0 !< Drag coefficient against ocean bottom
   real :: h_to_init_grounding
-  real :: frac_thres_n !normal fracture strain threshold
-  real :: frac_thres_t !tangential fracture strain threshold
-  logical :: debug_write !<Sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+  character(len=11) :: fracture_criterion='none' !<'damage','energy','stress','strain_rate','strain',or 'none'
+  real :: frac_thres_n=0.0 !normal fracture strain threshold
+  real :: frac_thres_t=0.0 !tangential fracture strain threshold
+  logical :: damage_test_1=.false. !< Sets initial damage for bonds that overlap y=17000.0
+  logical :: debug_write=.false. !< Sets traj_sample_hours=traj_write_hours & includes halo bergs in write
   real :: bond_coef !< Spring constant for iceberg bonds
   real :: radial_damping_coef !< Coefficient for relative iceberg motion damping (radial component) -Alon
   real :: tangental_damping_coef !< Coefficient for relative iceberg motion damping (tangential component) -Alon
@@ -540,10 +579,21 @@ module ice_bergs_framework
   real :: convergence_tolerance=1.e-8 !tolerance for the MTS convergence scheme
   ! DEM-mode parameters
   logical :: dem=.false. !if T, run in DEM-mode with angular terms, variable stiffness, etc
+  logical :: ignore_tangential_force=.false.
   real :: poisson=0.3 ! Poisson's ratio
   real :: dem_spring_coef=0.
   real :: dem_damping_coef=0.1
-  integer :: dem_beam_test=0 !1=Simply supported beam,2=cantilever beam,3=angular vel test
+  logical :: dem_shear_for_frac_only=.false. !< If true, DEM shear is calculated for fracture, but zeroed for berg interactions
+  integer :: dem_beam_test=0 !1=Simply supported beam,2=cantilever beam,3=angular vel tes
+  logical :: uniaxial_test=.false. !adds a tensile stress to the east-most berg element
+  real :: dem_tests_start_lon !starting lon of west-most berg element for uniaxial/dem tests
+  real :: dem_tests_end_lon !starting lon of east-most berg element for uniaxial/dem tests
+  ! Element interactions
+  logical :: constant_interaction_LW=.false. !< Use a constant element length & width during berg interactions
+  real :: constant_length=0.!< If constant_interaction_LW, the constant length. If 0, will be set to max initial length
+  real :: constant_width=0. !< If constant_interaction_LW, the constant width.  If 0, will be set to max initial width
+  ! Footloose calving parameters [England et al (2020) Modeling the breakup of tabular icebergs. Sci. Adv.]
+  !real ::
 end type icebergs
 
 !> Read original restarts. Needs to be module global so can be public to icebergs_mod.
@@ -623,12 +673,13 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: rho_bergs=850. ! Density of icebergs
 real :: spring_coef=1.e-8 ! Spring constant for iceberg interactions (this seems to be the highest stable value)
 real :: contact_spring_coef=0. !Spring coef for berg collisions (is set to spring_coef if not specified)
-character(len=11) :: fracture_criterion='none' !<'energy','stress','strain_rate','strain',or 'none'
 logical :: uniaxial_test=.false. !adds a tensile stress to the east-most berg element
 real :: cdrag_grounding=0.0 ! Drag coefficient against ocean bottom
 real :: h_to_init_grounding=100.0
+!character(len=11) :: fracture_criterion !<'energy','stress','strain_rate','strain',or 'none'
 real :: frac_thres_n=0.0 !normal fracture strain threshold
 real :: frac_thres_t=0.0 !tangential fracture strain threshold
+logical :: damage_test_1=.false. !< Sets initial damage for bonds that overlap y=17000.0
 real :: frac_thres_scaling=1.0 !scaling factor for frac_thres_n and frac_thres_t, useful for tuning
 logical :: debug_write=.false. !Sets traj_sample_hours=traj_write_hours & includes halo bergs in write
 real :: bond_coef=1.e-8 ! Spring constant for iceberg bonds - not being used right now
@@ -688,7 +739,7 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: halo_debugging=.False. ! Use for debugging halos (remove when its working)
 logical :: save_short_traj=.True. ! True saves only lon,lat,time,id in iceberg_trajectory.nc
 logical :: ignore_traj=.False. ! If true, then model does not traj trajectory data at all
-logical :: iceberg_bonds_on=.False. ! True=Allow icebergs to have bonds, False=don't allow.
+!logical :: iceberg_bonds_on=.False. ! True=Allow icebergs to have bonds, False=don't allow.
 logical :: manually_initialize_bonds=.False. ! True= Bonds are initialize manually.
 logical :: use_new_predictive_corrective =.False. ! Flag to use Bob's predictive corrective iceberg scheme- Added by Alon
 logical :: interactive_icebergs_on=.false. ! Turn on/off interactions between icebergs  - Added by Alon
@@ -713,10 +764,16 @@ subroutine ice_bergs_framework_init(bergs, &
 integer(kind=8) :: debug_iceberg_with_id = -1 ! If positive, monitors a berg with this id
 ! DEM-mode parameters
 !logical :: dem=.false. !if T, run in DEM-mode with angular terms, variable stiffness, etc
+logical :: ignore_tangential_force=.false.
 real :: poisson=0.3 ! Poisson's ratio
 real :: dem_spring_coef=0.
 real :: dem_damping_coef=0.1
+logical :: dem_shear_for_frac_only=.false. !< If true, DEM shear is calculated for fracture, but zeroed for berg interactions
 integer :: dem_beam_test=0 !1=Simply supported beam,2=cantilever beam,3=angular vel test
+! Element Interactions
+logical :: constant_interaction_LW=.false. !< Always use the initial, globally constant, element length & width during berg interactions
+real :: constant_length=0. !< If constant_interaction_LW, the constant length used. If zero in the nml, will be set to max initial L
+real :: constant_width=0. !< If constant_interaction_LW, the constant width used. If zero in the nml, will be set to max initial W
 
 namelist /icebergs_nml/ verbose, budget, halo,  traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,Static_icebergs,  &
          distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,bond_coef, radial_damping_coef, tangental_damping_coef, only_interactive_forces, &
@@ -731,9 +788,9 @@ subroutine ice_bergs_framework_init(bergs, &
          const_gamma, Gamma_T_3EQ, ignore_traj, debug_iceberg_with_id,use_updated_rolling_scheme, tip_parameter, read_old_restarts, tau_calving, read_ocean_depth_from_file, melt_cutoff,&
          apply_thickness_cutoff_to_gridded_melt, apply_thickness_cutoff_to_bergs_melt, use_mixed_melting, internal_bergs_for_drag, coastal_drift, tidal_drift,&
          mts,new_mts,ewsame,monitor_energy,mts_sub_steps,contact_distance,length_for_manually_initialize_bonds,manually_initialize_bonds_from_radii,contact_spring_coef,&
-         fracture_criterion, uniaxial_test, debug_write,cdrag_grounding,h_to_init_grounding,frac_thres_scaling,frac_thres_n,frac_thres_t,save_bond_traj,remove_unused_bergs,&
+         fracture_criterion, damage_test_1, uniaxial_test, debug_write,cdrag_grounding,h_to_init_grounding,frac_thres_scaling,frac_thres_n,frac_thres_t,save_bond_traj,remove_unused_bergs,&
          force_convergence,explicit_inner_mts,convergence_tolerance,&
-         dem,poisson,dem_spring_coef,dem_damping_coef,dem_beam_test
+         dem,ignore_tangential_force,poisson,dem_spring_coef,dem_damping_coef,dem_beam_test,constant_interaction_LW,constant_length,constant_width,dem_shear_for_frac_only,use_damage
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -1031,20 +1088,20 @@ subroutine ice_bergs_framework_init(bergs, &
     write(stderrunit,'(a,i3,a,4i4)') 'KID, icebergs_init: (',mpp_pe(),') [ij][se]c=', &
           grd%isc,grd%iec,grd%jsc,grd%jec
 
-    print *,'minval(grd%lon)',minval(grd%lon)
-    print *,'maxval(grd%lon)',maxval(grd%lon)
-    print *,'minval(grd%lat)',minval(grd%lat)
-    print *,'maxval(grd%lat)',maxval(grd%lat)
+    !print *,'minval(grd%lon)',minval(grd%lon)
+    !print *,'maxval(grd%lon)',maxval(grd%lon)
+    !print *,'minval(grd%lat)',minval(grd%lat)
+    !print *,'maxval(grd%lat)',maxval(grd%lat)
 
     write(stderrunit,'(a,4f10.2)') '[Lon|lat][min|max]=', &
           minval(grd%lon),maxval(grd%lon),minval(grd%lat),maxval(grd%lat)
   endif
 
-  if ( (mpp_pe() == 0) .and. (Lx .ne. -1.) .and. .not. (grid_is_latlon) ) then
-    print *,''
-    print *,'pe 0 x-domain after periodicity fix'
-    write(*,'(f12.2)') (grd%lon(i,grd%jsd), i=grd%isd,grd%ied)
-  end if
+ ! if ( (mpp_pe() == 0) .and. (Lx .ne. -1.) .and. .not. (grid_is_latlon) ) then
+ !   print *,''
+ !   print *,'pe 0 x-domain after periodicity fix'
+ !   write(*,'(f12.2)') (grd%lon(i,grd%jsd), i=grd%isd,grd%ied)
+ ! end if
 
  !if (mpp_pe().eq.5) then
  !  write(stderrunit,'(a3,32i7)') 'Lon',(i,i=grd%isd,grd%ied)
@@ -1106,21 +1163,45 @@ subroutine ice_bergs_framework_init(bergs, &
   endif
 endif
 if (.not. iceberg_bonds_on) then
-   max_bonds=0
+  max_bonds=0
 else
-  buffer_width=buffer_width+(max_bonds*10) ! Increase buffer width to include bonds being passed between processors
+  buffer_width=buffer_width+(max_bonds*5) ! Increase buffer width to include bonds being passed between processors
 endif
 if (save_short_traj) buffer_width_traj=6 ! This is the length of the short buffer used for abrevated traj
 if (ignore_traj) buffer_width_traj=0 ! If this is true, then all traj files should be ignored
 
+if (use_damage) then
+  buffer_width=buffer_width+(max_bonds*1)
+  buffer_width_bond_traj=buffer_width_bond_traj+1
+endif
+
 if (monitor_energy) then
   buffer_width=buffer_width+11+(max_bonds*6)
   buffer_width_traj=buffer_width_traj+6
-  buffer_width_bond_traj=buffer_width_bond_traj+2
+  !buffer_width_traj=buffer_width_traj+5 !if include temp terms
+  buffer_width_bond_traj=buffer_width_bond_traj+6
 endif
 
 if (dem) then
   buffer_width=buffer_width+3+(max_bonds*4)
+  buffer_width_traj=buffer_width_traj+3
+  buffer_width_bond_traj=buffer_width_bond_traj+4
+elseif (fracture_criterion .ne. 'none') then
+  buffer_width=buffer_width+1+(max_bonds*3)
+  buffer_width_traj=buffer_width_traj+1
+  buffer_width_bond_traj=buffer_width_bond_traj+3
+  if (fracture_criterion .eq. 'strain_rate') then
+    buffer_width=buffer_width+(max_bonds*1)
+    buffer_width_bond_traj=buffer_width_bond_traj+1
+  elseif (fracture_criterion .eq. 'energy') then
+    buffer_width=buffer_width+(max_bonds*1)
+    buffer_width_bond_traj=buffer_width_bond_traj+1
+  endif
+endif
+
+if (iceberg_bonds_on) then
+  buffer_width=buffer_width+1
+  buffer_width_traj=buffer_width_traj+1
 endif
 
 !must use verlet with mts - Alex
@@ -1131,7 +1212,7 @@ subroutine ice_bergs_framework_init(bergs, &
   !if mts_sub_steps is not given in the nml already,
   !then detemine according to the max dt according to the spring coef
   if (mts_sub_steps .eq. -1) then
-    mts_fast_dt = 2./sqrt(spring_coef)   !the (theoretical) maximum "fast" dt for mts scheme
+    mts_fast_dt = 0.3/sqrt(spring_coef)        !critical dt for mts scheme w/ safety multiplier of 0.75
     mts_sub_steps = ceiling(dt/mts_fast_dt)    !the number of substeps
   end if
 
@@ -1177,12 +1258,12 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%spring_coef=spring_coef
   bergs%contact_spring_coef=contact_spring_coef !Alex
   bergs%fracture_criterion=fracture_criterion
+  bergs%damage_test_1=damage_test_1
   bergs%uniaxial_test=uniaxial_test
   bergs%cdrag_grounding=cdrag_grounding
   bergs%h_to_init_grounding=h_to_init_grounding
   bergs%frac_thres_n=frac_thres_n*frac_thres_scaling
   bergs%frac_thres_t=frac_thres_t*frac_thres_scaling
-  if (mpp_pe()==0) print *,'FRAC_THRES: N,T:', bergs%frac_thres_n,bergs%frac_thres_t
   bergs%debug_write=debug_write
   bergs%bond_coef=bond_coef
   bergs%radial_damping_coef=radial_damping_coef
@@ -1255,11 +1336,16 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%convergence_tolerance=convergence_tolerance
   ! DEM-mode parameters
   bergs%dem=dem
+  bergs%ignore_tangential_force=ignore_tangential_force
   if (bergs%dem) bergs%explicit_inner_mts=.true.
   bergs%poisson=poisson
   bergs%dem_spring_coef=dem_spring_coef
   bergs%dem_damping_coef=dem_damping_coef
   bergs%dem_beam_test=dem_beam_test
+  bergs%constant_interaction_LW=constant_interaction_LW
+  bergs%constant_length=constant_length
+  bergs%constant_width=constant_width
+  bergs%dem_shear_for_frac_only=dem_shear_for_frac_only
 
   if (bergs%contact_distance>0) then
     dx_dlon=1; dy_dlat=1
@@ -2397,13 +2483,6 @@ subroutine energy_tests_init(bergs)
     this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
 
-      !test changing the radius
-      ! Vol=this%length*this%width*this%thickness
-      ! this%length=this%length*0.9
-      ! this%width=this%width*0.9
-      ! this%mass=(this%length*this%width*this%thickness/Vol)*this%mass
-
-
       this%uvel_old=this%uvel; this%uvel_prev=this%uvel
       this%vvel_old=this%vvel; this%vvel_prev=this%vvel
 
@@ -3009,9 +3088,6 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
   call push_buffer_value(buff%data(:,n), counter, id_cnt)
   call push_buffer_value(buff%data(:,n), counter, id_ij)
   call push_buffer_value(buff%data(:,n), counter, berg%od)
-  call push_buffer_value(buff%data(:,n), counter, berg%n_bonds)
-  call push_buffer_value(buff%data(:,n), counter, berg%accum_bond_rotation)
-
 
   if (mts) then
     call push_buffer_value(buff%data(:,n), counter, berg%conglom_id)
@@ -3033,6 +3109,10 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
     call push_buffer_value(buff%data(:,n), counter, berg%hi)
   endif
 
+  if (iceberg_bonds_on) then
+    call push_buffer_value(buff%data(:,n), counter, berg%n_bonds)
+  end if
+
   if (monitor_energy) then
     call push_buffer_value(buff%data(:,n), counter, berg%Ee)
     call push_buffer_value(buff%data(:,n), counter, berg%Ed)
@@ -3051,6 +3131,8 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
     call push_buffer_value(buff%data(:,n), counter, berg%ang_vel)
     call push_buffer_value(buff%data(:,n), counter, berg%ang_accel)
     call push_buffer_value(buff%data(:,n), counter, berg%rot)
+  elseif (fracture_criterion .ne. 'none') then
+    call push_buffer_value(buff%data(:,n), counter, berg%accum_bond_rotation)
   endif
 
   if (max_bonds .gt. 0) then
@@ -3063,11 +3145,10 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
         call push_buffer_value(buff%data(:,n), counter, current_bond%other_berg_ine)
         call push_buffer_value(buff%data(:,n), counter, current_bond%other_berg_jne)
         call push_buffer_value(buff%data(:,n), counter, current_bond%length)
-        call push_buffer_value(buff%data(:,n), counter, current_bond%rotation)
-        call push_buffer_value(buff%data(:,n), counter, current_bond%rel_rotation)
-        call push_buffer_value(buff%data(:,n), counter, current_bond%n_strain)
-        call push_buffer_value(buff%data(:,n), counter, current_bond%n_strain_rate)
-        call push_buffer_value(buff%data(:,n), counter, current_bond%spring_pe)
+
+        if (use_damage) then
+          call push_buffer_value(buff%data(:,n), counter, current_bond%damage)
+        endif
 
         if (monitor_energy) then
           call push_buffer_value(buff%data(:,n), counter, current_bond%Ee)
@@ -3083,6 +3164,16 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
           call push_buffer_value(buff%data(:,n), counter, current_bond%tangd2)
           call push_buffer_value(buff%data(:,n), counter, current_bond%nstress)
           call push_buffer_value(buff%data(:,n), counter, current_bond%sstress)
+        elseif (fracture_criterion .ne. 'none') then
+          call push_buffer_value(buff%data(:,n), counter, current_bond%rotation)
+          call push_buffer_value(buff%data(:,n), counter, current_bond%rel_rotation)
+          call push_buffer_value(buff%data(:,n), counter, current_bond%n_frac_var)
+          if (fracture_criterion .eq. 'strain_rate') then
+            call push_buffer_value(buff%data(:,n), counter, current_bond%n_strain_rate)
+          endif
+          if (fracture_criterion .eq. 'energy') then
+            call push_buffer_value(buff%data(:,n), counter, current_bond%spring_pe)
+          endif
         endif
 
         current_bond=>current_bond%next_bond
@@ -3092,11 +3183,10 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
         call push_buffer_value(buff%data(:,n), counter, 0)
         call push_buffer_value(buff%data(:,n), counter, 0)
         call push_buffer_value(buff%data(:,n), counter, 0)
-        call push_buffer_value(buff%data(:,n), counter, 0)
-        call push_buffer_value(buff%data(:,n), counter, 0)
-        call push_buffer_value(buff%data(:,n), counter, 0)
-        call push_buffer_value(buff%data(:,n), counter, 0)
-        call push_buffer_value(buff%data(:,n), counter, 0)
+
+        if (use_damage) then
+          call push_buffer_value(buff%data(:,n), counter, 0)
+        endif
 
         if (monitor_energy) then
           call push_buffer_value(buff%data(:,n), counter, 0)
@@ -3112,6 +3202,16 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
           call push_buffer_value(buff%data(:,n), counter, 0)
           call push_buffer_value(buff%data(:,n), counter, 0)
           call push_buffer_value(buff%data(:,n), counter, 0)
+        elseif (fracture_criterion .ne. 'none') then
+          call push_buffer_value(buff%data(:,n), counter, 0)
+          call push_buffer_value(buff%data(:,n), counter, 0)
+          call push_buffer_value(buff%data(:,n), counter, 0)
+          if (fracture_criterion .eq. 'strain_rate') then
+            call push_buffer_value(buff%data(:,n), counter, 0)
+          endif
+          if (fracture_criterion .eq. 'energy') then
+            call push_buffer_value(buff%data(:,n), counter, 0)
+          endif
         endif
 
       endif
@@ -3230,7 +3330,6 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
 integer :: stderrunit
 logical :: force_app,duplicate
 real :: temp_lon,temp_lat,length
-real :: rotation,rel_rotation,n_strain,n_strain_rate,spring_pe
 
   ! Get the stderr unit number
   stderrunit = stderr()
@@ -3241,6 +3340,14 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
   force_app = .false.
   if(present(force_append)) force_app = force_append
 
+  if (mts) then
+    allocate(localberg%axn_fast,localberg%ayn_fast,localberg%bxn_fast,localberg%byn_fast,localberg%conglom_id)
+  endif
+
+  if (iceberg_bonds_on) then
+    allocate(localberg%n_bonds)
+  endif
+
   if (monitor_energy) then
     allocate(localberg%Ee,localberg%Ed,localberg%Eext,localberg%Ee_contact,localberg%Ed_contact,localberg%Efrac,&
       localberg%Ee_temp,localberg%Ed_temp,localberg%Eext_temp,localberg%Ee_contact_temp,localberg%Ed_contact_temp)
@@ -3248,6 +3355,8 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
 
   if (dem) then
     allocate(localberg%ang_vel,localberg%ang_accel,localberg%rot)
+  elseif (fracture_criterion .ne. 'none') then
+    allocate(localberg%accum_bond_rotation)
   endif
 
   counter = 0
@@ -3285,8 +3394,6 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
   call pull_buffer_value(buff%data(:,n), counter, id_ij)
   localberg%id = id_from_2_ints(id_cnt, id_ij)
   call pull_buffer_value(buff%data(:,n), counter, localberg%od)
-  call pull_buffer_value(buff%data(:,n), counter, localberg%n_bonds)
-  call pull_buffer_value(buff%data(:,n), counter, localberg%accum_bond_rotation)
 
   if (bergs%mts) then
     call pull_buffer_value(buff%data(:,n), counter, localberg%conglom_id)
@@ -3308,6 +3415,10 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
     call pull_buffer_value(buff%data(:,n), counter, localberg%hi)
   endif
 
+  if (iceberg_bonds_on) then
+    call pull_buffer_value(buff%data(:,n), counter, localberg%n_bonds)
+  endif
+
   if (monitor_energy) then
     call pull_buffer_value(buff%data(:,n), counter, localberg%Ee)
     call pull_buffer_value(buff%data(:,n), counter, localberg%Ed)
@@ -3326,6 +3437,8 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
     call pull_buffer_value(buff%data(:,n), counter, localberg%ang_vel)
     call pull_buffer_value(buff%data(:,n), counter, localberg%ang_accel)
     call pull_buffer_value(buff%data(:,n), counter, localberg%rot)
+  elseif (fracture_criterion .ne. 'none') then
+    call pull_buffer_value(buff%data(:,n), counter, localberg%accum_bond_rotation)
   endif
 
   !These quantities no longer need to be passed between processors
@@ -3439,21 +3552,15 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
       call pull_buffer_value(buff%data(:,n), counter, other_berg_ine)
       call pull_buffer_value(buff%data(:,n), counter, other_berg_jne)
       call pull_buffer_value(buff%data(:,n), counter, length)
-      call pull_buffer_value(buff%data(:,n), counter, rotation)
-      call pull_buffer_value(buff%data(:,n), counter, rel_rotation)
-      call pull_buffer_value(buff%data(:,n), counter, n_strain)
-      call pull_buffer_value(buff%data(:,n), counter, n_strain_rate)
-      call pull_buffer_value(buff%data(:,n), counter, spring_pe)
 
       if (id_ij > 0) then
         call form_a_bond(this, id, other_berg_ine, other_berg_jne)
         current_bond=>this%first_bond
         current_bond%length=length
-        current_bond%rotation=rotation
-        current_bond%rel_rotation=rel_rotation
-        current_bond%n_strain=n_strain
-        current_bond%n_strain_rate=n_strain_rate
-        current_bond%spring_pe=spring_pe
+
+        if (use_damage) then
+          call pull_buffer_value(buff%data(:,n), counter, current_bond%damage)
+        endif
 
         if (monitor_energy) then
           call pull_buffer_value(buff%data(:,n), counter, current_bond%Ee)
@@ -3467,8 +3574,18 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
         if (dem) then
           call pull_buffer_value(buff%data(:,n), counter, current_bond%tangd1)
           call pull_buffer_value(buff%data(:,n), counter, current_bond%tangd2)
-          call pull_buffer_value(buff%data(:,n), counter, current_bond%sstress)
           call pull_buffer_value(buff%data(:,n), counter, current_bond%nstress)
+          call pull_buffer_value(buff%data(:,n), counter, current_bond%sstress)
+        elseif (fracture_criterion .ne. 'none') then
+          call pull_buffer_value(buff%data(:,n), counter, current_bond%rotation)
+          call pull_buffer_value(buff%data(:,n), counter, current_bond%rel_rotation)
+          call pull_buffer_value(buff%data(:,n), counter, current_bond%n_frac_var)
+          if (fracture_criterion .eq. 'strain_rate') then
+            call pull_buffer_value(buff%data(:,n), counter, current_bond%n_strain_rate)
+          endif
+          if (fracture_criterion .eq. 'energy') then
+            call pull_buffer_value(buff%data(:,n), counter, current_bond%spring_pe)
+          endif
         endif
       endif
     enddo
@@ -3571,16 +3688,18 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj)
     call push_buffer_value(buff%data(:,n),counter,traj%halo_berg)
     call push_buffer_value(buff%data(:,n),counter,traj%static_berg)
     call push_buffer_value(buff%data(:,n),counter,traj%od)
-    call push_buffer_value(buff%data(:,n),counter,traj%n_bonds)
-    call push_buffer_value(buff%data(:,n),counter,traj%accum_bond_rotation)
 
     if (mts) then
-      call push_buffer_value(buff%data(:,n),counter,traj%axn_fast)
-      call push_buffer_value(buff%data(:,n),counter,traj%ayn_fast)
-      call push_buffer_value(buff%data(:,n),counter,traj%bxn_fast)
-      call push_buffer_value(buff%data(:,n),counter,traj%byn_fast)
+      call push_buffer_value(buff%data(:,n), counter, traj%axn_fast)
+      call push_buffer_value(buff%data(:,n), counter, traj%ayn_fast)
+      call push_buffer_value(buff%data(:,n), counter, traj%bxn_fast)
+      call push_buffer_value(buff%data(:,n), counter, traj%byn_fast)
     endif
 
+    if (iceberg_bonds_on) then
+      call push_buffer_value(buff%data(:,n), counter, traj%n_bonds)
+    end if
+
     if (monitor_energy) then
       call push_buffer_value(buff%data(:,n), counter, traj%Ee)
       call push_buffer_value(buff%data(:,n), counter, traj%Ed)
@@ -3588,6 +3707,19 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj)
       call push_buffer_value(buff%data(:,n), counter, traj%Ee_contact)
       call push_buffer_value(buff%data(:,n), counter, traj%Ed_contact)
       call push_buffer_value(buff%data(:,n), counter, traj%Efrac)
+      ! call push_buffer_value(buff%data(:,n), counter, traj%Ee_contact_temp)
+      ! call push_buffer_value(buff%data(:,n), counter, traj%Ed_contact_temp)
+      ! call push_buffer_value(buff%data(:,n), counter, traj%Ee_temp)
+      ! call push_buffer_value(buff%data(:,n), counter, traj%Ed_temp)
+      ! call push_buffer_value(buff%data(:,n), counter, traj%Eext_temp)
+    endif
+
+    if (dem) then
+      call push_buffer_value(buff%data(:,n), counter, traj%ang_vel)
+      call push_buffer_value(buff%data(:,n), counter, traj%ang_accel)
+      call push_buffer_value(buff%data(:,n), counter, traj%rot)
+    elseif (fracture_criterion .ne. 'none') then
+      call push_buffer_value(buff%data(:,n), counter, traj%accum_bond_rotation)
     endif
 
   endif
@@ -3606,8 +3738,23 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj)
   integer :: counter ! Position in stack
   integer :: cnt, ij
 
+  if (mts) then
+    allocate(traj%axn_fast,traj%ayn_fast,traj%bxn_fast,traj%byn_fast)
+  endif
+
+  if (iceberg_bonds_on) then
+    allocate(traj%n_bonds)
+  endif
+
   if (monitor_energy) then
     allocate(traj%Ee,traj%Ed,traj%Eext,traj%Ee_contact,traj%Ed_contact,traj%Efrac)
+    !allocate(traj%Ee_temp,traj%Ed_temp,traj%Eext_temp,traj%Ee_contact_temp,traj%Ed_contact_temp)
+  endif
+
+  if (dem) then
+    allocate(traj%ang_vel,traj%ang_accel,traj%rot)
+  elseif (fracture_criterion .ne. 'none') then
+    allocate(traj%accum_bond_rotation)
   endif
 
   counter = 0
@@ -3648,16 +3795,18 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj)
     call pull_buffer_value(buff%data(:,n),counter,traj%halo_berg)
     call pull_buffer_value(buff%data(:,n),counter,traj%static_berg)
     call pull_buffer_value(buff%data(:,n),counter,traj%od)
-    call pull_buffer_value(buff%data(:,n),counter,traj%n_bonds)
-    call pull_buffer_value(buff%data(:,n),counter,traj%accum_bond_rotation)
 
     if (mts) then
-      call pull_buffer_value(buff%data(:,n),counter,traj%axn_fast)
-      call pull_buffer_value(buff%data(:,n),counter,traj%ayn_fast)
-      call pull_buffer_value(buff%data(:,n),counter,traj%bxn_fast)
-      call pull_buffer_value(buff%data(:,n),counter,traj%byn_fast)
+      call pull_buffer_value(buff%data(:,n), counter, traj%axn_fast)
+      call pull_buffer_value(buff%data(:,n), counter, traj%ayn_fast)
+      call pull_buffer_value(buff%data(:,n), counter, traj%bxn_fast)
+      call pull_buffer_value(buff%data(:,n), counter, traj%byn_fast)
     endif
 
+    if (iceberg_bonds_on) then
+      call pull_buffer_value(buff%data(:,n), counter, traj%n_bonds)
+    end if
+
     if (monitor_energy) then
       call pull_buffer_value(buff%data(:,n), counter, traj%Ee)
       call pull_buffer_value(buff%data(:,n), counter, traj%Ed)
@@ -3665,6 +3814,19 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj)
       call pull_buffer_value(buff%data(:,n), counter, traj%Ee_contact)
       call pull_buffer_value(buff%data(:,n), counter, traj%Ed_contact)
       call pull_buffer_value(buff%data(:,n), counter, traj%Efrac)
+      ! call pull_buffer_value(buff%data(:,n), counter, traj%Ee_contact_temp)
+      ! call pull_buffer_value(buff%data(:,n), counter, traj%Ed_contact_temp)
+      ! call pull_buffer_value(buff%data(:,n), counter, traj%Ee_temp)
+      ! call pull_buffer_value(buff%data(:,n), counter, traj%Ed_temp)
+      ! call pull_buffer_value(buff%data(:,n), counter, traj%Eext_temp)
+    endif
+
+    if (dem) then
+      call pull_buffer_value(buff%data(:,n), counter, traj%ang_vel)
+      call pull_buffer_value(buff%data(:,n), counter, traj%ang_accel)
+      call pull_buffer_value(buff%data(:,n), counter, traj%rot)
+    elseif (fracture_criterion .ne. 'none') then
+      call pull_buffer_value(buff%data(:,n), counter, traj%accum_bond_rotation)
     endif
   endif
   call append_posn(first, traj)
@@ -3692,11 +3854,6 @@ subroutine pack_bond_traj_into_buffer2(bond_traj, buff, n)
   call push_buffer_value(buff%data(:,n),counter,bond_traj%length)
   call push_buffer_value(buff%data(:,n),counter,bond_traj%n1)
   call push_buffer_value(buff%data(:,n),counter,bond_traj%n2)
-  call push_buffer_value(buff%data(:,n),counter,bond_traj%rotation)
-  call push_buffer_value(buff%data(:,n),counter,bond_traj%rel_rotation)
-  call push_buffer_value(buff%data(:,n),counter,bond_traj%n_strain)
-  call push_buffer_value(buff%data(:,n),counter,bond_traj%n_strain_rate)
-  call push_buffer_value(buff%data(:,n),counter,bond_traj%spring_pe)
 
   call split_id(bond_traj%id1, cnt1, ij1)
   call push_buffer_value(buff%data(:,n),counter,cnt1)
@@ -3705,9 +3862,33 @@ subroutine pack_bond_traj_into_buffer2(bond_traj, buff, n)
   call push_buffer_value(buff%data(:,n),counter,cnt2)
   call push_buffer_value(buff%data(:,n),counter,ij2)
 
+  if (use_damage) then
+    call push_buffer_value(buff%data(:,n),counter,bond_traj%damage)
+  endif
+
   if (monitor_energy) then
     call push_buffer_value(buff%data(:,n),counter,bond_traj%Ee)
     call push_buffer_value(buff%data(:,n),counter,bond_traj%Ed)
+    call push_buffer_value(buff%data(:,n),counter,bond_traj%axn_fast)
+    call push_buffer_value(buff%data(:,n),counter,bond_traj%ayn_fast)
+    call push_buffer_value(buff%data(:,n),counter,bond_traj%bxn_fast)
+    call push_buffer_value(buff%data(:,n),counter,bond_traj%byn_fast)
+  endif
+
+  if (dem) then
+    call push_buffer_value(buff%data(:,n),counter,bond_traj%tangd1)
+    call push_buffer_value(buff%data(:,n),counter,bond_traj%tangd2)
+    call push_buffer_value(buff%data(:,n),counter,bond_traj%nstress)
+    call push_buffer_value(buff%data(:,n),counter,bond_traj%sstress)
+  elseif (fracture_criterion.ne.'none') then
+    call push_buffer_value(buff%data(:,n),counter,bond_traj%rotation)
+    call push_buffer_value(buff%data(:,n),counter,bond_traj%rel_rotation)
+    call push_buffer_value(buff%data(:,n),counter,bond_traj%n_frac_var)
+    if (fracture_criterion.eq.'strain_rate') then
+      call push_buffer_value(buff%data(:,n),counter,bond_traj%n_strain_rate)
+    elseif (fracture_criterion.eq.'energy') then
+      call push_buffer_value(buff%data(:,n),counter,bond_traj%spring_pe)
+    endif
   endif
 
 end subroutine pack_bond_traj_into_buffer2
@@ -3723,7 +3904,22 @@ subroutine unpack_bond_traj_from_buffer2(first, buff, n)
   integer :: counter ! Position in stack
   integer :: cnt1, ij1, cnt2, ij2
 
-if (monitor_energy) allocate(bond_traj%Ee,bond_traj%Ed)
+  if (use_damage) then
+    allocate(bond_traj%damage)
+  endif
+  if (monitor_energy) then
+    allocate(bond_traj%Ee,bond_traj%Ed,bond_traj%axn_fast,bond_traj%ayn_fast,bond_traj%bxn_fast,bond_traj%byn_fast)
+  endif
+  if (dem) then
+    allocate(bond_traj%tangd1,bond_traj%tangd2,bond_traj%nstress,bond_traj%sstress)
+  elseif (fracture_criterion.ne.'none') then
+    allocate(bond_traj%rotation,bond_traj%rel_rotation,bond_traj%n_frac_var)
+    if (fracture_criterion.eq.'strain_rate') then
+      allocate(bond_traj%n_strain_rate)
+    elseif (fracture_criterion.eq.'energy') then
+      allocate(bond_traj%spring_pe)
+    endif
+  endif
 
   counter = 0
   call pull_buffer_value(buff%data(:,n),counter,bond_traj%lon)
@@ -3733,11 +3929,6 @@ subroutine unpack_bond_traj_from_buffer2(first, buff, n)
   call pull_buffer_value(buff%data(:,n),counter,bond_traj%length)
   call pull_buffer_value(buff%data(:,n),counter,bond_traj%n1)
   call pull_buffer_value(buff%data(:,n),counter,bond_traj%n2)
-  call pull_buffer_value(buff%data(:,n),counter,bond_traj%rotation)
-  call pull_buffer_value(buff%data(:,n),counter,bond_traj%rel_rotation)
-  call pull_buffer_value(buff%data(:,n),counter,bond_traj%n_strain)
-  call pull_buffer_value(buff%data(:,n),counter,bond_traj%n_strain_rate)
-
   call pull_buffer_value(buff%data(:,n),counter,cnt1)
   call pull_buffer_value(buff%data(:,n),counter,ij1)
   bond_traj%id1 = id_from_2_ints(cnt1, ij1)
@@ -3745,9 +3936,33 @@ subroutine unpack_bond_traj_from_buffer2(first, buff, n)
   call pull_buffer_value(buff%data(:,n),counter,ij2)
   bond_traj%id2 = id_from_2_ints(cnt2, ij2)
 
+  if (use_damage) then
+    call pull_buffer_value(buff%data(:,n),counter,bond_traj%damage)
+  endif
+
   if (monitor_energy) then
     call pull_buffer_value(buff%data(:,n),counter,bond_traj%Ee)
     call pull_buffer_value(buff%data(:,n),counter,bond_traj%Ed)
+    call pull_buffer_value(buff%data(:,n),counter,bond_traj%axn_fast)
+    call pull_buffer_value(buff%data(:,n),counter,bond_traj%ayn_fast)
+    call pull_buffer_value(buff%data(:,n),counter,bond_traj%bxn_fast)
+    call pull_buffer_value(buff%data(:,n),counter,bond_traj%byn_fast)
+  endif
+
+  if (dem) then
+    call pull_buffer_value(buff%data(:,n),counter,bond_traj%tangd1)
+    call pull_buffer_value(buff%data(:,n),counter,bond_traj%tangd2)
+    call pull_buffer_value(buff%data(:,n),counter,bond_traj%nstress)
+    call pull_buffer_value(buff%data(:,n),counter,bond_traj%sstress)
+  elseif (fracture_criterion.ne.'none') then
+    call pull_buffer_value(buff%data(:,n),counter,bond_traj%rotation)
+    call pull_buffer_value(buff%data(:,n),counter,bond_traj%rel_rotation)
+    call pull_buffer_value(buff%data(:,n),counter,bond_traj%n_frac_var)
+    if (fracture_criterion.eq.'strain_rate') then
+      call pull_buffer_value(buff%data(:,n),counter,bond_traj%n_strain_rate)
+    elseif (fracture_criterion.eq.'energy') then
+      call pull_buffer_value(buff%data(:,n),counter,bond_traj%spring_pe)
+    endif
   endif
 
   call append_bond_posn(first, bond_traj)
@@ -4205,12 +4420,24 @@ subroutine create_iceberg(berg, bergvals)
     call error_mesg('KID, create_iceberg', 'berg already associated. This should not happen!', FATAL)
   endif
   allocate(berg)
+
+  if (mts) then
+    allocate(berg%axn_fast,berg%ayn_fast,berg%bxn_fast,berg%byn_fast,berg%conglom_id)
+  endif
+
+  if (iceberg_bonds_on) then
+    allocate(berg%n_bonds)
+    berg%n_bonds=0
+  endif
+
   if (monitor_energy) then
     allocate(berg%Ee,berg%Ed,berg%Eext,berg%Ee_contact,berg%Ed_contact,berg%Efrac,&
       berg%Ee_temp,berg%Ed_temp,berg%Eext_temp,berg%Ee_contact_temp,berg%Ed_contact_temp)
   endif
   if (dem) then
     allocate(berg%ang_vel,berg%ang_accel,berg%rot)
+  elseif (fracture_criterion .ne. 'none') then
+    allocate(berg%accum_bond_rotation)
   endif
   berg=bergvals
   berg%prev=>null()
@@ -4329,7 +4556,7 @@ subroutine print_bergs(iochan, bergs, label)
 
 end subroutine print_bergs
 
-
+!> Set initial length of the bond
 subroutine orig_bond_length(bergs)
 type(icebergs), pointer :: bergs !< Container for all types and memory
 type(iceberg), pointer :: other_berg, berg
@@ -4360,7 +4587,7 @@ end subroutine orig_bond_length
 !> Initialize fracture parameters for non-DEM style fracture
 subroutine fracture_testing_initialization(bergs)
 type(icebergs), pointer :: bergs !< Container for all types and memory
-type(iceberg), pointer :: this, other_berg
+type(iceberg), pointer :: this
 type(bond) , pointer :: current_bond
 type(icebergs_gridded), pointer :: grd
 integer :: grdi, grdj
@@ -4374,7 +4601,7 @@ subroutine fracture_testing_initialization(bergs)
       do while (associated(current_bond)) ! loop over all bonds
         current_bond%rotation=0.0
         current_bond%rel_rotation=0.0
-        current_bond%n_strain=0.0
+        current_bond%n_frac_var=0.0
         current_bond%n_strain_rate=0.0
         current_bond=>current_bond%next_bond
       enddo
@@ -4383,6 +4610,35 @@ subroutine fracture_testing_initialization(bergs)
   enddo;enddo
 end subroutine fracture_testing_initialization
 
+!< Sets initial damage for bonds that overlap y=17000.0
+subroutine damage_test_1_init(bergs)
+type(icebergs), pointer :: bergs !< Container for all types and memory
+type(iceberg), pointer :: berg, other_berg
+type(bond) , pointer :: current_bond
+type(icebergs_gridded), pointer :: grd
+integer :: grdi, grdj
+
+  print *,'DAMAGE TEST 1 INITIALIZATION'
+  grd=>bergs%grd
+  do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+    berg=>bergs%list(grdi,grdj)%first
+    do while (associated(berg)) ! loop over all bergs
+      current_bond=>berg%first_bond
+      do while (associated(current_bond)) ! loop over all bonds
+        other_berg=>current_bond%other_berg
+        if (associated(current_bond%other_berg)) then
+          if ((other_berg%lat>17000.0 .and. berg%lat<=17000.0) .or. &
+            (berg%lat>17000.0 .and. other_berg%lat<=17000.0)) then
+            current_bond%damage=0.75
+          endif
+        endif
+        current_bond=>current_bond%next_bond
+      enddo
+      berg=>berg%next
+    enddo
+  enddo; enddo
+end subroutine damage_test_1_init
+
 !> Save number of bonds on element
 subroutine assign_n_bonds(bergs)
 type(icebergs), pointer :: bergs !< Container for all types and memory
@@ -4406,6 +4662,42 @@ subroutine assign_n_bonds(bergs)
   enddo;enddo
 end subroutine assign_n_bonds
 
+!> For if using constant_LW_for_interactions: if constant_length and constant_width
+!! are not given in the nml or are both set to zero, determine their values here
+subroutine set_constant_interaction_length_and_width(bergs)
+type(icebergs), pointer :: bergs !< Container for all types and memory
+type(iceberg), pointer :: this
+type(icebergs_gridded), pointer :: grd
+integer :: grdi, grdj
+real :: elem_sum, l_sum, w_sum
+
+  ! constant_length/constant_width are set to the mean values of the lengths/widths
+  ! that are currently initialized on the domain. Note that using the mean should be
+  ! overkill because ideally, the initialized elements should all have the same
+  ! length and width anyway...
+
+  if (.not. bergs%constant_interaction_LW) return
+
+  elem_sum = 0. !counter for number of elements
+  l_sum = 0.    !sum of lengths
+  w_sum = 0.    !sum of widths
+  grd=>bergs%grd
+  do grdj=grd%jsc,grd%jec ; do grdi=grd%isc,grd%iec!loop over all cells
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this)) ! loop over all bergs in cell
+      elem_sum=elem_sum+1.
+      l_sum=l_sum+this%length
+      w_sum=w_sum+this%width
+      this=>this%next
+    enddo
+  enddo;enddo
+
+  call mpp_sum(elem_sum); call mpp_sum(l_sum); call mpp_sum(w_sum)
+  bergs%constant_length = l_sum/elem_sum
+  bergs%constant_width  = w_sum/elem_sum
+
+end subroutine set_constant_interaction_length_and_width
+
 !> Initialization for the DEM beam tests
 subroutine dem_tests_init(bergs)
 type(icebergs), pointer :: bergs !< Container for all types and memory
@@ -4514,7 +4806,7 @@ subroutine update_bond_angles(bergs)
   grd=>bergs%grd
 
   if (.not. bergs%grd%grid_is_latlon) then
-    dx_dlon=1.0; dy_dlat=1.0; !dx_dlon1=1.0; dx_dlon2=1.0;
+    dx_dlon=1.0; dy_dlat=1.0
   else
     dy_dlat=pi_180*Rearth
   endif
@@ -4571,7 +4863,7 @@ subroutine update_and_break_bonds(bergs)
   integer :: grdi, grdj
   type(bond) , pointer :: current_bond,other_bond,kick_the_bucket
   real :: frac_thres_n,frac_thres_t,spring_coef
-  real :: inv_dt, rdenom, mean_denom, R1, R2, n_strain, BondEetot
+  real :: inv_dt, rdenom, mean_denom, R1, R2, n_frac_var, BondEetot
 
   frac_thres_n=bergs%frac_thres_n; frac_thres_t=bergs%frac_thres_t
   if (frac_thres_n<=0.0 .and. frac_thres_t<=0.0) return !all fracture ignored
@@ -4639,25 +4931,25 @@ subroutine update_and_break_bonds(bergs)
           !normal strain or strain-rate: note original length is taken as the sum of the
           !radii (calculated according to area) of the two bergs the bond connects.
           if (bergs%fracture_criterion=='strain_rate') then
-            n_strain=current_bond%length/(R1+R2) - 1.0
-            current_bond%n_strain_rate=(n_strain-current_bond%n_strain)*inv_dt
-            current_bond%n_strain=n_strain
-            n_strain=current_bond%n_strain_rate
+            n_frac_var=current_bond%length/(R1+R2) - 1.0
+            current_bond%n_strain_rate=(n_frac_var-current_bond%n_frac_var)*inv_dt
+            current_bond%n_frac_var=n_frac_var
+            n_frac_var=current_bond%n_strain_rate
           elseif (bergs%fracture_criterion=='strain') then
-            n_strain=current_bond%length/(R1+R2) - 1.0
-            current_bond%n_strain=n_strain
+            n_frac_var=current_bond%length/(R1+R2) - 1.0
+            current_bond%n_frac_var=n_frac_var
           elseif (bergs%fracture_criterion=='stress') then
-            n_strain=(current_bond%length-(R1+R2))*min(this%mass,other_berg%mass)*&
-              (bergs%spring_coef)/(R1+R2)
+            n_frac_var=(current_bond%length-(R1+R2))*min(this%mass,other_berg%mass)*&
+              (bergs%spring_coef)/(min(this%thickness,other_berg%thickness)*(R1+R2))
             current_bond%rel_rotation = current_bond%rel_rotation*R1*min(this%mass,other_berg%mass)*&
-              bergs%spring_coef/(R1+R2)
-            current_bond%n_strain=n_strain
+              bergs%spring_coef/(min(this%thickness,other_berg%thickness)*(R1+R2))
+            current_bond%n_frac_var=n_frac_var
           elseif (bergs%fracture_criterion=='energy') then
-            current_bond%n_strain=current_bond%spring_pe
+            current_bond%n_frac_var=current_bond%spring_pe
           endif
 
         !mark bond and matching bond on other_berg as fractured
-        if (abs(current_bond%rel_rotation)>frac_thres_t.or.n_strain>frac_thres_n) then
+        if (abs(current_bond%rel_rotation)>frac_thres_t.or.n_frac_var>frac_thres_n) then
           current_bond%other_id=-1
 
           !mark matching bond on other_berg
@@ -4683,18 +4975,18 @@ subroutine update_and_break_bonds(bergs)
         if (current_bond%other_id==-1) then
           if (grdj>=grd%jsc .and. grdj<=grd%jec .and. grdi>=grd%isc .and. grdi<=grd%iec) then
             if (bergs%fracture_criterion=='strain_rate') then
-              n_strain=current_bond%n_strain_rate
+              n_frac_var=current_bond%n_strain_rate
             else
-              n_strain=current_bond%n_strain
+              n_frac_var=current_bond%n_frac_var
             endif
-            if (abs(current_bond%rel_rotation)>frac_thres_t.and.n_strain>frac_thres_n) then
-              print *,'angle and n_strain break',current_bond%rel_rotation,n_strain,this%id
+            if (abs(current_bond%rel_rotation)>frac_thres_t.and.n_frac_var>frac_thres_n) then
+              print *,'angle and n_frac_var break',current_bond%rel_rotation,n_frac_var,this%id
             elseif (abs(current_bond%rel_rotation)>frac_thres_t) then
-              print *,'angle break',current_bond%rel_rotation,n_strain,this%id
-            elseif (n_strain>frac_thres_n) then
-              print *,'n_strain break',current_bond%rel_rotation,n_strain,this%id
+              print *,'angle break',current_bond%rel_rotation,n_frac_var,this%id
+            elseif (n_frac_var>frac_thres_n) then
+              print *,'n_frac_var break',current_bond%rel_rotation,n_frac_var,this%id
             else
-              print *,'break due to bond match',current_bond%rel_rotation,n_strain,this%id
+              print *,'break due to bond match',current_bond%rel_rotation,n_frac_var,this%id
             endif
           endif
           this%accum_bond_rotation=this%accum_bond_rotation-current_bond%rotation
@@ -4740,29 +5032,37 @@ subroutine break_bonds_dem(bergs)
       current_bond=>this%first_bond
       do while (associated(current_bond)) ! loop over all bonds
 
-        if ((current_bond%other_id .ne. -1) .and. &
-          (current_bond%nstress>frac_thres_n .or. current_bond%sstress>frac_thres_t)) then
-          if (current_bond%nstress>frac_thres_n .and. current_bond%sstress>frac_thres_t) then
-            print *,'normal and shear stress break',this%id,current_bond%nstress,current_bond%sstress
-          elseif (current_bond%nstress>frac_thres_n) then
-            print *,'normal stress break',this%id,current_bond%nstress,current_bond%sstress
-          else
-            print *,'shear stress break',this%id,current_bond%nstress,current_bond%sstress
+        if (use_damage) then
+          frac_thres_n=bergs%frac_thres_n*(1.-current_bond%damage)
+          frac_thres_t=bergs%frac_thres_t*(1.-current_bond%damage)
+        endif
+
+        if (current_bond%other_id.ne.-1) then
+
+          if (current_bond%nstress>frac_thres_n .or. current_bond%sstress>frac_thres_t) then
+            if (current_bond%nstress>frac_thres_n .and. current_bond%sstress>frac_thres_t) then
+              print *,'normal and shear stress break',this%id,current_bond%nstress,current_bond%sstress
+            elseif (current_bond%nstress>frac_thres_n) then
+              print *,'normal stress break',this%id,current_bond%nstress,current_bond%sstress
+            else
+              print *,'shear stress break',this%id,current_bond%nstress,current_bond%sstress
+            endif
+            current_bond%other_id=-1
           endif
 
-          current_bond%other_id=-1
-          other_berg=>current_bond%other_berg
-          if (associated(other_berg)) then
-            !mark matching bond on other_berg
-            other_bond=>other_berg%first_bond
-            do while (associated(other_bond)) ! loop over all bonds
-              if (other_bond%other_id.eq.this%id) other_bond%other_id=-1
-              other_bond=>other_bond%next_bond
-            enddo
+          if (current_bond%other_id.eq.-1) then
+            other_berg=>current_bond%other_berg
+            if (associated(other_berg)) then
+              !mark matching bond on other_berg
+              other_bond=>other_berg%first_bond
+              do while (associated(other_bond)) ! loop over all bonds
+                if (other_bond%other_id.eq.this%id) other_bond%other_id=-1
+                other_bond=>other_bond%next_bond
+              enddo
+            endif
           endif
-        else
-          current_bond=>current_bond%next_bond
         endif
+        current_bond=>current_bond%next_bond
       enddo
       this=>this%next
     enddo
@@ -4828,6 +5128,9 @@ subroutine form_a_bond(berg, other_id, other_berg_ine, other_berg_jne, other_ber
 
   ! Step 1: Create a new bond
   allocate(new_bond)
+  if (use_damage) then
+    allocate(new_bond%damage); new_bond%damage=0.
+  endif
   if (monitor_energy) then
     allocate(new_bond%Ee,new_bond%Ed,new_bond%axn_fast,new_bond%ayn_fast,new_bond%bxn_fast,new_bond%byn_fast)
     new_bond%Ee=0.; new_bond%Ed=0.; new_bond%axn_fast=0.; new_bond%ayn_fast=0.; new_bond%bxn_fast=0.; new_bond%byn_fast=0.
@@ -4838,6 +5141,17 @@ subroutine form_a_bond(berg, other_id, other_berg_ine, other_berg_jne, other_ber
     new_bond%tangd1=0.; new_bond%tangd2=0.
     allocate(new_bond%nstress,new_bond%sstress)
     new_bond%nstress=0.; new_bond%sstress=0.
+  elseif (fracture_criterion.ne.'none') then
+    allocate(new_bond%rotation,new_bond%rel_rotation,new_bond%n_frac_var)
+    new_bond%rotation=0.; new_bond%rel_rotation=0.; new_bond%n_frac_var=0.
+    if (fracture_criterion.eq.'strain_rate') then
+      allocate(new_bond%n_strain_rate)
+      new_bond%n_strain_rate=0.
+    endif
+    if (fracture_criterion.eq.'energy') then
+      allocate(new_bond%spring_pe)
+      new_bond%spring_pe=0.
+    endif
   endif
 
   new_bond%other_id=other_id
@@ -5301,10 +5615,38 @@ subroutine record_posn(bergs)
   js=bergs%grd%jsc;   je=bergs%grd%jec; is=bergs%grd%isc;   ie=bergs%grd%iec
 endif
 
-if (monitor_energy) then
-  allocate(posn%Ee,posn%Ed,posn%Eext,posn%Ee_contact,posn%Ed_contact,posn%Efrac)
-  if (save_bond_traj) allocate(bond_posn%Ee,bond_posn%Ed)
-endif
+  if (mts) then
+    allocate(posn%axn_fast,posn%ayn_fast,posn%bxn_fast,posn%byn_fast)
+  endif
+
+  if (iceberg_bonds_on) then
+    allocate(posn%n_bonds)
+  endif
+
+  if (monitor_energy) then
+    allocate(posn%Ee,posn%Ed,posn%Eext,posn%Ee_contact,posn%Ed_contact,posn%Efrac)
+    !allocate(posn%Ee_temp,posn%Ed_temp,posn%Eext_temp,posn%Ee_contact_temp,posn%Ed_contact_temp)
+  endif
+
+  if (dem) then
+    allocate(posn%ang_vel,posn%ang_accel,posn%rot)
+  elseif (fracture_criterion .ne. 'none') then
+    allocate(posn%accum_bond_rotation)
+  endif
+
+  if (save_bond_traj) then
+    if (use_damage) allocate(bond_posn%damage)
+    if (monitor_energy) then
+      allocate(bond_posn%Ee,bond_posn%Ed,bond_posn%axn_fast,bond_posn%ayn_fast,bond_posn%bxn_fast,bond_posn%byn_fast)
+    endif
+    if (dem) then
+      allocate(bond_posn%tangd1,bond_posn%tangd2,bond_posn%nstress,bond_posn%sstress)
+    elseif (fracture_criterion.ne.'none') then
+      allocate(bond_posn%rotation,bond_posn%rel_rotation,bond_posn%n_frac_var)
+      if (fracture_criterion.eq.'strain_rate') allocate(bond_posn%n_strain_rate)
+      if (fracture_criterion.eq.'energy') allocate(bond_posn%spring_pe)
+    endif
+  endif
 
   do grdj = js,je ; do grdi = is,ie
     this=>bergs%list(grdi,grdj)%first
@@ -5344,8 +5686,7 @@ subroutine record_posn(bergs)
         posn%halo_berg=this%halo_berg
         posn%static_berg=this%static_berg
         posn%od=this%od
-        posn%n_bonds=this%n_bonds
-        posn%accum_bond_rotation=this%accum_bond_rotation
+
         if (bergs%mts) then
           posn%axn_fast=this%axn_fast
           posn%ayn_fast=this%ayn_fast
@@ -5353,6 +5694,10 @@ subroutine record_posn(bergs)
           posn%byn_fast=this%byn_fast
         endif
 
+        if (iceberg_bonds_on) then
+          posn%n_bonds=this%n_bonds
+        end if
+
         if (monitor_energy) then
           posn%Ee=this%Ee
           posn%Ed=this%Ed
@@ -5360,6 +5705,19 @@ subroutine record_posn(bergs)
           posn%Ee_contact=this%Ee_contact
           posn%Ed_contact=this%Ed_contact
           posn%Efrac=this%Efrac
+          ! posn%Ee_contact_temp=this%Ee_contact_temp
+          ! posn%Ed_contact_temp=this%Ed_contact_temp
+          ! posn%Ee_temp=this%Ee_temp
+          ! posn%Ed_temp=this%Ed_temp
+          ! posn%Eext_temp=this%Eext_temp
+        endif
+
+        if (dem) then
+          posn%ang_vel=this%ang_vel
+          posn%ang_accel=this%ang_accel
+          posn%rot=this%rot
+        elseif (fracture_criterion .ne. 'none') then
+          posn%accum_bond_rotation=this%accum_bond_rotation
         endif
       endif
 
@@ -5385,15 +5743,32 @@ subroutine record_posn(bergs)
             bond_posn%year=bergs%current_year;    bond_posn%day=bergs%current_yearday
             bond_posn%length=current_bond%length;
             bond_posn%n1=n1;                      bond_posn%n2=n2
-            bond_posn%rotation=current_bond%rotation
-            bond_posn%rel_rotation=current_bond%rel_rotation
-            bond_posn%n_strain=current_bond%n_strain
-            bond_posn%n_strain_rate=current_bond%n_strain_rate
             bond_posn%id1=this%id;                bond_posn%id2=other_berg%id
 
+            if (use_damage) then
+              bond_posn%damage=current_bond%damage
+            endif
+
             if (monitor_energy) then
               bond_posn%Ee=current_bond%Ee
               bond_posn%Ed=current_bond%Ed
+              bond_posn%axn_fast=current_bond%axn_fast
+              bond_posn%ayn_fast=current_bond%ayn_fast
+              bond_posn%bxn_fast=current_bond%bxn_fast
+              bond_posn%byn_fast=current_bond%byn_fast
+            endif
+
+            if (dem) then
+              bond_posn%tangd1=current_bond%tangd1
+              bond_posn%tangd2=current_bond%tangd2
+              bond_posn%nstress=current_bond%nstress
+              bond_posn%sstress=current_bond%sstress
+            elseif (fracture_criterion.ne.'none') then
+              bond_posn%rotation=current_bond%rotation
+              bond_posn%rel_rotation=current_bond%rel_rotation
+              bond_posn%n_frac_var=current_bond%n_frac_var
+              if (fracture_criterion.eq.'strain_rate') bond_posn%n_strain_rate=current_bond%n_strain_rate
+              if (fracture_criterion.eq.'energy') bond_posn%spring_pe=current_bond%spring_pe
             endif
 
             call push_bond_posn(current_bond%bond_trajectory, bond_posn)
@@ -5417,9 +5792,26 @@ subroutine push_posn(trajectory, posn_vals)
 type(xyt), pointer :: new_posn
 
   allocate(new_posn)
+
+  if (mts) then
+    allocate(new_posn%axn_fast,new_posn%ayn_fast,new_posn%bxn_fast,new_posn%byn_fast)
+  endif
+
+  if (iceberg_bonds_on) then
+    allocate(new_posn%n_bonds)
+  endif
+
   if (monitor_energy) then
     allocate(new_posn%Ee,new_posn%Ed,new_posn%Eext,new_posn%Ee_contact,new_posn%Ed_contact,new_posn%Efrac)
+    !allocate(new_posn%Ee_temp,new_posn%Ed_temp,new_posn%Eext_temp,new_posn%Ee_contact_temp,new_posn%Ed_contact_temp)
+  endif
+
+  if (dem) then
+    allocate(new_posn%ang_vel,new_posn%ang_accel,new_posn%rot)
+  elseif (fracture_criterion .ne. 'none') then
+    allocate(new_posn%accum_bond_rotation)
   endif
+
   new_posn=posn_vals
   new_posn%next=>trajectory
   trajectory=>new_posn
@@ -5435,7 +5827,20 @@ subroutine push_bond_posn(bond_trajectory, bond_posn_vals)
 type(bond_xyt), pointer :: new_bond_posn
 
   allocate(new_bond_posn)
-  if (monitor_energy) allocate(new_bond_posn%Ee,new_bond_posn%Ed)
+
+  if (use_damage) allocate(new_bond_posn%damage)
+  if (monitor_energy) then
+    allocate(new_bond_posn%Ee,new_bond_posn%Ed,new_bond_posn%axn_fast,new_bond_posn%ayn_fast,&
+      new_bond_posn%bxn_fast,new_bond_posn%byn_fast)
+  endif
+  if (dem) then
+    allocate(new_bond_posn%tangd1,new_bond_posn%tangd2,new_bond_posn%nstress,new_bond_posn%sstress)
+  elseif (fracture_criterion.ne.'none') then
+    allocate(new_bond_posn%rotation,new_bond_posn%rel_rotation,new_bond_posn%n_frac_var)
+    if (fracture_criterion.eq.'strain_rate') allocate(new_bond_posn%n_strain_rate)
+    if (fracture_criterion.eq.'energy') allocate(new_bond_posn%spring_pe)
+  endif
+
   new_bond_posn=bond_posn_vals
   new_bond_posn%next=>bond_trajectory
   bond_trajectory=>new_bond_posn
@@ -5452,9 +5857,26 @@ subroutine append_posn(trajectory, posn_vals)
 type(xyt), pointer :: new_posn,next,last
 
   allocate(new_posn)
+
+  if (mts) then
+    allocate(new_posn%axn_fast,new_posn%ayn_fast,new_posn%bxn_fast,new_posn%byn_fast)
+  endif
+
+  if (iceberg_bonds_on) then
+    allocate(new_posn%n_bonds)
+  endif
+
   if (monitor_energy) then
     allocate(new_posn%Ee,new_posn%Ed,new_posn%Eext,new_posn%Ee_contact,new_posn%Ed_contact,new_posn%Efrac)
+    !allocate(new_posn%Ee_temp,new_posn%Ed_temp,new_posn%Eext_temp,new_posn%Ee_contact_temp,new_posn%Ed_contact_temp)
+  endif
+
+  if (dem) then
+    allocate(new_posn%ang_vel,new_posn%ang_accel,new_posn%rot)
+  elseif (fracture_criterion .ne. 'none' .and. (.not. dem)) then
+    allocate(new_posn%accum_bond_rotation)
   endif
+
   new_posn=posn_vals
   new_posn%next=>null()
   if(.NOT. associated(trajectory)) then
@@ -5480,7 +5902,20 @@ subroutine append_bond_posn(bond_trajectory, bond_posn_vals)
 type(bond_xyt), pointer :: new_bond_posn,next,last
 
   allocate(new_bond_posn)
-  if (monitor_energy) allocate(new_bond_posn%Ee,new_bond_posn%Ed)
+
+  if (use_damage) allocate(new_bond_posn%damage)
+  if (monitor_energy) then
+    allocate(new_bond_posn%Ee,new_bond_posn%Ed,new_bond_posn%axn_fast,new_bond_posn%ayn_fast,&
+      new_bond_posn%bxn_fast,new_bond_posn%byn_fast)
+  endif
+  if (dem) then
+    allocate(new_bond_posn%tangd1,new_bond_posn%tangd2,new_bond_posn%nstress,new_bond_posn%sstress)
+  elseif (fracture_criterion.ne.'none') then
+    allocate(new_bond_posn%rotation,new_bond_posn%rel_rotation,new_bond_posn%n_frac_var)
+    if (fracture_criterion.eq.'strain_rate') allocate(new_bond_posn%n_strain_rate)
+    if (fracture_criterion.eq.'energy') allocate(new_bond_posn%spring_pe)
+  endif
+
   new_bond_posn=bond_posn_vals
   new_bond_posn%next=>null()
   if(.NOT. associated(bond_trajectory)) then
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index c65d8f6..8c4b608 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -40,10 +40,11 @@ module ice_bergs_io
 use ice_bergs_framework, only: force_all_pes_traj
 use ice_bergs_framework, only: check_for_duplicates_in_parallel
 use ice_bergs_framework, only: split_id, id_from_2_ints, generate_id
-use ice_bergs_framework, only: mts,save_bond_traj !-Alex
-use ice_bergs_framework, only: push_bond_posn, append_bond_posn !-Alex
-use ice_bergs_framework, only: pack_bond_traj_into_buffer2,unpack_bond_traj_from_buffer2 !-Alex
-use ice_bergs_framework, only: monitor_energy
+! for MTS/DEM/fracture:
+use ice_bergs_framework, only: mts,save_bond_traj
+use ice_bergs_framework, only: push_bond_posn, append_bond_posn
+use ice_bergs_framework, only: pack_bond_traj_into_buffer2,unpack_bond_traj_from_buffer2
+use ice_bergs_framework, only: monitor_energy, use_damage, dem, fracture_criterion, iceberg_bonds_on
 
 implicit none ; private
 
@@ -147,7 +148,27 @@ subroutine write_restart(bergs, time_stamp)
                                    mass_scaling, &
                                    mass_of_bits, &
                                    static_berg,  &
-                                   heat_density
+                                   heat_density, &
+                                   axn_fast,     &
+                                   ayn_fast,     &
+                                   bxn_fast,     &
+                                   byn_fast,     &
+                                   damage,       &
+                                   ang_vel,      &
+                                   ang_accel,    &
+                                   rot,          &
+                                   lon_prev,     &
+                                   lat_prev,     &
+                                   accum_bond_rotation, &
+                                   tangd1,       &
+                                   tangd2,       &
+                                   nstress,      &
+                                   sstress,      &
+                                   rotation,     &
+                                   rel_rotation, &
+                                   n_frac_var,   &
+                                   n_strain_rate,&
+                                   spring_pe
 
 integer, allocatable, dimension(:) :: ine,              &
                                       jne,              &
@@ -210,6 +231,21 @@ subroutine write_restart(bergs, time_stamp)
    allocate(id_cnt(nbergs))
    allocate(id_ij(nbergs))
 
+   if (mts) then
+     allocate(axn_fast(nbergs))
+     allocate(ayn_fast(nbergs))
+     allocate(bxn_fast(nbergs))
+     allocate(byn_fast(nbergs))
+   endif
+   if (dem) then
+     allocate(ang_vel(nbergs))
+     allocate(ang_accel(nbergs))
+     allocate(rot(nbergs))
+   elseif (fracture_criterion.ne.'none') then
+     allocate(lon_prev(nbergs))
+     allocate(lat_prev(nbergs))
+     allocate(accum_bond_rotation(nbergs))
+   endif
 
   filename = trim("icebergs.res.nc")
   call set_domain(bergs%grd%domain)
@@ -229,7 +265,7 @@ subroutine write_restart(bergs, time_stamp)
   if (.not. bergs%Runge_not_Verlet) then
     id = register_restart_field(bergs_restart,filename,'axn',axn,longname='explicit zonal acceleration',units='m/s^2')
     id = register_restart_field(bergs_restart,filename,'ayn',ayn,longname='explicit meridional acceleration',units='m/s^2')
-    id = register_restart_field(bergs_restart,filename,'bxn',bxn,longname='inplicit zonal acceleration',units='m/s^2')
+    id = register_restart_field(bergs_restart,filename,'bxn',bxn,longname='implicit zonal acceleration',units='m/s^2')
     id = register_restart_field(bergs_restart,filename,'byn',byn,longname='implicit meridional acceleration',units='m/s^2')
   endif
   id = register_restart_field(bergs_restart,filename,'ine',ine,longname='i index',units='none')
@@ -258,6 +294,31 @@ subroutine write_restart(bergs, time_stamp)
   id = register_restart_field(bergs_restart,filename,'heat_density',heat_density, &
                                             longname='heat density',units='J/kg')
 
+  if (mts) then
+    id = register_restart_field(bergs_restart,filename,'axn_fast',axn_fast,&
+      longname='sub-step explicit zonal acceleration',units='m/s^2')
+    id = register_restart_field(bergs_restart,filename,'ayn_fast',ayn_fast,&
+      longname='sub-step explicit meridional acceleration',units='m/s^2')
+    id = register_restart_field(bergs_restart,filename,'bxn_fast',bxn_fast,&
+      longname='sub-step implicit zonal acceleration',units='m/s^2')
+    id = register_restart_field(bergs_restart,filename,'byn_fast',byn_fast,&
+      longname='sub-step implicit meridional acceleration',units='m/s^2')
+  endif
+
+  if (dem) then
+    id = register_restart_field(bergs_restart,filename,'ang_vel',ang_vel,&
+      longname='dem angular velocity',units='rad/s')
+    id = register_restart_field(bergs_restart,filename,'ang_accel',ang_accel,&
+      longname='dem angular acceleration',units='rad/s^2')
+    id = register_restart_field(bergs_restart,filename,'rot',rot,&
+      longname='dem accumulated rotation',units='rad')
+  elseif (fracture_criterion.ne.'none') then
+    id = register_restart_field(bergs_restart,filename,'lon_prev',lon_prev,longname='previous longitude',units='degrees_E')
+    id = register_restart_field(bergs_restart,filename,'lat_prev',lat_prev,longname='previous latitude',units='degrees_N')
+    id = register_restart_field(bergs_restart,filename,'accum_bond_rotation',accum_bond_rotation,&
+      longname='accumulated bond rotation',units='rad')
+  endif
+
   !Checking if any icebergs are static in order to decide whether to save static_berg
   n_static_bergs = 0
   do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
@@ -292,6 +353,21 @@ subroutine write_restart(bergs, time_stamp)
       static_berg(i) = this%static_berg
       call split_id(this%id, id_cnt(i), id_ij(i))
       mass_of_bits(i) = this%mass_of_bits; heat_density(i) = this%heat_density
+      if (mts) then
+        axn_fast(i) = this%axn_fast
+        ayn_fast(i) = this%ayn_fast
+        bxn_fast(i) = this%bxn_fast
+        byn_fast(i) = this%byn_fast
+      endif
+      if (dem) then
+        ang_vel(i) = this%ang_vel
+        ang_accel(i) = this%ang_accel
+        rot(i) = this%rot
+      elseif (fracture_criterion.ne.'none') then
+        lon_prev(i) = this%lon_prev
+        lat_prev(i) = this%lat_prev
+        accum_bond_rotation(i) = this%accum_bond_rotation
+      endif
       this=>this%next
     enddo
   enddo ; enddo
@@ -320,7 +396,25 @@ subroutine write_restart(bergs, time_stamp)
              mass_scaling, &
              mass_of_bits, &
              static_berg,  &
-             heat_density )
+             heat_density)
+  if (mts) then
+    deallocate(            &
+             axn_fast,     &
+             ayn_fast,     &
+             bxn_fast,     &
+             byn_fast)
+  endif
+  if (dem) then
+    deallocate(            &
+             ang_vel,      &
+             ang_accel,    &
+             rot)
+  elseif (fracture_criterion.ne.'none') then
+    deallocate(            &
+             lon_prev,     &
+             lat_prev,     &
+             accum_bond_rotation)
+  endif
 
   deallocate(           &
              ine,       &
@@ -348,6 +442,23 @@ subroutine write_restart(bergs, time_stamp)
   allocate(other_berg_ine(nbonds))
   allocate(other_berg_jne(nbonds))
 
+  if (use_damage) allocate(damage(nbonds))
+  if (dem) then
+    allocate(tangd1(nbonds))
+    allocate(tangd2(nbonds))
+    allocate(nstress(nbonds))
+    allocate(sstress(nbonds))
+  elseif (fracture_criterion.ne.'none') then
+    allocate(rotation(nbonds))
+    allocate(rel_rotation(nbonds))
+    allocate(n_frac_var(nbonds))
+    if (fracture_criterion.eq.'strain_rate') then
+      allocate(n_strain_rate(nbonds))
+    elseif (fracture_criterion.eq.'energy') then
+      allocate(spring_pe(nbonds))
+    endif
+  endif
+
   call get_instance_filename("bonds_iceberg.res.nc", filename_bonds)
   call set_domain(bergs%grd%domain)
   call register_restart_axis(bergs_bond_restart,filename,'i',nbonds)
@@ -366,6 +477,34 @@ subroutine write_restart(bergs, time_stamp)
   id = register_restart_field(bergs_bond_restart,filename_bonds,'other_id_cnt',other_id_cnt,longname='counter component of iceberg id second berg in bond',units='dimensionless')
   id = register_restart_field(bergs_bond_restart,filename_bonds,'other_id_ij',other_id_ij,longname='position component of iceberg id second berg in bond',units='dimensionless')
 
+  if (use_damage) then
+    id = register_restart_field(bergs_bond_restart,filename_bonds,'damage',damage,&
+      longname='damage',units='dimensionless')
+  endif
+  if (dem) then
+    id = register_restart_field(bergs_bond_restart,filename_bonds,'tangd1',tangd1,&
+      longname='zonal tangential displacement',units='m')
+    id = register_restart_field(bergs_bond_restart,filename_bonds,'tangd2',tangd2,&
+      longname='meridional tangential displacement',units='m')
+    id = register_restart_field(bergs_bond_restart,filename_bonds,'nstress',nstress,&
+      longname='normal stress',units='Pa')
+    id = register_restart_field(bergs_bond_restart,filename_bonds,'sstress',sstress,&
+      longname='shear stress',units='Pa')
+  elseif (fracture_criterion.ne.'none') then
+    id = register_restart_field(bergs_bond_restart,filename_bonds,'rotation',rotation,&
+      longname='rotation',units='rad')
+    id = register_restart_field(bergs_bond_restart,filename_bonds,'rel_rotation',rel_rotation,&
+      longname='relative rotation',units='rad')
+    id = register_restart_field(bergs_bond_restart,filename_bonds,'n_frac_var',n_frac_var,&
+      longname='normal fracture variable',units='dimensionless/s^-1/Pa/J')
+    if (fracture_criterion.eq.'strain_rate') then
+      id = register_restart_field(bergs_bond_restart,filename_bonds,'n_strain_rate',n_strain_rate,&
+        longname='normal strain-rate',units='1/seconds')
+    elseif (fracture_criterion.eq.'energy') then
+      id = register_restart_field(bergs_bond_restart,filename_bonds,'spring_pe',spring_pe,&
+        longname='spring potential energy',units='J')
+    endif
+  endif
 
   ! Write variables
 
@@ -383,6 +522,23 @@ subroutine write_restart(bergs, time_stamp)
         other_berg_ine(i)=current_bond%other_berg%ine
         other_berg_jne(i)=current_bond%other_berg%jne
 
+        if (use_damage) damage(i)=current_bond%damage
+        if (dem) then
+          tangd1(i)=current_bond%tangd1
+          tangd2(i)=current_bond%tangd2
+          nstress(i)=current_bond%nstress
+          sstress(i)=current_bond%sstress
+        elseif (fracture_criterion.ne.'none') then
+          rotation(i)=current_bond%rotation
+          rel_rotation(i)=current_bond%rel_rotation
+          n_frac_var(i)=current_bond%n_frac_var
+          if (fracture_criterion.eq.'strain_rate') then
+            n_strain_rate(i)=current_bond%n_strain_rate
+          elseif (fracture_criterion.eq.'energy') then
+            spring_pe(i)=current_bond%spring_pe
+          endif
+        endif
+
         current_bond=>current_bond%next_bond
       enddo !End of loop over bonds
       this=>this%next
@@ -400,8 +556,24 @@ subroutine write_restart(bergs, time_stamp)
              first_berg_ine,        &
              first_berg_jne,        &
              other_berg_ine,        &
-             other_berg_jne )
-
+             other_berg_jne)
+  if (dem) then
+    deallocate(                     &
+             tangd1,                &
+             tangd2,                &
+             nstress,               &
+             sstress)
+  elseif (fracture_criterion.ne.'none') then
+    deallocate(                     &
+             rotation,              &
+             rel_rotation,          &
+             n_frac_var)
+    if (fracture_criterion.eq.'strain_rate') then
+      deallocate(n_strain_rate)
+    elseif (fracture_criterion.eq.'energy') then
+      deallocate(spring_pe)
+    endif
+  endif
 
   call nullify_domain()
   endif
@@ -492,7 +664,18 @@ subroutine read_restart_bergs(bergs,Time)
                                    mass_scaling, &
                                    mass_of_bits, &
                                    static_berg,  &
-                                   heat_density
+                                   heat_density, &
+                                   axn_fast,     &
+                                   ayn_fast,     &
+                                   bxn_fast,     &
+                                   byn_fast,     &
+                                   ang_vel,      &
+                                   ang_accel,    &
+                                   rot,          &
+                                   lon_prev,     &
+                                   lat_prev,     &
+                                   accum_bond_rotation
+
 integer, allocatable, dimension(:) :: ine,        &
                                       jne,        &
                                       iceberg_num,&
@@ -552,6 +735,45 @@ subroutine read_restart_bergs(bergs,Time)
        allocate(id_ij(nbergs_in_file))
      endif
 
+      if (iceberg_bonds_on) then
+        allocate(localberg%n_bonds)
+        localberg%n_bonds=0.
+      end if
+
+      if (monitor_energy) then
+        allocate(localberg%Ee,localberg%Ed,localberg%Eext,localberg%Ee_contact,localberg%Ed_contact,localberg%Efrac,&
+          localberg%Ee_temp,localberg%Ed_temp,localberg%Eext_temp,localberg%Ee_contact_temp,localberg%Ed_contact_temp)
+        localberg%Ee=0.0; localberg%Ed=0.0; localberg%Eext=0.0; localberg%Ee_contact=0.0; localberg%Ed_contact=0.0
+        localberg%Efrac=0.0; localberg%Ee_temp=0.0; localberg%Ed_temp=0.0; localberg%Eext_temp=0.0
+        localberg%Ee_contact_temp=0.0; localberg%Ed_contact_temp=0.0
+      endif
+
+      if (mts) then
+        allocate(localberg%axn_fast)
+        allocate(localberg%ayn_fast)
+        allocate(localberg%bxn_fast)
+        allocate(localberg%byn_fast)
+        allocate(localberg%conglom_id)
+        localberg%conglom_id=0.
+
+       allocate(axn_fast(nbergs_in_file))
+       allocate(ayn_fast(nbergs_in_file))
+       allocate(bxn_fast(nbergs_in_file))
+       allocate(byn_fast(nbergs_in_file))
+     endif
+     if (dem) then
+       allocate(localberg%ang_vel)
+       allocate(localberg%ang_accel)
+       allocate(localberg%rot)
+       allocate(ang_vel(nbergs_in_file))
+       allocate(ang_accel(nbergs_in_file))
+       allocate(rot(nbergs_in_file))
+     elseif (fracture_criterion.ne.'none') then
+       allocate(lon_prev(nbergs_in_file))
+       allocate(lat_prev(nbergs_in_file))
+       allocate(accum_bond_rotation(nbergs_in_file))
+     endif
+
      call read_unlimited_axis(filename,'lon',lon,domain=grd%domain)
      call read_unlimited_axis(filename,'lat',lat,domain=grd%domain)
      call read_unlimited_axis(filename,'uvel',uvel,domain=grd%domain)
@@ -581,10 +803,30 @@ subroutine read_restart_bergs(bergs,Time)
        call read_int_vector(filename,'id_ij',id_ij,grd%domain)
      endif
      call read_real_vector(filename,'static_berg',static_berg,grd%domain,value_if_not_in_file=0.)
+
+     if (mts) then
+       call read_real_vector(filename,'axn_fast',axn_fast,grd%domain,value_if_not_in_file=0.)
+       call read_real_vector(filename,'ayn_fast',ayn_fast,grd%domain,value_if_not_in_file=0.)
+       call read_real_vector(filename,'bxn_fast',bxn_fast,grd%domain,value_if_not_in_file=0.)
+       call read_real_vector(filename,'byn_fast',byn_fast,grd%domain,value_if_not_in_file=0.)
+     endif
+
+     if (dem) then
+       call read_real_vector(filename,'ang_vel'  ,ang_vel  ,grd%domain,value_if_not_in_file=0.)
+       call read_real_vector(filename,'ang_accel',ang_accel,grd%domain,value_if_not_in_file=0.)
+       call read_real_vector(filename,'rot'      ,rot      ,grd%domain,value_if_not_in_file=0.)
+     elseif (fracture_criterion.ne.'none') then
+       call read_real_vector(filename,'lon_prev',lon_prev,grd%domain,value_if_not_in_file=0.)
+       call read_real_vector(filename,'lat_prev',lat_prev,grd%domain,value_if_not_in_file=0.)
+       call read_real_vector(filename,'accum_bond_rotation',accum_bond_rotation,grd%domain,value_if_not_in_file=0.)
+     endif
   elseif (bergs%require_restart) then
      stop 'read_restart_bergs, RESTART NOT FOUND!'
   endif
 
+   if (all(lon_prev.eq.0)) lon_prev=lon
+   if (all(lat_prev.eq.0)) lat_prev=lat
+
   ! Find approx outer bounds for tile
   lon0=minval( grd%lon(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
   lon1=maxval( grd%lon(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
@@ -649,6 +891,23 @@ subroutine read_restart_bergs(bergs,Time)
       localberg%heat_density=heat_density(k)
       localberg%first_bond=>null()
 
+     if (mts) then
+       localberg%axn_fast=axn_fast(k)
+       localberg%ayn_fast=ayn_fast(k)
+       localberg%bxn_fast=bxn_fast(k)
+       localberg%byn_fast=byn_fast(k)
+     endif
+
+     if (dem) then
+       localberg%ang_vel  =ang_vel(k)
+       localberg%ang_accel=ang_accel(k)
+       localberg%rot      =rot(k)
+     elseif (fracture_criterion.ne.'none') then
+       localberg%lon_prev=lon_prev(k)
+       localberg%lat_prev=lat_prev(k)
+       localberg%accum_bond_rotation=accum_bond_rotation(k)
+     endif
+
       if (really_debug) lres=is_point_in_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, explain=.true.)
       lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
       !call add_new_berg_to_list(bergs%first, localberg)
@@ -693,6 +952,25 @@ subroutine read_restart_bergs(bergs,Time)
                jne,          &
                start_year )
 
+    if (mts) then
+      deallocate(            &
+               axn_fast,     &
+               ayn_fast,     &
+               bxn_fast,     &
+               byn_fast)
+    endif
+    if (dem) then
+      deallocate(            &
+               ang_vel,      &
+               ang_accel,    &
+               rot)
+    elseif (fracture_criterion.ne.'none') then
+      deallocate(            &
+               lon_prev,     &
+               lat_prev,     &
+               accum_bond_rotation)
+    endif
+
     if (replace_iceberg_num) then
       deallocate(iceberg_num)
     else
@@ -784,6 +1062,20 @@ subroutine generate_bergs(bergs,Time)
 
   call get_date(Time, iyr, imon, iday, ihr, imin, isec)
 
+  if (mts) then
+    allocate(localberg%axn_fast)
+    allocate(localberg%ayn_fast)
+    allocate(localberg%bxn_fast)
+    allocate(localberg%byn_fast)
+  endif
+  if (dem) then
+    allocate(localberg%ang_vel)
+    allocate(localberg%ang_accel)
+    allocate(localberg%rot)
+  elseif (fracture_criterion.ne.'none') then
+    allocate(localberg%accum_bond_rotation)
+  endif
+
   do j=grd%jsc,grd%jec; do i=grd%isc,grd%iec
     if (grd%msk(i,j)>0. .and. abs(grd%latc(i,j))>80.0) then
       if (max(grd%lat(i,j),grd%lat(i-1,j),grd%lat(i,j-1),grd%lat(i-1,j-1))>89.999) cycle ! Cannot use this at Pole cells
@@ -795,8 +1087,6 @@ subroutine generate_bergs(bergs,Time)
       localberg%lat=grd%latc(i,j)
       localberg%lon_old=localberg%lon
       localberg%lat_old=localberg%lat
-      localberg%lon_prev=localberg%lon
-      localberg%lat_prev=localberg%lat
       localberg%mass=bergs%initial_mass(1)
       localberg%thickness=bergs%initial_thickness(1)
       localberg%width=bergs%initial_width(1)
@@ -819,10 +1109,22 @@ subroutine generate_bergs(bergs,Time)
       localberg%byn=0. !Alon
       localberg%uvel_prev=0. !Alon
       localberg%vvel_prev=0. !Alon
-      localberg%axn_fast=0. !Alex
-      localberg%ayn_fast=0. !Alex
-      localberg%bxn_fast=0. !Alex
-      localberg%byn_fast=0. !Alex
+      localberg%lon_prev=0.
+      localberg%lat_prev=0.
+
+      if (mts) then
+        localberg%axn_fast=0.
+        localberg%ayn_fast=0.
+        localberg%bxn_fast=0.
+        localberg%byn_fast=0.
+      endif
+      if (dem) then
+        localberg%ang_vel=0.
+        localberg%ang_accel=0.
+        localberg%rot=0.
+      elseif (fracture_criterion.ne.'none') then
+        localberg%accum_bond_rotation=0.
+      endif
 
       !Berg A
       call loc_set_berg_pos(grd, 0.9, 0.5, 1., 0., localberg)
@@ -916,6 +1218,15 @@ subroutine read_restart_bonds(bergs,Time)
                                       first_berg_ine,   &
                                       other_berg_jne,   &
                                       other_berg_ine
+real, allocatable, dimension(:) ::    tangd1,           &
+                                      tangd2,           &
+                                      nstress,          &
+                                      sstress,          &
+                                      rotation,         &
+                                      rel_rotation,     &
+                                      n_frac_var,       &
+                                      n_strain_rate,    &
+                                      spring_pe
 integer(kind=8), allocatable, dimension(:) :: first_id,   &
                                               other_id
 !integer, allocatable, dimension(:,:) :: iceberg_counter_grd
@@ -954,6 +1265,21 @@ subroutine read_restart_bonds(bergs,Time)
     allocate(other_berg_ine(nbonds_in_file))
     allocate(other_berg_jne(nbonds_in_file))
 
+    if (dem) then
+      allocate(tangd1(nbonds_in_file))
+      allocate(tangd2(nbonds_in_file))
+      allocate(nstress(nbonds_in_file))
+      allocate(sstress(nbonds_in_file))
+    elseif (fracture_criterion.ne.'none') then
+      allocate(rotation(nbonds_in_file))
+      allocate(rel_rotation(nbonds_in_file))
+      allocate(n_frac_var(nbonds_in_file))
+      if (fracture_criterion.eq.'strain_rate') then
+        allocate(n_strain_rate(nbonds_in_file))
+      elseif (fracture_criterion.eq.'energy') then
+        allocate(spring_pe(nbonds_in_file))
+      endif
+    endif
 
     call read_unlimited_axis(filename,'first_id_cnt',id_cnt,domain=grd%domain)
     call read_unlimited_axis(filename,'first_id_ij',id_ij,domain=grd%domain)
@@ -971,6 +1297,22 @@ subroutine read_restart_bonds(bergs,Time)
     call read_unlimited_axis(filename,'other_berg_jne',other_berg_jne,domain=grd%domain)
     call read_unlimited_axis(filename,'other_berg_ine',other_berg_ine,domain=grd%domain)
 
+    if (dem) then
+      call read_real_vector(filename,'tangd1',tangd1,grd%domain,value_if_not_in_file=0.)
+      call read_real_vector(filename,'tangd2',tangd2,grd%domain,value_if_not_in_file=0.)
+      call read_real_vector(filename,'nstress',nstress,grd%domain,value_if_not_in_file=0.)
+      call read_real_vector(filename,'sstress',sstress,grd%domain,value_if_not_in_file=0.)
+    elseif (fracture_criterion.ne.'none') then
+      call read_real_vector(filename,'rotation',rotation,grd%domain,value_if_not_in_file=0.)
+      call read_real_vector(filename,'rel_rotation',rel_rotation,grd%domain,value_if_not_in_file=0.)
+      call read_real_vector(filename,'n_frac_var',n_frac_var,grd%domain,value_if_not_in_file=0.)
+      if (fracture_criterion.eq.'strain_rate') then
+        call read_real_vector(filename,'n_strain_rate',n_strain_rate,grd%domain,value_if_not_in_file=0.)
+      elseif (fracture_criterion.eq.'energy') then
+        call read_real_vector(filename,'spring_pe',spring_pe,grd%domain,value_if_not_in_file=0.)
+      endif
+    endif
+
     number_first_bonds_matched=0
     number_second_bonds_matched=0
     number_perfect_bonds=0
@@ -1064,6 +1406,24 @@ subroutine read_restart_bonds(bergs,Time)
             call form_a_bond(first_berg, other_id(k), other_berg_ine(k), other_berg_jne(k),  second_berg)
             number_perfect_bonds=number_perfect_bonds+1
 
+            current_bond=>this%first_bond
+
+            if (dem) then
+              current_bond%tangd1=tangd1(k)
+              current_bond%tangd2=tangd2(k)
+              current_bond%nstress=nstress(k)
+              current_bond%sstress=sstress(k)
+            elseif (fracture_criterion.ne.'none') then
+              current_bond%tangd1=rotation(k)
+              current_bond%tangd2=rel_rotation(k)
+              current_bond%nstress=n_frac_var(k)
+              if (fracture_criterion.eq.'strain_rate') then
+                current_bond%n_strain_rate=n_strain_rate(k)
+              elseif (fracture_criterion.eq.'energy') then
+                current_bond%spring_pe=spring_pe(k)
+              endif
+            endif
+
             !Counting number of bonds where the first bond is in the computational domain
             if ( (first_berg_ine(k)>=grd%isc) .and. (first_berg_ine(k)<=grd%iec) .and. &
               (first_berg_jne(k)>=grd%jsc) .and. (first_berg_jne(k)<=grd%jec) ) then
@@ -1113,10 +1473,30 @@ subroutine read_restart_bonds(bergs,Time)
     endif
 
     deallocate(               &
+            first_id,         &
+            other_id,         &
             first_berg_ine,   &
             first_berg_jne,   &
-            other_berg_ine,  &
+            other_berg_ine,   &
             other_berg_jne )
+
+    if (dem) then
+      deallocate(                     &
+               tangd1,                &
+               tangd2,                &
+               nstress,               &
+               sstress)
+    elseif (fracture_criterion.ne.'none') then
+      deallocate(                     &
+               rotation,              &
+               rel_rotation,          &
+               n_frac_var)
+      if (fracture_criterion.eq.'strain_rate') then
+        deallocate(n_strain_rate)
+      elseif (fracture_criterion.eq.'energy') then
+        deallocate(spring_pe)
+      endif
+    endif
   endif
 
   if (mpp_pe() .eq. mpp_root_pe()) then
@@ -1268,9 +1648,11 @@ subroutine write_trajectory(trajectory, save_short_traj)
 integer :: uvelpid,vvelpid
 integer :: uoid, void, uiid, viid, uaid, vaid, sshxid, sshyid, sstid, sssid
 integer :: cnid, hiid, hsid
-integer :: mid, did, wid, lid, mbid, hdid, nbid, odid, abrid
+integer :: mid, did, wid, lid, mbid, hdid, nbid, odid
 integer :: axnid,aynid,bxnid,bynid,axnfid,aynfid,bxnfid,bynfid
-integer :: eecid,edcid,eeid,edid,aeid,efid !energy vars
+integer :: eecid,edcid,eeid,edid,aeid,efid
+integer :: eectid, edctid, eetid, edtid, aetid
+integer :: avid, aaid, rid, abrid
 character(len=37) :: filename
 character(len=7) :: pe_name
 type(xyt), pointer :: this, next
@@ -1417,8 +1799,6 @@ subroutine write_trajectory(trajectory, save_short_traj)
         bynid = inq_varid(ncid, 'byn')
         hsid = inq_varid(ncid, 'halo_berg')
         odid = inq_varid(ncid, 'od')
-        nbid = inq_varid(ncid, 'n_bonds')
-        abrid = inq_varid(ncid, 'accum_bond_rotation')
 
         if (mts) then
           axnfid = inq_varid(ncid, 'axn_fast')
@@ -1427,6 +1807,10 @@ subroutine write_trajectory(trajectory, save_short_traj)
           bynfid = inq_varid(ncid, 'byn_fast')
         endif
 
+        if (iceberg_bonds_on) then
+          nbid = inq_varid(ncid, 'n_bonds')
+        end if
+
         if (monitor_energy) then
           eeid = inq_varid(ncid, 'Ee')
           edid = inq_varid(ncid, 'Ed')
@@ -1434,7 +1818,21 @@ subroutine write_trajectory(trajectory, save_short_traj)
           eecid = inq_varid(ncid, 'Ee_contact')
           edcid = inq_varid(ncid, 'Ed_contact')
           efid =  inq_varid(ncid, 'Efrac')
+          ! eectid = inq_varid(ncid, 'Ee_contact_temp')
+          ! edctid = inq_varid(ncid, 'Ed_contact_temp')
+          ! eetid= inq_varid(ncid, 'Ee_temp')
+          ! edtid= inq_varid(ncid, 'Ed_temp')
+          ! aetid= inq_varid(ncid, 'Eext_temp')
         endif
+
+        if (dem) then
+          avid = inq_varid(ncid, 'ang_vel')
+          aaid = inq_varid(ncid, 'ang_accel')
+          rid  = inq_varid(ncid, 'rot')
+        elseif (fracture_criterion .ne. 'none') then
+          abrid = inq_varid(ncid, 'accum_bond_rotation')
+        endif
+
       endif
     else
       ! Dimensions
@@ -1477,8 +1875,6 @@ subroutine write_trajectory(trajectory, save_short_traj)
         bynid = def_var(ncid, 'byn', NF_DOUBLE, i_dim)
         hsid = def_var(ncid, 'halo_berg', NF_DOUBLE, i_dim)
         odid = def_var(ncid, 'od', NF_DOUBLE, i_dim)
-        nbid = def_var(ncid, 'n_bonds', NF_INT, i_dim)
-        abrid = def_var(ncid, 'accum_bond_rotation', NF_DOUBLE, i_dim)
 
         if (mts) then
           axnfid = def_var(ncid, 'axn_fast', NF_DOUBLE, i_dim)
@@ -1487,6 +1883,10 @@ subroutine write_trajectory(trajectory, save_short_traj)
           bynfid = def_var(ncid, 'byn_fast', NF_DOUBLE, i_dim)
         endif
 
+        if (iceberg_bonds_on) then
+          nbid = def_var(ncid, 'n_bonds', NF_INT, i_dim)
+        end if
+
         if (monitor_energy) then
           eeid = def_var(ncid, 'Ee', NF_DOUBLE, i_dim)
           edid = def_var(ncid, 'Ed', NF_DOUBLE, i_dim)
@@ -1494,6 +1894,19 @@ subroutine write_trajectory(trajectory, save_short_traj)
           eecid = def_var(ncid, 'Ee_contact', NF_DOUBLE, i_dim)
           edcid = def_var(ncid, 'Ed_contact', NF_DOUBLE, i_dim)
           efid = def_var(ncid, 'Efrac', NF_DOUBLE, i_dim)
+          ! eectid = def_var(ncid, 'Ee_contact_temp', NF_DOUBLE, i_dim)
+          ! edctid = def_var(ncid, 'Ed_contact_temp', NF_DOUBLE, i_dim)
+          ! eetid= def_var(ncid, 'Ee_temp', NF_DOUBLE, i_dim)
+          ! edtid= def_var(ncid, 'Ed_temp', NF_DOUBLE, i_dim)
+          ! aetid= def_var(ncid, 'Eext_temp', NF_DOUBLE, i_dim)
+        endif
+
+        if (dem) then
+          avid = def_var(ncid, 'ang_vel', NF_DOUBLE, i_dim)
+          aaid = def_var(ncid, 'ang_accel', NF_DOUBLE, i_dim)
+          rid  = def_var(ncid, 'rot', NF_DOUBLE, i_dim)
+        elseif (fracture_criterion .ne. 'none') then
+          abrid = def_var(ncid, 'accum_bond_rotation', NF_DOUBLE, i_dim)
         endif
       endif
 
@@ -1566,10 +1979,7 @@ subroutine write_trajectory(trajectory, save_short_traj)
         call put_att(ncid, hsid, 'units', 'non-dim')
         call put_att(ncid, odid, 'long_name', 'ocean_depth')
         call put_att(ncid, odid, 'units', 'm')
-        call put_att(ncid, nbid, 'long_name', 'number of bonds')
-        call put_att(ncid, nbid, 'units', 'dimensionless')
-        call put_att(ncid, abrid, 'long_name', 'accumulated bond rotation')
-        call put_att(ncid, abrid, 'units', 'radians')
+
         if (mts) then
           call put_att(ncid, uvelpid, 'long_name', 'zonal speed mts')
           call put_att(ncid, uvelpid, 'units', 'm/s')
@@ -1584,6 +1994,12 @@ subroutine write_trajectory(trajectory, save_short_traj)
           call put_att(ncid, bynfid, 'long_name', 'implicit fast step meridional acceleration')
           call put_att(ncid, bynfid, 'units', 'm')
         endif
+
+        if (iceberg_bonds_on) then
+          call put_att(ncid, nbid, 'long_name', 'number of bonds')
+          call put_att(ncid, nbid, 'units', 'dimensionless')
+        end if
+
         if (monitor_energy) then
           call put_att(ncid, eeid, 'long_name', 'bonded elastic energy')
           call put_att(ncid, eeid, 'units', 'J')
@@ -1597,6 +2013,28 @@ subroutine write_trajectory(trajectory, save_short_traj)
           call put_att(ncid, edcid, 'units', 'J')
           call put_att(ncid, efid, 'long_name', 'dissipated fracture energy')
           call put_att(ncid, efid, 'units', 'J')
+          ! call put_att(ncid, eectid, 'long_name', 'contact elastic energy temp')
+          ! call put_att(ncid, eectid, 'units', 'J')
+          ! call put_att(ncid, edctid, 'long_name', 'contact damping energy temp')
+          ! call put_att(ncid, edctid, 'units', 'J')
+          ! call put_att(ncid, eetid, 'long_name', 'bonded elastic energy temp')
+          ! call put_att(ncid, eetid, 'units', 'J')
+          ! call put_att(ncid, edtid, 'long_name', 'bonded damping energy temp')
+          ! call put_att(ncid, edtid, 'units', 'J')
+          ! call put_att(ncid, aetid, 'long_name', 'external energy temp')
+          ! call put_att(ncid, aetid, 'units', 'J')
+        endif
+
+        if (dem) then
+          call put_att(ncid, avid, 'long_name', 'angular velocity')
+          call put_att(ncid, avid, 'units', 'rad/s')
+          call put_att(ncid, aaid, 'long_name', 'angular acceleration')
+          call put_att(ncid, aaid, 'units', 'rad/s^2')
+          call put_att(ncid, rid, 'long_name', 'accumulated rotation')
+          call put_att(ncid, rid, 'units', 'rad')
+        elseif (fracture_criterion .ne. 'none') then
+          call put_att(ncid, abrid, 'long_name', 'accumulated bond rotation')
+          call put_att(ncid, abrid, 'units', 'radians')
         endif
       endif
     endif
@@ -1649,8 +2087,6 @@ subroutine write_trajectory(trajectory, save_short_traj)
         call put_double(ncid, bynid, i, this%byn)
         call put_double(ncid, hsid, i, this%halo_berg)
         call put_double(ncid, odid, i, this%od)
-        call put_int(ncid, nbid, i, this%n_bonds)
-        call put_double(ncid, abrid, i, this%accum_bond_rotation)
 
         if (mts) then
           call put_double(ncid, axnfid, i, this%axn_fast)
@@ -1659,13 +2095,30 @@ subroutine write_trajectory(trajectory, save_short_traj)
           call put_double(ncid, bynfid, i, this%byn_fast)
         endif
 
+        if (iceberg_bonds_on) then
+          call put_int(ncid, nbid, i, this%n_bonds)
+        end if
+
         if (monitor_energy) then
-          call put_double(ncid, eeid, i, this%Ee)
-          call put_double(ncid, edid, i, this%Ed)
-          call put_double(ncid, aeid, i, this%Eext)
-          call put_double(ncid, eecid, i, this%Ee_contact)
-          call put_double(ncid, edcid, i, this%Ed_contact)
-          call put_double(ncid, efid, i, this%Efrac)
+          call put_double(ncid, eeid,   i, this%Ee)
+          call put_double(ncid, edid,   i, this%Ed)
+          call put_double(ncid, aeid,   i, this%Eext)
+          call put_double(ncid, eecid,  i, this%Ee_contact)
+          call put_double(ncid, edcid,  i, this%Ed_contact)
+          call put_double(ncid, efid,   i, this%Efrac)
+          ! call put_double(ncid, eectid, i, this%Ee_contact_temp)
+          ! call put_double(ncid, edctid, i, this%Ed_contact_temp)
+          ! call put_double(ncid, eetid,  i, this%Ee_temp)
+          ! call put_double(ncid, edtid,  i, this%Ed_temp)
+          ! call put_double(ncid, aetid,  i, this%Eext_temp)
+        endif
+
+        if (dem) then
+          call put_double(ncid, avid, i, this%ang_vel)
+          call put_double(ncid, aaid, i, this%ang_accel)
+          call put_double(ncid, rid,  i, this%rot)
+        elseif (fracture_criterion .ne. 'none') then
+          call put_double(ncid, abrid, i, this%accum_bond_rotation)
         endif
 
       endif
@@ -1690,8 +2143,10 @@ subroutine write_bond_trajectory(trajectory)
 ! Local variables
 integer :: iret, ncid, i_dim, i
 integer :: lonid, latid, yearid, dayid, lenid,n1id, n2id, peid
-integer :: rotid,rrotid,nsid,nsrid
+integer :: rotid,rrotid,nsid,nsrid, damid
 integer :: idcnt1_id, idcnt2_id, idij1_id, idij2_id, eeid, edid
+integer :: axid,ayid,bxid,byid
+integer :: td1id,td2id,dnsid,dssid
 character(len=34) :: filename
 character(len=7) :: pe_name
 type(bond_xyt), pointer :: this, next
@@ -1803,16 +2258,30 @@ subroutine write_bond_trajectory(trajectory)
       lenid = inq_varid(ncid, 'length');
       n1id = inq_varid(ncid, 'n1');           n2id = inq_varid(ncid, 'n2')
 
-      !fracture params
-      rotid = inq_varid(ncid, 'rotation');    rrotid = inq_varid(ncid, 'rel_rotation')
-      nsid = inq_varid(ncid, 'n_strain');     nsrid = inq_varid(ncid, 'n_strain_rate')
-      peid = inq_varid(ncid, 'spring_pe');
-
       idcnt1_id = inq_varid(ncid, 'id_cnt1'); idij1_id = inq_varid(ncid, 'id_ij1')
       idcnt2_id = inq_varid(ncid, 'id_cnt2'); idij2_id = inq_varid(ncid, 'id_ij2')
 
+      if (use_damage) then
+        damid = inq_varid(ncid, 'damage')
+      endif
+
       if (monitor_energy) then
-        eeid = inq_varid(ncid, 'Ee'); edid = inq_varid(ncid, 'Ed')
+        eeid = inq_varid(ncid, 'Ee');       edid = inq_varid(ncid, 'Ed')
+        axid = inq_varid(ncid, 'axn_fast'); ayid = inq_varid(ncid, 'ayn_fast')
+        bxid = inq_varid(ncid, 'bxn_fast'); byid = inq_varid(ncid, 'byn_fast')
+      endif
+
+      if (dem) then
+        td1id = inq_varid(ncid, 'tangd1');  td2id = inq_varid(ncid, 'tangd2')
+        dnsid = inq_varid(ncid, 'nstress'); dssid = inq_varid(ncid, 'sstress')
+      elseif (fracture_criterion.ne.'none') then
+        rotid = inq_varid(ncid, 'rotation');    rrotid = inq_varid(ncid, 'rel_rotation')
+        nsid = inq_varid(ncid, 'n_frac_var')
+        if (fracture_criterion.eq.'strain_rate') then
+          nsrid = inq_varid(ncid, 'n_strain_rate')
+        elseif (fracture_criterion.eq.'energy') then
+          peid = inq_varid(ncid, 'spring_pe')
+        endif
       endif
 
     else
@@ -1826,16 +2295,30 @@ subroutine write_bond_trajectory(trajectory)
       lenid = def_var(ncid, 'length', NF_DOUBLE, i_dim);
       n1id = def_var(ncid, 'n1', NF_DOUBLE, i_dim);        n2id = def_var(ncid, 'n2', NF_DOUBLE, i_dim)
 
-      !fracture params
-      rotid = def_var(ncid, 'rotation', NF_DOUBLE, i_dim); rrotid = def_var(ncid, 'rel_rotation', NF_DOUBLE, i_dim)
-      nsid = def_var(ncid, 'n_strain', NF_DOUBLE, i_dim);  nsrid = def_var(ncid, 'n_strain_rate', NF_DOUBLE, i_dim)
-      peid = def_var(ncid, 'spring_pe', NF_DOUBLE, i_dim);
-
       idcnt1_id = def_var(ncid, 'id_cnt1', NF_INT, i_dim); idij1_id = def_var(ncid, 'id_ij1', NF_INT, i_dim)
       idcnt2_id = def_var(ncid, 'id_cnt2', NF_INT, i_dim); idij2_id = def_var(ncid, 'id_ij2', NF_INT, i_dim)
 
+      if (use_damage) then
+        damid = def_var(ncid, 'damage', NF_DOUBLE, i_dim)
+      endif
+
       if (monitor_energy) then
-        eeid = def_var(ncid, 'Ee', NF_DOUBLE, i_dim); edid = def_var(ncid, 'Ed', NF_DOUBLE, i_dim)
+        eeid = def_var(ncid, 'Ee', NF_DOUBLE, i_dim);       edid = def_var(ncid, 'Ed', NF_DOUBLE, i_dim)
+        axid = def_var(ncid, 'axn_fast', NF_DOUBLE, i_dim); ayid = def_var(ncid, 'ayn_fast', NF_DOUBLE, i_dim)
+        bxid = def_var(ncid, 'bxn_fast', NF_DOUBLE, i_dim); byid = def_var(ncid, 'byn_fast', NF_DOUBLE, i_dim)
+      endif
+
+      if (dem) then
+        td1id = def_var(ncid, 'tangd1',  NF_DOUBLE, i_dim); td2id = def_var(ncid, 'tangd2',  NF_DOUBLE, i_dim)
+        dnsid = def_var(ncid, 'nstress', NF_DOUBLE, i_dim); dssid = def_var(ncid, 'sstress', NF_DOUBLE, i_dim)
+      elseif (fracture_criterion.ne.'none') then
+        rotid = def_var(ncid, 'rotation', NF_DOUBLE, i_dim); rrotid = def_var(ncid, 'rel_rotation', NF_DOUBLE, i_dim)
+        nsid = def_var(ncid, 'n_frac_var', NF_DOUBLE, i_dim)
+        if (fracture_criterion.eq.'strain_rate') then
+          nsrid = def_var(ncid, 'n_strain_rate', NF_DOUBLE, i_dim)
+        elseif (fracture_criterion.eq.'energy') then
+          peid = def_var(ncid, 'spring_pe', NF_DOUBLE, i_dim)
+        endif
       endif
 
       ! Attributes
@@ -1849,13 +2332,6 @@ subroutine write_bond_trajectory(trajectory)
       call put_att(ncid, n1id, 'long_name', 'unit vector 1'); call put_att(ncid, n1id, 'units', 'non-dim')
       call put_att(ncid, n2id, 'long_name', 'unit vector 2'); call put_att(ncid, n2id, 'units', 'non-dim')
 
-      !fracture params
-      call put_att(ncid, rotid, 'long_name', 'rotation');           call put_att(ncid, rotid, 'units', 'rad')
-      call put_att(ncid, rrotid, 'long_name', 'relative rotation'); call put_att(ncid, rrotid, 'units', 'rad')
-      call put_att(ncid, nsid, 'long_name', 'normal strain');       call put_att(ncid, nsid, 'units', 'non-dim')
-      call put_att(ncid, nsrid, 'long_name', 'normal strain-rate'); call put_att(ncid, nsrid, 'units', '1/seconds')
-      call put_att(ncid, peid, 'long_name', 'spring potential energy'); call put_att(ncid, peid, 'units', 'J')
-
       call put_att(ncid, idcnt1_id, 'long_name', 'counter component of first connected iceberg id')
       call put_att(ncid, idcnt1_id, 'units', 'dimensionless')
       call put_att(ncid, idij1_id, 'long_name', 'position component of first connected iceberg id')
@@ -1865,11 +2341,40 @@ subroutine write_bond_trajectory(trajectory)
       call put_att(ncid, idij2_id, 'long_name', 'position component of second connected iceberg id')
       call put_att(ncid, idij2_id, 'units', 'dimensionless')
 
+      if (use_damage) then
+        call put_att(ncid, damid, 'long_name', 'damage')
+        call put_att(ncid, damid, 'units', 'none')
+      endif
+
       if (monitor_energy) then
-        call put_att(ncid, eeid, 'long_name', 'elastic energy')
-        call put_att(ncid, eeid, 'units', 'J')
-        call put_att(ncid, edid, 'long_name', 'damping energy')
-        call put_att(ncid, edid, 'units', 'J')
+        call put_att(ncid, eeid, 'long_name', 'elastic energy'); call put_att(ncid, eeid, 'units', 'J')
+        call put_att(ncid, edid, 'long_name', 'damping energy'); call put_att(ncid, edid, 'units', 'J')
+        call put_att(ncid, axid, 'long_name', 'explicit short-step zonal acceleration')
+        call put_att(ncid, axid, 'units', 'm/s^2')
+        call put_att(ncid, ayid, 'long_name', 'explicit short-step meridional acceleration')
+        call put_att(ncid, ayid, 'units', 'm/s^2')
+        call put_att(ncid, bxid, 'long_name', 'implicit short-step zonal acceleration')
+        call put_att(ncid, bxid, 'units', 'm/s^2')
+        call put_att(ncid, byid, 'long_name', 'implicit short-step meridional acceleration')
+        call put_att(ncid, byid, 'units', 'm/s^2')
+      endif
+
+      if (dem) then
+        call put_att(ncid, td1id, 'long_name', 'zonal tangential displacement')
+        call put_att(ncid, td1id, 'units', 'm')
+        call put_att(ncid, td2id, 'long_name', 'meridional tangential displacement')
+        call put_att(ncid, td2id, 'units', 'm')
+        call put_att(ncid, dnsid, 'long_name', 'normal stress'); call put_att(ncid, dnsid, 'units', 'Pa')
+        call put_att(ncid, dssid, 'long_name', 'shear stress');  call put_att(ncid, dssid, 'units', 'Pa')
+      elseif (fracture_criterion.ne.'none') then
+        call put_att(ncid, rotid, 'long_name', 'rotation');                call put_att(ncid, rotid, 'units', 'rad')
+        call put_att(ncid, rrotid, 'long_name', 'relative rotation');      call put_att(ncid, rrotid, 'units', 'rad')
+        call put_att(ncid, nsid, 'long_name', 'normal fracture variable'); call put_att(ncid, nsid, 'units', 'varies')
+        if (fracture_criterion.eq.'strain_rate') then
+          call put_att(ncid, nsrid, 'long_name', 'normal strain-rate'); call put_att(ncid, nsrid, 'units', '1/seconds')
+        elseif (fracture_criterion.eq.'energy') then
+          call put_att(ncid, peid, 'long_name', 'spring potential energy'); call put_att(ncid, peid, 'units', 'J')
+        endif
       endif
     endif
 
@@ -1891,18 +2396,32 @@ subroutine write_bond_trajectory(trajectory)
       call put_double(ncid, lenid, i, this%length);
       call put_double(ncid, n1id, i, this%n1);      call put_double(ncid, n2id, i, this%n2)
 
-      !fracture params
-      call put_double(ncid,rotid,i,this%rotation);  call put_double(ncid,rrotid,i,this%rel_rotation)
-      call put_double(ncid,nsid,i,this%n_strain);   call put_double(ncid,nsrid,i,this%n_strain_rate)
-      call put_double(ncid,peid,i,this%spring_pe)
-
       call split_id(this%id1, cnt, ij)
       call put_int(ncid, idcnt1_id, i, cnt);        call put_int(ncid, idij1_id, i, ij)
       call split_id(this%id2, cnt, ij)
       call put_int(ncid, idcnt2_id, i, cnt);        call put_int(ncid, idij2_id, i, ij)
 
+      if (use_damage) then
+        call put_double(ncid,damid,i,this%damage)
+      endif
+
       if (monitor_energy) then
-        call put_double(ncid,eeid,i,this%Ee);   call put_double(ncid,edid,i,this%Ed)
+        call put_double(ncid,eeid,i,this%Ee);       call put_double(ncid,edid,i,this%Ed)
+        call put_double(ncid,axid,i,this%axn_fast); call put_double(ncid,ayid,i,this%ayn_fast)
+        call put_double(ncid,bxid,i,this%bxn_fast); call put_double(ncid,byid,i,this%byn_fast)
+      endif
+
+      if (dem) then
+        call put_double(ncid,td1id,i,this%tangd1);  call put_double(ncid,td2id,i,this%tangd2)
+        call put_double(ncid,dnsid,i,this%nstress); call put_double(ncid,dssid,i,this%sstress)
+      elseif (fracture_criterion.ne.'none') then
+        call put_double(ncid,rotid,i,this%rotation);  call put_double(ncid,rrotid,i,this%rel_rotation)
+        call put_double(ncid,nsid,i,this%n_frac_var)
+        if (fracture_criterion.eq.'strain_rate') then
+          call put_double(ncid,nsrid,i,this%n_strain_rate)
+        elseif (fracture_criterion.eq.'energy') then
+          call put_double(ncid,peid,i,this%spring_pe)
+        endif
       endif
 
       next=>this%next
diff --git a/tests/collision_test_mts/input.nml b/tests/collision_test_mts/input.nml
index 2421207..d844dea 100644
--- a/tests/collision_test_mts/input.nml
+++ b/tests/collision_test_mts/input.nml
@@ -101,7 +101,7 @@
     verbose=.true. !(F) Be verbose to stderr
     verbose_hrs=24 ! (24) Period between verbose messages
     traj_sample_hrs=0.5 !1 !(24) sampling period for trajectory storage
-    traj_write_hrs=0 ! (480) Period for writing sampled trajectories to disk
+    traj_write_hrs=-1 ! (480) Period for writing sampled trajectories to disk
     budget=.true. !(T) Calculate budgets
     debug=.false. !(F) Turn on debugging
     really_debug=.false. !(F) Turn on debugging
diff --git a/tests/dem_ground_frac_test/input.nml b/tests/dem_ground_frac_test/input.nml
index e94afc9..bcc2b3e 100644
--- a/tests/dem_ground_frac_test/input.nml
+++ b/tests/dem_ground_frac_test/input.nml
@@ -20,19 +20,25 @@
 
 &icebergs_nml
 
+    !use_damage=.true.
+    !damage_test_1=.true.
 
     dem=.true.
+    ignore_tangential_force=.true.
     poisson=0.3
-    dem_damping_coef=0.99
+    dem_damping_coef=0. !1.0
     rho_bergs=850. ! (850) iceberg density
-    dem_spring_coef=1000.0
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    dem_spring_coef=4471.938678723104 !1000.0 
     spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
 
     monitor_energy=.false.
     !defaults given in parentheses:
     new_mts=.true.
     mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=500 !300 !1000 !(-1) # of mts sub-steps
+    mts_sub_steps=100!75 !(-1) # of mts sub-steps
     !mts_sub_steps=10
     force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
     convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
@@ -40,14 +46,15 @@
     contact_distance=1.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
     contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
     debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=3.16e6 !for power-law-type friction
+    cdrag_grounding=1.e3!3.16e6 !for power-law-type friction
     h_to_init_grounding=200.0
     ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
     remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
 
     fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_n = 12.
-    frac_thres_t = 12.
+    frac_thres_scaling = 1. 
+    frac_thres_n = 70. !2.1e4 !12.
+    frac_thres_t = 0. !12.
 
     !!fracture_criterion='strain'
     !!frac_thres_n = 0.0162
@@ -61,10 +68,10 @@
     Static_icebergs=.False. ! (T) True=icebergs do no move
 
     bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
     tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
     scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    critical_interaction_damping_on=.false. !(T) Sets damping on rel berg vel to crit val
     tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
     LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
     bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
@@ -85,7 +92,7 @@
     tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
     tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
     grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=1.0 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    coastal_drift=0.1 !(0.)Vel added to currents to cause bergs to drift away from land cells
     tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
     Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
     use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
@@ -118,8 +125,8 @@
 
     verbose=.false. !(F) Be verbose to stderr
     verbose_hrs=24000 ! (24) Period between verbose messages
-    traj_sample_hrs=0!0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=0!0!6 !(480) Period for writing sampled trajectories to disk
+    traj_sample_hrs=-1!0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=-1!0!6 !(480) Period for writing sampled trajectories to disk
     save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
     budget=.false. !(T) Calculate budgets
     debug=.false. !(F) Turn on debugging
diff --git a/tests/dem_ground_frac_test/input_dem.nml b/tests/dem_ground_frac_test/input_dem.nml
index 8c267fd..95ae26d 100644
--- a/tests/dem_ground_frac_test/input_dem.nml
+++ b/tests/dem_ground_frac_test/input_dem.nml
@@ -15,38 +15,44 @@
   debug=.true.
   collision_test=.false.
   grounding_test=.true.
-  bump_depth=200.0 !(m) depth of top of gaussian bump below sea level 
+  bump_depth=200.0 !(m) depth of top of gaussian bump below sea level
 /
 
 &icebergs_nml
 
+    !use_damage=.true.
+    !damage_test_1=.true.
 
     dem=.true.
     poisson=0.3
-    dem_damping_coef=0.99
+    dem_damping_coef=1.0
     rho_bergs=850. ! (850) iceberg density
-    dem_spring_coef=1000.0
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    dem_spring_coef=4471.938678723104 !1000.0
+   ! ignore_tangential_force=.true.
     spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
 
-
     monitor_energy=.false.
     !defaults given in parentheses:
     new_mts=.true.
     mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=500 !300 !1000 !(-1) # of mts sub-steps
+    mts_sub_steps=75 !(-1) # of mts sub-steps
     !mts_sub_steps=10
     force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
     convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
-    
+
     contact_distance=1.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
     contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
     debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=3.16e6 !for power-law-type friction
+    cdrag_grounding=1.e3!3.16e6 !for power-law-type friction
     h_to_init_grounding=200.0
     ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
     remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
 
     fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 4.  
     frac_thres_n = 12.
     frac_thres_t = 12.
 
@@ -86,7 +92,7 @@
     tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
     tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
     grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=1.0 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    coastal_drift=0.1 !(0.)Vel added to currents to cause bergs to drift away from land cells
     tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
     Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
     use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
@@ -119,8 +125,8 @@
 
     verbose=.false. !(F) Be verbose to stderr
     verbose_hrs=24000 ! (24) Period between verbose messages
-    traj_sample_hrs=0!0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=0!0!6 !(480) Period for writing sampled trajectories to disk
+    traj_sample_hrs=-1!0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=-1!0!6 !(480) Period for writing sampled trajectories to disk
     save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
     budget=.false. !(T) Calculate budgets
     debug=.false. !(F) Turn on debugging
diff --git a/tests/dem_ground_frac_test/input_dem_comp.nml b/tests/dem_ground_frac_test/input_dem_comp.nml
new file mode 100644
index 0000000..bcc2b3e
--- /dev/null
+++ b/tests/dem_ground_frac_test/input_dem_comp.nml
@@ -0,0 +1,192 @@
+
+&icebergs_driver_nml
+  ni=45 !30 !number of elements, x direction
+  nj=45 !30 !number of elements, y direction
+  ibdt=1800.0 !seconds
+  ibuo=0.1 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=999999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.true.
+  collision_test=.false.
+  grounding_test=.true.
+  bump_depth=200.0 !(m) depth of top of gaussian bump below sea level
+/
+
+&icebergs_nml
+
+    !use_damage=.true.
+    !damage_test_1=.true.
+
+    dem=.true.
+    ignore_tangential_force=.true.
+    poisson=0.3
+    dem_damping_coef=0. !1.0
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    dem_spring_coef=4471.938678723104 !1000.0 
+    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=100!75 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=1.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=200.0
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 1. 
+    frac_thres_n = 70. !2.1e4 !12.
+    frac_thres_t = 0. !12.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.false. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0.1 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=24000 ! (24) Period between verbose messages
+    traj_sample_hrs=-1!0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=-1!0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/dem_ground_frac_test/input_dem_orig.nml b/tests/dem_ground_frac_test/input_dem_orig.nml
new file mode 100644
index 0000000..404c2d4
--- /dev/null
+++ b/tests/dem_ground_frac_test/input_dem_orig.nml
@@ -0,0 +1,191 @@
+
+&icebergs_driver_nml
+  ni=90 !45 !30 !number of elements, x direction
+  nj=90 !45 !30 !number of elements, y direction
+  ibdt=1800.0 !seconds
+  ibuo=0.1 !05 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=999999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.true.
+  collision_test=.false.
+  grounding_test=.true.
+  bump_depth=200.0 !(m) depth of top of gaussian bump below sea level
+/
+
+&icebergs_nml
+
+    !use_damage=.true.
+    !damage_test_1=.true.
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    dem_spring_coef=1000.0 !4471.938678723104 !1000.0
+    !ignore_tangential_force=.true.
+    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=100 !(-1) # of mts sub-steps
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=1.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=200.0
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 1.  
+    frac_thres_n = 12. !0.!500.0 !12. !200.
+    frac_thres_t = 12. !0.!1000.0 !12. !200.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=90000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0.1 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=24000 ! (24) Period between verbose messages
+    traj_sample_hrs=-1!0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=-1!0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/dem_ground_frac_test/input_reg.nml b/tests/dem_ground_frac_test/input_reg.nml
index 332d03e..d0f4978 100644
--- a/tests/dem_ground_frac_test/input_reg.nml
+++ b/tests/dem_ground_frac_test/input_reg.nml
@@ -33,16 +33,16 @@
     !defaults given in parentheses:
     new_mts=.true.
     mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    !mts_sub_steps=1000 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
-    mts_sub_steps=300
+    mts_sub_steps=100 !50 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
     force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    explicit_inner_mts=.true. !If T, inner MTS iterations are treated explicitly
     convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
     
-    contact_distance=500.!1.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_distance=1.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
 
     contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
     debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=3.16e6 !for power-law-type friction
+    cdrag_grounding=1.e3 !3.16e6 !for power-law-type friction
     h_to_init_grounding=200.0
     ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
     remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
@@ -50,15 +50,16 @@
     !frac_thres_n = 12.
     !frac_thres_t = 12.
 
-    frac_thres_scaling=0.8 !h=300
-    fracture_criterion='strain' !('none') 'strain_rate','strain',or 'none'    
-    frac_thres_n = 0.0162
-    frac_thres_t = 0.0!457
+    !frac_thres_scaling=0.25 !h=300
+    !fracture_criterion='strain' !('none') 'strain_rate','strain',or 'none'    
+    !frac_thres_n = 0.0162
+    !frac_thres_t = 0.0!457
 
-    !fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    !frac_thres_scaling=1.0 !h=300 to 200, stress
-    !frac_thres_n = 2.5e3
-    !frac_thres_t = 0.0
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling=0.0033333 !this scaling corresponds w/ fixed stress calculation
+    !1.0 !h=300 to 200, stress
+    frac_thres_n = 3.5e3 !2.5e3
+    frac_thres_t = 50.e3!0.0
 
     halo=3 !(4) halo width
     Lx=45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
@@ -125,8 +126,8 @@
 
     verbose=.false. !(F) Be verbose to stderr
     verbose_hrs=24000 ! (24) Period between verbose messages
-    traj_sample_hrs=0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=0!6 !(480) Period for writing sampled trajectories to disk
+    traj_sample_hrs=-1!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=-1!6 !(480) Period for writing sampled trajectories to disk
     save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
     budget=.false. !(T) Calculate budgets
     debug=.false. !(F) Turn on debugging
diff --git a/tests/dem_ground_frac_test/input_reg_comp.nml b/tests/dem_ground_frac_test/input_reg_comp.nml
new file mode 100644
index 0000000..f54001b
--- /dev/null
+++ b/tests/dem_ground_frac_test/input_reg_comp.nml
@@ -0,0 +1,192 @@
+
+&icebergs_driver_nml
+  ni=45 !30 !number of elements, x direction
+  nj=45 !30 !number of elements, y direction
+  ibdt=1800.0 !seconds
+  ibuo=0.1 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=999999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.true.
+  collision_test=.false.
+  grounding_test=.true.
+  bump_depth=200.0 !(m) depth of top of gaussian bump below sea level 
+/
+
+&icebergs_nml
+
+
+    !dem=.true.
+    !poisson=0.3
+    !dem_damping_coef=0.99
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=1000.0
+    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=100 !50 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    explicit_inner_mts=.true. !If T, inner MTS iterations are treated explicitly
+    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
+    
+    contact_distance=1.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=1.e3 !3.16e6 !for power-law-type friction
+    h_to_init_grounding=200.0
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    !frac_thres_n = 12.
+    !frac_thres_t = 12.
+
+    !frac_thres_scaling=0.25 !h=300
+    !fracture_criterion='strain' !('none') 'strain_rate','strain',or 'none'    
+    !frac_thres_n = 0.0162
+    !frac_thres_t = 0.0!457
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling=1.0 !h=300 to 200, stress
+    frac_thres_n = 70. !2.1e4!3.5e3 !2.5e3
+    frac_thres_t = 0. !50.e3!0.0
+
+    halo=3 !(4) halo width
+    Lx=45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.false. !.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=1.0 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=24000 ! (24) Period between verbose messages
+    traj_sample_hrs=-1!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=-1!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/dem_ground_frac_test/input_reg_stress.nml b/tests/dem_ground_frac_test/input_reg_stress.nml
index 0b71d12..284f95c 100644
--- a/tests/dem_ground_frac_test/input_reg_stress.nml
+++ b/tests/dem_ground_frac_test/input_reg_stress.nml
@@ -33,16 +33,16 @@
     !defaults given in parentheses:
     new_mts=.true.
     mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    !mts_sub_steps=1000 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
-    mts_sub_steps=10 !300
+    mts_sub_steps=100 !50 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
     force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    explicit_inner_mts=.true. !If T, inner MTS iterations are treated explicitly
     convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
     
     contact_distance=1.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
 
     contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
     debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=3.16e6 !for power-law-type friction
+    cdrag_grounding=1.e3 !3.16e6 !for power-law-type friction
     h_to_init_grounding=200.0
     ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
     remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
@@ -125,8 +125,8 @@
 
     verbose=.false. !(F) Be verbose to stderr
     verbose_hrs=24000 ! (24) Period between verbose messages
-    traj_sample_hrs=0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=0!6 !(480) Period for writing sampled trajectories to disk
+    traj_sample_hrs=-1!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=-1!6 !(480) Period for writing sampled trajectories to disk
     save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
     budget=.false. !(T) Calculate budgets
     debug=.false. !(F) Turn on debugging
diff --git a/tests/dem_ground_frac_test/makeberg/makeberg.py b/tests/dem_ground_frac_test/makeberg/makeberg.py
index de25628..7d89aec 100755
--- a/tests/dem_ground_frac_test/makeberg/makeberg.py
+++ b/tests/dem_ground_frac_test/makeberg/makeberg.py
@@ -257,8 +257,8 @@ def create_empty_iceberg_restart_file(Empty_restart_filename):
 #R_frac=0.5*0.45 #2nd option
 radius=(np.sqrt(3)/2.)*(R_frac*grdres) #S is < 0.5 grid res
 #radius2=(np.sqrt(3)/2.)*(R_frac2*grdres) #S is < 0.5 grid res
-thickness1=300.0
-thickness2=300.0
+thickness1=200.0
+thickness2=200.0
 rho_ice=850.0
 
 
diff --git a/tests/dem_ssbeam_test/input.nml b/tests/dem_ssbeam_test/input.nml
index a6c18cd..5323907 100644
--- a/tests/dem_ssbeam_test/input.nml
+++ b/tests/dem_ssbeam_test/input.nml
@@ -116,8 +116,8 @@
 
     verbose=.false. !(F) Be verbose to stderr
     verbose_hrs=24000 ! (24) Period between verbose messages
-    traj_sample_hrs=0.0!5 !(24) sampling period for trajectory storage
-    traj_write_hrs=0.0!5 !(480) Period for writing sampled trajectories to disk
+    traj_sample_hrs=-1!5 !(24) sampling period for trajectory storage
+    traj_write_hrs=-1!5 !(480) Period for writing sampled trajectories to disk
     save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
     budget=.false. !(T) Calculate budgets
     debug=.false. !(F) Turn on debugging
diff --git a/tests/energy_test/input.nml b/tests/energy_test/input.nml
index 070b0f9..cd17b87 100644
--- a/tests/energy_test/input.nml
+++ b/tests/energy_test/input.nml
@@ -114,8 +114,8 @@
 
     verbose=.false. !(F) Be verbose to stderr
     verbose_hrs=24000 ! (24) Period between verbose messages
-    traj_sample_hrs=0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=0!6 !(480) Period for writing sampled trajectories to disk
+    traj_sample_hrs=-1!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=-1!6 !(480) Period for writing sampled trajectories to disk
     save_bond_traj=.false.!.true. !(F) If T, saves bond trajectories in a separate file
     budget=.false. !(T) Calculate budgets
     debug=.false. !(F) Turn on debugging
diff --git a/tests/energy_test2/input.nml b/tests/energy_test2/input.nml
index 6bd133d..1fc142e 100644
--- a/tests/energy_test2/input.nml
+++ b/tests/energy_test2/input.nml
@@ -109,8 +109,8 @@
 
     verbose=.false. !(F) Be verbose to stderr
     verbose_hrs=24000 ! (24) Period between verbose messages
-    traj_sample_hrs=0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=0!6 !(480) Period for writing sampled trajectories to disk
+    traj_sample_hrs=-1!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=-1!6 !(480) Period for writing sampled trajectories to disk
     save_bond_traj=.false.!.true. !(F) If T, saves bond trajectories in a separate file
     budget=.false. !(T) Calculate budgets
     debug=.false. !(F) Turn on debugging
diff --git a/tests/energy_test3/input.nml b/tests/energy_test3/input.nml
index 4edbd32..f56121b 100644
--- a/tests/energy_test3/input.nml
+++ b/tests/energy_test3/input.nml
@@ -130,8 +130,8 @@
 
     verbose=.false. !(F) Be verbose to stderr
     verbose_hrs=24000 ! (24) Period between verbose messages
-    traj_sample_hrs=0 !(24) sampling period for trajectory storage
-    traj_write_hrs=0 !(480) Period for writing sampled trajectories to disk
+    traj_sample_hrs=-1 !(24) sampling period for trajectory storage
+    traj_write_hrs=-1 !(480) Period for writing sampled trajectories to disk
     save_bond_traj=.true. !(F) If T, saves bond trajectories in a separate file
     budget=.false. !(T) Calculate budgets
     debug=.false. !(F) Turn on debugging
diff --git a/tests/frac_test/input.nml b/tests/frac_test/input.nml
index 0ea5017..0d6aab7 100644
--- a/tests/frac_test/input.nml
+++ b/tests/frac_test/input.nml
@@ -119,8 +119,8 @@
 
     verbose=.false. !(F) Be verbose to stderr
     verbose_hrs=24000 ! (24) Period between verbose messages
-    traj_sample_hrs=0 !(24) sampling period for trajectory storage
-    traj_write_hrs=0 !(480) Period for writing sampled trajectories to disk
+    traj_sample_hrs=-1 !(24) sampling period for trajectory storage
+    traj_write_hrs=-1 !(480) Period for writing sampled trajectories to disk
     save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
     budget=.false. !(T) Calculate budgets
     debug=.false. !(F) Turn on debugging
diff --git a/tests/ground_frac_test/input.nml b/tests/ground_frac_test/input.nml
index 1c15148..b8403a4 100644
--- a/tests/ground_frac_test/input.nml
+++ b/tests/ground_frac_test/input.nml
@@ -115,8 +115,8 @@
 
     verbose=.false. !(F) Be verbose to stderr
     verbose_hrs=24000 ! (24) Period between verbose messages
-    traj_sample_hrs=0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=0!6 !(480) Period for writing sampled trajectories to disk
+    traj_sample_hrs=-1!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=-1!6 !(480) Period for writing sampled trajectories to disk
     save_bond_traj=.true. !(F) If T, saves bond trajectories in a separate file
     budget=.false. !(T) Calculate budgets
     debug=.false. !(F) Turn on debugging

From b705b609259e94c0301ce8dbe494af4fb27f50aa Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Thu, 18 Feb 2021 20:09:52 -0500
Subject: [PATCH 278/361] partial fix for bond restart

---
 src/icebergs.F90                     | 6 +-----
 src/icebergs_io.F90                  | 2 +-
 tests/dem_ground_frac_test/input.nml | 4 ++--
 3 files changed, 4 insertions(+), 8 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 797fd85..be586b7 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -160,11 +160,7 @@ subroutine icebergs_init(bergs, &
       call read_restart_bonds(bergs,Time)
     endif
     call update_halo_icebergs(bergs)
-    if (bergs%manually_initialize_bonds) then
-      call initialize_iceberg_bonds(bergs)
-    else
-      call read_restart_bonds(bergs,Time)
-    endif
+    if (bergs%manually_initialize_bonds) call initialize_iceberg_bonds(bergs)
     if (bergs%mts) then
       call transfer_mts_bergs(bergs)
     else
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index 8c4b608..0cfaa40 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -1406,7 +1406,7 @@ subroutine read_restart_bonds(bergs,Time)
             call form_a_bond(first_berg, other_id(k), other_berg_ine(k), other_berg_jne(k),  second_berg)
             number_perfect_bonds=number_perfect_bonds+1
 
-            current_bond=>this%first_bond
+            current_bond=>first_berg%first_bond
 
             if (dem) then
               current_bond%tangd1=tangd1(k)
diff --git a/tests/dem_ground_frac_test/input.nml b/tests/dem_ground_frac_test/input.nml
index bcc2b3e..4bce62c 100644
--- a/tests/dem_ground_frac_test/input.nml
+++ b/tests/dem_ground_frac_test/input.nml
@@ -141,8 +141,8 @@
     ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
     require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
     use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
+    manually_initialize_bonds=.false.!.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.false.!.true.
     !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
     ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
     generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file

From 693179a831e4dec4770bf60244d5b9a2e39f8aa9 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Fri, 19 Feb 2021 09:49:30 -0500
Subject: [PATCH 279/361] assigned initial value of 'none' for
 fracture_criterion

---
 src/icebergs_framework.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 27384ae..6ca67cd 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -52,7 +52,7 @@ module ice_bergs_framework
 logical :: monitor_energy=.false. !<monitors energies: elastic (spring+collision), external, dissipated, fracture
 logical :: iceberg_bonds_on=.False. ! True=Allow icebergs to have bonds, False=don't allow.
 logical :: dem=.false. !< If T, run in DEM-mode with angular terms, variable stiffness, etc
-character(len=11) :: fracture_criterion !<'energy','stress','strain_rate','strain',or 'none'
+character(len=11) :: fracture_criterion='none' !<'energy','stress','strain_rate','strain',or 'none'
 logical :: use_damage=.false. !< Damage on bonds. Can evolve and serve as fracture criterion, or just to represent weaker bond
 
 !Public params !Niki: write a subroutine to expose these

From d2071bd917c8432231a8efeca8bb54c74b7c61b6 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Fri, 19 Feb 2021 15:56:28 -0500
Subject: [PATCH 280/361] Fixed angular velocity/rotation terms for dem-mode.
 Corrected which velocities are used for damping. A bit more development for
 constant_interaction_LW.

---
 src/icebergs.F90                     | 76 ++++++++++++++++++----------
 src/icebergs_framework.F90           | 11 ++++
 tests/dem_ground_frac_test/input.nml | 12 ++---
 tests/ground_frac_test/input.nml     |  1 +
 4 files changed, 67 insertions(+), 33 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index be586b7..130ae0e 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -654,7 +654,7 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
     !call rotpos_to_tang(lon2,lat2,x2,y2)
     u2=other_berg%uvel_old;  v2=other_berg%vvel_old !Old values are used to make it order invariant
 
-    if (bergs%constant_interaction_LW) then
+    if (bergs%constant_interaction_LW .and. bergs%mts .and. bonded) then
       ! use constant length and width here, just for interactions
       A1=bergs%constant_length*bergs%constant_width !Berg 1 area
       M1=A1*T1*bergs%rho_bergs                      !Berg 1 mass
@@ -893,10 +893,10 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
     !Rmin=min(R1,R2) !old
     if (R1<R2) then
       Rmin=R1
-      !T_Rmin=T1 !thickness of element w/ minimum radius
+      T_Rmin=T1 !thickness of element w/ minimum radius
     else
       Rmin=R2
-      !T_Rmin=T2
+      T_Rmin=T2
     endif
     l0=R1+R2
     delta=l0-r_dist
@@ -909,13 +909,15 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
     !bond width (determined at contact point)
     L=2.0*(Rmin+(Rmin-0.5*delta)*abs(R1-R2)/r_dist)
 
-    !Thick=T_Rmin+(Rmin-0.5*delta)*abs(T1-T2)/r_dist !the thickness (determined at contact point)
-    Thick=min(T1,T2) !minimum thickness makes more sense?
+    Thick=T_Rmin+(Rmin-0.5*delta)*abs(T1-T2)/r_dist !thickness as determined at contact point
+    !Thick=min(T1,T2) !minimum thickness
+    !Thick=0.5*(T1+T2) !average thickness
 
     youngs=bergs%dem_spring_coef
 
     !normal force:
     !Fn_x=youngs*Thick*delta*n1*L/l0 !Fn_y=youngs*Thick*delta*n2*L/l0
+    !normal stiffness is youngs*Thick*L/l0
     if (savestress) current_bond%nstress=-youngs*delta/l0 !normal stress
     Fn_x=youngs*Thick*delta*L/l0; Fn_y=Fn_x*n2; Fn_x=Fn_x*n1
 
@@ -951,7 +953,7 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
     endif
 
     !shear terms
-    ss_factor=-L*Thick*youngs/(l0*2.0*(1.0+bergs%poisson))
+    ss_factor=-L*Thick*youngs/(l0*2.0*(1.0+bergs%poisson)) !shear stiffness
     if (bergs%ignore_tangential_force) ss_factor=0.
     Fs_x=ss_factor*current_bond%tangd1; Fs_y=ss_factor*current_bond%tangd2 !shear forces
     if (savestress) current_bond%sstress=sqrt(Fs_x**2+Fs_y**2)/(L*Thick) !shear stress
@@ -1068,7 +1070,7 @@ subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, d
   real :: dragfrac, N_bonds, N_max, groundfrac, c_gnd, drag_gnd, scaling
   real :: minfricvel=3.17e-12 !m/s (~0.0001 m/a)
   type(bond), pointer :: current_bond
-  real :: IAd_x, IAd_y, sum_bond_Ee, sum_bond_Ed, oneoverkn
+  real :: IAd_x, IAd_y, sum_bond_Ee, sum_bond_Ed, oneoverkn, M2
   type(iceberg), pointer :: other_berg
 
   Runge_not_Verlet=bergs%Runge_not_Verlet  ! Loading directly from namelist/default , Alon
@@ -1309,7 +1311,14 @@ subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, d
     if (monitor_energy .or. bergs%fracture_criterion=='energy') then
       sum_bond_Ee=0.0
       sum_bond_Ed=0.0
-      M=berg%mass
+
+      if (bergs%constant_interaction_LW) then
+        ! mass according to constant length and width here, just for interactions
+        M=bergs%constant_length*bergs%constant_width*berg%thickness*bergs%rho_bergs
+      else
+        M=berg%mass
+      endif
+
       current_bond=>berg%first_bond
       do while (associated(current_bond)) ! loop over all bonds
         other_berg=>current_bond%other_berg
@@ -1338,6 +1347,13 @@ subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, d
 
         if (bergs%fracture_criterion=='energy') then
           oneoverkn = 1./bergs%spring_coef
+          if (bergs%constant_interaction_LW) then
+            ! other_berg mass according to constant length and width here, just for interactions
+            M2=bergs%constant_length*bergs%constant_width*other_berg%thickness*bergs%rho_bergs
+          else
+            M2=other_berg%mass
+          endif
+
           oneoverkn=oneoverkn*(M/min(M,other_berg%mass))
           current_bond%spring_pe = 0.5*((M*IA_x)**2+(M*IA_y)**2)*oneoverkn
         endif
@@ -1546,7 +1562,7 @@ subroutine accel_explicit_inner_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel,
   real :: P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y    !Added by Alon
   integer :: stderrunit
   type(bond), pointer :: current_bond
-  real :: IAd_x, IAd_y, sum_bond_Ee, sum_bond_Ed, oneoverkn
+  real :: IAd_x, IAd_y, sum_bond_Ee, sum_bond_Ed, oneoverkn, M2
   type(iceberg), pointer :: other_berg
   integer :: grdi,grdj
   logical :: bonded
@@ -1653,8 +1669,13 @@ subroutine accel_explicit_inner_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel,
       endif
     endif
 
-    !M=berg%thickness*(pi*R1**2)*bergs%rho_bergs
-    M=berg%mass
+    if (bergs%constant_interaction_LW) then
+      ! mass according to constant length and width here, just for interactions
+      M=bergs%constant_length*bergs%constant_width*berg%thickness*bergs%rho_bergs
+    else
+      M=berg%mass
+    endif
+
     IA_x=IA_x+F_x/M; IA_y=IA_y+F_y/M
     IAd_x=IAd_x+Fd_x/M; IAd_y=IAd_y+Fd_y/M
 
@@ -1677,7 +1698,6 @@ subroutine accel_explicit_inner_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel,
 
     !save bond energies
     if (monitor_energy .or. bergs%fracture_criterion=='energy') then
-      M=berg%mass
       current_bond=>berg%first_bond
       do while (associated(current_bond)) ! loop over all bonds
         other_berg=>current_bond%other_berg
@@ -1740,8 +1760,15 @@ subroutine accel_explicit_inner_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel,
         endif
 
         if (bergs%fracture_criterion=='energy') then
+          if (bergs%constant_interaction_LW) then
+            ! other_berg mass according to constant length and width here, just for interactions
+            M2=bergs%constant_length*bergs%constant_width*other_berg%thickness*bergs%rho_bergs
+          else
+            M2=other_berg%mass
+          endif
+
           oneoverkn = 1./bergs%spring_coef
-          oneoverkn=oneoverkn*(M/min(M,other_berg%mass))
+          oneoverkn=oneoverkn*(M/min(M,M2))
           current_bond%spring_pe = 0.5*((M*IA_x)**2+(M*IA_y)**2)*oneoverkn
         endif
 
@@ -5698,18 +5725,13 @@ subroutine evolve_icebergs_mts(bergs)
           berg%lon=lonn      ;  berg%lat=latn
           berg%lon_old=lonn  ;  berg%lat_old=latn
 
-          ! Set uvel_old to ustar for berg interactions?
-          ! if (new_mts) then
-          !   berg%uvel_old=berg%uvel+dt_2*(berg%axn_fast+berg%bxn_fast)
-          !   berg%vvel_old=berg%vvel+dt_2*(berg%ayn_fast+berg%bxn_fast)
-          ! else
-          !   berg%uvel_old=berg%uvel+dt_2*(berg%axn_fast)
-          !   berg%vvel_old=berg%vvel+dt_2*(berg%ayn_fast)
-          ! endif
-
-          if (bergs%dem) then
-            berg%ang_vel=berg%ang_vel+dt_2*berg%ang_accel
-            berg%rot=berg%rot+dt_2*berg%ang_vel
+          !Set uvel_old to ustar for berg interactions?
+          if (new_mts) then
+            berg%uvel_old=berg%uvel+dt_2*(berg%axn_fast+berg%bxn_fast)
+            berg%vvel_old=berg%vvel+dt_2*(berg%ayn_fast+berg%bxn_fast)
+          else
+            berg%uvel_old=berg%uvel+dt_2*(berg%axn_fast)
+            berg%vvel_old=berg%vvel+dt_2*(berg%ayn_fast)
           endif
         end if
         berg=>berg%next
@@ -5851,8 +5873,8 @@ subroutine evolve_icebergs_mts(bergs)
           berg%uvel_old=berg%uvel; berg%vvel_old=berg%vvel
 
           if (bergs%dem) then
-            berg%ang_vel=berg%ang_vel+dt_2*berg%ang_accel
-            berg%rot=berg%rot+dt_2*berg%ang_vel
+            berg%ang_vel=berg%ang_vel+dt*berg%ang_accel
+            berg%rot=berg%rot+dt*berg%ang_vel
           endif
 
           if (bergs%force_convergence) then
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 6ca67cd..7cbdf0f 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -1347,6 +1347,17 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%constant_width=constant_width
   bergs%dem_shear_for_frac_only=dem_shear_for_frac_only
 
+  if (monitor_energy) then
+    if (bergs%constant_interaction_LW) then
+      call error_mesg('KID, ice_bergs_framework_init', &
+        'cannot use monitor_energy with constant_interaction_LW yet', FATAL)
+    endif
+    if (bergs%dem .and. .not. bergs%ignore_tangential_force) then
+      call error_mesg('KID, ice_bergs_framework_init', &
+        'monitor_energy does not yet account for dem tangential force terms', FATAL)
+    endif
+  endif
+
   if (bergs%contact_distance>0) then
     dx_dlon=1; dy_dlat=1
     if (grd%grid_is_latlon) dy_dlat=pi_180*Rearth
diff --git a/tests/dem_ground_frac_test/input.nml b/tests/dem_ground_frac_test/input.nml
index 4bce62c..102fbe5 100644
--- a/tests/dem_ground_frac_test/input.nml
+++ b/tests/dem_ground_frac_test/input.nml
@@ -24,9 +24,9 @@
     !damage_test_1=.true.
 
     dem=.true.
-    ignore_tangential_force=.true.
+    ignore_tangential_force=.false.!.true.
     poisson=0.3
-    dem_damping_coef=0. !1.0
+    dem_damping_coef=1.0
     rho_bergs=850. ! (850) iceberg density
     !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
     !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
@@ -38,7 +38,7 @@
     !defaults given in parentheses:
     new_mts=.true.
     mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=100!75 !(-1) # of mts sub-steps
+    mts_sub_steps=10!75 !(-1) # of mts sub-steps
     !mts_sub_steps=10
     force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
     convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
@@ -53,7 +53,7 @@
 
     fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
     frac_thres_scaling = 1. 
-    frac_thres_n = 70. !2.1e4 !12.
+    frac_thres_n = 0.!70. !2.1e4 !12.
     frac_thres_t = 0. !12.
 
     !!fracture_criterion='strain'
@@ -141,8 +141,8 @@
     ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
     require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
     use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.false.!.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.false.!.true.
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
     !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
     ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
     generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
diff --git a/tests/ground_frac_test/input.nml b/tests/ground_frac_test/input.nml
index b8403a4..ad6aafa 100644
--- a/tests/ground_frac_test/input.nml
+++ b/tests/ground_frac_test/input.nml
@@ -1,3 +1,4 @@
+!NOTE: this result is from when we did NOT set uvel_old to ustar for berg interactions
 !KID, bergs_chksum: write_restart berg chksum=              32083975 chksum2=            2055392101 chksum3=           -2018330166 chksum4=           -2018330166 chksum5=           -1470408987 #=                    67
 !KID, grd_chksum2:    # of bergs/cell chksum=                     0 chksum2=                     0 min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
 ! Total number of bonds is:          286 

From 22909f77da411e2033bfa96e106cc851f34d84da Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Thu, 4 Mar 2021 16:27:33 -0500
Subject: [PATCH 281/361] added parameterization for footloose calving (England
 et al 2020). Works for non-bonded, TODO: finish footloose for bonded
 conglomerates. Moved rolling to separate solver.

---
 src/icebergs.F90                              | 541 ++++++++++++++++--
 src/icebergs_framework.F90                    |  28 +-
 src/icebergs_io.F90                           |  18 +-
 tests/footloose_no_bond_test/README           |   9 +
 tests/footloose_no_bond_test/RUN              |   5 +
 tests/footloose_no_bond_test/RUN1p            |   5 +
 .../animate_trajectories.py                   | 151 +++++
 tests/footloose_no_bond_test/diag_table       |   3 +
 tests/footloose_no_bond_test/input.nml        | 164 ++++++
 tests/footloose_no_bond_test/makeberg/RUN     |   5 +
 .../makeberg/makeberg.py                      | 278 +++++++++
 11 files changed, 1139 insertions(+), 68 deletions(-)
 create mode 100644 tests/footloose_no_bond_test/README
 create mode 100755 tests/footloose_no_bond_test/RUN
 create mode 100755 tests/footloose_no_bond_test/RUN1p
 create mode 100755 tests/footloose_no_bond_test/animate_trajectories.py
 create mode 100644 tests/footloose_no_bond_test/diag_table
 create mode 100644 tests/footloose_no_bond_test/input.nml
 create mode 100755 tests/footloose_no_bond_test/makeberg/RUN
 create mode 100755 tests/footloose_no_bond_test/makeberg/makeberg.py

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 130ae0e..cd9f468 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -14,6 +14,7 @@ module ice_bergs
 use mpp_mod, only: mpp_clock_begin, mpp_clock_end, mpp_clock_id
 use mpp_mod, only: CLOCK_COMPONENT, CLOCK_SUBCOMPONENT, CLOCK_LOOP
 use random_numbers_mod, only: initializeRandomNumberStream, getRandomNumbers, randomNumberStream
+use random_numbers_mod, only: constructSeed
 use mpp_mod, only: mpp_gather
 use fms_mod, only: clock_flag_default
 use fms_io_mod, only: get_instance_filename
@@ -506,17 +507,20 @@ subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
   logical :: critical_interaction_damping_on
   integer :: grdi, grdj
   logical :: iceberg_bonds_on
-  logical :: bonded !,contact_eligible,c_crit_dist
+  logical :: bonded
   integer :: nc_x,nc_y
 
-  nc_x=bergs%contact_cells_lon; nc_y=bergs%contact_cells_lat
-  iceberg_bonds_on=bergs%iceberg_bonds_on
-
-  IA_x=0.
-  IA_y=0.
+  IA_x=0.; IA_y=0.
   P_ia_11=0. ; P_ia_12=0. ;  P_ia_21=0.;  P_ia_22=0.
   P_ia_times_u_x=0. ; P_ia_times_u_y=0.
 
+  !no interactive force allowed for footloose child bergs until they are out of contact range of any of other berg
+  !at least once.
+  if (berg%fl_k.eq.-1) return
+
+  nc_x=bergs%contact_cells_lon; nc_y=bergs%contact_cells_lat
+  iceberg_bonds_on=bergs%iceberg_bonds_on
+
   if (bergs%mts .or. (bergs%contact_distance>0.) .or. (bergs%contact_spring_coef .ne. bergs%spring_coef) ) then
 
     ! Interactions for bonded berg elements only. For the mts scheme, this is only called if mts_part==3
@@ -641,7 +645,7 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
   real :: spring_coef, accel_spring, radial_damping_coef, p_ia_coef, tangental_damping_coef, bond_coef
   real :: crit_dist, vr1,vr2,vn,vn1,vn2,vt1,vt2
 
-  if (berg%id .ne. other_berg%id) then
+  if ((berg%id .ne. other_berg%id) .and. (berg%fl_k.ne.-1) .and. (other_berg%fl_k.ne.-1)) then
     ! From Berg 1
     T1=berg%thickness
     lon1=berg%lon_old; lat1=berg%lat_old
@@ -842,7 +846,7 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
   !relative particle rotation. Forces and torques were further modified here to depend
   !on ice thickness.
 
-  if (berg%id .ne. other_berg%id) then
+  if ((berg%id .ne. other_berg%id) .and. (berg%fl_k.ne.-1) .and. (other_berg%fl_k.ne.-1)) then
 
     ! From Berg 1
     T1=berg%thickness
@@ -2371,6 +2375,276 @@ subroutine dump_locvel(grd, i0, j0, A, lbl)
   enddo
 end subroutine dump_locvel
 
+
+!> Footloose (FL) mechanism
+!> Based on England et al. (2020) Modeling the breakup of tabular icebergs. Sci. Adv.
+subroutine footloose_calving(bergs, time)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  type(time_type), intent(in) :: time !< Model time
+  ! Local Variables
+  type(iceberg), pointer :: this
+  type(icebergs_gridded), pointer :: grd
+  type(bond), pointer :: current_bond
+  real, save :: N_max, youngs, poisson, l_c, lw_c, B_c, exp_nlambda
+  type(randomNumberStream),save :: rns ! Random numbers for stochastic tidal parameterization
+  logical, save :: Visited=.false.
+  integer :: grdi, grdj
+  integer, dimension(8) :: seed
+  real :: T, W, L, N_bonds, Ln, rn
+  real :: IC, max_k, k, Lr_fl, l_w, l_b, pu
+
+  ! For convenience
+  grd=>bergs%grd
+
+  if (.not. Visited) then
+    !define some constants:
+    !Maximum number of bonds that element can form based on shape
+    if (bergs%iceberg_bonds_on) then
+      if (bergs%hexagonal_icebergs) then
+        N_max=6.0
+      else
+        N_max=4.0
+      endif
+    else
+      N_max=0.0
+    endif
+
+    youngs=1.e8; poisson=0.3
+    l_c  = pi/(2.*sqrt(2.)) !for length-scale of child iceberg
+    lw_c = 1./(gravity*rho_seawater) !for buoyancy length
+    B_c  = youngs/(12.*(1.-poisson**2.)) !for bending stiffness
+    exp_nlambda=exp(-bergs%fl_r) !e^(-r*dt)
+    seed = constructSeed(1,1,time) !Seed random numbers for Poisson distribution
+    rns = initializeRandomNumberStream(seed)
+
+    Visited=.true.
+  endif
+
+  do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec !computational domain only
+    this=>bergs%list(grdi,grdj)%first
+    do while(associated(this))
+
+      !only non-static, non-footloose-child bergs are eligible for footloose calving:
+      if (.not. (this%static_berg.eq.1 .or. this%fl_k.lt.0)) then
+
+        T=this%thickness; W=this%width; L=this%length
+
+        N_bonds=0
+        if (bergs%iceberg_bonds_on) then
+          N_bonds=this%n_bonds
+          if (N_bonds>0) then
+            call error_mesg('KID,footloose_calving', &
+              'Bonded footloose calving not yet fully implemented!', FATAL)
+          endif
+        endif
+
+        l_w  = (lw_c*B_c*(T**3.))**0.25  !buoyancy length
+        l_b  = l_c*l_w                   !length of child icebergs
+
+
+        !---Determine k, the number of child bergs to calve via the footloose mechanism---!
+        !Bergs%fl_r is the average number of bergs to calve over the time increment
+        !given in seconds by bergs%fl_r_s. K is set according to a Poisson distribution
+        !or may be set directly equal to bergs%fl_r.
+        !England et al., 2020 used fl_r=4, fl_r_s= 86400 seconds (1 day), and daily
+        !timesteps, so that k (a whole number) gave the number of bergs to calve each
+        !timestep. Here, smaller timesteps are typically used, so k is scaled accordingly.
+        !Therefore, k is no longer a whole number, and is instead accumulated over time
+        !on this%fl_k. Then, floor(this%fl_k) child bergs are calved each timestep, after
+        !which, this number of child bergs is subtracted from this%fl_k
+
+        !A max possible number of child bergs to calve, max_k, is set to prevent footloose
+        !calving on very small icebergs or interior elements of bonded conglomerates:
+        if (bergs%iceberg_bonds_on .and. N_bonds>0.) then
+          if (N_bonds==N_max) then
+            max_k=0          !no FL calving allowed for interior bergs
+          else
+            call max_k_for_edge_elements
+          endif
+        else
+          !non-bonded berg must be larger than 3*(l_b) for FL calving. Set max_k accordingly.
+          max_k = max(floor((L - 3*(l_b**2.)/W))+1,0)
+        endif
+
+        if (max_k==0) then
+          k=0
+          this%fl_k=0
+        else
+          ! If sea ice concentration is <=50%, generate footloose child bergs
+          IC=min(1.,this%cn+bergs%sicn_shift)
+          if (.not. IC>0.5) then
+
+            if (bergs%fl_use_poisson_distribution) then
+              k=0; pu=1.0
+              do while (pu >= exp_nlambda)
+                call getRandomNumbers(rns, rn)
+                pu=pu*rn
+                k=k+1
+              enddo
+              k=k-1.0 !FL calving rate (per day or year)
+            else
+              k=bergs%fl_r
+            endif
+
+            !reduce FL calving rate based on number of bonds
+            if (bergs%iceberg_bonds_on) k=k*((N_max-N_bonds)/N_max)
+
+            k=k*(bergs%dt/bergs%fl_r_s) !scale k to dt
+            this%fl_k=this%fl_k+k       !update fl_k
+          endif
+
+          k=floor(this%fl_k)
+        endif
+
+
+        if (k>max_k) then
+          k=max_k
+          this%fl_k=0.
+        else
+          this%fl_k=this%fl_k-k !save the remainder for the next timestep
+        endif
+
+        !if there is footloose calving, create the new bergs and reduce length of parent berg
+        if (k>0) then
+
+          Lr_fl = k*3.*(l_b**2.)/W !FL mechanism length reduction for parent berg
+
+          call calve_fl_icebergs(bergs,this,k,l_b)
+
+          Ln=L-Lr_fl !new length
+          if (Ln .le. 0) then
+            if (N_bonds==0) then
+              call error_mesg('KID,footloose_calving', &
+                'non-edge element has fully calved from footloose mechanism', FATAL)
+            endif
+            this%fl_k=-3 !marks this berg to be deleted later
+          else
+            !update length, width, thickness,and mass of parent berg
+            if (bergs%allow_bergs_to_roll .and. N_bonds.eq.0.) call rolling(bergs,T,W,Ln)
+            this%thickness=T; this%width=min(W,Ln); this%length=max(W,Ln)
+            this%mass=this%length*this%width*this%thickness*bergs%rho_bergs
+          endif
+        endif
+      endif
+      this=>this%next
+    enddo
+  enddo; enddo
+
+contains
+
+  !TODO: finish this
+  subroutine max_k_for_edge_elements
+    max_k=huge(1.0)
+  end subroutine max_k_for_edge_elements
+
+end subroutine footloose_calving
+
+!> Delete any edge elements that fully calved from the footloose mechanism
+subroutine delete_fully_fl_calved_edge_elements(bergs)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  ! Local Variables
+  type(iceberg), pointer :: this, kick_the_bucket
+  type(icebergs_gridded), pointer :: grd
+  integer :: grdi,grdj
+
+  ! For convenience
+  grd=>bergs%grd
+
+  do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this)) ! loop over all bergs
+      if (this%fl_k==-3) then
+        !berg is marked to delete
+        kick_the_bucket=>this
+        this=>this%next
+        print *,'deleting berg',this%id
+        call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
+      else
+        this=>this%next
+      endif
+    enddo
+  enddo; enddo
+end subroutine delete_fully_fl_calved_edge_elements
+
+!> Adjust footloose child bergs to be eligible for contact interactions once they are
+!> out of contact range of any other berg for the first time
+subroutine adjust_fl_berg_interactivity(bergs)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  ! Local Variables
+  type(iceberg), pointer :: this, other_berg
+  type(icebergs_gridded), pointer :: grd
+  integer :: grdi, grdj, grdi2, grdj2, nc_x, nc_y
+  logical :: contact,radial_contact
+  real :: lat1,lat2,lon1,lon2,dlon,dlat,dx_dlon,dy_dlat,lat_ref
+  real :: r_dist,crit_dist,R1,R2,rdenom
+
+  ! For convenience
+  grd=>bergs%grd
+
+  nc_x=bergs%contact_cells_lon; nc_y=bergs%contact_cells_lat
+
+  if (nc_x.eq.1 .and. nc_y.eq.1) then
+    radial_contact=.true. !contact based on berg radii can occur
+    if (bergs%hexagonal_icebergs) then
+      rdenom=1./(2.*sqrt(3.))
+    else
+      !rdenom=1./pi
+      rdenom=1./4.
+    endif
+  else
+    radial_contact=.false.
+    crit_dist=bergs%contact_distance**2
+  endif
+
+  do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this))
+      if (this%fl_k.eq.-1) then
+        !It is a non-interactive, footloose child berg. Test if within contact range of another berg
+        contact=.false.
+        lat1=this%lat; lon1=this%lon
+        if (radial_contact) R1=sqrt(this%length*this%width*rdenom) !radius of current berg
+        do grdj2=max(grdj-nc_y,grd%jsd+1),min(grdj+nc_y,grd%jed)
+          do grdi2=max(grdi-nc_x,grd%isd+1),min(grdi+nc_x,grd%ied)
+            other_berg=>bergs%list(grdi2,grdj2)%first
+            do while (associated(other_berg))
+              if (other_berg%id.ne.this%id) then
+                lat2=other_berg%lat; lon2=other_berg%lon
+                dlon=lon2-lon1; dlat=lat2-lat1
+                if (radial_contact) then
+                  R2=sqrt(other_berg%length*other_berg%width*rdenom)
+                  crit_dist=max(R1+R2,bergs%contact_distance)**2
+                endif
+                if (bergs%grd%grid_is_latlon) then
+                  lat_ref=0.5*(lat1+lat2)
+                  dx_dlon=pi_180*Rearth*cos(lat_ref*pi_180); dy_dlat=pi_180*Rearth
+                  r_dist=(dlon*dx_dlon)**2 + (dlat*dy_dlat)**2
+                else
+                  r_dist=dlon**2 + dlat**2
+                endif
+                if (r_dist<crit_dist) then
+                  contact=.true.
+                  exit
+                endif
+              endif
+              other_berg=>other_berg%next
+            enddo
+            if (contact) exit
+          enddo
+          if (contact) exit
+        enddo
+        !if outside of contact range, mark the berg eligible for future interaction/contact
+        if (.not. contact) this%fl_k=-2
+      endif
+      this=>this%next
+    enddo
+  enddo; enddo
+
+end subroutine adjust_fl_berg_interactivity
+
 !> Steps forward thermodynamic state of all bergs
 subroutine thermodynamics(bergs)
   ! Arguments
@@ -2382,9 +2656,7 @@ subroutine thermodynamics(bergs)
   real :: Mv, Me, Mb, melt, dvo, dva, dM, Ss, dMe, dMb, dMv
   real :: Mnew, Mnew1, Mnew2, Hocean
   real :: Mbits, nMbits, dMbitsE, dMbitsM, Lbits, Abits, Mbb
-  real :: tip_parameter
   real :: Ms, N_bonds, N_max !Ice shelf melt, Number of bonds, Max_number of bonds
-  real :: Delta, q
   integer :: i,j, stderrunit
   type(iceberg), pointer :: this, next
   real, parameter :: perday=1./86400.
@@ -2575,44 +2847,8 @@ subroutine thermodynamics(bergs)
         call error_mesg('KID, thermodynamics', 'berg appears to have grounded!', FATAL)
       endif
 
-      ! Rolling
-      !There are now 3 iceberg rolling schemes:
-      !1) Rolling based on aspect ratio threshold (iceberg of constant density)
-      !2) Rolling based on corrected Weeks and Mellor scheme
-      !3) Rolling based on incorrect Weeks and Mellor scheme - kept for legacy reasons
-      if (bergs%allow_bergs_to_roll .and. N_bonds.eq.0.) then !only allow non-bonded,non-static bergs to roll
-        Dn=(bergs%rho_bergs/rho_seawater)*Tn ! draught (keel depth)
-        if ( Dn>0. ) then
-          if ( (.not.bergs%use_updated_rolling_scheme) .and. (bergs%tip_parameter<999.) ) then    !Use Rolling Scheme 3
-              if ( max(Wn,Ln)<sqrt(0.92*(Dn**2)+58.32*Dn) ) then
-                call swap_variables(Tn,Wn)
-              endif
-          else
-            if (Wn>Ln) call swap_variables(Ln,Wn)  !Make sure that Wn is the smaller dimension
-
-            if ( (.not.bergs%use_updated_rolling_scheme) .and. (bergs%tip_parameter>=999.) ) then    !Use Rolling Scheme 2
-              q=bergs%rho_bergs/rho_seawater
-              Delta=6.0
-              if (Wn<sqrt((6.0*q*(1-q)*(Tn**2))-(12*Delta*q*Tn))) then
-                  call swap_variables(Tn,Wn)
-              endif
-            endif
-
-            if (bergs%use_updated_rolling_scheme) then    !Use Rolling Scheme 1
-              if (bergs%tip_parameter>0.) then
-                tip_parameter=bergs%tip_parameter
-              else
-                ! Equation 27 from Burton et al 2012, or equivolently, Weeks and Mellor 1979 with constant density
-                tip_parameter=sqrt(6*(bergs%rho_bergs/rho_seawater)*(1-(bergs%rho_bergs/rho_seawater)))   !using default values gives 0.92
-              endif
-              if ((tip_parameter*Tn)>Wn)  then     !note that we use the Thickness instead of the Draft
-                  call swap_variables(Tn,Wn)
-              endif
-            endif
-          endif
-          Dn=(bergs%rho_bergs/rho_seawater)*Tn ! re-calculate draught (keel depth) for grounding
-        endif
-      endif
+      if (bergs%allow_bergs_to_roll .and. N_bonds.eq.0.) call rolling(bergs,Tn,Wn,Ln)
+      !Dn=(bergs%rho_bergs/rho_seawater)*Tn ! re-calculate draught (keel depth) for grounding
 
       !This option allows iceberg melt fluxes to enter the ocean without the icebergs changing shape
       if (bergs%Iceberg_melt_without_decay) then
@@ -2655,8 +2891,57 @@ subroutine thermodynamics(bergs)
       this=>next
     enddo
   enddo ; enddo
+end subroutine thermodynamics
 
-  contains
+!> Rolling
+!> There are now 3 iceberg rolling schemes:
+!> 1) Rolling based on aspect ratio threshold (iceberg of constant density)
+!> 2) Rolling based on corrected Weeks and Mellor scheme
+!> 3) Rolling based on incorrect Weeks and Mellor scheme - kept for legacy reasons
+subroutine rolling(bergs,Tn,Wn,Ln)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  real :: N_bonds !< Number of bonds
+  real :: Tn !< Berg thickness
+  real :: Wn !< Berg width
+  real :: Ln !< Berg length
+  ! Local variables
+  real, parameter :: Delta=6.0
+  real :: Dn, q, tip_parameter
+
+  Dn=(bergs%rho_bergs/rho_seawater)*Tn ! draught (keel depth)
+  if ( Dn>0. ) then
+    if ( (.not.bergs%use_updated_rolling_scheme) .and. (bergs%tip_parameter<999.) ) then    !Use Rolling Scheme 3
+      if ( max(Wn,Ln)<sqrt(0.92*(Dn**2)+58.32*Dn) ) then
+        call swap_variables(Tn,Wn)
+      endif
+    else
+      if (Wn>Ln) call swap_variables(Ln,Wn)  !Make sure that Wn is the smaller dimension
+
+      if ( (.not.bergs%use_updated_rolling_scheme) .and. (bergs%tip_parameter>=999.) ) then    !Use Rolling Scheme 2
+        q=bergs%rho_bergs/rho_seawater
+        if (Wn<sqrt((6.0*q*(1-q)*(Tn**2))-(12*Delta*q*Tn))) then
+          call swap_variables(Tn,Wn)
+        endif
+      endif
+
+      if (bergs%use_updated_rolling_scheme) then    !Use Rolling Scheme 1
+        if (bergs%tip_parameter>0.) then
+          tip_parameter=bergs%tip_parameter
+        else
+          ! Equation 27 from Burton et al 2012, or equivalently, Weeks and Mellor 1979 with constant density
+          ! Tip_parameter=0.92 if using default values
+          tip_parameter=sqrt(6*(bergs%rho_bergs/rho_seawater)*(1-(bergs%rho_bergs/rho_seawater)))
+        endif
+        if ((tip_parameter*Tn)>Wn)  then     !note that we use the Thickness instead of the Draft
+          call swap_variables(Tn,Wn)
+        endif
+      endif
+    endif
+    !Dn=(bergs%rho_bergs/rho_seawater)*Tn ! re-calculate draught (keel depth) for grounding
+  endif
+
+contains
 
   subroutine swap_variables(x,y)
     ! Arguments
@@ -2666,8 +2951,7 @@ subroutine swap_variables(x,y)
     x=y
     y=temp
   end subroutine swap_variables
-
-end subroutine thermodynamics
+end subroutine rolling
 
 subroutine create_gridded_icebergs_fields(bergs)
 ! Arguments
@@ -4630,6 +4914,12 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 
   call send_bergs_to_other_pes(bergs)
   if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after send_bergs() ')
+
+  ! Footloose mechanism part 1: calve the child icebergs
+  if (bergs%fl_r>0.) then
+    call footloose_calving(bergs, time)
+  endif
+
   if (bergs%mts) then
     call interp_gridded_fields_to_bergs(bergs)
     call transfer_mts_bergs(bergs)
@@ -4651,6 +4941,15 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   if (debug) call checksum_gridded(bergs%grd, 's/r run after exchange')
   call mpp_clock_end(bergs%clock_com)
 
+  ! Footloose mechanism part 2:
+  if (bergs%fl_r>0.) then
+    !delete any edge elements that have fully calved from the footloose mechanism
+    if (bergs%iceberg_bonds_on) call delete_fully_fl_calved_edge_elements(bergs)
+    !child bergs become interactive once they are out of contact range of any other
+    !berg for the first time
+    if (bergs%interactive_icebergs_on) call adjust_fl_berg_interactivity(bergs)
+  endif
+
   if (bergs%find_melt_using_spread_mass .or. bergs%mts) then
     call calculate_mass_on_ocean(bergs, with_diagnostics=.false.)
   end if
@@ -5382,18 +5681,22 @@ subroutine calve_icebergs(bergs)
           newberg%yj=yj
           newberg%uvel=0.
           newberg%vvel=0.
-          newberg%uvel_prev=0.  !Added by Alex
-          newberg%vvel_prev=0.  !Added by Alex
-          newberg%uvel_old=0.  !Added by Alex
-          newberg%vvel_old=0.  !Added by Alex
-          newberg%lon_prev=newberg%lon  !Added by Alex
-          newberg%lat_prev=newberg%lat  !Added by Alex
-          newberg%lon_old=newberg%lon  !Added by Alex
-          newberg%lat_old=newberg%lat  !Added by Alex
-          newberg%axn=0. !Added by Alon
-          newberg%ayn=0. !Added by Alon
-          newberg%bxn=0. !Added by Alon
-          newberg%byn=0. !Added by Alon
+          !--added by Alex:
+          newberg%uvel_prev=0.
+          newberg%vvel_prev=0.
+          newberg%uvel_old=0.
+          newberg%vvel_old=0.
+          newberg%lon_prev=newberg%lon
+          newberg%lat_prev=newberg%lat
+          newberg%lon_old=newberg%lon
+          newberg%lat_old=newberg%lat
+          newberg%fl_k=0.
+          !--added by Alon
+          newberg%axn=0.
+          newberg%ayn=0.
+          newberg%bxn=0.
+          newberg%byn=0.
+          !---
           newberg%mass=bergs%initial_mass(k)
           newberg%thickness=bergs%initial_thickness(k)
           newberg%width=bergs%initial_width(k)
@@ -5465,6 +5768,118 @@ subroutine calve_icebergs(bergs)
 
 end subroutine calve_icebergs
 
+  !> Calve footloose icebergs from parent berg
+subroutine calve_fl_icebergs(bergs,pberg,k,l_b)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  type(iceberg), pointer :: pberg !< Parent berg
+  type(real),intent(in) :: k !< Number of child bergs to calve
+  type(real),intent(in) :: l_b !< The width, and 1/3 the length, of a child berg
+  ! Local variables
+  type(iceberg) :: cberg ! The new child berg
+  type(icebergs_gridded), pointer :: grd
+
+  ! For convenience
+  grd=>bergs%grd
+
+  !A new child berg (cberg) that calves from the footloose mechanism initially has same position as the parent berg.
+  !Initially, cberg%fl_k is set to -1 to mark the berg as a child berg.
+  !If fl_k<0, the berg will is not eligible to decay via footloose calving (see subroutine footloose_calving)
+  !If fl_k==-1, the berg will also not interact with other berg elements. This is necessary because the child berg
+  !will initially overlap its parent berg, which would otherwise result in unrealistic contact forces.
+  !However, if (bergs%interactive_icebergs_on), a berg with fl_k==-1 will be set to fl_k=-2 once it is out of
+  !contact range of any other berg. With fl_k=-2, interactive contact forces may now be applied
+
+  !Set variable values for the new child berg:
+
+  !different values from parent:
+  cberg%width        = l_b/3.
+  cberg%length       = l_b
+  cberg%mass         = cberg%width * cberg%length * pberg%thickness * bergs%rho_bergs
+  cberg%start_lon    = pberg%lon
+  cberg%start_lat    = pberg%lat
+  cberg%start_day    = bergs%current_yearday
+  cberg%start_mass   = cberg%mass
+  cberg%mass_scaling = k !k is the number of icebergs cberg represents
+  cberg%mass_of_bits = 0.0
+  cberg%fl_k         = -1.0
+  cberg%start_year   = bergs%current_year
+  cberg%id           = generate_id(grd, pberg%ine, pberg%jne)
+
+  !same values as parent:
+  cberg%thickness    = pberg%thickness
+  cberg%lon          = pberg%lon
+  cberg%lat          = pberg%lat
+  cberg%lon_prev     = pberg%lon_prev
+  cberg%lat_prev     = pberg%lat_prev
+  cberg%uvel         = pberg%uvel
+  cberg%vvel         = pberg%vvel
+  cberg%axn          = pberg%axn
+  cberg%ayn          = pberg%ayn
+  cberg%bxn          = pberg%bxn
+  cberg%byn          = pberg%byn
+  cberg%uvel_prev    = pberg%uvel_prev
+  cberg%vvel_prev    = pberg%vvel_prev
+  cberg%uvel_old     = pberg%uvel_old
+  cberg%vvel_old     = pberg%vvel_old
+  cberg%lon_old      = pberg%lon_old
+  cberg%lat_old      = pberg%lat_old
+  cberg%heat_density = pberg%heat_density
+  cberg%halo_berg    = pberg%halo_berg
+  cberg%static_berg  = pberg%static_berg
+  cberg%ine          = pberg%ine
+  cberg%jne          = pberg%jne
+  cberg%xi           = pberg%xi
+  cberg%yj           = pberg%yj
+  cberg%uo           = pberg%uo
+  cberg%vo           = pberg%vo
+  cberg%ui           = pberg%ui
+  cberg%vi           = pberg%vi
+  cberg%ua           = pberg%ua
+  cberg%va           = pberg%va
+  cberg%ssh_x        = pberg%ssh_x
+  cberg%ssh_y        = pberg%ssh_y
+  cberg%sst          = pberg%sst
+  cberg%sss          = pberg%sss
+  cberg%cn           = pberg%cn
+  cberg%hi           = pberg%hi
+  cberg%od           = pberg%od
+
+  !optional variables
+  if (bergs%mts) then
+    allocate(cberg%axn_fast,cberg%ayn_fast,cberg%bxn_fast,cberg%byn_fast,cberg%conglom_id)
+    cberg%axn_fast=pberg%axn_fast
+    cberg%ayn_fast=pberg%ayn_fast
+    cberg%bxn_fast=pberg%bxn_fast
+    cberg%byn_fast=pberg%byn_fast
+    cberg%conglom_id=pberg%conglom_id
+  endif
+
+  if (bergs%iceberg_bonds_on) then
+    allocate(cberg%n_bonds)
+    cberg%n_bonds=0
+  endif
+
+  if (bergs%dem) then
+    allocate(cberg%ang_vel,cberg%ang_accel,cberg%rot)
+    cberg%ang_vel=0.; cberg%ang_accel=0.; cberg%rot=0.
+  endif
+
+  if (monitor_energy) then
+    allocate(cberg%Ee,cberg%Ed,cberg%Eext,cberg%Ee_contact,cberg%Ed_contact,cberg%Efrac,&
+      cberg%Ee_temp,cberg%Ed_temp,cberg%Eext_temp,cberg%Ee_contact_temp,cberg%Ed_contact_temp)
+    cberg%Ee=0.; cberg%Ed=0.; cberg%Eext=0.; cberg%Ee_contact=0.; cberg%Ed_contact=0.
+    cberg%Efrac=0.; cberg%Ee_temp=0.; cberg%Ed_temp=0.;cberg%Eext_temp=0.;
+    cberg%Ee_contact_temp=0.; cberg%Ed_contact_temp =0.
+  endif
+
+  if (bergs%fracture_criterion .ne. 'none' .and. (.not. bergs%dem)) then
+    allocate(cberg%accum_bond_rotation)
+    cberg%accum_bond_rotation=0.
+  endif
+
+  call add_new_berg_to_list(bergs%list(cberg%ine,cberg%jne)%first, cberg)
+end subroutine calve_fl_icebergs
 
 !> Evolves icebergs forward by updating velocity and position with a multiple-time-step Velocity Verlet
 !! scheme. Experimental option: each short/long step can be iterated until a given convergence tolerance
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 7cbdf0f..c8a1fe0 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -18,8 +18,8 @@ module ice_bergs_framework
 
 implicit none ; private
 
-integer :: buffer_width=33 ! This should be a parameter
-integer :: buffer_width_traj=35 ! This should be a parameter
+integer :: buffer_width=34 ! This should be a parameter
+integer :: buffer_width_traj=36 ! This should be a parameter
 integer :: buffer_width_bond_traj=11 !This should be a parameter
 integer, parameter :: nclasses=10 ! Number of ice bergs classes
 
@@ -221,6 +221,7 @@ module ice_bergs_framework
   real :: byn
   real :: uvel_prev
   real :: vvel_prev
+  real :: fl_k
   real :: uo !< Zonal velocity of ocean (m/s)
   real :: vo !< Meridional velocity of ocean (m/s)
   real :: ui !< Zonal velocity of ice (m/s)
@@ -300,6 +301,7 @@ module ice_bergs_framework
   real :: start_mass !< Mass berg had when created (kg)
   real :: mass_scaling !< Multiplier to scale mass when interpreting berg as a cloud of bergs (nondim)
   real :: mass_of_bits !< Mass of bergy bits following berg (kg)
+  real :: fl_k !< Cumulative number of footloose bergs to calve
   real :: heat_density !< Heat density of berg (J/kg)
   real :: halo_berg  ! Equal to zero for bergs on computational domain, and =1 for bergs on the halo
   real :: static_berg  ! Equal to 1 for icebergs which are static (not allowed to move). Might be extended to grounding later.
@@ -593,7 +595,9 @@ module ice_bergs_framework
   real :: constant_length=0.!< If constant_interaction_LW, the constant length. If 0, will be set to max initial length
   real :: constant_width=0. !< If constant_interaction_LW, the constant width.  If 0, will be set to max initial width
   ! Footloose calving parameters [England et al (2020) Modeling the breakup of tabular icebergs. Sci. Adv.]
-  !real ::
+  logical :: fl_use_poisson_distribution=.true. !< fl_r is (T) mean of Poisson distribution to determine k, or (F) k=fl_r
+  real :: fl_r=0. !< footloose average number of bergs calved per fl_r_s
+  real :: fl_r_s=0. !< seconds over which fl_r footloose bergs calve
 end type icebergs
 
 !> Read original restarts. Needs to be module global so can be public to icebergs_mod.
@@ -774,6 +778,10 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: constant_interaction_LW=.false. !< Always use the initial, globally constant, element length & width during berg interactions
 real :: constant_length=0. !< If constant_interaction_LW, the constant length used. If zero in the nml, will be set to max initial L
 real :: constant_width=0. !< If constant_interaction_LW, the constant width used. If zero in the nml, will be set to max initial W
+! Footloose calving parameters [England et al (2020) Modeling the breakup of tabular icebergs. Sci. Adv.]
+logical :: fl_use_poisson_distribution=.true. !< fl_r is (T) mean of Poisson distribution to determine k, or (F) k=fl_r
+real :: fl_r=0. !< footloose average number of bergs calved per fl_r_s
+real :: fl_r_s=0. !< seconds over which fl_r footloose bergs calve
 
 namelist /icebergs_nml/ verbose, budget, halo,  traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,Static_icebergs,  &
          distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,bond_coef, radial_damping_coef, tangental_damping_coef, only_interactive_forces, &
@@ -790,7 +798,7 @@ subroutine ice_bergs_framework_init(bergs, &
          mts,new_mts,ewsame,monitor_energy,mts_sub_steps,contact_distance,length_for_manually_initialize_bonds,manually_initialize_bonds_from_radii,contact_spring_coef,&
          fracture_criterion, damage_test_1, uniaxial_test, debug_write,cdrag_grounding,h_to_init_grounding,frac_thres_scaling,frac_thres_n,frac_thres_t,save_bond_traj,remove_unused_bergs,&
          force_convergence,explicit_inner_mts,convergence_tolerance,&
-         dem,ignore_tangential_force,poisson,dem_spring_coef,dem_damping_coef,dem_beam_test,constant_interaction_LW,constant_length,constant_width,dem_shear_for_frac_only,use_damage
+         dem,ignore_tangential_force,poisson,dem_spring_coef,dem_damping_coef,dem_beam_test,constant_interaction_LW,constant_length,constant_width,dem_shear_for_frac_only,use_damage, fl_use_poisson_distribution, fl_r, fl_r_s
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -1346,6 +1354,10 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%constant_length=constant_length
   bergs%constant_width=constant_width
   bergs%dem_shear_for_frac_only=dem_shear_for_frac_only
+  ! Footloose calving parameters
+  bergs%fl_use_poisson_distribution=fl_use_poisson_distribution
+  bergs%fl_r=fl_r
+  bergs%fl_r_s=fl_r_s
 
   if (monitor_energy) then
     if (bergs%constant_interaction_LW) then
@@ -3084,6 +3096,7 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
   call push_buffer_value(buff%data(:,n), counter, berg%thickness)
   call push_buffer_value(buff%data(:,n), counter, berg%width)
   call push_buffer_value(buff%data(:,n), counter, berg%length)
+  call push_buffer_value(buff%data(:,n), counter, berg%fl_k)
   call push_buffer_value(buff%data(:,n), counter, berg%mass_scaling)
   call push_buffer_value(buff%data(:,n), counter, berg%mass_of_bits)
   call push_buffer_value(buff%data(:,n), counter, berg%heat_density)
@@ -3305,6 +3318,9 @@ subroutine clear_berg_from_partners_bonds(berg)
           !write(stderrunit,*) , 'Clearing', berg%id, matching_bond%other_id,other_berg%id, mpp_pe()
           matching_bond%other_berg=>null()
           matching_bond=>null()
+          if (iceberg_bonds_on) then !should not find bonds unless they are on anyway, but just to be safe...
+            if (other_berg%n_bonds>0) other_berg%n_bonds=other_berg%n_bonds-1
+          endif
         else
           matching_bond=>matching_bond%next_bond
         endif
@@ -3390,6 +3406,7 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
   call pull_buffer_value(buff%data(:,n), counter, localberg%thickness)
   call pull_buffer_value(buff%data(:,n), counter, localberg%width)
   call pull_buffer_value(buff%data(:,n), counter, localberg%length)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%fl_k)
   call pull_buffer_value(buff%data(:,n), counter, localberg%mass_scaling)
   call pull_buffer_value(buff%data(:,n), counter, localberg%mass_of_bits)
   call pull_buffer_value(buff%data(:,n), counter, localberg%heat_density)
@@ -3680,6 +3697,7 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj)
     call push_buffer_value(buff%data(:,n),counter,traj%thickness)
     call push_buffer_value(buff%data(:,n),counter,traj%width)
     call push_buffer_value(buff%data(:,n),counter,traj%length)
+    call push_buffer_value(buff%data(:,n),counter,traj%fl_k)
     call push_buffer_value(buff%data(:,n),counter,traj%uo)
     call push_buffer_value(buff%data(:,n),counter,traj%vo)
     call push_buffer_value(buff%data(:,n),counter,traj%ui)
@@ -3787,6 +3805,7 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj)
     call pull_buffer_value(buff%data(:,n),counter,traj%thickness)
     call pull_buffer_value(buff%data(:,n),counter,traj%width)
     call pull_buffer_value(buff%data(:,n),counter,traj%length)
+    call pull_buffer_value(buff%data(:,n),counter,traj%fl_k)
     call pull_buffer_value(buff%data(:,n),counter,traj%uo)
     call pull_buffer_value(buff%data(:,n),counter,traj%vo)
     call pull_buffer_value(buff%data(:,n),counter,traj%ui)
@@ -5678,6 +5697,7 @@ subroutine record_posn(bergs)
         posn%thickness=this%thickness
         posn%width=this%width
         posn%length=this%length
+        posn%fl_k=this%fl_k
         posn%uo=this%uo
         posn%vo=this%vo
         posn%ui=this%ui
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index 0cfaa40..5647452 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -141,6 +141,7 @@ subroutine write_restart(bergs, time_stamp)
                                    thickness,    &
                                    width,        &
                                    length,       &
+                                   fl_k,         &
                                    start_lon,    &
                                    start_lat,    &
                                    start_day,    &
@@ -216,6 +217,7 @@ subroutine write_restart(bergs, time_stamp)
    allocate(thickness(nbergs))
    allocate(width(nbergs))
    allocate(length(nbergs))
+   allocate(fl_k(nbergs))
    allocate(start_lon(nbergs))
    allocate(start_lat(nbergs))
    allocate(start_day(nbergs))
@@ -273,6 +275,7 @@ subroutine write_restart(bergs, time_stamp)
   id = register_restart_field(bergs_restart,filename,'thickness',thickness,longname='thickness',units='m')
   id = register_restart_field(bergs_restart,filename,'width',width,longname='width',units='m')
   id = register_restart_field(bergs_restart,filename,'length',length,longname='length',units='m')
+  id = register_restart_field(bergs_restart,filename,'fl_k',fl_k,longname='footloose calving k',units='m')
   id = register_restart_field(bergs_restart,filename,'start_lon',start_lon, &
                                             longname='longitude of calving location',units='degrees_E')
   id = register_restart_field(bergs_restart,filename,'start_lat',start_lat, &
@@ -347,6 +350,7 @@ subroutine write_restart(bergs, time_stamp)
       axn(i) = this%axn; ayn(i) = this%ayn !Added by Alon
       bxn(i) = this%bxn; byn(i) = this%byn !Added by Alon
       width(i) = this%width; length(i) = this%length
+      fl_k(i) = this%fl_k
       start_lon(i) = this%start_lon; start_lat(i) = this%start_lat
       start_year(i) = this%start_year; start_day(i) = this%start_day
       start_mass(i) = this%start_mass; mass_scaling(i) = this%mass_scaling
@@ -389,6 +393,7 @@ subroutine write_restart(bergs, time_stamp)
              thickness,    &
              width,        &
              length,       &
+             fl_k,         &
              start_lon,    &
              start_lat,    &
              start_day,    &
@@ -657,6 +662,7 @@ subroutine read_restart_bergs(bergs,Time)
                                    thickness,    &
                                    width,        &
                                    length,       &
+                                   fl_k,         &
                                    start_lon,    &
                                    start_lat,    &
                                    start_day,    &
@@ -716,6 +722,7 @@ subroutine read_restart_bergs(bergs,Time)
      allocate(thickness(nbergs_in_file))
      allocate(width(nbergs_in_file))
      allocate(length(nbergs_in_file))
+     allocate(fl_k(nbergs_in_file))
      allocate(start_lon(nbergs_in_file))
      allocate(start_lat(nbergs_in_file))
      allocate(start_day(nbergs_in_file))
@@ -786,6 +793,7 @@ subroutine read_restart_bergs(bergs,Time)
      call read_unlimited_axis(filename,'thickness',thickness,domain=grd%domain)
      call read_unlimited_axis(filename,'width',width,domain=grd%domain)
      call read_unlimited_axis(filename,'length',length,domain=grd%domain)
+     call read_real_vector(filename,'fl_k',fl_k,grd%domain,value_if_not_in_file=0.)
      call read_unlimited_axis(filename,'start_lon',start_lon,domain=grd%domain)
      call read_unlimited_axis(filename,'start_lat',start_lat,domain=grd%domain)
      call read_unlimited_axis(filename,'start_day',start_day,domain=grd%domain)
@@ -874,6 +882,7 @@ subroutine read_restart_bergs(bergs,Time)
       localberg%thickness=thickness(k)
       localberg%width=width(k)
       localberg%length=length(k)
+      localberg%fl_k=fl_k(k)
       localberg%start_lon=start_lon(k)
       localberg%start_lat=start_lat(k)
       localberg%start_year=start_year(k)
@@ -940,6 +949,7 @@ subroutine read_restart_bergs(bergs,Time)
                thickness,    &
                width,        &
                length,       &
+               fl_k,         &
                start_lon,    &
                start_lat,    &
                start_day,    &
@@ -1091,6 +1101,7 @@ subroutine generate_bergs(bergs,Time)
       localberg%thickness=bergs%initial_thickness(1)
       localberg%width=bergs%initial_width(1)
       localberg%length=bergs%initial_length(1)
+      localberg%fl_k=0.
       localberg%start_lon=localberg%lon
       localberg%start_lat=localberg%lat
       localberg%start_year=iyr
@@ -1648,7 +1659,7 @@ subroutine write_trajectory(trajectory, save_short_traj)
 integer :: uvelpid,vvelpid
 integer :: uoid, void, uiid, viid, uaid, vaid, sshxid, sshyid, sstid, sssid
 integer :: cnid, hiid, hsid
-integer :: mid, did, wid, lid, mbid, hdid, nbid, odid
+integer :: mid, did, wid, lid, mbid, hdid, nbid, odid, flkid
 integer :: axnid,aynid,bxnid,bynid,axnfid,aynfid,bxnfid,bynfid
 integer :: eecid,edcid,eeid,edid,aeid,efid
 integer :: eectid, edctid, eetid, edtid, aetid
@@ -1787,6 +1798,7 @@ subroutine write_trajectory(trajectory, save_short_traj)
         did = inq_varid(ncid, 'thickness')
         wid = inq_varid(ncid, 'width')
         lid = inq_varid(ncid, 'length')
+        flkid = inq_varid(ncid, 'fl_k')
         sshxid = inq_varid(ncid, 'ssh_x')
         sshyid = inq_varid(ncid, 'ssh_y')
         sstid = inq_varid(ncid, 'sst')
@@ -1863,6 +1875,7 @@ subroutine write_trajectory(trajectory, save_short_traj)
         did = def_var(ncid, 'thickness', NF_DOUBLE, i_dim)
         wid = def_var(ncid, 'width', NF_DOUBLE, i_dim)
         lid = def_var(ncid, 'length', NF_DOUBLE, i_dim)
+        flkid = def_var(ncid, 'fl_k', NF_DOUBLE, i_dim)
         sshxid = def_var(ncid, 'ssh_x', NF_DOUBLE, i_dim)
         sshyid = def_var(ncid, 'ssh_y', NF_DOUBLE, i_dim)
         sstid = def_var(ncid, 'sst', NF_DOUBLE, i_dim)
@@ -1955,6 +1968,8 @@ subroutine write_trajectory(trajectory, save_short_traj)
         call put_att(ncid, wid, 'units', 'm')
         call put_att(ncid, lid, 'long_name', 'length')
         call put_att(ncid, lid, 'units', 'm')
+        call put_att(ncid, flkid, 'long_name', 'footloose calving k')
+        call put_att(ncid, flkid, 'units', 'm')
         call put_att(ncid, sshxid, 'long_name', 'sea surface height gradient_x')
         call put_att(ncid, sshxid, 'units', 'non-dim')
         call put_att(ncid, sshyid, 'long_name', 'sea surface height gradient_y')
@@ -2075,6 +2090,7 @@ subroutine write_trajectory(trajectory, save_short_traj)
         call put_double(ncid, did, i, this%thickness)
         call put_double(ncid, wid, i, this%width)
         call put_double(ncid, lid, i, this%length)
+        call put_double(ncid, flkid, i, this%fl_k)
         call put_double(ncid, sshxid, i, this%ssh_x)
         call put_double(ncid, sshyid, i, this%ssh_y)
         call put_double(ncid, sstid, i, this%sst)
diff --git a/tests/footloose_no_bond_test/README b/tests/footloose_no_bond_test/README
new file mode 100644
index 0000000..8a46a3d
--- /dev/null
+++ b/tests/footloose_no_bond_test/README
@@ -0,0 +1,9 @@
+Testing for footloose mechanism parameterization in (non-bonded mode only)
+
+1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
+2.(optional) edit input.nml
+3. run the model: ./RUN
+4. animate the results: animate_trajectories.py
+
+
+
diff --git a/tests/footloose_no_bond_test/RUN b/tests/footloose_no_bond_test/RUN
new file mode 100755
index 0000000..090c034
--- /dev/null
+++ b/tests/footloose_no_bond_test/RUN
@@ -0,0 +1,5 @@
+rm iceberg_trajectories.nc
+rm iceberg_trajectories.nc.*
+srun -n4 ./../../build/bergs.x
+
+
diff --git a/tests/footloose_no_bond_test/RUN1p b/tests/footloose_no_bond_test/RUN1p
new file mode 100755
index 0000000..c3bf53e
--- /dev/null
+++ b/tests/footloose_no_bond_test/RUN1p
@@ -0,0 +1,5 @@
+rm iceberg_trajectories.nc
+rm iceberg_trajectories.nc.*
+srun -n1 ./../../build/bergs.x
+
+
diff --git a/tests/footloose_no_bond_test/animate_trajectories.py b/tests/footloose_no_bond_test/animate_trajectories.py
new file mode 100755
index 0000000..27bf850
--- /dev/null
+++ b/tests/footloose_no_bond_test/animate_trajectories.py
@@ -0,0 +1,151 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+import matplotlib.pyplot as plt
+from matplotlib.animation import FuncAnimation
+from mpl_toolkits.axes_grid1 import make_axes_locatable
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
+                    help=''' provide filename to plot''')
+    parser.add_argument('-s', type=int, default='1450',
+                        help='''plotted particle size''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+
+
+def main(args):
+
+    print('reading file')
+
+    filename=args.fname
+    psize=args.s
+    #filename = 'iceberg_trajectories.nc'
+    field = 'lon'
+    field2 = 'lat'
+
+    with nc.Dataset(filename) as file:
+        x = file.variables['lon'][:]/1.e3
+        y = file.variables['lat'][:]/1.e3
+        day = file.variables['day'][:]
+        bid = file.variables['id_ij'][:]
+        vo = file.variables['fl_k'][:]
+        length = file.variables['length'][:]
+        width = file.variables['width'][:]
+
+    ud = np.unique(day)
+    ub = np.unique(bid)
+    t = ud[0]
+
+    radius = length*width*(1./(2*np.sqrt(3)))
+
+    urad=np.unique(radius)
+    #print('urad',urad)
+
+    # frame info
+    num_frames = len(ud)
+    movie_len = 10.0 #seconds
+    frame_len = 1000.0*movie_len/num_frames
+
+    xmin = 0 #np.floor(min(min(x),min(y),0))
+    xmax = 20 #np.ceil(max(max(x),max(y),20))
+    ymin = xmin
+    ymax = xmax
+
+    anim_running = True
+
+    def animate(i):
+
+        x1 = x[day == ud[i]]
+        y1 = y[day == ud[i]]
+        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
+
+        scat.set_offsets(data)
+
+        vo1 = vo[day == ud[i]]
+        scat.set_edgecolor('k')
+        scat.set_color(cmap(norm(vo1)))
+
+        r1 = radius[day == ud[i]]
+        scat.set_sizes(r1/psize)
+
+        t = ud[i]
+        time_text.set_text('time = %.1f days' % t )
+        return scat,time_text
+
+    def init():
+        scat.set_offsets([])
+        return scat,
+
+    def onClick(event):
+        global anim_running
+        if anim_running:
+            ani.event_source.stop()
+            anim_running = False
+        else:
+            ani.event_source.start()
+            anim_running = True
+
+    # Now we can do the plotting!
+    f = plt.figure(figsize=(5,5))
+    f.tight_layout()
+    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
+    div = make_axes_locatable(ax1)
+    cax = div.append_axes('right', '5%', '5%')
+    scat = ax1.scatter([],[],marker='o')
+    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
+
+    cmap = plt.cm.get_cmap('RdYlBu')
+    norm = plt.Normalize(vo.min(), vo.max())
+    cb1 = matplotlib.colorbar.ColorbarBase(cax, cmap=cmap,
+                                           norm=norm,
+                                           orientation='vertical')
+
+
+    # Change major ticks to show every 20.
+    ax1.xaxis.set_major_locator(MultipleLocator(5))
+    ax1.yaxis.set_major_locator(MultipleLocator(5))
+
+    ax1.xaxis.set_minor_locator(MultipleLocator(1))
+    ax1.yaxis.set_minor_locator(MultipleLocator(1))
+
+    # Turn grid on for both major and minor ticks and style minor slightly
+    # differently.
+    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
+    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
+
+    ax1.set_xlabel('x (km)')
+    ax1.set_ylabel('y (km)')
+    ax1.set_title('Iceberg trajectory')
+
+    f.canvas.mpl_connect('button_press_event', onClick)
+
+    ani = FuncAnimation(
+        f,animate,init_func=init,frames=num_frames,
+        interval=frame_len,blit=True,repeat=True)
+
+    print('time',t)
+
+    plt.show()
+    #animation.save("iceberg_traj_animation.mp4")
+
+
+print('Script complete')
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
diff --git a/tests/footloose_no_bond_test/diag_table b/tests/footloose_no_bond_test/diag_table
new file mode 100644
index 0000000..c1c8819
--- /dev/null
+++ b/tests/footloose_no_bond_test/diag_table
@@ -0,0 +1,3 @@
+"icebergs test"
+1 1 1 0 0 0
+
diff --git a/tests/footloose_no_bond_test/input.nml b/tests/footloose_no_bond_test/input.nml
new file mode 100644
index 0000000..dcaeaa3
--- /dev/null
+++ b/tests/footloose_no_bond_test/input.nml
@@ -0,0 +1,164 @@
+!note: to test this without bonds and without interactive bergs, set:
+!>iceberg_bonds_on=.true.
+!>interactive_icebergs_on=.false.
+!>manually_initialize_bonds=.true.
+!>length_for_manually_initialize_bonds<1
+
+
+&icebergs_driver_nml
+  ni=20 !number of elements, x direction
+  nj=20 !number of elements, y direction
+  ibdt=10.0 !1800.0 !86400.0 !seconds
+  ibuo=0.05 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=4800 !total simulation hours
+  nmax=99999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.false.
+  gridres=1000.
+  collision_test=.false. !specific to the current test, must be true here
+/
+
+
+&icebergs_nml
+
+    !defaults given in parentheses:
+
+    fl_r=4        !(4) average number of footloose bergs to calve per fl_r_s seconds
+    fl_r_s=86400  !(86400) time in s over which to calve, on average, fl_r footloose bergs
+
+    mts=.false. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=1 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
+    !contact_distance=0 !3.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    !contact_spring_coef=1.e-5!(default=spring_coeff) Berg spring coeff for collisions
+
+    halo=3 !(4) halo width
+    Lx=20000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.True. !(T) Point in cell can be found assuming regular Cartesian grid
+    !hexagonal_icebergs=.True. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    rho_bergs=850. ! (850) iceberg density
+    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0.0 !4 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true.!.false. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+
+    verbose=.true. !(F) Be verbose to stderr
+    verbose_hrs=24 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !1 !(24) sampling period for trajectory storage
+    traj_write_hrs=1 ! (480) Period for writing sampled trajectories to disk
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    length_for_manually_initialize_bonds=-1.e3!0.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/footloose_no_bond_test/makeberg/RUN b/tests/footloose_no_bond_test/makeberg/RUN
new file mode 100755
index 0000000..750e29e
--- /dev/null
+++ b/tests/footloose_no_bond_test/makeberg/RUN
@@ -0,0 +1,5 @@
+
+rm ./output_files/Generic*
+./makeberg.py
+
+cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
\ No newline at end of file
diff --git a/tests/footloose_no_bond_test/makeberg/makeberg.py b/tests/footloose_no_bond_test/makeberg/makeberg.py
new file mode 100755
index 0000000..dd146fc
--- /dev/null
+++ b/tests/footloose_no_bond_test/makeberg/makeberg.py
@@ -0,0 +1,278 @@
+#!/usr/bin/env python
+import numpy as np
+import math
+from netCDF4 import Dataset
+from pylab import *
+#import pdb
+import netCDF4 as nc
+
+#
+# Initialize 2 iceberg elements, which can later be bonded in the fortran code if needed
+#
+
+def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
+
+	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
+	# To copy the global attributes of the netCDF file
+
+	#Input and output files
+	#Create Empty restart file. This is later read so that the attributes can be used.
+	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
+	create_empty_iceberg_restart_file(Empty_restart_filename)
+	#Empty_restart_filename='input_files/icebergs.res.nc'
+
+	#Read empty restart file
+	f=Dataset(Empty_restart_filename,'r') # r is for read only
+	#Write a new restart file
+	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
+
+	for attname in f.ncattrs():
+		    setattr(g,attname,getattr(f,attname))
+
+
+	# To copy the dimension of the netCDF file
+	for dimname,dim in f.dimensions.iteritems():
+		# if you want to make changes in the dimensions of the new file
+		# you should add your own conditions here before the creation of the dimension.
+		#g.createDimension(dimname,len(dim))
+		g.createDimension(dimname,Number_of_bergs)
+
+	# To copy the variables of the netCDF file
+
+	for varname,ncvar in f.variables.iteritems():
+		# if you want to make changes in the variables of the new file
+		# you should add your own conditions here before the creation of the variable.
+		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
+		#Proceed to copy the variable attributes
+		for attname in ncvar.ncattrs():
+			setattr(var,attname,getattr(ncvar,attname))
+		#Finally copy the variable data to the new created variable
+		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
+
+		if varname=='i':
+			var[:]=Number_of_bergs
+
+		if varname=='iceberg_num':
+			for j in range(Number_of_bergs):
+				#var[j]=j+1
+				var[j]=iceberg_num[j]
+
+		if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
+		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
+		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
+		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
+			var[:]=0
+
+                if varname=='uvel':
+                        var[:]=uvel
+
+                if varname=='vvel':
+                        var[:]=vvel
+
+		if varname=='mass_scaling':
+			var[:]=mass_scaling
+
+		if varname=='thickness':
+			for j in range(Number_of_bergs):
+				var[j]=thickness[j]
+
+		if varname=='mass':
+			for j in range(Number_of_bergs):
+				var[j]=mass[j]
+
+		if varname=='width'  or varname=='length':
+			for j in range(Number_of_bergs):
+				var[j]=width[j]
+
+		if varname=='lon':
+			for j in range(Number_of_bergs):
+				var[j]=lon[j]
+
+		if varname=='lat':
+			for j in range(Number_of_bergs):
+				var[j]=lat[j]
+
+		if varname=='static_berg':
+			for j in range(Number_of_bergs):
+				var[j]=static_berg[j]
+
+
+	f.close()
+	g.close()
+
+
+def create_empty_iceberg_restart_file(Empty_restart_filename):
+
+	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
+
+	i=f.createDimension('i', None)
+	lon=f.createVariable('i','i')
+
+	lon=f.createVariable('lon','d',('i'))
+	lon.long_name = "longitude" ;
+	lon.units = "degrees_E" ;
+	lon.checksum = "               0" ;
+
+	lat=f.createVariable('lat','d',('i'))
+	lat.long_name = "latitude" ;
+	lat.units = "degrees_N" ;
+	lat.checksum = "               0" ;
+
+	uvel=f.createVariable('uvel','d',('i'))
+	uvel.long_name = "zonal velocity" ;
+	uvel.units = "m/s" ;
+	uvel.checksum = "               0" ;
+
+	vvel=f.createVariable('vvel','d',('i'))
+	vvel.long_name = "meridional velocity" ;
+	vvel.units = "m/s" ;
+	vvel.checksum = "               0" ;
+
+	mass=f.createVariable('mass','d',('i'))
+	mass.long_name = "mass" ;
+	mass.units = "kg" ;
+	mass.checksum = "               0" ;
+
+	axn=f.createVariable('axn','d',('i'))
+	axn.long_name = "explicit zonal acceleration" ;
+	axn.units = "m/s^2" ;
+	axn.checksum = "               0" ;
+
+	ayn=f.createVariable('ayn','d',('i'))
+	ayn.long_name = "explicit meridional acceleration" ;
+	ayn.units = "m/s^2" ;
+	ayn.checksum = "               0" ;
+
+	bxn=f.createVariable('bxn','d',('i'))
+	bxn.long_name = "inplicit zonal acceleration" ;
+	bxn.units = "m/s^2" ;
+	bxn.checksum = "               0" ;
+
+	byn=f.createVariable('byn','d',('i'))
+	byn.long_name = "implicit meridional acceleration" ;
+	byn.units = "m/s^2" ;
+	byn.checksum = "               0" ;
+
+	ine=f.createVariable('ine','i',('i'))
+	ine.long_name = "i index" ;
+	ine.units = "none" ;
+	ine.packing = 0 ;
+	ine.checksum = "               0" ;
+
+	jne=f.createVariable('jne','i',('i'))
+	jne.long_name = "j index" ;
+	jne.units = "none" ;
+	jne.packing = 0 ;
+	jne.checksum = "               0" ;
+
+	thickness=f.createVariable('thickness','d',('i'))
+	thickness.long_name = "thickness" ;
+	thickness.units = "m" ;
+	thickness.checksum = "               0" ;
+
+	width=f.createVariable('width','d',('i'))
+	width.long_name = "width" ;
+	width.units = "m" ;
+	width.checksum = "               0" ;
+
+	length=f.createVariable('length','d',('i'))
+	length.long_name = "length" ;
+	length.units = "m" ;
+	length.checksum = "               0" ;
+
+	start_lon=f.createVariable('start_lon','d',('i'))
+	start_lon.long_name = "longitude of calving location" ;
+	start_lon.units = "degrees_E" ;
+	start_lon.checksum = "               0" ;
+
+	start_lat=f.createVariable('start_lat','d',('i'))
+	start_lat.long_name = "latitude of calving location" ;
+	start_lat.units = "degrees_N" ;
+	start_lat.checksum = "               0" ;
+
+	start_year=f.createVariable('start_year','i',('i'))
+	start_year.long_name = "calendar year of calving event" ;
+	start_year.units = "years" ;
+	start_year.packing = 0 ;
+	start_year.checksum = "               0" ;
+
+	iceberg_num=f.createVariable('iceberg_num','i',('i'))
+	iceberg_num.long_name = "identification of the iceberg" ;
+	iceberg_num.units = "dimensionless" ;
+	iceberg_num.packing = 0 ;
+	iceberg_num.checksum = "               0" ;
+
+	start_day=f.createVariable('start_day','d',('i'))
+	start_day.long_name = "year day of calving event" ;
+	start_day.units = "days" ;
+	start_day.checksum = "               0" ;
+
+	start_mass=f.createVariable('start_mass','d',('i'))
+	start_mass.long_name = "initial mass of calving berg" ;
+	start_mass.units = "kg" ;
+	start_mass.checksum = "               0" ;
+
+	mass_scaling=f.createVariable('mass_scaling','d',('i'))
+	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
+	mass_scaling.units = "none" ;
+	mass_scaling.checksum = "               0" ;
+
+	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
+	mass_of_bits.long_name = "mass of bergy bits" ;
+	mass_of_bits.units = "kg" ;
+	mass_of_bits.checksum = "               0" ;
+
+	heat_density=f.createVariable('heat_density','d',('i'))
+	heat_density.long_name = "heat density" ;
+	heat_density.units = "J/kg" ;
+	heat_density.checksum = "               0" ;
+
+	halo_berg=f.createVariable('halo_berg','d',('i'))
+	halo_berg.long_name = "halo_berg" ;
+	halo_berg.units = "dimensionless" ;
+	halo_berg.checksum = "               0" ;
+
+	static_berg=f.createVariable('static_berg','d',('i'))
+	static_berg.long_name = "static_berg" ;
+	static_berg.units = "dimensionless" ;
+	static_berg.checksum = "               0" ;
+
+	f.sync()
+	f.close()
+
+
+
+#-----------------------------------#
+#               Main                #
+#-----------------------------------#
+
+grdres=5000.0
+xc=10000.1
+yc=10000.1
+R_frac=0.45
+radius=(np.sqrt(3)/2.)*(R_frac*grdres) #S is < 0.5 grid res
+element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*radius**2)
+width=np.sqrt(element_area)
+thickness=300.0
+rhoi=850.0
+mass=thickness*rhoi*element_area
+
+berg_count=2
+berg_x=[xc-radius,xc+radius]
+berg_y=[yc,yc]
+berg_h=[thickness,thickness]
+berg_width=[width,width]
+berg_mass=[mass,mass]
+berg_mass_scaling=[1,1]
+berg_id=[1,2]
+berg_static=[0,0]
+berg_uvel=[0,0]
+berg_vvel=[0,0]
+
+print('Number of bergs',berg_count)
+print('berg_x,berg_y',berg_x,berg_y)
+print('width',width)
+
+#Create iceberg restart file
+Ice_geometry_source='Generic'
+Create_iceberg_restart_file(berg_count,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)

From 09a6bae5b75bf6670c5dd7243fb1a3e52ff1c425 Mon Sep 17 00:00:00 2001
From: alex-huth <ahuth@princeton.edu>
Date: Thu, 4 Mar 2021 16:36:08 -0500
Subject: [PATCH 282/361] Update input.nml

---
 tests/footloose_no_bond_test/input.nml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/footloose_no_bond_test/input.nml b/tests/footloose_no_bond_test/input.nml
index dcaeaa3..2b45fdd 100644
--- a/tests/footloose_no_bond_test/input.nml
+++ b/tests/footloose_no_bond_test/input.nml
@@ -2,7 +2,7 @@
 !>iceberg_bonds_on=.true.
 !>interactive_icebergs_on=.false.
 !>manually_initialize_bonds=.true.
-!>length_for_manually_initialize_bonds<1
+!>length_for_manually_initialize_bonds<0
 
 
 &icebergs_driver_nml

From 27c7f75ec594b5369b35c16a0034d013c6b30461 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Thu, 4 Mar 2021 16:42:28 -0500
Subject: [PATCH 283/361] Update input.nml

---
 tests/footloose_no_bond_test/input.nml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/footloose_no_bond_test/input.nml b/tests/footloose_no_bond_test/input.nml
index dcaeaa3..2b45fdd 100644
--- a/tests/footloose_no_bond_test/input.nml
+++ b/tests/footloose_no_bond_test/input.nml
@@ -2,7 +2,7 @@
 !>iceberg_bonds_on=.true.
 !>interactive_icebergs_on=.false.
 !>manually_initialize_bonds=.true.
-!>length_for_manually_initialize_bonds<1
+!>length_for_manually_initialize_bonds<0
 
 
 &icebergs_driver_nml

From 32f0e56dd58b90fde833d823e5ea955fafd03c96 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Fri, 5 Mar 2021 14:09:24 -0500
Subject: [PATCH 284/361] fix mass scaling bug in creation of footloose child
 bergs

---
 src/icebergs.F90 | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index cd9f468..355a1e6 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -2901,7 +2901,6 @@ end subroutine thermodynamics
 subroutine rolling(bergs,Tn,Wn,Ln)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
-  real :: N_bonds !< Number of bonds
   real :: Tn !< Berg thickness
   real :: Wn !< Berg width
   real :: Ln !< Berg length
@@ -5800,7 +5799,7 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b)
   cberg%start_lat    = pberg%lat
   cberg%start_day    = bergs%current_yearday
   cberg%start_mass   = cberg%mass
-  cberg%mass_scaling = k !k is the number of icebergs cberg represents
+  cberg%mass_scaling = pberg%mass_scaling * k !k is the number of icebergs cberg represents
   cberg%mass_of_bits = 0.0
   cberg%fl_k         = -1.0
   cberg%start_year   = bergs%current_year

From b72ee3c3335835b606102231f38d652c34814077 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Wed, 10 Mar 2021 11:11:18 -0500
Subject: [PATCH 285/361] length fix for footloose child bergs

---
 src/icebergs.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 355a1e6..5c91032 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -5792,7 +5792,7 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b)
   !Set variable values for the new child berg:
 
   !different values from parent:
-  cberg%width        = l_b/3.
+  cberg%width        = l_b*3.
   cberg%length       = l_b
   cberg%mass         = cberg%width * cberg%length * pberg%thickness * bergs%rho_bergs
   cberg%start_lon    = pberg%lon

From a58fa5a3dd1867964ae4f354b0c0e29c04694695 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Tue, 30 Mar 2021 13:38:50 -0400
Subject: [PATCH 286/361] added option to position new footloose child bergs to
 a random corner of the parent berg, rather than having the child berg inherit
 the exact same position of the parent berg

---
 src/icebergs.F90                       | 94 +++++++++++++++++++-------
 src/icebergs_framework.F90             |  7 +-
 tests/footloose_no_bond_test/input.nml |  1 +
 3 files changed, 75 insertions(+), 27 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 5c91032..2e8a701 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -29,7 +29,7 @@ module ice_bergs
 use ice_bergs_framework, only: ice_bergs_framework_init
 use ice_bergs_framework, only: icebergs_gridded, xyt, iceberg, icebergs, buffer, bond
 use ice_bergs_framework, only: verbose, really_debug,debug,old_bug_rotated_weights,budget,use_roundoff_fix
-use ice_bergs_framework, only: find_cell,find_cell_by_search,count_bergs,is_point_in_cell,pos_within_cell
+use ice_bergs_framework, only: find_cell,find_cell_by_search,find_cell_wide,count_bergs,is_point_in_cell,pos_within_cell
 use ice_bergs_framework, only: count_bonds, form_a_bond,connect_all_bonds,show_all_bonds, bond_address_update
 use ice_bergs_framework, only: nclasses,old_bug_bilin
 use ice_bergs_framework, only: sum_mass,sum_heat,bilin,yearday,count_bergs,bergs_chksum,count_bergs_in_list
@@ -2393,6 +2393,7 @@ subroutine footloose_calving(bergs, time)
   integer, dimension(8) :: seed
   real :: T, W, L, N_bonds, Ln, rn
   real :: IC, max_k, k, Lr_fl, l_w, l_b, pu
+  real :: fl_disp_x, fl_disp_y
 
   ! For convenience
   grd=>bergs%grd
@@ -2421,6 +2422,8 @@ subroutine footloose_calving(bergs, time)
     Visited=.true.
   endif
 
+
+
   do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec !computational domain only
     this=>bergs%list(grdi,grdj)%first
     do while(associated(this))
@@ -2510,7 +2513,22 @@ subroutine footloose_calving(bergs, time)
 
           Lr_fl = k*3.*(l_b**2.)/W !FL mechanism length reduction for parent berg
 
-          call calve_fl_icebergs(bergs,this,k,l_b)
+          !if (bergs%displace_fl_bergs), new FL bergs are positioned at a randomly assigned corner of the parent berg.
+
+          if (.not. bergs%displace_fl_bergs) then
+            fl_disp_x=0.0; fl_disp_y=0.0
+          else
+            !call assign_fl_disp
+            fl_disp_x=0.5*this%length; fl_disp_y=0.5*this%width
+            if (rn<0.5) then
+              fl_disp_x=-fl_disp_x
+              if (rn<0.25) fl_disp_y=-fl_disp_y
+            elseif (rn<0.75) then
+              fl_disp_y=-fl_disp_y
+            end if
+          endif
+
+          call calve_fl_icebergs(bergs,this,k,l_b,fl_disp_x,fl_disp_y)
 
           Ln=L-Lr_fl !new length
           if (Ln .le. 0) then
@@ -2535,9 +2553,9 @@ subroutine footloose_calving(bergs, time)
 
   !TODO: finish this
   subroutine max_k_for_edge_elements
+    !for most edge elements, maxk=huge(1.0). If the k
     max_k=huge(1.0)
   end subroutine max_k_for_edge_elements
-
 end subroutine footloose_calving
 
 !> Delete any edge elements that fully calved from the footloose mechanism
@@ -4911,14 +4929,14 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   call mpp_clock_begin(bergs%clock_com)
   if (bergs%iceberg_bonds_on)  call  bond_address_update(bergs)
 
-  call send_bergs_to_other_pes(bergs)
-  if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after send_bergs() ')
-
   ! Footloose mechanism part 1: calve the child icebergs
   if (bergs%fl_r>0.) then
     call footloose_calving(bergs, time)
   endif
 
+  call send_bergs_to_other_pes(bergs)
+  if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after send_bergs() ')
+
   if (bergs%mts) then
     call interp_gridded_fields_to_bergs(bergs)
     call transfer_mts_bergs(bergs)
@@ -5768,35 +5786,71 @@ subroutine calve_icebergs(bergs)
 end subroutine calve_icebergs
 
   !> Calve footloose icebergs from parent berg
-subroutine calve_fl_icebergs(bergs,pberg,k,l_b)
+subroutine calve_fl_icebergs(bergs,pberg,k,l_b,fl_disp_x,fl_disp_y)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
   type(iceberg), pointer :: pberg !< Parent berg
   type(real),intent(in) :: k !< Number of child bergs to calve
   type(real),intent(in) :: l_b !< The width, and 1/3 the length, of a child berg
+  type(real),intent(in) :: fl_disp_x !< Child berg x-displacement from parent berg
+  type(real),intent(in) :: fl_disp_y !< Child berg x-displacement from parent berg
   ! Local variables
   type(iceberg) :: cberg ! The new child berg
   type(icebergs_gridded), pointer :: grd
+  logical :: lres
 
   ! For convenience
   grd=>bergs%grd
 
-  !A new child berg (cberg) that calves from the footloose mechanism initially has same position as the parent berg.
   !Initially, cberg%fl_k is set to -1 to mark the berg as a child berg.
-  !If fl_k<0, the berg will is not eligible to decay via footloose calving (see subroutine footloose_calving)
+  !If fl_k<0, the berg is not eligible to decay via footloose calving (see subroutine footloose_calving)
   !If fl_k==-1, the berg will also not interact with other berg elements. This is necessary because the child berg
-  !will initially overlap its parent berg, which would otherwise result in unrealistic contact forces.
+  !may initially overlap its parent berg, which would otherwise result in unrealistic contact forces.
   !However, if (bergs%interactive_icebergs_on), a berg with fl_k==-1 will be set to fl_k=-2 once it is out of
   !contact range of any other berg. With fl_k=-2, interactive contact forces may now be applied
 
   !Set variable values for the new child berg:
 
-  !different values from parent:
+  !Lat/lon and cell position for new berg:
+  if (bergs%displace_fl_bergs) then
+    cberg%lon = pberg%lon + fl_disp_x
+    cberg%lat = pberg%lat + fl_disp_y
+    lres= find_cell_wide(grd, cberg%lon, cberg%lat, cberg%ine, cberg%jne)
+    if (lres) then       !child berg is located on the data domain of the current PE
+      lres=pos_within_cell(grd, cberg%lon, cberg%lat, cberg%ine, cberg%jne, cberg%xi, cberg%yj)
+    else
+      !child berg is NOT located on the data domain of the current PE. Assign it to the closest halo element for now.
+      !It will later be transferred to the neighboring PE and reassigned to the correct cell
+      if (cberg%lon > grd%lon(grd%ied,grd%jed)) then
+        cberg%ine = grd%ied
+      elseif (cberg%lon < grd%lon(grd%isd,grd%jsd)) then
+        cberg%ine = grd%isd+1
+      endif
+      if (cberg%lat > grd%lat(grd%ied,grd%jed)) then
+        cberg%jne = grd%jed
+      elseif (cberg%lat < grd%lat(grd%isd,grd%jsd)) then
+        cberg%jne = grd%jsd+1
+      endif
+      cberg%xi=0.5; cberg%yj=0.5 !fake values. Will be updated on new PE.
+    endif
+  else
+    cberg%lon = pberg%lon
+    cberg%lat = pberg%lat
+    cberg%ine = pberg%ine
+    cberg%jne = pberg%jne
+    cberg%xi  = pberg%xi
+    cberg%yj  = pberg%yj
+  endif
+
   cberg%width        = l_b*3.
   cberg%length       = l_b
   cberg%mass         = cberg%width * cberg%length * pberg%thickness * bergs%rho_bergs
-  cberg%start_lon    = pberg%lon
-  cberg%start_lat    = pberg%lat
+  cberg%start_lon    = cberg%lon
+  cberg%start_lat    = cberg%lat
+  cberg%lon_prev     = pberg%lon_prev + fl_disp_x
+  cberg%lat_prev     = pberg%lat_prev + fl_disp_y
+  cberg%lon_old      = pberg%lon_old  + fl_disp_x
+  cberg%lat_old      = pberg%lat_old  + fl_disp_y
   cberg%start_day    = bergs%current_yearday
   cberg%start_mass   = cberg%mass
   cberg%mass_scaling = pberg%mass_scaling * k !k is the number of icebergs cberg represents
@@ -5804,13 +5858,10 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b)
   cberg%fl_k         = -1.0
   cberg%start_year   = bergs%current_year
   cberg%id           = generate_id(grd, pberg%ine, pberg%jne)
+  cberg%halo_berg    = 0.0
 
-  !same values as parent:
+  !always same values as parent:
   cberg%thickness    = pberg%thickness
-  cberg%lon          = pberg%lon
-  cberg%lat          = pberg%lat
-  cberg%lon_prev     = pberg%lon_prev
-  cberg%lat_prev     = pberg%lat_prev
   cberg%uvel         = pberg%uvel
   cberg%vvel         = pberg%vvel
   cberg%axn          = pberg%axn
@@ -5821,15 +5872,8 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b)
   cberg%vvel_prev    = pberg%vvel_prev
   cberg%uvel_old     = pberg%uvel_old
   cberg%vvel_old     = pberg%vvel_old
-  cberg%lon_old      = pberg%lon_old
-  cberg%lat_old      = pberg%lat_old
   cberg%heat_density = pberg%heat_density
-  cberg%halo_berg    = pberg%halo_berg
   cberg%static_berg  = pberg%static_berg
-  cberg%ine          = pberg%ine
-  cberg%jne          = pberg%jne
-  cberg%xi           = pberg%xi
-  cberg%yj           = pberg%yj
   cberg%uo           = pberg%uo
   cberg%vo           = pberg%vo
   cberg%ui           = pberg%ui
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index c8a1fe0..f1f8f13 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -77,7 +77,7 @@ module ice_bergs_framework
 public print_fld,print_berg, print_bergs,record_posn, push_posn, append_posn, check_position
 public move_trajectory, move_all_trajectories
 public form_a_bond, connect_all_bonds, show_all_bonds, bond_address_update
-public find_cell, find_cell_by_search, count_bergs, is_point_in_cell, pos_within_cell, count_bonds
+public find_cell, find_cell_by_search, find_cell_wide, count_bergs, is_point_in_cell, pos_within_cell, count_bonds
 public sum_mass, sum_heat, bilin, yearday, bergs_chksum, list_chksum, count_bergs_in_list
 public checksum_gridded
 public grd_chksum2,grd_chksum3
@@ -598,6 +598,7 @@ module ice_bergs_framework
   logical :: fl_use_poisson_distribution=.true. !< fl_r is (T) mean of Poisson distribution to determine k, or (F) k=fl_r
   real :: fl_r=0. !< footloose average number of bergs calved per fl_r_s
   real :: fl_r_s=0. !< seconds over which fl_r footloose bergs calve
+  logical :: displace_fl_bergs=.true. !< footloose berg positions are assigned to a corner of parent berg
 end type icebergs
 
 !> Read original restarts. Needs to be module global so can be public to icebergs_mod.
@@ -782,6 +783,7 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: fl_use_poisson_distribution=.true. !< fl_r is (T) mean of Poisson distribution to determine k, or (F) k=fl_r
 real :: fl_r=0. !< footloose average number of bergs calved per fl_r_s
 real :: fl_r_s=0. !< seconds over which fl_r footloose bergs calve
+logical :: displace_fl_bergs=.true. !< footloose berg positions are assigned to a corner of parent berg
 
 namelist /icebergs_nml/ verbose, budget, halo,  traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,Static_icebergs,  &
          distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,bond_coef, radial_damping_coef, tangental_damping_coef, only_interactive_forces, &
@@ -798,7 +800,7 @@ subroutine ice_bergs_framework_init(bergs, &
          mts,new_mts,ewsame,monitor_energy,mts_sub_steps,contact_distance,length_for_manually_initialize_bonds,manually_initialize_bonds_from_radii,contact_spring_coef,&
          fracture_criterion, damage_test_1, uniaxial_test, debug_write,cdrag_grounding,h_to_init_grounding,frac_thres_scaling,frac_thres_n,frac_thres_t,save_bond_traj,remove_unused_bergs,&
          force_convergence,explicit_inner_mts,convergence_tolerance,&
-         dem,ignore_tangential_force,poisson,dem_spring_coef,dem_damping_coef,dem_beam_test,constant_interaction_LW,constant_length,constant_width,dem_shear_for_frac_only,use_damage, fl_use_poisson_distribution, fl_r, fl_r_s
+         dem,ignore_tangential_force,poisson,dem_spring_coef,dem_damping_coef,dem_beam_test,constant_interaction_LW,constant_length,constant_width,dem_shear_for_frac_only,use_damage, fl_use_poisson_distribution, fl_r, fl_r_s, displace_fl_bergs
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -1358,6 +1360,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%fl_use_poisson_distribution=fl_use_poisson_distribution
   bergs%fl_r=fl_r
   bergs%fl_r_s=fl_r_s
+  bergs%displace_fl_bergs=displace_fl_bergs
 
   if (monitor_energy) then
     if (bergs%constant_interaction_LW) then
diff --git a/tests/footloose_no_bond_test/input.nml b/tests/footloose_no_bond_test/input.nml
index 2b45fdd..d8ff071 100644
--- a/tests/footloose_no_bond_test/input.nml
+++ b/tests/footloose_no_bond_test/input.nml
@@ -29,6 +29,7 @@
 
     fl_r=4        !(4) average number of footloose bergs to calve per fl_r_s seconds
     fl_r_s=86400  !(86400) time in s over which to calve, on average, fl_r footloose bergs
+    displace_fl_bergs=.true. !(T) randomly assign FL berg positions to a corner of parent berg
 
     mts=.false. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
     mts_sub_steps=1 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)

From fefb646184ca140f3b6a75ac98ee53ad05069d07 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Tue, 30 Mar 2021 16:45:24 -0400
Subject: [PATCH 287/361] amended previous footloose option for assigning child
 berg positions to random corners of parent berg. Now, assign to random
 positions along edges of parent berg

---
 src/icebergs.F90                       | 42 +++++++++++++++++++-------
 src/icebergs_framework.F90             |  4 +--
 tests/footloose_no_bond_test/input.nml |  2 +-
 3 files changed, 34 insertions(+), 14 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 2e8a701..da7b52d 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -2393,7 +2393,7 @@ subroutine footloose_calving(bergs, time)
   integer, dimension(8) :: seed
   real :: T, W, L, N_bonds, Ln, rn
   real :: IC, max_k, k, Lr_fl, l_w, l_b, pu
-  real :: fl_disp_x, fl_disp_y
+  real :: fl_disp_x, fl_disp_y, interp_loc
 
   ! For convenience
   grd=>bergs%grd
@@ -2513,19 +2513,39 @@ subroutine footloose_calving(bergs, time)
 
           Lr_fl = k*3.*(l_b**2.)/W !FL mechanism length reduction for parent berg
 
-          !if (bergs%displace_fl_bergs), new FL bergs are positioned at a randomly assigned corner of the parent berg.
+          !if (bergs%displace_fl_bergs), new FL bergs are positioned at a randomly assigned
+          !locations on edges of parent berg.
 
           if (.not. bergs%displace_fl_bergs) then
             fl_disp_x=0.0; fl_disp_y=0.0
           else
-            !call assign_fl_disp
-            fl_disp_x=0.5*this%length; fl_disp_y=0.5*this%width
-            if (rn<0.5) then
-              fl_disp_x=-fl_disp_x
-              if (rn<0.25) fl_disp_y=-fl_disp_y
-            elseif (rn<0.75) then
-              fl_disp_y=-fl_disp_y
-            end if
+            !get displace to a random location along one of the sides of the square berg
+            if (rn<0.25) then !north side
+              interp_loc=4.*rn
+              fl_disp_x=this%length*(interp_loc-0.5)
+              fl_disp_y=0.5*this%width
+            elseif (rn<0.5) then !east side
+              interp_loc=4.*(rn-0.25)
+              fl_disp_x=0.5*this%length
+              fl_disp_y=this%width*(interp_loc-0.5)
+            elseif (rn<0.75) then !south side
+              interp_loc=4.*(rn-0.5)
+              fl_disp_x=this%length*(interp_loc-0.5)
+              fl_disp_y=-0.5*this%width
+            else !west side
+              interp_loc=4.*(rn-0.75)
+              fl_disp_x=-0.5*this%length
+              fl_disp_y=0.5*this%width*(interp_loc-0.5)
+            endif
+
+            ! Old version, assigning to corners
+            ! fl_disp_x=0.5*this%length; fl_disp_y=0.5*this%width
+            ! if (rn<0.5) then
+            !   fl_disp_x=-fl_disp_x
+            !   if (rn<0.25) fl_disp_y=-fl_disp_y
+            ! elseif (rn<0.75) then
+            !   fl_disp_y=-fl_disp_y
+            ! end if
           endif
 
           call calve_fl_icebergs(bergs,this,k,l_b,fl_disp_x,fl_disp_y)
@@ -2553,7 +2573,7 @@ subroutine footloose_calving(bergs, time)
 
   !TODO: finish this
   subroutine max_k_for_edge_elements
-    !for most edge elements, maxk=huge(1.0). If the k
+    !for most edge elements, maxk=huge(1.0)
     max_k=huge(1.0)
   end subroutine max_k_for_edge_elements
 end subroutine footloose_calving
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index f1f8f13..3963fe9 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -598,7 +598,7 @@ module ice_bergs_framework
   logical :: fl_use_poisson_distribution=.true. !< fl_r is (T) mean of Poisson distribution to determine k, or (F) k=fl_r
   real :: fl_r=0. !< footloose average number of bergs calved per fl_r_s
   real :: fl_r_s=0. !< seconds over which fl_r footloose bergs calve
-  logical :: displace_fl_bergs=.true. !< footloose berg positions are assigned to a corner of parent berg
+  logical :: displace_fl_bergs=.true. !< footloose berg positions are randomly assigned along edges of parent berg
 end type icebergs
 
 !> Read original restarts. Needs to be module global so can be public to icebergs_mod.
@@ -783,7 +783,7 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: fl_use_poisson_distribution=.true. !< fl_r is (T) mean of Poisson distribution to determine k, or (F) k=fl_r
 real :: fl_r=0. !< footloose average number of bergs calved per fl_r_s
 real :: fl_r_s=0. !< seconds over which fl_r footloose bergs calve
-logical :: displace_fl_bergs=.true. !< footloose berg positions are assigned to a corner of parent berg
+logical :: displace_fl_bergs=.true. !< footloose berg positions are randomly assigned along edges of parent berg
 
 namelist /icebergs_nml/ verbose, budget, halo,  traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,Static_icebergs,  &
          distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,bond_coef, radial_damping_coef, tangental_damping_coef, only_interactive_forces, &
diff --git a/tests/footloose_no_bond_test/input.nml b/tests/footloose_no_bond_test/input.nml
index d8ff071..a261bf6 100644
--- a/tests/footloose_no_bond_test/input.nml
+++ b/tests/footloose_no_bond_test/input.nml
@@ -29,7 +29,7 @@
 
     fl_r=4        !(4) average number of footloose bergs to calve per fl_r_s seconds
     fl_r_s=86400  !(86400) time in s over which to calve, on average, fl_r footloose bergs
-    displace_fl_bergs=.true. !(T) randomly assign FL berg positions to a corner of parent berg
+    displace_fl_bergs=.true. !(T) randomly assign FL berg positions to sides of parent berg
 
     mts=.false. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
     mts_sub_steps=1 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)

From 7828b3f91226348cdd93115e3382463cd5993e80 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Wed, 31 Mar 2021 10:43:48 -0400
Subject: [PATCH 288/361] added footloose displacement for lat/lon coords as
 well as cartesian

---
 src/icebergs.F90           | 74 ++++++++++++++++++++++----------------
 src/icebergs_framework.F90 |  2 +-
 2 files changed, 45 insertions(+), 31 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index da7b52d..7ff99b9 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -2513,39 +2513,12 @@ subroutine footloose_calving(bergs, time)
 
           Lr_fl = k*3.*(l_b**2.)/W !FL mechanism length reduction for parent berg
 
-          !if (bergs%displace_fl_bergs), new FL bergs are positioned at a randomly assigned
-          !locations on edges of parent berg.
-
           if (.not. bergs%displace_fl_bergs) then
+            !newly calved FL bergs take same position as parent berg
             fl_disp_x=0.0; fl_disp_y=0.0
           else
-            !get displace to a random location along one of the sides of the square berg
-            if (rn<0.25) then !north side
-              interp_loc=4.*rn
-              fl_disp_x=this%length*(interp_loc-0.5)
-              fl_disp_y=0.5*this%width
-            elseif (rn<0.5) then !east side
-              interp_loc=4.*(rn-0.25)
-              fl_disp_x=0.5*this%length
-              fl_disp_y=this%width*(interp_loc-0.5)
-            elseif (rn<0.75) then !south side
-              interp_loc=4.*(rn-0.5)
-              fl_disp_x=this%length*(interp_loc-0.5)
-              fl_disp_y=-0.5*this%width
-            else !west side
-              interp_loc=4.*(rn-0.75)
-              fl_disp_x=-0.5*this%length
-              fl_disp_y=0.5*this%width*(interp_loc-0.5)
-            endif
-
-            ! Old version, assigning to corners
-            ! fl_disp_x=0.5*this%length; fl_disp_y=0.5*this%width
-            ! if (rn<0.5) then
-            !   fl_disp_x=-fl_disp_x
-            !   if (rn<0.25) fl_disp_y=-fl_disp_y
-            ! elseif (rn<0.75) then
-            !   fl_disp_y=-fl_disp_y
-            ! end if
+            !newly calved FL bergs are randomly assigned positions along the edges of the parent berg
+            call get_footloose_displacement
           endif
 
           call calve_fl_icebergs(bergs,this,k,l_b,fl_disp_x,fl_disp_y)
@@ -2576,6 +2549,47 @@ subroutine max_k_for_edge_elements
     !for most edge elements, maxk=huge(1.0)
     max_k=huge(1.0)
   end subroutine max_k_for_edge_elements
+
+  subroutine get_footloose_displacement
+    real :: lon1,lat1,x1,y1,dxdl1,dydl,xdot2,ydot2
+    logical :: on_tangential_plane
+
+    !displace child berg to a random location along one of the sides of the rectangular berg
+    if (rn<0.25) then !north side
+      interp_loc=4.*rn
+      fl_disp_x=this%length*(interp_loc-0.5)
+      fl_disp_y=0.5*this%width
+    elseif (rn<0.5) then !east side
+      interp_loc=4.*(rn-0.25)
+      fl_disp_x=0.5*this%length
+      fl_disp_y=this%width*(interp_loc-0.5)
+    elseif (rn<0.75) then !south side
+      interp_loc=4.*(rn-0.5)
+      fl_disp_x=this%length*(interp_loc-0.5)
+      fl_disp_y=-0.5*this%width
+    else !west side
+      interp_loc=4.*(rn-0.75)
+      fl_disp_x=-0.5*this%length
+      fl_disp_y=0.5*this%width*(interp_loc-0.5)
+    endif
+
+    if (grd%grid_is_latlon) then
+      on_tangential_plane=.false.
+      if ((this%lat>89.) .and. (grd%grid_is_latlon)) on_tangential_plane=.true.
+      lon1=this%lon; lat1=this%lat
+      if (on_tangential_plane) call rotpos_to_tang(lon1,lat1,x1,y1,this%id)
+      call convert_from_meters_to_grid(lat1,grd%grid_is_latlon,dxdl1,dydl)
+      if (on_tangential_plane) then
+        call rotvec_to_tang(lon1,fl_disp_x,fl_disp_y,xdot2,ydot2)
+        x1=x1+xdot2; y1=y1+ydot2
+        call rotpos_from_tang(x1,y1,lon1,lat1) !lon1 & lat1 = new FL berg position
+      else
+        lon1=lon1+fl_disp_x*dxdl1; lat1=lat1+fl_disp_y*dydl !new FL berg position
+      endif
+      fl_disp_x=lon1-this%lon; fl_disp_y=lat1-this%lat !convert back to displacement from parent berg
+    endif
+
+  end subroutine get_footloose_displacement
 end subroutine footloose_calving
 
 !> Delete any edge elements that fully calved from the footloose mechanism
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 3963fe9..b38508c 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -1402,7 +1402,7 @@ subroutine ice_bergs_framework_init(bergs, &
     bergs%contact_cells_lat = 1
   endif
 
-  print *,'# contact cells lon/lat',bergs%contact_cells_lon,bergs%contact_cells_lat
+  !print *,'# contact cells lon/lat',bergs%contact_cells_lon,bergs%contact_cells_lat
 
   !necessary?
   if (.not. mts) then

From a6ec49ddd03a1bcbb34c84d186d486ef2e1acd78 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Wed, 31 Mar 2021 12:56:45 -0400
Subject: [PATCH 289/361] fix that should prevent displaced footloose bergs
 from initializing into land cells. Added option to just convert footloose
 bergs into bergy bits. Partially implemented option to track footloose bergs
 similarly to (but separately from) bergy bits, where footloose bergs are
 tracked with the parent berg, and melted/eroded as a group

---
 src/icebergs.F90                       | 57 ++++++++++++++++++--------
 src/icebergs_framework.F90             | 24 +++++++----
 src/icebergs_io.F90                    | 22 ++++++++--
 tests/footloose_no_bond_test/input.nml |  1 +
 4 files changed, 77 insertions(+), 27 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 7ff99b9..56ab3bc 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -2416,7 +2416,7 @@ subroutine footloose_calving(bergs, time)
     lw_c = 1./(gravity*rho_seawater) !for buoyancy length
     B_c  = youngs/(12.*(1.-poisson**2.)) !for bending stiffness
     exp_nlambda=exp(-bergs%fl_r) !e^(-r*dt)
-    seed = constructSeed(1,1,time) !Seed random numbers for Poisson distribution
+    seed = constructSeed(mpp_pe(),mpp_pe(),time) !Seed random numbers for Poisson distribution
     rns = initializeRandomNumberStream(seed)
 
     Visited=.true.
@@ -2521,7 +2521,15 @@ subroutine footloose_calving(bergs, time)
             call get_footloose_displacement
           endif
 
-          call calve_fl_icebergs(bergs,this,k,l_b,fl_disp_x,fl_disp_y)
+          if (bergs%fl_style.eq.'bergy_bits') then
+            this%mass_of_bits=this%mass_of_bits+(bergs%rho_bergs*W*T*(L-Lr_fl))
+          elseif (bergs%fl_style.eq.'fl_bits') then
+            call error_mesg('KID,footloose_calving', &
+              'fl_style = "fl_bits" not yet fully implemented!', FATAL)
+            this%mass_of_fl_bits=this%mass_of_fl_bits+(bergs%rho_bergs*W*T*(L-Lr_fl))
+          else
+            call calve_fl_icebergs(bergs,this,k,l_b,fl_disp_x,fl_disp_y)
+          endif
 
           Ln=L-Lr_fl !new length
           if (Ln .le. 0) then
@@ -5826,12 +5834,12 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b,fl_disp_x,fl_disp_y)
   type(iceberg), pointer :: pberg !< Parent berg
   type(real),intent(in) :: k !< Number of child bergs to calve
   type(real),intent(in) :: l_b !< The width, and 1/3 the length, of a child berg
-  type(real),intent(in) :: fl_disp_x !< Child berg x-displacement from parent berg
-  type(real),intent(in) :: fl_disp_y !< Child berg x-displacement from parent berg
+  type(real) :: fl_disp_x !< Child berg x-displacement from parent berg
+  type(real) :: fl_disp_y !< Child berg x-displacement from parent berg
   ! Local variables
   type(iceberg) :: cberg ! The new child berg
   type(icebergs_gridded), pointer :: grd
-  logical :: lres
+  logical :: lres, displace
 
   ! For convenience
   grd=>bergs%grd
@@ -5845,29 +5853,41 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b,fl_disp_x,fl_disp_y)
 
   !Set variable values for the new child berg:
 
+  displace=bergs%displace_fl_bergs
   !Lat/lon and cell position for new berg:
-  if (bergs%displace_fl_bergs) then
+  if (displace) then
     cberg%lon = pberg%lon + fl_disp_x
     cberg%lat = pberg%lat + fl_disp_y
     lres= find_cell_wide(grd, cberg%lon, cberg%lat, cberg%ine, cberg%jne)
-    if (lres) then       !child berg is located on the data domain of the current PE
-      lres=pos_within_cell(grd, cberg%lon, cberg%lat, cberg%ine, cberg%jne, cberg%xi, cberg%yj)
-    else
-      !child berg is NOT located on the data domain of the current PE. Assign it to the closest halo element for now.
-      !It will later be transferred to the neighboring PE and reassigned to the correct cell
+
+    !If new berg is not on current PE, correct it so that it is. This correction is just a
+    !safety measure to make sure it is not within a grounded cell on the other PE.
+    if (.not. lres) then
+      !The choice of 75% and 25% weighting here is completely arbitrary...
       if (cberg%lon > grd%lon(grd%ied,grd%jed)) then
-        cberg%ine = grd%ied
+        cberg%lon = 0.75*grd%lon(grd%ied,grd%jed) + 0.25*pberg%lon
       elseif (cberg%lon < grd%lon(grd%isd,grd%jsd)) then
-        cberg%ine = grd%isd+1
+        cberg%lon = 0.75*grd%lon(grd%isd,grd%jsd) + 0.25*pberg%lon
       endif
       if (cberg%lat > grd%lat(grd%ied,grd%jed)) then
-        cberg%jne = grd%jed
+        cberg%lat = 0.75*grd%lat(grd%ied,grd%jed) + 0.25*pberg%lat
       elseif (cberg%lat < grd%lat(grd%isd,grd%jsd)) then
-        cberg%jne = grd%jsd+1
+        cberg%lat = 0.75*grd%lat(grd%isd,grd%jsd) + 0.25*pberg%lat
       endif
-      cberg%xi=0.5; cberg%yj=0.5 !fake values. Will be updated on new PE.
+      lres= find_cell_wide(grd, cberg%lon, cberg%lat, cberg%ine, cberg%jne)
+      if (.not. lres) call error_mesg('KID, calve_fl_icebergs', &
+        'corrected new berg position still not on current PE!', FATAL)
     endif
-  else
+
+    !if new berg is located within a grounded cell, change its position to the same as the parent berg
+    if (grd%area(cberg%ine,cberg%jne).eq.0.) then
+      fl_disp_x=0.0; fl_disp_y=0.0; displace=.false.
+    else
+      lres=pos_within_cell(grd, cberg%lon, cberg%lat, cberg%ine, cberg%jne, cberg%xi, cberg%yj)
+    endif
+  endif
+
+  if (.not. displace) then
     cberg%lon = pberg%lon
     cberg%lat = pberg%lat
     cberg%ine = pberg%ine
@@ -5881,6 +5901,9 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b,fl_disp_x,fl_disp_y)
   cberg%mass         = cberg%width * cberg%length * pberg%thickness * bergs%rho_bergs
   cberg%start_lon    = cberg%lon
   cberg%start_lat    = cberg%lat
+  !pberg%lon is saved on cberg%lon_prev in case the displacement of the new FL child berg causes it to ground,
+  !so that cberg%lon can then be corrected back to equal pberg%lon (same process for lat)
+  !Note lon_prev is otherwise only used for updating bond angles for fracture (not applicable to child bergs)
   cberg%lon_prev     = pberg%lon_prev + fl_disp_x
   cberg%lat_prev     = pberg%lat_prev + fl_disp_y
   cberg%lon_old      = pberg%lon_old  + fl_disp_x
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index b38508c..48bb298 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -18,8 +18,8 @@ module ice_bergs_framework
 
 implicit none ; private
 
-integer :: buffer_width=34 ! This should be a parameter
-integer :: buffer_width_traj=36 ! This should be a parameter
+integer :: buffer_width=35 ! This should be a parameter
+integer :: buffer_width_traj=37 ! This should be a parameter
 integer :: buffer_width_bond_traj=11 !This should be a parameter
 integer, parameter :: nclasses=10 ! Number of ice bergs classes
 
@@ -237,6 +237,7 @@ module ice_bergs_framework
   real :: halo_berg
   real :: static_berg
   real :: mass_of_bits !< Mass of bergy bits (kg)
+  real :: mass_of_fl_bits !< Mass of footloose bergy bits (kg)
   real :: heat_density !< Heat density of berg (J/kg)
   real :: od !< Ocean depth
   integer :: year !< Year of this record (years)
@@ -301,6 +302,7 @@ module ice_bergs_framework
   real :: start_mass !< Mass berg had when created (kg)
   real :: mass_scaling !< Multiplier to scale mass when interpreting berg as a cloud of bergs (nondim)
   real :: mass_of_bits !< Mass of bergy bits following berg (kg)
+  real :: mass_of_fl_bits !< Mass of footloose bergy bits following berg (kg)
   real :: fl_k !< Cumulative number of footloose bergs to calve
   real :: heat_density !< Heat density of berg (J/kg)
   real :: halo_berg  ! Equal to zero for bergs on computational domain, and =1 for bergs on the halo
@@ -599,6 +601,7 @@ module ice_bergs_framework
   real :: fl_r=0. !< footloose average number of bergs calved per fl_r_s
   real :: fl_r_s=0. !< seconds over which fl_r footloose bergs calve
   logical :: displace_fl_bergs=.true. !< footloose berg positions are randomly assigned along edges of parent berg
+  character(len=11) :: fl_style='new_bergs' !< Evolve footloose bergs individually as 'new_bergs', or as a group with size 'bergy_bits' or 'fl_bits'
 end type icebergs
 
 !> Read original restarts. Needs to be module global so can be public to icebergs_mod.
@@ -784,6 +787,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: fl_r=0. !< footloose average number of bergs calved per fl_r_s
 real :: fl_r_s=0. !< seconds over which fl_r footloose bergs calve
 logical :: displace_fl_bergs=.true. !< footloose berg positions are randomly assigned along edges of parent berg
+character(len=11) :: fl_style='new_bergs' !< Evolve footloose bergs individually as 'fl_bits', or as a group with size 'bergy_bits' or 'mean_size'
 
 namelist /icebergs_nml/ verbose, budget, halo,  traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,Static_icebergs,  &
          distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,bond_coef, radial_damping_coef, tangental_damping_coef, only_interactive_forces, &
@@ -800,7 +804,7 @@ subroutine ice_bergs_framework_init(bergs, &
          mts,new_mts,ewsame,monitor_energy,mts_sub_steps,contact_distance,length_for_manually_initialize_bonds,manually_initialize_bonds_from_radii,contact_spring_coef,&
          fracture_criterion, damage_test_1, uniaxial_test, debug_write,cdrag_grounding,h_to_init_grounding,frac_thres_scaling,frac_thres_n,frac_thres_t,save_bond_traj,remove_unused_bergs,&
          force_convergence,explicit_inner_mts,convergence_tolerance,&
-         dem,ignore_tangential_force,poisson,dem_spring_coef,dem_damping_coef,dem_beam_test,constant_interaction_LW,constant_length,constant_width,dem_shear_for_frac_only,use_damage, fl_use_poisson_distribution, fl_r, fl_r_s, displace_fl_bergs
+         dem,ignore_tangential_force,poisson,dem_spring_coef,dem_damping_coef,dem_beam_test,constant_interaction_LW,constant_length,constant_width,dem_shear_for_frac_only,use_damage, fl_use_poisson_distribution, fl_r, fl_r_s, displace_fl_bergs,fl_style
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -1361,6 +1365,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%fl_r=fl_r
   bergs%fl_r_s=fl_r_s
   bergs%displace_fl_bergs=displace_fl_bergs
+  bergs%fl_style=fl_style
 
   if (monitor_energy) then
     if (bergs%constant_interaction_LW) then
@@ -3102,6 +3107,7 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
   call push_buffer_value(buff%data(:,n), counter, berg%fl_k)
   call push_buffer_value(buff%data(:,n), counter, berg%mass_scaling)
   call push_buffer_value(buff%data(:,n), counter, berg%mass_of_bits)
+  call push_buffer_value(buff%data(:,n), counter, berg%mass_of_fl_bits)
   call push_buffer_value(buff%data(:,n), counter, berg%heat_density)
   call push_buffer_value(buff%data(:,n), counter, berg%ine)
   call push_buffer_value(buff%data(:,n), counter, berg%jne)
@@ -3412,6 +3418,7 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
   call pull_buffer_value(buff%data(:,n), counter, localberg%fl_k)
   call pull_buffer_value(buff%data(:,n), counter, localberg%mass_scaling)
   call pull_buffer_value(buff%data(:,n), counter, localberg%mass_of_bits)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%mass_of_fl_bits)
   call pull_buffer_value(buff%data(:,n), counter, localberg%heat_density)
   call pull_buffer_value(buff%data(:,n), counter, localberg%ine)
   call pull_buffer_value(buff%data(:,n), counter, localberg%jne)
@@ -3696,6 +3703,7 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj)
     call push_buffer_value(buff%data(:,n),counter,traj%vvel_prev)
     call push_buffer_value(buff%data(:,n),counter,traj%mass)
     call push_buffer_value(buff%data(:,n),counter,traj%mass_of_bits)
+    call push_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bits)
     call push_buffer_value(buff%data(:,n),counter,traj%heat_density)
     call push_buffer_value(buff%data(:,n),counter,traj%thickness)
     call push_buffer_value(buff%data(:,n),counter,traj%width)
@@ -3804,6 +3812,7 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj)
     call pull_buffer_value(buff%data(:,n),counter,traj%vvel_prev)
     call pull_buffer_value(buff%data(:,n),counter,traj%mass)
     call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_bits)
+    call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bits)
     call pull_buffer_value(buff%data(:,n),counter,traj%heat_density)
     call pull_buffer_value(buff%data(:,n),counter,traj%thickness)
     call pull_buffer_value(buff%data(:,n),counter,traj%width)
@@ -5696,6 +5705,7 @@ subroutine record_posn(bergs)
         posn%vvel_prev=this%vvel_prev
         posn%mass=this%mass
         posn%mass_of_bits=this%mass_of_bits
+        posn%mass_of_fl_bits=this%mass_of_fl_bits
         posn%heat_density=this%heat_density
         posn%thickness=this%thickness
         posn%width=this%width
@@ -6977,9 +6987,9 @@ real function sum_mass(bergs, justbits, justbergs)
       if (present(justbergs)) then
         sum_mass=sum_mass+this%mass*this%mass_scaling
       elseif (present(justbits)) then
-        sum_mass=sum_mass+this%mass_of_bits*this%mass_scaling
+        sum_mass=sum_mass+(this%mass_of_bits+this%mass_of_fl_bits)*this%mass_scaling
       else
-        sum_mass=sum_mass+(this%mass+this%mass_of_bits)*this%mass_scaling
+        sum_mass=sum_mass+(this%mass+this%mass_of_bits+this%mass_of_fl_bits)*this%mass_scaling
       endif
       this=>this%next
     enddo
@@ -7006,9 +7016,9 @@ real function sum_heat(bergs,justbits,justbergs)
       if (present(justbergs)) then
         dm=this%mass*this%mass_scaling
       elseif (present(justbits)) then
-        dm=this%mass_of_bits*this%mass_scaling
+        dm=(this%mass_of_bits+this%mass_of_fl_bits)*this%mass_scaling
       else
-        dm=(this%mass+this%mass_of_bits)*this%mass_scaling
+        dm=(this%mass+this%mass_of_bits+this%mass_of_fl_bits)*this%mass_scaling
       endif
       sum_heat=sum_heat+dm*this%heat_density
       this=>this%next
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index 5647452..3f4eb02 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -148,6 +148,7 @@ subroutine write_restart(bergs, time_stamp)
                                    start_mass,   &
                                    mass_scaling, &
                                    mass_of_bits, &
+                                   mass_of_fl_bits, &
                                    static_berg,  &
                                    heat_density, &
                                    axn_fast,     &
@@ -224,6 +225,7 @@ subroutine write_restart(bergs, time_stamp)
    allocate(start_mass(nbergs))
    allocate(mass_scaling(nbergs))
    allocate(mass_of_bits(nbergs))
+   allocate(mass_of_fl_bits(nbergs))
    allocate(heat_density(nbergs))
    allocate(static_berg(nbergs))
 
@@ -293,7 +295,9 @@ subroutine write_restart(bergs, time_stamp)
   id = register_restart_field(bergs_restart,filename,'mass_scaling',mass_scaling, &
                                             longname='scaling factor for mass of calving berg',units='none')
   id = register_restart_field(bergs_restart,filename,'mass_of_bits',mass_of_bits, &
-                                            longname='mass of bergy bits',units='kg')
+    longname='mass of bergy bits',units='kg')
+  id = register_restart_field(bergs_restart,filename,'mass_of_fl_bits',mass_of_fl_bits, &
+                                            longname='mass of footloose bits',units='kg')
   id = register_restart_field(bergs_restart,filename,'heat_density',heat_density, &
                                             longname='heat density',units='J/kg')
 
@@ -356,7 +360,8 @@ subroutine write_restart(bergs, time_stamp)
       start_mass(i) = this%start_mass; mass_scaling(i) = this%mass_scaling
       static_berg(i) = this%static_berg
       call split_id(this%id, id_cnt(i), id_ij(i))
-      mass_of_bits(i) = this%mass_of_bits; heat_density(i) = this%heat_density
+      mass_of_bits(i) = this%mass_of_bits; mass_of_fl_bits(i) = this%mass_of_fl_bits
+      heat_density(i) = this%heat_density
       if (mts) then
         axn_fast(i) = this%axn_fast
         ayn_fast(i) = this%ayn_fast
@@ -400,6 +405,7 @@ subroutine write_restart(bergs, time_stamp)
              start_mass,   &
              mass_scaling, &
              mass_of_bits, &
+             mass_of_fl_bits, &
              static_berg,  &
              heat_density)
   if (mts) then
@@ -669,6 +675,7 @@ subroutine read_restart_bergs(bergs,Time)
                                    start_mass,   &
                                    mass_scaling, &
                                    mass_of_bits, &
+                                   mass_of_fl_bits, &
                                    static_berg,  &
                                    heat_density, &
                                    axn_fast,     &
@@ -729,6 +736,7 @@ subroutine read_restart_bergs(bergs,Time)
      allocate(start_mass(nbergs_in_file))
      allocate(mass_scaling(nbergs_in_file))
      allocate(mass_of_bits(nbergs_in_file))
+     allocate(mass_of_fl_bits(nbergs_in_file))
      allocate(static_berg(nbergs_in_file))
      allocate(heat_density(nbergs_in_file))
      allocate(ine(nbergs_in_file))
@@ -800,6 +808,7 @@ subroutine read_restart_bergs(bergs,Time)
      call read_unlimited_axis(filename,'start_mass',start_mass,domain=grd%domain)
      call read_unlimited_axis(filename,'mass_scaling',mass_scaling,domain=grd%domain)
      call read_real_vector(filename,'mass_of_bits',mass_of_bits,domain=grd%domain,value_if_not_in_file=0.)
+     call read_real_vector(filename,'mass_of_fl_bits',mass_of_fl_bits,domain=grd%domain,value_if_not_in_file=0.)
      call read_real_vector(filename,'heat_density',heat_density,domain=grd%domain,value_if_not_in_file=0.)
      call read_unlimited_axis(filename,'ine',ine,domain=grd%domain)
      call read_unlimited_axis(filename,'jne',jne,domain=grd%domain)
@@ -895,6 +904,7 @@ subroutine read_restart_bergs(bergs,Time)
       localberg%start_mass=start_mass(k)
       localberg%mass_scaling=mass_scaling(k)
       localberg%mass_of_bits=mass_of_bits(k)
+      localberg%mass_of_fl_bits=mass_of_fl_bits(k)
       localberg%halo_berg=0.
       localberg%static_berg=static_berg(k)
       localberg%heat_density=heat_density(k)
@@ -956,6 +966,7 @@ subroutine read_restart_bergs(bergs,Time)
                start_mass,   &
                mass_scaling, &
                mass_of_bits, &
+               mass_of_fl_bits, &
                static_berg,  &
                heat_density, &
                ine,          &
@@ -1109,6 +1120,7 @@ subroutine generate_bergs(bergs,Time)
       localberg%start_mass=localberg%mass
       localberg%mass_scaling=bergs%mass_scaling(1)
       localberg%mass_of_bits=0.
+      localberg%mass_of_fl_bits=0.
       localberg%halo_berg=0.
       localberg%static_berg=0.
       localberg%heat_density=0.
@@ -1659,7 +1671,7 @@ subroutine write_trajectory(trajectory, save_short_traj)
 integer :: uvelpid,vvelpid
 integer :: uoid, void, uiid, viid, uaid, vaid, sshxid, sshyid, sstid, sssid
 integer :: cnid, hiid, hsid
-integer :: mid, did, wid, lid, mbid, hdid, nbid, odid, flkid
+integer :: mid, did, wid, lid, mbid, mflbid, hdid, nbid, odid, flkid
 integer :: axnid,aynid,bxnid,bynid,axnfid,aynfid,bxnfid,bynfid
 integer :: eecid,edcid,eeid,edid,aeid,efid
 integer :: eectid, edctid, eetid, edtid, aetid
@@ -1794,6 +1806,7 @@ subroutine write_trajectory(trajectory, save_short_traj)
         vaid = inq_varid(ncid, 'va')
         mid = inq_varid(ncid, 'mass')
         mbid = inq_varid(ncid, 'mass_of_bits')
+        mflbid = inq_varid(ncid, 'mass_of_fl_bits')
         hdid = inq_varid(ncid, 'heat_density')
         did = inq_varid(ncid, 'thickness')
         wid = inq_varid(ncid, 'width')
@@ -1871,6 +1884,7 @@ subroutine write_trajectory(trajectory, save_short_traj)
         vaid = def_var(ncid, 'va', NF_DOUBLE, i_dim)
         mid = def_var(ncid, 'mass', NF_DOUBLE, i_dim)
         mbid = def_var(ncid, 'mass_of_bits', NF_DOUBLE, i_dim)
+        mflbid = def_var(ncid, 'mass_of_fl_bits', NF_DOUBLE, i_dim)
         hdid = def_var(ncid, 'heat_density', NF_DOUBLE, i_dim)
         did = def_var(ncid, 'thickness', NF_DOUBLE, i_dim)
         wid = def_var(ncid, 'width', NF_DOUBLE, i_dim)
@@ -1960,6 +1974,8 @@ subroutine write_trajectory(trajectory, save_short_traj)
         call put_att(ncid, mid, 'units', 'kg')
         call put_att(ncid, mbid, 'long_name', 'mass_of_bits')
         call put_att(ncid, mbid, 'units', 'kg')
+        call put_att(ncid, mflbid, 'long_name', 'mass_of_fl_bits')
+        call put_att(ncid, mflbid, 'units', 'kg')
         call put_att(ncid, hdid, 'long_name', 'heat_density')
         call put_att(ncid, hdid, 'units', 'J/kg')
         call put_att(ncid, did, 'long_name', 'thickness')
diff --git a/tests/footloose_no_bond_test/input.nml b/tests/footloose_no_bond_test/input.nml
index a261bf6..35938e6 100644
--- a/tests/footloose_no_bond_test/input.nml
+++ b/tests/footloose_no_bond_test/input.nml
@@ -30,6 +30,7 @@
     fl_r=4        !(4) average number of footloose bergs to calve per fl_r_s seconds
     fl_r_s=86400  !(86400) time in s over which to calve, on average, fl_r footloose bergs
     displace_fl_bergs=.true. !(T) randomly assign FL berg positions to sides of parent berg
+    fl_style='new_bergs' !('new_bergs'). Can also group FL bergs into 'bergy_bits' or 'fl_bits'
 
     mts=.false. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
     mts_sub_steps=1 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)

From 0c6c9644d2c2701db8d208d425c87c7f3f6d7fd4 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Thu, 1 Apr 2021 11:23:15 -0400
Subject: [PATCH 290/361] quick fix of a mass calculation error for option
 where footloose mass added to bergy bits

---
 src/icebergs.F90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 56ab3bc..042901c 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -2522,11 +2522,11 @@ subroutine footloose_calving(bergs, time)
           endif
 
           if (bergs%fl_style.eq.'bergy_bits') then
-            this%mass_of_bits=this%mass_of_bits+(bergs%rho_bergs*W*T*(L-Lr_fl))
+            this%mass_of_bits=this%mass_of_bits+(bergs%rho_bergs*W*T*Lr_fl)
           elseif (bergs%fl_style.eq.'fl_bits') then
             call error_mesg('KID,footloose_calving', &
               'fl_style = "fl_bits" not yet fully implemented!', FATAL)
-            this%mass_of_fl_bits=this%mass_of_fl_bits+(bergs%rho_bergs*W*T*(L-Lr_fl))
+            !this%mass_of_fl_bits=this%mass_of_fl_bits+(bergs%rho_bergs*W*T*Lr_fl)
           else
             call calve_fl_icebergs(bergs,this,k,l_b,fl_disp_x,fl_disp_y)
           endif

From e720f7eb78782e67166f2e0f505f2ae4d1e36bba Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Thu, 1 Apr 2021 19:44:23 -0400
Subject: [PATCH 291/361] finished preliminary footloose bits option, where
 footloose bergs are tracked and evolved as a group without advecting away
 from their parent bergs

---
 src/icebergs.F90 | 74 ++++++++++++++++++++++++++++++++++++++++++++----
 1 file changed, 68 insertions(+), 6 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 042901c..f1b6bf5 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -2524,9 +2524,7 @@ subroutine footloose_calving(bergs, time)
           if (bergs%fl_style.eq.'bergy_bits') then
             this%mass_of_bits=this%mass_of_bits+(bergs%rho_bergs*W*T*Lr_fl)
           elseif (bergs%fl_style.eq.'fl_bits') then
-            call error_mesg('KID,footloose_calving', &
-              'fl_style = "fl_bits" not yet fully implemented!', FATAL)
-            !this%mass_of_fl_bits=this%mass_of_fl_bits+(bergs%rho_bergs*W*T*Lr_fl)
+            this%mass_of_fl_bits=this%mass_of_fl_bits+(bergs%rho_bergs*W*T*Lr_fl)
           else
             call calve_fl_icebergs(bergs,this,k,l_b,fl_disp_x,fl_disp_y)
           endif
@@ -2722,10 +2720,26 @@ subroutine thermodynamics(bergs)
   real, parameter :: perday=1./86400.
   integer :: grdi, grdj
   real :: SSS !Temporarily here
+  ! Footloose bits stuff
+  real :: youngs,poisson
+  real, save :: l_c, lw_c, B_c
+  logical, save :: Visited=.false.
+  real :: l_w,l_b,L_fl,W_fl,T_fl,M_fl,Vol_fl,Mb_fl,Tn_fl,nVol_fl,Mnew1_fl,dMb_fl
+  real :: Ln_fl,Wn_fl,Mnew2_fl,dMv_fl,Mnew_fl,dMe_fl,dM_fl
 
   ! For convenience
   grd=>bergs%grd
 
+  if (bergs%fl_style.eq.'fl_bits' .and. .not. Visited) then
+    !define some constants for footloose bits:
+    youngs=1.e8; poisson=0.3
+    l_c  = pi/(2.*sqrt(2.)) !for length-scale of child iceberg
+    lw_c = 1./(gravity*rho_seawater) !for buoyancy length
+    B_c  = youngs/(12.*(1.-poisson**2.)) !for bending stiffness
+    Visited=.true.
+  endif
+
+
   !Initializing
   grd%Uvel_on_ocean(:,:,:)=0.
   grd%Vvel_on_ocean(:,:,:)=0.
@@ -2849,6 +2863,53 @@ subroutine thermodynamics(bergs)
         dMv=(M/Vol)*(T*(W+L))*Mv*bergs%dt ! approx. mass loss to buoyant convection (kg)
       endif
 
+      ! Footloose bits (FL bits). Uses operator splitting.
+      ! For now, FL bits do not spawn bergy bits.
+      if (bergs%fl_style.eq.'fl_bits') then
+        !dimensions
+        l_w  = (lw_c*B_c*(T**3.))**0.25  !buoyancy length
+        l_b  = l_c*l_w !length of a freshly calved footloose child berg
+
+        !Estimate the dimenstions of a representative FL berg that will give roughly the same
+        !freshwater flux as the actual group of FL bergs of all different sizes:
+        !this may not be appropriate for very small FL bergs or dense sea ice cover
+        L_fl = 3.*l_b; W_fl=l_b; T_fl=T
+        call rolling(bergs,T_fl,W_fl,L_fl)
+        L_fl = L_fl*0.8; W_fl=W_fl*0.45; T_fl=T_fl*0.65
+        M_fl=this%mass_of_fl_bits; Vol_fl=L_fl*W_fl*T_fl
+
+        !FL bits melt rates in m/s
+        Mb_fl=max( 0.58*(dvo**0.8)*(SST+4.0)/(L_fl**0.2), 0.) *perday ! Basal turbulent melting
+        !Mv and Me are the same as above
+
+        Tn_fl=max(T_fl-Mb_fl*bergs%dt,0.) ! new total thickness (m)
+        nVol_fl=Tn_fl*W_fl*L_fl ! new volume (m^3)
+        Mnew1_fl=(nVol_fl/Vol_fl)*M_fl ! new mass (kg)
+        dMb_fl=M_fl-Mnew1_fl ! mass lost to basal melting (>0) (kg)
+
+        Ln_fl=max(L_fl-Mv*bergs%dt,0.) ! new length (m)
+        Wn_fl=max(W_fl-Mv*bergs%dt,0.) ! new width (m)
+        nVol_fl=Tn_fl*Wn_fl*Ln_fl ! new volume (m^3)
+        Mnew2_fl=(nVol_fl/Vol_fl)*M_fl ! new mass (kg)
+        dMv_fl=Mnew1_fl-Mnew2_fl ! mass lost to buoyant convection (>0) (kg)
+
+        Ln_fl=max(Ln_fl-Me*bergs%dt,0.) ! new length (m)
+        Wn_fl=max(Wn_fl-Me*bergs%dt,0.) ! new width (m)
+        nVol_fl=Tn_fl*Wn_fl*Ln_fl ! new volume (m^3)
+        Mnew_fl=(nVol_fl/Vol_fl)*M_fl ! new mass (kg)
+        dMe_fl=Mnew2_fl-Mnew_fl ! mass lost to erosion (>0) (kg)
+        dM_fl=M_fl-Mnew_fl ! mass lost to all erosion and melting (>0) (kg)
+
+        !Add FL mass loss terms to total mass loss terms
+        dMb=dMb+dMb_fl !from basal melt
+        dMv=dMv+dMv_fl !from buoyant convection
+        dMe=dMe+dMe_fl !from erosion
+        dM=dM+dM_fl    !overall mass loss
+      else
+        dM_fl=0.
+        Mnew_fl=0.
+      endif
+
       ! Bergy bits
       if (bergs%bergy_bit_erosion_fraction>0.) then
         Mbits=this%mass_of_bits ! mass of bergy bits (kg)
@@ -2918,7 +2979,7 @@ subroutine thermodynamics(bergs)
         !before reseting
         if (bergs%find_melt_using_spread_mass) then
           if (Mnew>0.) then !If the berg still exists
-            call spread_mass_across_ocean_cells(bergs,this, i, j, this%xi, this%yj,Mnew , nMbits, this%mass_scaling, Ln*Wn,  Tn)
+            call spread_mass_across_ocean_cells(bergs,this, i, j, this%xi, this%yj,Mnew+Mnew_fl , nMbits, this%mass_scaling, Ln*Wn,  Tn)
           endif
         endif
         !Reset all the values
@@ -2936,6 +2997,7 @@ subroutine thermodynamics(bergs)
         ! Store the new state of iceberg (with L>W)
         this%mass=Mnew
         this%mass_of_bits=nMbits
+        this%mass_of_fl_bits=Mnew_fl
         this%thickness=Tn
         this%width=min(Wn,Ln)
         this%length=max(Wn,Ln)
@@ -5896,8 +5958,8 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b,fl_disp_x,fl_disp_y)
     cberg%yj  = pberg%yj
   endif
 
-  cberg%width        = l_b*3.
-  cberg%length       = l_b
+  cberg%length       = l_b*3.
+  cberg%width        = l_b
   cberg%mass         = cberg%width * cberg%length * pberg%thickness * bergs%rho_bergs
   cberg%start_lon    = cberg%lon
   cberg%start_lat    = cberg%lat

From 1003d75c6dc51c1701bde64feab74b1cd6fdb51a Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Thu, 8 Apr 2021 19:16:29 -0400
Subject: [PATCH 292/361] separated footloose bits fully from bergy bits,
 though footloose bits can still be melted as bergy bits with new nml
 parameter fl_melt_as_bergy_bits. Added fl_bits_scale_l, fl_bits_scale_w, and
 fl_bits_scale_t nml parameters for specifying scaled dimensions of
 representative FL bits berg for melting vs. the dimensions of a new fl berg.
 Modified all budgets code to accomodate fl bits separately from bergy bits

---
 src/icebergs.F90                       | 239 +++++++++++++++----------
 src/icebergs_framework.F90             |  55 +++++-
 src/icebergs_io.F90                    |   2 +
 tests/footloose_no_bond_test/input.nml |   7 +-
 4 files changed, 195 insertions(+), 108 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index f1b6bf5..033d4be 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -2393,7 +2393,7 @@ subroutine footloose_calving(bergs, time)
   integer, dimension(8) :: seed
   real :: T, W, L, N_bonds, Ln, rn
   real :: IC, max_k, k, Lr_fl, l_w, l_b, pu
-  real :: fl_disp_x, fl_disp_y, interp_loc
+  real :: fl_disp_x, fl_disp_y, interp_loc, dM_fl_bits
 
   ! For convenience
   grd=>bergs%grd
@@ -2422,8 +2422,6 @@ subroutine footloose_calving(bergs, time)
     Visited=.true.
   endif
 
-
-
   do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec !computational domain only
     this=>bergs%list(grdi,grdj)%first
     do while(associated(this))
@@ -2500,7 +2498,6 @@ subroutine footloose_calving(bergs, time)
           k=floor(this%fl_k)
         endif
 
-
         if (k>max_k) then
           k=max_k
           this%fl_k=0.
@@ -2513,20 +2510,23 @@ subroutine footloose_calving(bergs, time)
 
           Lr_fl = k*3.*(l_b**2.)/W !FL mechanism length reduction for parent berg
 
-          if (.not. bergs%displace_fl_bergs) then
-            !newly calved FL bergs take same position as parent berg
-            fl_disp_x=0.0; fl_disp_y=0.0
-          else
-            !newly calved FL bergs are randomly assigned positions along the edges of the parent berg
-            call get_footloose_displacement
-          endif
-
-          if (bergs%fl_style.eq.'bergy_bits') then
-            this%mass_of_bits=this%mass_of_bits+(bergs%rho_bergs*W*T*Lr_fl)
-          elseif (bergs%fl_style.eq.'fl_bits') then
-            this%mass_of_fl_bits=this%mass_of_fl_bits+(bergs%rho_bergs*W*T*Lr_fl)
-          else
+          if (bergs%fl_style.eq.'new_bergs') then
+            !calve and track footloose bergs
+            if (.not. bergs%displace_fl_bergs) then
+              fl_disp_x=0.0; fl_disp_y=0.0    !new FL bergs take same position as parent berg
+            else
+              call get_footloose_displacement !new FL bergs given random position along parent berg edges
+            endif
             call calve_fl_icebergs(bergs,this,k,l_b,fl_disp_x,fl_disp_y)
+          else
+            !put FL berg mass in footloose bergs bits.
+            dM_fl_bits=bergs%rho_bergs*W*T*Lr_fl
+            this%mass_of_fl_bits=this%mass_of_fl_bits+dM_fl_bits
+            ! mass flux into fl bits (kg/m2/s)
+            if (grd%area(grdi,grdj).ne.0.) then
+              grd%fl_bits_src(grdi,grdj)=grd%fl_bits_src(grdi,grdj)+&
+                dM_fl_bits/(bergs%dt*grd%area(grdi,grdj))*this%mass_scaling
+            endif
           endif
 
           Ln=L-Lr_fl !new length
@@ -2721,25 +2721,11 @@ subroutine thermodynamics(bergs)
   integer :: grdi, grdj
   real :: SSS !Temporarily here
   ! Footloose bits stuff
-  real :: youngs,poisson
-  real, save :: l_c, lw_c, B_c
-  logical, save :: Visited=.false.
-  real :: l_w,l_b,L_fl,W_fl,T_fl,M_fl,Vol_fl,Mb_fl,Tn_fl,nVol_fl,Mnew1_fl,dMb_fl
-  real :: Ln_fl,Wn_fl,Mnew2_fl,dMv_fl,Mnew_fl,dMe_fl,dM_fl
+  real :: Lfl, Wfl, Tfl, Mfl, Afl, Mb_fl, dMfl, nMfl, Volfl, Lnfl, Wnfl, Tnfl, nVolfl
 
   ! For convenience
   grd=>bergs%grd
 
-  if (bergs%fl_style.eq.'fl_bits' .and. .not. Visited) then
-    !define some constants for footloose bits:
-    youngs=1.e8; poisson=0.3
-    l_c  = pi/(2.*sqrt(2.)) !for length-scale of child iceberg
-    lw_c = 1./(gravity*rho_seawater) !for buoyancy length
-    B_c  = youngs/(12.*(1.-poisson**2.)) !for bending stiffness
-    Visited=.true.
-  endif
-
-
   !Initializing
   grd%Uvel_on_ocean(:,:,:)=0.
   grd%Vvel_on_ocean(:,:,:)=0.
@@ -2863,51 +2849,36 @@ subroutine thermodynamics(bergs)
         dMv=(M/Vol)*(T*(W+L))*Mv*bergs%dt ! approx. mass loss to buoyant convection (kg)
       endif
 
-      ! Footloose bits (FL bits). Uses operator splitting.
-      ! For now, FL bits do not spawn bergy bits.
+      ! Footloose bits (FL bits). For now, FL bits do not erode into bergy bits.
       if (bergs%fl_style.eq.'fl_bits') then
-        !dimensions
-        l_w  = (lw_c*B_c*(T**3.))**0.25  !buoyancy length
-        l_b  = l_c*l_w !length of a freshly calved footloose child berg
-
-        !Estimate the dimenstions of a representative FL berg that will give roughly the same
-        !freshwater flux as the actual group of FL bergs of all different sizes:
-        !this may not be appropriate for very small FL bergs or dense sea ice cover
-        L_fl = 3.*l_b; W_fl=l_b; T_fl=T
-        call rolling(bergs,T_fl,W_fl,L_fl)
-        L_fl = L_fl*0.8; W_fl=W_fl*0.45; T_fl=T_fl*0.65
-        M_fl=this%mass_of_fl_bits; Vol_fl=L_fl*W_fl*T_fl
-
-        !FL bits melt rates in m/s
-        Mb_fl=max( 0.58*(dvo**0.8)*(SST+4.0)/(L_fl**0.2), 0.) *perday ! Basal turbulent melting
-        !Mv and Me are the same as above
-
-        Tn_fl=max(T_fl-Mb_fl*bergs%dt,0.) ! new total thickness (m)
-        nVol_fl=Tn_fl*W_fl*L_fl ! new volume (m^3)
-        Mnew1_fl=(nVol_fl/Vol_fl)*M_fl ! new mass (kg)
-        dMb_fl=M_fl-Mnew1_fl ! mass lost to basal melting (>0) (kg)
-
-        Ln_fl=max(L_fl-Mv*bergs%dt,0.) ! new length (m)
-        Wn_fl=max(W_fl-Mv*bergs%dt,0.) ! new width (m)
-        nVol_fl=Tn_fl*Wn_fl*Ln_fl ! new volume (m^3)
-        Mnew2_fl=(nVol_fl/Vol_fl)*M_fl ! new mass (kg)
-        dMv_fl=Mnew1_fl-Mnew2_fl ! mass lost to buoyant convection (>0) (kg)
-
-        Ln_fl=max(Ln_fl-Me*bergs%dt,0.) ! new length (m)
-        Wn_fl=max(Wn_fl-Me*bergs%dt,0.) ! new width (m)
-        nVol_fl=Tn_fl*Wn_fl*Ln_fl ! new volume (m^3)
-        Mnew_fl=(nVol_fl/Vol_fl)*M_fl ! new mass (kg)
-        dMe_fl=Mnew2_fl-Mnew_fl ! mass lost to erosion (>0) (kg)
-        dM_fl=M_fl-Mnew_fl ! mass lost to all erosion and melting (>0) (kg)
-
-        !Add FL mass loss terms to total mass loss terms
-        dMb=dMb+dMb_fl !from basal melt
-        dMv=dMv+dMv_fl !from buoyant convection
-        dMe=dMe+dMe_fl !from erosion
-        dM=dM+dM_fl    !overall mass loss
+
+        call fl_bits_dimensions(bergs,this,Lfl,Wfl,Tfl)
+        Mfl=this%mass_of_fl_bits
+
+        if (bergs%fl_melt_as_bergy_bits) then
+          Afl=(Mfl/bergs%rho_bergs)/Lfl
+          Mb_fl=max( 0.58*(dvo**0.8)*(SST+2.0)/(Lfl**0.2), 0.) *perday ! FL bits basal turbulent melting
+          Mb_fl=bergs%rho_bergs*Afl*Mb_fl ! in kg/s
+          dMfl=min(Mb_fl*bergs%dt,Mfl) ! bergy bits mass lost to melting (kg)
+          nMfl=Mfl-dMfl ! remove mass lost to bergy bits melt
+        else
+          Volfl=Lfl*Wfl*Tfl
+          Mb_fl=max( 0.58*(dvo**0.8)*(SST+4.0)/(Lfl**0.2), 0.) *perday  ! FL bits basal turbulent melting
+          Lnfl=max(Lfl-(Mv+Me)*bergs%dt,0.) ! (m)
+          Wnfl=max(Wfl-(Mv+Me)*bergs%dt,0.) ! (m)
+          Tnfl=max(Tfl-  Mb_fl*bergs%dt,0.) ! (m)
+          ! Update volume and mass of footloose berg
+          nVolfl=Tnfl*Wnfl*Lnfl ! (m^3)
+          nMfl=(nVolfl/Volfl)*Mfl ! (kg)
+          dMfl=Mfl-nMfl ! total footloose mass lost
+        endif
+        if (Mnew==0.) then ! if parent berg has completely melted then
+          dMfl= Mfl ! instantly melt all the bergy bits
+          nMfl=0.
+        endif
       else
-        dM_fl=0.
-        Mnew_fl=0.
+        dMfl=0.
+        nMfl=this%mass_of_fl_bits ! retain previous value incase non-zero
       endif
 
       ! Bergy bits
@@ -2946,6 +2917,8 @@ subroutine thermodynamics(bergs)
         grd%bergy_src(i,j)=grd%bergy_src(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
         melt=dMbitsM/bergs%dt ! melt rate of bergy bits in kg/s
         grd%bergy_melt(i,j)=grd%bergy_melt(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+        melt=dMfl/bergs%dt ! melt+erosion rate of fl bits in kg/s
+        grd%fl_bits_melt(i,j)=grd%fl_bits_melt(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
         if(grd%id_melt_buoy>0) then
           melt=dMb/bergs%dt ! melt rate due to buoyancy term in kg/s
           grd%melt_buoy(i,j)=grd%melt_buoy(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
@@ -2979,7 +2952,7 @@ subroutine thermodynamics(bergs)
         !before reseting
         if (bergs%find_melt_using_spread_mass) then
           if (Mnew>0.) then !If the berg still exists
-            call spread_mass_across_ocean_cells(bergs,this, i, j, this%xi, this%yj,Mnew+Mnew_fl , nMbits, this%mass_scaling, Ln*Wn,  Tn)
+            call spread_mass_across_ocean_cells(bergs,this, i, j, this%xi, this%yj,Mnew , nMbits+nMfl, this%mass_scaling, Ln*Wn,  Tn)
           endif
         endif
         !Reset all the values
@@ -2993,11 +2966,13 @@ subroutine thermodynamics(bergs)
           Lbits=min(L,W,T,40.) ! assume bergy bits are smallest dimension or 40 meters
           Abits=(Mbits/bergs%rho_bergs)/Lbits ! Effective bottom area (assuming T=Lbits)
         endif
+        nMfl=this%mass_of_fl_bits
+        Mfl=this%mass_of_fl_bits
       else
         ! Store the new state of iceberg (with L>W)
         this%mass=Mnew
         this%mass_of_bits=nMbits
-        this%mass_of_fl_bits=Mnew_fl
+        this%mass_of_fl_bits=nMfl
         this%thickness=Tn
         this%width=min(Wn,Ln)
         this%length=max(Wn,Ln)
@@ -3074,6 +3049,36 @@ subroutine swap_variables(x,y)
   end subroutine swap_variables
 end subroutine rolling
 
+!> Estimate the dimenstions of a representative FL berg that will give roughly the same
+!! freshwater flux as the actual group of FL bergs of all different sizes:
+!! this may not be appropriate for very small FL bergs or dense sea ice cover
+subroutine fl_bits_dimensions(bergs,this,L_fl,W_fl,T_fl)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  type(iceberg), pointer :: this
+  real :: L_fl !< Footloose berg bits length
+  real :: W_fl !< Footloose berg bits width
+  real :: T_fl !< Footloose berg bits thickness
+  ! Local variables
+  real,parameter :: l_c=pi/(2.*sqrt(2.)), lw_c = 1./(gravity*rho_seawater)
+  real,parameter :: B_c=1.e8/(12.*(1.-0.3**2.)) !youngs=1.e8, poisson=0.3
+  real :: l_w,l_b
+
+  if (bergs%fl_melt_as_bergy_bits) then
+    L_fl=min(this%length,this%width,this%thickness,40.)
+    T_fl=L_fl; W_fl=(this%mass_of_fl_bits/bergs%rho_bergs)/(L_fl*T_fl)
+  else
+    l_w  = (lw_c*B_c*(this%thickness**3.))**0.25  !buoyancy length
+    l_b  = l_c*l_w !length of a freshly calved footloose child berg
+    L_fl = 3.*l_b; W_fl=l_b; T_fl=this%thickness
+    call rolling(bergs,T_fl,W_fl,L_fl)
+    L_fl = bergs%fl_bits_scale_l*L_fl
+    W_fl = bergs%fl_bits_scale_w*W_fl
+    T_fl = bergs%fl_bits_scale_t*T_fl
+  endif
+end subroutine fl_bits_dimensions
+
+
 subroutine create_gridded_icebergs_fields(bergs)
 ! Arguments
 type(icebergs), pointer :: bergs !< Container for all types and memory
@@ -3588,7 +3593,7 @@ subroutine spread_mass_across_ocean_cells(bergs, berg, i, j, x, y, Mberg, Mbits,
   real, intent(in) :: x !< Longitude of berg (degree E)
   real, intent(in) :: y !< Latitude of berg (degree N)
   real, intent(in) :: Mberg !< Mass of berg (kg)
-  real, intent(in) :: Mbits !< Mass of bergy bits (kg)
+  real, intent(in) :: Mbits !< Combined mass of bergy and footloose bits (kg)
   real, intent(in) :: scaling !< Multiplier to scale mass (nondim)
   real, intent(in) :: Area !< Area of berg (m2)
   real, intent(in) :: Tn !< Thickness of berg (m)
@@ -4618,7 +4623,7 @@ subroutine calculate_mass_on_ocean(bergs, with_diagnostics)
 
           !Increasing Mass on ocean
           if ((bergs%add_weight_to_ocean .and. .not. bergs%time_average_weight) .or.(bergs%find_melt_using_spread_mass)) then
-            call spread_mass_across_ocean_cells(bergs, berg, berg%ine, berg%jne, berg%xi, berg%yj, berg%mass,berg%mass_of_bits, berg%mass_scaling, &
+            call spread_mass_across_ocean_cells(bergs, berg, berg%ine, berg%jne, berg%xi, berg%yj, berg%mass,berg%mass_of_bits+berg%mass_of_fl_bits, berg%mass_scaling, &
               berg%length*berg%width, berg%thickness)
           endif
 
@@ -4642,7 +4647,8 @@ subroutine calculate_sum_over_bergs_diagnositcs(bergs, grd, berg, i, j)
   integer, intent(in) :: i !< i-index of cell containing berg
   integer, intent(in) :: j !< j-index of cell containing berg
   ! Local variables
-  real ::  Abits, Lbits, Mbits
+  real ::  Abits, Abits_fl, Lbits, Mbits
+  real :: L_fl,W_fl,T_fl
 
   !Virtual area diagnostic
   if (grd%id_virtual_area>0) then
@@ -4652,7 +4658,13 @@ subroutine calculate_sum_over_bergs_diagnositcs(bergs, grd, berg, i, j)
     else
       Abits=0.0
     endif
-    grd%virtual_area(i,j)=grd%virtual_area(i,j)+(berg%width*berg%length+Abits)*berg%mass_scaling ! m^2
+    if (bergs%fl_style.eq.'fl_bits') then
+      call fl_bits_dimensions(bergs,berg,L_fl,W_fl,T_fl)
+      Abits_fl=(berg%mass_of_fl_bits/bergs%rho_bergs)/T_fl ! Effective bottom area
+    else
+      Abits_fl=0.0
+    endif
+    grd%virtual_area(i,j)=grd%virtual_area(i,j)+(berg%width*berg%length+Abits+Abits_fl)*berg%mass_scaling ! m^2
   endif
 
   !Mass diagnostic (also used in u_iceberg, v_iceberg
@@ -4667,7 +4679,11 @@ subroutine calculate_sum_over_bergs_diagnositcs(bergs, grd, berg, i, j)
 
   !Mass of bergy bits
   if (grd%id_bergy_mass>0 .or. bergs%add_weight_to_ocean)&
-       & grd%bergy_mass(i,j)=grd%bergy_mass(i,j)+berg%mass_of_bits/grd%area(i,j)*berg%mass_scaling ! kg/m2
+    & grd%bergy_mass(i,j)=grd%bergy_mass(i,j)+berg%mass_of_bits/grd%area(i,j)*berg%mass_scaling ! kg/m2
+
+  !Mass of footloose bits
+  if (grd%id_fl_bits_mass>0 .or. bergs%add_weight_to_ocean)&
+    & grd%fl_bits_mass(i,j)=grd%fl_bits_mass(i,j)+berg%mass_of_fl_bits/grd%area(i,j)*berg%mass_scaling ! kg/m2
 end subroutine calculate_sum_over_bergs_diagnositcs
 
 !> The main driver the steps updates icebergs
@@ -4698,7 +4714,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   integer :: iyr, imon, iday, ihr, imin, isec, k
   type(icebergs_gridded), pointer :: grd
   logical :: lerr, sample_traj, write_traj, lbudget, lverbose, check_bond_quality
-  real :: unused_calving, tmpsum, grdd_berg_mass, grdd_bergy_mass,grdd_spread_mass, grdd_spread_area
+  real :: unused_calving, tmpsum, grdd_berg_mass, grdd_bergy_mass, grdd_fl_bits_mass, grdd_spread_mass, grdd_spread_area
   real :: grdd_u_iceberg, grdd_v_iceberg, grdd_ustar_iceberg, grdd_spread_uvel, grdd_spread_vvel
   integer :: i, j, Iu, ju, iv, Jv, Iu_off, ju_off, iv_off, Jv_off
   real :: mask, max_SST
@@ -4730,6 +4746,9 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   grd%bergy_src(:,:)=0.
   grd%bergy_melt(:,:)=0.
   grd%bergy_mass(:,:)=0.
+  grd%fl_bits_src(:,:)=0.
+  grd%fl_bits_melt(:,:)=0.
+  grd%fl_bits_mass(:,:)=0.
   grd%spread_mass_old(:,:)=0.
   !grd%spread_mass(:,:)=0.  !Don't zero this out yet, because we can first use this an add it onto the SSH
   grd%spread_area(:,:)=0.
@@ -5033,14 +5052,12 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   call mpp_clock_begin(bergs%clock_com)
   if (bergs%iceberg_bonds_on)  call  bond_address_update(bergs)
 
-  ! Footloose mechanism part 1: calve the child icebergs
-  if (bergs%fl_r>0.) then
-    call footloose_calving(bergs, time)
-  endif
-
   call send_bergs_to_other_pes(bergs)
   if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after send_bergs() ')
 
+  ! Footloose mechanism part 1: calve the child icebergs
+  if (bergs%fl_r>0.) call footloose_calving(bergs, time)
+
   if (bergs%mts) then
     call interp_gridded_fields_to_bergs(bergs)
     call transfer_mts_bergs(bergs)
@@ -5151,6 +5168,12 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     lerr=send_data(grd%id_bergy_melt, grd%bergy_melt(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   if (grd%id_bergy_mass>0) &
     lerr=send_data(grd%id_bergy_mass, grd%bergy_mass(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_fl_bits_src>0) &
+    lerr=send_data(grd%id_fl_bits_src, grd%fl_bits_src(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_fl_bits_melt>0) &
+    lerr=send_data(grd%id_fl_bits_melt, grd%fl_bits_melt(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_fl_bits_mass>0) &
+    lerr=send_data(grd%id_fl_bits_mass, grd%fl_bits_mass(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   if (grd%id_spread_mass>0) &
     lerr=send_data(grd%id_spread_mass, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   if (grd%id_spread_area>0) &
@@ -5256,6 +5279,10 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   bergs%bergy_src=bergs%bergy_src+tmpsum*bergs%dt
   tmpsum=sum( grd%bergy_melt(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
   bergs%bergy_melt=bergs%bergy_melt+tmpsum*bergs%dt
+  tmpsum=sum( grd%fl_bits_src(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
+  bergs%fl_bits_src=bergs%fl_bits_src+tmpsum*bergs%dt
+  tmpsum=sum( grd%fl_bits_melt(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
+  bergs%fl_bits_melt=bergs%fl_bits_melt+tmpsum*bergs%dt
   tmpsum=sum( calving(:,:)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
   bergs%net_calving_returned=bergs%net_calving_returned+tmpsum*bergs%dt
   tmpsum=sum( grd%calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
@@ -5268,6 +5295,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     bergs%floating_mass_end=sum_mass(bergs)
     bergs%icebergs_mass_end=sum_mass(bergs,justbergs=.true.)
     bergs%bergy_mass_end=sum_mass(bergs,justbits=.true.)
+    bergs%fl_bits_mass_end=sum_mass(bergs,justflbits=.true.)
     !bergs%spread_mass_end=sum_mass(bergs) !Not sure what this is
     !bergs%spread_area_end=sum_mass(bergs) !Not sure what this is
     !bergs%u_iceberg_end=sum_mass(bergs) !Not sure what this is
@@ -5290,6 +5318,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     call mpp_sum(bergs%floating_mass_end)
     call mpp_sum(bergs%icebergs_mass_end)
     call mpp_sum(bergs%bergy_mass_end)
+    call mpp_sum(bergs%fl_bits_mass_end)
     call mpp_sum(bergs%spread_mass_end)
     call mpp_sum(bergs%spread_area_end)
     call mpp_sum(bergs%u_iceberg_end)
@@ -5319,10 +5348,14 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     call mpp_sum(bergs%berg_melt)
     call mpp_sum(bergs%bergy_src)
     call mpp_sum(bergs%bergy_melt)
+    call mpp_sum(bergs%fl_bits_src)
+    call mpp_sum(bergs%fl_bits_melt)
     grdd_berg_mass=sum( grd%mass(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
     call mpp_sum(grdd_berg_mass)
     grdd_bergy_mass=sum( grd%bergy_mass(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
     call mpp_sum(grdd_bergy_mass)
+    grdd_fl_bits_mass=sum( grd%fl_bits_mass(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
+    call mpp_sum(grdd_fl_bits_mass)
     grdd_spread_mass=sum( grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
     call mpp_sum(grdd_spread_mass)
     grdd_spread_area=sum( grd%spread_area(grd%isc:grd%iec,grd%jsc:grd%jec)*grd%area(grd%isc:grd%iec,grd%jsc:grd%jec) )
@@ -5334,6 +5367,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
       call report_state('floating','kg','',bergs%floating_mass_start,'',bergs%floating_mass_end,'',bergs%nbergs_end)
       call report_state('icebergs','kg','',bergs%icebergs_mass_start,'',bergs%icebergs_mass_end,'')
       call report_state('bits','kg','',bergs%bergy_mass_start,'',bergs%bergy_mass_end,'')
+      call report_state('fl_bits','kg','',bergs%fl_bits_mass_start,'',bergs%fl_bits_mass_end,'')
       call report_state('spread icebergs','kg','',bergs%spread_mass_start,'',bergs%spread_mass_end,'')
       call report_state('spread icebergs','m^2','',bergs%spread_area_start,'',bergs%spread_area_end,'')
       call report_istate('berg #','',bergs%nbergs_start,'',bergs%nbergs_end,'')
@@ -5352,6 +5386,9 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
       call report_budget('bits mass','kg','eros used',bergs%bergy_src, &
                                           'bergs',bergs%bergy_melt, &
                                           'stored mass',bergs%bergy_mass_start,bergs%bergy_mass_end)
+      call report_budget('fl bits mass','kg','fl calving',bergs%fl_bits_src, &
+                                          'fl melt+eros',bergs%fl_bits_melt, &
+                                          'fl mass',bergs%fl_bits_mass_start,bergs%fl_bits_mass_end)
       call report_budget('net mass','kg','recvd',bergs%net_calving_received, &
                                          'rtrnd',bergs%net_calving_returned, &
                                          'net mass',bergs%stored_start+bergs%floating_mass_start, &
@@ -5360,6 +5397,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
       call report_consistant('spread mass','kg','gridded',grdd_spread_mass,'bergs',bergs%spread_mass_end)
       call report_consistant('spread area','kg','gridded',grdd_spread_area,'bergs',bergs%spread_area_end)
       call report_consistant('bits mass','kg','gridded',grdd_bergy_mass,'bits',bergs%bergy_mass_end)
+      call report_consistant('fl bits mass','kg','gridded',grdd_fl_bits_mass,'fl bits',bergs%fl_bits_mass_end)
       call report_consistant('wieght','kg','returned',bergs%returned_mass_on_ocean,'floating',bergs%floating_mass_end)
       call report_state('net heat','J','',bergs%stored_heat_start+bergs%floating_heat_start,'',&
            & bergs%stored_heat_end+bergs%floating_heat_end,'')
@@ -5394,6 +5432,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     bergs%floating_mass_start=bergs%floating_mass_end
     bergs%icebergs_mass_start=bergs%icebergs_mass_end
     bergs%bergy_mass_start=bergs%bergy_mass_end
+    bergs%fl_bits_mass_start=bergs%fl_bits_mass_end
     bergs%spread_mass_start=bergs%spread_mass_end
     bergs%spread_area_start=bergs%spread_area_end
     bergs%net_calving_used=0.
@@ -5411,6 +5450,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     bergs%berg_melt=0.
     bergs%bergy_melt=0.
     bergs%bergy_src=0.
+    bergs%fl_bits_melt=0.
+    bergs%fl_bits_src=0.
 
     if (bergs%iceberg_bonds_on) then
       check_bond_quality=.true.
@@ -5830,6 +5871,7 @@ subroutine calve_icebergs(bergs)
           newberg%start_mass=bergs%initial_mass(k)
           newberg%mass_scaling=bergs%mass_scaling(k)
           newberg%mass_of_bits=0.
+          newberg%mass_of_fl_bits=0.
           newberg%halo_berg=0.
           newberg%static_berg=0.
           newberg%heat_density=grd%stored_heat(i,j)/grd%stored_ice(i,j,k) ! This is in J/kg
@@ -5922,8 +5964,7 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b,fl_disp_x,fl_disp_y)
     cberg%lat = pberg%lat + fl_disp_y
     lres= find_cell_wide(grd, cberg%lon, cberg%lat, cberg%ine, cberg%jne)
 
-    !If new berg is not on current PE, correct it so that it is. This correction is just a
-    !safety measure to make sure it is not within a grounded cell on the other PE.
+    !If new berg is not on current PE, correct it so that it is.
     if (.not. lres) then
       !The choice of 75% and 25% weighting here is completely arbitrary...
       if (cberg%lon > grd%lon(grd%ied,grd%jed)) then
@@ -5939,6 +5980,7 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b,fl_disp_x,fl_disp_y)
       lres= find_cell_wide(grd, cberg%lon, cberg%lat, cberg%ine, cberg%jne)
       if (.not. lres) call error_mesg('KID, calve_fl_icebergs', &
         'corrected new berg position still not on current PE!', FATAL)
+      fl_disp_x=pberg%lon-cberg%lon; fl_disp_y=pberg%lat-cberg%lat
     endif
 
     !if new berg is located within a grounded cell, change its position to the same as the parent berg
@@ -5963,9 +6005,6 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b,fl_disp_x,fl_disp_y)
   cberg%mass         = cberg%width * cberg%length * pberg%thickness * bergs%rho_bergs
   cberg%start_lon    = cberg%lon
   cberg%start_lat    = cberg%lat
-  !pberg%lon is saved on cberg%lon_prev in case the displacement of the new FL child berg causes it to ground,
-  !so that cberg%lon can then be corrected back to equal pberg%lon (same process for lat)
-  !Note lon_prev is otherwise only used for updating bond angles for fracture (not applicable to child bergs)
   cberg%lon_prev     = pberg%lon_prev + fl_disp_x
   cberg%lat_prev     = pberg%lat_prev + fl_disp_y
   cberg%lon_old      = pberg%lon_old  + fl_disp_x
@@ -5974,6 +6013,7 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b,fl_disp_x,fl_disp_y)
   cberg%start_mass   = cberg%mass
   cberg%mass_scaling = pberg%mass_scaling * k !k is the number of icebergs cberg represents
   cberg%mass_of_bits = 0.0
+  cberg%mass_of_fl_bits = 0.0
   cberg%fl_k         = -1.0
   cberg%start_year   = bergs%current_year
   cberg%id           = generate_id(grd, pberg%ine, pberg%jne)
@@ -6815,7 +6855,7 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln, rx, ry)
   ! Note, the mass scaling is equal to 1 (rather than 0.25 as in RK), since
   ! this is only called once in Verlet stepping.
   if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 1.0*berg%mass_scaling,berg%length*berg%width, berg%thickness)
+    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits+berg%mass_of_fl_bits, 1.0*berg%mass_scaling,berg%length*berg%width, berg%thickness)
 
   ! Calling the acceleration   (note that the velocity is converted to u_star inside the accel script)
   call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, ax1, ay1, axn, ayn, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
@@ -6945,7 +6985,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
   if ((berg%lat>89.) .and. (bergs%grd%grid_is_latlon)) on_tangential_plane=.true.
   i1=i;j1=j
   if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, berg%thickness)
+    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits+berg%mass_of_fl_bits, 0.25*berg%mass_scaling,berg%length*berg%width, berg%thickness)
 
   ! Loading past accelerations - Alon
   axn=berg%axn; ayn=berg%ayn !Alon
@@ -6983,7 +7023,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
   call adjust_index_and_ground(grd, lon2, lat2, uvel2, vvel2, i, j, xi, yj, bounced, error_flag, berg%id)
   i2=i; j2=j
   if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, berg%thickness)
+    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits+berg%mass_of_fl_bits, 0.25*berg%mass_scaling,berg%length*berg%width, berg%thickness)
   ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon2,lat2,x2,y2)
   if (.not.error_flag) then
     if (debug .and. .not. is_point_in_cell(bergs%grd, lon2, lat2, i, j)) error_flag=.true.
@@ -7040,7 +7080,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
   call adjust_index_and_ground(grd, lon3, lat3, uvel3, vvel3, i, j, xi, yj, bounced, error_flag, berg%id)
   i3=i; j3=j
   if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, berg%thickness)
+    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits+berg%mass_of_fl_bits, 0.25*berg%mass_scaling,berg%length*berg%width, berg%thickness)
   ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon3,lat3,x3,y3)
   if (.not.error_flag) then
     if (debug .and. .not. is_point_in_cell(bergs%grd, lon3, lat3, i, j)) error_flag=.true.
@@ -7170,7 +7210,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
   i=i1;j=j1;xi=berg%xi;yj=berg%yj
   call adjust_index_and_ground(grd, lonn, latn, uveln, vveln, i, j, xi, yj, bounced, error_flag, berg%id)
   if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, berg%thickness)
+    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits+berg%mass_of_fl_bits, 0.25*berg%mass_scaling,berg%length*berg%width, berg%thickness)
 
   if (.not.error_flag) then
     if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j)) error_flag=.true.
@@ -7746,6 +7786,9 @@ subroutine icebergs_end(bergs)
   deallocate(bergs%grd%bergy_src)
   deallocate(bergs%grd%bergy_melt)
   deallocate(bergs%grd%bergy_mass)
+  deallocate(bergs%grd%fl_bits_src)
+  deallocate(bergs%grd%fl_bits_melt)
+  deallocate(bergs%grd%fl_bits_mass)
   deallocate(bergs%grd%spread_mass)
   deallocate(bergs%grd%spread_mass_old)
   deallocate(bergs%grd%spread_area)
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 48bb298..55a6003 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -155,6 +155,9 @@ module ice_bergs_framework
   real, dimension(:,:), pointer :: bergy_src=>null() !< Mass flux from berg erosion into bergy bits (kg/s/m^2)
   real, dimension(:,:), pointer :: bergy_melt=>null() !< Melting rate of bergy bits (kg/s/m^2)
   real, dimension(:,:), pointer :: bergy_mass=>null() !< Mass distribution of bergy bits (kg/s/m^2)
+  real, dimension(:,:), pointer :: fl_bits_src=>null() !< Mass flux from berg into footloose bits (kg/s/m^2)
+  real, dimension(:,:), pointer :: fl_bits_melt=>null() !< Melting rate of footloose bits (kg/s/m^2)
+  real, dimension(:,:), pointer :: fl_bits_mass=>null() !< Mass distribution of footloose bits (kg/s/m^2)
   real, dimension(:,:), pointer :: spread_mass=>null() !< Mass of icebergs after spreading (kg/m^2)
   real, dimension(:,:), pointer :: spread_mass_old=>null() !< Mass of icebergs after spreading old (kg/m^2)
   real, dimension(:,:), pointer :: spread_area=>null() !< Area of icebergs after spreading (m^2/m^2)
@@ -191,6 +194,7 @@ module ice_bergs_framework
   integer :: id_calving_hflx_in=-1, id_stored_heat=-1, id_melt_hflx=-1, id_heat_content=-1
   integer :: id_mass=-1, id_ui=-1, id_vi=-1, id_ua=-1, id_va=-1, id_sst=-1, id_cn=-1, id_hi=-1
   integer :: id_bergy_src=-1, id_bergy_melt=-1, id_bergy_mass=-1, id_berg_melt=-1
+  integer :: id_fl_bits_src=-1, id_fl_bits_melt=-1, id_fl_bits_mass=-1
   integer :: id_rmean_calving=-1, id_rmean_calving_hflx=-1
   integer :: id_spread_mass=-1, id_spread_area=-1
   integer :: id_ssh=-1, id_fax=-1, id_fay=-1
@@ -555,6 +559,7 @@ module ice_bergs_framework
   real :: floating_heat_start=0., floating_heat_end=0.
   real :: icebergs_mass_start=0., icebergs_mass_end=0.
   real :: bergy_mass_start=0., bergy_mass_end=0.
+  real :: fl_bits_mass_start=0., fl_bits_mass_end=0.
   real :: spread_mass_start=0., spread_mass_end=0.
   real :: spread_area_start=0., spread_area_end=0.
   real :: u_iceberg_start=0., u_iceberg_end=0.
@@ -565,6 +570,7 @@ module ice_bergs_framework
   real :: returned_mass_on_ocean=0.
   real :: returned_area_on_ocean=0.
   real :: net_melt=0., berg_melt=0., bergy_src=0., bergy_melt=0.
+  real :: fl_bits_src=0., fl_bits_melt=0.
   integer :: nbergs_calved=0, nbergs_melted=0, nbergs_start=0, nbergs_end=0
   integer :: nspeeding_tickets=0
   integer :: nbonds=0
@@ -601,7 +607,11 @@ module ice_bergs_framework
   real :: fl_r=0. !< footloose average number of bergs calved per fl_r_s
   real :: fl_r_s=0. !< seconds over which fl_r footloose bergs calve
   logical :: displace_fl_bergs=.true. !< footloose berg positions are randomly assigned along edges of parent berg
-  character(len=11) :: fl_style='new_bergs' !< Evolve footloose bergs individually as 'new_bergs', or as a group with size 'bergy_bits' or 'fl_bits'
+  character(len=11) :: fl_style='new_bergs' !< Evolve footloose bergs individually as 'new_bergs', or as a group with size 'fl_bits'
+  logical :: fl_melt_as_bergy_bits=.false. !< Melt footloose bits as bergy_bits
+  real :: fl_bits_scale_l=0.8  !< For determining dimensions of FL bits berg; FL_bits length = fl_bits_scale_l*3*l_b
+  real :: fl_bits_scale_w=0.45 !< For determining dimensions of FL bits berg; FL_bits width = fl_bits_scale_l*3*l_b
+  real :: fl_bits_scale_t=0.65 !< For determining dimensions of FL bits berg; FL_bits thickness = fl_bits_scale_l*T
 end type icebergs
 
 !> Read original restarts. Needs to be module global so can be public to icebergs_mod.
@@ -788,6 +798,10 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: fl_r_s=0. !< seconds over which fl_r footloose bergs calve
 logical :: displace_fl_bergs=.true. !< footloose berg positions are randomly assigned along edges of parent berg
 character(len=11) :: fl_style='new_bergs' !< Evolve footloose bergs individually as 'fl_bits', or as a group with size 'bergy_bits' or 'mean_size'
+logical :: fl_melt_as_bergy_bits=.false. !< Melt footloose bits as bergy_bits
+real :: fl_bits_scale_l=0.8 !< For determining dimensions of FL bits berg; FL_bits length = fl_bits_scale_l*3*l_b
+real :: fl_bits_scale_w=0.45 !< For determining dimensions of FL bits berg; FL_bits width = fl_bits_scale_l*3*l_b
+real :: fl_bits_scale_t=0.65 !< For determining dimensions of FL bits berg; FL_bits thickness = fl_bits_scale_l*T
 
 namelist /icebergs_nml/ verbose, budget, halo,  traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,Static_icebergs,  &
          distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,bond_coef, radial_damping_coef, tangental_damping_coef, only_interactive_forces, &
@@ -804,7 +818,8 @@ subroutine ice_bergs_framework_init(bergs, &
          mts,new_mts,ewsame,monitor_energy,mts_sub_steps,contact_distance,length_for_manually_initialize_bonds,manually_initialize_bonds_from_radii,contact_spring_coef,&
          fracture_criterion, damage_test_1, uniaxial_test, debug_write,cdrag_grounding,h_to_init_grounding,frac_thres_scaling,frac_thres_n,frac_thres_t,save_bond_traj,remove_unused_bergs,&
          force_convergence,explicit_inner_mts,convergence_tolerance,&
-         dem,ignore_tangential_force,poisson,dem_spring_coef,dem_damping_coef,dem_beam_test,constant_interaction_LW,constant_length,constant_width,dem_shear_for_frac_only,use_damage, fl_use_poisson_distribution, fl_r, fl_r_s, displace_fl_bergs,fl_style
+         dem,ignore_tangential_force,poisson,dem_spring_coef,dem_damping_coef,dem_beam_test,constant_interaction_LW,constant_length,constant_width,dem_shear_for_frac_only,use_damage, fl_use_poisson_distribution, fl_r, fl_r_s, displace_fl_bergs,fl_style,&
+         fl_melt_as_bergy_bits,fl_bits_scale_l,fl_bits_scale_w,fl_bits_scale_t
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -921,6 +936,9 @@ subroutine ice_bergs_framework_init(bergs, &
   allocate( grd%bergy_src(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%bergy_src(:,:)=0.
   allocate( grd%bergy_melt(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%bergy_melt(:,:)=0.
   allocate( grd%bergy_mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%bergy_mass(:,:)=0.
+  allocate( grd%fl_bits_src(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%fl_bits_src(:,:)=0.
+  allocate( grd%fl_bits_melt(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%fl_bits_melt(:,:)=0.
+  allocate( grd%fl_bits_mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%fl_bits_mass(:,:)=0.
   allocate( grd%spread_mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_mass(:,:)=0.
   allocate( grd%spread_mass_old(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_mass_old(:,:)=0.
   allocate( grd%spread_area(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_area(:,:)=0.
@@ -1366,6 +1384,14 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%fl_r_s=fl_r_s
   bergs%displace_fl_bergs=displace_fl_bergs
   bergs%fl_style=fl_style
+  bergs%fl_melt_as_bergy_bits=fl_melt_as_bergy_bits
+  if (fl_style.ne.'new_bergs') then
+    displace_fl_bergs=.false.
+    bergs%fl_melt_as_bergy_bits=.false.
+  endif
+  bergs%fl_bits_scale_l=fl_bits_scale_l
+  bergs%fl_bits_scale_w=fl_bits_scale_w
+  bergs%fl_bits_scale_t=fl_bits_scale_t
 
   if (monitor_energy) then
     if (bergs%constant_interaction_LW) then
@@ -1470,7 +1496,13 @@ subroutine ice_bergs_framework_init(bergs, &
   grd%id_bergy_melt=register_diag_field('icebergs', 'bergy_melt', axes, Time, &
      'Melt rate of bergy bits', 'kg/(m^2*s)')
   grd%id_bergy_mass=register_diag_field('icebergs', 'bergy_mass', axes, Time, &
-     'Bergy bit density field', 'kg/(m^2)')
+    'Bergy bit density field', 'kg/(m^2)')
+  grd%id_fl_bits_src=register_diag_field('icebergs', 'fl_bits_src', axes, Time, &
+     'Mass source of footloose bits', 'kg/(m^2*s)')
+  grd%id_fl_bits_melt=register_diag_field('icebergs', 'fl_bits_melt', axes, Time, &
+     'Melt rate of footloose bits', 'kg/(m^2*s)')
+  grd%id_fl_bits_mass=register_diag_field('icebergs', 'fl_bits_mass', axes, Time, &
+    'Footloose bits density field', 'kg/(m^2)')
   grd%id_spread_mass=register_diag_field('icebergs', 'spread_mass', axes, Time, &
      'Iceberg mass after spreading', 'kg/(m^2)')
   grd%id_spread_area=register_diag_field('icebergs', 'spread_area', axes, Time, &
@@ -6971,10 +7003,11 @@ subroutine check_position(grd, berg, label, il, jl)
 end subroutine check_position
 
 !> Add up the mass of bergs and/or bergy bits
-real function sum_mass(bergs, justbits, justbergs)
+real function sum_mass(bergs, justbits, justflbits, justbergs)
 ! Arguments
 type(icebergs), pointer :: bergs !< Container for all types and memory
 logical, intent(in), optional :: justbits !< If present, add up mass of just bergy bits
+logical, intent(in), optional :: justflbits !< If present, add up mass of just footloose bits
 logical, intent(in), optional :: justbergs !< If present, add up mass of just bergs
 ! Local variables
 type(iceberg), pointer :: this
@@ -6987,7 +7020,9 @@ real function sum_mass(bergs, justbits, justbergs)
       if (present(justbergs)) then
         sum_mass=sum_mass+this%mass*this%mass_scaling
       elseif (present(justbits)) then
-        sum_mass=sum_mass+(this%mass_of_bits+this%mass_of_fl_bits)*this%mass_scaling
+        sum_mass=sum_mass+this%mass_of_bits*this%mass_scaling
+      elseif (present(justflbits)) then
+        sum_mass=sum_mass+this%mass_of_fl_bits*this%mass_scaling
       else
         sum_mass=sum_mass+(this%mass+this%mass_of_bits+this%mass_of_fl_bits)*this%mass_scaling
       endif
@@ -6998,10 +7033,11 @@ real function sum_mass(bergs, justbits, justbergs)
 end function sum_mass
 
 !> Add up the heat content of bergs and/or bergy bits
-real function sum_heat(bergs,justbits,justbergs)
+real function sum_heat(bergs,justbits,justflbits, justbergs)
 ! Arguments
 type(icebergs), pointer :: bergs !< Container for all types and memory
 logical, intent(in), optional :: justbits !< If present, add up heat content of just bergy bits
+logical, intent(in), optional :: justflbits !< If present, add up mass of just footloose bits
 logical, intent(in), optional :: justbergs !< If present, add up heat content of just bergs
 ! Local variables
 type(iceberg), pointer :: this
@@ -7016,7 +7052,9 @@ real function sum_heat(bergs,justbits,justbergs)
       if (present(justbergs)) then
         dm=this%mass*this%mass_scaling
       elseif (present(justbits)) then
-        dm=(this%mass_of_bits+this%mass_of_fl_bits)*this%mass_scaling
+        dm=this%mass_of_bits*this%mass_scaling
+      elseif (present(justflbits)) then
+        dm=this%mass_of_fl_bits*this%mass_scaling
       else
         dm=(this%mass+this%mass_of_bits+this%mass_of_fl_bits)*this%mass_scaling
       endif
@@ -7083,6 +7121,9 @@ subroutine checksum_gridded(grd, label)
   call grd_chksum2(grd, grd%bergy_src, 'bergy_src')
   call grd_chksum2(grd, grd%bergy_melt, 'bergy_melt')
   call grd_chksum2(grd, grd%bergy_mass, 'bergy_mass')
+  call grd_chksum2(grd, grd%fl_bits_src, 'fl_bits_src')
+  call grd_chksum2(grd, grd%fl_bits_melt, 'fl_bits_melt')
+  call grd_chksum2(grd, grd%fl_bits_mass, 'fl_bits_mass')
   call grd_chksum2(grd, grd%spread_mass, 'spread_mass')
   call grd_chksum2(grd, grd%spread_area, 'spread_area')
   call grd_chksum2(grd, grd%u_iceberg, 'u_iceberg')
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index 3f4eb02..ba1fc28 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -1032,6 +1032,8 @@ subroutine read_restart_bergs(bergs,Time)
   call mpp_sum( bergs%icebergs_mass_start )
   bergs%bergy_mass_start=sum_mass(bergs,justbits=.true.)
   call mpp_sum( bergs%bergy_mass_start )
+  bergs%fl_bits_mass_start=sum_mass(bergs,justflbits=.true.)
+  call mpp_sum( bergs%fl_bits_mass_start )
   if (mpp_pe().eq.mpp_root_pe().and.verbose) write(*,'(a)') 'KID, read_restart_bergs: completed'
 
 end subroutine read_restart_bergs
diff --git a/tests/footloose_no_bond_test/input.nml b/tests/footloose_no_bond_test/input.nml
index 35938e6..d0819d6 100644
--- a/tests/footloose_no_bond_test/input.nml
+++ b/tests/footloose_no_bond_test/input.nml
@@ -30,7 +30,8 @@
     fl_r=4        !(4) average number of footloose bergs to calve per fl_r_s seconds
     fl_r_s=86400  !(86400) time in s over which to calve, on average, fl_r footloose bergs
     displace_fl_bergs=.true. !(T) randomly assign FL berg positions to sides of parent berg
-    fl_style='new_bergs' !('new_bergs'). Can also group FL bergs into 'bergy_bits' or 'fl_bits'
+    fl_style='fl_bits' !('new_bergs'). Can also group FL bergs into 'fl_bits'
+    fl_melt_as_bergy_bits=.false.!true. !(F) If fl_style==fl_bits, melt the fl_bits as bergy bits
 
     mts=.false. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
     mts_sub_steps=1 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
@@ -51,7 +52,7 @@
     tangental_damping_coef=2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
     critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
     LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    bergy_bit_erosion_fraction=0.0 ! (0.) Fraction of erosion melt flux to divert to bergy bits
     sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
     u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
     v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
@@ -103,7 +104,7 @@
     verbose_hrs=24 ! (24) Period between verbose messages
     traj_sample_hrs=1 !1 !(24) sampling period for trajectory storage
     traj_write_hrs=1 ! (480) Period for writing sampled trajectories to disk
-    budget=.false. !(T) Calculate budgets
+    budget=.true.!.false. !(T) Calculate budgets
     debug=.false. !(F) Turn on debugging
     really_debug=.false. !(F) Turn on debugging
     halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)

From 81f5b841f30cd531af0da5c786c1357fef9c88de Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Fri, 9 Apr 2021 14:41:16 -0400
Subject: [PATCH 293/361] some minor edits to budgets. Added SST as nml
 parameter in the driver

---
 driver/icebergs_driver.F90             | 15 ++++++++-------
 src/icebergs.F90                       |  4 ++--
 tests/footloose_no_bond_test/input.nml |  7 ++++---
 3 files changed, 14 insertions(+), 12 deletions(-)

diff --git a/driver/icebergs_driver.F90 b/driver/icebergs_driver.F90
index a026efd..e419182 100644
--- a/driver/icebergs_driver.F90
+++ b/driver/icebergs_driver.F90
@@ -64,13 +64,14 @@ program icebergs_driver
 real :: ibui=0.0
 real :: ibvi=0.0
 real :: gridres=1.e3
-real :: bump_deptht=0
+real :: bump_depth=0
+real :: sst=-2
 integer :: ibhrs=2
 integer :: nmax = 2000000000 !<max number of iteration
 integer :: write_time_inc=1
 namelist /icebergs_driver_nml/ debug, ni, nj, halo, ibhrs, ibdt, ibuo, ibvo, nmax, &
   saverestart,ibui,ibvi,collision_test,chaotic_test,grounding_test,&
-  gridres,write_time_inc,bump_depth
+  gridres,write_time_inc,bump_depth, sst
 ! For loops
 integer :: isc !< Start of i-index for computational domain (used for loops)
 integer :: iec !< End of i-index for computational domain (used for loops)
@@ -104,7 +105,7 @@ program icebergs_driver
 real, dimension(:,:), allocatable :: ui,vi !<zonal and meridonal ice velocities (m/s)
 real, dimension(:,:), allocatable :: tauxa,tauya !< Zonal and meridonal wind stress (Pa)
 real, dimension(:,:), allocatable :: ssh !< Effective sea-surface height (m)
-real, dimension(:,:), allocatable :: sst !< Sea-surface temperature (C or K)
+real, dimension(:,:), allocatable :: sstemp !< Sea-surface temperature (C or K)
 real, dimension(:,:), allocatable :: cn !< Sea-ice concentration (nondim)
 real, dimension(:,:), allocatable :: hi !< Sea-ice thickness (m)
 real, dimension(:,:), allocatable :: calving_hflx !< Calving heat flux (W/m2)
@@ -244,7 +245,7 @@ program icebergs_driver
 allocate( tauxa(isd:ied,jsd:jed) )
 allocate( tauya(isd:ied,jsd:jed) )
 allocate( ssh(isd:ied,jsd:jed) )
-allocate( sst(isd:ied,jsd:jed) )
+allocate( sstemp(isd:ied,jsd:jed) )
 allocate( cn(isd:ied,jsd:jed) )
 allocate( hi(isd:ied,jsd:jed) )
 allocate( calving_hflx(isd:ied,jsd:jed) )
@@ -257,7 +258,7 @@ program icebergs_driver
 tauxa = 0.0 !zonal wind stress (Pa)
 tauya = 0.0 !meridonal wind stress (Pa)
 ssh = 0.0 !eff sea-surf height
-sst = -2.0 !sea surface temperature (C or K; if K, will automatically adjust to C)
+sstemp = sst !sea surface temperature (C or K; if K, will automatically adjust to C)
 cn = 0.0 !sea-ice concentration (nondim)
 hi = 0.0 !sea-ice thickness (m)
 calving_hflx = 0.0 !calving heat flux (W/m2)
@@ -344,12 +345,12 @@ program icebergs_driver
                     uo(isc-1:iec+1,jsc-1:jec+1), vo(isc-1:iec+1,jsc-1:jec+1), &
                     ui(isc-1:iec+1,jsc-1:jec+1), vi(isc-1:iec+1,jsc-1:jec+1), &
                     tauxa(isc:iec,jsc:jec), tauya(isc:iec,jsc:jec), &
-                    ssh(isc-1:iec+1,jsc-1:jec+1), sst(isc:iec,jsc:jec), &
+                    ssh(isc-1:iec+1,jsc-1:jec+1), sstemp(isc:iec,jsc:jec), &
                     calving_hflx(isc:iec,jsc:jec), &
                     cn(isc-1:iec+1,jsc-1:jec+1), hi(isc-1:iec+1,jsc-1:jec+1))
 
   ! full form, with optional vars:
-  ! call icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh, sst, &
+  ! call icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh, sstemp, &
   ! calving_hflx, cn, hi,stagger, stress_stagger, sss, mass_berg, ustar_berg, area_berg)
 
   Time = Time + real_to_time_type(dt)
diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 033d4be..a6e8bb7 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -2906,7 +2906,7 @@ subroutine thermodynamics(bergs)
 
       ! Add melting to the grid and field diagnostics
       if (grd%area(i,j).ne.0.) then
-        melt=(dM-(dMbitsE-dMbitsM))/bergs%dt ! kg/s
+        melt=(dM+dMfl-(dMbitsE-dMbitsM))/bergs%dt ! kg/s
         grd%floating_melt(i,j)=grd%floating_melt(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
         melt=melt*this%heat_density ! kg/s x J/kg = J/s
         grd%calving_hflx(i,j)=grd%calving_hflx(i,j)+melt/grd%area(i,j)*this%mass_scaling ! W/m2
@@ -5381,7 +5381,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
                                               'bergs',bergs%net_melt, &
                                               'stored mass',bergs%floating_mass_start,bergs%floating_mass_end)
       call report_budget('berg mass','kg','calving',bergs%net_calving_to_bergs, &
-                                          'melt+eros',bergs%berg_melt, &
+                                          'melt+eros+fl',bergs%berg_melt+bergs%fl_bits_src, &
                                           'berg mass',bergs%icebergs_mass_start,bergs%icebergs_mass_end)
       call report_budget('bits mass','kg','eros used',bergs%bergy_src, &
                                           'bergs',bergs%bergy_melt, &
diff --git a/tests/footloose_no_bond_test/input.nml b/tests/footloose_no_bond_test/input.nml
index d0819d6..b1a4600 100644
--- a/tests/footloose_no_bond_test/input.nml
+++ b/tests/footloose_no_bond_test/input.nml
@@ -19,6 +19,7 @@
   halo=3
   debug=.false.
   gridres=1000.
+  sst=-2
   collision_test=.false. !specific to the current test, must be true here
 /
 
@@ -29,7 +30,7 @@
 
     fl_r=4        !(4) average number of footloose bergs to calve per fl_r_s seconds
     fl_r_s=86400  !(86400) time in s over which to calve, on average, fl_r footloose bergs
-    displace_fl_bergs=.true. !(T) randomly assign FL berg positions to sides of parent berg
+    displace_fl_bergs=.false. !(T) randomly assign FL berg positions to sides of parent berg
     fl_style='fl_bits' !('new_bergs'). Can also group FL bergs into 'fl_bits'
     fl_melt_as_bergy_bits=.false.!true. !(F) If fl_style==fl_bits, melt the fl_bits as bergy bits
 
@@ -64,7 +65,7 @@
     const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
     use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
     add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    passive_mode=.true. ! (F) Add weight of icebergs + bits to ocean
     time_average_weight=.false. ! (F) Time average the weight on the ocean
     speed_limit=0. ! (0.) CFL speed limit for a berg
     tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
@@ -93,7 +94,7 @@
     set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
 
     iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true.!.false. ! (F) Turn on/off interactions between icebergs
+    interactive_icebergs_on=.false.!.true.!.false. ! (F) Turn on/off interactions between icebergs
     only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
     use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
     input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist

From a9deeea9e977a7bb73ad2c3e1304ecce838f5913 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Thu, 15 Apr 2021 16:41:45 -0400
Subject: [PATCH 294/361] a few minor changes to footloose bits regarding
 scaling and rolling. Separated the Me and Mv melt functions for footloose
 bits from parent berg, as these melt terms will be different for the parent
 berg if there is bonding. Added in footloose bits area when spreading berg
 mass to grid, assuming that footloose bits have the same thickness as the
 parent berg (Note this is just an approximation, as FL bergs should not have
 the same thickness, but not sure at this point if including FL area makes a
 difference, anyway)

---
 src/icebergs.F90 | 35 +++++++++++++++++++++--------------
 1 file changed, 21 insertions(+), 14 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index a6e8bb7..64c487d 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -2721,7 +2721,7 @@ subroutine thermodynamics(bergs)
   integer :: grdi, grdj
   real :: SSS !Temporarily here
   ! Footloose bits stuff
-  real :: Lfl, Wfl, Tfl, Mfl, Afl, Mb_fl, dMfl, nMfl, Volfl, Lnfl, Wnfl, Tnfl, nVolfl
+  real :: Lfl, Wfl, Tfl, Mfl, Afl, Me_fl, Mv_fl, Mb_fl, dMfl, nMfl, Volfl, Lnfl, Wnfl, Tnfl, nVolfl
 
   ! For convenience
   grd=>bergs%grd
@@ -2773,6 +2773,12 @@ subroutine thermodynamics(bergs)
       Me=max( 1./12.*(SST+2.)*Ss*(1+cos(pi*(IC**3))) ,0.) &! Wave erosion
           *perday ! convert to m/s
 
+      !same these values Mv and Me separately for footloose bits,
+      !in case Mv and Me change later due to number of bonds:
+      if (this%mass_of_fl_bits>0.) then
+        Mv_fl=Mv; Me_fl=Me !Note: Mb_fl is calculated below
+      endif
+
         if (bergs%use_mixed_melting .or. bergs%allow_bergs_to_roll) then
           N_bonds=0.
           if (bergs%iceberg_bonds_on) then
@@ -2850,7 +2856,7 @@ subroutine thermodynamics(bergs)
       endif
 
       ! Footloose bits (FL bits). For now, FL bits do not erode into bergy bits.
-      if (bergs%fl_style.eq.'fl_bits') then
+      if (this%mass_of_fl_bits>0.) then
 
         call fl_bits_dimensions(bergs,this,Lfl,Wfl,Tfl)
         Mfl=this%mass_of_fl_bits
@@ -2864,8 +2870,8 @@ subroutine thermodynamics(bergs)
         else
           Volfl=Lfl*Wfl*Tfl
           Mb_fl=max( 0.58*(dvo**0.8)*(SST+4.0)/(Lfl**0.2), 0.) *perday  ! FL bits basal turbulent melting
-          Lnfl=max(Lfl-(Mv+Me)*bergs%dt,0.) ! (m)
-          Wnfl=max(Wfl-(Mv+Me)*bergs%dt,0.) ! (m)
+          Lnfl=max(Lfl-(Mv_fl+Me_fl)*bergs%dt,0.) ! (m)
+          Wnfl=max(Wfl-(Mv_fl+Me_fl)*bergs%dt,0.) ! (m)
           Tnfl=max(Tfl-  Mb_fl*bergs%dt,0.) ! (m)
           ! Update volume and mass of footloose berg
           nVolfl=Tnfl*Wnfl*Lnfl ! (m^3)
@@ -2952,7 +2958,7 @@ subroutine thermodynamics(bergs)
         !before reseting
         if (bergs%find_melt_using_spread_mass) then
           if (Mnew>0.) then !If the berg still exists
-            call spread_mass_across_ocean_cells(bergs,this, i, j, this%xi, this%yj,Mnew , nMbits+nMfl, this%mass_scaling, Ln*Wn,  Tn)
+            call spread_mass_across_ocean_cells(bergs,this, i, j, this%xi, this%yj,Mnew , nMbits+nMfl, this%mass_scaling, Ln*Wn+nMfl/(Tn*bergs%rho_bergs),  Tn)
           endif
         endif
         !Reset all the values
@@ -3062,7 +3068,7 @@ subroutine fl_bits_dimensions(bergs,this,L_fl,W_fl,T_fl)
   ! Local variables
   real,parameter :: l_c=pi/(2.*sqrt(2.)), lw_c = 1./(gravity*rho_seawater)
   real,parameter :: B_c=1.e8/(12.*(1.-0.3**2.)) !youngs=1.e8, poisson=0.3
-  real :: l_w,l_b
+  real :: l_w,l_b,L_fl_temp
 
   if (bergs%fl_melt_as_bergy_bits) then
     L_fl=min(this%length,this%width,this%thickness,40.)
@@ -3072,8 +3078,9 @@ subroutine fl_bits_dimensions(bergs,this,L_fl,W_fl,T_fl)
     l_b  = l_c*l_w !length of a freshly calved footloose child berg
     L_fl = 3.*l_b; W_fl=l_b; T_fl=this%thickness
     call rolling(bergs,T_fl,W_fl,L_fl)
-    L_fl = bergs%fl_bits_scale_l*L_fl
-    W_fl = bergs%fl_bits_scale_w*W_fl
+    L_fl_temp = bergs%fl_bits_scale_l*max(L_fl,W_fl)
+    W_fl = bergs%fl_bits_scale_w*min(W_fl,L_fl)
+    L_fl = max(L_fl_temp,W_fl); W_fl=min(L_fl_temp,W_fl)
     T_fl = bergs%fl_bits_scale_t*T_fl
   endif
 end subroutine fl_bits_dimensions
@@ -4624,7 +4631,7 @@ subroutine calculate_mass_on_ocean(bergs, with_diagnostics)
           !Increasing Mass on ocean
           if ((bergs%add_weight_to_ocean .and. .not. bergs%time_average_weight) .or.(bergs%find_melt_using_spread_mass)) then
             call spread_mass_across_ocean_cells(bergs, berg, berg%ine, berg%jne, berg%xi, berg%yj, berg%mass,berg%mass_of_bits+berg%mass_of_fl_bits, berg%mass_scaling, &
-              berg%length*berg%width, berg%thickness)
+              berg%length*berg%width+berg%mass_of_fl_bits/(berg%thickness*bergs%rho_bergs), berg%thickness)
           endif
 
           !Calculated some iceberg diagnositcs
@@ -6855,7 +6862,7 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln, rx, ry)
   ! Note, the mass scaling is equal to 1 (rather than 0.25 as in RK), since
   ! this is only called once in Verlet stepping.
   if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits+berg%mass_of_fl_bits, 1.0*berg%mass_scaling,berg%length*berg%width, berg%thickness)
+    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits+berg%mass_of_fl_bits, 1.0*berg%mass_scaling,berg%length*berg%width+berg%mass_of_fl_bits/(berg%thickness*bergs%rho_bergs), berg%thickness)
 
   ! Calling the acceleration   (note that the velocity is converted to u_star inside the accel script)
   call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, ax1, ay1, axn, ayn, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
@@ -6985,7 +6992,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
   if ((berg%lat>89.) .and. (bergs%grd%grid_is_latlon)) on_tangential_plane=.true.
   i1=i;j1=j
   if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits+berg%mass_of_fl_bits, 0.25*berg%mass_scaling,berg%length*berg%width, berg%thickness)
+    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits+berg%mass_of_fl_bits, 0.25*berg%mass_scaling,berg%length*berg%width+berg%mass_of_fl_bits/(berg%thickness*bergs%rho_bergs), berg%thickness)
 
   ! Loading past accelerations - Alon
   axn=berg%axn; ayn=berg%ayn !Alon
@@ -7023,7 +7030,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
   call adjust_index_and_ground(grd, lon2, lat2, uvel2, vvel2, i, j, xi, yj, bounced, error_flag, berg%id)
   i2=i; j2=j
   if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits+berg%mass_of_fl_bits, 0.25*berg%mass_scaling,berg%length*berg%width, berg%thickness)
+    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits+berg%mass_of_fl_bits, 0.25*berg%mass_scaling,berg%length*berg%width+berg%mass_of_fl_bits/(berg%thickness*bergs%rho_bergs), berg%thickness)
   ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon2,lat2,x2,y2)
   if (.not.error_flag) then
     if (debug .and. .not. is_point_in_cell(bergs%grd, lon2, lat2, i, j)) error_flag=.true.
@@ -7080,7 +7087,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
   call adjust_index_and_ground(grd, lon3, lat3, uvel3, vvel3, i, j, xi, yj, bounced, error_flag, berg%id)
   i3=i; j3=j
   if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits+berg%mass_of_fl_bits, 0.25*berg%mass_scaling,berg%length*berg%width, berg%thickness)
+    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits+berg%mass_of_fl_bits, 0.25*berg%mass_scaling,berg%length*berg%width+berg%mass_of_fl_bits/(berg%thickness*bergs%rho_bergs), berg%thickness)
   ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon3,lat3,x3,y3)
   if (.not.error_flag) then
     if (debug .and. .not. is_point_in_cell(bergs%grd, lon3, lat3, i, j)) error_flag=.true.
@@ -7210,7 +7217,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
   i=i1;j=j1;xi=berg%xi;yj=berg%yj
   call adjust_index_and_ground(grd, lonn, latn, uveln, vveln, i, j, xi, yj, bounced, error_flag, berg%id)
   if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits+berg%mass_of_fl_bits, 0.25*berg%mass_scaling,berg%length*berg%width, berg%thickness)
+    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits+berg%mass_of_fl_bits, 0.25*berg%mass_scaling,berg%length*berg%width+berg%mass_of_fl_bits/(berg%thickness*bergs%rho_bergs), berg%thickness)
 
   if (.not.error_flag) then
     if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j)) error_flag=.true.

From cf1ce3309ae1043559851add75b537e265e09d45 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Mon, 19 Apr 2021 16:42:14 -0400
Subject: [PATCH 295/361] The mass associated with erosion of FL bits can now
 be added to bergy bits, rather than melting immediately. Rewrote
 initialization/calving of new bergs so that values of parameters (initial
 dimensions, distribution, mass scaling, etc) can be specified separately each
 hemisphere.

---
 src/icebergs.F90           | 133 +++++++++++++++++++++++++------------
 src/icebergs_framework.F90 |  73 +++++++++++++++-----
 src/icebergs_io.F90        |  23 +++++--
 3 files changed, 163 insertions(+), 66 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 64c487d..d3295cd 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -2721,7 +2721,8 @@ subroutine thermodynamics(bergs)
   integer :: grdi, grdj
   real :: SSS !Temporarily here
   ! Footloose bits stuff
-  real :: Lfl, Wfl, Tfl, Mfl, Afl, Me_fl, Mv_fl, Mb_fl, dMfl, nMfl, Volfl, Lnfl, Wnfl, Tnfl, nVolfl
+  real :: Lfl, Wfl, Tfl, Mfl, Afl, Me_fl, Mv_fl, Mb_fl, dMfl, nMfl
+  real :: Volfl, Lnfl, Wnfl, Tnfl, nVolfl, nMfl2, dMe_fl
 
   ! For convenience
   grd=>bergs%grd
@@ -2865,32 +2866,50 @@ subroutine thermodynamics(bergs)
           Afl=(Mfl/bergs%rho_bergs)/Lfl
           Mb_fl=max( 0.58*(dvo**0.8)*(SST+2.0)/(Lfl**0.2), 0.) *perday ! FL bits basal turbulent melting
           Mb_fl=bergs%rho_bergs*Afl*Mb_fl ! in kg/s
-          dMfl=min(Mb_fl*bergs%dt,Mfl) ! bergy bits mass lost to melting (kg)
-          nMfl=Mfl-dMfl ! remove mass lost to bergy bits melt
+          dMfl=min(Mb_fl*bergs%dt,Mfl) ! FL bergy bits mass lost to melting (kg)
+          nMfl=Mfl-dMfl ! remove mass lost to FL bergy bits melt
+          dMe_fl=0.
         else
           Volfl=Lfl*Wfl*Tfl
-          Mb_fl=max( 0.58*(dvo**0.8)*(SST+4.0)/(Lfl**0.2), 0.) *perday  ! FL bits basal turbulent melting
-          Lnfl=max(Lfl-(Mv_fl+Me_fl)*bergs%dt,0.) ! (m)
-          Wnfl=max(Wfl-(Mv_fl+Me_fl)*bergs%dt,0.) ! (m)
-          Tnfl=max(Tfl-  Mb_fl*bergs%dt,0.) ! (m)
-          ! Update volume and mass of footloose berg
-          nVolfl=Tnfl*Wnfl*Lnfl ! (m^3)
-          nMfl=(nVolfl/Volfl)*Mfl ! (kg)
-          dMfl=Mfl-nMfl ! total footloose mass lost
+          !basal turbulent melting
+          Mb_fl=max( 0.58*(dvo**0.8)*(SST+4.0)/(Lfl**0.2), 0.) *perday
+          Tnfl=max(Tfl-  Mb_fl*bergs%dt,0.) ! new FL thickness (m)
+          nVolfl=Tnfl*Wnfl*Lnfl ! new footloose volume (m^
+          if (bergs%use_operator_splitting) then
+            !buoyant convection
+            Lnfl=max(Lfl-Mv_fl*bergs%dt,0.) ! new FL length (m)
+            Wnfl=max(Wfl-Mv_fl*bergs%dt,0.) ! new FL width (m)
+            nVolfl=Tnfl*Wnfl*Lnfl ! new footloose volume (m^3)
+            nMfl2=(nVolfl/Volfl)*Mfl !new FL mass (kg), after buoyant convection
+            !erosion
+            Lnfl=max(Lfl-Me_fl*bergs%dt,0.) ! new FL length (m)
+            Wnfl=max(Wfl-Me_fl*bergs%dt,0.) ! new FL width (m)
+            nVolfl=Tnfl*Wnfl*Lnfl ! new footloose volume (m^3)
+            nMfl=(nVolfl/Volfl)*Mfl !new FL mass (kg), after all melt and erosion
+            dMe_fl=nMfl2-nMfl !FL mass lost to erosion (>0) (kg)
+          else
+            Lnfl=max(Lfl-(Mv_fl+Me_fl)*bergs%dt,0.) ! (m)
+            Wnfl=max(Wfl-(Mv_fl+Me_fl)*bergs%dt,0.) ! (m)
+            nVolfl=Tnfl*Wnfl*Lnfl ! new footloose volume (m^3)
+            nMfl=(nVolfl/Volfl)*Mfl ! new footloose mass (kg)
+            dMe_fl=(Mfl/Volfl)*(Tfl*(Wfl+Lfl))*Me_fl*bergs%dt !approx. FL mass loss to erosion
+          endif
+          dMfl=Mfl-nMfl ! total footloose mass lost to all erosion and melting (>0) (kg)
+          if (.not. bergs%fl_bits_erosion_to_bergy_bits) dMe_fl=0.
         endif
         if (Mnew==0.) then ! if parent berg has completely melted then
-          dMfl= Mfl ! instantly melt all the bergy bits
+          dMfl= Mfl ! instantly melt all the footloose bergy bits
           nMfl=0.
         endif
       else
-        dMfl=0.
+        dMfl=0.; dMe_fl=0.
         nMfl=this%mass_of_fl_bits ! retain previous value incase non-zero
       endif
 
       ! Bergy bits
       if (bergs%bergy_bit_erosion_fraction>0.) then
         Mbits=this%mass_of_bits ! mass of bergy bits (kg)
-        dMbitsE=bergs%bergy_bit_erosion_fraction*dMe ! change in mass of bits (kg)
+        dMbitsE=bergs%bergy_bit_erosion_fraction*(dMe+dMe_fl) ! change in mass of bits (kg)
         nMbits=Mbits+dMbitsE ! add new bergy bits to mass (kg)
         Lbits=min(L,W,T,40.) ! assume bergy bits are smallest dimension or 40 meters
         Abits=(Mbits/bergs%rho_bergs)/Lbits ! Effective bottom area (assuming T=Lbits)
@@ -5337,7 +5356,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     call mpp_sum(bergs%returned_mass_on_ocean)
     call mpp_sum(bergs%nbergs_end)
     call mpp_sum(bergs%nbergs_calved)
-    do k=1,nclasses; call mpp_sum(bergs%nbergs_calved_by_class(k)); enddo
+    do k=1,nclasses; call mpp_sum(bergs%nbergs_calved_by_class_s(k)); enddo
+    do k=1,nclasses; call mpp_sum(bergs%nbergs_calved_by_class_n(k)); enddo
     call mpp_sum(bergs%nbergs_melted)
     call mpp_sum(bergs%nspeeding_tickets)
     call mpp_sum(bergs%net_calving_returned)
@@ -5425,14 +5445,16 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
              & bergs%net_calving_received)
         call report_consistant('bot interface','kg','sent',bergs%net_outgoing_calving,'seen by SIS',bergs%net_calving_returned)
       endif
-      write(*,'("KID: calved by class = ",i4,20(",",i4))') (bergs%nbergs_calved_by_class(k),k=1,nclasses)
+      write(*,'("KID: calved by class S. hemisphere = ",i4,20(",",i4))') (bergs%nbergs_calved_by_class_s(k),k=1,nclasses)
+      write(*,'("KID: calved by class N. hemisphere = ",i4,20(",",i4))') (bergs%nbergs_calved_by_class_n(k),k=1,nclasses)
       if (bergs%nspeeding_tickets>0) write(*,'("KID: speeding tickets issued = ",i4)') bergs%nspeeding_tickets
     endif
     bergs%nbergs_start=bergs%nbergs_end
     bergs%stored_start=bergs%stored_end
     bergs%nbergs_melted=0
     bergs%nbergs_calved=0
-    bergs%nbergs_calved_by_class(:)=0
+    bergs%nbergs_calved_by_class_s(:)=0
+    bergs%nbergs_calved_by_class_n(:)=0
     bergs%nspeeding_tickets=0
     bergs%stored_heat_start=bergs%stored_heat_end
     bergs%floating_heat_start=bergs%floating_heat_end
@@ -5741,7 +5763,7 @@ subroutine accumulate_calving(bergs)
   type(icebergs), pointer :: bergs !< Container for all types and memory
   ! Local variables
   type(icebergs_gridded), pointer :: grd
-  real :: remaining_dist, net_calving_used
+  real :: remaining_dist_s, remaining_dist_n, net_calving_used
   integer :: k, i, j
   logical, save :: first_call=.true.
   integer :: stderrunit
@@ -5774,25 +5796,35 @@ subroutine accumulate_calving(bergs)
         'KID, accumulate_calving: initial stored heat=',bergs%stored_heat_start,' J'
    endif
 
-  remaining_dist=1.
+  remaining_dist_s=1.; remaining_dist_n=1.
   do k=1, nclasses
-    grd%stored_ice(:,:,k)=grd%stored_ice(:,:,k)+bergs%dt*grd%calving(:,:)*bergs%distribution(k)
-    remaining_dist=remaining_dist-bergs%distribution(k)
+    where (grd%lon<0.)
+      grd%stored_ice(:,:,k)=grd%stored_ice(:,:,k)+bergs%dt*grd%calving(:,:)*bergs%distribution_s(k)
+    elsewhere
+      grd%stored_ice(:,:,k)=grd%stored_ice(:,:,k)+bergs%dt*grd%calving(:,:)*bergs%distribution_n(k)
+    end where
+    remaining_dist_s=remaining_dist_s-bergs%distribution_s(k)
+    remaining_dist_n=remaining_dist_n-bergs%distribution_n(k)
   enddo
-  if (remaining_dist.lt.0.) then
-    write(stderrunit,*) 'KID, accumulate_calving: sum(distribution)>1!!!',remaining_dist
+  if (remaining_dist_s.lt.0. .or. remaining_dist_n.lt.0.) then
+    write(stderrunit,*) 'KID, accumulate_calving: sum(distribution)>1!!!',remaining_dist_s, remaining_dist_n
     call error_mesg('KID, accumulate_calving', 'calving is OVER distributed!', WARNING)
   endif
-  net_calving_used=sum( grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec) )*(1.-remaining_dist)
+  where (grd%lon<0.)
+    grd%tmp=remaining_dist_s
+  elsewhere
+    grd%tmp=remaining_dist_n
+  end where
+  net_calving_used=sum( grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec) *(1.-grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec)))
   bergs%net_calving_used=bergs%net_calving_used+net_calving_used*bergs%dt
   ! Remove the calving accounted for by accumulation
-  grd%calving(:,:)=grd%calving(:,:)*remaining_dist
+  grd%calving(:,:)=grd%calving(:,:)*grd%tmp(:,:)
 
   ! Do the same for heat (no separate classes needed)
-  grd%tmp(:,:)=bergs%dt*grd%calving_hflx(:,:)*grd%area(:,:)*(1.-remaining_dist)
+  grd%calving_hflx(:,:)=grd%calving_hflx(:,:)*grd%tmp(:,:)
+  grd%tmp(:,:)=bergs%dt*grd%calving_hflx(:,:)*grd%area(:,:)*(1.-grd%tmp(:,:))
   bergs%net_incoming_calving_heat_used=bergs%net_incoming_calving_heat_used+sum( grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec) )
   grd%stored_heat(:,:)=grd%stored_heat(:,:)+grd%tmp(:,:) ! +=bergs%dt*grd%calving_hflx(:,:)*grd%area(:,:)*(1.-remaining_dist)
-  grd%calving_hflx(:,:)=grd%calving_hflx(:,:)*remaining_dist
 
 end subroutine accumulate_calving
 
@@ -5808,6 +5840,7 @@ subroutine calve_icebergs(bergs)
   logical :: lret
   real :: xi, yj, ddt, calving_to_bergs, calved_to_berg, heat_to_bergs, heat_to_berg
   integer :: stderrunit
+  real, pointer :: initial_mass, mass_scaling, initial_thickness, initial_width, initial_length
 
   ! Get the stderr unit number
   stderrunit = stderr()
@@ -5827,7 +5860,16 @@ subroutine calve_icebergs(bergs)
     do j=grd%jsc, grd%jec
       do i=grd%isc, grd%iec
         ddt=0.; icnt=0
-        do while (grd%stored_ice(i,j,k).ge.bergs%initial_mass(k)*bergs%mass_scaling(k))
+        if (grd%lon(i,j)<0.) then
+          initial_mass=>bergs%initial_mass_s(k); mass_scaling=>bergs%mass_scaling_s(k)
+          initial_thickness=>bergs%initial_thickness_s(k)
+          initial_width=>bergs%initial_width_s(k); initial_length=>bergs%initial_length_s(k)
+        else
+          initial_mass=>bergs%initial_mass_n(k); mass_scaling=>bergs%mass_scaling_n(k)
+          initial_thickness=>bergs%initial_thickness_n(k)
+          initial_width=>bergs%initial_width_n(k); initial_length=>bergs%initial_length_n(k)
+        endif
+        do while (grd%stored_ice(i,j,k).ge.initial_mass*mass_scaling)
           newberg%lon=0.25*((grd%lon(i,j)+grd%lon(i-1,j-1))+(grd%lon(i-1,j)+grd%lon(i,j-1)))
           newberg%lat=0.25*((grd%lat(i,j)+grd%lat(i-1,j-1))+(grd%lat(i-1,j)+grd%lat(i,j-1)))
          !write(stderr(),*) 'KID, calve_icebergs: creating new iceberg at ',newberg%lon,newberg%lat
@@ -5866,17 +5908,17 @@ subroutine calve_icebergs(bergs)
           newberg%bxn=0.
           newberg%byn=0.
           !---
-          newberg%mass=bergs%initial_mass(k)
-          newberg%thickness=bergs%initial_thickness(k)
-          newberg%width=bergs%initial_width(k)
-          newberg%length=bergs%initial_length(k)
+          newberg%mass=initial_mass
+          newberg%thickness=initial_thickness
+          newberg%width=initial_width
+          newberg%length=initial_length
           newberg%start_lon=newberg%lon
           newberg%start_lat=newberg%lat
           newberg%start_year=bergs%current_year
           newberg%id = generate_id(grd, i, j)
           newberg%start_day=bergs%current_yearday+ddt/86400.
-          newberg%start_mass=bergs%initial_mass(k)
-          newberg%mass_scaling=bergs%mass_scaling(k)
+          newberg%start_mass=initial_mass
+          newberg%mass_scaling=mass_scaling
           newberg%mass_of_bits=0.
           newberg%mass_of_fl_bits=0.
           newberg%halo_berg=0.
@@ -5912,7 +5954,7 @@ subroutine calve_icebergs(bergs)
           endif
 
           call add_new_berg_to_list(bergs%list(i,j)%first, newberg)
-          calved_to_berg=bergs%initial_mass(k)*bergs%mass_scaling(k) ! Units of kg
+          calved_to_berg=initial_mass*mass_scaling ! Units of kg
           ! Heat content
           heat_to_berg=calved_to_berg*newberg%heat_density ! Units of J
           grd%stored_heat(i,j)=grd%stored_heat(i,j)-heat_to_berg
@@ -5924,7 +5966,11 @@ subroutine calve_icebergs(bergs)
           ddt=ddt-bergs%dt*2./17. ! Minor offset to start day (negative offsets)
           icnt=icnt+1
           bergs%nbergs_calved=bergs%nbergs_calved+1
-          bergs%nbergs_calved_by_class(k)=bergs%nbergs_calved_by_class(k)+1
+          if (grd%lon(i,j)<0.) then
+            bergs%nbergs_calved_by_class_s(k)=bergs%nbergs_calved_by_class_s(k)+1
+          else
+            bergs%nbergs_calved_by_class_n(k)=bergs%nbergs_calved_by_class_n(k)+1
+          endif
         enddo
         icntmax=max(icntmax,icnt)
       enddo
@@ -7822,11 +7868,16 @@ subroutine icebergs_end(bergs)
   deallocate(bergs%grd%hi)
   deallocate(bergs%grd%domain)
   deallocate(bergs%grd)
-  deallocate(bergs%initial_mass)
-  deallocate(bergs%distribution)
-  deallocate(bergs%initial_thickness)
-  deallocate(bergs%initial_width)
-  deallocate(bergs%initial_length)
+  deallocate(bergs%initial_mass_s)
+  deallocate(bergs%distribution_s)
+  deallocate(bergs%initial_thickness_s)
+  deallocate(bergs%initial_width_s)
+  deallocate(bergs%initial_length_s)
+  deallocate(bergs%initial_mass_n)
+  deallocate(bergs%distribution_n)
+  deallocate(bergs%initial_thickness_n)
+  deallocate(bergs%initial_width_n)
+  deallocate(bergs%initial_length_n)
   call dealloc_buffer(bergs%obuffer_n)
   call dealloc_buffer(bergs%obuffer_s)
   call dealloc_buffer(bergs%obuffer_e)
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 55a6003..8088627 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -485,8 +485,11 @@ module ice_bergs_framework
   real :: Gamma_T_3EQ=0.022 !< Non-dimensional heat-transfer coefficient
   real :: melt_cutoff=-1.0 !< Minimum ocean thickness for melting to occur (is not applied for values < 0)
   logical :: const_gamma=.True. !< If true uses a constant heat transfer coefficient, from which the salt transfer is calculated
-  real, dimension(:), pointer :: initial_mass, distribution, mass_scaling
-  real, dimension(:), pointer :: initial_thickness, initial_width, initial_length
+  real, dimension(:), pointer :: initial_mass_s, distribution_s, mass_scaling_s !< Southern hemisphere
+  real, dimension(:), pointer :: initial_thickness_s, initial_width_s, initial_length_s !< Southern hemisphere
+  logical :: separate_distrib_for_n_hemisphere=.False. ! Flag to use a separate berg distribution/mass/mass scaling/init thickness for N hemisphere
+  real, dimension(:), pointer :: initial_mass_n, distribution_n, mass_scaling_n !< Northern hemisphere
+  real, dimension(:), pointer :: initial_thickness_n, initial_width_n, initial_length_n !< Northern hemisphere
   logical :: restarted=.false. !< Indicate whether we read state from a restart or not
   logical :: use_operator_splitting=.true. !< Use first order operator splitting for thermodynamics
   logical :: add_weight_to_ocean=.true. !< Add weight of bergs to ocean
@@ -574,7 +577,8 @@ module ice_bergs_framework
   integer :: nbergs_calved=0, nbergs_melted=0, nbergs_start=0, nbergs_end=0
   integer :: nspeeding_tickets=0
   integer :: nbonds=0
-  integer, dimension(:), pointer :: nbergs_calved_by_class=>null()
+  integer, dimension(:), pointer :: nbergs_calved_by_class_s=>null()
+  integer, dimension(:), pointer :: nbergs_calved_by_class_n=>null()
   ! mts parameters - added by Alex
   logical :: mts=.false. !< Use multiple timestepping scheme (substep size is automatically determined)
   integer :: mts_sub_steps
@@ -609,6 +613,7 @@ module ice_bergs_framework
   logical :: displace_fl_bergs=.true. !< footloose berg positions are randomly assigned along edges of parent berg
   character(len=11) :: fl_style='new_bergs' !< Evolve footloose bergs individually as 'new_bergs', or as a group with size 'fl_bits'
   logical :: fl_melt_as_bergy_bits=.false. !< Melt footloose bits as bergy_bits
+  logical :: fl_bits_erosion_to_bergy_bits=.true. !< Erosion from footloose bits becomes bergy bits
   real :: fl_bits_scale_l=0.8  !< For determining dimensions of FL bits berg; FL_bits length = fl_bits_scale_l*3*l_b
   real :: fl_bits_scale_w=0.45 !< For determining dimensions of FL bits berg; FL_bits width = fl_bits_scale_l*3*l_b
   real :: fl_bits_scale_t=0.65 !< For determining dimensions of FL bits berg; FL_bits thickness = fl_bits_scale_l*T
@@ -775,10 +780,17 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: force_convergence=.false. ! Experimental MTS convergence scheme that better preserves momentum during collisions
 logical :: explicit_inner_mts=.false. !If T, inner MTS iterations are treated explicitly
 real :: convergence_tolerance=1.e-8 ! Tolerance for the MTS force_convergence scheme
+! Initial mass, distribution, scaling, thickness at calving. Default is gladstone et al 2001 for Southern hemisphere:
 real, dimension(nclasses) :: initial_mass=(/8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11/) ! Mass thresholds between iceberg classes (kg)
 real, dimension(nclasses) :: distribution=(/0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02/) ! Fraction of calving to apply to this class (non-dim) ,
 real, dimension(nclasses) :: mass_scaling=(/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) ! Ratio between effective and real iceberg mass (non-dim)
 real, dimension(nclasses) :: initial_thickness=(/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) ! Total thickness of newly calved bergs (m)
+!Default is Bigg et al 1997 for Northern hemisphere:
+logical :: separate_distrib_for_n_hemisphere=.False. ! Flag to use a separate berg distribution/mass/mass scaling/init thickness for N hemisphere
+real, dimension(nclasses) :: initial_mass_n=(/4.58e8, 3.61e9, 1.22e10, 2.91e10, 5.09e10, 7.34e10, 1.15e11, 1.65e11, 2.94e11, 5.59e11/) !for N hemisphere
+real, dimension(nclasses) :: distribution_n=(/0.14, 0.15, 0.20, 0.15, 0.08, 0.07, 0.05, 0.05, 0.05, 0.05/) ! for N hemisphere
+real, dimension(nclasses) :: mass_scaling_n=(/200, 50, 25, 13, 8, 5, 2, 1, 1, 1/) ! for N hemisphere
+real, dimension(nclasses) :: initial_thickness_n=(/80, 159.5, 240, 320, 360, 360, 360, 360, 360/) ! for N hemisphere
 integer(kind=8) :: debug_iceberg_with_id = -1 ! If positive, monitors a berg with this id
 ! DEM-mode parameters
 !logical :: dem=.false. !if T, run in DEM-mode with angular terms, variable stiffness, etc
@@ -799,8 +811,9 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: displace_fl_bergs=.true. !< footloose berg positions are randomly assigned along edges of parent berg
 character(len=11) :: fl_style='new_bergs' !< Evolve footloose bergs individually as 'fl_bits', or as a group with size 'bergy_bits' or 'mean_size'
 logical :: fl_melt_as_bergy_bits=.false. !< Melt footloose bits as bergy_bits
+logical :: fl_bits_erosion_to_bergy_bits=.true. !< Erosion from footloose bits becomes bergy bits
 real :: fl_bits_scale_l=0.8 !< For determining dimensions of FL bits berg; FL_bits length = fl_bits_scale_l*3*l_b
-real :: fl_bits_scale_w=0.45 !< For determining dimensions of FL bits berg; FL_bits width = fl_bits_scale_l*3*l_b
+real :: fl_bits_scale_w=0.45 !< For determining dimensions of FL bits berg; FL_bits width = fl_bits_scale_l*l_b
 real :: fl_bits_scale_t=0.65 !< For determining dimensions of FL bits berg; FL_bits thickness = fl_bits_scale_l*T
 
 namelist /icebergs_nml/ verbose, budget, halo,  traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,Static_icebergs,  &
@@ -819,7 +832,8 @@ subroutine ice_bergs_framework_init(bergs, &
          fracture_criterion, damage_test_1, uniaxial_test, debug_write,cdrag_grounding,h_to_init_grounding,frac_thres_scaling,frac_thres_n,frac_thres_t,save_bond_traj,remove_unused_bergs,&
          force_convergence,explicit_inner_mts,convergence_tolerance,&
          dem,ignore_tangential_force,poisson,dem_spring_coef,dem_damping_coef,dem_beam_test,constant_interaction_LW,constant_length,constant_width,dem_shear_for_frac_only,use_damage, fl_use_poisson_distribution, fl_r, fl_r_s, displace_fl_bergs,fl_style,&
-         fl_melt_as_bergy_bits,fl_bits_scale_l,fl_bits_scale_w,fl_bits_scale_t
+         fl_melt_as_bergy_bits,fl_bits_erosion_to_bergy_bits,fl_bits_scale_l,fl_bits_scale_w,fl_bits_scale_t,&
+         separate_distrib_for_n_hemisphere, initial_mass_n, distribution_n, mass_scaling_n, initial_thickness_n
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -827,7 +841,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: lon_mod, big_number
 logical :: lerr
 integer :: stdlogunit, stderrunit
-real :: Total_mass  !Added by Alon
+real :: Total_mass_s, Total_mass_n
 real :: mts_fast_dt=0.0 !Added by Alex
 real :: maxlon_c,minlon_c !Added by Alex, for mts verlet periodicity
 integer :: k,maxk
@@ -970,7 +984,8 @@ subroutine ice_bergs_framework_init(bergs, &
   allocate( grd%hi(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%hi(:,:)=0.
   allocate( grd%tmp(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%tmp(:,:)=0.
   allocate( grd%tmpc(grd%isc:grd%iec, grd%jsc:grd%jec) ); grd%tmpc(:,:)=0.
-  allocate( bergs%nbergs_calved_by_class(nclasses) ); bergs%nbergs_calved_by_class(:)=0
+  allocate( bergs%nbergs_calved_by_class_s(nclasses) ); bergs%nbergs_calved_by_class_s(:)=0
+  allocate( bergs%nbergs_calved_by_class_n(nclasses) ); bergs%nbergs_calved_by_class_n(:)=0
   allocate( grd%parity_x(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%parity_x(:,:)=1.
   allocate( grd%parity_y(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%parity_y(:,:)=1.
   allocate( grd%iceberg_counter_grd(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%iceberg_counter_grd(:,:)=0
@@ -1163,14 +1178,24 @@ subroutine ice_bergs_framework_init(bergs, &
   enddo; enddo
 
 
+  ! If a separate calving distribution for the northern hemisphere is not used, the following northern
+  ! hemisphere parameters inherit the values of their respective southern hemisphere parameters
+  if (.not. bergs%separate_distrib_for_n_hemisphere) then
+    initial_mass_n=initial_mass; distribution_n=distribution
+    mass_scaling_n=mass_scaling; initial_thickness_n=initial_thickness
+  endif
+
+
 !Added by Alon  - If a freq distribution is input, we have to convert the freq distribution to a mass flux distribution)
 if (input_freq_distribution) then
-     Total_mass=0.
+     Total_mass_s=0.; Total_mass_n=0.
      do j=1,nclasses
-          Total_mass=Total_mass+(distribution(j)*initial_mass(j))
+          Total_mass_s=Total_mass_s+(distribution(j)*initial_mass(j))
+          Total_mass_n=Total_mass_n+(distribution_n(j)*initial_mass_n(j))
      enddo
      do j=1,nclasses
-           distribution(j)=(distribution(j)*initial_mass(j))/Total_mass
+           distribution(j)=(distribution(j)*initial_mass(j))/Total_mass_s
+           distribution_n(j)=(distribution_n(j)*initial_mass_n(j))/Total_mass_n
      enddo
 endif
 
@@ -1301,6 +1326,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%radial_damping_coef=radial_damping_coef
   bergs%tangental_damping_coef=tangental_damping_coef
   bergs%LoW_ratio=LoW_ratio
+  bergs%separate_distrib_for_n_hemisphere=separate_distrib_for_n_hemisphere
   bergs%use_operator_splitting=use_operator_splitting
   bergs%bergy_bit_erosion_fraction=bergy_bit_erosion_fraction
   bergs%sicn_shift=sicn_shift
@@ -1385,6 +1411,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%displace_fl_bergs=displace_fl_bergs
   bergs%fl_style=fl_style
   bergs%fl_melt_as_bergy_bits=fl_melt_as_bergy_bits
+  bergs%fl_bits_erosion_to_bergy_bits=fl_bits_erosion_to_bergy_bits
   if (fl_style.ne.'new_bergs') then
     displace_fl_bergs=.false.
     bergs%fl_melt_as_bergy_bits=.false.
@@ -1448,14 +1475,24 @@ subroutine ice_bergs_framework_init(bergs, &
       endif
     endif
   endif
-  allocate( bergs%initial_mass(nclasses) ); bergs%initial_mass(:)=initial_mass(:)
-  allocate( bergs%distribution(nclasses) ); bergs%distribution(:)=distribution(:)
-  allocate( bergs%mass_scaling(nclasses) ); bergs%mass_scaling(:)=mass_scaling(:)
-  allocate( bergs%initial_thickness(nclasses) ); bergs%initial_thickness(:)=initial_thickness(:)
-  allocate( bergs%initial_width(nclasses) )
-  allocate( bergs%initial_length(nclasses) )
-  bergs%initial_width(:)=sqrt(initial_mass(:)/(LoW_ratio*rho_bergs*initial_thickness(:)))
-  bergs%initial_length(:)=LoW_ratio*bergs%initial_width(:)
+  allocate( bergs%initial_mass_s(nclasses) ); bergs%initial_mass_s(:)=initial_mass(:)
+  allocate( bergs%distribution_s(nclasses) ); bergs%distribution_s(:)=distribution(:)
+  allocate( bergs%mass_scaling_s(nclasses) ); bergs%mass_scaling_s(:)=mass_scaling(:)
+  allocate( bergs%initial_thickness_s(nclasses) ); bergs%initial_thickness_s(:)=initial_thickness(:)
+  allocate( bergs%initial_width_s(nclasses) )
+  allocate( bergs%initial_length_s(nclasses) )
+  bergs%initial_width_s(:)=sqrt(initial_mass(:)/(LoW_ratio*rho_bergs*initial_thickness(:)))
+  bergs%initial_length_s(:)=LoW_ratio*bergs%initial_width_s(:)
+
+  allocate( bergs%initial_mass_n(nclasses) ); bergs%initial_mass_n(:)=initial_mass_n(:)
+  allocate( bergs%distribution_n(nclasses) ); bergs%distribution_n(:)=distribution_n(:)
+  allocate( bergs%mass_scaling_n(nclasses) ); bergs%mass_scaling_n(:)=mass_scaling_n(:)
+  allocate( bergs%initial_thickness_n(nclasses) ); bergs%initial_thickness_n(:)=initial_thickness_n(:)
+  allocate( bergs%initial_width_n(nclasses) )
+  allocate( bergs%initial_length_n(nclasses) )
+  bergs%initial_width_n(:)=sqrt(initial_mass_n(:)/(LoW_ratio*rho_bergs*initial_thickness_n(:)))
+  bergs%initial_length_n(:)=LoW_ratio*bergs%initial_width_n(:)
+
   bergs%writeandstop=.false.
   grd%coastal_drift = coastal_drift
   grd%tidal_drift = tidal_drift
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index ba1fc28..1d4ca3d 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -1110,17 +1110,17 @@ subroutine generate_bergs(bergs,Time)
       localberg%lat=grd%latc(i,j)
       localberg%lon_old=localberg%lon
       localberg%lat_old=localberg%lat
-      localberg%mass=bergs%initial_mass(1)
-      localberg%thickness=bergs%initial_thickness(1)
-      localberg%width=bergs%initial_width(1)
-      localberg%length=bergs%initial_length(1)
+      localberg%mass=bergs%initial_mass_s(1)
+      localberg%thickness=bergs%initial_thickness_s(1)
+      localberg%width=bergs%initial_width_s(1)
+      localberg%length=bergs%initial_length_s(1)
       localberg%fl_k=0.
       localberg%start_lon=localberg%lon
       localberg%start_lat=localberg%lat
       localberg%start_year=iyr
       localberg%start_day=float(iday)+(float(ihr)+float(imin)/60.)/24.
       localberg%start_mass=localberg%mass
-      localberg%mass_scaling=bergs%mass_scaling(1)
+      localberg%mass_scaling=bergs%mass_scaling_s(1)
       localberg%mass_of_bits=0.
       localberg%mass_of_fl_bits=0.
       localberg%halo_berg=0.
@@ -1599,7 +1599,11 @@ subroutine read_restart_calving(bergs)
              rns=initializeRandomNumberStream(i+10000*j)
              call getRandomNumbers(rns,randnum(1,:))
              do k=1, nclasses
-                grd%stored_ice(i,j,k)=randnum(1,k) * grd%msk(i,j) * bergs%initial_mass(k) * bergs%mass_scaling(k)
+               if (grd%lon(i,j)<0.) then
+                 grd%stored_ice(i,j,k)=randnum(1,k) * grd%msk(i,j) * bergs%initial_mass_s(k) * bergs%mass_scaling_s(k)
+               else
+                 grd%stored_ice(i,j,k)=randnum(1,k) * grd%msk(i,j) * bergs%initial_mass_n(k) * bergs%mass_scaling_n(k)
+               endif
              end do
           end do
        end do
@@ -1609,8 +1613,13 @@ subroutine read_restart_calving(bergs)
           rns = initializeRandomNumberStream(i)
           call getRandomNumbers(rns,randnum)
           do k=1, nclasses
+            where (grd%lon(i,grd%jsc:grd%jec)<0.)
              grd%stored_ice(i,grd%jsc:grd%jec,k) = randnum(:,k) * grd%msk(i,grd%jsc:grd%jec) * &
-                  & bergs%initial_mass(k) * bergs%mass_scaling(k)
+               & bergs%initial_mass_s(k) * bergs%mass_scaling_s(k)
+           elsewhere
+             grd%stored_ice(i,grd%jsc:grd%jec,k) = randnum(:,k) * grd%msk(i,grd%jsc:grd%jec) * &
+               & bergs%initial_mass_n(k) * bergs%mass_scaling_n(k)
+           end where
           end do
        end do
     end if

From 21336416cbe1f08e92ee70047f68ce6f0ab83642 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Mon, 19 Apr 2021 17:15:21 -0400
Subject: [PATCH 296/361] quick fix to default N hemisphere initial
 thicknesses. Removed unnecessary line in footloose part of thermodynamics

---
 src/icebergs.F90           | 1 -
 src/icebergs_framework.F90 | 2 +-
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index d3295cd..03b2478 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -2874,7 +2874,6 @@ subroutine thermodynamics(bergs)
           !basal turbulent melting
           Mb_fl=max( 0.58*(dvo**0.8)*(SST+4.0)/(Lfl**0.2), 0.) *perday
           Tnfl=max(Tfl-  Mb_fl*bergs%dt,0.) ! new FL thickness (m)
-          nVolfl=Tnfl*Wnfl*Lnfl ! new footloose volume (m^
           if (bergs%use_operator_splitting) then
             !buoyant convection
             Lnfl=max(Lfl-Mv_fl*bergs%dt,0.) ! new FL length (m)
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 8088627..fc6f869 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -790,7 +790,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real, dimension(nclasses) :: initial_mass_n=(/4.58e8, 3.61e9, 1.22e10, 2.91e10, 5.09e10, 7.34e10, 1.15e11, 1.65e11, 2.94e11, 5.59e11/) !for N hemisphere
 real, dimension(nclasses) :: distribution_n=(/0.14, 0.15, 0.20, 0.15, 0.08, 0.07, 0.05, 0.05, 0.05, 0.05/) ! for N hemisphere
 real, dimension(nclasses) :: mass_scaling_n=(/200, 50, 25, 13, 8, 5, 2, 1, 1, 1/) ! for N hemisphere
-real, dimension(nclasses) :: initial_thickness_n=(/80, 159.5, 240, 320, 360, 360, 360, 360, 360/) ! for N hemisphere
+real, dimension(nclasses) :: initial_thickness_n=(/80.4, 159.5, 240., 320., 360., 360., 360., 360., 360., 360./) ! for N hemisphere
 integer(kind=8) :: debug_iceberg_with_id = -1 ! If positive, monitors a berg with this id
 ! DEM-mode parameters
 !logical :: dem=.false. !if T, run in DEM-mode with angular terms, variable stiffness, etc

From 80928aeef4fe55924b93ce3369770791cf900149 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Tue, 20 Apr 2021 10:55:43 -0400
Subject: [PATCH 297/361] fixed operator splitting error in footloose
 thermodynamics

---
 src/icebergs.F90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 03b2478..fcf6e49 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -2881,8 +2881,8 @@ subroutine thermodynamics(bergs)
             nVolfl=Tnfl*Wnfl*Lnfl ! new footloose volume (m^3)
             nMfl2=(nVolfl/Volfl)*Mfl !new FL mass (kg), after buoyant convection
             !erosion
-            Lnfl=max(Lfl-Me_fl*bergs%dt,0.) ! new FL length (m)
-            Wnfl=max(Wfl-Me_fl*bergs%dt,0.) ! new FL width (m)
+            Lnfl=max(Lnfl-Me_fl*bergs%dt,0.) ! new FL length (m)
+            Wnfl=max(Wnfl-Me_fl*bergs%dt,0.) ! new FL width (m)
             nVolfl=Tnfl*Wnfl*Lnfl ! new footloose volume (m^3)
             nMfl=(nVolfl/Volfl)*Mfl !new FL mass (kg), after all melt and erosion
             dMe_fl=nMfl2-nMfl !FL mass lost to erosion (>0) (kg)

From a43341ed05b3ddb2761842e489c4e6b0afc13eaf Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Wed, 21 Apr 2021 11:11:55 -0400
Subject: [PATCH 298/361] fix lon/lat mixup for n/s hemisphere berg calving
 distribution/initial thickness&mass

---
 src/icebergs.F90    | 8 ++++----
 src/icebergs_io.F90 | 4 ++--
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index fcf6e49..f79d907 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -5797,7 +5797,7 @@ subroutine accumulate_calving(bergs)
 
   remaining_dist_s=1.; remaining_dist_n=1.
   do k=1, nclasses
-    where (grd%lon<0.)
+    where (grd%lat<0.)
       grd%stored_ice(:,:,k)=grd%stored_ice(:,:,k)+bergs%dt*grd%calving(:,:)*bergs%distribution_s(k)
     elsewhere
       grd%stored_ice(:,:,k)=grd%stored_ice(:,:,k)+bergs%dt*grd%calving(:,:)*bergs%distribution_n(k)
@@ -5809,7 +5809,7 @@ subroutine accumulate_calving(bergs)
     write(stderrunit,*) 'KID, accumulate_calving: sum(distribution)>1!!!',remaining_dist_s, remaining_dist_n
     call error_mesg('KID, accumulate_calving', 'calving is OVER distributed!', WARNING)
   endif
-  where (grd%lon<0.)
+  where (grd%lat<0.)
     grd%tmp=remaining_dist_s
   elsewhere
     grd%tmp=remaining_dist_n
@@ -5859,7 +5859,7 @@ subroutine calve_icebergs(bergs)
     do j=grd%jsc, grd%jec
       do i=grd%isc, grd%iec
         ddt=0.; icnt=0
-        if (grd%lon(i,j)<0.) then
+        if (grd%lat(i,j)<0.) then
           initial_mass=>bergs%initial_mass_s(k); mass_scaling=>bergs%mass_scaling_s(k)
           initial_thickness=>bergs%initial_thickness_s(k)
           initial_width=>bergs%initial_width_s(k); initial_length=>bergs%initial_length_s(k)
@@ -5965,7 +5965,7 @@ subroutine calve_icebergs(bergs)
           ddt=ddt-bergs%dt*2./17. ! Minor offset to start day (negative offsets)
           icnt=icnt+1
           bergs%nbergs_calved=bergs%nbergs_calved+1
-          if (grd%lon(i,j)<0.) then
+          if (grd%lat(i,j)<0.) then
             bergs%nbergs_calved_by_class_s(k)=bergs%nbergs_calved_by_class_s(k)+1
           else
             bergs%nbergs_calved_by_class_n(k)=bergs%nbergs_calved_by_class_n(k)+1
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index 1d4ca3d..fe79ea4 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -1599,7 +1599,7 @@ subroutine read_restart_calving(bergs)
              rns=initializeRandomNumberStream(i+10000*j)
              call getRandomNumbers(rns,randnum(1,:))
              do k=1, nclasses
-               if (grd%lon(i,j)<0.) then
+               if (grd%lat(i,j)<0.) then
                  grd%stored_ice(i,j,k)=randnum(1,k) * grd%msk(i,j) * bergs%initial_mass_s(k) * bergs%mass_scaling_s(k)
                else
                  grd%stored_ice(i,j,k)=randnum(1,k) * grd%msk(i,j) * bergs%initial_mass_n(k) * bergs%mass_scaling_n(k)
@@ -1613,7 +1613,7 @@ subroutine read_restart_calving(bergs)
           rns = initializeRandomNumberStream(i)
           call getRandomNumbers(rns,randnum)
           do k=1, nclasses
-            where (grd%lon(i,grd%jsc:grd%jec)<0.)
+            where (grd%lat(i,grd%jsc:grd%jec)<0.)
              grd%stored_ice(i,grd%jsc:grd%jec,k) = randnum(:,k) * grd%msk(i,grd%jsc:grd%jec) * &
                & bergs%initial_mass_s(k) * bergs%mass_scaling_s(k)
            elsewhere

From 53cb93c13a5708e9198335211aea61cbc36ed231 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Thu, 22 Apr 2021 11:38:12 -0400
Subject: [PATCH 299/361] When approximating the dimensions of footloose bits,
 now apply scaling of length, width, and thickness before rolling correction,
 rather than after

---
 src/icebergs.F90 | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index f79d907..431410c 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -2863,6 +2863,7 @@ subroutine thermodynamics(bergs)
         Mfl=this%mass_of_fl_bits
 
         if (bergs%fl_melt_as_bergy_bits) then
+          Lfl=min(L,W,T,40.)
           Afl=(Mfl/bergs%rho_bergs)/Lfl
           Mb_fl=max( 0.58*(dvo**0.8)*(SST+2.0)/(Lfl**0.2), 0.) *perday ! FL bits basal turbulent melting
           Mb_fl=bergs%rho_bergs*Afl*Mb_fl ! in kg/s
@@ -3094,12 +3095,11 @@ subroutine fl_bits_dimensions(bergs,this,L_fl,W_fl,T_fl)
   else
     l_w  = (lw_c*B_c*(this%thickness**3.))**0.25  !buoyancy length
     l_b  = l_c*l_w !length of a freshly calved footloose child berg
-    L_fl = 3.*l_b; W_fl=l_b; T_fl=this%thickness
+    L_fl = bergs%fl_bits_scale_l*3.*l_b; W_fl=bergs%fl_bits_scale_w*l_b
+    T_fl=bergs%fl_bits_scale_t*this%thickness
     call rolling(bergs,T_fl,W_fl,L_fl)
-    L_fl_temp = bergs%fl_bits_scale_l*max(L_fl,W_fl)
-    W_fl = bergs%fl_bits_scale_w*min(W_fl,L_fl)
-    L_fl = max(L_fl_temp,W_fl); W_fl=min(L_fl_temp,W_fl)
-    T_fl = bergs%fl_bits_scale_t*T_fl
+    L_fl_temp = max(L_fl,W_fl)
+    W_fl = min(W_fl,L_fl); L_fl = L_fl_temp
   endif
 end subroutine fl_bits_dimensions
 

From 7a3f26745ea46c21705377dfed1e1de325959354 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Wed, 5 May 2021 14:25:22 -0400
Subject: [PATCH 300/361] =?UTF-8?q?(1)=20Fixed=20an=20error=20in=20the=20c?=
 =?UTF-8?q?alculation=20for=20the=20max=20number=20of=20footloose=20child?=
 =?UTF-8?q?=20bergs=20that=20could=20be=20calved=20from=20a=20parent=20ber?=
 =?UTF-8?q?g=20over=20a=20time=20step.=20(2)=20Switched=20to=20using=20the?=
 =?UTF-8?q?=20grid-based=20(rather=20than=20particle-based)=20sea-ice=20co?=
 =?UTF-8?q?ncentration=20during=20subroutine=20footloose=5Fcalving.=20The?=
 =?UTF-8?q?=20old,=20particle-based=20definition=20resulted=20in=20incorre?=
 =?UTF-8?q?ct=20sea-ice=20concentrations=20of=20zero=20for=20bergs=20that?=
 =?UTF-8?q?=20had=20just=20transferred=20between=20PEs.=20Given=20that=20s?=
 =?UTF-8?q?ea-ice=20concentrations=20>=200.5=20suppress=20FL=20calving,=20?=
 =?UTF-8?q?the=20particle-based=20definition=20was=20resulting=20in=20some?=
 =?UTF-8?q?=20extra=20FL=20calving.=20The=20grid-based=20approach=20solves?=
 =?UTF-8?q?=20this=20issue,=20but=20is=20otherwise=20identical.=20(3)=20Ad?=
 =?UTF-8?q?ded=20an=20option=20(fl=5Fk=5Fscale=5Fby=5Fperimeter)=20to=20sc?=
 =?UTF-8?q?ale=20the=20number=20of=20footloose=20bergs=20that=20a=20parent?=
 =?UTF-8?q?=20berg=20calves=20over=20a=20time=20step=20by=20the=20perimete?=
 =?UTF-8?q?r=20(2*(length+width))=20of=20the=20parent=20berg.=20(4)=20Adde?=
 =?UTF-8?q?d=20parameter=20track=20the=20number=20of=20footloose=20bergs?=
 =?UTF-8?q?=20calved=20(bergs%nbergs=5Fcalved=5Ffl).=20This=20parameter=20?=
 =?UTF-8?q?is=20now=20included=20when=20reporting=20the=20number=20of=20be?=
 =?UTF-8?q?rgs=20calved=20vs.=20melted.=20(5)=20Edited=20subroutine=20roll?=
 =?UTF-8?q?ing=20to=20automatically=20swap=20berg=20length=20and=20width?=
 =?UTF-8?q?=20if=20width=20is=20greater.=20(6)=20Added=20an=20option=20to?=
 =?UTF-8?q?=20convert=20footloose=20bits=20to=20a=20new=20berg=20if=20thei?=
 =?UTF-8?q?r=20mass=20exceeds=20a=20threshold=20(bergs%new=5Fberg=5Ffrom?=
 =?UTF-8?q?=5Ffl=5Fbits=5Fmass=5Fthres).=20(7)=20Added=20some=20new=20cloc?=
 =?UTF-8?q?ks=20to=20time=20subroutines=20for=20footloose=20and=20communic?=
 =?UTF-8?q?ation=20between=20processors.=20(8)=20Added=20(experimental)=20?=
 =?UTF-8?q?option=20to=20treat=20berg=20contact=20with=20land=20as=20if=20?=
 =?UTF-8?q?it=20was=20contact=20with=20another=20berg,=20to=20prevent=20gr?=
 =?UTF-8?q?ounding.=20(9)=20Fixed=20issue=20in=20subroutine=20calve=5Ficeb?=
 =?UTF-8?q?ergs,=20regarding=20allocations=20for=20new=20bergs=20when=20th?=
 =?UTF-8?q?e=20model=20was=20run=20in=20MTS=20mode,=20bonded=20mode,=20DEM?=
 =?UTF-8?q?=20mode,=20or=20with=20fracture=20or=20monitor=5Fenergy.=20(10)?=
 =?UTF-8?q?=20Split=20the=20definition=20of=20=E2=80=9Csquare=E2=80=9D=20i?=
 =?UTF-8?q?ceberg=20radius=20using=20into=20two=20options:=20(a)=20For=20b?=
 =?UTF-8?q?onded=20models=20using=20square=20packing:=20the=20radius=20cor?=
 =?UTF-8?q?responds=20to=20a=20circle=20inscribed=20within=20a=20square=20?=
 =?UTF-8?q?(b)=20For=20non-bonded=20models:=20the=20original=20definition,?=
 =?UTF-8?q?=20where=20radius=20corresponds=20to=20the=20true=20iceberg=20a?=
 =?UTF-8?q?rea=20(L*W).=20(11)=20Cleaned=20up=20the=20line=20lengths=20whe?=
 =?UTF-8?q?re=20namelist=20parameters=20are=20listed=20in=20icebergs=5Ffra?=
 =?UTF-8?q?mework.F90?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 src/icebergs.F90           | 332 +++++++++++++++++++++++++++++++------
 src/icebergs_framework.F90 |  87 +++++++---
 2 files changed, 344 insertions(+), 75 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 431410c..9cfba76 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -503,6 +503,7 @@ subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
   real, intent(out) :: P_ia_times_u_y !< Meridional damping projection (without new berg velocity) (kg m/s)
   ! Local variables
   type(bond), pointer :: current_bond
+  type(icebergs_gridded), pointer :: grd
   real :: u2, v2
   logical :: critical_interaction_damping_on
   integer :: grdi, grdj
@@ -578,6 +579,14 @@ subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
           other_berg=>other_berg%next
         enddo
       enddo; enddo
+      if (bergs%use_spring_for_land_contact) then
+        grd=>bergs%grd
+        do grdj = max(berg%jne-nc_y,bergs%grd%jsd),min(berg%jne+nc_y,bergs%grd%jed);&
+          do grdi = max(berg%ine-nc_x,bergs%grd%isd),min(berg%ine+nc_x,bergs%grd%ied)
+          if (grd%msk(grdi,grdj)==0) call calculate_force_land_contact(bergs, berg, grd, grdi, grdj, &
+            IA_x, IA_y, P_ia_11, P_ia_12, P_ia_21, P_ia_22) !, P_ia_times_u_x, P_ia_times_u_y)
+        enddo; enddo
+      endif
     endif
 
   else
@@ -607,6 +616,14 @@ subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
         current_bond=>current_bond%next_bond
       enddo
     endif
+    if (bergs%use_spring_for_land_contact) then
+      grd=>bergs%grd
+      do grdj = max(berg%jne-nc_y,bergs%grd%jsd),min(berg%jne+nc_y,bergs%grd%jed);&
+        do grdi = max(berg%ine-nc_x,bergs%grd%isd),min(berg%ine+nc_x,bergs%grd%ied)
+        if (grd%msk(grdi,grdj)==0) call calculate_force_land_contact(bergs, berg, grd, grdi, grdj, &
+          IA_x, IA_y, P_ia_11, P_ia_12, P_ia_21, P_ia_22) !, P_ia_times_u_x, P_ia_times_u_y)
+      enddo; enddo
+    endif
   endif
 end subroutine interactive_force
 
@@ -689,10 +706,13 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
       R1=sqrt(A1/(2.*sqrt(3.)))
       R2=sqrt(A2/(2.*sqrt(3.)))
     else !square packing
-      !R1=sqrt(A1/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
-      !R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
-      R1=0.5*sqrt(A1)
-      R2=0.5*sqrt(A2)
+      if (bergs%iceberg_bonds_on) then
+        R1=0.5*sqrt(A1)
+        R2=0.5*sqrt(A2)
+      else
+        R1=sqrt(A1/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
+        R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
+      endif
     endif
     !!!!!!!!!!!!!!!!!!!!!!!!!!!debugging!!!!!!!!!!!!!!!!!!!!!!!!!!MP1
     ! if (berg%id .eq. 1) then
@@ -888,10 +908,13 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
       R1=sqrt(A1/(2.*sqrt(3.)))
       R2=sqrt(A2/(2.*sqrt(3.)))
     else !square packing
-      !R1=sqrt(A1/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
-      !R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
-      R1=0.5*sqrt(A1)
-      R2=0.5*sqrt(A2)
+      if (bergs%iceberg_bonds_on) then
+        R1=0.5*sqrt(A1)
+        R2=0.5*sqrt(A2)
+      else
+        R1=sqrt(A1/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
+        R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
+      endif
     endif
 
     !Rmin=min(R1,R2) !old
@@ -988,6 +1011,148 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
 
 end subroutine calculate_force_dem
 
+!> Experimental subroutine to calculate interactive force between a berg and a land cell
+!> Should prevent grounding.
+subroutine calculate_force_land_contact(bergs, berg, grd, i, j, IA_x, IA_y, &
+  P_ia_11, P_ia_12, P_ia_21, P_ia_22) !, P_ia_times_u_x, P_ia_times_u_y)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  type(iceberg), pointer :: berg !< Primary berg
+  type(icebergs_gridded), pointer :: grd
+  integer, intent(in) :: i !< Grid cell i to contact
+  integer, intent(in) :: j !< Grid cell j to contact
+  real, intent(inout) :: IA_x !< Net zonal acceleration of berg due to interactions (m/s2)
+  real, intent(inout) :: IA_y !< Net meridional acceleration of berg due to interactions (m/s2)
+  real, intent(inout) :: P_ia_11 !< Damping projection matrix, xx component (kg/s)
+  real, intent(inout) :: P_ia_12 !< Damping projection matrix, xy component (kg/s)
+  real, intent(inout) :: P_ia_22 !< Damping projection matrix, yy component (kg/s)
+  real, intent(inout) :: P_ia_21 !< Damping projection matrix, yx component (kg/s)
+  !not needed because "other" iceberg is assumed to have velocity = 0
+  !real, intent(inout) :: P_ia_times_u_x !< Zonal damping projection (without new berg velocity) (kg m/s)
+  !real, intent(inout) :: P_ia_times_u_y !< Meridional damping projection (without new berg velocity) (kg m/s)
+
+  ! Local variables
+  real :: T1, L1, W1, lon1, lat1, R1, A1 ! Current iceberg
+  real :: lon2, lat2 ! "Other" iceberg
+  real :: dlon, dlat
+  real :: r_dist_x, r_dist_y, r_dist
+  real :: P_11, P_12, P_21, P_22
+  !real :: u2, v2
+  real :: lat_ref, dx_dlon, dy_dlat, crit_dist
+  logical :: critical_interaction_damping_on
+  real :: spring_coef, accel_spring, radial_damping_coef, p_ia_coef, tangental_damping_coef
+
+  if (i == berg%ine .and. j == berg%jne) return
+
+  lon1=berg%lon_old; lat1=berg%lat_old  ! From Berg 1
+
+  ! Find the location on the edge/corner of the land cell that is closest to the berg. The force is
+  ! calculated  as if there is a second berg at this location, with identical size to the input berg,
+  ! but with velocities set to zero
+  !u2=0;  v2=0 !"other berg" velocities are assumed to be zero
+  if (berg%ine==i) then
+    lon2=lon1
+    if (berg%jne>j) then !N of cell
+      lat2=grd%lat(i,j)
+    else !S of cell
+      lat2=grd%lat(i,j-1)
+    endif
+  elseif (berg%ine>i) then
+    if (berg%jne==j) then !E of cell
+      lon2=grd%lon(i,j)
+      lat2=lat1
+    elseif (berg%jne>j) then !NE of cell
+      lon2=grd%lon(i,j)
+      lat2=grd%lat(i,j)
+    else !SE of cell
+      lon2=grd%lon(i,j-1)
+      lat2=grd%lat(i,j-1)
+    endif
+  else
+    if (berg%jne==j) then !W of cell
+      lon2=grd%lon(i-1,j)
+      lat2=lat1
+    elseif (berg%jne>j) then !NW of cell
+      lon2=grd%lon(i-1,j)
+      lat2=grd%lat(i-1,j)
+    else !SW of cell
+      lon2=grd%lon(i-1,j-1)
+      lat2=grd%lat(i-1,j-1)
+    endif
+  endif
+
+  L1=berg%length; W1=berg%width; A1=L1*W1
+  dlon=lon1-lon2; dlat=lat1-lat2
+
+  ! Note that this is not the exact distance along a great circle.
+  ! Approximation for small distances. Should be fine.
+  lat_ref=0.5*(lat1+lat2)
+  call convert_from_grid_to_meters(lat_ref,bergs%grd%grid_is_latlon,dx_dlon,dy_dlat)
+
+  r_dist_x=dlon*dx_dlon; r_dist_y=dlat*dy_dlat
+  r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) ) !(Stern et al 2017, Eqn 3)
+
+  !Stern et al 2017, Eqn 4: radius of circle inscribed within hexagon or square with area A1 or A2
+  if (bergs%hexagonal_icebergs) then
+    R1=sqrt(A1/(2.*sqrt(3.)))
+  else !square packing
+    if (bergs%iceberg_bonds_on) then
+      R1=0.5*sqrt(A1)
+    else
+      R1=sqrt(A1/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
+    endif
+  endif
+
+  !Calculating spring force (Stern et al 2017, Eqn 6):
+  spring_coef=bergs%contact_spring_coef
+  crit_dist=max(2*R1,bergs%contact_distance)
+
+  radial_damping_coef=bergs%radial_damping_coef
+  tangental_damping_coef=bergs%tangental_damping_coef
+  critical_interaction_damping_on=bergs%critical_interaction_damping_on
+
+  ! Using critical values for damping rather than manually setting the damping.
+  if (critical_interaction_damping_on) then
+    radial_damping_coef=2.*sqrt(spring_coef) ! Critical damping
+    if (bergs%tang_crit_int_damp_on) then
+      tangental_damping_coef=(2.*sqrt(spring_coef))/4 ! Critical damping (just a guess)
+    endif
+  endif
+
+  if  (r_dist<crit_dist) then
+    !Spring force (Stern et al 2017, Eqn 7):
+    accel_spring=spring_coef*(crit_dist-r_dist)
+    IA_x=IA_x+(accel_spring*(r_dist_x/r_dist))
+    IA_y=IA_y+(accel_spring*(r_dist_y/r_dist))
+
+    ! Damping force (Stern et al 2017, Eqn 8):
+    ! Parallel velocity
+    !projection matrix in Stern et al 2017, Eqn 8:
+    P_11=(r_dist_x*r_dist_x)/(r_dist**2)
+    P_12=(r_dist_x*r_dist_y)/(r_dist**2)
+    P_21=(r_dist_x*r_dist_y)/(r_dist**2)
+    P_22=(r_dist_y*r_dist_y)/(r_dist**2)
+    p_ia_coef=radial_damping_coef
+    P_ia_11=P_ia_11+p_ia_coef*P_11
+    P_ia_12=P_ia_12+p_ia_coef*P_12
+    P_ia_21=P_ia_21+p_ia_coef*P_21
+    P_ia_22=P_ia_22+p_ia_coef*P_22
+    !not needed because u2 and v2 are zero
+    !P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
+    !P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
+
+    ! Normal velocities
+    P_11=1-P_11  ;  P_12=-P_12 ; P_21= -P_21 ;    P_22=1-P_22
+    p_ia_coef=tangental_damping_coef
+    P_ia_11=P_ia_11+p_ia_coef*P_11
+    P_ia_12=P_ia_12+p_ia_coef*P_12
+    P_ia_21=P_ia_21+p_ia_coef*P_21
+    P_ia_22=P_ia_22+p_ia_coef*P_22
+    !not needed because u2 and v2 are zero
+    !P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
+    !P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
+  endif
+end subroutine calculate_force_land_contact
 
 !> Calculates area of overlap between two circular bergs
 subroutine overlap_area(R1, R2, d, A, trapped)
@@ -1642,8 +1807,11 @@ subroutine accel_explicit_inner_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel,
     if (bergs%hexagonal_icebergs) then
       R1=sqrt(berg%length*berg%width/(2.*sqrt(3.)))
     else !square packing
-      !R1=sqrt(berg%length*berg%width/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
-      R1=0.5*sqrt(berg%length*berg%width)
+      if (bergs%iceberg_bonds_on) then
+        R1=0.5*sqrt(berg%length*berg%width)
+      else
+        R1=sqrt(berg%length*berg%width/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
+      endif
     endif
 
     if (bergs%dem_beam_test>0) then
@@ -2443,7 +2611,6 @@ subroutine footloose_calving(bergs, time)
         l_w  = (lw_c*B_c*(T**3.))**0.25  !buoyancy length
         l_b  = l_c*l_w                   !length of child icebergs
 
-
         !---Determine k, the number of child bergs to calve via the footloose mechanism---!
         !Bergs%fl_r is the average number of bergs to calve over the time increment
         !given in seconds by bergs%fl_r_s. K is set according to a Poisson distribution
@@ -2465,7 +2632,7 @@ subroutine footloose_calving(bergs, time)
           endif
         else
           !non-bonded berg must be larger than 3*(l_b) for FL calving. Set max_k accordingly.
-          max_k = max(floor((L - 3*(l_b**2.)/W))+1,0)
+          max_k = max(floor((L-3*l_b)*W/(3*l_b**2.)),0)
         endif
 
         if (max_k==0) then
@@ -2473,7 +2640,7 @@ subroutine footloose_calving(bergs, time)
           this%fl_k=0
         else
           ! If sea ice concentration is <=50%, generate footloose child bergs
-          IC=min(1.,this%cn+bergs%sicn_shift)
+          IC=min(1.,grd%cn(grdi,grdj)+bergs%sicn_shift) !sea ice only known on grid when this routine is called
           if (.not. IC>0.5) then
 
             if (bergs%fl_use_poisson_distribution) then
@@ -2488,10 +2655,9 @@ subroutine footloose_calving(bergs, time)
               k=bergs%fl_r
             endif
 
-            !reduce FL calving rate based on number of bonds
-            if (bergs%iceberg_bonds_on) k=k*((N_max-N_bonds)/N_max)
-
+            if (bergs%iceberg_bonds_on) k=k*((N_max-N_bonds)/N_max) !reduce FL calve rate by number of bonds
             k=k*(bergs%dt/bergs%fl_r_s) !scale k to dt
+            if (bergs%fl_k_scale_by_perimeter>0) k = k * (2.*(L+W)/bergs%fl_k_scale_by_perimeter)
             this%fl_k=this%fl_k+k       !update fl_k
           endif
 
@@ -2512,12 +2678,9 @@ subroutine footloose_calving(bergs, time)
 
           if (bergs%fl_style.eq.'new_bergs') then
             !calve and track footloose bergs
-            if (.not. bergs%displace_fl_bergs) then
-              fl_disp_x=0.0; fl_disp_y=0.0    !new FL bergs take same position as parent berg
-            else
-              call get_footloose_displacement !new FL bergs given random position along parent berg edges
-            endif
+            call get_footloose_displacement
             call calve_fl_icebergs(bergs,this,k,l_b,fl_disp_x,fl_disp_y)
+            bergs%nbergs_calved_fl=bergs%nbergs_calved_fl+1
           else
             !put FL berg mass in footloose bergs bits.
             dM_fl_bits=bergs%rho_bergs*W*T*Lr_fl
@@ -2539,11 +2702,21 @@ subroutine footloose_calving(bergs, time)
           else
             !update length, width, thickness,and mass of parent berg
             if (bergs%allow_bergs_to_roll .and. N_bonds.eq.0.) call rolling(bergs,T,W,Ln)
-            this%thickness=T; this%width=min(W,Ln); this%length=max(W,Ln)
+            this%thickness=T; this%width=W; this%length=Ln
             this%mass=this%length*this%width*this%thickness*bergs%rho_bergs
           endif
         endif
       endif
+
+      !Optionally, create a new berg from the FL bits if their mass exceeds a threshold
+      if (this%mass_of_fl_bits*this%mass_scaling > bergs%new_berg_from_fl_bits_mass_thres) then
+        call get_footloose_displacement
+        k=1
+        call calve_fl_icebergs(bergs,this,k,l_b,fl_disp_x,fl_disp_y,berg_from_bits=.true.)
+        bergs%nbergs_calved_fl=bergs%nbergs_calved_fl+1
+        this%mass_of_fl_bits=this%mass_of_fl_bits-bergs%new_berg_from_fl_bits_mass_thres/this%mass_scaling
+      endif
+
       this=>this%next
     enddo
   enddo; enddo
@@ -2560,6 +2733,11 @@ subroutine get_footloose_displacement
     real :: lon1,lat1,x1,y1,dxdl1,dydl,xdot2,ydot2
     logical :: on_tangential_plane
 
+    if (.not. bergs%displace_fl_bergs) then
+      fl_disp_x=0.0; fl_disp_y=0.0
+      return
+    endif
+
     !displace child berg to a random location along one of the sides of the rectangular berg
     if (rn<0.25) then !north side
       interp_loc=4.*rn
@@ -2649,8 +2827,11 @@ subroutine adjust_fl_berg_interactivity(bergs)
     if (bergs%hexagonal_icebergs) then
       rdenom=1./(2.*sqrt(3.))
     else
-      !rdenom=1./pi
-      rdenom=1./4.
+      if (bergs%iceberg_bonds_on) then
+        rdenom=1./pi
+      else
+        rdenom=1./4.
+      endif
     endif
   else
     radial_contact=.false.
@@ -3035,6 +3216,7 @@ subroutine rolling(bergs,Tn,Wn,Ln)
     if ( (.not.bergs%use_updated_rolling_scheme) .and. (bergs%tip_parameter<999.) ) then    !Use Rolling Scheme 3
       if ( max(Wn,Ln)<sqrt(0.92*(Dn**2)+58.32*Dn) ) then
         call swap_variables(Tn,Wn)
+        if (Wn>Ln) call swap_variables(Wn,Ln)
       endif
     else
       if (Wn>Ln) call swap_variables(Ln,Wn)  !Make sure that Wn is the smaller dimension
@@ -3043,6 +3225,7 @@ subroutine rolling(bergs,Tn,Wn,Ln)
         q=bergs%rho_bergs/rho_seawater
         if (Wn<sqrt((6.0*q*(1-q)*(Tn**2))-(12*Delta*q*Tn))) then
           call swap_variables(Tn,Wn)
+          if (Wn>Ln) call swap_variables(Wn,Ln)
         endif
       endif
 
@@ -3056,6 +3239,7 @@ subroutine rolling(bergs,Tn,Wn,Ln)
         endif
         if ((tip_parameter*Tn)>Wn)  then     !note that we use the Thickness instead of the Draft
           call swap_variables(Tn,Wn)
+          if (Wn>Ln) call swap_variables(Wn,Ln)
         endif
       endif
     endif
@@ -3087,7 +3271,7 @@ subroutine fl_bits_dimensions(bergs,this,L_fl,W_fl,T_fl)
   ! Local variables
   real,parameter :: l_c=pi/(2.*sqrt(2.)), lw_c = 1./(gravity*rho_seawater)
   real,parameter :: B_c=1.e8/(12.*(1.-0.3**2.)) !youngs=1.e8, poisson=0.3
-  real :: l_w,l_b,L_fl_temp
+  real :: l_w,l_b
 
   if (bergs%fl_melt_as_bergy_bits) then
     L_fl=min(this%length,this%width,this%thickness,40.)
@@ -3098,8 +3282,6 @@ subroutine fl_bits_dimensions(bergs,this,L_fl,W_fl,T_fl)
     L_fl = bergs%fl_bits_scale_l*3.*l_b; W_fl=bergs%fl_bits_scale_w*l_b
     T_fl=bergs%fl_bits_scale_t*this%thickness
     call rolling(bergs,T_fl,W_fl,L_fl)
-    L_fl_temp = max(L_fl,W_fl)
-    W_fl = min(W_fl,L_fl); L_fl = L_fl_temp
   endif
 end subroutine fl_bits_dimensions
 
@@ -5074,15 +5256,19 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   call mpp_clock_end(bergs%clock_mom)
 
   ! Send bergs to other PEs
-  call mpp_clock_begin(bergs%clock_com)
+  call mpp_clock_begin(bergs%clock_com1)
   if (bergs%iceberg_bonds_on)  call  bond_address_update(bergs)
 
   call send_bergs_to_other_pes(bergs)
   if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after send_bergs() ')
+  call mpp_clock_end(bergs%clock_com1)
 
+  call mpp_clock_begin(bergs%clock_fl1)
   ! Footloose mechanism part 1: calve the child icebergs
   if (bergs%fl_r>0.) call footloose_calving(bergs, time)
+  call mpp_clock_end(bergs%clock_fl1)
 
+  call mpp_clock_begin(bergs%clock_com2)
   if (bergs%mts) then
     call interp_gridded_fields_to_bergs(bergs)
     call transfer_mts_bergs(bergs)
@@ -5102,8 +5288,9 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   endif
   if (debug) call bergs_chksum(bergs, 'run bergs (exchanged)')
   if (debug) call checksum_gridded(bergs%grd, 's/r run after exchange')
-  call mpp_clock_end(bergs%clock_com)
+  call mpp_clock_end(bergs%clock_com2)
 
+  call mpp_clock_begin(bergs%clock_fl2)
   ! Footloose mechanism part 2:
   if (bergs%fl_r>0.) then
     !delete any edge elements that have fully calved from the footloose mechanism
@@ -5112,6 +5299,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     !berg for the first time
     if (bergs%interactive_icebergs_on) call adjust_fl_berg_interactivity(bergs)
   endif
+  call mpp_clock_end(bergs%clock_fl2)
 
   if (bergs%find_melt_using_spread_mass .or. bergs%mts) then
     call calculate_mass_on_ocean(bergs, with_diagnostics=.false.)
@@ -5355,6 +5543,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     call mpp_sum(bergs%returned_mass_on_ocean)
     call mpp_sum(bergs%nbergs_end)
     call mpp_sum(bergs%nbergs_calved)
+    call mpp_sum(bergs%nbergs_calved_fl)
     do k=1,nclasses; call mpp_sum(bergs%nbergs_calved_by_class_s(k)); enddo
     do k=1,nclasses; call mpp_sum(bergs%nbergs_calved_by_class_n(k)); enddo
     call mpp_sum(bergs%nbergs_melted)
@@ -5398,6 +5587,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
       call report_state('spread icebergs','m^2','',bergs%spread_area_start,'',bergs%spread_area_end,'')
       call report_istate('berg #','',bergs%nbergs_start,'',bergs%nbergs_end,'')
       call report_ibudget('berg #','calved',bergs%nbergs_calved, &
+                                   'FL calved',bergs%nbergs_calved_fl, &
                                    'melted',bergs%nbergs_melted, &
                                    '#',bergs%nbergs_start,bergs%nbergs_end)
       call report_budget('stored mass','kg','calving used',bergs%net_calving_used, &
@@ -5452,6 +5642,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     bergs%stored_start=bergs%stored_end
     bergs%nbergs_melted=0
     bergs%nbergs_calved=0
+    bergs%nbergs_calved_fl=0
     bergs%nbergs_calved_by_class_s(:)=0
     bergs%nbergs_calved_by_class_n(:)=0
     bergs%nspeeding_tickets=0
@@ -5579,11 +5770,13 @@ subroutine report_istate(budgetstr, startstr, startval, endstr, endval, delstr)
 end subroutine report_istate
 
 !> Prints a budget
-subroutine report_ibudget(budgetstr,instr,inval,outstr,outval,delstr,startval,endval)
+subroutine report_ibudget(budgetstr,instr1,inval1,instr2,inval2,outstr,outval,delstr,startval,endval)
   ! Arguments
   character*(*), intent(in) :: budgetstr !< Budget title
-  character*(*), intent(in) :: instr !< Incoming label
-  integer, intent(in) :: inval !< Incoming value
+  character*(*), intent(in) :: instr1 !< Incoming label 1
+  integer, intent(in) :: inval1 !< Incoming value 1
+  character*(*), intent(in) :: instr2 !< Incoming label 2
+  integer, intent(in) :: inval2 !< Incoming value 2
   character*(*), intent(in) :: outstr !< Outgoing label
   integer, intent(in) :: outval !< Outgoing value
   character*(*), intent(in) :: delstr !< Delta label
@@ -5591,10 +5784,11 @@ subroutine report_ibudget(budgetstr,instr,inval,outstr,outval,delstr,startval,en
   integer, intent(in) :: endval !< End value for budget
   ! Local variables
   write(*,200) budgetstr//' budget:', &
-                      instr//' in',inval, &
+                      instr1//' in',inval1, &
+                      instr2//' in',inval2, &
                       outstr//' out',outval, &
-                      'Delta '//delstr,inval-outval, &
-                      'error',((endval-startval)-(inval-outval))
+                      'Delta '//delstr,inval1+inval2-outval, &
+                      'error',((endval-startval)-(inval1+inval2-outval))
   200 format("KID: ",a19,10(a18,"=",i14,x,:,","))
 end subroutine report_ibudget
 
@@ -5840,6 +6034,7 @@ subroutine calve_icebergs(bergs)
   real :: xi, yj, ddt, calving_to_bergs, calved_to_berg, heat_to_bergs, heat_to_berg
   integer :: stderrunit
   real, pointer :: initial_mass, mass_scaling, initial_thickness, initial_width, initial_length
+  logical :: allocations_done
 
   ! Get the stderr unit number
   stderrunit = stderr()
@@ -5855,6 +6050,8 @@ subroutine calve_icebergs(bergs)
   heat_to_bergs=0.
   icntmax=0
 
+  allocations_done=.false.
+
   do k=1, nclasses
     do j=grd%jsc, grd%jec
       do i=grd%isc, grd%iec
@@ -5925,30 +6122,56 @@ subroutine calve_icebergs(bergs)
           newberg%heat_density=grd%stored_heat(i,j)/grd%stored_ice(i,j,k) ! This is in J/kg
 
           if (bergs%mts) then
-            allocate(newberg%axn_fast,newberg%ayn_fast,newberg%bxn_fast,newberg%byn_fast,newberg%conglom_id)
+            if (.not. allocations_done) then
+              if (.not. allocated(newberg%axn_fast)) allocate(newberg%axn_fast)
+              if (.not. allocated(newberg%ayn_fast)) allocate(newberg%ayn_fast)
+              if (.not. allocated(newberg%bxn_fast)) allocate(newberg%bxn_fast)
+              if (.not. allocated(newberg%byn_fast)) allocate(newberg%byn_fast)
+              if (.not. allocated(newberg%conglom_id)) allocate(newberg%conglom_id)
+            endif
             newberg%axn_fast=0.; newberg%ayn_fast=0.; newberg%bxn_fast=0.; newberg%byn_fast=0.; newberg%conglom_id=0
           endif
 
           if (bergs%iceberg_bonds_on) then
-            allocate(newberg%n_bonds)
+            if (.not. allocations_done) then
+              if (.not. allocated(newberg%n_bonds))  allocate(newberg%n_bonds)
+            endif
             newberg%n_bonds=0
           endif
 
           if (bergs%dem) then
-            allocate(newberg%ang_vel,newberg%ang_accel,newberg%rot)
+            if (.not. allocations_done) then
+              if (.not. allocated(newberg%ang_vel)) allocate(newberg%ang_vel)
+              if (.not. allocated(newberg%ang_accel)) allocate(newberg%ang_accel)
+              if (.not. allocated(newberg%rot)) allocate(newberg%rot)
+            endif
             newberg%ang_vel=0.; newberg%ang_accel=0.; newberg%rot=0.
           endif
 
           if (monitor_energy) then
-            allocate(newberg%Ee,newberg%Ed,newberg%Eext,newberg%Ee_contact,newberg%Ed_contact,newberg%Efrac,&
-              newberg%Ee_temp,newberg%Ed_temp,newberg%Eext_temp,newberg%Ee_contact_temp,newberg%Ed_contact_temp)
+            if (.not. allocations_done) then
+              if (.not. allocated(newberg%Ee)) allocate(newberg%Ee)
+              if (.not. allocated(newberg%Ed)) allocate(newberg%Ed)
+              if (.not. allocated(newberg%Eext)) allocate(newberg%Eext)
+              if (.not. allocated(newberg%Ee_contact)) allocate(newberg%Ee_contact)
+              if (.not. allocated(newberg%Ed_contact)) allocate(newberg%Ed_contact)
+              if (.not. allocated(newberg%Efrac)) allocate(newberg%Efrac)
+              if (.not. allocated(newberg%Ee_temp)) allocate(newberg%Ee_temp)
+              if (.not. allocated(newberg%Ed_temp)) allocate(newberg%Ed_temp)
+              if (.not. allocated(newberg%Eext_temp)) allocate(newberg%Eext_temp)
+              if (.not. allocated(newberg%Ee_contact_temp)) allocate(newberg%Ee_contact_temp)
+              if (.not. allocated(newberg%Ed_contact_temp)) allocate(newberg%Ed_contact_temp)
+            endif
+
             newberg%Ee=0.; newberg%Ed=0.; newberg%Eext=0.; newberg%Ee_contact=0.; newberg%Ed_contact=0.
             newberg%Efrac=0.; newberg%Ee_temp=0.; newberg%Ed_temp=0.;newberg%Eext_temp=0.;
             newberg%Ee_contact_temp=0.; newberg%Ed_contact_temp =0.
           endif
 
           if (bergs%fracture_criterion .ne. 'none' .and. (.not. bergs%dem)) then
-            allocate(newberg%accum_bond_rotation)
+            if (.not. allocations_done) then
+              if (.not. allocated(newberg%accum_bond_rotation)) allocate(newberg%accum_bond_rotation)
+            endif
             newberg%accum_bond_rotation=0.
           endif
 
@@ -5970,6 +6193,8 @@ subroutine calve_icebergs(bergs)
           else
             bergs%nbergs_calved_by_class_n(k)=bergs%nbergs_calved_by_class_n(k)+1
           endif
+
+          allocations_done=.true.
         enddo
         icntmax=max(icntmax,icnt)
       enddo
@@ -5984,7 +6209,7 @@ subroutine calve_icebergs(bergs)
 end subroutine calve_icebergs
 
   !> Calve footloose icebergs from parent berg
-subroutine calve_fl_icebergs(bergs,pberg,k,l_b,fl_disp_x,fl_disp_y)
+subroutine calve_fl_icebergs(bergs,pberg,k,l_b,fl_disp_x,fl_disp_y,berg_from_bits)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
   type(iceberg), pointer :: pberg !< Parent berg
@@ -5992,10 +6217,12 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b,fl_disp_x,fl_disp_y)
   type(real),intent(in) :: l_b !< The width, and 1/3 the length, of a child berg
   type(real) :: fl_disp_x !< Child berg x-displacement from parent berg
   type(real) :: fl_disp_y !< Child berg x-displacement from parent berg
+  logical, optional, intent(in) :: berg_from_bits
   ! Local variables
   type(iceberg) :: cberg ! The new child berg
   type(icebergs_gridded), pointer :: grd
   logical :: lres, displace
+  real :: Lfl, Wfl, Tfl
 
   ! For convenience
   grd=>bergs%grd
@@ -6052,9 +6279,20 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b,fl_disp_x,fl_disp_y)
     cberg%yj  = pberg%yj
   endif
 
-  cberg%length       = l_b*3.
-  cberg%width        = l_b
-  cberg%mass         = cberg%width * cberg%length * pberg%thickness * bergs%rho_bergs
+  if (present(berg_from_bits)) then
+    !use scaling for fl_bits to calculate new berg T,L,W, and M. Also affects mass scaling.
+    call fl_bits_dimensions(bergs,pberg,Lfl,Wfl,Tfl)
+    cberg%length = Lfl; cberg%width = Wfl; cberg%thickness = Tfl
+    cberg%mass = Tfl * Lfl * Wfl * bergs%rho_bergs
+    cberg%mass_scaling = bergs%new_berg_from_fl_bits_mass_thres/cberg%mass
+  else
+    cberg%length       = l_b*3.
+    cberg%width        = l_b
+    cberg%thickness    = pberg%thickness
+    cberg%mass         = cberg%width * cberg%length * pberg%thickness * bergs%rho_bergs
+    cberg%mass_scaling = pberg%mass_scaling * k !k is the number of icebergs cberg represents
+  endif
+
   cberg%start_lon    = cberg%lon
   cberg%start_lat    = cberg%lat
   cberg%lon_prev     = pberg%lon_prev + fl_disp_x
@@ -6062,8 +6300,7 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b,fl_disp_x,fl_disp_y)
   cberg%lon_old      = pberg%lon_old  + fl_disp_x
   cberg%lat_old      = pberg%lat_old  + fl_disp_y
   cberg%start_day    = bergs%current_yearday
-  cberg%start_mass   = cberg%mass
-  cberg%mass_scaling = pberg%mass_scaling * k !k is the number of icebergs cberg represents
+  cberg%start_mass   = pberg%mass !used for tracking the different size classes calved from grounded ice, so set to pberg.
   cberg%mass_of_bits = 0.0
   cberg%mass_of_fl_bits = 0.0
   cberg%fl_k         = -1.0
@@ -6072,7 +6309,6 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b,fl_disp_x,fl_disp_y)
   cberg%halo_berg    = 0.0
 
   !always same values as parent:
-  cberg%thickness    = pberg%thickness
   cberg%uvel         = pberg%uvel
   cberg%vvel         = pberg%vvel
   cberg%axn          = pberg%axn
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index fc6f869..5ee7791 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -455,7 +455,8 @@ module ice_bergs_framework
   integer :: max_bonds
   !>@{
   !! Handles for clocks
-  integer :: clock, clock_mom, clock_the, clock_int, clock_cal, clock_com, clock_ini, clock_ior, clock_iow, clock_dia
+  integer :: clock, clock_mom, clock_the, clock_int, clock_cal, clock_com1, clock_fl1, clock_com2, clock_fl2
+  integer :: clock_ini, clock_ior, clock_iow, clock_dia
   integer :: clock_trw, clock_trp
   integer :: clock_btrw, clock_btrp
   !>@}
@@ -574,7 +575,7 @@ module ice_bergs_framework
   real :: returned_area_on_ocean=0.
   real :: net_melt=0., berg_melt=0., bergy_src=0., bergy_melt=0.
   real :: fl_bits_src=0., fl_bits_melt=0.
-  integer :: nbergs_calved=0, nbergs_melted=0, nbergs_start=0, nbergs_end=0
+  integer :: nbergs_calved=0, nbergs_calved_fl=0, nbergs_melted=0, nbergs_start=0, nbergs_end=0
   integer :: nspeeding_tickets=0
   integer :: nbonds=0
   integer, dimension(:), pointer :: nbergs_calved_by_class_s=>null()
@@ -606,14 +607,18 @@ module ice_bergs_framework
   logical :: constant_interaction_LW=.false. !< Use a constant element length & width during berg interactions
   real :: constant_length=0.!< If constant_interaction_LW, the constant length. If 0, will be set to max initial length
   real :: constant_width=0. !< If constant_interaction_LW, the constant width.  If 0, will be set to max initial width
+  logical :: use_spring_for_land_contact=.false. !< Treat contact with masked (land) cells like contact with a static berg
   ! Footloose calving parameters [England et al (2020) Modeling the breakup of tabular icebergs. Sci. Adv.]
   logical :: fl_use_poisson_distribution=.true. !< fl_r is (T) mean of Poisson distribution to determine k, or (F) k=fl_r
+  logical :: fl_use_perimeter=.false. !< scale number of footloose bergs to calve by perimeter of the parent berg
   real :: fl_r=0. !< footloose average number of bergs calved per fl_r_s
   real :: fl_r_s=0. !< seconds over which fl_r footloose bergs calve
   logical :: displace_fl_bergs=.true. !< footloose berg positions are randomly assigned along edges of parent berg
   character(len=11) :: fl_style='new_bergs' !< Evolve footloose bergs individually as 'new_bergs', or as a group with size 'fl_bits'
   logical :: fl_melt_as_bergy_bits=.false. !< Melt footloose bits as bergy_bits
   logical :: fl_bits_erosion_to_bergy_bits=.true. !< Erosion from footloose bits becomes bergy bits
+  real :: fl_k_scale_by_perimeter=0 !< If greater than 0, scales FL k by (berg perimeter (m))/(this scaling (m))
+  real :: new_berg_from_fl_bits_mass_thres=huge(0.) ! Create a new berg from FL bits when mass_of_fl_bits exceeds this value
   real :: fl_bits_scale_l=0.8  !< For determining dimensions of FL bits berg; FL_bits length = fl_bits_scale_l*3*l_b
   real :: fl_bits_scale_w=0.45 !< For determining dimensions of FL bits berg; FL_bits width = fl_bits_scale_l*3*l_b
   real :: fl_bits_scale_t=0.65 !< For determining dimensions of FL bits berg; FL_bits thickness = fl_bits_scale_l*T
@@ -804,36 +809,48 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: constant_interaction_LW=.false. !< Always use the initial, globally constant, element length & width during berg interactions
 real :: constant_length=0. !< If constant_interaction_LW, the constant length used. If zero in the nml, will be set to max initial L
 real :: constant_width=0. !< If constant_interaction_LW, the constant width used. If zero in the nml, will be set to max initial W
+logical :: use_spring_for_land_contact=.false. !< Treat contact with masked (land) cells like contact with a static berg
 ! Footloose calving parameters [England et al (2020) Modeling the breakup of tabular icebergs. Sci. Adv.]
 logical :: fl_use_poisson_distribution=.true. !< fl_r is (T) mean of Poisson distribution to determine k, or (F) k=fl_r
+logical :: fl_use_perimeter=.false. !< scale number of footloose bergs to calve by perimeter of the parent berg
 real :: fl_r=0. !< footloose average number of bergs calved per fl_r_s
 real :: fl_r_s=0. !< seconds over which fl_r footloose bergs calve
 logical :: displace_fl_bergs=.true. !< footloose berg positions are randomly assigned along edges of parent berg
 character(len=11) :: fl_style='new_bergs' !< Evolve footloose bergs individually as 'fl_bits', or as a group with size 'bergy_bits' or 'mean_size'
 logical :: fl_melt_as_bergy_bits=.false. !< Melt footloose bits as bergy_bits
 logical :: fl_bits_erosion_to_bergy_bits=.true. !< Erosion from footloose bits becomes bergy bits
+real :: fl_k_scale_by_perimeter=0 !< If greater than 0, scales FL k by (berg perimeter (m))/(this scaling (m))
+real :: new_berg_from_fl_bits_mass_thres=huge(0.) ! Create a new berg from FL bits when mass_of_fl_bits exceeds this value
 real :: fl_bits_scale_l=0.8 !< For determining dimensions of FL bits berg; FL_bits length = fl_bits_scale_l*3*l_b
 real :: fl_bits_scale_w=0.45 !< For determining dimensions of FL bits berg; FL_bits width = fl_bits_scale_l*l_b
 real :: fl_bits_scale_t=0.65 !< For determining dimensions of FL bits berg; FL_bits thickness = fl_bits_scale_l*T
 
-namelist /icebergs_nml/ verbose, budget, halo,  traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,Static_icebergs,  &
-         distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,bond_coef, radial_damping_coef, tangental_damping_coef, only_interactive_forces, &
-         rho_bergs, LoW_ratio, debug, really_debug, use_operator_splitting, bergy_bit_erosion_fraction, iceberg_bonds_on, manually_initialize_bonds, ignore_missing_restart_bergs, &
-         parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, ignore_ij_restart, use_new_predictive_corrective, halo_debugging, hexagonal_icebergs, &
-         time_average_weight, generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, interactive_icebergs_on, scale_damping_by_pmag,&
-         critical_interaction_damping_on, tang_crit_int_damp_on, require_restart, &
-         old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,grounding_fraction, input_freq_distribution, force_all_pes_traj, &
-         allow_bergs_to_roll,set_melt_rates_to_zero,lat_ref,initial_orientation,rotate_icebergs_for_mass_spreading,grid_is_latlon,Lx,use_f_plane,use_old_spreading, &
-         grid_is_regular,override_iceberg_velocities,u_override,v_override,add_iceberg_thickness_to_SSH,Iceberg_melt_without_decay,melt_icebergs_as_ice_shelf, &
-         Use_three_equation_model,find_melt_using_spread_mass,use_mixed_layer_salinity_for_thermo,utide_icebergs,ustar_icebergs_bg,cdrag_icebergs, pass_fields_to_ocean_model, &
-         const_gamma, Gamma_T_3EQ, ignore_traj, debug_iceberg_with_id,use_updated_rolling_scheme, tip_parameter, read_old_restarts, tau_calving, read_ocean_depth_from_file, melt_cutoff,&
-         apply_thickness_cutoff_to_gridded_melt, apply_thickness_cutoff_to_bergs_melt, use_mixed_melting, internal_bergs_for_drag, coastal_drift, tidal_drift,&
-         mts,new_mts,ewsame,monitor_energy,mts_sub_steps,contact_distance,length_for_manually_initialize_bonds,manually_initialize_bonds_from_radii,contact_spring_coef,&
-         fracture_criterion, damage_test_1, uniaxial_test, debug_write,cdrag_grounding,h_to_init_grounding,frac_thres_scaling,frac_thres_n,frac_thres_t,save_bond_traj,remove_unused_bergs,&
-         force_convergence,explicit_inner_mts,convergence_tolerance,&
-         dem,ignore_tangential_force,poisson,dem_spring_coef,dem_damping_coef,dem_beam_test,constant_interaction_LW,constant_length,constant_width,dem_shear_for_frac_only,use_damage, fl_use_poisson_distribution, fl_r, fl_r_s, displace_fl_bergs,fl_style,&
-         fl_melt_as_bergy_bits,fl_bits_erosion_to_bergy_bits,fl_bits_scale_l,fl_bits_scale_w,fl_bits_scale_t,&
-         separate_distrib_for_n_hemisphere, initial_mass_n, distribution_n, mass_scaling_n, initial_thickness_n
+namelist /icebergs_nml/ verbose, budget, halo,  traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,&
+         Static_icebergs,distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,bond_coef, &
+         radial_damping_coef, tangental_damping_coef, only_interactive_forces, rho_bergs, LoW_ratio, debug, really_debug, &
+         use_operator_splitting, bergy_bit_erosion_fraction, iceberg_bonds_on, manually_initialize_bonds, &
+         ignore_missing_restart_bergs,  parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, &
+         ignore_ij_restart, use_new_predictive_corrective, halo_debugging, hexagonal_icebergs, time_average_weight, &
+         generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, interactive_icebergs_on,&
+         scale_damping_by_pmag, critical_interaction_damping_on, tang_crit_int_damp_on, require_restart,&
+         old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,&
+         grounding_fraction, input_freq_distribution, force_all_pes_traj,allow_bergs_to_roll,set_melt_rates_to_zero,lat_ref,&
+         initial_orientation,rotate_icebergs_for_mass_spreading,grid_is_latlon,Lx,use_f_plane,use_old_spreading,&
+         grid_is_regular,override_iceberg_velocities,u_override,v_override,add_iceberg_thickness_to_SSH,&
+         Iceberg_melt_without_decay,melt_icebergs_as_ice_shelf, Use_three_equation_model,find_melt_using_spread_mass,&
+         use_mixed_layer_salinity_for_thermo,utide_icebergs,ustar_icebergs_bg,cdrag_icebergs, pass_fields_to_ocean_model, &
+         const_gamma, Gamma_T_3EQ, ignore_traj, debug_iceberg_with_id,use_updated_rolling_scheme, tip_parameter, &
+         read_old_restarts, tau_calving, read_ocean_depth_from_file, melt_cutoff,apply_thickness_cutoff_to_gridded_melt, &
+         apply_thickness_cutoff_to_bergs_melt, use_mixed_melting, internal_bergs_for_drag, coastal_drift, tidal_drift,&
+         mts,new_mts,ewsame,monitor_energy,mts_sub_steps,contact_distance,length_for_manually_initialize_bonds,&
+         manually_initialize_bonds_from_radii,contact_spring_coef,fracture_criterion, damage_test_1, uniaxial_test, &
+         debug_write,cdrag_grounding,h_to_init_grounding,frac_thres_scaling,frac_thres_n,frac_thres_t,save_bond_traj,&
+         remove_unused_bergs,force_convergence,explicit_inner_mts,convergence_tolerance,dem,ignore_tangential_force,poisson,&
+         dem_spring_coef,dem_damping_coef,dem_beam_test,constant_interaction_LW,constant_length,constant_width,&
+         dem_shear_for_frac_only,use_damage,fl_use_poisson_distribution, fl_use_perimeter, fl_r, fl_r_s,displace_fl_bergs,&
+         fl_style,fl_melt_as_bergy_bits,fl_bits_erosion_to_bergy_bits,fl_k_scale_by_perimeter,use_spring_for_land_contact,&
+         new_berg_from_fl_bits_mass_thres,fl_bits_scale_l,fl_bits_scale_w,fl_bits_scale_t,separate_distrib_for_n_hemisphere,&
+         initial_mass_n, distribution_n, mass_scaling_n, initial_thickness_n
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -882,7 +899,10 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%clock_the=mpp_clock_id( 'Icebergs-thermodyn', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
   bergs%clock_int=mpp_clock_id( 'Icebergs-interface', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
   bergs%clock_cal=mpp_clock_id( 'Icebergs-calving', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
-  bergs%clock_com=mpp_clock_id( 'Icebergs-communication', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+  bergs%clock_com1=mpp_clock_id( 'Icebergs-communication1', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+  bergs%clock_fl1=mpp_clock_id( 'Icebergs-footloose1', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+  bergs%clock_com2=mpp_clock_id( 'Icebergs-communication2', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+  bergs%clock_fl2=mpp_clock_id( 'Icebergs-footloose2', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
   bergs%clock_ini=mpp_clock_id( 'Icebergs-initialization', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
   bergs%clock_ior=mpp_clock_id( 'Icebergs-I/O read', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
   bergs%clock_iow=mpp_clock_id( 'Icebergs-I/O write', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
@@ -1383,6 +1403,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%add_weight_to_ocean=add_weight_to_ocean
   bergs%use_old_spreading=use_old_spreading
   bergs%debug_iceberg_with_id=debug_iceberg_with_id
+  bergs%use_spring_for_land_contact=use_spring_for_land_contact
   bergs%mts=mts
   bergs%mts_fast_dt = mts_fast_dt
   bergs%mts_sub_steps = mts_sub_steps
@@ -1406,6 +1427,8 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%dem_shear_for_frac_only=dem_shear_for_frac_only
   ! Footloose calving parameters
   bergs%fl_use_poisson_distribution=fl_use_poisson_distribution
+  bergs%fl_use_perimeter=fl_use_perimeter
+  bergs%new_berg_from_fl_bits_mass_thres=new_berg_from_fl_bits_mass_thres
   bergs%fl_r=fl_r
   bergs%fl_r_s=fl_r_s
   bergs%displace_fl_bergs=displace_fl_bergs
@@ -1416,6 +1439,7 @@ subroutine ice_bergs_framework_init(bergs, &
     displace_fl_bergs=.false.
     bergs%fl_melt_as_bergy_bits=.false.
   endif
+  bergs%fl_k_scale_by_perimeter=fl_k_scale_by_perimeter
   bergs%fl_bits_scale_l=fl_bits_scale_l
   bergs%fl_bits_scale_w=fl_bits_scale_w
   bergs%fl_bits_scale_t=fl_bits_scale_t
@@ -2426,8 +2450,11 @@ recursive subroutine mts_pack_contact_bergs(bergs, berg, dir, pfix, nbergs_to_se
     if (bergs%hexagonal_icebergs) then
       rdenom=1./(2.*sqrt(3.))
     else
-      !rdenom=1./pi
-      rdenom=1./4.
+      if (bergs%iceberg_bonds_on) then
+        rdenom=1./4.
+      else
+        rdenom=1./pi
+      endif
     endif
     if (nc_x.eq.1 .and. nc_y.eq.1) then
       radial_contact=.true. !contact based on berg radii can occur
@@ -2645,8 +2672,11 @@ subroutine mts_remove_unused_bergs(bergs)
     if (bergs%hexagonal_icebergs) then
       rdenom=1./(2.*sqrt(3.))
     else
-      !rdenom=1./pi
-      rdenom=1./4.
+      if (bergs%iceberg_bonds_on) then
+        rdenom=1./4.
+      else
+        rdenom=1./pi
+      endif
     endif
   else
     radial_contact=.false.
@@ -4992,8 +5022,11 @@ subroutine update_and_break_bonds(bergs)
   if (bergs%hexagonal_icebergs) then
     rdenom=1./(2.*sqrt(3.))
   else
-    !rdenom=1./pi
-    rdenom=1./4.
+    if (bergs%iceberg_bonds_on) then
+      rdenom=1./4.
+    else
+      rdenom=1./pi
+    endif
   endif
 
   grd=>bergs%grd

From 8c92a8cea20a1ea0522d8bb85a6fe6c38f465eb2 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Wed, 5 May 2021 15:43:45 -0400
Subject: [PATCH 301/361] A few fixes to displace_fl_bergs to ensure new child
 berg is calved onto the computational domain. Added testing of the option to
 convert footloose bits to a new berg upon accumulating enough mass.

---
 src/icebergs.F90                       | 30 ++++++++++++++------------
 tests/footloose_no_bond_test/input.nml |  4 +++-
 2 files changed, 19 insertions(+), 15 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 9cfba76..526eaba 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -2554,12 +2554,12 @@ subroutine footloose_calving(bergs, time)
   type(iceberg), pointer :: this
   type(icebergs_gridded), pointer :: grd
   type(bond), pointer :: current_bond
-  real, save :: N_max, youngs, poisson, l_c, lw_c, B_c, exp_nlambda
+  real, save :: N_max, youngs, poisson, l_c, lw_c, B_c, exp_nlambda, rn
   type(randomNumberStream),save :: rns ! Random numbers for stochastic tidal parameterization
   logical, save :: Visited=.false.
   integer :: grdi, grdj
   integer, dimension(8) :: seed
-  real :: T, W, L, N_bonds, Ln, rn
+  real :: T, W, L, N_bonds, Ln
   real :: IC, max_k, k, Lr_fl, l_w, l_b, pu
   real :: fl_disp_x, fl_disp_y, interp_loc, dM_fl_bits
 
@@ -2586,7 +2586,7 @@ subroutine footloose_calving(bergs, time)
     exp_nlambda=exp(-bergs%fl_r) !e^(-r*dt)
     seed = constructSeed(mpp_pe(),mpp_pe(),time) !Seed random numbers for Poisson distribution
     rns = initializeRandomNumberStream(seed)
-
+    call getRandomNumbers(rns, rn)
     Visited=.true.
   endif
 
@@ -2678,6 +2678,7 @@ subroutine footloose_calving(bergs, time)
 
           if (bergs%fl_style.eq.'new_bergs') then
             !calve and track footloose bergs
+            if (bergs%displace_fl_bergs .and. .not. bergs%fl_use_poisson_distribution) call getRandomNumbers(rns, rn)
             call get_footloose_displacement
             call calve_fl_icebergs(bergs,this,k,l_b,fl_disp_x,fl_disp_y)
             bergs%nbergs_calved_fl=bergs%nbergs_calved_fl+1
@@ -2710,6 +2711,7 @@ subroutine footloose_calving(bergs, time)
 
       !Optionally, create a new berg from the FL bits if their mass exceeds a threshold
       if (this%mass_of_fl_bits*this%mass_scaling > bergs%new_berg_from_fl_bits_mass_thres) then
+        if (bergs%displace_fl_bergs .and. .not. bergs%fl_use_poisson_distribution) call getRandomNumbers(rns, rn)
         call get_footloose_displacement
         k=1
         call calve_fl_icebergs(bergs,this,k,l_b,fl_disp_x,fl_disp_y,berg_from_bits=.true.)
@@ -6241,22 +6243,22 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b,fl_disp_x,fl_disp_y,berg_from_bit
   if (displace) then
     cberg%lon = pberg%lon + fl_disp_x
     cberg%lat = pberg%lat + fl_disp_y
-    lres= find_cell_wide(grd, cberg%lon, cberg%lat, cberg%ine, cberg%jne)
+    lres= find_cell(grd, cberg%lon, cberg%lat, cberg%ine, cberg%jne)
 
-    !If new berg is not on current PE, correct it so that it is.
+    !If new berg is not on current PE (computational domain), correct it so that it is.
     if (.not. lres) then
       !The choice of 75% and 25% weighting here is completely arbitrary...
-      if (cberg%lon > grd%lon(grd%ied,grd%jed)) then
-        cberg%lon = 0.75*grd%lon(grd%ied,grd%jed) + 0.25*pberg%lon
-      elseif (cberg%lon < grd%lon(grd%isd,grd%jsd)) then
-        cberg%lon = 0.75*grd%lon(grd%isd,grd%jsd) + 0.25*pberg%lon
+      if (cberg%lon > grd%lon(grd%iec,grd%jec)) then
+        cberg%lon = 0.75*grd%lon(grd%iec,grd%jec) + 0.25*pberg%lon
+      elseif (cberg%lon < grd%lon(grd%isc-1,grd%jsc-1)) then
+        cberg%lon = 0.75*grd%lon(grd%isc-1,grd%jsc-1) + 0.25*pberg%lon
       endif
-      if (cberg%lat > grd%lat(grd%ied,grd%jed)) then
-        cberg%lat = 0.75*grd%lat(grd%ied,grd%jed) + 0.25*pberg%lat
-      elseif (cberg%lat < grd%lat(grd%isd,grd%jsd)) then
-        cberg%lat = 0.75*grd%lat(grd%isd,grd%jsd) + 0.25*pberg%lat
+      if (cberg%lat > grd%lat(grd%iec,grd%jec)) then
+        cberg%lat = 0.75*grd%lat(grd%iec,grd%jec) + 0.25*pberg%lat
+      elseif (cberg%lat < grd%lat(grd%isc-1,grd%jsc-1)) then
+        cberg%lat = 0.75*grd%lat(grd%isc-1,grd%jsc-1) + 0.25*pberg%lat
       endif
-      lres= find_cell_wide(grd, cberg%lon, cberg%lat, cberg%ine, cberg%jne)
+      lres= find_cell(grd, cberg%lon, cberg%lat, cberg%ine, cberg%jne)
       if (.not. lres) call error_mesg('KID, calve_fl_icebergs', &
         'corrected new berg position still not on current PE!', FATAL)
       fl_disp_x=pberg%lon-cberg%lon; fl_disp_y=pberg%lat-cberg%lat
diff --git a/tests/footloose_no_bond_test/input.nml b/tests/footloose_no_bond_test/input.nml
index b1a4600..2813527 100644
--- a/tests/footloose_no_bond_test/input.nml
+++ b/tests/footloose_no_bond_test/input.nml
@@ -30,9 +30,11 @@
 
     fl_r=4        !(4) average number of footloose bergs to calve per fl_r_s seconds
     fl_r_s=86400  !(86400) time in s over which to calve, on average, fl_r footloose bergs
-    displace_fl_bergs=.false. !(T) randomly assign FL berg positions to sides of parent berg
+    displace_fl_bergs=.true. !(T) randomly assign FL berg positions to sides of parent berg
     fl_style='fl_bits' !('new_bergs'). Can also group FL bergs into 'fl_bits'
     fl_melt_as_bergy_bits=.false.!true. !(F) If fl_style==fl_bits, melt the fl_bits as bergy bits
+    new_berg_from_fl_bits_mass_thres=8.e11
+    fl_use_poisson_distribution=.true.!.false.
 
     mts=.false. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
     mts_sub_steps=1 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)

From be72c6c60ad8b11b039b1716b78f1c513e25ad5e Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Wed, 5 May 2021 16:39:33 -0400
Subject: [PATCH 302/361] Small changes involving creating a new berg from FL
 bits once their mass accumulates enough: allow k>1, and modify fl_bits_src on
 grid after calving the new berg so that the FL bits budget is still correct

---
 src/icebergs.F90 | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 526eaba..9548621 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -2713,10 +2713,14 @@ subroutine footloose_calving(bergs, time)
       if (this%mass_of_fl_bits*this%mass_scaling > bergs%new_berg_from_fl_bits_mass_thres) then
         if (bergs%displace_fl_bergs .and. .not. bergs%fl_use_poisson_distribution) call getRandomNumbers(rns, rn)
         call get_footloose_displacement
-        k=1
+        k=floor(this%mass_of_fl_bits*this%mass_scaling/bergs%new_berg_from_fl_bits_mass_thres)
         call calve_fl_icebergs(bergs,this,k,l_b,fl_disp_x,fl_disp_y,berg_from_bits=.true.)
         bergs%nbergs_calved_fl=bergs%nbergs_calved_fl+1
-        this%mass_of_fl_bits=this%mass_of_fl_bits-bergs%new_berg_from_fl_bits_mass_thres/this%mass_scaling
+        this%mass_of_fl_bits=this%mass_of_fl_bits-k*bergs%new_berg_from_fl_bits_mass_thres/this%mass_scaling
+        if (grd%area(grdi,grdj).ne.0.) then
+          grd%fl_bits_src(grdi,grdj)=grd%fl_bits_src(grdi,grdj)-&
+            k*bergs%new_berg_from_fl_bits_mass_thres/(bergs%dt*grd%area(grdi,grdj))
+        endif
       endif
 
       this=>this%next
@@ -6286,7 +6290,7 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b,fl_disp_x,fl_disp_y,berg_from_bit
     call fl_bits_dimensions(bergs,pberg,Lfl,Wfl,Tfl)
     cberg%length = Lfl; cberg%width = Wfl; cberg%thickness = Tfl
     cberg%mass = Tfl * Lfl * Wfl * bergs%rho_bergs
-    cberg%mass_scaling = bergs%new_berg_from_fl_bits_mass_thres/cberg%mass
+    cberg%mass_scaling = k*bergs%new_berg_from_fl_bits_mass_thres/cberg%mass
   else
     cberg%length       = l_b*3.
     cberg%width        = l_b

From e27b158db9dee27380604d4bb9fe0f2169f9fcf3 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Thu, 6 May 2021 18:42:58 -0400
Subject: [PATCH 303/361] -Fixed an error (again) in the calculation for the
 max number of footloose child bergs that can be calved from a parent berg
 over a time step. The previous way was often enforcing one less footloose
 event that it should have, according to England 2020.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Several “minor” changes that ended up requiring widespread modification to the code:
-Added a separate berg variable for bergy bits associated with footloose bits (mass_of_fl_bergy_bits), rather than treating all bergy bits as if they were associated with the parent berg. Footloose bergy bits evolve separately from the regular bergy bits, which is more accurate, and allows bergy bits to be properly redistributed in the case that a portion of footloose bit is converted to new, separately-tracked berg.
-Some changes to spread_mass_across_ocean_cells, needed due to the addition of the mass_of_fl_bergy_bits variable.
-In subroutine thermodynamics, convert footloose bits into a new berg if the parent berg melts first.
-New diagnostic grid variables for: melt_by_class, child vs. parent melt, and footloose melt due to buoyant convection vs. basal melting vs. erosion.
-New, larger, default values for the footloose bits scaling factors (all set to 0.9)
---
 src/icebergs.F90           | 317 ++++++++++++++++++++++++++++++-------
 src/icebergs_framework.F90 |  81 ++++++++--
 src/icebergs_io.F90        |  21 ++-
 3 files changed, 339 insertions(+), 80 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 9548621..50b6935 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -2632,7 +2632,7 @@ subroutine footloose_calving(bergs, time)
           endif
         else
           !non-bonded berg must be larger than 3*(l_b) for FL calving. Set max_k accordingly.
-          max_k = max(floor((L-3*l_b)*W/(3*l_b**2.)),0)
+          max_k = max(ceiling((L-3*l_b)*W/(3*l_b**2.)),0)
         endif
 
         if (max_k==0) then
@@ -2716,7 +2716,6 @@ subroutine footloose_calving(bergs, time)
         k=floor(this%mass_of_fl_bits*this%mass_scaling/bergs%new_berg_from_fl_bits_mass_thres)
         call calve_fl_icebergs(bergs,this,k,l_b,fl_disp_x,fl_disp_y,berg_from_bits=.true.)
         bergs%nbergs_calved_fl=bergs%nbergs_calved_fl+1
-        this%mass_of_fl_bits=this%mass_of_fl_bits-k*bergs%new_berg_from_fl_bits_mass_thres/this%mass_scaling
         if (grd%area(grdi,grdj).ne.0.) then
           grd%fl_bits_src(grdi,grdj)=grd%fl_bits_src(grdi,grdj)-&
             k*bergs%new_berg_from_fl_bits_mass_thres/(bergs%dt*grd%area(grdi,grdj))
@@ -2905,11 +2904,14 @@ subroutine thermodynamics(bergs)
   integer :: i,j, stderrunit
   type(iceberg), pointer :: this, next
   real, parameter :: perday=1./86400.
-  integer :: grdi, grdj
+  integer :: grdi, grdj, k
   real :: SSS !Temporarily here
   ! Footloose bits stuff
-  real :: Lfl, Wfl, Tfl, Mfl, Afl, Me_fl, Mv_fl, Mb_fl, dMfl, nMfl
-  real :: Volfl, Lnfl, Wnfl, Tnfl, nVolfl, nMfl2, dMe_fl
+  real :: Lfl, Wfl, Tfl, Mfl, Afl, Me_fl, Mv_fl, Mb_fl, dMfl
+  real :: Volfl, Lnfl, Wnfl, Tnfl, nVolfl, Mnew1_fl, Mnew2_fl, Mnew_fl
+  real :: dMb_fl, dMv_fl, dMe_fl
+  real :: Mbits_fl, dMbitsE_fl, nMbits_fl, Lbits_fl, Abits_fl, Mbb_fl, dMbitsM_fl
+  real :: prev_mass_of_fl_bits, prev_mass_of_fl_bergy_bits, M_edit, Mscale_edit
 
   ! For convenience
   grd=>bergs%grd
@@ -3055,48 +3057,55 @@ subroutine thermodynamics(bergs)
           Mb_fl=max( 0.58*(dvo**0.8)*(SST+2.0)/(Lfl**0.2), 0.) *perday ! FL bits basal turbulent melting
           Mb_fl=bergs%rho_bergs*Afl*Mb_fl ! in kg/s
           dMfl=min(Mb_fl*bergs%dt,Mfl) ! FL bergy bits mass lost to melting (kg)
-          nMfl=Mfl-dMfl ! remove mass lost to FL bergy bits melt
-          dMe_fl=0.
+          Mnew_fl=Mfl-dMfl ! remove mass lost to FL bergy bits melt
+          dMe_fl=0.; dMb_fl=dMfl; dMv_fl=0.
+          if (Mnew==0.) then ! if parent berg has completely melted then
+            dMfl=Mfl ! instantly melt all of these footloose bits
+            Mnew_fl=0.
+          endif
         else
           Volfl=Lfl*Wfl*Tfl
           !basal turbulent melting
           Mb_fl=max( 0.58*(dvo**0.8)*(SST+4.0)/(Lfl**0.2), 0.) *perday
           Tnfl=max(Tfl-  Mb_fl*bergs%dt,0.) ! new FL thickness (m)
           if (bergs%use_operator_splitting) then
+            !basal turbulent melting, continued
+            nVolfl=Tnfl*Wfl*Lfl ! new volume (m^3)
+            Mnew1_fl=(nVolfl/Volfl)*Mfl ! new mass (kg)
+            dMb_fl=Mfl-Mnew1_fl ! mass lost to basal melting (>0) (kg)
             !buoyant convection
             Lnfl=max(Lfl-Mv_fl*bergs%dt,0.) ! new FL length (m)
             Wnfl=max(Wfl-Mv_fl*bergs%dt,0.) ! new FL width (m)
             nVolfl=Tnfl*Wnfl*Lnfl ! new footloose volume (m^3)
-            nMfl2=(nVolfl/Volfl)*Mfl !new FL mass (kg), after buoyant convection
+            Mnew2_fl=(nVolfl/Volfl)*Mfl !new FL mass (kg), after buoyant convection
+            dMv_fl=Mnew1_fl-Mnew2_fl
             !erosion
             Lnfl=max(Lnfl-Me_fl*bergs%dt,0.) ! new FL length (m)
             Wnfl=max(Wnfl-Me_fl*bergs%dt,0.) ! new FL width (m)
             nVolfl=Tnfl*Wnfl*Lnfl ! new footloose volume (m^3)
-            nMfl=(nVolfl/Volfl)*Mfl !new FL mass (kg), after all melt and erosion
-            dMe_fl=nMfl2-nMfl !FL mass lost to erosion (>0) (kg)
+            Mnew_fl=(nVolfl/Volfl)*Mfl !new FL mass (kg), after all melt and erosion
+            dMe_fl=Mnew2_fl-Mnew_fl !FL mass lost to erosion (>0) (kg)
           else
             Lnfl=max(Lfl-(Mv_fl+Me_fl)*bergs%dt,0.) ! (m)
             Wnfl=max(Wfl-(Mv_fl+Me_fl)*bergs%dt,0.) ! (m)
             nVolfl=Tnfl*Wnfl*Lnfl ! new footloose volume (m^3)
-            nMfl=(nVolfl/Volfl)*Mfl ! new footloose mass (kg)
-            dMe_fl=(Mfl/Volfl)*(Tfl*(Wfl+Lfl))*Me_fl*bergs%dt !approx. FL mass loss to erosion
+            Mnew_fl=(nVolfl/Volfl)*Mfl ! new footloose mass (kg)
+            dMb_fl=(Mfl/Volfl)*(Wfl*Lfl)*Mb_fl*bergs%dt       !approx. FL mass loss to basal melting (kg)
+            dMe_fl=(Mfl/Volfl)*(Tfl*(Wfl+Lfl))*Me_fl*bergs%dt !approx. FL mass loss to erosion (kg)
+            dMv_fl=(Mfl/Volfl)*(Tfl*(Wfl+Lfl))*Mv_fl*bergs%dt !approx. FL mass loss to buoyant convection (kg)
           endif
-          dMfl=Mfl-nMfl ! total footloose mass lost to all erosion and melting (>0) (kg)
-          if (.not. bergs%fl_bits_erosion_to_bergy_bits) dMe_fl=0.
-        endif
-        if (Mnew==0.) then ! if parent berg has completely melted then
-          dMfl= Mfl ! instantly melt all the footloose bergy bits
-          nMfl=0.
+          dMfl=Mfl-Mnew_fl ! total footloose mass lost to all erosion and melting (>0) (kg)
         endif
       else
-        dMfl=0.; dMe_fl=0.
-        nMfl=this%mass_of_fl_bits ! retain previous value incase non-zero
+        dMfl=0.; dMb_fl=0.; dMv_fl=0.; dMe_fl=0.
+        Mnew_fl=this%mass_of_fl_bits ! retain previous value incase non-zero
       endif
 
       ! Bergy bits
       if (bergs%bergy_bit_erosion_fraction>0.) then
+        !Parent Berg bergy bits
         Mbits=this%mass_of_bits ! mass of bergy bits (kg)
-        dMbitsE=bergs%bergy_bit_erosion_fraction*(dMe+dMe_fl) ! change in mass of bits (kg)
+        dMbitsE=bergs%bergy_bit_erosion_fraction*dMe ! change in mass of bits (kg)
         nMbits=Mbits+dMbitsE ! add new bergy bits to mass (kg)
         Lbits=min(L,W,T,40.) ! assume bergy bits are smallest dimension or 40 meters
         Abits=(Mbits/bergs%rho_bergs)/Lbits ! Effective bottom area (assuming T=Lbits)
@@ -3109,39 +3118,123 @@ subroutine thermodynamics(bergs)
           dMbitsM=dMbitsM+nMbits ! instantly melt all the bergy bits
           nMbits=0.
         endif
+
+        !Footloose bits bergy bits
+        if (this%mass_of_fl_bits>0.) then
+          Mbits_fl=this%mass_of_fl_bergy_bits ! mass of footloose bergy bits (kg)
+          dMbitsE_fl=bergs%bergy_bit_erosion_fraction*dMe_fl ! change in mass of bits (kg)
+          nMbits_fl=Mbits_fl+dMbitsE_fl ! add new bergy bits to mass (kg)
+          Lbits_fl=min(Lfl,Wfl,Tfl,40.) ! assume bergy bits are smallest dimension or 40 meters
+          Abits_fl=(Mbits_fl/bergs%rho_bergs)/Lbits_fl ! Effective bottom area (assuming T=Lbits)
+          Mbb_fl=max( 0.58*(dvo**0.8)*(SST+2.0)/(Lbits_fl**0.2), 0.) &! Basal turbulent melting (for bits)
+            *perday ! convert to m/s
+          Mbb_fl=bergs%rho_bergs*Abits_fl*Mbb_fl ! in kg/s
+          dMbitsM_fl=min(Mbb_fl*bergs%dt,nMbits_fl) ! bergy bits mass lost to melting (kg)
+          nMbits_fl=nMbits_fl-dMbitsM_fl ! remove mass lost to bergy bits melt
+          if (Mnew_fl==0.) then ! if FL berg associated with these bits has completely melted then
+            dMbitsM_fl=dMbitsM_fl+nMbits_fl ! instantly melt all the bergy bits
+            nMbits_fl=0.
+          endif
+        else
+          dMbitsE_fl=0.; dMbitsM_fl=0.; Abits_fl=0.; nMbits_fl=0.
+        endif
       else
-        Abits=0.
-        dMbitsE=0.
-        dMbitsM=0.
-        nMbits=this%mass_of_bits ! retain previous value incase non-zero
+        ! retain previous value incase non-zero
+        Abits=0.;    dMbitsE=0.;    dMbitsM=0.;    nMbits=this%mass_of_bits
+        Abits_fl=0.; dMbitsE_fl=0.; dMbitsM_fl=0.; nMbits_fl=this%mass_of_fl_bergy_bits
       endif
 
       ! Add melting to the grid and field diagnostics
       if (grd%area(i,j).ne.0.) then
-        melt=(dM+dMfl-(dMbitsE-dMbitsM))/bergs%dt ! kg/s
+
+        melt=(dM-(dMbitsE-dMbitsM)+dMfl-(dMbitsE_fl-dMbitsM_fl))/bergs%dt ! kg/s
         grd%floating_melt(i,j)=grd%floating_melt(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+
+        if (grd%id_melt_by_class>0) then
+          if (this%lat<0.) then
+            k=minloc(abs(bergs%initial_mass_s-this%start_mass),1)
+          else
+            k=minloc(abs(bergs%initial_mass_n-this%start_mass),1)
+          endif
+          grd%melt_by_class(i,j,k)=grd%melt_by_class(i,j,k)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+        endif
+
         melt=melt*this%heat_density ! kg/s x J/kg = J/s
         grd%calving_hflx(i,j)=grd%calving_hflx(i,j)+melt/grd%area(i,j)*this%mass_scaling ! W/m2
         bergs%net_heat_to_ocean=bergs%net_heat_to_ocean+melt*this%mass_scaling*bergs%dt ! J
+
         melt=dM/bergs%dt ! kg/s
         grd%berg_melt(i,j)=grd%berg_melt(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
-        melt=dMbitsE/bergs%dt ! mass flux into bergy bits in kg/s
+
+        melt=(dMbitsE+dMbitsE_fl)/bergs%dt ! mass flux into bergy bits in kg/s
         grd%bergy_src(i,j)=grd%bergy_src(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
-        melt=dMbitsM/bergs%dt ! melt rate of bergy bits in kg/s
+
+        melt=(dMbitsM+dMbitsM_fl)/bergs%dt ! melt rate of bergy bits in kg/s
         grd%bergy_melt(i,j)=grd%bergy_melt(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+
         melt=dMfl/bergs%dt ! melt+erosion rate of fl bits in kg/s
         grd%fl_bits_melt(i,j)=grd%fl_bits_melt(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
-        if(grd%id_melt_buoy>0) then
-          melt=dMb/bergs%dt ! melt rate due to buoyancy term in kg/s
-          grd%melt_buoy(i,j)=grd%melt_buoy(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
-        endif
-        if(grd%id_melt_eros>0) then
-          melt=dMe/bergs%dt ! erosion rate in kg/s
-          grd%melt_eros(i,j)=grd%melt_eros(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+
+        if (this%fl_k>=0) then
+          !Non-footloose berg:
+          if(grd%id_fl_parent_melt>0) then
+            melt=(dM-(dMbitsE-dMbitsM))/bergs%dt !total melt of the "parent" berg
+            grd%fl_parent_melt(i,j)=grd%fl_parent_melt(i,j)+melt/grd%area(i,j)*this%mass_scaling !kg/m2/s
+          endif
+          if(grd%id_fl_child_melt>0) then
+            melt=(dMfl-(dMbitsE_fl-dMbitsM_fl))/bergs%dt !total melt of the "child" FL bits
+            grd%fl_child_melt(i,j)=grd%fl_child_melt(i,j)+melt/grd%area(i,j)*this%mass_scaling !kg/m2/s
+          endif
+          if(grd%id_melt_buoy>0) then
+            melt=dMb/bergs%dt ! melt rate due to buoyancy term in kg/s
+            grd%melt_buoy(i,j)=grd%melt_buoy(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+          endif
+          if(grd%id_melt_eros>0) then
+            melt=dMe/bergs%dt ! erosion rate in kg/s
+            grd%melt_eros(i,j)=grd%melt_eros(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+          endif
+          if(grd%id_melt_conv>0) then
+            melt=dMv/bergs%dt ! melt rate due to convection term in kg/s
+            grd%melt_conv(i,j)=grd%melt_conv(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+          endif
+        else
+          !Independently-tracked footloose "child" berg:
+          if(grd%id_fl_child_melt>0) then
+            melt=(dM-(dMbitsE-dMbitsM))/bergs%dt !total melt of the "child" berg (here, melts like a parent berg)
+            grd%fl_child_melt(i,j)=grd%fl_child_melt(i,j)+melt/grd%area(i,j)*this%mass_scaling !kg/m2/s
+          endif
+          if(grd%id_melt_buoy>0) then
+            melt=dMb/bergs%dt ! melt rate due to buoyancy term in kg/s
+            grd%melt_buoy_fl(i,j)=grd%melt_buoy_fl(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+          endif
+          if(grd%id_melt_eros>0) then
+            melt=dMe/bergs%dt ! erosion rate in kg/s
+            grd%melt_eros_fl(i,j)=grd%melt_eros_fl(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+          endif
+          if(grd%id_melt_conv>0) then
+            melt=dMv/bergs%dt ! melt rate due to convection term in kg/s
+            grd%melt_conv_fl(i,j)=grd%melt_conv_fl(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+          endif
         endif
-        if(grd%id_melt_conv>0) then
-          melt=dMv/bergs%dt ! melt rate due to convection term in kg/s
-          grd%melt_conv(i,j)=grd%melt_conv(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+
+        if (dMfl>0) then
+          ! Footloose bit:
+          if(grd%id_fl_child_melt>0) then
+            melt=(dM-(dMbitsE-dMbitsM))/bergs%dt !total melt of the "child" FL bits
+            grd%fl_child_melt(i,j)=grd%fl_child_melt(i,j)+melt/grd%area(i,j)*this%mass_scaling !kg/m2/s
+          endif
+          if(grd%id_melt_buoy>0) then
+            melt=dMb_fl/bergs%dt ! melt rate due to buoyancy term in kg/s
+            grd%melt_buoy_fl(i,j)=grd%melt_buoy_fl(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+          endif
+          if(grd%id_melt_eros>0) then
+            melt=dMe_fl/bergs%dt ! erosion rate in kg/s
+            grd%melt_eros_fl(i,j)=grd%melt_eros_fl(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+          endif
+          if(grd%id_melt_conv>0) then
+            melt=dMv_fl/bergs%dt ! melt rate due to convection term in kg/s
+            grd%melt_conv_fl(i,j)=grd%melt_conv_fl(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+          endif
         endif
       else
         stderrunit = stderr()
@@ -3162,14 +3255,32 @@ subroutine thermodynamics(bergs)
         !the thermodynamics are applied.
         !If the spread_mass is being used to calculate melt, we calculate this
         !before reseting
+
+        !temporarily update the iceberg's footloose and footloose bergy bits masses, which are added
+        !to the total mass within subroutine spread_mass_across_ocean_cells:
+        prev_mass_of_fl_bits = this%mass_of_fl_bits; prev_mass_of_fl_bergy_bits    = this%mass_of_fl_bergy_bits
+        this%mass_of_fl_bits = Mnew_fl;              this%mass_of_fl_bergy_bits = nMbits_fl
+
         if (bergs%find_melt_using_spread_mass) then
           if (Mnew>0.) then !If the berg still exists
-            call spread_mass_across_ocean_cells(bergs,this, i, j, this%xi, this%yj,Mnew , nMbits+nMfl, this%mass_scaling, Ln*Wn+nMfl/(Tn*bergs%rho_bergs),  Tn)
+            call spread_mass_across_ocean_cells(bergs,this, i, j, this%xi, this%yj, Mnew, &
+              nMbits, this%mass_scaling, Ln*Wn,  Tn, addfootloose=.true.)
+          elseif (Mnew_fl>0.) then
+            !In the unlikely case that the parent berg has melted completely, but footloose bits still
+            !exist, spread mass using footloose in place of the parent berg.
+            M_edit=Lnfl*Wnfl*Tnfl*bergs%rho_bergs
+            Mscale_edit = Mnew_fl*this%mass_scaling/M_edit
+            call spread_mass_across_ocean_cells(bergs,this, i, j, this%xi, this%yj, M_edit, &
+              nMbits, Mscale_edit, Lnfl*Wnfl,  Tnfl, addfootloose=.false.)
           endif
         endif
         !Reset all the values
+        this%mass_of_fl_bits=prev_mass_of_fl_bits
+        this%mass_of_fl_bergy_bits=prev_mass_of_fl_bergy_bits
         Mnew=this%mass
         nMbits=this%mass_of_bits
+        Mnew_fl=this%mass_of_fl_bits
+        nMbits_fl=this%mass_of_fl_bergy_bits
         Tn=this%thickness
         Wn=this%width
         Ln=this%length
@@ -3177,14 +3288,18 @@ subroutine thermodynamics(bergs)
           Mbits=this%mass_of_bits ! mass of bergy bits (kg)
           Lbits=min(L,W,T,40.) ! assume bergy bits are smallest dimension or 40 meters
           Abits=(Mbits/bergs%rho_bergs)/Lbits ! Effective bottom area (assuming T=Lbits)
+          if (this%mass_of_fl_bits>0.) then
+            Mbits_fl=this%mass_of_fl_bergy_bits ! mass of footloose bergy bits (kg)
+            Lbits_fl=min(Lfl,Wfl,Tfl,40.) ! assume bergy bits are smallest dimension or 40 meters
+            Abits_fl=(Mbits_fl/bergs%rho_bergs)/Lbits_fl ! Effective bottom area (assuming T=Lbits)
+          endif
         endif
-        nMfl=this%mass_of_fl_bits
-        Mfl=this%mass_of_fl_bits
       else
         ! Store the new state of iceberg (with L>W)
         this%mass=Mnew
         this%mass_of_bits=nMbits
-        this%mass_of_fl_bits=nMfl
+        this%mass_of_fl_bits=Mnew_fl
+        this%mass_of_fl_bergy_bits=nMbits_fl
         this%thickness=Tn
         this%width=min(Wn,Ln)
         this%length=max(Wn,Ln)
@@ -3192,9 +3307,26 @@ subroutine thermodynamics(bergs)
       next=>this%next
 
       ! Did berg completely melt?
-      if (Mnew<=0.) then ! Delete the berg
-        if (.not. bergs%debug_write) call move_trajectory(bergs, this)
-        call delete_iceberg_from_list(bergs%list(grdi,grdj)%first, this)
+      if (Mnew<=0.) then
+        if (Mnew_fl>0) then
+          ! The parent berg is melted, but the associated footloose bergs are not.
+          ! Replace the parent with the footloose
+          bergs%nbergs_calved_fl=bergs%nbergs_calved_fl+1
+          this%mass=Lnfl*Wnfl*Tnfl*bergs%rho_bergs
+          this%length=Lnfl; this%width=Wnfl; this%thickness=Tnfl
+          nMbits_fl=nMbits_fl*this%mass_scaling
+          this%mass_scaling = Mnew_fl*this%mass_scaling/this%mass
+          this%mass_of_bits=nMbits_fl/this%mass_scaling
+          this%mass_of_fl_bits=0.
+          this%mass_of_fl_bergy_bits=0.
+          this%fl_k=-1.
+          this%start_year=bergs%current_year
+          this%start_day=bergs%current_yearday
+        else
+          ! Delete the berg
+          if (.not. bergs%debug_write) call move_trajectory(bergs, this)
+          call delete_iceberg_from_list(bergs%list(grdi,grdj)%first, this)
+        endif
         bergs%nbergs_melted=bergs%nbergs_melted+1
       endif
       this=>next
@@ -3797,7 +3929,7 @@ subroutine find_orientation_using_iceberg_bonds(grd, berg, orientation)
 end subroutine find_orientation_using_iceberg_bonds
 
 !> Spread mass of a berg around cells centered on i,j
-subroutine spread_mass_across_ocean_cells(bergs, berg, i, j, x, y, Mberg, Mbits, scaling, Area, Tn)
+subroutine spread_mass_across_ocean_cells(bergs, berg, i, j, x, y, Mberg, Mbits, scaling, Area, Tn, addfootloose)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
   type(iceberg), pointer :: berg !< Berg whose mass is being considered
@@ -3806,10 +3938,11 @@ subroutine spread_mass_across_ocean_cells(bergs, berg, i, j, x, y, Mberg, Mbits,
   real, intent(in) :: x !< Longitude of berg (degree E)
   real, intent(in) :: y !< Latitude of berg (degree N)
   real, intent(in) :: Mberg !< Mass of berg (kg)
-  real, intent(in) :: Mbits !< Combined mass of bergy and footloose bits (kg)
+  real, intent(in) :: Mbits !< Combined mass of bergy and footloose bergy bits (kg)
   real, intent(in) :: scaling !< Multiplier to scale mass (nondim)
   real, intent(in) :: Area !< Area of berg (m2)
   real, intent(in) :: Tn !< Thickness of berg (m)
+  logical, intent(in) :: addfootloose !< Add contributions of footloose bergs
   ! Local variables
   type(icebergs_gridded), pointer :: grd
   real :: xL, xC, xR, yD, yC, yU, Mass, L
@@ -3824,6 +3957,7 @@ subroutine spread_mass_across_ocean_cells(bergs, berg, i, j, x, y, Mberg, Mbits,
   integer :: stderrunit
   logical :: debug
   real :: orientation, Mass_berg
+  real :: Mfl,Lfl,Wfl,Tfl,Mbits_fl
 
   ! Get the stderr unit number
   stderrunit = stderr()
@@ -3832,14 +3966,29 @@ subroutine spread_mass_across_ocean_cells(bergs, berg, i, j, x, y, Mberg, Mbits,
   grd=>bergs%grd
   Mass_berg=Mberg
 
+  if (addfootloose) then
+    Mfl=berg%mass_of_fl_bits
+    Mbits_fl=berg%mass_of_fl_bergy_bits
+  else
+    Mfl=0.
+    Mbits_fl=0.
+  endif
+
   ! Trimming icebergs to account for grounded fraction.
   if (bergs%grounding_fraction>0.) then
     Hocean=bergs%grounding_fraction*(grd%ocean_depth(i,j)+grd%ssh(i,j))
     Dn=(bergs%rho_bergs/rho_seawater)*Tn ! re-calculate draught (keel depth)
-    if (Dn>Hocean) Mass_berg=Mberg*min(1.,Hocean/Dn)
+    if (Dn>Hocean) Mass_berg=Mass_berg*min(1.,Hocean/Dn)
+    if (Mfl>0. .and. addfootloose) then
+      call fl_bits_dimensions(bergs,berg,Lfl,Wfl,Tfl)
+      Dn=(bergs%rho_bergs/rho_seawater)*Tfl ! re-calculate draught (keel depth) for FL bits
+      if (Dn>Hocean) Mfl=Mfl*min(1.,Hocean/Dn)
+    endif
   endif
 
-  Mass=(Mass_berg+Mbits)*scaling
+  Mass_berg=Mass_berg+Mfl
+
+  Mass=(Mass_berg+Mbits+Mbits_fl)*scaling
   ! This line attempts to "clip" the weight felt by the ocean. The concept of
   ! clipping is non-physical and this step should be replaced by grounding.
   if (grd%clipping_depth>0.) Mass=min(Mass,grd%clipping_depth*grd%area(i,j)*rho_seawater)
@@ -4836,8 +4985,8 @@ subroutine calculate_mass_on_ocean(bergs, with_diagnostics)
 
           !Increasing Mass on ocean
           if ((bergs%add_weight_to_ocean .and. .not. bergs%time_average_weight) .or.(bergs%find_melt_using_spread_mass)) then
-            call spread_mass_across_ocean_cells(bergs, berg, berg%ine, berg%jne, berg%xi, berg%yj, berg%mass,berg%mass_of_bits+berg%mass_of_fl_bits, berg%mass_scaling, &
-              berg%length*berg%width+berg%mass_of_fl_bits/(berg%thickness*bergs%rho_bergs), berg%thickness)
+            call spread_mass_across_ocean_cells(bergs, berg, berg%ine, berg%jne, berg%xi, berg%yj, berg%mass,&
+              berg%mass_of_bits, berg%mass_scaling, berg%length*berg%width, berg%thickness,addfootloose=.true.)
           endif
 
           !Calculated some iceberg diagnositcs
@@ -4860,7 +5009,7 @@ subroutine calculate_sum_over_bergs_diagnositcs(bergs, grd, berg, i, j)
   integer, intent(in) :: i !< i-index of cell containing berg
   integer, intent(in) :: j !< j-index of cell containing berg
   ! Local variables
-  real ::  Abits, Abits_fl, Lbits, Mbits
+  real ::  Abits, Abits_fl, Abits_fl_bergy, Lbits, Mbits
   real :: L_fl,W_fl,T_fl
 
   !Virtual area diagnostic
@@ -4874,10 +5023,18 @@ subroutine calculate_sum_over_bergs_diagnositcs(bergs, grd, berg, i, j)
     if (bergs%fl_style.eq.'fl_bits') then
       call fl_bits_dimensions(bergs,berg,L_fl,W_fl,T_fl)
       Abits_fl=(berg%mass_of_fl_bits/bergs%rho_bergs)/T_fl ! Effective bottom area
+      if (bergs%bergy_bit_erosion_fraction>0.) then
+        Lbits=min(L_fl,W_fl,T_fl,40.)
+        Abits_fl_bergy=(berg%mass_of_fl_bergy_bits/bergs%rho_bergs)/Lbits
+      else
+        Abits_fl_bergy=0.0
+      endif
     else
       Abits_fl=0.0
+      Abits_fl_bergy=0.0
     endif
-    grd%virtual_area(i,j)=grd%virtual_area(i,j)+(berg%width*berg%length+Abits+Abits_fl)*berg%mass_scaling ! m^2
+    grd%virtual_area(i,j)=grd%virtual_area(i,j)+&
+      (berg%width*berg%length+Abits+Abits_fl+Abits_fl_bergy)*berg%mass_scaling ! m^2
   endif
 
   !Mass diagnostic (also used in u_iceberg, v_iceberg
@@ -4897,6 +5054,10 @@ subroutine calculate_sum_over_bergs_diagnositcs(bergs, grd, berg, i, j)
   !Mass of footloose bits
   if (grd%id_fl_bits_mass>0 .or. bergs%add_weight_to_ocean)&
     & grd%fl_bits_mass(i,j)=grd%fl_bits_mass(i,j)+berg%mass_of_fl_bits/grd%area(i,j)*berg%mass_scaling ! kg/m2
+
+  !Mass of footloose bits
+  if (grd%id_fl_bergy_bits_mass>0 .or. bergs%add_weight_to_ocean)&
+    & grd%fl_bergy_bits_mass(i,j)=grd%fl_bergy_bits_mass(i,j)+berg%mass_of_fl_bergy_bits/grd%area(i,j)*berg%mass_scaling ! kg/m2
 end subroutine calculate_sum_over_bergs_diagnositcs
 
 !> The main driver the steps updates icebergs
@@ -4962,6 +5123,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   grd%fl_bits_src(:,:)=0.
   grd%fl_bits_melt(:,:)=0.
   grd%fl_bits_mass(:,:)=0.
+  grd%fl_bergy_bits_mass(:,:)=0.
   grd%spread_mass_old(:,:)=0.
   !grd%spread_mass(:,:)=0.  !Don't zero this out yet, because we can first use this an add it onto the SSH
   grd%spread_area(:,:)=0.
@@ -4972,6 +5134,12 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   grd%ustar_iceberg(:,:)=0.
   grd%mass(:,:)=0.
   grd%virtual_area(:,:)=0.
+  grd%melt_by_class(:,:,:)=0.
+  grd%melt_buoy_fl(:,:)=0.
+  grd%melt_eros_fl(:,:)=0.
+  grd%melt_conv_fl(:,:)=0.
+  grd%fl_parent_melt(:,:)=0.
+  grd%fl_child_melt(:,:)=0.
 
   !Initializing _on_ocean_fields
   grd%mass_on_ocean(:,:,:)=0. ;   grd%area_on_ocean(:,:,:)=0.
@@ -5393,6 +5561,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     lerr=send_data(grd%id_fl_bits_melt, grd%fl_bits_melt(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   if (grd%id_fl_bits_mass>0) &
     lerr=send_data(grd%id_fl_bits_mass, grd%fl_bits_mass(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_fl_bergy_bits_mass>0) &
+    lerr=send_data(grd%id_fl_bergy_bits_mass, grd%fl_bergy_bits_mass(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   if (grd%id_spread_mass>0) &
     lerr=send_data(grd%id_spread_mass, grd%spread_mass(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   if (grd%id_spread_area>0) &
@@ -5423,6 +5593,18 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     lerr=send_data(grd%id_fax, tauxa(:,:), Time)
   if (grd%id_fay>0) &
     lerr=send_data(grd%id_fay, tauya(:,:), Time)
+  if (grd%id_melt_by_class<0) &
+    lerr=send_data(grd%id_melt_by_class, grd%melt_by_class(grd%isc:grd%iec,grd%jsc:grd%jec,:), Time)
+  if (grd%id_melt_buoy_fl>0) &
+    lerr=send_data(grd%id_melt_buoy_fl, grd%melt_buoy_fl(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_melt_eros_fl>0) &
+    lerr=send_data(grd%id_melt_eros_fl, grd%melt_eros_fl(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_melt_conv_fl>0) &
+    lerr=send_data(grd%id_melt_conv_fl, grd%melt_conv_fl(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_fl_parent_melt>0) &
+    lerr=send_data(grd%id_fl_parent_melt, grd%fl_parent_melt(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
+  if (grd%id_fl_child_melt>0) &
+    lerr=send_data(grd%id_fl_child_melt, grd%fl_child_melt(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
   if (grd%id_count>0) then
     allocate( iCount(grd%isc:grd%iec,grd%jsc:grd%jec) ); iCount(:,:)=0
     do j = grd%jsc, grd%jec ; do i = grd%isc, grd%iec
@@ -6123,6 +6305,7 @@ subroutine calve_icebergs(bergs)
           newberg%mass_scaling=mass_scaling
           newberg%mass_of_bits=0.
           newberg%mass_of_fl_bits=0.
+          newberg%mass_of_fl_bergy_bits=0.
           newberg%halo_berg=0.
           newberg%static_berg=0.
           newberg%heat_density=grd%stored_heat(i,j)/grd%stored_ice(i,j,k) ! This is in J/kg
@@ -6228,7 +6411,7 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b,fl_disp_x,fl_disp_y,berg_from_bit
   type(iceberg) :: cberg ! The new child berg
   type(icebergs_gridded), pointer :: grd
   logical :: lres, displace
-  real :: Lfl, Wfl, Tfl
+  real :: Lfl, Wfl, Tfl, percent_fl
 
   ! For convenience
   grd=>bergs%grd
@@ -6291,12 +6474,18 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b,fl_disp_x,fl_disp_y,berg_from_bit
     cberg%length = Lfl; cberg%width = Wfl; cberg%thickness = Tfl
     cberg%mass = Tfl * Lfl * Wfl * bergs%rho_bergs
     cberg%mass_scaling = k*bergs%new_berg_from_fl_bits_mass_thres/cberg%mass
+    !the new berg will take a fraction of the parent berg footloose bergy bits mass as bergy bits mass
+    percent_fl = (cberg%mass*cberg%mass_scaling)/(pberg%mass_of_fl_bits*pberg%mass_scaling)
+    cberg%mass_of_bits = (percent_fl * pberg%mass_of_fl_bergy_bits*pberg%mass_scaling)/cberg%mass_scaling
+    pberg%mass_of_fl_bergy_bits = (1-percent_fl)*pberg%mass_of_fl_bergy_bits
+    pberg%mass_of_fl_bits=pberg%mass_of_fl_bits-k*bergs%new_berg_from_fl_bits_mass_thres/pberg%mass_scaling
   else
     cberg%length       = l_b*3.
     cberg%width        = l_b
     cberg%thickness    = pberg%thickness
     cberg%mass         = cberg%width * cberg%length * pberg%thickness * bergs%rho_bergs
     cberg%mass_scaling = pberg%mass_scaling * k !k is the number of icebergs cberg represents
+    cberg%mass_of_bits = 0.0
   endif
 
   cberg%start_lon    = cberg%lon
@@ -6307,8 +6496,8 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b,fl_disp_x,fl_disp_y,berg_from_bit
   cberg%lat_old      = pberg%lat_old  + fl_disp_y
   cberg%start_day    = bergs%current_yearday
   cberg%start_mass   = pberg%mass !used for tracking the different size classes calved from grounded ice, so set to pberg.
-  cberg%mass_of_bits = 0.0
   cberg%mass_of_fl_bits = 0.0
+  cberg%mass_of_fl_bergy_bits = 0.0
   cberg%fl_k         = -1.0
   cberg%start_year   = bergs%current_year
   cberg%id           = generate_id(grd, pberg%ine, pberg%jne)
@@ -7149,7 +7338,8 @@ subroutine verlet_stepping(bergs,berg, axn, ayn, bxn, byn, uveln, vveln, rx, ry)
   ! Note, the mass scaling is equal to 1 (rather than 0.25 as in RK), since
   ! this is only called once in Verlet stepping.
   if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits+berg%mass_of_fl_bits, 1.0*berg%mass_scaling,berg%length*berg%width+berg%mass_of_fl_bits/(berg%thickness*bergs%rho_bergs), berg%thickness)
+    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 1.0*berg%mass_scaling,&
+    berg%length*berg%width, berg%thickness, addfootloose=.true.)
 
   ! Calling the acceleration   (note that the velocity is converted to u_star inside the accel script)
   call accel(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, ax1, ay1, axn, ayn, bxn, byn) !axn, ayn, bxn, byn - Added by Alon
@@ -7279,7 +7469,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
   if ((berg%lat>89.) .and. (bergs%grd%grid_is_latlon)) on_tangential_plane=.true.
   i1=i;j1=j
   if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits+berg%mass_of_fl_bits, 0.25*berg%mass_scaling,berg%length*berg%width+berg%mass_of_fl_bits/(berg%thickness*bergs%rho_bergs), berg%thickness)
+    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, berg%thickness, addfootloose=.true.)
 
   ! Loading past accelerations - Alon
   axn=berg%axn; ayn=berg%ayn !Alon
@@ -7317,7 +7507,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
   call adjust_index_and_ground(grd, lon2, lat2, uvel2, vvel2, i, j, xi, yj, bounced, error_flag, berg%id)
   i2=i; j2=j
   if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits+berg%mass_of_fl_bits, 0.25*berg%mass_scaling,berg%length*berg%width+berg%mass_of_fl_bits/(berg%thickness*bergs%rho_bergs), berg%thickness)
+    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, berg%thickness, addfootloose=.true.)
   ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon2,lat2,x2,y2)
   if (.not.error_flag) then
     if (debug .and. .not. is_point_in_cell(bergs%grd, lon2, lat2, i, j)) error_flag=.true.
@@ -7374,7 +7564,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
   call adjust_index_and_ground(grd, lon3, lat3, uvel3, vvel3, i, j, xi, yj, bounced, error_flag, berg%id)
   i3=i; j3=j
   if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits+berg%mass_of_fl_bits, 0.25*berg%mass_scaling,berg%length*berg%width+berg%mass_of_fl_bits/(berg%thickness*bergs%rho_bergs), berg%thickness)
+    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, berg%thickness,addfootloose=.true.)
   ! if (bounced.and.on_tangential_plane) call rotpos_to_tang(lon3,lat3,x3,y3)
   if (.not.error_flag) then
     if (debug .and. .not. is_point_in_cell(bergs%grd, lon3, lat3, i, j)) error_flag=.true.
@@ -7504,7 +7694,7 @@ subroutine Runge_Kutta_stepping(bergs, berg, axn, ayn, bxn, byn, uveln, vveln, l
   i=i1;j=j1;xi=berg%xi;yj=berg%yj
   call adjust_index_and_ground(grd, lonn, latn, uveln, vveln, i, j, xi, yj, bounced, error_flag, berg%id)
   if (bergs%add_weight_to_ocean .and. bergs%time_average_weight) &
-    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits+berg%mass_of_fl_bits, 0.25*berg%mass_scaling,berg%length*berg%width+berg%mass_of_fl_bits/(berg%thickness*bergs%rho_bergs), berg%thickness)
+    call spread_mass_across_ocean_cells(bergs, berg, i, j, xi, yj, berg%mass, berg%mass_of_bits, 0.25*berg%mass_scaling,berg%length*berg%width, berg%thickness, addfootloose=.true.)
 
   if (.not.error_flag) then
     if (.not. is_point_in_cell(bergs%grd, lonn, latn, i, j)) error_flag=.true.
@@ -8083,6 +8273,7 @@ subroutine icebergs_end(bergs)
   deallocate(bergs%grd%fl_bits_src)
   deallocate(bergs%grd%fl_bits_melt)
   deallocate(bergs%grd%fl_bits_mass)
+  deallocate(bergs%grd%fl_bergy_bits_mass)
   deallocate(bergs%grd%spread_mass)
   deallocate(bergs%grd%spread_mass_old)
   deallocate(bergs%grd%spread_area)
@@ -8107,6 +8298,12 @@ subroutine icebergs_end(bergs)
   deallocate(bergs%grd%sss)
   deallocate(bergs%grd%cn)
   deallocate(bergs%grd%hi)
+  deallocate(bergs%grd%melt_by_class)
+  deallocate(bergs%grd%melt_buoy_fl)
+  deallocate(bergs%grd%melt_eros_fl)
+  deallocate(bergs%grd%melt_conv_fl)
+  deallocate(bergs%grd%fl_parent_melt)
+  deallocate(bergs%grd%fl_child_melt)
   deallocate(bergs%grd%domain)
   deallocate(bergs%grd)
   deallocate(bergs%initial_mass_s)
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 5ee7791..e757601 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -18,8 +18,8 @@ module ice_bergs_framework
 
 implicit none ; private
 
-integer :: buffer_width=35 ! This should be a parameter
-integer :: buffer_width_traj=37 ! This should be a parameter
+integer :: buffer_width=36 ! This should be a parameter
+integer :: buffer_width_traj=38 ! This should be a parameter
 integer :: buffer_width_bond_traj=11 !This should be a parameter
 integer, parameter :: nclasses=10 ! Number of ice bergs classes
 
@@ -145,10 +145,16 @@ module ice_bergs_framework
   real, dimension(:,:), pointer :: sss=>null() !< Sea surface salinity (psu)
   real, dimension(:,:), pointer :: cn=>null() !< Sea-ice concentration (0 to 1)
   real, dimension(:,:), pointer :: hi=>null() !< Sea-ice thickness (m)
+  real, dimension(:,:,:), pointer :: melt_by_class=>null() !< Total icebergs melt rate by mass class (kg/s/m^2)
+  real, dimension(:,:), pointer :: melt_buoy_fl=>null() !< Footloose bergs buoyancy component of melting rate (kg/s/m^2)
+  real, dimension(:,:), pointer :: melt_eros_fl=>null() !< Footloose bergs erosion component of melting rate (kg/s/m^2)
+  real, dimension(:,:), pointer :: melt_conv_fl=>null() !< Footloose bergs convective component of melting rate (kg/s/m^2)
+  real, dimension(:,:), pointer :: fl_parent_melt=>null() !< Footloose parent bergs melting rate (kg/s/m^2)
+  real, dimension(:,:), pointer :: fl_child_melt=>null() !< Footloose child bergs melting rate (kg/s/m^2)
   real, dimension(:,:), pointer :: calving=>null() !< Calving mass rate [frozen runoff] (kg/s) (into stored ice)
   real, dimension(:,:), pointer :: calving_hflx=>null() !< Calving heat flux [heat content of calving] (W/m2) (into stored ice)
   real, dimension(:,:), pointer :: floating_melt=>null() !< Net melting rate to icebergs + bits (kg/s/m^2)
-  real, dimension(:,:), pointer :: berg_melt=>null() !< Melting+erosion rate of icebergs (kg/s/m^2)
+  real, dimension(:,:), pointer :: berg_melt=>null() !< Melting+erosion rate of parent icebergs (kg/s/m^2)
   real, dimension(:,:), pointer :: melt_buoy=>null() !< Buoyancy component of melting rate (kg/s/m^2)
   real, dimension(:,:), pointer :: melt_eros=>null() !< Erosion component of melting rate (kg/s/m^2)
   real, dimension(:,:), pointer :: melt_conv=>null() !< Convective component of melting rate (kg/s/m^2)
@@ -158,6 +164,7 @@ module ice_bergs_framework
   real, dimension(:,:), pointer :: fl_bits_src=>null() !< Mass flux from berg into footloose bits (kg/s/m^2)
   real, dimension(:,:), pointer :: fl_bits_melt=>null() !< Melting rate of footloose bits (kg/s/m^2)
   real, dimension(:,:), pointer :: fl_bits_mass=>null() !< Mass distribution of footloose bits (kg/s/m^2)
+  real, dimension(:,:), pointer :: fl_bergy_bits_mass=>null() !< Mass distribution of footloose bergy bits (kg/s/m^2)
   real, dimension(:,:), pointer :: spread_mass=>null() !< Mass of icebergs after spreading (kg/m^2)
   real, dimension(:,:), pointer :: spread_mass_old=>null() !< Mass of icebergs after spreading old (kg/m^2)
   real, dimension(:,:), pointer :: spread_area=>null() !< Area of icebergs after spreading (m^2/m^2)
@@ -194,7 +201,7 @@ module ice_bergs_framework
   integer :: id_calving_hflx_in=-1, id_stored_heat=-1, id_melt_hflx=-1, id_heat_content=-1
   integer :: id_mass=-1, id_ui=-1, id_vi=-1, id_ua=-1, id_va=-1, id_sst=-1, id_cn=-1, id_hi=-1
   integer :: id_bergy_src=-1, id_bergy_melt=-1, id_bergy_mass=-1, id_berg_melt=-1
-  integer :: id_fl_bits_src=-1, id_fl_bits_melt=-1, id_fl_bits_mass=-1
+  integer :: id_fl_bits_src=-1, id_fl_bits_melt=-1, id_fl_bits_mass=-1, id_fl_bergy_bits_mass=-1
   integer :: id_rmean_calving=-1, id_rmean_calving_hflx=-1
   integer :: id_spread_mass=-1, id_spread_area=-1
   integer :: id_ssh=-1, id_fax=-1, id_fay=-1
@@ -202,6 +209,8 @@ module ice_bergs_framework
   integer :: id_spread_uvel=-1, id_spread_vvel=-1
   integer :: id_melt_m_per_year=-1
   integer :: id_ocean_depth=-1
+  integer :: id_melt_by_class=-1, id_melt_buoy_fl=-1, id_melt_eros_fl=-1, id_melt_conv_fl=-1
+  integer :: id_fl_parent_melt=-1, id_fl_child_melt=-1
   !>@}
 
   real :: clipping_depth=0. !< The effective depth at which to clip the weight felt by the ocean [m].
@@ -241,7 +250,8 @@ module ice_bergs_framework
   real :: halo_berg
   real :: static_berg
   real :: mass_of_bits !< Mass of bergy bits (kg)
-  real :: mass_of_fl_bits !< Mass of footloose bergy bits (kg)
+  real :: mass_of_fl_bits !< Mass of footloose bits (kg)
+  real :: mass_of_fl_bergy_bits !< Mass of bergy bits associated with the footloose bits (kg)
   real :: heat_density !< Heat density of berg (J/kg)
   real :: od !< Ocean depth
   integer :: year !< Year of this record (years)
@@ -307,6 +317,7 @@ module ice_bergs_framework
   real :: mass_scaling !< Multiplier to scale mass when interpreting berg as a cloud of bergs (nondim)
   real :: mass_of_bits !< Mass of bergy bits following berg (kg)
   real :: mass_of_fl_bits !< Mass of footloose bergy bits following berg (kg)
+  real :: mass_of_fl_bergy_bits !< Mass of bergy bits associated with the footloose bits (kg)
   real :: fl_k !< Cumulative number of footloose bergs to calve
   real :: heat_density !< Heat density of berg (J/kg)
   real :: halo_berg  ! Equal to zero for bergs on computational domain, and =1 for bergs on the halo
@@ -619,9 +630,9 @@ module ice_bergs_framework
   logical :: fl_bits_erosion_to_bergy_bits=.true. !< Erosion from footloose bits becomes bergy bits
   real :: fl_k_scale_by_perimeter=0 !< If greater than 0, scales FL k by (berg perimeter (m))/(this scaling (m))
   real :: new_berg_from_fl_bits_mass_thres=huge(0.) ! Create a new berg from FL bits when mass_of_fl_bits exceeds this value
-  real :: fl_bits_scale_l=0.8  !< For determining dimensions of FL bits berg; FL_bits length = fl_bits_scale_l*3*l_b
-  real :: fl_bits_scale_w=0.45 !< For determining dimensions of FL bits berg; FL_bits width = fl_bits_scale_l*3*l_b
-  real :: fl_bits_scale_t=0.65 !< For determining dimensions of FL bits berg; FL_bits thickness = fl_bits_scale_l*T
+  real :: fl_bits_scale_l=0.9  !< For determining dimensions of FL bits berg; FL_bits length = fl_bits_scale_l*3*l_b
+  real :: fl_bits_scale_w=0.9 !< For determining dimensions of FL bits berg; FL_bits width = fl_bits_scale_l*3*l_b
+  real :: fl_bits_scale_t=0.9 !< For determining dimensions of FL bits berg; FL_bits thickness = fl_bits_scale_l*T
 end type icebergs
 
 !> Read original restarts. Needs to be module global so can be public to icebergs_mod.
@@ -821,9 +832,9 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: fl_bits_erosion_to_bergy_bits=.true. !< Erosion from footloose bits becomes bergy bits
 real :: fl_k_scale_by_perimeter=0 !< If greater than 0, scales FL k by (berg perimeter (m))/(this scaling (m))
 real :: new_berg_from_fl_bits_mass_thres=huge(0.) ! Create a new berg from FL bits when mass_of_fl_bits exceeds this value
-real :: fl_bits_scale_l=0.8 !< For determining dimensions of FL bits berg; FL_bits length = fl_bits_scale_l*3*l_b
-real :: fl_bits_scale_w=0.45 !< For determining dimensions of FL bits berg; FL_bits width = fl_bits_scale_l*l_b
-real :: fl_bits_scale_t=0.65 !< For determining dimensions of FL bits berg; FL_bits thickness = fl_bits_scale_l*T
+real :: fl_bits_scale_l=0.9 !< For determining dimensions of FL bits berg; FL_bits length = fl_bits_scale_l*3*l_b
+real :: fl_bits_scale_w=0.9 !< For determining dimensions of FL bits berg; FL_bits width = fl_bits_scale_l*l_b
+real :: fl_bits_scale_t=0.9 !< For determining dimensions of FL bits berg; FL_bits thickness = fl_bits_scale_l*T
 
 namelist /icebergs_nml/ verbose, budget, halo,  traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,&
          Static_icebergs,distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,bond_coef, &
@@ -973,6 +984,7 @@ subroutine ice_bergs_framework_init(bergs, &
   allocate( grd%fl_bits_src(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%fl_bits_src(:,:)=0.
   allocate( grd%fl_bits_melt(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%fl_bits_melt(:,:)=0.
   allocate( grd%fl_bits_mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%fl_bits_mass(:,:)=0.
+  allocate( grd%fl_bergy_bits_mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%fl_bergy_bits_mass(:,:)=0.
   allocate( grd%spread_mass(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_mass(:,:)=0.
   allocate( grd%spread_mass_old(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_mass_old(:,:)=0.
   allocate( grd%spread_area(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%spread_area(:,:)=0.
@@ -1002,6 +1014,12 @@ subroutine ice_bergs_framework_init(bergs, &
   allocate( grd%sss(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%sss(:,:)=0.
   allocate( grd%cn(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%cn(:,:)=0.
   allocate( grd%hi(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%hi(:,:)=0.
+  allocate( grd%melt_by_class(grd%isd:grd%ied, grd%jsd:grd%jed, nclasses) ); grd%melt_by_class(:,:,:)=0.
+  allocate( grd%melt_buoy_fl(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%melt_buoy_fl(:,:)=0.
+  allocate( grd%melt_eros_fl(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%melt_eros_fl(:,:)=0.
+  allocate( grd%melt_conv_fl(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%melt_conv_fl(:,:)=0.
+  allocate( grd%fl_parent_melt(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%fl_parent_melt(:,:)=0.
+  allocate( grd%fl_child_melt(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%fl_child_melt(:,:)=0.
   allocate( grd%tmp(grd%isd:grd%ied, grd%jsd:grd%jed) ); grd%tmp(:,:)=0.
   allocate( grd%tmpc(grd%isc:grd%iec, grd%jsc:grd%jec) ); grd%tmpc(:,:)=0.
   allocate( bergs%nbergs_calved_by_class_s(nclasses) ); bergs%nbergs_calved_by_class_s(:)=0
@@ -1564,6 +1582,8 @@ subroutine ice_bergs_framework_init(bergs, &
      'Melt rate of footloose bits', 'kg/(m^2*s)')
   grd%id_fl_bits_mass=register_diag_field('icebergs', 'fl_bits_mass', axes, Time, &
     'Footloose bits density field', 'kg/(m^2)')
+  grd%id_fl_bergy_bits_mass=register_diag_field('icebergs', 'fl_bergy_bits_mass', axes, Time, &
+    'Footloose bergy bits density field', 'kg/(m^2)')
   grd%id_spread_mass=register_diag_field('icebergs', 'spread_mass', axes, Time, &
      'Iceberg mass after spreading', 'kg/(m^2)')
   grd%id_spread_area=register_diag_field('icebergs', 'spread_area', axes, Time, &
@@ -1583,9 +1603,11 @@ subroutine ice_bergs_framework_init(bergs, &
   grd%id_mass=register_diag_field('icebergs', 'mass', axes, Time, &
      'Iceberg density field', 'kg/(m^2)')
   grd%id_stored_ice=register_diag_field('icebergs', 'stored_ice', axes3d, Time, &
-     'Accumulated ice mass by class', 'kg')
+     'Accumulated ice mass by class (z-axis labels correspond to Southern hemisphere classes)', &
+     'kg')
   grd%id_real_calving=register_diag_field('icebergs', 'real_calving', axes3d, Time, &
-     'Calving into iceberg class', 'kg/s')
+     'Calving into iceberg class (z-axis labels correspond to Southern hemisphere classes)', &
+     'kg/s')
   grd%id_rmean_calving=register_diag_field('icebergs', 'running_mean_calving', axes, Time, &
      'Running mean of calving', 'kg/s')
   grd%id_rmean_calving_hflx=register_diag_field('icebergs', 'running_mean_calving_hflx', axes, Time, &
@@ -1622,6 +1644,19 @@ subroutine ice_bergs_framework_init(bergs, &
      'Y-stress on ice from atmosphere', 'N m^-2')
   grd%id_ocean_depth=register_diag_field('icebergs', 'Depth', axes, Time, &
      'Ocean Depth', 'm')
+  grd%id_melt_by_class=register_diag_field('icebergs', 'melt_by_class', axes3d, Time, &
+     'Total ice melt (bergs+bits+FL_bits) by class (z-axis labels correspond to Southern hemisphere classes)', &
+     'kg/(m^2*s)')
+  grd%id_melt_buoy_fl=register_diag_field('icebergs', 'melt_buoy_fl', axes, Time, &
+     'Buoyancy component of footloose iceberg melt rate', 'kg/(m^2*s)')
+  grd%id_melt_eros_fl=register_diag_field('icebergs', 'melt_eros_fl', axes, Time, &
+     'Erosion component of footloose iceberg melt rate', 'kg/(m^2*s)')
+  grd%id_melt_conv_fl=register_diag_field('icebergs', 'melt_conv_fl', axes, Time, &
+     'Convective component of footloose iceberg melt rate', 'kg/(m^2*s)')
+  grd%id_fl_parent_melt=register_diag_field('icebergs', 'fl_parent_melt', axes, Time, &
+     'Melt rate of footloose parent bergs', 'kg/(m^2*s)')
+  grd%id_fl_child_melt=register_diag_field('icebergs', 'fl_child_melt', axes, Time, &
+     'Melt rate of footloose child bergs', 'kg/(m^2*s)')
 
   ! Static fields
   id_class=register_static_field('icebergs', 'lon', axes, &
@@ -3207,6 +3242,7 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
   call push_buffer_value(buff%data(:,n), counter, berg%mass_scaling)
   call push_buffer_value(buff%data(:,n), counter, berg%mass_of_bits)
   call push_buffer_value(buff%data(:,n), counter, berg%mass_of_fl_bits)
+  call push_buffer_value(buff%data(:,n), counter, berg%mass_of_fl_bergy_bits)
   call push_buffer_value(buff%data(:,n), counter, berg%heat_density)
   call push_buffer_value(buff%data(:,n), counter, berg%ine)
   call push_buffer_value(buff%data(:,n), counter, berg%jne)
@@ -3518,6 +3554,7 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
   call pull_buffer_value(buff%data(:,n), counter, localberg%mass_scaling)
   call pull_buffer_value(buff%data(:,n), counter, localberg%mass_of_bits)
   call pull_buffer_value(buff%data(:,n), counter, localberg%mass_of_fl_bits)
+  call pull_buffer_value(buff%data(:,n), counter, localberg%mass_of_fl_bergy_bits)
   call pull_buffer_value(buff%data(:,n), counter, localberg%heat_density)
   call pull_buffer_value(buff%data(:,n), counter, localberg%ine)
   call pull_buffer_value(buff%data(:,n), counter, localberg%jne)
@@ -3803,6 +3840,7 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj)
     call push_buffer_value(buff%data(:,n),counter,traj%mass)
     call push_buffer_value(buff%data(:,n),counter,traj%mass_of_bits)
     call push_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bits)
+    call push_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bergy_bits)
     call push_buffer_value(buff%data(:,n),counter,traj%heat_density)
     call push_buffer_value(buff%data(:,n),counter,traj%thickness)
     call push_buffer_value(buff%data(:,n),counter,traj%width)
@@ -3912,6 +3950,7 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj)
     call pull_buffer_value(buff%data(:,n),counter,traj%mass)
     call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_bits)
     call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bits)
+    call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bergy_bits)
     call pull_buffer_value(buff%data(:,n),counter,traj%heat_density)
     call pull_buffer_value(buff%data(:,n),counter,traj%thickness)
     call pull_buffer_value(buff%data(:,n),counter,traj%width)
@@ -5808,6 +5847,7 @@ subroutine record_posn(bergs)
         posn%mass=this%mass
         posn%mass_of_bits=this%mass_of_bits
         posn%mass_of_fl_bits=this%mass_of_fl_bits
+        posn%mass_of_fl_bergy_bits=this%mass_of_fl_bergy_bits
         posn%heat_density=this%heat_density
         posn%thickness=this%thickness
         posn%width=this%width
@@ -7090,11 +7130,11 @@ real function sum_mass(bergs, justbits, justflbits, justbergs)
       if (present(justbergs)) then
         sum_mass=sum_mass+this%mass*this%mass_scaling
       elseif (present(justbits)) then
-        sum_mass=sum_mass+this%mass_of_bits*this%mass_scaling
+        sum_mass=sum_mass+(this%mass_of_bits+this%mass_of_fl_bergy_bits)*this%mass_scaling
       elseif (present(justflbits)) then
         sum_mass=sum_mass+this%mass_of_fl_bits*this%mass_scaling
       else
-        sum_mass=sum_mass+(this%mass+this%mass_of_bits+this%mass_of_fl_bits)*this%mass_scaling
+        sum_mass=sum_mass+(this%mass+this%mass_of_bits+this%mass_of_fl_bits+this%mass_of_fl_bergy_bits)*this%mass_scaling
       endif
       this=>this%next
     enddo
@@ -7122,11 +7162,11 @@ real function sum_heat(bergs,justbits,justflbits, justbergs)
       if (present(justbergs)) then
         dm=this%mass*this%mass_scaling
       elseif (present(justbits)) then
-        dm=this%mass_of_bits*this%mass_scaling
+        dm=(this%mass_of_bits+this%mass_of_fl_bergy_bits)*this%mass_scaling
       elseif (present(justflbits)) then
         dm=this%mass_of_fl_bits*this%mass_scaling
       else
-        dm=(this%mass+this%mass_of_bits+this%mass_of_fl_bits)*this%mass_scaling
+        dm=(this%mass+this%mass_of_bits+this%mass_of_fl_bits+this%mass_of_fl_bergy_bits)*this%mass_scaling
       endif
       sum_heat=sum_heat+dm*this%heat_density
       this=>this%next
@@ -7194,6 +7234,7 @@ subroutine checksum_gridded(grd, label)
   call grd_chksum2(grd, grd%fl_bits_src, 'fl_bits_src')
   call grd_chksum2(grd, grd%fl_bits_melt, 'fl_bits_melt')
   call grd_chksum2(grd, grd%fl_bits_mass, 'fl_bits_mass')
+  call grd_chksum2(grd, grd%fl_bergy_bits_mass, 'fl_bergy_bits_mass')
   call grd_chksum2(grd, grd%spread_mass, 'spread_mass')
   call grd_chksum2(grd, grd%spread_area, 'spread_area')
   call grd_chksum2(grd, grd%u_iceberg, 'u_iceberg')
@@ -7204,6 +7245,12 @@ subroutine checksum_gridded(grd, label)
   call grd_chksum2(grd, grd%virtual_area, 'varea')
   call grd_chksum2(grd, grd%floating_melt, 'floating_melt')
   call grd_chksum2(grd, grd%berg_melt, 'berg_melt')
+  call grd_chksum3(grd, grd%melt_by_class, 'melt_by_class')
+  call grd_chksum2(grd, grd%melt_buoy_fl, 'melt_b_fl')
+  call grd_chksum2(grd, grd%melt_eros_fl, 'melt_e_fl')
+  call grd_chksum2(grd, grd%melt_conv_fl, 'melt_v_fl')
+  call grd_chksum2(grd, grd%fl_parent_melt, 'fl_parent_melt')
+  call grd_chksum2(grd, grd%fl_child_melt, 'fl_child_melt')
 
   ! static
   call grd_chksum2(grd, grd%lon, 'lon')
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index fe79ea4..3a1a662 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -149,6 +149,7 @@ subroutine write_restart(bergs, time_stamp)
                                    mass_scaling, &
                                    mass_of_bits, &
                                    mass_of_fl_bits, &
+                                   mass_of_fl_bergy_bits, &
                                    static_berg,  &
                                    heat_density, &
                                    axn_fast,     &
@@ -226,6 +227,7 @@ subroutine write_restart(bergs, time_stamp)
    allocate(mass_scaling(nbergs))
    allocate(mass_of_bits(nbergs))
    allocate(mass_of_fl_bits(nbergs))
+   allocate(mass_of_fl_bergy_bits(nbergs))
    allocate(heat_density(nbergs))
    allocate(static_berg(nbergs))
 
@@ -295,9 +297,11 @@ subroutine write_restart(bergs, time_stamp)
   id = register_restart_field(bergs_restart,filename,'mass_scaling',mass_scaling, &
                                             longname='scaling factor for mass of calving berg',units='none')
   id = register_restart_field(bergs_restart,filename,'mass_of_bits',mass_of_bits, &
-    longname='mass of bergy bits',units='kg')
+                                            longname='mass of bergy bits',units='kg')
   id = register_restart_field(bergs_restart,filename,'mass_of_fl_bits',mass_of_fl_bits, &
                                             longname='mass of footloose bits',units='kg')
+  id = register_restart_field(bergs_restart,filename,'mass_of_fl_bergy_bits',mass_of_fl_bergy_bits, &
+                                            longname='mass of bergy bits associated with footloose bits',units='kg')
   id = register_restart_field(bergs_restart,filename,'heat_density',heat_density, &
                                             longname='heat density',units='J/kg')
 
@@ -361,7 +365,7 @@ subroutine write_restart(bergs, time_stamp)
       static_berg(i) = this%static_berg
       call split_id(this%id, id_cnt(i), id_ij(i))
       mass_of_bits(i) = this%mass_of_bits; mass_of_fl_bits(i) = this%mass_of_fl_bits
-      heat_density(i) = this%heat_density
+      mass_of_fl_bergy_bits(i) = this%mass_of_fl_bergy_bits; heat_density(i) = this%heat_density
       if (mts) then
         axn_fast(i) = this%axn_fast
         ayn_fast(i) = this%ayn_fast
@@ -406,6 +410,7 @@ subroutine write_restart(bergs, time_stamp)
              mass_scaling, &
              mass_of_bits, &
              mass_of_fl_bits, &
+             mass_of_fl_bergy_bits, &
              static_berg,  &
              heat_density)
   if (mts) then
@@ -676,6 +681,7 @@ subroutine read_restart_bergs(bergs,Time)
                                    mass_scaling, &
                                    mass_of_bits, &
                                    mass_of_fl_bits, &
+                                   mass_of_fl_bergy_bits, &
                                    static_berg,  &
                                    heat_density, &
                                    axn_fast,     &
@@ -737,6 +743,7 @@ subroutine read_restart_bergs(bergs,Time)
      allocate(mass_scaling(nbergs_in_file))
      allocate(mass_of_bits(nbergs_in_file))
      allocate(mass_of_fl_bits(nbergs_in_file))
+     allocate(mass_of_fl_bergy_bits(nbergs_in_file))
      allocate(static_berg(nbergs_in_file))
      allocate(heat_density(nbergs_in_file))
      allocate(ine(nbergs_in_file))
@@ -809,6 +816,7 @@ subroutine read_restart_bergs(bergs,Time)
      call read_unlimited_axis(filename,'mass_scaling',mass_scaling,domain=grd%domain)
      call read_real_vector(filename,'mass_of_bits',mass_of_bits,domain=grd%domain,value_if_not_in_file=0.)
      call read_real_vector(filename,'mass_of_fl_bits',mass_of_fl_bits,domain=grd%domain,value_if_not_in_file=0.)
+     call read_real_vector(filename,'mass_of_fl_bergy_bits',mass_of_fl_bergy_bits,domain=grd%domain,value_if_not_in_file=0.)
      call read_real_vector(filename,'heat_density',heat_density,domain=grd%domain,value_if_not_in_file=0.)
      call read_unlimited_axis(filename,'ine',ine,domain=grd%domain)
      call read_unlimited_axis(filename,'jne',jne,domain=grd%domain)
@@ -905,6 +913,7 @@ subroutine read_restart_bergs(bergs,Time)
       localberg%mass_scaling=mass_scaling(k)
       localberg%mass_of_bits=mass_of_bits(k)
       localberg%mass_of_fl_bits=mass_of_fl_bits(k)
+      localberg%mass_of_fl_bergy_bits=mass_of_fl_bergy_bits(k)
       localberg%halo_berg=0.
       localberg%static_berg=static_berg(k)
       localberg%heat_density=heat_density(k)
@@ -967,6 +976,7 @@ subroutine read_restart_bergs(bergs,Time)
                mass_scaling, &
                mass_of_bits, &
                mass_of_fl_bits, &
+               mass_of_fl_bergy_bits, &
                static_berg,  &
                heat_density, &
                ine,          &
@@ -1123,6 +1133,7 @@ subroutine generate_bergs(bergs,Time)
       localberg%mass_scaling=bergs%mass_scaling_s(1)
       localberg%mass_of_bits=0.
       localberg%mass_of_fl_bits=0.
+      localberg%mass_of_fl_bergy_bits=0.
       localberg%halo_berg=0.
       localberg%static_berg=0.
       localberg%heat_density=0.
@@ -1682,7 +1693,7 @@ subroutine write_trajectory(trajectory, save_short_traj)
 integer :: uvelpid,vvelpid
 integer :: uoid, void, uiid, viid, uaid, vaid, sshxid, sshyid, sstid, sssid
 integer :: cnid, hiid, hsid
-integer :: mid, did, wid, lid, mbid, mflbid, hdid, nbid, odid, flkid
+integer :: mid, did, wid, lid, mbid, mflbid, mflbbid, hdid, nbid, odid, flkid
 integer :: axnid,aynid,bxnid,bynid,axnfid,aynfid,bxnfid,bynfid
 integer :: eecid,edcid,eeid,edid,aeid,efid
 integer :: eectid, edctid, eetid, edtid, aetid
@@ -1818,6 +1829,7 @@ subroutine write_trajectory(trajectory, save_short_traj)
         mid = inq_varid(ncid, 'mass')
         mbid = inq_varid(ncid, 'mass_of_bits')
         mflbid = inq_varid(ncid, 'mass_of_fl_bits')
+        mflbbid = inq_varid(ncid, 'mass_of_fl_bergy_bits')
         hdid = inq_varid(ncid, 'heat_density')
         did = inq_varid(ncid, 'thickness')
         wid = inq_varid(ncid, 'width')
@@ -1896,6 +1908,7 @@ subroutine write_trajectory(trajectory, save_short_traj)
         mid = def_var(ncid, 'mass', NF_DOUBLE, i_dim)
         mbid = def_var(ncid, 'mass_of_bits', NF_DOUBLE, i_dim)
         mflbid = def_var(ncid, 'mass_of_fl_bits', NF_DOUBLE, i_dim)
+        mflbbid = def_var(ncid, 'mass_of_fl_bergy_bits', NF_DOUBLE, i_dim)
         hdid = def_var(ncid, 'heat_density', NF_DOUBLE, i_dim)
         did = def_var(ncid, 'thickness', NF_DOUBLE, i_dim)
         wid = def_var(ncid, 'width', NF_DOUBLE, i_dim)
@@ -1987,6 +2000,8 @@ subroutine write_trajectory(trajectory, save_short_traj)
         call put_att(ncid, mbid, 'units', 'kg')
         call put_att(ncid, mflbid, 'long_name', 'mass_of_fl_bits')
         call put_att(ncid, mflbid, 'units', 'kg')
+        call put_att(ncid, mflbbid, 'long_name', 'mass_of_fl_bergy_bits')
+        call put_att(ncid, mflbbid, 'units', 'kg')
         call put_att(ncid, hdid, 'long_name', 'heat_density')
         call put_att(ncid, hdid, 'units', 'J/kg')
         call put_att(ncid, did, 'long_name', 'thickness')

From 429dff692c07355673d021de23012fcf160ef930 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Sat, 8 May 2021 10:27:17 -0400
Subject: [PATCH 304/361] Added FL and mass parameters to save_short_traj
 trajectory output (TODO: make a save_fl_traj option, instead). In subroutine
 footloose_calving, added an adjustment to max_k to make sure it does not
 result in negative parent berg length. Fixed bug where send_data for
 grd%melt_by_class was not called. Slight edit to how new FL berg positions
 are initialized in relation to the parent berg: if the random initialization
 scheme fails to initialize the new berg on the current PE, an attempt is made
 to initialize it at one of the parent berg corners on the current PE.

---
 src/icebergs.F90           | 65 +++++++++++++++++++++----------
 src/icebergs_framework.F90 | 53 +++++++++++++++++--------
 src/icebergs_io.F90        | 80 ++++++++++++++++++++++++++------------
 3 files changed, 136 insertions(+), 62 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 50b6935..a2bc53b 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -2633,6 +2633,10 @@ subroutine footloose_calving(bergs, time)
         else
           !non-bonded berg must be larger than 3*(l_b) for FL calving. Set max_k accordingly.
           max_k = max(ceiling((L-3*l_b)*W/(3*l_b**2.)),0)
+
+          if (L-max_k*3.*(l_b**2.)/W<=0.) then
+            max_k = max_k-1
+          endif
         endif
 
         if (max_k==0) then
@@ -2696,6 +2700,7 @@ subroutine footloose_calving(bergs, time)
           Ln=L-Lr_fl !new length
           if (Ln .le. 0) then
             if (N_bonds==0) then
+              print *,'l_b,L,W,k,max_k',l_b,L,W,k,max_k
               call error_mesg('KID,footloose_calving', &
                 'non-edge element has fully calved from footloose mechanism', FATAL)
             endif
@@ -3322,6 +3327,10 @@ subroutine thermodynamics(bergs)
           this%fl_k=-1.
           this%start_year=bergs%current_year
           this%start_day=bergs%current_yearday
+          if (grd%area(i,j).ne.0.) then
+            grd%fl_bits_src(i,j)=grd%fl_bits_src(i,j)-&
+              this%mass*this%mass_scaling/(bergs%dt*grd%area(i,j))
+          endif
         else
           ! Delete the berg
           if (.not. bergs%debug_write) call move_trajectory(bergs, this)
@@ -5593,7 +5602,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     lerr=send_data(grd%id_fax, tauxa(:,:), Time)
   if (grd%id_fay>0) &
     lerr=send_data(grd%id_fay, tauya(:,:), Time)
-  if (grd%id_melt_by_class<0) &
+  if (grd%id_melt_by_class>0) &
     lerr=send_data(grd%id_melt_by_class, grd%melt_by_class(grd%isc:grd%iec,grd%jsc:grd%jec,:), Time)
   if (grd%id_melt_buoy_fl>0) &
     lerr=send_data(grd%id_melt_buoy_fl, grd%melt_buoy_fl(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
@@ -6434,28 +6443,41 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b,fl_disp_x,fl_disp_y,berg_from_bit
 
     !If new berg is not on current PE (computational domain), correct it so that it is.
     if (.not. lres) then
-      !The choice of 75% and 25% weighting here is completely arbitrary...
-      if (cberg%lon > grd%lon(grd%iec,grd%jec)) then
-        cberg%lon = 0.75*grd%lon(grd%iec,grd%jec) + 0.25*pberg%lon
-      elseif (cberg%lon < grd%lon(grd%isc-1,grd%jsc-1)) then
-        cberg%lon = 0.75*grd%lon(grd%isc-1,grd%jsc-1) + 0.25*pberg%lon
+      !try the corners
+      cberg%lon = pberg%lon - 0.5*pberg%length
+      cberg%lat = pberg%lat - 0.5*pberg%width
+      lres= find_cell(grd, cberg%lon, cberg%lat, cberg%ine, cberg%jne)
+      if (.not. lres) then
+        cberg%lon = pberg%lon - 0.5*pberg%length
+        cberg%lat = pberg%lat + 0.5*pberg%width
+        lres= find_cell(grd, cberg%lon, cberg%lat, cberg%ine, cberg%jne)
+        if (.not. lres) then
+          cberg%lon = pberg%lon + 0.5*pberg%length
+          cberg%lat = pberg%lat + 0.5*pberg%width
+          lres= find_cell(grd, cberg%lon, cberg%lat, cberg%ine, cberg%jne)
+          if (.not. lres) then
+            cberg%lon = pberg%lon + 0.5*pberg%length
+            cberg%lat = pberg%lat - 0.5*pberg%width
+            lres= find_cell(grd, cberg%lon, cberg%lat, cberg%ine, cberg%jne)
+          endif
+        endif
       endif
-      if (cberg%lat > grd%lat(grd%iec,grd%jec)) then
-        cberg%lat = 0.75*grd%lat(grd%iec,grd%jec) + 0.25*pberg%lat
-      elseif (cberg%lat < grd%lat(grd%isc-1,grd%jsc-1)) then
-        cberg%lat = 0.75*grd%lat(grd%isc-1,grd%jsc-1) + 0.25*pberg%lat
+      if (.not. lres) then
+        !if all else fails, give the child berg the same coords as the parent
+        fl_disp_x=0.0; fl_disp_y=0.0; displace=.false.
+        !call error_mesg('KID, calve_fl_icebergs', &
+        !'corrected new berg position still not on current PE!', FATAL)
+      else
+        fl_disp_x=pberg%lon-cberg%lon; fl_disp_y=pberg%lat-cberg%lat
       endif
-      lres= find_cell(grd, cberg%lon, cberg%lat, cberg%ine, cberg%jne)
-      if (.not. lres) call error_mesg('KID, calve_fl_icebergs', &
-        'corrected new berg position still not on current PE!', FATAL)
-      fl_disp_x=pberg%lon-cberg%lon; fl_disp_y=pberg%lat-cberg%lat
     endif
-
-    !if new berg is located within a grounded cell, change its position to the same as the parent berg
-    if (grd%area(cberg%ine,cberg%jne).eq.0.) then
-      fl_disp_x=0.0; fl_disp_y=0.0; displace=.false.
-    else
-      lres=pos_within_cell(grd, cberg%lon, cberg%lat, cberg%ine, cberg%jne, cberg%xi, cberg%yj)
+    if (displace) then
+      !if new berg is located within a grounded cell, change its position to the same as the parent berg
+      if (grd%area(cberg%ine,cberg%jne).eq.0.) then
+        fl_disp_x=0.0; fl_disp_y=0.0; displace=.false.
+      else
+        lres=pos_within_cell(grd, cberg%lon, cberg%lat, cberg%ine, cberg%jne, cberg%xi, cberg%yj)
+      endif
     endif
   endif
 
@@ -6495,7 +6517,7 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b,fl_disp_x,fl_disp_y,berg_from_bit
   cberg%lon_old      = pberg%lon_old  + fl_disp_x
   cberg%lat_old      = pberg%lat_old  + fl_disp_y
   cberg%start_day    = bergs%current_yearday
-  cberg%start_mass   = pberg%mass !used for tracking the different size classes calved from grounded ice, so set to pberg.
+
   cberg%mass_of_fl_bits = 0.0
   cberg%mass_of_fl_bergy_bits = 0.0
   cberg%fl_k         = -1.0
@@ -6504,6 +6526,7 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b,fl_disp_x,fl_disp_y,berg_from_bit
   cberg%halo_berg    = 0.0
 
   !always same values as parent:
+  cberg%start_mass   = pberg%start_mass !used for tracking the different size classes calved from grounded ice, so set to pberg.
   cberg%uvel         = pberg%uvel
   cberg%vvel         = pberg%vvel
   cberg%axn          = pberg%axn
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index e757601..52c813b 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -19,7 +19,7 @@ module ice_bergs_framework
 implicit none ; private
 
 integer :: buffer_width=36 ! This should be a parameter
-integer :: buffer_width_traj=38 ! This should be a parameter
+integer :: buffer_width_traj=39 ! This should be a parameter
 integer :: buffer_width_bond_traj=11 !This should be a parameter
 integer, parameter :: nclasses=10 ! Number of ice bergs classes
 
@@ -254,6 +254,7 @@ module ice_bergs_framework
   real :: mass_of_fl_bergy_bits !< Mass of bergy bits associated with the footloose bits (kg)
   real :: heat_density !< Heat density of berg (J/kg)
   real :: od !< Ocean depth
+  real :: start_mass
   integer :: year !< Year of this record (years)
   integer(kind=8) :: id = -1 !< Iceberg identifier
   type(xyt), pointer :: next=>null() !< Next link in list
@@ -1262,7 +1263,7 @@ subroutine ice_bergs_framework_init(bergs, &
 else
   buffer_width=buffer_width+(max_bonds*5) ! Increase buffer width to include bonds being passed between processors
 endif
-if (save_short_traj) buffer_width_traj=6 ! This is the length of the short buffer used for abrevated traj
+if (save_short_traj) buffer_width_traj=12 ! This is the length of the short buffer used for abrevated traj
 if (ignore_traj) buffer_width_traj=0 ! If this is true, then all traj files should be ignored
 
 if (use_damage) then
@@ -3832,20 +3833,26 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj)
   call split_id(traj%id, cnt, ij)
   call push_buffer_value(buff%data(:,n),counter,cnt)
   call push_buffer_value(buff%data(:,n),counter,ij)
+  call push_buffer_value(buff%data(:,n),counter,traj%mass)
+  call push_buffer_value(buff%data(:,n),counter,traj%start_mass)
+  call push_buffer_value(buff%data(:,n),counter,traj%mass_of_bits)
+  call push_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bits)
+  call push_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bergy_bits)
+  call push_buffer_value(buff%data(:,n),counter,traj%fl_k)
   if (.not. save_short_traj) then
     call push_buffer_value(buff%data(:,n),counter,traj%uvel)
     call push_buffer_value(buff%data(:,n),counter,traj%vvel)
     call push_buffer_value(buff%data(:,n),counter,traj%uvel_prev)
     call push_buffer_value(buff%data(:,n),counter,traj%vvel_prev)
-    call push_buffer_value(buff%data(:,n),counter,traj%mass)
-    call push_buffer_value(buff%data(:,n),counter,traj%mass_of_bits)
-    call push_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bits)
-    call push_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bergy_bits)
+    ! call push_buffer_value(buff%data(:,n),counter,traj%mass)
+    ! call push_buffer_value(buff%data(:,n),counter,traj%mass_of_bits)
+    ! call push_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bits)
+    ! call push_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bergy_bits)
     call push_buffer_value(buff%data(:,n),counter,traj%heat_density)
     call push_buffer_value(buff%data(:,n),counter,traj%thickness)
     call push_buffer_value(buff%data(:,n),counter,traj%width)
     call push_buffer_value(buff%data(:,n),counter,traj%length)
-    call push_buffer_value(buff%data(:,n),counter,traj%fl_k)
+    ! call push_buffer_value(buff%data(:,n),counter,traj%fl_k)
     call push_buffer_value(buff%data(:,n),counter,traj%uo)
     call push_buffer_value(buff%data(:,n),counter,traj%vo)
     call push_buffer_value(buff%data(:,n),counter,traj%ui)
@@ -3942,20 +3949,26 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj)
   call pull_buffer_value(buff%data(:,n),counter,cnt)
   call pull_buffer_value(buff%data(:,n),counter,ij)
   traj%id = id_from_2_ints(cnt, ij)
+  call pull_buffer_value(buff%data(:,n),counter,traj%mass)
+  call pull_buffer_value(buff%data(:,n),counter,traj%start_mass)
+  call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_bits)
+  call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bits)
+  call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bergy_bits)
+  call pull_buffer_value(buff%data(:,n),counter,traj%fl_k)
   if (.not. save_short_traj) then
     call pull_buffer_value(buff%data(:,n),counter,traj%uvel)
     call pull_buffer_value(buff%data(:,n),counter,traj%vvel)
     call pull_buffer_value(buff%data(:,n),counter,traj%uvel_prev)
     call pull_buffer_value(buff%data(:,n),counter,traj%vvel_prev)
-    call pull_buffer_value(buff%data(:,n),counter,traj%mass)
-    call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_bits)
-    call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bits)
-    call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bergy_bits)
+    ! call pull_buffer_value(buff%data(:,n),counter,traj%mass)
+    ! call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_bits)
+    ! call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bits)
+    ! call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bergy_bits)
     call pull_buffer_value(buff%data(:,n),counter,traj%heat_density)
     call pull_buffer_value(buff%data(:,n),counter,traj%thickness)
     call pull_buffer_value(buff%data(:,n),counter,traj%width)
     call pull_buffer_value(buff%data(:,n),counter,traj%length)
-    call pull_buffer_value(buff%data(:,n),counter,traj%fl_k)
+    ! call pull_buffer_value(buff%data(:,n),counter,traj%fl_k)
     call pull_buffer_value(buff%data(:,n),counter,traj%uo)
     call pull_buffer_value(buff%data(:,n),counter,traj%vo)
     call pull_buffer_value(buff%data(:,n),counter,traj%ui)
@@ -5839,20 +5852,26 @@ subroutine record_posn(bergs)
       posn%year=bergs%current_year
       posn%day=bergs%current_yearday
       posn%id=this%id
+      posn%mass=this%mass
+      posn%start_mass=this%start_mass
+      posn%mass_of_bits=this%mass_of_bits
+      posn%mass_of_fl_bits=this%mass_of_fl_bits
+      posn%mass_of_fl_bergy_bits=this%mass_of_fl_bergy_bits
+      posn%fl_k=this%fl_k
       if (.not. bergs%save_short_traj) then !Not totally sure that this is correct
         posn%uvel=this%uvel
         posn%vvel=this%vvel
         posn%uvel_prev=this%uvel_prev
         posn%vvel_prev=this%vvel_prev
-        posn%mass=this%mass
-        posn%mass_of_bits=this%mass_of_bits
-        posn%mass_of_fl_bits=this%mass_of_fl_bits
-        posn%mass_of_fl_bergy_bits=this%mass_of_fl_bergy_bits
+        ! posn%mass=this%mass
+        ! posn%mass_of_bits=this%mass_of_bits
+        ! posn%mass_of_fl_bits=this%mass_of_fl_bits
+        ! posn%mass_of_fl_bergy_bits=this%mass_of_fl_bergy_bits
         posn%heat_density=this%heat_density
         posn%thickness=this%thickness
         posn%width=this%width
         posn%length=this%length
-        posn%fl_k=this%fl_k
+        ! posn%fl_k=this%fl_k
         posn%uo=this%uo
         posn%vo=this%vo
         posn%ui=this%ui
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index 3a1a662..c78b413 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -1693,7 +1693,7 @@ subroutine write_trajectory(trajectory, save_short_traj)
 integer :: uvelpid,vvelpid
 integer :: uoid, void, uiid, viid, uaid, vaid, sshxid, sshyid, sstid, sssid
 integer :: cnid, hiid, hsid
-integer :: mid, did, wid, lid, mbid, mflbid, mflbbid, hdid, nbid, odid, flkid
+integer :: mid, smid, did, wid, lid, mbid, mflbid, mflbbid, hdid, nbid, odid, flkid
 integer :: axnid,aynid,bxnid,bynid,axnfid,aynfid,bxnfid,bynfid
 integer :: eecid,edcid,eeid,edid,aeid,efid
 integer :: eectid, edctid, eetid, edtid, aetid
@@ -1815,6 +1815,12 @@ subroutine write_trajectory(trajectory, save_short_traj)
       dayid = inq_varid(ncid, 'day')
       idcntid = inq_varid(ncid, 'id_cnt')
       idijid = inq_varid(ncid, 'id_ij')
+      mid = inq_varid(ncid, 'mass')
+      smid = inq_varid(ncid, 'start_mass')
+      mbid = inq_varid(ncid, 'mass_of_bits')
+      mflbid = inq_varid(ncid, 'mass_of_fl_bits')
+      mflbbid = inq_varid(ncid, 'mass_of_fl_bergy_bits')
+      flkid = inq_varid(ncid, 'fl_k')
       if (.not.save_short_traj) then
         uvelid = inq_varid(ncid, 'uvel')
         vvelid = inq_varid(ncid, 'vvel')
@@ -1826,15 +1832,15 @@ subroutine write_trajectory(trajectory, save_short_traj)
         viid = inq_varid(ncid, 'vi')
         uaid = inq_varid(ncid, 'ua')
         vaid = inq_varid(ncid, 'va')
-        mid = inq_varid(ncid, 'mass')
-        mbid = inq_varid(ncid, 'mass_of_bits')
-        mflbid = inq_varid(ncid, 'mass_of_fl_bits')
-        mflbbid = inq_varid(ncid, 'mass_of_fl_bergy_bits')
+        ! mid = inq_varid(ncid, 'mass')
+        ! mbid = inq_varid(ncid, 'mass_of_bits')
+        ! mflbid = inq_varid(ncid, 'mass_of_fl_bits')
+        ! mflbbid = inq_varid(ncid, 'mass_of_fl_bergy_bits')
         hdid = inq_varid(ncid, 'heat_density')
         did = inq_varid(ncid, 'thickness')
         wid = inq_varid(ncid, 'width')
         lid = inq_varid(ncid, 'length')
-        flkid = inq_varid(ncid, 'fl_k')
+        ! flkid = inq_varid(ncid, 'fl_k')
         sshxid = inq_varid(ncid, 'ssh_x')
         sshyid = inq_varid(ncid, 'ssh_y')
         sstid = inq_varid(ncid, 'sst')
@@ -1894,6 +1900,12 @@ subroutine write_trajectory(trajectory, save_short_traj)
       dayid = def_var(ncid, 'day', NF_DOUBLE, i_dim)
       idcntid = def_var(ncid, 'id_cnt', NF_INT, i_dim)
       idijid = def_var(ncid, 'id_ij', NF_INT, i_dim)
+      mid = def_var(ncid, 'mass', NF_DOUBLE, i_dim)
+      smid = def_var(ncid, 'start_mass', NF_DOUBLE, i_dim)
+      mbid = def_var(ncid, 'mass_of_bits', NF_DOUBLE, i_dim)
+      mflbid = def_var(ncid, 'mass_of_fl_bits', NF_DOUBLE, i_dim)
+      mflbbid = def_var(ncid, 'mass_of_fl_bergy_bits', NF_DOUBLE, i_dim)
+      flkid = def_var(ncid, 'fl_k', NF_DOUBLE, i_dim)
       if (.not. save_short_traj) then
         uvelid = def_var(ncid, 'uvel', NF_DOUBLE, i_dim)
         vvelid = def_var(ncid, 'vvel', NF_DOUBLE, i_dim)
@@ -1905,15 +1917,15 @@ subroutine write_trajectory(trajectory, save_short_traj)
         viid = def_var(ncid, 'vi', NF_DOUBLE, i_dim)
         uaid = def_var(ncid, 'ua', NF_DOUBLE, i_dim)
         vaid = def_var(ncid, 'va', NF_DOUBLE, i_dim)
-        mid = def_var(ncid, 'mass', NF_DOUBLE, i_dim)
-        mbid = def_var(ncid, 'mass_of_bits', NF_DOUBLE, i_dim)
-        mflbid = def_var(ncid, 'mass_of_fl_bits', NF_DOUBLE, i_dim)
-        mflbbid = def_var(ncid, 'mass_of_fl_bergy_bits', NF_DOUBLE, i_dim)
+        ! mid = def_var(ncid, 'mass', NF_DOUBLE, i_dim)
+        ! mbid = def_var(ncid, 'mass_of_bits', NF_DOUBLE, i_dim)
+        ! mflbid = def_var(ncid, 'mass_of_fl_bits', NF_DOUBLE, i_dim)
+        ! mflbbid = def_var(ncid, 'mass_of_fl_bergy_bits', NF_DOUBLE, i_dim)
         hdid = def_var(ncid, 'heat_density', NF_DOUBLE, i_dim)
         did = def_var(ncid, 'thickness', NF_DOUBLE, i_dim)
         wid = def_var(ncid, 'width', NF_DOUBLE, i_dim)
         lid = def_var(ncid, 'length', NF_DOUBLE, i_dim)
-        flkid = def_var(ncid, 'fl_k', NF_DOUBLE, i_dim)
+        ! flkid = def_var(ncid, 'fl_k', NF_DOUBLE, i_dim)
         sshxid = def_var(ncid, 'ssh_x', NF_DOUBLE, i_dim)
         sshyid = def_var(ncid, 'ssh_y', NF_DOUBLE, i_dim)
         sstid = def_var(ncid, 'sst', NF_DOUBLE, i_dim)
@@ -1976,7 +1988,18 @@ subroutine write_trajectory(trajectory, save_short_traj)
       call put_att(ncid, idcntid, 'units', 'dimensionless')
       call put_att(ncid, idijid, 'long_name', 'position component of iceberg id')
       call put_att(ncid, idijid, 'units', 'dimensionless')
-
+      call put_att(ncid, mid, 'long_name', 'mass')
+      call put_att(ncid, mid, 'units', 'kg')
+      call put_att(ncid, smid, 'long_name', 'start_mass')
+      call put_att(ncid, smid, 'units', 'kg')
+      call put_att(ncid, mbid, 'long_name', 'mass_of_bits')
+      call put_att(ncid, mbid, 'units', 'kg')
+      call put_att(ncid, mflbid, 'long_name', 'mass_of_fl_bits')
+      call put_att(ncid, mflbid, 'units', 'kg')
+      call put_att(ncid, mflbbid, 'long_name', 'mass_of_fl_bergy_bits')
+      call put_att(ncid, mflbbid, 'units', 'kg')
+      call put_att(ncid, flkid, 'long_name', 'footloose calving k')
+      call put_att(ncid, flkid, 'units', 'none')
       if (.not. save_short_traj) then
         call put_att(ncid, uvelid, 'long_name', 'zonal spped')
         call put_att(ncid, uvelid, 'units', 'm/s')
@@ -1994,14 +2017,14 @@ subroutine write_trajectory(trajectory, save_short_traj)
         call put_att(ncid, uaid, 'units', 'm/s')
         call put_att(ncid, vaid, 'long_name', 'atmos meridional spped')
         call put_att(ncid, vaid, 'units', 'm/s')
-        call put_att(ncid, mid, 'long_name', 'mass')
-        call put_att(ncid, mid, 'units', 'kg')
-        call put_att(ncid, mbid, 'long_name', 'mass_of_bits')
-        call put_att(ncid, mbid, 'units', 'kg')
-        call put_att(ncid, mflbid, 'long_name', 'mass_of_fl_bits')
-        call put_att(ncid, mflbid, 'units', 'kg')
-        call put_att(ncid, mflbbid, 'long_name', 'mass_of_fl_bergy_bits')
-        call put_att(ncid, mflbbid, 'units', 'kg')
+        ! call put_att(ncid, mid, 'long_name', 'mass')
+        ! call put_att(ncid, mid, 'units', 'kg')
+        ! call put_att(ncid, mbid, 'long_name', 'mass_of_bits')
+        ! call put_att(ncid, mbid, 'units', 'kg')
+        ! call put_att(ncid, mflbid, 'long_name', 'mass_of_fl_bits')
+        ! call put_att(ncid, mflbid, 'units', 'kg')
+        ! call put_att(ncid, mflbbid, 'long_name', 'mass_of_fl_bergy_bits')
+        ! call put_att(ncid, mflbbid, 'units', 'kg')
         call put_att(ncid, hdid, 'long_name', 'heat_density')
         call put_att(ncid, hdid, 'units', 'J/kg')
         call put_att(ncid, did, 'long_name', 'thickness')
@@ -2010,8 +2033,8 @@ subroutine write_trajectory(trajectory, save_short_traj)
         call put_att(ncid, wid, 'units', 'm')
         call put_att(ncid, lid, 'long_name', 'length')
         call put_att(ncid, lid, 'units', 'm')
-        call put_att(ncid, flkid, 'long_name', 'footloose calving k')
-        call put_att(ncid, flkid, 'units', 'm')
+        ! call put_att(ncid, flkid, 'long_name', 'footloose calving k')
+        ! call put_att(ncid, flkid, 'units', 'none')
         call put_att(ncid, sshxid, 'long_name', 'sea surface height gradient_x')
         call put_att(ncid, sshxid, 'units', 'non-dim')
         call put_att(ncid, sshyid, 'long_name', 'sea surface height gradient_y')
@@ -2116,6 +2139,12 @@ subroutine write_trajectory(trajectory, save_short_traj)
       call split_id(this%id, cnt, ij)
       call put_int(ncid, idcntid, i, cnt)
       call put_int(ncid, idijid, i, ij)
+      call put_double(ncid, mid, i, this%mass)
+      call put_double(ncid, smid, i, this%start_mass)
+      call put_double(ncid, mbid, i, this%mass_of_bits)
+      call put_double(ncid, mflbid, i, this%mass_of_fl_bits)
+      call put_double(ncid, mflbbid, i, this%mass_of_fl_bergy_bits)
+      call put_double(ncid, flkid, i, this%fl_k)
       if (.not. save_short_traj) then
         call put_double(ncid, uvelid, i, this%uvel)
         call put_double(ncid, vvelid, i, this%vvel)
@@ -2127,12 +2156,15 @@ subroutine write_trajectory(trajectory, save_short_traj)
         call put_double(ncid, viid, i, this%vi)
         call put_double(ncid, uaid, i, this%ua)
         call put_double(ncid, vaid, i, this%va)
-        call put_double(ncid, mid, i, this%mass)
+        ! call put_double(ncid, mid, i, this%mass)
+        ! call put_double(ncid, mbid, i, this%mass_of_bits)
+        ! call put_double(ncid, mflbid, i, this%mass_of_fl_bits)
+        ! call put_double(ncid, mflbbid, i, this%mass_of_fl_bergy_bits)
         call put_double(ncid, hdid, i, this%heat_density)
         call put_double(ncid, did, i, this%thickness)
         call put_double(ncid, wid, i, this%width)
         call put_double(ncid, lid, i, this%length)
-        call put_double(ncid, flkid, i, this%fl_k)
+        ! call put_double(ncid, flkid, i, this%fl_k)
         call put_double(ncid, sshxid, i, this%ssh_x)
         call put_double(ncid, sshyid, i, this%ssh_y)
         call put_double(ncid, sstid, i, this%sst)

From f631618a232d17c8f0196281157a2a067c7d8e6b Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Mon, 10 May 2021 14:17:57 -0400
Subject: [PATCH 305/361] removed useless nml parameter fl_melt_as_bergy_bits.
 Added nml parameter save_fl_traj to save masses and footloose parameters in
 the berg trajectories.

---
 src/icebergs.F90           |  95 ++++++++++++++---------------------
 src/icebergs_framework.F90 |  80 +++++++++++++----------------
 src/icebergs_io.F90        | 100 ++++++++++++++++---------------------
 3 files changed, 114 insertions(+), 161 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index a2bc53b..620bfd3 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -188,7 +188,7 @@ subroutine debugwriteandstop(bergs)
   bergs%debug_write=.true.
   call record_posn(bergs)
   call move_all_trajectories(bergs)
-  call write_trajectory(bergs%trajectories, bergs%save_short_traj)
+  call write_trajectory(bergs%trajectories, bergs%save_short_traj, bergs%save_fl_traj)
   if (save_bond_traj) call write_bond_trajectory(bergs%bond_trajectories)
   call mpp_sync()
   call error_mesg('KID', 'WRITE AND STOP!!!', FATAL)
@@ -3052,55 +3052,39 @@ subroutine thermodynamics(bergs)
 
       ! Footloose bits (FL bits). For now, FL bits do not erode into bergy bits.
       if (this%mass_of_fl_bits>0.) then
-
         call fl_bits_dimensions(bergs,this,Lfl,Wfl,Tfl)
         Mfl=this%mass_of_fl_bits
-
-        if (bergs%fl_melt_as_bergy_bits) then
-          Lfl=min(L,W,T,40.)
-          Afl=(Mfl/bergs%rho_bergs)/Lfl
-          Mb_fl=max( 0.58*(dvo**0.8)*(SST+2.0)/(Lfl**0.2), 0.) *perday ! FL bits basal turbulent melting
-          Mb_fl=bergs%rho_bergs*Afl*Mb_fl ! in kg/s
-          dMfl=min(Mb_fl*bergs%dt,Mfl) ! FL bergy bits mass lost to melting (kg)
-          Mnew_fl=Mfl-dMfl ! remove mass lost to FL bergy bits melt
-          dMe_fl=0.; dMb_fl=dMfl; dMv_fl=0.
-          if (Mnew==0.) then ! if parent berg has completely melted then
-            dMfl=Mfl ! instantly melt all of these footloose bits
-            Mnew_fl=0.
-          endif
+        Volfl=Lfl*Wfl*Tfl
+        !basal turbulent melting
+        Mb_fl=max( 0.58*(dvo**0.8)*(SST+4.0)/(Lfl**0.2), 0.) *perday
+        Tnfl=max(Tfl-  Mb_fl*bergs%dt,0.) ! new FL thickness (m)
+        if (bergs%use_operator_splitting) then
+          !basal turbulent melting, continued
+          nVolfl=Tnfl*Wfl*Lfl ! new volume (m^3)
+          Mnew1_fl=(nVolfl/Volfl)*Mfl ! new mass (kg)
+          dMb_fl=Mfl-Mnew1_fl ! mass lost to basal melting (>0) (kg)
+          !buoyant convection
+          Lnfl=max(Lfl-Mv_fl*bergs%dt,0.) ! new FL length (m)
+          Wnfl=max(Wfl-Mv_fl*bergs%dt,0.) ! new FL width (m)
+          nVolfl=Tnfl*Wnfl*Lnfl ! new footloose volume (m^3)
+          Mnew2_fl=(nVolfl/Volfl)*Mfl !new FL mass (kg), after buoyant convection
+          dMv_fl=Mnew1_fl-Mnew2_fl
+          !erosion
+          Lnfl=max(Lnfl-Me_fl*bergs%dt,0.) ! new FL length (m)
+          Wnfl=max(Wnfl-Me_fl*bergs%dt,0.) ! new FL width (m)
+          nVolfl=Tnfl*Wnfl*Lnfl ! new footloose volume (m^3)
+          Mnew_fl=(nVolfl/Volfl)*Mfl !new FL mass (kg), after all melt and erosion
+          dMe_fl=Mnew2_fl-Mnew_fl !FL mass lost to erosion (>0) (kg)
         else
-          Volfl=Lfl*Wfl*Tfl
-          !basal turbulent melting
-          Mb_fl=max( 0.58*(dvo**0.8)*(SST+4.0)/(Lfl**0.2), 0.) *perday
-          Tnfl=max(Tfl-  Mb_fl*bergs%dt,0.) ! new FL thickness (m)
-          if (bergs%use_operator_splitting) then
-            !basal turbulent melting, continued
-            nVolfl=Tnfl*Wfl*Lfl ! new volume (m^3)
-            Mnew1_fl=(nVolfl/Volfl)*Mfl ! new mass (kg)
-            dMb_fl=Mfl-Mnew1_fl ! mass lost to basal melting (>0) (kg)
-            !buoyant convection
-            Lnfl=max(Lfl-Mv_fl*bergs%dt,0.) ! new FL length (m)
-            Wnfl=max(Wfl-Mv_fl*bergs%dt,0.) ! new FL width (m)
-            nVolfl=Tnfl*Wnfl*Lnfl ! new footloose volume (m^3)
-            Mnew2_fl=(nVolfl/Volfl)*Mfl !new FL mass (kg), after buoyant convection
-            dMv_fl=Mnew1_fl-Mnew2_fl
-            !erosion
-            Lnfl=max(Lnfl-Me_fl*bergs%dt,0.) ! new FL length (m)
-            Wnfl=max(Wnfl-Me_fl*bergs%dt,0.) ! new FL width (m)
-            nVolfl=Tnfl*Wnfl*Lnfl ! new footloose volume (m^3)
-            Mnew_fl=(nVolfl/Volfl)*Mfl !new FL mass (kg), after all melt and erosion
-            dMe_fl=Mnew2_fl-Mnew_fl !FL mass lost to erosion (>0) (kg)
-          else
-            Lnfl=max(Lfl-(Mv_fl+Me_fl)*bergs%dt,0.) ! (m)
-            Wnfl=max(Wfl-(Mv_fl+Me_fl)*bergs%dt,0.) ! (m)
-            nVolfl=Tnfl*Wnfl*Lnfl ! new footloose volume (m^3)
-            Mnew_fl=(nVolfl/Volfl)*Mfl ! new footloose mass (kg)
-            dMb_fl=(Mfl/Volfl)*(Wfl*Lfl)*Mb_fl*bergs%dt       !approx. FL mass loss to basal melting (kg)
-            dMe_fl=(Mfl/Volfl)*(Tfl*(Wfl+Lfl))*Me_fl*bergs%dt !approx. FL mass loss to erosion (kg)
-            dMv_fl=(Mfl/Volfl)*(Tfl*(Wfl+Lfl))*Mv_fl*bergs%dt !approx. FL mass loss to buoyant convection (kg)
-          endif
-          dMfl=Mfl-Mnew_fl ! total footloose mass lost to all erosion and melting (>0) (kg)
+          Lnfl=max(Lfl-(Mv_fl+Me_fl)*bergs%dt,0.) ! (m)
+          Wnfl=max(Wfl-(Mv_fl+Me_fl)*bergs%dt,0.) ! (m)
+          nVolfl=Tnfl*Wnfl*Lnfl ! new footloose volume (m^3)
+          Mnew_fl=(nVolfl/Volfl)*Mfl ! new footloose mass (kg)
+          dMb_fl=(Mfl/Volfl)*(Wfl*Lfl)*Mb_fl*bergs%dt       !approx. FL mass loss to basal melting (kg)
+          dMe_fl=(Mfl/Volfl)*(Tfl*(Wfl+Lfl))*Me_fl*bergs%dt !approx. FL mass loss to erosion (kg)
+          dMv_fl=(Mfl/Volfl)*(Tfl*(Wfl+Lfl))*Mv_fl*bergs%dt !approx. FL mass loss to buoyant convection (kg)
         endif
+        dMfl=Mfl-Mnew_fl ! total footloose mass lost to all erosion and melting (>0) (kg)
       else
         dMfl=0.; dMb_fl=0.; dMv_fl=0.; dMe_fl=0.
         Mnew_fl=this%mass_of_fl_bits ! retain previous value incase non-zero
@@ -3420,16 +3404,11 @@ subroutine fl_bits_dimensions(bergs,this,L_fl,W_fl,T_fl)
   real,parameter :: B_c=1.e8/(12.*(1.-0.3**2.)) !youngs=1.e8, poisson=0.3
   real :: l_w,l_b
 
-  if (bergs%fl_melt_as_bergy_bits) then
-    L_fl=min(this%length,this%width,this%thickness,40.)
-    T_fl=L_fl; W_fl=(this%mass_of_fl_bits/bergs%rho_bergs)/(L_fl*T_fl)
-  else
-    l_w  = (lw_c*B_c*(this%thickness**3.))**0.25  !buoyancy length
-    l_b  = l_c*l_w !length of a freshly calved footloose child berg
-    L_fl = bergs%fl_bits_scale_l*3.*l_b; W_fl=bergs%fl_bits_scale_w*l_b
-    T_fl=bergs%fl_bits_scale_t*this%thickness
-    call rolling(bergs,T_fl,W_fl,L_fl)
-  endif
+  l_w  = (lw_c*B_c*(this%thickness**3.))**0.25  !buoyancy length
+  l_b  = l_c*l_w !length of a freshly calved footloose child berg
+  L_fl = bergs%fl_bits_scale_l*3.*l_b; W_fl=bergs%fl_bits_scale_w*l_b
+  T_fl=bergs%fl_bits_scale_t*this%thickness
+  call rolling(bergs,T_fl,W_fl,L_fl)
 end subroutine fl_bits_dimensions
 
 
@@ -5513,7 +5492,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   if (sample_traj .or. bergs%writeandstop) call record_posn(bergs)
   if (write_traj .or. bergs%writeandstop) then
     call move_all_trajectories(bergs)
-    call write_trajectory(bergs%trajectories, bergs%save_short_traj)
+    call write_trajectory(bergs%trajectories, bergs%save_short_traj, bergs%save_fl_traj)
     if (save_bond_traj) call write_bond_trajectory(bergs%bond_trajectories)
   endif
 
@@ -8267,7 +8246,7 @@ subroutine icebergs_end(bergs)
   call move_all_trajectories(bergs, delete_bergs=.true.)
 
   if (.not. bergs%ignore_traj) then
-    call write_trajectory(bergs%trajectories, bergs%save_short_traj)
+    call write_trajectory(bergs%trajectories, bergs%save_short_traj, bergs%save_fl_traj)
     if (save_bond_traj) call write_bond_trajectory(bergs%bond_trajectories)
   endif
 
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 52c813b..e7bb83c 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -19,7 +19,7 @@ module ice_bergs_framework
 implicit none ; private
 
 integer :: buffer_width=36 ! This should be a parameter
-integer :: buffer_width_traj=39 ! This should be a parameter
+integer :: buffer_width_traj=27 ! This should be a parameter
 integer :: buffer_width_bond_traj=11 !This should be a parameter
 integer, parameter :: nclasses=10 ! Number of ice bergs classes
 
@@ -533,6 +533,7 @@ module ice_bergs_framework
   logical :: only_interactive_forces=.False. !< Icebergs only feel interactive forces, and not ocean, wind...
   logical :: halo_debugging=.False. !< Use for debugging halos (remove when its working)
   logical :: save_short_traj=.True. !< True saves only lon,lat,time,id in iceberg_trajectory.nc
+  logical :: save_fl_traj=.False. ! True saves short traj, plus masses and footloose parameters in iceberg_trajectory.nc
   logical :: ignore_traj=.False. !< If true, then model does not write trajectory data at all
   logical :: iceberg_bonds_on=.False. !< True=Allow icebergs to have bonds, False=don't allow.
   logical :: manually_initialize_bonds=.False. !< True= Bonds are initialize manually.
@@ -627,7 +628,6 @@ module ice_bergs_framework
   real :: fl_r_s=0. !< seconds over which fl_r footloose bergs calve
   logical :: displace_fl_bergs=.true. !< footloose berg positions are randomly assigned along edges of parent berg
   character(len=11) :: fl_style='new_bergs' !< Evolve footloose bergs individually as 'new_bergs', or as a group with size 'fl_bits'
-  logical :: fl_melt_as_bergy_bits=.false. !< Melt footloose bits as bergy_bits
   logical :: fl_bits_erosion_to_bergy_bits=.true. !< Erosion from footloose bits becomes bergy bits
   real :: fl_k_scale_by_perimeter=0 !< If greater than 0, scales FL k by (berg perimeter (m))/(this scaling (m))
   real :: new_berg_from_fl_bits_mass_thres=huge(0.) ! Create a new berg from FL bits when mass_of_fl_bits exceeds this value
@@ -778,6 +778,7 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: only_interactive_forces=.False. ! Icebergs only feel interactive forces, and not ocean, wind...
 logical :: halo_debugging=.False. ! Use for debugging halos (remove when its working)
 logical :: save_short_traj=.True. ! True saves only lon,lat,time,id in iceberg_trajectory.nc
+logical :: save_fl_traj=.False. ! True saves short traj, plus masses and footloose parameters in iceberg_trajectory.nc
 logical :: ignore_traj=.False. ! If true, then model does not traj trajectory data at all
 !logical :: iceberg_bonds_on=.False. ! True=Allow icebergs to have bonds, False=don't allow.
 logical :: manually_initialize_bonds=.False. ! True= Bonds are initialize manually.
@@ -829,7 +830,6 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: fl_r_s=0. !< seconds over which fl_r footloose bergs calve
 logical :: displace_fl_bergs=.true. !< footloose berg positions are randomly assigned along edges of parent berg
 character(len=11) :: fl_style='new_bergs' !< Evolve footloose bergs individually as 'fl_bits', or as a group with size 'bergy_bits' or 'mean_size'
-logical :: fl_melt_as_bergy_bits=.false. !< Melt footloose bits as bergy_bits
 logical :: fl_bits_erosion_to_bergy_bits=.true. !< Erosion from footloose bits becomes bergy bits
 real :: fl_k_scale_by_perimeter=0 !< If greater than 0, scales FL k by (berg perimeter (m))/(this scaling (m))
 real :: new_berg_from_fl_bits_mass_thres=huge(0.) ! Create a new berg from FL bits when mass_of_fl_bits exceeds this value
@@ -860,7 +860,7 @@ subroutine ice_bergs_framework_init(bergs, &
          remove_unused_bergs,force_convergence,explicit_inner_mts,convergence_tolerance,dem,ignore_tangential_force,poisson,&
          dem_spring_coef,dem_damping_coef,dem_beam_test,constant_interaction_LW,constant_length,constant_width,&
          dem_shear_for_frac_only,use_damage,fl_use_poisson_distribution, fl_use_perimeter, fl_r, fl_r_s,displace_fl_bergs,&
-         fl_style,fl_melt_as_bergy_bits,fl_bits_erosion_to_bergy_bits,fl_k_scale_by_perimeter,use_spring_for_land_contact,&
+         fl_style,fl_bits_erosion_to_bergy_bits,fl_k_scale_by_perimeter,use_spring_for_land_contact, save_fl_traj,&
          new_berg_from_fl_bits_mass_thres,fl_bits_scale_l,fl_bits_scale_w,fl_bits_scale_t,separate_distrib_for_n_hemisphere,&
          initial_mass_n, distribution_n, mass_scaling_n, initial_thickness_n
 
@@ -1263,7 +1263,8 @@ subroutine ice_bergs_framework_init(bergs, &
 else
   buffer_width=buffer_width+(max_bonds*5) ! Increase buffer width to include bonds being passed between processors
 endif
-if (save_short_traj) buffer_width_traj=12 ! This is the length of the short buffer used for abrevated traj
+if (save_short_traj) buffer_width_traj=6 ! This is the length of the short buffer used for abrevated traj
+if (save_fl_traj) buffer_width_traj=buffer_width_traj+6
 if (ignore_traj) buffer_width_traj=0 ! If this is true, then all traj files should be ignored
 
 if (use_damage) then
@@ -1343,6 +1344,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%traj_sample_hrs=traj_sample_hrs
   bergs%traj_write_hrs=traj_write_hrs
   bergs%save_short_traj=save_short_traj
+  bergs%save_fl_traj=save_fl_traj
   bergs%ignore_traj=ignore_traj
   bergs%verbose_hrs=verbose_hrs
   bergs%grd%halo=halo
@@ -1452,12 +1454,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%fl_r_s=fl_r_s
   bergs%displace_fl_bergs=displace_fl_bergs
   bergs%fl_style=fl_style
-  bergs%fl_melt_as_bergy_bits=fl_melt_as_bergy_bits
   bergs%fl_bits_erosion_to_bergy_bits=fl_bits_erosion_to_bergy_bits
-  if (fl_style.ne.'new_bergs') then
-    displace_fl_bergs=.false.
-    bergs%fl_melt_as_bergy_bits=.false.
-  endif
   bergs%fl_k_scale_by_perimeter=fl_k_scale_by_perimeter
   bergs%fl_bits_scale_l=fl_bits_scale_l
   bergs%fl_bits_scale_w=fl_bits_scale_w
@@ -3812,12 +3809,13 @@ subroutine increase_ibuffer(old, num_bergs, width)
 end subroutine increase_ibuffer
 
 !> Packs a trajectory entry into a buffer
-subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj)
+subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj, save_fl_traj)
   ! Arguments
   type(xyt), pointer :: traj !< Trajectory entry to pack
   type(buffer), pointer :: buff !< Buffer to pack entry into
   integer, intent(in) :: n !< Position in buffer to place entry
   logical, intent(in) :: save_short_traj !< If true, only use a subset of trajectory data
+  logical, intent(in) :: save_fl_traj !< If true, save masses and footloose parameters
   ! Local variables
   integer :: counter ! Position in stack
   integer :: cnt, ij
@@ -3833,26 +3831,23 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj)
   call split_id(traj%id, cnt, ij)
   call push_buffer_value(buff%data(:,n),counter,cnt)
   call push_buffer_value(buff%data(:,n),counter,ij)
-  call push_buffer_value(buff%data(:,n),counter,traj%mass)
-  call push_buffer_value(buff%data(:,n),counter,traj%start_mass)
-  call push_buffer_value(buff%data(:,n),counter,traj%mass_of_bits)
-  call push_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bits)
-  call push_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bergy_bits)
-  call push_buffer_value(buff%data(:,n),counter,traj%fl_k)
+  if (save_fl_traj) then
+    call push_buffer_value(buff%data(:,n),counter,traj%mass)
+    call push_buffer_value(buff%data(:,n),counter,traj%start_mass)
+    call push_buffer_value(buff%data(:,n),counter,traj%mass_of_bits)
+    call push_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bits)
+    call push_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bergy_bits)
+    call push_buffer_value(buff%data(:,n),counter,traj%fl_k)
+  endif
   if (.not. save_short_traj) then
     call push_buffer_value(buff%data(:,n),counter,traj%uvel)
     call push_buffer_value(buff%data(:,n),counter,traj%vvel)
     call push_buffer_value(buff%data(:,n),counter,traj%uvel_prev)
     call push_buffer_value(buff%data(:,n),counter,traj%vvel_prev)
-    ! call push_buffer_value(buff%data(:,n),counter,traj%mass)
-    ! call push_buffer_value(buff%data(:,n),counter,traj%mass_of_bits)
-    ! call push_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bits)
-    ! call push_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bergy_bits)
     call push_buffer_value(buff%data(:,n),counter,traj%heat_density)
     call push_buffer_value(buff%data(:,n),counter,traj%thickness)
     call push_buffer_value(buff%data(:,n),counter,traj%width)
     call push_buffer_value(buff%data(:,n),counter,traj%length)
-    ! call push_buffer_value(buff%data(:,n),counter,traj%fl_k)
     call push_buffer_value(buff%data(:,n),counter,traj%uo)
     call push_buffer_value(buff%data(:,n),counter,traj%vo)
     call push_buffer_value(buff%data(:,n),counter,traj%ui)
@@ -3911,12 +3906,13 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj)
 end subroutine pack_traj_into_buffer2
 
 !> Unpacks a trajectory entry from a buffer
-subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj)
+subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj, save_fl_traj)
   ! Arguments
   type(xyt), pointer :: first !< Trajectory list
   type(buffer), pointer :: buff !< Buffer from which to unpack
   integer, intent(in) :: n !< Position in buffer to unpack
   logical, intent(in) :: save_short_traj !< If true, only use a subset of trajectory data
+  logical, intent(in) :: save_fl_traj !< If true, save masses and footloose parameters
   ! Local variables
   type(xyt) :: traj
   integer :: counter ! Position in stack
@@ -3949,26 +3945,23 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj)
   call pull_buffer_value(buff%data(:,n),counter,cnt)
   call pull_buffer_value(buff%data(:,n),counter,ij)
   traj%id = id_from_2_ints(cnt, ij)
-  call pull_buffer_value(buff%data(:,n),counter,traj%mass)
-  call pull_buffer_value(buff%data(:,n),counter,traj%start_mass)
-  call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_bits)
-  call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bits)
-  call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bergy_bits)
-  call pull_buffer_value(buff%data(:,n),counter,traj%fl_k)
+  if (save_fl_traj) then
+    call pull_buffer_value(buff%data(:,n),counter,traj%mass)
+    call pull_buffer_value(buff%data(:,n),counter,traj%start_mass)
+    call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_bits)
+    call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bits)
+    call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bergy_bits)
+    call pull_buffer_value(buff%data(:,n),counter,traj%fl_k)
+  endif
   if (.not. save_short_traj) then
     call pull_buffer_value(buff%data(:,n),counter,traj%uvel)
     call pull_buffer_value(buff%data(:,n),counter,traj%vvel)
     call pull_buffer_value(buff%data(:,n),counter,traj%uvel_prev)
     call pull_buffer_value(buff%data(:,n),counter,traj%vvel_prev)
-    ! call pull_buffer_value(buff%data(:,n),counter,traj%mass)
-    ! call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_bits)
-    ! call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bits)
-    ! call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bergy_bits)
     call pull_buffer_value(buff%data(:,n),counter,traj%heat_density)
     call pull_buffer_value(buff%data(:,n),counter,traj%thickness)
     call pull_buffer_value(buff%data(:,n),counter,traj%width)
     call pull_buffer_value(buff%data(:,n),counter,traj%length)
-    ! call pull_buffer_value(buff%data(:,n),counter,traj%fl_k)
     call pull_buffer_value(buff%data(:,n),counter,traj%uo)
     call pull_buffer_value(buff%data(:,n),counter,traj%vo)
     call pull_buffer_value(buff%data(:,n),counter,traj%ui)
@@ -5852,26 +5845,23 @@ subroutine record_posn(bergs)
       posn%year=bergs%current_year
       posn%day=bergs%current_yearday
       posn%id=this%id
-      posn%mass=this%mass
-      posn%start_mass=this%start_mass
-      posn%mass_of_bits=this%mass_of_bits
-      posn%mass_of_fl_bits=this%mass_of_fl_bits
-      posn%mass_of_fl_bergy_bits=this%mass_of_fl_bergy_bits
-      posn%fl_k=this%fl_k
+      if (bergs%save_fl_traj) then
+        posn%mass=this%mass
+        posn%start_mass=this%start_mass
+        posn%mass_of_bits=this%mass_of_bits
+        posn%mass_of_fl_bits=this%mass_of_fl_bits
+        posn%mass_of_fl_bergy_bits=this%mass_of_fl_bergy_bits
+        posn%fl_k=this%fl_k
+      endif
       if (.not. bergs%save_short_traj) then !Not totally sure that this is correct
         posn%uvel=this%uvel
         posn%vvel=this%vvel
         posn%uvel_prev=this%uvel_prev
         posn%vvel_prev=this%vvel_prev
-        ! posn%mass=this%mass
-        ! posn%mass_of_bits=this%mass_of_bits
-        ! posn%mass_of_fl_bits=this%mass_of_fl_bits
-        ! posn%mass_of_fl_bergy_bits=this%mass_of_fl_bergy_bits
         posn%heat_density=this%heat_density
         posn%thickness=this%thickness
         posn%width=this%width
         posn%length=this%length
-        ! posn%fl_k=this%fl_k
         posn%uo=this%uo
         posn%vo=this%vo
         posn%ui=this%ui
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index c78b413..64aeed8 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -1683,10 +1683,11 @@ subroutine read_ocean_depth(grd)
 end subroutine read_ocean_depth
 
 !> Write a trajectory-based diagnostics file
-subroutine write_trajectory(trajectory, save_short_traj)
+subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj)
 ! Arguments
 type(xyt), pointer :: trajectory !< An iceberg trajectory
 logical, intent(in) :: save_short_traj !< If true, record less data
+logical, intent(in) :: save_fl_traj !< If true, save masses and footloose data
 ! Local variables
 integer :: iret, ncid, i_dim, i
 integer :: lonid, latid, yearid, dayid, uvelid, vvelid, idcntid, idijid
@@ -1745,7 +1746,7 @@ subroutine write_trajectory(trajectory, save_short_traj)
            call increase_ibuffer(ibuffer_io, ntrajs_rcvd_io,buffer_width_traj)
            call mpp_recv(ibuffer_io%data, ntrajs_rcvd_io*buffer_width_traj,from_pe=from_pe, tag=COMM_TAG_12)
            do i=1, ntrajs_rcvd_io
-              call unpack_traj_from_buffer2(traj4io, ibuffer_io, i, save_short_traj)
+              call unpack_traj_from_buffer2(traj4io, ibuffer_io, i, save_short_traj, save_fl_traj)
            enddo
        endif
      enddo
@@ -1753,7 +1754,7 @@ subroutine write_trajectory(trajectory, save_short_traj)
      ! Pack and send trajectories to the root PE for this I/O tile
      do while (associated(trajectory))
        ntrajs_sent_io = ntrajs_sent_io +1
-       call pack_traj_into_buffer2(trajectory, obuffer_io, ntrajs_sent_io, save_short_traj)
+       call pack_traj_into_buffer2(trajectory, obuffer_io, ntrajs_sent_io, save_short_traj, save_fl_traj)
        this => trajectory ! Need to keep pointer in order to free up the links memory
        trajectory => trajectory%next ! This will eventually result in trajectory => null()
        deallocate(this) ! Delete the link from memory
@@ -1815,12 +1816,14 @@ subroutine write_trajectory(trajectory, save_short_traj)
       dayid = inq_varid(ncid, 'day')
       idcntid = inq_varid(ncid, 'id_cnt')
       idijid = inq_varid(ncid, 'id_ij')
-      mid = inq_varid(ncid, 'mass')
-      smid = inq_varid(ncid, 'start_mass')
-      mbid = inq_varid(ncid, 'mass_of_bits')
-      mflbid = inq_varid(ncid, 'mass_of_fl_bits')
-      mflbbid = inq_varid(ncid, 'mass_of_fl_bergy_bits')
-      flkid = inq_varid(ncid, 'fl_k')
+      if (save_fl_traj) then
+        mid = inq_varid(ncid, 'mass')
+        smid = inq_varid(ncid, 'start_mass')
+        mbid = inq_varid(ncid, 'mass_of_bits')
+        mflbid = inq_varid(ncid, 'mass_of_fl_bits')
+        mflbbid = inq_varid(ncid, 'mass_of_fl_bergy_bits')
+        flkid = inq_varid(ncid, 'fl_k')
+      endif
       if (.not.save_short_traj) then
         uvelid = inq_varid(ncid, 'uvel')
         vvelid = inq_varid(ncid, 'vvel')
@@ -1832,15 +1835,10 @@ subroutine write_trajectory(trajectory, save_short_traj)
         viid = inq_varid(ncid, 'vi')
         uaid = inq_varid(ncid, 'ua')
         vaid = inq_varid(ncid, 'va')
-        ! mid = inq_varid(ncid, 'mass')
-        ! mbid = inq_varid(ncid, 'mass_of_bits')
-        ! mflbid = inq_varid(ncid, 'mass_of_fl_bits')
-        ! mflbbid = inq_varid(ncid, 'mass_of_fl_bergy_bits')
         hdid = inq_varid(ncid, 'heat_density')
         did = inq_varid(ncid, 'thickness')
         wid = inq_varid(ncid, 'width')
         lid = inq_varid(ncid, 'length')
-        ! flkid = inq_varid(ncid, 'fl_k')
         sshxid = inq_varid(ncid, 'ssh_x')
         sshyid = inq_varid(ncid, 'ssh_y')
         sstid = inq_varid(ncid, 'sst')
@@ -1900,12 +1898,14 @@ subroutine write_trajectory(trajectory, save_short_traj)
       dayid = def_var(ncid, 'day', NF_DOUBLE, i_dim)
       idcntid = def_var(ncid, 'id_cnt', NF_INT, i_dim)
       idijid = def_var(ncid, 'id_ij', NF_INT, i_dim)
-      mid = def_var(ncid, 'mass', NF_DOUBLE, i_dim)
-      smid = def_var(ncid, 'start_mass', NF_DOUBLE, i_dim)
-      mbid = def_var(ncid, 'mass_of_bits', NF_DOUBLE, i_dim)
-      mflbid = def_var(ncid, 'mass_of_fl_bits', NF_DOUBLE, i_dim)
-      mflbbid = def_var(ncid, 'mass_of_fl_bergy_bits', NF_DOUBLE, i_dim)
-      flkid = def_var(ncid, 'fl_k', NF_DOUBLE, i_dim)
+      if (save_fl_traj) then
+        mid = def_var(ncid, 'mass', NF_DOUBLE, i_dim)
+        smid = def_var(ncid, 'start_mass', NF_DOUBLE, i_dim)
+        mbid = def_var(ncid, 'mass_of_bits', NF_DOUBLE, i_dim)
+        mflbid = def_var(ncid, 'mass_of_fl_bits', NF_DOUBLE, i_dim)
+        mflbbid = def_var(ncid, 'mass_of_fl_bergy_bits', NF_DOUBLE, i_dim)
+        flkid = def_var(ncid, 'fl_k', NF_DOUBLE, i_dim)
+      endif
       if (.not. save_short_traj) then
         uvelid = def_var(ncid, 'uvel', NF_DOUBLE, i_dim)
         vvelid = def_var(ncid, 'vvel', NF_DOUBLE, i_dim)
@@ -1917,15 +1917,10 @@ subroutine write_trajectory(trajectory, save_short_traj)
         viid = def_var(ncid, 'vi', NF_DOUBLE, i_dim)
         uaid = def_var(ncid, 'ua', NF_DOUBLE, i_dim)
         vaid = def_var(ncid, 'va', NF_DOUBLE, i_dim)
-        ! mid = def_var(ncid, 'mass', NF_DOUBLE, i_dim)
-        ! mbid = def_var(ncid, 'mass_of_bits', NF_DOUBLE, i_dim)
-        ! mflbid = def_var(ncid, 'mass_of_fl_bits', NF_DOUBLE, i_dim)
-        ! mflbbid = def_var(ncid, 'mass_of_fl_bergy_bits', NF_DOUBLE, i_dim)
         hdid = def_var(ncid, 'heat_density', NF_DOUBLE, i_dim)
         did = def_var(ncid, 'thickness', NF_DOUBLE, i_dim)
         wid = def_var(ncid, 'width', NF_DOUBLE, i_dim)
         lid = def_var(ncid, 'length', NF_DOUBLE, i_dim)
-        ! flkid = def_var(ncid, 'fl_k', NF_DOUBLE, i_dim)
         sshxid = def_var(ncid, 'ssh_x', NF_DOUBLE, i_dim)
         sshyid = def_var(ncid, 'ssh_y', NF_DOUBLE, i_dim)
         sstid = def_var(ncid, 'sst', NF_DOUBLE, i_dim)
@@ -1988,18 +1983,20 @@ subroutine write_trajectory(trajectory, save_short_traj)
       call put_att(ncid, idcntid, 'units', 'dimensionless')
       call put_att(ncid, idijid, 'long_name', 'position component of iceberg id')
       call put_att(ncid, idijid, 'units', 'dimensionless')
-      call put_att(ncid, mid, 'long_name', 'mass')
-      call put_att(ncid, mid, 'units', 'kg')
-      call put_att(ncid, smid, 'long_name', 'start_mass')
-      call put_att(ncid, smid, 'units', 'kg')
-      call put_att(ncid, mbid, 'long_name', 'mass_of_bits')
-      call put_att(ncid, mbid, 'units', 'kg')
-      call put_att(ncid, mflbid, 'long_name', 'mass_of_fl_bits')
-      call put_att(ncid, mflbid, 'units', 'kg')
-      call put_att(ncid, mflbbid, 'long_name', 'mass_of_fl_bergy_bits')
-      call put_att(ncid, mflbbid, 'units', 'kg')
-      call put_att(ncid, flkid, 'long_name', 'footloose calving k')
-      call put_att(ncid, flkid, 'units', 'none')
+      if (save_fl_traj) then
+        call put_att(ncid, mid, 'long_name', 'mass')
+        call put_att(ncid, mid, 'units', 'kg')
+        call put_att(ncid, smid, 'long_name', 'start_mass')
+        call put_att(ncid, smid, 'units', 'kg')
+        call put_att(ncid, mbid, 'long_name', 'mass_of_bits')
+        call put_att(ncid, mbid, 'units', 'kg')
+        call put_att(ncid, mflbid, 'long_name', 'mass_of_fl_bits')
+        call put_att(ncid, mflbid, 'units', 'kg')
+        call put_att(ncid, mflbbid, 'long_name', 'mass_of_fl_bergy_bits')
+        call put_att(ncid, mflbbid, 'units', 'kg')
+        call put_att(ncid, flkid, 'long_name', 'footloose calving k')
+        call put_att(ncid, flkid, 'units', 'none')
+      endif
       if (.not. save_short_traj) then
         call put_att(ncid, uvelid, 'long_name', 'zonal spped')
         call put_att(ncid, uvelid, 'units', 'm/s')
@@ -2017,14 +2014,6 @@ subroutine write_trajectory(trajectory, save_short_traj)
         call put_att(ncid, uaid, 'units', 'm/s')
         call put_att(ncid, vaid, 'long_name', 'atmos meridional spped')
         call put_att(ncid, vaid, 'units', 'm/s')
-        ! call put_att(ncid, mid, 'long_name', 'mass')
-        ! call put_att(ncid, mid, 'units', 'kg')
-        ! call put_att(ncid, mbid, 'long_name', 'mass_of_bits')
-        ! call put_att(ncid, mbid, 'units', 'kg')
-        ! call put_att(ncid, mflbid, 'long_name', 'mass_of_fl_bits')
-        ! call put_att(ncid, mflbid, 'units', 'kg')
-        ! call put_att(ncid, mflbbid, 'long_name', 'mass_of_fl_bergy_bits')
-        ! call put_att(ncid, mflbbid, 'units', 'kg')
         call put_att(ncid, hdid, 'long_name', 'heat_density')
         call put_att(ncid, hdid, 'units', 'J/kg')
         call put_att(ncid, did, 'long_name', 'thickness')
@@ -2033,8 +2022,6 @@ subroutine write_trajectory(trajectory, save_short_traj)
         call put_att(ncid, wid, 'units', 'm')
         call put_att(ncid, lid, 'long_name', 'length')
         call put_att(ncid, lid, 'units', 'm')
-        ! call put_att(ncid, flkid, 'long_name', 'footloose calving k')
-        ! call put_att(ncid, flkid, 'units', 'none')
         call put_att(ncid, sshxid, 'long_name', 'sea surface height gradient_x')
         call put_att(ncid, sshxid, 'units', 'non-dim')
         call put_att(ncid, sshyid, 'long_name', 'sea surface height gradient_y')
@@ -2139,12 +2126,14 @@ subroutine write_trajectory(trajectory, save_short_traj)
       call split_id(this%id, cnt, ij)
       call put_int(ncid, idcntid, i, cnt)
       call put_int(ncid, idijid, i, ij)
-      call put_double(ncid, mid, i, this%mass)
-      call put_double(ncid, smid, i, this%start_mass)
-      call put_double(ncid, mbid, i, this%mass_of_bits)
-      call put_double(ncid, mflbid, i, this%mass_of_fl_bits)
-      call put_double(ncid, mflbbid, i, this%mass_of_fl_bergy_bits)
-      call put_double(ncid, flkid, i, this%fl_k)
+      if (save_fl_traj) then
+        call put_double(ncid, mid, i, this%mass)
+        call put_double(ncid, smid, i, this%start_mass)
+        call put_double(ncid, mbid, i, this%mass_of_bits)
+        call put_double(ncid, mflbid, i, this%mass_of_fl_bits)
+        call put_double(ncid, mflbbid, i, this%mass_of_fl_bergy_bits)
+        call put_double(ncid, flkid, i, this%fl_k)
+      endif
       if (.not. save_short_traj) then
         call put_double(ncid, uvelid, i, this%uvel)
         call put_double(ncid, vvelid, i, this%vvel)
@@ -2156,15 +2145,10 @@ subroutine write_trajectory(trajectory, save_short_traj)
         call put_double(ncid, viid, i, this%vi)
         call put_double(ncid, uaid, i, this%ua)
         call put_double(ncid, vaid, i, this%va)
-        ! call put_double(ncid, mid, i, this%mass)
-        ! call put_double(ncid, mbid, i, this%mass_of_bits)
-        ! call put_double(ncid, mflbid, i, this%mass_of_fl_bits)
-        ! call put_double(ncid, mflbbid, i, this%mass_of_fl_bergy_bits)
         call put_double(ncid, hdid, i, this%heat_density)
         call put_double(ncid, did, i, this%thickness)
         call put_double(ncid, wid, i, this%width)
         call put_double(ncid, lid, i, this%length)
-        ! call put_double(ncid, flkid, i, this%fl_k)
         call put_double(ncid, sshxid, i, this%ssh_x)
         call put_double(ncid, sshyid, i, this%ssh_y)
         call put_double(ncid, sstid, i, this%sst)

From 677fdb1ab9fd104f0094e52ce7b026e00653265b Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Mon, 10 May 2021 14:41:39 -0400
Subject: [PATCH 306/361] fix traj buffer width

---
 src/icebergs_framework.F90             | 2 +-
 tests/footloose_no_bond_test/input.nml | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index e7bb83c..c3cef50 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -19,7 +19,7 @@ module ice_bergs_framework
 implicit none ; private
 
 integer :: buffer_width=36 ! This should be a parameter
-integer :: buffer_width_traj=27 ! This should be a parameter
+integer :: buffer_width_traj=33 ! This should be a parameter
 integer :: buffer_width_bond_traj=11 !This should be a parameter
 integer, parameter :: nclasses=10 ! Number of ice bergs classes
 
diff --git a/tests/footloose_no_bond_test/input.nml b/tests/footloose_no_bond_test/input.nml
index 2813527..64159c7 100644
--- a/tests/footloose_no_bond_test/input.nml
+++ b/tests/footloose_no_bond_test/input.nml
@@ -32,7 +32,6 @@
     fl_r_s=86400  !(86400) time in s over which to calve, on average, fl_r footloose bergs
     displace_fl_bergs=.true. !(T) randomly assign FL berg positions to sides of parent berg
     fl_style='fl_bits' !('new_bergs'). Can also group FL bergs into 'fl_bits'
-    fl_melt_as_bergy_bits=.false.!true. !(F) If fl_style==fl_bits, melt the fl_bits as bergy bits
     new_berg_from_fl_bits_mass_thres=8.e11
     fl_use_poisson_distribution=.true.!.false.
 
@@ -55,7 +54,7 @@
     tangental_damping_coef=2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
     critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
     LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0.0 ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    bergy_bit_erosion_fraction=1.0 ! (0.) Fraction of erosion melt flux to divert to bergy bits
     sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
     u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
     v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
@@ -115,6 +114,7 @@
 
     parallel_reprod=.true. !(T) Reproduce across different PE decompositions
     save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    save_fl_traj=.true. !(T) True save masses and footloose parameters in iceberg_trajectory.nc
     ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
 
     ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart

From 40e0d449bf902a35f9aa543d04ce09ea327cfddc Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Tue, 11 May 2021 12:18:20 -0400
Subject: [PATCH 307/361] (1) Added real nml parameter traj_area_thres, a
 threshold for berg area (km^2) that must be exceeded to save a non-bonded
 berg trajectory. This will reduce computational cost of producing trajectory
 data, by ignoring trajectories of small bergs. The BYU/NIC database of berg
 trajectories ignores bergs with areas less than 5 km^2, so setting
 traj_area_thres=5 would be appropriate to generate modeled trajectories for
 comparison. (2) Added documentation where it was missing.

---
 src/icebergs.F90           |  16 +-
 src/icebergs_framework.F90 | 324 +++++++++++++++++++------------------
 src/icebergs_io.F90        |   7 +-
 3 files changed, 184 insertions(+), 163 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 620bfd3..fda6ebb 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -2733,12 +2733,14 @@ subroutine footloose_calving(bergs, time)
 
 contains
 
-  !TODO: finish this
+  !> Get maximum number of footloose bergs that can calve over a timestep for bonded edge elements.
+  !> \todo finish this
   subroutine max_k_for_edge_elements
     !for most edge elements, maxk=huge(1.0)
     max_k=huge(1.0)
   end subroutine max_k_for_edge_elements
 
+  !> Determine random displacement of footloose child bergs from parent berg
   subroutine get_footloose_displacement
     real :: lon1,lat1,x1,y1,dxdl1,dydl,xdot2,ydot2
     logical :: on_tangential_plane
@@ -3379,9 +3381,11 @@ subroutine rolling(bergs,Tn,Wn,Ln)
 
 contains
 
+  !> swap values between two parameters
   subroutine swap_variables(x,y)
     ! Arguments
-    real, intent(inout) :: x, y
+    real, intent(inout) :: x !< first parameter
+    real, intent(inout) :: y !< second parameter
     real :: temp
     temp=x
     x=y
@@ -3411,7 +3415,7 @@ subroutine fl_bits_dimensions(bergs,this,L_fl,W_fl,T_fl)
   call rolling(bergs,T_fl,W_fl,L_fl)
 end subroutine fl_bits_dimensions
 
-
+!> Generate gridded fields from icebergs
 subroutine create_gridded_icebergs_fields(bergs)
 ! Arguments
 type(icebergs), pointer :: bergs !< Container for all types and memory
@@ -4694,6 +4698,7 @@ subroutine Hexagon_into_quadrants_using_triangles(x0, y0, H, theta, Area_hex ,Ar
 
  end subroutine Hexagon_into_quadrants_using_triangles
 
+!> Loop through all bergs and call interp_flds
 subroutine interp_gridded_fields_to_bergs(bergs)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
@@ -4732,7 +4737,7 @@ subroutine interp_gridded_fields_to_bergs(bergs)
 
 end subroutine interp_gridded_fields_to_bergs
 
-
+!> Interpolate ocean, sea ice, and atmosphere fields from grid to iceberg
 subroutine interp_flds(grd, x, y, i, j, xi, yj, rx, ry, uo, vo, ui, vi, ua, va, ssh_x, ssh_y, sst, sss, cn, hi, od)
   ! Arguments
   type(icebergs_gridded), pointer :: grd !< Container for gridded fields
@@ -8335,9 +8340,10 @@ subroutine icebergs_end(bergs)
 
 end subroutine icebergs_end
 
+!> deallocate a buffer
 subroutine dealloc_buffer(buff)
   ! Arguments
-  type(buffer), pointer :: buff
+  type(buffer), pointer :: buff !< the buffer
   ! Local variables
     if (associated(buff)) then
       if (associated(buff%data)) deallocate(buff%data)
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index c3cef50..00e895e 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -461,6 +461,7 @@ module ice_bergs_framework
              !! \todo Should make dt adaptive?
   integer :: current_year !< Current year (years)
   real :: current_yearday !< Current year-day, 1.00-365.99, (days)
+  real :: traj_area_thres !< Threshold for berg area (km^2) that must be exceeded to save a non-bonded berg trajectory
   real :: traj_sample_hrs !< Period between sampling for trajectories (hours)
   real :: traj_write_hrs !< Period between writing of trajectories (hours)
   real :: verbose_hrs !< Period between terminal status reports (hours)
@@ -631,9 +632,9 @@ module ice_bergs_framework
   logical :: fl_bits_erosion_to_bergy_bits=.true. !< Erosion from footloose bits becomes bergy bits
   real :: fl_k_scale_by_perimeter=0 !< If greater than 0, scales FL k by (berg perimeter (m))/(this scaling (m))
   real :: new_berg_from_fl_bits_mass_thres=huge(0.) ! Create a new berg from FL bits when mass_of_fl_bits exceeds this value
-  real :: fl_bits_scale_l=0.9  !< For determining dimensions of FL bits berg; FL_bits length = fl_bits_scale_l*3*l_b
-  real :: fl_bits_scale_w=0.9 !< For determining dimensions of FL bits berg; FL_bits width = fl_bits_scale_l*3*l_b
-  real :: fl_bits_scale_t=0.9 !< For determining dimensions of FL bits berg; FL_bits thickness = fl_bits_scale_l*T
+  real :: fl_bits_scale_l=0.9 !< For determining dimensions of FL bits berg; FL_bits length    = fl_bits_scale_l * 3*l_b
+  real :: fl_bits_scale_w=0.9 !< For determining dimensions of FL bits berg; FL_bits width     = fl_bits_scale_w * 3*l_b
+  real :: fl_bits_scale_t=0.9 !< For determining dimensions of FL bits berg; FL_bits thickness = fl_bits_scale_t * T
 end type icebergs
 
 !> Read original restarts. Needs to be module global so can be public to icebergs_mod.
@@ -706,6 +707,7 @@ subroutine ice_bergs_framework_init(bergs, &
 
 ! Namelist parameters (and defaults)
 integer :: halo=4 ! Width of halo region
+real :: traj_area_thres=0. ! Threshold for berg area (km^2) that must be exceeded to save a non-bonded berg trajectory
 real :: traj_sample_hrs=24. ! Period between sampling of position for trajectory storage
 real :: traj_write_hrs=480. ! Period between writing sampled trajectories to disk
 real :: verbose_hrs=24. ! Period between verbose messages
@@ -716,10 +718,10 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: uniaxial_test=.false. !adds a tensile stress to the east-most berg element
 real :: cdrag_grounding=0.0 ! Drag coefficient against ocean bottom
 real :: h_to_init_grounding=100.0
-!character(len=11) :: fracture_criterion !<'energy','stress','strain_rate','strain',or 'none'
+!character(len=11) :: fracture_criterion ! 'energy','stress','strain_rate','strain',or 'none'
 real :: frac_thres_n=0.0 !normal fracture strain threshold
 real :: frac_thres_t=0.0 !tangential fracture strain threshold
-logical :: damage_test_1=.false. !< Sets initial damage for bonds that overlap y=17000.0
+logical :: damage_test_1=.false. ! Sets initial damage for bonds that overlap y=17000.0
 real :: frac_thres_scaling=1.0 !scaling factor for frac_thres_n and frac_thres_t, useful for tuning
 logical :: debug_write=.false. !Sets traj_sample_hours=traj_write_hours & includes halo bergs in write
 real :: bond_coef=1.e-8 ! Spring constant for iceberg bonds - not being used right now
@@ -743,8 +745,8 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: add_weight_to_ocean=.true. ! Add weight of icebergs + bits to ocean
 logical :: passive_mode=.false. ! Add weight of icebergs + bits to ocean
 logical :: time_average_weight=.false. ! Time average the weight on the ocean
-real :: length_for_manually_initialize_bonds=1000.0 !<if manually init bonds, only  bond if dist between particles is .lt. this length - Alex
-logical :: manually_initialize_bonds_from_radii=.false. !<if manually init bonds, form bonds if dist between particles is < 1.25x the smaller radii - Alex
+real :: length_for_manually_initialize_bonds=1000.0 ! if manually init bonds, only  bond if dist between particles is .lt. this length - Alex
+logical :: manually_initialize_bonds_from_radii=.false. ! if manually init bonds, form bonds if dist between particles is < 1.25x the smaller radii - Alex
 real :: speed_limit=0. ! CFL speed limit for a berg
 real :: tau_calving=0. ! Time scale for smoothing out calving field (years)
 real :: tip_parameter=0. ! Parameter to override iceberg rolling critical ratio (use zero to get parameter directly from ice and seawater densities
@@ -753,7 +755,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: tidal_drift=0. ! Amplitude of a stochastic tidal velocity added to ocean currents to cause bergs to drift randomly
 logical :: Runge_not_Verlet=.True. ! True=Runge Kutta, False=Verlet.
 logical :: use_mixed_melting=.False. ! If true, then the melt is determined partly using 3 eq model partly using iceberg parameterizations (according to iceberg bond number)
-logical :: internal_bergs_for_drag=.False. !< True=reduces side drag for bonded elements in momentum equation.
+logical :: internal_bergs_for_drag=.False. ! True=reduces side drag for bonded elements in momentum equation.
 logical :: apply_thickness_cutoff_to_gridded_melt=.False. ! Prevents melt for ocean thickness below melt_cuttoff (applied to gridded melt fields)
 logical :: apply_thickness_cutoff_to_bergs_melt=.False. ! Prevents melt for ocean thickness below melt_cuttoff (applied to bergs)
 logical :: use_updated_rolling_scheme=.false. ! Use the corrected Rolling Scheme rather than the erroneous one
@@ -816,33 +818,33 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: poisson=0.3 ! Poisson's ratio
 real :: dem_spring_coef=0.
 real :: dem_damping_coef=0.1
-logical :: dem_shear_for_frac_only=.false. !< If true, DEM shear is calculated for fracture, but zeroed for berg interactions
+logical :: dem_shear_for_frac_only=.false. ! If true, DEM shear is calculated for fracture, but zeroed for berg interactions
 integer :: dem_beam_test=0 !1=Simply supported beam,2=cantilever beam,3=angular vel test
 ! Element Interactions
-logical :: constant_interaction_LW=.false. !< Always use the initial, globally constant, element length & width during berg interactions
-real :: constant_length=0. !< If constant_interaction_LW, the constant length used. If zero in the nml, will be set to max initial L
-real :: constant_width=0. !< If constant_interaction_LW, the constant width used. If zero in the nml, will be set to max initial W
-logical :: use_spring_for_land_contact=.false. !< Treat contact with masked (land) cells like contact with a static berg
+logical :: constant_interaction_LW=.false. ! Always use the initial, globally constant, element length & width during berg interactions
+real :: constant_length=0. ! If constant_interaction_LW, the constant length used. If zero in the nml, will be set to max initial L
+real :: constant_width=0. ! If constant_interaction_LW, the constant width used. If zero in the nml, will be set to max initial W
+logical :: use_spring_for_land_contact=.false. ! Treat contact with masked (land) cells like contact with a static berg
 ! Footloose calving parameters [England et al (2020) Modeling the breakup of tabular icebergs. Sci. Adv.]
-logical :: fl_use_poisson_distribution=.true. !< fl_r is (T) mean of Poisson distribution to determine k, or (F) k=fl_r
-logical :: fl_use_perimeter=.false. !< scale number of footloose bergs to calve by perimeter of the parent berg
-real :: fl_r=0. !< footloose average number of bergs calved per fl_r_s
-real :: fl_r_s=0. !< seconds over which fl_r footloose bergs calve
-logical :: displace_fl_bergs=.true. !< footloose berg positions are randomly assigned along edges of parent berg
-character(len=11) :: fl_style='new_bergs' !< Evolve footloose bergs individually as 'fl_bits', or as a group with size 'bergy_bits' or 'mean_size'
-logical :: fl_bits_erosion_to_bergy_bits=.true. !< Erosion from footloose bits becomes bergy bits
-real :: fl_k_scale_by_perimeter=0 !< If greater than 0, scales FL k by (berg perimeter (m))/(this scaling (m))
+logical :: fl_use_poisson_distribution=.true. ! fl_r is (T) mean of Poisson distribution to determine k, or (F) k=fl_r
+logical :: fl_use_perimeter=.false. ! scale number of footloose bergs to calve by perimeter of the parent berg
+real :: fl_r=0. ! footloose average number of bergs calved per fl_r_s
+real :: fl_r_s=0. ! seconds over which fl_r footloose bergs calve
+logical :: displace_fl_bergs=.true. ! footloose berg positions are randomly assigned along edges of parent berg
+character(len=11) :: fl_style='new_bergs' ! Evolve footloose bergs individually as 'fl_bits', or as a group with size 'bergy_bits' or 'mean_size'
+logical :: fl_bits_erosion_to_bergy_bits=.true. ! Erosion from footloose bits becomes bergy bits
+real :: fl_k_scale_by_perimeter=0 ! If greater than 0, scales FL k by (berg perimeter (m))/(this scaling (m))
 real :: new_berg_from_fl_bits_mass_thres=huge(0.) ! Create a new berg from FL bits when mass_of_fl_bits exceeds this value
-real :: fl_bits_scale_l=0.9 !< For determining dimensions of FL bits berg; FL_bits length = fl_bits_scale_l*3*l_b
-real :: fl_bits_scale_w=0.9 !< For determining dimensions of FL bits berg; FL_bits width = fl_bits_scale_l*l_b
-real :: fl_bits_scale_t=0.9 !< For determining dimensions of FL bits berg; FL_bits thickness = fl_bits_scale_l*T
+real :: fl_bits_scale_l=0.9 ! For determining dimensions of FL bits berg; FL_bits length    = fl_bits_scale_l * 3*l_b
+real :: fl_bits_scale_w=0.9 ! For determining dimensions of FL bits berg; FL_bits width     = fl_bits_scale_w * l_b
+real :: fl_bits_scale_t=0.9 ! For determining dimensions of FL bits berg; FL_bits thickness = fl_bits_scale_t * T
 
 namelist /icebergs_nml/ verbose, budget, halo,  traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,&
-         Static_icebergs,distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,bond_coef, &
-         radial_damping_coef, tangental_damping_coef, only_interactive_forces, rho_bergs, LoW_ratio, debug, really_debug, &
-         use_operator_splitting, bergy_bit_erosion_fraction, iceberg_bonds_on, manually_initialize_bonds, &
-         ignore_missing_restart_bergs,  parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode, &
-         ignore_ij_restart, use_new_predictive_corrective, halo_debugging, hexagonal_icebergs, time_average_weight, &
+         traj_area_thres, Static_icebergs,distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,bond_coef,&
+         radial_damping_coef, tangental_damping_coef, only_interactive_forces, rho_bergs, LoW_ratio, debug, really_debug,&
+         use_operator_splitting, bergy_bit_erosion_fraction, iceberg_bonds_on, manually_initialize_bonds,&
+         ignore_missing_restart_bergs,  parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode,&
+         ignore_ij_restart, use_new_predictive_corrective, halo_debugging, hexagonal_icebergs, time_average_weight,&
          generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, interactive_icebergs_on,&
          scale_damping_by_pmag, critical_interaction_damping_on, tang_crit_int_damp_on, require_restart,&
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,&
@@ -850,9 +852,9 @@ subroutine ice_bergs_framework_init(bergs, &
          initial_orientation,rotate_icebergs_for_mass_spreading,grid_is_latlon,Lx,use_f_plane,use_old_spreading,&
          grid_is_regular,override_iceberg_velocities,u_override,v_override,add_iceberg_thickness_to_SSH,&
          Iceberg_melt_without_decay,melt_icebergs_as_ice_shelf, Use_three_equation_model,find_melt_using_spread_mass,&
-         use_mixed_layer_salinity_for_thermo,utide_icebergs,ustar_icebergs_bg,cdrag_icebergs, pass_fields_to_ocean_model, &
+         use_mixed_layer_salinity_for_thermo,utide_icebergs,ustar_icebergs_bg,cdrag_icebergs, pass_fields_to_ocean_model,&
          const_gamma, Gamma_T_3EQ, ignore_traj, debug_iceberg_with_id,use_updated_rolling_scheme, tip_parameter, &
-         read_old_restarts, tau_calving, read_ocean_depth_from_file, melt_cutoff,apply_thickness_cutoff_to_gridded_melt, &
+         read_old_restarts, tau_calving, read_ocean_depth_from_file, melt_cutoff,apply_thickness_cutoff_to_gridded_melt,&
          apply_thickness_cutoff_to_bergs_melt, use_mixed_melting, internal_bergs_for_drag, coastal_drift, tidal_drift,&
          mts,new_mts,ewsame,monitor_energy,mts_sub_steps,contact_distance,length_for_manually_initialize_bonds,&
          manually_initialize_bonds_from_radii,contact_spring_coef,fracture_criterion, damage_test_1, uniaxial_test, &
@@ -1341,6 +1343,7 @@ subroutine ice_bergs_framework_init(bergs, &
 
  ! Parameters
   bergs%dt=dt
+  bergs%traj_area_thres=traj_area_thres
   bergs%traj_sample_hrs=traj_sample_hrs
   bergs%traj_write_hrs=traj_write_hrs
   bergs%save_short_traj=save_short_traj
@@ -3439,9 +3442,10 @@ subroutine pull_buffer_ivalue(vbuf, counter, val)
 
 end subroutine pull_buffer_ivalue
 
+!> Nullify the other_berg pointer for a bond pointing to the current berg
 subroutine clear_berg_from_partners_bonds(berg)
 ! Arguments
-type(iceberg), intent(in), pointer :: berg
+type(iceberg), intent(in), pointer :: berg !< Iceberg to clear from partner bonds
 ! Local variables
 type(iceberg), pointer :: other_berg
 type(bond), pointer :: current_bond, matching_bond
@@ -4245,7 +4249,7 @@ subroutine unpack_duplicate_check(bergs,localberg,duplicate)
   type(iceberg) :: localberg !< Input iceberg
   logical :: duplicate !< True if a duplicate is detected
   ! Local variables
-  type(iceberg), pointer :: this !<bergs for comparison
+  type(iceberg), pointer :: this ! bergs for comparison
 
   duplicate=.false.
   if (.not. bergs%mts) return
@@ -4513,7 +4517,7 @@ end function inorder
 !! \todo Should be able to remove this function if using identifiers properly
 real function time_hash(berg)!  Alon: Think about removing this.
 ! Arguments
-type(iceberg), pointer :: berg
+type(iceberg), pointer :: berg !< An iceberg
   time_hash=berg%start_day+366.*float(berg%start_year)
 end function time_hash
 
@@ -4949,7 +4953,7 @@ subroutine init_dem_params(bergs)
   enddo;enddo
 end subroutine init_dem_params
 
-
+!> Set the accumulated bond rotation to zero for all bergs
 subroutine reset_bond_rotation(bergs)
 type(icebergs), pointer :: bergs !< Container for all types and memory
 type(iceberg), pointer :: this, other_berg
@@ -5300,13 +5304,16 @@ subroutine delete_bond_from_list(berg,bond_to_delete)
   deallocate(bond_to_delete)
 end subroutine delete_bond_from_list
 
+!> Bond two bergs together
 subroutine form_a_bond(berg, other_id, other_berg_ine, other_berg_jne, other_berg)
 ! Arguments
-type(iceberg), pointer :: berg
-type(iceberg), optional,  pointer :: other_berg
+type(iceberg), pointer :: berg !< first berg
+integer(kind=8), intent(in) :: other_id !< ID of the other other berg
+integer, optional  :: other_berg_ine !< second berg zonal cell index
+integer, optional :: other_berg_jne !< second berg meridional cell index
+type(iceberg), optional,  pointer :: other_berg !< second berg
+! Local variables
 type(bond) , pointer :: new_bond, first_bond
-integer(kind=8), intent(in) :: other_id
-integer, optional  :: other_berg_ine, other_berg_jne
 integer :: stderrunit
 
  stderrunit = stderr()
@@ -5794,6 +5801,7 @@ subroutine record_posn(bergs)
 integer :: grdi, grdj
 integer :: js,je,is,ie
 type(bond) , pointer :: current_bond
+real :: area_thres
 ! Local bond variables
 type(bond_xyt) :: bond_posn
 real :: dx_dlon,dy_dlat,lat_ref,dx,dy,n1,n2,id1,id2
@@ -5837,139 +5845,143 @@ subroutine record_posn(bergs)
     endif
   endif
 
+  area_thres=bergs%traj_area_thres*1.e6 ! convert from km^2 to m^2
+
   do grdj = js,je ; do grdi = is,ie
     this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
-      posn%lon=this%lon
-      posn%lat=this%lat
-      posn%year=bergs%current_year
-      posn%day=bergs%current_yearday
-      posn%id=this%id
-      if (bergs%save_fl_traj) then
-        posn%mass=this%mass
-        posn%start_mass=this%start_mass
-        posn%mass_of_bits=this%mass_of_bits
-        posn%mass_of_fl_bits=this%mass_of_fl_bits
-        posn%mass_of_fl_bergy_bits=this%mass_of_fl_bergy_bits
-        posn%fl_k=this%fl_k
-      endif
-      if (.not. bergs%save_short_traj) then !Not totally sure that this is correct
-        posn%uvel=this%uvel
-        posn%vvel=this%vvel
-        posn%uvel_prev=this%uvel_prev
-        posn%vvel_prev=this%vvel_prev
-        posn%heat_density=this%heat_density
-        posn%thickness=this%thickness
-        posn%width=this%width
-        posn%length=this%length
-        posn%uo=this%uo
-        posn%vo=this%vo
-        posn%ui=this%ui
-        posn%vi=this%vi
-        posn%ua=this%ua
-        posn%va=this%va
-        posn%ssh_x=this%ssh_x
-        posn%ssh_y=this%ssh_y
-        posn%sst=this%sst
-        posn%sss=this%sss
-        posn%cn=this%cn
-        posn%hi=this%hi
-        posn%axn=this%axn
-        posn%ayn=this%ayn
-        posn%bxn=this%bxn
-        posn%byn=this%byn
-        posn%halo_berg=this%halo_berg
-        posn%static_berg=this%static_berg
-        posn%od=this%od
-
-        if (bergs%mts) then
-          posn%axn_fast=this%axn_fast
-          posn%ayn_fast=this%ayn_fast
-          posn%bxn_fast=this%bxn_fast
-          posn%byn_fast=this%byn_fast
+      current_bond=>this%first_bond
+      if ( (this%mass/(bergs%rho_bergs*this%thickness)) >= area_thres .or. associated(current_bond) ) then
+        posn%lon=this%lon
+        posn%lat=this%lat
+        posn%year=bergs%current_year
+        posn%day=bergs%current_yearday
+        posn%id=this%id
+        if (bergs%save_fl_traj) then
+          posn%mass=this%mass
+          posn%start_mass=this%start_mass
+          posn%mass_of_bits=this%mass_of_bits
+          posn%mass_of_fl_bits=this%mass_of_fl_bits
+          posn%mass_of_fl_bergy_bits=this%mass_of_fl_bergy_bits
+          posn%fl_k=this%fl_k
         endif
+        if (.not. bergs%save_short_traj) then !Not totally sure that this is correct
+          posn%uvel=this%uvel
+          posn%vvel=this%vvel
+          posn%uvel_prev=this%uvel_prev
+          posn%vvel_prev=this%vvel_prev
+          posn%heat_density=this%heat_density
+          posn%thickness=this%thickness
+          posn%width=this%width
+          posn%length=this%length
+          posn%uo=this%uo
+          posn%vo=this%vo
+          posn%ui=this%ui
+          posn%vi=this%vi
+          posn%ua=this%ua
+          posn%va=this%va
+          posn%ssh_x=this%ssh_x
+          posn%ssh_y=this%ssh_y
+          posn%sst=this%sst
+          posn%sss=this%sss
+          posn%cn=this%cn
+          posn%hi=this%hi
+          posn%axn=this%axn
+          posn%ayn=this%ayn
+          posn%bxn=this%bxn
+          posn%byn=this%byn
+          posn%halo_berg=this%halo_berg
+          posn%static_berg=this%static_berg
+          posn%od=this%od
 
-        if (iceberg_bonds_on) then
-          posn%n_bonds=this%n_bonds
-        end if
+          if (bergs%mts) then
+            posn%axn_fast=this%axn_fast
+            posn%ayn_fast=this%ayn_fast
+            posn%bxn_fast=this%bxn_fast
+            posn%byn_fast=this%byn_fast
+          endif
 
-        if (monitor_energy) then
-          posn%Ee=this%Ee
-          posn%Ed=this%Ed
-          posn%Eext=this%Eext
-          posn%Ee_contact=this%Ee_contact
-          posn%Ed_contact=this%Ed_contact
-          posn%Efrac=this%Efrac
-          ! posn%Ee_contact_temp=this%Ee_contact_temp
-          ! posn%Ed_contact_temp=this%Ed_contact_temp
-          ! posn%Ee_temp=this%Ee_temp
-          ! posn%Ed_temp=this%Ed_temp
-          ! posn%Eext_temp=this%Eext_temp
-        endif
+          if (iceberg_bonds_on) then
+            posn%n_bonds=this%n_bonds
+          end if
 
-        if (dem) then
-          posn%ang_vel=this%ang_vel
-          posn%ang_accel=this%ang_accel
-          posn%rot=this%rot
-        elseif (fracture_criterion .ne. 'none') then
-          posn%accum_bond_rotation=this%accum_bond_rotation
+          if (monitor_energy) then
+            posn%Ee=this%Ee
+            posn%Ed=this%Ed
+            posn%Eext=this%Eext
+            posn%Ee_contact=this%Ee_contact
+            posn%Ed_contact=this%Ed_contact
+            posn%Efrac=this%Efrac
+            ! posn%Ee_contact_temp=this%Ee_contact_temp
+            ! posn%Ed_contact_temp=this%Ed_contact_temp
+            ! posn%Ee_temp=this%Ee_temp
+            ! posn%Ed_temp=this%Ed_temp
+            ! posn%Eext_temp=this%Eext_temp
+          endif
+
+          if (dem) then
+            posn%ang_vel=this%ang_vel
+            posn%ang_accel=this%ang_accel
+            posn%rot=this%rot
+          elseif (fracture_criterion .ne. 'none') then
+            posn%accum_bond_rotation=this%accum_bond_rotation
+          endif
         endif
-      endif
 
-      call push_posn(this%trajectory, posn)
+        call push_posn(this%trajectory, posn)
 
-      if (save_bond_traj) then
-        current_bond=>this%first_bond
-        do while (associated(current_bond)) ! loop over all bonds
-          if  (associated(current_bond%other_berg)) then
-            other_berg=>current_bond%other_berg
+        if (save_bond_traj) then
+          do while (associated(current_bond)) ! loop over all bonds
+            if  (associated(current_bond%other_berg)) then
+              other_berg=>current_bond%other_berg
 
-            ! From icebergs.F90 --> subroutine convert_from_grid_to_meters
-            if (bergs%grd%grid_is_latlon) then
-              lat_ref=0.5*(this%lat+other_berg%lat)
-              dx_dlon=pi_180*Rearth*cos(lat_ref*pi_180);  dy_dlat=pi_180*Rearth
-            else
-              dx_dlon=1.0;                                dy_dlat=1.0
-            endif
+              ! From icebergs.F90 --> subroutine convert_from_grid_to_meters
+              if (bergs%grd%grid_is_latlon) then
+                lat_ref=0.5*(this%lat+other_berg%lat)
+                dx_dlon=pi_180*Rearth*cos(lat_ref*pi_180);  dy_dlat=pi_180*Rearth
+              else
+                dx_dlon=1.0;                                dy_dlat=1.0
+              endif
 
-            dx=(this%lon-other_berg%lon)*dx_dlon; dy=(this%lat-other_berg%lat)*dy_dlat
-            n1=dx/this%length; n2=dy/this%length !unit vector
-            bond_posn%lon=this%lon-dx/2;          bond_posn%lat=this%lat-dy/2
-            bond_posn%year=bergs%current_year;    bond_posn%day=bergs%current_yearday
-            bond_posn%length=current_bond%length;
-            bond_posn%n1=n1;                      bond_posn%n2=n2
-            bond_posn%id1=this%id;                bond_posn%id2=other_berg%id
+              dx=(this%lon-other_berg%lon)*dx_dlon; dy=(this%lat-other_berg%lat)*dy_dlat
+              n1=dx/this%length; n2=dy/this%length !unit vector
+              bond_posn%lon=this%lon-dx/2;          bond_posn%lat=this%lat-dy/2
+              bond_posn%year=bergs%current_year;    bond_posn%day=bergs%current_yearday
+              bond_posn%length=current_bond%length;
+              bond_posn%n1=n1;                      bond_posn%n2=n2
+              bond_posn%id1=this%id;                bond_posn%id2=other_berg%id
 
-            if (use_damage) then
-              bond_posn%damage=current_bond%damage
-            endif
+              if (use_damage) then
+                bond_posn%damage=current_bond%damage
+              endif
 
-            if (monitor_energy) then
-              bond_posn%Ee=current_bond%Ee
-              bond_posn%Ed=current_bond%Ed
-              bond_posn%axn_fast=current_bond%axn_fast
-              bond_posn%ayn_fast=current_bond%ayn_fast
-              bond_posn%bxn_fast=current_bond%bxn_fast
-              bond_posn%byn_fast=current_bond%byn_fast
-            endif
+              if (monitor_energy) then
+                bond_posn%Ee=current_bond%Ee
+                bond_posn%Ed=current_bond%Ed
+                bond_posn%axn_fast=current_bond%axn_fast
+                bond_posn%ayn_fast=current_bond%ayn_fast
+                bond_posn%bxn_fast=current_bond%bxn_fast
+                bond_posn%byn_fast=current_bond%byn_fast
+              endif
 
-            if (dem) then
-              bond_posn%tangd1=current_bond%tangd1
-              bond_posn%tangd2=current_bond%tangd2
-              bond_posn%nstress=current_bond%nstress
-              bond_posn%sstress=current_bond%sstress
-            elseif (fracture_criterion.ne.'none') then
-              bond_posn%rotation=current_bond%rotation
-              bond_posn%rel_rotation=current_bond%rel_rotation
-              bond_posn%n_frac_var=current_bond%n_frac_var
-              if (fracture_criterion.eq.'strain_rate') bond_posn%n_strain_rate=current_bond%n_strain_rate
-              if (fracture_criterion.eq.'energy') bond_posn%spring_pe=current_bond%spring_pe
-            endif
+              if (dem) then
+                bond_posn%tangd1=current_bond%tangd1
+                bond_posn%tangd2=current_bond%tangd2
+                bond_posn%nstress=current_bond%nstress
+                bond_posn%sstress=current_bond%sstress
+              elseif (fracture_criterion.ne.'none') then
+                bond_posn%rotation=current_bond%rotation
+                bond_posn%rel_rotation=current_bond%rel_rotation
+                bond_posn%n_frac_var=current_bond%n_frac_var
+                if (fracture_criterion.eq.'strain_rate') bond_posn%n_strain_rate=current_bond%n_strain_rate
+                if (fracture_criterion.eq.'energy') bond_posn%spring_pe=current_bond%spring_pe
+              endif
 
-            call push_bond_posn(current_bond%bond_trajectory, bond_posn)
-          endif
-          current_bond=>current_bond%next_bond
-        enddo
+              call push_bond_posn(current_bond%bond_trajectory, bond_posn)
+            endif
+            current_bond=>current_bond%next_bond
+          enddo
+        endif
       endif
 
       this=>this%next
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index 64aeed8..08fab02 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -634,8 +634,10 @@ end function last_berg
 
 !> Read a real value from a file and optionally return a default value if variable is missing
 real function get_real_from_file(ncid, varid, k, value_if_not_in_file)
-integer, intent(in) :: ncid, varid, k
-real, optional :: value_if_not_in_file
+integer, intent(in) :: ncid !< file id
+integer, intent(in) :: varid !< variable id
+integer, intent(in) :: k !< index
+real, optional :: value_if_not_in_file !< default value, if variable missing in file
 
 if (varid<1.and.present(value_if_not_in_file)) then
   get_real_from_file=value_if_not_in_file
@@ -1188,6 +1190,7 @@ subroutine generate_bergs(bergs,Time)
 
 end subroutine generate_bergs
 
+!> For generating bergs for debugging, assign initial berg positions and velocities
 subroutine loc_set_berg_pos(grd, xi, yj, uvel, vvel, berg)
   type(icebergs_gridded), pointer :: grd !< Container for gridded fields
   real, intent(in) :: xi !< Non-dimensional x-position within cell to give berg

From 6585a867bff31f651b5b1597783e67164dce6c2f Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Tue, 11 May 2021 15:20:55 -0400
Subject: [PATCH 308/361] more documentation

---
 src/icebergs.F90 | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index fda6ebb..266f10e 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -1018,7 +1018,7 @@ subroutine calculate_force_land_contact(bergs, berg, grd, i, j, IA_x, IA_y, &
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
   type(iceberg), pointer :: berg !< Primary berg
-  type(icebergs_gridded), pointer :: grd
+  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
   integer, intent(in) :: i !< Grid cell i to contact
   integer, intent(in) :: j !< Grid cell j to contact
   real, intent(inout) :: IA_x !< Net zonal acceleration of berg due to interactions (m/s2)
@@ -3393,13 +3393,14 @@ subroutine swap_variables(x,y)
   end subroutine swap_variables
 end subroutine rolling
 
-!> Estimate the dimenstions of a representative FL berg that will give roughly the same
-!! freshwater flux as the actual group of FL bergs of all different sizes:
-!! this may not be appropriate for very small FL bergs or dense sea ice cover
+!> Estimate the dimensions of a footloose berg that represents the footloose bits.
+!! The goal is that the meltwater flux from this representative berg, multiplied by
+!! (the mass of all footloose bits)/(mass of the representative berg), matches the meltwater
+!! flux of all footloose bits (which if they were individually tracked, could vary in size).
 subroutine fl_bits_dimensions(bergs,this,L_fl,W_fl,T_fl)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
-  type(iceberg), pointer :: this
+  type(iceberg), pointer :: this !< Parent berg to the footloose bits
   real :: L_fl !< Footloose berg bits length
   real :: W_fl !< Footloose berg bits width
   real :: T_fl !< Footloose berg bits thickness
@@ -6399,7 +6400,7 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b,fl_disp_x,fl_disp_y,berg_from_bit
   type(real),intent(in) :: l_b !< The width, and 1/3 the length, of a child berg
   type(real) :: fl_disp_x !< Child berg x-displacement from parent berg
   type(real) :: fl_disp_y !< Child berg x-displacement from parent berg
-  logical, optional, intent(in) :: berg_from_bits
+  logical, optional, intent(in) :: berg_from_bits !< True to create new berg from footloose bits
   ! Local variables
   type(iceberg) :: cberg ! The new child berg
   type(icebergs_gridded), pointer :: grd

From 16e94cc033e600322c79f637ad0b2fb0b89114b0 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Tue, 18 May 2021 19:27:10 -0400
Subject: [PATCH 309/361] -Modified perimeter scaling so that the new parent
 berg shape is determined by subtracting ice from both the length and width,
 rather than just the length. -Rearranged code so that interpolations from
 grid to particles occurs outside of evolve_icebergs -set default for
 input_freq_distribution to True, in accordance with the given default
 distribution and distribution_n. -Output thickness with trajectories if and
 only if save_fl_traj=.True. -Set the defauly for save_fl_traj to .True.

---
 src/icebergs.F90           | 133 +++++++++++++++++++++++++------------
 src/icebergs_framework.F90 |  16 ++---
 src/icebergs_io.F90        |  10 +--
 3 files changed, 104 insertions(+), 55 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 266f10e..a52761a 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -50,7 +50,7 @@ module ice_bergs
 use ice_bergs_framework, only: fracture_testing_initialization, orig_bond_length
 use ice_bergs_framework, only: update_and_break_bonds,break_bonds_dem,assign_n_bonds,reset_bond_rotation
 use ice_bergs_framework, only: update_bond_angles
-use ice_bergs_framework, only: monitor_energy, energy_tests_init, new_mts
+use ice_bergs_framework, only: monitor_energy, energy_tests_init, mts, new_mts
 use ice_bergs_framework, only: dem_tests_init
 use ice_bergs_framework, only: dem, init_dem_params
 use ice_bergs_framework, only: set_constant_interaction_length_and_width
@@ -1265,7 +1265,6 @@ subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, d
     scaling=1.0
   endif
 
-
   ! Initializing accelerations
   axn=0.; ayn=0.; bxn=0.; byn=0.
 
@@ -2081,14 +2080,14 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
   grd=>bergs%grd
 
   ! Interpolate gridded fields to berg
-  if (bergs%mts) then
+  !if (bergs%mts) then
     !gridded fields already saved on berg
     uo=berg%uo; vo=berg%vo; ua=berg%ua; va=berg%va; ui=berg%ui; vi=berg%vi;
     ssh_x=berg%ssh_x; ssh_y=berg%ssh_y; sst=berg%sst; sss=berg%sss;  cn=berg%cn; hi=berg%hi; od=berg%od
-  else
-    call interp_flds(grd, berg%lon, berg%lat, i, j, xi, yj, rx, ry, uo, vo, ui, vi, ua, va, ssh_x, &
-      ssh_y, sst, sss, cn, hi, od)
-  end if
+  !else
+  !  call interp_flds(grd, berg%lon, berg%lat, i, j, xi, yj, rx, ry, uo, vo, ui, vi, ua, va, ssh_x, &
+  !    ssh_y, sst, sss, cn, hi, od)
+  !end if
 
   if ((grd%grid_is_latlon) .and. (.not. bergs%use_f_plane)) then
      f_cori=(2.*omega)*sin(pi_180*lat)
@@ -2560,7 +2559,7 @@ subroutine footloose_calving(bergs, time)
   integer :: grdi, grdj
   integer, dimension(8) :: seed
   real :: T, W, L, N_bonds, Ln
-  real :: IC, max_k, k, Lr_fl, l_w, l_b, pu
+  real :: IC, max_k, k, l_w, l_b, pu, c, l_b3, Lmin, Wmin, ds, Wn, dA
   real :: fl_disp_x, fl_disp_y, interp_loc, dM_fl_bits
 
   ! For convenience
@@ -2610,6 +2609,7 @@ subroutine footloose_calving(bergs, time)
 
         l_w  = (lw_c*B_c*(T**3.))**0.25  !buoyancy length
         l_b  = l_c*l_w                   !length of child icebergs
+        l_b3 = 3*l_b
 
         !---Determine k, the number of child bergs to calve via the footloose mechanism---!
         !Bergs%fl_r is the average number of bergs to calve over the time increment
@@ -2631,11 +2631,16 @@ subroutine footloose_calving(bergs, time)
             call max_k_for_edge_elements
           endif
         else
-          !non-bonded berg must be larger than 3*(l_b) for FL calving. Set max_k accordingly.
-          max_k = max(ceiling((L-3*l_b)*W/(3*l_b**2.)),0)
+          !non-bonded berg length must be greater than 3*(l_b) for FL calving. Set max_k accordingly.
+          if (bergs%fl_k_scale_by_perimeter>0) then
+            !the minimum length and width the parent berg can have after footloose
+            c = ceiling((L-l_b3)/l_b3); Lmin = L - c*l_b3;
+            c = ceiling((W-l_b3)/l_b3); Wmin = W - c*l_b3;
 
-          if (L-max_k*3.*(l_b**2.)/W<=0.) then
-            max_k = max_k-1
+            max_k = max(floor((L*W - Lmin*Wmin)/(l_b3*l_b)),0)
+          else
+            max_k = max(ceiling((L-l_b3)*W/(3*l_b**2.)),0)
+            if (L-max_k*3.*(l_b**2.)/W<=0.) max_k = max_k-1
           endif
         endif
 
@@ -2661,7 +2666,14 @@ subroutine footloose_calving(bergs, time)
 
             if (bergs%iceberg_bonds_on) k=k*((N_max-N_bonds)/N_max) !reduce FL calve rate by number of bonds
             k=k*(bergs%dt/bergs%fl_r_s) !scale k to dt
-            if (bergs%fl_k_scale_by_perimeter>0) k = k * (2.*(L+W)/bergs%fl_k_scale_by_perimeter)
+            if (bergs%fl_k_scale_by_perimeter>0) then
+              if (c == 0) then
+                !W not eligible for footloose, so only scale by length
+                k = k * 2.*L/bergs%fl_k_scale_by_perimeter
+              else
+                k = k * 2.*(L+W)/bergs%fl_k_scale_by_perimeter
+              endif
+            endif
             this%fl_k=this%fl_k+k       !update fl_k
           endif
 
@@ -2678,7 +2690,22 @@ subroutine footloose_calving(bergs, time)
         !if there is footloose calving, create the new bergs and reduce length of parent berg
         if (k>0) then
 
-          Lr_fl = k*3.*(l_b**2.)/W !FL mechanism length reduction for parent berg
+          !new parent berg length (Ln) and width (Wn), and change in area (dA):
+          if (bergs%fl_k_scale_by_perimeter>0 .and. c>0) then
+            !for scale by perimeter, both the length and width are reduced by ds
+            ds = 0.5*( (L+W) - sqrt( (L+W)**2. - 4. * (l_b3*l_b*k) ) )
+            Ln = L-ds; Wn=W-ds
+            !Corrections to keep Wn >= Wmin. Ln is adjusted accordingly to retain the same dA.
+            if (Wn<Wmin) then
+              Ln=Ln*(1-(Wmin-Wn)/Wmin)
+              Wn=Wmin
+            endif
+          else
+            ds = k*3.*(l_b**2.)/W !FL mechanism length reduction for parent berg
+            Ln=L-ds
+            Wn=W
+          endif
+          dA = L*W - Ln*Wn !change in area. Should equal k*3*l_b**2
 
           if (bergs%fl_style.eq.'new_bergs') then
             !calve and track footloose bergs
@@ -2688,7 +2715,7 @@ subroutine footloose_calving(bergs, time)
             bergs%nbergs_calved_fl=bergs%nbergs_calved_fl+1
           else
             !put FL berg mass in footloose bergs bits.
-            dM_fl_bits=bergs%rho_bergs*W*T*Lr_fl
+            dM_fl_bits=bergs%rho_bergs*T*dA
             this%mass_of_fl_bits=this%mass_of_fl_bits+dM_fl_bits
             ! mass flux into fl bits (kg/m2/s)
             if (grd%area(grdi,grdj).ne.0.) then
@@ -2697,8 +2724,7 @@ subroutine footloose_calving(bergs, time)
             endif
           endif
 
-          Ln=L-Lr_fl !new length
-          if (Ln .le. 0) then
+          if (Ln .le. 0 .or. Wn .le. 0) then
             if (N_bonds==0) then
               print *,'l_b,L,W,k,max_k',l_b,L,W,k,max_k
               call error_mesg('KID,footloose_calving', &
@@ -2707,8 +2733,8 @@ subroutine footloose_calving(bergs, time)
             this%fl_k=-3 !marks this berg to be deleted later
           else
             !update length, width, thickness,and mass of parent berg
-            if (bergs%allow_bergs_to_roll .and. N_bonds.eq.0.) call rolling(bergs,T,W,Ln)
-            this%thickness=T; this%width=W; this%length=Ln
+            if (bergs%allow_bergs_to_roll .and. N_bonds.eq.0.) call rolling(bergs,T,Wn,Ln)
+            this%thickness=T; this%width=Wn; this%length=Ln
             this%mass=this%length*this%width*this%thickness*bergs%rho_bergs
           endif
         endif
@@ -2941,9 +2967,9 @@ subroutine thermodynamics(bergs)
     this=>bergs%list(grdi,grdj)%first
     do while(associated(this))
       if (debug) call check_position(grd, this, 'thermodynamics (top)')
-      call interp_flds(grd, this%lon, this%lat, this%ine, this%jne, this%xi, this%yj, 0., 0., &
-                       this%uo, this%vo, this%ui, this%vi, this%ua, this%va, this%ssh_x, &
-                       this%ssh_y, this%sst, this%sss,this%cn, this%hi)
+      ! call interp_flds(grd, this%lon, this%lat, this%ine, this%jne, this%xi, this%yj, 0., 0., &
+      !                  this%uo, this%vo, this%ui, this%vi, this%ua, this%va, this%ssh_x, &
+      !                  this%ssh_y, this%sst, this%sss,this%cn, this%hi)
       SST=this%sst
       SSS=this%sss
       IC=min(1.,this%cn+bergs%sicn_shift) ! Shift sea-ice concentration
@@ -4706,7 +4732,7 @@ subroutine interp_gridded_fields_to_bergs(bergs)
   ! Local variables
   type(icebergs_gridded), pointer :: grd
   type(iceberg), pointer :: berg
-  integer :: grdj,grdi,i
+  integer :: grdj,grdi,i,is,ie,js,je
   type(randomNumberStream) :: rns ! Random numbers for stochastic tidal parameterization
   real :: rx,ry
 
@@ -4714,7 +4740,13 @@ subroutine interp_gridded_fields_to_bergs(bergs)
   grd=>bergs%grd
   rx=0.0; ry=0.0;
 
-  do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec ! just for computational domain
+  if (bergs%mts) then
+    is=grd%isc; ie=grd%iec; js=grd%jsc; je=grd%jec
+  else
+    is=grd%isc-1; ie=grd%iec+1; js=grd%jsc-1; je=grd%jec+1
+  endif
+
+  do grdj = js,je ; do grdi = is,ie ! just for computational domain
     berg=>bergs%list(grdi,grdj)%first
     if (associated(berg) .and. grd%tidal_drift>0.) then
       ! Seed random numbers based on space and "time"
@@ -4902,8 +4934,13 @@ subroutine interp_flds(grd, x, y, i, j, xi, yj, rx, ry, uo, vo, ui, vi, ua, va,
   endif
 
   ! Quadratic interpolation of ocean depth+sea surface height (A-grid)
+  ! Ocean depth is only needed for grounding friction, used with the MTS model only?
   if (present(od)) then
-    od=quad_interp_from_agrid(grd,grd%ocean_depth,x,y,i,j,xi,yj)+quad_interp_from_agrid(grd,grd%ssh,x,y,i,j,xi,yj)
+    if (mts) then
+      od=quad_interp_from_agrid(grd,grd%ocean_depth,x,y,i,j,xi,yj)+quad_interp_from_agrid(grd,grd%ssh,x,y,i,j,xi,yj)
+    else
+      od=grd%ocean_depth(i,j)+grd%ssh(i,j)
+    endif
   endif
 end subroutine interp_flds
 
@@ -5367,22 +5404,6 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   if (debug) call bergs_chksum(bergs, 'run bergs (top)')
   if (debug) call checksum_gridded(bergs%grd, 'top of s/r run')
 
-  !If MTS VV and first visit, perform initial interp of gridded fields to bergs
-  if (.not. Visited) then
-    Visited=.true.
-    if (bergs%mts) then
-      call interp_gridded_fields_to_bergs(bergs)
-      call transfer_mts_bergs(bergs)
-    elseif ((bergs%contact_distance>0.) .or. (bergs%contact_spring_coef .ne. bergs%spring_coef)) then
-      call set_conglom_ids(bergs)
-    endif
-    if (bergs%iceberg_bonds_on) call orig_bond_length(bergs)
-
-    if (monitor_energy) then
-      call energy_tests_init(bergs)
-    endif
-  endif
-
   ! Accumulate ice from calving
   call accumulate_calving(bergs)
   if (grd%id_accum>0) then
@@ -5404,6 +5425,22 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after calving()    ')
   call mpp_clock_end(bergs%clock_cal)
 
+  !need to redo MTS transfers after a restart
+  if (.not. Visited) then
+    Visited=.true.
+    if (bergs%mts) then
+      call interp_gridded_fields_to_bergs(bergs)
+      call transfer_mts_bergs(bergs)
+    elseif ((bergs%contact_distance>0.) .or. (bergs%contact_spring_coef .ne. bergs%spring_coef)) then
+      call set_conglom_ids(bergs)
+    endif
+    if (bergs%iceberg_bonds_on) call orig_bond_length(bergs)
+    if (monitor_energy) call energy_tests_init(bergs)
+    if (mpp_pe()==0) write(*,'(a)') 'KID, iceberg_run: completed first visit initialization'
+  endif
+
+  if (.not. bergs%mts) call interp_gridded_fields_to_bergs(bergs)
+
   ! For each berg, evolve
   call mpp_clock_begin(bergs%clock_mom)
 
@@ -5453,6 +5490,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
         call set_conglom_ids(bergs)
       endif
     endif
+    call interp_gridded_fields_to_bergs(bergs)
   endif
   if (debug) call bergs_chksum(bergs, 'run bergs (exchanged)')
   if (debug) call checksum_gridded(bergs%grd, 's/r run after exchange')
@@ -5507,7 +5545,6 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     call error_mesg('KID', 'WRITE AND STOP!!!', FATAL)
   endif
 
-
   ! Gridded diagnostics
   if (grd%id_uo>0) &
     lerr=send_data(grd%id_uo, grd%uo(grd%isc:grd%iec,grd%jsc:grd%jec), Time)
@@ -6217,6 +6254,8 @@ subroutine calve_icebergs(bergs)
   integer :: stderrunit
   real, pointer :: initial_mass, mass_scaling, initial_thickness, initial_width, initial_length
   logical :: allocations_done
+  type(randomNumberStream) :: rns ! Random numbers for stochastic tidal parameterization
+  real :: rx,ry
 
   ! Get the stderr unit number
   stderrunit = stderr()
@@ -6358,6 +6397,16 @@ subroutine calve_icebergs(bergs)
             newberg%accum_bond_rotation=0.
           endif
 
+          !interpolate gridded variables to new iceberg
+          if (grd%tidal_drift>0.) then
+            call getRandomNumbers(rns, rx)
+            call getRandomNumbers(rns, ry)
+            rx = 2.*rx - 1.; ry = 2.*ry - 1.
+          endif
+          call interp_flds(grd, newberg%lon, newberg%lat, i, j, xi, yj, rx, ry, newberg%uo, newberg%vo, newberg%ui, &
+            newberg%vi, newberg%ua, newberg%va, newberg%ssh_x, newberg%ssh_y, newberg%sst, newberg%sss, newberg%cn, &
+            newberg%hi, newberg%od)
+
           call add_new_berg_to_list(bergs%list(i,j)%first, newberg)
           calved_to_berg=initial_mass*mass_scaling ! Units of kg
           ! Heat content
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 00e895e..b54cb0a 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -19,7 +19,7 @@ module ice_bergs_framework
 implicit none ; private
 
 integer :: buffer_width=36 ! This should be a parameter
-integer :: buffer_width_traj=33 ! This should be a parameter
+integer :: buffer_width_traj=32 ! This should be a parameter
 integer :: buffer_width_bond_traj=11 !This should be a parameter
 integer, parameter :: nclasses=10 ! Number of ice bergs classes
 
@@ -534,7 +534,7 @@ module ice_bergs_framework
   logical :: only_interactive_forces=.False. !< Icebergs only feel interactive forces, and not ocean, wind...
   logical :: halo_debugging=.False. !< Use for debugging halos (remove when its working)
   logical :: save_short_traj=.True. !< True saves only lon,lat,time,id in iceberg_trajectory.nc
-  logical :: save_fl_traj=.False. ! True saves short traj, plus masses and footloose parameters in iceberg_trajectory.nc
+  logical :: save_fl_traj=.True. ! True saves short traj, plus masses and footloose parameters in iceberg_trajectory.nc
   logical :: ignore_traj=.False. !< If true, then model does not write trajectory data at all
   logical :: iceberg_bonds_on=.False. !< True=Allow icebergs to have bonds, False=don't allow.
   logical :: manually_initialize_bonds=.False. !< True= Bonds are initialize manually.
@@ -780,7 +780,7 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: only_interactive_forces=.False. ! Icebergs only feel interactive forces, and not ocean, wind...
 logical :: halo_debugging=.False. ! Use for debugging halos (remove when its working)
 logical :: save_short_traj=.True. ! True saves only lon,lat,time,id in iceberg_trajectory.nc
-logical :: save_fl_traj=.False. ! True saves short traj, plus masses and footloose parameters in iceberg_trajectory.nc
+logical :: save_fl_traj=.True. ! True saves short traj, plus masses and footloose parameters in iceberg_trajectory.nc
 logical :: ignore_traj=.False. ! If true, then model does not traj trajectory data at all
 !logical :: iceberg_bonds_on=.False. ! True=Allow icebergs to have bonds, False=don't allow.
 logical :: manually_initialize_bonds=.False. ! True= Bonds are initialize manually.
@@ -790,7 +790,7 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: critical_interaction_damping_on=.true. ! Sets the damping on relative iceberg velocity to critical value - Added by Alon
 logical :: tang_crit_int_damp_on=.true. ! Critical interaction damping for tangential component?
 logical :: do_unit_tests=.false. ! Conduct some unit tests
-logical :: input_freq_distribution=.false. ! Flag to show if input distribution is freq or mass dist (=1 if input is a freq dist, =0 to use an input mass dist)
+logical :: input_freq_distribution=.true. ! Flag to show if input distribution is freq or mass dist (=1 if input is a freq dist, =0 to use an input mass dist)
 logical :: read_old_restarts=.false. ! Legacy option that does nothing
 logical :: use_old_spreading=.true. ! If true, spreads iceberg mass as if the berg is one grid cell wide
 logical :: read_ocean_depth_from_file=.false. ! If true, ocean depth is read from a file.
@@ -1266,7 +1266,7 @@ subroutine ice_bergs_framework_init(bergs, &
   buffer_width=buffer_width+(max_bonds*5) ! Increase buffer width to include bonds being passed between processors
 endif
 if (save_short_traj) buffer_width_traj=6 ! This is the length of the short buffer used for abrevated traj
-if (save_fl_traj) buffer_width_traj=buffer_width_traj+6
+if (save_fl_traj) buffer_width_traj=buffer_width_traj+7
 if (ignore_traj) buffer_width_traj=0 ! If this is true, then all traj files should be ignored
 
 if (use_damage) then
@@ -3842,6 +3842,7 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj, save_fl_traj)
     call push_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bits)
     call push_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bergy_bits)
     call push_buffer_value(buff%data(:,n),counter,traj%fl_k)
+    call push_buffer_value(buff%data(:,n),counter,traj%thickness)
   endif
   if (.not. save_short_traj) then
     call push_buffer_value(buff%data(:,n),counter,traj%uvel)
@@ -3849,7 +3850,6 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj, save_fl_traj)
     call push_buffer_value(buff%data(:,n),counter,traj%uvel_prev)
     call push_buffer_value(buff%data(:,n),counter,traj%vvel_prev)
     call push_buffer_value(buff%data(:,n),counter,traj%heat_density)
-    call push_buffer_value(buff%data(:,n),counter,traj%thickness)
     call push_buffer_value(buff%data(:,n),counter,traj%width)
     call push_buffer_value(buff%data(:,n),counter,traj%length)
     call push_buffer_value(buff%data(:,n),counter,traj%uo)
@@ -3956,6 +3956,7 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj, save_fl_tra
     call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bits)
     call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bergy_bits)
     call pull_buffer_value(buff%data(:,n),counter,traj%fl_k)
+    call pull_buffer_value(buff%data(:,n),counter,traj%thickness)
   endif
   if (.not. save_short_traj) then
     call pull_buffer_value(buff%data(:,n),counter,traj%uvel)
@@ -3963,7 +3964,6 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj, save_fl_tra
     call pull_buffer_value(buff%data(:,n),counter,traj%uvel_prev)
     call pull_buffer_value(buff%data(:,n),counter,traj%vvel_prev)
     call pull_buffer_value(buff%data(:,n),counter,traj%heat_density)
-    call pull_buffer_value(buff%data(:,n),counter,traj%thickness)
     call pull_buffer_value(buff%data(:,n),counter,traj%width)
     call pull_buffer_value(buff%data(:,n),counter,traj%length)
     call pull_buffer_value(buff%data(:,n),counter,traj%uo)
@@ -5864,6 +5864,7 @@ subroutine record_posn(bergs)
           posn%mass_of_fl_bits=this%mass_of_fl_bits
           posn%mass_of_fl_bergy_bits=this%mass_of_fl_bergy_bits
           posn%fl_k=this%fl_k
+          posn%thickness=this%thickness
         endif
         if (.not. bergs%save_short_traj) then !Not totally sure that this is correct
           posn%uvel=this%uvel
@@ -5871,7 +5872,6 @@ subroutine record_posn(bergs)
           posn%uvel_prev=this%uvel_prev
           posn%vvel_prev=this%vvel_prev
           posn%heat_density=this%heat_density
-          posn%thickness=this%thickness
           posn%width=this%width
           posn%length=this%length
           posn%uo=this%uo
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index 08fab02..df322a4 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -1826,6 +1826,7 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj)
         mflbid = inq_varid(ncid, 'mass_of_fl_bits')
         mflbbid = inq_varid(ncid, 'mass_of_fl_bergy_bits')
         flkid = inq_varid(ncid, 'fl_k')
+        did = inq_varid(ncid, 'thickness')
       endif
       if (.not.save_short_traj) then
         uvelid = inq_varid(ncid, 'uvel')
@@ -1839,7 +1840,6 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj)
         uaid = inq_varid(ncid, 'ua')
         vaid = inq_varid(ncid, 'va')
         hdid = inq_varid(ncid, 'heat_density')
-        did = inq_varid(ncid, 'thickness')
         wid = inq_varid(ncid, 'width')
         lid = inq_varid(ncid, 'length')
         sshxid = inq_varid(ncid, 'ssh_x')
@@ -1908,6 +1908,7 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj)
         mflbid = def_var(ncid, 'mass_of_fl_bits', NF_DOUBLE, i_dim)
         mflbbid = def_var(ncid, 'mass_of_fl_bergy_bits', NF_DOUBLE, i_dim)
         flkid = def_var(ncid, 'fl_k', NF_DOUBLE, i_dim)
+        did = def_var(ncid, 'thickness', NF_DOUBLE, i_dim)
       endif
       if (.not. save_short_traj) then
         uvelid = def_var(ncid, 'uvel', NF_DOUBLE, i_dim)
@@ -1921,7 +1922,6 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj)
         uaid = def_var(ncid, 'ua', NF_DOUBLE, i_dim)
         vaid = def_var(ncid, 'va', NF_DOUBLE, i_dim)
         hdid = def_var(ncid, 'heat_density', NF_DOUBLE, i_dim)
-        did = def_var(ncid, 'thickness', NF_DOUBLE, i_dim)
         wid = def_var(ncid, 'width', NF_DOUBLE, i_dim)
         lid = def_var(ncid, 'length', NF_DOUBLE, i_dim)
         sshxid = def_var(ncid, 'ssh_x', NF_DOUBLE, i_dim)
@@ -1999,6 +1999,8 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj)
         call put_att(ncid, mflbbid, 'units', 'kg')
         call put_att(ncid, flkid, 'long_name', 'footloose calving k')
         call put_att(ncid, flkid, 'units', 'none')
+        call put_att(ncid, did, 'long_name', 'thickness')
+        call put_att(ncid, did, 'units', 'm')
       endif
       if (.not. save_short_traj) then
         call put_att(ncid, uvelid, 'long_name', 'zonal spped')
@@ -2019,8 +2021,6 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj)
         call put_att(ncid, vaid, 'units', 'm/s')
         call put_att(ncid, hdid, 'long_name', 'heat_density')
         call put_att(ncid, hdid, 'units', 'J/kg')
-        call put_att(ncid, did, 'long_name', 'thickness')
-        call put_att(ncid, did, 'units', 'm')
         call put_att(ncid, wid, 'long_name', 'width')
         call put_att(ncid, wid, 'units', 'm')
         call put_att(ncid, lid, 'long_name', 'length')
@@ -2136,6 +2136,7 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj)
         call put_double(ncid, mflbid, i, this%mass_of_fl_bits)
         call put_double(ncid, mflbbid, i, this%mass_of_fl_bergy_bits)
         call put_double(ncid, flkid, i, this%fl_k)
+        call put_double(ncid, did, i, this%thickness)
       endif
       if (.not. save_short_traj) then
         call put_double(ncid, uvelid, i, this%uvel)
@@ -2149,7 +2150,6 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj)
         call put_double(ncid, uaid, i, this%ua)
         call put_double(ncid, vaid, i, this%va)
         call put_double(ncid, hdid, i, this%heat_density)
-        call put_double(ncid, did, i, this%thickness)
         call put_double(ncid, wid, i, this%width)
         call put_double(ncid, lid, i, this%length)
         call put_double(ncid, sshxid, i, this%ssh_x)

From 239632713f985bc8e6c8159cb4617737bcd2b00c Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Fri, 30 Jul 2021 14:45:40 -0400
Subject: [PATCH 310/361] -Added youngs modulus and ice strength for footloose
 as nml parameters (fl_youngs and fl_strength) -footloose now based on
 horizontal area lost to side wave erosion/melt (see nml parameters
 fl_use_l_scale, fl_l_scale, fl_l_scale_erosion_only; thermodynamics and
 footloose subroutines) -Added more options for saving trajectories: (1)
 specify an area threshold that must be exceeded to save, (2) save all
 trajectories when some year is passed (nml parameter save_all_traj_year), 
 (3) save all trajectories by initial mass class (see nml parameters
 save_nonfl_traj_by_class, save_traj_by_class_start_mass_thres_n,
 save_traj_by_class_start_mass_thres_s, traj_area_thres_sntbc) -Added a fix
 for a floating-error for that sometimes occurred when using
 input_freq_distribution, where the recalculated distributions would not add
 up to one.

---
 src/icebergs.F90           | 206 ++++++++++++++++++++++++++-----------
 src/icebergs_framework.F90 | 142 +++++++++++++++++++++----
 src/icebergs_io.F90        |  62 ++++++-----
 3 files changed, 307 insertions(+), 103 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index a52761a..e9a7c63 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -188,7 +188,7 @@ subroutine debugwriteandstop(bergs)
   bergs%debug_write=.true.
   call record_posn(bergs)
   call move_all_trajectories(bergs)
-  call write_trajectory(bergs%trajectories, bergs%save_short_traj, bergs%save_fl_traj)
+  call write_trajectory(bergs%trajectories, bergs%save_short_traj, bergs%save_fl_traj, bergs%fl_r)
   if (save_bond_traj) call write_bond_trajectory(bergs%bond_trajectories)
   call mpp_sync()
   call error_mesg('KID', 'WRITE AND STOP!!!', FATAL)
@@ -851,7 +851,7 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
   real :: A2,T2,M2,u2,v2,lon2,lat2,R2 ! Other iceberg
   real :: dlon, dlat, lat_ref, dx_dlon, dy_dlat
   real :: r_dist_x, r_dist_y, r_dist
-  real :: Rmin, delta, L, l0, youngs, Thick, T_Rmin, n1, n2
+  real :: Rmin, delta, L, l0, youngs_dem, Thick, T_Rmin, n1, n2
   real :: ur, vr, up, vp, rotu, rotv, rtu, rtv, RR1, RR2
   real :: ur2, vr2
   real :: ss_factor, ss1, ss2
@@ -940,13 +940,13 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
     !Thick=min(T1,T2) !minimum thickness
     !Thick=0.5*(T1+T2) !average thickness
 
-    youngs=bergs%dem_spring_coef
+    youngs_dem=bergs%dem_spring_coef
 
     !normal force:
-    !Fn_x=youngs*Thick*delta*n1*L/l0 !Fn_y=youngs*Thick*delta*n2*L/l0
-    !normal stiffness is youngs*Thick*L/l0
-    if (savestress) current_bond%nstress=-youngs*delta/l0 !normal stress
-    Fn_x=youngs*Thick*delta*L/l0; Fn_y=Fn_x*n2; Fn_x=Fn_x*n1
+    !Fn_x=youngs_dem*Thick*delta*n1*L/l0 !Fn_y=youngs_dem*Thick*delta*n2*L/l0
+    !normal stiffness is youngs_dem*Thick*L/l0
+    if (savestress) current_bond%nstress=-youngs_dem*delta/l0 !normal stress
+    Fn_x=youngs_dem*Thick*delta*L/l0; Fn_y=Fn_x*n2; Fn_x=Fn_x*n1
 
     !relative translational velocity
     ur=berg%uvel_old-other_berg%uvel_old; vr=berg%vvel_old-other_berg%vvel_old
@@ -980,7 +980,7 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
     endif
 
     !shear terms
-    ss_factor=-L*Thick*youngs/(l0*2.0*(1.0+bergs%poisson)) !shear stiffness
+    ss_factor=-L*Thick*youngs_dem/(l0*2.0*(1.0+bergs%poisson)) !shear stiffness
     if (bergs%ignore_tangential_force) ss_factor=0.
     Fs_x=ss_factor*current_bond%tangd1; Fs_y=ss_factor*current_bond%tangd2 !shear forces
     if (savestress) current_bond%sstress=sqrt(Fs_x**2+Fs_y**2)/(L*Thick) !shear stress
@@ -989,10 +989,10 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
     Ts = -(RR1x*Fs_y-RR1y*Fs_x)
 
     !Torque from relative particle rotation
-    Tr = -youngs*Thick*(L*L*L)*sin(berg%rot-other_berg%rot)/(12.*l0)
+    Tr = -youngs_dem*Thick*(L*L*L)*sin(berg%rot-other_berg%rot)/(12.*l0)
 
     !damping
-    K_damp = 2.*youngs/(3.*(1.-bergs%poisson**2)) !damping factor
+    K_damp = 2.*youngs_dem/(3.*(1.-bergs%poisson**2)) !damping factor
     Meff = M1*M2/(M1+M2) !effective mass
 
     damping_coef = bergs%dem_damping_coef*sqrt(K_damp*Meff)
@@ -2554,6 +2554,8 @@ subroutine footloose_calving(bergs, time)
   type(icebergs_gridded), pointer :: grd
   type(bond), pointer :: current_bond
   real, save :: N_max, youngs, poisson, l_c, lw_c, B_c, exp_nlambda, rn
+  real, save :: e1, drho, sigmay, lfootparam
+  real :: foot_l,foot_mass, foot_area
   type(randomNumberStream),save :: rns ! Random numbers for stochastic tidal parameterization
   logical, save :: Visited=.false.
   integer :: grdi, grdj
@@ -2578,7 +2580,14 @@ subroutine footloose_calving(bergs, time)
       N_max=0.0
     endif
 
-    youngs=1.e8; poisson=0.3
+    !for fl_use_l_scale
+    e1=exp(0.25*pi)
+    drho=rho_seawater-bergs%rho_bergs
+    sigmay=bergs%fl_strength*1000 !strength (Pa)
+    !to get foot length for calving, multiply lfootparam by thickness/l_w
+    lfootparam=e1*rho_seawater*sigmay/(6*bergs%rho_bergs*gravity*drho)
+
+    poisson=0.3; youngs=bergs%fl_youngs
     l_c  = pi/(2.*sqrt(2.)) !for length-scale of child iceberg
     lw_c = 1./(gravity*rho_seawater) !for buoyancy length
     B_c  = youngs/(12.*(1.-poisson**2.)) !for bending stiffness
@@ -2644,47 +2653,73 @@ subroutine footloose_calving(bergs, time)
           endif
         endif
 
-        if (max_k==0) then
-          k=0
-          this%fl_k=0
+        if (bergs%fl_use_l_scale) then
+          if (max_k==0) then
+            k=0
+          else
+            ! !here, fl_k is the accumulated mass from side melt/erosion
+            ! foot_l = lfootparam*T/l_w
+            ! !this is the mass of side melt/erosion needed to calve a single footloose berg
+            ! foot_mass = foot_l * T*(1.-bergs%rho_bergs/rho_seawater) * l_b3 * bergs%rho_bergs
+            ! !If bergs%fl_l_scale=1, all side mass loss is above sea level, and goes into creating the
+            ! !foot. Adjust to >1 if some mass loss evenly melts the sides at all depths...
+            ! foot_mass = bergs%fl_l_scale * foot_mass/T
+            ! k=floor(this%fl_k/foot_mass)
+            ! if (k>max_k) k=max_k
+            ! this%fl_k=this%fl_k-k*foot_mass
+
+            !here, fl_k is the accumulated mass from side melt/erosion
+            foot_l = lfootparam*T/l_w
+            !this is the area of side melt/erosion needed to calve a single footloose berg
+            foot_area = foot_l * l_b3
+            foot_area = bergs%fl_l_scale * foot_area
+            k=floor(this%fl_k/foot_area)
+            if (k>max_k) k=max_k
+            this%fl_k=this%fl_k-k*foot_area
+          endif
         else
-          ! If sea ice concentration is <=50%, generate footloose child bergs
-          IC=min(1.,grd%cn(grdi,grdj)+bergs%sicn_shift) !sea ice only known on grid when this routine is called
-          if (.not. IC>0.5) then
-
-            if (bergs%fl_use_poisson_distribution) then
-              k=0; pu=1.0
-              do while (pu >= exp_nlambda)
-                call getRandomNumbers(rns, rn)
-                pu=pu*rn
-                k=k+1
-              enddo
-              k=k-1.0 !FL calving rate (per day or year)
-            else
-              k=bergs%fl_r
-            endif
-
-            if (bergs%iceberg_bonds_on) k=k*((N_max-N_bonds)/N_max) !reduce FL calve rate by number of bonds
-            k=k*(bergs%dt/bergs%fl_r_s) !scale k to dt
-            if (bergs%fl_k_scale_by_perimeter>0) then
-              if (c == 0) then
-                !W not eligible for footloose, so only scale by length
-                k = k * 2.*L/bergs%fl_k_scale_by_perimeter
+          if (max_k==0) then
+            k=0
+            this%fl_k=0
+          else
+            ! If sea ice concentration is <=50%, generate footloose child bergs
+            IC=min(1.,grd%cn(grdi,grdj)+bergs%sicn_shift) !sea ice only known on grid when this routine is called
+            if (.not. IC>0.5) then
+
+              if (bergs%fl_use_poisson_distribution) then
+                k=0; pu=1.0
+                do while (pu >= exp_nlambda)
+                  call getRandomNumbers(rns, rn)
+                  pu=pu*rn
+                  k=k+1
+                enddo
+                k=k-1.0 !FL calving rate (per day or year)
               else
-                k = k * 2.*(L+W)/bergs%fl_k_scale_by_perimeter
+                k=bergs%fl_r
               endif
-            endif
-            this%fl_k=this%fl_k+k       !update fl_k
-          endif
 
-          k=floor(this%fl_k)
-        endif
+              if (bergs%iceberg_bonds_on) k=k*((N_max-N_bonds)/N_max) !reduce FL calve rate by number of bonds
+              k=k*(bergs%dt/bergs%fl_r_s) !scale k to dt
+              if (bergs%fl_k_scale_by_perimeter>0) then
+                if (c == 0) then
+                  !W not eligible for footloose, so only scale by length
+                  k = k * 2.*L/bergs%fl_k_scale_by_perimeter
+                else
+                  k = k * 2.*(L+W)/bergs%fl_k_scale_by_perimeter
+                endif
+              endif
+              this%fl_k=this%fl_k+k       !update fl_k
+            end if
 
-        if (k>max_k) then
-          k=max_k
-          this%fl_k=0.
-        else
-          this%fl_k=this%fl_k-k !save the remainder for the next timestep
+            k=floor(this%fl_k)
+          endif
+
+          if (k>max_k) then
+            k=max_k
+            this%fl_k=0.
+          else
+            this%fl_k=this%fl_k-k !save the remainder for the next timestep
+          endif
         endif
 
         !if there is footloose calving, create the new bergs and reduce length of parent berg
@@ -2929,7 +2964,7 @@ subroutine thermodynamics(bergs)
   ! Local variables
   type(icebergs_gridded), pointer :: grd
   type(bond), pointer :: current_bond
-  real :: M, T, W, L, SST, Vol, Ln, Wn, Tn, nVol, IC, Dn
+  real :: M, T, W, L, SST, Vol, Ln, Ln1, Wn, Wn1, Tn, nVol, IC, Dn
   real :: Mv, Me, Mb, melt, dvo, dva, dM, Ss, dMe, dMb, dMv
   real :: Mnew, Mnew1, Mnew2, Hocean
   real :: Mbits, nMbits, dMbitsE, dMbitsM, Lbits, Abits, Mbb
@@ -2942,9 +2977,10 @@ subroutine thermodynamics(bergs)
   ! Footloose bits stuff
   real :: Lfl, Wfl, Tfl, Mfl, Afl, Me_fl, Mv_fl, Mb_fl, dMfl
   real :: Volfl, Lnfl, Wnfl, Tnfl, nVolfl, Mnew1_fl, Mnew2_fl, Mnew_fl
-  real :: dMb_fl, dMv_fl, dMe_fl
+  real :: dMb_fl, dMv_fl, dMe_fl, dMe_l, dMv_l
   real :: Mbits_fl, dMbitsE_fl, nMbits_fl, Lbits_fl, Abits_fl, Mbb_fl, dMbitsM_fl
-  real :: prev_mass_of_fl_bits, prev_mass_of_fl_bergy_bits, M_edit, Mscale_edit
+  real :: prev_mass_of_fl_bits, prev_mass_of_fl_bergy_bits, M_edit, Mscale_edit,l_b3,fb, kd
+  real, parameter :: l_c=pi/(2.*sqrt(2.)),lw_c = 1./(gravity*rho_seawater),B_c=1./(12.*(1.-0.3**2.))
 
   ! For convenience
   grd=>bergs%grd
@@ -3052,14 +3088,14 @@ subroutine thermodynamics(bergs)
         Mnew1=(nVol/Vol)*M ! new mass (kg)
         dMb=M-Mnew1 ! mass lost to basal melting (>0) (kg)
 
-        Ln=max(L-Mv*bergs%dt,0.) ! new length (m)
-        Wn=max(W-Mv*bergs%dt,0.) ! new width (m)
-        nVol=Tn*Wn*Ln ! new volume (m^3)
+        Ln1=max(L-Mv*bergs%dt,0.) ! new length (m)
+        Wn1=max(W-Mv*bergs%dt,0.) ! new width (m)
+        nVol=Tn*Wn1*Ln1 ! new volume (m^3)
         Mnew2=(nVol/Vol)*M ! new mass (kg)
         dMv=Mnew1-Mnew2 ! mass lost to buoyant convection (>0) (kg)
 
-        Ln=max(Ln-Me*bergs%dt,0.) ! new length (m)
-        Wn=max(Wn-Me*bergs%dt,0.) ! new width (m)
+        Ln=max(Ln1-Me*bergs%dt,0.) ! new length (m)
+        Wn=max(Wn1-Me*bergs%dt,0.) ! new width (m)
         nVol=Tn*Wn*Ln ! new volume (m^3)
         Mnew=(nVol/Vol)*M ! new mass (kg)
         dMe=Mnew2-Mnew ! mass lost to erosion (>0) (kg)
@@ -3078,6 +3114,58 @@ subroutine thermodynamics(bergs)
         dMv=(M/Vol)*(T*(W+L))*Mv*bergs%dt ! approx. mass loss to buoyant convection (kg)
       endif
 
+      ! !if footloose is based on length of foot, accumulate side mass loss on fl_k
+      ! !note: this only works when bergs%use_operator_splitting=.true.
+      ! if (bergs%fl_use_l_scale .and. this%fl_k>=0) then
+      !   l_b3 = 3.*l_c*(lw_c*bergs%fl_youngs*B_c*(Tn**3.))**0.25 !child berg length x 3
+      !   if (L>l_b3) then !do not accumulate side made loss for sides < l_b3
+      !     if (W>l_b3) then
+      !       if (bergs%fl_l_scale_erosion_only) then
+      !         this%fl_k=this%fl_k + (dMe - dMv)/Tn
+      !         if (this%fl_k<0) this%fl_k=0
+      !       else
+      !         this%fl_k= this%fl_k + (dMe + dMv)/Tn
+      !       endif
+      !     else
+      !       dMv_l=dMv*(Wn1 + W)/(2.*(Ln1 + W)) !mass loss from length from buoyant convection
+      !       dMe_l=dMe*(Wn+ Wn1)/(2.*(Ln+ Wn1)) !mass loss from length from erosion
+      !       if (bergs%fl_l_scale_erosion_only) then
+      !         this%fl_k=this%fl_k + (dMe_l - dMv_l)/Tn
+      !         if (this%fl_k<0) this%fl_k=0
+      !       else
+      !         this%fl_k= this%fl_k + (dMe_l + dMv_l)/Tn
+      !       endif
+      !     endif
+      !   endif
+      ! endif
+
+      !if footloose is based on length of foot, accumulate side mass loss on fl_k
+      !note: this only works when bergs%use_operator_splitting=.true.
+      if (bergs%fl_use_l_scale .and. this%fl_k>=0) then
+        l_b3 = 3.*l_c*(lw_c*bergs%fl_youngs*B_c*(Tn**3.))**0.25 !child berg length x 3
+        if (L>l_b3) then !do not accumulate side made loss for sides < l_b3
+          fb = Tn*(1.-bergs%rho_bergs/rho_seawater) !freeboard
+          kd = Tn-fb !keel depth
+          if (W>l_b3) then
+            if (bergs%fl_l_scale_erosion_only) then
+              this%fl_k=this%fl_k + (dMe/fb - dMv/kd)/bergs%rho_bergs !horiz area from erosion - from buoy conv
+              if (this%fl_k<0) this%fl_k=0
+            else
+              this%fl_k= this%fl_k + (dMe + dMv)/Tn
+            endif
+          else
+            dMv_l=dMv*(Wn1 + W)/(2.*(Ln1 + W)) !mass loss from length from buoyant convection
+            dMe_l=dMe*(Wn+ Wn1)/(2.*(Ln+ Wn1)) !mass loss from length from erosion
+            if (bergs%fl_l_scale_erosion_only) then
+              this%fl_k=this%fl_k + (dMe_l/fb - dMv_l/kd)/bergs%rho_bergs
+              if (this%fl_k<0) this%fl_k=0
+            else
+              this%fl_k= this%fl_k + (dMe_l + dMv_l)/Tn
+            endif
+          endif
+        endif
+      endif
+
       ! Footloose bits (FL bits). For now, FL bits do not erode into bergy bits.
       if (this%mass_of_fl_bits>0.) then
         call fl_bits_dimensions(bergs,this,Lfl,Wfl,Tfl)
@@ -3432,10 +3520,10 @@ subroutine fl_bits_dimensions(bergs,this,L_fl,W_fl,T_fl)
   real :: T_fl !< Footloose berg bits thickness
   ! Local variables
   real,parameter :: l_c=pi/(2.*sqrt(2.)), lw_c = 1./(gravity*rho_seawater)
-  real,parameter :: B_c=1.e8/(12.*(1.-0.3**2.)) !youngs=1.e8, poisson=0.3
+  real,parameter :: B_c=1./(12.*(1.-0.3**2.)) !poisson=0.3
   real :: l_w,l_b
 
-  l_w  = (lw_c*B_c*(this%thickness**3.))**0.25  !buoyancy length
+  l_w  = (lw_c*bergs%fl_youngs*B_c*(this%thickness**3.))**0.25  !buoyancy length
   l_b  = l_c*l_w !length of a freshly calved footloose child berg
   L_fl = bergs%fl_bits_scale_l*3.*l_b; W_fl=bergs%fl_bits_scale_w*l_b
   T_fl=bergs%fl_bits_scale_t*this%thickness
@@ -5536,7 +5624,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   if (sample_traj .or. bergs%writeandstop) call record_posn(bergs)
   if (write_traj .or. bergs%writeandstop) then
     call move_all_trajectories(bergs)
-    call write_trajectory(bergs%trajectories, bergs%save_short_traj, bergs%save_fl_traj)
+    call write_trajectory(bergs%trajectories, bergs%save_short_traj, bergs%save_fl_traj, bergs%fl_r)
     if (save_bond_traj) call write_bond_trajectory(bergs%bond_trajectories)
   endif
 
@@ -8301,7 +8389,7 @@ subroutine icebergs_end(bergs)
   call move_all_trajectories(bergs, delete_bergs=.true.)
 
   if (.not. bergs%ignore_traj) then
-    call write_trajectory(bergs%trajectories, bergs%save_short_traj, bergs%save_fl_traj)
+    call write_trajectory(bergs%trajectories, bergs%save_short_traj, bergs%save_fl_traj, bergs%fl_r)
     if (save_bond_traj) call write_bond_trajectory(bergs%bond_trajectories)
   endif
 
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index b54cb0a..30ba6c6 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -255,6 +255,7 @@ module ice_bergs_framework
   real :: heat_density !< Heat density of berg (J/kg)
   real :: od !< Ocean depth
   real :: start_mass
+  real :: mass_scaling
   integer :: year !< Year of this record (years)
   integer(kind=8) :: id = -1 !< Iceberg identifier
   type(xyt), pointer :: next=>null() !< Next link in list
@@ -462,6 +463,7 @@ module ice_bergs_framework
   integer :: current_year !< Current year (years)
   real :: current_yearday !< Current year-day, 1.00-365.99, (days)
   real :: traj_area_thres !< Threshold for berg area (km^2) that must be exceeded to save a non-bonded berg trajectory
+  real :: traj_area_thres_sntbc !< Threshold for berg area (km^2) for saving trajectory when using save_nonfl_traj_by_class
   real :: traj_sample_hrs !< Period between sampling for trajectories (hours)
   real :: traj_write_hrs !< Period between writing of trajectories (hours)
   real :: verbose_hrs !< Period between terminal status reports (hours)
@@ -535,6 +537,10 @@ module ice_bergs_framework
   logical :: halo_debugging=.False. !< Use for debugging halos (remove when its working)
   logical :: save_short_traj=.True. !< True saves only lon,lat,time,id in iceberg_trajectory.nc
   logical :: save_fl_traj=.True. ! True saves short traj, plus masses and footloose parameters in iceberg_trajectory.nc
+  real :: save_all_traj_year=huge(0.0) ! Year at which all trajectories (for all berg areas) are saved
+  logical :: save_nonfl_traj_by_class=.false. ! Save non-footloose trajectories based on initial mass class
+  real :: save_traj_by_class_start_mass_thres_n=0.0 ! The northern hemisphere mass thres for save_nonfl_traj_by_class
+  real :: save_traj_by_class_start_mass_thres_s=0.0 ! The southern hemisphere mass thres for save_nonfl_traj_by_class
   logical :: ignore_traj=.False. !< If true, then model does not write trajectory data at all
   logical :: iceberg_bonds_on=.False. !< True=Allow icebergs to have bonds, False=don't allow.
   logical :: manually_initialize_bonds=.False. !< True= Bonds are initialize manually.
@@ -625,6 +631,11 @@ module ice_bergs_framework
   ! Footloose calving parameters [England et al (2020) Modeling the breakup of tabular icebergs. Sci. Adv.]
   logical :: fl_use_poisson_distribution=.true. !< fl_r is (T) mean of Poisson distribution to determine k, or (F) k=fl_r
   logical :: fl_use_perimeter=.false. !< scale number of footloose bergs to calve by perimeter of the parent berg
+  real :: fl_youngs=1.e8 !< Young's modulus for footloose calculations (Pa)
+  real :: fl_strength=500. !< yield stress for footloose calculations (kPa)
+  logical :: fl_use_l_scale=.false. !< footloose based on side melt and/or erosion
+  real :: fl_l_scale=1. !< scaling factor for footloose based on side melt
+  logical :: fl_l_scale_erosion_only=.true. !< fl according to erosion - buoyant convection
   real :: fl_r=0. !< footloose average number of bergs calved per fl_r_s
   real :: fl_r_s=0. !< seconds over which fl_r footloose bergs calve
   logical :: displace_fl_bergs=.true. !< footloose berg positions are randomly assigned along edges of parent berg
@@ -708,6 +719,7 @@ subroutine ice_bergs_framework_init(bergs, &
 ! Namelist parameters (and defaults)
 integer :: halo=4 ! Width of halo region
 real :: traj_area_thres=0. ! Threshold for berg area (km^2) that must be exceeded to save a non-bonded berg trajectory
+real :: traj_area_thres_sntbc=0. !< Threshold for berg area (km^2) for saving trajectory when using save_nonfl_traj_by_class
 real :: traj_sample_hrs=24. ! Period between sampling of position for trajectory storage
 real :: traj_write_hrs=480. ! Period between writing sampled trajectories to disk
 real :: verbose_hrs=24. ! Period between verbose messages
@@ -781,6 +793,10 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: halo_debugging=.False. ! Use for debugging halos (remove when its working)
 logical :: save_short_traj=.True. ! True saves only lon,lat,time,id in iceberg_trajectory.nc
 logical :: save_fl_traj=.True. ! True saves short traj, plus masses and footloose parameters in iceberg_trajectory.nc
+real :: save_all_traj_year=huge(0.0) ! Year at which all trajectories (for all berg areas) are saved
+logical :: save_nonfl_traj_by_class=.false. ! Save non-footloose trajectories based on initial mass class
+real :: save_traj_by_class_start_mass_thres_n=0.0 ! The northern hemisphere mass thres for save_nonfl_traj_by_class
+real :: save_traj_by_class_start_mass_thres_s=0.0 ! The southern hemisphere mass thres for save_nonfl_traj_by_class
 logical :: ignore_traj=.False. ! If true, then model does not traj trajectory data at all
 !logical :: iceberg_bonds_on=.False. ! True=Allow icebergs to have bonds, False=don't allow.
 logical :: manually_initialize_bonds=.False. ! True= Bonds are initialize manually.
@@ -828,6 +844,11 @@ subroutine ice_bergs_framework_init(bergs, &
 ! Footloose calving parameters [England et al (2020) Modeling the breakup of tabular icebergs. Sci. Adv.]
 logical :: fl_use_poisson_distribution=.true. ! fl_r is (T) mean of Poisson distribution to determine k, or (F) k=fl_r
 logical :: fl_use_perimeter=.false. ! scale number of footloose bergs to calve by perimeter of the parent berg
+real :: fl_youngs=1.e8 !< Young's modulus for footloose calculations (Pa)
+real :: fl_strength=500. !< yield stress for footloose calculations (kPa)
+logical :: fl_use_l_scale=.false. !< footloose based on side melt
+real :: fl_l_scale=1. !< scaling factor for footloose based on side melt and/or erosion
+logical :: fl_l_scale_erosion_only=.true. !< fl according to erosion - buoyant convection
 real :: fl_r=0. ! footloose average number of bergs calved per fl_r_s
 real :: fl_r_s=0. ! seconds over which fl_r footloose bergs calve
 logical :: displace_fl_bergs=.true. ! footloose berg positions are randomly assigned along edges of parent berg
@@ -864,7 +885,9 @@ subroutine ice_bergs_framework_init(bergs, &
          dem_shear_for_frac_only,use_damage,fl_use_poisson_distribution, fl_use_perimeter, fl_r, fl_r_s,displace_fl_bergs,&
          fl_style,fl_bits_erosion_to_bergy_bits,fl_k_scale_by_perimeter,use_spring_for_land_contact, save_fl_traj,&
          new_berg_from_fl_bits_mass_thres,fl_bits_scale_l,fl_bits_scale_w,fl_bits_scale_t,separate_distrib_for_n_hemisphere,&
-         initial_mass_n, distribution_n, mass_scaling_n, initial_thickness_n
+         initial_mass_n, distribution_n, mass_scaling_n, initial_thickness_n, fl_use_l_scale, fl_l_scale,&
+         fl_l_scale_erosion_only, fl_youngs, fl_strength,  save_all_traj_year, save_nonfl_traj_by_class,&
+         save_traj_by_class_start_mass_thres_n, save_traj_by_class_start_mass_thres_s,traj_area_thres_sntbc
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -873,6 +896,8 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: lerr
 integer :: stdlogunit, stderrunit
 real :: Total_mass_s, Total_mass_n
+real :: remaining_dist_s,remaining_dist_n
+integer :: last_dist_j, last_dist_j_n
 real :: mts_fast_dt=0.0 !Added by Alex
 real :: maxlon_c,minlon_c !Added by Alex, for mts verlet periodicity
 integer :: k,maxk
@@ -1221,7 +1246,7 @@ subroutine ice_bergs_framework_init(bergs, &
 
   ! If a separate calving distribution for the northern hemisphere is not used, the following northern
   ! hemisphere parameters inherit the values of their respective southern hemisphere parameters
-  if (.not. bergs%separate_distrib_for_n_hemisphere) then
+  if (.not. separate_distrib_for_n_hemisphere) then
     initial_mass_n=initial_mass; distribution_n=distribution
     mass_scaling_n=mass_scaling; initial_thickness_n=initial_thickness
   endif
@@ -1238,6 +1263,33 @@ subroutine ice_bergs_framework_init(bergs, &
            distribution(j)=(distribution(j)*initial_mass(j))/Total_mass_s
            distribution_n(j)=(distribution_n(j)*initial_mass_n(j))/Total_mass_n
      enddo
+
+     if (mpp_pe()==0) then
+       print *,'uncorrected distribution_s',distribution
+       print *,'uncorrected distribution_n',distribution_n
+     endif
+     !floating point fix: correct the distributions so that
+     !remaining_dist_s and remaining_dist_n in icebergs.F90/accumulate_calving are >= 0
+     do j=1,nclasses
+       if (distribution(j)>0.) last_dist_j=j
+       if (distribution_n(j)>0.) last_dist_j_n=j
+     enddo
+     remaining_dist_s=1.; remaining_dist_n=1.
+     do j=1,last_dist_j-1
+       remaining_dist_s=remaining_dist_s-distribution(j)
+     enddo
+     distribution(last_dist_j)=remaining_dist_s
+     do j=1,last_dist_j_n-1
+       remaining_dist_n=remaining_dist_n-distribution_n(j)
+     enddo
+     distribution_n(last_dist_j_n)=remaining_dist_n
+     if (mpp_pe()==0) then
+       print *,'remaining_dist_s, last_dist_j_s, remaining_dist_n','last_dist_j_n',&
+         remaining_dist_s-distribution(last_dist_j),last_dist_j,&
+         remaining_dist_n-distribution_n(last_dist_j_n),last_dist_j_n
+       print *,'corrected distribution_s',distribution
+       print *,'corrected distribution_n',distribution_n
+     endif
 endif
 
 if ((halo .lt. 3) .and. (rotate_icebergs_for_mass_spreading .and. iceberg_bonds_on) )   then
@@ -1266,7 +1318,13 @@ subroutine ice_bergs_framework_init(bergs, &
   buffer_width=buffer_width+(max_bonds*5) ! Increase buffer width to include bonds being passed between processors
 endif
 if (save_short_traj) buffer_width_traj=6 ! This is the length of the short buffer used for abrevated traj
-if (save_fl_traj) buffer_width_traj=buffer_width_traj+7
+if (save_fl_traj) then
+  if (fl_r>0) then
+    buffer_width_traj=buffer_width_traj+8
+  else
+    buffer_width_traj=buffer_width_traj+4
+  endif
+endif
 if (ignore_traj) buffer_width_traj=0 ! If this is true, then all traj files should be ignored
 
 if (use_damage) then
@@ -1344,10 +1402,15 @@ subroutine ice_bergs_framework_init(bergs, &
  ! Parameters
   bergs%dt=dt
   bergs%traj_area_thres=traj_area_thres
+  bergs%traj_area_thres_sntbc=traj_area_thres_sntbc
   bergs%traj_sample_hrs=traj_sample_hrs
   bergs%traj_write_hrs=traj_write_hrs
   bergs%save_short_traj=save_short_traj
   bergs%save_fl_traj=save_fl_traj
+  bergs%save_all_traj_year=save_all_traj_year
+  bergs%save_nonfl_traj_by_class=save_nonfl_traj_by_class
+  bergs%save_traj_by_class_start_mass_thres_n=save_traj_by_class_start_mass_thres_n
+  bergs%save_traj_by_class_start_mass_thres_s=save_traj_by_class_start_mass_thres_s
   bergs%ignore_traj=ignore_traj
   bergs%verbose_hrs=verbose_hrs
   bergs%grd%halo=halo
@@ -1452,6 +1515,11 @@ subroutine ice_bergs_framework_init(bergs, &
   ! Footloose calving parameters
   bergs%fl_use_poisson_distribution=fl_use_poisson_distribution
   bergs%fl_use_perimeter=fl_use_perimeter
+  bergs%fl_youngs=fl_youngs
+  bergs%fl_strength=fl_strength
+  bergs%fl_use_l_scale=fl_use_l_scale
+  bergs%fl_l_scale=fl_l_scale
+  bergs%fl_l_scale_erosion_only=fl_l_scale_erosion_only
   bergs%new_berg_from_fl_bits_mass_thres=new_berg_from_fl_bits_mass_thres
   bergs%fl_r=fl_r
   bergs%fl_r_s=fl_r_s
@@ -1462,6 +1530,14 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%fl_bits_scale_l=fl_bits_scale_l
   bergs%fl_bits_scale_w=fl_bits_scale_w
   bergs%fl_bits_scale_t=fl_bits_scale_t
+  if (bergs%fl_use_l_scale) then
+    bergs%fl_use_perimeter=.true.
+    bergs%fl_k_scale_by_perimeter=1
+    if (.not. bergs%use_operator_splitting) then
+      call error_mesg('KID, ice_bergs_framework_init', &
+        'use_operator_splitting must be true when fl_use_l_scale=.true.', FATAL)
+    endif
+  endif
 
   if (monitor_energy) then
     if (bergs%constant_interaction_LW) then
@@ -3813,13 +3889,14 @@ subroutine increase_ibuffer(old, num_bergs, width)
 end subroutine increase_ibuffer
 
 !> Packs a trajectory entry into a buffer
-subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj, save_fl_traj)
+subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj, save_fl_traj, fl_r)
   ! Arguments
   type(xyt), pointer :: traj !< Trajectory entry to pack
   type(buffer), pointer :: buff !< Buffer to pack entry into
   integer, intent(in) :: n !< Position in buffer to place entry
   logical, intent(in) :: save_short_traj !< If true, only use a subset of trajectory data
   logical, intent(in) :: save_fl_traj !< If true, save masses and footloose parameters
+  real, intent(in) :: fl_r !< If >0 and save_fl_traj, save footloose parameters
   ! Local variables
   integer :: counter ! Position in stack
   integer :: cnt, ij
@@ -3838,11 +3915,14 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj, save_fl_traj)
   if (save_fl_traj) then
     call push_buffer_value(buff%data(:,n),counter,traj%mass)
     call push_buffer_value(buff%data(:,n),counter,traj%start_mass)
-    call push_buffer_value(buff%data(:,n),counter,traj%mass_of_bits)
-    call push_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bits)
-    call push_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bergy_bits)
-    call push_buffer_value(buff%data(:,n),counter,traj%fl_k)
     call push_buffer_value(buff%data(:,n),counter,traj%thickness)
+    call push_buffer_value(buff%data(:,n),counter,traj%mass_of_bits)
+    if (fl_r>0) then
+      call push_buffer_value(buff%data(:,n),counter,traj%mass_scaling)
+      call push_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bits)
+      call push_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bergy_bits)
+      call push_buffer_value(buff%data(:,n),counter,traj%fl_k)
+    endif
   endif
   if (.not. save_short_traj) then
     call push_buffer_value(buff%data(:,n),counter,traj%uvel)
@@ -3910,13 +3990,14 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj, save_fl_traj)
 end subroutine pack_traj_into_buffer2
 
 !> Unpacks a trajectory entry from a buffer
-subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj, save_fl_traj)
+subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj, save_fl_traj, fl_r)
   ! Arguments
   type(xyt), pointer :: first !< Trajectory list
   type(buffer), pointer :: buff !< Buffer from which to unpack
   integer, intent(in) :: n !< Position in buffer to unpack
   logical, intent(in) :: save_short_traj !< If true, only use a subset of trajectory data
   logical, intent(in) :: save_fl_traj !< If true, save masses and footloose parameters
+  real, intent(in) :: fl_r !< If >0 and save_fl_traj, save footloose parameters
   ! Local variables
   type(xyt) :: traj
   integer :: counter ! Position in stack
@@ -3952,11 +4033,14 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj, save_fl_tra
   if (save_fl_traj) then
     call pull_buffer_value(buff%data(:,n),counter,traj%mass)
     call pull_buffer_value(buff%data(:,n),counter,traj%start_mass)
-    call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_bits)
-    call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bits)
-    call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bergy_bits)
-    call pull_buffer_value(buff%data(:,n),counter,traj%fl_k)
     call pull_buffer_value(buff%data(:,n),counter,traj%thickness)
+    call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_bits)
+    if (fl_r>0) then
+      call pull_buffer_value(buff%data(:,n),counter,traj%mass_scaling)
+      call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bits)
+      call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bergy_bits)
+      call pull_buffer_value(buff%data(:,n),counter,traj%fl_k)
+    endif
   endif
   if (.not. save_short_traj) then
     call pull_buffer_value(buff%data(:,n),counter,traj%uvel)
@@ -5801,10 +5885,11 @@ subroutine record_posn(bergs)
 integer :: grdi, grdj
 integer :: js,je,is,ie
 type(bond) , pointer :: current_bond
-real :: area_thres
+real :: area_thres,area_thres2
 ! Local bond variables
 type(bond_xyt) :: bond_posn
-real :: dx_dlon,dy_dlat,lat_ref,dx,dy,n1,n2,id1,id2
+real :: dx_dlon,dy_dlat,lat_ref,dx,dy,n1,n2,id1,id2,berg_area
+logical :: loc_save_nonfl_traj_by_class
 
 if (bergs%debug_write) then
   js=bergs%grd%jsd+1; je=bergs%grd%jed; is=bergs%grd%isd+1; ie=bergs%grd%ied
@@ -5846,12 +5931,26 @@ subroutine record_posn(bergs)
   endif
 
   area_thres=bergs%traj_area_thres*1.e6 ! convert from km^2 to m^2
+  area_thres2=bergs%traj_area_thres_sntbc*1.e6
+  loc_save_nonfl_traj_by_class=.false.
 
   do grdj = js,je ; do grdi = is,ie
     this=>bergs%list(grdi,grdj)%first
     do while (associated(this))
+      berg_area=this%mass/(bergs%rho_bergs*this%thickness)
+      if (bergs%save_nonfl_traj_by_class) then
+        loc_save_nonfl_traj_by_class=.false.
+        if (this%fl_k>=0. .and. berg_area>area_thres2) then
+          if (this%lat<0.) then
+            if (this%start_mass>=bergs%save_traj_by_class_start_mass_thres_s) loc_save_nonfl_traj_by_class=.true.
+          else
+            if (this%start_mass>=bergs%save_traj_by_class_start_mass_thres_n) loc_save_nonfl_traj_by_class=.true.
+          endif
+        endif
+      endif
       current_bond=>this%first_bond
-      if ( (this%mass/(bergs%rho_bergs*this%thickness)) >= area_thres .or. associated(current_bond) ) then
+      if ( bergs%current_year>bergs%save_all_traj_year .or. loc_save_nonfl_traj_by_class .or. &
+        berg_area >= area_thres .or. associated(current_bond) ) then
         posn%lon=this%lon
         posn%lat=this%lat
         posn%year=bergs%current_year
@@ -5860,11 +5959,14 @@ subroutine record_posn(bergs)
         if (bergs%save_fl_traj) then
           posn%mass=this%mass
           posn%start_mass=this%start_mass
-          posn%mass_of_bits=this%mass_of_bits
-          posn%mass_of_fl_bits=this%mass_of_fl_bits
-          posn%mass_of_fl_bergy_bits=this%mass_of_fl_bergy_bits
-          posn%fl_k=this%fl_k
           posn%thickness=this%thickness
+          posn%mass_of_bits=this%mass_of_bits
+          if (bergs%fl_r>0) then
+            posn%mass_scaling=this%mass_scaling
+            posn%mass_of_fl_bits=this%mass_of_fl_bits
+            posn%mass_of_fl_bergy_bits=this%mass_of_fl_bergy_bits
+            posn%fl_k=this%fl_k
+          endif
         endif
         if (.not. bergs%save_short_traj) then !Not totally sure that this is correct
           posn%uvel=this%uvel
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index df322a4..c8a07c3 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -1686,11 +1686,12 @@ subroutine read_ocean_depth(grd)
 end subroutine read_ocean_depth
 
 !> Write a trajectory-based diagnostics file
-subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj)
+subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r)
 ! Arguments
 type(xyt), pointer :: trajectory !< An iceberg trajectory
 logical, intent(in) :: save_short_traj !< If true, record less data
 logical, intent(in) :: save_fl_traj !< If true, save masses and footloose data
+real, intent(in) :: fl_r !< If >0 and save_fl_traj, save footloose params
 ! Local variables
 integer :: iret, ncid, i_dim, i
 integer :: lonid, latid, yearid, dayid, uvelid, vvelid, idcntid, idijid
@@ -1698,7 +1699,7 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj)
 integer :: uoid, void, uiid, viid, uaid, vaid, sshxid, sshyid, sstid, sssid
 integer :: cnid, hiid, hsid
 integer :: mid, smid, did, wid, lid, mbid, mflbid, mflbbid, hdid, nbid, odid, flkid
-integer :: axnid,aynid,bxnid,bynid,axnfid,aynfid,bxnfid,bynfid
+integer :: axnid,aynid,bxnid,bynid,axnfid,aynfid,bxnfid,bynfid, msid
 integer :: eecid,edcid,eeid,edid,aeid,efid
 integer :: eectid, edctid, eetid, edtid, aetid
 integer :: avid, aaid, rid, abrid
@@ -1749,7 +1750,7 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj)
            call increase_ibuffer(ibuffer_io, ntrajs_rcvd_io,buffer_width_traj)
            call mpp_recv(ibuffer_io%data, ntrajs_rcvd_io*buffer_width_traj,from_pe=from_pe, tag=COMM_TAG_12)
            do i=1, ntrajs_rcvd_io
-              call unpack_traj_from_buffer2(traj4io, ibuffer_io, i, save_short_traj, save_fl_traj)
+              call unpack_traj_from_buffer2(traj4io, ibuffer_io, i, save_short_traj, save_fl_traj, fl_r)
            enddo
        endif
      enddo
@@ -1757,7 +1758,7 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj)
      ! Pack and send trajectories to the root PE for this I/O tile
      do while (associated(trajectory))
        ntrajs_sent_io = ntrajs_sent_io +1
-       call pack_traj_into_buffer2(trajectory, obuffer_io, ntrajs_sent_io, save_short_traj, save_fl_traj)
+       call pack_traj_into_buffer2(trajectory, obuffer_io, ntrajs_sent_io, save_short_traj, save_fl_traj, fl_r)
        this => trajectory ! Need to keep pointer in order to free up the links memory
        trajectory => trajectory%next ! This will eventually result in trajectory => null()
        deallocate(this) ! Delete the link from memory
@@ -1822,11 +1823,14 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj)
       if (save_fl_traj) then
         mid = inq_varid(ncid, 'mass')
         smid = inq_varid(ncid, 'start_mass')
-        mbid = inq_varid(ncid, 'mass_of_bits')
-        mflbid = inq_varid(ncid, 'mass_of_fl_bits')
-        mflbbid = inq_varid(ncid, 'mass_of_fl_bergy_bits')
-        flkid = inq_varid(ncid, 'fl_k')
         did = inq_varid(ncid, 'thickness')
+        mbid = inq_varid(ncid, 'mass_of_bits')
+        if (fl_r>0) then
+          msid = inq_varid(ncid, 'mass_scaling')
+          mflbid = inq_varid(ncid, 'mass_of_fl_bits')
+          mflbbid = inq_varid(ncid, 'mass_of_fl_bergy_bits')
+          flkid = inq_varid(ncid, 'fl_k')
+        endif
       endif
       if (.not.save_short_traj) then
         uvelid = inq_varid(ncid, 'uvel')
@@ -1904,11 +1908,14 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj)
       if (save_fl_traj) then
         mid = def_var(ncid, 'mass', NF_DOUBLE, i_dim)
         smid = def_var(ncid, 'start_mass', NF_DOUBLE, i_dim)
-        mbid = def_var(ncid, 'mass_of_bits', NF_DOUBLE, i_dim)
-        mflbid = def_var(ncid, 'mass_of_fl_bits', NF_DOUBLE, i_dim)
-        mflbbid = def_var(ncid, 'mass_of_fl_bergy_bits', NF_DOUBLE, i_dim)
-        flkid = def_var(ncid, 'fl_k', NF_DOUBLE, i_dim)
         did = def_var(ncid, 'thickness', NF_DOUBLE, i_dim)
+        mbid = def_var(ncid, 'mass_of_bits', NF_DOUBLE, i_dim)
+        if (fl_r>0) then
+          msid = def_var(ncid, 'mass_scaling', NF_DOUBLE, i_dim)
+          mflbid = def_var(ncid, 'mass_of_fl_bits', NF_DOUBLE, i_dim)
+          mflbbid = def_var(ncid, 'mass_of_fl_bergy_bits', NF_DOUBLE, i_dim)
+          flkid = def_var(ncid, 'fl_k', NF_DOUBLE, i_dim)
+        endif
       endif
       if (.not. save_short_traj) then
         uvelid = def_var(ncid, 'uvel', NF_DOUBLE, i_dim)
@@ -1991,16 +1998,20 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj)
         call put_att(ncid, mid, 'units', 'kg')
         call put_att(ncid, smid, 'long_name', 'start_mass')
         call put_att(ncid, smid, 'units', 'kg')
-        call put_att(ncid, mbid, 'long_name', 'mass_of_bits')
-        call put_att(ncid, mbid, 'units', 'kg')
-        call put_att(ncid, mflbid, 'long_name', 'mass_of_fl_bits')
-        call put_att(ncid, mflbid, 'units', 'kg')
-        call put_att(ncid, mflbbid, 'long_name', 'mass_of_fl_bergy_bits')
-        call put_att(ncid, mflbbid, 'units', 'kg')
-        call put_att(ncid, flkid, 'long_name', 'footloose calving k')
-        call put_att(ncid, flkid, 'units', 'none')
         call put_att(ncid, did, 'long_name', 'thickness')
         call put_att(ncid, did, 'units', 'm')
+        call put_att(ncid, mbid, 'long_name', 'mass_of_bits')
+        call put_att(ncid, mbid, 'units', 'kg')
+        if (fl_r>0) then
+          call put_att(ncid, msid, 'long_name', 'mass_scaling')
+          call put_att(ncid, msid, 'units', 'dimensionless')
+          call put_att(ncid, mflbid, 'long_name', 'mass_of_fl_bits')
+          call put_att(ncid, mflbid, 'units', 'kg')
+          call put_att(ncid, mflbbid, 'long_name', 'mass_of_fl_bergy_bits')
+          call put_att(ncid, mflbbid, 'units', 'kg')
+          call put_att(ncid, flkid, 'long_name', 'footloose calving k')
+          call put_att(ncid, flkid, 'units', 'none')
+        endif
       endif
       if (.not. save_short_traj) then
         call put_att(ncid, uvelid, 'long_name', 'zonal spped')
@@ -2132,11 +2143,14 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj)
       if (save_fl_traj) then
         call put_double(ncid, mid, i, this%mass)
         call put_double(ncid, smid, i, this%start_mass)
-        call put_double(ncid, mbid, i, this%mass_of_bits)
-        call put_double(ncid, mflbid, i, this%mass_of_fl_bits)
-        call put_double(ncid, mflbbid, i, this%mass_of_fl_bergy_bits)
-        call put_double(ncid, flkid, i, this%fl_k)
         call put_double(ncid, did, i, this%thickness)
+        call put_double(ncid, mbid, i, this%mass_of_bits)
+        if (fl_r>0) then
+          call put_double(ncid, msid, i, this%mass_scaling)
+          call put_double(ncid, mflbid, i, this%mass_of_fl_bits)
+          call put_double(ncid, mflbbid, i, this%mass_of_fl_bergy_bits)
+          call put_double(ncid, flkid, i, this%fl_k)
+        endif
       endif
       if (.not. save_short_traj) then
         call put_double(ncid, uvelid, i, this%uvel)

From b3e639594886cde971639e709ee298cf9228dab3 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Thu, 12 Aug 2021 10:06:01 -0400
Subject: [PATCH 311/361] fix diagnostic for gridded melt associated with
 footloose child bergs

---
 src/icebergs.F90 | 68 ++++++++++++++----------------------------------
 1 file changed, 19 insertions(+), 49 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index e9a7c63..575d1a8 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -3114,31 +3114,6 @@ subroutine thermodynamics(bergs)
         dMv=(M/Vol)*(T*(W+L))*Mv*bergs%dt ! approx. mass loss to buoyant convection (kg)
       endif
 
-      ! !if footloose is based on length of foot, accumulate side mass loss on fl_k
-      ! !note: this only works when bergs%use_operator_splitting=.true.
-      ! if (bergs%fl_use_l_scale .and. this%fl_k>=0) then
-      !   l_b3 = 3.*l_c*(lw_c*bergs%fl_youngs*B_c*(Tn**3.))**0.25 !child berg length x 3
-      !   if (L>l_b3) then !do not accumulate side made loss for sides < l_b3
-      !     if (W>l_b3) then
-      !       if (bergs%fl_l_scale_erosion_only) then
-      !         this%fl_k=this%fl_k + (dMe - dMv)/Tn
-      !         if (this%fl_k<0) this%fl_k=0
-      !       else
-      !         this%fl_k= this%fl_k + (dMe + dMv)/Tn
-      !       endif
-      !     else
-      !       dMv_l=dMv*(Wn1 + W)/(2.*(Ln1 + W)) !mass loss from length from buoyant convection
-      !       dMe_l=dMe*(Wn+ Wn1)/(2.*(Ln+ Wn1)) !mass loss from length from erosion
-      !       if (bergs%fl_l_scale_erosion_only) then
-      !         this%fl_k=this%fl_k + (dMe_l - dMv_l)/Tn
-      !         if (this%fl_k<0) this%fl_k=0
-      !       else
-      !         this%fl_k= this%fl_k + (dMe_l + dMv_l)/Tn
-      !       endif
-      !     endif
-      !   endif
-      ! endif
-
       !if footloose is based on length of foot, accumulate side mass loss on fl_k
       !note: this only works when bergs%use_operator_splitting=.true.
       if (bergs%fl_use_l_scale .and. this%fl_k>=0) then
@@ -3166,7 +3141,7 @@ subroutine thermodynamics(bergs)
         endif
       endif
 
-      ! Footloose bits (FL bits). For now, FL bits do not erode into bergy bits.
+      ! Footloose bits (FL bits).
       if (this%mass_of_fl_bits>0.) then
         call fl_bits_dimensions(bergs,this,Lfl,Wfl,Tfl)
         Mfl=this%mass_of_fl_bits
@@ -3302,45 +3277,40 @@ subroutine thermodynamics(bergs)
             melt=dMv/bergs%dt ! melt rate due to convection term in kg/s
             grd%melt_conv(i,j)=grd%melt_conv(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
           endif
+
+          if (dMfl>0) then
+            if(grd%id_melt_buoy_fl>0) then
+              melt=dMb_fl/bergs%dt ! melt rate due to buoyancy term in kg/s
+              grd%melt_buoy_fl(i,j)=grd%melt_buoy_fl(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+            endif
+            if(grd%id_melt_eros_fl>0) then
+              melt=dMe_fl/bergs%dt ! erosion rate in kg/s
+              grd%melt_eros_fl(i,j)=grd%melt_eros_fl(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+            endif
+            if(grd%id_melt_conv_fl>0) then
+              melt=dMv_fl/bergs%dt ! melt rate due to convection term in kg/s
+              grd%melt_conv_fl(i,j)=grd%melt_conv_fl(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
+            endif
+          endif
         else
           !Independently-tracked footloose "child" berg:
           if(grd%id_fl_child_melt>0) then
             melt=(dM-(dMbitsE-dMbitsM))/bergs%dt !total melt of the "child" berg (here, melts like a parent berg)
             grd%fl_child_melt(i,j)=grd%fl_child_melt(i,j)+melt/grd%area(i,j)*this%mass_scaling !kg/m2/s
           endif
-          if(grd%id_melt_buoy>0) then
+          if(grd%id_melt_buoy_fl>0) then
             melt=dMb/bergs%dt ! melt rate due to buoyancy term in kg/s
             grd%melt_buoy_fl(i,j)=grd%melt_buoy_fl(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
           endif
-          if(grd%id_melt_eros>0) then
+          if(grd%id_melt_eros_fl>0) then
             melt=dMe/bergs%dt ! erosion rate in kg/s
             grd%melt_eros_fl(i,j)=grd%melt_eros_fl(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
           endif
-          if(grd%id_melt_conv>0) then
+          if(grd%id_melt_conv_fl>0) then
             melt=dMv/bergs%dt ! melt rate due to convection term in kg/s
             grd%melt_conv_fl(i,j)=grd%melt_conv_fl(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
           endif
         endif
-
-        if (dMfl>0) then
-          ! Footloose bit:
-          if(grd%id_fl_child_melt>0) then
-            melt=(dM-(dMbitsE-dMbitsM))/bergs%dt !total melt of the "child" FL bits
-            grd%fl_child_melt(i,j)=grd%fl_child_melt(i,j)+melt/grd%area(i,j)*this%mass_scaling !kg/m2/s
-          endif
-          if(grd%id_melt_buoy>0) then
-            melt=dMb_fl/bergs%dt ! melt rate due to buoyancy term in kg/s
-            grd%melt_buoy_fl(i,j)=grd%melt_buoy_fl(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
-          endif
-          if(grd%id_melt_eros>0) then
-            melt=dMe_fl/bergs%dt ! erosion rate in kg/s
-            grd%melt_eros_fl(i,j)=grd%melt_eros_fl(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
-          endif
-          if(grd%id_melt_conv>0) then
-            melt=dMv_fl/bergs%dt ! melt rate due to convection term in kg/s
-            grd%melt_conv_fl(i,j)=grd%melt_conv_fl(i,j)+melt/grd%area(i,j)*this%mass_scaling ! kg/m2/s
-          endif
-        endif
       else
         stderrunit = stderr()
         write(stderrunit,*) 'KID, thermodynamics: berg appears to have grounded!!!! PE=',mpp_pe(),i,j

From 50d8c2894ae06c6446cda3e25d9b259c951e6045 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Wed, 25 Aug 2021 17:20:12 -0400
Subject: [PATCH 312/361] added footloose bergy bits to grd%bergy_mass
 diagnostic

---
 src/icebergs.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 575d1a8..aed84cd 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -5138,7 +5138,7 @@ subroutine calculate_sum_over_bergs_diagnositcs(bergs, grd, berg, i, j)
 
   !Mass of bergy bits
   if (grd%id_bergy_mass>0 .or. bergs%add_weight_to_ocean)&
-    & grd%bergy_mass(i,j)=grd%bergy_mass(i,j)+berg%mass_of_bits/grd%area(i,j)*berg%mass_scaling ! kg/m2
+    & grd%bergy_mass(i,j)=grd%bergy_mass(i,j)+(berg%mass_of_bits+berg%mass_of_fl_bergy_bits)/grd%area(i,j)*berg%mass_scaling ! kg/m2
 
   !Mass of footloose bits
   if (grd%id_fl_bits_mass>0 .or. bergs%add_weight_to_ocean)&

From be810d96d61c71e00f56f39fe0ea71260983b29e Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Tue, 28 Sep 2021 13:21:40 -0400
Subject: [PATCH 313/361] added berg velocities to save_short_traj. added
 option to save trajectories of footloose child bergs with areas exceeding a
 given threshold

---
 src/icebergs_framework.F90 | 40 ++++++++++++++++++++++++++------------
 src/icebergs_io.F90        | 30 ++++++++++++++++++----------
 2 files changed, 48 insertions(+), 22 deletions(-)

diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 30ba6c6..193fcb8 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -464,6 +464,7 @@ module ice_bergs_framework
   real :: current_yearday !< Current year-day, 1.00-365.99, (days)
   real :: traj_area_thres !< Threshold for berg area (km^2) that must be exceeded to save a non-bonded berg trajectory
   real :: traj_area_thres_sntbc !< Threshold for berg area (km^2) for saving trajectory when using save_nonfl_traj_by_class
+  real :: traj_area_thres_fl !< Threshold for berg area (km^2) that must be exceeded to save a non-bonded FL berg trajectory
   real :: traj_sample_hrs !< Period between sampling for trajectories (hours)
   real :: traj_write_hrs !< Period between writing of trajectories (hours)
   real :: verbose_hrs !< Period between terminal status reports (hours)
@@ -720,6 +721,7 @@ subroutine ice_bergs_framework_init(bergs, &
 integer :: halo=4 ! Width of halo region
 real :: traj_area_thres=0. ! Threshold for berg area (km^2) that must be exceeded to save a non-bonded berg trajectory
 real :: traj_area_thres_sntbc=0. !< Threshold for berg area (km^2) for saving trajectory when using save_nonfl_traj_by_class
+real :: traj_area_thres_fl=huge(0.0) ! Threshold for berg area (km^2) that must be exceeded to save a non-bonded FL berg trajectory
 real :: traj_sample_hrs=24. ! Period between sampling of position for trajectory storage
 real :: traj_write_hrs=480. ! Period between writing sampled trajectories to disk
 real :: verbose_hrs=24. ! Period between verbose messages
@@ -887,7 +889,8 @@ subroutine ice_bergs_framework_init(bergs, &
          new_berg_from_fl_bits_mass_thres,fl_bits_scale_l,fl_bits_scale_w,fl_bits_scale_t,separate_distrib_for_n_hemisphere,&
          initial_mass_n, distribution_n, mass_scaling_n, initial_thickness_n, fl_use_l_scale, fl_l_scale,&
          fl_l_scale_erosion_only, fl_youngs, fl_strength,  save_all_traj_year, save_nonfl_traj_by_class,&
-         save_traj_by_class_start_mass_thres_n, save_traj_by_class_start_mass_thres_s,traj_area_thres_sntbc
+         save_traj_by_class_start_mass_thres_n, save_traj_by_class_start_mass_thres_s,traj_area_thres_sntbc,&
+         traj_area_thres_fl
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -1320,9 +1323,9 @@ subroutine ice_bergs_framework_init(bergs, &
 if (save_short_traj) buffer_width_traj=6 ! This is the length of the short buffer used for abrevated traj
 if (save_fl_traj) then
   if (fl_r>0) then
-    buffer_width_traj=buffer_width_traj+8
+    buffer_width_traj=buffer_width_traj+8+2
   else
-    buffer_width_traj=buffer_width_traj+4
+    buffer_width_traj=buffer_width_traj+4+2
   endif
 endif
 if (ignore_traj) buffer_width_traj=0 ! If this is true, then all traj files should be ignored
@@ -1403,6 +1406,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%dt=dt
   bergs%traj_area_thres=traj_area_thres
   bergs%traj_area_thres_sntbc=traj_area_thres_sntbc
+  bergs%traj_area_thres_fl=traj_area_thres_fl
   bergs%traj_sample_hrs=traj_sample_hrs
   bergs%traj_write_hrs=traj_write_hrs
   bergs%save_short_traj=save_short_traj
@@ -3917,6 +3921,8 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj, save_fl_traj,
     call push_buffer_value(buff%data(:,n),counter,traj%start_mass)
     call push_buffer_value(buff%data(:,n),counter,traj%thickness)
     call push_buffer_value(buff%data(:,n),counter,traj%mass_of_bits)
+    call push_buffer_value(buff%data(:,n),counter,traj%uvel)
+    call push_buffer_value(buff%data(:,n),counter,traj%vvel)
     if (fl_r>0) then
       call push_buffer_value(buff%data(:,n),counter,traj%mass_scaling)
       call push_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bits)
@@ -3925,8 +3931,8 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj, save_fl_traj,
     endif
   endif
   if (.not. save_short_traj) then
-    call push_buffer_value(buff%data(:,n),counter,traj%uvel)
-    call push_buffer_value(buff%data(:,n),counter,traj%vvel)
+    !call push_buffer_value(buff%data(:,n),counter,traj%uvel)
+    !call push_buffer_value(buff%data(:,n),counter,traj%vvel)
     call push_buffer_value(buff%data(:,n),counter,traj%uvel_prev)
     call push_buffer_value(buff%data(:,n),counter,traj%vvel_prev)
     call push_buffer_value(buff%data(:,n),counter,traj%heat_density)
@@ -4035,6 +4041,8 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj, save_fl_tra
     call pull_buffer_value(buff%data(:,n),counter,traj%start_mass)
     call pull_buffer_value(buff%data(:,n),counter,traj%thickness)
     call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_bits)
+    call pull_buffer_value(buff%data(:,n),counter,traj%uvel)
+    call pull_buffer_value(buff%data(:,n),counter,traj%vvel)
     if (fl_r>0) then
       call pull_buffer_value(buff%data(:,n),counter,traj%mass_scaling)
       call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bits)
@@ -4043,8 +4051,8 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj, save_fl_tra
     endif
   endif
   if (.not. save_short_traj) then
-    call pull_buffer_value(buff%data(:,n),counter,traj%uvel)
-    call pull_buffer_value(buff%data(:,n),counter,traj%vvel)
+    !call pull_buffer_value(buff%data(:,n),counter,traj%uvel)
+    !call pull_buffer_value(buff%data(:,n),counter,traj%vvel)
     call pull_buffer_value(buff%data(:,n),counter,traj%uvel_prev)
     call pull_buffer_value(buff%data(:,n),counter,traj%vvel_prev)
     call pull_buffer_value(buff%data(:,n),counter,traj%heat_density)
@@ -5885,11 +5893,11 @@ subroutine record_posn(bergs)
 integer :: grdi, grdj
 integer :: js,je,is,ie
 type(bond) , pointer :: current_bond
-real :: area_thres,area_thres2
+real :: area_thres,area_thres2,area_thres3
 ! Local bond variables
 type(bond_xyt) :: bond_posn
 real :: dx_dlon,dy_dlat,lat_ref,dx,dy,n1,n2,id1,id2,berg_area
-logical :: loc_save_nonfl_traj_by_class
+logical :: loc_save_nonfl_traj_by_class,save_fl_berg
 
 if (bergs%debug_write) then
   js=bergs%grd%jsd+1; je=bergs%grd%jed; is=bergs%grd%isd+1; ie=bergs%grd%ied
@@ -5932,6 +5940,7 @@ subroutine record_posn(bergs)
 
   area_thres=bergs%traj_area_thres*1.e6 ! convert from km^2 to m^2
   area_thres2=bergs%traj_area_thres_sntbc*1.e6
+  area_thres3=bergs%traj_area_thres_fl*1.e6
   loc_save_nonfl_traj_by_class=.false.
 
   do grdj = js,je ; do grdi = is,ie
@@ -5948,9 +5957,14 @@ subroutine record_posn(bergs)
           endif
         endif
       endif
+      if (this%fl_k<0 .and. berg_area>area_thres3) then
+        save_fl_berg=.true.
+      else
+        save_fl_berg=.false.
+      endif
       current_bond=>this%first_bond
       if ( bergs%current_year>bergs%save_all_traj_year .or. loc_save_nonfl_traj_by_class .or. &
-        berg_area >= area_thres .or. associated(current_bond) ) then
+        berg_area >= area_thres .or. associated(current_bond) .or. save_fl_berg) then
         posn%lon=this%lon
         posn%lat=this%lat
         posn%year=bergs%current_year
@@ -5961,6 +5975,8 @@ subroutine record_posn(bergs)
           posn%start_mass=this%start_mass
           posn%thickness=this%thickness
           posn%mass_of_bits=this%mass_of_bits
+          posn%uvel=this%uvel
+          posn%vvel=this%vvel
           if (bergs%fl_r>0) then
             posn%mass_scaling=this%mass_scaling
             posn%mass_of_fl_bits=this%mass_of_fl_bits
@@ -5969,8 +5985,8 @@ subroutine record_posn(bergs)
           endif
         endif
         if (.not. bergs%save_short_traj) then !Not totally sure that this is correct
-          posn%uvel=this%uvel
-          posn%vvel=this%vvel
+          !posn%uvel=this%uvel
+          !posn%vvel=this%vvel
           posn%uvel_prev=this%uvel_prev
           posn%vvel_prev=this%vvel_prev
           posn%heat_density=this%heat_density
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index c8a07c3..f3eb132 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -1825,6 +1825,8 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r)
         smid = inq_varid(ncid, 'start_mass')
         did = inq_varid(ncid, 'thickness')
         mbid = inq_varid(ncid, 'mass_of_bits')
+        uvelid = inq_varid(ncid, 'uvel')
+        vvelid = inq_varid(ncid, 'vvel')
         if (fl_r>0) then
           msid = inq_varid(ncid, 'mass_scaling')
           mflbid = inq_varid(ncid, 'mass_of_fl_bits')
@@ -1833,8 +1835,8 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r)
         endif
       endif
       if (.not.save_short_traj) then
-        uvelid = inq_varid(ncid, 'uvel')
-        vvelid = inq_varid(ncid, 'vvel')
+        !uvelid = inq_varid(ncid, 'uvel')
+        !vvelid = inq_varid(ncid, 'vvel')
         uvelpid = inq_varid(ncid, 'uvel_prev')
         vvelpid = inq_varid(ncid, 'vvel_prev')
         uoid = inq_varid(ncid, 'uo')
@@ -1910,6 +1912,8 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r)
         smid = def_var(ncid, 'start_mass', NF_DOUBLE, i_dim)
         did = def_var(ncid, 'thickness', NF_DOUBLE, i_dim)
         mbid = def_var(ncid, 'mass_of_bits', NF_DOUBLE, i_dim)
+        uvelid = def_var(ncid, 'uvel', NF_DOUBLE, i_dim)
+        vvelid = def_var(ncid, 'vvel', NF_DOUBLE, i_dim)
         if (fl_r>0) then
           msid = def_var(ncid, 'mass_scaling', NF_DOUBLE, i_dim)
           mflbid = def_var(ncid, 'mass_of_fl_bits', NF_DOUBLE, i_dim)
@@ -1918,8 +1922,8 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r)
         endif
       endif
       if (.not. save_short_traj) then
-        uvelid = def_var(ncid, 'uvel', NF_DOUBLE, i_dim)
-        vvelid = def_var(ncid, 'vvel', NF_DOUBLE, i_dim)
+        !uvelid = def_var(ncid, 'uvel', NF_DOUBLE, i_dim)
+        !vvelid = def_var(ncid, 'vvel', NF_DOUBLE, i_dim)
         uvelpid = def_var(ncid, 'uvel_prev', NF_DOUBLE, i_dim)
         vvelpid = def_var(ncid, 'vvel_prev', NF_DOUBLE, i_dim)
         uoid = def_var(ncid, 'uo', NF_DOUBLE, i_dim)
@@ -2002,6 +2006,10 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r)
         call put_att(ncid, did, 'units', 'm')
         call put_att(ncid, mbid, 'long_name', 'mass_of_bits')
         call put_att(ncid, mbid, 'units', 'kg')
+        call put_att(ncid, uvelid, 'long_name', 'zonal spped')
+        call put_att(ncid, uvelid, 'units', 'm/s')
+        call put_att(ncid, vvelid, 'long_name', 'meridional spped')
+        call put_att(ncid, vvelid, 'units', 'm/s')
         if (fl_r>0) then
           call put_att(ncid, msid, 'long_name', 'mass_scaling')
           call put_att(ncid, msid, 'units', 'dimensionless')
@@ -2014,10 +2022,10 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r)
         endif
       endif
       if (.not. save_short_traj) then
-        call put_att(ncid, uvelid, 'long_name', 'zonal spped')
-        call put_att(ncid, uvelid, 'units', 'm/s')
-        call put_att(ncid, vvelid, 'long_name', 'meridional spped')
-        call put_att(ncid, vvelid, 'units', 'm/s')
+        ! call put_att(ncid, uvelid, 'long_name', 'zonal spped')
+        ! call put_att(ncid, uvelid, 'units', 'm/s')
+        ! call put_att(ncid, vvelid, 'long_name', 'meridional spped')
+        ! call put_att(ncid, vvelid, 'units', 'm/s')
         call put_att(ncid, uoid, 'long_name', 'ocean zonal spped')
         call put_att(ncid, uoid, 'units', 'm/s')
         call put_att(ncid, void, 'long_name', 'ocean meridional spped')
@@ -2145,6 +2153,8 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r)
         call put_double(ncid, smid, i, this%start_mass)
         call put_double(ncid, did, i, this%thickness)
         call put_double(ncid, mbid, i, this%mass_of_bits)
+        call put_double(ncid, uvelid, i, this%uvel)
+        call put_double(ncid, vvelid, i, this%vvel)
         if (fl_r>0) then
           call put_double(ncid, msid, i, this%mass_scaling)
           call put_double(ncid, mflbid, i, this%mass_of_fl_bits)
@@ -2153,8 +2163,8 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r)
         endif
       endif
       if (.not. save_short_traj) then
-        call put_double(ncid, uvelid, i, this%uvel)
-        call put_double(ncid, vvelid, i, this%vvel)
+        ! call put_double(ncid, uvelid, i, this%uvel)
+        ! call put_double(ncid, vvelid, i, this%vvel)
         call put_double(ncid, uvelpid, i, this%uvel_prev)
         call put_double(ncid, vvelpid, i, this%vvel_prev)
         call put_double(ncid, uoid, i, this%uo)

From 30e22b3c9e8c39809839e75aebc1f3cb2c3a7c83 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Wed, 5 Jan 2022 12:07:20 -0500
Subject: [PATCH 314/361] =?UTF-8?q?-Added=20A68=20breakup=20test=20case.?=
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---
 build/README.md                               |    7 +-
 build/a68_dims__genmod.f90                    |   12 +
 build/handle_err__genmod.f90                  |   10 +
 driver/driver_data.f90                        |  245 +++
 driver/icebergs_driver.F90                    |  321 ++-
 src/.gitignore                                |    2 +
 src/icebergs.F90                              | 1073 ++++++++--
 src/icebergs_framework.F90                    |  335 ++-
 src/icebergs_io.F90                           |   97 +-
 tests/.gitignore                              |    3 +
 .../__pycache__/hexagon_area.cpython-38.pyc   |  Bin 0 -> 23834 bytes
 .../Scripts_and_analysis/hexagon_area.py      |  488 ++---
 .../Scripts_and_analysis/hexagon_area.pyc     |  Bin 33356 -> 30221 bytes
 tests/Iceberg_repository/hexagon_area.py      |  282 +--
 tests/a68/.gitignore                          |    4 +
 tests/a68/README                              |   26 +
 tests/a68/RUN                                 |    7 +
 tests/a68/RUN1p                               |    7 +
 tests/a68/RUN_check_ss.sh                     |   18 +
 tests/a68/RUN_check_ss2.sh                    |   18 +
 tests/a68/RUN_check_ss_new.sh                 |   18 +
 tests/a68/RUN_loop.sh                         |   53 +
 tests/a68/RUN_loop2.sh                        |   35 +
 tests/a68/RUN_loop_noground.sh                |   28 +
 tests/a68/RUN_lsf_hex.sh                      |   33 +
 tests/a68/RUN_lsf_square.sh                   |   47 +
 tests/a68/RUN_lsf_square_comp.sh              |   36 +
 tests/a68/RUN_restart_for_paper.sh            |   34 +
 tests/a68/RUN_ssf_hex.sh                      |   64 +
 tests/a68/RUN_ssf_square.sh                   |   66 +
 tests/a68/RUN_ssfrac.sh                       |   30 +
 tests/a68/RUN_ssfrac2.sh                      |   30 +
 tests/a68/RUN_test_init_for_paper.sh          |   19 +
 tests/a68/animate_trajectories.py             |  317 +++
 tests/a68/check_ss.nml                        |  212 ++
 tests/a68/check_ss2.nml                       |  212 ++
 tests/a68/check_ss3.nml                       |  212 ++
 tests/a68/check_ss3_nofrac.nml                |  212 ++
 tests/a68/check_ss3_ssf.nml                   |  214 ++
 tests/a68/check_ss_new.nml                    |  212 ++
 tests/a68/check_ss_orig.nml                   |  211 ++
 tests/a68/diag_table                          |    3 +
 tests/a68/hex_4restart.sh                     |   40 +
 tests/a68/hex_r_lsf.nml                       |  214 ++
 tests/a68/hex_r_ssf.nml                       |  230 ++
 tests/a68/hex_wgs84_frac_specs.nml            |  209 ++
 tests/a68/input.nml                           |  216 ++
 tests/a68/input_fill.nml                      |  205 ++
 tests/a68/input_fill2.nml                     |  212 ++
 tests/a68/input_fill_hex.nml                  |  216 ++
 tests/a68/input_fill_hex_4restart.nml         |  210 ++
 tests/a68/input_fill_hex_noground.nml         |  213 ++
 .../makeberg-checkpoint.ipynb                 |  441 ++++
 tests/a68/makeberg/RUN                        |   89 +
 tests/a68/makeberg/RUN_for_paper              |    6 +
 tests/a68/makeberg/make_one_berg.py           |  399 ++++
 tests/a68/makeberg/makeberg.ipynb             |  441 ++++
 tests/a68/makeberg/makeberg.py                | 1900 +++++++++++++++++
 tests/a68/n6000_t2500.nml                     |  194 ++
 tests/a68/nov3_tests.nml                      |  197 ++
 tests/a68/restart_for_nco.py                  |   19 +
 tests/a68/save_input.nml                      |  192 ++
 tests/a68/square_for_restart.nml              |  210 ++
 .../a68/square_for_restart_od_17.8_ydn.1.nml  |  211 ++
 ...quare_for_restart_od_19.5_tn_ng_ydn.05.nml |  211 ++
 ...square_for_restart_od_21.25_tn_ng_noyd.nml |  211 ++
 tests/a68/square_r_lsf.nml                    |  215 ++
 tests/a68/square_r_lsf_comp.nml               |  208 ++
 tests/a68/square_r_ssf.nml                    |  209 ++
 tests/a68/tau_is.nml                          |  197 ++
 tests/a68/test1.nml                           |  194 ++
 tests/a68/test2.nml                           |  196 ++
 tests/a68/test2_updated.nml                   |  201 ++
 tests/a68/test3.nml                           |  198 ++
 tests/a68/test4_curl.nml                      |  199 ++
 tests/a68/test_new.nml                        |  204 ++
 tests/a68/test_new2.nml                       |  204 ++
 tests/a68/test_no_bonds.nml                   |  211 ++
 tests/dem_cbeam_test/input.nml                |    2 +
 tests/dem_ground_frac_test_big/.gitignore     |    1 +
 tests/dem_ground_frac_test_big/README         |    7 +
 tests/dem_ground_frac_test_big/RUN            |    7 +
 .../animate_trajectories.py                   |  161 ++
 tests/dem_ground_frac_test_big/diag_table     |    3 +
 tests/dem_ground_frac_test_big/input.nml      |  199 ++
 tests/dem_ground_frac_test_big/makeberg/RUN   |    3 +
 .../makeberg/makeberg.py                      |  376 ++++
 tests/dem_ground_frac_test_big/save1.nml      |  199 ++
 tests/dem_ground_frac_test_big/save2.nml      |  199 ++
 tests/dem_ground_frac_test_big/save3.nml      |  199 ++
 tests/ground_frac_test/RUN                    |   10 +-
 tests/ground_frac_test/input.nml              |   42 +-
 tests/ground_frac_test/input_save.nml         |  182 ++
 tests/nc2csv.py                               |   13 +-
 tests/nc2csv_bonds.py                         |   34 +-
 95 files changed, 15285 insertions(+), 727 deletions(-)
 create mode 100644 build/a68_dims__genmod.f90
 create mode 100644 build/handle_err__genmod.f90
 create mode 100644 driver/driver_data.f90
 create mode 100644 src/.gitignore
 create mode 100644 tests/Iceberg_repository/Scripts_and_analysis/__pycache__/hexagon_area.cpython-38.pyc
 create mode 100644 tests/a68/.gitignore
 create mode 100644 tests/a68/README
 create mode 100755 tests/a68/RUN
 create mode 100755 tests/a68/RUN1p
 create mode 100755 tests/a68/RUN_check_ss.sh
 create mode 100755 tests/a68/RUN_check_ss2.sh
 create mode 100755 tests/a68/RUN_check_ss_new.sh
 create mode 100755 tests/a68/RUN_loop.sh
 create mode 100755 tests/a68/RUN_loop2.sh
 create mode 100755 tests/a68/RUN_loop_noground.sh
 create mode 100755 tests/a68/RUN_lsf_hex.sh
 create mode 100755 tests/a68/RUN_lsf_square.sh
 create mode 100755 tests/a68/RUN_lsf_square_comp.sh
 create mode 100644 tests/a68/RUN_restart_for_paper.sh
 create mode 100755 tests/a68/RUN_ssf_hex.sh
 create mode 100755 tests/a68/RUN_ssf_square.sh
 create mode 100755 tests/a68/RUN_ssfrac.sh
 create mode 100755 tests/a68/RUN_ssfrac2.sh
 create mode 100644 tests/a68/RUN_test_init_for_paper.sh
 create mode 100755 tests/a68/animate_trajectories.py
 create mode 100644 tests/a68/check_ss.nml
 create mode 100644 tests/a68/check_ss2.nml
 create mode 100644 tests/a68/check_ss3.nml
 create mode 100644 tests/a68/check_ss3_nofrac.nml
 create mode 100644 tests/a68/check_ss3_ssf.nml
 create mode 100644 tests/a68/check_ss_new.nml
 create mode 100644 tests/a68/check_ss_orig.nml
 create mode 100644 tests/a68/diag_table
 create mode 100755 tests/a68/hex_4restart.sh
 create mode 100644 tests/a68/hex_r_lsf.nml
 create mode 100644 tests/a68/hex_r_ssf.nml
 create mode 100644 tests/a68/hex_wgs84_frac_specs.nml
 create mode 100644 tests/a68/input.nml
 create mode 100644 tests/a68/input_fill.nml
 create mode 100644 tests/a68/input_fill2.nml
 create mode 100644 tests/a68/input_fill_hex.nml
 create mode 100644 tests/a68/input_fill_hex_4restart.nml
 create mode 100644 tests/a68/input_fill_hex_noground.nml
 create mode 100644 tests/a68/makeberg/.ipynb_checkpoints/makeberg-checkpoint.ipynb
 create mode 100755 tests/a68/makeberg/RUN
 create mode 100755 tests/a68/makeberg/RUN_for_paper
 create mode 100755 tests/a68/makeberg/make_one_berg.py
 create mode 100644 tests/a68/makeberg/makeberg.ipynb
 create mode 100755 tests/a68/makeberg/makeberg.py
 create mode 100644 tests/a68/n6000_t2500.nml
 create mode 100644 tests/a68/nov3_tests.nml
 create mode 100755 tests/a68/restart_for_nco.py
 create mode 100644 tests/a68/save_input.nml
 create mode 100644 tests/a68/square_for_restart.nml
 create mode 100644 tests/a68/square_for_restart_od_17.8_ydn.1.nml
 create mode 100644 tests/a68/square_for_restart_od_19.5_tn_ng_ydn.05.nml
 create mode 100644 tests/a68/square_for_restart_od_21.25_tn_ng_noyd.nml
 create mode 100644 tests/a68/square_r_lsf.nml
 create mode 100644 tests/a68/square_r_lsf_comp.nml
 create mode 100644 tests/a68/square_r_ssf.nml
 create mode 100644 tests/a68/tau_is.nml
 create mode 100644 tests/a68/test1.nml
 create mode 100644 tests/a68/test2.nml
 create mode 100644 tests/a68/test2_updated.nml
 create mode 100644 tests/a68/test3.nml
 create mode 100644 tests/a68/test4_curl.nml
 create mode 100644 tests/a68/test_new.nml
 create mode 100644 tests/a68/test_new2.nml
 create mode 100644 tests/a68/test_no_bonds.nml
 create mode 100644 tests/dem_ground_frac_test_big/.gitignore
 create mode 100644 tests/dem_ground_frac_test_big/README
 create mode 100755 tests/dem_ground_frac_test_big/RUN
 create mode 100755 tests/dem_ground_frac_test_big/animate_trajectories.py
 create mode 100644 tests/dem_ground_frac_test_big/diag_table
 create mode 100644 tests/dem_ground_frac_test_big/input.nml
 create mode 100755 tests/dem_ground_frac_test_big/makeberg/RUN
 create mode 100755 tests/dem_ground_frac_test_big/makeberg/makeberg.py
 create mode 100644 tests/dem_ground_frac_test_big/save1.nml
 create mode 100644 tests/dem_ground_frac_test_big/save2.nml
 create mode 100644 tests/dem_ground_frac_test_big/save3.nml
 create mode 100644 tests/ground_frac_test/input_save.nml

diff --git a/build/README.md b/build/README.md
index 5b43574..c3f26c4 100644
--- a/build/README.md
+++ b/build/README.md
@@ -16,5 +16,8 @@ To create a `Makefile`:
 To compile a "debug" executable:
 ```
 make DEBUG=1 -j
-##make NETCDF=3 DEBUG=1 bergs.x -j
-```
\ No newline at end of file
+#or
+source mkcmd
+#source mkcmd runs the following:
+#make NETCDF=3 DEBUG=1 bergs.x -j
+```
diff --git a/build/a68_dims__genmod.f90 b/build/a68_dims__genmod.f90
new file mode 100644
index 0000000..3e781da
--- /dev/null
+++ b/build/a68_dims__genmod.f90
@@ -0,0 +1,12 @@
+        !COMPILER-GENERATED INTERFACE MODULE: Fri Oct  1 13:21:29 2021
+        ! This source file is for reference only and may not completely
+        ! represent the generated interface used by the compiler.
+        MODULE A68_DIMS__genmod
+          INTERFACE 
+            SUBROUTINE A68_DIMS(DATA_DIR,NI,NJ)
+              CHARACTER(LEN=1000) :: DATA_DIR
+              INTEGER(KIND=4), INTENT(OUT) :: NI
+              INTEGER(KIND=4), INTENT(OUT) :: NJ
+            END SUBROUTINE A68_DIMS
+          END INTERFACE 
+        END MODULE A68_DIMS__genmod
diff --git a/build/handle_err__genmod.f90 b/build/handle_err__genmod.f90
new file mode 100644
index 0000000..0dd846d
--- /dev/null
+++ b/build/handle_err__genmod.f90
@@ -0,0 +1,10 @@
+        !COMPILER-GENERATED INTERFACE MODULE: Fri Oct  1 13:21:29 2021
+        ! This source file is for reference only and may not completely
+        ! represent the generated interface used by the compiler.
+        MODULE HANDLE_ERR__genmod
+          INTERFACE 
+            SUBROUTINE HANDLE_ERR(STATUS)
+              INTEGER(KIND=4), INTENT(IN) :: STATUS
+            END SUBROUTINE HANDLE_ERR
+          END INTERFACE 
+        END MODULE HANDLE_ERR__genmod
diff --git a/driver/driver_data.f90 b/driver/driver_data.f90
new file mode 100644
index 0000000..f68d3dc
--- /dev/null
+++ b/driver/driver_data.f90
@@ -0,0 +1,245 @@
+module driver_data
+
+use fms_mod, only : read_data
+use fms_mod, only : file_exist
+use fms_mod, only : field_exist
+use fms_mod, only : error_mesg
+use fms_mod, only : FATAL
+use mpp_domains_mod, only : domain2D
+use mpp_mod, only : mpp_pe
+use mpp_mod, only : mpp_root_pe
+use mpp_mod, only: mpp_sync
+use constants_mod, only: pi
+use netcdf
+!include 'netcdf.inc'
+
+implicit none
+
+contains
+
+  subroutine a68_dims(data_dir,ni,nj)
+    ! Arguments
+    character(len=*) :: data_dir
+    integer, intent(out):: ni,nj
+    ! Local variables
+    character(len=1000):: infile
+    integer(kind=4) :: ncid
+    integer :: status
+
+    infile=trim(trim(data_dir)//'a68_experiment_ll_p125_grid.nc')
+
+    !Open netCDF file
+    call handle_err(nf90_open(infile, nf90_nowrite, ncid))
+    !Inquire about the dimensions
+    call handle_err(nf90_inquire_dimension(ncid,1,len=nj))
+    call handle_err(nf90_inquire_dimension(ncid,2,len=ni))
+    !Close netCDF file
+    call handle_err(nf90_close(ncid))
+  end subroutine a68_dims
+
+  subroutine handle_err(status)
+    integer, intent (in) :: status
+
+    if(status /= nf90_noerr) then
+      print *, trim(nf90_strerror(status))
+      stop "Stopped"
+    end if
+  end subroutine handle_err
+
+
+  subroutine a68_prep(data_dir,mpp_domain,lon,lat,dx,dy,area,depth,uo,vo,tauxa,tauya,ssh,&
+    vert_int_ocean_vel,tau_is_velocity,Old_wrong_Rearth_and_SSH,REarth)
+    !mom_Rearth)
+  ! Arguments
+  character(len=*) :: data_dir
+  type(domain2D) :: mpp_domain
+  real :: lon(:,:) !< Longitude or position in x
+  real :: lat(:,:) !< Latitude or position in y
+  real :: dx(:,:) !< Length of northern edge of cell (m)
+  real :: dy(:,:) !< Length of eatern edge of cell (m)
+  real :: area(:,:) !< Area of cell (m2)
+  real :: depth(:,:) !< Depth of ocean (m)
+  real :: uo(:,:) !< Zonal ocean velocities (m/s)
+  real :: vo(:,:) !< Meridional ocean velocities (m/s)
+  real :: tauxa(:,:) !< Zonal wind stress (Pa)
+  real :: tauya(:,:) !< Meridional wind stress (Pa)
+  real :: ssh(:,:) !< Effective sea surface height (m)
+  logical :: Old_wrong_Rearth_and_SSH !< use Rearth=6.36e6 and SSH on B grid
+  logical :: mom_Rearth !< Use Rearth=6.378e6
+  logical :: vert_int_ocean_vel !< If true, use ocean velocity vertically-integrated over berg draft
+  logical :: tau_is_velocity !< If true, read in JRA-55 wind velocity (m/s), not ORAS5 stress (Pa)
+  real :: REarth
+  ! Local variables
+  character(len=1000) :: filename
+  real, parameter :: gres=0.125
+
+  !Grid specs: lon,lat,dx,dy,area
+  filename=trim(trim(data_dir)//'a68_experiment_ll_p125_grid.nc')
+  call read_a68_data(mpp_domain,filename,'longitude',lon)
+  lon=lon+360
+  call read_a68_data(mpp_domain,filename,'latitude',lat)
+
+  call haversine_dist_and_area(REarth,gres,lon,lat,dx,dy,area)
+
+  ! if (Old_wrong_Rearth_and_SSH) then
+  !   call read_a68_data(mpp_domain,filename,'dx_Rold',dx)
+  !   call read_a68_data(mpp_domain,filename,'dy_Rold',dy)
+  !   call read_a68_data(mpp_domain,filename,'area_Rold',area)
+  ! elseif (mom_Rearth) then
+  !   call read_a68_data(mpp_domain,filename,'dx_mom',dx)
+  !   call read_a68_data(mpp_domain,filename,'dy_mom',dy)
+  !   call read_a68_data(mpp_domain,filename,'area_mom',area)
+  ! else
+  !   call read_a68_data(mpp_domain,filename,'dx',dx)
+  !   call read_a68_data(mpp_domain,filename,'dy',dy)
+  !   call read_a68_data(mpp_domain,filename,'area',area)
+  ! endif
+
+  !Depth
+  filename=trim(trim(data_dir)//'a68_experiment_gebco_ll_p125.nc')
+  call read_a68_data(mpp_domain,filename,'elevation',depth)
+  depth=-depth !depth is negative in the data, but needs to be positive in the model
+
+  !Ocean velocity
+  !(vertically-integrated over draft of 200 m berg if vert_int_ocean_vel==true, otherwise, surface vel)
+  filename=trim(trim(data_dir)//'a68_experiment_ocean_surf_and_mean_vel_fixed_oras5_dec2020_ll_p125.nc')
+  !filename=trim(trim(data_dir)//'a68_experiment_ocean_test_vel.nc')
+
+  if (vert_int_ocean_vel) then
+    call read_a68_data(mpp_domain,filename,'uo_mean_over_berg_depth',uo)
+    call read_a68_data(mpp_domain,filename,'vo_mean_over_berg_depth',vo)
+  else
+    call read_a68_data(mpp_domain,filename,'uo',uo)
+    call read_a68_data(mpp_domain,filename,'vo',vo)
+  end if
+
+  if (tau_is_velocity) then
+  !Wind velocities -- note this is saved on tauxa and tauya, the wind stress variables.
+  !However, these variables are interpreted in the code as wind velocity if
+  !tau_is_velocity=.true. in the nml,
+    filename=trim(trim(data_dir)//'a68_experiment_wind_vel_jra55_dec2020_ll_p125.nc')
+    call read_a68_data(mpp_domain,filename,'ua',tauxa)
+    call read_a68_data(mpp_domain,filename,'va',tauya)
+  else
+    filename=trim(trim(data_dir)//'a68_experiment_wind_stress_oras5_dec2020_ll_p125.nc')
+    call read_a68_data(mpp_domain,filename,'taux',tauxa)
+    call read_a68_data(mpp_domain,filename,'tauy',tauya)
+  endif
+
+  !Effect sea surface height
+  filename=trim(trim(data_dir)//'a68_experiment_ssh_oras5_dec2020_ll_p125.nc')
+  if (Old_wrong_Rearth_and_SSH) then
+    call read_a68_data(mpp_domain,filename,'ssh_bgrid',ssh)
+  else
+    call read_a68_data(mpp_domain,filename,'SSH',ssh)
+  endif
+end subroutine a68_prep
+
+subroutine haversine_dist_and_area(REarth,gres,lon1,lat1,dx,dy,area)
+  !Arguments
+  real, intent(in) :: REarth    !Earth radius (m)
+  real, intent(in) :: gres      !grid resolution (degrees)
+  real, intent(in) :: lon1(:,:) !grid longitude
+  real, intent(in) :: lat1(:,:) !grid latitude
+  real, intent(out) :: dx(:,:)  !grid dx (m)
+  real, intent(out) :: dy(:,:)   !grid dy (m)
+  real, intent(out) :: area(:,:) !grid area (m^2)
+  ! Local variables
+  real, parameter :: pi_180=pi/180.
+  real, dimension(size(lon1,1),size(lon1,2)) :: lon2,lat2,p1,p2,dp,dm,a,c
+
+  !calculate dx
+  lon2=lon1-gres
+  lat2=lat1
+  p1 = lat1 * pi_180; p2 = lat2 * pi_180; dp = (lat2-lat1) * pi_180; dm = (lon2-lon1) * pi_180
+  a = sin(0.5*dp)**2. + cos(p1) * cos(p2) * sin(0.5*dm)**2.; c = 2. * atan2(sqrt(a), sqrt(1-a))
+  dx = REarth * c
+
+  !calculate dy
+  lat2=lat1-gres
+  lon2=lon1
+  p1 = lat1 * pi_180; p2 = lat2 * pi_180; dp = (lat2-lat1) * pi_180; dm = (lon2-lon1) * pi_180
+  a = sin(0.5*dp)**2. + cos(p1) * cos(p2) * sin(0.5*dm)**2.; c = 2. * atan2(sqrt(a), sqrt(1-a))
+  dy = REarth * c
+
+  !calculate area
+  area=pi_180*(REarth**2.)*abs(sin(lat1*pi_180)-sin(lat2*pi_180))*abs(gres)
+end subroutine haversine_dist_and_area
+
+
+!> Read ocean and atmospheric data for A68 experiment from file
+subroutine read_a68_data(domain,filename,var,field)
+  ! Arguments
+  type(domain2D) :: domain !< Parallel decomposition
+  character(len=*), intent(in) :: filename, var
+  real :: field(:,:)
+
+  call mpp_sync()
+  if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') 'icebergs_driver: Reading ',var
+  if (file_exist(filename)) then
+    if (field_exist(filename, var)) then
+      call read_data(filename, var, field, domain)
+    else
+      if (mpp_pe().eq.mpp_root_pe()) then
+        call error_mesg('icebergs_driver:','Variable missing in file!', FATAL)
+      endif
+    endif
+  else
+    if (mpp_pe().eq.mpp_root_pe()) then
+      call error_mesg('icebergs_driver:','File for variable not found!', FATAL)
+    endif
+  endif
+  call mpp_sync()
+end subroutine read_a68_data
+
+subroutine a68_prep_3d(data_dir,mpp_domain,tauxa_hr,tauya_hr,uo_hr,vo_hr,ssh_hr)
+  ! Arguments
+  character(len=*) :: data_dir
+
+  type(domain2D) :: mpp_domain
+  real :: tauxa_hr(:,:,:) !< Zonal jra55 wind velocity (m/s, hourly)
+  real :: tauya_hr(:,:,:) !< Meridional jra55 wind velocity (m/s, hourly)
+  real :: uo_hr(:,:,:) !< Zonal OSCAR ocean surface velocity (m/s, hourly)
+  real :: vo_hr(:,:,:) !< Meridional OSCAR ocean surface velocity (m/s, hourly)
+  real :: ssh_hr(:,:,:) !< Effective sea surface height (m, hourly)
+  ! Local variables
+  character(len=1000) :: filename
+
+  !filename=trim(trim(data_dir)//'a68_experiment_wind_vel_jra55_dec2020_HOURLY_ll_p125.nc')
+  filename=trim(trim(data_dir)//'a68_experiment_wind_vel_ncep_10m_dec2020_HOURLY_ll_p125.nc')
+  call read_a68_data_3d(mpp_domain,filename,'ua',tauxa_hr)
+  call read_a68_data_3d(mpp_domain,filename,'va',tauya_hr)
+
+  filename=trim(trim(data_dir)//'a68_experiment_ocean_surf_vel_oscar_dec2020_HOURLY_ll_p125.nc')
+  call read_a68_data_3d(mpp_domain,filename,'uo',uo_hr)
+  call read_a68_data_3d(mpp_domain,filename,'vo',vo_hr)
+
+  filename=trim(trim(data_dir)//'a68_experiment_ssh_duacs_dec2020_HOURLY_ll_p125.nc')
+  call read_a68_data_3d(mpp_domain,filename,'SSH',ssh_hr)
+end subroutine a68_prep_3d
+
+subroutine read_a68_data_3d(domain,filename,var,field)
+  ! Arguments
+  type(domain2D) :: domain !< Parallel decomposition
+  character(len=*), intent(in) :: filename, var
+  real :: field(:,:,:)
+
+  call mpp_sync()
+  if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') 'icebergs_driver: Reading ',var
+  if (file_exist(filename)) then
+    if (field_exist(filename, var)) then
+      call read_data(filename, var, field, domain)
+    else
+      if (mpp_pe().eq.mpp_root_pe()) then
+        call error_mesg('icebergs_driver:','Variable missing in file!', FATAL)
+      endif
+    endif
+  else
+    if (mpp_pe().eq.mpp_root_pe()) then
+      call error_mesg('icebergs_driver:','File for variable not found!', FATAL)
+    endif
+  endif
+  call mpp_sync()
+end subroutine read_a68_data_3d
+
+end module driver_data
diff --git a/driver/icebergs_driver.F90 b/driver/icebergs_driver.F90
index e419182..042bcc5 100644
--- a/driver/icebergs_driver.F90
+++ b/driver/icebergs_driver.F90
@@ -17,6 +17,7 @@ program icebergs_driver
 use mpp_mod, only : mpp_npes
 use mpp_mod, only : mpp_pe
 use mpp_mod, only : mpp_root_pe
+use mpp_mod, only: mpp_sync
 use time_manager_mod, only : time_type
 use time_manager_mod, only : set_date
 use time_manager_mod, only : set_calendar_type
@@ -33,6 +34,7 @@ program icebergs_driver
 use ice_bergs, only : icebergs_run
 use ice_bergs, only : icebergs_end
 use ice_bergs, only : icebergs_save_restart
+use driver_data
 
 ! For parallelism
 integer :: nprocs !< Number of processes
@@ -57,21 +59,35 @@ program icebergs_driver
 logical :: collision_test=.false.
 logical :: chaotic_test=.false.
 logical :: grounding_test=.false.
+logical :: big_grounding_test=.false.
+logical :: a68_test=.false.
+logical :: vert_int_ocean_vel=.false.
+logical :: tau_is_velocity=.true.
+logical :: reverse_a68_forcings=.false.
+character(len=1000) :: data_dir = 'data/'
+integer :: transient_a68_data_start_ind=0 !<set to .gt. 0 to use the hourly JRA-55 wind data for the A68
+!! test. The values indicate the time index to start from in the hourly data
 integer :: halo=1 !< Width of halo in parallel decomposition
 real :: ibdt=3600.0
-real :: ibuo=0.1
+real :: ibuo=0.0
 real :: ibvo=0.0
 real :: ibui=0.0
 real :: ibvi=0.0
 real :: gridres=1.e3
 real :: bump_depth=0
 real :: sst=-2
+logical :: Old_wrong_Rearth_and_SSH=.false. !< use Rearth=6.36e6 and SSH on B grid
+real :: REarth=6.378e6
+!logical :: mom_Rearth=.false. !< Use Rearth=6.378e6
+logical :: no_wind=.false.
 integer :: ibhrs=2
 integer :: nmax = 2000000000 !<max number of iteration
 integer :: write_time_inc=1
 namelist /icebergs_driver_nml/ debug, ni, nj, halo, ibhrs, ibdt, ibuo, ibvo, nmax, &
   saverestart,ibui,ibvi,collision_test,chaotic_test,grounding_test,&
-  gridres,write_time_inc,bump_depth, sst
+  gridres,write_time_inc,bump_depth, sst, a68_test, data_dir, vert_int_ocean_vel,&
+  reverse_a68_forcings,tau_is_velocity,transient_a68_data_start_ind,&
+  Old_wrong_Rearth_and_SSH,no_wind,REarth,big_grounding_test !mom_Rearth
 ! For loops
 integer :: isc !< Start of i-index for computational domain (used for loops)
 integer :: iec !< End of i-index for computational domain (used for loops)
@@ -82,6 +98,7 @@ program icebergs_driver
 type(time_type) :: Time_end  !<end time for the experiment (s)
 real :: dt !<time increment
 integer :: ns !<timestep counter
+real :: ns2
 integer :: iyr, imon, iday, ihr, imin, isec
 real :: time_begin, time_finish
 ! For icebergs
@@ -96,7 +113,7 @@ program icebergs_driver
 real, allocatable :: sin_rot(:,:) !< Sine of angle of grid orientation
 real, allocatable :: depth(:,:) !< Depth of ocean (m)
 ! Work variables
-integer :: i,j
+integer :: i,j, dit
 real, allocatable :: coord(:) !< One dimensional coordinate for initializing diagnostics
 
 ! For icebergs_run
@@ -104,7 +121,10 @@ program icebergs_driver
 real, dimension(:,:), allocatable :: uo,vo !<zonal and meridonal ocean velocities (m/s)
 real, dimension(:,:), allocatable :: ui,vi !<zonal and meridonal ice velocities (m/s)
 real, dimension(:,:), allocatable :: tauxa,tauya !< Zonal and meridonal wind stress (Pa)
+real, dimension(:,:,:), allocatable :: tauxa_hr,tauya_hr !< Hourly jra-55 zonal and meridonal wind velocity (m/s) for A68 test
+real, dimension(:,:,:), allocatable :: uo_hr,vo_hr !<Hourly OSCAR zonal and meridonal ocean surface velocities (m/s) for A68 test
 real, dimension(:,:), allocatable :: ssh !< Effective sea-surface height (m)
+real, dimension(:,:,:), allocatable :: ssh_hr !< Effective sea-surface height (m, hourly)
 real, dimension(:,:), allocatable :: sstemp !< Sea-surface temperature (C or K)
 real, dimension(:,:), allocatable :: cn !< Sea-ice concentration (nondim)
 real, dimension(:,:), allocatable :: hi !< Sea-ice thickness (m)
@@ -128,6 +148,13 @@ program icebergs_driver
 nmunit = open_namelist_file(file='input.nml')
 read(nmunit, nml=icebergs_driver_nml)
 call close_file(nmunit)
+
+if (a68_test) then
+  call a68_dims(data_dir,ni,nj)
+  if (mpp_pe()==0) print *,'ni,nj',ni,nj
+  iflags=0
+endif
+
 if (min(ni,nj)<1) call error_mesg('icebergs_driver:', &
   'Both ni,nj must be positive in icebergs_driver_nml namelist', FATAL)
 
@@ -172,6 +199,7 @@ program icebergs_driver
 if (debug .and. mpp_root_pe()==0) print *,'isd,isc,iec,ied=',isd,isc,iec,ied
 if (debug .and. mpp_root_pe()==0) print *,'jsd,jsc,jec,jed=',jsd,jsc,jec,jed
 
+! for icebergs_init
 allocate( lon(isd:ied,jsd:jed) )
 allocate( lat(isd:ied,jsd:jed) )
 allocate( wet(isd:ied,jsd:jed) )
@@ -182,60 +210,6 @@ program icebergs_driver
 allocate( sin_rot(isd:ied,jsd:jed) )
 allocate( depth(isd:ied,jsd:jed) )
 
-do j = jsd, jed
-  do i = isd, ied
-    lon(i,j) = gridres*real(i)
-    lat(i,j) = gridres*real(j)
-    dx(i,j) = gridres
-    dy(i,j) = gridres
-    area(i,j) = gridres*gridres
-    wet(i,j) = 1.0
-    cos_rot(i,j) = 1.0
-    sin_rot(i,j) = 0.0
-    depth(i,j) = 1000.
-  enddo
-enddo
-
-if (chaotic_test) then
-  !assign land cells at the N and S portions of the domain.
-  !input.nml: set coastal drift parameter to prevent grounding
-  do j=jsd,jed; do i=isd,ied
-    if (lat(i,j)<=0.0+2*gridres .or. lat(i,j)>=1000.e3-2*gridres) wet(i,j)=0.0
-  enddo;enddo
-endif
-
-if (grounding_test) then
-  lat(:,:)=lat(:,:)-15000.0
-  !assign land cells at the N and S portions of the domain.
-  !input.nml: set coastal drift parameter to prevent grounding
-  do j=jsd,jed; do i=isd,ied
-    if (lat(i,j)<=0.0+2*gridres .or. lat(i,j)>=30.e3-2*gridres) wet(i,j)=0.0
-  enddo;enddo
-
-  !introduce gaussian bump to bathymetry
-  a = 1000.0-bump_depth !max height(m)
-  c = 2.5e3; !controls width
-  bx = 15.e3; by = 15.e3
-  do j=jsd,jed; do i=isd,ied
-    xc=lon(i,j)-(gridres/2.); yc=lat(i,j)-(gridres/2.) !define at cell centers
-    depth(i,j)=a*exp(-((xc-bx)*(xc-bx)/(2.*c*c)+(yc-by)*(yc-by)/(2.*c*c)))
-  enddo; enddo
-  print *,'min, max depth',minval(depth(:,:)),maxval(depth(:,:))
-  depth = 1000.0-depth
-endif
-
-
-call set_calendar_type(THIRTY_DAY_MONTHS)
-time = set_date(1,1,1,0,0,0)
-dt = ibdt
-
-call icebergs_init(bergs, &
-                   ni, nj, layout, io_layout, axes, iflags, jflags, dt, time, &
-                   lon(isc:iec,jsc:jec), lat(isc:iec,jsc:jec), wet(isc-1:iec+1,jsc-1:jec+1), &
-                   dx(isc-1:iec+1,jsc-1:jec+1), dy(isc-1:iec+1,jsc-1:jec+1), area(isc:iec,jsc:jec), &
-                   cos_rot(isc-1:iec+1,jsc-1:jec+1), sin_rot(isc-1:iec+1,jsc-1:jec+1), &
-                   depth(isc:iec,jsc:jec), fractional_area=.false.)
-
 ! for icebergs_run:
 allocate( calving(isd:ied,jsd:jed) )
 allocate( uo(isd:ied,jsd:jed) )
@@ -263,6 +237,153 @@ program icebergs_driver
 hi = 0.0 !sea-ice thickness (m)
 calving_hflx = 0.0 !calving heat flux (W/m2)
 
+! optional:
+! allocate( sss(isd:ied,jsd:jed) )
+! allocate( mass_berg(isd:ied,jsd:jed) )
+! allocate( ustar_berg(isd:ied,jsd:jed) )
+! allocate( area_berg(isd:ied,jsd:jed) )
+! stagger =  !scalar integer
+! stress_stagger = !scalar integer
+! sss = !sea surface salinity (1e-3)
+! mass_berg = !mass of bergs (kg)
+! ustar_berg = !Friction velocity on base of bergs (m/s)
+! area_berg = !Area of bergs (m2)
+
+if (a68_test) then
+  if (Old_wrong_Rearth_and_SSH) REarth=6360000.
+  call mpp_sync()
+  call a68_prep(data_dir,mpp_domain,lon,lat,dx,dy,area,depth,uo,vo,tauxa,tauya,ssh,vert_int_ocean_vel,tau_is_velocity,Old_wrong_Rearth_and_SSH,REarth)
+  !mom_Rearth)
+  call mpp_sync()
+  if (no_wind) then
+    tauxa=0.0; tauya=0.0
+  endif
+  !where (lon<(-37.6+360.))
+  !  depth=depth+1000.
+  !end where
+  wet=1.0
+  cos_rot=1.0
+  sin_rot=0.0
+  if (reverse_a68_forcings) then
+    uo=-uo; vo=-vo
+    tauxa=-tauxa; tauya=-tauya
+  endif
+
+  if (transient_a68_data_start_ind>0) then
+    if (.not. (ibdt==3600.0 .or. ibdt==1800.0)) then
+      call error_mesg('icebergs_driver:', &
+      'in order to use transient_a68_data_start_ind>0, timestep must be 30 min or 1 hr', FATAL)
+    endif
+    if (.not. tau_is_velocity) call error_mesg('icebergs_driver:', &
+      'tau_is_velocity must be true if transient_a68_data_start_ind>-1', FATAL)
+    allocate( tauxa_hr(isd:ied,jsd:jed,739) )
+    allocate( tauya_hr(isd:ied,jsd:jed,739) )
+    allocate( uo_hr(isd:ied,jsd:jed,744) )
+    allocate( vo_hr(isd:ied,jsd:jed,744) )
+    allocate( ssh_hr(isd:ied,jsd:jed,744) )
+    call a68_prep_3d(data_dir,mpp_domain,tauxa_hr,tauya_hr,uo_hr,vo_hr,ssh_hr)
+    if (reverse_a68_forcings) then
+      tauxa_hr=-tauxa_hr; tauya_hr=-tauya_hr
+      uo_hr=-uo_hr; vo_hr=-vo_hr
+      ssh_hr=-ssh_hr
+      dit=-1
+    else
+      dit=1
+    endif
+    if (no_wind) then
+      tauxa_hr=0.0; tauya_hr=0.0
+    endif
+  endif
+
+  !print *,'lon min/max',minval(lon),maxval(lon)
+  !print *,'lat min/max',minval(lat),maxval(lat)
+  !print *,'lon(isd:isc+1,jsc+1)',lon(isd:isc+1,jsc+1)
+  !print *,'depth(isd:isc+1,jsc+1)',depth(isd:isc+1,jsc+1)
+  !print *,'lon(isd,jsd),lat(isd,jsd)',lon(isd,jsd),lat(isd,jsd)
+  !print *,'lon(ied,jed),lat(ied,jed)',lon(ied,jed),lat(ied,jed)
+  !iceberg vel: ub: 0.0362195771130627 vb: -0.04608364827503143
+else
+  do j = jsd, jed
+    do i = isd, ied
+      lon(i,j) = gridres*real(i)
+      lat(i,j) = gridres*real(j)
+      dx(i,j) = gridres
+      dy(i,j) = gridres
+      area(i,j) = gridres*gridres
+      wet(i,j) = 1.0
+      cos_rot(i,j) = 1.0
+      sin_rot(i,j) = 0.0
+      depth(i,j) = 1000.
+    enddo
+  enddo
+
+  if (chaotic_test) then
+    !assign land cells at the N and S portions of the domain.
+    !input.nml: set coastal drift parameter to prevent grounding
+    do j=jsd,jed; do i=isd,ied
+      if (lat(i,j)<=0.0+2*gridres .or. lat(i,j)>=1000.e3-2*gridres) wet(i,j)=0.0
+    enddo;enddo
+  endif
+
+  if (big_grounding_test) then
+    lat(:,:)=lat(:,:)-0.45 !-25000.1
+    lon(:,:)=lon(:,:)-0.45
+    !assign land cells at the N and S portions of the domain.
+    !input.nml: set coastal drift parameter to prevent grounding
+    do j=jsd,jed; do i=isd,ied
+      if (lat(i,j)<=(-5.e3) .or. lat(i,j)>=(220.e3)) wet(i,j)=0.0
+    enddo;enddo
+
+    !introduce gaussian bump to bathymetry
+    a = 1000.0-bump_depth !max height(m)
+    c = 5e3; !controls width
+    bx = 63.e3; by = 60.e3 !50.e3
+    do j=jsd,jed; do i=isd,ied
+      xc=lon(i,j)-(gridres/2.); yc=lat(i,j)-(gridres/2.) !define at cell centers
+      depth(i,j)=a*exp(-((xc-bx)*(xc-bx)/(2.*c*c)+(yc-by)*(yc-by)/(2.*c*c)))
+    enddo; enddo
+    print *,'min, max depth',minval(depth(:,:)),maxval(depth(:,:))
+    depth = 1000.0-depth
+  endif
+
+  if (grounding_test) then
+    lat(:,:)=lat(:,:)-15000.0
+    !assign land cells at the N and S portions of the domain.
+    !input.nml: set coastal drift parameter to prevent grounding
+    do j=jsd,jed; do i=isd,ied
+      if (lat(i,j)<=0.0+2*gridres .or. lat(i,j)>=30.e3-2*gridres) wet(i,j)=0.0
+    enddo;enddo
+
+    !introduce gaussian bump to bathymetry
+    a = 1000.0-bump_depth !max height(m)
+    c = 2.5e3; !controls width
+    bx = 15.e3; by = 15.e3
+    do j=jsd,jed; do i=isd,ied
+      xc=lon(i,j)-(gridres/2.); yc=lat(i,j)-(gridres/2.) !define at cell centers
+      depth(i,j)=a*exp(-((xc-bx)*(xc-bx)/(2.*c*c)+(yc-by)*(yc-by)/(2.*c*c)))
+    enddo; enddo
+    print *,'min, max depth',minval(depth(:,:)),maxval(depth(:,:))
+    depth = 1000.0-depth
+  endif
+endif
+
+
+call set_calendar_type(THIRTY_DAY_MONTHS)
+
+if (transient_a68_data_start_ind==355) then
+  time = set_date(1,1,7,5,0,0)
+else
+  time = set_date(1,1,1,0,0,0)
+endif
+dt = ibdt
+
+call icebergs_init(bergs, &
+                   ni, nj, layout, io_layout, axes, iflags, jflags, dt, time, &
+                   lon(isc:iec,jsc:jec), lat(isc:iec,jsc:jec), wet(isc-1:iec+1,jsc-1:jec+1), &
+                   dx(isc-1:iec+1,jsc-1:jec+1), dy(isc-1:iec+1,jsc-1:jec+1), area(isc:iec,jsc:jec), &
+                   cos_rot(isc-1:iec+1,jsc-1:jec+1), sin_rot(isc-1:iec+1,jsc-1:jec+1), &
+                   depth(isc:iec,jsc:jec), fractional_area=.false.)
+
 if (collision_test .or. grounding_test) then
   if (grounding_test) then
     mid=15.e3
@@ -281,7 +402,7 @@ program icebergs_driver
       !   endif
       ! endif
 
-     else
+    else
       if (lat(i,j)>mid) then
         vo(i,j)=-ibvo
       else
@@ -311,24 +432,27 @@ program icebergs_driver
   enddo;enddo
 endif
 
-! optional:
-! allocate( sss(isd:ied,jsd:jed) )
-! allocate( mass_berg(isd:ied,jsd:jed) )
-! allocate( ustar_berg(isd:ied,jsd:jed) )
-! allocate( area_berg(isd:ied,jsd:jed) )
-! stagger =  !scalar integer
-! stress_stagger = !scalar integer
-! sss = !sea surface salinity (1e-3)
-! mass_berg = !mass of bergs (kg)
-! ustar_berg = !Friction velocity on base of bergs (m/s)
-! area_berg = !Area of bergs (m2)
-
 ns = 1 !timestep counter
+if (transient_a68_data_start_ind>0) ns2 = 1
+
+!uo=0.;vo=0.ui=0.;vi=0.;ssh=0.;tauxa=0.;tauya=0.;depth=-1000000
+!tauxa=0.; tauya=0.; ssh_hr=0.
+
+!uo_hr=0.2; vo_hr=0.
 
 ! Time_end = increment_date(Time, years, months, days, hours, minutes, seconds)
 Time_end = increment_date(Time,0,0,0,ibhrs,0,0)
 
-do while ((ns < nmax) .and. (Time < Time_end))
+! if (mpp_pe()==0) then
+!   print *,'shape(tauxa_hr)', shape(tauxa_hr)
+!   print *,'shape(tauya_hr)', shape(tauya_hr)
+!   print *,'shape(tauxa)', shape(tauxa)
+!   print *,'shape(tauya)', shape(tauya)
+!   print *,'lon(isc:isc+2,jsc:jsc+2)',lon(isc:isc+2,jsc:jsc+2)-360
+!   print *,'lat(isc:isc+2,jsc:jsc+2)',lat(isc:isc+2,jsc:jsc+2)
+! endif
+
+do while ((ns <= nmax) .and. (Time < Time_end))
   if (mpp_pe()==0 .and. debug .and. mod(ns-1,write_time_inc)==0) then
     call get_date(Time, iyr, imon, iday, ihr, imin, isec)
     write(*,*) ''
@@ -336,10 +460,34 @@ program icebergs_driver
     write(*,'(a,i5)')' Timestep   ',ns
     write(*,'(a,i5,a,i5,a,i5)')' year',iyr,'  month ',imon,'  day   ',iday
     write(*,'(a,i5,a,i5,a,i5)')' hour',ihr,'  minute',imin,'  second',isec
+    call cpu_time(time_finish)
+    write(*,*) 'cpu time elapsed: ', (time_finish - time_begin)/60., 'minutes'
     write(*,'(a)') '-------------------------------------------'
     write(*,*) ''
   end if
 
+  if (transient_a68_data_start_ind>0) then
+
+    if ((ibdt==3600.0) .or. (mod(ns2,1.)==0)) then
+      tauxa=tauxa_hr(:,:,transient_a68_data_start_ind+dit*(int(ns2)-1))
+      tauya=tauya_hr(:,:,transient_a68_data_start_ind+dit*(int(ns2)-1))
+      uo=uo_hr(:,:,transient_a68_data_start_ind+dit*(int(ns2)-1))
+      vo=vo_hr(:,:,transient_a68_data_start_ind+dit*(int(ns2)-1))
+      ssh=ssh_hr(:,:,transient_a68_data_start_ind+dit*(int(ns2)-1))
+    else
+      tauxa=0.5*(tauxa+tauxa_hr(:,:,transient_a68_data_start_ind+dit*(int(ceiling(ns2))-1)))
+      tauya=0.5*(tauya+tauya_hr(:,:,transient_a68_data_start_ind+dit*(int(ceiling(ns2))-1)))
+      uo=0.5*(uo+uo_hr(:,:,transient_a68_data_start_ind+dit*(int(ceiling(ns2))-1)))
+      vo=0.5*(vo+vo_hr(:,:,transient_a68_data_start_ind+dit*(int(ceiling(ns2))-1)))
+      ssh=ssh_hr(:,:,transient_a68_data_start_ind+dit*(int(ns2)-1))
+    endif
+    ! if (mpp_pe()==0) then
+    !   print *,'index',transient_a68_data_start_ind+dit*(ns-1)
+    !   print *,'tauxa(isc:isc+2,jsc:jsc+2)',tauxa(isc:isc+2,jsc:jsc+2)
+    !   print *,'tauya(isc:isc+2,jsc:jsc+2)',tauya(isc:isc+2,jsc:jsc+2)
+    ! endif
+  endif
+
   ! The main driver the steps updates icebergs
   call icebergs_run(bergs, time, calving(isc:iec,jsc:jec), &
                     uo(isc-1:iec+1,jsc-1:jec+1), vo(isc-1:iec+1,jsc-1:jec+1), &
@@ -355,10 +503,41 @@ program icebergs_driver
 
   Time = Time + real_to_time_type(dt)
   ns = ns+1
+
+  if (transient_a68_data_start_ind>0) then
+    if (ibdt==3600.0) then
+      ns2=ns2+1
+    elseif (ibdt==1800.0) then
+      ns2=ns2+0.5
+      !if (mod(ns,2)>0) then
+      !  ns2=ns2+1
+      !endif
+    endif
+  endif
+
 enddo
 
 if (saverestart) call icebergs_save_restart(bergs)
 
+call get_date(Time, iyr, imon, iday, ihr, imin, isec)
+write(*,*) ''
+write(*,'(a)') '-------------------------------------------'
+write(*,'(a,i5)')' Saving after timestep   ',ns-1
+print *,' ns2   ',ns2
+if (mod(ns2,1.)==0) then
+  print *,'transient_a68_data_start_ind+dit*(int(ns2)-1)',&
+    transient_a68_data_start_ind+dit*(int(ns2)-1)
+else
+  print *,'transient_a68_data_start_ind+dit*(int(ceiling(ns2))-1))',&
+    transient_a68_data_start_ind+dit*(int(ceiling(ns2))-1)
+endif
+write(*,'(a)')' Restart time is:'
+write(*,'(a,i5,a,i5,a,i5)')' year',iyr,'  month ',imon,'  day   ',iday
+write(*,'(a,i5,a,i5,a,i5)')' hour',ihr,'  minute',imin,'  second',isec
+write(*,'(a)') '-------------------------------------------'
+write(*,*) ''
+
+
 !Deallocate all memory and disassociated pointer
 call icebergs_end(bergs)
 
diff --git a/src/.gitignore b/src/.gitignore
new file mode 100644
index 0000000..6e2beee
--- /dev/null
+++ b/src/.gitignore
@@ -0,0 +1,2 @@
+temp.F90
+*~
\ No newline at end of file
diff --git a/src/icebergs.F90 b/src/icebergs.F90
index aed84cd..c1edf2a 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -39,13 +39,14 @@ module ice_bergs
 use ice_bergs_framework, only: record_posn,check_position,print_berg,print_bergs,print_fld
 use ice_bergs_framework, only: add_new_berg_to_list,delete_iceberg_from_list,destroy_iceberg
 use ice_bergs_framework, only: grd_chksum2,grd_chksum3
-use ice_bergs_framework, only: fix_restart_dates, offset_berg_dates
+use ice_bergs_framework, only: Rearth, fix_restart_dates, offset_berg_dates
 use ice_bergs_framework, only: orig_read  ! Remove when backward compatibility no longer needed
 use ice_bergs_framework, only: monitor_a_berg
 use ice_bergs_framework, only: is_point_within_xi_yj_bounds
 use ice_bergs_framework, only: test_check_for_duplicate_ids_in_list
 use ice_bergs_framework, only: generate_id
-use ice_bergs_framework, only: update_latlon,set_conglom_ids,transfer_mts_bergs,quad_interp_from_agrid
+use ice_bergs_framework, only: update_latlon,set_conglom_ids,transfer_mts_bergs
+use ice_bergs_framework, only: quad_interp_from_agrid
 use ice_bergs_framework, only: save_bond_traj
 use ice_bergs_framework, only: fracture_testing_initialization, orig_bond_length
 use ice_bergs_framework, only: update_and_break_bonds,break_bonds_dem,assign_n_bonds,reset_bond_rotation
@@ -53,8 +54,11 @@ module ice_bergs
 use ice_bergs_framework, only: monitor_energy, energy_tests_init, mts, new_mts
 use ice_bergs_framework, only: dem_tests_init
 use ice_bergs_framework, only: dem, init_dem_params
-use ice_bergs_framework, only: set_constant_interaction_length_and_width
-use ice_bergs_framework, only: use_damage, damage_test_1_init
+use ice_bergs_framework, only: orig_dem_moment_of_inertia, no_frac_first_ts
+use ice_bergs_framework, only: A68_test, A68_xdisp, A68_ydisp
+use ice_bergs_framework, only: set_constant_interaction_length_and_width, skip_first_outer_mts_step
+use ice_bergs_framework, only: use_damage, damage_test_1_init, break_bonds_on_sub_steps
+use ice_bergs_framework, only: power_ground, short_step_mts_grounding, radius_based_drag
 
 use ice_bergs_io,        only: ice_bergs_io_init, write_restart, write_trajectory, write_bond_trajectory
 use ice_bergs_io,        only: read_restart_bergs, read_restart_calving
@@ -68,7 +72,7 @@ module ice_bergs
 
 real, parameter :: pi_180=pi/180.  !< Converts degrees to radians
 real, parameter :: r180_pi=180./pi !< Converts radians to degrees
-real, parameter :: Rearth=6360000. !< Radius of earth (m)
+!real, parameter :: Rearth=6360000. !< Radius of earth (m) (now specified in nml, see icebergs_framework)
 real, parameter :: rho_ice=916.7 !< Density of fresh ice @ 0oC (kg/m^3)
 real, parameter :: rho_water=999.8 !< Density of fresh water @ 0oC (kg/m^3)
 real, parameter :: rho_air=1.1 !< Density of air @ 0oC (kg/m^3)
@@ -152,7 +156,7 @@ subroutine icebergs_init(bergs, &
   if (bergs%read_ocean_depth_from_file) call read_ocean_depth(bergs%grd)
 
   if (monitor_energy) call energy_tests_init(bergs)
-  if (bergs%dem) call init_dem_params(bergs)
+  !if (bergs%dem) call init_dem_params(bergs)
 
   if (bergs%iceberg_bonds_on) then
     if (bergs%manually_initialize_bonds) then
@@ -188,8 +192,8 @@ subroutine debugwriteandstop(bergs)
   bergs%debug_write=.true.
   call record_posn(bergs)
   call move_all_trajectories(bergs)
-  call write_trajectory(bergs%trajectories, bergs%save_short_traj, bergs%save_fl_traj, bergs%fl_r)
-  if (save_bond_traj) call write_bond_trajectory(bergs%bond_trajectories)
+  call write_trajectory(bergs%trajectories, bergs%save_short_traj, bergs%save_fl_traj, bergs%fl_r, bergs%traj_name)
+  if (save_bond_traj) call write_bond_trajectory(bergs%bond_trajectories, bergs%bond_traj_name)
   call mpp_sync()
   call error_mesg('KID', 'WRITE AND STOP!!!', FATAL)
 end subroutine debugwriteandstop
@@ -429,7 +433,7 @@ subroutine initialize_iceberg_bonds(bergs)
                 radius1=sqrt(berg%length*berg%width*rdenom)
                 radius2=sqrt(other_berg%length*other_berg%width*rdenom)
                 !radius=sqrt(min(berg%length*berg%width,other_berg%length*other_berg%width))
-                if (r_dist.lt.1.1*(radius1+radius2)) &
+                if (r_dist.lt.1.25*(radius1+radius2)) &
                   call form_a_bond(berg, other_berg%id, other_berg%ine, other_berg%jne, other_berg)
               elseif (r_dist.lt.bergs%length_for_manually_initialize_bonds) then
                 ! If the bergs are closer than bergs%length_for_manually_initialize_bonds, then form a bond -Alex
@@ -564,7 +568,8 @@ subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
       endif
     endif
 
-    ! Interactions for non-bonded berg elements only. For the mts scheme, this is only called if mts_part==1
+    ! Interactions (collision) between berg elements of different conglomerates only.
+    ! For the mts scheme, this is only called if mts_part==1
     if (.not. (bergs%mts .and. bergs%mts_part .eq. 3)) then
       bonded=.false. ! Interactions for non-bonded berg elements
       do grdj = max(berg%jne-nc_y,bergs%grd%jsd),min(berg%jne+nc_y,bergs%grd%jed);&
@@ -829,9 +834,383 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
 
 end subroutine calculate_force
 
+!> Calculate interactive forces between two bergs
+subroutine calculate_unbonded_same_conglom_dem_force(bergs, berg, other_berg, IA_x, IA_y, &
+  IAd_x, IAd_y, u0, v0, u1, v1)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  type(iceberg), pointer :: berg !< Primary berg
+  type(iceberg), pointer :: other_berg !< Berg that primary is interacting with
+  real, intent(inout) :: IA_x !< Net zonal acceleration of berg due to interactions (m/s2)
+  real, intent(inout) :: IA_y !< Net meridional acceleration of berg due to interactions (m/s2)
+  real, intent(inout) :: IAd_x !< Damping of net zonal acceleration of berg due to interactions (m/s2)
+  real, intent(inout) :: IAd_y !< Damping of net meridional acceleration of berg due to interactions (m/s2)
+  real, intent(in) :: u0 !< Zonal velocity of primary berg (m/s)
+  real, intent(in) :: v0 !< Meridional velocity of primary berg (m/s)
+  real, intent(in) :: u1 !< Zonal velocity of other berg (m/s)
+  real, intent(in) :: v1 !< Meridional velocity of other berg (m/s)
+  ! Local variables
+  real :: T1, L1, W1, lon1, lat1, x1, y1, R1, A1 ! Current iceberg
+  real :: T2, L2, W2, lon2, lat2, x2, y2, R2, A2 ! Other iceberg
+  real :: dlon, dlat
+  real :: r_dist_x, r_dist_y, r_dist, A_o, A_min, trapped, T_min
+  real :: P_ia_11, P_ia_12, P_ia_22, P_ia_21
+  real :: P_11, P_12, P_21, P_22
+  real :: M1, M2, M_min
+  real :: u2, v2
+  real :: lat_ref, dx_dlon, dy_dlat
+  logical :: critical_interaction_damping_on,crit_dist_from_radius_only
+  real :: spring_coef, accel_spring, radial_damping_coef, p_ia_coef, tangental_damping_coef
+  real :: crit_dist, vr1,vr2,vn,vn1,vn2,vt1,vt2
+
+  if ((berg%id .ne. other_berg%id) .and. (berg%fl_k.ne.-1) .and. (other_berg%fl_k.ne.-1)) then
+
+    ! Calculate distance first, so that we return if out of range:
+
+    dlon=berg%lon_old-other_berg%lon_old
+    dlat=berg%lat_old-other_berg%lat_old
+
+    ! Note that this is not the exact distance along a great circle.
+    ! Approximation for small distances. Should be fine.
+    !r_dist_x=x1-x2 ; r_dist_y=y1-y2
+    !r_dist=sqrt( ((x1-x2)**2) + ((y1-y2)**2) )
+    lat_ref=0.5*(berg%lat_old+other_berg%lat_old)
+    call convert_from_grid_to_meters(lat_ref,bergs%grd%grid_is_latlon,dx_dlon,dy_dlat)
+
+    r_dist_x=dlon*dx_dlon
+    r_dist_y=dlat*dy_dlat
+    r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) ) !(Stern et al 2017, Eqn 3)
+
+    if (bergs%constant_interaction_LW) then
+      if ( (2*bergs%constant_radius)<=r_dist ) return
+      R1=bergs%constant_radius
+      A1=bergs%constant_area
+      M1=A1*berg%thickness*bergs%rho_bergs                      !Berg 1 mass
+      A2=A1                                         !Berg 2 area
+      M2=A2*other_berg%thickness*bergs%rho_bergs                      !Berg 2 mass
+      R2=R1
+    else
+      ! use actual length and width of bergs
+      L1=berg%length; W1=berg%width; A1=L1*W1                   !From Berg 1
+      L2=other_berg%length; W2=other_berg%width;  A2=L2*W2 !From Berg 2
+
+      !Stern et al 2017, Eqn 4: radius of circle inscribed within hexagon or square with area A1 or A2
+      if (bergs%hexagonal_icebergs) then
+        R1=sqrt(A1/(2.*sqrt(3.)))
+        R2=sqrt(A2/(2.*sqrt(3.)))
+      else !square packing
+        if (bergs%iceberg_bonds_on) then
+          R1=0.5*sqrt(A1)
+          R2=0.5*sqrt(A2)
+        else
+          R1=sqrt(A1/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
+          R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
+        endif
+      endif
+      if ((R1+R2)<=r_dist) return
+      M1=berg%mass; M2=other_berg%mass;
+    endif
+
+    u2=other_berg%uvel_old;  v2=other_berg%vvel_old !Old values are used to make it order invariant
+
+    M_min=min(M1,M2)
+
+    crit_dist=R1+R2
+    spring_coef=bergs%spring_coef
+
+    radial_damping_coef=bergs%radial_damping_coef
+    tangental_damping_coef=bergs%tangental_damping_coef
+    critical_interaction_damping_on=bergs%critical_interaction_damping_on
+
+    ! Using critical values for damping rather than manually setting the damping.
+    if (critical_interaction_damping_on) then
+      radial_damping_coef=2.*sqrt(spring_coef) ! Critical damping
+      if (bergs%tang_crit_int_damp_on) then
+        tangental_damping_coef=(2.*sqrt(spring_coef))/4 ! Critical damping (just a guess)
+      endif
+    endif
+
+    if (bergs%uniaxial_test) then
+      if (berg%start_lon==bergs%dem_tests_start_lon) IA_x=IA_x-1.e-5
+      if (berg%start_lon==bergs%dem_tests_end_lon)   IA_x=IA_x+1.e-5
+    endif
+
+    if  ((r_dist>0.) .and. (r_dist<crit_dist)) then
+
+      !Spring force (Stern et al 2017, Eqn 7):
+      !accel_spring=spring_coef*(T_min/berg%thickness)*(A_o/A1) ! Old version dependent on area
+      accel_spring=spring_coef*(M_min/M1)*(crit_dist-r_dist)
+      IA_x=IA_x+(accel_spring*(r_dist_x/r_dist))
+      IA_y=IA_y+(accel_spring*(r_dist_y/r_dist))
+
+      ! if (r_dist < 5*(R1+R2)) then
+        ! Damping force (Stern et al 2017, Eqn 8):
+        ! Paralel velocity
+        !projection matrix in Stern et al 2017, Eqn 8:
+        P_11=(r_dist_x*r_dist_x)/(r_dist**2)
+        P_12=(r_dist_x*r_dist_y)/(r_dist**2)
+        P_21=(r_dist_x*r_dist_y)/(r_dist**2)
+        P_22=(r_dist_y*r_dist_y)/(r_dist**2)
+        !p_ia_coef=radial_damping_coef*(T_min/berg%thickness)*(A_min/A1)
+        p_ia_coef=radial_damping_coef*(M_min/M1)
+        !the following was done originally, but it is wrong:
+        if (bergs%scale_damping_by_pmag) then
+          p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2)) &
+            + sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
+        endif
+
+        P_ia_11=p_ia_coef*P_11
+        P_ia_12=p_ia_coef*P_12
+        P_ia_21=p_ia_coef*P_21
+        P_ia_22=p_ia_coef*P_22
+        ! P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
+        ! P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
+
+        ! Normal velocities
+        P_11=1-P_11  ;  P_12=-P_12 ; P_21= -P_21 ;    P_22=1-P_22
+        p_ia_coef=tangental_damping_coef*(M_min/M1)
+        !the following was done originally, but it is wrong:
+        if (bergs%scale_damping_by_pmag) then
+          p_ia_coef=p_ia_coef*(0.5*(sqrt((((P_11*(u2-u1))+(P_12*(v2-v1)))**2)+ (((P_12*(u2-u1))+(P_22*(v2-v1)))**2))  &
+            + sqrt((((P_11*(u2-u0))+(P_12*(v2-v0)))**2)+(((P_12*(u2-u0)) +(P_22*(v2-v0)))**2))))
+        endif
+        P_ia_11=P_ia_11+p_ia_coef*P_11
+        P_ia_12=P_ia_12+p_ia_coef*P_12
+        P_ia_21=P_ia_21+p_ia_coef*P_21
+        P_ia_22=P_ia_22+p_ia_coef*P_22
+        ! P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
+        ! P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
+
+        IAd_x=IAd_x+P_ia_11*(other_berg%uvel_old-berg%uvel_old)+P_ia_12*(other_berg%vvel_old-berg%vvel_old)
+        IAd_y=IAd_y+P_ia_12*(other_berg%uvel_old-berg%uvel_old)+P_ia_22*(other_berg%vvel_old-berg%vvel_old)
+    endif
+  endif
+
+end subroutine calculate_unbonded_same_conglom_dem_force
+
 !> Calculate interactive forces between two bergs using a discrete element method (DEM)
 !> that includes additional terms for tangential forces and torque.
 subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
+  dt, F_x, F_y, T, Fd_x, Fd_y, T_d, savestress)
+  ! Arguments
+  type(icebergs), pointer :: bergs !< Container for all types and memory
+  type(iceberg), pointer :: berg !< Primary berg
+  type(iceberg), pointer :: other_berg !< Berg that primary is interacting with
+  type(bond), pointer :: current_bond !< Bond being processed
+  real, intent(in) :: dt !< Time step size
+  real, intent(inout) :: F_x !< Net x-force without damping (N)
+  real, intent(inout) :: F_y !< Net y-force without damping (N)
+  real, intent(inout) :: T !< Net torque without damping (Nm)
+  real, intent(inout) :: Fd_x !< Net x-force from damping (N)
+  real, intent(inout) :: Fd_y !< Net y-force from damping (N)
+  real, intent(inout) :: T_d !< Net torque from damping (Nm)
+  logical, intent(in) :: savestress !< Save stress/tangential displacement on bond or not
+  ! Local variables
+  real :: A1,T1,M1,u1,v1,lon1,lat1,R1 ! Current iceberg
+  real :: A2,T2,M2,u2,v2,lon2,lat2,R2 ! Other iceberg
+  real :: dlon, dlat, lat_ref, dx_dlon, dy_dlat
+  real :: r_dist_x, r_dist_y, r_dist
+  real :: Rmin, delta, L, l0, youngs_dem, Thick, T_Rmin, n1, n2
+  real :: ur, vr, up, vp, rotu, rotv, rtu, rtv, RR1, RR2
+  real :: ur2, vr2, Rsig, Rtau
+  real :: ss_factor, ss1, ss2
+  real :: Meff, damping_coef
+  real :: Fn_x, Fn_y, Fs_x, Fs_y, Ts, Tr
+  real :: tangdotnt,tangd1p,tangd2p, tmag, tmagp, t_rat, Area
+  real :: RR1x,RR1y,RR2x,RR2y,theta, half_delta, K_damp, theta_old
+  real, parameter :: hexdenom=1./(2.*sqrt(3.))
+
+  !This DEM formulation follows Wang 2020 "A scale-invariant bonded particle model for
+  !simulating large deformation and failure of continua", which differs from "classic"
+  !DEM (e.g. Potyondy & Cundall, 2004) in its definition of bond width and torque from
+  !relative particle rotation. Forces and torques were further modified here to depend
+  !on ice thickness.
+
+  if ((berg%id .ne. other_berg%id) .and. (berg%fl_k.ne.-1) .and. (other_berg%fl_k.ne.-1)) then
+
+    if (bergs%constant_interaction_LW) then
+      ! use constant length and width here, just for interactions
+      M1=bergs%constant_area*berg%thickness*bergs%rho_bergs                      !Berg 1 mass
+      M2=bergs%constant_area*other_berg%thickness*bergs%rho_bergs                !Berg 2 mass
+      R1=bergs%constant_radius
+      R2=R1
+      Rmin=R1
+      l0=2*R1
+      T_Rmin=other_berg%thickness
+    else
+      ! use actual length and width of bergs
+      M1=berg%mass; A1=berg%length*berg%width                   !From Berg 1
+      M2=other_berg%mass; A2=other_berg%length*other_berg%width !From Berg 2
+
+      !Stern et al 2017, Eqn 4: radius of circle inscribed within hexagon or square with area A1 or A2
+      if (bergs%hexagonal_icebergs) then
+        R1=sqrt(A1*hexdenom)
+        R2=sqrt(A2*hexdenom)
+      else !square packing
+        !if (bergs%iceberg_bonds_on) then
+        R1=0.5*sqrt(A1)
+        R2=0.5*sqrt(A2)
+        ! else
+        !   R1=sqrt(A1/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
+        !   R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
+        ! endif
+      endif
+          !Rmin=min(R1,R2) !old
+      if (R1<R2) then
+        Rmin=R1
+        T_Rmin=berg%thickness !thickness of element w/ minimum radius
+      else
+        Rmin=R2
+        T_Rmin=other_berg%thickness
+      endif
+      l0=R1+R2
+    endif
+
+    !dlon=berg%lon_old-other_berg%lon_old; dlat=berg%lat_old-other_berg%lat_old
+
+    ! Note that this is not the exact distance along a great circle.
+    ! Approximation for small distances. Should be fine.
+    lat_ref=0.5*(berg%lat_old+other_berg%lat_old)
+    call convert_from_grid_to_meters(lat_ref,bergs%grd%grid_is_latlon,dx_dlon,dy_dlat)
+
+    r_dist_x=(berg%lon_old-other_berg%lon_old)*dx_dlon
+    r_dist_y=(berg%lat_old-other_berg%lat_old)*dy_dlat
+    current_bond%length=sqrt( (r_dist_x**2) + (r_dist_y**2) ) !(Stern et al 2017, Eqn 3)
+
+    if (current_bond%length==0) print *,'r_dist,berg%lat_old,berg%lon_old,other_berg%lat_old,other_berg%lon_old',current_bond%length,berg%lat,berg%lon,other_berg%lat,other_berg%lon
+    !unit vec
+    n1=r_dist_x/current_bond%length; n2=r_dist_y/current_bond%length
+
+    half_delta=0.5*(l0-current_bond%length)
+
+    !element distances to contact point
+    RR1=R1-half_delta; RR2=R2-half_delta !magnitude
+    RR1x=RR1*n1;  RR1y=RR1*n2 !element 1 components
+    RR2x=RR2*n1;  RR2y=RR2*n2 !element 2 components
+
+    !bond width (determined at contact point)
+    L=2.0*(Rmin+(Rmin-half_delta)*abs(R1-R2)/current_bond%length)
+
+    Thick=T_Rmin+(Rmin-half_delta)*abs(berg%thickness-other_berg%thickness)/current_bond%length !thickness as determined at contact point
+    !Thick=min(berg%thickness,other_berg%thickness) !minimum thickness
+    !Thick=0.5*(berg%thickness+other_berg%thickness) !average thickness
+
+    !normal force:
+    !Fn_x=bergs%dem_spring_coef*Thick*delta*n1*L/l0 !Fn_y=bergs%dem_spring_coef*Thick*delta*n2*L/l0
+    !normal stiffness is bergs%dem_spring_coef*Thick*L/l0
+    Fn_x=bergs%dem_spring_coef*Thick*2.*half_delta*L/l0; Fn_y=Fn_x*n2; Fn_x=Fn_x*n1
+
+    !relative translational velocity
+    ur=berg%uvel_old-other_berg%uvel_old; vr=berg%vvel_old-other_berg%vvel_old
+
+    if (savestress) then
+      !Rotation of contact plane:
+      tmag=current_bond%tangd1**2+current_bond%tangd2**2 !old magnitude
+      !project old tangential displacement to current tangent plane
+      tangdotnt=current_bond%tangd1*n1+current_bond%tangd2*n2
+      tangd1p=current_bond%tangd1-tangdotnt*n1; tangd2p=current_bond%tangd2-tangdotnt*n2
+      !rescale to the old magnitude
+      tmagp=tangd1p**2+tangd2p**2
+
+      if (tmagp>0.) then
+        t_rat=sqrt(tmag/tmagp)
+        tangd1p=t_rat*tangd1p; tangd2p=t_rat*tangd2p
+      else
+        tangd1p=0.; tangd2p=0.
+      endif
+      !current_bond%tangd1=tangd1p; current_bond%tangd2=tangd2p
+
+      !relative tangential velocities from rotation
+      rotu=RR1y*berg%ang_vel + RR2y*other_berg%ang_vel
+      rotv=-(RR1x*berg%ang_vel + RR2x*other_berg%ang_vel)
+      ur2=ur+rotu; vr2=vr+rotv
+
+      !'parallel' velocity = dot(relative velocity,unit vec)*unit vec
+      up=ur2*n1+vr2*n2; vp=up*n2; up=up*n1
+      ! rtu=ur2-up; rtv=vr2-vp !the relative tangential velocities
+      ! !add the new tangential displacement
+      ! current_bond%tangd1=current_bond%tangd1+rtu*dt; current_bond%tangd2=current_bond%tangd2+rtv*dt
+
+      !faster:
+      !add the new tangential displacement
+      current_bond%tangd1=tangd1p+(ur2-up)*dt; current_bond%tangd2=tangd2p+(vr2-vp)*dt
+    endif
+
+    !shear terms
+    ss_factor=-L*Thick*bergs%dem_spring_coef/(l0*2.0*(1.0+bergs%poisson)) !shear stiffness
+    if (bergs%ignore_tangential_force) ss_factor=0.
+    Fs_x=ss_factor*current_bond%tangd1; Fs_y=ss_factor*current_bond%tangd2 !shear forces
+    if (savestress) current_bond%sstress=sqrt(Fs_x**2+Fs_y**2)/(L*Thick) !shear stress
+
+    !Torque from shearing force: Ts = R .cross. Fs
+    Ts = -(RR1x*Fs_y-RR1y*Fs_x)
+
+    current_bond%rel_rotation=current_bond%rel_rotation+(berg%ang_vel-other_berg%ang_vel)*dt
+
+    !Torque from relative particle rotation
+    if (.not. orig_dem_moment_of_inertia) then
+      theta=sin(berg%rot-other_berg%rot)
+      !theta_old=sin(berg%rot-other_berg%rot)
+      !theta=sin(current_bond%rel_rotation)
+      Tr = -bergs%dem_spring_coef*(L**3.)*Thick*theta/(12.*l0) !should be same as below, except for theta
+    else
+      !For testing purposes. All particles should have same radius and thickness.
+      theta=berg%rot-other_berg%rot
+      !theta_old=berg%rot-other_berg%rot
+      !theta=current_bond%rel_rotation
+      Tr = -(bergs%dem_spring_coef/l0)*(2./3.)*((0.5*L)**3.)*Thick*theta
+    endif
+
+!!$    if (abs(theta-theta_old) > abs(theta*0.05)) then
+!!$      print *,'theta mismatch!', theta_old, theta
+!!$    endif
+
+    !if (savestress) current_bond%nstress=-bergs%dem_spring_coef*delta/l0 + abs(bergs%dem_spring_coef/l0*theta*0.5*L)
+    if (savestress) current_bond%nstress=(bergs%dem_spring_coef/l0)*(-2*half_delta + abs(theta*0.5*L))
+
+    !max tensile stress
+
+    if (break_bonds_on_sub_steps) then
+      if (bergs%fracture_criterion=='computed') then
+        Rsig=current_bond%nstress/bergs%frac_thres_n
+        Rtau=current_bond%sstress/bergs%frac_thres_t
+        if ((0.5*Rsig+sqrt((0.5*Rsig)**2. + Rtau**2.)) > 1) return
+      elseif (bergs%fracture_criterion=='computed_s') then
+        Rsig=current_bond%nstress/bergs%frac_thres_n
+        Rtau=current_bond%sstress/bergs%frac_thres_t
+        if (sqrt(Rsig**2. + Rtau**2.) > 1) return
+      elseif (bergs%fracture_criterion=='stress') then
+        if (current_bond%nstress>bergs%frac_thres_n .or. current_bond%sstress>bergs%frac_thres_t) then
+          return !Broken bond. Return without adding forces and torques
+        endif
+      else
+        call error_mesg('KID, calculate_force_dem', &
+          'break_bond_on_sub_steps currently only possible with fracture critera=computed or stress', FATAL)
+      endif
+    endif
+
+    !damping
+
+    !Meff = M1*M2/(M1+M2) !effective mass
+    damping_coef = bergs%dem_damping_coef*sqrt(bergs%dem_K_damp*M1*M2/(M1+M2))
+
+    Fd_x = Fd_x-damping_coef*ur; Fd_y = Fd_y-damping_coef*vr  !linear damping force
+    T_d  = T_d-damping_coef*(berg%ang_vel-other_berg%ang_vel) !damping torque
+
+    if (bergs%dem_shear_for_frac_only) then
+      Fs_x=0.; Fs_y=0.
+    endif
+
+    !final forces
+    T = T + (Ts + Tr) !torque
+    F_x = F_x + Fn_x + Fs_x; F_y = F_y + Fn_y + Fs_y !linear forces
+  endif
+
+end subroutine calculate_force_dem
+
+!> Calculate interactive forces between two bergs using a discrete element method (DEM)
+!> that includes additional terms for tangential forces and torque.
+subroutine calculate_force_dem2(bergs, berg, other_berg, current_bond, &
   dt, F_x, F_y, T, Fd_x, Fd_y, T_d, savestress)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
@@ -858,7 +1237,7 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
   real :: K_damp, Meff, damping_coef
   real :: Fn_x, Fn_y, Fs_x, Fs_y, Ts, Tr
   real :: tangdotnt,tangd1p,tangd2p, tmag, tmagp
-  real :: RR1x,RR1y,RR2x,RR2y
+  real :: RR1x,RR1y,RR2x,RR2y,theta
 
   !This DEM formulation follows Wang 2020 "A scale-invariant bonded particle model for
   !simulating large deformation and failure of continua", which differs from "classic"
@@ -900,6 +1279,7 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
     r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) ) !(Stern et al 2017, Eqn 3)
     current_bond%length=r_dist
 
+    if (r_dist==0) print *,'r_dist,lat1,lon1,lat2,lon2',r_dist,berg%lat,berg%lon,other_berg%lat,other_berg%lon
     !unit vec
     n1=r_dist_x/r_dist; n2=r_dist_y/r_dist
 
@@ -945,7 +1325,6 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
     !normal force:
     !Fn_x=youngs_dem*Thick*delta*n1*L/l0 !Fn_y=youngs_dem*Thick*delta*n2*L/l0
     !normal stiffness is youngs_dem*Thick*L/l0
-    if (savestress) current_bond%nstress=-youngs_dem*delta/l0 !normal stress
     Fn_x=youngs_dem*Thick*delta*L/l0; Fn_y=Fn_x*n2; Fn_x=Fn_x*n1
 
     !relative translational velocity
@@ -989,7 +1368,18 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
     Ts = -(RR1x*Fs_y-RR1y*Fs_x)
 
     !Torque from relative particle rotation
-    Tr = -youngs_dem*Thick*(L*L*L)*sin(berg%rot-other_berg%rot)/(12.*l0)
+    if (.not. orig_dem_moment_of_inertia) then
+      theta=sin(berg%rot-other_berg%rot)
+      Tr = -youngs_dem*(L**3.)*Thick*theta/(12.*l0) !should be same as below, except for theta
+    else
+      !For testing purposes. All particles should have same radius and thickness.
+      theta=berg%rot-other_berg%rot
+      Tr = -(youngs_dem/l0)*(2./3.)*((0.5*L)**3.)*Thick*theta
+    endif
+
+    !if (savestress) current_bond%nstress=-youngs_dem*delta/l0 + abs(youngs_dem/l0*theta*0.5*L)
+    if (savestress) current_bond%nstress=(youngs_dem/l0)*(-delta + abs(theta*0.5*L))
+    !max tensile stress
 
     !damping
     K_damp = 2.*youngs_dem/(3.*(1.-bergs%poisson**2)) !damping factor
@@ -1009,7 +1399,7 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
     F_x = F_x + Fn_x + Fs_x; F_y = F_y + Fn_y + Fs_y !linear forces
   endif
 
-end subroutine calculate_force_dem
+end subroutine calculate_force_dem2
 
 !> Experimental subroutine to calculate interactive force between a berg and a land cell
 !> Should prevent grounding.
@@ -1241,6 +1631,7 @@ subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, d
   type(bond), pointer :: current_bond
   real :: IAd_x, IAd_y, sum_bond_Ee, sum_bond_Ed, oneoverkn, M2
   type(iceberg), pointer :: other_berg
+  real :: L2,W2
 
   Runge_not_Verlet=bergs%Runge_not_Verlet  ! Loading directly from namelist/default , Alon
   interactive_icebergs_on=bergs%interactive_icebergs_on  ! Loading directly from namelist/default , Alon
@@ -1289,6 +1680,14 @@ subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, d
     hi=min(hi,D)
     D_hi=max(0.,D-hi)
 
+    if (bergs%dem .and. bergs%hexagonal_icebergs .and. radius_based_drag) then
+      !L2=W2=2*radius. This makes things (sort of) consistent with square packing.
+      L2=2.*sqrt(berg%length*berg%width/(2.*sqrt(3.)))
+      W2=L2
+    else
+      !for square bergs in DEM mode, L2=W2=2*radius already. In non-DEM mode, this is business as usual.
+      L2=L; W2=W
+    endif
 
     !start to feel grounded with draught of bergs%h_to_init_grounding meters of the sea floor topography
     !at groundfrac=0, apply no grounding force. at groundfrac=1, apply max grounding force
@@ -1307,6 +1706,13 @@ subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, d
     else
       c_gnd=0.0
     endif
+    if (short_step_mts_grounding) c_gnd=0.
+
+    !For testing sensitivity to number of short steps 
+    ! if ((groundfrac.ne.0.) .and. (bergs%mts_sub_steps>200)) then
+    !   print *,'changing # of ss to 200'
+    !   bergs%mts_sub_steps=200
+    ! endif
 
     ! Wave radiation (Stern et al 2017, Eqs A4-A5)
     uwave=ua-uo; vwave=va-vo  ! Use wind speed rel. to ocean for wave model (aja)
@@ -1317,9 +1723,9 @@ subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, d
     ! http://www4.ncsu.edu/eos/users/c/ceknowle/public/chapter10/part2.html
     Lcutoff=0.125*Lwavelength
     Ltop=0.25*Lwavelength
-    Cr=Cr0*min(max(0.,(L-Lcutoff)/((Ltop-Lcutoff)+1.e-30)),1.) ! Wave radiation coefficient fitted to
+    Cr=Cr0*min(max(0.,(L2-Lcutoff)/((Ltop-Lcutoff)+1.e-30)),1.) ! Wave radiation coefficient fitted to
     ! graph from Carrieres et al.,  POAC Drift Model.
-    wave_rad=0.5*rho_seawater/M*Cr*gravity*ampl*min(ampl,F)*(2.*W*L)/(W+L)
+    wave_rad=0.5*rho_seawater/M*Cr*gravity*ampl*min(ampl,F)*(2.*W2*L2)/(W2+L2)
     wmod = sqrt(ua*ua+va*va) ! Wind speed
     if (wmod.ne.0.) then
       uwave=ua/wmod ! Wave radiation force acts in wind direction ...
@@ -1343,12 +1749,12 @@ subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, d
     endif
 
     ! Weighted drag coefficients (Stern et al 2017, Eqs A1-A3)
-    c_ocn=rho_seawater/M*(0.5*Cd_wv*dragfrac*W*(D_hi)+Cd_wh*W*L)
-    c_atm=rho_air     /M*(0.5*Cd_av*dragfrac*W*F     +Cd_ah*W*L)
+    c_ocn=rho_seawater/M*bergs%ocean_drag_scale*(0.5*Cd_wv*dragfrac*W2*(D_hi)+Cd_wh*W*L)
+    c_atm=rho_air     /M*(0.5*Cd_av*dragfrac*W2*F     +Cd_ah*W*L)
     if (abs(hi).eq.0.) then
       c_ice=0.
     else
-      c_ice=rho_ice   /M*(0.5*Cd_iv*dragfrac*W*hi              )
+      c_ice=rho_ice   /M*(0.5*Cd_iv*dragfrac*W2*hi              )
     endif
     if (abs(ui)+abs(vi).eq.0.) c_ice=0.
 
@@ -1403,7 +1809,10 @@ subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, d
       drag_ocn=c_ocn*0.5*(sqrt( (uveln-uo)**2+(vveln-vo)**2 )+sqrt( (uvel0-uo)**2+(vvel0-vo)**2 ))
       drag_atm=c_atm*0.5*(sqrt( (uveln-ua)**2+(vveln-va)**2 )+sqrt( (uvel0-ua)**2+(vvel0-va)**2 ))
       drag_ice=c_ice*0.5*(sqrt( (uveln-ui)**2+(vveln-vi)**2 )+sqrt( (uvel0-ui)**2+(vvel0-vi)**2 ))
-      drag_gnd=c_gnd*max(0.5*(sqrt(uveln**2+vveln**2)+sqrt(uvel0**2+vvel0**2)),minfricvel)**(1.0/3.0 - 1.0)
+      drag_gnd=c_gnd
+      if (power_ground) then
+        drag_gnd=c_gnd*max(0.5*(sqrt(uveln**2+vveln**2)+sqrt(uvel0**2+vvel0**2)),minfricvel)**(-2./3.)
+      endif
       !RHS ~ similar to accel terms in Stern et al 2017, Eqn B5
       RHS_x=(axn/2) + scaling*(-drag_ocn*(u_star-uo) -drag_atm*(u_star-ua) -drag_ice*(u_star-ui) -drag_gnd*u_star)
       RHS_y=(ayn/2) + scaling*(-drag_ocn*(v_star-vo) -drag_atm*(v_star-va) -drag_ice*(v_star-vi) -drag_gnd*v_star)
@@ -1730,12 +2139,12 @@ subroutine accel_explicit_inner_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel,
   real :: P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y    !Added by Alon
   integer :: stderrunit
   type(bond), pointer :: current_bond
-  real :: IAd_x, IAd_y, sum_bond_Ee, sum_bond_Ed, oneoverkn, M2
+  real :: IAd_x, IAd_y, sum_bond_Ee, sum_bond_Ed, oneoverkn, M2, D, groundfrac
   type(iceberg), pointer :: other_berg
   integer :: grdi,grdj
   logical :: bonded
   ! DEM-mode local variables
-  real :: F_x, F_y, T, Fd_x, Fd_y, T_d, R1, at
+  real :: F_x, F_y, T, Fd_x, Fd_y, T_d, R1, at, dragfrac
 
   u_star=uvel0+(axn*(dt/2.)); v_star=vvel0+(ayn*(dt/2.))  !Alon
   stderrunit = stderr()   ! Get the stderr unit number.
@@ -1781,12 +2190,17 @@ subroutine accel_explicit_inner_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel,
       other_berg=>bergs%list(grdi,grdj)%first
       do while (associated(other_berg))
         if (other_berg%id>0 .and. other_berg%conglom_id.eq.berg%conglom_id) then
-          P_ia_11=0. ; P_ia_12=0. ;  P_ia_21=0.;  P_ia_22=0.
-          P_ia_times_u_x=0. ; P_ia_times_u_y=0.
-          call calculate_force(bergs, berg, other_berg, IA_x, IA_y, uvel0, vvel0, uvel0, vvel0,  &
-            P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded,c_crit_dist=.true.)
-          IAd_x=IAd_x+P_ia_11*(other_berg%uvel_old-berg%uvel_old)+P_ia_12*(other_berg%vvel_old-berg%vvel_old)
-          IAd_y=IAd_y+P_ia_12*(other_berg%uvel_old-berg%uvel_old)+P_ia_22*(other_berg%vvel_old-berg%vvel_old)
+          if (bergs%dem) then
+            call calculate_unbonded_same_conglom_dem_force(bergs, berg, other_berg, &
+              IA_x, IA_y, IAd_x, IAd_y, uvel0, vvel0, uvel0, vvel0)
+          else
+            P_ia_11=0. ; P_ia_12=0. ;  P_ia_21=0.;  P_ia_22=0.
+            P_ia_times_u_x=0. ; P_ia_times_u_y=0.
+            call calculate_force(bergs, berg, other_berg, IA_x, IA_y, uvel0, vvel0, uvel0, vvel0,  &
+              P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded,c_crit_dist=.true.)
+            IAd_x=IAd_x+P_ia_11*(other_berg%uvel_old-berg%uvel_old)+P_ia_12*(other_berg%vvel_old-berg%vvel_old)
+            IAd_y=IAd_y+P_ia_12*(other_berg%uvel_old-berg%uvel_old)+P_ia_22*(other_berg%vvel_old-berg%vvel_old)
+          endif
         endif
         other_berg=>other_berg%next
       enddo
@@ -1803,16 +2217,6 @@ subroutine accel_explicit_inner_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel,
 
   if (bergs%dem) then
 
-    if (bergs%hexagonal_icebergs) then
-      R1=sqrt(berg%length*berg%width/(2.*sqrt(3.)))
-    else !square packing
-      if (bergs%iceberg_bonds_on) then
-        R1=0.5*sqrt(berg%length*berg%width)
-      else
-        R1=sqrt(berg%length*berg%width/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
-      endif
-    endif
-
     if (bergs%dem_beam_test>0) then
       if (bergs%dem_beam_test==1) then
         !3.1 (Wang,2020): Simply supported beam test
@@ -1843,13 +2247,64 @@ subroutine accel_explicit_inner_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel,
     if (bergs%constant_interaction_LW) then
       ! mass according to constant length and width here, just for interactions
       M=bergs%constant_length*bergs%constant_width*berg%thickness*bergs%rho_bergs
+      if (bergs%hexagonal_icebergs) then
+        R1=sqrt(bergs%constant_length*bergs%constant_width/(2.*sqrt(3.)))
+      else !square packing
+        if (bergs%iceberg_bonds_on) then
+          R1=0.5*sqrt(bergs%constant_length*bergs%constant_width)
+        else
+          R1=sqrt(bergs%constant_length*bergs%constant_width/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
+        endif
+      endif
     else
       M=berg%mass
+      if (bergs%hexagonal_icebergs) then
+        R1=sqrt(berg%length*berg%width/(2.*sqrt(3.)))
+      else !square packing
+        if (bergs%iceberg_bonds_on) then
+          R1=0.5*sqrt(berg%length*berg%width)
+        else
+          R1=sqrt(berg%length*berg%width/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
+        endif
+      endif
     endif
 
     IA_x=IA_x+F_x/M; IA_y=IA_y+F_y/M
     IAd_x=IAd_x+Fd_x/M; IAd_y=IAd_y+Fd_y/M
 
+    if (bergs%add_curl_to_torque) then
+      dragfrac = 1.0
+      if ((bergs%iceberg_bonds_on) .and. (bergs%internal_bergs_for_drag)) then
+        dragfrac = 1. - berg%n_bonds/bergs%max_bonds
+      else
+        dragfrac = 1.0
+      endif
+      T = T + (R1**4.)*rho_seawater*bergs%ocean_drag_scale*&
+        (0.2*pi*R1*Cd_wh + 0.5*Cd_wv*dragfrac*berg%thickness*(bergs%rho_bergs/rho_seawater)) * &
+        (0.5*berg%curl_o-berg%ang_vel)*abs(0.5*berg%curl_o-berg%ang_vel)
+    endif
+
+    ! !torque from grounding drag
+    ! !start to feel grounded with draught of bergs%h_to_init_grounding meters of the sea floor topography
+    ! !at groundfrac=0, apply no grounding force. at groundfrac=1, apply max grounding force
+    ! D=(bergs%rho_bergs/rho_seawater)*berg%thickness ! draught (keel depth)
+    ! if (bergs%h_to_init_grounding>0.0) then
+    !   groundfrac=1.0-(berg%od-D)/bergs%h_to_init_grounding
+    !   groundfrac=max(groundfrac,0.0); groundfrac=min(groundfrac,1.0)
+    ! else
+    !   if (D>berg%od) then
+    !     groundfrac=1.0
+    !   else
+    !     groundfrac=0.0
+    !   endif
+    ! endif
+    ! if (groundfrac>0.0) then
+    !   print *,'T_prev,T_d,groundfrac,nbonds,angvel',T,T_d,groundfrac,berg%n_bonds,berg%ang_vel
+    !   print *,'T ground',-bergs%cdrag_grounding*groundfrac*0.5*pi*(R1**4.)*berg%ang_vel
+    !   T=T-bergs%cdrag_grounding*groundfrac*0.5*pi*(R1**4.)*berg%ang_vel !treat berg as disk?
+    !   print *,'T_after',T
+    ! endif
+
     at=(T+T_d)/(0.5*M*R1**2) !torque acceleration
     berg%ang_accel = at
   endif
@@ -2165,7 +2620,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
   endif
 
   ! Weighted drag coefficients (Stern et al 2017, Eqs A1-A3)
-  c_ocn=rho_seawater/M*(0.5*Cd_wv*dragfrac*W*(D_hi)+Cd_wh*W*L)
+  c_ocn=rho_seawater/M*bergs%ocean_drag_scale*(0.5*Cd_wv*dragfrac*W*(D_hi)+Cd_wh*W*L)
   c_atm=rho_air     /M*(0.5*Cd_av*dragfrac*W*F     +Cd_ah*W*L)
   if (abs(hi).eq.0.) then
     c_ice=0.
@@ -2235,14 +2690,20 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
     drag_ocn=c_ocn*0.5*(sqrt( (uveln-uo)**2+(vveln-vo)**2 )+sqrt( (uvel0-uo)**2+(vvel0-vo)**2 ))
     drag_atm=c_atm*0.5*(sqrt( (uveln-ua)**2+(vveln-va)**2 )+sqrt( (uvel0-ua)**2+(vvel0-va)**2 ))
     drag_ice=c_ice*0.5*(sqrt( (uveln-ui)**2+(vveln-vi)**2 )+sqrt( (uvel0-ui)**2+(vvel0-vi)**2 ))
-    drag_gnd=c_gnd*max(0.5*(sqrt(uveln**2+vveln**2)+sqrt(uvel0**2+vvel0**2)),minfricvel)**(1.0/3.0 - 1.0)
+    drag_gnd=c_gnd
+    if (power_ground) then
+      drag_gnd=c_gnd*max(0.5*(sqrt(uveln**2+vveln**2)+sqrt(uvel0**2+vvel0**2)),minfricvel)**(1.0/3.0 - 1.0)
+    endif
   else
     !Original Scheme
     us=0.5*(uveln+uvel); vs=0.5*(vveln+vvel)
     drag_ocn=c_ocn*sqrt( (us-uo)**2+(vs-vo)**2 )
     drag_atm=c_atm*sqrt( (us-ua)**2+(vs-va)**2 )
     drag_ice=c_ice*sqrt( (us-ui)**2+(vs-vi)**2 )
-    drag_gnd=c_gnd*max(sqrt(us**2+vs**2),minfricvel)**(1.0/3.0 - 1.0)
+    drag_gnd=c_gnd
+    if (power_ground) then
+      drag_gnd=c_gnd*max(sqrt(us**2+vs**2),minfricvel)**(1.0/3.0 - 1.0)
+    endif
   endif
 
   !RHS ~ similar to accel terms in Stern et al 2017, Eqn B5
@@ -2657,22 +3118,11 @@ subroutine footloose_calving(bergs, time)
           if (max_k==0) then
             k=0
           else
-            ! !here, fl_k is the accumulated mass from side melt/erosion
-            ! foot_l = lfootparam*T/l_w
-            ! !this is the mass of side melt/erosion needed to calve a single footloose berg
-            ! foot_mass = foot_l * T*(1.-bergs%rho_bergs/rho_seawater) * l_b3 * bergs%rho_bergs
-            ! !If bergs%fl_l_scale=1, all side mass loss is above sea level, and goes into creating the
-            ! !foot. Adjust to >1 if some mass loss evenly melts the sides at all depths...
-            ! foot_mass = bergs%fl_l_scale * foot_mass/T
-            ! k=floor(this%fl_k/foot_mass)
-            ! if (k>max_k) k=max_k
-            ! this%fl_k=this%fl_k-k*foot_mass
-
-            !here, fl_k is the accumulated mass from side melt/erosion
+            !here, fl_k is the accumulated foot area from erosion - side melt
             foot_l = lfootparam*T/l_w
-            !this is the area of side melt/erosion needed to calve a single footloose berg
+            !this is the foot area needed to calve a single footloose berg
             foot_area = foot_l * l_b3
-            foot_area = bergs%fl_l_scale * foot_area
+            foot_area = bergs%fl_l_scale * foot_area !option to scale the foot area needed to calve
             k=floor(this%fl_k/foot_area)
             if (k>max_k) k=max_k
             this%fl_k=this%fl_k-k*foot_area
@@ -2901,9 +3351,9 @@ subroutine adjust_fl_berg_interactivity(bergs)
       rdenom=1./(2.*sqrt(3.))
     else
       if (bergs%iceberg_bonds_on) then
-        rdenom=1./pi
-      else
         rdenom=1./4.
+      else
+        rdenom=1./pi
       endif
     endif
   else
@@ -4821,6 +5271,7 @@ subroutine interp_gridded_fields_to_bergs(bergs)
         endif
         call interp_flds(grd, berg%lon, berg%lat, berg%ine, berg%jne, berg%xi, berg%yj, rx, ry, berg%uo, berg%vo, &
           berg%ui, berg%vi, berg%ua, berg%va, berg%ssh_x, berg%ssh_y, berg%sst, berg%sss, berg%cn, berg%hi, berg%od)
+        if (bergs%add_curl_to_torque) call interp_curl(grd,berg)
       endif
       berg=>berg%next
     enddo
@@ -4862,6 +5313,8 @@ subroutine interp_flds(grd, x, y, i, j, xi, yj, rx, ry, uo, vo, ui, vi, ua, va,
   real :: hxm, hxp, ssh
   integer :: stderrunit
   integer :: ii, jj
+  real :: p1x=322.67292, p2x=322.94692, p3x=322.86458, p1y=-55.01042, p2y=-55.01042, p3y=-54.93958
+  real :: alpha, beta, gamma
 
   ! Get the stderr unit number
   stderrunit = stderr()
@@ -4952,9 +5405,9 @@ subroutine interp_flds(grd, x, y, i, j, xi, yj, rx, ry, uo, vo, ui, vi, ua, va,
 
   ! Estimate SSH gradient in Y direction
 #ifdef USE_OLD_SSH_GRADIENT
-  dxp=0.5*(grd%dy(i,j+1)+grd%dy(i-1,j+1))
-  dx0=0.5*(grd%dy(i,j)+grd%dy(i-1,j))
-  dxm=0.5*(grd%dy(i,j-1)+grd%dy(i-1,j-1))
+  dxp=0.5*(grd%dy(i,j+1)+grd%dy(i-1,j+1)) !dy of middle of cell above
+  dx0=0.5*(grd%dy(i,j)+grd%dy(i-1,j))     !dy of middle of cell
+  dxm=0.5*(grd%dy(i,j-1)+grd%dy(i-1,j-1)) !dy of middle of cell below
   hxm=2.*(grd%ssh(i,j)-grd%ssh(i,j-1))/(dx0+dxm)*grd%msk(i,j-1) &
         +(-ssh_coast)/(dx0+dxm)*(1.-grd%msk(i,j-1)) ! force to drive bergs away from coasts
   hxp=2.*(grd%ssh(i,j+1)-grd%ssh(i,j))/(dx0+dxp)*grd%msk(i,j+1) &
@@ -4988,20 +5441,153 @@ subroutine interp_flds(grd, x, y, i, j, xi, yj, rx, ry, uo, vo, ui, vi, ua, va,
     write(stderrunit,*) 'KID, Error in interpolate: ua,va,ssh_x,ssh_y', ua, va, ssh_x, ssh_y
     write(stderrunit,*) 'KID, Error in interpolate: sst,cn,hi', sst, sss, cn, hi, mpp_pe()
     call error_mesg('KID, interp fields', 'field interpaolations has NaNs', FATAL)
-
   endif
 
   ! Quadratic interpolation of ocean depth+sea surface height (A-grid)
   ! Ocean depth is only needed for grounding friction, used with the MTS model only?
   if (present(od)) then
     if (mts) then
-      od=quad_interp_from_agrid(grd,grd%ocean_depth,x,y,i,j,xi,yj)+quad_interp_from_agrid(grd,grd%ssh,x,y,i,j,xi,yj)
+      !od=quad_interp_from_agrid(grd,grd%ocean_depth,x,y,i,j,xi,yj)+quad_interp_from_agrid(grd,grd%ssh,x,y,i,j,xi,yj)
+
+      !od=quad_interp_from_agrid(grd,grd%ocean_depth+grd%ssh,x,y,i,j,xi,yj)
+
+      if (A68_test) then
+
+        ! if (x<(-37.1+360) .and. x>(-37.38+360) .and. y<-54.68 .and. y>-54.86) then
+        !   od=0
+        ! else
+        !   od=1000
+        ! endif
+
+        od=1000.
+        !if ((x>-37.3861+360).and.(y>-54.9778)) od=0.
+        !if ((x>-37.2752+360).and.(y>-55.1341)) od=0.
+        !if ((x>-37.3458+360).and.(y>-55.1038)) od=0.
+
+        !od17.8 dy=-0.1
+        !if ((x>-37.2954+360).and.(y>-55.2975)) od=0.
+        if ((x>A68_xdisp+360).and.(y>A68_ydisp)) od=0.
+
+        ! p1y=p1y+A68_ydisp; p2y=p2y+A68_ydisp; p3y=p3y+A68_ydisp
+        ! p1x=p1x+A68_xdisp; p2x=p2x+A68_xdisp; p3x=p3x+A68_xdisp
+
+        ! od=1000.0
+        ! if (x>p1x .and. x<p2x .and. y>p1y .and. y<p3y) then
+        !   alpha = ((p2y - p3y)*(x - p3x) + (p3x - p2x)*(y - p3y)) /&
+        !     ((p2y - p3y)*(p1x - p3x) + (p3x - p2x)*(p1y - p3y))
+        !   if (alpha>0.) then
+        !     beta = ((p3y - p1y)*(x - p3x) + (p1x - p3x)*(y - p3y)) /&
+        !       ((p2y - p3y)*(p1x - p3x) + (p3x - p2x)*(p1y - p3y))
+        !     if (beta>0.) then
+        !       gamma = 1. - alpha - beta
+        !       if (gamma>0.) then
+        !         od=0.
+        !       endif
+        !     endif
+        !   endif
+        ! endif
+
+        ! p1y=p1y-A68_ydisp; p2y=p2y-A68_ydisp; p3y=p3y-A68_ydisp
+        ! p1x=p1x-A68_xdisp; p2x=p2x-A68_xdisp; p3x=p3x-A68_xdisp
+      else
+        od=quad_interp_from_agrid(grd,grd%ocean_depth+grd%ssh,x,y,i,j,xi,yj)
+      endif
+
     else
       od=grd%ocean_depth(i,j)+grd%ssh(i,j)
     endif
   endif
 end subroutine interp_flds
 
+!> Interpolates ocean (and atmospheric?) torque fields to an iceberg (DEM-mode required)
+subroutine interp_curl(grd,berg)
+  type(icebergs_gridded), pointer :: grd
+  type(iceberg), pointer :: berg
+  ! Local variables
+  integer :: i,j
+  real :: xi,yj
+  real :: hxp_o, hxp_a, hxm_o, hxm_a
+  real :: duo_dy, dua_dy, duo_dx, dua_dx
+  real :: dvo_dy, dva_dy, dvo_dx, dva_dx
+  real :: cos_rot, sin_rot
+
+  i =berg%ine;  j=berg%jne
+  xi=berg%xi;  yj=berg%yj
+
+  if (yj>=0.5) then
+    hxp_o=(yj-0.5)*ddx_v_point(grd,grd%vo,i  ,j+1,.true. )+(1.5-yj)*ddx_v_point(grd,grd%vo,i  ,j  ,.true. )
+    hxm_o=(yj-0.5)*ddx_v_point(grd,grd%vo,i-1,j+1,.true. )+(1.5-yj)*ddx_v_point(grd,grd%vo,i-1,j  ,.true. )
+    !hxp_a=(yj-0.5)*ddx_v_point(grd,grd%va,i  ,j+1,.false.)+(1.5-yj)*ddx_v_point(grd,grd%va,i  ,j  ,.false.)
+    !hxm_a=(yj-0.5)*ddx_v_point(grd,grd%va,i-1,j+1,.false.)+(1.5-yj)*ddx_v_point(grd,grd%va,i-1,j  ,.false.)
+  else
+    hxp_o=(yj+0.5)*ddx_v_point(grd,grd%vo,i  ,j  ,.true. )+(0.5-yj)*ddx_v_point(grd,grd%vo,i  ,j-1,.true. )
+    hxm_o=(yj+0.5)*ddx_v_point(grd,grd%vo,i-1,j  ,.true. )+(0.5-yj)*ddx_v_point(grd,grd%vo,i-1,j-1,.true. )
+    !hxp_a=(yj+0.5)*ddx_v_point(grd,grd%va,i  ,j  ,.false.)+(0.5-yj)*ddx_v_point(grd,grd%va,i  ,j-1,.false.)
+    !hxm_a=(yj+0.5)*ddx_v_point(grd,grd%va,i-1,j  ,.false.)+(0.5-yj)*ddx_v_point(grd,grd%va,i-1,j-1,.false.)
+  endif
+  dvo_dx=xi*hxp_o+(1.-xi)*hxm_o
+  !dva_dx=xi*hxp_a+(1.-xi)*hxm_a
+  if (xi>=0.5) then
+    hxp_o=(xi-0.5)*ddy_u_point(grd,grd%uo,i+1,j  ,.true. )+(1.5-xi)*ddy_u_point(grd,grd%uo,i  ,j  ,.true. )
+    hxm_o=(xi-0.5)*ddy_u_point(grd,grd%uo,i+1,j-1,.true. )+(1.5-xi)*ddy_u_point(grd,grd%uo,i  ,j-1,.true. )
+    !hxp_a=(xi-0.5)*ddy_u_point(grd,grd%ua,i+1,j  ,.false.)+(1.5-xi)*ddy_u_point(grd,grd%ua,i  ,j  ,.false.)
+    !hxm_a=(xi-0.5)*ddy_u_point(grd,grd%ua,i+1,j-1,.false.)+(1.5-xi)*ddy_u_point(grd,grd%ua,i  ,j-1,.false.)
+  else
+    hxp_o=(xi+0.5)*ddy_u_point(grd,grd%uo,i  ,j  ,.true. )+(0.5-xi)*ddy_u_point(grd,grd%uo,i-1,j  ,.true. )
+    hxm_o=(xi+0.5)*ddy_u_point(grd,grd%uo,i  ,j-1,.true. )+(0.5-xi)*ddy_u_point(grd,grd%uo,i-1,j-1,.true. )
+    !hxp_a=(xi+0.5)*ddy_u_point(grd,grd%ua,i  ,j  ,.false.)+(0.5-xi)*ddy_u_point(grd,grd%uo,i-1,j  ,.false.)
+    !hxm_a=(xi+0.5)*ddy_u_point(grd,grd%ua,i  ,j-1,.false.)+(0.5-xi)*ddy_u_point(grd,grd%uo,i-1,j-1,.false.)
+  endif
+  duo_dy=yj*hxp_o+(1.-yj)*hxm_o
+  !dua_dy=yj*hxp_a+(1.-yj)*hxm_a
+
+  cos_rot=bilin(grd, grd%cos, i, j, xi, yj) ! If true, uses the inverted bilin function
+  sin_rot=bilin(grd, grd%sin, i, j, xi, yj)
+
+  if ((cos_rot .ne. 1.0) .or. (sin_rot .ne. 0.0)) then
+    if (yj>=0.5) then
+      hxp_o=(yj-0.5)*ddx_v_point(grd,grd%uo,i  ,j+1,.true. )+(1.5-yj)*ddx_v_point(grd,grd%uo,i  ,j  ,.true. )
+      hxm_o=(yj-0.5)*ddx_v_point(grd,grd%uo,i-1,j+1,.true. )+(1.5-yj)*ddx_v_point(grd,grd%uo,i-1,j  ,.true. )
+      !hxp_a=(yj-0.5)*ddx_v_point(grd,grd%ua,i  ,j+1,.false.)+(1.5-yj)*ddx_v_point(grd,grd%ua,i  ,j  ,.false.)
+      !hxm_a=(yj-0.5)*ddx_v_point(grd,grd%ua,i-1,j+1,.false.)+(1.5-yj)*ddx_v_point(grd,grd%ua,i-1,j  ,.false.)
+    else
+      hxp_o=(yj+0.5)*ddx_v_point(grd,grd%uo,i  ,j  ,.true. )+(0.5-yj)*ddx_v_point(grd,grd%uo,i  ,j-1,.true. )
+      hxm_o=(yj+0.5)*ddx_v_point(grd,grd%uo,i-1,j  ,.true. )+(0.5-yj)*ddx_v_point(grd,grd%uo,i-1,j-1,.true. )
+      !hxp_a=(yj+0.5)*ddx_v_point(grd,grd%ua,i  ,j  ,.false.)+(0.5-yj)*ddx_v_point(grd,grd%ua,i  ,j-1,.false.)
+      !hxm_a=(yj+0.5)*ddx_v_point(grd,grd%ua,i-1,j  ,.false.)+(0.5-yj)*ddx_v_point(grd,grd%ua,i-1,j-1,.false.)
+    endif
+    duo_dx=xi*hxp_o+(1.-xi)*hxm_o
+    !dua_dx=xi*hxp_a+(1.-xi)*hxm_a
+    if (xi>=0.5) then
+      hxp_o=(xi-0.5)*ddy_u_point(grd,grd%vo,i+1,j,  .true. )+(1.5-xi)*ddy_u_point(grd,grd%vo,i  ,j,  .true. )
+      hxm_o=(xi-0.5)*ddy_u_point(grd,grd%vo,i+1,j-1,.true. )+(1.5-xi)*ddy_u_point(grd,grd%vo,i  ,j-1,.true. )
+      !hxp_a=(xi-0.5)*ddy_u_point(grd,grd%va,i+1,j,  .false.)+(1.5-xi)*ddy_u_point(grd,grd%va,i  ,j,  .false.)
+      !hxm_a=(xi-0.5)*ddy_u_point(grd,grd%va,i+1,j-1,.false.)+(1.5-xi)*ddy_u_point(grd,grd%va,i  ,j-1,.false.)
+    else
+      hxp_o=(xi+0.5)*ddy_u_point(grd,grd%vo,i  ,j,  .true. )+(0.5-xi)*ddy_u_point(grd,grd%vo,i-1,j,  .true. )
+      hxm_o=(xi+0.5)*ddy_u_point(grd,grd%vo,i  ,j-1,.true. )+(0.5-xi)*ddy_u_point(grd,grd%vo,i-1,j-1,.true. )
+      !hxp_a=(xi+0.5)*ddy_u_point(grd,grd%va,i  ,j,  .false.)+(0.5-xi)*ddy_u_point(grd,grd%vo,i-1,j,  .false.)
+      !hxm_a=(xi+0.5)*ddy_u_point(grd,grd%va,i  ,j-1,.false.)+(0.5-xi)*ddy_u_point(grd,grd%vo,i-1,j-1,.false.)
+    endif
+    dvo_dy=yj*hxp_o+(1.-yj)*hxm_o
+    !dva_dy=yj*hxp_a+(1.-yj)*hxm_a
+    call rotate(duo_dx, dvo_dx, cos_rot, sin_rot)
+    call rotate(duo_dy, dvo_dy, cos_rot, sin_rot)
+    !call rotate(dua_dx, dva_dx, cos_rot, sin_rot)
+    !call rotate(dua_dy, dva_dy, cos_rot, sin_rot)
+  endif
+
+  if ((dvo_dx.ne.dvo_dx) .or. (duo_dy.ne.duo_dy)) then
+    dvo_dx=0.; duo_dy=0.
+  endif
+  !if ((dva_dx.ne.dva_dx) .or. (dua_dy.ne.dua_dy)) then
+  !  dva_dx=0.; dua_dy=0.
+  !endif
+
+  berg%curl_o=dvo_dx-duo_dy
+  !berg%curl_a=dva_dx-dua_dy
+end subroutine interp_curl
+
 !> Returns zonal slope of sea-surface height across the east face of cell i,j
 real function ddx_ssh(grd,i,j)
   ! Arguments
@@ -5028,6 +5614,30 @@ real function ddy_ssh(grd,i,j)
   ddy_ssh=2.*(grd%ssh(i,j+1)-grd%ssh(i,j))/(dy0+dyp)*grd%msk(i,j+1)*grd%msk(i,j)
 end function ddy_ssh
 
+!> Returns zonal slope of a grid variable defined at i,j at the v point of the grid cell
+real function ddx_v_point(grd,fld,i,j,mask)
+  ! Arguments
+  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+  real, intent(in) :: fld(grd%isd:grd%ied,grd%jsd:grd%jed) !< Field to interpolate
+  integer, intent(in) :: i !< i-index of cell
+  integer, intent(in) :: j !< j-index of cell
+  logical, intent(in) :: mask !< if true, mask land cells
+  ddx_v_point=(fld(i,j)-fld(i-1,j))/grd%dx(i,j)
+  if (mask) ddx_v_point=ddx_v_point*grd%msk(i-1,j)*grd%msk(i,j)
+end function ddx_v_point
+
+!> Returns meridional slope of a grid variable defined at i,j at the u point of the grid cell
+real function ddy_u_point(grd,fld,i,j,mask)
+  ! Arguments
+  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+  real, intent(in) :: fld(grd%isd:grd%ied,grd%jsd:grd%jed) !< Field to interpolate
+  integer, intent(in) :: i !< i-index of cell
+  integer, intent(in) :: j !< j-index of cell
+  logical, intent(in) :: mask !< if true, mask land cells
+  ddy_u_point=(fld(i,j)-fld(i,j-1))/grd%dy(i,j)
+  if (mask) ddy_u_point=ddy_u_point*grd%msk(i,j-1)*grd%msk(i,j)
+end function ddy_u_point
+
 ! Rotates vector (u,v) using rotation matrix with elements cos_rot and sin_rot
 subroutine rotate(u, v, cos_rot, sin_rot)
   ! Arguments
@@ -5397,7 +6007,9 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   call mpp_update_domains(grd%uo, grd%vo, grd%domain, gridtype=BGRID_NE)
   call mpp_update_domains(grd%ui, grd%vi, grd%domain, gridtype=BGRID_NE)
 
-  call invert_tau_for_du(grd%ua, grd%va) ! Note rough conversion from stress to speed
+  if (.not. bergs%tau_is_velocity) then
+    call invert_tau_for_du(grd%ua, grd%va) ! Note rough conversion from stress to speed
+  endif
  !grd%ua(grd%isc:grd%iec,grd%jsc:grd%jec)=sign(sqrt(abs(tauxa(:,:))/0.01),tauxa(:,:))  ! Note rough conversion from stress to speed
  !grd%va(grd%isc:grd%iec,grd%jsc:grd%jec)=sign(sqrt(abs(tauya(:,:))/0.01),tauya(:,:))  ! Note rough conversion from stress to speed
   call mpp_update_domains(grd%ua, grd%va, grd%domain, gridtype=BGRID_NE)
@@ -5594,8 +6206,8 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   if (sample_traj .or. bergs%writeandstop) call record_posn(bergs)
   if (write_traj .or. bergs%writeandstop) then
     call move_all_trajectories(bergs)
-    call write_trajectory(bergs%trajectories, bergs%save_short_traj, bergs%save_fl_traj, bergs%fl_r)
-    if (save_bond_traj) call write_bond_trajectory(bergs%bond_trajectories)
+    call write_trajectory(bergs%trajectories, bergs%save_short_traj, bergs%save_fl_traj, bergs%fl_r, bergs%traj_name)
+    if (save_bond_traj) call write_bond_trajectory(bergs%bond_trajectories, bergs%bond_traj_name)
   endif
 
   if (bergs%writeandstop) then
@@ -6663,6 +7275,10 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b,fl_disp_x,fl_disp_y,berg_from_bit
   if (bergs%dem) then
     allocate(cberg%ang_vel,cberg%ang_accel,cberg%rot)
     cberg%ang_vel=0.; cberg%ang_accel=0.; cberg%rot=0.
+    if (bergs%add_curl_to_torque) then
+      allocate(cberg%curl_o)!,cberg%curl_a)
+      cberg%curl_o=pberg%curl_o!; cberg%curl_a=pberg%curl_a;
+    endif
   endif
 
   if (monitor_energy) then
@@ -6712,7 +7328,8 @@ subroutine evolve_icebergs_mts(bergs)
   real :: Fex_i, Fey_i, Fec_x, Fec_y, Fdc_x, Fdc_y, ustar, vstar, uveln_star, vveln_star
   integer :: ii,jj,maxii,minii,maxjj,minjj
   real :: usum,usum1,usum2,normchange,denom
-  logical :: finished,last_iter
+  real :: MM,AA,R1,groundfrac,gdrag,D
+  logical :: finished,last_iter,had_collision
 
   ! Multiple Time Step Velocity Verlet:
   ! NOTE: To avoid the need for computationally expensive transfers between processors
@@ -6734,6 +7351,30 @@ subroutine evolve_icebergs_mts(bergs)
   do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec ! just for computational domain
     berg=>bergs%list(grdi,grdj)%first
     do while (associated(berg)) ! loop over all bergs
+
+!!$      if (.not. short_step_mts_grounding) then
+!!$        !set fully-grounded particles to static
+!!$        D=(bergs%rho_bergs/rho_seawater)*berg%thickness ! draught (keel depth)
+!!$        if (bergs%h_to_init_grounding>0.0) then
+!!$          groundfrac=1.0-(berg%od-D)/bergs%h_to_init_grounding
+!!$          groundfrac=max(groundfrac,0.0); groundfrac=min(groundfrac,1.0)
+!!$        else
+!!$          if (D>berg%od) then
+!!$            groundfrac=1.0
+!!$          else
+!!$            groundfrac=0.0
+!!$          endif
+!!$        endif
+!!$
+!!$        if (groundfrac==1.0) then
+!!$          berg%static_berg=1.0
+!!$          berg%uvel=0.; berg%vvel=0.; berg%axn=0.; berg%ayn=0.; berg%bxn=0.; berg%byn=0.
+!!$          berg%uvel_prev=0.; berg%vvel_prev=0.; berg%uvel_old=0.; berg%vvel_old=0.
+!!$          berg%axn_fast=0.; berg%ayn_fast=0.; berg%bxn_fast=0.; berg%byn_fast=0.
+!!$          berg%ang_vel=0.; berg%ang_accel=0.
+!!$        endif
+!!$      endif
+
       if (berg%static_berg .lt. 0.5 .and. berg%halo_berg .lt. 0.5) then
         if (.not. is_point_in_cell(bergs%grd, berg%lon, berg%lat, berg%ine, berg%jne) ) then
           write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lon',(i,i=grd%isd,grd%ied)
@@ -6765,6 +7406,7 @@ subroutine evolve_icebergs_mts(bergs)
   save_bond_energy=.false.
   usum=0.0; usum1=0.0; usum2=0.0
   finished=.false.
+  had_collision=.false.
 
   if (bergs%force_convergence) then
     last_iter=.false.
@@ -6772,124 +7414,138 @@ subroutine evolve_icebergs_mts(bergs)
     last_iter=.true.
   endif
 
-  do while (.not. finished)
+  if (.not. skip_first_outer_mts_step) then
 
-    ii=ii+1
+    do while (.not. finished)
 
-    do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
-      berg=>bergs%list(grdi,grdj)%first
-      do while (associated(berg)) ! loop over all bergs
-        !only evolve non-static bergs that overlap, or are part of a conglom that overlaps, the computational domain:
-        if (berg%static_berg .lt. 0.5 .and. (berg%conglom_id.ne.0 .or. bergs%force_convergence)) then
-          latn = berg%lat ;   lonn = berg%lon
-          uvel1=berg%uvel ;   vvel1=berg%vvel !V_n (previous cycle)
-          axn  = 0.0      ;   ayn  = 0.0 !note these are redefined at the start of subroutine accel_mts
-          bxn  = 0.0      ;   byn  = 0.0
-          i=berg%ine      ;   j=berg%jne
-          xi=berg%xi      ;   yj=berg%yj
+      ii=ii+1
 
-          call accel_mts(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, &
-            ax1, ay1, axn, ayn, bxn, byn, save_bond_energy,Fec_x, Fec_y, Fdc_x, Fdc_y)
+      do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+        berg=>bergs%list(grdi,grdj)%first
+        do while (associated(berg)) ! loop over all bergs
+          !only evolve non-static bergs that overlap, or are part of a conglom that overlaps, the computational domain:
+          if (berg%static_berg .lt. 0.5 .and. (berg%conglom_id.ne.0 .or. bergs%force_convergence)) then
+            latn = berg%lat ;   lonn = berg%lon
+            uvel1=berg%uvel ;   vvel1=berg%vvel !V_n (previous cycle)
+            axn  = 0.0      ;   ayn  = 0.0 !note these are redefined at the start of subroutine accel_mts
+            bxn  = 0.0      ;   byn  = 0.0
+            i=berg%ine      ;   j=berg%jne
+            xi=berg%xi      ;   yj=berg%yj
 
-          if (monitor_energy .and. last_iter) &
-            call mts_energy_part_1(bergs,berg,ax1,ay1,axn,ayn,bxn,byn,Fec_x,Fec_y,Fdc_x,Fdc_y)
+            call accel_mts(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, &
+              ax1, ay1, axn, ayn, bxn, byn, save_bond_energy,Fec_x, Fec_y, Fdc_x, Fdc_y)
 
-          ! Saving all the iceberg variables
-          berg%axn=axn; berg%ayn=ayn
-          berg%bxn=bxn; berg%byn=byn
+            if (Fdc_x .ne. 0. .or. Fdc_y .ne. 0.) had_collision=.true.
+            if (monitor_energy .and. last_iter) &
+              call mts_energy_part_1(bergs,berg,ax1,ay1,axn,ayn,bxn,byn,Fec_x,Fec_y,Fdc_x,Fdc_y)
 
-          if (bergs%force_convergence) then
-            berg%uvel_prev=berg%uvel+(dt*ax1); berg%vvel_prev=berg%vvel+(dt*ay1) !the new velocity
-            if (ii==1) usum=usum+berg%uvel_old**2 + berg%vvel_old**2
-            usum1=usum1+berg%uvel_prev**2+berg%vvel_prev**2
-            usum2=usum2+(berg%uvel_prev-berg%uvel_old)**2+(berg%vvel_prev-berg%vvel_old)**2
-          else
-            berg%uvel=berg%uvel+(dt*ax1); berg%vvel=berg%vvel+(dt*ay1)
+            ! Saving all the iceberg variables
+            berg%axn=axn; berg%ayn=ayn
+            berg%bxn=bxn; berg%byn=byn
 
-            !The final velocity from the previous cycle, which can be used
-            !during post-processing to calculate kinetic energy and momentum
-            berg%uvel_prev=berg%uvel    ; berg%vvel_prev=berg%vvel
-          endif
-        endif
-        berg=>berg%next
-      enddo ! loop over all bergs
-    enddo; enddo
+            if (bergs%force_convergence) then
+              berg%uvel_prev=berg%uvel+(dt*ax1); berg%vvel_prev=berg%vvel+(dt*ay1) !the new velocity
+              if (ii==1) usum=usum+berg%uvel_old**2 + berg%vvel_old**2
+              usum1=usum1+berg%uvel_prev**2+berg%vvel_prev**2
+              usum2=usum2+(berg%uvel_prev-berg%uvel_old)**2+(berg%vvel_prev-berg%vvel_old)**2
+            else
+              berg%uvel=berg%uvel+(dt*ax1); berg%vvel=berg%vvel+(dt*ay1)
 
-    !update uvel_old and vvel_old for damping interaction with other elements
-    if (bergs%force_convergence) then
-      do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
-        berg=>bergs%list(grdi,grdj)%first
-        do while (associated(berg)) ! loop over all bergs
-          if (berg%static_berg .lt. 0.5) then
-            berg%uvel_old=berg%uvel_prev; berg%vvel_old=berg%vvel_prev
+              !The final velocity from the previous cycle, which can be used
+              !during post-processing to calculate kinetic energy and momentum
+              berg%uvel_prev=berg%uvel    ; berg%vvel_prev=berg%vvel
+            endif
           endif
           berg=>berg%next
-        enddo
+        enddo ! loop over all bergs
       enddo; enddo
-    endif
 
-    if (bergs%force_convergence .and. .not. last_iter) then
-      if (ii>1) then
-        denom=sqrt(usum)+sqrt(usum1)
-        if (denom>0) then
-          normchange=2.0*sqrt(usum2)/denom
-        else
-          normchange=0.0
+      !update uvel_old and vvel_old for damping interaction with other elements
+      if (bergs%force_convergence) then
+        do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+          berg=>bergs%list(grdi,grdj)%first
+          do while (associated(berg)) ! loop over all bergs
+            if (berg%static_berg .lt. 0.5) then
+              berg%uvel_old=berg%uvel_prev; berg%vvel_old=berg%vvel_prev
+            endif
+            berg=>berg%next
+          enddo
+        enddo; enddo
+      endif
+
+      if (bergs%force_convergence .and. (.not. last_iter) .and. had_collision) then
+        if (ii>1) then
+          denom=sqrt(usum)+sqrt(usum1)
+          if (denom>0) then
+            normchange=2.0*sqrt(usum2)/denom
+          else
+            normchange=0.0
+          endif
+          if (normchange<bergs%convergence_tolerance) last_iter=.true.
         endif
-        if (normchange<bergs%convergence_tolerance) last_iter=.true.
+        usum=usum1 !previous norm (squared)
+      else
+        finished=.true.
       endif
-      usum=usum1 !previous norm (squared)
-    else
-      finished=.true.
-    endif
 
-    if (last_iter .and. .not. monitor_energy) finished=.true.
+      if (last_iter .and. .not. monitor_energy) finished=.true.
 
-    usum1=0.0; usum2=0.0
+      usum1=0.0; usum2=0.0
 
-  enddo
+    enddo
 
+    !  print *,'iters',ii
 
-  if (.not. bergs%dem) then
-    call update_bond_angles(bergs)
-    call update_and_break_bonds(bergs)
-  else
-    call break_bonds_dem(bergs)
-  endif
+    if (.not. bergs%dem) then
+      call update_bond_angles(bergs)
+      call update_and_break_bonds(bergs)
+    else
+      if (.not. break_bonds_on_sub_steps) then
+        call break_bonds_dem(bergs)
+      endif
+    endif
 
-  !PART 2: X_0 and V_0, before fast sub-steps
-  !X_0=X_n (no change)
-  !update V_0 on uvel_old and vvel_old
-  !update lat and lon with implicit slow force component
-  do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
-    berg=>bergs%list(grdi,grdj)%first
-    do while (associated(berg)) ! loop over all bergs
-      if (berg%static_berg .lt. 0.5 .and. berg%conglom_id.ne.0) then
-        berg%lat_prev = berg%lat; berg%lon_prev = berg%lon
-        berg%uvel=berg%uvel_prev; berg%vvel=berg%vvel_prev
+    !PART 2: X_0 and V_0, before fast sub-steps
+    !X_0=X_n (no change)
+    !update V_0 on uvel_old and vvel_old
+    !update lat and lon with implicit slow force component
+    do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+      berg=>bergs%list(grdi,grdj)%first
+      do while (associated(berg)) ! loop over all bergs
+        if (berg%static_berg .lt. 0.5 .and. berg%conglom_id.ne.0) then
+          berg%lat_prev = berg%lat; berg%lon_prev = berg%lon
+          berg%uvel=berg%uvel_prev; berg%vvel=berg%vvel_prev
 
-        if (new_mts) then
-          berg%uvel = berg%uvel + dt_2*(berg%axn+berg%bxn)
-          berg%vvel = berg%vvel + dt_2*(berg%ayn+berg%byn)
-        else
-          berg%uvel = berg%uvel + dt_2*berg%axn
-          berg%vvel = berg%vvel + dt_2*berg%ayn
-          berg%lat = berg%lat + 0.5*(dt**2)*berg%byn
-          berg%lon = berg%lon + 0.5*(dt**2)*berg%bxn
-        endif
+          if (new_mts) then
+            berg%uvel = berg%uvel + dt_2*(berg%axn+berg%bxn)
+            berg%vvel = berg%vvel + dt_2*(berg%ayn+berg%byn)
+          else
+            ! TODO: make this work with latlon coords (or just get rid of the depreciated non-new_mts option)
+            if (grd%grid_is_latlon) stop
+            berg%uvel = berg%uvel + dt_2*berg%axn
+            berg%vvel = berg%vvel + dt_2*berg%ayn
+            berg%lat = berg%lat + 0.5*(dt**2)*berg%byn
+            berg%lon = berg%lon + 0.5*(dt**2)*berg%bxn
+          endif
 
-        berg%uvel_old=berg%uvel; berg%vvel_old=berg%vvel
+          berg%uvel_old=berg%uvel; berg%vvel_old=berg%vvel
+
+          if (bergs%force_convergence) then
+            berg%axn=berg%axn_fast; berg%ayn=berg%ayn_fast
+            berg%bxn=berg%bxn_fast; berg%byn=berg%byn_fast
+          endif
 
-        if (bergs%force_convergence) then
-          berg%axn=berg%axn_fast; berg%ayn=berg%ayn_fast
-          berg%bxn=berg%bxn_fast; berg%byn=berg%byn_fast
+          !if (monitor energy): already did energy update in part I
         endif
+        berg=>berg%next
+      enddo
+    enddo; enddo
+
+  else
+    print *,'skipping first outer step'
+    skip_first_outer_mts_step=.false.
+  endif
 
-        !if (monitor energy): already did energy update in part I
-      endif
-      berg=>berg%next
-    enddo
-  enddo; enddo
 
 
   ! PART 3: MTS fast sub-steps (bonded interactions only):
@@ -6982,6 +7638,10 @@ subroutine evolve_icebergs_mts(bergs)
           i=berg%ine      ;   j=berg%jne
           xi=berg%xi      ;   yj=berg%yj
 
+          ! if (latn>50.e3 .or. latn<10.e3 .or. lonn > 45.e3) then
+          !   print *,'id,lat,lon',berg%id,latn,lonn
+          ! endif
+
           if (new_mts) then
             axn = axn+bxn; ayn=ayn+byn
           endif
@@ -6995,13 +7655,42 @@ subroutine evolve_icebergs_mts(bergs)
           if (bergs%explicit_inner_mts) then
             call accel_explicit_inner_mts(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, &
               ax1, ay1, axn, ayn, save_bond_energy)
-              bxn=0.; byn=0.
+            bxn=0.; byn=0.
+
+            if (short_step_mts_grounding) then
+              D=(bergs%rho_bergs/rho_seawater)*berg%thickness ! draught (keel depth)
+              if (bergs%h_to_init_grounding>0.0) then
+                groundfrac=1.0-(berg%od-D)/bergs%h_to_init_grounding
+                groundfrac=max(groundfrac,0.0); groundfrac=min(groundfrac,1.0)
+              else
+                if (D>berg%od) then
+                  groundfrac=1.0
+                else
+                  groundfrac=0.0
+                endif
+              endif
+              if (groundfrac>0.0) then
+                if (bergs%constant_interaction_LW) then
+                  ! mass according to constant length and width here, just for interactions
+                  MM=bergs%constant_length*bergs%constant_width*berg%thickness*bergs%rho_bergs
+                  AA=bergs%constant_width*bergs%constant_length
+                else
+                  MM=berg%mass
+                  AA=berg%length*berg%width
+                endif
+                gdrag=-bergs%cdrag_grounding*groundfrac*AA/MM
+              else
+                gdrag=0.
+              endif
+              axn=axn+uvel1*gdrag; ayn=ayn+vvel1*gdrag
+              ax1=0.5*axn; ay1=0.5*ayn
+            endif
+
           else
             call accel_mts(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, &
               ax1, ay1, axn, ayn, bxn, byn, save_bond_energy)
           endif
 
-
           ! Solving for the new velocity (Stern et al 2017, Eqn B5)
           on_tangential_plane=.false.
           if ((berg%lat>89.) .and. (bergs%grd%grid_is_latlon)) on_tangential_plane=.true.
@@ -7087,8 +7776,58 @@ subroutine evolve_icebergs_mts(bergs)
         if (berg%static_berg .lt. 0.5 .and. berg%conglom_id.ne.0) then
           berg%uvel_old=berg%uvel; berg%vvel_old=berg%vvel
 
+          if (bergs%use_grounding_torque) then
+            !torque from grounding drag
+            !start to feel grounded with draught of bergs%h_to_init_grounding meters of the sea floor topography
+            !at groundfrac=0, apply no grounding force. at groundfrac=1, apply max grounding force
+            D=(bergs%rho_bergs/rho_seawater)*berg%thickness ! draught (keel depth)
+            if (bergs%h_to_init_grounding>0.0) then
+              groundfrac=1.0-(berg%od-D)/bergs%h_to_init_grounding
+              groundfrac=max(groundfrac,0.0); groundfrac=min(groundfrac,1.0)
+            else
+              if (D>berg%od) then
+                groundfrac=1.0
+              else
+                groundfrac=0.0
+              endif
+            endif
+            if (groundfrac>0.0) then
+              if (bergs%constant_interaction_LW) then
+                ! mass according to constant length and width here, just for interactions
+                MM=bergs%constant_length*bergs%constant_width*berg%thickness*bergs%rho_bergs
+                if (bergs%hexagonal_icebergs) then
+                  R1=sqrt(bergs%constant_length*bergs%constant_width/(2.*sqrt(3.)))
+                else !square packing
+                  if (bergs%iceberg_bonds_on) then
+                    R1=0.5*sqrt(bergs%constant_length*bergs%constant_width)
+                  else
+                    R1=sqrt(bergs%constant_length*bergs%constant_width/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
+                  endif
+                endif
+              else
+                MM=berg%mass
+                if (bergs%hexagonal_icebergs) then
+                  R1=sqrt(berg%length*berg%width/(2.*sqrt(3.)))
+                else !square packing
+                  if (bergs%iceberg_bonds_on) then
+                    R1=0.5*sqrt(berg%length*berg%width)
+                  else
+                    R1=sqrt(berg%length*berg%width/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
+                  endif
+                endif
+              endif
+              gdrag=-bergs%cdrag_grounding*groundfrac*pi*(R1**2.)/MM
+            else
+              gdrag=0.
+            endif
+          else
+            gdrag=0.
+          endif
+
           if (bergs%dem) then
-            berg%ang_vel=berg%ang_vel+dt*berg%ang_accel
+            berg%ang_vel=berg%ang_vel+dt*berg%ang_accel !explicit
+            !implicit (add grounding drag):
+            berg%ang_vel=berg%ang_vel/(1.-gdrag*dt)
             berg%rot=berg%rot+dt*berg%ang_vel
           endif
 
@@ -7100,13 +7839,13 @@ subroutine evolve_icebergs_mts(bergs)
         berg=>berg%next
       enddo ! loop over all bergs
     enddo; enddo ! update 'old' velocities
+
+    if (break_bonds_on_sub_steps) call break_bonds_dem(bergs)
   enddo ! loop over sub-steps
 
   !reset interactive_forces
   bergs%only_interactive_forces=only_interactive_forces
 
-  !call update_and_break_bonds(bergs)
-
   !update indices
   do grdj = grd%jsc,grd%jec ; do grdi = grd%isc,grd%iec
     !no reason to worry about halo/conglomerate bergs here
@@ -7129,7 +7868,7 @@ subroutine evolve_icebergs_mts(bergs)
     enddo ! loop over all bergs
   enddo; enddo ! update 'old' velocities
 
-
+  no_frac_first_ts=.false.
   ! for testing:
   ! maxii=ii; minii=ii
   ! call mpp_max(maxii); call mpp_min(minii); call mpp_max(maxjj); call mpp_min(minjj)
@@ -8359,8 +9098,8 @@ subroutine icebergs_end(bergs)
   call move_all_trajectories(bergs, delete_bergs=.true.)
 
   if (.not. bergs%ignore_traj) then
-    call write_trajectory(bergs%trajectories, bergs%save_short_traj, bergs%save_fl_traj, bergs%fl_r)
-    if (save_bond_traj) call write_bond_trajectory(bergs%bond_trajectories)
+    call write_trajectory(bergs%trajectories, bergs%save_short_traj, bergs%save_fl_traj, bergs%fl_r, bergs%traj_name)
+    if (save_bond_traj) call write_bond_trajectory(bergs%bond_trajectories, bergs%bond_traj_name)
   endif
 
   deallocate(bergs%grd%lon)
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 193fcb8..9569c3b 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -38,10 +38,10 @@ module ice_bergs_framework
 logical :: old_bug_rotated_weights=.false. !< Skip the rotation of off-center weights for rotated halo updates
 logical :: make_calving_reproduce=.false. !< Make the calving.res.nc file reproduce across pe count changes.
 logical :: old_bug_bilin=.true. !< If true, uses the inverted bilinear function (use False to get correct answer)
-character(len=10) :: restart_input_dir = 'INPUT/' !< Directory to look for restart files
+character(len=20) :: restart_input_dir = 'INPUT/' !< Directory to look for restart files
 integer, parameter :: delta_buf=25 !< Size by which to increment buffers
 real, parameter :: pi_180=pi/180. !< Converts degrees to radians
-real, parameter :: Rearth=6360000. !< Radius of earth (m)
+real :: Rearth=6360000. !< Radius of earth (m)
 logical :: fix_restart_dates=.true. !< After a restart, check that bergs were created before the current model date
 logical :: do_unit_tests=.false. !< Conduct some unit tests
 logical :: force_all_pes_traj=.false. !< Force all pes write trajectory files regardless of io_layout
@@ -52,8 +52,20 @@ module ice_bergs_framework
 logical :: monitor_energy=.false. !<monitors energies: elastic (spring+collision), external, dissipated, fracture
 logical :: iceberg_bonds_on=.False. ! True=Allow icebergs to have bonds, False=don't allow.
 logical :: dem=.false. !< If T, run in DEM-mode with angular terms, variable stiffness, etc
+logical :: power_ground=.false.
+logical :: short_step_mts_grounding=.false.
+logical :: radius_based_drag=.false. !if T, hex bergs, and dem, 2r is used as the area of the vert face for drag/wave forces
+logical :: A68_test=.false. !< If True, grounding will not be allowed west of 38 deg W nor North of 54.85 S
+real :: A68_xdisp=0.
+real :: A68_ydisp=0.
+logical :: rev_mind=.false.
+logical :: add_curl_to_torque=.false. !include torque from the curl of ocean and atmospheric velocities (DEM-mode only)
 character(len=11) :: fracture_criterion='none' !<'energy','stress','strain_rate','strain',or 'none'
 logical :: use_damage=.false. !< Damage on bonds. Can evolve and serve as fracture criterion, or just to represent weaker bond
+logical :: orig_dem_moment_of_inertia=.false.
+logical :: break_bonds_on_sub_steps=.false.
+logical :: skip_first_outer_mts_step=.false.
+logical :: no_frac_first_ts=.false.
 
 !Public params !Niki: write a subroutine to expose these
 public nclasses,buffer_width,buffer_width_traj,buffer_width_bond_traj
@@ -61,7 +73,9 @@ module ice_bergs_framework
 public ignore_ij_restart, use_slow_find,generate_test_icebergs,old_bug_rotated_weights,budget
 public orig_read, force_all_pes_traj
 public mts,new_mts,save_bond_traj,ewsame,monitor_energy,iceberg_bonds_on
-public dem, fracture_criterion
+public dem, add_curl_to_torque, fracture_criterion, orig_dem_moment_of_inertia
+public power_ground, short_step_mts_grounding, radius_based_drag
+public A68_test, A68_xdisp, A68_ydisp
 
 !Public types
 public icebergs_gridded, xyt, iceberg, icebergs, buffer, bond, bond_xyt
@@ -81,7 +95,7 @@ module ice_bergs_framework
 public sum_mass, sum_heat, bilin, yearday, bergs_chksum, list_chksum, count_bergs_in_list
 public checksum_gridded
 public grd_chksum2,grd_chksum3
-public fix_restart_dates, offset_berg_dates
+public Rearth, fix_restart_dates, offset_berg_dates
 public move_berg_between_cells
 public find_individual_iceberg
 public monitor_a_berg
@@ -96,6 +110,7 @@ module ice_bergs_framework
 public energy_tests_init,dem_tests_init
 public init_dem_params
 public set_constant_interaction_length_and_width,use_damage,damage_test_1_init
+public break_bonds_on_sub_steps, skip_first_outer_mts_step, no_frac_first_ts
 
 !> Container for gridded fields
 type :: icebergs_gridded
@@ -285,6 +300,8 @@ module ice_bergs_framework
   real, allocatable :: ang_vel !< Angular velocity
   real, allocatable :: ang_accel !< Angular acceleration
   real, allocatable :: rot !< Accumulated rotation
+  real, allocatable :: curl_o !< curl of ocean velocity
+  real, allocatable :: curl_a !< curl of atmospheric velocity
 end type xyt
 
 !> An iceberg object, used as a link in a linked list
@@ -373,6 +390,8 @@ module ice_bergs_framework
   real, allocatable :: ang_vel !< Angular velocity
   real, allocatable :: ang_accel !< Angular acceleration
   real, allocatable :: rot !< Accumulated rotation
+  real, allocatable :: curl_o !< curl of ocean velocity
+  real, allocatable :: curl_a !< curl of atmospheric velocity
 end type iceberg
 
 !> A bond object connecting two bergs, used as a link in a linked list
@@ -390,7 +409,8 @@ module ice_bergs_framework
   !in which case the following correspond to only the most recent timestep and units are s^(-1)
   real, allocatable :: damage
   real, allocatable :: rotation !radians
-  real, allocatable :: rel_rotation !<rotation relative to the mean of all bonds for a berg
+  real, allocatable :: rel_rotation !<non-dem mode: rotation relative to the mean of all bonds for a berg
+  !!dem-mode: relative rotation between two bonded particles (radians)
   real, allocatable :: n_frac_var !<normal strain, stress, or spring energy
   real, allocatable :: n_strain_rate !<for fracture_criterion=='strain_rate' only
   real, allocatable :: spring_pe
@@ -537,6 +557,8 @@ module ice_bergs_framework
   logical :: only_interactive_forces=.False. !< Icebergs only feel interactive forces, and not ocean, wind...
   logical :: halo_debugging=.False. !< Use for debugging halos (remove when its working)
   logical :: save_short_traj=.True. !< True saves only lon,lat,time,id in iceberg_trajectory.nc
+  character(len=70) :: traj_name='iceberg_trajectories.nc'
+  character(len=70) :: bond_traj_name='bond_trajectories.nc'
   logical :: save_fl_traj=.True. ! True saves short traj, plus masses and footloose parameters in iceberg_trajectory.nc
   real :: save_all_traj_year=huge(0.0) ! Year at which all trajectories (for all berg areas) are saved
   logical :: save_nonfl_traj_by_class=.false. ! Save non-footloose trajectories based on initial mass class
@@ -557,6 +579,7 @@ module ice_bergs_framework
   real :: length_for_manually_initialize_bonds=1000.0 !< If manually initialing bonds, only  bond if dist between particles is < this length -Added by Alex
   logical :: manually_initialize_bonds_from_radii=.false. !< If manually initialing bonds, form bonds if dist between particles is < 1.25x the smaller radii-Alex
   real :: speed_limit=0. !< CFL speed limit for a berg [m/s]
+  logical :: tau_is_velocity=.false. !< If True, then wind stress input is actually velocity (m/s)
   real :: tau_calving=0. !< Time scale for smoothing out calving field (years)
   real :: tip_parameter=0. !< If non-zero, overrides iceberg rolling critical ratio (use zero to get parameter directly from ice and seawater densities)
   real :: grounding_fraction=0. !< Fraction of water column depth at which grounding occurs
@@ -615,7 +638,9 @@ module ice_bergs_framework
   real :: convergence_tolerance=1.e-8 !tolerance for the MTS convergence scheme
   ! DEM-mode parameters
   logical :: dem=.false. !if T, run in DEM-mode with angular terms, variable stiffness, etc
+  logical :: use_grounding_torque=.false.
   logical :: ignore_tangential_force=.false.
+  real :: dem_K_damp !damping parameter
   real :: poisson=0.3 ! Poisson's ratio
   real :: dem_spring_coef=0.
   real :: dem_damping_coef=0.1
@@ -624,12 +649,16 @@ module ice_bergs_framework
   logical :: uniaxial_test=.false. !adds a tensile stress to the east-most berg element
   real :: dem_tests_start_lon !starting lon of west-most berg element for uniaxial/dem tests
   real :: dem_tests_end_lon !starting lon of east-most berg element for uniaxial/dem tests
+  logical :: add_curl_to_torque=.false. !include torque from the curl of ocean and atmospheric velocities
   ! Element interactions
   logical :: constant_interaction_LW=.false. !< Use a constant element length & width during berg interactions
   real :: constant_length=0.!< If constant_interaction_LW, the constant length. If 0, will be set to max initial length
   real :: constant_width=0. !< If constant_interaction_LW, the constant width.  If 0, will be set to max initial width
+  real :: constant_area
+  real :: constant_radius
+  real :: ocean_drag_scale=1. !< Scaling factor for the ocean drag coefficients
   logical :: use_spring_for_land_contact=.false. !< Treat contact with masked (land) cells like contact with a static berg
-  ! Footloose calving parameters [England et al (2020) Modeling the breakup of tabular icebergs. Sci. Adv.]
+  ! Footloose calving parameters
   logical :: fl_use_poisson_distribution=.true. !< fl_r is (T) mean of Poisson distribution to determine k, or (F) k=fl_r
   logical :: fl_use_perimeter=.false. !< scale number of footloose bergs to calve by perimeter of the parent berg
   real :: fl_youngs=1.e8 !< Young's modulus for footloose calculations (Pa)
@@ -721,7 +750,7 @@ subroutine ice_bergs_framework_init(bergs, &
 integer :: halo=4 ! Width of halo region
 real :: traj_area_thres=0. ! Threshold for berg area (km^2) that must be exceeded to save a non-bonded berg trajectory
 real :: traj_area_thres_sntbc=0. !< Threshold for berg area (km^2) for saving trajectory when using save_nonfl_traj_by_class
-real :: traj_area_thres_fl=huge(0.0) ! Threshold for berg area (km^2) that must be exceeded to save a non-bonded FL berg trajectory
+real :: traj_area_thres_fl=1.e9 ! Threshold for berg area (km^2) that must be exceeded to save a non-bonded FL berg trajectory
 real :: traj_sample_hrs=24. ! Period between sampling of position for trajectory storage
 real :: traj_write_hrs=480. ! Period between writing sampled trajectories to disk
 real :: verbose_hrs=24. ! Period between verbose messages
@@ -762,6 +791,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: length_for_manually_initialize_bonds=1000.0 ! if manually init bonds, only  bond if dist between particles is .lt. this length - Alex
 logical :: manually_initialize_bonds_from_radii=.false. ! if manually init bonds, form bonds if dist between particles is < 1.25x the smaller radii - Alex
 real :: speed_limit=0. ! CFL speed limit for a berg
+logical :: tau_is_velocity=.false. !< If True, then wind stress input is actually velocity (m/s)
 real :: tau_calving=0. ! Time scale for smoothing out calving field (years)
 real :: tip_parameter=0. ! Parameter to override iceberg rolling critical ratio (use zero to get parameter directly from ice and seawater densities
 real :: grounding_fraction=0. ! Fraction of water column depth at which grounding occurs
@@ -794,6 +824,8 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: only_interactive_forces=.False. ! Icebergs only feel interactive forces, and not ocean, wind...
 logical :: halo_debugging=.False. ! Use for debugging halos (remove when its working)
 logical :: save_short_traj=.True. ! True saves only lon,lat,time,id in iceberg_trajectory.nc
+character(len=70) :: traj_name='iceberg_trajectories.nc'
+character(len=70) :: bond_traj_name='bond_trajectories.nc'
 logical :: save_fl_traj=.True. ! True saves short traj, plus masses and footloose parameters in iceberg_trajectory.nc
 real :: save_all_traj_year=huge(0.0) ! Year at which all trajectories (for all berg areas) are saved
 logical :: save_nonfl_traj_by_class=.false. ! Save non-footloose trajectories based on initial mass class
@@ -832,6 +864,7 @@ subroutine ice_bergs_framework_init(bergs, &
 integer(kind=8) :: debug_iceberg_with_id = -1 ! If positive, monitors a berg with this id
 ! DEM-mode parameters
 !logical :: dem=.false. !if T, run in DEM-mode with angular terms, variable stiffness, etc
+logical :: use_grounding_torque=.false.
 logical :: ignore_tangential_force=.false.
 real :: poisson=0.3 ! Poisson's ratio
 real :: dem_spring_coef=0.
@@ -842,6 +875,7 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: constant_interaction_LW=.false. ! Always use the initial, globally constant, element length & width during berg interactions
 real :: constant_length=0. ! If constant_interaction_LW, the constant length used. If zero in the nml, will be set to max initial L
 real :: constant_width=0. ! If constant_interaction_LW, the constant width used. If zero in the nml, will be set to max initial W
+real :: ocean_drag_scale=1. !< Scaling factor for the ocean drag coefficients
 logical :: use_spring_for_land_contact=.false. ! Treat contact with masked (land) cells like contact with a static berg
 ! Footloose calving parameters [England et al (2020) Modeling the breakup of tabular icebergs. Sci. Adv.]
 logical :: fl_use_poisson_distribution=.true. ! fl_r is (T) mean of Poisson distribution to determine k, or (F) k=fl_r
@@ -862,13 +896,14 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: fl_bits_scale_w=0.9 ! For determining dimensions of FL bits berg; FL_bits width     = fl_bits_scale_w * l_b
 real :: fl_bits_scale_t=0.9 ! For determining dimensions of FL bits berg; FL_bits thickness = fl_bits_scale_t * T
 
-namelist /icebergs_nml/ verbose, budget, halo,  traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,&
+
+namelist /icebergs_nml/ verbose, budget, halo,  traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,traj_name,bond_traj_name,&
          traj_area_thres, Static_icebergs,distribution, mass_scaling, initial_thickness, verbose_hrs, spring_coef,bond_coef,&
          radial_damping_coef, tangental_damping_coef, only_interactive_forces, rho_bergs, LoW_ratio, debug, really_debug,&
          use_operator_splitting, bergy_bit_erosion_fraction, iceberg_bonds_on, manually_initialize_bonds,&
          ignore_missing_restart_bergs,  parallel_reprod, use_slow_find, sicn_shift, add_weight_to_ocean, passive_mode,&
          ignore_ij_restart, use_new_predictive_corrective, halo_debugging, hexagonal_icebergs, time_average_weight,&
-         generate_test_icebergs, speed_limit, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, interactive_icebergs_on,&
+         generate_test_icebergs, speed_limit, Rearth, fix_restart_dates, use_roundoff_fix, Runge_not_Verlet, interactive_icebergs_on,&
          scale_damping_by_pmag, critical_interaction_damping_on, tang_crit_int_damp_on, require_restart,&
          old_bug_rotated_weights, make_calving_reproduce,restart_input_dir, orig_read, old_bug_bilin,do_unit_tests,&
          grounding_fraction, input_freq_distribution, force_all_pes_traj,allow_bergs_to_roll,set_melt_rates_to_zero,lat_ref,&
@@ -890,7 +925,10 @@ subroutine ice_bergs_framework_init(bergs, &
          initial_mass_n, distribution_n, mass_scaling_n, initial_thickness_n, fl_use_l_scale, fl_l_scale,&
          fl_l_scale_erosion_only, fl_youngs, fl_strength,  save_all_traj_year, save_nonfl_traj_by_class,&
          save_traj_by_class_start_mass_thres_n, save_traj_by_class_start_mass_thres_s,traj_area_thres_sntbc,&
-         traj_area_thres_fl
+         traj_area_thres_fl,tau_is_velocity, add_curl_to_torque,ocean_drag_scale, A68_test, &
+         A68_xdisp,A68_ydisp,&
+         orig_dem_moment_of_inertia, break_bonds_on_sub_steps, skip_first_outer_mts_step, rev_mind, &
+         no_frac_first_ts, use_grounding_torque, power_ground, short_step_mts_grounding, radius_based_drag
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -1345,7 +1383,11 @@ subroutine ice_bergs_framework_init(bergs, &
 if (dem) then
   buffer_width=buffer_width+3+(max_bonds*4)
   buffer_width_traj=buffer_width_traj+3
-  buffer_width_bond_traj=buffer_width_bond_traj+4
+  buffer_width_bond_traj=buffer_width_bond_traj+4+1
+  if (add_curl_to_torque) then
+    buffer_width=buffer_width+1 !2
+    buffer_width_traj=buffer_width_traj+1 !2
+  endif
 elseif (fracture_criterion .ne. 'none') then
   buffer_width=buffer_width+1+(max_bonds*3)
   buffer_width_traj=buffer_width_traj+1
@@ -1410,6 +1452,8 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%traj_sample_hrs=traj_sample_hrs
   bergs%traj_write_hrs=traj_write_hrs
   bergs%save_short_traj=save_short_traj
+  bergs%traj_name=traj_name
+  bergs%bond_traj_name=bond_traj_name
   bergs%save_fl_traj=save_fl_traj
   bergs%save_all_traj_year=save_all_traj_year
   bergs%save_nonfl_traj_by_class=save_nonfl_traj_by_class
@@ -1444,6 +1488,7 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%passive_mode=passive_mode
   bergs%time_average_weight=time_average_weight
   bergs%speed_limit=speed_limit
+  bergs%tau_is_velocity=tau_is_velocity
   bergs%tau_calving=tau_calving
   bergs%tip_parameter=tip_parameter
   bergs%use_updated_rolling_scheme=use_updated_rolling_scheme  !Alon
@@ -1506,16 +1551,32 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%convergence_tolerance=convergence_tolerance
   ! DEM-mode parameters
   bergs%dem=dem
+  bergs%use_grounding_torque=use_grounding_torque
   bergs%ignore_tangential_force=ignore_tangential_force
   if (bergs%dem) bergs%explicit_inner_mts=.true.
   bergs%poisson=poisson
   bergs%dem_spring_coef=dem_spring_coef
+  bergs%dem_K_damp=2.*bergs%dem_spring_coef/(3.*(1.-bergs%poisson**2)) !damping factor
   bergs%dem_damping_coef=dem_damping_coef
   bergs%dem_beam_test=dem_beam_test
   bergs%constant_interaction_LW=constant_interaction_LW
   bergs%constant_length=constant_length
   bergs%constant_width=constant_width
+  if (bergs%constant_interaction_LW) then
+    bergs%constant_area=bergs%constant_length*bergs%constant_width
+    if (bergs%hexagonal_icebergs) then
+      bergs%constant_radius=sqrt(bergs%constant_area/(2.*sqrt(3.)))
+    else
+      if (bergs%iceberg_bonds_on) then
+        bergs%constant_radius=0.5*sqrt(bergs%constant_area)
+      else
+        bergs%constant_radius=sqrt(bergs%constant_area/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
+      endif
+    endif
+  endif
+  bergs%ocean_drag_scale=ocean_drag_scale
   bergs%dem_shear_for_frac_only=dem_shear_for_frac_only
+  bergs%add_curl_to_torque=add_curl_to_torque
   ! Footloose calving parameters
   bergs%fl_use_poisson_distribution=fl_use_poisson_distribution
   bergs%fl_use_perimeter=fl_use_perimeter
@@ -3380,6 +3441,10 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
     call push_buffer_value(buff%data(:,n), counter, berg%ang_vel)
     call push_buffer_value(buff%data(:,n), counter, berg%ang_accel)
     call push_buffer_value(buff%data(:,n), counter, berg%rot)
+    if (add_curl_to_torque) then
+      call push_buffer_value(buff%data(:,n), counter, berg%curl_o)
+      !call push_buffer_value(buff%data(:,n), counter, berg%curl_a)
+    endif
   elseif (fracture_criterion .ne. 'none') then
     call push_buffer_value(buff%data(:,n), counter, berg%accum_bond_rotation)
   endif
@@ -3413,6 +3478,7 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
           call push_buffer_value(buff%data(:,n), counter, current_bond%tangd2)
           call push_buffer_value(buff%data(:,n), counter, current_bond%nstress)
           call push_buffer_value(buff%data(:,n), counter, current_bond%sstress)
+          call push_buffer_value(buff%data(:,n), counter, current_bond%rel_rotation)
         elseif (fracture_criterion .ne. 'none') then
           call push_buffer_value(buff%data(:,n), counter, current_bond%rotation)
           call push_buffer_value(buff%data(:,n), counter, current_bond%rel_rotation)
@@ -3608,6 +3674,9 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
 
   if (dem) then
     allocate(localberg%ang_vel,localberg%ang_accel,localberg%rot)
+    if (add_curl_to_torque) then
+      allocate(localberg%curl_o) !,localberg%curl_a)
+    endif
   elseif (fracture_criterion .ne. 'none') then
     allocate(localberg%accum_bond_rotation)
   endif
@@ -3693,6 +3762,10 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
     call pull_buffer_value(buff%data(:,n), counter, localberg%ang_vel)
     call pull_buffer_value(buff%data(:,n), counter, localberg%ang_accel)
     call pull_buffer_value(buff%data(:,n), counter, localberg%rot)
+    if (add_curl_to_torque) then
+      call pull_buffer_value(buff%data(:,n), counter, localberg%curl_o)
+      !call pull_buffer_value(buff%data(:,n), counter, localberg%curl_a)
+    endif
   elseif (fracture_criterion .ne. 'none') then
     call pull_buffer_value(buff%data(:,n), counter, localberg%accum_bond_rotation)
   endif
@@ -3832,6 +3905,7 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
           call pull_buffer_value(buff%data(:,n), counter, current_bond%tangd2)
           call pull_buffer_value(buff%data(:,n), counter, current_bond%nstress)
           call pull_buffer_value(buff%data(:,n), counter, current_bond%sstress)
+          call pull_buffer_value(buff%data(:,n), counter, current_bond%rel_rotation)
         elseif (fracture_criterion .ne. 'none') then
           call pull_buffer_value(buff%data(:,n), counter, current_bond%rotation)
           call pull_buffer_value(buff%data(:,n), counter, current_bond%rel_rotation)
@@ -3987,6 +4061,10 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj, save_fl_traj,
       call push_buffer_value(buff%data(:,n), counter, traj%ang_vel)
       call push_buffer_value(buff%data(:,n), counter, traj%ang_accel)
       call push_buffer_value(buff%data(:,n), counter, traj%rot)
+      if (add_curl_to_torque) then
+        call push_buffer_value(buff%data(:,n), counter, traj%curl_o)
+        !call push_buffer_value(buff%data(:,n), counter, traj%curl_a)
+      endif
     elseif (fracture_criterion .ne. 'none') then
       call push_buffer_value(buff%data(:,n), counter, traj%accum_bond_rotation)
     endif
@@ -4024,6 +4102,7 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj, save_fl_tra
 
   if (dem) then
     allocate(traj%ang_vel,traj%ang_accel,traj%rot)
+    if (add_curl_to_torque) allocate(traj%curl_o) !,traj%curl_a)
   elseif (fracture_criterion .ne. 'none') then
     allocate(traj%accum_bond_rotation)
   endif
@@ -4107,6 +4186,10 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj, save_fl_tra
       call pull_buffer_value(buff%data(:,n), counter, traj%ang_vel)
       call pull_buffer_value(buff%data(:,n), counter, traj%ang_accel)
       call pull_buffer_value(buff%data(:,n), counter, traj%rot)
+      if (add_curl_to_torque) then
+        call pull_buffer_value(buff%data(:,n), counter, traj%curl_o)
+        !call pull_buffer_value(buff%data(:,n), counter, traj%curl_a)
+      endif
     elseif (fracture_criterion .ne. 'none') then
       call pull_buffer_value(buff%data(:,n), counter, traj%accum_bond_rotation)
     endif
@@ -4162,6 +4245,7 @@ subroutine pack_bond_traj_into_buffer2(bond_traj, buff, n)
     call push_buffer_value(buff%data(:,n),counter,bond_traj%tangd2)
     call push_buffer_value(buff%data(:,n),counter,bond_traj%nstress)
     call push_buffer_value(buff%data(:,n),counter,bond_traj%sstress)
+    call push_buffer_value(buff%data(:,n),counter,bond_traj%rel_rotation)
   elseif (fracture_criterion.ne.'none') then
     call push_buffer_value(buff%data(:,n),counter,bond_traj%rotation)
     call push_buffer_value(buff%data(:,n),counter,bond_traj%rel_rotation)
@@ -4193,7 +4277,7 @@ subroutine unpack_bond_traj_from_buffer2(first, buff, n)
     allocate(bond_traj%Ee,bond_traj%Ed,bond_traj%axn_fast,bond_traj%ayn_fast,bond_traj%bxn_fast,bond_traj%byn_fast)
   endif
   if (dem) then
-    allocate(bond_traj%tangd1,bond_traj%tangd2,bond_traj%nstress,bond_traj%sstress)
+    allocate(bond_traj%tangd1,bond_traj%tangd2,bond_traj%nstress,bond_traj%sstress,bond_traj%rel_rotation)
   elseif (fracture_criterion.ne.'none') then
     allocate(bond_traj%rotation,bond_traj%rel_rotation,bond_traj%n_frac_var)
     if (fracture_criterion.eq.'strain_rate') then
@@ -4236,6 +4320,7 @@ subroutine unpack_bond_traj_from_buffer2(first, buff, n)
     call pull_buffer_value(buff%data(:,n),counter,bond_traj%tangd2)
     call pull_buffer_value(buff%data(:,n),counter,bond_traj%nstress)
     call pull_buffer_value(buff%data(:,n),counter,bond_traj%sstress)
+    call pull_buffer_value(buff%data(:,n),counter,bond_traj%rel_rotation)
   elseif (fracture_criterion.ne.'none') then
     call pull_buffer_value(buff%data(:,n),counter,bond_traj%rotation)
     call pull_buffer_value(buff%data(:,n),counter,bond_traj%rel_rotation)
@@ -4718,6 +4803,7 @@ subroutine create_iceberg(berg, bergvals)
   endif
   if (dem) then
     allocate(berg%ang_vel,berg%ang_accel,berg%rot)
+    if (add_curl_to_torque) allocate(berg%curl_o) !,berg%curl_a)
   elseif (fracture_criterion .ne. 'none') then
     allocate(berg%accum_bond_rotation)
   endif
@@ -4978,6 +5064,17 @@ subroutine set_constant_interaction_length_and_width(bergs)
   bergs%constant_length = l_sum/elem_sum
   bergs%constant_width  = w_sum/elem_sum
 
+  bergs%constant_area=bergs%constant_length*bergs%constant_width
+  if (bergs%hexagonal_icebergs) then
+    bergs%constant_radius=sqrt(bergs%constant_area/(2.*sqrt(3.)))
+  else
+    if (bergs%iceberg_bonds_on) then
+      bergs%constant_radius=0.5*sqrt(bergs%constant_area)
+    else
+      bergs%constant_radius=sqrt(bergs%constant_area/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
+    endif
+  endif
+
 end subroutine set_constant_interaction_length_and_width
 
 !> Initialization for the DEM beam tests
@@ -5037,7 +5134,7 @@ subroutine init_dem_params(bergs)
   do grdj=grd%jsd,grd%jed ; do grdi=grd%isd,grd%ied !loop over all cells
     this=>bergs%list(grdi,grdj)%first
     do while (associated(this)) ! loop over all bergs in cell
-      this%ang_vel=0.
+      !this%ang_vel=0.
       this%ang_accel=0.
       this%rot=0.
       this=>this%next
@@ -5304,6 +5401,11 @@ subroutine break_bonds_dem(bergs)
   integer :: grdi, grdj
   type(bond) , pointer :: current_bond,other_bond,kick_the_bucket
   real :: frac_thres_n,frac_thres_t
+  real :: Rsig,Rtau,frac
+
+  if (no_frac_first_ts) then
+    return
+  endif
 
   frac_thres_n=bergs%frac_thres_n; frac_thres_t=bergs%frac_thres_t
 
@@ -5324,15 +5426,33 @@ subroutine break_bonds_dem(bergs)
 
         if (current_bond%other_id.ne.-1) then
 
-          if (current_bond%nstress>frac_thres_n .or. current_bond%sstress>frac_thres_t) then
-            if (current_bond%nstress>frac_thres_n .and. current_bond%sstress>frac_thres_t) then
-              print *,'normal and shear stress break',this%id,current_bond%nstress,current_bond%sstress
-            elseif (current_bond%nstress>frac_thres_n) then
-              print *,'normal stress break',this%id,current_bond%nstress,current_bond%sstress
-            else
-              print *,'shear stress break',this%id,current_bond%nstress,current_bond%sstress
+          if (bergs%fracture_criterion=='computed') then
+            Rsig=current_bond%nstress/frac_thres_n
+            Rtau=current_bond%sstress/frac_thres_t
+            frac=0.5*Rsig+sqrt((0.5*Rsig)**2. + Rtau**2.)
+            if (frac > 1.) then
+              print *,'BREAK',this%lat,frac,Rsig,Rtau
+              current_bond%other_id=-1
+            endif
+          elseif (bergs%fracture_criterion=='computed_s') then
+            Rsig=current_bond%nstress/bergs%frac_thres_n
+            Rtau=current_bond%sstress/bergs%frac_thres_t
+            frac=sqrt(Rsig**2. + Rtau**2.)
+            if (frac > 1.) then
+              print *,'BREAK',this%lat,frac,Rsig,Rtau
+              current_bond%other_id=-1
             endif
-            current_bond%other_id=-1
+          else
+              if (current_bond%nstress>frac_thres_n .or. current_bond%sstress>frac_thres_t) then
+                if (current_bond%nstress>frac_thres_n .and. current_bond%sstress>frac_thres_t) then
+                  print *,'T and S break',this%lat,current_bond%nstress,current_bond%sstress
+                elseif (current_bond%nstress>frac_thres_n) then
+                  print *,'TENSILE break',this%lat,current_bond%nstress,current_bond%sstress
+                else
+                  print *,'SHEAR   break',this%lat,current_bond%nstress,current_bond%sstress
+                endif
+                current_bond%other_id=-1
+              endif
           endif
 
           if (current_bond%other_id.eq.-1) then
@@ -5341,7 +5461,28 @@ subroutine break_bonds_dem(bergs)
               !mark matching bond on other_berg
               other_bond=>other_berg%first_bond
               do while (associated(other_bond)) ! loop over all bonds
-                if (other_bond%other_id.eq.this%id) other_bond%other_id=-1
+                if (other_bond%other_id.eq.this%id) then
+                  other_bond%other_id=-1
+                  if (bergs%fracture_criterion=='computed') then
+                    Rsig=other_bond%nstress/frac_thres_n
+                    Rtau=other_bond%sstress/frac_thres_t
+                    frac=0.5*Rsig+sqrt((0.5*Rsig)**2. + Rtau**2.)
+                    if (frac <= 1.) then
+                      print *,'Other bond did not fracture!'
+                    endif
+                  elseif(bergs%fracture_criterion=='computed_s') then
+                    Rsig=current_bond%nstress/bergs%frac_thres_n
+                    Rtau=current_bond%sstress/bergs%frac_thres_t
+                    frac=sqrt(Rsig**2. + Rtau**2.)
+                    if (frac <= 1.) then
+                      print *,'Other bond did not fracture!'
+                    endif
+                  elseif (other_bond%nstress<=frac_thres_n .and. other_bond%sstress<=frac_thres_t) then
+                    print *,'Other bond did not fracture!'
+                    print *,'current and other bond nstress,',current_bond%nstress, other_bond%nstress
+                    print *,'current and other bond sstress,',current_bond%sstress, other_bond%sstress
+                  endif
+                endif
                 other_bond=>other_bond%next_bond
               enddo
             endif
@@ -5429,6 +5570,8 @@ subroutine form_a_bond(berg, other_id, other_berg_ine, other_berg_jne, other_ber
     new_bond%tangd1=0.; new_bond%tangd2=0.
     allocate(new_bond%nstress,new_bond%sstress)
     new_bond%nstress=0.; new_bond%sstress=0.
+    allocate(new_bond%rel_rotation)
+    new_bond%rel_rotation=0.
   elseif (fracture_criterion.ne.'none') then
     allocate(new_bond%rotation,new_bond%rel_rotation,new_bond%n_frac_var)
     new_bond%rotation=0.; new_bond%rel_rotation=0.; new_bond%n_frac_var=0.
@@ -5920,6 +6063,7 @@ subroutine record_posn(bergs)
 
   if (dem) then
     allocate(posn%ang_vel,posn%ang_accel,posn%rot)
+    if (add_curl_to_torque) allocate(posn%curl_o) !,posn%curl_a)
   elseif (fracture_criterion .ne. 'none') then
     allocate(posn%accum_bond_rotation)
   endif
@@ -5930,7 +6074,7 @@ subroutine record_posn(bergs)
       allocate(bond_posn%Ee,bond_posn%Ed,bond_posn%axn_fast,bond_posn%ayn_fast,bond_posn%bxn_fast,bond_posn%byn_fast)
     endif
     if (dem) then
-      allocate(bond_posn%tangd1,bond_posn%tangd2,bond_posn%nstress,bond_posn%sstress)
+      allocate(bond_posn%tangd1,bond_posn%tangd2,bond_posn%nstress,bond_posn%sstress,bond_posn%rel_rotation)
     elseif (fracture_criterion.ne.'none') then
       allocate(bond_posn%rotation,bond_posn%rel_rotation,bond_posn%n_frac_var)
       if (fracture_criterion.eq.'strain_rate') allocate(bond_posn%n_strain_rate)
@@ -6041,6 +6185,10 @@ subroutine record_posn(bergs)
             posn%ang_vel=this%ang_vel
             posn%ang_accel=this%ang_accel
             posn%rot=this%rot
+            if (add_curl_to_torque) then
+              posn%curl_o=this%curl_o
+              !posn%curl_a=this%curl_a
+            endif
           elseif (fracture_criterion .ne. 'none') then
             posn%accum_bond_rotation=this%accum_bond_rotation
           endif
@@ -6063,7 +6211,8 @@ subroutine record_posn(bergs)
 
               dx=(this%lon-other_berg%lon)*dx_dlon; dy=(this%lat-other_berg%lat)*dy_dlat
               n1=dx/this%length; n2=dy/this%length !unit vector
-              bond_posn%lon=this%lon-dx/2;          bond_posn%lat=this%lat-dy/2
+              bond_posn%lon=0.5*(this%lon+other_berg%lon)
+              bond_posn%lat=0.5*(this%lat+other_berg%lat)
               bond_posn%year=bergs%current_year;    bond_posn%day=bergs%current_yearday
               bond_posn%length=current_bond%length;
               bond_posn%n1=n1;                      bond_posn%n2=n2
@@ -6087,6 +6236,7 @@ subroutine record_posn(bergs)
                 bond_posn%tangd2=current_bond%tangd2
                 bond_posn%nstress=current_bond%nstress
                 bond_posn%sstress=current_bond%sstress
+                bond_posn%rel_rotation=current_bond%rel_rotation
               elseif (fracture_criterion.ne.'none') then
                 bond_posn%rotation=current_bond%rotation
                 bond_posn%rel_rotation=current_bond%rel_rotation
@@ -6133,6 +6283,7 @@ subroutine push_posn(trajectory, posn_vals)
 
   if (dem) then
     allocate(new_posn%ang_vel,new_posn%ang_accel,new_posn%rot)
+    if (add_curl_to_torque) allocate(new_posn%curl_o) !,new_posn%curl_a)
   elseif (fracture_criterion .ne. 'none') then
     allocate(new_posn%accum_bond_rotation)
   endif
@@ -6159,7 +6310,7 @@ subroutine push_bond_posn(bond_trajectory, bond_posn_vals)
       new_bond_posn%bxn_fast,new_bond_posn%byn_fast)
   endif
   if (dem) then
-    allocate(new_bond_posn%tangd1,new_bond_posn%tangd2,new_bond_posn%nstress,new_bond_posn%sstress)
+    allocate(new_bond_posn%tangd1,new_bond_posn%tangd2,new_bond_posn%nstress,new_bond_posn%sstress,new_bond_posn%rel_rotation)
   elseif (fracture_criterion.ne.'none') then
     allocate(new_bond_posn%rotation,new_bond_posn%rel_rotation,new_bond_posn%n_frac_var)
     if (fracture_criterion.eq.'strain_rate') allocate(new_bond_posn%n_strain_rate)
@@ -6198,6 +6349,7 @@ subroutine append_posn(trajectory, posn_vals)
 
   if (dem) then
     allocate(new_posn%ang_vel,new_posn%ang_accel,new_posn%rot)
+    if (add_curl_to_torque) allocate(new_posn%curl_o) !,new_posn%curl_a)
   elseif (fracture_criterion .ne. 'none' .and. (.not. dem)) then
     allocate(new_posn%accum_bond_rotation)
   endif
@@ -6234,7 +6386,7 @@ subroutine append_bond_posn(bond_trajectory, bond_posn_vals)
       new_bond_posn%bxn_fast,new_bond_posn%byn_fast)
   endif
   if (dem) then
-    allocate(new_bond_posn%tangd1,new_bond_posn%tangd2,new_bond_posn%nstress,new_bond_posn%sstress)
+    allocate(new_bond_posn%tangd1,new_bond_posn%tangd2,new_bond_posn%nstress,new_bond_posn%sstress,new_bond_posn%rel_rotation)
   elseif (fracture_criterion.ne.'none') then
     allocate(new_bond_posn%rotation,new_bond_posn%rel_rotation,new_bond_posn%n_frac_var)
     if (fracture_criterion.eq.'strain_rate') allocate(new_bond_posn%n_strain_rate)
@@ -6639,13 +6791,13 @@ logical function check_and_find_cell(grd, x, y, oi, oj)
 endif
 
 !find cell for structured grid without looping:
-oi=floor((x-grd%lon(grd%isd,grd%jsd))/(grd%lon(grd%isd+1,grd%jsd+1)-grd%lon(grd%isd,grd%jsd)))+grd%isd+1
-oj=floor((y-grd%lat(grd%isd,grd%jsd))/(grd%lat(grd%isd+1,grd%jsd+1)-grd%lat(grd%isd,grd%jsd)))+grd%jsd+1
-if (.not. (oi-1.lt.grd%isd.or.oi.gt.grd%ied.or.oj-1.lt.grd%jsd.or.oj.gt.grd%jed)) then
-  if (is_point_in_cell(grd, x, y, oi, oj)) then
-    check_and_find_cell=.true.; return
-  endif
-endif
+! oi=floor((x-grd%lon(grd%isd,grd%jsd))/(grd%lon(grd%isd+1,grd%jsd+1)-grd%lon(grd%isd,grd%jsd)))+grd%isd+1
+! oj=floor((y-grd%lat(grd%isd,grd%jsd))/(grd%lat(grd%isd+1,grd%jsd+1)-grd%lat(grd%isd,grd%jsd)))+grd%jsd+1
+! if (.not. (oi-1.lt.grd%isd.or.oi.gt.grd%ied.or.oj-1.lt.grd%jsd.or.oj.gt.grd%jed)) then
+!   if (is_point_in_cell(grd, x, y, oi, oj)) then
+!     check_and_find_cell=.true.; return
+!   endif
+! endif
 
   oi=-999; oj=-999
   do j=grd%jsd+1,grd%jed; do i=grd%isd+1,grd%ied
@@ -6671,13 +6823,13 @@ logical function find_cell(grd, x, y, oi, oj)
 
 
 !find cell for structured grid without looping:
-oi=floor((x-grd%lon(grd%isd,grd%jsd))/(grd%lon(grd%isd+1,grd%jsd+1)-grd%lon(grd%isd,grd%jsd)))+grd%isd+1
-oj=floor((y-grd%lat(grd%isd,grd%jsd))/(grd%lat(grd%isd+1,grd%jsd+1)-grd%lat(grd%isd,grd%jsd)))+grd%jsd+1
-if (oi>grd%isc-1 .and. oi<grd%iec+1 .and. oj>grd%jsc-1 .and. oj<grd%jec+1) then
-  if (is_point_in_cell(grd, x, y, oi, oj)) then
-    find_cell=.true.; return
-  endif
-endif
+! oi=floor((x-grd%lon(grd%isd,grd%jsd))/(grd%lon(grd%isd+1,grd%jsd+1)-grd%lon(grd%isd,grd%jsd)))+grd%isd+1
+! oj=floor((y-grd%lat(grd%isd,grd%jsd))/(grd%lat(grd%isd+1,grd%jsd+1)-grd%lat(grd%isd,grd%jsd)))+grd%jsd+1
+! if (oi>grd%isc-1 .and. oi<grd%iec+1 .and. oj>grd%jsc-1 .and. oj<grd%jec+1) then
+!   if (is_point_in_cell(grd, x, y, oi, oj)) then
+!     find_cell=.true.; return
+!   endif
+! endif
 
   oi=-999; oj=-999
   do j=grd%jsc,grd%jec; do i=grd%isc,grd%iec
@@ -6702,13 +6854,13 @@ logical function find_cell_wide(grd, x, y, oi, oj)
 
 find_cell_wide=.false.
 !find cell for structured grid without looping:
-oi=floor((x-grd%lon(grd%isd,grd%jsd))/(grd%lon(grd%isd+1,grd%jsd+1)-grd%lon(grd%isd,grd%jsd)))+grd%isd+1
-oj=floor((y-grd%lat(grd%isd,grd%jsd))/(grd%lat(grd%isd+1,grd%jsd+1)-grd%lat(grd%isd,grd%jsd)))+grd%jsd+1
-if (.not. (oi-1.lt.grd%isd.or.oi.gt.grd%ied.or.oj-1.lt.grd%jsd.or.oj.gt.grd%jed)) then
-  if (is_point_in_cell(grd, x, y, oi, oj)) then
-    find_cell_wide=.true.; return
-  endif
-endif
+! oi=floor((x-grd%lon(grd%isd,grd%jsd))/(grd%lon(grd%isd+1,grd%jsd+1)-grd%lon(grd%isd,grd%jsd)))+grd%isd+1
+! oj=floor((y-grd%lat(grd%isd,grd%jsd))/(grd%lat(grd%isd+1,grd%jsd+1)-grd%lat(grd%isd,grd%jsd)))+grd%jsd+1
+! if (.not. (oi-1.lt.grd%isd.or.oi.gt.grd%ied.or.oj-1.lt.grd%jsd.or.oj.gt.grd%jed)) then
+!   if (is_point_in_cell(grd, x, y, oi, oj)) then
+!     find_cell_wide=.true.; return
+!   endif
+! endif
 
 oi=-999; oj=-999
 
@@ -7736,6 +7888,78 @@ real function bilin(grd, fld, i, j, xi, yj)
   endif
 end function bilin
 
+!> Bilinear interpolation of an A-grid field to a location within a cell (not tested!)
+real function bilin_interp_from_agrid(grd, fld, x, y, i, j, xi, yj)
+! Arguments
+type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+real, intent(in) :: fld(grd%isd:grd%ied,grd%jsd:grd%jed) !< Field to interpolate
+real, intent(in) :: x !<Longitude of position
+real, intent(in) :: y !<Latitude of position
+real, intent(in) :: xi !< Non-dimensional x-position within cell
+real, intent(in) :: yj !< Non-dimensional y-position within cell
+integer, intent(in) :: i !< i-index of cell
+integer, intent(in) :: j !< j-index of cell
+! Local variables
+integer :: is,ie,js,je
+real :: x1,x2,x3,x4,y1,y2,y3,y4
+real :: dx,dy,Delta_x,xx,yy
+real :: xloc,yloc !local coords
+real :: xb(2,2), yb(2,2) !basis functions
+
+!Uses bilinear lagrange basis functions (like in FEM), where the 4
+!nodes of an "element" are defined by a 2x2 array of neigboring cell-centers
+
+if (xi>=0.5) then
+  is=i; ie=i+1
+else
+  is=i-1; ie=i
+endif
+
+if (yj>=0.5) then
+  js=j; je=j+1
+else
+  js=j-1; je=j
+endif
+
+!four corners
+x1=grd%lonc(is,js); y1=grd%latc(is,js)
+x2=grd%lonc(ie,js); y2=grd%latc(ie,js)
+x3=grd%lonc(ie,je); y3=grd%latc(ie,je)
+x4=grd%lonc(is,je); y4=grd%latc(is,je)
+
+!get non-dimensional, local (natural) coords xloc and yloc:
+!largely copied from to pos_within_cell
+if ((.not. grd%grid_is_latlon) .and. (grd%grid_is_regular))  then
+  dx=abs(x3-x4); dy=abs(y3-y2)
+  x1=x3-(dx/2); y1=y3-(dy/2)
+  Delta_x= apply_modulo_around_point(x,x1,grd%Lx)-x1
+  xloc=((Delta_x)/dx)+0.5; yloc=((y-y1)/dy)+0.5
+elseif ((max(y1,y2,y3,y4)<89.999) .or.(.not. grd%grid_is_latlon)) then
+  ! This returns non-dimensional position xi,yj for quad cells (not at a pole)
+  call calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x, y, xloc, yloc, grd%Lx)
+else
+  ! One of the cell corners is at the north pole so we switch to a tangent plane with
+  ! co-latitude as a radial coordinate.
+  xx=(90.-y)*cos(x*pi_180); yy=(90.-y)*sin(x*pi_180)
+  x1=(90.-y1)*cos(grd%lon(is,js)*pi_180); y1=(90.-y1)*sin(grd%lon(is,js)*pi_180)
+  x2=(90.-y2)*cos(grd%lon(ie,je)*pi_180); y2=(90.-y2)*sin(grd%lon(ie,je)*pi_180)
+  x3=(90.-y3)*cos(grd%lon(ie,je)*pi_180); y3=(90.-y3)*sin(grd%lon(ie,je)*pi_180)
+  x4=(90.-y4)*cos(grd%lon(is,je)*pi_180); y4=(90.-y4)*sin(grd%lon(is,je)*pi_180)
+  call calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, xx, yy, xloc, yloc, grd%Lx)
+endif
+
+!convert local coords to lie within the range [-1,1] rather than [0,1]
+xloc=xloc*2-1; yloc=yloc*2-1
+
+!basis functions:
+xb(1,:)=1-xloc; yb(:,1)=1-yloc
+xb(2,:)=1+xloc; yb(:,2)=1+yloc
+
+!interpolate:
+bilin_interp_from_agrid=sum(0.25*xb*yb*fld(is:ie,js:je))
+
+end function bilin_interp_from_agrid
+
 !> Quadratic interpolation of an A-grid field to a location within a cell
 real function quad_interp_from_agrid(grd, fld, x, y, i, j, xi, yj)
 ! Arguments
@@ -7753,12 +7977,23 @@ real function quad_interp_from_agrid(grd, fld, x, y, i, j, xi, yj)
 real :: dx,dy,Delta_x,xx,yy
 real :: xloc,yloc !local coords
 real :: xb(3,3), yb(3,3) !basis functions
+integer :: mind!=1
 
 !Uses bi-quadratic lagrange quadrilateral basis functions (like in FEM), where the 9
-!nodes of an "element" are defined by a 3x3 array of neigboring cell-centers
+!nodes of an "element" are defined by a 3x3 array of neigboring cell-centers. Note that a
+!perfect quadrilateral is assumed for simplicity (4 straight sides). This assumption
+!is imperfect when using a geographic grid (local coordinates may be slightly wrong),
+!but is probably good enough to approximate the bathymetry at a point, which is the
+!main purpose of this subroutine. Note that even the bilinear interpolations used elsewhere
+!are inaccurate, given the curved coordinate system...
 
 !bounds of "node" array (is:ie,js:je).
-if (mod(i,2)==1) then
+ if (rev_mind) then
+   mind=0
+ else
+   mind=1
+ endif
+if (mod(i,2)==mind) then
   if (xi>=0.5) then
     is=i; ie=i+2
   else
@@ -7767,7 +8002,7 @@ real function quad_interp_from_agrid(grd, fld, x, y, i, j, xi, yj)
 else
   is=i-1; ie=i+1
 endif
-if (mod(j,2)==1) then
+if (mod(j,2)==mind) then
   if (yj>=0.5) then
     js=j; je=j+2
   else
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index f3eb132..06ff4d2 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -44,7 +44,7 @@ module ice_bergs_io
 use ice_bergs_framework, only: mts,save_bond_traj
 use ice_bergs_framework, only: push_bond_posn, append_bond_posn
 use ice_bergs_framework, only: pack_bond_traj_into_buffer2,unpack_bond_traj_from_buffer2
-use ice_bergs_framework, only: monitor_energy, use_damage, dem, fracture_criterion, iceberg_bonds_on
+use ice_bergs_framework, only: monitor_energy, use_damage, dem, add_curl_to_torque, fracture_criterion, iceberg_bonds_on
 
 implicit none ; private
 
@@ -160,6 +160,8 @@ subroutine write_restart(bergs, time_stamp)
                                    ang_vel,      &
                                    ang_accel,    &
                                    rot,          &
+                                   curl_o,       &
+                                   !curl_a,       &
                                    lon_prev,     &
                                    lat_prev,     &
                                    accum_bond_rotation, &
@@ -247,6 +249,10 @@ subroutine write_restart(bergs, time_stamp)
      allocate(ang_vel(nbergs))
      allocate(ang_accel(nbergs))
      allocate(rot(nbergs))
+     if (add_curl_to_torque) then
+       allocate(curl_o(nbergs))
+       !allocate(curl_a(nbergs))
+    endif
    elseif (fracture_criterion.ne.'none') then
      allocate(lon_prev(nbergs))
      allocate(lat_prev(nbergs))
@@ -323,6 +329,12 @@ subroutine write_restart(bergs, time_stamp)
       longname='dem angular acceleration',units='rad/s^2')
     id = register_restart_field(bergs_restart,filename,'rot',rot,&
       longname='dem accumulated rotation',units='rad')
+    if (add_curl_to_torque) then
+      id = register_restart_field(bergs_restart,filename,'curl_o',curl_o,&
+        longname='curl of ocean velocity',units='1/s')
+      !id = register_restart_field(bergs_restart,filename,'curl_a',curl_a,&
+      !  longname='curl of atmospheric velocity',units='1/s')
+    endif
   elseif (fracture_criterion.ne.'none') then
     id = register_restart_field(bergs_restart,filename,'lon_prev',lon_prev,longname='previous longitude',units='degrees_E')
     id = register_restart_field(bergs_restart,filename,'lat_prev',lat_prev,longname='previous latitude',units='degrees_N')
@@ -376,6 +388,10 @@ subroutine write_restart(bergs, time_stamp)
         ang_vel(i) = this%ang_vel
         ang_accel(i) = this%ang_accel
         rot(i) = this%rot
+        if (add_curl_to_torque) then
+          curl_o(i) = this%curl_o
+          !curl_a(i) = this%curl_a
+        endif
       elseif (fracture_criterion.ne.'none') then
         lon_prev(i) = this%lon_prev
         lat_prev(i) = this%lat_prev
@@ -425,6 +441,11 @@ subroutine write_restart(bergs, time_stamp)
              ang_vel,      &
              ang_accel,    &
              rot)
+    if (add_curl_to_torque) then
+      deallocate(          &
+             curl_o) !,       &
+             !curl_a)
+    endif
   elseif (fracture_criterion.ne.'none') then
     deallocate(            &
              lon_prev,     &
@@ -464,6 +485,7 @@ subroutine write_restart(bergs, time_stamp)
     allocate(tangd2(nbonds))
     allocate(nstress(nbonds))
     allocate(sstress(nbonds))
+    allocate(rel_rotation(nbonds))
   elseif (fracture_criterion.ne.'none') then
     allocate(rotation(nbonds))
     allocate(rel_rotation(nbonds))
@@ -506,6 +528,8 @@ subroutine write_restart(bergs, time_stamp)
       longname='normal stress',units='Pa')
     id = register_restart_field(bergs_bond_restart,filename_bonds,'sstress',sstress,&
       longname='shear stress',units='Pa')
+    id = register_restart_field(bergs_bond_restart,filename_bonds,'rel_rotation',rel_rotation,&
+      longname='relative rotation',units='rad')
   elseif (fracture_criterion.ne.'none') then
     id = register_restart_field(bergs_bond_restart,filename_bonds,'rotation',rotation,&
       longname='rotation',units='rad')
@@ -544,6 +568,7 @@ subroutine write_restart(bergs, time_stamp)
           tangd2(i)=current_bond%tangd2
           nstress(i)=current_bond%nstress
           sstress(i)=current_bond%sstress
+          rel_rotation(i)=current_bond%rel_rotation
         elseif (fracture_criterion.ne.'none') then
           rotation(i)=current_bond%rotation
           rel_rotation(i)=current_bond%rel_rotation
@@ -578,7 +603,8 @@ subroutine write_restart(bergs, time_stamp)
              tangd1,                &
              tangd2,                &
              nstress,               &
-             sstress)
+             sstress,               &
+             rel_rotation)
   elseif (fracture_criterion.ne.'none') then
     deallocate(                     &
              rotation,              &
@@ -658,7 +684,7 @@ subroutine read_restart_bergs(bergs,Time)
 logical :: multiPErestart  ! Not needed with new restart read; currently kept for compatibility
 real :: lon0, lon1, lat0, lat1
 real :: pos_is_good, pos_is_good_all_pe
-character(len=33) :: filename, filename_base
+character(len=53) :: filename, filename_base
 type(icebergs_gridded), pointer :: grd
 type(iceberg) :: localberg ! NOT a pointer but an actual local variable
 integer :: stderrunit, i, j, cnt, ij
@@ -792,6 +818,10 @@ subroutine read_restart_bergs(bergs,Time)
        allocate(ang_vel(nbergs_in_file))
        allocate(ang_accel(nbergs_in_file))
        allocate(rot(nbergs_in_file))
+       if (add_curl_to_torque) then
+         allocate(localberg%curl_o)!, localberg%curl_a)
+         localberg%curl_o=0.0!; localberg%curl_a=0.0
+       endif
      elseif (fracture_criterion.ne.'none') then
        allocate(lon_prev(nbergs_in_file))
        allocate(lat_prev(nbergs_in_file))
@@ -884,6 +914,7 @@ subroutine read_restart_bergs(bergs,Time)
            & ' on PE ',mpp_pe()
       write(stderrunit,*) 'KID, read_restart_bergs: lres = ',lres
     endif
+
     if (lres) then ! true if we reside on this PE grid
       localberg%uvel=uvel(k)
       localberg%vvel=vvel(k)
@@ -1107,6 +1138,10 @@ subroutine generate_bergs(bergs,Time)
     allocate(localberg%ang_vel)
     allocate(localberg%ang_accel)
     allocate(localberg%rot)
+    if (add_curl_to_torque) then
+      allocate(localberg%curl_o)
+      !allocate(localberg%curl_a)
+    endif
   elseif (fracture_criterion.ne.'none') then
     allocate(localberg%accum_bond_rotation)
   endif
@@ -1160,6 +1195,10 @@ subroutine generate_bergs(bergs,Time)
         localberg%ang_vel=0.
         localberg%ang_accel=0.
         localberg%rot=0.
+        if (add_curl_to_torque) then
+          localberg%curl_o=0.
+          !localberg%curl_a=0.
+        endif
       elseif (fracture_criterion.ne.'none') then
         localberg%accum_bond_rotation=0.
       endif
@@ -1235,7 +1274,7 @@ subroutine read_restart_bonds(bergs,Time)
 logical :: first_berg_found, second_berg_found
 logical :: multiPErestart  ! Not needed with new restart read; currently kept for compatibility
 real :: lon0, lon1, lat0, lat1
-character(len=33) :: filename, filename_base
+character(len=53) :: filename, filename_base
 type(icebergs_gridded), pointer :: grd
 type(iceberg) :: localberg ! NOT a pointer but an actual local variable
 type(iceberg) , pointer :: this, first_berg, second_berg
@@ -1309,6 +1348,7 @@ subroutine read_restart_bonds(bergs,Time)
       allocate(tangd2(nbonds_in_file))
       allocate(nstress(nbonds_in_file))
       allocate(sstress(nbonds_in_file))
+      allocate(rel_rotation(nbonds_in_file))
     elseif (fracture_criterion.ne.'none') then
       allocate(rotation(nbonds_in_file))
       allocate(rel_rotation(nbonds_in_file))
@@ -1341,6 +1381,7 @@ subroutine read_restart_bonds(bergs,Time)
       call read_real_vector(filename,'tangd2',tangd2,grd%domain,value_if_not_in_file=0.)
       call read_real_vector(filename,'nstress',nstress,grd%domain,value_if_not_in_file=0.)
       call read_real_vector(filename,'sstress',sstress,grd%domain,value_if_not_in_file=0.)
+      call read_real_vector(filename,'rel_rotation',rel_rotation,grd%domain,value_if_not_in_file=0.)
     elseif (fracture_criterion.ne.'none') then
       call read_real_vector(filename,'rotation',rotation,grd%domain,value_if_not_in_file=0.)
       call read_real_vector(filename,'rel_rotation',rel_rotation,grd%domain,value_if_not_in_file=0.)
@@ -1452,10 +1493,11 @@ subroutine read_restart_bonds(bergs,Time)
               current_bond%tangd2=tangd2(k)
               current_bond%nstress=nstress(k)
               current_bond%sstress=sstress(k)
+              current_bond%rel_rotation=rel_rotation(k)
             elseif (fracture_criterion.ne.'none') then
-              current_bond%tangd1=rotation(k)
-              current_bond%tangd2=rel_rotation(k)
-              current_bond%nstress=n_frac_var(k)
+              current_bond%rotation=rotation(k)
+              current_bond%rel_rotation=rel_rotation(k)
+              current_bond%n_frac_var=n_frac_var(k)
               if (fracture_criterion.eq.'strain_rate') then
                 current_bond%n_strain_rate=n_strain_rate(k)
               elseif (fracture_criterion.eq.'energy') then
@@ -1524,7 +1566,8 @@ subroutine read_restart_bonds(bergs,Time)
                tangd1,                &
                tangd2,                &
                nstress,               &
-               sstress)
+               sstress,               &
+               rel_rotation)
     elseif (fracture_criterion.ne.'none') then
       deallocate(                     &
                rotation,              &
@@ -1686,7 +1729,7 @@ subroutine read_ocean_depth(grd)
 end subroutine read_ocean_depth
 
 !> Write a trajectory-based diagnostics file
-subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r)
+subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r, traj_name)
 ! Arguments
 type(xyt), pointer :: trajectory !< An iceberg trajectory
 logical, intent(in) :: save_short_traj !< If true, record less data
@@ -1695,7 +1738,7 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r)
 ! Local variables
 integer :: iret, ncid, i_dim, i
 integer :: lonid, latid, yearid, dayid, uvelid, vvelid, idcntid, idijid
-integer :: uvelpid,vvelpid
+integer :: uvelpid,vvelpid, curloid, curlaid
 integer :: uoid, void, uiid, viid, uaid, vaid, sshxid, sshyid, sstid, sssid
 integer :: cnid, hiid, hsid
 integer :: mid, smid, did, wid, lid, mbid, mflbid, mflbbid, hdid, nbid, odid, flkid
@@ -1703,7 +1746,7 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r)
 integer :: eecid,edcid,eeid,edid,aeid,efid
 integer :: eectid, edctid, eetid, edtid, aetid
 integer :: avid, aaid, rid, abrid
-character(len=37) :: filename
+character(len=70) :: filename, traj_name
 character(len=7) :: pe_name
 type(xyt), pointer :: this, next
 integer :: stderrunit, cnt, ij
@@ -1779,7 +1822,8 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r)
 
   if((force_all_pes_traj .OR. is_io_tile_root_pe) .AND. associated(traj4io)) then
 
-    call get_instance_filename("iceberg_trajectories.nc", filename)
+    !call get_instance_filename("iceberg_trajectories.nc", filename)
+    call get_instance_filename(traj_name, filename)
     if(io_tile_id(1) .ge. 0 .AND. .NOT. force_all_pes_traj) then !io_tile_root_pes write
        if(io_npes .gt. 1) then !attach tile_id  to filename only if there is more than one I/O pe
           if (io_tile_id(1)<10000) then
@@ -1890,6 +1934,10 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r)
           avid = inq_varid(ncid, 'ang_vel')
           aaid = inq_varid(ncid, 'ang_accel')
           rid  = inq_varid(ncid, 'rot')
+          if (add_curl_to_torque) then
+            curloid = inq_varid(ncid, 'curl_o')
+            !curlaid = inq_varid(ncid, 'curl_a')
+          endif
         elseif (fracture_criterion .ne. 'none') then
           abrid = inq_varid(ncid, 'accum_bond_rotation')
         endif
@@ -1977,6 +2025,10 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r)
           avid = def_var(ncid, 'ang_vel', NF_DOUBLE, i_dim)
           aaid = def_var(ncid, 'ang_accel', NF_DOUBLE, i_dim)
           rid  = def_var(ncid, 'rot', NF_DOUBLE, i_dim)
+          if (add_curl_to_torque) then
+            curloid = def_var(ncid, 'curl_o', NF_DOUBLE, i_dim)
+            !curlaid = def_var(ncid, 'curl_a', NF_DOUBLE, i_dim)
+          endif
         elseif (fracture_criterion .ne. 'none') then
           abrid = def_var(ncid, 'accum_bond_rotation', NF_DOUBLE, i_dim)
         endif
@@ -2121,6 +2173,12 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r)
           call put_att(ncid, aaid, 'units', 'rad/s^2')
           call put_att(ncid, rid, 'long_name', 'accumulated rotation')
           call put_att(ncid, rid, 'units', 'rad')
+          if (add_curl_to_torque) then
+            call put_att(ncid, curloid, 'long_name', 'curl of ocean velocity')
+            call put_att(ncid, curloid, 'units', '1/s')
+            !call put_att(ncid, curlaid, 'long_name', 'curl of atmospheric velocity')
+            !call put_att(ncid, curlaid, 'units', '1/s')
+          endif
         elseif (fracture_criterion .ne. 'none') then
           call put_att(ncid, abrid, 'long_name', 'accumulated bond rotation')
           call put_att(ncid, abrid, 'units', 'radians')
@@ -2218,6 +2276,10 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r)
           call put_double(ncid, avid, i, this%ang_vel)
           call put_double(ncid, aaid, i, this%ang_accel)
           call put_double(ncid, rid,  i, this%rot)
+          if (add_curl_to_torque) then
+            call put_double(ncid, curloid, i, this%curl_o)
+            !call put_double(ncid, curlaid, i, this%curl_a)
+          endif
         elseif (fracture_criterion .ne. 'none') then
           call put_double(ncid, abrid, i, this%accum_bond_rotation)
         endif
@@ -2238,7 +2300,7 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r)
 end subroutine write_trajectory
 
 !> Write a trajectory-based diagnostics file for bonds
-subroutine write_bond_trajectory(trajectory)
+subroutine write_bond_trajectory(trajectory, bond_traj_name)
 ! Arguments
 type(bond_xyt), pointer :: trajectory !< An iceberg bond trajectory
 ! Local variables
@@ -2248,7 +2310,7 @@ subroutine write_bond_trajectory(trajectory)
 integer :: idcnt1_id, idcnt2_id, idij1_id, idij2_id, eeid, edid
 integer :: axid,ayid,bxid,byid
 integer :: td1id,td2id,dnsid,dssid
-character(len=34) :: filename
+character(len=70) :: filename, bond_traj_name
 character(len=7) :: pe_name
 type(bond_xyt), pointer :: this, next
 integer :: stderrunit, cnt, ij
@@ -2319,7 +2381,8 @@ subroutine write_bond_trajectory(trajectory)
 
   if((force_all_pes_traj .OR. is_io_tile_root_pe) .AND. associated(traj4io)) then
 
-    call get_instance_filename("bond_trajectories.nc", filename)
+    !call get_instance_filename("bond_trajectories.nc", filename)
+    call get_instance_filename(bond_traj_name, filename)
     if(io_tile_id(1) .ge. 0 .AND. .NOT. force_all_pes_traj) then !io_tile_root_pes write
       if(io_npes .gt. 1) then !attach tile_id  to filename only if there is more than one I/O pe
         if (io_tile_id(1)<10000) then
@@ -2375,6 +2438,7 @@ subroutine write_bond_trajectory(trajectory)
       if (dem) then
         td1id = inq_varid(ncid, 'tangd1');  td2id = inq_varid(ncid, 'tangd2')
         dnsid = inq_varid(ncid, 'nstress'); dssid = inq_varid(ncid, 'sstress')
+        rrotid = inq_varid(ncid, 'rel_rotation')
       elseif (fracture_criterion.ne.'none') then
         rotid = inq_varid(ncid, 'rotation');    rrotid = inq_varid(ncid, 'rel_rotation')
         nsid = inq_varid(ncid, 'n_frac_var')
@@ -2412,6 +2476,7 @@ subroutine write_bond_trajectory(trajectory)
       if (dem) then
         td1id = def_var(ncid, 'tangd1',  NF_DOUBLE, i_dim); td2id = def_var(ncid, 'tangd2',  NF_DOUBLE, i_dim)
         dnsid = def_var(ncid, 'nstress', NF_DOUBLE, i_dim); dssid = def_var(ncid, 'sstress', NF_DOUBLE, i_dim)
+        rrotid = def_var(ncid, 'rel_rotation', NF_DOUBLE, i_dim)
       elseif (fracture_criterion.ne.'none') then
         rotid = def_var(ncid, 'rotation', NF_DOUBLE, i_dim); rrotid = def_var(ncid, 'rel_rotation', NF_DOUBLE, i_dim)
         nsid = def_var(ncid, 'n_frac_var', NF_DOUBLE, i_dim)
@@ -2467,6 +2532,7 @@ subroutine write_bond_trajectory(trajectory)
         call put_att(ncid, td2id, 'units', 'm')
         call put_att(ncid, dnsid, 'long_name', 'normal stress'); call put_att(ncid, dnsid, 'units', 'Pa')
         call put_att(ncid, dssid, 'long_name', 'shear stress');  call put_att(ncid, dssid, 'units', 'Pa')
+        call put_att(ncid, rrotid, 'long_name', 'relative rotation');      call put_att(ncid, rrotid, 'units', 'rad')
       elseif (fracture_criterion.ne.'none') then
         call put_att(ncid, rotid, 'long_name', 'rotation');                call put_att(ncid, rotid, 'units', 'rad')
         call put_att(ncid, rrotid, 'long_name', 'relative rotation');      call put_att(ncid, rrotid, 'units', 'rad')
@@ -2515,6 +2581,7 @@ subroutine write_bond_trajectory(trajectory)
       if (dem) then
         call put_double(ncid,td1id,i,this%tangd1);  call put_double(ncid,td2id,i,this%tangd2)
         call put_double(ncid,dnsid,i,this%nstress); call put_double(ncid,dssid,i,this%sstress)
+        call put_double(ncid,rrotid,i,this%rel_rotation)
       elseif (fracture_criterion.ne.'none') then
         call put_double(ncid,rotid,i,this%rotation);  call put_double(ncid,rrotid,i,this%rel_rotation)
         call put_double(ncid,nsid,i,this%n_frac_var)
diff --git a/tests/.gitignore b/tests/.gitignore
index b733a1e..5bdd1c4 100644
--- a/tests/.gitignore
+++ b/tests/.gitignore
@@ -7,3 +7,6 @@ single_test/
 size_test_tab/
 steady_test/
 uniaxial_test/
+a68_2/
+a68_3/
+a68_old/
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/__pycache__/hexagon_area.cpython-38.pyc b/tests/Iceberg_repository/Scripts_and_analysis/__pycache__/hexagon_area.cpython-38.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..7cc14f60f06a6e09242e1a18e1cc3491c5eb89b7
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diff --git a/tests/Iceberg_repository/Scripts_and_analysis/hexagon_area.py b/tests/Iceberg_repository/Scripts_and_analysis/hexagon_area.py
index 08ef572..0315036 100755
--- a/tests/Iceberg_repository/Scripts_and_analysis/hexagon_area.py
+++ b/tests/Iceberg_repository/Scripts_and_analysis/hexagon_area.py
@@ -6,7 +6,7 @@
 import matplotlib
 import math
 import os
-matplotlib.use("GTKAgg")
+matplotlib.use("tkagg")
 #from pylab import *
 #import matplotlib.pyplot as plt
 import pdb
@@ -18,8 +18,8 @@
 
 def Divide_hexagon_into_4_quadrants_old(x0,y0,H):
 	S=(2/np.sqrt(3))*H
-	Area_hex=3*(np.sqrt(3)/2)*(S**2)  #Area of the hexagon (should be equal to Area/grid_area, since it is not dim)  - check this
-	#print 'y0,H',y0, H	
+	Area_hex=3*(np.sqrt(3)/2)*(S**2)  #Area of the hexagon (should be equal to Area/grid_area, since it is not dim)	 - check this
+	#print( 'y0,H',y0, H	
 	#Defining boundaries of hexagon, and if statements to see which side of the boundary you are on
 	W1= False ; W2=False ;W3=False ;W4=False ;W5=False ;W6=False ;H1=False ;V1=False ;V2=False
 	W1=(-y0<-np.sqrt(3)*(-x0) + ((np.sqrt(3)*(S))));#upper right
@@ -40,9 +40,9 @@ def Divide_hexagon_into_4_quadrants_old(x0,y0,H):
 	V2=(x0<(S/2));
 	  
 	#Deciding if the origin is within the hexagon
-	#print W1 , W2 , W3 , W4 , W5 , W6
+	#print( W1 , W2 , W3 , W4 , W5 , W6
 	#if In_hex:
-	#	print In_hex
+	#	print( In_hex
 		
 	#Calculating the area of the top and bottom half of the hexagon, 2 Cases for the majority above and below the y0=0 line
 	#(and two more for the hexagon totally above and below the y0=0 line)
@@ -116,11 +116,11 @@ def Divide_hexagon_into_4_quadrants_old(x0,y0,H):
 		
 
 		#yCxC=1.
-		#print 'out of hex'
+		#print( 'out of hex'
 
 	else:
 		#Determine which sector within the hexagon you are in. (sectors 1 to 6 go counter clockwise starting with top right)
-		if (H1==True):  #Bottom half
+		if (H1==True):	#Bottom half
 			if V1:
 				#if W1==False:
 				if ((y0+(np.sqrt(3)*(x0+S)))<=0.):
@@ -151,7 +151,7 @@ def Divide_hexagon_into_4_quadrants_old(x0,y0,H):
 				else:
 					Sector=6;
 
-		#print Sector
+		#print( Sector
 
 		#If the hexagon is in Sector 1,3,4 or 6, then the intersetion of the hexagon and the corresponding sector forms a baby triangle
 		#If the hexagon is in Sector 2,5 then the intersetion of the hexagon and the corresponding sector forms a baby trapesoid
@@ -239,21 +239,21 @@ def Divide_hexagon_into_4_quadrants_old(x0,y0,H):
 			Area_Q1=Area_right;
 			Area_Q2=Area_left-Area_Q3;
 
-		#print x0,y0,Sector
+		#print( x0,y0,Sector
 	return [Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4]
 
 
 
-def Hexagon_into_quadrants_using_triangles_across_lines(x0,y0,H,theta,  Px, Py, Qx, Qy, Rx, Ry, Sx, Sy ):
+def Hexagon_into_quadrants_using_triangles_across_lines(x0,y0,H,theta,	Px, Py, Qx, Qy, Rx, Ry, Sx, Sy ):
 	#In this routine, the hexagon is divided across lines PQ, RS.	 
 	#Length of side of Hexagon
 	S=(2/np.sqrt(3))*H;  
 
 	#Finding positions of corners
-	C1x=S           ; C1y=0.  #Corner 1 (right)
+	C1x=S		; C1y=0.  #Corner 1 (right)
 	C2x=H/np.sqrt(3.)  ; C2y=H;  #Corner 2 (top right)
 	C3x=-H/np.sqrt(3.) ; C3y=H;  #Corner 3 (top left)
-	C4x=-S          ; C4y=0.; #Corner 4 (left)
+	C4x=-S		; C4y=0.; #Corner 4 (left)
 	C5x=-H/np.sqrt(3.) ; C5y=-H; #Corner 5 (bottom right)
 	C6x=H/np.sqrt(3.)  ; C6y=-H; #Corner 6 (bottom right)
 
@@ -274,18 +274,18 @@ def Hexagon_into_quadrants_using_triangles_across_lines(x0,y0,H,theta,  Px, Py,
 	[T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4]=Triangle_divided_into_four_parts(x0,y0,C6x,C6y,C1x,C1y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
 	
 	#Area of Hexagon is the sum of the triangles
-	#print '1:', Triangle_divided_into_four_parts(x0,y0,C1x,C1y,C2x,C2y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T012
-	#print '1b:', Triangle_divided_into_four_quadrants(x0,y0,C1x,C1y,C2x,C2y); #T012
-	#print '2', Triangle_divided_into_four_parts(x0,y0,C2x,C2y,C3x,C3y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
-	#print '2b',Triangle_divided_into_four_quadrants(x0,y0,C2x,C2y,C3x,C3y); #T023
-	#print '3:',Triangle_divided_into_four_parts(x0,y0,C3x,C3y,C4x,C4y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T034
-	#print '3b',Triangle_divided_into_four_quadrants(x0,y0,C3x,C3y,C4x,C4y); #T034
-	#print '4',Triangle_divided_into_four_parts(x0,y0,C4x,C4y,C5x,C5y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
-	#print '4b:',Triangle_divided_into_four_quadrants(x0,y0,C4x,C4y,C5x,C5y); #T023
-	#print '5', Triangle_divided_into_four_parts(x0,y0,C5x,C5y,C6x,C6y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
-	#print '5b',Triangle_divided_into_four_quadrants(x0,y0,C5x,C5y,C6x,C6y); #T023
-	#print '6:',Triangle_divided_into_four_parts(x0,y0,C6x,C6y,C1x,C1y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
-	#print '6b',Triangle_divided_into_four_quadrants(x0,y0,C6x,C6y,C1x,C1y); #T023
+	#print( '1:', Triangle_divided_into_four_parts(x0,y0,C1x,C1y,C2x,C2y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T012
+	#print( '1b:', Triangle_divided_into_four_quadrants(x0,y0,C1x,C1y,C2x,C2y); #T012
+	#print( '2', Triangle_divided_into_four_parts(x0,y0,C2x,C2y,C3x,C3y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
+	#print( '2b',Triangle_divided_into_four_quadrants(x0,y0,C2x,C2y,C3x,C3y); #T023
+	#print( '3:',Triangle_divided_into_four_parts(x0,y0,C3x,C3y,C4x,C4y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T034
+	#print( '3b',Triangle_divided_into_four_quadrants(x0,y0,C3x,C3y,C4x,C4y); #T034
+	#print( '4',Triangle_divided_into_four_parts(x0,y0,C4x,C4y,C5x,C5y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
+	#print( '4b:',Triangle_divided_into_four_quadrants(x0,y0,C4x,C4y,C5x,C5y); #T023
+	#print( '5', Triangle_divided_into_four_parts(x0,y0,C5x,C5y,C6x,C6y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
+	#print( '5b',Triangle_divided_into_four_quadrants(x0,y0,C5x,C5y,C6x,C6y); #T023
+	#print( '6:',Triangle_divided_into_four_parts(x0,y0,C6x,C6y,C1x,C1y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
+	#print( '6b',Triangle_divided_into_four_quadrants(x0,y0,C6x,C6y,C1x,C1y); #T023
 
 	#Summing up
 	Area_hex=T12_Area+T23_Area+T34_Area+T45_Area+T56_Area+T61_Area;
@@ -299,19 +299,19 @@ def Hexagon_into_quadrants_using_triangles_across_lines(x0,y0,H,theta,  Px, Py,
 
 
 	#if  (abs(x0-(-0.186672393129))<0.00001)  and (abs(y0-(-0.436171))<0.00001):
-	#	print 'Triangle 1,xo,y0',x0,y0 
-	#	print 'Triangle 1H,S',H,S 
-	#	print 'Triangle 1,Corners',C1x,C1y,C2x,C2y 
-	#	print 'Triangle 1, Area full', T12_Area
-	#	print 'Triangle 1, Area T1', T12_Q1
-	#	print 'Triangle 1, Area T2', T12_Q2
-	#	print 'Triangle 1, Area T3', T12_Q3
-	#	print 'Triangle 1, Area T4', T12_Q4 
-	#	#print 'Triangle 2',x0,y0,C2x,C2y,C3x,C3y,T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4
-	#	#print 'Triangle 3',x0,y0,C3x,C3y,C4x,C4y,T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4 
-	#	#print 'Triangle 4',x0,y0,C4x,C4y,C5x,C5y,T45_Area,T45_Q1,T45_Q2,T45_Q3,T45_Q4
-	#	#print 'Triangle 5',x0,y0,C5x,C5y,C6x,C6y,T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4 
-	#	#print 'Triangle 6',x0,y0,C6x,C6y,C1x,C1y,T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4
+	#	print( 'Triangle 1,xo,y0',x0,y0 
+	#	print( 'Triangle 1H,S',H,S 
+	#	print( 'Triangle 1,Corners',C1x,C1y,C2x,C2y 
+	#	print( 'Triangle 1, Area full', T12_Area
+	#	print( 'Triangle 1, Area T1', T12_Q1
+	#	print( 'Triangle 1, Area T2', T12_Q2
+	#	print( 'Triangle 1, Area T3', T12_Q3
+	#	print( 'Triangle 1, Area T4', T12_Q4 
+	#	#print( 'Triangle 2',x0,y0,C2x,C2y,C3x,C3y,T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4
+	#	#print( 'Triangle 3',x0,y0,C3x,C3y,C4x,C4y,T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4 
+	#	#print( 'Triangle 4',x0,y0,C4x,C4y,C5x,C5y,T45_Area,T45_Q1,T45_Q2,T45_Q3,T45_Q4
+	#	#print( 'Triangle 5',x0,y0,C5x,C5y,C6x,C6y,T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4 
+	#	#print( 'Triangle 6',x0,y0,C6x,C6y,C1x,C1y,T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4
 
 	Area_Q1=max(Area_Q1,0.);
 	Area_Q2=max(Area_Q2,0.);
@@ -321,32 +321,32 @@ def Hexagon_into_quadrants_using_triangles_across_lines(x0,y0,H,theta,  Px, Py,
 
 	Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
 	if (abs(Error)>0.01):
-		print  'diamonds, hex error, H,x0,y0, Error', H, x0 , y0, Error
-        	print 'diamonds, hex error, Areas',Area_hex, (Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
-	      	print 'Hexagon error is large!!'
+		print(	'diamonds, hex error, H,x0,y0, Error', H, x0 , y0, Error)
+		print( 'diamonds, hex error, Areas',Area_hex, (Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,	 Area_Q4)
+		print( 'Hexagon error is large!!')
 
 
 
 	#Adjust Areas so that the error is zero by subtracting the error from the largest sector.
 	if  (((Area_Q1>=Area_Q2) and (Area_Q1>=Area_Q3)) and (Area_Q1>=Area_Q4)):
-		#print 'fix1',Error
+		#print( 'fix1',Error
 		Area_Q1=Area_Q1+Error
 	elif  (((Area_Q2>=Area_Q1) and (Area_Q2>=Area_Q3)) and (Area_Q2>=Area_Q4)):
-		#print 'fix2', Error
+		#print( 'fix2', Error
 		Area_Q2=Area_Q2+Error
 	elif  (((Area_Q3>=Area_Q1) and (Area_Q3>=Area_Q2)) and (Area_Q3>=Area_Q4)):
-		#print 'fix3',Error
+		#print( 'fix3',Error
 		Area_Q3=Area_Q3+Error
-   	elif  (((Area_Q4>=Area_Q1) and (Area_Q4>=Area_Q2)) and (Area_Q4>=Area_Q3)):
-		#print 'fix4',Error
+	elif  (((Area_Q4>=Area_Q1) and (Area_Q4>=Area_Q2)) and (Area_Q4>=Area_Q3)):
+		#print( 'fix4',Error
 		Area_Q4=Area_Q4+Error
 	else:
-		print 'There is some thing wrong with this hexagon. Something very wrong'
+		print( 'There is some thing wrong with this hexagon. Something very wrong')
 
 	#Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
 	Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
 	if ((abs(Error)>0.01)):
-		print 'The hexagon error is still too large!!!', Error
+		print( 'The hexagon error is still too large!!!', Error)
 
 
 
@@ -358,10 +358,10 @@ def Hexagon_into_quadrants_using_triangles(x0,y0,H,theta):
 	S=(2/np.sqrt(3))*H;  
 
 	#Finding positions of corners
-	C1x=S           ; C1y=0.  #Corner 1 (right)
+	C1x=S		; C1y=0.  #Corner 1 (right)
 	C2x=H/np.sqrt(3.)  ; C2y=H;  #Corner 2 (top right)
 	C3x=-H/np.sqrt(3.) ; C3y=H;  #Corner 3 (top left)
-	C4x=-S          ; C4y=0.; #Corner 4 (left)
+	C4x=-S		; C4y=0.; #Corner 4 (left)
 	C5x=-H/np.sqrt(3.) ; C5y=-H; #Corner 5 (bottom right)
 	C6x=H/np.sqrt(3.)  ; C6y=-H; #Corner 6 (bottom right)
 
@@ -393,19 +393,19 @@ def Hexagon_into_quadrants_using_triangles(x0,y0,H,theta):
 
 
 	#if  (abs(x0-(-0.186672393129))<0.00001)  and (abs(y0-(-0.436171))<0.00001):
-	#	print 'Triangle 1,xo,y0',x0,y0 
-	#	print 'Triangle 1H,S',H,S 
-	#	print 'Triangle 1,Corners',C1x,C1y,C2x,C2y 
-	#	print 'Triangle 1, Area full', T12_Area
-	#	print 'Triangle 1, Area T1', T12_Q1
-	#	print 'Triangle 1, Area T2', T12_Q2
-	#	print 'Triangle 1, Area T3', T12_Q3
-	#	print 'Triangle 1, Area T4', T12_Q4 
-	#	#print 'Triangle 2',x0,y0,C2x,C2y,C3x,C3y,T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4
-	#	#print 'Triangle 3',x0,y0,C3x,C3y,C4x,C4y,T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4 
-	#	#print 'Triangle 4',x0,y0,C4x,C4y,C5x,C5y,T45_Area,T45_Q1,T45_Q2,T45_Q3,T45_Q4
-	#	#print 'Triangle 5',x0,y0,C5x,C5y,C6x,C6y,T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4 
-	#	#print 'Triangle 6',x0,y0,C6x,C6y,C1x,C1y,T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4
+	#	print( 'Triangle 1,xo,y0',x0,y0 
+	#	print( 'Triangle 1H,S',H,S 
+	#	print( 'Triangle 1,Corners',C1x,C1y,C2x,C2y 
+	#	print( 'Triangle 1, Area full', T12_Area
+	#	print( 'Triangle 1, Area T1', T12_Q1
+	#	print( 'Triangle 1, Area T2', T12_Q2
+	#	print( 'Triangle 1, Area T3', T12_Q3
+	#	print( 'Triangle 1, Area T4', T12_Q4 
+	#	#print( 'Triangle 2',x0,y0,C2x,C2y,C3x,C3y,T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4
+	#	#print( 'Triangle 3',x0,y0,C3x,C3y,C4x,C4y,T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4 
+	#	#print( 'Triangle 4',x0,y0,C4x,C4y,C5x,C5y,T45_Area,T45_Q1,T45_Q2,T45_Q3,T45_Q4
+	#	#print( 'Triangle 5',x0,y0,C5x,C5y,C6x,C6y,T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4 
+	#	#print( 'Triangle 6',x0,y0,C6x,C6y,C1x,C1y,T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4
 
 	Area_Q1=max(Area_Q1,0.);
 	Area_Q2=max(Area_Q2,0.);
@@ -415,32 +415,32 @@ def Hexagon_into_quadrants_using_triangles(x0,y0,H,theta):
 
 	Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
 	if (abs(Error)>0.01):
-		print  'diamonds, hex error, H,x0,y0, Error', H, x0 , y0, Error
-        	print 'diamonds, hex error, Areas',Area_hex, (Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
-	      	print 'Hexagon error is large!!'
+		print(	'diamonds, hex error, H,x0,y0, Error', H, x0 , y0, Error)
+		print( 'diamonds, hex error, Areas',Area_hex, (Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,	 Area_Q4)
+		print( 'Hexagon error is large!!')
 
 
 
 	#Adjust Areas so that the error is zero by subtracting the error from the largest sector.
 	if  (((Area_Q1>=Area_Q2) and (Area_Q1>=Area_Q3)) and (Area_Q1>=Area_Q4)):
-		#print 'fix1',Error
+		#print( 'fix1',Error
 		Area_Q1=Area_Q1+Error
 	elif  (((Area_Q2>=Area_Q1) and (Area_Q2>=Area_Q3)) and (Area_Q2>=Area_Q4)):
-		#print 'fix2', Error
+		#print( 'fix2', Error
 		Area_Q2=Area_Q2+Error
 	elif  (((Area_Q3>=Area_Q1) and (Area_Q3>=Area_Q2)) and (Area_Q3>=Area_Q4)):
-		#print 'fix3',Error
+		#print( 'fix3',Error
 		Area_Q3=Area_Q3+Error
-   	elif  (((Area_Q4>=Area_Q1) and (Area_Q4>=Area_Q2)) and (Area_Q4>=Area_Q3)):
-		#print 'fix4',Error
+	elif  (((Area_Q4>=Area_Q1) and (Area_Q4>=Area_Q2)) and (Area_Q4>=Area_Q3)):
+		#print( 'fix4',Error
 		Area_Q4=Area_Q4+Error
 	else:
-		print 'There is some thing wrong with this hexagon. Something very wrong'
+		print( 'There is some thing wrong with this hexagon. Something very wrong')
 
 	#Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
 	Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
 	if ((abs(Error)>0.01)):
-		print 'The hexagon error is still too large!!!', Error
+		print( 'The hexagon error is still too large!!!', Error)
 
 
 
@@ -468,7 +468,7 @@ def find_intersect_using_metric(Ax,Ay, Bx, By, Cx, Cy):
 	elif M_BC<=min(M_AC, M_AB):
 		return BC_px, BC_py, BC_qx, BC_qy
 	else: 
-		print 'You should not get here'
+		print( 'You should not get here')
 		halt
 
 def find_intersect_using_metric_and_lines(Ax,Ay, Bx, By, Cx, Cy,Px, Py, Qx, Qy, Rx, Ry, Sx, Sy):
@@ -492,14 +492,14 @@ def find_intersect_using_metric_and_lines(Ax,Ay, Bx, By, Cx, Cy,Px, Py, Qx, Qy,
 	elif M_BC<=min(M_AC, M_AB):
 		return BC_px, BC_py, BC_qx, BC_qy
 	else: 
-		print 'You should not get here'
+		print( 'You should not get here')
 		halt
 
 
 def point_in_interval_metric(Ax,Ay,Bx,By,px,py,qx,qy):
 	metric=0.0
-	#print 'Ax,Ay,Bx,By',Ax,Ay,Bx,By,px,py,qx,qy
-	#print 'px,py,qx,qy',px,py,qx,qy
+	#print( 'Ax,Ay,Bx,By',Ax,Ay,Bx,By,px,py,qx,qy
+	#print( 'px,py,qx,qy',px,py,qx,qy
 
 	#Finds a metric for how close a point is to being inside an interval. If it is inside, then metric is equal to zero.
 	Mx1= max(px - max(Ax,Bx),0.)  #Zero is px <= max(Ax,Bx)
@@ -507,7 +507,7 @@ def point_in_interval_metric(Ax,Ay,Bx,By,px,py,qx,qy):
 	My1= max(py - max(Ay,By),0.)  #Zero is px <= max(Ax,Bx)
 	My2= max( min(Ay,By)-py ,0.)  #Zero is px <= max(Ax,Bx)
 	p_metric=abs(Mx1)+abs(Mx2)+abs(My1)+abs(My2)
-	#print 'Mx1, Mx2, My1, My2', Mx1, Mx2, My1, My2 
+	#print( 'Mx1, Mx2, My1, My2', Mx1, Mx2, My1, My2 
 
 	#Finds a metric for how close a point is to being inside an interval. If it is inside, then metric is equal to zero.
 	Mx1= max(qx - max(Ax,Bx),0.)  #Zero is qx <= max(Ax,Bx)
@@ -533,11 +533,11 @@ def Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy):
 	[Area_Right ,Area_Left]=divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,'y');
 	 
 	#Decide if the origin is in the triangle
-	if point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.):  #Then you have to divide area 4 ways.
+	if point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.):	#Then you have to divide area 4 ways.
 		#Find a line in the triangle that cuts both axes in/on the trianlge
-	    	[px, py]=intercept_of_a_line(Ax,Ay,Bx,By,'x'); #x_intercept
-	    	[qx, qy]=intercept_of_a_line(Ax,Ay,Bx,By,'y'); #y_intercept
-	    	if (point_in_interval(Ax,Ay,Bx,By,px,py) & point_in_interval(Ax,Ay,Bx,By,qx,qy))==False:
+		[px, py]=intercept_of_a_line(Ax,Ay,Bx,By,'x'); #x_intercept
+		[qx, qy]=intercept_of_a_line(Ax,Ay,Bx,By,'y'); #y_intercept
+		if (point_in_interval(Ax,Ay,Bx,By,px,py) & point_in_interval(Ax,Ay,Bx,By,qx,qy))==False:
 			[px, py]=intercept_of_a_line(Ax,Ay,Cx,Cy,'x'); #x_intercept
 			[qx, qy]=intercept_of_a_line(Ax,Ay,Cx,Cy,'y'); #y_intercept
 			if (point_in_interval(Ax,Ay,Cx,Cy,px,py) & point_in_interval(Ax,Ay,Cx,Cy,qx,qy))==False:
@@ -546,7 +546,7 @@ def Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy):
 				if (point_in_interval(Bx,By,Cx,Cy,px,py) & point_in_interval(Bx,By,Cx,Cy,qx,qy))==False:
 					#point_in_interval_metric
 					[px, py, qx, qy]= find_intersect_using_metric(Ax,Ay, Bx, By, Cx, Cy)
-					#print 'Houston, we have a problem'
+					#print( 'Houston, we have a problem'
 					#plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy)
 					#halt
 
@@ -555,27 +555,27 @@ def Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy):
 		if Area_key_quadrant>0.0:
 			if px>=0. and qy>=0.: #First quadrant
 				Key_quadrant=1;
-			elif px<0. and qy>=0.:  #Second quadrant
+			elif px<0. and qy>=0.:	#Second quadrant
 				Key_quadrant=2;
 			elif px<0. and qy<0.:
-				Key_quadrant=3;  #Third quadrant
+				Key_quadrant=3;	 #Third quadrant
 			else:
-				Key_quadrant=4;  #Forth quadrant
+				Key_quadrant=4;	 #Forth quadrant
 	    
 	#if (point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.) is False) or (Area_key_quadrant==0):
 	if Area_key_quadrant==0:
-	#else:  #Then at least one quadrant is empty, and this can be used to find the areas in the other quadrant.  Assigning quadrants. Key_quadrant is the empty quadrant.
-		#print 'Mother...'
-		#print 'Ax, Ay',Ax,Ay
-		#print 'Bx, By',Bx,By
-		#print 'Cx, Cy',Cx,Cy
+	#else:	#Then at least one quadrant is empty, and this can be used to find the areas in the other quadrant.  Assigning quadrants. Key_quadrant is the empty quadrant.
+		#print( 'Mother...'
+		#print( 'Ax, Ay',Ax,Ay
+		#print( 'Bx, By',Bx,By
+		#print( 'Cx, Cy',Cx,Cy
 		Area_key_quadrant=0;
 		if (((Ax>0. and Ay>0.) or (Bx>0. and By>0.) or (Cx>0. and Cy>0.))==False)  and (Area_Upper+Area_Right<=Area_triangle):
 		#if (((Ax>=0. and Ay>=0.) or (Bx>=0. and By>=0.) or (Cx>=0. and Cy>=0.))==False)  and (Area_Upper+Area_Right<=Area_triangle):
 			#No points land in this quadrant and triangle does not cross the quadrant
 			Key_quadrant=1;
 		elif  (((Ax<0. and Ay>0) or (Bx<0. and By>0.) or (Cx<0. and Cy>0.))==False)  and (Area_Upper+Area_Left<=Area_triangle):
-			#elif  (((Ax<0. and Ay>=0) or (Bx<0. and By>=0.) or (Cx<0. and Cy>=0.))==False)  and (Area_Upper+Area_Left<=Area_triangle):
+			#elif  (((Ax<0. and Ay>=0) or (Bx<0. and By>=0.) or (Cx<0. and Cy>=0.))==False)	 and (Area_Upper+Area_Left<=Area_triangle):
 			Key_quadrant=2;
 		elif (((Ax<0. and Ay<0.) or (Bx<0. and By<0.) or (Cx<0. and Cy<0.))==False) & (Area_Lower+Area_Left<=Area_triangle):
 			#elif (((Ax<0. and Ay<0.) or (Bx<0. and By<0.) or (Cx<0. and Cy<0.))==False) & (Area_Lower+Area_Left<=Area_triangle):
@@ -609,7 +609,7 @@ def Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy):
 		#Area_Q3=Area_Left-Area_Q2;
 		Area_Q3=Area_triangle-Area_Q1-Area_Q2-Area_Q4;
 	else:
-	    print 'Help, I need somebody, help!'
+	    print( 'Help, I need somebody, help!')
 	    halt
 	
 	Area_Q1=max(Area_Q1,0.); 
@@ -621,14 +621,14 @@ def Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy):
 	#Marker 1
 	if Error>1e-15:
 	#if True:
-		print 'The triangles are not accurate enough. This is a problem!'
-		print 'Triangle corners: ' ,Ax,Ay,Bx,By,Cx,Cy
-		print 'Error',Error
-		print 'Key_quadrant', Key_quadrant 
-		print 'Area Key_quadrant', Area_key_quadrant 
-		print 'Upper, Lower',Area_Upper ,Area_Lower
-		print 'Left, Right ', Area_Right ,Area_Left
-		print 'Point in triangle', point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.)
+		print( 'The triangles are not accurate enough. This is a problem!')
+		print( 'Triangle corners: ' ,Ax,Ay,Bx,By,Cx,Cy)
+		print( 'Error',Error)
+		print( 'Key_quadrant', Key_quadrant )
+		print( 'Area Key_quadrant', Area_key_quadrant )
+		print( 'Upper, Lower',Area_Upper ,Area_Lower)
+		print( 'Left, Right ', Area_Right ,Area_Left)
+		print( 'Point in triangle', point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.))
 		#plt.plot(np.array([Ax,Bx,Cx,Ax]),np.array([Ay, By, Cy,Ay]))
 		#plt.plot(np.array([-0.5,0.5]),np.array([0.,0.]),'k')
 		#plt.plot(np.array([0.,0.]),np.array([-0.5,0.5]),'k')
@@ -653,13 +653,13 @@ def find_quadrant_using_lines(x0 , y0 , Px, Py, Qx, Qy, Rx, Ry, Sx, Sy): #Findin
 	elif (above_PQ==-1) and (above_RS==1):
 		quadrant=4
 	else:
-		#print 'Point not in a quadrant!'
+		#print( 'Point not in a quadrant!'
 		quadrant=0
 		#halt
 
 	return quadrant
 
-def Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ):#Divides the triangle into 4 parts, across two intersecting lines. PQ, RS intersect at origin (for now)
+def Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy	):#Divides the triangle into 4 parts, across two intersecting lines. PQ, RS intersect at origin (for now)
 	Area_key_quadrant=0.0
 	Area_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
 	#if Area_triangle==0.0:
@@ -672,18 +672,18 @@ def Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry,
 	[Area_Right ,Area_Left] =divding_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Rx, Ry, Sx, Sy);
 	 
 	#Decide if the origin is in the triangle
-	if point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.):  #Then you have to divide area 4 ways.
+	if point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.):	#Then you have to divide area 4 ways.
 		#Find a line in the triangle that cuts both axes in/on the trianlge
-	    	[px, py]=intercept_of_two_lines(Ax,Ay,Bx,By,Px, Py, Qx, Qy); #PQ_intercept
-	    	[qx, qy]=intercept_of_two_lines(Ax,Ay,Bx,By,Rx, Ry, Sx, Sy); #RS_intercept
-	    	if (point_in_interval(Ax,Ay,Bx,By,px,py) & point_in_interval(Ax,Ay,Bx,By,qx,qy))==False:
+		[px, py]=intercept_of_two_lines(Ax,Ay,Bx,By,Px, Py, Qx, Qy); #PQ_intercept
+		[qx, qy]=intercept_of_two_lines(Ax,Ay,Bx,By,Rx, Ry, Sx, Sy); #RS_intercept
+		if (point_in_interval(Ax,Ay,Bx,By,px,py) & point_in_interval(Ax,Ay,Bx,By,qx,qy))==False:
 			[px, py]=intercept_of_two_lines(Ax,Ay,Cx,Cy,Px, Py, Qx, Qy); #PQ_intercept
 			[qx, qy]=intercept_of_two_lines(Ax,Ay,Cx,Cy,Rx, Ry, Sx, Sy); #RS_intercept
 			if (point_in_interval(Ax,Ay,Cx,Cy,px,py) & point_in_interval(Ax,Ay,Cx,Cy,qx,qy))==False:
 				[px, py]=intercept_of_two_lines(Bx,By,Cx,Cy,Px, Py, Qx, Qy); #PQ_intercept
 				[qx, qy]=intercept_of_two_lines(Bx,By,Cx,Cy,Rx, Ry, Sx, Sy); #RS_intercept
 				if (point_in_interval(Bx,By,Cx,Cy,px,py) & point_in_interval(Bx,By,Cx,Cy,qx,qy))==False:
-					#print 'Houston, we have a problem'
+					#print( 'Houston, we have a problem'
 					[px, py, qx, qy]= find_intersect_using_metric_and_lines(Ax,Ay, Bx, By, Cx, Cy,Px, Py, Qx, Qy, Rx, Ry, Sx, Sy)
 					#plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy)
 					#halt
@@ -692,27 +692,27 @@ def Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry,
 		Area_key_quadrant=Area_of_triangle(px,py,qx,qy,0.,0.);
 		if px>=0. and qy>=0.: #First quadrant  (I think the zeros here are because the PQ, RS intersect at zero)
 			Key_quadrant=1;
-		elif px<0. and qy>=0.:  #Second quadrant
+		elif px<0. and qy>=0.:	#Second quadrant
 			Key_quadrant=2;
 		elif px<0. and qy<0.:
-			Key_quadrant=3;  #Third quadrant
+			Key_quadrant=3;	 #Third quadrant
 		else:
-			Key_quadrant=4;  #Forth quadrant
+			Key_quadrant=4;	 #Forth quadrant
 	    
 	if Area_key_quadrant==0:
-		#else:  #Then at least one quadrant is empty, and this can be used to find the areas in the other quadrant.  Assigning quadrants. Key_quadrant is the empty quadrant.
-		#print 'Mother...'
-		#print 'Ax, Ay',Ax,Ay
-		#print 'Bx, By',Bx,By
-		#print 'Cx, Cy',Cx,Cy
+		#else:	#Then at least one quadrant is empty, and this can be used to find the areas in the other quadrant.  Assigning quadrants. Key_quadrant is the empty quadrant.
+		#print( 'Mother...'
+		#print( 'Ax, Ay',Ax,Ay
+		#print( 'Bx, By',Bx,By
+		#print( 'Cx, Cy',Cx,Cy
 		Area_key_quadrant=0;
 		#Finding which quadrant the triangle points fall in.
 		A_quad = find_quadrant_using_lines(Ax,Ay,Px, Py, Qx, Qy, Rx, Ry, Sx, Sy)
 		B_quad = find_quadrant_using_lines(Bx,By,Px, Py, Qx, Qy, Rx, Ry, Sx, Sy)
 		C_quad = find_quadrant_using_lines(Cx,Cy,Px, Py, Qx, Qy, Rx, Ry, Sx, Sy)
-		#print 'A_quad, B_quad, C_quad',A_quad, B_quad, C_quad
+		#print( 'A_quad, B_quad, C_quad',A_quad, B_quad, C_quad
 
-		if (((A_quad==1) or (B_quad==1) or (C_quad==1))==False)  and (Area_Upper+Area_Right<=Area_triangle):
+		if (((A_quad==1) or (B_quad==1) or (C_quad==1))==False)	 and (Area_Upper+Area_Right<=Area_triangle):
 			#No points land in this quadrant and triangle does not cross the quadrant
 			Key_quadrant=1;
 		elif  (((A_quad==2) or (B_quad==2) or (C_quad==2))==False)  and (Area_Upper+Area_Left<=Area_triangle):
@@ -722,7 +722,7 @@ def Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry,
 		else:
 			Key_quadrant=4;
 	
-		#print Key_quadrant
+		#print( Key_quadrant
 	#Assign values to quadrants
 	if Key_quadrant==1:
 		Area_Q1=Area_key_quadrant;
@@ -749,7 +749,7 @@ def Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry,
 		#Area_Q3=Area_Left-Area_Q2;
 		Area_Q3=Area_triangle-Area_Q1-Area_Q2-Area_Q4;
 	else:
-	    print 'Help, I need somebody, help!'
+	    print( 'Help, I need somebody, help!')
 	    halt
 	
 	Area_Q1=max(Area_Q1,0.); 
@@ -760,30 +760,30 @@ def Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry,
 	Error=abs(Area_Q1+Area_Q2+Area_Q3+Area_Q4-Area_triangle)
 	if Error>1e-15:
 	#if True:
-		print 'The triangles are not accurate enough. This is a problem!'
-		print 'Triangle corners: ' ,Ax,Ay,Bx,By,Cx,Cy
-		print 'Error',Error
-		print 'Key_quadrant', Key_quadrant 
-		print 'Area Key_quadrant', Area_key_quadrant 
-		print 'Upper, Lower',Area_Upper ,Area_Lower
-		print 'Left, Right ', Area_Right ,Area_Left
-		print 'Point in triangle', point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.)
+		print( 'The triangles are not accurate enough. This is a problem!')
+		print( 'Triangle corners: ' ,Ax,Ay,Bx,By,Cx,Cy)
+		print( 'Error',Error)
+		print( 'Key_quadrant', Key_quadrant )
+		print( 'Area Key_quadrant', Area_key_quadrant )
+		print( 'Upper, Lower',Area_Upper ,Area_Lower)
+		print( 'Left, Right ', Area_Right ,Area_Left)
+		print( 'Point in triangle', point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.))
 		#return
 
 	return [Area_triangle, Area_Q1, Area_Q2 ,Area_Q3 ,Area_Q4]
 
 def divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1):
-	if axes1=='x':  #Use the y-coordinates for if statements to see which side of the line you are on
+	if axes1=='x':	#Use the y-coordinates for if statements to see which side of the line you are on
 		A0=Ay; B0=By;  C0=Cy;
-	if axes1=='y':  #Use the y-coordinates for if statements to see which side of the line you are on
+	if axes1=='y':	#Use the y-coordinates for if statements to see which side of the line you are on
 		A0=Ax; B0=Bx;  C0=Cx;
  
-	#print 'A0,B0,C0', A0,B0,C0
+	#print( 'A0,B0,C0', A0,B0,C0
 	A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
-	if B0*C0>0.: #then B and C are on the same side  (and non-zero)
-		#print 'HHHH1'	
+	if B0*C0>0.: #then B and C are on the same side	 (and non-zero)
+		#print( 'HHHH1'	
 		if A0*B0>=0.: #then all three on the the same side (if it equals zero, then A0=0 and the otehrs are not)
-			if (A0>0.)  or  (A0==0. and  B0>0.):
+			if (A0>0.)  or	(A0==0. and  B0>0.):
 				Area_positive= A_triangle;
 				Area_negative= 0.;
 			else:
@@ -793,43 +793,43 @@ def divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1):
 			[Area_positive, Area_negative]=Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1);
 
 	elif B0*C0<0.: #then B and C are on the opposite sides
-		#print 'HHHH2'	
+		#print( 'HHHH2'	
 		if A0*B0>=0.:  #then C is all alone
 			[Area_positive, Area_negative]=Area_of_triangle_across_axes(Cx,Cy,Bx,By,Ax,Ay,axes1);
 		else: #then B is all alone
 			[Area_positive, Area_negative]=Area_of_triangle_across_axes(Bx,By,Cx,Cy,Ax,Ay,axes1);
 
 	else:  #This is the case when either B or C is equal to zero (or both), A0 could be zero too.
-		#print 'HHHH3'	
+		#print( 'HHHH3'	
 		if (A0==0. and B0==0. and C0==0.):
 			Area_positive= 0.;
 			Area_negative= 0.;
-		elif (A0*B0<0.)  or  (A0*C0<0.):    #A, B are on opposite sides, and C is zero.  OR  A, C are on opposite sides, and B is zero.
+		elif (A0*B0<0.)	 or  (A0*C0<0.):    #A, B are on opposite sides, and C is zero.	 OR  A, C are on opposite sides, and B is zero.
 			[Area_positive, Area_negative]=Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1);
-			#print 'HHHH6'	
+			#print( 'HHHH6'	
 		elif (A0*B0>0.) or (A0*C0>0.) or (abs(A0)>0. and (B0==0.) and (C0==0.)):
-			#print 'HHHH7'	
-		        if (A0>0.):
-		        	Area_positive= A_triangle;
+			#print( 'HHHH7'	
+			if (A0>0.):
+				Area_positive= A_triangle;
 				Area_negative= 0.;
-        		else:
+			else:
 				Area_positive= 0.;
 				Area_negative= A_triangle;
     
-    		elif A0==0.:  #(Also, one of B,C is zero too)
-			#print 'HHHH8'	
+		elif A0==0.:  #(Also, one of B,C is zero too)
+			#print( 'HHHH8'	
 			if B0>0. or C0>0.:
 				Area_positive= A_triangle;
 				Area_negative= 0.;
 			elif B0<0. or C0<0.:
 				Area_positive= 0.;
 				Area_negative= A_triangle;
-		        else:
-				print 'You should not get here1'
+			else:
+				print( 'You should not get here1')
 				halt
-    		else:
-			print 'You should not get here2'
-			print Ax,Ay,Bx,By,Cx,Cy
+		else:
+			print( 'You should not get here2')
+			print( Ax,Ay,Bx,By,Cx,Cy)
 			halt
 	
 	return [Area_positive, Area_negative]
@@ -839,14 +839,14 @@ def divding_triangle_across_line2(Ax,Ay,Bx,By,Cx,Cy,  Px, Py, Qx, Qy ):
 	B0= Above_on_below_line(Bx,By, Px, Py, Qx, Qy)
 	C0= Above_on_below_line(Cx,Cy, Px, Py, Qx, Qy) 
 	
-	#print 'A0,B0,C0', A0,B0,C0
-	#print Px, Py, Qx, Qy
+	#print( 'A0,B0,C0', A0,B0,C0
+	#print( Px, Py, Qx, Qy
  
 	A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
-	if B0*C0>0.: #then B and C are on the same side  (and non-zero)
-		#print 'GGG1'
+	if B0*C0>0.: #then B and C are on the same side	 (and non-zero)
+		#print( 'GGG1'
 		if A0*B0>=0.: #then all three on the the same side (if it equals zero, then A0=0 and the otehrs are not)
-			if (A0>0.)  or  (A0==0. and  B0>0.):
+			if (A0>0.)  or	(A0==0. and  B0>0.):
 				Area_positive= A_triangle;
 				Area_negative= 0.;
 			else:
@@ -856,66 +856,66 @@ def divding_triangle_across_line2(Ax,Ay,Bx,By,Cx,Cy,  Px, Py, Qx, Qy ):
 			[Area_positive, Area_negative]=Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy );
 
 	elif B0*C0<0.: #then B and C are on the opposite sides
-		#print 'GGG2'
+		#print( 'GGG2'
 		if A0*B0>=0.:  #then C is all alone
 			[Area_positive, Area_negative]=Area_of_triangle_across_line(Cx,Cy,Bx,By,Ax,Ay, Px, Py, Qx, Qy );
 		else: #then B is all alone
 			[Area_positive, Area_negative]=Area_of_triangle_across_line(Bx,By,Cx,Cy,Ax,Ay, Px, Py, Qx, Qy );
 
 	else:  #This is the case when either B or C is equal to zero (or both), A0 could be zero too.
-		#print 'GGG3'
+		#print( 'GGG3'
 		if (A0==0. and B0==0. and C0==0.):
 			Area_positive= 0.;
 			Area_negative= 0.;
-		elif (A0*B0<0.)  or  (A0*C0<0.):    #A, B are on opposite sides, and C is zero.  OR  A, C are on opposite sides, and B is zero.
+		elif (A0*B0<0.)	 or  (A0*C0<0.):    #A, B are on opposite sides, and C is zero.	 OR  A, C are on opposite sides, and B is zero.
 			[Area_positive, Area_negative]=Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy);
-			#print 'GGG5', Area_positive, Area_negative
+			#print( 'GGG5', Area_positive, Area_negative
 		elif (A0*B0>0.) or (A0*C0>0.) or (abs(A0)>0. and (B0==0.) and (C0==0.)):
-		        if (A0>0.):
-		        	Area_positive= A_triangle;
+			if (A0>0.):
+				Area_positive= A_triangle;
 				Area_negative= 0.;
-        		else:
+			else:
 				Area_positive= 0.;
 				Area_negative= A_triangle;
     
-    		elif A0==0.:  #(Also, one of B,C is zero too)
+		elif A0==0.:  #(Also, one of B,C is zero too)
 			if B0>0. or C0>0.:
 				Area_positive= A_triangle;
 				Area_negative= 0.;
 			elif B0<0. or C0<0.:
 				Area_positive= 0.;
 				Area_negative= A_triangle;
-		        else:
-				print 'You should not get here1'
+			else:
+				print( 'You should not get here1')
 				halt
-    		else:
-			print 'You should not get here2'
-			print Ax,Ay,Bx,By,Cx,Cy
+		else:
+			print( 'You should not get here2')
+			print( Ax,Ay,Bx,By,Cx,Cy)
 			halt
 	
 	return [Area_positive, Area_negative]
 
 
-def divding_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy,   Px, Py, Qx, Qy ):  #Triangle is ABC, line is PQ
+def divding_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy,   Px, Py, Qx, Qy ):	 #Triangle is ABC, line is PQ
 	A0= Above_on_below_line(Ax,Ay, Px, Py, Qx, Qy)
 	B0= Above_on_below_line(Bx,By, Px, Py, Qx, Qy)
 	C0= Above_on_below_line(Cx,Cy, Px, Py, Qx, Qy) 
-	#print 'BBB0', A0, B0, C0
+	#print( 'BBB0', A0, B0, C0
 
 	A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
 	# B and C are on the same side of the line
 	#if (Point_above_line(Bx,By, Px, Py, Qx, Qy)==Point_above_line(Cx,Cy, Px, Py, Qx, Qy)) :
-	#if ((B0==C0) and (B0!=0))  or ((B0==0 or C0==0) and np.max(B0,C0)>0.5)   :
+	#if ((B0==C0) and (B0!=0))  or ((B0==0 or C0==0) and np.max(B0,C0)>0.5)	  :
 	if ((B0==C0) and (B0!=0))  or ((B0==0 or C0==0))   : #B and C on the same side or B or C is zero
-		#print 'BBB1'
+		#print( 'BBB1'
 		[Area_positive, Area_negative]=Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy);
 	else: #then B and C are on the opposite sides
 		#if Point_above_line(Ax,Ay, Px, Py, Qx, Qy)==Point_above_line(Bx,By, Px, Py, Qx, Qy):  #then C is all alone
 		if A0*B0>=0.:  #then C is all alone
-			#print 'BBB2'
+			#print( 'BBB2'
 			[Area_positive, Area_negative]=Area_of_triangle_across_line(Cx,Cy,Bx,By,Ax,Ay, Px, Py, Qx, Qy);
 		else: #then B is all alone
-			#print 'BBB3'
+			#print( 'BBB3'
 			[Area_positive, Area_negative]=Area_of_triangle_across_line(Bx,By,Cx,Cy,Ax,Ay, Px, Py, Qx, Qy);
 
 	return [Area_positive, Area_negative]
@@ -958,7 +958,7 @@ def intercept_of_a_line(Ax,Ay,Bx,By,axes1):
 	if axes1=='y': #y intercept
 		if (Ax==Bx)==False:
 			x0=0.; 
-			y0=-(((Ay-By)/(Ax-Bx))*Ax)+Ay;  
+			y0=-(((Ay-By)/(Ax-Bx))*Ax)+Ay;	
 		else:
 			x0=No_intercept_val;
 			y0=No_intercept_val;
@@ -990,18 +990,18 @@ def intercept_of_two_lines(Ax,Ay,Bx,By,Px,Py,Qx,Qy):
 		else:
 			m1=(Ay-By)/(Ax-Bx)
 			if (Px==Qx):
-				print 'Stop2'
+				print( 'Stop2')
 				(x0 , y0) =intercept_of_a_line(Ax-Px,Ay,Bx-Px,By,'y')
 				x0=Px
 			else:
 				m2=(Py-Qy)/(Px-Qx)
 				if m1==m2:
-					print 'Stop3'
+					print( 'Stop3')
 					x0=No_intercept_val;
 					y0=No_intercept_val;
 					halt2
 				else:
-					print 'Stop4'
+					print( 'Stop4')
 					x0=(1/(m1-m2))*( (m1*Ax -Ay) -(m2*Px - Py))
 					y0=m1*(x0-Ax)+Ay
 	
@@ -1009,7 +1009,7 @@ def intercept_of_two_lines(Ax,Ay,Bx,By,Px,Py,Qx,Qy):
 
 
 def Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axis1):#In this fuction, A is the point on one side of the axis, and B,C are on the opposite sides
-	#print 'Area_of_triangle_across_axes' ,Ax,Ay,Bx,By,Cx,Cy
+	#print( 'Area_of_triangle_across_axes' ,Ax,Ay,Bx,By,Cx,Cy
 	A_triangle2=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
 	[pABx, pABy]=intercept_of_a_line(Ax,Ay,Bx,By,axis1);
 	[pACx, pACy]=intercept_of_a_line(Ax,Ay,Cx,Cy,axis1);
@@ -1018,7 +1018,7 @@ def Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axis1):#In this fuction, A is
 	if axis1=='y':
 		A0=Ax; #Value used for if statements (deciding up/down vs left/right)
 	
-	#print 'QQQ', Ax,Ay,pABx,pABy,pACx,pACy
+	#print( 'QQQ', Ax,Ay,pABx,pABy,pACx,pACy
 	A_half_triangle=Area_of_triangle(Ax,Ay,pABx,pABy,pACx,pACy);
 	if (A0>=0.):
 		Area_positive= A_half_triangle;
@@ -1068,21 +1068,21 @@ def Point_above_line(x,y,Px, Py, Qx, Qy): #If the point is above the line, then
 def Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px,Py, Qx, Qy, debug=False):
 	#In this fuction, B and C are the same side of the line. (I think this works even if B and/or C are on the line too)
 	#A is unknown. PQ is the line.
-	#print 'RRR Area_of_triangle_across_line' ,Ax,Ay,Bx,By,Cx,Cy
+	#print( 'RRR Area_of_triangle_across_line' ,Ax,Ay,Bx,By,Cx,Cy
 	
 	if (Ax==Bx and Ay==By) or (Ax==Cx and Ay==Cy) or (Cx==Bx and Cy==By):
-		#print 'AAA1'
+		#print( 'AAA1'
 		Area_positive=0.0
 		Area_negative=0.0
 	else:
-		#print 'AAA2'
+		#print( 'AAA2'
 		A0= Above_on_below_line(Ax,Ay, Px, Py, Qx, Qy)
 		B0= Above_on_below_line(Bx,By, Px, Py, Qx, Qy)
 		C0= Above_on_below_line(Cx,Cy, Px, Py, Qx, Qy) 
 		A_triangle2=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
 
 		if check_if_point_is_on_the_line(Px,Py,Qx,Qy, Ax,Ay):  #Is point A on the line?
-			#print 'AAA3'
+			#print( 'AAA3'
 			#if Point_above_line(Bx,By, Px,Py, Qx, Qy) or Point_above_line(Cx,Cy, Px,Py, Qx, Qy):
 			if B0==1 or C0==1:
 				Area_positive= A_triangle2;
@@ -1093,9 +1093,9 @@ def Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px,Py, Qx, Qy, debug=False):
 		else: #If A is not on the line
 			#If A is on the same side of the line as B and C
 			#All on the same side of the line
-			if ((A0==B0 and A0==C0)  or (A0==B0 and C0==0) or (A0==C0 and B0==0)):  
-			#if Point_above_line(Ax,Ay, Px,Py, Qx, Qy) == Point_above_line( Bx,By, Px,Py, Qx, Qy)  and (Point_above_line(Ax,Ay,Px,Py,Qx,Qy)==Point_above_line(Cx,Cy,Px,Py,Qx,Qy)):  
-				#print 'AAA4'
+			if ((A0==B0 and A0==C0)	 or (A0==B0 and C0==0) or (A0==C0 and B0==0)):	
+			#if Point_above_line(Ax,Ay, Px,Py, Qx, Qy) == Point_above_line( Bx,By, Px,Py, Qx, Qy)  and (Point_above_line(Ax,Ay,Px,Py,Qx,Qy)==Point_above_line(Cx,Cy,Px,Py,Qx,Qy)):	
+				#print( 'AAA4'
 				#if Point_above_line(Bx,By, Px,Py, Qx, Qy) or Point_above_line(Cx,Cy, Px,Py, Qx, Qy):
 				if A0==1 or C0==1:
 					Area_positive= A_triangle2;
@@ -1103,7 +1103,7 @@ def Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px,Py, Qx, Qy, debug=False):
 				else:
 					Area_positive= 0.0;
 					Area_negative= A_triangle2;
-			elif (C0==0 and B0==0 and (abs(A0)>0)):  
+			elif (C0==0 and B0==0 and (abs(A0)>0)):	 
 				if Point_above_line(Ax,Ay, Px,Py, Qx, Qy):
 					Area_positive= A_triangle2;
 					Area_negative= 0.0;
@@ -1112,10 +1112,10 @@ def Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px,Py, Qx, Qy, debug=False):
 					Area_negative= A_triangle2;
 
 			else:  #If A is not on the same side of the line as B and C
-				#print 'AAA5'
+				#print( 'AAA5'
 				[pABx, pABy]=intercept_of_two_lines(Ax,Ay,Bx,By, Px, Py, Qx, Qy);
 				[pACx, pACy]=intercept_of_two_lines(Ax,Ay,Cx,Cy, Px, Py, Qx, Qy);
-				#print 'Tri2', Ax,Ay,pABx,pABy,pACx,pACy
+				#print( 'Tri2', Ax,Ay,pABx,pABy,pACx,pACy
 				
 				A_half_triangle=Area_of_triangle(Ax,Ay,pABx,pABy,pACx,pACy);
 				if Point_above_line(Ax,Ay , Px,Py,Qx,Qy):
@@ -1128,17 +1128,17 @@ def Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px,Py, Qx, Qy, debug=False):
 	return [Area_positive, Area_negative]
 
 def Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy):
-	Area    =   abs(    0.5*((Ax*(By-Cy))+(Bx*(Cy-Ay))+(Cx*(Ay-By))) );
+	Area	=   abs(    0.5*((Ax*(By-Cy))+(Bx*(Cy-Ay))+(Cx*(Ay-By))) );
 	return Area
 
 
 def point_in_interval(Ax,Ay,Bx,By,px,py):
 	point_is_in_interval=False
-	#print 'NNN1'
+	#print( 'NNN1'
 	if ((px <= max(Ax,Bx)) and (px >= min(Ax,Bx))):
-		#print 'NNN2', 'py=', py,  'max=',max(Ay,By), 'XXX', (py - max(Ay,By))
+		#print( 'NNN2', 'py=', py,  'max=',max(Ay,By), 'XXX', (py - max(Ay,By))
 		if ((py <= max(Ay,By)) and (py >= min(Ay,By))):
-			##print 'NNN3'
+			##print( 'NNN3'
 			point_is_in_interval=True
 	return point_is_in_interval
 
@@ -1154,7 +1154,7 @@ def rotate_and_translate(px,py,theta,x0,y0):
 def point_in_triangle_old(Ax,Ay,Bx,By,Cx,Cy,qx,qy):
 	#if False:
 	if (Ax==qx and Ay==qy) or (Bx==qx and By==qy) or (Cx==qx and Cy==qy):  #Exclude the pathelogical case
-	        	point_is_in_triangle = 0.;
+			point_is_in_triangle = 0.;
 	else:
 		if (check_if_point_is_on_the_line(Ax,Ay,Bx,By,qx,qy) or (check_if_point_is_on_the_line(Ax,Ay,Cx,Cy,qx,qy)) or (check_if_point_is_on_the_line(Bx,By,Cx,Cy,qx,qy))):
 			point_is_in_triangle = 0;
@@ -1188,7 +1188,7 @@ def point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,qx,qy):
 	point_is_in_triangle = 0;
 
 	if (Ax==qx and Ay==qy) or (Bx==qx and By==qy) or (Cx==qx and Cy==qy):  #Exclude the pathelogical case
-	        	point_is_in_triangle = 0.;
+			point_is_in_triangle = 0.;
 	else:
 		if (check_if_point_is_on_the_line(Ax,Ay,Bx,By,qx,qy) or (check_if_point_is_on_the_line(Ax,Ay,Cx,Cy,qx,qy)) or (check_if_point_is_on_the_line(Bx,By,Cx,Cy,qx,qy))):
 			point_is_in_triangle = 0;
@@ -1221,16 +1221,16 @@ def roundoff(x,sig_fig):
 
 def square_spreading_calculation(x,y,L):
 	xL=min(0.5, max(0., 0.5-(x/L)))
-        xR=min(0.5, max(0., (x/L)+(0.5-(1/L) )))
-        xC=max(0., 1.-(xL+xR))
-        yD=min(0.5, max(0., 0.5-(y/L)))
-        yU=min(0.5, max(0., (y/L)+(0.5-(1/L) )))
-        yC=max(0., 1.-(yD+yU))
+	xR=min(0.5, max(0., (x/L)+(0.5-(1/L) )))
+	xC=max(0., 1.-(xL+xR))
+	yD=min(0.5, max(0., 0.5-(y/L)))
+	yU=min(0.5, max(0., (y/L)+(0.5-(1/L) )))
+	yC=max(0., 1.-(yD+yU))
 
 def plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy, Px=None, Py=None, Qx=None, Qy=None, Rx=None, Ry=None, Sx=None, Sy=None):
 	if Px is None:
 		Px=-1. ; Py=0. ; Qx=1. ; Qy=0. #x-axis 
-                Rx=0. ; Ry=-1. ; Sx=0. ; Sy=1. #y-axis 
+		Rx=0. ; Ry=-1. ; Sx=0. ; Sy=1. #y-axis 
 	plt.plot(np.array([Px, Qx]), np.array([Py, Qy]))
 	plt.plot(np.array([Rx, Sx]), np.array([Ry, Sy]))
 	plt.plot(np.array([Ax, Bx, Cx, Ax]), np.array([Ay, By, Cy, Ay]))
@@ -1268,7 +1268,7 @@ def main():
 		#plt.plot(Px,Py,'*')
 		#plt.plot(Qx,Qy,'*')
 
-		print 'x0, y0' , x0 , y0
+		print( 'x0, y0' , x0 , y0)
 		plt.show()
 
 
@@ -1294,16 +1294,16 @@ def main():
 									x=divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1)
 									y=divding_triangle_across_line2(Ax,Ay,Bx,By,Cx,Cy, Px,Py, Qx, Qy)
 									#y=divding_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px,Py, Qx, Qy)
-									#if abs(x[0]-y[0])>0 or  abs(x[1]-y[1])>0 or  abs(x[0]-z[0])>0 or  abs(x[1]-z[1])>0:
-									if abs(x[0]-y[0])>0 or  abs(x[1]-y[1])>0:
-										print 'Broken!!!: ', 'Ax, Ay =', Ax, Ay, 'Bx, By =' , Bx, By, 'Cx, Cy =' ,Cx, Cy
-										print 'count', count
-										print x
-										print y
+									#if abs(x[0]-y[0])>0 or	 abs(x[1]-y[1])>0 or  abs(x[0]-z[0])>0 or  abs(x[1]-z[1])>0:
+									if abs(x[0]-y[0])>0 or	abs(x[1]-y[1])>0:
+										print( 'Broken!!!: ', 'Ax, Ay =', Ax, Ay, 'Bx, By =' , Bx, By, 'Cx, Cy =' ,Cx, Cy)
+										print( 'count', count)
+										print( x)
+										print( y)
 										plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy)
 										halt
 
-		print 'Test Successful'
+		print( 'Test Successful')
 
 
 
@@ -1320,22 +1320,22 @@ def main():
 						for Cx in np.linspace(-0.5 , 0.5 , N):
 							for Cy in np.linspace(-0.5 , 0.5 , N):
 								count=count+1
-								#print count
+								#print( count
 								if count>0:
 									x=Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy)
 									y=Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy )
 									Error=abs(x[1]+x[2]+x[3]+x[4]-x[0])
 									#if Error>1e-15:
-									if abs(x[0]-y[0])>0 or  abs(x[1]-y[1])>0 or abs(x[2]-y[2])>0 or  abs(x[3]-y[3])>0 or  abs(x[4]-y[4])>0 :
-										print 'Broken!!!: ', 'Ax, Ay =', Ax, Ay, 'Bx, By =' , Bx, By, 'Cx, Cy =' ,Cx, Cy
-										print 'count=', count
-										#print 'Error = ', Error
-										print x
-										#print y
+									if abs(x[0]-y[0])>0 or	abs(x[1]-y[1])>0 or abs(x[2]-y[2])>0 or	 abs(x[3]-y[3])>0 or  abs(x[4]-y[4])>0 :
+										print( 'Broken!!!: ', 'Ax, Ay =', Ax, Ay, 'Bx, By =' , Bx, By, 'Cx, Cy =' ,Cx, Cy)
+										print( 'count=', count)
+										#print( 'Error = ', Error
+										print( x)
+										#print( y
 										plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy)
 										halt
 
-		print 'Triangle_into_fours Test Successful'
+		print( 'Triangle_into_fours Test Successful')
 
 		#[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]=Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy); 
 		#[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]= Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  )
@@ -1343,8 +1343,8 @@ def main():
 	if test_case=='Point_above_line':
 		x0=0.1 ;y0=0.3 ; Px=0.4; Py=-1.0; Qx=0.2; Qy=2.2
 		plt.plot(np.array([Px, Qx]), np.array([Py, Qy]))
-                plt.plot(x0,y0,'*')
-		print Point_above_line(x0,y0,Px, Py, Qx, Qy)
+		plt.plot(x0,y0,'*')
+		print( Point_above_line(x0,y0,Px, Py, Qx, Qy))
 		plt.show()
 
 
@@ -1360,7 +1360,7 @@ def main():
 			for y0 in np.linspace(-0.5 , 0.5 , N):
 				for H in np.linspace(0.0 , 0.5 , N):
 					count=count+1
-					#print count
+					#print( count
 					if count>0:
 						C5x=-H/np.sqrt(3.) ; C5y=-H; #Corner 5 (bottom right)
 						C6x=H/np.sqrt(3.)  ; C6y=-H; #Corner 6 (bottom right)
@@ -1368,8 +1368,8 @@ def main():
 						[C6x,C6y]=rotate_and_translate(C6x,C6y,theta,x0,y0)
 						#x = Triangle_divided_into_four_parts(x0,y0,C5x,C5y,C6x,C6y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
 						#y = Triangle_divided_into_four_quadrants(x0,y0,C5x,C5y,C6x,C6y); #T023
-						#print x
-						#print y
+						#print( x
+						#print( y
 						#Ax=x0 ;  Ay=y0
 						#Bx=C5x ; By=C5y ;
 						#Cx=C6x ; Cy=C6y ;
@@ -1382,14 +1382,14 @@ def main():
 						#eps=0.0
 						#if abs(Area_hex-Area_hexb)>eps or  abs(Area_Q1-Area_Q1b)>eps or abs(Area_Q2-Area_Q2b)>eps \
 						#		or  abs(Area_Q3-Area_Q3b)>eps or  abs(Area_Q4-Area_Q4b)>eps :
-						if abs(x[0]-y[0])>0 or  abs(x[1]-y[1])>0 or abs(x[2]-y[2])>0 or  abs(x[3]-y[3])>0 or  abs(x[4]-y[4])>0 :
-							print 'Broken!!!: ', x0, y0, H
-							print Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4 
-							print Area_hexb, Area_Q1b, Area_Q2b, Area_Q3b, Area_Q4b
-							print 'count=', count
+						if abs(x[0]-y[0])>0 or	abs(x[1]-y[1])>0 or abs(x[2]-y[2])>0 or	 abs(x[3]-y[3])>0 or  abs(x[4]-y[4])>0 :
+							print( 'Broken!!!: ', x0, y0, H)
+							print( Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4) 
+							print( Area_hexb, Area_Q1b, Area_Q2b, Area_Q3b, Area_Q4b)
+							print( 'count=', count)
 							halt
 		
-		print 'Many_Hexagons Test Successful'
+		print( 'Many_Hexagons Test Successful')
 
 
 	if test_case=='hexagon':
@@ -1398,17 +1398,17 @@ def main():
 		x0=0.
 		y0=0.
 		#(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Divide_hexagon_into_4_quadrants_old(x0,y0,H)
-		#print x0,y0,H
-		#print 'First version', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+		#print( x0,y0,H
+		#print( 'First version', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
 		(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Hexagon_into_quadrants_using_triangles(x0,y0,H,theta=0)
-		print 'Triangle version1',Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+		print( 'Triangle version1',Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
 		(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Hexagon_into_quadrants_using_triangles(x0,y0,H,theta=90.)
-		print 'Triangle version2',Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+		print( 'Triangle version2',Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
 		
-		#print 'Analysis'	
-		#print 'sum of quadrants: ', (Area_Q1+Area_Q2+Area_Q3+Area_Q4)
-		print 'Scaled areas: '
-		print (Area_Q1+Area_Q2+Area_Q3+Area_Q4)/Area_hex, Area_Q1/Area_hex, Area_Q2/Area_hex, Area_Q3/Area_hex, Area_Q4/Area_hex
+		#print( 'Analysis'	
+		#print( 'sum of quadrants: ', (Area_Q1+Area_Q2+Area_Q3+Area_Q4)
+		print( 'Scaled areas: ')
+		print( (Area_Q1+Area_Q2+Area_Q3+Area_Q4)/Area_hex, Area_Q1/Area_hex, Area_Q2/Area_hex, Area_Q3/Area_hex, Area_Q4/Area_hex)
 		
 
 	elif test_case=='square':
@@ -1429,15 +1429,15 @@ def main():
 
 		[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]=Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy); #T023
 
-		#Px=1. ; Py=0. ; Qx=2. ; Qy=0.  
-		#Rx=0. ; Ry=1. ; Sx=0. ; Sy=2.  
+		#Px=1. ; Py=0. ; Qx=2. ; Qy=0.	
+		#Rx=0. ; Ry=1. ; Sx=0. ; Sy=2.	
 		#[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]= Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  )
 
-		print 'Triangle 2: ',Ax,Ay,Bx,By,Cx,Cy
-		print 'Full',T23_Q1+T23_Q2+T23_Q3+T23_Q4
-		print 'Q1, Q2,Q3,Q4',T23_Q1,T23_Q2,T23_Q3,T23_Q4
-		print 'Full triangle area',T23_Area
-		print 'Error',(T23_Q1+T23_Q2+T23_Q3+T23_Q4-T23_Area)
+		print( 'Triangle 2: ',Ax,Ay,Bx,By,Cx,Cy)
+		print( 'Full',T23_Q1+T23_Q2+T23_Q3+T23_Q4)
+		print( 'Q1, Q2,Q3,Q4',T23_Q1,T23_Q2,T23_Q3,T23_Q4)
+		print( 'Full triangle area',T23_Area)
+		print( 'Error',(T23_Q1+T23_Q2+T23_Q3+T23_Q4-T23_Area))
 		
 		
 
@@ -1448,10 +1448,10 @@ def main():
 		By= -8.433062639672301E-002
 		Cx=0.249999999997304
 		Cy=6.000694090068343E-002
-		print 'Point in triangle', point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.)
+		print( 'Point in triangle', point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.))
 
 
-	print 'Script complete'
+	print( 'Script complete')
 
 if __name__ == '__main__':
 	main()
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/hexagon_area.pyc b/tests/Iceberg_repository/Scripts_and_analysis/hexagon_area.pyc
index 97776014762ca5b310f73cbd13d88dce6ef061a2..06e4f5193c982779a1816a464418162e1a1aa352 100644
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diff --git a/tests/Iceberg_repository/hexagon_area.py b/tests/Iceberg_repository/hexagon_area.py
index 08020cc..83d444d 100755
--- a/tests/Iceberg_repository/hexagon_area.py
+++ b/tests/Iceberg_repository/hexagon_area.py
@@ -6,7 +6,7 @@
 import matplotlib
 import math
 import os
-matplotlib.use("GTKAgg")
+matplotlib.use("tkagg")
 from pylab import *
 #import matplotlib.pyplot as plt
 import pdb
@@ -18,7 +18,7 @@
 
 def Divide_hexagon_into_4_quadrants_old(x0,y0,H):
 	S=(2/sqrt(3))*H
-	Area_hex=3*(np.sqrt(3)/2)*(S**2)  #Area of the hexagon (should be equal to Area/grid_area, since it is not dim)  - check this
+	Area_hex=3*(np.sqrt(3)/2)*(S**2)  #Area of the hexagon (should be equal to Area/grid_area, since it is not dim)	 - check this
 	#print 'y0,H',y0, H	
 	#Defining boundaries of hexagon, and if statements to see which side of the boundary you are on
 	W1= False ; W2=False ;W3=False ;W4=False ;W5=False ;W6=False ;H1=False ;V1=False ;V2=False
@@ -120,7 +120,7 @@ def Divide_hexagon_into_4_quadrants_old(x0,y0,H):
 
 	else:
 		#Determine which sector within the hexagon you are in. (sectors 1 to 6 go counter clockwise starting with top right)
-		if (H1==True):  #Bottom half
+		if (H1==True):	#Bottom half
 			if V1:
 				#if W1==False:
 				if ((y0+(sqrt(3)*(x0+S)))<=0.):
@@ -244,18 +244,18 @@ def Divide_hexagon_into_4_quadrants_old(x0,y0,H):
 
 
 
-def Hexagon_into_quadrants_using_triangles_across_lines(x0,y0,H,theta,  Px, Py, Qx, Qy, Rx, Ry, Sx, Sy ):
+def Hexagon_into_quadrants_using_triangles_across_lines(x0,y0,H,theta,	Px, Py, Qx, Qy, Rx, Ry, Sx, Sy ):
 	#In this routine, the hexagon is divided across lines PQ, RS.	 
 	#Length of side of Hexagon
 	S=(2/sqrt(3))*H;  
 
 	#Finding positions of corners
-	C1x=S           ; C1y=0.  #Corner 1 (right)
-	C2x=H/sqrt(3.)  ; C2y=H;  #Corner 2 (top right)
+	C1x=S		; C1y=0.  #Corner 1 (right)
+	C2x=H/sqrt(3.)	; C2y=H;  #Corner 2 (top right)
 	C3x=-H/sqrt(3.) ; C3y=H;  #Corner 3 (top left)
-	C4x=-S          ; C4y=0.; #Corner 4 (left)
+	C4x=-S		; C4y=0.; #Corner 4 (left)
 	C5x=-H/sqrt(3.) ; C5y=-H; #Corner 5 (bottom right)
-	C6x=H/sqrt(3.)  ; C6y=-H; #Corner 6 (bottom right)
+	C6x=H/sqrt(3.)	; C6y=-H; #Corner 6 (bottom right)
 
 	#Finding positions of corners
 	[C1x,C1y]=rotate_and_translate(C1x,C1y,theta,x0,y0)
@@ -321,9 +321,9 @@ def Hexagon_into_quadrants_using_triangles_across_lines(x0,y0,H,theta,  Px, Py,
 
 	Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
 	if (abs(Error)>0.01):
-		print  'diamonds, hex error, H,x0,y0, Error', H, x0 , y0, Error
-        	print 'diamonds, hex error, Areas',Area_hex, (Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
-	      	print 'Hexagon error is large!!'
+		print  ('diamonds, hex error, H,x0,y0, Error', H, x0 , y0, Error)
+		print ('diamonds, hex error, Areas',Area_hex, (Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,	 Area_Q4)
+		print ('Hexagon error is large!!')
 
 
 
@@ -337,16 +337,16 @@ def Hexagon_into_quadrants_using_triangles_across_lines(x0,y0,H,theta,  Px, Py,
 	elif  (((Area_Q3>=Area_Q1) and (Area_Q3>=Area_Q2)) and (Area_Q3>=Area_Q4)):
 		#print 'fix3',Error
 		Area_Q3=Area_Q3+Error
-   	elif  (((Area_Q4>=Area_Q1) and (Area_Q4>=Area_Q2)) and (Area_Q4>=Area_Q3)):
+	elif  (((Area_Q4>=Area_Q1) and (Area_Q4>=Area_Q2)) and (Area_Q4>=Area_Q3)):
 		#print 'fix4',Error
 		Area_Q4=Area_Q4+Error
 	else:
-		print 'There is some thing wrong with this hexagon. Something very wrong'
+		print ('There is some thing wrong with this hexagon. Something very wrong')
 
 	#Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
 	Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
 	if ((abs(Error)>0.01)):
-		print 'The hexagon error is still too large!!!', Error
+		print ('The hexagon error is still too large!!!', Error)
 
 
 
@@ -358,12 +358,12 @@ def Hexagon_into_quadrants_using_triangles(x0,y0,H,theta):
 	S=(2/sqrt(3))*H;  
 
 	#Finding positions of corners
-	C1x=S           ; C1y=0.  #Corner 1 (right)
-	C2x=H/sqrt(3.)  ; C2y=H;  #Corner 2 (top right)
+	C1x=S		; C1y=0.  #Corner 1 (right)
+	C2x=H/sqrt(3.)	; C2y=H;  #Corner 2 (top right)
 	C3x=-H/sqrt(3.) ; C3y=H;  #Corner 3 (top left)
-	C4x=-S          ; C4y=0.; #Corner 4 (left)
+	C4x=-S		; C4y=0.; #Corner 4 (left)
 	C5x=-H/sqrt(3.) ; C5y=-H; #Corner 5 (bottom right)
-	C6x=H/sqrt(3.)  ; C6y=-H; #Corner 6 (bottom right)
+	C6x=H/sqrt(3.)	; C6y=-H; #Corner 6 (bottom right)
 
 	#Finding positions of corners
 	[C1x,C1y]=rotate_and_translate(C1x,C1y,theta,x0,y0)
@@ -415,9 +415,9 @@ def Hexagon_into_quadrants_using_triangles(x0,y0,H,theta):
 
 	Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
 	if (abs(Error)>0.01):
-		print  'diamonds, hex error, H,x0,y0, Error', H, x0 , y0, Error
-        	print 'diamonds, hex error, Areas',Area_hex, (Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,  Area_Q4
-	      	print 'Hexagon error is large!!'
+		print ( 'diamonds, hex error, H,x0,y0, Error', H, x0 , y0, Error)
+		print ('diamonds, hex error, Areas',Area_hex, (Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,	 Area_Q4)
+		print ('Hexagon error is large!!')
 
 
 
@@ -431,16 +431,16 @@ def Hexagon_into_quadrants_using_triangles(x0,y0,H,theta):
 	elif  (((Area_Q3>=Area_Q1) and (Area_Q3>=Area_Q2)) and (Area_Q3>=Area_Q4)):
 		#print 'fix3',Error
 		Area_Q3=Area_Q3+Error
-   	elif  (((Area_Q4>=Area_Q1) and (Area_Q4>=Area_Q2)) and (Area_Q4>=Area_Q3)):
+	elif  (((Area_Q4>=Area_Q1) and (Area_Q4>=Area_Q2)) and (Area_Q4>=Area_Q3)):
 		#print 'fix4',Error
 		Area_Q4=Area_Q4+Error
 	else:
-		print 'There is some thing wrong with this hexagon. Something very wrong'
+		print ('There is some thing wrong with this hexagon. Something very wrong')
 
 	#Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
 	Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
 	if ((abs(Error)>0.01)):
-		print 'The hexagon error is still too large!!!', Error
+		print ('The hexagon error is still too large!!!', Error)
 
 
 
@@ -468,7 +468,7 @@ def find_intersect_using_metric(Ax,Ay, Bx, By, Cx, Cy):
 	elif M_BC<=min(M_AC, M_AB):
 		return BC_px, BC_py, BC_qx, BC_qy
 	else: 
-		print 'You should not get here'
+		print ('You should not get here')
 		halt
 
 def find_intersect_using_metric_and_lines(Ax,Ay, Bx, By, Cx, Cy,Px, Py, Qx, Qy, Rx, Ry, Sx, Sy):
@@ -492,7 +492,7 @@ def find_intersect_using_metric_and_lines(Ax,Ay, Bx, By, Cx, Cy,Px, Py, Qx, Qy,
 	elif M_BC<=min(M_AC, M_AB):
 		return BC_px, BC_py, BC_qx, BC_qy
 	else: 
-		print 'You should not get here'
+		print ('You should not get here')
 		halt
 
 
@@ -533,11 +533,11 @@ def Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy):
 	[Area_Right ,Area_Left]=divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,'y');
 	 
 	#Decide if the origin is in the triangle
-	if point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.):  #Then you have to divide area 4 ways.
+	if point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.):	#Then you have to divide area 4 ways.
 		#Find a line in the triangle that cuts both axes in/on the trianlge
-	    	[px, py]=intercept_of_a_line(Ax,Ay,Bx,By,'x'); #x_intercept
-	    	[qx, qy]=intercept_of_a_line(Ax,Ay,Bx,By,'y'); #y_intercept
-	    	if (point_in_interval(Ax,Ay,Bx,By,px,py) & point_in_interval(Ax,Ay,Bx,By,qx,qy))==False:
+		[px, py]=intercept_of_a_line(Ax,Ay,Bx,By,'x'); #x_intercept
+		[qx, qy]=intercept_of_a_line(Ax,Ay,Bx,By,'y'); #y_intercept
+		if (point_in_interval(Ax,Ay,Bx,By,px,py) & point_in_interval(Ax,Ay,Bx,By,qx,qy))==False:
 			[px, py]=intercept_of_a_line(Ax,Ay,Cx,Cy,'x'); #x_intercept
 			[qx, qy]=intercept_of_a_line(Ax,Ay,Cx,Cy,'y'); #y_intercept
 			if (point_in_interval(Ax,Ay,Cx,Cy,px,py) & point_in_interval(Ax,Ay,Cx,Cy,qx,qy))==False:
@@ -555,16 +555,16 @@ def Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy):
 		if Area_key_quadrant>0.0:
 			if px>=0. and qy>=0.: #First quadrant
 				Key_quadrant=1;
-			elif px<0. and qy>=0.:  #Second quadrant
+			elif px<0. and qy>=0.:	#Second quadrant
 				Key_quadrant=2;
 			elif px<0. and qy<0.:
-				Key_quadrant=3;  #Third quadrant
+				Key_quadrant=3;	 #Third quadrant
 			else:
-				Key_quadrant=4;  #Forth quadrant
+				Key_quadrant=4;	 #Forth quadrant
 	    
 	#if (point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.) is False) or (Area_key_quadrant==0):
 	if Area_key_quadrant==0:
-	#else:  #Then at least one quadrant is empty, and this can be used to find the areas in the other quadrant.  Assigning quadrants. Key_quadrant is the empty quadrant.
+	#else:	#Then at least one quadrant is empty, and this can be used to find the areas in the other quadrant.  Assigning quadrants. Key_quadrant is the empty quadrant.
 		#print 'Mother...'
 		#print 'Ax, Ay',Ax,Ay
 		#print 'Bx, By',Bx,By
@@ -575,7 +575,7 @@ def Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy):
 			#No points land in this quadrant and triangle does not cross the quadrant
 			Key_quadrant=1;
 		elif  (((Ax<0. and Ay>0) or (Bx<0. and By>0.) or (Cx<0. and Cy>0.))==False)  and (Area_Upper+Area_Left<=Area_triangle):
-			#elif  (((Ax<0. and Ay>=0) or (Bx<0. and By>=0.) or (Cx<0. and Cy>=0.))==False)  and (Area_Upper+Area_Left<=Area_triangle):
+			#elif  (((Ax<0. and Ay>=0) or (Bx<0. and By>=0.) or (Cx<0. and Cy>=0.))==False)	 and (Area_Upper+Area_Left<=Area_triangle):
 			Key_quadrant=2;
 		elif (((Ax<0. and Ay<0.) or (Bx<0. and By<0.) or (Cx<0. and Cy<0.))==False) & (Area_Lower+Area_Left<=Area_triangle):
 			#elif (((Ax<0. and Ay<0.) or (Bx<0. and By<0.) or (Cx<0. and Cy<0.))==False) & (Area_Lower+Area_Left<=Area_triangle):
@@ -609,7 +609,7 @@ def Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy):
 		#Area_Q3=Area_Left-Area_Q2;
 		Area_Q3=Area_triangle-Area_Q1-Area_Q2-Area_Q4;
 	else:
-	    print 'Help, I need somebody, help!'
+	    print( 'Help, I need somebody, help!')
 	    halt
 	
 	Area_Q1=max(Area_Q1,0.); 
@@ -621,14 +621,14 @@ def Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy):
 	#Marker 1
 	if Error>1e-15:
 	#if True:
-		print 'The triangles are not accurate enough. This is a problem!'
-		print 'Triangle corners: ' ,Ax,Ay,Bx,By,Cx,Cy
-		print 'Error',Error
-		print 'Key_quadrant', Key_quadrant 
-		print 'Area Key_quadrant', Area_key_quadrant 
-		print 'Upper, Lower',Area_Upper ,Area_Lower
-		print 'Left, Right ', Area_Right ,Area_Left
-		print 'Point in triangle', point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.)
+		print ('The triangles are not accurate enough. This is a problem!')
+		print ('Triangle corners: ' ,Ax,Ay,Bx,By,Cx,Cy)
+		print ('Error',Error)
+		print ('Key_quadrant', Key_quadrant )
+		print ('Area Key_quadrant', Area_key_quadrant) 
+		print ('Upper, Lower',Area_Upper ,Area_Lower)
+		print ('Left, Right ', Area_Right ,Area_Left)
+		print ('Point in triangle', point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.))
 		#plt.plot(np.array([Ax,Bx,Cx,Ax]),np.array([Ay, By, Cy,Ay]))
 		#plt.plot(np.array([-0.5,0.5]),np.array([0.,0.]),'k')
 		#plt.plot(np.array([0.,0.]),np.array([-0.5,0.5]),'k')
@@ -659,7 +659,7 @@ def find_quadrant_using_lines(x0 , y0 , Px, Py, Qx, Qy, Rx, Ry, Sx, Sy): #Findin
 
 	return quadrant
 
-def Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ):#Divides the triangle into 4 parts, across two intersecting lines. PQ, RS intersect at origin (for now)
+def Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy	):#Divides the triangle into 4 parts, across two intersecting lines. PQ, RS intersect at origin (for now)
 	Area_key_quadrant=0.0
 	Area_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
 	#if Area_triangle==0.0:
@@ -672,11 +672,11 @@ def Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry,
 	[Area_Right ,Area_Left] =divding_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Rx, Ry, Sx, Sy);
 	 
 	#Decide if the origin is in the triangle
-	if point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.):  #Then you have to divide area 4 ways.
+	if point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.):	#Then you have to divide area 4 ways.
 		#Find a line in the triangle that cuts both axes in/on the trianlge
-	    	[px, py]=intercept_of_two_lines(Ax,Ay,Bx,By,Px, Py, Qx, Qy); #PQ_intercept
-	    	[qx, qy]=intercept_of_two_lines(Ax,Ay,Bx,By,Rx, Ry, Sx, Sy); #RS_intercept
-	    	if (point_in_interval(Ax,Ay,Bx,By,px,py) & point_in_interval(Ax,Ay,Bx,By,qx,qy))==False:
+		[px, py]=intercept_of_two_lines(Ax,Ay,Bx,By,Px, Py, Qx, Qy); #PQ_intercept
+		[qx, qy]=intercept_of_two_lines(Ax,Ay,Bx,By,Rx, Ry, Sx, Sy); #RS_intercept
+		if (point_in_interval(Ax,Ay,Bx,By,px,py) & point_in_interval(Ax,Ay,Bx,By,qx,qy))==False:
 			[px, py]=intercept_of_two_lines(Ax,Ay,Cx,Cy,Px, Py, Qx, Qy); #PQ_intercept
 			[qx, qy]=intercept_of_two_lines(Ax,Ay,Cx,Cy,Rx, Ry, Sx, Sy); #RS_intercept
 			if (point_in_interval(Ax,Ay,Cx,Cy,px,py) & point_in_interval(Ax,Ay,Cx,Cy,qx,qy))==False:
@@ -692,15 +692,15 @@ def Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry,
 		Area_key_quadrant=Area_of_triangle(px,py,qx,qy,0.,0.);
 		if px>=0. and qy>=0.: #First quadrant  (I think the zeros here are because the PQ, RS intersect at zero)
 			Key_quadrant=1;
-		elif px<0. and qy>=0.:  #Second quadrant
+		elif px<0. and qy>=0.:	#Second quadrant
 			Key_quadrant=2;
 		elif px<0. and qy<0.:
-			Key_quadrant=3;  #Third quadrant
+			Key_quadrant=3;	 #Third quadrant
 		else:
-			Key_quadrant=4;  #Forth quadrant
+			Key_quadrant=4;	 #Forth quadrant
 	    
 	if Area_key_quadrant==0:
-		#else:  #Then at least one quadrant is empty, and this can be used to find the areas in the other quadrant.  Assigning quadrants. Key_quadrant is the empty quadrant.
+		#else:	#Then at least one quadrant is empty, and this can be used to find the areas in the other quadrant.  Assigning quadrants. Key_quadrant is the empty quadrant.
 		#print 'Mother...'
 		#print 'Ax, Ay',Ax,Ay
 		#print 'Bx, By',Bx,By
@@ -712,7 +712,7 @@ def Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry,
 		C_quad = find_quadrant_using_lines(Cx,Cy,Px, Py, Qx, Qy, Rx, Ry, Sx, Sy)
 		#print 'A_quad, B_quad, C_quad',A_quad, B_quad, C_quad
 
-		if (((A_quad==1) or (B_quad==1) or (C_quad==1))==False)  and (Area_Upper+Area_Right<=Area_triangle):
+		if (((A_quad==1) or (B_quad==1) or (C_quad==1))==False)	 and (Area_Upper+Area_Right<=Area_triangle):
 			#No points land in this quadrant and triangle does not cross the quadrant
 			Key_quadrant=1;
 		elif  (((A_quad==2) or (B_quad==2) or (C_quad==2))==False)  and (Area_Upper+Area_Left<=Area_triangle):
@@ -749,7 +749,7 @@ def Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry,
 		#Area_Q3=Area_Left-Area_Q2;
 		Area_Q3=Area_triangle-Area_Q1-Area_Q2-Area_Q4;
 	else:
-	    print 'Help, I need somebody, help!'
+	    print ('Help, I need somebody, help!')
 	    halt
 	
 	Area_Q1=max(Area_Q1,0.); 
@@ -760,30 +760,30 @@ def Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry,
 	Error=abs(Area_Q1+Area_Q2+Area_Q3+Area_Q4-Area_triangle)
 	if Error>1e-15:
 	#if True:
-		print 'The triangles are not accurate enough. This is a problem!'
-		print 'Triangle corners: ' ,Ax,Ay,Bx,By,Cx,Cy
-		print 'Error',Error
-		print 'Key_quadrant', Key_quadrant 
-		print 'Area Key_quadrant', Area_key_quadrant 
-		print 'Upper, Lower',Area_Upper ,Area_Lower
-		print 'Left, Right ', Area_Right ,Area_Left
-		print 'Point in triangle', point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.)
+		print ('The triangles are not accurate enough. This is a problem!')
+		print ('Triangle corners: ' ,Ax,Ay,Bx,By,Cx,Cy)
+		print ('Error',Error)
+		print ('Key_quadrant', Key_quadrant )
+		print ('Area Key_quadrant', Area_key_quadrant )
+		print ('Upper, Lower',Area_Upper ,Area_Lower)
+		print ('Left, Right ', Area_Right ,Area_Left)
+		print ('Point in triangle', point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.))
 		#return
 
 	return [Area_triangle, Area_Q1, Area_Q2 ,Area_Q3 ,Area_Q4]
 
 def divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1):
-	if axes1=='x':  #Use the y-coordinates for if statements to see which side of the line you are on
+	if axes1=='x':	#Use the y-coordinates for if statements to see which side of the line you are on
 		A0=Ay; B0=By;  C0=Cy;
-	if axes1=='y':  #Use the y-coordinates for if statements to see which side of the line you are on
+	if axes1=='y':	#Use the y-coordinates for if statements to see which side of the line you are on
 		A0=Ax; B0=Bx;  C0=Cx;
  
 	#print 'A0,B0,C0', A0,B0,C0
 	A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
-	if B0*C0>0.: #then B and C are on the same side  (and non-zero)
+	if B0*C0>0.: #then B and C are on the same side	 (and non-zero)
 		#print 'HHHH1'	
 		if A0*B0>=0.: #then all three on the the same side (if it equals zero, then A0=0 and the otehrs are not)
-			if (A0>0.)  or  (A0==0. and  B0>0.):
+			if (A0>0.)  or	(A0==0. and  B0>0.):
 				Area_positive= A_triangle;
 				Area_negative= 0.;
 			else:
@@ -804,19 +804,19 @@ def divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1):
 		if (A0==0. and B0==0. and C0==0.):
 			Area_positive= 0.;
 			Area_negative= 0.;
-		elif (A0*B0<0.)  or  (A0*C0<0.):    #A, B are on opposite sides, and C is zero.  OR  A, C are on opposite sides, and B is zero.
+		elif (A0*B0<0.)	 or  (A0*C0<0.):    #A, B are on opposite sides, and C is zero.	 OR  A, C are on opposite sides, and B is zero.
 			[Area_positive, Area_negative]=Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1);
 			#print 'HHHH6'	
 		elif (A0*B0>0.) or (A0*C0>0.) or (abs(A0)>0. and (B0==0.) and (C0==0.)):
 			#print 'HHHH7'	
-		        if (A0>0.):
-		        	Area_positive= A_triangle;
+			if (A0>0.):
+				Area_positive= A_triangle;
 				Area_negative= 0.;
-        		else:
+			else:
 				Area_positive= 0.;
 				Area_negative= A_triangle;
     
-    		elif A0==0.:  #(Also, one of B,C is zero too)
+		elif A0==0.:  #(Also, one of B,C is zero too)
 			#print 'HHHH8'	
 			if B0>0. or C0>0.:
 				Area_positive= A_triangle;
@@ -824,12 +824,12 @@ def divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1):
 			elif B0<0. or C0<0.:
 				Area_positive= 0.;
 				Area_negative= A_triangle;
-		        else:
+			else:
 				print 'You should not get here1'
 				halt
-    		else:
-			print 'You should not get here2'
-			print Ax,Ay,Bx,By,Cx,Cy
+		else:
+			print ('You should not get here2')
+			print (Ax,Ay,Bx,By,Cx,Cy)
 			halt
 	
 	return [Area_positive, Area_negative]
@@ -843,10 +843,10 @@ def divding_triangle_across_line2(Ax,Ay,Bx,By,Cx,Cy,  Px, Py, Qx, Qy ):
 	#print Px, Py, Qx, Qy
  
 	A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
-	if B0*C0>0.: #then B and C are on the same side  (and non-zero)
+	if B0*C0>0.: #then B and C are on the same side	 (and non-zero)
 		#print 'GGG1'
 		if A0*B0>=0.: #then all three on the the same side (if it equals zero, then A0=0 and the otehrs are not)
-			if (A0>0.)  or  (A0==0. and  B0>0.):
+			if (A0>0.)  or	(A0==0. and  B0>0.):
 				Area_positive= A_triangle;
 				Area_negative= 0.;
 			else:
@@ -867,36 +867,36 @@ def divding_triangle_across_line2(Ax,Ay,Bx,By,Cx,Cy,  Px, Py, Qx, Qy ):
 		if (A0==0. and B0==0. and C0==0.):
 			Area_positive= 0.;
 			Area_negative= 0.;
-		elif (A0*B0<0.)  or  (A0*C0<0.):    #A, B are on opposite sides, and C is zero.  OR  A, C are on opposite sides, and B is zero.
+		elif (A0*B0<0.)	 or  (A0*C0<0.):    #A, B are on opposite sides, and C is zero.	 OR  A, C are on opposite sides, and B is zero.
 			[Area_positive, Area_negative]=Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy);
 			#print 'GGG5', Area_positive, Area_negative
 		elif (A0*B0>0.) or (A0*C0>0.) or (abs(A0)>0. and (B0==0.) and (C0==0.)):
-		        if (A0>0.):
-		        	Area_positive= A_triangle;
+			if (A0>0.):
+				Area_positive= A_triangle;
 				Area_negative= 0.;
-        		else:
+			else:
 				Area_positive= 0.;
 				Area_negative= A_triangle;
     
-    		elif A0==0.:  #(Also, one of B,C is zero too)
+		elif A0==0.:  #(Also, one of B,C is zero too)
 			if B0>0. or C0>0.:
 				Area_positive= A_triangle;
 				Area_negative= 0.;
 			elif B0<0. or C0<0.:
 				Area_positive= 0.;
 				Area_negative= A_triangle;
-		        else:
-				print 'You should not get here1'
+			else:
+				print ('You should not get here1')
 				halt
-    		else:
-			print 'You should not get here2'
-			print Ax,Ay,Bx,By,Cx,Cy
+		else:
+			print ('You should not get here2')
+			print (Ax,Ay,Bx,By,Cx,Cy)
 			halt
 	
 	return [Area_positive, Area_negative]
 
 
-def divding_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy,   Px, Py, Qx, Qy ):  #Triangle is ABC, line is PQ
+def divding_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy,   Px, Py, Qx, Qy ):	 #Triangle is ABC, line is PQ
 	A0= Above_on_below_line(Ax,Ay, Px, Py, Qx, Qy)
 	B0= Above_on_below_line(Bx,By, Px, Py, Qx, Qy)
 	C0= Above_on_below_line(Cx,Cy, Px, Py, Qx, Qy) 
@@ -905,7 +905,7 @@ def divding_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy,   Px, Py, Qx, Qy ):  #Triang
 	A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
 	# B and C are on the same side of the line
 	#if (Point_above_line(Bx,By, Px, Py, Qx, Qy)==Point_above_line(Cx,Cy, Px, Py, Qx, Qy)) :
-	#if ((B0==C0) and (B0!=0))  or ((B0==0 or C0==0) and np.max(B0,C0)>0.5)   :
+	#if ((B0==C0) and (B0!=0))  or ((B0==0 or C0==0) and np.max(B0,C0)>0.5)	  :
 	if ((B0==C0) and (B0!=0))  or ((B0==0 or C0==0))   : #B and C on the same side or B or C is zero
 		#print 'BBB1'
 		[Area_positive, Area_negative]=Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy);
@@ -958,7 +958,7 @@ def intercept_of_a_line(Ax,Ay,Bx,By,axes1):
 	if axes1=='y': #y intercept
 		if (Ax==Bx)==False:
 			x0=0.; 
-			y0=-(((Ay-By)/(Ax-Bx))*Ax)+Ay;  
+			y0=-(((Ay-By)/(Ax-Bx))*Ax)+Ay;	
 		else:
 			x0=No_intercept_val;
 			y0=No_intercept_val;
@@ -990,18 +990,18 @@ def intercept_of_two_lines(Ax,Ay,Bx,By,Px,Py,Qx,Qy):
 		else:
 			m1=(Ay-By)/(Ax-Bx)
 			if (Px==Qx):
-				print 'Stop2'
+				print ('Stop2')
 				(x0 , y0) =intercept_of_a_line(Ax-Px,Ay,Bx-Px,By,'y')
 				x0=Px
 			else:
 				m2=(Py-Qy)/(Px-Qx)
 				if m1==m2:
-					print 'Stop3'
+					print( 'Stop3')
 					x0=No_intercept_val;
 					y0=No_intercept_val;
 					halt2
 				else:
-					print 'Stop4'
+					print( 'Stop4')
 					x0=(1/(m1-m2))*( (m1*Ax -Ay) -(m2*Px - Py))
 					y0=m1*(x0-Ax)+Ay
 	
@@ -1093,8 +1093,8 @@ def Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px,Py, Qx, Qy, debug=False):
 		else: #If A is not on the line
 			#If A is on the same side of the line as B and C
 			#All on the same side of the line
-			if ((A0==B0 and A0==C0)  or (A0==B0 and C0==0) or (A0==C0 and B0==0)):  
-			#if Point_above_line(Ax,Ay, Px,Py, Qx, Qy) == Point_above_line( Bx,By, Px,Py, Qx, Qy)  and (Point_above_line(Ax,Ay,Px,Py,Qx,Qy)==Point_above_line(Cx,Cy,Px,Py,Qx,Qy)):  
+			if ((A0==B0 and A0==C0)	 or (A0==B0 and C0==0) or (A0==C0 and B0==0)):	
+			#if Point_above_line(Ax,Ay, Px,Py, Qx, Qy) == Point_above_line( Bx,By, Px,Py, Qx, Qy)  and (Point_above_line(Ax,Ay,Px,Py,Qx,Qy)==Point_above_line(Cx,Cy,Px,Py,Qx,Qy)):	
 				#print 'AAA4'
 				#if Point_above_line(Bx,By, Px,Py, Qx, Qy) or Point_above_line(Cx,Cy, Px,Py, Qx, Qy):
 				if A0==1 or C0==1:
@@ -1103,7 +1103,7 @@ def Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px,Py, Qx, Qy, debug=False):
 				else:
 					Area_positive= 0.0;
 					Area_negative= A_triangle2;
-			elif (C0==0 and B0==0 and (abs(A0)>0)):  
+			elif (C0==0 and B0==0 and (abs(A0)>0)):	 
 				if Point_above_line(Ax,Ay, Px,Py, Qx, Qy):
 					Area_positive= A_triangle2;
 					Area_negative= 0.0;
@@ -1128,7 +1128,7 @@ def Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px,Py, Qx, Qy, debug=False):
 	return [Area_positive, Area_negative]
 
 def Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy):
-	Area    =   abs(    0.5*((Ax*(By-Cy))+(Bx*(Cy-Ay))+(Cx*(Ay-By))) );
+	Area	=   abs(    0.5*((Ax*(By-Cy))+(Bx*(Cy-Ay))+(Cx*(Ay-By))) );
 	return Area
 
 
@@ -1154,7 +1154,7 @@ def rotate_and_translate(px,py,theta,x0,y0):
 def point_in_triangle_old(Ax,Ay,Bx,By,Cx,Cy,qx,qy):
 	#if False:
 	if (Ax==qx and Ay==qy) or (Bx==qx and By==qy) or (Cx==qx and Cy==qy):  #Exclude the pathelogical case
-	        	point_is_in_triangle = 0.;
+			point_is_in_triangle = 0.;
 	else:
 		if (check_if_point_is_on_the_line(Ax,Ay,Bx,By,qx,qy) or (check_if_point_is_on_the_line(Ax,Ay,Cx,Cy,qx,qy)) or (check_if_point_is_on_the_line(Bx,By,Cx,Cy,qx,qy))):
 			point_is_in_triangle = 0;
@@ -1188,7 +1188,7 @@ def point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,qx,qy):
 	point_is_in_triangle = 0;
 
 	if (Ax==qx and Ay==qy) or (Bx==qx and By==qy) or (Cx==qx and Cy==qy):  #Exclude the pathelogical case
-	        	point_is_in_triangle = 0.;
+			point_is_in_triangle = 0.;
 	else:
 		if (check_if_point_is_on_the_line(Ax,Ay,Bx,By,qx,qy) or (check_if_point_is_on_the_line(Ax,Ay,Cx,Cy,qx,qy)) or (check_if_point_is_on_the_line(Bx,By,Cx,Cy,qx,qy))):
 			point_is_in_triangle = 0;
@@ -1221,16 +1221,16 @@ def roundoff(x,sig_fig):
 
 def square_spreading_calculation(x,y,L):
 	xL=min(0.5, max(0., 0.5-(x/L)))
-        xR=min(0.5, max(0., (x/L)+(0.5-(1/L) )))
-        xC=max(0., 1.-(xL+xR))
-        yD=min(0.5, max(0., 0.5-(y/L)))
-        yU=min(0.5, max(0., (y/L)+(0.5-(1/L) )))
-        yC=max(0., 1.-(yD+yU))
+	xR=min(0.5, max(0., (x/L)+(0.5-(1/L) )))
+	xC=max(0., 1.-(xL+xR))
+	yD=min(0.5, max(0., 0.5-(y/L)))
+	yU=min(0.5, max(0., (y/L)+(0.5-(1/L) )))
+	yC=max(0., 1.-(yD+yU))
 
 def plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy, Px=None, Py=None, Qx=None, Qy=None, Rx=None, Ry=None, Sx=None, Sy=None):
 	if Px is None:
 		Px=-1. ; Py=0. ; Qx=1. ; Qy=0. #x-axis 
-                Rx=0. ; Ry=-1. ; Sx=0. ; Sy=1. #y-axis 
+		Rx=0. ; Ry=-1. ; Sx=0. ; Sy=1. #y-axis 
 	plt.plot(np.array([Px, Qx]), np.array([Py, Qy]))
 	plt.plot(np.array([Rx, Sx]), np.array([Ry, Sy]))
 	plt.plot(np.array([Ax, Bx, Cx, Ax]), np.array([Ay, By, Cy, Ay]))
@@ -1268,7 +1268,7 @@ def main():
 		#plt.plot(Px,Py,'*')
 		#plt.plot(Qx,Qy,'*')
 
-		print 'x0, y0' , x0 , y0
+		print ('x0, y0' , x0 , y0)
 		plt.show()
 
 
@@ -1294,16 +1294,16 @@ def main():
 									x=divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1)
 									y=divding_triangle_across_line2(Ax,Ay,Bx,By,Cx,Cy, Px,Py, Qx, Qy)
 									#y=divding_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px,Py, Qx, Qy)
-									#if abs(x[0]-y[0])>0 or  abs(x[1]-y[1])>0 or  abs(x[0]-z[0])>0 or  abs(x[1]-z[1])>0:
-									if abs(x[0]-y[0])>0 or  abs(x[1]-y[1])>0:
-										print 'Broken!!!: ', 'Ax, Ay =', Ax, Ay, 'Bx, By =' , Bx, By, 'Cx, Cy =' ,Cx, Cy
-										print 'count', count
-										print x
-										print y
+									#if abs(x[0]-y[0])>0 or	 abs(x[1]-y[1])>0 or  abs(x[0]-z[0])>0 or  abs(x[1]-z[1])>0:
+									if abs(x[0]-y[0])>0 or	abs(x[1]-y[1])>0:
+										print ('Broken!!!: ', 'Ax, Ay =', Ax, Ay, 'Bx, By =' , Bx, By, 'Cx, Cy =' ,Cx, Cy)
+										print ('count', count)
+										print (x)
+										print( y)
 										plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy)
 										halt
 
-		print 'Test Successful'
+		print ('Test Successful')
 
 
 
@@ -1326,16 +1326,16 @@ def main():
 									y=Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy )
 									Error=abs(x[1]+x[2]+x[3]+x[4]-x[0])
 									#if Error>1e-15:
-									if abs(x[0]-y[0])>0 or  abs(x[1]-y[1])>0 or abs(x[2]-y[2])>0 or  abs(x[3]-y[3])>0 or  abs(x[4]-y[4])>0 :
-										print 'Broken!!!: ', 'Ax, Ay =', Ax, Ay, 'Bx, By =' , Bx, By, 'Cx, Cy =' ,Cx, Cy
-										print 'count=', count
+									if abs(x[0]-y[0])>0 or	abs(x[1]-y[1])>0 or abs(x[2]-y[2])>0 or	 abs(x[3]-y[3])>0 or  abs(x[4]-y[4])>0 :
+										print ('Broken!!!: ', 'Ax, Ay =', Ax, Ay, 'Bx, By =' , Bx, By, 'Cx, Cy =' ,Cx, Cy)
+										print( 'count=', count)
 										#print 'Error = ', Error
-										print x
+										print( x)
 										#print y
 										plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy)
 										halt
 
-		print 'Triangle_into_fours Test Successful'
+		print ('Triangle_into_fours Test Successful')
 
 		#[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]=Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy); 
 		#[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]= Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  )
@@ -1343,8 +1343,8 @@ def main():
 	if test_case=='Point_above_line':
 		x0=0.1 ;y0=0.3 ; Px=0.4; Py=-1.0; Qx=0.2; Qy=2.2
 		plt.plot(np.array([Px, Qx]), np.array([Py, Qy]))
-                plt.plot(x0,y0,'*')
-		print Point_above_line(x0,y0,Px, Py, Qx, Qy)
+		plt.plot(x0,y0,'*')
+		print (Point_above_line(x0,y0,Px, Py, Qx, Qy))
 		plt.show()
 
 
@@ -1363,7 +1363,7 @@ def main():
 					#print count
 					if count>0:
 						C5x=-H/sqrt(3.) ; C5y=-H; #Corner 5 (bottom right)
-						C6x=H/sqrt(3.)  ; C6y=-H; #Corner 6 (bottom right)
+						C6x=H/sqrt(3.)	; C6y=-H; #Corner 6 (bottom right)
 						[C5x,C5y]=rotate_and_translate(C5x,C5y,theta,x0,y0)
 						[C6x,C6y]=rotate_and_translate(C6x,C6y,theta,x0,y0)
 						#x = Triangle_divided_into_four_parts(x0,y0,C5x,C5y,C6x,C6y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
@@ -1382,14 +1382,14 @@ def main():
 						#eps=0.0
 						#if abs(Area_hex-Area_hexb)>eps or  abs(Area_Q1-Area_Q1b)>eps or abs(Area_Q2-Area_Q2b)>eps \
 						#		or  abs(Area_Q3-Area_Q3b)>eps or  abs(Area_Q4-Area_Q4b)>eps :
-						if abs(x[0]-y[0])>0 or  abs(x[1]-y[1])>0 or abs(x[2]-y[2])>0 or  abs(x[3]-y[3])>0 or  abs(x[4]-y[4])>0 :
-							print 'Broken!!!: ', x0, y0, H
-							print Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4 
-							print Area_hexb, Area_Q1b, Area_Q2b, Area_Q3b, Area_Q4b
-							print 'count=', count
+						if abs(x[0]-y[0])>0 or	abs(x[1]-y[1])>0 or abs(x[2]-y[2])>0 or	 abs(x[3]-y[3])>0 or  abs(x[4]-y[4])>0 :
+							print ('Broken!!!: ', x0, y0, H)
+							print (Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4 )
+							print (Area_hexb, Area_Q1b, Area_Q2b, Area_Q3b, Area_Q4b)
+							print ('count=', count)
 							halt
 		
-		print 'Many_Hexagons Test Successful'
+		print ('Many_Hexagons Test Successful')
 
 
 	if test_case=='hexagon':
@@ -1401,14 +1401,14 @@ def main():
 		#print x0,y0,H
 		#print 'First version', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
 		(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Hexagon_into_quadrants_using_triangles(x0,y0,H,theta=0)
-		print 'Triangle version1',Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+		print ('Triangle version1',Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
 		(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Hexagon_into_quadrants_using_triangles(x0,y0,H,theta=90.)
-		print 'Triangle version2',Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+		print ('Triangle version2',Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
 		
 		#print 'Analysis'	
 		#print 'sum of quadrants: ', (Area_Q1+Area_Q2+Area_Q3+Area_Q4)
-		print 'Scaled areas: '
-		print (Area_Q1+Area_Q2+Area_Q3+Area_Q4)/Area_hex, Area_Q1/Area_hex, Area_Q2/Area_hex, Area_Q3/Area_hex, Area_Q4/Area_hex
+		print ('Scaled areas: ')
+		print( (Area_Q1+Area_Q2+Area_Q3+Area_Q4)/Area_hex, Area_Q1/Area_hex, Area_Q2/Area_hex, Area_Q3/Area_hex, Area_Q4/Area_hex)
 		
 
 	elif test_case=='square':
@@ -1429,15 +1429,15 @@ def main():
 
 		[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]=Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy); #T023
 
-		#Px=1. ; Py=0. ; Qx=2. ; Qy=0.  
-		#Rx=0. ; Ry=1. ; Sx=0. ; Sy=2.  
+		#Px=1. ; Py=0. ; Qx=2. ; Qy=0.	
+		#Rx=0. ; Ry=1. ; Sx=0. ; Sy=2.	
 		#[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]= Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  )
 
-		print 'Triangle 2: ',Ax,Ay,Bx,By,Cx,Cy
-		print 'Full',T23_Q1+T23_Q2+T23_Q3+T23_Q4
-		print 'Q1, Q2,Q3,Q4',T23_Q1,T23_Q2,T23_Q3,T23_Q4
-		print 'Full triangle area',T23_Area
-		print 'Error',(T23_Q1+T23_Q2+T23_Q3+T23_Q4-T23_Area)
+		print ('Triangle 2: ',Ax,Ay,Bx,By,Cx,Cy)
+		print ('Full',T23_Q1+T23_Q2+T23_Q3+T23_Q4)
+		print ('Q1, Q2,Q3,Q4',T23_Q1,T23_Q2,T23_Q3,T23_Q4)
+		print ('Full triangle area',T23_Area)
+		print ('Error',(T23_Q1+T23_Q2+T23_Q3+T23_Q4-T23_Area))
 		
 		
 
@@ -1448,10 +1448,10 @@ def main():
 		By= -8.433062639672301E-002
 		Cx=0.249999999997304
 		Cy=6.000694090068343E-002
-		print 'Point in triangle', point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.)
+		print ('Point in triangle', point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.))
 
 
-	print 'Script complete'
+	print ('Script complete')
 
 if __name__ == '__main__':
 	main()
diff --git a/tests/a68/.gitignore b/tests/a68/.gitignore
new file mode 100644
index 0000000..577f3bd
--- /dev/null
+++ b/tests/a68/.gitignore
@@ -0,0 +1,4 @@
+results/
+oldnc/
+oldnc2/
+csvresults/
\ No newline at end of file
diff --git a/tests/a68/README b/tests/a68/README
new file mode 100644
index 0000000..8d990cb
--- /dev/null
+++ b/tests/a68/README
@@ -0,0 +1,26 @@
+TO RUN THE EXPERIMENT IN THE PAPER/AGU 2021:
+
+1. Make the iceberg input files:
+   cd makeberg; ./RUN_for_paper; cd ..
+
+2. (optional) Run the spinup without fracture or grounding, and test different ocean scaling, etc. These tests are used to determine which simulation best follows the observed A68:
+   ./RUN_test_init_for_paper.sh
+
+3. Run the selected spinup (which uses ocean_scaling=17.8) to the point for restart:
+   cp square_for_restart_od_17.8_ydn.1.nml input.nml
+   ./RUN_1p.sh
+
+4. Copy the restart to a new directory:
+   cp INPUT/ S_17.8_ydn.1_r/
+
+5. Rerun the simulation from the restart, this time activating grounding and fracture:
+   ./RUN_restart_for_paper.sh
+
+6. animate the results:
+   ./animate_trajectories.py -fname=sq_ssf_ssg1.e4_od17.8_addsm.true._rectx-37.5285_y-55.2166_n23_t10.nc
+
+
+Warning: steps 1 and 6 probably require different versions of python or packages. TODO: fix this.
+
+
+
diff --git a/tests/a68/RUN b/tests/a68/RUN
new file mode 100755
index 0000000..03f559f
--- /dev/null
+++ b/tests/a68/RUN
@@ -0,0 +1,7 @@
+rm iceberg_trajectories.nc
+rm iceberg_trajectories.nc.*
+rm bond_trajectories.nc
+rm bond_trajectories.nc.*
+srun -n16 ./../../build/bergs.x
+
+
diff --git a/tests/a68/RUN1p b/tests/a68/RUN1p
new file mode 100755
index 0000000..3dfc97d
--- /dev/null
+++ b/tests/a68/RUN1p
@@ -0,0 +1,7 @@
+rm iceberg_trajectories.nc
+rm iceberg_trajectories.nc.*
+rm bond_trajectories.nc
+rm bond_trajectories.nc.*
+srun -n1 ./../../build/bergs.x
+
+
diff --git a/tests/a68/RUN_check_ss.sh b/tests/a68/RUN_check_ss.sh
new file mode 100755
index 0000000..4c33e77
--- /dev/null
+++ b/tests/a68/RUN_check_ss.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+
+#ocean drag values
+ss=(200 300 400 750 500 100 1000)
+name=(sstest_200.nc sstest_300.nc sstest_400.nc sstest_750.nc sstest_500.nc sstest_100.nc sstest_1000.nc)
+
+for ((i = 0; i < ${#ss[@]}; ++i)); do
+    substeps=(${ss[$i]})
+    fname2=(${name[$i]})
+
+    echo $substeps
+    echo $fname2
+
+    sed  "s/<ss>/$substeps/; s/<fname>/$fname2/g" \
+	 check_ss.nml > input.nml
+    ./RUN1p
+    # &>/dev/null &
+done
diff --git a/tests/a68/RUN_check_ss2.sh b/tests/a68/RUN_check_ss2.sh
new file mode 100755
index 0000000..a9a1d82
--- /dev/null
+++ b/tests/a68/RUN_check_ss2.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+
+#ocean drag values
+ss=(200 300 400 750 500 100 1000)
+name=(sstest2_200.nc sstest2_300.nc sstest2_400.nc sstest2_750.nc sstest2_500.nc sstest2_100.nc sstest2_1000.nc)
+
+for ((i = 0; i < ${#ss[@]}; ++i)); do
+    substeps=(${ss[$i]})
+    fname2=(${name[$i]})
+
+    echo $substeps
+    echo $fname2
+
+    sed  "s/<ss>/$substeps/; s/<fname>/$fname2/g" \
+	 check_ss2.nml > input.nml
+    ./RUN1p
+    # &>/dev/null &
+done
diff --git a/tests/a68/RUN_check_ss_new.sh b/tests/a68/RUN_check_ss_new.sh
new file mode 100755
index 0000000..c4cc32a
--- /dev/null
+++ b/tests/a68/RUN_check_ss_new.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+
+#ocean drag values
+ss=(200)
+name=(sstest_200.nc)
+
+for ((i = 0; i < ${#ss[@]}; ++i)); do
+    substeps=(${ss[$i]})
+    fname2=(${name[$i]})
+
+    echo $substeps
+    echo $fname2
+
+    sed  "s/<ss>/$substeps/; s/<fname>/$fname2/g" \
+	 check_ss.nml > input.nml
+    ./RUN1p
+    # &>/dev/null &
+done
diff --git a/tests/a68/RUN_loop.sh b/tests/a68/RUN_loop.sh
new file mode 100755
index 0000000..ce98aa4
--- /dev/null
+++ b/tests/a68/RUN_loop.sh
@@ -0,0 +1,53 @@
+#!/bin/bash
+
+#ocean drag values
+#odrag=(6.5 6 5 7 4 8 3 1)
+#name=(hex_wgs84_nofrac_od6.5.nc hex_wgs84_nofrac_od6.nc hex_wgs84_nofrac_od5.nc hex_wgs84_nofrac_od7.nc hex_wgs84_nofrac_od4.nc hex_wgs84_nofrac_od8.nc hex_wgs84_nofrac_od3.nc hex_wgs84_nofrac_od1.nc)
+
+#odrag=(6 6.5 7)
+#name=(hex_ydn.5_wgs84_nofrac_od6.nc hex_ydn.5_wgs84_nofrac_od6.5.nc hex_ydn.5_wgs84_nofrac_od7.nc)
+
+#this was to test having rev_mind=.true. and rev_mind=.false., to determine where it places the seamount.
+#odrag=(6.)
+#name=(test_rm2_false.nc)
+
+#odrag=(6.075 6.025)
+#name=(hex_yn.075_nf_od6.075.nc hex_yn.075_nf_od6.025.nc)
+
+#odrag=(6. 6.5 5.5)
+#name=(hex_yn.1_nf_od6.nc hex_yn.1_nf_od6.5.nc hex_yn.1_nf_od5.5.nc)
+
+#odrag=(4.75 4.85)
+#name=(hex_yn.125_nf_od4.75.nc hex_yn.125_nf_od4.85.nc)
+
+#odrag=(2.9 2.95)
+#name=(hex_yn.175_nf_od2.9.nc hex_yn.175_nf_od2.95.nc)
+
+odrag=(9.5 10.5)
+name=(hex_yn.1_nf_od9.5_rad_drag_E1e6.nc hex_yn.1_nf_od10.5_rad_drag_E1e6.nc)
+
+
+#odrag=(5.5 5)
+#name=(hex_yn.1_nf_od5.5_radius_drag.nc hex_yn.1_nf_od5_radius_drag.nc)
+
+
+radius=6363827
+damp=1
+gc=0
+
+echo $radius
+echo $damp
+echo $gc
+
+for ((i = 0; i < ${#odrag[@]}; ++i)); do
+    drag=(${odrag[$i]})
+    fname=(${name[$i]})
+
+    echo $drag
+    echo $fname
+
+    sed  "s/<od>/$drag/; s/<gc>/$gc/; s/<rad>/$radius/; s/<damp>/$damp/; s/<name>/$fname/g" \
+	 input_fill_hex.nml > input.nml
+    ./RUN1p
+    # &>/dev/null &
+done
diff --git a/tests/a68/RUN_loop2.sh b/tests/a68/RUN_loop2.sh
new file mode 100755
index 0000000..df50ee6
--- /dev/null
+++ b/tests/a68/RUN_loop2.sh
@@ -0,0 +1,35 @@
+#!/bin/bash
+
+#ocean drag values
+#odrag=(20 22 24 26 28)
+#name=(od_20_tn_ng_nw.nc od_22_tn_ng_nw.nc od_24_tn_ng_nw.nc od_26_tn_ng_nw.nc od_28_tn_ng_nw.nc)
+
+# odrag=(1 5 10 15 20 22 24 26)
+# name=(od_1_tn_ng_ellr.nc od_5_tn_ng_ellr.nc od_10_tn_ng_ellr.nc od_15_tn_ng_ellr.nc od_20_tn_ng_ellr.nc od_22_tn_ng_ellr.nc od_24_tn_ng_ellr.nc od_26_tn_ng_ellr.nc)
+
+# odrag=(15 17.5 20)
+# name=(od_15_tn_ng_noyd.nc od_17.5_tn_ng_noyd.nc od_20_tn_ng_noyd.nc)
+
+#odrag=(19.7)
+#name=(od_19.7_tn_ng_yd.05.nc)
+
+#odrag=(13 14 15)
+#name=(ydp.5_od_13.nc ydp.5_od_14.nc ydp.5_od_15.nc)
+
+Rearth=6363827
+odrag=(17.8 17.9)
+name=(od_17.8_tn_ng_ydn.1.nc od_17.9_tn_ng_ydn.1.nc)
+
+for ((i = 0; i < ${#odrag[@]}; ++i)); do
+    drag=(${odrag[$i]})
+    fname=(${name[$i]})
+
+    echo $drag
+    echo $fname
+    echo $Rearth
+
+    sed  "s/<od>/$drag/; s/<re>/$Rearth/; s/<name>/$fname/g" \
+	 input_fill2.nml > input.nml
+    ./RUN1p
+    # &>/dev/null &
+done
diff --git a/tests/a68/RUN_loop_noground.sh b/tests/a68/RUN_loop_noground.sh
new file mode 100755
index 0000000..c258e44
--- /dev/null
+++ b/tests/a68/RUN_loop_noground.sh
@@ -0,0 +1,28 @@
+#!/bin/bash
+
+#ocean drag values
+odrag=(7)
+#(12 15 20 1)
+name=(test_5e6_od7_hex_check.nc)
+#(h_yn.05_ss100e1e6_nf_od12.nc h_yn.05ss100e1e6_nf_od15.nc h_yn.05ss100e1e6_nf_od20.nc h_yn.05ss100e1e6_nf_od1.nc)
+youngs=5e6
+#5e6
+#odrag=(7.2)
+#name=(hex_ydn.05_wgs84_gc0_nofrac_od7.2.nc)
+
+radius=6363827
+
+echo $radius
+
+for ((i = 0; i < ${#odrag[@]}; ++i)); do
+    drag=(${odrag[$i]})
+    fname=(${name[$i]})
+
+    echo $drag
+    echo $fname
+
+    sed  "s/<od>/$drag/; s/<rad>/$radius/; s/<sc>/$youngs/; s/<name>/$fname/g" \
+	 input_fill_hex_noground.nml > input.nml
+    ./RUN1p
+    # &>/dev/null &
+done
diff --git a/tests/a68/RUN_lsf_hex.sh b/tests/a68/RUN_lsf_hex.sh
new file mode 100755
index 0000000..46b213c
--- /dev/null
+++ b/tests/a68/RUN_lsf_hex.sh
@@ -0,0 +1,33 @@
+#!/bin/bash
+
+#ocean drag values
+ss=(10000)
+gcoef=(1.e20)
+nstress=(68000)
+tstress=(50000)
+damp=(0.1)
+name=(zh_lsf_10kss_el_gl1e20_t50k_n68k_od7_gt_realloc_dc.1.nc)
+#name=(zhex_lsf_el_g1e60_t50k_n400k_od7_2kss.nc)
+radius=6363827
+#6.371229e6
+
+for ((i = 0; i < ${#ss[@]}; ++i)); do
+    substeps=(${ss[$i]})
+    gc=(${gcoef[$i]})
+    fname2=(${name[$i]})
+    ns=(${nstress[$i]})
+    ts=(${tstress[$i]})
+    dc=(${damp[$i]})
+
+    echo $substeps
+    echo $gc
+    echo $fname2
+    echo $ns
+    echo $ts
+
+    sed  "s/<ss>/$substeps/; s/<gc>/$gc/; s/<dc>/$dc/; s/<rad>/$radius/; s/<ns>/$ns/; s/<ts>/$ts/; s/<fname>/$fname2/g" \
+	 hex_r_lsf.nml > input.nml
+    rm $fname2
+    ./RUN1p
+    # &>/dev/null &
+done
diff --git a/tests/a68/RUN_lsf_square.sh b/tests/a68/RUN_lsf_square.sh
new file mode 100755
index 0000000..d28cc3d
--- /dev/null
+++ b/tests/a68/RUN_lsf_square.sh
@@ -0,0 +1,47 @@
+#!/bin/bash
+
+#ocean drag values
+ss=(200)
+gcoef=(1.e6)
+odrag=(15)
+nstress=(18)
+tstress=(2.75)
+# A68dy=0.
+# A68dx=0.
+a68=.false.
+#.true.
+A68dx=0.
+#-0.4017
+A68dy=0.
+#-0.05
+dxw=0.
+#n.4017
+dyw=0.
+#n.05
+#name=(sq_lsf_gc1e6_od15_n18k_t2.75k_cd4e3.nc)
+Eradius=6.378e6
+#6363827
+
+for ((i = 0; i < ${#ss[@]}; ++i)); do
+    substeps=(${ss[$i]})
+    gc=(${gcoef[$i]})
+    fname2=(${name[$i]})
+    #bname2=(${bond_name[$i]})
+    ns=(${nstress[$i]})
+    ts=(${tstress[$i]})
+    od=(${odrag[$i]})
+
+    echo $substeps
+    echo $gc
+    echo $fname2
+    echo $ns
+    echo $ts
+    echo $od
+    echo $a68
+
+    sed  "s/<ss>/$substeps/;  s/<a68>/$a68/; s/<xd>/$A68dx/; s/<yd>/$A68dy/; s/<xdw>/$dxw/; s/<ydw>/$dyw/; s/<gc>/$gc/; s/<rad>/$Eradius/; s/<od>/$od/; s/<ns>/$ns/; s/<ts>/$ts/; s/<name>/$fname2/g" \
+	 square_r_lsf.nml > input.nml
+    rm $fname2
+    #rm $bname2
+    ./RUN1p
+done
diff --git a/tests/a68/RUN_lsf_square_comp.sh b/tests/a68/RUN_lsf_square_comp.sh
new file mode 100755
index 0000000..be5e763
--- /dev/null
+++ b/tests/a68/RUN_lsf_square_comp.sh
@@ -0,0 +1,36 @@
+#!/bin/bash
+
+#ocean drag values
+ss=(200)
+gcoef=(1.e8)
+odrag=(15)
+nstress=(8000)
+tstress=(8000)
+A68dy=0.
+A68dx=0.
+name=(sq_lsf_gc1e8_od15_c8k.nc)
+Eradius=6.378e6
+#6363827
+
+for ((i = 0; i < ${#ss[@]}; ++i)); do
+    substeps=(${ss[$i]})
+    gc=(${gcoef[$i]})
+    fname2=(${name[$i]})
+    #bname2=(${bond_name[$i]})
+    ns=(${nstress[$i]})
+    ts=(${tstress[$i]})
+    od=(${odrag[$i]})
+
+    echo $substeps
+    echo $gc
+    echo $fname2
+    echo $ns
+    echo $ts
+    echo $od
+
+    sed  "s/<ss>/$substeps/;  s/<xd>/$A68dx/; s/<yd>/$A68dy/; s/<gc>/$gc/; s/<rad>/$Eradius/; s/<od>/$od/; s/<ns>/$ns/; s/<ts>/$ts/; s/<name>/$fname2/g" \
+	 square_r_lsf_comp.nml > input.nml
+    rm $fname2
+    #rm $bname2
+    ./RUN1p
+done
diff --git a/tests/a68/RUN_restart_for_paper.sh b/tests/a68/RUN_restart_for_paper.sh
new file mode 100644
index 0000000..5748090
--- /dev/null
+++ b/tests/a68/RUN_restart_for_paper.sh
@@ -0,0 +1,34 @@
+#!/bin/bash
+
+#ocean drag values
+ss=200
+gcoef=(1.e4)
+rdir=S_17.8_ydn.1_r
+odrag=17.8
+nstress=(23)
+tstress=(10)
+a68=.true.
+
+A68dx=-37.5285
+A68dy=-55.2166
+
+fname2=sq_ssf_ssg1.e4_od17.8_addsm.true._rectx-37.5285_y-55.2166_n23_t10.nc
+Eradius=6363827
+pg=.false.
+
+for ((i = 0; i < ${#nstress[@]}; ++i)); do
+    gc=(${gcoef[$i]})
+    ns=(${nstress[$i]})
+    ts=(${tstress[$i]})
+
+    echo $gc
+    echo $a68
+    echo $ns
+    echo $ts
+    echo $pg
+    echo $rdir
+
+    sed  "s/<ss>/$ss/; s/<a68>/$a68/; s/<pg>/$pg/; s/<xd>/$A68dx/; s/<yd>/$A68dy/; s/<rdir>/$rdir/; s/<gc>/$gc/; s/<rad>/$Eradius/; s/<od>/$odrag/; s/<ns>/$ns/; s/<ts>/$ts/; s/<name>/$fname2/g" \
+	 square_r_ssf.nml > input.nml
+    ./RUN1p
+done
diff --git a/tests/a68/RUN_ssf_hex.sh b/tests/a68/RUN_ssf_hex.sh
new file mode 100755
index 0000000..0e29104
--- /dev/null
+++ b/tests/a68/RUN_ssf_hex.sh
@@ -0,0 +1,64 @@
+#!/bin/bash
+
+# odrag=(7.2)
+# nstress=(82000)
+# tstress=(82000)
+# A68dy=0.1
+# A68dx=-0.08
+# name=(zh_ssf_el_gl1e30_od7.2_compd82.k_tripy.1xn.08_cspr1en7_10e3cd_powgnd.nc)
+# radius=6363827
+
+#ocean drag values
+ss=(200)
+gcoef=(1.e4)
+pg=.false.
+#.true.
+odrag=(6)
+#5
+nstress=105
+#(85)
+tstress=55
+#(55)
+a68=.true.
+#.false.
+ssg=.true.
+#.true.
+A68dy=0.06792000000000087
+#-0.02 #for 5.4
+#0.06
+A68dx=-0.27071999999997587
+#-0.323
+#-0.15 #for 5.4
+#-0.2
+
+#name=(zzh_ssf_yn.075_gl1e10_od6_nt80k_a68_y.06xn.2.nc)
+#name=(zzh_ssf_yn.1_gl1e10_od5.4_nt82k_a68_yn.02xn.15.nc)
+#name=(hz_ssf_yn.1_gl1e6_od5_n90_t60_a68.nc)
+radius=6363827
+
+for ((i = 0; i < ${#ss[@]}; ++i)); do
+    substeps=(${ss[$i]})
+    gc=(${gcoef[$i]})
+    #fname2=(${name[$i]})
+    #bname2=(${bond_name[$i]})
+    ns=(${nstress[$i]})
+    ts=(${tstress[$i]})
+    od=(${odrag[$i]})
+
+    echo $substeps
+    echo $gc
+    #echo $fname2
+    echo $ns
+    echo $ts
+    echo $od
+    echo $A68dx
+    echo $A68dy
+    echo $pg
+    echo $ssg
+
+    sed  "s/<ss>/$substeps/; s/<pg>/$pg/; s/<a68>/$a68/; s/<xd>/$A68dx/; s/<yd>/$A68dy/; s/<gc>/$gc/; s/<rad>/$radius/; s/<ssg>/$ssg/; s/<od>/$od/; s/<ns>/$ns/; s/<ts>/$ts/g" \
+	 hex_r_ssf.nml > input.nml
+    rm $fname2
+    rm $bname2
+    ./RUN1p
+done
diff --git a/tests/a68/RUN_ssf_square.sh b/tests/a68/RUN_ssf_square.sh
new file mode 100755
index 0000000..69dba14
--- /dev/null
+++ b/tests/a68/RUN_ssf_square.sh
@@ -0,0 +1,66 @@
+#!/bin/bash
+
+#ocean drag values
+ss=200
+gcoef=(1.e4 5.e3 1.e1)
+#gcoef=(1.e4 5.e3 1.e1)
+rdir=S_17.8_ydn.1_r
+odrag=17.8
+#19.5
+#21.25
+#15
+nstress=(24 23 23)
+#25
+#(25 30 35 30 25)
+tstress=(6.5 6.5 6.5)
+#tstress=(7 7 7)
+#7
+#(6 5 5 4 4)
+#nstress=(50000)
+#tstress=(3000)
+a68=.true.
+#.false
+
+# A68dx=-0.01872
+# A68dy=-0.09338
+
+#A68dx=-37.2954
+#A68dy=-55.2975
+
+A68dx=-37.5285
+A68dy=-55.2166
+
+
+#name=(sq_ssf_gc1e6_od15_n20k_t5k.nc)
+fname2=loop
+#Eradius=6.378e6
+Eradius=6363827
+pg=.false.
+#.true.
+#6363827
+
+for ((i = 0; i < ${#nstress[@]}; ++i)); do
+    #substeps=(${ss[$i]})
+    gc=(${gcoef[$i]})
+    #fname2=(${name[$i]})
+    #bname2=(${bond_name[$i]})
+    ns=(${nstress[$i]})
+    ts=(${tstress[$i]})
+    #od=(${odrag[$i]})
+
+    #echo $substeps
+    echo $gc
+    #echo $fname2
+    echo $a68
+    echo $ns
+    echo $ts
+    echo $pg
+    echo $rdir
+    #echo $od
+
+    sed  "s/<ss>/$ss/; s/<a68>/$a68/; s/<pg>/$pg/; s/<xd>/$A68dx/; s/<yd>/$A68dy/; s/<rdir>/$rdir/; s/<gc>/$gc/; s/<rad>/$Eradius/; s/<od>/$odrag/; s/<ns>/$ns/; s/<ts>/$ts/; s/<name>/$fname2/g" \
+	 square_r_ssf.nml > input.nml
+    #rm $fname2
+    #rm $bname2
+    ./RUN1p
+done
diff --git a/tests/a68/RUN_ssfrac.sh b/tests/a68/RUN_ssfrac.sh
new file mode 100755
index 0000000..6126cb8
--- /dev/null
+++ b/tests/a68/RUN_ssfrac.sh
@@ -0,0 +1,30 @@
+#!/bin/bash
+
+#ocean drag values
+ss=(200)
+# 400 500 1000)
+gcoef=(1.e6)
+nstress=(9000)
+tstress=(2500)
+name=(lsf_nsf_200_gc1e5_t2.5k_n9k.nc)
+# sstest_400_ssf.nc sstest_500_ssf.nc sstest_1000_ssf.nc)
+
+for ((i = 0; i < ${#ss[@]}; ++i)); do
+    substeps=(${ss[$i]})
+    gc=(${gcoef[$i]})
+    fname2=(${name[$i]})
+    ns=(${nstress[$i]})
+    ts=(${tstress[$i]})
+
+    echo $substeps
+    echo $gc
+    echo $fname2
+    echo $ns
+    echo $ts
+
+    sed  "s/<ss>/$substeps/; s/<gc>/$gc/; s/<ns>/$ns/; s/<ts>/$ts/; s/<fname>/$fname2/g" \
+	 check_ss3.nml > input.nml
+    rm $fname2
+    ./RUN1p
+    # &>/dev/null &
+done
diff --git a/tests/a68/RUN_ssfrac2.sh b/tests/a68/RUN_ssfrac2.sh
new file mode 100755
index 0000000..779b85a
--- /dev/null
+++ b/tests/a68/RUN_ssfrac2.sh
@@ -0,0 +1,30 @@
+#!/bin/bash
+
+#ocean drag values
+ss=(200)
+#(100 300 750)
+gcoef=(1.e6)
+nstress=(20000)
+tstress=(8000)
+name=(ssf_nstressfix_200_gc1e6_t8k_n20k.nc)
+#(sstest_100_ssf.nc sstest_300_ssf.nc sstest_750_ssf.nc)
+
+for ((i = 0; i < ${#ss[@]}; ++i)); do
+    substeps=(${ss[$i]})
+    gc=(${gcoef[$i]})
+    fname2=(${name[$i]})
+    ns=(${nstress[$i]})
+    ts=(${tstress[$i]})
+
+    echo $substeps
+    echo $gc
+    echo $fname2
+    echo $ns
+    echo $ts
+
+    sed  "s/<ss>/$substeps/;  s/<gc>/$gc/; s/<ns>/$ns/; s/<ts>/$ts/; s/<fname>/$fname2/g" \
+	 check_ss3_ssf.nml > input.nml
+    rm $fname2
+    ./RUN1p
+    # &>/dev/null &
+done
diff --git a/tests/a68/RUN_test_init_for_paper.sh b/tests/a68/RUN_test_init_for_paper.sh
new file mode 100644
index 0000000..3b7bfab
--- /dev/null
+++ b/tests/a68/RUN_test_init_for_paper.sh
@@ -0,0 +1,19 @@
+#!/bin/bash
+
+Rearth=6363827
+odrag=(17.8)
+name=(od_17.8_tn_ng_ydn.1.nc)
+
+for ((i = 0; i < ${#odrag[@]}; ++i)); do
+    drag=(${odrag[$i]})
+    fname=(${name[$i]})
+
+    echo $drag
+    echo $fname
+    echo $Rearth
+
+    sed  "s/<od>/$drag/; s/<re>/$Rearth/; s/<name>/$fname/g" \
+	 input_fill2.nml > input.nml
+    ./RUN1p
+    # &>/dev/null &
+done
diff --git a/tests/a68/animate_trajectories.py b/tests/a68/animate_trajectories.py
new file mode 100755
index 0000000..a30ca3b
--- /dev/null
+++ b/tests/a68/animate_trajectories.py
@@ -0,0 +1,317 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+import matplotlib.pyplot as plt
+from matplotlib.animation import FuncAnimation
+import argparse
+import xarray as xr
+from mpl_toolkits.axes_grid1.axes_divider import make_axes_locatable
+
+import cartopy.crs as ccrs
+import copy
+from matplotlib.figure import figaspect
+from matplotlib import ticker
+from cartopy.mpl.gridliner import LONGITUDE_FORMATTER, LATITUDE_FORMATTER
+from cartopy.mpl.ticker import LongitudeFormatter, LatitudeFormatter
+import matplotlib.ticker as mticker
+import matplotlib.colors as mcolors
+from matplotlib.colors import LinearSegmentedColormap
+
+from pyproj import Transformer
+#from scipy import stats
+#import pandas as pd
+import matplotlib.ticker as plticker
+
+
+from matplotlib.gridspec import GridSpec
+import matplotlib.path as mpath
+import matplotlib.dates as mdates
+import cartopy.mpl.ticker as ctk
+
+def parseCommandLine():
+    t0=9+13./24
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
+                    help=''' provide filename to plot''')
+    parser.add_argument('-s', type=int, default='400',
+                        help='''plotted particle size''')
+    parser.add_argument('-t0', type=float, default=t0,
+                        help=''' initial time (days)''')
+    parser.add_argument('-plotvar', type=bool, default=False,
+                        help=''' plot a var''')
+    parser.add_argument('-zoom', type=bool, default=False,
+                        help=''' zoom to A68 grounding point''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+
+
+def main(args):
+
+    print('reading file')
+
+    filename=args.fname
+    psize=args.s
+    t0=args.t0
+    pvar=args.plotvar
+    zoom=args.zoom
+    #if (zoom):
+    #    psize=75
+    #filename = 'iceberg_trajectories.nc'
+    field = 'lon'
+    field2 = 'lat'
+
+    with nc.Dataset(filename) as file:
+        x = file.variables['lon'][:]-360 #/1.e3
+        y = file.variables['lat'][:] #/1.e3
+        day = file.variables['day'][:]
+        length = file.variables['length'][:]
+        width = file.variables['width'][:]
+        thick = file.variables['thickness'][:]
+        od = file.variables['od'][:]
+        nbonds = file.variables['n_bonds'][:]
+        #uvel = file.variables['uvel_prev'][:]
+        #vvel = file.variables['vvel_prev'][:]
+
+    print('min day',day.min())
+    day=day+t0
+
+    thevar=nbonds
+    # thres=17.5
+    # x=x[day<thres]
+    # y=y[day<thres]
+    # length=length[day<thres]
+    # width=width[day<thres]
+    # thick=thick[day<thres]
+    # od=od[day<thres]
+    # day=day[day<thres]
+
+    ud = np.unique(day)
+    t = ud[0]
+
+    #print('uinit',uvel[day==t])
+    #print('vinit',vvel[day==t])
+
+    # print('lon',x)
+    # print('lat',y)
+    radius = np.sqrt(length*width/4)#*(1./(2*np.sqrt(3)))
+
+    #for determining if grounded:
+    rho_bergs=850.
+    rho_seawater=1025.
+    h_to_ground=30.
+    draught=(rho_bergs/rho_seawater)*thick
+    groundfrac=1.-(od-draught)/h_to_ground
+    groundfrac[groundfrac<0.]=0.
+    groundfrac[groundfrac>1.]=1.
+
+    groundfrac2=groundfrac*0
+    groundfrac2[draught>od]=1.
+
+    #groundfrac[thick<200.]=0.
+    #groundfrac[thick>=200.]=1.
+
+
+    # frame info
+    num_frames = len(ud)
+    movie_len = 5 #seconds
+    #frame_len = 1000.0*movie_len/num_frames/10000000
+    frame_len = movie_len/num_frames/1000
+
+    if (zoom):
+        xmin = -39 #38.5
+        xmax = -36
+        ymin = -57 #-56.5
+        ymax = -54
+    else:
+        xmin = -41
+        xmax = -36
+        ymin = -58
+        ymax = -54
+
+    anim_running = True
+
+    def animate(i):
+
+        x1 = x[day == ud[i]]
+        y1 = y[day == ud[i]]
+        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
+
+        scat.set_offsets(data)
+
+        #t = ud[i]+14+13./24
+        #t = ud[i]+16#9+13./24
+        t=ud[i]
+        time_text.set_text('date = Dec %.3f' % t )
+
+        r1 = radius[day == ud[i]]
+        scat.set_sizes(r1/psize)
+
+        hstat = groundfrac[day == ud[i]]
+        hstat2 = groundfrac2[day == ud[i]]
+        cstring=[]
+        cstring2=[]
+
+        if pvar==True:
+        #var1=od[day==ud[i]]
+            var1=thevar[day==ud[i]]
+            scat.set_color(cmap(norm(var1)))
+        else:
+            for j in range(len(hstat)):
+                if (hstat2[j]==0):
+                    if (hstat[j]==0):
+                        cstring.append("none")
+                        cstring2.append('r')
+                    else:
+                        cstring.append("b")
+                        cstring2.append('b')
+                else:
+                    cstring.append("c")
+                    cstring2.append('c')
+            scat.set_color(cstring)
+            scat.set_edgecolor(cstring2)
+
+        return scat,time_text
+
+    def init():
+        scat.set_offsets([])
+        return scat,
+
+    def onClick(event):
+        global anim_running
+        if anim_running:
+            ani.event_source.stop()
+            anim_running = False
+        else:
+            ani.event_source.start()
+            anim_running = True
+
+
+    minlon = xmin
+    maxlon = xmax
+    midlon = (minlon+maxlon)/2
+
+    minlat = ymin
+    maxlat = ymax
+    midlat = (ymin+ymax)/2
+
+    extent=[xmin, xmax, ymin, ymax]
+    extent2=[xmin-1, xmax+1, ymin-1, ymax+1]
+    extent3=[xmin-1, ymin-1, xmax+1, ymax+1]
+
+    subplot_kws=dict(projection=ccrs.NearsidePerspective(central_longitude=midlon, central_latitude=midlat))
+
+    bottom_x=np.vstack(np.linspace(minlon,maxlon,3)); bottom_y=bottom_x*0+minlat
+    top_x=np.vstack(np.linspace(maxlon,minlon,3)); top_y=top_x*0+maxlat
+    lons=np.vstack((bottom_x,top_x)); lats=np.vstack((bottom_y,top_y))
+    boundary_path=np.hstack((lons,lats))
+    boundary_path = mpath.Path(boundary_path)
+
+    old=False
+    
+    # Now we can do the plotting!
+    f = plt.figure(figsize=(8,8))
+    f.tight_layout()
+
+    if old:
+        ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
+        scat = ax1.scatter([],[],marker='o')#,edgecolor='red')        
+    else:
+        ax1 = plt.axes(projection=ccrs.NearsidePerspective(central_longitude=midlon, central_latitude=midlat))
+        scat = ax1.scatter([],[],transform=ccrs.PlateCarree(),marker='o')#,edgecolor='red')        
+
+    if pvar==True:
+        div = make_axes_locatable(ax1)
+        cax = div.append_axes('right', '5%', '5%')
+        cmap = plt.cm.get_cmap('RdYlBu')
+        norm = plt.Normalize(thevar.min(), thevar.max())
+        #norm = plt.Normalize(165.7, 165.8)
+        cb1 = matplotlib.colorbar.ColorbarBase(cax, cmap=cmap,
+                                               norm=norm,
+                                               orientation='vertical')
+
+
+    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
+
+
+    #plt.scatter(323.4-360,-56.6,marker='o')
+    #plt.scatter(322.52-360,-55.39,marker='o')
+
+    xt=np.array([-37.32708,-37.05308,-37.13542,-37.32708])
+    yt=np.array([-55.01042,-55.01042,-54.93958,-55.01042])
+    plt.plot(xt,yt)
+
+
+    if (pvar==False):
+        dir='./data'
+        oscar=xr.load_dataset(f'{dir}/a68_experiment_ocean_surf_vel_oscar_dec2020_HOURLY_ll_p125.nc')
+        #oscar.isel(time=400).plot.quiver(x="lon",y="lat",u="uo",v="vo",hue='vel',vmax=0.2, scale=8)
+        vv=oscar.isel(time=400)
+        norm=plt.cm.colors.Normalize(vmin=0,vmax=0.35)
+        if (old==False):
+            ax1.quiver(vv.lon.values,vv.lat.values,vv.uo.values,vv.vo.values,vv.vel.values,scale=8,cmap='viridis',norm=norm,transform=ccrs.PlateCarree())
+        else:
+            ax1.quiver(vv.lon,vv.lat,vv.uo,vv.vo,vv.vel,scale=8,cmap='viridis',norm=norm)
+        f.colorbar(plt.cm.ScalarMappable(norm=norm, cmap='viridis'),ax=ax1, shrink=0.75)        
+        #330 is dec 14th at 5PM. 408 is dec 16th at 5 PM
+
+
+    if old==True:
+        ax1.set_aspect('equal', adjustable='box')
+
+        # Change major ticks to show every 20.
+        ax1.xaxis.set_major_locator(MultipleLocator(5))
+        ax1.yaxis.set_major_locator(MultipleLocator(5))
+
+        ax1.xaxis.set_minor_locator(MultipleLocator(1))
+        ax1.yaxis.set_minor_locator(MultipleLocator(1))
+
+        # Turn grid on for both major and minor ticks and style minor slightly
+        # differently.
+        ax1.grid(which='major', color='#CCCCCC', linestyle=':')
+        ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
+
+        ax1.set_xlabel('lon')
+        ax1.set_ylabel('lat')
+        ax1.set_title('Iceberg trajectory')
+    else:
+        xticks=list(range(minlon,maxlon+1)); yticks=list(range(minlat,maxlat+1))
+        dir_labels=True
+        proj_to_data = ccrs.PlateCarree()._as_mpl_transform(ax1) - ax1.transData
+        bound_in_target = proj_to_data.transform_path(boundary_path)
+        ax1.set_extent(extent2, crs=ccrs.PlateCarree())
+        ax1.set_boundary(bound_in_target)
+        g=ax1.gridlines(color='black',alpha=0.5,linestyle='--',draw_labels=True,x_inline=False, y_inline=False,xlocs=xticks,ylocs=yticks)
+        g.top_labels=False; g.right_labels=False; g.rotate_labels=False
+        #g.xformatter=LongitudeFormatter(direction_label=dir_labels); g.yformatter=LatitudeFormatter(direction_label=dir_labels)
+        g.xlabel_style = {'size': 12, 'color': 'gray'}; g.ylabel_style = {'size': 12, 'color': 'gray'}
+
+
+    f.canvas.mpl_connect('button_press_event', onClick)
+
+    ani = FuncAnimation(
+        f,animate,init_func=init,frames=num_frames,
+        interval=frame_len,blit=True,repeat=True)
+
+    print('time',t)
+
+    plt.show()
+    #animation.save("iceberg_traj_animation.mp4")
+
+
+print('Script complete')
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
diff --git a/tests/a68/check_ss.nml b/tests/a68/check_ss.nml
new file mode 100644
index 0000000..7cad116
--- /dev/null
+++ b/tests/a68/check_ss.nml
@@ -0,0 +1,212 @@
+&icebergs_driver_nml
+  a68_test=.true.
+  vert_int_ocean_vel=.false.!.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  Old_wrong_Rearth_and_SSH=.false.
+  Rearth=6.378e6
+  !mom_Rearth=.true.
+  no_wind=.false.
+  tau_is_velocity=.true.!.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=1200 !310 !999999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=361 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
+/
+
+&icebergs_nml
+
+    A68_test=.true.
+    Rearth=6.378e6 !6.371229e6 !6.36e6 !6.378e6
+    tau_is_velocity=.true.!.false.
+    ocean_drag_scale=15 !20. !1
+
+    add_curl_to_torque=.false.
+
+    constant_interaction_LW=.true.
+
+    !traj_name=od_15_tn_ng_momr_for_restart_b.nc
+    traj_name=<fname>
+    !od_15_tn_ng_momr_res_n9k_s3k_500ss.nc
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
+    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=<ss>!500!125!75 !75 !150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=30!15!50. !15.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 1.0
+    frac_thres_n = 7500.0 !25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
+    frac_thres_t = 2800.0 !11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.false. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    !restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    !manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    !manually_initialize_bonds_from_radii=.true.   
+    restart_input_dir='./S_OD15b/'
+    manually_initialize_bonds=.false. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.false.!.true.
+    
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/a68/check_ss2.nml b/tests/a68/check_ss2.nml
new file mode 100644
index 0000000..4d00bac
--- /dev/null
+++ b/tests/a68/check_ss2.nml
@@ -0,0 +1,212 @@
+&icebergs_driver_nml
+  a68_test=.true.
+  vert_int_ocean_vel=.false.!.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  Old_wrong_Rearth_and_SSH=.false.
+  Rearth=6.378e6
+  !mom_Rearth=.true.
+  no_wind=.false.
+  tau_is_velocity=.true.!.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=1200 !310 !999999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=361 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
+/
+
+&icebergs_nml
+
+    A68_test=.true.
+    Rearth=6.378e6 !6.371229e6 !6.36e6 !6.378e6
+    tau_is_velocity=.true.!.false.
+    ocean_drag_scale=15 !20. !1
+
+    add_curl_to_torque=.false.
+
+    constant_interaction_LW=.true.
+
+    !traj_name=od_15_tn_ng_momr_for_restart_b.nc
+    traj_name=<fname>
+    !od_15_tn_ng_momr_res_n9k_s3k_500ss.nc
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
+    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=<ss>!500!125!75 !75 !150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=30!15!50. !15.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 0.9 !1.0
+    frac_thres_n = 7500.0 !25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
+    frac_thres_t = 2800.0 !11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.false. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    !restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    !manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    !manually_initialize_bonds_from_radii=.true.   
+    restart_input_dir='./S_OD15b/'
+    manually_initialize_bonds=.false. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.false.!.true.
+    
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/a68/check_ss3.nml b/tests/a68/check_ss3.nml
new file mode 100644
index 0000000..50b23df
--- /dev/null
+++ b/tests/a68/check_ss3.nml
@@ -0,0 +1,212 @@
+&icebergs_driver_nml
+  a68_test=.true.
+  vert_int_ocean_vel=.false.!.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  Old_wrong_Rearth_and_SSH=.false.
+  Rearth=6.378e6
+  !mom_Rearth=.true.
+  no_wind=.false.
+  tau_is_velocity=.true.!.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=120 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=1200 !310 !999999999 !max number of timesteps
+  saverestart=.false.!.true.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=361 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
+/
+
+&icebergs_nml
+
+    A68_test=.true.
+    Rearth=6.378e6 !6.371229e6 !6.36e6 !6.378e6
+    tau_is_velocity=.true.!.false.
+    ocean_drag_scale=15 !20. !1
+
+    add_curl_to_torque=.false.
+
+    constant_interaction_LW=.true.
+
+    !traj_name=od_15_tn_ng_momr_for_restart_b.nc
+    traj_name=<fname>
+    !od_15_tn_ng_momr_res_n9k_s3k_500ss.nc
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
+    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=<ss>!500!125!75 !75 !150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=<gc> !1.e7 !6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=30!15!50. !15.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 1.
+    frac_thres_n = <ns> !9000.0 !11250.0
+    frac_thres_t = <ts> !3000.0 !10000.0
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.false. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    !restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    !manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    !manually_initialize_bonds_from_radii=.true.   
+    restart_input_dir='./S_OD15b/'
+    manually_initialize_bonds=.false. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.false.!.true.
+    
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/a68/check_ss3_nofrac.nml b/tests/a68/check_ss3_nofrac.nml
new file mode 100644
index 0000000..f500a95
--- /dev/null
+++ b/tests/a68/check_ss3_nofrac.nml
@@ -0,0 +1,212 @@
+&icebergs_driver_nml
+  a68_test=.true.
+  vert_int_ocean_vel=.false.!.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  Old_wrong_Rearth_and_SSH=.false.
+  Rearth=6.378e6
+  !mom_Rearth=.true.
+  no_wind=.false.
+  tau_is_velocity=.true.!.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=120 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=1200 !310 !999999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=361 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
+/
+
+&icebergs_nml
+
+    A68_test=.true.
+    Rearth=6.378e6 !6.371229e6 !6.36e6 !6.378e6
+    tau_is_velocity=.true.!.false.
+    ocean_drag_scale=15 !20. !1
+
+    add_curl_to_torque=.false.
+
+    constant_interaction_LW=.true.
+
+    !traj_name=od_15_tn_ng_momr_for_restart_b.nc
+    traj_name=<fname>
+    !od_15_tn_ng_momr_res_n9k_s3k_500ss.nc
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
+    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=<ss>!500!125!75 !75 !150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=30!15!50. !15.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 1.
+    frac_thres_n = -1 !15000.0 !11250.0
+    frac_thres_t = -1 !7500.0
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.false. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    !restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    !manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    !manually_initialize_bonds_from_radii=.true.   
+    restart_input_dir='./S_OD15b/'
+    manually_initialize_bonds=.false. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.false.!.true.
+    
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/a68/check_ss3_ssf.nml b/tests/a68/check_ss3_ssf.nml
new file mode 100644
index 0000000..881c16b
--- /dev/null
+++ b/tests/a68/check_ss3_ssf.nml
@@ -0,0 +1,214 @@
+&icebergs_driver_nml
+  a68_test=.true.
+  vert_int_ocean_vel=.false.!.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  Old_wrong_Rearth_and_SSH=.false.
+  Rearth=6.378e6
+  !mom_Rearth=.true.
+  no_wind=.false.
+  tau_is_velocity=.true.!.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=120 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=1200 !310 !999999999 !max number of timesteps
+  saverestart=.false.!.true.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=361 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
+/
+
+&icebergs_nml
+
+    A68_test=.true.
+    Rearth=6.378e6 !6.371229e6 !6.36e6 !6.378e6
+    tau_is_velocity=.true.!.false.
+    ocean_drag_scale=15 !20. !1
+
+    add_curl_to_torque=.false.
+
+    constant_interaction_LW=.true.
+
+    break_bonds_on_sub_steps=.true.
+
+    !traj_name=od_15_tn_ng_momr_for_restart_b.nc
+    traj_name=<fname>
+    !od_15_tn_ng_momr_res_n9k_s3k_500ss.nc
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
+    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=<ss>!500!125!75 !75 !150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=<gc>!1.e7!6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=30 !15!50. !15.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 1.
+    frac_thres_n = <ns> !16000.0 !11250.0
+    frac_thres_t = <ts> !7500.0 !10000.0
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.false. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    !restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    !manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    !manually_initialize_bonds_from_radii=.true.   
+    restart_input_dir='./S_OD15b/'
+    manually_initialize_bonds=.false. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.false.!.true.
+    
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/a68/check_ss_new.nml b/tests/a68/check_ss_new.nml
new file mode 100644
index 0000000..7cad116
--- /dev/null
+++ b/tests/a68/check_ss_new.nml
@@ -0,0 +1,212 @@
+&icebergs_driver_nml
+  a68_test=.true.
+  vert_int_ocean_vel=.false.!.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  Old_wrong_Rearth_and_SSH=.false.
+  Rearth=6.378e6
+  !mom_Rearth=.true.
+  no_wind=.false.
+  tau_is_velocity=.true.!.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=1200 !310 !999999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=361 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
+/
+
+&icebergs_nml
+
+    A68_test=.true.
+    Rearth=6.378e6 !6.371229e6 !6.36e6 !6.378e6
+    tau_is_velocity=.true.!.false.
+    ocean_drag_scale=15 !20. !1
+
+    add_curl_to_torque=.false.
+
+    constant_interaction_LW=.true.
+
+    !traj_name=od_15_tn_ng_momr_for_restart_b.nc
+    traj_name=<fname>
+    !od_15_tn_ng_momr_res_n9k_s3k_500ss.nc
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
+    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=<ss>!500!125!75 !75 !150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=30!15!50. !15.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 1.0
+    frac_thres_n = 7500.0 !25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
+    frac_thres_t = 2800.0 !11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.false. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    !restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    !manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    !manually_initialize_bonds_from_radii=.true.   
+    restart_input_dir='./S_OD15b/'
+    manually_initialize_bonds=.false. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.false.!.true.
+    
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/a68/check_ss_orig.nml b/tests/a68/check_ss_orig.nml
new file mode 100644
index 0000000..78161d7
--- /dev/null
+++ b/tests/a68/check_ss_orig.nml
@@ -0,0 +1,211 @@
+&icebergs_driver_nml
+  a68_test=.true.
+  vert_int_ocean_vel=.false.!.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  Old_wrong_Rearth_and_SSH=.false.
+  Rearth=6.378e6
+  !mom_Rearth=.true.
+  no_wind=.false.
+  tau_is_velocity=.true.!.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=1200 !310 !999999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=361 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
+/
+
+&icebergs_nml
+
+    A68_test=.true.
+    Rearth=6.378e6 !6.371229e6 !6.36e6 !6.378e6
+    tau_is_velocity=.true.!.false.
+    ocean_drag_scale=15 !20. !1
+
+    add_curl_to_torque=.false.
+
+    constant_interaction_LW=.true.
+
+    !traj_name=od_15_tn_ng_momr_for_restart_b.nc
+    traj_name=od_15_tn_ng_momr_res_n9k_s3k_500ss.nc
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
+    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=500!125!75 !75 !150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=30!15!50. !15.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 1.5
+    frac_thres_n = 6000.0 !25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
+    frac_thres_t = 2000.0 !11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.false. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    !restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    !manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    !manually_initialize_bonds_from_radii=.true.   
+    restart_input_dir='./S_OD15b/'
+    manually_initialize_bonds=.false. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.false.!.true.
+    
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/a68/diag_table b/tests/a68/diag_table
new file mode 100644
index 0000000..c1c8819
--- /dev/null
+++ b/tests/a68/diag_table
@@ -0,0 +1,3 @@
+"icebergs test"
+1 1 1 0 0 0
+
diff --git a/tests/a68/hex_4restart.sh b/tests/a68/hex_4restart.sh
new file mode 100755
index 0000000..6755381
--- /dev/null
+++ b/tests/a68/hex_4restart.sh
@@ -0,0 +1,40 @@
+#!/bin/bash
+
+#ocean drag values
+#odrag=(6.5 6 5 7 4 8 3 1)
+#name=(hex_wgs84_nofrac_od6.5.nc hex_wgs84_nofrac_od6.nc hex_wgs84_nofrac_od5.nc hex_wgs84_nofrac_od7.nc hex_wgs84_nofrac_od4.nc hex_wgs84_nofrac_od8.nc hex_wgs84_nofrac_od3.nc hex_wgs84_nofrac_od1.nc)
+
+#odrag=(7.2)
+#name=(hex_ydn.05_wgs84_nf_od7.2_4restart.nc)
+
+# odrag=(6)
+# name=(hex_yn.075_nf_od6_4restart.nc)
+# bond_name=(hex_yn.075_nf_od6_4restart_bonds.nc)
+# radius=6363827
+
+# odrag=(5.4)
+# name=(hex_yn.1_nf_od5.4_4restart.nc)
+# bond_name=(hex_yn.1_nf_od5.4_4restart_bonds.nc)
+# radius=6363827
+
+odrag=(5)
+name=(hex_yn.1_nf_od5_4restart.nc)
+bond_name=(hex_yn.1_nf_od5_4restart_bonds.nc)
+radius=6363827
+
+echo $radius
+
+for ((i = 0; i < ${#odrag[@]}; ++i)); do
+    drag=(${odrag[$i]})
+    fname=(${name[$i]})
+    bname=(${bond_name[$i]})
+    echo $drag
+    echo $fname
+
+    sed  "s/<od>/$drag/; s/<rad>/$radius/; s/<bname>/$bname/; s/<name>/$fname/g" \
+	 input_fill_hex_4restart.nml > input.nml
+    rm $fname
+    rm $bname
+    ./RUN1p
+    # &>/dev/null &
+done
diff --git a/tests/a68/hex_r_lsf.nml b/tests/a68/hex_r_lsf.nml
new file mode 100644
index 0000000..16d0ccc
--- /dev/null
+++ b/tests/a68/hex_r_lsf.nml
@@ -0,0 +1,214 @@
+&icebergs_driver_nml
+  a68_test=.true.
+  vert_int_ocean_vel=.false.!.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  Old_wrong_Rearth_and_SSH=.false.
+  Rearth=<rad>
+  !6.371229e6 !6.378e6
+  no_wind=.false.
+  tau_is_velocity=.true.!.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=120 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=1200 !310 !999999999 !max number of timesteps
+  saverestart=.false.!.true.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=355 !361 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
+/
+
+&icebergs_nml
+
+    A68_test=.true.!.false.!.true.
+    Rearth=<rad>
+    !6.371229e6 !6.378e6 !6.371229e6 !6.36e6 !6.378e6
+    tau_is_velocity=.true.!.false.
+    ocean_drag_scale=7 !6.5 !20. !1
+
+    add_curl_to_torque=.false.
+    constant_interaction_LW=.true.
+
+    no_frac_first_ts=.true.
+    !orig_dem_moment_of_inertia=.true.
+
+    traj_name=<fname>
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=<dc>
+    !1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    !spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7, r=1500, and square pack?
+    spring_coef=0.0007547062342348049 !if dem_spring_coef=0.5e7, r=1500, and hex pack?    
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=<ss>!500!125!75 !75 !150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=<gc>!1.e7!6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=0 !15!50. !15.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 1.
+    frac_thres_n = <ns> !16000.0 !11250.0
+    frac_thres_t = <ts> !7500.0 !10000.0
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true.!.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=-1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=2 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.false. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.false. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    !restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    !manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    !manually_initialize_bonds_from_radii=.true.
+    restart_input_dir='./HEX7_r/' !'./S_OD15b/'
+    manually_initialize_bonds=.false. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.false.!.true.
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/a68/hex_r_ssf.nml b/tests/a68/hex_r_ssf.nml
new file mode 100644
index 0000000..b9c3e44
--- /dev/null
+++ b/tests/a68/hex_r_ssf.nml
@@ -0,0 +1,230 @@
+&icebergs_driver_nml
+  a68_test=.true.
+  vert_int_ocean_vel=.false.!.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  Old_wrong_Rearth_and_SSH=.false.
+  Rearth=<rad>
+  !6.371229e6 !6.378e6
+  !mom_Rearth=.true.
+  no_wind=.false.
+  tau_is_velocity=.true.!.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=120 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=1200 !310 !999999999 !max number of timesteps
+  saverestart=.false.!.true.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=355 !361 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
+  !transient_a68_data_start_ind=331
+/
+
+&icebergs_nml
+
+    A68_test=<a68> !.false.!.true.
+    A68_xdisp=<xd>
+    A68_ydisp=<yd>
+    !orig_dem_moment_of_inertia=.true.
+    Rearth=<rad>
+    !6.371229e6 !6.378e6 !6.371229e6 !6.36e6 !6.378e6
+    tau_is_velocity=.true.!.false.
+    ocean_drag_scale=<od> !7. !6.5 !20. !1
+
+    add_curl_to_torque=.false.
+
+    constant_interaction_LW=.true.
+
+    no_frac_first_ts=.true.
+    power_ground=<pg>
+    
+    break_bonds_on_sub_steps=.true.
+    short_step_mts_grounding=<ssg>
+
+    !use_grounding_torque=.true.
+
+    !traj_name=od_15_tn_ng_momr_for_restart_b.nc
+    !traj_name=<fname>
+    traj_name=hz_ssf_g<gc>_addsm<a68>_od<od>_n<ns>t<ts>_pg<pg>_ssg<ssg>.nc
+    !bond_traj_name=<bname>
+    !od_15_tn_ng_momr_res_n9k_s3k_500ss.nc
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    !spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7, r=1500, and square pack?
+    spring_coef=0.0007547062342348049 !if dem_spring_coef=5e6, r=1500, and hex pack?    
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=<ss>!500!125!75 !75 !150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-4 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=10.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7 !(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=<gc>!1.e7!6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=1. !0 !15!50. !15.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !'computed' !'stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 1.
+    frac_thres_n = <ns>e3 !16000.0 !11250.0
+    frac_thres_t = <ts>e3 !7500.0 !10000.0
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=-1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=2 !6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false.!.true. !.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.false. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    !restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    !manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    !manually_initialize_bonds_from_radii=.true.
+    !restart_input_dir='H<od>_yn.1_r/'
+    restart_input_dir='H<od>_yn.75_r/'
+    !restart_input_dir='HEX<od>_r/'
+    manually_initialize_bonds=.false. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.false.!.true.
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/a68/hex_wgs84_frac_specs.nml b/tests/a68/hex_wgs84_frac_specs.nml
new file mode 100644
index 0000000..0fae617
--- /dev/null
+++ b/tests/a68/hex_wgs84_frac_specs.nml
@@ -0,0 +1,209 @@
+&icebergs_driver_nml
+  a68_test=.true.
+  vert_int_ocean_vel=.false.!.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  Old_wrong_Rearth_and_SSH=.false.
+  no_wind=.false.  
+  tau_is_velocity=.true.!.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=360 !120 !360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=298 !432 !298 !310 !99999 !310 !999999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=206 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
+  Rearth=6363827
+  !6.371229e6
+/
+
+&icebergs_nml
+
+    A68_test=.false.
+    Rearth=6363827
+    tau_is_velocity=.true.!.false.
+    ocean_drag_scale=6.5 !20. !1
+
+    add_curl_to_torque=.false.
+
+    skip_first_outer_mts_step=.true.
+
+    constant_interaction_LW=.true.
+
+    traj_name=hex_wgs84_nofrac_od6.5_for_restart.nc
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    !spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7, r=1500, and square pack?
+    spring_coef=0.0007547062342348049 !if dem_spring_coef=0.5e7, r=1500, and hex pack?
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=200 !125!75 !75 !150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=30!15!50. !15.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 100000
+    frac_thres_n = 25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
+    frac_thres_t = 11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.false. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/a68/input.nml b/tests/a68/input.nml
new file mode 100644
index 0000000..b4eae13
--- /dev/null
+++ b/tests/a68/input.nml
@@ -0,0 +1,216 @@
+&icebergs_driver_nml
+  a68_test=.true.
+  vert_int_ocean_vel=.false.!.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  Old_wrong_Rearth_and_SSH=.false.
+  no_wind=.false.  
+  tau_is_velocity=.true.!.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=360 !120 !360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=432 !298 !310 !99999 !310 !999999999 !max number of timesteps
+  saverestart=.false.!.true.!.false.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=206 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
+  Rearth=6363827
+  !6.371229e6
+/
+
+&icebergs_nml
+
+    A68_test=.false. !.true. !.false.
+    short_step_mts_grounding=.true.
+    !rev_mind=.true.
+    Rearth=6363827
+    tau_is_velocity=.true.!.false.
+    ocean_drag_scale=10 !20. !1
+
+    add_curl_to_torque=.false.
+
+    skip_first_outer_mts_step=.true.
+
+    constant_interaction_LW=.true.
+
+    traj_name=hex_yn.1_nf_od10_rad_drag_E1e6.nc
+
+    radius_based_drag=.true.
+    !orig_dem_moment_of_inertia=.true.
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1
+    !1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=1.e6 !5e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    !spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7, r=1500, and square pack
+    !spring_coef=0.0007547062342348049 !if dem_spring_coef=0.5e7, r=1500, and hex pack
+    spring_coef=0.00037735311711740245 !if dem_spring_coef=2.5e6, r=1500, and hex pack
+    
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=200 !125!75 !75 !150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-4 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=0
+    h_to_init_grounding=0.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 10000000000
+    frac_thres_n = 25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
+    frac_thres_t = 11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.false. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/a68/input_fill.nml b/tests/a68/input_fill.nml
new file mode 100644
index 0000000..fa0473a
--- /dev/null
+++ b/tests/a68/input_fill.nml
@@ -0,0 +1,205 @@
+&icebergs_driver_nml
+  a68_test=.true.
+  vert_int_ocean_vel=.false.!.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  Old_wrong_Rearth_and_SSH=.false.
+  mom_Rearth=.false.
+  no_wind=.false.  
+  tau_is_velocity=.true.!.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=999999999 !max number of timesteps
+  saverestart=.false.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=206 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
+/
+
+&icebergs_nml
+
+    Rearth=6.371229e6 !6.36e6 !6.378e6
+    tau_is_velocity=.true.!.false.
+    ocean_drag_scale=<od> !20. !1
+
+    add_curl_to_torque=.false.
+
+    constant_interaction_LW=.true.
+
+    traj_name=<name>
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
+    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=125!75 !75 !150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=30!15!50. !15.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 1
+    frac_thres_n = 25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
+    frac_thres_t = 11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.false. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/a68/input_fill2.nml b/tests/a68/input_fill2.nml
new file mode 100644
index 0000000..c991c1a
--- /dev/null
+++ b/tests/a68/input_fill2.nml
@@ -0,0 +1,212 @@
+&icebergs_driver_nml
+  a68_test=.true.
+  vert_int_ocean_vel=.false.!.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  Old_wrong_Rearth_and_SSH=.false.
+  !mom_Rearth=.true.
+  Rearth=<re>
+  !6363827 !6.378e6
+  no_wind=.false.
+  tau_is_velocity=.true.!.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=432 !360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=999999999 !max number of timesteps
+  saverestart=.false.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=206 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
+/
+
+&icebergs_nml
+
+    Rearth=<re>
+    !6363827 !6.378e6 !6.371229e6 !6.36e6 !6.378e6
+    A68_test=.true.
+    short_step_mts_grounding=.true.
+    
+    tau_is_velocity=.true.!.false.
+    ocean_drag_scale=<od> !20. !1
+
+    skip_first_outer_mts_step=.true.
+    add_curl_to_torque=.false.
+
+    constant_interaction_LW=.true.
+
+    traj_name=<name>
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
+    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=200 !75 !75 !150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-4 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=0.!1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=0!30!15!50. !15.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 10000000
+    frac_thres_n = 25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
+    frac_thres_t = 11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.false. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/a68/input_fill_hex.nml b/tests/a68/input_fill_hex.nml
new file mode 100644
index 0000000..a57be74
--- /dev/null
+++ b/tests/a68/input_fill_hex.nml
@@ -0,0 +1,216 @@
+&icebergs_driver_nml
+  a68_test=.true.
+  vert_int_ocean_vel=.false.!.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  Old_wrong_Rearth_and_SSH=.false.
+  no_wind=.false.  
+  tau_is_velocity=.true.!.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=360 !120 !360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=432 !298 !310 !99999 !310 !999999999 !max number of timesteps
+  saverestart=.false.!.true.!.false.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=206 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
+  Rearth=<rad>
+  !6.371229e6
+/
+
+&icebergs_nml
+
+    A68_test=.false. !.true. !.false.
+    short_step_mts_grounding=.true.
+    !rev_mind=.true.
+    Rearth=<rad>
+    tau_is_velocity=.true.!.false.
+    ocean_drag_scale=<od> !20. !1
+
+    add_curl_to_torque=.false.
+
+    skip_first_outer_mts_step=.true.
+
+    constant_interaction_LW=.true.
+
+    traj_name=<name>
+
+    radius_based_drag=.true.
+    !orig_dem_moment_of_inertia=.true.
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=<damp>
+    !1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=1.e6 !5e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    !spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7, r=1500, and square pack
+    !spring_coef=0.0007547062342348049 !if dem_spring_coef=0.5e7, r=1500, and hex pack
+    spring_coef=0.00037735311711740245 !if dem_spring_coef=2.5e6, r=1500, and hex pack
+    
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=200 !125!75 !75 !150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-4 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=<gc>
+    h_to_init_grounding=0.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 10000000000
+    frac_thres_n = 25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
+    frac_thres_t = 11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.false. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/a68/input_fill_hex_4restart.nml b/tests/a68/input_fill_hex_4restart.nml
new file mode 100644
index 0000000..1c3b6f8
--- /dev/null
+++ b/tests/a68/input_fill_hex_4restart.nml
@@ -0,0 +1,210 @@
+&icebergs_driver_nml
+  a68_test=.true.
+  vert_int_ocean_vel=.false.!.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  Old_wrong_Rearth_and_SSH=.false.
+  no_wind=.false.  
+  tau_is_velocity=.true.!.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=360 !120 !360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  !nmax=298
+  nmax=250 !1 day earlier than usual
+  saverestart=.true.!.false.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=206 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
+  Rearth=<rad>
+/
+
+&icebergs_nml
+
+    A68_test=.true.
+    Rearth=<rad>
+    tau_is_velocity=.true.
+    ocean_drag_scale=<od>
+
+    add_curl_to_torque=.false.
+
+    skip_first_outer_mts_step=.true.
+
+    constant_interaction_LW=.true.
+
+    traj_name=<name>
+    bond_traj_name=<bname>	    
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    !spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7, r=1500, and square pack?
+    spring_coef=0.0007547062342348049 !if dem_spring_coef=0.5e7, r=1500, and hex pack?
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=200 !125!75 !75 !150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=0 !1.e6 !3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=0!30!15!50. !15.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='none' !'stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 100000
+    frac_thres_n = 25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
+    frac_thres_t = 11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.true. !.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.false. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/a68/input_fill_hex_noground.nml b/tests/a68/input_fill_hex_noground.nml
new file mode 100644
index 0000000..4521d92
--- /dev/null
+++ b/tests/a68/input_fill_hex_noground.nml
@@ -0,0 +1,213 @@
+&icebergs_driver_nml
+  a68_test=.true.
+  vert_int_ocean_vel=.false.!.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  Old_wrong_Rearth_and_SSH=.false.
+  no_wind=.false.  
+  tau_is_velocity=.true.!.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=360 !120 !360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=432 !298 !310 !99999 !310 !999999999 !max number of timesteps
+  saverestart=.false.!.true.!.false.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=206 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
+  Rearth=<rad>
+  !6.371229e6
+/
+
+&icebergs_nml
+
+    A68_test=.true.!.false.
+    Rearth=<rad>
+    tau_is_velocity=.true.!.false.
+    ocean_drag_scale=<od> !20. !1
+
+    no_frac_first_ts=.true.
+    add_curl_to_torque=.false.
+
+    skip_first_outer_mts_step=.true.
+
+    constant_interaction_LW=.true.
+
+    traj_name=<name>
+
+    !break_bonds_on_sub_steps=.true.
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=<sc> !5e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    !spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7, r=1500, and square pack?
+    !spring_coef=0.00015094124684696098
+    spring_coef=0.0007547062342348049 !if dem_spring_coef=0.5e7, r=1500, and hex pack?
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=200 !125!75 !75 !150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=0.!1.e6 !3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=0!15!50. !15.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 1 !00000
+    frac_thres_n = 90000. !25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
+    frac_thres_t = 45000. !11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.false. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/a68/makeberg/.ipynb_checkpoints/makeberg-checkpoint.ipynb b/tests/a68/makeberg/.ipynb_checkpoints/makeberg-checkpoint.ipynb
new file mode 100644
index 0000000..70a29cb
--- /dev/null
+++ b/tests/a68/makeberg/.ipynb_checkpoints/makeberg-checkpoint.ipynb
@@ -0,0 +1,441 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "2abe9955",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "Matplotlib is building the font cache; this may take a moment.\n"
+     ]
+    }
+   ],
+   "source": [
+    "import numpy as np\n",
+    "import math\n",
+    "from netCDF4 import Dataset\n",
+    "from pylab import *\n",
+    "import netCDF4 as nc\n",
+    "import xarray as xr"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "184ddcbc",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data'\n",
+    "a68_experiment_berg_2020_12_14_gridded_ll_p0625_cropped.nc  \n",
+    "a68_experiment_ocean_vel_oras5_dec2020_ll_p125.nc\n",
+    "a68_experiment_gebco_ll_p125.nc                             \n",
+    "a68_experiment_wind_vel_jra55_dec2020_ll_p125.nc"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8bb3e5dc",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#!/usr/bin/env python\n",
+    "\n",
+    "\n",
+    "#\n",
+    "# Initialize 2 iceberg elements, which can later be bonded in the fortran code if needed\n",
+    "#\n",
+    "\n",
+    "def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):\n",
+    "\n",
+    "    print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'\n",
+    "    # To copy the global attributes of the netCDF file\n",
+    "\n",
+    "    #Input and output files\n",
+    "    #Create Empty restart file. This is later read so that the attributes can be used.\n",
+    "    Empty_restart_filename='output_files/Empty_icebergs.res.nc'\n",
+    "    create_empty_iceberg_restart_file(Empty_restart_filename)\n",
+    "    #Empty_restart_filename='input_files/icebergs.res.nc'\n",
+    "\n",
+    "    #Read empty restart file\n",
+    "    f=Dataset(Empty_restart_filename,'r') # r is for read only\n",
+    "    #Write a new restart file\n",
+    "    g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file\n",
+    "\n",
+    "    for attname in f.ncattrs():\n",
+    "            setattr(g,attname,getattr(f,attname))\n",
+    "\n",
+    "\n",
+    "    # To copy the dimension of the netCDF file\n",
+    "    for dimname,dim in f.dimensions.iteritems():\n",
+    "        # if you want to make changes in the dimensions of the new file\n",
+    "        # you should add your own conditions here before the creation of the dimension.\n",
+    "        #g.createDimension(dimname,len(dim))\n",
+    "        g.createDimension(dimname,Number_of_bergs)\n",
+    "\n",
+    "    # To copy the variables of the netCDF file\n",
+    "\n",
+    "    for varname,ncvar in f.variables.iteritems():\n",
+    "        # if you want to make changes in the variables of the new file\n",
+    "        # you should add your own conditions here before the creation of the variable.\n",
+    "        var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)\n",
+    "        #Proceed to copy the variable attributes\n",
+    "        for attname in ncvar.ncattrs():\n",
+    "            setattr(var,attname,getattr(ncvar,attname))\n",
+    "        #Finally copy the variable data to the new created variable\n",
+    "        #var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.\n",
+    "\n",
+    "        if varname=='i':\n",
+    "            var[:]=Number_of_bergs\n",
+    "\n",
+    "        if varname=='iceberg_num':\n",
+    "            for j in range(Number_of_bergs):\n",
+    "                #var[j]=j+1\n",
+    "                var[j]=iceberg_num[j]\n",
+    "\n",
+    "        if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\\\n",
+    "        or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \\\n",
+    "        or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \\\n",
+    "        or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\\\n",
+    "            var[:]=0\n",
+    "\n",
+    "                if varname=='uvel':\n",
+    "                        var[:]=uvel\n",
+    "\n",
+    "                if varname=='vvel':\n",
+    "                        var[:]=vvel\n",
+    "\n",
+    "        if varname=='mass_scaling':\n",
+    "            var[:]=mass_scaling\n",
+    "\n",
+    "        if varname=='thickness':\n",
+    "            for j in range(Number_of_bergs):\n",
+    "                var[j]=thickness[j]\n",
+    "\n",
+    "        if varname=='mass':\n",
+    "            for j in range(Number_of_bergs):\n",
+    "                var[j]=mass[j]\n",
+    "\n",
+    "        if varname=='width'  or varname=='length':\n",
+    "            for j in range(Number_of_bergs):\n",
+    "                var[j]=width[j]\n",
+    "\n",
+    "        if varname=='lon':\n",
+    "            for j in range(Number_of_bergs):\n",
+    "                var[j]=lon[j]\n",
+    "\n",
+    "        if varname=='lat':\n",
+    "            for j in range(Number_of_bergs):\n",
+    "                var[j]=lat[j]\n",
+    "\n",
+    "        if varname=='static_berg':\n",
+    "            for j in range(Number_of_bergs):\n",
+    "                var[j]=static_berg[j]\n",
+    "\n",
+    "\n",
+    "    f.close()\n",
+    "    g.close()\n",
+    "\n",
+    "\n",
+    "def create_empty_iceberg_restart_file(Empty_restart_filename):\n",
+    "\n",
+    "    f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')\n",
+    "\n",
+    "    i=f.createDimension('i', None)\n",
+    "    lon=f.createVariable('i','i')\n",
+    "\n",
+    "    lon=f.createVariable('lon','d',('i'))\n",
+    "    lon.long_name = \"longitude\" ;\n",
+    "    lon.units = \"degrees_E\" ;\n",
+    "    lon.checksum = \"               0\" ;\n",
+    "\n",
+    "    lat=f.createVariable('lat','d',('i'))\n",
+    "    lat.long_name = \"latitude\" ;\n",
+    "    lat.units = \"degrees_N\" ;\n",
+    "    lat.checksum = \"               0\" ;\n",
+    "\n",
+    "    uvel=f.createVariable('uvel','d',('i'))\n",
+    "    uvel.long_name = \"zonal velocity\" ;\n",
+    "    uvel.units = \"m/s\" ;\n",
+    "    uvel.checksum = \"               0\" ;\n",
+    "\n",
+    "    vvel=f.createVariable('vvel','d',('i'))\n",
+    "    vvel.long_name = \"meridional velocity\" ;\n",
+    "    vvel.units = \"m/s\" ;\n",
+    "    vvel.checksum = \"               0\" ;\n",
+    "\n",
+    "    mass=f.createVariable('mass','d',('i'))\n",
+    "    mass.long_name = \"mass\" ;\n",
+    "    mass.units = \"kg\" ;\n",
+    "    mass.checksum = \"               0\" ;\n",
+    "\n",
+    "    axn=f.createVariable('axn','d',('i'))\n",
+    "    axn.long_name = \"explicit zonal acceleration\" ;\n",
+    "    axn.units = \"m/s^2\" ;\n",
+    "    axn.checksum = \"               0\" ;\n",
+    "\n",
+    "    ayn=f.createVariable('ayn','d',('i'))\n",
+    "    ayn.long_name = \"explicit meridional acceleration\" ;\n",
+    "    ayn.units = \"m/s^2\" ;\n",
+    "    ayn.checksum = \"               0\" ;\n",
+    "\n",
+    "    bxn=f.createVariable('bxn','d',('i'))\n",
+    "    bxn.long_name = \"inplicit zonal acceleration\" ;\n",
+    "    bxn.units = \"m/s^2\" ;\n",
+    "    bxn.checksum = \"               0\" ;\n",
+    "\n",
+    "    byn=f.createVariable('byn','d',('i'))\n",
+    "    byn.long_name = \"implicit meridional acceleration\" ;\n",
+    "    byn.units = \"m/s^2\" ;\n",
+    "    byn.checksum = \"               0\" ;\n",
+    "\n",
+    "    ine=f.createVariable('ine','i',('i'))\n",
+    "    ine.long_name = \"i index\" ;\n",
+    "    ine.units = \"none\" ;\n",
+    "    ine.packing = 0 ;\n",
+    "    ine.checksum = \"               0\" ;\n",
+    "\n",
+    "    jne=f.createVariable('jne','i',('i'))\n",
+    "    jne.long_name = \"j index\" ;\n",
+    "    jne.units = \"none\" ;\n",
+    "    jne.packing = 0 ;\n",
+    "    jne.checksum = \"               0\" ;\n",
+    "\n",
+    "    thickness=f.createVariable('thickness','d',('i'))\n",
+    "    thickness.long_name = \"thickness\" ;\n",
+    "    thickness.units = \"m\" ;\n",
+    "    thickness.checksum = \"               0\" ;\n",
+    "\n",
+    "    width=f.createVariable('width','d',('i'))\n",
+    "    width.long_name = \"width\" ;\n",
+    "    width.units = \"m\" ;\n",
+    "    width.checksum = \"               0\" ;\n",
+    "\n",
+    "    length=f.createVariable('length','d',('i'))\n",
+    "    length.long_name = \"length\" ;\n",
+    "    length.units = \"m\" ;\n",
+    "    length.checksum = \"               0\" ;\n",
+    "\n",
+    "    start_lon=f.createVariable('start_lon','d',('i'))\n",
+    "    start_lon.long_name = \"longitude of calving location\" ;\n",
+    "    start_lon.units = \"degrees_E\" ;\n",
+    "    start_lon.checksum = \"               0\" ;\n",
+    "\n",
+    "    start_lat=f.createVariable('start_lat','d',('i'))\n",
+    "    start_lat.long_name = \"latitude of calving location\" ;\n",
+    "    start_lat.units = \"degrees_N\" ;\n",
+    "    start_lat.checksum = \"               0\" ;\n",
+    "\n",
+    "    start_year=f.createVariable('start_year','i',('i'))\n",
+    "    start_year.long_name = \"calendar year of calving event\" ;\n",
+    "    start_year.units = \"years\" ;\n",
+    "    start_year.packing = 0 ;\n",
+    "    start_year.checksum = \"               0\" ;\n",
+    "\n",
+    "    iceberg_num=f.createVariable('iceberg_num','i',('i'))\n",
+    "    iceberg_num.long_name = \"identification of the iceberg\" ;\n",
+    "    iceberg_num.units = \"dimensionless\" ;\n",
+    "    iceberg_num.packing = 0 ;\n",
+    "    iceberg_num.checksum = \"               0\" ;\n",
+    "\n",
+    "    start_day=f.createVariable('start_day','d',('i'))\n",
+    "    start_day.long_name = \"year day of calving event\" ;\n",
+    "    start_day.units = \"days\" ;\n",
+    "    start_day.checksum = \"               0\" ;\n",
+    "\n",
+    "    start_mass=f.createVariable('start_mass','d',('i'))\n",
+    "    start_mass.long_name = \"initial mass of calving berg\" ;\n",
+    "    start_mass.units = \"kg\" ;\n",
+    "    start_mass.checksum = \"               0\" ;\n",
+    "\n",
+    "    mass_scaling=f.createVariable('mass_scaling','d',('i'))\n",
+    "    mass_scaling.long_name = \"scaling factor for mass of calving berg\" ;\n",
+    "    mass_scaling.units = \"none\" ;\n",
+    "    mass_scaling.checksum = \"               0\" ;\n",
+    "\n",
+    "    mass_of_bits=f.createVariable('mass_of_bits','d',('i'))\n",
+    "    mass_of_bits.long_name = \"mass of bergy bits\" ;\n",
+    "    mass_of_bits.units = \"kg\" ;\n",
+    "    mass_of_bits.checksum = \"               0\" ;\n",
+    "\n",
+    "    heat_density=f.createVariable('heat_density','d',('i'))\n",
+    "    heat_density.long_name = \"heat density\" ;\n",
+    "    heat_density.units = \"J/kg\" ;\n",
+    "    heat_density.checksum = \"               0\" ;\n",
+    "\n",
+    "    halo_berg=f.createVariable('halo_berg','d',('i'))\n",
+    "    halo_berg.long_name = \"halo_berg\" ;\n",
+    "    halo_berg.units = \"dimensionless\" ;\n",
+    "    halo_berg.checksum = \"               0\" ;\n",
+    "\n",
+    "    static_berg=f.createVariable('static_berg','d',('i'))\n",
+    "    static_berg.long_name = \"static_berg\" ;\n",
+    "    static_berg.units = \"dimensionless\" ;\n",
+    "    static_berg.checksum = \"               0\" ;\n",
+    "\n",
+    "    f.sync()\n",
+    "    f.close()\n",
+    "\n",
+    "\n",
+    "\n",
+    "#-----------------------------------#\n",
+    "#               Main                #\n",
+    "#-----------------------------------#\n",
+    "\n",
+    "# just2particles=False\n",
+    "# flip2ndconglom=True#False\n",
+    "# offset2ndconglom=True#False\n",
+    "\n",
+    "grdxmin=0; grdxmax=45000e3\n",
+    "grdymin=0; grdymax=45000e3\n",
+    "grdres=1000.0\n",
+    "R_frac=0.45 #1st option\n",
+    "#R_frac=0.5*0.45 #2nd option\n",
+    "radius=(np.sqrt(3)/2.)*(R_frac*grdres) #S is < 0.5 grid res\n",
+    "#radius2=(np.sqrt(3)/2.)*(R_frac2*grdres) #S is < 0.5 grid res\n",
+    "thickness1=200.0\n",
+    "thickness2=200.0\n",
+    "rho_ice=850.0\n",
+    "\n",
+    "\n",
+    "nbergs=1 #number of conglomerates\n",
+    "\n",
+    "#center coords of each (rectangular) conglomerate berg (CB=conglomerate berg)\n",
+    "CBxc=np.array([3500]); CByc=np.array([15000])\n",
+    "#side lengths\n",
+    "CBxl=np.array([4000]); CByl=np.array([8000])\n",
+    "\n",
+    "\n",
+    "CByl=CByl.astype(int); CBxl=CBxl.astype(int)\n",
+    "\n",
+    "#--- xmax, xmin, ymax, ymin for each CB --\n",
+    "CBxmin=CBxc-(0.5*CBxl); CBxmax=CBxc+(0.5*CBxl)\n",
+    "CBymin=CByc-(0.5*CByl); CBymax=CByc+(0.5*CByl)\n",
+    "#this shouldn't happen:\n",
+    "CBxmin[CBxmin<grdxmin]=grdxmin; CBxmax[CBxmax>grdxmax]=grdxmax\n",
+    "CBymin[CBxmin<grdymin]=grdymin; CBymax[CBymax>grdymax]=grdymax\n",
+    "CBxc=0.5*(CBxmin+CBxmax); CByc=0.5*(CBymin+CBymax)\n",
+    "\n",
+    "# #if just want one particle per CB\n",
+    "# if just2particles:\n",
+    "#         CBxmin=CBxc; CBxmax=CBxc\n",
+    "#         CBymin=CByc; CBymax=CByc\n",
+    "\n",
+    "#--- min and max thicknesses for each CB ---\n",
+    "h1=thickness1\n",
+    "h2=thickness2\n",
+    "CBhmax=np.array([h1]); CBhmin=np.array([h2])\n",
+    "\n",
+    "#radii\n",
+    "CBrad=np.array([radius])\n",
+    "print('radii',CBrad)\n",
+    "\n",
+    "berg_x=[]; berg_y=[]\n",
+    "berg_id=[]; berg_static=[]\n",
+    "berg_width=[]; berg_bonds=[]\n",
+    "berg_h=[]; berg_mass_scaling=[]\n",
+    "berg_mass=[]\n",
+    "berg_uvel=[]; berg_vvel=[]\n",
+    "\n",
+    "berg_count=0\n",
+    "\n",
+    "for i in range(nbergs):\n",
+    "        x_start=CBxmin[i]+(CBrad[i]*2./np.sqrt(3))\n",
+    "\n",
+    "        # if flip2ndconglom and i>0:\n",
+    "        #         x_start=CBxmax[i]-(CBrad[i]*2./np.sqrt(3))\n",
+    "\n",
+    "        #pdb.set_trace()\n",
+    "        if x_start>CBxmax[i]:\n",
+    "                x_start=CBxmax[i]\n",
+    "        y_start0=CBymin[i]+CBrad[i]\n",
+    "        if y_start0>CBymax[i]:\n",
+    "                y_start0=CBymax[i]\n",
+    "        element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*(CBrad[i])**2)\n",
+    "        #H (thickness) is a linear function of a berg element's position from the\n",
+    "        #center of the CB. H=Hmax at the center of the CB and H=Hmin at a corner of the\n",
+    "        #CB, where the dist of a corner from the center is:\n",
+    "        cdistb=np.sqrt((CBxmin[i]-CBxc[i])**2+(CBymin[i]-CByc[i])**2)\n",
+    "        j=0\n",
+    "        x_val=x_start\n",
+    "        offset=0.0\n",
+    "        # if (i==0):\n",
+    "        uvel=0.#1\n",
+    "        # else:\n",
+    "        #         uvel=-0.15#-0.05\n",
+    "        #         if (offset2ndconglom):\n",
+    "        #                 offset=250.0\n",
+    "        vvel=0.0#25\n",
+    "        #uvel=0;vvel=0\n",
+    "        #berg_count_start=berg_count\n",
+    "        while x_val<=CBxmax[i] and x_val>=CBxmin[i]:\n",
+    "                y_start=y_start0+((j%2)*CBrad[i])+offset\n",
+    "                k=0\n",
+    "                y_val=y_start\n",
+    "                while y_val<=(CBymax[i]+offset):\n",
+    "                        berg_count=berg_count+1\n",
+    "                        berg_id.append(berg_count)\n",
+    "                        berg_x.append(x_val)\n",
+    "                        berg_y.append(y_val)\n",
+    "                        berg_width.append(sqrt(element_area))\n",
+    "                        #dist of berg elem from center of CB\n",
+    "                        bdistc=np.sqrt((x_val-CBxc[i])**2+(y_val-CByc[i])**2)\n",
+    "                        bh=CBhmin[i]*bdistc/cdistb + CBhmax[i]*(1-bdistc/cdistb)\n",
+    "                        # if (just2particles):\n",
+    "                        #         bh=h1\n",
+    "                        berg_h.append(bh) #thickness\n",
+    "                        berg_mass_scaling.append(1)\n",
+    "                        berg_mass.append(bh*rho_ice*element_area)\n",
+    "                        berg_static.append(0)\n",
+    "                        berg_uvel.append(uvel)\n",
+    "                        berg_vvel.append(vvel)\n",
+    "                        # if (x_val<22000):\n",
+    "                        #         berg_vvel.append(vvel)\n",
+    "                        # else:\n",
+    "                        #         berg_vvel.append(0.4)\n",
+    "                        #berg_CBid.append(i)\n",
+    "                        k=k+1\n",
+    "                        y_val=y_start+(2*k*CBrad[i])\n",
+    "                j=j+1\n",
+    "                # if flip2ndconglom and i>0:\n",
+    "                #         x_val=x_start-(np.sqrt(3)*CBrad[i]*j)\n",
+    "                # else:\n",
+    "                x_val=x_start+(np.sqrt(3)*CBrad[i]*j)\n",
+    "\n",
+    "print('Number of bergs',berg_count)\n",
+    "\n",
+    "#pdb.set_trace()\n",
+    "\n",
+    "#Create iceberg restart file\n",
+    "Ice_geometry_source='Generic'\n",
+    "Create_iceberg_restart_file(berg_count,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)\n"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.8"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/tests/a68/makeberg/RUN b/tests/a68/makeberg/RUN
new file mode 100755
index 0000000..bc3883d
--- /dev/null
+++ b/tests/a68/makeberg/RUN
@@ -0,0 +1,89 @@
+rm ./output_files/Generic*
+
+#OPTION 1: SET CONSTANT THICKNESS TO 200 m
+#-------------------------------------------
+
+
+#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_09_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -lat_ref_grid_to_cartesian=-55.2 -uvel=0.2 -R_earth=6378000.
+
+#6.371229e6
+
+#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='hexagon' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_09_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -R_earth=6.371229e6 -lat_ref_grid_to_cartesian=-55.2 -uvel=0.2 -dx=3500.
+
+#for Rearth at 55 S for WGS84 ellipsoid
+#Change lon_init and lat_init to be displaced by dx/2 for this one!!
+#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='hexagon' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_09_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -lat_ref_grid_to_cartesian=-55.2 -uvel=0.22 -dx=3500. -R_earth=6363827. -displace_y=-0.05 -icethres=0.5
+
+#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='hexagon' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_09_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -lat_ref_grid_to_cartesian=-55.2 -uvel=0.22 -dx=3500. -R_earth=6363827. -displace_y=-0.025 -icethres=0.6
+
+#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='hexagon' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_09_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -lat_ref_grid_to_cartesian=-55.2 -uvel=0.22 -dx=3540. -R_earth=6363827. -displace_y=-0.0625 -icethres=0.9
+
+#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='hexagon' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_09_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -lat_ref_grid_to_cartesian=-55.2 -uvel=0.22 -dx=3540. -R_earth=6363827. -displace_y=-0.075 -icethres=0.9
+
+./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='hexagon' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_09_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -lat_ref_grid_to_cartesian=-55.2 -uvel=0.22 -dx=3540. -R_earth=6363827. -displace_y=-0.1 -icethres=0.9
+
+# AGU hex test:
+#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='hexagon' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_09_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -lat_ref_grid_to_cartesian=-55.2 -uvel=0.22 -dx=3540. -R_earth=6363827. -displace_y=-0.175 -icethres=0.9
+
+
+#For testing rev_mind=.true. vs. rev_mind=.false.
+#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='hexagon' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_14_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -lat_ref_grid_to_cartesian=-55.2 -dx=3500. -R_earth=6363827. -set_all_domain_to_ice=True -set_all_bergs_static_by_default=True
+
+#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_09_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=False -Radius=1500 -lat_ref_grid_to_cartesian=-55.2 -uvel=0.22 -dx=500. -R_earth=6363827. -icethres=0.8
+
+
+# THIS IS THE ONE USED FOR AGU AND IN THE PAPER!!
+#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_09_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=False -Radius=1500 -lat_ref_grid_to_cartesian=-55.2 -uvel=0.22 -dx=500. -R_earth=6363827. -icethres=0.5 -displace_y=-0.1
+
+#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_09_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=False -Radius=1500 -lat_ref_grid_to_cartesian=-55.2 -uvel=0.22 -dx=500. -R_earth=6378000. -icethres=0.5 -displace_y=-0.1
+
+#for Rearth at 55 S for WGS84 ellipsoid
+ #this was the displacement for ./../oldnc2/od_##_tn_ng_ellr.nc??
+#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_09_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -lat_ref_grid_to_cartesian=-55.2 -uvel=0.22 -dx=250. -R_earth=6363827. -displace_y=-0.05
+
+#-lat_ref_grid_to_cartesian=-55.2 -uvel=0.2 -vvel=0.0
+
+#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_14_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_thickness=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -R_earth=6.371229e6 -lat_ref_grid_to_cartesian=-55.8
+
+#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_14a_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_thickness=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -R_earth=6.371229e6 -lat_ref_grid_to_cartesian=-55.8
+
+#-uvel=0.2 -vvel=-0.2
+
+#-uvel=0.2 -vvel=-0.2 -ang_vel_prescribed=-7.5e-5
+
+#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_13_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_thickness=False -plot_ice_mask=False -plot_icebergs_positions=True -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -R_earth=6.371229e6 -lat_ref_grid_to_cartesian=-55.8
+
+
+#-uvel=0.1 -vvel=0.4
+#-uvel=0.18 -vvel=-0.23 -R_earth=6360000
+#-ang_vel_prescribed=-7.5e-5
+#-uvel=0.2 -vvel=-0.2
+
+# -R_earth=6360000
+
+#-R_earth=6378000.
+
+#-uvel=0.18 -vvel=-0.23
+#-uvel=0.254 -vvel=-0.08
+#-R_earth=6360000 -uvel=0.18 -vvel=-0.23
+#-uvel=0.24 -vvel=-0.08
+
+#OPTION 2: VARY THICKESS
+#-----------------------
+
+#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_09_gridded_ll_p0625_cropped_hvary.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=False -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=False -plot_icebergs_positions=True -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -R_earth=6.371229e6 -lat_ref_grid_to_cartesian=-55.8
+#-uvel=0.2 -vvel=0.
+
+#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_14_gridded_ll_p0625_cropped_hvary.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=False -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=False -plot_icebergs_positions=True -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -R_earth=6.371229e6 -lat_ref_grid_to_cartesian=-55.8
+
+#-uvel=0.24 -vvel=-0.08
+#-uvel=0.18 -vvel=-0.23
+
+#-Radius=2000
+#-uvel=0.18 -vvel=-0.23 #correct?
+#-uvel=0.036 -vvel=-0.046 #wrong?
+#-uvel=0. -vvel=0
+
+#./make_one_berg.py
+
+cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
diff --git a/tests/a68/makeberg/RUN_for_paper b/tests/a68/makeberg/RUN_for_paper
new file mode 100755
index 0000000..4e2be66
--- /dev/null
+++ b/tests/a68/makeberg/RUN_for_paper
@@ -0,0 +1,6 @@
+rm ./output_files/Generic*
+
+# THIS IS THE BERG USED FOR AGU 2021 AND IN THE PAPER!!
+./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_09_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=False -Radius=1500 -lat_ref_grid_to_cartesian=-55.2 -uvel=0.22 -dx=500. -R_earth=6363827. -icethres=0.5 -displace_y=-0.1
+
+cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
diff --git a/tests/a68/makeberg/make_one_berg.py b/tests/a68/makeberg/make_one_berg.py
new file mode 100755
index 0000000..e39ec35
--- /dev/null
+++ b/tests/a68/makeberg/make_one_berg.py
@@ -0,0 +1,399 @@
+#!/usr/bin/env python
+import numpy as np
+import math
+from netCDF4 import Dataset
+from pylab import *
+#import pdb
+import netCDF4 as nc
+
+#
+# Initialize 2 iceberg elements, which can later be bonded in the fortran code if needed
+#
+
+def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
+
+        print('Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..')
+        # To copy the global attributes of the netCDF file
+
+        #Input and output files
+        #Create Empty restart file. This is later read so that the attributes can be used.
+        Empty_restart_filename='output_files/Empty_icebergs.res.nc'
+        create_empty_iceberg_restart_file(Empty_restart_filename)
+        #Empty_restart_filename='input_files/icebergs.res.nc'
+
+        #Read empty restart file
+        f=Dataset(Empty_restart_filename,'r') # r is for read only
+        #Write a new restart file
+        g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
+
+        for attname in f.ncattrs():
+                    setattr(g,attname,getattr(f,attname))
+
+
+        # To copy the dimension of the netCDF file
+        for dimname,dim in f.dimensions.iteritems():
+                # if you want to make changes in the dimensions of the new file
+                # you should add your own conditions here before the creation of the dimension.
+                #g.createDimension(dimname,len(dim))
+                g.createDimension(dimname,Number_of_bergs)
+
+        # To copy the variables of the netCDF file
+
+        for varname,ncvar in f.variables.iteritems():
+                # if you want to make changes in the variables of the new file
+                # you should add your own conditions here before the creation of the variable.
+                var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
+                #Proceed to copy the variable attributes
+                for attname in ncvar.ncattrs():
+                        setattr(var,attname,getattr(ncvar,attname))
+                #Finally copy the variable data to the new created variable
+                #var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
+
+                if varname=='i':
+                        var[:]=Number_of_bergs
+
+                if varname=='iceberg_num':
+                        for j in range(Number_of_bergs):
+                                #var[j]=j+1
+                                var[j]=iceberg_num[j]
+
+                if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
+                or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
+                or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
+                or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
+                        var[:]=0
+
+                if varname=='uvel':
+                        var[:]=uvel
+
+                if varname=='vvel':
+                        var[:]=vvel
+
+                if varname=='mass_scaling':
+                        var[:]=mass_scaling
+
+                if varname=='thickness':
+                        for j in range(Number_of_bergs):
+                                var[j]=thickness[j]
+
+                if varname=='mass':
+                        for j in range(Number_of_bergs):
+                                var[j]=mass[j]
+
+                if varname=='width'  or varname=='length':
+                        for j in range(Number_of_bergs):
+                                var[j]=width[j]
+
+                if varname=='lon':
+                        for j in range(Number_of_bergs):
+                                var[j]=lon[j]
+
+                if varname=='lat':
+                        for j in range(Number_of_bergs):
+                                var[j]=lat[j]
+
+                if varname=='static_berg':
+                        for j in range(Number_of_bergs):
+                                var[j]=static_berg[j]
+
+
+        f.close()
+        g.close()
+
+
+def create_empty_iceberg_restart_file(Empty_restart_filename):
+
+        f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
+
+        i=f.createDimension('i', None)
+        lon=f.createVariable('i','i')
+
+        lon=f.createVariable('lon','d',('i'))
+        lon.long_name = "longitude" ;
+        lon.units = "degrees_E" ;
+        lon.checksum = "               0" ;
+
+        lat=f.createVariable('lat','d',('i'))
+        lat.long_name = "latitude" ;
+        lat.units = "degrees_N" ;
+        lat.checksum = "               0" ;
+
+        uvel=f.createVariable('uvel','d',('i'))
+        uvel.long_name = "zonal velocity" ;
+        uvel.units = "m/s" ;
+        uvel.checksum = "               0" ;
+
+        vvel=f.createVariable('vvel','d',('i'))
+        vvel.long_name = "meridional velocity" ;
+        vvel.units = "m/s" ;
+        vvel.checksum = "               0" ;
+
+        mass=f.createVariable('mass','d',('i'))
+        mass.long_name = "mass" ;
+        mass.units = "kg" ;
+        mass.checksum = "               0" ;
+
+        axn=f.createVariable('axn','d',('i'))
+        axn.long_name = "explicit zonal acceleration" ;
+        axn.units = "m/s^2" ;
+        axn.checksum = "               0" ;
+
+        ayn=f.createVariable('ayn','d',('i'))
+        ayn.long_name = "explicit meridional acceleration" ;
+        ayn.units = "m/s^2" ;
+        ayn.checksum = "               0" ;
+
+        bxn=f.createVariable('bxn','d',('i'))
+        bxn.long_name = "inplicit zonal acceleration" ;
+        bxn.units = "m/s^2" ;
+        bxn.checksum = "               0" ;
+
+        byn=f.createVariable('byn','d',('i'))
+        byn.long_name = "implicit meridional acceleration" ;
+        byn.units = "m/s^2" ;
+        byn.checksum = "               0" ;
+
+        ine=f.createVariable('ine','i',('i'))
+        ine.long_name = "i index" ;
+        ine.units = "none" ;
+        ine.packing = 0 ;
+        ine.checksum = "               0" ;
+
+        jne=f.createVariable('jne','i',('i'))
+        jne.long_name = "j index" ;
+        jne.units = "none" ;
+        jne.packing = 0 ;
+        jne.checksum = "               0" ;
+
+        thickness=f.createVariable('thickness','d',('i'))
+        thickness.long_name = "thickness" ;
+        thickness.units = "m" ;
+        thickness.checksum = "               0" ;
+
+        width=f.createVariable('width','d',('i'))
+        width.long_name = "width" ;
+        width.units = "m" ;
+        width.checksum = "               0" ;
+
+        length=f.createVariable('length','d',('i'))
+        length.long_name = "length" ;
+        length.units = "m" ;
+        length.checksum = "               0" ;
+
+        start_lon=f.createVariable('start_lon','d',('i'))
+        start_lon.long_name = "longitude of calving location" ;
+        start_lon.units = "degrees_E" ;
+        start_lon.checksum = "               0" ;
+
+        start_lat=f.createVariable('start_lat','d',('i'))
+        start_lat.long_name = "latitude of calving location" ;
+        start_lat.units = "degrees_N" ;
+        start_lat.checksum = "               0" ;
+
+        start_year=f.createVariable('start_year','i',('i'))
+        start_year.long_name = "calendar year of calving event" ;
+        start_year.units = "years" ;
+        start_year.packing = 0 ;
+        start_year.checksum = "               0" ;
+
+        iceberg_num=f.createVariable('iceberg_num','i',('i'))
+        iceberg_num.long_name = "identification of the iceberg" ;
+        iceberg_num.units = "dimensionless" ;
+        iceberg_num.packing = 0 ;
+        iceberg_num.checksum = "               0" ;
+
+        start_day=f.createVariable('start_day','d',('i'))
+        start_day.long_name = "year day of calving event" ;
+        start_day.units = "days" ;
+        start_day.checksum = "               0" ;
+
+        start_mass=f.createVariable('start_mass','d',('i'))
+        start_mass.long_name = "initial mass of calving berg" ;
+        start_mass.units = "kg" ;
+        start_mass.checksum = "               0" ;
+
+        mass_scaling=f.createVariable('mass_scaling','d',('i'))
+        mass_scaling.long_name = "scaling factor for mass of calving berg" ;
+        mass_scaling.units = "none" ;
+        mass_scaling.checksum = "               0" ;
+
+        mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
+        mass_of_bits.long_name = "mass of bergy bits" ;
+        mass_of_bits.units = "kg" ;
+        mass_of_bits.checksum = "               0" ;
+
+        heat_density=f.createVariable('heat_density','d',('i'))
+        heat_density.long_name = "heat density" ;
+        heat_density.units = "J/kg" ;
+        heat_density.checksum = "               0" ;
+
+        halo_berg=f.createVariable('halo_berg','d',('i'))
+        halo_berg.long_name = "halo_berg" ;
+        halo_berg.units = "dimensionless" ;
+        halo_berg.checksum = "               0" ;
+
+        static_berg=f.createVariable('static_berg','d',('i'))
+        static_berg.long_name = "static_berg" ;
+        static_berg.units = "dimensionless" ;
+        static_berg.checksum = "               0" ;
+
+        f.sync()
+        f.close()
+
+
+
+#-----------------------------------#
+#               Main                #
+#-----------------------------------#
+
+# just2particles=False
+# flip2ndconglom=True#False
+# offset2ndconglom=True#False
+
+grdxmin=0; grdxmax=45000e3
+grdymin=0; grdymax=45000e3
+grdres=0.125 #degrees
+#hexagonal
+#R_frac=0.45 #1st option
+#radius=(np.sqrt(3)/2.)*(R_frac*grdres) #S is < 0.5 grid res
+
+#square
+radius=1000
+thickness1=200.0
+thickness2=200.0
+
+rho_ice=850.0
+
+
+nbergs=1 #number of conglomerates
+
+#center coords of each (rectangular) conglomerate berg (CB=conglomerate berg)
+CBxc=np.array([4000]); CByc=np.array([4000])
+#side lengths
+CBxl=np.array([4000]); CByl=np.array([4000])
+
+
+CByl=CByl.astype(int); CBxl=CBxl.astype(int)
+
+#--- xmax, xmin, ymax, ymin for each CB --
+CBxmin=CBxc-(0.5*CBxl); CBxmax=CBxc+(0.5*CBxl)
+CBymin=CByc-(0.5*CByl); CBymax=CByc+(0.5*CByl)
+#this shouldn't happen:
+CBxmin[CBxmin<grdxmin]=grdxmin; CBxmax[CBxmax>grdxmax]=grdxmax
+CBymin[CBxmin<grdymin]=grdymin; CBymax[CBymax>grdymax]=grdymax
+CBxc=0.5*(CBxmin+CBxmax); CByc=0.5*(CBymin+CBymax)
+
+# #if just want one particle per CB
+# if just2particles:
+#         CBxmin=CBxc; CBxmax=CBxc
+#         CBymin=CByc; CBymax=CByc
+
+#--- min and max thicknesses for each CB ---
+h1=thickness1
+h2=thickness2
+CBhmax=np.array([h1]); CBhmin=np.array([h2])
+
+#radii
+CBrad=np.array([radius])
+print('radii',CBrad)
+
+berg_x=[]; berg_y=[]
+berg_id=[]; berg_static=[]
+berg_width=[]; berg_bonds=[]
+berg_h=[]; berg_mass_scaling=[]
+berg_mass=[]
+berg_uvel=[]; berg_vvel=[]
+
+berg_count=0
+
+
+#Test a single particle to start
+berg_count=1
+x_val=-38.1+360
+y_val=-54.9
+uvel=0.036
+vvel=-0.046
+element_area=(2.*radius)**2
+bh=h1
+berg_id.append(berg_count)
+berg_x.append(x_val)
+berg_y.append(y_val)
+berg_width.append(np.sqrt(element_area))
+#dist of berg elem from center of CB
+berg_h.append(h1) #thickness
+berg_mass_scaling.append(1)
+berg_mass.append(bh*rho_ice*element_area)
+berg_static.append(0)
+berg_uvel.append(uvel)
+berg_vvel.append(vvel)
+
+# for i in range(nbergs):
+#         x_start=CBxmin[i]+(CBrad[i]*2./np.sqrt(3))
+
+#         # if flip2ndconglom and i>0:
+#         #         x_start=CBxmax[i]-(CBrad[i]*2./np.sqrt(3))
+
+#         #pdb.set_trace()
+#         if x_start>CBxmax[i]:
+#                 x_start=CBxmax[i]
+#         y_start0=CBymin[i]+CBrad[i]
+#         if y_start0>CBymax[i]:
+#                 y_start0=CBymax[i]
+#         element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*(CBrad[i])**2)
+#         #H (thickness) is a linear function of a berg element's position from the
+#         #center of the CB. H=Hmax at the center of the CB and H=Hmin at a corner of the
+#         #CB, where the dist of a corner from the center is:
+#         cdistb=np.sqrt((CBxmin[i]-CBxc[i])**2+(CBymin[i]-CByc[i])**2)
+#         j=0
+#         x_val=x_start
+#         offset=0.0
+#         # if (i==0):
+#         uvel=0.036
+#         # else:
+#         #         uvel=-0.15#-0.05
+#         #         if (offset2ndconglom):
+#         #                 offset=250.0
+#         vvel=-0.046
+#         #uvel=0;vvel=0
+#         #berg_count_start=berg_count
+#         while x_val<=CBxmax[i] and x_val>=CBxmin[i]:
+#                 y_start=y_start0+((j%2)*CBrad[i])+offset
+#                 k=0
+#                 y_val=y_start
+#                 while y_val<=(CBymax[i]+offset):
+#                         berg_count=berg_count+1
+#                         berg_id.append(berg_count)
+#                         berg_x.append(x_val)
+#                         berg_y.append(y_val)
+#                         berg_width.append(sqrt(element_area))
+#                         #dist of berg elem from center of CB
+#                         bdistc=np.sqrt((x_val-CBxc[i])**2+(y_val-CByc[i])**2)
+#                         bh=CBhmin[i]*bdistc/cdistb + CBhmax[i]*(1-bdistc/cdistb)
+#                         # if (just2particles):
+#                         #         bh=h1
+#                         berg_h.append(bh) #thickness
+#                         berg_mass_scaling.append(1)
+#                         berg_mass.append(bh*rho_ice*element_area)
+#                         berg_static.append(0)
+#                         berg_uvel.append(uvel)
+#                         berg_vvel.append(vvel)
+#                         # if (x_val<22000):
+#                         #         berg_vvel.append(vvel)
+#                         # else:
+#                         #         berg_vvel.append(0.4)
+#                         #berg_CBid.append(i)
+#                         k=k+1
+#                         y_val=y_start+(2*k*CBrad[i])
+#                 j=j+1
+#                 # if flip2ndconglom and i>0:
+#                 #         x_val=x_start-(np.sqrt(3)*CBrad[i]*j)
+#                 # else:
+#                 x_val=x_start+(np.sqrt(3)*CBrad[i]*j)
+
+print('Number of bergs',berg_count)
+
+#pdb.set_trace()
+
+#Create iceberg restart file
+Ice_geometry_source='Generic'
+Create_iceberg_restart_file(berg_count,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)
diff --git a/tests/a68/makeberg/makeberg.ipynb b/tests/a68/makeberg/makeberg.ipynb
new file mode 100644
index 0000000..70a29cb
--- /dev/null
+++ b/tests/a68/makeberg/makeberg.ipynb
@@ -0,0 +1,441 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "2abe9955",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "Matplotlib is building the font cache; this may take a moment.\n"
+     ]
+    }
+   ],
+   "source": [
+    "import numpy as np\n",
+    "import math\n",
+    "from netCDF4 import Dataset\n",
+    "from pylab import *\n",
+    "import netCDF4 as nc\n",
+    "import xarray as xr"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "184ddcbc",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data'\n",
+    "a68_experiment_berg_2020_12_14_gridded_ll_p0625_cropped.nc  \n",
+    "a68_experiment_ocean_vel_oras5_dec2020_ll_p125.nc\n",
+    "a68_experiment_gebco_ll_p125.nc                             \n",
+    "a68_experiment_wind_vel_jra55_dec2020_ll_p125.nc"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8bb3e5dc",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#!/usr/bin/env python\n",
+    "\n",
+    "\n",
+    "#\n",
+    "# Initialize 2 iceberg elements, which can later be bonded in the fortran code if needed\n",
+    "#\n",
+    "\n",
+    "def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):\n",
+    "\n",
+    "    print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'\n",
+    "    # To copy the global attributes of the netCDF file\n",
+    "\n",
+    "    #Input and output files\n",
+    "    #Create Empty restart file. This is later read so that the attributes can be used.\n",
+    "    Empty_restart_filename='output_files/Empty_icebergs.res.nc'\n",
+    "    create_empty_iceberg_restart_file(Empty_restart_filename)\n",
+    "    #Empty_restart_filename='input_files/icebergs.res.nc'\n",
+    "\n",
+    "    #Read empty restart file\n",
+    "    f=Dataset(Empty_restart_filename,'r') # r is for read only\n",
+    "    #Write a new restart file\n",
+    "    g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file\n",
+    "\n",
+    "    for attname in f.ncattrs():\n",
+    "            setattr(g,attname,getattr(f,attname))\n",
+    "\n",
+    "\n",
+    "    # To copy the dimension of the netCDF file\n",
+    "    for dimname,dim in f.dimensions.iteritems():\n",
+    "        # if you want to make changes in the dimensions of the new file\n",
+    "        # you should add your own conditions here before the creation of the dimension.\n",
+    "        #g.createDimension(dimname,len(dim))\n",
+    "        g.createDimension(dimname,Number_of_bergs)\n",
+    "\n",
+    "    # To copy the variables of the netCDF file\n",
+    "\n",
+    "    for varname,ncvar in f.variables.iteritems():\n",
+    "        # if you want to make changes in the variables of the new file\n",
+    "        # you should add your own conditions here before the creation of the variable.\n",
+    "        var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)\n",
+    "        #Proceed to copy the variable attributes\n",
+    "        for attname in ncvar.ncattrs():\n",
+    "            setattr(var,attname,getattr(ncvar,attname))\n",
+    "        #Finally copy the variable data to the new created variable\n",
+    "        #var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.\n",
+    "\n",
+    "        if varname=='i':\n",
+    "            var[:]=Number_of_bergs\n",
+    "\n",
+    "        if varname=='iceberg_num':\n",
+    "            for j in range(Number_of_bergs):\n",
+    "                #var[j]=j+1\n",
+    "                var[j]=iceberg_num[j]\n",
+    "\n",
+    "        if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\\\n",
+    "        or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \\\n",
+    "        or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \\\n",
+    "        or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\\\n",
+    "            var[:]=0\n",
+    "\n",
+    "                if varname=='uvel':\n",
+    "                        var[:]=uvel\n",
+    "\n",
+    "                if varname=='vvel':\n",
+    "                        var[:]=vvel\n",
+    "\n",
+    "        if varname=='mass_scaling':\n",
+    "            var[:]=mass_scaling\n",
+    "\n",
+    "        if varname=='thickness':\n",
+    "            for j in range(Number_of_bergs):\n",
+    "                var[j]=thickness[j]\n",
+    "\n",
+    "        if varname=='mass':\n",
+    "            for j in range(Number_of_bergs):\n",
+    "                var[j]=mass[j]\n",
+    "\n",
+    "        if varname=='width'  or varname=='length':\n",
+    "            for j in range(Number_of_bergs):\n",
+    "                var[j]=width[j]\n",
+    "\n",
+    "        if varname=='lon':\n",
+    "            for j in range(Number_of_bergs):\n",
+    "                var[j]=lon[j]\n",
+    "\n",
+    "        if varname=='lat':\n",
+    "            for j in range(Number_of_bergs):\n",
+    "                var[j]=lat[j]\n",
+    "\n",
+    "        if varname=='static_berg':\n",
+    "            for j in range(Number_of_bergs):\n",
+    "                var[j]=static_berg[j]\n",
+    "\n",
+    "\n",
+    "    f.close()\n",
+    "    g.close()\n",
+    "\n",
+    "\n",
+    "def create_empty_iceberg_restart_file(Empty_restart_filename):\n",
+    "\n",
+    "    f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')\n",
+    "\n",
+    "    i=f.createDimension('i', None)\n",
+    "    lon=f.createVariable('i','i')\n",
+    "\n",
+    "    lon=f.createVariable('lon','d',('i'))\n",
+    "    lon.long_name = \"longitude\" ;\n",
+    "    lon.units = \"degrees_E\" ;\n",
+    "    lon.checksum = \"               0\" ;\n",
+    "\n",
+    "    lat=f.createVariable('lat','d',('i'))\n",
+    "    lat.long_name = \"latitude\" ;\n",
+    "    lat.units = \"degrees_N\" ;\n",
+    "    lat.checksum = \"               0\" ;\n",
+    "\n",
+    "    uvel=f.createVariable('uvel','d',('i'))\n",
+    "    uvel.long_name = \"zonal velocity\" ;\n",
+    "    uvel.units = \"m/s\" ;\n",
+    "    uvel.checksum = \"               0\" ;\n",
+    "\n",
+    "    vvel=f.createVariable('vvel','d',('i'))\n",
+    "    vvel.long_name = \"meridional velocity\" ;\n",
+    "    vvel.units = \"m/s\" ;\n",
+    "    vvel.checksum = \"               0\" ;\n",
+    "\n",
+    "    mass=f.createVariable('mass','d',('i'))\n",
+    "    mass.long_name = \"mass\" ;\n",
+    "    mass.units = \"kg\" ;\n",
+    "    mass.checksum = \"               0\" ;\n",
+    "\n",
+    "    axn=f.createVariable('axn','d',('i'))\n",
+    "    axn.long_name = \"explicit zonal acceleration\" ;\n",
+    "    axn.units = \"m/s^2\" ;\n",
+    "    axn.checksum = \"               0\" ;\n",
+    "\n",
+    "    ayn=f.createVariable('ayn','d',('i'))\n",
+    "    ayn.long_name = \"explicit meridional acceleration\" ;\n",
+    "    ayn.units = \"m/s^2\" ;\n",
+    "    ayn.checksum = \"               0\" ;\n",
+    "\n",
+    "    bxn=f.createVariable('bxn','d',('i'))\n",
+    "    bxn.long_name = \"inplicit zonal acceleration\" ;\n",
+    "    bxn.units = \"m/s^2\" ;\n",
+    "    bxn.checksum = \"               0\" ;\n",
+    "\n",
+    "    byn=f.createVariable('byn','d',('i'))\n",
+    "    byn.long_name = \"implicit meridional acceleration\" ;\n",
+    "    byn.units = \"m/s^2\" ;\n",
+    "    byn.checksum = \"               0\" ;\n",
+    "\n",
+    "    ine=f.createVariable('ine','i',('i'))\n",
+    "    ine.long_name = \"i index\" ;\n",
+    "    ine.units = \"none\" ;\n",
+    "    ine.packing = 0 ;\n",
+    "    ine.checksum = \"               0\" ;\n",
+    "\n",
+    "    jne=f.createVariable('jne','i',('i'))\n",
+    "    jne.long_name = \"j index\" ;\n",
+    "    jne.units = \"none\" ;\n",
+    "    jne.packing = 0 ;\n",
+    "    jne.checksum = \"               0\" ;\n",
+    "\n",
+    "    thickness=f.createVariable('thickness','d',('i'))\n",
+    "    thickness.long_name = \"thickness\" ;\n",
+    "    thickness.units = \"m\" ;\n",
+    "    thickness.checksum = \"               0\" ;\n",
+    "\n",
+    "    width=f.createVariable('width','d',('i'))\n",
+    "    width.long_name = \"width\" ;\n",
+    "    width.units = \"m\" ;\n",
+    "    width.checksum = \"               0\" ;\n",
+    "\n",
+    "    length=f.createVariable('length','d',('i'))\n",
+    "    length.long_name = \"length\" ;\n",
+    "    length.units = \"m\" ;\n",
+    "    length.checksum = \"               0\" ;\n",
+    "\n",
+    "    start_lon=f.createVariable('start_lon','d',('i'))\n",
+    "    start_lon.long_name = \"longitude of calving location\" ;\n",
+    "    start_lon.units = \"degrees_E\" ;\n",
+    "    start_lon.checksum = \"               0\" ;\n",
+    "\n",
+    "    start_lat=f.createVariable('start_lat','d',('i'))\n",
+    "    start_lat.long_name = \"latitude of calving location\" ;\n",
+    "    start_lat.units = \"degrees_N\" ;\n",
+    "    start_lat.checksum = \"               0\" ;\n",
+    "\n",
+    "    start_year=f.createVariable('start_year','i',('i'))\n",
+    "    start_year.long_name = \"calendar year of calving event\" ;\n",
+    "    start_year.units = \"years\" ;\n",
+    "    start_year.packing = 0 ;\n",
+    "    start_year.checksum = \"               0\" ;\n",
+    "\n",
+    "    iceberg_num=f.createVariable('iceberg_num','i',('i'))\n",
+    "    iceberg_num.long_name = \"identification of the iceberg\" ;\n",
+    "    iceberg_num.units = \"dimensionless\" ;\n",
+    "    iceberg_num.packing = 0 ;\n",
+    "    iceberg_num.checksum = \"               0\" ;\n",
+    "\n",
+    "    start_day=f.createVariable('start_day','d',('i'))\n",
+    "    start_day.long_name = \"year day of calving event\" ;\n",
+    "    start_day.units = \"days\" ;\n",
+    "    start_day.checksum = \"               0\" ;\n",
+    "\n",
+    "    start_mass=f.createVariable('start_mass','d',('i'))\n",
+    "    start_mass.long_name = \"initial mass of calving berg\" ;\n",
+    "    start_mass.units = \"kg\" ;\n",
+    "    start_mass.checksum = \"               0\" ;\n",
+    "\n",
+    "    mass_scaling=f.createVariable('mass_scaling','d',('i'))\n",
+    "    mass_scaling.long_name = \"scaling factor for mass of calving berg\" ;\n",
+    "    mass_scaling.units = \"none\" ;\n",
+    "    mass_scaling.checksum = \"               0\" ;\n",
+    "\n",
+    "    mass_of_bits=f.createVariable('mass_of_bits','d',('i'))\n",
+    "    mass_of_bits.long_name = \"mass of bergy bits\" ;\n",
+    "    mass_of_bits.units = \"kg\" ;\n",
+    "    mass_of_bits.checksum = \"               0\" ;\n",
+    "\n",
+    "    heat_density=f.createVariable('heat_density','d',('i'))\n",
+    "    heat_density.long_name = \"heat density\" ;\n",
+    "    heat_density.units = \"J/kg\" ;\n",
+    "    heat_density.checksum = \"               0\" ;\n",
+    "\n",
+    "    halo_berg=f.createVariable('halo_berg','d',('i'))\n",
+    "    halo_berg.long_name = \"halo_berg\" ;\n",
+    "    halo_berg.units = \"dimensionless\" ;\n",
+    "    halo_berg.checksum = \"               0\" ;\n",
+    "\n",
+    "    static_berg=f.createVariable('static_berg','d',('i'))\n",
+    "    static_berg.long_name = \"static_berg\" ;\n",
+    "    static_berg.units = \"dimensionless\" ;\n",
+    "    static_berg.checksum = \"               0\" ;\n",
+    "\n",
+    "    f.sync()\n",
+    "    f.close()\n",
+    "\n",
+    "\n",
+    "\n",
+    "#-----------------------------------#\n",
+    "#               Main                #\n",
+    "#-----------------------------------#\n",
+    "\n",
+    "# just2particles=False\n",
+    "# flip2ndconglom=True#False\n",
+    "# offset2ndconglom=True#False\n",
+    "\n",
+    "grdxmin=0; grdxmax=45000e3\n",
+    "grdymin=0; grdymax=45000e3\n",
+    "grdres=1000.0\n",
+    "R_frac=0.45 #1st option\n",
+    "#R_frac=0.5*0.45 #2nd option\n",
+    "radius=(np.sqrt(3)/2.)*(R_frac*grdres) #S is < 0.5 grid res\n",
+    "#radius2=(np.sqrt(3)/2.)*(R_frac2*grdres) #S is < 0.5 grid res\n",
+    "thickness1=200.0\n",
+    "thickness2=200.0\n",
+    "rho_ice=850.0\n",
+    "\n",
+    "\n",
+    "nbergs=1 #number of conglomerates\n",
+    "\n",
+    "#center coords of each (rectangular) conglomerate berg (CB=conglomerate berg)\n",
+    "CBxc=np.array([3500]); CByc=np.array([15000])\n",
+    "#side lengths\n",
+    "CBxl=np.array([4000]); CByl=np.array([8000])\n",
+    "\n",
+    "\n",
+    "CByl=CByl.astype(int); CBxl=CBxl.astype(int)\n",
+    "\n",
+    "#--- xmax, xmin, ymax, ymin for each CB --\n",
+    "CBxmin=CBxc-(0.5*CBxl); CBxmax=CBxc+(0.5*CBxl)\n",
+    "CBymin=CByc-(0.5*CByl); CBymax=CByc+(0.5*CByl)\n",
+    "#this shouldn't happen:\n",
+    "CBxmin[CBxmin<grdxmin]=grdxmin; CBxmax[CBxmax>grdxmax]=grdxmax\n",
+    "CBymin[CBxmin<grdymin]=grdymin; CBymax[CBymax>grdymax]=grdymax\n",
+    "CBxc=0.5*(CBxmin+CBxmax); CByc=0.5*(CBymin+CBymax)\n",
+    "\n",
+    "# #if just want one particle per CB\n",
+    "# if just2particles:\n",
+    "#         CBxmin=CBxc; CBxmax=CBxc\n",
+    "#         CBymin=CByc; CBymax=CByc\n",
+    "\n",
+    "#--- min and max thicknesses for each CB ---\n",
+    "h1=thickness1\n",
+    "h2=thickness2\n",
+    "CBhmax=np.array([h1]); CBhmin=np.array([h2])\n",
+    "\n",
+    "#radii\n",
+    "CBrad=np.array([radius])\n",
+    "print('radii',CBrad)\n",
+    "\n",
+    "berg_x=[]; berg_y=[]\n",
+    "berg_id=[]; berg_static=[]\n",
+    "berg_width=[]; berg_bonds=[]\n",
+    "berg_h=[]; berg_mass_scaling=[]\n",
+    "berg_mass=[]\n",
+    "berg_uvel=[]; berg_vvel=[]\n",
+    "\n",
+    "berg_count=0\n",
+    "\n",
+    "for i in range(nbergs):\n",
+    "        x_start=CBxmin[i]+(CBrad[i]*2./np.sqrt(3))\n",
+    "\n",
+    "        # if flip2ndconglom and i>0:\n",
+    "        #         x_start=CBxmax[i]-(CBrad[i]*2./np.sqrt(3))\n",
+    "\n",
+    "        #pdb.set_trace()\n",
+    "        if x_start>CBxmax[i]:\n",
+    "                x_start=CBxmax[i]\n",
+    "        y_start0=CBymin[i]+CBrad[i]\n",
+    "        if y_start0>CBymax[i]:\n",
+    "                y_start0=CBymax[i]\n",
+    "        element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*(CBrad[i])**2)\n",
+    "        #H (thickness) is a linear function of a berg element's position from the\n",
+    "        #center of the CB. H=Hmax at the center of the CB and H=Hmin at a corner of the\n",
+    "        #CB, where the dist of a corner from the center is:\n",
+    "        cdistb=np.sqrt((CBxmin[i]-CBxc[i])**2+(CBymin[i]-CByc[i])**2)\n",
+    "        j=0\n",
+    "        x_val=x_start\n",
+    "        offset=0.0\n",
+    "        # if (i==0):\n",
+    "        uvel=0.#1\n",
+    "        # else:\n",
+    "        #         uvel=-0.15#-0.05\n",
+    "        #         if (offset2ndconglom):\n",
+    "        #                 offset=250.0\n",
+    "        vvel=0.0#25\n",
+    "        #uvel=0;vvel=0\n",
+    "        #berg_count_start=berg_count\n",
+    "        while x_val<=CBxmax[i] and x_val>=CBxmin[i]:\n",
+    "                y_start=y_start0+((j%2)*CBrad[i])+offset\n",
+    "                k=0\n",
+    "                y_val=y_start\n",
+    "                while y_val<=(CBymax[i]+offset):\n",
+    "                        berg_count=berg_count+1\n",
+    "                        berg_id.append(berg_count)\n",
+    "                        berg_x.append(x_val)\n",
+    "                        berg_y.append(y_val)\n",
+    "                        berg_width.append(sqrt(element_area))\n",
+    "                        #dist of berg elem from center of CB\n",
+    "                        bdistc=np.sqrt((x_val-CBxc[i])**2+(y_val-CByc[i])**2)\n",
+    "                        bh=CBhmin[i]*bdistc/cdistb + CBhmax[i]*(1-bdistc/cdistb)\n",
+    "                        # if (just2particles):\n",
+    "                        #         bh=h1\n",
+    "                        berg_h.append(bh) #thickness\n",
+    "                        berg_mass_scaling.append(1)\n",
+    "                        berg_mass.append(bh*rho_ice*element_area)\n",
+    "                        berg_static.append(0)\n",
+    "                        berg_uvel.append(uvel)\n",
+    "                        berg_vvel.append(vvel)\n",
+    "                        # if (x_val<22000):\n",
+    "                        #         berg_vvel.append(vvel)\n",
+    "                        # else:\n",
+    "                        #         berg_vvel.append(0.4)\n",
+    "                        #berg_CBid.append(i)\n",
+    "                        k=k+1\n",
+    "                        y_val=y_start+(2*k*CBrad[i])\n",
+    "                j=j+1\n",
+    "                # if flip2ndconglom and i>0:\n",
+    "                #         x_val=x_start-(np.sqrt(3)*CBrad[i]*j)\n",
+    "                # else:\n",
+    "                x_val=x_start+(np.sqrt(3)*CBrad[i]*j)\n",
+    "\n",
+    "print('Number of bergs',berg_count)\n",
+    "\n",
+    "#pdb.set_trace()\n",
+    "\n",
+    "#Create iceberg restart file\n",
+    "Ice_geometry_source='Generic'\n",
+    "Create_iceberg_restart_file(berg_count,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)\n"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.8"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/tests/a68/makeberg/makeberg.py b/tests/a68/makeberg/makeberg.py
new file mode 100755
index 0000000..9b6c6bc
--- /dev/null
+++ b/tests/a68/makeberg/makeberg.py
@@ -0,0 +1,1900 @@
+#!/usr/bin/env python
+
+#First import the netcdf4 library
+from netCDF4 import Dataset  # http://code.google.com/p/netcdf4-python/
+import numpy as np  # http://code.google.com/p/netcdf4-python/
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+from scipy import interpolate
+#import matplotlib.pyplot as plt
+import argparse
+import pdb
+import netCDF4 as nc
+
+
+import sys
+pypath = '/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/Iceberg_repository'
+for dir_name in os.listdir(pypath):
+        dir_path = os.path.join(pypath, dir_name)
+        if os.path.isdir(dir_path):
+                sys.path.insert(0, dir_path)
+
+from hexagon_area import Divide_hexagon_into_4_quadrants_old
+from hexagon_area import Hexagon_into_quadrants_using_triangles
+
+
+def parseCommandLine():
+        """
+        Parse the command line positional and optional arguments.
+        This is the highest level procedure invoked from the very end of the script.
+        """
+
+        parser = argparse.ArgumentParser(description=
+        '''
+        Generate files for iceberg and bond restart files, matching given ice thickness fields.
+        ''',
+        epilog='Written by Alon Stern, Dec. 2016.')
+
+        #Adding an extra boolian type argument
+        #p = argparse.ArgumentParser()
+        parser.register('type','bool',str2bool) # add type keyword to registries
+        #p.add_argument('-b',type='bool')  # do not use 'type=bool'
+
+        #Flags
+        parser.add_argument('-save_restart_files', type='bool', default=True,
+                          help=''' Writes an iceberg restart file,  icebergs.res ''')
+
+        parser.add_argument('-save_new_h_ice_file', type='bool', default=True,
+                          help=''' Writes a new gridded ice thickness file, which is what the ice thickness after the berg mass is interpolated back onto the grid''')
+
+        parser.add_argument('-Convert_to_lat_lon', type='bool', default=False,
+                          help=''' Converts the iceberg positions to lat / lon coordinates  ''')
+
+        parser.add_argument('-input_is_cartesian', type='bool', default=True,
+                          help=''' The positions in the ice thickness input file is given in cartesian coordiantes''')
+        parser.add_argument('-lat_ref_grid_to_cartesian', type=float, default=-9999,
+                          help='''Reference latitude for converting to cartesian grid   ''')
+
+        parser.add_argument('-A68', type='bool', default=False,
+                          help=''' Use velocities and angular velocities for A68 experiment''')
+
+        parser.add_argument('-displace_y', type=float, default=0.0,
+                          help='''displace the y coords of the berg (meters)   ''')
+
+        parser.add_argument('-ang_vel_prescribed', type=float, default=0.0,
+                          help='''Prescibed angular velocity   ''')
+        
+        parser.add_argument('-dx', type=float, default=250.0,
+                          help='''dx for regrid   ''')
+        
+        parser.add_argument('-icethres', type=float, default=0.5,
+                          help='''threshold for whether a grid cell is ice or not   ''')
+        
+        #Iceberg setup flags
+        parser.add_argument('-only_choose_one_berg', type='bool', default=False,
+                          help=''' When true, only one iceberg (with number chosen_berg_num) is written to icebergs.res. This is for debugging  ''')
+
+        parser.add_argument('-chosen_berg_num', type=int, default=1,
+                          help='''When only_choose_one_berg=True, then only the iceberg with this number is written to the icebergs.res file  ''')
+
+        parser.add_argument('-scale_the_grid_to_lat_lon', type='bool', default=False,
+                          help=''' This option scales dimensions by a fixed amount. Option should be removed   ''')
+
+        parser.add_argument('-adjust_lat_ref', type='bool', default=True,
+                          help=''' This option is only used when Convert_to_lat_lon is true. If true, then the reference latitudes depends on iceberg position.\
+                                          This still needs to be tested using lat lon test cases.''')
+
+        parser.add_argument('-set_all_thicknesses_to_one', type='bool', default=False,
+                          help=''' Sets all non-zero ice thickness to Th_prescibed (default 1), useful for debugging.  ''')
+
+        parser.add_argument('-Th_prescribed', type=float, default=1.0,
+                          help='''Prescibed ice thickness used when the flag set_all_thicknesses_to_one=True   ''')
+
+        parser.add_argument('-uvel', type=float, default=0.0,
+                          help='''Prescibed ice u velocity (m/s)''')
+
+        parser.add_argument('-vvel', type=float, default=0.0,
+                          help='''Prescibed ice v velocity (m/s)''')
+
+        parser.add_argument('-Interpolate_from_four_corners', type='bool', default=True,
+                          help=''' The thickness of an iceberg is calcaulated from the 4 corners of the gridded thickness. When flag is false, the near thickness is used  ''')
+
+        parser.add_argument('-Switch_x_and_y_to_rotate_90', type='bool', default=False,
+                          help=''' Rotates the whole domain by 90 degrees by switching lat and lon of icebergs.  ''')
+
+        parser.add_argument('-set_all_domain_to_ice', type='bool', default=False,
+                          help=''' Sets the ice thickness = Th_prescibed (default 1) throughout the entire domain. Applied only when flag set_all_thicknesses_to_one=True   ''')
+
+        parser.add_argument('-Use_default_radius', type='bool', default=False,
+                          help=''' Calculates an appropriate ice element radius based on the ocean grid spacing.   ''')
+
+        parser.add_argument('-Remove_stationary_bergs', type='bool', default=False,
+                          help=''' All stationary icebergs are removed.  ''')
+
+        #Static vs non-static flags (These are needed for calving away from Static shelf)
+        parser.add_argument('-set_all_bergs_static_by_default', type='bool', default=True,
+                        help='''Bergs are static unless instructed otherwise (e.g.: after applying calving)   ''')
+
+        parser.add_argument('-set_some_bergs_static_by_default', type='bool', default=False,
+                          help=''' Bergs in part of the domain are set to static by default (see subroutine for details)  ''')
+
+        parser.add_argument('-Make_icebergs_non_static_later', type='bool', default=False,
+                        help=''' Run subroutine which makes some icebergs non-static later (eg: icebergs around calved tabular icebergs).  Note that bonds are \
+                                        only created for non_static, so by making bergs non_static later, it means they can move, but are not bonded.  ''')
+
+        #Mass spreadng flags
+        parser.add_argument('-Switch_regridding_element_type', type='bool', default=False,
+                          help=''' When true, element shape is switched from hexagon to square (and visa versa) before regridding. Used in debugging to see if having \
+                          the wrond elemnt type makes a bid difference. Maybe this option should be removed(?)''')
+
+        parser.add_argument('-Fill_in_the_boundaries', type='bool', default=True,
+                          help=''' Adds extra (static)  ice elements at the edges of the domain when the ice shelf extends right up until the boundaries of the domain.\
+                                          Only used with hexagonal ice elements (for now).''')
+
+        parser.add_argument('-regrid_icebergs_onto_grid', type='bool', default=True,
+                          help=''' After icebergs have been defined, the iceberg mass is interpolated back onto the ocean grid  ''')
+
+        parser.add_argument('-element_type', type=str, default='hexagon',
+                        help='''Shape of element used in mass spreading. Options are: 'hexagon' or 'square'   ''')
+
+
+        #Plotting flags - Only affect how the ice elements are plotted and does not affect files created by this script
+        parser.add_argument('-Run_plotting_subroutine', type='bool', default=True,
+                          help=''' Subrouting is run plots icebergs and ice thickness. All other plotting flags require this to be true.  ''')
+
+        parser.add_argument('-plot_circles', type='bool', default=False,
+                          help=''' Circles are plotted to scale which show how large each ice element is. (Useful when converting to lat lon)  ''')
+
+        parser.add_argument('-plot_ice_mask', type='bool', default=False,
+                          help=''' The ice mask (showing where ice shelf is present) is plotted under iceberg positions. Option may be removed.  ''')
+
+        parser.add_argument('-plot_ice_thickness', type='bool', default=True,
+                          help=''' The ice thickness is plotted under iceberg positions   ''')
+
+        parser.add_argument('-plot_icebergs_positions', type='bool', default=True,
+                          help='''  Positions of ice elements are plotted  ''')
+
+        parser.add_argument('-plot_h_ice_new', type='bool', default=True,
+                          help='''  The newly interpolated ice thickness is plotted under iceberg positions ''')
+
+        parser.add_argument('-plot_bonds', type='bool', default=False,
+                          help=''' Bonds are plotted between the ice elements   ''')
+
+        #Bond related flags
+        parser.add_argument('-Create_icebergs_bonds', type='bool', default=True,
+                          help=''' Bonds are created between icebergs  ''')
+
+        parser.add_argument('-break_some_bonds', type='bool', default=True,
+                          help=''' After the bonds have been set up, some are broken. This simulates a iceberg / ice shelf calving.\
+                                          Note that this flag is also used to make a calving event even if bonds are not used since \
+                                          the "calving" process also sets some icebergs to static and others to non-static''')
+
+        parser.add_argument('-Allow_bonds_for_static_iceberg', type='bool', default=False,
+                          help=''' If True then bonds are allowed for ice elements which are static.   ''')
+
+        parser.add_argument('-Allow_bonds_with_boundary_bergs', type='bool', default=False,
+                          help=''' When true, bonds are allowed to form with elements close to the boundary. \
+                                          When false, bonds are allowed for bergs closer with i,j < N_bergs_before_bd.\
+                                          This option is a little confusing and might need to be removed (>)''')
+
+        #Experimental setup flags
+        parser.add_argument('-Ice_geometry_source', type=str, default='ISOMIP',
+                        help=''' Name of experiment which is being run. Options are 'ISOMIP', 'Generic' and 'Weddell'\
+                                        These experiments override some of the flags above and have standary input files  (see below).\
+                                        This will be made more general later so that ice thickness files are passed into the script with standarized formate through driver.\
+                                        ''')
+
+        parser.add_argument('-ISOMIP_ice_geometry_filename', type=str, default='input_files/Isomip_ice_geometry.nc',
+                        help=''' Ice thickness from the ISOMIP experiment, given on ice grid, rather than ocean grid.  ''')
+
+        parser.add_argument('-ISOMIP_reduced_ice_geometry_filename', type=str, default='input_files/Ocean1_3D_no_calving_trimmed.nc',
+                        help=''' Ice thickness from ISOMIP experiment, given on ocean grid. Later all input files will be made to have this format\
+                                        (or to specify if they are on the ice grid, what format the ocean should have)''')
+
+        parser.add_argument('-Weddell_ice_geometry_filename', type=str, default='input_files/Bedmap2_gridded_subset_Weddell_Sea_Region.nc',
+                        help='''  Ice thickness from the ice shelves in the Weddell Sea, given on ice grid, rather than ocean grid.  ''')
+
+        parser.add_argument('-Generic_ice_geometry_filename', type=str, \
+                        default='/lustre/f1/unswept/Alon.Stern/MOM6-examples_Alon/ice_ocean_SIS2/Drifting_tabular/python_scripts/output_files/Ice_shelf_file.nc',
+                        help=''' Ice thickness used in a generic setup.   ''')
+
+
+        parser.add_argument('-ISOMIP_reduced', type='bool', default=True,
+                        help=''' Flag which specifies that we are using the reduced ISOMIP file (on the ocean grid), rather than geomety on the ice grid. \
+                                        Reduced uses 2X2 grid, not reduced uses 1X1 grid \
+                                        This should be made more general later.''')
+
+        #Parameters
+        parser.add_argument('-Radius', type=float, default='850.0',
+                        help='''Radius of ice element (m). This is overriden if Use_default_radius=True\
+                                        Note that Hexagon only valid if the Radius, S< half gridcell  (about 0.85 using 2km grid)''')
+
+        parser.add_argument('-rho_ice', type=float, default=850.0,
+                        help=''' Density of icebergs (kg/m^3)  ''')
+
+        parser.add_argument('-gravity', type=float, default=9.8,
+                        help=''' Gravitational acceleration  (m/s^2)''')
+
+        parser.add_argument('-mass_scaling', type=float, default=1.0,
+                        help=''' Number of icebergs represented by one ice element  ''')
+
+        #parser.add_argument('-R_earth', type=float, default=6360000.,
+        #                 help=''' Radius of the earch (m) - used in Lat/Lon conversions.   ''')
+
+        parser.add_argument('-R_earth', type=float, default=6378000.,
+                        help=''' Radius of the earch (m) - used in Lat/Lon conversions.   ''')
+
+        parser.add_argument('-buffer_number', type=int, default=0,
+                        help=''' Amount of points from the boundaries where ice thickness is set to zero for debugging. This should be removed.  ''')
+
+        parser.add_argument('-IA_scaling', type=float, default=1.,
+                        help='''  A scaling parameter which allows the interactive radius be different from radius for testing the bonds.\
+                                        (This has not been used in a long while, and perhaps should be removed)''')
+
+        optCmdLineArgs = parser.parse_args()
+        return optCmdLineArgs
+
+def str2bool(string):
+        if string.lower() in  ("yes", "true", "t", "1"):
+                Value=True
+        elif string.lower() in ("no", "false", "f", "0"):
+                Value=False
+        else:
+                print( '**********************************************************************')
+                print( 'The input variable ' ,str(string) ,  ' is not suitable for boolean conversion, using default')
+                print( '**********************************************************************')
+
+                Value=None
+                return
+
+        return Value
+
+
+
+def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,ang_vel_in,uvel_out,vvel_out,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg):
+
+        print( 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..')
+        # To copy the global attributes of the netCDF file
+
+        #Input and output files
+        #Create Empty restart file. This is later read so that the attributes can be used.
+        Empty_restart_filename='output_files/Empty_icebergs.res.nc'
+        create_empty_iceberg_restart_file(Empty_restart_filename)
+        #Empty_restart_filename='input_files/icebergs.res.nc'
+
+        #Read empty restart file
+        f=Dataset(Empty_restart_filename,'r') # r is for read only
+        #Write a new restart file
+        print('Ice_geometry_source',Ice_geometry_source)
+        g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
+
+        for attname in f.ncattrs():
+                    setattr(g,attname,getattr(f,attname))
+
+
+        # To copy the dimension of the netCDF file
+        for dimname,dim in f.dimensions.iteritems():
+                # if you want to make changes in the dimensions of the new file
+                # you should add your own conditions here before the creation of the dimension.
+                #g.createDimension(dimname,len(dim))
+                g.createDimension(dimname,Number_of_bergs)
+
+        # To copy the variables of the netCDF file
+
+        for varname,ncvar in f.variables.iteritems():
+                # if you want to make changes in the variables of the new file
+                # you should add your own conditions here before the creation of the variable.
+                var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
+                #Proceed to copy the variable attributes
+                for attname in ncvar.ncattrs():
+                        setattr(var,attname,getattr(ncvar,attname))
+                #Finally copy the variable data to the new created variable
+                #var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
+
+                if varname=='i':
+                        var[:]=Number_of_bergs
+
+                if varname=='iceberg_num':
+                        for j in range(Number_of_bergs):
+                                #var[j]=j+1
+                                var[j]=iceberg_num[j]
+
+                if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
+                or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
+                or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
+                or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
+                        var[:]=0
+
+                if varname=='ang_vel':
+                        for j in range(Number_of_bergs):
+                                var[j]=ang_vel_in #1.0.#ang_vel_out[j]
+
+                if varname=='uvel':
+                        for j in range(Number_of_bergs):
+                                var[j]=uvel_out[j]
+
+                if varname=='vvel':
+                        for j in range(Number_of_bergs):
+                                var[j]=vvel_out[j]
+
+                if varname=='mass_scaling':
+                        var[:]=mass_scaling
+
+                if varname=='thickness':
+                        for j in range(Number_of_bergs):
+                                var[j]=thickness[j]
+
+                if varname=='mass':
+                        for j in range(Number_of_bergs):
+                                var[j]=mass[j]
+
+                if varname=='width'  or varname=='length':
+                        for j in range(Number_of_bergs):
+                                var[j]=width[j]
+
+                if varname=='lon':
+                        for j in range(Number_of_bergs):
+                                var[j]=lon[j]
+
+                if varname=='lat':
+                        for j in range(Number_of_bergs):
+                                var[j]=lat[j]
+
+                if varname=='static_berg':
+                        for j in range(Number_of_bergs):
+                                var[j]=static_berg[j]
+
+
+        f.close()
+        g.close()
+
+
+
+def Create_bond_restart_file(Number_of_bonds,first_berg_num,first_berg_ine,first_berg_jne,other_berg_ine,other_berg_jne,iceberg_num,other_berg_num,Ice_geometry_source):
+        #Creating the bond restart file
+
+        print( 'Writing bond restart files with  ', Number_of_bonds, ' Bonds')
+        # To copy the global attributes of the netCDF file
+
+        #Input and output files
+        #Create Empty restart file. This is later read so that the attributes can be used.
+        Empty_bond_restart_filename='output_files/Empty_bonds_icebergs.res.nc'
+        create_empty_bond_restart_file(Empty_bond_restart_filename)
+        #Empty_bond_restart_filename='input_files/bonds_iceberg.res.nc'
+
+        h=Dataset(Empty_bond_restart_filename,'r') # r is for read only
+        q=Dataset('output_files/' + Ice_geometry_source + '_bonds_iceberg.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
+
+        for attname in h.ncattrs():
+                    setattr(q,attname,getattr(h,attname))
+
+
+        # To copy the dimension of the netCDF file
+        for dimname,dim in h.dimensions.iteritems():
+                # if you want to make changes in the dimensions of the new file
+                # you should add your own conditions here before the creation of the dimension.
+                #g.createDimension(dimname,len(dim))
+                q.createDimension(dimname,Number_of_bonds)
+
+        # To copy the variables of the netCDF file
+
+        for varname,ncvar in h.variables.iteritems():
+                # if you want to make changes in the variables of the new file
+                # you should add your own conditions here before the creation of the variable.
+                var = q.createVariable(varname,ncvar.dtype,ncvar.dimensions)
+                #Proceed to copy the variable attributes
+                for attname in ncvar.ncattrs():
+                        setattr(var,attname,getattr(ncvar,attname))
+                #Finally copy the variable data to the new created variable
+                #var[:] = ncvar[0]
+                var[:] = 0.
+
+                if varname=='i':
+                        var[:]=Number_of_bonds
+
+                if varname=='first_berg_num':
+                        for j in range(Number_of_bonds):
+                                var[j]=first_berg_num[j]
+
+                if varname=='first_berg_ine':
+                        for j in range(Number_of_bonds):
+                                var[j]=first_berg_ine[j]
+
+                if varname=='first_berg_jne':
+                        for j in range(Number_of_bonds):
+                                var[j]=first_berg_jne[j]
+
+                if varname=='other_berg_num':
+                        for j in range(Number_of_bonds):
+                                var[j]=other_berg_num[j]
+
+                if varname=='other_berg_ine':
+                        for j in range(Number_of_bonds):
+                                var[j]=other_berg_ine[j]
+
+                if varname=='other_berg_jne':
+                        for j in range(Number_of_bonds):
+                                var[j]=other_berg_jne[j]
+
+        h.close()
+        q.close()
+
+
+def create_empty_iceberg_restart_file(Empty_restart_filename):
+
+        f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
+
+        i=f.createDimension('i', None)
+        lon=f.createVariable('i','i')
+
+        lon=f.createVariable('lon','d',('i'))
+        lon.long_name = "longitude" ;
+        lon.units = "degrees_E" ;
+        lon.checksum = "               0" ;
+
+        lat=f.createVariable('lat','d',('i'))
+        lat.long_name = "latitude" ;
+        lat.units = "degrees_N" ;
+        lat.checksum = "               0" ;
+
+        ang_vel=f.createVariable('ang_vel','d',('i'))
+        ang_vel.long_name = "angular velocity" ;
+        ang_vel.units = "rad/s" ;
+        ang_vel.checksum = "               0" ;
+
+        uvel=f.createVariable('uvel','d',('i'))
+        uvel.long_name = "zonal velocity" ;
+        uvel.units = "m/s" ;
+        uvel.checksum = "               0" ;
+
+        vvel=f.createVariable('vvel','d',('i'))
+        vvel.long_name = "meridional velocity" ;
+        vvel.units = "m/s" ;
+        vvel.checksum = "               0" ;
+
+        mass=f.createVariable('mass','d',('i'))
+        mass.long_name = "mass" ;
+        mass.units = "kg" ;
+        mass.checksum = "               0" ;
+
+        axn=f.createVariable('axn','d',('i'))
+        axn.long_name = "explicit zonal acceleration" ;
+        axn.units = "m/s^2" ;
+        axn.checksum = "               0" ;
+
+        ayn=f.createVariable('ayn','d',('i'))
+        ayn.long_name = "explicit meridional acceleration" ;
+        ayn.units = "m/s^2" ;
+        ayn.checksum = "               0" ;
+
+        bxn=f.createVariable('bxn','d',('i'))
+        bxn.long_name = "inplicit zonal acceleration" ;
+        bxn.units = "m/s^2" ;
+        bxn.checksum = "               0" ;
+
+        byn=f.createVariable('byn','d',('i'))
+        byn.long_name = "implicit meridional acceleration" ;
+        byn.units = "m/s^2" ;
+        byn.checksum = "               0" ;
+
+        ine=f.createVariable('ine','i',('i'))
+        ine.long_name = "i index" ;
+        ine.units = "none" ;
+        ine.packing = 0 ;
+        ine.checksum = "               0" ;
+
+        jne=f.createVariable('jne','i',('i'))
+        jne.long_name = "j index" ;
+        jne.units = "none" ;
+        jne.packing = 0 ;
+        jne.checksum = "               0" ;
+
+        thickness=f.createVariable('thickness','d',('i'))
+        thickness.long_name = "thickness" ;
+        thickness.units = "m" ;
+        thickness.checksum = "               0" ;
+
+        width=f.createVariable('width','d',('i'))
+        width.long_name = "width" ;
+        width.units = "m" ;
+        width.checksum = "               0" ;
+
+        length=f.createVariable('length','d',('i'))
+        length.long_name = "length" ;
+        length.units = "m" ;
+        length.checksum = "               0" ;
+
+        start_lon=f.createVariable('start_lon','d',('i'))
+        start_lon.long_name = "longitude of calving location" ;
+        start_lon.units = "degrees_E" ;
+        start_lon.checksum = "               0" ;
+
+        start_lat=f.createVariable('start_lat','d',('i'))
+        start_lat.long_name = "latitude of calving location" ;
+        start_lat.units = "degrees_N" ;
+        start_lat.checksum = "               0" ;
+
+        start_year=f.createVariable('start_year','i',('i'))
+        start_year.long_name = "calendar year of calving event" ;
+        start_year.units = "years" ;
+        start_year.packing = 0 ;
+        start_year.checksum = "               0" ;
+
+        iceberg_num=f.createVariable('iceberg_num','i',('i'))
+        iceberg_num.long_name = "identification of the iceberg" ;
+        iceberg_num.units = "dimensionless" ;
+        iceberg_num.packing = 0 ;
+        iceberg_num.checksum = "               0" ;
+
+        start_day=f.createVariable('start_day','d',('i'))
+        start_day.long_name = "year day of calving event" ;
+        start_day.units = "days" ;
+        start_day.checksum = "               0" ;
+
+        start_mass=f.createVariable('start_mass','d',('i'))
+        start_mass.long_name = "initial mass of calving berg" ;
+        start_mass.units = "kg" ;
+        start_mass.checksum = "               0" ;
+
+        mass_scaling=f.createVariable('mass_scaling','d',('i'))
+        mass_scaling.long_name = "scaling factor for mass of calving berg" ;
+        mass_scaling.units = "none" ;
+        mass_scaling.checksum = "               0" ;
+
+        mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
+        mass_of_bits.long_name = "mass of bergy bits" ;
+        mass_of_bits.units = "kg" ;
+        mass_of_bits.checksum = "               0" ;
+
+        heat_density=f.createVariable('heat_density','d',('i'))
+        heat_density.long_name = "heat density" ;
+        heat_density.units = "J/kg" ;
+        heat_density.checksum = "               0" ;
+
+        halo_berg=f.createVariable('halo_berg','d',('i'))
+        halo_berg.long_name = "halo_berg" ;
+        halo_berg.units = "dimensionless" ;
+        halo_berg.checksum = "               0" ;
+
+        static_berg=f.createVariable('static_berg','d',('i'))
+        static_berg.long_name = "static_berg" ;
+        static_berg.units = "dimensionless" ;
+        static_berg.checksum = "               0" ;
+
+        f.sync()
+        f.close()
+
+def create_empty_bond_restart_file(Empty_bond_restart_filename):
+
+        f = Dataset(Empty_bond_restart_filename,'w', format='NETCDF3_CLASSIC')
+
+        i=f.createDimension('i', None)
+        i=f.createVariable('i','i')
+
+        first_berg_ine=f.createVariable('first_berg_ine','i',('i'))
+        first_berg_ine.long_name = "iceberg ine of first berg in bond" ;
+        first_berg_ine.units = "dimensionless" ;
+        first_berg_ine.packing = 0 ;
+        first_berg_ine.checksum = "               0" ;
+
+        first_berg_jne=f.createVariable('first_berg_jne','i',('i'))
+        first_berg_jne.long_name = "iceberg jne of first berg in bond" ;
+        first_berg_jne.units = "dimensionless" ;
+        first_berg_jne.packing = 0 ;
+        first_berg_jne.checksum = "               0" ;
+
+        first_berg_num=f.createVariable('first_berg_num','i',('i'))
+        first_berg_num.long_name = "iceberg id first berg in bond" ;
+        first_berg_num.units = "dimensionless" ;
+        first_berg_num.packing = 0 ;
+        first_berg_num.checksum = "               0" ;
+
+        other_berg_ine=f.createVariable('other_berg_ine','i',('i'))
+        other_berg_ine.long_name = "iceberg ine of second berg in bond" ;
+        other_berg_ine.units = "dimensionless" ;
+        other_berg_ine.packing = 0 ;
+        other_berg_ine.checksum = "               0" ;
+
+        other_berg_jne=f.createVariable('other_berg_jne','i',('i'))
+        other_berg_jne.long_name = "iceberg jne of second berg in bond" ;
+        other_berg_jne.units = "dimensionless" ;
+        other_berg_jne.packing = 0 ;
+        other_berg_jne.checksum = "                0" ;
+
+        other_berg_num=f.createVariable('other_berg_num','i',('i'))
+        other_berg_num.long_name = "iceberg id second berg in bond" ;
+        other_berg_num.units = "dimensionless" ;
+        other_berg_num.packing = 0 ;
+        other_berg_num.checksum = "               0" ;
+
+        f.sync()
+        f.close()
+
+def Define_iceberg_thickness_and_mass(Number_of_bergs,dx_berg,dy_berg,rho_ice,Radius,h_ice,A68,uvel_in,vvel_in,x,y,\
+                width,Interpolate_from_four_corners,element_area,element_type,static_berg):
+        thickness=[]
+        mass=[]
+        uvel_out=[]
+        vvel_out=[]
+        ang_vel_out=[]
+        ny,nx=h_ice.shape
+        dx=x[1]-x[0]
+        grid_area=dx*dx
+        for berg_count in range(Number_of_bergs):
+                x_val=dx_berg[berg_count] ; y_val=dy_berg[berg_count]
+                i_val=int(floor(x_val/dx))
+                j_val=int(floor(y_val/dx))
+
+                #Interpolate thickness from 4 corners - possibly do this later, but I worry about when you are between a shelf and non shelf piece.
+                if Interpolate_from_four_corners==True:
+
+                        x_cell=(x_val-x[i_val])/sqrt(grid_area)+0.5
+                        y_cell=(y_val-y[j_val])/sqrt(grid_area)+0.5
+
+                        mass_on_ocean=np.zeros([nx,ny,10])   #Setting up matrix to spread mass to ocean.  Note that I have used 10 points  so that I can ignore 0 and match with python numbering
+                        mass_val=1.
+                        mass_on_ocean=spread_mass_to_ocean(nx,ny,i_val,j_val,mass_on_ocean,x_cell,y_cell,element_area,mass_val,element_type,grid_area,static_berg[berg_count])
+                        Th=0.
+                        h=np.array([0,0,0,0,0,0,0,0,0,0])
+                        if i_val>0 and j_val>0:
+                                h[1]=h_ice[j_val-1,i_val-1]
+                        if j_val>0:
+                                h[2]=h_ice[j_val-1,i_val]
+                        if j_val>0 and i_val<(nx-1):
+                                h[3]=h_ice[j_val-1,i_val+1]
+                        if i_val>0:
+                                h[4]=h_ice[j_val,i_val-1]
+                        if True:
+                                h[5]=h_ice[j_val,i_val]
+                        if i_val<(nx-1):
+                                h[6]=h_ice[j_val,i_val+1]
+                        if i_val>0 and j_val<(ny-1):
+                                h[7]=h_ice[j_val+1,i_val-1]
+                        if j_val<(ny-1):
+                                h[8]=h_ice[j_val+1,i_val]
+                        if i_val<(nx-1) and j_val<(ny-1):
+                                h[9]=h_ice[j_val+1,i_val+1]
+                        for k in range(1,10):
+                                Th=Th+(mass_on_ocean[i_val,j_val,k]*h[k])
+                                #print i_val,j_val,k,mass_on_ocean[i_val,j_val,k]
+                        #if abs(Th-1)>0.0000001:
+                        #       print 'Thickness',Th-1,i_val,j_val
+                        #       test=0.
+                        #       for k in range(1,10):
+                        #               print k,mass_on_ocean[i_val,j_val,k], h[k]
+                        #               test=test+(mass_on_ocean[i_val,j_val,k])
+                        #       print test
+                        #       halt
+
+
+                Th=h_ice[j_val,i_val]
+                thickness.append(Th)
+
+                if (A68):
+                        uvel_out.append(uvel_in)
+                        vvel_out.append(vvel_in)
+                        ang_vel_out.append(0)
+                else:
+                        uvel_out.append(uvel_in)
+                        vvel_out.append(vvel_in)
+                        ang_vel_out.append(0)
+                #Check that all thicknesses are positive
+                if Th<=0:
+                        print ('Thickness is less than or equal to zero,0!',i_val, j_val,x_val,y_val)
+                        halt
+                #mass.append(Th*rho_ice*element_area)
+                mass.append(Th*rho_ice*(width[berg_count])**2)
+                #if element_type=='square':
+                #       mass.append(Th*rho_ice*((2*Radius)**2)) # For square elements
+                #else:
+                #       mass.append(Th*rho_ice*np.pi*(Radius**2))  #For circular elements
+        return [thickness, mass, uvel_out, vvel_out, ang_vel_out]
+
+
+def check_if_it_is_in_domain(x_val,y_val,x_min,x_max,y_min,y_max,R_earth,lat_init,adjust_lat_ref,dx,dy):
+        point_is_in_domain=True
+
+        if (x_val >= (x_max-x_min+(dx))) or (x_val<= 0) or  (y_val >= (y_max-y_min+(dy))) or (y_val <= 0):
+                point_is_in_domain=False
+
+        return point_is_in_domain
+
+def check_if_it_is_ice(x_val,y_val,ice_mask,dx,icethres):
+        i_val=int(floor(x_val/dx))
+        j_val=int(floor(y_val/dx))
+        #print('jval',j_val,'ival',i_val)
+
+
+############# ##### ####### #########
+
+        if ice_mask[j_val,i_val]>icethres: #0.5:#99:
+                it_is_ice=True
+        else:
+                it_is_ice=False
+        return it_is_ice
+
+def calculate_element_area(element_type,Radius):
+        if element_type=='square':
+                element_area=(2*Radius)**2
+        elif element_type=='hexagon':
+                element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*(Radius)**2) #Area of hexagon around circle (used for packing)
+                #Another derivation uses innner hexagon with two more triangles added, which is a 1/6 of the hexagon area each (two since there are 6, shared by 3 each)
+                #element_area=(4./3.)*H_i, where H_i=(3.*np.sqrt(3.)/2.)*((Radius)**2)  is the area of the inner hexagon (with sides equal to the radius)
+
+        return element_area
+
+def add_and_extra_boundary_berg(i,j,New_thickness,y_shift,x_shift,Nbh_thickness_value,Nbh_mass_value,New_mass,berg_count,dx_berg,dy_berg,\
+                iceberg_num,thickness,width,mass,static_berg,grid_area,rho_ice):
+        tol=0.0000000000001
+        if New_thickness[j,i]>1.+tol:
+                print( 'The new thickness is too big!!!', i,j,  New_thickness[j,i])
+                halt
+        if ((Nbh_thickness_value-New_thickness[j,i])>tol):
+                y_val=y_shift[j]
+                x_val=x_shift[i]
+                if Nbh_thickness_value>0. and (abs(Nbh_thickness_value-1)<tol) and (Nbh_mass_value>New_mass[j,i]):
+                        berg_count=berg_count+1
+                        dx_berg.append(x_val)
+                        dy_berg.append(y_val)
+                        iceberg_num.append(berg_count)
+                        width_val=np.sqrt((Nbh_thickness_value-New_thickness[j,i])*grid_area)
+                        if Nbh_thickness_value-New_thickness[j,i]<0:
+                                print( 'Stop', Nbh_thickness_value, New_thickness[j,i],i,j)
+                        mass_val=Nbh_mass_value-New_mass[j,i]
+                        thickness_val=mass_val/(width_val*width_val*rho_ice)
+                        thickness.append(thickness_val)
+                        width.append(width_val)
+                        mass.append(mass_val)
+                        static_berg.append(1.)
+        return [berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg]
+
+
+def add_extra_bergs_on_boundary(dx,dy,x,y,Number_of_bergs,element_area,rho_ice,X_min,X_max,Y_min,Y_max,R_earth,lat_init,adjust_lat_ref,ice_mask,\
+                iceberg_num,width,dx_berg,dy_berg,h_ice,element_type,static_berg,thickness,mass):
+        eps=0.000001
+        grid_area=dx*dy
+        Nx=len(x)  ; Ny=len(y)
+        x_shift=(x-np.min(x))+(dx/2) ; y_shift=(y-np.min(y))+(dy/2)
+
+        thickness_temp= [1. for i in range(Number_of_bergs)] ;
+        mass_temp= [element_area*rho_ice*1. for i in range(Number_of_bergs)] ;
+        New_area=regrid_iceberg_thickness(dy_berg,dx_berg,Number_of_bergs,thickness_temp,mass_temp,h_ice,x_shift,y_shift,rho_ice,element_type,static_berg,plot_outcome=False)
+        New_thickness=(New_area)/(rho_ice*grid_area)  #Should be equal to one everywhere where there is ice shelf.
+        New_mass=regrid_iceberg_thickness(dy_berg,dx_berg,Number_of_bergs,thickness,mass,h_ice,x_shift,y_shift,rho_ice,element_type,static_berg,plot_outcome=False)
+        berg_count=Number_of_bergs
+
+
+        #Vertical boundary
+        for i in np.array([0,Nx-1]):
+                #for j in range(Ny):
+                for j in range(1,Ny-1):
+                        Nbh_mass_value=h_ice[j,i]*rho_ice*grid_area  #Neighbouring shelf value
+                        if i==0:
+                                Nbh_thickness_value=New_thickness[j,1]  #Neighbouring shelf value
+                                #x_val=0+(eps*dx)
+                        if i==Nx-1:
+                                Nbh_thickness_value=New_thickness[j,Nx-2]  #Neighbouring shelf value
+                                #x_val=x_shift[i]+(dx/2)-eps
+                        [berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg]=add_and_extra_boundary_berg(i,j,New_thickness,y_shift,x_shift,\
+                                        Nbh_thickness_value,Nbh_mass_value,New_mass,berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg,grid_area,rho_ice)
+
+        ##Horizontal boundary
+        for j in np.array([0,Ny-1]):
+                #for i in range(1,Nx-1):
+                for i in range(1,Nx-1):
+                        Nbh_mass_value=h_ice[j,i]*rho_ice*grid_area  #Neighbouring shelf value
+                        if j==0:
+                                Nbh_thickness_value=New_thickness[1,i]  #Neighbouring shelf value
+                                #y_val=0+(eps*dy)
+                        if j==Ny-1:
+                                Nbh_thickness_value=New_thickness[Ny-2,i]  #Neighbouring shelf value
+                                #y_val=y_shift[j]+(dy/2)-eps
+                        #Nbh_thickness_value=np.mean(New_thickness[range(1,Ny-1),i])  #Neighbouring shelf value
+                        [berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg]=add_and_extra_boundary_berg(i,j,New_thickness,y_shift,x_shift,\
+                                        Nbh_thickness_value,Nbh_mass_value,New_mass,berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg,grid_area,rho_ice)
+
+        #Doing the corners seperately
+        for j in np.array([0,Ny-1]):
+                #for i in range(1,Nx-1):
+                for i in np.array([0,Nx-1]):
+                        Nbh_mass_value=h_ice[j,i]*rho_ice*grid_area  #Neighbouring shelf value
+                        if j==0 and i==0:
+                                Nbh_thickness_value=New_thickness[1,1]  #Neighbouring shelf value
+                        if j==0 and i==Nx-1:
+                                Nbh_thickness_value=New_thickness[1,Nx-2]  #Neighbouring shelf value
+                        if j==Ny-1 and i==0:
+                                Nbh_thickness_value=New_thickness[Ny-2,1]  #Neighbouring shelf value
+                        if j==Ny-1 and i==Nx-1:
+                                Nbh_thickness_value=New_thickness[Ny-2,Nx-2]  #Neighbouring shelf value
+                        [berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg]=add_and_extra_boundary_berg(i,j,New_thickness,y_shift,x_shift,\
+                                        Nbh_thickness_value,Nbh_mass_value,New_mass,berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg,grid_area,rho_ice)
+
+
+        Number_of_bergs=berg_count
+
+        return [dx_berg, dy_berg,iceberg_num, width,Number_of_bergs,static_berg,thickness,mass]
+
+
+def remove_stationary_bergs(dx_berg, dy_berg,iceberg_num,width,Number_of_bergs,static_berg):
+        dx_berg_new=[]
+        dy_berg_new=[]
+        iceberg_num_new=[]
+        width_new=[]
+        static_berg_new=[]
+        for i in range(Number_of_bergs):
+                if static_berg[i]<0.5:
+                        dx_berg_new.append(dx_berg[i])
+                        dy_berg_new.append(dy_berg[i])
+                        iceberg_num_new.append(iceberg_num[i])
+                        width_new.append(width[i])
+                        static_berg_new.append(static_berg[i])
+
+        Number_of_bergs_new=len(iceberg_num_new)
+        return [dx_berg_new, dy_berg_new,iceberg_num_new, width_new,Number_of_bergs_new,static_berg_new]
+
+def Create_icebergs(lon_init,lat_init,Radius,R_earth, x, y,ice_mask,h_ice,A68,uvel_in,vvel_in,Convert_to_lat_lon,rho_ice,\
+                element_type,scale_the_grid_to_lat_lon,lat_ref,adjust_lat_ref,Interpolate_from_four_corners,\
+                Fill_in_the_boundaries,set_all_bergs_static_by_default,break_some_bonds,Remove_stationary_bergs,set_some_bergs_static_by_default,icethres):
+        print( 'Starting to create icebergs...')
+        dx_berg=[]  #x distance in cartesian of berg from lon_init
+        dy_berg=[]  #y distance in cartesian of berg from lat_init
+        dlon_berg=[] #x distance in lon of berg from lon_init
+        #dlat_berg=[] #y distance in lat of berg from lat_init
+        lon=[] #Longitude of iceberg
+        lat=[] #Latitude of iceberg
+        iceberg_num=[] #ID of iceberg
+
+        element_area=calculate_element_area(element_type,Radius)
+        #width=np.sqrt(element_area)
+        width=[]
+
+        #dx=x[1]-x[0]  ;dy=y[1]-y[0]
+        #X_min=np.min(x)-dx; X_max=np.max(x)+dx  #In lat lon or cartesian
+        #Y_min=np.min(y)-dy; Y_max=np.max(y)+dy  #In lat lon or cartesian
+        X_min=np.min(x); X_max=np.max(x)  #In lat lon or cartesian
+        Y_min=np.min(y); Y_max=np.max(y)  #In lat lon or cartesian
+
+        #N=2*int(ceil((R_max)/(2*Radius))+2)
+
+        if element_type=='square':
+                N=int(ceil((X_max-X_min)/(Radius)))
+                M=int(ceil((Y_max-Y_min)/(Radius)))
+        else:
+                N=2*int(ceil((X_max-X_min)/(Radius)))
+                M=2*int(ceil((Y_max-Y_min)/(Radius)))
+
+        #N=10
+        #M=6
+        #MP4
+        dx=x[1]-x[0]
+        dy=y[1]-y[0]
+        Lx=X_max+dx
+        Ly=Y_max+dx
+
+        berg_count=0
+        #for j in range(N):
+        for i in range(N):
+                if element_type=='square':
+                        x_start=Radius#+Radius/2
+                        y_start=Radius#+Radius/2
+                        x_val=x_start+(2*i*Radius)
+
+                #Hexagonal
+                else:
+                        y_start=(Radius)+(((i%2)*Radius))
+                        x_start=((2/sqrt(3))*Radius)
+                        x_val=x_start + (np.sqrt(3)*Radius*i)
+
+                for j in range(M):
+                #for i in range(M):
+                        #x_val=x_start+(2*i*Radius)  ; y_val=y_start
+                        y_val=y_start+(2*j*Radius)  ;# x_val=x_start + (np.sqrt(3)*Radius*i)
+                        if check_if_it_is_in_domain(x_val,y_val,X_min,X_max,Y_min,Y_max,R_earth,lat_init,adjust_lat_ref,dx,dy):
+                        #if True:
+                                #R_val=np.sqrt(((x_val-x0)**2) +((y_val-y0)**2))
+                                if check_if_it_is_ice(x_val,y_val,ice_mask,dx,icethres):
+                                        #Don't allow points closer than R from the boundary (these are sorted out later)
+                                        #if abs(y_val-Ly)<Radius or  ((abs(x_val-Lx)<((2/sqrt(3))*Radius)) and element_type=='hexagon') or ((abs(x_val-Lx)<Radius) and element_type=='square'):
+                                        berg_count=berg_count+1
+                                        iceberg_num.append(berg_count)
+                                        dx_berg.append(x_val)
+                                        dy_berg.append(y_val)
+                                        width.append(np.sqrt(element_area))
+        #print 'dx_berg',dx_berg
+        #print 'dy_berg',dy_berg
+
+
+
+        Number_of_bergs=berg_count
+        print( 'Icebergs created. Number of bergs = ', Number_of_bergs)
+
+        #Deciding if icebergs are static or not
+        static_berg = [0. for i in dx_berg]
+        if set_all_bergs_static_by_default==True:
+                static_berg = [1. for i in static_berg]
+        if set_some_bergs_static_by_default is True:
+                for i in range(len(dx_berg)):
+                        if dx_berg[i]>Lx/2:
+                                static_berg[i]=1.
+        if break_some_bonds==True:
+                #static_berg =Change_static_berg_after_calving(Number_of_bergs,lat,lon, static_berg)
+                static_berg =Change_static_berg_after_calving(Number_of_bergs,dy_berg,dx_berg, static_berg)
+                static_berg=static_berg[0]
+
+        if Remove_stationary_bergs is True:
+                Fill_in_the_boundaries=False
+                [dx_berg, dy_berg,iceberg_num, width,Number_of_bergs,static_berg]=remove_stationary_bergs(dx_berg, dy_berg,iceberg_num,\
+                                width,Number_of_bergs,static_berg)
+                print( 'After purge  Number of bergs = ', Number_of_bergs)
+
+        #Defining the thickness of the icebergs
+        (thickness, mass, uvel_out, vvel_out,ang_vel_out)=Define_iceberg_thickness_and_mass(Number_of_bergs,dx_berg,dy_berg,rho_ice,Radius, h_ice,A68,uvel_in,vvel_in,x,y,\
+                        width,Interpolate_from_four_corners,element_area,element_type,static_berg)
+
+        N_bergs_before_bd=Number_of_bergs
+        if Fill_in_the_boundaries==True and element_type=='hexagon':
+                [dx_berg, dy_berg,iceberg_num, width,Number_of_bergs,static_berg,thickness,mass]= add_extra_bergs_on_boundary(dx,dy,x,y,Number_of_bergs,element_area,rho_ice,X_min,X_max,Y_min,\
+                                Y_max,R_earth,lat_init,adjust_lat_ref,ice_mask,iceberg_num,width,dx_berg,dy_berg,\
+                                h_ice,element_type,static_berg,thickness,mass)
+                print( 'Number of icebergs after accounting for boundaries = ', Number_of_bergs)
+
+
+
+        if Convert_to_lat_lon==True:
+                #Defining lon lat positions:
+                #dlat_berg=(180/np.pi)*(1/R_earth)*dy_berg
+                #dlon_berg=(180/np.pi)*(1/R_earth)*(1/cos(lat_init*np.pi/180))*dx_berg
+                for i in range(Number_of_bergs):
+                        #Finding latittude
+                        dlat_dy=(180/np.pi)*(1/R_earth)
+
+                        lat.append(lat_init+(dlat_dy*dy_berg[i]))
+
+                        #Finding longitude
+                        if adjust_lat_ref==True:
+                                lat_ref=lat_init+(dlat_dy*dy_berg[i])
+                                #print lat_ref
+                        dlon_dx=(180/np.pi)*(1/R_earth)*(1/np.cos(lat_ref*np.pi/180)) #Note that this depends on the latitude of the iceberg. Could approx this with lat_init.
+                        lon.append(lon_init+(dlon_dx*dx_berg[i] ))
+
+                        #dlon_berg.append(dlon_dx*dx_berg[i])
+                        #lon.append(lon_init+dlon_berg[i])
+        else:
+                if scale_the_grid_to_lat_lon==True:
+                        Scale_up=1./2000.
+                        Radius=Radius*Scale_up
+                        dx_berg = [(i*Scale_up) for i in dx_berg] ; dy_berg = [i*Scale_up for i in dy_berg]
+                        x=x*Scale_up ; y=y*Scale_up
+                        dx=dx*Scale_up ;dy=dy*Scale_up
+                x=(x-np.min(x))+(dx/2) ; y=(y-np.min(y))+(dy/2)
+                lon=dx_berg  ; lat=dy_berg
+
+        #Note that static_berg calculations used to be here, after the conversion. I have moved them. I hope that this does not affect answers.
+
+        return (Number_of_bergs,lon,lat,iceberg_num,dx_berg,dy_berg,thickness,ang_vel_out,uvel_out,vvel_out,mass,width,x,y,Radius,static_berg,N_bergs_before_bd)
+
+
+
+def Create_calving_event(lat1,lon1,lat2,lon2):
+        [R_calve, Calve_lon, Calve_lat]=get_calving_parameters()
+
+        #Circular calving from ice front
+        R1=np.sqrt((lon1-Calve_lon)**2+ (lat1-Calve_lat)**2)
+        R2=np.sqrt((lon2-Calve_lon)**2+ (lat2-Calve_lat)**2)
+
+        #Iceberg splitting down the midde (length wise)
+        #R1=lat1
+        #R2=lat2
+        #R_calve=500*1000
+        #Iceberg splitting down the midde (width wise)
+        R1=lon1
+        R2=lon2
+        R_calve=250*1000
+
+        bond_broken=False
+        if ((R1 < R_calve)*(R2>R_calve) )  > 0.5 :
+                bond_broken=True
+        if ((R2 < R_calve)*(R1>R_calve) )  > 0.5 :
+                bond_broken=True
+
+        return bond_broken
+
+def get_calving_parameters():
+        #Calve_lat =20
+        #Calve_lon=160
+        #R_calve=15
+        Calve_lat =20.2*2000
+        Calve_lon=165*2000
+        R_calve=12*2000
+        #R_calve=15.*2000.
+        #R_calve=1.*2000.
+
+        return [R_calve, Calve_lon, Calve_lat]
+
+def Change_static_berg_after_calving(Number_of_bergs,lat,lon, static_berg):
+        [R_calve, Calve_lon, Calve_lat]=get_calving_parameters()
+        count=0.
+        for i in range(Number_of_bergs):
+                R1=np.sqrt((lon[i]-Calve_lon)**2+ (lat[i]-Calve_lat)**2)
+                #Making calved icebergs not be static.
+                if R1<R_calve:
+                        count=count+1.
+                        #print 'An iceberg is now static!'
+                        static_berg[i]=0.
+        print( 'Amount of unstatic icebergs after calving = ', count)
+
+        return [static_berg]
+
+def Change_static_berg_after_bonding(Number_of_bergs,lat,lon, static_berg):
+        #For now, it just uses a bigger circle.
+        multiplier=1.2
+        [R_calve, Calve_lon, Calve_lat]=get_calving_parameters()
+        count=0.
+        for i in range(Number_of_bergs):
+                R1=np.sqrt((lon[i]-Calve_lon)**2+ (lat[i]-Calve_lat)**2)
+                #Making calved icebergs not be static.
+                if R1<(R_calve*multiplier):
+                        count=count+1.
+                        #print 'An iceberg is now static!'
+                        static_berg[i]=0.
+        print ('Amount of unstatic icebergs after bonding and restatic= ', count)
+
+        return [static_berg]
+
+def find_max_number_of_bonds(first_berg_num,Number_of_bonds):
+        count=1
+        best_count=1
+        sorted_bonds=np.sort(first_berg_num)
+        for k in range(1,Number_of_bonds):
+                previous_berg=sorted_bonds[k-1]
+                #print k, sorted_bonds[k]
+                if sorted_bonds[k] == sorted_bonds[k-1]:
+                        count=count+1
+                        best_count=max(count,best_count)
+                else:
+                        count=1
+        Max_number_of_bonds=best_count
+        return Max_number_of_bonds
+
+def Define_iceberg_bonds(Number_of_bergs,iceberg_num,lat,lon,dx_berg, dy_berg,Radius,break_some_bonds,static_berg, Allow_bonds_for_static_iceberg\
+                ,N_bergs_before_bd,Allow_bonds_with_boundary_bergs):
+        print( 'Starting to create bonds...')
+        #Defining Bonds:
+        Bond=np.zeros((Number_of_bergs, Number_of_bergs))
+        bond_broken=False
+        first_berg_num=[]  # Initializing bond list first berg
+        first_berg_ine=[]  # Initializing bond list first berg
+        first_berg_jne=[]  # Initializing bond list first berg
+        first_berg_lat=[]  # Initializing bond list first berg
+        first_berg_lon=[]  # Initializing bond list first berg
+        other_berg_num=[]  # Initializing bond list other berg
+        other_berg_ine=[]  # Initializing bond list other berg
+        other_berg_jne=[]  # Initializing bond list other berg
+        other_berg_lat=[]  # Initializing bond list other berg
+        other_berg_lon=[]  # Initializing bond list other berg
+        bond_count=0
+        for i in range(Number_of_bergs):
+                if (static_berg[i]<0.5) or (Allow_bonds_for_static_iceberg is True):
+                        #for j in range(Number_of_bergs):
+                        for j in range(i):
+                                if (static_berg[j]<0.5) or (Allow_bonds_for_static_iceberg is True):
+                                        if i!=j:
+                                                if ((i <N_bergs_before_bd) and (j <N_bergs_before_bd))  or (Allow_bonds_with_boundary_bergs is True):
+                                                        R_dist=np.sqrt(((dx_berg[i]-dx_berg[j])**2) + ((dy_berg[i]-dy_berg[j])**2))
+                                                        if break_some_bonds==True:
+                                                                bond_broken=Create_calving_event(lat[i],lon[i],lat[j],lon[j])
+                                                        if R_dist < (2.01*Radius) and (bond_broken==False):
+                                                                bond_count=bond_count+2
+                                                                #Connect bond in the first direction
+                                                                first_berg_num.append(iceberg_num[i]);  first_berg_ine.append(999);
+                                                                other_berg_num.append(iceberg_num[j]);  other_berg_ine.append(999);
+                                                                first_berg_jne.append(999);first_berg_lat.append(lat[i]); first_berg_lon.append(lon[i])
+                                                                other_berg_jne.append(999);other_berg_lat.append(lat[j]); other_berg_lon.append(lon[j])
+                                                                #Connect bond in the other direction
+                                                                first_berg_num.append(iceberg_num[j]);  first_berg_ine.append(999);
+                                                                other_berg_num.append(iceberg_num[i]);  other_berg_ine.append(999);
+                                                                first_berg_jne.append(999);first_berg_lat.append(lat[j]); first_berg_lon.append(lon[j])
+                                                                other_berg_jne.append(999);other_berg_lat.append(lat[i]); other_berg_lon.append(lon[i])
+        Number_of_bonds=bond_count
+        Max_number_of_bonds=find_max_number_of_bonds(first_berg_num,Number_of_bonds)
+        print( 'Number of bonds created = ' , Number_of_bonds)
+        print( 'Maximum number of bonds = ' ,  Max_number_of_bonds)
+
+        return [ Number_of_bonds, first_berg_num,first_berg_ine,first_berg_jne,first_berg_lat,first_berg_lon, other_berg_num,other_berg_ine, other_berg_jne,other_berg_lat,other_berg_lon]
+
+def load_ISOMIP_ice_geometry(filename,buffer_number):
+        with nc.Dataset(filename) as file:
+                ocean_mask = file.variables['openOceanMask'][:,:]
+                upperSurface = file.variables['upperSurface'][:,:]
+                lowerSurface = file.variables['lowerSurface'][:,:]
+                x = file.variables['x'][:]
+                y = file.variables['y'][:]
+
+        ice_mask=1-ocean_mask #one if it ice, zero if it is ocean
+        h_ice=upperSurface-lowerSurface #The ice thickness
+        M=ice_mask.shape
+
+        #Setting the boundaries to non-ice
+        A=np.arange(0,buffer_number)
+        B=np.arange(M[0]-buffer_number,M[0])
+        C=np.arange(M[1]-buffer_number,M[1])
+        ice_mask[A,:]=0; ice_mask[B,:]=0
+        ice_mask[:,A]=0; ice_mask[:,C]=0
+
+        return [x,y,ice_mask,h_ice]
+
+
+def create_clipped_icethickness_file(h_ice,area,mass,grid_area,gravity,Ice_geometry_source):
+        #Creating clipped file
+        [ny, nx]= h_ice.shape ;
+
+        New_ice_thickness_filename='output_files/'+ Ice_geometry_source +'_Ice_Shelf_clipped.nc'
+        g=Dataset(New_ice_thickness_filename,'w') # w if for creating a file
+
+        g.createDimension('nx',nx)
+        g.createDimension('ny',ny)
+
+        thick_h=g.createVariable('thick','f8',('ny','nx'))
+        area_h=g.createVariable('area','f8',('ny','nx'))
+        p_surf_h=g.createVariable('p_surf','f8',('ny','nx'))
+
+        thick_h.units = 'm'
+        thick_h.standard_name = 'ice shelf thickness (clipped)'
+        area_h.units = 'm2'
+        area_h.standard_name = 'ice shelf area'
+        p_surf_h.units = 'Pa'
+        p_surf_h.standard_name = 'surface pressure due to ice shelf'
+
+        p_surf=(gravity*mass)/grid_area
+        g.variables['thick'][:]=h_ice
+        g.variables['area'][:]=area
+        g.variables['p_surf'][:]=p_surf
+        print ('Creating clipped ice file: ' , New_ice_thickness_filename)
+
+        g.sync()
+        g.close()
+
+
+def load_ISOMIP_reduced_ice_geometry(ice_filename,buffer_number):
+        with nc.Dataset(ice_filename) as file:
+                h_ice = file.variables['thick'][:,:]
+                area =  file.variables['area'][:,:]
+                M=h_ice.shape
+
+        y=np.linspace(1000,79000,M[0],endpoint=True)
+        #x=np.linspace(321000,799000,M[1],endpoint=True)
+        x=np.linspace(1000,479000,M[1],endpoint=True)
+        ice_mask=h_ice>0.
+
+
+        count=0. #MP1
+        #Setting the boundaries to non-ice
+        A=np.arange(0,buffer_number)
+        B=np.arange(M[0]-buffer_number,M[0])
+        C=np.arange(M[1]-buffer_number,M[1])
+        #if buffer_number>0:
+        ice_mask[A,:]=0; ice_mask[B,:]=0
+        ice_mask[:,A]=0; ice_mask[:,C]=0
+
+        return [x,y,ice_mask,h_ice]
+
+def load_generic_ice_geometry(filename,y_disp):
+        print( 'Loading from ' , filename)
+        with nc.Dataset(filename) as file:
+                #h_ice = file.variables['thick'][:]
+                #area = file.variables['area'][:,:]
+                h_ice = file.variables['b_id'][:]
+                x = file.variables['lon'][:]
+                y = file.variables['lat'][:]+y_disp
+
+                ice_mask=h_ice>0
+                ice_mask[np.where(ice_mask<0)]=0.
+                #ice_mask=1-ocean_mask #one if it ice, zero if it is ocean
+                h_ice[np.where(np.isnan(h_ice))]=0.
+                ice_mask[np.where(np.isnan(ice_mask))]=0.
+                dx=x[1]-x[0]
+                #lon_init=x[0]-(dx/2.)+360
+                #lat_init=y[0]-(dx/2.)
+                lon_init=x[0]+360
+                lat_init=y[0]
+
+                #dy=y[1]-y[0]
+                lon_init=x[0]-(dx/2.)+360
+                lat_init=y[0]-(dx/2.)
+                print( 'Bottom corner = [ ', lon_init,' , ' , lat_init, ' dx = ' , dx)
+
+        return [x,y,ice_mask,h_ice,lon_init, lat_init]
+
+def load_Weddel_ice_geometry(filename):
+        with nc.Dataset(filename) as file:
+                h_ice = file.variables['thickness'][:,:]
+                ice_mask = file.variables['icemask_grounded_and_shelves'][:,:]
+                x = file.variables['lon'][:]
+                y = file.variables['lat'][:]
+
+                ice_mask[np.where(ice_mask<-1)]=0.
+                #ice_mask=1-ocean_mask #one if it ice, zero if it is ocean
+                h_ice[np.where(np.isnan(h_ice))]=0.
+                ice_mask[np.where(np.isnan(ice_mask))]=0.
+
+        return [x,y,ice_mask,h_ice]
+
+def Select_just_one_berg(lon,lat,thickness,width,mass,iceberg_num,chosen_berg_num,static_berg):
+        print ('You have chosen to choose just one icebergs!!!')
+        for k in range(len(lat)):
+                if iceberg_num[k]==chosen_berg_num:
+                        berg_ind=k
+        lon_temp=lon[berg_ind]; lon=[] ; lon.append(lon_temp)
+        lat_temp=lat[berg_ind]; lat=[] ; lat.append(lat_temp)
+        thickness_temp=thickness[berg_ind]; thickness=[] ; thickness.append(thickness_temp)
+        mass_temp=mass[berg_ind]; mass=[] ; mass.append(mass_temp)
+        width_temp=width[berg_ind]; width=[] ; width.append(width_temp)
+        static_berg_temp=static_berg[berg_ind]; static_berg=[] ; static_berg.append(static_berg_temp)
+        iceberg_num_temp=iceberg_num[berg_ind]; iceberg_num=[] ; iceberg_num.append(iceberg_num_temp)
+        Number_of_bergs=1
+        return [Number_of_bergs,lon,lat,thickness,width,mass,iceberg_num]
+
+def plotting_iceberg_positions(lat,lon,Number_of_bergs,R_earth,Radius,IA_scaling,Convert_to_lat_lon, \
+                plot_circles,h_ice,ice_mask,x,y,plot_ice_mask,plot_ice_thickness,thickness,plot_icebergs_positions,static_berg,h_ice_new,plot_h_ice_new):
+        print ('Starting to plot...')
+        Radius=Radius*IA_scaling
+        circ_ind=np.linspace(0,2*pi,100);
+
+        if plot_ice_mask==True:
+                print(shape(x),shape(y),shape(ice_mask))
+                cNorm = mpl.colors.Normalize(vmin=0., vmax=1.)
+                plt.pcolor(x,y,ice_mask,norm=cNorm)
+                plt.title('Ice mask')
+
+        elif plot_h_ice_new is True: # Ice thickness after interpolation
+                cNorm = mpl.colors.Normalize(vmin=np.min(h_ice_new), vmax=np.max(h_ice_new))
+                plt.pcolor(x,y,h_ice_new , norm=cNorm)
+                plt.title('New thickness')
+
+        elif plot_ice_thickness==True:
+                cNorm = mpl.colors.Normalize(vmin=0., vmax=1000.)
+                plt.pcolor(x,y,h_ice,cmap='jet',norm=cNorm)
+                plt.title('Old thickness')
+
+        if plot_icebergs_positions==True:
+                variable=thickness
+                #variable=static_berg
+                plt.scatter(lon, lat,color='yellow')
+                cNorm = mpl.colors.Normalize(vmin=0., vmax=np.max(variable))
+                plt.scatter(lon, lat,c=variable,norm=cNorm,cmap='jet',s=150)
+                #cNorm = mpl.colors.Normalize(vmin=-1, vmax=1.)
+                #plt.scatter(lon, lat,c=static_berg,norm=cNorm,cmap='jet',s=150)
+                #plt.title('Iceberg positions')
+
+        #plt.plot(lon, lat,'bo-',linewidth=5)
+        if plot_circles==True:
+                for k in range(Number_of_bergs):
+                        if Convert_to_lat_lon==True:
+                                dR_lat=(Radius/R_earth)*(180/np.pi)
+                                dR_lon=(Radius/R_earth)*(180/np.pi)*(1/np.cos(lat[k]*np.pi/180))
+                                plt.plot(lon[k]+(dR_lon*cos(circ_ind)),lat[k]+(dR_lat*sin(circ_ind)),'c');
+                        else:
+                                plt.plot(lon[k]+(Radius*cos(circ_ind)),lat[k]+(Radius*sin(circ_ind)),'c');
+
+
+
+        #plt.plot(lon, lat,'bo-')
+        if Convert_to_lat_lon==True:
+                plt.xlabel('longitude (deg)')
+                plt.ylabel('latitude (deg)')
+        else:
+                plt.xlabel('longitude (m)')
+                plt.ylabel('latitude (m)')
+        plt.colorbar()
+        plt.grid(True)
+
+
+def plotting_iceberg_bonds(first_berg_lat,first_berg_lon,other_berg_lat,other_berg_lon,Number_of_bonds):
+
+        for k in range(Number_of_bonds):
+                x_bond=[]
+                y_bond=[]
+                x_bond.append(first_berg_lon[k])
+                x_bond.append(other_berg_lon[k])
+                y_bond.append(first_berg_lat[k])
+                y_bond.append(other_berg_lat[k])
+                plt.plot(x_bond, y_bond,'r',linewidth=5)
+
+
+def spread_mass_to_ocean(Nx,Ny,i,j,mass_on_ocean,x,y,Area,Mass,element_type,grid_area,static_berg):
+                #Note that the x,y coming into this routine are the position within a cell (from 0 to 1), with 0.5,0.5 being in the center of the cell.
+
+                #Initialize weights for each cell
+                yDxL=0.  ; yDxC=0. ; yDxR=0. ; yCxL=0. ; yCxR=0.
+                yUxL=0.  ; yUxC=0. ; yUxR=0. ; yCxC=1.
+
+                if element_type=='square':
+                #if True:
+                        L = min(( (np.sqrt(Area)  / np.sqrt(grid_area))),1) ;  #Non dimensionalize element length by grid area. (This gives the non-dim length of the square)
+                        xL=min(0.5, max(0., 0.5-(x/L)))
+                        xR=min(0.5, max(0., (x/L)+(0.5-(1/L) )))
+                        xC=max(0., 1.-(xL+xR))
+                        yD=min(0.5, max(0., 0.5-(y/L)))
+                        yU=min(0.5, max(0., (y/L)+(0.5-(1/L) )))
+                        yC=max(0., 1.-(yD+yU))
+
+                        yDxL=yD*xL#*grd%msk[i-1,j-1]
+                        yDxC=yD*xC#*grd%msk[i  ,j-1]
+                        yDxR=yD*xR#*grd%msk[i+1,j-1]
+                        yCxL=yC*xL#*grd%msk[i-1,j  ]
+                        yCxR=yC*xR#*grd%msk[i+1,j  ]
+                        yUxL=yU*xL#*grd%msk[i-1,j+1]
+                        yUxC=yU*xC#*grd%msk[i  ,j+1]
+                        yUxR=yU*xR#*grd%msk(i+1,j+1]
+                        yCxC=1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )
+
+                if element_type=='hexagon':
+                #if False:#element_type=='hexagon':
+                        H = min(( (np.sqrt(Area/(2*sqrt(3)))  / np.sqrt(grid_area))),1) ;  #Non dimensionalize element length by grid area. (This gives the non-dim Apothen of the hexagon)
+                        S=(2/np.sqrt(3))*H #Side of the hexagon
+                        if S>0.5:
+                                print( 'Elements must be smaller than a whole gridcell', 'i.e.: S= ' , S , '>=0.5',i,j)
+                                halt
+
+                        #Subtracting the position of the nearest corner from x,y
+                        origin_x=1 ; origin_y=1
+                        if x<0.5:
+                                origin_x=0
+                        if y<0.5:
+                                origin_y=0
+
+                        x0=(x-origin_x) #Position of the hexagon center, relative to origin at the nearest vertex
+                        y0=(y-origin_y)
+
+                        #(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Divide_hexagon_into_4_quadrants_old(x0,y0,H)
+                        (Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Hexagon_into_quadrants_using_triangles(x0,y0,H,0.)
+                        if min(min(Area_Q1,Area_Q2),min(Area_Q3, Area_Q4)) <0:
+                                print( 'Yolo')
+                                print( x0,y0,H)
+                                #print min(min(Area_Q1,Area_Q2),min(Area_Q3, Area_Q4))
+                                print( Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
+
+                        Area_Q1=Area_Q1/Area_hex
+                        Area_Q2=Area_Q2/Area_hex
+                        Area_Q3=Area_Q3/Area_hex
+                        Area_Q4=Area_Q4/Area_hex
+
+
+                        #Now, you decide which quadrant belongs to which mass on ocean cell.
+                        #Top right vertex
+                        if x>=0.5 and y>= 0.5:
+                                yUxR=Area_Q1
+                                yUxC=Area_Q2
+                                yCxC=Area_Q3
+                                yCxR=Area_Q4
+
+                        #Top left vertex
+                        if x<0.5 and y>= 0.5:
+                                yUxC=Area_Q1
+                                yUxL=Area_Q2
+                                yCxL=Area_Q3
+                                yCxC=Area_Q4
+
+                        #Bottom left vertex
+                        if x<0.5 and y< 0.5:
+                                yCxC=Area_Q1
+                                yCxL=Area_Q2
+                                yDxL=Area_Q3
+                                yDxC=Area_Q4
+
+                        #Bottom right vertex
+                        if x>=0.5 and y< 0.5:
+                                yCxR=Area_Q1
+                                yCxC=Area_Q2
+                                yDxC=Area_Q3
+                                yDxR=Area_Q4
+
+                        #if Sector<4 and Sector>-1:
+                        #       print Sector
+
+
+                        #Check that this is true
+                        if abs(yCxC-(1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )))>0.001:
+                                print ('All the mass is not being used!!!')
+                                #print W1 , W2 , W3 , W4 , W5 , W6
+                                #print Area_Upper, Area_Lower, Area_right, Area_left
+                                print( 'Areas: ',Area_hex,Area_hex*Area_Q1, Area_hex*Area_Q2, Area_hex*Area_Q3, Area_hex*Area_Q4)
+                                print( 'x0=',x0, 'y0=',y0, 'H=', H)
+                                print ('Total area= ',(Area_Q1+Area_Q2+Area_Q3+Area_Q4))#, Sector
+
+
+                #Accounting for masked points
+                a=1. ; b=1. ; c=1. ; d=1.
+                if i==0:
+                        a=0.;
+                if j==0:
+                        b=0.;
+                if i==Nx-1:
+                        c=0;
+                if j==Ny-1:
+                        d=0;
+
+                fraction_used= ((yDxL*a*b) + (yDxC*b) + (yDxR*b*c) +(yCxL*a) + (yCxR*c) + (yUxL*a*d) + (yUxC*d) + (yUxR*c*d) + (yCxC))
+                if static_berg>0.5:
+                        fraction_used=1.
+
+                mass_on_ocean[i,j,1]=mass_on_ocean[i,j,1]+(a*b*yDxL*Mass/fraction_used)
+                mass_on_ocean[i,j,2]=mass_on_ocean[i,j,2]+(b*yDxC*Mass/fraction_used)
+                mass_on_ocean[i,j,3]=mass_on_ocean[i,j,3]+(b*c*yDxR*Mass/fraction_used)
+                mass_on_ocean[i,j,4]=mass_on_ocean[i,j,4]+(a*yCxL*Mass/fraction_used)
+                mass_on_ocean[i,j,5]=mass_on_ocean[i,j,5]+(yCxC*Mass/fraction_used)
+                mass_on_ocean[i,j,6]=mass_on_ocean[i,j,6]+(c*yCxR*Mass/fraction_used)
+                mass_on_ocean[i,j,7]=mass_on_ocean[i,j,7]+(a*d*yUxL*Mass/fraction_used)
+                mass_on_ocean[i,j,8]=mass_on_ocean[i,j,8]+(d*yUxC*Mass/fraction_used)
+                mass_on_ocean[i,j,9]=mass_on_ocean[i,j,9]+(c*d*yUxR*Mass/fraction_used)
+
+
+                return mass_on_ocean
+
+
+def calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x, y, Lx):
+
+        Lx_2=Lx/2.
+
+        alpha=x2-x1
+        delta=y2-y1
+        beta=x4-x1
+        epsilon=y4-y1
+        gamma=(x3-x1)-(alpha+beta)
+        kappa=(y3-y1)-(delta+epsilon)
+
+        a=(kappa*beta-gamma*epsilon)
+        dx=np.mod(x-(x1-Lx_2),Lx)+(x1-Lx_2)-x1
+        dy=y-y1
+        b=(delta*beta-alpha*epsilon)-(kappa*dx-gamma*dy)
+        c=(alpha*dy-delta*dx)
+
+        #print 'alpha,beta,gamma',alpha,beta,gamma
+        #print 'delta,epsilon,kappa',delta,epsilon,kappa
+        #print 'dx,dy',dx,dy
+        #print 'A,B,C,',a,b,c
+
+        if (abs(a)>1.e-12):
+                d=0.25*(b**2)-a*c
+                if (d>=0.):
+                        yy1=-(0.5*b+sqrt(d))/a
+                        yy2=-(0.5*b-sqrt(d))/a
+                        if (abs(yy1-0.5).lt.abs(yy2-0.5)):
+                                yj=yy1;
+                        else:
+                                yj=yy2;
+                else:
+                        print ('ERROR', halt)
+        else:
+                if (b!=0.):
+                        yj=-c/b
+                else:
+                        yj=0.
+
+        a=(alpha+gamma*yj)
+        b=(delta+kappa*yj)
+        if (a!=0.):
+                xi=(dx-beta*yj)/a
+        elif (b!=0.):
+                xi=(dy-epsilon*yj)/b
+        else:
+                c=(epsilon*alpha-beta*delta)+(epsilon*gamma-beta*kappa)*yj
+                if (c!=0.):
+                        xi=(epsilon*dx-beta*dy)/c
+                else:
+                        print( 'ERROR', halt2)
+
+        return xi,yj
+
+
+
+def regrid_iceberg_thickness(lat,lon,Number_of_bergs,thickness,mass,h_ice,x,y,rho_ice,element_type,static_berg,plot_outcome=True):
+        Nx=len(x)  ; Ny=len(y)
+        dx=x[1]-x[0]    ;dy=y[1]-y[0]
+        New_mass=h_ice*0 #Initializing regrided field to zero
+        Area = [(mass[i]/(rho_ice*thickness[i])) for i in range(Number_of_bergs)] ;
+        grid_area=dx*dy #Assuming a regular grid
+        Orig_mass=h_ice*rho_ice*grid_area
+
+        mass_on_ocean=np.zeros([Nx,Ny,10])   #Setting up matrix to spread mass to ocean.  Note that I have used 10 points  so that I can ignore 0 and match with python numbering
+        #mass_on_ocean=np.zeros([Nx,Ny])   #Setting up matrix to spread mass to ocean.
+        #Note: You may want to import the grid that the ocean model actually sees.
+        for berg_count in range(Number_of_bergs):
+                x_val=lon[berg_count]
+                y_val=lat[berg_count]
+                Area_val=Area[berg_count]
+                mass_val=mass[berg_count]
+
+                j_val=int(floor(y_val/dy))
+                i_val=int(floor(x_val/dx))
+                x_cell=(x_val-x[i_val])/sqrt(grid_area)+0.5
+                y_cell=(y_val-y[j_val])/sqrt(grid_area)+0.5
+
+                #if plot_outcome==True:
+                #       print 'YOLO0', x_val-123626.65521,y_val
+                #       print 'YOLO1', x[i_val],y[j_val]
+                #       print 'YOLO2', x_cell,y_cell
+
+                #Using the same interpolation as in the model
+                #x1=x[i_val]-(dx/2.)   ; y1=y[j_val]-(dx/2.)
+                #x2=x[i_val]+(dx/2.) ; y2=y[j_val]-(dx/2.)
+                #x3=x[i_val]+(dx/2.) ; y3=y[j_val]+(dx/2.)
+                #x4=x[i_val]-(dx/2.) ; y4=y[j_val]+(dx/2.)
+                #[xi,yj]=calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x_val, y_val, Lx=100000000000000.)
+                #[x_cell,y_cell]=calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x_val, y_val, Lx=100000000000000.)
+                #print 'YOLO:x1,x2,x3,x4',x1,x2,x3,x4
+                #print 'YOLO:y1,y2,y3,y4',y1,y2,y3,y4
+                #print 'YOLO:xi,yj,x_cell,y_cell', xi,yj, x_cell,y_cell
+
+                mass_on_ocean=spread_mass_to_ocean(Nx,Ny,i_val,j_val,mass_on_ocean,x_cell,y_cell,Area_val,mass_val,element_type,grid_area,static_berg[berg_count])
+
+        #Adding mass_onto_ocean
+        for i in range(1,Nx-1):
+                for j in range(1,Ny-1):
+                        New_mass[j,i]=mass_on_ocean[i,j,5]  \
+                                        +  ( ( (mass_on_ocean[i-1,j-1,9]+mass_on_ocean[i+1,j+1,1])   \
+                                        +  (mass_on_ocean[i+1,j-1,7]+mass_on_ocean[i-1,j+1,3]) ) \
+                                        +   ( (mass_on_ocean[i-1,j  ,6]+mass_on_ocean[i+1,j  ,4])   \
+                                        +  (mass_on_ocean[i  ,j-1,8]+mass_on_ocean[i  ,j+1,2]) ) )
+
+        #Adding mass to boundary cells
+        for j in range(1,Ny-1):
+                i=0
+                New_mass[j,i]=mass_on_ocean[i,j,5] +  mass_on_ocean[i+1,j+1,1] +  mass_on_ocean[i+1,j-1,7] \
+                        +  mass_on_ocean[i+1,j  ,4]     +  mass_on_ocean[i  ,j-1,8] + mass_on_ocean[i  ,j+1,2]
+                i=Nx-1
+                New_mass[j,i]=mass_on_ocean[i,j,5] +  mass_on_ocean[i-1,j-1,9] + mass_on_ocean[i-1,j+1,3] \
+                                        +   mass_on_ocean[i-1,j ,6] + mass_on_ocean[i ,j-1,8]+mass_on_ocean[i ,j+1,2]
+
+        for i in range(1,Nx-1):
+                j=0
+                New_mass[j,i]=mass_on_ocean[i,j,5] +   mass_on_ocean[i+1,j+1,1] +  mass_on_ocean[i-1,j+1,3]  \
+                                +  mass_on_ocean[i-1,j  ,6] + mass_on_ocean[i+1,j  ,4] +  mass_on_ocean[i  ,j+1,2]
+
+                j=Ny-1
+                New_mass[j,i]=mass_on_ocean[i,j,5] +  mass_on_ocean[i-1,j-1,9]  +  mass_on_ocean[i+1,j-1,7] + \
+                                mass_on_ocean[i-1,j  ,6]+mass_on_ocean[i+1,j  ,4] +  mass_on_ocean[i  ,j-1,8]
+
+        #Corners
+        i=0 ;j=0
+        New_mass[j,i]=mass_on_ocean[i,j,5] + mass_on_ocean[i+1,j+1,1] + mass_on_ocean[i+1,j  ,4] + mass_on_ocean[i  ,j+1,2]
+        i=0 ;j=Ny-1
+        New_mass[j,i]=mass_on_ocean[i,j,5] + mass_on_ocean[i+1,j-1,7] + mass_on_ocean[i+1,j  ,4] + mass_on_ocean[i  ,j-1,8]
+        i=Nx-1; j=0
+        New_mass[j,i]=mass_on_ocean[i,j,5] + mass_on_ocean[i-1,j+1,3] + mass_on_ocean[i-1,j  ,6] + mass_on_ocean[i  ,j+1,2]
+        i=Nx-1; j=Ny-1
+        New_mass[j,i]=mass_on_ocean[i,j,5] + mass_on_ocean[i-1,j-1,9] + mass_on_ocean[i-1,j  ,6] + mass_on_ocean[i  ,j-1,8]
+
+
+        if plot_outcome==True: #MP2
+                #print 'Warning: the interpolation scheme is not the same as the one used in the model'
+
+                plot_data=(Orig_mass-New_mass)/Orig_mass
+                cNorm = mpl.colors.Normalize(vmin=-.1, vmax=.1)
+                vmax=np.max(abs(plot_data))
+                plt.pcolormesh(x,y,plot_data,cmap='bwr',norm=cNorm)
+                plt.title('Error between bergs and shelf')
+
+                #plot_data=(New_mass/New_thickness/rho_ice)
+                #vmax=np.max(abs(plot_data))
+                #cNorm = mpl.colors.Normalize(vmin=-vmax, vmax=vmax)
+                #plt.pcolormesh(x,y,plot_data,cmap='jet',norm=cNorm)
+                #plt.title('h_ice')
+
+                #plot_data=(New_mass-Orig_mass)/(rho_ice*grid_area)
+                #cNorm = mpl.colors.Normalize(vmin=-0.00000000001, vmax=0.00000000001)
+                #vmax=np.max(abs(plot_data))
+                #plt.pcolormesh(x,y,plot_data,cmap='bwr',norm=cNorm)
+
+                plt.colorbar()
+                #plt.xlim([min(x)-,max(x)])
+                #plt.ylim([min(y),max(y)])
+                #plt.show()
+
+        return New_mass
+
+def Switch_x_and_y_directions(lat,lon, A, B, C):
+        print( 'Switching x and y directions!!!')
+        lat_new=[]
+        lon_new=[]
+        for i in range(len(lat)):
+                lat_new.append(lon[i])
+                lon_new.append(lat[i])
+        M=A.shape
+        A_new=np.zeros([M[1],M[0]])
+        B_new=np.zeros([M[1],M[0]])
+        C_new=np.zeros([M[1],M[0]])
+        for i in range(M[0]):
+                for j in range(M[1]):
+                        A_new[j,i]=A[i,j]
+                        B_new[j,i]=B[i,j]
+                        C_new[j,i]=C[i,j]
+
+        return  [lat_new,lon_new,A_new,B_new, C_new]
+
+def interpolate_field_onto_new_grid(x,y,x_new,y_new,field):
+        xx, yy = np.meshgrid(x, y)
+        #f = interpolate.interp2d(x, y, field, kind='cubic')
+        f = interpolate.interp2d(x, y, field, kind='linear')
+        field_new = f(x_new, y_new)
+        return field_new
+
+def convert_input_to_catesian_coordinates(lon,lat,ice_mask,h_ice,R_earth,dx,lat_ref):
+        #Parameters
+        thickness_threshhold=0.01
+
+        lon_max=np.max(lon) ; lon_min=np.min(lon)
+        lat_max=np.max(lat) ; lat_min=np.min(lat)
+        #lat_ref=np.mean(lat)
+
+        #55.8 one more element of support near finger
+        #lat_ref=-55.75
+        print('lat_ref',lat_ref)
+        #llon,llat=np.meshgrid(lon,lat)
+        #lat_ref=np.mean(llat[np.where(h_ice>0.01)])
+        #print('lat_ref new',lat_ref)
+
+        #Converting to cartesian grid
+        x=(np.pi/180)*R_earth*np.cos(lat_ref*np.pi/180.)*lon
+        y=(np.pi/180)*R_earth*lat
+
+        # x=R_earth*np.cos(lat*np.pi/180)*np.cos(lon*np.pi/180)
+        # y=R_earth*np.cos(lon*np.pi/180)*np.cos(lat*np.pi/180)
+
+        print('minx',np.min(x))
+        print('maxx',np.max(x))
+        print('miny',np.min(y))
+        print('maxy',np.max(y))
+        #x=x-np.min(x)
+        #y=y-np.min(y)
+
+        #Creating regular grid
+        x_new=np.linspace(np.min(x), np.max(x), num=len(x))
+        y_new=np.linspace(np.min(y),np.max(y), num=len(y))
+        x_new=np.arange(np.min(x), np.max(x), step=dx)
+        y_new=np.arange(np.min(y), np.max(y), step=dx)
+
+        h_ice_new=interpolate_field_onto_new_grid(x,y,x_new,y_new,h_ice)
+        h_ice_new[np.where(h_ice_new<thickness_threshhold)]=0.
+        ice_mask_new=interpolate_field_onto_new_grid(x,y,x_new,y_new,ice_mask)
+        #ice_mask_new=np.round(ice_mask_new)
+        #print ice_mask_new[50,:]
+
+        return [x_new,y_new,ice_mask_new,h_ice_new]
+
+
+####################################################################################################################################################
+##########################################################  Main Program   #########################################################################
+####################################################################################################################################################
+
+def main(args):
+
+        #Flags
+        save_restart_files=args.save_restart_files
+        save_new_h_ice_file=args.save_new_h_ice_file
+        Convert_to_lat_lon=args.Convert_to_lat_lon
+        input_is_cartesian=args.input_is_cartesian
+        A68=args.A68
+
+        #Iceberg setup flags
+        only_choose_one_berg=args.only_choose_one_berg  ; chosen_berg_num=args.chosen_berg_num
+        scale_the_grid_to_lat_lon=args.scale_the_grid_to_lat_lon
+        adjust_lat_ref=args.adjust_lat_ref
+        set_all_thicknesses_to_one=args.set_all_thicknesses_to_one   ; Th_prescribed=args.Th_prescribed
+        uvel_in=args.uvel; vvel_in=args.vvel
+        Interpolate_from_four_corners=args.Interpolate_from_four_corners
+        Switch_x_and_y_to_rotate_90=args.Switch_x_and_y_to_rotate_90
+        set_all_domain_to_ice=args.set_all_domain_to_ice
+        Use_default_radius=args.Use_default_radius
+
+        #Static vs non-static flags
+        set_all_bergs_static_by_default=args.set_all_bergs_static_by_default
+        set_some_bergs_static_by_default=args.set_some_bergs_static_by_default
+        Make_icebergs_non_static_later=args.Make_icebergs_non_static_later
+
+        #Mass spreadng flags
+        element_type=args.element_type
+        Switch_regridding_element_type=args.Switch_regridding_element_type
+        Fill_in_the_boundaries=args.Fill_in_the_boundaries
+        regrid_icebergs_onto_grid=args.regrid_icebergs_onto_grid
+
+        #Plotting flags
+        Run_plotting_subroutine=args.Run_plotting_subroutine
+        plot_circles=args.plot_circles
+        plot_ice_mask=args.plot_ice_mask
+        plot_ice_thickness=args.plot_ice_thickness
+        plot_icebergs_positions=args.plot_icebergs_positions
+        plot_h_ice_new=args.plot_h_ice_new
+        plot_bonds=args.plot_bonds
+
+        #Bond related flags
+        Create_icebergs_bonds=args.Create_icebergs_bonds
+        break_some_bonds=args.break_some_bonds
+        Remove_stationary_bergs=args.Remove_stationary_bergs
+        Allow_bonds_for_static_iceberg=args.Allow_bonds_for_static_iceberg
+        Allow_bonds_with_boundary_bergs=args.Allow_bonds_with_boundary_bergs
+
+
+        #Which experiment
+        Ice_geometry_source=args.Ice_geometry_source
+        ISOMIP_reduced=args.ISOMIP_reduced
+        ISOMIP_ice_geometry_filename=args.ISOMIP_ice_geometry_filename
+        ISOMIP_reduced_ice_geometry_filename=args.ISOMIP_reduced_ice_geometry_filename
+        Weddell_ice_geometry_filename=args.Weddell_ice_geometry_filename
+        Generic_ice_geometry_filename=args.Generic_ice_geometry_filename
+
+
+        #Parameters
+        Radius=args.Radius
+        rho_ice=args.rho_ice
+        gravity=args.gravity
+        mass_scaling=args.mass_scaling
+        R_earth=args.R_earth
+        print('R_earth',R_earth)
+        buffer_number=args.buffer_number
+        ang_vel_in=args.ang_vel_prescribed
+        y_disp=args.displace_y
+        lat_ref=args.lat_ref_grid_to_cartesian
+        dx_in=args.dx
+        icethres=args.icethres
+
+        #Let interactive radius be different from radius for testing the model:
+        IA_scaling=args.IA_scaling
+
+        #Applying some special case flags
+        if Ice_geometry_source=='ISOMIP':
+                Convert_to_lat_lon=False       ; input_is_cartesian=True ;
+        if Ice_geometry_source=='Generic':
+                Convert_to_lat_lon=True       ; input_is_cartesian=False ; set_all_bergs_static_by_default=False ; Fill_in_the_boundaries=False ; Use_default_radius=False
+        if Ice_geometry_source=='Weddell':
+                Convert_to_lat_lon=False        ; input_is_cartesian=False
+
+        #Applying Warnings
+        if element_type=='square' and Interpolate_from_four_corners==True:
+                print ('Square packing with R dividing dx, works best with interpolation off.')
+
+        print( 'Element type= ', element_type, ';  Switched_regridding= ', Switch_regridding_element_type)
+        if break_some_bonds==True:
+                print ('Some bonds are being broken')
+
+        #####################################################################################
+        #####################################################################################
+        Radius=Radius/IA_scaling
+
+        if  Ice_geometry_source=='ISOMIP':
+                if ISOMIP_reduced==False:
+                        lon_init=0  ; lat_init=-70.  #latitude  of bottom left corner of iceberg
+                        (x,y,ice_mask,h_ice)=load_ISOMIP_ice_geometry(ISOMIP_ice_geometry_filename,buffer_number)
+                        ice_filename=ISOMIP_ice_geometry_filename
+                else:
+                        lon_init=0  ; lat_init=-70.  #latitude  of bottom left corner of iceberg
+                        (x,y,ice_mask,h_ice)=load_ISOMIP_reduced_ice_geometry(ISOMIP_reduced_ice_geometry_filename,buffer_number)
+                        ice_filename=ISOMIP_reduced_ice_geometry_filename
+
+        if  Ice_geometry_source=='Weddell':
+                lon_init=-32.9  ; lat_init=-70.  #latitude  of bottom left corner of iceberg
+                (x,y,ice_mask,h_ice)=load_Weddel_ice_geometry(Weddell_ice_geometry_filename)
+                ice_filename=Weddell_ice_geometry_filename
+                Radius=0.5*10000.
+
+        if  Ice_geometry_source=='Generic':
+                (x,y,ice_mask,h_ice, lon_init, lat_init)=load_generic_ice_geometry(Generic_ice_geometry_filename,y_disp)
+
+        if input_is_cartesian is False:
+                dx=dx_in #3500. #250. #1000.0 #2000.0 #4000.#1000.
+                if (lat_ref==-9999):
+                        lat_ref=np.mean(y)
+                lat_grid=y.copy() ; lon_grid=x.copy()+360; ice_mask_grid=h_ice.copy()
+                #print('ice_mask_grid',ice_mask_grid)
+                (x,y,ice_mask,h_ice)=convert_input_to_catesian_coordinates(x,y,ice_mask,h_ice,R_earth,dx,lat_ref)
+
+        if set_all_thicknesses_to_one==True:
+                print( 'All thicknesses being set equal to 1')
+                if set_all_domain_to_ice is True:
+                        ice_mask[:,:]=1.
+                h_ice[np.where(ice_mask>0.5)]=Th_prescribed
+
+        if Use_default_radius is True:
+                dx=x[1]-x[0]  #This is used as the ocean grid size
+                R_frac=0.45
+                if element_type=='square':
+                        Radius=R_frac*dx  #(less than half the grid size)
+                if element_type=='hexagon':
+                        Radius= (np.sqrt(3)/2.) *(R_frac*dx)   #(S is < half the grid size)
+        print ('Radius set to R= ' , Radius)
+
+        #lat_ref=np.max(y)
+        #Define the positions,thickness, mass,  of the icebergs
+
+        (Number_of_bergs,lon,lat,iceberg_num,dx_berg, dy_berg,thickness,ang_vel_out,uvel_out,vvel_out,mass,width,x,y,Radius,static_berg,N_bergs_before_bd)= Create_icebergs(lon_init,lat_init,\
+                                                                                                                                                                            Radius,R_earth, x, y,ice_mask,h_ice,A68,uvel_in,vvel_in,Convert_to_lat_lon,rho_ice,element_type,scale_the_grid_to_lat_lon,lat_ref,adjust_lat_ref,\
+                                                                                                                                                                            Interpolate_from_four_corners,Fill_in_the_boundaries, set_all_bergs_static_by_default,break_some_bonds,Remove_stationary_bergs,set_some_bergs_static_by_default,icethres)
+
+        print ('Maximum thickness:', np.max(thickness), np.min(thickness))
+        #Define the positions of the iceberg bonds
+        if Create_icebergs_bonds==True:
+                (Number_of_bonds, first_berg_num,first_berg_ine,first_berg_jne,first_berg_lat,first_berg_lon, other_berg_num,other_berg_ine, other_berg_jne,other_berg_lat,other_berg_lon)=\
+                                Define_iceberg_bonds(Number_of_bergs,iceberg_num,lat,lon,dx_berg, dy_berg,Radius,break_some_bonds,static_berg,Allow_bonds_for_static_iceberg\
+                                ,N_bergs_before_bd,Allow_bonds_with_boundary_bergs)
+
+        if Make_icebergs_non_static_later is True:
+                Change_static_berg_after_bonding(Number_of_bergs,lat,lon, static_berg)
+
+
+        temp_mass=[mass[i]/thickness[i] for i in range(len(thickness))]
+        if only_choose_one_berg==True:
+                (Number_of_bergs,lon,lat,thickness,width,mass,iceberg_num)= Select_just_one_berg(lon,lat,thickness,width,mass,iceberg_num,chosen_berg_num,static_berg)
+
+
+        if regrid_icebergs_onto_grid==True:
+                if scale_the_grid_to_lat_lon==True:
+                        print ('Regridding should be run with scale_the_grid_to_lat_lon off')
+                else:
+                        if Switch_regridding_element_type==True:
+                                if element_type=='square':
+                                        element_type='hexagon'
+                                else:
+                                        element_type='square'
+                        temp_thickness=[1. for i in thickness]
+                        temp_mass=[mass[i]/(thickness[i]*rho_ice) for i in range(len(thickness))]
+                        temp_rho_ice=1.
+                        New_area=regrid_iceberg_thickness(lat,lon,Number_of_bergs,temp_thickness,temp_mass,h_ice,x,y,temp_rho_ice,element_type,static_berg,plot_outcome=False)
+                        New_mass=regrid_iceberg_thickness(lat,lon,Number_of_bergs,thickness,mass,h_ice,x,y,rho_ice,element_type,static_berg,plot_outcome=False)
+                if save_new_h_ice_file==True:
+                        grid_area=(x[1]-x[0])*(x[1]-x[0])
+                        h_ice_new=New_mass*0
+                        M=h_ice.shape
+                        for j in range(M[0]):
+                                for i in range(M[1]):
+                                        if New_area[j,i]>0:
+                                                h_ice_new[j,i]=New_mass[j,i]/(rho_ice*New_area[j,i])
+
+        if Switch_x_and_y_to_rotate_90 is True:
+                [lat,lon, h_ice_new,New_area,New_mass]=Switch_x_and_y_directions(lat,lon, h_ice_new,New_area,New_mass)
+
+
+        if save_restart_files==True:
+
+                #Creating iceberg restart file
+                Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,ang_vel_in,uvel_out,vvel_out,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg)
+
+                #Creating bond restart file
+                if Create_icebergs_bonds==True:
+                        Create_bond_restart_file(Number_of_bonds,first_berg_num,first_berg_ine,first_berg_jne,other_berg_ine,other_berg_jne,iceberg_num,other_berg_num,Ice_geometry_source)
+
+                if save_new_h_ice_file==True:
+                        create_clipped_icethickness_file(h_ice_new,New_area,New_mass,grid_area,gravity,Ice_geometry_source)
+
+        # Plotting the positions and bonds of the newly formed formation
+        if Run_plotting_subroutine==True:
+                if Convert_to_lat_lon==True:
+                        plotting_iceberg_positions(lat,lon,Number_of_bergs,R_earth,Radius,IA_scaling,Convert_to_lat_lon,\
+                                                   plot_circles,h_ice,ice_mask_grid,lon_grid,lat_grid,plot_ice_mask,\
+                                                   plot_ice_thickness,thickness,plot_icebergs_positions,static_berg,\
+                                                   h_ice_new,plot_h_ice_new)
+                        # plotting_iceberg_positions(lat,lon,Number_of_bergs,R_earth,Radius,IA_scaling,Convert_to_lat_lon,\
+                        #                            plot_circles,h_ice,ice_mask,x,y,plot_ice_mask,plot_ice_thickness,\
+                        #                            thickness,plot_icebergs_positions,static_berg,h_ice_new,plot_h_ice_new)
+                if (plot_bonds==True) and (Create_icebergs_bonds):
+                        plotting_iceberg_bonds(first_berg_lat,first_berg_lon,other_berg_lat,other_berg_lon,Number_of_bonds)
+
+        #field=New_mass/(rho_ice*grid_area)
+        field=New_area/grid_area -1.
+        M=field.shape
+        #print 'field',(field[M[0]-1,:])
+        #print 'field',(field[M[0]-2,:])
+        #print 'h_ice',h_ice_new[:,:]
+        #print 'h_ice-1',h_ice_new[:,:]-1.
+        if Run_plotting_subroutine:
+                plt.show()
+        print ('Script complete')
+
+
+
+if __name__ == '__main__':
+        optCmdLineArgs= parseCommandLine()
+        main(optCmdLineArgs)
+        #sys.exit(main())
diff --git a/tests/a68/n6000_t2500.nml b/tests/a68/n6000_t2500.nml
new file mode 100644
index 0000000..97aafa3
--- /dev/null
+++ b/tests/a68/n6000_t2500.nml
@@ -0,0 +1,194 @@
+!#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_14_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=True -plot_circles=True -plot_h_ice_new=True -plot_ice_thickness=False -plot_ice_mask=False -plot_icebergs_positions=True -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -uvel=0.036 -vvel=-0.056
+&icebergs_driver_nml
+  !ni=45 !30 !number of elements, x direction
+  !nj=45 !30 !number of elements, y direction
+  a68_test=.true.
+  vert_int_ocean_vel=.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  ibdt=1800.0 !seconds
+  !ibuo=0.1 !ocean x velocity
+  !ibvo=0.0 !ocean y velocity
+  !ibui=0.0 !ice x velocity
+  !ibvi=0.0 !ice y velocity
+  ibhrs=720 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=999999999 !max number of timesteps
+  saverestart=.false.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+/
+
+&icebergs_nml
+
+    tau_is_velocity=.true.
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=1e6!1e7!34000.0 !4471.938678723104 !1000.0
+    spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=75!150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+    
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=25.!200.0
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 1.
+    frac_thres_n = 6000. !3000. !2.1e4 !12.
+    frac_thres_t = 2500. !1750. !35000. !12.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=1 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/a68/nov3_tests.nml b/tests/a68/nov3_tests.nml
new file mode 100644
index 0000000..dbe4e96
--- /dev/null
+++ b/tests/a68/nov3_tests.nml
@@ -0,0 +1,197 @@
+
+&icebergs_driver_nml
+  !ni=45 !30 !number of elements, x direction
+  !nj=45 !30 !number of elements, y direction
+  a68_test=.true.
+  vert_int_ocean_vel=.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  tau_is_velocity=.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=720 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=999999999 !max number of timesteps
+  saverestart=.false.
+  halo=4
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=0 !206 !326 !206 !206 for dec09_1PM, 326 for dec14_1PM !0 for static
+/
+
+&icebergs_nml
+
+    Rearth=6.378e6
+    tau_is_velocity=.true.
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=1e6!1e7!34000.0 !4471.938678723104 !1000.0
+    spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=200!75!150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-6!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=1.e4!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=25 !25.!200.0
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 1000000.0
+    frac_thres_n = 20000.0 !8000.0 !5575. !3000. !2.1e4 !12.
+    frac_thres_t = 6000.0 !4000.0 !5575. !1750. !35000. !12.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=4 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=2 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/a68/restart_for_nco.py b/tests/a68/restart_for_nco.py
new file mode 100755
index 0000000..a8bea5f
--- /dev/null
+++ b/tests/a68/restart_for_nco.py
@@ -0,0 +1,19 @@
+#!/usr/bin/env python
+
+import xarray as xr
+fname='./square_for_restart_od17.8_ydn.1.nc'
+test=xr.load_dataset(fname,decode_timedelta=False,decode_times=False)
+test2=test.copy()
+test2=test2.where(test2.day<test2.day.max(),drop=True)
+test2.to_netcdf('./square_for_restart_od17.8_ydn.1_without_last_ts.nc', format='NETCDF3_CLASSIC')
+
+
+# import xarray as xr
+# fname='./sq_ssf_ssg1.e4_od17.8_addsm.true._rectx-37.5285_y-55.2166_n23_t10.nc'
+# test=xr.load_dataset(fname,decode_timedelta=False,decode_times=False)
+# test2=test.copy()
+# test2=test2.where(test2.day<test2.day.max(),drop=True)
+# test2.to_netcdf('./sq_ssf_ssg1.e4_od17.8_addsm.true._rectx-37.5285_y-55.2166_n23_t10_without_last_ts.nc', format='NETCDF3_CLASSIC')
+
+
+# ncrcat square_for_restart_od17.8_ydn.1_without_last_ts.nc sq_ssf_ssg1.e4_od17.8_addsm.true._rectx-37.5285_y-55.2166_n23_t10_without_last_ts.nc sq_ssf_ssg1.e4_od17.8_addsm.true._rectx-37.5285_y-55.2166_n23_t10_full2.nc
diff --git a/tests/a68/save_input.nml b/tests/a68/save_input.nml
new file mode 100644
index 0000000..c862a41
--- /dev/null
+++ b/tests/a68/save_input.nml
@@ -0,0 +1,192 @@
+
+&icebergs_driver_nml
+  !ni=45 !30 !number of elements, x direction
+  !nj=45 !30 !number of elements, y direction
+  a68_test=.true.
+  vert_int_ocean_vel=.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  ibdt=1800.0 !seconds
+  !ibuo=0.1 !ocean x velocity
+  !ibvo=0.0 !ocean y velocity
+  !ibui=0.0 !ice x velocity
+  !ibvi=0.0 !ice y velocity
+  ibhrs=720 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=999999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.true.
+/
+
+&icebergs_nml
+
+    tau_is_velocity=.true.
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=1e7!34000.0 !4471.938678723104 !1000.0
+    spring_coef=1.e-4 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=100 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
+    
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=1.e5!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=10. !50.!200.0
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 1.
+    frac_thres_n = 4000. !3000. !2.1e4 !12.
+    frac_thres_t = 2000. !1750. !35000. !12.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=1 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/a68/square_for_restart.nml b/tests/a68/square_for_restart.nml
new file mode 100644
index 0000000..5462787
--- /dev/null
+++ b/tests/a68/square_for_restart.nml
@@ -0,0 +1,210 @@
+&icebergs_driver_nml
+  a68_test=.true.
+  vert_int_ocean_vel=.false.!.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  Old_wrong_Rearth_and_SSH=.false.
+  !mom_Rearth=.false.
+  !Rearth=6363827
+  Rearth=6.378e6
+  no_wind=.false.
+  tau_is_velocity=.true.!.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=298 !max number of timesteps
+  saverestart=.true. !.false. !.true. !.false.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=206 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
+/
+
+&icebergs_nml
+
+    !Rearth=6363827 !6.378e6 !6.371229e6 !6.36e6 !6.378e6
+    Rearth=6.378e6
+    A68_test=.false.
+    tau_is_velocity=.true.!.false.
+    ocean_drag_scale=15 !<od> !20. !1
+
+    add_curl_to_torque=.false.
+
+    constant_interaction_LW=.true.
+
+    traj_name='square_for_restart.nc' !<name>
+    bond_traj_name='square_for_restart_bonds.nc'
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
+    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=200 !75 !75 !150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=0.!1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=30!15!50. !15.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='none' !'stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 1
+    frac_thres_n = 25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
+    frac_thres_t = 11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.true. !.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='SQUARE_INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.false. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/a68/square_for_restart_od_17.8_ydn.1.nml b/tests/a68/square_for_restart_od_17.8_ydn.1.nml
new file mode 100644
index 0000000..2770143
--- /dev/null
+++ b/tests/a68/square_for_restart_od_17.8_ydn.1.nml
@@ -0,0 +1,211 @@
+&icebergs_driver_nml
+  a68_test=.true.
+  vert_int_ocean_vel=.false.!.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  Old_wrong_Rearth_and_SSH=.false.
+  !mom_Rearth=.false.
+  Rearth=6363827
+  no_wind=.false.
+  tau_is_velocity=.true.!.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=298 !max number of timesteps
+  saverestart=.true. !.false. !.true. !.false.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=206 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
+/
+
+&icebergs_nml
+
+    Rearth=6363827
+    A68_test=.true.
+    short_step_mts_grounding=.true.
+    
+    tau_is_velocity=.true.
+    ocean_drag_scale=17.8 !19.5 !<od>
+
+    skip_first_outer_mts_step=.true.
+    add_curl_to_torque=.false.
+
+    constant_interaction_LW=.true.
+
+    traj_name='square_for_restart_od17.8_ydn.1.nc' !<name>
+    bond_traj_name='square_for_restart_od17.8_ydn.1_bonds.nc'
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
+    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=200 !75 !75 !150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-4 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=0.!1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=0!30!15!50. !15.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 10000000
+    frac_thres_n = 25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
+    frac_thres_t = 11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.true. !.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.false. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/a68/square_for_restart_od_19.5_tn_ng_ydn.05.nml b/tests/a68/square_for_restart_od_19.5_tn_ng_ydn.05.nml
new file mode 100644
index 0000000..115c931
--- /dev/null
+++ b/tests/a68/square_for_restart_od_19.5_tn_ng_ydn.05.nml
@@ -0,0 +1,211 @@
+&icebergs_driver_nml
+  a68_test=.true.
+  vert_int_ocean_vel=.false.!.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  Old_wrong_Rearth_and_SSH=.false.
+  !mom_Rearth=.false.
+  Rearth=6363827
+  no_wind=.false.
+  tau_is_velocity=.true.!.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=298 !max number of timesteps
+  saverestart=.true. !.false. !.true. !.false.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=206 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
+/
+
+&icebergs_nml
+
+    Rearth=6363827
+    A68_test=.true.
+    short_step_mts_grounding=.true.
+    
+    tau_is_velocity=.true.
+    ocean_drag_scale=19.5 !<od>
+
+    skip_first_outer_mts_step=.true.
+    add_curl_to_torque=.false.
+
+    constant_interaction_LW=.true.
+
+    traj_name='square_for_restart_od19.5_ydn.05.nc' !<name>
+    bond_traj_name='square_for_restart_od19.5_ydn.05_bonds.nc'
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
+    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=200 !75 !75 !150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-4 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=0.!1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=0!30!15!50. !15.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 10000000
+    frac_thres_n = 25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
+    frac_thres_t = 11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.true. !.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.false. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/a68/square_for_restart_od_21.25_tn_ng_noyd.nml b/tests/a68/square_for_restart_od_21.25_tn_ng_noyd.nml
new file mode 100644
index 0000000..6a32b9a
--- /dev/null
+++ b/tests/a68/square_for_restart_od_21.25_tn_ng_noyd.nml
@@ -0,0 +1,211 @@
+&icebergs_driver_nml
+  a68_test=.true.
+  vert_int_ocean_vel=.false.!.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  Old_wrong_Rearth_and_SSH=.false.
+  !mom_Rearth=.false.
+  Rearth=6363827
+  no_wind=.false.
+  tau_is_velocity=.true.!.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=297 !8 !max number of timesteps
+  saverestart=.true. !.false. !.true. !.false.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=206 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
+/
+
+&icebergs_nml
+
+    Rearth=6363827
+    A68_test=.true.
+    short_step_mts_grounding=.true.
+    
+    tau_is_velocity=.true.
+    ocean_drag_scale=21.25 !<od>
+
+    skip_first_outer_mts_step=.true.
+    add_curl_to_torque=.false.
+
+    constant_interaction_LW=.true.
+
+    traj_name='square_for_restart_od21.25.nc' !<name>
+    bond_traj_name='square_for_restart_bonds_od21.25.nc'
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
+    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=200 !75 !75 !150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-4 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=0.!1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=0!30!15!50. !15.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 10000000
+    frac_thres_n = 25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
+    frac_thres_t = 11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.true. !.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.false. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/a68/square_r_lsf.nml b/tests/a68/square_r_lsf.nml
new file mode 100644
index 0000000..c0ceaac
--- /dev/null
+++ b/tests/a68/square_r_lsf.nml
@@ -0,0 +1,215 @@
+&icebergs_driver_nml
+  a68_test=.true.
+  vert_int_ocean_vel=.false.!.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  Old_wrong_Rearth_and_SSH=.false.
+  !mom_Rearth=.false.
+  !Rearth=6363827
+  Rearth=<rad>
+  !6.378e6
+  no_wind=.false.
+  tau_is_velocity=.true.!.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=120 !360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=999999999 !max number of timesteps
+  saverestart=.false. !.true. !.false.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=355 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
+/
+
+&icebergs_nml
+
+    Rearth=<rad> !6.378e6
+    A68_test=<a68> !.false.
+    A68_xdisp=<xd>
+    A68_ydisp=<yd>
+    tau_is_velocity=.true.!.false.
+    ocean_drag_scale=<od> !15
+
+    add_curl_to_torque=.false.
+
+    constant_interaction_LW=.true.
+
+    traj_name=sq_lsf_g<gc>_addsm<a68>_<xdw>_<ydw>_od<od>_n<ns>t<ts>.nc
+    !<name>
+    !bond_traj_name=<bname>
+    
+    no_frac_first_ts=.true.
+    break_bonds_on_sub_steps=.false. !.true.
+    
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
+    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=<ss> !75 !75 !150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-4 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=<gc>!1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=0!15!50. !15.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 1
+    frac_thres_n = <ns>e3
+    !75000.0
+    frac_thres_t = <ts>e3
+    !28000.
+
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='S_<od>_r/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.false. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/a68/square_r_lsf_comp.nml b/tests/a68/square_r_lsf_comp.nml
new file mode 100644
index 0000000..c273f5b
--- /dev/null
+++ b/tests/a68/square_r_lsf_comp.nml
@@ -0,0 +1,208 @@
+&icebergs_driver_nml
+  a68_test=.true.
+  vert_int_ocean_vel=.false.!.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  Old_wrong_Rearth_and_SSH=.false.
+  Rearth=<rad>
+  no_wind=.false.
+  tau_is_velocity=.true.!.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=120 !360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=999999999 !max number of timesteps
+  saverestart=.false. !.true. !.false.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=355 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
+/
+
+&icebergs_nml
+
+    Rearth=<rad> !6.378e6
+    A68_test=.false.
+    A68_xdisp=<xd>
+    A68_ydisp=<yd>
+    tau_is_velocity=.true.!.false.
+    ocean_drag_scale=<od> !15
+
+    add_curl_to_torque=.false.
+
+    constant_interaction_LW=.true.
+
+    traj_name=<name>
+    !bond_traj_name=<bname>
+    
+    no_frac_first_ts=.true.
+    break_bonds_on_sub_steps=.false. !.true.
+    
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
+    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=<ss> !75 !75 !150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-4 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=6.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=<gc>!1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=0!15!50. !15.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='computed' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 1
+    frac_thres_n = <ns>
+    frac_thres_t = <ts>
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='S_<od>_r/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.false. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/a68/square_r_ssf.nml b/tests/a68/square_r_ssf.nml
new file mode 100644
index 0000000..f39cef9
--- /dev/null
+++ b/tests/a68/square_r_ssf.nml
@@ -0,0 +1,209 @@
+&icebergs_driver_nml
+  a68_test=.true.
+  vert_int_ocean_vel=.false.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  Old_wrong_Rearth_and_SSH=.false.
+  Rearth=<rad>
+  no_wind=.false.
+  tau_is_velocity=.true.!.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=240 !360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=999999999 !max number of timesteps
+  saverestart=.false. !.true. !.false.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=355 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
+/
+
+&icebergs_nml
+    Rearth=<rad>
+    A68_test=<a68>
+    A68_xdisp=<xd>
+    A68_ydisp=<yd>
+    tau_is_velocity=.true.
+    ocean_drag_scale=<od>
+    short_step_mts_grounding=.true.
+
+    add_curl_to_torque=.false.
+
+    constant_interaction_LW=.true.
+
+    traj_name=sq_ssf_ssg<gc>_od<od>_addsm<a68>_rectx<xd>_y<yd>_n<ns>_t<ts>.nc
+    !bond_traj_name=<bname>
+
+    no_frac_first_ts=.true.
+    break_bonds_on_sub_steps=.true.
+    power_ground=<pg>
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
+    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=<ss> !75 !75 !150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-4 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=<gc>!1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=0!15!50. !15.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 1
+    frac_thres_n = <ns>e3
+    frac_thres_t = <ts>e3
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.false.!.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.false.!.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.false.!.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='<rdir>/' !'S_17.8_ydn.1_r/' !'S_19.5_ydn.05_r/' !'S_<od>_r/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.false. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/a68/tau_is.nml b/tests/a68/tau_is.nml
new file mode 100644
index 0000000..8a98758
--- /dev/null
+++ b/tests/a68/tau_is.nml
@@ -0,0 +1,197 @@
+&icebergs_driver_nml
+  a68_test=.true.
+  vert_int_ocean_vel=.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  Old_wrong_Rearth_and_SSH=.false.
+  tau_is_velocity=.true.!.false.!.true.!.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=720 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=400 !999999999 !max number of timesteps
+  saverestart=.false.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=0 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326
+/
+
+&icebergs_nml
+
+    Rearth=6.371229e6 !6.36e6 !6.378e6
+    tau_is_velocity=.true.!.false.!.true.!.false.
+
+    add_curl_to_torque=.false.!.true.
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=1e6!1e7!34000.0 !4471.938678723104 !1000.0
+    spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=75 !75 !150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=50. !15.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 1.0 !1.0
+    frac_thres_n = 6000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
+    frac_thres_t = 2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/a68/test1.nml b/tests/a68/test1.nml
new file mode 100644
index 0000000..96446d8
--- /dev/null
+++ b/tests/a68/test1.nml
@@ -0,0 +1,194 @@
+
+&icebergs_driver_nml
+  !ni=45 !30 !number of elements, x direction
+  !nj=45 !30 !number of elements, y direction
+  a68_test=.true.
+  vert_int_ocean_vel=.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  ibdt=1800.0 !seconds
+  !ibuo=0.1 !ocean x velocity
+  !ibvo=0.0 !ocean y velocity
+  !ibui=0.0 !ice x velocity
+  !ibvi=0.0 !ice y velocity
+  ibhrs=720 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=999999999 !max number of timesteps
+  saverestart=.false.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+/
+
+&icebergs_nml
+
+    tau_is_velocity=.true.
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=1e6!1e7!34000.0 !4471.938678723104 !1000.0
+    spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=75!150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+    
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=25.!200.0
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 1.
+    frac_thres_n = 12000. !3000. !2.1e4 !12.
+    frac_thres_t = 3000. !1750. !35000. !12.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=1 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/a68/test2.nml b/tests/a68/test2.nml
new file mode 100644
index 0000000..838de5a
--- /dev/null
+++ b/tests/a68/test2.nml
@@ -0,0 +1,196 @@
+!probably used an initial -uvel=0.18 -vvel=-0.23
+
+!./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_14_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_thickness=False -plot_ice_mask=False -plot_icebergs_positions=True -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -uvel=0.18 -vvel=-0.23 -R_earth=6360000
+&icebergs_driver_nml
+  !ni=45 !30 !number of elements, x direction
+  !nj=45 !30 !number of elements, y direction
+  a68_test=.true.
+  vert_int_ocean_vel=.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  ibdt=1800.0 !seconds
+  !ibuo=0.1 !ocean x velocity
+  !ibvo=0.0 !ocean y velocity
+  !ibui=0.0 !ice x velocity
+  !ibvi=0.0 !ice y velocity
+  ibhrs=720 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=999999999 !max number of timesteps
+  saverestart=.false.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+/
+
+&icebergs_nml
+
+    tau_is_velocity=.true.
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=1e6!1e7!34000.0 !4471.938678723104 !1000.0
+    spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=75!150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+    
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=25 !35!25.!200.0
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 1.
+    frac_thres_n = 6000. !3000. !2.1e4 !12.
+    frac_thres_t = 2500. !1750. !35000. !12.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=24 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/a68/test2_updated.nml b/tests/a68/test2_updated.nml
new file mode 100644
index 0000000..1cd6474
--- /dev/null
+++ b/tests/a68/test2_updated.nml
@@ -0,0 +1,201 @@
+#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_14_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_thickness=False -plot_ice_mask=False -plot_icebergs_positions=True -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -uvel=0.18 -vvel=-0.23 -R_earth=6360000
+
+&icebergs_driver_nml
+  !ni=45 !30 !number of elements, x direction
+  !nj=45 !30 !number of elements, y direction
+  a68_test=.true.
+  vert_int_ocean_vel=.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  Old_wrong_Rearth_and_SSH=.true.
+  tau_is_velocity=.true.!.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=720 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=400 !999999999 !max number of timesteps
+  saverestart=.false.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=0!305 !0 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326 !0 for static
+/
+
+&icebergs_nml
+
+    Rearth=6.36e6 !6.378e6
+    tau_is_velocity=.true.!.false.
+
+    add_curl_to_torque=.false.!.true.
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=1e6!1e7!34000.0 !4471.938678723104 !1000.0
+    spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=75 !150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=25.!200.0
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 1.0
+    frac_thres_n = 6000. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
+    frac_thres_t = 2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/a68/test3.nml b/tests/a68/test3.nml
new file mode 100644
index 0000000..4878421
--- /dev/null
+++ b/tests/a68/test3.nml
@@ -0,0 +1,198 @@
+!this test used the transient jra, but not the transient oscar surf vel data
+!./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_14_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=True -plot_circles=True -plot_h_ice_new=True -plot_ice_thickness=False -plot_ice_mask=False -plot_icebergs_positions=True -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -uvel=0.24 -vvel=-0.08
+
+&icebergs_driver_nml
+  !ni=45 !30 !number of elements, x direction
+  !nj=45 !30 !number of elements, y direction
+  a68_test=.true.
+  vert_int_ocean_vel=.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  tau_is_velocity=.true.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=720 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=999999999 !max number of timesteps
+  saverestart=.false.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=326!206 !206 for dec09_1PM, 326 for dec14_1PM
+/
+
+&icebergs_nml
+
+    tau_is_velocity=.true.
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=1e6!1e7!34000.0 !4471.938678723104 !1000.0
+    spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=100!75!150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-6!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=25 !25.!200.0
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 1.0
+    frac_thres_n = 8000.0 !8000.0 !5575. !3000. !2.1e4 !12.
+    frac_thres_t = 2500.0 !4000.0 !5575. !1750. !35000. !12.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false.!.true. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0!-56. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/a68/test4_curl.nml b/tests/a68/test4_curl.nml
new file mode 100644
index 0000000..bd67b9a
--- /dev/null
+++ b/tests/a68/test4_curl.nml
@@ -0,0 +1,199 @@
+
+&icebergs_driver_nml
+  !ni=45 !30 !number of elements, x direction
+  !nj=45 !30 !number of elements, y direction
+  a68_test=.true.
+  vert_int_ocean_vel=.false.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  tau_is_velocity=.true.!.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=720 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=400 !999999999 !max number of timesteps
+  saverestart=.false.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=305 !0 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326 !0 for static
+/
+
+&icebergs_nml
+
+    Rearth=6.378e6
+    tau_is_velocity=.true.!.false.
+
+    add_curl_to_torque=.true.!.false.!.true.
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=0.5e7!1e7!34000.0 !4471.938678723104 !1000.0
+    spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=100 !75 !150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-6!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=25.!200.0
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 1.0
+    frac_thres_n = 12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
+    frac_thres_t = 6000.0 !4000.0 !5575. !1750. !35000. !12.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/a68/test_new.nml b/tests/a68/test_new.nml
new file mode 100644
index 0000000..48da578
--- /dev/null
+++ b/tests/a68/test_new.nml
@@ -0,0 +1,204 @@
+!./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_14a_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_thickness=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -R_earth=6.371229e6 -lat_ref_grid_to_cartesian=-55.8 -uvel=0.2 -vvel=-0.2 !
+
+!in makeberg.py
+!if ice_mask[j_val,i_val]>0.5:#99:
+!                it_is_ice=True
+!dx=250.
+
+&icebergs_driver_nml
+  a68_test=.true.
+  vert_int_ocean_vel=.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  Old_wrong_Rearth_and_SSH=.false.
+  tau_is_velocity=.false.!.true.!.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=720 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=400 !999999999 !max number of timesteps
+  saverestart=.false.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=0 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326
+/
+
+&icebergs_nml
+
+    Rearth=6.371229e6 !6.36e6 !6.378e6
+    tau_is_velocity=.false.!.true.!.false.
+
+    add_curl_to_torque=.false.!.true.
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=1e6!1e7!34000.0 !4471.938678723104 !1000.0
+    spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=75 !75 !150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=15.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 1.0 !1.0
+    frac_thres_n = 6000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
+    frac_thres_t = 2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/a68/test_new2.nml b/tests/a68/test_new2.nml
new file mode 100644
index 0000000..b801bfe
--- /dev/null
+++ b/tests/a68/test_new2.nml
@@ -0,0 +1,204 @@
+!./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_14a_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_thickness=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -R_earth=6.371229e6 -lat_ref_grid_to_cartesian=-55.8 -uvel=0.2 -vvel=-0.2
+
+&icebergs_driver_nml
+  a68_test=.true.
+  vert_int_ocean_vel=.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  Old_wrong_Rearth_and_SSH=.false.
+  tau_is_velocity=.false. !.true.!.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=360 !15 days !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=400 !999999999 !max number of timesteps
+  saverestart=.false.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=0!330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
+/
+
+&icebergs_nml
+
+    Rearth=6.371229e6 !6.36e6 !6.378e6
+    tau_is_velocity=.false.!.true.!.false.
+
+    add_curl_to_torque=.false.
+
+    constant_interaction_LW=.true.
+
+    !traj_name="traj_p5e7.nc"
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=1e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
+    !spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=75 !75 !150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=15!50. !15.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 1.0
+    frac_thres_n = 4750.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
+    frac_thres_t = 2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.false. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/a68/test_no_bonds.nml b/tests/a68/test_no_bonds.nml
new file mode 100644
index 0000000..762d2c1
--- /dev/null
+++ b/tests/a68/test_no_bonds.nml
@@ -0,0 +1,211 @@
+&icebergs_driver_nml
+  a68_test=.true.
+  vert_int_ocean_vel=.false.!.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  Old_wrong_Rearth_and_SSH=.false.
+  !mom_Rearth=.false.
+  Rearth=6363827
+  no_wind=.false.
+  tau_is_velocity=.true.!.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=432 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=999999 !max number of timesteps
+  saverestart=.false.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=206 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
+/
+
+&icebergs_nml
+
+    Rearth=6363827
+    A68_test=.true.
+    short_step_mts_grounding=.true.
+    
+    tau_is_velocity=.true.
+    ocean_drag_scale=17.8 !19.5 !<od>
+
+    skip_first_outer_mts_step=.true.
+    add_curl_to_torque=.false.
+
+    constant_interaction_LW=.true.
+
+    traj_name='test_no_bonds.nc' !<name>
+    !bond_traj_name='square_for_restart_od17.8_ydn.1_bonds.nc'
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=1.e-30 !5e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
+    spring_coef=1.e-30 !0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=200 !75 !75 !150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-4 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=0.1 !4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=0.!1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=0!30!15!50. !15.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 10000000
+    frac_thres_n = 25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
+    frac_thres_t = 11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.false. !.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.false. !.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.false !.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.false. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/dem_cbeam_test/input.nml b/tests/dem_cbeam_test/input.nml
index 50d2e0f..3dea833 100644
--- a/tests/dem_cbeam_test/input.nml
+++ b/tests/dem_cbeam_test/input.nml
@@ -20,6 +20,8 @@
 
 &icebergs_nml
 
+    orig_dem_moment_of_inertia=.true.
+
     !defaults given in parentheses:
     dem_beam_test=2
     dem=.true.
diff --git a/tests/dem_ground_frac_test_big/.gitignore b/tests/dem_ground_frac_test_big/.gitignore
new file mode 100644
index 0000000..68bcbc9
--- /dev/null
+++ b/tests/dem_ground_frac_test_big/.gitignore
@@ -0,0 +1 @@
+results/
\ No newline at end of file
diff --git a/tests/dem_ground_frac_test_big/README b/tests/dem_ground_frac_test_big/README
new file mode 100644
index 0000000..ec575a8
--- /dev/null
+++ b/tests/dem_ground_frac_test_big/README
@@ -0,0 +1,7 @@
+1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
+2.(optional) edit input.nml
+3. run the model: ./RUN
+4, animate the results: animate_trajectories.py
+
+This is a good test for visualizing fracture dependence on particle size. Try running makeberg.py with the full radius and then half the radius, and with regular vs dem nmls. Make sure to edit the nmls so that contact distance is halved when radius is halved
+
diff --git a/tests/dem_ground_frac_test_big/RUN b/tests/dem_ground_frac_test_big/RUN
new file mode 100755
index 0000000..3dfc97d
--- /dev/null
+++ b/tests/dem_ground_frac_test_big/RUN
@@ -0,0 +1,7 @@
+rm iceberg_trajectories.nc
+rm iceberg_trajectories.nc.*
+rm bond_trajectories.nc
+rm bond_trajectories.nc.*
+srun -n1 ./../../build/bergs.x
+
+
diff --git a/tests/dem_ground_frac_test_big/animate_trajectories.py b/tests/dem_ground_frac_test_big/animate_trajectories.py
new file mode 100755
index 0000000..d163b57
--- /dev/null
+++ b/tests/dem_ground_frac_test_big/animate_trajectories.py
@@ -0,0 +1,161 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+import matplotlib.pyplot as plt
+from matplotlib.animation import FuncAnimation
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
+                    help=''' provide filename to plot''')
+    parser.add_argument('-s', type=int, default='14000',
+                        help='''plotted particle size''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+
+
+def main(args):
+
+    print('reading file')
+
+    filename=args.fname
+    psize=args.s
+    #filename = 'iceberg_trajectories.nc'
+    field = 'lon'
+    field2 = 'lat'
+
+    with nc.Dataset(filename) as file:
+        x = file.variables['lon'][:]/1.e3
+        y = file.variables['lat'][:]/1.e3
+        day = file.variables['day'][:]
+        length = file.variables['length'][:]
+        width = file.variables['width'][:]
+        thick = file.variables['thickness'][:]
+        od = file.variables['od'][:]
+
+    ud = np.unique(day)
+    t = ud[0]
+
+    radius = length*width*(1./(2*np.sqrt(3)))
+
+    #for determining if grounded:
+    rho_bergs=850.
+    rho_seawater=1025.
+    h_to_ground=20 #200.
+    draught=(rho_bergs/rho_seawater)*thick
+    if (h_to_ground==0):
+        groundfrac=draught-od
+    else:
+        groundfrac=1.-(od-draught)/h_to_ground
+    groundfrac[groundfrac<0.]=0.
+    groundfrac[groundfrac>1.]=1.
+
+    #groundfrac[thick<200.]=0.
+    #groundfrac[thick>=200.]=1.
+
+
+    # frame info
+    num_frames = len(ud)
+    movie_len = 5 #seconds
+    #frame_len = 1000.0*movie_len/num_frames/10000000
+    frame_len = movie_len/num_frames/1000
+
+    xmin = 40
+    xmax = 100
+    ymin = 20 #xmin
+    ymax = 80 #xmax
+
+    anim_running = True
+
+    def animate(i):
+
+        x1 = x[day == ud[i]]
+        y1 = y[day == ud[i]]
+        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
+
+        scat.set_offsets(data)
+
+        t = ud[i]
+        time_text.set_text('time = %.1f days' % t )
+
+        r1 = radius[day == ud[i]]
+        scat.set_sizes(r1/psize)
+
+        hstat = groundfrac[day == ud[i]]
+        cstring=[]
+        for j in range(len(hstat)):
+            if (hstat[j]==0):
+                cstring.append("none")
+            else:
+                cstring.append("b")
+        scat.set_color(cstring)
+        scat.set_edgecolor('r')
+
+        return scat,time_text
+
+    def init():
+        scat.set_offsets([])
+        return scat,
+
+    def onClick(event):
+        global anim_running
+        if anim_running:
+            ani.event_source.stop()
+            anim_running = False
+        else:
+            ani.event_source.start()
+            anim_running = True
+
+    # Now we can do the plotting!
+    f = plt.figure(figsize=(5,5))
+    f.tight_layout()
+    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
+    scat = ax1.scatter([],[],marker='o')#,edgecolor='red')
+    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
+
+    # Change major ticks to show every 20.
+    ax1.xaxis.set_major_locator(MultipleLocator(5))
+    ax1.yaxis.set_major_locator(MultipleLocator(5))
+
+    ax1.xaxis.set_minor_locator(MultipleLocator(1))
+    ax1.yaxis.set_minor_locator(MultipleLocator(1))
+
+    # Turn grid on for both major and minor ticks and style minor slightly
+    # differently.
+    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
+    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
+
+    ax1.set_xlabel('x (km)')
+    ax1.set_ylabel('y (km)')
+    ax1.set_title('Iceberg trajectory')
+
+    f.canvas.mpl_connect('button_press_event', onClick)
+
+    ani = FuncAnimation(
+        f,animate,init_func=init,frames=num_frames,
+        interval=frame_len,blit=True,repeat=True)
+
+    print('time',t)
+
+    plt.show()
+    #animation.save("iceberg_traj_animation.mp4")
+
+
+print('Script complete')
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
diff --git a/tests/dem_ground_frac_test_big/diag_table b/tests/dem_ground_frac_test_big/diag_table
new file mode 100644
index 0000000..c1c8819
--- /dev/null
+++ b/tests/dem_ground_frac_test_big/diag_table
@@ -0,0 +1,3 @@
+"icebergs test"
+1 1 1 0 0 0
+
diff --git a/tests/dem_ground_frac_test_big/input.nml b/tests/dem_ground_frac_test_big/input.nml
new file mode 100644
index 0000000..5464dbd
--- /dev/null
+++ b/tests/dem_ground_frac_test_big/input.nml
@@ -0,0 +1,199 @@
+
+&icebergs_driver_nml
+  ni=45 !30 !number of elements, x direction
+  nj=45 !30 !number of elements, y direction
+  gridres=5000.0
+  ibdt=1800.0 !seconds
+  ibuo=0.1 !ocean x velocity
+  ibvo=0.1 !-0.1 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=999999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.true.
+  collision_test=.false.
+  big_grounding_test=.true.
+  bump_depth=50. !200.0 !(m) depth of top of gaussian bump below sea level
+/
+
+&icebergs_nml
+
+    constant_interaction_LW=.true.
+    !traj_name=test_dem.nc
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    break_bonds_on_sub_steps=.true.
+    
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5. A=L*W always works?
+    dem_spring_coef=5e6 !5e6 !1e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=0.00015094124684696098 !dem_spring_coef=1.e6, r=1500, and hex pack
+    !spring_coef=0.0030188249369392196 !dem_spring_coef=5.e6, r=750, and hex pack!
+    !spring_coef=0.0006037649873878439 !dem_spring_coef=1.e6, r=750, and hex pack
+    spring_coef=0.0007547062342348049 !if dem_spring_coef=5e6, r=1500, and hex pack?
+    !spring_coef=0.0015094124684696098 !dem_spring_coef=1.e7, r=1500, and hex pack
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=200 !75 !(-1) # of mts sub-steps
+    explicit_inner_mts=.true.
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=6.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-8 !(default=spring_coeff) Berg spring coeff for collisions
+
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=1.e5 !3.16e6 !for power-law-type friction
+    h_to_init_grounding=20 !200.0
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.false.!.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='computed_s' !'stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 1.05 !0.75 !0.5
+    frac_thres_n = 2000 !1850 !!!1000 !2250 !4100
+    frac_thres_t = 1000 !1200 !1450 !500 !!!1500 !800 !10000000 !800 !1400
+
+
+    halo=3 !(4) halo width
+    Lx=225000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0.1 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=24000 ! (24) Period between verbose messages
+    traj_sample_hrs=0.5 !-1!0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=0.5 !-1!0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=1600.0!800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/dem_ground_frac_test_big/makeberg/RUN b/tests/dem_ground_frac_test_big/makeberg/RUN
new file mode 100755
index 0000000..520d671
--- /dev/null
+++ b/tests/dem_ground_frac_test_big/makeberg/RUN
@@ -0,0 +1,3 @@
+rm ./output_files/Generic*
+./makeberg.py
+cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
diff --git a/tests/dem_ground_frac_test_big/makeberg/makeberg.py b/tests/dem_ground_frac_test_big/makeberg/makeberg.py
new file mode 100755
index 0000000..1fe1baa
--- /dev/null
+++ b/tests/dem_ground_frac_test_big/makeberg/makeberg.py
@@ -0,0 +1,376 @@
+#!/usr/bin/env python
+import numpy as np
+import math
+from netCDF4 import Dataset
+from pylab import *
+#import pdb
+import netCDF4 as nc
+
+#
+# Initialize 2 iceberg elements, which can later be bonded in the fortran code if needed
+#
+
+def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
+
+	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
+	# To copy the global attributes of the netCDF file
+
+	#Input and output files
+	#Create Empty restart file. This is later read so that the attributes can be used.
+	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
+	create_empty_iceberg_restart_file(Empty_restart_filename)
+	#Empty_restart_filename='input_files/icebergs.res.nc'
+
+	#Read empty restart file
+	f=Dataset(Empty_restart_filename,'r') # r is for read only
+	#Write a new restart file
+	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
+
+	for attname in f.ncattrs():
+		    setattr(g,attname,getattr(f,attname))
+
+
+	# To copy the dimension of the netCDF file
+	for dimname,dim in f.dimensions.iteritems():
+		# if you want to make changes in the dimensions of the new file
+		# you should add your own conditions here before the creation of the dimension.
+		#g.createDimension(dimname,len(dim))
+		g.createDimension(dimname,Number_of_bergs)
+
+	# To copy the variables of the netCDF file
+
+	for varname,ncvar in f.variables.iteritems():
+		# if you want to make changes in the variables of the new file
+		# you should add your own conditions here before the creation of the variable.
+		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
+		#Proceed to copy the variable attributes
+		for attname in ncvar.ncattrs():
+			setattr(var,attname,getattr(ncvar,attname))
+		#Finally copy the variable data to the new created variable
+		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
+
+		if varname=='i':
+			var[:]=Number_of_bergs
+
+		if varname=='iceberg_num':
+			for j in range(Number_of_bergs):
+				#var[j]=j+1
+				var[j]=iceberg_num[j]
+
+		if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
+		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
+		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
+		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
+			var[:]=0
+
+                if varname=='uvel':
+                        var[:]=uvel
+
+                if varname=='vvel':
+                        var[:]=vvel
+
+		if varname=='mass_scaling':
+			var[:]=mass_scaling
+
+		if varname=='thickness':
+			for j in range(Number_of_bergs):
+				var[j]=thickness[j]
+
+		if varname=='mass':
+			for j in range(Number_of_bergs):
+				var[j]=mass[j]
+
+		if varname=='width'  or varname=='length':
+			for j in range(Number_of_bergs):
+				var[j]=width[j]
+
+		if varname=='lon':
+			for j in range(Number_of_bergs):
+				var[j]=lon[j]
+
+		if varname=='lat':
+			for j in range(Number_of_bergs):
+				var[j]=lat[j]
+
+		if varname=='static_berg':
+			for j in range(Number_of_bergs):
+				var[j]=static_berg[j]
+
+
+	f.close()
+	g.close()
+
+
+def create_empty_iceberg_restart_file(Empty_restart_filename):
+
+	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
+
+	i=f.createDimension('i', None)
+	lon=f.createVariable('i','i')
+
+	lon=f.createVariable('lon','d',('i'))
+	lon.long_name = "longitude" ;
+	lon.units = "degrees_E" ;
+	lon.checksum = "               0" ;
+
+	lat=f.createVariable('lat','d',('i'))
+	lat.long_name = "latitude" ;
+	lat.units = "degrees_N" ;
+	lat.checksum = "               0" ;
+
+	uvel=f.createVariable('uvel','d',('i'))
+	uvel.long_name = "zonal velocity" ;
+	uvel.units = "m/s" ;
+	uvel.checksum = "               0" ;
+
+	vvel=f.createVariable('vvel','d',('i'))
+	vvel.long_name = "meridional velocity" ;
+	vvel.units = "m/s" ;
+	vvel.checksum = "               0" ;
+
+	mass=f.createVariable('mass','d',('i'))
+	mass.long_name = "mass" ;
+	mass.units = "kg" ;
+	mass.checksum = "               0" ;
+
+	axn=f.createVariable('axn','d',('i'))
+	axn.long_name = "explicit zonal acceleration" ;
+	axn.units = "m/s^2" ;
+	axn.checksum = "               0" ;
+
+	ayn=f.createVariable('ayn','d',('i'))
+	ayn.long_name = "explicit meridional acceleration" ;
+	ayn.units = "m/s^2" ;
+	ayn.checksum = "               0" ;
+
+	bxn=f.createVariable('bxn','d',('i'))
+	bxn.long_name = "inplicit zonal acceleration" ;
+	bxn.units = "m/s^2" ;
+	bxn.checksum = "               0" ;
+
+	byn=f.createVariable('byn','d',('i'))
+	byn.long_name = "implicit meridional acceleration" ;
+	byn.units = "m/s^2" ;
+	byn.checksum = "               0" ;
+
+	ine=f.createVariable('ine','i',('i'))
+	ine.long_name = "i index" ;
+	ine.units = "none" ;
+	ine.packing = 0 ;
+	ine.checksum = "               0" ;
+
+	jne=f.createVariable('jne','i',('i'))
+	jne.long_name = "j index" ;
+	jne.units = "none" ;
+	jne.packing = 0 ;
+	jne.checksum = "               0" ;
+
+	thickness=f.createVariable('thickness','d',('i'))
+	thickness.long_name = "thickness" ;
+	thickness.units = "m" ;
+	thickness.checksum = "               0" ;
+
+	width=f.createVariable('width','d',('i'))
+	width.long_name = "width" ;
+	width.units = "m" ;
+	width.checksum = "               0" ;
+
+	length=f.createVariable('length','d',('i'))
+	length.long_name = "length" ;
+	length.units = "m" ;
+	length.checksum = "               0" ;
+
+	start_lon=f.createVariable('start_lon','d',('i'))
+	start_lon.long_name = "longitude of calving location" ;
+	start_lon.units = "degrees_E" ;
+	start_lon.checksum = "               0" ;
+
+	start_lat=f.createVariable('start_lat','d',('i'))
+	start_lat.long_name = "latitude of calving location" ;
+	start_lat.units = "degrees_N" ;
+	start_lat.checksum = "               0" ;
+
+	start_year=f.createVariable('start_year','i',('i'))
+	start_year.long_name = "calendar year of calving event" ;
+	start_year.units = "years" ;
+	start_year.packing = 0 ;
+	start_year.checksum = "               0" ;
+
+	iceberg_num=f.createVariable('iceberg_num','i',('i'))
+	iceberg_num.long_name = "identification of the iceberg" ;
+	iceberg_num.units = "dimensionless" ;
+	iceberg_num.packing = 0 ;
+	iceberg_num.checksum = "               0" ;
+
+	start_day=f.createVariable('start_day','d',('i'))
+	start_day.long_name = "year day of calving event" ;
+	start_day.units = "days" ;
+	start_day.checksum = "               0" ;
+
+	start_mass=f.createVariable('start_mass','d',('i'))
+	start_mass.long_name = "initial mass of calving berg" ;
+	start_mass.units = "kg" ;
+	start_mass.checksum = "               0" ;
+
+	mass_scaling=f.createVariable('mass_scaling','d',('i'))
+	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
+	mass_scaling.units = "none" ;
+	mass_scaling.checksum = "               0" ;
+
+	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
+	mass_of_bits.long_name = "mass of bergy bits" ;
+	mass_of_bits.units = "kg" ;
+	mass_of_bits.checksum = "               0" ;
+
+	heat_density=f.createVariable('heat_density','d',('i'))
+	heat_density.long_name = "heat density" ;
+	heat_density.units = "J/kg" ;
+	heat_density.checksum = "               0" ;
+
+	halo_berg=f.createVariable('halo_berg','d',('i'))
+	halo_berg.long_name = "halo_berg" ;
+	halo_berg.units = "dimensionless" ;
+	halo_berg.checksum = "               0" ;
+
+	static_berg=f.createVariable('static_berg','d',('i'))
+	static_berg.long_name = "static_berg" ;
+	static_berg.units = "dimensionless" ;
+	static_berg.checksum = "               0" ;
+
+	f.sync()
+	f.close()
+
+
+
+#-----------------------------------#
+#               Main                #
+#-----------------------------------#
+
+# just2particles=False
+# flip2ndconglom=True#False
+# offset2ndconglom=True#False
+
+grdxmin=0; grdxmax=225000e3
+grdymin=0; grdymax=225000e3
+grdres=5000.0
+R_frac=0.45 #1st option
+#R_frac=0.5*0.45 #2nd option
+#radius=(np.sqrt(3)/2.)*(R_frac*grdres) #S is < 0.5 grid res
+radius=1.5e3 #/2
+#radius2=(np.sqrt(3)/2.)*(R_frac2*grdres) #S is < 0.5 grid res
+thickness1=200.0
+thickness2=200.0
+rho_ice=850.0
+
+
+nbergs=1 #number of conglomerates
+
+#center coords of each (rectangular) conglomerate berg (CB=conglomerate berg)
+CBxc=np.array([50000]); CByc=np.array([50000])
+#side lengths
+CBxl=np.array([15000]); CByl=np.array([35000])
+
+
+CByl=CByl.astype(int); CBxl=CBxl.astype(int)
+
+#--- xmax, xmin, ymax, ymin for each CB --
+CBxmin=CBxc-(0.5*CBxl); CBxmax=CBxc+(0.5*CBxl)
+CBymin=CByc-(0.5*CByl); CBymax=CByc+(0.5*CByl)
+#this shouldn't happen:
+CBxmin[CBxmin<grdxmin]=grdxmin; CBxmax[CBxmax>grdxmax]=grdxmax
+CBymin[CBxmin<grdymin]=grdymin; CBymax[CBymax>grdymax]=grdymax
+CBxc=0.5*(CBxmin+CBxmax); CByc=0.5*(CBymin+CBymax)
+
+# #if just want one particle per CB
+# if just2particles:
+#         CBxmin=CBxc; CBxmax=CBxc
+#         CBymin=CByc; CBymax=CByc
+
+#--- min and max thicknesses for each CB ---
+h1=thickness1
+h2=thickness2
+CBhmax=np.array([h1]); CBhmin=np.array([h2])
+
+#radii
+CBrad=np.array([radius])
+print('radii',CBrad)
+
+berg_x=[]; berg_y=[]
+berg_id=[]; berg_static=[]
+berg_width=[]; berg_bonds=[]
+berg_h=[]; berg_mass_scaling=[]
+berg_mass=[]
+berg_uvel=[]; berg_vvel=[]
+
+berg_count=0
+
+for i in range(nbergs):
+        x_start=CBxmin[i]+(CBrad[i]*2./np.sqrt(3))
+
+        # if flip2ndconglom and i>0:
+        #         x_start=CBxmax[i]-(CBrad[i]*2./np.sqrt(3))
+
+        #pdb.set_trace()
+        if x_start>CBxmax[i]:
+                x_start=CBxmax[i]
+        y_start0=CBymin[i]+CBrad[i]
+        if y_start0>CBymax[i]:
+                y_start0=CBymax[i]
+        element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*(CBrad[i])**2)
+        #H (thickness) is a linear function of a berg element's position from the
+        #center of the CB. H=Hmax at the center of the CB and H=Hmin at a corner of the
+        #CB, where the dist of a corner from the center is:
+        cdistb=np.sqrt((CBxmin[i]-CBxc[i])**2+(CBymin[i]-CByc[i])**2)
+        j=0
+        x_val=x_start
+        offset=0.0
+        # if (i==0):
+        uvel=0.1#1
+        # else:
+        #         uvel=-0.15#-0.05
+        #         if (offset2ndconglom):
+        #                 offset=250.0
+        vvel=0.0#25
+        #uvel=0;vvel=0
+        #berg_count_start=berg_count
+        while x_val<=CBxmax[i] and x_val>=CBxmin[i]:
+                y_start=y_start0+((j%2)*CBrad[i])+offset
+                k=0
+                y_val=y_start
+                while y_val<=(CBymax[i]+offset):
+                        berg_count=berg_count+1
+                        berg_id.append(berg_count)
+                        berg_x.append(x_val)
+                        berg_y.append(y_val)
+                        berg_width.append(sqrt(element_area))
+                        #dist of berg elem from center of CB
+                        bdistc=np.sqrt((x_val-CBxc[i])**2+(y_val-CByc[i])**2)
+                        bh=CBhmin[i]*bdistc/cdistb + CBhmax[i]*(1-bdistc/cdistb)
+                        # if (just2particles):
+                        #         bh=h1
+                        berg_h.append(bh) #thickness
+                        berg_mass_scaling.append(1)
+                        berg_mass.append(bh*rho_ice*element_area)
+                        berg_static.append(0)
+                        berg_uvel.append(uvel)
+                        berg_vvel.append(vvel)
+                        # if (x_val<22000):
+                        #         berg_vvel.append(vvel)
+                        # else:
+                        #         berg_vvel.append(0.4)
+                        #berg_CBid.append(i)
+                        k=k+1
+                        y_val=y_start+(2*k*CBrad[i])
+                j=j+1
+                # if flip2ndconglom and i>0:
+                #         x_val=x_start-(np.sqrt(3)*CBrad[i]*j)
+                # else:
+                x_val=x_start+(np.sqrt(3)*CBrad[i]*j)
+
+print('Number of bergs',berg_count)
+
+#pdb.set_trace()
+
+#Create iceberg restart file
+Ice_geometry_source='Generic'
+Create_iceberg_restart_file(berg_count,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)
diff --git a/tests/dem_ground_frac_test_big/save1.nml b/tests/dem_ground_frac_test_big/save1.nml
new file mode 100644
index 0000000..23f330e
--- /dev/null
+++ b/tests/dem_ground_frac_test_big/save1.nml
@@ -0,0 +1,199 @@
+
+&icebergs_driver_nml
+  ni=45 !30 !number of elements, x direction
+  nj=45 !30 !number of elements, y direction
+  gridres=5000.0
+  ibdt=1800.0 !seconds
+  ibuo=0.1 !ocean x velocity
+  ibvo=0.0 !-0.1 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=999999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.true.
+  collision_test=.false.
+  big_grounding_test=.true.
+  bump_depth=100. !200.0 !(m) depth of top of gaussian bump below sea level
+/
+
+&icebergs_nml
+
+    constant_interaction_LW=.true.
+    !traj_name=test_dem.nc
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    break_bonds_on_sub_steps=.true.
+    
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5. A=L*W always works?
+    dem_spring_coef=5e6 !1e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=0.00015094124684696098 !dem_spring_coef=1.e6, r=1500, and hex pack
+    !spring_coef=0.0030188249369392196 !dem_spring_coef=5.r6, r=750, and hex pack!
+    !spring_coef=0.0006037649873878439 !dem_spring_coef=1.e6, r=750, and hex pack
+    spring_coef=0.0007547062342348049 !if dem_spring_coef=0.5e7, r=1500, and hex pack?
+    
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=200 !75 !(-1) # of mts sub-steps
+    explicit_inner_mts=.true.
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-2 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-8 !(default=spring_coeff) Berg spring coeff for collisions
+
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=1.e5 !3.16e6 !for power-law-type friction
+    h_to_init_grounding=20 !200.0
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.false.!.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 0.75 !1. !0.75 !0.5
+    frac_thres_n = 2250 !1000 !2250 !4100
+    frac_thres_t = 800 !10000000 !800 !1400
+
+
+    halo=3 !(4) halo width
+    Lx=225000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.false. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0.1 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=24000 ! (24) Period between verbose messages
+    traj_sample_hrs=0.5 !-1!0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=0.5 !-1!0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=1600.0!800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/dem_ground_frac_test_big/save2.nml b/tests/dem_ground_frac_test_big/save2.nml
new file mode 100644
index 0000000..38bd29c
--- /dev/null
+++ b/tests/dem_ground_frac_test_big/save2.nml
@@ -0,0 +1,199 @@
+
+&icebergs_driver_nml
+  ni=45 !30 !number of elements, x direction
+  nj=45 !30 !number of elements, y direction
+  gridres=5000.0
+  ibdt=1800.0 !seconds
+  ibuo=0.1 !ocean x velocity
+  ibvo=0.1 !-0.1 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=999999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.true.
+  collision_test=.false.
+  big_grounding_test=.true.
+  bump_depth=50. !200.0 !(m) depth of top of gaussian bump below sea level
+/
+
+&icebergs_nml
+
+    constant_interaction_LW=.true.
+    !traj_name=test_dem.nc
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    break_bonds_on_sub_steps=.true.
+    
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5. A=L*W always works?
+    dem_spring_coef=5e6 !5e6 !1e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=0.00015094124684696098 !dem_spring_coef=1.e6, r=1500, and hex pack
+    !spring_coef=0.0030188249369392196 !dem_spring_coef=5.e6, r=750, and hex pack!
+    !spring_coef=0.0006037649873878439 !dem_spring_coef=1.e6, r=750, and hex pack
+    spring_coef=0.0007547062342348049 !if dem_spring_coef=5e6, r=1500, and hex pack?
+    !spring_coef=0.0015094124684696098 !dem_spring_coef=1.e7, r=1500, and hex pack
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=200 !75 !(-1) # of mts sub-steps
+    explicit_inner_mts=.true.
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-2 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-8 !(default=spring_coeff) Berg spring coeff for collisions
+
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=1.e5 !3.16e6 !for power-law-type friction
+    h_to_init_grounding=20 !200.0
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.false.!.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 1.0 !0.75 !1. !0.75 !0.5
+    frac_thres_n = 1850 !1000 !2250 !4100
+    frac_thres_t = 500 !1500 !800 !10000000 !800 !1400
+
+
+    halo=3 !(4) halo width
+    Lx=225000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.false. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0.1 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=24000 ! (24) Period between verbose messages
+    traj_sample_hrs=0.5 !-1!0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=0.5 !-1!0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=1600.0!800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/dem_ground_frac_test_big/save3.nml b/tests/dem_ground_frac_test_big/save3.nml
new file mode 100644
index 0000000..bb7f660
--- /dev/null
+++ b/tests/dem_ground_frac_test_big/save3.nml
@@ -0,0 +1,199 @@
+
+&icebergs_driver_nml
+  ni=45 !30 !number of elements, x direction
+  nj=45 !30 !number of elements, y direction
+  gridres=5000.0
+  ibdt=1800.0 !seconds
+  ibuo=0.1 !ocean x velocity
+  ibvo=0.1 !-0.1 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=999999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.true.
+  collision_test=.false.
+  big_grounding_test=.true.
+  bump_depth=50. !200.0 !(m) depth of top of gaussian bump below sea level
+/
+
+&icebergs_nml
+
+    constant_interaction_LW=.true.
+    !traj_name=test_dem.nc
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=0.1 !1.0
+    explicit_inner_mts=.true.
+    break_bonds_on_sub_steps=.true.
+    
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5. A=L*W always works?
+    dem_spring_coef=5e6 !5e6 !1e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=0.00015094124684696098 !dem_spring_coef=1.e6, r=1500, and hex pack
+    !spring_coef=0.0030188249369392196 !dem_spring_coef=5.e6, r=750, and hex pack!
+    !spring_coef=0.0006037649873878439 !dem_spring_coef=1.e6, r=750, and hex pack
+    spring_coef=0.0007547062342348049 !if dem_spring_coef=5e6, r=1500, and hex pack?
+    !spring_coef=0.0015094124684696098 !dem_spring_coef=1.e7, r=1500, and hex pack
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=200 !75 !(-1) # of mts sub-steps
+    explicit_inner_mts=.true.
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-2 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-8 !(default=spring_coeff) Berg spring coeff for collisions
+
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=1.e5 !3.16e6 !for power-law-type friction
+    h_to_init_grounding=20 !200.0
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.false.!.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 1.4 !0.75 !1. !0.75 !0.5
+    frac_thres_n = 1850 !1000 !2250 !4100
+    frac_thres_t = 500 !1500 !800 !10000000 !800 !1400
+
+
+    halo=3 !(4) halo width
+    Lx=225000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.false. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0.1 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=24000 ! (24) Period between verbose messages
+    traj_sample_hrs=0.5 !-1!0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=0.5 !-1!0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=1600.0!800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/ground_frac_test/RUN b/tests/ground_frac_test/RUN
index f881323..3f4dc1d 100755
--- a/tests/ground_frac_test/RUN
+++ b/tests/ground_frac_test/RUN
@@ -1,7 +1,7 @@
-rm iceberg_trajectories.nc
-rm iceberg_trajectories.nc.*
-rm bond_trajectories.nc
-rm bond_trajectories.nc.*
-srun -n9 ./../../build/bergs.x
+#rm iceberg_trajectories.nc
+#rm iceberg_trajectories.nc.*
+#rm bond_trajectories.nc
+#rm bond_trajectories.nc.*
+srun -n1 ./../../build/bergs.x
 
 
diff --git a/tests/ground_frac_test/input.nml b/tests/ground_frac_test/input.nml
index ad6aafa..3969650 100644
--- a/tests/ground_frac_test/input.nml
+++ b/tests/ground_frac_test/input.nml
@@ -26,10 +26,33 @@
 !200 n:0.0278 vo=.1
 !200 n:0.0325 or 0.03 vo=0
     monitor_energy=.false.
+
+    constant_interaction_LW=.true.
+    traj_name=test_dem.nc
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5. A=L*W always works?
+    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    !spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7, r=1500, and square pack?
+    spring_coef=0.01118 !if dem_spring_coef=0.5e7, L=A=725.334717, and hex pack?  
+    !0.0007547062342348049 !if dem_spring_coef=0.5e7, r=1500, and hex pack?  
+
     !defaults given in parentheses:
     new_mts=.true.
     mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=10 !20 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
+    mts_sub_steps=250000 !10 !20 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
     contact_distance=1.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
     contact_spring_coef=1.e-7 !!5.e-7!(default=spring_coeff) Berg spring coeff for collisions
     debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
@@ -38,15 +61,10 @@
     ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
     remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
 
-    fracture_criterion='strain' !('none') 'strain_rate','strain',or 'none'
-
-    !for scale_damping_by_pmag=.false., old_mts
-    !frac_thres_n = 0.018 !0.02
-    !frac_thres_t = 0.05076 !0.0564
-
-    !scale_damping_by_pmag=.false., new_mts
-    frac_thres_n = 0.0162
-    frac_thres_t = 0.0457
+    fracture_criterion='stress' !('none') 'strain_rate','stress,'strain',or 'none'
+    frac_thres_scaling = 1.
+    frac_thres_n = 20000.
+    frac_thres_t = 20000.
 
     halo=3 !(4) halo width
     Lx=45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
@@ -56,10 +74,10 @@
     Static_icebergs=.False. ! (T) True=icebergs do no move
 
     rho_bergs=850. ! (850) iceberg density
-    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    !spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
     !tangent_spring_coef=3.85e-6 !10 !6
     bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
     tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
     scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
     critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
diff --git a/tests/ground_frac_test/input_save.nml b/tests/ground_frac_test/input_save.nml
new file mode 100644
index 0000000..ad6aafa
--- /dev/null
+++ b/tests/ground_frac_test/input_save.nml
@@ -0,0 +1,182 @@
+!NOTE: this result is from when we did NOT set uvel_old to ustar for berg interactions
+!KID, bergs_chksum: write_restart berg chksum=              32083975 chksum2=            2055392101 chksum3=           -2018330166 chksum4=           -2018330166 chksum5=           -1470408987 #=                    67
+!KID, grd_chksum2:    # of bergs/cell chksum=                     0 chksum2=                     0 min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
+! Total number of bonds is:          286 
+
+&icebergs_driver_nml
+  ni=45 !30 !number of elements, x direction
+  nj=45 !30 !number of elements, y direction
+  ibdt=1800.0 !seconds
+  ibuo=0.1 !ocean x velocity
+  ibvo=0.0 !1 !2 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=999999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.true.
+  collision_test=.false.
+  grounding_test=.true.
+  bump_depth=200.0 !(m) depth of top of gaussian bump below sea level 
+/
+
+&icebergs_nml
+!200 n:0.0278 vo=.1
+!200 n:0.0325 or 0.03 vo=0
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=10 !20 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
+    contact_distance=1.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7 !!5.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=3.16e6 !200.0 !for power-law-type friction
+    h_to_init_grounding=200.0 !300.0 !150.0 !300.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='strain' !('none') 'strain_rate','strain',or 'none'
+
+    !for scale_damping_by_pmag=.false., old_mts
+    !frac_thres_n = 0.018 !0.02
+    !frac_thres_t = 0.05076 !0.0564
+
+    !scale_damping_by_pmag=.false., new_mts
+    frac_thres_n = 0.0162
+    frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    rho_bergs=850. ! (850) iceberg density
+    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    !tangent_spring_coef=3.85e-6 !10 !6
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=1.0 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=24000 ! (24) Period between verbose messages
+    traj_sample_hrs=-1!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=-1!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.true. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/nc2csv.py b/tests/nc2csv.py
index be5f7bc..d5d390c 100755
--- a/tests/nc2csv.py
+++ b/tests/nc2csv.py
@@ -90,9 +90,9 @@ def main(args ):
                 aynf = file.variables['ayn_fast'][:]
                 bxnf = file.variables['bxn_fast'][:]
                 bynf = file.variables['byn_fast'][:]
-                tot_axn = file.variables['tot_accel_x'][:]
-                tot_ayn = file.variables['tot_accel_y'][:]
-                fields = ['x','y','time','id','uv','vv','mass','H','W','L','axn','ayn','bxn','byn','ocean_depth','axnf','aynf','bxnf','bynf','nbonds_id','accelx','accely']
+                #tot_axn = file.variables['tot_accel_x'][:]
+                #tot_ayn = file.variables['tot_accel_y'][:]
+                fields = ['x','y','time','id','uv','vv','mass','H','W','L','axn','ayn','bxn','byn','ocean_depth','axnf','aynf','bxnf','bynf','nbonds_id']#,'accelx','accely']
             else:
                 fields = ['x','y','time','id','uv','vv','mass','H','W','L','axn','ayn','bxn','byn','ocean_depth']
 
@@ -124,8 +124,8 @@ def main(args ):
                 ayf = aynf[ptime == utime[i]]
                 bxf = bxnf[ptime == utime[i]]
                 byf = bynf[ptime == utime[i]]
-                tot_ax = tot_axn[ptime == utime[i]]
-                tot_ay = tot_ayn[ptime == utime[i]]
+                #tot_ax = tot_axn[ptime == utime[i]]
+                #tot_ay = tot_ayn[ptime == utime[i]]
         filename = fout+str(i)+".csv"
         with open(filename, 'w') as file:
             writer = csv.writer(file)
@@ -136,7 +136,8 @@ def main(args ):
             else:
                 if mts==True:
                     for j in range(len(x)):
-                        writer.writerow([x[j],y[j],time[j],pid[j],uv[j],vv[j],mass[j],H[j],W[j],L[j],ax[j],ay[j],bx[j],by[j],od[j],axf[j],ayf[j],bxf[j],byf[j],nb[j],tot_ax[j],tot_ay[j]])
+                        writer.writerow([x[j],y[j],time[j],pid[j],uv[j],vv[j],mass[j],H[j],W[j],L[j],ax[j],ay[j],bx[j],by[j],od[j],axf[j],ayf[j],bxf[j],byf[j],nb[j]])
+                                        #,tot_ax[j],tot_ay[j]])
                 else:
                     for j in range(len(x)):
                         writer.writerow([x[j],y[j],time[j],pid[j],uv[j],vv[j],mass[j],H[j],W[j],L[j],ax[j],ay[j],bx[j],by[j],od[j]])
diff --git a/tests/nc2csv_bonds.py b/tests/nc2csv_bonds.py
index b8caa0e..29c719a 100755
--- a/tests/nc2csv_bonds.py
+++ b/tests/nc2csv_bonds.py
@@ -47,16 +47,18 @@ def main(args ):
         length = file.variables['length'][:]
         n1 = file.variables['n1'][:]
         n2 = file.variables['n2'][:]
-        rot = file.variables['rotation'][:]
-        rrot = file.variables['rel_rotation'][:]
-        ns = file.variables['n_strain'][:]
-        nsr = file.variables['n_strain_rate'][:]
+        #rot = file.variables['rotation'][:]
+        #rrot = file.variables['rel_rotation'][:]
+        #ns = file.variables['n_strain'][:]
+        #nsr = file.variables['n_strain_rate'][:]
+        ns = file.variables['nstress'][:]
+        ss = file.variables['sstress'][:]
         id_cnt1 = file.variables['id_cnt1'][:]
         id_ij1 = file.variables['id_ij1'][:]
         id_cnt2 = file.variables['id_cnt2'][:]
         id_ij2 = file.variables['id_ij2'][:]
-        fields = ['x','y','time','len','n1','n2','rot','rrot','ns','nsr','berg_id1','berg_id2']
-
+        #fields = ['x','y','time','len','n1','n2','rot','rrot','ns','nsr','berg_id1','berg_id2']
+        fields = ['x','y','time','len','n1','n2','ns','ss','berg_id1','berg_id2']
     idmid=int('2',8)**32
     btime=year+day/365.15
     bidin1=id_cnt1*idmid+id_ij1
@@ -77,10 +79,12 @@ def main(args ):
     length = length[biddiff>0]
     n1 = n1[biddiff>0]
     n2 = n2[biddiff>0]
-    rot=rot[biddiff>0]
-    rrot=rrot[biddiff>0]
+    # rot=rot[biddiff>0]
+    # rrot=rrot[biddiff>0]
+    # ns=ns[biddiff>0]
+    # nsr=nsr[biddiff>0]
     ns=ns[biddiff>0]
-    nsr=nsr[biddiff>0]
+    ss=ss[biddiff>0]
     bidin1 = bidin1[biddiff>0]
     bidin2 = bidin2[biddiff>0]
 
@@ -93,10 +97,12 @@ def main(args ):
         blen = length[btime == utime[i]]
         bn1 = n1[btime == utime[i]]
         bn2 = n2[btime == utime[i]]
-        brot = rot[btime == utime[i]]
-        brrot = rrot[btime == utime[i]]
+        # brot = rot[btime == utime[i]]
+        # brrot = rrot[btime == utime[i]]
+        # bns = ns[btime == utime[i]]
+        # bnsr = nsr[btime == utime[i]]
         bns = ns[btime == utime[i]]
-        bnsr = nsr[btime == utime[i]]
+        bss = ss[btime == utime[i]]
         bid1 = bidin1[btime == utime[i]]
         bid2 = bidin2[btime == utime[i]]
 
@@ -105,8 +111,8 @@ def main(args ):
             writer = csv.writer(file)
             writer.writerow(fields)
             for j in range(len(x)):
-                writer.writerow([x[j],y[j],time[j],blen[j],bn1[j],bn2[j],brot[j],brrot[j],bns[j],bnsr[j],bid1[j],bid2[j]])
-
+               # writer.writerow([x[j],y[j],time[j],blen[j],bn1[j],bn2[j],brot[j],brrot[j],bns[j],bnsr[j],bid1[j],bid2[j]])
+                writer.writerow([x[j],y[j],time[j],blen[j],bn1[j],bn2[j],bns[j],bss[j],bid1[j],bid2[j]])
 print('Script complete')
 
 def str2bool(string):

From 1a0238444ef1991b334db17dd5bc788a76579bdb Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Fri, 14 Jan 2022 17:28:14 -0500
Subject: [PATCH 315/361] -Tuned new run for paper using fewer MTS sub-steps
 (90 vs 200). Adjusted README accordingly. -Achieved about a 5x speedup by
 changing code so that forces for only one of the two bonds in a pair have to
 be evaluated during sub-steps, eliminating the call to process MTS sub-step
 contact with other elements in the same conglomerate for interior
 (fully-bonded) elements (to which this contact does not apply), and reducing
 the search range for this contact when it is needed (for non-fully bonded
 elements). -Increased parallelization buffer width +1*number_of_bonds to
 accomodate variable for relative rotation of bonds

---
 driver/icebergs_driver.F90                    |  75 ++--
 src/icebergs.F90                              | 410 ++++++------------
 src/icebergs_framework.F90                    | 196 ++++++---
 tests/a68/README                              |  31 +-
 tests/a68/RUN_for_restart_paper.sh            |   7 +
 tests/a68/RUN_loop.sh                         |   4 +-
 tests/a68/RUN_restart_for_paper.sh            |  35 +-
 tests/a68/RUN_test_init_for_paper.sh          |   8 +-
 tests/a68/animate_trajectories.py             |  13 +-
 tests/a68/input.nml                           |  73 ++--
 tests/a68/input_fill2.nml                     |   4 +-
 tests/a68/long_run.nml                        | 217 +++++++++
 tests/a68/long_run_for_paper.sh               |  30 ++
 .../square_for_restart_od_17.8_ydn.1_ss90.nml | 211 +++++++++
 tests/a68/square_r_ssf.nml                    |   5 +-
 15 files changed, 868 insertions(+), 451 deletions(-)
 create mode 100755 tests/a68/RUN_for_restart_paper.sh
 mode change 100644 => 100755 tests/a68/RUN_restart_for_paper.sh
 mode change 100644 => 100755 tests/a68/RUN_test_init_for_paper.sh
 create mode 100644 tests/a68/long_run.nml
 create mode 100755 tests/a68/long_run_for_paper.sh
 create mode 100644 tests/a68/square_for_restart_od_17.8_ydn.1_ss90.nml

diff --git a/driver/icebergs_driver.F90 b/driver/icebergs_driver.F90
index 042bcc5..42815b4 100644
--- a/driver/icebergs_driver.F90
+++ b/driver/icebergs_driver.F90
@@ -139,8 +139,6 @@ program icebergs_driver
 !grounding/collision tests
 real :: mid
 
-call cpu_time(time_begin)
-
 ! Boot FMS
 call fms_init()
 
@@ -294,14 +292,6 @@ program icebergs_driver
       tauxa_hr=0.0; tauya_hr=0.0
     endif
   endif
-
-  !print *,'lon min/max',minval(lon),maxval(lon)
-  !print *,'lat min/max',minval(lat),maxval(lat)
-  !print *,'lon(isd:isc+1,jsc+1)',lon(isd:isc+1,jsc+1)
-  !print *,'depth(isd:isc+1,jsc+1)',depth(isd:isc+1,jsc+1)
-  !print *,'lon(isd,jsd),lat(isd,jsd)',lon(isd,jsd),lat(isd,jsd)
-  !print *,'lon(ied,jed),lat(ied,jed)',lon(ied,jed),lat(ied,jed)
-  !iceberg vel: ub: 0.0362195771130627 vb: -0.04608364827503143
 else
   do j = jsd, jed
     do i = isd, ied
@@ -435,22 +425,10 @@ program icebergs_driver
 ns = 1 !timestep counter
 if (transient_a68_data_start_ind>0) ns2 = 1
 
-!uo=0.;vo=0.ui=0.;vi=0.;ssh=0.;tauxa=0.;tauya=0.;depth=-1000000
-!tauxa=0.; tauya=0.; ssh_hr=0.
-
-!uo_hr=0.2; vo_hr=0.
-
 ! Time_end = increment_date(Time, years, months, days, hours, minutes, seconds)
 Time_end = increment_date(Time,0,0,0,ibhrs,0,0)
 
-! if (mpp_pe()==0) then
-!   print *,'shape(tauxa_hr)', shape(tauxa_hr)
-!   print *,'shape(tauya_hr)', shape(tauya_hr)
-!   print *,'shape(tauxa)', shape(tauxa)
-!   print *,'shape(tauya)', shape(tauya)
-!   print *,'lon(isc:isc+2,jsc:jsc+2)',lon(isc:isc+2,jsc:jsc+2)-360
-!   print *,'lat(isc:isc+2,jsc:jsc+2)',lat(isc:isc+2,jsc:jsc+2)
-! endif
+call cpu_time(time_begin)
 
 do while ((ns <= nmax) .and. (Time < Time_end))
   if (mpp_pe()==0 .and. debug .and. mod(ns-1,write_time_inc)==0) then
@@ -461,7 +439,7 @@ program icebergs_driver
     write(*,'(a,i5,a,i5,a,i5)')' year',iyr,'  month ',imon,'  day   ',iday
     write(*,'(a,i5,a,i5,a,i5)')' hour',ihr,'  minute',imin,'  second',isec
     call cpu_time(time_finish)
-    write(*,*) 'cpu time elapsed: ', (time_finish - time_begin)/60., 'minutes'
+    write(*,*) 'clock-time elapsed: ', (time_finish - time_begin)/60., 'minutes'
     write(*,'(a)') '-------------------------------------------'
     write(*,*) ''
   end if
@@ -481,11 +459,6 @@ program icebergs_driver
       vo=0.5*(vo+vo_hr(:,:,transient_a68_data_start_ind+dit*(int(ceiling(ns2))-1)))
       ssh=ssh_hr(:,:,transient_a68_data_start_ind+dit*(int(ns2)-1))
     endif
-    ! if (mpp_pe()==0) then
-    !   print *,'index',transient_a68_data_start_ind+dit*(ns-1)
-    !   print *,'tauxa(isc:isc+2,jsc:jsc+2)',tauxa(isc:isc+2,jsc:jsc+2)
-    !   print *,'tauya(isc:isc+2,jsc:jsc+2)',tauya(isc:isc+2,jsc:jsc+2)
-    ! endif
   endif
 
   ! The main driver the steps updates icebergs
@@ -509,34 +482,36 @@ program icebergs_driver
       ns2=ns2+1
     elseif (ibdt==1800.0) then
       ns2=ns2+0.5
-      !if (mod(ns,2)>0) then
-      !  ns2=ns2+1
-      !endif
     endif
   endif
-
 enddo
 
-if (saverestart) call icebergs_save_restart(bergs)
 
-call get_date(Time, iyr, imon, iday, ihr, imin, isec)
-write(*,*) ''
-write(*,'(a)') '-------------------------------------------'
-write(*,'(a,i5)')' Saving after timestep   ',ns-1
-print *,' ns2   ',ns2
-if (mod(ns2,1.)==0) then
-  print *,'transient_a68_data_start_ind+dit*(int(ns2)-1)',&
-    transient_a68_data_start_ind+dit*(int(ns2)-1)
-else
-  print *,'transient_a68_data_start_ind+dit*(int(ceiling(ns2))-1))',&
-    transient_a68_data_start_ind+dit*(int(ceiling(ns2))-1)
+if (a68_test) then
+  call cpu_time(time_finish)
+  call get_date(Time, iyr, imon, iday, ihr, imin, isec)
+  write(*,*) ''
+  write(*,'(a)') '-------------------------------------------'
+  write(*,'(a,i5)')' Saving after timestep   ',ns-1
+  print *,' ns2   ',ns2
+  if (mod(ns2,1.)==0) then
+    print *,'transient_a68_data_start_ind+dit*(int(ns2)-1)',&
+      transient_a68_data_start_ind+dit*(int(ns2)-1)
+  else
+    print *,'transient_a68_data_start_ind+dit*(int(ceiling(ns2))-1))',&
+      transient_a68_data_start_ind+dit*(int(ceiling(ns2))-1)
+  endif
+  write(*,'(a)')' Restart time is:'
+  write(*,'(a,i5,a,i5,a,i5)')' year',iyr,'  month ',imon,'  day   ',iday
+  write(*,'(a,i5,a,i5,a,i5)')' hour',ihr,'  minute',imin,'  second',isec
+  write(*,*) ''
+  write(*,*) 'clock-time elapsed: ', (time_finish - time_begin)/60., 'minutes'
+  write(*,*) 'clock-time per day: ', (time_finish - time_begin)/(ns-1)*(60*60*24)/ibdt
+  write(*,'(a)') '-------------------------------------------'
+  write(*,*) ''
 endif
-write(*,'(a)')' Restart time is:'
-write(*,'(a,i5,a,i5,a,i5)')' year',iyr,'  month ',imon,'  day   ',iday
-write(*,'(a,i5,a,i5,a,i5)')' hour',ihr,'  minute',imin,'  second',isec
-write(*,'(a)') '-------------------------------------------'
-write(*,*) ''
 
+if (saverestart) call icebergs_save_restart(bergs)
 
 !Deallocate all memory and disassociated pointer
 call icebergs_end(bergs)
diff --git a/src/icebergs.F90 b/src/icebergs.F90
index c1edf2a..fedc1b2 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -53,7 +53,7 @@ module ice_bergs
 use ice_bergs_framework, only: update_bond_angles
 use ice_bergs_framework, only: monitor_energy, energy_tests_init, mts, new_mts
 use ice_bergs_framework, only: dem_tests_init
-use ice_bergs_framework, only: dem, init_dem_params
+use ice_bergs_framework, only: dem, init_dem_params, save_bond_forces
 use ice_bergs_framework, only: orig_dem_moment_of_inertia, no_frac_first_ts
 use ice_bergs_framework, only: A68_test, A68_xdisp, A68_ydisp
 use ice_bergs_framework, only: set_constant_interaction_length_and_width, skip_first_outer_mts_step
@@ -170,7 +170,7 @@ subroutine icebergs_init(bergs, &
       call transfer_mts_bergs(bergs)
     else
       call update_halo_icebergs(bergs)
-      call connect_all_bonds(bergs)
+      call connect_all_bonds(bergs, match_bond_pairs=.true.)
     endif
     nbonds=0
     check_bond_quality=.True.
@@ -879,10 +879,10 @@ subroutine calculate_unbonded_same_conglom_dem_force(bergs, berg, other_berg, IA
 
     r_dist_x=dlon*dx_dlon
     r_dist_y=dlat*dy_dlat
-    r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) ) !(Stern et al 2017, Eqn 3)
+    r_dist= (r_dist_x**2) + (r_dist_y**2)
 
     if (bergs%constant_interaction_LW) then
-      if ( (2*bergs%constant_radius)<=r_dist ) return
+      if ( (2*bergs%constant_radius)**2<=r_dist ) return
       R1=bergs%constant_radius
       A1=bergs%constant_area
       M1=A1*berg%thickness*bergs%rho_bergs                      !Berg 1 mass
@@ -907,10 +907,12 @@ subroutine calculate_unbonded_same_conglom_dem_force(bergs, berg, other_berg, IA
           R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
         endif
       endif
-      if ((R1+R2)<=r_dist) return
+      if ((R1+R2)**2<=r_dist) return
       M1=berg%mass; M2=other_berg%mass;
     endif
 
+    r_dist=sqrt(r_dist)
+
     u2=other_berg%uvel_old;  v2=other_berg%vvel_old !Old values are used to make it order invariant
 
     M_min=min(M1,M2)
@@ -1161,27 +1163,62 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
       Tr = -(bergs%dem_spring_coef/l0)*(2./3.)*((0.5*L)**3.)*Thick*theta
     endif
 
-!!$    if (abs(theta-theta_old) > abs(theta*0.05)) then
-!!$      print *,'theta mismatch!', theta_old, theta
-!!$    endif
-
     !if (savestress) current_bond%nstress=-bergs%dem_spring_coef*delta/l0 + abs(bergs%dem_spring_coef/l0*theta*0.5*L)
     if (savestress) current_bond%nstress=(bergs%dem_spring_coef/l0)*(-2*half_delta + abs(theta*0.5*L))
 
     !max tensile stress
 
     if (break_bonds_on_sub_steps) then
-      if (bergs%fracture_criterion=='computed') then
+
+      if (bergs%fracture_criterion=='stress') then
+        if (current_bond%nstress>bergs%frac_thres_n .or. current_bond%sstress>bergs%frac_thres_t) then
+          bergs%bond_break_detected=.true.
+
+          if (current_bond%nstress<0) then
+            !if fail under shear with normal compression, then should still feel contact force
+            Fd_x = Fd_x-damping_coef*ur; Fd_y = Fd_y-damping_coef*vr  !linear damping force
+            F_x = F_x + Fn_x; F_y = F_y + Fn_y !linear forces
+          endif
+
+          if (savestress .and. save_bond_forces) then
+            current_bond%T=0.; current_bond%T_d=0.
+            if (current_bond%nstress<0) then
+              current_bond%F_x=Fn_x; current_bond%F_y=Fn_y
+              current_bond%Fd_x=-damping_coef*ur; current_bond%Fd_y=-damping_coef*vr;
+            else
+              current_bond%F_x=0.; current_bond%F_y=0.
+              current_bond%Fd_x=0.; current_bond%Fd_y=0.
+            endif
+            current_bond%other_bond%F_x  = -current_bond%F_x
+            current_bond%other_bond%F_y  = -current_bond%F_y
+            current_bond%other_bond%Fd_x = -current_bond%Fd_x
+            current_bond%other_bond%Fd_y = -current_bond%Fd_y
+            current_bond%other_bond%T=0.; current_bond%other_bond%T_d=0.
+            current_bond%other_bond%nstress      = current_bond%nstress
+            current_bond%other_bond%sstress      = current_bond%sstress
+            current_bond%other_bond%rel_rotation = -current_bond%rel_rotation
+            current_bond%other_bond%tangd1       = -current_bond%tangd1
+            current_bond%other_bond%tangd2       = -current_bond%tangd2
+            current_bond%other_bond%length       = current_bond%length
+            current_bond%other_bond%other_id=-current_bond%other_bond%other_id
+          endif
+          return !Broken bond. Return without adding forces and torques
+        endif
+      elseif (bergs%fracture_criterion=='computed') then
         Rsig=current_bond%nstress/bergs%frac_thres_n
         Rtau=current_bond%sstress/bergs%frac_thres_t
-        if ((0.5*Rsig+sqrt((0.5*Rsig)**2. + Rtau**2.)) > 1) return
+        if ((0.5*Rsig+sqrt((0.5*Rsig)**2. + Rtau**2.)) > 1) then
+          bergs%bond_break_detected=.true.
+          if (save_bond_forces) current_bond%other_bond%other_id=-current_bond%other_bond%other_id
+          return
+        endif
       elseif (bergs%fracture_criterion=='computed_s') then
         Rsig=current_bond%nstress/bergs%frac_thres_n
         Rtau=current_bond%sstress/bergs%frac_thres_t
-        if (sqrt(Rsig**2. + Rtau**2.) > 1) return
-      elseif (bergs%fracture_criterion=='stress') then
-        if (current_bond%nstress>bergs%frac_thres_n .or. current_bond%sstress>bergs%frac_thres_t) then
-          return !Broken bond. Return without adding forces and torques
+        if (sqrt(Rsig**2. + Rtau**2.) > 1) then
+          if (save_bond_forces) current_bond%other_bond%other_id=-current_bond%other_bond%other_id
+          bergs%bond_break_detected=.true.
+          return
         endif
       else
         call error_mesg('KID, calculate_force_dem', &
@@ -1194,199 +1231,30 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
     !Meff = M1*M2/(M1+M2) !effective mass
     damping_coef = bergs%dem_damping_coef*sqrt(bergs%dem_K_damp*M1*M2/(M1+M2))
 
-    Fd_x = Fd_x-damping_coef*ur; Fd_y = Fd_y-damping_coef*vr  !linear damping force
-    T_d  = T_d-damping_coef*(berg%ang_vel-other_berg%ang_vel) !damping torque
-
-    if (bergs%dem_shear_for_frac_only) then
-      Fs_x=0.; Fs_y=0.
-    endif
-
-    !final forces
-    T = T + (Ts + Tr) !torque
-    F_x = F_x + Fn_x + Fs_x; F_y = F_y + Fn_y + Fs_y !linear forces
-  endif
-
-end subroutine calculate_force_dem
-
-!> Calculate interactive forces between two bergs using a discrete element method (DEM)
-!> that includes additional terms for tangential forces and torque.
-subroutine calculate_force_dem2(bergs, berg, other_berg, current_bond, &
-  dt, F_x, F_y, T, Fd_x, Fd_y, T_d, savestress)
-  ! Arguments
-  type(icebergs), pointer :: bergs !< Container for all types and memory
-  type(iceberg), pointer :: berg !< Primary berg
-  type(iceberg), pointer :: other_berg !< Berg that primary is interacting with
-  type(bond), pointer :: current_bond !< Bond being processed
-  real, intent(in) :: dt !< Time step size
-  real, intent(inout) :: F_x !< Net x-force without damping (N)
-  real, intent(inout) :: F_y !< Net y-force without damping (N)
-  real, intent(inout) :: T !< Net torque without damping (Nm)
-  real, intent(inout) :: Fd_x !< Net x-force from damping (N)
-  real, intent(inout) :: Fd_y !< Net y-force from damping (N)
-  real, intent(inout) :: T_d !< Net torque from damping (Nm)
-  logical, intent(in) :: savestress !< Save stress/tangential displacement on bond or not
-  ! Local variables
-  real :: A1,T1,M1,u1,v1,lon1,lat1,R1 ! Current iceberg
-  real :: A2,T2,M2,u2,v2,lon2,lat2,R2 ! Other iceberg
-  real :: dlon, dlat, lat_ref, dx_dlon, dy_dlat
-  real :: r_dist_x, r_dist_y, r_dist
-  real :: Rmin, delta, L, l0, youngs_dem, Thick, T_Rmin, n1, n2
-  real :: ur, vr, up, vp, rotu, rotv, rtu, rtv, RR1, RR2
-  real :: ur2, vr2
-  real :: ss_factor, ss1, ss2
-  real :: K_damp, Meff, damping_coef
-  real :: Fn_x, Fn_y, Fs_x, Fs_y, Ts, Tr
-  real :: tangdotnt,tangd1p,tangd2p, tmag, tmagp
-  real :: RR1x,RR1y,RR2x,RR2y,theta
-
-  !This DEM formulation follows Wang 2020 "A scale-invariant bonded particle model for
-  !simulating large deformation and failure of continua", which differs from "classic"
-  !DEM (e.g. Potyondy & Cundall, 2004) in its definition of bond width and torque from
-  !relative particle rotation. Forces and torques were further modified here to depend
-  !on ice thickness.
-
-  if ((berg%id .ne. other_berg%id) .and. (berg%fl_k.ne.-1) .and. (other_berg%fl_k.ne.-1)) then
-
-    ! From Berg 1
-    T1=berg%thickness
-    lon1=berg%lon_old; lat1=berg%lat_old
-
-    ! From Berg 2
-    T2=other_berg%thickness
-    lon2=other_berg%lon_old; lat2=other_berg%lat_old
-
-    if (bergs%constant_interaction_LW) then
-      ! use constant length and width here, just for interactions
-      A1=bergs%constant_length*bergs%constant_width !Berg 1 area
-      M1=A1*T1*bergs%rho_bergs                      !Berg 1 mass
-      A2=A1                                         !Berg 2 area
-      M2=A2*T2*bergs%rho_bergs                      !Berg 2 mass
-    else
-      ! use actual length and width of bergs
-      M1=berg%mass; A1=berg%length*berg%width                   !From Berg 1
-      M2=other_berg%mass; A2=other_berg%length*other_berg%width !From Berg 2
-    endif
-
-    dlon=lon1-lon2; dlat=lat1-lat2
-
-    ! Note that this is not the exact distance along a great circle.
-    ! Approximation for small distances. Should be fine.
-    lat_ref=0.5*(lat1+lat2)
-    call convert_from_grid_to_meters(lat_ref,bergs%grd%grid_is_latlon,dx_dlon,dy_dlat)
-
-    r_dist_x=dlon*dx_dlon
-    r_dist_y=dlat*dy_dlat
-    r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) ) !(Stern et al 2017, Eqn 3)
-    current_bond%length=r_dist
-
-    if (r_dist==0) print *,'r_dist,lat1,lon1,lat2,lon2',r_dist,berg%lat,berg%lon,other_berg%lat,other_berg%lon
-    !unit vec
-    n1=r_dist_x/r_dist; n2=r_dist_y/r_dist
-
-    !Stern et al 2017, Eqn 4: radius of circle inscribed within hexagon or square with area A1 or A2
-    if (bergs%hexagonal_icebergs) then
-      R1=sqrt(A1/(2.*sqrt(3.)))
-      R2=sqrt(A2/(2.*sqrt(3.)))
-    else !square packing
-      if (bergs%iceberg_bonds_on) then
-        R1=0.5*sqrt(A1)
-        R2=0.5*sqrt(A2)
-      else
-        R1=sqrt(A1/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
-        R2=sqrt(A2/pi) ! Interaction radius of the other iceberg
-      endif
+    if (savestress .and. save_bond_forces) then
+      current_bond%F_x  = Fn_x + Fs_x
+      current_bond%F_y  = Fn_y + Fs_y
+      current_bond%Fd_x = -damping_coef*ur
+      current_bond%Fd_y = -damping_coef*vr
+      current_bond%T    = Ts+Tr
+      current_bond%T_d  = -damping_coef*(berg%ang_vel-other_berg%ang_vel)
+
+      current_bond%other_bond%F_x  = -current_bond%F_x
+      current_bond%other_bond%F_y  = -current_bond%F_y
+      current_bond%other_bond%Fd_x = -current_bond%Fd_x
+      current_bond%other_bond%Fd_y = -current_bond%Fd_y
+      current_bond%other_bond%T    = Ts-Tr
+      current_bond%other_bond%T_d  = -current_bond%T_d
+
+      current_bond%other_bond%nstress      = current_bond%nstress
+      current_bond%other_bond%sstress      = current_bond%sstress
+      current_bond%other_bond%rel_rotation = -current_bond%rel_rotation
+      current_bond%other_bond%tangd1       = -current_bond%tangd1
+      current_bond%other_bond%tangd2       = -current_bond%tangd2
+      current_bond%other_bond%length       = current_bond%length
+      current_bond%other_bond%other_id=-current_bond%other_bond%other_id !mark matching bond as processed
     endif
 
-    !Rmin=min(R1,R2) !old
-    if (R1<R2) then
-      Rmin=R1
-      T_Rmin=T1 !thickness of element w/ minimum radius
-    else
-      Rmin=R2
-      T_Rmin=T2
-    endif
-    l0=R1+R2
-    delta=l0-r_dist
-
-    !element distances to contact point
-    RR1=R1-0.5*delta; RR2=R2-0.5*delta !magnitude
-    RR1x=RR1*n1;  RR1y=RR1*n2 !element 1 components
-    RR2x=RR2*n1;  RR2y=RR2*n2 !element 2 components
-
-    !bond width (determined at contact point)
-    L=2.0*(Rmin+(Rmin-0.5*delta)*abs(R1-R2)/r_dist)
-
-    Thick=T_Rmin+(Rmin-0.5*delta)*abs(T1-T2)/r_dist !thickness as determined at contact point
-    !Thick=min(T1,T2) !minimum thickness
-    !Thick=0.5*(T1+T2) !average thickness
-
-    youngs_dem=bergs%dem_spring_coef
-
-    !normal force:
-    !Fn_x=youngs_dem*Thick*delta*n1*L/l0 !Fn_y=youngs_dem*Thick*delta*n2*L/l0
-    !normal stiffness is youngs_dem*Thick*L/l0
-    Fn_x=youngs_dem*Thick*delta*L/l0; Fn_y=Fn_x*n2; Fn_x=Fn_x*n1
-
-    !relative translational velocity
-    ur=berg%uvel_old-other_berg%uvel_old; vr=berg%vvel_old-other_berg%vvel_old
-
-    if (savestress) then
-      !Rotation of contact plane:
-      tmag=sqrt(current_bond%tangd1**2+current_bond%tangd2**2) !old magnitude
-      !project old tangential displacement to current tangent plane
-      tangdotnt=current_bond%tangd1*n1+current_bond%tangd2*n2
-      tangd1p=current_bond%tangd1-tangdotnt*n1; tangd2p=current_bond%tangd2-tangdotnt*n2
-      !rescale to the old magnitude
-      tmagp=sqrt(tangd1p**2+tangd2p**2)
-      if (tmagp>0.) then
-        tangd1p=(tmag/tmagp)*tangd1p; tangd2p=(tmag/tmagp)*tangd2p
-      else
-        tangd1p=0.; tangd2p=0.
-      endif
-      current_bond%tangd1=tangd1p; current_bond%tangd2=tangd2p
-
-      !relative tangential velocities from rotation
-      rotu=RR1y*berg%ang_vel + RR2y*other_berg%ang_vel
-      rotv=-(RR1x*berg%ang_vel + RR2x*other_berg%ang_vel)
-      ur2=ur+rotu; vr2=vr+rotv
-
-      !'parallel' velocity = dot(relative velocity,unit vec)*unit vec
-      up=ur2*n1+vr2*n2; vp=up*n2; up=up*n1
-      rtu=ur2-up; rtv=vr2-vp !the relative tangential velocities
-
-      !add the new tangential displacement
-      current_bond%tangd1=current_bond%tangd1+rtu*dt; current_bond%tangd2=current_bond%tangd2+rtv*dt
-    endif
-
-    !shear terms
-    ss_factor=-L*Thick*youngs_dem/(l0*2.0*(1.0+bergs%poisson)) !shear stiffness
-    if (bergs%ignore_tangential_force) ss_factor=0.
-    Fs_x=ss_factor*current_bond%tangd1; Fs_y=ss_factor*current_bond%tangd2 !shear forces
-    if (savestress) current_bond%sstress=sqrt(Fs_x**2+Fs_y**2)/(L*Thick) !shear stress
-
-    !Torque from shearing force: Ts = R .cross. Fs
-    Ts = -(RR1x*Fs_y-RR1y*Fs_x)
-
-    !Torque from relative particle rotation
-    if (.not. orig_dem_moment_of_inertia) then
-      theta=sin(berg%rot-other_berg%rot)
-      Tr = -youngs_dem*(L**3.)*Thick*theta/(12.*l0) !should be same as below, except for theta
-    else
-      !For testing purposes. All particles should have same radius and thickness.
-      theta=berg%rot-other_berg%rot
-      Tr = -(youngs_dem/l0)*(2./3.)*((0.5*L)**3.)*Thick*theta
-    endif
-
-    !if (savestress) current_bond%nstress=-youngs_dem*delta/l0 + abs(youngs_dem/l0*theta*0.5*L)
-    if (savestress) current_bond%nstress=(youngs_dem/l0)*(-delta + abs(theta*0.5*L))
-    !max tensile stress
-
-    !damping
-    K_damp = 2.*youngs_dem/(3.*(1.-bergs%poisson**2)) !damping factor
-    Meff = M1*M2/(M1+M2) !effective mass
-
-    damping_coef = bergs%dem_damping_coef*sqrt(K_damp*Meff)
-
     Fd_x = Fd_x-damping_coef*ur; Fd_y = Fd_y-damping_coef*vr  !linear damping force
     T_d  = T_d-damping_coef*(berg%ang_vel-other_berg%ang_vel) !damping torque
 
@@ -1399,7 +1267,7 @@ subroutine calculate_force_dem2(bergs, berg, other_berg, current_bond, &
     F_x = F_x + Fn_x + Fs_x; F_y = F_y + Fn_y + Fs_y !linear forces
   endif
 
-end subroutine calculate_force_dem2
+end subroutine calculate_force_dem
 
 !> Experimental subroutine to calculate interactive force between a berg and a land cell
 !> Should prevent grounding.
@@ -1708,7 +1576,7 @@ subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, d
     endif
     if (short_step_mts_grounding) c_gnd=0.
 
-    !For testing sensitivity to number of short steps 
+    !For testing sensitivity to number of short steps
     ! if ((groundfrac.ne.0.) .and. (bergs%mts_sub_steps>200)) then
     !   print *,'changing # of ss to 200'
     !   bergs%mts_sub_steps=200
@@ -2142,7 +2010,7 @@ subroutine accel_explicit_inner_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel,
   real :: IAd_x, IAd_y, sum_bond_Ee, sum_bond_Ed, oneoverkn, M2, D, groundfrac
   type(iceberg), pointer :: other_berg
   integer :: grdi,grdj
-  logical :: bonded
+  logical :: bonded, bond_matched, run_contact
   ! DEM-mode local variables
   real :: F_x, F_y, T, Fd_x, Fd_y, T_d, R1, at, dragfrac
 
@@ -2159,52 +2027,85 @@ subroutine accel_explicit_inner_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel,
   endif
 
   bonded=.true.
+  bond_matched=.false.
   if (bergs%iceberg_bonds_on) then
     current_bond=>berg%first_bond
     do while (associated(current_bond)) ! loop over all bonds
-      other_berg=>current_bond%other_berg
-      if (.not. associated(other_berg)) then
-        call error_mesg('KID,bond interactions', 'Trying to do Bond interactions with unassosiated berg!' ,FATAL)
-      else
+
+      if (save_bond_forces) then
+        bond_matched=.false.
         if (bergs%dem) then
-          call calculate_force_dem(bergs,berg,other_berg,current_bond,&
-            dt,F_x,F_y,T,Fd_x,Fd_y,T_d,savestress=.true.)
-          other_berg%id=-other_berg%id !mark, as to not repeat in contact search below
-        else
-          P_ia_11=0. ; P_ia_12=0. ;  P_ia_21=0.;  P_ia_22=0.
-          P_ia_times_u_x=0. ; P_ia_times_u_y=0.
-          call calculate_force(bergs, berg, other_berg, IA_x, IA_y, uvel0, vvel0, uvel0, vvel0,  &
-            P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded)
-          other_berg%id=-other_berg%id !mark, as to not repeat in contact search below
-          IAd_x=IAd_x+P_ia_11*(other_berg%uvel_old-berg%uvel_old)+P_ia_12*(other_berg%vvel_old-berg%vvel_old)
-          IAd_y=IAd_y+P_ia_12*(other_berg%uvel_old-berg%uvel_old)+P_ia_22*(other_berg%vvel_old-berg%vvel_old)
+          if (current_bond%other_id<0) then
+            current_bond%other_id=-current_bond%other_id
+            other_berg=>current_bond%other_berg
+            other_berg%id=-other_berg%id !mark, as to not repeat in contact search below
+
+            bond_matched=.true.
+            F_x=F_x+current_bond%F_x; F_y=F_y+current_bond%F_y
+            Fd_x=Fd_x+current_bond%Fd_x; Fd_y=Fd_y+current_bond%Fd_y
+            T=T+current_bond%T; T_d=T_d+current_bond%T_d
+          endif
         endif
       endif
-      current_bond=>current_bond%next_bond
-    enddo
-    !contact search: find any surrounding non-bonded bergs in the same conglom, and processes
-    !them for contact using the regular (non-contact) spring constant and crit_dist based on radii
-    bonded=.false.
-    do grdj = max(berg%jne-2,bergs%grd%jsd+1),min(berg%jne+2,bergs%grd%jed);&
-      do grdi = max(berg%ine-2,bergs%grd%isd+1),min(berg%ine+2,bergs%grd%ied)
-      other_berg=>bergs%list(grdi,grdj)%first
-      do while (associated(other_berg))
-        if (other_berg%id>0 .and. other_berg%conglom_id.eq.berg%conglom_id) then
+
+      if (.not. bond_matched) then
+        other_berg=>current_bond%other_berg
+        if (.not. associated(other_berg)) then
+          call error_mesg('KID,bond interactions', 'Trying to do Bond interactions with unassosiated berg!' ,FATAL)
+        else
           if (bergs%dem) then
-            call calculate_unbonded_same_conglom_dem_force(bergs, berg, other_berg, &
-              IA_x, IA_y, IAd_x, IAd_y, uvel0, vvel0, uvel0, vvel0)
+            call calculate_force_dem(bergs,berg,other_berg,current_bond,&
+              dt,F_x,F_y,T,Fd_x,Fd_y,T_d,savestress=.true.)
+            other_berg%id=-other_berg%id !mark, as to not repeat in contact search below
           else
             P_ia_11=0. ; P_ia_12=0. ;  P_ia_21=0.;  P_ia_22=0.
             P_ia_times_u_x=0. ; P_ia_times_u_y=0.
             call calculate_force(bergs, berg, other_berg, IA_x, IA_y, uvel0, vvel0, uvel0, vvel0,  &
-              P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded,c_crit_dist=.true.)
+              P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded)
+            other_berg%id=-other_berg%id !mark, as to not repeat in contact search below
             IAd_x=IAd_x+P_ia_11*(other_berg%uvel_old-berg%uvel_old)+P_ia_12*(other_berg%vvel_old-berg%vvel_old)
             IAd_y=IAd_y+P_ia_12*(other_berg%uvel_old-berg%uvel_old)+P_ia_22*(other_berg%vvel_old-berg%vvel_old)
           endif
         endif
-        other_berg=>other_berg%next
-      enddo
-    enddo;enddo
+      endif
+      current_bond=>current_bond%next_bond
+    enddo
+    !contact search: find any surrounding non-bonded bergs in the same conglom, and processes
+    !them for contact using the regular (non-contact) spring constant and crit_dist based on radii
+    bonded=.false.
+
+    !for dem-mode, do not bother running the contact algorithm if the particle is within interior of conglomerate
+    if (bergs%iceberg_bonds_on .and. bergs%dem) then
+      if (berg%n_bonds .eq. bergs%max_bonds) then
+        run_contact=.false.
+      else
+        run_contact=.true.
+      endif
+    else
+      run_contact=.true.
+    endif
+    if (run_contact) then
+      do grdj = max(berg%jne-1,bergs%grd%jsd+1),min(berg%jne+1,bergs%grd%jed);&
+        do grdi = max(berg%ine-1,bergs%grd%isd+1),min(berg%ine+1,bergs%grd%ied)
+        other_berg=>bergs%list(grdi,grdj)%first
+        do while (associated(other_berg))
+          if (other_berg%id>0 .and. other_berg%conglom_id.eq.berg%conglom_id) then
+            if (bergs%dem) then
+              call calculate_unbonded_same_conglom_dem_force(bergs, berg, other_berg, &
+                IA_x, IA_y, IAd_x, IAd_y, uvel0, vvel0, uvel0, vvel0)
+            else
+              P_ia_11=0. ; P_ia_12=0. ;  P_ia_21=0.;  P_ia_22=0.
+              P_ia_times_u_x=0. ; P_ia_times_u_y=0.
+              call calculate_force(bergs, berg, other_berg, IA_x, IA_y, uvel0, vvel0, uvel0, vvel0,  &
+                P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded,c_crit_dist=.true.)
+              IAd_x=IAd_x+P_ia_11*(other_berg%uvel_old-berg%uvel_old)+P_ia_12*(other_berg%vvel_old-berg%vvel_old)
+              IAd_y=IAd_y+P_ia_12*(other_berg%uvel_old-berg%uvel_old)+P_ia_22*(other_berg%vvel_old-berg%vvel_old)
+            endif
+          endif
+          other_berg=>other_berg%next
+        enddo
+      enddo;enddo
+    endif
 
     !unmark the bonded bergs
     current_bond=>berg%first_bond
@@ -6152,7 +6053,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
       call update_halo_icebergs(bergs)
       if (bergs%debug_iceberg_with_id>0) call monitor_a_berg(bergs, 'icebergs_run, after update_halo()')
       if (bergs%iceberg_bonds_on) then
-        call connect_all_bonds(bergs)
+        call connect_all_bonds(bergs,match_bond_pairs=.true.)
       else
         if (grd%Lx>0.) call update_latlon(bergs)
       endif
@@ -7352,29 +7253,6 @@ subroutine evolve_icebergs_mts(bergs)
     berg=>bergs%list(grdi,grdj)%first
     do while (associated(berg)) ! loop over all bergs
 
-!!$      if (.not. short_step_mts_grounding) then
-!!$        !set fully-grounded particles to static
-!!$        D=(bergs%rho_bergs/rho_seawater)*berg%thickness ! draught (keel depth)
-!!$        if (bergs%h_to_init_grounding>0.0) then
-!!$          groundfrac=1.0-(berg%od-D)/bergs%h_to_init_grounding
-!!$          groundfrac=max(groundfrac,0.0); groundfrac=min(groundfrac,1.0)
-!!$        else
-!!$          if (D>berg%od) then
-!!$            groundfrac=1.0
-!!$          else
-!!$            groundfrac=0.0
-!!$          endif
-!!$        endif
-!!$
-!!$        if (groundfrac==1.0) then
-!!$          berg%static_berg=1.0
-!!$          berg%uvel=0.; berg%vvel=0.; berg%axn=0.; berg%ayn=0.; berg%bxn=0.; berg%byn=0.
-!!$          berg%uvel_prev=0.; berg%vvel_prev=0.; berg%uvel_old=0.; berg%vvel_old=0.
-!!$          berg%axn_fast=0.; berg%ayn_fast=0.; berg%bxn_fast=0.; berg%byn_fast=0.
-!!$          berg%ang_vel=0.; berg%ang_accel=0.
-!!$        endif
-!!$      endif
-
       if (berg%static_berg .lt. 0.5 .and. berg%halo_berg .lt. 0.5) then
         if (.not. is_point_in_cell(bergs%grd, berg%lon, berg%lat, berg%ine, berg%jne) ) then
           write(stderrunit,'(i4,a4,32i7)') mpp_pe(),'Lon',(i,i=grd%isd,grd%ied)
@@ -7624,7 +7502,7 @@ subroutine evolve_icebergs_mts(bergs)
       jj=jj+1
 
       if (monitor_energy .and. last_iter) save_bond_energy=.true.
-
+      bergs%bond_break_detected=.false.
     ! update velocities
     do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
       berg=>bergs%list(grdi,grdj)%first
@@ -7840,7 +7718,7 @@ subroutine evolve_icebergs_mts(bergs)
       enddo ! loop over all bergs
     enddo; enddo ! update 'old' velocities
 
-    if (break_bonds_on_sub_steps) call break_bonds_dem(bergs)
+    if (break_bonds_on_sub_steps .and. bergs%bond_break_detected) call break_bonds_dem(bergs)
   enddo ! loop over sub-steps
 
   !reset interactive_forces
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 9569c3b..c7133bc 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -52,6 +52,7 @@ module ice_bergs_framework
 logical :: monitor_energy=.false. !<monitors energies: elastic (spring+collision), external, dissipated, fracture
 logical :: iceberg_bonds_on=.False. ! True=Allow icebergs to have bonds, False=don't allow.
 logical :: dem=.false. !< If T, run in DEM-mode with angular terms, variable stiffness, etc
+logical :: save_bond_forces=.true. !< If T, saves forces on bonds (TODO save on bond traj, too), so that only 1 of 2 bonds in a pair need to be processed during DEM-MTS explicit sub-steps
 logical :: power_ground=.false.
 logical :: short_step_mts_grounding=.false.
 logical :: radius_based_drag=.false. !if T, hex bergs, and dem, 2r is used as the area of the vert face for drag/wave forces
@@ -73,7 +74,7 @@ module ice_bergs_framework
 public ignore_ij_restart, use_slow_find,generate_test_icebergs,old_bug_rotated_weights,budget
 public orig_read, force_all_pes_traj
 public mts,new_mts,save_bond_traj,ewsame,monitor_energy,iceberg_bonds_on
-public dem, add_curl_to_torque, fracture_criterion, orig_dem_moment_of_inertia
+public dem, save_bond_forces, add_curl_to_torque, fracture_criterion, orig_dem_moment_of_inertia
 public power_ground, short_step_mts_grounding, radius_based_drag
 public A68_test, A68_xdisp, A68_ydisp
 
@@ -426,6 +427,14 @@ module ice_bergs_framework
   real, allocatable :: tangd2 !< Accumulated tangential displacement, y-component (m)
   real, allocatable :: nstress !< Normal stress (Pa)
   real, allocatable :: sstress !< Shear stress (Pa)
+  type(bond), pointer :: other_bond=>null() !< Matching bond
+  ! If save_bond_forces
+  real, allocatable :: F_x !< Zonal force
+  real, allocatable :: F_y !< Meridional force
+  real, allocatable :: Fd_x !< Zonal damping force
+  real, allocatable :: Fd_y !< Meridional damping force
+  real, allocatable :: T !< Torque
+  real, allocatable :: T_d !< Torque (damping)
 end type bond
 
 !> A link in the bond trajectory record (diagnostic)
@@ -644,6 +653,7 @@ module ice_bergs_framework
   real :: poisson=0.3 ! Poisson's ratio
   real :: dem_spring_coef=0.
   real :: dem_damping_coef=0.1
+  logical :: bond_break_detected=.false.
   logical :: dem_shear_for_frac_only=.false. !< If true, DEM shear is calculated for fracture, but zeroed for berg interactions
   integer :: dem_beam_test=0 !1=Simply supported beam,2=cantilever beam,3=angular vel tes
   logical :: uniaxial_test=.false. !adds a tensile stress to the east-most berg element
@@ -928,7 +938,7 @@ subroutine ice_bergs_framework_init(bergs, &
          traj_area_thres_fl,tau_is_velocity, add_curl_to_torque,ocean_drag_scale, A68_test, &
          A68_xdisp,A68_ydisp,&
          orig_dem_moment_of_inertia, break_bonds_on_sub_steps, skip_first_outer_mts_step, rev_mind, &
-         no_frac_first_ts, use_grounding_torque, power_ground, short_step_mts_grounding, radius_based_drag
+         no_frac_first_ts, use_grounding_torque, power_ground, short_step_mts_grounding, radius_based_drag, save_bond_forces
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -1381,7 +1391,7 @@ subroutine ice_bergs_framework_init(bergs, &
 endif
 
 if (dem) then
-  buffer_width=buffer_width+3+(max_bonds*4)
+  buffer_width=buffer_width+3+(max_bonds*5)
   buffer_width_traj=buffer_width_traj+3
   buffer_width_bond_traj=buffer_width_bond_traj+4+1
   if (add_curl_to_torque) then
@@ -2321,9 +2331,9 @@ Subroutine transfer_mts_bergs(bergs)
   enddo
 
   if (debug) then
-    call connect_all_bonds(bergs,ignore_unmatched=.false.)
+    call connect_all_bonds(bergs,ignore_unmatched=.false.,match_bond_pairs=.true.)
   else
-    call connect_all_bonds(bergs,ignore_unmatched=.true.)
+    call connect_all_bonds(bergs,ignore_unmatched=.true.,match_bond_pairs=.true.)
   endif
 
   call set_conglom_ids(bergs)
@@ -3517,6 +3527,7 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
           call push_buffer_value(buff%data(:,n), counter, 0)
           call push_buffer_value(buff%data(:,n), counter, 0)
           call push_buffer_value(buff%data(:,n), counter, 0)
+          call push_buffer_value(buff%data(:,n), counter, 0)
         elseif (fracture_criterion .ne. 'none') then
           call push_buffer_value(buff%data(:,n), counter, 0)
           call push_buffer_value(buff%data(:,n), counter, 0)
@@ -5426,7 +5437,18 @@ subroutine break_bonds_dem(bergs)
 
         if (current_bond%other_id.ne.-1) then
 
-          if (bergs%fracture_criterion=='computed') then
+          if (bergs%fracture_criterion=='stress') then
+            if (current_bond%nstress>frac_thres_n .or. current_bond%sstress>frac_thres_t) then
+              if (current_bond%nstress>frac_thres_n .and. current_bond%sstress>frac_thres_t) then
+                print *,'T and S break',this%lat,current_bond%nstress,current_bond%sstress
+              elseif (current_bond%nstress>frac_thres_n) then
+                print *,'TENSILE break',this%lat,current_bond%nstress,current_bond%sstress
+              else
+                print *,'SHEAR   break',this%lat,current_bond%nstress,current_bond%sstress
+              endif
+              current_bond%other_id=-1
+            endif
+          elseif (bergs%fracture_criterion=='computed') then
             Rsig=current_bond%nstress/frac_thres_n
             Rtau=current_bond%sstress/frac_thres_t
             frac=0.5*Rsig+sqrt((0.5*Rsig)**2. + Rtau**2.)
@@ -5443,48 +5465,45 @@ subroutine break_bonds_dem(bergs)
               current_bond%other_id=-1
             endif
           else
-              if (current_bond%nstress>frac_thres_n .or. current_bond%sstress>frac_thres_t) then
-                if (current_bond%nstress>frac_thres_n .and. current_bond%sstress>frac_thres_t) then
-                  print *,'T and S break',this%lat,current_bond%nstress,current_bond%sstress
-                elseif (current_bond%nstress>frac_thres_n) then
-                  print *,'TENSILE break',this%lat,current_bond%nstress,current_bond%sstress
-                else
-                  print *,'SHEAR   break',this%lat,current_bond%nstress,current_bond%sstress
-                endif
-                current_bond%other_id=-1
-              endif
+            call error_mesg('KID, break_bonds_dem','fracture criterion not supported for DEM!',FATAL)
           endif
 
-          if (current_bond%other_id.eq.-1) then
-            other_berg=>current_bond%other_berg
-            if (associated(other_berg)) then
-              !mark matching bond on other_berg
-              other_bond=>other_berg%first_bond
-              do while (associated(other_bond)) ! loop over all bonds
-                if (other_bond%other_id.eq.this%id) then
-                  other_bond%other_id=-1
-                  if (bergs%fracture_criterion=='computed') then
-                    Rsig=other_bond%nstress/frac_thres_n
-                    Rtau=other_bond%sstress/frac_thres_t
-                    frac=0.5*Rsig+sqrt((0.5*Rsig)**2. + Rtau**2.)
-                    if (frac <= 1.) then
-                      print *,'Other bond did not fracture!'
-                    endif
-                  elseif(bergs%fracture_criterion=='computed_s') then
-                    Rsig=current_bond%nstress/bergs%frac_thres_n
-                    Rtau=current_bond%sstress/bergs%frac_thres_t
-                    frac=sqrt(Rsig**2. + Rtau**2.)
-                    if (frac <= 1.) then
-                      print *,'Other bond did not fracture!'
+          if (save_bond_forces) then
+            if (current_bond%other_id.eq.-1) current_bond%other_bond%other_id=-1
+          else
+            if (current_bond%other_id.eq.-1) then
+              other_berg=>current_bond%other_berg
+              if (associated(other_berg)) then
+                !mark matching bond on other_berg
+                other_bond=>other_berg%first_bond
+                do while (associated(other_bond)) ! loop over all bonds
+                  if (other_bond%other_id.eq.this%id) then
+                    other_bond%other_id=-1
+                    if (debug) then
+                      if (bergs%fracture_criterion=='computed') then
+                        Rsig=other_bond%nstress/frac_thres_n
+                        Rtau=other_bond%sstress/frac_thres_t
+                        frac=0.5*Rsig+sqrt((0.5*Rsig)**2. + Rtau**2.)
+                        if (frac <= 1.) then
+                          print *,'Other bond did not fracture!'
+                        endif
+                      elseif(bergs%fracture_criterion=='computed_s') then
+                        Rsig=current_bond%nstress/bergs%frac_thres_n
+                        Rtau=current_bond%sstress/bergs%frac_thres_t
+                        frac=sqrt(Rsig**2. + Rtau**2.)
+                        if (frac <= 1.) then
+                          print *,'Other bond did not fracture!'
+                        endif
+                      elseif (other_bond%nstress<=frac_thres_n .and. other_bond%sstress<=frac_thres_t) then
+                        print *,'Other bond did not fracture!'
+                        print *,'current and other bond nstress,',current_bond%nstress, other_bond%nstress
+                        print *,'current and other bond sstress,',current_bond%sstress, other_bond%sstress
+                      endif
                     endif
-                  elseif (other_bond%nstress<=frac_thres_n .and. other_bond%sstress<=frac_thres_t) then
-                    print *,'Other bond did not fracture!'
-                    print *,'current and other bond nstress,',current_bond%nstress, other_bond%nstress
-                    print *,'current and other bond sstress,',current_bond%sstress, other_bond%sstress
                   endif
-                endif
-                other_bond=>other_bond%next_bond
-              enddo
+                  other_bond=>other_bond%next_bond
+                enddo
+              endif
             endif
           endif
         endif
@@ -5572,6 +5591,10 @@ subroutine form_a_bond(berg, other_id, other_berg_ine, other_berg_jne, other_ber
     new_bond%nstress=0.; new_bond%sstress=0.
     allocate(new_bond%rel_rotation)
     new_bond%rel_rotation=0.
+    if (save_bond_forces) then
+      allocate(new_bond%F_x, new_bond%F_y, new_bond%Fd_x, new_bond%Fd_y, new_bond%T, new_bond%T_d)
+      new_bond%F_x=0.; new_bond%F_y=0.; new_bond%Fd_x=0.; new_bond%Fd_y=0.; new_bond%T=0.; new_bond%T_d=0.
+    endif
   elseif (fracture_criterion.ne.'none') then
     allocate(new_bond%rotation,new_bond%rel_rotation,new_bond%n_frac_var)
     new_bond%rotation=0.; new_bond%rel_rotation=0.; new_bond%n_frac_var=0.
@@ -5695,23 +5718,28 @@ subroutine show_all_bonds(bergs)
 end subroutine show_all_bonds
 
 !> Sweep across all bergs filling in bond data
-subroutine connect_all_bonds(bergs, ignore_unmatched)
+subroutine connect_all_bonds(bergs, ignore_unmatched, match_bond_pairs)
 type(icebergs), pointer :: bergs !< Container for all types and memory
 logical,optional :: ignore_unmatched !< If true, do not call error if the other berg in a bond is not found
+logical,optional :: match_bond_pairs !< If true, point identical bonds (bond pairs) to each other
 ! Local variables
 type(iceberg), pointer :: other_berg, berg
 type(icebergs_gridded), pointer :: grd
 integer :: i, j
 integer :: grdi, grdj
 integer :: grdi_inner, grdj_inner
-type(bond) , pointer :: current_bond, other_berg_bond
-logical :: bond_matched, missing_bond, check_bond_quality,check_match
+type(bond) , pointer :: current_bond, other_bond
+logical :: bond_matched, missing_bond, check_bond_quality,check_match,link_bond_pairs
 integer nbonds
 
   check_match = .true.
   if (present(ignore_unmatched)) then
     if (ignore_unmatched) check_match = .false.
   end if
+  link_bond_pairs=.false.
+  if (present(match_bond_pairs)) then
+    if (match_bond_pairs) link_bond_pairs=.true.
+  endif
 
 missing_bond=.false.
 bond_matched=.false.
@@ -5820,6 +5848,38 @@ subroutine connect_all_bonds(bergs, ignore_unmatched)
     nbonds=0
     call count_bonds(bergs, nbonds,check_bond_quality)
   endif
+
+  if (save_bond_forces .and. link_bond_pairs) then
+    do grdj = grd%jsd+1,grd%jed ; do grdi = grd%isd+1,grd%ied
+      berg=>bergs%list(grdi,grdj)%first
+      do while (associated(berg)) ! loop over all bergs
+        if (berg%halo_berg.ne.10) then
+          current_bond=>berg%first_bond
+          do while (associated(current_bond)) ! loop over all bonds
+            if (.not.associated(current_bond%other_bond)) then
+              other_berg=>current_bond%other_berg
+              if (associated(other_berg)) then
+                other_bond=>other_berg%first_bond
+                do while (associated(other_bond)) ! loop over all bonds
+                  if (other_bond%other_id.eq.berg%id) then
+                    other_bond%other_bond=>current_bond
+                    current_bond%other_bond=>other_bond
+                    other_bond=>null()
+                  else
+                    other_bond=>other_bond%next_bond
+                  endif
+                enddo
+              else
+                call error_mesg('KID, connect_all_bonds', 'A bond is missing its second berg !!!', WARNING)
+              endif
+            endif
+            current_bond=>current_bond%next_bond
+          enddo
+        endif
+        berg=>berg%next
+      enddo
+    enddo;enddo
+  endif
 end subroutine connect_all_bonds
 
 !> If periodic domain, update lat & lon for bergs located beyond Lx - Alex
@@ -6791,13 +6851,13 @@ logical function check_and_find_cell(grd, x, y, oi, oj)
 endif
 
 !find cell for structured grid without looping:
-! oi=floor((x-grd%lon(grd%isd,grd%jsd))/(grd%lon(grd%isd+1,grd%jsd+1)-grd%lon(grd%isd,grd%jsd)))+grd%isd+1
-! oj=floor((y-grd%lat(grd%isd,grd%jsd))/(grd%lat(grd%isd+1,grd%jsd+1)-grd%lat(grd%isd,grd%jsd)))+grd%jsd+1
-! if (.not. (oi-1.lt.grd%isd.or.oi.gt.grd%ied.or.oj-1.lt.grd%jsd.or.oj.gt.grd%jed)) then
-!   if (is_point_in_cell(grd, x, y, oi, oj)) then
-!     check_and_find_cell=.true.; return
-!   endif
-! endif
+oi=floor((x-grd%lon(grd%isd,grd%jsd))/(grd%lon(grd%isd+1,grd%jsd+1)-grd%lon(grd%isd,grd%jsd)))+grd%isd+1
+oj=floor((y-grd%lat(grd%isd,grd%jsd))/(grd%lat(grd%isd+1,grd%jsd+1)-grd%lat(grd%isd,grd%jsd)))+grd%jsd+1
+if (.not. (oi-1.lt.grd%isd.or.oi.gt.grd%ied.or.oj-1.lt.grd%jsd.or.oj.gt.grd%jed)) then
+  if (is_point_in_cell(grd, x, y, oi, oj)) then
+    check_and_find_cell=.true.; return
+  endif
+endif
 
   oi=-999; oj=-999
   do j=grd%jsd+1,grd%jed; do i=grd%isd+1,grd%ied
@@ -6823,13 +6883,13 @@ logical function find_cell(grd, x, y, oi, oj)
 
 
 !find cell for structured grid without looping:
-! oi=floor((x-grd%lon(grd%isd,grd%jsd))/(grd%lon(grd%isd+1,grd%jsd+1)-grd%lon(grd%isd,grd%jsd)))+grd%isd+1
-! oj=floor((y-grd%lat(grd%isd,grd%jsd))/(grd%lat(grd%isd+1,grd%jsd+1)-grd%lat(grd%isd,grd%jsd)))+grd%jsd+1
-! if (oi>grd%isc-1 .and. oi<grd%iec+1 .and. oj>grd%jsc-1 .and. oj<grd%jec+1) then
-!   if (is_point_in_cell(grd, x, y, oi, oj)) then
-!     find_cell=.true.; return
-!   endif
-! endif
+oi=floor((x-grd%lon(grd%isd,grd%jsd))/(grd%lon(grd%isd+1,grd%jsd+1)-grd%lon(grd%isd,grd%jsd)))+grd%isd+1
+oj=floor((y-grd%lat(grd%isd,grd%jsd))/(grd%lat(grd%isd+1,grd%jsd+1)-grd%lat(grd%isd,grd%jsd)))+grd%jsd+1
+if (oi>grd%isc-1 .and. oi<grd%iec+1 .and. oj>grd%jsc-1 .and. oj<grd%jec+1) then
+  if (is_point_in_cell(grd, x, y, oi, oj)) then
+    find_cell=.true.; return
+  endif
+endif
 
   oi=-999; oj=-999
   do j=grd%jsc,grd%jec; do i=grd%isc,grd%iec
@@ -6854,13 +6914,13 @@ logical function find_cell_wide(grd, x, y, oi, oj)
 
 find_cell_wide=.false.
 !find cell for structured grid without looping:
-! oi=floor((x-grd%lon(grd%isd,grd%jsd))/(grd%lon(grd%isd+1,grd%jsd+1)-grd%lon(grd%isd,grd%jsd)))+grd%isd+1
-! oj=floor((y-grd%lat(grd%isd,grd%jsd))/(grd%lat(grd%isd+1,grd%jsd+1)-grd%lat(grd%isd,grd%jsd)))+grd%jsd+1
-! if (.not. (oi-1.lt.grd%isd.or.oi.gt.grd%ied.or.oj-1.lt.grd%jsd.or.oj.gt.grd%jed)) then
-!   if (is_point_in_cell(grd, x, y, oi, oj)) then
-!     find_cell_wide=.true.; return
-!   endif
-! endif
+oi=floor((x-grd%lon(grd%isd,grd%jsd))/(grd%lon(grd%isd+1,grd%jsd+1)-grd%lon(grd%isd,grd%jsd)))+grd%isd+1
+oj=floor((y-grd%lat(grd%isd,grd%jsd))/(grd%lat(grd%isd+1,grd%jsd+1)-grd%lat(grd%isd,grd%jsd)))+grd%jsd+1
+if (.not. (oi-1.lt.grd%isd.or.oi.gt.grd%ied.or.oj-1.lt.grd%jsd.or.oj.gt.grd%jed)) then
+  if (is_point_in_cell(grd, x, y, oi, oj)) then
+    find_cell_wide=.true.; return
+  endif
+endif
 
 oi=-999; oj=-999
 
diff --git a/tests/a68/README b/tests/a68/README
index 8d990cb..995a5d5 100644
--- a/tests/a68/README
+++ b/tests/a68/README
@@ -1,26 +1,33 @@
-TO RUN THE EXPERIMENT IN THE PAPER/AGU 2021:
+TO RUN THE EXPERIMENT IN THE PAPER:
 
-1. Make the iceberg input files:
+I. Make the iceberg input files:
    cd makeberg; ./RUN_for_paper; cd ..
 
-2. (optional) Run the spinup without fracture or grounding, and test different ocean scaling, etc. These tests are used to determine which simulation best follows the observed A68:
+II. The full run from the paper:
+   ./long_run_for_paper.sh
+
+III. Animate the results:
+./animate_trajectories.py -fname=longrun_od_17.8_tn_ng_ydn.1_ss90_ns18_rx-37.51_ry-55.2166.nc
+
+
+
+ADVANCED: TUNING EXPERIMENTS:
+
+1. Tuning ocean drag coefficients (by scaling the default point-particle coefficients) and Youngs Modulus: run the simulation without fracture or grounding, and test different parameter values. The following run without fracture/grounding was used for tuning in the paper:
    ./RUN_test_init_for_paper.sh
 
-3. Run the selected spinup (which uses ocean_scaling=17.8) to the point for restart:
-   cp square_for_restart_od_17.8_ydn.1.nml input.nml
+2. Spinup for fracture tuning: Repeat the run from (1) to just before the first breakup to create a restart file, which will be used by experiments to tune the fracture parameters (step 6, below). To run the spinup used for the paper:
+   cp square_for_restart_od_17.8_ydn.1_ss90.nml input.nml
    ./RUN_1p.sh
 
-4. Copy the restart to a new directory:
-   cp INPUT/ S_17.8_ydn.1_r/
+3. Copy the restart to a new directory:
+   cp INPUT/ S_17.8_ydn.1_ss90_r/
 
-5. Rerun the simulation from the restart, this time activating grounding and fracture:
+5. Rerun the simulation from the restart, this time activating grounding and fracture.
    ./RUN_restart_for_paper.sh
 
 6. animate the results:
-   ./animate_trajectories.py -fname=sq_ssf_ssg1.e4_od17.8_addsm.true._rectx-37.5285_y-55.2166_n23_t10.nc
+   ./animate_trajectories.py -fname=sq_ssfg_gc1.e4_od17.8_rx-37.51_y-55.2166_n18_t10_ss90.nc
 
 
 Warning: steps 1 and 6 probably require different versions of python or packages. TODO: fix this.
-
-
-
diff --git a/tests/a68/RUN_for_restart_paper.sh b/tests/a68/RUN_for_restart_paper.sh
new file mode 100755
index 0000000..e1852ae
--- /dev/null
+++ b/tests/a68/RUN_for_restart_paper.sh
@@ -0,0 +1,7 @@
+#cp square_for_restart_od_17.8_ydn.1_ss90.nml input.nml
+#./RUN1p
+#cp ./RESTART/* ./S_17.8_ydn.1_ss90_r/
+
+cp square_for_restart_od_17.8_ydn.1.nml input.nml
+./RUN1p
+cp ./RESTART/* ./S_17.8_ydn.1_r/
diff --git a/tests/a68/RUN_loop.sh b/tests/a68/RUN_loop.sh
index ce98aa4..4a074de 100755
--- a/tests/a68/RUN_loop.sh
+++ b/tests/a68/RUN_loop.sh
@@ -23,8 +23,8 @@
 #odrag=(2.9 2.95)
 #name=(hex_yn.175_nf_od2.9.nc hex_yn.175_nf_od2.95.nc)
 
-odrag=(9.5 10.5)
-name=(hex_yn.1_nf_od9.5_rad_drag_E1e6.nc hex_yn.1_nf_od10.5_rad_drag_E1e6.nc)
+odrag=(10.9 10.95)
+name=(hex_yn.1_nf_od10.9_rad_drag_E1e6.nc hex_yn.1_nf_od10.95_rad_drag_E1e6.nc)
 
 
 #odrag=(5.5 5)
diff --git a/tests/a68/RUN_restart_for_paper.sh b/tests/a68/RUN_restart_for_paper.sh
old mode 100644
new mode 100755
index 5748090..823420f
--- a/tests/a68/RUN_restart_for_paper.sh
+++ b/tests/a68/RUN_restart_for_paper.sh
@@ -1,19 +1,24 @@
 #!/bin/bash
 
-#ocean drag values
-ss=200
+#grounding coef
 gcoef=(1.e4)
-rdir=S_17.8_ydn.1_r
+#number of substeps
+ss=90
+#restart directory
+rdir=S_17.8_ydn.1_ss90_r
+#scale factor for ocean drag coefficients
 odrag=17.8
-nstress=(23)
+#normal and shear stress thresholds (kPa)
+nstress=(18)
 tstress=(10)
+#Use A68a grounding zone?
 a68=.true.
-
-A68dx=-37.5285
+#lower-left coords of grounding zone
+A68dx=-37.51
 A68dy=-55.2166
-
-fname2=sq_ssf_ssg1.e4_od17.8_addsm.true._rectx-37.5285_y-55.2166_n23_t10.nc
+#Earth radius
 Eradius=6363827
+#Use power-law grounding drag? If false, uses linear grounding drag.
 pg=.false.
 
 for ((i = 0; i < ${#nstress[@]}; ++i)); do
@@ -27,8 +32,20 @@ for ((i = 0; i < ${#nstress[@]}; ++i)); do
     echo $ts
     echo $pg
     echo $rdir
+    echo $ss
+    echo $A68dx
+    echo $A68dy
 
-    sed  "s/<ss>/$ss/; s/<a68>/$a68/; s/<pg>/$pg/; s/<xd>/$A68dx/; s/<yd>/$A68dy/; s/<rdir>/$rdir/; s/<gc>/$gc/; s/<rad>/$Eradius/; s/<od>/$odrag/; s/<ns>/$ns/; s/<ts>/$ts/; s/<name>/$fname2/g" \
+    sed  "s/<ss>/$ss/; s/<a68>/$a68/; s/<pg>/$pg/; s/<xd>/$A68dx/; s/<yd>/$A68dy/; s/<rdir>/$rdir/; s/<gc>/$gc/; s/<rad>/$Eradius/; s/<od>/$odrag/; s/<ns>/$ns/; s/<ts>/$ts/g" \
 	 square_r_ssf.nml > input.nml
     ./RUN1p
 done
+
+##Another good run, with more sub-steps:
+#gcoef=(1.e4)
+#ss=200
+#rdir=S_17.8_ydn.1_r
+#A68dx=-37.5285
+#A68dy=-55.2166
+#Eradius=6363827
+#pg=.false.
diff --git a/tests/a68/RUN_test_init_for_paper.sh b/tests/a68/RUN_test_init_for_paper.sh
old mode 100644
new mode 100755
index 3b7bfab..f54b94a
--- a/tests/a68/RUN_test_init_for_paper.sh
+++ b/tests/a68/RUN_test_init_for_paper.sh
@@ -2,7 +2,10 @@
 
 Rearth=6363827
 odrag=(17.8)
-name=(od_17.8_tn_ng_ydn.1.nc)
+#name=(od_17.8_tn_ng_ydn.1.nc)
+#ss=200
+name=(od_17.8_tn_ng_ydn.1_ss90.nc)
+ss=90
 
 for ((i = 0; i < ${#odrag[@]}; ++i)); do
     drag=(${odrag[$i]})
@@ -11,8 +14,9 @@ for ((i = 0; i < ${#odrag[@]}; ++i)); do
     echo $drag
     echo $fname
     echo $Rearth
+    echo $ss
 
-    sed  "s/<od>/$drag/; s/<re>/$Rearth/; s/<name>/$fname/g" \
+    sed  "s/<od>/$drag/; s/<re>/$Rearth/; s/<ss>/$ss/; s/<name>/$fname/g" \
 	 input_fill2.nml > input.nml
     ./RUN1p
     # &>/dev/null &
diff --git a/tests/a68/animate_trajectories.py b/tests/a68/animate_trajectories.py
index a30ca3b..23497ef 100755
--- a/tests/a68/animate_trajectories.py
+++ b/tests/a68/animate_trajectories.py
@@ -218,21 +218,24 @@ def onClick(event):
     boundary_path = mpath.Path(boundary_path)
 
     old=False
-    
+
+    if pvar==True:
+        old=True
+
     # Now we can do the plotting!
     f = plt.figure(figsize=(8,8))
     f.tight_layout()
 
     if old:
         ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
-        scat = ax1.scatter([],[],marker='o')#,edgecolor='red')        
+        scat = ax1.scatter([],[],marker='o')#,edgecolor='red')
     else:
         ax1 = plt.axes(projection=ccrs.NearsidePerspective(central_longitude=midlon, central_latitude=midlat))
-        scat = ax1.scatter([],[],transform=ccrs.PlateCarree(),marker='o')#,edgecolor='red')        
+        scat = ax1.scatter([],[],transform=ccrs.PlateCarree(),marker='o')#,edgecolor='red')
 
     if pvar==True:
         div = make_axes_locatable(ax1)
-        cax = div.append_axes('right', '5%', '5%')
+        cax = div.append_axes('right', size='5%', pad='5%')
         cmap = plt.cm.get_cmap('RdYlBu')
         norm = plt.Normalize(thevar.min(), thevar.max())
         #norm = plt.Normalize(165.7, 165.8)
@@ -262,7 +265,7 @@ def onClick(event):
             ax1.quiver(vv.lon.values,vv.lat.values,vv.uo.values,vv.vo.values,vv.vel.values,scale=8,cmap='viridis',norm=norm,transform=ccrs.PlateCarree())
         else:
             ax1.quiver(vv.lon,vv.lat,vv.uo,vv.vo,vv.vel,scale=8,cmap='viridis',norm=norm)
-        f.colorbar(plt.cm.ScalarMappable(norm=norm, cmap='viridis'),ax=ax1, shrink=0.75)        
+        f.colorbar(plt.cm.ScalarMappable(norm=norm, cmap='viridis'),ax=ax1, shrink=0.75)
         #330 is dec 14th at 5PM. 408 is dec 16th at 5 PM
 
 
diff --git a/tests/a68/input.nml b/tests/a68/input.nml
index b4eae13..f216136 100644
--- a/tests/a68/input.nml
+++ b/tests/a68/input.nml
@@ -3,49 +3,55 @@
   vert_int_ocean_vel=.false.!.true.
   data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
   Old_wrong_Rearth_and_SSH=.false.
-  no_wind=.false.  
+  !mom_Rearth=.true.
+  Rearth=6363827
+  !6363827 !6.378e6
+  no_wind=.false.
   tau_is_velocity=.true.!.false.
   ibdt=1800.0 !seconds
   ibuo=0.0 !ocean x velocity
   ibvo=0.0 !ocean y velocity
   ibui=0.0 !ice x velocity
   ibvi=0.0 !ice y velocity
-  ibhrs=360 !120 !360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  ibhrs=432 !360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
   write_time_inc = 48 !increment at which time is written to screen
-  nmax=432 !298 !310 !99999 !310 !999999999 !max number of timesteps
-  saverestart=.false.!.true.!.false.
+  nmax=999999999 !max number of timesteps
+  saverestart=.false.
   halo=3
   debug=.true.
   reverse_a68_forcings=.false.
   transient_a68_data_start_ind=206 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
-  Rearth=6363827
-  !6.371229e6
 /
 
 &icebergs_nml
 
-    A68_test=.false. !.true. !.false.
-    short_step_mts_grounding=.true.
-    !rev_mind=.true.
     Rearth=6363827
-    tau_is_velocity=.true.!.false.
-    ocean_drag_scale=10 !20. !1
+    !6363827 !6.378e6 !6.371229e6 !6.36e6 !6.378e6
+    A68_test=.true.
+    A68_xdisp=-37.51
+    A68_ydisp=-55.2166
+    short_step_mts_grounding=.true.
 
-    add_curl_to_torque=.false.
+    tau_is_velocity=.true.!.false.
+    ocean_drag_scale=17.8 !20. !1
 
     skip_first_outer_mts_step=.true.
+    add_curl_to_torque=.false.
 
     constant_interaction_LW=.true.
 
-    traj_name=hex_yn.1_nf_od10_rad_drag_E1e6.nc
+    traj_name=longrun_od_17.8_tn_ng_ydn.1_ss90_ns18_rx-37.51_ry-55.2166_1p.nc
+    bond_traj_name=longrun_od_17.8_tn_ng_ydn.1_ss90_ns18_rx-37.51_ry-55.2166_bonds_1p.nc
+    
+    break_bonds_on_sub_steps=.true.
+
+    power_ground=.false.
 
-    radius_based_drag=.true.
-    !orig_dem_moment_of_inertia=.true.
+    save_bond_forces=.true.
 
     dem=.true.
     poisson=0.3
-    dem_damping_coef=1
-    !1.0
+    dem_damping_coef=1.0
     explicit_inner_mts=.true.
     rho_bergs=850. ! (850) iceberg density
     !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
@@ -53,17 +59,16 @@
     !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
     !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
     !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=1.e6 !5e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
     !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    !spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7, r=1500, and square pack
-    !spring_coef=0.0007547062342348049 !if dem_spring_coef=0.5e7, r=1500, and hex pack
-    spring_coef=0.00037735311711740245 !if dem_spring_coef=2.5e6, r=1500, and hex pack
-    
+    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
+    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
+
     monitor_energy=.false.
     !defaults given in parentheses:
     new_mts=.true.
     mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=200 !125!75 !75 !150 !50 !(-1) # of mts sub-steps
+    mts_sub_steps=90 !200 !75 !75 !150 !50 !(-1) # of mts sub-steps
     !mts_sub_steps=10
     force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
     convergence_tolerance=1e-4 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
@@ -71,15 +76,15 @@
     contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
     contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
     debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=0
-    h_to_init_grounding=0.
+    cdrag_grounding=1.e4 !0.!1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=0!30!15!50. !15.
     ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
     remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
 
     fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 10000000000
-    frac_thres_n = 25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
-    frac_thres_t = 11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
+    frac_thres_scaling = 1 !0000000
+    frac_thres_n = 18e3 !25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
+    frac_thres_t = 100e3 !1000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
 
     !!fracture_criterion='strain'
     !!frac_thres_n = 0.0162
@@ -89,7 +94,7 @@
     Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
     grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
     grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.true. !.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
     Static_icebergs=.False. ! (T) True=icebergs do no move
 
     bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
@@ -145,14 +150,14 @@
     use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
     input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
     use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors
+    max_bonds=4 ! (6) Max # of bonds passed between processors
     internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
 
     verbose=.false. !(F) Be verbose to stderr
     verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    traj_sample_hrs=0!1 !(24) sampling period for trajectory storage
+    traj_write_hrs=0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.true. !.false. !(F) If T, saves bond trajectories in a separate file
     budget=.false. !(T) Calculate budgets
     debug=.false. !(F) Turn on debugging
     really_debug=.false. !(F) Turn on debugging
@@ -210,7 +215,7 @@
 /
 
  &fms_nml
-       clock_grain='MODULE'
+       clock_grain='NONE'
        domains_stack_size = 2000000
        clock_flags='SYNC'
 /
\ No newline at end of file
diff --git a/tests/a68/input_fill2.nml b/tests/a68/input_fill2.nml
index c991c1a..ff6747d 100644
--- a/tests/a68/input_fill2.nml
+++ b/tests/a68/input_fill2.nml
@@ -29,7 +29,7 @@
     !6363827 !6.378e6 !6.371229e6 !6.36e6 !6.378e6
     A68_test=.true.
     short_step_mts_grounding=.true.
-    
+
     tau_is_velocity=.true.!.false.
     ocean_drag_scale=<od> !20. !1
 
@@ -59,7 +59,7 @@
     !defaults given in parentheses:
     new_mts=.true.
     mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=200 !75 !75 !150 !50 !(-1) # of mts sub-steps
+    mts_sub_steps=<ss> !200 !75 !75 !150 !50 !(-1) # of mts sub-steps
     !mts_sub_steps=10
     force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
     convergence_tolerance=1e-4 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
diff --git a/tests/a68/long_run.nml b/tests/a68/long_run.nml
new file mode 100644
index 0000000..507561d
--- /dev/null
+++ b/tests/a68/long_run.nml
@@ -0,0 +1,217 @@
+&icebergs_driver_nml
+  a68_test=.true.
+  vert_int_ocean_vel=.false.!.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  Old_wrong_Rearth_and_SSH=.false.
+  !mom_Rearth=.true.
+  Rearth=<re>
+  !6363827 !6.378e6
+  no_wind=.false.
+  tau_is_velocity=.true.!.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=432 !360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=999999999 !max number of timesteps
+  saverestart=.false.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=206 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
+/
+
+&icebergs_nml
+
+    Rearth=<re>
+    !6363827 !6.378e6 !6.371229e6 !6.36e6 !6.378e6
+    A68_test=.true.
+    A68_xdisp=<xd>
+    A68_ydisp=<yd>
+    short_step_mts_grounding=.true.
+
+    tau_is_velocity=.true.
+    ocean_drag_scale=<od>
+
+    skip_first_outer_mts_step=.true.
+    add_curl_to_torque=.false.
+
+    constant_interaction_LW=.true.
+
+    traj_name=<name>_1p.nc
+    bond_traj_name=<name>_bonds_1p.nc
+    
+    break_bonds_on_sub_steps=.true.
+
+    power_ground=.false.
+
+    save_bond_forces=.true.
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
+    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=<ss> !200 !75 !75 !150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-4 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=<gc> !0.!1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=0!30!15!50. !15.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 1
+    frac_thres_n = <ns>e3
+    frac_thres_t = 100e3
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=0!1 !(24) sampling period for trajectory storage
+    traj_write_hrs=0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.true. !.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.false. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='NONE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/a68/long_run_for_paper.sh b/tests/a68/long_run_for_paper.sh
new file mode 100755
index 0000000..dc9d45d
--- /dev/null
+++ b/tests/a68/long_run_for_paper.sh
@@ -0,0 +1,30 @@
+#!/bin/bash
+
+Rearth=6363827
+odrag=(17.8)
+name=(longrun_od_17.8_tn_ng_ydn.1_ss90_ns18_rx-37.51_ry-55.2166)
+ss=90
+gcoef=(1.e4)
+nstress=(18)
+A68dx=-37.51
+A68dy=-55.2166
+
+for ((i = 0; i < ${#odrag[@]}; ++i)); do
+    drag=(${odrag[$i]})
+    fname=(${name[$i]})
+    gc=(${gcoef[$i]})
+    ns=(${nstress[$i]})
+
+    echo $drag
+    echo $fname
+    echo $Rearth
+    echo $ss
+    echo $A68dx
+    echo $A68dy
+    echo $ns
+
+    sed  "s/<od>/$drag/; s/<re>/$Rearth/; s/<ss>/$ss/; s/<ns>/$ns/; s/<gc>/$gc/; s/<xd>/$A68dx/; s/<yd>/$A68dy/; s/<name>/$fname/g" \
+	 long_run.nml > input.nml
+    ./RUN1p
+    # &>/dev/null &
+done
diff --git a/tests/a68/square_for_restart_od_17.8_ydn.1_ss90.nml b/tests/a68/square_for_restart_od_17.8_ydn.1_ss90.nml
new file mode 100644
index 0000000..87d92bd
--- /dev/null
+++ b/tests/a68/square_for_restart_od_17.8_ydn.1_ss90.nml
@@ -0,0 +1,211 @@
+&icebergs_driver_nml
+  a68_test=.true.
+  vert_int_ocean_vel=.false.!.true.
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  Old_wrong_Rearth_and_SSH=.false.
+  !mom_Rearth=.false.
+  Rearth=6363827
+  no_wind=.false.
+  tau_is_velocity=.true.!.false.
+  ibdt=1800.0 !seconds
+  ibuo=0.0 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=298 !max number of timesteps
+  saverestart=.true. !.false. !.true. !.false.
+  halo=3
+  debug=.true.
+  reverse_a68_forcings=.false.
+  transient_a68_data_start_ind=206 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
+/
+
+&icebergs_nml
+
+    Rearth=6363827
+    A68_test=.true.
+    short_step_mts_grounding=.true.
+    
+    tau_is_velocity=.true.
+    ocean_drag_scale=17.8 !19.5 !<od>
+
+    skip_first_outer_mts_step=.true.
+    add_curl_to_torque=.false.
+
+    constant_interaction_LW=.true.
+
+    traj_name='square_for_restart_od17.8_ydn.1_ss90.nc' !<name>
+    bond_traj_name='square_for_restart_od17.8_ydn.1_bonds.nc'
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
+    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
+    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=90 !75 !75 !150 !50 !(-1) # of mts sub-steps
+    !mts_sub_steps=10
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-4 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=0.!1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    h_to_init_grounding=0!30!15!50. !15.
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 10000000
+    frac_thres_n = 25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
+    frac_thres_t = 11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
+
+    !!fracture_criterion='strain'
+    !!frac_thres_n = 0.0162
+    !!frac_thres_t = 0.0457
+
+    halo=3 !(4) halo width
+    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=4 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=0 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !.true. !.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.false. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
\ No newline at end of file
diff --git a/tests/a68/square_r_ssf.nml b/tests/a68/square_r_ssf.nml
index f39cef9..b51894c 100644
--- a/tests/a68/square_r_ssf.nml
+++ b/tests/a68/square_r_ssf.nml
@@ -34,13 +34,16 @@
 
     constant_interaction_LW=.true.
 
-    traj_name=sq_ssf_ssg<gc>_od<od>_addsm<a68>_rectx<xd>_y<yd>_n<ns>_t<ts>.nc
+    !traj_name=sq_ssf_ssg<gc>_od<od>_addsm<a68>_rectx<xd>_y<yd>_n<ns>_t<ts>.nc
+    traj_name=sq_ssfg_gc<gc>_od<od>_rx<xd>_y<yd>_n<ns>_t<ts>_ss<ss>.nc
     !bond_traj_name=<bname>
 
     no_frac_first_ts=.true.
     break_bonds_on_sub_steps=.true.
     power_ground=<pg>
 
+    save_bond_forces=.true.
+
     dem=.true.
     poisson=0.3
     dem_damping_coef=1.0

From 684e66cc48fe57c209c5d0c9df21d2142fa2eab4 Mon Sep 17 00:00:00 2001
From: Alex Huth <ahuth@princeton.edu>
Date: Thu, 20 Jan 2022 17:24:33 -0500
Subject: [PATCH 316/361] Delete makeberg.ipynb

---
 tests/a68/makeberg/makeberg.ipynb | 441 ------------------------------
 1 file changed, 441 deletions(-)
 delete mode 100644 tests/a68/makeberg/makeberg.ipynb

diff --git a/tests/a68/makeberg/makeberg.ipynb b/tests/a68/makeberg/makeberg.ipynb
deleted file mode 100644
index 70a29cb..0000000
--- a/tests/a68/makeberg/makeberg.ipynb
+++ /dev/null
@@ -1,441 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": 1,
-   "id": "2abe9955",
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "Matplotlib is building the font cache; this may take a moment.\n"
-     ]
-    }
-   ],
-   "source": [
-    "import numpy as np\n",
-    "import math\n",
-    "from netCDF4 import Dataset\n",
-    "from pylab import *\n",
-    "import netCDF4 as nc\n",
-    "import xarray as xr"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "184ddcbc",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data'\n",
-    "a68_experiment_berg_2020_12_14_gridded_ll_p0625_cropped.nc  \n",
-    "a68_experiment_ocean_vel_oras5_dec2020_ll_p125.nc\n",
-    "a68_experiment_gebco_ll_p125.nc                             \n",
-    "a68_experiment_wind_vel_jra55_dec2020_ll_p125.nc"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "8bb3e5dc",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#!/usr/bin/env python\n",
-    "\n",
-    "\n",
-    "#\n",
-    "# Initialize 2 iceberg elements, which can later be bonded in the fortran code if needed\n",
-    "#\n",
-    "\n",
-    "def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):\n",
-    "\n",
-    "    print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'\n",
-    "    # To copy the global attributes of the netCDF file\n",
-    "\n",
-    "    #Input and output files\n",
-    "    #Create Empty restart file. This is later read so that the attributes can be used.\n",
-    "    Empty_restart_filename='output_files/Empty_icebergs.res.nc'\n",
-    "    create_empty_iceberg_restart_file(Empty_restart_filename)\n",
-    "    #Empty_restart_filename='input_files/icebergs.res.nc'\n",
-    "\n",
-    "    #Read empty restart file\n",
-    "    f=Dataset(Empty_restart_filename,'r') # r is for read only\n",
-    "    #Write a new restart file\n",
-    "    g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file\n",
-    "\n",
-    "    for attname in f.ncattrs():\n",
-    "            setattr(g,attname,getattr(f,attname))\n",
-    "\n",
-    "\n",
-    "    # To copy the dimension of the netCDF file\n",
-    "    for dimname,dim in f.dimensions.iteritems():\n",
-    "        # if you want to make changes in the dimensions of the new file\n",
-    "        # you should add your own conditions here before the creation of the dimension.\n",
-    "        #g.createDimension(dimname,len(dim))\n",
-    "        g.createDimension(dimname,Number_of_bergs)\n",
-    "\n",
-    "    # To copy the variables of the netCDF file\n",
-    "\n",
-    "    for varname,ncvar in f.variables.iteritems():\n",
-    "        # if you want to make changes in the variables of the new file\n",
-    "        # you should add your own conditions here before the creation of the variable.\n",
-    "        var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)\n",
-    "        #Proceed to copy the variable attributes\n",
-    "        for attname in ncvar.ncattrs():\n",
-    "            setattr(var,attname,getattr(ncvar,attname))\n",
-    "        #Finally copy the variable data to the new created variable\n",
-    "        #var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.\n",
-    "\n",
-    "        if varname=='i':\n",
-    "            var[:]=Number_of_bergs\n",
-    "\n",
-    "        if varname=='iceberg_num':\n",
-    "            for j in range(Number_of_bergs):\n",
-    "                #var[j]=j+1\n",
-    "                var[j]=iceberg_num[j]\n",
-    "\n",
-    "        if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\\\n",
-    "        or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \\\n",
-    "        or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \\\n",
-    "        or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\\\n",
-    "            var[:]=0\n",
-    "\n",
-    "                if varname=='uvel':\n",
-    "                        var[:]=uvel\n",
-    "\n",
-    "                if varname=='vvel':\n",
-    "                        var[:]=vvel\n",
-    "\n",
-    "        if varname=='mass_scaling':\n",
-    "            var[:]=mass_scaling\n",
-    "\n",
-    "        if varname=='thickness':\n",
-    "            for j in range(Number_of_bergs):\n",
-    "                var[j]=thickness[j]\n",
-    "\n",
-    "        if varname=='mass':\n",
-    "            for j in range(Number_of_bergs):\n",
-    "                var[j]=mass[j]\n",
-    "\n",
-    "        if varname=='width'  or varname=='length':\n",
-    "            for j in range(Number_of_bergs):\n",
-    "                var[j]=width[j]\n",
-    "\n",
-    "        if varname=='lon':\n",
-    "            for j in range(Number_of_bergs):\n",
-    "                var[j]=lon[j]\n",
-    "\n",
-    "        if varname=='lat':\n",
-    "            for j in range(Number_of_bergs):\n",
-    "                var[j]=lat[j]\n",
-    "\n",
-    "        if varname=='static_berg':\n",
-    "            for j in range(Number_of_bergs):\n",
-    "                var[j]=static_berg[j]\n",
-    "\n",
-    "\n",
-    "    f.close()\n",
-    "    g.close()\n",
-    "\n",
-    "\n",
-    "def create_empty_iceberg_restart_file(Empty_restart_filename):\n",
-    "\n",
-    "    f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')\n",
-    "\n",
-    "    i=f.createDimension('i', None)\n",
-    "    lon=f.createVariable('i','i')\n",
-    "\n",
-    "    lon=f.createVariable('lon','d',('i'))\n",
-    "    lon.long_name = \"longitude\" ;\n",
-    "    lon.units = \"degrees_E\" ;\n",
-    "    lon.checksum = \"               0\" ;\n",
-    "\n",
-    "    lat=f.createVariable('lat','d',('i'))\n",
-    "    lat.long_name = \"latitude\" ;\n",
-    "    lat.units = \"degrees_N\" ;\n",
-    "    lat.checksum = \"               0\" ;\n",
-    "\n",
-    "    uvel=f.createVariable('uvel','d',('i'))\n",
-    "    uvel.long_name = \"zonal velocity\" ;\n",
-    "    uvel.units = \"m/s\" ;\n",
-    "    uvel.checksum = \"               0\" ;\n",
-    "\n",
-    "    vvel=f.createVariable('vvel','d',('i'))\n",
-    "    vvel.long_name = \"meridional velocity\" ;\n",
-    "    vvel.units = \"m/s\" ;\n",
-    "    vvel.checksum = \"               0\" ;\n",
-    "\n",
-    "    mass=f.createVariable('mass','d',('i'))\n",
-    "    mass.long_name = \"mass\" ;\n",
-    "    mass.units = \"kg\" ;\n",
-    "    mass.checksum = \"               0\" ;\n",
-    "\n",
-    "    axn=f.createVariable('axn','d',('i'))\n",
-    "    axn.long_name = \"explicit zonal acceleration\" ;\n",
-    "    axn.units = \"m/s^2\" ;\n",
-    "    axn.checksum = \"               0\" ;\n",
-    "\n",
-    "    ayn=f.createVariable('ayn','d',('i'))\n",
-    "    ayn.long_name = \"explicit meridional acceleration\" ;\n",
-    "    ayn.units = \"m/s^2\" ;\n",
-    "    ayn.checksum = \"               0\" ;\n",
-    "\n",
-    "    bxn=f.createVariable('bxn','d',('i'))\n",
-    "    bxn.long_name = \"inplicit zonal acceleration\" ;\n",
-    "    bxn.units = \"m/s^2\" ;\n",
-    "    bxn.checksum = \"               0\" ;\n",
-    "\n",
-    "    byn=f.createVariable('byn','d',('i'))\n",
-    "    byn.long_name = \"implicit meridional acceleration\" ;\n",
-    "    byn.units = \"m/s^2\" ;\n",
-    "    byn.checksum = \"               0\" ;\n",
-    "\n",
-    "    ine=f.createVariable('ine','i',('i'))\n",
-    "    ine.long_name = \"i index\" ;\n",
-    "    ine.units = \"none\" ;\n",
-    "    ine.packing = 0 ;\n",
-    "    ine.checksum = \"               0\" ;\n",
-    "\n",
-    "    jne=f.createVariable('jne','i',('i'))\n",
-    "    jne.long_name = \"j index\" ;\n",
-    "    jne.units = \"none\" ;\n",
-    "    jne.packing = 0 ;\n",
-    "    jne.checksum = \"               0\" ;\n",
-    "\n",
-    "    thickness=f.createVariable('thickness','d',('i'))\n",
-    "    thickness.long_name = \"thickness\" ;\n",
-    "    thickness.units = \"m\" ;\n",
-    "    thickness.checksum = \"               0\" ;\n",
-    "\n",
-    "    width=f.createVariable('width','d',('i'))\n",
-    "    width.long_name = \"width\" ;\n",
-    "    width.units = \"m\" ;\n",
-    "    width.checksum = \"               0\" ;\n",
-    "\n",
-    "    length=f.createVariable('length','d',('i'))\n",
-    "    length.long_name = \"length\" ;\n",
-    "    length.units = \"m\" ;\n",
-    "    length.checksum = \"               0\" ;\n",
-    "\n",
-    "    start_lon=f.createVariable('start_lon','d',('i'))\n",
-    "    start_lon.long_name = \"longitude of calving location\" ;\n",
-    "    start_lon.units = \"degrees_E\" ;\n",
-    "    start_lon.checksum = \"               0\" ;\n",
-    "\n",
-    "    start_lat=f.createVariable('start_lat','d',('i'))\n",
-    "    start_lat.long_name = \"latitude of calving location\" ;\n",
-    "    start_lat.units = \"degrees_N\" ;\n",
-    "    start_lat.checksum = \"               0\" ;\n",
-    "\n",
-    "    start_year=f.createVariable('start_year','i',('i'))\n",
-    "    start_year.long_name = \"calendar year of calving event\" ;\n",
-    "    start_year.units = \"years\" ;\n",
-    "    start_year.packing = 0 ;\n",
-    "    start_year.checksum = \"               0\" ;\n",
-    "\n",
-    "    iceberg_num=f.createVariable('iceberg_num','i',('i'))\n",
-    "    iceberg_num.long_name = \"identification of the iceberg\" ;\n",
-    "    iceberg_num.units = \"dimensionless\" ;\n",
-    "    iceberg_num.packing = 0 ;\n",
-    "    iceberg_num.checksum = \"               0\" ;\n",
-    "\n",
-    "    start_day=f.createVariable('start_day','d',('i'))\n",
-    "    start_day.long_name = \"year day of calving event\" ;\n",
-    "    start_day.units = \"days\" ;\n",
-    "    start_day.checksum = \"               0\" ;\n",
-    "\n",
-    "    start_mass=f.createVariable('start_mass','d',('i'))\n",
-    "    start_mass.long_name = \"initial mass of calving berg\" ;\n",
-    "    start_mass.units = \"kg\" ;\n",
-    "    start_mass.checksum = \"               0\" ;\n",
-    "\n",
-    "    mass_scaling=f.createVariable('mass_scaling','d',('i'))\n",
-    "    mass_scaling.long_name = \"scaling factor for mass of calving berg\" ;\n",
-    "    mass_scaling.units = \"none\" ;\n",
-    "    mass_scaling.checksum = \"               0\" ;\n",
-    "\n",
-    "    mass_of_bits=f.createVariable('mass_of_bits','d',('i'))\n",
-    "    mass_of_bits.long_name = \"mass of bergy bits\" ;\n",
-    "    mass_of_bits.units = \"kg\" ;\n",
-    "    mass_of_bits.checksum = \"               0\" ;\n",
-    "\n",
-    "    heat_density=f.createVariable('heat_density','d',('i'))\n",
-    "    heat_density.long_name = \"heat density\" ;\n",
-    "    heat_density.units = \"J/kg\" ;\n",
-    "    heat_density.checksum = \"               0\" ;\n",
-    "\n",
-    "    halo_berg=f.createVariable('halo_berg','d',('i'))\n",
-    "    halo_berg.long_name = \"halo_berg\" ;\n",
-    "    halo_berg.units = \"dimensionless\" ;\n",
-    "    halo_berg.checksum = \"               0\" ;\n",
-    "\n",
-    "    static_berg=f.createVariable('static_berg','d',('i'))\n",
-    "    static_berg.long_name = \"static_berg\" ;\n",
-    "    static_berg.units = \"dimensionless\" ;\n",
-    "    static_berg.checksum = \"               0\" ;\n",
-    "\n",
-    "    f.sync()\n",
-    "    f.close()\n",
-    "\n",
-    "\n",
-    "\n",
-    "#-----------------------------------#\n",
-    "#               Main                #\n",
-    "#-----------------------------------#\n",
-    "\n",
-    "# just2particles=False\n",
-    "# flip2ndconglom=True#False\n",
-    "# offset2ndconglom=True#False\n",
-    "\n",
-    "grdxmin=0; grdxmax=45000e3\n",
-    "grdymin=0; grdymax=45000e3\n",
-    "grdres=1000.0\n",
-    "R_frac=0.45 #1st option\n",
-    "#R_frac=0.5*0.45 #2nd option\n",
-    "radius=(np.sqrt(3)/2.)*(R_frac*grdres) #S is < 0.5 grid res\n",
-    "#radius2=(np.sqrt(3)/2.)*(R_frac2*grdres) #S is < 0.5 grid res\n",
-    "thickness1=200.0\n",
-    "thickness2=200.0\n",
-    "rho_ice=850.0\n",
-    "\n",
-    "\n",
-    "nbergs=1 #number of conglomerates\n",
-    "\n",
-    "#center coords of each (rectangular) conglomerate berg (CB=conglomerate berg)\n",
-    "CBxc=np.array([3500]); CByc=np.array([15000])\n",
-    "#side lengths\n",
-    "CBxl=np.array([4000]); CByl=np.array([8000])\n",
-    "\n",
-    "\n",
-    "CByl=CByl.astype(int); CBxl=CBxl.astype(int)\n",
-    "\n",
-    "#--- xmax, xmin, ymax, ymin for each CB --\n",
-    "CBxmin=CBxc-(0.5*CBxl); CBxmax=CBxc+(0.5*CBxl)\n",
-    "CBymin=CByc-(0.5*CByl); CBymax=CByc+(0.5*CByl)\n",
-    "#this shouldn't happen:\n",
-    "CBxmin[CBxmin<grdxmin]=grdxmin; CBxmax[CBxmax>grdxmax]=grdxmax\n",
-    "CBymin[CBxmin<grdymin]=grdymin; CBymax[CBymax>grdymax]=grdymax\n",
-    "CBxc=0.5*(CBxmin+CBxmax); CByc=0.5*(CBymin+CBymax)\n",
-    "\n",
-    "# #if just want one particle per CB\n",
-    "# if just2particles:\n",
-    "#         CBxmin=CBxc; CBxmax=CBxc\n",
-    "#         CBymin=CByc; CBymax=CByc\n",
-    "\n",
-    "#--- min and max thicknesses for each CB ---\n",
-    "h1=thickness1\n",
-    "h2=thickness2\n",
-    "CBhmax=np.array([h1]); CBhmin=np.array([h2])\n",
-    "\n",
-    "#radii\n",
-    "CBrad=np.array([radius])\n",
-    "print('radii',CBrad)\n",
-    "\n",
-    "berg_x=[]; berg_y=[]\n",
-    "berg_id=[]; berg_static=[]\n",
-    "berg_width=[]; berg_bonds=[]\n",
-    "berg_h=[]; berg_mass_scaling=[]\n",
-    "berg_mass=[]\n",
-    "berg_uvel=[]; berg_vvel=[]\n",
-    "\n",
-    "berg_count=0\n",
-    "\n",
-    "for i in range(nbergs):\n",
-    "        x_start=CBxmin[i]+(CBrad[i]*2./np.sqrt(3))\n",
-    "\n",
-    "        # if flip2ndconglom and i>0:\n",
-    "        #         x_start=CBxmax[i]-(CBrad[i]*2./np.sqrt(3))\n",
-    "\n",
-    "        #pdb.set_trace()\n",
-    "        if x_start>CBxmax[i]:\n",
-    "                x_start=CBxmax[i]\n",
-    "        y_start0=CBymin[i]+CBrad[i]\n",
-    "        if y_start0>CBymax[i]:\n",
-    "                y_start0=CBymax[i]\n",
-    "        element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*(CBrad[i])**2)\n",
-    "        #H (thickness) is a linear function of a berg element's position from the\n",
-    "        #center of the CB. H=Hmax at the center of the CB and H=Hmin at a corner of the\n",
-    "        #CB, where the dist of a corner from the center is:\n",
-    "        cdistb=np.sqrt((CBxmin[i]-CBxc[i])**2+(CBymin[i]-CByc[i])**2)\n",
-    "        j=0\n",
-    "        x_val=x_start\n",
-    "        offset=0.0\n",
-    "        # if (i==0):\n",
-    "        uvel=0.#1\n",
-    "        # else:\n",
-    "        #         uvel=-0.15#-0.05\n",
-    "        #         if (offset2ndconglom):\n",
-    "        #                 offset=250.0\n",
-    "        vvel=0.0#25\n",
-    "        #uvel=0;vvel=0\n",
-    "        #berg_count_start=berg_count\n",
-    "        while x_val<=CBxmax[i] and x_val>=CBxmin[i]:\n",
-    "                y_start=y_start0+((j%2)*CBrad[i])+offset\n",
-    "                k=0\n",
-    "                y_val=y_start\n",
-    "                while y_val<=(CBymax[i]+offset):\n",
-    "                        berg_count=berg_count+1\n",
-    "                        berg_id.append(berg_count)\n",
-    "                        berg_x.append(x_val)\n",
-    "                        berg_y.append(y_val)\n",
-    "                        berg_width.append(sqrt(element_area))\n",
-    "                        #dist of berg elem from center of CB\n",
-    "                        bdistc=np.sqrt((x_val-CBxc[i])**2+(y_val-CByc[i])**2)\n",
-    "                        bh=CBhmin[i]*bdistc/cdistb + CBhmax[i]*(1-bdistc/cdistb)\n",
-    "                        # if (just2particles):\n",
-    "                        #         bh=h1\n",
-    "                        berg_h.append(bh) #thickness\n",
-    "                        berg_mass_scaling.append(1)\n",
-    "                        berg_mass.append(bh*rho_ice*element_area)\n",
-    "                        berg_static.append(0)\n",
-    "                        berg_uvel.append(uvel)\n",
-    "                        berg_vvel.append(vvel)\n",
-    "                        # if (x_val<22000):\n",
-    "                        #         berg_vvel.append(vvel)\n",
-    "                        # else:\n",
-    "                        #         berg_vvel.append(0.4)\n",
-    "                        #berg_CBid.append(i)\n",
-    "                        k=k+1\n",
-    "                        y_val=y_start+(2*k*CBrad[i])\n",
-    "                j=j+1\n",
-    "                # if flip2ndconglom and i>0:\n",
-    "                #         x_val=x_start-(np.sqrt(3)*CBrad[i]*j)\n",
-    "                # else:\n",
-    "                x_val=x_start+(np.sqrt(3)*CBrad[i]*j)\n",
-    "\n",
-    "print('Number of bergs',berg_count)\n",
-    "\n",
-    "#pdb.set_trace()\n",
-    "\n",
-    "#Create iceberg restart file\n",
-    "Ice_geometry_source='Generic'\n",
-    "Create_iceberg_restart_file(berg_count,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)\n"
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.8"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}

From b857d370fb3349bc1ee63615ce9f559ab01e9ede Mon Sep 17 00:00:00 2001
From: Alex Huth <ahuth@princeton.edu>
Date: Thu, 20 Jan 2022 17:24:51 -0500
Subject: [PATCH 317/361] Delete makeberg-checkpoint.ipynb

---
 .../makeberg-checkpoint.ipynb                 | 441 ------------------
 1 file changed, 441 deletions(-)
 delete mode 100644 tests/a68/makeberg/.ipynb_checkpoints/makeberg-checkpoint.ipynb

diff --git a/tests/a68/makeberg/.ipynb_checkpoints/makeberg-checkpoint.ipynb b/tests/a68/makeberg/.ipynb_checkpoints/makeberg-checkpoint.ipynb
deleted file mode 100644
index 70a29cb..0000000
--- a/tests/a68/makeberg/.ipynb_checkpoints/makeberg-checkpoint.ipynb
+++ /dev/null
@@ -1,441 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": 1,
-   "id": "2abe9955",
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "Matplotlib is building the font cache; this may take a moment.\n"
-     ]
-    }
-   ],
-   "source": [
-    "import numpy as np\n",
-    "import math\n",
-    "from netCDF4 import Dataset\n",
-    "from pylab import *\n",
-    "import netCDF4 as nc\n",
-    "import xarray as xr"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "184ddcbc",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data'\n",
-    "a68_experiment_berg_2020_12_14_gridded_ll_p0625_cropped.nc  \n",
-    "a68_experiment_ocean_vel_oras5_dec2020_ll_p125.nc\n",
-    "a68_experiment_gebco_ll_p125.nc                             \n",
-    "a68_experiment_wind_vel_jra55_dec2020_ll_p125.nc"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "8bb3e5dc",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#!/usr/bin/env python\n",
-    "\n",
-    "\n",
-    "#\n",
-    "# Initialize 2 iceberg elements, which can later be bonded in the fortran code if needed\n",
-    "#\n",
-    "\n",
-    "def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):\n",
-    "\n",
-    "    print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'\n",
-    "    # To copy the global attributes of the netCDF file\n",
-    "\n",
-    "    #Input and output files\n",
-    "    #Create Empty restart file. This is later read so that the attributes can be used.\n",
-    "    Empty_restart_filename='output_files/Empty_icebergs.res.nc'\n",
-    "    create_empty_iceberg_restart_file(Empty_restart_filename)\n",
-    "    #Empty_restart_filename='input_files/icebergs.res.nc'\n",
-    "\n",
-    "    #Read empty restart file\n",
-    "    f=Dataset(Empty_restart_filename,'r') # r is for read only\n",
-    "    #Write a new restart file\n",
-    "    g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file\n",
-    "\n",
-    "    for attname in f.ncattrs():\n",
-    "            setattr(g,attname,getattr(f,attname))\n",
-    "\n",
-    "\n",
-    "    # To copy the dimension of the netCDF file\n",
-    "    for dimname,dim in f.dimensions.iteritems():\n",
-    "        # if you want to make changes in the dimensions of the new file\n",
-    "        # you should add your own conditions here before the creation of the dimension.\n",
-    "        #g.createDimension(dimname,len(dim))\n",
-    "        g.createDimension(dimname,Number_of_bergs)\n",
-    "\n",
-    "    # To copy the variables of the netCDF file\n",
-    "\n",
-    "    for varname,ncvar in f.variables.iteritems():\n",
-    "        # if you want to make changes in the variables of the new file\n",
-    "        # you should add your own conditions here before the creation of the variable.\n",
-    "        var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)\n",
-    "        #Proceed to copy the variable attributes\n",
-    "        for attname in ncvar.ncattrs():\n",
-    "            setattr(var,attname,getattr(ncvar,attname))\n",
-    "        #Finally copy the variable data to the new created variable\n",
-    "        #var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.\n",
-    "\n",
-    "        if varname=='i':\n",
-    "            var[:]=Number_of_bergs\n",
-    "\n",
-    "        if varname=='iceberg_num':\n",
-    "            for j in range(Number_of_bergs):\n",
-    "                #var[j]=j+1\n",
-    "                var[j]=iceberg_num[j]\n",
-    "\n",
-    "        if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\\\n",
-    "        or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \\\n",
-    "        or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \\\n",
-    "        or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\\\n",
-    "            var[:]=0\n",
-    "\n",
-    "                if varname=='uvel':\n",
-    "                        var[:]=uvel\n",
-    "\n",
-    "                if varname=='vvel':\n",
-    "                        var[:]=vvel\n",
-    "\n",
-    "        if varname=='mass_scaling':\n",
-    "            var[:]=mass_scaling\n",
-    "\n",
-    "        if varname=='thickness':\n",
-    "            for j in range(Number_of_bergs):\n",
-    "                var[j]=thickness[j]\n",
-    "\n",
-    "        if varname=='mass':\n",
-    "            for j in range(Number_of_bergs):\n",
-    "                var[j]=mass[j]\n",
-    "\n",
-    "        if varname=='width'  or varname=='length':\n",
-    "            for j in range(Number_of_bergs):\n",
-    "                var[j]=width[j]\n",
-    "\n",
-    "        if varname=='lon':\n",
-    "            for j in range(Number_of_bergs):\n",
-    "                var[j]=lon[j]\n",
-    "\n",
-    "        if varname=='lat':\n",
-    "            for j in range(Number_of_bergs):\n",
-    "                var[j]=lat[j]\n",
-    "\n",
-    "        if varname=='static_berg':\n",
-    "            for j in range(Number_of_bergs):\n",
-    "                var[j]=static_berg[j]\n",
-    "\n",
-    "\n",
-    "    f.close()\n",
-    "    g.close()\n",
-    "\n",
-    "\n",
-    "def create_empty_iceberg_restart_file(Empty_restart_filename):\n",
-    "\n",
-    "    f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')\n",
-    "\n",
-    "    i=f.createDimension('i', None)\n",
-    "    lon=f.createVariable('i','i')\n",
-    "\n",
-    "    lon=f.createVariable('lon','d',('i'))\n",
-    "    lon.long_name = \"longitude\" ;\n",
-    "    lon.units = \"degrees_E\" ;\n",
-    "    lon.checksum = \"               0\" ;\n",
-    "\n",
-    "    lat=f.createVariable('lat','d',('i'))\n",
-    "    lat.long_name = \"latitude\" ;\n",
-    "    lat.units = \"degrees_N\" ;\n",
-    "    lat.checksum = \"               0\" ;\n",
-    "\n",
-    "    uvel=f.createVariable('uvel','d',('i'))\n",
-    "    uvel.long_name = \"zonal velocity\" ;\n",
-    "    uvel.units = \"m/s\" ;\n",
-    "    uvel.checksum = \"               0\" ;\n",
-    "\n",
-    "    vvel=f.createVariable('vvel','d',('i'))\n",
-    "    vvel.long_name = \"meridional velocity\" ;\n",
-    "    vvel.units = \"m/s\" ;\n",
-    "    vvel.checksum = \"               0\" ;\n",
-    "\n",
-    "    mass=f.createVariable('mass','d',('i'))\n",
-    "    mass.long_name = \"mass\" ;\n",
-    "    mass.units = \"kg\" ;\n",
-    "    mass.checksum = \"               0\" ;\n",
-    "\n",
-    "    axn=f.createVariable('axn','d',('i'))\n",
-    "    axn.long_name = \"explicit zonal acceleration\" ;\n",
-    "    axn.units = \"m/s^2\" ;\n",
-    "    axn.checksum = \"               0\" ;\n",
-    "\n",
-    "    ayn=f.createVariable('ayn','d',('i'))\n",
-    "    ayn.long_name = \"explicit meridional acceleration\" ;\n",
-    "    ayn.units = \"m/s^2\" ;\n",
-    "    ayn.checksum = \"               0\" ;\n",
-    "\n",
-    "    bxn=f.createVariable('bxn','d',('i'))\n",
-    "    bxn.long_name = \"inplicit zonal acceleration\" ;\n",
-    "    bxn.units = \"m/s^2\" ;\n",
-    "    bxn.checksum = \"               0\" ;\n",
-    "\n",
-    "    byn=f.createVariable('byn','d',('i'))\n",
-    "    byn.long_name = \"implicit meridional acceleration\" ;\n",
-    "    byn.units = \"m/s^2\" ;\n",
-    "    byn.checksum = \"               0\" ;\n",
-    "\n",
-    "    ine=f.createVariable('ine','i',('i'))\n",
-    "    ine.long_name = \"i index\" ;\n",
-    "    ine.units = \"none\" ;\n",
-    "    ine.packing = 0 ;\n",
-    "    ine.checksum = \"               0\" ;\n",
-    "\n",
-    "    jne=f.createVariable('jne','i',('i'))\n",
-    "    jne.long_name = \"j index\" ;\n",
-    "    jne.units = \"none\" ;\n",
-    "    jne.packing = 0 ;\n",
-    "    jne.checksum = \"               0\" ;\n",
-    "\n",
-    "    thickness=f.createVariable('thickness','d',('i'))\n",
-    "    thickness.long_name = \"thickness\" ;\n",
-    "    thickness.units = \"m\" ;\n",
-    "    thickness.checksum = \"               0\" ;\n",
-    "\n",
-    "    width=f.createVariable('width','d',('i'))\n",
-    "    width.long_name = \"width\" ;\n",
-    "    width.units = \"m\" ;\n",
-    "    width.checksum = \"               0\" ;\n",
-    "\n",
-    "    length=f.createVariable('length','d',('i'))\n",
-    "    length.long_name = \"length\" ;\n",
-    "    length.units = \"m\" ;\n",
-    "    length.checksum = \"               0\" ;\n",
-    "\n",
-    "    start_lon=f.createVariable('start_lon','d',('i'))\n",
-    "    start_lon.long_name = \"longitude of calving location\" ;\n",
-    "    start_lon.units = \"degrees_E\" ;\n",
-    "    start_lon.checksum = \"               0\" ;\n",
-    "\n",
-    "    start_lat=f.createVariable('start_lat','d',('i'))\n",
-    "    start_lat.long_name = \"latitude of calving location\" ;\n",
-    "    start_lat.units = \"degrees_N\" ;\n",
-    "    start_lat.checksum = \"               0\" ;\n",
-    "\n",
-    "    start_year=f.createVariable('start_year','i',('i'))\n",
-    "    start_year.long_name = \"calendar year of calving event\" ;\n",
-    "    start_year.units = \"years\" ;\n",
-    "    start_year.packing = 0 ;\n",
-    "    start_year.checksum = \"               0\" ;\n",
-    "\n",
-    "    iceberg_num=f.createVariable('iceberg_num','i',('i'))\n",
-    "    iceberg_num.long_name = \"identification of the iceberg\" ;\n",
-    "    iceberg_num.units = \"dimensionless\" ;\n",
-    "    iceberg_num.packing = 0 ;\n",
-    "    iceberg_num.checksum = \"               0\" ;\n",
-    "\n",
-    "    start_day=f.createVariable('start_day','d',('i'))\n",
-    "    start_day.long_name = \"year day of calving event\" ;\n",
-    "    start_day.units = \"days\" ;\n",
-    "    start_day.checksum = \"               0\" ;\n",
-    "\n",
-    "    start_mass=f.createVariable('start_mass','d',('i'))\n",
-    "    start_mass.long_name = \"initial mass of calving berg\" ;\n",
-    "    start_mass.units = \"kg\" ;\n",
-    "    start_mass.checksum = \"               0\" ;\n",
-    "\n",
-    "    mass_scaling=f.createVariable('mass_scaling','d',('i'))\n",
-    "    mass_scaling.long_name = \"scaling factor for mass of calving berg\" ;\n",
-    "    mass_scaling.units = \"none\" ;\n",
-    "    mass_scaling.checksum = \"               0\" ;\n",
-    "\n",
-    "    mass_of_bits=f.createVariable('mass_of_bits','d',('i'))\n",
-    "    mass_of_bits.long_name = \"mass of bergy bits\" ;\n",
-    "    mass_of_bits.units = \"kg\" ;\n",
-    "    mass_of_bits.checksum = \"               0\" ;\n",
-    "\n",
-    "    heat_density=f.createVariable('heat_density','d',('i'))\n",
-    "    heat_density.long_name = \"heat density\" ;\n",
-    "    heat_density.units = \"J/kg\" ;\n",
-    "    heat_density.checksum = \"               0\" ;\n",
-    "\n",
-    "    halo_berg=f.createVariable('halo_berg','d',('i'))\n",
-    "    halo_berg.long_name = \"halo_berg\" ;\n",
-    "    halo_berg.units = \"dimensionless\" ;\n",
-    "    halo_berg.checksum = \"               0\" ;\n",
-    "\n",
-    "    static_berg=f.createVariable('static_berg','d',('i'))\n",
-    "    static_berg.long_name = \"static_berg\" ;\n",
-    "    static_berg.units = \"dimensionless\" ;\n",
-    "    static_berg.checksum = \"               0\" ;\n",
-    "\n",
-    "    f.sync()\n",
-    "    f.close()\n",
-    "\n",
-    "\n",
-    "\n",
-    "#-----------------------------------#\n",
-    "#               Main                #\n",
-    "#-----------------------------------#\n",
-    "\n",
-    "# just2particles=False\n",
-    "# flip2ndconglom=True#False\n",
-    "# offset2ndconglom=True#False\n",
-    "\n",
-    "grdxmin=0; grdxmax=45000e3\n",
-    "grdymin=0; grdymax=45000e3\n",
-    "grdres=1000.0\n",
-    "R_frac=0.45 #1st option\n",
-    "#R_frac=0.5*0.45 #2nd option\n",
-    "radius=(np.sqrt(3)/2.)*(R_frac*grdres) #S is < 0.5 grid res\n",
-    "#radius2=(np.sqrt(3)/2.)*(R_frac2*grdres) #S is < 0.5 grid res\n",
-    "thickness1=200.0\n",
-    "thickness2=200.0\n",
-    "rho_ice=850.0\n",
-    "\n",
-    "\n",
-    "nbergs=1 #number of conglomerates\n",
-    "\n",
-    "#center coords of each (rectangular) conglomerate berg (CB=conglomerate berg)\n",
-    "CBxc=np.array([3500]); CByc=np.array([15000])\n",
-    "#side lengths\n",
-    "CBxl=np.array([4000]); CByl=np.array([8000])\n",
-    "\n",
-    "\n",
-    "CByl=CByl.astype(int); CBxl=CBxl.astype(int)\n",
-    "\n",
-    "#--- xmax, xmin, ymax, ymin for each CB --\n",
-    "CBxmin=CBxc-(0.5*CBxl); CBxmax=CBxc+(0.5*CBxl)\n",
-    "CBymin=CByc-(0.5*CByl); CBymax=CByc+(0.5*CByl)\n",
-    "#this shouldn't happen:\n",
-    "CBxmin[CBxmin<grdxmin]=grdxmin; CBxmax[CBxmax>grdxmax]=grdxmax\n",
-    "CBymin[CBxmin<grdymin]=grdymin; CBymax[CBymax>grdymax]=grdymax\n",
-    "CBxc=0.5*(CBxmin+CBxmax); CByc=0.5*(CBymin+CBymax)\n",
-    "\n",
-    "# #if just want one particle per CB\n",
-    "# if just2particles:\n",
-    "#         CBxmin=CBxc; CBxmax=CBxc\n",
-    "#         CBymin=CByc; CBymax=CByc\n",
-    "\n",
-    "#--- min and max thicknesses for each CB ---\n",
-    "h1=thickness1\n",
-    "h2=thickness2\n",
-    "CBhmax=np.array([h1]); CBhmin=np.array([h2])\n",
-    "\n",
-    "#radii\n",
-    "CBrad=np.array([radius])\n",
-    "print('radii',CBrad)\n",
-    "\n",
-    "berg_x=[]; berg_y=[]\n",
-    "berg_id=[]; berg_static=[]\n",
-    "berg_width=[]; berg_bonds=[]\n",
-    "berg_h=[]; berg_mass_scaling=[]\n",
-    "berg_mass=[]\n",
-    "berg_uvel=[]; berg_vvel=[]\n",
-    "\n",
-    "berg_count=0\n",
-    "\n",
-    "for i in range(nbergs):\n",
-    "        x_start=CBxmin[i]+(CBrad[i]*2./np.sqrt(3))\n",
-    "\n",
-    "        # if flip2ndconglom and i>0:\n",
-    "        #         x_start=CBxmax[i]-(CBrad[i]*2./np.sqrt(3))\n",
-    "\n",
-    "        #pdb.set_trace()\n",
-    "        if x_start>CBxmax[i]:\n",
-    "                x_start=CBxmax[i]\n",
-    "        y_start0=CBymin[i]+CBrad[i]\n",
-    "        if y_start0>CBymax[i]:\n",
-    "                y_start0=CBymax[i]\n",
-    "        element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*(CBrad[i])**2)\n",
-    "        #H (thickness) is a linear function of a berg element's position from the\n",
-    "        #center of the CB. H=Hmax at the center of the CB and H=Hmin at a corner of the\n",
-    "        #CB, where the dist of a corner from the center is:\n",
-    "        cdistb=np.sqrt((CBxmin[i]-CBxc[i])**2+(CBymin[i]-CByc[i])**2)\n",
-    "        j=0\n",
-    "        x_val=x_start\n",
-    "        offset=0.0\n",
-    "        # if (i==0):\n",
-    "        uvel=0.#1\n",
-    "        # else:\n",
-    "        #         uvel=-0.15#-0.05\n",
-    "        #         if (offset2ndconglom):\n",
-    "        #                 offset=250.0\n",
-    "        vvel=0.0#25\n",
-    "        #uvel=0;vvel=0\n",
-    "        #berg_count_start=berg_count\n",
-    "        while x_val<=CBxmax[i] and x_val>=CBxmin[i]:\n",
-    "                y_start=y_start0+((j%2)*CBrad[i])+offset\n",
-    "                k=0\n",
-    "                y_val=y_start\n",
-    "                while y_val<=(CBymax[i]+offset):\n",
-    "                        berg_count=berg_count+1\n",
-    "                        berg_id.append(berg_count)\n",
-    "                        berg_x.append(x_val)\n",
-    "                        berg_y.append(y_val)\n",
-    "                        berg_width.append(sqrt(element_area))\n",
-    "                        #dist of berg elem from center of CB\n",
-    "                        bdistc=np.sqrt((x_val-CBxc[i])**2+(y_val-CByc[i])**2)\n",
-    "                        bh=CBhmin[i]*bdistc/cdistb + CBhmax[i]*(1-bdistc/cdistb)\n",
-    "                        # if (just2particles):\n",
-    "                        #         bh=h1\n",
-    "                        berg_h.append(bh) #thickness\n",
-    "                        berg_mass_scaling.append(1)\n",
-    "                        berg_mass.append(bh*rho_ice*element_area)\n",
-    "                        berg_static.append(0)\n",
-    "                        berg_uvel.append(uvel)\n",
-    "                        berg_vvel.append(vvel)\n",
-    "                        # if (x_val<22000):\n",
-    "                        #         berg_vvel.append(vvel)\n",
-    "                        # else:\n",
-    "                        #         berg_vvel.append(0.4)\n",
-    "                        #berg_CBid.append(i)\n",
-    "                        k=k+1\n",
-    "                        y_val=y_start+(2*k*CBrad[i])\n",
-    "                j=j+1\n",
-    "                # if flip2ndconglom and i>0:\n",
-    "                #         x_val=x_start-(np.sqrt(3)*CBrad[i]*j)\n",
-    "                # else:\n",
-    "                x_val=x_start+(np.sqrt(3)*CBrad[i]*j)\n",
-    "\n",
-    "print('Number of bergs',berg_count)\n",
-    "\n",
-    "#pdb.set_trace()\n",
-    "\n",
-    "#Create iceberg restart file\n",
-    "Ice_geometry_source='Generic'\n",
-    "Create_iceberg_restart_file(berg_count,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)\n"
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.8"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}

From 26862457b0dff7f8b8e118914efdf7873e539be6 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Wed, 9 Mar 2022 12:41:45 -0500
Subject: [PATCH 318/361] added test dem_test_contact, for varying L_ij, the
 critical-interactive-length scale, for MTS-DEM simulations. Artifically
 increasing L_ij is needed to prevent overlapping of conglomerates under
 contact if their particle radii are low. Also added
 long_run_no_inc_contact_dist.sh and .nml in tests/a68, to test A68a test
 without increaing L_ij (it has essentially no effect, given the large
 particle radii). Some edits to icebergs.F90 to increase computational
 efficiency.

---
 driver/icebergs_driver.F90                    |  38 +-
 src/icebergs.F90                              |  76 ++--
 tests/a68/long_run.nml                        |  14 +-
 ...t.nml => long_run_no_inc_contact_dist.nml} |  48 +--
 tests/a68/long_run_no_inc_contact_dist.sh     |  40 ++
 tests/chaotic_test/.gitignore                 |   4 +-
 tests/dem_test_contact/.gitignore             |   1 +
 tests/dem_test_contact/README                 |   7 +
 tests/dem_test_contact/RUN                    |   7 +
 .../dem_test_contact/animate_trajectories.py  | 161 +++++++
 tests/dem_test_contact/diag_table             |   3 +
 tests/dem_test_contact/input.nml              | 200 +++++++++
 tests/dem_test_contact/makeberg/RUN           |   3 +
 tests/dem_test_contact/makeberg/makeberg.py   | 395 ++++++++++++++++++
 tests/nc2csv.py                               |   6 +-
 15 files changed, 928 insertions(+), 75 deletions(-)
 rename tests/a68/{input.nml => long_run_no_inc_contact_dist.nml} (89%)
 create mode 100755 tests/a68/long_run_no_inc_contact_dist.sh
 create mode 100644 tests/dem_test_contact/.gitignore
 create mode 100644 tests/dem_test_contact/README
 create mode 100755 tests/dem_test_contact/RUN
 create mode 100755 tests/dem_test_contact/animate_trajectories.py
 create mode 100644 tests/dem_test_contact/diag_table
 create mode 100644 tests/dem_test_contact/input.nml
 create mode 100755 tests/dem_test_contact/makeberg/RUN
 create mode 100755 tests/dem_test_contact/makeberg/makeberg.py

diff --git a/driver/icebergs_driver.F90 b/driver/icebergs_driver.F90
index 42815b4..e112545 100644
--- a/driver/icebergs_driver.F90
+++ b/driver/icebergs_driver.F90
@@ -18,6 +18,7 @@ program icebergs_driver
 use mpp_mod, only : mpp_pe
 use mpp_mod, only : mpp_root_pe
 use mpp_mod, only: mpp_sync
+use mpp_mod, only: mpp_exit
 use time_manager_mod, only : time_type
 use time_manager_mod, only : set_date
 use time_manager_mod, only : set_calendar_type
@@ -60,6 +61,7 @@ program icebergs_driver
 logical :: chaotic_test=.false.
 logical :: grounding_test=.false.
 logical :: big_grounding_test=.false.
+logical :: dem_test_contact=.false.
 logical :: a68_test=.false.
 logical :: vert_int_ocean_vel=.false.
 logical :: tau_is_velocity=.true.
@@ -87,7 +89,7 @@ program icebergs_driver
   saverestart,ibui,ibvi,collision_test,chaotic_test,grounding_test,&
   gridres,write_time_inc,bump_depth, sst, a68_test, data_dir, vert_int_ocean_vel,&
   reverse_a68_forcings,tau_is_velocity,transient_a68_data_start_ind,&
-  Old_wrong_Rearth_and_SSH,no_wind,REarth,big_grounding_test !mom_Rearth
+  Old_wrong_Rearth_and_SSH,no_wind,REarth,big_grounding_test,dem_test_contact !mom_Rearth
 ! For loops
 integer :: isc !< Start of i-index for computational domain (used for loops)
 integer :: iec !< End of i-index for computational domain (used for loops)
@@ -334,6 +336,32 @@ program icebergs_driver
     enddo; enddo
     print *,'min, max depth',minval(depth(:,:)),maxval(depth(:,:))
     depth = 1000.0-depth
+  endif
+
+   if (dem_test_contact) then
+    lat(:,:)=lat(:,:)-0.45 !-25000.1
+    lon(:,:)=lon(:,:)-0.45
+    !assign land cells at the N and S portions of the domain.
+    !input.nml: set coastal drift parameter to prevent grounding
+    do j=jsd,jed; do i=isd,ied
+      if (lat(i,j)<=(-5.e3) .or. lat(i,j)>=(220.e3)) wet(i,j)=0.0
+    enddo;enddo
+
+    mid=50.e3
+
+    do j=jsd,jed; do i=isd,ied
+      if (lon(i,j)>65 .or. lat(i,j)==mid) then
+        vo(i,j)=0.0
+      else
+        if (lat(i,j)>mid) then
+          vo(i,j)=-ibvo
+        else
+          vo(i,j)=ibvo
+        endif
+      endif
+  enddo;enddo
+
+
   endif
 
   if (grounding_test) then
@@ -513,13 +541,15 @@ program icebergs_driver
 
 if (saverestart) call icebergs_save_restart(bergs)
 
-!Deallocate all memory and disassociated pointer
-call icebergs_end(bergs)
-
 call cpu_time(time_finish)
 
 if (mpp_pe()==0) then
   write(*,*) 'Simulation finished in ', (time_finish - time_begin)/60., 'minutes'
 end if
 
+call mpp_exit()
+
+!Deallocate all memory and disassociated pointer
+call icebergs_end(bergs)
+
 end program icebergs_driver
diff --git a/src/icebergs.F90 b/src/icebergs.F90
index fedc1b2..f13a2eb 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -1176,6 +1176,7 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
 
           if (current_bond%nstress<0) then
             !if fail under shear with normal compression, then should still feel contact force
+            damping_coef = bergs%dem_damping_coef*sqrt(bergs%dem_K_damp*M1*M2/(M1+M2))
             Fd_x = Fd_x-damping_coef*ur; Fd_y = Fd_y-damping_coef*vr  !linear damping force
             F_x = F_x + Fn_x; F_y = F_y + Fn_y !linear forces
           endif
@@ -2089,7 +2090,7 @@ subroutine accel_explicit_inner_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel,
         do grdi = max(berg%ine-1,bergs%grd%isd+1),min(berg%ine+1,bergs%grd%ied)
         other_berg=>bergs%list(grdi,grdj)%first
         do while (associated(other_berg))
-          if (other_berg%id>0 .and. other_berg%conglom_id.eq.berg%conglom_id) then
+          if (other_berg%id>0 .and. other_berg%conglom_id.eq.berg%conglom_id .and. other_berg%n_bonds<bergs%max_bonds) then
             if (bergs%dem) then
               call calculate_unbonded_same_conglom_dem_force(bergs, berg, other_berg, &
                 IA_x, IA_y, IAd_x, IAd_y, uvel0, vvel0, uvel0, vvel0)
@@ -3392,12 +3393,13 @@ subroutine thermodynamics(bergs)
         if (bergs%use_mixed_melting .or. bergs%allow_bergs_to_roll) then
           N_bonds=0.
           if (bergs%iceberg_bonds_on) then
+            N_bonds=this%n_bonds
             ! Determining number of bonds
-            current_bond=>this%first_bond
-            do while (associated(current_bond)) ! loop over all bonds
-              N_bonds=N_bonds+1.0
-              current_bond=>current_bond%next_bond
-            enddo
+            ! current_bond=>this%first_bond
+            ! do while (associated(current_bond)) ! loop over all bonds
+            !   N_bonds=N_bonds+1.0
+            !   current_bond=>current_bond%next_bond
+            ! enddo
           endif
           if  (this%static_berg .eq. 1)  N_bonds=N_max  !Static icebergs melt like ice shelves
         endif
@@ -7303,35 +7305,40 @@ subroutine evolve_icebergs_mts(bergs)
         do while (associated(berg)) ! loop over all bergs
           !only evolve non-static bergs that overlap, or are part of a conglom that overlaps, the computational domain:
           if (berg%static_berg .lt. 0.5 .and. (berg%conglom_id.ne.0 .or. bergs%force_convergence)) then
-            latn = berg%lat ;   lonn = berg%lon
-            uvel1=berg%uvel ;   vvel1=berg%vvel !V_n (previous cycle)
-            axn  = 0.0      ;   ayn  = 0.0 !note these are redefined at the start of subroutine accel_mts
-            bxn  = 0.0      ;   byn  = 0.0
-            i=berg%ine      ;   j=berg%jne
-            xi=berg%xi      ;   yj=berg%yj
-
-            call accel_mts(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, &
-              ax1, ay1, axn, ayn, bxn, byn, save_bond_energy,Fec_x, Fec_y, Fdc_x, Fdc_y)
-
-            if (Fdc_x .ne. 0. .or. Fdc_y .ne. 0.) had_collision=.true.
-            if (monitor_energy .and. last_iter) &
-              call mts_energy_part_1(bergs,berg,ax1,ay1,axn,ayn,bxn,byn,Fec_x,Fec_y,Fdc_x,Fdc_y)
-
-            ! Saving all the iceberg variables
-            berg%axn=axn; berg%ayn=ayn
-            berg%bxn=bxn; berg%byn=byn
-
-            if (bergs%force_convergence) then
-              berg%uvel_prev=berg%uvel+(dt*ax1); berg%vvel_prev=berg%vvel+(dt*ay1) !the new velocity
-              if (ii==1) usum=usum+berg%uvel_old**2 + berg%vvel_old**2
-              usum1=usum1+berg%uvel_prev**2+berg%vvel_prev**2
-              usum2=usum2+(berg%uvel_prev-berg%uvel_old)**2+(berg%vvel_prev-berg%vvel_old)**2
-            else
-              berg%uvel=berg%uvel+(dt*ax1); berg%vvel=berg%vvel+(dt*ay1)
+            if (ii==1 .or. berg%static_berg==0.1) then
+              latn = berg%lat ;   lonn = berg%lon
+              uvel1=berg%uvel ;   vvel1=berg%vvel !V_n (previous cycle)
+              axn  = 0.0      ;   ayn  = 0.0 !note these are redefined at the start of subroutine accel_mts
+              bxn  = 0.0      ;   byn  = 0.0
+              i=berg%ine      ;   j=berg%jne
+              xi=berg%xi      ;   yj=berg%yj
+
+              call accel_mts(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, &
+                ax1, ay1, axn, ayn, bxn, byn, save_bond_energy,Fec_x, Fec_y, Fdc_x, Fdc_y)
+
+              if (Fdc_x .ne. 0. .or. Fdc_y .ne. 0. .and. bergs%force_convergence) then
+                had_collision=.true.
+                berg%static_berg=0.1
+              endif
+              if (monitor_energy .and. last_iter) &
+                call mts_energy_part_1(bergs,berg,ax1,ay1,axn,ayn,bxn,byn,Fec_x,Fec_y,Fdc_x,Fdc_y)
+
+              ! Saving all the iceberg variables
+              berg%axn=axn; berg%ayn=ayn
+              berg%bxn=bxn; berg%byn=byn
+
+              if (bergs%force_convergence) then
+                berg%uvel_prev=berg%uvel+(dt*ax1); berg%vvel_prev=berg%vvel+(dt*ay1) !the new velocity
+                if (ii==1) usum=usum+berg%uvel_old**2 + berg%vvel_old**2
+                usum1=usum1+berg%uvel_prev**2+berg%vvel_prev**2
+                usum2=usum2+(berg%uvel_prev-berg%uvel_old)**2+(berg%vvel_prev-berg%vvel_old)**2
+              else
+                berg%uvel=berg%uvel+(dt*ax1); berg%vvel=berg%vvel+(dt*ay1)
 
-              !The final velocity from the previous cycle, which can be used
-              !during post-processing to calculate kinetic energy and momentum
-              berg%uvel_prev=berg%uvel    ; berg%vvel_prev=berg%vvel
+                !The final velocity from the previous cycle, which can be used
+                !during post-processing to calculate kinetic energy and momentum
+                berg%uvel_prev=berg%uvel    ; berg%vvel_prev=berg%vvel
+              endif
             endif
           endif
           berg=>berg%next
@@ -7345,6 +7352,7 @@ subroutine evolve_icebergs_mts(bergs)
           do while (associated(berg)) ! loop over all bergs
             if (berg%static_berg .lt. 0.5) then
               berg%uvel_old=berg%uvel_prev; berg%vvel_old=berg%vvel_prev
+              if (last_iter .and. berg%static_berg==0.1) berg%static_berg=0.
             endif
             berg=>berg%next
           enddo
diff --git a/tests/a68/long_run.nml b/tests/a68/long_run.nml
index 507561d..e85f80a 100644
--- a/tests/a68/long_run.nml
+++ b/tests/a68/long_run.nml
@@ -26,7 +26,7 @@
 &icebergs_nml
 
     Rearth=<re>
-    !6363827 !6.378e6 !6.371229e6 !6.36e6 !6.378e6
+
     A68_test=.true.
     A68_xdisp=<xd>
     A68_ydisp=<yd>
@@ -40,9 +40,9 @@
 
     constant_interaction_LW=.true.
 
-    traj_name=<name>_1p.nc
-    bond_traj_name=<name>_bonds_1p.nc
-    
+    traj_name=<name>.nc
+    bond_traj_name=<name>_bonds.nc
+
     break_bonds_on_sub_steps=.true.
 
     power_ground=.false.
@@ -121,7 +121,7 @@
     coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
     tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
     Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    use_mixed_melting=.true. !.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
     apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
     apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
     melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
@@ -153,7 +153,7 @@
     verbose_hrs=1!24000 ! (24) Period between verbose messages
     traj_sample_hrs=0!1 !(24) sampling period for trajectory storage
     traj_write_hrs=0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.true. !.false. !(F) If T, saves bond trajectories in a separate file
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
     budget=.false. !(T) Calculate budgets
     debug=.false. !(F) Turn on debugging
     really_debug=.false. !(F) Turn on debugging
@@ -211,7 +211,7 @@
 /
 
  &fms_nml
-       clock_grain='NONE'
+       clock_grain='MODULE'
        domains_stack_size = 2000000
        clock_flags='SYNC'
 /
\ No newline at end of file
diff --git a/tests/a68/input.nml b/tests/a68/long_run_no_inc_contact_dist.nml
similarity index 89%
rename from tests/a68/input.nml
rename to tests/a68/long_run_no_inc_contact_dist.nml
index f216136..12de105 100644
--- a/tests/a68/input.nml
+++ b/tests/a68/long_run_no_inc_contact_dist.nml
@@ -4,11 +4,11 @@
   data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
   Old_wrong_Rearth_and_SSH=.false.
   !mom_Rearth=.true.
-  Rearth=6363827
+  Rearth=<re>
   !6363827 !6.378e6
   no_wind=.false.
   tau_is_velocity=.true.!.false.
-  ibdt=1800.0 !seconds
+  ibdt=<ibdt> !3600.0 !1800.0 !seconds
   ibuo=0.0 !ocean x velocity
   ibvo=0.0 !ocean y velocity
   ibui=0.0 !ice x velocity
@@ -25,24 +25,24 @@
 
 &icebergs_nml
 
-    Rearth=6363827
-    !6363827 !6.378e6 !6.371229e6 !6.36e6 !6.378e6
+    Rearth=<re>
+
     A68_test=.true.
-    A68_xdisp=-37.51
-    A68_ydisp=-55.2166
+    A68_xdisp=<xd>
+    A68_ydisp=<yd>
     short_step_mts_grounding=.true.
 
-    tau_is_velocity=.true.!.false.
-    ocean_drag_scale=17.8 !20. !1
+    tau_is_velocity=.true.
+    ocean_drag_scale=<od>
 
     skip_first_outer_mts_step=.true.
     add_curl_to_torque=.false.
 
     constant_interaction_LW=.true.
 
-    traj_name=longrun_od_17.8_tn_ng_ydn.1_ss90_ns18_rx-37.51_ry-55.2166_1p.nc
-    bond_traj_name=longrun_od_17.8_tn_ng_ydn.1_ss90_ns18_rx-37.51_ry-55.2166_bonds_1p.nc
-    
+    traj_name=<name>.nc
+    bond_traj_name=<name>_bonds.nc
+
     break_bonds_on_sub_steps=.true.
 
     power_ground=.false.
@@ -68,27 +68,23 @@
     !defaults given in parentheses:
     new_mts=.true.
     mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=90 !200 !75 !75 !150 !50 !(-1) # of mts sub-steps
+    mts_sub_steps=<ss> !200 !75 !75 !150 !50 !(-1) # of mts sub-steps
     !mts_sub_steps=10
     force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
     convergence_tolerance=1e-4 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
 
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_distance=0.!4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
     contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
     debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e4 !0.!1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    cdrag_grounding=<gc> !0.!1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
     h_to_init_grounding=0!30!15!50. !15.
     ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
     remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
 
     fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1 !0000000
-    frac_thres_n = 18e3 !25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
-    frac_thres_t = 100e3 !1000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
+    frac_thres_scaling = 1
+    frac_thres_n = <ns>e3
+    frac_thres_t = 1000e3
 
     halo=3 !(4) halo width
     Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
@@ -125,7 +121,7 @@
     coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
     tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
     Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    use_mixed_melting=.true. !.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
     apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
     apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
     melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
@@ -155,9 +151,9 @@
 
     verbose=.false. !(F) Be verbose to stderr
     verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=0!1 !(24) sampling period for trajectory storage
-    traj_write_hrs=0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.true. !.false. !(F) If T, saves bond trajectories in a separate file
+    traj_sample_hrs=1 !0!1 !(24) sampling period for trajectory storage
+    traj_write_hrs=1 !0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
     budget=.false. !(T) Calculate budgets
     debug=.false. !(F) Turn on debugging
     really_debug=.false. !(F) Turn on debugging
@@ -215,7 +211,7 @@
 /
 
  &fms_nml
-       clock_grain='NONE'
+       clock_grain='MODULE'
        domains_stack_size = 2000000
        clock_flags='SYNC'
 /
\ No newline at end of file
diff --git a/tests/a68/long_run_no_inc_contact_dist.sh b/tests/a68/long_run_no_inc_contact_dist.sh
new file mode 100755
index 0000000..9d02863
--- /dev/null
+++ b/tests/a68/long_run_no_inc_contact_dist.sh
@@ -0,0 +1,40 @@
+#!/bin/bash
+
+Rearth=6363827
+odrag=(17.8)
+ss=90
+name=(lrun_nicd_od_17.8_tn_ng_ydn.1_ss90_ns18_rx-37.51_ry-55.2166)
+ibdt=1800.0
+
+gcoef=(1.e4)
+nstress=(18)
+A68dx=-37.51
+A68dy=-55.2166
+
+odrag=(10.35)
+ss=180
+name=(lrun_nicd_hrtest)
+ibdt=3600.0
+nstress=(24.) #(22.5)
+A68dx=-37.5
+A68dy=-55.1
+
+for ((i = 0; i < ${#odrag[@]}; ++i)); do
+    drag=(${odrag[$i]})
+    fname=(${name[$i]})
+    gc=(${gcoef[$i]})
+    ns=(${nstress[$i]})
+
+    echo $drag
+    echo $fname
+    echo $Rearth
+    echo $ss
+    echo $A68dx
+    echo $A68dy
+    echo $ns
+
+    sed  "s/<od>/$drag/; s/<re>/$Rearth/; s/<ss>/$ss/; s/<ns>/$ns/; s/<gc>/$gc/; s/<xd>/$A68dx/; s/<yd>/$A68dy/; s/<ibdt>/$ibdt/; s/<name>/$fname/g" \
+	 long_run_no_inc_contact_dist.nml > input.nml
+    ./RUN1p
+    # &>/dev/null &
+done
diff --git a/tests/chaotic_test/.gitignore b/tests/chaotic_test/.gitignore
index 68bcbc9..f395a63 100644
--- a/tests/chaotic_test/.gitignore
+++ b/tests/chaotic_test/.gitignore
@@ -1 +1,3 @@
-results/
\ No newline at end of file
+results/
+csvresults/
+csvresults2/
\ No newline at end of file
diff --git a/tests/dem_test_contact/.gitignore b/tests/dem_test_contact/.gitignore
new file mode 100644
index 0000000..68bcbc9
--- /dev/null
+++ b/tests/dem_test_contact/.gitignore
@@ -0,0 +1 @@
+results/
\ No newline at end of file
diff --git a/tests/dem_test_contact/README b/tests/dem_test_contact/README
new file mode 100644
index 0000000..ec575a8
--- /dev/null
+++ b/tests/dem_test_contact/README
@@ -0,0 +1,7 @@
+1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
+2.(optional) edit input.nml
+3. run the model: ./RUN
+4, animate the results: animate_trajectories.py
+
+This is a good test for visualizing fracture dependence on particle size. Try running makeberg.py with the full radius and then half the radius, and with regular vs dem nmls. Make sure to edit the nmls so that contact distance is halved when radius is halved
+
diff --git a/tests/dem_test_contact/RUN b/tests/dem_test_contact/RUN
new file mode 100755
index 0000000..3dfc97d
--- /dev/null
+++ b/tests/dem_test_contact/RUN
@@ -0,0 +1,7 @@
+rm iceberg_trajectories.nc
+rm iceberg_trajectories.nc.*
+rm bond_trajectories.nc
+rm bond_trajectories.nc.*
+srun -n1 ./../../build/bergs.x
+
+
diff --git a/tests/dem_test_contact/animate_trajectories.py b/tests/dem_test_contact/animate_trajectories.py
new file mode 100755
index 0000000..d163b57
--- /dev/null
+++ b/tests/dem_test_contact/animate_trajectories.py
@@ -0,0 +1,161 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+import matplotlib.pyplot as plt
+from matplotlib.animation import FuncAnimation
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
+                    help=''' provide filename to plot''')
+    parser.add_argument('-s', type=int, default='14000',
+                        help='''plotted particle size''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+
+
+def main(args):
+
+    print('reading file')
+
+    filename=args.fname
+    psize=args.s
+    #filename = 'iceberg_trajectories.nc'
+    field = 'lon'
+    field2 = 'lat'
+
+    with nc.Dataset(filename) as file:
+        x = file.variables['lon'][:]/1.e3
+        y = file.variables['lat'][:]/1.e3
+        day = file.variables['day'][:]
+        length = file.variables['length'][:]
+        width = file.variables['width'][:]
+        thick = file.variables['thickness'][:]
+        od = file.variables['od'][:]
+
+    ud = np.unique(day)
+    t = ud[0]
+
+    radius = length*width*(1./(2*np.sqrt(3)))
+
+    #for determining if grounded:
+    rho_bergs=850.
+    rho_seawater=1025.
+    h_to_ground=20 #200.
+    draught=(rho_bergs/rho_seawater)*thick
+    if (h_to_ground==0):
+        groundfrac=draught-od
+    else:
+        groundfrac=1.-(od-draught)/h_to_ground
+    groundfrac[groundfrac<0.]=0.
+    groundfrac[groundfrac>1.]=1.
+
+    #groundfrac[thick<200.]=0.
+    #groundfrac[thick>=200.]=1.
+
+
+    # frame info
+    num_frames = len(ud)
+    movie_len = 5 #seconds
+    #frame_len = 1000.0*movie_len/num_frames/10000000
+    frame_len = movie_len/num_frames/1000
+
+    xmin = 40
+    xmax = 100
+    ymin = 20 #xmin
+    ymax = 80 #xmax
+
+    anim_running = True
+
+    def animate(i):
+
+        x1 = x[day == ud[i]]
+        y1 = y[day == ud[i]]
+        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
+
+        scat.set_offsets(data)
+
+        t = ud[i]
+        time_text.set_text('time = %.1f days' % t )
+
+        r1 = radius[day == ud[i]]
+        scat.set_sizes(r1/psize)
+
+        hstat = groundfrac[day == ud[i]]
+        cstring=[]
+        for j in range(len(hstat)):
+            if (hstat[j]==0):
+                cstring.append("none")
+            else:
+                cstring.append("b")
+        scat.set_color(cstring)
+        scat.set_edgecolor('r')
+
+        return scat,time_text
+
+    def init():
+        scat.set_offsets([])
+        return scat,
+
+    def onClick(event):
+        global anim_running
+        if anim_running:
+            ani.event_source.stop()
+            anim_running = False
+        else:
+            ani.event_source.start()
+            anim_running = True
+
+    # Now we can do the plotting!
+    f = plt.figure(figsize=(5,5))
+    f.tight_layout()
+    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
+    scat = ax1.scatter([],[],marker='o')#,edgecolor='red')
+    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
+
+    # Change major ticks to show every 20.
+    ax1.xaxis.set_major_locator(MultipleLocator(5))
+    ax1.yaxis.set_major_locator(MultipleLocator(5))
+
+    ax1.xaxis.set_minor_locator(MultipleLocator(1))
+    ax1.yaxis.set_minor_locator(MultipleLocator(1))
+
+    # Turn grid on for both major and minor ticks and style minor slightly
+    # differently.
+    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
+    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
+
+    ax1.set_xlabel('x (km)')
+    ax1.set_ylabel('y (km)')
+    ax1.set_title('Iceberg trajectory')
+
+    f.canvas.mpl_connect('button_press_event', onClick)
+
+    ani = FuncAnimation(
+        f,animate,init_func=init,frames=num_frames,
+        interval=frame_len,blit=True,repeat=True)
+
+    print('time',t)
+
+    plt.show()
+    #animation.save("iceberg_traj_animation.mp4")
+
+
+print('Script complete')
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
diff --git a/tests/dem_test_contact/diag_table b/tests/dem_test_contact/diag_table
new file mode 100644
index 0000000..c1c8819
--- /dev/null
+++ b/tests/dem_test_contact/diag_table
@@ -0,0 +1,3 @@
+"icebergs test"
+1 1 1 0 0 0
+
diff --git a/tests/dem_test_contact/input.nml b/tests/dem_test_contact/input.nml
new file mode 100644
index 0000000..e3e1133
--- /dev/null
+++ b/tests/dem_test_contact/input.nml
@@ -0,0 +1,200 @@
+
+&icebergs_driver_nml
+  ni=45 !30 !number of elements, x direction
+  nj=45 !30 !number of elements, y direction
+  gridres=5000.0
+  ibdt=1800.0 !seconds
+  ibuo=0.2 !ocean x velocity
+  ibvo=0.2 !-0.1 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  write_time_inc = 48 !increment at which time is written to screen
+  nmax=999999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.true.
+  collision_test=.false.
+  !big_grounding_test=.true.
+  dem_test_contact=.true.
+  bump_depth=50. !200.0 !(m) depth of top of gaussian bump below sea level
+/
+
+&icebergs_nml
+
+    constant_interaction_LW=.true.
+    !traj_name=test_dem.nc
+
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    break_bonds_on_sub_steps=.true.
+
+    rho_bergs=850. ! (850) iceberg density
+    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5. A=L*W always works?
+    dem_spring_coef=5e6 !5e6 !1e6 !1e7!34000.0 !4471.938678723104 !1000.0
+    !spring_coef=0.00015094124684696098 !dem_spring_coef=1.e6, r=1500, and hex pack
+    !spring_coef=0.0030188249369392196 !dem_spring_coef=5.e6, r=750, and hex pack!
+    !spring_coef=0.0006037649873878439 !dem_spring_coef=1.e6, r=750, and hex pack
+    spring_coef=0.0007547062342348049 !if dem_spring_coef=5e6, r=1500, and hex pack?
+    !spring_coef=0.0015094124684696098 !dem_spring_coef=1.e7, r=1500, and hex pack
+
+    monitor_energy=.false.
+    !defaults given in parentheses:
+    new_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=500 !90 # of mts sub-steps #use 90 for 1.5km radii, 500 works for 500 m radii
+    explicit_inner_mts=.true.
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(a68) !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!1.e-7!(a68)!6!8 !(default=spring_coeff) Berg spring coeff for collisions
+
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    cdrag_grounding=1.e5 !3.16e6 !for power-law-type friction
+    h_to_init_grounding=20 !200.0
+    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
+    remove_unused_bergs=.false.!.true. !(T) remove unneeded bergs after PEs transfers
+
+    fracture_criterion='stress' !none' !'stress' !('none') 'strain_rate','strain',or 'none'
+    frac_thres_scaling = 99999999 !1.05 !0.75 !0.5
+    frac_thres_n = 2000 !1850 !!!1000 !2250 !4100
+    frac_thres_t = 1000 !1200 !1450 !500 !!!1500 !800 !10000000 !800 !1400
+
+
+    halo=3 !(4) halo width
+    Lx=225000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0.1 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.false. !(F) Be verbose to stderr
+    verbose_hrs=24000 ! (24) Period between verbose messages
+    traj_sample_hrs=0.5 !-1!0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=0.5 !-1!0!6 !(480) Period for writing sampled trajectories to disk
+    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    manually_initialize_bonds_from_radii=.true.
+    !length_for_manually_initialize_bonds=1600.0!800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/dem_test_contact/makeberg/RUN b/tests/dem_test_contact/makeberg/RUN
new file mode 100755
index 0000000..520d671
--- /dev/null
+++ b/tests/dem_test_contact/makeberg/RUN
@@ -0,0 +1,3 @@
+rm ./output_files/Generic*
+./makeberg.py
+cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
diff --git a/tests/dem_test_contact/makeberg/makeberg.py b/tests/dem_test_contact/makeberg/makeberg.py
new file mode 100755
index 0000000..b0de588
--- /dev/null
+++ b/tests/dem_test_contact/makeberg/makeberg.py
@@ -0,0 +1,395 @@
+#!/usr/bin/env python
+import numpy as np
+import math
+from netCDF4 import Dataset
+from pylab import *
+#import pdb
+import netCDF4 as nc
+
+#
+# Initialize 2 iceberg elements, which can later be bonded in the fortran code if needed
+#
+
+def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,berg_uvel,berg_vvel):
+
+	#print('Writing iceberg restart files, with ' , Number_of_bergs	, 'icebergs..')
+        print 'Writing iceberg restart files, with ' , Number_of_bergs	, 'icebergs..'
+	# To copy the global attributes of the netCDF file
+
+	#Input and output files
+	#Create Empty restart file. This is later read so that the attributes can be used.
+	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
+	create_empty_iceberg_restart_file(Empty_restart_filename)
+	#Empty_restart_filename='input_files/icebergs.res.nc'
+
+	#Read empty restart file
+	f=Dataset(Empty_restart_filename,'r') # r is for read only
+	#Write a new restart file
+	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
+
+	for attname in f.ncattrs():
+		    setattr(g,attname,getattr(f,attname))
+
+
+	# To copy the dimension of the netCDF file
+	for dimname,dim in f.dimensions.iteritems():
+		# if you want to make changes in the dimensions of the new file
+		# you should add your own conditions here before the creation of the dimension.
+		#g.createDimension(dimname,len(dim))
+		g.createDimension(dimname,Number_of_bergs)
+
+	# To copy the variables of the netCDF file
+
+	for varname,ncvar in f.variables.iteritems():
+		# if you want to make changes in the variables of the new file
+		# you should add your own conditions here before the creation of the variable.
+		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
+		#Proceed to copy the variable attributes
+		for attname in ncvar.ncattrs():
+			setattr(var,attname,getattr(ncvar,attname))
+		#Finally copy the variable data to the new created variable
+		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
+
+		if varname=='i':
+			var[:]=Number_of_bergs
+
+		if varname=='iceberg_num':
+			for j in range(Number_of_bergs):
+				#var[j]=j+1
+				var[j]=iceberg_num[j]
+
+		if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
+		or varname=='bxn' or varname=='byn' or	varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
+		or varname=='mass_of_bits' or varname=='start_mass' or	varname=='start_day' or varname=='start_year' or varname=='start_lon' \
+		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
+			var[:]=0
+
+		if varname=='uvel':
+			for j in range(Number_of_bergs):
+				var[j]=berg_uvel[j]
+			#var[:]=berg_uvel[j]
+
+		if varname=='vvel':
+			for j in range(Number_of_bergs):
+				var[j]=berg_vvel[j]
+			#var[:]=berg_vvel[j]
+
+		if varname=='mass_scaling':
+			for j in range(Number_of_bergs):
+				var[j]=mass_scaling[j]
+			#var[:]=mass_scaling[j]
+
+		if varname=='thickness':
+			for j in range(Number_of_bergs):
+				var[j]=thickness[j]
+
+		if varname=='mass':
+			for j in range(Number_of_bergs):
+				var[j]=mass[j]
+
+		if varname=='width'  or varname=='length':
+			for j in range(Number_of_bergs):
+				var[j]=width[j]
+
+		if varname=='lon':
+			for j in range(Number_of_bergs):
+				var[j]=lon[j]
+
+		if varname=='lat':
+			for j in range(Number_of_bergs):
+				var[j]=lat[j]
+
+		if varname=='static_berg':
+			for j in range(Number_of_bergs):
+				var[j]=static_berg[j]
+
+
+	f.close()
+	g.close()
+
+
+def create_empty_iceberg_restart_file(Empty_restart_filename):
+
+        f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
+
+        i=f.createDimension('i', None)
+        lon=f.createVariable('i','i')
+
+        lon=f.createVariable('lon','d',('i'))
+        lon.long_name = "longitude" ;
+        lon.units = "degrees_E" ;
+        lon.checksum = "               0" ;
+
+        lat=f.createVariable('lat','d',('i'))
+        lat.long_name = "latitude" ;
+        lat.units = "degrees_N" ;
+        lat.checksum = "               0" ;
+
+        uvel=f.createVariable('uvel','d',('i'))
+        uvel.long_name = "zonal velocity" ;
+        uvel.units = "m/s" ;
+        uvel.checksum = "               0" ;
+
+        vvel=f.createVariable('vvel','d',('i'))
+        vvel.long_name = "meridional velocity" ;
+        vvel.units = "m/s" ;
+        vvel.checksum = "               0" ;
+
+        mass=f.createVariable('mass','d',('i'))
+        mass.long_name = "mass" ;
+        mass.units = "kg" ;
+        mass.checksum = "               0" ;
+
+        axn=f.createVariable('axn','d',('i'))
+        axn.long_name = "explicit zonal acceleration" ;
+        axn.units = "m/s^2" ;
+        axn.checksum = "               0" ;
+
+        ayn=f.createVariable('ayn','d',('i'))
+        ayn.long_name = "explicit meridional acceleration" ;
+        ayn.units = "m/s^2" ;
+        ayn.checksum = "               0" ;
+
+        bxn=f.createVariable('bxn','d',('i'))
+        bxn.long_name = "inplicit zonal acceleration" ;
+        bxn.units = "m/s^2" ;
+        bxn.checksum = "               0" ;
+
+        byn=f.createVariable('byn','d',('i'))
+        byn.long_name = "implicit meridional acceleration" ;
+        byn.units = "m/s^2" ;
+        byn.checksum = "               0" ;
+
+        ine=f.createVariable('ine','i',('i'))
+        ine.long_name = "i index" ;
+        ine.units = "none" ;
+        ine.packing = 0 ;
+        ine.checksum = "               0" ;
+
+        jne=f.createVariable('jne','i',('i'))
+        jne.long_name = "j index" ;
+        jne.units = "none" ;
+        jne.packing = 0 ;
+        jne.checksum = "               0" ;
+
+        thickness=f.createVariable('thickness','d',('i'))
+        thickness.long_name = "thickness" ;
+        thickness.units = "m" ;
+        thickness.checksum = "               0" ;
+
+        width=f.createVariable('width','d',('i'))
+        width.long_name = "width" ;
+        width.units = "m" ;
+        width.checksum = "               0" ;
+
+        length=f.createVariable('length','d',('i'))
+        length.long_name = "length" ;
+        length.units = "m" ;
+        length.checksum = "               0" ;
+
+        start_lon=f.createVariable('start_lon','d',('i'))
+        start_lon.long_name = "longitude of calving location" ;
+        start_lon.units = "degrees_E" ;
+        start_lon.checksum = "               0" ;
+
+        start_lat=f.createVariable('start_lat','d',('i'))
+        start_lat.long_name = "latitude of calving location" ;
+        start_lat.units = "degrees_N" ;
+        start_lat.checksum = "               0" ;
+
+        start_year=f.createVariable('start_year','i',('i'))
+        start_year.long_name = "calendar year of calving event" ;
+        start_year.units = "years" ;
+        start_year.packing = 0 ;
+        start_year.checksum = "               0" ;
+
+        iceberg_num=f.createVariable('iceberg_num','i',('i'))
+        iceberg_num.long_name = "identification of the iceberg" ;
+        iceberg_num.units = "dimensionless" ;
+        iceberg_num.packing = 0 ;
+        iceberg_num.checksum = "               0" ;
+
+        start_day=f.createVariable('start_day','d',('i'))
+        start_day.long_name = "year day of calving event" ;
+        start_day.units = "days" ;
+        start_day.checksum = "               0" ;
+
+        start_mass=f.createVariable('start_mass','d',('i'))
+        start_mass.long_name = "initial mass of calving berg" ;
+        start_mass.units = "kg" ;
+        start_mass.checksum = "               0" ;
+
+        mass_scaling=f.createVariable('mass_scaling','d',('i'))
+        mass_scaling.long_name = "scaling factor for mass of calving berg" ;
+        mass_scaling.units = "none" ;
+        mass_scaling.checksum = "               0" ;
+
+        mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
+        mass_of_bits.long_name = "mass of bergy bits" ;
+        mass_of_bits.units = "kg" ;
+        mass_of_bits.checksum = "               0" ;
+
+        heat_density=f.createVariable('heat_density','d',('i'))
+        heat_density.long_name = "heat density" ;
+        heat_density.units = "J/kg" ;
+        heat_density.checksum = "               0" ;
+
+        halo_berg=f.createVariable('halo_berg','d',('i'))
+        halo_berg.long_name = "halo_berg" ;
+        halo_berg.units = "dimensionless" ;
+        halo_berg.checksum = "               0" ;
+
+        static_berg=f.createVariable('static_berg','d',('i'))
+        static_berg.long_name = "static_berg" ;
+        static_berg.units = "dimensionless" ;
+        static_berg.checksum = "               0" ;
+
+	f.sync()
+	f.close()
+
+
+
+#-----------------------------------#
+#		Main		    #
+#-----------------------------------#
+
+# just2particles=False
+# flip2ndconglom=True#False
+# offset2ndconglom=True#False
+
+grdxmin=0; grdxmax=225000e3
+grdymin=0; grdymax=225000e3
+grdres=5000.0
+R_frac=0.45 #1st option
+#R_frac=0.5*0.45 #2nd option
+#radius=(np.sqrt(3)/2.)*(R_frac*grdres) #S is < 0.5 grid res
+radius=500 #1.5e3 #/2
+#radius2=(np.sqrt(3)/2.)*(R_frac2*grdres) #S is < 0.5 grid res
+thickness1=300.0
+thickness2=30.0
+rho_ice=850.0
+
+
+nbergs=2 #number of conglomerates
+
+#center coords of each (rectangular) conglomerate berg (CB=conglomerate berg)
+CBxc=np.array([52500,52500]); CByc=np.array([27500,72500])
+#side lengths
+CBxl=np.array([15000,15000]); CByl=np.array([15000,15000])
+
+
+CByl=CByl.astype(int); CBxl=CBxl.astype(int)
+
+#--- xmax, xmin, ymax, ymin for each CB --
+CBxmin=CBxc-(0.5*CBxl); CBxmax=CBxc+(0.5*CBxl)
+CBymin=CByc-(0.5*CByl); CBymax=CByc+(0.5*CByl)
+#this shouldn't happen:
+CBxmin[CBxmin<grdxmin]=grdxmin; CBxmax[CBxmax>grdxmax]=grdxmax
+CBymin[CBxmin<grdymin]=grdymin; CBymax[CBymax>grdymax]=grdymax
+CBxc=0.5*(CBxmin+CBxmax); CByc=0.5*(CBymin+CBymax)
+
+# #if just want one particle per CB
+# if just2particles:
+#	  CBxmin=CBxc; CBxmax=CBxc
+#	  CBymin=CByc; CBymax=CByc
+
+#--- min and max thicknesses for each CB ---
+h1=thickness1
+h2=thickness2
+CBhmax=np.array([h1,h2]); CBhmin=np.array([h1,h2])
+
+#radii
+CBrad=np.array([radius,radius])
+#print('radii',CBrad)
+
+berg_x=[]; berg_y=[]
+berg_id=[]; berg_static=[]
+berg_width=[]; berg_bonds=[]
+berg_h=[]; berg_mass_scaling=[]
+berg_mass=[]
+berg_uvel=[]; berg_vvel=[]
+berg_uvel_in=np.array([0.2,0.2]); berg_vvel_in=np.array([0.2,-0.2])
+
+berg_count=0
+
+for i in range(nbergs):
+	# if (i>0):
+	# 	print('num bergs in 1st conglom',berg_count)
+
+	x_start=CBxmin[i]+(CBrad[i]*2./np.sqrt(3))
+
+        if (i>0):
+                x_start=x_start+1.5e3
+
+	# if flip2ndconglom and i>0:
+	#	  x_start=CBxmax[i]-(CBrad[i]*2./np.sqrt(3))
+
+	#pdb.set_trace()
+	if x_start>CBxmax[i]:
+		x_start=CBxmax[i]
+	y_start0=CBymin[i]+CBrad[i]
+	if y_start0>CBymax[i]:
+		y_start0=CBymax[i]
+	element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*(CBrad[i])**2)
+	#H (thickness) is a linear function of a berg element's position from the
+	#center of the CB. H=Hmax at the center of the CB and H=Hmin at a corner of the
+	#CB, where the dist of a corner from the center is:
+	cdistb=np.sqrt((CBxmin[i]-CBxc[i])**2+(CBymin[i]-CByc[i])**2)
+	j=0
+	x_val=x_start
+	offset=0.0
+	# if (i==0):
+	uvel=berg_uvel_in[i]
+	#0.1#1
+	# else:
+	#	  uvel=-0.15#-0.05
+	#	  if (offset2ndconglom):
+	#		  offset=250.0
+	vvel=berg_vvel_in[i]
+
+	#print('uvel vvel',uvel,vvel)
+	#0.0#25
+	#uvel=0;vvel=0
+	#berg_count_start=berg_count
+	while x_val<=CBxmax[i] and x_val>=CBxmin[i]:
+		y_start=y_start0+((j%2)*CBrad[i])+offset
+		k=0
+		y_val=y_start
+		while y_val<=(CBymax[i]+offset):
+			berg_count=berg_count+1
+			berg_id.append(berg_count)
+			berg_x.append(x_val)
+			berg_y.append(y_val)
+			berg_width.append(sqrt(element_area))
+			#dist of berg elem from center of CB
+			bdistc=np.sqrt((x_val-CBxc[i])**2+(y_val-CByc[i])**2)
+			bh=CBhmin[i]*bdistc/cdistb + CBhmax[i]*(1-bdistc/cdistb)
+			# if (just2particles):
+			#	  bh=h1
+			berg_h.append(bh) #thickness
+			berg_mass_scaling.append(1)
+			berg_mass.append(bh*rho_ice*element_area)
+			berg_static.append(0)
+			berg_uvel.append(uvel)
+			berg_vvel.append(vvel)
+			# if (x_val<22000):
+			#	  berg_vvel.append(vvel)
+			# else:
+			#	  berg_vvel.append(0.4)
+			#berg_CBid.append(i)
+			k=k+1
+			y_val=y_start+(2*k*CBrad[i])
+		j=j+1
+		# if flip2ndconglom and i>0:
+		#	  x_val=x_start-(np.sqrt(3)*CBrad[i]*j)
+		# else:
+		x_val=x_start+(np.sqrt(3)*CBrad[i]*j)
+
+#print('Number of bergs',berg_count)
+print 'Number of bergs',berg_count
+
+#pdb.set_trace()
+
+#Create iceberg restart file
+Ice_geometry_source='Generic'
+Create_iceberg_restart_file(berg_count,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)
diff --git a/tests/nc2csv.py b/tests/nc2csv.py
index d5d390c..05a9602 100755
--- a/tests/nc2csv.py
+++ b/tests/nc2csv.py
@@ -150,9 +150,9 @@ def str2bool(string):
 	elif string.lower() in ("no", "false", "f", "0"):
 		Value=False
 	else:
-		print '**********************************************************************'
-		print 'The input variable ' ,str(string) ,  ' is not suitable for boolean conversion, using default'
-		print '**********************************************************************'
+		print( '**********************************************************************')
+		print( 'The input variable ' ,str(string) ,  ' is not suitable for boolean conversion, using default')
+		print( '**********************************************************************')
 
 		Value=None
 		return

From b5a4bec54784b4911d8b4b049567cab96a840f28 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Thu, 17 Nov 2022 18:33:22 -0500
Subject: [PATCH 319/361] Cleanup of beam tests

---
 tests/dem_cbeam_test/README                   |   5 +-
 tests/dem_cbeam_test/RUN                      |   2 +-
 .../dem_cbeam_test/animate_trajectories_1l.py | 187 ----------
 tests/dem_cbeam_test/input.nml                |  10 +-
 tests/dem_rbeam_test/.gitignore               |   1 -
 tests/dem_rbeam_test/README                   |   8 -
 tests/dem_rbeam_test/RUN                      |   5 -
 tests/dem_rbeam_test/animate_trajectories.py  | 164 ---------
 tests/dem_rbeam_test/diag_table               |   3 -
 tests/dem_rbeam_test/input.nml                | 184 ----------
 tests/dem_rbeam_test/makeberg/RUN             |   3 -
 tests/dem_rbeam_test/makeberg/makeberg.py     | 321 ------------------
 tests/dem_ssbeam_test/README                  |   6 +-
 tests/dem_ssbeam_test/RUN                     |   2 +-
 tests/dem_ssbeam_test/animate_trajectories.py |   7 +-
 tests/dem_ssbeam_test/input.nml               |   9 +-
 16 files changed, 31 insertions(+), 886 deletions(-)
 delete mode 100755 tests/dem_cbeam_test/animate_trajectories_1l.py
 delete mode 100644 tests/dem_rbeam_test/.gitignore
 delete mode 100644 tests/dem_rbeam_test/README
 delete mode 100755 tests/dem_rbeam_test/RUN
 delete mode 100755 tests/dem_rbeam_test/animate_trajectories.py
 delete mode 100644 tests/dem_rbeam_test/diag_table
 delete mode 100644 tests/dem_rbeam_test/input.nml
 delete mode 100755 tests/dem_rbeam_test/makeberg/RUN
 delete mode 100755 tests/dem_rbeam_test/makeberg/makeberg.py

diff --git a/tests/dem_cbeam_test/README b/tests/dem_cbeam_test/README
index be1f91d..9fbeafc 100644
--- a/tests/dem_cbeam_test/README
+++ b/tests/dem_cbeam_test/README
@@ -1,2 +1,5 @@
-This is the cantilever beam test from Section 3.2 of Wang 2020 "A scale-invariant bonded particle model for simulating large deformation and failure of continua"
+This is the cantilever beam test from Section 3.2 of Wang 2020 "A scale-invariant bonded particle model for simulating large deformation and failure of continua" https://doi.org/10.1016/j.compgeo.2020.103735. It tests the discrete-element/bonded-particle model that underlies iKID.
 
+When the results are animated (animate_trajectories.py), the beam should bend into alignment with the plotted line.
+
+By default, run with 4 PEs
diff --git a/tests/dem_cbeam_test/RUN b/tests/dem_cbeam_test/RUN
index 0ffc895..32c463c 100755
--- a/tests/dem_cbeam_test/RUN
+++ b/tests/dem_cbeam_test/RUN
@@ -2,4 +2,4 @@ rm iceberg_trajectories.nc
 rm iceberg_trajectories.nc.*
 rm bond_trajectories.nc
 rm bond_trajectories.nc.*
-srun -n1 ./../../build/bergs.x
+srun -n4 ./../../build/bergs.x
diff --git a/tests/dem_cbeam_test/animate_trajectories_1l.py b/tests/dem_cbeam_test/animate_trajectories_1l.py
deleted file mode 100755
index 501a507..0000000
--- a/tests/dem_cbeam_test/animate_trajectories_1l.py
+++ /dev/null
@@ -1,187 +0,0 @@
-#!/usr/bin/env python
-
-from netCDF4 import Dataset
-import pdb
-import netCDF4 as nc
-import numpy as np
-import matplotlib
-import math
-import os
-matplotlib.use("tkagg")
-from pylab import *
-import matplotlib.pyplot as plt
-from matplotlib.animation import FuncAnimation
-import argparse
-
-def parseCommandLine():
-    parser = argparse.ArgumentParser(description=
-    '''Generate animation of iceberg trajectories.''',
-    epilog='Written by Alex Huth, 2020')
-    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
-                    help=''' provide filename to plot''')
-    parser.add_argument('-s', type=int, default='100000',
-                    help='''plotted particle size''')
-    optCmdLineArgs = parser.parse_args()
-    return optCmdLineArgs
-
-
-def main(args):
-
-    print('reading file')
-
-    filename=args.fname
-    psize=args.s
-    #filename = 'iceberg_trajectories.nc'
-    field = 'lon'
-    field2 = 'lat'
-
-    with nc.Dataset(filename) as file:
-        x = file.variables['lon'][:]/1.e3
-        y = file.variables['lat'][:]/1.e3
-        day = file.variables['day'][:]
-        length = file.variables['length'][:]
-        width = file.variables['width'][:]
-        hs = file.variables['thickness'][:]
-
-
-    radius = length*width*(1./(2*np.sqrt(3)))
-
-    #print('day',day)
-    crop=False
-    tc=1.25
-    if crop:
-        x=x[day<=tc]
-        y=y[day<=tc]
-        day=day[day<=tc]
-
-    ud = np.unique(day)
-    #print('ud',ud)
-    t = ud[0]
-
-    # frame info
-    num_frames = len(ud)
-    movie_len = 4.0 #seconds
-    frame_len = 1000.0*movie_len/num_frames
-
-    d=5000.0
-    r=d/2.
-    xshift=101
-    yshift=(151.e3+2*r)/1.e3
-
-    xmin = 90-xshift
-    xmax = 260-xshift
-    ymin = 0-yshift
-    ymax = 170-yshift
-
-    x=x-xshift
-    y=y-yshift
-
-    anim_running = True
-
-    def animate(i):
-
-        x1 = x[day == ud[i]]
-        y1 = y[day == ud[i]]
-        # hstat = hs[day == ud[i]]
-        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
-        hstat= day[day == ud[i]]
-
-        ud_max=np.max(ud)
-
-        cstring=[]
-        # for j in range(len(hstat)):
-        #     if (hstat[j]<=200):
-        #         cstring.append("r")
-        #     else:
-        #         cstring.append("b")
-
-        for j in range(len(hstat)):
-            if (hstat[j]<ud_max):
-                cstring.append("r")
-            else:
-                cstring.append("b")
-
-        scat.set_offsets(data)
-        scat.set_color(cstring)
-        scat.set_edgecolor('k')
-        #scat2.set_offsets(data)
-
-        t = ud[i]
-        time_text.set_text('time = %.1f days' % t )
-
-        r1 = radius[day == ud[i]]
-
-        scat.set_sizes(r1/psize)
-        return scat,time_text #,scat2
-
-    def init():
-        scat.set_offsets([])
-        return scat,
-
-    def onClick(event):
-        global anim_running
-        if anim_running:
-            ani.event_source.stop()
-            anim_running = False
-        else:
-            ani.event_source.start()
-            anim_running = True
-
-    # Now we can do the plotting!
-    f = plt.figure(figsize=(5,5))
-    f.tight_layout()
-    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
-    #scat = ax1.scatter([],[],marker='o',facecolor='w',s=psize,edgecolor='red')
-    scat = ax1.scatter([],[],marker='o')#,facecolor='w',edgecolor='red')
-    #scat2 = ax1.scatter([],[],marker='.',color='k',s=5)
-    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
-
-    # Change major ticks to show every 20.
-    ax1.xaxis.set_major_locator(MultipleLocator(50))
-    ax1.yaxis.set_major_locator(MultipleLocator(50))
-
-    ax1.xaxis.set_minor_locator(MultipleLocator(10))
-    ax1.yaxis.set_minor_locator(MultipleLocator(10))
-
-    # Turn grid on for both major and minor ticks and style minor slightly
-    # differently.
-    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
-    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
-
-    ax1.set_xlabel('x (km)')
-    ax1.set_ylabel('displacement (km)')
-    ax1.set_title('Iceberg trajectory')
-
-
-    #analytical solution
-    thick=4
-    xa=np.linspace(0,150000,100)
-    P=-(1.5e10)/3. #Newtons
-    l=29*d #total beam length (m) between center of start and end particles (x-dir)
-    h=d  #total beam height (m) between center of start and end particles (y-dir)
-    AI= thick*(h**3)/12. #second  moment of area
-    YM=1.e9 #young's modulus (Pa)
-    w= P*(xa**2.)*(3.*l-xa)/(6.*YM*AI) #deflection
-
-    xa=(xa)/1.e3
-    w=w/1.e3
-    ax1.plot(xa,w)
-
-    f.canvas.mpl_connect('button_press_event', onClick)
-    ani = FuncAnimation(
-        f,animate,init_func=init,frames=num_frames,
-        interval=frame_len,blit=True,repeat=False)
-
-
-    print('time',t)
-
-    plt.show()
-    #animation.save("iceberg_traj_animation.mp4")
-
-
-print('Script complete')
-
-if __name__ == '__main__':
-    optCmdLineArgs=	parseCommandLine()
-    anim_running = True
-    main(optCmdLineArgs)
diff --git a/tests/dem_cbeam_test/input.nml b/tests/dem_cbeam_test/input.nml
index 3dea833..437eefb 100644
--- a/tests/dem_cbeam_test/input.nml
+++ b/tests/dem_cbeam_test/input.nml
@@ -1,3 +1,9 @@
+! KID, bergs_chksum: write_restart berg chksum=545105294 chksum2=-884448578 chksum3=-1504290914 chksum4=-1504290914 chksum5=-845603363 #=90
+! KID, grd_chksum2:# of bergs/cell chksum=0 chksum2=0 min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
+!  Total number of bonds is: 294
+!  All iceberg bonds are connected and working well
+! KID, grd_chksum3:   write stored_ice chksum=-540079793 chksum2=-1237287029 min= 6.393358811E+05 max= 7.380127765E+11 mean= 8.033602570E+10 rms= 1.613270384E+11 sd= 1.399018810E+11
+
 &icebergs_driver_nml
   ni=20 !number of elements, x direction
   nj=20 !number of elements, y direction
@@ -7,8 +13,8 @@
   ibui=0.0 !ice x velocity
   ibvi=0.0 !ice y velocity
   ibhrs=200 !total simulation hours
-  write_time_inc = 600 !increment at which time is written to screen
-  nmax=1200  !max number of timesteps
+  write_time_inc = 25 !increment at which time is written to screen
+  nmax=300  !max number of timesteps
   saverestart=.true.
   halo=3
   debug=.true.
diff --git a/tests/dem_rbeam_test/.gitignore b/tests/dem_rbeam_test/.gitignore
deleted file mode 100644
index 68bcbc9..0000000
--- a/tests/dem_rbeam_test/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-results/
\ No newline at end of file
diff --git a/tests/dem_rbeam_test/README b/tests/dem_rbeam_test/README
deleted file mode 100644
index c59aa7d..0000000
--- a/tests/dem_rbeam_test/README
+++ /dev/null
@@ -1,8 +0,0 @@
-Testing of angular/rotational terms in DEM mode. In ./makeberg, a "1-D" conglomerate with 30 elements is initialized.
-There are two tests using this configuration, where the test is specified by setting dem_beam_test to either 3 or 4 in the nml. See nml for details.
-
-1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
-2.(optional) edit input.nml
-3. run the model: ./RUN
-4, animate the results: animate_trajectories.py
-
diff --git a/tests/dem_rbeam_test/RUN b/tests/dem_rbeam_test/RUN
deleted file mode 100755
index 0ffc895..0000000
--- a/tests/dem_rbeam_test/RUN
+++ /dev/null
@@ -1,5 +0,0 @@
-rm iceberg_trajectories.nc
-rm iceberg_trajectories.nc.*
-rm bond_trajectories.nc
-rm bond_trajectories.nc.*
-srun -n1 ./../../build/bergs.x
diff --git a/tests/dem_rbeam_test/animate_trajectories.py b/tests/dem_rbeam_test/animate_trajectories.py
deleted file mode 100755
index 5cae233..0000000
--- a/tests/dem_rbeam_test/animate_trajectories.py
+++ /dev/null
@@ -1,164 +0,0 @@
-#!/usr/bin/env python
-
-from netCDF4 import Dataset
-import pdb
-import netCDF4 as nc
-import numpy as np
-import matplotlib
-import math
-import os
-matplotlib.use("tkagg")
-from pylab import *
-import matplotlib.pyplot as plt
-from matplotlib.animation import FuncAnimation
-import argparse
-
-def parseCommandLine():
-    parser = argparse.ArgumentParser(description=
-    '''Generate animation of iceberg trajectories.''',
-    epilog='Written by Alex Huth, 2020')
-    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
-                    help=''' provide filename to plot''')
-    parser.add_argument('-s', type=int, default='100000',
-                    help='''plotted particle size''')
-    optCmdLineArgs = parser.parse_args()
-    return optCmdLineArgs
-
-
-def main(args):
-
-    print('reading file')
-
-    filename=args.fname
-    psize=args.s
-    #filename = 'iceberg_trajectories.nc'
-    field = 'lon'
-    field2 = 'lat'
-
-    with nc.Dataset(filename) as file:
-        x = file.variables['lon'][:]/1.e3
-        y = file.variables['lat'][:]/1.e3
-        day = file.variables['day'][:]
-        length = file.variables['length'][:]
-        width = file.variables['width'][:]
-        hs = file.variables['thickness'][:]
-
-
-    radius = length*width*(1./(2*np.sqrt(3)))
-
-    #print('day',day)
-    crop=False
-    tc=1.25
-    if crop:
-        x=x[day<=tc]
-        y=y[day<=tc]
-        day=day[day<=tc]
-
-    ud = np.unique(day)
-    #print('ud',ud)
-    t = ud[0]
-
-    # frame info
-    num_frames = len(ud)
-    movie_len = 4.0 #seconds
-    frame_len = 1000.0*movie_len/num_frames
-
-    d=5000.0
-    r=d/2.
-    xshift=101
-    yshift=(151.e3+2*r)/1.e3
-
-    xmin = 90-xshift
-    xmax = 260-xshift
-    ymin = 0-yshift
-    ymax = 170-yshift
-
-    x=x-xshift
-    y=y-yshift
-
-    anim_running = True
-
-    def animate(i):
-
-        x1 = x[day == ud[i]]
-        y1 = y[day == ud[i]]
-        # hstat = hs[day == ud[i]]
-        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
-        hstat= day[day == ud[i]]
-
-        ud_max=np.max(ud)
-
-        cstring=[]
-
-        for j in range(len(hstat)):
-            if (hstat[j]<ud_max):
-                cstring.append("r")
-            else:
-                cstring.append("b")
-
-        scat.set_offsets(data)
-        scat.set_color(cstring)
-        scat.set_edgecolor('k')
-
-        t = ud[i]
-        time_text.set_text('time = %.1f days' % t )
-
-        r1 = radius[day == ud[i]]
-
-        scat.set_sizes(r1/psize)
-        return scat,time_text
-
-    def init():
-        scat.set_offsets([])
-        return scat,
-
-    def onClick(event):
-        global anim_running
-        if anim_running:
-            ani.event_source.stop()
-            anim_running = False
-        else:
-            ani.event_source.start()
-            anim_running = True
-
-    # Now we can do the plotting!
-    f = plt.figure(figsize=(5,5))
-    f.tight_layout()
-    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
-    scat = ax1.scatter([],[],marker='o')
-    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
-
-    # Change major ticks to show every 20.
-    ax1.xaxis.set_major_locator(MultipleLocator(50))
-    ax1.yaxis.set_major_locator(MultipleLocator(50))
-
-    ax1.xaxis.set_minor_locator(MultipleLocator(10))
-    ax1.yaxis.set_minor_locator(MultipleLocator(10))
-
-    # Turn grid on for both major and minor ticks and style minor slightly
-    # differently.
-    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
-    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
-
-    ax1.set_xlabel('x (km)')
-    ax1.set_ylabel('displacement (km)')
-    ax1.set_title('Iceberg trajectory')
-
-    f.canvas.mpl_connect('button_press_event', onClick)
-    ani = FuncAnimation(
-        f,animate,init_func=init,frames=num_frames,
-        interval=frame_len,blit=True,repeat=False)
-
-
-    print('time',t)
-
-    plt.show()
-    #animation.save("iceberg_traj_animation.mp4")
-
-
-print('Script complete')
-
-if __name__ == '__main__':
-    optCmdLineArgs=	parseCommandLine()
-    anim_running = True
-    main(optCmdLineArgs)
diff --git a/tests/dem_rbeam_test/diag_table b/tests/dem_rbeam_test/diag_table
deleted file mode 100644
index c1c8819..0000000
--- a/tests/dem_rbeam_test/diag_table
+++ /dev/null
@@ -1,3 +0,0 @@
-"icebergs test"
-1 1 1 0 0 0
-
diff --git a/tests/dem_rbeam_test/input.nml b/tests/dem_rbeam_test/input.nml
deleted file mode 100644
index b1d2542..0000000
--- a/tests/dem_rbeam_test/input.nml
+++ /dev/null
@@ -1,184 +0,0 @@
-&icebergs_driver_nml
-  ni=20 !number of elements, x direction
-  nj=20 !number of elements, y direction
-  ibdt=10. !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=200 !total simulation hours
-  write_time_inc = 600 !increment at which time is written to screen
-  nmax=12000  !max number of timesteps
-  saverestart=.true.
-  halo=3
-  debug=.true.
-  collision_test=.false.
-  grounding_test=.false.
-  bump_depth=9999.0 !(m) depth of top of gaussian bump below sea level
-  gridres=15000
-/
-
-&icebergs_nml
-
-    !defaults given in parentheses:
-    !For this test, two options for dem_beam_test:
-    !3=1st element has rotation=-pi/2. Other elements adjust accordingly.
-    !4=vvel is always zero for 1st element. Last element initialized with vvel=-40 m/s
-    dem_beam_test=3
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=0.7
-    rho_bergs=900. ! (850) iceberg density
-    dem_spring_coef=1.e9 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-
-    monitor_energy=.false. !(F)save total elastic (spring+collision),external,dissipated,&fracture energy
-    new_mts=.true. !(F) If T, implicit accel is added 50% at the current time step and 50% at the next time step
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=200  !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=2000.0 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-8 !(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=3.16e6 !friction drag param
-    h_to_init_grounding=200.0 !300.0 !150.0 !300.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.false. !(T) remove unneeded bergs after PEs transfers
-
-
-    fracture_criterion='none' !('none') 'strain_rate','strain','stress',or 'none'
-    !here, try setting scaling 1.0 if force_convergence=.false., 0.5 if force_convergence=.true.
-    frac_thres_scaling = 1.0 !(1) scales frac_thres_n and frac_thres_t
-    frac_thres_n = 0. !1.e7  !normal fracture strain threshold
-    frac_thres_t = 0. !5.e7 !tangential fracture strain threshold
-
-    halo=3 !(4) halo width
-    Lx=300.e3 ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.false. ! (T) True=icebergs do no move
-
-    spring_coef=1.e-5
-    radial_damping_coef=0.0 !(1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.false. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0.0 !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.false. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.false. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.true. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=4 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=24000 ! (24) Period between verbose messages
-    traj_sample_hrs=0.05 !(24) sampling period for trajectory storage
-    traj_write_hrs=0.05 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.!(F) Init bond b/w bergs if dist<1.1*radius
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/dem_rbeam_test/makeberg/RUN b/tests/dem_rbeam_test/makeberg/RUN
deleted file mode 100755
index 9456794..0000000
--- a/tests/dem_rbeam_test/makeberg/RUN
+++ /dev/null
@@ -1,3 +0,0 @@
-rm ./output_files/Generic*
-./makeberg.py -t=1
-cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
diff --git a/tests/dem_rbeam_test/makeberg/makeberg.py b/tests/dem_rbeam_test/makeberg/makeberg.py
deleted file mode 100755
index 1f68b34..0000000
--- a/tests/dem_rbeam_test/makeberg/makeberg.py
+++ /dev/null
@@ -1,321 +0,0 @@
-#!/usr/bin/env python
-import numpy as np
-import math
-from netCDF4 import Dataset
-from pylab import *
-#import pdb
-import netCDF4 as nc
-import argparse
-
-def parseCommandLine():
-    parser = argparse.ArgumentParser(description=
-    '''Generate animation of iceberg trajectories.''',
-    epilog='Written by Alex Huth, 2020')
-    parser.add_argument('-t', type=int, default='1',
-                    help='''which test case''')
-    optCmdLineArgs = parser.parse_args()
-    return optCmdLineArgs
-
-def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
-
-	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
-	# To copy the global attributes of the netCDF file
-
-	#Input and output files
-	#Create Empty restart file. This is later read so that the attributes can be used.
-	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
-	create_empty_iceberg_restart_file(Empty_restart_filename)
-	#Empty_restart_filename='input_files/icebergs.res.nc'
-
-	#Read empty restart file
-	f=Dataset(Empty_restart_filename,'r') # r is for read only
-	#Write a new restart file
-	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
-
-	for attname in f.ncattrs():
-		    setattr(g,attname,getattr(f,attname))
-
-
-	# To copy the dimension of the netCDF file
-	for dimname,dim in f.dimensions.iteritems():
-		# if you want to make changes in the dimensions of the new file
-		# you should add your own conditions here before the creation of the dimension.
-		#g.createDimension(dimname,len(dim))
-		g.createDimension(dimname,Number_of_bergs)
-
-	# To copy the variables of the netCDF file
-
-	for varname,ncvar in f.variables.iteritems():
-		# if you want to make changes in the variables of the new file
-		# you should add your own conditions here before the creation of the variable.
-		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
-		#Proceed to copy the variable attributes
-		for attname in ncvar.ncattrs():
-			setattr(var,attname,getattr(ncvar,attname))
-		#Finally copy the variable data to the new created variable
-		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
-
-		if varname=='i':
-			var[:]=Number_of_bergs
-
-		if varname=='iceberg_num':
-			for j in range(Number_of_bergs):
-				#var[j]=j+1
-				var[j]=iceberg_num[j]
-
-		if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
-		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
-		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
-		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
-			var[:]=0
-
-                if varname=='uvel':
-			for j in range(Number_of_bergs):
-				var[j]=uvel[j]
-
-                if varname=='vvel':
-			for j in range(Number_of_bergs):
-				var[j]=vvel[j]
-
-		if varname=='mass_scaling':
-			for j in range(Number_of_bergs):
-				var[j]=mass_scaling[j]
-
-		if varname=='thickness':
-			for j in range(Number_of_bergs):
-				var[j]=thickness[j]
-
-		if varname=='mass':
-			for j in range(Number_of_bergs):
-				var[j]=mass[j]
-
-		if varname=='width'  or varname=='length':
-			for j in range(Number_of_bergs):
-				var[j]=width[j]
-
-		if varname=='lon':
-			for j in range(Number_of_bergs):
-				var[j]=lon[j]
-
-		if varname=='lat':
-			for j in range(Number_of_bergs):
-				var[j]=lat[j]
-
-		if varname=='static_berg':
-			for j in range(Number_of_bergs):
-				var[j]=static_berg[j]
-
-
-	f.close()
-	g.close()
-
-
-def create_empty_iceberg_restart_file(Empty_restart_filename):
-
-	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
-
-	i=f.createDimension('i', None)
-	lon=f.createVariable('i','i')
-
-	lon=f.createVariable('lon','d',('i'))
-	lon.long_name = "longitude" ;
-	lon.units = "degrees_E" ;
-	lon.checksum = "               0" ;
-
-	lat=f.createVariable('lat','d',('i'))
-	lat.long_name = "latitude" ;
-	lat.units = "degrees_N" ;
-	lat.checksum = "               0" ;
-
-	uvel=f.createVariable('uvel','d',('i'))
-	uvel.long_name = "zonal velocity" ;
-	uvel.units = "m/s" ;
-	uvel.checksum = "               0" ;
-
-	vvel=f.createVariable('vvel','d',('i'))
-	vvel.long_name = "meridional velocity" ;
-	vvel.units = "m/s" ;
-	vvel.checksum = "               0" ;
-
-	mass=f.createVariable('mass','d',('i'))
-	mass.long_name = "mass" ;
-	mass.units = "kg" ;
-	mass.checksum = "               0" ;
-
-	axn=f.createVariable('axn','d',('i'))
-	axn.long_name = "explicit zonal acceleration" ;
-	axn.units = "m/s^2" ;
-	axn.checksum = "               0" ;
-
-	ayn=f.createVariable('ayn','d',('i'))
-	ayn.long_name = "explicit meridional acceleration" ;
-	ayn.units = "m/s^2" ;
-	ayn.checksum = "               0" ;
-
-	bxn=f.createVariable('bxn','d',('i'))
-	bxn.long_name = "inplicit zonal acceleration" ;
-	bxn.units = "m/s^2" ;
-	bxn.checksum = "               0" ;
-
-	byn=f.createVariable('byn','d',('i'))
-	byn.long_name = "implicit meridional acceleration" ;
-	byn.units = "m/s^2" ;
-	byn.checksum = "               0" ;
-
-	ine=f.createVariable('ine','i',('i'))
-	ine.long_name = "i index" ;
-	ine.units = "none" ;
-	ine.packing = 0 ;
-	ine.checksum = "               0" ;
-
-	jne=f.createVariable('jne','i',('i'))
-	jne.long_name = "j index" ;
-	jne.units = "none" ;
-	jne.packing = 0 ;
-	jne.checksum = "               0" ;
-
-	thickness=f.createVariable('thickness','d',('i'))
-	thickness.long_name = "thickness" ;
-	thickness.units = "m" ;
-	thickness.checksum = "               0" ;
-
-	width=f.createVariable('width','d',('i'))
-	width.long_name = "width" ;
-	width.units = "m" ;
-	width.checksum = "               0" ;
-
-	length=f.createVariable('length','d',('i'))
-	length.long_name = "length" ;
-	length.units = "m" ;
-	length.checksum = "               0" ;
-
-	start_lon=f.createVariable('start_lon','d',('i'))
-	start_lon.long_name = "longitude of calving location" ;
-	start_lon.units = "degrees_E" ;
-	start_lon.checksum = "               0" ;
-
-	start_lat=f.createVariable('start_lat','d',('i'))
-	start_lat.long_name = "latitude of calving location" ;
-	start_lat.units = "degrees_N" ;
-	start_lat.checksum = "               0" ;
-
-	start_year=f.createVariable('start_year','i',('i'))
-	start_year.long_name = "calendar year of calving event" ;
-	start_year.units = "years" ;
-	start_year.packing = 0 ;
-	start_year.checksum = "               0" ;
-
-	iceberg_num=f.createVariable('iceberg_num','i',('i'))
-	iceberg_num.long_name = "identification of the iceberg" ;
-	iceberg_num.units = "dimensionless" ;
-	iceberg_num.packing = 0 ;
-	iceberg_num.checksum = "               0" ;
-
-	start_day=f.createVariable('start_day','d',('i'))
-	start_day.long_name = "year day of calving event" ;
-	start_day.units = "days" ;
-	start_day.checksum = "               0" ;
-
-	start_mass=f.createVariable('start_mass','d',('i'))
-	start_mass.long_name = "initial mass of calving berg" ;
-	start_mass.units = "kg" ;
-	start_mass.checksum = "               0" ;
-
-	mass_scaling=f.createVariable('mass_scaling','d',('i'))
-	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
-	mass_scaling.units = "none" ;
-	mass_scaling.checksum = "               0" ;
-
-	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
-	mass_of_bits.long_name = "mass of bergy bits" ;
-	mass_of_bits.units = "kg" ;
-	mass_of_bits.checksum = "               0" ;
-
-	heat_density=f.createVariable('heat_density','d',('i'))
-	heat_density.long_name = "heat density" ;
-	heat_density.units = "J/kg" ;
-	heat_density.checksum = "               0" ;
-
-	halo_berg=f.createVariable('halo_berg','d',('i'))
-	halo_berg.long_name = "halo_berg" ;
-	halo_berg.units = "dimensionless" ;
-	halo_berg.checksum = "               0" ;
-
-	static_berg=f.createVariable('static_berg','d',('i'))
-	static_berg.long_name = "static_berg" ;
-	static_berg.units = "dimensionless" ;
-	static_berg.checksum = "               0" ;
-
-	f.sync()
-	f.close()
-
-
-def main(args):
-
-    #SQUARE PACKING
-
-        test=args.t
-        grdres=20.e3
-        r=2500.0#/3.
-
-        #start coords
-        xs=101.e3
-        ys=151.e3
-
-        h=4. #thickness
-        rho_ice=900.0
-
-
-        if test==1:
-            #5 particles w/ large radius
-            nbergs=30#90
-            width=r*2.
-            length=r*2.
-
-        #radii for evenly distrib cases
-        #element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*r**2)
-        element_area=(2.*r)**2
-
-        berg_x=[]; berg_y=[]
-        berg_id=[]; berg_static=[]
-        berg_width=[]; berg_bonds=[]
-        berg_h=[]; berg_mass_scaling=[]
-        berg_mass=[]
-        berg_uvel=[]; berg_vvel=[]
-
-        x=xs
-        y=ys#-2*r
-
-        berg_count=0.
-        while berg_count<nbergs:
-                berg_count=berg_count+1
-                if berg_count==1:
-                    #x=xs
-                    y=y+2*r
-                    static=1
-                else:
-                    static=0
-                    x=x+2*r
-
-                berg_x.append(x)
-                berg_y.append(y)
-                berg_width.append(sqrt(element_area))
-                berg_h.append(h)
-                berg_mass_scaling.append(1)
-                berg_mass.append(h*rho_ice*element_area)
-                berg_static.append(static)
-                berg_uvel.append(0)
-                berg_vvel.append(0)
-                berg_id.append(berg_count)
-
-        print('Number of bergs',berg_count)
-
-        #Create iceberg restart file
-        Ice_geometry_source='Generic'
-        Create_iceberg_restart_file(nbergs,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)
-
-
-if __name__ == '__main__':
-    optCmdLineArgs=	parseCommandLine()
-    anim_running = True
-    main(optCmdLineArgs)
diff --git a/tests/dem_ssbeam_test/README b/tests/dem_ssbeam_test/README
index 38ed5d7..8d6267c 100644
--- a/tests/dem_ssbeam_test/README
+++ b/tests/dem_ssbeam_test/README
@@ -1 +1,5 @@
-This is the simply supported beam test from Section 3.1 of Wang 2020 "A scale-invariant bonded particle model for simulating large deformation and failure of continua"
\ No newline at end of file
+This is the simply supported beam test from Section 3.1 of Wang 2020 "A scale-invariant bonded particle model for simulating large deformation and failure of continua" https://doi.org/10.1016/j.compgeo.2020.103735. It tests the discrete-element/bonded-particle model that underlies iKID.
+
+When the results are animated (animate_trajectories.py), the beam should bend into alignment with the plotted line.
+
+By default, run with 4 PEs
diff --git a/tests/dem_ssbeam_test/RUN b/tests/dem_ssbeam_test/RUN
index 0ffc895..32c463c 100755
--- a/tests/dem_ssbeam_test/RUN
+++ b/tests/dem_ssbeam_test/RUN
@@ -2,4 +2,4 @@ rm iceberg_trajectories.nc
 rm iceberg_trajectories.nc.*
 rm bond_trajectories.nc
 rm bond_trajectories.nc.*
-srun -n1 ./../../build/bergs.x
+srun -n4 ./../../build/bergs.x
diff --git a/tests/dem_ssbeam_test/animate_trajectories.py b/tests/dem_ssbeam_test/animate_trajectories.py
index 9b8cf0d..259c410 100755
--- a/tests/dem_ssbeam_test/animate_trajectories.py
+++ b/tests/dem_ssbeam_test/animate_trajectories.py
@@ -38,7 +38,7 @@ def main(args):
     with nc.Dataset(filename) as file:
         x = file.variables['lon'][:] #/1.e3
         y = file.variables['lat'][:] #/1.e3
-        day = file.variables['day'][:]
+        day = file.variables['day'][:]*24*60*60
         length = file.variables['length'][:]
         width = file.variables['width'][:]
         hs = file.variables['thickness'][:]
@@ -48,10 +48,11 @@ def main(args):
 
     #print('day',day)
     crop=False
-    tc=1.25
+    tc=2e-5#1.25
     if crop:
         x=x[day<=tc]
         y=y[day<=tc]
+        radius=radius[day<=tc]
         day=day[day<=tc]
 
     ud = np.unique(day)
@@ -97,7 +98,7 @@ def animate(i):
         scat.set_edgecolor('k')
 
         t = ud[i]
-        time_text.set_text('time = %.1f days' % t )
+        time_text.set_text('time = %.1f sec' % t )
 
         r1 = radius[day == ud[i]]
         scat.set_sizes(r1/psize)
diff --git a/tests/dem_ssbeam_test/input.nml b/tests/dem_ssbeam_test/input.nml
index 5323907..7f36f5c 100644
--- a/tests/dem_ssbeam_test/input.nml
+++ b/tests/dem_ssbeam_test/input.nml
@@ -1,3 +1,10 @@
+! KID, bergs_chksum: write_restart berg chksum=1546149565 chksum2=-1486497579 chksum3=-1459704404 chksum4=-1459704404 chksum5=0 #=29
+! KID, grd_chksum2: # of bergs/cell chksum=0 chksum2=0 min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
+!  Total number of bonds is:56
+!  All iceberg bonds are connected and working well
+! KID, grd_chksum3:   write stored_ice chksum=-540079793 chksum2=-1237287029 min= 6.393358811E+05 max= 7.380127765E+11 mean= 8.033602570E+10 rms= 1.613270384E+11 sd= 1.399018810E+11
+
+
 &icebergs_driver_nml
   ni=20 !number of elements, x direction
   nj=20 !number of elements, y direction
@@ -8,7 +15,7 @@
   ibvi=0.0 !ice y velocity
   ibhrs=200 !total simulation hours
   write_time_inc = 1 !600 !increment at which time is written to screen
-  nmax=30 !1200  !max number of timesteps
+  nmax=10 !1200  !max number of timesteps
   saverestart=.true.
   halo=3
   debug=.true.

From 1ee47c1a25f227c0451160df1100009e55ee4e52 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Fri, 18 Nov 2022 15:30:27 -0500
Subject: [PATCH 320/361] merged in mpp_self_sync modification from dev/gfdl

---
 src/icebergs_io.F90 | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index 06ff4d2..0d635da 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -8,7 +8,7 @@ module ice_bergs_io
 use mpp_domains_mod, only: mpp_get_tile_pelist,mpp_get_tile_npes,mpp_get_io_domain,mpp_get_tile_id
 
 use mpp_mod, only: mpp_npes, mpp_pe, mpp_root_pe, mpp_sum, mpp_min, mpp_max, NULL_PE
-use mpp_mod, only: mpp_send, mpp_recv, mpp_gather, mpp_chksum
+use mpp_mod, only: mpp_send, mpp_recv, mpp_gather, mpp_chksum, mpp_sync_self
 use mpp_mod, only: COMM_TAG_11, COMM_TAG_12, COMM_TAG_13, COMM_TAG_14
 
 use fms_mod, only: stdlog, stderr, error_mesg, FATAL, WARNING, NOTE
@@ -1752,10 +1752,10 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r, tra
 integer :: stderrunit, cnt, ij
 !I/O vars
 type(xyt), pointer :: traj4io=>null()
-integer :: ntrajs_sent_io,ntrajs_rcvd_io
 integer :: from_pe,np
 type(buffer), pointer :: obuffer_io=>null(), ibuffer_io=>null()
 logical :: io_is_in_append_mode
+integer :: ntrajs_sent_io,ntrajs_rcvd_io
 
   ! Get the stderr unit number
   stderrunit=stderr()
@@ -1812,7 +1812,7 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r, tra
         call mpp_send(obuffer_io%data, ntrajs_sent_io*buffer_width_traj, to_pe=io_tile_root_pe, tag=COMM_TAG_12)
      endif
   endif
-
+  call mpp_sync_self()
   endif !.NOT. force_all_pes_traj
 
   call mpp_clock_end(clock_trp)

From 20cb3455cef9e9062f4ed70ae9e0a70ffced4f2e Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Fri, 18 Nov 2022 16:27:51 -0500
Subject: [PATCH 321/361] reset input_freq_distribution to false, the old
 default

---
 src/icebergs_framework.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index c7133bc..3b23c26 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -850,7 +850,7 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: critical_interaction_damping_on=.true. ! Sets the damping on relative iceberg velocity to critical value - Added by Alon
 logical :: tang_crit_int_damp_on=.true. ! Critical interaction damping for tangential component?
 logical :: do_unit_tests=.false. ! Conduct some unit tests
-logical :: input_freq_distribution=.true. ! Flag to show if input distribution is freq or mass dist (=1 if input is a freq dist, =0 to use an input mass dist)
+logical :: input_freq_distribution=.false. ! Flag to show if input distribution is freq or mass dist (=1 if input is a freq dist, =0 to use an input mass dist)
 logical :: read_old_restarts=.false. ! Legacy option that does nothing
 logical :: use_old_spreading=.true. ! If true, spreads iceberg mass as if the berg is one grid cell wide
 logical :: read_ocean_depth_from_file=.false. ! If true, ocean depth is read from a file.

From e730ef20fabc9d7dead9e624a3aafe74ec28df18 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Fri, 18 Nov 2022 17:11:46 -0500
Subject: [PATCH 322/361] documented file name variables for particle and bond
 trajectories

---
 src/icebergs_io.F90 | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index 0d635da..09abcb3 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -1735,6 +1735,7 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r, tra
 logical, intent(in) :: save_short_traj !< If true, record less data
 logical, intent(in) :: save_fl_traj !< If true, save masses and footloose data
 real, intent(in) :: fl_r !< If >0 and save_fl_traj, save footloose params
+character(len=70) :: traj_name !< name of trajectory file
 ! Local variables
 integer :: iret, ncid, i_dim, i
 integer :: lonid, latid, yearid, dayid, uvelid, vvelid, idcntid, idijid
@@ -1746,7 +1747,7 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r, tra
 integer :: eecid,edcid,eeid,edid,aeid,efid
 integer :: eectid, edctid, eetid, edtid, aetid
 integer :: avid, aaid, rid, abrid
-character(len=70) :: filename, traj_name
+character(len=70) :: filename
 character(len=7) :: pe_name
 type(xyt), pointer :: this, next
 integer :: stderrunit, cnt, ij
@@ -2303,6 +2304,7 @@ end subroutine write_trajectory
 subroutine write_bond_trajectory(trajectory, bond_traj_name)
 ! Arguments
 type(bond_xyt), pointer :: trajectory !< An iceberg bond trajectory
+character(len=70) :: bond_traj_name !<file name of bond trajectories
 ! Local variables
 integer :: iret, ncid, i_dim, i
 integer :: lonid, latid, yearid, dayid, lenid,n1id, n2id, peid
@@ -2310,7 +2312,7 @@ subroutine write_bond_trajectory(trajectory, bond_traj_name)
 integer :: idcnt1_id, idcnt2_id, idij1_id, idij2_id, eeid, edid
 integer :: axid,ayid,bxid,byid
 integer :: td1id,td2id,dnsid,dssid
-character(len=70) :: filename, bond_traj_name
+character(len=70) :: filename
 character(len=7) :: pe_name
 type(bond_xyt), pointer :: this, next
 integer :: stderrunit, cnt, ij

From 28a755d94f3d04d84d9ed71c7a9e231c2356ee51 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Mon, 21 Nov 2022 15:30:04 -0500
Subject: [PATCH 323/361] changes towards passing om4p5 jra55 regression tests.
 In absence of DEM,MTS, or footloose, reset when grid to particle
 intepolations occur to the original convention. Only save footloose variables
 in restart files if footloose is active.

---
 src/icebergs.F90           | 45 ++++++++++++++++++++++++++------------
 src/icebergs_framework.F90 |  6 +++++
 src/icebergs_io.F90        | 44 +++++++++++++++++++++++++------------
 3 files changed, 67 insertions(+), 28 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index f13a2eb..59436cf 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -2437,14 +2437,22 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
   grd=>bergs%grd
 
   ! Interpolate gridded fields to berg
-  !if (bergs%mts) then
-    !gridded fields already saved on berg
+  ! !if (bergs%mts) then
+  !   !gridded fields already saved on berg
+  !   uo=berg%uo; vo=berg%vo; ua=berg%ua; va=berg%va; ui=berg%ui; vi=berg%vi;
+  !   ssh_x=berg%ssh_x; ssh_y=berg%ssh_y; sst=berg%sst; sss=berg%sss;  cn=berg%cn; hi=berg%hi; od=berg%od
+  ! !else
+  ! !  call interp_flds(grd, berg%lon, berg%lat, i, j, xi, yj, rx, ry, uo, vo, ui, vi, ua, va, ssh_x, &
+  ! !    ssh_y, sst, sss, cn, hi, od)
+  !   !end if
+
+  if (bergs%old_interp_flds_order) then
+    call interp_flds(grd, berg%lon, berg%lat, i, j, xi, yj, rx, ry, uo, vo, ui, vi, ua, va, ssh_x, &
+      ssh_y, sst, sss, cn, hi, od)
+  else
     uo=berg%uo; vo=berg%vo; ua=berg%ua; va=berg%va; ui=berg%ui; vi=berg%vi;
     ssh_x=berg%ssh_x; ssh_y=berg%ssh_y; sst=berg%sst; sss=berg%sss;  cn=berg%cn; hi=berg%hi; od=berg%od
-  !else
-  !  call interp_flds(grd, berg%lon, berg%lat, i, j, xi, yj, rx, ry, uo, vo, ui, vi, ua, va, ssh_x, &
-  !    ssh_y, sst, sss, cn, hi, od)
-  !end if
+  end if
 
   if ((grd%grid_is_latlon) .and. (.not. bergs%use_f_plane)) then
      f_cori=(2.*omega)*sin(pi_180*lat)
@@ -3355,9 +3363,13 @@ subroutine thermodynamics(bergs)
     this=>bergs%list(grdi,grdj)%first
     do while(associated(this))
       if (debug) call check_position(grd, this, 'thermodynamics (top)')
-      ! call interp_flds(grd, this%lon, this%lat, this%ine, this%jne, this%xi, this%yj, 0., 0., &
-      !                  this%uo, this%vo, this%ui, this%vi, this%ua, this%va, this%ssh_x, &
-      !                  this%ssh_y, this%sst, this%sss,this%cn, this%hi)
+
+      if (bergs%old_interp_flds_order) then
+        call interp_flds(grd, this%lon, this%lat, this%ine, this%jne, this%xi, this%yj, 0., 0., &
+          this%uo, this%vo, this%ui, this%vi, this%ua, this%va, this%ssh_x, &
+          this%ssh_y, this%sst, this%sss,this%cn, this%hi)
+      end if
+
       SST=this%sst
       SSS=this%sss
       IC=min(1.,this%cn+bergs%sicn_shift) ! Shift sea-ice concentration
@@ -6012,7 +6024,9 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     if (mpp_pe()==0) write(*,'(a)') 'KID, iceberg_run: completed first visit initialization'
   endif
 
-  if (.not. bergs%mts) call interp_gridded_fields_to_bergs(bergs)
+  !if (.not. bergs%mts) call interp_gridded_fields_to_bergs(bergs)
+  !call this for footloose
+  if ((.not. bergs%mts) .and. (.not. bergs%old_interp_flds_order)) call interp_gridded_fields_to_bergs(bergs)
 
   ! For each berg, evolve
   call mpp_clock_begin(bergs%clock_mom)
@@ -6063,7 +6077,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
         call set_conglom_ids(bergs)
       endif
     endif
-    call interp_gridded_fields_to_bergs(bergs)
+    if (.not. bergs%old_interp_flds_order) call interp_gridded_fields_to_bergs(bergs)
   endif
   if (debug) call bergs_chksum(bergs, 'run bergs (exchanged)')
   if (debug) call checksum_gridded(bergs%grd, 's/r run after exchange')
@@ -6976,9 +6990,12 @@ subroutine calve_icebergs(bergs)
             call getRandomNumbers(rns, ry)
             rx = 2.*rx - 1.; ry = 2.*ry - 1.
           endif
-          call interp_flds(grd, newberg%lon, newberg%lat, i, j, xi, yj, rx, ry, newberg%uo, newberg%vo, newberg%ui, &
-            newberg%vi, newberg%ua, newberg%va, newberg%ssh_x, newberg%ssh_y, newberg%sst, newberg%sss, newberg%cn, &
-            newberg%hi, newberg%od)
+
+          if (.not. bergs%old_interp_flds_order) then
+            call interp_flds(grd, newberg%lon, newberg%lat, i, j, xi, yj, rx, ry, newberg%uo, newberg%vo, newberg%ui, &
+              newberg%vi, newberg%ua, newberg%va, newberg%ssh_x, newberg%ssh_y, newberg%sst, newberg%sss, newberg%cn, &
+              newberg%hi, newberg%od)
+          end if
 
           call add_new_berg_to_list(bergs%list(i,j)%first, newberg)
           calved_to_berg=initial_mass*mass_scaling ! Units of kg
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 3b23c26..d6cc554 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -686,6 +686,9 @@ module ice_bergs_framework
   real :: fl_bits_scale_l=0.9 !< For determining dimensions of FL bits berg; FL_bits length    = fl_bits_scale_l * 3*l_b
   real :: fl_bits_scale_w=0.9 !< For determining dimensions of FL bits berg; FL_bits width     = fl_bits_scale_w * 3*l_b
   real :: fl_bits_scale_t=0.9 !< For determining dimensions of FL bits berg; FL_bits thickness = fl_bits_scale_t * T
+
+  !backwards compatibility
+  logical :: old_interp_flds_order=.false. !< Use old order of when to interpolate grid variables to bergs. Will be false if MTS, DEM, or footloose (.not. fl_r>0)
 end type icebergs
 
 !> Read original restarts. Needs to be module global so can be public to icebergs_mod.
@@ -1625,6 +1628,9 @@ subroutine ice_bergs_framework_init(bergs, &
     endif
   endif
 
+  !backwards compatibility
+  if (.not. (bergs%mts .or. bergs%dem .or. bergs%fl_r>0.)) bergs%old_interp_flds_order=.true.
+
   if (bergs%contact_distance>0) then
     dx_dlon=1; dy_dlat=1
     if (grd%grid_is_latlon) dy_dlat=pi_180*Rearth
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index 0d635da..1cd4267 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -221,15 +221,12 @@ subroutine write_restart(bergs, time_stamp)
    allocate(thickness(nbergs))
    allocate(width(nbergs))
    allocate(length(nbergs))
-   allocate(fl_k(nbergs))
    allocate(start_lon(nbergs))
    allocate(start_lat(nbergs))
    allocate(start_day(nbergs))
    allocate(start_mass(nbergs))
    allocate(mass_scaling(nbergs))
    allocate(mass_of_bits(nbergs))
-   allocate(mass_of_fl_bits(nbergs))
-   allocate(mass_of_fl_bergy_bits(nbergs))
    allocate(heat_density(nbergs))
    allocate(static_berg(nbergs))
 
@@ -239,6 +236,12 @@ subroutine write_restart(bergs, time_stamp)
    allocate(id_cnt(nbergs))
    allocate(id_ij(nbergs))
 
+   if (bergs%fl_r>0) then
+     allocate(fl_k(nbergs))
+     allocate(mass_of_fl_bits(nbergs))
+     allocate(mass_of_fl_bergy_bits(nbergs))
+   end if
+
    if (mts) then
      allocate(axn_fast(nbergs))
      allocate(ayn_fast(nbergs))
@@ -285,7 +288,6 @@ subroutine write_restart(bergs, time_stamp)
   id = register_restart_field(bergs_restart,filename,'thickness',thickness,longname='thickness',units='m')
   id = register_restart_field(bergs_restart,filename,'width',width,longname='width',units='m')
   id = register_restart_field(bergs_restart,filename,'length',length,longname='length',units='m')
-  id = register_restart_field(bergs_restart,filename,'fl_k',fl_k,longname='footloose calving k',units='m')
   id = register_restart_field(bergs_restart,filename,'start_lon',start_lon, &
                                             longname='longitude of calving location',units='degrees_E')
   id = register_restart_field(bergs_restart,filename,'start_lat',start_lat, &
@@ -304,13 +306,17 @@ subroutine write_restart(bergs, time_stamp)
                                             longname='scaling factor for mass of calving berg',units='none')
   id = register_restart_field(bergs_restart,filename,'mass_of_bits',mass_of_bits, &
                                             longname='mass of bergy bits',units='kg')
-  id = register_restart_field(bergs_restart,filename,'mass_of_fl_bits',mass_of_fl_bits, &
-                                            longname='mass of footloose bits',units='kg')
-  id = register_restart_field(bergs_restart,filename,'mass_of_fl_bergy_bits',mass_of_fl_bergy_bits, &
-                                            longname='mass of bergy bits associated with footloose bits',units='kg')
   id = register_restart_field(bergs_restart,filename,'heat_density',heat_density, &
                                             longname='heat density',units='J/kg')
 
+  if (bergs%fl_r>0) then
+    id = register_restart_field(bergs_restart,filename,'fl_k',fl_k,longname='footloose calving k',units='m')
+    id = register_restart_field(bergs_restart,filename,'mass_of_fl_bits',mass_of_fl_bits, &
+      longname='mass of footloose bits',units='kg')
+    id = register_restart_field(bergs_restart,filename,'mass_of_fl_bergy_bits',mass_of_fl_bergy_bits, &
+      longname='mass of bergy bits associated with footloose bits',units='kg')
+   end if
+
   if (mts) then
     id = register_restart_field(bergs_restart,filename,'axn_fast',axn_fast,&
       longname='sub-step explicit zonal acceleration',units='m/s^2')
@@ -370,14 +376,20 @@ subroutine write_restart(bergs, time_stamp)
       axn(i) = this%axn; ayn(i) = this%ayn !Added by Alon
       bxn(i) = this%bxn; byn(i) = this%byn !Added by Alon
       width(i) = this%width; length(i) = this%length
-      fl_k(i) = this%fl_k
       start_lon(i) = this%start_lon; start_lat(i) = this%start_lat
       start_year(i) = this%start_year; start_day(i) = this%start_day
       start_mass(i) = this%start_mass; mass_scaling(i) = this%mass_scaling
       static_berg(i) = this%static_berg
       call split_id(this%id, id_cnt(i), id_ij(i))
-      mass_of_bits(i) = this%mass_of_bits; mass_of_fl_bits(i) = this%mass_of_fl_bits
-      mass_of_fl_bergy_bits(i) = this%mass_of_fl_bergy_bits; heat_density(i) = this%heat_density
+      mass_of_bits(i) = this%mass_of_bits
+      heat_density(i) = this%heat_density
+
+      if (bergs%fl_r>0) then
+        fl_k(i) = this%fl_k
+        mass_of_fl_bits(i) = this%mass_of_fl_bits
+        mass_of_fl_bergy_bits(i) = this%mass_of_fl_bergy_bits
+      end if
+
       if (mts) then
         axn_fast(i) = this%axn_fast
         ayn_fast(i) = this%ayn_fast
@@ -418,17 +430,21 @@ subroutine write_restart(bergs, time_stamp)
              thickness,    &
              width,        &
              length,       &
-             fl_k,         &
              start_lon,    &
              start_lat,    &
              start_day,    &
              start_mass,   &
              mass_scaling, &
              mass_of_bits, &
-             mass_of_fl_bits, &
-             mass_of_fl_bergy_bits, &
              static_berg,  &
              heat_density)
+
+  if (bergs%fl_r>0.) then
+    deallocate(                   &
+                 fl_k,            &
+                 mass_of_fl_bits, &
+                 mass_of_fl_bergy_bits)
+  end if
   if (mts) then
     deallocate(            &
              axn_fast,     &

From 2bf5e752145125cfe38999e24ac89e9064d31720 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Wed, 23 Nov 2022 14:03:12 -0500
Subject: [PATCH 324/361] Added separate test cases for footloose_poisson
 (calve child bergs from iceberg edges similarly to England et al., 2020, with
 some geometric features from Huth et al., 2022) and footloose_physical
 (physically based parameterization of footloose calving of child bergs from
 iceberg edges, following Huth et al., 2022). Removed the A68a test case from
 the driver

---
 driver/icebergs_driver.F90                    | 283 ++++++------------
 src/icebergs.F90                              |   2 +-
 .../README                                    |   0
 .../RUN                                       |   0
 .../RUN1p                                     |   0
 .../animate_trajectories.py                   |   0
 .../diag_table                                |   0
 tests/footloose_physical/input.nml            | 172 +++++++++++
 .../input_old.nml}                            |   0
 .../makeberg/RUN                              |   0
 .../makeberg/makeberg.py                      |   0
 tests/footloose_poisson/README                |   9 +
 tests/footloose_poisson/RUN                   |   5 +
 tests/footloose_poisson/RUN1p                 |   5 +
 .../footloose_poisson/animate_trajectories.py | 151 ++++++++++
 tests/footloose_poisson/diag_table            |   3 +
 tests/footloose_poisson/input.nml             | 167 +++++++++++
 tests/footloose_poisson/input_old.nml         | 170 +++++++++++
 tests/footloose_poisson/makeberg/RUN          |   5 +
 tests/footloose_poisson/makeberg/makeberg.py  | 278 +++++++++++++++++
 20 files changed, 1054 insertions(+), 196 deletions(-)
 rename tests/{footloose_no_bond_test => footloose_physical}/README (100%)
 rename tests/{footloose_no_bond_test => footloose_physical}/RUN (100%)
 rename tests/{footloose_no_bond_test => footloose_physical}/RUN1p (100%)
 rename tests/{footloose_no_bond_test => footloose_physical}/animate_trajectories.py (100%)
 rename tests/{footloose_no_bond_test => footloose_physical}/diag_table (100%)
 create mode 100644 tests/footloose_physical/input.nml
 rename tests/{footloose_no_bond_test/input.nml => footloose_physical/input_old.nml} (100%)
 rename tests/{footloose_no_bond_test => footloose_physical}/makeberg/RUN (100%)
 rename tests/{footloose_no_bond_test => footloose_physical}/makeberg/makeberg.py (100%)
 create mode 100644 tests/footloose_poisson/README
 create mode 100755 tests/footloose_poisson/RUN
 create mode 100755 tests/footloose_poisson/RUN1p
 create mode 100755 tests/footloose_poisson/animate_trajectories.py
 create mode 100644 tests/footloose_poisson/diag_table
 create mode 100644 tests/footloose_poisson/input.nml
 create mode 100644 tests/footloose_poisson/input_old.nml
 create mode 100755 tests/footloose_poisson/makeberg/RUN
 create mode 100755 tests/footloose_poisson/makeberg/makeberg.py

diff --git a/driver/icebergs_driver.F90 b/driver/icebergs_driver.F90
index e112545..e83e9fe 100644
--- a/driver/icebergs_driver.F90
+++ b/driver/icebergs_driver.F90
@@ -62,19 +62,19 @@ program icebergs_driver
 logical :: grounding_test=.false.
 logical :: big_grounding_test=.false.
 logical :: dem_test_contact=.false.
-logical :: a68_test=.false.
 logical :: vert_int_ocean_vel=.false.
 logical :: tau_is_velocity=.true.
-logical :: reverse_a68_forcings=.false.
+logical :: sin_test=.false.
+logical :: fl_test=.false.
 character(len=1000) :: data_dir = 'data/'
-integer :: transient_a68_data_start_ind=0 !<set to .gt. 0 to use the hourly JRA-55 wind data for the A68
-!! test. The values indicate the time index to start from in the hourly data
 integer :: halo=1 !< Width of halo in parallel decomposition
 real :: ibdt=3600.0
 real :: ibuo=0.0
 real :: ibvo=0.0
 real :: ibui=0.0
 real :: ibvi=0.0
+real :: ibua=0.0
+real :: ibuy=0.0
 real :: gridres=1.e3
 real :: bump_depth=0
 real :: sst=-2
@@ -87,8 +87,8 @@ program icebergs_driver
 integer :: write_time_inc=1
 namelist /icebergs_driver_nml/ debug, ni, nj, halo, ibhrs, ibdt, ibuo, ibvo, nmax, &
   saverestart,ibui,ibvi,collision_test,chaotic_test,grounding_test,&
-  gridres,write_time_inc,bump_depth, sst, a68_test, data_dir, vert_int_ocean_vel,&
-  reverse_a68_forcings,tau_is_velocity,transient_a68_data_start_ind,&
+  gridres,write_time_inc,bump_depth, sst, data_dir, vert_int_ocean_vel,&
+  sin_test,fl_test,tau_is_velocity,ibua,ibuy,&
   Old_wrong_Rearth_and_SSH,no_wind,REarth,big_grounding_test,dem_test_contact !mom_Rearth
 ! For loops
 integer :: isc !< Start of i-index for computational domain (used for loops)
@@ -123,8 +123,6 @@ program icebergs_driver
 real, dimension(:,:), allocatable :: uo,vo !<zonal and meridonal ocean velocities (m/s)
 real, dimension(:,:), allocatable :: ui,vi !<zonal and meridonal ice velocities (m/s)
 real, dimension(:,:), allocatable :: tauxa,tauya !< Zonal and meridonal wind stress (Pa)
-real, dimension(:,:,:), allocatable :: tauxa_hr,tauya_hr !< Hourly jra-55 zonal and meridonal wind velocity (m/s) for A68 test
-real, dimension(:,:,:), allocatable :: uo_hr,vo_hr !<Hourly OSCAR zonal and meridonal ocean surface velocities (m/s) for A68 test
 real, dimension(:,:), allocatable :: ssh !< Effective sea-surface height (m)
 real, dimension(:,:,:), allocatable :: ssh_hr !< Effective sea-surface height (m, hourly)
 real, dimension(:,:), allocatable :: sstemp !< Sea-surface temperature (C or K)
@@ -149,12 +147,6 @@ program icebergs_driver
 read(nmunit, nml=icebergs_driver_nml)
 call close_file(nmunit)
 
-if (a68_test) then
-  call a68_dims(data_dir,ni,nj)
-  if (mpp_pe()==0) print *,'ni,nj',ni,nj
-  iflags=0
-endif
-
 if (min(ni,nj)<1) call error_mesg('icebergs_driver:', &
   'Both ni,nj must be positive in icebergs_driver_nml namelist', FATAL)
 
@@ -229,8 +221,8 @@ program icebergs_driver
 vo = ibvo !meridonal ocean velocities (m/s)
 ui = ibui !zonal ice velocities (m/s)
 vi = ibvi !meridonal ice velocities (m/s)
-tauxa = 0.0 !zonal wind stress (Pa)
-tauya = 0.0 !meridonal wind stress (Pa)
+tauxa = ibua !zonal wind velocity (m/s) or stress (Pa) if tau_is_velocity=.false,
+tauya = ibuy !meridonal wind velocity (m/s) or stress (Pa) if tau_is_velocity=.false,
 ssh = 0.0 !eff sea-surf height
 sstemp = sst !sea surface temperature (C or K; if K, will automatically adjust to C)
 cn = 0.0 !sea-ice concentration (nondim)
@@ -249,150 +241,102 @@ program icebergs_driver
 ! ustar_berg = !Friction velocity on base of bergs (m/s)
 ! area_berg = !Area of bergs (m2)
 
-if (a68_test) then
-  if (Old_wrong_Rearth_and_SSH) REarth=6360000.
-  call mpp_sync()
-  call a68_prep(data_dir,mpp_domain,lon,lat,dx,dy,area,depth,uo,vo,tauxa,tauya,ssh,vert_int_ocean_vel,tau_is_velocity,Old_wrong_Rearth_and_SSH,REarth)
-  !mom_Rearth)
-  call mpp_sync()
-  if (no_wind) then
-    tauxa=0.0; tauya=0.0
-  endif
-  !where (lon<(-37.6+360.))
-  !  depth=depth+1000.
-  !end where
-  wet=1.0
-  cos_rot=1.0
-  sin_rot=0.0
-  if (reverse_a68_forcings) then
-    uo=-uo; vo=-vo
-    tauxa=-tauxa; tauya=-tauya
-  endif
-
-  if (transient_a68_data_start_ind>0) then
-    if (.not. (ibdt==3600.0 .or. ibdt==1800.0)) then
-      call error_mesg('icebergs_driver:', &
-      'in order to use transient_a68_data_start_ind>0, timestep must be 30 min or 1 hr', FATAL)
-    endif
-    if (.not. tau_is_velocity) call error_mesg('icebergs_driver:', &
-      'tau_is_velocity must be true if transient_a68_data_start_ind>-1', FATAL)
-    allocate( tauxa_hr(isd:ied,jsd:jed,739) )
-    allocate( tauya_hr(isd:ied,jsd:jed,739) )
-    allocate( uo_hr(isd:ied,jsd:jed,744) )
-    allocate( vo_hr(isd:ied,jsd:jed,744) )
-    allocate( ssh_hr(isd:ied,jsd:jed,744) )
-    call a68_prep_3d(data_dir,mpp_domain,tauxa_hr,tauya_hr,uo_hr,vo_hr,ssh_hr)
-    if (reverse_a68_forcings) then
-      tauxa_hr=-tauxa_hr; tauya_hr=-tauya_hr
-      uo_hr=-uo_hr; vo_hr=-vo_hr
-      ssh_hr=-ssh_hr
-      dit=-1
-    else
-      dit=1
-    endif
-    if (no_wind) then
-      tauxa_hr=0.0; tauya_hr=0.0
-    endif
-  endif
-else
-  do j = jsd, jed
-    do i = isd, ied
-      lon(i,j) = gridres*real(i)
-      lat(i,j) = gridres*real(j)
-      dx(i,j) = gridres
-      dy(i,j) = gridres
-      area(i,j) = gridres*gridres
-      wet(i,j) = 1.0
-      cos_rot(i,j) = 1.0
-      sin_rot(i,j) = 0.0
-      depth(i,j) = 1000.
-    enddo
+do j = jsd, jed
+  do i = isd, ied
+    lon(i,j) = gridres*real(i)
+    lat(i,j) = gridres*real(j)
+    dx(i,j) = gridres
+    dy(i,j) = gridres
+    area(i,j) = gridres*gridres
+    wet(i,j) = 1.0
+    cos_rot(i,j) = 1.0
+    sin_rot(i,j) = 0.0
+    depth(i,j) = 1000.
   enddo
+enddo
 
-  if (chaotic_test) then
-    !assign land cells at the N and S portions of the domain.
-    !input.nml: set coastal drift parameter to prevent grounding
-    do j=jsd,jed; do i=isd,ied
-      if (lat(i,j)<=0.0+2*gridres .or. lat(i,j)>=1000.e3-2*gridres) wet(i,j)=0.0
-    enddo;enddo
-  endif
+if (chaotic_test) then
+  !assign land cells at the N and S portions of the domain.
+  !input.nml: set coastal drift parameter to prevent grounding
+  do j=jsd,jed; do i=isd,ied
+    if (lat(i,j)<=0.0+2*gridres .or. lat(i,j)>=1000.e3-2*gridres) wet(i,j)=0.0
+  enddo;enddo
+endif
 
-  if (big_grounding_test) then
-    lat(:,:)=lat(:,:)-0.45 !-25000.1
-    lon(:,:)=lon(:,:)-0.45
-    !assign land cells at the N and S portions of the domain.
-    !input.nml: set coastal drift parameter to prevent grounding
-    do j=jsd,jed; do i=isd,ied
-      if (lat(i,j)<=(-5.e3) .or. lat(i,j)>=(220.e3)) wet(i,j)=0.0
-    enddo;enddo
-
-    !introduce gaussian bump to bathymetry
-    a = 1000.0-bump_depth !max height(m)
-    c = 5e3; !controls width
-    bx = 63.e3; by = 60.e3 !50.e3
-    do j=jsd,jed; do i=isd,ied
-      xc=lon(i,j)-(gridres/2.); yc=lat(i,j)-(gridres/2.) !define at cell centers
-      depth(i,j)=a*exp(-((xc-bx)*(xc-bx)/(2.*c*c)+(yc-by)*(yc-by)/(2.*c*c)))
-    enddo; enddo
-    print *,'min, max depth',minval(depth(:,:)),maxval(depth(:,:))
-    depth = 1000.0-depth
-  endif
+if (big_grounding_test) then
+  lat(:,:)=lat(:,:)-0.45 !-25000.1
+  lon(:,:)=lon(:,:)-0.45
+  !assign land cells at the N and S portions of the domain.
+  !input.nml: set coastal drift parameter to prevent grounding
+  do j=jsd,jed; do i=isd,ied
+    if (lat(i,j)<=(-5.e3) .or. lat(i,j)>=(220.e3)) wet(i,j)=0.0
+  enddo;enddo
+
+  !introduce gaussian bump to bathymetry
+  a = 1000.0-bump_depth !max height(m)
+  c = 5e3; !controls width
+  bx = 63.e3; by = 60.e3 !50.e3
+  do j=jsd,jed; do i=isd,ied
+    xc=lon(i,j)-(gridres/2.); yc=lat(i,j)-(gridres/2.) !define at cell centers
+    depth(i,j)=a*exp(-((xc-bx)*(xc-bx)/(2.*c*c)+(yc-by)*(yc-by)/(2.*c*c)))
+  enddo; enddo
+  print *,'min, max depth',minval(depth(:,:)),maxval(depth(:,:))
+  depth = 1000.0-depth
+endif
 
-   if (dem_test_contact) then
-    lat(:,:)=lat(:,:)-0.45 !-25000.1
-    lon(:,:)=lon(:,:)-0.45
-    !assign land cells at the N and S portions of the domain.
-    !input.nml: set coastal drift parameter to prevent grounding
-    do j=jsd,jed; do i=isd,ied
-      if (lat(i,j)<=(-5.e3) .or. lat(i,j)>=(220.e3)) wet(i,j)=0.0
-    enddo;enddo
+if (dem_test_contact) then
+  lat(:,:)=lat(:,:)-0.45 !-25000.1
+  lon(:,:)=lon(:,:)-0.45
+  !assign land cells at the N and S portions of the domain.
+  !input.nml: set coastal drift parameter to prevent grounding
+  do j=jsd,jed; do i=isd,ied
+    if (lat(i,j)<=(-5.e3) .or. lat(i,j)>=(220.e3)) wet(i,j)=0.0
+  enddo;enddo
 
-    mid=50.e3
+  mid=50.e3
 
-    do j=jsd,jed; do i=isd,ied
-      if (lon(i,j)>65 .or. lat(i,j)==mid) then
-        vo(i,j)=0.0
+  do j=jsd,jed; do i=isd,ied
+    if (lon(i,j)>65 .or. lat(i,j)==mid) then
+      vo(i,j)=0.0
+    else
+      if (lat(i,j)>mid) then
+        vo(i,j)=-ibvo
       else
-        if (lat(i,j)>mid) then
-          vo(i,j)=-ibvo
-        else
-          vo(i,j)=ibvo
-        endif
+        vo(i,j)=ibvo
       endif
+    endif
   enddo;enddo
+endif
 
+if (grounding_test) then
+  lat(:,:)=lat(:,:)-15000.0
+  !assign land cells at the N and S portions of the domain.
+  !input.nml: set coastal drift parameter to prevent grounding
+  do j=jsd,jed; do i=isd,ied
+    if (lat(i,j)<=0.0+2*gridres .or. lat(i,j)>=30.e3-2*gridres) wet(i,j)=0.0
+  enddo;enddo
 
-  endif
-
-  if (grounding_test) then
-    lat(:,:)=lat(:,:)-15000.0
-    !assign land cells at the N and S portions of the domain.
-    !input.nml: set coastal drift parameter to prevent grounding
-    do j=jsd,jed; do i=isd,ied
-      if (lat(i,j)<=0.0+2*gridres .or. lat(i,j)>=30.e3-2*gridres) wet(i,j)=0.0
-    enddo;enddo
-
-    !introduce gaussian bump to bathymetry
-    a = 1000.0-bump_depth !max height(m)
-    c = 2.5e3; !controls width
-    bx = 15.e3; by = 15.e3
-    do j=jsd,jed; do i=isd,ied
-      xc=lon(i,j)-(gridres/2.); yc=lat(i,j)-(gridres/2.) !define at cell centers
-      depth(i,j)=a*exp(-((xc-bx)*(xc-bx)/(2.*c*c)+(yc-by)*(yc-by)/(2.*c*c)))
-    enddo; enddo
-    print *,'min, max depth',minval(depth(:,:)),maxval(depth(:,:))
-    depth = 1000.0-depth
-  endif
+  !introduce gaussian bump to bathymetry
+  a = 1000.0-bump_depth !max height(m)
+  c = 2.5e3; !controls width
+  bx = 15.e3; by = 15.e3
+  do j=jsd,jed; do i=isd,ied
+    xc=lon(i,j)-(gridres/2.); yc=lat(i,j)-(gridres/2.) !define at cell centers
+    depth(i,j)=a*exp(-((xc-bx)*(xc-bx)/(2.*c*c)+(yc-by)*(yc-by)/(2.*c*c)))
+  enddo; enddo
+  print *,'min, max depth',minval(depth(:,:)),maxval(depth(:,:))
+  depth = 1000.0-depth
 endif
 
+if (sin_test) vo = vo * sin(lat*2*pi/(20.0*gridres) + gridres)
+
+if (fl_test) then
+  where(lon>10000) vo=-vo
+endif
 
 call set_calendar_type(THIRTY_DAY_MONTHS)
 
-if (transient_a68_data_start_ind==355) then
-  time = set_date(1,1,7,5,0,0)
-else
-  time = set_date(1,1,1,0,0,0)
-endif
+time = set_date(1,1,1,0,0,0)
 dt = ibdt
 
 call icebergs_init(bergs, &
@@ -451,7 +395,6 @@ program icebergs_driver
 endif
 
 ns = 1 !timestep counter
-if (transient_a68_data_start_ind>0) ns2 = 1
 
 ! Time_end = increment_date(Time, years, months, days, hours, minutes, seconds)
 Time_end = increment_date(Time,0,0,0,ibhrs,0,0)
@@ -472,23 +415,6 @@ program icebergs_driver
     write(*,*) ''
   end if
 
-  if (transient_a68_data_start_ind>0) then
-
-    if ((ibdt==3600.0) .or. (mod(ns2,1.)==0)) then
-      tauxa=tauxa_hr(:,:,transient_a68_data_start_ind+dit*(int(ns2)-1))
-      tauya=tauya_hr(:,:,transient_a68_data_start_ind+dit*(int(ns2)-1))
-      uo=uo_hr(:,:,transient_a68_data_start_ind+dit*(int(ns2)-1))
-      vo=vo_hr(:,:,transient_a68_data_start_ind+dit*(int(ns2)-1))
-      ssh=ssh_hr(:,:,transient_a68_data_start_ind+dit*(int(ns2)-1))
-    else
-      tauxa=0.5*(tauxa+tauxa_hr(:,:,transient_a68_data_start_ind+dit*(int(ceiling(ns2))-1)))
-      tauya=0.5*(tauya+tauya_hr(:,:,transient_a68_data_start_ind+dit*(int(ceiling(ns2))-1)))
-      uo=0.5*(uo+uo_hr(:,:,transient_a68_data_start_ind+dit*(int(ceiling(ns2))-1)))
-      vo=0.5*(vo+vo_hr(:,:,transient_a68_data_start_ind+dit*(int(ceiling(ns2))-1)))
-      ssh=ssh_hr(:,:,transient_a68_data_start_ind+dit*(int(ns2)-1))
-    endif
-  endif
-
   ! The main driver the steps updates icebergs
   call icebergs_run(bergs, time, calving(isc:iec,jsc:jec), &
                     uo(isc-1:iec+1,jsc-1:jec+1), vo(isc-1:iec+1,jsc-1:jec+1), &
@@ -504,41 +430,8 @@ program icebergs_driver
 
   Time = Time + real_to_time_type(dt)
   ns = ns+1
-
-  if (transient_a68_data_start_ind>0) then
-    if (ibdt==3600.0) then
-      ns2=ns2+1
-    elseif (ibdt==1800.0) then
-      ns2=ns2+0.5
-    endif
-  endif
 enddo
 
-
-if (a68_test) then
-  call cpu_time(time_finish)
-  call get_date(Time, iyr, imon, iday, ihr, imin, isec)
-  write(*,*) ''
-  write(*,'(a)') '-------------------------------------------'
-  write(*,'(a,i5)')' Saving after timestep   ',ns-1
-  print *,' ns2   ',ns2
-  if (mod(ns2,1.)==0) then
-    print *,'transient_a68_data_start_ind+dit*(int(ns2)-1)',&
-      transient_a68_data_start_ind+dit*(int(ns2)-1)
-  else
-    print *,'transient_a68_data_start_ind+dit*(int(ceiling(ns2))-1))',&
-      transient_a68_data_start_ind+dit*(int(ceiling(ns2))-1)
-  endif
-  write(*,'(a)')' Restart time is:'
-  write(*,'(a,i5,a,i5,a,i5)')' year',iyr,'  month ',imon,'  day   ',iday
-  write(*,'(a,i5,a,i5,a,i5)')' hour',ihr,'  minute',imin,'  second',isec
-  write(*,*) ''
-  write(*,*) 'clock-time elapsed: ', (time_finish - time_begin)/60., 'minutes'
-  write(*,*) 'clock-time per day: ', (time_finish - time_begin)/(ns-1)*(60*60*24)/ibdt
-  write(*,'(a)') '-------------------------------------------'
-  write(*,*) ''
-endif
-
 if (saverestart) call icebergs_save_restart(bergs)
 
 call cpu_time(time_finish)
diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 59436cf..6935f0b 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -3364,7 +3364,7 @@ subroutine thermodynamics(bergs)
     do while(associated(this))
       if (debug) call check_position(grd, this, 'thermodynamics (top)')
 
-      if (bergs%old_interp_flds_order) then
+      if (bergs%old_interp_flds_order .or. (.not. mts .and. .not. dem .and. this%halo_berg.ge.0.5)) then
         call interp_flds(grd, this%lon, this%lat, this%ine, this%jne, this%xi, this%yj, 0., 0., &
           this%uo, this%vo, this%ui, this%vi, this%ua, this%va, this%ssh_x, &
           this%ssh_y, this%sst, this%sss,this%cn, this%hi)
diff --git a/tests/footloose_no_bond_test/README b/tests/footloose_physical/README
similarity index 100%
rename from tests/footloose_no_bond_test/README
rename to tests/footloose_physical/README
diff --git a/tests/footloose_no_bond_test/RUN b/tests/footloose_physical/RUN
similarity index 100%
rename from tests/footloose_no_bond_test/RUN
rename to tests/footloose_physical/RUN
diff --git a/tests/footloose_no_bond_test/RUN1p b/tests/footloose_physical/RUN1p
similarity index 100%
rename from tests/footloose_no_bond_test/RUN1p
rename to tests/footloose_physical/RUN1p
diff --git a/tests/footloose_no_bond_test/animate_trajectories.py b/tests/footloose_physical/animate_trajectories.py
similarity index 100%
rename from tests/footloose_no_bond_test/animate_trajectories.py
rename to tests/footloose_physical/animate_trajectories.py
diff --git a/tests/footloose_no_bond_test/diag_table b/tests/footloose_physical/diag_table
similarity index 100%
rename from tests/footloose_no_bond_test/diag_table
rename to tests/footloose_physical/diag_table
diff --git a/tests/footloose_physical/input.nml b/tests/footloose_physical/input.nml
new file mode 100644
index 0000000..270111d
--- /dev/null
+++ b/tests/footloose_physical/input.nml
@@ -0,0 +1,172 @@
+!!KID, bergs_chksum: write_restart berg chksum=-461793748 chksum2=-461793748 chksum3=-1042515716 chksum4=-1042515716 chksum5=0 #=12
+
+
+&icebergs_driver_nml
+  ni=20 !number of elements, x direction
+  nj=20 !number of elements, y direction
+  ibdt=10.0 !1800.0 !86400.0 !seconds
+  ibuo=1.0 !ocean x velocity
+  ibvo=0.1 !ocean y velocity (if sin_test=true, will vary as ibvo*sin(y*2*pi/(4*gridres)) + gridres )
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibua=-1.0 !wind x velocity
+  ibuy=0.0  !wind y velocity
+  ibhrs=192 !total simulation hours
+  nmax=99999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.false.
+  gridres=1000.
+  sst=-0.5
+  fl_test=.true.
+/
+
+
+&icebergs_nml
+
+    !defaults given in parentheses:
+
+    fl_r=1        !(4) average number of footloose bergs to calve per fl_r_s seconds
+    fl_r_s=0  !(86400) time in s over which to calve, on average, fl_r footloose bergs
+    displace_fl_bergs=.true. !(T) randomly assign FL berg positions to sides of parent berg
+    fl_style='fl_bits' !'fl_bits' !('new_bergs'). Can also group FL bergs into 'fl_bits'
+    fl_youngs=1.e8 !Young's modulus for footloose calculations (Pa)
+    fl_strength=250. !yield stress for footloose calculations (kPa)
+    fl_use_l_scale=.true. !scaling factor for footloose based on side melt
+    fl_k_scale_by_perimeter=1 !If greater than 0, scales FL k by (berg perimeter (m))/(this scaling (m))
+    new_berg_from_fl_bits_mass_thres=3.e11  !Create a new berg from FL bits when mass_of_fl_bits exceeds this value
+    fl_l_scale_erosion_only=.true. !fl according to erosion - buoyant convection
+    fl_use_poisson_distribution=.false. !fl_r is (T) mean of Poisson distribution to determine k, or (F) k=fl_r
+    mts=.false. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=1 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
+    !contact_distance=0 !3.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    !contact_spring_coef=1.e-5!(default=spring_coeff) Berg spring coeff for collisions
+
+    halo=3 !(4) halo width
+    Lx=20000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.True. !(T) Point in cell can be found assuming regular Cartesian grid
+    !hexagonal_icebergs=.True. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    rho_bergs=850. ! (850) iceberg density
+    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=1.0 ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.true. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0.0 !4 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.false.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.false.!.true.!.false. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+
+    verbose=.true. !(F) Be verbose to stderr
+    verbose_hrs=24 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !1 !(24) sampling period for trajectory storage
+    traj_write_hrs=24 ! (480) Period for writing sampled trajectories to disk
+    budget=.true.!.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    save_fl_traj=.true. !(T) True save masses and footloose parameters in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    length_for_manually_initialize_bonds=-1.e3!0.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/footloose_no_bond_test/input.nml b/tests/footloose_physical/input_old.nml
similarity index 100%
rename from tests/footloose_no_bond_test/input.nml
rename to tests/footloose_physical/input_old.nml
diff --git a/tests/footloose_no_bond_test/makeberg/RUN b/tests/footloose_physical/makeberg/RUN
similarity index 100%
rename from tests/footloose_no_bond_test/makeberg/RUN
rename to tests/footloose_physical/makeberg/RUN
diff --git a/tests/footloose_no_bond_test/makeberg/makeberg.py b/tests/footloose_physical/makeberg/makeberg.py
similarity index 100%
rename from tests/footloose_no_bond_test/makeberg/makeberg.py
rename to tests/footloose_physical/makeberg/makeberg.py
diff --git a/tests/footloose_poisson/README b/tests/footloose_poisson/README
new file mode 100644
index 0000000..8a46a3d
--- /dev/null
+++ b/tests/footloose_poisson/README
@@ -0,0 +1,9 @@
+Testing for footloose mechanism parameterization in (non-bonded mode only)
+
+1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
+2.(optional) edit input.nml
+3. run the model: ./RUN
+4. animate the results: animate_trajectories.py
+
+
+
diff --git a/tests/footloose_poisson/RUN b/tests/footloose_poisson/RUN
new file mode 100755
index 0000000..090c034
--- /dev/null
+++ b/tests/footloose_poisson/RUN
@@ -0,0 +1,5 @@
+rm iceberg_trajectories.nc
+rm iceberg_trajectories.nc.*
+srun -n4 ./../../build/bergs.x
+
+
diff --git a/tests/footloose_poisson/RUN1p b/tests/footloose_poisson/RUN1p
new file mode 100755
index 0000000..c3bf53e
--- /dev/null
+++ b/tests/footloose_poisson/RUN1p
@@ -0,0 +1,5 @@
+rm iceberg_trajectories.nc
+rm iceberg_trajectories.nc.*
+srun -n1 ./../../build/bergs.x
+
+
diff --git a/tests/footloose_poisson/animate_trajectories.py b/tests/footloose_poisson/animate_trajectories.py
new file mode 100755
index 0000000..27bf850
--- /dev/null
+++ b/tests/footloose_poisson/animate_trajectories.py
@@ -0,0 +1,151 @@
+#!/usr/bin/env python
+
+from netCDF4 import Dataset
+import pdb
+import netCDF4 as nc
+import numpy as np
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+import matplotlib.pyplot as plt
+from matplotlib.animation import FuncAnimation
+from mpl_toolkits.axes_grid1 import make_axes_locatable
+import argparse
+
+def parseCommandLine():
+    parser = argparse.ArgumentParser(description=
+    '''Generate animation of iceberg trajectories.''',
+    epilog='Written by Alex Huth, 2020')
+    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
+                    help=''' provide filename to plot''')
+    parser.add_argument('-s', type=int, default='1450',
+                        help='''plotted particle size''')
+    optCmdLineArgs = parser.parse_args()
+    return optCmdLineArgs
+
+
+
+def main(args):
+
+    print('reading file')
+
+    filename=args.fname
+    psize=args.s
+    #filename = 'iceberg_trajectories.nc'
+    field = 'lon'
+    field2 = 'lat'
+
+    with nc.Dataset(filename) as file:
+        x = file.variables['lon'][:]/1.e3
+        y = file.variables['lat'][:]/1.e3
+        day = file.variables['day'][:]
+        bid = file.variables['id_ij'][:]
+        vo = file.variables['fl_k'][:]
+        length = file.variables['length'][:]
+        width = file.variables['width'][:]
+
+    ud = np.unique(day)
+    ub = np.unique(bid)
+    t = ud[0]
+
+    radius = length*width*(1./(2*np.sqrt(3)))
+
+    urad=np.unique(radius)
+    #print('urad',urad)
+
+    # frame info
+    num_frames = len(ud)
+    movie_len = 10.0 #seconds
+    frame_len = 1000.0*movie_len/num_frames
+
+    xmin = 0 #np.floor(min(min(x),min(y),0))
+    xmax = 20 #np.ceil(max(max(x),max(y),20))
+    ymin = xmin
+    ymax = xmax
+
+    anim_running = True
+
+    def animate(i):
+
+        x1 = x[day == ud[i]]
+        y1 = y[day == ud[i]]
+        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
+
+        scat.set_offsets(data)
+
+        vo1 = vo[day == ud[i]]
+        scat.set_edgecolor('k')
+        scat.set_color(cmap(norm(vo1)))
+
+        r1 = radius[day == ud[i]]
+        scat.set_sizes(r1/psize)
+
+        t = ud[i]
+        time_text.set_text('time = %.1f days' % t )
+        return scat,time_text
+
+    def init():
+        scat.set_offsets([])
+        return scat,
+
+    def onClick(event):
+        global anim_running
+        if anim_running:
+            ani.event_source.stop()
+            anim_running = False
+        else:
+            ani.event_source.start()
+            anim_running = True
+
+    # Now we can do the plotting!
+    f = plt.figure(figsize=(5,5))
+    f.tight_layout()
+    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
+    div = make_axes_locatable(ax1)
+    cax = div.append_axes('right', '5%', '5%')
+    scat = ax1.scatter([],[],marker='o')
+    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
+
+    cmap = plt.cm.get_cmap('RdYlBu')
+    norm = plt.Normalize(vo.min(), vo.max())
+    cb1 = matplotlib.colorbar.ColorbarBase(cax, cmap=cmap,
+                                           norm=norm,
+                                           orientation='vertical')
+
+
+    # Change major ticks to show every 20.
+    ax1.xaxis.set_major_locator(MultipleLocator(5))
+    ax1.yaxis.set_major_locator(MultipleLocator(5))
+
+    ax1.xaxis.set_minor_locator(MultipleLocator(1))
+    ax1.yaxis.set_minor_locator(MultipleLocator(1))
+
+    # Turn grid on for both major and minor ticks and style minor slightly
+    # differently.
+    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
+    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
+
+    ax1.set_xlabel('x (km)')
+    ax1.set_ylabel('y (km)')
+    ax1.set_title('Iceberg trajectory')
+
+    f.canvas.mpl_connect('button_press_event', onClick)
+
+    ani = FuncAnimation(
+        f,animate,init_func=init,frames=num_frames,
+        interval=frame_len,blit=True,repeat=True)
+
+    print('time',t)
+
+    plt.show()
+    #animation.save("iceberg_traj_animation.mp4")
+
+
+print('Script complete')
+
+if __name__ == '__main__':
+    optCmdLineArgs=	parseCommandLine()
+    anim_running = True
+    main(optCmdLineArgs)
diff --git a/tests/footloose_poisson/diag_table b/tests/footloose_poisson/diag_table
new file mode 100644
index 0000000..c1c8819
--- /dev/null
+++ b/tests/footloose_poisson/diag_table
@@ -0,0 +1,3 @@
+"icebergs test"
+1 1 1 0 0 0
+
diff --git a/tests/footloose_poisson/input.nml b/tests/footloose_poisson/input.nml
new file mode 100644
index 0000000..3e6a416
--- /dev/null
+++ b/tests/footloose_poisson/input.nml
@@ -0,0 +1,167 @@
+!!KID, bergs_chksum: write_restart berg chksum=1239600118 chksum2=1239600118 chksum3=-1474195494 chksum4=-1474195494 chksum5=0 #=8
+
+
+&icebergs_driver_nml
+  ni=20 !number of elements, x direction
+  nj=20 !number of elements, y direction
+  ibdt=10.0 !1800.0 !86400.0 !seconds
+  ibuo=0.1 !ocean x velocity
+  ibvo=0.05 !ocean y velocity (if sin_test=true, will vary as ibvo*sin(y*2*pi/(4*gridres)) + gridres )
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=192 !total simulation hours
+  nmax=99999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.false.
+  gridres=1000.
+  sst=-2
+  !sin_test=.true.
+  fl_test=.true.
+/
+
+
+&icebergs_nml
+
+    !defaults given in parentheses:
+
+    fl_r=4        !(4) average number of footloose bergs to calve per fl_r_s seconds
+    fl_r_s=86400  !(86400) time in s over which to calve, on average, fl_r footloose bergs
+    displace_fl_bergs=.true. !(T) randomly assign FL berg positions to sides of parent berg
+    fl_style='fl_bits' !('new_bergs'). Can also group FL bergs into 'fl_bits'
+    new_berg_from_fl_bits_mass_thres=8.e11 !Create a new berg from FL bits when mass_of_fl_bits exceeds this value
+    fl_use_poisson_distribution=.true.
+
+    mts=.false. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=1 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
+    !contact_distance=0 !3.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    !contact_spring_coef=1.e-5!(default=spring_coeff) Berg spring coeff for collisions
+
+    halo=3 !(4) halo width
+    Lx=20000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.True. !(T) Point in cell can be found assuming regular Cartesian grid
+    !hexagonal_icebergs=.True. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    rho_bergs=850. ! (850) iceberg density
+    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=1.0 ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.true. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0.0 !4 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.false.!.true.!.false. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+
+    verbose=.true. !(F) Be verbose to stderr
+    verbose_hrs=24 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !1 !(24) sampling period for trajectory storage
+    traj_write_hrs=24 ! (480) Period for writing sampled trajectories to disk
+    budget=.true.!.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    save_fl_traj=.true. !(T) True save masses and footloose parameters in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    length_for_manually_initialize_bonds=-1.e3!0.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/footloose_poisson/input_old.nml b/tests/footloose_poisson/input_old.nml
new file mode 100644
index 0000000..64159c7
--- /dev/null
+++ b/tests/footloose_poisson/input_old.nml
@@ -0,0 +1,170 @@
+!note: to test this without bonds and without interactive bergs, set:
+!>iceberg_bonds_on=.true.
+!>interactive_icebergs_on=.false.
+!>manually_initialize_bonds=.true.
+!>length_for_manually_initialize_bonds<0
+
+
+&icebergs_driver_nml
+  ni=20 !number of elements, x direction
+  nj=20 !number of elements, y direction
+  ibdt=10.0 !1800.0 !86400.0 !seconds
+  ibuo=0.05 !ocean x velocity
+  ibvo=0.0 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=4800 !total simulation hours
+  nmax=99999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.false.
+  gridres=1000.
+  sst=-2
+  collision_test=.false. !specific to the current test, must be true here
+/
+
+
+&icebergs_nml
+
+    !defaults given in parentheses:
+
+    fl_r=4        !(4) average number of footloose bergs to calve per fl_r_s seconds
+    fl_r_s=86400  !(86400) time in s over which to calve, on average, fl_r footloose bergs
+    displace_fl_bergs=.true. !(T) randomly assign FL berg positions to sides of parent berg
+    fl_style='fl_bits' !('new_bergs'). Can also group FL bergs into 'fl_bits'
+    new_berg_from_fl_bits_mass_thres=8.e11
+    fl_use_poisson_distribution=.true.!.false.
+
+    mts=.false. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=1 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
+    !contact_distance=0 !3.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    !contact_spring_coef=1.e-5!(default=spring_coeff) Berg spring coeff for collisions
+
+    halo=3 !(4) halo width
+    Lx=20000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.True. !(T) Point in cell can be found assuming regular Cartesian grid
+    !hexagonal_icebergs=.True. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    rho_bergs=850. ! (850) iceberg density
+    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=1.0 ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.true. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0.0 !4 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.false.!.true.!.false. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+
+    verbose=.true. !(F) Be verbose to stderr
+    verbose_hrs=24 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !1 !(24) sampling period for trajectory storage
+    traj_write_hrs=1 ! (480) Period for writing sampled trajectories to disk
+    budget=.true.!.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    save_fl_traj=.true. !(T) True save masses and footloose parameters in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    length_for_manually_initialize_bonds=-1.e3!0.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/footloose_poisson/makeberg/RUN b/tests/footloose_poisson/makeberg/RUN
new file mode 100755
index 0000000..750e29e
--- /dev/null
+++ b/tests/footloose_poisson/makeberg/RUN
@@ -0,0 +1,5 @@
+
+rm ./output_files/Generic*
+./makeberg.py
+
+cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
\ No newline at end of file
diff --git a/tests/footloose_poisson/makeberg/makeberg.py b/tests/footloose_poisson/makeberg/makeberg.py
new file mode 100755
index 0000000..dd146fc
--- /dev/null
+++ b/tests/footloose_poisson/makeberg/makeberg.py
@@ -0,0 +1,278 @@
+#!/usr/bin/env python
+import numpy as np
+import math
+from netCDF4 import Dataset
+from pylab import *
+#import pdb
+import netCDF4 as nc
+
+#
+# Initialize 2 iceberg elements, which can later be bonded in the fortran code if needed
+#
+
+def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
+
+	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
+	# To copy the global attributes of the netCDF file
+
+	#Input and output files
+	#Create Empty restart file. This is later read so that the attributes can be used.
+	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
+	create_empty_iceberg_restart_file(Empty_restart_filename)
+	#Empty_restart_filename='input_files/icebergs.res.nc'
+
+	#Read empty restart file
+	f=Dataset(Empty_restart_filename,'r') # r is for read only
+	#Write a new restart file
+	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
+
+	for attname in f.ncattrs():
+		    setattr(g,attname,getattr(f,attname))
+
+
+	# To copy the dimension of the netCDF file
+	for dimname,dim in f.dimensions.iteritems():
+		# if you want to make changes in the dimensions of the new file
+		# you should add your own conditions here before the creation of the dimension.
+		#g.createDimension(dimname,len(dim))
+		g.createDimension(dimname,Number_of_bergs)
+
+	# To copy the variables of the netCDF file
+
+	for varname,ncvar in f.variables.iteritems():
+		# if you want to make changes in the variables of the new file
+		# you should add your own conditions here before the creation of the variable.
+		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
+		#Proceed to copy the variable attributes
+		for attname in ncvar.ncattrs():
+			setattr(var,attname,getattr(ncvar,attname))
+		#Finally copy the variable data to the new created variable
+		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
+
+		if varname=='i':
+			var[:]=Number_of_bergs
+
+		if varname=='iceberg_num':
+			for j in range(Number_of_bergs):
+				#var[j]=j+1
+				var[j]=iceberg_num[j]
+
+		if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
+		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
+		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
+		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
+			var[:]=0
+
+                if varname=='uvel':
+                        var[:]=uvel
+
+                if varname=='vvel':
+                        var[:]=vvel
+
+		if varname=='mass_scaling':
+			var[:]=mass_scaling
+
+		if varname=='thickness':
+			for j in range(Number_of_bergs):
+				var[j]=thickness[j]
+
+		if varname=='mass':
+			for j in range(Number_of_bergs):
+				var[j]=mass[j]
+
+		if varname=='width'  or varname=='length':
+			for j in range(Number_of_bergs):
+				var[j]=width[j]
+
+		if varname=='lon':
+			for j in range(Number_of_bergs):
+				var[j]=lon[j]
+
+		if varname=='lat':
+			for j in range(Number_of_bergs):
+				var[j]=lat[j]
+
+		if varname=='static_berg':
+			for j in range(Number_of_bergs):
+				var[j]=static_berg[j]
+
+
+	f.close()
+	g.close()
+
+
+def create_empty_iceberg_restart_file(Empty_restart_filename):
+
+	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
+
+	i=f.createDimension('i', None)
+	lon=f.createVariable('i','i')
+
+	lon=f.createVariable('lon','d',('i'))
+	lon.long_name = "longitude" ;
+	lon.units = "degrees_E" ;
+	lon.checksum = "               0" ;
+
+	lat=f.createVariable('lat','d',('i'))
+	lat.long_name = "latitude" ;
+	lat.units = "degrees_N" ;
+	lat.checksum = "               0" ;
+
+	uvel=f.createVariable('uvel','d',('i'))
+	uvel.long_name = "zonal velocity" ;
+	uvel.units = "m/s" ;
+	uvel.checksum = "               0" ;
+
+	vvel=f.createVariable('vvel','d',('i'))
+	vvel.long_name = "meridional velocity" ;
+	vvel.units = "m/s" ;
+	vvel.checksum = "               0" ;
+
+	mass=f.createVariable('mass','d',('i'))
+	mass.long_name = "mass" ;
+	mass.units = "kg" ;
+	mass.checksum = "               0" ;
+
+	axn=f.createVariable('axn','d',('i'))
+	axn.long_name = "explicit zonal acceleration" ;
+	axn.units = "m/s^2" ;
+	axn.checksum = "               0" ;
+
+	ayn=f.createVariable('ayn','d',('i'))
+	ayn.long_name = "explicit meridional acceleration" ;
+	ayn.units = "m/s^2" ;
+	ayn.checksum = "               0" ;
+
+	bxn=f.createVariable('bxn','d',('i'))
+	bxn.long_name = "inplicit zonal acceleration" ;
+	bxn.units = "m/s^2" ;
+	bxn.checksum = "               0" ;
+
+	byn=f.createVariable('byn','d',('i'))
+	byn.long_name = "implicit meridional acceleration" ;
+	byn.units = "m/s^2" ;
+	byn.checksum = "               0" ;
+
+	ine=f.createVariable('ine','i',('i'))
+	ine.long_name = "i index" ;
+	ine.units = "none" ;
+	ine.packing = 0 ;
+	ine.checksum = "               0" ;
+
+	jne=f.createVariable('jne','i',('i'))
+	jne.long_name = "j index" ;
+	jne.units = "none" ;
+	jne.packing = 0 ;
+	jne.checksum = "               0" ;
+
+	thickness=f.createVariable('thickness','d',('i'))
+	thickness.long_name = "thickness" ;
+	thickness.units = "m" ;
+	thickness.checksum = "               0" ;
+
+	width=f.createVariable('width','d',('i'))
+	width.long_name = "width" ;
+	width.units = "m" ;
+	width.checksum = "               0" ;
+
+	length=f.createVariable('length','d',('i'))
+	length.long_name = "length" ;
+	length.units = "m" ;
+	length.checksum = "               0" ;
+
+	start_lon=f.createVariable('start_lon','d',('i'))
+	start_lon.long_name = "longitude of calving location" ;
+	start_lon.units = "degrees_E" ;
+	start_lon.checksum = "               0" ;
+
+	start_lat=f.createVariable('start_lat','d',('i'))
+	start_lat.long_name = "latitude of calving location" ;
+	start_lat.units = "degrees_N" ;
+	start_lat.checksum = "               0" ;
+
+	start_year=f.createVariable('start_year','i',('i'))
+	start_year.long_name = "calendar year of calving event" ;
+	start_year.units = "years" ;
+	start_year.packing = 0 ;
+	start_year.checksum = "               0" ;
+
+	iceberg_num=f.createVariable('iceberg_num','i',('i'))
+	iceberg_num.long_name = "identification of the iceberg" ;
+	iceberg_num.units = "dimensionless" ;
+	iceberg_num.packing = 0 ;
+	iceberg_num.checksum = "               0" ;
+
+	start_day=f.createVariable('start_day','d',('i'))
+	start_day.long_name = "year day of calving event" ;
+	start_day.units = "days" ;
+	start_day.checksum = "               0" ;
+
+	start_mass=f.createVariable('start_mass','d',('i'))
+	start_mass.long_name = "initial mass of calving berg" ;
+	start_mass.units = "kg" ;
+	start_mass.checksum = "               0" ;
+
+	mass_scaling=f.createVariable('mass_scaling','d',('i'))
+	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
+	mass_scaling.units = "none" ;
+	mass_scaling.checksum = "               0" ;
+
+	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
+	mass_of_bits.long_name = "mass of bergy bits" ;
+	mass_of_bits.units = "kg" ;
+	mass_of_bits.checksum = "               0" ;
+
+	heat_density=f.createVariable('heat_density','d',('i'))
+	heat_density.long_name = "heat density" ;
+	heat_density.units = "J/kg" ;
+	heat_density.checksum = "               0" ;
+
+	halo_berg=f.createVariable('halo_berg','d',('i'))
+	halo_berg.long_name = "halo_berg" ;
+	halo_berg.units = "dimensionless" ;
+	halo_berg.checksum = "               0" ;
+
+	static_berg=f.createVariable('static_berg','d',('i'))
+	static_berg.long_name = "static_berg" ;
+	static_berg.units = "dimensionless" ;
+	static_berg.checksum = "               0" ;
+
+	f.sync()
+	f.close()
+
+
+
+#-----------------------------------#
+#               Main                #
+#-----------------------------------#
+
+grdres=5000.0
+xc=10000.1
+yc=10000.1
+R_frac=0.45
+radius=(np.sqrt(3)/2.)*(R_frac*grdres) #S is < 0.5 grid res
+element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*radius**2)
+width=np.sqrt(element_area)
+thickness=300.0
+rhoi=850.0
+mass=thickness*rhoi*element_area
+
+berg_count=2
+berg_x=[xc-radius,xc+radius]
+berg_y=[yc,yc]
+berg_h=[thickness,thickness]
+berg_width=[width,width]
+berg_mass=[mass,mass]
+berg_mass_scaling=[1,1]
+berg_id=[1,2]
+berg_static=[0,0]
+berg_uvel=[0,0]
+berg_vvel=[0,0]
+
+print('Number of bergs',berg_count)
+print('berg_x,berg_y',berg_x,berg_y)
+print('width',width)
+
+#Create iceberg restart file
+Ice_geometry_source='Generic'
+Create_iceberg_restart_file(berg_count,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)

From c94cc78483f426b31b46cc9791cd2c245173517b Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Fri, 25 Nov 2022 14:04:25 -0500
Subject: [PATCH 325/361] fixed up dem_ground_frac_test: consolidated to a
 single test, tuned, and recorded chksum

---
 tests/dem_ground_frac_test/RUN                |   2 +-
 .../animate_trajectories.py                   |  17 +-
 tests/dem_ground_frac_test/input.nml          |  65 +--
 tests/dem_ground_frac_test/input_dem.nml      | 192 ---------
 tests/dem_ground_frac_test/input_dem_comp.nml | 192 ---------
 tests/dem_ground_frac_test/input_dem_orig.nml | 191 ---------
 tests/dem_ground_frac_test/input_reg.nml      | 193 ---------
 tests/dem_ground_frac_test/input_reg_comp.nml | 192 ---------
 .../dem_ground_frac_test/input_reg_stress.nml | 192 ---------
 .../dem_ground_frac_test/makeberg/makeberg.py |  15 +-
 tests/dem_ground_frac_test_big/.gitignore     |   1 -
 tests/dem_ground_frac_test_big/README         |   7 -
 tests/dem_ground_frac_test_big/RUN            |   7 -
 .../animate_trajectories.py                   | 161 --------
 tests/dem_ground_frac_test_big/diag_table     |   3 -
 tests/dem_ground_frac_test_big/input.nml      | 199 ---------
 tests/dem_ground_frac_test_big/makeberg/RUN   |   3 -
 .../makeberg/makeberg.py                      | 376 ------------------
 tests/dem_ground_frac_test_big/save1.nml      | 199 ---------
 tests/dem_ground_frac_test_big/save2.nml      | 199 ---------
 tests/dem_ground_frac_test_big/save3.nml      | 199 ---------
 21 files changed, 54 insertions(+), 2551 deletions(-)
 delete mode 100644 tests/dem_ground_frac_test/input_dem.nml
 delete mode 100644 tests/dem_ground_frac_test/input_dem_comp.nml
 delete mode 100644 tests/dem_ground_frac_test/input_dem_orig.nml
 delete mode 100644 tests/dem_ground_frac_test/input_reg.nml
 delete mode 100644 tests/dem_ground_frac_test/input_reg_comp.nml
 delete mode 100644 tests/dem_ground_frac_test/input_reg_stress.nml
 delete mode 100644 tests/dem_ground_frac_test_big/.gitignore
 delete mode 100644 tests/dem_ground_frac_test_big/README
 delete mode 100755 tests/dem_ground_frac_test_big/RUN
 delete mode 100755 tests/dem_ground_frac_test_big/animate_trajectories.py
 delete mode 100644 tests/dem_ground_frac_test_big/diag_table
 delete mode 100644 tests/dem_ground_frac_test_big/input.nml
 delete mode 100755 tests/dem_ground_frac_test_big/makeberg/RUN
 delete mode 100755 tests/dem_ground_frac_test_big/makeberg/makeberg.py
 delete mode 100644 tests/dem_ground_frac_test_big/save1.nml
 delete mode 100644 tests/dem_ground_frac_test_big/save2.nml
 delete mode 100644 tests/dem_ground_frac_test_big/save3.nml

diff --git a/tests/dem_ground_frac_test/RUN b/tests/dem_ground_frac_test/RUN
index f881323..3cc561d 100755
--- a/tests/dem_ground_frac_test/RUN
+++ b/tests/dem_ground_frac_test/RUN
@@ -2,6 +2,6 @@ rm iceberg_trajectories.nc
 rm iceberg_trajectories.nc.*
 rm bond_trajectories.nc
 rm bond_trajectories.nc.*
-srun -n9 ./../../build/bergs.x
+srun -n4 ./../../build/bergs.x
 
 
diff --git a/tests/dem_ground_frac_test/animate_trajectories.py b/tests/dem_ground_frac_test/animate_trajectories.py
index 815b6d6..d163b57 100755
--- a/tests/dem_ground_frac_test/animate_trajectories.py
+++ b/tests/dem_ground_frac_test/animate_trajectories.py
@@ -19,7 +19,7 @@ def parseCommandLine():
     epilog='Written by Alex Huth, 2020')
     parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
                     help=''' provide filename to plot''')
-    parser.add_argument('-s', type=int, default='3500',
+    parser.add_argument('-s', type=int, default='14000',
                         help='''plotted particle size''')
     optCmdLineArgs = parser.parse_args()
     return optCmdLineArgs
@@ -53,9 +53,12 @@ def main(args):
     #for determining if grounded:
     rho_bergs=850.
     rho_seawater=1025.
-    h_to_ground=200.
+    h_to_ground=20 #200.
     draught=(rho_bergs/rho_seawater)*thick
-    groundfrac=1.-(od-draught)/h_to_ground
+    if (h_to_ground==0):
+        groundfrac=draught-od
+    else:
+        groundfrac=1.-(od-draught)/h_to_ground
     groundfrac[groundfrac<0.]=0.
     groundfrac[groundfrac>1.]=1.
 
@@ -69,10 +72,10 @@ def main(args):
     #frame_len = 1000.0*movie_len/num_frames/10000000
     frame_len = movie_len/num_frames/1000
 
-    xmin = 0
-    xmax = 30
-    ymin = xmin
-    ymax = xmax
+    xmin = 40
+    xmax = 100
+    ymin = 20 #xmin
+    ymax = 80 #xmax
 
     anim_running = True
 
diff --git a/tests/dem_ground_frac_test/input.nml b/tests/dem_ground_frac_test/input.nml
index 102fbe5..00040b2 100644
--- a/tests/dem_ground_frac_test/input.nml
+++ b/tests/dem_ground_frac_test/input.nml
@@ -1,67 +1,72 @@
+!!KID, bergs_chksum: write_restart berg chksum=751155043 chksum2=1054759942 chksum3=946244516 chksum4=946244516 chksum5=0 #=69
 
 &icebergs_driver_nml
   ni=45 !30 !number of elements, x direction
   nj=45 !30 !number of elements, y direction
+  gridres=5000.0
   ibdt=1800.0 !seconds
   ibuo=0.1 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
+  ibvo=0.1 !ocean y velocity
   ibui=0.0 !ice x velocity
   ibvi=0.0 !ice y velocity
-  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  ibhrs=72 !total simulation hours
   write_time_inc = 48 !increment at which time is written to screen
   nmax=999999999 !max number of timesteps
   saverestart=.true.
   halo=3
   debug=.true.
   collision_test=.false.
-  grounding_test=.true.
-  bump_depth=200.0 !(m) depth of top of gaussian bump below sea level
+  big_grounding_test=.true.
+  bump_depth=50.!(m) depth of top of gaussian bump below sea level
 /
 
 &icebergs_nml
 
-    !use_damage=.true.
-    !damage_test_1=.true.
+    constant_interaction_LW=.true.
 
     dem=.true.
-    ignore_tangential_force=.false.!.true.
     poisson=0.3
     dem_damping_coef=1.0
+    explicit_inner_mts=.true.
+    break_bonds_on_sub_steps=.true.
+    short_step_mts_grounding=.true.
+    
     rho_bergs=850. ! (850) iceberg density
     !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
     !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
     !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    dem_spring_coef=4471.938678723104 !1000.0 
-    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5. A=L*W always works?
+    dem_spring_coef=5e6
+    spring_coef=0.0007547062342348049 !if dem_spring_coef=5e6, r=1500, and hex pack?
+    !spring_coef=0.00065359477124183  !if dem_spring_coef=5e6, r=1500, and square pack?
+    
     monitor_energy=.false.
     !defaults given in parentheses:
     new_mts=.true.
     mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=10!75 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
+    mts_sub_steps=200 !(-1) # of mts sub-steps
+    explicit_inner_mts=.true.
     force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
+    convergence_tolerance=1e-2 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=5.e-8 !(default=spring_coeff) Berg spring coeff for collisions
 
-    contact_distance=1.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
     debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=200.0
+    cdrag_grounding=1.e4
+    h_to_init_grounding=0 !0 !200.0
     ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
+    remove_unused_bergs=.false. !(T) remove unneeded bergs after PEs transfers
 
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1. 
-    frac_thres_n = 0.!70. !2.1e4 !12.
-    frac_thres_t = 0. !12.
+    fracture_criterion='stress' !('none')
+    frac_thres_scaling = 1
+    frac_thres_n = 1850
+    frac_thres_t = 1000
 
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
 
     halo=3 !(4) halo width
-    Lx=45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    Lx=225000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
     grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
     grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
     hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
@@ -71,7 +76,7 @@
     radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
     tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
     scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.false. !(T) Sets damping on rel berg vel to crit val
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
     tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
     LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
     bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
@@ -125,8 +130,8 @@
 
     verbose=.false. !(F) Be verbose to stderr
     verbose_hrs=24000 ! (24) Period between verbose messages
-    traj_sample_hrs=-1!0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=-1!0!6 !(480) Period for writing sampled trajectories to disk
+    traj_sample_hrs=0.5 !-1!0!6 !(24) sampling period for trajectory storage
+    traj_write_hrs=0.5 !-1!0!6 !(480) Period for writing sampled trajectories to disk
     save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
     budget=.false. !(T) Calculate budgets
     debug=.false. !(F) Turn on debugging
@@ -143,7 +148,7 @@
     use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
     manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
     manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    !length_for_manually_initialize_bonds=1600.0!800.0 !(1e3)Dist b/w bergs to init bonds manually
     ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
     generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
     fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
diff --git a/tests/dem_ground_frac_test/input_dem.nml b/tests/dem_ground_frac_test/input_dem.nml
deleted file mode 100644
index 95ae26d..0000000
--- a/tests/dem_ground_frac_test/input_dem.nml
+++ /dev/null
@@ -1,192 +0,0 @@
-
-&icebergs_driver_nml
-  ni=45 !30 !number of elements, x direction
-  nj=45 !30 !number of elements, y direction
-  ibdt=1800.0 !seconds
-  ibuo=0.1 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=999999999 !max number of timesteps
-  saverestart=.true.
-  halo=3
-  debug=.true.
-  collision_test=.false.
-  grounding_test=.true.
-  bump_depth=200.0 !(m) depth of top of gaussian bump below sea level
-/
-
-&icebergs_nml
-
-    !use_damage=.true.
-    !damage_test_1=.true.
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    dem_spring_coef=4471.938678723104 !1000.0
-   ! ignore_tangential_force=.true.
-    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=75 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=1.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=200.0
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 4.  
-    frac_thres_n = 12.
-    frac_thres_t = 12.
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0.1 !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=24000 ! (24) Period between verbose messages
-    traj_sample_hrs=-1!0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=-1!0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/dem_ground_frac_test/input_dem_comp.nml b/tests/dem_ground_frac_test/input_dem_comp.nml
deleted file mode 100644
index bcc2b3e..0000000
--- a/tests/dem_ground_frac_test/input_dem_comp.nml
+++ /dev/null
@@ -1,192 +0,0 @@
-
-&icebergs_driver_nml
-  ni=45 !30 !number of elements, x direction
-  nj=45 !30 !number of elements, y direction
-  ibdt=1800.0 !seconds
-  ibuo=0.1 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=999999999 !max number of timesteps
-  saverestart=.true.
-  halo=3
-  debug=.true.
-  collision_test=.false.
-  grounding_test=.true.
-  bump_depth=200.0 !(m) depth of top of gaussian bump below sea level
-/
-
-&icebergs_nml
-
-    !use_damage=.true.
-    !damage_test_1=.true.
-
-    dem=.true.
-    ignore_tangential_force=.true.
-    poisson=0.3
-    dem_damping_coef=0. !1.0
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    dem_spring_coef=4471.938678723104 !1000.0 
-    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=100!75 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=1.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=200.0
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1. 
-    frac_thres_n = 70. !2.1e4 !12.
-    frac_thres_t = 0. !12.
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.false. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0.1 !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=24000 ! (24) Period between verbose messages
-    traj_sample_hrs=-1!0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=-1!0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/dem_ground_frac_test/input_dem_orig.nml b/tests/dem_ground_frac_test/input_dem_orig.nml
deleted file mode 100644
index 404c2d4..0000000
--- a/tests/dem_ground_frac_test/input_dem_orig.nml
+++ /dev/null
@@ -1,191 +0,0 @@
-
-&icebergs_driver_nml
-  ni=90 !45 !30 !number of elements, x direction
-  nj=90 !45 !30 !number of elements, y direction
-  ibdt=1800.0 !seconds
-  ibuo=0.1 !05 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=999999999 !max number of timesteps
-  saverestart=.true.
-  halo=3
-  debug=.true.
-  collision_test=.false.
-  grounding_test=.true.
-  bump_depth=200.0 !(m) depth of top of gaussian bump below sea level
-/
-
-&icebergs_nml
-
-    !use_damage=.true.
-    !damage_test_1=.true.
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    dem_spring_coef=1000.0 !4471.938678723104 !1000.0
-    !ignore_tangential_force=.true.
-    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=100 !(-1) # of mts sub-steps
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=1.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=200.0
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1.  
-    frac_thres_n = 12. !0.!500.0 !12. !200.
-    frac_thres_t = 12. !0.!1000.0 !12. !200.
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=90000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0.1 !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=24000 ! (24) Period between verbose messages
-    traj_sample_hrs=-1!0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=-1!0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/dem_ground_frac_test/input_reg.nml b/tests/dem_ground_frac_test/input_reg.nml
deleted file mode 100644
index d0f4978..0000000
--- a/tests/dem_ground_frac_test/input_reg.nml
+++ /dev/null
@@ -1,193 +0,0 @@
-
-&icebergs_driver_nml
-  ni=45 !30 !number of elements, x direction
-  nj=45 !30 !number of elements, y direction
-  ibdt=1800.0 !seconds
-  ibuo=0.1 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=999999999 !max number of timesteps
-  saverestart=.true.
-  halo=3
-  debug=.true.
-  collision_test=.false.
-  grounding_test=.true.
-  bump_depth=200.0 !(m) depth of top of gaussian bump below sea level 
-/
-
-&icebergs_nml
-
-
-    !dem=.true.
-    !poisson=0.3
-    !dem_damping_coef=0.99
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=1000.0
-    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=100 !50 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    explicit_inner_mts=.true. !If T, inner MTS iterations are treated explicitly
-    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
-    
-    contact_distance=1.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e3 !3.16e6 !for power-law-type friction
-    h_to_init_grounding=200.0
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    !frac_thres_n = 12.
-    !frac_thres_t = 12.
-
-    !frac_thres_scaling=0.25 !h=300
-    !fracture_criterion='strain' !('none') 'strain_rate','strain',or 'none'    
-    !frac_thres_n = 0.0162
-    !frac_thres_t = 0.0!457
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling=0.0033333 !this scaling corresponds w/ fixed stress calculation
-    !1.0 !h=300 to 200, stress
-    frac_thres_n = 3.5e3 !2.5e3
-    frac_thres_t = 50.e3!0.0
-
-    halo=3 !(4) halo width
-    Lx=45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=1.0 !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=24000 ! (24) Period between verbose messages
-    traj_sample_hrs=-1!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=-1!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/dem_ground_frac_test/input_reg_comp.nml b/tests/dem_ground_frac_test/input_reg_comp.nml
deleted file mode 100644
index f54001b..0000000
--- a/tests/dem_ground_frac_test/input_reg_comp.nml
+++ /dev/null
@@ -1,192 +0,0 @@
-
-&icebergs_driver_nml
-  ni=45 !30 !number of elements, x direction
-  nj=45 !30 !number of elements, y direction
-  ibdt=1800.0 !seconds
-  ibuo=0.1 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=999999999 !max number of timesteps
-  saverestart=.true.
-  halo=3
-  debug=.true.
-  collision_test=.false.
-  grounding_test=.true.
-  bump_depth=200.0 !(m) depth of top of gaussian bump below sea level 
-/
-
-&icebergs_nml
-
-
-    !dem=.true.
-    !poisson=0.3
-    !dem_damping_coef=0.99
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=1000.0
-    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=100 !50 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    explicit_inner_mts=.true. !If T, inner MTS iterations are treated explicitly
-    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
-    
-    contact_distance=1.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e3 !3.16e6 !for power-law-type friction
-    h_to_init_grounding=200.0
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    !frac_thres_n = 12.
-    !frac_thres_t = 12.
-
-    !frac_thres_scaling=0.25 !h=300
-    !fracture_criterion='strain' !('none') 'strain_rate','strain',or 'none'    
-    !frac_thres_n = 0.0162
-    !frac_thres_t = 0.0!457
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling=1.0 !h=300 to 200, stress
-    frac_thres_n = 70. !2.1e4!3.5e3 !2.5e3
-    frac_thres_t = 0. !50.e3!0.0
-
-    halo=3 !(4) halo width
-    Lx=45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.false. !.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=1.0 !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=24000 ! (24) Period between verbose messages
-    traj_sample_hrs=-1!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=-1!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/dem_ground_frac_test/input_reg_stress.nml b/tests/dem_ground_frac_test/input_reg_stress.nml
deleted file mode 100644
index 284f95c..0000000
--- a/tests/dem_ground_frac_test/input_reg_stress.nml
+++ /dev/null
@@ -1,192 +0,0 @@
-
-&icebergs_driver_nml
-  ni=45 !30 !number of elements, x direction
-  nj=45 !30 !number of elements, y direction
-  ibdt=1800.0 !seconds
-  ibuo=0.1 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=999999999 !max number of timesteps
-  saverestart=.true.
-  halo=3
-  debug=.true.
-  collision_test=.false.
-  grounding_test=.true.
-  bump_depth=200.0 !(m) depth of top of gaussian bump below sea level 
-/
-
-&icebergs_nml
-
-
-    !dem=.true.
-    !poisson=0.3
-    !dem_damping_coef=0.99
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=1000.0
-    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=100 !50 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    explicit_inner_mts=.true. !If T, inner MTS iterations are treated explicitly
-    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
-    
-    contact_distance=1.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e3 !3.16e6 !for power-law-type friction
-    h_to_init_grounding=200.0
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    !frac_thres_n = 12.
-    !frac_thres_t = 12.
-
-    !frac_thres_scaling=0.25 !h=300
-    !fracture_criterion='strain' !('none') 'strain_rate','strain',or 'none'    
-    !frac_thres_n = 0.0162
-    !frac_thres_t = 0.0!457
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling=1.0 !h=300 to 200, stress
-    frac_thres_n = 3.5e3 !2.5e3
-    frac_thres_t = 50.e3!0.0
-
-    halo=3 !(4) halo width
-    Lx=45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=1.0 !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=24000 ! (24) Period between verbose messages
-    traj_sample_hrs=-1!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=-1!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/dem_ground_frac_test/makeberg/makeberg.py b/tests/dem_ground_frac_test/makeberg/makeberg.py
index 7d89aec..1fe1baa 100755
--- a/tests/dem_ground_frac_test/makeberg/makeberg.py
+++ b/tests/dem_ground_frac_test/makeberg/makeberg.py
@@ -250,12 +250,13 @@ def create_empty_iceberg_restart_file(Empty_restart_filename):
 # flip2ndconglom=True#False
 # offset2ndconglom=True#False
 
-grdxmin=0; grdxmax=45000e3
-grdymin=0; grdymax=45000e3
-grdres=1000.0
+grdxmin=0; grdxmax=225000e3
+grdymin=0; grdymax=225000e3
+grdres=5000.0
 R_frac=0.45 #1st option
 #R_frac=0.5*0.45 #2nd option
-radius=(np.sqrt(3)/2.)*(R_frac*grdres) #S is < 0.5 grid res
+#radius=(np.sqrt(3)/2.)*(R_frac*grdres) #S is < 0.5 grid res
+radius=1.5e3 #/2
 #radius2=(np.sqrt(3)/2.)*(R_frac2*grdres) #S is < 0.5 grid res
 thickness1=200.0
 thickness2=200.0
@@ -265,9 +266,9 @@ def create_empty_iceberg_restart_file(Empty_restart_filename):
 nbergs=1 #number of conglomerates
 
 #center coords of each (rectangular) conglomerate berg (CB=conglomerate berg)
-CBxc=np.array([3500]); CByc=np.array([15000])
+CBxc=np.array([50000]); CByc=np.array([50000])
 #side lengths
-CBxl=np.array([4000]); CByl=np.array([8000])
+CBxl=np.array([15000]); CByl=np.array([35000])
 
 
 CByl=CByl.astype(int); CBxl=CBxl.astype(int)
@@ -324,7 +325,7 @@ def create_empty_iceberg_restart_file(Empty_restart_filename):
         x_val=x_start
         offset=0.0
         # if (i==0):
-        uvel=0.#1
+        uvel=0.1#1
         # else:
         #         uvel=-0.15#-0.05
         #         if (offset2ndconglom):
diff --git a/tests/dem_ground_frac_test_big/.gitignore b/tests/dem_ground_frac_test_big/.gitignore
deleted file mode 100644
index 68bcbc9..0000000
--- a/tests/dem_ground_frac_test_big/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-results/
\ No newline at end of file
diff --git a/tests/dem_ground_frac_test_big/README b/tests/dem_ground_frac_test_big/README
deleted file mode 100644
index ec575a8..0000000
--- a/tests/dem_ground_frac_test_big/README
+++ /dev/null
@@ -1,7 +0,0 @@
-1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
-2.(optional) edit input.nml
-3. run the model: ./RUN
-4, animate the results: animate_trajectories.py
-
-This is a good test for visualizing fracture dependence on particle size. Try running makeberg.py with the full radius and then half the radius, and with regular vs dem nmls. Make sure to edit the nmls so that contact distance is halved when radius is halved
-
diff --git a/tests/dem_ground_frac_test_big/RUN b/tests/dem_ground_frac_test_big/RUN
deleted file mode 100755
index 3dfc97d..0000000
--- a/tests/dem_ground_frac_test_big/RUN
+++ /dev/null
@@ -1,7 +0,0 @@
-rm iceberg_trajectories.nc
-rm iceberg_trajectories.nc.*
-rm bond_trajectories.nc
-rm bond_trajectories.nc.*
-srun -n1 ./../../build/bergs.x
-
-
diff --git a/tests/dem_ground_frac_test_big/animate_trajectories.py b/tests/dem_ground_frac_test_big/animate_trajectories.py
deleted file mode 100755
index d163b57..0000000
--- a/tests/dem_ground_frac_test_big/animate_trajectories.py
+++ /dev/null
@@ -1,161 +0,0 @@
-#!/usr/bin/env python
-
-from netCDF4 import Dataset
-import pdb
-import netCDF4 as nc
-import numpy as np
-import matplotlib
-import math
-import os
-matplotlib.use("tkagg")
-from pylab import *
-import matplotlib.pyplot as plt
-from matplotlib.animation import FuncAnimation
-import argparse
-
-def parseCommandLine():
-    parser = argparse.ArgumentParser(description=
-    '''Generate animation of iceberg trajectories.''',
-    epilog='Written by Alex Huth, 2020')
-    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
-                    help=''' provide filename to plot''')
-    parser.add_argument('-s', type=int, default='14000',
-                        help='''plotted particle size''')
-    optCmdLineArgs = parser.parse_args()
-    return optCmdLineArgs
-
-
-
-def main(args):
-
-    print('reading file')
-
-    filename=args.fname
-    psize=args.s
-    #filename = 'iceberg_trajectories.nc'
-    field = 'lon'
-    field2 = 'lat'
-
-    with nc.Dataset(filename) as file:
-        x = file.variables['lon'][:]/1.e3
-        y = file.variables['lat'][:]/1.e3
-        day = file.variables['day'][:]
-        length = file.variables['length'][:]
-        width = file.variables['width'][:]
-        thick = file.variables['thickness'][:]
-        od = file.variables['od'][:]
-
-    ud = np.unique(day)
-    t = ud[0]
-
-    radius = length*width*(1./(2*np.sqrt(3)))
-
-    #for determining if grounded:
-    rho_bergs=850.
-    rho_seawater=1025.
-    h_to_ground=20 #200.
-    draught=(rho_bergs/rho_seawater)*thick
-    if (h_to_ground==0):
-        groundfrac=draught-od
-    else:
-        groundfrac=1.-(od-draught)/h_to_ground
-    groundfrac[groundfrac<0.]=0.
-    groundfrac[groundfrac>1.]=1.
-
-    #groundfrac[thick<200.]=0.
-    #groundfrac[thick>=200.]=1.
-
-
-    # frame info
-    num_frames = len(ud)
-    movie_len = 5 #seconds
-    #frame_len = 1000.0*movie_len/num_frames/10000000
-    frame_len = movie_len/num_frames/1000
-
-    xmin = 40
-    xmax = 100
-    ymin = 20 #xmin
-    ymax = 80 #xmax
-
-    anim_running = True
-
-    def animate(i):
-
-        x1 = x[day == ud[i]]
-        y1 = y[day == ud[i]]
-        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
-
-        scat.set_offsets(data)
-
-        t = ud[i]
-        time_text.set_text('time = %.1f days' % t )
-
-        r1 = radius[day == ud[i]]
-        scat.set_sizes(r1/psize)
-
-        hstat = groundfrac[day == ud[i]]
-        cstring=[]
-        for j in range(len(hstat)):
-            if (hstat[j]==0):
-                cstring.append("none")
-            else:
-                cstring.append("b")
-        scat.set_color(cstring)
-        scat.set_edgecolor('r')
-
-        return scat,time_text
-
-    def init():
-        scat.set_offsets([])
-        return scat,
-
-    def onClick(event):
-        global anim_running
-        if anim_running:
-            ani.event_source.stop()
-            anim_running = False
-        else:
-            ani.event_source.start()
-            anim_running = True
-
-    # Now we can do the plotting!
-    f = plt.figure(figsize=(5,5))
-    f.tight_layout()
-    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
-    scat = ax1.scatter([],[],marker='o')#,edgecolor='red')
-    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
-
-    # Change major ticks to show every 20.
-    ax1.xaxis.set_major_locator(MultipleLocator(5))
-    ax1.yaxis.set_major_locator(MultipleLocator(5))
-
-    ax1.xaxis.set_minor_locator(MultipleLocator(1))
-    ax1.yaxis.set_minor_locator(MultipleLocator(1))
-
-    # Turn grid on for both major and minor ticks and style minor slightly
-    # differently.
-    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
-    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
-
-    ax1.set_xlabel('x (km)')
-    ax1.set_ylabel('y (km)')
-    ax1.set_title('Iceberg trajectory')
-
-    f.canvas.mpl_connect('button_press_event', onClick)
-
-    ani = FuncAnimation(
-        f,animate,init_func=init,frames=num_frames,
-        interval=frame_len,blit=True,repeat=True)
-
-    print('time',t)
-
-    plt.show()
-    #animation.save("iceberg_traj_animation.mp4")
-
-
-print('Script complete')
-
-if __name__ == '__main__':
-    optCmdLineArgs=	parseCommandLine()
-    anim_running = True
-    main(optCmdLineArgs)
diff --git a/tests/dem_ground_frac_test_big/diag_table b/tests/dem_ground_frac_test_big/diag_table
deleted file mode 100644
index c1c8819..0000000
--- a/tests/dem_ground_frac_test_big/diag_table
+++ /dev/null
@@ -1,3 +0,0 @@
-"icebergs test"
-1 1 1 0 0 0
-
diff --git a/tests/dem_ground_frac_test_big/input.nml b/tests/dem_ground_frac_test_big/input.nml
deleted file mode 100644
index 5464dbd..0000000
--- a/tests/dem_ground_frac_test_big/input.nml
+++ /dev/null
@@ -1,199 +0,0 @@
-
-&icebergs_driver_nml
-  ni=45 !30 !number of elements, x direction
-  nj=45 !30 !number of elements, y direction
-  gridres=5000.0
-  ibdt=1800.0 !seconds
-  ibuo=0.1 !ocean x velocity
-  ibvo=0.1 !-0.1 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=999999999 !max number of timesteps
-  saverestart=.true.
-  halo=3
-  debug=.true.
-  collision_test=.false.
-  big_grounding_test=.true.
-  bump_depth=50. !200.0 !(m) depth of top of gaussian bump below sea level
-/
-
-&icebergs_nml
-
-    constant_interaction_LW=.true.
-    !traj_name=test_dem.nc
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    break_bonds_on_sub_steps=.true.
-    
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5. A=L*W always works?
-    dem_spring_coef=5e6 !5e6 !1e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=0.00015094124684696098 !dem_spring_coef=1.e6, r=1500, and hex pack
-    !spring_coef=0.0030188249369392196 !dem_spring_coef=5.e6, r=750, and hex pack!
-    !spring_coef=0.0006037649873878439 !dem_spring_coef=1.e6, r=750, and hex pack
-    spring_coef=0.0007547062342348049 !if dem_spring_coef=5e6, r=1500, and hex pack?
-    !spring_coef=0.0015094124684696098 !dem_spring_coef=1.e7, r=1500, and hex pack
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=200 !75 !(-1) # of mts sub-steps
-    explicit_inner_mts=.true.
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=6.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-8 !(default=spring_coeff) Berg spring coeff for collisions
-
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e5 !3.16e6 !for power-law-type friction
-    h_to_init_grounding=20 !200.0
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.false.!.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='computed_s' !'stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1.05 !0.75 !0.5
-    frac_thres_n = 2000 !1850 !!!1000 !2250 !4100
-    frac_thres_t = 1000 !1200 !1450 !500 !!!1500 !800 !10000000 !800 !1400
-
-
-    halo=3 !(4) halo width
-    Lx=225000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0.1 !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=24000 ! (24) Period between verbose messages
-    traj_sample_hrs=0.5 !-1!0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=0.5 !-1!0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=1600.0!800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/dem_ground_frac_test_big/makeberg/RUN b/tests/dem_ground_frac_test_big/makeberg/RUN
deleted file mode 100755
index 520d671..0000000
--- a/tests/dem_ground_frac_test_big/makeberg/RUN
+++ /dev/null
@@ -1,3 +0,0 @@
-rm ./output_files/Generic*
-./makeberg.py
-cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
diff --git a/tests/dem_ground_frac_test_big/makeberg/makeberg.py b/tests/dem_ground_frac_test_big/makeberg/makeberg.py
deleted file mode 100755
index 1fe1baa..0000000
--- a/tests/dem_ground_frac_test_big/makeberg/makeberg.py
+++ /dev/null
@@ -1,376 +0,0 @@
-#!/usr/bin/env python
-import numpy as np
-import math
-from netCDF4 import Dataset
-from pylab import *
-#import pdb
-import netCDF4 as nc
-
-#
-# Initialize 2 iceberg elements, which can later be bonded in the fortran code if needed
-#
-
-def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
-
-	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
-	# To copy the global attributes of the netCDF file
-
-	#Input and output files
-	#Create Empty restart file. This is later read so that the attributes can be used.
-	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
-	create_empty_iceberg_restart_file(Empty_restart_filename)
-	#Empty_restart_filename='input_files/icebergs.res.nc'
-
-	#Read empty restart file
-	f=Dataset(Empty_restart_filename,'r') # r is for read only
-	#Write a new restart file
-	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
-
-	for attname in f.ncattrs():
-		    setattr(g,attname,getattr(f,attname))
-
-
-	# To copy the dimension of the netCDF file
-	for dimname,dim in f.dimensions.iteritems():
-		# if you want to make changes in the dimensions of the new file
-		# you should add your own conditions here before the creation of the dimension.
-		#g.createDimension(dimname,len(dim))
-		g.createDimension(dimname,Number_of_bergs)
-
-	# To copy the variables of the netCDF file
-
-	for varname,ncvar in f.variables.iteritems():
-		# if you want to make changes in the variables of the new file
-		# you should add your own conditions here before the creation of the variable.
-		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
-		#Proceed to copy the variable attributes
-		for attname in ncvar.ncattrs():
-			setattr(var,attname,getattr(ncvar,attname))
-		#Finally copy the variable data to the new created variable
-		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
-
-		if varname=='i':
-			var[:]=Number_of_bergs
-
-		if varname=='iceberg_num':
-			for j in range(Number_of_bergs):
-				#var[j]=j+1
-				var[j]=iceberg_num[j]
-
-		if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
-		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
-		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
-		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
-			var[:]=0
-
-                if varname=='uvel':
-                        var[:]=uvel
-
-                if varname=='vvel':
-                        var[:]=vvel
-
-		if varname=='mass_scaling':
-			var[:]=mass_scaling
-
-		if varname=='thickness':
-			for j in range(Number_of_bergs):
-				var[j]=thickness[j]
-
-		if varname=='mass':
-			for j in range(Number_of_bergs):
-				var[j]=mass[j]
-
-		if varname=='width'  or varname=='length':
-			for j in range(Number_of_bergs):
-				var[j]=width[j]
-
-		if varname=='lon':
-			for j in range(Number_of_bergs):
-				var[j]=lon[j]
-
-		if varname=='lat':
-			for j in range(Number_of_bergs):
-				var[j]=lat[j]
-
-		if varname=='static_berg':
-			for j in range(Number_of_bergs):
-				var[j]=static_berg[j]
-
-
-	f.close()
-	g.close()
-
-
-def create_empty_iceberg_restart_file(Empty_restart_filename):
-
-	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
-
-	i=f.createDimension('i', None)
-	lon=f.createVariable('i','i')
-
-	lon=f.createVariable('lon','d',('i'))
-	lon.long_name = "longitude" ;
-	lon.units = "degrees_E" ;
-	lon.checksum = "               0" ;
-
-	lat=f.createVariable('lat','d',('i'))
-	lat.long_name = "latitude" ;
-	lat.units = "degrees_N" ;
-	lat.checksum = "               0" ;
-
-	uvel=f.createVariable('uvel','d',('i'))
-	uvel.long_name = "zonal velocity" ;
-	uvel.units = "m/s" ;
-	uvel.checksum = "               0" ;
-
-	vvel=f.createVariable('vvel','d',('i'))
-	vvel.long_name = "meridional velocity" ;
-	vvel.units = "m/s" ;
-	vvel.checksum = "               0" ;
-
-	mass=f.createVariable('mass','d',('i'))
-	mass.long_name = "mass" ;
-	mass.units = "kg" ;
-	mass.checksum = "               0" ;
-
-	axn=f.createVariable('axn','d',('i'))
-	axn.long_name = "explicit zonal acceleration" ;
-	axn.units = "m/s^2" ;
-	axn.checksum = "               0" ;
-
-	ayn=f.createVariable('ayn','d',('i'))
-	ayn.long_name = "explicit meridional acceleration" ;
-	ayn.units = "m/s^2" ;
-	ayn.checksum = "               0" ;
-
-	bxn=f.createVariable('bxn','d',('i'))
-	bxn.long_name = "inplicit zonal acceleration" ;
-	bxn.units = "m/s^2" ;
-	bxn.checksum = "               0" ;
-
-	byn=f.createVariable('byn','d',('i'))
-	byn.long_name = "implicit meridional acceleration" ;
-	byn.units = "m/s^2" ;
-	byn.checksum = "               0" ;
-
-	ine=f.createVariable('ine','i',('i'))
-	ine.long_name = "i index" ;
-	ine.units = "none" ;
-	ine.packing = 0 ;
-	ine.checksum = "               0" ;
-
-	jne=f.createVariable('jne','i',('i'))
-	jne.long_name = "j index" ;
-	jne.units = "none" ;
-	jne.packing = 0 ;
-	jne.checksum = "               0" ;
-
-	thickness=f.createVariable('thickness','d',('i'))
-	thickness.long_name = "thickness" ;
-	thickness.units = "m" ;
-	thickness.checksum = "               0" ;
-
-	width=f.createVariable('width','d',('i'))
-	width.long_name = "width" ;
-	width.units = "m" ;
-	width.checksum = "               0" ;
-
-	length=f.createVariable('length','d',('i'))
-	length.long_name = "length" ;
-	length.units = "m" ;
-	length.checksum = "               0" ;
-
-	start_lon=f.createVariable('start_lon','d',('i'))
-	start_lon.long_name = "longitude of calving location" ;
-	start_lon.units = "degrees_E" ;
-	start_lon.checksum = "               0" ;
-
-	start_lat=f.createVariable('start_lat','d',('i'))
-	start_lat.long_name = "latitude of calving location" ;
-	start_lat.units = "degrees_N" ;
-	start_lat.checksum = "               0" ;
-
-	start_year=f.createVariable('start_year','i',('i'))
-	start_year.long_name = "calendar year of calving event" ;
-	start_year.units = "years" ;
-	start_year.packing = 0 ;
-	start_year.checksum = "               0" ;
-
-	iceberg_num=f.createVariable('iceberg_num','i',('i'))
-	iceberg_num.long_name = "identification of the iceberg" ;
-	iceberg_num.units = "dimensionless" ;
-	iceberg_num.packing = 0 ;
-	iceberg_num.checksum = "               0" ;
-
-	start_day=f.createVariable('start_day','d',('i'))
-	start_day.long_name = "year day of calving event" ;
-	start_day.units = "days" ;
-	start_day.checksum = "               0" ;
-
-	start_mass=f.createVariable('start_mass','d',('i'))
-	start_mass.long_name = "initial mass of calving berg" ;
-	start_mass.units = "kg" ;
-	start_mass.checksum = "               0" ;
-
-	mass_scaling=f.createVariable('mass_scaling','d',('i'))
-	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
-	mass_scaling.units = "none" ;
-	mass_scaling.checksum = "               0" ;
-
-	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
-	mass_of_bits.long_name = "mass of bergy bits" ;
-	mass_of_bits.units = "kg" ;
-	mass_of_bits.checksum = "               0" ;
-
-	heat_density=f.createVariable('heat_density','d',('i'))
-	heat_density.long_name = "heat density" ;
-	heat_density.units = "J/kg" ;
-	heat_density.checksum = "               0" ;
-
-	halo_berg=f.createVariable('halo_berg','d',('i'))
-	halo_berg.long_name = "halo_berg" ;
-	halo_berg.units = "dimensionless" ;
-	halo_berg.checksum = "               0" ;
-
-	static_berg=f.createVariable('static_berg','d',('i'))
-	static_berg.long_name = "static_berg" ;
-	static_berg.units = "dimensionless" ;
-	static_berg.checksum = "               0" ;
-
-	f.sync()
-	f.close()
-
-
-
-#-----------------------------------#
-#               Main                #
-#-----------------------------------#
-
-# just2particles=False
-# flip2ndconglom=True#False
-# offset2ndconglom=True#False
-
-grdxmin=0; grdxmax=225000e3
-grdymin=0; grdymax=225000e3
-grdres=5000.0
-R_frac=0.45 #1st option
-#R_frac=0.5*0.45 #2nd option
-#radius=(np.sqrt(3)/2.)*(R_frac*grdres) #S is < 0.5 grid res
-radius=1.5e3 #/2
-#radius2=(np.sqrt(3)/2.)*(R_frac2*grdres) #S is < 0.5 grid res
-thickness1=200.0
-thickness2=200.0
-rho_ice=850.0
-
-
-nbergs=1 #number of conglomerates
-
-#center coords of each (rectangular) conglomerate berg (CB=conglomerate berg)
-CBxc=np.array([50000]); CByc=np.array([50000])
-#side lengths
-CBxl=np.array([15000]); CByl=np.array([35000])
-
-
-CByl=CByl.astype(int); CBxl=CBxl.astype(int)
-
-#--- xmax, xmin, ymax, ymin for each CB --
-CBxmin=CBxc-(0.5*CBxl); CBxmax=CBxc+(0.5*CBxl)
-CBymin=CByc-(0.5*CByl); CBymax=CByc+(0.5*CByl)
-#this shouldn't happen:
-CBxmin[CBxmin<grdxmin]=grdxmin; CBxmax[CBxmax>grdxmax]=grdxmax
-CBymin[CBxmin<grdymin]=grdymin; CBymax[CBymax>grdymax]=grdymax
-CBxc=0.5*(CBxmin+CBxmax); CByc=0.5*(CBymin+CBymax)
-
-# #if just want one particle per CB
-# if just2particles:
-#         CBxmin=CBxc; CBxmax=CBxc
-#         CBymin=CByc; CBymax=CByc
-
-#--- min and max thicknesses for each CB ---
-h1=thickness1
-h2=thickness2
-CBhmax=np.array([h1]); CBhmin=np.array([h2])
-
-#radii
-CBrad=np.array([radius])
-print('radii',CBrad)
-
-berg_x=[]; berg_y=[]
-berg_id=[]; berg_static=[]
-berg_width=[]; berg_bonds=[]
-berg_h=[]; berg_mass_scaling=[]
-berg_mass=[]
-berg_uvel=[]; berg_vvel=[]
-
-berg_count=0
-
-for i in range(nbergs):
-        x_start=CBxmin[i]+(CBrad[i]*2./np.sqrt(3))
-
-        # if flip2ndconglom and i>0:
-        #         x_start=CBxmax[i]-(CBrad[i]*2./np.sqrt(3))
-
-        #pdb.set_trace()
-        if x_start>CBxmax[i]:
-                x_start=CBxmax[i]
-        y_start0=CBymin[i]+CBrad[i]
-        if y_start0>CBymax[i]:
-                y_start0=CBymax[i]
-        element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*(CBrad[i])**2)
-        #H (thickness) is a linear function of a berg element's position from the
-        #center of the CB. H=Hmax at the center of the CB and H=Hmin at a corner of the
-        #CB, where the dist of a corner from the center is:
-        cdistb=np.sqrt((CBxmin[i]-CBxc[i])**2+(CBymin[i]-CByc[i])**2)
-        j=0
-        x_val=x_start
-        offset=0.0
-        # if (i==0):
-        uvel=0.1#1
-        # else:
-        #         uvel=-0.15#-0.05
-        #         if (offset2ndconglom):
-        #                 offset=250.0
-        vvel=0.0#25
-        #uvel=0;vvel=0
-        #berg_count_start=berg_count
-        while x_val<=CBxmax[i] and x_val>=CBxmin[i]:
-                y_start=y_start0+((j%2)*CBrad[i])+offset
-                k=0
-                y_val=y_start
-                while y_val<=(CBymax[i]+offset):
-                        berg_count=berg_count+1
-                        berg_id.append(berg_count)
-                        berg_x.append(x_val)
-                        berg_y.append(y_val)
-                        berg_width.append(sqrt(element_area))
-                        #dist of berg elem from center of CB
-                        bdistc=np.sqrt((x_val-CBxc[i])**2+(y_val-CByc[i])**2)
-                        bh=CBhmin[i]*bdistc/cdistb + CBhmax[i]*(1-bdistc/cdistb)
-                        # if (just2particles):
-                        #         bh=h1
-                        berg_h.append(bh) #thickness
-                        berg_mass_scaling.append(1)
-                        berg_mass.append(bh*rho_ice*element_area)
-                        berg_static.append(0)
-                        berg_uvel.append(uvel)
-                        berg_vvel.append(vvel)
-                        # if (x_val<22000):
-                        #         berg_vvel.append(vvel)
-                        # else:
-                        #         berg_vvel.append(0.4)
-                        #berg_CBid.append(i)
-                        k=k+1
-                        y_val=y_start+(2*k*CBrad[i])
-                j=j+1
-                # if flip2ndconglom and i>0:
-                #         x_val=x_start-(np.sqrt(3)*CBrad[i]*j)
-                # else:
-                x_val=x_start+(np.sqrt(3)*CBrad[i]*j)
-
-print('Number of bergs',berg_count)
-
-#pdb.set_trace()
-
-#Create iceberg restart file
-Ice_geometry_source='Generic'
-Create_iceberg_restart_file(berg_count,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)
diff --git a/tests/dem_ground_frac_test_big/save1.nml b/tests/dem_ground_frac_test_big/save1.nml
deleted file mode 100644
index 23f330e..0000000
--- a/tests/dem_ground_frac_test_big/save1.nml
+++ /dev/null
@@ -1,199 +0,0 @@
-
-&icebergs_driver_nml
-  ni=45 !30 !number of elements, x direction
-  nj=45 !30 !number of elements, y direction
-  gridres=5000.0
-  ibdt=1800.0 !seconds
-  ibuo=0.1 !ocean x velocity
-  ibvo=0.0 !-0.1 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=999999999 !max number of timesteps
-  saverestart=.true.
-  halo=3
-  debug=.true.
-  collision_test=.false.
-  big_grounding_test=.true.
-  bump_depth=100. !200.0 !(m) depth of top of gaussian bump below sea level
-/
-
-&icebergs_nml
-
-    constant_interaction_LW=.true.
-    !traj_name=test_dem.nc
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    break_bonds_on_sub_steps=.true.
-    
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5. A=L*W always works?
-    dem_spring_coef=5e6 !1e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=0.00015094124684696098 !dem_spring_coef=1.e6, r=1500, and hex pack
-    !spring_coef=0.0030188249369392196 !dem_spring_coef=5.r6, r=750, and hex pack!
-    !spring_coef=0.0006037649873878439 !dem_spring_coef=1.e6, r=750, and hex pack
-    spring_coef=0.0007547062342348049 !if dem_spring_coef=0.5e7, r=1500, and hex pack?
-    
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=200 !75 !(-1) # of mts sub-steps
-    explicit_inner_mts=.true.
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-2 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-8 !(default=spring_coeff) Berg spring coeff for collisions
-
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e5 !3.16e6 !for power-law-type friction
-    h_to_init_grounding=20 !200.0
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.false.!.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 0.75 !1. !0.75 !0.5
-    frac_thres_n = 2250 !1000 !2250 !4100
-    frac_thres_t = 800 !10000000 !800 !1400
-
-
-    halo=3 !(4) halo width
-    Lx=225000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.false. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0.1 !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=24000 ! (24) Period between verbose messages
-    traj_sample_hrs=0.5 !-1!0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=0.5 !-1!0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=1600.0!800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/dem_ground_frac_test_big/save2.nml b/tests/dem_ground_frac_test_big/save2.nml
deleted file mode 100644
index 38bd29c..0000000
--- a/tests/dem_ground_frac_test_big/save2.nml
+++ /dev/null
@@ -1,199 +0,0 @@
-
-&icebergs_driver_nml
-  ni=45 !30 !number of elements, x direction
-  nj=45 !30 !number of elements, y direction
-  gridres=5000.0
-  ibdt=1800.0 !seconds
-  ibuo=0.1 !ocean x velocity
-  ibvo=0.1 !-0.1 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=999999999 !max number of timesteps
-  saverestart=.true.
-  halo=3
-  debug=.true.
-  collision_test=.false.
-  big_grounding_test=.true.
-  bump_depth=50. !200.0 !(m) depth of top of gaussian bump below sea level
-/
-
-&icebergs_nml
-
-    constant_interaction_LW=.true.
-    !traj_name=test_dem.nc
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    break_bonds_on_sub_steps=.true.
-    
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5. A=L*W always works?
-    dem_spring_coef=5e6 !5e6 !1e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=0.00015094124684696098 !dem_spring_coef=1.e6, r=1500, and hex pack
-    !spring_coef=0.0030188249369392196 !dem_spring_coef=5.e6, r=750, and hex pack!
-    !spring_coef=0.0006037649873878439 !dem_spring_coef=1.e6, r=750, and hex pack
-    spring_coef=0.0007547062342348049 !if dem_spring_coef=5e6, r=1500, and hex pack?
-    !spring_coef=0.0015094124684696098 !dem_spring_coef=1.e7, r=1500, and hex pack
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=200 !75 !(-1) # of mts sub-steps
-    explicit_inner_mts=.true.
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-2 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-8 !(default=spring_coeff) Berg spring coeff for collisions
-
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e5 !3.16e6 !for power-law-type friction
-    h_to_init_grounding=20 !200.0
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.false.!.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1.0 !0.75 !1. !0.75 !0.5
-    frac_thres_n = 1850 !1000 !2250 !4100
-    frac_thres_t = 500 !1500 !800 !10000000 !800 !1400
-
-
-    halo=3 !(4) halo width
-    Lx=225000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.false. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0.1 !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=24000 ! (24) Period between verbose messages
-    traj_sample_hrs=0.5 !-1!0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=0.5 !-1!0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=1600.0!800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/dem_ground_frac_test_big/save3.nml b/tests/dem_ground_frac_test_big/save3.nml
deleted file mode 100644
index bb7f660..0000000
--- a/tests/dem_ground_frac_test_big/save3.nml
+++ /dev/null
@@ -1,199 +0,0 @@
-
-&icebergs_driver_nml
-  ni=45 !30 !number of elements, x direction
-  nj=45 !30 !number of elements, y direction
-  gridres=5000.0
-  ibdt=1800.0 !seconds
-  ibuo=0.1 !ocean x velocity
-  ibvo=0.1 !-0.1 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=999999999 !max number of timesteps
-  saverestart=.true.
-  halo=3
-  debug=.true.
-  collision_test=.false.
-  big_grounding_test=.true.
-  bump_depth=50. !200.0 !(m) depth of top of gaussian bump below sea level
-/
-
-&icebergs_nml
-
-    constant_interaction_LW=.true.
-    !traj_name=test_dem.nc
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=0.1 !1.0
-    explicit_inner_mts=.true.
-    break_bonds_on_sub_steps=.true.
-    
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5. A=L*W always works?
-    dem_spring_coef=5e6 !5e6 !1e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=0.00015094124684696098 !dem_spring_coef=1.e6, r=1500, and hex pack
-    !spring_coef=0.0030188249369392196 !dem_spring_coef=5.e6, r=750, and hex pack!
-    !spring_coef=0.0006037649873878439 !dem_spring_coef=1.e6, r=750, and hex pack
-    spring_coef=0.0007547062342348049 !if dem_spring_coef=5e6, r=1500, and hex pack?
-    !spring_coef=0.0015094124684696098 !dem_spring_coef=1.e7, r=1500, and hex pack
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=200 !75 !(-1) # of mts sub-steps
-    explicit_inner_mts=.true.
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-2 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-8 !(default=spring_coeff) Berg spring coeff for collisions
-
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e5 !3.16e6 !for power-law-type friction
-    h_to_init_grounding=20 !200.0
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.false.!.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1.4 !0.75 !1. !0.75 !0.5
-    frac_thres_n = 1850 !1000 !2250 !4100
-    frac_thres_t = 500 !1500 !800 !10000000 !800 !1400
-
-
-    halo=3 !(4) halo width
-    Lx=225000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.false. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0.1 !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=24000 ! (24) Period between verbose messages
-    traj_sample_hrs=0.5 !-1!0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=0.5 !-1!0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=1600.0!800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/

From 9399b38b435a2a3ebf5b847cada8554960206b60 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Fri, 25 Nov 2022 18:18:00 -0500
Subject: [PATCH 326/361] Combined the footloose tests into one directory. Also
 completed a directory of tests for collision using either the original KID
 scheme, KID+MTS, or iKID. Eliminated unused tests.

---
 src/icebergs_framework.F90                    |   2 +-
 tests/.gitignore                              |   1 +
 tests/2p_collision_test/README                |   5 -
 tests/2p_collision_test/RUN1p                 |   5 -
 .../2p_collision_test/animate_trajectories.py | 158 -------
 tests/2p_collision_test/input.nml             | 166 -------
 tests/2p_collision_test/makeberg/RUN          |  13 -
 .../Scripts_and_analysis/hexagon_area.pyc     | Bin 30221 -> 33353 bytes
 tests/chaotic_test/.gitignore                 |   3 -
 tests/chaotic_test/README                     |   5 -
 tests/chaotic_test/RUN                        |   5 -
 tests/chaotic_test/animate_trajectories.py    | 121 ------
 .../chaotic_test/animate_trajectories_1pe.py  | 158 -------
 tests/chaotic_test/makeberg/RUN               |   3 -
 tests/chaotic_test/makeberg/makeberg.py       | 406 ------------------
 tests/collision_test/README                   |   5 -
 tests/collision_test/RUN                      |   5 -
 tests/collision_test/RUN1p                    |   5 -
 tests/collision_test/RUN_tstest.sh            |  33 --
 .../animate_trajectories_1pe.py               | 175 --------
 tests/collision_test/diag_table               |   3 -
 tests/collision_test/input_tstest.nml         | 151 -------
 tests/collision_test/makeberg/makeberg.py     |  77 ----
 tests/collision_test_mts/.gitignore           |   1 -
 tests/collision_test_mts/README               |   5 -
 tests/collision_test_mts/RUN1p                |   5 -
 tests/collision_test_mts/RUN_tstest.sh        |  33 --
 .../animate_trajectories.py                   | 121 ------
 .../animate_trajectories_1pe.py               | 175 --------
 tests/collision_test_mts/diag_table           |   3 -
 tests/collision_test_mts/input_tstest.nml     | 159 -------
 tests/collision_test_mts/makeberg/RUN         |  12 -
 tests/collision_test_mts/makeberg/makeberg.py |  77 ----
 .../.gitignore                                |   0
 tests/collision_tests/README                  |  22 +
 .../RUN => collision_tests/RUN_KID}           |   1 +
 .../RUN => collision_tests/RUN_MTS_KID}       |   1 +
 .../RUN => collision_tests/RUN_iKID}          |   1 +
 .../animate_trajectories.py                   |   0
 .../animate_trajectories_1pe.py               |   0
 .../diag_table                                |   0
 .../input_KID.nml}                            |  69 +--
 .../input_MTS_KID.nml}                        |  60 +--
 .../input_iKID.nml}                           |  31 +-
 .../makeberg/RUN                              |   0
 .../makeberg/makeberg.py                      |   0
 tests/dem_test_contact/.gitignore             |   1 -
 tests/dem_test_contact/README                 |   7 -
 tests/dem_test_contact/RUN                    |   7 -
 .../dem_test_contact/animate_trajectories.py  | 161 -------
 tests/dem_test_contact/diag_table             |   3 -
 tests/dem_test_contact/input.nml              | 200 ---------
 tests/dem_test_contact/makeberg/RUN           |   3 -
 tests/dem_test_contact/makeberg/makeberg.py   | 395 -----------------
 tests/energy_test/.gitignore                  |   1 -
 tests/energy_test/README                      |   7 -
 tests/energy_test/RUN                         |   7 -
 tests/energy_test/animate_trajectories.py     | 121 ------
 tests/energy_test/animate_trajectories_1pe.py | 180 --------
 tests/energy_test/diag_table                  |   3 -
 tests/energy_test/input.nml                   | 181 --------
 tests/energy_test/makeberg/README             |   4 -
 tests/energy_test/makeberg/RUN                |   3 -
 tests/energy_test/makeberg/RUN2               |   3 -
 tests/energy_test/makeberg/makeberg.py        | 374 ----------------
 tests/energy_test/makeberg/makeberg2.py       | 276 ------------
 tests/energy_test2/.gitignore                 |   1 -
 tests/energy_test2/README                     |   9 -
 tests/energy_test2/RUN                        |   7 -
 tests/energy_test2/animate_trajectories.py    | 121 ------
 .../energy_test2/animate_trajectories_1pe.py  | 180 --------
 tests/energy_test2/diag_table                 |   3 -
 tests/energy_test2/input.nml                  | 176 --------
 tests/energy_test2/makeberg/RUN               |   3 -
 tests/energy_test2/makeberg/makeberg.py       | 367 ----------------
 tests/energy_test3/.gitignore                 |   1 -
 tests/energy_test3/README                     |   9 -
 tests/energy_test3/RUN                        |   7 -
 tests/energy_test3/RUN1p                      |   7 -
 tests/energy_test3/animate_trajectories.py    | 141 ------
 .../energy_test3/animate_trajectories_1pe.py  | 189 --------
 tests/energy_test3/diag_table                 |   3 -
 tests/energy_test3/input.nml                  | 197 ---------
 tests/energy_test3/makeberg/RUN               |   3 -
 tests/energy_test3/makeberg/makeberg.py       | 377 ----------------
 tests/footloose_physical/README               |   9 -
 tests/footloose_physical/RUN1p                |   5 -
 tests/footloose_physical/diag_table           |   3 -
 tests/footloose_physical/input_old.nml        | 170 --------
 tests/footloose_poisson/README                |   9 -
 tests/footloose_poisson/RUN                   |   5 -
 tests/footloose_poisson/RUN1p                 |   5 -
 .../footloose_poisson/animate_trajectories.py | 151 -------
 tests/footloose_poisson/diag_table            |   3 -
 tests/footloose_poisson/input_old.nml         | 170 --------
 tests/footloose_poisson/makeberg/RUN          |   5 -
 tests/footloose_poisson/makeberg/makeberg.py  | 278 ------------
 tests/footloose_tests/.gitignore              |   1 +
 tests/footloose_tests/README                  |  25 ++
 tests/footloose_tests/RUN_FL_physical         |   4 +
 tests/footloose_tests/RUN_FL_poisson          |   4 +
 .../animate_trajectories.py                   |   0
 .../diag_table                                |   0
 .../input_FL_physical.nml}                    |   3 +
 .../input_FL_poisson.nml}                     |   3 +
 .../makeberg/RUN                              |   0
 .../makeberg/makeberg.py                      |   0
 tests/frac_test/.gitignore                    |   1 -
 tests/frac_test/README                        |   9 -
 tests/frac_test/RUN                           |   7 -
 tests/frac_test/RUN1p                         |   7 -
 tests/frac_test/animate_trajectories.py       | 140 ------
 tests/frac_test/animate_trajectories_1pe.py   | 189 --------
 tests/frac_test/diag_table                    |   3 -
 tests/frac_test/input.nml                     | 186 --------
 tests/frac_test/makeberg/RUN                  |   3 -
 tests/frac_test/makeberg/makeberg.py          | 376 ----------------
 tests/ground_frac_test/.gitignore             |   1 -
 tests/ground_frac_test/README                 |   5 -
 tests/ground_frac_test/RUN                    |   7 -
 .../ground_frac_test/animate_trajectories.py  | 121 ------
 .../animate_trajectories_1pe.py               | 180 --------
 tests/ground_frac_test/diag_table             |   3 -
 tests/ground_frac_test/input.nml              | 200 ---------
 tests/ground_frac_test/input_save.nml         | 182 --------
 tests/ground_frac_test/makeberg/RUN           |  12 -
 tests/ground_frac_test/makeberg/makeberg.py   |  89 ----
 tests/ground_frac_test/reference_input.nml    | 183 --------
 tests/plot_energy.py                          |   6 +-
 129 files changed, 155 insertions(+), 8627 deletions(-)
 delete mode 100644 tests/2p_collision_test/README
 delete mode 100755 tests/2p_collision_test/RUN1p
 delete mode 100755 tests/2p_collision_test/animate_trajectories.py
 delete mode 100644 tests/2p_collision_test/input.nml
 delete mode 100755 tests/2p_collision_test/makeberg/RUN
 delete mode 100644 tests/chaotic_test/.gitignore
 delete mode 100644 tests/chaotic_test/README
 delete mode 100755 tests/chaotic_test/RUN
 delete mode 100755 tests/chaotic_test/animate_trajectories.py
 delete mode 100755 tests/chaotic_test/animate_trajectories_1pe.py
 delete mode 100755 tests/chaotic_test/makeberg/RUN
 delete mode 100755 tests/chaotic_test/makeberg/makeberg.py
 delete mode 100644 tests/collision_test/README
 delete mode 100755 tests/collision_test/RUN
 delete mode 100755 tests/collision_test/RUN1p
 delete mode 100755 tests/collision_test/RUN_tstest.sh
 delete mode 100755 tests/collision_test/animate_trajectories_1pe.py
 delete mode 100644 tests/collision_test/diag_table
 delete mode 100644 tests/collision_test/input_tstest.nml
 delete mode 100755 tests/collision_test/makeberg/makeberg.py
 delete mode 100644 tests/collision_test_mts/.gitignore
 delete mode 100644 tests/collision_test_mts/README
 delete mode 100755 tests/collision_test_mts/RUN1p
 delete mode 100755 tests/collision_test_mts/RUN_tstest.sh
 delete mode 100755 tests/collision_test_mts/animate_trajectories.py
 delete mode 100755 tests/collision_test_mts/animate_trajectories_1pe.py
 delete mode 100644 tests/collision_test_mts/diag_table
 delete mode 100644 tests/collision_test_mts/input_tstest.nml
 delete mode 100755 tests/collision_test_mts/makeberg/RUN
 delete mode 100755 tests/collision_test_mts/makeberg/makeberg.py
 rename tests/{collision_test => collision_tests}/.gitignore (100%)
 create mode 100644 tests/collision_tests/README
 rename tests/{collision_test_mts/RUN => collision_tests/RUN_KID} (76%)
 rename tests/{footloose_physical/RUN => collision_tests/RUN_MTS_KID} (74%)
 rename tests/{2p_collision_test/RUN => collision_tests/RUN_iKID} (76%)
 rename tests/{collision_test => collision_tests}/animate_trajectories.py (100%)
 rename tests/{2p_collision_test => collision_tests}/animate_trajectories_1pe.py (100%)
 rename tests/{2p_collision_test => collision_tests}/diag_table (100%)
 rename tests/{collision_test/input.nml => collision_tests/input_KID.nml} (83%)
 rename tests/{chaotic_test/input.nml => collision_tests/input_MTS_KID.nml} (79%)
 rename tests/{collision_test_mts/input.nml => collision_tests/input_iKID.nml} (88%)
 rename tests/{collision_test => collision_tests}/makeberg/RUN (100%)
 rename tests/{2p_collision_test => collision_tests}/makeberg/makeberg.py (100%)
 delete mode 100644 tests/dem_test_contact/.gitignore
 delete mode 100644 tests/dem_test_contact/README
 delete mode 100755 tests/dem_test_contact/RUN
 delete mode 100755 tests/dem_test_contact/animate_trajectories.py
 delete mode 100644 tests/dem_test_contact/diag_table
 delete mode 100644 tests/dem_test_contact/input.nml
 delete mode 100755 tests/dem_test_contact/makeberg/RUN
 delete mode 100755 tests/dem_test_contact/makeberg/makeberg.py
 delete mode 100644 tests/energy_test/.gitignore
 delete mode 100644 tests/energy_test/README
 delete mode 100755 tests/energy_test/RUN
 delete mode 100755 tests/energy_test/animate_trajectories.py
 delete mode 100755 tests/energy_test/animate_trajectories_1pe.py
 delete mode 100644 tests/energy_test/diag_table
 delete mode 100644 tests/energy_test/input.nml
 delete mode 100644 tests/energy_test/makeberg/README
 delete mode 100755 tests/energy_test/makeberg/RUN
 delete mode 100755 tests/energy_test/makeberg/RUN2
 delete mode 100755 tests/energy_test/makeberg/makeberg.py
 delete mode 100755 tests/energy_test/makeberg/makeberg2.py
 delete mode 100644 tests/energy_test2/.gitignore
 delete mode 100644 tests/energy_test2/README
 delete mode 100755 tests/energy_test2/RUN
 delete mode 100755 tests/energy_test2/animate_trajectories.py
 delete mode 100755 tests/energy_test2/animate_trajectories_1pe.py
 delete mode 100644 tests/energy_test2/diag_table
 delete mode 100644 tests/energy_test2/input.nml
 delete mode 100755 tests/energy_test2/makeberg/RUN
 delete mode 100755 tests/energy_test2/makeberg/makeberg.py
 delete mode 100644 tests/energy_test3/.gitignore
 delete mode 100644 tests/energy_test3/README
 delete mode 100755 tests/energy_test3/RUN
 delete mode 100755 tests/energy_test3/RUN1p
 delete mode 100755 tests/energy_test3/animate_trajectories.py
 delete mode 100755 tests/energy_test3/animate_trajectories_1pe.py
 delete mode 100644 tests/energy_test3/diag_table
 delete mode 100644 tests/energy_test3/input.nml
 delete mode 100755 tests/energy_test3/makeberg/RUN
 delete mode 100755 tests/energy_test3/makeberg/makeberg.py
 delete mode 100644 tests/footloose_physical/README
 delete mode 100755 tests/footloose_physical/RUN1p
 delete mode 100644 tests/footloose_physical/diag_table
 delete mode 100644 tests/footloose_physical/input_old.nml
 delete mode 100644 tests/footloose_poisson/README
 delete mode 100755 tests/footloose_poisson/RUN
 delete mode 100755 tests/footloose_poisson/RUN1p
 delete mode 100755 tests/footloose_poisson/animate_trajectories.py
 delete mode 100644 tests/footloose_poisson/diag_table
 delete mode 100644 tests/footloose_poisson/input_old.nml
 delete mode 100755 tests/footloose_poisson/makeberg/RUN
 delete mode 100755 tests/footloose_poisson/makeberg/makeberg.py
 create mode 100644 tests/footloose_tests/.gitignore
 create mode 100644 tests/footloose_tests/README
 create mode 100755 tests/footloose_tests/RUN_FL_physical
 create mode 100755 tests/footloose_tests/RUN_FL_poisson
 rename tests/{footloose_physical => footloose_tests}/animate_trajectories.py (100%)
 rename tests/{chaotic_test => footloose_tests}/diag_table (100%)
 rename tests/{footloose_physical/input.nml => footloose_tests/input_FL_physical.nml} (99%)
 rename tests/{footloose_poisson/input.nml => footloose_tests/input_FL_poisson.nml} (99%)
 rename tests/{footloose_physical => footloose_tests}/makeberg/RUN (100%)
 rename tests/{footloose_physical => footloose_tests}/makeberg/makeberg.py (100%)
 delete mode 100644 tests/frac_test/.gitignore
 delete mode 100644 tests/frac_test/README
 delete mode 100755 tests/frac_test/RUN
 delete mode 100755 tests/frac_test/RUN1p
 delete mode 100755 tests/frac_test/animate_trajectories.py
 delete mode 100755 tests/frac_test/animate_trajectories_1pe.py
 delete mode 100644 tests/frac_test/diag_table
 delete mode 100644 tests/frac_test/input.nml
 delete mode 100755 tests/frac_test/makeberg/RUN
 delete mode 100755 tests/frac_test/makeberg/makeberg.py
 delete mode 100644 tests/ground_frac_test/.gitignore
 delete mode 100644 tests/ground_frac_test/README
 delete mode 100755 tests/ground_frac_test/RUN
 delete mode 100755 tests/ground_frac_test/animate_trajectories.py
 delete mode 100755 tests/ground_frac_test/animate_trajectories_1pe.py
 delete mode 100644 tests/ground_frac_test/diag_table
 delete mode 100644 tests/ground_frac_test/input.nml
 delete mode 100644 tests/ground_frac_test/input_save.nml
 delete mode 100755 tests/ground_frac_test/makeberg/RUN
 delete mode 100755 tests/ground_frac_test/makeberg/makeberg.py
 delete mode 100644 tests/ground_frac_test/reference_input.nml

diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index d6cc554..549caea 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -5855,7 +5855,7 @@ subroutine connect_all_bonds(bergs, ignore_unmatched, match_bond_pairs)
     call count_bonds(bergs, nbonds,check_bond_quality)
   endif
 
-  if (save_bond_forces .and. link_bond_pairs) then
+  if (save_bond_forces .and. link_bond_pairs .and. bergs%dem) then
     do grdj = grd%jsd+1,grd%jed ; do grdi = grd%isd+1,grd%ied
       berg=>bergs%list(grdi,grdj)%first
       do while (associated(berg)) ! loop over all bergs
diff --git a/tests/.gitignore b/tests/.gitignore
index 5bdd1c4..97068f3 100644
--- a/tests/.gitignore
+++ b/tests/.gitignore
@@ -10,3 +10,4 @@ uniaxial_test/
 a68_2/
 a68_3/
 a68_old/
+other_tests/
diff --git a/tests/2p_collision_test/README b/tests/2p_collision_test/README
deleted file mode 100644
index 83093c2..0000000
--- a/tests/2p_collision_test/README
+++ /dev/null
@@ -1,5 +0,0 @@
-1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
-2.(optional) edit input.nml
-3. run the model: ./RUN
-4, animate the results: animate_trajectories.py
-
diff --git a/tests/2p_collision_test/RUN1p b/tests/2p_collision_test/RUN1p
deleted file mode 100755
index c3bf53e..0000000
--- a/tests/2p_collision_test/RUN1p
+++ /dev/null
@@ -1,5 +0,0 @@
-rm iceberg_trajectories.nc
-rm iceberg_trajectories.nc.*
-srun -n1 ./../../build/bergs.x
-
-
diff --git a/tests/2p_collision_test/animate_trajectories.py b/tests/2p_collision_test/animate_trajectories.py
deleted file mode 100755
index b41d801..0000000
--- a/tests/2p_collision_test/animate_trajectories.py
+++ /dev/null
@@ -1,158 +0,0 @@
-#!/usr/bin/env python
-
-from netCDF4 import Dataset
-import pdb
-import netCDF4 as nc
-import numpy as np
-import matplotlib
-import math
-import os
-matplotlib.use("tkagg")
-from pylab import *
-import matplotlib.pyplot as plt
-from matplotlib.animation import FuncAnimation
-from mpl_toolkits.axes_grid1 import make_axes_locatable
-import argparse
-
-def parseCommandLine():
-    parser = argparse.ArgumentParser(description=
-    '''Generate animation of iceberg trajectories.''',
-    epilog='Written by Alex Huth, 2020')
-    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
-                    help=''' provide filename to plot''')
-    optCmdLineArgs = parser.parse_args()
-    return optCmdLineArgs
-
-
-
-def main(args):
-    
-    print('reading file')
-
-    filename=args.fname
-    #filename = 'iceberg_trajectories.nc'
-    field = 'lon'
-    field2 = 'lat'
-
-    with nc.Dataset(filename) as file:
-        x = file.variables['lon'][:]/1.e3
-        y = file.variables['lat'][:]/1.e3
-        day = file.variables['day'][:]
-        bid = file.variables['id_ij'][:]
-        #vo = file.variables['vvel'][:]
-        #vo = file.variables['vvel_prev'][:]
-        vo = file.variables['id_ij'][:]
-
-    ud = np.unique(day)
-    ub = np.unique(bid)
-    t = ud[0]
-
-
-    # frame info
-    num_frames = len(ud)
-    movie_len = 20.0 #seconds
-    frame_len = 1000.0*movie_len/num_frames
-    
-    xmin = 0 #np.floor(min(min(x),min(y),0))
-    xmax = 20 #np.ceil(max(max(x),max(y),20))
-    ymin = xmin
-    ymax = xmax
-
-    anim_running = True
-
-    def animate(i):
-
-        x1 = x[day == ud[i]]
-        y1 = y[day == ud[i]]
-        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
-
-        scat.set_offsets(data)
-        
-        # bid1 = bid[day == ud[i]]        
-        # cstring=[]
-        # for j in range(len(bid1)):
-        #     if (bid1[j]==ub[1]):
-        #         cstring.append("b")
-        #     else:                 
-        #         cstring.append("r")
-        # scat.set_color(cstring)
-
-        vo1 = vo[day == ud[i]]
-        scat.set_edgecolor('k')
-        scat.set_color(cmap(norm(vo1)))
-
-        t = ud[i]
-        time_text.set_text('time = %.1f days' % t )        
-        return scat,time_text
-
-    def init():
-        scat.set_offsets([])
-        return scat,
-
-    def onClick(event):
-        global anim_running
-        if anim_running:
-            ani.event_source.stop()
-            anim_running = False
-        else:
-            ani.event_source.start()
-            anim_running = True       
-    
-    # Now we can do the plotting!    
-    f = plt.figure(figsize=(5,5))
-    f.tight_layout()
-    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
-    div = make_axes_locatable(ax1)
-    cax = div.append_axes('right', '5%', '5%') 
-    scat = ax1.scatter([],[],c=[],marker='o',s=100) #,edgecolor='k')
-    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
-
-    cmap = plt.cm.get_cmap('RdYlBu')
-    norm = plt.Normalize(vo.min(), vo.max())
-    cb1 = matplotlib.colorbar.ColorbarBase(cax, cmap=cmap,
-                                           norm=norm,
-                                           orientation='vertical')      
-
-   
-    # Change major ticks to show every 20.
-    ax1.xaxis.set_major_locator(MultipleLocator(5))
-    ax1.yaxis.set_major_locator(MultipleLocator(5))
-
-    ax1.xaxis.set_minor_locator(MultipleLocator(1))
-    ax1.yaxis.set_minor_locator(MultipleLocator(1))
-
-    # Turn grid on for both major and minor ticks and style minor slightly
-    # differently.
-    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
-    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
-
-    ax1.set_xlabel('x (km)')
-    ax1.set_ylabel('y (km)')
-    ax1.set_title('Iceberg trajectory')
- 
-    f.canvas.mpl_connect('button_press_event', onClick)
-
-    ani = FuncAnimation(
-        f,animate,init_func=init,frames=num_frames,
-        interval=frame_len,blit=True,repeat=True)
-
-    print('time',t)
-
-    plt.show()
-    #animation.save("iceberg_traj_animation.mp4")
-
-
-print('Script complete')
-
-if __name__ == '__main__':
-    optCmdLineArgs=	parseCommandLine()
-    anim_running = True
-    main(optCmdLineArgs)
-
-
-
-
-
-
-
-
diff --git a/tests/2p_collision_test/input.nml b/tests/2p_collision_test/input.nml
deleted file mode 100644
index 2d4ab32..0000000
--- a/tests/2p_collision_test/input.nml
+++ /dev/null
@@ -1,166 +0,0 @@
-!test that the mts and sts velocity verlet schemes agree, when mts is run with a single inner loop
-! note that chksums will not agree. TODO: modify chksums to be invariant to mts vs sts
-
-! for mts=.false.:
-! KID, bergs_chksum: write_restart berg chksum= -982041486 chksum2=  -982041486 chksum3=           -1680028706 chksum4=           -1680028706 chksum5=                     0 #=2
-
-!for mts=.true.:
-! KID, bergs_chksum: write_restart berg chksum=  160896535 chksum2=   160896535 chksum3=           -1680028706 chksum4=           -1680028706 chksum5=                     0 #=2
-
-! for both
-! KID, grd_chksum2:    # of bergs/cell chksum=           0 chksum2=           0 min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
-! KID, grd_chksum3:   write stored_ice chksum=  -540079793 chksum2= -1237287029 min= 6.393358811E+05 max= 7.380127765E+11 mean= 8.033602570E+10 rms= 1.613270384E+11 sd= 1.399018810E+11
-! KID, grd_chksum2:  write stored_heat chksum=           0 chksum2=           0 min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
-
-&icebergs_driver_nml
-  ni=20 !number of elements, x direction
-  nj=20 !number of elements, y direction
-  ibdt=600.0 !seconds
-  ibuo=0.2 !ocean x velocity
-  ibvo=0.2 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=48 !total simulation hours
-  nmax=99999999 !max number of timesteps
-  saverestart=.true. 
-  halo=3
-  debug=.false.   
-  collision_test=.true. !specific to the current test, must be true here
-/
-
-
-&icebergs_nml
-
-    !defaults given in parentheses:
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=1 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
-    contact_distance=0 !3.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-5!(default=spring_coeff) Berg spring coeff for collisions
-
-    halo=3 !(4) halo width
-    Lx=20000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.True. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move    
-    
-    rho_bergs=850. ! (850) iceberg density
-    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val 
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0.4 !4 !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #) 
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met    
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)    
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread			
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.false. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...       
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors    
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=24 ! (24) Period between verbose messages
-    traj_sample_hrs=0.5 !1 !(24) sampling period for trajectory storage
-    traj_write_hrs=0.5 ! (480) Period for writing sampled trajectories to disk    
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id    
-    
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.true. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all    
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart 
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.false. ! (F) True= Bonds are initialize manually.
-    length_for_manually_initialize_bonds=0.0 !(1e3)Dist b/w bergs to init bonds manually    
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.      
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-    
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-    
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-    
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-    
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
- 
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/2p_collision_test/makeberg/RUN b/tests/2p_collision_test/makeberg/RUN
deleted file mode 100755
index d998794..0000000
--- a/tests/2p_collision_test/makeberg/RUN
+++ /dev/null
@@ -1,13 +0,0 @@
-./makeberg.py
-
-rm ./output_files/Generic*
-
-./../../Iceberg_repository/Scripts_and_analysis/initialize_bergs_in_pattern.py \
-	-set_all_bergs_static_by_default=False -Run_plotting_subroutine=False \
-	-break_some_bonds=False -Ice_geometry_source='Generic' \
-	-Generic_ice_geometry_filename='./testtabularberg.nc' \
-	-ISOMIP_reduced=False -collision_test=True \
-	-select_just_min_and_max_lat_berg=True
-
-cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
-cp ./output_files/Generic_bonds_iceberg.res.nc ./../INPUT/bonds_iceberg.res.nc
\ No newline at end of file
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/hexagon_area.pyc b/tests/Iceberg_repository/Scripts_and_analysis/hexagon_area.pyc
index 06e4f5193c982779a1816a464418162e1a1aa352..f0183b2e91e5919cba386d292db458999496b1a3 100644
GIT binary patch
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diff --git a/tests/chaotic_test/.gitignore b/tests/chaotic_test/.gitignore
deleted file mode 100644
index f395a63..0000000
--- a/tests/chaotic_test/.gitignore
+++ /dev/null
@@ -1,3 +0,0 @@
-results/
-csvresults/
-csvresults2/
\ No newline at end of file
diff --git a/tests/chaotic_test/README b/tests/chaotic_test/README
deleted file mode 100644
index 83093c2..0000000
--- a/tests/chaotic_test/README
+++ /dev/null
@@ -1,5 +0,0 @@
-1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
-2.(optional) edit input.nml
-3. run the model: ./RUN
-4, animate the results: animate_trajectories.py
-
diff --git a/tests/chaotic_test/RUN b/tests/chaotic_test/RUN
deleted file mode 100755
index 208e8a7..0000000
--- a/tests/chaotic_test/RUN
+++ /dev/null
@@ -1,5 +0,0 @@
-rm iceberg_trajectories.nc
-rm iceberg_trajectories.nc.*
-srun -n100 ./../../build/bergs.x
-
-
diff --git a/tests/chaotic_test/animate_trajectories.py b/tests/chaotic_test/animate_trajectories.py
deleted file mode 100755
index 28ab658..0000000
--- a/tests/chaotic_test/animate_trajectories.py
+++ /dev/null
@@ -1,121 +0,0 @@
-#!/usr/bin/env python
-
-from netCDF4 import Dataset
-import pdb
-import netCDF4 as nc
-import numpy as np
-import matplotlib
-import math
-import os
-matplotlib.use("tkagg")
-from pylab import *
-import matplotlib.pyplot as plt
-from matplotlib.animation import FuncAnimation
-import argparse
-
-def parseCommandLine():
-    parser = argparse.ArgumentParser(description=
-    '''Generate animation of iceberg trajectories.''',
-    epilog='Written by Alex Huth, 2020')
-    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
-                    help=''' provide filename to plot''')
-    optCmdLineArgs = parser.parse_args()
-    return optCmdLineArgs
-
-
-
-def main(args ):
-
-    print('reading file')
-
-    filename=args.fname
-    #filename = 'iceberg_trajectories.nc'
-    field = 'lon'
-    field2 = 'lat'
-
-    with nc.Dataset(filename) as file:
-        x = file.variables['lon'][:]/1.e4
-        y = file.variables['lat'][:]/1.e4 #10km
-        day = file.variables['day'][:]
-
-    ud = np.unique(day)
-    t = ud[0]
-
-    # frame info
-    num_frames = len(ud)
-    movie_len = 5.0 #seconds
-    frame_len = 1000.0*movie_len/num_frames
-
-    xmin = 0 #np.floor(min(min(x),min(y),0))
-    xmax = 100 #20 #np.ceil(max(max(x),max(y),20))
-    ymin = xmin
-    ymax = xmax
-
-    anim_running = True
-
-    def animate(i):
-
-        x1 = x[day == ud[i]]
-        y1 = y[day == ud[i]]
-        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
-
-        scat.set_offsets(data)
-
-        t = ud[i]
-        time_text.set_text('time = %.1f days' % t )
-        return scat,time_text
-
-    def init():
-        scat.set_offsets([])
-        return scat,
-
-    def onClick(event):
-        global anim_running
-        if anim_running:
-            ani.event_source.stop()
-            anim_running = False
-        else:
-            ani.event_source.start()
-            anim_running = True
-
-    # Now we can do the plotting!
-    f = plt.figure(figsize=(5,5))
-    f.tight_layout()
-    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
-    scat = ax1.scatter([],[],marker='o',facecolor='w',s=10,edgecolor='red')
-    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
-
-    # Change major ticks 
-    ax1.xaxis.set_major_locator(MultipleLocator(10))
-    ax1.yaxis.set_major_locator(MultipleLocator(10))
-
-    ax1.xaxis.set_minor_locator(MultipleLocator(5))
-    ax1.yaxis.set_minor_locator(MultipleLocator(5))
-
-    # Turn grid on for both major and minor ticks and style minor slightly
-    # differently.
-    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
-    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
-
-    ax1.set_xlabel('x (10 km)')
-    ax1.set_ylabel('y (10 km)')
-    ax1.set_title('Iceberg trajectory')
-
-    f.canvas.mpl_connect('button_press_event', onClick)
-
-    ani = FuncAnimation(
-        f,animate,init_func=init,frames=num_frames,
-        interval=frame_len,blit=True,repeat=True)
-
-    print('time',t)
-
-    plt.show()
-    #animation.save("iceberg_traj_animation.mp4")
-
-
-print('Script complete')
-
-if __name__ == '__main__':
-    optCmdLineArgs=	parseCommandLine()
-    anim_running = True
-    main(optCmdLineArgs)
diff --git a/tests/chaotic_test/animate_trajectories_1pe.py b/tests/chaotic_test/animate_trajectories_1pe.py
deleted file mode 100755
index e115e29..0000000
--- a/tests/chaotic_test/animate_trajectories_1pe.py
+++ /dev/null
@@ -1,158 +0,0 @@
-#!/usr/bin/env python
-
-from netCDF4 import Dataset
-import pdb
-import netCDF4 as nc
-import numpy as np
-import matplotlib
-import math
-import os
-matplotlib.use("tkagg")
-from pylab import *
-import matplotlib.pyplot as plt
-from matplotlib.animation import FuncAnimation
-import argparse
-
-def parseCommandLine():
-    parser = argparse.ArgumentParser(description=
-    '''Generate animation of iceberg trajectories.''',
-    epilog='Written by Alex Huth, 2020')
-    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc.0000',
-                    help=''' provide filename to plot''')
-    optCmdLineArgs = parser.parse_args()
-    return optCmdLineArgs
-
-
-
-def main(args):
-
-    print('reading file')
-
-    filename=args.fname
-    field = 'lon'
-    field2 = 'lat'
-
-    with nc.Dataset(filename) as file:
-        x = file.variables['lon'][:]/1.e4
-        y = file.variables['lat'][:]/1.e4
-        day = file.variables['day'][:]
-        hs = file.variables['halo_berg'][:]
-        idij = file.variables['id_ij'][:]
-        idcnt = file.variables['id_cnt'][:]
-
-    ud = np.unique(day)
-    t = ud[0]
-
-    print('unique hs',np.unique(hs))
-
-    # frame info
-    num_frames = len(ud)
-    movie_len = 5.0 #seconds
-    frame_len = 1000.0*movie_len/num_frames
-
-    xmin = 25
-    xmax = 65
-    ymin = 40
-    ymax = 70
-
-    anim_running = True
-
-    def animate(i):
-
-        x1 = x[day == ud[i]]
-        y1 = y[day == ud[i]]
-        hstat = hs[day == ud[i]]
-        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
-        idd = idij[day == ud[i]]
-        idc = idcnt[day == ud[i]]
-
-        cstring=[]
-        for j in range(len(hstat)):
-
-            if (hstat[j]<0):
-                cstring.append("y")
-            elif (hstat[j]==0):
-                cstring.append("b")
-            elif (hstat[j]==1):
-                cstring.append("r")
-            elif (hstat[j]==2):
-                cstring.append("g")
-            elif (hstat[j]==10):
-                cstring.append("c")
-            else:
-                cstring.append("k")
-
-        scat.set_offsets(data)
-        scat.set_color(cstring)
-        scat.set_edgecolor('none')
-
-        t = ud[i]
-        time_text.set_text('time = %.1f days' % t )
-        return scat,time_text
-
-    def init():
-        scat.set_offsets([])
-        return scat,
-
-    def onClick(event):
-        global anim_running
-        if anim_running:
-            ani.event_source.stop()
-            anim_running = False
-        else:
-            ani.event_source.start()
-            anim_running = True
-
-    # Now we can do the plotting!
-    f = plt.figure(figsize=(5,5))
-    f.tight_layout()
-    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
-    scat = ax1.scatter([],[],marker='o',s=6)
-    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
-
-    # Turn grid on for both major and minor ticks and style minor slightly
-    # differently.
-    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
-    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
-
-    ax1.set_xlabel('x (km)')
-    ax1.set_ylabel('y (km)')
-    ax1.set_title('Iceberg trajectory')
-
-    f.canvas.mpl_connect('button_press_event', onClick)
-
-    ani = FuncAnimation(
-        f,animate,init_func=init,frames=num_frames,
-        interval=frame_len,blit=True,repeat=False)
-
-    print('time',t)
-
-    jsd=49
-    jsc=50
-    jec=60
-    jed=61.5
-    isd=39
-    isc=40
-    iec=50
-    ied=51.5
-
-    plt.plot([isc,isc],[jsc,jec],'k-',lw=1)
-    plt.plot([iec,iec],[jsc,jec],'k-',lw=1)
-    plt.plot([isc,iec],[jsc,jsc],'k-',lw=1)
-    plt.plot([isc,iec],[jec,jec],'k-',lw=1)
-
-    plt.plot([isd,isd],[jsd,jed],'b:',lw=1)
-    plt.plot([ied,ied],[jsd,jed],'b:',lw=1)
-    plt.plot([isd,ied],[jsd,jsd],'b:',lw=1)
-    plt.plot([isd,ied],[jed,jed],'b:',lw=1)
-
-    plt.show()
-    #animation.save("iceberg_traj_animation.mp4")
-
-
-print('Script complete')
-
-if __name__ == '__main__':
-    optCmdLineArgs=	parseCommandLine()
-    anim_running = True
-    main(optCmdLineArgs)
diff --git a/tests/chaotic_test/makeberg/RUN b/tests/chaotic_test/makeberg/RUN
deleted file mode 100755
index d985f3f..0000000
--- a/tests/chaotic_test/makeberg/RUN
+++ /dev/null
@@ -1,3 +0,0 @@
-rm ./output_files/Generic*
-./makeberg.py
-cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
\ No newline at end of file
diff --git a/tests/chaotic_test/makeberg/makeberg.py b/tests/chaotic_test/makeberg/makeberg.py
deleted file mode 100755
index 90efab7..0000000
--- a/tests/chaotic_test/makeberg/makeberg.py
+++ /dev/null
@@ -1,406 +0,0 @@
-#!/usr/bin/env python
-import numpy as np
-import math
-from netCDF4 import Dataset
-from pylab import *
-#import pdb
-import netCDF4 as nc
-
-#based on a simple Lehmer "random" number generator
-#where the final result is scaled from 0 to 1
-def lrng(count,m,a,initval):
-
-        r = m % a
-        q = m // a
-
-        z=np.zeros(count+1)
-        z[0]=initval
-
-        for i in range(0,count):
-                t = a * (z[i] % q) - r * (z[i] // q)
-                if (t > 0):
-                        z[i+1]=t
-                else:
-                        z[i+1]=t+m
-        #z = z/m
-
-        #normalize within [0,1]
-        z=z-np.min(z)
-        z=z/(np.max(z))
-
-        return z
-
-def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg):
-
-	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
-	# To copy the global attributes of the netCDF file
-
-	#Input and output files
-	#Create Empty restart file. This is later read so that the attributes can be used.
-	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
-	create_empty_iceberg_restart_file(Empty_restart_filename)
-	#Empty_restart_filename='input_files/icebergs.res.nc'
-
-	#Read empty restart file
-	f=Dataset(Empty_restart_filename,'r') # r is for read only
-	#Write a new restart file
-	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
-
-	for attname in f.ncattrs():
-		    setattr(g,attname,getattr(f,attname))
-
-
-	# To copy the dimension of the netCDF file
-	for dimname,dim in f.dimensions.iteritems():
-		# if you want to make changes in the dimensions of the new file
-		# you should add your own conditions here before the creation of the dimension.
-		#g.createDimension(dimname,len(dim))
-		g.createDimension(dimname,Number_of_bergs)
-
-	# To copy the variables of the netCDF file
-
-	for varname,ncvar in f.variables.iteritems():
-		# if you want to make changes in the variables of the new file
-		# you should add your own conditions here before the creation of the variable.
-		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
-		#Proceed to copy the variable attributes
-		for attname in ncvar.ncattrs():
-			setattr(var,attname,getattr(ncvar,attname))
-		#Finally copy the variable data to the new created variable
-		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
-
-		if varname=='i':
-			var[:]=Number_of_bergs
-
-		if varname=='iceberg_num':
-			for j in range(Number_of_bergs):
-				#var[j]=j+1
-				var[j]=iceberg_num[j]
-
-		if varname=='uvel' or varname=='vvel' or varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
-		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
-		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
-		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
-			var[:]=0
-
-		if varname=='mass_scaling':
-			var[:]=mass_scaling
-
-		if varname=='thickness':
-			for j in range(Number_of_bergs):
-				var[j]=thickness[j]
-
-		if varname=='mass':
-			for j in range(Number_of_bergs):
-				var[j]=mass[j]
-
-		if varname=='width'  or varname=='length':
-			for j in range(Number_of_bergs):
-				var[j]=width[j]
-
-		if varname=='lon':
-			for j in range(Number_of_bergs):
-				var[j]=lon[j]
-
-		if varname=='lat':
-			for j in range(Number_of_bergs):
-				var[j]=lat[j]
-
-		if varname=='static_berg':
-			for j in range(Number_of_bergs):
-				var[j]=static_berg[j]
-
-
-	f.close()
-	g.close()
-
-
-def create_empty_iceberg_restart_file(Empty_restart_filename):
-
-	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
-
-	i=f.createDimension('i', None)
-	lon=f.createVariable('i','i')
-
-	lon=f.createVariable('lon','d',('i'))
-	lon.long_name = "longitude" ;
-	lon.units = "degrees_E" ;
-	lon.checksum = "               0" ;
-
-	lat=f.createVariable('lat','d',('i'))
-	lat.long_name = "latitude" ;
-	lat.units = "degrees_N" ;
-	lat.checksum = "               0" ;
-
-	uvel=f.createVariable('uvel','d',('i'))
-	uvel.long_name = "zonal velocity" ;
-	uvel.units = "m/s" ;
-	uvel.checksum = "               0" ;
-
-	vvel=f.createVariable('vvel','d',('i'))
-	vvel.long_name = "meridional velocity" ;
-	vvel.units = "m/s" ;
-	vvel.checksum = "               0" ;
-
-	mass=f.createVariable('mass','d',('i'))
-	mass.long_name = "mass" ;
-	mass.units = "kg" ;
-	mass.checksum = "               0" ;
-
-	axn=f.createVariable('axn','d',('i'))
-	axn.long_name = "explicit zonal acceleration" ;
-	axn.units = "m/s^2" ;
-	axn.checksum = "               0" ;
-
-	ayn=f.createVariable('ayn','d',('i'))
-	ayn.long_name = "explicit meridional acceleration" ;
-	ayn.units = "m/s^2" ;
-	ayn.checksum = "               0" ;
-
-	bxn=f.createVariable('bxn','d',('i'))
-	bxn.long_name = "inplicit zonal acceleration" ;
-	bxn.units = "m/s^2" ;
-	bxn.checksum = "               0" ;
-
-	byn=f.createVariable('byn','d',('i'))
-	byn.long_name = "implicit meridional acceleration" ;
-	byn.units = "m/s^2" ;
-	byn.checksum = "               0" ;
-
-	ine=f.createVariable('ine','i',('i'))
-	ine.long_name = "i index" ;
-	ine.units = "none" ;
-	ine.packing = 0 ;
-	ine.checksum = "               0" ;
-
-	jne=f.createVariable('jne','i',('i'))
-	jne.long_name = "j index" ;
-	jne.units = "none" ;
-	jne.packing = 0 ;
-	jne.checksum = "               0" ;
-
-	thickness=f.createVariable('thickness','d',('i'))
-	thickness.long_name = "thickness" ;
-	thickness.units = "m" ;
-	thickness.checksum = "               0" ;
-
-	width=f.createVariable('width','d',('i'))
-	width.long_name = "width" ;
-	width.units = "m" ;
-	width.checksum = "               0" ;
-
-	length=f.createVariable('length','d',('i'))
-	length.long_name = "length" ;
-	length.units = "m" ;
-	length.checksum = "               0" ;
-
-	start_lon=f.createVariable('start_lon','d',('i'))
-	start_lon.long_name = "longitude of calving location" ;
-	start_lon.units = "degrees_E" ;
-	start_lon.checksum = "               0" ;
-
-	start_lat=f.createVariable('start_lat','d',('i'))
-	start_lat.long_name = "latitude of calving location" ;
-	start_lat.units = "degrees_N" ;
-	start_lat.checksum = "               0" ;
-
-	start_year=f.createVariable('start_year','i',('i'))
-	start_year.long_name = "calendar year of calving event" ;
-	start_year.units = "years" ;
-	start_year.packing = 0 ;
-	start_year.checksum = "               0" ;
-
-	iceberg_num=f.createVariable('iceberg_num','i',('i'))
-	iceberg_num.long_name = "identification of the iceberg" ;
-	iceberg_num.units = "dimensionless" ;
-	iceberg_num.packing = 0 ;
-	iceberg_num.checksum = "               0" ;
-
-	start_day=f.createVariable('start_day','d',('i'))
-	start_day.long_name = "year day of calving event" ;
-	start_day.units = "days" ;
-	start_day.checksum = "               0" ;
-
-	start_mass=f.createVariable('start_mass','d',('i'))
-	start_mass.long_name = "initial mass of calving berg" ;
-	start_mass.units = "kg" ;
-	start_mass.checksum = "               0" ;
-
-	mass_scaling=f.createVariable('mass_scaling','d',('i'))
-	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
-	mass_scaling.units = "none" ;
-	mass_scaling.checksum = "               0" ;
-
-	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
-	mass_of_bits.long_name = "mass of bergy bits" ;
-	mass_of_bits.units = "kg" ;
-	mass_of_bits.checksum = "               0" ;
-
-	heat_density=f.createVariable('heat_density','d',('i'))
-	heat_density.long_name = "heat density" ;
-	heat_density.units = "J/kg" ;
-	heat_density.checksum = "               0" ;
-
-	halo_berg=f.createVariable('halo_berg','d',('i'))
-	halo_berg.long_name = "halo_berg" ;
-	halo_berg.units = "dimensionless" ;
-	halo_berg.checksum = "               0" ;
-
-	static_berg=f.createVariable('static_berg','d',('i'))
-	static_berg.long_name = "static_berg" ;
-	static_berg.units = "dimensionless" ;
-	static_berg.checksum = "               0" ;
-
-	f.sync()
-	f.close()
-
-
-
-#-----------------------------------#
-#               Main                #
-#-----------------------------------#
-
-#ice params
-rho_ice=850
-
-#grid parameters (m)
-grdres=5000
-grdxmin=0; grdxmax=1000e3
-grdymin=0; grdymax=1000e3
-
-#--- berg locs: ---
-nbergs_x=10 #num of conglomerate bergs in x-dir
-nbergs_y=10 #num of conglomerate bergs in y-dir
-nbergs=nbergs_x*nbergs_y
-start=50e3; end=950e3; #m
-#center coords of each (rectangular) conglomerate berg (CB=conglomerate berg)
-CBxc=np.linspace(start,end,num=nbergs_x); CByc=np.linspace(start,end,num=nbergs_y)
-#CBxc=np.tile(CBxc,nbergs_y); CByc=np.tile(CByc,nbergs_x)
-CBxc,CByc=np.meshgrid(CBxc,CByc)
-CBxc=CBxc.flatten()
-CByc=CByc.flatten()
-
-#reduced version
-# mask = abs(500e3-CByc)
-# CBxc=CBxc[mask<100e3]
-# CByc=CByc[mask<100e3]
-# mask = abs(500e3-CBxc)
-# CBxc=CBxc[mask<300e3]
-# CByc=CByc[mask<300e3]
-# nbergs=len(CBxc)
-
-#reduced version 2
-#CBxc=CBxc[CByc<100e3]
-#CByc=CByc[CByc<100e3]
-#nbergs=len(CBxc)
-
-#--- Lehmer pseudo-random number generator params ---
-m=2147483647; a=16807l
-iv=a #first value
-
-#--- side lengths for the rectangular bergs ---
-m=2147483647; a=16807 #Lehmer pseudo-random number generator params
-rn=lrng(nbergs+1,m,a,iv) #the pseudo-random numbers
-minn=5e3; maxn=60e3 #bounds of side lengths, in m (diag should be < length of a processor)
-start=0; end=nbergs #slice of random number array with which to work
-CBxl=(maxn-minn)*rn[start:end]+minn #array of berg lengths in the x-dir, adjusted for bounds
-CByl=rn[start+1:end+1] #array of berg lengths in the y-dir
-CByl[CByl<0.33]=0.33 #keep the aspect ratio somewhat realistic
-CBxl=np.around(CBxl)
-CByl=CByl*CBxl
-CByl=np.around(CByl)
-CByl[CByl<minn]=minn
-CByl=CByl.astype(int); CBxl=CBxl.astype(int)
-#flip CBxl and CByl for half of them, so that CBxl is not always > CByl
-yl2=CByl.copy(); xl2=CBxl.copy()
-CByl[start:end:2]=xl2[start:end:2]; CBxl[start:end:2]=yl2[start:end:2]
-
-#--- xmax, xmin, ymax, ymin for each CB --
-CBxmin=CBxc-(0.5*CBxl); CBxmax=CBxc+(0.5*CBxl)
-CBymin=CByc-(0.5*CByl); CBymax=CByc+(0.5*CByl)
-#this shouldn't happen:
-CBxmin[CBxmin<grdxmin]=grdxmin; CBxmax[CBxmax>grdxmax]=grdxmax
-CBymin[CBxmin<grdymin]=grdymin; CBymax[CBymax>grdymax]=grdymax
-CBxc=0.5*(CBxmin+CBxmax); CByc=0.5*(CBymin+CBymax)
-
-#--- min and max thicknesses for each CB ---
-minn=50; maxn=350
-#minn=250; maxn=250
-iv=rn[-1]; rn=lrng(nbergs+1,m,a,iv)
-h1=(maxn-minn)*rn[start:end]+minn
-h2=(maxn-minn)*rn[start+1:end+1]+minn
-CBhmax=np.maximum(h1,h2); CBhmin=np.minimum(h1,h2)
-
-#--- berg element radii ---
-R_frac=0.45
-maxn=(np.sqrt(3)/2.)*(R_frac*grdres) #S is < 0.5 grid res
-minn=maxn/2 # smaller radii are allowed
-iv=rn[-1]; rn=lrng(nbergs+1,m,a,iv)
-CBrad=(maxn-minn)*rn[start:end]+minn
-
-print('maxn,minn',maxn,minn)
-
-#-- create berg elements for each conglomerate berg --
-# CBxc,CByc=center coords for each conglom berg
-# CByl,CBxl=side lengths for each conglom berg
-# CBhmax,CBhmin=max and min thicknesses on each berg
-# CBrad=radius of each berg element
-# CBnx,CBny=number of bergs in each dir
-# CBxmin,CBxmax,CBymin,CBymax
-
-berg_x=[]; berg_y=[]
-berg_id=[]; berg_static=[]
-berg_width=[]; berg_bonds=[]
-berg_h=[]; berg_mass_scaling=[]
-berg_mass=[]
-
-#berg_CBid=[];
-berg_count=0
-
-for i in range(nbergs):
-        x_start=CBxmin[i]+(CBrad[i]*2./np.sqrt(3))
-
-        #pdb.set_trace()
-        if x_start>CBxmax[i]:
-                x_start=CBxmax[i]
-        y_start0=CBymin[i]+CBrad[i]
-        if y_start0>CBymax[i]:
-                y_start0=CBymax[i]
-        element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*(CBrad[i])**2)
-        #H (thickness) is a linear function of a berg element's position from the
-        #center of the CB. H=Hmax at the center of the CB and H=Hmin at a corner of the
-        #CB, where the dist of a corner from the center is:
-        cdistb=np.sqrt((CBxmin[i]-CBxc[i])**2+(CBymin[i]-CByc[i])**2)
-        j=0
-        x_val=x_start
-        #berg_count_start=berg_count
-        while x_val<=CBxmax[i]:
-                y_start=y_start0+((j%2)*CBrad[i])
-                k=0
-                y_val=y_start
-                while y_val<CBymax[i]:
-                        berg_count=berg_count+1
-                        berg_id.append(berg_count)
-                        berg_x.append(x_val)
-                        berg_y.append(y_val)
-                        berg_width.append(sqrt(element_area))
-                        #dist of berg elem from center of CB
-                        bdistc=np.sqrt((x_val-CBxc[i])**2+(y_val-CByc[i])**2)
-                        bh=CBhmin[i]*bdistc/cdistb + CBhmax[i]*(1-bdistc/cdistb)
-                        berg_h.append(bh) #thickness
-                        berg_mass_scaling.append(1)
-                        berg_mass.append(bh*rho_ice*element_area)
-                        berg_static.append(0)
-                        #berg_CBid.append(i)
-                        k=k+1
-                        y_val=y_start+(2*k*CBrad[i])
-                j=j+1
-                x_val=x_start+(np.sqrt(3)*CBrad[i]*j)
-
-print('Number of bergs',berg_count)
-
-#pdb.set_trace()
-
-#Create iceberg restart file
-Ice_geometry_source='Generic'
-Create_iceberg_restart_file(berg_count,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static)
diff --git a/tests/collision_test/README b/tests/collision_test/README
deleted file mode 100644
index 83093c2..0000000
--- a/tests/collision_test/README
+++ /dev/null
@@ -1,5 +0,0 @@
-1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
-2.(optional) edit input.nml
-3. run the model: ./RUN
-4, animate the results: animate_trajectories.py
-
diff --git a/tests/collision_test/RUN b/tests/collision_test/RUN
deleted file mode 100755
index 090c034..0000000
--- a/tests/collision_test/RUN
+++ /dev/null
@@ -1,5 +0,0 @@
-rm iceberg_trajectories.nc
-rm iceberg_trajectories.nc.*
-srun -n4 ./../../build/bergs.x
-
-
diff --git a/tests/collision_test/RUN1p b/tests/collision_test/RUN1p
deleted file mode 100755
index c3bf53e..0000000
--- a/tests/collision_test/RUN1p
+++ /dev/null
@@ -1,5 +0,0 @@
-rm iceberg_trajectories.nc
-rm iceberg_trajectories.nc.*
-srun -n1 ./../../build/bergs.x
-
-
diff --git a/tests/collision_test/RUN_tstest.sh b/tests/collision_test/RUN_tstest.sh
deleted file mode 100755
index fe5f81c..0000000
--- a/tests/collision_test/RUN_tstest.sh
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/bin/bash
-
-rm iceberg_trajectories.nc
-
-space="s_"
-nc="c_.nc"
-r="./results/iceberg_trajectories_"
-
-s1='10' # 960' #'10 30 60 90'
-c1='1.e-5' # 1.e-4'
-
-for i in $s1
-do
-	for j in $c1
-	do
-	    	result="$r$i$space$j$nc"
-		echo $i
-		echo $j
-		echo $result
-
-		sed "s/<sec>/$i/; s/<coef>/$j/g" \
-		    input_tstest.nml > input.nml
-
-		srun -n4 ./../../build/bergs.x
-
-		mv iceberg_trajectories.nc $result
-	done
-done
-
-
-
-
-
diff --git a/tests/collision_test/animate_trajectories_1pe.py b/tests/collision_test/animate_trajectories_1pe.py
deleted file mode 100755
index 19db84d..0000000
--- a/tests/collision_test/animate_trajectories_1pe.py
+++ /dev/null
@@ -1,175 +0,0 @@
-#!/usr/bin/env python
-
-from netCDF4 import Dataset
-import pdb
-import netCDF4 as nc
-import numpy as np
-import matplotlib
-import math
-import os
-matplotlib.use("tkagg")
-from pylab import *
-import matplotlib.pyplot as plt
-from matplotlib.animation import FuncAnimation
-import argparse
-
-def parseCommandLine():
-    parser = argparse.ArgumentParser(description=
-    '''Generate animation of iceberg trajectories.''',
-    epilog='Written by Alex Huth, 2020')
-    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc.0000',
-                    help=''' provide filename to plot''')
-    optCmdLineArgs = parser.parse_args()
-    return optCmdLineArgs
-
-
-
-def main(args):
-    
-    print('reading file')
-
-    filename=args.fname
-    #filename = 'iceberg_trajectories.nc'
-    field = 'lon'
-    field2 = 'lat'
-
-    with nc.Dataset(filename) as file:
-        x = file.variables['lon'][:]/1.e3
-        y = file.variables['lat'][:]/1.e3
-        day = file.variables['day'][:]
-        hs = file.variables['halo_berg'][:]
-
-    #hs = hs+1
-    ud = np.unique(day)
-    t = ud[0]
-
-    print('unique hs',np.unique(hs))
-
-    # frame info
-    num_frames = len(ud)
-    movie_len = 5.0 #seconds
-    frame_len = 1000.0*movie_len/num_frames
-    
-    xmin = np.floor(min(min(x),min(y),-5))
-    xmax = np.ceil(max(max(x),max(y),25))
-    ymin = xmin
-    ymax = xmax
-
-    anim_running = True
-
-    def animate(i):
-
-        x1 = x[day == ud[i]]
-        y1 = y[day == ud[i]]
-        hstat = hs[day == ud[i]]
-        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
-
-        cstring=[]
-        for j in range(len(hstat)):
-            if (hstat[j]<0):
-                cstring.append("y")
-            elif (hstat[j]==0):                 
-                cstring.append("b")
-            elif (hstat[j]==1):
-                cstring.append("r")
-            elif (hstat[j]==2):
-                cstring.append("g")
-            elif (hstat[j]==3):
-                cstring.append("k")
-            elif (hstat[j]==4):
-                cstring.append("m")
-            else:
-                cstring.append("c")
-                                                           
-        scat.set_offsets(data)
-        scat.set_color(cstring)
-        scat.set_edgecolor('k')
-        
-        t = ud[i]
-        time_text.set_text('time = %.1f days' % t )        
-        return scat,time_text
-
-    def init():
-        scat.set_offsets([])
-        return scat,
-
-    def onClick(event):
-        global anim_running
-        if anim_running:
-            ani.event_source.stop()
-            anim_running = False
-        else:
-            ani.event_source.start()
-            anim_running = True       
-    
-    # Now we can do the plotting!
-    f = plt.figure(figsize=(5,5))
-    f.tight_layout()
-    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
-    scat = ax1.scatter([],[],marker='o',s=60) 
-    #scat = ax1.scatter([],[],marker='o',facecolor='w',s=60,edgecolor='red')
-    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
-
-    # Change major ticks to show every 20.
-    ax1.xaxis.set_major_locator(MultipleLocator(5))
-    ax1.yaxis.set_major_locator(MultipleLocator(5))
-
-    ax1.xaxis.set_minor_locator(MultipleLocator(1))
-    ax1.yaxis.set_minor_locator(MultipleLocator(1))
-
-    # Turn grid on for both major and minor ticks and style minor slightly
-    # differently.
-    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
-    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
-
-    ax1.set_xlabel('x (km)')
-    ax1.set_ylabel('y (km)')
-    ax1.set_title('Iceberg trajectory')
- 
-    f.canvas.mpl_connect('button_press_event', onClick)
-
-    ani = FuncAnimation(
-        f,animate,init_func=init,frames=num_frames,
-        interval=frame_len,blit=True,repeat=True)
-
-    print('time',t)
-
-    plt.plot([0,0],[0,20],'k-',lw=1)
-    plt.plot([10,10],[0,20],'k-',lw=1)
-    plt.plot([20,20],[0,20],'k-',lw=1)
-    plt.plot([0,0],[0,20],'k-',lw=1)
-    plt.plot([20,20],[0,20],'k-',lw=1)
-    plt.plot([0,0],[0,20],'k-',lw=1)
-    plt.plot([0,20],[10,10],'k-',lw=1)
-    plt.plot([0,20],[20,20],'k-',lw=1)
-    plt.plot([0,20],[0,0],'k-',lw=1)
-    plt.plot([0,20],[20,20],'k-',lw=1)
-
-    plt.plot([-2,-2],[-2,23],'b:',lw=1)
-    plt.plot([8,8],[-2,23],'b:',lw=1)
-    plt.plot([13,13],[-2,23],'b:',lw=1)
-    plt.plot([23,23],[-2,23],'b:',lw=1)
-    plt.plot([-2,23],[-2,-2],'b:',lw=1)
-    plt.plot([-2,23],[8,8],'b:',lw=1)
-    plt.plot([-2,23],[13,13],'b:',lw=1)
-    plt.plot([-2,23],[23,23],'b:',lw=1)      
- 
-    
-    plt.show()
-    #animation.save("iceberg_traj_animation.mp4")
-
-
-print('Script complete')
-
-if __name__ == '__main__':
-    optCmdLineArgs=	parseCommandLine()
-    anim_running = True
-    main(optCmdLineArgs)
-
-
-
-
-
-
-
-
diff --git a/tests/collision_test/diag_table b/tests/collision_test/diag_table
deleted file mode 100644
index c1c8819..0000000
--- a/tests/collision_test/diag_table
+++ /dev/null
@@ -1,3 +0,0 @@
-"icebergs test"
-1 1 1 0 0 0
-
diff --git a/tests/collision_test/input_tstest.nml b/tests/collision_test/input_tstest.nml
deleted file mode 100644
index 792b4f2..0000000
--- a/tests/collision_test/input_tstest.nml
+++ /dev/null
@@ -1,151 +0,0 @@
-&icebergs_driver_nml
-  ni=20 !number of elements, x direction
-  nj=20 !number of elements, y direction
-  ibdt=<sec>.0 !10.0 !seconds
-  ibuo=0.2 !ocean x velocity
-  ibvo=0.2 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=48 !total simulation hours
-  nmax=99999999 !max number of timesteps
-  saverestart=.false. 
-  halo=3
-  debug=.false.  
-  collision_test=.true. !specific to the current test, must be true here
-/
-
-
-&icebergs_nml
-
-    !defaults given in parentheses:
-    
-    !vectorized=.true. !(F) use vectorized version of the code
-    !mts=.false. !(F) use multiple timestepping scheme (substep size is automatically determined)
-
-    halo=3 !(4) halo width
-    Lx=20000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.True. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move    
-    
-    rho_bergs=850. ! (850) iceberg density
-    spring_coef=<coef> !1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs= 0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs =  1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0.4 !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #) 
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. ! (T) Allows bergs toroll over when rolling conditions are met    
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.False. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)    
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread			
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.False. !(F)Bergs only feel interactive forces, not ocean, wind...    
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val    
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors    
-
-    verbose=.true. !(F) Be verbose to stderr
-    verbose_hrs=1 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !(24) sampling period for trajectory storage
-    traj_write_hrs=1 ! (480) Period for writing sampled trajectories to disk    
-    budget=.true. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1 !12884902036 ! If positive, monitors a berg with this id    
-    
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.True. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.False. ! (F) If true, then model does not traj trajectory data at all    
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart 
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually    
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir = 'INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.    
-    do_unit_tests=.true. ! (F) Conduct some unit tests    
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-    
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-    
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-    
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-    
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
- 
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
\ No newline at end of file
diff --git a/tests/collision_test/makeberg/makeberg.py b/tests/collision_test/makeberg/makeberg.py
deleted file mode 100755
index 423b6a5..0000000
--- a/tests/collision_test/makeberg/makeberg.py
+++ /dev/null
@@ -1,77 +0,0 @@
-#!/usr/bin/env python
-
-from netCDF4 import Dataset  
-import numpy as np 
-import math
-#import os
-from pylab import *
-#import pdb
-import netCDF4 as nc
-
-nx = 20
-ny = 20
-New_ice_thickness_filename='testberg.nc'
-grid_res = 1.e3 #1 km 
-grid_area = grid_res * grid_res
-h_ice = 300.0
-
-New_ice_thickness_filename='testtabularberg.nc'
-g=Dataset(New_ice_thickness_filename,'w') # w if for creating a file
-
-g.createDimension('nx',nx)
-g.createDimension('ny',ny)
-thick_h=g.createVariable('thick','f8',('ny','nx'))
-area_h=g.createVariable('area','f8',('ny','nx'))
-lat_h=g.createVariable('lat','f8','ny')
-lon_h=g.createVariable('lon','f8','nx')
-#lat_h=g.createVariable('lat','f8',('ny','nx'))
-#lon_h=g.createVariable('lon','f8',('ny','nx'))
-
-thick_h.units = 'm'
-thick_h.standard_name = 'ice shelf thickness'
-area_h.units = 'm2'
-area_h.standard_name = 'ice shelf area'
-lon_h.unit = 'm'
-lon_h.standard_name = 'longitude'
-lat_h.unit = 'm'
-lat_h.standard_name = 'latitude'
-
-
-
-#g.variables['thick'][:]=h_ice
-g.variables['area'][:,:]=grid_area
-
-#create a circular tabular berg centered on the following coords (km)
-cy = 4.5e3
-cx = 4.5e3
-#cx2 = 15.5e3
-
-for i in range(nx):
-
-        tx = float(i) * grid_res 
-        g.variables['lon'][i] = tx
-        
-        for j in range(ny):
-               
-                ty = float(j) * grid_res 
-                dist = sqrt((tx-cx)*(tx-cx) + (ty-cy)*(ty-cy))
-                #dist2 =  sqrt((tx-cx2)*(tx-cx2) + (ty-cy)*(ty-cy))
-                #g.variables['lon'][i,j] = tx
-                #g.variables['lat'][i,j] = ty
-        
-                if (dist <1.e3): #or dist2<1.e3):
-                        g.variables['thick'][i,j]=h_ice
-                else:
-                        g.variables['thick'][i,j]=0.0
-
-                        
-
-for j in range(ny):
-        g.variables['lat'][j] = float(j) * grid_res 
-
-print('Creating file: ' , New_ice_thickness_filename)
-
-g.sync()
-g.close()
-
-        
diff --git a/tests/collision_test_mts/.gitignore b/tests/collision_test_mts/.gitignore
deleted file mode 100644
index 68bcbc9..0000000
--- a/tests/collision_test_mts/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-results/
\ No newline at end of file
diff --git a/tests/collision_test_mts/README b/tests/collision_test_mts/README
deleted file mode 100644
index 83093c2..0000000
--- a/tests/collision_test_mts/README
+++ /dev/null
@@ -1,5 +0,0 @@
-1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
-2.(optional) edit input.nml
-3. run the model: ./RUN
-4, animate the results: animate_trajectories.py
-
diff --git a/tests/collision_test_mts/RUN1p b/tests/collision_test_mts/RUN1p
deleted file mode 100755
index c3bf53e..0000000
--- a/tests/collision_test_mts/RUN1p
+++ /dev/null
@@ -1,5 +0,0 @@
-rm iceberg_trajectories.nc
-rm iceberg_trajectories.nc.*
-srun -n1 ./../../build/bergs.x
-
-
diff --git a/tests/collision_test_mts/RUN_tstest.sh b/tests/collision_test_mts/RUN_tstest.sh
deleted file mode 100755
index fe5f81c..0000000
--- a/tests/collision_test_mts/RUN_tstest.sh
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/bin/bash
-
-rm iceberg_trajectories.nc
-
-space="s_"
-nc="c_.nc"
-r="./results/iceberg_trajectories_"
-
-s1='10' # 960' #'10 30 60 90'
-c1='1.e-5' # 1.e-4'
-
-for i in $s1
-do
-	for j in $c1
-	do
-	    	result="$r$i$space$j$nc"
-		echo $i
-		echo $j
-		echo $result
-
-		sed "s/<sec>/$i/; s/<coef>/$j/g" \
-		    input_tstest.nml > input.nml
-
-		srun -n4 ./../../build/bergs.x
-
-		mv iceberg_trajectories.nc $result
-	done
-done
-
-
-
-
-
diff --git a/tests/collision_test_mts/animate_trajectories.py b/tests/collision_test_mts/animate_trajectories.py
deleted file mode 100755
index 50831d8..0000000
--- a/tests/collision_test_mts/animate_trajectories.py
+++ /dev/null
@@ -1,121 +0,0 @@
-#!/usr/bin/env python
-
-from netCDF4 import Dataset
-import pdb
-import netCDF4 as nc
-import numpy as np
-import matplotlib
-import math
-import os
-matplotlib.use("tkagg")
-from pylab import *
-import matplotlib.pyplot as plt
-from matplotlib.animation import FuncAnimation
-import argparse
-
-def parseCommandLine():
-    parser = argparse.ArgumentParser(description=
-    '''Generate animation of iceberg trajectories.''',
-    epilog='Written by Alex Huth, 2020')
-    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
-                    help=''' provide filename to plot''')
-    optCmdLineArgs = parser.parse_args()
-    return optCmdLineArgs
-
-
-
-def main(args):
-
-    print('reading file')
-
-    filename=args.fname
-    #filename = 'iceberg_trajectories.nc'
-    field = 'lon'
-    field2 = 'lat'
-
-    with nc.Dataset(filename) as file:
-        x = file.variables['lon'][:]/1.e3
-        y = file.variables['lat'][:]/1.e3
-        day = file.variables['day'][:]
-
-    ud = np.unique(day)
-    t = ud[0]
-
-    # frame info
-    num_frames = len(ud)
-    movie_len = 5.0 #seconds
-    frame_len = 1000.0*movie_len/num_frames
-
-    xmin = 0 #np.floor(min(min(x),min(y),0))
-    xmax = 20 #np.ceil(max(max(x),max(y),20))
-    ymin = xmin
-    ymax = xmax
-
-    anim_running = True
-
-    def animate(i):
-
-        x1 = x[day == ud[i]]
-        y1 = y[day == ud[i]]
-        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
-
-        scat.set_offsets(data)
-
-        t = ud[i]
-        time_text.set_text('time = %.1f days' % t )
-        return scat,time_text
-
-    def init():
-        scat.set_offsets([])
-        return scat,
-
-    def onClick(event):
-        global anim_running
-        if anim_running:
-            ani.event_source.stop()
-            anim_running = False
-        else:
-            ani.event_source.start()
-            anim_running = True
-
-    # Now we can do the plotting!
-    f = plt.figure(figsize=(5,5))
-    f.tight_layout()
-    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
-    scat = ax1.scatter([],[],marker='o',facecolor='w',s=100,edgecolor='red')
-    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
-
-    # Change major ticks to show every 20.
-    ax1.xaxis.set_major_locator(MultipleLocator(5))
-    ax1.yaxis.set_major_locator(MultipleLocator(5))
-
-    ax1.xaxis.set_minor_locator(MultipleLocator(1))
-    ax1.yaxis.set_minor_locator(MultipleLocator(1))
-
-    # Turn grid on for both major and minor ticks and style minor slightly
-    # differently.
-    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
-    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
-
-    ax1.set_xlabel('x (km)')
-    ax1.set_ylabel('y (km)')
-    ax1.set_title('Iceberg trajectory')
-
-    f.canvas.mpl_connect('button_press_event', onClick)
-
-    ani = FuncAnimation(
-        f,animate,init_func=init,frames=num_frames,
-        interval=frame_len,blit=True,repeat=True)
-
-    print('time',t)
-
-    plt.show()
-    #animation.save("iceberg_traj_animation.mp4")
-
-
-print('Script complete')
-
-if __name__ == '__main__':
-    optCmdLineArgs=	parseCommandLine()
-    anim_running = True
-    main(optCmdLineArgs)
diff --git a/tests/collision_test_mts/animate_trajectories_1pe.py b/tests/collision_test_mts/animate_trajectories_1pe.py
deleted file mode 100755
index c3839d0..0000000
--- a/tests/collision_test_mts/animate_trajectories_1pe.py
+++ /dev/null
@@ -1,175 +0,0 @@
-#!/usr/bin/env python
-
-from netCDF4 import Dataset
-import pdb
-import netCDF4 as nc
-import numpy as np
-import matplotlib
-import math
-import os
-matplotlib.use("tkagg")
-from pylab import *
-import matplotlib.pyplot as plt
-from matplotlib.animation import FuncAnimation
-import argparse
-
-def parseCommandLine():
-    parser = argparse.ArgumentParser(description=
-    '''Generate animation of iceberg trajectories.''',
-    epilog='Written by Alex Huth, 2020')
-    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc.0000',
-                    help=''' provide filename to plot''')
-    optCmdLineArgs = parser.parse_args()
-    return optCmdLineArgs
-
-
-
-def main(args):
-    
-    print('reading file')
-
-    filename=args.fname
-    #filename = 'iceberg_trajectories.nc'
-    field = 'lon'
-    field2 = 'lat'
-
-    with nc.Dataset(filename) as file:
-        x = file.variables['lon'][:]/1.e3
-        y = file.variables['lat'][:]/1.e3
-        day = file.variables['day'][:]
-        hs = file.variables['halo_berg'][:]
-
-    #hs = hs+1
-    ud = np.unique(day)
-    t = ud[0]
-
-    print('unique hs',np.unique(hs))
-
-    # frame info
-    num_frames = len(ud)
-    movie_len = 5.0 #seconds
-    frame_len = 1000.0*movie_len/num_frames
-    
-    xmin = np.floor(min(min(x),min(y),-5))
-    xmax = np.ceil(max(max(x),max(y),25))
-    ymin = xmin
-    ymax = xmax
-
-    anim_running = True
-
-    def animate(i):
-
-        x1 = x[day == ud[i]]
-        y1 = y[day == ud[i]]
-        hstat = hs[day == ud[i]]
-        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
-
-        cstring=[]
-        for j in range(len(hstat)):
-            if (hstat[j]<0):
-                cstring.append("m")
-            elif (hstat[j]==0):                 
-                cstring.append("b")
-            elif (hstat[j]==1):
-                cstring.append("r")
-            elif (hstat[j]==2):
-                cstring.append("g")
-            elif (hstat[j]==3):
-                cstring.append("k")
-            elif (hstat[j]==10):
-                cstring.append("c")
-            else:
-                cstring.append("y")
-                                                           
-        scat.set_offsets(data)
-        scat.set_color(cstring)
-        scat.set_edgecolor('k')
-        
-        t = ud[i]
-        time_text.set_text('time = %.1f days' % t )        
-        return scat,time_text
-
-    def init():
-        scat.set_offsets([])
-        return scat,
-
-    def onClick(event):
-        global anim_running
-        if anim_running:
-            ani.event_source.stop()
-            anim_running = False
-        else:
-            ani.event_source.start()
-            anim_running = True       
-    
-    # Now we can do the plotting!
-    f = plt.figure(figsize=(5,5))
-    f.tight_layout()
-    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
-    scat = ax1.scatter([],[],marker='o',s=60) 
-    #scat = ax1.scatter([],[],marker='o',facecolor='w',s=60,edgecolor='red')
-    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
-
-    # Change major ticks to show every 20.
-    ax1.xaxis.set_major_locator(MultipleLocator(5))
-    ax1.yaxis.set_major_locator(MultipleLocator(5))
-
-    ax1.xaxis.set_minor_locator(MultipleLocator(1))
-    ax1.yaxis.set_minor_locator(MultipleLocator(1))
-
-    # Turn grid on for both major and minor ticks and style minor slightly
-    # differently.
-    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
-    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
-
-    ax1.set_xlabel('x (km)')
-    ax1.set_ylabel('y (km)')
-    ax1.set_title('Iceberg trajectory')
- 
-    f.canvas.mpl_connect('button_press_event', onClick)
-
-    ani = FuncAnimation(
-        f,animate,init_func=init,frames=num_frames,
-        interval=frame_len,blit=True,repeat=True)
-
-    print('time',t)
-
-    plt.plot([0,0],[0,20],'k-',lw=1)
-    plt.plot([10,10],[0,20],'k-',lw=1)
-    plt.plot([20,20],[0,20],'k-',lw=1)
-    plt.plot([0,0],[0,20],'k-',lw=1)
-    plt.plot([20,20],[0,20],'k-',lw=1)
-    plt.plot([0,0],[0,20],'k-',lw=1)
-    plt.plot([0,20],[10,10],'k-',lw=1)
-    plt.plot([0,20],[20,20],'k-',lw=1)
-    plt.plot([0,20],[0,0],'k-',lw=1)
-    plt.plot([0,20],[20,20],'k-',lw=1)
-
-    plt.plot([-2,-2],[-2,23],'b:',lw=1)
-    plt.plot([8,8],[-2,23],'b:',lw=1)
-    plt.plot([13,13],[-2,23],'b:',lw=1)
-    plt.plot([23,23],[-2,23],'b:',lw=1)
-    plt.plot([-2,23],[-2,-2],'b:',lw=1)
-    plt.plot([-2,23],[8,8],'b:',lw=1)
-    plt.plot([-2,23],[13,13],'b:',lw=1)
-    plt.plot([-2,23],[23,23],'b:',lw=1)      
- 
-    
-    plt.show()
-    #animation.save("iceberg_traj_animation.mp4")
-
-
-print('Script complete')
-
-if __name__ == '__main__':
-    optCmdLineArgs=	parseCommandLine()
-    anim_running = True
-    main(optCmdLineArgs)
-
-
-
-
-
-
-
-
diff --git a/tests/collision_test_mts/diag_table b/tests/collision_test_mts/diag_table
deleted file mode 100644
index c1c8819..0000000
--- a/tests/collision_test_mts/diag_table
+++ /dev/null
@@ -1,3 +0,0 @@
-"icebergs test"
-1 1 1 0 0 0
-
diff --git a/tests/collision_test_mts/input_tstest.nml b/tests/collision_test_mts/input_tstest.nml
deleted file mode 100644
index bd13bd4..0000000
--- a/tests/collision_test_mts/input_tstest.nml
+++ /dev/null
@@ -1,159 +0,0 @@
-!TARGET CHKSUM:
-!Total number of bonds is:           52 
-!KID, bergs_chksum: write_restart berg chksum = 892128108  chksum2= -515180265  chksum3= 1707263945  chksum4= 1707263945  chksum5 = 0           #= 16
-!KID, grd_chksum2 : # of bergs/cell chksum    = 0          chksum2= 0           min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
-!KID, grd_chksum3 : write stored_ice chksum   = -540079793 chksum2= -1237287029 min= 6.393358811E+05 max= 7.380127765E+11 mean= 8.033602570E+10 rms= 1.613270384E+11 sd= 1.399018810E+11
-!KID, grd_chksum2 : write stored_heat chksum  = 0          chksum2= 0           min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
-
-
-&icebergs_driver_nml
-  ni=20 !number of elements, x direction
-  nj=20 !number of elements, y direction
-  ibdt=<sec>.0 !10.0 !seconds
-  ibuo=0.2 !ocean x velocity
-  ibvo=0.2 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=48 !total simulation hours
-  nmax=99999999 !max number of timesteps
-  saverestart=.false. 
-  halo=3
-  debug=.false.  
-  collision_test=.true. !specific to the current test, must be true here
-/
-
-
-&icebergs_nml
-
-    !defaults given in parentheses:
-    
-    !vectorized=.true. !(F) use vectorized version of the code
-    !mts=.false. !(F) use multiple timestepping scheme (substep size is automatically determined)
-
-    halo=3 !(4) halo width
-    Lx=20000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.True. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move    
-    
-    rho_bergs=850. ! (850) iceberg density
-    spring_coef=<coef> !1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs= 0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs =  1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0.4 !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #) 
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. ! (T) Allows bergs toroll over when rolling conditions are met    
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.False. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)    
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread			
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.False. !(F)Bergs only feel interactive forces, not ocean, wind...    
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val    
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors    
-
-    verbose=.true. !(F) Be verbose to stderr
-    verbose_hrs=1 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !(24) sampling period for trajectory storage
-    traj_write_hrs=1 ! (480) Period for writing sampled trajectories to disk    
-    budget=.true. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1 !12884902036 ! If positive, monitors a berg with this id    
-    
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.True. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.False. ! (F) If true, then model does not traj trajectory data at all    
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart 
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually    
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir = 'INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.    
-    do_unit_tests=.true. ! (F) Conduct some unit tests    
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-    
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-    
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-    
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-    
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
- 
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
\ No newline at end of file
diff --git a/tests/collision_test_mts/makeberg/RUN b/tests/collision_test_mts/makeberg/RUN
deleted file mode 100755
index ae7808f..0000000
--- a/tests/collision_test_mts/makeberg/RUN
+++ /dev/null
@@ -1,12 +0,0 @@
-./makeberg.py
-
-rm ./output_files/Generic*
-
-./../../Iceberg_repository/Scripts_and_analysis/initialize_bergs_in_pattern.py \
-	-set_all_bergs_static_by_default=False -Run_plotting_subroutine=False \
-	-break_some_bonds=False -Ice_geometry_source='Generic' \
-	-Generic_ice_geometry_filename='./testtabularberg.nc' \
-	-ISOMIP_reduced=False -collision_test=True
-
-cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
-cp ./output_files/Generic_bonds_iceberg.res.nc ./../INPUT/bonds_iceberg.res.nc
\ No newline at end of file
diff --git a/tests/collision_test_mts/makeberg/makeberg.py b/tests/collision_test_mts/makeberg/makeberg.py
deleted file mode 100755
index 423b6a5..0000000
--- a/tests/collision_test_mts/makeberg/makeberg.py
+++ /dev/null
@@ -1,77 +0,0 @@
-#!/usr/bin/env python
-
-from netCDF4 import Dataset  
-import numpy as np 
-import math
-#import os
-from pylab import *
-#import pdb
-import netCDF4 as nc
-
-nx = 20
-ny = 20
-New_ice_thickness_filename='testberg.nc'
-grid_res = 1.e3 #1 km 
-grid_area = grid_res * grid_res
-h_ice = 300.0
-
-New_ice_thickness_filename='testtabularberg.nc'
-g=Dataset(New_ice_thickness_filename,'w') # w if for creating a file
-
-g.createDimension('nx',nx)
-g.createDimension('ny',ny)
-thick_h=g.createVariable('thick','f8',('ny','nx'))
-area_h=g.createVariable('area','f8',('ny','nx'))
-lat_h=g.createVariable('lat','f8','ny')
-lon_h=g.createVariable('lon','f8','nx')
-#lat_h=g.createVariable('lat','f8',('ny','nx'))
-#lon_h=g.createVariable('lon','f8',('ny','nx'))
-
-thick_h.units = 'm'
-thick_h.standard_name = 'ice shelf thickness'
-area_h.units = 'm2'
-area_h.standard_name = 'ice shelf area'
-lon_h.unit = 'm'
-lon_h.standard_name = 'longitude'
-lat_h.unit = 'm'
-lat_h.standard_name = 'latitude'
-
-
-
-#g.variables['thick'][:]=h_ice
-g.variables['area'][:,:]=grid_area
-
-#create a circular tabular berg centered on the following coords (km)
-cy = 4.5e3
-cx = 4.5e3
-#cx2 = 15.5e3
-
-for i in range(nx):
-
-        tx = float(i) * grid_res 
-        g.variables['lon'][i] = tx
-        
-        for j in range(ny):
-               
-                ty = float(j) * grid_res 
-                dist = sqrt((tx-cx)*(tx-cx) + (ty-cy)*(ty-cy))
-                #dist2 =  sqrt((tx-cx2)*(tx-cx2) + (ty-cy)*(ty-cy))
-                #g.variables['lon'][i,j] = tx
-                #g.variables['lat'][i,j] = ty
-        
-                if (dist <1.e3): #or dist2<1.e3):
-                        g.variables['thick'][i,j]=h_ice
-                else:
-                        g.variables['thick'][i,j]=0.0
-
-                        
-
-for j in range(ny):
-        g.variables['lat'][j] = float(j) * grid_res 
-
-print('Creating file: ' , New_ice_thickness_filename)
-
-g.sync()
-g.close()
-
-        
diff --git a/tests/collision_test/.gitignore b/tests/collision_tests/.gitignore
similarity index 100%
rename from tests/collision_test/.gitignore
rename to tests/collision_tests/.gitignore
diff --git a/tests/collision_tests/README b/tests/collision_tests/README
new file mode 100644
index 0000000..aa826d5
--- /dev/null
+++ b/tests/collision_tests/README
@@ -0,0 +1,22 @@
+Model the contact between two bonded-particle iceberg conglomerates using the original "KID" scheme (Stern et al, 2017), the "MTS-KID" multiple-timestepping scheme (without angular momentum terms), or the "iKID" discrete-element-style scheme (Huth et al, 2022; MTS-KID with angular momentum terms).
+
+1. Make the iceberg input files: cd makeberg; ./RUN; cd ..
+2. run the model: ./RUN_KID or ./RUN_MTS_KID or ./RUN_iKID
+3. animate the results:
+./animate_trajectories.py -fname="KID.nc"
+or
+./animate_trajectories.py -fname="MTS_KID.nc"
+or
+./animate_trajectories.py -fname="iKID.nc"
+
+!!for regression testing:
+Note the "write_restart berg" chksums in each of the .nml files that are called by the model run commands, and also printed below:
+
+KID:
+chksum = -1211104969 chksum2= -1211104969 chksum3= 1964715299  chksum4= 1964715299  chksum5= 0#= 16
+
+MTS_KID:
+chksum=-1441819690 chksum2=-1441819690 chksum3=1124700946 chksum4=1124700946 chksum5=0 #=16
+
+iKID:
+chksum=1560193269 chksum2=-1064844053 chksum3=-1070230468 chksum4=-1070230468 chksum5=0 #=16
diff --git a/tests/collision_test_mts/RUN b/tests/collision_tests/RUN_KID
similarity index 76%
rename from tests/collision_test_mts/RUN
rename to tests/collision_tests/RUN_KID
index 090c034..bd8f615 100755
--- a/tests/collision_test_mts/RUN
+++ b/tests/collision_tests/RUN_KID
@@ -1,5 +1,6 @@
 rm iceberg_trajectories.nc
 rm iceberg_trajectories.nc.*
+cp input_KID.nml input.nml
 srun -n4 ./../../build/bergs.x
 
 
diff --git a/tests/footloose_physical/RUN b/tests/collision_tests/RUN_MTS_KID
similarity index 74%
rename from tests/footloose_physical/RUN
rename to tests/collision_tests/RUN_MTS_KID
index 090c034..c797f65 100755
--- a/tests/footloose_physical/RUN
+++ b/tests/collision_tests/RUN_MTS_KID
@@ -1,5 +1,6 @@
 rm iceberg_trajectories.nc
 rm iceberg_trajectories.nc.*
+cp input_MTS_KID.nml input.nml
 srun -n4 ./../../build/bergs.x
 
 
diff --git a/tests/2p_collision_test/RUN b/tests/collision_tests/RUN_iKID
similarity index 76%
rename from tests/2p_collision_test/RUN
rename to tests/collision_tests/RUN_iKID
index 090c034..b617edb 100755
--- a/tests/2p_collision_test/RUN
+++ b/tests/collision_tests/RUN_iKID
@@ -1,5 +1,6 @@
 rm iceberg_trajectories.nc
 rm iceberg_trajectories.nc.*
+cp input_iKID.nml input.nml
 srun -n4 ./../../build/bergs.x
 
 
diff --git a/tests/collision_test/animate_trajectories.py b/tests/collision_tests/animate_trajectories.py
similarity index 100%
rename from tests/collision_test/animate_trajectories.py
rename to tests/collision_tests/animate_trajectories.py
diff --git a/tests/2p_collision_test/animate_trajectories_1pe.py b/tests/collision_tests/animate_trajectories_1pe.py
similarity index 100%
rename from tests/2p_collision_test/animate_trajectories_1pe.py
rename to tests/collision_tests/animate_trajectories_1pe.py
diff --git a/tests/2p_collision_test/diag_table b/tests/collision_tests/diag_table
similarity index 100%
rename from tests/2p_collision_test/diag_table
rename to tests/collision_tests/diag_table
diff --git a/tests/collision_test/input.nml b/tests/collision_tests/input_KID.nml
similarity index 83%
rename from tests/collision_test/input.nml
rename to tests/collision_tests/input_KID.nml
index 98b0b11..328c2cd 100644
--- a/tests/collision_test/input.nml
+++ b/tests/collision_tests/input_KID.nml
@@ -1,10 +1,4 @@
-!TARGET CHKSUM (60 s time increments, non-MTS):
-!Total number of bonds is:           52 
-!KID, bergs_chksum: write_restart berg chksum = -1211104969 chksum2= -1211104969 chksum3= 1964715299  chksum4= 1964715299  chksum5= 0            #= 16
-!KID, grd_chksum2 : # of bergs/cell chksum    = 0           chksum2= 0           min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
-!KID, grd_chksum3 : write stored_ice chksum   = -540079793  chksum2= -1237287029 min= 6.393358811E+05 max= 7.380127765E+11 mean= 8.033602570E+10 rms= 1.613270384E+11 sd= 1.399018810E+11
-!KID, grd_chksum2 : write stored_heat chksum  = 0           chksum2= 0           min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
-
+!!KID, bergs_chksum: write_restart berg chksum = -1211104969 chksum2= -1211104969 chksum3= 1964715299  chksum4= 1964715299  chksum5= 0#= 16
 
 &icebergs_driver_nml
   ni=20 !number of elements, x direction
@@ -16,34 +10,41 @@
   ibvi=0.0 !ice y velocity
   ibhrs=48 !total simulation hours
   nmax=99999999 !max number of timesteps
-  saverestart=.true. 
+  saverestart=.true.
   halo=3
-  debug=.false.   
+  debug=.false.
   collision_test=.true. !specific to the current test, must be true here
 /
 
 
 &icebergs_nml
 
+    traj_name=KID.nc
+    bond_traj_name=KID_bonds.nc
+
     !defaults given in parentheses:
-    !mts=.false. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    !mts_sub_steps=0 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
-    !contact_distance=0 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    !contact_spring_coef=1.e-5!(default=spring_coeff) Berg spring coeff for collisions    
+    ! explicit_inner_mts=.true.
+    ! new_mts=.true.
+    ! mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    ! mts_sub_steps=60 !1 !30 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
+    ! contact_distance=1.75e3 !2.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    ! contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    ! debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    ! remove_unused_bergs=.false. !(T) remove unneeded bergs after PEs transfers
 
     halo=3 !(4) halo width
     Lx=20000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
     grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
     grid_is_regular=.True. !(T) Point in cell can be found assuming regular Cartesian grid
     hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move    
-    
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
     rho_bergs=850. ! (850) iceberg density
     spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
     bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
     radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
     tangental_damping_coef=2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val 
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
     LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
     bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
     sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
@@ -66,11 +67,11 @@
     coastal_drift=0.4 !(0.)Vel added to currents to cause bergs to drift away from land cells
     tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
     Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #) 
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
     apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
     apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
     melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. ! (T) Allows bergs toroll over when rolling conditions are met    
+    allow_bergs_to_roll=.true. ! (T) Allows bergs toroll over when rolling conditions are met
     use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
     pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
     use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
@@ -81,45 +82,45 @@
     add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
     override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
     use_f_plane=.False. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)    
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread			
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
     set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
 
     iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
     interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...       
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
     use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
     input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
     use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors    
+    max_bonds=6 ! (6) Max # of bonds passed between processors
 
     verbose=.true. !(F) Be verbose to stderr
     verbose_hrs=1 ! (24) Period between verbose messages
     traj_sample_hrs=1 !1 !(24) sampling period for trajectory storage
-    traj_write_hrs=6 ! (480) Period for writing sampled trajectories to disk    
+    traj_write_hrs=6 ! (480) Period for writing sampled trajectories to disk
     budget=.true. !(T) Calculate budgets
     debug=.false. !(F) Turn on debugging
     really_debug=.false. !(F) Turn on debugging
     halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id    
-    
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
     parallel_reprod=.true. !(T) Reproduce across different PE decompositions
     save_short_traj=.true. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.False. ! (F) If true, then model does not track trajectory data at all    
+    ignore_traj=.False. ! (F) If true, then model does not track trajectory data at all
 
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart 
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
     require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
     use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
     manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually    
+    length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
     ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
     generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
     fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
     restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.      
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
     orig_read=.false. !(F) Legacy option that does nothing
     read_old_restarts=.false. ! (F) Legacy option that does nothing
-    
+
     use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
     old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
     make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
@@ -130,15 +131,15 @@
     ! Mass thresholds between iceberg classes (kg):
     !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
     initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-    
+
     ! Fraction of calving to apply to this class (non-dim):
     !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
     distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-    
+
     ! Ratio between effective and real iceberg mass (non-dim):
     !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
     mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-    
+
     ! Total thickness of newly calved bergs (m):
     !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
     initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
@@ -152,7 +153,7 @@
          fms_netcdf_restart=.false.
          threading_read='multi'
 /
- 
+
  &fms_nml
        clock_grain='MODULE'
        domains_stack_size = 2000000
diff --git a/tests/chaotic_test/input.nml b/tests/collision_tests/input_MTS_KID.nml
similarity index 79%
rename from tests/chaotic_test/input.nml
rename to tests/collision_tests/input_MTS_KID.nml
index bcde5cb..1fedaf8 100644
--- a/tests/chaotic_test/input.nml
+++ b/tests/collision_tests/input_MTS_KID.nml
@@ -1,40 +1,42 @@
-!KID, bergs_chksum: write_restart berg chksum=            1999445081 chksum2=           -1410727016 chksum3=             622127949 chksum4=             622127949 chksum5=            2101409293 #=                 11795
-!KID, grd_chksum2:    # of bergs/cell chksum=                     0 chksum2=                     0 min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
-! All iceberg bonds are connected and working well
-!KID, write_restart: writing calving.res.nc                     
-!KID, grd_chksum3:   write stored_ice chksum=             879111700 chksum2=           -1289231459 min= 0.000000000E+00 max= 7.399978449E+11 mean= 7.819993372E+10 rms= 1.579219025E+11 sd= 1.372009390E+11
+!!KID, bergs_chksum: write_restart berg chksum=-1441819690 chksum2=-1441819690 chksum3=1124700946 chksum4=1124700946 chksum5=0 #=16
 
 &icebergs_driver_nml
-  ni=200 !number of elements, x direction
-  nj=200 !number of elements, y direction
-  ibdt=1800.0 !seconds
+  ni=20 !number of elements, x direction
+  nj=20 !number of elements, y direction
+  ibdt=3600.0 !seconds
   ibuo=0.2 !ocean x velocity
   ibvo=0.2 !ocean y velocity
   ibui=0.0 !ice x velocity
   ibvi=0.0 !ice y velocity
-  ibhrs=1460 !~2 months !8760!1 year !total simulation hours
+  ibhrs=48 !total simulation hours
   nmax=99999999 !max number of timesteps
   saverestart=.true.
   halo=3
-  debug=.true.
-  collision_test=.false.
-  chaotic_test=.true.
-  gridres=5.e3
+  debug=.false.
+  collision_test=.true. !specific to the current test, must be true here
 /
 
 &icebergs_nml
 
+    traj_name=MTS_KID.nc
+    bond_traj_name=MTS_KID_bonds.nc
+
     !defaults given in parentheses:
+    explicit_inner_mts=.true.
+    new_mts=.true.
     mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=40 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
-    contact_distance=8.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7 !(default=spring_coeff) Berg spring coeff for collisions
+    mts_sub_steps=60 !1 !30 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
+    contact_distance=1.75e3 !2.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
     debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    remove_unused_bergs=.false. !(T) remove unneeded bergs after PEs transfers
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
 
     halo=3 !(4) halo width
-    Lx=1000.e3 ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    Lx=20000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
     grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
+    grid_is_regular=.True. !(T) Point in cell can be found assuming regular Cartesian grid
     hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
     Static_icebergs=.False. ! (T) True=icebergs do no move
 
@@ -63,7 +65,7 @@
     tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
     tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
     grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=2.0 !0.4 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    coastal_drift=0.4 !(0.)Vel added to currents to cause bergs to drift away from land cells
     tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
     Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
     use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
@@ -92,13 +94,12 @@
     input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
     use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
     max_bonds=6 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.false. !(F) True reduces side drag for bonded bergs in momentum eqn.    
+    internal_bergs_for_drag=.false. !(F) True reduces side drag for bonded bergs in momentum eqn.
 
     verbose=.true. !(F) Be verbose to stderr
     verbose_hrs=24 ! (24) Period between verbose messages
-    traj_sample_hrs=24 !.5 !1 !(24) sampling period for trajectory storage
-    traj_write_hrs=24 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.true.
+    traj_sample_hrs=0.5 !1 !(24) sampling period for trajectory storage
+    traj_write_hrs=-1 ! (480) Period for writing sampled trajectories to disk
     budget=.true. !(T) Calculate budgets
     debug=.false. !(F) Turn on debugging
     really_debug=.false. !(F) Turn on debugging
@@ -108,14 +109,12 @@
     parallel_reprod=.true. !(T) Reproduce across different PE decompositions
     save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
     ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
 
     ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
     require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
     use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
     manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.!(F) Init bond b/w bergs if dist<1.25*radius
-    length_for_manually_initialize_bonds=0.0 !(1e3)Dist b/w bergs to init bonds manually
+    length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
     ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
     generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
     fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
@@ -129,6 +128,7 @@
     make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
     old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
     do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
 
     ! Mass thresholds between iceberg classes (kg):
     !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
@@ -152,12 +152,12 @@
 /
 
  &fms_io_nml
-       fms_netcdf_restart=.false.
-       threading_read='multi'
+         fms_netcdf_restart=.false.
+         threading_read='multi'
 /
 
  &fms_nml
-       clock_grain='MODULE' !'ROUTINE'
-       domains_stack_size = 200000
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
        clock_flags='SYNC'
 /
diff --git a/tests/collision_test_mts/input.nml b/tests/collision_tests/input_iKID.nml
similarity index 88%
rename from tests/collision_test_mts/input.nml
rename to tests/collision_tests/input_iKID.nml
index d844dea..3393971 100644
--- a/tests/collision_test_mts/input.nml
+++ b/tests/collision_tests/input_iKID.nml
@@ -1,11 +1,4 @@
-!chksum different than below after setting uvel0=u_star at start of accel_mts for bergs%MTS_part==1
-
-!TARGET CHKSUM (1 hr time increments, MTS w/ 20 sub-steps, contact at 1.5e3 m, contact spring 1.e-7, spring_coef 1.0e-5):
-!Total number of bonds is:           52
-!KID, bergs_chksum: write_restart berg chksum = -1984749888 chksum2= 2128479089 chksum3= 609798238  chksum4= 609798238  chksum5= 0            #= 16
-!KID, grd_chksum2 : # of bergs/cell chksum    = 0           chksum2= 0           min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
-!KID, grd_chksum3 : write stored_ice chksum   = -540079793  chksum2= -1237287029 min= 6.393358811E+05 max= 7.380127765E+11 mean= 8.033602570E+10 rms= 1.613270384E+11 sd= 1.399018810E+11
-!KID, grd_chksum2 : write stored_heat chksum  = 0           chksum2= 0           min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
+!!KID, bergs_chksum: write_restart berg chksum=1560193269 chksum2=-1064844053 chksum3=-1070230468 chksum4=-1070230468 chksum5=0 #=16
 
 
 &icebergs_driver_nml
@@ -26,14 +19,30 @@
 
 &icebergs_nml
 
+    traj_name=iKID.nc
+    bond_traj_name=iKID_bonds.nc
+
     !defaults given in parentheses:
-    new_mts=.false.
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5. A=L*W always works?
+    dem_spring_coef=4471.94
+    spring_coef=1.e-5 !if dem_spring_coef=5e6, r=1500, and hex pack?
+
+    explicit_inner_mts=.true.
+    new_mts=.true.
     mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=20 !1 !30 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
-    contact_distance=1.5e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    mts_sub_steps=60 !1 !30 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
+    contact_distance=1.75e3 !2.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
     contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
     debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
     remove_unused_bergs=.false. !(T) remove unneeded bergs after PEs transfers
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
 
     halo=3 !(4) halo width
     Lx=20000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
diff --git a/tests/collision_test/makeberg/RUN b/tests/collision_tests/makeberg/RUN
similarity index 100%
rename from tests/collision_test/makeberg/RUN
rename to tests/collision_tests/makeberg/RUN
diff --git a/tests/2p_collision_test/makeberg/makeberg.py b/tests/collision_tests/makeberg/makeberg.py
similarity index 100%
rename from tests/2p_collision_test/makeberg/makeberg.py
rename to tests/collision_tests/makeberg/makeberg.py
diff --git a/tests/dem_test_contact/.gitignore b/tests/dem_test_contact/.gitignore
deleted file mode 100644
index 68bcbc9..0000000
--- a/tests/dem_test_contact/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-results/
\ No newline at end of file
diff --git a/tests/dem_test_contact/README b/tests/dem_test_contact/README
deleted file mode 100644
index ec575a8..0000000
--- a/tests/dem_test_contact/README
+++ /dev/null
@@ -1,7 +0,0 @@
-1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
-2.(optional) edit input.nml
-3. run the model: ./RUN
-4, animate the results: animate_trajectories.py
-
-This is a good test for visualizing fracture dependence on particle size. Try running makeberg.py with the full radius and then half the radius, and with regular vs dem nmls. Make sure to edit the nmls so that contact distance is halved when radius is halved
-
diff --git a/tests/dem_test_contact/RUN b/tests/dem_test_contact/RUN
deleted file mode 100755
index 3dfc97d..0000000
--- a/tests/dem_test_contact/RUN
+++ /dev/null
@@ -1,7 +0,0 @@
-rm iceberg_trajectories.nc
-rm iceberg_trajectories.nc.*
-rm bond_trajectories.nc
-rm bond_trajectories.nc.*
-srun -n1 ./../../build/bergs.x
-
-
diff --git a/tests/dem_test_contact/animate_trajectories.py b/tests/dem_test_contact/animate_trajectories.py
deleted file mode 100755
index d163b57..0000000
--- a/tests/dem_test_contact/animate_trajectories.py
+++ /dev/null
@@ -1,161 +0,0 @@
-#!/usr/bin/env python
-
-from netCDF4 import Dataset
-import pdb
-import netCDF4 as nc
-import numpy as np
-import matplotlib
-import math
-import os
-matplotlib.use("tkagg")
-from pylab import *
-import matplotlib.pyplot as plt
-from matplotlib.animation import FuncAnimation
-import argparse
-
-def parseCommandLine():
-    parser = argparse.ArgumentParser(description=
-    '''Generate animation of iceberg trajectories.''',
-    epilog='Written by Alex Huth, 2020')
-    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
-                    help=''' provide filename to plot''')
-    parser.add_argument('-s', type=int, default='14000',
-                        help='''plotted particle size''')
-    optCmdLineArgs = parser.parse_args()
-    return optCmdLineArgs
-
-
-
-def main(args):
-
-    print('reading file')
-
-    filename=args.fname
-    psize=args.s
-    #filename = 'iceberg_trajectories.nc'
-    field = 'lon'
-    field2 = 'lat'
-
-    with nc.Dataset(filename) as file:
-        x = file.variables['lon'][:]/1.e3
-        y = file.variables['lat'][:]/1.e3
-        day = file.variables['day'][:]
-        length = file.variables['length'][:]
-        width = file.variables['width'][:]
-        thick = file.variables['thickness'][:]
-        od = file.variables['od'][:]
-
-    ud = np.unique(day)
-    t = ud[0]
-
-    radius = length*width*(1./(2*np.sqrt(3)))
-
-    #for determining if grounded:
-    rho_bergs=850.
-    rho_seawater=1025.
-    h_to_ground=20 #200.
-    draught=(rho_bergs/rho_seawater)*thick
-    if (h_to_ground==0):
-        groundfrac=draught-od
-    else:
-        groundfrac=1.-(od-draught)/h_to_ground
-    groundfrac[groundfrac<0.]=0.
-    groundfrac[groundfrac>1.]=1.
-
-    #groundfrac[thick<200.]=0.
-    #groundfrac[thick>=200.]=1.
-
-
-    # frame info
-    num_frames = len(ud)
-    movie_len = 5 #seconds
-    #frame_len = 1000.0*movie_len/num_frames/10000000
-    frame_len = movie_len/num_frames/1000
-
-    xmin = 40
-    xmax = 100
-    ymin = 20 #xmin
-    ymax = 80 #xmax
-
-    anim_running = True
-
-    def animate(i):
-
-        x1 = x[day == ud[i]]
-        y1 = y[day == ud[i]]
-        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
-
-        scat.set_offsets(data)
-
-        t = ud[i]
-        time_text.set_text('time = %.1f days' % t )
-
-        r1 = radius[day == ud[i]]
-        scat.set_sizes(r1/psize)
-
-        hstat = groundfrac[day == ud[i]]
-        cstring=[]
-        for j in range(len(hstat)):
-            if (hstat[j]==0):
-                cstring.append("none")
-            else:
-                cstring.append("b")
-        scat.set_color(cstring)
-        scat.set_edgecolor('r')
-
-        return scat,time_text
-
-    def init():
-        scat.set_offsets([])
-        return scat,
-
-    def onClick(event):
-        global anim_running
-        if anim_running:
-            ani.event_source.stop()
-            anim_running = False
-        else:
-            ani.event_source.start()
-            anim_running = True
-
-    # Now we can do the plotting!
-    f = plt.figure(figsize=(5,5))
-    f.tight_layout()
-    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
-    scat = ax1.scatter([],[],marker='o')#,edgecolor='red')
-    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
-
-    # Change major ticks to show every 20.
-    ax1.xaxis.set_major_locator(MultipleLocator(5))
-    ax1.yaxis.set_major_locator(MultipleLocator(5))
-
-    ax1.xaxis.set_minor_locator(MultipleLocator(1))
-    ax1.yaxis.set_minor_locator(MultipleLocator(1))
-
-    # Turn grid on for both major and minor ticks and style minor slightly
-    # differently.
-    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
-    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
-
-    ax1.set_xlabel('x (km)')
-    ax1.set_ylabel('y (km)')
-    ax1.set_title('Iceberg trajectory')
-
-    f.canvas.mpl_connect('button_press_event', onClick)
-
-    ani = FuncAnimation(
-        f,animate,init_func=init,frames=num_frames,
-        interval=frame_len,blit=True,repeat=True)
-
-    print('time',t)
-
-    plt.show()
-    #animation.save("iceberg_traj_animation.mp4")
-
-
-print('Script complete')
-
-if __name__ == '__main__':
-    optCmdLineArgs=	parseCommandLine()
-    anim_running = True
-    main(optCmdLineArgs)
diff --git a/tests/dem_test_contact/diag_table b/tests/dem_test_contact/diag_table
deleted file mode 100644
index c1c8819..0000000
--- a/tests/dem_test_contact/diag_table
+++ /dev/null
@@ -1,3 +0,0 @@
-"icebergs test"
-1 1 1 0 0 0
-
diff --git a/tests/dem_test_contact/input.nml b/tests/dem_test_contact/input.nml
deleted file mode 100644
index e3e1133..0000000
--- a/tests/dem_test_contact/input.nml
+++ /dev/null
@@ -1,200 +0,0 @@
-
-&icebergs_driver_nml
-  ni=45 !30 !number of elements, x direction
-  nj=45 !30 !number of elements, y direction
-  gridres=5000.0
-  ibdt=1800.0 !seconds
-  ibuo=0.2 !ocean x velocity
-  ibvo=0.2 !-0.1 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=999999999 !max number of timesteps
-  saverestart=.true.
-  halo=3
-  debug=.true.
-  collision_test=.false.
-  !big_grounding_test=.true.
-  dem_test_contact=.true.
-  bump_depth=50. !200.0 !(m) depth of top of gaussian bump below sea level
-/
-
-&icebergs_nml
-
-    constant_interaction_LW=.true.
-    !traj_name=test_dem.nc
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    break_bonds_on_sub_steps=.true.
-
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5. A=L*W always works?
-    dem_spring_coef=5e6 !5e6 !1e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=0.00015094124684696098 !dem_spring_coef=1.e6, r=1500, and hex pack
-    !spring_coef=0.0030188249369392196 !dem_spring_coef=5.e6, r=750, and hex pack!
-    !spring_coef=0.0006037649873878439 !dem_spring_coef=1.e6, r=750, and hex pack
-    spring_coef=0.0007547062342348049 !if dem_spring_coef=5e6, r=1500, and hex pack?
-    !spring_coef=0.0015094124684696098 !dem_spring_coef=1.e7, r=1500, and hex pack
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=500 !90 # of mts sub-steps #use 90 for 1.5km radii, 500 works for 500 m radii
-    explicit_inner_mts=.true.
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(a68) !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!1.e-7!(a68)!6!8 !(default=spring_coeff) Berg spring coeff for collisions
-
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e5 !3.16e6 !for power-law-type friction
-    h_to_init_grounding=20 !200.0
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.false.!.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !none' !'stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 99999999 !1.05 !0.75 !0.5
-    frac_thres_n = 2000 !1850 !!!1000 !2250 !4100
-    frac_thres_t = 1000 !1200 !1450 !500 !!!1500 !800 !10000000 !800 !1400
-
-
-    halo=3 !(4) halo width
-    Lx=225000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0.1 !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=24000 ! (24) Period between verbose messages
-    traj_sample_hrs=0.5 !-1!0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=0.5 !-1!0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=1600.0!800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/dem_test_contact/makeberg/RUN b/tests/dem_test_contact/makeberg/RUN
deleted file mode 100755
index 520d671..0000000
--- a/tests/dem_test_contact/makeberg/RUN
+++ /dev/null
@@ -1,3 +0,0 @@
-rm ./output_files/Generic*
-./makeberg.py
-cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
diff --git a/tests/dem_test_contact/makeberg/makeberg.py b/tests/dem_test_contact/makeberg/makeberg.py
deleted file mode 100755
index b0de588..0000000
--- a/tests/dem_test_contact/makeberg/makeberg.py
+++ /dev/null
@@ -1,395 +0,0 @@
-#!/usr/bin/env python
-import numpy as np
-import math
-from netCDF4 import Dataset
-from pylab import *
-#import pdb
-import netCDF4 as nc
-
-#
-# Initialize 2 iceberg elements, which can later be bonded in the fortran code if needed
-#
-
-def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,berg_uvel,berg_vvel):
-
-	#print('Writing iceberg restart files, with ' , Number_of_bergs	, 'icebergs..')
-        print 'Writing iceberg restart files, with ' , Number_of_bergs	, 'icebergs..'
-	# To copy the global attributes of the netCDF file
-
-	#Input and output files
-	#Create Empty restart file. This is later read so that the attributes can be used.
-	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
-	create_empty_iceberg_restart_file(Empty_restart_filename)
-	#Empty_restart_filename='input_files/icebergs.res.nc'
-
-	#Read empty restart file
-	f=Dataset(Empty_restart_filename,'r') # r is for read only
-	#Write a new restart file
-	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
-
-	for attname in f.ncattrs():
-		    setattr(g,attname,getattr(f,attname))
-
-
-	# To copy the dimension of the netCDF file
-	for dimname,dim in f.dimensions.iteritems():
-		# if you want to make changes in the dimensions of the new file
-		# you should add your own conditions here before the creation of the dimension.
-		#g.createDimension(dimname,len(dim))
-		g.createDimension(dimname,Number_of_bergs)
-
-	# To copy the variables of the netCDF file
-
-	for varname,ncvar in f.variables.iteritems():
-		# if you want to make changes in the variables of the new file
-		# you should add your own conditions here before the creation of the variable.
-		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
-		#Proceed to copy the variable attributes
-		for attname in ncvar.ncattrs():
-			setattr(var,attname,getattr(ncvar,attname))
-		#Finally copy the variable data to the new created variable
-		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
-
-		if varname=='i':
-			var[:]=Number_of_bergs
-
-		if varname=='iceberg_num':
-			for j in range(Number_of_bergs):
-				#var[j]=j+1
-				var[j]=iceberg_num[j]
-
-		if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
-		or varname=='bxn' or varname=='byn' or	varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
-		or varname=='mass_of_bits' or varname=='start_mass' or	varname=='start_day' or varname=='start_year' or varname=='start_lon' \
-		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
-			var[:]=0
-
-		if varname=='uvel':
-			for j in range(Number_of_bergs):
-				var[j]=berg_uvel[j]
-			#var[:]=berg_uvel[j]
-
-		if varname=='vvel':
-			for j in range(Number_of_bergs):
-				var[j]=berg_vvel[j]
-			#var[:]=berg_vvel[j]
-
-		if varname=='mass_scaling':
-			for j in range(Number_of_bergs):
-				var[j]=mass_scaling[j]
-			#var[:]=mass_scaling[j]
-
-		if varname=='thickness':
-			for j in range(Number_of_bergs):
-				var[j]=thickness[j]
-
-		if varname=='mass':
-			for j in range(Number_of_bergs):
-				var[j]=mass[j]
-
-		if varname=='width'  or varname=='length':
-			for j in range(Number_of_bergs):
-				var[j]=width[j]
-
-		if varname=='lon':
-			for j in range(Number_of_bergs):
-				var[j]=lon[j]
-
-		if varname=='lat':
-			for j in range(Number_of_bergs):
-				var[j]=lat[j]
-
-		if varname=='static_berg':
-			for j in range(Number_of_bergs):
-				var[j]=static_berg[j]
-
-
-	f.close()
-	g.close()
-
-
-def create_empty_iceberg_restart_file(Empty_restart_filename):
-
-        f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
-
-        i=f.createDimension('i', None)
-        lon=f.createVariable('i','i')
-
-        lon=f.createVariable('lon','d',('i'))
-        lon.long_name = "longitude" ;
-        lon.units = "degrees_E" ;
-        lon.checksum = "               0" ;
-
-        lat=f.createVariable('lat','d',('i'))
-        lat.long_name = "latitude" ;
-        lat.units = "degrees_N" ;
-        lat.checksum = "               0" ;
-
-        uvel=f.createVariable('uvel','d',('i'))
-        uvel.long_name = "zonal velocity" ;
-        uvel.units = "m/s" ;
-        uvel.checksum = "               0" ;
-
-        vvel=f.createVariable('vvel','d',('i'))
-        vvel.long_name = "meridional velocity" ;
-        vvel.units = "m/s" ;
-        vvel.checksum = "               0" ;
-
-        mass=f.createVariable('mass','d',('i'))
-        mass.long_name = "mass" ;
-        mass.units = "kg" ;
-        mass.checksum = "               0" ;
-
-        axn=f.createVariable('axn','d',('i'))
-        axn.long_name = "explicit zonal acceleration" ;
-        axn.units = "m/s^2" ;
-        axn.checksum = "               0" ;
-
-        ayn=f.createVariable('ayn','d',('i'))
-        ayn.long_name = "explicit meridional acceleration" ;
-        ayn.units = "m/s^2" ;
-        ayn.checksum = "               0" ;
-
-        bxn=f.createVariable('bxn','d',('i'))
-        bxn.long_name = "inplicit zonal acceleration" ;
-        bxn.units = "m/s^2" ;
-        bxn.checksum = "               0" ;
-
-        byn=f.createVariable('byn','d',('i'))
-        byn.long_name = "implicit meridional acceleration" ;
-        byn.units = "m/s^2" ;
-        byn.checksum = "               0" ;
-
-        ine=f.createVariable('ine','i',('i'))
-        ine.long_name = "i index" ;
-        ine.units = "none" ;
-        ine.packing = 0 ;
-        ine.checksum = "               0" ;
-
-        jne=f.createVariable('jne','i',('i'))
-        jne.long_name = "j index" ;
-        jne.units = "none" ;
-        jne.packing = 0 ;
-        jne.checksum = "               0" ;
-
-        thickness=f.createVariable('thickness','d',('i'))
-        thickness.long_name = "thickness" ;
-        thickness.units = "m" ;
-        thickness.checksum = "               0" ;
-
-        width=f.createVariable('width','d',('i'))
-        width.long_name = "width" ;
-        width.units = "m" ;
-        width.checksum = "               0" ;
-
-        length=f.createVariable('length','d',('i'))
-        length.long_name = "length" ;
-        length.units = "m" ;
-        length.checksum = "               0" ;
-
-        start_lon=f.createVariable('start_lon','d',('i'))
-        start_lon.long_name = "longitude of calving location" ;
-        start_lon.units = "degrees_E" ;
-        start_lon.checksum = "               0" ;
-
-        start_lat=f.createVariable('start_lat','d',('i'))
-        start_lat.long_name = "latitude of calving location" ;
-        start_lat.units = "degrees_N" ;
-        start_lat.checksum = "               0" ;
-
-        start_year=f.createVariable('start_year','i',('i'))
-        start_year.long_name = "calendar year of calving event" ;
-        start_year.units = "years" ;
-        start_year.packing = 0 ;
-        start_year.checksum = "               0" ;
-
-        iceberg_num=f.createVariable('iceberg_num','i',('i'))
-        iceberg_num.long_name = "identification of the iceberg" ;
-        iceberg_num.units = "dimensionless" ;
-        iceberg_num.packing = 0 ;
-        iceberg_num.checksum = "               0" ;
-
-        start_day=f.createVariable('start_day','d',('i'))
-        start_day.long_name = "year day of calving event" ;
-        start_day.units = "days" ;
-        start_day.checksum = "               0" ;
-
-        start_mass=f.createVariable('start_mass','d',('i'))
-        start_mass.long_name = "initial mass of calving berg" ;
-        start_mass.units = "kg" ;
-        start_mass.checksum = "               0" ;
-
-        mass_scaling=f.createVariable('mass_scaling','d',('i'))
-        mass_scaling.long_name = "scaling factor for mass of calving berg" ;
-        mass_scaling.units = "none" ;
-        mass_scaling.checksum = "               0" ;
-
-        mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
-        mass_of_bits.long_name = "mass of bergy bits" ;
-        mass_of_bits.units = "kg" ;
-        mass_of_bits.checksum = "               0" ;
-
-        heat_density=f.createVariable('heat_density','d',('i'))
-        heat_density.long_name = "heat density" ;
-        heat_density.units = "J/kg" ;
-        heat_density.checksum = "               0" ;
-
-        halo_berg=f.createVariable('halo_berg','d',('i'))
-        halo_berg.long_name = "halo_berg" ;
-        halo_berg.units = "dimensionless" ;
-        halo_berg.checksum = "               0" ;
-
-        static_berg=f.createVariable('static_berg','d',('i'))
-        static_berg.long_name = "static_berg" ;
-        static_berg.units = "dimensionless" ;
-        static_berg.checksum = "               0" ;
-
-	f.sync()
-	f.close()
-
-
-
-#-----------------------------------#
-#		Main		    #
-#-----------------------------------#
-
-# just2particles=False
-# flip2ndconglom=True#False
-# offset2ndconglom=True#False
-
-grdxmin=0; grdxmax=225000e3
-grdymin=0; grdymax=225000e3
-grdres=5000.0
-R_frac=0.45 #1st option
-#R_frac=0.5*0.45 #2nd option
-#radius=(np.sqrt(3)/2.)*(R_frac*grdres) #S is < 0.5 grid res
-radius=500 #1.5e3 #/2
-#radius2=(np.sqrt(3)/2.)*(R_frac2*grdres) #S is < 0.5 grid res
-thickness1=300.0
-thickness2=30.0
-rho_ice=850.0
-
-
-nbergs=2 #number of conglomerates
-
-#center coords of each (rectangular) conglomerate berg (CB=conglomerate berg)
-CBxc=np.array([52500,52500]); CByc=np.array([27500,72500])
-#side lengths
-CBxl=np.array([15000,15000]); CByl=np.array([15000,15000])
-
-
-CByl=CByl.astype(int); CBxl=CBxl.astype(int)
-
-#--- xmax, xmin, ymax, ymin for each CB --
-CBxmin=CBxc-(0.5*CBxl); CBxmax=CBxc+(0.5*CBxl)
-CBymin=CByc-(0.5*CByl); CBymax=CByc+(0.5*CByl)
-#this shouldn't happen:
-CBxmin[CBxmin<grdxmin]=grdxmin; CBxmax[CBxmax>grdxmax]=grdxmax
-CBymin[CBxmin<grdymin]=grdymin; CBymax[CBymax>grdymax]=grdymax
-CBxc=0.5*(CBxmin+CBxmax); CByc=0.5*(CBymin+CBymax)
-
-# #if just want one particle per CB
-# if just2particles:
-#	  CBxmin=CBxc; CBxmax=CBxc
-#	  CBymin=CByc; CBymax=CByc
-
-#--- min and max thicknesses for each CB ---
-h1=thickness1
-h2=thickness2
-CBhmax=np.array([h1,h2]); CBhmin=np.array([h1,h2])
-
-#radii
-CBrad=np.array([radius,radius])
-#print('radii',CBrad)
-
-berg_x=[]; berg_y=[]
-berg_id=[]; berg_static=[]
-berg_width=[]; berg_bonds=[]
-berg_h=[]; berg_mass_scaling=[]
-berg_mass=[]
-berg_uvel=[]; berg_vvel=[]
-berg_uvel_in=np.array([0.2,0.2]); berg_vvel_in=np.array([0.2,-0.2])
-
-berg_count=0
-
-for i in range(nbergs):
-	# if (i>0):
-	# 	print('num bergs in 1st conglom',berg_count)
-
-	x_start=CBxmin[i]+(CBrad[i]*2./np.sqrt(3))
-
-        if (i>0):
-                x_start=x_start+1.5e3
-
-	# if flip2ndconglom and i>0:
-	#	  x_start=CBxmax[i]-(CBrad[i]*2./np.sqrt(3))
-
-	#pdb.set_trace()
-	if x_start>CBxmax[i]:
-		x_start=CBxmax[i]
-	y_start0=CBymin[i]+CBrad[i]
-	if y_start0>CBymax[i]:
-		y_start0=CBymax[i]
-	element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*(CBrad[i])**2)
-	#H (thickness) is a linear function of a berg element's position from the
-	#center of the CB. H=Hmax at the center of the CB and H=Hmin at a corner of the
-	#CB, where the dist of a corner from the center is:
-	cdistb=np.sqrt((CBxmin[i]-CBxc[i])**2+(CBymin[i]-CByc[i])**2)
-	j=0
-	x_val=x_start
-	offset=0.0
-	# if (i==0):
-	uvel=berg_uvel_in[i]
-	#0.1#1
-	# else:
-	#	  uvel=-0.15#-0.05
-	#	  if (offset2ndconglom):
-	#		  offset=250.0
-	vvel=berg_vvel_in[i]
-
-	#print('uvel vvel',uvel,vvel)
-	#0.0#25
-	#uvel=0;vvel=0
-	#berg_count_start=berg_count
-	while x_val<=CBxmax[i] and x_val>=CBxmin[i]:
-		y_start=y_start0+((j%2)*CBrad[i])+offset
-		k=0
-		y_val=y_start
-		while y_val<=(CBymax[i]+offset):
-			berg_count=berg_count+1
-			berg_id.append(berg_count)
-			berg_x.append(x_val)
-			berg_y.append(y_val)
-			berg_width.append(sqrt(element_area))
-			#dist of berg elem from center of CB
-			bdistc=np.sqrt((x_val-CBxc[i])**2+(y_val-CByc[i])**2)
-			bh=CBhmin[i]*bdistc/cdistb + CBhmax[i]*(1-bdistc/cdistb)
-			# if (just2particles):
-			#	  bh=h1
-			berg_h.append(bh) #thickness
-			berg_mass_scaling.append(1)
-			berg_mass.append(bh*rho_ice*element_area)
-			berg_static.append(0)
-			berg_uvel.append(uvel)
-			berg_vvel.append(vvel)
-			# if (x_val<22000):
-			#	  berg_vvel.append(vvel)
-			# else:
-			#	  berg_vvel.append(0.4)
-			#berg_CBid.append(i)
-			k=k+1
-			y_val=y_start+(2*k*CBrad[i])
-		j=j+1
-		# if flip2ndconglom and i>0:
-		#	  x_val=x_start-(np.sqrt(3)*CBrad[i]*j)
-		# else:
-		x_val=x_start+(np.sqrt(3)*CBrad[i]*j)
-
-#print('Number of bergs',berg_count)
-print 'Number of bergs',berg_count
-
-#pdb.set_trace()
-
-#Create iceberg restart file
-Ice_geometry_source='Generic'
-Create_iceberg_restart_file(berg_count,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)
diff --git a/tests/energy_test/.gitignore b/tests/energy_test/.gitignore
deleted file mode 100644
index 68bcbc9..0000000
--- a/tests/energy_test/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-results/
\ No newline at end of file
diff --git a/tests/energy_test/README b/tests/energy_test/README
deleted file mode 100644
index b95ec8e..0000000
--- a/tests/energy_test/README
+++ /dev/null
@@ -1,7 +0,0 @@
-A simple test for momentum and energy conservation. In ./makeberg, a conglomerate berg with 60 (./makeberg/RUN) or 2 (./makeberg/RUN2) elements can be initialized. The right half of each conglomerate of elements has an initial x-velocity of 0.2, while all other element velocities are zero.
-
-1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
-2.(optional) edit input.nml
-3. run the model: ./RUN
-4, animate the results: animate_trajectories.py
-
diff --git a/tests/energy_test/RUN b/tests/energy_test/RUN
deleted file mode 100755
index f881323..0000000
--- a/tests/energy_test/RUN
+++ /dev/null
@@ -1,7 +0,0 @@
-rm iceberg_trajectories.nc
-rm iceberg_trajectories.nc.*
-rm bond_trajectories.nc
-rm bond_trajectories.nc.*
-srun -n9 ./../../build/bergs.x
-
-
diff --git a/tests/energy_test/animate_trajectories.py b/tests/energy_test/animate_trajectories.py
deleted file mode 100755
index 8b9aa7d..0000000
--- a/tests/energy_test/animate_trajectories.py
+++ /dev/null
@@ -1,121 +0,0 @@
-#!/usr/bin/env python
-
-from netCDF4 import Dataset
-import pdb
-import netCDF4 as nc
-import numpy as np
-import matplotlib
-import math
-import os
-matplotlib.use("tkagg")
-from pylab import *
-import matplotlib.pyplot as plt
-from matplotlib.animation import FuncAnimation
-import argparse
-
-def parseCommandLine():
-    parser = argparse.ArgumentParser(description=
-    '''Generate animation of iceberg trajectories.''',
-    epilog='Written by Alex Huth, 2020')
-    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
-                    help=''' provide filename to plot''')
-    optCmdLineArgs = parser.parse_args()
-    return optCmdLineArgs
-
-
-
-def main(args):
-
-    print('reading file')
-
-    filename=args.fname
-    #filename = 'iceberg_trajectories.nc'
-    field = 'lon'
-    field2 = 'lat'
-
-    with nc.Dataset(filename) as file:
-        x = file.variables['lon'][:]/1.e3
-        y = file.variables['lat'][:]/1.e3
-        day = file.variables['day'][:]
-
-    ud = np.unique(day)
-    t = ud[0]
-
-    # frame info
-    num_frames = len(ud)
-    movie_len = 10.0 #seconds
-    frame_len = 1000.0*movie_len/num_frames
-
-    xmin = 0
-    xmax = 30
-    ymin = xmin
-    ymax = xmax
-
-    anim_running = True
-
-    def animate(i):
-
-        x1 = x[day == ud[i]]
-        y1 = y[day == ud[i]]
-        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
-
-        scat.set_offsets(data)
-
-        t = ud[i]
-        time_text.set_text('time = %.1f days' % t )
-        return scat,time_text
-
-    def init():
-        scat.set_offsets([])
-        return scat,
-
-    def onClick(event):
-        global anim_running
-        if anim_running:
-            ani.event_source.stop()
-            anim_running = False
-        else:
-            ani.event_source.start()
-            anim_running = True
-
-    # Now we can do the plotting!
-    f = plt.figure(figsize=(5,5))
-    f.tight_layout()
-    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
-    scat = ax1.scatter([],[],marker='o',facecolor='w',s=50,edgecolor='red')
-    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
-
-    # Change major ticks to show every 20.
-    ax1.xaxis.set_major_locator(MultipleLocator(5))
-    ax1.yaxis.set_major_locator(MultipleLocator(5))
-
-    ax1.xaxis.set_minor_locator(MultipleLocator(1))
-    ax1.yaxis.set_minor_locator(MultipleLocator(1))
-
-    # Turn grid on for both major and minor ticks and style minor slightly
-    # differently.
-    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
-    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
-
-    ax1.set_xlabel('x (km)')
-    ax1.set_ylabel('y (km)')
-    ax1.set_title('Iceberg trajectory')
-
-    f.canvas.mpl_connect('button_press_event', onClick)
-
-    ani = FuncAnimation(
-        f,animate,init_func=init,frames=num_frames,
-        interval=frame_len,blit=True,repeat=True)
-
-    print('time',t)
-
-    plt.show()
-    #animation.save("iceberg_traj_animation.mp4")
-
-
-print('Script complete')
-
-if __name__ == '__main__':
-    optCmdLineArgs=	parseCommandLine()
-    anim_running = True
-    main(optCmdLineArgs)
diff --git a/tests/energy_test/animate_trajectories_1pe.py b/tests/energy_test/animate_trajectories_1pe.py
deleted file mode 100755
index beee932..0000000
--- a/tests/energy_test/animate_trajectories_1pe.py
+++ /dev/null
@@ -1,180 +0,0 @@
-#!/usr/bin/env python
-
-from netCDF4 import Dataset
-import pdb
-import netCDF4 as nc
-import numpy as np
-import matplotlib
-import math
-import os
-matplotlib.use("tkagg")
-from pylab import *
-import matplotlib.pyplot as plt
-from matplotlib.animation import FuncAnimation
-import argparse
-
-def parseCommandLine():
-    parser = argparse.ArgumentParser(description=
-    '''Generate animation of iceberg trajectories.''',
-    epilog='Written by Alex Huth, 2020')
-    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc.0000',
-                    help=''' provide filename to plot''')
-    optCmdLineArgs = parser.parse_args()
-    return optCmdLineArgs
-
-
-
-def main(args):
-
-    print('reading file')
-
-    filename=args.fname
-    #filename = 'iceberg_trajectories.nc'
-    field = 'lon'
-    field2 = 'lat'
-
-    with nc.Dataset(filename) as file:
-        x = file.variables['lon'][:]/1.e3
-        y = file.variables['lat'][:]/1.e3
-        day = file.variables['day'][:]
-        hs = file.variables['halo_berg'][:]
-        #hs = file.variables['n_bonds'][:]        
-
-    #hs = hs+1
-    ud = np.unique(day)
-    t = ud[0]
-
-    print('unique hs',np.unique(hs))
-
-    # frame info
-    num_frames = len(ud)
-    movie_len = 10.0 #seconds
-    frame_len = 1000.0*movie_len/num_frames
-
-    xmin = np.floor(min(min(x),min(y),-5))
-    xmax = np.ceil(max(max(x),max(y),35))
-    ymin = xmin
-    ymax = xmax
-
-    anim_running = True
-
-    def animate(i):
-
-        x1 = x[day == ud[i]]
-        y1 = y[day == ud[i]]
-        hstat = hs[day == ud[i]]
-        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
-
-        cstring=[]
-        for j in range(len(hstat)):
-            if (hstat[j]<0):
-                cstring.append("m")
-            elif (hstat[j]==0):
-                cstring.append("b")
-            elif (hstat[j]==1):
-                cstring.append("r")
-            elif (hstat[j]==2):
-                cstring.append("g")
-            elif (hstat[j]==3):
-                cstring.append("k")
-            elif (hstat[j]==4):
-                cstring.append("c")
-            elif (hstat[j]==5):
-                cstring.append("y")
-            elif (hstat[j]==6):
-                cstring.append("w")
-            elif (hstat[j]==10):                
-                cstring.append("c")
-            # else:
-            #     cstring.append("y")
-
-        scat.set_offsets(data)
-        scat.set_color(cstring)
-        scat.set_edgecolor('k')
-
-        t = ud[i]
-        time_text.set_text('time = %.1f days' % t )
-        return scat,time_text
-
-    def init():
-        scat.set_offsets([])
-        return scat,
-
-    def onClick(event):
-        global anim_running
-        if anim_running:
-            ani.event_source.stop()
-            anim_running = False
-        else:
-            ani.event_source.start()
-            anim_running = True
-
-    # Now we can do the plotting!
-    f = plt.figure(figsize=(5,5))
-    f.tight_layout()
-    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
-    scat = ax1.scatter([],[],marker='o',s=60)
-    #scat = ax1.scatter([],[],marker='o',facecolor='w',s=60,edgecolor='red')
-    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
-
-    # Change major ticks to show every 20.
-    ax1.xaxis.set_major_locator(MultipleLocator(5))
-    ax1.yaxis.set_major_locator(MultipleLocator(5))
-
-    ax1.xaxis.set_minor_locator(MultipleLocator(1))
-    ax1.yaxis.set_minor_locator(MultipleLocator(1))
-
-    # Turn grid on for both major and minor ticks and style minor slightly
-    # differently.
-    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
-    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
-
-    ax1.set_xlabel('x (km)')
-    ax1.set_ylabel('y (km)')
-    ax1.set_title('Iceberg trajectory')
-
-    f.canvas.mpl_connect('button_press_event', onClick)
-
-    ani = FuncAnimation(
-        f,animate,init_func=init,frames=num_frames,
-        interval=frame_len,blit=True,repeat=True)
-
-    print('time',t)
-
-    plt.plot([0,0],[0,30],'k-',lw=1)
-    plt.plot([10,10],[0,30],'k-',lw=1)
-    plt.plot([20,20],[0,30],'k-',lw=1)
-    plt.plot([30,30],[0,30],'k-',lw=1)
-    plt.plot([0,30],[0,0],'k-',lw=1)
-    plt.plot([0,30],[10,10],'k-',lw=1)
-    plt.plot([0,30],[20,20],'k-',lw=1)
-    plt.plot([0,30],[30,30],'k-',lw=1)
-
-    plt.plot([-2,-2],[-2,33],'b:',lw=1)
-    plt.plot([3,3],[-2,33],'b:',lw=1)
-    plt.plot([8,8],[-2,33],'b:',lw=1)
-    plt.plot([13,13],[-2,33],'b:',lw=1)
-    plt.plot([18,18],[-2,33],'b:',lw=1)
-    plt.plot([23,23],[-2,33],'b:',lw=1)
-    plt.plot([28,28],[-2,33],'b:',lw=1)
-    plt.plot([33,33],[-2,33],'b:',lw=1)    
-
-    plt.plot([-2,33],[-2,-2],'b:',lw=1)
-    plt.plot([-2,33],[3,3],'b:',lw=1)
-    plt.plot([-2,33],[8,8],'b:',lw=1)
-    plt.plot([-2,33],[13,13],'b:',lw=1)
-    plt.plot([-2,33],[18,18],'b:',lw=1)
-    plt.plot([-2,33],[23,23],'b:',lw=1)
-    plt.plot([-2,33],[28,28],'b:',lw=1)
-    plt.plot([-2,33],[33,33],'b:',lw=1)
-
-    plt.show()
-    #animation.save("iceberg_traj_animation.mp4")
-
-
-print('Script complete')
-
-if __name__ == '__main__':
-    optCmdLineArgs=	parseCommandLine()
-    anim_running = True
-    main(optCmdLineArgs)
diff --git a/tests/energy_test/diag_table b/tests/energy_test/diag_table
deleted file mode 100644
index c1c8819..0000000
--- a/tests/energy_test/diag_table
+++ /dev/null
@@ -1,3 +0,0 @@
-"icebergs test"
-1 1 1 0 0 0
-
diff --git a/tests/energy_test/input.nml b/tests/energy_test/input.nml
deleted file mode 100644
index cd17b87..0000000
--- a/tests/energy_test/input.nml
+++ /dev/null
@@ -1,181 +0,0 @@
-!For the 60 element test:
-!KID, bergs_chksum: write_restart berg chksum=            1143158595 chksum2=           -1591676389 chksum3=            1858541605 chksum4=            1858541605 chksum5=                     0 #=                    60
-!KID, grd_chksum2:    # of bergs/cell chksum=                     0 chksum2=                     0 min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
-!Total number of bonds is:          298 
-
-
-
-&icebergs_driver_nml
-  ni=45 !30 !number of elements, x direction
-  nj=45 !30 !number of elements, y direction
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=999999999 !max number of timesteps
-  saverestart=.true.
-  halo=3
-  debug=.true.
-  collision_test=.false.
-  grounding_test=.false.
-  bump_depth=9999.0 !(m) depth of top of gaussian bump below sea level 
-/
-
-&icebergs_nml
-
-    !defaults given in parentheses:
-    monitor_energy=.true. !(F)
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=10 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
-
-    !force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    !convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=1.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7 !!5.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=3.16e6 !friction drag param
-    h_to_init_grounding=200.0
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='strain' !('none') 'strain_rate','strain',or 'none'
-    !frac_thres_n = 0.018
-    !frac_thres_t = 0.05076
-
-    halo=3 !(4) halo width
-    Lx=45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    rho_bergs=850. ! (850) iceberg density
-    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.0!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=1.0 !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true.!.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.true. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=24000 ! (24) Period between verbose messages
-    traj_sample_hrs=-1!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=-1!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false.!.true. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.!(F) Init bond b/w bergs if dist<1.25*radius
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/energy_test/makeberg/README b/tests/energy_test/makeberg/README
deleted file mode 100644
index 4d7f3fe..0000000
--- a/tests/energy_test/makeberg/README
+++ /dev/null
@@ -1,4 +0,0 @@
-RUN makes a conglomerate berg with 60 elements
-RUN2 makes a conglomerate berg with 2 elements
-
-For both conglomerate, the right half of the particles are initialized with an x-velocity>0, which the left half has x-velocity=0. All y-velocity is zero.
\ No newline at end of file
diff --git a/tests/energy_test/makeberg/RUN b/tests/energy_test/makeberg/RUN
deleted file mode 100755
index 520d671..0000000
--- a/tests/energy_test/makeberg/RUN
+++ /dev/null
@@ -1,3 +0,0 @@
-rm ./output_files/Generic*
-./makeberg.py
-cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
diff --git a/tests/energy_test/makeberg/RUN2 b/tests/energy_test/makeberg/RUN2
deleted file mode 100755
index 0a6834e..0000000
--- a/tests/energy_test/makeberg/RUN2
+++ /dev/null
@@ -1,3 +0,0 @@
-rm ./output_files/Generic*
-./makeberg2.py
-cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
diff --git a/tests/energy_test/makeberg/makeberg.py b/tests/energy_test/makeberg/makeberg.py
deleted file mode 100755
index 4ef99eb..0000000
--- a/tests/energy_test/makeberg/makeberg.py
+++ /dev/null
@@ -1,374 +0,0 @@
-#!/usr/bin/env python
-import numpy as np
-import math
-from netCDF4 import Dataset
-from pylab import *
-#import pdb
-import netCDF4 as nc
-
-#
-# Initialize 2 iceberg elements, which can later be bonded in the fortran code if needed
-#
-
-def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
-
-	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
-	# To copy the global attributes of the netCDF file
-
-	#Input and output files
-	#Create Empty restart file. This is later read so that the attributes can be used.
-	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
-	create_empty_iceberg_restart_file(Empty_restart_filename)
-	#Empty_restart_filename='input_files/icebergs.res.nc'
-
-	#Read empty restart file
-	f=Dataset(Empty_restart_filename,'r') # r is for read only
-	#Write a new restart file
-	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
-
-	for attname in f.ncattrs():
-		    setattr(g,attname,getattr(f,attname))
-
-
-	# To copy the dimension of the netCDF file
-	for dimname,dim in f.dimensions.iteritems():
-		# if you want to make changes in the dimensions of the new file
-		# you should add your own conditions here before the creation of the dimension.
-		#g.createDimension(dimname,len(dim))
-		g.createDimension(dimname,Number_of_bergs)
-
-	# To copy the variables of the netCDF file
-
-	for varname,ncvar in f.variables.iteritems():
-		# if you want to make changes in the variables of the new file
-		# you should add your own conditions here before the creation of the variable.
-		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
-		#Proceed to copy the variable attributes
-		for attname in ncvar.ncattrs():
-			setattr(var,attname,getattr(ncvar,attname))
-		#Finally copy the variable data to the new created variable
-		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
-
-		if varname=='i':
-			var[:]=Number_of_bergs
-
-		if varname=='iceberg_num':
-			for j in range(Number_of_bergs):
-				#var[j]=j+1
-				var[j]=iceberg_num[j]
-
-		if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
-		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
-		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
-		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
-			var[:]=0
-
-                if varname=='uvel':
-                        var[:]=uvel
-
-                if varname=='vvel':
-                        var[:]=vvel
-
-		if varname=='mass_scaling':
-			var[:]=mass_scaling
-
-		if varname=='thickness':
-			for j in range(Number_of_bergs):
-				var[j]=thickness[j]
-
-		if varname=='mass':
-			for j in range(Number_of_bergs):
-				var[j]=mass[j]
-
-		if varname=='width'  or varname=='length':
-			for j in range(Number_of_bergs):
-				var[j]=width[j]
-
-		if varname=='lon':
-			for j in range(Number_of_bergs):
-				var[j]=lon[j]
-
-		if varname=='lat':
-			for j in range(Number_of_bergs):
-				var[j]=lat[j]
-
-		if varname=='static_berg':
-			for j in range(Number_of_bergs):
-				var[j]=static_berg[j]
-
-
-	f.close()
-	g.close()
-
-
-def create_empty_iceberg_restart_file(Empty_restart_filename):
-
-	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
-
-	i=f.createDimension('i', None)
-	lon=f.createVariable('i','i')
-
-	lon=f.createVariable('lon','d',('i'))
-	lon.long_name = "longitude" ;
-	lon.units = "degrees_E" ;
-	lon.checksum = "               0" ;
-
-	lat=f.createVariable('lat','d',('i'))
-	lat.long_name = "latitude" ;
-	lat.units = "degrees_N" ;
-	lat.checksum = "               0" ;
-
-	uvel=f.createVariable('uvel','d',('i'))
-	uvel.long_name = "zonal velocity" ;
-	uvel.units = "m/s" ;
-	uvel.checksum = "               0" ;
-
-	vvel=f.createVariable('vvel','d',('i'))
-	vvel.long_name = "meridional velocity" ;
-	vvel.units = "m/s" ;
-	vvel.checksum = "               0" ;
-
-	mass=f.createVariable('mass','d',('i'))
-	mass.long_name = "mass" ;
-	mass.units = "kg" ;
-	mass.checksum = "               0" ;
-
-	axn=f.createVariable('axn','d',('i'))
-	axn.long_name = "explicit zonal acceleration" ;
-	axn.units = "m/s^2" ;
-	axn.checksum = "               0" ;
-
-	ayn=f.createVariable('ayn','d',('i'))
-	ayn.long_name = "explicit meridional acceleration" ;
-	ayn.units = "m/s^2" ;
-	ayn.checksum = "               0" ;
-
-	bxn=f.createVariable('bxn','d',('i'))
-	bxn.long_name = "inplicit zonal acceleration" ;
-	bxn.units = "m/s^2" ;
-	bxn.checksum = "               0" ;
-
-	byn=f.createVariable('byn','d',('i'))
-	byn.long_name = "implicit meridional acceleration" ;
-	byn.units = "m/s^2" ;
-	byn.checksum = "               0" ;
-
-	ine=f.createVariable('ine','i',('i'))
-	ine.long_name = "i index" ;
-	ine.units = "none" ;
-	ine.packing = 0 ;
-	ine.checksum = "               0" ;
-
-	jne=f.createVariable('jne','i',('i'))
-	jne.long_name = "j index" ;
-	jne.units = "none" ;
-	jne.packing = 0 ;
-	jne.checksum = "               0" ;
-
-	thickness=f.createVariable('thickness','d',('i'))
-	thickness.long_name = "thickness" ;
-	thickness.units = "m" ;
-	thickness.checksum = "               0" ;
-
-	width=f.createVariable('width','d',('i'))
-	width.long_name = "width" ;
-	width.units = "m" ;
-	width.checksum = "               0" ;
-
-	length=f.createVariable('length','d',('i'))
-	length.long_name = "length" ;
-	length.units = "m" ;
-	length.checksum = "               0" ;
-
-	start_lon=f.createVariable('start_lon','d',('i'))
-	start_lon.long_name = "longitude of calving location" ;
-	start_lon.units = "degrees_E" ;
-	start_lon.checksum = "               0" ;
-
-	start_lat=f.createVariable('start_lat','d',('i'))
-	start_lat.long_name = "latitude of calving location" ;
-	start_lat.units = "degrees_N" ;
-	start_lat.checksum = "               0" ;
-
-	start_year=f.createVariable('start_year','i',('i'))
-	start_year.long_name = "calendar year of calving event" ;
-	start_year.units = "years" ;
-	start_year.packing = 0 ;
-	start_year.checksum = "               0" ;
-
-	iceberg_num=f.createVariable('iceberg_num','i',('i'))
-	iceberg_num.long_name = "identification of the iceberg" ;
-	iceberg_num.units = "dimensionless" ;
-	iceberg_num.packing = 0 ;
-	iceberg_num.checksum = "               0" ;
-
-	start_day=f.createVariable('start_day','d',('i'))
-	start_day.long_name = "year day of calving event" ;
-	start_day.units = "days" ;
-	start_day.checksum = "               0" ;
-
-	start_mass=f.createVariable('start_mass','d',('i'))
-	start_mass.long_name = "initial mass of calving berg" ;
-	start_mass.units = "kg" ;
-	start_mass.checksum = "               0" ;
-
-	mass_scaling=f.createVariable('mass_scaling','d',('i'))
-	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
-	mass_scaling.units = "none" ;
-	mass_scaling.checksum = "               0" ;
-
-	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
-	mass_of_bits.long_name = "mass of bergy bits" ;
-	mass_of_bits.units = "kg" ;
-	mass_of_bits.checksum = "               0" ;
-
-	heat_density=f.createVariable('heat_density','d',('i'))
-	heat_density.long_name = "heat density" ;
-	heat_density.units = "J/kg" ;
-	heat_density.checksum = "               0" ;
-
-	halo_berg=f.createVariable('halo_berg','d',('i'))
-	halo_berg.long_name = "halo_berg" ;
-	halo_berg.units = "dimensionless" ;
-	halo_berg.checksum = "               0" ;
-
-	static_berg=f.createVariable('static_berg','d',('i'))
-	static_berg.long_name = "static_berg" ;
-	static_berg.units = "dimensionless" ;
-	static_berg.checksum = "               0" ;
-
-	f.sync()
-	f.close()
-
-
-
-#-----------------------------------#
-#               Main                #
-#-----------------------------------#
-
-just2particles=False
-flip2ndconglom=False
-offset2ndconglom=False
-
-grdxmin=0; grdxmax=45000e3
-grdymin=0; grdymax=45000e3
-grdres=1000.0
-R_frac=0.45
-radius=(np.sqrt(3)/2.)*(R_frac*grdres) #S is < 0.5 grid res
-element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*radius**2)
-width=np.sqrt(element_area)
-thickness1=300.0
-thickness2=300.0
-rho_ice=850.0
-
-
-nbergs=1 #number of conglomerates
-
-#center coords of each (rectangular) conglomerate berg (CB=conglomerate berg)
-CBxc=np.array([8000]); CByc=np.array([15000])
-
-
-#side lengths
-CBxl=np.array([4000]); CByl=np.array([8000])
-
-CByl=CByl.astype(int); CBxl=CBxl.astype(int)
-
-#--- xmax, xmin, ymax, ymin for each CB --
-CBxmin=CBxc-(0.5*CBxl); CBxmax=CBxc+(0.5*CBxl)
-CBymin=CByc-(0.5*CByl); CBymax=CByc+(0.5*CByl)
-#this shouldn't happen:
-CBxmin[CBxmin<grdxmin]=grdxmin; CBxmax[CBxmax>grdxmax]=grdxmax
-CBymin[CBxmin<grdymin]=grdymin; CBymax[CBymax>grdymax]=grdymax
-CBxc=0.5*(CBxmin+CBxmax); CByc=0.5*(CBymin+CBymax)
-
-#if just want one particle per CB
-if just2particles:
-        CBxmin=CBxc; CBxmax=CBxc
-        CBymin=CByc; CBymax=CByc
-
-#--- min and max thicknesses for each CB ---
-h1=thickness1; h2=thickness2
-CBhmax=np.array([h1]); CBhmin=np.array([h2])
-
-#radii
-CBrad=np.array([radius])
-
-berg_x=[]; berg_y=[]
-berg_id=[]; berg_static=[]
-berg_width=[]; berg_bonds=[]
-berg_h=[]; berg_mass_scaling=[]
-berg_mass=[]
-berg_uvel=[]; berg_vvel=[]
-
-berg_count=0
-
-for i in range(nbergs):
-
-        x_start=CBxmin[i]+(CBrad[i]*2./np.sqrt(3))
-
-        if flip2ndconglom and i>0:
-                x_start=CBxmax[i]-(CBrad[i]*2./np.sqrt(3))
-
-        #pdb.set_trace()
-        if x_start>CBxmax[i]:
-                x_start=CBxmax[i]
-        y_start0=CBymin[i]+CBrad[i]
-        if y_start0>CBymax[i]:
-                y_start0=CBymax[i]
-        element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*(CBrad[i])**2)
-        #H (thickness) is a linear function of a berg element's position from the
-        #center of the CB. H=Hmax at the center of the CB and H=Hmin at a corner of the
-        #CB, where the dist of a corner from the center is:
-        cdistb=np.sqrt((CBxmin[i]-CBxc[i])**2+(CBymin[i]-CByc[i])**2)
-        j=0
-        x_val=x_start
-        offset=0.0
-        if (i==0):
-                uvel=0.
-        else:
-                uvel=0.
-                if (offset2ndconglom):
-                        offset=250.0
-        vvel=0
-        #berg_count_start=berg_count
-        while x_val<=CBxmax[i] and x_val>=CBxmin[i]:
-                y_start=y_start0+((j%2)*CBrad[i])+offset
-                k=0
-                y_val=y_start
-                while y_val<=(CBymax[i]+offset):
-                        berg_count=berg_count+1
-                        berg_id.append(berg_count)
-                        berg_x.append(x_val)
-                        berg_y.append(y_val)
-                        berg_width.append(sqrt(element_area))
-                        #dist of berg elem from center of CB
-                        bdistc=np.sqrt((x_val-CBxc[i])**2+(y_val-CByc[i])**2)
-                        bh=CBhmin[i]*bdistc/cdistb + CBhmax[i]*(1-bdistc/cdistb)
-                        if (just2particles):
-                                bh=h1
-                        berg_h.append(bh) #thickness
-                        berg_mass_scaling.append(1)
-                        berg_mass.append(bh*rho_ice*element_area)
-                        berg_static.append(0)
-                        #berg_uvel.append(uvel)
-                        berg_vvel.append(vvel)
-                        if (x_val>8000):
-                                berg_uvel.append(0.2)
-                        else:
-                                berg_uvel.append(uvel)
-
-                        k=k+1
-                        y_val=y_start+(2*k*CBrad[i])
-                j=j+1
-                if flip2ndconglom and i>0:
-                        x_val=x_start-(np.sqrt(3)*CBrad[i]*j)
-                else:
-                        x_val=x_start+(np.sqrt(3)*CBrad[i]*j)
-
-print('Number of bergs',berg_count)
-
-#pdb.set_trace()
-
-#Create iceberg restart file
-Ice_geometry_source='Generic'
-Create_iceberg_restart_file(berg_count,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)
diff --git a/tests/energy_test/makeberg/makeberg2.py b/tests/energy_test/makeberg/makeberg2.py
deleted file mode 100755
index 635a5b7..0000000
--- a/tests/energy_test/makeberg/makeberg2.py
+++ /dev/null
@@ -1,276 +0,0 @@
-#!/usr/bin/env python
-import numpy as np
-import math
-from netCDF4 import Dataset
-from pylab import *
-#import pdb
-import netCDF4 as nc
-
-#
-# Initialize 2 iceberg elements, which can later be bonded in the fortran code if needed
-#
-
-def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
-
-	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
-	# To copy the global attributes of the netCDF file
-
-	#Input and output files
-	#Create Empty restart file. This is later read so that the attributes can be used.
-	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
-	create_empty_iceberg_restart_file(Empty_restart_filename)
-	#Empty_restart_filename='input_files/icebergs.res.nc'
-
-	#Read empty restart file
-	f=Dataset(Empty_restart_filename,'r') # r is for read only
-	#Write a new restart file
-	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
-
-	for attname in f.ncattrs():
-		    setattr(g,attname,getattr(f,attname))
-
-
-	# To copy the dimension of the netCDF file
-	for dimname,dim in f.dimensions.iteritems():
-		# if you want to make changes in the dimensions of the new file
-		# you should add your own conditions here before the creation of the dimension.
-		#g.createDimension(dimname,len(dim))
-		g.createDimension(dimname,Number_of_bergs)
-
-	# To copy the variables of the netCDF file
-
-	for varname,ncvar in f.variables.iteritems():
-		# if you want to make changes in the variables of the new file
-		# you should add your own conditions here before the creation of the variable.
-		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
-		#Proceed to copy the variable attributes
-		for attname in ncvar.ncattrs():
-			setattr(var,attname,getattr(ncvar,attname))
-		#Finally copy the variable data to the new created variable
-		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
-
-		if varname=='i':
-			var[:]=Number_of_bergs
-
-		if varname=='iceberg_num':
-			for j in range(Number_of_bergs):
-				#var[j]=j+1
-				var[j]=iceberg_num[j]
-
-		if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
-		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
-		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
-		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
-			var[:]=0
-
-                if varname=='uvel':
-                        var[:]=uvel
-
-                if varname=='vvel':
-                        var[:]=vvel
-
-		if varname=='mass_scaling':
-			var[:]=mass_scaling
-
-		if varname=='thickness':
-			for j in range(Number_of_bergs):
-				var[j]=thickness[j]
-
-		if varname=='mass':
-			for j in range(Number_of_bergs):
-				var[j]=mass[j]
-
-		if varname=='width'  or varname=='length':
-			for j in range(Number_of_bergs):
-				var[j]=width[j]
-
-		if varname=='lon':
-			for j in range(Number_of_bergs):
-				var[j]=lon[j]
-
-		if varname=='lat':
-			for j in range(Number_of_bergs):
-				var[j]=lat[j]
-
-		if varname=='static_berg':
-			for j in range(Number_of_bergs):
-				var[j]=static_berg[j]
-
-
-	f.close()
-	g.close()
-
-
-def create_empty_iceberg_restart_file(Empty_restart_filename):
-
-	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
-
-	i=f.createDimension('i', None)
-	lon=f.createVariable('i','i')
-
-	lon=f.createVariable('lon','d',('i'))
-	lon.long_name = "longitude" ;
-	lon.units = "degrees_E" ;
-	lon.checksum = "               0" ;
-
-	lat=f.createVariable('lat','d',('i'))
-	lat.long_name = "latitude" ;
-	lat.units = "degrees_N" ;
-	lat.checksum = "               0" ;
-
-	uvel=f.createVariable('uvel','d',('i'))
-	uvel.long_name = "zonal velocity" ;
-	uvel.units = "m/s" ;
-	uvel.checksum = "               0" ;
-
-	vvel=f.createVariable('vvel','d',('i'))
-	vvel.long_name = "meridional velocity" ;
-	vvel.units = "m/s" ;
-	vvel.checksum = "               0" ;
-
-	mass=f.createVariable('mass','d',('i'))
-	mass.long_name = "mass" ;
-	mass.units = "kg" ;
-	mass.checksum = "               0" ;
-
-	axn=f.createVariable('axn','d',('i'))
-	axn.long_name = "explicit zonal acceleration" ;
-	axn.units = "m/s^2" ;
-	axn.checksum = "               0" ;
-
-	ayn=f.createVariable('ayn','d',('i'))
-	ayn.long_name = "explicit meridional acceleration" ;
-	ayn.units = "m/s^2" ;
-	ayn.checksum = "               0" ;
-
-	bxn=f.createVariable('bxn','d',('i'))
-	bxn.long_name = "inplicit zonal acceleration" ;
-	bxn.units = "m/s^2" ;
-	bxn.checksum = "               0" ;
-
-	byn=f.createVariable('byn','d',('i'))
-	byn.long_name = "implicit meridional acceleration" ;
-	byn.units = "m/s^2" ;
-	byn.checksum = "               0" ;
-
-	ine=f.createVariable('ine','i',('i'))
-	ine.long_name = "i index" ;
-	ine.units = "none" ;
-	ine.packing = 0 ;
-	ine.checksum = "               0" ;
-
-	jne=f.createVariable('jne','i',('i'))
-	jne.long_name = "j index" ;
-	jne.units = "none" ;
-	jne.packing = 0 ;
-	jne.checksum = "               0" ;
-
-	thickness=f.createVariable('thickness','d',('i'))
-	thickness.long_name = "thickness" ;
-	thickness.units = "m" ;
-	thickness.checksum = "               0" ;
-
-	width=f.createVariable('width','d',('i'))
-	width.long_name = "width" ;
-	width.units = "m" ;
-	width.checksum = "               0" ;
-
-	length=f.createVariable('length','d',('i'))
-	length.long_name = "length" ;
-	length.units = "m" ;
-	length.checksum = "               0" ;
-
-	start_lon=f.createVariable('start_lon','d',('i'))
-	start_lon.long_name = "longitude of calving location" ;
-	start_lon.units = "degrees_E" ;
-	start_lon.checksum = "               0" ;
-
-	start_lat=f.createVariable('start_lat','d',('i'))
-	start_lat.long_name = "latitude of calving location" ;
-	start_lat.units = "degrees_N" ;
-	start_lat.checksum = "               0" ;
-
-	start_year=f.createVariable('start_year','i',('i'))
-	start_year.long_name = "calendar year of calving event" ;
-	start_year.units = "years" ;
-	start_year.packing = 0 ;
-	start_year.checksum = "               0" ;
-
-	iceberg_num=f.createVariable('iceberg_num','i',('i'))
-	iceberg_num.long_name = "identification of the iceberg" ;
-	iceberg_num.units = "dimensionless" ;
-	iceberg_num.packing = 0 ;
-	iceberg_num.checksum = "               0" ;
-
-	start_day=f.createVariable('start_day','d',('i'))
-	start_day.long_name = "year day of calving event" ;
-	start_day.units = "days" ;
-	start_day.checksum = "               0" ;
-
-	start_mass=f.createVariable('start_mass','d',('i'))
-	start_mass.long_name = "initial mass of calving berg" ;
-	start_mass.units = "kg" ;
-	start_mass.checksum = "               0" ;
-
-	mass_scaling=f.createVariable('mass_scaling','d',('i'))
-	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
-	mass_scaling.units = "none" ;
-	mass_scaling.checksum = "               0" ;
-
-	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
-	mass_of_bits.long_name = "mass of bergy bits" ;
-	mass_of_bits.units = "kg" ;
-	mass_of_bits.checksum = "               0" ;
-
-	heat_density=f.createVariable('heat_density','d',('i'))
-	heat_density.long_name = "heat density" ;
-	heat_density.units = "J/kg" ;
-	heat_density.checksum = "               0" ;
-
-	halo_berg=f.createVariable('halo_berg','d',('i'))
-	halo_berg.long_name = "halo_berg" ;
-	halo_berg.units = "dimensionless" ;
-	halo_berg.checksum = "               0" ;
-
-	static_berg=f.createVariable('static_berg','d',('i'))
-	static_berg.long_name = "static_berg" ;
-	static_berg.units = "dimensionless" ;
-	static_berg.checksum = "               0" ;
-
-	f.sync()
-	f.close()
-
-
-
-#-----------------------------------#
-#               Main                #
-#-----------------------------------#
-
-grdres=1000.0
-xc=4500.0
-yc=15001.0
-R_frac=0.45
-radius=(np.sqrt(3)/2.)*(R_frac*grdres) #S is < 0.5 grid res
-element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*radius**2)
-width=np.sqrt(element_area)
-thickness=300.0
-rhoi=850.0
-mass=thickness*rhoi*element_area
-
-berg_count=2
-berg_x=[xc-radius,xc+radius]
-berg_y=[yc,yc]
-berg_h=[thickness,thickness]
-berg_width=[width,width]
-berg_mass=[mass,mass]
-berg_mass_scaling=[1,1]
-berg_id=[1,2]
-berg_static=[0,0]
-berg_uvel=[0,0.2]
-berg_vvel=[0,0]
-
-print('Number of bergs',berg_count)
-
-#Create iceberg restart file
-Ice_geometry_source='Generic'
-Create_iceberg_restart_file(berg_count,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)
diff --git a/tests/energy_test2/.gitignore b/tests/energy_test2/.gitignore
deleted file mode 100644
index 68bcbc9..0000000
--- a/tests/energy_test2/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-results/
\ No newline at end of file
diff --git a/tests/energy_test2/README b/tests/energy_test2/README
deleted file mode 100644
index d555978..0000000
--- a/tests/energy_test2/README
+++ /dev/null
@@ -1,9 +0,0 @@
-Collision and (subsequent fracture?) of two conglomerate bergs. For testing a scheme where the implicit part of the MTS solution is iterated to convergence to help conserve momentum conservation when collisions occur. Also for testing fracture scheme (e.g. effects of particle size, fracture thresholds, sensitivity to violation of momentum conservation). Set force_convergence to true and specify a convergence tolerance.
-
-Unlike in energy_test3, this test conserves momentum during collision even without the iterative scheme.
-
-1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
-2.(optional) edit input.nml
-3. run the model: ./RUN
-4. animate the results: animate_trajectories.py
-
diff --git a/tests/energy_test2/RUN b/tests/energy_test2/RUN
deleted file mode 100755
index f881323..0000000
--- a/tests/energy_test2/RUN
+++ /dev/null
@@ -1,7 +0,0 @@
-rm iceberg_trajectories.nc
-rm iceberg_trajectories.nc.*
-rm bond_trajectories.nc
-rm bond_trajectories.nc.*
-srun -n9 ./../../build/bergs.x
-
-
diff --git a/tests/energy_test2/animate_trajectories.py b/tests/energy_test2/animate_trajectories.py
deleted file mode 100755
index dacd0ca..0000000
--- a/tests/energy_test2/animate_trajectories.py
+++ /dev/null
@@ -1,121 +0,0 @@
-#!/usr/bin/env python
-
-from netCDF4 import Dataset
-import pdb
-import netCDF4 as nc
-import numpy as np
-import matplotlib
-import math
-import os
-matplotlib.use("tkagg")
-from pylab import *
-import matplotlib.pyplot as plt
-from matplotlib.animation import FuncAnimation
-import argparse
-
-def parseCommandLine():
-    parser = argparse.ArgumentParser(description=
-    '''Generate animation of iceberg trajectories.''',
-    epilog='Written by Alex Huth, 2020')
-    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
-                    help=''' provide filename to plot''')
-    optCmdLineArgs = parser.parse_args()
-    return optCmdLineArgs
-
-
-
-def main(args):
-
-    print('reading file')
-
-    filename=args.fname
-    #filename = 'iceberg_trajectories.nc'
-    field = 'lon'
-    field2 = 'lat'
-
-    with nc.Dataset(filename) as file:
-        x = file.variables['lon'][:]/1.e3
-        y = file.variables['lat'][:]/1.e3
-        day = file.variables['day'][:]
-
-    ud = np.unique(day)
-    t = ud[0]
-
-    # frame info
-    num_frames = len(ud)
-    movie_len = 10.0 #seconds
-    frame_len = 1000.0*movie_len/num_frames
-
-    xmin = 0
-    xmax = 30
-    ymin = 7.5
-    ymax = 37.5
-
-    anim_running = True
-
-    def animate(i):
-
-        x1 = x[day == ud[i]]
-        y1 = y[day == ud[i]]
-        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
-
-        scat.set_offsets(data)
-
-        t = ud[i]
-        time_text.set_text('time = %.1f days' % t )
-        return scat,time_text
-
-    def init():
-        scat.set_offsets([])
-        return scat,
-
-    def onClick(event):
-        global anim_running
-        if anim_running:
-            ani.event_source.stop()
-            anim_running = False
-        else:
-            ani.event_source.start()
-            anim_running = True
-
-    # Now we can do the plotting!
-    f = plt.figure(figsize=(5,5))
-    f.tight_layout()
-    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
-    scat = ax1.scatter([],[],marker='o',facecolor='w',s=50,edgecolor='red')
-    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
-
-    # Change major ticks to show every 20.
-    ax1.xaxis.set_major_locator(MultipleLocator(5))
-    ax1.yaxis.set_major_locator(MultipleLocator(5))
-
-    ax1.xaxis.set_minor_locator(MultipleLocator(1))
-    ax1.yaxis.set_minor_locator(MultipleLocator(1))
-
-    # Turn grid on for both major and minor ticks and style minor slightly
-    # differently.
-    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
-    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
-
-    ax1.set_xlabel('x (km)')
-    ax1.set_ylabel('y (km)')
-    ax1.set_title('Iceberg trajectory')
-
-    f.canvas.mpl_connect('button_press_event', onClick)
-
-    ani = FuncAnimation(
-        f,animate,init_func=init,frames=num_frames,
-        interval=frame_len,blit=True,repeat=True)
-
-    print('time',t)
-
-    plt.show()
-    #animation.save("iceberg_traj_animation.mp4")
-
-
-print('Script complete')
-
-if __name__ == '__main__':
-    optCmdLineArgs=	parseCommandLine()
-    anim_running = True
-    main(optCmdLineArgs)
diff --git a/tests/energy_test2/animate_trajectories_1pe.py b/tests/energy_test2/animate_trajectories_1pe.py
deleted file mode 100755
index 93480db..0000000
--- a/tests/energy_test2/animate_trajectories_1pe.py
+++ /dev/null
@@ -1,180 +0,0 @@
-#!/usr/bin/env python
-
-from netCDF4 import Dataset
-import pdb
-import netCDF4 as nc
-import numpy as np
-import matplotlib
-import math
-import os
-matplotlib.use("tkagg")
-from pylab import *
-import matplotlib.pyplot as plt
-from matplotlib.animation import FuncAnimation
-import argparse
-
-def parseCommandLine():
-    parser = argparse.ArgumentParser(description=
-    '''Generate animation of iceberg trajectories.''',
-    epilog='Written by Alex Huth, 2020')
-    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc.0000',
-                    help=''' provide filename to plot''')
-    optCmdLineArgs = parser.parse_args()
-    return optCmdLineArgs
-
-
-
-def main(args):
-
-    print('reading file')
-
-    filename=args.fname
-    #filename = 'iceberg_trajectories.nc'
-    field = 'lon'
-    field2 = 'lat'
-
-    with nc.Dataset(filename) as file:
-        x = file.variables['lon'][:]/1.e3
-        y = file.variables['lat'][:]/1.e3
-        day = file.variables['day'][:]
-        hs = file.variables['halo_berg'][:]
-        #hs = file.variables['conglom_id'][:]        
-
-    #hs = hs+1
-    ud = np.unique(day)
-    t = ud[0]
-
-    print('unique hs',np.unique(hs))
-
-    # frame info
-    num_frames = len(ud)
-    movie_len = 10.0 #seconds
-    frame_len = 1000.0*movie_len/num_frames
-
-    xmin = np.floor(min(min(x),min(y),-5))
-    xmax = np.ceil(max(max(x),max(y),35))
-    ymin = xmin
-    ymax = xmax
-
-    anim_running = True
-
-    def animate(i):
-
-        x1 = x[day == ud[i]]
-        y1 = y[day == ud[i]]
-        hstat = hs[day == ud[i]]
-        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
-
-        cstring=[]
-        for j in range(len(hstat)):
-            if (hstat[j]<0):
-                cstring.append("m")
-            elif (hstat[j]==0):
-                cstring.append("b")
-            elif (hstat[j]==1):
-                cstring.append("r")
-            elif (hstat[j]==2):
-                cstring.append("g")
-            elif (hstat[j]==3):
-                cstring.append("k")
-            elif (hstat[j]==4):
-                cstring.append("c")
-            elif (hstat[j]==5):
-                cstring.append("y")
-            elif (hstat[j]==6):
-                cstring.append("w")
-            elif (hstat[j]==10):                
-                cstring.append("c")
-            # else:
-            #     cstring.append("y")
-
-        scat.set_offsets(data)
-        scat.set_color(cstring)
-        scat.set_edgecolor('k')
-
-        t = ud[i]
-        time_text.set_text('time = %.1f days' % t )
-        return scat,time_text
-
-    def init():
-        scat.set_offsets([])
-        return scat,
-
-    def onClick(event):
-        global anim_running
-        if anim_running:
-            ani.event_source.stop()
-            anim_running = False
-        else:
-            ani.event_source.start()
-            anim_running = True
-
-    # Now we can do the plotting!
-    f = plt.figure(figsize=(5,5))
-    f.tight_layout()
-    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
-    scat = ax1.scatter([],[],marker='o',s=30)
-    #scat = ax1.scatter([],[],marker='o',facecolor='w',s=60,edgecolor='red')
-    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
-
-    # Change major ticks to show every 20.
-    ax1.xaxis.set_major_locator(MultipleLocator(5))
-    ax1.yaxis.set_major_locator(MultipleLocator(5))
-
-    ax1.xaxis.set_minor_locator(MultipleLocator(1))
-    ax1.yaxis.set_minor_locator(MultipleLocator(1))
-
-    # Turn grid on for both major and minor ticks and style minor slightly
-    # differently.
-    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
-    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
-
-    ax1.set_xlabel('x (km)')
-    ax1.set_ylabel('y (km)')
-    ax1.set_title('Iceberg trajectory')
-
-    f.canvas.mpl_connect('button_press_event', onClick)
-
-    ani = FuncAnimation(
-        f,animate,init_func=init,frames=num_frames,
-        interval=frame_len,blit=True,repeat=True)
-
-    print('time',t)
-
-    plt.plot([0,0],[0,30],'k-',lw=1)
-    plt.plot([10,10],[0,30],'k-',lw=1)
-    plt.plot([20,20],[0,30],'k-',lw=1)
-    plt.plot([30,30],[0,30],'k-',lw=1)
-    plt.plot([0,30],[0,0],'k-',lw=1)
-    plt.plot([0,30],[10,10],'k-',lw=1)
-    plt.plot([0,30],[20,20],'k-',lw=1)
-    plt.plot([0,30],[30,30],'k-',lw=1)
-
-    plt.plot([-2,-2],[-2,33],'b:',lw=1)
-    plt.plot([3,3],[-2,33],'b:',lw=1)
-    plt.plot([8,8],[-2,33],'b:',lw=1)
-    plt.plot([13,13],[-2,33],'b:',lw=1)
-    plt.plot([18,18],[-2,33],'b:',lw=1)
-    plt.plot([23,23],[-2,33],'b:',lw=1)
-    plt.plot([28,28],[-2,33],'b:',lw=1)
-    plt.plot([33,33],[-2,33],'b:',lw=1)    
-
-    plt.plot([-2,33],[-2,-2],'b:',lw=1)
-    plt.plot([-2,33],[3,3],'b:',lw=1)
-    plt.plot([-2,33],[8,8],'b:',lw=1)
-    plt.plot([-2,33],[13,13],'b:',lw=1)
-    plt.plot([-2,33],[18,18],'b:',lw=1)
-    plt.plot([-2,33],[23,23],'b:',lw=1)
-    plt.plot([-2,33],[28,28],'b:',lw=1)
-    plt.plot([-2,33],[33,33],'b:',lw=1)
-
-    plt.show()
-    #animation.save("iceberg_traj_animation.mp4")
-
-
-print('Script complete')
-
-if __name__ == '__main__':
-    optCmdLineArgs=	parseCommandLine()
-    anim_running = True
-    main(optCmdLineArgs)
diff --git a/tests/energy_test2/diag_table b/tests/energy_test2/diag_table
deleted file mode 100644
index c1c8819..0000000
--- a/tests/energy_test2/diag_table
+++ /dev/null
@@ -1,3 +0,0 @@
-"icebergs test"
-1 1 1 0 0 0
-
diff --git a/tests/energy_test2/input.nml b/tests/energy_test2/input.nml
deleted file mode 100644
index 1fc142e..0000000
--- a/tests/energy_test2/input.nml
+++ /dev/null
@@ -1,176 +0,0 @@
-
-&icebergs_driver_nml
-  ni=45 !number of elements, x direction
-  nj=45 !number of elements, y direction
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=46 !total simulation hours
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=999999999 !max number of timesteps
-  saverestart=.true.
-  halo=4
-  debug=.true.
-  collision_test=.false.
-  grounding_test=.false.
-  bump_depth=9999.0 !(m) depth of top of gaussian bump below sea level 
-/
-
-&icebergs_nml
-
-    !defaults given in parentheses:
-    monitor_energy=.true. !(F)save total elastic (spring+collision),external,dissipated,&fracture energy
-    new_mts=.true. !(F) If T, implicit accel is added 50% at the current time step and 50% at the next time step
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=20  !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
-
-    force_convergence=.false. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=3e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-8!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=3.16e6 !friction drag param
-    h_to_init_grounding=200.0
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='strain' !('none') 'strain_rate','strain',or 'none'
-    !frac_thres_scaling = 1.0 !(1) scales frac_thres_n and frac_thres_t
-    !frac_thres_n = 0.018  !normal fracture strain threshold
-    !frac_thres_t = 0.05076 !tangential fracture strain threshold    
-
-    halo=4 !(4) halo width
-    Lx=45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    rho_bergs=850. ! (850) iceberg density
-    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.0!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.true. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0.0 !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.false. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.false. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true.!.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.true. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.false. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=24000 ! (24) Period between verbose messages
-    traj_sample_hrs=-1!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=-1!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false.!.true. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.!(F) Init bond b/w bergs if dist<1.25*radius
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/energy_test2/makeberg/RUN b/tests/energy_test2/makeberg/RUN
deleted file mode 100755
index d985f3f..0000000
--- a/tests/energy_test2/makeberg/RUN
+++ /dev/null
@@ -1,3 +0,0 @@
-rm ./output_files/Generic*
-./makeberg.py
-cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
\ No newline at end of file
diff --git a/tests/energy_test2/makeberg/makeberg.py b/tests/energy_test2/makeberg/makeberg.py
deleted file mode 100755
index 61605f9..0000000
--- a/tests/energy_test2/makeberg/makeberg.py
+++ /dev/null
@@ -1,367 +0,0 @@
-#!/usr/bin/env python
-import numpy as np
-import math
-from netCDF4 import Dataset
-from pylab import *
-#import pdb
-import netCDF4 as nc
-
-#
-# Initialize 2 iceberg elements, which can later be bonded in the fortran code if needed
-#
-
-def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
-
-	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
-	# To copy the global attributes of the netCDF file
-
-	#Input and output files
-	#Create Empty restart file. This is later read so that the attributes can be used.
-	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
-	create_empty_iceberg_restart_file(Empty_restart_filename)
-	#Empty_restart_filename='input_files/icebergs.res.nc'
-
-	#Read empty restart file
-	f=Dataset(Empty_restart_filename,'r') # r is for read only
-	#Write a new restart file
-	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
-
-	for attname in f.ncattrs():
-		    setattr(g,attname,getattr(f,attname))
-
-
-	# To copy the dimension of the netCDF file
-	for dimname,dim in f.dimensions.iteritems():
-		# if you want to make changes in the dimensions of the new file
-		# you should add your own conditions here before the creation of the dimension.
-		#g.createDimension(dimname,len(dim))
-		g.createDimension(dimname,Number_of_bergs)
-
-	# To copy the variables of the netCDF file
-
-	for varname,ncvar in f.variables.iteritems():
-		# if you want to make changes in the variables of the new file
-		# you should add your own conditions here before the creation of the variable.
-		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
-		#Proceed to copy the variable attributes
-		for attname in ncvar.ncattrs():
-			setattr(var,attname,getattr(ncvar,attname))
-		#Finally copy the variable data to the new created variable
-		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
-
-		if varname=='i':
-			var[:]=Number_of_bergs
-
-		if varname=='iceberg_num':
-			for j in range(Number_of_bergs):
-				#var[j]=j+1
-				var[j]=iceberg_num[j]
-
-		if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
-		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
-		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
-		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
-			var[:]=0
-
-                if varname=='uvel':
-                        var[:]=uvel
-
-                if varname=='vvel':
-                        var[:]=vvel
-
-		if varname=='mass_scaling':
-			var[:]=mass_scaling
-
-		if varname=='thickness':
-			for j in range(Number_of_bergs):
-				var[j]=thickness[j]
-
-		if varname=='mass':
-			for j in range(Number_of_bergs):
-				var[j]=mass[j]
-
-		if varname=='width'  or varname=='length':
-			for j in range(Number_of_bergs):
-				var[j]=width[j]
-
-		if varname=='lon':
-			for j in range(Number_of_bergs):
-				var[j]=lon[j]
-
-		if varname=='lat':
-			for j in range(Number_of_bergs):
-				var[j]=lat[j]
-
-		if varname=='static_berg':
-			for j in range(Number_of_bergs):
-				var[j]=static_berg[j]
-
-
-	f.close()
-	g.close()
-
-
-def create_empty_iceberg_restart_file(Empty_restart_filename):
-
-	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
-
-	i=f.createDimension('i', None)
-	lon=f.createVariable('i','i')
-
-	lon=f.createVariable('lon','d',('i'))
-	lon.long_name = "longitude" ;
-	lon.units = "degrees_E" ;
-	lon.checksum = "               0" ;
-
-	lat=f.createVariable('lat','d',('i'))
-	lat.long_name = "latitude" ;
-	lat.units = "degrees_N" ;
-	lat.checksum = "               0" ;
-
-	uvel=f.createVariable('uvel','d',('i'))
-	uvel.long_name = "zonal velocity" ;
-	uvel.units = "m/s" ;
-	uvel.checksum = "               0" ;
-
-	vvel=f.createVariable('vvel','d',('i'))
-	vvel.long_name = "meridional velocity" ;
-	vvel.units = "m/s" ;
-	vvel.checksum = "               0" ;
-
-	mass=f.createVariable('mass','d',('i'))
-	mass.long_name = "mass" ;
-	mass.units = "kg" ;
-	mass.checksum = "               0" ;
-
-	axn=f.createVariable('axn','d',('i'))
-	axn.long_name = "explicit zonal acceleration" ;
-	axn.units = "m/s^2" ;
-	axn.checksum = "               0" ;
-
-	ayn=f.createVariable('ayn','d',('i'))
-	ayn.long_name = "explicit meridional acceleration" ;
-	ayn.units = "m/s^2" ;
-	ayn.checksum = "               0" ;
-
-	bxn=f.createVariable('bxn','d',('i'))
-	bxn.long_name = "inplicit zonal acceleration" ;
-	bxn.units = "m/s^2" ;
-	bxn.checksum = "               0" ;
-
-	byn=f.createVariable('byn','d',('i'))
-	byn.long_name = "implicit meridional acceleration" ;
-	byn.units = "m/s^2" ;
-	byn.checksum = "               0" ;
-
-	ine=f.createVariable('ine','i',('i'))
-	ine.long_name = "i index" ;
-	ine.units = "none" ;
-	ine.packing = 0 ;
-	ine.checksum = "               0" ;
-
-	jne=f.createVariable('jne','i',('i'))
-	jne.long_name = "j index" ;
-	jne.units = "none" ;
-	jne.packing = 0 ;
-	jne.checksum = "               0" ;
-
-	thickness=f.createVariable('thickness','d',('i'))
-	thickness.long_name = "thickness" ;
-	thickness.units = "m" ;
-	thickness.checksum = "               0" ;
-
-	width=f.createVariable('width','d',('i'))
-	width.long_name = "width" ;
-	width.units = "m" ;
-	width.checksum = "               0" ;
-
-	length=f.createVariable('length','d',('i'))
-	length.long_name = "length" ;
-	length.units = "m" ;
-	length.checksum = "               0" ;
-
-	start_lon=f.createVariable('start_lon','d',('i'))
-	start_lon.long_name = "longitude of calving location" ;
-	start_lon.units = "degrees_E" ;
-	start_lon.checksum = "               0" ;
-
-	start_lat=f.createVariable('start_lat','d',('i'))
-	start_lat.long_name = "latitude of calving location" ;
-	start_lat.units = "degrees_N" ;
-	start_lat.checksum = "               0" ;
-
-	start_year=f.createVariable('start_year','i',('i'))
-	start_year.long_name = "calendar year of calving event" ;
-	start_year.units = "years" ;
-	start_year.packing = 0 ;
-	start_year.checksum = "               0" ;
-
-	iceberg_num=f.createVariable('iceberg_num','i',('i'))
-	iceberg_num.long_name = "identification of the iceberg" ;
-	iceberg_num.units = "dimensionless" ;
-	iceberg_num.packing = 0 ;
-	iceberg_num.checksum = "               0" ;
-
-	start_day=f.createVariable('start_day','d',('i'))
-	start_day.long_name = "year day of calving event" ;
-	start_day.units = "days" ;
-	start_day.checksum = "               0" ;
-
-	start_mass=f.createVariable('start_mass','d',('i'))
-	start_mass.long_name = "initial mass of calving berg" ;
-	start_mass.units = "kg" ;
-	start_mass.checksum = "               0" ;
-
-	mass_scaling=f.createVariable('mass_scaling','d',('i'))
-	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
-	mass_scaling.units = "none" ;
-	mass_scaling.checksum = "               0" ;
-
-	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
-	mass_of_bits.long_name = "mass of bergy bits" ;
-	mass_of_bits.units = "kg" ;
-	mass_of_bits.checksum = "               0" ;
-
-	heat_density=f.createVariable('heat_density','d',('i'))
-	heat_density.long_name = "heat density" ;
-	heat_density.units = "J/kg" ;
-	heat_density.checksum = "               0" ;
-
-	halo_berg=f.createVariable('halo_berg','d',('i'))
-	halo_berg.long_name = "halo_berg" ;
-	halo_berg.units = "dimensionless" ;
-	halo_berg.checksum = "               0" ;
-
-	static_berg=f.createVariable('static_berg','d',('i'))
-	static_berg.long_name = "static_berg" ;
-	static_berg.units = "dimensionless" ;
-	static_berg.checksum = "               0" ;
-
-	f.sync()
-	f.close()
-
-
-
-#-----------------------------------#
-#               Main                #
-#-----------------------------------#
-
-just2particles=False
-flip2ndconglom=True
-offset2ndconglom=True
-
-grdxmin=0; grdxmax=45000e3
-grdymin=0; grdymax=45000e3
-grdres=1000.0
-R_frac=0.45
-radius=(np.sqrt(3)/2.)*(R_frac*grdres) #S is < 0.5 grid res
-element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*radius**2)
-width=np.sqrt(element_area)
-thickness1=300.0
-thickness2=300.0
-rho_ice=850.0
-
-
-nbergs=2 #number of conglomerates
-
-#center coords of each (rectangular) conglomerate berg (CB=conglomerate berg)
-CBxc=np.array([9500, 17500]); CByc=np.array([22500, 22500])
-
-#side lengths
-#CBxl=np.array([2500, 10000]); CByl=np.array([10000, 2500])
-CBxl=np.array([3000, 3000]); CByl=np.array([3000, 3000])
-CByl=CByl.astype(int); CBxl=CBxl.astype(int)
-
-#--- xmax, xmin, ymax, ymin for each CB --
-CBxmin=CBxc-(0.5*CBxl); CBxmax=CBxc+(0.5*CBxl)
-CBymin=CByc-(0.5*CByl); CBymax=CByc+(0.5*CByl)
-#this shouldn't happen:
-CBxmin[CBxmin<grdxmin]=grdxmin; CBxmax[CBxmax>grdxmax]=grdxmax
-CBymin[CBxmin<grdymin]=grdymin; CBymax[CBymax>grdymax]=grdymax
-CBxc=0.5*(CBxmin+CBxmax); CByc=0.5*(CBymin+CBymax)
-
-#if just want one particle per CB
-if just2particles:
-        CBxmin=CBxc; CBxmax=CBxc
-        CBymin=CByc; CBymax=CByc
-
-#--- min and max thicknesses for each CB ---
-h1=thickness1; h2=thickness2
-CBhmax=np.array([h1,h1]); CBhmin=np.array([h2,h2])
-
-#radii
-CBrad=np.array([radius,radius])
-
-berg_x=[]; berg_y=[]
-berg_id=[]; berg_static=[]
-berg_width=[]; berg_bonds=[]
-berg_h=[]; berg_mass_scaling=[]
-berg_mass=[]; berg_uvel=[]; berg_vvel=[]
-
-berg_count=0
-
-for i in range(nbergs):
-        x_start=CBxmin[i]+(CBrad[i]*2./np.sqrt(3))
-
-        if flip2ndconglom and i>0:
-                x_start=CBxmax[i]-(CBrad[i]*2./np.sqrt(3))
-
-        #pdb.set_trace()
-        if x_start>CBxmax[i]:
-                x_start=CBxmax[i]
-        y_start0=CBymin[i]+CBrad[i]
-        if y_start0>CBymax[i]:
-                y_start0=CBymax[i]
-        element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*(CBrad[i])**2)
-        #H (thickness) is a linear function of a berg element's position from the
-        #center of the CB. H=Hmax at the center of the CB and H=Hmin at a corner of the
-        #CB, where the dist of a corner from the center is:
-        cdistb=np.sqrt((CBxmin[i]-CBxc[i])**2+(CBymin[i]-CByc[i])**2)
-        j=0
-        x_val=x_start
-        offset=0.0
-        vvel=0.025
-        if (i==0):
-                uvel=0.05
-        else:
-                uvel=-0.15
-                if (offset2ndconglom):
-                        offset=2000.0 #250.0
-        #berg_count_start=berg_count
-        while x_val<=CBxmax[i] and x_val>=CBxmin[i]:
-                y_start=y_start0+((j%2)*CBrad[i])+offset
-                k=0
-                y_val=y_start
-                while y_val<=(CBymax[i]+offset):
-                        berg_count=berg_count+1
-                        berg_id.append(berg_count)
-                        berg_x.append(x_val)
-                        berg_y.append(y_val)
-                        berg_width.append(sqrt(element_area))
-                        #dist of berg elem from center of CB
-                        bdistc=np.sqrt((x_val-CBxc[i])**2+(y_val-CByc[i])**2)
-                        bh=CBhmin[i]*bdistc/cdistb + CBhmax[i]*(1-bdistc/cdistb)
-                        if (just2particles):
-                                bh=h1
-                        berg_h.append(bh) #thickness
-                        berg_mass_scaling.append(1)
-                        berg_mass.append(bh*rho_ice*element_area)
-                        berg_static.append(0)
-                        berg_uvel.append(uvel)
-                        berg_vvel.append(vvel)
-                        #berg_CBid.append(i)
-                        k=k+1
-                        y_val=y_start+(2*k*CBrad[i])
-                j=j+1
-                if flip2ndconglom and i>0:
-                        x_val=x_start-(np.sqrt(3)*CBrad[i]*j)
-                else:
-                        x_val=x_start+(np.sqrt(3)*CBrad[i]*j)
-
-print('Number of bergs',berg_count)
-
-#pdb.set_trace()
-
-#Create iceberg restart file
-Ice_geometry_source='Generic'
-Create_iceberg_restart_file(berg_count,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)
diff --git a/tests/energy_test3/.gitignore b/tests/energy_test3/.gitignore
deleted file mode 100644
index 68bcbc9..0000000
--- a/tests/energy_test3/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-results/
\ No newline at end of file
diff --git a/tests/energy_test3/README b/tests/energy_test3/README
deleted file mode 100644
index 7482b12..0000000
--- a/tests/energy_test3/README
+++ /dev/null
@@ -1,9 +0,0 @@
-Collision and subsequent fracture of two conglomerate bergs. For testing a scheme where the MTS solution is iterated to convergence in order to help conserve momentum conservation when collisions occur. Also for testing fracture scheme (e.g. effects of particle size, fracture thresholds, sensitivity to violation of momentum conservation). Set force_convergence to true and specify a convergence tolerance. Iterations will stop once convergence tolerance is reached.
-
-Unlike in energy_test2, this test will not conserve momentum sufficiently during collision unless the iterative scheme is used.
-
-1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
-2.(optional) edit input.nml
-3. run the model: ./RUN
-4, animate the results: animate_trajectories.py
-
diff --git a/tests/energy_test3/RUN b/tests/energy_test3/RUN
deleted file mode 100755
index f881323..0000000
--- a/tests/energy_test3/RUN
+++ /dev/null
@@ -1,7 +0,0 @@
-rm iceberg_trajectories.nc
-rm iceberg_trajectories.nc.*
-rm bond_trajectories.nc
-rm bond_trajectories.nc.*
-srun -n9 ./../../build/bergs.x
-
-
diff --git a/tests/energy_test3/RUN1p b/tests/energy_test3/RUN1p
deleted file mode 100755
index 3dfc97d..0000000
--- a/tests/energy_test3/RUN1p
+++ /dev/null
@@ -1,7 +0,0 @@
-rm iceberg_trajectories.nc
-rm iceberg_trajectories.nc.*
-rm bond_trajectories.nc
-rm bond_trajectories.nc.*
-srun -n1 ./../../build/bergs.x
-
-
diff --git a/tests/energy_test3/animate_trajectories.py b/tests/energy_test3/animate_trajectories.py
deleted file mode 100755
index 3bcce56..0000000
--- a/tests/energy_test3/animate_trajectories.py
+++ /dev/null
@@ -1,141 +0,0 @@
-#!/usr/bin/env python
-
-from netCDF4 import Dataset
-import pdb
-import netCDF4 as nc
-import numpy as np
-import matplotlib
-import math
-import os
-matplotlib.use("tkagg")
-from pylab import *
-import matplotlib.pyplot as plt
-from matplotlib.animation import FuncAnimation
-import argparse
-
-def parseCommandLine():
-    parser = argparse.ArgumentParser(description=
-    '''Generate animation of iceberg trajectories.''',
-    epilog='Written by Alex Huth, 2020')
-    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
-                    help=''' provide filename to plot''')
-    parser.add_argument('-s', type=int, default='4000',
-                    help='''plotted particle size''')
-    optCmdLineArgs = parser.parse_args()    
-    optCmdLineArgs = parser.parse_args()
-    return optCmdLineArgs
-
-
-def main(args):
-
-    print('reading file')
-
-    filename=args.fname
-    psize=args.s
-    #filename = 'iceberg_trajectories.nc'
-    field = 'lon'
-    field2 = 'lat'
-
-    with nc.Dataset(filename) as file:
-        x = file.variables['lon'][:]/1.e3
-        y = file.variables['lat'][:]/1.e3
-        day = file.variables['day'][:]
-        length = file.variables['length'][:]
-        width = file.variables['width'][:]
-
-        
-    radius = length*width*(1/(2*np.sqrt(3)))
-
-    crop=False
-    tc=1.25
-    if crop:
-        x=x[day<=tc]
-        y=y[day<=tc]
-        day=day[day<=tc]
-
-    ud = np.unique(day)
-    t = ud[0]
-
-    # frame info
-    num_frames = len(ud)
-    movie_len = 10.0 #seconds
-    frame_len = 1000.0*movie_len/num_frames
-
-    xmin = 0
-    xmax = 30 #45 #30
-    ymin = 7.5 #0 #7.5
-    ymax = 37.5 #45 #37.5
-
-    anim_running = True
-
-    def animate(i):
-
-        x1 = x[day == ud[i]]
-        y1 = y[day == ud[i]]
-        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
-
-        scat.set_offsets(data)
-
-        t = ud[i]
-        time_text.set_text('time = %.1f days' % t )
-
-        r1 = radius[day == ud[i]]
-        
-        scat.set_sizes(r1/psize)
-        return scat,time_text
-
-    def init():
-        scat.set_offsets([])
-        return scat,
-
-    def onClick(event):
-        global anim_running
-        if anim_running:
-            ani.event_source.stop()
-            anim_running = False
-        else:
-            ani.event_source.start()
-            anim_running = True
-
-    # Now we can do the plotting!
-    f = plt.figure(figsize=(5,5))
-    f.tight_layout()
-    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
-    #scat = ax1.scatter([],[],marker='o',facecolor='w',s=psize,edgecolor='red')
-    scat = ax1.scatter([],[],marker='o',facecolor='w',edgecolor='red')    
-    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
-
-    # Change major ticks to show every 20.
-    ax1.xaxis.set_major_locator(MultipleLocator(5))
-    ax1.yaxis.set_major_locator(MultipleLocator(5))
-
-    ax1.xaxis.set_minor_locator(MultipleLocator(1))
-    ax1.yaxis.set_minor_locator(MultipleLocator(1))
-
-    # Turn grid on for both major and minor ticks and style minor slightly
-    # differently.
-    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
-    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
-
-    ax1.set_xlabel('x (km)')
-    ax1.set_ylabel('y (km)')
-    ax1.set_title('Iceberg trajectory')
-
-    f.canvas.mpl_connect('button_press_event', onClick)
-
-    ani = FuncAnimation(
-        f,animate,init_func=init,frames=num_frames,
-        interval=frame_len,blit=True,repeat=True)
-
-    print('time',t)
-
-    plt.show()
-    #animation.save("iceberg_traj_animation.mp4")
-
-
-print('Script complete')
-
-if __name__ == '__main__':
-    optCmdLineArgs=	parseCommandLine()
-    anim_running = True
-    main(optCmdLineArgs)
diff --git a/tests/energy_test3/animate_trajectories_1pe.py b/tests/energy_test3/animate_trajectories_1pe.py
deleted file mode 100755
index 931c727..0000000
--- a/tests/energy_test3/animate_trajectories_1pe.py
+++ /dev/null
@@ -1,189 +0,0 @@
-#!/usr/bin/env python
-
-from netCDF4 import Dataset
-import pdb
-import netCDF4 as nc
-import numpy as np
-import matplotlib
-import math
-import os
-matplotlib.use("tkagg")
-from pylab import *
-import matplotlib.pyplot as plt
-from matplotlib.animation import FuncAnimation
-import argparse
-
-def parseCommandLine():
-    parser = argparse.ArgumentParser(description=
-    '''Generate animation of iceberg trajectories.''',
-    epilog='Written by Alex Huth, 2020')
-    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc.0000',
-                    help=''' provide filename to plot''')
-    optCmdLineArgs = parser.parse_args()
-    return optCmdLineArgs
-
-
-
-def main(args):
-
-    print('reading file')
-
-    filename=args.fname
-    #filename = 'iceberg_trajectories.nc'
-    field = 'lon'
-    field2 = 'lat'
-
-    with nc.Dataset(filename) as file:
-        x = file.variables['lon'][:]/1.e3
-        y = file.variables['lat'][:]/1.e3
-        day = file.variables['day'][:]
-        hs = file.variables['halo_berg'][:]
-        #hs = file.variables['conglom_id'][:]        
-
-    #hs = hs+1
-    ud = np.unique(day)
-    t = ud[0]
-
-    print('unique hs',np.unique(hs))
-
-    # frame info
-    num_frames = len(ud)
-    movie_len = 10.0 #seconds
-    frame_len = 1000.0*movie_len/num_frames
-
-    xmin = np.floor(min(min(x),min(y),-5))
-    xmax = np.ceil(max(max(x),max(y),35))
-    ymin = xmin
-    ymax = xmax
-
-    anim_running = True
-
-    def animate(i):
-
-        x1 = x[day == ud[i]]
-        y1 = y[day == ud[i]]
-        hstat = hs[day == ud[i]]
-        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
-
-        cstring=[]
-        for j in range(len(hstat)):
-            if (hstat[j]<0):
-                cstring.append("m")
-            elif (hstat[j]==0):
-                cstring.append("b")
-            elif (hstat[j]==1):
-                cstring.append("r")
-            elif (hstat[j]==2):
-                cstring.append("g")
-            elif (hstat[j]==3):
-                cstring.append("k")
-            elif (hstat[j]==4):
-                cstring.append("c")
-            elif (hstat[j]==5):
-                cstring.append("y")
-            elif (hstat[j]==6):
-                cstring.append("w")
-            elif (hstat[j]==10):                
-                cstring.append("c")
-            # else:
-            #     cstring.append("y")
-
-        scat.set_offsets(data)
-        scat.set_color(cstring)
-        scat.set_edgecolor('k')
-
-        t = ud[i]
-        time_text.set_text('time = %.1f days' % t )
-        return scat,time_text
-
-    def init():
-        scat.set_offsets([])
-        return scat,
-
-    def onClick(event):
-        global anim_running
-        if anim_running:
-            ani.event_source.stop()
-            anim_running = False
-        else:
-            ani.event_source.start()
-            anim_running = True
-
-    # Now we can do the plotting!
-    f = plt.figure(figsize=(5,5))
-    f.tight_layout()
-    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
-    scat = ax1.scatter([],[],marker='o',s=30)
-    #scat = ax1.scatter([],[],marker='o',facecolor='w',s=60,edgecolor='red')
-    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
-
-    # Change major ticks to show every 20.
-    ax1.xaxis.set_major_locator(MultipleLocator(5))
-    ax1.yaxis.set_major_locator(MultipleLocator(5))
-
-    ax1.xaxis.set_minor_locator(MultipleLocator(1))
-    ax1.yaxis.set_minor_locator(MultipleLocator(1))
-
-    # Turn grid on for both major and minor ticks and style minor slightly
-    # differently.
-    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
-    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
-
-    ax1.set_xlabel('x (km)')
-    ax1.set_ylabel('y (km)')
-    ax1.set_title('Iceberg trajectory')
-
-    f.canvas.mpl_connect('button_press_event', onClick)
-
-    ani = FuncAnimation(
-        f,animate,init_func=init,frames=num_frames,
-        interval=frame_len,blit=True,repeat=True)
-
-    print('time',t)
-
-    plt.plot([0,0],[0,30],'k-',lw=1)
-    plt.plot([10,10],[0,30],'k-',lw=1)
-    plt.plot([20,20],[0,30],'k-',lw=1)
-    plt.plot([30,30],[0,30],'k-',lw=1)
-    plt.plot([0,30],[0,0],'k-',lw=1)
-    plt.plot([0,30],[10,10],'k-',lw=1)
-    plt.plot([0,30],[20,20],'k-',lw=1)
-    plt.plot([0,30],[30,30],'k-',lw=1)
-
-
-    h=3 #halo width
-    w=h-1
-
-    x1=0; x2=10; x3=20; x4=30
-    y1=0; y2=10; y3=20; y4=30    
-    
-
-    plt.plot([x1-w,x1-w],[y1-w,y4+h],'b:',lw=1)
-    plt.plot([x1+h,x1+h],[y1-w,y4+h],'b:',lw=1)
-    plt.plot([x2-w,x2-w],[y1-w,y4+h],'b:',lw=1)
-    plt.plot([x2+h,x2+h],[y1-w,y4+h],'b:',lw=1)
-    plt.plot([x3-w,x3-w],[y1-w,y4+h],'b:',lw=1)
-    plt.plot([x3+h,x3+h],[y1-w,y4+h],'b:',lw=1)
-    plt.plot([x4-w,x4-w],[y1-w,y4+h],'b:',lw=1)
-    plt.plot([x4+h,x4+h],[y1-w,y4+h],'b:',lw=1) 
-       
-
-    plt.plot([x1-w,x4+h],[y1-w,y1-w],'b:',lw=1)
-    plt.plot([x1-w,x4+h],[y1+h,y1+h],'b:',lw=1)
-    plt.plot([x1-w,x4+h],[y2-w,y2-w],'b:',lw=1)
-    plt.plot([x1-w,x4+h],[y2+h,y2+h],'b:',lw=1)
-    plt.plot([x1-w,x4+h],[y3-w,y3-w],'b:',lw=1)
-    plt.plot([x1-w,x4+h],[y3+h,y3+h],'b:',lw=1)
-    plt.plot([x1-w,x4+h],[y4-w,y4-w],'b:',lw=1)
-    plt.plot([x1-w,x4+h],[y4+h,y4+h],'b:',lw=1)
-
-    plt.show()
-    #animation.save("iceberg_traj_animation.mp4")
-
-
-print('Script complete')
-
-if __name__ == '__main__':
-    optCmdLineArgs=	parseCommandLine()
-    anim_running = True
-    main(optCmdLineArgs)
diff --git a/tests/energy_test3/diag_table b/tests/energy_test3/diag_table
deleted file mode 100644
index c1c8819..0000000
--- a/tests/energy_test3/diag_table
+++ /dev/null
@@ -1,3 +0,0 @@
-"icebergs test"
-1 1 1 0 0 0
-
diff --git a/tests/energy_test3/input.nml b/tests/energy_test3/input.nml
deleted file mode 100644
index f56121b..0000000
--- a/tests/energy_test3/input.nml
+++ /dev/null
@@ -1,197 +0,0 @@
-!KID, bergs_chksum: write_restart berg chksum=           -1918812055 chksum2=             743944572 chksum3=             -78785014 chksum4=             -78785014 chksum5=                     0 #=                    71
-!KID, grd_chksum2:    # of bergs/cell chksum=                     0 chksum2=                     0 min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
-! Total number of bonds is:          276
-
-!test: replace uvel_old and vvel_old during damping with ustar and vstar
-!KID, bergs_chksum: write_restart berg chksum=           -1514198739 chksum2=            -764201033 chksum3=             -78785014 chksum4=             -78785014 chksum5=                     0 #=                    71
-!KID, grd_chksum2:    # of bergs/cell chksum=                     0 chksum2=                     0 min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
-! Total number of bonds is:          276 
-
-
-&icebergs_driver_nml
-  ni=45 !number of elements, x direction
-  nj=45 !number of elements, y direction
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=24 !total simulation hours
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=999999999 !max number of timesteps
-  saverestart=.true.
-  halo=3
-  debug=.true.
-  collision_test=.false.
-  grounding_test=.false.
-  bump_depth=9999.0 !(m) depth of top of gaussian bump below sea level
-/
-
-&icebergs_nml
-
-    !defaults given in parentheses:
-    explicit_inner_mts=.false. !(F) If T, inner MTS iterations are treated explicitly
-
-    monitor_energy=.true. !(F)save total elastic (spring+collision),external,dissipated,&fracture energy
-    new_mts=.true. !(F) If T, implicit accel is added 50% at the current time step and 50% at the next time step
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=20  !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1.e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=2000 !2500 !2500 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-8 !(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=3.16e6 !friction drag param
-    h_to_init_grounding=200.0 !300.0 !150.0 !300.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.false. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='strain' !('none') 'strain_rate','strain','stress',or 'none'
-    !here, try setting scaling 1.0 if force_convergence=.false., 0.5 if force_convergence=.true.
-    frac_thres_scaling = 0.5 !(1) scales frac_thres_n and frac_thres_t
-    frac_thres_n = 0.018  !normal fracture strain threshold
-    frac_thres_t = 0.05076 !tangential fracture strain threshold
-
-    !fracture_criterion='strain_rate' !('none') 'strain_rate','strain','stress',or 'none'
-    !frac_thres_scaling = 1 !(1) scales frac_thres_n and frac_thres_t
-    !frac_thres_n = 2.e-6  !normal fracture strain threshold
-    !frac_thres_t = 0!1.e-5 !tangential fracture strain threshold
-
-    !fracture_criterion='stress' !('none') 'strain_rate','strain','stress',or 'none'
-    !here, try setting scaling 1.0 if force_convergence=.false., 0.5 if force_convergence=.true.
-    !frac_thres_scaling = 1.0 !(1) scales frac_thres_n and frac_thres_t
-    !frac_thres_n = 8000.0  !normal fracture strain threshold
-    !frac_thres_t = 0.!12000.0 !0.05076 !tangential fracture strain threshold
-
-    halo=3 !(4) halo width
-    Lx=45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    rho_bergs=850. ! (850) iceberg density
-    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    radial_damping_coef=0.0 !(1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0.0 !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.false. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.false. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.true. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=24000 ! (24) Period between verbose messages
-    traj_sample_hrs=-1 !(24) sampling period for trajectory storage
-    traj_write_hrs=-1 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.true. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.!(F) Init bond b/w bergs if dist<1.25*radius
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/energy_test3/makeberg/RUN b/tests/energy_test3/makeberg/RUN
deleted file mode 100755
index d985f3f..0000000
--- a/tests/energy_test3/makeberg/RUN
+++ /dev/null
@@ -1,3 +0,0 @@
-rm ./output_files/Generic*
-./makeberg.py
-cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
\ No newline at end of file
diff --git a/tests/energy_test3/makeberg/makeberg.py b/tests/energy_test3/makeberg/makeberg.py
deleted file mode 100755
index 829fe4c..0000000
--- a/tests/energy_test3/makeberg/makeberg.py
+++ /dev/null
@@ -1,377 +0,0 @@
-#!/usr/bin/env python
-import numpy as np
-import math
-from netCDF4 import Dataset
-from pylab import *
-#import pdb
-import netCDF4 as nc
-
-#
-# Initialize 2 iceberg elements, which can later be bonded in the fortran code if needed
-#
-
-def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
-
-	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
-	# To copy the global attributes of the netCDF file
-
-	#Input and output files
-	#Create Empty restart file. This is later read so that the attributes can be used.
-	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
-	create_empty_iceberg_restart_file(Empty_restart_filename)
-	#Empty_restart_filename='input_files/icebergs.res.nc'
-
-	#Read empty restart file
-	f=Dataset(Empty_restart_filename,'r') # r is for read only
-	#Write a new restart file
-	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
-
-	for attname in f.ncattrs():
-		    setattr(g,attname,getattr(f,attname))
-
-
-	# To copy the dimension of the netCDF file
-	for dimname,dim in f.dimensions.iteritems():
-		# if you want to make changes in the dimensions of the new file
-		# you should add your own conditions here before the creation of the dimension.
-		#g.createDimension(dimname,len(dim))
-		g.createDimension(dimname,Number_of_bergs)
-
-	# To copy the variables of the netCDF file
-
-	for varname,ncvar in f.variables.iteritems():
-		# if you want to make changes in the variables of the new file
-		# you should add your own conditions here before the creation of the variable.
-		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
-		#Proceed to copy the variable attributes
-		for attname in ncvar.ncattrs():
-			setattr(var,attname,getattr(ncvar,attname))
-		#Finally copy the variable data to the new created variable
-		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
-
-		if varname=='i':
-			var[:]=Number_of_bergs
-
-		if varname=='iceberg_num':
-			for j in range(Number_of_bergs):
-				#var[j]=j+1
-				var[j]=iceberg_num[j]
-
-		if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
-		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
-		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
-		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
-			var[:]=0
-
-                if varname=='uvel':
-                        var[:]=uvel
-
-                if varname=='vvel':
-                        var[:]=vvel
-
-		if varname=='mass_scaling':
-			var[:]=mass_scaling
-
-		if varname=='thickness':
-			for j in range(Number_of_bergs):
-				var[j]=thickness[j]
-
-		if varname=='mass':
-			for j in range(Number_of_bergs):
-				var[j]=mass[j]
-
-		if varname=='width'  or varname=='length':
-			for j in range(Number_of_bergs):
-				var[j]=width[j]
-
-		if varname=='lon':
-			for j in range(Number_of_bergs):
-				var[j]=lon[j]
-
-		if varname=='lat':
-			for j in range(Number_of_bergs):
-				var[j]=lat[j]
-
-		if varname=='static_berg':
-			for j in range(Number_of_bergs):
-				var[j]=static_berg[j]
-
-
-	f.close()
-	g.close()
-
-
-def create_empty_iceberg_restart_file(Empty_restart_filename):
-
-	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
-
-	i=f.createDimension('i', None)
-	lon=f.createVariable('i','i')
-
-	lon=f.createVariable('lon','d',('i'))
-	lon.long_name = "longitude" ;
-	lon.units = "degrees_E" ;
-	lon.checksum = "               0" ;
-
-	lat=f.createVariable('lat','d',('i'))
-	lat.long_name = "latitude" ;
-	lat.units = "degrees_N" ;
-	lat.checksum = "               0" ;
-
-	uvel=f.createVariable('uvel','d',('i'))
-	uvel.long_name = "zonal velocity" ;
-	uvel.units = "m/s" ;
-	uvel.checksum = "               0" ;
-
-	vvel=f.createVariable('vvel','d',('i'))
-	vvel.long_name = "meridional velocity" ;
-	vvel.units = "m/s" ;
-	vvel.checksum = "               0" ;
-
-	mass=f.createVariable('mass','d',('i'))
-	mass.long_name = "mass" ;
-	mass.units = "kg" ;
-	mass.checksum = "               0" ;
-
-	axn=f.createVariable('axn','d',('i'))
-	axn.long_name = "explicit zonal acceleration" ;
-	axn.units = "m/s^2" ;
-	axn.checksum = "               0" ;
-
-	ayn=f.createVariable('ayn','d',('i'))
-	ayn.long_name = "explicit meridional acceleration" ;
-	ayn.units = "m/s^2" ;
-	ayn.checksum = "               0" ;
-
-	bxn=f.createVariable('bxn','d',('i'))
-	bxn.long_name = "inplicit zonal acceleration" ;
-	bxn.units = "m/s^2" ;
-	bxn.checksum = "               0" ;
-
-	byn=f.createVariable('byn','d',('i'))
-	byn.long_name = "implicit meridional acceleration" ;
-	byn.units = "m/s^2" ;
-	byn.checksum = "               0" ;
-
-	ine=f.createVariable('ine','i',('i'))
-	ine.long_name = "i index" ;
-	ine.units = "none" ;
-	ine.packing = 0 ;
-	ine.checksum = "               0" ;
-
-	jne=f.createVariable('jne','i',('i'))
-	jne.long_name = "j index" ;
-	jne.units = "none" ;
-	jne.packing = 0 ;
-	jne.checksum = "               0" ;
-
-	thickness=f.createVariable('thickness','d',('i'))
-	thickness.long_name = "thickness" ;
-	thickness.units = "m" ;
-	thickness.checksum = "               0" ;
-
-	width=f.createVariable('width','d',('i'))
-	width.long_name = "width" ;
-	width.units = "m" ;
-	width.checksum = "               0" ;
-
-	length=f.createVariable('length','d',('i'))
-	length.long_name = "length" ;
-	length.units = "m" ;
-	length.checksum = "               0" ;
-
-	start_lon=f.createVariable('start_lon','d',('i'))
-	start_lon.long_name = "longitude of calving location" ;
-	start_lon.units = "degrees_E" ;
-	start_lon.checksum = "               0" ;
-
-	start_lat=f.createVariable('start_lat','d',('i'))
-	start_lat.long_name = "latitude of calving location" ;
-	start_lat.units = "degrees_N" ;
-	start_lat.checksum = "               0" ;
-
-	start_year=f.createVariable('start_year','i',('i'))
-	start_year.long_name = "calendar year of calving event" ;
-	start_year.units = "years" ;
-	start_year.packing = 0 ;
-	start_year.checksum = "               0" ;
-
-	iceberg_num=f.createVariable('iceberg_num','i',('i'))
-	iceberg_num.long_name = "identification of the iceberg" ;
-	iceberg_num.units = "dimensionless" ;
-	iceberg_num.packing = 0 ;
-	iceberg_num.checksum = "               0" ;
-
-	start_day=f.createVariable('start_day','d',('i'))
-	start_day.long_name = "year day of calving event" ;
-	start_day.units = "days" ;
-	start_day.checksum = "               0" ;
-
-	start_mass=f.createVariable('start_mass','d',('i'))
-	start_mass.long_name = "initial mass of calving berg" ;
-	start_mass.units = "kg" ;
-	start_mass.checksum = "               0" ;
-
-	mass_scaling=f.createVariable('mass_scaling','d',('i'))
-	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
-	mass_scaling.units = "none" ;
-	mass_scaling.checksum = "               0" ;
-
-	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
-	mass_of_bits.long_name = "mass of bergy bits" ;
-	mass_of_bits.units = "kg" ;
-	mass_of_bits.checksum = "               0" ;
-
-	heat_density=f.createVariable('heat_density','d',('i'))
-	heat_density.long_name = "heat density" ;
-	heat_density.units = "J/kg" ;
-	heat_density.checksum = "               0" ;
-
-	halo_berg=f.createVariable('halo_berg','d',('i'))
-	halo_berg.long_name = "halo_berg" ;
-	halo_berg.units = "dimensionless" ;
-	halo_berg.checksum = "               0" ;
-
-	static_berg=f.createVariable('static_berg','d',('i'))
-	static_berg.long_name = "static_berg" ;
-	static_berg.units = "dimensionless" ;
-	static_berg.checksum = "               0" ;
-
-	f.sync()
-	f.close()
-
-
-
-#-----------------------------------#
-#               Main                #
-#-----------------------------------#
-
-just2particles=False
-flip2ndconglom=True#False
-offset2ndconglom=True#False
-
-grdxmin=0; grdxmax=45000e3
-grdymin=0; grdymax=45000e3
-grdres=1000.0
-R_frac=0.45
-radius=(np.sqrt(3)/2.)*(R_frac*grdres) #S is < 0.5 grid res
-element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*radius**2)
-width=np.sqrt(element_area)
-thickness1=300.0
-thickness2=300.0
-rho_ice=850.0
-
-#mass
-mass=thickness1*element_area*rho_ice
-print('mass',mass)
-
-nbergs=2 #number of conglomerates
-
-#center coords of each (rectangular) conglomerate berg (CB=conglomerate berg)
-CBxc=np.array([10500, 22500]); CByc=np.array([22500, 22500])
-#CBxc=np.array([9500, 17500]); CByc=np.array([22500, 22500])
-
-#side lengths
-CBxl=np.array([2500, 7500]); CByl=np.array([7500, 2500])
-#CBxl=np.array([2500, 2500]); CByl=np.array([7500, 7500])
-#CBxl=np.array([3000, 3000]); CByl=np.array([3000, 3000])
-CByl=CByl.astype(int); CBxl=CBxl.astype(int)
-
-#--- xmax, xmin, ymax, ymin for each CB --
-CBxmin=CBxc-(0.5*CBxl); CBxmax=CBxc+(0.5*CBxl)
-CBymin=CByc-(0.5*CByl); CBymax=CByc+(0.5*CByl)
-#this shouldn't happen:
-CBxmin[CBxmin<grdxmin]=grdxmin; CBxmax[CBxmax>grdxmax]=grdxmax
-CBymin[CBxmin<grdymin]=grdymin; CBymax[CBymax>grdymax]=grdymax
-CBxc=0.5*(CBxmin+CBxmax); CByc=0.5*(CBymin+CBymax)
-
-#if just want one particle per CB
-if just2particles:
-        CBxmin=CBxc; CBxmax=CBxc
-        CBymin=CByc; CBymax=CByc
-
-#--- min and max thicknesses for each CB ---
-h1=thickness1; h2=thickness2
-CBhmax=np.array([h1,h1]); CBhmin=np.array([h2,h2])
-
-#radii
-CBrad=np.array([radius,radius])
-
-berg_x=[]; berg_y=[]
-berg_id=[]; berg_static=[]
-berg_width=[]; berg_bonds=[]
-berg_h=[]; berg_mass_scaling=[]
-berg_mass=[]
-berg_uvel=[]; berg_vvel=[]
-
-berg_count=0
-
-for i in range(nbergs):
-        x_start=CBxmin[i]+(CBrad[i]*2./np.sqrt(3))
-
-        if flip2ndconglom and i>0:
-                x_start=CBxmax[i]-(CBrad[i]*2./np.sqrt(3))
-
-        #pdb.set_trace()
-        if x_start>CBxmax[i]:
-                x_start=CBxmax[i]
-        y_start0=CBymin[i]+CBrad[i]
-        if y_start0>CBymax[i]:
-                y_start0=CBymax[i]
-        element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*(CBrad[i])**2)
-        #H (thickness) is a linear function of a berg element's position from the
-        #center of the CB. H=Hmax at the center of the CB and H=Hmin at a corner of the
-        #CB, where the dist of a corner from the center is:
-        cdistb=np.sqrt((CBxmin[i]-CBxc[i])**2+(CBymin[i]-CByc[i])**2)
-        j=0
-        x_val=x_start
-        offset=0.0
-        if (i==0):
-                uvel=0.05#0.075
-        else:
-                uvel=-0.15#-0.05
-                if (offset2ndconglom):
-                        offset=250.0
-        vvel=0.025#0.01
-        #berg_count_start=berg_count
-        while x_val<=CBxmax[i] and x_val>=CBxmin[i]:
-                y_start=y_start0+((j%2)*CBrad[i])+offset
-                k=0
-                y_val=y_start
-                while y_val<=(CBymax[i]+offset):
-                        berg_count=berg_count+1
-                        berg_id.append(berg_count)
-                        berg_x.append(x_val)
-                        berg_y.append(y_val)
-                        berg_width.append(sqrt(element_area))
-                        #dist of berg elem from center of CB
-                        bdistc=np.sqrt((x_val-CBxc[i])**2+(y_val-CByc[i])**2)
-                        bh=CBhmin[i]*bdistc/cdistb + CBhmax[i]*(1-bdistc/cdistb)
-                        if (just2particles):
-                                bh=h1
-                        berg_h.append(bh) #thickness
-                        berg_mass_scaling.append(1)
-                        berg_mass.append(bh*rho_ice*element_area)
-                        berg_static.append(0)
-                        berg_uvel.append(uvel)
-                        berg_vvel.append(vvel)
-                        # if (x_val<22000):
-                        #         berg_vvel.append(vvel)
-                        # else:
-                        #         berg_vvel.append(0.4)
-                        #berg_CBid.append(i)
-                        k=k+1
-                        y_val=y_start+(2*k*CBrad[i])
-                j=j+1
-                if flip2ndconglom and i>0:
-                        x_val=x_start-(np.sqrt(3)*CBrad[i]*j)
-                else:
-                        x_val=x_start+(np.sqrt(3)*CBrad[i]*j)
-
-print('Number of bergs',berg_count)
-
-#pdb.set_trace()
-
-#Create iceberg restart file
-Ice_geometry_source='Generic'
-Create_iceberg_restart_file(berg_count,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)
diff --git a/tests/footloose_physical/README b/tests/footloose_physical/README
deleted file mode 100644
index 8a46a3d..0000000
--- a/tests/footloose_physical/README
+++ /dev/null
@@ -1,9 +0,0 @@
-Testing for footloose mechanism parameterization in (non-bonded mode only)
-
-1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
-2.(optional) edit input.nml
-3. run the model: ./RUN
-4. animate the results: animate_trajectories.py
-
-
-
diff --git a/tests/footloose_physical/RUN1p b/tests/footloose_physical/RUN1p
deleted file mode 100755
index c3bf53e..0000000
--- a/tests/footloose_physical/RUN1p
+++ /dev/null
@@ -1,5 +0,0 @@
-rm iceberg_trajectories.nc
-rm iceberg_trajectories.nc.*
-srun -n1 ./../../build/bergs.x
-
-
diff --git a/tests/footloose_physical/diag_table b/tests/footloose_physical/diag_table
deleted file mode 100644
index c1c8819..0000000
--- a/tests/footloose_physical/diag_table
+++ /dev/null
@@ -1,3 +0,0 @@
-"icebergs test"
-1 1 1 0 0 0
-
diff --git a/tests/footloose_physical/input_old.nml b/tests/footloose_physical/input_old.nml
deleted file mode 100644
index 64159c7..0000000
--- a/tests/footloose_physical/input_old.nml
+++ /dev/null
@@ -1,170 +0,0 @@
-!note: to test this without bonds and without interactive bergs, set:
-!>iceberg_bonds_on=.true.
-!>interactive_icebergs_on=.false.
-!>manually_initialize_bonds=.true.
-!>length_for_manually_initialize_bonds<0
-
-
-&icebergs_driver_nml
-  ni=20 !number of elements, x direction
-  nj=20 !number of elements, y direction
-  ibdt=10.0 !1800.0 !86400.0 !seconds
-  ibuo=0.05 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=4800 !total simulation hours
-  nmax=99999999 !max number of timesteps
-  saverestart=.true.
-  halo=3
-  debug=.false.
-  gridres=1000.
-  sst=-2
-  collision_test=.false. !specific to the current test, must be true here
-/
-
-
-&icebergs_nml
-
-    !defaults given in parentheses:
-
-    fl_r=4        !(4) average number of footloose bergs to calve per fl_r_s seconds
-    fl_r_s=86400  !(86400) time in s over which to calve, on average, fl_r footloose bergs
-    displace_fl_bergs=.true. !(T) randomly assign FL berg positions to sides of parent berg
-    fl_style='fl_bits' !('new_bergs'). Can also group FL bergs into 'fl_bits'
-    new_berg_from_fl_bits_mass_thres=8.e11
-    fl_use_poisson_distribution=.true.!.false.
-
-    mts=.false. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=1 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
-    !contact_distance=0 !3.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    !contact_spring_coef=1.e-5!(default=spring_coeff) Berg spring coeff for collisions
-
-    halo=3 !(4) halo width
-    Lx=20000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.True. !(T) Point in cell can be found assuming regular Cartesian grid
-    !hexagonal_icebergs=.True. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    rho_bergs=850. ! (850) iceberg density
-    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=1.0 ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.true. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0.0 !4 !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.false.!.true.!.false. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors
-
-    verbose=.true. !(F) Be verbose to stderr
-    verbose_hrs=24 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !1 !(24) sampling period for trajectory storage
-    traj_write_hrs=1 ! (480) Period for writing sampled trajectories to disk
-    budget=.true.!.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    save_fl_traj=.true. !(T) True save masses and footloose parameters in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    length_for_manually_initialize_bonds=-1.e3!0.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/footloose_poisson/README b/tests/footloose_poisson/README
deleted file mode 100644
index 8a46a3d..0000000
--- a/tests/footloose_poisson/README
+++ /dev/null
@@ -1,9 +0,0 @@
-Testing for footloose mechanism parameterization in (non-bonded mode only)
-
-1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
-2.(optional) edit input.nml
-3. run the model: ./RUN
-4. animate the results: animate_trajectories.py
-
-
-
diff --git a/tests/footloose_poisson/RUN b/tests/footloose_poisson/RUN
deleted file mode 100755
index 090c034..0000000
--- a/tests/footloose_poisson/RUN
+++ /dev/null
@@ -1,5 +0,0 @@
-rm iceberg_trajectories.nc
-rm iceberg_trajectories.nc.*
-srun -n4 ./../../build/bergs.x
-
-
diff --git a/tests/footloose_poisson/RUN1p b/tests/footloose_poisson/RUN1p
deleted file mode 100755
index c3bf53e..0000000
--- a/tests/footloose_poisson/RUN1p
+++ /dev/null
@@ -1,5 +0,0 @@
-rm iceberg_trajectories.nc
-rm iceberg_trajectories.nc.*
-srun -n1 ./../../build/bergs.x
-
-
diff --git a/tests/footloose_poisson/animate_trajectories.py b/tests/footloose_poisson/animate_trajectories.py
deleted file mode 100755
index 27bf850..0000000
--- a/tests/footloose_poisson/animate_trajectories.py
+++ /dev/null
@@ -1,151 +0,0 @@
-#!/usr/bin/env python
-
-from netCDF4 import Dataset
-import pdb
-import netCDF4 as nc
-import numpy as np
-import matplotlib
-import math
-import os
-matplotlib.use("tkagg")
-from pylab import *
-import matplotlib.pyplot as plt
-from matplotlib.animation import FuncAnimation
-from mpl_toolkits.axes_grid1 import make_axes_locatable
-import argparse
-
-def parseCommandLine():
-    parser = argparse.ArgumentParser(description=
-    '''Generate animation of iceberg trajectories.''',
-    epilog='Written by Alex Huth, 2020')
-    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
-                    help=''' provide filename to plot''')
-    parser.add_argument('-s', type=int, default='1450',
-                        help='''plotted particle size''')
-    optCmdLineArgs = parser.parse_args()
-    return optCmdLineArgs
-
-
-
-def main(args):
-
-    print('reading file')
-
-    filename=args.fname
-    psize=args.s
-    #filename = 'iceberg_trajectories.nc'
-    field = 'lon'
-    field2 = 'lat'
-
-    with nc.Dataset(filename) as file:
-        x = file.variables['lon'][:]/1.e3
-        y = file.variables['lat'][:]/1.e3
-        day = file.variables['day'][:]
-        bid = file.variables['id_ij'][:]
-        vo = file.variables['fl_k'][:]
-        length = file.variables['length'][:]
-        width = file.variables['width'][:]
-
-    ud = np.unique(day)
-    ub = np.unique(bid)
-    t = ud[0]
-
-    radius = length*width*(1./(2*np.sqrt(3)))
-
-    urad=np.unique(radius)
-    #print('urad',urad)
-
-    # frame info
-    num_frames = len(ud)
-    movie_len = 10.0 #seconds
-    frame_len = 1000.0*movie_len/num_frames
-
-    xmin = 0 #np.floor(min(min(x),min(y),0))
-    xmax = 20 #np.ceil(max(max(x),max(y),20))
-    ymin = xmin
-    ymax = xmax
-
-    anim_running = True
-
-    def animate(i):
-
-        x1 = x[day == ud[i]]
-        y1 = y[day == ud[i]]
-        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
-
-        scat.set_offsets(data)
-
-        vo1 = vo[day == ud[i]]
-        scat.set_edgecolor('k')
-        scat.set_color(cmap(norm(vo1)))
-
-        r1 = radius[day == ud[i]]
-        scat.set_sizes(r1/psize)
-
-        t = ud[i]
-        time_text.set_text('time = %.1f days' % t )
-        return scat,time_text
-
-    def init():
-        scat.set_offsets([])
-        return scat,
-
-    def onClick(event):
-        global anim_running
-        if anim_running:
-            ani.event_source.stop()
-            anim_running = False
-        else:
-            ani.event_source.start()
-            anim_running = True
-
-    # Now we can do the plotting!
-    f = plt.figure(figsize=(5,5))
-    f.tight_layout()
-    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
-    div = make_axes_locatable(ax1)
-    cax = div.append_axes('right', '5%', '5%')
-    scat = ax1.scatter([],[],marker='o')
-    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
-
-    cmap = plt.cm.get_cmap('RdYlBu')
-    norm = plt.Normalize(vo.min(), vo.max())
-    cb1 = matplotlib.colorbar.ColorbarBase(cax, cmap=cmap,
-                                           norm=norm,
-                                           orientation='vertical')
-
-
-    # Change major ticks to show every 20.
-    ax1.xaxis.set_major_locator(MultipleLocator(5))
-    ax1.yaxis.set_major_locator(MultipleLocator(5))
-
-    ax1.xaxis.set_minor_locator(MultipleLocator(1))
-    ax1.yaxis.set_minor_locator(MultipleLocator(1))
-
-    # Turn grid on for both major and minor ticks and style minor slightly
-    # differently.
-    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
-    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
-
-    ax1.set_xlabel('x (km)')
-    ax1.set_ylabel('y (km)')
-    ax1.set_title('Iceberg trajectory')
-
-    f.canvas.mpl_connect('button_press_event', onClick)
-
-    ani = FuncAnimation(
-        f,animate,init_func=init,frames=num_frames,
-        interval=frame_len,blit=True,repeat=True)
-
-    print('time',t)
-
-    plt.show()
-    #animation.save("iceberg_traj_animation.mp4")
-
-
-print('Script complete')
-
-if __name__ == '__main__':
-    optCmdLineArgs=	parseCommandLine()
-    anim_running = True
-    main(optCmdLineArgs)
diff --git a/tests/footloose_poisson/diag_table b/tests/footloose_poisson/diag_table
deleted file mode 100644
index c1c8819..0000000
--- a/tests/footloose_poisson/diag_table
+++ /dev/null
@@ -1,3 +0,0 @@
-"icebergs test"
-1 1 1 0 0 0
-
diff --git a/tests/footloose_poisson/input_old.nml b/tests/footloose_poisson/input_old.nml
deleted file mode 100644
index 64159c7..0000000
--- a/tests/footloose_poisson/input_old.nml
+++ /dev/null
@@ -1,170 +0,0 @@
-!note: to test this without bonds and without interactive bergs, set:
-!>iceberg_bonds_on=.true.
-!>interactive_icebergs_on=.false.
-!>manually_initialize_bonds=.true.
-!>length_for_manually_initialize_bonds<0
-
-
-&icebergs_driver_nml
-  ni=20 !number of elements, x direction
-  nj=20 !number of elements, y direction
-  ibdt=10.0 !1800.0 !86400.0 !seconds
-  ibuo=0.05 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=4800 !total simulation hours
-  nmax=99999999 !max number of timesteps
-  saverestart=.true.
-  halo=3
-  debug=.false.
-  gridres=1000.
-  sst=-2
-  collision_test=.false. !specific to the current test, must be true here
-/
-
-
-&icebergs_nml
-
-    !defaults given in parentheses:
-
-    fl_r=4        !(4) average number of footloose bergs to calve per fl_r_s seconds
-    fl_r_s=86400  !(86400) time in s over which to calve, on average, fl_r footloose bergs
-    displace_fl_bergs=.true. !(T) randomly assign FL berg positions to sides of parent berg
-    fl_style='fl_bits' !('new_bergs'). Can also group FL bergs into 'fl_bits'
-    new_berg_from_fl_bits_mass_thres=8.e11
-    fl_use_poisson_distribution=.true.!.false.
-
-    mts=.false. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=1 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
-    !contact_distance=0 !3.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    !contact_spring_coef=1.e-5!(default=spring_coeff) Berg spring coeff for collisions
-
-    halo=3 !(4) halo width
-    Lx=20000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.True. !(T) Point in cell can be found assuming regular Cartesian grid
-    !hexagonal_icebergs=.True. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    rho_bergs=850. ! (850) iceberg density
-    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=1.0 ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.true. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0.0 !4 !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.false.!.true.!.false. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors
-
-    verbose=.true. !(F) Be verbose to stderr
-    verbose_hrs=24 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !1 !(24) sampling period for trajectory storage
-    traj_write_hrs=1 ! (480) Period for writing sampled trajectories to disk
-    budget=.true.!.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    save_fl_traj=.true. !(T) True save masses and footloose parameters in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    length_for_manually_initialize_bonds=-1.e3!0.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/footloose_poisson/makeberg/RUN b/tests/footloose_poisson/makeberg/RUN
deleted file mode 100755
index 750e29e..0000000
--- a/tests/footloose_poisson/makeberg/RUN
+++ /dev/null
@@ -1,5 +0,0 @@
-
-rm ./output_files/Generic*
-./makeberg.py
-
-cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
\ No newline at end of file
diff --git a/tests/footloose_poisson/makeberg/makeberg.py b/tests/footloose_poisson/makeberg/makeberg.py
deleted file mode 100755
index dd146fc..0000000
--- a/tests/footloose_poisson/makeberg/makeberg.py
+++ /dev/null
@@ -1,278 +0,0 @@
-#!/usr/bin/env python
-import numpy as np
-import math
-from netCDF4 import Dataset
-from pylab import *
-#import pdb
-import netCDF4 as nc
-
-#
-# Initialize 2 iceberg elements, which can later be bonded in the fortran code if needed
-#
-
-def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
-
-	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
-	# To copy the global attributes of the netCDF file
-
-	#Input and output files
-	#Create Empty restart file. This is later read so that the attributes can be used.
-	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
-	create_empty_iceberg_restart_file(Empty_restart_filename)
-	#Empty_restart_filename='input_files/icebergs.res.nc'
-
-	#Read empty restart file
-	f=Dataset(Empty_restart_filename,'r') # r is for read only
-	#Write a new restart file
-	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
-
-	for attname in f.ncattrs():
-		    setattr(g,attname,getattr(f,attname))
-
-
-	# To copy the dimension of the netCDF file
-	for dimname,dim in f.dimensions.iteritems():
-		# if you want to make changes in the dimensions of the new file
-		# you should add your own conditions here before the creation of the dimension.
-		#g.createDimension(dimname,len(dim))
-		g.createDimension(dimname,Number_of_bergs)
-
-	# To copy the variables of the netCDF file
-
-	for varname,ncvar in f.variables.iteritems():
-		# if you want to make changes in the variables of the new file
-		# you should add your own conditions here before the creation of the variable.
-		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
-		#Proceed to copy the variable attributes
-		for attname in ncvar.ncattrs():
-			setattr(var,attname,getattr(ncvar,attname))
-		#Finally copy the variable data to the new created variable
-		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
-
-		if varname=='i':
-			var[:]=Number_of_bergs
-
-		if varname=='iceberg_num':
-			for j in range(Number_of_bergs):
-				#var[j]=j+1
-				var[j]=iceberg_num[j]
-
-		if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
-		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
-		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
-		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
-			var[:]=0
-
-                if varname=='uvel':
-                        var[:]=uvel
-
-                if varname=='vvel':
-                        var[:]=vvel
-
-		if varname=='mass_scaling':
-			var[:]=mass_scaling
-
-		if varname=='thickness':
-			for j in range(Number_of_bergs):
-				var[j]=thickness[j]
-
-		if varname=='mass':
-			for j in range(Number_of_bergs):
-				var[j]=mass[j]
-
-		if varname=='width'  or varname=='length':
-			for j in range(Number_of_bergs):
-				var[j]=width[j]
-
-		if varname=='lon':
-			for j in range(Number_of_bergs):
-				var[j]=lon[j]
-
-		if varname=='lat':
-			for j in range(Number_of_bergs):
-				var[j]=lat[j]
-
-		if varname=='static_berg':
-			for j in range(Number_of_bergs):
-				var[j]=static_berg[j]
-
-
-	f.close()
-	g.close()
-
-
-def create_empty_iceberg_restart_file(Empty_restart_filename):
-
-	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
-
-	i=f.createDimension('i', None)
-	lon=f.createVariable('i','i')
-
-	lon=f.createVariable('lon','d',('i'))
-	lon.long_name = "longitude" ;
-	lon.units = "degrees_E" ;
-	lon.checksum = "               0" ;
-
-	lat=f.createVariable('lat','d',('i'))
-	lat.long_name = "latitude" ;
-	lat.units = "degrees_N" ;
-	lat.checksum = "               0" ;
-
-	uvel=f.createVariable('uvel','d',('i'))
-	uvel.long_name = "zonal velocity" ;
-	uvel.units = "m/s" ;
-	uvel.checksum = "               0" ;
-
-	vvel=f.createVariable('vvel','d',('i'))
-	vvel.long_name = "meridional velocity" ;
-	vvel.units = "m/s" ;
-	vvel.checksum = "               0" ;
-
-	mass=f.createVariable('mass','d',('i'))
-	mass.long_name = "mass" ;
-	mass.units = "kg" ;
-	mass.checksum = "               0" ;
-
-	axn=f.createVariable('axn','d',('i'))
-	axn.long_name = "explicit zonal acceleration" ;
-	axn.units = "m/s^2" ;
-	axn.checksum = "               0" ;
-
-	ayn=f.createVariable('ayn','d',('i'))
-	ayn.long_name = "explicit meridional acceleration" ;
-	ayn.units = "m/s^2" ;
-	ayn.checksum = "               0" ;
-
-	bxn=f.createVariable('bxn','d',('i'))
-	bxn.long_name = "inplicit zonal acceleration" ;
-	bxn.units = "m/s^2" ;
-	bxn.checksum = "               0" ;
-
-	byn=f.createVariable('byn','d',('i'))
-	byn.long_name = "implicit meridional acceleration" ;
-	byn.units = "m/s^2" ;
-	byn.checksum = "               0" ;
-
-	ine=f.createVariable('ine','i',('i'))
-	ine.long_name = "i index" ;
-	ine.units = "none" ;
-	ine.packing = 0 ;
-	ine.checksum = "               0" ;
-
-	jne=f.createVariable('jne','i',('i'))
-	jne.long_name = "j index" ;
-	jne.units = "none" ;
-	jne.packing = 0 ;
-	jne.checksum = "               0" ;
-
-	thickness=f.createVariable('thickness','d',('i'))
-	thickness.long_name = "thickness" ;
-	thickness.units = "m" ;
-	thickness.checksum = "               0" ;
-
-	width=f.createVariable('width','d',('i'))
-	width.long_name = "width" ;
-	width.units = "m" ;
-	width.checksum = "               0" ;
-
-	length=f.createVariable('length','d',('i'))
-	length.long_name = "length" ;
-	length.units = "m" ;
-	length.checksum = "               0" ;
-
-	start_lon=f.createVariable('start_lon','d',('i'))
-	start_lon.long_name = "longitude of calving location" ;
-	start_lon.units = "degrees_E" ;
-	start_lon.checksum = "               0" ;
-
-	start_lat=f.createVariable('start_lat','d',('i'))
-	start_lat.long_name = "latitude of calving location" ;
-	start_lat.units = "degrees_N" ;
-	start_lat.checksum = "               0" ;
-
-	start_year=f.createVariable('start_year','i',('i'))
-	start_year.long_name = "calendar year of calving event" ;
-	start_year.units = "years" ;
-	start_year.packing = 0 ;
-	start_year.checksum = "               0" ;
-
-	iceberg_num=f.createVariable('iceberg_num','i',('i'))
-	iceberg_num.long_name = "identification of the iceberg" ;
-	iceberg_num.units = "dimensionless" ;
-	iceberg_num.packing = 0 ;
-	iceberg_num.checksum = "               0" ;
-
-	start_day=f.createVariable('start_day','d',('i'))
-	start_day.long_name = "year day of calving event" ;
-	start_day.units = "days" ;
-	start_day.checksum = "               0" ;
-
-	start_mass=f.createVariable('start_mass','d',('i'))
-	start_mass.long_name = "initial mass of calving berg" ;
-	start_mass.units = "kg" ;
-	start_mass.checksum = "               0" ;
-
-	mass_scaling=f.createVariable('mass_scaling','d',('i'))
-	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
-	mass_scaling.units = "none" ;
-	mass_scaling.checksum = "               0" ;
-
-	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
-	mass_of_bits.long_name = "mass of bergy bits" ;
-	mass_of_bits.units = "kg" ;
-	mass_of_bits.checksum = "               0" ;
-
-	heat_density=f.createVariable('heat_density','d',('i'))
-	heat_density.long_name = "heat density" ;
-	heat_density.units = "J/kg" ;
-	heat_density.checksum = "               0" ;
-
-	halo_berg=f.createVariable('halo_berg','d',('i'))
-	halo_berg.long_name = "halo_berg" ;
-	halo_berg.units = "dimensionless" ;
-	halo_berg.checksum = "               0" ;
-
-	static_berg=f.createVariable('static_berg','d',('i'))
-	static_berg.long_name = "static_berg" ;
-	static_berg.units = "dimensionless" ;
-	static_berg.checksum = "               0" ;
-
-	f.sync()
-	f.close()
-
-
-
-#-----------------------------------#
-#               Main                #
-#-----------------------------------#
-
-grdres=5000.0
-xc=10000.1
-yc=10000.1
-R_frac=0.45
-radius=(np.sqrt(3)/2.)*(R_frac*grdres) #S is < 0.5 grid res
-element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*radius**2)
-width=np.sqrt(element_area)
-thickness=300.0
-rhoi=850.0
-mass=thickness*rhoi*element_area
-
-berg_count=2
-berg_x=[xc-radius,xc+radius]
-berg_y=[yc,yc]
-berg_h=[thickness,thickness]
-berg_width=[width,width]
-berg_mass=[mass,mass]
-berg_mass_scaling=[1,1]
-berg_id=[1,2]
-berg_static=[0,0]
-berg_uvel=[0,0]
-berg_vvel=[0,0]
-
-print('Number of bergs',berg_count)
-print('berg_x,berg_y',berg_x,berg_y)
-print('width',width)
-
-#Create iceberg restart file
-Ice_geometry_source='Generic'
-Create_iceberg_restart_file(berg_count,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)
diff --git a/tests/footloose_tests/.gitignore b/tests/footloose_tests/.gitignore
new file mode 100644
index 0000000..69f2275
--- /dev/null
+++ b/tests/footloose_tests/.gitignore
@@ -0,0 +1 @@
+old/
\ No newline at end of file
diff --git a/tests/footloose_tests/README b/tests/footloose_tests/README
new file mode 100644
index 0000000..5bb4c4f
--- /dev/null
+++ b/tests/footloose_tests/README
@@ -0,0 +1,25 @@
+Testing for footloose mechanism parameterization in (non-bonded mode only).
+
+"FL_poisson" tests a scheme similar to England et al 2020, where footloose child bergs are created according to a Poisson distribution.
+
+"FL_physical" tests the Huth et al 2022 scheme, where beam theory is used to determine when to calve footloose child bergs according to the size of the underwater foot on the parent berg, which is determined by tracking side melt and erosion over time.
+
+In both tests, we use the Huth et al 2022 footloose child berg binning scheme.
+
+1. Make the iceberg input files: cd makeberg; ./RUN; cd ..
+2. run the model: ./RUN_FL_poisson or ./RUN_FL_physical
+3. animate the results:
+
+./animate_trajectories.py -fname="FL_poisson.nc"
+or
+./animate_trajectories.py -fname="FL_physical.nc"
+
+
+!!for regression testing:
+Note the "write_restart berg" chksums in each of the .nml files that are called by the model run commands, and also printed below:
+
+FL_poisson:
+chksum=1239600118 chksum2=1239600118 chksum3=-1474195494 chksum4=-1474195494 chksum5=0 #=8
+
+FL_physical:
+chksum=-461793748 chksum2=-461793748 chksum3=-1042515716 chksum4=-1042515716 chksum5=0 #=12
diff --git a/tests/footloose_tests/RUN_FL_physical b/tests/footloose_tests/RUN_FL_physical
new file mode 100755
index 0000000..c0fdd06
--- /dev/null
+++ b/tests/footloose_tests/RUN_FL_physical
@@ -0,0 +1,4 @@
+rm iceberg_trajectories.nc
+rm iceberg_trajectories.nc.*
+cp input_FL_physical.nml input.nml
+srun -n4 ./../../build/bergs.x
\ No newline at end of file
diff --git a/tests/footloose_tests/RUN_FL_poisson b/tests/footloose_tests/RUN_FL_poisson
new file mode 100755
index 0000000..6029355
--- /dev/null
+++ b/tests/footloose_tests/RUN_FL_poisson
@@ -0,0 +1,4 @@
+rm iceberg_trajectories.nc
+rm iceberg_trajectories.nc.*
+cp input_FL_poisson.nml input.nml
+srun -n4 ./../../build/bergs.x
\ No newline at end of file
diff --git a/tests/footloose_physical/animate_trajectories.py b/tests/footloose_tests/animate_trajectories.py
similarity index 100%
rename from tests/footloose_physical/animate_trajectories.py
rename to tests/footloose_tests/animate_trajectories.py
diff --git a/tests/chaotic_test/diag_table b/tests/footloose_tests/diag_table
similarity index 100%
rename from tests/chaotic_test/diag_table
rename to tests/footloose_tests/diag_table
diff --git a/tests/footloose_physical/input.nml b/tests/footloose_tests/input_FL_physical.nml
similarity index 99%
rename from tests/footloose_physical/input.nml
rename to tests/footloose_tests/input_FL_physical.nml
index 270111d..c3d53fe 100644
--- a/tests/footloose_physical/input.nml
+++ b/tests/footloose_tests/input_FL_physical.nml
@@ -24,6 +24,9 @@
 
 &icebergs_nml
 
+    traj_name=FL_physical.nc
+    bond_traj_name=FL_physical_bonds.nc
+
     !defaults given in parentheses:
 
     fl_r=1        !(4) average number of footloose bergs to calve per fl_r_s seconds
diff --git a/tests/footloose_poisson/input.nml b/tests/footloose_tests/input_FL_poisson.nml
similarity index 99%
rename from tests/footloose_poisson/input.nml
rename to tests/footloose_tests/input_FL_poisson.nml
index 3e6a416..5cfc651 100644
--- a/tests/footloose_poisson/input.nml
+++ b/tests/footloose_tests/input_FL_poisson.nml
@@ -23,6 +23,9 @@
 
 &icebergs_nml
 
+    traj_name=FL_poisson.nc
+    bond_traj_name=FL_poisson_bonds.nc
+    
     !defaults given in parentheses:
 
     fl_r=4        !(4) average number of footloose bergs to calve per fl_r_s seconds
diff --git a/tests/footloose_physical/makeberg/RUN b/tests/footloose_tests/makeberg/RUN
similarity index 100%
rename from tests/footloose_physical/makeberg/RUN
rename to tests/footloose_tests/makeberg/RUN
diff --git a/tests/footloose_physical/makeberg/makeberg.py b/tests/footloose_tests/makeberg/makeberg.py
similarity index 100%
rename from tests/footloose_physical/makeberg/makeberg.py
rename to tests/footloose_tests/makeberg/makeberg.py
diff --git a/tests/frac_test/.gitignore b/tests/frac_test/.gitignore
deleted file mode 100644
index 68bcbc9..0000000
--- a/tests/frac_test/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-results/
\ No newline at end of file
diff --git a/tests/frac_test/README b/tests/frac_test/README
deleted file mode 100644
index 7482b12..0000000
--- a/tests/frac_test/README
+++ /dev/null
@@ -1,9 +0,0 @@
-Collision and subsequent fracture of two conglomerate bergs. For testing a scheme where the MTS solution is iterated to convergence in order to help conserve momentum conservation when collisions occur. Also for testing fracture scheme (e.g. effects of particle size, fracture thresholds, sensitivity to violation of momentum conservation). Set force_convergence to true and specify a convergence tolerance. Iterations will stop once convergence tolerance is reached.
-
-Unlike in energy_test2, this test will not conserve momentum sufficiently during collision unless the iterative scheme is used.
-
-1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
-2.(optional) edit input.nml
-3. run the model: ./RUN
-4, animate the results: animate_trajectories.py
-
diff --git a/tests/frac_test/RUN b/tests/frac_test/RUN
deleted file mode 100755
index f881323..0000000
--- a/tests/frac_test/RUN
+++ /dev/null
@@ -1,7 +0,0 @@
-rm iceberg_trajectories.nc
-rm iceberg_trajectories.nc.*
-rm bond_trajectories.nc
-rm bond_trajectories.nc.*
-srun -n9 ./../../build/bergs.x
-
-
diff --git a/tests/frac_test/RUN1p b/tests/frac_test/RUN1p
deleted file mode 100755
index 3dfc97d..0000000
--- a/tests/frac_test/RUN1p
+++ /dev/null
@@ -1,7 +0,0 @@
-rm iceberg_trajectories.nc
-rm iceberg_trajectories.nc.*
-rm bond_trajectories.nc
-rm bond_trajectories.nc.*
-srun -n1 ./../../build/bergs.x
-
-
diff --git a/tests/frac_test/animate_trajectories.py b/tests/frac_test/animate_trajectories.py
deleted file mode 100755
index ca7d5cd..0000000
--- a/tests/frac_test/animate_trajectories.py
+++ /dev/null
@@ -1,140 +0,0 @@
-#!/usr/bin/env python
-
-from netCDF4 import Dataset
-import pdb
-import netCDF4 as nc
-import numpy as np
-import matplotlib
-import math
-import os
-matplotlib.use("tkagg")
-from pylab import *
-import matplotlib.pyplot as plt
-from matplotlib.animation import FuncAnimation
-import argparse
-
-def parseCommandLine():
-    parser = argparse.ArgumentParser(description=
-    '''Generate animation of iceberg trajectories.''',
-    epilog='Written by Alex Huth, 2020')
-    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
-                    help=''' provide filename to plot''')
-    parser.add_argument('-s', type=int, default='4000',
-                    help='''plotted particle size''')  
-    optCmdLineArgs = parser.parse_args()
-    return optCmdLineArgs
-
-
-def main(args):
-
-    print('reading file')
-
-    filename=args.fname
-    psize=args.s
-    #filename = 'iceberg_trajectories.nc'
-    field = 'lon'
-    field2 = 'lat'
-
-    with nc.Dataset(filename) as file:
-        x = file.variables['lon'][:]/1.e3
-        y = file.variables['lat'][:]/1.e3
-        day = file.variables['day'][:]
-        length = file.variables['length'][:]
-        width = file.variables['width'][:]
-
-        
-    radius = length*width*(1/(2*np.sqrt(3)))
-
-    crop=False
-    tc=1.25
-    if crop:
-        x=x[day<=tc]
-        y=y[day<=tc]
-        day=day[day<=tc]
-
-    ud = np.unique(day)
-    t = ud[0]
-
-    # frame info
-    num_frames = len(ud)
-    movie_len = 10.0 #seconds
-    frame_len = 1000.0*movie_len/num_frames
-
-    xmin = 0
-    xmax = 30 #45 #30
-    ymin = 7.5 #0 #7.5
-    ymax = 37.5 #45 #37.5
-
-    anim_running = True
-
-    def animate(i):
-
-        x1 = x[day == ud[i]]
-        y1 = y[day == ud[i]]
-        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
-
-        scat.set_offsets(data)
-
-        t = ud[i]
-        time_text.set_text('time = %.1f days' % t )
-
-        r1 = radius[day == ud[i]]
-        
-        scat.set_sizes(r1/psize)
-        return scat,time_text
-
-    def init():
-        scat.set_offsets([])
-        return scat,
-
-    def onClick(event):
-        global anim_running
-        if anim_running:
-            ani.event_source.stop()
-            anim_running = False
-        else:
-            ani.event_source.start()
-            anim_running = True
-
-    # Now we can do the plotting!
-    f = plt.figure(figsize=(5,5))
-    f.tight_layout()
-    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
-    #scat = ax1.scatter([],[],marker='o',facecolor='w',s=psize,edgecolor='red')
-    scat = ax1.scatter([],[],marker='o',facecolor='w',edgecolor='red')    
-    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
-
-    # Change major ticks to show every 20.
-    ax1.xaxis.set_major_locator(MultipleLocator(5))
-    ax1.yaxis.set_major_locator(MultipleLocator(5))
-
-    ax1.xaxis.set_minor_locator(MultipleLocator(1))
-    ax1.yaxis.set_minor_locator(MultipleLocator(1))
-
-    # Turn grid on for both major and minor ticks and style minor slightly
-    # differently.
-    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
-    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
-
-    ax1.set_xlabel('x (km)')
-    ax1.set_ylabel('y (km)')
-    ax1.set_title('Iceberg trajectory')
-
-    f.canvas.mpl_connect('button_press_event', onClick)
-
-    ani = FuncAnimation(
-        f,animate,init_func=init,frames=num_frames,
-        interval=frame_len,blit=True,repeat=True)
-
-    print('time',t)
-
-    plt.show()
-    #animation.save("iceberg_traj_animation.mp4")
-
-
-print('Script complete')
-
-if __name__ == '__main__':
-    optCmdLineArgs=	parseCommandLine()
-    anim_running = True
-    main(optCmdLineArgs)
diff --git a/tests/frac_test/animate_trajectories_1pe.py b/tests/frac_test/animate_trajectories_1pe.py
deleted file mode 100755
index 931c727..0000000
--- a/tests/frac_test/animate_trajectories_1pe.py
+++ /dev/null
@@ -1,189 +0,0 @@
-#!/usr/bin/env python
-
-from netCDF4 import Dataset
-import pdb
-import netCDF4 as nc
-import numpy as np
-import matplotlib
-import math
-import os
-matplotlib.use("tkagg")
-from pylab import *
-import matplotlib.pyplot as plt
-from matplotlib.animation import FuncAnimation
-import argparse
-
-def parseCommandLine():
-    parser = argparse.ArgumentParser(description=
-    '''Generate animation of iceberg trajectories.''',
-    epilog='Written by Alex Huth, 2020')
-    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc.0000',
-                    help=''' provide filename to plot''')
-    optCmdLineArgs = parser.parse_args()
-    return optCmdLineArgs
-
-
-
-def main(args):
-
-    print('reading file')
-
-    filename=args.fname
-    #filename = 'iceberg_trajectories.nc'
-    field = 'lon'
-    field2 = 'lat'
-
-    with nc.Dataset(filename) as file:
-        x = file.variables['lon'][:]/1.e3
-        y = file.variables['lat'][:]/1.e3
-        day = file.variables['day'][:]
-        hs = file.variables['halo_berg'][:]
-        #hs = file.variables['conglom_id'][:]        
-
-    #hs = hs+1
-    ud = np.unique(day)
-    t = ud[0]
-
-    print('unique hs',np.unique(hs))
-
-    # frame info
-    num_frames = len(ud)
-    movie_len = 10.0 #seconds
-    frame_len = 1000.0*movie_len/num_frames
-
-    xmin = np.floor(min(min(x),min(y),-5))
-    xmax = np.ceil(max(max(x),max(y),35))
-    ymin = xmin
-    ymax = xmax
-
-    anim_running = True
-
-    def animate(i):
-
-        x1 = x[day == ud[i]]
-        y1 = y[day == ud[i]]
-        hstat = hs[day == ud[i]]
-        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
-
-        cstring=[]
-        for j in range(len(hstat)):
-            if (hstat[j]<0):
-                cstring.append("m")
-            elif (hstat[j]==0):
-                cstring.append("b")
-            elif (hstat[j]==1):
-                cstring.append("r")
-            elif (hstat[j]==2):
-                cstring.append("g")
-            elif (hstat[j]==3):
-                cstring.append("k")
-            elif (hstat[j]==4):
-                cstring.append("c")
-            elif (hstat[j]==5):
-                cstring.append("y")
-            elif (hstat[j]==6):
-                cstring.append("w")
-            elif (hstat[j]==10):                
-                cstring.append("c")
-            # else:
-            #     cstring.append("y")
-
-        scat.set_offsets(data)
-        scat.set_color(cstring)
-        scat.set_edgecolor('k')
-
-        t = ud[i]
-        time_text.set_text('time = %.1f days' % t )
-        return scat,time_text
-
-    def init():
-        scat.set_offsets([])
-        return scat,
-
-    def onClick(event):
-        global anim_running
-        if anim_running:
-            ani.event_source.stop()
-            anim_running = False
-        else:
-            ani.event_source.start()
-            anim_running = True
-
-    # Now we can do the plotting!
-    f = plt.figure(figsize=(5,5))
-    f.tight_layout()
-    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
-    scat = ax1.scatter([],[],marker='o',s=30)
-    #scat = ax1.scatter([],[],marker='o',facecolor='w',s=60,edgecolor='red')
-    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
-
-    # Change major ticks to show every 20.
-    ax1.xaxis.set_major_locator(MultipleLocator(5))
-    ax1.yaxis.set_major_locator(MultipleLocator(5))
-
-    ax1.xaxis.set_minor_locator(MultipleLocator(1))
-    ax1.yaxis.set_minor_locator(MultipleLocator(1))
-
-    # Turn grid on for both major and minor ticks and style minor slightly
-    # differently.
-    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
-    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
-
-    ax1.set_xlabel('x (km)')
-    ax1.set_ylabel('y (km)')
-    ax1.set_title('Iceberg trajectory')
-
-    f.canvas.mpl_connect('button_press_event', onClick)
-
-    ani = FuncAnimation(
-        f,animate,init_func=init,frames=num_frames,
-        interval=frame_len,blit=True,repeat=True)
-
-    print('time',t)
-
-    plt.plot([0,0],[0,30],'k-',lw=1)
-    plt.plot([10,10],[0,30],'k-',lw=1)
-    plt.plot([20,20],[0,30],'k-',lw=1)
-    plt.plot([30,30],[0,30],'k-',lw=1)
-    plt.plot([0,30],[0,0],'k-',lw=1)
-    plt.plot([0,30],[10,10],'k-',lw=1)
-    plt.plot([0,30],[20,20],'k-',lw=1)
-    plt.plot([0,30],[30,30],'k-',lw=1)
-
-
-    h=3 #halo width
-    w=h-1
-
-    x1=0; x2=10; x3=20; x4=30
-    y1=0; y2=10; y3=20; y4=30    
-    
-
-    plt.plot([x1-w,x1-w],[y1-w,y4+h],'b:',lw=1)
-    plt.plot([x1+h,x1+h],[y1-w,y4+h],'b:',lw=1)
-    plt.plot([x2-w,x2-w],[y1-w,y4+h],'b:',lw=1)
-    plt.plot([x2+h,x2+h],[y1-w,y4+h],'b:',lw=1)
-    plt.plot([x3-w,x3-w],[y1-w,y4+h],'b:',lw=1)
-    plt.plot([x3+h,x3+h],[y1-w,y4+h],'b:',lw=1)
-    plt.plot([x4-w,x4-w],[y1-w,y4+h],'b:',lw=1)
-    plt.plot([x4+h,x4+h],[y1-w,y4+h],'b:',lw=1) 
-       
-
-    plt.plot([x1-w,x4+h],[y1-w,y1-w],'b:',lw=1)
-    plt.plot([x1-w,x4+h],[y1+h,y1+h],'b:',lw=1)
-    plt.plot([x1-w,x4+h],[y2-w,y2-w],'b:',lw=1)
-    plt.plot([x1-w,x4+h],[y2+h,y2+h],'b:',lw=1)
-    plt.plot([x1-w,x4+h],[y3-w,y3-w],'b:',lw=1)
-    plt.plot([x1-w,x4+h],[y3+h,y3+h],'b:',lw=1)
-    plt.plot([x1-w,x4+h],[y4-w,y4-w],'b:',lw=1)
-    plt.plot([x1-w,x4+h],[y4+h,y4+h],'b:',lw=1)
-
-    plt.show()
-    #animation.save("iceberg_traj_animation.mp4")
-
-
-print('Script complete')
-
-if __name__ == '__main__':
-    optCmdLineArgs=	parseCommandLine()
-    anim_running = True
-    main(optCmdLineArgs)
diff --git a/tests/frac_test/diag_table b/tests/frac_test/diag_table
deleted file mode 100644
index c1c8819..0000000
--- a/tests/frac_test/diag_table
+++ /dev/null
@@ -1,3 +0,0 @@
-"icebergs test"
-1 1 1 0 0 0
-
diff --git a/tests/frac_test/input.nml b/tests/frac_test/input.nml
deleted file mode 100644
index 0d6aab7..0000000
--- a/tests/frac_test/input.nml
+++ /dev/null
@@ -1,186 +0,0 @@
-
-&icebergs_driver_nml
-  ni=45 !number of elements, x direction
-  nj=45 !number of elements, y direction
-  ibdt=900!1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=24 !total simulation hours
-  write_time_inc = 1!48 !increment at which time is written to screen
-  nmax=999999999 !max number of timesteps
-  saverestart=.true.
-  halo=3
-  debug=.true.
-  collision_test=.false.
-  grounding_test=.false.
-  bump_depth=9999.0 !(m) depth of top of gaussian bump below sea level
-/
-
-&icebergs_nml
-
-    !defaults given in parentheses:
-    monitor_energy=.true. !(F)save total elastic (spring+collision),external,dissipated,&fracture energy
-    new_mts=.true. !(F) If T, implicit accel is added 50% at the current time step and 50% at the next time step
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=20  !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=2000 !2500 !2500 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=0.5e-8!4.471938678723104 !0.5e-8 !1.e-8 !(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=3.16e6 !friction drag param
-    h_to_init_grounding=200.0 !300.0 !150.0 !300.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.false. !(T) remove unneeded bergs after PEs transfers
-
-    !fracture_criterion='strain' !('none') 'strain_rate','strain','stress',or 'none'
-    !!here, try setting scaling 1.0 if force_convergence=.false., 0.5 if force_convergence=.true.
-    !frac_thres_scaling = 0.5 !(1) scales frac_thres_n and frac_thres_t
-    !frac_thres_n = 0.018  !normal fracture strain threshold
-    !frac_thres_t = 0.!0.05076 !tangential fracture strain threshold
-
-    !fracture_criterion='strain_rate' !('none') 'strain_rate','strain','stress',or 'none'
-    !frac_thres_scaling = 1 !(1) scales frac_thres_n and frac_thres_t
-    !frac_thres_n = 2.e-6  !normal fracture strain threshold
-    !frac_thres_t = 0!1.e-5 !tangential fracture strain threshold
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain','stress',or 'none'
-    !here, try setting scaling 1.0 if force_convergence=.false., 0.5 if force_convergence=.true.
-    frac_thres_scaling = 1.0 !(1) scales frac_thres_n and frac_thres_t
-    frac_thres_n = 0.!8000.0  !normal fracture strain threshold
-    frac_thres_t = 0.!12000.0 !0.05076 !tangential fracture strain threshold
-
-    halo=3 !(4) halo width
-    Lx=45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    rho_bergs=850. ! (850) iceberg density
-    spring_coef=1.e-5!4471.938678723104 !7.8e-3(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    radial_damping_coef=0.0 !(1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.false. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0.0 !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.false. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.false. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.true. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=24000 ! (24) Period between verbose messages
-    traj_sample_hrs=-1 !(24) sampling period for trajectory storage
-    traj_write_hrs=-1 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    !require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.!(F) Init bond b/w bergs if dist<1.25*radius
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/frac_test/makeberg/RUN b/tests/frac_test/makeberg/RUN
deleted file mode 100755
index d985f3f..0000000
--- a/tests/frac_test/makeberg/RUN
+++ /dev/null
@@ -1,3 +0,0 @@
-rm ./output_files/Generic*
-./makeberg.py
-cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
\ No newline at end of file
diff --git a/tests/frac_test/makeberg/makeberg.py b/tests/frac_test/makeberg/makeberg.py
deleted file mode 100755
index be410b2..0000000
--- a/tests/frac_test/makeberg/makeberg.py
+++ /dev/null
@@ -1,376 +0,0 @@
-#!/usr/bin/env python
-import numpy as np
-import math
-from netCDF4 import Dataset
-from pylab import *
-#import pdb
-import netCDF4 as nc
-
-#
-# Initialize 2 iceberg elements, which can later be bonded in the fortran code if needed
-#
-
-def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
-
-	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
-	# To copy the global attributes of the netCDF file
-
-	#Input and output files
-	#Create Empty restart file. This is later read so that the attributes can be used.
-	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
-	create_empty_iceberg_restart_file(Empty_restart_filename)
-	#Empty_restart_filename='input_files/icebergs.res.nc'
-
-	#Read empty restart file
-	f=Dataset(Empty_restart_filename,'r') # r is for read only
-	#Write a new restart file
-	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
-
-	for attname in f.ncattrs():
-		    setattr(g,attname,getattr(f,attname))
-
-
-	# To copy the dimension of the netCDF file
-	for dimname,dim in f.dimensions.iteritems():
-		# if you want to make changes in the dimensions of the new file
-		# you should add your own conditions here before the creation of the dimension.
-		#g.createDimension(dimname,len(dim))
-		g.createDimension(dimname,Number_of_bergs)
-
-	# To copy the variables of the netCDF file
-
-	for varname,ncvar in f.variables.iteritems():
-		# if you want to make changes in the variables of the new file
-		# you should add your own conditions here before the creation of the variable.
-		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
-		#Proceed to copy the variable attributes
-		for attname in ncvar.ncattrs():
-			setattr(var,attname,getattr(ncvar,attname))
-		#Finally copy the variable data to the new created variable
-		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
-
-		if varname=='i':
-			var[:]=Number_of_bergs
-
-		if varname=='iceberg_num':
-			for j in range(Number_of_bergs):
-				#var[j]=j+1
-				var[j]=iceberg_num[j]
-
-		if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
-		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
-		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
-		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
-			var[:]=0
-
-                if varname=='uvel':
-                        var[:]=uvel
-
-                if varname=='vvel':
-                        var[:]=vvel
-
-		if varname=='mass_scaling':
-			var[:]=mass_scaling
-
-		if varname=='thickness':
-			for j in range(Number_of_bergs):
-				var[j]=thickness[j]
-
-		if varname=='mass':
-			for j in range(Number_of_bergs):
-				var[j]=mass[j]
-
-		if varname=='width'  or varname=='length':
-			for j in range(Number_of_bergs):
-				var[j]=width[j]
-
-		if varname=='lon':
-			for j in range(Number_of_bergs):
-				var[j]=lon[j]
-
-		if varname=='lat':
-			for j in range(Number_of_bergs):
-				var[j]=lat[j]
-
-		if varname=='static_berg':
-			for j in range(Number_of_bergs):
-				var[j]=static_berg[j]
-
-
-	f.close()
-	g.close()
-
-
-def create_empty_iceberg_restart_file(Empty_restart_filename):
-
-	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
-
-	i=f.createDimension('i', None)
-	lon=f.createVariable('i','i')
-
-	lon=f.createVariable('lon','d',('i'))
-	lon.long_name = "longitude" ;
-	lon.units = "degrees_E" ;
-	lon.checksum = "               0" ;
-
-	lat=f.createVariable('lat','d',('i'))
-	lat.long_name = "latitude" ;
-	lat.units = "degrees_N" ;
-	lat.checksum = "               0" ;
-
-	uvel=f.createVariable('uvel','d',('i'))
-	uvel.long_name = "zonal velocity" ;
-	uvel.units = "m/s" ;
-	uvel.checksum = "               0" ;
-
-	vvel=f.createVariable('vvel','d',('i'))
-	vvel.long_name = "meridional velocity" ;
-	vvel.units = "m/s" ;
-	vvel.checksum = "               0" ;
-
-	mass=f.createVariable('mass','d',('i'))
-	mass.long_name = "mass" ;
-	mass.units = "kg" ;
-	mass.checksum = "               0" ;
-
-	axn=f.createVariable('axn','d',('i'))
-	axn.long_name = "explicit zonal acceleration" ;
-	axn.units = "m/s^2" ;
-	axn.checksum = "               0" ;
-
-	ayn=f.createVariable('ayn','d',('i'))
-	ayn.long_name = "explicit meridional acceleration" ;
-	ayn.units = "m/s^2" ;
-	ayn.checksum = "               0" ;
-
-	bxn=f.createVariable('bxn','d',('i'))
-	bxn.long_name = "inplicit zonal acceleration" ;
-	bxn.units = "m/s^2" ;
-	bxn.checksum = "               0" ;
-
-	byn=f.createVariable('byn','d',('i'))
-	byn.long_name = "implicit meridional acceleration" ;
-	byn.units = "m/s^2" ;
-	byn.checksum = "               0" ;
-
-	ine=f.createVariable('ine','i',('i'))
-	ine.long_name = "i index" ;
-	ine.units = "none" ;
-	ine.packing = 0 ;
-	ine.checksum = "               0" ;
-
-	jne=f.createVariable('jne','i',('i'))
-	jne.long_name = "j index" ;
-	jne.units = "none" ;
-	jne.packing = 0 ;
-	jne.checksum = "               0" ;
-
-	thickness=f.createVariable('thickness','d',('i'))
-	thickness.long_name = "thickness" ;
-	thickness.units = "m" ;
-	thickness.checksum = "               0" ;
-
-	width=f.createVariable('width','d',('i'))
-	width.long_name = "width" ;
-	width.units = "m" ;
-	width.checksum = "               0" ;
-
-	length=f.createVariable('length','d',('i'))
-	length.long_name = "length" ;
-	length.units = "m" ;
-	length.checksum = "               0" ;
-
-	start_lon=f.createVariable('start_lon','d',('i'))
-	start_lon.long_name = "longitude of calving location" ;
-	start_lon.units = "degrees_E" ;
-	start_lon.checksum = "               0" ;
-
-	start_lat=f.createVariable('start_lat','d',('i'))
-	start_lat.long_name = "latitude of calving location" ;
-	start_lat.units = "degrees_N" ;
-	start_lat.checksum = "               0" ;
-
-	start_year=f.createVariable('start_year','i',('i'))
-	start_year.long_name = "calendar year of calving event" ;
-	start_year.units = "years" ;
-	start_year.packing = 0 ;
-	start_year.checksum = "               0" ;
-
-	iceberg_num=f.createVariable('iceberg_num','i',('i'))
-	iceberg_num.long_name = "identification of the iceberg" ;
-	iceberg_num.units = "dimensionless" ;
-	iceberg_num.packing = 0 ;
-	iceberg_num.checksum = "               0" ;
-
-	start_day=f.createVariable('start_day','d',('i'))
-	start_day.long_name = "year day of calving event" ;
-	start_day.units = "days" ;
-	start_day.checksum = "               0" ;
-
-	start_mass=f.createVariable('start_mass','d',('i'))
-	start_mass.long_name = "initial mass of calving berg" ;
-	start_mass.units = "kg" ;
-	start_mass.checksum = "               0" ;
-
-	mass_scaling=f.createVariable('mass_scaling','d',('i'))
-	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
-	mass_scaling.units = "none" ;
-	mass_scaling.checksum = "               0" ;
-
-	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
-	mass_of_bits.long_name = "mass of bergy bits" ;
-	mass_of_bits.units = "kg" ;
-	mass_of_bits.checksum = "               0" ;
-
-	heat_density=f.createVariable('heat_density','d',('i'))
-	heat_density.long_name = "heat density" ;
-	heat_density.units = "J/kg" ;
-	heat_density.checksum = "               0" ;
-
-	halo_berg=f.createVariable('halo_berg','d',('i'))
-	halo_berg.long_name = "halo_berg" ;
-	halo_berg.units = "dimensionless" ;
-	halo_berg.checksum = "               0" ;
-
-	static_berg=f.createVariable('static_berg','d',('i'))
-	static_berg.long_name = "static_berg" ;
-	static_berg.units = "dimensionless" ;
-	static_berg.checksum = "               0" ;
-
-	f.sync()
-	f.close()
-
-
-
-#-----------------------------------#
-#               Main                #
-#-----------------------------------#
-
-just2particles=False
-flip2ndconglom=True#False
-offset2ndconglom=True#False
-
-grdxmin=0; grdxmax=45000e3
-grdymin=0; grdymax=45000e3
-grdres=1000.0
-R_frac=0.3375 #225
-R_frac2=0.3375 #45
-radius=(np.sqrt(3)/2.)*(R_frac*grdres) #S is < 0.5 grid res
-radius2=(np.sqrt(3)/2.)*(R_frac2*grdres) #S is < 0.5 grid res
-thickness1=300.0
-thickness2=200.0
-rho_ice=850.0
-
-
-nbergs=2 #number of conglomerates
-
-#center coords of each (rectangular) conglomerate berg (CB=conglomerate berg)
-CBxc=np.array([10500, 22500]); CByc=np.array([22500, 22500])
-#CBxc=np.array([9500, 17500]); CByc=np.array([22500, 22500])
-
-#side lengths
-CBxl=np.array([2500, 7500]); CByl=np.array([7500, 2500])
-#CBxl=np.array([2500, 2500]); CByl=np.array([7500, 7500])
-#CBxl=np.array([3000, 3000]); CByl=np.array([3000, 3000])
-CByl=CByl.astype(int); CBxl=CBxl.astype(int)
-
-#--- xmax, xmin, ymax, ymin for each CB --
-CBxmin=CBxc-(0.5*CBxl); CBxmax=CBxc+(0.5*CBxl)
-CBymin=CByc-(0.5*CByl); CBymax=CByc+(0.5*CByl)
-#this shouldn't happen:
-CBxmin[CBxmin<grdxmin]=grdxmin; CBxmax[CBxmax>grdxmax]=grdxmax
-CBymin[CBxmin<grdymin]=grdymin; CBymax[CBymax>grdymax]=grdymax
-CBxc=0.5*(CBxmin+CBxmax); CByc=0.5*(CBymin+CBymax)
-
-#if just want one particle per CB
-if just2particles:
-        CBxmin=CBxc; CBxmax=CBxc
-        CBymin=CByc; CBymax=CByc
-
-#--- min and max thicknesses for each CB ---
-h1=thickness1; h2=thickness2
-CBhmax=np.array([h1,h2]); CBhmin=np.array([h1,h2])
-
-#radii
-CBrad=np.array([radius,radius2])
-print('radii',CBrad)
-
-berg_x=[]; berg_y=[]
-berg_id=[]; berg_static=[]
-berg_width=[]; berg_bonds=[]
-berg_h=[]; berg_mass_scaling=[]
-berg_mass=[]
-berg_uvel=[]; berg_vvel=[]
-
-berg_count=0
-
-for i in range(nbergs):
-        x_start=CBxmin[i]+(CBrad[i]*2./np.sqrt(3))
-
-        if flip2ndconglom and i>0:
-                x_start=CBxmax[i]-(CBrad[i]*2./np.sqrt(3))
-
-        #pdb.set_trace()
-        if x_start>CBxmax[i]:
-                x_start=CBxmax[i]
-        y_start0=CBymin[i]+CBrad[i]
-        if y_start0>CBymax[i]:
-                y_start0=CBymax[i]
-        element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*(CBrad[i])**2)
-        #H (thickness) is a linear function of a berg element's position from the
-        #center of the CB. H=Hmax at the center of the CB and H=Hmin at a corner of the
-        #CB, where the dist of a corner from the center is:
-        cdistb=np.sqrt((CBxmin[i]-CBxc[i])**2+(CBymin[i]-CByc[i])**2)
-        j=0
-        x_val=x_start
-        offset=0.0
-        if (i==0):
-                uvel=0.05#0.075
-        else:
-                uvel=-0.15#-0.05
-                if (offset2ndconglom):
-                        offset=250.0
-        vvel=0.025#0.01
-        #uvel=0;vvel=0
-        #berg_count_start=berg_count
-        while x_val<=CBxmax[i] and x_val>=CBxmin[i]:
-                y_start=y_start0+((j%2)*CBrad[i])+offset
-                k=0
-                y_val=y_start
-                while y_val<=(CBymax[i]+offset):
-                        berg_count=berg_count+1
-                        berg_id.append(berg_count)
-                        berg_x.append(x_val)
-                        berg_y.append(y_val)
-                        berg_width.append(sqrt(element_area))
-                        #dist of berg elem from center of CB
-                        bdistc=np.sqrt((x_val-CBxc[i])**2+(y_val-CByc[i])**2)
-                        bh=CBhmin[i]*bdistc/cdistb + CBhmax[i]*(1-bdistc/cdistb)
-                        if (just2particles):
-                                bh=h1
-                        berg_h.append(bh) #thickness
-                        berg_mass_scaling.append(1)
-                        berg_mass.append(bh*rho_ice*element_area)
-                        berg_static.append(0)
-                        berg_uvel.append(uvel)
-                        berg_vvel.append(vvel)
-                        # if (x_val<22000):
-                        #         berg_vvel.append(vvel)
-                        # else:
-                        #         berg_vvel.append(0.4)
-                        #berg_CBid.append(i)
-                        k=k+1
-                        y_val=y_start+(2*k*CBrad[i])
-                j=j+1
-                if flip2ndconglom and i>0:
-                        x_val=x_start-(np.sqrt(3)*CBrad[i]*j)
-                else:
-                        x_val=x_start+(np.sqrt(3)*CBrad[i]*j)
-
-print('Number of bergs',berg_count)
-
-#pdb.set_trace()
-
-#Create iceberg restart file
-Ice_geometry_source='Generic'
-Create_iceberg_restart_file(berg_count,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)
diff --git a/tests/ground_frac_test/.gitignore b/tests/ground_frac_test/.gitignore
deleted file mode 100644
index 68bcbc9..0000000
--- a/tests/ground_frac_test/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-results/
\ No newline at end of file
diff --git a/tests/ground_frac_test/README b/tests/ground_frac_test/README
deleted file mode 100644
index 83093c2..0000000
--- a/tests/ground_frac_test/README
+++ /dev/null
@@ -1,5 +0,0 @@
-1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
-2.(optional) edit input.nml
-3. run the model: ./RUN
-4, animate the results: animate_trajectories.py
-
diff --git a/tests/ground_frac_test/RUN b/tests/ground_frac_test/RUN
deleted file mode 100755
index 3f4dc1d..0000000
--- a/tests/ground_frac_test/RUN
+++ /dev/null
@@ -1,7 +0,0 @@
-#rm iceberg_trajectories.nc
-#rm iceberg_trajectories.nc.*
-#rm bond_trajectories.nc
-#rm bond_trajectories.nc.*
-srun -n1 ./../../build/bergs.x
-
-
diff --git a/tests/ground_frac_test/animate_trajectories.py b/tests/ground_frac_test/animate_trajectories.py
deleted file mode 100755
index 8b9aa7d..0000000
--- a/tests/ground_frac_test/animate_trajectories.py
+++ /dev/null
@@ -1,121 +0,0 @@
-#!/usr/bin/env python
-
-from netCDF4 import Dataset
-import pdb
-import netCDF4 as nc
-import numpy as np
-import matplotlib
-import math
-import os
-matplotlib.use("tkagg")
-from pylab import *
-import matplotlib.pyplot as plt
-from matplotlib.animation import FuncAnimation
-import argparse
-
-def parseCommandLine():
-    parser = argparse.ArgumentParser(description=
-    '''Generate animation of iceberg trajectories.''',
-    epilog='Written by Alex Huth, 2020')
-    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
-                    help=''' provide filename to plot''')
-    optCmdLineArgs = parser.parse_args()
-    return optCmdLineArgs
-
-
-
-def main(args):
-
-    print('reading file')
-
-    filename=args.fname
-    #filename = 'iceberg_trajectories.nc'
-    field = 'lon'
-    field2 = 'lat'
-
-    with nc.Dataset(filename) as file:
-        x = file.variables['lon'][:]/1.e3
-        y = file.variables['lat'][:]/1.e3
-        day = file.variables['day'][:]
-
-    ud = np.unique(day)
-    t = ud[0]
-
-    # frame info
-    num_frames = len(ud)
-    movie_len = 10.0 #seconds
-    frame_len = 1000.0*movie_len/num_frames
-
-    xmin = 0
-    xmax = 30
-    ymin = xmin
-    ymax = xmax
-
-    anim_running = True
-
-    def animate(i):
-
-        x1 = x[day == ud[i]]
-        y1 = y[day == ud[i]]
-        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
-
-        scat.set_offsets(data)
-
-        t = ud[i]
-        time_text.set_text('time = %.1f days' % t )
-        return scat,time_text
-
-    def init():
-        scat.set_offsets([])
-        return scat,
-
-    def onClick(event):
-        global anim_running
-        if anim_running:
-            ani.event_source.stop()
-            anim_running = False
-        else:
-            ani.event_source.start()
-            anim_running = True
-
-    # Now we can do the plotting!
-    f = plt.figure(figsize=(5,5))
-    f.tight_layout()
-    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
-    scat = ax1.scatter([],[],marker='o',facecolor='w',s=50,edgecolor='red')
-    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
-
-    # Change major ticks to show every 20.
-    ax1.xaxis.set_major_locator(MultipleLocator(5))
-    ax1.yaxis.set_major_locator(MultipleLocator(5))
-
-    ax1.xaxis.set_minor_locator(MultipleLocator(1))
-    ax1.yaxis.set_minor_locator(MultipleLocator(1))
-
-    # Turn grid on for both major and minor ticks and style minor slightly
-    # differently.
-    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
-    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
-
-    ax1.set_xlabel('x (km)')
-    ax1.set_ylabel('y (km)')
-    ax1.set_title('Iceberg trajectory')
-
-    f.canvas.mpl_connect('button_press_event', onClick)
-
-    ani = FuncAnimation(
-        f,animate,init_func=init,frames=num_frames,
-        interval=frame_len,blit=True,repeat=True)
-
-    print('time',t)
-
-    plt.show()
-    #animation.save("iceberg_traj_animation.mp4")
-
-
-print('Script complete')
-
-if __name__ == '__main__':
-    optCmdLineArgs=	parseCommandLine()
-    anim_running = True
-    main(optCmdLineArgs)
diff --git a/tests/ground_frac_test/animate_trajectories_1pe.py b/tests/ground_frac_test/animate_trajectories_1pe.py
deleted file mode 100755
index beee932..0000000
--- a/tests/ground_frac_test/animate_trajectories_1pe.py
+++ /dev/null
@@ -1,180 +0,0 @@
-#!/usr/bin/env python
-
-from netCDF4 import Dataset
-import pdb
-import netCDF4 as nc
-import numpy as np
-import matplotlib
-import math
-import os
-matplotlib.use("tkagg")
-from pylab import *
-import matplotlib.pyplot as plt
-from matplotlib.animation import FuncAnimation
-import argparse
-
-def parseCommandLine():
-    parser = argparse.ArgumentParser(description=
-    '''Generate animation of iceberg trajectories.''',
-    epilog='Written by Alex Huth, 2020')
-    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc.0000',
-                    help=''' provide filename to plot''')
-    optCmdLineArgs = parser.parse_args()
-    return optCmdLineArgs
-
-
-
-def main(args):
-
-    print('reading file')
-
-    filename=args.fname
-    #filename = 'iceberg_trajectories.nc'
-    field = 'lon'
-    field2 = 'lat'
-
-    with nc.Dataset(filename) as file:
-        x = file.variables['lon'][:]/1.e3
-        y = file.variables['lat'][:]/1.e3
-        day = file.variables['day'][:]
-        hs = file.variables['halo_berg'][:]
-        #hs = file.variables['n_bonds'][:]        
-
-    #hs = hs+1
-    ud = np.unique(day)
-    t = ud[0]
-
-    print('unique hs',np.unique(hs))
-
-    # frame info
-    num_frames = len(ud)
-    movie_len = 10.0 #seconds
-    frame_len = 1000.0*movie_len/num_frames
-
-    xmin = np.floor(min(min(x),min(y),-5))
-    xmax = np.ceil(max(max(x),max(y),35))
-    ymin = xmin
-    ymax = xmax
-
-    anim_running = True
-
-    def animate(i):
-
-        x1 = x[day == ud[i]]
-        y1 = y[day == ud[i]]
-        hstat = hs[day == ud[i]]
-        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
-
-        cstring=[]
-        for j in range(len(hstat)):
-            if (hstat[j]<0):
-                cstring.append("m")
-            elif (hstat[j]==0):
-                cstring.append("b")
-            elif (hstat[j]==1):
-                cstring.append("r")
-            elif (hstat[j]==2):
-                cstring.append("g")
-            elif (hstat[j]==3):
-                cstring.append("k")
-            elif (hstat[j]==4):
-                cstring.append("c")
-            elif (hstat[j]==5):
-                cstring.append("y")
-            elif (hstat[j]==6):
-                cstring.append("w")
-            elif (hstat[j]==10):                
-                cstring.append("c")
-            # else:
-            #     cstring.append("y")
-
-        scat.set_offsets(data)
-        scat.set_color(cstring)
-        scat.set_edgecolor('k')
-
-        t = ud[i]
-        time_text.set_text('time = %.1f days' % t )
-        return scat,time_text
-
-    def init():
-        scat.set_offsets([])
-        return scat,
-
-    def onClick(event):
-        global anim_running
-        if anim_running:
-            ani.event_source.stop()
-            anim_running = False
-        else:
-            ani.event_source.start()
-            anim_running = True
-
-    # Now we can do the plotting!
-    f = plt.figure(figsize=(5,5))
-    f.tight_layout()
-    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
-    scat = ax1.scatter([],[],marker='o',s=60)
-    #scat = ax1.scatter([],[],marker='o',facecolor='w',s=60,edgecolor='red')
-    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
-
-    # Change major ticks to show every 20.
-    ax1.xaxis.set_major_locator(MultipleLocator(5))
-    ax1.yaxis.set_major_locator(MultipleLocator(5))
-
-    ax1.xaxis.set_minor_locator(MultipleLocator(1))
-    ax1.yaxis.set_minor_locator(MultipleLocator(1))
-
-    # Turn grid on for both major and minor ticks and style minor slightly
-    # differently.
-    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
-    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
-
-    ax1.set_xlabel('x (km)')
-    ax1.set_ylabel('y (km)')
-    ax1.set_title('Iceberg trajectory')
-
-    f.canvas.mpl_connect('button_press_event', onClick)
-
-    ani = FuncAnimation(
-        f,animate,init_func=init,frames=num_frames,
-        interval=frame_len,blit=True,repeat=True)
-
-    print('time',t)
-
-    plt.plot([0,0],[0,30],'k-',lw=1)
-    plt.plot([10,10],[0,30],'k-',lw=1)
-    plt.plot([20,20],[0,30],'k-',lw=1)
-    plt.plot([30,30],[0,30],'k-',lw=1)
-    plt.plot([0,30],[0,0],'k-',lw=1)
-    plt.plot([0,30],[10,10],'k-',lw=1)
-    plt.plot([0,30],[20,20],'k-',lw=1)
-    plt.plot([0,30],[30,30],'k-',lw=1)
-
-    plt.plot([-2,-2],[-2,33],'b:',lw=1)
-    plt.plot([3,3],[-2,33],'b:',lw=1)
-    plt.plot([8,8],[-2,33],'b:',lw=1)
-    plt.plot([13,13],[-2,33],'b:',lw=1)
-    plt.plot([18,18],[-2,33],'b:',lw=1)
-    plt.plot([23,23],[-2,33],'b:',lw=1)
-    plt.plot([28,28],[-2,33],'b:',lw=1)
-    plt.plot([33,33],[-2,33],'b:',lw=1)    
-
-    plt.plot([-2,33],[-2,-2],'b:',lw=1)
-    plt.plot([-2,33],[3,3],'b:',lw=1)
-    plt.plot([-2,33],[8,8],'b:',lw=1)
-    plt.plot([-2,33],[13,13],'b:',lw=1)
-    plt.plot([-2,33],[18,18],'b:',lw=1)
-    plt.plot([-2,33],[23,23],'b:',lw=1)
-    plt.plot([-2,33],[28,28],'b:',lw=1)
-    plt.plot([-2,33],[33,33],'b:',lw=1)
-
-    plt.show()
-    #animation.save("iceberg_traj_animation.mp4")
-
-
-print('Script complete')
-
-if __name__ == '__main__':
-    optCmdLineArgs=	parseCommandLine()
-    anim_running = True
-    main(optCmdLineArgs)
diff --git a/tests/ground_frac_test/diag_table b/tests/ground_frac_test/diag_table
deleted file mode 100644
index c1c8819..0000000
--- a/tests/ground_frac_test/diag_table
+++ /dev/null
@@ -1,3 +0,0 @@
-"icebergs test"
-1 1 1 0 0 0
-
diff --git a/tests/ground_frac_test/input.nml b/tests/ground_frac_test/input.nml
deleted file mode 100644
index 3969650..0000000
--- a/tests/ground_frac_test/input.nml
+++ /dev/null
@@ -1,200 +0,0 @@
-!NOTE: this result is from when we did NOT set uvel_old to ustar for berg interactions
-!KID, bergs_chksum: write_restart berg chksum=              32083975 chksum2=            2055392101 chksum3=           -2018330166 chksum4=           -2018330166 chksum5=           -1470408987 #=                    67
-!KID, grd_chksum2:    # of bergs/cell chksum=                     0 chksum2=                     0 min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
-! Total number of bonds is:          286 
-
-&icebergs_driver_nml
-  ni=45 !30 !number of elements, x direction
-  nj=45 !30 !number of elements, y direction
-  ibdt=1800.0 !seconds
-  ibuo=0.1 !ocean x velocity
-  ibvo=0.0 !1 !2 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=999999999 !max number of timesteps
-  saverestart=.true.
-  halo=3
-  debug=.true.
-  collision_test=.false.
-  grounding_test=.true.
-  bump_depth=200.0 !(m) depth of top of gaussian bump below sea level 
-/
-
-&icebergs_nml
-!200 n:0.0278 vo=.1
-!200 n:0.0325 or 0.03 vo=0
-    monitor_energy=.false.
-
-    constant_interaction_LW=.true.
-    traj_name=test_dem.nc
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5. A=L*W always works?
-    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    !spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7, r=1500, and square pack?
-    spring_coef=0.01118 !if dem_spring_coef=0.5e7, L=A=725.334717, and hex pack?  
-    !0.0007547062342348049 !if dem_spring_coef=0.5e7, r=1500, and hex pack?  
-
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=250000 !10 !20 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=1.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7 !!5.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=3.16e6 !200.0 !for power-law-type friction
-    h_to_init_grounding=200.0 !300.0 !150.0 !300.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','stress,'strain',or 'none'
-    frac_thres_scaling = 1.
-    frac_thres_n = 20000.
-    frac_thres_t = 20000.
-
-    halo=3 !(4) halo width
-    Lx=45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    rho_bergs=850. ! (850) iceberg density
-    !spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    !tangent_spring_coef=3.85e-6 !10 !6
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=1.0 !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=24000 ! (24) Period between verbose messages
-    traj_sample_hrs=-1!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=-1!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.true. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/ground_frac_test/input_save.nml b/tests/ground_frac_test/input_save.nml
deleted file mode 100644
index ad6aafa..0000000
--- a/tests/ground_frac_test/input_save.nml
+++ /dev/null
@@ -1,182 +0,0 @@
-!NOTE: this result is from when we did NOT set uvel_old to ustar for berg interactions
-!KID, bergs_chksum: write_restart berg chksum=              32083975 chksum2=            2055392101 chksum3=           -2018330166 chksum4=           -2018330166 chksum5=           -1470408987 #=                    67
-!KID, grd_chksum2:    # of bergs/cell chksum=                     0 chksum2=                     0 min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
-! Total number of bonds is:          286 
-
-&icebergs_driver_nml
-  ni=45 !30 !number of elements, x direction
-  nj=45 !30 !number of elements, y direction
-  ibdt=1800.0 !seconds
-  ibuo=0.1 !ocean x velocity
-  ibvo=0.0 !1 !2 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=999999999 !max number of timesteps
-  saverestart=.true.
-  halo=3
-  debug=.true.
-  collision_test=.false.
-  grounding_test=.true.
-  bump_depth=200.0 !(m) depth of top of gaussian bump below sea level 
-/
-
-&icebergs_nml
-!200 n:0.0278 vo=.1
-!200 n:0.0325 or 0.03 vo=0
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=10 !20 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
-    contact_distance=1.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7 !!5.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=3.16e6 !200.0 !for power-law-type friction
-    h_to_init_grounding=200.0 !300.0 !150.0 !300.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='strain' !('none') 'strain_rate','strain',or 'none'
-
-    !for scale_damping_by_pmag=.false., old_mts
-    !frac_thres_n = 0.018 !0.02
-    !frac_thres_t = 0.05076 !0.0564
-
-    !scale_damping_by_pmag=.false., new_mts
-    frac_thres_n = 0.0162
-    frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    rho_bergs=850. ! (850) iceberg density
-    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    !tangent_spring_coef=3.85e-6 !10 !6
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=1.0 !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=24000 ! (24) Period between verbose messages
-    traj_sample_hrs=-1!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=-1!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.true. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/ground_frac_test/makeberg/RUN b/tests/ground_frac_test/makeberg/RUN
deleted file mode 100755
index 24c0f15..0000000
--- a/tests/ground_frac_test/makeberg/RUN
+++ /dev/null
@@ -1,12 +0,0 @@
-./makeberg.py
-
-rm ./output_files/Generic*
-
-./../../Iceberg_repository/Scripts_and_analysis/initialize_bergs_in_pattern.py \
-	-set_all_bergs_static_by_default=False -Run_plotting_subroutine=False \
-	-break_some_bonds=False -Ice_geometry_source='Generic' \
-	-Generic_ice_geometry_filename='./testtabularberg.nc' \
-	-ISOMIP_reduced=False -collision_test=False -grounding_test=true
-
-cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
-cp ./output_files/Generic_bonds_iceberg.res.nc ./../INPUT/bonds_iceberg.res.nc
diff --git a/tests/ground_frac_test/makeberg/makeberg.py b/tests/ground_frac_test/makeberg/makeberg.py
deleted file mode 100755
index b38e604..0000000
--- a/tests/ground_frac_test/makeberg/makeberg.py
+++ /dev/null
@@ -1,89 +0,0 @@
-#!/usr/bin/env python
-
-from netCDF4 import Dataset  
-import numpy as np 
-import math
-#import os
-from pylab import *
-#import pdb
-import netCDF4 as nc
-
-nx = 30
-ny = 30
-New_ice_thickness_filename='testberg.nc'
-grid_res = 1.e3 #1 km 
-grid_area = grid_res * grid_res
-h_ice = 300.0
-
-New_ice_thickness_filename='testtabularberg.nc'
-g=Dataset(New_ice_thickness_filename,'w') # w if for creating a file
-
-g.createDimension('nx',nx)
-g.createDimension('ny',ny)
-thick_h=g.createVariable('thick','f8',('ny','nx'))
-area_h=g.createVariable('area','f8',('ny','nx'))
-lat_h=g.createVariable('lat','f8','ny')
-lon_h=g.createVariable('lon','f8','nx')
-#lat_h=g.createVariable('lat','f8',('ny','nx'))
-#lon_h=g.createVariable('lon','f8',('ny','nx'))
-
-thick_h.units = 'm'
-thick_h.standard_name = 'ice shelf thickness'
-area_h.units = 'm2'
-area_h.standard_name = 'ice shelf area'
-lon_h.unit = 'm'
-lon_h.standard_name = 'longitude'
-lat_h.unit = 'm'
-lat_h.standard_name = 'latitude'
-
-
-
-#g.variables['thick'][:]=h_ice
-g.variables['area'][:,:]=grid_area
-
-#create a circular tabular berg centered on the following coords (km)
-cy = 3.5e3
-cx = 15.0e3
-xl = 8.e3 #7.0e3 #5.0e3
-yl = 4.e3 #5.0e3
-xmin=cx-xl/2
-xmax=cx+xl/2
-ymin=cy-yl/2
-ymax=cy+yl/2
-maxh=h_ice
-minh=300 #100
-slopedist=sqrt((xl/2)**2 + (yl/2)**2)
-slope=(minh-h_ice)/slopedist
-
-#cx2 = 15.5e3
-
-for i in range(nx):
-
-        tx = float(i) * grid_res 
-        g.variables['lon'][i] = tx
-        
-        for j in range(ny):
-               
-                ty = float(j) * grid_res
-
-                # dist = sqrt((tx-cx)*(tx-cx) + (ty-cy)*(ty-cy))
-                # if (dist <1.e3): #or dist2<1.e3):
-                #         g.variables['thick'][i,j]=h_ice
-                if (tx>=xmin and tx<=xmax and ty>=ymin and ty<=ymax):
-                        dist = sqrt((tx-cx)*(tx-cx) + (ty-cy)*(ty-cy))                         
-                        g.variables['thick'][i,j]=slope*dist+h_ice
-                                               
-                else:
-                        g.variables['thick'][i,j]=0.0
-
-                        
-
-for j in range(ny):
-        g.variables['lat'][j] = float(j) * grid_res 
-
-print('Creating file: ' , New_ice_thickness_filename)
-
-g.sync()
-g.close()
-
-        
diff --git a/tests/ground_frac_test/reference_input.nml b/tests/ground_frac_test/reference_input.nml
deleted file mode 100644
index 3921603..0000000
--- a/tests/ground_frac_test/reference_input.nml
+++ /dev/null
@@ -1,183 +0,0 @@
-!KID, bergs_chksum: write_restart berg chksum=            -195625967 chksum2=            1455880446 chksum3=            -243405929 chksum4=            -243405929 chksum5=            -495829423 #=                    67
-!KID, grd_chksum2:    # of bergs/cell chksum=                     0 chksum2=                     0 min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
-! Total number of bonds is:          240 
-! All iceberg bonds are connected and working well
-!KID, grd_chksum3:   write stored_ice chksum=             859876028 chksum2=            -702294156 min= 0.000000000E+00 max= 7.389503907E+11 mean= 4.320307812E+10 rms= 1.148723635E+11 sd= 1.064384984E+11
-
-
-&icebergs_driver_nml
-  ni=45 !30 !number of elements, x direction
-  nj=45 !30 !number of elements, y direction
-  ibdt=1800.0 !seconds
-  ibuo=0.1 !ocean x velocity
-  ibvo=0.0 !1 !2 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=212!480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=999999999 !max number of timesteps
-  saverestart=.true.
-  halo=3
-  debug=.true.
-  collision_test=.false.
-  grounding_test=.true.
-  bump_depth=200.0 !(m) depth of top of gaussian bump below sea level 
-/
-
-&icebergs_nml
-!200 n:0.0278 vo=.1
-!200 n:0.0325 or 0.03 vo=0
-    !defaults given in parentheses:
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=10 !20 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
-    contact_distance=1.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7 !!5.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=3.16e6 !200.0 !for power-law-type friction
-    h_to_init_grounding=200.0 !300.0 !150.0 !300.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='strain' !('none') 'strain_rate','strain',or 'none'
-    !old !frac_thres_n strain, 200 m bd  0.045, 0.04, 
-    !old !frac_trhes_t strain, 200 m bd: 0.08 , 0.1 .
-    !old !frac_thres_n sr, 200 m bd: 2.5e-5 
-    !old !frac_thres_t sr, 200 m bd: 5.e-5
-    frac_thres_n= 0.025 !0.04 !0.0415 !0.045 !0.05
-    frac_thres_t= 0.0705 !0.095 !0.0925 !0.1 !0.09
-
-    !for scale_damping_by_pmag=.false.
-    !frac_thres_n = 0.018 !0.02
-    !frac_thres_t = 0.05076 !0.0564
-
-    halo=3 !(4) halo width
-    Lx=45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.true. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    rho_bergs=850. ! (850) iceberg density
-    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    !tangent_spring_coef=3.85e-6 !10 !6
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.true. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.true. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=1.0 !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=24000 ! (24) Period between verbose messages
-    traj_sample_hrs=6 !(24) sampling period for trajectory storage
-    traj_write_hrs=6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.true. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/plot_energy.py b/tests/plot_energy.py
index 358e1f5..13dc8ed 100755
--- a/tests/plot_energy.py
+++ b/tests/plot_energy.py
@@ -185,7 +185,7 @@ def main(args):
     fig2 = plt.figure(2)
     ax = plt.subplot(111)
     ax.plot(ud[step0:], tot_momentum_x[step0:],  color='k', label='x momentum')
-    #ax.plot(ud[step0:], tot_momentum_x2[step0:],  color='y', label='x momentum 2', linestyle='dashed')
+    ax.plot(ud[step0:], tot_momentum_x2[step0:],  color='y', label='x momentum 2', linestyle='dashed')
     chartBox = ax.get_position()
     ax.set_position([chartBox.x0, chartBox.y0, chartBox.width*0.6, chartBox.height])
     ax.legend(loc='upper center', bbox_to_anchor=(1.45, 0.8), shadow=True, ncol=1)
@@ -194,8 +194,8 @@ def main(args):
     fig3 = plt.figure(3)
     ax = plt.subplot(111)
     ax.plot(ud[step0:], tot_momentum_y[step0:],  color='k', label='y momentum')
-    #if (abs(mom_y0_tot2)>0):
-    #    ax.plot(ud[step0:], tot_momentum_y2[step0:],  color='y', label='y momentum 2', linestyle='dashed')
+    if (abs(mom_y0_tot2)>0):
+        ax.plot(ud[step0:], tot_momentum_y2[step0:],  color='y', label='y momentum 2', linestyle='dashed')
     chartBox = ax.get_position()
     ax.set_position([chartBox.x0, chartBox.y0, chartBox.width*0.6, chartBox.height])
     ax.legend(loc='upper center', bbox_to_anchor=(1.45, 0.8), shadow=True, ncol=1)

From 33a8bca3bccd2e142a76483dfe8cd4c0a9d368b1 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Thu, 22 Dec 2022 11:53:57 -0500
Subject: [PATCH 327/361] removed experimental option to account for ocean/wind
 curl on particle torque, because it has minimal effect and is therefore
 unused anyway

---
 src/icebergs.F90           | 106 -------------------------------------
 src/icebergs_framework.F90 |  43 +--------------
 src/icebergs_io.F90        |  55 +------------------
 tests/.gitignore           |   5 ++
 4 files changed, 9 insertions(+), 200 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 6935f0b..5910afb 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -2174,18 +2174,6 @@ subroutine accel_explicit_inner_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel,
     IA_x=IA_x+F_x/M; IA_y=IA_y+F_y/M
     IAd_x=IAd_x+Fd_x/M; IAd_y=IAd_y+Fd_y/M
 
-    if (bergs%add_curl_to_torque) then
-      dragfrac = 1.0
-      if ((bergs%iceberg_bonds_on) .and. (bergs%internal_bergs_for_drag)) then
-        dragfrac = 1. - berg%n_bonds/bergs%max_bonds
-      else
-        dragfrac = 1.0
-      endif
-      T = T + (R1**4.)*rho_seawater*bergs%ocean_drag_scale*&
-        (0.2*pi*R1*Cd_wh + 0.5*Cd_wv*dragfrac*berg%thickness*(bergs%rho_bergs/rho_seawater)) * &
-        (0.5*berg%curl_o-berg%ang_vel)*abs(0.5*berg%curl_o-berg%ang_vel)
-    endif
-
     ! !torque from grounding drag
     ! !start to feel grounded with draught of bergs%h_to_init_grounding meters of the sea floor topography
     ! !at groundfrac=0, apply no grounding force. at groundfrac=1, apply max grounding force
@@ -5186,7 +5174,6 @@ subroutine interp_gridded_fields_to_bergs(bergs)
         endif
         call interp_flds(grd, berg%lon, berg%lat, berg%ine, berg%jne, berg%xi, berg%yj, rx, ry, berg%uo, berg%vo, &
           berg%ui, berg%vi, berg%ua, berg%va, berg%ssh_x, berg%ssh_y, berg%sst, berg%sss, berg%cn, berg%hi, berg%od)
-        if (bergs%add_curl_to_torque) call interp_curl(grd,berg)
       endif
       berg=>berg%next
     enddo
@@ -5414,95 +5401,6 @@ subroutine interp_flds(grd, x, y, i, j, xi, yj, rx, ry, uo, vo, ui, vi, ua, va,
   endif
 end subroutine interp_flds
 
-!> Interpolates ocean (and atmospheric?) torque fields to an iceberg (DEM-mode required)
-subroutine interp_curl(grd,berg)
-  type(icebergs_gridded), pointer :: grd
-  type(iceberg), pointer :: berg
-  ! Local variables
-  integer :: i,j
-  real :: xi,yj
-  real :: hxp_o, hxp_a, hxm_o, hxm_a
-  real :: duo_dy, dua_dy, duo_dx, dua_dx
-  real :: dvo_dy, dva_dy, dvo_dx, dva_dx
-  real :: cos_rot, sin_rot
-
-  i =berg%ine;  j=berg%jne
-  xi=berg%xi;  yj=berg%yj
-
-  if (yj>=0.5) then
-    hxp_o=(yj-0.5)*ddx_v_point(grd,grd%vo,i  ,j+1,.true. )+(1.5-yj)*ddx_v_point(grd,grd%vo,i  ,j  ,.true. )
-    hxm_o=(yj-0.5)*ddx_v_point(grd,grd%vo,i-1,j+1,.true. )+(1.5-yj)*ddx_v_point(grd,grd%vo,i-1,j  ,.true. )
-    !hxp_a=(yj-0.5)*ddx_v_point(grd,grd%va,i  ,j+1,.false.)+(1.5-yj)*ddx_v_point(grd,grd%va,i  ,j  ,.false.)
-    !hxm_a=(yj-0.5)*ddx_v_point(grd,grd%va,i-1,j+1,.false.)+(1.5-yj)*ddx_v_point(grd,grd%va,i-1,j  ,.false.)
-  else
-    hxp_o=(yj+0.5)*ddx_v_point(grd,grd%vo,i  ,j  ,.true. )+(0.5-yj)*ddx_v_point(grd,grd%vo,i  ,j-1,.true. )
-    hxm_o=(yj+0.5)*ddx_v_point(grd,grd%vo,i-1,j  ,.true. )+(0.5-yj)*ddx_v_point(grd,grd%vo,i-1,j-1,.true. )
-    !hxp_a=(yj+0.5)*ddx_v_point(grd,grd%va,i  ,j  ,.false.)+(0.5-yj)*ddx_v_point(grd,grd%va,i  ,j-1,.false.)
-    !hxm_a=(yj+0.5)*ddx_v_point(grd,grd%va,i-1,j  ,.false.)+(0.5-yj)*ddx_v_point(grd,grd%va,i-1,j-1,.false.)
-  endif
-  dvo_dx=xi*hxp_o+(1.-xi)*hxm_o
-  !dva_dx=xi*hxp_a+(1.-xi)*hxm_a
-  if (xi>=0.5) then
-    hxp_o=(xi-0.5)*ddy_u_point(grd,grd%uo,i+1,j  ,.true. )+(1.5-xi)*ddy_u_point(grd,grd%uo,i  ,j  ,.true. )
-    hxm_o=(xi-0.5)*ddy_u_point(grd,grd%uo,i+1,j-1,.true. )+(1.5-xi)*ddy_u_point(grd,grd%uo,i  ,j-1,.true. )
-    !hxp_a=(xi-0.5)*ddy_u_point(grd,grd%ua,i+1,j  ,.false.)+(1.5-xi)*ddy_u_point(grd,grd%ua,i  ,j  ,.false.)
-    !hxm_a=(xi-0.5)*ddy_u_point(grd,grd%ua,i+1,j-1,.false.)+(1.5-xi)*ddy_u_point(grd,grd%ua,i  ,j-1,.false.)
-  else
-    hxp_o=(xi+0.5)*ddy_u_point(grd,grd%uo,i  ,j  ,.true. )+(0.5-xi)*ddy_u_point(grd,grd%uo,i-1,j  ,.true. )
-    hxm_o=(xi+0.5)*ddy_u_point(grd,grd%uo,i  ,j-1,.true. )+(0.5-xi)*ddy_u_point(grd,grd%uo,i-1,j-1,.true. )
-    !hxp_a=(xi+0.5)*ddy_u_point(grd,grd%ua,i  ,j  ,.false.)+(0.5-xi)*ddy_u_point(grd,grd%uo,i-1,j  ,.false.)
-    !hxm_a=(xi+0.5)*ddy_u_point(grd,grd%ua,i  ,j-1,.false.)+(0.5-xi)*ddy_u_point(grd,grd%uo,i-1,j-1,.false.)
-  endif
-  duo_dy=yj*hxp_o+(1.-yj)*hxm_o
-  !dua_dy=yj*hxp_a+(1.-yj)*hxm_a
-
-  cos_rot=bilin(grd, grd%cos, i, j, xi, yj) ! If true, uses the inverted bilin function
-  sin_rot=bilin(grd, grd%sin, i, j, xi, yj)
-
-  if ((cos_rot .ne. 1.0) .or. (sin_rot .ne. 0.0)) then
-    if (yj>=0.5) then
-      hxp_o=(yj-0.5)*ddx_v_point(grd,grd%uo,i  ,j+1,.true. )+(1.5-yj)*ddx_v_point(grd,grd%uo,i  ,j  ,.true. )
-      hxm_o=(yj-0.5)*ddx_v_point(grd,grd%uo,i-1,j+1,.true. )+(1.5-yj)*ddx_v_point(grd,grd%uo,i-1,j  ,.true. )
-      !hxp_a=(yj-0.5)*ddx_v_point(grd,grd%ua,i  ,j+1,.false.)+(1.5-yj)*ddx_v_point(grd,grd%ua,i  ,j  ,.false.)
-      !hxm_a=(yj-0.5)*ddx_v_point(grd,grd%ua,i-1,j+1,.false.)+(1.5-yj)*ddx_v_point(grd,grd%ua,i-1,j  ,.false.)
-    else
-      hxp_o=(yj+0.5)*ddx_v_point(grd,grd%uo,i  ,j  ,.true. )+(0.5-yj)*ddx_v_point(grd,grd%uo,i  ,j-1,.true. )
-      hxm_o=(yj+0.5)*ddx_v_point(grd,grd%uo,i-1,j  ,.true. )+(0.5-yj)*ddx_v_point(grd,grd%uo,i-1,j-1,.true. )
-      !hxp_a=(yj+0.5)*ddx_v_point(grd,grd%ua,i  ,j  ,.false.)+(0.5-yj)*ddx_v_point(grd,grd%ua,i  ,j-1,.false.)
-      !hxm_a=(yj+0.5)*ddx_v_point(grd,grd%ua,i-1,j  ,.false.)+(0.5-yj)*ddx_v_point(grd,grd%ua,i-1,j-1,.false.)
-    endif
-    duo_dx=xi*hxp_o+(1.-xi)*hxm_o
-    !dua_dx=xi*hxp_a+(1.-xi)*hxm_a
-    if (xi>=0.5) then
-      hxp_o=(xi-0.5)*ddy_u_point(grd,grd%vo,i+1,j,  .true. )+(1.5-xi)*ddy_u_point(grd,grd%vo,i  ,j,  .true. )
-      hxm_o=(xi-0.5)*ddy_u_point(grd,grd%vo,i+1,j-1,.true. )+(1.5-xi)*ddy_u_point(grd,grd%vo,i  ,j-1,.true. )
-      !hxp_a=(xi-0.5)*ddy_u_point(grd,grd%va,i+1,j,  .false.)+(1.5-xi)*ddy_u_point(grd,grd%va,i  ,j,  .false.)
-      !hxm_a=(xi-0.5)*ddy_u_point(grd,grd%va,i+1,j-1,.false.)+(1.5-xi)*ddy_u_point(grd,grd%va,i  ,j-1,.false.)
-    else
-      hxp_o=(xi+0.5)*ddy_u_point(grd,grd%vo,i  ,j,  .true. )+(0.5-xi)*ddy_u_point(grd,grd%vo,i-1,j,  .true. )
-      hxm_o=(xi+0.5)*ddy_u_point(grd,grd%vo,i  ,j-1,.true. )+(0.5-xi)*ddy_u_point(grd,grd%vo,i-1,j-1,.true. )
-      !hxp_a=(xi+0.5)*ddy_u_point(grd,grd%va,i  ,j,  .false.)+(0.5-xi)*ddy_u_point(grd,grd%vo,i-1,j,  .false.)
-      !hxm_a=(xi+0.5)*ddy_u_point(grd,grd%va,i  ,j-1,.false.)+(0.5-xi)*ddy_u_point(grd,grd%vo,i-1,j-1,.false.)
-    endif
-    dvo_dy=yj*hxp_o+(1.-yj)*hxm_o
-    !dva_dy=yj*hxp_a+(1.-yj)*hxm_a
-    call rotate(duo_dx, dvo_dx, cos_rot, sin_rot)
-    call rotate(duo_dy, dvo_dy, cos_rot, sin_rot)
-    !call rotate(dua_dx, dva_dx, cos_rot, sin_rot)
-    !call rotate(dua_dy, dva_dy, cos_rot, sin_rot)
-  endif
-
-  if ((dvo_dx.ne.dvo_dx) .or. (duo_dy.ne.duo_dy)) then
-    dvo_dx=0.; duo_dy=0.
-  endif
-  !if ((dva_dx.ne.dva_dx) .or. (dua_dy.ne.dua_dy)) then
-  !  dva_dx=0.; dua_dy=0.
-  !endif
-
-  berg%curl_o=dvo_dx-duo_dy
-  !berg%curl_a=dva_dx-dua_dy
-end subroutine interp_curl
-
 !> Returns zonal slope of sea-surface height across the east face of cell i,j
 real function ddx_ssh(grd,i,j)
   ! Arguments
@@ -7195,10 +7093,6 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b,fl_disp_x,fl_disp_y,berg_from_bit
   if (bergs%dem) then
     allocate(cberg%ang_vel,cberg%ang_accel,cberg%rot)
     cberg%ang_vel=0.; cberg%ang_accel=0.; cberg%rot=0.
-    if (bergs%add_curl_to_torque) then
-      allocate(cberg%curl_o)!,cberg%curl_a)
-      cberg%curl_o=pberg%curl_o!; cberg%curl_a=pberg%curl_a;
-    endif
   endif
 
   if (monitor_energy) then
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 549caea..d4ce54a 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -60,7 +60,6 @@ module ice_bergs_framework
 real :: A68_xdisp=0.
 real :: A68_ydisp=0.
 logical :: rev_mind=.false.
-logical :: add_curl_to_torque=.false. !include torque from the curl of ocean and atmospheric velocities (DEM-mode only)
 character(len=11) :: fracture_criterion='none' !<'energy','stress','strain_rate','strain',or 'none'
 logical :: use_damage=.false. !< Damage on bonds. Can evolve and serve as fracture criterion, or just to represent weaker bond
 logical :: orig_dem_moment_of_inertia=.false.
@@ -74,7 +73,7 @@ module ice_bergs_framework
 public ignore_ij_restart, use_slow_find,generate_test_icebergs,old_bug_rotated_weights,budget
 public orig_read, force_all_pes_traj
 public mts,new_mts,save_bond_traj,ewsame,monitor_energy,iceberg_bonds_on
-public dem, save_bond_forces, add_curl_to_torque, fracture_criterion, orig_dem_moment_of_inertia
+public dem, save_bond_forces, fracture_criterion, orig_dem_moment_of_inertia
 public power_ground, short_step_mts_grounding, radius_based_drag
 public A68_test, A68_xdisp, A68_ydisp
 
@@ -301,8 +300,6 @@ module ice_bergs_framework
   real, allocatable :: ang_vel !< Angular velocity
   real, allocatable :: ang_accel !< Angular acceleration
   real, allocatable :: rot !< Accumulated rotation
-  real, allocatable :: curl_o !< curl of ocean velocity
-  real, allocatable :: curl_a !< curl of atmospheric velocity
 end type xyt
 
 !> An iceberg object, used as a link in a linked list
@@ -391,8 +388,6 @@ module ice_bergs_framework
   real, allocatable :: ang_vel !< Angular velocity
   real, allocatable :: ang_accel !< Angular acceleration
   real, allocatable :: rot !< Accumulated rotation
-  real, allocatable :: curl_o !< curl of ocean velocity
-  real, allocatable :: curl_a !< curl of atmospheric velocity
 end type iceberg
 
 !> A bond object connecting two bergs, used as a link in a linked list
@@ -659,7 +654,6 @@ module ice_bergs_framework
   logical :: uniaxial_test=.false. !adds a tensile stress to the east-most berg element
   real :: dem_tests_start_lon !starting lon of west-most berg element for uniaxial/dem tests
   real :: dem_tests_end_lon !starting lon of east-most berg element for uniaxial/dem tests
-  logical :: add_curl_to_torque=.false. !include torque from the curl of ocean and atmospheric velocities
   ! Element interactions
   logical :: constant_interaction_LW=.false. !< Use a constant element length & width during berg interactions
   real :: constant_length=0.!< If constant_interaction_LW, the constant length. If 0, will be set to max initial length
@@ -938,7 +932,7 @@ subroutine ice_bergs_framework_init(bergs, &
          initial_mass_n, distribution_n, mass_scaling_n, initial_thickness_n, fl_use_l_scale, fl_l_scale,&
          fl_l_scale_erosion_only, fl_youngs, fl_strength,  save_all_traj_year, save_nonfl_traj_by_class,&
          save_traj_by_class_start_mass_thres_n, save_traj_by_class_start_mass_thres_s,traj_area_thres_sntbc,&
-         traj_area_thres_fl,tau_is_velocity, add_curl_to_torque,ocean_drag_scale, A68_test, &
+         traj_area_thres_fl,tau_is_velocity, ocean_drag_scale, A68_test, &
          A68_xdisp,A68_ydisp,&
          orig_dem_moment_of_inertia, break_bonds_on_sub_steps, skip_first_outer_mts_step, rev_mind, &
          no_frac_first_ts, use_grounding_torque, power_ground, short_step_mts_grounding, radius_based_drag, save_bond_forces
@@ -1397,10 +1391,6 @@ subroutine ice_bergs_framework_init(bergs, &
   buffer_width=buffer_width+3+(max_bonds*5)
   buffer_width_traj=buffer_width_traj+3
   buffer_width_bond_traj=buffer_width_bond_traj+4+1
-  if (add_curl_to_torque) then
-    buffer_width=buffer_width+1 !2
-    buffer_width_traj=buffer_width_traj+1 !2
-  endif
 elseif (fracture_criterion .ne. 'none') then
   buffer_width=buffer_width+1+(max_bonds*3)
   buffer_width_traj=buffer_width_traj+1
@@ -1589,7 +1579,6 @@ subroutine ice_bergs_framework_init(bergs, &
   endif
   bergs%ocean_drag_scale=ocean_drag_scale
   bergs%dem_shear_for_frac_only=dem_shear_for_frac_only
-  bergs%add_curl_to_torque=add_curl_to_torque
   ! Footloose calving parameters
   bergs%fl_use_poisson_distribution=fl_use_poisson_distribution
   bergs%fl_use_perimeter=fl_use_perimeter
@@ -3457,10 +3446,6 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
     call push_buffer_value(buff%data(:,n), counter, berg%ang_vel)
     call push_buffer_value(buff%data(:,n), counter, berg%ang_accel)
     call push_buffer_value(buff%data(:,n), counter, berg%rot)
-    if (add_curl_to_torque) then
-      call push_buffer_value(buff%data(:,n), counter, berg%curl_o)
-      !call push_buffer_value(buff%data(:,n), counter, berg%curl_a)
-    endif
   elseif (fracture_criterion .ne. 'none') then
     call push_buffer_value(buff%data(:,n), counter, berg%accum_bond_rotation)
   endif
@@ -3691,9 +3676,6 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
 
   if (dem) then
     allocate(localberg%ang_vel,localberg%ang_accel,localberg%rot)
-    if (add_curl_to_torque) then
-      allocate(localberg%curl_o) !,localberg%curl_a)
-    endif
   elseif (fracture_criterion .ne. 'none') then
     allocate(localberg%accum_bond_rotation)
   endif
@@ -3779,10 +3761,6 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
     call pull_buffer_value(buff%data(:,n), counter, localberg%ang_vel)
     call pull_buffer_value(buff%data(:,n), counter, localberg%ang_accel)
     call pull_buffer_value(buff%data(:,n), counter, localberg%rot)
-    if (add_curl_to_torque) then
-      call pull_buffer_value(buff%data(:,n), counter, localberg%curl_o)
-      !call pull_buffer_value(buff%data(:,n), counter, localberg%curl_a)
-    endif
   elseif (fracture_criterion .ne. 'none') then
     call pull_buffer_value(buff%data(:,n), counter, localberg%accum_bond_rotation)
   endif
@@ -4078,10 +4056,6 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj, save_fl_traj,
       call push_buffer_value(buff%data(:,n), counter, traj%ang_vel)
       call push_buffer_value(buff%data(:,n), counter, traj%ang_accel)
       call push_buffer_value(buff%data(:,n), counter, traj%rot)
-      if (add_curl_to_torque) then
-        call push_buffer_value(buff%data(:,n), counter, traj%curl_o)
-        !call push_buffer_value(buff%data(:,n), counter, traj%curl_a)
-      endif
     elseif (fracture_criterion .ne. 'none') then
       call push_buffer_value(buff%data(:,n), counter, traj%accum_bond_rotation)
     endif
@@ -4119,7 +4093,6 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj, save_fl_tra
 
   if (dem) then
     allocate(traj%ang_vel,traj%ang_accel,traj%rot)
-    if (add_curl_to_torque) allocate(traj%curl_o) !,traj%curl_a)
   elseif (fracture_criterion .ne. 'none') then
     allocate(traj%accum_bond_rotation)
   endif
@@ -4203,10 +4176,6 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj, save_fl_tra
       call pull_buffer_value(buff%data(:,n), counter, traj%ang_vel)
       call pull_buffer_value(buff%data(:,n), counter, traj%ang_accel)
       call pull_buffer_value(buff%data(:,n), counter, traj%rot)
-      if (add_curl_to_torque) then
-        call pull_buffer_value(buff%data(:,n), counter, traj%curl_o)
-        !call pull_buffer_value(buff%data(:,n), counter, traj%curl_a)
-      endif
     elseif (fracture_criterion .ne. 'none') then
       call pull_buffer_value(buff%data(:,n), counter, traj%accum_bond_rotation)
     endif
@@ -4820,7 +4789,6 @@ subroutine create_iceberg(berg, bergvals)
   endif
   if (dem) then
     allocate(berg%ang_vel,berg%ang_accel,berg%rot)
-    if (add_curl_to_torque) allocate(berg%curl_o) !,berg%curl_a)
   elseif (fracture_criterion .ne. 'none') then
     allocate(berg%accum_bond_rotation)
   endif
@@ -6129,7 +6097,6 @@ subroutine record_posn(bergs)
 
   if (dem) then
     allocate(posn%ang_vel,posn%ang_accel,posn%rot)
-    if (add_curl_to_torque) allocate(posn%curl_o) !,posn%curl_a)
   elseif (fracture_criterion .ne. 'none') then
     allocate(posn%accum_bond_rotation)
   endif
@@ -6251,10 +6218,6 @@ subroutine record_posn(bergs)
             posn%ang_vel=this%ang_vel
             posn%ang_accel=this%ang_accel
             posn%rot=this%rot
-            if (add_curl_to_torque) then
-              posn%curl_o=this%curl_o
-              !posn%curl_a=this%curl_a
-            endif
           elseif (fracture_criterion .ne. 'none') then
             posn%accum_bond_rotation=this%accum_bond_rotation
           endif
@@ -6349,7 +6312,6 @@ subroutine push_posn(trajectory, posn_vals)
 
   if (dem) then
     allocate(new_posn%ang_vel,new_posn%ang_accel,new_posn%rot)
-    if (add_curl_to_torque) allocate(new_posn%curl_o) !,new_posn%curl_a)
   elseif (fracture_criterion .ne. 'none') then
     allocate(new_posn%accum_bond_rotation)
   endif
@@ -6415,7 +6377,6 @@ subroutine append_posn(trajectory, posn_vals)
 
   if (dem) then
     allocate(new_posn%ang_vel,new_posn%ang_accel,new_posn%rot)
-    if (add_curl_to_torque) allocate(new_posn%curl_o) !,new_posn%curl_a)
   elseif (fracture_criterion .ne. 'none' .and. (.not. dem)) then
     allocate(new_posn%accum_bond_rotation)
   endif
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index a1911ed..d7761af 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -44,7 +44,7 @@ module ice_bergs_io
 use ice_bergs_framework, only: mts,save_bond_traj
 use ice_bergs_framework, only: push_bond_posn, append_bond_posn
 use ice_bergs_framework, only: pack_bond_traj_into_buffer2,unpack_bond_traj_from_buffer2
-use ice_bergs_framework, only: monitor_energy, use_damage, dem, add_curl_to_torque, fracture_criterion, iceberg_bonds_on
+use ice_bergs_framework, only: monitor_energy, use_damage, dem, fracture_criterion, iceberg_bonds_on
 
 implicit none ; private
 
@@ -160,8 +160,6 @@ subroutine write_restart(bergs, time_stamp)
                                    ang_vel,      &
                                    ang_accel,    &
                                    rot,          &
-                                   curl_o,       &
-                                   !curl_a,       &
                                    lon_prev,     &
                                    lat_prev,     &
                                    accum_bond_rotation, &
@@ -252,10 +250,6 @@ subroutine write_restart(bergs, time_stamp)
      allocate(ang_vel(nbergs))
      allocate(ang_accel(nbergs))
      allocate(rot(nbergs))
-     if (add_curl_to_torque) then
-       allocate(curl_o(nbergs))
-       !allocate(curl_a(nbergs))
-    endif
    elseif (fracture_criterion.ne.'none') then
      allocate(lon_prev(nbergs))
      allocate(lat_prev(nbergs))
@@ -335,12 +329,6 @@ subroutine write_restart(bergs, time_stamp)
       longname='dem angular acceleration',units='rad/s^2')
     id = register_restart_field(bergs_restart,filename,'rot',rot,&
       longname='dem accumulated rotation',units='rad')
-    if (add_curl_to_torque) then
-      id = register_restart_field(bergs_restart,filename,'curl_o',curl_o,&
-        longname='curl of ocean velocity',units='1/s')
-      !id = register_restart_field(bergs_restart,filename,'curl_a',curl_a,&
-      !  longname='curl of atmospheric velocity',units='1/s')
-    endif
   elseif (fracture_criterion.ne.'none') then
     id = register_restart_field(bergs_restart,filename,'lon_prev',lon_prev,longname='previous longitude',units='degrees_E')
     id = register_restart_field(bergs_restart,filename,'lat_prev',lat_prev,longname='previous latitude',units='degrees_N')
@@ -400,10 +388,6 @@ subroutine write_restart(bergs, time_stamp)
         ang_vel(i) = this%ang_vel
         ang_accel(i) = this%ang_accel
         rot(i) = this%rot
-        if (add_curl_to_torque) then
-          curl_o(i) = this%curl_o
-          !curl_a(i) = this%curl_a
-        endif
       elseif (fracture_criterion.ne.'none') then
         lon_prev(i) = this%lon_prev
         lat_prev(i) = this%lat_prev
@@ -457,11 +441,6 @@ subroutine write_restart(bergs, time_stamp)
              ang_vel,      &
              ang_accel,    &
              rot)
-    if (add_curl_to_torque) then
-      deallocate(          &
-             curl_o) !,       &
-             !curl_a)
-    endif
   elseif (fracture_criterion.ne.'none') then
     deallocate(            &
              lon_prev,     &
@@ -834,10 +813,6 @@ subroutine read_restart_bergs(bergs,Time)
        allocate(ang_vel(nbergs_in_file))
        allocate(ang_accel(nbergs_in_file))
        allocate(rot(nbergs_in_file))
-       if (add_curl_to_torque) then
-         allocate(localberg%curl_o)!, localberg%curl_a)
-         localberg%curl_o=0.0!; localberg%curl_a=0.0
-       endif
      elseif (fracture_criterion.ne.'none') then
        allocate(lon_prev(nbergs_in_file))
        allocate(lat_prev(nbergs_in_file))
@@ -1154,10 +1129,6 @@ subroutine generate_bergs(bergs,Time)
     allocate(localberg%ang_vel)
     allocate(localberg%ang_accel)
     allocate(localberg%rot)
-    if (add_curl_to_torque) then
-      allocate(localberg%curl_o)
-      !allocate(localberg%curl_a)
-    endif
   elseif (fracture_criterion.ne.'none') then
     allocate(localberg%accum_bond_rotation)
   endif
@@ -1211,10 +1182,6 @@ subroutine generate_bergs(bergs,Time)
         localberg%ang_vel=0.
         localberg%ang_accel=0.
         localberg%rot=0.
-        if (add_curl_to_torque) then
-          localberg%curl_o=0.
-          !localberg%curl_a=0.
-        endif
       elseif (fracture_criterion.ne.'none') then
         localberg%accum_bond_rotation=0.
       endif
@@ -1755,7 +1722,7 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r, tra
 ! Local variables
 integer :: iret, ncid, i_dim, i
 integer :: lonid, latid, yearid, dayid, uvelid, vvelid, idcntid, idijid
-integer :: uvelpid,vvelpid, curloid, curlaid
+integer :: uvelpid,vvelpid
 integer :: uoid, void, uiid, viid, uaid, vaid, sshxid, sshyid, sstid, sssid
 integer :: cnid, hiid, hsid
 integer :: mid, smid, did, wid, lid, mbid, mflbid, mflbbid, hdid, nbid, odid, flkid
@@ -1951,10 +1918,6 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r, tra
           avid = inq_varid(ncid, 'ang_vel')
           aaid = inq_varid(ncid, 'ang_accel')
           rid  = inq_varid(ncid, 'rot')
-          if (add_curl_to_torque) then
-            curloid = inq_varid(ncid, 'curl_o')
-            !curlaid = inq_varid(ncid, 'curl_a')
-          endif
         elseif (fracture_criterion .ne. 'none') then
           abrid = inq_varid(ncid, 'accum_bond_rotation')
         endif
@@ -2042,10 +2005,6 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r, tra
           avid = def_var(ncid, 'ang_vel', NF_DOUBLE, i_dim)
           aaid = def_var(ncid, 'ang_accel', NF_DOUBLE, i_dim)
           rid  = def_var(ncid, 'rot', NF_DOUBLE, i_dim)
-          if (add_curl_to_torque) then
-            curloid = def_var(ncid, 'curl_o', NF_DOUBLE, i_dim)
-            !curlaid = def_var(ncid, 'curl_a', NF_DOUBLE, i_dim)
-          endif
         elseif (fracture_criterion .ne. 'none') then
           abrid = def_var(ncid, 'accum_bond_rotation', NF_DOUBLE, i_dim)
         endif
@@ -2190,12 +2149,6 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r, tra
           call put_att(ncid, aaid, 'units', 'rad/s^2')
           call put_att(ncid, rid, 'long_name', 'accumulated rotation')
           call put_att(ncid, rid, 'units', 'rad')
-          if (add_curl_to_torque) then
-            call put_att(ncid, curloid, 'long_name', 'curl of ocean velocity')
-            call put_att(ncid, curloid, 'units', '1/s')
-            !call put_att(ncid, curlaid, 'long_name', 'curl of atmospheric velocity')
-            !call put_att(ncid, curlaid, 'units', '1/s')
-          endif
         elseif (fracture_criterion .ne. 'none') then
           call put_att(ncid, abrid, 'long_name', 'accumulated bond rotation')
           call put_att(ncid, abrid, 'units', 'radians')
@@ -2293,10 +2246,6 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r, tra
           call put_double(ncid, avid, i, this%ang_vel)
           call put_double(ncid, aaid, i, this%ang_accel)
           call put_double(ncid, rid,  i, this%rot)
-          if (add_curl_to_torque) then
-            call put_double(ncid, curloid, i, this%curl_o)
-            !call put_double(ncid, curlaid, i, this%curl_a)
-          endif
         elseif (fracture_criterion .ne. 'none') then
           call put_double(ncid, abrid, i, this%accum_bond_rotation)
         endif
diff --git a/tests/.gitignore b/tests/.gitignore
index 97068f3..3247cd1 100644
--- a/tests/.gitignore
+++ b/tests/.gitignore
@@ -7,7 +7,12 @@ single_test/
 size_test_tab/
 steady_test/
 uniaxial_test/
+a68/
+collision_tests_2/
 a68_2/
 a68_3/
 a68_old/
 other_tests/
+nc2csv_bonds.py
+plot_bond_strain.py
+plot_energy.py
\ No newline at end of file

From 6d4d4d4b05a18cfc867a148dc57cfa30872e67fc Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Tue, 27 Dec 2022 13:52:58 -0500
Subject: [PATCH 328/361] Added bond variable 'broken' to track if a bond is
 broken (1) or intact (0). Added namelist option
 'use_broken_bonds_for_substep_contact', which if true, identifies a pair of
 particles as contacting during the sub-steps if and only if the bond between
 them is broken (according to the new 'broken' variable'). This is more
 computationally-efficient than searching for contact pairs in the current and
 neighboring grid cells. Both the new 'broken' variable and
 'use_broken_bonds_for_substep_contact' option can only be used for iKID
 multiple time step runs in dem-mode (dem=.true.).

---
 src/icebergs.F90                     |  99 +++++++++-------
 src/icebergs_framework.F90           | 167 +++++++++++++++++++--------
 src/icebergs_io.F90                  |  27 +++--
 tests/collision_tests/.gitignore     |   3 +-
 tests/collision_tests/input.nml      | 161 ++++++++++++++++++++++++++
 tests/dem_ground_frac_test/README    |   9 +-
 tests/dem_ground_frac_test/input.nml |  17 ++-
 tests/footloose_tests/.gitignore     |   3 +-
 8 files changed, 379 insertions(+), 107 deletions(-)
 create mode 100644 tests/collision_tests/input.nml

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 5910afb..d881b89 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -1174,6 +1174,17 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
         if (current_bond%nstress>bergs%frac_thres_n .or. current_bond%sstress>bergs%frac_thres_t) then
           bergs%bond_break_detected=.true.
 
+          if (current_bond%broken.ne.1) then
+            current_bond%broken=1
+            if (current_bond%nstress>bergs%frac_thres_n .and. current_bond%sstress>bergs%frac_thres_t) then
+              print *,'T and S break',berg%lat,current_bond%nstress,current_bond%sstress
+            elseif (current_bond%nstress>bergs%frac_thres_n) then
+              print *,'TENSILE break',berg%lat,current_bond%nstress,current_bond%sstress
+            else
+              print *,'SHEAR   break',berg%lat,current_bond%nstress,current_bond%sstress
+            endif
+          endif
+
           if (current_bond%nstress<0) then
             !if fail under shear with normal compression, then should still feel contact force
             damping_coef = bergs%dem_damping_coef*sqrt(bergs%dem_K_damp*M1*M2/(M1+M2))
@@ -1181,6 +1192,8 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
             F_x = F_x + Fn_x; F_y = F_y + Fn_y !linear forces
           endif
 
+          if (bergs%use_broken_bonds_for_substep_contact) berg%n_bonds=berg%n_bonds-1
+
           if (savestress .and. save_bond_forces) then
             current_bond%T=0.; current_bond%T_d=0.
             if (current_bond%nstress<0) then
@@ -1201,29 +1214,17 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
             current_bond%other_bond%tangd1       = -current_bond%tangd1
             current_bond%other_bond%tangd2       = -current_bond%tangd2
             current_bond%other_bond%length       = current_bond%length
+            current_bond%other_bond%broken=1
             current_bond%other_bond%other_id=-current_bond%other_bond%other_id
+            if (bergs%use_broken_bonds_for_substep_contact) then
+              current_bond%other_berg%n_bonds=current_bond%other_berg%n_bonds-1
+            endif
           endif
           return !Broken bond. Return without adding forces and torques
         endif
-      elseif (bergs%fracture_criterion=='computed') then
-        Rsig=current_bond%nstress/bergs%frac_thres_n
-        Rtau=current_bond%sstress/bergs%frac_thres_t
-        if ((0.5*Rsig+sqrt((0.5*Rsig)**2. + Rtau**2.)) > 1) then
-          bergs%bond_break_detected=.true.
-          if (save_bond_forces) current_bond%other_bond%other_id=-current_bond%other_bond%other_id
-          return
-        endif
-      elseif (bergs%fracture_criterion=='computed_s') then
-        Rsig=current_bond%nstress/bergs%frac_thres_n
-        Rtau=current_bond%sstress/bergs%frac_thres_t
-        if (sqrt(Rsig**2. + Rtau**2.) > 1) then
-          if (save_bond_forces) current_bond%other_bond%other_id=-current_bond%other_bond%other_id
-          bergs%bond_break_detected=.true.
-          return
-        endif
       else
         call error_mesg('KID, calculate_force_dem', &
-          'break_bond_on_sub_steps currently only possible with fracture critera=computed or stress', FATAL)
+          'break_bond_on_sub_steps currently only possible with fracture critera=stress', FATAL)
       endif
     endif
 
@@ -1611,7 +1612,11 @@ subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, d
       ! Determining number of bonds
       current_bond=>berg%first_bond
       do while (associated(current_bond)) ! loop over all bonds
-        N_bonds=N_bonds+1.0
+        if (bergs%dem) then
+          if (current_bond%broken.ne.1) N_bonds=N_bonds+1.0
+        else
+          N_bonds=N_bonds+1.0
+        endif
         current_bond=>current_bond%next_bond
       enddo
       dragfrac = ((N_max-N_bonds)/N_max)
@@ -2039,7 +2044,9 @@ subroutine accel_explicit_inner_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel,
           if (current_bond%other_id<0) then
             current_bond%other_id=-current_bond%other_id
             other_berg=>current_bond%other_berg
-            other_berg%id=-other_berg%id !mark, as to not repeat in contact search below
+            if (.not. bergs%use_broken_bonds_for_substep_contact) then
+              other_berg%id=-other_berg%id !mark, as to not repeat in contact search below
+            endif
 
             bond_matched=.true.
             F_x=F_x+current_bond%F_x; F_y=F_y+current_bond%F_y
@@ -2055,15 +2062,22 @@ subroutine accel_explicit_inner_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel,
           call error_mesg('KID,bond interactions', 'Trying to do Bond interactions with unassosiated berg!' ,FATAL)
         else
           if (bergs%dem) then
-            call calculate_force_dem(bergs,berg,other_berg,current_bond,&
-              dt,F_x,F_y,T,Fd_x,Fd_y,T_d,savestress=.true.)
-            other_berg%id=-other_berg%id !mark, as to not repeat in contact search below
+            if (current_bond%broken.eq.1) then
+              call calculate_unbonded_same_conglom_dem_force(bergs, berg, other_berg, &
+                IA_x, IA_y, IAd_x, IAd_y, uvel0, vvel0, uvel0, vvel0)
+            else
+              call calculate_force_dem(bergs,berg,other_berg,current_bond,&
+                dt,F_x,F_y,T,Fd_x,Fd_y,T_d,savestress=.true.)
+            endif
+            if (.not. bergs%use_broken_bonds_for_substep_contact) then
+              other_berg%id=-other_berg%id !mark, as to not repeat in contact search below
+            endif
           else
             P_ia_11=0. ; P_ia_12=0. ;  P_ia_21=0.;  P_ia_22=0.
             P_ia_times_u_x=0. ; P_ia_times_u_y=0.
             call calculate_force(bergs, berg, other_berg, IA_x, IA_y, uvel0, vvel0, uvel0, vvel0,  &
               P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded)
-            other_berg%id=-other_berg%id !mark, as to not repeat in contact search below
+            other_berg%id=-other_berg%id !mark, as to not repeat in contact search below (dem required for use_broken_bonds_for_substep_contact)
             IAd_x=IAd_x+P_ia_11*(other_berg%uvel_old-berg%uvel_old)+P_ia_12*(other_berg%vvel_old-berg%vvel_old)
             IAd_y=IAd_y+P_ia_12*(other_berg%uvel_old-berg%uvel_old)+P_ia_22*(other_berg%vvel_old-berg%vvel_old)
           endif
@@ -2077,7 +2091,7 @@ subroutine accel_explicit_inner_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel,
 
     !for dem-mode, do not bother running the contact algorithm if the particle is within interior of conglomerate
     if (bergs%iceberg_bonds_on .and. bergs%dem) then
-      if (berg%n_bonds .eq. bergs%max_bonds) then
+      if ((berg%n_bonds .eq. bergs%max_bonds).or. bergs%use_broken_bonds_for_substep_contact) then
         run_contact=.false.
       else
         run_contact=.true.
@@ -2107,14 +2121,15 @@ subroutine accel_explicit_inner_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel,
         enddo
       enddo;enddo
     endif
-
-    !unmark the bonded bergs
-    current_bond=>berg%first_bond
-    do while (associated(current_bond))
-      other_berg=>current_bond%other_berg
-      other_berg%id=abs(other_berg%id)
-      current_bond=>current_bond%next_bond
-    enddo
+    if (.not. bergs%use_broken_bonds_for_substep_contact) then
+      !unmark the bonded bergs
+      current_bond=>berg%first_bond
+      do while (associated(current_bond))
+        other_berg=>current_bond%other_berg
+        other_berg%id=abs(other_berg%id)
+        current_bond=>current_bond%next_bond
+      enddo
+    endif
   endif
 
   if (bergs%dem) then
@@ -2511,7 +2526,11 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
     ! Determining number of bonds
     current_bond=>berg%first_bond
     do while (associated(current_bond)) ! loop over all bonds
-      N_bonds=N_bonds+1.0
+      if (bergs%dem) then
+        if (current_bond%broken.ne.1) N_bonds=N_bonds+1.0
+      else
+        N_bonds=N_bonds+1.0
+      endif
       current_bond=>current_bond%next_bond
     enddo
     dragfrac = ((N_max-N_bonds)/N_max)
@@ -3397,7 +3416,11 @@ subroutine thermodynamics(bergs)
             ! Determining number of bonds
             ! current_bond=>this%first_bond
             ! do while (associated(current_bond)) ! loop over all bonds
+            ! if (bergs%dem) then
+            !   if (current_bond%broken.ne.1) N_bonds=N_bonds+1.0
+            ! else
             !   N_bonds=N_bonds+1.0
+            ! endif
             !   current_bond=>current_bond%next_bond
             ! enddo
           endif
@@ -7343,8 +7366,6 @@ subroutine evolve_icebergs_mts(bergs)
     skip_first_outer_mts_step=.false.
   endif
 
-
-
   ! PART 3: MTS fast sub-steps (bonded interactions only):
   ! Position and velocity are updated by:
   ! X2 = X1+dt*V1+((dt^2)/2)*a_k +((dt^2)/2)*b_k
@@ -7435,10 +7456,6 @@ subroutine evolve_icebergs_mts(bergs)
           i=berg%ine      ;   j=berg%jne
           xi=berg%xi      ;   yj=berg%yj
 
-          ! if (latn>50.e3 .or. latn<10.e3 .or. lonn > 45.e3) then
-          !   print *,'id,lat,lon',berg%id,latn,lonn
-          ! endif
-
           if (new_mts) then
             axn = axn+bxn; ayn=ayn+byn
           endif
@@ -7637,7 +7654,9 @@ subroutine evolve_icebergs_mts(bergs)
       enddo ! loop over all bergs
     enddo; enddo ! update 'old' velocities
 
-    if (break_bonds_on_sub_steps .and. bergs%bond_break_detected) call break_bonds_dem(bergs)
+    if (.not. bergs%use_broken_bonds_for_substep_contact) then
+      if (break_bonds_on_sub_steps .and. bergs%bond_break_detected) call break_bonds_dem(bergs)
+    endif
   enddo ! loop over sub-steps
 
   !reset interactive_forces
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index d4ce54a..3b3618a 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -422,6 +422,7 @@ module ice_bergs_framework
   real, allocatable :: tangd2 !< Accumulated tangential displacement, y-component (m)
   real, allocatable :: nstress !< Normal stress (Pa)
   real, allocatable :: sstress !< Shear stress (Pa)
+  integer, allocatable :: broken !< Is a bond broken (1) or not (0)?
   type(bond), pointer :: other_bond=>null() !< Matching bond
   ! If save_bond_forces
   real, allocatable :: F_x !< Zonal force
@@ -463,6 +464,7 @@ module ice_bergs_framework
   real, allocatable :: tangd2 !< Accumulated tangential displacement, y-component (m)
   real, allocatable :: nstress
   real, allocatable :: sstress
+  integer, allocatable :: broken !< Is bond broken (1) or not(0)?
 end type bond_xyt
 
 ! A dynamic buffer, used for communication, that packs types into rectangular memory
@@ -648,6 +650,7 @@ module ice_bergs_framework
   real :: poisson=0.3 ! Poisson's ratio
   real :: dem_spring_coef=0.
   real :: dem_damping_coef=0.1
+  logical :: use_broken_bonds_for_substep_contact=.false. !only evaluate sub-step contact between particles with a broken bond
   logical :: bond_break_detected=.false.
   logical :: dem_shear_for_frac_only=.false. !< If true, DEM shear is calculated for fracture, but zeroed for berg interactions
   integer :: dem_beam_test=0 !1=Simply supported beam,2=cantilever beam,3=angular vel tes
@@ -768,7 +771,6 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: uniaxial_test=.false. !adds a tensile stress to the east-most berg element
 real :: cdrag_grounding=0.0 ! Drag coefficient against ocean bottom
 real :: h_to_init_grounding=100.0
-!character(len=11) :: fracture_criterion ! 'energy','stress','strain_rate','strain',or 'none'
 real :: frac_thres_n=0.0 !normal fracture strain threshold
 real :: frac_thres_t=0.0 !tangential fracture strain threshold
 logical :: damage_test_1=.false. ! Sets initial damage for bonds that overlap y=17000.0
@@ -876,6 +878,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: poisson=0.3 ! Poisson's ratio
 real :: dem_spring_coef=0.
 real :: dem_damping_coef=0.1
+logical :: use_broken_bonds_for_substep_contact=.false. ! only evaluate sub-step contact between particles with a broken bond
 logical :: dem_shear_for_frac_only=.false. ! If true, DEM shear is calculated for fracture, but zeroed for berg interactions
 integer :: dem_beam_test=0 !1=Simply supported beam,2=cantilever beam,3=angular vel test
 ! Element Interactions
@@ -933,7 +936,7 @@ subroutine ice_bergs_framework_init(bergs, &
          fl_l_scale_erosion_only, fl_youngs, fl_strength,  save_all_traj_year, save_nonfl_traj_by_class,&
          save_traj_by_class_start_mass_thres_n, save_traj_by_class_start_mass_thres_s,traj_area_thres_sntbc,&
          traj_area_thres_fl,tau_is_velocity, ocean_drag_scale, A68_test, &
-         A68_xdisp,A68_ydisp,&
+         A68_xdisp,A68_ydisp,use_broken_bonds_for_substep_contact,&
          orig_dem_moment_of_inertia, break_bonds_on_sub_steps, skip_first_outer_mts_step, rev_mind, &
          no_frac_first_ts, use_grounding_torque, power_ground, short_step_mts_grounding, radius_based_drag, save_bond_forces
 
@@ -1388,9 +1391,9 @@ subroutine ice_bergs_framework_init(bergs, &
 endif
 
 if (dem) then
-  buffer_width=buffer_width+3+(max_bonds*5)
+  buffer_width=buffer_width+3+(max_bonds*6)
   buffer_width_traj=buffer_width_traj+3
-  buffer_width_bond_traj=buffer_width_bond_traj+4+1
+  buffer_width_bond_traj=buffer_width_bond_traj+6
 elseif (fracture_criterion .ne. 'none') then
   buffer_width=buffer_width+1+(max_bonds*3)
   buffer_width_traj=buffer_width_traj+1
@@ -1561,6 +1564,16 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%dem_spring_coef=dem_spring_coef
   bergs%dem_K_damp=2.*bergs%dem_spring_coef/(3.*(1.-bergs%poisson**2)) !damping factor
   bergs%dem_damping_coef=dem_damping_coef
+  if (break_bonds_on_sub_steps) then
+    if (use_broken_bonds_for_substep_contact .and. .not. (bergs%dem .and. bergs%iceberg_bonds_on)) then
+      call error_mesg('KID, framework', &
+        'use_broken_bonds_for_substep_contact requires dem and iceberg_bonds_on', FATAL)
+    else
+      bergs%use_broken_bonds_for_substep_contact=use_broken_bonds_for_substep_contact
+    endif
+  else
+    bergs%use_broken_bonds_for_substep_contact=.false.
+  end if
   bergs%dem_beam_test=dem_beam_test
   bergs%constant_interaction_LW=constant_interaction_LW
   bergs%constant_length=constant_length
@@ -2772,6 +2785,18 @@ subroutine set_conglom_ids(bergs)
     enddo
   enddo;enddo
 
+  if (bergs%use_broken_bonds_for_substep_contact) then
+    do grdj = grd%jsd,grd%jed; do grdi = grd%isd,grd%ied
+      this=>bergs%list(grdi,grdj)%first
+      do while (associated(this))
+        if (this%n_bonds<bergs%max_bonds) then
+          call remove_broken_bonds_between_congloms(this)
+        endif
+        this=>this%next
+      enddo
+    enddo;enddo
+  endif
+
 end subroutine set_conglom_ids
 
 !> Assign initial velocities and energies for energy tracking tests
@@ -2819,19 +2844,84 @@ recursive subroutine label_conglomerates(berg, new_conglom_id)
   type(iceberg), pointer :: other_berg
   type(bond) , pointer :: current_bond
 
+  current_bond=>berg%first_bond
+
+  if (dem) then
+    do while (associated(current_bond))
+      if (current_bond%broken.ne.1) then
+        if  (associated(current_bond%other_berg)) then
+          other_berg=>current_bond%other_berg
+          if (other_berg%conglom_id.ne.new_conglom_id) then
+            other_berg%conglom_id=new_conglom_id
+            if (other_berg%halo_berg==10) other_berg%halo_berg=2
+            call label_conglomerates(other_berg,new_conglom_id)
+          endif
+        endif
+      endif
+      current_bond=>current_bond%next_bond
+    enddo
+  else
+    !same as above with no broken bond check
+    do while (associated(current_bond))
+      if  (associated(current_bond%other_berg)) then
+        other_berg=>current_bond%other_berg
+        if (other_berg%conglom_id.ne.new_conglom_id) then
+          other_berg%conglom_id=new_conglom_id
+          if (other_berg%halo_berg==10) other_berg%halo_berg=2
+          call label_conglomerates(other_berg,new_conglom_id)
+        endif
+      endif
+      current_bond=>current_bond%next_bond
+    enddo
+  endif
+end subroutine label_conglomerates
+
+!> Remove broken bonds between two different conglomerates
+subroutine remove_broken_bonds_between_congloms(berg)
+  type(iceberg), pointer :: berg !< Berg to start search from
+  ! Local variables
+  type(iceberg), pointer :: other_berg
+  type(bond) , pointer :: current_bond, other_bond, kick_the_bucket
+
   current_bond=>berg%first_bond
   do while (associated(current_bond))
-    if  (associated(current_bond%other_berg)) then
-      other_berg=>current_bond%other_berg
-      if (other_berg%conglom_id.ne.new_conglom_id) then
-        other_berg%conglom_id=new_conglom_id
-        if (other_berg%halo_berg==10) other_berg%halo_berg=2
-        call label_conglomerates(other_berg,new_conglom_id)
+
+    if (current_bond%broken.eq.1) then
+      if  (associated(current_bond%other_berg)) then
+        other_berg=>current_bond%other_berg
+        if (other_berg%conglom_id.ne.berg%conglom_id) then
+          !broken bond exists between two different conglomerates
+          !remove matching bond from other berg
+          if (save_bond_forces .and. associated(current_bond%other_bond)) then
+            other_bond=>current_bond%other_bond
+            call delete_bond_from_list(other_berg,other_bond)
+          else
+            other_bond=>other_berg%first_bond
+            do while (associated(other_bond)) ! loop over all bonds
+              if (other_bond%other_id.eq.berg%id) then
+                kick_the_bucket=>other_bond
+                other_bond=>null()
+                call delete_bond_from_list(other_berg,kick_the_bucket)
+              else
+                other_bond=>other_bond%next_bond
+              endif
+            enddo
+          endif
+          !remove bond from current berg
+          kick_the_bucket=>current_bond
+          current_bond=>current_bond%next_bond
+          call delete_bond_from_list(berg,kick_the_bucket)
+        else
+          current_bond=>current_bond%next_bond
+        endif
+      else
+        current_bond=>current_bond%next_bond
       endif
+    else
+      current_bond=>current_bond%next_bond
     endif
-    current_bond=>current_bond%next_bond
   enddo
-end subroutine label_conglomerates
+end subroutine remove_broken_bonds_between_congloms
 
 !> Keep only the bergs which are part of, or within contact distance of, a conglomerate that overlaps
 !! the computational domain, or which are halo_berg=1
@@ -3480,6 +3570,7 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
           call push_buffer_value(buff%data(:,n), counter, current_bond%nstress)
           call push_buffer_value(buff%data(:,n), counter, current_bond%sstress)
           call push_buffer_value(buff%data(:,n), counter, current_bond%rel_rotation)
+          call push_buffer_value(buff%data(:,n), counter, current_bond%broken)
         elseif (fracture_criterion .ne. 'none') then
           call push_buffer_value(buff%data(:,n), counter, current_bond%rotation)
           call push_buffer_value(buff%data(:,n), counter, current_bond%rel_rotation)
@@ -3519,6 +3610,7 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
           call push_buffer_value(buff%data(:,n), counter, 0)
           call push_buffer_value(buff%data(:,n), counter, 0)
           call push_buffer_value(buff%data(:,n), counter, 0)
+          call push_buffer_value(buff%data(:,n), counter, 0)
         elseif (fracture_criterion .ne. 'none') then
           call push_buffer_value(buff%data(:,n), counter, 0)
           call push_buffer_value(buff%data(:,n), counter, 0)
@@ -3901,6 +3993,7 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
           call pull_buffer_value(buff%data(:,n), counter, current_bond%nstress)
           call pull_buffer_value(buff%data(:,n), counter, current_bond%sstress)
           call pull_buffer_value(buff%data(:,n), counter, current_bond%rel_rotation)
+          call pull_buffer_value(buff%data(:,n), counter, current_bond%broken)
         elseif (fracture_criterion .ne. 'none') then
           call pull_buffer_value(buff%data(:,n), counter, current_bond%rotation)
           call pull_buffer_value(buff%data(:,n), counter, current_bond%rel_rotation)
@@ -4232,6 +4325,7 @@ subroutine pack_bond_traj_into_buffer2(bond_traj, buff, n)
     call push_buffer_value(buff%data(:,n),counter,bond_traj%nstress)
     call push_buffer_value(buff%data(:,n),counter,bond_traj%sstress)
     call push_buffer_value(buff%data(:,n),counter,bond_traj%rel_rotation)
+    call push_buffer_value(buff%data(:,n),counter,bond_traj%broken)
   elseif (fracture_criterion.ne.'none') then
     call push_buffer_value(buff%data(:,n),counter,bond_traj%rotation)
     call push_buffer_value(buff%data(:,n),counter,bond_traj%rel_rotation)
@@ -4307,6 +4401,7 @@ subroutine unpack_bond_traj_from_buffer2(first, buff, n)
     call pull_buffer_value(buff%data(:,n),counter,bond_traj%nstress)
     call pull_buffer_value(buff%data(:,n),counter,bond_traj%sstress)
     call pull_buffer_value(buff%data(:,n),counter,bond_traj%rel_rotation)
+    call pull_buffer_value(buff%data(:,n),counter,bond_traj%broken)
   elseif (fracture_criterion.ne.'none') then
     call pull_buffer_value(buff%data(:,n),counter,bond_traj%rotation)
     call pull_buffer_value(buff%data(:,n),counter,bond_traj%rel_rotation)
@@ -5413,29 +5508,13 @@ subroutine break_bonds_dem(bergs)
 
           if (bergs%fracture_criterion=='stress') then
             if (current_bond%nstress>frac_thres_n .or. current_bond%sstress>frac_thres_t) then
-              if (current_bond%nstress>frac_thres_n .and. current_bond%sstress>frac_thres_t) then
-                print *,'T and S break',this%lat,current_bond%nstress,current_bond%sstress
-              elseif (current_bond%nstress>frac_thres_n) then
-                print *,'TENSILE break',this%lat,current_bond%nstress,current_bond%sstress
-              else
-                print *,'SHEAR   break',this%lat,current_bond%nstress,current_bond%sstress
-              endif
-              current_bond%other_id=-1
-            endif
-          elseif (bergs%fracture_criterion=='computed') then
-            Rsig=current_bond%nstress/frac_thres_n
-            Rtau=current_bond%sstress/frac_thres_t
-            frac=0.5*Rsig+sqrt((0.5*Rsig)**2. + Rtau**2.)
-            if (frac > 1.) then
-              print *,'BREAK',this%lat,frac,Rsig,Rtau
-              current_bond%other_id=-1
-            endif
-          elseif (bergs%fracture_criterion=='computed_s') then
-            Rsig=current_bond%nstress/bergs%frac_thres_n
-            Rtau=current_bond%sstress/bergs%frac_thres_t
-            frac=sqrt(Rsig**2. + Rtau**2.)
-            if (frac > 1.) then
-              print *,'BREAK',this%lat,frac,Rsig,Rtau
+              ! if (current_bond%nstress>frac_thres_n .and. current_bond%sstress>frac_thres_t) then
+              !   print *,'T and S break',this%lat,current_bond%nstress,current_bond%sstress
+              ! elseif (current_bond%nstress>frac_thres_n) then
+              !   print *,'TENSILE break',this%lat,current_bond%nstress,current_bond%sstress
+              ! else
+              !   print *,'SHEAR   break',this%lat,current_bond%nstress,current_bond%sstress
+              ! endif
               current_bond%other_id=-1
             endif
           else
@@ -5454,21 +5533,7 @@ subroutine break_bonds_dem(bergs)
                   if (other_bond%other_id.eq.this%id) then
                     other_bond%other_id=-1
                     if (debug) then
-                      if (bergs%fracture_criterion=='computed') then
-                        Rsig=other_bond%nstress/frac_thres_n
-                        Rtau=other_bond%sstress/frac_thres_t
-                        frac=0.5*Rsig+sqrt((0.5*Rsig)**2. + Rtau**2.)
-                        if (frac <= 1.) then
-                          print *,'Other bond did not fracture!'
-                        endif
-                      elseif(bergs%fracture_criterion=='computed_s') then
-                        Rsig=current_bond%nstress/bergs%frac_thres_n
-                        Rtau=current_bond%sstress/bergs%frac_thres_t
-                        frac=sqrt(Rsig**2. + Rtau**2.)
-                        if (frac <= 1.) then
-                          print *,'Other bond did not fracture!'
-                        endif
-                      elseif (other_bond%nstress<=frac_thres_n .and. other_bond%sstress<=frac_thres_t) then
+                      if (other_bond%nstress<=frac_thres_n .and. other_bond%sstress<=frac_thres_t) then
                         print *,'Other bond did not fracture!'
                         print *,'current and other bond nstress,',current_bond%nstress, other_bond%nstress
                         print *,'current and other bond sstress,',current_bond%sstress, other_bond%sstress
@@ -5565,6 +5630,8 @@ subroutine form_a_bond(berg, other_id, other_berg_ine, other_berg_jne, other_ber
     new_bond%nstress=0.; new_bond%sstress=0.
     allocate(new_bond%rel_rotation)
     new_bond%rel_rotation=0.
+    allocate(new_bond%broken)
+    new_bond%broken=0
     if (save_bond_forces) then
       allocate(new_bond%F_x, new_bond%F_y, new_bond%Fd_x, new_bond%Fd_y, new_bond%T, new_bond%T_d)
       new_bond%F_x=0.; new_bond%F_y=0.; new_bond%Fd_x=0.; new_bond%Fd_y=0.; new_bond%T=0.; new_bond%T_d=0.
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index d7761af..0e48343 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -185,7 +185,8 @@ subroutine write_restart(bergs, time_stamp)
                                       first_berg_jne,         &
                                       first_berg_ine,         &
                                       other_berg_jne,         &
-                                      other_berg_ine
+                                      other_berg_ine,         &
+                                      broken
 
 
 integer :: grdi, grdj
@@ -481,6 +482,7 @@ subroutine write_restart(bergs, time_stamp)
     allocate(nstress(nbonds))
     allocate(sstress(nbonds))
     allocate(rel_rotation(nbonds))
+    allocate(broken(nbonds))
   elseif (fracture_criterion.ne.'none') then
     allocate(rotation(nbonds))
     allocate(rel_rotation(nbonds))
@@ -525,6 +527,8 @@ subroutine write_restart(bergs, time_stamp)
       longname='shear stress',units='Pa')
     id = register_restart_field(bergs_bond_restart,filename_bonds,'rel_rotation',rel_rotation,&
       longname='relative rotation',units='rad')
+     id = register_restart_field(bergs_bond_restart,filename_bonds,'broken',broken,&
+      longname='broken status',units='none')
   elseif (fracture_criterion.ne.'none') then
     id = register_restart_field(bergs_bond_restart,filename_bonds,'rotation',rotation,&
       longname='rotation',units='rad')
@@ -564,6 +568,7 @@ subroutine write_restart(bergs, time_stamp)
           nstress(i)=current_bond%nstress
           sstress(i)=current_bond%sstress
           rel_rotation(i)=current_bond%rel_rotation
+          broken(i)=current_bond%broken
         elseif (fracture_criterion.ne.'none') then
           rotation(i)=current_bond%rotation
           rel_rotation(i)=current_bond%rel_rotation
@@ -599,7 +604,8 @@ subroutine write_restart(bergs, time_stamp)
              tangd2,                &
              nstress,               &
              sstress,               &
-             rel_rotation)
+             rel_rotation,          &
+             broken)
   elseif (fracture_criterion.ne.'none') then
     deallocate(                     &
              rotation,              &
@@ -1278,7 +1284,8 @@ subroutine read_restart_bonds(bergs,Time)
                                       first_berg_jne,   &
                                       first_berg_ine,   &
                                       other_berg_jne,   &
-                                      other_berg_ine
+                                      other_berg_ine,   &
+                                      broken
 real, allocatable, dimension(:) ::    tangd1,           &
                                       tangd2,           &
                                       nstress,          &
@@ -1332,6 +1339,7 @@ subroutine read_restart_bonds(bergs,Time)
       allocate(nstress(nbonds_in_file))
       allocate(sstress(nbonds_in_file))
       allocate(rel_rotation(nbonds_in_file))
+      allocate(broken(nbonds_in_file))
     elseif (fracture_criterion.ne.'none') then
       allocate(rotation(nbonds_in_file))
       allocate(rel_rotation(nbonds_in_file))
@@ -1365,6 +1373,7 @@ subroutine read_restart_bonds(bergs,Time)
       call read_real_vector(filename,'nstress',nstress,grd%domain,value_if_not_in_file=0.)
       call read_real_vector(filename,'sstress',sstress,grd%domain,value_if_not_in_file=0.)
       call read_real_vector(filename,'rel_rotation',rel_rotation,grd%domain,value_if_not_in_file=0.)
+      call read_int_vector(filename,'broken',broken,grd%domain,value_if_not_in_file=0)
     elseif (fracture_criterion.ne.'none') then
       call read_real_vector(filename,'rotation',rotation,grd%domain,value_if_not_in_file=0.)
       call read_real_vector(filename,'rel_rotation',rel_rotation,grd%domain,value_if_not_in_file=0.)
@@ -1477,6 +1486,7 @@ subroutine read_restart_bonds(bergs,Time)
               current_bond%nstress=nstress(k)
               current_bond%sstress=sstress(k)
               current_bond%rel_rotation=rel_rotation(k)
+              current_bond%broken=broken(k)
             elseif (fracture_criterion.ne.'none') then
               current_bond%rotation=rotation(k)
               current_bond%rel_rotation=rel_rotation(k)
@@ -1550,7 +1560,8 @@ subroutine read_restart_bonds(bergs,Time)
                tangd2,                &
                nstress,               &
                sstress,               &
-               rel_rotation)
+               rel_rotation,          &
+               broken)
     elseif (fracture_criterion.ne.'none') then
       deallocate(                     &
                rotation,              &
@@ -2273,7 +2284,7 @@ subroutine write_bond_trajectory(trajectory, bond_traj_name)
 ! Local variables
 integer :: iret, ncid, i_dim, i
 integer :: lonid, latid, yearid, dayid, lenid,n1id, n2id, peid
-integer :: rotid,rrotid,nsid,nsrid, damid
+integer :: rotid,rrotid,nsid,nsrid, damid, brid
 integer :: idcnt1_id, idcnt2_id, idij1_id, idij2_id, eeid, edid
 integer :: axid,ayid,bxid,byid
 integer :: td1id,td2id,dnsid,dssid
@@ -2405,7 +2416,7 @@ subroutine write_bond_trajectory(trajectory, bond_traj_name)
       if (dem) then
         td1id = inq_varid(ncid, 'tangd1');  td2id = inq_varid(ncid, 'tangd2')
         dnsid = inq_varid(ncid, 'nstress'); dssid = inq_varid(ncid, 'sstress')
-        rrotid = inq_varid(ncid, 'rel_rotation')
+        rrotid = inq_varid(ncid, 'rel_rotation'); brid = inq_varid(ncid, 'broken')
       elseif (fracture_criterion.ne.'none') then
         rotid = inq_varid(ncid, 'rotation');    rrotid = inq_varid(ncid, 'rel_rotation')
         nsid = inq_varid(ncid, 'n_frac_var')
@@ -2444,6 +2455,7 @@ subroutine write_bond_trajectory(trajectory, bond_traj_name)
         td1id = def_var(ncid, 'tangd1',  NF_DOUBLE, i_dim); td2id = def_var(ncid, 'tangd2',  NF_DOUBLE, i_dim)
         dnsid = def_var(ncid, 'nstress', NF_DOUBLE, i_dim); dssid = def_var(ncid, 'sstress', NF_DOUBLE, i_dim)
         rrotid = def_var(ncid, 'rel_rotation', NF_DOUBLE, i_dim)
+        brid = def_var(ncid, 'broken', NF_INT, i_dim)
       elseif (fracture_criterion.ne.'none') then
         rotid = def_var(ncid, 'rotation', NF_DOUBLE, i_dim); rrotid = def_var(ncid, 'rel_rotation', NF_DOUBLE, i_dim)
         nsid = def_var(ncid, 'n_frac_var', NF_DOUBLE, i_dim)
@@ -2500,6 +2512,7 @@ subroutine write_bond_trajectory(trajectory, bond_traj_name)
         call put_att(ncid, dnsid, 'long_name', 'normal stress'); call put_att(ncid, dnsid, 'units', 'Pa')
         call put_att(ncid, dssid, 'long_name', 'shear stress');  call put_att(ncid, dssid, 'units', 'Pa')
         call put_att(ncid, rrotid, 'long_name', 'relative rotation');      call put_att(ncid, rrotid, 'units', 'rad')
+        call put_att(ncid, brid, 'long_name', 'broken status');      call put_att(ncid, brid, 'units', 'none')
       elseif (fracture_criterion.ne.'none') then
         call put_att(ncid, rotid, 'long_name', 'rotation');                call put_att(ncid, rotid, 'units', 'rad')
         call put_att(ncid, rrotid, 'long_name', 'relative rotation');      call put_att(ncid, rrotid, 'units', 'rad')
@@ -2548,7 +2561,7 @@ subroutine write_bond_trajectory(trajectory, bond_traj_name)
       if (dem) then
         call put_double(ncid,td1id,i,this%tangd1);  call put_double(ncid,td2id,i,this%tangd2)
         call put_double(ncid,dnsid,i,this%nstress); call put_double(ncid,dssid,i,this%sstress)
-        call put_double(ncid,rrotid,i,this%rel_rotation)
+        call put_double(ncid,rrotid,i,this%rel_rotation); call put_int(ncid,brid,i,this%broken)
       elseif (fracture_criterion.ne.'none') then
         call put_double(ncid,rotid,i,this%rotation);  call put_double(ncid,rrotid,i,this%rel_rotation)
         call put_double(ncid,nsid,i,this%n_frac_var)
diff --git a/tests/collision_tests/.gitignore b/tests/collision_tests/.gitignore
index 68bcbc9..75188aa 100644
--- a/tests/collision_tests/.gitignore
+++ b/tests/collision_tests/.gitignore
@@ -1 +1,2 @@
-results/
\ No newline at end of file
+results/
+input.nml
\ No newline at end of file
diff --git a/tests/collision_tests/input.nml b/tests/collision_tests/input.nml
new file mode 100644
index 0000000..328c2cd
--- /dev/null
+++ b/tests/collision_tests/input.nml
@@ -0,0 +1,161 @@
+!!KID, bergs_chksum: write_restart berg chksum = -1211104969 chksum2= -1211104969 chksum3= 1964715299  chksum4= 1964715299  chksum5= 0#= 16
+
+&icebergs_driver_nml
+  ni=20 !number of elements, x direction
+  nj=20 !number of elements, y direction
+  ibdt=60.0 !seconds
+  ibuo=0.2 !ocean x velocity
+  ibvo=0.2 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=48 !total simulation hours
+  nmax=99999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.false.
+  collision_test=.true. !specific to the current test, must be true here
+/
+
+
+&icebergs_nml
+
+    traj_name=KID.nc
+    bond_traj_name=KID_bonds.nc
+
+    !defaults given in parentheses:
+    ! explicit_inner_mts=.true.
+    ! new_mts=.true.
+    ! mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    ! mts_sub_steps=60 !1 !30 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
+    ! contact_distance=1.75e3 !2.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    ! contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    ! debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    ! remove_unused_bergs=.false. !(T) remove unneeded bergs after PEs transfers
+
+    halo=3 !(4) halo width
+    Lx=20000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.True. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    rho_bergs=850. ! (850) iceberg density
+    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0.4 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.False. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+
+    verbose=.true. !(F) Be verbose to stderr
+    verbose_hrs=1 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !1 !(24) sampling period for trajectory storage
+    traj_write_hrs=6 ! (480) Period for writing sampled trajectories to disk
+    budget=.true. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.true. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.False. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/dem_ground_frac_test/README b/tests/dem_ground_frac_test/README
index ec575a8..ef744e9 100644
--- a/tests/dem_ground_frac_test/README
+++ b/tests/dem_ground_frac_test/README
@@ -1,7 +1,6 @@
-1. Make the iceberg input files: cd makeberg; ./RUN; cd .. 
+A bonded-particle iceberg drifts east and collides with a seamount, fracturing (rift-calving) into fragments that drift away. Tests the iKID multiple-time stepping scheme with grounding, fracture, and interal sub-step forces evaluated using the parallel-bond discrete element method. Also tests the option 'use_broken_bonds_for_substep_contact' (see input.nml).
+
+1. Make the iceberg input files: cd makeberg; ./RUN; cd ..
 2.(optional) edit input.nml
 3. run the model: ./RUN
-4, animate the results: animate_trajectories.py
-
-This is a good test for visualizing fracture dependence on particle size. Try running makeberg.py with the full radius and then half the radius, and with regular vs dem nmls. Make sure to edit the nmls so that contact distance is halved when radius is halved
-
+4. animate the results: animate_trajectories.py
diff --git a/tests/dem_ground_frac_test/input.nml b/tests/dem_ground_frac_test/input.nml
index 00040b2..afdfcbe 100644
--- a/tests/dem_ground_frac_test/input.nml
+++ b/tests/dem_ground_frac_test/input.nml
@@ -1,3 +1,12 @@
+!! test with and without use_broken_bonds_for_substep_contact.
+!! The simulations should be nearly identical except use_broken_bonds_for_substep_contact=.true. only evaluates sub-step contact between particles that have broken bonds.
+!! This is more computationally-efficient than searching for contact pairs each substep (use_broken_bonds_for_substep_contact=.false.).
+!! The only difference between the simulations should end up being the order at which contact is evaluated between particles, which does result in a slightly different chksum due to rounding error.
+
+!! if use_broken_bonds_for_substep_contact=.true.
+!!KID, bergs_chksum: write_restart berg chksum=52588724 chksum2=-1645779216 chksum3=946244516 chksum4=946244516 chksum5=0 #=69
+
+!! if use_broken_bonds_for_substep_contact=.false.
 !!KID, bergs_chksum: write_restart berg chksum=751155043 chksum2=1054759942 chksum3=946244516 chksum4=946244516 chksum5=0 #=69
 
 &icebergs_driver_nml
@@ -22,6 +31,8 @@
 
 &icebergs_nml
 
+    use_broken_bonds_for_substep_contact=.true.
+
     constant_interaction_LW=.true.
 
     dem=.true.
@@ -30,7 +41,7 @@
     explicit_inner_mts=.true.
     break_bonds_on_sub_steps=.true.
     short_step_mts_grounding=.true.
-    
+
     rho_bergs=850. ! (850) iceberg density
     !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
     !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
@@ -40,7 +51,7 @@
     dem_spring_coef=5e6
     spring_coef=0.0007547062342348049 !if dem_spring_coef=5e6, r=1500, and hex pack?
     !spring_coef=0.00065359477124183  !if dem_spring_coef=5e6, r=1500, and square pack?
-    
+
     monitor_energy=.false.
     !defaults given in parentheses:
     new_mts=.true.
@@ -57,7 +68,7 @@
     cdrag_grounding=1.e4
     h_to_init_grounding=0 !0 !200.0
     ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.false. !(T) remove unneeded bergs after PEs transfers
+    remove_unused_bergs=.true.!.false. !(T) remove unneeded bergs after PEs transfers
 
     fracture_criterion='stress' !('none')
     frac_thres_scaling = 1
diff --git a/tests/footloose_tests/.gitignore b/tests/footloose_tests/.gitignore
index 69f2275..6734d90 100644
--- a/tests/footloose_tests/.gitignore
+++ b/tests/footloose_tests/.gitignore
@@ -1 +1,2 @@
-old/
\ No newline at end of file
+old/
+input.nml
\ No newline at end of file

From d7a8babcc6d32b07364474c19deb25778c1752aa Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Tue, 27 Dec 2022 17:37:56 -0500
Subject: [PATCH 329/361] Added A68 test back into repository and driver.
 Tested it with new nml option 'use_broken_bonds_for_substep_contact=.true.',
 which yielded about a 15% speedup compared to previously

---
 driver/icebergs_driver.F90                    |  270 ++-
 tests/a68/.gitignore                          |    4 -
 tests/a68/README                              |   33 -
 tests/a68/RUN                                 |    7 -
 tests/a68/RUN_check_ss.sh                     |   18 -
 tests/a68/RUN_check_ss2.sh                    |   18 -
 tests/a68/RUN_check_ss_new.sh                 |   18 -
 tests/a68/RUN_for_restart_paper.sh            |    7 -
 tests/a68/RUN_loop.sh                         |   53 -
 tests/a68/RUN_loop2.sh                        |   35 -
 tests/a68/RUN_loop_noground.sh                |   28 -
 tests/a68/RUN_lsf_hex.sh                      |   33 -
 tests/a68/RUN_lsf_square.sh                   |   47 -
 tests/a68/RUN_lsf_square_comp.sh              |   36 -
 tests/a68/RUN_restart_for_paper.sh            |   51 -
 tests/a68/RUN_ssf_hex.sh                      |   64 -
 tests/a68/RUN_ssf_square.sh                   |   66 -
 tests/a68/RUN_ssfrac.sh                       |   30 -
 tests/a68/RUN_ssfrac2.sh                      |   30 -
 tests/a68/RUN_test_init_for_paper.sh          |   23 -
 tests/a68/check_ss.nml                        |  212 ---
 tests/a68/check_ss2.nml                       |  212 ---
 tests/a68/check_ss3.nml                       |  212 ---
 tests/a68/check_ss3_nofrac.nml                |  212 ---
 tests/a68/check_ss3_ssf.nml                   |  214 ---
 tests/a68/check_ss_new.nml                    |  212 ---
 tests/a68/check_ss_orig.nml                   |  211 ---
 tests/a68/hex_4restart.sh                     |   40 -
 tests/a68/hex_r_lsf.nml                       |  214 ---
 tests/a68/hex_r_ssf.nml                       |  230 ---
 tests/a68/hex_wgs84_frac_specs.nml            |  209 ---
 tests/a68/input_fill.nml                      |  205 ---
 tests/a68/input_fill_hex.nml                  |  216 ---
 tests/a68/input_fill_hex_4restart.nml         |  210 ---
 tests/a68/input_fill_hex_noground.nml         |  213 ---
 tests/a68/long_run_no_inc_contact_dist.nml    |  217 ---
 tests/a68/long_run_no_inc_contact_dist.sh     |   40 -
 tests/a68/makeberg/RUN                        |   89 -
 tests/a68/makeberg/make_one_berg.py           |  399 -----
 tests/a68/n6000_t2500.nml                     |  194 ---
 tests/a68/nov3_tests.nml                      |  197 ---
 tests/a68/restart_for_nco.py                  |   19 -
 tests/a68/save_input.nml                      |  192 ---
 tests/a68/square_for_restart.nml              |  210 ---
 .../a68/square_for_restart_od_17.8_ydn.1.nml  |  211 ---
 .../square_for_restart_od_17.8_ydn.1_ss90.nml |  211 ---
 ...quare_for_restart_od_19.5_tn_ng_ydn.05.nml |  211 ---
 ...square_for_restart_od_21.25_tn_ng_noyd.nml |  211 ---
 tests/a68/square_r_lsf.nml                    |  215 ---
 tests/a68/square_r_lsf_comp.nml               |  208 ---
 tests/a68/square_r_ssf.nml                    |  212 ---
 tests/a68/tau_is.nml                          |  197 ---
 tests/a68/test1.nml                           |  194 ---
 tests/a68/test2.nml                           |  196 ---
 tests/a68/test2_updated.nml                   |  201 ---
 tests/a68/test3.nml                           |  198 ---
 tests/a68/test4_curl.nml                      |  199 ---
 tests/a68/test_new.nml                        |  204 ---
 tests/a68/test_new2.nml                       |  204 ---
 tests/a68/test_no_bonds.nml                   |  211 ---
 tests/a68_test/README                         |   14 +
 tests/{a68 => a68_test}/RUN1p                 |    0
 .../{a68 => a68_test}/animate_trajectories.py |    1 +
 tests/a68_test/data/.gitignore                |    5 +
 tests/a68_test/data/recombine_nc.sh           |   12 +
 tests/{a68 => a68_test}/diag_table            |    0
 .../input_fill2.nml => a68_test/input.nml}    |   74 +-
 tests/{a68 => a68_test}/long_run.nml          |   38 +-
 tests/{a68 => a68_test}/long_run_for_paper.sh |    0
 .../{a68 => a68_test}/makeberg/RUN_for_paper  |    2 +-
 tests/a68_test/makeberg/hexagon_area.py       | 1458 +++++++++++++++++
 tests/a68_test/makeberg/hexagon_area.pyc      |  Bin 0 -> 32612 bytes
 tests/{a68 => a68_test}/makeberg/makeberg.py  |    8 +-
 73 files changed, 1752 insertions(+), 8593 deletions(-)
 delete mode 100644 tests/a68/.gitignore
 delete mode 100644 tests/a68/README
 delete mode 100755 tests/a68/RUN
 delete mode 100755 tests/a68/RUN_check_ss.sh
 delete mode 100755 tests/a68/RUN_check_ss2.sh
 delete mode 100755 tests/a68/RUN_check_ss_new.sh
 delete mode 100755 tests/a68/RUN_for_restart_paper.sh
 delete mode 100755 tests/a68/RUN_loop.sh
 delete mode 100755 tests/a68/RUN_loop2.sh
 delete mode 100755 tests/a68/RUN_loop_noground.sh
 delete mode 100755 tests/a68/RUN_lsf_hex.sh
 delete mode 100755 tests/a68/RUN_lsf_square.sh
 delete mode 100755 tests/a68/RUN_lsf_square_comp.sh
 delete mode 100755 tests/a68/RUN_restart_for_paper.sh
 delete mode 100755 tests/a68/RUN_ssf_hex.sh
 delete mode 100755 tests/a68/RUN_ssf_square.sh
 delete mode 100755 tests/a68/RUN_ssfrac.sh
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diff --git a/driver/icebergs_driver.F90 b/driver/icebergs_driver.F90
index e83e9fe..eeef73c 100644
--- a/driver/icebergs_driver.F90
+++ b/driver/icebergs_driver.F90
@@ -62,11 +62,15 @@ program icebergs_driver
 logical :: grounding_test=.false.
 logical :: big_grounding_test=.false.
 logical :: dem_test_contact=.false.
+logical :: a68_test=.false.
 logical :: vert_int_ocean_vel=.false.
 logical :: tau_is_velocity=.true.
+logical :: reverse_a68_forcings=.false.
 logical :: sin_test=.false.
 logical :: fl_test=.false.
 character(len=1000) :: data_dir = 'data/'
+integer :: transient_a68_data_start_ind=0 !<set to .gt. 0 to use the hourly JRA-55 wind data for the A68
+!! test. The values indicate the time index to start from in the hourly data
 integer :: halo=1 !< Width of halo in parallel decomposition
 real :: ibdt=3600.0
 real :: ibuo=0.0
@@ -87,8 +91,8 @@ program icebergs_driver
 integer :: write_time_inc=1
 namelist /icebergs_driver_nml/ debug, ni, nj, halo, ibhrs, ibdt, ibuo, ibvo, nmax, &
   saverestart,ibui,ibvi,collision_test,chaotic_test,grounding_test,&
-  gridres,write_time_inc,bump_depth, sst, data_dir, vert_int_ocean_vel,&
-  sin_test,fl_test,tau_is_velocity,ibua,ibuy,&
+  gridres,write_time_inc,bump_depth, sst, a68_test, data_dir, vert_int_ocean_vel,&
+  reverse_a68_forcings,sin_test,fl_test,tau_is_velocity,transient_a68_data_start_ind,ibua,ibuy,&
   Old_wrong_Rearth_and_SSH,no_wind,REarth,big_grounding_test,dem_test_contact !mom_Rearth
 ! For loops
 integer :: isc !< Start of i-index for computational domain (used for loops)
@@ -123,6 +127,8 @@ program icebergs_driver
 real, dimension(:,:), allocatable :: uo,vo !<zonal and meridonal ocean velocities (m/s)
 real, dimension(:,:), allocatable :: ui,vi !<zonal and meridonal ice velocities (m/s)
 real, dimension(:,:), allocatable :: tauxa,tauya !< Zonal and meridonal wind stress (Pa)
+real, dimension(:,:,:), allocatable :: tauxa_hr,tauya_hr !< Hourly jra-55 zonal and meridonal wind velocity (m/s) for A68 test
+real, dimension(:,:,:), allocatable :: uo_hr,vo_hr !<Hourly OSCAR zonal and meridonal ocean surface velocities (m/s) for A68 test
 real, dimension(:,:), allocatable :: ssh !< Effective sea-surface height (m)
 real, dimension(:,:,:), allocatable :: ssh_hr !< Effective sea-surface height (m, hourly)
 real, dimension(:,:), allocatable :: sstemp !< Sea-surface temperature (C or K)
@@ -147,6 +153,12 @@ program icebergs_driver
 read(nmunit, nml=icebergs_driver_nml)
 call close_file(nmunit)
 
+if (a68_test) then
+  call a68_dims(data_dir,ni,nj)
+  if (mpp_pe()==0) print *,'ni,nj',ni,nj
+  iflags=0
+endif
+
 if (min(ni,nj)<1) call error_mesg('icebergs_driver:', &
   'Both ni,nj must be positive in icebergs_driver_nml namelist', FATAL)
 
@@ -241,91 +253,140 @@ program icebergs_driver
 ! ustar_berg = !Friction velocity on base of bergs (m/s)
 ! area_berg = !Area of bergs (m2)
 
-do j = jsd, jed
-  do i = isd, ied
-    lon(i,j) = gridres*real(i)
-    lat(i,j) = gridres*real(j)
-    dx(i,j) = gridres
-    dy(i,j) = gridres
-    area(i,j) = gridres*gridres
-    wet(i,j) = 1.0
-    cos_rot(i,j) = 1.0
-    sin_rot(i,j) = 0.0
-    depth(i,j) = 1000.
-  enddo
-enddo
+if (a68_test) then
+  if (Old_wrong_Rearth_and_SSH) REarth=6360000.
+  call mpp_sync()
+  call a68_prep(data_dir,mpp_domain,lon,lat,dx,dy,area,depth,uo,vo,tauxa,tauya,ssh,vert_int_ocean_vel,tau_is_velocity,Old_wrong_Rearth_and_SSH,REarth)
+  !mom_Rearth)
+  call mpp_sync()
+  if (no_wind) then
+    tauxa=0.0; tauya=0.0
+  endif
+  !where (lon<(-37.6+360.))
+  !  depth=depth+1000.
+  !end where
+  wet=1.0
+  cos_rot=1.0
+  sin_rot=0.0
+  if (reverse_a68_forcings) then
+    uo=-uo; vo=-vo
+    tauxa=-tauxa; tauya=-tauya
+  endif
 
-if (chaotic_test) then
-  !assign land cells at the N and S portions of the domain.
-  !input.nml: set coastal drift parameter to prevent grounding
-  do j=jsd,jed; do i=isd,ied
-    if (lat(i,j)<=0.0+2*gridres .or. lat(i,j)>=1000.e3-2*gridres) wet(i,j)=0.0
-  enddo;enddo
-endif
+  if (transient_a68_data_start_ind>0) then
+    if (.not. (ibdt==3600.0 .or. ibdt==1800.0)) then
+      call error_mesg('icebergs_driver:', &
+      'in order to use transient_a68_data_start_ind>0, timestep must be 30 min or 1 hr', FATAL)
+    endif
+    if (.not. tau_is_velocity) call error_mesg('icebergs_driver:', &
+      'tau_is_velocity must be true if transient_a68_data_start_ind>-1', FATAL)
+    allocate( tauxa_hr(isd:ied,jsd:jed,739) )
+    allocate( tauya_hr(isd:ied,jsd:jed,739) )
+    allocate( uo_hr(isd:ied,jsd:jed,744) )
+    allocate( vo_hr(isd:ied,jsd:jed,744) )
+    allocate( ssh_hr(isd:ied,jsd:jed,744) )
+    call a68_prep_3d(data_dir,mpp_domain,tauxa_hr,tauya_hr,uo_hr,vo_hr,ssh_hr)
+    if (reverse_a68_forcings) then
+      tauxa_hr=-tauxa_hr; tauya_hr=-tauya_hr
+      uo_hr=-uo_hr; vo_hr=-vo_hr
+      ssh_hr=-ssh_hr
+      dit=-1
+    else
+      dit=1
+    endif
+    if (no_wind) then
+      tauxa_hr=0.0; tauya_hr=0.0
+    endif
+  endif
+else
+  do j = jsd, jed
+    do i = isd, ied
+      lon(i,j) = gridres*real(i)
+      lat(i,j) = gridres*real(j)
+      dx(i,j) = gridres
+      dy(i,j) = gridres
+      area(i,j) = gridres*gridres
+      wet(i,j) = 1.0
+      cos_rot(i,j) = 1.0
+      sin_rot(i,j) = 0.0
+      depth(i,j) = 1000.
+    enddo
+  enddo
 
-if (big_grounding_test) then
-  lat(:,:)=lat(:,:)-0.45 !-25000.1
-  lon(:,:)=lon(:,:)-0.45
-  !assign land cells at the N and S portions of the domain.
-  !input.nml: set coastal drift parameter to prevent grounding
-  do j=jsd,jed; do i=isd,ied
-    if (lat(i,j)<=(-5.e3) .or. lat(i,j)>=(220.e3)) wet(i,j)=0.0
-  enddo;enddo
+  if (chaotic_test) then
+    !assign land cells at the N and S portions of the domain.
+    !input.nml: set coastal drift parameter to prevent grounding
+    do j=jsd,jed; do i=isd,ied
+      if (lat(i,j)<=0.0+2*gridres .or. lat(i,j)>=1000.e3-2*gridres) wet(i,j)=0.0
+    enddo;enddo
+  endif
 
-  !introduce gaussian bump to bathymetry
-  a = 1000.0-bump_depth !max height(m)
-  c = 5e3; !controls width
-  bx = 63.e3; by = 60.e3 !50.e3
-  do j=jsd,jed; do i=isd,ied
-    xc=lon(i,j)-(gridres/2.); yc=lat(i,j)-(gridres/2.) !define at cell centers
-    depth(i,j)=a*exp(-((xc-bx)*(xc-bx)/(2.*c*c)+(yc-by)*(yc-by)/(2.*c*c)))
-  enddo; enddo
-  print *,'min, max depth',minval(depth(:,:)),maxval(depth(:,:))
-  depth = 1000.0-depth
-endif
+  if (big_grounding_test) then
+    lat(:,:)=lat(:,:)-0.45 !-25000.1
+    lon(:,:)=lon(:,:)-0.45
+    !assign land cells at the N and S portions of the domain.
+    !input.nml: set coastal drift parameter to prevent grounding
+    do j=jsd,jed; do i=isd,ied
+      if (lat(i,j)<=(-5.e3) .or. lat(i,j)>=(220.e3)) wet(i,j)=0.0
+    enddo;enddo
+
+    !introduce gaussian bump to bathymetry
+    a = 1000.0-bump_depth !max height(m)
+    c = 5e3; !controls width
+    bx = 63.e3; by = 60.e3 !50.e3
+    do j=jsd,jed; do i=isd,ied
+      xc=lon(i,j)-(gridres/2.); yc=lat(i,j)-(gridres/2.) !define at cell centers
+      depth(i,j)=a*exp(-((xc-bx)*(xc-bx)/(2.*c*c)+(yc-by)*(yc-by)/(2.*c*c)))
+    enddo; enddo
+    print *,'min, max depth',minval(depth(:,:)),maxval(depth(:,:))
+    depth = 1000.0-depth
+  endif
 
-if (dem_test_contact) then
-  lat(:,:)=lat(:,:)-0.45 !-25000.1
-  lon(:,:)=lon(:,:)-0.45
-  !assign land cells at the N and S portions of the domain.
-  !input.nml: set coastal drift parameter to prevent grounding
-  do j=jsd,jed; do i=isd,ied
-    if (lat(i,j)<=(-5.e3) .or. lat(i,j)>=(220.e3)) wet(i,j)=0.0
-  enddo;enddo
+   if (dem_test_contact) then
+    lat(:,:)=lat(:,:)-0.45 !-25000.1
+    lon(:,:)=lon(:,:)-0.45
+    !assign land cells at the N and S portions of the domain.
+    !input.nml: set coastal drift parameter to prevent grounding
+    do j=jsd,jed; do i=isd,ied
+      if (lat(i,j)<=(-5.e3) .or. lat(i,j)>=(220.e3)) wet(i,j)=0.0
+    enddo;enddo
 
-  mid=50.e3
+    mid=50.e3
 
-  do j=jsd,jed; do i=isd,ied
-    if (lon(i,j)>65 .or. lat(i,j)==mid) then
-      vo(i,j)=0.0
-    else
-      if (lat(i,j)>mid) then
-        vo(i,j)=-ibvo
+    do j=jsd,jed; do i=isd,ied
+      if (lon(i,j)>65 .or. lat(i,j)==mid) then
+        vo(i,j)=0.0
       else
-        vo(i,j)=ibvo
+        if (lat(i,j)>mid) then
+          vo(i,j)=-ibvo
+        else
+          vo(i,j)=ibvo
+        endif
       endif
-    endif
   enddo;enddo
-endif
 
-if (grounding_test) then
-  lat(:,:)=lat(:,:)-15000.0
-  !assign land cells at the N and S portions of the domain.
-  !input.nml: set coastal drift parameter to prevent grounding
-  do j=jsd,jed; do i=isd,ied
-    if (lat(i,j)<=0.0+2*gridres .or. lat(i,j)>=30.e3-2*gridres) wet(i,j)=0.0
-  enddo;enddo
 
-  !introduce gaussian bump to bathymetry
-  a = 1000.0-bump_depth !max height(m)
-  c = 2.5e3; !controls width
-  bx = 15.e3; by = 15.e3
-  do j=jsd,jed; do i=isd,ied
-    xc=lon(i,j)-(gridres/2.); yc=lat(i,j)-(gridres/2.) !define at cell centers
-    depth(i,j)=a*exp(-((xc-bx)*(xc-bx)/(2.*c*c)+(yc-by)*(yc-by)/(2.*c*c)))
-  enddo; enddo
-  print *,'min, max depth',minval(depth(:,:)),maxval(depth(:,:))
-  depth = 1000.0-depth
+  endif
+
+  if (grounding_test) then
+    lat(:,:)=lat(:,:)-15000.0
+    !assign land cells at the N and S portions of the domain.
+    !input.nml: set coastal drift parameter to prevent grounding
+    do j=jsd,jed; do i=isd,ied
+      if (lat(i,j)<=0.0+2*gridres .or. lat(i,j)>=30.e3-2*gridres) wet(i,j)=0.0
+    enddo;enddo
+
+    !introduce gaussian bump to bathymetry
+    a = 1000.0-bump_depth !max height(m)
+    c = 2.5e3; !controls width
+    bx = 15.e3; by = 15.e3
+    do j=jsd,jed; do i=isd,ied
+      xc=lon(i,j)-(gridres/2.); yc=lat(i,j)-(gridres/2.) !define at cell centers
+      depth(i,j)=a*exp(-((xc-bx)*(xc-bx)/(2.*c*c)+(yc-by)*(yc-by)/(2.*c*c)))
+    enddo; enddo
+    print *,'min, max depth',minval(depth(:,:)),maxval(depth(:,:))
+    depth = 1000.0-depth
+  endif
 endif
 
 if (sin_test) vo = vo * sin(lat*2*pi/(20.0*gridres) + gridres)
@@ -336,7 +397,11 @@ program icebergs_driver
 
 call set_calendar_type(THIRTY_DAY_MONTHS)
 
-time = set_date(1,1,1,0,0,0)
+if (transient_a68_data_start_ind==355) then
+  time = set_date(1,1,7,5,0,0)
+else
+  time = set_date(1,1,1,0,0,0)
+endif
 dt = ibdt
 
 call icebergs_init(bergs, &
@@ -395,6 +460,7 @@ program icebergs_driver
 endif
 
 ns = 1 !timestep counter
+if (transient_a68_data_start_ind>0) ns2 = 1
 
 ! Time_end = increment_date(Time, years, months, days, hours, minutes, seconds)
 Time_end = increment_date(Time,0,0,0,ibhrs,0,0)
@@ -415,6 +481,23 @@ program icebergs_driver
     write(*,*) ''
   end if
 
+  if (transient_a68_data_start_ind>0) then
+
+    if ((ibdt==3600.0) .or. (mod(ns2,1.)==0)) then
+      tauxa=tauxa_hr(:,:,transient_a68_data_start_ind+dit*(int(ns2)-1))
+      tauya=tauya_hr(:,:,transient_a68_data_start_ind+dit*(int(ns2)-1))
+      uo=uo_hr(:,:,transient_a68_data_start_ind+dit*(int(ns2)-1))
+      vo=vo_hr(:,:,transient_a68_data_start_ind+dit*(int(ns2)-1))
+      ssh=ssh_hr(:,:,transient_a68_data_start_ind+dit*(int(ns2)-1))
+    else
+      tauxa=0.5*(tauxa+tauxa_hr(:,:,transient_a68_data_start_ind+dit*(int(ceiling(ns2))-1)))
+      tauya=0.5*(tauya+tauya_hr(:,:,transient_a68_data_start_ind+dit*(int(ceiling(ns2))-1)))
+      uo=0.5*(uo+uo_hr(:,:,transient_a68_data_start_ind+dit*(int(ceiling(ns2))-1)))
+      vo=0.5*(vo+vo_hr(:,:,transient_a68_data_start_ind+dit*(int(ceiling(ns2))-1)))
+      ssh=ssh_hr(:,:,transient_a68_data_start_ind+dit*(int(ns2)-1))
+    endif
+  endif
+
   ! The main driver the steps updates icebergs
   call icebergs_run(bergs, time, calving(isc:iec,jsc:jec), &
                     uo(isc-1:iec+1,jsc-1:jec+1), vo(isc-1:iec+1,jsc-1:jec+1), &
@@ -430,8 +513,41 @@ program icebergs_driver
 
   Time = Time + real_to_time_type(dt)
   ns = ns+1
+
+  if (transient_a68_data_start_ind>0) then
+    if (ibdt==3600.0) then
+      ns2=ns2+1
+    elseif (ibdt==1800.0) then
+      ns2=ns2+0.5
+    endif
+  endif
 enddo
 
+
+if (a68_test) then
+  call cpu_time(time_finish)
+  call get_date(Time, iyr, imon, iday, ihr, imin, isec)
+  write(*,*) ''
+  write(*,'(a)') '-------------------------------------------'
+  write(*,'(a,i5)')' Saving after timestep   ',ns-1
+  print *,' ns2   ',ns2
+  if (mod(ns2,1.)==0) then
+    print *,'transient_a68_data_start_ind+dit*(int(ns2)-1)',&
+      transient_a68_data_start_ind+dit*(int(ns2)-1)
+  else
+    print *,'transient_a68_data_start_ind+dit*(int(ceiling(ns2))-1))',&
+      transient_a68_data_start_ind+dit*(int(ceiling(ns2))-1)
+  endif
+  write(*,'(a)')' Restart time is:'
+  write(*,'(a,i5,a,i5,a,i5)')' year',iyr,'  month ',imon,'  day   ',iday
+  write(*,'(a,i5,a,i5,a,i5)')' hour',ihr,'  minute',imin,'  second',isec
+  write(*,*) ''
+  write(*,*) 'clock-time elapsed: ', (time_finish - time_begin)/60., 'minutes'
+  write(*,*) 'clock-time per day: ', (time_finish - time_begin)/(ns-1)*(60*60*24)/ibdt
+  write(*,'(a)') '-------------------------------------------'
+  write(*,*) ''
+endif
+
 if (saverestart) call icebergs_save_restart(bergs)
 
 call cpu_time(time_finish)
diff --git a/tests/a68/.gitignore b/tests/a68/.gitignore
deleted file mode 100644
index 577f3bd..0000000
--- a/tests/a68/.gitignore
+++ /dev/null
@@ -1,4 +0,0 @@
-results/
-oldnc/
-oldnc2/
-csvresults/
\ No newline at end of file
diff --git a/tests/a68/README b/tests/a68/README
deleted file mode 100644
index 995a5d5..0000000
--- a/tests/a68/README
+++ /dev/null
@@ -1,33 +0,0 @@
-TO RUN THE EXPERIMENT IN THE PAPER:
-
-I. Make the iceberg input files:
-   cd makeberg; ./RUN_for_paper; cd ..
-
-II. The full run from the paper:
-   ./long_run_for_paper.sh
-
-III. Animate the results:
-./animate_trajectories.py -fname=longrun_od_17.8_tn_ng_ydn.1_ss90_ns18_rx-37.51_ry-55.2166.nc
-
-
-
-ADVANCED: TUNING EXPERIMENTS:
-
-1. Tuning ocean drag coefficients (by scaling the default point-particle coefficients) and Youngs Modulus: run the simulation without fracture or grounding, and test different parameter values. The following run without fracture/grounding was used for tuning in the paper:
-   ./RUN_test_init_for_paper.sh
-
-2. Spinup for fracture tuning: Repeat the run from (1) to just before the first breakup to create a restart file, which will be used by experiments to tune the fracture parameters (step 6, below). To run the spinup used for the paper:
-   cp square_for_restart_od_17.8_ydn.1_ss90.nml input.nml
-   ./RUN_1p.sh
-
-3. Copy the restart to a new directory:
-   cp INPUT/ S_17.8_ydn.1_ss90_r/
-
-5. Rerun the simulation from the restart, this time activating grounding and fracture.
-   ./RUN_restart_for_paper.sh
-
-6. animate the results:
-   ./animate_trajectories.py -fname=sq_ssfg_gc1.e4_od17.8_rx-37.51_y-55.2166_n18_t10_ss90.nc
-
-
-Warning: steps 1 and 6 probably require different versions of python or packages. TODO: fix this.
diff --git a/tests/a68/RUN b/tests/a68/RUN
deleted file mode 100755
index 03f559f..0000000
--- a/tests/a68/RUN
+++ /dev/null
@@ -1,7 +0,0 @@
-rm iceberg_trajectories.nc
-rm iceberg_trajectories.nc.*
-rm bond_trajectories.nc
-rm bond_trajectories.nc.*
-srun -n16 ./../../build/bergs.x
-
-
diff --git a/tests/a68/RUN_check_ss.sh b/tests/a68/RUN_check_ss.sh
deleted file mode 100755
index 4c33e77..0000000
--- a/tests/a68/RUN_check_ss.sh
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/bin/bash
-
-#ocean drag values
-ss=(200 300 400 750 500 100 1000)
-name=(sstest_200.nc sstest_300.nc sstest_400.nc sstest_750.nc sstest_500.nc sstest_100.nc sstest_1000.nc)
-
-for ((i = 0; i < ${#ss[@]}; ++i)); do
-    substeps=(${ss[$i]})
-    fname2=(${name[$i]})
-
-    echo $substeps
-    echo $fname2
-
-    sed  "s/<ss>/$substeps/; s/<fname>/$fname2/g" \
-	 check_ss.nml > input.nml
-    ./RUN1p
-    # &>/dev/null &
-done
diff --git a/tests/a68/RUN_check_ss2.sh b/tests/a68/RUN_check_ss2.sh
deleted file mode 100755
index a9a1d82..0000000
--- a/tests/a68/RUN_check_ss2.sh
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/bin/bash
-
-#ocean drag values
-ss=(200 300 400 750 500 100 1000)
-name=(sstest2_200.nc sstest2_300.nc sstest2_400.nc sstest2_750.nc sstest2_500.nc sstest2_100.nc sstest2_1000.nc)
-
-for ((i = 0; i < ${#ss[@]}; ++i)); do
-    substeps=(${ss[$i]})
-    fname2=(${name[$i]})
-
-    echo $substeps
-    echo $fname2
-
-    sed  "s/<ss>/$substeps/; s/<fname>/$fname2/g" \
-	 check_ss2.nml > input.nml
-    ./RUN1p
-    # &>/dev/null &
-done
diff --git a/tests/a68/RUN_check_ss_new.sh b/tests/a68/RUN_check_ss_new.sh
deleted file mode 100755
index c4cc32a..0000000
--- a/tests/a68/RUN_check_ss_new.sh
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/bin/bash
-
-#ocean drag values
-ss=(200)
-name=(sstest_200.nc)
-
-for ((i = 0; i < ${#ss[@]}; ++i)); do
-    substeps=(${ss[$i]})
-    fname2=(${name[$i]})
-
-    echo $substeps
-    echo $fname2
-
-    sed  "s/<ss>/$substeps/; s/<fname>/$fname2/g" \
-	 check_ss.nml > input.nml
-    ./RUN1p
-    # &>/dev/null &
-done
diff --git a/tests/a68/RUN_for_restart_paper.sh b/tests/a68/RUN_for_restart_paper.sh
deleted file mode 100755
index e1852ae..0000000
--- a/tests/a68/RUN_for_restart_paper.sh
+++ /dev/null
@@ -1,7 +0,0 @@
-#cp square_for_restart_od_17.8_ydn.1_ss90.nml input.nml
-#./RUN1p
-#cp ./RESTART/* ./S_17.8_ydn.1_ss90_r/
-
-cp square_for_restart_od_17.8_ydn.1.nml input.nml
-./RUN1p
-cp ./RESTART/* ./S_17.8_ydn.1_r/
diff --git a/tests/a68/RUN_loop.sh b/tests/a68/RUN_loop.sh
deleted file mode 100755
index 4a074de..0000000
--- a/tests/a68/RUN_loop.sh
+++ /dev/null
@@ -1,53 +0,0 @@
-#!/bin/bash
-
-#ocean drag values
-#odrag=(6.5 6 5 7 4 8 3 1)
-#name=(hex_wgs84_nofrac_od6.5.nc hex_wgs84_nofrac_od6.nc hex_wgs84_nofrac_od5.nc hex_wgs84_nofrac_od7.nc hex_wgs84_nofrac_od4.nc hex_wgs84_nofrac_od8.nc hex_wgs84_nofrac_od3.nc hex_wgs84_nofrac_od1.nc)
-
-#odrag=(6 6.5 7)
-#name=(hex_ydn.5_wgs84_nofrac_od6.nc hex_ydn.5_wgs84_nofrac_od6.5.nc hex_ydn.5_wgs84_nofrac_od7.nc)
-
-#this was to test having rev_mind=.true. and rev_mind=.false., to determine where it places the seamount.
-#odrag=(6.)
-#name=(test_rm2_false.nc)
-
-#odrag=(6.075 6.025)
-#name=(hex_yn.075_nf_od6.075.nc hex_yn.075_nf_od6.025.nc)
-
-#odrag=(6. 6.5 5.5)
-#name=(hex_yn.1_nf_od6.nc hex_yn.1_nf_od6.5.nc hex_yn.1_nf_od5.5.nc)
-
-#odrag=(4.75 4.85)
-#name=(hex_yn.125_nf_od4.75.nc hex_yn.125_nf_od4.85.nc)
-
-#odrag=(2.9 2.95)
-#name=(hex_yn.175_nf_od2.9.nc hex_yn.175_nf_od2.95.nc)
-
-odrag=(10.9 10.95)
-name=(hex_yn.1_nf_od10.9_rad_drag_E1e6.nc hex_yn.1_nf_od10.95_rad_drag_E1e6.nc)
-
-
-#odrag=(5.5 5)
-#name=(hex_yn.1_nf_od5.5_radius_drag.nc hex_yn.1_nf_od5_radius_drag.nc)
-
-
-radius=6363827
-damp=1
-gc=0
-
-echo $radius
-echo $damp
-echo $gc
-
-for ((i = 0; i < ${#odrag[@]}; ++i)); do
-    drag=(${odrag[$i]})
-    fname=(${name[$i]})
-
-    echo $drag
-    echo $fname
-
-    sed  "s/<od>/$drag/; s/<gc>/$gc/; s/<rad>/$radius/; s/<damp>/$damp/; s/<name>/$fname/g" \
-	 input_fill_hex.nml > input.nml
-    ./RUN1p
-    # &>/dev/null &
-done
diff --git a/tests/a68/RUN_loop2.sh b/tests/a68/RUN_loop2.sh
deleted file mode 100755
index df50ee6..0000000
--- a/tests/a68/RUN_loop2.sh
+++ /dev/null
@@ -1,35 +0,0 @@
-#!/bin/bash
-
-#ocean drag values
-#odrag=(20 22 24 26 28)
-#name=(od_20_tn_ng_nw.nc od_22_tn_ng_nw.nc od_24_tn_ng_nw.nc od_26_tn_ng_nw.nc od_28_tn_ng_nw.nc)
-
-# odrag=(1 5 10 15 20 22 24 26)
-# name=(od_1_tn_ng_ellr.nc od_5_tn_ng_ellr.nc od_10_tn_ng_ellr.nc od_15_tn_ng_ellr.nc od_20_tn_ng_ellr.nc od_22_tn_ng_ellr.nc od_24_tn_ng_ellr.nc od_26_tn_ng_ellr.nc)
-
-# odrag=(15 17.5 20)
-# name=(od_15_tn_ng_noyd.nc od_17.5_tn_ng_noyd.nc od_20_tn_ng_noyd.nc)
-
-#odrag=(19.7)
-#name=(od_19.7_tn_ng_yd.05.nc)
-
-#odrag=(13 14 15)
-#name=(ydp.5_od_13.nc ydp.5_od_14.nc ydp.5_od_15.nc)
-
-Rearth=6363827
-odrag=(17.8 17.9)
-name=(od_17.8_tn_ng_ydn.1.nc od_17.9_tn_ng_ydn.1.nc)
-
-for ((i = 0; i < ${#odrag[@]}; ++i)); do
-    drag=(${odrag[$i]})
-    fname=(${name[$i]})
-
-    echo $drag
-    echo $fname
-    echo $Rearth
-
-    sed  "s/<od>/$drag/; s/<re>/$Rearth/; s/<name>/$fname/g" \
-	 input_fill2.nml > input.nml
-    ./RUN1p
-    # &>/dev/null &
-done
diff --git a/tests/a68/RUN_loop_noground.sh b/tests/a68/RUN_loop_noground.sh
deleted file mode 100755
index c258e44..0000000
--- a/tests/a68/RUN_loop_noground.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/bin/bash
-
-#ocean drag values
-odrag=(7)
-#(12 15 20 1)
-name=(test_5e6_od7_hex_check.nc)
-#(h_yn.05_ss100e1e6_nf_od12.nc h_yn.05ss100e1e6_nf_od15.nc h_yn.05ss100e1e6_nf_od20.nc h_yn.05ss100e1e6_nf_od1.nc)
-youngs=5e6
-#5e6
-#odrag=(7.2)
-#name=(hex_ydn.05_wgs84_gc0_nofrac_od7.2.nc)
-
-radius=6363827
-
-echo $radius
-
-for ((i = 0; i < ${#odrag[@]}; ++i)); do
-    drag=(${odrag[$i]})
-    fname=(${name[$i]})
-
-    echo $drag
-    echo $fname
-
-    sed  "s/<od>/$drag/; s/<rad>/$radius/; s/<sc>/$youngs/; s/<name>/$fname/g" \
-	 input_fill_hex_noground.nml > input.nml
-    ./RUN1p
-    # &>/dev/null &
-done
diff --git a/tests/a68/RUN_lsf_hex.sh b/tests/a68/RUN_lsf_hex.sh
deleted file mode 100755
index 46b213c..0000000
--- a/tests/a68/RUN_lsf_hex.sh
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/bin/bash
-
-#ocean drag values
-ss=(10000)
-gcoef=(1.e20)
-nstress=(68000)
-tstress=(50000)
-damp=(0.1)
-name=(zh_lsf_10kss_el_gl1e20_t50k_n68k_od7_gt_realloc_dc.1.nc)
-#name=(zhex_lsf_el_g1e60_t50k_n400k_od7_2kss.nc)
-radius=6363827
-#6.371229e6
-
-for ((i = 0; i < ${#ss[@]}; ++i)); do
-    substeps=(${ss[$i]})
-    gc=(${gcoef[$i]})
-    fname2=(${name[$i]})
-    ns=(${nstress[$i]})
-    ts=(${tstress[$i]})
-    dc=(${damp[$i]})
-
-    echo $substeps
-    echo $gc
-    echo $fname2
-    echo $ns
-    echo $ts
-
-    sed  "s/<ss>/$substeps/; s/<gc>/$gc/; s/<dc>/$dc/; s/<rad>/$radius/; s/<ns>/$ns/; s/<ts>/$ts/; s/<fname>/$fname2/g" \
-	 hex_r_lsf.nml > input.nml
-    rm $fname2
-    ./RUN1p
-    # &>/dev/null &
-done
diff --git a/tests/a68/RUN_lsf_square.sh b/tests/a68/RUN_lsf_square.sh
deleted file mode 100755
index d28cc3d..0000000
--- a/tests/a68/RUN_lsf_square.sh
+++ /dev/null
@@ -1,47 +0,0 @@
-#!/bin/bash
-
-#ocean drag values
-ss=(200)
-gcoef=(1.e6)
-odrag=(15)
-nstress=(18)
-tstress=(2.75)
-# A68dy=0.
-# A68dx=0.
-a68=.false.
-#.true.
-A68dx=0.
-#-0.4017
-A68dy=0.
-#-0.05
-dxw=0.
-#n.4017
-dyw=0.
-#n.05
-#name=(sq_lsf_gc1e6_od15_n18k_t2.75k_cd4e3.nc)
-Eradius=6.378e6
-#6363827
-
-for ((i = 0; i < ${#ss[@]}; ++i)); do
-    substeps=(${ss[$i]})
-    gc=(${gcoef[$i]})
-    fname2=(${name[$i]})
-    #bname2=(${bond_name[$i]})
-    ns=(${nstress[$i]})
-    ts=(${tstress[$i]})
-    od=(${odrag[$i]})
-
-    echo $substeps
-    echo $gc
-    echo $fname2
-    echo $ns
-    echo $ts
-    echo $od
-    echo $a68
-
-    sed  "s/<ss>/$substeps/;  s/<a68>/$a68/; s/<xd>/$A68dx/; s/<yd>/$A68dy/; s/<xdw>/$dxw/; s/<ydw>/$dyw/; s/<gc>/$gc/; s/<rad>/$Eradius/; s/<od>/$od/; s/<ns>/$ns/; s/<ts>/$ts/; s/<name>/$fname2/g" \
-	 square_r_lsf.nml > input.nml
-    rm $fname2
-    #rm $bname2
-    ./RUN1p
-done
diff --git a/tests/a68/RUN_lsf_square_comp.sh b/tests/a68/RUN_lsf_square_comp.sh
deleted file mode 100755
index be5e763..0000000
--- a/tests/a68/RUN_lsf_square_comp.sh
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/bin/bash
-
-#ocean drag values
-ss=(200)
-gcoef=(1.e8)
-odrag=(15)
-nstress=(8000)
-tstress=(8000)
-A68dy=0.
-A68dx=0.
-name=(sq_lsf_gc1e8_od15_c8k.nc)
-Eradius=6.378e6
-#6363827
-
-for ((i = 0; i < ${#ss[@]}; ++i)); do
-    substeps=(${ss[$i]})
-    gc=(${gcoef[$i]})
-    fname2=(${name[$i]})
-    #bname2=(${bond_name[$i]})
-    ns=(${nstress[$i]})
-    ts=(${tstress[$i]})
-    od=(${odrag[$i]})
-
-    echo $substeps
-    echo $gc
-    echo $fname2
-    echo $ns
-    echo $ts
-    echo $od
-
-    sed  "s/<ss>/$substeps/;  s/<xd>/$A68dx/; s/<yd>/$A68dy/; s/<gc>/$gc/; s/<rad>/$Eradius/; s/<od>/$od/; s/<ns>/$ns/; s/<ts>/$ts/; s/<name>/$fname2/g" \
-	 square_r_lsf_comp.nml > input.nml
-    rm $fname2
-    #rm $bname2
-    ./RUN1p
-done
diff --git a/tests/a68/RUN_restart_for_paper.sh b/tests/a68/RUN_restart_for_paper.sh
deleted file mode 100755
index 823420f..0000000
--- a/tests/a68/RUN_restart_for_paper.sh
+++ /dev/null
@@ -1,51 +0,0 @@
-#!/bin/bash
-
-#grounding coef
-gcoef=(1.e4)
-#number of substeps
-ss=90
-#restart directory
-rdir=S_17.8_ydn.1_ss90_r
-#scale factor for ocean drag coefficients
-odrag=17.8
-#normal and shear stress thresholds (kPa)
-nstress=(18)
-tstress=(10)
-#Use A68a grounding zone?
-a68=.true.
-#lower-left coords of grounding zone
-A68dx=-37.51
-A68dy=-55.2166
-#Earth radius
-Eradius=6363827
-#Use power-law grounding drag? If false, uses linear grounding drag.
-pg=.false.
-
-for ((i = 0; i < ${#nstress[@]}; ++i)); do
-    gc=(${gcoef[$i]})
-    ns=(${nstress[$i]})
-    ts=(${tstress[$i]})
-
-    echo $gc
-    echo $a68
-    echo $ns
-    echo $ts
-    echo $pg
-    echo $rdir
-    echo $ss
-    echo $A68dx
-    echo $A68dy
-
-    sed  "s/<ss>/$ss/; s/<a68>/$a68/; s/<pg>/$pg/; s/<xd>/$A68dx/; s/<yd>/$A68dy/; s/<rdir>/$rdir/; s/<gc>/$gc/; s/<rad>/$Eradius/; s/<od>/$odrag/; s/<ns>/$ns/; s/<ts>/$ts/g" \
-	 square_r_ssf.nml > input.nml
-    ./RUN1p
-done
-
-##Another good run, with more sub-steps:
-#gcoef=(1.e4)
-#ss=200
-#rdir=S_17.8_ydn.1_r
-#A68dx=-37.5285
-#A68dy=-55.2166
-#Eradius=6363827
-#pg=.false.
diff --git a/tests/a68/RUN_ssf_hex.sh b/tests/a68/RUN_ssf_hex.sh
deleted file mode 100755
index 0e29104..0000000
--- a/tests/a68/RUN_ssf_hex.sh
+++ /dev/null
@@ -1,64 +0,0 @@
-#!/bin/bash
-
-# odrag=(7.2)
-# nstress=(82000)
-# tstress=(82000)
-# A68dy=0.1
-# A68dx=-0.08
-# name=(zh_ssf_el_gl1e30_od7.2_compd82.k_tripy.1xn.08_cspr1en7_10e3cd_powgnd.nc)
-# radius=6363827
-
-#ocean drag values
-ss=(200)
-gcoef=(1.e4)
-pg=.false.
-#.true.
-odrag=(6)
-#5
-nstress=105
-#(85)
-tstress=55
-#(55)
-a68=.true.
-#.false.
-ssg=.true.
-#.true.
-A68dy=0.06792000000000087
-#-0.02 #for 5.4
-#0.06
-A68dx=-0.27071999999997587
-#-0.323
-#-0.15 #for 5.4
-#-0.2
-
-#name=(zzh_ssf_yn.075_gl1e10_od6_nt80k_a68_y.06xn.2.nc)
-#name=(zzh_ssf_yn.1_gl1e10_od5.4_nt82k_a68_yn.02xn.15.nc)
-#name=(hz_ssf_yn.1_gl1e6_od5_n90_t60_a68.nc)
-radius=6363827
-
-for ((i = 0; i < ${#ss[@]}; ++i)); do
-    substeps=(${ss[$i]})
-    gc=(${gcoef[$i]})
-    #fname2=(${name[$i]})
-    #bname2=(${bond_name[$i]})
-    ns=(${nstress[$i]})
-    ts=(${tstress[$i]})
-    od=(${odrag[$i]})
-
-    echo $substeps
-    echo $gc
-    #echo $fname2
-    echo $ns
-    echo $ts
-    echo $od
-    echo $A68dx
-    echo $A68dy
-    echo $pg
-    echo $ssg
-
-    sed  "s/<ss>/$substeps/; s/<pg>/$pg/; s/<a68>/$a68/; s/<xd>/$A68dx/; s/<yd>/$A68dy/; s/<gc>/$gc/; s/<rad>/$radius/; s/<ssg>/$ssg/; s/<od>/$od/; s/<ns>/$ns/; s/<ts>/$ts/g" \
-	 hex_r_ssf.nml > input.nml
-    rm $fname2
-    rm $bname2
-    ./RUN1p
-done
diff --git a/tests/a68/RUN_ssf_square.sh b/tests/a68/RUN_ssf_square.sh
deleted file mode 100755
index 69dba14..0000000
--- a/tests/a68/RUN_ssf_square.sh
+++ /dev/null
@@ -1,66 +0,0 @@
-#!/bin/bash
-
-#ocean drag values
-ss=200
-gcoef=(1.e4 5.e3 1.e1)
-#gcoef=(1.e4 5.e3 1.e1)
-rdir=S_17.8_ydn.1_r
-odrag=17.8
-#19.5
-#21.25
-#15
-nstress=(24 23 23)
-#25
-#(25 30 35 30 25)
-tstress=(6.5 6.5 6.5)
-#tstress=(7 7 7)
-#7
-#(6 5 5 4 4)
-#nstress=(50000)
-#tstress=(3000)
-a68=.true.
-#.false
-
-# A68dx=-0.01872
-# A68dy=-0.09338
-
-#A68dx=-37.2954
-#A68dy=-55.2975
-
-A68dx=-37.5285
-A68dy=-55.2166
-
-
-#name=(sq_ssf_gc1e6_od15_n20k_t5k.nc)
-fname2=loop
-#Eradius=6.378e6
-Eradius=6363827
-pg=.false.
-#.true.
-#6363827
-
-for ((i = 0; i < ${#nstress[@]}; ++i)); do
-    #substeps=(${ss[$i]})
-    gc=(${gcoef[$i]})
-    #fname2=(${name[$i]})
-    #bname2=(${bond_name[$i]})
-    ns=(${nstress[$i]})
-    ts=(${tstress[$i]})
-    #od=(${odrag[$i]})
-
-    #echo $substeps
-    echo $gc
-    #echo $fname2
-    echo $a68
-    echo $ns
-    echo $ts
-    echo $pg
-    echo $rdir
-    #echo $od
-
-    sed  "s/<ss>/$ss/; s/<a68>/$a68/; s/<pg>/$pg/; s/<xd>/$A68dx/; s/<yd>/$A68dy/; s/<rdir>/$rdir/; s/<gc>/$gc/; s/<rad>/$Eradius/; s/<od>/$odrag/; s/<ns>/$ns/; s/<ts>/$ts/; s/<name>/$fname2/g" \
-	 square_r_ssf.nml > input.nml
-    #rm $fname2
-    #rm $bname2
-    ./RUN1p
-done
diff --git a/tests/a68/RUN_ssfrac.sh b/tests/a68/RUN_ssfrac.sh
deleted file mode 100755
index 6126cb8..0000000
--- a/tests/a68/RUN_ssfrac.sh
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/bin/bash
-
-#ocean drag values
-ss=(200)
-# 400 500 1000)
-gcoef=(1.e6)
-nstress=(9000)
-tstress=(2500)
-name=(lsf_nsf_200_gc1e5_t2.5k_n9k.nc)
-# sstest_400_ssf.nc sstest_500_ssf.nc sstest_1000_ssf.nc)
-
-for ((i = 0; i < ${#ss[@]}; ++i)); do
-    substeps=(${ss[$i]})
-    gc=(${gcoef[$i]})
-    fname2=(${name[$i]})
-    ns=(${nstress[$i]})
-    ts=(${tstress[$i]})
-
-    echo $substeps
-    echo $gc
-    echo $fname2
-    echo $ns
-    echo $ts
-
-    sed  "s/<ss>/$substeps/; s/<gc>/$gc/; s/<ns>/$ns/; s/<ts>/$ts/; s/<fname>/$fname2/g" \
-	 check_ss3.nml > input.nml
-    rm $fname2
-    ./RUN1p
-    # &>/dev/null &
-done
diff --git a/tests/a68/RUN_ssfrac2.sh b/tests/a68/RUN_ssfrac2.sh
deleted file mode 100755
index 779b85a..0000000
--- a/tests/a68/RUN_ssfrac2.sh
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/bin/bash
-
-#ocean drag values
-ss=(200)
-#(100 300 750)
-gcoef=(1.e6)
-nstress=(20000)
-tstress=(8000)
-name=(ssf_nstressfix_200_gc1e6_t8k_n20k.nc)
-#(sstest_100_ssf.nc sstest_300_ssf.nc sstest_750_ssf.nc)
-
-for ((i = 0; i < ${#ss[@]}; ++i)); do
-    substeps=(${ss[$i]})
-    gc=(${gcoef[$i]})
-    fname2=(${name[$i]})
-    ns=(${nstress[$i]})
-    ts=(${tstress[$i]})
-
-    echo $substeps
-    echo $gc
-    echo $fname2
-    echo $ns
-    echo $ts
-
-    sed  "s/<ss>/$substeps/;  s/<gc>/$gc/; s/<ns>/$ns/; s/<ts>/$ts/; s/<fname>/$fname2/g" \
-	 check_ss3_ssf.nml > input.nml
-    rm $fname2
-    ./RUN1p
-    # &>/dev/null &
-done
diff --git a/tests/a68/RUN_test_init_for_paper.sh b/tests/a68/RUN_test_init_for_paper.sh
deleted file mode 100755
index f54b94a..0000000
--- a/tests/a68/RUN_test_init_for_paper.sh
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/bin/bash
-
-Rearth=6363827
-odrag=(17.8)
-#name=(od_17.8_tn_ng_ydn.1.nc)
-#ss=200
-name=(od_17.8_tn_ng_ydn.1_ss90.nc)
-ss=90
-
-for ((i = 0; i < ${#odrag[@]}; ++i)); do
-    drag=(${odrag[$i]})
-    fname=(${name[$i]})
-
-    echo $drag
-    echo $fname
-    echo $Rearth
-    echo $ss
-
-    sed  "s/<od>/$drag/; s/<re>/$Rearth/; s/<ss>/$ss/; s/<name>/$fname/g" \
-	 input_fill2.nml > input.nml
-    ./RUN1p
-    # &>/dev/null &
-done
diff --git a/tests/a68/check_ss.nml b/tests/a68/check_ss.nml
deleted file mode 100644
index 7cad116..0000000
--- a/tests/a68/check_ss.nml
+++ /dev/null
@@ -1,212 +0,0 @@
-&icebergs_driver_nml
-  a68_test=.true.
-  vert_int_ocean_vel=.false.!.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  Old_wrong_Rearth_and_SSH=.false.
-  Rearth=6.378e6
-  !mom_Rearth=.true.
-  no_wind=.false.
-  tau_is_velocity=.true.!.false.
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=1200 !310 !999999999 !max number of timesteps
-  saverestart=.true.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=361 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
-/
-
-&icebergs_nml
-
-    A68_test=.true.
-    Rearth=6.378e6 !6.371229e6 !6.36e6 !6.378e6
-    tau_is_velocity=.true.!.false.
-    ocean_drag_scale=15 !20. !1
-
-    add_curl_to_torque=.false.
-
-    constant_interaction_LW=.true.
-
-    !traj_name=od_15_tn_ng_momr_for_restart_b.nc
-    traj_name=<fname>
-    !od_15_tn_ng_momr_res_n9k_s3k_500ss.nc
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
-    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=<ss>!500!125!75 !75 !150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=30!15!50. !15.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1.0
-    frac_thres_n = 7500.0 !25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
-    frac_thres_t = 2800.0 !11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=4 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.false. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    !restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    !manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    !manually_initialize_bonds_from_radii=.true.   
-    restart_input_dir='./S_OD15b/'
-    manually_initialize_bonds=.false. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.false.!.true.
-    
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
\ No newline at end of file
diff --git a/tests/a68/check_ss2.nml b/tests/a68/check_ss2.nml
deleted file mode 100644
index 4d00bac..0000000
--- a/tests/a68/check_ss2.nml
+++ /dev/null
@@ -1,212 +0,0 @@
-&icebergs_driver_nml
-  a68_test=.true.
-  vert_int_ocean_vel=.false.!.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  Old_wrong_Rearth_and_SSH=.false.
-  Rearth=6.378e6
-  !mom_Rearth=.true.
-  no_wind=.false.
-  tau_is_velocity=.true.!.false.
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=1200 !310 !999999999 !max number of timesteps
-  saverestart=.true.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=361 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
-/
-
-&icebergs_nml
-
-    A68_test=.true.
-    Rearth=6.378e6 !6.371229e6 !6.36e6 !6.378e6
-    tau_is_velocity=.true.!.false.
-    ocean_drag_scale=15 !20. !1
-
-    add_curl_to_torque=.false.
-
-    constant_interaction_LW=.true.
-
-    !traj_name=od_15_tn_ng_momr_for_restart_b.nc
-    traj_name=<fname>
-    !od_15_tn_ng_momr_res_n9k_s3k_500ss.nc
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
-    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=<ss>!500!125!75 !75 !150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=30!15!50. !15.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 0.9 !1.0
-    frac_thres_n = 7500.0 !25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
-    frac_thres_t = 2800.0 !11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=4 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.false. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    !restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    !manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    !manually_initialize_bonds_from_radii=.true.   
-    restart_input_dir='./S_OD15b/'
-    manually_initialize_bonds=.false. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.false.!.true.
-    
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
\ No newline at end of file
diff --git a/tests/a68/check_ss3.nml b/tests/a68/check_ss3.nml
deleted file mode 100644
index 50b23df..0000000
--- a/tests/a68/check_ss3.nml
+++ /dev/null
@@ -1,212 +0,0 @@
-&icebergs_driver_nml
-  a68_test=.true.
-  vert_int_ocean_vel=.false.!.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  Old_wrong_Rearth_and_SSH=.false.
-  Rearth=6.378e6
-  !mom_Rearth=.true.
-  no_wind=.false.
-  tau_is_velocity=.true.!.false.
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=120 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=1200 !310 !999999999 !max number of timesteps
-  saverestart=.false.!.true.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=361 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
-/
-
-&icebergs_nml
-
-    A68_test=.true.
-    Rearth=6.378e6 !6.371229e6 !6.36e6 !6.378e6
-    tau_is_velocity=.true.!.false.
-    ocean_drag_scale=15 !20. !1
-
-    add_curl_to_torque=.false.
-
-    constant_interaction_LW=.true.
-
-    !traj_name=od_15_tn_ng_momr_for_restart_b.nc
-    traj_name=<fname>
-    !od_15_tn_ng_momr_res_n9k_s3k_500ss.nc
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
-    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=<ss>!500!125!75 !75 !150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=<gc> !1.e7 !6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=30!15!50. !15.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1.
-    frac_thres_n = <ns> !9000.0 !11250.0
-    frac_thres_t = <ts> !3000.0 !10000.0
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=4 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.false. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    !restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    !manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    !manually_initialize_bonds_from_radii=.true.   
-    restart_input_dir='./S_OD15b/'
-    manually_initialize_bonds=.false. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.false.!.true.
-    
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
\ No newline at end of file
diff --git a/tests/a68/check_ss3_nofrac.nml b/tests/a68/check_ss3_nofrac.nml
deleted file mode 100644
index f500a95..0000000
--- a/tests/a68/check_ss3_nofrac.nml
+++ /dev/null
@@ -1,212 +0,0 @@
-&icebergs_driver_nml
-  a68_test=.true.
-  vert_int_ocean_vel=.false.!.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  Old_wrong_Rearth_and_SSH=.false.
-  Rearth=6.378e6
-  !mom_Rearth=.true.
-  no_wind=.false.
-  tau_is_velocity=.true.!.false.
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=120 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=1200 !310 !999999999 !max number of timesteps
-  saverestart=.true.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=361 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
-/
-
-&icebergs_nml
-
-    A68_test=.true.
-    Rearth=6.378e6 !6.371229e6 !6.36e6 !6.378e6
-    tau_is_velocity=.true.!.false.
-    ocean_drag_scale=15 !20. !1
-
-    add_curl_to_torque=.false.
-
-    constant_interaction_LW=.true.
-
-    !traj_name=od_15_tn_ng_momr_for_restart_b.nc
-    traj_name=<fname>
-    !od_15_tn_ng_momr_res_n9k_s3k_500ss.nc
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
-    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=<ss>!500!125!75 !75 !150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=30!15!50. !15.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1.
-    frac_thres_n = -1 !15000.0 !11250.0
-    frac_thres_t = -1 !7500.0
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=4 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.false. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    !restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    !manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    !manually_initialize_bonds_from_radii=.true.   
-    restart_input_dir='./S_OD15b/'
-    manually_initialize_bonds=.false. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.false.!.true.
-    
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
\ No newline at end of file
diff --git a/tests/a68/check_ss3_ssf.nml b/tests/a68/check_ss3_ssf.nml
deleted file mode 100644
index 881c16b..0000000
--- a/tests/a68/check_ss3_ssf.nml
+++ /dev/null
@@ -1,214 +0,0 @@
-&icebergs_driver_nml
-  a68_test=.true.
-  vert_int_ocean_vel=.false.!.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  Old_wrong_Rearth_and_SSH=.false.
-  Rearth=6.378e6
-  !mom_Rearth=.true.
-  no_wind=.false.
-  tau_is_velocity=.true.!.false.
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=120 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=1200 !310 !999999999 !max number of timesteps
-  saverestart=.false.!.true.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=361 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
-/
-
-&icebergs_nml
-
-    A68_test=.true.
-    Rearth=6.378e6 !6.371229e6 !6.36e6 !6.378e6
-    tau_is_velocity=.true.!.false.
-    ocean_drag_scale=15 !20. !1
-
-    add_curl_to_torque=.false.
-
-    constant_interaction_LW=.true.
-
-    break_bonds_on_sub_steps=.true.
-
-    !traj_name=od_15_tn_ng_momr_for_restart_b.nc
-    traj_name=<fname>
-    !od_15_tn_ng_momr_res_n9k_s3k_500ss.nc
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
-    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=<ss>!500!125!75 !75 !150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=<gc>!1.e7!6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=30 !15!50. !15.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1.
-    frac_thres_n = <ns> !16000.0 !11250.0
-    frac_thres_t = <ts> !7500.0 !10000.0
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=4 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.false. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    !restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    !manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    !manually_initialize_bonds_from_radii=.true.   
-    restart_input_dir='./S_OD15b/'
-    manually_initialize_bonds=.false. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.false.!.true.
-    
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
\ No newline at end of file
diff --git a/tests/a68/check_ss_new.nml b/tests/a68/check_ss_new.nml
deleted file mode 100644
index 7cad116..0000000
--- a/tests/a68/check_ss_new.nml
+++ /dev/null
@@ -1,212 +0,0 @@
-&icebergs_driver_nml
-  a68_test=.true.
-  vert_int_ocean_vel=.false.!.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  Old_wrong_Rearth_and_SSH=.false.
-  Rearth=6.378e6
-  !mom_Rearth=.true.
-  no_wind=.false.
-  tau_is_velocity=.true.!.false.
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=1200 !310 !999999999 !max number of timesteps
-  saverestart=.true.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=361 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
-/
-
-&icebergs_nml
-
-    A68_test=.true.
-    Rearth=6.378e6 !6.371229e6 !6.36e6 !6.378e6
-    tau_is_velocity=.true.!.false.
-    ocean_drag_scale=15 !20. !1
-
-    add_curl_to_torque=.false.
-
-    constant_interaction_LW=.true.
-
-    !traj_name=od_15_tn_ng_momr_for_restart_b.nc
-    traj_name=<fname>
-    !od_15_tn_ng_momr_res_n9k_s3k_500ss.nc
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
-    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=<ss>!500!125!75 !75 !150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=30!15!50. !15.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1.0
-    frac_thres_n = 7500.0 !25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
-    frac_thres_t = 2800.0 !11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=4 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.false. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    !restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    !manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    !manually_initialize_bonds_from_radii=.true.   
-    restart_input_dir='./S_OD15b/'
-    manually_initialize_bonds=.false. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.false.!.true.
-    
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
\ No newline at end of file
diff --git a/tests/a68/check_ss_orig.nml b/tests/a68/check_ss_orig.nml
deleted file mode 100644
index 78161d7..0000000
--- a/tests/a68/check_ss_orig.nml
+++ /dev/null
@@ -1,211 +0,0 @@
-&icebergs_driver_nml
-  a68_test=.true.
-  vert_int_ocean_vel=.false.!.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  Old_wrong_Rearth_and_SSH=.false.
-  Rearth=6.378e6
-  !mom_Rearth=.true.
-  no_wind=.false.
-  tau_is_velocity=.true.!.false.
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=1200 !310 !999999999 !max number of timesteps
-  saverestart=.true.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=361 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
-/
-
-&icebergs_nml
-
-    A68_test=.true.
-    Rearth=6.378e6 !6.371229e6 !6.36e6 !6.378e6
-    tau_is_velocity=.true.!.false.
-    ocean_drag_scale=15 !20. !1
-
-    add_curl_to_torque=.false.
-
-    constant_interaction_LW=.true.
-
-    !traj_name=od_15_tn_ng_momr_for_restart_b.nc
-    traj_name=od_15_tn_ng_momr_res_n9k_s3k_500ss.nc
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
-    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=500!125!75 !75 !150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=30!15!50. !15.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1.5
-    frac_thres_n = 6000.0 !25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
-    frac_thres_t = 2000.0 !11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=4 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.false. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    !restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    !manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    !manually_initialize_bonds_from_radii=.true.   
-    restart_input_dir='./S_OD15b/'
-    manually_initialize_bonds=.false. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.false.!.true.
-    
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
\ No newline at end of file
diff --git a/tests/a68/hex_4restart.sh b/tests/a68/hex_4restart.sh
deleted file mode 100755
index 6755381..0000000
--- a/tests/a68/hex_4restart.sh
+++ /dev/null
@@ -1,40 +0,0 @@
-#!/bin/bash
-
-#ocean drag values
-#odrag=(6.5 6 5 7 4 8 3 1)
-#name=(hex_wgs84_nofrac_od6.5.nc hex_wgs84_nofrac_od6.nc hex_wgs84_nofrac_od5.nc hex_wgs84_nofrac_od7.nc hex_wgs84_nofrac_od4.nc hex_wgs84_nofrac_od8.nc hex_wgs84_nofrac_od3.nc hex_wgs84_nofrac_od1.nc)
-
-#odrag=(7.2)
-#name=(hex_ydn.05_wgs84_nf_od7.2_4restart.nc)
-
-# odrag=(6)
-# name=(hex_yn.075_nf_od6_4restart.nc)
-# bond_name=(hex_yn.075_nf_od6_4restart_bonds.nc)
-# radius=6363827
-
-# odrag=(5.4)
-# name=(hex_yn.1_nf_od5.4_4restart.nc)
-# bond_name=(hex_yn.1_nf_od5.4_4restart_bonds.nc)
-# radius=6363827
-
-odrag=(5)
-name=(hex_yn.1_nf_od5_4restart.nc)
-bond_name=(hex_yn.1_nf_od5_4restart_bonds.nc)
-radius=6363827
-
-echo $radius
-
-for ((i = 0; i < ${#odrag[@]}; ++i)); do
-    drag=(${odrag[$i]})
-    fname=(${name[$i]})
-    bname=(${bond_name[$i]})
-    echo $drag
-    echo $fname
-
-    sed  "s/<od>/$drag/; s/<rad>/$radius/; s/<bname>/$bname/; s/<name>/$fname/g" \
-	 input_fill_hex_4restart.nml > input.nml
-    rm $fname
-    rm $bname
-    ./RUN1p
-    # &>/dev/null &
-done
diff --git a/tests/a68/hex_r_lsf.nml b/tests/a68/hex_r_lsf.nml
deleted file mode 100644
index 16d0ccc..0000000
--- a/tests/a68/hex_r_lsf.nml
+++ /dev/null
@@ -1,214 +0,0 @@
-&icebergs_driver_nml
-  a68_test=.true.
-  vert_int_ocean_vel=.false.!.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  Old_wrong_Rearth_and_SSH=.false.
-  Rearth=<rad>
-  !6.371229e6 !6.378e6
-  no_wind=.false.
-  tau_is_velocity=.true.!.false.
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=120 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=1200 !310 !999999999 !max number of timesteps
-  saverestart=.false.!.true.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=355 !361 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
-/
-
-&icebergs_nml
-
-    A68_test=.true.!.false.!.true.
-    Rearth=<rad>
-    !6.371229e6 !6.378e6 !6.371229e6 !6.36e6 !6.378e6
-    tau_is_velocity=.true.!.false.
-    ocean_drag_scale=7 !6.5 !20. !1
-
-    add_curl_to_torque=.false.
-    constant_interaction_LW=.true.
-
-    no_frac_first_ts=.true.
-    !orig_dem_moment_of_inertia=.true.
-
-    traj_name=<fname>
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=<dc>
-    !1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    !spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7, r=1500, and square pack?
-    spring_coef=0.0007547062342348049 !if dem_spring_coef=0.5e7, r=1500, and hex pack?    
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=<ss>!500!125!75 !75 !150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=<gc>!1.e7!6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=0 !15!50. !15.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1.
-    frac_thres_n = <ns> !16000.0 !11250.0
-    frac_thres_t = <ts> !7500.0 !10000.0
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.true.!.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=-1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=2 !12 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.false. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.false. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    !restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    !manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    !manually_initialize_bonds_from_radii=.true.
-    restart_input_dir='./HEX7_r/' !'./S_OD15b/'
-    manually_initialize_bonds=.false. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.false.!.true.
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
\ No newline at end of file
diff --git a/tests/a68/hex_r_ssf.nml b/tests/a68/hex_r_ssf.nml
deleted file mode 100644
index b9c3e44..0000000
--- a/tests/a68/hex_r_ssf.nml
+++ /dev/null
@@ -1,230 +0,0 @@
-&icebergs_driver_nml
-  a68_test=.true.
-  vert_int_ocean_vel=.false.!.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  Old_wrong_Rearth_and_SSH=.false.
-  Rearth=<rad>
-  !6.371229e6 !6.378e6
-  !mom_Rearth=.true.
-  no_wind=.false.
-  tau_is_velocity=.true.!.false.
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=120 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=1200 !310 !999999999 !max number of timesteps
-  saverestart=.false.!.true.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=355 !361 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
-  !transient_a68_data_start_ind=331
-/
-
-&icebergs_nml
-
-    A68_test=<a68> !.false.!.true.
-    A68_xdisp=<xd>
-    A68_ydisp=<yd>
-    !orig_dem_moment_of_inertia=.true.
-    Rearth=<rad>
-    !6.371229e6 !6.378e6 !6.371229e6 !6.36e6 !6.378e6
-    tau_is_velocity=.true.!.false.
-    ocean_drag_scale=<od> !7. !6.5 !20. !1
-
-    add_curl_to_torque=.false.
-
-    constant_interaction_LW=.true.
-
-    no_frac_first_ts=.true.
-    power_ground=<pg>
-    
-    break_bonds_on_sub_steps=.true.
-    short_step_mts_grounding=<ssg>
-
-    !use_grounding_torque=.true.
-
-    !traj_name=od_15_tn_ng_momr_for_restart_b.nc
-    !traj_name=<fname>
-    traj_name=hz_ssf_g<gc>_addsm<a68>_od<od>_n<ns>t<ts>_pg<pg>_ssg<ssg>.nc
-    !bond_traj_name=<bname>
-    !od_15_tn_ng_momr_res_n9k_s3k_500ss.nc
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    !spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7, r=1500, and square pack?
-    spring_coef=0.0007547062342348049 !if dem_spring_coef=5e6, r=1500, and hex pack?    
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=<ss>!500!125!75 !75 !150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-4 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=10.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7 !(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=<gc>!1.e7!6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=1. !0 !15!50. !15.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !'computed' !'stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1.
-    frac_thres_n = <ns>e3 !16000.0 !11250.0
-    frac_thres_t = <ts>e3 !7500.0 !10000.0
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=-1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=2 !6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false.!.true. !.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.false. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    !restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    !manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    !manually_initialize_bonds_from_radii=.true.
-    !restart_input_dir='H<od>_yn.1_r/'
-    restart_input_dir='H<od>_yn.75_r/'
-    !restart_input_dir='HEX<od>_r/'
-    manually_initialize_bonds=.false. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.false.!.true.
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
\ No newline at end of file
diff --git a/tests/a68/hex_wgs84_frac_specs.nml b/tests/a68/hex_wgs84_frac_specs.nml
deleted file mode 100644
index 0fae617..0000000
--- a/tests/a68/hex_wgs84_frac_specs.nml
+++ /dev/null
@@ -1,209 +0,0 @@
-&icebergs_driver_nml
-  a68_test=.true.
-  vert_int_ocean_vel=.false.!.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  Old_wrong_Rearth_and_SSH=.false.
-  no_wind=.false.  
-  tau_is_velocity=.true.!.false.
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=360 !120 !360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=298 !432 !298 !310 !99999 !310 !999999999 !max number of timesteps
-  saverestart=.true.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=206 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
-  Rearth=6363827
-  !6.371229e6
-/
-
-&icebergs_nml
-
-    A68_test=.false.
-    Rearth=6363827
-    tau_is_velocity=.true.!.false.
-    ocean_drag_scale=6.5 !20. !1
-
-    add_curl_to_torque=.false.
-
-    skip_first_outer_mts_step=.true.
-
-    constant_interaction_LW=.true.
-
-    traj_name=hex_wgs84_nofrac_od6.5_for_restart.nc
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    !spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7, r=1500, and square pack?
-    spring_coef=0.0007547062342348049 !if dem_spring_coef=0.5e7, r=1500, and hex pack?
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=200 !125!75 !75 !150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=30!15!50. !15.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 100000
-    frac_thres_n = 25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
-    frac_thres_t = 11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.true. !.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.false. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
\ No newline at end of file
diff --git a/tests/a68/input_fill.nml b/tests/a68/input_fill.nml
deleted file mode 100644
index fa0473a..0000000
--- a/tests/a68/input_fill.nml
+++ /dev/null
@@ -1,205 +0,0 @@
-&icebergs_driver_nml
-  a68_test=.true.
-  vert_int_ocean_vel=.false.!.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  Old_wrong_Rearth_and_SSH=.false.
-  mom_Rearth=.false.
-  no_wind=.false.  
-  tau_is_velocity=.true.!.false.
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=999999999 !max number of timesteps
-  saverestart=.false.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=206 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
-/
-
-&icebergs_nml
-
-    Rearth=6.371229e6 !6.36e6 !6.378e6
-    tau_is_velocity=.true.!.false.
-    ocean_drag_scale=<od> !20. !1
-
-    add_curl_to_torque=.false.
-
-    constant_interaction_LW=.true.
-
-    traj_name=<name>
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
-    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=125!75 !75 !150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=30!15!50. !15.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1
-    frac_thres_n = 25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
-    frac_thres_t = 11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=4 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.false. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
\ No newline at end of file
diff --git a/tests/a68/input_fill_hex.nml b/tests/a68/input_fill_hex.nml
deleted file mode 100644
index a57be74..0000000
--- a/tests/a68/input_fill_hex.nml
+++ /dev/null
@@ -1,216 +0,0 @@
-&icebergs_driver_nml
-  a68_test=.true.
-  vert_int_ocean_vel=.false.!.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  Old_wrong_Rearth_and_SSH=.false.
-  no_wind=.false.  
-  tau_is_velocity=.true.!.false.
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=360 !120 !360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=432 !298 !310 !99999 !310 !999999999 !max number of timesteps
-  saverestart=.false.!.true.!.false.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=206 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
-  Rearth=<rad>
-  !6.371229e6
-/
-
-&icebergs_nml
-
-    A68_test=.false. !.true. !.false.
-    short_step_mts_grounding=.true.
-    !rev_mind=.true.
-    Rearth=<rad>
-    tau_is_velocity=.true.!.false.
-    ocean_drag_scale=<od> !20. !1
-
-    add_curl_to_torque=.false.
-
-    skip_first_outer_mts_step=.true.
-
-    constant_interaction_LW=.true.
-
-    traj_name=<name>
-
-    radius_based_drag=.true.
-    !orig_dem_moment_of_inertia=.true.
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=<damp>
-    !1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=1.e6 !5e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    !spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7, r=1500, and square pack
-    !spring_coef=0.0007547062342348049 !if dem_spring_coef=0.5e7, r=1500, and hex pack
-    spring_coef=0.00037735311711740245 !if dem_spring_coef=2.5e6, r=1500, and hex pack
-    
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=200 !125!75 !75 !150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-4 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=<gc>
-    h_to_init_grounding=0.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 10000000000
-    frac_thres_n = 25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
-    frac_thres_t = 11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.true. !.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.false. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
\ No newline at end of file
diff --git a/tests/a68/input_fill_hex_4restart.nml b/tests/a68/input_fill_hex_4restart.nml
deleted file mode 100644
index 1c3b6f8..0000000
--- a/tests/a68/input_fill_hex_4restart.nml
+++ /dev/null
@@ -1,210 +0,0 @@
-&icebergs_driver_nml
-  a68_test=.true.
-  vert_int_ocean_vel=.false.!.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  Old_wrong_Rearth_and_SSH=.false.
-  no_wind=.false.  
-  tau_is_velocity=.true.!.false.
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=360 !120 !360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  !nmax=298
-  nmax=250 !1 day earlier than usual
-  saverestart=.true.!.false.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=206 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
-  Rearth=<rad>
-/
-
-&icebergs_nml
-
-    A68_test=.true.
-    Rearth=<rad>
-    tau_is_velocity=.true.
-    ocean_drag_scale=<od>
-
-    add_curl_to_torque=.false.
-
-    skip_first_outer_mts_step=.true.
-
-    constant_interaction_LW=.true.
-
-    traj_name=<name>
-    bond_traj_name=<bname>	    
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    !spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7, r=1500, and square pack?
-    spring_coef=0.0007547062342348049 !if dem_spring_coef=0.5e7, r=1500, and hex pack?
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=200 !125!75 !75 !150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=0 !1.e6 !3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=0!30!15!50. !15.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='none' !'stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 100000
-    frac_thres_n = 25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
-    frac_thres_t = 11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.true. !.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.true. !.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.false. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
\ No newline at end of file
diff --git a/tests/a68/input_fill_hex_noground.nml b/tests/a68/input_fill_hex_noground.nml
deleted file mode 100644
index 4521d92..0000000
--- a/tests/a68/input_fill_hex_noground.nml
+++ /dev/null
@@ -1,213 +0,0 @@
-&icebergs_driver_nml
-  a68_test=.true.
-  vert_int_ocean_vel=.false.!.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  Old_wrong_Rearth_and_SSH=.false.
-  no_wind=.false.  
-  tau_is_velocity=.true.!.false.
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=360 !120 !360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=432 !298 !310 !99999 !310 !999999999 !max number of timesteps
-  saverestart=.false.!.true.!.false.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=206 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
-  Rearth=<rad>
-  !6.371229e6
-/
-
-&icebergs_nml
-
-    A68_test=.true.!.false.
-    Rearth=<rad>
-    tau_is_velocity=.true.!.false.
-    ocean_drag_scale=<od> !20. !1
-
-    no_frac_first_ts=.true.
-    add_curl_to_torque=.false.
-
-    skip_first_outer_mts_step=.true.
-
-    constant_interaction_LW=.true.
-
-    traj_name=<name>
-
-    !break_bonds_on_sub_steps=.true.
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=<sc> !5e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    !spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7, r=1500, and square pack?
-    !spring_coef=0.00015094124684696098
-    spring_coef=0.0007547062342348049 !if dem_spring_coef=0.5e7, r=1500, and hex pack?
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=200 !125!75 !75 !150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=0.!1.e6 !3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=0!15!50. !15.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1 !00000
-    frac_thres_n = 90000. !25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
-    frac_thres_t = 45000. !11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.true. !.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.false. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
\ No newline at end of file
diff --git a/tests/a68/long_run_no_inc_contact_dist.nml b/tests/a68/long_run_no_inc_contact_dist.nml
deleted file mode 100644
index 12de105..0000000
--- a/tests/a68/long_run_no_inc_contact_dist.nml
+++ /dev/null
@@ -1,217 +0,0 @@
-&icebergs_driver_nml
-  a68_test=.true.
-  vert_int_ocean_vel=.false.!.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  Old_wrong_Rearth_and_SSH=.false.
-  !mom_Rearth=.true.
-  Rearth=<re>
-  !6363827 !6.378e6
-  no_wind=.false.
-  tau_is_velocity=.true.!.false.
-  ibdt=<ibdt> !3600.0 !1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=432 !360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=999999999 !max number of timesteps
-  saverestart=.false.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=206 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
-/
-
-&icebergs_nml
-
-    Rearth=<re>
-
-    A68_test=.true.
-    A68_xdisp=<xd>
-    A68_ydisp=<yd>
-    short_step_mts_grounding=.true.
-
-    tau_is_velocity=.true.
-    ocean_drag_scale=<od>
-
-    skip_first_outer_mts_step=.true.
-    add_curl_to_torque=.false.
-
-    constant_interaction_LW=.true.
-
-    traj_name=<name>.nc
-    bond_traj_name=<name>_bonds.nc
-
-    break_bonds_on_sub_steps=.true.
-
-    power_ground=.false.
-
-    save_bond_forces=.true.
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
-    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=<ss> !200 !75 !75 !150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-4 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=0.!4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=<gc> !0.!1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=0!30!15!50. !15.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1
-    frac_thres_n = <ns>e3
-    frac_thres_t = 1000e3
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.true. !.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=4 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!1 !(24) sampling period for trajectory storage
-    traj_write_hrs=1 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.false. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
\ No newline at end of file
diff --git a/tests/a68/long_run_no_inc_contact_dist.sh b/tests/a68/long_run_no_inc_contact_dist.sh
deleted file mode 100755
index 9d02863..0000000
--- a/tests/a68/long_run_no_inc_contact_dist.sh
+++ /dev/null
@@ -1,40 +0,0 @@
-#!/bin/bash
-
-Rearth=6363827
-odrag=(17.8)
-ss=90
-name=(lrun_nicd_od_17.8_tn_ng_ydn.1_ss90_ns18_rx-37.51_ry-55.2166)
-ibdt=1800.0
-
-gcoef=(1.e4)
-nstress=(18)
-A68dx=-37.51
-A68dy=-55.2166
-
-odrag=(10.35)
-ss=180
-name=(lrun_nicd_hrtest)
-ibdt=3600.0
-nstress=(24.) #(22.5)
-A68dx=-37.5
-A68dy=-55.1
-
-for ((i = 0; i < ${#odrag[@]}; ++i)); do
-    drag=(${odrag[$i]})
-    fname=(${name[$i]})
-    gc=(${gcoef[$i]})
-    ns=(${nstress[$i]})
-
-    echo $drag
-    echo $fname
-    echo $Rearth
-    echo $ss
-    echo $A68dx
-    echo $A68dy
-    echo $ns
-
-    sed  "s/<od>/$drag/; s/<re>/$Rearth/; s/<ss>/$ss/; s/<ns>/$ns/; s/<gc>/$gc/; s/<xd>/$A68dx/; s/<yd>/$A68dy/; s/<ibdt>/$ibdt/; s/<name>/$fname/g" \
-	 long_run_no_inc_contact_dist.nml > input.nml
-    ./RUN1p
-    # &>/dev/null &
-done
diff --git a/tests/a68/makeberg/RUN b/tests/a68/makeberg/RUN
deleted file mode 100755
index bc3883d..0000000
--- a/tests/a68/makeberg/RUN
+++ /dev/null
@@ -1,89 +0,0 @@
-rm ./output_files/Generic*
-
-#OPTION 1: SET CONSTANT THICKNESS TO 200 m
-#-------------------------------------------
-
-
-#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_09_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -lat_ref_grid_to_cartesian=-55.2 -uvel=0.2 -R_earth=6378000.
-
-#6.371229e6
-
-#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='hexagon' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_09_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -R_earth=6.371229e6 -lat_ref_grid_to_cartesian=-55.2 -uvel=0.2 -dx=3500.
-
-#for Rearth at 55 S for WGS84 ellipsoid
-#Change lon_init and lat_init to be displaced by dx/2 for this one!!
-#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='hexagon' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_09_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -lat_ref_grid_to_cartesian=-55.2 -uvel=0.22 -dx=3500. -R_earth=6363827. -displace_y=-0.05 -icethres=0.5
-
-#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='hexagon' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_09_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -lat_ref_grid_to_cartesian=-55.2 -uvel=0.22 -dx=3500. -R_earth=6363827. -displace_y=-0.025 -icethres=0.6
-
-#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='hexagon' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_09_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -lat_ref_grid_to_cartesian=-55.2 -uvel=0.22 -dx=3540. -R_earth=6363827. -displace_y=-0.0625 -icethres=0.9
-
-#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='hexagon' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_09_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -lat_ref_grid_to_cartesian=-55.2 -uvel=0.22 -dx=3540. -R_earth=6363827. -displace_y=-0.075 -icethres=0.9
-
-./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='hexagon' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_09_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -lat_ref_grid_to_cartesian=-55.2 -uvel=0.22 -dx=3540. -R_earth=6363827. -displace_y=-0.1 -icethres=0.9
-
-# AGU hex test:
-#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='hexagon' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_09_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -lat_ref_grid_to_cartesian=-55.2 -uvel=0.22 -dx=3540. -R_earth=6363827. -displace_y=-0.175 -icethres=0.9
-
-
-#For testing rev_mind=.true. vs. rev_mind=.false.
-#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='hexagon' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_14_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -lat_ref_grid_to_cartesian=-55.2 -dx=3500. -R_earth=6363827. -set_all_domain_to_ice=True -set_all_bergs_static_by_default=True
-
-#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_09_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=False -Radius=1500 -lat_ref_grid_to_cartesian=-55.2 -uvel=0.22 -dx=500. -R_earth=6363827. -icethres=0.8
-
-
-# THIS IS THE ONE USED FOR AGU AND IN THE PAPER!!
-#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_09_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=False -Radius=1500 -lat_ref_grid_to_cartesian=-55.2 -uvel=0.22 -dx=500. -R_earth=6363827. -icethres=0.5 -displace_y=-0.1
-
-#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_09_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=False -Radius=1500 -lat_ref_grid_to_cartesian=-55.2 -uvel=0.22 -dx=500. -R_earth=6378000. -icethres=0.5 -displace_y=-0.1
-
-#for Rearth at 55 S for WGS84 ellipsoid
- #this was the displacement for ./../oldnc2/od_##_tn_ng_ellr.nc??
-#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_09_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -lat_ref_grid_to_cartesian=-55.2 -uvel=0.22 -dx=250. -R_earth=6363827. -displace_y=-0.05
-
-#-lat_ref_grid_to_cartesian=-55.2 -uvel=0.2 -vvel=0.0
-
-#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_14_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_thickness=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -R_earth=6.371229e6 -lat_ref_grid_to_cartesian=-55.8
-
-#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_14a_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_thickness=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -R_earth=6.371229e6 -lat_ref_grid_to_cartesian=-55.8
-
-#-uvel=0.2 -vvel=-0.2
-
-#-uvel=0.2 -vvel=-0.2 -ang_vel_prescribed=-7.5e-5
-
-#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_13_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_thickness=False -plot_ice_mask=False -plot_icebergs_positions=True -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -R_earth=6.371229e6 -lat_ref_grid_to_cartesian=-55.8
-
-
-#-uvel=0.1 -vvel=0.4
-#-uvel=0.18 -vvel=-0.23 -R_earth=6360000
-#-ang_vel_prescribed=-7.5e-5
-#-uvel=0.2 -vvel=-0.2
-
-# -R_earth=6360000
-
-#-R_earth=6378000.
-
-#-uvel=0.18 -vvel=-0.23
-#-uvel=0.254 -vvel=-0.08
-#-R_earth=6360000 -uvel=0.18 -vvel=-0.23
-#-uvel=0.24 -vvel=-0.08
-
-#OPTION 2: VARY THICKESS
-#-----------------------
-
-#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_09_gridded_ll_p0625_cropped_hvary.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=False -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=False -plot_icebergs_positions=True -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -R_earth=6.371229e6 -lat_ref_grid_to_cartesian=-55.8
-#-uvel=0.2 -vvel=0.
-
-#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_14_gridded_ll_p0625_cropped_hvary.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=False -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=False -plot_icebergs_positions=True -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -R_earth=6.371229e6 -lat_ref_grid_to_cartesian=-55.8
-
-#-uvel=0.24 -vvel=-0.08
-#-uvel=0.18 -vvel=-0.23
-
-#-Radius=2000
-#-uvel=0.18 -vvel=-0.23 #correct?
-#-uvel=0.036 -vvel=-0.046 #wrong?
-#-uvel=0. -vvel=0
-
-#./make_one_berg.py
-
-cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
diff --git a/tests/a68/makeberg/make_one_berg.py b/tests/a68/makeberg/make_one_berg.py
deleted file mode 100755
index e39ec35..0000000
--- a/tests/a68/makeberg/make_one_berg.py
+++ /dev/null
@@ -1,399 +0,0 @@
-#!/usr/bin/env python
-import numpy as np
-import math
-from netCDF4 import Dataset
-from pylab import *
-#import pdb
-import netCDF4 as nc
-
-#
-# Initialize 2 iceberg elements, which can later be bonded in the fortran code if needed
-#
-
-def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
-
-        print('Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..')
-        # To copy the global attributes of the netCDF file
-
-        #Input and output files
-        #Create Empty restart file. This is later read so that the attributes can be used.
-        Empty_restart_filename='output_files/Empty_icebergs.res.nc'
-        create_empty_iceberg_restart_file(Empty_restart_filename)
-        #Empty_restart_filename='input_files/icebergs.res.nc'
-
-        #Read empty restart file
-        f=Dataset(Empty_restart_filename,'r') # r is for read only
-        #Write a new restart file
-        g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
-
-        for attname in f.ncattrs():
-                    setattr(g,attname,getattr(f,attname))
-
-
-        # To copy the dimension of the netCDF file
-        for dimname,dim in f.dimensions.iteritems():
-                # if you want to make changes in the dimensions of the new file
-                # you should add your own conditions here before the creation of the dimension.
-                #g.createDimension(dimname,len(dim))
-                g.createDimension(dimname,Number_of_bergs)
-
-        # To copy the variables of the netCDF file
-
-        for varname,ncvar in f.variables.iteritems():
-                # if you want to make changes in the variables of the new file
-                # you should add your own conditions here before the creation of the variable.
-                var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
-                #Proceed to copy the variable attributes
-                for attname in ncvar.ncattrs():
-                        setattr(var,attname,getattr(ncvar,attname))
-                #Finally copy the variable data to the new created variable
-                #var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
-
-                if varname=='i':
-                        var[:]=Number_of_bergs
-
-                if varname=='iceberg_num':
-                        for j in range(Number_of_bergs):
-                                #var[j]=j+1
-                                var[j]=iceberg_num[j]
-
-                if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
-                or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
-                or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
-                or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
-                        var[:]=0
-
-                if varname=='uvel':
-                        var[:]=uvel
-
-                if varname=='vvel':
-                        var[:]=vvel
-
-                if varname=='mass_scaling':
-                        var[:]=mass_scaling
-
-                if varname=='thickness':
-                        for j in range(Number_of_bergs):
-                                var[j]=thickness[j]
-
-                if varname=='mass':
-                        for j in range(Number_of_bergs):
-                                var[j]=mass[j]
-
-                if varname=='width'  or varname=='length':
-                        for j in range(Number_of_bergs):
-                                var[j]=width[j]
-
-                if varname=='lon':
-                        for j in range(Number_of_bergs):
-                                var[j]=lon[j]
-
-                if varname=='lat':
-                        for j in range(Number_of_bergs):
-                                var[j]=lat[j]
-
-                if varname=='static_berg':
-                        for j in range(Number_of_bergs):
-                                var[j]=static_berg[j]
-
-
-        f.close()
-        g.close()
-
-
-def create_empty_iceberg_restart_file(Empty_restart_filename):
-
-        f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
-
-        i=f.createDimension('i', None)
-        lon=f.createVariable('i','i')
-
-        lon=f.createVariable('lon','d',('i'))
-        lon.long_name = "longitude" ;
-        lon.units = "degrees_E" ;
-        lon.checksum = "               0" ;
-
-        lat=f.createVariable('lat','d',('i'))
-        lat.long_name = "latitude" ;
-        lat.units = "degrees_N" ;
-        lat.checksum = "               0" ;
-
-        uvel=f.createVariable('uvel','d',('i'))
-        uvel.long_name = "zonal velocity" ;
-        uvel.units = "m/s" ;
-        uvel.checksum = "               0" ;
-
-        vvel=f.createVariable('vvel','d',('i'))
-        vvel.long_name = "meridional velocity" ;
-        vvel.units = "m/s" ;
-        vvel.checksum = "               0" ;
-
-        mass=f.createVariable('mass','d',('i'))
-        mass.long_name = "mass" ;
-        mass.units = "kg" ;
-        mass.checksum = "               0" ;
-
-        axn=f.createVariable('axn','d',('i'))
-        axn.long_name = "explicit zonal acceleration" ;
-        axn.units = "m/s^2" ;
-        axn.checksum = "               0" ;
-
-        ayn=f.createVariable('ayn','d',('i'))
-        ayn.long_name = "explicit meridional acceleration" ;
-        ayn.units = "m/s^2" ;
-        ayn.checksum = "               0" ;
-
-        bxn=f.createVariable('bxn','d',('i'))
-        bxn.long_name = "inplicit zonal acceleration" ;
-        bxn.units = "m/s^2" ;
-        bxn.checksum = "               0" ;
-
-        byn=f.createVariable('byn','d',('i'))
-        byn.long_name = "implicit meridional acceleration" ;
-        byn.units = "m/s^2" ;
-        byn.checksum = "               0" ;
-
-        ine=f.createVariable('ine','i',('i'))
-        ine.long_name = "i index" ;
-        ine.units = "none" ;
-        ine.packing = 0 ;
-        ine.checksum = "               0" ;
-
-        jne=f.createVariable('jne','i',('i'))
-        jne.long_name = "j index" ;
-        jne.units = "none" ;
-        jne.packing = 0 ;
-        jne.checksum = "               0" ;
-
-        thickness=f.createVariable('thickness','d',('i'))
-        thickness.long_name = "thickness" ;
-        thickness.units = "m" ;
-        thickness.checksum = "               0" ;
-
-        width=f.createVariable('width','d',('i'))
-        width.long_name = "width" ;
-        width.units = "m" ;
-        width.checksum = "               0" ;
-
-        length=f.createVariable('length','d',('i'))
-        length.long_name = "length" ;
-        length.units = "m" ;
-        length.checksum = "               0" ;
-
-        start_lon=f.createVariable('start_lon','d',('i'))
-        start_lon.long_name = "longitude of calving location" ;
-        start_lon.units = "degrees_E" ;
-        start_lon.checksum = "               0" ;
-
-        start_lat=f.createVariable('start_lat','d',('i'))
-        start_lat.long_name = "latitude of calving location" ;
-        start_lat.units = "degrees_N" ;
-        start_lat.checksum = "               0" ;
-
-        start_year=f.createVariable('start_year','i',('i'))
-        start_year.long_name = "calendar year of calving event" ;
-        start_year.units = "years" ;
-        start_year.packing = 0 ;
-        start_year.checksum = "               0" ;
-
-        iceberg_num=f.createVariable('iceberg_num','i',('i'))
-        iceberg_num.long_name = "identification of the iceberg" ;
-        iceberg_num.units = "dimensionless" ;
-        iceberg_num.packing = 0 ;
-        iceberg_num.checksum = "               0" ;
-
-        start_day=f.createVariable('start_day','d',('i'))
-        start_day.long_name = "year day of calving event" ;
-        start_day.units = "days" ;
-        start_day.checksum = "               0" ;
-
-        start_mass=f.createVariable('start_mass','d',('i'))
-        start_mass.long_name = "initial mass of calving berg" ;
-        start_mass.units = "kg" ;
-        start_mass.checksum = "               0" ;
-
-        mass_scaling=f.createVariable('mass_scaling','d',('i'))
-        mass_scaling.long_name = "scaling factor for mass of calving berg" ;
-        mass_scaling.units = "none" ;
-        mass_scaling.checksum = "               0" ;
-
-        mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
-        mass_of_bits.long_name = "mass of bergy bits" ;
-        mass_of_bits.units = "kg" ;
-        mass_of_bits.checksum = "               0" ;
-
-        heat_density=f.createVariable('heat_density','d',('i'))
-        heat_density.long_name = "heat density" ;
-        heat_density.units = "J/kg" ;
-        heat_density.checksum = "               0" ;
-
-        halo_berg=f.createVariable('halo_berg','d',('i'))
-        halo_berg.long_name = "halo_berg" ;
-        halo_berg.units = "dimensionless" ;
-        halo_berg.checksum = "               0" ;
-
-        static_berg=f.createVariable('static_berg','d',('i'))
-        static_berg.long_name = "static_berg" ;
-        static_berg.units = "dimensionless" ;
-        static_berg.checksum = "               0" ;
-
-        f.sync()
-        f.close()
-
-
-
-#-----------------------------------#
-#               Main                #
-#-----------------------------------#
-
-# just2particles=False
-# flip2ndconglom=True#False
-# offset2ndconglom=True#False
-
-grdxmin=0; grdxmax=45000e3
-grdymin=0; grdymax=45000e3
-grdres=0.125 #degrees
-#hexagonal
-#R_frac=0.45 #1st option
-#radius=(np.sqrt(3)/2.)*(R_frac*grdres) #S is < 0.5 grid res
-
-#square
-radius=1000
-thickness1=200.0
-thickness2=200.0
-
-rho_ice=850.0
-
-
-nbergs=1 #number of conglomerates
-
-#center coords of each (rectangular) conglomerate berg (CB=conglomerate berg)
-CBxc=np.array([4000]); CByc=np.array([4000])
-#side lengths
-CBxl=np.array([4000]); CByl=np.array([4000])
-
-
-CByl=CByl.astype(int); CBxl=CBxl.astype(int)
-
-#--- xmax, xmin, ymax, ymin for each CB --
-CBxmin=CBxc-(0.5*CBxl); CBxmax=CBxc+(0.5*CBxl)
-CBymin=CByc-(0.5*CByl); CBymax=CByc+(0.5*CByl)
-#this shouldn't happen:
-CBxmin[CBxmin<grdxmin]=grdxmin; CBxmax[CBxmax>grdxmax]=grdxmax
-CBymin[CBxmin<grdymin]=grdymin; CBymax[CBymax>grdymax]=grdymax
-CBxc=0.5*(CBxmin+CBxmax); CByc=0.5*(CBymin+CBymax)
-
-# #if just want one particle per CB
-# if just2particles:
-#         CBxmin=CBxc; CBxmax=CBxc
-#         CBymin=CByc; CBymax=CByc
-
-#--- min and max thicknesses for each CB ---
-h1=thickness1
-h2=thickness2
-CBhmax=np.array([h1]); CBhmin=np.array([h2])
-
-#radii
-CBrad=np.array([radius])
-print('radii',CBrad)
-
-berg_x=[]; berg_y=[]
-berg_id=[]; berg_static=[]
-berg_width=[]; berg_bonds=[]
-berg_h=[]; berg_mass_scaling=[]
-berg_mass=[]
-berg_uvel=[]; berg_vvel=[]
-
-berg_count=0
-
-
-#Test a single particle to start
-berg_count=1
-x_val=-38.1+360
-y_val=-54.9
-uvel=0.036
-vvel=-0.046
-element_area=(2.*radius)**2
-bh=h1
-berg_id.append(berg_count)
-berg_x.append(x_val)
-berg_y.append(y_val)
-berg_width.append(np.sqrt(element_area))
-#dist of berg elem from center of CB
-berg_h.append(h1) #thickness
-berg_mass_scaling.append(1)
-berg_mass.append(bh*rho_ice*element_area)
-berg_static.append(0)
-berg_uvel.append(uvel)
-berg_vvel.append(vvel)
-
-# for i in range(nbergs):
-#         x_start=CBxmin[i]+(CBrad[i]*2./np.sqrt(3))
-
-#         # if flip2ndconglom and i>0:
-#         #         x_start=CBxmax[i]-(CBrad[i]*2./np.sqrt(3))
-
-#         #pdb.set_trace()
-#         if x_start>CBxmax[i]:
-#                 x_start=CBxmax[i]
-#         y_start0=CBymin[i]+CBrad[i]
-#         if y_start0>CBymax[i]:
-#                 y_start0=CBymax[i]
-#         element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*(CBrad[i])**2)
-#         #H (thickness) is a linear function of a berg element's position from the
-#         #center of the CB. H=Hmax at the center of the CB and H=Hmin at a corner of the
-#         #CB, where the dist of a corner from the center is:
-#         cdistb=np.sqrt((CBxmin[i]-CBxc[i])**2+(CBymin[i]-CByc[i])**2)
-#         j=0
-#         x_val=x_start
-#         offset=0.0
-#         # if (i==0):
-#         uvel=0.036
-#         # else:
-#         #         uvel=-0.15#-0.05
-#         #         if (offset2ndconglom):
-#         #                 offset=250.0
-#         vvel=-0.046
-#         #uvel=0;vvel=0
-#         #berg_count_start=berg_count
-#         while x_val<=CBxmax[i] and x_val>=CBxmin[i]:
-#                 y_start=y_start0+((j%2)*CBrad[i])+offset
-#                 k=0
-#                 y_val=y_start
-#                 while y_val<=(CBymax[i]+offset):
-#                         berg_count=berg_count+1
-#                         berg_id.append(berg_count)
-#                         berg_x.append(x_val)
-#                         berg_y.append(y_val)
-#                         berg_width.append(sqrt(element_area))
-#                         #dist of berg elem from center of CB
-#                         bdistc=np.sqrt((x_val-CBxc[i])**2+(y_val-CByc[i])**2)
-#                         bh=CBhmin[i]*bdistc/cdistb + CBhmax[i]*(1-bdistc/cdistb)
-#                         # if (just2particles):
-#                         #         bh=h1
-#                         berg_h.append(bh) #thickness
-#                         berg_mass_scaling.append(1)
-#                         berg_mass.append(bh*rho_ice*element_area)
-#                         berg_static.append(0)
-#                         berg_uvel.append(uvel)
-#                         berg_vvel.append(vvel)
-#                         # if (x_val<22000):
-#                         #         berg_vvel.append(vvel)
-#                         # else:
-#                         #         berg_vvel.append(0.4)
-#                         #berg_CBid.append(i)
-#                         k=k+1
-#                         y_val=y_start+(2*k*CBrad[i])
-#                 j=j+1
-#                 # if flip2ndconglom and i>0:
-#                 #         x_val=x_start-(np.sqrt(3)*CBrad[i]*j)
-#                 # else:
-#                 x_val=x_start+(np.sqrt(3)*CBrad[i]*j)
-
-print('Number of bergs',berg_count)
-
-#pdb.set_trace()
-
-#Create iceberg restart file
-Ice_geometry_source='Generic'
-Create_iceberg_restart_file(berg_count,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)
diff --git a/tests/a68/n6000_t2500.nml b/tests/a68/n6000_t2500.nml
deleted file mode 100644
index 97aafa3..0000000
--- a/tests/a68/n6000_t2500.nml
+++ /dev/null
@@ -1,194 +0,0 @@
-!#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_14_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=True -plot_circles=True -plot_h_ice_new=True -plot_ice_thickness=False -plot_ice_mask=False -plot_icebergs_positions=True -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -uvel=0.036 -vvel=-0.056
-&icebergs_driver_nml
-  !ni=45 !30 !number of elements, x direction
-  !nj=45 !30 !number of elements, y direction
-  a68_test=.true.
-  vert_int_ocean_vel=.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  ibdt=1800.0 !seconds
-  !ibuo=0.1 !ocean x velocity
-  !ibvo=0.0 !ocean y velocity
-  !ibui=0.0 !ice x velocity
-  !ibvi=0.0 !ice y velocity
-  ibhrs=720 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=999999999 !max number of timesteps
-  saverestart=.false.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-/
-
-&icebergs_nml
-
-    tau_is_velocity=.true.
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=1e6!1e7!34000.0 !4471.938678723104 !1000.0
-    spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=75!150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-    
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=25.!200.0
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1.
-    frac_thres_n = 6000. !3000. !2.1e4 !12.
-    frac_thres_t = 2500. !1750. !35000. !12.
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=4 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=1 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/a68/nov3_tests.nml b/tests/a68/nov3_tests.nml
deleted file mode 100644
index dbe4e96..0000000
--- a/tests/a68/nov3_tests.nml
+++ /dev/null
@@ -1,197 +0,0 @@
-
-&icebergs_driver_nml
-  !ni=45 !30 !number of elements, x direction
-  !nj=45 !30 !number of elements, y direction
-  a68_test=.true.
-  vert_int_ocean_vel=.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  tau_is_velocity=.false.
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=720 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=999999999 !max number of timesteps
-  saverestart=.false.
-  halo=4
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=0 !206 !326 !206 !206 for dec09_1PM, 326 for dec14_1PM !0 for static
-/
-
-&icebergs_nml
-
-    Rearth=6.378e6
-    tau_is_velocity=.true.
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=1e6!1e7!34000.0 !4471.938678723104 !1000.0
-    spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=200!75!150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-6!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e4!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=25 !25.!200.0
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1000000.0
-    frac_thres_n = 20000.0 !8000.0 !5575. !3000. !2.1e4 !12.
-    frac_thres_t = 6000.0 !4000.0 !5575. !1750. !35000. !12.
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=4 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=4 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=2 !12 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/a68/restart_for_nco.py b/tests/a68/restart_for_nco.py
deleted file mode 100755
index a8bea5f..0000000
--- a/tests/a68/restart_for_nco.py
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env python
-
-import xarray as xr
-fname='./square_for_restart_od17.8_ydn.1.nc'
-test=xr.load_dataset(fname,decode_timedelta=False,decode_times=False)
-test2=test.copy()
-test2=test2.where(test2.day<test2.day.max(),drop=True)
-test2.to_netcdf('./square_for_restart_od17.8_ydn.1_without_last_ts.nc', format='NETCDF3_CLASSIC')
-
-
-# import xarray as xr
-# fname='./sq_ssf_ssg1.e4_od17.8_addsm.true._rectx-37.5285_y-55.2166_n23_t10.nc'
-# test=xr.load_dataset(fname,decode_timedelta=False,decode_times=False)
-# test2=test.copy()
-# test2=test2.where(test2.day<test2.day.max(),drop=True)
-# test2.to_netcdf('./sq_ssf_ssg1.e4_od17.8_addsm.true._rectx-37.5285_y-55.2166_n23_t10_without_last_ts.nc', format='NETCDF3_CLASSIC')
-
-
-# ncrcat square_for_restart_od17.8_ydn.1_without_last_ts.nc sq_ssf_ssg1.e4_od17.8_addsm.true._rectx-37.5285_y-55.2166_n23_t10_without_last_ts.nc sq_ssf_ssg1.e4_od17.8_addsm.true._rectx-37.5285_y-55.2166_n23_t10_full2.nc
diff --git a/tests/a68/save_input.nml b/tests/a68/save_input.nml
deleted file mode 100644
index c862a41..0000000
--- a/tests/a68/save_input.nml
+++ /dev/null
@@ -1,192 +0,0 @@
-
-&icebergs_driver_nml
-  !ni=45 !30 !number of elements, x direction
-  !nj=45 !30 !number of elements, y direction
-  a68_test=.true.
-  vert_int_ocean_vel=.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  ibdt=1800.0 !seconds
-  !ibuo=0.1 !ocean x velocity
-  !ibvo=0.0 !ocean y velocity
-  !ibui=0.0 !ice x velocity
-  !ibvi=0.0 !ice y velocity
-  ibhrs=720 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=999999999 !max number of timesteps
-  saverestart=.true.
-  halo=3
-  debug=.true.
-/
-
-&icebergs_nml
-
-    tau_is_velocity=.true.
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=1e7!34000.0 !4471.938678723104 !1000.0
-    spring_coef=1.e-4 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=100 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
-    
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e5!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=10. !50.!200.0
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1.
-    frac_thres_n = 4000. !3000. !2.1e4 !12.
-    frac_thres_t = 2000. !1750. !35000. !12.
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=4 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=1 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/a68/square_for_restart.nml b/tests/a68/square_for_restart.nml
deleted file mode 100644
index 5462787..0000000
--- a/tests/a68/square_for_restart.nml
+++ /dev/null
@@ -1,210 +0,0 @@
-&icebergs_driver_nml
-  a68_test=.true.
-  vert_int_ocean_vel=.false.!.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  Old_wrong_Rearth_and_SSH=.false.
-  !mom_Rearth=.false.
-  !Rearth=6363827
-  Rearth=6.378e6
-  no_wind=.false.
-  tau_is_velocity=.true.!.false.
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=298 !max number of timesteps
-  saverestart=.true. !.false. !.true. !.false.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=206 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
-/
-
-&icebergs_nml
-
-    !Rearth=6363827 !6.378e6 !6.371229e6 !6.36e6 !6.378e6
-    Rearth=6.378e6
-    A68_test=.false.
-    tau_is_velocity=.true.!.false.
-    ocean_drag_scale=15 !<od> !20. !1
-
-    add_curl_to_torque=.false.
-
-    constant_interaction_LW=.true.
-
-    traj_name='square_for_restart.nc' !<name>
-    bond_traj_name='square_for_restart_bonds.nc'
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
-    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=200 !75 !75 !150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=0.!1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=30!15!50. !15.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='none' !'stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1
-    frac_thres_n = 25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
-    frac_thres_t = 11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=4 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.true. !.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='SQUARE_INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.false. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
\ No newline at end of file
diff --git a/tests/a68/square_for_restart_od_17.8_ydn.1.nml b/tests/a68/square_for_restart_od_17.8_ydn.1.nml
deleted file mode 100644
index 2770143..0000000
--- a/tests/a68/square_for_restart_od_17.8_ydn.1.nml
+++ /dev/null
@@ -1,211 +0,0 @@
-&icebergs_driver_nml
-  a68_test=.true.
-  vert_int_ocean_vel=.false.!.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  Old_wrong_Rearth_and_SSH=.false.
-  !mom_Rearth=.false.
-  Rearth=6363827
-  no_wind=.false.
-  tau_is_velocity=.true.!.false.
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=298 !max number of timesteps
-  saverestart=.true. !.false. !.true. !.false.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=206 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
-/
-
-&icebergs_nml
-
-    Rearth=6363827
-    A68_test=.true.
-    short_step_mts_grounding=.true.
-    
-    tau_is_velocity=.true.
-    ocean_drag_scale=17.8 !19.5 !<od>
-
-    skip_first_outer_mts_step=.true.
-    add_curl_to_torque=.false.
-
-    constant_interaction_LW=.true.
-
-    traj_name='square_for_restart_od17.8_ydn.1.nc' !<name>
-    bond_traj_name='square_for_restart_od17.8_ydn.1_bonds.nc'
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
-    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=200 !75 !75 !150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-4 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=0.!1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=0!30!15!50. !15.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 10000000
-    frac_thres_n = 25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
-    frac_thres_t = 11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=4 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.true. !.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.false. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
\ No newline at end of file
diff --git a/tests/a68/square_for_restart_od_17.8_ydn.1_ss90.nml b/tests/a68/square_for_restart_od_17.8_ydn.1_ss90.nml
deleted file mode 100644
index 87d92bd..0000000
--- a/tests/a68/square_for_restart_od_17.8_ydn.1_ss90.nml
+++ /dev/null
@@ -1,211 +0,0 @@
-&icebergs_driver_nml
-  a68_test=.true.
-  vert_int_ocean_vel=.false.!.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  Old_wrong_Rearth_and_SSH=.false.
-  !mom_Rearth=.false.
-  Rearth=6363827
-  no_wind=.false.
-  tau_is_velocity=.true.!.false.
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=298 !max number of timesteps
-  saverestart=.true. !.false. !.true. !.false.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=206 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
-/
-
-&icebergs_nml
-
-    Rearth=6363827
-    A68_test=.true.
-    short_step_mts_grounding=.true.
-    
-    tau_is_velocity=.true.
-    ocean_drag_scale=17.8 !19.5 !<od>
-
-    skip_first_outer_mts_step=.true.
-    add_curl_to_torque=.false.
-
-    constant_interaction_LW=.true.
-
-    traj_name='square_for_restart_od17.8_ydn.1_ss90.nc' !<name>
-    bond_traj_name='square_for_restart_od17.8_ydn.1_bonds.nc'
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
-    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=90 !75 !75 !150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-4 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=0.!1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=0!30!15!50. !15.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 10000000
-    frac_thres_n = 25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
-    frac_thres_t = 11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=4 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=0 !12 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !.true. !.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.false. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
\ No newline at end of file
diff --git a/tests/a68/square_for_restart_od_19.5_tn_ng_ydn.05.nml b/tests/a68/square_for_restart_od_19.5_tn_ng_ydn.05.nml
deleted file mode 100644
index 115c931..0000000
--- a/tests/a68/square_for_restart_od_19.5_tn_ng_ydn.05.nml
+++ /dev/null
@@ -1,211 +0,0 @@
-&icebergs_driver_nml
-  a68_test=.true.
-  vert_int_ocean_vel=.false.!.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  Old_wrong_Rearth_and_SSH=.false.
-  !mom_Rearth=.false.
-  Rearth=6363827
-  no_wind=.false.
-  tau_is_velocity=.true.!.false.
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=298 !max number of timesteps
-  saverestart=.true. !.false. !.true. !.false.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=206 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
-/
-
-&icebergs_nml
-
-    Rearth=6363827
-    A68_test=.true.
-    short_step_mts_grounding=.true.
-    
-    tau_is_velocity=.true.
-    ocean_drag_scale=19.5 !<od>
-
-    skip_first_outer_mts_step=.true.
-    add_curl_to_torque=.false.
-
-    constant_interaction_LW=.true.
-
-    traj_name='square_for_restart_od19.5_ydn.05.nc' !<name>
-    bond_traj_name='square_for_restart_od19.5_ydn.05_bonds.nc'
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
-    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=200 !75 !75 !150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-4 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=0.!1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=0!30!15!50. !15.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 10000000
-    frac_thres_n = 25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
-    frac_thres_t = 11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=4 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.true. !.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.false. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
\ No newline at end of file
diff --git a/tests/a68/square_for_restart_od_21.25_tn_ng_noyd.nml b/tests/a68/square_for_restart_od_21.25_tn_ng_noyd.nml
deleted file mode 100644
index 6a32b9a..0000000
--- a/tests/a68/square_for_restart_od_21.25_tn_ng_noyd.nml
+++ /dev/null
@@ -1,211 +0,0 @@
-&icebergs_driver_nml
-  a68_test=.true.
-  vert_int_ocean_vel=.false.!.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  Old_wrong_Rearth_and_SSH=.false.
-  !mom_Rearth=.false.
-  Rearth=6363827
-  no_wind=.false.
-  tau_is_velocity=.true.!.false.
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=297 !8 !max number of timesteps
-  saverestart=.true. !.false. !.true. !.false.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=206 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
-/
-
-&icebergs_nml
-
-    Rearth=6363827
-    A68_test=.true.
-    short_step_mts_grounding=.true.
-    
-    tau_is_velocity=.true.
-    ocean_drag_scale=21.25 !<od>
-
-    skip_first_outer_mts_step=.true.
-    add_curl_to_torque=.false.
-
-    constant_interaction_LW=.true.
-
-    traj_name='square_for_restart_od21.25.nc' !<name>
-    bond_traj_name='square_for_restart_bonds_od21.25.nc'
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
-    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=200 !75 !75 !150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-4 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=0.!1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=0!30!15!50. !15.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 10000000
-    frac_thres_n = 25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
-    frac_thres_t = 11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=4 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.true. !.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.false. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
\ No newline at end of file
diff --git a/tests/a68/square_r_lsf.nml b/tests/a68/square_r_lsf.nml
deleted file mode 100644
index c0ceaac..0000000
--- a/tests/a68/square_r_lsf.nml
+++ /dev/null
@@ -1,215 +0,0 @@
-&icebergs_driver_nml
-  a68_test=.true.
-  vert_int_ocean_vel=.false.!.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  Old_wrong_Rearth_and_SSH=.false.
-  !mom_Rearth=.false.
-  !Rearth=6363827
-  Rearth=<rad>
-  !6.378e6
-  no_wind=.false.
-  tau_is_velocity=.true.!.false.
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=120 !360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=999999999 !max number of timesteps
-  saverestart=.false. !.true. !.false.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=355 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
-/
-
-&icebergs_nml
-
-    Rearth=<rad> !6.378e6
-    A68_test=<a68> !.false.
-    A68_xdisp=<xd>
-    A68_ydisp=<yd>
-    tau_is_velocity=.true.!.false.
-    ocean_drag_scale=<od> !15
-
-    add_curl_to_torque=.false.
-
-    constant_interaction_LW=.true.
-
-    traj_name=sq_lsf_g<gc>_addsm<a68>_<xdw>_<ydw>_od<od>_n<ns>t<ts>.nc
-    !<name>
-    !bond_traj_name=<bname>
-    
-    no_frac_first_ts=.true.
-    break_bonds_on_sub_steps=.false. !.true.
-    
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
-    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=<ss> !75 !75 !150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-4 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=<gc>!1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=0!15!50. !15.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1
-    frac_thres_n = <ns>e3
-    !75000.0
-    frac_thres_t = <ts>e3
-    !28000.
-
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=4 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='S_<od>_r/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.false. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
\ No newline at end of file
diff --git a/tests/a68/square_r_lsf_comp.nml b/tests/a68/square_r_lsf_comp.nml
deleted file mode 100644
index c273f5b..0000000
--- a/tests/a68/square_r_lsf_comp.nml
+++ /dev/null
@@ -1,208 +0,0 @@
-&icebergs_driver_nml
-  a68_test=.true.
-  vert_int_ocean_vel=.false.!.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  Old_wrong_Rearth_and_SSH=.false.
-  Rearth=<rad>
-  no_wind=.false.
-  tau_is_velocity=.true.!.false.
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=120 !360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=999999999 !max number of timesteps
-  saverestart=.false. !.true. !.false.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=355 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
-/
-
-&icebergs_nml
-
-    Rearth=<rad> !6.378e6
-    A68_test=.false.
-    A68_xdisp=<xd>
-    A68_ydisp=<yd>
-    tau_is_velocity=.true.!.false.
-    ocean_drag_scale=<od> !15
-
-    add_curl_to_torque=.false.
-
-    constant_interaction_LW=.true.
-
-    traj_name=<name>
-    !bond_traj_name=<bname>
-    
-    no_frac_first_ts=.true.
-    break_bonds_on_sub_steps=.false. !.true.
-    
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
-    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=<ss> !75 !75 !150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-4 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=6.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=<gc>!1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=0!15!50. !15.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='computed' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1
-    frac_thres_n = <ns>
-    frac_thres_t = <ts>
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=4 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='S_<od>_r/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.false. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
\ No newline at end of file
diff --git a/tests/a68/square_r_ssf.nml b/tests/a68/square_r_ssf.nml
deleted file mode 100644
index b51894c..0000000
--- a/tests/a68/square_r_ssf.nml
+++ /dev/null
@@ -1,212 +0,0 @@
-&icebergs_driver_nml
-  a68_test=.true.
-  vert_int_ocean_vel=.false.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  Old_wrong_Rearth_and_SSH=.false.
-  Rearth=<rad>
-  no_wind=.false.
-  tau_is_velocity=.true.!.false.
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=240 !360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=999999999 !max number of timesteps
-  saverestart=.false. !.true. !.false.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=355 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
-/
-
-&icebergs_nml
-    Rearth=<rad>
-    A68_test=<a68>
-    A68_xdisp=<xd>
-    A68_ydisp=<yd>
-    tau_is_velocity=.true.
-    ocean_drag_scale=<od>
-    short_step_mts_grounding=.true.
-
-    add_curl_to_torque=.false.
-
-    constant_interaction_LW=.true.
-
-    !traj_name=sq_ssf_ssg<gc>_od<od>_addsm<a68>_rectx<xd>_y<yd>_n<ns>_t<ts>.nc
-    traj_name=sq_ssfg_gc<gc>_od<od>_rx<xd>_y<yd>_n<ns>_t<ts>_ss<ss>.nc
-    !bond_traj_name=<bname>
-
-    no_frac_first_ts=.true.
-    break_bonds_on_sub_steps=.true.
-    power_ground=<pg>
-
-    save_bond_forces=.true.
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
-    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=<ss> !75 !75 !150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-4 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=<gc>!1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=0!15!50. !15.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1
-    frac_thres_n = <ns>e3
-    frac_thres_t = <ts>e3
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=4 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.false.!.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.false.!.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.false.!.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='<rdir>/' !'S_17.8_ydn.1_r/' !'S_19.5_ydn.05_r/' !'S_<od>_r/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.false. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
\ No newline at end of file
diff --git a/tests/a68/tau_is.nml b/tests/a68/tau_is.nml
deleted file mode 100644
index 8a98758..0000000
--- a/tests/a68/tau_is.nml
+++ /dev/null
@@ -1,197 +0,0 @@
-&icebergs_driver_nml
-  a68_test=.true.
-  vert_int_ocean_vel=.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  Old_wrong_Rearth_and_SSH=.false.
-  tau_is_velocity=.true.!.false.!.true.!.false.
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=720 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=400 !999999999 !max number of timesteps
-  saverestart=.false.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=0 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326
-/
-
-&icebergs_nml
-
-    Rearth=6.371229e6 !6.36e6 !6.378e6
-    tau_is_velocity=.true.!.false.!.true.!.false.
-
-    add_curl_to_torque=.false.!.true.
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=1e6!1e7!34000.0 !4471.938678723104 !1000.0
-    spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=75 !75 !150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=50. !15.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1.0 !1.0
-    frac_thres_n = 6000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
-    frac_thres_t = 2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=4 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
\ No newline at end of file
diff --git a/tests/a68/test1.nml b/tests/a68/test1.nml
deleted file mode 100644
index 96446d8..0000000
--- a/tests/a68/test1.nml
+++ /dev/null
@@ -1,194 +0,0 @@
-
-&icebergs_driver_nml
-  !ni=45 !30 !number of elements, x direction
-  !nj=45 !30 !number of elements, y direction
-  a68_test=.true.
-  vert_int_ocean_vel=.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  ibdt=1800.0 !seconds
-  !ibuo=0.1 !ocean x velocity
-  !ibvo=0.0 !ocean y velocity
-  !ibui=0.0 !ice x velocity
-  !ibvi=0.0 !ice y velocity
-  ibhrs=720 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=999999999 !max number of timesteps
-  saverestart=.false.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-/
-
-&icebergs_nml
-
-    tau_is_velocity=.true.
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=1e6!1e7!34000.0 !4471.938678723104 !1000.0
-    spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=75!150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-    
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=25.!200.0
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1.
-    frac_thres_n = 12000. !3000. !2.1e4 !12.
-    frac_thres_t = 3000. !1750. !35000. !12.
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=4 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=1 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/a68/test2.nml b/tests/a68/test2.nml
deleted file mode 100644
index 838de5a..0000000
--- a/tests/a68/test2.nml
+++ /dev/null
@@ -1,196 +0,0 @@
-!probably used an initial -uvel=0.18 -vvel=-0.23
-
-!./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_14_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_thickness=False -plot_ice_mask=False -plot_icebergs_positions=True -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -uvel=0.18 -vvel=-0.23 -R_earth=6360000
-&icebergs_driver_nml
-  !ni=45 !30 !number of elements, x direction
-  !nj=45 !30 !number of elements, y direction
-  a68_test=.true.
-  vert_int_ocean_vel=.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  ibdt=1800.0 !seconds
-  !ibuo=0.1 !ocean x velocity
-  !ibvo=0.0 !ocean y velocity
-  !ibui=0.0 !ice x velocity
-  !ibvi=0.0 !ice y velocity
-  ibhrs=720 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=999999999 !max number of timesteps
-  saverestart=.false.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-/
-
-&icebergs_nml
-
-    tau_is_velocity=.true.
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=1e6!1e7!34000.0 !4471.938678723104 !1000.0
-    spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=75!150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-    
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=25 !35!25.!200.0
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1.
-    frac_thres_n = 6000. !3000. !2.1e4 !12.
-    frac_thres_t = 2500. !1750. !35000. !12.
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=4 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=24 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/a68/test2_updated.nml b/tests/a68/test2_updated.nml
deleted file mode 100644
index 1cd6474..0000000
--- a/tests/a68/test2_updated.nml
+++ /dev/null
@@ -1,201 +0,0 @@
-#./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_14_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_thickness=False -plot_ice_mask=False -plot_icebergs_positions=True -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -uvel=0.18 -vvel=-0.23 -R_earth=6360000
-
-&icebergs_driver_nml
-  !ni=45 !30 !number of elements, x direction
-  !nj=45 !30 !number of elements, y direction
-  a68_test=.true.
-  vert_int_ocean_vel=.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  Old_wrong_Rearth_and_SSH=.true.
-  tau_is_velocity=.true.!.false.
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=720 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=400 !999999999 !max number of timesteps
-  saverestart=.false.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=0!305 !0 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326 !0 for static
-/
-
-&icebergs_nml
-
-    Rearth=6.36e6 !6.378e6
-    tau_is_velocity=.true.!.false.
-
-    add_curl_to_torque=.false.!.true.
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=1e6!1e7!34000.0 !4471.938678723104 !1000.0
-    spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=75 !150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=25.!200.0
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1.0
-    frac_thres_n = 6000. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
-    frac_thres_t = 2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=4 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/a68/test3.nml b/tests/a68/test3.nml
deleted file mode 100644
index 4878421..0000000
--- a/tests/a68/test3.nml
+++ /dev/null
@@ -1,198 +0,0 @@
-!this test used the transient jra, but not the transient oscar surf vel data
-!./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_14_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=True -plot_circles=True -plot_h_ice_new=True -plot_ice_thickness=False -plot_ice_mask=False -plot_icebergs_positions=True -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -uvel=0.24 -vvel=-0.08
-
-&icebergs_driver_nml
-  !ni=45 !30 !number of elements, x direction
-  !nj=45 !30 !number of elements, y direction
-  a68_test=.true.
-  vert_int_ocean_vel=.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  tau_is_velocity=.true.
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=720 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=999999999 !max number of timesteps
-  saverestart=.false.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=326!206 !206 for dec09_1PM, 326 for dec14_1PM
-/
-
-&icebergs_nml
-
-    tau_is_velocity=.true.
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=1e6!1e7!34000.0 !4471.938678723104 !1000.0
-    spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=100!75!150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-6!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=25 !25.!200.0
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1.0
-    frac_thres_n = 8000.0 !8000.0 !5575. !3000. !2.1e4 !12.
-    frac_thres_t = 2500.0 !4000.0 !5575. !1750. !35000. !12.
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false.!.true. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0!-56. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=4 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=12 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/a68/test4_curl.nml b/tests/a68/test4_curl.nml
deleted file mode 100644
index bd67b9a..0000000
--- a/tests/a68/test4_curl.nml
+++ /dev/null
@@ -1,199 +0,0 @@
-
-&icebergs_driver_nml
-  !ni=45 !30 !number of elements, x direction
-  !nj=45 !30 !number of elements, y direction
-  a68_test=.true.
-  vert_int_ocean_vel=.false.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  tau_is_velocity=.true.!.false.
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=720 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=400 !999999999 !max number of timesteps
-  saverestart=.false.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=305 !0 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326 !0 for static
-/
-
-&icebergs_nml
-
-    Rearth=6.378e6
-    tau_is_velocity=.true.!.false.
-
-    add_curl_to_torque=.true.!.false.!.true.
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=0.5e7!1e7!34000.0 !4471.938678723104 !1000.0
-    spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=100 !75 !150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-6!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=25.!200.0
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1.0
-    frac_thres_n = 12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
-    frac_thres_t = 6000.0 !4000.0 !5575. !1750. !35000. !12.
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=4 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/a68/test_new.nml b/tests/a68/test_new.nml
deleted file mode 100644
index 48da578..0000000
--- a/tests/a68/test_new.nml
+++ /dev/null
@@ -1,204 +0,0 @@
-!./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_14a_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_thickness=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -R_earth=6.371229e6 -lat_ref_grid_to_cartesian=-55.8 -uvel=0.2 -vvel=-0.2 !
-
-!in makeberg.py
-!if ice_mask[j_val,i_val]>0.5:#99:
-!                it_is_ice=True
-!dx=250.
-
-&icebergs_driver_nml
-  a68_test=.true.
-  vert_int_ocean_vel=.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  Old_wrong_Rearth_and_SSH=.false.
-  tau_is_velocity=.false.!.true.!.false.
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=720 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=400 !999999999 !max number of timesteps
-  saverestart=.false.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=0 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326
-/
-
-&icebergs_nml
-
-    Rearth=6.371229e6 !6.36e6 !6.378e6
-    tau_is_velocity=.false.!.true.!.false.
-
-    add_curl_to_torque=.false.!.true.
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=1e6!1e7!34000.0 !4471.938678723104 !1000.0
-    spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=75 !75 !150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=15.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1.0 !1.0
-    frac_thres_n = 6000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
-    frac_thres_t = 2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=4 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
\ No newline at end of file
diff --git a/tests/a68/test_new2.nml b/tests/a68/test_new2.nml
deleted file mode 100644
index b801bfe..0000000
--- a/tests/a68/test_new2.nml
+++ /dev/null
@@ -1,204 +0,0 @@
-!./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_14a_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_thickness=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=True -Radius=1500 -R_earth=6.371229e6 -lat_ref_grid_to_cartesian=-55.8 -uvel=0.2 -vvel=-0.2
-
-&icebergs_driver_nml
-  a68_test=.true.
-  vert_int_ocean_vel=.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  Old_wrong_Rearth_and_SSH=.false.
-  tau_is_velocity=.false. !.true.!.false.
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=360 !15 days !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=400 !999999999 !max number of timesteps
-  saverestart=.false.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=0!330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
-/
-
-&icebergs_nml
-
-    Rearth=6.371229e6 !6.36e6 !6.378e6
-    tau_is_velocity=.false.!.true.!.false.
-
-    add_curl_to_torque=.false.
-
-    constant_interaction_LW=.true.
-
-    !traj_name="traj_p5e7.nc"
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=1e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
-    !spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=75 !75 !150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-2 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=15!50. !15.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1.0
-    frac_thres_n = 4750.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
-    frac_thres_t = 2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=4 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.false. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
\ No newline at end of file
diff --git a/tests/a68/test_no_bonds.nml b/tests/a68/test_no_bonds.nml
deleted file mode 100644
index 762d2c1..0000000
--- a/tests/a68/test_no_bonds.nml
+++ /dev/null
@@ -1,211 +0,0 @@
-&icebergs_driver_nml
-  a68_test=.true.
-  vert_int_ocean_vel=.false.!.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
-  Old_wrong_Rearth_and_SSH=.false.
-  !mom_Rearth=.false.
-  Rearth=6363827
-  no_wind=.false.
-  tau_is_velocity=.true.!.false.
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=432 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=999999 !max number of timesteps
-  saverestart=.false.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=206 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
-/
-
-&icebergs_nml
-
-    Rearth=6363827
-    A68_test=.true.
-    short_step_mts_grounding=.true.
-    
-    tau_is_velocity=.true.
-    ocean_drag_scale=17.8 !19.5 !<od>
-
-    skip_first_outer_mts_step=.true.
-    add_curl_to_torque=.false.
-
-    constant_interaction_LW=.true.
-
-    traj_name='test_no_bonds.nc' !<name>
-    !bond_traj_name='square_for_restart_od17.8_ydn.1_bonds.nc'
-
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=1.e-30 !5e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
-    spring_coef=1.e-30 !0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=200 !75 !75 !150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-4 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    contact_distance=0.1 !4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=0.!1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=0!30!15!50. !15.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 10000000
-    frac_thres_n = 25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
-    frac_thres_t = 11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
-
-    halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.false. !.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=4 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.false. !.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.false !.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.false. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
\ No newline at end of file
diff --git a/tests/a68_test/README b/tests/a68_test/README
new file mode 100644
index 0000000..f770f07
--- /dev/null
+++ b/tests/a68_test/README
@@ -0,0 +1,14 @@
+TO RUN THE EXPERIMENT IN THE PAPER:
+
+I. Make the iceberg input files:
+   cd makeberg; ./RUN_for_paper; cd ..
+
+II. Some quick processing of the hourly data
+   cd data; source recombine_nc.sh; cd ..
+   (note that the recombine_nc.sh requires cdo or nco -- edit it accordingly)
+
+III. The full run from the paper:
+   ./long_run_for_paper.sh
+
+IV. Animate the results:
+./animate_trajectories.py -fname=longrun_od_17.8_tn_ng_ydn.1_ss90_ns18_rx-37.51_ry-55.2166.nc
diff --git a/tests/a68/RUN1p b/tests/a68_test/RUN1p
similarity index 100%
rename from tests/a68/RUN1p
rename to tests/a68_test/RUN1p
diff --git a/tests/a68/animate_trajectories.py b/tests/a68_test/animate_trajectories.py
similarity index 99%
rename from tests/a68/animate_trajectories.py
rename to tests/a68_test/animate_trajectories.py
index 23497ef..2f4478e 100755
--- a/tests/a68/animate_trajectories.py
+++ b/tests/a68_test/animate_trajectories.py
@@ -260,6 +260,7 @@ def onClick(event):
         oscar=xr.load_dataset(f'{dir}/a68_experiment_ocean_surf_vel_oscar_dec2020_HOURLY_ll_p125.nc')
         #oscar.isel(time=400).plot.quiver(x="lon",y="lat",u="uo",v="vo",hue='vel',vmax=0.2, scale=8)
         vv=oscar.isel(time=400)
+        vv['vel']=np.sqrt(vv.uo*vv.uo+vv.vo*vv.vo)
         norm=plt.cm.colors.Normalize(vmin=0,vmax=0.35)
         if (old==False):
             ax1.quiver(vv.lon.values,vv.lat.values,vv.uo.values,vv.vo.values,vv.vel.values,scale=8,cmap='viridis',norm=norm,transform=ccrs.PlateCarree())
diff --git a/tests/a68_test/data/.gitignore b/tests/a68_test/data/.gitignore
new file mode 100644
index 0000000..e143a14
--- /dev/null
+++ b/tests/a68_test/data/.gitignore
@@ -0,0 +1,5 @@
+!*.nc
+a68_experiment_ocean_surf_vel_oscar_dec2020_HOURLY_ll_p125.nc
+a68_experiment_ssh_duacs_dec2020_HOURLY_ll_p125.nc
+a68_experiment_wind_vel_ncep_10m_dec2020_HOURLY_ll_p125.nc
+split_script.sh
\ No newline at end of file
diff --git a/tests/a68_test/data/recombine_nc.sh b/tests/a68_test/data/recombine_nc.sh
new file mode 100644
index 0000000..46e25ee
--- /dev/null
+++ b/tests/a68_test/data/recombine_nc.sh
@@ -0,0 +1,12 @@
+
+#using cdo
+cdo mergetime ./split_files/ocean*.nc a68_experiment_ocean_surf_vel_oscar_dec2020_HOURLY_ll_p125.nc
+cdo mergetime ./split_files/ssh*.nc a68_experiment_ssh_duacs_dec2020_HOURLY_ll_p125.nc
+cdo mergetime ./split_files/wind*.nc a68_experiment_wind_vel_ncep_10m_dec2020_HOURLY_ll_p125.nc
+
+#using ncrcat (nco)
+#ncrcat ./split_files/ocean00000?.nc a68_experiment_ocean_surf_vel_oscar_dec2020_HOURLY_ll_p125.nc
+#ncrcat ./split_files/ssh00000?.nc a68_experiment_ssh_duacs_dec2020_HOURLY_ll_p125.nc
+#ncrcat ./split_files/wind00000?.nc a68_experiment_wind_vel_ncep_10m_dec2020_HOURLY_ll_p125.nc
+
+ln -s a68_experiment_ocean_surf_vel_oscar_dec2020_HOURLY_ll_p125.nc ../../../postprocessing/data/a68_experiment_ocean_surf_vel_oscar_dec2020_HOURLY_ll_p125.nc
diff --git a/tests/a68/diag_table b/tests/a68_test/diag_table
similarity index 100%
rename from tests/a68/diag_table
rename to tests/a68_test/diag_table
diff --git a/tests/a68/input_fill2.nml b/tests/a68_test/input.nml
similarity index 83%
rename from tests/a68/input_fill2.nml
rename to tests/a68_test/input.nml
index ff6747d..5f38abe 100644
--- a/tests/a68/input_fill2.nml
+++ b/tests/a68_test/input.nml
@@ -1,10 +1,17 @@
+!! with short_step_mts_grounding=.true. :
+!! KID, bergs_chksum: write_restart berg chksum=2003283855 chksum2=-936278869 chksum3=399994109 chksum4=399994109 chksum5=0 #=472
+
+!! without short_step_mts_grounding=.true :
+
+
 &icebergs_driver_nml
   a68_test=.true.
   vert_int_ocean_vel=.false.!.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  !specify your data dir (ocean currents, winds, etc)
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68_test/data/'
   Old_wrong_Rearth_and_SSH=.false.
   !mom_Rearth=.true.
-  Rearth=<re>
+  Rearth=6363827
   !6363827 !6.378e6
   no_wind=.false.
   tau_is_velocity=.true.!.false.
@@ -13,10 +20,10 @@
   ibvo=0.0 !ocean y velocity
   ibui=0.0 !ice x velocity
   ibvi=0.0 !ice y velocity
-  ibhrs=432 !360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  ibhrs=432 !total simulation hours
   write_time_inc = 48 !increment at which time is written to screen
   nmax=999999999 !max number of timesteps
-  saverestart=.false.
+  saverestart=.true.!.false.
   halo=3
   debug=.true.
   reverse_a68_forcings=.false.
@@ -25,21 +32,28 @@
 
 &icebergs_nml
 
-    Rearth=<re>
-    !6363827 !6.378e6 !6.371229e6 !6.36e6 !6.378e6
+    Rearth=6363827
+
     A68_test=.true.
+    A68_xdisp=-37.51
+    A68_ydisp=-55.2166
     short_step_mts_grounding=.true.
 
-    tau_is_velocity=.true.!.false.
-    ocean_drag_scale=<od> !20. !1
+    tau_is_velocity=.true.
+    ocean_drag_scale=17.8
 
     skip_first_outer_mts_step=.true.
-    add_curl_to_torque=.false.
 
     constant_interaction_LW=.true.
 
-    traj_name=<name>
+    traj_name=longrun_od_17.8_tn_ng_ydn.1_ss90_ns18_rx-37.51_ry-55.2166.nc
+    bond_traj_name=longrun_od_17.8_tn_ng_ydn.1_ss90_ns18_rx-37.51_ry-55.2166_bonds.nc
 
+    break_bonds_on_sub_steps=.true.
+
+    save_bond_forces=.true.
+    use_broken_bonds_for_substep_contact=.true.
+    
     dem=.true.
     poisson=0.3
     dem_damping_coef=1.0
@@ -50,39 +64,37 @@
     !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
     !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
     !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
-    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
+    dem_spring_coef=5e6 !Young's Modulus
+
+    !As coded, the short-step contact model is the same as the long-step contact, but really
+    !we want the short-step contact model to be the same as the short-step bonded-interaction model
+    !for A68a, which is accomplished by setting this short-step spring constant as follows:
+    !(TODO: replace the short-step contact model to be the same as the short-step bonded interactions?)
+    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500, with square packing
 
     monitor_energy=.false.
     !defaults given in parentheses:
     new_mts=.true.
     mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=<ss> !200 !75 !75 !150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
+    mts_sub_steps=90 !# of mts sub-steps
     force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-4 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+    convergence_tolerance=1e-4 ! tolerance for the MTS force_convergence scheme
 
     contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
     contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
     debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=0.!1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
+    cdrag_grounding=1.e4 !0.!1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
     h_to_init_grounding=0!30!15!50. !15.
     ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
     remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
 
     fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 10000000
-    frac_thres_n = 25000.0 !5000.0 !4250. !12000.0 !8000.0 !5575. !3000. !2.1e4 !12.
-    frac_thres_t = 11000. !2000.0 !2500. !6000.0 !4000.0 !5575. !1750. !35000. !12.
-
-    !!fracture_criterion='strain'
-    !!frac_thres_n = 0.0162
-    !!frac_thres_t = 0.0457
+    frac_thres_scaling = 1
+    frac_thres_n = 18e3
+    frac_thres_t = 100e3
 
     halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    Lx=360 !(360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
     grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
     grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
     hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
@@ -116,11 +128,11 @@
     coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
     tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
     Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    use_mixed_melting=.true. !(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
     apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
     apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
     melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    allow_bergs_to_roll=.true. ! (T) Allows bergs toroll over when rolling conditions are met
     use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
     pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
     use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
@@ -145,9 +157,9 @@
     internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
 
     verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !0!6 !(24) sampling period for trajectory storage
-    traj_write_hrs=6 !12 !0!6 !(480) Period for writing sampled trajectories to disk
+    verbose_hrs=1! (24) Period between verbose messages
+    traj_sample_hrs=0!1 !(24) sampling period for trajectory storage
+    traj_write_hrs=0!6 !(480) Period for writing sampled trajectories to disk
     save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
     budget=.false. !(T) Calculate budgets
     debug=.false. !(F) Turn on debugging
diff --git a/tests/a68/long_run.nml b/tests/a68_test/long_run.nml
similarity index 89%
rename from tests/a68/long_run.nml
rename to tests/a68_test/long_run.nml
index e85f80a..9632450 100644
--- a/tests/a68/long_run.nml
+++ b/tests/a68_test/long_run.nml
@@ -1,7 +1,11 @@
+!! using either short_step_mts_grounding=.true. or .false. gives identical chksum here:
+!! KID, bergs_chksum: write_restart berg chksum=2003283855 chksum2=-936278869 chksum3=399994109 chksum4=399994109 chksum5=0 #=472
+
 &icebergs_driver_nml
   a68_test=.true.
   vert_int_ocean_vel=.false.!.true.
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68/data/'
+  !specify your data dir (ocean currents, winds, etc)
+  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68_test/data/'
   Old_wrong_Rearth_and_SSH=.false.
   !mom_Rearth=.true.
   Rearth=<re>
@@ -13,10 +17,10 @@
   ibvo=0.0 !ocean y velocity
   ibui=0.0 !ice x velocity
   ibvi=0.0 !ice y velocity
-  ibhrs=432 !360 !480 !20 days !1440 !960 !total simulation hours (60 !40 days)
+  ibhrs=432 !total simulation hours
   write_time_inc = 48 !increment at which time is written to screen
   nmax=999999999 !max number of timesteps
-  saverestart=.false.
+  saverestart=.true.!.false.
   halo=3
   debug=.true.
   reverse_a68_forcings=.false.
@@ -36,7 +40,6 @@
     ocean_drag_scale=<od>
 
     skip_first_outer_mts_step=.true.
-    add_curl_to_torque=.false.
 
     constant_interaction_LW=.true.
 
@@ -45,9 +48,8 @@
 
     break_bonds_on_sub_steps=.true.
 
-    power_ground=.false.
-
     save_bond_forces=.true.
+    use_broken_bonds_for_substep_contact=.true.
 
     dem=.true.
     poisson=0.3
@@ -59,19 +61,21 @@
     !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
     !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
     !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=5e6 !1e7!34000.0 !4471.938678723104 !1000.0
-    !spring_coef=1.e-6 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    !spring_coef=0.00013071895424836603!if dem_spring_coef=1e6 and r=1500?
-    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500?
+    dem_spring_coef=5e6 !Young's Modulus
+
+    !As coded, the short-step contact model is the same as the long-step contact, but really
+    !we want the short-step contact model to be the same as the short-step bonded-interaction model
+    !for A68a, which is accomplished by setting this short-step spring constant as follows:
+    !(TODO: replace the short-step contact model to be the same as the short-step bonded interactions?)
+    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500, with square packing
 
     monitor_energy=.false.
     !defaults given in parentheses:
     new_mts=.true.
     mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=<ss> !200 !75 !75 !150 !50 !(-1) # of mts sub-steps
-    !mts_sub_steps=10
+    mts_sub_steps=<ss> !# of mts sub-steps
     force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-4 !8 !(1.e-8) tolerance for the MTS force_convergence scheme
+    convergence_tolerance=1e-4 ! tolerance for the MTS force_convergence scheme
 
     contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
     contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
@@ -87,7 +91,7 @@
     frac_thres_t = 100e3
 
     halo=3 !(4) halo width
-    Lx=360 !28.875!45000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    Lx=360 !(360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
     grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
     grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
     hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
@@ -121,11 +125,11 @@
     coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
     tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
     Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.true. !.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    use_mixed_melting=.true. !(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
     apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
     apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
     melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    allow_bergs_to_roll=.true. ! (T) Allows bergs toroll over when rolling conditions are met
     use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
     pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
     use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
@@ -150,7 +154,7 @@
     internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
 
     verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1!24000 ! (24) Period between verbose messages
+    verbose_hrs=1! (24) Period between verbose messages
     traj_sample_hrs=0!1 !(24) sampling period for trajectory storage
     traj_write_hrs=0!6 !(480) Period for writing sampled trajectories to disk
     save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
diff --git a/tests/a68/long_run_for_paper.sh b/tests/a68_test/long_run_for_paper.sh
similarity index 100%
rename from tests/a68/long_run_for_paper.sh
rename to tests/a68_test/long_run_for_paper.sh
diff --git a/tests/a68/makeberg/RUN_for_paper b/tests/a68_test/makeberg/RUN_for_paper
similarity index 87%
rename from tests/a68/makeberg/RUN_for_paper
rename to tests/a68_test/makeberg/RUN_for_paper
index 4e2be66..2cbc068 100755
--- a/tests/a68/makeberg/RUN_for_paper
+++ b/tests/a68_test/makeberg/RUN_for_paper
@@ -1,6 +1,6 @@
 rm ./output_files/Generic*
 
-# THIS IS THE BERG USED FOR AGU 2021 AND IN THE PAPER!!
+# THIS IS THE BERG USED IN HUTH ET AL, 2022 OCEAN CURRENTS BREAK UP A TABULAR ICEBERG. SCIENCE ADVANCES:
 ./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_09_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=False -Radius=1500 -lat_ref_grid_to_cartesian=-55.2 -uvel=0.22 -dx=500. -R_earth=6363827. -icethres=0.5 -displace_y=-0.1
 
 cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
diff --git a/tests/a68_test/makeberg/hexagon_area.py b/tests/a68_test/makeberg/hexagon_area.py
new file mode 100755
index 0000000..5db6cec
--- /dev/null
+++ b/tests/a68_test/makeberg/hexagon_area.py
@@ -0,0 +1,1458 @@
+#!/usr/bin/env python
+
+#First import the netcdf4 library
+from netCDF4 import Dataset  # http://code.google.com/p/netcdf4-python/
+import numpy as np  # http://code.google.com/p/netcdf4-python/
+import matplotlib
+import math
+import os
+matplotlib.use("tkagg")
+from pylab import *
+#import matplotlib.pyplot as plt
+import pdb
+import netCDF4 as nc
+
+
+
+#######################
+
+def Divide_hexagon_into_4_quadrants_old(x0,y0,H):
+	S=(2/sqrt(3))*H
+	Area_hex=3*(np.sqrt(3)/2)*(S**2)  #Area of the hexagon (should be equal to Area/grid_area, since it is not dim)	 - check this
+	#print 'y0,H',y0, H
+	#Defining boundaries of hexagon, and if statements to see which side of the boundary you are on
+	W1= False ; W2=False ;W3=False ;W4=False ;W5=False ;W6=False ;H1=False ;V1=False ;V2=False
+	W1=(-y0<-sqrt(3)*(-x0) + ((sqrt(3)*(S))));#upper right
+	W2=(-y0<(H));#Top
+	W3=(-y0<sqrt(3)*(-x0) + ((sqrt(3)*(S))));#Upper left
+	W4=(-y0<sqrt(3)*(-x0) + (-(sqrt(3)*(S))));#Lower right
+	W5=(-y0>-H);#Bottom
+	W6=(-y0<-sqrt(3)*(-x0) + (-(sqrt(3)*(S))));#Lower left
+
+
+	T1=(-x0<S) #Right
+	T2=(-y0<(H));#Top
+	T3= (-x0>-S) #Left
+	T4=(-y0>-H);#Bottom
+
+	H1=(y0<0);
+	V1=(x0<-(S/2));
+	V2=(x0<(S/2));
+
+	#Deciding if the origin is within the hexagon
+	#print W1 , W2 , W3 , W4 , W5 , W6
+	#if In_hex:
+	#	print In_hex
+
+	#Calculating the area of the top and bottom half of the hexagon, 2 Cases for the majority above and below the y0=0 line
+	#(and two more for the hexagon totally above and below the y0=0 line)
+	if abs(y0)<H:
+		Trapesium=((sqrt(3)*H)-(abs(y0)/sqrt(3)))*(H-abs(y0));
+		if y0>=0:
+			Area_Lower=Trapesium;
+			Area_Upper=Area_hex-Trapesium;
+		else:
+			Area_Upper=Trapesium;
+			Area_Lower=Area_hex-Trapesium;
+	else:
+		if y0>=0:
+			Area_Lower=0.;
+			Area_Upper=Area_hex;
+		else:
+			Area_Lower=Area_hex;
+			Area_Upper=0.;
+
+	#Calcularing Left and Right area of the hexagon, about the x0=0 line, 3 cases:
+	#(and two more for when the hexagon is totally to the left or right of the x0=0 line)
+	if abs(x0)<S:
+		if abs(x0)<S/2:
+			Rectangle=(abs(x0)*2*H);
+			Big_side =(Area_hex/2) +Rectangle;
+			Small_side=Area_hex-Big_side;
+		else:
+			Triangle=(sqrt(3))*((S-abs(x0))**2);
+			Small_side=Triangle;
+			Big_side=Area_hex-Small_side;
+		if x0>=0.:
+			Area_right=Big_side;
+			Area_left=Small_side;
+		else:
+			Area_right=Small_side;
+			Area_left=Big_side;
+	else:
+		if x0>=0.:
+			Area_right=Area_hex;
+			Area_left=0.;
+		else:
+			Area_right=0.;
+			Area_left=Area_hex;
+
+	In_hex= W1 & W2 & W3 & W4 & W5 & W6;
+	In_hex_box=T1 & T2 & T3 & T4
+	Area_Q1=0.; Area_Q2=0. ; Area_Q3=0.; Area_Q4=0.;
+	Sector=0
+	#if In_hex==False: #Then the hexagon is completely contained in the middle cell
+	if In_hex_box==False: #Then the hexagon is completely contained in the middle cell
+		Sector=-1
+		#mass_on_ocean[i,j,5]=mass_on_ocean[i,j,5]+Mass
+		if min(Area_Upper,Area_Lower)==0.:
+			Sector=-2
+			if Area_Upper==0.:
+				Area_Q3=Area_left;
+				Area_Q4=Area_right;
+			if Area_Lower==0.:
+				Area_Q1=Area_right;
+				Area_Q2=Area_left;
+
+		elif min(Area_right,Area_left)==0.:
+			Sector=-3
+			if Area_right==0.:
+				Area_Q2=Area_Upper;
+				Area_Q3=Area_Lower;
+
+			if Area_left==0.:
+				Area_Q1=Area_Upper;
+				Area_Q4=Area_Lower;
+
+
+		#yCxC=1.
+		#print 'out of hex'
+
+	else:
+		#Determine which sector within the hexagon you are in. (sectors 1 to 6 go counter clockwise starting with top right)
+		if (H1==True):	#Bottom half
+			if V1:
+				#if W1==False:
+				if ((y0+(sqrt(3)*(x0+S)))<=0.):
+					Sector=1;
+				else:
+					Sector=2;
+			elif (V1==False) & (V2==True):
+				Sector=3;
+			else:
+				#if (W3==True):
+				if ((y0-(sqrt(3)*(x0-S)))>=0.):
+					Sector=4;
+				else:
+					Sector=5;
+		else:  #Bottom half
+			if V1:
+				#if W6==False:
+				if ((y0 -(sqrt(3)*(x0+S)))>=0.):
+					Sector=10;
+				else:
+					Sector=9;
+			elif (V1==False) & (V2==True):
+				Sector=8;
+			else:
+				#if (W4==True):
+				if ((y0+(sqrt(3)*(x0-S)))<=0.):
+					Sector=7;
+				else:
+					Sector=6;
+
+		#print Sector
+
+		#If the hexagon is in Sector 1,3,4 or 6, then the intersetion of the hexagon and the corresponding sector forms a baby triangle
+		#If the hexagon is in Sector 2,5 then the intersetion of the hexagon and the corresponding sector forms a baby trapesoid
+		if Sector==2 or Sector==4  or Sector==7 or Sector==9:
+			Baby_triangle=(1/(2*sqrt(3)))*((-abs(y0)+(sqrt(3)*(S-abs(x0))))**2);
+		else:
+			#Baby_trap= (H-abs(y0)) * ((-H-abs(y0)+(2*sqrt(3)*(S-abs(x0))))/(2*sqrt(3)));
+			Baby_trap=(H-abs(y0))*((S-abs(x0) - ((H+abs(y0))/(2*sqrt(3))))) ;
+
+		#Finally, we assign the correct areas in each quadrant (Q1,Q2,Q3,Q4), depending on which sector you are in.
+		C1=0.;C2=0.;C3=0.;C4=0.;
+
+		#Corner cases
+		if Sector==2:
+			Area_Q1=Baby_triangle;
+			Area_Q2=Area_Upper-Area_Q1
+			Area_Q3=Area_left-Area_Q2
+			Area_Q4=Area_right-Area_Q1
+
+		if Sector==4:
+			Area_Q2=Baby_triangle;
+			Area_Q1=Area_Upper-Area_Q2
+			Area_Q3=Area_left-Area_Q2
+			Area_Q4=Area_right-Area_Q1
+
+		if Sector==7:
+			Area_Q3=Baby_triangle;
+			Area_Q2=Area_left-Area_Q3
+			Area_Q1=Area_Upper-Area_Q2
+			Area_Q4=Area_right-Area_Q1
+
+		if Sector==9:
+			Area_Q4=Baby_triangle;
+			Area_Q1=Area_right-Area_Q4
+			Area_Q2=Area_Upper-Area_Q1
+			Area_Q3=Area_left-Area_Q2
+
+		#Center cases
+		if Sector==3:
+			if x0<=0.:
+				Area_Q1=Baby_trap;
+				Area_Q2=Area_Upper-Area_Q1;
+				Area_Q3=Area_left-Area_Q2;
+				Area_Q4=Area_right-Area_Q1;
+			else:
+				Area_Q2=Baby_trap;
+				Area_Q1=Area_Upper-Area_Q2;
+				Area_Q3=Area_left-Area_Q2;
+				Area_Q4=Area_right-Area_Q1;
+
+		if Sector==8:
+			if x0<=0.:
+				Area_Q4=Baby_trap;
+				Area_Q3=Area_Lower-Area_Q4;
+				Area_Q1=Area_right-Area_Q4;
+				Area_Q2=Area_Upper-Area_Q1;
+			else:
+				Area_Q3=Baby_trap;
+				Area_Q4=Area_Lower-Area_Q3;
+				Area_Q1=Area_right-Area_Q4;
+				Area_Q2=Area_Upper-Area_Q1;
+
+		#Outside triangle cases:
+		if Sector==1:
+			Area_Q1=0.;
+			Area_Q2=Area_Upper;
+			Area_Q4=Area_right;
+			Area_Q3=Area_left-Area_Q2;
+
+		if Sector==5:
+			Area_Q2=0.;
+			Area_Q1=Area_Upper;
+			Area_Q3=Area_left;
+			Area_Q4=Area_Lower-Area_Q3;
+
+		if Sector==6:
+			Area_Q3=0.;
+			Area_Q2=Area_left;
+			Area_Q4=Area_Lower;
+			Area_Q1=Area_right-Area_Q4;
+
+		if Sector==10:
+			Area_Q4=0.;
+			Area_Q3=Area_Lower;
+			Area_Q1=Area_right;
+			Area_Q2=Area_left-Area_Q3;
+
+		#print x0,y0,Sector
+	return [Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4]
+
+
+
+def Hexagon_into_quadrants_using_triangles_across_lines(x0,y0,H,theta,	Px, Py, Qx, Qy, Rx, Ry, Sx, Sy ):
+	#In this routine, the hexagon is divided across lines PQ, RS.
+	#Length of side of Hexagon
+	S=(2/sqrt(3))*H;
+
+	#Finding positions of corners
+	C1x=S		; C1y=0.  #Corner 1 (right)
+	C2x=H/sqrt(3.)	; C2y=H;  #Corner 2 (top right)
+	C3x=-H/sqrt(3.) ; C3y=H;  #Corner 3 (top left)
+	C4x=-S		; C4y=0.; #Corner 4 (left)
+	C5x=-H/sqrt(3.) ; C5y=-H; #Corner 5 (bottom right)
+	C6x=H/sqrt(3.)	; C6y=-H; #Corner 6 (bottom right)
+
+	#Finding positions of corners
+	[C1x,C1y]=rotate_and_translate(C1x,C1y,theta,x0,y0)
+	[C2x,C2y]=rotate_and_translate(C2x,C2y,theta,x0,y0)
+	[C3x,C3y]=rotate_and_translate(C3x,C3y,theta,x0,y0)
+	[C4x,C4y]=rotate_and_translate(C4x,C4y,theta,x0,y0)
+	[C5x,C5y]=rotate_and_translate(C5x,C5y,theta,x0,y0)
+	[C6x,C6y]=rotate_and_translate(C6x,C6y,theta,x0,y0)
+
+	#Area of Hexagon is the sum of the triangles
+	[T12_Area,T12_Q1,T12_Q2,T12_Q3,T12_Q4]=Triangle_divided_into_four_parts(x0,y0,C1x,C1y,C2x,C2y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T012
+	[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]=Triangle_divided_into_four_parts(x0,y0,C2x,C2y,C3x,C3y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
+	[T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4]=Triangle_divided_into_four_parts(x0,y0,C3x,C3y,C4x,C4y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T034
+	[T45_Area,T45_Q1,T45_Q2,T45_Q3,T45_Q4]=Triangle_divided_into_four_parts(x0,y0,C4x,C4y,C5x,C5y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
+	[T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4]=Triangle_divided_into_four_parts(x0,y0,C5x,C5y,C6x,C6y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
+	[T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4]=Triangle_divided_into_four_parts(x0,y0,C6x,C6y,C1x,C1y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
+
+	#Area of Hexagon is the sum of the triangles
+	#print '1:', Triangle_divided_into_four_parts(x0,y0,C1x,C1y,C2x,C2y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T012
+	#print '1b:', Triangle_divided_into_four_quadrants(x0,y0,C1x,C1y,C2x,C2y); #T012
+	#print '2', Triangle_divided_into_four_parts(x0,y0,C2x,C2y,C3x,C3y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
+	#print '2b',Triangle_divided_into_four_quadrants(x0,y0,C2x,C2y,C3x,C3y); #T023
+	#print '3:',Triangle_divided_into_four_parts(x0,y0,C3x,C3y,C4x,C4y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T034
+	#print '3b',Triangle_divided_into_four_quadrants(x0,y0,C3x,C3y,C4x,C4y); #T034
+	#print '4',Triangle_divided_into_four_parts(x0,y0,C4x,C4y,C5x,C5y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
+	#print '4b:',Triangle_divided_into_four_quadrants(x0,y0,C4x,C4y,C5x,C5y); #T023
+	#print '5', Triangle_divided_into_four_parts(x0,y0,C5x,C5y,C6x,C6y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
+	#print '5b',Triangle_divided_into_four_quadrants(x0,y0,C5x,C5y,C6x,C6y); #T023
+	#print '6:',Triangle_divided_into_four_parts(x0,y0,C6x,C6y,C1x,C1y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
+	#print '6b',Triangle_divided_into_four_quadrants(x0,y0,C6x,C6y,C1x,C1y); #T023
+
+	#Summing up
+	Area_hex=T12_Area+T23_Area+T34_Area+T45_Area+T56_Area+T61_Area;
+	Area_Q1=T12_Q1+T23_Q1+T34_Q1+T45_Q1+T56_Q1+T61_Q1;
+	Area_Q2=T12_Q2+T23_Q2+T34_Q2+T45_Q2+T56_Q2+T61_Q2;
+	Area_Q3=T12_Q3+T23_Q3+T34_Q3+T45_Q3+T56_Q3+T61_Q3;
+	Area_Q4=T12_Q4+T23_Q4+T34_Q4+T45_Q4+T56_Q4+T61_Q4;
+	#Area_Q4=Area_hex-(Area_Q1+Area_Q2+Area_Q3)
+
+
+
+
+	#if  (abs(x0-(-0.186672393129))<0.00001)  and (abs(y0-(-0.436171))<0.00001):
+	#	print 'Triangle 1,xo,y0',x0,y0
+	#	print 'Triangle 1H,S',H,S
+	#	print 'Triangle 1,Corners',C1x,C1y,C2x,C2y
+	#	print 'Triangle 1, Area full', T12_Area
+	#	print 'Triangle 1, Area T1', T12_Q1
+	#	print 'Triangle 1, Area T2', T12_Q2
+	#	print 'Triangle 1, Area T3', T12_Q3
+	#	print 'Triangle 1, Area T4', T12_Q4
+	#	#print 'Triangle 2',x0,y0,C2x,C2y,C3x,C3y,T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4
+	#	#print 'Triangle 3',x0,y0,C3x,C3y,C4x,C4y,T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4
+	#	#print 'Triangle 4',x0,y0,C4x,C4y,C5x,C5y,T45_Area,T45_Q1,T45_Q2,T45_Q3,T45_Q4
+	#	#print 'Triangle 5',x0,y0,C5x,C5y,C6x,C6y,T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4
+	#	#print 'Triangle 6',x0,y0,C6x,C6y,C1x,C1y,T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4
+
+	Area_Q1=max(Area_Q1,0.);
+	Area_Q2=max(Area_Q2,0.);
+	Area_Q3=max(Area_Q3,0.);
+	Area_Q4=max(Area_Q4,0.);
+
+
+	Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
+	if (abs(Error)>0.01):
+		print  ('diamonds, hex error, H,x0,y0, Error', H, x0 , y0, Error)
+		print ('diamonds, hex error, Areas',Area_hex, (Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,	 Area_Q4)
+		print ('Hexagon error is large!!')
+
+
+
+	#Adjust Areas so that the error is zero by subtracting the error from the largest sector.
+	if  (((Area_Q1>=Area_Q2) and (Area_Q1>=Area_Q3)) and (Area_Q1>=Area_Q4)):
+		#print 'fix1',Error
+		Area_Q1=Area_Q1+Error
+	elif  (((Area_Q2>=Area_Q1) and (Area_Q2>=Area_Q3)) and (Area_Q2>=Area_Q4)):
+		#print 'fix2', Error
+		Area_Q2=Area_Q2+Error
+	elif  (((Area_Q3>=Area_Q1) and (Area_Q3>=Area_Q2)) and (Area_Q3>=Area_Q4)):
+		#print 'fix3',Error
+		Area_Q3=Area_Q3+Error
+	elif  (((Area_Q4>=Area_Q1) and (Area_Q4>=Area_Q2)) and (Area_Q4>=Area_Q3)):
+		#print 'fix4',Error
+		Area_Q4=Area_Q4+Error
+	else:
+		print ('There is some thing wrong with this hexagon. Something very wrong')
+
+	#Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
+	Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
+	if ((abs(Error)>0.01)):
+		print ('The hexagon error is still too large!!!', Error)
+
+
+
+	return [Area_hex ,Area_Q1, Area_Q2, Area_Q3, Area_Q4]
+
+def Hexagon_into_quadrants_using_triangles(x0,y0,H,theta):
+
+	#Length of side of Hexagon
+	S=(2/sqrt(3))*H;
+
+	#Finding positions of corners
+	C1x=S		; C1y=0.  #Corner 1 (right)
+	C2x=H/sqrt(3.)	; C2y=H;  #Corner 2 (top right)
+	C3x=-H/sqrt(3.) ; C3y=H;  #Corner 3 (top left)
+	C4x=-S		; C4y=0.; #Corner 4 (left)
+	C5x=-H/sqrt(3.) ; C5y=-H; #Corner 5 (bottom right)
+	C6x=H/sqrt(3.)	; C6y=-H; #Corner 6 (bottom right)
+
+	#Finding positions of corners
+	[C1x,C1y]=rotate_and_translate(C1x,C1y,theta,x0,y0)
+	[C2x,C2y]=rotate_and_translate(C2x,C2y,theta,x0,y0)
+	[C3x,C3y]=rotate_and_translate(C3x,C3y,theta,x0,y0)
+	[C4x,C4y]=rotate_and_translate(C4x,C4y,theta,x0,y0)
+	[C5x,C5y]=rotate_and_translate(C5x,C5y,theta,x0,y0)
+	[C6x,C6y]=rotate_and_translate(C6x,C6y,theta,x0,y0)
+
+	#Area of Hexagon is the sum of the triangles
+	[T12_Area,T12_Q1,T12_Q2,T12_Q3,T12_Q4]=Triangle_divided_into_four_quadrants(x0,y0,C1x,C1y,C2x,C2y); #T012
+	[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]=Triangle_divided_into_four_quadrants(x0,y0,C2x,C2y,C3x,C3y); #T023
+	[T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4]=Triangle_divided_into_four_quadrants(x0,y0,C3x,C3y,C4x,C4y); #T034
+	[T45_Area,T45_Q1,T45_Q2,T45_Q3,T45_Q4]=Triangle_divided_into_four_quadrants(x0,y0,C4x,C4y,C5x,C5y); #T023
+	[T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4]=Triangle_divided_into_four_quadrants(x0,y0,C5x,C5y,C6x,C6y); #T023
+	[T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4]=Triangle_divided_into_four_quadrants(x0,y0,C6x,C6y,C1x,C1y); #T023
+
+	#Summing up
+	Area_hex=T12_Area+T23_Area+T34_Area+T45_Area+T56_Area+T61_Area;
+	Area_Q1=T12_Q1+T23_Q1+T34_Q1+T45_Q1+T56_Q1+T61_Q1;
+	Area_Q2=T12_Q2+T23_Q2+T34_Q2+T45_Q2+T56_Q2+T61_Q2;
+	Area_Q3=T12_Q3+T23_Q3+T34_Q3+T45_Q3+T56_Q3+T61_Q3;
+	Area_Q4=T12_Q4+T23_Q4+T34_Q4+T45_Q4+T56_Q4+T61_Q4;
+	#Area_Q4=Area_hex-(Area_Q1+Area_Q2+Area_Q3)
+
+
+
+
+	#if  (abs(x0-(-0.186672393129))<0.00001)  and (abs(y0-(-0.436171))<0.00001):
+	#	print 'Triangle 1,xo,y0',x0,y0
+	#	print 'Triangle 1H,S',H,S
+	#	print 'Triangle 1,Corners',C1x,C1y,C2x,C2y
+	#	print 'Triangle 1, Area full', T12_Area
+	#	print 'Triangle 1, Area T1', T12_Q1
+	#	print 'Triangle 1, Area T2', T12_Q2
+	#	print 'Triangle 1, Area T3', T12_Q3
+	#	print 'Triangle 1, Area T4', T12_Q4
+	#	#print 'Triangle 2',x0,y0,C2x,C2y,C3x,C3y,T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4
+	#	#print 'Triangle 3',x0,y0,C3x,C3y,C4x,C4y,T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4
+	#	#print 'Triangle 4',x0,y0,C4x,C4y,C5x,C5y,T45_Area,T45_Q1,T45_Q2,T45_Q3,T45_Q4
+	#	#print 'Triangle 5',x0,y0,C5x,C5y,C6x,C6y,T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4
+	#	#print 'Triangle 6',x0,y0,C6x,C6y,C1x,C1y,T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4
+
+	Area_Q1=max(Area_Q1,0.);
+	Area_Q2=max(Area_Q2,0.);
+	Area_Q3=max(Area_Q3,0.);
+	Area_Q4=max(Area_Q4,0.);
+
+
+	Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
+	if (abs(Error)>0.01):
+		print ( 'diamonds, hex error, H,x0,y0, Error', H, x0 , y0, Error)
+		print ('diamonds, hex error, Areas',Area_hex, (Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,	 Area_Q4)
+		print ('Hexagon error is large!!')
+
+
+
+	#Adjust Areas so that the error is zero by subtracting the error from the largest sector.
+	if  (((Area_Q1>=Area_Q2) and (Area_Q1>=Area_Q3)) and (Area_Q1>=Area_Q4)):
+		#print 'fix1',Error
+		Area_Q1=Area_Q1+Error
+	elif  (((Area_Q2>=Area_Q1) and (Area_Q2>=Area_Q3)) and (Area_Q2>=Area_Q4)):
+		#print 'fix2', Error
+		Area_Q2=Area_Q2+Error
+	elif  (((Area_Q3>=Area_Q1) and (Area_Q3>=Area_Q2)) and (Area_Q3>=Area_Q4)):
+		#print 'fix3',Error
+		Area_Q3=Area_Q3+Error
+	elif  (((Area_Q4>=Area_Q1) and (Area_Q4>=Area_Q2)) and (Area_Q4>=Area_Q3)):
+		#print 'fix4',Error
+		Area_Q4=Area_Q4+Error
+	else:
+		print ('There is some thing wrong with this hexagon. Something very wrong')
+
+	#Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
+	Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
+	if ((abs(Error)>0.01)):
+		print ('The hexagon error is still too large!!!', Error)
+
+
+
+	return [Area_hex ,Area_Q1, Area_Q2, Area_Q3, Area_Q4]
+
+
+def find_intersect_using_metric(Ax,Ay, Bx, By, Cx, Cy):
+	#Line AB
+	[AB_px, AB_py]=intercept_of_a_line(Ax,Ay,Bx,By,'x'); #x_intercept
+	[AB_qx, AB_qy]=intercept_of_a_line(Ax,Ay,Bx,By,'y'); #y_intercept
+	M_AB=point_in_interval_metric(Ax,Ay,Bx,By,AB_px,AB_py, AB_qx, AB_qy)
+	#Line AC
+	[AC_px, AC_py]=intercept_of_a_line(Ax,Ay,Cx,Cy,'x'); #x_intercept
+	[AC_qx, AC_qy]=intercept_of_a_line(Ax,Ay,Cx,Cy,'y'); #y_intercept
+	M_AC=point_in_interval_metric(Ax,Ay,Cx,Cy,AC_px, AC_py,AC_qx, AC_qy)
+	#Line AB
+	[BC_px, BC_py]=intercept_of_a_line(Bx,By,Cx,Cy,'x'); #x_intercept
+	[BC_qx, BC_qy]=intercept_of_a_line(Bx,By,Cx,Cy,'y'); #y_intercept
+	M_BC=point_in_interval_metric(Bx,By,Cx,Cy,BC_px,BC_py,BC_qx, BC_qy)
+
+	if M_AB<=min(M_BC, M_AC):
+		return AB_px, AB_py, AB_qx, AB_qy
+	elif M_AC<=min(M_BC, M_AB):
+		return AC_px, AC_py, AC_qx, AC_qy
+	elif M_BC<=min(M_AC, M_AB):
+		return BC_px, BC_py, BC_qx, BC_qy
+	else:
+		print ('You should not get here')
+		halt
+
+def find_intersect_using_metric_and_lines(Ax,Ay, Bx, By, Cx, Cy,Px, Py, Qx, Qy, Rx, Ry, Sx, Sy):
+	#Line AB
+	[AB_px, AB_py]=intercept_of_two_lines(Ax,Ay,Bx,By,Px, Py, Qx, Qy); #PQ_intercept
+	[AB_qx, AB_qy]=intercept_of_two_lines(Ax,Ay,Bx,By,Rx, Ry, Sx, Sy); #RS_intercept
+	M_AB=point_in_interval_metric(Ax,Ay,Bx,By,AB_px,AB_py, AB_qx, AB_qy)
+	#Line AC
+	[AC_px, AC_py]=intercept_of_two_lines(Ax,Ay,Cx,Cy,Px, Py, Qx, Qy); #PQ_intercept
+	[AC_qx, AC_qy]=intercept_of_two_lines(Ax,Ay,Cx,Cy, Rx, Ry, Sx, Sy); #RS_intercept
+	M_AC=point_in_interval_metric(Ax,Ay,Cx,Cy,AC_px, AC_py,AC_qx, AC_qy)
+	#Line AB
+	[BC_px, BC_py]=intercept_of_two_lines(Bx,By,Cx,Cy,Px, Py, Qx, Qy); #PQ_intercept
+	[BC_qx, BC_qy]=intercept_of_two_lines(Bx,By,Cx,Cy, Rx, Ry, Sx, Sy); #RS_intercept
+	M_BC=point_in_interval_metric(Bx,By,Cx,Cy,BC_px,BC_py,BC_qx, BC_qy)
+
+	if M_AB<=min(M_BC, M_AC):
+		return AB_px, AB_py, AB_qx, AB_qy
+	elif M_AC<=min(M_BC, M_AB):
+		return AC_px, AC_py, AC_qx, AC_qy
+	elif M_BC<=min(M_AC, M_AB):
+		return BC_px, BC_py, BC_qx, BC_qy
+	else:
+		print ('You should not get here')
+		halt
+
+
+def point_in_interval_metric(Ax,Ay,Bx,By,px,py,qx,qy):
+	metric=0.0
+	#print 'Ax,Ay,Bx,By',Ax,Ay,Bx,By,px,py,qx,qy
+	#print 'px,py,qx,qy',px,py,qx,qy
+
+	#Finds a metric for how close a point is to being inside an interval. If it is inside, then metric is equal to zero.
+	Mx1= max(px - max(Ax,Bx),0.)  #Zero is px <= max(Ax,Bx)
+	Mx2= max( min(Ax,Bx)-px ,0.)  #Zero is px <= max(Ax,Bx)
+	My1= max(py - max(Ay,By),0.)  #Zero is px <= max(Ax,Bx)
+	My2= max( min(Ay,By)-py ,0.)  #Zero is px <= max(Ax,Bx)
+	p_metric=abs(Mx1)+abs(Mx2)+abs(My1)+abs(My2)
+	#print 'Mx1, Mx2, My1, My2', Mx1, Mx2, My1, My2
+
+	#Finds a metric for how close a point is to being inside an interval. If it is inside, then metric is equal to zero.
+	Mx1= max(qx - max(Ax,Bx),0.)  #Zero is qx <= max(Ax,Bx)
+	Mx2= max( min(Ax,Bx)-qx ,0.)  #Zero is qx <= max(Ax,Bx)
+	My1= max(qy - max(Ay,By),0.)  #Zero is qx <= max(Ax,Bx)
+	My2= max( min(Ay,By)-qy ,0.)  #Zero is qx <= max(Ax,Bx)
+	q_metric=abs(Mx1)+abs(Mx2)+abs(My1)+abs(My2)
+
+	metric=p_metric+q_metric
+	return metric
+
+
+def Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy):
+	Area_key_quadrant=0.0 #Initializing
+	Area_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
+	#if Area_triangle==0.0:
+	#	Area_triangle=0.0 ; Area_Q1=0.0 ; Area_Q2=0.0; Area_Q3=0.0; Area_Q4= 0.0
+	#	return [Area_triangle, Area_Q1, Area_Q2 ,Area_Q3 ,Area_Q4]
+
+
+	#Calculating area across axes
+	[Area_Upper ,Area_Lower]=divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,'x');
+	[Area_Right ,Area_Left]=divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,'y');
+
+	#Decide if the origin is in the triangle
+	if point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.):	#Then you have to divide area 4 ways.
+		#Find a line in the triangle that cuts both axes in/on the trianlge
+		[px, py]=intercept_of_a_line(Ax,Ay,Bx,By,'x'); #x_intercept
+		[qx, qy]=intercept_of_a_line(Ax,Ay,Bx,By,'y'); #y_intercept
+		if (point_in_interval(Ax,Ay,Bx,By,px,py) & point_in_interval(Ax,Ay,Bx,By,qx,qy))==False:
+			[px, py]=intercept_of_a_line(Ax,Ay,Cx,Cy,'x'); #x_intercept
+			[qx, qy]=intercept_of_a_line(Ax,Ay,Cx,Cy,'y'); #y_intercept
+			if (point_in_interval(Ax,Ay,Cx,Cy,px,py) & point_in_interval(Ax,Ay,Cx,Cy,qx,qy))==False:
+				[px, py]=intercept_of_a_line(Bx,By,Cx,Cy,'x'); #x_intercept
+				[qx, qy]=intercept_of_a_line(Bx,By,Cx,Cy,'y'); #y_intercept
+				if (point_in_interval(Bx,By,Cx,Cy,px,py) & point_in_interval(Bx,By,Cx,Cy,qx,qy))==False:
+					#point_in_interval_metric
+					[px, py, qx, qy]= find_intersect_using_metric(Ax,Ay, Bx, By, Cx, Cy)
+					#print 'Houston, we have a problem'
+					#plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy)
+					#halt
+
+		#Assigning quadrants. Key_quadrant is the quadrant with the baby triangle in it.
+		Area_key_quadrant=Area_of_triangle(px,py,qx,qy,0.,0.);
+		if Area_key_quadrant>0.0:
+			if px>=0. and qy>=0.: #First quadrant
+				Key_quadrant=1;
+			elif px<0. and qy>=0.:	#Second quadrant
+				Key_quadrant=2;
+			elif px<0. and qy<0.:
+				Key_quadrant=3;	 #Third quadrant
+			else:
+				Key_quadrant=4;	 #Forth quadrant
+
+	#if (point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.) is False) or (Area_key_quadrant==0):
+	if Area_key_quadrant==0:
+	#else:	#Then at least one quadrant is empty, and this can be used to find the areas in the other quadrant.  Assigning quadrants. Key_quadrant is the empty quadrant.
+		#print 'Mother...'
+		#print 'Ax, Ay',Ax,Ay
+		#print 'Bx, By',Bx,By
+		#print 'Cx, Cy',Cx,Cy
+		Area_key_quadrant=0;
+		if (((Ax>0. and Ay>0.) or (Bx>0. and By>0.) or (Cx>0. and Cy>0.))==False)  and (Area_Upper+Area_Right<=Area_triangle):
+		#if (((Ax>=0. and Ay>=0.) or (Bx>=0. and By>=0.) or (Cx>=0. and Cy>=0.))==False)  and (Area_Upper+Area_Right<=Area_triangle):
+			#No points land in this quadrant and triangle does not cross the quadrant
+			Key_quadrant=1;
+		elif  (((Ax<0. and Ay>0) or (Bx<0. and By>0.) or (Cx<0. and Cy>0.))==False)  and (Area_Upper+Area_Left<=Area_triangle):
+			#elif  (((Ax<0. and Ay>=0) or (Bx<0. and By>=0.) or (Cx<0. and Cy>=0.))==False)	 and (Area_Upper+Area_Left<=Area_triangle):
+			Key_quadrant=2;
+		elif (((Ax<0. and Ay<0.) or (Bx<0. and By<0.) or (Cx<0. and Cy<0.))==False) & (Area_Lower+Area_Left<=Area_triangle):
+			#elif (((Ax<0. and Ay<0.) or (Bx<0. and By<0.) or (Cx<0. and Cy<0.))==False) & (Area_Lower+Area_Left<=Area_triangle):
+			Key_quadrant=3;
+		else:
+			Key_quadrant=4;
+
+	#Assign values to quadrants
+	if Key_quadrant==1:
+		Area_Q1=Area_key_quadrant;
+		Area_Q2=Area_Upper-Area_Q1;
+		Area_Q4=Area_Right-Area_Q1;
+		#Area_Q3=Area_Left-Area_Q2;
+		Area_Q3=Area_triangle-Area_Q1-Area_Q2-Area_Q4;
+	elif Key_quadrant==2:
+		Area_Q2=Area_key_quadrant;
+		Area_Q1=Area_Upper-Area_Q2;
+		Area_Q4=Area_Right-Area_Q1;
+		#Area_Q3=Area_Left-Area_Q2;
+		Area_Q3=Area_triangle-Area_Q1-Area_Q2-Area_Q4;
+	elif Key_quadrant==3:
+		Area_Q3=Area_key_quadrant;
+		Area_Q2=Area_Left-Area_Q3;
+		Area_Q1=Area_Upper-Area_Q2;
+		#Area_Q4=Area_Right-Area_Q1;
+		Area_Q4=Area_triangle-Area_Q1-Area_Q2-Area_Q3;
+	elif Key_quadrant==4:
+		Area_Q4=Area_key_quadrant;
+		Area_Q1=Area_Right-Area_Q4;
+		Area_Q2=Area_Upper-Area_Q1;
+		#Area_Q3=Area_Left-Area_Q2;
+		Area_Q3=Area_triangle-Area_Q1-Area_Q2-Area_Q4;
+	else:
+	    print( 'Help, I need somebody, help!')
+	    halt
+
+	Area_Q1=max(Area_Q1,0.);
+	Area_Q2=max(Area_Q2,0.);
+	Area_Q3=max(Area_Q3,0.);
+	Area_Q4=max(Area_Q4,0.);
+
+	Error=abs(Area_Q1+Area_Q2+Area_Q3+Area_Q4-Area_triangle)
+	#Marker 1
+	if Error>1e-15:
+	#if True:
+		print ('The triangles are not accurate enough. This is a problem!')
+		print ('Triangle corners: ' ,Ax,Ay,Bx,By,Cx,Cy)
+		print ('Error',Error)
+		print ('Key_quadrant', Key_quadrant )
+		print ('Area Key_quadrant', Area_key_quadrant)
+		print ('Upper, Lower',Area_Upper ,Area_Lower)
+		print ('Left, Right ', Area_Right ,Area_Left)
+		print ('Point in triangle', point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.))
+		#plt.plot(np.array([Ax,Bx,Cx,Ax]),np.array([Ay, By, Cy,Ay]))
+		#plt.plot(np.array([-0.5,0.5]),np.array([0.,0.]),'k')
+		#plt.plot(np.array([0.,0.]),np.array([-0.5,0.5]),'k')
+		#plt.plot(0,0,'*')
+		#plt.show()
+		#halt
+		#return
+
+	return [Area_triangle, Area_Q1, Area_Q2 ,Area_Q3 ,Area_Q4]
+
+def find_quadrant_using_lines(x0 , y0 , Px, Py, Qx, Qy, Rx, Ry, Sx, Sy): #Finding "quadrant" of point using lines PQ, RS as axes.  (This assumes PQ is like the x axis and RS like the y axis)
+	#above_PQ=Point_above_line(x0,y0, Px, Py, Qx, Qy)
+	#above_RS=Point_above_line(x0,y0, Rx, Ry, Sx, Sy)
+	above_PQ=Above_on_below_line(x0,y0, Px, Py, Qx, Qy)
+	above_RS=Above_on_below_line(x0,y0, Rx, Ry, Sx, Sy)
+	if (above_PQ==1) and (above_RS==1):
+		quadrant=1
+	elif (above_PQ==1) and (above_RS==-1):
+		quadrant=2
+	elif (above_PQ==-1) and (above_RS==-1):
+		quadrant=3
+	elif (above_PQ==-1) and (above_RS==1):
+		quadrant=4
+	else:
+		#print 'Point not in a quadrant!'
+		quadrant=0
+		#halt
+
+	return quadrant
+
+def Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy	):#Divides the triangle into 4 parts, across two intersecting lines. PQ, RS intersect at origin (for now)
+	Area_key_quadrant=0.0
+	Area_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
+	#if Area_triangle==0.0:
+	#	Area_triangle=0.0 ; Area_Q1=0.0 ; Area_Q2=0.0; Area_Q3=0.0; Area_Q4= 0.0
+	#	return [Area_triangle, Area_Q1, Area_Q2 ,Area_Q3 ,Area_Q4]
+
+
+	#Calculating area across axes
+	[Area_Upper ,Area_Lower]=divding_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy);
+	[Area_Right ,Area_Left] =divding_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Rx, Ry, Sx, Sy);
+
+	#Decide if the origin is in the triangle
+	if point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.):	#Then you have to divide area 4 ways.
+		#Find a line in the triangle that cuts both axes in/on the trianlge
+		[px, py]=intercept_of_two_lines(Ax,Ay,Bx,By,Px, Py, Qx, Qy); #PQ_intercept
+		[qx, qy]=intercept_of_two_lines(Ax,Ay,Bx,By,Rx, Ry, Sx, Sy); #RS_intercept
+		if (point_in_interval(Ax,Ay,Bx,By,px,py) & point_in_interval(Ax,Ay,Bx,By,qx,qy))==False:
+			[px, py]=intercept_of_two_lines(Ax,Ay,Cx,Cy,Px, Py, Qx, Qy); #PQ_intercept
+			[qx, qy]=intercept_of_two_lines(Ax,Ay,Cx,Cy,Rx, Ry, Sx, Sy); #RS_intercept
+			if (point_in_interval(Ax,Ay,Cx,Cy,px,py) & point_in_interval(Ax,Ay,Cx,Cy,qx,qy))==False:
+				[px, py]=intercept_of_two_lines(Bx,By,Cx,Cy,Px, Py, Qx, Qy); #PQ_intercept
+				[qx, qy]=intercept_of_two_lines(Bx,By,Cx,Cy,Rx, Ry, Sx, Sy); #RS_intercept
+				if (point_in_interval(Bx,By,Cx,Cy,px,py) & point_in_interval(Bx,By,Cx,Cy,qx,qy))==False:
+					#print 'Houston, we have a problem'
+					[px, py, qx, qy]= find_intersect_using_metric_and_lines(Ax,Ay, Bx, By, Cx, Cy,Px, Py, Qx, Qy, Rx, Ry, Sx, Sy)
+					#plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy)
+					#halt
+
+		#Assigning quadrants. Key_quadrant is the quadrant with the baby triangle in it.
+		Area_key_quadrant=Area_of_triangle(px,py,qx,qy,0.,0.);
+		if px>=0. and qy>=0.: #First quadrant  (I think the zeros here are because the PQ, RS intersect at zero)
+			Key_quadrant=1;
+		elif px<0. and qy>=0.:	#Second quadrant
+			Key_quadrant=2;
+		elif px<0. and qy<0.:
+			Key_quadrant=3;	 #Third quadrant
+		else:
+			Key_quadrant=4;	 #Forth quadrant
+
+	if Area_key_quadrant==0:
+		#else:	#Then at least one quadrant is empty, and this can be used to find the areas in the other quadrant.  Assigning quadrants. Key_quadrant is the empty quadrant.
+		#print 'Mother...'
+		#print 'Ax, Ay',Ax,Ay
+		#print 'Bx, By',Bx,By
+		#print 'Cx, Cy',Cx,Cy
+		Area_key_quadrant=0;
+		#Finding which quadrant the triangle points fall in.
+		A_quad = find_quadrant_using_lines(Ax,Ay,Px, Py, Qx, Qy, Rx, Ry, Sx, Sy)
+		B_quad = find_quadrant_using_lines(Bx,By,Px, Py, Qx, Qy, Rx, Ry, Sx, Sy)
+		C_quad = find_quadrant_using_lines(Cx,Cy,Px, Py, Qx, Qy, Rx, Ry, Sx, Sy)
+		#print 'A_quad, B_quad, C_quad',A_quad, B_quad, C_quad
+
+		if (((A_quad==1) or (B_quad==1) or (C_quad==1))==False)	 and (Area_Upper+Area_Right<=Area_triangle):
+			#No points land in this quadrant and triangle does not cross the quadrant
+			Key_quadrant=1;
+		elif  (((A_quad==2) or (B_quad==2) or (C_quad==2))==False)  and (Area_Upper+Area_Left<=Area_triangle):
+			Key_quadrant=2;
+		elif (((A_quad==3) or (B_quad==3) or (C_quad==3))==False) & (Area_Lower+Area_Left<=Area_triangle):
+			Key_quadrant=3;
+		else:
+			Key_quadrant=4;
+
+		#print Key_quadrant
+	#Assign values to quadrants
+	if Key_quadrant==1:
+		Area_Q1=Area_key_quadrant;
+		Area_Q2=Area_Upper-Area_Q1;
+		Area_Q4=Area_Right-Area_Q1;
+		#Area_Q3=Area_Left-Area_Q2;
+		Area_Q3=Area_triangle-Area_Q1-Area_Q2-Area_Q4;
+	elif Key_quadrant==2:
+		Area_Q2=Area_key_quadrant;
+		Area_Q1=Area_Upper-Area_Q2;
+		Area_Q4=Area_Right-Area_Q1;
+		#Area_Q3=Area_Left-Area_Q2;
+		Area_Q3=Area_triangle-Area_Q1-Area_Q2-Area_Q4;
+	elif Key_quadrant==3:
+		Area_Q3=Area_key_quadrant;
+		Area_Q2=Area_Left-Area_Q3;
+		Area_Q1=Area_Upper-Area_Q2;
+		#Area_Q4=Area_Right-Area_Q1;
+		Area_Q4=Area_triangle-Area_Q1-Area_Q2-Area_Q3;
+	elif Key_quadrant==4:
+		Area_Q4=Area_key_quadrant;
+		Area_Q1=Area_Right-Area_Q4;
+		Area_Q2=Area_Upper-Area_Q1;
+		#Area_Q3=Area_Left-Area_Q2;
+		Area_Q3=Area_triangle-Area_Q1-Area_Q2-Area_Q4;
+	else:
+	    print ('Help, I need somebody, help!')
+	    halt
+
+	Area_Q1=max(Area_Q1,0.);
+	Area_Q2=max(Area_Q2,0.);
+	Area_Q3=max(Area_Q3,0.);
+	Area_Q4=max(Area_Q4,0.);
+
+	Error=abs(Area_Q1+Area_Q2+Area_Q3+Area_Q4-Area_triangle)
+	if Error>1e-15:
+	#if True:
+		print ('The triangles are not accurate enough. This is a problem!')
+		print ('Triangle corners: ' ,Ax,Ay,Bx,By,Cx,Cy)
+		print ('Error',Error)
+		print ('Key_quadrant', Key_quadrant )
+		print ('Area Key_quadrant', Area_key_quadrant )
+		print ('Upper, Lower',Area_Upper ,Area_Lower)
+		print ('Left, Right ', Area_Right ,Area_Left)
+		print ('Point in triangle', point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.))
+		#return
+
+	return [Area_triangle, Area_Q1, Area_Q2 ,Area_Q3 ,Area_Q4]
+
+def divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1):
+	if axes1=='x':	#Use the y-coordinates for if statements to see which side of the line you are on
+		A0=Ay; B0=By;  C0=Cy;
+	if axes1=='y':	#Use the y-coordinates for if statements to see which side of the line you are on
+		A0=Ax; B0=Bx;  C0=Cx;
+
+	#print 'A0,B0,C0', A0,B0,C0
+	A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
+	if B0*C0>0.: #then B and C are on the same side	 (and non-zero)
+		#print 'HHHH1'
+		if A0*B0>=0.: #then all three on the the same side (if it equals zero, then A0=0 and the otehrs are not)
+			if (A0>0.)  or	(A0==0. and  B0>0.):
+				Area_positive= A_triangle;
+				Area_negative= 0.;
+			else:
+				Area_positive= 0.;
+				Area_negative= A_triangle;
+		else:  #A is on the opposite side to B and C
+			[Area_positive, Area_negative]=Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1);
+
+	elif B0*C0<0.: #then B and C are on the opposite sides
+		#print 'HHHH2'
+		if A0*B0>=0.:  #then C is all alone
+			[Area_positive, Area_negative]=Area_of_triangle_across_axes(Cx,Cy,Bx,By,Ax,Ay,axes1);
+		else: #then B is all alone
+			[Area_positive, Area_negative]=Area_of_triangle_across_axes(Bx,By,Cx,Cy,Ax,Ay,axes1);
+
+	else:  #This is the case when either B or C is equal to zero (or both), A0 could be zero too.
+		#print 'HHHH3'
+		if (A0==0. and B0==0. and C0==0.):
+			Area_positive= 0.;
+			Area_negative= 0.;
+		elif (A0*B0<0.)	 or  (A0*C0<0.):    #A, B are on opposite sides, and C is zero.	 OR  A, C are on opposite sides, and B is zero.
+			[Area_positive, Area_negative]=Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1);
+			#print 'HHHH6'
+		elif (A0*B0>0.) or (A0*C0>0.) or (abs(A0)>0. and (B0==0.) and (C0==0.)):
+			#print 'HHHH7'
+			if (A0>0.):
+				Area_positive= A_triangle;
+				Area_negative= 0.;
+			else:
+				Area_positive= 0.;
+				Area_negative= A_triangle;
+
+		elif A0==0.:  #(Also, one of B,C is zero too)
+			#print 'HHHH8'
+			if B0>0. or C0>0.:
+				Area_positive= A_triangle;
+				Area_negative= 0.;
+			elif B0<0. or C0<0.:
+				Area_positive= 0.;
+				Area_negative= A_triangle;
+			else:
+				print 'You should not get here1'
+				halt
+		else:
+			print ('You should not get here2')
+			print (Ax,Ay,Bx,By,Cx,Cy)
+			halt
+
+	return [Area_positive, Area_negative]
+
+def divding_triangle_across_line2(Ax,Ay,Bx,By,Cx,Cy,  Px, Py, Qx, Qy ):
+	A0= Above_on_below_line(Ax,Ay, Px, Py, Qx, Qy)
+	B0= Above_on_below_line(Bx,By, Px, Py, Qx, Qy)
+	C0= Above_on_below_line(Cx,Cy, Px, Py, Qx, Qy)
+
+	#print 'A0,B0,C0', A0,B0,C0
+	#print Px, Py, Qx, Qy
+
+	A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
+	if B0*C0>0.: #then B and C are on the same side	 (and non-zero)
+		#print 'GGG1'
+		if A0*B0>=0.: #then all three on the the same side (if it equals zero, then A0=0 and the otehrs are not)
+			if (A0>0.)  or	(A0==0. and  B0>0.):
+				Area_positive= A_triangle;
+				Area_negative= 0.;
+			else:
+				Area_positive= 0.;
+				Area_negative= A_triangle;
+		else:  #A is on the opposite side to B and C
+			[Area_positive, Area_negative]=Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy );
+
+	elif B0*C0<0.: #then B and C are on the opposite sides
+		#print 'GGG2'
+		if A0*B0>=0.:  #then C is all alone
+			[Area_positive, Area_negative]=Area_of_triangle_across_line(Cx,Cy,Bx,By,Ax,Ay, Px, Py, Qx, Qy );
+		else: #then B is all alone
+			[Area_positive, Area_negative]=Area_of_triangle_across_line(Bx,By,Cx,Cy,Ax,Ay, Px, Py, Qx, Qy );
+
+	else:  #This is the case when either B or C is equal to zero (or both), A0 could be zero too.
+		#print 'GGG3'
+		if (A0==0. and B0==0. and C0==0.):
+			Area_positive= 0.;
+			Area_negative= 0.;
+		elif (A0*B0<0.)	 or  (A0*C0<0.):    #A, B are on opposite sides, and C is zero.	 OR  A, C are on opposite sides, and B is zero.
+			[Area_positive, Area_negative]=Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy);
+			#print 'GGG5', Area_positive, Area_negative
+		elif (A0*B0>0.) or (A0*C0>0.) or (abs(A0)>0. and (B0==0.) and (C0==0.)):
+			if (A0>0.):
+				Area_positive= A_triangle;
+				Area_negative= 0.;
+			else:
+				Area_positive= 0.;
+				Area_negative= A_triangle;
+
+		elif A0==0.:  #(Also, one of B,C is zero too)
+			if B0>0. or C0>0.:
+				Area_positive= A_triangle;
+				Area_negative= 0.;
+			elif B0<0. or C0<0.:
+				Area_positive= 0.;
+				Area_negative= A_triangle;
+			else:
+				print ('You should not get here1')
+				halt
+		else:
+			print ('You should not get here2')
+			print (Ax,Ay,Bx,By,Cx,Cy)
+			halt
+
+	return [Area_positive, Area_negative]
+
+
+def divding_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy,   Px, Py, Qx, Qy ):	 #Triangle is ABC, line is PQ
+	A0= Above_on_below_line(Ax,Ay, Px, Py, Qx, Qy)
+	B0= Above_on_below_line(Bx,By, Px, Py, Qx, Qy)
+	C0= Above_on_below_line(Cx,Cy, Px, Py, Qx, Qy)
+	#print 'BBB0', A0, B0, C0
+
+	A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
+	# B and C are on the same side of the line
+	#if (Point_above_line(Bx,By, Px, Py, Qx, Qy)==Point_above_line(Cx,Cy, Px, Py, Qx, Qy)) :
+	#if ((B0==C0) and (B0!=0))  or ((B0==0 or C0==0) and np.max(B0,C0)>0.5)	  :
+	if ((B0==C0) and (B0!=0))  or ((B0==0 or C0==0))   : #B and C on the same side or B or C is zero
+		#print 'BBB1'
+		[Area_positive, Area_negative]=Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy);
+	else: #then B and C are on the opposite sides
+		#if Point_above_line(Ax,Ay, Px, Py, Qx, Qy)==Point_above_line(Bx,By, Px, Py, Qx, Qy):  #then C is all alone
+		if A0*B0>=0.:  #then C is all alone
+			#print 'BBB2'
+			[Area_positive, Area_negative]=Area_of_triangle_across_line(Cx,Cy,Bx,By,Ax,Ay, Px, Py, Qx, Qy);
+		else: #then B is all alone
+			#print 'BBB3'
+			[Area_positive, Area_negative]=Area_of_triangle_across_line(Bx,By,Cx,Cy,Ax,Ay, Px, Py, Qx, Qy);
+
+	return [Area_positive, Area_negative]
+
+
+def check_if_point_is_on_the_line(Ax,Ay,Bx,By,qx,qy,repeat_calculation=False):
+
+	tol=0.00000000000000;
+	dxc = qx - Ax;
+	dyc = qy - Ay;
+
+	dxl = Bx - Ax;
+	dyl = By - Ay;
+
+	cross = dxc * dyl - dyc * dxl;
+
+	if abs(cross)<=tol:
+		point_is_on_line=True
+	else:
+		point_is_on_line=False
+
+	if repeat_calculation is False:
+		if point_is_on_line != check_if_point_is_on_the_line(Bx,By,Ax,Ay,qx,qy, True):
+			point_is_on_line=True
+
+	return point_is_on_line
+
+def intercept_of_a_line(Ax,Ay,Bx,By,axes1):
+	No_intercept_val=100000000000.; #Huge value used to make sure that the intercept is outside the triange in the parralel case.
+	#No_intercept_val=np.NaN;
+
+	if axes1=='x': #x intercept
+		if (Ay==By)==False:
+			x0=Ax -(((Ax-Bx)/(Ay-By))*Ay);
+			y0=0.;
+		else:
+			x0=No_intercept_val;
+			y0=No_intercept_val;
+
+	if axes1=='y': #y intercept
+		if (Ax==Bx)==False:
+			x0=0.;
+			y0=-(((Ay-By)/(Ax-Bx))*Ax)+Ay;
+		else:
+			x0=No_intercept_val;
+			y0=No_intercept_val;
+
+	return [x0, y0]
+
+def intercept_of_two_lines(Ax,Ay,Bx,By,Px,Py,Qx,Qy):
+	No_intercept_val=100000000000.; #Huge value used to make sure that the intercept is outside the triange in the parralel case.
+	#No_intercept_val=np.NaN;
+
+	#One of the lines is actually a point:
+	if ((Ax==Bx) and (Ay==By)) or ((Px==Qx) and (Py==Qy)):
+		x0=No_intercept_val; y0=No_intercept_val;
+		halt6
+	else:
+		if (Ax==Bx):
+			(x0 , y0) =intercept_of_a_line(Px-Ax,Py,Qx-Ax,Qy,'y')
+			x0=Ax
+		#Here we check the other three directions to make code agree to machine precision with old version. The code could skip straight to the else.
+		elif (Px==Qx):
+			(x0 , y0) =intercept_of_a_line(Ax-Px,Ay,Bx-Px,By,'y')
+			x0=Px
+		elif (Ay==By):
+			(x0 , y0) =intercept_of_a_line(Px,Py-Ay,Qx,Qy-Ay,'x')
+			y0=Ay
+		elif (Py==Qy):
+			(x0 , y0) =intercept_of_a_line(Ax,Ay-Py,Bx,By-Py,'x')
+			y0=Py
+		else:
+			m1=(Ay-By)/(Ax-Bx)
+			if (Px==Qx):
+				print ('Stop2')
+				(x0 , y0) =intercept_of_a_line(Ax-Px,Ay,Bx-Px,By,'y')
+				x0=Px
+			else:
+				m2=(Py-Qy)/(Px-Qx)
+				if m1==m2:
+					print( 'Stop3')
+					x0=No_intercept_val;
+					y0=No_intercept_val;
+					halt2
+				else:
+					print( 'Stop4')
+					x0=(1/(m1-m2))*( (m1*Ax -Ay) -(m2*Px - Py))
+					y0=m1*(x0-Ax)+Ay
+
+	return [x0, y0]
+
+
+def Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axis1):#In this fuction, A is the point on one side of the axis, and B,C are on the opposite sides
+	#print 'Area_of_triangle_across_axes' ,Ax,Ay,Bx,By,Cx,Cy
+	A_triangle2=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
+	[pABx, pABy]=intercept_of_a_line(Ax,Ay,Bx,By,axis1);
+	[pACx, pACy]=intercept_of_a_line(Ax,Ay,Cx,Cy,axis1);
+	if axis1=='x':
+		A0=Ay; #Value used for if statements (deciding up/down vs left/right)
+	if axis1=='y':
+		A0=Ax; #Value used for if statements (deciding up/down vs left/right)
+
+	#print 'QQQ', Ax,Ay,pABx,pABy,pACx,pACy
+	A_half_triangle=Area_of_triangle(Ax,Ay,pABx,pABy,pACx,pACy);
+	if (A0>=0.):
+		Area_positive= A_half_triangle;
+		Area_negative= A_triangle2-A_half_triangle;
+
+	else:
+		Area_positive= A_triangle2-A_half_triangle;
+		Area_negative= A_half_triangle;
+
+	return [Area_positive, Area_negative]
+
+def Above_on_below_line(x,y,Px, Py, Qx, Qy): #If the point is above the line, then returns True, otherwise false
+	if Px==Qx:
+		if x>Px:
+			Point_above_line=1.0
+		elif x<Px:
+			Point_above_line=-1.0
+		else:
+			Point_above_line=0.0
+	else:
+		m=(Py-Qy)/(Px-Qx)
+		if y > m*(x-Px) + Py:
+			Point_above_line=1.0
+		elif y < m*(x-Px) + Py:
+			Point_above_line=-1.0
+		else:
+			Point_above_line=0.0
+
+	return Point_above_line
+
+def Point_above_line(x,y,Px, Py, Qx, Qy): #If the point is above the line, then returns True, otherwise false
+	if Px==Qx:
+		if x>=Px:
+			Point_above_line=True
+		else:
+			Point_above_line=False
+	else:
+		m=(Py-Qy)/(Px-Qx)
+		if y >= m*(x-Px) + Py:
+			Point_above_line=True
+		else:
+			Point_above_line=False
+
+	return Point_above_line
+
+
+def Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px,Py, Qx, Qy, debug=False):
+	#In this fuction, B and C are the same side of the line. (I think this works even if B and/or C are on the line too)
+	#A is unknown. PQ is the line.
+	#print 'RRR Area_of_triangle_across_line' ,Ax,Ay,Bx,By,Cx,Cy
+
+	if (Ax==Bx and Ay==By) or (Ax==Cx and Ay==Cy) or (Cx==Bx and Cy==By):
+		#print 'AAA1'
+		Area_positive=0.0
+		Area_negative=0.0
+	else:
+		#print 'AAA2'
+		A0= Above_on_below_line(Ax,Ay, Px, Py, Qx, Qy)
+		B0= Above_on_below_line(Bx,By, Px, Py, Qx, Qy)
+		C0= Above_on_below_line(Cx,Cy, Px, Py, Qx, Qy)
+		A_triangle2=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
+
+		if check_if_point_is_on_the_line(Px,Py,Qx,Qy, Ax,Ay):  #Is point A on the line?
+			#print 'AAA3'
+			#if Point_above_line(Bx,By, Px,Py, Qx, Qy) or Point_above_line(Cx,Cy, Px,Py, Qx, Qy):
+			if B0==1 or C0==1:
+				Area_positive= A_triangle2;
+				Area_negative= 0.0;
+			else:
+				Area_positive= 0.0;
+				Area_negative= A_triangle2;
+		else: #If A is not on the line
+			#If A is on the same side of the line as B and C
+			#All on the same side of the line
+			if ((A0==B0 and A0==C0)	 or (A0==B0 and C0==0) or (A0==C0 and B0==0)):
+			#if Point_above_line(Ax,Ay, Px,Py, Qx, Qy) == Point_above_line( Bx,By, Px,Py, Qx, Qy)  and (Point_above_line(Ax,Ay,Px,Py,Qx,Qy)==Point_above_line(Cx,Cy,Px,Py,Qx,Qy)):
+				#print 'AAA4'
+				#if Point_above_line(Bx,By, Px,Py, Qx, Qy) or Point_above_line(Cx,Cy, Px,Py, Qx, Qy):
+				if A0==1 or C0==1:
+					Area_positive= A_triangle2;
+					Area_negative= 0.0;
+				else:
+					Area_positive= 0.0;
+					Area_negative= A_triangle2;
+			elif (C0==0 and B0==0 and (abs(A0)>0)):
+				if Point_above_line(Ax,Ay, Px,Py, Qx, Qy):
+					Area_positive= A_triangle2;
+					Area_negative= 0.0;
+				else:
+					Area_positive= 0.0;
+					Area_negative= A_triangle2;
+
+			else:  #If A is not on the same side of the line as B and C
+				#print 'AAA5'
+				[pABx, pABy]=intercept_of_two_lines(Ax,Ay,Bx,By, Px, Py, Qx, Qy);
+				[pACx, pACy]=intercept_of_two_lines(Ax,Ay,Cx,Cy, Px, Py, Qx, Qy);
+				#print 'Tri2', Ax,Ay,pABx,pABy,pACx,pACy
+
+				A_half_triangle=Area_of_triangle(Ax,Ay,pABx,pABy,pACx,pACy);
+				if Point_above_line(Ax,Ay , Px,Py,Qx,Qy):
+					Area_positive= A_half_triangle;
+					Area_negative= A_triangle2-A_half_triangle;
+				else:
+					Area_positive= A_triangle2-A_half_triangle;
+					Area_negative= A_half_triangle;
+
+	return [Area_positive, Area_negative]
+
+def Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy):
+	Area	=   abs(    0.5*((Ax*(By-Cy))+(Bx*(Cy-Ay))+(Cx*(Ay-By))) );
+	return Area
+
+
+def point_in_interval(Ax,Ay,Bx,By,px,py):
+	point_is_in_interval=False
+	#print 'NNN1'
+	if ((px <= max(Ax,Bx)) and (px >= min(Ax,Bx))):
+		#print 'NNN2', 'py=', py,  'max=',max(Ay,By), 'XXX', (py - max(Ay,By))
+		if ((py <= max(Ay,By)) and (py >= min(Ay,By))):
+			##print 'NNN3'
+			point_is_in_interval=True
+	return point_is_in_interval
+
+def rotate_and_translate(px,py,theta,x0,y0):
+	#This function takes a point px,py, and rotates it clockwise around the origin by theta degrees, and then translates by (x0,y0)
+	 px_temp = (cos(theta*pi/180.)*px) + (sin(theta*pi/180.)*py)
+	 py_temp = (-sin(theta*pi/180.)*px) + (cos(theta*pi/180.)*py)
+	 px= px_temp +x0
+	 py= py_temp +y0
+	 return [px,py]
+
+
+def point_in_triangle_old(Ax,Ay,Bx,By,Cx,Cy,qx,qy):
+	#if False:
+	if (Ax==qx and Ay==qy) or (Bx==qx and By==qy) or (Cx==qx and Cy==qy):  #Exclude the pathelogical case
+			point_is_in_triangle = 0.;
+	else:
+		if (check_if_point_is_on_the_line(Ax,Ay,Bx,By,qx,qy) or (check_if_point_is_on_the_line(Ax,Ay,Cx,Cy,qx,qy)) or (check_if_point_is_on_the_line(Bx,By,Cx,Cy,qx,qy))):
+			point_is_in_triangle = 0;
+		else:
+			#Compute vectors
+			v0x=Cx-Ax;
+			v1x=Bx-Ax;
+			v2x=qx-Ax;
+			v0y=Cy-Ay;
+			v1y=By-Ay;
+			v2y=qy-Ay;
+
+			#%Compute dot products
+			dot00 = (v0x*v0x)+(v0y*v0y);
+			dot01 = (v0x*v1x)+(v0y*v1y);
+			dot02 = (v0x*v2x)+(v0y*v2y);
+			dot11 = (v1x*v1x)+(v1y*v1y);
+			dot12 = (v1x*v2x)+(v1y*v2y);
+
+			#Compute barycentric coordinates
+			invDenom= 1 / ((dot00 * dot11) - (dot01*dot01));
+			u=((dot11*dot02)-(dot01*dot12))*invDenom;
+			v=((dot00*dot12)-(dot01*dot02))*invDenom;
+
+			point_is_in_triangle = (((u)>=0) & ((v)>=0) & ((u+v)<(1)));
+	return point_is_in_triangle
+
+
+
+def point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,qx,qy):
+	point_is_in_triangle = 0;
+
+	if (Ax==qx and Ay==qy) or (Bx==qx and By==qy) or (Cx==qx and Cy==qy):  #Exclude the pathelogical case
+			point_is_in_triangle = 0.;
+	else:
+		if (check_if_point_is_on_the_line(Ax,Ay,Bx,By,qx,qy) or (check_if_point_is_on_the_line(Ax,Ay,Cx,Cy,qx,qy)) or (check_if_point_is_on_the_line(Bx,By,Cx,Cy,qx,qy))):
+			point_is_in_triangle = 0;
+		else:
+			l0=(qx-Ax)*(By-Ay)-(qy-Ay)*(Bx-Ax)
+			l1=(qx-Bx)*(Cy-By)-(qy-By)*(Cx-Bx)
+			l2=(qx-Cx)*(Ay-Cy)-(qy-Cy)*(Ax-Cx)
+
+			p0=np.sign( l0);
+			p1=np.sign( l1);
+			p2=np.sign( l2);
+			if (l0 == 0.):
+				p0=0.
+			if (l1==0.):
+				p1=0.
+			if (l2==0.):
+				p2=0.
+
+			if ( (abs(p0)+abs(p2))+(abs(p1)) == abs((p0+p2)+(p1)) ):
+				point_is_in_triangle = 1;
+	return point_is_in_triangle
+
+
+def roundoff(x,sig_fig):
+	x_roundoff=round(x*(10**(sig_fig)))/(10**(sig_fig))
+	#x_roundoff=(FLOAT (INT(x * (10.**sig_fig) + 0.5)) / (10.**sig_fig))
+	return x_roundoff
+
+
+
+def square_spreading_calculation(x,y,L):
+	xL=min(0.5, max(0., 0.5-(x/L)))
+	xR=min(0.5, max(0., (x/L)+(0.5-(1/L) )))
+	xC=max(0., 1.-(xL+xR))
+	yD=min(0.5, max(0., 0.5-(y/L)))
+	yU=min(0.5, max(0., (y/L)+(0.5-(1/L) )))
+	yC=max(0., 1.-(yD+yU))
+
+def plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy, Px=None, Py=None, Qx=None, Qy=None, Rx=None, Ry=None, Sx=None, Sy=None):
+	if Px is None:
+		Px=-1. ; Py=0. ; Qx=1. ; Qy=0. #x-axis
+		Rx=0. ; Ry=-1. ; Sx=0. ; Sy=1. #y-axis
+	plt.plot(np.array([Px, Qx]), np.array([Py, Qy]))
+	plt.plot(np.array([Rx, Sx]), np.array([Ry, Sy]))
+	plt.plot(np.array([Ax, Bx, Cx, Ax]), np.array([Ay, By, Cy, Ay]))
+	plt.plot(np.array([Ax, Bx, Cx, Ax]), np.array([Ay, By, Cy, Ay]),'8')
+	text(Ax,Ay,'A',fontsize=20)
+	text(Bx,By,'B',fontsize=20)
+	text(Cx,Cy,'C',fontsize=20)
+	plt.show()
+
+####################################################################################################################################################
+##########################################################  Main Program   #########################################################################
+####################################################################################################################################################
+
+def main():
+
+	#test_case='hexagon'
+	#test_case='triangle'
+	#test_case='square'
+	#test_case='point_in_triangle'
+	#test_case='line_intercept'
+	#test_case='Point_above_line'
+	#test_case='Triangle_across_line'
+	#test_case='Triangle_into_fours'
+	test_case='many_hexagons'
+
+	if test_case=='line_intercept':
+		Ax=1. ; Ay=1.5 ; Bx=1. ; By=-3.4
+		Px=0.2; Py=-1.0; Qx=0.2; Qy=2.2
+		(x0,y0)=intercept_of_two_lines(Ax,Ay,Bx,By,Px,Py,Qx,Qy)
+		plt.plot( np.array([Ax, Bx])  , np.array([Ay, By]))
+		plt.plot(np.array([Px, Qx]), np.array([Py, Qy]))
+		plt.plot(x0,y0,'*')
+		#plt.plot(Ax,Ay,'*')
+		#plt.plot(Bx,By,'*')
+		#plt.plot(Px,Py,'*')
+		#plt.plot(Qx,Qy,'*')
+
+		print ('x0, y0' , x0 , y0)
+		plt.show()
+
+
+	if test_case=='Triangle_across_line':
+		#y-axis
+		Px=0.0 ; Py=-1.0 ;Qx=0.0 ;Qy=1.0
+		axes1='y'
+
+		#x-axis
+		#Px=-1.0 ; Py=0.0 ;Qx=1.0 ;Qy=0.0
+		#axes1='x'
+
+		N=11 #Choose an odd number
+		count=0
+		for Ax in np.linspace(-0.5 , 0.5 , N):
+			for Ay in np.linspace(-0.5 , 0.5 , N):
+				for Bx in np.linspace(-0.5 , 0.5 , N):
+					for By in np.linspace(-0.5 , 0.5 , N):
+						for Cx in np.linspace(-0.5 , 0.5 , N):
+							for Cy in np.linspace(-0.5 , 0.5 , N):
+								count=count+1
+								if count>0:
+									x=divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1)
+									y=divding_triangle_across_line2(Ax,Ay,Bx,By,Cx,Cy, Px,Py, Qx, Qy)
+									#y=divding_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px,Py, Qx, Qy)
+									#if abs(x[0]-y[0])>0 or	 abs(x[1]-y[1])>0 or  abs(x[0]-z[0])>0 or  abs(x[1]-z[1])>0:
+									if abs(x[0]-y[0])>0 or	abs(x[1]-y[1])>0:
+										print ('Broken!!!: ', 'Ax, Ay =', Ax, Ay, 'Bx, By =' , Bx, By, 'Cx, Cy =' ,Cx, Cy)
+										print ('count', count)
+										print (x)
+										print( y)
+										plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy)
+										halt
+
+		print ('Test Successful')
+
+
+
+	if test_case=='Triangle_into_fours':
+		Px=1. ; Py=0. ; Qx=2. ; Qy=0. #x-axis
+		Rx=0. ; Ry=1. ; Sx=0. ; Sy=2. #y-axis
+
+		count=0
+		N=11 #Use an odd number
+		for Ax in np.linspace(-0.5 , 0.5 , N):
+			for Ay in np.linspace(-0.5 , 0.5 , N):
+				for Bx in np.linspace(-0.5 , 0.5 , N):
+					for By in np.linspace(-0.5 , 0.5 , N):
+						for Cx in np.linspace(-0.5 , 0.5 , N):
+							for Cy in np.linspace(-0.5 , 0.5 , N):
+								count=count+1
+								#print count
+								if count>0:
+									x=Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy)
+									y=Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy )
+									Error=abs(x[1]+x[2]+x[3]+x[4]-x[0])
+									#if Error>1e-15:
+									if abs(x[0]-y[0])>0 or	abs(x[1]-y[1])>0 or abs(x[2]-y[2])>0 or	 abs(x[3]-y[3])>0 or  abs(x[4]-y[4])>0 :
+										print ('Broken!!!: ', 'Ax, Ay =', Ax, Ay, 'Bx, By =' , Bx, By, 'Cx, Cy =' ,Cx, Cy)
+										print( 'count=', count)
+										#print 'Error = ', Error
+										print( x)
+										#print y
+										plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy)
+										halt
+
+		print ('Triangle_into_fours Test Successful')
+
+		#[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]=Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy);
+		#[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]= Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  )
+
+	if test_case=='Point_above_line':
+		x0=0.1 ;y0=0.3 ; Px=0.4; Py=-1.0; Qx=0.2; Qy=2.2
+		plt.plot(np.array([Px, Qx]), np.array([Py, Qy]))
+		plt.plot(x0,y0,'*')
+		print (Point_above_line(x0,y0,Px, Py, Qx, Qy))
+		plt.show()
+
+
+
+
+	if test_case=='many_hexagons':
+		Px=-1. ; Py=0. ; Qx=1. ; Qy=0. #x-axis
+		Rx=0. ; Ry=-1. ; Sx=0. ; Sy=1. #y-axis
+		N=101
+		theta=0.0
+		count=0
+		for x0 in np.linspace(-0.5 , 0.5 , N):
+			for y0 in np.linspace(-0.5 , 0.5 , N):
+				for H in np.linspace(0.0 , 0.5 , N):
+					count=count+1
+					#print count
+					if count>0:
+						C5x=-H/sqrt(3.) ; C5y=-H; #Corner 5 (bottom right)
+						C6x=H/sqrt(3.)	; C6y=-H; #Corner 6 (bottom right)
+						[C5x,C5y]=rotate_and_translate(C5x,C5y,theta,x0,y0)
+						[C6x,C6y]=rotate_and_translate(C6x,C6y,theta,x0,y0)
+						#x = Triangle_divided_into_four_parts(x0,y0,C5x,C5y,C6x,C6y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
+						#y = Triangle_divided_into_four_quadrants(x0,y0,C5x,C5y,C6x,C6y); #T023
+						#print x
+						#print y
+						#Ax=x0 ;  Ay=y0
+						#Bx=C5x ; By=C5y ;
+						#Cx=C6x ; Cy=C6y ;
+						#plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy)
+						#(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)=Hexagon_into_quadrants_using_triangles_across_lines(x0,y0,H,theta,  Px, Py, Qx, Qy, Rx, Ry, Sx, Sy )
+						#(Area_hexb, Area_Q1b, Area_Q2b, Area_Q3b, Area_Q4b)= Hexagon_into_quadrants_using_triangles(x0,y0,H,theta=0)
+						x=Hexagon_into_quadrants_using_triangles_across_lines(x0,y0,H,theta,  Px, Py, Qx, Qy, Rx, Ry, Sx, Sy )
+						y= Hexagon_into_quadrants_using_triangles(x0,y0,H,theta=0)
+						eps=1e-15
+						#eps=0.0
+						#if abs(Area_hex-Area_hexb)>eps or  abs(Area_Q1-Area_Q1b)>eps or abs(Area_Q2-Area_Q2b)>eps \
+						#		or  abs(Area_Q3-Area_Q3b)>eps or  abs(Area_Q4-Area_Q4b)>eps :
+						if abs(x[0]-y[0])>0 or	abs(x[1]-y[1])>0 or abs(x[2]-y[2])>0 or	 abs(x[3]-y[3])>0 or  abs(x[4]-y[4])>0 :
+							print ('Broken!!!: ', x0, y0, H)
+							print (Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4 )
+							print (Area_hexb, Area_Q1b, Area_Q2b, Area_Q3b, Area_Q4b)
+							print ('count=', count)
+							halt
+
+		print ('Many_Hexagons Test Successful')
+
+
+	if test_case=='hexagon':
+		H=1.
+		S=2.*H/sqrt(3.)
+		x0=0.
+		y0=0.
+		#(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Divide_hexagon_into_4_quadrants_old(x0,y0,H)
+		#print x0,y0,H
+		#print 'First version', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
+		(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Hexagon_into_quadrants_using_triangles(x0,y0,H,theta=0)
+		print ('Triangle version1',Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
+		(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Hexagon_into_quadrants_using_triangles(x0,y0,H,theta=90.)
+		print ('Triangle version2',Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
+
+		#print 'Analysis'
+		#print 'sum of quadrants: ', (Area_Q1+Area_Q2+Area_Q3+Area_Q4)
+		print ('Scaled areas: ')
+		print( (Area_Q1+Area_Q2+Area_Q3+Area_Q4)/Area_hex, Area_Q1/Area_hex, Area_Q2/Area_hex, Area_Q3/Area_hex, Area_Q4/Area_hex)
+
+
+	elif test_case=='square':
+
+		x0=0.6999999999999
+		y0=0.3
+		L=0.6
+		square_spreading_calculation(x0,y0,L)
+
+	elif test_case=='triangle':
+		Ax=-0.5
+		Ay=-0.3 -((8./9.)/10.)
+		Bx=-0.277777777778
+		By= -0.5
+
+		Cx=0.5
+		Cy=0.3 +((8./9.)/10.)
+
+		[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]=Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy); #T023
+
+		#Px=1. ; Py=0. ; Qx=2. ; Qy=0.
+		#Rx=0. ; Ry=1. ; Sx=0. ; Sy=2.
+		#[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]= Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  )
+
+		print ('Triangle 2: ',Ax,Ay,Bx,By,Cx,Cy)
+		print ('Full',T23_Q1+T23_Q2+T23_Q3+T23_Q4)
+		print ('Q1, Q2,Q3,Q4',T23_Q1,T23_Q2,T23_Q3,T23_Q4)
+		print ('Full triangle area',T23_Area)
+		print ('Error',(T23_Q1+T23_Q2+T23_Q3+T23_Q4-T23_Area))
+
+
+
+	elif test_case=='point_in_triangle':
+		Ax= -2.695732526092343E-012
+		Ay=0.204344508198090
+		Bx=-2.695750202346321E-012
+		By= -8.433062639672301E-002
+		Cx=0.249999999997304
+		Cy=6.000694090068343E-002
+		print ('Point in triangle', point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.))
+
+
+	print ('Script complete')
+
+if __name__ == '__main__':
+	main()
+	#sys.exit(main())
diff --git a/tests/a68_test/makeberg/hexagon_area.pyc b/tests/a68_test/makeberg/hexagon_area.pyc
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zQNN)=NAyb7&C=OM3Y}~&VZ&u>?!L~Qgi_o+cH`Yc$-FmjoIO6SRvaI9M(v^<(N>*#
z{53~Qkp9Cp)$7;h7F}T_ZoD?pkYZ<M`m)IjtXECJ%GP%t@9X?hru15Ki!&3K&1J59
z*#cB2ONa4j4mAH{+56-+E5nB7Cq&u!{IDn+!apKPiTZvC3XxbAJSXboGQKF|(=t9J
z!@k0x4eioz$<R<N{jLlfnJ<Ylk+2QUiQAz%ajil-;I%GCcB~YSUYjjnpQ*e`++BYo
z#%4Rdrz3nDxKYBpv**9{%=C=+4EOBdd8TKeXTIlE{O#!9-m|^u6+GK|Hut}(r=zF0
Vr>AFc&+eYCp6<O{dcM*h{U2C-!2AFJ

literal 0
HcmV?d00001

diff --git a/tests/a68/makeberg/makeberg.py b/tests/a68_test/makeberg/makeberg.py
similarity index 99%
rename from tests/a68/makeberg/makeberg.py
rename to tests/a68_test/makeberg/makeberg.py
index 9b6c6bc..d34547c 100755
--- a/tests/a68/makeberg/makeberg.py
+++ b/tests/a68_test/makeberg/makeberg.py
@@ -16,7 +16,7 @@
 
 
 import sys
-pypath = '/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/Iceberg_repository'
+pypath = '.'
 for dir_name in os.listdir(pypath):
         dir_path = os.path.join(pypath, dir_name)
         if os.path.isdir(dir_path):
@@ -66,13 +66,13 @@ def parseCommandLine():
 
         parser.add_argument('-ang_vel_prescribed', type=float, default=0.0,
                           help='''Prescibed angular velocity   ''')
-        
+
         parser.add_argument('-dx', type=float, default=250.0,
                           help='''dx for regrid   ''')
-        
+
         parser.add_argument('-icethres', type=float, default=0.5,
                           help='''threshold for whether a grid cell is ice or not   ''')
-        
+
         #Iceberg setup flags
         parser.add_argument('-only_choose_one_berg', type='bool', default=False,
                           help=''' When true, only one iceberg (with number chosen_berg_num) is written to icebergs.res. This is for debugging  ''')

From e13d1b610fbcae429a4e02998aea810340289597 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Wed, 28 Dec 2022 12:15:04 -0500
Subject: [PATCH 330/361] Removed experimental use_damage and power_ground
 options

---
 src/icebergs.F90                            |  14 +-
 src/icebergs_framework.F90                  |  91 +-------
 src/icebergs_io.F90                         |  28 +--
 tests/a68_test/.gitignore                   |   1 +
 tests/a68_test/input.nml                    | 224 --------------------
 tests/footloose_tests/input_FL_physical.nml |   2 +-
 tests/footloose_tests/input_FL_poisson.nml  |   2 +-
 7 files changed, 13 insertions(+), 349 deletions(-)
 create mode 100644 tests/a68_test/.gitignore
 delete mode 100644 tests/a68_test/input.nml

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index d881b89..a608c70 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -57,8 +57,8 @@ module ice_bergs
 use ice_bergs_framework, only: orig_dem_moment_of_inertia, no_frac_first_ts
 use ice_bergs_framework, only: A68_test, A68_xdisp, A68_ydisp
 use ice_bergs_framework, only: set_constant_interaction_length_and_width, skip_first_outer_mts_step
-use ice_bergs_framework, only: use_damage, damage_test_1_init, break_bonds_on_sub_steps
-use ice_bergs_framework, only: power_ground, short_step_mts_grounding, radius_based_drag
+use ice_bergs_framework, only: break_bonds_on_sub_steps
+use ice_bergs_framework, only: short_step_mts_grounding, radius_based_drag
 
 use ice_bergs_io,        only: ice_bergs_io_init, write_restart, write_trajectory, write_bond_trajectory
 use ice_bergs_io,        only: read_restart_bergs, read_restart_calving
@@ -180,7 +180,6 @@ subroutine icebergs_init(bergs, &
   endif
 
   if (bergs%uniaxial_test .or. bergs%dem_beam_test>0) call dem_tests_init(bergs)
-  if (bergs%damage_test_1) call damage_test_1_init(bergs)
 
   if (bergs%constant_interaction_LW .and. (bergs%constant_length==0. .or. bergs%constant_width==0.)) then
     call set_constant_interaction_length_and_width(bergs)
@@ -1684,9 +1683,6 @@ subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, d
       drag_atm=c_atm*0.5*(sqrt( (uveln-ua)**2+(vveln-va)**2 )+sqrt( (uvel0-ua)**2+(vvel0-va)**2 ))
       drag_ice=c_ice*0.5*(sqrt( (uveln-ui)**2+(vveln-vi)**2 )+sqrt( (uvel0-ui)**2+(vvel0-vi)**2 ))
       drag_gnd=c_gnd
-      if (power_ground) then
-        drag_gnd=c_gnd*max(0.5*(sqrt(uveln**2+vveln**2)+sqrt(uvel0**2+vvel0**2)),minfricvel)**(-2./3.)
-      endif
       !RHS ~ similar to accel terms in Stern et al 2017, Eqn B5
       RHS_x=(axn/2) + scaling*(-drag_ocn*(u_star-uo) -drag_atm*(u_star-ua) -drag_ice*(u_star-ui) -drag_gnd*u_star)
       RHS_y=(ayn/2) + scaling*(-drag_ocn*(v_star-vo) -drag_atm*(v_star-va) -drag_ice*(v_star-vi) -drag_gnd*v_star)
@@ -2608,9 +2604,6 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
     drag_atm=c_atm*0.5*(sqrt( (uveln-ua)**2+(vveln-va)**2 )+sqrt( (uvel0-ua)**2+(vvel0-va)**2 ))
     drag_ice=c_ice*0.5*(sqrt( (uveln-ui)**2+(vveln-vi)**2 )+sqrt( (uvel0-ui)**2+(vvel0-vi)**2 ))
     drag_gnd=c_gnd
-    if (power_ground) then
-      drag_gnd=c_gnd*max(0.5*(sqrt(uveln**2+vveln**2)+sqrt(uvel0**2+vvel0**2)),minfricvel)**(1.0/3.0 - 1.0)
-    endif
   else
     !Original Scheme
     us=0.5*(uveln+uvel); vs=0.5*(vveln+vvel)
@@ -2618,9 +2611,6 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
     drag_atm=c_atm*sqrt( (us-ua)**2+(vs-va)**2 )
     drag_ice=c_ice*sqrt( (us-ui)**2+(vs-vi)**2 )
     drag_gnd=c_gnd
-    if (power_ground) then
-      drag_gnd=c_gnd*max(sqrt(us**2+vs**2),minfricvel)**(1.0/3.0 - 1.0)
-    endif
   endif
 
   !RHS ~ similar to accel terms in Stern et al 2017, Eqn B5
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 3b3618a..d32938b 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -53,7 +53,6 @@ module ice_bergs_framework
 logical :: iceberg_bonds_on=.False. ! True=Allow icebergs to have bonds, False=don't allow.
 logical :: dem=.false. !< If T, run in DEM-mode with angular terms, variable stiffness, etc
 logical :: save_bond_forces=.true. !< If T, saves forces on bonds (TODO save on bond traj, too), so that only 1 of 2 bonds in a pair need to be processed during DEM-MTS explicit sub-steps
-logical :: power_ground=.false.
 logical :: short_step_mts_grounding=.false.
 logical :: radius_based_drag=.false. !if T, hex bergs, and dem, 2r is used as the area of the vert face for drag/wave forces
 logical :: A68_test=.false. !< If True, grounding will not be allowed west of 38 deg W nor North of 54.85 S
@@ -61,7 +60,6 @@ module ice_bergs_framework
 real :: A68_ydisp=0.
 logical :: rev_mind=.false.
 character(len=11) :: fracture_criterion='none' !<'energy','stress','strain_rate','strain',or 'none'
-logical :: use_damage=.false. !< Damage on bonds. Can evolve and serve as fracture criterion, or just to represent weaker bond
 logical :: orig_dem_moment_of_inertia=.false.
 logical :: break_bonds_on_sub_steps=.false.
 logical :: skip_first_outer_mts_step=.false.
@@ -74,7 +72,7 @@ module ice_bergs_framework
 public orig_read, force_all_pes_traj
 public mts,new_mts,save_bond_traj,ewsame,monitor_energy,iceberg_bonds_on
 public dem, save_bond_forces, fracture_criterion, orig_dem_moment_of_inertia
-public power_ground, short_step_mts_grounding, radius_based_drag
+public short_step_mts_grounding, radius_based_drag
 public A68_test, A68_xdisp, A68_ydisp
 
 !Public types
@@ -109,7 +107,7 @@ module ice_bergs_framework
 public fracture_testing_initialization, orig_bond_length
 public energy_tests_init,dem_tests_init
 public init_dem_params
-public set_constant_interaction_length_and_width,use_damage,damage_test_1_init
+public set_constant_interaction_length_and_width
 public break_bonds_on_sub_steps, skip_first_outer_mts_step, no_frac_first_ts
 
 !> Container for gridded fields
@@ -403,7 +401,6 @@ module ice_bergs_framework
   ! Fracture parameters:
   !The following are accumulated over all timesteps, unless fracture_criterion=='strain_rate',
   !in which case the following correspond to only the most recent timestep and units are s^(-1)
-  real, allocatable :: damage
   real, allocatable :: rotation !radians
   real, allocatable :: rel_rotation !<non-dem mode: rotation relative to the mean of all bonds for a berg
   !!dem-mode: relative rotation between two bonded particles (radians)
@@ -446,7 +443,6 @@ module ice_bergs_framework
   integer(kind=8) :: id2 !<ID of second berg
   type(bond_xyt), pointer :: next=>null() !< Next link in list
   ! Fracture parameters:
-  real, allocatable :: damage
   real, allocatable :: rotation !radians
   real, allocatable :: rel_rotation !<rotation relative to the mean of all bonds for a berg
   real, allocatable :: n_frac_var !<normal strain, stress, or spring energy
@@ -507,10 +503,9 @@ module ice_bergs_framework
   real :: contact_spring_coef !<Spring coefficient for berg collisions -Alex
   real :: cdrag_grounding=0.0 !< Drag coefficient against ocean bottom
   real :: h_to_init_grounding
-  character(len=11) :: fracture_criterion='none' !<'damage','energy','stress','strain_rate','strain',or 'none'
+  character(len=11) :: fracture_criterion='none' !<'energy','stress','strain_rate','strain',or 'none'
   real :: frac_thres_n=0.0 !normal fracture strain threshold
   real :: frac_thres_t=0.0 !tangential fracture strain threshold
-  logical :: damage_test_1=.false. !< Sets initial damage for bonds that overlap y=17000.0
   logical :: debug_write=.false. !< Sets traj_sample_hours=traj_write_hours & includes halo bergs in write
   real :: bond_coef !< Spring constant for iceberg bonds
   real :: radial_damping_coef !< Coefficient for relative iceberg motion damping (radial component) -Alon
@@ -773,7 +768,6 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: h_to_init_grounding=100.0
 real :: frac_thres_n=0.0 !normal fracture strain threshold
 real :: frac_thres_t=0.0 !tangential fracture strain threshold
-logical :: damage_test_1=.false. ! Sets initial damage for bonds that overlap y=17000.0
 real :: frac_thres_scaling=1.0 !scaling factor for frac_thres_n and frac_thres_t, useful for tuning
 logical :: debug_write=.false. !Sets traj_sample_hours=traj_write_hours & includes halo bergs in write
 real :: bond_coef=1.e-8 ! Spring constant for iceberg bonds - not being used right now
@@ -925,11 +919,11 @@ subroutine ice_bergs_framework_init(bergs, &
          read_old_restarts, tau_calving, read_ocean_depth_from_file, melt_cutoff,apply_thickness_cutoff_to_gridded_melt,&
          apply_thickness_cutoff_to_bergs_melt, use_mixed_melting, internal_bergs_for_drag, coastal_drift, tidal_drift,&
          mts,new_mts,ewsame,monitor_energy,mts_sub_steps,contact_distance,length_for_manually_initialize_bonds,&
-         manually_initialize_bonds_from_radii,contact_spring_coef,fracture_criterion, damage_test_1, uniaxial_test, &
+         manually_initialize_bonds_from_radii,contact_spring_coef,fracture_criterion, uniaxial_test, &
          debug_write,cdrag_grounding,h_to_init_grounding,frac_thres_scaling,frac_thres_n,frac_thres_t,save_bond_traj,&
          remove_unused_bergs,force_convergence,explicit_inner_mts,convergence_tolerance,dem,ignore_tangential_force,poisson,&
          dem_spring_coef,dem_damping_coef,dem_beam_test,constant_interaction_LW,constant_length,constant_width,&
-         dem_shear_for_frac_only,use_damage,fl_use_poisson_distribution, fl_use_perimeter, fl_r, fl_r_s,displace_fl_bergs,&
+         dem_shear_for_frac_only,fl_use_poisson_distribution, fl_use_perimeter, fl_r, fl_r_s,displace_fl_bergs,&
          fl_style,fl_bits_erosion_to_bergy_bits,fl_k_scale_by_perimeter,use_spring_for_land_contact, save_fl_traj,&
          new_berg_from_fl_bits_mass_thres,fl_bits_scale_l,fl_bits_scale_w,fl_bits_scale_t,separate_distrib_for_n_hemisphere,&
          initial_mass_n, distribution_n, mass_scaling_n, initial_thickness_n, fl_use_l_scale, fl_l_scale,&
@@ -938,7 +932,7 @@ subroutine ice_bergs_framework_init(bergs, &
          traj_area_thres_fl,tau_is_velocity, ocean_drag_scale, A68_test, &
          A68_xdisp,A68_ydisp,use_broken_bonds_for_substep_contact,&
          orig_dem_moment_of_inertia, break_bonds_on_sub_steps, skip_first_outer_mts_step, rev_mind, &
-         no_frac_first_ts, use_grounding_torque, power_ground, short_step_mts_grounding, radius_based_drag, save_bond_forces
+         no_frac_first_ts, use_grounding_torque, short_step_mts_grounding, radius_based_drag, save_bond_forces
 
 ! Local variables
 integer :: ierr, iunit, i, j, id_class, axes3d(3), is,ie,js,je,np
@@ -1378,11 +1372,6 @@ subroutine ice_bergs_framework_init(bergs, &
 endif
 if (ignore_traj) buffer_width_traj=0 ! If this is true, then all traj files should be ignored
 
-if (use_damage) then
-  buffer_width=buffer_width+(max_bonds*1)
-  buffer_width_bond_traj=buffer_width_bond_traj+1
-endif
-
 if (monitor_energy) then
   buffer_width=buffer_width+11+(max_bonds*6)
   buffer_width_traj=buffer_width_traj+6
@@ -1476,7 +1465,6 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%spring_coef=spring_coef
   bergs%contact_spring_coef=contact_spring_coef !Alex
   bergs%fracture_criterion=fracture_criterion
-  bergs%damage_test_1=damage_test_1
   bergs%uniaxial_test=uniaxial_test
   bergs%cdrag_grounding=cdrag_grounding
   bergs%h_to_init_grounding=h_to_init_grounding
@@ -3551,10 +3539,6 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
         call push_buffer_value(buff%data(:,n), counter, current_bond%other_berg_jne)
         call push_buffer_value(buff%data(:,n), counter, current_bond%length)
 
-        if (use_damage) then
-          call push_buffer_value(buff%data(:,n), counter, current_bond%damage)
-        endif
-
         if (monitor_energy) then
           call push_buffer_value(buff%data(:,n), counter, current_bond%Ee)
           call push_buffer_value(buff%data(:,n), counter, current_bond%Ed)
@@ -3591,10 +3575,6 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
         call push_buffer_value(buff%data(:,n), counter, 0)
         call push_buffer_value(buff%data(:,n), counter, 0)
 
-        if (use_damage) then
-          call push_buffer_value(buff%data(:,n), counter, 0)
-        endif
-
         if (monitor_energy) then
           call push_buffer_value(buff%data(:,n), counter, 0)
           call push_buffer_value(buff%data(:,n), counter, 0)
@@ -3974,10 +3954,6 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
         current_bond=>this%first_bond
         current_bond%length=length
 
-        if (use_damage) then
-          call pull_buffer_value(buff%data(:,n), counter, current_bond%damage)
-        endif
-
         if (monitor_energy) then
           call pull_buffer_value(buff%data(:,n), counter, current_bond%Ee)
           call pull_buffer_value(buff%data(:,n), counter, current_bond%Ed)
@@ -4306,10 +4282,6 @@ subroutine pack_bond_traj_into_buffer2(bond_traj, buff, n)
   call push_buffer_value(buff%data(:,n),counter,cnt2)
   call push_buffer_value(buff%data(:,n),counter,ij2)
 
-  if (use_damage) then
-    call push_buffer_value(buff%data(:,n),counter,bond_traj%damage)
-  endif
-
   if (monitor_energy) then
     call push_buffer_value(buff%data(:,n),counter,bond_traj%Ee)
     call push_buffer_value(buff%data(:,n),counter,bond_traj%Ed)
@@ -4350,9 +4322,6 @@ subroutine unpack_bond_traj_from_buffer2(first, buff, n)
   integer :: counter ! Position in stack
   integer :: cnt1, ij1, cnt2, ij2
 
-  if (use_damage) then
-    allocate(bond_traj%damage)
-  endif
   if (monitor_energy) then
     allocate(bond_traj%Ee,bond_traj%Ed,bond_traj%axn_fast,bond_traj%ayn_fast,bond_traj%bxn_fast,bond_traj%byn_fast)
   endif
@@ -4382,10 +4351,6 @@ subroutine unpack_bond_traj_from_buffer2(first, buff, n)
   call pull_buffer_value(buff%data(:,n),counter,ij2)
   bond_traj%id2 = id_from_2_ints(cnt2, ij2)
 
-  if (use_damage) then
-    call pull_buffer_value(buff%data(:,n),counter,bond_traj%damage)
-  endif
-
   if (monitor_energy) then
     call pull_buffer_value(buff%data(:,n),counter,bond_traj%Ee)
     call pull_buffer_value(buff%data(:,n),counter,bond_traj%Ed)
@@ -5058,35 +5023,6 @@ subroutine fracture_testing_initialization(bergs)
   enddo;enddo
 end subroutine fracture_testing_initialization
 
-!< Sets initial damage for bonds that overlap y=17000.0
-subroutine damage_test_1_init(bergs)
-type(icebergs), pointer :: bergs !< Container for all types and memory
-type(iceberg), pointer :: berg, other_berg
-type(bond) , pointer :: current_bond
-type(icebergs_gridded), pointer :: grd
-integer :: grdi, grdj
-
-  print *,'DAMAGE TEST 1 INITIALIZATION'
-  grd=>bergs%grd
-  do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
-    berg=>bergs%list(grdi,grdj)%first
-    do while (associated(berg)) ! loop over all bergs
-      current_bond=>berg%first_bond
-      do while (associated(current_bond)) ! loop over all bonds
-        other_berg=>current_bond%other_berg
-        if (associated(current_bond%other_berg)) then
-          if ((other_berg%lat>17000.0 .and. berg%lat<=17000.0) .or. &
-            (berg%lat>17000.0 .and. other_berg%lat<=17000.0)) then
-            current_bond%damage=0.75
-          endif
-        endif
-        current_bond=>current_bond%next_bond
-      enddo
-      berg=>berg%next
-    enddo
-  enddo; enddo
-end subroutine damage_test_1_init
-
 !> Save number of bonds on element
 subroutine assign_n_bonds(bergs)
 type(icebergs), pointer :: bergs !< Container for all types and memory
@@ -5499,11 +5435,6 @@ subroutine break_bonds_dem(bergs)
       current_bond=>this%first_bond
       do while (associated(current_bond)) ! loop over all bonds
 
-        if (use_damage) then
-          frac_thres_n=bergs%frac_thres_n*(1.-current_bond%damage)
-          frac_thres_t=bergs%frac_thres_t*(1.-current_bond%damage)
-        endif
-
         if (current_bond%other_id.ne.-1) then
 
           if (bergs%fracture_criterion=='stress') then
@@ -5615,9 +5546,6 @@ subroutine form_a_bond(berg, other_id, other_berg_ine, other_berg_jne, other_ber
 
   ! Step 1: Create a new bond
   allocate(new_bond)
-  if (use_damage) then
-    allocate(new_bond%damage); new_bond%damage=0.
-  endif
   if (monitor_energy) then
     allocate(new_bond%Ee,new_bond%Ed,new_bond%axn_fast,new_bond%ayn_fast,new_bond%bxn_fast,new_bond%byn_fast)
     new_bond%Ee=0.; new_bond%Ed=0.; new_bond%axn_fast=0.; new_bond%ayn_fast=0.; new_bond%bxn_fast=0.; new_bond%byn_fast=0.
@@ -6169,7 +6097,6 @@ subroutine record_posn(bergs)
   endif
 
   if (save_bond_traj) then
-    if (use_damage) allocate(bond_posn%damage)
     if (monitor_energy) then
       allocate(bond_posn%Ee,bond_posn%Ed,bond_posn%axn_fast,bond_posn%ayn_fast,bond_posn%bxn_fast,bond_posn%byn_fast)
     endif
@@ -6314,10 +6241,6 @@ subroutine record_posn(bergs)
               bond_posn%n1=n1;                      bond_posn%n2=n2
               bond_posn%id1=this%id;                bond_posn%id2=other_berg%id
 
-              if (use_damage) then
-                bond_posn%damage=current_bond%damage
-              endif
-
               if (monitor_energy) then
                 bond_posn%Ee=current_bond%Ee
                 bond_posn%Ed=current_bond%Ed
@@ -6399,7 +6322,6 @@ subroutine push_bond_posn(bond_trajectory, bond_posn_vals)
 
   allocate(new_bond_posn)
 
-  if (use_damage) allocate(new_bond_posn%damage)
   if (monitor_energy) then
     allocate(new_bond_posn%Ee,new_bond_posn%Ed,new_bond_posn%axn_fast,new_bond_posn%ayn_fast,&
       new_bond_posn%bxn_fast,new_bond_posn%byn_fast)
@@ -6474,7 +6396,6 @@ subroutine append_bond_posn(bond_trajectory, bond_posn_vals)
 
   allocate(new_bond_posn)
 
-  if (use_damage) allocate(new_bond_posn%damage)
   if (monitor_energy) then
     allocate(new_bond_posn%Ee,new_bond_posn%Ed,new_bond_posn%axn_fast,new_bond_posn%ayn_fast,&
       new_bond_posn%bxn_fast,new_bond_posn%byn_fast)
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index 0e48343..c0eec7f 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -44,7 +44,7 @@ module ice_bergs_io
 use ice_bergs_framework, only: mts,save_bond_traj
 use ice_bergs_framework, only: push_bond_posn, append_bond_posn
 use ice_bergs_framework, only: pack_bond_traj_into_buffer2,unpack_bond_traj_from_buffer2
-use ice_bergs_framework, only: monitor_energy, use_damage, dem, fracture_criterion, iceberg_bonds_on
+use ice_bergs_framework, only: monitor_energy, dem, fracture_criterion, iceberg_bonds_on
 
 implicit none ; private
 
@@ -156,7 +156,6 @@ subroutine write_restart(bergs, time_stamp)
                                    ayn_fast,     &
                                    bxn_fast,     &
                                    byn_fast,     &
-                                   damage,       &
                                    ang_vel,      &
                                    ang_accel,    &
                                    rot,          &
@@ -475,7 +474,6 @@ subroutine write_restart(bergs, time_stamp)
   allocate(other_berg_ine(nbonds))
   allocate(other_berg_jne(nbonds))
 
-  if (use_damage) allocate(damage(nbonds))
   if (dem) then
     allocate(tangd1(nbonds))
     allocate(tangd2(nbonds))
@@ -512,10 +510,6 @@ subroutine write_restart(bergs, time_stamp)
   id = register_restart_field(bergs_bond_restart,filename_bonds,'other_id_cnt',other_id_cnt,longname='counter component of iceberg id second berg in bond',units='dimensionless')
   id = register_restart_field(bergs_bond_restart,filename_bonds,'other_id_ij',other_id_ij,longname='position component of iceberg id second berg in bond',units='dimensionless')
 
-  if (use_damage) then
-    id = register_restart_field(bergs_bond_restart,filename_bonds,'damage',damage,&
-      longname='damage',units='dimensionless')
-  endif
   if (dem) then
     id = register_restart_field(bergs_bond_restart,filename_bonds,'tangd1',tangd1,&
       longname='zonal tangential displacement',units='m')
@@ -561,7 +555,6 @@ subroutine write_restart(bergs, time_stamp)
         other_berg_ine(i)=current_bond%other_berg%ine
         other_berg_jne(i)=current_bond%other_berg%jne
 
-        if (use_damage) damage(i)=current_bond%damage
         if (dem) then
           tangd1(i)=current_bond%tangd1
           tangd2(i)=current_bond%tangd2
@@ -2284,7 +2277,7 @@ subroutine write_bond_trajectory(trajectory, bond_traj_name)
 ! Local variables
 integer :: iret, ncid, i_dim, i
 integer :: lonid, latid, yearid, dayid, lenid,n1id, n2id, peid
-integer :: rotid,rrotid,nsid,nsrid, damid, brid
+integer :: rotid,rrotid,nsid,nsrid, brid
 integer :: idcnt1_id, idcnt2_id, idij1_id, idij2_id, eeid, edid
 integer :: axid,ayid,bxid,byid
 integer :: td1id,td2id,dnsid,dssid
@@ -2403,10 +2396,6 @@ subroutine write_bond_trajectory(trajectory, bond_traj_name)
       idcnt1_id = inq_varid(ncid, 'id_cnt1'); idij1_id = inq_varid(ncid, 'id_ij1')
       idcnt2_id = inq_varid(ncid, 'id_cnt2'); idij2_id = inq_varid(ncid, 'id_ij2')
 
-      if (use_damage) then
-        damid = inq_varid(ncid, 'damage')
-      endif
-
       if (monitor_energy) then
         eeid = inq_varid(ncid, 'Ee');       edid = inq_varid(ncid, 'Ed')
         axid = inq_varid(ncid, 'axn_fast'); ayid = inq_varid(ncid, 'ayn_fast')
@@ -2441,10 +2430,6 @@ subroutine write_bond_trajectory(trajectory, bond_traj_name)
       idcnt1_id = def_var(ncid, 'id_cnt1', NF_INT, i_dim); idij1_id = def_var(ncid, 'id_ij1', NF_INT, i_dim)
       idcnt2_id = def_var(ncid, 'id_cnt2', NF_INT, i_dim); idij2_id = def_var(ncid, 'id_ij2', NF_INT, i_dim)
 
-      if (use_damage) then
-        damid = def_var(ncid, 'damage', NF_DOUBLE, i_dim)
-      endif
-
       if (monitor_energy) then
         eeid = def_var(ncid, 'Ee', NF_DOUBLE, i_dim);       edid = def_var(ncid, 'Ed', NF_DOUBLE, i_dim)
         axid = def_var(ncid, 'axn_fast', NF_DOUBLE, i_dim); ayid = def_var(ncid, 'ayn_fast', NF_DOUBLE, i_dim)
@@ -2486,11 +2471,6 @@ subroutine write_bond_trajectory(trajectory, bond_traj_name)
       call put_att(ncid, idij2_id, 'long_name', 'position component of second connected iceberg id')
       call put_att(ncid, idij2_id, 'units', 'dimensionless')
 
-      if (use_damage) then
-        call put_att(ncid, damid, 'long_name', 'damage')
-        call put_att(ncid, damid, 'units', 'none')
-      endif
-
       if (monitor_energy) then
         call put_att(ncid, eeid, 'long_name', 'elastic energy'); call put_att(ncid, eeid, 'units', 'J')
         call put_att(ncid, edid, 'long_name', 'damping energy'); call put_att(ncid, edid, 'units', 'J')
@@ -2548,10 +2528,6 @@ subroutine write_bond_trajectory(trajectory, bond_traj_name)
       call split_id(this%id2, cnt, ij)
       call put_int(ncid, idcnt2_id, i, cnt);        call put_int(ncid, idij2_id, i, ij)
 
-      if (use_damage) then
-        call put_double(ncid,damid,i,this%damage)
-      endif
-
       if (monitor_energy) then
         call put_double(ncid,eeid,i,this%Ee);       call put_double(ncid,edid,i,this%Ed)
         call put_double(ncid,axid,i,this%axn_fast); call put_double(ncid,ayid,i,this%ayn_fast)
diff --git a/tests/a68_test/.gitignore b/tests/a68_test/.gitignore
new file mode 100644
index 0000000..3ca2294
--- /dev/null
+++ b/tests/a68_test/.gitignore
@@ -0,0 +1 @@
+input.nml
\ No newline at end of file
diff --git a/tests/a68_test/input.nml b/tests/a68_test/input.nml
deleted file mode 100644
index 5f38abe..0000000
--- a/tests/a68_test/input.nml
+++ /dev/null
@@ -1,224 +0,0 @@
-!! with short_step_mts_grounding=.true. :
-!! KID, bergs_chksum: write_restart berg chksum=2003283855 chksum2=-936278869 chksum3=399994109 chksum4=399994109 chksum5=0 #=472
-
-!! without short_step_mts_grounding=.true :
-
-
-&icebergs_driver_nml
-  a68_test=.true.
-  vert_int_ocean_vel=.false.!.true.
-  !specify your data dir (ocean currents, winds, etc)
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68_test/data/'
-  Old_wrong_Rearth_and_SSH=.false.
-  !mom_Rearth=.true.
-  Rearth=6363827
-  !6363827 !6.378e6
-  no_wind=.false.
-  tau_is_velocity=.true.!.false.
-  ibdt=1800.0 !seconds
-  ibuo=0.0 !ocean x velocity
-  ibvo=0.0 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=432 !total simulation hours
-  write_time_inc = 48 !increment at which time is written to screen
-  nmax=999999999 !max number of timesteps
-  saverestart=.true.!.false.
-  halo=3
-  debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=206 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
-/
-
-&icebergs_nml
-
-    Rearth=6363827
-
-    A68_test=.true.
-    A68_xdisp=-37.51
-    A68_ydisp=-55.2166
-    short_step_mts_grounding=.true.
-
-    tau_is_velocity=.true.
-    ocean_drag_scale=17.8
-
-    skip_first_outer_mts_step=.true.
-
-    constant_interaction_LW=.true.
-
-    traj_name=longrun_od_17.8_tn_ng_ydn.1_ss90_ns18_rx-37.51_ry-55.2166.nc
-    bond_traj_name=longrun_od_17.8_tn_ng_ydn.1_ss90_ns18_rx-37.51_ry-55.2166_bonds.nc
-
-    break_bonds_on_sub_steps=.true.
-
-    save_bond_forces=.true.
-    use_broken_bonds_for_substep_contact=.true.
-    
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    explicit_inner_mts=.true.
-    rho_bergs=850. ! (850) iceberg density
-    !dem_spring_coef=E=youngs. For hexagonal packing and a constant radius and density for all elements,
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5
-    dem_spring_coef=5e6 !Young's Modulus
-
-    !As coded, the short-step contact model is the same as the long-step contact, but really
-    !we want the short-step contact model to be the same as the short-step bonded-interaction model
-    !for A68a, which is accomplished by setting this short-step spring constant as follows:
-    !(TODO: replace the short-step contact model to be the same as the short-step bonded interactions?)
-    spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500, with square packing
-
-    monitor_energy=.false.
-    !defaults given in parentheses:
-    new_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=90 !# of mts sub-steps
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-4 ! tolerance for the MTS force_convergence scheme
-
-    contact_distance=4.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    cdrag_grounding=1.e4 !0.!1.e6!3.16e6!1.e6!1.e3!3.16e6 !for power-law-type friction
-    h_to_init_grounding=0!30!15!50. !15.
-    ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
-
-    fracture_criterion='stress' !('none') 'strain_rate','strain',or 'none'
-    frac_thres_scaling = 1
-    frac_thres_n = 18e3
-    frac_thres_t = 100e3
-
-    halo=3 !(4) halo width
-    Lx=360 !(360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.true. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.false. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.false. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=0.!1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=0.0!2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    scale_damping_by_pmag=.false. !(T) Scales damping by mag of (proj matrix \cdot relvel)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    tang_crit_int_damp_on=.false. !(F) critical interaction tamping for tangential component?
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0. !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.true. !(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=4 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.true. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.false. !(F) Be verbose to stderr
-    verbose_hrs=1! (24) Period between verbose messages
-    traj_sample_hrs=0!1 !(24) sampling period for trajectory storage
-    traj_write_hrs=0!6 !(480) Period for writing sampled trajectories to disk
-    save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    manually_initialize_bonds_from_radii=.true.
-    !length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.false. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
\ No newline at end of file
diff --git a/tests/footloose_tests/input_FL_physical.nml b/tests/footloose_tests/input_FL_physical.nml
index c3d53fe..6b4d7f5 100644
--- a/tests/footloose_tests/input_FL_physical.nml
+++ b/tests/footloose_tests/input_FL_physical.nml
@@ -111,7 +111,7 @@
     verbose_hrs=24 ! (24) Period between verbose messages
     traj_sample_hrs=1 !1 !(24) sampling period for trajectory storage
     traj_write_hrs=24 ! (480) Period for writing sampled trajectories to disk
-    budget=.true.!.false. !(T) Calculate budgets
+    budget=.false. !(T) Calculate budgets
     debug=.false. !(F) Turn on debugging
     really_debug=.false. !(F) Turn on debugging
     halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
diff --git a/tests/footloose_tests/input_FL_poisson.nml b/tests/footloose_tests/input_FL_poisson.nml
index 5cfc651..feace6a 100644
--- a/tests/footloose_tests/input_FL_poisson.nml
+++ b/tests/footloose_tests/input_FL_poisson.nml
@@ -106,7 +106,7 @@
     verbose_hrs=24 ! (24) Period between verbose messages
     traj_sample_hrs=1 !1 !(24) sampling period for trajectory storage
     traj_write_hrs=24 ! (480) Period for writing sampled trajectories to disk
-    budget=.true.!.false. !(T) Calculate budgets
+    budget=.false. !(T) Calculate budgets
     debug=.false. !(F) Turn on debugging
     really_debug=.false. !(F) Turn on debugging
     halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)

From 51cba6b7f4d1c6bcff09094f490edcdbc0f6ecdc Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Wed, 28 Dec 2022 16:27:44 -0500
Subject: [PATCH 331/361] more clean up -removed 'dem_shear_for_frac_only' -set
 new_mts to default -converted some print statements into write statements
 -removed some old commented code -cleaned up A68a code in icebergs.F90 -added
 comments for some namelist options -added option 'print_fracture' to write
 bond/particle info to screen when fracture occurs

---
 src/icebergs.F90                        | 310 ++++++------------------
 src/icebergs_framework.F90              |  58 ++---
 tests/a68_test/long_run.nml             |   1 -
 tests/collision_tests/input.nml         |   1 -
 tests/collision_tests/input_KID.nml     |   1 -
 tests/collision_tests/input_MTS_KID.nml |   1 -
 tests/collision_tests/input_iKID.nml    |   1 -
 tests/dem_cbeam_test/input.nml          |   7 +-
 tests/dem_ground_frac_test/input.nml    |   1 -
 tests/dem_ssbeam_test/input.nml         |   1 -
 10 files changed, 100 insertions(+), 282 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index a608c70..202107c 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -51,7 +51,7 @@ module ice_bergs
 use ice_bergs_framework, only: fracture_testing_initialization, orig_bond_length
 use ice_bergs_framework, only: update_and_break_bonds,break_bonds_dem,assign_n_bonds,reset_bond_rotation
 use ice_bergs_framework, only: update_bond_angles
-use ice_bergs_framework, only: monitor_energy, energy_tests_init, mts, new_mts
+use ice_bergs_framework, only: monitor_energy, energy_tests_init, mts
 use ice_bergs_framework, only: dem_tests_init
 use ice_bergs_framework, only: dem, init_dem_params, save_bond_forces
 use ice_bergs_framework, only: orig_dem_moment_of_inertia, no_frac_first_ts
@@ -1078,7 +1078,7 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
     r_dist_y=(berg%lat_old-other_berg%lat_old)*dy_dlat
     current_bond%length=sqrt( (r_dist_x**2) + (r_dist_y**2) ) !(Stern et al 2017, Eqn 3)
 
-    if (current_bond%length==0) print *,'r_dist,berg%lat_old,berg%lon_old,other_berg%lat_old,other_berg%lon_old',current_bond%length,berg%lat,berg%lon,other_berg%lat,other_berg%lon
+    if (current_bond%length==0) call error_mesg('KID, calculate_force_dem', 'bond with zero length!', FATAL)
     !unit vec
     n1=r_dist_x/current_bond%length; n2=r_dist_y/current_bond%length
 
@@ -1175,12 +1175,17 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
 
           if (current_bond%broken.ne.1) then
             current_bond%broken=1
-            if (current_bond%nstress>bergs%frac_thres_n .and. current_bond%sstress>bergs%frac_thres_t) then
-              print *,'T and S break',berg%lat,current_bond%nstress,current_bond%sstress
-            elseif (current_bond%nstress>bergs%frac_thres_n) then
-              print *,'TENSILE break',berg%lat,current_bond%nstress,current_bond%sstress
-            else
-              print *,'SHEAR   break',berg%lat,current_bond%nstress,current_bond%sstress
+            if (bergs%print_fracture) then
+              if (current_bond%nstress>bergs%frac_thres_n .and. current_bond%sstress>bergs%frac_thres_t) then
+                write(*,'(a,4(x,a,es12.2))'),'T and S break: ',&
+                  'lat',berg%lat,'lon',berg%lon,'nstress',current_bond%nstress,'sstress',current_bond%sstress
+              elseif (current_bond%nstress>bergs%frac_thres_n) then
+                write(*,'(a,4(x,a,es12.2))'),'TENSILE break: ',&
+                  'lat',berg%lat,'lon',berg%lon,'nstress',current_bond%nstress,'sstress',current_bond%sstress
+              else
+                write(*,'(a,4(x,a,es12.2))'),'SHEAR break:   ',&
+                  'lat',berg%lat,'lon',berg%lon,'nstress',current_bond%nstress,'sstress',current_bond%sstress
+              endif
             endif
           endif
 
@@ -1259,10 +1264,6 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
     Fd_x = Fd_x-damping_coef*ur; Fd_y = Fd_y-damping_coef*vr  !linear damping force
     T_d  = T_d-damping_coef*(berg%ang_vel-other_berg%ang_vel) !damping torque
 
-    if (bergs%dem_shear_for_frac_only) then
-      Fs_x=0.; Fs_y=0.
-    endif
-
     !final forces
     T = T + (Ts + Tr) !torque
     F_x = F_x + Fn_x + Fs_x; F_y = F_y + Fn_y + Fs_y !linear forces
@@ -1495,7 +1496,7 @@ subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, d
   logical :: use_new_predictive_corrective !Flad to use Bob's predictive corrective scheme. (default off)
   integer :: itloop
   integer :: stderrunit
-  real :: dragfrac, N_bonds, N_max, groundfrac, c_gnd, drag_gnd, scaling
+  real :: dragfrac, N_bonds, N_max, groundfrac, c_gnd, drag_gnd, scaling=0.5
   real :: minfricvel=3.17e-12 !m/s (~0.0001 m/a)
   type(bond), pointer :: current_bond
   real :: IAd_x, IAd_y, sum_bond_Ee, sum_bond_Ed, oneoverkn, M2
@@ -1519,12 +1520,6 @@ subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, d
     uvel=berg%uvel;   vvel=berg%vvel
   endif
 
-  if (new_mts) then
-    scaling=0.5
-  else
-    scaling=1.0
-  endif
-
   ! Initializing accelerations
   axn=0.; ayn=0.; bxn=0.; byn=0.
 
@@ -1577,12 +1572,6 @@ subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, d
     endif
     if (short_step_mts_grounding) c_gnd=0.
 
-    !For testing sensitivity to number of short steps
-    ! if ((groundfrac.ne.0.) .and. (bergs%mts_sub_steps>200)) then
-    !   print *,'changing # of ss to 200'
-    !   bergs%mts_sub_steps=200
-    ! endif
-
     ! Wave radiation (Stern et al 2017, Eqs A4-A5)
     uwave=ua-uo; vwave=va-vo  ! Use wind speed rel. to ocean for wave model (aja)
     wmod=uwave*uwave+vwave*vwave ! The wave amplitude and length depend on the wind speed relative to the ocean current
@@ -1732,15 +1721,9 @@ subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, d
     axn=axn+f_cori*vveln; ayn=ayn-f_cori*uveln    !for Crank Nicolson Coriolis
   endif
 
-  if (new_mts) then
-    !ax = 0.5*(axn + bxn)
-    !where uvel_new = uvel_old + dt*ax
-    bxn = 2*ax-axn; byn = 2*ay-ayn
-  else
-    !ax = axn/2 + bxn
-    !where uvel_new = uvel_old + dt*ax
-    bxn= ax-(axn/2); byn= ay-(ayn/2) !Alon
-  endif
+  !ax = 0.5*(axn + bxn)
+  !where uvel_new = uvel_old + dt*ax
+  bxn = 2*ax-axn; byn = 2*ay-ayn
 
   if (bergs%mts_part==1) then
     !collisional elastic forces
@@ -1776,11 +1759,11 @@ subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, d
             (uvel0 + u_star)*M*current_bond%axn_fast +&
             (vvel0 + v_star)*M*current_bond%ayn_fast)
 
-          if (new_mts) then
-            current_bond%Ed=current_bond%Ed - 0.25*dt*(&
-              (uvel0 + u_star)*M*current_bond%bxn_fast +&
-              (vvel0 + v_star)*M*current_bond%byn_fast)
-          endif
+
+          current_bond%Ed=current_bond%Ed - 0.25*dt*(&
+            (uvel0 + u_star)*M*current_bond%bxn_fast +&
+            (vvel0 + v_star)*M*current_bond%byn_fast)
+
         endif
 
         !the rest:
@@ -1811,17 +1794,10 @@ subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, d
             (u_star + uveln)*M*IA_x + &
             (v_star + vveln)*M*IA_y)
 
-
-          if (new_mts) then
-            !V{i+0.5} to V{i+1}
-            current_bond%Ed=current_bond%Ed- 0.25*dt*(&
-              (u_star + uveln)*M*IAd_x + &
-              (v_star + vveln)*M*IAd_y)
-          else
-            current_bond%Ed=current_bond%Ed - 0.5*dt*(&
-              (u_star + uveln)*M*IAd_x + &
-              (v_star + vveln)*M*IAd_y)
-          endif
+          !V{i+0.5} to V{i+1}
+          current_bond%Ed=current_bond%Ed- 0.25*dt*(&
+            (u_star + uveln)*M*IAd_x + &
+            (v_star + vveln)*M*IAd_y)
 
           sum_bond_Ee = sum_bond_Ee + current_bond%Ee
           sum_bond_Ed = sum_bond_Ed + current_bond%Ed
@@ -2185,27 +2161,6 @@ subroutine accel_explicit_inner_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel,
     IA_x=IA_x+F_x/M; IA_y=IA_y+F_y/M
     IAd_x=IAd_x+Fd_x/M; IAd_y=IAd_y+Fd_y/M
 
-    ! !torque from grounding drag
-    ! !start to feel grounded with draught of bergs%h_to_init_grounding meters of the sea floor topography
-    ! !at groundfrac=0, apply no grounding force. at groundfrac=1, apply max grounding force
-    ! D=(bergs%rho_bergs/rho_seawater)*berg%thickness ! draught (keel depth)
-    ! if (bergs%h_to_init_grounding>0.0) then
-    !   groundfrac=1.0-(berg%od-D)/bergs%h_to_init_grounding
-    !   groundfrac=max(groundfrac,0.0); groundfrac=min(groundfrac,1.0)
-    ! else
-    !   if (D>berg%od) then
-    !     groundfrac=1.0
-    !   else
-    !     groundfrac=0.0
-    !   endif
-    ! endif
-    ! if (groundfrac>0.0) then
-    !   print *,'T_prev,T_d,groundfrac,nbonds,angvel',T,T_d,groundfrac,berg%n_bonds,berg%ang_vel
-    !   print *,'T ground',-bergs%cdrag_grounding*groundfrac*0.5*pi*(R1**4.)*berg%ang_vel
-    !   T=T-bergs%cdrag_grounding*groundfrac*0.5*pi*(R1**4.)*berg%ang_vel !treat berg as disk?
-    !   print *,'T_after',T
-    ! endif
-
     at=(T+T_d)/(0.5*M*R1**2) !torque acceleration
     berg%ang_accel = at
   endif
@@ -2213,11 +2168,7 @@ subroutine accel_explicit_inner_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel,
   axn=IA_x+IAd_x; ayn=IA_y+IAd_y
   bxn=0.0; byn=0.0
 
-  if (new_mts) then
-    ax=0.5*(axn+bxn); ay=0.5*(ayn+byn)
-  else
-    ax=0.5*axn+bxn; ay=0.5*ayn+byn
-  endif
+  ax=0.5*(axn+bxn); ay=0.5*(ayn+byn)
 
   uveln=u_star+dt*ax; vveln=v_star+dt*ay
 
@@ -2235,12 +2186,10 @@ subroutine accel_explicit_inner_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel,
             (uvel0 + u_star)*M*current_bond%axn_fast +&
             (vvel0 + v_star)*M*current_bond%ayn_fast)
 
-          if (new_mts) then
-            !here, bxn_fast and byn_fast are explicit damping accel (not implicit!)
-            current_bond%Ed=current_bond%Ed - 0.25*dt*(&
-              (uvel0 + u_star)*M*current_bond%bxn_fast +&
-              (vvel0 + v_star)*M*current_bond%byn_fast)
-          endif
+          !here, bxn_fast and byn_fast are explicit damping accel (not implicit!)
+          current_bond%Ed=current_bond%Ed - 0.25*dt*(&
+            (uvel0 + u_star)*M*current_bond%bxn_fast +&
+            (vvel0 + v_star)*M*current_bond%byn_fast)
         endif
 
         !the rest:
@@ -2305,17 +2254,10 @@ subroutine accel_explicit_inner_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel,
             (u_star + uveln)*M*IA_x + &
             (v_star + vveln)*M*IA_y)
 
-
-          if (new_mts) then
-            !V{i+0.5} to V{i+1}
-            current_bond%Ed=current_bond%Ed- 0.25*dt*(&
-              (u_star + uveln)*M*IAd_x + &
-              (v_star + vveln)*M*IAd_y)
-          else
-            current_bond%Ed=current_bond%Ed - 0.5*dt*(&
-              (u_star + uveln)*M*IAd_x + &
-              (v_star + vveln)*M*IAd_y)
-          endif
+          !V{i+0.5} to V{i+1}
+          current_bond%Ed=current_bond%Ed- 0.25*dt*(&
+            (u_star + uveln)*M*IAd_x + &
+            (v_star + vveln)*M*IAd_y)
 
           current_bond%axn_fast=IA_x;  current_bond%ayn_fast=IA_y
 
@@ -3225,7 +3167,6 @@ subroutine delete_fully_fl_calved_edge_elements(bergs)
         !berg is marked to delete
         kick_the_bucket=>this
         this=>this%next
-        print *,'deleting berg',this%id
         call delete_iceberg_from_list(bergs%list(grdi,grdj)%first,kick_the_bucket)
       else
         this=>this%next
@@ -5362,52 +5303,17 @@ subroutine interp_flds(grd, x, y, i, j, xi, yj, rx, ry, uo, vo, ui, vi, ua, va,
   ! Ocean depth is only needed for grounding friction, used with the MTS model only?
   if (present(od)) then
     if (mts) then
-      !od=quad_interp_from_agrid(grd,grd%ocean_depth,x,y,i,j,xi,yj)+quad_interp_from_agrid(grd,grd%ssh,x,y,i,j,xi,yj)
-
-      !od=quad_interp_from_agrid(grd,grd%ocean_depth+grd%ssh,x,y,i,j,xi,yj)
-
       if (A68_test) then
-
-        ! if (x<(-37.1+360) .and. x>(-37.38+360) .and. y<-54.68 .and. y>-54.86) then
-        !   od=0
-        ! else
-        !   od=1000
-        ! endif
-
-        od=1000.
-        !if ((x>-37.3861+360).and.(y>-54.9778)) od=0.
-        !if ((x>-37.2752+360).and.(y>-55.1341)) od=0.
-        !if ((x>-37.3458+360).and.(y>-55.1038)) od=0.
-
-        !od17.8 dy=-0.1
-        !if ((x>-37.2954+360).and.(y>-55.2975)) od=0.
-        if ((x>A68_xdisp+360).and.(y>A68_ydisp)) od=0.
-
-        ! p1y=p1y+A68_ydisp; p2y=p2y+A68_ydisp; p3y=p3y+A68_ydisp
-        ! p1x=p1x+A68_xdisp; p2x=p2x+A68_xdisp; p3x=p3x+A68_xdisp
-
-        ! od=1000.0
-        ! if (x>p1x .and. x<p2x .and. y>p1y .and. y<p3y) then
-        !   alpha = ((p2y - p3y)*(x - p3x) + (p3x - p2x)*(y - p3y)) /&
-        !     ((p2y - p3y)*(p1x - p3x) + (p3x - p2x)*(p1y - p3y))
-        !   if (alpha>0.) then
-        !     beta = ((p3y - p1y)*(x - p3x) + (p1x - p3x)*(y - p3y)) /&
-        !       ((p2y - p3y)*(p1x - p3x) + (p3x - p2x)*(p1y - p3y))
-        !     if (beta>0.) then
-        !       gamma = 1. - alpha - beta
-        !       if (gamma>0.) then
-        !         od=0.
-        !       endif
-        !     endif
-        !   endif
-        ! endif
-
-        ! p1y=p1y-A68_ydisp; p2y=p2y-A68_ydisp; p3y=p3y-A68_ydisp
-        ! p1x=p1x-A68_xdisp; p2x=p2x-A68_xdisp; p3x=p3x-A68_xdisp
+        if ((x>A68_xdisp+360).and.(y>A68_ydisp)) then
+          !ocean depth of the grounding zone
+          od=0.
+        else
+          !ocean depth elsewhere, sufficient to prevent grounding
+          od=1000.
+        endif
       else
         od=quad_interp_from_agrid(grd,grd%ocean_depth+grd%ssh,x,y,i,j,xi,yj)
       endif
-
     else
       od=grd%ocean_depth(i,j)+grd%ssh(i,j)
     endif
@@ -7326,17 +7232,8 @@ subroutine evolve_icebergs_mts(bergs)
           berg%lat_prev = berg%lat; berg%lon_prev = berg%lon
           berg%uvel=berg%uvel_prev; berg%vvel=berg%vvel_prev
 
-          if (new_mts) then
-            berg%uvel = berg%uvel + dt_2*(berg%axn+berg%bxn)
-            berg%vvel = berg%vvel + dt_2*(berg%ayn+berg%byn)
-          else
-            ! TODO: make this work with latlon coords (or just get rid of the depreciated non-new_mts option)
-            if (grd%grid_is_latlon) stop
-            berg%uvel = berg%uvel + dt_2*berg%axn
-            berg%vvel = berg%vvel + dt_2*berg%ayn
-            berg%lat = berg%lat + 0.5*(dt**2)*berg%byn
-            berg%lon = berg%lon + 0.5*(dt**2)*berg%bxn
-          endif
+          berg%uvel = berg%uvel + dt_2*(berg%axn+berg%bxn)
+          berg%vvel = berg%vvel + dt_2*(berg%ayn+berg%byn)
 
           berg%uvel_old=berg%uvel; berg%vvel_old=berg%vvel
 
@@ -7405,13 +7302,8 @@ subroutine evolve_icebergs_mts(bergs)
           berg%lon_old=lonn  ;  berg%lat_old=latn
 
           !Set uvel_old to ustar for berg interactions?
-          if (new_mts) then
-            berg%uvel_old=berg%uvel+dt_2*(berg%axn_fast+berg%bxn_fast)
-            berg%vvel_old=berg%vvel+dt_2*(berg%ayn_fast+berg%bxn_fast)
-          else
-            berg%uvel_old=berg%uvel+dt_2*(berg%axn_fast)
-            berg%vvel_old=berg%vvel+dt_2*(berg%ayn_fast)
-          endif
+          berg%uvel_old=berg%uvel+dt_2*(berg%axn_fast+berg%bxn_fast)
+          berg%vvel_old=berg%vvel+dt_2*(berg%ayn_fast+berg%bxn_fast)
         end if
         berg=>berg%next
       enddo !loop over all bergs
@@ -7446,9 +7338,7 @@ subroutine evolve_icebergs_mts(bergs)
           i=berg%ine      ;   j=berg%jne
           xi=berg%xi      ;   yj=berg%yj
 
-          if (new_mts) then
-            axn = axn+bxn; ayn=ayn+byn
-          endif
+          axn = axn+bxn; ayn=ayn+byn
 
           ! Turn the velocities into u_star, v_star.(uvel3 is v_star) - (possible issues with tangent plane?)
           uvel3=uvel1+(dt_2*axn)                  !(Stern et al 2017, Eq B4)
@@ -7552,13 +7442,8 @@ subroutine evolve_icebergs_mts(bergs)
             !update old velocities for interactions
             berg%uvel_old=berg%uvel; berg%vvel_old=berg%vvel
 
-            if (new_mts) then
-              berg%uvel=berg%uvel-dt_2*(berg%axn_fast+berg%bxn_fast)-dt_2*(berg%axn+berg%bxn)
-              berg%vvel=berg%vvel-dt_2*(berg%ayn_fast+berg%byn_fast)-dt_2*(berg%ayn+berg%byn)
-            else
-              berg%uvel=berg%uvel-dt_2*(berg%axn_fast+2.0*berg%bxn_fast)-dt_2*berg%axn
-              berg%vvel=berg%vvel-dt_2*(berg%ayn_fast+2.0*berg%byn_fast)-dt_2*berg%ayn
-            endif
+            berg%uvel=berg%uvel-dt_2*(berg%axn_fast+berg%bxn_fast)-dt_2*(berg%axn+berg%bxn)
+            berg%vvel=berg%vvel-dt_2*(berg%ayn_fast+berg%byn_fast)-dt_2*(berg%ayn+berg%byn)
             berg%axn_fast=berg%axn; berg%ayn_fast=berg%ayn
             berg%bxn_fast=berg%bxn; berg%byn_fast=berg%byn
           endif
@@ -7581,7 +7466,7 @@ subroutine evolve_icebergs_mts(bergs)
           berg%uvel_old=berg%uvel; berg%vvel_old=berg%vvel
 
           if (bergs%use_grounding_torque) then
-            !torque from grounding drag
+            !torque from grounding drag (WARNING: EXPERIMENTAL)
             !start to feel grounded with draught of bergs%h_to_init_grounding meters of the sea floor topography
             !at groundfrac=0, apply no grounding force. at groundfrac=1, apply max grounding force
             D=(bergs%rho_bergs/rho_seawater)*berg%thickness ! draught (keel depth)
@@ -7675,11 +7560,6 @@ subroutine evolve_icebergs_mts(bergs)
   enddo; enddo ! update 'old' velocities
 
   no_frac_first_ts=.false.
-  ! for testing:
-  ! maxii=ii; minii=ii
-  ! call mpp_max(maxii); call mpp_min(minii); call mpp_max(maxjj); call mpp_min(minjj)
-  !if (maxii>2 .or. maxjj>2) print *,'outer max iters, inner max iters',maxii,maxjj
-
 end subroutine evolve_icebergs_mts
 
 
@@ -7711,69 +7591,35 @@ subroutine mts_energy_part_1(bergs, berg, ax1, ay1, axn, ayn, bxn, byn, Fec_x, F
 
   !derived from Mayrhofer,Hager, and Kloss 2017 (MHK17) and Asmar et al 2003
   M = berg%mass
-  if (new_mts) then
-    Fex = M * 2*ax1; Fey = M * 2*ay1 !external forces
-    Fex = Fex - Fec_x - Fdc_x; Fey = Fey - Fec_y - Fdc_y !external forces minus collisional
-
-    uveln=berg%uvel+(dt*ax1); vveln=berg%vvel+(dt*ay1)
-    ustar=berg%uvel; vstar=berg%vvel
-
-    !dEext=0.5*(V_{i+1} + V_{i+0.5})*F_{ext,i+1}*dt/2
-    berg%Eext=berg%Eext_temp - 0.25*dt*(&
-      (uveln + ustar)*Fex + (vveln + vstar)*Fey)
-
-    berg%Ee_contact=berg%Ee_contact_temp - 0.25*dt*(&
-      (uveln + ustar)*Fec_x + (vveln + vstar)*Fec_y)
-
-    berg%Ed_contact=berg%Ed_contact_temp - 0.25*dt*(&
-      (uveln + ustar)*Fdc_x + (vveln + vstar)*Fdc_y)
-
-    !The following is for part II
-    !V{i+1.5}
-    uveln_star = uveln + dt*ax1; vveln_star = vveln + dt*ay1
 
-    berg%Eext_temp=berg%Eext - 0.25*dt*(&
-      (uveln + uveln_star)*Fex + (vveln + vveln_star)*Fey)
+  Fex = M * 2*ax1; Fey = M * 2*ay1 !external forces
+  Fex = Fex - Fec_x - Fdc_x; Fey = Fey - Fec_y - Fdc_y !external forces minus collisional
 
-    berg%Ee_contact_temp=berg%Ee_contact - 0.25*dt*(&
-      (uveln + uveln_star)*Fec_x + (vveln + vveln_star)*Fec_y)
+  uveln=berg%uvel+(dt*ax1); vveln=berg%vvel+(dt*ay1)
+  ustar=berg%uvel; vstar=berg%vvel
 
-    berg%Ed_contact_temp=berg%Ed_contact - 0.25*dt*(&
-      (uveln + uveln_star)*Fdc_x + (vveln + vveln_star)*Fdc_y)
+  !dEext=0.5*(V_{i+1} + V_{i+0.5})*F_{ext,i+1}*dt/2
+  berg%Eext=berg%Eext_temp - 0.25*dt*(&
+    (uveln + ustar)*Fex + (vveln + vstar)*Fey)
 
-  else
-    Fex = M * axn; Fey = M * ayn !explicit forces
-    Fex = Fex - Fec_x; Fey = Fey - Fec_y !explicit forces minus collisional elastic
-    Fex_i = M * bxn;     Fey_i= M * byn !implicit forces
-    Fex_i = Fex_i - Fdc_x; Fey_i = Fey_i - Fdc_y !implicit forces minus collisional damping
-
-    uveln=berg%uvel+(dt*ax1); vveln=berg%vvel+(dt*ay1)
-    ustar=berg%uvel; vstar=berg%vvel
+  berg%Ee_contact=berg%Ee_contact_temp - 0.25*dt*(&
+    (uveln + ustar)*Fec_x + (vveln + vstar)*Fec_y)
 
-    !explicit:
-    !dEext=0.5*(V_{i+1} + V_{i+0.5})*F_{ext,i+1}*dt/2
-    berg%Eext=berg%Eext_temp - 0.25*dt*(&
-      (uveln + ustar)*Fex + (vveln + vstar)*Fey)
+  berg%Ed_contact=berg%Ed_contact_temp - 0.25*dt*(&
+    (uveln + ustar)*Fdc_x + (vveln + vstar)*Fdc_y)
 
-    berg%Ee_contact=berg%Ee_contact_temp - 0.25*dt*(&
-      (uveln + ustar)*Fec_x + (vveln + vstar)*Fec_y)
+  !The following is for part II
+  !V{i+1.5}
+  uveln_star = uveln + dt*ax1; vveln_star = vveln + dt*ay1
 
-    berg%Eext=berg%Eext - 0.5*dt*(&
-      (uveln + ustar)*Fex_i + (vveln + vstar)*Fey_i)
+  berg%Eext_temp=berg%Eext - 0.25*dt*(&
+    (uveln + uveln_star)*Fex + (vveln + vveln_star)*Fey)
 
-    berg%Ed_contact=berg%Ed_contact - 0.5*dt*(&
-      (uveln + ustar)*Fdc_x + (vveln + vstar)*Fdc_y)
+  berg%Ee_contact_temp=berg%Ee_contact - 0.25*dt*(&
+    (uveln + uveln_star)*Fec_x + (vveln + vveln_star)*Fec_y)
 
-    !The following is for part II
-    !V{i+1.5}
-    uveln_star = uveln + 0.5*dt*axn; vveln_star = vveln + 0.5*dt*ayn
-
-    berg%Eext_temp=berg%Eext - 0.25*dt*(&
-      (uveln + uveln_star)*Fex + (vveln + vveln_star)*Fey)
-
-    berg%Ee_contact_temp=berg%Ee_contact - 0.25*dt*(&
-      (uveln + uveln_star)*Fec_x + (vveln + vveln_star)*Fec_y)
-  endif
+  berg%Ed_contact_temp=berg%Ed_contact - 0.25*dt*(&
+    (uveln + uveln_star)*Fdc_x + (vveln + vveln_star)*Fdc_y)
 
   berg%Ee=berg%Ee_temp; berg%Ed=berg%Ed_temp
 end subroutine mts_energy_part_1
@@ -7800,17 +7646,11 @@ subroutine mts_energy_part_3(bergs,berg,ustar,vstar,wt)
     (ustar + berg%uvel)*Fex + &
     (vstar + berg%vvel)*Fey)
 
-  if (new_mts) then   !for i to i+1/2 or i+1/2 to i+1
-    Fdx = M * berg%bxn_fast; Fdy = M * berg%byn_fast !damping forces
-    berg%Ed_temp=berg%Ed_temp - 0.25*dt*(&
-      (ustar + berg%uvel)*Fdx + &
-      (vstar + berg%vvel)*Fdy)
-  elseif (wt==2) then !for i+1/2 to i+1
-    Fdx = M * berg%bxn_fast; Fdy = M * berg%byn_fast !damping forces
-    berg%Ed_temp=berg%Ed_temp - 0.5*dt*(&
-      (ustar + berg%uvel)*Fdx + &
-      (vstar + berg%vvel)*Fdy)
-  endif
+  Fdx = M * berg%bxn_fast; Fdy = M * berg%byn_fast !damping forces
+  berg%Ed_temp=berg%Ed_temp - 0.25*dt*(&
+    (ustar + berg%uvel)*Fdx + &
+    (vstar + berg%vvel)*Fdy)
+
 end subroutine mts_energy_part_3
 
 !> Evolves icebergs forward by updating velocity and position with a time-stepping scheme
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index d32938b..880811e 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -46,21 +46,20 @@ module ice_bergs_framework
 logical :: do_unit_tests=.false. !< Conduct some unit tests
 logical :: force_all_pes_traj=.false. !< Force all pes write trajectory files regardless of io_layout
 logical :: mts=.false. !< Use multiple time stepping scheme
-logical :: new_mts=.false. !If T, implicit accel is added 50% at the current time step and 50% at the next time step
 logical :: save_bond_traj=.false. !<Save trajectory files for bonds
 logical :: ewsame=.false. !<(F) set T if periodic and 2 PEs along the x direction (zonal) (i.e. E/W PEs are the same)
 logical :: monitor_energy=.false. !<monitors energies: elastic (spring+collision), external, dissipated, fracture
 logical :: iceberg_bonds_on=.False. ! True=Allow icebergs to have bonds, False=don't allow.
 logical :: dem=.false. !< If T, run in DEM-mode with angular terms, variable stiffness, etc
-logical :: save_bond_forces=.true. !< If T, saves forces on bonds (TODO save on bond traj, too), so that only 1 of 2 bonds in a pair need to be processed during DEM-MTS explicit sub-steps
+logical :: save_bond_forces=.true. !< Saves forces on bonds so only 1 of 2 bonds in a pair need processing during DEM-MTS explicit sub-steps
 logical :: short_step_mts_grounding=.false.
 logical :: radius_based_drag=.false. !if T, hex bergs, and dem, 2r is used as the area of the vert face for drag/wave forces
-logical :: A68_test=.false. !< If True, grounding will not be allowed west of 38 deg W nor North of 54.85 S
-real :: A68_xdisp=0.
-real :: A68_ydisp=0.
-logical :: rev_mind=.false.
+logical :: A68_test=.false. !< If True, enforces grounding zone in the A68 test case (Huth et al., 2022)
+real :: A68_xdisp=0. !< longitude of the SW corner of the grounding zone in the A68 test case
+real :: A68_ydisp=0. !< latitude of the SW corner of the grounding zone in the A68 test case
+logical :: rev_mind=.false. !< Alterate option for staggering the 3x3 cells used for quadratic mapping of ocean depth to particles
 character(len=11) :: fracture_criterion='none' !<'energy','stress','strain_rate','strain',or 'none'
-logical :: orig_dem_moment_of_inertia=.false.
+logical :: orig_dem_moment_of_inertia=.false. !< Use Potyondy & Cundall,2004 torque from relative particle rotation (rather than Wang, 2020)
 logical :: break_bonds_on_sub_steps=.false.
 logical :: skip_first_outer_mts_step=.false.
 logical :: no_frac_first_ts=.false.
@@ -70,7 +69,7 @@ module ice_bergs_framework
 public verbose, really_debug, debug, restart_input_dir,make_calving_reproduce,old_bug_bilin,use_roundoff_fix
 public ignore_ij_restart, use_slow_find,generate_test_icebergs,old_bug_rotated_weights,budget
 public orig_read, force_all_pes_traj
-public mts,new_mts,save_bond_traj,ewsame,monitor_energy,iceberg_bonds_on
+public mts,save_bond_traj,ewsame,monitor_energy,iceberg_bonds_on
 public dem, save_bond_forces, fracture_criterion, orig_dem_moment_of_inertia
 public short_step_mts_grounding, radius_based_drag
 public A68_test, A68_xdisp, A68_ydisp
@@ -646,8 +645,8 @@ module ice_bergs_framework
   real :: dem_spring_coef=0.
   real :: dem_damping_coef=0.1
   logical :: use_broken_bonds_for_substep_contact=.false. !only evaluate sub-step contact between particles with a broken bond
+  logical :: print_fracture=.true. !when a bond breaks, print fracture type, lat, lon, and stresses
   logical :: bond_break_detected=.false.
-  logical :: dem_shear_for_frac_only=.false. !< If true, DEM shear is calculated for fracture, but zeroed for berg interactions
   integer :: dem_beam_test=0 !1=Simply supported beam,2=cantilever beam,3=angular vel tes
   logical :: uniaxial_test=.false. !adds a tensile stress to the east-most berg element
   real :: dem_tests_start_lon !starting lon of west-most berg element for uniaxial/dem tests
@@ -873,7 +872,7 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: dem_spring_coef=0.
 real :: dem_damping_coef=0.1
 logical :: use_broken_bonds_for_substep_contact=.false. ! only evaluate sub-step contact between particles with a broken bond
-logical :: dem_shear_for_frac_only=.false. ! If true, DEM shear is calculated for fracture, but zeroed for berg interactions
+logical :: print_fracture=.true. !when a bond breaks, print fracture type, lat, lon, and stresses
 integer :: dem_beam_test=0 !1=Simply supported beam,2=cantilever beam,3=angular vel test
 ! Element Interactions
 logical :: constant_interaction_LW=.false. ! Always use the initial, globally constant, element length & width during berg interactions
@@ -918,19 +917,19 @@ subroutine ice_bergs_framework_init(bergs, &
          const_gamma, Gamma_T_3EQ, ignore_traj, debug_iceberg_with_id,use_updated_rolling_scheme, tip_parameter, &
          read_old_restarts, tau_calving, read_ocean_depth_from_file, melt_cutoff,apply_thickness_cutoff_to_gridded_melt,&
          apply_thickness_cutoff_to_bergs_melt, use_mixed_melting, internal_bergs_for_drag, coastal_drift, tidal_drift,&
-         mts,new_mts,ewsame,monitor_energy,mts_sub_steps,contact_distance,length_for_manually_initialize_bonds,&
+         mts,ewsame,monitor_energy,mts_sub_steps,contact_distance,length_for_manually_initialize_bonds,&
          manually_initialize_bonds_from_radii,contact_spring_coef,fracture_criterion, uniaxial_test, &
          debug_write,cdrag_grounding,h_to_init_grounding,frac_thres_scaling,frac_thres_n,frac_thres_t,save_bond_traj,&
          remove_unused_bergs,force_convergence,explicit_inner_mts,convergence_tolerance,dem,ignore_tangential_force,poisson,&
          dem_spring_coef,dem_damping_coef,dem_beam_test,constant_interaction_LW,constant_length,constant_width,&
-         dem_shear_for_frac_only,fl_use_poisson_distribution, fl_use_perimeter, fl_r, fl_r_s,displace_fl_bergs,&
+         fl_use_poisson_distribution, fl_use_perimeter, fl_r, fl_r_s,displace_fl_bergs,&
          fl_style,fl_bits_erosion_to_bergy_bits,fl_k_scale_by_perimeter,use_spring_for_land_contact, save_fl_traj,&
          new_berg_from_fl_bits_mass_thres,fl_bits_scale_l,fl_bits_scale_w,fl_bits_scale_t,separate_distrib_for_n_hemisphere,&
          initial_mass_n, distribution_n, mass_scaling_n, initial_thickness_n, fl_use_l_scale, fl_l_scale,&
          fl_l_scale_erosion_only, fl_youngs, fl_strength,  save_all_traj_year, save_nonfl_traj_by_class,&
          save_traj_by_class_start_mass_thres_n, save_traj_by_class_start_mass_thres_s,traj_area_thres_sntbc,&
          traj_area_thres_fl,tau_is_velocity, ocean_drag_scale, A68_test, &
-         A68_xdisp,A68_ydisp,use_broken_bonds_for_substep_contact,&
+         A68_xdisp,A68_ydisp,use_broken_bonds_for_substep_contact,print_fracture,&
          orig_dem_moment_of_inertia, break_bonds_on_sub_steps, skip_first_outer_mts_step, rev_mind, &
          no_frac_first_ts, use_grounding_torque, short_step_mts_grounding, radius_based_drag, save_bond_forces
 
@@ -1180,8 +1179,7 @@ subroutine ice_bergs_framework_init(bergs, &
 
 
   if ( (mpp_pe() == 0) .and. (Lx .ne. 360.) .and. .not. (grid_is_latlon) ) then
-    print *,''
-    print *,'pe0 x-domain before periodicity fix'
+    write(*,'(/,a)') 'pe0 x-domain before periodicity fix'
     write(*,'(f12.2)') (grd%lon(i,grd%jsd), i=grd%isd,grd%ied)
   endif
 
@@ -1246,21 +1244,10 @@ subroutine ice_bergs_framework_init(bergs, &
     write(stderrunit,'(a,i3,a,4i4)') 'KID, icebergs_init: (',mpp_pe(),') [ij][se]c=', &
           grd%isc,grd%iec,grd%jsc,grd%jec
 
-    !print *,'minval(grd%lon)',minval(grd%lon)
-    !print *,'maxval(grd%lon)',maxval(grd%lon)
-    !print *,'minval(grd%lat)',minval(grd%lat)
-    !print *,'maxval(grd%lat)',maxval(grd%lat)
-
     write(stderrunit,'(a,4f10.2)') '[Lon|lat][min|max]=', &
           minval(grd%lon),maxval(grd%lon),minval(grd%lat),maxval(grd%lat)
   endif
 
- ! if ( (mpp_pe() == 0) .and. (Lx .ne. -1.) .and. .not. (grid_is_latlon) ) then
- !   print *,''
- !   print *,'pe 0 x-domain after periodicity fix'
- !   write(*,'(f12.2)') (grd%lon(i,grd%jsd), i=grd%isd,grd%ied)
- ! end if
-
  !if (mpp_pe().eq.5) then
  !  write(stderrunit,'(a3,32i7)') 'Lon',(i,i=grd%isd,grd%ied)
  !  do j=grd%jed,grd%jsd,-1
@@ -1562,6 +1549,7 @@ subroutine ice_bergs_framework_init(bergs, &
   else
     bergs%use_broken_bonds_for_substep_contact=.false.
   end if
+  bergs%print_fracture=print_fracture
   bergs%dem_beam_test=dem_beam_test
   bergs%constant_interaction_LW=constant_interaction_LW
   bergs%constant_length=constant_length
@@ -1579,7 +1567,6 @@ subroutine ice_bergs_framework_init(bergs, &
     endif
   endif
   bergs%ocean_drag_scale=ocean_drag_scale
-  bergs%dem_shear_for_frac_only=dem_shear_for_frac_only
   ! Footloose calving parameters
   bergs%fl_use_poisson_distribution=fl_use_poisson_distribution
   bergs%fl_use_perimeter=fl_use_perimeter
@@ -1650,8 +1637,6 @@ subroutine ice_bergs_framework_init(bergs, &
     bergs%contact_cells_lat = 1
   endif
 
-  !print *,'# contact cells lon/lat',bergs%contact_cells_lon,bergs%contact_cells_lat
-
   !necessary?
   if (.not. mts) then
     if ((halo-1)<bergs%contact_cells_lon .or. (halo-1)<bergs%contact_cells_lat) then
@@ -5418,6 +5403,7 @@ subroutine break_bonds_dem(bergs)
   type(bond) , pointer :: current_bond,other_bond,kick_the_bucket
   real :: frac_thres_n,frac_thres_t
   real :: Rsig,Rtau,frac
+  integer :: stderrunit
 
   if (no_frac_first_ts) then
     return
@@ -5439,13 +5425,6 @@ subroutine break_bonds_dem(bergs)
 
           if (bergs%fracture_criterion=='stress') then
             if (current_bond%nstress>frac_thres_n .or. current_bond%sstress>frac_thres_t) then
-              ! if (current_bond%nstress>frac_thres_n .and. current_bond%sstress>frac_thres_t) then
-              !   print *,'T and S break',this%lat,current_bond%nstress,current_bond%sstress
-              ! elseif (current_bond%nstress>frac_thres_n) then
-              !   print *,'TENSILE break',this%lat,current_bond%nstress,current_bond%sstress
-              ! else
-              !   print *,'SHEAR   break',this%lat,current_bond%nstress,current_bond%sstress
-              ! endif
               current_bond%other_id=-1
             endif
           else
@@ -5465,9 +5444,10 @@ subroutine break_bonds_dem(bergs)
                     other_bond%other_id=-1
                     if (debug) then
                       if (other_bond%nstress<=frac_thres_n .and. other_bond%sstress<=frac_thres_t) then
-                        print *,'Other bond did not fracture!'
-                        print *,'current and other bond nstress,',current_bond%nstress, other_bond%nstress
-                        print *,'current and other bond sstress,',current_bond%sstress, other_bond%sstress
+                        stderrunit=stderr()
+                        call error_mesg('KID, break_bonds_dem', 'Other bond did not fracture!', WARNING)
+                        write(stderrunit,*) 'current and other bond nstress',current_bond%nstress, other_bond%nstress
+                        write(stderrunit,*) 'current and other bond sstress',current_bond%sstress, other_bond%sstress
                       endif
                     endif
                   endif
diff --git a/tests/a68_test/long_run.nml b/tests/a68_test/long_run.nml
index 9632450..594ae81 100644
--- a/tests/a68_test/long_run.nml
+++ b/tests/a68_test/long_run.nml
@@ -71,7 +71,6 @@
 
     monitor_energy=.false.
     !defaults given in parentheses:
-    new_mts=.true.
     mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
     mts_sub_steps=<ss> !# of mts sub-steps
     force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
diff --git a/tests/collision_tests/input.nml b/tests/collision_tests/input.nml
index 328c2cd..2b66aed 100644
--- a/tests/collision_tests/input.nml
+++ b/tests/collision_tests/input.nml
@@ -24,7 +24,6 @@
 
     !defaults given in parentheses:
     ! explicit_inner_mts=.true.
-    ! new_mts=.true.
     ! mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
     ! mts_sub_steps=60 !1 !30 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
     ! contact_distance=1.75e3 !2.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
diff --git a/tests/collision_tests/input_KID.nml b/tests/collision_tests/input_KID.nml
index 328c2cd..2b66aed 100644
--- a/tests/collision_tests/input_KID.nml
+++ b/tests/collision_tests/input_KID.nml
@@ -24,7 +24,6 @@
 
     !defaults given in parentheses:
     ! explicit_inner_mts=.true.
-    ! new_mts=.true.
     ! mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
     ! mts_sub_steps=60 !1 !30 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
     ! contact_distance=1.75e3 !2.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
diff --git a/tests/collision_tests/input_MTS_KID.nml b/tests/collision_tests/input_MTS_KID.nml
index 1fedaf8..c806ac5 100644
--- a/tests/collision_tests/input_MTS_KID.nml
+++ b/tests/collision_tests/input_MTS_KID.nml
@@ -23,7 +23,6 @@
 
     !defaults given in parentheses:
     explicit_inner_mts=.true.
-    new_mts=.true.
     mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
     mts_sub_steps=60 !1 !30 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
     contact_distance=1.75e3 !2.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
diff --git a/tests/collision_tests/input_iKID.nml b/tests/collision_tests/input_iKID.nml
index 3393971..b51271c 100644
--- a/tests/collision_tests/input_iKID.nml
+++ b/tests/collision_tests/input_iKID.nml
@@ -34,7 +34,6 @@
     spring_coef=1.e-5 !if dem_spring_coef=5e6, r=1500, and hex pack?
 
     explicit_inner_mts=.true.
-    new_mts=.true.
     mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
     mts_sub_steps=60 !1 !30 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
     contact_distance=1.75e3 !2.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
diff --git a/tests/dem_cbeam_test/input.nml b/tests/dem_cbeam_test/input.nml
index 437eefb..636195e 100644
--- a/tests/dem_cbeam_test/input.nml
+++ b/tests/dem_cbeam_test/input.nml
@@ -1,4 +1,10 @@
+!! with orig_dem_moment_of_inertia=.false.
+!!KID, bergs_chksum: write_restart berg chksum=-1959001450 chksum2=-472027384 chksum3=-1504290914 chksum4=-1504290914 chksum5=-81885495 #=90
+
+!! with orig_dem_moment_of_inertia=.true.
 ! KID, bergs_chksum: write_restart berg chksum=545105294 chksum2=-884448578 chksum3=-1504290914 chksum4=-1504290914 chksum5=-845603363 #=90
+
+!! in either case:
 ! KID, grd_chksum2:# of bergs/cell chksum=0 chksum2=0 min= 0.000000000E+00 max= 0.000000000E+00 mean= 0.000000000E+00 rms= 0.000000000E+00 sd= 0.000000000E+00
 !  Total number of bonds is: 294
 !  All iceberg bonds are connected and working well
@@ -37,7 +43,6 @@
     dem_spring_coef=1.e9 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
 
     monitor_energy=.false. !(F)save total elastic (spring+collision),external,dissipated,&fracture energy
-    new_mts=.true. !(F) If T, implicit accel is added 50% at the current time step and 50% at the next time step
     mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
     mts_sub_steps=2000  !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
     force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
diff --git a/tests/dem_ground_frac_test/input.nml b/tests/dem_ground_frac_test/input.nml
index afdfcbe..62b2f46 100644
--- a/tests/dem_ground_frac_test/input.nml
+++ b/tests/dem_ground_frac_test/input.nml
@@ -54,7 +54,6 @@
 
     monitor_energy=.false.
     !defaults given in parentheses:
-    new_mts=.true.
     mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
     mts_sub_steps=200 !(-1) # of mts sub-steps
     explicit_inner_mts=.true.
diff --git a/tests/dem_ssbeam_test/input.nml b/tests/dem_ssbeam_test/input.nml
index 7f36f5c..ca5af1c 100644
--- a/tests/dem_ssbeam_test/input.nml
+++ b/tests/dem_ssbeam_test/input.nml
@@ -36,7 +36,6 @@
     dem_spring_coef=1.e9 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
 
     monitor_energy=.false. !(F)save total elastic (spring+collision),external,dissipated,&fracture energy
-    new_mts=.true. !(F) If T, implicit accel is added 50% at the current time step and 50% at the next time step
     mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
     mts_sub_steps=1e5 !20 !00  !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
 

From b07c13203015ae7cb40dbd389fd590fc2427d3b7 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Wed, 28 Dec 2022 17:38:28 -0500
Subject: [PATCH 332/361] removed several unused/experimental functions and
 features: fracture_testing_initialization, init_dem_params,
 uniaxial_test,use_spring_land_contact,and calculate_force_land_contact

---
 src/icebergs.F90           | 191 +++----------------------------------
 src/icebergs_framework.F90 |  63 +-----------
 2 files changed, 17 insertions(+), 237 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 202107c..f269d73 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -48,12 +48,12 @@ module ice_bergs
 use ice_bergs_framework, only: update_latlon,set_conglom_ids,transfer_mts_bergs
 use ice_bergs_framework, only: quad_interp_from_agrid
 use ice_bergs_framework, only: save_bond_traj
-use ice_bergs_framework, only: fracture_testing_initialization, orig_bond_length
+use ice_bergs_framework, only: orig_bond_length
 use ice_bergs_framework, only: update_and_break_bonds,break_bonds_dem,assign_n_bonds,reset_bond_rotation
 use ice_bergs_framework, only: update_bond_angles
 use ice_bergs_framework, only: monitor_energy, energy_tests_init, mts
 use ice_bergs_framework, only: dem_tests_init
-use ice_bergs_framework, only: dem, init_dem_params, save_bond_forces
+use ice_bergs_framework, only: dem, save_bond_forces
 use ice_bergs_framework, only: orig_dem_moment_of_inertia, no_frac_first_ts
 use ice_bergs_framework, only: A68_test, A68_xdisp, A68_ydisp
 use ice_bergs_framework, only: set_constant_interaction_length_and_width, skip_first_outer_mts_step
@@ -156,7 +156,6 @@ subroutine icebergs_init(bergs, &
   if (bergs%read_ocean_depth_from_file) call read_ocean_depth(bergs%grd)
 
   if (monitor_energy) call energy_tests_init(bergs)
-  !if (bergs%dem) call init_dem_params(bergs)
 
   if (bergs%iceberg_bonds_on) then
     if (bergs%manually_initialize_bonds) then
@@ -176,16 +175,16 @@ subroutine icebergs_init(bergs, &
     check_bond_quality=.True.
     call count_bonds(bergs, nbonds,check_bond_quality)
     call assign_n_bonds(bergs)
-    !call fracture_testing_initialization(bergs)
   endif
 
-  if (bergs%uniaxial_test .or. bergs%dem_beam_test>0) call dem_tests_init(bergs)
+  if (bergs%dem_beam_test>0) call dem_tests_init(bergs)
 
   if (bergs%constant_interaction_LW .and. (bergs%constant_length==0. .or. bergs%constant_width==0.)) then
     call set_constant_interaction_length_and_width(bergs)
   endif
 end subroutine icebergs_init
 
+!> For debugging. Call to write all particle and bond trajectories, including within halos. Then, end the simulation.
 subroutine debugwriteandstop(bergs)
   type(icebergs), pointer :: bergs !< Container for all types and memory
   bergs%debug_write=.true.
@@ -197,7 +196,6 @@ subroutine debugwriteandstop(bergs)
   call error_mesg('KID', 'WRITE AND STOP!!!', FATAL)
 end subroutine debugwriteandstop
 
-
 !> Invoke some unit testing
 subroutine unit_testing(bergs)
   ! Arguments
@@ -583,14 +581,6 @@ subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
           other_berg=>other_berg%next
         enddo
       enddo; enddo
-      if (bergs%use_spring_for_land_contact) then
-        grd=>bergs%grd
-        do grdj = max(berg%jne-nc_y,bergs%grd%jsd),min(berg%jne+nc_y,bergs%grd%jed);&
-          do grdi = max(berg%ine-nc_x,bergs%grd%isd),min(berg%ine+nc_x,bergs%grd%ied)
-          if (grd%msk(grdi,grdj)==0) call calculate_force_land_contact(bergs, berg, grd, grdi, grdj, &
-            IA_x, IA_y, P_ia_11, P_ia_12, P_ia_21, P_ia_22) !, P_ia_times_u_x, P_ia_times_u_y)
-        enddo; enddo
-      endif
     endif
 
   else
@@ -620,14 +610,6 @@ subroutine interactive_force(bergs, berg, IA_x, IA_y, u0, v0, u1, v1,&
         current_bond=>current_bond%next_bond
       enddo
     endif
-    if (bergs%use_spring_for_land_contact) then
-      grd=>bergs%grd
-      do grdj = max(berg%jne-nc_y,bergs%grd%jsd),min(berg%jne+nc_y,bergs%grd%jed);&
-        do grdi = max(berg%ine-nc_x,bergs%grd%isd),min(berg%ine+nc_x,bergs%grd%ied)
-        if (grd%msk(grdi,grdj)==0) call calculate_force_land_contact(bergs, berg, grd, grdi, grdj, &
-          IA_x, IA_y, P_ia_11, P_ia_12, P_ia_21, P_ia_22) !, P_ia_times_u_x, P_ia_times_u_y)
-      enddo; enddo
-    endif
   endif
 end subroutine interactive_force
 
@@ -770,11 +752,6 @@ subroutine calculate_force(bergs, berg, other_berg, IA_x, IA_y, u0, v0, u1, v1,
       if (.not. (r_dist>crit_dist)) tbonded=.false.
     endif
 
-    if (bergs%uniaxial_test) then
-      if (berg%start_lon==bergs%dem_tests_start_lon) IA_x=IA_x-1.e-5
-      if (berg%start_lon==bergs%dem_tests_end_lon)   IA_x=IA_x+1.e-5
-    endif
-
     if  ((r_dist>0.) .and. ( tbonded .or. (r_dist<crit_dist .and. .not. bonded) )) then
 
       !Spring force (Stern et al 2017, Eqn 7):
@@ -931,11 +908,6 @@ subroutine calculate_unbonded_same_conglom_dem_force(bergs, berg, other_berg, IA
       endif
     endif
 
-    if (bergs%uniaxial_test) then
-      if (berg%start_lon==bergs%dem_tests_start_lon) IA_x=IA_x-1.e-5
-      if (berg%start_lon==bergs%dem_tests_end_lon)   IA_x=IA_x+1.e-5
-    endif
-
     if  ((r_dist>0.) .and. (r_dist<crit_dist)) then
 
       !Spring force (Stern et al 2017, Eqn 7):
@@ -1092,8 +1064,11 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
     !bond width (determined at contact point)
     L=2.0*(Rmin+(Rmin-half_delta)*abs(R1-R2)/current_bond%length)
 
-    Thick=T_Rmin+(Rmin-half_delta)*abs(berg%thickness-other_berg%thickness)/current_bond%length !thickness as determined at contact point
-    !Thick=min(berg%thickness,other_berg%thickness) !minimum thickness
+    !thickness as determined at contact point
+    Thick=T_Rmin+(Rmin-half_delta)*abs(berg%thickness-other_berg%thickness)/current_bond%length
+
+    !some other possible definitions of thickness:
+    !Thick=min(berg%thickness,other_berg%thickness)  !minimum thickness
     !Thick=0.5*(berg%thickness+other_berg%thickness) !average thickness
 
     !normal force:
@@ -1150,11 +1125,13 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
 
     !Torque from relative particle rotation
     if (.not. orig_dem_moment_of_inertia) then
+      !Wang, 2020
       theta=sin(berg%rot-other_berg%rot)
       !theta_old=sin(berg%rot-other_berg%rot)
       !theta=sin(current_bond%rel_rotation)
       Tr = -bergs%dem_spring_coef*(L**3.)*Thick*theta/(12.*l0) !should be same as below, except for theta
     else
+      !Potyondy & Cundall, 2004
       !For testing purposes. All particles should have same radius and thickness.
       theta=berg%rot-other_berg%rot
       !theta_old=berg%rot-other_berg%rot
@@ -1271,149 +1248,6 @@ subroutine calculate_force_dem(bergs, berg, other_berg, current_bond, &
 
 end subroutine calculate_force_dem
 
-!> Experimental subroutine to calculate interactive force between a berg and a land cell
-!> Should prevent grounding.
-subroutine calculate_force_land_contact(bergs, berg, grd, i, j, IA_x, IA_y, &
-  P_ia_11, P_ia_12, P_ia_21, P_ia_22) !, P_ia_times_u_x, P_ia_times_u_y)
-  ! Arguments
-  type(icebergs), pointer :: bergs !< Container for all types and memory
-  type(iceberg), pointer :: berg !< Primary berg
-  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
-  integer, intent(in) :: i !< Grid cell i to contact
-  integer, intent(in) :: j !< Grid cell j to contact
-  real, intent(inout) :: IA_x !< Net zonal acceleration of berg due to interactions (m/s2)
-  real, intent(inout) :: IA_y !< Net meridional acceleration of berg due to interactions (m/s2)
-  real, intent(inout) :: P_ia_11 !< Damping projection matrix, xx component (kg/s)
-  real, intent(inout) :: P_ia_12 !< Damping projection matrix, xy component (kg/s)
-  real, intent(inout) :: P_ia_22 !< Damping projection matrix, yy component (kg/s)
-  real, intent(inout) :: P_ia_21 !< Damping projection matrix, yx component (kg/s)
-  !not needed because "other" iceberg is assumed to have velocity = 0
-  !real, intent(inout) :: P_ia_times_u_x !< Zonal damping projection (without new berg velocity) (kg m/s)
-  !real, intent(inout) :: P_ia_times_u_y !< Meridional damping projection (without new berg velocity) (kg m/s)
-
-  ! Local variables
-  real :: T1, L1, W1, lon1, lat1, R1, A1 ! Current iceberg
-  real :: lon2, lat2 ! "Other" iceberg
-  real :: dlon, dlat
-  real :: r_dist_x, r_dist_y, r_dist
-  real :: P_11, P_12, P_21, P_22
-  !real :: u2, v2
-  real :: lat_ref, dx_dlon, dy_dlat, crit_dist
-  logical :: critical_interaction_damping_on
-  real :: spring_coef, accel_spring, radial_damping_coef, p_ia_coef, tangental_damping_coef
-
-  if (i == berg%ine .and. j == berg%jne) return
-
-  lon1=berg%lon_old; lat1=berg%lat_old  ! From Berg 1
-
-  ! Find the location on the edge/corner of the land cell that is closest to the berg. The force is
-  ! calculated  as if there is a second berg at this location, with identical size to the input berg,
-  ! but with velocities set to zero
-  !u2=0;  v2=0 !"other berg" velocities are assumed to be zero
-  if (berg%ine==i) then
-    lon2=lon1
-    if (berg%jne>j) then !N of cell
-      lat2=grd%lat(i,j)
-    else !S of cell
-      lat2=grd%lat(i,j-1)
-    endif
-  elseif (berg%ine>i) then
-    if (berg%jne==j) then !E of cell
-      lon2=grd%lon(i,j)
-      lat2=lat1
-    elseif (berg%jne>j) then !NE of cell
-      lon2=grd%lon(i,j)
-      lat2=grd%lat(i,j)
-    else !SE of cell
-      lon2=grd%lon(i,j-1)
-      lat2=grd%lat(i,j-1)
-    endif
-  else
-    if (berg%jne==j) then !W of cell
-      lon2=grd%lon(i-1,j)
-      lat2=lat1
-    elseif (berg%jne>j) then !NW of cell
-      lon2=grd%lon(i-1,j)
-      lat2=grd%lat(i-1,j)
-    else !SW of cell
-      lon2=grd%lon(i-1,j-1)
-      lat2=grd%lat(i-1,j-1)
-    endif
-  endif
-
-  L1=berg%length; W1=berg%width; A1=L1*W1
-  dlon=lon1-lon2; dlat=lat1-lat2
-
-  ! Note that this is not the exact distance along a great circle.
-  ! Approximation for small distances. Should be fine.
-  lat_ref=0.5*(lat1+lat2)
-  call convert_from_grid_to_meters(lat_ref,bergs%grd%grid_is_latlon,dx_dlon,dy_dlat)
-
-  r_dist_x=dlon*dx_dlon; r_dist_y=dlat*dy_dlat
-  r_dist=sqrt( (r_dist_x**2) + (r_dist_y**2) ) !(Stern et al 2017, Eqn 3)
-
-  !Stern et al 2017, Eqn 4: radius of circle inscribed within hexagon or square with area A1 or A2
-  if (bergs%hexagonal_icebergs) then
-    R1=sqrt(A1/(2.*sqrt(3.)))
-  else !square packing
-    if (bergs%iceberg_bonds_on) then
-      R1=0.5*sqrt(A1)
-    else
-      R1=sqrt(A1/pi) ! Interaction radius of the iceberg (assuming circular icebergs)
-    endif
-  endif
-
-  !Calculating spring force (Stern et al 2017, Eqn 6):
-  spring_coef=bergs%contact_spring_coef
-  crit_dist=max(2*R1,bergs%contact_distance)
-
-  radial_damping_coef=bergs%radial_damping_coef
-  tangental_damping_coef=bergs%tangental_damping_coef
-  critical_interaction_damping_on=bergs%critical_interaction_damping_on
-
-  ! Using critical values for damping rather than manually setting the damping.
-  if (critical_interaction_damping_on) then
-    radial_damping_coef=2.*sqrt(spring_coef) ! Critical damping
-    if (bergs%tang_crit_int_damp_on) then
-      tangental_damping_coef=(2.*sqrt(spring_coef))/4 ! Critical damping (just a guess)
-    endif
-  endif
-
-  if  (r_dist<crit_dist) then
-    !Spring force (Stern et al 2017, Eqn 7):
-    accel_spring=spring_coef*(crit_dist-r_dist)
-    IA_x=IA_x+(accel_spring*(r_dist_x/r_dist))
-    IA_y=IA_y+(accel_spring*(r_dist_y/r_dist))
-
-    ! Damping force (Stern et al 2017, Eqn 8):
-    ! Parallel velocity
-    !projection matrix in Stern et al 2017, Eqn 8:
-    P_11=(r_dist_x*r_dist_x)/(r_dist**2)
-    P_12=(r_dist_x*r_dist_y)/(r_dist**2)
-    P_21=(r_dist_x*r_dist_y)/(r_dist**2)
-    P_22=(r_dist_y*r_dist_y)/(r_dist**2)
-    p_ia_coef=radial_damping_coef
-    P_ia_11=P_ia_11+p_ia_coef*P_11
-    P_ia_12=P_ia_12+p_ia_coef*P_12
-    P_ia_21=P_ia_21+p_ia_coef*P_21
-    P_ia_22=P_ia_22+p_ia_coef*P_22
-    !not needed because u2 and v2 are zero
-    !P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
-    !P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
-
-    ! Normal velocities
-    P_11=1-P_11  ;  P_12=-P_12 ; P_21= -P_21 ;    P_22=1-P_22
-    p_ia_coef=tangental_damping_coef
-    P_ia_11=P_ia_11+p_ia_coef*P_11
-    P_ia_12=P_ia_12+p_ia_coef*P_12
-    P_ia_21=P_ia_21+p_ia_coef*P_21
-    P_ia_22=P_ia_22+p_ia_coef*P_22
-    !not needed because u2 and v2 are zero
-    !P_ia_times_u_x=P_ia_times_u_x+ (p_ia_coef* ((P_11*u2) +(P_12*v2)))
-    !P_ia_times_u_y=P_ia_times_u_y+ (p_ia_coef* ((P_12*u2) +(P_22*v2)))
-  endif
-end subroutine calculate_force_land_contact
-
 !> Calculates area of overlap between two circular bergs
 subroutine overlap_area(R1, R2, d, A, trapped)
   ! Arguments
@@ -2385,7 +2219,7 @@ subroutine accel(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, r
   ! !else
   ! !  call interp_flds(grd, berg%lon, berg%lat, i, j, xi, yj, rx, ry, uo, vo, ui, vi, ua, va, ssh_x, &
   ! !    ssh_y, sst, sss, cn, hi, od)
-  !   !end if
+  ! !end if
 
   if (bergs%old_interp_flds_order) then
     call interp_flds(grd, berg%lon, berg%lat, i, j, xi, yj, rx, ry, uo, vo, ui, vi, ua, va, ssh_x, &
@@ -5841,7 +5675,6 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
     if (mpp_pe()==0) write(*,'(a)') 'KID, iceberg_run: completed first visit initialization'
   endif
 
-  !if (.not. bergs%mts) call interp_gridded_fields_to_bergs(bergs)
   !call this for footloose
   if ((.not. bergs%mts) .and. (.not. bergs%old_interp_flds_order)) call interp_gridded_fields_to_bergs(bergs)
 
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 880811e..22dce06 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -103,9 +103,8 @@ module ice_bergs_framework
 public update_latlon,set_conglom_ids,transfer_mts_bergs,quad_interp_from_agrid
 public pack_bond_traj_into_buffer2, unpack_bond_traj_from_buffer2, push_bond_posn, append_bond_posn
 public update_and_break_bonds,break_bonds_dem,assign_n_bonds,reset_bond_rotation,update_bond_angles
-public fracture_testing_initialization, orig_bond_length
+public orig_bond_length
 public energy_tests_init,dem_tests_init
-public init_dem_params
 public set_constant_interaction_length_and_width
 public break_bonds_on_sub_steps, skip_first_outer_mts_step, no_frac_first_ts
 
@@ -648,9 +647,8 @@ module ice_bergs_framework
   logical :: print_fracture=.true. !when a bond breaks, print fracture type, lat, lon, and stresses
   logical :: bond_break_detected=.false.
   integer :: dem_beam_test=0 !1=Simply supported beam,2=cantilever beam,3=angular vel tes
-  logical :: uniaxial_test=.false. !adds a tensile stress to the east-most berg element
-  real :: dem_tests_start_lon !starting lon of west-most berg element for uniaxial/dem tests
-  real :: dem_tests_end_lon !starting lon of east-most berg element for uniaxial/dem tests
+  real :: dem_tests_start_lon !starting lon of west-most berg element for dem tests
+  real :: dem_tests_end_lon !starting lon of east-most berg element for dem tests
   ! Element interactions
   logical :: constant_interaction_LW=.false. !< Use a constant element length & width during berg interactions
   real :: constant_length=0.!< If constant_interaction_LW, the constant length. If 0, will be set to max initial length
@@ -658,7 +656,6 @@ module ice_bergs_framework
   real :: constant_area
   real :: constant_radius
   real :: ocean_drag_scale=1. !< Scaling factor for the ocean drag coefficients
-  logical :: use_spring_for_land_contact=.false. !< Treat contact with masked (land) cells like contact with a static berg
   ! Footloose calving parameters
   logical :: fl_use_poisson_distribution=.true. !< fl_r is (T) mean of Poisson distribution to determine k, or (F) k=fl_r
   logical :: fl_use_perimeter=.false. !< scale number of footloose bergs to calve by perimeter of the parent berg
@@ -762,7 +759,6 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: rho_bergs=850. ! Density of icebergs
 real :: spring_coef=1.e-8 ! Spring constant for iceberg interactions (this seems to be the highest stable value)
 real :: contact_spring_coef=0. !Spring coef for berg collisions (is set to spring_coef if not specified)
-logical :: uniaxial_test=.false. !adds a tensile stress to the east-most berg element
 real :: cdrag_grounding=0.0 ! Drag coefficient against ocean bottom
 real :: h_to_init_grounding=100.0
 real :: frac_thres_n=0.0 !normal fracture strain threshold
@@ -879,7 +875,6 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: constant_length=0. ! If constant_interaction_LW, the constant length used. If zero in the nml, will be set to max initial L
 real :: constant_width=0. ! If constant_interaction_LW, the constant width used. If zero in the nml, will be set to max initial W
 real :: ocean_drag_scale=1. !< Scaling factor for the ocean drag coefficients
-logical :: use_spring_for_land_contact=.false. ! Treat contact with masked (land) cells like contact with a static berg
 ! Footloose calving parameters [England et al (2020) Modeling the breakup of tabular icebergs. Sci. Adv.]
 logical :: fl_use_poisson_distribution=.true. ! fl_r is (T) mean of Poisson distribution to determine k, or (F) k=fl_r
 logical :: fl_use_perimeter=.false. ! scale number of footloose bergs to calve by perimeter of the parent berg
@@ -918,12 +913,12 @@ subroutine ice_bergs_framework_init(bergs, &
          read_old_restarts, tau_calving, read_ocean_depth_from_file, melt_cutoff,apply_thickness_cutoff_to_gridded_melt,&
          apply_thickness_cutoff_to_bergs_melt, use_mixed_melting, internal_bergs_for_drag, coastal_drift, tidal_drift,&
          mts,ewsame,monitor_energy,mts_sub_steps,contact_distance,length_for_manually_initialize_bonds,&
-         manually_initialize_bonds_from_radii,contact_spring_coef,fracture_criterion, uniaxial_test, &
+         manually_initialize_bonds_from_radii,contact_spring_coef,fracture_criterion, &
          debug_write,cdrag_grounding,h_to_init_grounding,frac_thres_scaling,frac_thres_n,frac_thres_t,save_bond_traj,&
          remove_unused_bergs,force_convergence,explicit_inner_mts,convergence_tolerance,dem,ignore_tangential_force,poisson,&
          dem_spring_coef,dem_damping_coef,dem_beam_test,constant_interaction_LW,constant_length,constant_width,&
          fl_use_poisson_distribution, fl_use_perimeter, fl_r, fl_r_s,displace_fl_bergs,&
-         fl_style,fl_bits_erosion_to_bergy_bits,fl_k_scale_by_perimeter,use_spring_for_land_contact, save_fl_traj,&
+         fl_style,fl_bits_erosion_to_bergy_bits,fl_k_scale_by_perimeter, save_fl_traj,&
          new_berg_from_fl_bits_mass_thres,fl_bits_scale_l,fl_bits_scale_w,fl_bits_scale_t,separate_distrib_for_n_hemisphere,&
          initial_mass_n, distribution_n, mass_scaling_n, initial_thickness_n, fl_use_l_scale, fl_l_scale,&
          fl_l_scale_erosion_only, fl_youngs, fl_strength,  save_all_traj_year, save_nonfl_traj_by_class,&
@@ -1452,7 +1447,6 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%spring_coef=spring_coef
   bergs%contact_spring_coef=contact_spring_coef !Alex
   bergs%fracture_criterion=fracture_criterion
-  bergs%uniaxial_test=uniaxial_test
   bergs%cdrag_grounding=cdrag_grounding
   bergs%h_to_init_grounding=h_to_init_grounding
   bergs%frac_thres_n=frac_thres_n*frac_thres_scaling
@@ -1520,7 +1514,6 @@ subroutine ice_bergs_framework_init(bergs, &
   bergs%add_weight_to_ocean=add_weight_to_ocean
   bergs%use_old_spreading=use_old_spreading
   bergs%debug_iceberg_with_id=debug_iceberg_with_id
-  bergs%use_spring_for_land_contact=use_spring_for_land_contact
   bergs%mts=mts
   bergs%mts_fast_dt = mts_fast_dt
   bergs%mts_sub_steps = mts_sub_steps
@@ -4982,32 +4975,6 @@ subroutine orig_bond_length(bergs)
   enddo; enddo
 end subroutine orig_bond_length
 
-!> Initialize fracture parameters for non-DEM style fracture
-subroutine fracture_testing_initialization(bergs)
-type(icebergs), pointer :: bergs !< Container for all types and memory
-type(iceberg), pointer :: this
-type(bond) , pointer :: current_bond
-type(icebergs_gridded), pointer :: grd
-integer :: grdi, grdj
-
-  grd=>bergs%grd
-  do grdj=grd%jsd,grd%jed ; do grdi=grd%isd,grd%ied !loop over all cells
-    this=>bergs%list(grdi,grdj)%first
-    do while (associated(this)) ! loop over all bergs in cell
-      this%accum_bond_rotation=0.0
-      current_bond=>this%first_bond
-      do while (associated(current_bond)) ! loop over all bonds
-        current_bond%rotation=0.0
-        current_bond%rel_rotation=0.0
-        current_bond%n_frac_var=0.0
-        current_bond%n_strain_rate=0.0
-        current_bond=>current_bond%next_bond
-      enddo
-      this=>this%next
-    enddo
-  enddo;enddo
-end subroutine fracture_testing_initialization
-
 !> Save number of bonds on element
 subroutine assign_n_bonds(bergs)
 type(icebergs), pointer :: bergs !< Container for all types and memory
@@ -5123,26 +5090,6 @@ subroutine dem_tests_init(bergs)
 
 end subroutine dem_tests_init
 
-!> Initialize berg element parameters for DEM-style simulations
-subroutine init_dem_params(bergs)
-type(icebergs), pointer :: bergs !< Container for all types and memory
-type(iceberg), pointer :: this
-type(icebergs_gridded), pointer :: grd
-integer :: grdi, grdj
-real :: maxlon
-
-  grd=>bergs%grd
-  do grdj=grd%jsd,grd%jed ; do grdi=grd%isd,grd%ied !loop over all cells
-    this=>bergs%list(grdi,grdj)%first
-    do while (associated(this)) ! loop over all bergs in cell
-      !this%ang_vel=0.
-      this%ang_accel=0.
-      this%rot=0.
-      this=>this%next
-    enddo
-  enddo;enddo
-end subroutine init_dem_params
-
 !> Set the accumulated bond rotation to zero for all bergs
 subroutine reset_bond_rotation(bergs)
 type(icebergs), pointer :: bergs !< Container for all types and memory

From 7a52136e55eb38290c775aec85a2ef518590ed21 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Wed, 28 Dec 2022 19:05:26 -0500
Subject: [PATCH 333/361] Removed energy monitoring. While it was previously
 useful for development, it was also clunky, it only worked in non-DEM mode
 (without torques), and it added a dozen or so variables. Removed energy-based
 bond-breaking as well.

---
 src/icebergs.F90                     | 540 ++++++---------------------
 src/icebergs_framework.F90           | 335 +----------------
 src/icebergs_io.F90                  | 146 +-------
 tests/a68_test/long_run.nml          |   1 -
 tests/collision_tests/input.nml      | 160 --------
 tests/dem_cbeam_test/input.nml       |   1 -
 tests/dem_ground_frac_test/input.nml |   1 -
 tests/dem_ssbeam_test/input.nml      |   1 -
 8 files changed, 134 insertions(+), 1051 deletions(-)
 delete mode 100644 tests/collision_tests/input.nml

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index f269d73..8bcf421 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -51,7 +51,7 @@ module ice_bergs
 use ice_bergs_framework, only: orig_bond_length
 use ice_bergs_framework, only: update_and_break_bonds,break_bonds_dem,assign_n_bonds,reset_bond_rotation
 use ice_bergs_framework, only: update_bond_angles
-use ice_bergs_framework, only: monitor_energy, energy_tests_init, mts
+use ice_bergs_framework, only: mts
 use ice_bergs_framework, only: dem_tests_init
 use ice_bergs_framework, only: dem, save_bond_forces
 use ice_bergs_framework, only: orig_dem_moment_of_inertia, no_frac_first_ts
@@ -155,8 +155,6 @@ subroutine icebergs_init(bergs, &
   !Reading ocean depth from a file
   if (bergs%read_ocean_depth_from_file) call read_ocean_depth(bergs%grd)
 
-  if (monitor_energy) call energy_tests_init(bergs)
-
   if (bergs%iceberg_bonds_on) then
     if (bergs%manually_initialize_bonds) then
       call initialize_iceberg_bonds(bergs)
@@ -1283,7 +1281,7 @@ end subroutine overlap_area
 
 !> For the MTS scheme, calculates the instantaneous acceleration of an iceberg
 subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt, rx, ry, &
-  ax, ay, axn, ayn, bxn, byn, save_bond_energy, Fec_x, Fec_y, Fdc_x, Fdc_y, debug_flag)
+  ax, ay, axn, ayn, bxn, byn, Fec_x, Fec_y, Fdc_x, Fdc_y, debug_flag)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
   type(iceberg), pointer :: berg !< An iceberg
@@ -1305,7 +1303,6 @@ subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, d
   real, intent(inout) :: ayn !< Explicit estimate of meridional acceleration (m/s2)
   real, intent(inout) :: bxn !< Implicit component of zonal acceleration (m/s2)
   real, intent(inout) :: byn !< Implicit component of meridional acceleration (m/s2)
-  logical, intent(in) :: save_bond_energy !< Track energy terms for bonds (when monitor_energy==T)
   real, optional, intent(out) :: Fec_x !< If bergs%mts_part==1: Zonal collisional elastic force (N)
   real, optional, intent(out) :: Fec_y !< If bergs%mts_part==1: Meridional collisional elastic force (N)
   real, optional, intent(out) :: Fdc_x !< If bergs%mts_part==1: Zonal collisional damping force (N)
@@ -1333,7 +1330,7 @@ subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, d
   real :: dragfrac, N_bonds, N_max, groundfrac, c_gnd, drag_gnd, scaling=0.5
   real :: minfricvel=3.17e-12 !m/s (~0.0001 m/a)
   type(bond), pointer :: current_bond
-  real :: IAd_x, IAd_y, sum_bond_Ee, sum_bond_Ed, oneoverkn, M2
+  real :: IAd_x, IAd_y, oneoverkn, M2
   type(iceberg), pointer :: other_berg
   real :: L2,W2
 
@@ -1570,79 +1567,6 @@ subroutine accel_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, d
       Fdc_x=berg%mass*( P_ia_times_u_x - (P_ia_11*uveln+P_ia_12*vveln))
       Fdc_y=berg%mass*( P_ia_times_u_y - (P_ia_21*uveln+P_ia_22*vveln))
     endif
-  elseif (save_bond_energy) then
-    !save bond energies
-    if (monitor_energy .or. bergs%fracture_criterion=='energy') then
-      sum_bond_Ee=0.0
-      sum_bond_Ed=0.0
-
-      if (bergs%constant_interaction_LW) then
-        ! mass according to constant length and width here, just for interactions
-        M=bergs%constant_length*bergs%constant_width*berg%thickness*bergs%rho_bergs
-      else
-        M=berg%mass
-      endif
-
-      current_bond=>berg%first_bond
-      do while (associated(current_bond)) ! loop over all bonds
-        other_berg=>current_bond%other_berg
-
-        if (monitor_energy) then
-          !first, the half-step:
-          current_bond%Ee=current_bond%Ee - 0.25*dt*(&
-            (uvel0 + u_star)*M*current_bond%axn_fast +&
-            (vvel0 + v_star)*M*current_bond%ayn_fast)
-
-
-          current_bond%Ed=current_bond%Ed - 0.25*dt*(&
-            (uvel0 + u_star)*M*current_bond%bxn_fast +&
-            (vvel0 + v_star)*M*current_bond%byn_fast)
-
-        endif
-
-        !the rest:
-        IA_x=0.0; IA_y=0.0 !explicit elastic force
-        P_ia_11=0.0; P_ia_12=0.0; P_ia_21=0.0; P_ia_22=0.0
-        call calculate_force(bergs, berg, other_berg, IA_x, IA_y, uveln, vveln, uveln, vveln,  &
-          P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded=.true.)
-        !implicit damping force
-        IAd_x=P_ia_11*(other_berg%uvel_old-uveln)+P_ia_12*(other_berg%vvel_old-vveln)
-        IAd_y=P_ia_12*(other_berg%uvel_old-uveln)+P_ia_22*(other_berg%vvel_old-vveln)
-
-        if (bergs%fracture_criterion=='energy') then
-          oneoverkn = 1./bergs%spring_coef
-          if (bergs%constant_interaction_LW) then
-            ! other_berg mass according to constant length and width here, just for interactions
-            M2=bergs%constant_length*bergs%constant_width*other_berg%thickness*bergs%rho_bergs
-          else
-            M2=other_berg%mass
-          endif
-
-          oneoverkn=oneoverkn*(M/min(M,other_berg%mass))
-          current_bond%spring_pe = 0.5*((M*IA_x)**2+(M*IA_y)**2)*oneoverkn
-        endif
-
-        if (monitor_energy) then
-          !work
-          current_bond%Ee=current_bond%Ee - 0.25*dt*(&
-            (u_star + uveln)*M*IA_x + &
-            (v_star + vveln)*M*IA_y)
-
-          !V{i+0.5} to V{i+1}
-          current_bond%Ed=current_bond%Ed- 0.25*dt*(&
-            (u_star + uveln)*M*IAd_x + &
-            (v_star + vveln)*M*IAd_y)
-
-          sum_bond_Ee = sum_bond_Ee + current_bond%Ee
-          sum_bond_Ed = sum_bond_Ed + current_bond%Ed
-
-          current_bond%axn_fast=IA_x;  current_bond%ayn_fast=IA_y
-          current_bond%bxn_fast=IAd_x; current_bond%byn_fast=IAd_y
-        endif
-
-        current_bond=>current_bond%next_bond
-      enddo
-    endif
   endif
 
   ! Limit speed of bergs based on a CFL criteria
@@ -1789,7 +1713,7 @@ end subroutine accel_mts
 !> Calculates the instantaneous acceleration of an iceberg due to berg interactions
 !> For the inner steps of the mts scheme only. Explicit velocity verlet (no implicit terms)
 subroutine accel_explicit_inner_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel, uvel0, vvel0, dt,  &
-  ax, ay, axn, ayn, save_bond_energy, debug_flag)
+  ax, ay, axn, ayn, debug_flag)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
   type(iceberg), pointer :: berg !< An iceberg
@@ -1807,7 +1731,6 @@ subroutine accel_explicit_inner_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel,
   real, intent(out) :: ay !< Meridional acceleration (m/s2)
   real, intent(inout) :: axn !< Explicit estimate of zonal acceleration (m/s2)
   real, intent(inout) :: ayn !< Explicit estimate of meridional acceleration (m/s2)
-  logical, intent(in) :: save_bond_energy !< Track energy terms for bonds (when monitor_energy==T)
   logical, optional :: debug_flag !< If true, print debugging
   ! Local variables
   type(icebergs_gridded), pointer :: grd
@@ -1819,7 +1742,7 @@ subroutine accel_explicit_inner_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel,
   real :: P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y    !Added by Alon
   integer :: stderrunit
   type(bond), pointer :: current_bond
-  real :: IAd_x, IAd_y, sum_bond_Ee, sum_bond_Ed, oneoverkn, M2, D, groundfrac
+  real :: IAd_x, IAd_y, oneoverkn, M2, D, groundfrac
   type(iceberg), pointer :: other_berg
   integer :: grdi,grdj
   logical :: bonded, bond_matched, run_contact
@@ -2006,104 +1929,6 @@ subroutine accel_explicit_inner_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel,
 
   uveln=u_star+dt*ax; vveln=v_star+dt*ay
 
-  if (save_bond_energy) then
-
-    !save bond energies
-    if (monitor_energy .or. bergs%fracture_criterion=='energy') then
-      current_bond=>berg%first_bond
-      do while (associated(current_bond)) ! loop over all bonds
-        other_berg=>current_bond%other_berg
-
-        if (monitor_energy) then
-          !first, the half-step:
-          current_bond%Ee=current_bond%Ee - 0.25*dt*(&
-            (uvel0 + u_star)*M*current_bond%axn_fast +&
-            (vvel0 + v_star)*M*current_bond%ayn_fast)
-
-          !here, bxn_fast and byn_fast are explicit damping accel (not implicit!)
-          current_bond%Ed=current_bond%Ed - 0.25*dt*(&
-            (uvel0 + u_star)*M*current_bond%bxn_fast +&
-            (vvel0 + v_star)*M*current_bond%byn_fast)
-        endif
-
-        !the rest:
-
-        if (bergs%dem) then
-          F_x=0.; F_y=0.; T=0.; Fd_x=0.; Fd_y=0.; T_d=0.
-          call calculate_force_dem(bergs,berg,other_berg,current_bond,dt,&
-            F_x,F_y,T,Fd_x,Fd_y,T_d,savestress=.false.)
-          if (bergs%dem_beam_test>0) then
-            if (bergs%dem_beam_test==1) then
-              !3.1 (Wang,2020): Simply supported beam test
-              !no vertical load on ends of beam, add vertical load to center of beam
-              if (berg%start_lon==bergs%dem_tests_start_lon .or. berg%start_lon==bergs%dem_tests_end_lon) then
-                F_y=0.0; Fd_y=0.0
-              elseif (berg%start_lon==0.5*(bergs%dem_tests_start_lon+bergs%dem_tests_end_lon)) then
-                F_y = F_y - 1.5e5
-              endif
-            elseif (bergs%dem_beam_test==2) then
-              !3.2 (Wang,2020): Cantilever beam test
-              !add vertical load to end of the cantilever beam
-              if (berg%start_lon==bergs%dem_tests_end_lon) then
-                F_y = F_y - 1.5e10/3.
-              endif
-            elseif (bergs%dem_beam_test==3) then
-              !Angular velocity test (starting element has constant rot=-pi/2)
-              if (berg%start_lon==bergs%dem_tests_start_lon) then
-                T=0.0; T_d=0.0
-              endif
-            elseif (bergs%dem_beam_test==4) then
-              if (berg%start_lon==bergs%dem_tests_start_lon) then
-                F_y=0.0; Fd_y=0.0
-              endif
-            endif
-          endif
-          IA_x=F_x/M; IA_y=F_y/M; IAd_x=Fd_x/M; IAd_y=Fd_y/M
-        else
-          IA_x=0.0; IA_y=0.0 !explicit elastic force
-          P_ia_11=0.0; P_ia_12=0.0; P_ia_21=0.0; P_ia_22=0.0
-          call calculate_force(bergs, berg, other_berg, IA_x, IA_y, uvel0, vvel0, uvel0, vvel0,  &
-            P_ia_11, P_ia_12, P_ia_21, P_ia_22, P_ia_times_u_x, P_ia_times_u_y,bonded=.true.)
-          !damping force
-          IAd_x=P_ia_11*(other_berg%uvel_old-berg%uvel_old)+P_ia_12*(other_berg%vvel_old-berg%vvel_old)
-          IAd_y=P_ia_12*(other_berg%uvel_old-berg%uvel_old)+P_ia_22*(other_berg%vvel_old-berg%vvel_old)
-        endif
-
-        if (bergs%fracture_criterion=='energy') then
-          if (bergs%constant_interaction_LW) then
-            ! other_berg mass according to constant length and width here, just for interactions
-            M2=bergs%constant_length*bergs%constant_width*other_berg%thickness*bergs%rho_bergs
-          else
-            M2=other_berg%mass
-          endif
-
-          oneoverkn = 1./bergs%spring_coef
-          oneoverkn=oneoverkn*(M/min(M,M2))
-          current_bond%spring_pe = 0.5*((M*IA_x)**2+(M*IA_y)**2)*oneoverkn
-        endif
-
-        if (monitor_energy) then
-          !work
-          current_bond%Ee=current_bond%Ee - 0.25*dt*(&
-            (u_star + uveln)*M*IA_x + &
-            (v_star + vveln)*M*IA_y)
-
-          !V{i+0.5} to V{i+1}
-          current_bond%Ed=current_bond%Ed- 0.25*dt*(&
-            (u_star + uveln)*M*IAd_x + &
-            (v_star + vveln)*M*IAd_y)
-
-          current_bond%axn_fast=IA_x;  current_bond%ayn_fast=IA_y
-
-          !here, bxn_fast and byn_fast are explicit damping accel (not implicit!)
-          current_bond%bxn_fast=IAd_x; current_bond%byn_fast=IAd_y
-        endif
-
-        current_bond=>current_bond%next_bond
-      enddo
-    endif
-  endif
-
   ! Limit speed of bergs based on a CFL criteria
   if ((bergs%speed_limit>0.) .or. (bergs%speed_limit .eq.-1.)) then
     speed=sqrt(uveln*uveln+vveln*vveln) ! Speed of berg
@@ -5671,7 +5496,6 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
       call set_conglom_ids(bergs)
     endif
     if (bergs%iceberg_bonds_on) call orig_bond_length(bergs)
-    if (monitor_energy) call energy_tests_init(bergs)
     if (mpp_pe()==0) write(*,'(a)') 'KID, iceberg_run: completed first visit initialization'
   endif
 
@@ -6607,26 +6431,6 @@ subroutine calve_icebergs(bergs)
             newberg%ang_vel=0.; newberg%ang_accel=0.; newberg%rot=0.
           endif
 
-          if (monitor_energy) then
-            if (.not. allocations_done) then
-              if (.not. allocated(newberg%Ee)) allocate(newberg%Ee)
-              if (.not. allocated(newberg%Ed)) allocate(newberg%Ed)
-              if (.not. allocated(newberg%Eext)) allocate(newberg%Eext)
-              if (.not. allocated(newberg%Ee_contact)) allocate(newberg%Ee_contact)
-              if (.not. allocated(newberg%Ed_contact)) allocate(newberg%Ed_contact)
-              if (.not. allocated(newberg%Efrac)) allocate(newberg%Efrac)
-              if (.not. allocated(newberg%Ee_temp)) allocate(newberg%Ee_temp)
-              if (.not. allocated(newberg%Ed_temp)) allocate(newberg%Ed_temp)
-              if (.not. allocated(newberg%Eext_temp)) allocate(newberg%Eext_temp)
-              if (.not. allocated(newberg%Ee_contact_temp)) allocate(newberg%Ee_contact_temp)
-              if (.not. allocated(newberg%Ed_contact_temp)) allocate(newberg%Ed_contact_temp)
-            endif
-
-            newberg%Ee=0.; newberg%Ed=0.; newberg%Eext=0.; newberg%Ee_contact=0.; newberg%Ed_contact=0.
-            newberg%Efrac=0.; newberg%Ee_temp=0.; newberg%Ed_temp=0.;newberg%Eext_temp=0.;
-            newberg%Ee_contact_temp=0.; newberg%Ed_contact_temp =0.
-          endif
-
           if (bergs%fracture_criterion .ne. 'none' .and. (.not. bergs%dem)) then
             if (.not. allocations_done) then
               if (.not. allocated(newberg%accum_bond_rotation)) allocate(newberg%accum_bond_rotation)
@@ -6847,14 +6651,6 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b,fl_disp_x,fl_disp_y,berg_from_bit
     cberg%ang_vel=0.; cberg%ang_accel=0.; cberg%rot=0.
   endif
 
-  if (monitor_energy) then
-    allocate(cberg%Ee,cberg%Ed,cberg%Eext,cberg%Ee_contact,cberg%Ed_contact,cberg%Efrac,&
-      cberg%Ee_temp,cberg%Ed_temp,cberg%Eext_temp,cberg%Ee_contact_temp,cberg%Ed_contact_temp)
-    cberg%Ee=0.; cberg%Ed=0.; cberg%Eext=0.; cberg%Ee_contact=0.; cberg%Ed_contact=0.
-    cberg%Efrac=0.; cberg%Ee_temp=0.; cberg%Ed_temp=0.;cberg%Eext_temp=0.;
-    cberg%Ee_contact_temp=0.; cberg%Ed_contact_temp =0.
-  endif
-
   if (bergs%fracture_criterion .ne. 'none' .and. (.not. bergs%dem)) then
     allocate(cberg%accum_bond_rotation)
     cberg%accum_bond_rotation=0.
@@ -6888,10 +6684,7 @@ subroutine evolve_icebergs_mts(bergs)
   real :: ax1,ay1
   real :: dt, dt_2
   logical :: on_tangential_plane, error_flag, bounced
-  !energy stuff
-  real :: dx,dy,M,Fex,Fey,Fex_prev,Fey_prev,Fdx_prev,Fdy_prev,Fdx,Fdy,Fx_tot,Fy_tot,Fx_tot_prev,Fy_tot_prev
-  logical :: save_bond_energy
-  real :: Fex_i, Fey_i, Fec_x, Fec_y, Fdc_x, Fdc_y, ustar, vstar, uveln_star, vveln_star
+  real :: Fec_x, Fec_y, Fdc_x, Fdc_y, ustar, vstar, uveln_star, vveln_star
   integer :: ii,jj,maxii,minii,maxjj,minjj
   real :: usum,usum1,usum2,normchange,denom
   real :: MM,AA,R1,groundfrac,gdrag,D
@@ -6946,7 +6739,6 @@ subroutine evolve_icebergs_mts(bergs)
   dt_2=0.5*dt
   rx = 0.0; ry = 0.0 !not needed, because interp_gridded_fields_to_bergs was already called
   ii = 0
-  save_bond_energy=.false.
   usum=0.0; usum1=0.0; usum2=0.0
   finished=.false.
   had_collision=.false.
@@ -6977,14 +6769,12 @@ subroutine evolve_icebergs_mts(bergs)
               xi=berg%xi      ;   yj=berg%yj
 
               call accel_mts(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, &
-                ax1, ay1, axn, ayn, bxn, byn, save_bond_energy,Fec_x, Fec_y, Fdc_x, Fdc_y)
+                ax1, ay1, axn, ayn, bxn, byn,Fec_x, Fec_y, Fdc_x, Fdc_y)
 
               if (Fdc_x .ne. 0. .or. Fdc_y .ne. 0. .and. bergs%force_convergence) then
                 had_collision=.true.
                 berg%static_berg=0.1
               endif
-              if (monitor_energy .and. last_iter) &
-                call mts_energy_part_1(bergs,berg,ax1,ay1,axn,ayn,bxn,byn,Fec_x,Fec_y,Fdc_x,Fdc_y)
 
               ! Saving all the iceberg variables
               berg%axn=axn; berg%ayn=ayn
@@ -7037,7 +6827,7 @@ subroutine evolve_icebergs_mts(bergs)
         finished=.true.
       endif
 
-      if (last_iter .and. .not. monitor_energy) finished=.true.
+      if (last_iter) finished=.true.
 
       usum1=0.0; usum2=0.0
 
@@ -7075,7 +6865,6 @@ subroutine evolve_icebergs_mts(bergs)
             berg%bxn=berg%bxn_fast; berg%byn=berg%byn_fast
           endif
 
-          !if (monitor energy): already did energy update in part I
         endif
         berg=>berg%next
       enddo
@@ -7145,7 +6934,7 @@ subroutine evolve_icebergs_mts(bergs)
     jj=0
     usum=0.0; usum1=0.0; usum2=0.0
     finished=.false.
-    save_bond_energy=.false.
+
     if (bergs%force_convergence .and. (.not. bergs%explicit_inner_mts)) then
       last_iter=.false.
     else
@@ -7156,140 +6945,134 @@ subroutine evolve_icebergs_mts(bergs)
 
       jj=jj+1
 
-      if (monitor_energy .and. last_iter) save_bond_energy=.true.
       bergs%bond_break_detected=.false.
-    ! update velocities
-    do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
-      berg=>bergs%list(grdi,grdj)%first
-      do while (associated(berg)) ! loop over all bergs
-        if (berg%static_berg .lt. 0.5 .and. berg%conglom_id.ne.0) then
-
-          latn = berg%lat ;   lonn = berg%lon
-          axn  = berg%axn_fast ;   ayn  = berg%ayn_fast
-          bxn  = berg%bxn_fast ;   byn  = berg%byn_fast
-          uvel1=berg%uvel ;   vvel1=berg%vvel
-          i=berg%ine      ;   j=berg%jne
-          xi=berg%xi      ;   yj=berg%yj
-
-          axn = axn+bxn; ayn=ayn+byn
-
-          ! Turn the velocities into u_star, v_star.(uvel3 is v_star) - (possible issues with tangent plane?)
-          uvel3=uvel1+(dt_2*axn)                  !(Stern et al 2017, Eq B4)
-          vvel3=vvel1+(dt_2*ayn)
-
-          if (monitor_energy .and. last_iter) call mts_energy_part_3(bergs,berg,uvel3,vvel3,wt=1)
-
-          if (bergs%explicit_inner_mts) then
-            call accel_explicit_inner_mts(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, &
-              ax1, ay1, axn, ayn, save_bond_energy)
-            bxn=0.; byn=0.
+      ! update velocities
+      do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+        berg=>bergs%list(grdi,grdj)%first
+        do while (associated(berg)) ! loop over all bergs
+          if (berg%static_berg .lt. 0.5 .and. berg%conglom_id.ne.0) then
 
-            if (short_step_mts_grounding) then
-              D=(bergs%rho_bergs/rho_seawater)*berg%thickness ! draught (keel depth)
-              if (bergs%h_to_init_grounding>0.0) then
-                groundfrac=1.0-(berg%od-D)/bergs%h_to_init_grounding
-                groundfrac=max(groundfrac,0.0); groundfrac=min(groundfrac,1.0)
-              else
-                if (D>berg%od) then
-                  groundfrac=1.0
+            latn = berg%lat ;   lonn = berg%lon
+            axn  = berg%axn_fast ;   ayn  = berg%ayn_fast
+            bxn  = berg%bxn_fast ;   byn  = berg%byn_fast
+            uvel1=berg%uvel ;   vvel1=berg%vvel
+            i=berg%ine      ;   j=berg%jne
+            xi=berg%xi      ;   yj=berg%yj
+
+            axn = axn+bxn; ayn=ayn+byn
+
+            ! Turn the velocities into u_star, v_star.(uvel3 is v_star) - (possible issues with tangent plane?)
+            uvel3=uvel1+(dt_2*axn)                  !(Stern et al 2017, Eq B4)
+            vvel3=vvel1+(dt_2*ayn)
+
+            if (bergs%explicit_inner_mts) then
+              call accel_explicit_inner_mts(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, &
+                ax1, ay1, axn, ayn)
+              bxn=0.; byn=0.
+
+              if (short_step_mts_grounding) then
+                D=(bergs%rho_bergs/rho_seawater)*berg%thickness ! draught (keel depth)
+                if (bergs%h_to_init_grounding>0.0) then
+                  groundfrac=1.0-(berg%od-D)/bergs%h_to_init_grounding
+                  groundfrac=max(groundfrac,0.0); groundfrac=min(groundfrac,1.0)
                 else
-                  groundfrac=0.0
+                  if (D>berg%od) then
+                    groundfrac=1.0
+                  else
+                    groundfrac=0.0
+                  endif
                 endif
-              endif
-              if (groundfrac>0.0) then
-                if (bergs%constant_interaction_LW) then
-                  ! mass according to constant length and width here, just for interactions
-                  MM=bergs%constant_length*bergs%constant_width*berg%thickness*bergs%rho_bergs
-                  AA=bergs%constant_width*bergs%constant_length
+                if (groundfrac>0.0) then
+                  if (bergs%constant_interaction_LW) then
+                    ! mass according to constant length and width here, just for interactions
+                    MM=bergs%constant_length*bergs%constant_width*berg%thickness*bergs%rho_bergs
+                    AA=bergs%constant_width*bergs%constant_length
+                  else
+                    MM=berg%mass
+                    AA=berg%length*berg%width
+                  endif
+                  gdrag=-bergs%cdrag_grounding*groundfrac*AA/MM
                 else
-                  MM=berg%mass
-                  AA=berg%length*berg%width
+                  gdrag=0.
                 endif
-                gdrag=-bergs%cdrag_grounding*groundfrac*AA/MM
-              else
-                gdrag=0.
+                axn=axn+uvel1*gdrag; ayn=ayn+vvel1*gdrag
+                ax1=0.5*axn; ay1=0.5*ayn
               endif
-              axn=axn+uvel1*gdrag; ayn=ayn+vvel1*gdrag
-              ax1=0.5*axn; ay1=0.5*ayn
+
+            else
+              call accel_mts(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, &
+                ax1, ay1, axn, ayn, bxn, byn)
             endif
 
-          else
-            call accel_mts(bergs, berg, i, j, xi, yj, latn, uvel1, vvel1, uvel1, vvel1, dt, rx, ry, &
-              ax1, ay1, axn, ayn, bxn, byn, save_bond_energy)
-          endif
+            ! Solving for the new velocity (Stern et al 2017, Eqn B5)
+            on_tangential_plane=.false.
+            if ((berg%lat>89.) .and. (bergs%grd%grid_is_latlon)) on_tangential_plane=.true.
+            if (on_tangential_plane) then
+              call rotvec_to_tang(lonn,uvel3,vvel3,xdot3,ydot3)
+              call rotvec_to_tang(lonn,ax1,ay1,xddot1,yddot1)
+              xdotn=xdot3+(dt*xddot1); ydotn=ydot3+(dt*yddot1)
+              call rotvec_from_tang(lonn,xdotn,ydotn,uveln,vveln)
+            else
+              !uvel3, vvel3 become uveln and vveln after they are put into lat/lon co-ordinates
+              uveln=uvel3+(dt*ax1); vveln=vvel3+(dt*ay1)
+            endif
 
-          ! Solving for the new velocity (Stern et al 2017, Eqn B5)
-          on_tangential_plane=.false.
-          if ((berg%lat>89.) .and. (bergs%grd%grid_is_latlon)) on_tangential_plane=.true.
-          if (on_tangential_plane) then
-            call rotvec_to_tang(lonn,uvel3,vvel3,xdot3,ydot3)
-            call rotvec_to_tang(lonn,ax1,ay1,xddot1,yddot1)
-            xdotn=xdot3+(dt*xddot1); ydotn=ydot3+(dt*yddot1)
-            call rotvec_from_tang(lonn,xdotn,ydotn,uveln,vveln)
-          else
-            !uvel3, vvel3 become uveln and vveln after they are put into lat/lon co-ordinates
-            uveln=uvel3+(dt*ax1); vveln=vvel3+(dt*ay1)
-          endif
+            if (bergs%force_convergence .and. (.not. bergs%explicit_inner_mts)) then
+              if (jj==1) usum=usum+berg%uvel_old**2 + berg%vvel_old**2
+              usum1=usum1 + uveln**2 + vveln**2
+              usum2=usum2+(uveln-berg%uvel_old)**2+(vveln-berg%vvel_old)**2
+            endif
 
-          if (bergs%force_convergence .and. (.not. bergs%explicit_inner_mts)) then
-            if (jj==1) usum=usum+berg%uvel_old**2 + berg%vvel_old**2
-            usum1=usum1 + uveln**2 + vveln**2
-            usum2=usum2+(uveln-berg%uvel_old)**2+(vveln-berg%vvel_old)**2
+            ! Saving all the iceberg variables.
+            berg%axn_fast=axn; berg%ayn_fast=ayn
+            berg%bxn_fast=bxn; berg%byn_fast=byn
+            berg%uvel=uveln  ; berg%vvel=vveln
           endif
+          berg=>berg%next
+        enddo ! loop over all bergs
+      enddo; enddo ! update velocities
 
-          ! Saving all the iceberg variables.
-          berg%axn_fast=axn; berg%ayn_fast=ayn
-          berg%bxn_fast=bxn; berg%byn_fast=byn
-          berg%uvel=uveln  ; berg%vvel=vveln
-
-          if (monitor_energy .and. last_iter) call mts_energy_part_3(bergs,berg,uvel3,vvel3,wt=2)
-
-        endif
-        berg=>berg%next
-      enddo ! loop over all bergs
-    enddo; enddo ! update velocities
-
-    if (bergs%force_convergence .and. .not. last_iter) then
-      if (jj>1) then
-        denom=sqrt(usum)+sqrt(usum1)
-        if (denom>0) then
-          normchange=2.0*sqrt(usum2)/denom
-        else
-          normchange=0.0
+      if (bergs%force_convergence .and. .not. last_iter) then
+        if (jj>1) then
+          denom=sqrt(usum)+sqrt(usum1)
+          if (denom>0) then
+            normchange=2.0*sqrt(usum2)/denom
+          else
+            normchange=0.0
+          endif
+          if (normchange<bergs%convergence_tolerance) last_iter=.true.
         endif
-        if (normchange<bergs%convergence_tolerance) last_iter=.true.
+        usum=usum1 !previous norm (squared)
+      else
+        finished=.true.
       endif
-      usum=usum1 !previous norm (squared)
-    else
-      finished=.true.
-    endif
 
-    if (last_iter .and. .not. monitor_energy) finished=.true.
+      if (last_iter) finished=.true.
 
-    if (bergs%force_convergence .and. (.not. finished)) then
-      do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
-        berg=>bergs%list(grdi,grdj)%first
-        do while (associated(berg)) ! loop over all bergs
-          if (berg%static_berg .lt. 0.5 .and. berg%conglom_id.ne.0) then
+      if (bergs%force_convergence .and. (.not. finished)) then
+        do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
+          berg=>bergs%list(grdi,grdj)%first
+          do while (associated(berg)) ! loop over all bergs
+            if (berg%static_berg .lt. 0.5 .and. berg%conglom_id.ne.0) then
 
-            !update old velocities for interactions
-            berg%uvel_old=berg%uvel; berg%vvel_old=berg%vvel
+              !update old velocities for interactions
+              berg%uvel_old=berg%uvel; berg%vvel_old=berg%vvel
 
-            berg%uvel=berg%uvel-dt_2*(berg%axn_fast+berg%bxn_fast)-dt_2*(berg%axn+berg%bxn)
-            berg%vvel=berg%vvel-dt_2*(berg%ayn_fast+berg%byn_fast)-dt_2*(berg%ayn+berg%byn)
-            berg%axn_fast=berg%axn; berg%ayn_fast=berg%ayn
-            berg%bxn_fast=berg%bxn; berg%byn_fast=berg%byn
-          endif
-          berg=>berg%next
-        enddo
-      enddo; enddo
-    endif
+              berg%uvel=berg%uvel-dt_2*(berg%axn_fast+berg%bxn_fast)-dt_2*(berg%axn+berg%bxn)
+              berg%vvel=berg%vvel-dt_2*(berg%ayn_fast+berg%byn_fast)-dt_2*(berg%ayn+berg%byn)
+              berg%axn_fast=berg%axn; berg%ayn_fast=berg%ayn
+              berg%bxn_fast=berg%bxn; berg%byn_fast=berg%byn
+            endif
+            berg=>berg%next
+          enddo
+        enddo; enddo
+      endif
 
-    usum1=0.0; usum2=0.0
+      usum1=0.0; usum2=0.0
 
-    if (jj<minjj .and. finished) minjj=jj
-    if (jj>maxjj .and. finished) maxjj=jj
-  enddo
+      if (jj<minjj .and. finished) minjj=jj
+      if (jj>maxjj .and. finished) maxjj=jj
+    enddo
 
     !update 'old' velocities used for interactions
     do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
@@ -7395,97 +7178,6 @@ subroutine evolve_icebergs_mts(bergs)
   no_frac_first_ts=.false.
 end subroutine evolve_icebergs_mts
 
-
-!> Energy calculations for MTS_part==1
-subroutine mts_energy_part_1(bergs, berg, ax1, ay1, axn, ayn, bxn, byn, Fec_x, Fec_y, Fdc_x, Fdc_y)
-  ! Arguments
-  type(icebergs), pointer :: bergs !< Container for all types and memory
-  type(iceberg), pointer :: berg !< Berg for which to do calculations
-  real, intent(in) :: ax1 !< Zonal acceleration [m s-2]
-  real, intent(in) :: ay1 !< Meridional acceleration [m s-2]
-  real, intent(in) :: axn !< Explicit estimate of zonal acceleration [m s-2]
-  real, intent(in) :: ayn !< Explicit estimate of meridional acceleration [m s-2]
-  real, intent(in) :: bxn !< Implicit estimate of zonal acceleration [m s-2]
-  real, intent(in) :: byn !< Implicit estimate of meridional acceleration [m s-2]
-  real, intent(in) :: Fec_x !< Zonal elastic force from collision with other conglomerate [N]
-  real, intent(in) :: Fec_y !< Meridional elastic force from collision with other conglomerate [N]
-  real, intent(in) :: Fdc_x !< !< Zonal damping force from collision with other conglomerate [N]
-  real, intent(in) :: Fdc_y !< !< Meridional damping force from collision with other conglomerate [N]
-  ! Local
-  real :: dt, M, Fex, Fey, Fex_i, Fey_i
-  real :: uveln, vveln, uveln_star, vveln_star, ustar, vstar
-
-  dt=bergs%dt
-
-  !Again, MTS part 1 solves for V_n+1 from the previous timestep
-  !"Temp" energy variables are from the previous cycle
-  !At the end of MTS part 1, the non-"temp" energy variables are saved for post-processing/analysis
-  !see plot_energy.py
-
-  !derived from Mayrhofer,Hager, and Kloss 2017 (MHK17) and Asmar et al 2003
-  M = berg%mass
-
-  Fex = M * 2*ax1; Fey = M * 2*ay1 !external forces
-  Fex = Fex - Fec_x - Fdc_x; Fey = Fey - Fec_y - Fdc_y !external forces minus collisional
-
-  uveln=berg%uvel+(dt*ax1); vveln=berg%vvel+(dt*ay1)
-  ustar=berg%uvel; vstar=berg%vvel
-
-  !dEext=0.5*(V_{i+1} + V_{i+0.5})*F_{ext,i+1}*dt/2
-  berg%Eext=berg%Eext_temp - 0.25*dt*(&
-    (uveln + ustar)*Fex + (vveln + vstar)*Fey)
-
-  berg%Ee_contact=berg%Ee_contact_temp - 0.25*dt*(&
-    (uveln + ustar)*Fec_x + (vveln + vstar)*Fec_y)
-
-  berg%Ed_contact=berg%Ed_contact_temp - 0.25*dt*(&
-    (uveln + ustar)*Fdc_x + (vveln + vstar)*Fdc_y)
-
-  !The following is for part II
-  !V{i+1.5}
-  uveln_star = uveln + dt*ax1; vveln_star = vveln + dt*ay1
-
-  berg%Eext_temp=berg%Eext - 0.25*dt*(&
-    (uveln + uveln_star)*Fex + (vveln + vveln_star)*Fey)
-
-  berg%Ee_contact_temp=berg%Ee_contact - 0.25*dt*(&
-    (uveln + uveln_star)*Fec_x + (vveln + vveln_star)*Fec_y)
-
-  berg%Ed_contact_temp=berg%Ed_contact - 0.25*dt*(&
-    (uveln + uveln_star)*Fdc_x + (vveln + vveln_star)*Fdc_y)
-
-  berg%Ee=berg%Ee_temp; berg%Ed=berg%Ed_temp
-end subroutine mts_energy_part_1
-
-!> Energy calculations for MTS_part==3
-subroutine mts_energy_part_3(bergs,berg,ustar,vstar,wt)
-  ! Arguments
-  type(icebergs), pointer :: bergs !< Container for all types and memory
-  type(iceberg), pointer :: berg !< Berg to do calculations for
-  real,intent(in) :: ustar !< u-component of half-step velocity [m s-1]
-  real,intent(in) :: vstar !< v-component of half-step velocity [m s-1]
-  integer,intent(in) :: wt !< integrate from time i to i+1/2 (wt==1) or i+1/2 to i+1 (wt==2)
-  ! Local
-  real :: dt, M, Fex, Fey, Fdx, Fdy
-
-
-  !MTS sub-step forces
-  dt = bergs%mts_fast_dt
-  M = berg%mass
-  Fex = M * berg%axn_fast; Fey = M * berg%ayn_fast !elastic forces
-
-  !for i to i+1/2 or i+1/2 to i+1
-  berg%Ee_temp=berg%Ee_temp - 0.25*dt*(&
-    (ustar + berg%uvel)*Fex + &
-    (vstar + berg%vvel)*Fey)
-
-  Fdx = M * berg%bxn_fast; Fdy = M * berg%byn_fast !damping forces
-  berg%Ed_temp=berg%Ed_temp - 0.25*dt*(&
-    (ustar + berg%uvel)*Fdx + &
-    (vstar + berg%vvel)*Fdy)
-
-end subroutine mts_energy_part_3
-
 !> Evolves icebergs forward by updating velocity and position with a time-stepping scheme
 subroutine evolve_icebergs(bergs)
   ! Arguments
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 22dce06..4be126f 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -48,7 +48,6 @@ module ice_bergs_framework
 logical :: mts=.false. !< Use multiple time stepping scheme
 logical :: save_bond_traj=.false. !<Save trajectory files for bonds
 logical :: ewsame=.false. !<(F) set T if periodic and 2 PEs along the x direction (zonal) (i.e. E/W PEs are the same)
-logical :: monitor_energy=.false. !<monitors energies: elastic (spring+collision), external, dissipated, fracture
 logical :: iceberg_bonds_on=.False. ! True=Allow icebergs to have bonds, False=don't allow.
 logical :: dem=.false. !< If T, run in DEM-mode with angular terms, variable stiffness, etc
 logical :: save_bond_forces=.true. !< Saves forces on bonds so only 1 of 2 bonds in a pair need processing during DEM-MTS explicit sub-steps
@@ -58,7 +57,7 @@ module ice_bergs_framework
 real :: A68_xdisp=0. !< longitude of the SW corner of the grounding zone in the A68 test case
 real :: A68_ydisp=0. !< latitude of the SW corner of the grounding zone in the A68 test case
 logical :: rev_mind=.false. !< Alterate option for staggering the 3x3 cells used for quadratic mapping of ocean depth to particles
-character(len=11) :: fracture_criterion='none' !<'energy','stress','strain_rate','strain',or 'none'
+character(len=11) :: fracture_criterion='none' !<'stress' or 'none'. In non-dem-mode, 'strain_rate' and 'strain' are also options.
 logical :: orig_dem_moment_of_inertia=.false. !< Use Potyondy & Cundall,2004 torque from relative particle rotation (rather than Wang, 2020)
 logical :: break_bonds_on_sub_steps=.false.
 logical :: skip_first_outer_mts_step=.false.
@@ -69,7 +68,7 @@ module ice_bergs_framework
 public verbose, really_debug, debug, restart_input_dir,make_calving_reproduce,old_bug_bilin,use_roundoff_fix
 public ignore_ij_restart, use_slow_find,generate_test_icebergs,old_bug_rotated_weights,budget
 public orig_read, force_all_pes_traj
-public mts,save_bond_traj,ewsame,monitor_energy,iceberg_bonds_on
+public mts,save_bond_traj,ewsame,iceberg_bonds_on
 public dem, save_bond_forces, fracture_criterion, orig_dem_moment_of_inertia
 public short_step_mts_grounding, radius_based_drag
 public A68_test, A68_xdisp, A68_ydisp
@@ -104,7 +103,7 @@ module ice_bergs_framework
 public pack_bond_traj_into_buffer2, unpack_bond_traj_from_buffer2, push_bond_posn, append_bond_posn
 public update_and_break_bonds,break_bonds_dem,assign_n_bonds,reset_bond_rotation,update_bond_angles
 public orig_bond_length
-public energy_tests_init,dem_tests_init
+public dem_tests_init
 public set_constant_interaction_length_and_width
 public break_bonds_on_sub_steps, skip_first_outer_mts_step, no_frac_first_ts
 
@@ -280,18 +279,6 @@ module ice_bergs_framework
   integer, allocatable :: n_bonds
   ! If frac
   real, allocatable :: accum_bond_rotation
-  ! For optional energy monitoring
-  real, allocatable :: Ee !< Energy from bonds, elastic (J)
-  real, allocatable :: Ed !< Energy from bonds, damping (J)
-  real, allocatable :: Eext !< Energy from external forces (J)
-  real, allocatable :: Ee_contact !< Energy from contact, elastic (J)
-  real, allocatable :: Ed_contact !< Energy from contanct, damping (J)
-  real, allocatable :: Efrac !< Energy from breaking bonds (J)
-  real, allocatable :: Ee_temp !< Temporary storage: Energy from bonds, elastic (J)
-  real, allocatable :: Ed_temp !< Temporary storage: Energy from bonds, damping (J)
-  real, allocatable :: Eext_temp !< Temporary storage: Energy from external forces (J)
-  real, allocatable :: Ee_contact_temp !< Temporary storage: Energy from contact, elastic (J)
-  real, allocatable :: Ed_contact_temp !< Temporary storage: Energy from damping, elastic (J)
   ! For DEM-mode
   real, allocatable :: ang_vel !< Angular velocity
   real, allocatable :: ang_accel !< Angular acceleration
@@ -368,18 +355,6 @@ module ice_bergs_framework
   integer, allocatable :: n_bonds
   ! If frac
   real, allocatable :: accum_bond_rotation
-  ! For optional energy monitoring
-  real, allocatable :: Ee !< Energy from bonds, elastic (J)
-  real, allocatable :: Ed !< Energy from bonds, damping (J)
-  real, allocatable :: Eext !< Energy from external forces (J)
-  real, allocatable :: Ee_contact !< Energy from contact, elastic (J)
-  real, allocatable :: Ed_contact !< Energy from contanct, damping (J)
-  real, allocatable :: Efrac !< Energy from breaking bonds (J)
-  real, allocatable :: Ee_temp !< Temporary storage: Energy from bonds, elastic (J)
-  real, allocatable :: Ed_temp !< Temporary storage: Energy from bonds, damping (J)
-  real, allocatable :: Eext_temp !< Temporary storage: Energy from external forces (J)
-  real, allocatable :: Ee_contact_temp !< Temporary storage: Energy from contact, elastic (J)
-  real, allocatable :: Ed_contact_temp !< Temporary storage: Energy from damping, elastic (J)
   ! For DEM-mode
   real, allocatable :: ang_vel !< Angular velocity
   real, allocatable :: ang_accel !< Angular acceleration
@@ -399,19 +374,11 @@ module ice_bergs_framework
   ! Fracture parameters:
   !The following are accumulated over all timesteps, unless fracture_criterion=='strain_rate',
   !in which case the following correspond to only the most recent timestep and units are s^(-1)
-  real, allocatable :: rotation !radians
-  real, allocatable :: rel_rotation !<non-dem mode: rotation relative to the mean of all bonds for a berg
-  !!dem-mode: relative rotation between two bonded particles (radians)
-  real, allocatable :: n_frac_var !<normal strain, stress, or spring energy
+  real, allocatable :: rotation !radians (non-dem only)
+  real, allocatable :: rel_rotation !<non-dem: relative to the mean of all bonds for a berg. dem: relative to other particle
+  ! non-dem-mode fracture:
+  real, allocatable :: n_frac_var !<normal stress or strain
   real, allocatable :: n_strain_rate !<for fracture_criterion=='strain_rate' only
-  real, allocatable :: spring_pe
-  ! For optional energy monitoring
-  real, allocatable :: Ee !< Bond energy, elastic (J)
-  real, allocatable :: Ed !< Bond energy, damping (J)
-  real, allocatable :: axn_fast !< Zonal acceleration contribution to parent berg, explicit (m s^-2)
-  real, allocatable :: ayn_fast !< Meridional  acceleration contribution to parent berg, explicit (m s^-2)
-  real, allocatable :: bxn_fast !< Zonal acceleration contribution to parent berg, implicit (m s^-2)
-  real, allocatable :: byn_fast !< Meridional acceleration contribution to parent berg, implicit (m s^-2)
   ! For DEM-mode
   real, allocatable :: tangd1 !< Accumulated tangential displacement, x-component (m)
   real, allocatable :: tangd2 !< Accumulated tangential displacement, y-component (m)
@@ -440,19 +407,11 @@ module ice_bergs_framework
   integer(kind=8) :: id1 !<ID of first berg
   integer(kind=8) :: id2 !<ID of second berg
   type(bond_xyt), pointer :: next=>null() !< Next link in list
-  ! Fracture parameters:
-  real, allocatable :: rotation !radians
-  real, allocatable :: rel_rotation !<rotation relative to the mean of all bonds for a berg
-  real, allocatable :: n_frac_var !<normal strain, stress, or spring energy
+  real, allocatable :: rotation !radians (non-dem only)
+  real, allocatable :: rel_rotation !<non-dem: relative to the mean of all bonds for a berg. dem: relative to other particle
+  ! non-dem-mode fracture:
+  real, allocatable :: n_frac_var !<normal stress or strain
   real, allocatable :: n_strain_rate !<for fracture_criterion=='strain_rate' only
-  real, allocatable :: spring_pe
-  ! For optional energy monitoring
-  real, allocatable :: Ee !< Bond energy (elastic)
-  real, allocatable :: Ed !< Bond energy (damping)
-  real, allocatable :: axn_fast !< Zonal acceleration contribution to parent berg, explicit (m s^-2)
-  real, allocatable :: ayn_fast !< Meridional  acceleration contribution to parent berg, explicit (m s^-2)
-  real, allocatable :: bxn_fast !< Zonal acceleration contribution to parent berg, implicit (m s^-2)
-  real, allocatable :: byn_fast !< Meridional acceleration contribution to parent berg, implicit (m s^-2)
   ! For DEM-mode
   real, allocatable :: tangd1 !< Accumulated tangential displacement, x-component (m)
   real, allocatable :: tangd2 !< Accumulated tangential displacement, y-component (m)
@@ -501,7 +460,7 @@ module ice_bergs_framework
   real :: contact_spring_coef !<Spring coefficient for berg collisions -Alex
   real :: cdrag_grounding=0.0 !< Drag coefficient against ocean bottom
   real :: h_to_init_grounding
-  character(len=11) :: fracture_criterion='none' !<'energy','stress','strain_rate','strain',or 'none'
+  character(len=11) :: fracture_criterion='none' !<'stress' or 'none'. In non-dem-mode, 'strain_rate' and 'strain' are also options.
   real :: frac_thres_n=0.0 !normal fracture strain threshold
   real :: frac_thres_t=0.0 !tangential fracture strain threshold
   logical :: debug_write=.false. !< Sets traj_sample_hours=traj_write_hours & includes halo bergs in write
@@ -912,7 +871,7 @@ subroutine ice_bergs_framework_init(bergs, &
          const_gamma, Gamma_T_3EQ, ignore_traj, debug_iceberg_with_id,use_updated_rolling_scheme, tip_parameter, &
          read_old_restarts, tau_calving, read_ocean_depth_from_file, melt_cutoff,apply_thickness_cutoff_to_gridded_melt,&
          apply_thickness_cutoff_to_bergs_melt, use_mixed_melting, internal_bergs_for_drag, coastal_drift, tidal_drift,&
-         mts,ewsame,monitor_energy,mts_sub_steps,contact_distance,length_for_manually_initialize_bonds,&
+         mts,ewsame,mts_sub_steps,contact_distance,length_for_manually_initialize_bonds,&
          manually_initialize_bonds_from_radii,contact_spring_coef,fracture_criterion, &
          debug_write,cdrag_grounding,h_to_init_grounding,frac_thres_scaling,frac_thres_n,frac_thres_t,save_bond_traj,&
          remove_unused_bergs,force_convergence,explicit_inner_mts,convergence_tolerance,dem,ignore_tangential_force,poisson,&
@@ -1354,13 +1313,6 @@ subroutine ice_bergs_framework_init(bergs, &
 endif
 if (ignore_traj) buffer_width_traj=0 ! If this is true, then all traj files should be ignored
 
-if (monitor_energy) then
-  buffer_width=buffer_width+11+(max_bonds*6)
-  buffer_width_traj=buffer_width_traj+6
-  !buffer_width_traj=buffer_width_traj+5 !if include temp terms
-  buffer_width_bond_traj=buffer_width_bond_traj+6
-endif
-
 if (dem) then
   buffer_width=buffer_width+3+(max_bonds*6)
   buffer_width_traj=buffer_width_traj+3
@@ -1372,9 +1324,6 @@ subroutine ice_bergs_framework_init(bergs, &
   if (fracture_criterion .eq. 'strain_rate') then
     buffer_width=buffer_width+(max_bonds*1)
     buffer_width_bond_traj=buffer_width_bond_traj+1
-  elseif (fracture_criterion .eq. 'energy') then
-    buffer_width=buffer_width+(max_bonds*1)
-    buffer_width_bond_traj=buffer_width_bond_traj+1
   endif
 endif
 
@@ -1587,17 +1536,6 @@ subroutine ice_bergs_framework_init(bergs, &
     endif
   endif
 
-  if (monitor_energy) then
-    if (bergs%constant_interaction_LW) then
-      call error_mesg('KID, ice_bergs_framework_init', &
-        'cannot use monitor_energy with constant_interaction_LW yet', FATAL)
-    endif
-    if (bergs%dem .and. .not. bergs%ignore_tangential_force) then
-      call error_mesg('KID, ice_bergs_framework_init', &
-        'monitor_energy does not yet account for dem tangential force terms', FATAL)
-    endif
-  endif
-
   !backwards compatibility
   if (.not. (bergs%mts .or. bergs%dem .or. bergs%fl_r>0.)) bergs%old_interp_flds_order=.true.
 
@@ -2765,43 +2703,6 @@ subroutine set_conglom_ids(bergs)
 
 end subroutine set_conglom_ids
 
-!> Assign initial velocities and energies for energy tracking tests
-subroutine energy_tests_init(bergs)
-  ! Arguments
-  type(icebergs), pointer :: bergs !< Container for all types and memory
-  ! Local variables
-  type(icebergs_gridded), pointer :: grd
-  type(iceberg), pointer :: this
-  integer :: grdi,grdj
-  real :: vol
-  type(bond), pointer :: current_bond
-
-  grd=>bergs%grd
-
-  !Reset all conglom ids to zero
-  do grdj = grd%jsd,grd%jed; do grdi = grd%isd,grd%ied
-    this=>bergs%list(grdi,grdj)%first
-    do while (associated(this))
-
-      this%uvel_old=this%uvel; this%uvel_prev=this%uvel
-      this%vvel_old=this%vvel; this%vvel_prev=this%vvel
-
-      this%Ee=0.0; this%Ed=0.0; this%Eext=0.0; this%Ee_contact=0.0; this%Ed_contact=0.0; this%Efrac=0.0
-      this%Ee_temp=0.0; this%Ed_temp=0.0; this%Eext_temp=0.0; this%Ee_contact_temp=0.0; this%Ed_contact_temp=0.0
-
-      current_bond=>this%first_bond
-      do while (associated(current_bond)) ! loop over all bonds
-        current_bond%Ee=0.0; current_bond%Ed=0.0
-        current_bond%axn_fast=0.0; current_bond%ayn_fast=0.0
-        current_bond%bxn_fast=0.0; current_bond%byn_fast=0.0
-        current_bond=>current_bond%next_bond
-      enddo
-
-      this=>this%next
-    enddo
-  enddo;enddo
-end subroutine energy_tests_init
-
 !> Identify all bergs in the same conglomerate as the given berg, and assign them the given conglom_id
 recursive subroutine label_conglomerates(berg, new_conglom_id)
   type(iceberg), pointer :: berg !< Berg to start search from
@@ -3484,20 +3385,6 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
     call push_buffer_value(buff%data(:,n), counter, berg%n_bonds)
   end if
 
-  if (monitor_energy) then
-    call push_buffer_value(buff%data(:,n), counter, berg%Ee)
-    call push_buffer_value(buff%data(:,n), counter, berg%Ed)
-    call push_buffer_value(buff%data(:,n), counter, berg%Eext)
-    call push_buffer_value(buff%data(:,n), counter, berg%Ee_contact)
-    call push_buffer_value(buff%data(:,n), counter, berg%Ed_contact)
-    call push_buffer_value(buff%data(:,n), counter, berg%Efrac)
-    call push_buffer_value(buff%data(:,n), counter, berg%Ee_contact_temp)
-    call push_buffer_value(buff%data(:,n), counter, berg%Ed_contact_temp)
-    call push_buffer_value(buff%data(:,n), counter, berg%Ee_temp)
-    call push_buffer_value(buff%data(:,n), counter, berg%Ed_temp)
-    call push_buffer_value(buff%data(:,n), counter, berg%Eext_temp)
-  endif
-
   if (dem) then
     call push_buffer_value(buff%data(:,n), counter, berg%ang_vel)
     call push_buffer_value(buff%data(:,n), counter, berg%ang_accel)
@@ -3517,15 +3404,6 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
         call push_buffer_value(buff%data(:,n), counter, current_bond%other_berg_jne)
         call push_buffer_value(buff%data(:,n), counter, current_bond%length)
 
-        if (monitor_energy) then
-          call push_buffer_value(buff%data(:,n), counter, current_bond%Ee)
-          call push_buffer_value(buff%data(:,n), counter, current_bond%Ed)
-          call push_buffer_value(buff%data(:,n), counter, current_bond%axn_fast)
-          call push_buffer_value(buff%data(:,n), counter, current_bond%ayn_fast)
-          call push_buffer_value(buff%data(:,n), counter, current_bond%bxn_fast)
-          call push_buffer_value(buff%data(:,n), counter, current_bond%byn_fast)
-        endif
-
         if (dem) then
           call push_buffer_value(buff%data(:,n), counter, current_bond%tangd1)
           call push_buffer_value(buff%data(:,n), counter, current_bond%tangd2)
@@ -3540,9 +3418,6 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
           if (fracture_criterion .eq. 'strain_rate') then
             call push_buffer_value(buff%data(:,n), counter, current_bond%n_strain_rate)
           endif
-          if (fracture_criterion .eq. 'energy') then
-            call push_buffer_value(buff%data(:,n), counter, current_bond%spring_pe)
-          endif
         endif
 
         current_bond=>current_bond%next_bond
@@ -3553,15 +3428,6 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
         call push_buffer_value(buff%data(:,n), counter, 0)
         call push_buffer_value(buff%data(:,n), counter, 0)
 
-        if (monitor_energy) then
-          call push_buffer_value(buff%data(:,n), counter, 0)
-          call push_buffer_value(buff%data(:,n), counter, 0)
-          call push_buffer_value(buff%data(:,n), counter, 0)
-          call push_buffer_value(buff%data(:,n), counter, 0)
-          call push_buffer_value(buff%data(:,n), counter, 0)
-          call push_buffer_value(buff%data(:,n), counter, 0)
-        endif
-
         if (dem) then
           call push_buffer_value(buff%data(:,n), counter, 0)
           call push_buffer_value(buff%data(:,n), counter, 0)
@@ -3576,9 +3442,6 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
           if (fracture_criterion .eq. 'strain_rate') then
             call push_buffer_value(buff%data(:,n), counter, 0)
           endif
-          if (fracture_criterion .eq. 'energy') then
-            call push_buffer_value(buff%data(:,n), counter, 0)
-          endif
         endif
 
       endif
@@ -3719,11 +3582,6 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
     allocate(localberg%n_bonds)
   endif
 
-  if (monitor_energy) then
-    allocate(localberg%Ee,localberg%Ed,localberg%Eext,localberg%Ee_contact,localberg%Ed_contact,localberg%Efrac,&
-      localberg%Ee_temp,localberg%Ed_temp,localberg%Eext_temp,localberg%Ee_contact_temp,localberg%Ed_contact_temp)
-  endif
-
   if (dem) then
     allocate(localberg%ang_vel,localberg%ang_accel,localberg%rot)
   elseif (fracture_criterion .ne. 'none') then
@@ -3793,20 +3651,6 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
     call pull_buffer_value(buff%data(:,n), counter, localberg%n_bonds)
   endif
 
-  if (monitor_energy) then
-    call pull_buffer_value(buff%data(:,n), counter, localberg%Ee)
-    call pull_buffer_value(buff%data(:,n), counter, localberg%Ed)
-    call pull_buffer_value(buff%data(:,n), counter, localberg%Eext)
-    call pull_buffer_value(buff%data(:,n), counter, localberg%Ee_contact)
-    call pull_buffer_value(buff%data(:,n), counter, localberg%Ed_contact)
-    call pull_buffer_value(buff%data(:,n), counter, localberg%Efrac)
-    call pull_buffer_value(buff%data(:,n), counter, localberg%Ee_contact_temp)
-    call pull_buffer_value(buff%data(:,n), counter, localberg%Ed_contact_temp)
-    call pull_buffer_value(buff%data(:,n), counter, localberg%Ee_temp)
-    call pull_buffer_value(buff%data(:,n), counter, localberg%Ed_temp)
-    call pull_buffer_value(buff%data(:,n), counter, localberg%Eext_temp)
-  endif
-
   if (dem) then
     call pull_buffer_value(buff%data(:,n), counter, localberg%ang_vel)
     call pull_buffer_value(buff%data(:,n), counter, localberg%ang_accel)
@@ -3932,15 +3776,6 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
         current_bond=>this%first_bond
         current_bond%length=length
 
-        if (monitor_energy) then
-          call pull_buffer_value(buff%data(:,n), counter, current_bond%Ee)
-          call pull_buffer_value(buff%data(:,n), counter, current_bond%Ed)
-          call pull_buffer_value(buff%data(:,n), counter, current_bond%axn_fast)
-          call pull_buffer_value(buff%data(:,n), counter, current_bond%ayn_fast)
-          call pull_buffer_value(buff%data(:,n), counter, current_bond%bxn_fast)
-          call pull_buffer_value(buff%data(:,n), counter, current_bond%byn_fast)
-        endif
-
         if (dem) then
           call pull_buffer_value(buff%data(:,n), counter, current_bond%tangd1)
           call pull_buffer_value(buff%data(:,n), counter, current_bond%tangd2)
@@ -3955,9 +3790,6 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
           if (fracture_criterion .eq. 'strain_rate') then
             call pull_buffer_value(buff%data(:,n), counter, current_bond%n_strain_rate)
           endif
-          if (fracture_criterion .eq. 'energy') then
-            call pull_buffer_value(buff%data(:,n), counter, current_bond%spring_pe)
-          endif
         endif
       endif
     enddo
@@ -4085,20 +3917,6 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj, save_fl_traj,
       call push_buffer_value(buff%data(:,n), counter, traj%n_bonds)
     end if
 
-    if (monitor_energy) then
-      call push_buffer_value(buff%data(:,n), counter, traj%Ee)
-      call push_buffer_value(buff%data(:,n), counter, traj%Ed)
-      call push_buffer_value(buff%data(:,n), counter, traj%Eext)
-      call push_buffer_value(buff%data(:,n), counter, traj%Ee_contact)
-      call push_buffer_value(buff%data(:,n), counter, traj%Ed_contact)
-      call push_buffer_value(buff%data(:,n), counter, traj%Efrac)
-      ! call push_buffer_value(buff%data(:,n), counter, traj%Ee_contact_temp)
-      ! call push_buffer_value(buff%data(:,n), counter, traj%Ed_contact_temp)
-      ! call push_buffer_value(buff%data(:,n), counter, traj%Ee_temp)
-      ! call push_buffer_value(buff%data(:,n), counter, traj%Ed_temp)
-      ! call push_buffer_value(buff%data(:,n), counter, traj%Eext_temp)
-    endif
-
     if (dem) then
       call push_buffer_value(buff%data(:,n), counter, traj%ang_vel)
       call push_buffer_value(buff%data(:,n), counter, traj%ang_accel)
@@ -4133,11 +3951,6 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj, save_fl_tra
     allocate(traj%n_bonds)
   endif
 
-  if (monitor_energy) then
-    allocate(traj%Ee,traj%Ed,traj%Eext,traj%Ee_contact,traj%Ed_contact,traj%Efrac)
-    !allocate(traj%Ee_temp,traj%Ed_temp,traj%Eext_temp,traj%Ee_contact_temp,traj%Ed_contact_temp)
-  endif
-
   if (dem) then
     allocate(traj%ang_vel,traj%ang_accel,traj%rot)
   elseif (fracture_criterion .ne. 'none') then
@@ -4205,20 +4018,6 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj, save_fl_tra
       call pull_buffer_value(buff%data(:,n), counter, traj%n_bonds)
     end if
 
-    if (monitor_energy) then
-      call pull_buffer_value(buff%data(:,n), counter, traj%Ee)
-      call pull_buffer_value(buff%data(:,n), counter, traj%Ed)
-      call pull_buffer_value(buff%data(:,n), counter, traj%Eext)
-      call pull_buffer_value(buff%data(:,n), counter, traj%Ee_contact)
-      call pull_buffer_value(buff%data(:,n), counter, traj%Ed_contact)
-      call pull_buffer_value(buff%data(:,n), counter, traj%Efrac)
-      ! call pull_buffer_value(buff%data(:,n), counter, traj%Ee_contact_temp)
-      ! call pull_buffer_value(buff%data(:,n), counter, traj%Ed_contact_temp)
-      ! call pull_buffer_value(buff%data(:,n), counter, traj%Ee_temp)
-      ! call pull_buffer_value(buff%data(:,n), counter, traj%Ed_temp)
-      ! call pull_buffer_value(buff%data(:,n), counter, traj%Eext_temp)
-    endif
-
     if (dem) then
       call pull_buffer_value(buff%data(:,n), counter, traj%ang_vel)
       call pull_buffer_value(buff%data(:,n), counter, traj%ang_accel)
@@ -4260,15 +4059,6 @@ subroutine pack_bond_traj_into_buffer2(bond_traj, buff, n)
   call push_buffer_value(buff%data(:,n),counter,cnt2)
   call push_buffer_value(buff%data(:,n),counter,ij2)
 
-  if (monitor_energy) then
-    call push_buffer_value(buff%data(:,n),counter,bond_traj%Ee)
-    call push_buffer_value(buff%data(:,n),counter,bond_traj%Ed)
-    call push_buffer_value(buff%data(:,n),counter,bond_traj%axn_fast)
-    call push_buffer_value(buff%data(:,n),counter,bond_traj%ayn_fast)
-    call push_buffer_value(buff%data(:,n),counter,bond_traj%bxn_fast)
-    call push_buffer_value(buff%data(:,n),counter,bond_traj%byn_fast)
-  endif
-
   if (dem) then
     call push_buffer_value(buff%data(:,n),counter,bond_traj%tangd1)
     call push_buffer_value(buff%data(:,n),counter,bond_traj%tangd2)
@@ -4282,8 +4072,6 @@ subroutine pack_bond_traj_into_buffer2(bond_traj, buff, n)
     call push_buffer_value(buff%data(:,n),counter,bond_traj%n_frac_var)
     if (fracture_criterion.eq.'strain_rate') then
       call push_buffer_value(buff%data(:,n),counter,bond_traj%n_strain_rate)
-    elseif (fracture_criterion.eq.'energy') then
-      call push_buffer_value(buff%data(:,n),counter,bond_traj%spring_pe)
     endif
   endif
 
@@ -4300,17 +4088,12 @@ subroutine unpack_bond_traj_from_buffer2(first, buff, n)
   integer :: counter ! Position in stack
   integer :: cnt1, ij1, cnt2, ij2
 
-  if (monitor_energy) then
-    allocate(bond_traj%Ee,bond_traj%Ed,bond_traj%axn_fast,bond_traj%ayn_fast,bond_traj%bxn_fast,bond_traj%byn_fast)
-  endif
   if (dem) then
     allocate(bond_traj%tangd1,bond_traj%tangd2,bond_traj%nstress,bond_traj%sstress,bond_traj%rel_rotation)
   elseif (fracture_criterion.ne.'none') then
     allocate(bond_traj%rotation,bond_traj%rel_rotation,bond_traj%n_frac_var)
     if (fracture_criterion.eq.'strain_rate') then
       allocate(bond_traj%n_strain_rate)
-    elseif (fracture_criterion.eq.'energy') then
-      allocate(bond_traj%spring_pe)
     endif
   endif
 
@@ -4329,15 +4112,6 @@ subroutine unpack_bond_traj_from_buffer2(first, buff, n)
   call pull_buffer_value(buff%data(:,n),counter,ij2)
   bond_traj%id2 = id_from_2_ints(cnt2, ij2)
 
-  if (monitor_energy) then
-    call pull_buffer_value(buff%data(:,n),counter,bond_traj%Ee)
-    call pull_buffer_value(buff%data(:,n),counter,bond_traj%Ed)
-    call pull_buffer_value(buff%data(:,n),counter,bond_traj%axn_fast)
-    call pull_buffer_value(buff%data(:,n),counter,bond_traj%ayn_fast)
-    call pull_buffer_value(buff%data(:,n),counter,bond_traj%bxn_fast)
-    call pull_buffer_value(buff%data(:,n),counter,bond_traj%byn_fast)
-  endif
-
   if (dem) then
     call pull_buffer_value(buff%data(:,n),counter,bond_traj%tangd1)
     call pull_buffer_value(buff%data(:,n),counter,bond_traj%tangd2)
@@ -4351,8 +4125,6 @@ subroutine unpack_bond_traj_from_buffer2(first, buff, n)
     call pull_buffer_value(buff%data(:,n),counter,bond_traj%n_frac_var)
     if (fracture_criterion.eq.'strain_rate') then
       call pull_buffer_value(buff%data(:,n),counter,bond_traj%n_strain_rate)
-    elseif (fracture_criterion.eq.'energy') then
-      call pull_buffer_value(buff%data(:,n),counter,bond_traj%spring_pe)
     endif
   endif
 
@@ -4821,10 +4593,6 @@ subroutine create_iceberg(berg, bergvals)
     berg%n_bonds=0
   endif
 
-  if (monitor_energy) then
-    allocate(berg%Ee,berg%Ed,berg%Eext,berg%Ee_contact,berg%Ed_contact,berg%Efrac,&
-      berg%Ee_temp,berg%Ed_temp,berg%Eext_temp,berg%Ee_contact_temp,berg%Ed_contact_temp)
-  endif
   if (dem) then
     allocate(berg%ang_vel,berg%ang_accel,berg%rot)
   elseif (fracture_criterion .ne. 'none') then
@@ -5274,8 +5042,6 @@ subroutine update_and_break_bonds(bergs)
             current_bond%rel_rotation = current_bond%rel_rotation*R1*min(this%mass,other_berg%mass)*&
               bergs%spring_coef/(min(this%thickness,other_berg%thickness)*(R1+R2))
             current_bond%n_frac_var=n_frac_var
-          elseif (bergs%fracture_criterion=='energy') then
-            current_bond%n_frac_var=current_bond%spring_pe
           endif
 
         !mark bond and matching bond on other_berg as fractured
@@ -5321,13 +5087,6 @@ subroutine update_and_break_bonds(bergs)
           endif
           this%accum_bond_rotation=this%accum_bond_rotation-current_bond%rotation
           this%n_bonds=this%n_bonds-1
-          if (monitor_energy) then
-            !convert the elastic spring energy associated with the bond to dissipated energy
-            !on the parent element.
-            this%Ee=this%Ee-current_bond%Ee
-            this%Ee_temp=this%Ee_temp-current_bond%Ee
-            this%Efrac=this%Efrac+current_bond%Ee
-          endif
           kick_the_bucket=>current_bond
           current_bond=>current_bond%next_bond
           call delete_bond_from_list(this,kick_the_bucket)
@@ -5418,13 +5177,6 @@ subroutine break_bonds_dem(bergs)
       do while (associated(current_bond)) ! loop over all bonds
         if (current_bond%other_id.eq.-1) then
           this%n_bonds=this%n_bonds-1
-          if (monitor_energy) then
-            !convert the elastic spring energy associated with the bond to dissipated energy
-            !on the parent element.
-            this%Ee=this%Ee-current_bond%Ee
-            this%Ee_temp=this%Ee_temp-current_bond%Ee
-            this%Efrac=this%Efrac+current_bond%Ee
-          endif
           kick_the_bucket=>current_bond
           current_bond=>current_bond%next_bond
           call delete_bond_from_list(this,kick_the_bucket)
@@ -5473,10 +5225,6 @@ subroutine form_a_bond(berg, other_id, other_berg_ine, other_berg_jne, other_ber
 
   ! Step 1: Create a new bond
   allocate(new_bond)
-  if (monitor_energy) then
-    allocate(new_bond%Ee,new_bond%Ed,new_bond%axn_fast,new_bond%ayn_fast,new_bond%bxn_fast,new_bond%byn_fast)
-    new_bond%Ee=0.; new_bond%Ed=0.; new_bond%axn_fast=0.; new_bond%ayn_fast=0.; new_bond%bxn_fast=0.; new_bond%byn_fast=0.
-  endif
 
   if (dem) then
     allocate(new_bond%tangd1,new_bond%tangd2)
@@ -5498,10 +5246,6 @@ subroutine form_a_bond(berg, other_id, other_berg_ine, other_berg_jne, other_ber
       allocate(new_bond%n_strain_rate)
       new_bond%n_strain_rate=0.
     endif
-    if (fracture_criterion.eq.'energy') then
-      allocate(new_bond%spring_pe)
-      new_bond%spring_pe=0.
-    endif
   endif
 
   new_bond%other_id=other_id
@@ -6012,11 +5756,6 @@ subroutine record_posn(bergs)
     allocate(posn%n_bonds)
   endif
 
-  if (monitor_energy) then
-    allocate(posn%Ee,posn%Ed,posn%Eext,posn%Ee_contact,posn%Ed_contact,posn%Efrac)
-    !allocate(posn%Ee_temp,posn%Ed_temp,posn%Eext_temp,posn%Ee_contact_temp,posn%Ed_contact_temp)
-  endif
-
   if (dem) then
     allocate(posn%ang_vel,posn%ang_accel,posn%rot)
   elseif (fracture_criterion .ne. 'none') then
@@ -6024,15 +5763,11 @@ subroutine record_posn(bergs)
   endif
 
   if (save_bond_traj) then
-    if (monitor_energy) then
-      allocate(bond_posn%Ee,bond_posn%Ed,bond_posn%axn_fast,bond_posn%ayn_fast,bond_posn%bxn_fast,bond_posn%byn_fast)
-    endif
     if (dem) then
       allocate(bond_posn%tangd1,bond_posn%tangd2,bond_posn%nstress,bond_posn%sstress,bond_posn%rel_rotation)
     elseif (fracture_criterion.ne.'none') then
       allocate(bond_posn%rotation,bond_posn%rel_rotation,bond_posn%n_frac_var)
       if (fracture_criterion.eq.'strain_rate') allocate(bond_posn%n_strain_rate)
-      if (fracture_criterion.eq.'energy') allocate(bond_posn%spring_pe)
     endif
   endif
 
@@ -6121,20 +5856,6 @@ subroutine record_posn(bergs)
             posn%n_bonds=this%n_bonds
           end if
 
-          if (monitor_energy) then
-            posn%Ee=this%Ee
-            posn%Ed=this%Ed
-            posn%Eext=this%Eext
-            posn%Ee_contact=this%Ee_contact
-            posn%Ed_contact=this%Ed_contact
-            posn%Efrac=this%Efrac
-            ! posn%Ee_contact_temp=this%Ee_contact_temp
-            ! posn%Ed_contact_temp=this%Ed_contact_temp
-            ! posn%Ee_temp=this%Ee_temp
-            ! posn%Ed_temp=this%Ed_temp
-            ! posn%Eext_temp=this%Eext_temp
-          endif
-
           if (dem) then
             posn%ang_vel=this%ang_vel
             posn%ang_accel=this%ang_accel
@@ -6168,15 +5889,6 @@ subroutine record_posn(bergs)
               bond_posn%n1=n1;                      bond_posn%n2=n2
               bond_posn%id1=this%id;                bond_posn%id2=other_berg%id
 
-              if (monitor_energy) then
-                bond_posn%Ee=current_bond%Ee
-                bond_posn%Ed=current_bond%Ed
-                bond_posn%axn_fast=current_bond%axn_fast
-                bond_posn%ayn_fast=current_bond%ayn_fast
-                bond_posn%bxn_fast=current_bond%bxn_fast
-                bond_posn%byn_fast=current_bond%byn_fast
-              endif
-
               if (dem) then
                 bond_posn%tangd1=current_bond%tangd1
                 bond_posn%tangd2=current_bond%tangd2
@@ -6188,7 +5900,6 @@ subroutine record_posn(bergs)
                 bond_posn%rel_rotation=current_bond%rel_rotation
                 bond_posn%n_frac_var=current_bond%n_frac_var
                 if (fracture_criterion.eq.'strain_rate') bond_posn%n_strain_rate=current_bond%n_strain_rate
-                if (fracture_criterion.eq.'energy') bond_posn%spring_pe=current_bond%spring_pe
               endif
 
               call push_bond_posn(current_bond%bond_trajectory, bond_posn)
@@ -6222,11 +5933,6 @@ subroutine push_posn(trajectory, posn_vals)
     allocate(new_posn%n_bonds)
   endif
 
-  if (monitor_energy) then
-    allocate(new_posn%Ee,new_posn%Ed,new_posn%Eext,new_posn%Ee_contact,new_posn%Ed_contact,new_posn%Efrac)
-    !allocate(new_posn%Ee_temp,new_posn%Ed_temp,new_posn%Eext_temp,new_posn%Ee_contact_temp,new_posn%Ed_contact_temp)
-  endif
-
   if (dem) then
     allocate(new_posn%ang_vel,new_posn%ang_accel,new_posn%rot)
   elseif (fracture_criterion .ne. 'none') then
@@ -6249,16 +5955,11 @@ subroutine push_bond_posn(bond_trajectory, bond_posn_vals)
 
   allocate(new_bond_posn)
 
-  if (monitor_energy) then
-    allocate(new_bond_posn%Ee,new_bond_posn%Ed,new_bond_posn%axn_fast,new_bond_posn%ayn_fast,&
-      new_bond_posn%bxn_fast,new_bond_posn%byn_fast)
-  endif
   if (dem) then
     allocate(new_bond_posn%tangd1,new_bond_posn%tangd2,new_bond_posn%nstress,new_bond_posn%sstress,new_bond_posn%rel_rotation)
   elseif (fracture_criterion.ne.'none') then
     allocate(new_bond_posn%rotation,new_bond_posn%rel_rotation,new_bond_posn%n_frac_var)
     if (fracture_criterion.eq.'strain_rate') allocate(new_bond_posn%n_strain_rate)
-    if (fracture_criterion.eq.'energy') allocate(new_bond_posn%spring_pe)
   endif
 
   new_bond_posn=bond_posn_vals
@@ -6286,11 +5987,6 @@ subroutine append_posn(trajectory, posn_vals)
     allocate(new_posn%n_bonds)
   endif
 
-  if (monitor_energy) then
-    allocate(new_posn%Ee,new_posn%Ed,new_posn%Eext,new_posn%Ee_contact,new_posn%Ed_contact,new_posn%Efrac)
-    !allocate(new_posn%Ee_temp,new_posn%Ed_temp,new_posn%Eext_temp,new_posn%Ee_contact_temp,new_posn%Ed_contact_temp)
-  endif
-
   if (dem) then
     allocate(new_posn%ang_vel,new_posn%ang_accel,new_posn%rot)
   elseif (fracture_criterion .ne. 'none' .and. (.not. dem)) then
@@ -6323,16 +6019,11 @@ subroutine append_bond_posn(bond_trajectory, bond_posn_vals)
 
   allocate(new_bond_posn)
 
-  if (monitor_energy) then
-    allocate(new_bond_posn%Ee,new_bond_posn%Ed,new_bond_posn%axn_fast,new_bond_posn%ayn_fast,&
-      new_bond_posn%bxn_fast,new_bond_posn%byn_fast)
-  endif
   if (dem) then
     allocate(new_bond_posn%tangd1,new_bond_posn%tangd2,new_bond_posn%nstress,new_bond_posn%sstress,new_bond_posn%rel_rotation)
   elseif (fracture_criterion.ne.'none') then
     allocate(new_bond_posn%rotation,new_bond_posn%rel_rotation,new_bond_posn%n_frac_var)
     if (fracture_criterion.eq.'strain_rate') allocate(new_bond_posn%n_strain_rate)
-    if (fracture_criterion.eq.'energy') allocate(new_bond_posn%spring_pe)
   endif
 
   new_bond_posn=bond_posn_vals
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index c0eec7f..267085c 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -44,7 +44,7 @@ module ice_bergs_io
 use ice_bergs_framework, only: mts,save_bond_traj
 use ice_bergs_framework, only: push_bond_posn, append_bond_posn
 use ice_bergs_framework, only: pack_bond_traj_into_buffer2,unpack_bond_traj_from_buffer2
-use ice_bergs_framework, only: monitor_energy, dem, fracture_criterion, iceberg_bonds_on
+use ice_bergs_framework, only: dem, fracture_criterion, iceberg_bonds_on
 
 implicit none ; private
 
@@ -169,8 +169,7 @@ subroutine write_restart(bergs, time_stamp)
                                    rotation,     &
                                    rel_rotation, &
                                    n_frac_var,   &
-                                   n_strain_rate,&
-                                   spring_pe
+                                   n_strain_rate
 
 integer, allocatable, dimension(:) :: ine,              &
                                       jne,              &
@@ -487,8 +486,6 @@ subroutine write_restart(bergs, time_stamp)
     allocate(n_frac_var(nbonds))
     if (fracture_criterion.eq.'strain_rate') then
       allocate(n_strain_rate(nbonds))
-    elseif (fracture_criterion.eq.'energy') then
-      allocate(spring_pe(nbonds))
     endif
   endif
 
@@ -533,9 +530,6 @@ subroutine write_restart(bergs, time_stamp)
     if (fracture_criterion.eq.'strain_rate') then
       id = register_restart_field(bergs_bond_restart,filename_bonds,'n_strain_rate',n_strain_rate,&
         longname='normal strain-rate',units='1/seconds')
-    elseif (fracture_criterion.eq.'energy') then
-      id = register_restart_field(bergs_bond_restart,filename_bonds,'spring_pe',spring_pe,&
-        longname='spring potential energy',units='J')
     endif
   endif
 
@@ -568,8 +562,6 @@ subroutine write_restart(bergs, time_stamp)
           n_frac_var(i)=current_bond%n_frac_var
           if (fracture_criterion.eq.'strain_rate') then
             n_strain_rate(i)=current_bond%n_strain_rate
-          elseif (fracture_criterion.eq.'energy') then
-            spring_pe(i)=current_bond%spring_pe
           endif
         endif
 
@@ -606,8 +598,6 @@ subroutine write_restart(bergs, time_stamp)
              n_frac_var)
     if (fracture_criterion.eq.'strain_rate') then
       deallocate(n_strain_rate)
-    elseif (fracture_criterion.eq.'energy') then
-      deallocate(spring_pe)
     endif
   endif
 
@@ -784,14 +774,6 @@ subroutine read_restart_bergs(bergs,Time)
         localberg%n_bonds=0.
       end if
 
-      if (monitor_energy) then
-        allocate(localberg%Ee,localberg%Ed,localberg%Eext,localberg%Ee_contact,localberg%Ed_contact,localberg%Efrac,&
-          localberg%Ee_temp,localberg%Ed_temp,localberg%Eext_temp,localberg%Ee_contact_temp,localberg%Ed_contact_temp)
-        localberg%Ee=0.0; localberg%Ed=0.0; localberg%Eext=0.0; localberg%Ee_contact=0.0; localberg%Ed_contact=0.0
-        localberg%Efrac=0.0; localberg%Ee_temp=0.0; localberg%Ed_temp=0.0; localberg%Eext_temp=0.0
-        localberg%Ee_contact_temp=0.0; localberg%Ed_contact_temp=0.0
-      endif
-
       if (mts) then
         allocate(localberg%axn_fast)
         allocate(localberg%ayn_fast)
@@ -1286,8 +1268,7 @@ subroutine read_restart_bonds(bergs,Time)
                                       rotation,         &
                                       rel_rotation,     &
                                       n_frac_var,       &
-                                      n_strain_rate,    &
-                                      spring_pe
+                                      n_strain_rate
 integer(kind=8), allocatable, dimension(:) :: first_id,   &
                                               other_id
 !integer, allocatable, dimension(:,:) :: iceberg_counter_grd
@@ -1339,8 +1320,6 @@ subroutine read_restart_bonds(bergs,Time)
       allocate(n_frac_var(nbonds_in_file))
       if (fracture_criterion.eq.'strain_rate') then
         allocate(n_strain_rate(nbonds_in_file))
-      elseif (fracture_criterion.eq.'energy') then
-        allocate(spring_pe(nbonds_in_file))
       endif
     endif
 
@@ -1373,8 +1352,6 @@ subroutine read_restart_bonds(bergs,Time)
       call read_real_vector(filename,'n_frac_var',n_frac_var,grd%domain,value_if_not_in_file=0.)
       if (fracture_criterion.eq.'strain_rate') then
         call read_real_vector(filename,'n_strain_rate',n_strain_rate,grd%domain,value_if_not_in_file=0.)
-      elseif (fracture_criterion.eq.'energy') then
-        call read_real_vector(filename,'spring_pe',spring_pe,grd%domain,value_if_not_in_file=0.)
       endif
     endif
 
@@ -1486,8 +1463,6 @@ subroutine read_restart_bonds(bergs,Time)
               current_bond%n_frac_var=n_frac_var(k)
               if (fracture_criterion.eq.'strain_rate') then
                 current_bond%n_strain_rate=n_strain_rate(k)
-              elseif (fracture_criterion.eq.'energy') then
-                current_bond%spring_pe=spring_pe(k)
               endif
             endif
 
@@ -1562,8 +1537,6 @@ subroutine read_restart_bonds(bergs,Time)
                n_frac_var)
       if (fracture_criterion.eq.'strain_rate') then
         deallocate(n_strain_rate)
-      elseif (fracture_criterion.eq.'energy') then
-        deallocate(spring_pe)
       endif
     endif
   endif
@@ -1731,8 +1704,6 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r, tra
 integer :: cnid, hiid, hsid
 integer :: mid, smid, did, wid, lid, mbid, mflbid, mflbbid, hdid, nbid, odid, flkid
 integer :: axnid,aynid,bxnid,bynid,axnfid,aynfid,bxnfid,bynfid, msid
-integer :: eecid,edcid,eeid,edid,aeid,efid
-integer :: eectid, edctid, eetid, edtid, aetid
 integer :: avid, aaid, rid, abrid
 character(len=70) :: filename
 character(len=7) :: pe_name
@@ -1904,20 +1875,6 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r, tra
           nbid = inq_varid(ncid, 'n_bonds')
         end if
 
-        if (monitor_energy) then
-          eeid = inq_varid(ncid, 'Ee')
-          edid = inq_varid(ncid, 'Ed')
-          aeid = inq_varid(ncid, 'Eext')
-          eecid = inq_varid(ncid, 'Ee_contact')
-          edcid = inq_varid(ncid, 'Ed_contact')
-          efid =  inq_varid(ncid, 'Efrac')
-          ! eectid = inq_varid(ncid, 'Ee_contact_temp')
-          ! edctid = inq_varid(ncid, 'Ed_contact_temp')
-          ! eetid= inq_varid(ncid, 'Ee_temp')
-          ! edtid= inq_varid(ncid, 'Ed_temp')
-          ! aetid= inq_varid(ncid, 'Eext_temp')
-        endif
-
         if (dem) then
           avid = inq_varid(ncid, 'ang_vel')
           aaid = inq_varid(ncid, 'ang_accel')
@@ -1991,20 +1948,6 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r, tra
           nbid = def_var(ncid, 'n_bonds', NF_INT, i_dim)
         end if
 
-        if (monitor_energy) then
-          eeid = def_var(ncid, 'Ee', NF_DOUBLE, i_dim)
-          edid = def_var(ncid, 'Ed', NF_DOUBLE, i_dim)
-          aeid = def_var(ncid, 'Eext', NF_DOUBLE, i_dim)
-          eecid = def_var(ncid, 'Ee_contact', NF_DOUBLE, i_dim)
-          edcid = def_var(ncid, 'Ed_contact', NF_DOUBLE, i_dim)
-          efid = def_var(ncid, 'Efrac', NF_DOUBLE, i_dim)
-          ! eectid = def_var(ncid, 'Ee_contact_temp', NF_DOUBLE, i_dim)
-          ! edctid = def_var(ncid, 'Ed_contact_temp', NF_DOUBLE, i_dim)
-          ! eetid= def_var(ncid, 'Ee_temp', NF_DOUBLE, i_dim)
-          ! edtid= def_var(ncid, 'Ed_temp', NF_DOUBLE, i_dim)
-          ! aetid= def_var(ncid, 'Eext_temp', NF_DOUBLE, i_dim)
-        endif
-
         if (dem) then
           avid = def_var(ncid, 'ang_vel', NF_DOUBLE, i_dim)
           aaid = def_var(ncid, 'ang_accel', NF_DOUBLE, i_dim)
@@ -2121,31 +2064,6 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r, tra
           call put_att(ncid, nbid, 'units', 'dimensionless')
         end if
 
-        if (monitor_energy) then
-          call put_att(ncid, eeid, 'long_name', 'bonded elastic energy')
-          call put_att(ncid, eeid, 'units', 'J')
-          call put_att(ncid, edid, 'long_name', 'bonded damping energy')
-          call put_att(ncid, edid, 'units', 'J')
-          call put_att(ncid, aeid, 'long_name', 'external energy')
-          call put_att(ncid, aeid, 'units', 'J')
-          call put_att(ncid, eecid, 'long_name', 'contact elastic energy')
-          call put_att(ncid, eecid, 'units', 'J')
-          call put_att(ncid, edcid, 'long_name', 'contact damping energy')
-          call put_att(ncid, edcid, 'units', 'J')
-          call put_att(ncid, efid, 'long_name', 'dissipated fracture energy')
-          call put_att(ncid, efid, 'units', 'J')
-          ! call put_att(ncid, eectid, 'long_name', 'contact elastic energy temp')
-          ! call put_att(ncid, eectid, 'units', 'J')
-          ! call put_att(ncid, edctid, 'long_name', 'contact damping energy temp')
-          ! call put_att(ncid, edctid, 'units', 'J')
-          ! call put_att(ncid, eetid, 'long_name', 'bonded elastic energy temp')
-          ! call put_att(ncid, eetid, 'units', 'J')
-          ! call put_att(ncid, edtid, 'long_name', 'bonded damping energy temp')
-          ! call put_att(ncid, edtid, 'units', 'J')
-          ! call put_att(ncid, aetid, 'long_name', 'external energy temp')
-          ! call put_att(ncid, aetid, 'units', 'J')
-        endif
-
         if (dem) then
           call put_att(ncid, avid, 'long_name', 'angular velocity')
           call put_att(ncid, avid, 'units', 'rad/s')
@@ -2232,20 +2150,6 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r, tra
           call put_int(ncid, nbid, i, this%n_bonds)
         end if
 
-        if (monitor_energy) then
-          call put_double(ncid, eeid,   i, this%Ee)
-          call put_double(ncid, edid,   i, this%Ed)
-          call put_double(ncid, aeid,   i, this%Eext)
-          call put_double(ncid, eecid,  i, this%Ee_contact)
-          call put_double(ncid, edcid,  i, this%Ed_contact)
-          call put_double(ncid, efid,   i, this%Efrac)
-          ! call put_double(ncid, eectid, i, this%Ee_contact_temp)
-          ! call put_double(ncid, edctid, i, this%Ed_contact_temp)
-          ! call put_double(ncid, eetid,  i, this%Ee_temp)
-          ! call put_double(ncid, edtid,  i, this%Ed_temp)
-          ! call put_double(ncid, aetid,  i, this%Eext_temp)
-        endif
-
         if (dem) then
           call put_double(ncid, avid, i, this%ang_vel)
           call put_double(ncid, aaid, i, this%ang_accel)
@@ -2276,10 +2180,9 @@ subroutine write_bond_trajectory(trajectory, bond_traj_name)
 character(len=70) :: bond_traj_name !<file name of bond trajectories
 ! Local variables
 integer :: iret, ncid, i_dim, i
-integer :: lonid, latid, yearid, dayid, lenid,n1id, n2id, peid
+integer :: lonid, latid, yearid, dayid, lenid,n1id, n2id
 integer :: rotid,rrotid,nsid,nsrid, brid
-integer :: idcnt1_id, idcnt2_id, idij1_id, idij2_id, eeid, edid
-integer :: axid,ayid,bxid,byid
+integer :: idcnt1_id, idcnt2_id, idij1_id, idij2_id
 integer :: td1id,td2id,dnsid,dssid
 character(len=70) :: filename
 character(len=7) :: pe_name
@@ -2396,12 +2299,6 @@ subroutine write_bond_trajectory(trajectory, bond_traj_name)
       idcnt1_id = inq_varid(ncid, 'id_cnt1'); idij1_id = inq_varid(ncid, 'id_ij1')
       idcnt2_id = inq_varid(ncid, 'id_cnt2'); idij2_id = inq_varid(ncid, 'id_ij2')
 
-      if (monitor_energy) then
-        eeid = inq_varid(ncid, 'Ee');       edid = inq_varid(ncid, 'Ed')
-        axid = inq_varid(ncid, 'axn_fast'); ayid = inq_varid(ncid, 'ayn_fast')
-        bxid = inq_varid(ncid, 'bxn_fast'); byid = inq_varid(ncid, 'byn_fast')
-      endif
-
       if (dem) then
         td1id = inq_varid(ncid, 'tangd1');  td2id = inq_varid(ncid, 'tangd2')
         dnsid = inq_varid(ncid, 'nstress'); dssid = inq_varid(ncid, 'sstress')
@@ -2411,8 +2308,6 @@ subroutine write_bond_trajectory(trajectory, bond_traj_name)
         nsid = inq_varid(ncid, 'n_frac_var')
         if (fracture_criterion.eq.'strain_rate') then
           nsrid = inq_varid(ncid, 'n_strain_rate')
-        elseif (fracture_criterion.eq.'energy') then
-          peid = inq_varid(ncid, 'spring_pe')
         endif
       endif
 
@@ -2430,12 +2325,6 @@ subroutine write_bond_trajectory(trajectory, bond_traj_name)
       idcnt1_id = def_var(ncid, 'id_cnt1', NF_INT, i_dim); idij1_id = def_var(ncid, 'id_ij1', NF_INT, i_dim)
       idcnt2_id = def_var(ncid, 'id_cnt2', NF_INT, i_dim); idij2_id = def_var(ncid, 'id_ij2', NF_INT, i_dim)
 
-      if (monitor_energy) then
-        eeid = def_var(ncid, 'Ee', NF_DOUBLE, i_dim);       edid = def_var(ncid, 'Ed', NF_DOUBLE, i_dim)
-        axid = def_var(ncid, 'axn_fast', NF_DOUBLE, i_dim); ayid = def_var(ncid, 'ayn_fast', NF_DOUBLE, i_dim)
-        bxid = def_var(ncid, 'bxn_fast', NF_DOUBLE, i_dim); byid = def_var(ncid, 'byn_fast', NF_DOUBLE, i_dim)
-      endif
-
       if (dem) then
         td1id = def_var(ncid, 'tangd1',  NF_DOUBLE, i_dim); td2id = def_var(ncid, 'tangd2',  NF_DOUBLE, i_dim)
         dnsid = def_var(ncid, 'nstress', NF_DOUBLE, i_dim); dssid = def_var(ncid, 'sstress', NF_DOUBLE, i_dim)
@@ -2446,8 +2335,6 @@ subroutine write_bond_trajectory(trajectory, bond_traj_name)
         nsid = def_var(ncid, 'n_frac_var', NF_DOUBLE, i_dim)
         if (fracture_criterion.eq.'strain_rate') then
           nsrid = def_var(ncid, 'n_strain_rate', NF_DOUBLE, i_dim)
-        elseif (fracture_criterion.eq.'energy') then
-          peid = def_var(ncid, 'spring_pe', NF_DOUBLE, i_dim)
         endif
       endif
 
@@ -2471,19 +2358,6 @@ subroutine write_bond_trajectory(trajectory, bond_traj_name)
       call put_att(ncid, idij2_id, 'long_name', 'position component of second connected iceberg id')
       call put_att(ncid, idij2_id, 'units', 'dimensionless')
 
-      if (monitor_energy) then
-        call put_att(ncid, eeid, 'long_name', 'elastic energy'); call put_att(ncid, eeid, 'units', 'J')
-        call put_att(ncid, edid, 'long_name', 'damping energy'); call put_att(ncid, edid, 'units', 'J')
-        call put_att(ncid, axid, 'long_name', 'explicit short-step zonal acceleration')
-        call put_att(ncid, axid, 'units', 'm/s^2')
-        call put_att(ncid, ayid, 'long_name', 'explicit short-step meridional acceleration')
-        call put_att(ncid, ayid, 'units', 'm/s^2')
-        call put_att(ncid, bxid, 'long_name', 'implicit short-step zonal acceleration')
-        call put_att(ncid, bxid, 'units', 'm/s^2')
-        call put_att(ncid, byid, 'long_name', 'implicit short-step meridional acceleration')
-        call put_att(ncid, byid, 'units', 'm/s^2')
-      endif
-
       if (dem) then
         call put_att(ncid, td1id, 'long_name', 'zonal tangential displacement')
         call put_att(ncid, td1id, 'units', 'm')
@@ -2499,8 +2373,6 @@ subroutine write_bond_trajectory(trajectory, bond_traj_name)
         call put_att(ncid, nsid, 'long_name', 'normal fracture variable'); call put_att(ncid, nsid, 'units', 'varies')
         if (fracture_criterion.eq.'strain_rate') then
           call put_att(ncid, nsrid, 'long_name', 'normal strain-rate'); call put_att(ncid, nsrid, 'units', '1/seconds')
-        elseif (fracture_criterion.eq.'energy') then
-          call put_att(ncid, peid, 'long_name', 'spring potential energy'); call put_att(ncid, peid, 'units', 'J')
         endif
       endif
     endif
@@ -2528,12 +2400,6 @@ subroutine write_bond_trajectory(trajectory, bond_traj_name)
       call split_id(this%id2, cnt, ij)
       call put_int(ncid, idcnt2_id, i, cnt);        call put_int(ncid, idij2_id, i, ij)
 
-      if (monitor_energy) then
-        call put_double(ncid,eeid,i,this%Ee);       call put_double(ncid,edid,i,this%Ed)
-        call put_double(ncid,axid,i,this%axn_fast); call put_double(ncid,ayid,i,this%ayn_fast)
-        call put_double(ncid,bxid,i,this%bxn_fast); call put_double(ncid,byid,i,this%byn_fast)
-      endif
-
       if (dem) then
         call put_double(ncid,td1id,i,this%tangd1);  call put_double(ncid,td2id,i,this%tangd2)
         call put_double(ncid,dnsid,i,this%nstress); call put_double(ncid,dssid,i,this%sstress)
@@ -2543,8 +2409,6 @@ subroutine write_bond_trajectory(trajectory, bond_traj_name)
         call put_double(ncid,nsid,i,this%n_frac_var)
         if (fracture_criterion.eq.'strain_rate') then
           call put_double(ncid,nsrid,i,this%n_strain_rate)
-        elseif (fracture_criterion.eq.'energy') then
-          call put_double(ncid,peid,i,this%spring_pe)
         endif
       endif
 
diff --git a/tests/a68_test/long_run.nml b/tests/a68_test/long_run.nml
index 594ae81..f872eef 100644
--- a/tests/a68_test/long_run.nml
+++ b/tests/a68_test/long_run.nml
@@ -69,7 +69,6 @@
     !(TODO: replace the short-step contact model to be the same as the short-step bonded interactions?)
     spring_coef=0.00065359477124183 !if dem_spring_coef=0.5e7 and r=1500, with square packing
 
-    monitor_energy=.false.
     !defaults given in parentheses:
     mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
     mts_sub_steps=<ss> !# of mts sub-steps
diff --git a/tests/collision_tests/input.nml b/tests/collision_tests/input.nml
deleted file mode 100644
index 2b66aed..0000000
--- a/tests/collision_tests/input.nml
+++ /dev/null
@@ -1,160 +0,0 @@
-!!KID, bergs_chksum: write_restart berg chksum = -1211104969 chksum2= -1211104969 chksum3= 1964715299  chksum4= 1964715299  chksum5= 0#= 16
-
-&icebergs_driver_nml
-  ni=20 !number of elements, x direction
-  nj=20 !number of elements, y direction
-  ibdt=60.0 !seconds
-  ibuo=0.2 !ocean x velocity
-  ibvo=0.2 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=48 !total simulation hours
-  nmax=99999999 !max number of timesteps
-  saverestart=.true.
-  halo=3
-  debug=.false.
-  collision_test=.true. !specific to the current test, must be true here
-/
-
-
-&icebergs_nml
-
-    traj_name=KID.nc
-    bond_traj_name=KID_bonds.nc
-
-    !defaults given in parentheses:
-    ! explicit_inner_mts=.true.
-    ! mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    ! mts_sub_steps=60 !1 !30 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
-    ! contact_distance=1.75e3 !2.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    ! contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    ! debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    ! remove_unused_bergs=.false. !(T) remove unneeded bergs after PEs transfers
-
-    halo=3 !(4) halo width
-    Lx=20000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.True. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    rho_bergs=850. ! (850) iceberg density
-    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0.4 !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.False. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors
-
-    verbose=.true. !(F) Be verbose to stderr
-    verbose_hrs=1 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !1 !(24) sampling period for trajectory storage
-    traj_write_hrs=6 ! (480) Period for writing sampled trajectories to disk
-    budget=.true. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.true. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.False. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/dem_cbeam_test/input.nml b/tests/dem_cbeam_test/input.nml
index 636195e..c90bc74 100644
--- a/tests/dem_cbeam_test/input.nml
+++ b/tests/dem_cbeam_test/input.nml
@@ -42,7 +42,6 @@
     rho_bergs=900. ! (850) iceberg density
     dem_spring_coef=1.e9 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
 
-    monitor_energy=.false. !(F)save total elastic (spring+collision),external,dissipated,&fracture energy
     mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
     mts_sub_steps=2000  !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
     force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
diff --git a/tests/dem_ground_frac_test/input.nml b/tests/dem_ground_frac_test/input.nml
index 62b2f46..0525a05 100644
--- a/tests/dem_ground_frac_test/input.nml
+++ b/tests/dem_ground_frac_test/input.nml
@@ -52,7 +52,6 @@
     spring_coef=0.0007547062342348049 !if dem_spring_coef=5e6, r=1500, and hex pack?
     !spring_coef=0.00065359477124183  !if dem_spring_coef=5e6, r=1500, and square pack?
 
-    monitor_energy=.false.
     !defaults given in parentheses:
     mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
     mts_sub_steps=200 !(-1) # of mts sub-steps
diff --git a/tests/dem_ssbeam_test/input.nml b/tests/dem_ssbeam_test/input.nml
index ca5af1c..14a455b 100644
--- a/tests/dem_ssbeam_test/input.nml
+++ b/tests/dem_ssbeam_test/input.nml
@@ -35,7 +35,6 @@
     rho_bergs=800. ! (850) iceberg density
     dem_spring_coef=1.e9 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
 
-    monitor_energy=.false. !(F)save total elastic (spring+collision),external,dissipated,&fracture energy
     mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
     mts_sub_steps=1e5 !20 !00  !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
 

From 9bd3b77bea0789366a49db1bf85dd604b02f24fb Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Thu, 29 Dec 2022 12:09:38 -0500
Subject: [PATCH 334/361] Cleaned up the makeberg directories and files

---
 tests/.gitignore                              |  14 +-
 .../Scripts_and_analysis/hexagon_area.pyc     | Bin 33353 -> 33353 bytes
 tests/a68_test/{RUN1p => RUN}                 |   0
 tests/a68_test/long_run_for_paper.sh          |   3 +-
 tests/a68_test/makeberg/RUN_for_paper         |   6 -
 tests/a68_test/makeberg/hexagon_area.pyc      | Bin 32612 -> 32612 bytes
 tests/a68_test/makeberg/makeberg.py           |  12 +-
 tests/collision_tests/makeberg/makeberg.py    |  34 +-
 tests/dem_cbeam_test/makeberg/RUN_1l          |   3 -
 tests/dem_cbeam_test/makeberg/RUN_2p          |   3 -
 tests/dem_cbeam_test/makeberg/makeberg.py     |   6 +-
 tests/dem_cbeam_test/makeberg/makeberg_1l.py  | 321 ------------------
 tests/dem_cbeam_test/makeberg/makeberg_2p.py  | 300 ----------------
 .../dem_ground_frac_test/makeberg/makeberg.py |  55 +--
 tests/dem_ssbeam_test/makeberg/makeberg.py    |   7 +-
 tests/footloose_tests/.gitignore              |   1 -
 tests/footloose_tests/makeberg/makeberg.py    |   4 -
 tests/nc2csv.py                               | 165 ---------
 tests/nc2csv_bonds.py                         | 136 --------
 tests/plot_bond_strain.py                     |  79 -----
 tests/plot_energy.py                          | 219 ------------
 21 files changed, 31 insertions(+), 1337 deletions(-)
 rename tests/a68_test/{RUN1p => RUN} (100%)
 delete mode 100755 tests/a68_test/makeberg/RUN_for_paper
 delete mode 100755 tests/dem_cbeam_test/makeberg/RUN_1l
 delete mode 100755 tests/dem_cbeam_test/makeberg/RUN_2p
 delete mode 100755 tests/dem_cbeam_test/makeberg/makeberg_1l.py
 delete mode 100755 tests/dem_cbeam_test/makeberg/makeberg_2p.py
 delete mode 100755 tests/nc2csv.py
 delete mode 100755 tests/nc2csv_bonds.py
 delete mode 100755 tests/plot_bond_strain.py
 delete mode 100755 tests/plot_energy.py

diff --git a/tests/.gitignore b/tests/.gitignore
index 3247cd1..a93e4f9 100644
--- a/tests/.gitignore
+++ b/tests/.gitignore
@@ -3,16 +3,4 @@
 *.nc
 *.csv
 core
-single_test/
-size_test_tab/
-steady_test/
-uniaxial_test/
-a68/
-collision_tests_2/
-a68_2/
-a68_3/
-a68_old/
-other_tests/
-nc2csv_bonds.py
-plot_bond_strain.py
-plot_energy.py
\ No newline at end of file
+other_tests/
\ No newline at end of file
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/hexagon_area.pyc b/tests/Iceberg_repository/Scripts_and_analysis/hexagon_area.pyc
index f0183b2e91e5919cba386d292db458999496b1a3..c543d81695a6eecfb2bddea9f3b7ff88f8c90d00 100644
GIT binary patch
delta 18
ZcmX@v!gR8QiJkc~FIVu1wHw);ngBx{2KN8}

delta 18
ZcmX@v!gR8QiJkc~FIOpN#YT3gCICK(1|<Lh

diff --git a/tests/a68_test/RUN1p b/tests/a68_test/RUN
similarity index 100%
rename from tests/a68_test/RUN1p
rename to tests/a68_test/RUN
diff --git a/tests/a68_test/long_run_for_paper.sh b/tests/a68_test/long_run_for_paper.sh
index dc9d45d..df2581a 100755
--- a/tests/a68_test/long_run_for_paper.sh
+++ b/tests/a68_test/long_run_for_paper.sh
@@ -25,6 +25,5 @@ for ((i = 0; i < ${#odrag[@]}; ++i)); do
 
     sed  "s/<od>/$drag/; s/<re>/$Rearth/; s/<ss>/$ss/; s/<ns>/$ns/; s/<gc>/$gc/; s/<xd>/$A68dx/; s/<yd>/$A68dy/; s/<name>/$fname/g" \
 	 long_run.nml > input.nml
-    ./RUN1p
-    # &>/dev/null &
+    ./RUN
 done
diff --git a/tests/a68_test/makeberg/RUN_for_paper b/tests/a68_test/makeberg/RUN_for_paper
deleted file mode 100755
index 2cbc068..0000000
--- a/tests/a68_test/makeberg/RUN_for_paper
+++ /dev/null
@@ -1,6 +0,0 @@
-rm ./output_files/Generic*
-
-# THIS IS THE BERG USED IN HUTH ET AL, 2022 OCEAN CURRENTS BREAK UP A TABULAR ICEBERG. SCIENCE ADVANCES:
-./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_09_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=False -Radius=1500 -lat_ref_grid_to_cartesian=-55.2 -uvel=0.22 -dx=500. -R_earth=6363827. -icethres=0.5 -displace_y=-0.1
-
-cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
diff --git a/tests/a68_test/makeberg/hexagon_area.pyc b/tests/a68_test/makeberg/hexagon_area.pyc
index 5e8a8a0e8bdedd5f3635eb928331eabf50465379..e0a9f18723586ed28c47fc86fd9f873f180c213e 100644
GIT binary patch
delta 17
ZcmaFzkMYSrMmFZpyj&~mHnPRl0{~2<2bBN-

delta 17
YcmaFzkMYSrMmFZpyj<pC8`<LO0ZA|h`v3p{

diff --git a/tests/a68_test/makeberg/makeberg.py b/tests/a68_test/makeberg/makeberg.py
index d34547c..3db6dda 100755
--- a/tests/a68_test/makeberg/makeberg.py
+++ b/tests/a68_test/makeberg/makeberg.py
@@ -36,7 +36,7 @@ def parseCommandLine():
         '''
         Generate files for iceberg and bond restart files, matching given ice thickness fields.
         ''',
-        epilog='Written by Alon Stern, Dec. 2016.')
+        epilog='Written by Alex Huth, 2021, based on Iceberg_repository code from Alon Stern.')
 
         #Adding an extra boolian type argument
         #p = argparse.ArgumentParser()
@@ -1806,7 +1806,6 @@ def main(args):
                         Radius= (np.sqrt(3)/2.) *(R_frac*dx)   #(S is < half the grid size)
         print ('Radius set to R= ' , Radius)
 
-        #lat_ref=np.max(y)
         #Define the positions,thickness, mass,  of the icebergs
 
         (Number_of_bergs,lon,lat,iceberg_num,dx_berg, dy_berg,thickness,ang_vel_out,uvel_out,vvel_out,mass,width,x,y,Radius,static_berg,N_bergs_before_bd)= Create_icebergs(lon_init,lat_init,\
@@ -1875,19 +1874,12 @@ def main(args):
                                                    plot_circles,h_ice,ice_mask_grid,lon_grid,lat_grid,plot_ice_mask,\
                                                    plot_ice_thickness,thickness,plot_icebergs_positions,static_berg,\
                                                    h_ice_new,plot_h_ice_new)
-                        # plotting_iceberg_positions(lat,lon,Number_of_bergs,R_earth,Radius,IA_scaling,Convert_to_lat_lon,\
-                        #                            plot_circles,h_ice,ice_mask,x,y,plot_ice_mask,plot_ice_thickness,\
-                        #                            thickness,plot_icebergs_positions,static_berg,h_ice_new,plot_h_ice_new)
+
                 if (plot_bonds==True) and (Create_icebergs_bonds):
                         plotting_iceberg_bonds(first_berg_lat,first_berg_lon,other_berg_lat,other_berg_lon,Number_of_bonds)
 
-        #field=New_mass/(rho_ice*grid_area)
         field=New_area/grid_area -1.
         M=field.shape
-        #print 'field',(field[M[0]-1,:])
-        #print 'field',(field[M[0]-2,:])
-        #print 'h_ice',h_ice_new[:,:]
-        #print 'h_ice-1',h_ice_new[:,:]-1.
         if Run_plotting_subroutine:
                 plt.show()
         print ('Script complete')
diff --git a/tests/collision_tests/makeberg/makeberg.py b/tests/collision_tests/makeberg/makeberg.py
index 423b6a5..3aabdae 100755
--- a/tests/collision_tests/makeberg/makeberg.py
+++ b/tests/collision_tests/makeberg/makeberg.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
-from netCDF4 import Dataset  
-import numpy as np 
+from netCDF4 import Dataset
+import numpy as np
 import math
 #import os
 from pylab import *
@@ -10,8 +10,7 @@
 
 nx = 20
 ny = 20
-New_ice_thickness_filename='testberg.nc'
-grid_res = 1.e3 #1 km 
+grid_res = 1.e3 #1 km
 grid_area = grid_res * grid_res
 h_ice = 300.0
 
@@ -24,8 +23,6 @@
 area_h=g.createVariable('area','f8',('ny','nx'))
 lat_h=g.createVariable('lat','f8','ny')
 lon_h=g.createVariable('lon','f8','nx')
-#lat_h=g.createVariable('lat','f8',('ny','nx'))
-#lon_h=g.createVariable('lon','f8',('ny','nx'))
 
 thick_h.units = 'm'
 thick_h.standard_name = 'ice shelf thickness'
@@ -36,42 +33,33 @@
 lat_h.unit = 'm'
 lat_h.standard_name = 'latitude'
 
-
-
-#g.variables['thick'][:]=h_ice
 g.variables['area'][:,:]=grid_area
 
 #create a circular tabular berg centered on the following coords (km)
 cy = 4.5e3
 cx = 4.5e3
-#cx2 = 15.5e3
 
 for i in range(nx):
 
-        tx = float(i) * grid_res 
+        tx = float(i) * grid_res
         g.variables['lon'][i] = tx
-        
+
         for j in range(ny):
-               
-                ty = float(j) * grid_res 
+
+                ty = float(j) * grid_res
                 dist = sqrt((tx-cx)*(tx-cx) + (ty-cy)*(ty-cy))
-                #dist2 =  sqrt((tx-cx2)*(tx-cx2) + (ty-cy)*(ty-cy))
-                #g.variables['lon'][i,j] = tx
-                #g.variables['lat'][i,j] = ty
-        
-                if (dist <1.e3): #or dist2<1.e3):
+
+                if (dist <1.e3):
                         g.variables['thick'][i,j]=h_ice
                 else:
                         g.variables['thick'][i,j]=0.0
 
-                        
+
 
 for j in range(ny):
-        g.variables['lat'][j] = float(j) * grid_res 
+        g.variables['lat'][j] = float(j) * grid_res
 
 print('Creating file: ' , New_ice_thickness_filename)
 
 g.sync()
 g.close()
-
-        
diff --git a/tests/dem_cbeam_test/makeberg/RUN_1l b/tests/dem_cbeam_test/makeberg/RUN_1l
deleted file mode 100755
index 7a790b4..0000000
--- a/tests/dem_cbeam_test/makeberg/RUN_1l
+++ /dev/null
@@ -1,3 +0,0 @@
-rm ./output_files/Generic*
-./makeberg_1l.py -t=1
-cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
diff --git a/tests/dem_cbeam_test/makeberg/RUN_2p b/tests/dem_cbeam_test/makeberg/RUN_2p
deleted file mode 100755
index 72b7d99..0000000
--- a/tests/dem_cbeam_test/makeberg/RUN_2p
+++ /dev/null
@@ -1,3 +0,0 @@
-rm ./output_files/Generic*
-./makeberg_2p.py -t=1
-cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
diff --git a/tests/dem_cbeam_test/makeberg/makeberg.py b/tests/dem_cbeam_test/makeberg/makeberg.py
index 11ff0dc..c213556 100755
--- a/tests/dem_cbeam_test/makeberg/makeberg.py
+++ b/tests/dem_cbeam_test/makeberg/makeberg.py
@@ -9,8 +9,10 @@
 
 def parseCommandLine():
     parser = argparse.ArgumentParser(description=
-    '''Generate animation of iceberg trajectories.''',
-    epilog='Written by Alex Huth, 2020')
+    '''
+    Generate files for iceberg and bond restart files, matching given ice thickness fields.
+    ''',
+    epilog='Written by Alex Huth, 2021, based on Iceberg_repository code from Alon Stern.')
     parser.add_argument('-t', type=int, default='1',
                     help='''which test case''')
     optCmdLineArgs = parser.parse_args()
diff --git a/tests/dem_cbeam_test/makeberg/makeberg_1l.py b/tests/dem_cbeam_test/makeberg/makeberg_1l.py
deleted file mode 100755
index 79a39f2..0000000
--- a/tests/dem_cbeam_test/makeberg/makeberg_1l.py
+++ /dev/null
@@ -1,321 +0,0 @@
-#!/usr/bin/env python
-import numpy as np
-import math
-from netCDF4 import Dataset
-from pylab import *
-#import pdb
-import netCDF4 as nc
-import argparse
-
-def parseCommandLine():
-    parser = argparse.ArgumentParser(description=
-    '''Generate animation of iceberg trajectories.''',
-    epilog='Written by Alex Huth, 2020')
-    parser.add_argument('-t', type=int, default='1',
-                    help='''which test case''')
-    optCmdLineArgs = parser.parse_args()
-    return optCmdLineArgs
-
-def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
-
-	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
-	# To copy the global attributes of the netCDF file
-
-	#Input and output files
-	#Create Empty restart file. This is later read so that the attributes can be used.
-	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
-	create_empty_iceberg_restart_file(Empty_restart_filename)
-	#Empty_restart_filename='input_files/icebergs.res.nc'
-
-	#Read empty restart file
-	f=Dataset(Empty_restart_filename,'r') # r is for read only
-	#Write a new restart file
-	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
-
-	for attname in f.ncattrs():
-		    setattr(g,attname,getattr(f,attname))
-
-
-	# To copy the dimension of the netCDF file
-	for dimname,dim in f.dimensions.iteritems():
-		# if you want to make changes in the dimensions of the new file
-		# you should add your own conditions here before the creation of the dimension.
-		#g.createDimension(dimname,len(dim))
-		g.createDimension(dimname,Number_of_bergs)
-
-	# To copy the variables of the netCDF file
-
-	for varname,ncvar in f.variables.iteritems():
-		# if you want to make changes in the variables of the new file
-		# you should add your own conditions here before the creation of the variable.
-		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
-		#Proceed to copy the variable attributes
-		for attname in ncvar.ncattrs():
-			setattr(var,attname,getattr(ncvar,attname))
-		#Finally copy the variable data to the new created variable
-		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
-
-		if varname=='i':
-			var[:]=Number_of_bergs
-
-		if varname=='iceberg_num':
-			for j in range(Number_of_bergs):
-				#var[j]=j+1
-				var[j]=iceberg_num[j]
-
-		if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
-		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
-		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
-		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
-			var[:]=0
-
-                if varname=='uvel':
-			for j in range(Number_of_bergs):
-				var[j]=uvel[j]
-
-                if varname=='vvel':
-			for j in range(Number_of_bergs):
-				var[j]=vvel[j]
-
-		if varname=='mass_scaling':
-			for j in range(Number_of_bergs):
-				var[j]=mass_scaling[j]
-
-		if varname=='thickness':
-			for j in range(Number_of_bergs):
-				var[j]=thickness[j]
-
-		if varname=='mass':
-			for j in range(Number_of_bergs):
-				var[j]=mass[j]
-
-		if varname=='width'  or varname=='length':
-			for j in range(Number_of_bergs):
-				var[j]=width[j]
-
-		if varname=='lon':
-			for j in range(Number_of_bergs):
-				var[j]=lon[j]
-
-		if varname=='lat':
-			for j in range(Number_of_bergs):
-				var[j]=lat[j]
-
-		if varname=='static_berg':
-			for j in range(Number_of_bergs):
-				var[j]=static_berg[j]
-
-
-	f.close()
-	g.close()
-
-
-def create_empty_iceberg_restart_file(Empty_restart_filename):
-
-	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
-
-	i=f.createDimension('i', None)
-	lon=f.createVariable('i','i')
-
-	lon=f.createVariable('lon','d',('i'))
-	lon.long_name = "longitude" ;
-	lon.units = "degrees_E" ;
-	lon.checksum = "               0" ;
-
-	lat=f.createVariable('lat','d',('i'))
-	lat.long_name = "latitude" ;
-	lat.units = "degrees_N" ;
-	lat.checksum = "               0" ;
-
-	uvel=f.createVariable('uvel','d',('i'))
-	uvel.long_name = "zonal velocity" ;
-	uvel.units = "m/s" ;
-	uvel.checksum = "               0" ;
-
-	vvel=f.createVariable('vvel','d',('i'))
-	vvel.long_name = "meridional velocity" ;
-	vvel.units = "m/s" ;
-	vvel.checksum = "               0" ;
-
-	mass=f.createVariable('mass','d',('i'))
-	mass.long_name = "mass" ;
-	mass.units = "kg" ;
-	mass.checksum = "               0" ;
-
-	axn=f.createVariable('axn','d',('i'))
-	axn.long_name = "explicit zonal acceleration" ;
-	axn.units = "m/s^2" ;
-	axn.checksum = "               0" ;
-
-	ayn=f.createVariable('ayn','d',('i'))
-	ayn.long_name = "explicit meridional acceleration" ;
-	ayn.units = "m/s^2" ;
-	ayn.checksum = "               0" ;
-
-	bxn=f.createVariable('bxn','d',('i'))
-	bxn.long_name = "inplicit zonal acceleration" ;
-	bxn.units = "m/s^2" ;
-	bxn.checksum = "               0" ;
-
-	byn=f.createVariable('byn','d',('i'))
-	byn.long_name = "implicit meridional acceleration" ;
-	byn.units = "m/s^2" ;
-	byn.checksum = "               0" ;
-
-	ine=f.createVariable('ine','i',('i'))
-	ine.long_name = "i index" ;
-	ine.units = "none" ;
-	ine.packing = 0 ;
-	ine.checksum = "               0" ;
-
-	jne=f.createVariable('jne','i',('i'))
-	jne.long_name = "j index" ;
-	jne.units = "none" ;
-	jne.packing = 0 ;
-	jne.checksum = "               0" ;
-
-	thickness=f.createVariable('thickness','d',('i'))
-	thickness.long_name = "thickness" ;
-	thickness.units = "m" ;
-	thickness.checksum = "               0" ;
-
-	width=f.createVariable('width','d',('i'))
-	width.long_name = "width" ;
-	width.units = "m" ;
-	width.checksum = "               0" ;
-
-	length=f.createVariable('length','d',('i'))
-	length.long_name = "length" ;
-	length.units = "m" ;
-	length.checksum = "               0" ;
-
-	start_lon=f.createVariable('start_lon','d',('i'))
-	start_lon.long_name = "longitude of calving location" ;
-	start_lon.units = "degrees_E" ;
-	start_lon.checksum = "               0" ;
-
-	start_lat=f.createVariable('start_lat','d',('i'))
-	start_lat.long_name = "latitude of calving location" ;
-	start_lat.units = "degrees_N" ;
-	start_lat.checksum = "               0" ;
-
-	start_year=f.createVariable('start_year','i',('i'))
-	start_year.long_name = "calendar year of calving event" ;
-	start_year.units = "years" ;
-	start_year.packing = 0 ;
-	start_year.checksum = "               0" ;
-
-	iceberg_num=f.createVariable('iceberg_num','i',('i'))
-	iceberg_num.long_name = "identification of the iceberg" ;
-	iceberg_num.units = "dimensionless" ;
-	iceberg_num.packing = 0 ;
-	iceberg_num.checksum = "               0" ;
-
-	start_day=f.createVariable('start_day','d',('i'))
-	start_day.long_name = "year day of calving event" ;
-	start_day.units = "days" ;
-	start_day.checksum = "               0" ;
-
-	start_mass=f.createVariable('start_mass','d',('i'))
-	start_mass.long_name = "initial mass of calving berg" ;
-	start_mass.units = "kg" ;
-	start_mass.checksum = "               0" ;
-
-	mass_scaling=f.createVariable('mass_scaling','d',('i'))
-	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
-	mass_scaling.units = "none" ;
-	mass_scaling.checksum = "               0" ;
-
-	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
-	mass_of_bits.long_name = "mass of bergy bits" ;
-	mass_of_bits.units = "kg" ;
-	mass_of_bits.checksum = "               0" ;
-
-	heat_density=f.createVariable('heat_density','d',('i'))
-	heat_density.long_name = "heat density" ;
-	heat_density.units = "J/kg" ;
-	heat_density.checksum = "               0" ;
-
-	halo_berg=f.createVariable('halo_berg','d',('i'))
-	halo_berg.long_name = "halo_berg" ;
-	halo_berg.units = "dimensionless" ;
-	halo_berg.checksum = "               0" ;
-
-	static_berg=f.createVariable('static_berg','d',('i'))
-	static_berg.long_name = "static_berg" ;
-	static_berg.units = "dimensionless" ;
-	static_berg.checksum = "               0" ;
-
-	f.sync()
-	f.close()
-
-
-def main(args):
-
-    #SQUARE PACKING
-
-        test=args.t
-        grdres=20.e3
-        r=2500.0#/3.
-
-        #start coords
-        xs=101.e3
-        ys=151.e3
-
-        h=1. #thickness
-        rho_ice=900.0
-
-
-        if test==1:
-            #5 particles w/ large radius
-            nbergs=30#90
-            width=r*2.
-            length=r*2.
-
-        #radii for evenly distrib cases
-        #element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*r**2)
-        element_area=(2.*r)**2
-
-        berg_x=[]; berg_y=[]
-        berg_id=[]; berg_static=[]
-        berg_width=[]; berg_bonds=[]
-        berg_h=[]; berg_mass_scaling=[]
-        berg_mass=[]
-        berg_uvel=[]; berg_vvel=[]
-
-        x=xs
-        y=ys#-2*r
-
-        berg_count=0.
-        while berg_count<nbergs:
-                berg_count=berg_count+1
-                if berg_count==1:
-                    #x=xs
-                    y=y+2*r
-                    static=1
-                else:
-                    static=0
-                    x=x+2*r
-
-                berg_x.append(x)
-                berg_y.append(y)
-                berg_width.append(sqrt(element_area))
-                berg_h.append(h)
-                berg_mass_scaling.append(1)
-                berg_mass.append(h*rho_ice*element_area)
-                berg_static.append(static)
-                berg_uvel.append(0)
-                berg_vvel.append(0)
-                berg_id.append(berg_count)
-
-        print('Number of bergs',berg_count)
-
-        #Create iceberg restart file
-        Ice_geometry_source='Generic'
-        Create_iceberg_restart_file(nbergs,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)
-
-
-if __name__ == '__main__':
-    optCmdLineArgs=	parseCommandLine()
-    anim_running = True
-    main(optCmdLineArgs)
diff --git a/tests/dem_cbeam_test/makeberg/makeberg_2p.py b/tests/dem_cbeam_test/makeberg/makeberg_2p.py
deleted file mode 100755
index 0947559..0000000
--- a/tests/dem_cbeam_test/makeberg/makeberg_2p.py
+++ /dev/null
@@ -1,300 +0,0 @@
-#!/usr/bin/env python
-import numpy as np
-import math
-from netCDF4 import Dataset
-from pylab import *
-#import pdb
-import netCDF4 as nc
-import argparse
-
-def parseCommandLine():
-    parser = argparse.ArgumentParser(description=
-    '''Generate animation of iceberg trajectories.''',
-    epilog='Written by Alex Huth, 2020')
-    parser.add_argument('-t', type=int, default='1',
-                    help='''which test case''')
-    optCmdLineArgs = parser.parse_args()
-    return optCmdLineArgs
-
-def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
-
-	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
-	# To copy the global attributes of the netCDF file
-
-	#Input and output files
-	#Create Empty restart file. This is later read so that the attributes can be used.
-	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
-	create_empty_iceberg_restart_file(Empty_restart_filename)
-	#Empty_restart_filename='input_files/icebergs.res.nc'
-
-	#Read empty restart file
-	f=Dataset(Empty_restart_filename,'r') # r is for read only
-	#Write a new restart file
-	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
-
-	for attname in f.ncattrs():
-		    setattr(g,attname,getattr(f,attname))
-
-
-	# To copy the dimension of the netCDF file
-	for dimname,dim in f.dimensions.iteritems():
-		# if you want to make changes in the dimensions of the new file
-		# you should add your own conditions here before the creation of the dimension.
-		#g.createDimension(dimname,len(dim))
-		g.createDimension(dimname,Number_of_bergs)
-
-	# To copy the variables of the netCDF file
-
-	for varname,ncvar in f.variables.iteritems():
-		# if you want to make changes in the variables of the new file
-		# you should add your own conditions here before the creation of the variable.
-		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
-		#Proceed to copy the variable attributes
-		for attname in ncvar.ncattrs():
-			setattr(var,attname,getattr(ncvar,attname))
-		#Finally copy the variable data to the new created variable
-		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
-
-		if varname=='i':
-			var[:]=Number_of_bergs
-
-		if varname=='iceberg_num':
-			for j in range(Number_of_bergs):
-				#var[j]=j+1
-				var[j]=iceberg_num[j]
-
-		if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
-		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
-		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
-		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
-			var[:]=0
-
-                if varname=='uvel':
-			for j in range(Number_of_bergs):
-				var[j]=uvel[j]
-
-                if varname=='vvel':
-			for j in range(Number_of_bergs):
-				var[j]=vvel[j]
-
-		if varname=='mass_scaling':
-			for j in range(Number_of_bergs):
-				var[j]=mass_scaling[j]
-
-		if varname=='thickness':
-			for j in range(Number_of_bergs):
-				var[j]=thickness[j]
-
-		if varname=='mass':
-			for j in range(Number_of_bergs):
-				var[j]=mass[j]
-
-		if varname=='width'  or varname=='length':
-			for j in range(Number_of_bergs):
-				var[j]=width[j]
-
-		if varname=='lon':
-			for j in range(Number_of_bergs):
-				var[j]=lon[j]
-
-		if varname=='lat':
-			for j in range(Number_of_bergs):
-				var[j]=lat[j]
-
-		if varname=='static_berg':
-			for j in range(Number_of_bergs):
-				var[j]=static_berg[j]
-
-
-	f.close()
-	g.close()
-
-
-def create_empty_iceberg_restart_file(Empty_restart_filename):
-
-	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
-
-	i=f.createDimension('i', None)
-	lon=f.createVariable('i','i')
-
-	lon=f.createVariable('lon','d',('i'))
-	lon.long_name = "longitude" ;
-	lon.units = "degrees_E" ;
-	lon.checksum = "               0" ;
-
-	lat=f.createVariable('lat','d',('i'))
-	lat.long_name = "latitude" ;
-	lat.units = "degrees_N" ;
-	lat.checksum = "               0" ;
-
-	uvel=f.createVariable('uvel','d',('i'))
-	uvel.long_name = "zonal velocity" ;
-	uvel.units = "m/s" ;
-	uvel.checksum = "               0" ;
-
-	vvel=f.createVariable('vvel','d',('i'))
-	vvel.long_name = "meridional velocity" ;
-	vvel.units = "m/s" ;
-	vvel.checksum = "               0" ;
-
-	mass=f.createVariable('mass','d',('i'))
-	mass.long_name = "mass" ;
-	mass.units = "kg" ;
-	mass.checksum = "               0" ;
-
-	axn=f.createVariable('axn','d',('i'))
-	axn.long_name = "explicit zonal acceleration" ;
-	axn.units = "m/s^2" ;
-	axn.checksum = "               0" ;
-
-	ayn=f.createVariable('ayn','d',('i'))
-	ayn.long_name = "explicit meridional acceleration" ;
-	ayn.units = "m/s^2" ;
-	ayn.checksum = "               0" ;
-
-	bxn=f.createVariable('bxn','d',('i'))
-	bxn.long_name = "inplicit zonal acceleration" ;
-	bxn.units = "m/s^2" ;
-	bxn.checksum = "               0" ;
-
-	byn=f.createVariable('byn','d',('i'))
-	byn.long_name = "implicit meridional acceleration" ;
-	byn.units = "m/s^2" ;
-	byn.checksum = "               0" ;
-
-	ine=f.createVariable('ine','i',('i'))
-	ine.long_name = "i index" ;
-	ine.units = "none" ;
-	ine.packing = 0 ;
-	ine.checksum = "               0" ;
-
-	jne=f.createVariable('jne','i',('i'))
-	jne.long_name = "j index" ;
-	jne.units = "none" ;
-	jne.packing = 0 ;
-	jne.checksum = "               0" ;
-
-	thickness=f.createVariable('thickness','d',('i'))
-	thickness.long_name = "thickness" ;
-	thickness.units = "m" ;
-	thickness.checksum = "               0" ;
-
-	width=f.createVariable('width','d',('i'))
-	width.long_name = "width" ;
-	width.units = "m" ;
-	width.checksum = "               0" ;
-
-	length=f.createVariable('length','d',('i'))
-	length.long_name = "length" ;
-	length.units = "m" ;
-	length.checksum = "               0" ;
-
-	start_lon=f.createVariable('start_lon','d',('i'))
-	start_lon.long_name = "longitude of calving location" ;
-	start_lon.units = "degrees_E" ;
-	start_lon.checksum = "               0" ;
-
-	start_lat=f.createVariable('start_lat','d',('i'))
-	start_lat.long_name = "latitude of calving location" ;
-	start_lat.units = "degrees_N" ;
-	start_lat.checksum = "               0" ;
-
-	start_year=f.createVariable('start_year','i',('i'))
-	start_year.long_name = "calendar year of calving event" ;
-	start_year.units = "years" ;
-	start_year.packing = 0 ;
-	start_year.checksum = "               0" ;
-
-	iceberg_num=f.createVariable('iceberg_num','i',('i'))
-	iceberg_num.long_name = "identification of the iceberg" ;
-	iceberg_num.units = "dimensionless" ;
-	iceberg_num.packing = 0 ;
-	iceberg_num.checksum = "               0" ;
-
-	start_day=f.createVariable('start_day','d',('i'))
-	start_day.long_name = "year day of calving event" ;
-	start_day.units = "days" ;
-	start_day.checksum = "               0" ;
-
-	start_mass=f.createVariable('start_mass','d',('i'))
-	start_mass.long_name = "initial mass of calving berg" ;
-	start_mass.units = "kg" ;
-	start_mass.checksum = "               0" ;
-
-	mass_scaling=f.createVariable('mass_scaling','d',('i'))
-	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
-	mass_scaling.units = "none" ;
-	mass_scaling.checksum = "               0" ;
-
-	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
-	mass_of_bits.long_name = "mass of bergy bits" ;
-	mass_of_bits.units = "kg" ;
-	mass_of_bits.checksum = "               0" ;
-
-	heat_density=f.createVariable('heat_density','d',('i'))
-	heat_density.long_name = "heat density" ;
-	heat_density.units = "J/kg" ;
-	heat_density.checksum = "               0" ;
-
-	halo_berg=f.createVariable('halo_berg','d',('i'))
-	halo_berg.long_name = "halo_berg" ;
-	halo_berg.units = "dimensionless" ;
-	halo_berg.checksum = "               0" ;
-
-	static_berg=f.createVariable('static_berg','d',('i'))
-	static_berg.long_name = "static_berg" ;
-	static_berg.units = "dimensionless" ;
-	static_berg.checksum = "               0" ;
-
-	f.sync()
-	f.close()
-
-
-def main(args):
-
-    #SQUARE PACKING
-
-        test=args.t
-        grdres=20.e3
-        r=2500.0
-
-        #start coords
-        xs=101.e3
-        ys=101.e3
-
-        h=1 #thickness
-        rho_ice=900.0
-
-
-        if test==1:
-            #5 particles w/ large radius
-            nbergs=2
-            width=5000.0
-            length=5000.0
-
-        #radii for evenly distrib cases
-        #element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*r**2)
-        element_area=(2.*r)**2
-
-        berg_x=[xs,xs+2.*r]
-        berg_y=[ys,ys]
-        berg_width=[sqrt(element_area),sqrt(element_area)]
-        berg_h=[h,h]
-        berg_mass_scaling=[1,1]
-        berg_mass=[h*rho_ice*element_area,h*rho_ice*element_area]
-        berg_static=[0,0]
-        berg_uvel=[0,0]
-        berg_vvel=[0,0]
-        berg_id=[1,2]
-
-        nbergs=2
-
-        #Create iceberg restart file
-        Ice_geometry_source='Generic'
-        Create_iceberg_restart_file(nbergs,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)
-
-
-if __name__ == '__main__':
-    optCmdLineArgs=	parseCommandLine()
-    anim_running = True
-    main(optCmdLineArgs)
diff --git a/tests/dem_ground_frac_test/makeberg/makeberg.py b/tests/dem_ground_frac_test/makeberg/makeberg.py
index 1fe1baa..a729381 100755
--- a/tests/dem_ground_frac_test/makeberg/makeberg.py
+++ b/tests/dem_ground_frac_test/makeberg/makeberg.py
@@ -6,10 +6,6 @@
 #import pdb
 import netCDF4 as nc
 
-#
-# Initialize 2 iceberg elements, which can later be bonded in the fortran code if needed
-#
-
 def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
 
 	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
@@ -240,29 +236,19 @@ def create_empty_iceberg_restart_file(Empty_restart_filename):
 	f.sync()
 	f.close()
 
-
-
 #-----------------------------------#
 #               Main                #
 #-----------------------------------#
 
-# just2particles=False
-# flip2ndconglom=True#False
-# offset2ndconglom=True#False
-
 grdxmin=0; grdxmax=225000e3
 grdymin=0; grdymax=225000e3
 grdres=5000.0
-R_frac=0.45 #1st option
-#R_frac=0.5*0.45 #2nd option
-#radius=(np.sqrt(3)/2.)*(R_frac*grdres) #S is < 0.5 grid res
-radius=1.5e3 #/2
-#radius2=(np.sqrt(3)/2.)*(R_frac2*grdres) #S is < 0.5 grid res
+R_frac=0.45
+radius=1.5e3
 thickness1=200.0
 thickness2=200.0
 rho_ice=850.0
 
-
 nbergs=1 #number of conglomerates
 
 #center coords of each (rectangular) conglomerate berg (CB=conglomerate berg)
@@ -281,11 +267,6 @@ def create_empty_iceberg_restart_file(Empty_restart_filename):
 CBymin[CBxmin<grdymin]=grdymin; CBymax[CBymax>grdymax]=grdymax
 CBxc=0.5*(CBxmin+CBxmax); CByc=0.5*(CBymin+CBymax)
 
-# #if just want one particle per CB
-# if just2particles:
-#         CBxmin=CBxc; CBxmax=CBxc
-#         CBymin=CByc; CBymax=CByc
-
 #--- min and max thicknesses for each CB ---
 h1=thickness1
 h2=thickness2
@@ -307,10 +288,6 @@ def create_empty_iceberg_restart_file(Empty_restart_filename):
 for i in range(nbergs):
         x_start=CBxmin[i]+(CBrad[i]*2./np.sqrt(3))
 
-        # if flip2ndconglom and i>0:
-        #         x_start=CBxmax[i]-(CBrad[i]*2./np.sqrt(3))
-
-        #pdb.set_trace()
         if x_start>CBxmax[i]:
                 x_start=CBxmax[i]
         y_start0=CBymin[i]+CBrad[i]
@@ -324,15 +301,10 @@ def create_empty_iceberg_restart_file(Empty_restart_filename):
         j=0
         x_val=x_start
         offset=0.0
-        # if (i==0):
-        uvel=0.1#1
-        # else:
-        #         uvel=-0.15#-0.05
-        #         if (offset2ndconglom):
-        #                 offset=250.0
-        vvel=0.0#25
-        #uvel=0;vvel=0
-        #berg_count_start=berg_count
+
+        uvel=0.1
+        vvel=0.0
+
         while x_val<=CBxmax[i] and x_val>=CBxmin[i]:
                 y_start=y_start0+((j%2)*CBrad[i])+offset
                 k=0
@@ -346,31 +318,22 @@ def create_empty_iceberg_restart_file(Empty_restart_filename):
                         #dist of berg elem from center of CB
                         bdistc=np.sqrt((x_val-CBxc[i])**2+(y_val-CByc[i])**2)
                         bh=CBhmin[i]*bdistc/cdistb + CBhmax[i]*(1-bdistc/cdistb)
-                        # if (just2particles):
-                        #         bh=h1
+
                         berg_h.append(bh) #thickness
                         berg_mass_scaling.append(1)
                         berg_mass.append(bh*rho_ice*element_area)
                         berg_static.append(0)
                         berg_uvel.append(uvel)
                         berg_vvel.append(vvel)
-                        # if (x_val<22000):
-                        #         berg_vvel.append(vvel)
-                        # else:
-                        #         berg_vvel.append(0.4)
-                        #berg_CBid.append(i)
+
                         k=k+1
                         y_val=y_start+(2*k*CBrad[i])
                 j=j+1
-                # if flip2ndconglom and i>0:
-                #         x_val=x_start-(np.sqrt(3)*CBrad[i]*j)
-                # else:
+
                 x_val=x_start+(np.sqrt(3)*CBrad[i]*j)
 
 print('Number of bergs',berg_count)
 
-#pdb.set_trace()
-
 #Create iceberg restart file
 Ice_geometry_source='Generic'
 Create_iceberg_restart_file(berg_count,berg_x,berg_y,berg_h,berg_width,berg_mass,berg_mass_scaling,berg_id,Ice_geometry_source,berg_static,berg_uvel,berg_vvel)
diff --git a/tests/dem_ssbeam_test/makeberg/makeberg.py b/tests/dem_ssbeam_test/makeberg/makeberg.py
index 9b14fb3..7ac6b92 100755
--- a/tests/dem_ssbeam_test/makeberg/makeberg.py
+++ b/tests/dem_ssbeam_test/makeberg/makeberg.py
@@ -9,8 +9,8 @@
 
 def parseCommandLine():
     parser = argparse.ArgumentParser(description=
-    '''Generate animation of iceberg trajectories.''',
-    epilog='Written by Alex Huth, 2020')
+    '''Generate icebergs.''',
+    epilog='Written by Alex Huth, 2020. Based on code from Alon Stern.')
     parser.add_argument('-t', type=int, default='1',
                     help='''which test case''')
     optCmdLineArgs = parser.parse_args()
@@ -284,13 +284,12 @@ def main(args):
         berg_uvel=[]; berg_vvel=[]
 
         x=xs
-        y=ys#-2*r
+        y=ys
 
         berg_count=0.
         while berg_count<nbergs:
                 berg_count=berg_count+1
                 if berg_count==1:
-                    #x=xs
                     y=y+2*r
                     static=0
                 else:
diff --git a/tests/footloose_tests/.gitignore b/tests/footloose_tests/.gitignore
index 6734d90..3ca2294 100644
--- a/tests/footloose_tests/.gitignore
+++ b/tests/footloose_tests/.gitignore
@@ -1,2 +1 @@
-old/
 input.nml
\ No newline at end of file
diff --git a/tests/footloose_tests/makeberg/makeberg.py b/tests/footloose_tests/makeberg/makeberg.py
index dd146fc..10d0355 100755
--- a/tests/footloose_tests/makeberg/makeberg.py
+++ b/tests/footloose_tests/makeberg/makeberg.py
@@ -6,10 +6,6 @@
 #import pdb
 import netCDF4 as nc
 
-#
-# Initialize 2 iceberg elements, which can later be bonded in the fortran code if needed
-#
-
 def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
 
 	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
diff --git a/tests/nc2csv.py b/tests/nc2csv.py
deleted file mode 100755
index 05a9602..0000000
--- a/tests/nc2csv.py
+++ /dev/null
@@ -1,165 +0,0 @@
-#!/usr/bin/env python
-
-from netCDF4 import Dataset
-import pdb
-import netCDF4 as nc
-import numpy as np
-import csv
-import math
-import os
-import argparse
-
-#CONVERT BERG TRAJECTORIES FROM NETCDF TO CSV FILE FOR VISUALIZATION IN PARAVIEW
-#returns a series of csv files (one for each time step)
-#To view csv in paraview:
-#1. load all csv files in the series
-#2. Filters --> Table To Points
-#3. In the TableToPoints filter, assign x for X Column, and y for Y Column. Check 2D Points.
-
-
-def parseCommandLine():
-    parser = argparse.ArgumentParser(description=
-                                     '''Convert iceberg trajectories netcdf file to csv file.''',
-                                     epilog='Written by Alex Huth, 2020')
-    parser.register('type','bool',str2bool) # add type keyword to registries
-    parser.add_argument('-fin', type=str, default='iceberg_trajectories.nc',
-                        help=''' provide netcdf filename''')
-    parser.add_argument('-fout', type=str, default='./csvresults/iceberg_trajectories',
-                        help=''' provide filename prefix for csv''')
-    parser.add_argument('-short_traj', type='bool', default=False,
-		        help=''' indicate whether save_short_traj was used ''')
-    parser.add_argument('-mts', type='bool', default=True,
-       	                help=''' indicate whether mts was used ''')
-    optCmdLineArgs = parser.parse_args()
-    return optCmdLineArgs
-
-
-
-def main(args ):
-
-    print('reading file')
-
-    fin=args.fin
-    fout=args.fout
-    short_traj=args.short_traj
-    mts=args.mts
-    if short_traj==True:
-        mts=False
-
-    with nc.Dataset(fin) as file:
-        lon = file.variables['lon'][:]
-        lat = file.variables['lat'][:]
-        year = file.variables['year'][:]
-        day = file.variables['day'][:]
-        id_cnt = file.variables['id_cnt'][:]
-        id_ij = file.variables['id_ij'][:]
-        if short_traj==True:
-            fields = ['x','y','time','id']
-        else:
-            uvel = file.variables['uvel'][:]
-            vvel = file.variables['vvel'][:]
-            # uo = file.variables['uo'][:]
-            # vo = file.variables['vo'][:]
-            # ui = file.variables['ui'][:]
-            # vi = file.variables['vi'][:]
-            # ua = file.variables['ua'][:]
-            # va = file.variables['va'][:]
-            pmass = file.variables['mass'][:]
-            # mass_of_bits= file.variables['mass_of_bits'][:]
-            # heat_density= file.variables['heat_density'][:]
-            thickness = file.variables['thickness'][:]
-            width = file.variables['width'][:]
-            length = file.variables['length'][:]
-            # ssh_x = file.variables['ssh_x'][:]
-            # ssh_y = file.variables['ssh_y'][:]
-            # sst = file.variables['sst'][:]
-            # sss = file.variables['sss'][:]
-            # cn = file.variables['cn'][:]
-            # hi = file.variables['hi'][:]
-            axn = file.variables['axn'][:]
-            ayn = file.variables['ayn'][:]
-            bxn = file.variables['bxn'][:]
-            byn = file.variables['byn'][:]
-            #halo_berg = file.variables['halo_berg'][:]
-            ocean_depth  = file.variables['od'][:]
-            if mts==True:
-                nbonds_id = file.variables['n_bonds'][:]
-                #uvprev = file.variables['uvel_prev'][:]
-                #vvprev = file.variables['vvel_prev'][:]
-                axnf = file.variables['axn_fast'][:]
-                aynf = file.variables['ayn_fast'][:]
-                bxnf = file.variables['bxn_fast'][:]
-                bynf = file.variables['byn_fast'][:]
-                #tot_axn = file.variables['tot_accel_x'][:]
-                #tot_ayn = file.variables['tot_accel_y'][:]
-                fields = ['x','y','time','id','uv','vv','mass','H','W','L','axn','ayn','bxn','byn','ocean_depth','axnf','aynf','bxnf','bynf','nbonds_id']#,'accelx','accely']
-            else:
-                fields = ['x','y','time','id','uv','vv','mass','H','W','L','axn','ayn','bxn','byn','ocean_depth']
-
-    idmid=int('2',8)**32
-    ptime=year+day/365.15
-    pidin=id_cnt*idmid+id_ij
-    utime=np.unique(ptime)
-
-    for i in range(len(utime)):
-        x = lon[ptime == utime[i]]
-        y = lat[ptime == utime[i]]
-        time = ptime[ptime == utime[i]]
-        pid = pidin[ptime == utime[i]]
-        if short_traj==False:
-            uv = uvel[ptime == utime[i]]
-            vv = vvel[ptime == utime[i]]
-            mass = pmass[ptime == utime[i]]
-            H = thickness[ptime == utime[i]]
-            W = width[ptime == utime[i]]
-            L = length[ptime == utime[i]]
-            ax = axn[ptime == utime[i]]
-            ay = ayn[ptime == utime[i]]
-            bx = bxn[ptime == utime[i]]
-            by = byn[ptime == utime[i]]
-            od = ocean_depth[ptime == utime[i]]
-            if mts==True:
-                nb = nbonds_id[ptime == utime[i]]
-                axf = axnf[ptime == utime[i]]
-                ayf = aynf[ptime == utime[i]]
-                bxf = bxnf[ptime == utime[i]]
-                byf = bynf[ptime == utime[i]]
-                #tot_ax = tot_axn[ptime == utime[i]]
-                #tot_ay = tot_ayn[ptime == utime[i]]
-        filename = fout+str(i)+".csv"
-        with open(filename, 'w') as file:
-            writer = csv.writer(file)
-            writer.writerow(fields)
-            if short_traj==True:
-                for j in range(len(x)):
-                    writer.writerow([x[j],y[j],time[j],pid[j]])
-            else:
-                if mts==True:
-                    for j in range(len(x)):
-                        writer.writerow([x[j],y[j],time[j],pid[j],uv[j],vv[j],mass[j],H[j],W[j],L[j],ax[j],ay[j],bx[j],by[j],od[j],axf[j],ayf[j],bxf[j],byf[j],nb[j]])
-                                        #,tot_ax[j],tot_ay[j]])
-                else:
-                    for j in range(len(x)):
-                        writer.writerow([x[j],y[j],time[j],pid[j],uv[j],vv[j],mass[j],H[j],W[j],L[j],ax[j],ay[j],bx[j],by[j],od[j]])
-
-print('Script complete')
-
-def str2bool(string):
-	if string.lower() in  ("yes", "true", "t", "1"):
-		Value=True
-	elif string.lower() in ("no", "false", "f", "0"):
-		Value=False
-	else:
-		print( '**********************************************************************')
-		print( 'The input variable ' ,str(string) ,  ' is not suitable for boolean conversion, using default')
-		print( '**********************************************************************')
-
-		Value=None
-		return
-
-	return Value
-
-if __name__ == '__main__':
-    optCmdLineArgs=	parseCommandLine()
-    anim_running = True
-    main(optCmdLineArgs)
diff --git a/tests/nc2csv_bonds.py b/tests/nc2csv_bonds.py
deleted file mode 100755
index 29c719a..0000000
--- a/tests/nc2csv_bonds.py
+++ /dev/null
@@ -1,136 +0,0 @@
-#!/usr/bin/env python
-
-from netCDF4 import Dataset
-import pdb
-import netCDF4 as nc
-import numpy as np
-import csv
-import math
-import os
-import argparse
-
-#CONVERT BOND TRAJECTORIES FROM NETCDF TO CSV FILE FOR VISUALIZATION IN PARAVIEW
-#returns a series of csv files (one for each time step)
-#To view csv in paraview:
-#1. load all csv files in the series
-#2. Filters --> Table To Points
-#3. In the TableToPoints filter, assign x for X Column, and y for Y Column. Check 2D Points.
-#4. Use calculator to define a vector field for visualizing the bond:
-#   bond_vect = n1*iHat+n2*iHat
-#5. Make a line glyph w/ orientation given by bond_vect components and magnitude by length
-
-
-def parseCommandLine():
-    parser = argparse.ArgumentParser(description=
-                                     '''Convert iceberg bond trajectories netcdf file to csv file.''',
-                                     epilog='Written by Alex Huth, 2020')
-    parser.register('type','bool',str2bool) # add type keyword to registries
-    parser.add_argument('-fin', type=str, default='bond_trajectories.nc',
-                        help=''' provide netcdf filename''')
-    parser.add_argument('-fout', type=str, default='./csvresults/bond_trajectories',
-                        help=''' provide filename prefix for csv''')
-    optCmdLineArgs = parser.parse_args()
-    return optCmdLineArgs
-
-def main(args ):
-
-    print('reading file')
-
-    fin=args.fin
-    fout=args.fout
-
-    with nc.Dataset(fin) as file:
-        lon = file.variables['lon'][:]
-        lat = file.variables['lat'][:]
-        year = file.variables['year'][:]
-        day = file.variables['day'][:]
-        length = file.variables['length'][:]
-        n1 = file.variables['n1'][:]
-        n2 = file.variables['n2'][:]
-        #rot = file.variables['rotation'][:]
-        #rrot = file.variables['rel_rotation'][:]
-        #ns = file.variables['n_strain'][:]
-        #nsr = file.variables['n_strain_rate'][:]
-        ns = file.variables['nstress'][:]
-        ss = file.variables['sstress'][:]
-        id_cnt1 = file.variables['id_cnt1'][:]
-        id_ij1 = file.variables['id_ij1'][:]
-        id_cnt2 = file.variables['id_cnt2'][:]
-        id_ij2 = file.variables['id_ij2'][:]
-        #fields = ['x','y','time','len','n1','n2','rot','rrot','ns','nsr','berg_id1','berg_id2']
-        fields = ['x','y','time','len','n1','n2','ns','ss','berg_id1','berg_id2']
-    idmid=int('2',8)**32
-    btime=year+day/365.15
-    bidin1=id_cnt1*idmid+id_ij1
-    bidin2=id_cnt2*idmid+id_ij2
-
-    # uid=np.unique(bidin1)
-    # uid2=np.unique(bidin2)
-    # print('uid',uid)
-    # print('uid2',uid2)
-
-    #there are originally 2 copies of each bond (one copy for each particle in the bond)
-    #Remove the duplicates:
-    biddiff=bidin2-bidin1
-
-    lon = lon[biddiff>0]
-    lat = lat[biddiff>0]
-    btime = btime[biddiff>0]
-    length = length[biddiff>0]
-    n1 = n1[biddiff>0]
-    n2 = n2[biddiff>0]
-    # rot=rot[biddiff>0]
-    # rrot=rrot[biddiff>0]
-    # ns=ns[biddiff>0]
-    # nsr=nsr[biddiff>0]
-    ns=ns[biddiff>0]
-    ss=ss[biddiff>0]
-    bidin1 = bidin1[biddiff>0]
-    bidin2 = bidin2[biddiff>0]
-
-    utime=np.unique(btime)
-
-    for i in range(len(utime)):
-        x = lon[btime == utime[i]]
-        y = lat[btime == utime[i]]
-        time = btime[btime == utime[i]]
-        blen = length[btime == utime[i]]
-        bn1 = n1[btime == utime[i]]
-        bn2 = n2[btime == utime[i]]
-        # brot = rot[btime == utime[i]]
-        # brrot = rrot[btime == utime[i]]
-        # bns = ns[btime == utime[i]]
-        # bnsr = nsr[btime == utime[i]]
-        bns = ns[btime == utime[i]]
-        bss = ss[btime == utime[i]]
-        bid1 = bidin1[btime == utime[i]]
-        bid2 = bidin2[btime == utime[i]]
-
-        filename = fout+str(i)+".csv"
-        with open(filename, 'w') as file:
-            writer = csv.writer(file)
-            writer.writerow(fields)
-            for j in range(len(x)):
-               # writer.writerow([x[j],y[j],time[j],blen[j],bn1[j],bn2[j],brot[j],brrot[j],bns[j],bnsr[j],bid1[j],bid2[j]])
-                writer.writerow([x[j],y[j],time[j],blen[j],bn1[j],bn2[j],bns[j],bss[j],bid1[j],bid2[j]])
-print('Script complete')
-
-def str2bool(string):
-	if string.lower() in  ("yes", "true", "t", "1"):
-		Value=True
-	elif string.lower() in ("no", "false", "f", "0"):
-		Value=False
-	else:
-		print '**********************************************************************'
-		print 'The input variable ' ,str(string) ,  ' is not suitable for boolean conversion, using default'
-		print '**********************************************************************'
-
-		Value=None
-		return
-
-	return Value
-
-if __name__ == '__main__':
-    optCmdLineArgs=	parseCommandLine()
-    anim_running = True
-    main(optCmdLineArgs)
diff --git a/tests/plot_bond_strain.py b/tests/plot_bond_strain.py
deleted file mode 100755
index 49b2fe6..0000000
--- a/tests/plot_bond_strain.py
+++ /dev/null
@@ -1,79 +0,0 @@
-#!/usr/bin/env python3
-
-from netCDF4 import Dataset
-import pdb
-import netCDF4 as nc
-import numpy as np
-import matplotlib
-import math
-import os
-matplotlib.use("tkagg")
-from pylab import *
-import matplotlib.pyplot as plt
-import argparse
-
-def parseCommandLine():
-    parser = argparse.ArgumentParser(description=
-    '''Plot energy from bond trajectories.''',
-    epilog='Written by Alex Huth, 2020')
-    parser.add_argument('-fname', type=str, default='bond_trajectories.nc',
-                    help=''' provide filename to plot''')
-    optCmdLineArgs = parser.parse_args()
-    return optCmdLineArgs
-
-
-
-def main(args):
-
-    print('reading file')
-
-    filename=args.fname
-
-    with nc.Dataset(filename) as file:
-        rot    = file.variables['rotation'][:]
-        rrot    = file.variables['rel_rotation'][:]
-        ns  = file.variables['n_strain'][:]
-        nsr   = file.variables['n_strain_rate'][:]
-        day   = file.variables['day'][:]
-
-    print('rrotmin','rrotmax',np.min(nsr),np.max(nsr))
-
-    ud = np.unique(day)
-    dt = ud[1]-ud[0]
-
-    print('dt',dt)
-
-    fig = plt.figure(1)
-    ax = plt.subplot(111)
-    
-    for j in range(len(ud)):
-
-        #ENERGY STUFF
-        rot1 = rot[day == ud[j]]
-        rrot1 = rrot[day == ud[j]]
-        ns1 = ns[day == ud[j]]
-        nsr1 = nsr[day == ud[j]]
-        ud1 = day[day == ud[j]]
-
-
-        ax.plot(ud1, rot1,  color='k', label='rotation')
-        ax.plot(ud1, rrot1, color='c', label='relative rot', linestyle='dashed')
-        #ax.plot(ud1, ns1, color='b', label='normal strain', linestyle='dashed')
-        ax.plot(ud1, nsr1, color='g', label='normal strain rate', linestyle='dashed')
-
-
-    #ax.legend(loc="upper right")
-    chartBox = ax.get_position()
-    ax.set_position([chartBox.x0, chartBox.y0, chartBox.width*0.6, chartBox.height])
-    ax.legend(loc='upper center', bbox_to_anchor=(1.45, 0.8), shadow=True, ncol=1)
-    plt.xlabel('time (days)')
-    plt.ylabel('strains')
-
-    plt.show()
-
-print('Script complete')
-
-if __name__ == '__main__':
-    optCmdLineArgs=	parseCommandLine()
-    anim_running = True
-    main(optCmdLineArgs)
diff --git a/tests/plot_energy.py b/tests/plot_energy.py
deleted file mode 100755
index 13dc8ed..0000000
--- a/tests/plot_energy.py
+++ /dev/null
@@ -1,219 +0,0 @@
-#!/usr/bin/env python3
-
-from netCDF4 import Dataset
-import pdb
-import netCDF4 as nc
-import numpy as np
-import matplotlib
-import math
-import os
-matplotlib.use("tkagg")
-from pylab import *
-import matplotlib.pyplot as plt
-import argparse
-
-def parseCommandLine():
-    parser = argparse.ArgumentParser(description=
-    '''Plot energy from iceberg trajectories.''',
-    epilog='Written by Alex Huth, 2020')
-    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc',
-                    help=''' provide filename to plot''')
-    optCmdLineArgs = parser.parse_args()
-    return optCmdLineArgs
-
-
-
-def main(args):
-
-    print('reading file')
-
-    filename=args.fname
-
-    with nc.Dataset(filename) as file:
-        Ee    = file.variables['Ee'][:]
-        Ed    = file.variables['Ed'][:]
-        Eext  = file.variables['Eext'][:]
-        Eec   = file.variables['Ee_contact'][:]
-        Edc   = file.variables['Ed_contact'][:]
-        Efrac = file.variables['Efrac'][:]
-        day   = file.variables['day'][:]
-        vx    = file.variables['uvel_prev'][:]
-        vy    = file.variables['vvel_prev'][:]
-        mass  = file.variables['mass'][:]
-        x    = file.variables['lon'][:]
-        y    = file.variables['lat'][:]
-        vx2    = file.variables['uvel'][:]
-        vy2    = file.variables['vvel'][:]
-
-    crop=False
-    tc=1.0
-    if crop:
-        Ee = Ee[day<=tc]
-        Ed = Ed[day<=tc]
-        Eext=Eext[day<=tc]
-        Eec=Eec[day<=tc]
-        Edc=Edc[day<=tc]
-        Efrac=Efrac[day<=tc]
-        vx=vx[day<=tc]
-        vy=vy[day<=tc]
-        mass=mass[day<=tc]
-        x=x[day<=tc]
-        y=y[day<=tc]
-        vx2=vx2[day<=tc]
-        vy2=vy2[day<=tc]       
-        day=day[day<=tc]
-
-
-
-    # vx=np.copy(vx2); vy=np.copy(vy2)
-
-    ud = np.unique(day)
-    step0 = 0
-    dt = ud[1]-ud[0]
-
-    print('dt',dt)
-
-    tot_Ee = np.zeros(len(ud)-step0)
-    tot_Ed = np.zeros(len(ud)-step0)
-    tot_Eext = np.zeros(len(ud)-step0)
-    tot_Eec = np.zeros(len(ud)-step0)
-    tot_Edc = np.zeros(len(ud)-step0)
-    tot_Efrac = np.zeros(len(ud)-step0)
-    tot_Ek = np.zeros(len(ud)-step0)
-    tot_E  = np.zeros(len(ud)-step0)
-    tot_momentum_x = np.zeros(len(ud)-step0)
-    tot_momentum_y = np.zeros(len(ud)-step0)
-    tot_momentum = np.zeros(len(ud)-step0)
-    tot_momentum_x2 = np.zeros(len(ud)-step0)
-    tot_momentum_y2 = np.zeros(len(ud)-step0)
-    tot_momentum2 = np.zeros(len(ud)-step0)
-
-    # tot_vel_diff = np.zeros(len(ud)-step0)
-
-
-    #regular version
-    mom_x0 = mass[day == ud[step0]]*vx[day == ud[step0]]
-    mom_y0 = mass[day == ud[step0]]*vy[day == ud[step0]]
-    mom_x0_tot = np.sum(mom_x0); mom_y0_tot = np.sum(mom_y0)
-
-    #'uncorrected' version
-    mom_x02 = mom_x0; mom_y02=mom_y0
-    mom_x0_tot2=mom_x0_tot; mom_y0_tot2=mom_y0_tot
-
-    #if needed, 'correct' the regular version by changing the reference frame
-    #so that mom_x0_tot>0 and mom_y0_tot>0
-    dvx=0.0; dvy=0.0
-    if (mom_x0_tot==0):
-        print('changing x reference frame!')
-        dvx=0.01#e-8
-        mom_x0 = mass[day == ud[step0]]*(vx[day == ud[step0]]+dvx)
-        mom_x0_tot = np.sum(mom_x0)
-    if (mom_y0_tot==0):
-        print('changing y reference frame!')
-        dvy=0.01#e-8
-        mom_y0 = mass[day == ud[step0]]*(vy[day == ud[step0]]+dvy)
-        mom_y0_tot = np.sum(mom_y0)
-
-
-    for i in range(len(ud)-step0):
-
-        j=i+step0
-
-        #ENERGY STUFF
-        Ee1 = Ee[day == ud[j]]
-        Ed1 = Ed[day == ud[j]]
-        Eec1 = Eec[day == ud[j]]
-        Edc1 = Edc[day == ud[j]]
-        Efrac1 = Efrac[day == ud[j]]
-        Eext1 = Eext[day == ud[j]]
-        Ek1 = 0.5*mass[day == ud[j]]*(vx[day == ud[j]]**2+vy[day == ud[j]]**2)
-
-        tot_Ee[i] = np.sum(Ee1)
-        tot_Ed[i] = np.sum(Ed1)
-        tot_Eec[i] = np.sum(Eec1)
-        tot_Edc[i] = np.sum(Edc1)
-
-        tot_Efrac[i] = np.sum(Efrac1)
-        tot_Eext[i] = np.sum(Eext1)
-        tot_Ek[i] = np.sum(Ek1)
-
-        tot_E[i] = tot_Ee[i]+tot_Ed[i]+tot_Eec[i]+tot_Edc[i]+tot_Efrac[i]+tot_Eext[i]+tot_Ek[i]
-
-        #MOMENTUM STUFF
-
-        #--reg version, corrected--
-        mom_x = mass[day == ud[j]] * (vx[day == ud[j]]+dvx)
-        mom_y = mass[day == ud[j]] * (vy[day == ud[j]]+dvy)
-        tot_momentum_x[i] = (np.sum(mom_x)-mom_x0_tot)/mom_x0_tot
-        tot_momentum_y[i] = (np.sum(mom_y)-mom_y0_tot)/mom_y0_tot
-
-        #--reg version, uncorrected--
-        mom_x2 = mass[day == ud[j]] * (vx[day == ud[j]])
-        mom_y2 = mass[day == ud[j]] * (vy[day == ud[j]])
-        tot_momentum_x2[i] = (np.sum(mom_x2)-mom_x0_tot2)/mom_x0_tot2
-        tot_momentum_y2[i] = (np.sum(mom_y2)-mom_y0_tot2)/mom_y0_tot2
-
-        # ua =  vx[day == ud[j]]; va =  vy[day == ud[j]]
-        # ub = vx2[day == ud[j]]; vb = vy2[day == ud[j]]
-        # tot_vel_diff[i] = np.sum(sqrt((ua-ub)**2 + (va-vb)**2))
-
-
-    ud=ud[0:len(ud)-step0]
-
-    fig = plt.figure(1)
-    ax = plt.subplot(111)
-    ax.plot(ud, tot_E,  color='k', label='total')
-    ax.plot(ud, tot_Eext, color='c', label='external', linestyle='dashed')
-    ax.plot(ud, tot_Ee, color='b', label='elastic (bonded)', linestyle='dashed')
-    ax.plot(ud, tot_Ed, color='g', label='damping (bonded)', linestyle='dashed')
-    ax.plot(ud, tot_Eec, color='b', label='elastic (collision)', linestyle='dotted')
-    ax.plot(ud, tot_Edc, color='g', label='damping (collision)', linestyle='dotted')
-    ax.plot(ud, tot_Ek, color='r', label='kinetic', linestyle='dotted')
-    ax.plot(ud, tot_Efrac, color='m', label='dissipated fracture', linestyle='dotted')
-
-    print('min/max tot_E',np.min(tot_E),np.max(tot_E))
-
-    #ax.legend(loc="upper right")
-    chartBox = ax.get_position()
-    ax.set_position([chartBox.x0, chartBox.y0, chartBox.width*0.6, chartBox.height])
-    ax.legend(loc='upper center', bbox_to_anchor=(1.45, 0.8), shadow=True, ncol=1)
-    plt.xlabel('time (days)')
-    plt.ylabel('energy (J)')
-    #axes=plt.gca()
-    #axes.set_ylim([-1.e-14,1.e-14])
-
-    fig2 = plt.figure(2)
-    ax = plt.subplot(111)
-    ax.plot(ud[step0:], tot_momentum_x[step0:],  color='k', label='x momentum')
-    ax.plot(ud[step0:], tot_momentum_x2[step0:],  color='y', label='x momentum 2', linestyle='dashed')
-    chartBox = ax.get_position()
-    ax.set_position([chartBox.x0, chartBox.y0, chartBox.width*0.6, chartBox.height])
-    ax.legend(loc='upper center', bbox_to_anchor=(1.45, 0.8), shadow=True, ncol=1)
-
-
-    fig3 = plt.figure(3)
-    ax = plt.subplot(111)
-    ax.plot(ud[step0:], tot_momentum_y[step0:],  color='k', label='y momentum')
-    if (abs(mom_y0_tot2)>0):
-        ax.plot(ud[step0:], tot_momentum_y2[step0:],  color='y', label='y momentum 2', linestyle='dashed')
-    chartBox = ax.get_position()
-    ax.set_position([chartBox.x0, chartBox.y0, chartBox.width*0.6, chartBox.height])
-    ax.legend(loc='upper center', bbox_to_anchor=(1.45, 0.8), shadow=True, ncol=1)
-
-
-    # fig4 = plt.figure(4)
-    # ax = plt.subplot(111)
-    # ax.plot(ud[step0:], tot_vel_diff[step0:],  color='k', label='vel diff')
-    # chartBox = ax.get_position()
-    # ax.set_position([chartBox.x0, chartBox.y0, chartBox.width*0.6, chartBox.height])
-    # ax.legend(loc='upper center', bbox_to_anchor=(1.45, 0.8), shadow=True, ncol=1)
-
-
-    plt.show()
-
-print('Script complete')
-
-if __name__ == '__main__':
-    optCmdLineArgs=	parseCommandLine()
-    anim_running = True
-    main(optCmdLineArgs)

From dd55ccaebbaee8adc5c4928d1030d1d663995382 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Thu, 29 Dec 2022 13:50:26 -0500
Subject: [PATCH 335/361] tests/collision_tests/makeberg used to be dependent
 on Alon's scripts in tests/Iceberg_repository, but now moved those few
 scripts directly to tests/collision_tests/makeberg and deleted
 tests/Iceberg_repository. This deleted directory was Alon's KID/ice shelf
 tests on the ISOMIP geometry, which are outdated (e.g. they may rely on
 specific branches of the coupler and SIS2, and job scripts are not written
 for slurm)

---
 tests/Iceberg_repository/.gitignore           |    3 -
 .../Bergs/Layer/Empty_run/MOM_input           |    1 -
 .../Bergs/Layer/Empty_run/MOM_override        |   73 -
 .../Bergs/Layer/Empty_run/SIS_input           |    1 -
 .../Bergs/Layer/Empty_run/SIS_override        |    8 -
 .../Bergs/Layer/Empty_run/clean_MOM.sh        |    1 -
 .../Bergs/Layer/Empty_run/data_table          |    1 -
 .../Bergs/Layer/Empty_run/diag_table          |    1 -
 .../Bergs/Layer/Empty_run/field_table         |    1 -
 .../Bergs/Layer/Empty_run/input.nml           |  140 --
 .../Bergs/Layer/Empty_run/output              |   16 -
 .../Bergs/Layer/Empty_run/run_script.sh       |    1 -
 .../Bergs/Layer/Empty_run/submit_to_queue     |   25 -
 .../Bergs/Layer/Moving_berg_Bond/MOM_input    |    1 -
 .../Bergs/Layer/Moving_berg_Bond/MOM_override |   71 -
 .../Bergs/Layer/Moving_berg_Bond/README       |    4 -
 .../Bergs/Layer/Moving_berg_Bond/SIS_input    |    1 -
 .../Bergs/Layer/Moving_berg_Bond/SIS_override |    9 -
 .../Bergs/Layer/Moving_berg_Bond/clean_MOM.sh |    1 -
 .../Bergs/Layer/Moving_berg_Bond/data_table   |    1 -
 .../Bergs/Layer/Moving_berg_Bond/diag_table   |    1 -
 .../Bergs/Layer/Moving_berg_Bond/field_table  |    1 -
 .../Bergs/Layer/Moving_berg_Bond/input.nml    |  140 --
 .../Layer/Moving_berg_Bond/run_script.sh      |    1 -
 .../Layer/Moving_berg_Bond/submit_to_queue    |   25 -
 .../Bergs/Layer/Moving_berg_Collapse/README   |    7 -
 .../Layer/Moving_berg_Collapse/input.nml      |  140 --
 .../Bergs/Layer/Moving_berg_drift/MOM_input   |    1 -
 .../Layer/Moving_berg_drift/MOM_override      |   71 -
 .../Bergs/Layer/Moving_berg_drift/README      |    3 -
 .../Bergs/Layer/Moving_berg_drift/SIS_input   |    1 -
 .../Layer/Moving_berg_drift/SIS_override      |    9 -
 .../Layer/Moving_berg_drift/clean_MOM.sh      |    1 -
 .../Bergs/Layer/Moving_berg_drift/data_table  |    1 -
 .../Bergs/Layer/Moving_berg_drift/diag_table  |    1 -
 .../Bergs/Layer/Moving_berg_drift/field_table |    1 -
 .../Bergs/Layer/Moving_berg_drift/input.nml   |  140 --
 .../Layer/Moving_berg_drift/run_script.sh     |    1 -
 .../Layer/Moving_berg_drift/submit_to_queue   |   25 -
 .../Bergs/Layer/Moving_berg_fixed/MOM_input   |    1 -
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 rename tests/{Iceberg_repository => collision_tests/makeberg}/hexagon_area.py (96%)
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diff --git a/tests/Iceberg_repository/.gitignore b/tests/Iceberg_repository/.gitignore
deleted file mode 100644
index 3e14065..0000000
--- a/tests/Iceberg_repository/.gitignore
+++ /dev/null
@@ -1,3 +0,0 @@
-*~
-*.out
-*.nc
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/MOM_input b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/MOM_input
deleted file mode 120000
index a756962..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/MOM_input
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/MOM_input
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/MOM_override b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/MOM_override
deleted file mode 100644
index 45aaab7..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/MOM_override
+++ /dev/null
@@ -1,73 +0,0 @@
-! Blank file in which we can put "overrides" for parameters
-
-!TPY params
-#override NK = 72
-#override NKML = 4
-
-! TIME STEP
-!#override DT = 720
-!#override DT_THERM = 720
-#override DT = 10
-#override DT_THERM = 10
-#override DT_FORCING = 10
-
-! MIXING
-#override SMAGORINSKY_KH = False
-#override BIHARMONIC = False
-#override KH = 6.0  ! back. horiz. visc.
-#override KHTR = 1.0    ! back. horiz. diff.
-#override KD = 5.0E-5     ! back. diapycnal diff.
-#override KV = 1.0E-3     ! back. diapycnal visc.
-
-!WARM IC
-#override ISOMIP_T_SUR = -1.9
-#override ISOMIP_S_SUR = 33.8
-#override ISOMIP_T_BOT = 1.0
-#override ISOMIP_S_BOT = 34.7
-
-! ice shelf
-#override ICE_SHELF = False                !   [Boolean] default = False
-#override SHELF_THERMO = True
-#override SHELF_THREE_EQN = True
-#override SHELF_3EQ_GAMMA = False
-#override UTIDE = 0.01
-!SHELF_S_ROOT = True
-!#override USE_HMIX_SFC_PROP = True
-!#override HMIX_SFC_PROP = 10.
-
-! FRAZIL  - making sure sea ice does not form
-#override FRAZIL = False
-#override PRESSURE_DEPENDENT_FRAZIL = False
-
-! MIXED LAYER
-#override BULKMIXEDLAYER = True
-#override BULK_RI_ML = 0.25
-#override MIXEDLAYER_RESTRAT = True
-#override HMIX_MIN = 2.0
-!#override KV_TBL_MIN = 1.0E-2
-#override HTBL_SHELF_MIN = 2.0
-#override BOUND_SALINITY = True
- 
-! SHEAR MIXING
-#override USE_JACKSON_PARAM = True
-#override RINO_CRIT = 0.25
-!#override KD_KAPPA_SHEAR_0 = 1.0E-2
-
-! SPONGE
-#override SPONGE = True
-ISOMIP_SPONGE_FILE = "3D_LAYER_WARM_TPY_IC.nc"
-#override ISOMIP_TNUDG = 0.1
-!#override ISOMIP_SPONGE_TEMP_OFFSET=0.1
-
-
-! PASSIVE TRACERS
-USE_ISOMIP_TRACER = False
-
-! Simulation time
-#override DAYMAX = 730
-
-!#override FIT_SALINITY = False
-
-!Passing Iceberg field to ocean
-ICEBERGS_APPLY_RIGID_BOUNDARY=True !Different boundary condition is used under ice shelves
-ALLOW_ICEBERG_FLUX_DIAGNOSTICS=True
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/SIS_input b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/SIS_input
deleted file mode 120000
index ad3cd99..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/SIS_input
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/SIS_input
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/SIS_override b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/SIS_override
deleted file mode 100644
index fc641d7..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/SIS_override
+++ /dev/null
@@ -1,8 +0,0 @@
-# Blank file in which we can put "overrides" for parameters
-DO_ICEBERGS =True              !   If true, use the icebergs module.
-
-!Time Stepping
-!#override DT_FORCING = 10.0              !   [s] default = 0.0
-!#override DT_RHEOLOGY = 10.0             ! The sub-cycling time step, in s, for iterating
-
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/clean_MOM.sh b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/clean_MOM.sh
deleted file mode 120000
index c5370af..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/clean_MOM.sh
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/clean_MOM.sh
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/data_table b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/data_table
deleted file mode 120000
index 5b82b3c..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/data_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/data_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/diag_table b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/diag_table
deleted file mode 120000
index cff65fe..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/diag_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/diag_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/field_table b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/field_table
deleted file mode 120000
index b5ea991..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/field_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/field_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/input.nml b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/input.nml
deleted file mode 100644
index 7b69203..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/input.nml
+++ /dev/null
@@ -1,140 +0,0 @@
- &MOM_input_nml
-        output_directory = './',
-        input_filename = 'r'
-        restart_input_dir = 'INPUT/',
-        restart_output_dir = 'RESTART/',
-        parameter_filename = 'MOM_input',
-                             'MOM_override' /
-
- &SIS_input_nml
-        output_directory = './',
-        input_filename = 'r'
-        restart_input_dir = 'INPUT/',
-        restart_output_dir = 'RESTART/',
-        parameter_filename = 'SIS_input',
-                             'SIS_override' /
-
- &diag_manager_nml
-         max_output_fields=1000
-         max_input_fields=1000
-         max_num_axis_sets=1000
-	 flush_nc_files=.true.
-         max_files=1000
-         max_axes=2000
- /
-
- &coupler_nml
-            months = 0,
-            days   = 60,
-            current_date = 1,1,1,0,0,0,
-            hours = 0,
-            minutes =0, 
-            seconds = 0
-            calendar = 'NOLEAP',
-            dt_cpld  = 10.0,
-            dt_atmos = 10.0,
-            do_atmos = .false.,
-            do_land = .false.,
-            do_ice = .true.,
-            do_ocean = .true.,
-            atmos_npes = 0,
-            ocean_npes = 0,
-            concurrent = .false.
-            use_lag_fluxes=.false. /
-
-
- &icebergs_nml
-    verbose=.false.,
-    verbose_hrs=240,
-    traj_sample_hrs=24000,
-    ignore_ij_restart=.true.
-    halo=2,
-    save_short_traj=.true.
-    debug=.false.,
-    really_debug=.false.,
-    use_slow_find=.true.,
-    add_weight_to_ocean=.true.,
-    passive_mode=.false.,
-    Static_icebergs=.False.,
-    ignore_missing_restart_bergs=.false.,
-    generate_test_icebergs=.false.,
-    speed_limit=0.,
-    use_roundoff_fix=.true.,
-    make_calving_reproduce=.false.,
-    Runge_not_Verlet=.false.,
-    iceberg_bonds_on=.true.,
-    critical_interaction_damping_on=.true.,
-    use_new_predictive_corrective=.true.,
-    interactive_icebergs_on=.true.
-    halo_debugging=.false.
-    spring_coef=0.00001
-    distribution=0.0, 0.99, 0.0, 0.00, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11,
-    hexagonal_icebergs=.true.
-    allow_bergs_to_roll=.true.
-    set_melt_rates_to_zero=.false.
-    use_roundoff_fix=.false.
-    grid_is_latlon=.false.
-    grid_is_regular=.true.
-    initial_orientation=-0.
-    rotate_icebergs_for_mass_spreading=.false.
-    lat_ref=-75.0
-    u_override=0.00
-    v_override=0.00
-    override_iceberg_velocities=.false.
-    add_iceberg_thickness_to_SSH=.false.
-    max_bonds=6
-    Iceberg_melt_without_decay=.true.
-    melt_icebergs_as_ice_shelf=.true.
-    Use_three_equation_model=.true.
-    find_melt_using_spread_mass=.true.
-    use_mixed_layer_salinity_for_thermo=.true.
-    pass_fields_to_ocean_model=.true.
-    rho_bergs=918.0
-    utide_icebergs=0.01
-    ustar_icebergs_bg=0.000
-    cdrag_icebergs =0.0025
-    const_gamma=.false.
-    Gamma_T_3EQ=0.22
-    ignore_traj=.False.
-    read_ocean_depth_from_file=.true.
-    apply_thickness_cutoff_to_bergs_melt=.true.
-    apply_thickness_cutoff_to_gridded_melt=.true.
-    melt_cutoff=10.
-    read_old_restarts=.false.
-    internal_bergs_for_drag=.true.
-    use_mixed_melting=.true.
- &data_override_nml
-         /
-
- &fms_io_nml
-         fms_netcdf_restart=.true.
-         threading_read='multi'
- /
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC' /
-
- &ice_albedo_nml
-      t_range = 10. /
-
- &ice_model_nml
-           /
-
- &monin_obukhov_nml
-            neutral = .true. /
-
- &ocean_albedo_nml
-      ocean_albedo_option = 5 /
-
- &sat_vapor_pres_nml
-      construct_table_wrt_liq = .true.,
-      construct_table_wrt_liq_and_ice = .true. /
-
- &xgrid_nml
-            make_exchange_reproduce = .false.
-            interp_method = 'second_order' /
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/output b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/output
deleted file mode 100644
index 981abd1..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/output
+++ /dev/null
@@ -1,16 +0,0 @@
- 
-***NOTICE TO DDT USERS*** 
-With version 4.0 (and later) of DDT, the procedure for memory debugging has 
-changed.  You no longer need to compile with the ddtmem-cc, ddtmem-CC, 
-and ddtmem-ftn scripts.  Rather, just load the ddt-memdebug module (in 
-addition to this module) and compile as you normally would (with cc, 
-CC and/or ftn).  The appropriate memory debugging libraries will be 
-linked automatically. 
- 
-Please direct questions to help@olcf.ornl.gov 
- 
-python_scipy(3):ERROR:105: Unable to locate a modulefile for 'python_scipy/0.17.0'
-python_scipy(3):ERROR:105: Unable to locate a modulefile for 'python_scipy/0.17.0'
-python_scipy(3):ERROR:105: Unable to locate a modulefile for 'python_scipy/0.17.0'
-aprun: file ../../../../../build/intel/ice_ocean_SIS2/repro/old_executable/MOM6 not found
-aprun: Exiting due to errors. Application aborted
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/run_script.sh b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/run_script.sh
deleted file mode 120000
index 2a081b9..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/run_script.sh
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/run_script.sh
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/submit_to_queue b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/submit_to_queue
deleted file mode 100644
index d35f1b8..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Empty_run/submit_to_queue
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/bin/csh -f
-#PBS -r y                                                              #This job is restartable
-#PBS -j oe                                                             #STDOUT and STDERR are in the same file, specified below in the '-o' option
-#PBS -q batch                                                          #Do not change this - it tells your job where to run
-#PBS -S /bin/sh                                                        #Do not change this - it keeps your job from issuing a false alarm
-#PBS -E                                                                #Do not change this - it gives your job more and more useful Moab environment variables
-#PBS -N  Bergs_Empty_Run                                               #Job Name:             You may want to change this to reflect your job's purpose or relation to an experiment
-#PBS -l partition=c3
-#PBS -l size=4                                                        #You will need to change this to reflect your job's core requirements - 24 is the current core increment.
-#PBS -l walltime=16:00:00                                              #You MUST change this to reflect your job's expected run time, including copy time
-#PBS -m bea                                                            #Email options: You may want to change this to reduce your incoming email stream
-
-######################################################################################################################
-#
-#  Gaea c1ms batch skeleton version 0.9
-#  
-#  0.9 - Initial version - 20110906 - Daniel Gall - Daniel.Gall@noaa.gov
-#
-######################################################################################################################
-
-#Source the system initialization scripts (but not the user's so as to avoid interactive settings that can poison us)
-source /etc/csh.cshrc
-
-#Run the experiment
-aprun -n 128 ../../../../../build/intel/ice_ocean_SIS2/repro/MOM6
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/MOM_input b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/MOM_input
deleted file mode 120000
index a756962..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/MOM_input
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/MOM_input
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/MOM_override b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/MOM_override
deleted file mode 100644
index 1fec204..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/MOM_override
+++ /dev/null
@@ -1,71 +0,0 @@
-! Blank file in which we can put "overrides" for parameters
-
-!TPY params
-#override NK = 72
-#override NKML = 4
-
-! TIME STEP
-#override DT = 10
-#override DT_THERM = 10
-#override DT_FORCING = 10
-
-! MIXING
-#override SMAGORINSKY_KH = False
-#override BIHARMONIC = False
-#override KH = 6.0  ! back. horiz. visc.
-#override KHTR = 1.0    ! back. horiz. diff.
-#override KD = 5.0E-5     ! back. diapycnal diff.
-#override KV = 1.0E-3     ! back. diapycnal visc.
-
-!WARM IC
-#override ISOMIP_T_SUR = -1.9
-#override ISOMIP_S_SUR = 33.8
-#override ISOMIP_T_BOT = 1.0
-#override ISOMIP_S_BOT = 34.7
-
-! ice shelf
-#override ICE_SHELF = False                !   [Boolean] default = False
-#override SHELF_THERMO = True
-#override SHELF_THREE_EQN = True
-#override SHELF_3EQ_GAMMA = False
-#override UTIDE = 0.01
-!SHELF_S_ROOT = True
-!#override USE_HMIX_SFC_PROP = True
-!#override HMIX_SFC_PROP = 10.
-
-! FRAZIL  - making sure sea ice does not form
-#override FRAZIL = False
-#override PRESSURE_DEPENDENT_FRAZIL = False
-
-! MIXED LAYER
-#override BULKMIXEDLAYER = True
-#override BULK_RI_ML = 0.25
-#override MIXEDLAYER_RESTRAT = True
-#override HMIX_MIN = 2.0
-!#override KV_TBL_MIN = 1.0E-2
-#override HTBL_SHELF_MIN = 2.0
-#override BOUND_SALINITY = True
- 
-! SHEAR MIXING
-#override USE_JACKSON_PARAM = True
-#override RINO_CRIT = 0.25
-!#override KD_KAPPA_SHEAR_0 = 1.0E-2
-
-! SPONGE
-#override SPONGE = True
-ISOMIP_SPONGE_FILE = "3D_LAYER_WARM_TPY_IC.nc"
-#override ISOMIP_TNUDG = 0.1
-!#override ISOMIP_SPONGE_TEMP_OFFSET=0.1
-
-
-! PASSIVE TRACERS
-USE_ISOMIP_TRACER = False
-
-! Simulation time
-#override DAYMAX = 730
-
-!#override FIT_SALINITY = False
-
-!Passing Iceberg field to ocean
-ICEBERGS_APPLY_RIGID_BOUNDARY=True !Different boundary condition is used under ice shelves
-ALLOW_ICEBERG_FLUX_DIAGNOSTICS=True
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/README b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/README
deleted file mode 100644
index 0972054..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/README
+++ /dev/null
@@ -1,4 +0,0 @@
-A tabular icebergs breaks away from the ice shelf. The tabular icebergs is bonded together by numeric bonds. Icebergs are allowed to evolve freely
-
-Works best when started from restart file created by Static_berg simulation.
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/SIS_input b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/SIS_input
deleted file mode 120000
index ad3cd99..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/SIS_input
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/SIS_input
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/SIS_override b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/SIS_override
deleted file mode 100644
index 605ca84..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/SIS_override
+++ /dev/null
@@ -1,9 +0,0 @@
-# Blank file in which we can put "overrides" for parameters
-DO_ICEBERGS =True              !   If true, use the icebergs module.
-
-!Time Stepping
-#override DT_FORCING = 10.0              !   [s] default = 0.0
-#override DT_RHEOLOGY = 10.0             ! The sub-cycling time step, in s, for iterating
-#override DT_ICE_DYNAMICS = 10.0 
-
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/clean_MOM.sh b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/clean_MOM.sh
deleted file mode 120000
index c5370af..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/clean_MOM.sh
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/clean_MOM.sh
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/data_table b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/data_table
deleted file mode 120000
index 5b82b3c..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/data_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/data_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/diag_table b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/diag_table
deleted file mode 120000
index cff65fe..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/diag_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/diag_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/field_table b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/field_table
deleted file mode 120000
index b5ea991..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/field_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/field_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/input.nml b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/input.nml
deleted file mode 100644
index 7b69203..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/input.nml
+++ /dev/null
@@ -1,140 +0,0 @@
- &MOM_input_nml
-        output_directory = './',
-        input_filename = 'r'
-        restart_input_dir = 'INPUT/',
-        restart_output_dir = 'RESTART/',
-        parameter_filename = 'MOM_input',
-                             'MOM_override' /
-
- &SIS_input_nml
-        output_directory = './',
-        input_filename = 'r'
-        restart_input_dir = 'INPUT/',
-        restart_output_dir = 'RESTART/',
-        parameter_filename = 'SIS_input',
-                             'SIS_override' /
-
- &diag_manager_nml
-         max_output_fields=1000
-         max_input_fields=1000
-         max_num_axis_sets=1000
-	 flush_nc_files=.true.
-         max_files=1000
-         max_axes=2000
- /
-
- &coupler_nml
-            months = 0,
-            days   = 60,
-            current_date = 1,1,1,0,0,0,
-            hours = 0,
-            minutes =0, 
-            seconds = 0
-            calendar = 'NOLEAP',
-            dt_cpld  = 10.0,
-            dt_atmos = 10.0,
-            do_atmos = .false.,
-            do_land = .false.,
-            do_ice = .true.,
-            do_ocean = .true.,
-            atmos_npes = 0,
-            ocean_npes = 0,
-            concurrent = .false.
-            use_lag_fluxes=.false. /
-
-
- &icebergs_nml
-    verbose=.false.,
-    verbose_hrs=240,
-    traj_sample_hrs=24000,
-    ignore_ij_restart=.true.
-    halo=2,
-    save_short_traj=.true.
-    debug=.false.,
-    really_debug=.false.,
-    use_slow_find=.true.,
-    add_weight_to_ocean=.true.,
-    passive_mode=.false.,
-    Static_icebergs=.False.,
-    ignore_missing_restart_bergs=.false.,
-    generate_test_icebergs=.false.,
-    speed_limit=0.,
-    use_roundoff_fix=.true.,
-    make_calving_reproduce=.false.,
-    Runge_not_Verlet=.false.,
-    iceberg_bonds_on=.true.,
-    critical_interaction_damping_on=.true.,
-    use_new_predictive_corrective=.true.,
-    interactive_icebergs_on=.true.
-    halo_debugging=.false.
-    spring_coef=0.00001
-    distribution=0.0, 0.99, 0.0, 0.00, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11,
-    hexagonal_icebergs=.true.
-    allow_bergs_to_roll=.true.
-    set_melt_rates_to_zero=.false.
-    use_roundoff_fix=.false.
-    grid_is_latlon=.false.
-    grid_is_regular=.true.
-    initial_orientation=-0.
-    rotate_icebergs_for_mass_spreading=.false.
-    lat_ref=-75.0
-    u_override=0.00
-    v_override=0.00
-    override_iceberg_velocities=.false.
-    add_iceberg_thickness_to_SSH=.false.
-    max_bonds=6
-    Iceberg_melt_without_decay=.true.
-    melt_icebergs_as_ice_shelf=.true.
-    Use_three_equation_model=.true.
-    find_melt_using_spread_mass=.true.
-    use_mixed_layer_salinity_for_thermo=.true.
-    pass_fields_to_ocean_model=.true.
-    rho_bergs=918.0
-    utide_icebergs=0.01
-    ustar_icebergs_bg=0.000
-    cdrag_icebergs =0.0025
-    const_gamma=.false.
-    Gamma_T_3EQ=0.22
-    ignore_traj=.False.
-    read_ocean_depth_from_file=.true.
-    apply_thickness_cutoff_to_bergs_melt=.true.
-    apply_thickness_cutoff_to_gridded_melt=.true.
-    melt_cutoff=10.
-    read_old_restarts=.false.
-    internal_bergs_for_drag=.true.
-    use_mixed_melting=.true.
- &data_override_nml
-         /
-
- &fms_io_nml
-         fms_netcdf_restart=.true.
-         threading_read='multi'
- /
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC' /
-
- &ice_albedo_nml
-      t_range = 10. /
-
- &ice_model_nml
-           /
-
- &monin_obukhov_nml
-            neutral = .true. /
-
- &ocean_albedo_nml
-      ocean_albedo_option = 5 /
-
- &sat_vapor_pres_nml
-      construct_table_wrt_liq = .true.,
-      construct_table_wrt_liq_and_ice = .true. /
-
- &xgrid_nml
-            make_exchange_reproduce = .false.
-            interp_method = 'second_order' /
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/run_script.sh b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/run_script.sh
deleted file mode 120000
index 2a081b9..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/run_script.sh
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/run_script.sh
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/submit_to_queue b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/submit_to_queue
deleted file mode 100644
index cc5b649..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Bond/submit_to_queue
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/bin/csh -f
-#PBS -r y                                                              #This job is restartable
-#PBS -j oe                                                             #STDOUT and STDERR are in the same file, specified below in the '-o' option
-#PBS -q batch                                                          #Do not change this - it tells your job where to run
-#PBS -S /bin/sh                                                        #Do not change this - it keeps your job from issuing a false alarm
-#PBS -E                                                                #Do not change this - it gives your job more and more useful Moab environment variables
-#PBS -N  Bergs_Bond_layer                                              #Job Name:             You may want to change this to reflect your job's purpose or relation to an experiment
-#PBS -l partition=c3
-#PBS -l size=4                                                        #You will need to change this to reflect your job's core requirements - 24 is the current core increment.
-#PBS -l walltime=16:00:00                                              #You MUST change this to reflect your job's expected run time, including copy time
-#PBS -m bea                                                            #Email options: You may want to change this to reduce your incoming email stream
-
-######################################################################################################################
-#
-#  Gaea c1ms batch skeleton version 0.9
-#  
-#  0.9 - Initial version - 20110906 - Daniel Gall - Daniel.Gall@noaa.gov
-#
-######################################################################################################################
-
-#Source the system initialization scripts (but not the user's so as to avoid interactive settings that can poison us)
-source /etc/csh.cshrc
-
-#Run the experiment
-aprun -n 128 ../../../../../build/intel/ice_ocean_SIS2/repro/MOM6
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Collapse/README b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Collapse/README
deleted file mode 100644
index ac458b8..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Collapse/README
+++ /dev/null
@@ -1,7 +0,0 @@
-A tabular icebergs breaks away from the ice shelf. Smaller pieces also break away, which allows the tabular iceberg to move more easily. The tabular icebergs is bonded together by numeric bonds. Icebergs are allowed to evolve freely
-
-Works best when started from restart file created by Static_berg simulation.
-
-Experimental setup is exactly the same as Moving_berg_Bond simulation, except that when icebergs.res is created, use the command line flag:
-./initialize_bergs_in_pattern.py -Make_icebergs_non_static_later=True
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Collapse/input.nml b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Collapse/input.nml
deleted file mode 100644
index 7b69203..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_Collapse/input.nml
+++ /dev/null
@@ -1,140 +0,0 @@
- &MOM_input_nml
-        output_directory = './',
-        input_filename = 'r'
-        restart_input_dir = 'INPUT/',
-        restart_output_dir = 'RESTART/',
-        parameter_filename = 'MOM_input',
-                             'MOM_override' /
-
- &SIS_input_nml
-        output_directory = './',
-        input_filename = 'r'
-        restart_input_dir = 'INPUT/',
-        restart_output_dir = 'RESTART/',
-        parameter_filename = 'SIS_input',
-                             'SIS_override' /
-
- &diag_manager_nml
-         max_output_fields=1000
-         max_input_fields=1000
-         max_num_axis_sets=1000
-	 flush_nc_files=.true.
-         max_files=1000
-         max_axes=2000
- /
-
- &coupler_nml
-            months = 0,
-            days   = 60,
-            current_date = 1,1,1,0,0,0,
-            hours = 0,
-            minutes =0, 
-            seconds = 0
-            calendar = 'NOLEAP',
-            dt_cpld  = 10.0,
-            dt_atmos = 10.0,
-            do_atmos = .false.,
-            do_land = .false.,
-            do_ice = .true.,
-            do_ocean = .true.,
-            atmos_npes = 0,
-            ocean_npes = 0,
-            concurrent = .false.
-            use_lag_fluxes=.false. /
-
-
- &icebergs_nml
-    verbose=.false.,
-    verbose_hrs=240,
-    traj_sample_hrs=24000,
-    ignore_ij_restart=.true.
-    halo=2,
-    save_short_traj=.true.
-    debug=.false.,
-    really_debug=.false.,
-    use_slow_find=.true.,
-    add_weight_to_ocean=.true.,
-    passive_mode=.false.,
-    Static_icebergs=.False.,
-    ignore_missing_restart_bergs=.false.,
-    generate_test_icebergs=.false.,
-    speed_limit=0.,
-    use_roundoff_fix=.true.,
-    make_calving_reproduce=.false.,
-    Runge_not_Verlet=.false.,
-    iceberg_bonds_on=.true.,
-    critical_interaction_damping_on=.true.,
-    use_new_predictive_corrective=.true.,
-    interactive_icebergs_on=.true.
-    halo_debugging=.false.
-    spring_coef=0.00001
-    distribution=0.0, 0.99, 0.0, 0.00, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11,
-    hexagonal_icebergs=.true.
-    allow_bergs_to_roll=.true.
-    set_melt_rates_to_zero=.false.
-    use_roundoff_fix=.false.
-    grid_is_latlon=.false.
-    grid_is_regular=.true.
-    initial_orientation=-0.
-    rotate_icebergs_for_mass_spreading=.false.
-    lat_ref=-75.0
-    u_override=0.00
-    v_override=0.00
-    override_iceberg_velocities=.false.
-    add_iceberg_thickness_to_SSH=.false.
-    max_bonds=6
-    Iceberg_melt_without_decay=.true.
-    melt_icebergs_as_ice_shelf=.true.
-    Use_three_equation_model=.true.
-    find_melt_using_spread_mass=.true.
-    use_mixed_layer_salinity_for_thermo=.true.
-    pass_fields_to_ocean_model=.true.
-    rho_bergs=918.0
-    utide_icebergs=0.01
-    ustar_icebergs_bg=0.000
-    cdrag_icebergs =0.0025
-    const_gamma=.false.
-    Gamma_T_3EQ=0.22
-    ignore_traj=.False.
-    read_ocean_depth_from_file=.true.
-    apply_thickness_cutoff_to_bergs_melt=.true.
-    apply_thickness_cutoff_to_gridded_melt=.true.
-    melt_cutoff=10.
-    read_old_restarts=.false.
-    internal_bergs_for_drag=.true.
-    use_mixed_melting=.true.
- &data_override_nml
-         /
-
- &fms_io_nml
-         fms_netcdf_restart=.true.
-         threading_read='multi'
- /
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC' /
-
- &ice_albedo_nml
-      t_range = 10. /
-
- &ice_model_nml
-           /
-
- &monin_obukhov_nml
-            neutral = .true. /
-
- &ocean_albedo_nml
-      ocean_albedo_option = 5 /
-
- &sat_vapor_pres_nml
-      construct_table_wrt_liq = .true.,
-      construct_table_wrt_liq_and_ice = .true. /
-
- &xgrid_nml
-            make_exchange_reproduce = .false.
-            interp_method = 'second_order' /
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/MOM_input b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/MOM_input
deleted file mode 120000
index a756962..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/MOM_input
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/MOM_input
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/MOM_override b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/MOM_override
deleted file mode 100644
index 1fec204..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/MOM_override
+++ /dev/null
@@ -1,71 +0,0 @@
-! Blank file in which we can put "overrides" for parameters
-
-!TPY params
-#override NK = 72
-#override NKML = 4
-
-! TIME STEP
-#override DT = 10
-#override DT_THERM = 10
-#override DT_FORCING = 10
-
-! MIXING
-#override SMAGORINSKY_KH = False
-#override BIHARMONIC = False
-#override KH = 6.0  ! back. horiz. visc.
-#override KHTR = 1.0    ! back. horiz. diff.
-#override KD = 5.0E-5     ! back. diapycnal diff.
-#override KV = 1.0E-3     ! back. diapycnal visc.
-
-!WARM IC
-#override ISOMIP_T_SUR = -1.9
-#override ISOMIP_S_SUR = 33.8
-#override ISOMIP_T_BOT = 1.0
-#override ISOMIP_S_BOT = 34.7
-
-! ice shelf
-#override ICE_SHELF = False                !   [Boolean] default = False
-#override SHELF_THERMO = True
-#override SHELF_THREE_EQN = True
-#override SHELF_3EQ_GAMMA = False
-#override UTIDE = 0.01
-!SHELF_S_ROOT = True
-!#override USE_HMIX_SFC_PROP = True
-!#override HMIX_SFC_PROP = 10.
-
-! FRAZIL  - making sure sea ice does not form
-#override FRAZIL = False
-#override PRESSURE_DEPENDENT_FRAZIL = False
-
-! MIXED LAYER
-#override BULKMIXEDLAYER = True
-#override BULK_RI_ML = 0.25
-#override MIXEDLAYER_RESTRAT = True
-#override HMIX_MIN = 2.0
-!#override KV_TBL_MIN = 1.0E-2
-#override HTBL_SHELF_MIN = 2.0
-#override BOUND_SALINITY = True
- 
-! SHEAR MIXING
-#override USE_JACKSON_PARAM = True
-#override RINO_CRIT = 0.25
-!#override KD_KAPPA_SHEAR_0 = 1.0E-2
-
-! SPONGE
-#override SPONGE = True
-ISOMIP_SPONGE_FILE = "3D_LAYER_WARM_TPY_IC.nc"
-#override ISOMIP_TNUDG = 0.1
-!#override ISOMIP_SPONGE_TEMP_OFFSET=0.1
-
-
-! PASSIVE TRACERS
-USE_ISOMIP_TRACER = False
-
-! Simulation time
-#override DAYMAX = 730
-
-!#override FIT_SALINITY = False
-
-!Passing Iceberg field to ocean
-ICEBERGS_APPLY_RIGID_BOUNDARY=True !Different boundary condition is used under ice shelves
-ALLOW_ICEBERG_FLUX_DIAGNOSTICS=True
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/README b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/README
deleted file mode 100644
index b4eb12b..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/README
+++ /dev/null
@@ -1,3 +0,0 @@
-A piece of the ice shelf breaks off. The elements are not bonded together, so they move freely away. However, they do interact with one another.
-
-Works best when started from restart file created by Static_berg simulation.
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/SIS_input b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/SIS_input
deleted file mode 120000
index ad3cd99..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/SIS_input
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/SIS_input
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/SIS_override b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/SIS_override
deleted file mode 100644
index 605ca84..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/SIS_override
+++ /dev/null
@@ -1,9 +0,0 @@
-# Blank file in which we can put "overrides" for parameters
-DO_ICEBERGS =True              !   If true, use the icebergs module.
-
-!Time Stepping
-#override DT_FORCING = 10.0              !   [s] default = 0.0
-#override DT_RHEOLOGY = 10.0             ! The sub-cycling time step, in s, for iterating
-#override DT_ICE_DYNAMICS = 10.0 
-
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/clean_MOM.sh b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/clean_MOM.sh
deleted file mode 120000
index c5370af..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/clean_MOM.sh
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/clean_MOM.sh
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/data_table b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/data_table
deleted file mode 120000
index 5b82b3c..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/data_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/data_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/diag_table b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/diag_table
deleted file mode 120000
index cff65fe..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/diag_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/diag_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/field_table b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/field_table
deleted file mode 120000
index b5ea991..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/field_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/field_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/input.nml b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/input.nml
deleted file mode 100644
index 7424ccd..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/input.nml
+++ /dev/null
@@ -1,140 +0,0 @@
- &MOM_input_nml
-        output_directory = './',
-        input_filename = 'r'
-        restart_input_dir = 'INPUT/',
-        restart_output_dir = 'RESTART/',
-        parameter_filename = 'MOM_input',
-                             'MOM_override' /
-
- &SIS_input_nml
-        output_directory = './',
-        input_filename = 'r'
-        restart_input_dir = 'INPUT/',
-        restart_output_dir = 'RESTART/',
-        parameter_filename = 'SIS_input',
-                             'SIS_override' /
-
- &diag_manager_nml
-         max_output_fields=1000
-         max_input_fields=1000
-         max_num_axis_sets=1000
-	 flush_nc_files=.true.
-         max_files=1000
-         max_axes=2000
- /
-
- &coupler_nml
-            months = 0,
-            days   = 60,
-            current_date = 1,1,1,0,0,0,
-            hours = 0,
-            minutes =0, 
-            seconds = 0
-            calendar = 'NOLEAP',
-            dt_cpld  = 10.0,
-            dt_atmos = 10.0,
-            do_atmos = .false.,
-            do_land = .false.,
-            do_ice = .true.,
-            do_ocean = .true.,
-            atmos_npes = 0,
-            ocean_npes = 0,
-            concurrent = .false.
-            use_lag_fluxes=.false. /
-
-
- &icebergs_nml
-    verbose=.false.,
-    verbose_hrs=240,
-    traj_sample_hrs=24000,
-    ignore_ij_restart=.true.
-    halo=2,
-    save_short_traj=.true.
-    debug=.false.,
-    really_debug=.false.,
-    use_slow_find=.true.,
-    add_weight_to_ocean=.true.,
-    passive_mode=.false.,
-    Static_icebergs=.False.,
-    ignore_missing_restart_bergs=.false.,
-    generate_test_icebergs=.false.,
-    speed_limit=0.,
-    use_roundoff_fix=.true.,
-    make_calving_reproduce=.false.,
-    Runge_not_Verlet=.false.,
-    iceberg_bonds_on=.false.,
-    critical_interaction_damping_on=.true.,
-    use_new_predictive_corrective=.true.,
-    interactive_icebergs_on=.true.
-    halo_debugging=.false.
-    spring_coef=0.00001
-    distribution=0.0, 0.99, 0.0, 0.00, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11,
-    hexagonal_icebergs=.true.
-    allow_bergs_to_roll=.true.
-    set_melt_rates_to_zero=.false.
-    use_roundoff_fix=.false.
-    grid_is_latlon=.false.
-    grid_is_regular=.true.
-    initial_orientation=-0.
-    rotate_icebergs_for_mass_spreading=.false.
-    lat_ref=-75.0
-    u_override=0.00
-    v_override=0.00
-    override_iceberg_velocities=.false.
-    add_iceberg_thickness_to_SSH=.false.
-    max_bonds=6
-    Iceberg_melt_without_decay=.true.
-    melt_icebergs_as_ice_shelf=.true.
-    Use_three_equation_model=.true.
-    find_melt_using_spread_mass=.true.
-    use_mixed_layer_salinity_for_thermo=.true.
-    pass_fields_to_ocean_model=.true.
-    rho_bergs=918.0
-    utide_icebergs=0.01
-    ustar_icebergs_bg=0.000
-    cdrag_icebergs =0.0025
-    const_gamma=.false.
-    Gamma_T_3EQ=0.22
-    ignore_traj=.False.
-    read_ocean_depth_from_file=.true.
-    apply_thickness_cutoff_to_bergs_melt=.true.
-    apply_thickness_cutoff_to_gridded_melt=.true.
-    melt_cutoff=10.
-    read_old_restarts=.false.
-    internal_bergs_for_drag=.true.
-    use_mixed_melting=.true.
- &data_override_nml
-         /
-
- &fms_io_nml
-         fms_netcdf_restart=.true.
-         threading_read='multi'
- /
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC' /
-
- &ice_albedo_nml
-      t_range = 10. /
-
- &ice_model_nml
-           /
-
- &monin_obukhov_nml
-            neutral = .true. /
-
- &ocean_albedo_nml
-      ocean_albedo_option = 5 /
-
- &sat_vapor_pres_nml
-      construct_table_wrt_liq = .true.,
-      construct_table_wrt_liq_and_ice = .true. /
-
- &xgrid_nml
-            make_exchange_reproduce = .false.
-            interp_method = 'second_order' /
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/run_script.sh b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/run_script.sh
deleted file mode 120000
index 2a081b9..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/run_script.sh
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/run_script.sh
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/submit_to_queue b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/submit_to_queue
deleted file mode 100644
index 4895e94..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_drift/submit_to_queue
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/bin/csh -f
-#PBS -r y                                                              #This job is restartable
-#PBS -j oe                                                             #STDOUT and STDERR are in the same file, specified below in the '-o' option
-#PBS -q batch                                                          #Do not change this - it tells your job where to run
-#PBS -S /bin/sh                                                        #Do not change this - it keeps your job from issuing a false alarm
-#PBS -E                                                                #Do not change this - it gives your job more and more useful Moab environment variables
-#PBS -N  Bergs_drift_layer                                               #Job Name:             You may want to change this to reflect your job's purpose or relation to an experiment
-#PBS -l partition=c3
-#PBS -l size=4                                                        #You will need to change this to reflect your job's core requirements - 24 is the current core increment.
-#PBS -l walltime=16:00:00                                              #You MUST change this to reflect your job's expected run time, including copy time
-#PBS -m bea                                                            #Email options: You may want to change this to reduce your incoming email stream
-
-######################################################################################################################
-#
-#  Gaea c1ms batch skeleton version 0.9
-#  
-#  0.9 - Initial version - 20110906 - Daniel Gall - Daniel.Gall@noaa.gov
-#
-######################################################################################################################
-
-#Source the system initialization scripts (but not the user's so as to avoid interactive settings that can poison us)
-source /etc/csh.cshrc
-
-#Run the experiment
-aprun -n 128 ../../../../../build/intel/ice_ocean_SIS2/repro/MOM6
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/MOM_input b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/MOM_input
deleted file mode 120000
index a756962..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/MOM_input
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/MOM_input
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/MOM_override b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/MOM_override
deleted file mode 100644
index 1fec204..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/MOM_override
+++ /dev/null
@@ -1,71 +0,0 @@
-! Blank file in which we can put "overrides" for parameters
-
-!TPY params
-#override NK = 72
-#override NKML = 4
-
-! TIME STEP
-#override DT = 10
-#override DT_THERM = 10
-#override DT_FORCING = 10
-
-! MIXING
-#override SMAGORINSKY_KH = False
-#override BIHARMONIC = False
-#override KH = 6.0  ! back. horiz. visc.
-#override KHTR = 1.0    ! back. horiz. diff.
-#override KD = 5.0E-5     ! back. diapycnal diff.
-#override KV = 1.0E-3     ! back. diapycnal visc.
-
-!WARM IC
-#override ISOMIP_T_SUR = -1.9
-#override ISOMIP_S_SUR = 33.8
-#override ISOMIP_T_BOT = 1.0
-#override ISOMIP_S_BOT = 34.7
-
-! ice shelf
-#override ICE_SHELF = False                !   [Boolean] default = False
-#override SHELF_THERMO = True
-#override SHELF_THREE_EQN = True
-#override SHELF_3EQ_GAMMA = False
-#override UTIDE = 0.01
-!SHELF_S_ROOT = True
-!#override USE_HMIX_SFC_PROP = True
-!#override HMIX_SFC_PROP = 10.
-
-! FRAZIL  - making sure sea ice does not form
-#override FRAZIL = False
-#override PRESSURE_DEPENDENT_FRAZIL = False
-
-! MIXED LAYER
-#override BULKMIXEDLAYER = True
-#override BULK_RI_ML = 0.25
-#override MIXEDLAYER_RESTRAT = True
-#override HMIX_MIN = 2.0
-!#override KV_TBL_MIN = 1.0E-2
-#override HTBL_SHELF_MIN = 2.0
-#override BOUND_SALINITY = True
- 
-! SHEAR MIXING
-#override USE_JACKSON_PARAM = True
-#override RINO_CRIT = 0.25
-!#override KD_KAPPA_SHEAR_0 = 1.0E-2
-
-! SPONGE
-#override SPONGE = True
-ISOMIP_SPONGE_FILE = "3D_LAYER_WARM_TPY_IC.nc"
-#override ISOMIP_TNUDG = 0.1
-!#override ISOMIP_SPONGE_TEMP_OFFSET=0.1
-
-
-! PASSIVE TRACERS
-USE_ISOMIP_TRACER = False
-
-! Simulation time
-#override DAYMAX = 730
-
-!#override FIT_SALINITY = False
-
-!Passing Iceberg field to ocean
-ICEBERGS_APPLY_RIGID_BOUNDARY=True !Different boundary condition is used under ice shelves
-ALLOW_ICEBERG_FLUX_DIAGNOSTICS=True
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/README b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/README
deleted file mode 100644
index fa2bc28..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/README
+++ /dev/null
@@ -1,5 +0,0 @@
-A tabular iceberg breaks away from the ice shelf. The non-static icebergs move away from the ice shelf at a prescribed velocity. The time step is quite small (10s) in order to resolve ocean motions
-
-Works best when started from restart file created by Static_berg simulation.
-
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/SIS_input b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/SIS_input
deleted file mode 120000
index ad3cd99..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/SIS_input
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/SIS_input
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/SIS_override b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/SIS_override
deleted file mode 100644
index 605ca84..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/SIS_override
+++ /dev/null
@@ -1,9 +0,0 @@
-# Blank file in which we can put "overrides" for parameters
-DO_ICEBERGS =True              !   If true, use the icebergs module.
-
-!Time Stepping
-#override DT_FORCING = 10.0              !   [s] default = 0.0
-#override DT_RHEOLOGY = 10.0             ! The sub-cycling time step, in s, for iterating
-#override DT_ICE_DYNAMICS = 10.0 
-
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/clean_MOM.sh b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/clean_MOM.sh
deleted file mode 120000
index c5370af..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/clean_MOM.sh
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/clean_MOM.sh
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/data_table b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/data_table
deleted file mode 120000
index 5b82b3c..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/data_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/data_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/diag_table b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/diag_table
deleted file mode 120000
index cff65fe..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/diag_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/diag_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/field_table b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/field_table
deleted file mode 120000
index b5ea991..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/field_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/field_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/input.nml b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/input.nml
deleted file mode 100644
index 97afa25..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/input.nml
+++ /dev/null
@@ -1,140 +0,0 @@
- &MOM_input_nml
-        output_directory = './',
-        input_filename = 'r'
-        restart_input_dir = 'INPUT/',
-        restart_output_dir = 'RESTART/',
-        parameter_filename = 'MOM_input',
-                             'MOM_override' /
-
- &SIS_input_nml
-        output_directory = './',
-        input_filename = 'r'
-        restart_input_dir = 'INPUT/',
-        restart_output_dir = 'RESTART/',
-        parameter_filename = 'SIS_input',
-                             'SIS_override' /
-
- &diag_manager_nml
-         max_output_fields=1000
-         max_input_fields=1000
-         max_num_axis_sets=1000
-	 flush_nc_files=.true.
-         max_files=1000
-         max_axes=2000
- /
-
- &coupler_nml
-            months = 0,
-            days   = 60,
-            current_date = 1,1,1,0,0,0,
-            hours = 0,
-            minutes =0, 
-            seconds = 0
-            calendar = 'NOLEAP',
-            dt_cpld  = 10.0,
-            dt_atmos = 10.0,
-            do_atmos = .false.,
-            do_land = .false.,
-            do_ice = .true.,
-            do_ocean = .true.,
-            atmos_npes = 0,
-            ocean_npes = 0,
-            concurrent = .false.
-            use_lag_fluxes=.false. /
-
-
- &icebergs_nml
-    verbose=.false.,
-    verbose_hrs=240,
-    traj_sample_hrs=24000,
-    ignore_ij_restart=.true.
-    halo=2,
-    save_short_traj=.true.
-    debug=.false.,
-    really_debug=.false.,
-    use_slow_find=.true.,
-    add_weight_to_ocean=.true.,
-    passive_mode=.false.,
-    Static_icebergs=.False.,
-    ignore_missing_restart_bergs=.false.,
-    generate_test_icebergs=.false.,
-    speed_limit=0.,
-    use_roundoff_fix=.true.,
-    make_calving_reproduce=.false.,
-    Runge_not_Verlet=.false.,
-    iceberg_bonds_on=.false.,
-    critical_interaction_damping_on=.true.,
-    use_new_predictive_corrective=.true.,
-    interactive_icebergs_on=.false.
-    halo_debugging=.false.
-    spring_coef=0.00001
-    distribution=0.0, 0.99, 0.0, 0.00, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11,
-    hexagonal_icebergs=.true.
-    allow_bergs_to_roll=.true.
-    set_melt_rates_to_zero=.false.
-    use_roundoff_fix=.false.
-    grid_is_latlon=.false.
-    grid_is_regular=.true.
-    initial_orientation=-0.
-    rotate_icebergs_for_mass_spreading=.false.
-    lat_ref=-75.0
-    u_override=0.01
-    v_override=0.00
-    override_iceberg_velocities=.true.
-    add_iceberg_thickness_to_SSH=.false.
-    max_bonds=6
-    Iceberg_melt_without_decay=.true.
-    melt_icebergs_as_ice_shelf=.true.
-    Use_three_equation_model=.true.
-    find_melt_using_spread_mass=.true.
-    use_mixed_layer_salinity_for_thermo=.true.
-    pass_fields_to_ocean_model=.true.
-    rho_bergs=918.0
-    utide_icebergs=0.01
-    ustar_icebergs_bg=0.000
-    cdrag_icebergs =0.0025
-    const_gamma=.false.
-    Gamma_T_3EQ=0.22
-    ignore_traj=.False.
-    read_ocean_depth_from_file=.true.
-    apply_thickness_cutoff_to_bergs_melt=.true.
-    apply_thickness_cutoff_to_gridded_melt=.true.
-    melt_cutoff=10.
-    read_old_restarts=.false.
-    internal_bergs_for_drag=.true.
-    use_mixed_melting=.true.
- &data_override_nml
-         /
-
- &fms_io_nml
-         fms_netcdf_restart=.true.
-         threading_read='multi'
- /
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC' /
-
- &ice_albedo_nml
-      t_range = 10. /
-
- &ice_model_nml
-           /
-
- &monin_obukhov_nml
-            neutral = .true. /
-
- &ocean_albedo_nml
-      ocean_albedo_option = 5 /
-
- &sat_vapor_pres_nml
-      construct_table_wrt_liq = .true.,
-      construct_table_wrt_liq_and_ice = .true. /
-
- &xgrid_nml
-            make_exchange_reproduce = .false.
-            interp_method = 'second_order' /
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/run_script.sh b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/run_script.sh
deleted file mode 120000
index 2a081b9..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/run_script.sh
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/run_script.sh
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/submit_to_queue b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/submit_to_queue
deleted file mode 100644
index 2e508c9..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Moving_berg_fixed/submit_to_queue
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/bin/csh -f
-#PBS -r y                                                              #This job is restartable
-#PBS -j oe                                                             #STDOUT and STDERR are in the same file, specified below in the '-o' option
-#PBS -q batch                                                          #Do not change this - it tells your job where to run
-#PBS -S /bin/sh                                                        #Do not change this - it keeps your job from issuing a false alarm
-#PBS -E                                                                #Do not change this - it gives your job more and more useful Moab environment variables
-#PBS -N  Bergs_fixed_layer                                               #Job Name:             You may want to change this to reflect your job's purpose or relation to an experiment
-#PBS -l partition=c3
-#PBS -l size=4                                                        #You will need to change this to reflect your job's core requirements - 24 is the current core increment.
-#PBS -l walltime=16:00:00                                              #You MUST change this to reflect your job's expected run time, including copy time
-#PBS -m bea                                                            #Email options: You may want to change this to reduce your incoming email stream
-
-######################################################################################################################
-#
-#  Gaea c1ms batch skeleton version 0.9
-#  
-#  0.9 - Initial version - 20110906 - Daniel Gall - Daniel.Gall@noaa.gov
-#
-######################################################################################################################
-
-#Source the system initialization scripts (but not the user's so as to avoid interactive settings that can poison us)
-source /etc/csh.cshrc
-
-#Run the experiment
-aprun -n 128 ../../../../../build/intel/ice_ocean_SIS2/repro/MOM6
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/MOM_input b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/MOM_input
deleted file mode 120000
index a756962..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/MOM_input
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/MOM_input
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/MOM_override b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/MOM_override
deleted file mode 100644
index 5da8e97..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/MOM_override
+++ /dev/null
@@ -1,73 +0,0 @@
-! Blank file in which we can put "overrides" for parameters
-
-!TPY params
-#override NK = 72
-#override NKML = 4
-
-! TIME STEP
-!#override DT = 720
-!#override DT_THERM = 720
-#override DT = 360
-#override DT_THERM = 360
-#override DT_FORCING = 360
-
-! MIXING
-#override SMAGORINSKY_KH = False
-#override BIHARMONIC = False
-#override KH = 6.0  ! back. horiz. visc.
-#override KHTR = 1.0    ! back. horiz. diff.
-#override KD = 5.0E-5     ! back. diapycnal diff.
-#override KV = 1.0E-3     ! back. diapycnal visc.
-
-!WARM IC
-#override ISOMIP_T_SUR = -1.9
-#override ISOMIP_S_SUR = 33.8
-#override ISOMIP_T_BOT = 1.0
-#override ISOMIP_S_BOT = 34.7
-
-! ice shelf
-#override ICE_SHELF = False                !   [Boolean] default = False
-#override SHELF_THERMO = True
-#override SHELF_THREE_EQN = True
-#override SHELF_3EQ_GAMMA = False
-#override UTIDE = 0.01
-!SHELF_S_ROOT = True
-!#override USE_HMIX_SFC_PROP = True
-!#override HMIX_SFC_PROP = 10.
-
-! FRAZIL  - making sure sea ice does not form
-#override FRAZIL = False
-#override PRESSURE_DEPENDENT_FRAZIL = False
-
-! MIXED LAYER
-#override BULKMIXEDLAYER = True
-#override BULK_RI_ML = 0.25
-#override MIXEDLAYER_RESTRAT = True
-#override HMIX_MIN = 2.0
-!#override KV_TBL_MIN = 1.0E-2
-#override HTBL_SHELF_MIN = 2.0
-#override BOUND_SALINITY = True
- 
-! SHEAR MIXING
-#override USE_JACKSON_PARAM = True
-#override RINO_CRIT = 0.25
-!#override KD_KAPPA_SHEAR_0 = 1.0E-2
-
-! SPONGE
-#override SPONGE = True
-ISOMIP_SPONGE_FILE = "3D_LAYER_WARM_TPY_IC.nc"
-#override ISOMIP_TNUDG = 0.1
-!#override ISOMIP_SPONGE_TEMP_OFFSET=0.1
-
-
-! PASSIVE TRACERS
-USE_ISOMIP_TRACER = False
-
-! Simulation time
-#override DAYMAX = 730
-
-!#override FIT_SALINITY = False
-
-!Passing Iceberg field to ocean
-ICEBERGS_APPLY_RIGID_BOUNDARY=True !Different boundary condition is used under ice shelves
-ALLOW_ICEBERG_FLUX_DIAGNOSTICS=True
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/README b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/README
deleted file mode 100644
index c042733..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/README
+++ /dev/null
@@ -1 +0,0 @@
-Ice shelf does not move. Shelf melts using three equation model.
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/SIS_input b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/SIS_input
deleted file mode 120000
index ad3cd99..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/SIS_input
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/SIS_input
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/SIS_override b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/SIS_override
deleted file mode 100644
index fc641d7..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/SIS_override
+++ /dev/null
@@ -1,8 +0,0 @@
-# Blank file in which we can put "overrides" for parameters
-DO_ICEBERGS =True              !   If true, use the icebergs module.
-
-!Time Stepping
-!#override DT_FORCING = 10.0              !   [s] default = 0.0
-!#override DT_RHEOLOGY = 10.0             ! The sub-cycling time step, in s, for iterating
-
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/clean_MOM.sh b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/clean_MOM.sh
deleted file mode 120000
index c5370af..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/clean_MOM.sh
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/clean_MOM.sh
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/data_table b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/data_table
deleted file mode 120000
index 5b82b3c..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/data_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/data_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/diag_table b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/diag_table
deleted file mode 120000
index cff65fe..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/diag_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/diag_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/field_table b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/field_table
deleted file mode 120000
index b5ea991..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/field_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/field_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/input.nml b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/input.nml
deleted file mode 100644
index 3854fd4..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/input.nml
+++ /dev/null
@@ -1,140 +0,0 @@
- &MOM_input_nml
-        output_directory = './',
-        input_filename = 'r'
-        restart_input_dir = 'INPUT/',
-        restart_output_dir = 'RESTART/',
-        parameter_filename = 'MOM_input',
-                             'MOM_override' /
-
- &SIS_input_nml
-        output_directory = './',
-        input_filename = 'r'
-        restart_input_dir = 'INPUT/',
-        restart_output_dir = 'RESTART/',
-        parameter_filename = 'SIS_input',
-                             'SIS_override' /
-
- &diag_manager_nml
-         max_output_fields=1000
-         max_input_fields=1000
-         max_num_axis_sets=1000
-	 flush_nc_files=.true.
-         max_files=1000
-         max_axes=2000
- /
-
- &coupler_nml
-            months = 60,
-            days   = 0,
-            current_date = 1,1,1,0,0,0,
-            hours = 0,
-            minutes =0, 
-            seconds = 0
-            calendar = 'NOLEAP',
-            dt_cpld  = 360.0,
-            dt_atmos = 360.0,
-            do_atmos = .false.,
-            do_land = .false.,
-            do_ice = .true.,
-            do_ocean = .true.,
-            atmos_npes = 0,
-            ocean_npes = 0,
-            concurrent = .false.
-            use_lag_fluxes=.false. /
-
-
- &icebergs_nml
-    verbose=.false.,
-    verbose_hrs=240,
-    traj_sample_hrs=24000,
-    ignore_ij_restart=.true.
-    halo=2,
-    save_short_traj=.true.
-    debug=.false.,
-    really_debug=.false.,
-    use_slow_find=.true.,
-    add_weight_to_ocean=.true.,
-    passive_mode=.false.,
-    Static_icebergs=.True.,
-    ignore_missing_restart_bergs=.false.,
-    generate_test_icebergs=.false.,
-    speed_limit=0.,
-    use_roundoff_fix=.true.,
-    make_calving_reproduce=.false.,
-    Runge_not_Verlet=.false.,
-    iceberg_bonds_on=.false.,
-    critical_interaction_damping_on=.true.,
-    use_new_predictive_corrective=.true.,
-    interactive_icebergs_on=.false.
-    halo_debugging=.false.
-    spring_coef=0.00001
-    distribution=0.0, 0.99, 0.0, 0.00, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11,
-    hexagonal_icebergs=.true.
-    allow_bergs_to_roll=.true.
-    set_melt_rates_to_zero=.false.
-    use_roundoff_fix=.false.
-    grid_is_latlon=.false.
-    grid_is_regular=.true.
-    initial_orientation=-0.
-    rotate_icebergs_for_mass_spreading=.false.
-    lat_ref=-75.0
-    u_override=0.00
-    v_override=0.00
-    override_iceberg_velocities=.false.
-    add_iceberg_thickness_to_SSH=.false.
-    max_bonds=6
-    Iceberg_melt_without_decay=.true.
-    melt_icebergs_as_ice_shelf=.true.
-    Use_three_equation_model=.true.
-    find_melt_using_spread_mass=.true.
-    use_mixed_layer_salinity_for_thermo=.true.
-    pass_fields_to_ocean_model=.true.
-    rho_bergs=918.0
-    utide_icebergs=0.01
-    ustar_icebergs_bg=0.000
-    cdrag_icebergs =0.0025
-    const_gamma=.false.
-    Gamma_T_3EQ=0.22
-    ignore_traj=.False.
-    read_ocean_depth_from_file=.true.
-    apply_thickness_cutoff_to_bergs_melt=.true.
-    apply_thickness_cutoff_to_gridded_melt=.true.
-    melt_cutoff=10.
-    read_old_restarts=.false.
-    internal_bergs_for_drag=.true.
-    use_mixed_melting=.true.
- &data_override_nml
-         /
-
- &fms_io_nml
-         fms_netcdf_restart=.true.
-         threading_read='multi'
- /
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC' /
-
- &ice_albedo_nml
-      t_range = 10. /
-
- &ice_model_nml
-           /
-
- &monin_obukhov_nml
-            neutral = .true. /
-
- &ocean_albedo_nml
-      ocean_albedo_option = 5 /
-
- &sat_vapor_pres_nml
-      construct_table_wrt_liq = .true.,
-      construct_table_wrt_liq_and_ice = .true. /
-
- &xgrid_nml
-            make_exchange_reproduce = .false.
-            interp_method = 'second_order' /
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/run_script.sh b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/run_script.sh
deleted file mode 120000
index 2a081b9..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/run_script.sh
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/run_script.sh
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/submit_to_queue b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/submit_to_queue
deleted file mode 100644
index d35f1b8..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Layer/Static_shelf/submit_to_queue
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/bin/csh -f
-#PBS -r y                                                              #This job is restartable
-#PBS -j oe                                                             #STDOUT and STDERR are in the same file, specified below in the '-o' option
-#PBS -q batch                                                          #Do not change this - it tells your job where to run
-#PBS -S /bin/sh                                                        #Do not change this - it keeps your job from issuing a false alarm
-#PBS -E                                                                #Do not change this - it gives your job more and more useful Moab environment variables
-#PBS -N  Bergs_Empty_Run                                               #Job Name:             You may want to change this to reflect your job's purpose or relation to an experiment
-#PBS -l partition=c3
-#PBS -l size=4                                                        #You will need to change this to reflect your job's core requirements - 24 is the current core increment.
-#PBS -l walltime=16:00:00                                              #You MUST change this to reflect your job's expected run time, including copy time
-#PBS -m bea                                                            #Email options: You may want to change this to reduce your incoming email stream
-
-######################################################################################################################
-#
-#  Gaea c1ms batch skeleton version 0.9
-#  
-#  0.9 - Initial version - 20110906 - Daniel Gall - Daniel.Gall@noaa.gov
-#
-######################################################################################################################
-
-#Source the system initialization scripts (but not the user's so as to avoid interactive settings that can poison us)
-source /etc/csh.cshrc
-
-#Run the experiment
-aprun -n 128 ../../../../../build/intel/ice_ocean_SIS2/repro/MOM6
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/MOM_input b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/MOM_input
deleted file mode 120000
index a756962..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/MOM_input
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/MOM_input
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/MOM_override b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/MOM_override
deleted file mode 100644
index cd50151..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/MOM_override
+++ /dev/null
@@ -1,91 +0,0 @@
-! Blank file in which we can put "overrides" for parameters
-! z
-#override USE_REGRIDDING = True
-#override REGRIDDING_COORDINATE_MODE = "SIGMA_SHELF_ZSTAR" 
-#override INTERPOLATION_SCHEME = "PPM_H4"
-#override REMAPPING_SCHEME = "PPM_H4"
-
-
-!TPY params
-#override NK = 72
-#override NKML = 4
-
-! TIME STEP
-#override DT = 10
-#override DT_THERM = 10
-#override DT_FORCING = 10
-
-! MIXING
-#override SMAGORINSKY_KH = False
-#override BIHARMONIC = False
-#override KH = 6.0  ! back. horiz. visc.
-#override KHTR = 1.0    ! back. horiz. diff.
-#override KD = 5.0E-5     ! back. diapycnal diff.
-#override KV = 1.0E-3     ! back. diapycnal visc.
-
-!WARM IC
-#override ISOMIP_T_SUR = -1.9
-#override ISOMIP_S_SUR = 33.8
-#override ISOMIP_T_BOT = 1.0
-#override ISOMIP_S_BOT = 34.7
-
-! ice shelf
-#override ICE_SHELF = False                !   [Boolean] default = False
-#override SHELF_THERMO = TRUE
-#override SHELF_THREE_EQN = True
-#override SHELF_3EQ_GAMMA = False
-#override UTIDE = 0.01
-!SHELF_S_ROOT = True
-!#override USE_HMIX_SFC_PROP = True
-!#override HMIX_SFC_PROP = 10.
-
-! FRAZIL  - making sure sea ice does not form
-#override FRAZIL = False
-#override PRESSURE_DEPENDENT_FRAZIL = False
-
-! EPBL
-#override ENERGETICS_SFC_PBL = True       !   [Boolean] default = False
-                                ! If true, use an implied energetics planetary boundary
-                                ! layer scheme to determine the diffusivity and viscosity
-                                ! in the surface boundary layer.
-#override EPBL_IS_ADDITIVE = True         !   [Boolean] default = True
-                                ! If true, the diffusivity from ePBL is added to all
-                                ! other diffusivities. Otherwise, the larger of kappa-
-                                ! shear and ePBL diffusivities are used.
-#override USE_MLD_ITERATION = True        !   [Boolean] default = False
-                                ! A logical that determines whether or not to use the
-                                ! MLD to set the EPBL length scale.
-#override HTBL_SHELF_MIN = 10.0
-#override BOUND_SALINITY = True
-
-
-! SHEAR MIXING
-#override USE_JACKSON_PARAM = True
-#override RINO_CRIT = 0.25
-!#override KD_KAPPA_SHEAR_0 = 1.0E-2
-
-! SPONGE
-#override SPONGE = TRUE
-ISOMIP_SPONGE_FILE = "3D_LAYER_WARM_TPY_IC.nc"
-#override ISOMIP_TNUDG = 0.1
-#override ISOMIP_TNUDG = 0.1
-#override ISOMIP_S_SUR_SPONGE = 33.8      !   [not defined] default = 35.0
-                                ! Surface salinity in sponge layer.
-#override ISOMIP_S_BOT_SPONGE = 34.7      !   [not defined] default = 35.0
-                                ! Bottom salinity in sponge layer.
-#override ISOMIP_T_SUR_SPONGE = -1.9      !   [not defined] default = -1.9
-                                ! Surface temperature in sponge layer.
-#override ISOMIP_T_BOT_SPONGE = 1.0
-!#override ISOMIP_SPONGE_TEMP_OFFSET=0.1
-
-! PASSIVE TRACERS
-USE_ISOMIP_TRACER = False
-
-! Simulation time
-#override DAYMAX = 730
-
-!#override FIT_SALINITY = False
-
-!Passing Iceberg field to ocean
-ICEBERGS_APPLY_RIGID_BOUNDARY=True !Different boundary condition is used under ice shelves
-ALLOW_ICEBERG_FLUX_DIAGNOSTICS=True
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/SIS_input b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/SIS_input
deleted file mode 120000
index ad3cd99..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/SIS_input
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/SIS_input
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/SIS_override b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/SIS_override
deleted file mode 100644
index fc641d7..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/SIS_override
+++ /dev/null
@@ -1,8 +0,0 @@
-# Blank file in which we can put "overrides" for parameters
-DO_ICEBERGS =True              !   If true, use the icebergs module.
-
-!Time Stepping
-!#override DT_FORCING = 10.0              !   [s] default = 0.0
-!#override DT_RHEOLOGY = 10.0             ! The sub-cycling time step, in s, for iterating
-
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/clean_MOM.sh b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/clean_MOM.sh
deleted file mode 120000
index c5370af..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/clean_MOM.sh
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/clean_MOM.sh
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/data_table b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/data_table
deleted file mode 120000
index 5b82b3c..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/data_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/data_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/diag_table b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/diag_table
deleted file mode 120000
index cff65fe..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/diag_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/diag_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/field_table b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/field_table
deleted file mode 120000
index b5ea991..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/field_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/field_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/input.nml b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/input.nml
deleted file mode 100644
index 7b69203..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/input.nml
+++ /dev/null
@@ -1,140 +0,0 @@
- &MOM_input_nml
-        output_directory = './',
-        input_filename = 'r'
-        restart_input_dir = 'INPUT/',
-        restart_output_dir = 'RESTART/',
-        parameter_filename = 'MOM_input',
-                             'MOM_override' /
-
- &SIS_input_nml
-        output_directory = './',
-        input_filename = 'r'
-        restart_input_dir = 'INPUT/',
-        restart_output_dir = 'RESTART/',
-        parameter_filename = 'SIS_input',
-                             'SIS_override' /
-
- &diag_manager_nml
-         max_output_fields=1000
-         max_input_fields=1000
-         max_num_axis_sets=1000
-	 flush_nc_files=.true.
-         max_files=1000
-         max_axes=2000
- /
-
- &coupler_nml
-            months = 0,
-            days   = 60,
-            current_date = 1,1,1,0,0,0,
-            hours = 0,
-            minutes =0, 
-            seconds = 0
-            calendar = 'NOLEAP',
-            dt_cpld  = 10.0,
-            dt_atmos = 10.0,
-            do_atmos = .false.,
-            do_land = .false.,
-            do_ice = .true.,
-            do_ocean = .true.,
-            atmos_npes = 0,
-            ocean_npes = 0,
-            concurrent = .false.
-            use_lag_fluxes=.false. /
-
-
- &icebergs_nml
-    verbose=.false.,
-    verbose_hrs=240,
-    traj_sample_hrs=24000,
-    ignore_ij_restart=.true.
-    halo=2,
-    save_short_traj=.true.
-    debug=.false.,
-    really_debug=.false.,
-    use_slow_find=.true.,
-    add_weight_to_ocean=.true.,
-    passive_mode=.false.,
-    Static_icebergs=.False.,
-    ignore_missing_restart_bergs=.false.,
-    generate_test_icebergs=.false.,
-    speed_limit=0.,
-    use_roundoff_fix=.true.,
-    make_calving_reproduce=.false.,
-    Runge_not_Verlet=.false.,
-    iceberg_bonds_on=.true.,
-    critical_interaction_damping_on=.true.,
-    use_new_predictive_corrective=.true.,
-    interactive_icebergs_on=.true.
-    halo_debugging=.false.
-    spring_coef=0.00001
-    distribution=0.0, 0.99, 0.0, 0.00, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11,
-    hexagonal_icebergs=.true.
-    allow_bergs_to_roll=.true.
-    set_melt_rates_to_zero=.false.
-    use_roundoff_fix=.false.
-    grid_is_latlon=.false.
-    grid_is_regular=.true.
-    initial_orientation=-0.
-    rotate_icebergs_for_mass_spreading=.false.
-    lat_ref=-75.0
-    u_override=0.00
-    v_override=0.00
-    override_iceberg_velocities=.false.
-    add_iceberg_thickness_to_SSH=.false.
-    max_bonds=6
-    Iceberg_melt_without_decay=.true.
-    melt_icebergs_as_ice_shelf=.true.
-    Use_three_equation_model=.true.
-    find_melt_using_spread_mass=.true.
-    use_mixed_layer_salinity_for_thermo=.true.
-    pass_fields_to_ocean_model=.true.
-    rho_bergs=918.0
-    utide_icebergs=0.01
-    ustar_icebergs_bg=0.000
-    cdrag_icebergs =0.0025
-    const_gamma=.false.
-    Gamma_T_3EQ=0.22
-    ignore_traj=.False.
-    read_ocean_depth_from_file=.true.
-    apply_thickness_cutoff_to_bergs_melt=.true.
-    apply_thickness_cutoff_to_gridded_melt=.true.
-    melt_cutoff=10.
-    read_old_restarts=.false.
-    internal_bergs_for_drag=.true.
-    use_mixed_melting=.true.
- &data_override_nml
-         /
-
- &fms_io_nml
-         fms_netcdf_restart=.true.
-         threading_read='multi'
- /
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC' /
-
- &ice_albedo_nml
-      t_range = 10. /
-
- &ice_model_nml
-           /
-
- &monin_obukhov_nml
-            neutral = .true. /
-
- &ocean_albedo_nml
-      ocean_albedo_option = 5 /
-
- &sat_vapor_pres_nml
-      construct_table_wrt_liq = .true.,
-      construct_table_wrt_liq_and_ice = .true. /
-
- &xgrid_nml
-            make_exchange_reproduce = .false.
-            interp_method = 'second_order' /
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/run_script.sh b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/run_script.sh
deleted file mode 120000
index 2a081b9..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/run_script.sh
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/run_script.sh
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/submit_to_queue b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/submit_to_queue
deleted file mode 100644
index d35f1b8..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Empty_run/submit_to_queue
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/bin/csh -f
-#PBS -r y                                                              #This job is restartable
-#PBS -j oe                                                             #STDOUT and STDERR are in the same file, specified below in the '-o' option
-#PBS -q batch                                                          #Do not change this - it tells your job where to run
-#PBS -S /bin/sh                                                        #Do not change this - it keeps your job from issuing a false alarm
-#PBS -E                                                                #Do not change this - it gives your job more and more useful Moab environment variables
-#PBS -N  Bergs_Empty_Run                                               #Job Name:             You may want to change this to reflect your job's purpose or relation to an experiment
-#PBS -l partition=c3
-#PBS -l size=4                                                        #You will need to change this to reflect your job's core requirements - 24 is the current core increment.
-#PBS -l walltime=16:00:00                                              #You MUST change this to reflect your job's expected run time, including copy time
-#PBS -m bea                                                            #Email options: You may want to change this to reduce your incoming email stream
-
-######################################################################################################################
-#
-#  Gaea c1ms batch skeleton version 0.9
-#  
-#  0.9 - Initial version - 20110906 - Daniel Gall - Daniel.Gall@noaa.gov
-#
-######################################################################################################################
-
-#Source the system initialization scripts (but not the user's so as to avoid interactive settings that can poison us)
-source /etc/csh.cshrc
-
-#Run the experiment
-aprun -n 128 ../../../../../build/intel/ice_ocean_SIS2/repro/MOM6
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/MOM_input b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/MOM_input
deleted file mode 120000
index a756962..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/MOM_input
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/MOM_input
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/MOM_override b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/MOM_override
deleted file mode 100644
index cd50151..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/MOM_override
+++ /dev/null
@@ -1,91 +0,0 @@
-! Blank file in which we can put "overrides" for parameters
-! z
-#override USE_REGRIDDING = True
-#override REGRIDDING_COORDINATE_MODE = "SIGMA_SHELF_ZSTAR" 
-#override INTERPOLATION_SCHEME = "PPM_H4"
-#override REMAPPING_SCHEME = "PPM_H4"
-
-
-!TPY params
-#override NK = 72
-#override NKML = 4
-
-! TIME STEP
-#override DT = 10
-#override DT_THERM = 10
-#override DT_FORCING = 10
-
-! MIXING
-#override SMAGORINSKY_KH = False
-#override BIHARMONIC = False
-#override KH = 6.0  ! back. horiz. visc.
-#override KHTR = 1.0    ! back. horiz. diff.
-#override KD = 5.0E-5     ! back. diapycnal diff.
-#override KV = 1.0E-3     ! back. diapycnal visc.
-
-!WARM IC
-#override ISOMIP_T_SUR = -1.9
-#override ISOMIP_S_SUR = 33.8
-#override ISOMIP_T_BOT = 1.0
-#override ISOMIP_S_BOT = 34.7
-
-! ice shelf
-#override ICE_SHELF = False                !   [Boolean] default = False
-#override SHELF_THERMO = TRUE
-#override SHELF_THREE_EQN = True
-#override SHELF_3EQ_GAMMA = False
-#override UTIDE = 0.01
-!SHELF_S_ROOT = True
-!#override USE_HMIX_SFC_PROP = True
-!#override HMIX_SFC_PROP = 10.
-
-! FRAZIL  - making sure sea ice does not form
-#override FRAZIL = False
-#override PRESSURE_DEPENDENT_FRAZIL = False
-
-! EPBL
-#override ENERGETICS_SFC_PBL = True       !   [Boolean] default = False
-                                ! If true, use an implied energetics planetary boundary
-                                ! layer scheme to determine the diffusivity and viscosity
-                                ! in the surface boundary layer.
-#override EPBL_IS_ADDITIVE = True         !   [Boolean] default = True
-                                ! If true, the diffusivity from ePBL is added to all
-                                ! other diffusivities. Otherwise, the larger of kappa-
-                                ! shear and ePBL diffusivities are used.
-#override USE_MLD_ITERATION = True        !   [Boolean] default = False
-                                ! A logical that determines whether or not to use the
-                                ! MLD to set the EPBL length scale.
-#override HTBL_SHELF_MIN = 10.0
-#override BOUND_SALINITY = True
-
-
-! SHEAR MIXING
-#override USE_JACKSON_PARAM = True
-#override RINO_CRIT = 0.25
-!#override KD_KAPPA_SHEAR_0 = 1.0E-2
-
-! SPONGE
-#override SPONGE = TRUE
-ISOMIP_SPONGE_FILE = "3D_LAYER_WARM_TPY_IC.nc"
-#override ISOMIP_TNUDG = 0.1
-#override ISOMIP_TNUDG = 0.1
-#override ISOMIP_S_SUR_SPONGE = 33.8      !   [not defined] default = 35.0
-                                ! Surface salinity in sponge layer.
-#override ISOMIP_S_BOT_SPONGE = 34.7      !   [not defined] default = 35.0
-                                ! Bottom salinity in sponge layer.
-#override ISOMIP_T_SUR_SPONGE = -1.9      !   [not defined] default = -1.9
-                                ! Surface temperature in sponge layer.
-#override ISOMIP_T_BOT_SPONGE = 1.0
-!#override ISOMIP_SPONGE_TEMP_OFFSET=0.1
-
-! PASSIVE TRACERS
-USE_ISOMIP_TRACER = False
-
-! Simulation time
-#override DAYMAX = 730
-
-!#override FIT_SALINITY = False
-
-!Passing Iceberg field to ocean
-ICEBERGS_APPLY_RIGID_BOUNDARY=True !Different boundary condition is used under ice shelves
-ALLOW_ICEBERG_FLUX_DIAGNOSTICS=True
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/README b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/README
deleted file mode 100644
index 0972054..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/README
+++ /dev/null
@@ -1,4 +0,0 @@
-A tabular icebergs breaks away from the ice shelf. The tabular icebergs is bonded together by numeric bonds. Icebergs are allowed to evolve freely
-
-Works best when started from restart file created by Static_berg simulation.
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/SIS_input b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/SIS_input
deleted file mode 120000
index ad3cd99..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/SIS_input
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/SIS_input
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/SIS_override b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/SIS_override
deleted file mode 100644
index 605ca84..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/SIS_override
+++ /dev/null
@@ -1,9 +0,0 @@
-# Blank file in which we can put "overrides" for parameters
-DO_ICEBERGS =True              !   If true, use the icebergs module.
-
-!Time Stepping
-#override DT_FORCING = 10.0              !   [s] default = 0.0
-#override DT_RHEOLOGY = 10.0             ! The sub-cycling time step, in s, for iterating
-#override DT_ICE_DYNAMICS = 10.0 
-
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/clean_MOM.sh b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/clean_MOM.sh
deleted file mode 120000
index c5370af..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/clean_MOM.sh
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/clean_MOM.sh
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/data_table b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/data_table
deleted file mode 120000
index 5b82b3c..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/data_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/data_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/diag_table b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/diag_table
deleted file mode 120000
index cff65fe..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/diag_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/diag_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/field_table b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/field_table
deleted file mode 120000
index b5ea991..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/field_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/field_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/input.nml b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/input.nml
deleted file mode 100644
index 7b69203..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/input.nml
+++ /dev/null
@@ -1,140 +0,0 @@
- &MOM_input_nml
-        output_directory = './',
-        input_filename = 'r'
-        restart_input_dir = 'INPUT/',
-        restart_output_dir = 'RESTART/',
-        parameter_filename = 'MOM_input',
-                             'MOM_override' /
-
- &SIS_input_nml
-        output_directory = './',
-        input_filename = 'r'
-        restart_input_dir = 'INPUT/',
-        restart_output_dir = 'RESTART/',
-        parameter_filename = 'SIS_input',
-                             'SIS_override' /
-
- &diag_manager_nml
-         max_output_fields=1000
-         max_input_fields=1000
-         max_num_axis_sets=1000
-	 flush_nc_files=.true.
-         max_files=1000
-         max_axes=2000
- /
-
- &coupler_nml
-            months = 0,
-            days   = 60,
-            current_date = 1,1,1,0,0,0,
-            hours = 0,
-            minutes =0, 
-            seconds = 0
-            calendar = 'NOLEAP',
-            dt_cpld  = 10.0,
-            dt_atmos = 10.0,
-            do_atmos = .false.,
-            do_land = .false.,
-            do_ice = .true.,
-            do_ocean = .true.,
-            atmos_npes = 0,
-            ocean_npes = 0,
-            concurrent = .false.
-            use_lag_fluxes=.false. /
-
-
- &icebergs_nml
-    verbose=.false.,
-    verbose_hrs=240,
-    traj_sample_hrs=24000,
-    ignore_ij_restart=.true.
-    halo=2,
-    save_short_traj=.true.
-    debug=.false.,
-    really_debug=.false.,
-    use_slow_find=.true.,
-    add_weight_to_ocean=.true.,
-    passive_mode=.false.,
-    Static_icebergs=.False.,
-    ignore_missing_restart_bergs=.false.,
-    generate_test_icebergs=.false.,
-    speed_limit=0.,
-    use_roundoff_fix=.true.,
-    make_calving_reproduce=.false.,
-    Runge_not_Verlet=.false.,
-    iceberg_bonds_on=.true.,
-    critical_interaction_damping_on=.true.,
-    use_new_predictive_corrective=.true.,
-    interactive_icebergs_on=.true.
-    halo_debugging=.false.
-    spring_coef=0.00001
-    distribution=0.0, 0.99, 0.0, 0.00, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11,
-    hexagonal_icebergs=.true.
-    allow_bergs_to_roll=.true.
-    set_melt_rates_to_zero=.false.
-    use_roundoff_fix=.false.
-    grid_is_latlon=.false.
-    grid_is_regular=.true.
-    initial_orientation=-0.
-    rotate_icebergs_for_mass_spreading=.false.
-    lat_ref=-75.0
-    u_override=0.00
-    v_override=0.00
-    override_iceberg_velocities=.false.
-    add_iceberg_thickness_to_SSH=.false.
-    max_bonds=6
-    Iceberg_melt_without_decay=.true.
-    melt_icebergs_as_ice_shelf=.true.
-    Use_three_equation_model=.true.
-    find_melt_using_spread_mass=.true.
-    use_mixed_layer_salinity_for_thermo=.true.
-    pass_fields_to_ocean_model=.true.
-    rho_bergs=918.0
-    utide_icebergs=0.01
-    ustar_icebergs_bg=0.000
-    cdrag_icebergs =0.0025
-    const_gamma=.false.
-    Gamma_T_3EQ=0.22
-    ignore_traj=.False.
-    read_ocean_depth_from_file=.true.
-    apply_thickness_cutoff_to_bergs_melt=.true.
-    apply_thickness_cutoff_to_gridded_melt=.true.
-    melt_cutoff=10.
-    read_old_restarts=.false.
-    internal_bergs_for_drag=.true.
-    use_mixed_melting=.true.
- &data_override_nml
-         /
-
- &fms_io_nml
-         fms_netcdf_restart=.true.
-         threading_read='multi'
- /
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC' /
-
- &ice_albedo_nml
-      t_range = 10. /
-
- &ice_model_nml
-           /
-
- &monin_obukhov_nml
-            neutral = .true. /
-
- &ocean_albedo_nml
-      ocean_albedo_option = 5 /
-
- &sat_vapor_pres_nml
-      construct_table_wrt_liq = .true.,
-      construct_table_wrt_liq_and_ice = .true. /
-
- &xgrid_nml
-            make_exchange_reproduce = .false.
-            interp_method = 'second_order' /
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/run_script.sh b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/run_script.sh
deleted file mode 120000
index 2a081b9..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/run_script.sh
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/run_script.sh
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/submit_to_queue b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/submit_to_queue
deleted file mode 100644
index cc5b649..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Bond/submit_to_queue
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/bin/csh -f
-#PBS -r y                                                              #This job is restartable
-#PBS -j oe                                                             #STDOUT and STDERR are in the same file, specified below in the '-o' option
-#PBS -q batch                                                          #Do not change this - it tells your job where to run
-#PBS -S /bin/sh                                                        #Do not change this - it keeps your job from issuing a false alarm
-#PBS -E                                                                #Do not change this - it gives your job more and more useful Moab environment variables
-#PBS -N  Bergs_Bond_layer                                              #Job Name:             You may want to change this to reflect your job's purpose or relation to an experiment
-#PBS -l partition=c3
-#PBS -l size=4                                                        #You will need to change this to reflect your job's core requirements - 24 is the current core increment.
-#PBS -l walltime=16:00:00                                              #You MUST change this to reflect your job's expected run time, including copy time
-#PBS -m bea                                                            #Email options: You may want to change this to reduce your incoming email stream
-
-######################################################################################################################
-#
-#  Gaea c1ms batch skeleton version 0.9
-#  
-#  0.9 - Initial version - 20110906 - Daniel Gall - Daniel.Gall@noaa.gov
-#
-######################################################################################################################
-
-#Source the system initialization scripts (but not the user's so as to avoid interactive settings that can poison us)
-source /etc/csh.cshrc
-
-#Run the experiment
-aprun -n 128 ../../../../../build/intel/ice_ocean_SIS2/repro/MOM6
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Collapse/README b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Collapse/README
deleted file mode 100644
index ac458b8..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Collapse/README
+++ /dev/null
@@ -1,7 +0,0 @@
-A tabular icebergs breaks away from the ice shelf. Smaller pieces also break away, which allows the tabular iceberg to move more easily. The tabular icebergs is bonded together by numeric bonds. Icebergs are allowed to evolve freely
-
-Works best when started from restart file created by Static_berg simulation.
-
-Experimental setup is exactly the same as Moving_berg_Bond simulation, except that when icebergs.res is created, use the command line flag:
-./initialize_bergs_in_pattern.py -Make_icebergs_non_static_later=True
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Collapse/input.nml b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Collapse/input.nml
deleted file mode 100644
index 7b69203..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_Collapse/input.nml
+++ /dev/null
@@ -1,140 +0,0 @@
- &MOM_input_nml
-        output_directory = './',
-        input_filename = 'r'
-        restart_input_dir = 'INPUT/',
-        restart_output_dir = 'RESTART/',
-        parameter_filename = 'MOM_input',
-                             'MOM_override' /
-
- &SIS_input_nml
-        output_directory = './',
-        input_filename = 'r'
-        restart_input_dir = 'INPUT/',
-        restart_output_dir = 'RESTART/',
-        parameter_filename = 'SIS_input',
-                             'SIS_override' /
-
- &diag_manager_nml
-         max_output_fields=1000
-         max_input_fields=1000
-         max_num_axis_sets=1000
-	 flush_nc_files=.true.
-         max_files=1000
-         max_axes=2000
- /
-
- &coupler_nml
-            months = 0,
-            days   = 60,
-            current_date = 1,1,1,0,0,0,
-            hours = 0,
-            minutes =0, 
-            seconds = 0
-            calendar = 'NOLEAP',
-            dt_cpld  = 10.0,
-            dt_atmos = 10.0,
-            do_atmos = .false.,
-            do_land = .false.,
-            do_ice = .true.,
-            do_ocean = .true.,
-            atmos_npes = 0,
-            ocean_npes = 0,
-            concurrent = .false.
-            use_lag_fluxes=.false. /
-
-
- &icebergs_nml
-    verbose=.false.,
-    verbose_hrs=240,
-    traj_sample_hrs=24000,
-    ignore_ij_restart=.true.
-    halo=2,
-    save_short_traj=.true.
-    debug=.false.,
-    really_debug=.false.,
-    use_slow_find=.true.,
-    add_weight_to_ocean=.true.,
-    passive_mode=.false.,
-    Static_icebergs=.False.,
-    ignore_missing_restart_bergs=.false.,
-    generate_test_icebergs=.false.,
-    speed_limit=0.,
-    use_roundoff_fix=.true.,
-    make_calving_reproduce=.false.,
-    Runge_not_Verlet=.false.,
-    iceberg_bonds_on=.true.,
-    critical_interaction_damping_on=.true.,
-    use_new_predictive_corrective=.true.,
-    interactive_icebergs_on=.true.
-    halo_debugging=.false.
-    spring_coef=0.00001
-    distribution=0.0, 0.99, 0.0, 0.00, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11,
-    hexagonal_icebergs=.true.
-    allow_bergs_to_roll=.true.
-    set_melt_rates_to_zero=.false.
-    use_roundoff_fix=.false.
-    grid_is_latlon=.false.
-    grid_is_regular=.true.
-    initial_orientation=-0.
-    rotate_icebergs_for_mass_spreading=.false.
-    lat_ref=-75.0
-    u_override=0.00
-    v_override=0.00
-    override_iceberg_velocities=.false.
-    add_iceberg_thickness_to_SSH=.false.
-    max_bonds=6
-    Iceberg_melt_without_decay=.true.
-    melt_icebergs_as_ice_shelf=.true.
-    Use_three_equation_model=.true.
-    find_melt_using_spread_mass=.true.
-    use_mixed_layer_salinity_for_thermo=.true.
-    pass_fields_to_ocean_model=.true.
-    rho_bergs=918.0
-    utide_icebergs=0.01
-    ustar_icebergs_bg=0.000
-    cdrag_icebergs =0.0025
-    const_gamma=.false.
-    Gamma_T_3EQ=0.22
-    ignore_traj=.False.
-    read_ocean_depth_from_file=.true.
-    apply_thickness_cutoff_to_bergs_melt=.true.
-    apply_thickness_cutoff_to_gridded_melt=.true.
-    melt_cutoff=10.
-    read_old_restarts=.false.
-    internal_bergs_for_drag=.true.
-    use_mixed_melting=.true.
- &data_override_nml
-         /
-
- &fms_io_nml
-         fms_netcdf_restart=.true.
-         threading_read='multi'
- /
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC' /
-
- &ice_albedo_nml
-      t_range = 10. /
-
- &ice_model_nml
-           /
-
- &monin_obukhov_nml
-            neutral = .true. /
-
- &ocean_albedo_nml
-      ocean_albedo_option = 5 /
-
- &sat_vapor_pres_nml
-      construct_table_wrt_liq = .true.,
-      construct_table_wrt_liq_and_ice = .true. /
-
- &xgrid_nml
-            make_exchange_reproduce = .false.
-            interp_method = 'second_order' /
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/MOM_input b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/MOM_input
deleted file mode 120000
index a756962..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/MOM_input
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/MOM_input
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/MOM_override b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/MOM_override
deleted file mode 100644
index cd50151..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/MOM_override
+++ /dev/null
@@ -1,91 +0,0 @@
-! Blank file in which we can put "overrides" for parameters
-! z
-#override USE_REGRIDDING = True
-#override REGRIDDING_COORDINATE_MODE = "SIGMA_SHELF_ZSTAR" 
-#override INTERPOLATION_SCHEME = "PPM_H4"
-#override REMAPPING_SCHEME = "PPM_H4"
-
-
-!TPY params
-#override NK = 72
-#override NKML = 4
-
-! TIME STEP
-#override DT = 10
-#override DT_THERM = 10
-#override DT_FORCING = 10
-
-! MIXING
-#override SMAGORINSKY_KH = False
-#override BIHARMONIC = False
-#override KH = 6.0  ! back. horiz. visc.
-#override KHTR = 1.0    ! back. horiz. diff.
-#override KD = 5.0E-5     ! back. diapycnal diff.
-#override KV = 1.0E-3     ! back. diapycnal visc.
-
-!WARM IC
-#override ISOMIP_T_SUR = -1.9
-#override ISOMIP_S_SUR = 33.8
-#override ISOMIP_T_BOT = 1.0
-#override ISOMIP_S_BOT = 34.7
-
-! ice shelf
-#override ICE_SHELF = False                !   [Boolean] default = False
-#override SHELF_THERMO = TRUE
-#override SHELF_THREE_EQN = True
-#override SHELF_3EQ_GAMMA = False
-#override UTIDE = 0.01
-!SHELF_S_ROOT = True
-!#override USE_HMIX_SFC_PROP = True
-!#override HMIX_SFC_PROP = 10.
-
-! FRAZIL  - making sure sea ice does not form
-#override FRAZIL = False
-#override PRESSURE_DEPENDENT_FRAZIL = False
-
-! EPBL
-#override ENERGETICS_SFC_PBL = True       !   [Boolean] default = False
-                                ! If true, use an implied energetics planetary boundary
-                                ! layer scheme to determine the diffusivity and viscosity
-                                ! in the surface boundary layer.
-#override EPBL_IS_ADDITIVE = True         !   [Boolean] default = True
-                                ! If true, the diffusivity from ePBL is added to all
-                                ! other diffusivities. Otherwise, the larger of kappa-
-                                ! shear and ePBL diffusivities are used.
-#override USE_MLD_ITERATION = True        !   [Boolean] default = False
-                                ! A logical that determines whether or not to use the
-                                ! MLD to set the EPBL length scale.
-#override HTBL_SHELF_MIN = 10.0
-#override BOUND_SALINITY = True
-
-
-! SHEAR MIXING
-#override USE_JACKSON_PARAM = True
-#override RINO_CRIT = 0.25
-!#override KD_KAPPA_SHEAR_0 = 1.0E-2
-
-! SPONGE
-#override SPONGE = TRUE
-ISOMIP_SPONGE_FILE = "3D_LAYER_WARM_TPY_IC.nc"
-#override ISOMIP_TNUDG = 0.1
-#override ISOMIP_TNUDG = 0.1
-#override ISOMIP_S_SUR_SPONGE = 33.8      !   [not defined] default = 35.0
-                                ! Surface salinity in sponge layer.
-#override ISOMIP_S_BOT_SPONGE = 34.7      !   [not defined] default = 35.0
-                                ! Bottom salinity in sponge layer.
-#override ISOMIP_T_SUR_SPONGE = -1.9      !   [not defined] default = -1.9
-                                ! Surface temperature in sponge layer.
-#override ISOMIP_T_BOT_SPONGE = 1.0
-!#override ISOMIP_SPONGE_TEMP_OFFSET=0.1
-
-! PASSIVE TRACERS
-USE_ISOMIP_TRACER = False
-
-! Simulation time
-#override DAYMAX = 730
-
-!#override FIT_SALINITY = False
-
-!Passing Iceberg field to ocean
-ICEBERGS_APPLY_RIGID_BOUNDARY=True !Different boundary condition is used under ice shelves
-ALLOW_ICEBERG_FLUX_DIAGNOSTICS=True
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/README b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/README
deleted file mode 100644
index b4eb12b..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/README
+++ /dev/null
@@ -1,3 +0,0 @@
-A piece of the ice shelf breaks off. The elements are not bonded together, so they move freely away. However, they do interact with one another.
-
-Works best when started from restart file created by Static_berg simulation.
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/SIS_input b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/SIS_input
deleted file mode 120000
index ad3cd99..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/SIS_input
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/SIS_input
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/SIS_override b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/SIS_override
deleted file mode 100644
index 605ca84..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/SIS_override
+++ /dev/null
@@ -1,9 +0,0 @@
-# Blank file in which we can put "overrides" for parameters
-DO_ICEBERGS =True              !   If true, use the icebergs module.
-
-!Time Stepping
-#override DT_FORCING = 10.0              !   [s] default = 0.0
-#override DT_RHEOLOGY = 10.0             ! The sub-cycling time step, in s, for iterating
-#override DT_ICE_DYNAMICS = 10.0 
-
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/clean_MOM.sh b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/clean_MOM.sh
deleted file mode 120000
index c5370af..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/clean_MOM.sh
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/clean_MOM.sh
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/data_table b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/data_table
deleted file mode 120000
index 5b82b3c..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/data_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/data_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/diag_table b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/diag_table
deleted file mode 120000
index cff65fe..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/diag_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/diag_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/field_table b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/field_table
deleted file mode 120000
index b5ea991..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/field_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/field_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/input.nml b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/input.nml
deleted file mode 100644
index 7424ccd..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/input.nml
+++ /dev/null
@@ -1,140 +0,0 @@
- &MOM_input_nml
-        output_directory = './',
-        input_filename = 'r'
-        restart_input_dir = 'INPUT/',
-        restart_output_dir = 'RESTART/',
-        parameter_filename = 'MOM_input',
-                             'MOM_override' /
-
- &SIS_input_nml
-        output_directory = './',
-        input_filename = 'r'
-        restart_input_dir = 'INPUT/',
-        restart_output_dir = 'RESTART/',
-        parameter_filename = 'SIS_input',
-                             'SIS_override' /
-
- &diag_manager_nml
-         max_output_fields=1000
-         max_input_fields=1000
-         max_num_axis_sets=1000
-	 flush_nc_files=.true.
-         max_files=1000
-         max_axes=2000
- /
-
- &coupler_nml
-            months = 0,
-            days   = 60,
-            current_date = 1,1,1,0,0,0,
-            hours = 0,
-            minutes =0, 
-            seconds = 0
-            calendar = 'NOLEAP',
-            dt_cpld  = 10.0,
-            dt_atmos = 10.0,
-            do_atmos = .false.,
-            do_land = .false.,
-            do_ice = .true.,
-            do_ocean = .true.,
-            atmos_npes = 0,
-            ocean_npes = 0,
-            concurrent = .false.
-            use_lag_fluxes=.false. /
-
-
- &icebergs_nml
-    verbose=.false.,
-    verbose_hrs=240,
-    traj_sample_hrs=24000,
-    ignore_ij_restart=.true.
-    halo=2,
-    save_short_traj=.true.
-    debug=.false.,
-    really_debug=.false.,
-    use_slow_find=.true.,
-    add_weight_to_ocean=.true.,
-    passive_mode=.false.,
-    Static_icebergs=.False.,
-    ignore_missing_restart_bergs=.false.,
-    generate_test_icebergs=.false.,
-    speed_limit=0.,
-    use_roundoff_fix=.true.,
-    make_calving_reproduce=.false.,
-    Runge_not_Verlet=.false.,
-    iceberg_bonds_on=.false.,
-    critical_interaction_damping_on=.true.,
-    use_new_predictive_corrective=.true.,
-    interactive_icebergs_on=.true.
-    halo_debugging=.false.
-    spring_coef=0.00001
-    distribution=0.0, 0.99, 0.0, 0.00, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11,
-    hexagonal_icebergs=.true.
-    allow_bergs_to_roll=.true.
-    set_melt_rates_to_zero=.false.
-    use_roundoff_fix=.false.
-    grid_is_latlon=.false.
-    grid_is_regular=.true.
-    initial_orientation=-0.
-    rotate_icebergs_for_mass_spreading=.false.
-    lat_ref=-75.0
-    u_override=0.00
-    v_override=0.00
-    override_iceberg_velocities=.false.
-    add_iceberg_thickness_to_SSH=.false.
-    max_bonds=6
-    Iceberg_melt_without_decay=.true.
-    melt_icebergs_as_ice_shelf=.true.
-    Use_three_equation_model=.true.
-    find_melt_using_spread_mass=.true.
-    use_mixed_layer_salinity_for_thermo=.true.
-    pass_fields_to_ocean_model=.true.
-    rho_bergs=918.0
-    utide_icebergs=0.01
-    ustar_icebergs_bg=0.000
-    cdrag_icebergs =0.0025
-    const_gamma=.false.
-    Gamma_T_3EQ=0.22
-    ignore_traj=.False.
-    read_ocean_depth_from_file=.true.
-    apply_thickness_cutoff_to_bergs_melt=.true.
-    apply_thickness_cutoff_to_gridded_melt=.true.
-    melt_cutoff=10.
-    read_old_restarts=.false.
-    internal_bergs_for_drag=.true.
-    use_mixed_melting=.true.
- &data_override_nml
-         /
-
- &fms_io_nml
-         fms_netcdf_restart=.true.
-         threading_read='multi'
- /
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC' /
-
- &ice_albedo_nml
-      t_range = 10. /
-
- &ice_model_nml
-           /
-
- &monin_obukhov_nml
-            neutral = .true. /
-
- &ocean_albedo_nml
-      ocean_albedo_option = 5 /
-
- &sat_vapor_pres_nml
-      construct_table_wrt_liq = .true.,
-      construct_table_wrt_liq_and_ice = .true. /
-
- &xgrid_nml
-            make_exchange_reproduce = .false.
-            interp_method = 'second_order' /
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/run_script.sh b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/run_script.sh
deleted file mode 120000
index 2a081b9..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/run_script.sh
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/run_script.sh
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/submit_to_queue b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/submit_to_queue
deleted file mode 100644
index 4895e94..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_drift/submit_to_queue
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/bin/csh -f
-#PBS -r y                                                              #This job is restartable
-#PBS -j oe                                                             #STDOUT and STDERR are in the same file, specified below in the '-o' option
-#PBS -q batch                                                          #Do not change this - it tells your job where to run
-#PBS -S /bin/sh                                                        #Do not change this - it keeps your job from issuing a false alarm
-#PBS -E                                                                #Do not change this - it gives your job more and more useful Moab environment variables
-#PBS -N  Bergs_drift_layer                                               #Job Name:             You may want to change this to reflect your job's purpose or relation to an experiment
-#PBS -l partition=c3
-#PBS -l size=4                                                        #You will need to change this to reflect your job's core requirements - 24 is the current core increment.
-#PBS -l walltime=16:00:00                                              #You MUST change this to reflect your job's expected run time, including copy time
-#PBS -m bea                                                            #Email options: You may want to change this to reduce your incoming email stream
-
-######################################################################################################################
-#
-#  Gaea c1ms batch skeleton version 0.9
-#  
-#  0.9 - Initial version - 20110906 - Daniel Gall - Daniel.Gall@noaa.gov
-#
-######################################################################################################################
-
-#Source the system initialization scripts (but not the user's so as to avoid interactive settings that can poison us)
-source /etc/csh.cshrc
-
-#Run the experiment
-aprun -n 128 ../../../../../build/intel/ice_ocean_SIS2/repro/MOM6
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/MOM_input b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/MOM_input
deleted file mode 120000
index a756962..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/MOM_input
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/MOM_input
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/MOM_override b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/MOM_override
deleted file mode 100644
index cd50151..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/MOM_override
+++ /dev/null
@@ -1,91 +0,0 @@
-! Blank file in which we can put "overrides" for parameters
-! z
-#override USE_REGRIDDING = True
-#override REGRIDDING_COORDINATE_MODE = "SIGMA_SHELF_ZSTAR" 
-#override INTERPOLATION_SCHEME = "PPM_H4"
-#override REMAPPING_SCHEME = "PPM_H4"
-
-
-!TPY params
-#override NK = 72
-#override NKML = 4
-
-! TIME STEP
-#override DT = 10
-#override DT_THERM = 10
-#override DT_FORCING = 10
-
-! MIXING
-#override SMAGORINSKY_KH = False
-#override BIHARMONIC = False
-#override KH = 6.0  ! back. horiz. visc.
-#override KHTR = 1.0    ! back. horiz. diff.
-#override KD = 5.0E-5     ! back. diapycnal diff.
-#override KV = 1.0E-3     ! back. diapycnal visc.
-
-!WARM IC
-#override ISOMIP_T_SUR = -1.9
-#override ISOMIP_S_SUR = 33.8
-#override ISOMIP_T_BOT = 1.0
-#override ISOMIP_S_BOT = 34.7
-
-! ice shelf
-#override ICE_SHELF = False                !   [Boolean] default = False
-#override SHELF_THERMO = TRUE
-#override SHELF_THREE_EQN = True
-#override SHELF_3EQ_GAMMA = False
-#override UTIDE = 0.01
-!SHELF_S_ROOT = True
-!#override USE_HMIX_SFC_PROP = True
-!#override HMIX_SFC_PROP = 10.
-
-! FRAZIL  - making sure sea ice does not form
-#override FRAZIL = False
-#override PRESSURE_DEPENDENT_FRAZIL = False
-
-! EPBL
-#override ENERGETICS_SFC_PBL = True       !   [Boolean] default = False
-                                ! If true, use an implied energetics planetary boundary
-                                ! layer scheme to determine the diffusivity and viscosity
-                                ! in the surface boundary layer.
-#override EPBL_IS_ADDITIVE = True         !   [Boolean] default = True
-                                ! If true, the diffusivity from ePBL is added to all
-                                ! other diffusivities. Otherwise, the larger of kappa-
-                                ! shear and ePBL diffusivities are used.
-#override USE_MLD_ITERATION = True        !   [Boolean] default = False
-                                ! A logical that determines whether or not to use the
-                                ! MLD to set the EPBL length scale.
-#override HTBL_SHELF_MIN = 10.0
-#override BOUND_SALINITY = True
-
-
-! SHEAR MIXING
-#override USE_JACKSON_PARAM = True
-#override RINO_CRIT = 0.25
-!#override KD_KAPPA_SHEAR_0 = 1.0E-2
-
-! SPONGE
-#override SPONGE = TRUE
-ISOMIP_SPONGE_FILE = "3D_LAYER_WARM_TPY_IC.nc"
-#override ISOMIP_TNUDG = 0.1
-#override ISOMIP_TNUDG = 0.1
-#override ISOMIP_S_SUR_SPONGE = 33.8      !   [not defined] default = 35.0
-                                ! Surface salinity in sponge layer.
-#override ISOMIP_S_BOT_SPONGE = 34.7      !   [not defined] default = 35.0
-                                ! Bottom salinity in sponge layer.
-#override ISOMIP_T_SUR_SPONGE = -1.9      !   [not defined] default = -1.9
-                                ! Surface temperature in sponge layer.
-#override ISOMIP_T_BOT_SPONGE = 1.0
-!#override ISOMIP_SPONGE_TEMP_OFFSET=0.1
-
-! PASSIVE TRACERS
-USE_ISOMIP_TRACER = False
-
-! Simulation time
-#override DAYMAX = 730
-
-!#override FIT_SALINITY = False
-
-!Passing Iceberg field to ocean
-ICEBERGS_APPLY_RIGID_BOUNDARY=True !Different boundary condition is used under ice shelves
-ALLOW_ICEBERG_FLUX_DIAGNOSTICS=True
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/README b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/README
deleted file mode 100644
index fa2bc28..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/README
+++ /dev/null
@@ -1,5 +0,0 @@
-A tabular iceberg breaks away from the ice shelf. The non-static icebergs move away from the ice shelf at a prescribed velocity. The time step is quite small (10s) in order to resolve ocean motions
-
-Works best when started from restart file created by Static_berg simulation.
-
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/SIS_input b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/SIS_input
deleted file mode 120000
index ad3cd99..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/SIS_input
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/SIS_input
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/SIS_override b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/SIS_override
deleted file mode 100644
index 605ca84..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/SIS_override
+++ /dev/null
@@ -1,9 +0,0 @@
-# Blank file in which we can put "overrides" for parameters
-DO_ICEBERGS =True              !   If true, use the icebergs module.
-
-!Time Stepping
-#override DT_FORCING = 10.0              !   [s] default = 0.0
-#override DT_RHEOLOGY = 10.0             ! The sub-cycling time step, in s, for iterating
-#override DT_ICE_DYNAMICS = 10.0 
-
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/clean_MOM.sh b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/clean_MOM.sh
deleted file mode 120000
index c5370af..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/clean_MOM.sh
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/clean_MOM.sh
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/data_table b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/data_table
deleted file mode 120000
index 5b82b3c..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/data_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/data_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/diag_table b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/diag_table
deleted file mode 120000
index cff65fe..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/diag_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/diag_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/field_table b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/field_table
deleted file mode 120000
index b5ea991..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/field_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/field_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/input.nml b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/input.nml
deleted file mode 100644
index 97afa25..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/input.nml
+++ /dev/null
@@ -1,140 +0,0 @@
- &MOM_input_nml
-        output_directory = './',
-        input_filename = 'r'
-        restart_input_dir = 'INPUT/',
-        restart_output_dir = 'RESTART/',
-        parameter_filename = 'MOM_input',
-                             'MOM_override' /
-
- &SIS_input_nml
-        output_directory = './',
-        input_filename = 'r'
-        restart_input_dir = 'INPUT/',
-        restart_output_dir = 'RESTART/',
-        parameter_filename = 'SIS_input',
-                             'SIS_override' /
-
- &diag_manager_nml
-         max_output_fields=1000
-         max_input_fields=1000
-         max_num_axis_sets=1000
-	 flush_nc_files=.true.
-         max_files=1000
-         max_axes=2000
- /
-
- &coupler_nml
-            months = 0,
-            days   = 60,
-            current_date = 1,1,1,0,0,0,
-            hours = 0,
-            minutes =0, 
-            seconds = 0
-            calendar = 'NOLEAP',
-            dt_cpld  = 10.0,
-            dt_atmos = 10.0,
-            do_atmos = .false.,
-            do_land = .false.,
-            do_ice = .true.,
-            do_ocean = .true.,
-            atmos_npes = 0,
-            ocean_npes = 0,
-            concurrent = .false.
-            use_lag_fluxes=.false. /
-
-
- &icebergs_nml
-    verbose=.false.,
-    verbose_hrs=240,
-    traj_sample_hrs=24000,
-    ignore_ij_restart=.true.
-    halo=2,
-    save_short_traj=.true.
-    debug=.false.,
-    really_debug=.false.,
-    use_slow_find=.true.,
-    add_weight_to_ocean=.true.,
-    passive_mode=.false.,
-    Static_icebergs=.False.,
-    ignore_missing_restart_bergs=.false.,
-    generate_test_icebergs=.false.,
-    speed_limit=0.,
-    use_roundoff_fix=.true.,
-    make_calving_reproduce=.false.,
-    Runge_not_Verlet=.false.,
-    iceberg_bonds_on=.false.,
-    critical_interaction_damping_on=.true.,
-    use_new_predictive_corrective=.true.,
-    interactive_icebergs_on=.false.
-    halo_debugging=.false.
-    spring_coef=0.00001
-    distribution=0.0, 0.99, 0.0, 0.00, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11,
-    hexagonal_icebergs=.true.
-    allow_bergs_to_roll=.true.
-    set_melt_rates_to_zero=.false.
-    use_roundoff_fix=.false.
-    grid_is_latlon=.false.
-    grid_is_regular=.true.
-    initial_orientation=-0.
-    rotate_icebergs_for_mass_spreading=.false.
-    lat_ref=-75.0
-    u_override=0.01
-    v_override=0.00
-    override_iceberg_velocities=.true.
-    add_iceberg_thickness_to_SSH=.false.
-    max_bonds=6
-    Iceberg_melt_without_decay=.true.
-    melt_icebergs_as_ice_shelf=.true.
-    Use_three_equation_model=.true.
-    find_melt_using_spread_mass=.true.
-    use_mixed_layer_salinity_for_thermo=.true.
-    pass_fields_to_ocean_model=.true.
-    rho_bergs=918.0
-    utide_icebergs=0.01
-    ustar_icebergs_bg=0.000
-    cdrag_icebergs =0.0025
-    const_gamma=.false.
-    Gamma_T_3EQ=0.22
-    ignore_traj=.False.
-    read_ocean_depth_from_file=.true.
-    apply_thickness_cutoff_to_bergs_melt=.true.
-    apply_thickness_cutoff_to_gridded_melt=.true.
-    melt_cutoff=10.
-    read_old_restarts=.false.
-    internal_bergs_for_drag=.true.
-    use_mixed_melting=.true.
- &data_override_nml
-         /
-
- &fms_io_nml
-         fms_netcdf_restart=.true.
-         threading_read='multi'
- /
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC' /
-
- &ice_albedo_nml
-      t_range = 10. /
-
- &ice_model_nml
-           /
-
- &monin_obukhov_nml
-            neutral = .true. /
-
- &ocean_albedo_nml
-      ocean_albedo_option = 5 /
-
- &sat_vapor_pres_nml
-      construct_table_wrt_liq = .true.,
-      construct_table_wrt_liq_and_ice = .true. /
-
- &xgrid_nml
-            make_exchange_reproduce = .false.
-            interp_method = 'second_order' /
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/run_script.sh b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/run_script.sh
deleted file mode 120000
index 2a081b9..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/run_script.sh
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/run_script.sh
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/submit_to_queue b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/submit_to_queue
deleted file mode 100644
index 2e508c9..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Moving_berg_fixed/submit_to_queue
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/bin/csh -f
-#PBS -r y                                                              #This job is restartable
-#PBS -j oe                                                             #STDOUT and STDERR are in the same file, specified below in the '-o' option
-#PBS -q batch                                                          #Do not change this - it tells your job where to run
-#PBS -S /bin/sh                                                        #Do not change this - it keeps your job from issuing a false alarm
-#PBS -E                                                                #Do not change this - it gives your job more and more useful Moab environment variables
-#PBS -N  Bergs_fixed_layer                                               #Job Name:             You may want to change this to reflect your job's purpose or relation to an experiment
-#PBS -l partition=c3
-#PBS -l size=4                                                        #You will need to change this to reflect your job's core requirements - 24 is the current core increment.
-#PBS -l walltime=16:00:00                                              #You MUST change this to reflect your job's expected run time, including copy time
-#PBS -m bea                                                            #Email options: You may want to change this to reduce your incoming email stream
-
-######################################################################################################################
-#
-#  Gaea c1ms batch skeleton version 0.9
-#  
-#  0.9 - Initial version - 20110906 - Daniel Gall - Daniel.Gall@noaa.gov
-#
-######################################################################################################################
-
-#Source the system initialization scripts (but not the user's so as to avoid interactive settings that can poison us)
-source /etc/csh.cshrc
-
-#Run the experiment
-aprun -n 128 ../../../../../build/intel/ice_ocean_SIS2/repro/MOM6
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/MOM_input b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/MOM_input
deleted file mode 120000
index a756962..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/MOM_input
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/MOM_input
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/MOM_override b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/MOM_override
deleted file mode 100644
index 760b13d..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/MOM_override
+++ /dev/null
@@ -1,94 +0,0 @@
-! Blank file in which we can put "overrides" for parameters
-! z
-#override USE_REGRIDDING = True
-#override REGRIDDING_COORDINATE_MODE = "SIGMA_SHELF_ZSTAR" 
-#override INTERPOLATION_SCHEME = "PPM_H4"
-#override REMAPPING_SCHEME = "PPM_H4"
-
-
-!TPY params
-#override NK = 72
-#override NKML = 4
-
-! TIME STEP
-!#override DT = 10
-!#override DT_THERM = 10
-!#override DT_FORCING = 10
-#override DT = 360
-#override DT_THERM = 360
-#override DT_FORCING = 360
-
-! MIXING
-#override SMAGORINSKY_KH = False
-#override BIHARMONIC = False
-#override KH = 6.0  ! back. horiz. visc.
-#override KHTR = 1.0    ! back. horiz. diff.
-#override KD = 5.0E-5     ! back. diapycnal diff.
-#override KV = 1.0E-3     ! back. diapycnal visc.
-
-!WARM IC
-#override ISOMIP_T_SUR = -1.9
-#override ISOMIP_S_SUR = 33.8
-#override ISOMIP_T_BOT = 1.0
-#override ISOMIP_S_BOT = 34.7
-
-! ice shelf
-#override ICE_SHELF = False                !   [Boolean] default = False
-#override SHELF_THERMO = TRUE
-#override SHELF_THREE_EQN = True
-#override SHELF_3EQ_GAMMA = False
-#override UTIDE = 0.01
-!SHELF_S_ROOT = True
-!#override USE_HMIX_SFC_PROP = True
-!#override HMIX_SFC_PROP = 10.
-
-! FRAZIL  - making sure sea ice does not form
-#override FRAZIL = False
-#override PRESSURE_DEPENDENT_FRAZIL = False
-
-! EPBL
-#override ENERGETICS_SFC_PBL = True       !   [Boolean] default = False
-                                ! If true, use an implied energetics planetary boundary
-                                ! layer scheme to determine the diffusivity and viscosity
-                                ! in the surface boundary layer.
-#override EPBL_IS_ADDITIVE = True         !   [Boolean] default = True
-                                ! If true, the diffusivity from ePBL is added to all
-                                ! other diffusivities. Otherwise, the larger of kappa-
-                                ! shear and ePBL diffusivities are used.
-#override USE_MLD_ITERATION = True        !   [Boolean] default = False
-                                ! A logical that determines whether or not to use the
-                                ! MLD to set the EPBL length scale.
-#override HTBL_SHELF_MIN = 10.0
-#override BOUND_SALINITY = True
-
-
-! SHEAR MIXING
-#override USE_JACKSON_PARAM = True
-#override RINO_CRIT = 0.25
-!#override KD_KAPPA_SHEAR_0 = 1.0E-2
-
-! SPONGE
-#override SPONGE = TRUE
-ISOMIP_SPONGE_FILE = "3D_LAYER_WARM_TPY_IC.nc"
-#override ISOMIP_TNUDG = 0.1
-#override ISOMIP_TNUDG = 0.1
-#override ISOMIP_S_SUR_SPONGE = 33.8      !   [not defined] default = 35.0
-                                ! Surface salinity in sponge layer.
-#override ISOMIP_S_BOT_SPONGE = 34.7      !   [not defined] default = 35.0
-                                ! Bottom salinity in sponge layer.
-#override ISOMIP_T_SUR_SPONGE = -1.9      !   [not defined] default = -1.9
-                                ! Surface temperature in sponge layer.
-#override ISOMIP_T_BOT_SPONGE = 1.0
-!#override ISOMIP_SPONGE_TEMP_OFFSET=0.1
-
-! PASSIVE TRACERS
-USE_ISOMIP_TRACER = False
-
-! Simulation time
-#override DAYMAX = 730
-
-!#override FIT_SALINITY = False
-
-!Passing Iceberg field to ocean
-ICEBERGS_APPLY_RIGID_BOUNDARY=True !Different boundary condition is used under ice shelves
-ALLOW_ICEBERG_FLUX_DIAGNOSTICS=True
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/README b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/README
deleted file mode 100644
index c042733..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/README
+++ /dev/null
@@ -1 +0,0 @@
-Ice shelf does not move. Shelf melts using three equation model.
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/SIS_input b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/SIS_input
deleted file mode 120000
index ad3cd99..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/SIS_input
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/SIS_input
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/SIS_override b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/SIS_override
deleted file mode 100644
index fc641d7..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/SIS_override
+++ /dev/null
@@ -1,8 +0,0 @@
-# Blank file in which we can put "overrides" for parameters
-DO_ICEBERGS =True              !   If true, use the icebergs module.
-
-!Time Stepping
-!#override DT_FORCING = 10.0              !   [s] default = 0.0
-!#override DT_RHEOLOGY = 10.0             ! The sub-cycling time step, in s, for iterating
-
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/clean_MOM.sh b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/clean_MOM.sh
deleted file mode 120000
index c5370af..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/clean_MOM.sh
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/clean_MOM.sh
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/data_table b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/data_table
deleted file mode 120000
index 5b82b3c..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/data_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/data_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/diag_table b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/diag_table
deleted file mode 120000
index cff65fe..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/diag_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/diag_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/field_table b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/field_table
deleted file mode 120000
index b5ea991..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/field_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/field_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/input.nml b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/input.nml
deleted file mode 100644
index 3854fd4..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/input.nml
+++ /dev/null
@@ -1,140 +0,0 @@
- &MOM_input_nml
-        output_directory = './',
-        input_filename = 'r'
-        restart_input_dir = 'INPUT/',
-        restart_output_dir = 'RESTART/',
-        parameter_filename = 'MOM_input',
-                             'MOM_override' /
-
- &SIS_input_nml
-        output_directory = './',
-        input_filename = 'r'
-        restart_input_dir = 'INPUT/',
-        restart_output_dir = 'RESTART/',
-        parameter_filename = 'SIS_input',
-                             'SIS_override' /
-
- &diag_manager_nml
-         max_output_fields=1000
-         max_input_fields=1000
-         max_num_axis_sets=1000
-	 flush_nc_files=.true.
-         max_files=1000
-         max_axes=2000
- /
-
- &coupler_nml
-            months = 60,
-            days   = 0,
-            current_date = 1,1,1,0,0,0,
-            hours = 0,
-            minutes =0, 
-            seconds = 0
-            calendar = 'NOLEAP',
-            dt_cpld  = 360.0,
-            dt_atmos = 360.0,
-            do_atmos = .false.,
-            do_land = .false.,
-            do_ice = .true.,
-            do_ocean = .true.,
-            atmos_npes = 0,
-            ocean_npes = 0,
-            concurrent = .false.
-            use_lag_fluxes=.false. /
-
-
- &icebergs_nml
-    verbose=.false.,
-    verbose_hrs=240,
-    traj_sample_hrs=24000,
-    ignore_ij_restart=.true.
-    halo=2,
-    save_short_traj=.true.
-    debug=.false.,
-    really_debug=.false.,
-    use_slow_find=.true.,
-    add_weight_to_ocean=.true.,
-    passive_mode=.false.,
-    Static_icebergs=.True.,
-    ignore_missing_restart_bergs=.false.,
-    generate_test_icebergs=.false.,
-    speed_limit=0.,
-    use_roundoff_fix=.true.,
-    make_calving_reproduce=.false.,
-    Runge_not_Verlet=.false.,
-    iceberg_bonds_on=.false.,
-    critical_interaction_damping_on=.true.,
-    use_new_predictive_corrective=.true.,
-    interactive_icebergs_on=.false.
-    halo_debugging=.false.
-    spring_coef=0.00001
-    distribution=0.0, 0.99, 0.0, 0.00, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11,
-    hexagonal_icebergs=.true.
-    allow_bergs_to_roll=.true.
-    set_melt_rates_to_zero=.false.
-    use_roundoff_fix=.false.
-    grid_is_latlon=.false.
-    grid_is_regular=.true.
-    initial_orientation=-0.
-    rotate_icebergs_for_mass_spreading=.false.
-    lat_ref=-75.0
-    u_override=0.00
-    v_override=0.00
-    override_iceberg_velocities=.false.
-    add_iceberg_thickness_to_SSH=.false.
-    max_bonds=6
-    Iceberg_melt_without_decay=.true.
-    melt_icebergs_as_ice_shelf=.true.
-    Use_three_equation_model=.true.
-    find_melt_using_spread_mass=.true.
-    use_mixed_layer_salinity_for_thermo=.true.
-    pass_fields_to_ocean_model=.true.
-    rho_bergs=918.0
-    utide_icebergs=0.01
-    ustar_icebergs_bg=0.000
-    cdrag_icebergs =0.0025
-    const_gamma=.false.
-    Gamma_T_3EQ=0.22
-    ignore_traj=.False.
-    read_ocean_depth_from_file=.true.
-    apply_thickness_cutoff_to_bergs_melt=.true.
-    apply_thickness_cutoff_to_gridded_melt=.true.
-    melt_cutoff=10.
-    read_old_restarts=.false.
-    internal_bergs_for_drag=.true.
-    use_mixed_melting=.true.
- &data_override_nml
-         /
-
- &fms_io_nml
-         fms_netcdf_restart=.true.
-         threading_read='multi'
- /
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC' /
-
- &ice_albedo_nml
-      t_range = 10. /
-
- &ice_model_nml
-           /
-
- &monin_obukhov_nml
-            neutral = .true. /
-
- &ocean_albedo_nml
-      ocean_albedo_option = 5 /
-
- &sat_vapor_pres_nml
-      construct_table_wrt_liq = .true.,
-      construct_table_wrt_liq_and_ice = .true. /
-
- &xgrid_nml
-            make_exchange_reproduce = .false.
-            interp_method = 'second_order' /
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/run_script.sh b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/run_script.sh
deleted file mode 120000
index 2a081b9..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/run_script.sh
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/run_script.sh
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/submit_to_queue b/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/submit_to_queue
deleted file mode 100644
index d35f1b8..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Bergs/Sigma_Shelf_Star/Static_shelf/submit_to_queue
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/bin/csh -f
-#PBS -r y                                                              #This job is restartable
-#PBS -j oe                                                             #STDOUT and STDERR are in the same file, specified below in the '-o' option
-#PBS -q batch                                                          #Do not change this - it tells your job where to run
-#PBS -S /bin/sh                                                        #Do not change this - it keeps your job from issuing a false alarm
-#PBS -E                                                                #Do not change this - it gives your job more and more useful Moab environment variables
-#PBS -N  Bergs_Empty_Run                                               #Job Name:             You may want to change this to reflect your job's purpose or relation to an experiment
-#PBS -l partition=c3
-#PBS -l size=4                                                        #You will need to change this to reflect your job's core requirements - 24 is the current core increment.
-#PBS -l walltime=16:00:00                                              #You MUST change this to reflect your job's expected run time, including copy time
-#PBS -m bea                                                            #Email options: You may want to change this to reduce your incoming email stream
-
-######################################################################################################################
-#
-#  Gaea c1ms batch skeleton version 0.9
-#  
-#  0.9 - Initial version - 20110906 - Daniel Gall - Daniel.Gall@noaa.gov
-#
-######################################################################################################################
-
-#Source the system initialization scripts (but not the user's so as to avoid interactive settings that can poison us)
-source /etc/csh.cshrc
-
-#Run the experiment
-aprun -n 128 ../../../../../build/intel/ice_ocean_SIS2/repro/MOM6
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/MOM_input b/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/MOM_input
deleted file mode 120000
index a756962..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/MOM_input
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/MOM_input
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/MOM_override b/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/MOM_override
deleted file mode 100644
index 0e751df..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/MOM_override
+++ /dev/null
@@ -1,64 +0,0 @@
-! Blank file in which we can put "overrides" for parameters
-
-!TPY params
-#override NK = 72
-#override NKML = 4
-
-! TIME STEP
-#override DT = 720
-#override DT_THERM = 720
-
-! MIXING
-#override SMAGORINSKY_KH = False
-#override BIHARMONIC = False
-#override KH = 6.0  ! back. horiz. visc.
-#override KHTR = 1.0    ! back. horiz. diff.
-#override KD = 5.0E-5     ! back. diapycnal diff.
-#override KV = 1.0E-3     ! back. diapycnal visc.
-
-!WARM IC
-#override ISOMIP_T_SUR = -1.9
-#override ISOMIP_S_SUR = 33.8
-#override ISOMIP_T_BOT = 1.0
-#override ISOMIP_S_BOT = 34.7
-
-! ice shelf
-#override SHELF_THERMO = TRUE
-#override SHELF_THREE_EQN = True
-#override SHELF_3EQ_GAMMA = False
-#override UTIDE = 0.01
-!SHELF_S_ROOT = True
-!#override USE_HMIX_SFC_PROP = True
-!#override HMIX_SFC_PROP = 10.
-
-! FRAZIL  - making sure sea ice does not form
-#override FRAZIL = False
-#override PRESSURE_DEPENDENT_FRAZIL = False
-
-! MIXED LAYER
-#override BULKMIXEDLAYER = True
-#override BULK_RI_ML = 0.25
-#override MIXEDLAYER_RESTRAT = True
-#override HMIX_MIN = 2.0
-!#override KV_TBL_MIN = 1.0E-2
-#override HTBL_SHELF_MIN = 2.0
-#override BOUND_SALINITY = True
- 
-! SHEAR MIXING
-#override USE_JACKSON_PARAM = True
-#override RINO_CRIT = 0.25
-!#override KD_KAPPA_SHEAR_0 = 1.0E-2
-
-! SPONGE
-#override SPONGE = TRUE
-ISOMIP_SPONGE_FILE = "3D_LAYER_WARM_TPY_IC.nc"
-#override ISOMIP_TNUDG = 0.1
-!#override ISOMIP_SPONGE_TEMP_OFFSET=0.1
-
-! PASSIVE TRACERS
-USE_ISOMIP_TRACER = True
-
-! Simulation time
-#override DAYMAX = 730
-
-!#override FIT_SALINITY = False
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/README b/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/README
deleted file mode 100644
index c042733..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/README
+++ /dev/null
@@ -1 +0,0 @@
-Ice shelf does not move. Shelf melts using three equation model.
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/SIS_input b/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/SIS_input
deleted file mode 120000
index ad3cd99..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/SIS_input
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/SIS_input
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/SIS_override b/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/SIS_override
deleted file mode 100644
index f591eb2..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/SIS_override
+++ /dev/null
@@ -1,8 +0,0 @@
-# Blank file in which we can put "overrides" for parameters
-DO_ICEBERGS =False              !   If true, use the icebergs module.
-
-!Time Stepping
-!#override DT_FORCING = 10.0              !   [s] default = 0.0
-!#override DT_RHEOLOGY = 10.0             ! The sub-cycling time step, in s, for iterating
-
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/clean_MOM.sh b/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/clean_MOM.sh
deleted file mode 120000
index c5370af..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/clean_MOM.sh
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/clean_MOM.sh
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/data_table b/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/data_table
deleted file mode 120000
index 5b82b3c..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/data_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/data_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/diag_table b/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/diag_table
deleted file mode 120000
index cff65fe..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/diag_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/diag_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/field_table b/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/field_table
deleted file mode 120000
index b5ea991..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/field_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/field_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/input.nml b/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/input.nml
deleted file mode 100644
index 3854fd4..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/input.nml
+++ /dev/null
@@ -1,140 +0,0 @@
- &MOM_input_nml
-        output_directory = './',
-        input_filename = 'r'
-        restart_input_dir = 'INPUT/',
-        restart_output_dir = 'RESTART/',
-        parameter_filename = 'MOM_input',
-                             'MOM_override' /
-
- &SIS_input_nml
-        output_directory = './',
-        input_filename = 'r'
-        restart_input_dir = 'INPUT/',
-        restart_output_dir = 'RESTART/',
-        parameter_filename = 'SIS_input',
-                             'SIS_override' /
-
- &diag_manager_nml
-         max_output_fields=1000
-         max_input_fields=1000
-         max_num_axis_sets=1000
-	 flush_nc_files=.true.
-         max_files=1000
-         max_axes=2000
- /
-
- &coupler_nml
-            months = 60,
-            days   = 0,
-            current_date = 1,1,1,0,0,0,
-            hours = 0,
-            minutes =0, 
-            seconds = 0
-            calendar = 'NOLEAP',
-            dt_cpld  = 360.0,
-            dt_atmos = 360.0,
-            do_atmos = .false.,
-            do_land = .false.,
-            do_ice = .true.,
-            do_ocean = .true.,
-            atmos_npes = 0,
-            ocean_npes = 0,
-            concurrent = .false.
-            use_lag_fluxes=.false. /
-
-
- &icebergs_nml
-    verbose=.false.,
-    verbose_hrs=240,
-    traj_sample_hrs=24000,
-    ignore_ij_restart=.true.
-    halo=2,
-    save_short_traj=.true.
-    debug=.false.,
-    really_debug=.false.,
-    use_slow_find=.true.,
-    add_weight_to_ocean=.true.,
-    passive_mode=.false.,
-    Static_icebergs=.True.,
-    ignore_missing_restart_bergs=.false.,
-    generate_test_icebergs=.false.,
-    speed_limit=0.,
-    use_roundoff_fix=.true.,
-    make_calving_reproduce=.false.,
-    Runge_not_Verlet=.false.,
-    iceberg_bonds_on=.false.,
-    critical_interaction_damping_on=.true.,
-    use_new_predictive_corrective=.true.,
-    interactive_icebergs_on=.false.
-    halo_debugging=.false.
-    spring_coef=0.00001
-    distribution=0.0, 0.99, 0.0, 0.00, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11,
-    hexagonal_icebergs=.true.
-    allow_bergs_to_roll=.true.
-    set_melt_rates_to_zero=.false.
-    use_roundoff_fix=.false.
-    grid_is_latlon=.false.
-    grid_is_regular=.true.
-    initial_orientation=-0.
-    rotate_icebergs_for_mass_spreading=.false.
-    lat_ref=-75.0
-    u_override=0.00
-    v_override=0.00
-    override_iceberg_velocities=.false.
-    add_iceberg_thickness_to_SSH=.false.
-    max_bonds=6
-    Iceberg_melt_without_decay=.true.
-    melt_icebergs_as_ice_shelf=.true.
-    Use_three_equation_model=.true.
-    find_melt_using_spread_mass=.true.
-    use_mixed_layer_salinity_for_thermo=.true.
-    pass_fields_to_ocean_model=.true.
-    rho_bergs=918.0
-    utide_icebergs=0.01
-    ustar_icebergs_bg=0.000
-    cdrag_icebergs =0.0025
-    const_gamma=.false.
-    Gamma_T_3EQ=0.22
-    ignore_traj=.False.
-    read_ocean_depth_from_file=.true.
-    apply_thickness_cutoff_to_bergs_melt=.true.
-    apply_thickness_cutoff_to_gridded_melt=.true.
-    melt_cutoff=10.
-    read_old_restarts=.false.
-    internal_bergs_for_drag=.true.
-    use_mixed_melting=.true.
- &data_override_nml
-         /
-
- &fms_io_nml
-         fms_netcdf_restart=.true.
-         threading_read='multi'
- /
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC' /
-
- &ice_albedo_nml
-      t_range = 10. /
-
- &ice_model_nml
-           /
-
- &monin_obukhov_nml
-            neutral = .true. /
-
- &ocean_albedo_nml
-      ocean_albedo_option = 5 /
-
- &sat_vapor_pres_nml
-      construct_table_wrt_liq = .true.,
-      construct_table_wrt_liq_and_ice = .true. /
-
- &xgrid_nml
-            make_exchange_reproduce = .false.
-            interp_method = 'second_order' /
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/run_script.sh b/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/run_script.sh
deleted file mode 120000
index 2a081b9..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/run_script.sh
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/run_script.sh
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/submit_to_queue b/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/submit_to_queue
deleted file mode 100644
index d35f1b8..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Layer/Static_shelf/submit_to_queue
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/bin/csh -f
-#PBS -r y                                                              #This job is restartable
-#PBS -j oe                                                             #STDOUT and STDERR are in the same file, specified below in the '-o' option
-#PBS -q batch                                                          #Do not change this - it tells your job where to run
-#PBS -S /bin/sh                                                        #Do not change this - it keeps your job from issuing a false alarm
-#PBS -E                                                                #Do not change this - it gives your job more and more useful Moab environment variables
-#PBS -N  Bergs_Empty_Run                                               #Job Name:             You may want to change this to reflect your job's purpose or relation to an experiment
-#PBS -l partition=c3
-#PBS -l size=4                                                        #You will need to change this to reflect your job's core requirements - 24 is the current core increment.
-#PBS -l walltime=16:00:00                                              #You MUST change this to reflect your job's expected run time, including copy time
-#PBS -m bea                                                            #Email options: You may want to change this to reduce your incoming email stream
-
-######################################################################################################################
-#
-#  Gaea c1ms batch skeleton version 0.9
-#  
-#  0.9 - Initial version - 20110906 - Daniel Gall - Daniel.Gall@noaa.gov
-#
-######################################################################################################################
-
-#Source the system initialization scripts (but not the user's so as to avoid interactive settings that can poison us)
-source /etc/csh.cshrc
-
-#Run the experiment
-aprun -n 128 ../../../../../build/intel/ice_ocean_SIS2/repro/MOM6
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/MOM_input b/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/MOM_input
deleted file mode 120000
index a756962..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/MOM_input
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/MOM_input
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/MOM_override b/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/MOM_override
deleted file mode 100644
index e2277a9..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/MOM_override
+++ /dev/null
@@ -1,91 +0,0 @@
-! Blank file in which we can put "overrides" for parameters
-! z
-#override USE_REGRIDDING = True
-#override REGRIDDING_COORDINATE_MODE = "SIGMA_SHELF_ZSTAR" 
-#override INTERPOLATION_SCHEME = "PPM_H4"
-#override REMAPPING_SCHEME = "PPM_H4"
-
-
-!TPY params
-#override NK = 72
-#override NKML = 4
-
-! TIME STEP
-#override DT = 360
-#override DT_THERM = 360
-#override DT_FORCING = 360
-!#override DT = 10
-!#override DT_THERM = 10
-!#override DT_FORCING = 10
-
-! MIXING
-#override SMAGORINSKY_KH = False
-#override BIHARMONIC = False
-#override KH = 6.0  ! back. horiz. visc.
-#override KHTR = 1.0    ! back. horiz. diff.
-#override KD = 5.0E-5     ! back. diapycnal diff.
-#override KV = 1.0E-3     ! back. diapycnal visc.
-
-!WARM IC
-#override ISOMIP_T_SUR = -1.9
-#override ISOMIP_S_SUR = 33.8
-#override ISOMIP_T_BOT = 1.0
-#override ISOMIP_S_BOT = 34.7
-
-! ice shelf
-#override ICE_SHELF = True                !   [Boolean] default = False
-#override SHELF_THERMO = TRUE
-#override SHELF_THREE_EQN = True
-#override SHELF_3EQ_GAMMA = False
-#override UTIDE = 0.01
-!SHELF_S_ROOT = True
-!#override USE_HMIX_SFC_PROP = True
-!#override HMIX_SFC_PROP = 10.
-
-! FRAZIL  - making sure sea ice does not form
-#override FRAZIL = False
-#override PRESSURE_DEPENDENT_FRAZIL = False
-
-! EPBL
-#override ENERGETICS_SFC_PBL = True       !   [Boolean] default = False
-                                ! If true, use an implied energetics planetary boundary
-                                ! layer scheme to determine the diffusivity and viscosity
-                                ! in the surface boundary layer.
-#override EPBL_IS_ADDITIVE = True         !   [Boolean] default = True
-                                ! If true, the diffusivity from ePBL is added to all
-                                ! other diffusivities. Otherwise, the larger of kappa-
-                                ! shear and ePBL diffusivities are used.
-#override USE_MLD_ITERATION = True        !   [Boolean] default = False
-                                ! A logical that determines whether or not to use the
-                                ! MLD to set the EPBL length scale.
-#override HTBL_SHELF_MIN = 10.0
-#override BOUND_SALINITY = True
-
-
-! SHEAR MIXING
-#override USE_JACKSON_PARAM = True
-#override RINO_CRIT = 0.25
-!#override KD_KAPPA_SHEAR_0 = 1.0E-2
-
-! SPONGE
-#override SPONGE = TRUE
-ISOMIP_SPONGE_FILE = "3D_LAYER_WARM_TPY_IC.nc"
-#override ISOMIP_TNUDG = 0.1
-#override ISOMIP_TNUDG = 0.1
-#override ISOMIP_S_SUR_SPONGE = 33.8      !   [not defined] default = 35.0
-                                ! Surface salinity in sponge layer.
-#override ISOMIP_S_BOT_SPONGE = 34.7      !   [not defined] default = 35.0
-                                ! Bottom salinity in sponge layer.
-#override ISOMIP_T_SUR_SPONGE = -1.9      !   [not defined] default = -1.9
-                                ! Surface temperature in sponge layer.
-#override ISOMIP_T_BOT_SPONGE = 1.0
-!#override ISOMIP_SPONGE_TEMP_OFFSET=0.1
-
-! PASSIVE TRACERS
-USE_ISOMIP_TRACER = True
-
-! Simulation time
-#override DAYMAX = 730
-
-!#override FIT_SALINITY = False
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/README b/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/README
deleted file mode 100644
index c042733..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/README
+++ /dev/null
@@ -1 +0,0 @@
-Ice shelf does not move. Shelf melts using three equation model.
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/SIS_input b/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/SIS_input
deleted file mode 120000
index ad3cd99..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/SIS_input
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/SIS_input
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/SIS_override b/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/SIS_override
deleted file mode 100644
index f591eb2..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/SIS_override
+++ /dev/null
@@ -1,8 +0,0 @@
-# Blank file in which we can put "overrides" for parameters
-DO_ICEBERGS =False              !   If true, use the icebergs module.
-
-!Time Stepping
-!#override DT_FORCING = 10.0              !   [s] default = 0.0
-!#override DT_RHEOLOGY = 10.0             ! The sub-cycling time step, in s, for iterating
-
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/clean_MOM.sh b/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/clean_MOM.sh
deleted file mode 120000
index c5370af..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/clean_MOM.sh
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/clean_MOM.sh
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/data_table b/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/data_table
deleted file mode 120000
index 5b82b3c..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/data_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/data_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/diag_table b/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/diag_table
deleted file mode 120000
index cff65fe..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/diag_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/diag_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/field_table b/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/field_table
deleted file mode 120000
index b5ea991..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/field_table
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/field_table
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/input.nml b/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/input.nml
deleted file mode 100644
index 46b34b2..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/input.nml
+++ /dev/null
@@ -1,140 +0,0 @@
- &MOM_input_nml
-        output_directory = './',
-        input_filename = 'r'
-        restart_input_dir = 'INPUT/',
-        restart_output_dir = 'RESTART/',
-        parameter_filename = 'MOM_input',
-                             'MOM_override' /
-
- &SIS_input_nml
-        output_directory = './',
-        input_filename = 'r'
-        restart_input_dir = 'INPUT/',
-        restart_output_dir = 'RESTART/',
-        parameter_filename = 'SIS_input',
-                             'SIS_override' /
-
- &diag_manager_nml
-         max_output_fields=1000
-         max_input_fields=1000
-         max_num_axis_sets=1000
-	 flush_nc_files=.true.
-         max_files=1000
-         max_axes=2000
- /
-
- &coupler_nml
-            months = 60,
-            days   = 0,
-            current_date = 1,1,1,0,0,0,
-            hours = 0,
-            minutes =0, 
-            seconds = 0
-            calendar = 'NOLEAP',
-            dt_cpld  = 360.0,
-            dt_atmos = 3600.0,
-            do_atmos = .false.,
-            do_land = .false.,
-            do_ice = .true.,
-            do_ocean = .true.,
-            atmos_npes = 0,
-            ocean_npes = 0,
-            concurrent = .false.
-            use_lag_fluxes=.false. /
-
-
- &icebergs_nml
-    verbose=.false.,
-    verbose_hrs=240,
-    traj_sample_hrs=24000,
-    ignore_ij_restart=.true.
-    halo=2,
-    save_short_traj=.true.
-    debug=.false.,
-    really_debug=.false.,
-    use_slow_find=.true.,
-    add_weight_to_ocean=.true.,
-    passive_mode=.false.,
-    Static_icebergs=.True.,
-    ignore_missing_restart_bergs=.false.,
-    generate_test_icebergs=.false.,
-    speed_limit=0.,
-    use_roundoff_fix=.true.,
-    make_calving_reproduce=.false.,
-    Runge_not_Verlet=.false.,
-    iceberg_bonds_on=.false.,
-    critical_interaction_damping_on=.true.,
-    use_new_predictive_corrective=.true.,
-    interactive_icebergs_on=.false.
-    halo_debugging=.false.
-    spring_coef=0.00001
-    distribution=0.0, 0.99, 0.0, 0.00, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11,
-    hexagonal_icebergs=.true.
-    allow_bergs_to_roll=.true.
-    set_melt_rates_to_zero=.false.
-    use_roundoff_fix=.false.
-    grid_is_latlon=.false.
-    grid_is_regular=.true.
-    initial_orientation=-0.
-    rotate_icebergs_for_mass_spreading=.false.
-    lat_ref=-75.0
-    u_override=0.00
-    v_override=0.00
-    override_iceberg_velocities=.false.
-    add_iceberg_thickness_to_SSH=.false.
-    max_bonds=6
-    Iceberg_melt_without_decay=.true.
-    melt_icebergs_as_ice_shelf=.true.
-    Use_three_equation_model=.true.
-    find_melt_using_spread_mass=.true.
-    use_mixed_layer_salinity_for_thermo=.true.
-    pass_fields_to_ocean_model=.true.
-    rho_bergs=918.0
-    utide_icebergs=0.01
-    ustar_icebergs_bg=0.000
-    cdrag_icebergs =0.0025
-    const_gamma=.false.
-    Gamma_T_3EQ=0.22
-    ignore_traj=.False.
-    read_ocean_depth_from_file=.true.
-    apply_thickness_cutoff_to_bergs_melt=.true.
-    apply_thickness_cutoff_to_gridded_melt=.true.
-    melt_cutoff=10.
-    read_old_restarts=.false.
-    internal_bergs_for_drag=.true.
-    use_mixed_melting=.true.
- &data_override_nml
-         /
-
- &fms_io_nml
-         fms_netcdf_restart=.true.
-         threading_read='multi'
- /
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC' /
-
- &ice_albedo_nml
-      t_range = 10. /
-
- &ice_model_nml
-           /
-
- &monin_obukhov_nml
-            neutral = .true. /
-
- &ocean_albedo_nml
-      ocean_albedo_option = 5 /
-
- &sat_vapor_pres_nml
-      construct_table_wrt_liq = .true.,
-      construct_table_wrt_liq_and_ice = .true. /
-
- &xgrid_nml
-            make_exchange_reproduce = .false.
-            interp_method = 'second_order' /
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/run_script.sh b/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/run_script.sh
deleted file mode 120000
index 2a081b9..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/run_script.sh
+++ /dev/null
@@ -1 +0,0 @@
-../../../common/run_script.sh
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/submit_to_queue b/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/submit_to_queue
deleted file mode 100644
index d35f1b8..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/Shelf/Sigma_Shelf_Star/Static_shelf/submit_to_queue
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/bin/csh -f
-#PBS -r y                                                              #This job is restartable
-#PBS -j oe                                                             #STDOUT and STDERR are in the same file, specified below in the '-o' option
-#PBS -q batch                                                          #Do not change this - it tells your job where to run
-#PBS -S /bin/sh                                                        #Do not change this - it keeps your job from issuing a false alarm
-#PBS -E                                                                #Do not change this - it gives your job more and more useful Moab environment variables
-#PBS -N  Bergs_Empty_Run                                               #Job Name:             You may want to change this to reflect your job's purpose or relation to an experiment
-#PBS -l partition=c3
-#PBS -l size=4                                                        #You will need to change this to reflect your job's core requirements - 24 is the current core increment.
-#PBS -l walltime=16:00:00                                              #You MUST change this to reflect your job's expected run time, including copy time
-#PBS -m bea                                                            #Email options: You may want to change this to reduce your incoming email stream
-
-######################################################################################################################
-#
-#  Gaea c1ms batch skeleton version 0.9
-#  
-#  0.9 - Initial version - 20110906 - Daniel Gall - Daniel.Gall@noaa.gov
-#
-######################################################################################################################
-
-#Source the system initialization scripts (but not the user's so as to avoid interactive settings that can poison us)
-source /etc/csh.cshrc
-
-#Run the experiment
-aprun -n 128 ../../../../../build/intel/ice_ocean_SIS2/repro/MOM6
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/common/MOM_input b/tests/Iceberg_repository/ISOMIP_Calving/common/MOM_input
deleted file mode 100644
index 1b56f9f..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/common/MOM_input
+++ /dev/null
@@ -1,721 +0,0 @@
-/* This input file provides the adjustable run-time parameters for version 6 of
-   the Modular Ocean Model (MOM6), a numerical ocean model developed at NOAA-GFDL.
-   Where appropriate, parameters use usually given in MKS units.
-
-   This particular file is for the "quiet" rho ISOMIP test case.
-
-   This MOM_input file typically contains only the non-default values that are
-   needed to reproduce this example.  A full list of parameters for this example
-   can be found in the corresponding MOM_parameter_doc.all file which is
-   generated by the model at run-time. */
-
-REENTRANT_X = False             !   [Boolean] default = True
-                                ! If true, the domain is zonally reentrant.
-NIHALO = 4                      ! default = 2
-                                ! The number of halo points on each side in the
-                                ! x-direction.  With STATIC_MEMORY_ this is set as NIHALO_
-                                ! in MOM_memory.h at compile time; without STATIC_MEMORY_
-                                ! the default is NIHALO_ in MOM_memory.h (if defined) or 2.
-NJHALO = 4                      ! default = 2
-                                ! The number of halo points on each side in the
-                                ! y-direction.  With STATIC_MEMORY_ this is set as NJHALO_
-                                ! in MOM_memory.h at compile time; without STATIC_MEMORY_
-                                ! the default is NJHALO_ in MOM_memory.h (if defined) or 2.
-NIGLOBAL = 240                  !
-                                ! The total number of thickness grid points in the
-                                ! x-direction in the physical domain. With STATIC_MEMORY_
-                                ! this is set in MOM_memory.h at compile time.
-NJGLOBAL = 40                   !
-                                ! The total number of thickness grid points in the
-                                ! y-direction in the physical domain. With STATIC_MEMORY_
-                                ! this is set in MOM_memory.h at compile time.
-IO_LAYOUT = 1, 1                ! default = 0
-                                ! The processor layout to be used, or 0,0 to automatically
-                                ! set the io_layout to be the same as the layout.
-
-! === module MOM_grid ===
-
-! === module MOM_verticalGrid ===
-Z_OUTPUT_GRID_FILE = "ISOMIP_zgrid.nc" ! default = ""
-                                ! The file that specifies the vertical grid for
-                                ! depth-space diagnostics, or blank to disable
-                                ! depth-space output.
-! Parameters providing information about the vertical grid.
-RHO_0 = 1028.0                  !   [kg m-3] default = 1035.0
-                                ! The mean ocean density used with BOUSSINESQ true to
-                                ! calculate accelerations and the mass for conservation
-                                ! properties, or with BOUSSINSEQ false to convert some
-                                ! parameters from vertical units of m to kg m-2.
-ANGSTROM = 1.0E-15              !   [m] default = 1.0E-10
-                                ! The minumum layer thickness, usually one-Angstrom.
-NK = 36                         !   [nondim]
-                                ! The number of model layers.
-
-! === module MOM ===
-BULKMIXEDLAYER = False          !   [Boolean] default = True
-                                ! If true, use a Kraus-Turner-like bulk mixed layer
-                                ! with transitional buffer layers.  Layers 1 through
-                                ! NKML+NKBL have variable densities. There must be at
-                                ! least NKML+NKBL+1 layers if BULKMIXEDLAYER is true.
-                                ! The default is the same setting as ENABLE_THERMODYNAMICS.
-REGRID_USE_OLD_DIRECTION = False ! [Boolean] default = True
-                                ! This is an undocumented parameter.
-DT = 1000.0                      !   [s]
-                                ! The (baroclinic) dynamics time step.  The time-step that
-                                ! is actually used will be an integer fraction of the
-                                ! forcing time-step (DT_FORCING in ocean-only mode or the
-                                ! coupling timestep in coupled mode.)
-DEBUG = False                   !   [Boolean] default = False
-                                ! If true, write out verbose debugging data.
-DT_THERM = 1000.0                !   [s] default = 300.0
-                                ! The thermodynamic and tracer advection time step.
-                                ! Ideally DT_THERM should be an integer multiple of DT
-                                ! and less than the forcing or coupling time-step, unless
-                                ! THERMO_SPANS_COUPLING is true, in which case DT_THERM
-                                ! can be an integer multiple of the coupling timestep.  By
-                                ! default DT_THERM is set to DT.
-DTBT_RESET_PERIOD = 0.0         !   [s] default = 300.0
-                                ! The period between recalculations of DTBT (if DTBT <= 0).
-                                ! If DTBT_RESET_PERIOD is negative, DTBT is set based
-                                ! only on information available at initialization.  If
-                                ! dynamic, DTBT will be set at least every forcing time
-                                ! step, and if 0, every dynamics time step.  The default is
-                                ! set by DT_THERM.  This is only used if SPLIT is true.
-C_P = 3974.0                    !   [J kg-1 K-1] default = 3991.86795711963
-                                ! The heat capacity of sea water, approximated as a
-                                ! constant. This is only used if ENABLE_THERMODYNAMICS is
-                                ! true. The default value is from the TEOS-10 definition
-                                ! of conservative temperature.
-SAVE_INITIAL_CONDS = True       !   [Boolean] default = False
-                                ! If true, write the initial conditions to a file given
-                                ! by IC_OUTPUT_FILE.
-IC_OUTPUT_FILE = "ISOMIP_IC"    ! default = "MOM_IC"
-                                ! The file into which to write the initial conditions.
-HMIX_SFC_PROP = 1.0             !   [m] default = 1.0
-                                ! If BULKMIXEDLAYER is false, HMIX_SFC_PROP is the depth
-                                ! over which to average to find surface properties like
-                                ! SST and SSS or density and surface velocities.
-
-! === module MOM_tracer_registry ===
-EQN_OF_STATE = "LINEAR"         ! default = "WRIGHT"
-                                ! EQN_OF_STATE determines which ocean equation of state
-                                ! should be used.  Currently, the valid choices are
-                                ! "LINEAR", "UNESCO", and "WRIGHT".
-                                ! This is only used if USE_EOS is true.
-RHO_T0_S0 = 999.910681          !   [kg m-3] default = 1000.0
-                                ! When EQN_OF_STATE=LINEAR,
-                                ! this is the density at T=0, S=0.
-DRHO_DT = -0.038357             !   [kg m-3 K-1] default = -0.2
-                                ! When EQN_OF_STATE=LINEAR,
-                                ! this is the partial derivative of density with
-                                ! temperature.
-DRHO_DS = 0.805876              !   [kg m-3 PSU-1] default = 0.8
-                                ! When EQN_OF_STATE=LINEAR,
-                                ! this is the partial derivative of density with
-                                ! salinity.
-TFREEZE_FORM = "LINEAR"         ! default = "LINEAR"
-                                ! TFREEZE_FORM determines which expression should be
-                                ! used for the freezing point.  Currently, the valid
-                                ! choices are "LINEAR", "MILLERO_78".
-TFREEZE_S0_P0 = 0.0832          !   [deg C] default = 0.0
-                                ! When TFREEZE_FORM=LINEAR,
-                                ! this is the freezing potential temperature at
-                                ! S=0, P=0.
-DTFREEZE_DS = -0.0573           !   [deg C PSU-1] default = -0.054
-                                ! When TFREEZE_FORM=LINEAR,
-                                ! this is the derivative of the freezing potential
-                                ! temperature with salinity.
-DTFREEZE_DP = -7.53E-08         !   [deg C Pa-1] default = 0.0
-                                ! When TFREEZE_FORM=LINEAR,
-                                ! this is the derivative of the freezing potential
-                                ! temperature with pressure.
-! === module MOM_tracer_flow_control ===
-INPUTDIR = "INPUT"              ! default = "."
-                                ! The directory in which input files are found.
-
-! === module MOM_grid_init ===
-GRID_CONFIG = "cartesian"       !
-                                ! A character string that determines the method for
-                                ! defining the horizontal grid.  Current options are:
-                                !     mosaic - read the grid from a mosaic (supergrid)
-                                !              file set by GRID_FILE.
-                                !     cartesian - use a (flat) Cartesian grid.
-                                !     spherical - use a simple spherical grid.
-                                !     mercator - use a Mercator spherical grid.
-AXIS_UNITS = "k"                ! default = "degrees"
-                                ! The units for the Cartesian axes. Valid entries are:
-                                !     degrees - degrees of latitude and longitude
-                                !     m - meters
-                                !     k - kilometers
-SOUTHLAT = 0.0                  !   [k]
-                                ! The southern latitude of the domain or the equivalent
-                                ! starting value for the y-axis.
-LENLAT = 80.0                   !   [k]
-                                ! The latitudinal or y-direction length of the domain.
-WESTLON = 320.0                 !   [k] default = 0.0
-                                ! The western longitude of the domain or the equivalent
-                                ! starting value for the x-axis.
-LENLON = 480.0                  !   [k]
-                                ! The longitudinal or x-direction length of the domain.
-TOPO_CONFIG = "ISOMIP"          !
-                                ! This specifies how bathymetry is specified:
-                                !     file - read bathymetric information from the file
-                                !       specified by (TOPO_FILE).
-                                !     flat - flat bottom set to MAXIMUM_DEPTH.
-                                !     bowl - an analytically specified bowl-shaped basin
-                                !       ranging between MAXIMUM_DEPTH and MINIMUM_DEPTH.
-                                !     spoon - a similar shape to 'bowl', but with an vertical
-                                !       wall at the southern face.
-                                !     halfpipe - a zonally uniform channel with a half-sine
-                                !       profile in the meridional direction.
-                                !     benchmark - use the benchmark test case topography.
-                                !     DOME - use a slope and channel configuration for the
-                                !       DOME sill-overflow test case.
-                                !     ISOMIP - use a slope and channel configuration for the
-                                !       ISOMIP test case.
-                                !     DOME2D - use a shelf and slope configuration for the
-                                !       DOME2D gravity current/overflow test case.
-                                !     seamount - Gaussian bump for spontaneous motion test case.
-                                !     Phillips - ACC-like idealized topography used in the Phillips config.
-                                !     USER - call a user modified routine.
-
-! === module ISOMIP_initialize_topography ===
-MINIMUM_DEPTH = 1.0             !   [m] default = 0.0
-                                ! The minimum depth of the ocean.
-MAXIMUM_DEPTH = 720.0           !   [m]
-                                ! The maximum depth of the ocean.
-ROTATION = "beta"               ! default = "2omegasinlat"
-                                ! This specifies how the Coriolis parameter is specified:
-                                !     2omegasinlat - Use twice the planetary rotation rate
-                                !       times the sine of latitude.
-                                !     betaplane - Use a beta-plane or f-plane.
-                                !     USER - call a user modified routine.
-F_0 = -1.40871E-04              !   [s-1] default = 0.0
-                                ! The reference value of the Coriolis parameter with the
-                                ! betaplane option.
-COORD_CONFIG = "linear"         !
-                                ! This specifies how layers are to be defined:
-                                !     file - read coordinate information from the file
-                                !       specified by (COORD_FILE).
-                                !     linear - linear based on interfaces not layers
-                                !     layer_ref - linear based on layer densities
-                                !     ts_ref - use reference temperature and salinity
-                                !     ts_range - use range of temperature and salinity
-                                !       (T_REF and S_REF) to determine surface density
-                                !       and GINT calculate internal densities.
-                                !     gprime - use reference density (RHO_0) for surface
-                                !       density and GINT calculate internal densities.
-                                !     ts_profile - use temperature and salinity profiles
-                                !       (read from COORD_FILE) to set layer densities.
-                                !     USER - call a user modified routine.
-LIGHTEST_DENSITY = 1027.1524    !   [kg m-3] default = 1027.0
-                                ! The reference potential density used for the surface
-                                ! interface.
-DENSITY_RANGE = 0.7438856       !   [kg m-3] default = 2.0
-                                ! The range of reference potential densities across
-                                ! all interfaces.
-BOUNDARY_EXTRAPOLATION_PRESSURE = True !   [Boolean] default = True
-                                ! When defined, the reconstruction is extrapolated
-                                ! within boundary cells rather than assume PCM for the.
-                                ! calculation of pressure. e.g. if PPM is used, a
-                                ! PPM reconstruction will also be used within
-                                ! boundary cells.
-RECONSTRUCT_FOR_PRESSURE = True !   [Boolean] default = True
-                                ! If True, use vertical reconstruction of T/S within
-                                ! the integrals of teh FV pressure gradient calculation.
-                                ! If False, use the constant-by-layer algorithm.
-                                ! By default, this is True when using ALE and False otherwise.
-PRESSURE_RECONSTRUCTION_SCHEME = 1 ! default = 1
-                                ! Type of vertical reconstruction of T/S to use in integrals
-                                ! within the FV pressure gradient calculation. 1: PLM reconstruction.
-                                !  2: PPM reconstruction.
-REMAP_UV_USING_OLD_ALG = False  !   [Boolean] default = True
-                                ! If true, uses the old remapping-via-a-delta-z method for
-                                ! remapping u and v. If false, uses the new method that remaps
-                                ! between grids described by an old and new thickness.
-MIN_THICKNESS = 1.0E-12         !   [m] default = 0.001
-                                ! When regridding, this is the minimum layer
-                                ! thickness allowed.
-BOUNDARY_EXTRAPOLATION = True   !   [Boolean] default = False
-                                ! When defined, a proper high-order reconstruction
-                                ! scheme is used within boundary cells rather
-                                ! than PCM. E.g., if PPM is used for remapping, a
-                                ! PPM reconstruction will also be used within
-                                ! boundary cells.
-REMAP_AFTER_INITIALIZATION = False !   [Boolean] default = True
-                                ! If true, applies regridding and remapping immediately after
-                                ! initialization so that the state is ALE consistent. This is a
-                                ! legacy step and should not be needed if the initialization is
-                                ! consistent with the coordinate mode.
-THICKNESS_CONFIG = "ISOMIP"     !
-                                ! A string that determines how the initial layer
-                                ! thicknesses are specified for a new run:
-                                !     file - read interface heights from the file specified
-                                !     thickness_file - read thicknesses from the file specified
-                                !       by (THICKNESS_FILE).
-                                !     coord - determined by ALE coordinate.
-                                !     uniform - uniform thickness layers evenly distributed
-                                !       between the surface and MAXIMUM_DEPTH.
-                                !     DOME - use a slope and channel configuration for the
-                                !       DOME sill-overflow test case.
-                                !     ISOMIP - use a configuration for the
-                                !       ISOMIP test case.
-                                !     benchmark - use the benchmark test case thicknesses.
-                                !     search - search a density profile for the interface
-                                !       densities. This is not yet implemented.
-                                !     circle_obcs - the circle_obcs test case is used.
-                                !     DOME2D - 2D version of DOME initialization.
-                                !     adjustment2d - TBD AJA.
-                                !     sloshing - TBD AJA.
-                                !     seamount - TBD AJA.
-                                !     rossby_front - a mixed layer front in thermal wind balance.
-                                !     USER - call a user modified routine.
-SPONGE_CONFIG = "ISOMIP"    ! default = "file"
-                                ! A string that sets how the sponges are configured:
-                                !     ISOMIP - use a configuration for the
-                                !       ISOMIP test case.
-                                !     USER - call a user modified routine.
-ISOMIP_TNUDG = 0.1                     !  default = 0.0 (days)
-                                ! Nudging time scale for sponge layers.
-TS_CONFIG = "ISOMIP"            !
-                                ! A string that determines how the initial tempertures
-                                ! and salinities are specified for a new run:
-                                !     file - read velocities from the file specified
-                                !       by (TS_FILE).
-                                !     fit - find the temperatures that are consistent with
-                                !       the layer densities and salinity S_REF.
-                                !     TS_profile - use temperature and salinity profiles
-                                !       (read from TS_FILE) to set layer densities.
-                                !     benchmark - use the benchmark test case T & S.
-                                !     linear - linear in logical layer space.
-                                !     DOME2D - 2D DOME initialization.
-                                !     ISOMIP - ISOMIP initialization.
-                                !     adjustment2d - TBD AJA.
-                                !     sloshing - TBD AJA.
-                                !     seamount - TBD AJA.
-                                !     rossby_front - a mixed layer front in thermal wind balance.
-                                !     SCM_ideal_hurr - used in the SCM idealized hurricane test.
-                                !     USER - call a user modified routine.
-T_REF = -1.9                    !   [degC]
-                                ! A reference temperature used in initialization.
-FIT_SALINITY = True             ! If true, accept the prescribed temperature and fit the
-                                ! salinity; otherwise take salinity and fit temperature.
-VELOCITY_CONFIG = "zero"        ! default = "zero"
-                                ! A string that determines how the initial velocities
-                                ! are specified for a new run:
-                                !     file - read velocities from the file specified
-                                !       by (VELOCITY_FILE).
-                                !     zero - the fluid is initially at rest.
-                                !     uniform - the flow is uniform (determined by
-                                !       parameters INITIAL_U_CONST and INITIAL_V_CONST).
-                                !     rossby_front - a mixed layer front in thermal wind balance.
-                                !     USER - call a user modified routine.
-TRIM_IC_FOR_P_SURF = True       !   [Boolean] default = False
-                                ! If true, cuts way the top of the column for initial conditions
-                                ! at the depth where the hydrostatic presure matches the imposed
-                                ! surface pressure which is read from file.
-SURFACE_PRESSURE_FILE = "isomip_ice_shelf1_clipped.nc" !
-                                ! The initial condition file for the surface height.
-SURFACE_PRESSURE_VAR = "p_surf"!   [kg m-2] default = ""
-!SURFACE_PRESSURE_VAR = "thick"  !   [kg m-2] default = ""
-                                ! The initial condition variable for the surface height.
-!SURFACE_PRESSURE_SCALE = 8996.4 ! [file dependent] default = 1.0
-SURFACE_PRESSURE_SCALE = 1.0   ! [file dependent] default = 1.0
-                                ! A scaling factor to convert SURFACE_PRESSURE_VAR from
-                                ! file SURFACE_PRESSURE_FILE into a surface pressure.
-SPONGE = False                  !   [Boolean] default = False
-                                ! If true, sponges may be applied anywhere in the domain.
-                                ! The exact location and properties of those sponges are
-                                ! specified via SPONGE_CONFIG.
-
-! === module MOM_MEKE ===
-! === module MOM_set_visc ===
-BOTTOMDRAGLAW = True            !   [Boolean] default = True
-                                ! If true, the bottom stress is calculated with a drag
-                                ! law of the form c_drag*|u|*u. The velocity magnitude
-                                ! may be an assumed value or it may be based on the
-                                ! actual velocity in the bottommost HBBL, depending on
-                                ! LINEAR_DRAG.
-CHANNEL_DRAG = False            !   [Boolean] default = False
-                                ! If true, the bottom drag is exerted directly on each
-                                ! layer proportional to the fraction of the bottom it
-                                ! overlies.
-CDRAG = 0.0025                   !   [nondim] default = 0.003
-                                ! CDRAG is the drag coefficient relating the magnitude of
-                                ! the velocity field to the bottom stress. CDRAG is only
-                                ! used if BOTTOMDRAGLAW is defined.
-BBL_USE_EOS = True              !   [Boolean] default = False
-                                ! If true, use the equation of state in determining the
-                                ! properties of the bottom boundary layer.  Otherwise use
-                                ! the layer target potential densities.
-BBL_THICK_MIN = 2.0             !   [m] default = 0.0
-                                ! The minimum bottom boundary layer thickness that can be
-                                ! used with BOTTOMDRAGLAW. This might be
-                                ! Kv / (cdrag * drag_bg_vel) to give Kv as the minimum
-                                ! near-bottom viscosity.
-HTBL_SHELF_MIN = 2.0            !   [m] default = 2.0
-                                ! The minimum top boundary layer thickness that can be
-                                ! used with BOTTOMDRAGLAW. This might be
-                                ! Kv / (cdrag * drag_bg_vel) to give Kv as the minimum
-                                ! near-top viscosity.
-HTBL_SHELF = 2.0               !   [m] default = 10.0
-                                ! The thickness over which near-surface velocities are
-                                ! averaged for the drag law under an ice shelf.  By
-                                ! default this is the same as HBBL
-KV = 1.0E-06                    !   [m2 s-1]
-                                ! The background kinematic viscosity in the interior.
-                                ! The molecular value, ~1e-6 m2 s-1, may be used.
-BE = 0.7                        !   [nondim] default = 0.6
-                                ! If SPLIT is true, BE determines the relative weighting
-                                ! of a  2nd-order Runga-Kutta baroclinic time stepping
-                                ! scheme (0.5) and a backward Euler scheme (1) that is
-                                ! used for the Coriolis and inertial terms.  BE may be
-                                ! from 0.5 to 1, but instability may occur near 0.5.
-                                ! BE is also applicable if SPLIT is false and USE_RK2
-                                ! is true.
-ETA_TOLERANCE = 1.0E-12         !   [m] default = 1.25E-14
-                                ! The tolerance for the differences between the
-                                ! barotropic and baroclinic estimates of the sea surface
-                                ! height due to the fluxes through each face.  The total
-                                ! tolerance for SSH is 4 times this value.  The default
-                                ! is 0.5*NK*ANGSTROM, and this should not be set less x
-                                ! than about 10^-15*MAXIMUM_DEPTH.
-CORIOLIS_EN_DIS = True          !   [Boolean] default = False
-                                ! If true, two estimates of the thickness fluxes are used
-                                ! to estimate the Coriolis term, and the one that
-                                ! dissipates energy relative to the other one is used.
-CORIOLIS_SCHEME = "SADOURNY75_ENERGY" ! default = "SADOURNY75_ENERGY"
-                                ! CORIOLIS_SCHEME selects the discretization for the
-                                ! Coriolis terms. Valid values are:
-                                !    SADOURNY75_ENERGY - Sadourny, 1975; energy cons.
-                                !    ARAKAWA_HSU90     - Arakawa & Hsu, 1990
-                                !    SADOURNY75_ENSTRO - Sadourny, 1975; enstrophy cons.
-                                !    ARAKAWA_LAMB81    - Arakawa & Lamb, 1981; En. + Enst.
-                                !    ARAKAWA_LAMB_BLEND - A blend of Arakawa & Lamb with
-                                !                         Arakawa & Hsu and Sadourny energy
-BOUND_CORIOLIS = True           !   [Boolean] default = False
-                                ! If true, the Coriolis terms at u-points are bounded by
-                                ! the four estimates of (f+rv)v from the four neighboring
-                                ! v-points, and similarly at v-points.  This option is
-                                ! always effectively false with CORIOLIS_EN_DIS defined and
-                                ! CORIOLIS_SCHEME set to SADOURNY75_ENERGY.
-ANALYTIC_FV_PGF = True          !   [Boolean] default = True
-                                ! If true the pressure gradient forces are calculated
-                                ! with a finite volume form that analytically integrates
-                                ! the equations of state in pressure to avoid any
-                                ! possibility of numerical thermobaric instability, as
-                                ! described in Adcroft et al., O. Mod. (2008).
-MASS_WEIGHT_IN_PRESSURE_GRADIENT = True !   [Boolean] default = False
-                                ! If true, use mass weighting when interpolation T/S for
-                                ! top/bottom integrals in AFV pressure gradient calculation.
-
-! === module MOM_hor_visc ===
-LAPLACIAN = True                !   [Boolean] default = False
-                                ! If true, use a Laplacian horizontal viscosity.
-KH = 0.0                        !   [m2 s-1] default = 0.0
-                                ! The background Laplacian horizontal viscosity.
-KH_VEL_SCALE = 0.0              !   [m s-1] default = 0.0
-                                ! The velocity scale which is multiplied by the grid
-                                ! spacing to calculate the Laplacian viscosity.
-                                ! The final viscosity is the largest of this scaled
-                                ! viscosity, the Smagorinsky viscosity and KH.
-SMAGORINSKY_KH = True           !   [Boolean] default = False
-                                ! If true, use a Smagorinsky nonlinear eddy viscosity.
-SMAG_LAP_CONST = 0.15           !   [nondim] default = 0.0
-                                ! The nondimensional Laplacian Smagorinsky constant,
-                                ! often 0.15.
-BIHARMONIC = True               !   [Boolean] default = True
-                                ! If true, use a biharmonic horizontal viscosity.
-                                ! BIHARMONIC may be used with LAPLACIAN.
-AH = 0.0                        !   [m4 s-1] default = 0.0
-                                ! The background biharmonic horizontal viscosity.
-AH_VEL_SCALE = 0.005            !   [m s-1] default = 0.0
-                                ! The velocity scale which is multiplied by the cube of
-                                ! the grid spacing to calculate the biharmonic viscosity.
-                                ! The final viscosity is the largest of this scaled
-                                ! viscosity, the Smagorinsky viscosity and AH.
-SMAGORINSKY_AH = True           !   [Boolean] default = False
-                                ! If true, use a biharmonic Smagorinsky nonlinear eddy
-                                ! viscosity.
-SMAG_BI_CONST = 0.06            !   [nondim] default = 0.0
-                                ! The nondimensional biharmonic Smagorinsky constant,
-                                ! typically 0.015 - 0.06.
-
-! === module MOM_vert_friction ===
-U_TRUNC_FILE = "U_velocity_truncations" ! default = ""
-                                ! The absolute path to a file into which the accelerations
-                                ! leading to zonal velocity truncations are written.
-                                ! Undefine this for efficiency if this diagnostic is not
-                                ! needed.
-V_TRUNC_FILE = "V_velocity_truncations" ! default = ""
-                                ! The absolute path to a file into which the accelerations
-                                ! leading to meridional velocity truncations are written.
-                                ! Undefine this for efficiency if this diagnostic is not
-                                ! needed.
-HARMONIC_BL_SCALE = 1.0         !   [nondim] default = 0.0
-                                ! A scale to determine when water is in the boundary
-                                ! layers based solely on harmonic mean thicknesses for
-                                ! the purpose of determining the extent to which the
-                                ! thicknesses used in the viscosities are upwinded.
-HMIX_FIXED = 20.0               !   [m]
-                                ! The prescribed depth over which the near-surface
-                                ! viscosity and diffusivity are elevated when the bulk
-                                ! mixed layer is not used.
-!KVML = 1.0E-06                  !   [m2 s-1] default = 1.0E-04
-                                ! The kinematic viscosity in the mixed layer.  A typical
-                                ! value is ~1e-2 m2 s-1. KVML is not used if
-                                ! BULKMIXEDLAYER is true.  The default is set by KV.
-HBBL = 5.0                     !   [m]
-                                ! The thickness of a bottom boundary layer with a
-                                ! viscosity of KVBBL if BOTTOMDRAGLAW is not defined, or
-                                ! the thickness over which near-bottom velocities are
-                                ! averaged for the drag law if BOTTOMDRAGLAW is defined
-                                ! but LINEAR_DRAG is not.
-!KV_BBL_MIN = 1.0E-06            !   [m2 s-1] default = 0.0
-                                ! The minimum viscosities in the bottom boundary layer.
-!KV_TBL_MIN = 1.0E-06            !   [m2 s-1] default = 0.0
-                                ! The minimum viscosities in the top boundary layer.
-MAXVEL = 10.0                   !   [m s-1] default = 3.0E+08
-                                ! The maximum velocity allowed before the velocity
-                                ! components are truncated.
-
-! === module MOM_PointAccel ===
-
-! === module MOM_barotropic ===
-BOUND_BT_CORRECTION = True      !   [Boolean] default = False
-                                ! If true, the corrective pseudo mass-fluxes into the
-                                ! barotropic solver are limited to values that require
-                                ! less than maxCFL_BT_cont to be accommodated.
-USE_BT_CONT_TYPE = True         !   [Boolean] default = True
-                                ! If true, use a structure with elements that describe
-                                ! effective face areas from the summed continuity solver
-                                ! as a function the barotropic flow in coupling between
-                                ! the barotropic and baroclinic flow.  This is only used
-                                ! if SPLIT is true.
-DYNAMIC_SURFACE_PRESSURE = True !   [Boolean] default = False
-                                ! If true, add a dynamic pressure due to a viscous ice
-                                ! shelf, for instance.
-BT_THICK_SCHEME = "FROM_BT_CONT" ! default = "FROM_BT_CONT"
-                                ! A string describing the scheme that is used to set the
-                                ! open face areas used for barotropic transport and the
-                                ! relative weights of the accelerations. Valid values are:
-                                !    ARITHMETIC - arithmetic mean layer thicknesses
-                                !    HARMONIC - harmonic mean layer thicknesses
-                                !    HYBRID (the default) - use arithmetic means for
-                                !       layers above the shallowest bottom, the harmonic
-                                !       mean for layers below, and a weighted average for
-                                !       layers that straddle that depth
-                                !    FROM_BT_CONT - use the average thicknesses kept
-                                !       in the h_u and h_v fields of the BT_cont_type
-BEBT = 0.2                      !   [nondim] default = 0.1
-                                ! BEBT determines whether the barotropic time stepping
-                                ! uses the forward-backward time-stepping scheme or a
-                                ! backward Euler scheme. BEBT is valid in the range from
-                                ! 0 (for a forward-backward treatment of nonrotating
-                                ! gravity waves) to 1 (for a backward Euler treatment).
-                                ! In practice, BEBT must be greater than about 0.05.
-DTBT = -0.9                     !   [s or nondim] default = -0.98
-                                ! The barotropic time step, in s. DTBT is only used with
-                                ! the split explicit time stepping. To set the time step
-                                ! automatically based the maximum stable value use 0, or
-                                ! a negative value gives the fraction of the stable value.
-                                ! Setting DTBT to 0 is the same as setting it to -0.98.
-                                ! The value of DTBT that will actually be used is an
-                                ! integer fraction of DT, rounding down.
-
-! === module MOM_thickness_diffuse ===
-KHTH = 0.0                      !   [m2 s-1] default = 0.0
-                                ! The background horizontal thickness diffusivity.
-! === module MOM_diabatic_driver ===
-! The following parameters are used for diabatic processes.
-ENERGETICS_SFC_PBL = False      !   [Boolean] default = False
-                                ! If true, use an implied energetics planetary boundary
-                                ! layer scheme to determine the diffusivity and viscosity
-                                ! in the surface boundary layer.
-
-! === module MOM_KPP ===
-! This is the MOM wrapper to CVmix:KPP
-! See http://code.google.com/p/cvmix/
-USE_KPP = False                 !   [Boolean] default = False
-                                ! If true, turns on the [CVmix] KPP scheme of Large et al., 1994,
-                                ! to calculate diffusivities and non-local transport in the OBL.
-
-! === module MOM_diffConvection ===
-! This module implements enhanced diffusivity as a
-! function of static stability, N^2.
-CONVECTION%
-%CONVECTION
-
-! === module MOM_entrain_diffusive ===
-CORRECT_DENSITY = False         !   [Boolean] default = True
-                                ! If true, and USE_EOS is true, the layer densities are
-                                ! restored toward their target values by the diapycnal
-                                ! mixing, as described in Hallberg (MWR, 2000).
-MAX_ENT_IT = 20                 ! default = 5
-                                ! The maximum number of iterations that may be used to
-                                ! calculate the interior diapycnal entrainment.
-TOLERANCE_ENT = 1.0E-08         !   [m] default = 1.0E-13
-                                ! The tolerance with which to solve for entrainment values.
-BBL_EFFIC = 0.2                 !   [nondim] default = 0.2
-                                ! The efficiency with which the energy extracted by
-                                ! bottom drag drives BBL diffusion.  This is only
-                                ! used if BOTTOMDRAGLAW is true.
-KD = 0.0                        !   [m2 s-1]
-                                ! The background diapycnal diffusivity of density in the
-                                ! interior. Zero or the molecular value, ~1e-7 m2 s-1,
-                                ! may be used.
-KD_MIN = 5.0E-05
-! === module MOM_kappa_shear ===
-! Parameterization of shear-driven turbulence following Jackson, Hallberg and Legg, JPO 2008
-USE_JACKSON_PARAM = False       !   [Boolean] default = False
-                                ! If true, use the Jackson-Hallberg-Legg (JPO 2008)
-                                ! shear mixing parameterization.
-
-! === module MOM_diabatic_aux ===
-! The following parameters are used for auxiliary diabatic processes.
-
-! === module MOM_regularize_layers ===
-
-! === module MOM_opacity ===
-PEN_SW_SCALE = 15.0             !   [m] default = 0.0
-                                ! The vertical absorption e-folding depth of the
-                                ! penetrating shortwave radiation.
-PEN_SW_FRAC = 0.42              !   [nondim] default = 0.0
-                                ! The fraction of the shortwave radiation that penetrates
-                                ! below the surface.
-
-! === module MOM_tracer_advect ===
-
-! === module MOM_tracer_hor_diff ===
-
-! === module MOM_neutral_diffusion ===
-! This module implements neutral diffusion of tracers
-
-! === module MOM_surface_forcing ===
-VARIABLE_WINDS = False          !   [Boolean] default = True
-                                ! If true, the winds vary in time after the initialization.
-VARIABLE_BUOYFORCE = False      !   [Boolean] default = True
-                                ! If true, the buoyancy forcing varies in time after the
-                                ! initialization of the model.
-BUOY_CONFIG = "NONE"            !
-                                ! The character string that indicates how buoyancy forcing
-                                ! is specified. Valid options include (file), (zero),
-                                ! (linear), (USER), and (NONE).
-WIND_CONFIG = "zero"            !
-                                ! The character string that indicates how wind forcing
-                                ! is specified. Valid options include (file), (2gyre),
-                                ! (1gyre), (gyres), (zero), and (USER).
-GUST_CONST = 0.0               !   [Pa] default = 0.02
-                                ! The background gustiness in the winds.
-ICE_SHELF = True                !   [Boolean] default = False
-                                ! If true, enables the ice shelf model.
-!ZSTAR_RIGID_SURFACE_THRESHOLD = 10 !
-
-! === module MOM_grid ===
-! Parameters providing information about the lateral grid.
-
-! === module MOM_hor_index ===
-! Sets the horizontal array index types.
-
-! === module MOM_grid_init ===
-
-! === module MOM_ice_shelf ===
-DYNAMIC_SHELF_MASS = False      !   [Boolean] default = False
-                                ! If true, the ice sheet mass can evolve with time.
-SHELF_THERMO = TRUE            !   [Boolean] default = False
-                                ! If true, use a thermodynamically interactive ice shelf.
-SHELF_THREE_EQN = False         !   [Boolean] default = True
-                                ! If true, use the three equation expression of
-                                ! consistency to calculate the fluxes at the ice-ocean
-                                ! interface.
-SHELF_INSULATOR = True          !   [Boolean] default = False
-                                ! If true, the ice shelf is a perfect insulatior
-                                ! (no conduction).
-SHELF_3EQ_GAMMA = True          !   [Boolean] default = False
-                                ! If true, user specifies a constant nondimensional heat-transfer coefficient
-                                ! (GAMMA_T_3EQ), from which the salt-transfer coefficient is then computed
-                                !  as GAMMA_T_3EQ/35. This is used with SHELF_THREE_EQN.
-SHELF_3EQ_GAMMA_T = 0.22       !   [nondim.] default = 0.022
-                                ! Nondimensional heat-transfer coefficient.
-SHELF_2EQ_GAMMA_T = 0.0         !   [m s-1]
-                                ! If SHELF_THREE_EQN is false, this the fixed turbulent
-                                ! exchange velocity at the ice-ocean interface.
-ICE_SHELF_FLUX_FACTOR = 1.0     !   [none] default = 1.0
-                                ! Non-dimensional factor applied to shelf thermodynamic
-                                ! fluxes.
-ICE_SHELF_TEMPERATURE = -20.0   !   [degC] default = -15.0
-                                ! The temperature at the center of the ice shelf.
-DT_FORCING = 300.0              !   [s] default = 0.0
-                                ! The time step for changing forcing, coupling with other
-                                ! components, or potentially writing certain diagnostics.
-                                ! The default value is given by DT.
-COL_THICK_MELT_THRESHOLD = 10.0  !   [m] default = 0.0
-                                ! The minimum ML thickness where melting is allowed.
-WRITE_OUTPUT_TO_FILE = True     !   [Boolean] default = False
-                                ! for debugging purposes
-USTAR_SHELF_BG = 0.0            !   [m s-1] default = 0.0
-                                ! The minimum value of ustar under ice sheves.
-CDRAG_SHELF = 0.0025            !   [nondim] default = 0.003
-                                ! CDRAG is the drag coefficient relating the magnitude of
-                                ! the velocity field to the surface stress.
-UTIDE = 0.01                   !   [m s-1] default = 0.0
-                                ! The constant tidal amplitude used with INT_TIDE_DISSIPATION.
-MELTING_CUTOFF_DEPTH = 0      ! default = 0.0
-                                ! Depth above which the melt is set to zero (it must be >= 0)
-                                ! Default value won't affect the solution.
-! === module ISOMIP_initialize_topography ===
-ICE_PROFILE_CONFIG = "FILE"     !
-                                ! This specifies how the initial ice profile is specified.
-                                ! Valid values are: CHANNEL, FILE, and USER.
-ICE_THICKNESS_FILE = "isomip_ice_shelf1_clipped.nc" ! default = "ice_shelf_h.nc"
-                                ! The file from which the bathymetry is read.
-ICE_THICKNESS_VARNAME = "thick" ! default = "h_shelf"
-                                ! The name of the thickness variable in ICE_THICKNESS_FILE.
-ICE_AREA_VARNAME = "area"       ! default = "area_shelf_h"
-                                ! The name of the area variable in ICE_THICKNESS_FILE.
-SHELF_IC_OUTPUT_FILE = "MOM_Shelf_IC" ! default = "MOM_Shelf_IC"
-                                ! The name-root of the output file for the ice shelf
-                                ! initial conditions.
-DENSITY_ICE = 918.0             !   [kg m-3] default = 900.0
-                                ! A typical density of ice.
-! === module MOM_sum_output ===
-CALCULATE_APE = False           !   [Boolean] default = True
-                                ! If true, calculate the available potential energy of
-                                ! the interfaces.  Setting this to false reduces the
-                                ! memory footprint of high-PE-count models dramatically.
-MAXTRUNC = 5000                 !   [truncations save_interval-1] default = 0
-                                ! The run will be stopped, and the day set to a very
-                                ! large value if the velocity is truncated more than
-                                ! MAXTRUNC times between energy saves.  Set MAXTRUNC to 0
-                                ! to stop if there is any truncation of velocities.
-DATE_STAMPED_STDOUT = False     !   [Boolean] default = True
-                                ! If true, use dates (not times) in messages to stdout
-MAXCPU = -1.0                   !   [wall-clock seconds] default = -1.0
-                                ! The maximum amount of cpu time per processor for which
-                                ! MOM should run before saving a restart file and
-                                ! quitting with a return value that indicates that a
-                                ! further run is required to complete the simulation.
-                                ! If automatic restarts are not desired, use a negative
-                                ! value for MAXCPU.  MAXCPU has units of wall-clock
-                                ! seconds, so the actual CPU time used is larger by a
-                                ! factor of the number of processors used.
-
-! === module MOM_main (MOM_driver) ===
-DAYMAX = 365.0                   !   [days]
-                                ! The final time of the whole simulation, in units of
-                                ! TIMEUNIT seconds.  This also sets the potential end
-                                ! time of the present run segment if the end time is
-                                ! not set via ocean_solo_nml in input.nml.
-RESTART_CONTROL = 1             ! default = 1
-                                ! An integer whose bits encode which restart files are
-                                ! written. Add 2 (bit 1) for a time-stamped file, and odd
-                                ! (bit 0) for a non-time-stamped file. A non-time-stamped
-                                ! restart file is saved at the end of the run segment
-                                ! for any non-negative value.
-RESTINT = 365.0                 !   [days] default = 0.0
-                                ! The interval between saves of the restart file in units
-                                ! of TIMEUNIT.  Use 0 (the default) to not save
-                                ! incremental restart files at all.
-ENERGYSAVEDAYS = 2.0            !   [days] default = 0.0034722222222222
-                                ! The interval in units of TIMEUNIT between saves of the
-CALC_RHO_FOR_SEA_LEVEL=True
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/common/SIS_input b/tests/Iceberg_repository/ISOMIP_Calving/common/SIS_input
deleted file mode 100644
index 6c8a425..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/common/SIS_input
+++ /dev/null
@@ -1,125 +0,0 @@
-!********+*********+*********+*********+*********+*********+*********+*
-!*   This file determines the adjustable run-time parameters for the  *
-!* Sea Ice Simulator (SIS), versions 2 and later.  Where              *
-!* appropriate, MKS units are used.                                   *
-!********+*********+*********+*********+*********+*********+*********+*
-! >>> Baltic sea coupled ice-ocean SIS2 5 layer ice, 63 layer ocean test case.
-
-!  Specify properties of the physical domain.
-GRID_CONFIG = "mosaic"          !    Method for defining horizontal grid
-                                !  = file|cartesian|spherical|mercator
-                                !  file - read grid from file "GRID_FILE"
-                                !  cartesian - a Cartesian grid
-                                !  spherical - a spherical grid
-                                !  mercator  - a Mercator grid
-GRID_FILE = "ocean_hgrid.nc"
-                                !    Name of file to read horizontal grid data
-INPUTDIR = "INPUT"
-                                !    INPUTDIR is a directory in which NetCDF
-                                !  input files might be found.
-
-CGRID_ICE_DYNAMICS = True       !   If true, use a C-grid discretization of the
-                                ! sea-ice dynamics; if false use a B-grid
-                                ! discretization.
-
-!  Specify the numerical domain.
-NIGLOBAL = 240                   !    NIGLOBAL and NJGLOBAL are the number of thickness
-NJGLOBAL = 40                   !  grid points in the zonal and meridional
-                                !  directions of the physical domain.
-NCAT_ICE = 1                    !    The number of sea ice thickness categories.
-NIHALO = 2                      !    NIHALO and NJHALO are the number of halo
-NJHALO = 2                      !  points on each side in the x- and y-directions.
-                                !  If static memory allocation is used, these
-                                !  must match the values of NIHALO_ and NJHALO_
-                                !  in MOM_memory.h.
-IO_LAYOUT = 1, 1                !    The processor layout to be used, or 0,0 to automatically
-                                !  set the io_layout to be the same as the layout.
-
-REENTRANT_X = False             !    If defined, the domain is zonally reentrant.
-REENTRANT_Y = False             !    If defined, the domain is meridionally
-                                !  reentrant.
-TRIPOLAR_N = False              !    Use tripolar connectivity at the northern
-                                !  edge of the domain.  With TRIPOLAR_N, NIGLOBAL
-                                !  must be even.
-
-DEBUG = False                   !    If true, write out verbose debugging data.
-SEND_LOG_TO_STDOUT = False      !    If true write out log information to stdout.
-TIMEUNIT = 8.64E+04             !   [s] default = 8.64E+04
-ICE_STATS_INTERVAL = 0.25       !    The interval in units of TIMEUNIT between
-                                ! writes of the globally summed ice statistics
-                                ! and conservation checks.
-
-!  Specify the time integration scheme for the ice dynamics.
-DT_ICE_DYNAMICS = 300.0        ! The time step used for the slow ice dynamics, 
-                                ! including stepping the continuity equation and
-                                ! interactions between the ice mass field and 
-                                ! velocities, in s.
-INTERSPERSED_ICE_THERMO = False ! If true, the sea ice thermodynamic updates are applied
-                                ! after the new velocities are determined, but before the
-                                ! transport occurs.  Otherwise, the ice thermodynamic
-                                ! updates occur at the start of the slow ice update and
-                                ! dynamics and continuity can occur together.
-                                ! The default should be changed to false.
-
-DT_RHEOLOGY = 300.0             ! The sub-cycling time step, in s, for iterating
-                                ! the rheology and ice momentum equations. If
-                                ! DT_RHEOLOGY is negative, the time step is set
-                                ! via NSTEPS_DYN.
-PROJECT_ICE_DRAG_VEL = True     ! If true, project forward the ice velocity used in the
-                                ! drag calculation to avoid an instability that can occur
-                                ! when an finite stress is applied to thin ice moving with
-                                ! the velocity of the ocean.
-ICE_TDAMP_ELASTIC = 0.0         !   The damping timescale associated with the
-                                ! elastic terms in the sea-ice dynamics.
-
-SIS_TRACER_ADVECTION_SCHEME = "PPM:H3" ! The horizontal transport scheme for
-                                ! tracers.  Valid options include:
-                                !   UPWIND_2D - Non-directionally split upwind
-                                !   PCM    - Directionally split peicewise constant
-                                !   PLM    - Piecewise Linear Method
-                                !   PPM:H3 - Piecewise Parabolic Method (Huyhn 3rd order)
-SIS_CONTINUITY_SCHEME = "UPWIND_2D" ! default = "UPWIND_2D"
-                                ! The horizontal transport scheme used in continuity:
-                                !   UPWIND_2D - Non-directionally split upwind
-                                !   PCM       - Directionally split peicewise constant
-                                !   PPM:C2PD  - Positive definite PPM with 2nd order edge values
-                                !   PPM:C2MO  - Monotonic PPM with 2nd order edge values
-
-!  Specify the ice properties.
-ICE_STRENGTH_PSTAR = 2.75e4     !    ICE_STRENGTH_PSTAR is a constant in the
-                                !  expression for the ice strength, P* in
-                                !  Hunke & Dukowics '97, in Pa.
-RHO_OCEAN = 1030.0              !    RHO_OCEAN is used in the Boussinesq
-                                !  approximation to calculations of pressure and
-                                !  pressure gradients, in units of kg m-3.
-RHO_ICE = 905.0                 !    RHO_ICE is the nominal density of sea ice
-                                !  used in SIS, in units of kg m-3.
-RHO_SNOW = 330.0                !    RHO_SNOW is the nominal density of snow
-                                !  used in SIS, in units of kg m-3.
-CP_ICE = 2100.0                 !    The heat capacity of fresh ice, approximated
-                                !  as a constant, in J kg-1 K-1.
-CP_SEAWATER = 4200.0            !   The heat capacity of sea water, approximated
-                                !  as a constant, in J kg-1 K-1.
-ICE_BULK_SALINITY = 5.0         !    The fixed bulk salinity of sea ice, in g/kg.
-ICE_RELATIVE_SALINITY = 0.0     !    The initial salinity of sea ice as a
-                                ! fraction of the salinity of the seawater from
-                                ! which it formed.
-SIS2_FILLING_FRAZIL = True      !   If true, apply frazil to fill as many categories as
-                                ! possible to fill in a uniform (minimum) amount of ice
-                                ! in all the thinnest categories. Otherwise the frazil is
-                                ! always assigned to a single category.
-FILLING_FRAZIL_TIMESCALE = 8.64e4 !  A timescale with which the filling frazil
-                                ! causes the thinest cells to attain similar
-                                ! thicknesses, or a negative number to apply
-                                ! the frazil flux uniformly, in s.
-
-!  Specify the properties of the surface forcing.
-ICE_OCEAN_STRESS_STAGGER = "C"  ! default = "B"
-                                ! A case-insensitive character string to indicate the
-                                ! staggering of the stress field on the ocean that is
-                                ! returned to the coupler.  Valid values include
-                                ! 'A', 'B', or 'C'.
-ADD_DIURNAL_SW = False           !    If true, add a synthetic diurnal cycle to
-                                !  the shortwave radiation.
-!OMEGA = 0.0                     !   [s-1] default = 7.2921E-05
-PASS_ICEBERG_AREA_TO_OCEAN = True !Iceberg area is passed to the ocean through the coupler.
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/common/clean_MOM.sh b/tests/Iceberg_repository/ISOMIP_Calving/common/clean_MOM.sh
deleted file mode 100755
index 5ce2ea2..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/common/clean_MOM.sh
+++ /dev/null
@@ -1,14 +0,0 @@
-rm *.nc*
-rm available_diags.000000
-rm logfile.000000.out
-rm MOM_parameter_doc.*
-rm ocean.stats
-rm time_stamp.out
-rm V_velocity_truncations
-rm U_velocity_truncations
-rm output
-rm SIS_parameter_doc.*
-rm seaice.stats
-rm SIS.available_diags
-rm SIS_fast.available_diags
-rm TPY_*
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/common/data_table b/tests/Iceberg_repository/ISOMIP_Calving/common/data_table
deleted file mode 100644
index e28f42c..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/common/data_table
+++ /dev/null
@@ -1,47 +0,0 @@
-"ATM" , "p_surf"        , ""         , ""                             , .false. ,  100000000.0
-"ATM" , "p_bot"         , ""         , ""                             , .false. ,  100000000.0
-"ATM" , "t_bot"         , ""    , ""                             , .false. ,  273.0
-"ATM" , "sphum_bot"     , ""    , ""                             , .false. ,  1.e-3
-"ATM" , "u_bot"         , ""    , ""                             , .false. ,  0.0
-"ATM" , "v_bot"         , ""    , ""                             , .false. ,  0.0
-"ATM" , "z_bot"         , ""            , ""                             , .false. , 1.0
-"ATM" , "gust"          , ""            , ""                             , .false. ,  1.0
-"ICE" , "lprec"         , ""        , ""                            , .false. ,  0.0
-"ICE" , "fprec"         , ""        , ""                            , .false. ,  0.0
-"ICE" , "q_flux"         , ""        , ""                            , .false. ,  0.0
-"ICE" , "t_flux"         , ""        , ""                            , .false. ,  0.0
-"ICE" , "lw_flux"         , ""        , ""                            , .false. ,  0.0
-"ICE" , "u_flux"         , ""        , ""                            , .false. , -0.00000
-"ICE" , "v_flux"         , ""        , ""                            , .false. , -0.00000
-#"ICE" , "latent"         , ""        , ""                            , .false. ,  0.0
-#"ICE" , "runoff"        , ""            , ""                             , .false.  ,  0.0
-#"ICE" , "calving"       , ""     , ""                                     , .false.  ,  0.0
-#"ICE" , "calving_hflx"       , ""     , ""                                     , .false.  ,  0.0
-"ICE" , "dhdt"          , ""            , ""                             , .false.  ,  80.0
-"ICE" , "dedt"          , ""            , ""                             , .false.  ,  2.0e-6
-"ICE" , "drdt"          , ""            , ""                             , .false.  , 10.0
-#"ICE", "sic_obs"        , ""         , ""                             , .true. ,  0.00
-#"ICE", "sit_obs"        , ""         , ""                             , .true. ,  0.00
-#"ICE", "sst_obs"        , ""         , ""                             , .true. ,  -1.9
-"LND" , "t_surf"        , ""            , ""                             , .true.  ,  273.0
-"LND" , "t_ca"          , ""            , ""                             , .true.  ,  273.0
-"LND" , "q_ca"          , ""            , ""                             , .true.  ,  0.0
-"LND" , "rough_mom"     , ""            , ""                             , .true.  ,  0.01
-"LND" , "rough_heat"    , ""            , ""                             , .true.  ,  0.1
-"LND" , "albedo"        , ""            , ""                             , .true.  ,  0.1
-"LND" , "t_ca"          , ""            , ""                             , .true.  ,  273.0
-"LND" , "t_surf"        , ""            , ""                             , .true.  ,  273.0
-"LND" , "sphum_surf"    , ""            , ""                             , .true.  ,  0.0
-"LND" , "sphum_ca"      , ""            , ""                             , .true.  ,  0.0
-"LND" , "t_flux"        , ""            , ""                             , .true.  ,  0.0
-"LND" , "sphum_flux"    , ""            , ""                             , .true.  ,  0.0
-"LND" , "lw_flux"       , ""            , ""                             , .true.  ,  0.0
-"LND" , "sw_flux"       , ""            , ""                             , .true.  ,  0.0
-"LND" , "lprec"         , ""            , ""                             , .true.  ,  0.0
-"LND" , "fprec"         , ""            , ""                             , .true.  ,  0.0
-"LND" , "dhdt"          , ""            , ""                             , .true.  ,  5.0
-"LND" , "dedt"          , ""            , ""                             , .true.  ,  2e-6
-"LND" , "dedq"          , ""            , ""                             , .true.  ,  0.0
-"LND" , "drdt"          , ""            , ""                             , .true.  ,  0.0
-"LND" , "drag_q"        , ""            , ""                             , .true.  ,  0.0
-"LND" , "p_surf"        , ""            , ""                             , .true.  ,  1.e-5
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/common/diag_table b/tests/Iceberg_repository/ISOMIP_Calving/common/diag_table
deleted file mode 100644
index 129f3c1..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/common/diag_table
+++ /dev/null
@@ -1,453 +0,0 @@
-GOLD_SIS
-1 1 1 0 0 0 
-#output files
-#"prog",     1,"days",1,"days","time"
-#"ice_month",      1,  "months", 1, "days", "time",
-#"ocean_month",    1,  "months", 1, "days", "time",
-#"ocean_month_z",  1,  "months", 1, "days", "time",
-#"icebergs_month", 1, "months", 1, "days", "time",
-#"flux_month",     1,  "months", 1, "days", "time"
-#"ocean_sfc",    1,  "months", 1, "days", "time",
-
-"prog",           60,"minutes",1,"days","time"
-"ice_month",      60,  "minutes", 1, "days", "time",
-"icebergs_month", 60, "minutes", 1, "days", "time",
-"ocean_month",    60,  "minutes", 1, "days", "time",
-"ocean_month_z",  60,  "minutes", 1, "days", "time",
-"flux_month",     720,  "minutes", 1, "days", "time"
-"ocean_sfc",    720,  "minutes", 1, "days", "time",
-#
-#"prog",     720,"minutes",1,"days","time"
-#"ice_month",      720,  "minutes", 1, "days", "time",
-#"icebergs_month", 720, "minutes", 1, "days", "time",
-#"ocean_month",    720,  "minutes", 1, "days", "time",
-#"ocean_month_z",  720,  "minutes", 1, "days", "time",
-#"flux_month",     720,  "minutes", 1, "days", "time"
-#"ocean_sfc",    720,  "minutes", 1, "days", "time",
-#
-#"prog",     1,"days",1,"days","time"
-#"ice_month",      1,  "days", 1, "days", "time",
-#"icebergs_month", 1, "days", 1, "days", "time",
-#"ocean_month",    1,  "days", 1, "days", "time",
-#"ocean_sfc",    1,  "days", 1, "days", "time",
-#"ocean_month_z",  1,  "days", 1, "days", "time",
-#"flux_month",    1,  "days", 1, "days", "time"
-#
-"ocean_static",-1,  "days", 1, "days", "time",
-
-#"ocean_scalar", 1,  "months", 1, "days", "time"
-#
-#output variables
-#
-# OCEAN DIAGNOSTICS:
-#===================
-#===================
-#
-# Surface Ocean fields:
-#=========================
-"ocean_model","SSH","SSH","ocean_sfc","all",.true.,"none",2
-"ocean_model","SSU","SSU","ocean_sfc","all",.true.,"none",2
-"ocean_model","SSV","SSV","ocean_sfc","all",.true.,"none",2
-"ocean_model","SST","SST","ocean_sfc","all",.true.,"none",2
-"ocean_model","SSS","SSS","ocean_sfc","all",.true.,"none",2
-"ocean_model","speed","speed","ocean_sfc","all",.true.,"none",2
-
-# Prognostic Ocean fields:
-#=========================
-"ocean_model","u","u","ocean_month","all",.true.,"none",2
-"ocean_model","v","v","ocean_month","all",.true.,"none",2
-"ocean_model","h","h","ocean_month","all",.true.,"none",2
-"ocean_model","e","e","ocean_month","all",.true.,"none",2
-"ocean_model","temp","temp","ocean_month","all",.true.,"none",2
-"ocean_model","salt","salt","ocean_month","all",.true.,"none",2
-#"ocean_model","PRCmE","PRCmE","ocean_month","all",.true.,"none",2
-"ocean_model","melt","melt","ocean_month","all",.true.,"none",2
-#"ocean_model","mass_flux","mass_flux","ocean_month","all",.true.,"none",2
-#"ocean_model","frunoff","frunoff","ocean_month","all",.true.,"none",2
-#"ocean_model","heat_content_frunoff","heat_content_frunoff","ocean_month","all",.true.,"none",2
-#"ocean_model","net_heat_coupler","net_heat_coupler","ocean_month","all",.true.,"none",2
-#"ocean_model","tr_D1","tr1","ocean_month","all",.true.,"none",2
-#"ocean_model","tr_D2","tr2","ocean_month","all",.true.,"none",2
-"ocean_model","rhoinsitu","rhoinsitu","ocean_month","all",.true.,"none",2
-"ocean_model","ustar_shelf","ustar_shelf","ocean_month","all",.true.,"none",2
-#"ocean_model","exch_vel_s","exch_vel_s","ocean_month","all",.true.,"none",2
-#"ocean_model","exch_vel_t","exch_vel_t","ocean_month","all",.true.,"none",2
-"ocean_model","tfreeze","tfreeze","ocean_month","all",.true.,"none",2
-"ocean_model","u_ml","u_ml","ocean_month","all",.true.,"none",2
-"ocean_model","v_ml","v_ml","ocean_month","all",.true.,"none",2
-#"ocean_model","thermal_driving","thermal_driving","ocean_month","all",.true.,"none",2
-#"ocean_model","haline_driving","haline_driving","ocean_month","all",.true.,"none",2
-"ocean_model","h_ML","h_ML","ocean_month","all",.true.,"none",2
-#"ocean_model","ePBL_h_ML","ePBL_h_ML","ocean_month","all",.true.,"none",2
-"ocean_model","uhbt","uhbt","ocean_month","all",.true.,"none",2
-"ocean_model","vhbt","vhbt","ocean_month","all",.true.,"none",2
-#
-# Auxilary Tracers:
-#==================
-#"ocean_model","vintage","vintage","ocean_month","all",.true.,"none",2
-#"ocean_model","age","age","ocean_month","all",.true.,"none",2
-#
-# Z-space fields:
-#==================
-#"ocean_model_z_new","u","u","ocean_month_z","all",.true.,"none",2
-#"ocean_model_z_new","v","v","ocean_month_z","all",.true.,"none",2
-#"ocean_model_z_new","temp","temp","ocean_month_z","all",.true.,"none",2
-#"ocean_model_z_new","salt","salt","ocean_month_z","all",.true.,"none",2
-#"ocean_model_z_new","rhoinsitu","rhoinsitu","ocean_month_z","all",.true.,"none",2
-#"ocean_model_z","vintage","vintage","ocean_month_z","all",.true.,"none",2
-#"ocean_model_z","age","age","ocean_month_z","all",.true.,"none",2
-
-# Z-space fields:
-#==================
- "ocean_model_z","temp","temp","ocean_month_z","all",.true.,"none",2
- "ocean_model_z","salt","salt","ocean_month_z","all",.true.,"none",2
- "ocean_model_z","u","u","ocean_month_z","all",.true.,"none",2
- "ocean_model_z","uh","uh","ocean_month_z","all",.true.,"none",2
- "ocean_model_z","v","v","ocean_month_z","all",.true.,"none",2
- "ocean_model_z","vh","vh","ocean_month_z","all",.true.,"none",2 
-
-
-# Prognostic Ocean fields:
-#=========================
-"ocean_model","u","u","prog","all",.true.,"none",2
-"ocean_model","v","v","prog","all",.true.,"none",2
-"ocean_model","h","h","prog","all",.true.,"none",1
-"ocean_model","e","e","prog","all",.true.,"none",2
-"ocean_model","temp","temp","prog","all",.true.,"none",2
-"ocean_model","salt","salt","prog","all",.true.,"none",2
-"ocean_model","Rml","Rml","prog","all",.true.,"none",2
-#"ocean_model","tr_D1","tr1","prog","all",.true.,"none",2
-"ocean_model","tr_D2","tr2","prog","all",.true.,"none",2
-"ocean_model","rhoinsitu","rhoinsitu","prog","all",.true.,"none",2
-
-# Continuity Equation Terms:
-#===========================
-#"ocean_model","wd","wd","ocean_month","all",.true.,"none",2
-"ocean_model","uh","uh","ocean_month","all",.true.,"none",2
-"ocean_model","vh","vh","ocean_month","all",.true.,"none",2
-#"ocean_model","h_rho","h_rho","ocean_month","all",.true.,"none",2
-#"ocean_model","uh_rho","uh_rho","ocean_month","all",.true.,"none",2
-#"ocean_model","vh_rho","vh_rho","ocean_month","all",.true.,"none",2
-#"ocean_model","uhGM_rho","uhGM_rho","ocean_month","all",.true.,"none",2
-#"ocean_model","vhGM_rho","vhGM_rho","ocean_month","all",.true.,"none",2
-#"ocean_model","GMwork","GMwork","ocean_month","all",.true.,"none",2
-#
-# Mixed Layer TKE Budget Terms:
-#===========================
-"ocean_model","TKE_wind","TKE_wind","ocean_month","all",.true.,"none",2
-#"ocean_model","TKE_RiBulk","TKE_RiBulk","ocean_month","all",.true.,"none",2
-#"ocean_model","TKE_conv","TKE_conv","ocean_month","all",.true.,"none",2
-#"ocean_model","TKE_pen_SW","TKE_pen_SW","ocean_month","all",.true.,"none",2
-#"ocean_model","TKE_mixing","TKE_mixing","ocean_month","all",.true.,"none",2
-#"ocean_model","TKE_mech_decay","TKE_mech_decay","ocean_month","all",.true.,"none",2
-#"ocean_model","TKE_conv_decay","TKE_conv_decay","ocean_month","all",.true.,"none",2
-#"ocean_model","TKE_conv_s2","TKE_conv_s2","ocean_month","all",.true.,"none",2
-#"ocean_model","TKE_tidal","TKE_tidal","ocean_month","all",.true.,"none",2
-#"ocean_model","Kd_effective","Kd_effective","ocean_month","all",.true.,"none",2
-#
-# Tracer Fluxes:
-#==================
-#"ocean_model","T_adx",  "T_adx",  "ave_prog_%4yr_%3dy","all",.true.,"none",2
-#"ocean_model","T_ady",  "T_ady",  "ave_prog_%4yr_%3dy","all",.true.,"none",2
-#"ocean_model","T_diffx","T_diffx","ave_prog_%4yr_%3dy","all",.true.,"none",2
-#"ocean_model","T_diffy","T_diffy","ave_prog_%4yr_%3dy","all",.true.,"none",2
-#"ocean_model","S_adx",  "S_adx",  "ave_prog_%4yr_%3dy","all",.true.,"none",2
-#"ocean_model","S_ady",  "S_ady",  "ave_prog_%4yr_%3dy","all",.true.,"none",2
-#"ocean_model","S_diffx","S_diffx","ave_prog_%4yr_%3dy","all",.true.,"none",2
-#"ocean_model","S_diffy","S_diffy","ave_prog_%4yr_%3dy","all",.true.,"none",2
-
-
-# Momentum Balance Terms:
-#=======================
-#"ocean_model","dudt","dudt","ocean_month","all",.true.,"none",2
-#"ocean_model","dvdt","dvdt","ocean_month","all",.true.,"none",2
-#"ocean_model","CAu","CAu","ocean_month","all",.true.,"none",2
-#"ocean_model","CAv","CAv","ocean_month","all",.true.,"none",2
-#"ocean_model","PFu","PFu","ocean_month","all",.true.,"none",2
-#"ocean_model","PFv","PFv","ocean_month","all",.true.,"none",2
-#"ocean_model","du_dt_visc","du_dt_visc","ocean_month","all",.true.,"none",2
-#"ocean_model","dv_dt_visc","dv_dt_visc","ocean_month","all",.true.,"none",2
-#"ocean_model","diffu","diffu","ocean_month","all",.true.,"none",2
-#"ocean_model","diffv","diffv","ocean_month","all",.true.,"none",2
-#"ocean_model","dudt_dia","dudt_dia","ocean_month","all",.true.,"none",2
-#"ocean_model","dvdt_dia","dvdt_dia","ocean_month","all",.true.,"none",2
-# Subterms that should not be added to a closed budget.
-#"ocean_model","gKEu","gKEu","ocean_month","all",.true.,"none",2
-#"ocean_model","gKEv","gKEv","ocean_month","all",.true.,"none",2
-#"ocean_model","rvxu","rvxu","ocean_month","all",.true.,"none",2
-#"ocean_model","rvxv","rvxv","ocean_month","all",.true.,"none",2
-#"ocean_model","PFu_bc","PFu_bc","ocean_month","all",.true.,"none",2
-#"ocean_model","PFv_bc","PFv_bc","ocean_month","all",.true.,"none",2
-
-# Barotropic Momentum Balance Terms:
-# (only available with split time stepping.)
-#===========================================
-#"ocean_model","PFuBT","PFuBT","ocean_month","all",.true.,"none",2
-#"ocean_model","PFvBT","PFvBT","ocean_month","all",.true.,"none",2
-#"ocean_model","CoruBT","CoruBT","ocean_month","all",.true.,"none",2
-#"ocean_model","CorvBT","CorvBT","ocean_month","all",.true.,"none",2
-#"ocean_model","ubtforce","ubtforce","ocean_month","all",.true.,"none",2
-#"ocean_model","vbtforce","vbtforce","ocean_month","all",.true.,"none",2
-#"ocean_model","u_accel_bt","u_accel_bt","ocean_month","all",.true.,"none",2
-#"ocean_model","v_accel_bt","v_accel_bt","ocean_month","all",.true.,"none",2
-#
-# Viscosities and diffusivities:
-#===============================
-#"ocean_model","Kd","Kd","visc_%4yr_%3dy","all",.true.,"none",2
-#"ocean_model","Ahh","Ahh","visc_%4yr_%3dy","all",.true.,"none",2
-#"ocean_model","Ahq","Ahq","visc_%4yr_%3dy","all",.true.,"none",2
-#"ocean_model","Khh","Khh","visc_%4yr_%3dy","all",.true.,"none",2
-#"ocean_model","Khq","Khq","visc_%4yr_%3dy","all",.true.,"none",2
-#"ocean_model","bbl_thick_u","bbl_thick_u","visc_%4yr_%3dy","all",.true.,"none",2
-#"ocean_model","kv_bbl_u","kv_bbl_u","visc_%4yr_%3dy","all",.true.,"none",2
-#"ocean_model","bbl_thick_v","bbl_thick_v","visc_%4yr_%3dy","all",.true.,"none",2
-#"ocean_model","kv_bbl_v","kv_bbl_v","visc_%4yr_%3dy","all",.true.,"none",2
-#"ocean_model","av_visc","av_visc","visc_%4yr_%3dy","all",.true.,"none",2
-#"ocean_model","au_visc","au_visc","visc_%4yr_%3dy","all",.true.,"none",2
-#"ocean_model","FrictWork","FrictWork","ocean_month","all",.true.,"none",2
-#"ocean_model","SN_u","SN_u","ocean_month","all",.true.,"none",2
-#"ocean_model","SN_v","SN_v","ocean_month","all",.true.,"none",2
-#"ocean_model","NH","NH","ocean_month","all",.true.,"none",2
-#"ocean_model","Ld","Ld","ocean_month","all",.true.,"none",2
-#"ocean_model","Le","Le","ocean_month","all",.true.,"none",2
-#"ocean_model","L2u","L2u","ocean_month","all",.true.,"none",2
-#"ocean_model","L2v","L2v","ocean_month","all",.true.,"none",2
-#"ocean_model","S2u","S2u","ocean_month","all",.true.,"none",2
-#"ocean_model","S2v","S2v","ocean_month","all",.true.,"none",2
-#"ocean_model","eff_beta","eff_beta","ocean_month","all",.true.,"none",2
-#"ocean_model","KHTH_u","KHTH_u","ocean_month","all",.true.,"none",2
-#"ocean_model","KHTH_v","KHTH_v","ocean_month","all",.true.,"none",2
-#"ocean_model","KHTR_u","KHTR_u","ocean_month","all",.true.,"none",2
-#"ocean_model","KHTR_v","KHTR_v","ocean_month","all",.true.,"none",2
-
-# MEKE:
-#======
-# "ocean_model","MEKE","MEKE","ocean_month","all",.true.,"none",2
-# "ocean_model","MEKE_src","MEKE_src","ocean_month","all",.true.,"none",2
-# "ocean_model","MEKE_Kh","MEKE_Kh","ocean_month","all",.true.,"none",2
-#
-# Kinetic Energy Balance Terms:
-#=============================
-#"ocean_model","KE","KE","energy_%4yr_%3dy","all",.true.,"none",2
-#"ocean_model","dKE_dt","dKE_dt","energy_%4yr_%3dy","all",.true.,"none",2
-#"ocean_model","PE_to_KE","PE_to_KE","energy_%4yr_%3dy","all",.true.,"none",2
-#"ocean_model","KE_Coradv","KE_Coradv","energy_%4yr_%3dy","all",.true.,"none",2
-#"ocean_model","KE_adv","KE_adv","energy_%4yr_%3dy","all",.true.,"none",2
-#"ocean_model","KE_visc","KE_visc","energy_%4yr_%3dy","all",.true.,"none",2
-#"ocean_model","KE_horvisc","KE_horvisc","energy_%4yr_%3dy","all",.true.,"none",2
-#"ocean_model","KE_dia","KE_dia","energy_%4yr_%3dy","all",.true.,"none",2
-#
-# Surface Forcing:
-#=================
-"ocean_model","taux",     "taux",     "ocean_month","all",.true.,"none",2
-"ocean_model","tauy",     "tauy",     "ocean_month","all",.true.,"none",2
-"ocean_model","ustar",    "ustar",    "ocean_month","all",.true.,"none",2
-#"ocean_model","PRCmE",    "PRCmE",    "ocean_month","all",.true.,"none",2
-"ocean_model","SW",       "SW",       "ocean_month","all",.true.,"none",2
-"ocean_model","latent",   "latent",       "ocean_month","all",.true.,"none",2
-"ocean_model","latent_frunoff",   "latent_frunoff",       "ocean_month","all",.true.,"none",2
-"ocean_model","sensible",   "sensible",       "ocean_month","all",.true.,"none",2
-"ocean_model","LwLatSens","LwLatSens","ocean_month","all",.true.,"none",2
-"ocean_model","p_surf",   "p_surf",   "ocean_month","all",.true.,"none",2
-"ocean_model","salt_flux","salt_flux","ocean_month","all",.true.,"none",2
-"ocean_model","ustar_berg","ustar_berg","ocean_month","all",.true.,"none",2
-"ocean_model","area_berg","area_berg","ocean_month","all",.true.,"none",2
-"ocean_model","mass_berg","mass_berg","ocean_month","all",.true.,"none",2
-"ocean_model","ustar_ice_cover","ustar_ice_cover","ocean_month","all",.true.,"none",2
-"ocean_model","frac_ice_cover","frac_ice_cover","ocean_month","all",.true.,"none",2
-#"ocean_model","frunoff",   "frunoff",       "ocean_month","all",.true.,"none",2
-#"ocean_model","lrunoff",   "lrunoff",       "ocean_month","all",.true.,"none",2
-
-# Static ocean fields:
-#=====================
-"ocean_model", "geolon",      "geolon",      "ocean_static", "all", .true., "none", 2
-"ocean_model", "geolat",      "geolat",      "ocean_static", "all", .true., "none", 2
-"ocean_model", "geolon_c",    "geolon_c",    "ocean_static", "all", .true., "none", 2
-"ocean_model", "geolat_c",    "geolat_c",    "ocean_static", "all", .true., "none", 2
-"ocean_model", "geolon_u",    "geolon_u",    "ocean_static", "all", .true., "none", 2
-"ocean_model", "geolat_u",    "geolat_u",    "ocean_static", "all", .true., "none", 2
-"ocean_model", "geolon_v",    "geolon_v",    "ocean_static", "all", .true., "none", 2
-"ocean_model", "geolat_v",    "geolat_v",    "ocean_static", "all", .true., "none", 2
-"ocean_model", "area_t",      "area_t",      "ocean_static", "all", .true., "none", 2
-"ocean_model", "depth_ocean", "depth_ocean", "ocean_static", "all", .true., "none", 2
-"ocean_model", "wet",         "wet",         "ocean_static", "all", .true., "none", 2
-"ocean_model", "wet_c",       "wet_c",       "ocean_static", "all", .true., "none", 2
-"ocean_model", "wet_u",       "wet_u",       "ocean_static", "all", .true., "none", 2
-"ocean_model", "wet_v",       "wet_v",       "ocean_static", "all", .true., "none", 2
-"ocean_model", "Coriolis",    "Coriolis",    "ocean_static", "all", .true., "none", 2
-
-#
-# ICE DIAGNOSTICS:
-#=================
-#=================
-#"ice_model", "FRAZIL",     "FRAZIL",     "ice_month", "all", .true., "none", 2,
-"ice_model", "HI",         "HI",         "ice_month", "all", .true., "none", 2,
-#"ice_model", "HS",         "HS",         "ice_month", "all", .true., "none", 2,
-#"ice_model", "TS",         "TS",         "ice_month", "all", .true., "none", 2,
-#"ice_model", "T1",         "T1",         "ice_month", "all", .true., "none", 2,
-#"ice_model", "T2",         "T2",         "ice_month", "all", .true., "none", 2,
-"ice_model", "CN",         "CN",         "ice_month", "all", .true., "none", 2,
-#"ice_model", "EXT",        "EXT",        "ice_month", "all", .true., "none", 2,
-"ice_model", "MI",         "MI",         "ice_month", "all", .true., "none", 2,
-#"ice_model", "XPRT",       "XPRT",       "ice_month", "all", .true., "none", 2,
-#"ice_model", "LSRC",       "LSRC",       "ice_month", "all", .true., "none", 2,
-#"ice_model", "LSNK",       "LSNK",       "ice_month", "all", .true., "none", 2,
-#"ice_model", "BSNK",       "BSNK",       "ice_month", "all", .true., "none", 2,
-#"ice_model", "SN2IC",      "SN2IC",      "ice_month", "all", .true., "none", 2,
-#"ice_model", "ALB",        "ALB",        "ice_month", "all", .true., "none", 2,
-#"ice_model", "SW",         "SW",         "ice_month", "all", .true., "none", 2,
-"ice_model", "LW",         "LW",         "ice_month", "all", .true., "none", 2,
-"ice_model", "SH",         "SH",         "ice_month", "all", .true., "none", 2,
-#"ice_model", "LH",         "LH",         "ice_month", "all", .true., "none", 2,
-"ice_model", "TMELT",      "TMELT",      "ice_month", "all", .true., "none", 2,
-#"ice_model", "BMELT",      "BMELT",      "ice_month", "all", .true., "none", 2,
-#"ice_model", "BHEAT",      "BHEAT",      "ice_month", "all", .true., "none", 2,
-"ice_model", "UI",         "UI",         "ice_month", "all", .true., "none", 2,
-"ice_model", "VI",         "VI",         "ice_month", "all", .true., "none", 2,
-#"ice_model", "FA_X",       "FA_X",       "ice_month", "all", .true., "none", 2,
-#"ice_model", "FA_Y",       "FA_Y",       "ice_month", "all", .true., "none", 2,
-#"ice_model", "FI_X",       "FI_X",       "ice_month", "all", .true., "none", 2,
-#"ice_model", "FI_Y",       "FI_Y",       "ice_month", "all", .true., "none", 2,
-"ice_model", "SST",        "SST",        "ice_month", "all", .true., "none", 2,
-"ice_model", "SSS",        "SSS",        "ice_month", "all", .true., "none", 2,
-#"ice_model", "SSH",        "SSH",        "ice_month", "all", .true., "none", 2,
-"ice_model", "UO",         "UO",         "ice_month", "all", .true., "none", 2,
-"ice_model", "VO",         "VO",         "ice_month", "all", .true., "none", 2,
-"ice_model", "SNOWFL",     "SNOWFL",     "ice_month", "all", .true., "none", 2,
-#"ice_model", "RAIN",       "RAIN",       "ice_month", "all", .true., "none", 2,
-#"ice_model", "CALVING",    "CALVING",    "ice_month", "all", .true., "none", 2,
-#"ice_model", "RUNOFF",     "RUNOFF",     "ice_month", "all", .true., "none", 2,
-"ice_model", "CELL_AREA",  "CELL_AREA",  "ice_month", "all", .true., "none", 2,
-"ice_model", "GEOLON",     "GEOLON",     "ice_month", "all", .true., "none", 2,
-"ice_model", "GEOLAT",     "GEOLAT",     "ice_month", "all", .true., "none", 2,
-"ice_model", "SINROT",     "SINROT",     "ice_month", "all", .true., "none", 2,
-"ice_model", "COSROT",     "COSROT",     "ice_month", "all", .true., "none", 2,
-"ice_model", "SALTF",      "SALTF",      "ice_month", "all", .true., "none", 2,
-#"ice_model", "IX_TRANS",   "IX_TRANS",   "ice_month", "all", .true., "none", 2,
-#"ice_model", "IY_TRANS",   "IY_TRANS",   "ice_month", "all", .true., "none", 2,
-"ice_model", "MIB",   "MIB",   "ice_month", "all", .true., "none", 2,
-"ice_model", "USTAR_BERG",   "USTAR_BERG",   "ice_month", "all", .true., "none", 2,
-"ice_model", "AREA_BERG",   "AREA_BERG",   "ice_month", "all", .true., "none", 2,
-"ice_model", "MASS_BERG",   "MASS_BERG",   "ice_month", "all", .true., "none", 2,
-
-# ICEBERG DIAGNOSTICS:
-#=====================
-#=====================
-"icebergs", "calving",        "calving",        "icebergs_month", "all", .true., "none", 2,
-#"icebergs", "accum_calving",  "accum_calving",  "icebergs_month", "all", .true., "none", 2,
-#"icebergs", "unused_calving", "unused_calving", "icebergs_month", "all", .true., "none", 2,
-#"icebergs", "real_calving",   "real_calving",   "icebergs_month", "all", .true., "none", 2,
-#"icebergs", "stored_ice",     "stored_ice",     "icebergs_month", "all", .true., "none", 2,
-"icebergs", "hi",             "hi",             "icebergs_month", "all", .true., "none", 2,
-"icebergs", "cn",             "cn",             "icebergs_month", "all", .true., "none", 2,
-"icebergs", "ui",             "ui",             "icebergs_month", "all", .true., "none", 2,
-"icebergs", "vi",             "vi",             "icebergs_month", "all", .true., "none", 2,
-"icebergs", "ua",             "ua",             "icebergs_month", "all", .true., "none", 2,
-"icebergs", "va",             "va",             "icebergs_month", "all", .true., "none", 2,
-"icebergs", "uo",             "uo",             "icebergs_month", "all", .true., "none", 2,
-"icebergs", "vo",             "vo",             "icebergs_month", "all", .true., "none", 2,
-"icebergs", "sst",            "sst",            "icebergs_month", "all", .true., "none", 2,
-"icebergs", "sss",            "sss",            "icebergs_month", "all", .true., "none", 2,
-"icebergs", "ssh",            "ssh",            "icebergs_month", "all", .true., "none", 2,
-"icebergs", "mass",           "mass",           "icebergs_month", "all", .true., "none", 2,
-"icebergs", "virtual_area",   "virtual_area",   "icebergs_month", "all", .true., "none", 2,
-"icebergs", "melt",           "melt",           "icebergs_month", "all", .true., "none", 2,
-#"icebergs", "berg_melt",      "berg_melt",      "icebergs_month", "all", .true., "none", 2,
-"icebergs", "spread_mass",    "spread_mass",    "icebergs_month", "all", .true., "none", 2,
-"icebergs", "spread_area",    "spread_area",    "icebergs_month", "all", .true., "none", 2,
-#"icebergs", "melt_buoy",      "melt_buoy",      "icebergs_month", "all", .true., "none", 2,
-#"icebergs", "melt_eros",      "melt_eros",      "icebergs_month", "all", .true., "none", 2,
-#"icebergs", "melt_conv",      "melt_conv",      "icebergs_month", "all", .true., "none", 2,
-"icebergs", "melt_m_per_year","melt_m_per_year","icebergs_month", "all", .true., "none", 2,
-"icebergs", "mask",           "mask",           "icebergs_month", "all", .true., "none", 2,
-"icebergs", "area",           "area",           "icebergs_month", "all", .true., "none", 2,
-"icebergs", "lon",            "lon",            "icebergs_month", "all", .true., "none", 2,
-"icebergs", "lat",            "lat",            "icebergs_month", "all", .true., "none", 2,
-"icebergs", "u_iceberg",      "u_iceberg",      "icebergs_month", "all", .true., "none", 2,
-"icebergs", "v_iceberg",      "v_iceberg",      "icebergs_month", "all", .true., "none", 2,
-"icebergs", "spread_uvel",      "spread_uvel",      "icebergs_month", "all", .true., "none", 2,
-"icebergs", "spread_vvel",      "spread_vvel",      "icebergs_month", "all", .true., "none", 2,
-"icebergs", "ustar_iceberg",      "ustar_iceberg",      "icebergs_month", "all", .true., "none", 2,
-#"icebergs", "running_mean_calving",      "running_mean_calving",      "icebergs_month", "all", .true., "none", 2,
-#"icebergs", "running_mean_calving_hflx",      "running_mean_calving_hflx",      "icebergs_month", "all", .true., "none", 2,
-"icebergs", "ocean_depth", "ocean_depth", "icebergs_month", "all", .true., "none", 2,
-"icebergs", "Depth", "Depth", "icebergs_month", "all", .true., "none", 2,
-
-#
-#========================
-# ATMOSPHERE DIAGNOSTICS:
-#========================
-#========================
-# "flux",      "land_mask",   "land_mask",   "flux_month", "all", .true., "none", 2,
-# "flux",      "ice_mask",    "ice_mask",    "flux_month", "all", .true.,  "none", 2,
-# "flux",      "drag_moist",  "drag_moist",  "flux_month", "all", .true.,  "none", 2,
-# "flux",      "drag_heat",   "drag_heat",   "flux_month", "all", .true.,  "none", 2,
-# "flux",      "drag_mom",    "drag_mom",    "flux_month", "all", .true.,  "none", 2,
-# "flux",      "wind",        "wind",        "flux_month", "all", .true.,  "none", 2,
-# # "flux" forcing fields for land model: wind, q_ref atmos_8xdaily
-# #"flux",      "wind",        "wind",        "atmos_8xdaily", "all", .true., "none", 2,
-# #"flux",      "q_ref",       "q_ref",       "atmos_8xdaily", "all", .true., "none", 2,
-# "flux",      "tau_x",       "tau_x",       "flux_month", "all", .true.,  "none", 2,
-# "flux",      "tau_y",       "tau_y",       "flux_month", "all", .true.,  "none", 2,
-# "flux",      "shflx",       "shflx",       "flux_month", "all", .true.,  "none", 2,
-# "flux",      "evap",        "evap",        "flux_month", "all", .true.,  "none", 2,
-# "flux",      "lwflx",       "lwflx",       "flux_month", "all", .true.,  "none", 2,
-# "flux",      "rh_ref",      "rh_ref",      "flux_month", "all", .true.,  "none", 2,
-# "flux",      "u_ref",       "u_ref",       "flux_month", "all", .true.,  "none", 2,
-# "flux",      "v_ref",       "v_ref",       "flux_month", "all", .true.,  "none", 2,
-# "flux",      "u_atm",       "u_atm",       "flux_month", "all", .true.,"none", 2,
-# "flux",      "v_atm",       "v_atm",       "flux_month", "all", .true.,"none", 2,
-# "flux",      "t_atm",       "t_atm",       "flux_month", "all", .true.,"none", 2,
-# "flux",      "t_surf",      "t_surf",      "flux_month", "all", .true.,"none", 2,
-# "flux",      "q_atm",       "q_atm",       "flux_month", "all", .true.,"none", 2,
-#
-# For these "_col" fields, set do_cmip_diagnostics=.true. in &shortwave_driver_nml, and uncomment
-#"radiation", "organic_carbon_exopdep_col","org_crb_exdep_c", "atmos_month", "all", .true., "none", 2,
-#"radiation", "organic_carbon_abopdep_col","org_crb_abdep_c", "atmos_month", "all", .true., "none", 2,
-#"radiation", "black_carbon_exopdep_col",  "blk_crb_exdep_c", "atmos_month", "all", .true., "none", 2,
-#"radiation", "black_carbon_abopdep_col",  "blk_crb_abdep_c", "atmos_month", "all", .true., "none", 2,
-#"radiation", "sea_salt_exopdep_col",      "salt_exdep_c",    "atmos_month", "all", .true., "none", 2,
-#"radiation", "sea_salt_abopdep_col",      "salt_abdep_c",    "atmos_month", "all", .true., "none", 2,
-#"radiation", "so4_anthro_col",            "so4_ant_col",     "atmos_month", "all", .true., "none", 2,
-#"radiation", "so4_natural_col",           "so4_nat_col",     "atmos_month", "all", .true., "none", 2,
-#"radiation", "small_dust_exopdep_col",    "sm_dust_exdep_c", "atmos_month", "all", .true., "none", 2,
-#"radiation", "small_dust_abopdep_col",    "sm_dust_abdep_c", "atmos_month", "all", .true., "none", 2,
-#"radiation", "large_dust_exopdep_col",    "lg_dust_exdep_c", "atmos_month", "all", .true., "none", 2,
-#"radiation", "large_dust_abopdep_col",    "lg_dust_abdep_c", "atmos_month", "all", .true., "none", 2,
-#
-
-
-#=============================================================================================
-#
-#====> This file can be used with diag_manager/v2.0a (or higher) <====
-#
-#
-#  FORMATS FOR FILE ENTRIES (not all input values are used)
-#  ------------------------
-#
-#"file_name", output_freq, "output_units", format, "time_units", "long_name",
-#
-#
-#output_freq:  > 0  output frequency in "output_units"
-#              = 0  output frequency every time step
-#              =-1  output frequency at end of run
-#
-#output_units = units used for output frequency
-#               (years, months, days, minutes, hours, seconds)
-#
-#time_units   = units used to label the time axis
-#               (days, minutes, hours, seconds)
-#
-#
-#  FORMAT FOR FIELD ENTRIES (not all input values are used)
-#  ------------------------
-#
-#"module_name", "field_name", "output_name", "file_name" "time_sampling", time_avg, "other_opts", packing
-#
-#time_avg = .true. or .false.
-#
-#packing  = 1  double precision
-#         = 2  float
-#         = 4  packed 16-bit integers
-#         = 8  packed 1-byte (not tested?)
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/common/field_table b/tests/Iceberg_repository/ISOMIP_Calving/common/field_table
deleted file mode 100644
index a4e98a7..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/common/field_table
+++ /dev/null
@@ -1,71 +0,0 @@
-"diag_tracers","ocean_mod","frazil"
-
-file_in  = INPUT/ocean_frazil.res.nc
-file_out = RESTART/ocean_frazil.res.nc
-/
-
-
-"prog_tracers","ocean_mod","temp"
-
-horizontal-advection-scheme = mdfl_sweby
-vertical-advection-scheme = mdfl_sweby
-file_in  = INPUT/ocean_temp_salt.res.nc
-file_out = RESTART/ocean_temp_salt.res.nc
-/
-
-"prog_tracers","ocean_mod","salt"
-
-rizontal-advection-scheme = mdfl_sweby
-vertical-advection-scheme = mdfl_sweby
-file_in  = INPUT/ocean_temp_salt.res.nc
-file_out = RESTART/ocean_temp_salt.res.nc
-/
-
-
-"tracer_packages","ocean_mod","ocean_age_tracer"
-
-names = global
-horizontal-advection-scheme = mdfl_sweby
-vertical-advection-scheme = mdfl_sweby
-file_in  = INPUT/ocean_age.res.nc
-file_out = RESTART/ocean_age.res.nc
-min_tracer_limit=0.0
-/
-
-"prog_tracers","ocean_mod","age_global"
-
-const_init_tracer = t
-const_init_value = 0.0
-/
-
-"namelists","ocean_mod","ocean_age_tracer/global"
-
-slat = -90.0
-nlat =  90.0
-wlon =   0.0
-elon = 360.0
-/
-
- "TRACER", "atmos_mod", "sphum"
-           "longname",     "specific humidity"
-           "units",        "kg/kg" /
-
-# prognotic cloud scheme tracers
-  "TRACER", "atmos_mod", "liq_wat"
-            "longname",     "cloud liquid specific humidity"
-            "units",        "kg/kg" /
-  "TRACER", "atmos_mod", "ice_wat"
-            "longname",     "cloud ice water specific humidity"
-            "units",        "kg/kg" /
-  "TRACER", "atmos_mod", "cld_amt"
-            "longname",     "cloud fraction"
-            "units",        "none" /
-
-# test tracer for radon
-
-# "TRACER", "atmos_mod", "radon"
-#           "longname",     "radon test tracer"
-#           "units",        "kg/kg" /
-
- "TRACER", "land_mod", "sphum"/
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/common/input.nml b/tests/Iceberg_repository/ISOMIP_Calving/common/input.nml
deleted file mode 100644
index fd79354..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/common/input.nml
+++ /dev/null
@@ -1,137 +0,0 @@
- &MOM_input_nml
-        output_directory = './',
-        input_filename = 'r'
-        restart_input_dir = 'INPUT/',
-        restart_output_dir = 'RESTART/',
-        parameter_filename = 'MOM_input',
-                             'MOM_override' /
-
- &SIS_input_nml
-        output_directory = './',
-        input_filename = 'r'
-        restart_input_dir = 'INPUT/',
-        restart_output_dir = 'RESTART/',
-        parameter_filename = 'SIS_input',
-                             'SIS_override' /
-
- &diag_manager_nml
-         max_output_fields=1000
-         max_input_fields=1000
-         max_num_axis_sets=1000
-         conserve_water=.false.,
-         max_files=1000
-         max_axes=2000
- /
-
- &coupler_nml
-            months = 60,
-            days   = 0,
-            current_date = 1,1,1,0,0,0,
-            hours = 0,
-            minutes =0, 
-            seconds = 0
-            calendar = 'NOLEAP',
-            dt_cpld  = 300.0,
-            dt_atmos = 300.0,
-            do_atmos = .false.,
-            do_land = .false.,
-            do_ice = .true.,
-            do_ocean = .true.,
-            atmos_npes = 0,
-            ocean_npes = 0,
-            concurrent = .false.
-            use_lag_fluxes=.false. /
-
-
- &icebergs_nml
-    verbose=.false.,
-    verbose_hrs=24,
-    traj_sample_hrs=24000,
-    ignore_ij_restart=.true.
-    halo=2,
-    save_short_traj=.true.
-    debug=.false.,
-    really_debug=.false.,
-    use_slow_find=.true.,
-    add_weight_to_ocean=.true.,
-    passive_mode=.false.,
-    Static_icebergs=.True.,
-    ignore_missing_restart_bergs=.false.,
-    generate_test_icebergs=.false.,
-    speed_limit=0.,
-    use_roundoff_fix=.true.,
-    make_calving_reproduce=.false.,
-    Runge_not_Verlet=.false.,
-    iceberg_bonds_on=.false.,
-    critical_interaction_damping_on=.false.,
-    use_new_predictive_corrective=.true.,
-    interactive_icebergs_on=.false.
-    halo_debugging=.false.
-    spring_coef=0.000001
-    distribution=0.0, 0.99, 0.0, 0.00, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11,
-    hexagonal_icebergs=.true.
-    allow_bergs_to_roll=.false.
-    set_melt_rates_to_zero=.false.
-    use_roundoff_fix=.false.
-    grid_is_latlon=.false.
-    grid_is_regular=.true.
-    initial_orientation=-0.
-    rotate_icebergs_for_mass_spreading=.false.
-    lat_ref=-75.0
-    u_override=0.00
-    v_override=0.00
-    override_iceberg_velocities=.false.
-    add_iceberg_thickness_to_SSH=.true.
-    max_bonds=6
-    Iceberg_melt_without_decay=.true.
-    melt_icebergs_as_ice_shelf=.true.
-    Use_three_equation_model=.true.
-    find_melt_using_spread_mass=.true.
-    use_mixed_layer_salinity_for_thermo=.true.
-    pass_fields_to_ocean_model=.true.
-    rho_bergs=918.0
-    utide_icebergs=0.01
-    ustar_icebergs_bg=0.000
-    cdrag_icebergs =0.0025
-    const_gamma=.false.
-    Gamma_T_3EQ=0.22
-    ignore_traj=.False.
-    read_ocean_depth_from_file=.true.
-    apply_thickness_cutoff_to_bergs_melt=.true.
-    apply_thickness_cutoff_to_gridded_melt=.true.
-    melt_cutoff=10.
- &data_override_nml
-         /
-
- &fms_io_nml
-         fms_netcdf_restart=.true.
-         threading_read='multi'
- /
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC' /
-
- &ice_albedo_nml
-      t_range = 10. /
-
- &ice_model_nml
-           /
-
- &monin_obukhov_nml
-            neutral = .true. /
-
- &ocean_albedo_nml
-      ocean_albedo_option = 5 /
-
- &sat_vapor_pres_nml
-      construct_table_wrt_liq = .true.,
-      construct_table_wrt_liq_and_ice = .true. /
-
- &xgrid_nml
-            make_exchange_reproduce = .false.
-            interp_method = 'second_order' /
-
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/common/run_script.sh b/tests/Iceberg_repository/ISOMIP_Calving/common/run_script.sh
deleted file mode 100755
index 26e29af..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/common/run_script.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-#mv RESTART/* INPUT/
-#aprun -n 16 ../../build/intel/ice_ocean_SIS2/repro/MOM6
-aprun -n 128 ../../../../../build/intel/ice_ocean_SIS2/repro/old_executable/MOM6
-#aprun -n 32 MOM6
-#cp RESTART/* RESTART_BACKUP
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/common/submit_to_queue b/tests/Iceberg_repository/ISOMIP_Calving/common/submit_to_queue
deleted file mode 100644
index 3cb9f5f..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/common/submit_to_queue
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/bin/csh -f
-#PBS -r y                                                              #This job is restartable
-#PBS -j oe                                                             #STDOUT and STDERR are in the same file, specified below in the '-o' option
-#PBS -q batch                                                          #Do not change this - it tells your job where to run
-#PBS -S /bin/sh                                                        #Do not change this - it keeps your job from issuing a false alarm
-#PBS -E                                                                #Do not change this - it gives your job more and more useful Moab environment variables
-#PBS -N  Melt_with_decay                                                  #Job Name:             You may want to change this to reflect your job's purpose or relation to an experiment
-#PBS -l partition=c3
-#PBS -l size=4                                                        #You will need to change this to reflect your job's core requirements - 24 is the current core increment.
-#PBS -l walltime=16:00:00                                              #You MUST change this to reflect your job's expected run time, including copy time
-#PBS -m bea                                                            #Email options: You may want to change this to reduce your incoming email stream
-
-######################################################################################################################
-#
-#  Gaea c1ms batch skeleton version 0.9
-#  
-#  0.9 - Initial version - 20110906 - Daniel Gall - Daniel.Gall@noaa.gov
-#
-######################################################################################################################
-
-#Source the system initialization scripts (but not the user's so as to avoid interactive settings that can poison us)
-source /etc/csh.cshrc
-
-#Run the experiment
-aprun -n 128 ../../../../build/intel/ice_ocean_SIS2/repro/old_executable/MOM6
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/python_scripts/Create_mosaic.py b/tests/Iceberg_repository/ISOMIP_Calving/python_scripts/Create_mosaic.py
deleted file mode 120000
index bab5810..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/python_scripts/Create_mosaic.py
+++ /dev/null
@@ -1 +0,0 @@
-../../Scripts_and_analysis/Create_mosaic.py
\ No newline at end of file
diff --git a/tests/Iceberg_repository/ISOMIP_Calving/python_scripts/initialize_bergs_in_pattern.py b/tests/Iceberg_repository/ISOMIP_Calving/python_scripts/initialize_bergs_in_pattern.py
deleted file mode 120000
index 9824e45..0000000
--- a/tests/Iceberg_repository/ISOMIP_Calving/python_scripts/initialize_bergs_in_pattern.py
+++ /dev/null
@@ -1 +0,0 @@
-../../Scripts_and_analysis/initialize_bergs_in_pattern.py
\ No newline at end of file
diff --git a/tests/Iceberg_repository/README b/tests/Iceberg_repository/README
deleted file mode 100644
index 922b12f..0000000
--- a/tests/Iceberg_repository/README
+++ /dev/null
@@ -1,34 +0,0 @@
-
-- Alon's Iceberg Repository, edited for initializing a model setup for testing the iceberg driver.
-- 1. Initialize a berg using the scripts in one of the test directories
-- 2. Use ./Scripts_and_analysis/initialize_bergs_in_pattern.py to convert the berg into a restart (input)
-     file
-
-
-
------------------------------------------------------------
-
-
-
-
-Alon's readme:
-
-To set up the experiments, please run the setup_ISOMIP_calving.sh script. This will create all the netcdf files which are needed to run the simulations. To run the script, write the following at the command line:
-
-source setup_ISOMIP_calving.sh
-
-
-
-- Building an executable:
-
-You can create an executable using latest version of the code on dev/master, except for the coupler, which needs to be on the following branch
-
-Repository: git@github.com:sternalon/coupler.git
-Branch: passing_ustar_through_coupler
-
-These changes to the coupler have been added to Bob's branch
-Repository: git@github.com:NOAA-GFDL/coupler.git
-Branch: user/rwh/redesign_flux_exchange
-
-Note that there might be some incompatibility with the SIS code which require using a special branch. This is found on gitlab. 
-Branch: sis2_interface
diff --git a/tests/Iceberg_repository/RUN b/tests/Iceberg_repository/RUN
deleted file mode 100755
index 12706a3..0000000
--- a/tests/Iceberg_repository/RUN
+++ /dev/null
@@ -1,12 +0,0 @@
-#sample runfile:
-
-#rm ./output_files/Generic*
-
-#./Scripts_and_analysis/initialize_bergs_in_pattern.py -set_all_bergs_static_by_default=False -Run_plotting_subroutine=False \
-#				 -break_some_bonds=False -Ice_geometry_source='Generic' \
-#				 -Generic_ice_geometry_filename='./testberg/testtabularberg.nc' \
-#				 -ISOMIP_reduced=False \
-
-#copy iceberg and bond restart files to input directories
-#cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
-#cp ./output_files/Generic_bonds_iceberg.res.nc ./../INPUT/bonds_iceberg.res.nc
\ No newline at end of file
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/Create_a_cartesian_grid_and_mosaic.ipynb b/tests/Iceberg_repository/Scripts_and_analysis/Create_a_cartesian_grid_and_mosaic.ipynb
deleted file mode 100644
index 13ebeb2..0000000
--- a/tests/Iceberg_repository/Scripts_and_analysis/Create_a_cartesian_grid_and_mosaic.ipynb
+++ /dev/null
@@ -1,649 +0,0 @@
-{
- "metadata": {
-  "name": "",
-  "signature": "sha256:d2ef6bae770b9c56ac62500a0a35fe92d46b49ffb6124a589b7173e88a66994f"
- },
- "nbformat": 3,
- "nbformat_minor": 0,
- "worksheets": [
-  {
-   "cells": [
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
-      "import scipy.io.netcdf\n",
-      "import numpy\n",
-      "%pylab inline"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": [
-      {
-       "output_type": "stream",
-       "stream": "stdout",
-       "text": [
-        "Populating the interactive namespace from numpy and matplotlib\n"
-       ]
-      }
-     ],
-     "prompt_number": 1
-    },
-    {
-     "cell_type": "markdown",
-     "metadata": {},
-     "source": [
-      "Model grid will have ni x nj h-point grid cells"
-     ]
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
-      "nj,ni = 40,240"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 2
-    },
-    {
-     "cell_type": "markdown",
-     "metadata": {},
-     "source": [
-      "A mosaic file has a supergrid of an integer refinement (e.g. 2*ni x 2*nj cells)"
-     ]
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
-      "snj, sni = 2*nj, 2*ni"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 3
-    },
-    {
-     "cell_type": "markdown",
-     "metadata": {},
-     "source": [
-      "Uniform resolution of the ocean model grid will be dxo x dyo"
-     ]
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
-      "dxo = 2.e3\n",
-      "dyo = 2.e3"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 4
-    },
-    {
-     "cell_type": "markdown",
-     "metadata": {},
-     "source": [
-      "Number of land points used nl"
-     ]
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
-      "nl=0\n",
-      "Ocean_Depth=numpy.zeros((nj,ni))\n",
-      "Ocean_Depth[:,:]=1000.\n",
-      "#Define land points:\n",
-      "#Ocean_Depth[-1,:]=0  ;Ocean_Depth[0,:]=0  #Setting boundaries to zero\n",
-      "#Ocean_Depth[:,-1]=0  ;Ocean_Depth[:,0]=0  #Setting boundaries to zero\n",
-      "Ocean_Depth[0,0]=0.\n",
-      "for j in range(nj):\n",
-      "    for i in range(ni):\n",
-      "        if Ocean_Depth[j,i]==0:\n",
-      "            nl=nl+1"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 5
-    },
-    {
-     "cell_type": "markdown",
-     "metadata": {},
-     "source": [
-      "Using a supergrid refinement of 2, the grid lengths, area and coordinates are:"
-     ]
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
-      "dx = (0.5 * dxo) * numpy.ones((snj+1,sni))\n",
-      "dy = (0.5 * dyo) * numpy.ones((snj,sni+1))\n",
-      "area = (0.25 * (dxo * dyo)) * numpy.ones((snj,sni))\n",
-      "x = numpy.zeros((snj+1,sni+1))\n",
-      "x[:,1:] = numpy.cumsum( dx, axis=-1 )\n",
-      "y = numpy.zeros((snj+1,sni+1))\n",
-      "y[1:,:] = numpy.cumsum( dy, axis=-2 )"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 6
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
-      "# A helper function to use when writing strings in a netcdf file\n",
-      "def set_string(variable, value):\n",
-      "    \"\"\"Sets \"variable\" to \"value\" padded with blanks where\n",
-      "    \"variable\" is a netcdf variable object and \"value\" is a string.\"\"\"\n",
-      "    variable[:] = '\\000' * variable.shape[0]\n",
-      "    variable[:len(value)] = value"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 7
-    },
-    {
-     "cell_type": "markdown",
-     "metadata": {},
-     "source": [
-      "Create a netcdf3 horizontal ocean-grid file..."
-     ]
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
-      "rg = scipy.io.netcdf_file('ocean_hgrid.nc','w',version=2)"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 8
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
-      "rg.createDimension('nx',sni)\n",
-      "rg.createDimension('ny',snj)\n",
-      "rg.createDimension('nxp',sni+1)\n",
-      "rg.createDimension('nyp',snj+1)\n",
-      "rg.createDimension('string',255)"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 9
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
-      "dx_h = rg.createVariable('dx','f8',('nyp','nx',))\n",
-      "dx_h.units = 'm'\n",
-      "dy_h = rg.createVariable('dy','f8',('ny','nxp',))\n",
-      "dy_h.units = 'm'\n",
-      "area_h = rg.createVariable('area','f8',('ny','nx',))\n",
-      "area_h.units = 'm2'\n",
-      "x_h = rg.createVariable('x','f8',('nyp','nxp',))\n",
-      "x_h.units = 'm'\n",
-      "y_h = rg.createVariable('y','f8',('nyp','nxp',))\n",
-      "y_h.units = 'm'\n",
-      "tile = rg.createVariable('tile','c',('string',))"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 10
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
-      "dx_h[:,:] = dx[:,:]\n",
-      "dy_h[:,:] = dy[:,:]\n",
-      "area_h[:,:] = area[:,:]\n",
-      "x_h[:,:] = x[:,:]\n",
-      "y_h[:,:] = y[:,:]\n",
-      "tile[:] = '\\000' * 255\n",
-      "tile[:5] = 'tile1'\n",
-      "set_string(tile,'tile1')"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 11
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
-      "rg.close()"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 12
-    },
-    {
-     "cell_type": "markdown",
-     "metadata": {},
-     "source": [
-      "Create a netcdf3 ocean-mask file..."
-     ]
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
-      "rg = scipy.io.netcdf_file('ocean_mask.nc','w',version=2)\n",
-      "rg.createDimension('nx',ni)\n",
-      "rg.createDimension('ny',nj)\n",
-      "mask = rg.createVariable('mask','f4',('ny','nx',))\n",
-      "mask[:,:] = 1.\n",
-      "rg.close()"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 13
-    },
-    {
-     "cell_type": "markdown",
-     "metadata": {},
-     "source": [
-      "Create a mosaic description for the above grid file..."
-     ]
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
-      "rg = scipy.io.netcdf_file('ocean_mosaic.nc','w',version=2)\n",
-      "rg.createDimension('ntiles',1)\n",
-      "rg.createDimension('string',255)\n",
-      "mosaic = rg.createVariable('mosaic','c',('string',))\n",
-      "mosaic.standard_name = 'grid_mosaic_spec'\n",
-      "mosaic.children = 'contacts'\n",
-      "mosaic.grid_descriptor = ''\n",
-      "gridlocation = rg.createVariable('gridlocation','c',('string',))\n",
-      "gridlocation.standard_name = 'grid_file_location'\n",
-      "gridfiles = rg.createVariable('gridfiles','c',('ntiles','string',))\n",
-      "gridtiles = rg.createVariable('gridtiles','c',('ntiles','string',))\n",
-      "rg.grid_version = '0.2'\n",
-      "# Fill in data\n",
-      "mosaic[:] = '\\000' * 255\n",
-      "mosaic[:12] = 'ocean_mosaic'\n",
-      "gridlocation[:] = '\\000' * 255\n",
-      "gridlocation[:2] = './'\n",
-      "gridfiles[:] = '\\000' * 255\n",
-      "gridfiles[0,:14] = 'ocean_hgrid.nc'\n",
-      "gridtiles[:] = '\\000' * 255\n",
-      "gridtiles[0,:5] = 'tile1'\n",
-      "rg.close()"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 14
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
-      "!pwd"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": [
-      {
-       "output_type": "stream",
-       "stream": "stdout",
-       "text": [
-        "/home/aas/Iceberg_Project/ISOMIP/Create_mosaics\r\n"
-       ]
-      }
-     ],
-     "prompt_number": 15
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
-      "# Fake a ocean_topog.nc file\n",
-      "rg = scipy.io.netcdf_file('ocean_topog.nc','w',version=2)\n",
-      "rg.createDimension('nx',ni)\n",
-      "rg.createDimension('ny',nj)\n",
-      "rg.createDimension('ntiles',1)\n",
-      "depth = rg.createVariable('depth','f4',('ny','nx',))\n",
-      "depth[:,:] = 1000.\n",
-      "#depth[-1,-1] =0  #One point is being defined as a land point\n",
-      "rg.close()"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 16
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
-      "rg = scipy.io.netcdf_file('atmos_mosaic_tile1Xland_mosaic_tile1.nc','w',version=2) # atmos_mosaic_tile1Xland_mosaic_tile1.nc\n",
-      "rg.createDimension('string',255)\n",
-      "rg.createDimension('ncells',nl)  #It is unclear whether this works when nl=0. It does work for nl>0\n",
-      "rg.createDimension('two',2)\n",
-      "contact = rg.createVariable('contact','c',('string',))\n",
-      "contact.standard_name = 'grid_contact_spec'\n",
-      "contact.contact_type = 'exchange'\n",
-      "contact.parent1_cell = 'tile1_cell'\n",
-      "contact.parent2_cell = 'tile2_cell'\n",
-      "contact.xgrid_area_field = 'xgrid_area'\n",
-      "contact.distant_to_parent1_centroid = 'tile1_distance'\n",
-      "contact.distant_to_parent2_centroid = 'tile2_distance'\n",
-      "tile1_cell = rg.createVariable('tile1_cell','f8',('ncells','two',))\n",
-      "tile1_cell.standard_name = 'parent_cell_indices_in_mosaic1'\n",
-      "tile2_cell = rg.createVariable('tile2_cell','f8',('ncells','two',))\n",
-      "tile2_cell.standard_name = 'parent_cell_indices_in_mosaic2'\n",
-      "xgrid_area = rg.createVariable('xgrid_area','f8',('ncells',))\n",
-      "xgrid_area.standard_name = 'exchange_grid_area'\n",
-      "xgrid_area.units = 'm2'\n",
-      "tile1_distance = rg.createVariable('tile1_distance','f8',('ncells','two'))\n",
-      "tile1_distance.standard_name = 'distance_from_parent1_cell_centroid'\n",
-      "tile2_distance = rg.createVariable('tile2_distance','f8',('ncells','two'))\n",
-      "tile2_distance.standard_name = 'distance_from_parent2_cell_centroid'\n",
-      "rg.grid_version = '0.2'\n",
-      "# Fill in data\n",
-      "contact[:] = '\\000' * 255\n",
-      "contact[:37] = 'atmos_mosaic:tile1::land_mosaic:tile1'\n",
-      "tile1_cell[:] = [ni,nj]\n",
-      "tile2_cell[:] = [ni,nj]\n",
-      "xgrid_area[:] = dxo * dyo\n",
-      "tile1_distance[:] = 0.\n",
-      "tile2_distance[:] = 0.\n",
-      "rg.close()"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 17
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
-      "rg = scipy.io.netcdf_file('atmos_mosaic_tile1Xocean_mosaic_tile1.nc','w',version=2) # atmos_mosaic_tile1Xocean_mosaic_tile1.nc\n",
-      "rg.createDimension('string',255)\n",
-      "rg.createDimension('ncells',ni*nj-nl) # -1 is for a single land point\n",
-      "rg.createDimension('two',2)\n",
-      "contact = rg.createVariable('contact','c',('string',))\n",
-      "contact.standard_name = 'grid_contact_spec'\n",
-      "contact.contact_type = 'exchange'\n",
-      "contact.parent1_cell = 'tile1_cell'\n",
-      "contact.parent2_cell = 'tile2_cell'\n",
-      "contact.xgrid_area_field = 'xgrid_area'\n",
-      "contact.distant_to_parent1_centroid = 'tile1_distance'\n",
-      "contact.distant_to_parent2_centroid = 'tile2_distance'\n",
-      "tile1_cell = rg.createVariable('tile1_cell','f8',('ncells','two',))\n",
-      "tile1_cell.standard_name = 'parent_cell_indices_in_mosaic1'\n",
-      "tile2_cell = rg.createVariable('tile2_cell','f8',('ncells','two',))\n",
-      "tile2_cell.standard_name = 'parent_cell_indices_in_mosaic2'\n",
-      "xgrid_area = rg.createVariable('xgrid_area','f8',('ncells',))\n",
-      "xgrid_area.standard_name = 'exchange_grid_area'\n",
-      "xgrid_area.units = 'm2'\n",
-      "tile1_distance = rg.createVariable('tile1_distance','f8',('ncells','two'))\n",
-      "tile1_distance.standard_name = 'distance_from_parent1_cell_centroid'\n",
-      "tile2_distance = rg.createVariable('tile2_distance','f8',('ncells','two'))\n",
-      "tile2_distance.standard_name = 'distance_from_parent2_cell_centroid'\n",
-      "rg.grid_version = '0.2'\n",
-      "# Fill in data\n",
-      "contact[:] = '\\000' * 255\n",
-      "contact[:37] = 'atmos_mosaic:tile1::land_mosaic:tile1'\n",
-      "tile1_cell[:] = [ni,nj]\n",
-      "tile2_cell[:] = [ni,nj]\n",
-      "xgrid_area[:] = dxo * dyo\n",
-      "count=-1\n",
-      "for j in range(nj):\n",
-      "    for i in range(ni):\n",
-      "        if Ocean_Depth[j,i]!=0:\n",
-      "            count=count+1\n",
-      "            tile1_cell[count] = [i,j]\n",
-      "            tile2_cell[count] = [i,j]\n",
-      "            tile1_distance[count] = [0,0]\n",
-      "            tile2_distance[count] = [0,0]\n",
-      "            xgrid_area[count] = dxo * dyo\n",
-      "rg.close()"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 18
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
-      "rg = scipy.io.netcdf_file('land_mosaic_tile1Xocean_mosaic_tile1.nc','w',version=2) # land_mosaic_tile1Xocean_mosaic_tile1.nc\n",
-      "rg.createDimension('string',255)\n",
-      "rg.createDimension('ncells',ni*nj-nl) # -1 is for a single land point\n",
-      "rg.createDimension('two',2)\n",
-      "contact = rg.createVariable('contact','c',('string',))\n",
-      "contact.standard_name = 'grid_contact_spec'\n",
-      "contact.contact_type = 'exchange'\n",
-      "contact.parent1_cell = 'tile1_cell'\n",
-      "contact.parent2_cell = 'tile2_cell'\n",
-      "contact.xgrid_area_field = 'xgrid_area'\n",
-      "contact.distant_to_parent1_centroid = 'tile1_distance'\n",
-      "contact.distant_to_parent2_centroid = 'tile2_distance'\n",
-      "tile1_cell = rg.createVariable('tile1_cell','f8',('ncells','two',))\n",
-      "tile1_cell.standard_name = 'parent_cell_indices_in_mosaic1'\n",
-      "tile2_cell = rg.createVariable('tile2_cell','f8',('ncells','two',))\n",
-      "tile2_cell.standard_name = 'parent_cell_indices_in_mosaic2'\n",
-      "xgrid_area = rg.createVariable('xgrid_area','f8',('ncells',))\n",
-      "xgrid_area.standard_name = 'exchange_grid_area'\n",
-      "xgrid_area.units = 'm2'\n",
-      "tile1_distance = rg.createVariable('tile1_distance','f8',('ncells','two'))\n",
-      "tile1_distance.standard_name = 'distance_from_parent1_cell_centroid'\n",
-      "tile2_distance = rg.createVariable('tile2_distance','f8',('ncells','two'))\n",
-      "tile2_distance.standard_name = 'distance_from_parent2_cell_centroid'\n",
-      "rg.grid_version = '0.2'\n",
-      "# Fill in data\n",
-      "contact[:] = '\\000' * 255\n",
-      "contact[:37] = 'atmos_mosaic:tile1::land_mosaic:tile1'\n",
-      "tile1_cell[:] = [ni,nj]\n",
-      "tile2_cell[:] = [ni,nj]\n",
-      "xgrid_area[:] = dxo * dyo\n",
-      "count=-1\n",
-      "for j in range(nj):\n",
-      "    for i in range(ni):\n",
-      "        if Ocean_Depth[j,i]!=0:\n",
-      "            count=count+1\n",
-      "            tile1_cell[count] = [i,j]\n",
-      "            tile2_cell[count] = [i,j]\n",
-      "            tile1_distance[count] = [0,0]\n",
-      "            tile2_distance[count] = [0,0]\n",
-      "            xgrid_area[count] = dxo * dyo\n",
-      "rg.close()"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 19
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
-      "rg = scipy.io.netcdf_file('mosaic.nc','w',version=2) # land_mosaic_tile1Xocean_mosaic_tile1.nc\n",
-      "rg.createDimension('string',255)\n",
-      "rg.createDimension('nfile_aXo',1) # -1 is for a single land point\n",
-      "rg.createDimension('nfile_aXl',1) # -1 is for a single land point\n",
-      "rg.createDimension('nfile_lXo',1) # -1 is for a single land point\n",
-      "\n",
-      "atm_mosaic_dir = rg.createVariable('atm_mosaic_dir','c',('string',))\n",
-      "atm_mosaic_dir.standard_name = 'directory_storing_atmosphere_mosaic'\n",
-      "\n",
-      "atm_mosaic_file = rg.createVariable('atm_mosaic_file','c',('string',))\n",
-      "atm_mosaic_file.standard_name = 'atmosphere_mosaic_file_name'\n",
-      "\n",
-      "atm_mosaic = rg.createVariable('atm_mosaic','c',('string',))\n",
-      "atm_mosaic.standard_name = 'atmosphere_mosaic_name'\n",
-      "\n",
-      "lnd_mosaic_dir = rg.createVariable('lnd_mosaic_dir','c',('string',))\n",
-      "lnd_mosaic_dir.standard_name = 'directory_storing_land_mosaic'\n",
-      "\n",
-      "lnd_mosaic_file = rg.createVariable('lnd_mosaic_file','c',('string',))\n",
-      "lnd_mosaic_file.standard_name = 'land_mosaic_file_name'\n",
-      "\n",
-      "lnd_mosaic = rg.createVariable('lnd_mosaic','c',('string',))\n",
-      "lnd_mosaic.standard_name = 'land_mosaic_name'\n",
-      "\n",
-      "ocn_mosaic_dir = rg.createVariable('ocn_mosaic_dir','c',('string',))\n",
-      "ocn_mosaic_dir.standard_name = 'directory_storing_ocean_mosaic'\n",
-      "\n",
-      "ocn_mosaic_file = rg.createVariable('ocn_mosaic_file','c',('string',))\n",
-      "ocn_mosaic_file.standard_name = 'ocean_mosaic_file_name'\n",
-      "\n",
-      "ocn_mosaic = rg.createVariable('ocn_mosaic','c',('string',))\n",
-      "ocn_mosaic.standard_name = 'ocean_mosaic_name'\n",
-      "\n",
-      "\n",
-      "ocn_topog_dir = rg.createVariable('ocn_topog_dir','c',('string',))\n",
-      "ocn_mosaic_dir.standard_name = 'directory_storing_ocean_topog'\n",
-      "\n",
-      "ocn_topog_file = rg.createVariable('ocn_topog_file','c',('string',))\n",
-      "ocn_topog_file.standard_name = 'ocean_topog_file_name'\n",
-      "\n",
-      "aXo_file = rg.createVariable('aXo_file','c',('nfile_aXo','string',))\n",
-      "aXo_file.standard_name = 'atmXocn_exchange_grid_file'\n",
-      "\n",
-      "aXl_file = rg.createVariable('aXl_file','c',('nfile_aXl','string',))\n",
-      "aXl_file.standard_name = 'atmXlnd_exchange_grid_file'\n",
-      "\n",
-      "lXo_file = rg.createVariable('lXo_file','c',('nfile_lXo','string',))\n",
-      "lXo_file.standard_name = 'lndXocn_exchange_grid_file'\n",
-      "\n",
-      "#Global attributes\n",
-      "rg.grid_version = '0.2'\n",
-      "rg.code_version = \"$Name:  $\"\n",
-      "rg.history = \"/net2/aja/workspace/MOM6-examples/ice_ocean_SIS2/OM4_025/preprocessing/fre_nctools/tools/make_quick_mosaic/make_quick_mosaic --input_mosaic ocean_mosaic.nc --ocean_topog ocean_topog.nc\"\n",
-      "# Fill in data\n",
-      "atm_mosaic_dir[:] = '\\000' * 255\n",
-      "atm_mosaic_dir[:2] = './'\n",
-      "\n",
-      "atm_mosaic_file[:] = '\\000' * 255\n",
-      "atm_mosaic_file[:15] = 'ocean_mosaic.nc'\n",
-      "\n",
-      "atm_mosaic[:] = '\\000' * 255\n",
-      "atm_mosaic[:12] = 'atmos_mosaic'\n",
-      "\n",
-      "lnd_mosaic_dir[:] = '\\000' * 255\n",
-      "lnd_mosaic_dir[:2] = './'\n",
-      "\n",
-      "lnd_mosaic_file[:] = '\\000' * 255\n",
-      "lnd_mosaic_file[:15] = 'ocean_mosaic.nc'\n",
-      "\n",
-      "lnd_mosaic[:] = '\\000' * 255\n",
-      "lnd_mosaic[:11] = 'land_mosaic'\n",
-      "\n",
-      "ocn_mosaic_dir[:] = '\\000' * 255\n",
-      "ocn_mosaic_dir[:2] = './'\n",
-      "\n",
-      "ocn_mosaic_file[:] = '\\000' * 255\n",
-      "ocn_mosaic_file[:15] = 'ocean_mosaic.nc'\n",
-      "\n",
-      "ocn_mosaic[:] = '\\000' * 255\n",
-      "ocn_mosaic[:12] = 'ocean_mosaic'\n",
-      "\n",
-      "ocn_topog_dir[:] = '\\000' * 255\n",
-      "ocn_topog_dir[:2] = './'\n",
-      "\n",
-      "ocn_topog_file[:] = '\\000' * 255\n",
-      "ocn_topog_file[:14] = 'ocean_topog.nc'\n",
-      "\n",
-      "aXo_file[:,:] = '\\000' * 255\n",
-      "aXo_file[:,:40] = 'atmos_mosaic_tile1Xocean_mosaic_tile1.nc'\n",
-      "\n",
-      "aXl_file[:,:] = '\\000' * 255\n",
-      "aXl_file[:,:39] = 'atmos_mosaic_tile1Xland_mosaic_tile1.nc'\n",
-      "\n",
-      "lXo_file[:,:] = '\\000' * 255\n",
-      "lXo_file[:,:39] = 'land_mosaic_tile1Xocean_mosaic_tile1.nc'\n",
-      "\n",
-      "rg.close()\n",
-      "\n"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 20
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 20
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 20
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 20
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 20
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 20
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 20
-    }
-   ],
-   "metadata": {}
-  }
- ]
-}
\ No newline at end of file
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/Create_mosaic.py b/tests/Iceberg_repository/Scripts_and_analysis/Create_mosaic.py
deleted file mode 100755
index eab8050..0000000
--- a/tests/Iceberg_repository/Scripts_and_analysis/Create_mosaic.py
+++ /dev/null
@@ -1,1387 +0,0 @@
-#!/usr/bin/env python
-
-# generate files for Idealized Ice Shelf problem.
-# Gustavo Marques
-
-#import matplotlib
-#matplotlib.use('Agg')
-import argparse
-from netCDF4 import MFDataset, Dataset
-from scipy.interpolate import interp1d
-from scipy.ndimage.filters import gaussian_filter
-from scipy.optimize import curve_fit
-import numpy as np
-import matplotlib.pyplot as plt
-#import wright_eos as eos
-#import gsw
-import warnings
-import os
-
-def parseCommandLine():
-  """
-  Parse the command line positional and optional arguments.
-  This is the highest level procedure invoked from the very end of the script.
-  """
-  parser = argparse.ArgumentParser(description=
-      '''
-      Generate files for ocean-ice simulations.
-      ''',
-  epilog='Written by Gustavo Marques and Alon Stern, Dec. 2016.')
-
-  parser.add_argument('-nx', type=int, default=300,
-      help='''The total number of grid points in the x direction (default = 1200).''')
-
-  parser.add_argument('-ny', type=int, default=200,
-      help='''The total number of grid points in the y direction (default = 2400).''')
-
-  parser.add_argument('-nz', type=int, default=36,
-      help='''Number of model layers (default = 63).''')
-  
-  parser.add_argument('-W', type=float, default=1500.,
-      help='''Domain width in the x direction (km). Default is 1500.''')
-  
-  parser.add_argument('-L', type=float, default=1000.,
-      help='''Domain lenght in the y direction (km). Default is 1.2E3''')
-
-  parser.add_argument('-cshelf_lenght', type=float, default=000.,
-      help='''Continental shelf lenght in the y direction (km). Default is 500.''')
-
-  parser.add_argument('-slope_lenght', type=float, default=50.,
-      help='''Continental shelf slope lenght in the y direction (km). Default is 50.''')
-
-  parser.add_argument('-u10_asf', type=float, default=-5.0,
-      help='''Max. wind speed at the ASF (m/2). Default is -5.0''')
-  
-  parser.add_argument('-ISL', type=float, default=0.,
-      help='''Ice shelf legnth (km). Default is 0.0E3''')
-
-  parser.add_argument('-max_depth', type=float, default=3.0e3,
-      help='''Maximum ocean depth (m). Default is 3E3.''')
-
-  parser.add_argument('-min_depth', type=float, default=1000.0,
-      help='''Minimum ocean depth (m). Default is 500.''')
-
-  parser.add_argument('-land_width', type=float, default=100.0,
-      help='''Widht of land region next to ice shelf (km)- this also controls the shape
-      of the ice shelf. Default is 100.''')
-
-  parser.add_argument('-coupled_run', help='''Generate all the files needed to run an ocean_SIS2 simulation.''', action="store_true")
-  
-  parser.add_argument('-create_wind_files', help='''Generate wind iles.''', action="store_true")
-  
-  parser.add_argument('-create_TS_files', help='''Generate initial T/S files.''', action="store_true")
-  
-  parser.add_argument('-create_forcing_files', help='''Generate forcing files.''', action="store_true")
-  
-  parser.add_argument('-debug', help='''Adds prints and plots to help debug.''', action="store_true")
-
-  parser.add_argument('-freeze_ic', help='''Sets the temp to the freezing point in the upper 50 m of the IC.''', action="store_true")
-
-  parser.add_argument('-trough', help='''Adds a trough cutting the continental shelf.''', action="store_true")
-  
-  parser.add_argument('-homogeneous_ts', help='''Make the initial T/S homogeneous in the horizontal.''', action="store_true")
-
-  optCmdLineArgs = parser.parse_args()
-  driver(optCmdLineArgs)
-
-def driver(args):
-   """
-   This is where all the action happends, i.e., calls to different functions that generate
-   files that are needed.
-   """
-   nx = args.nx ; ny = args.ny; nz = args.nz
-   L = args.L; W = args.W; D = args.max_depth
-
-   dy = L/ny; dx = W/nx
-   y = np.arange(dy/2.,L,dy)
-   x = np.arange(dx/2.,W,dx)
-
-   # create dir. to place figures
-   #os.system('mkdir PNG')
-
-   # create ice shelf
-   #make_ice_shelf(x,y,args)
-
-   # create topography
-   Ocean_Depth = make_topo(x,y,args)
-   
-   #Create wind forcing
-   if args.create_wind_files:
-	   make_wind(x,y,args) 
-
-   if args.coupled_run:
-   	make_mosaic(x,y,Ocean_Depth,args) 
-
-   # initial T/S
-   if args.create_TS_files:
-   	make_ts(x,y,args)
-
-   # create forcing
-   if args.create_forcing_files:
-   	make_forcing(x,y,args) 
-   
-
-   print 'Driver section complete'
-   
-   return
-
-def make_ice_shelf(x,y,args):
-   '''
-   Here is a slightly different version but with constants
-   H(x) = H0 *(Q0)^(1/4) / [Q0+4*H0^4*C^3*x]^(1/4)
-   where H0 is ice thickness at the grounding line Q0 = U0*H0 is ice flux at the grounding line, C = rho*g*(1-rho/rho_w)/4/Bbar, rho is the ice density, rho_w is the sea-water density, Bbar is ice stiffness parameter.
-   for the following parameters 
-   rho = 917 kg/m^3
-   rho_w = 1028 kg/m^3
-   Bbar = 1.68e8
-   C = 1.4440e-06
-   U0= 700 m/yr = 2.2182e-05 m/s
-   H0 = 1500 m
-   Q0 = 0.0333 m^2/s
-   rho = 917. #kg/m^3
-   rho_w = 1028. #kg/m^3
-   Bbar = 1.68e8
-   '''
-   x = x * 1.0e3 # im m
-   y = y * 1.0e3 # im m
-   C = 1.4440e-06
-   H0 = 2000.0 #m
-   Q0 = 0.03327 #m^2/s
-   gp = 20.e3 # grouding line position
-   dy = y[1]-y[0]
-   dx = x[1]-x[0]
-   Lice = 200.0e3
-   h =  H0 *(Q0)**(1./4.) / (Q0+100*H0**4*C**3*(y-gp))**(1./4.)
-   h[y<gp] = H0
-   h[y>Lice] = 0.0 
-   # smooth
-   h_smooth = gaussian_filter(h,2)
-   h_smooth[y<gp] = H0
-   h_smooth[h_smooth<50.0] = 0.0
-   # find meridional lenght of ice shelf
-   tmp = np.nonzero(h_smooth==0.0)[0][0]
-   args.ISL = x[tmp] / 1.0e3
-   print 'Ice shelf meridional lenght is (km):',x[tmp] / 1.0e3
-   
-   if args.debug:
-      plt.plot(y,h,'k',y,h_smooth,'r')
-      plt.savefig('PNG/ice_shelf_profile.png')
-
-   area_tmp = np.ones(args.ny) * dx * dy
-   area_tmp[h_smooth == 0.0] = 0.0
-
-   # Create a netcdf horizontal ocean-grid file
-   name = 'IC_IS'
-   ncfile = Dataset('output_files/'+name+'.nc','w')
-   ncfile.createDimension('nx',args.nx)
-   ncfile.createDimension('ny',args.ny)
-   thick = ncfile.createVariable('thick','double',('ny','nx',))
-   thick.units = 'm'
-   thick.standard_name =  'ice shelf thickness'
-   area = ncfile.createVariable('area','double',('ny','nx',))
-   area.units = 'm2'
-   area.standard_name =  'ice shelf area'  
-
-   # write into nc file
-   for i in range(args.nx):
-        thick[:,i] = h_smooth[:]
-        area[:,i] = area_tmp[:]
-
-   ncfile.sync()
-   ncfile.close()
-   print ('*** SUCCESS creating '+name+'.nc!') 
-
-def make_mosaic(x,y,Ocean_Depth,args):
-   '''
-   Create files used in coupled ice/ocean runs.
-   '''
-   ni = args.nx;   nj = args.ny
-   snj, sni = 2*nj, 2*ni
-   dxo = (x[1] - x[0]) * 1.0e3 # in m
-   dyo = (y[1] - y[0]) * 1.0e3 # in m
-
-   # Number of land points used nl GM: There has to be at least ONE land point
-   nl=0
-   #Define land points:
-   Ocean_Depth[0,0]=0.0
-   for j in range(nj):
-      for i in range(ni):
-          if Ocean_Depth[j,i]==0:
-              nl=nl+1
-
-   # Using a supergrid refinement of 2, the grid lengths, area and coordinates are:
-   dx = (0.5 * dxo) * np.ones((snj+1,sni))
-   dy = (0.5 * dyo) * np.ones((snj,sni+1))
-   area = (0.25 * (dxo * dyo)) * np.ones((snj,sni))
-   x = np.zeros((snj+1,sni+1))
-   x[:,1:] = np.cumsum( dx, axis=-1 )
-   y = np.zeros((snj+1,sni+1))
-   y[1:,:] = np.cumsum( dy, axis=-2 )
-
-   # Create a netcdf horizontal ocean-grid file
-   name = 'ocean_hgrid'
-   ncfile = Dataset('output_files/' +name+'.nc','w')
-   ncfile.createDimension('nx',sni)
-   ncfile.createDimension('ny',snj)
-   ncfile.createDimension('nxp',sni+1)
-   ncfile.createDimension('nyp',snj+1)
-   ncfile.createDimension('string',255)
-   dx_h = ncfile.createVariable('dx','f8',('nyp','nx',))
-   dx_h.units = 'm'
-   dy_h = ncfile.createVariable('dy','f8',('ny','nxp',))
-   dy_h.units = 'm'
-   area_h = ncfile.createVariable('area','f8',('ny','nx',))
-   area_h.units = 'm2'
-   x_h = ncfile.createVariable('x','f8',('nyp','nxp',))
-   x_h.units = 'm'
-   y_h = ncfile.createVariable('y','f8',('nyp','nxp',))
-   y_h.units = 'm'
-   tile = ncfile.createVariable('tile','c',('string',)) 
-   dx_h[:,:] = dx[:,:]
-   dy_h[:,:] = dy[:,:]
-   area_h[:,:] = area[:,:]
-   x_h[:,:] = x[:,:]
-   y_h[:,:] = y[:,:]
-   tile[:] = '\000' * 255
-   tile[:5] = 'tile1'
-   set_string(tile,'tile1')
-   ncfile.close()
-   print ('*** SUCCESS creating '+name+'.nc!')
-
-   # create ocean_mask file
-   name = 'ocean_mask'
-   rg = Dataset('output_files/' +name+'.nc','w')
-   rg.createDimension('nx',ni)
-   rg.createDimension('ny',nj)
-   mask = rg.createVariable('mask','f4',('ny','nx',))
-   mask[:,:] = 1.
-   rg.close()
-   print ('*** SUCCESS creating '+name+'.nc!')
-
-   # Create a mosaic description for the grid file
-   name = 'ocean_mosaic'
-   rg = Dataset('output_files/' +name+'.nc','w')
-   rg.createDimension('ntiles',1)
-   rg.createDimension('string',255)
-   mosaic = rg.createVariable('mosaic','c',('string',))
-   mosaic.standard_name = 'grid_mosaic_spec'
-   mosaic.children = 'contacts'
-   mosaic.grid_descriptor = ''
-   gridlocation = rg.createVariable('gridlocation','c',('string',))
-   gridlocation.standard_name = 'grid_file_location'
-   gridfiles = rg.createVariable('gridfiles','c',('ntiles','string',))
-   gridtiles = rg.createVariable('gridtiles','c',('ntiles','string',))
-   rg.grid_version = '0.2'
-   # Fill in data
-   mosaic[:] = '\000' * 255
-   mosaic[:12] = 'ocean_mosaic'
-   gridlocation[:] = '\000' * 255
-   gridlocation[:2] = './'
-   gridfiles[:] = '\000' * 255
-   gridfiles[0,:14] = 'ocean_hgrid.nc'
-   gridtiles[:] = '\000' * 255
-   gridtiles[0,:5] = 'tile1'
-   rg.close()
-   print ('*** SUCCESS creating '+name+'.nc!')
-
-   name = 'atmos_mosaic_tile1Xland_mosaic_tile1'
-   rg = Dataset('output_files/' + name+'.nc','w')
-   rg.createDimension('string',255)
-   rg.createDimension('ncells',nl)  #It is unclear whether this works when nl=0. It does work for nl>0
-   rg.createDimension('two',2)
-   contact = rg.createVariable('contact','c',('string',))
-   contact.standard_name = 'grid_contact_spec'
-   contact.contact_type = 'exchange'
-   contact.parent1_cell = 'tile1_cell'
-   contact.parent2_cell = 'tile2_cell'
-   contact.xgrid_area_field = 'xgrid_area'
-   contact.distant_to_parent1_centroid = 'tile1_distance'
-   contact.distant_to_parent2_centroid = 'tile2_distance'
-   tile1_cell = rg.createVariable('tile1_cell','f8',('ncells','two'))
-   tile1_cell.standard_name = 'parent_cell_indices_in_mosaic1'
-   tile2_cell = rg.createVariable('tile2_cell','f8',('ncells','two'))
-   tile2_cell.standard_name = 'parent_cell_indices_in_mosaic2'
-   xgrid_area = rg.createVariable('xgrid_area','f8',('ncells'))
-   xgrid_area.standard_name = 'exchange_grid_area'
-   xgrid_area.units = 'm2'
-   tile1_distance = rg.createVariable('tile1_distance','f8',('ncells','two'))
-   tile1_distance.standard_name = 'distance_from_parent1_cell_centroid'
-   tile2_distance = rg.createVariable('tile2_distance','f8',('ncells','two'))
-   tile2_distance.standard_name = 'distance_from_parent2_cell_centroid'
-   rg.grid_version = '0.2'
-   # Fill in data
-   contact[:] = '\000' * 255
-   contact[:37] = 'atmos_mosaic:tile1::land_mosaic:tile1'
-   for i in range(nl):
-      tile1_cell[i,:] = [ni,nj]
-      tile2_cell[i,:] = [ni,nj]
-
-   xgrid_area[:] = dxo * dyo
-   tile1_distance[:] = 0.
-   tile2_distance[:] = 0.
-   rg.close()
-   print ('*** SUCCESS creating '+name+'.nc!')
-
-   name = 'atmos_mosaic_tile1Xocean_mosaic_tile1'
-   rg = Dataset('output_files/' + name+'.nc','w')
-   rg.createDimension('string',255)
-   rg.createDimension('ncells',ni*nj-nl) # -1 is for a single land point
-   rg.createDimension('two',2)
-   contact = rg.createVariable('contact','c',('string',))
-   contact.standard_name = 'grid_contact_spec'
-   contact.contact_type = 'exchange'
-   contact.parent1_cell = 'tile1_cell'
-   contact.parent2_cell = 'tile2_cell'
-   contact.xgrid_area_field = 'xgrid_area'
-   contact.distant_to_parent1_centroid = 'tile1_distance'
-   contact.distant_to_parent2_centroid = 'tile2_distance'
-   tile1_cell = rg.createVariable('tile1_cell','f8',('ncells','two',))
-   tile1_cell.standard_name = 'parent_cell_indices_in_mosaic1'
-   tile2_cell = rg.createVariable('tile2_cell','f8',('ncells','two',))
-   tile2_cell.standard_name = 'parent_cell_indices_in_mosaic2'
-   xgrid_area = rg.createVariable('xgrid_area','f8',('ncells',))
-   xgrid_area.standard_name = 'exchange_grid_area'
-   xgrid_area.units = 'm2'
-   tile1_distance = rg.createVariable('tile1_distance','f8',('ncells','two'))
-   tile1_distance.standard_name = 'distance_from_parent1_cell_centroid'
-   tile2_distance = rg.createVariable('tile2_distance','f8',('ncells','two'))
-   tile2_distance.standard_name = 'distance_from_parent2_cell_centroid'
-   rg.grid_version = '0.2'
-   # Fill in data
-   contact[:] = '\000' * 255
-   contact[:37] = 'atmos_mosaic:tile1::land_mosaic:tile1'
-   for i in range(nl):
-      tile1_cell[i,:] = [ni,nj]
-      tile2_cell[i,:] = [ni,nj]
-   
-   xgrid_area[:] = dxo * dyo
-   count=-1
-   for j in range(nj):
-       for i in range(ni):
-          if Ocean_Depth[j,i]!=0:
-            count=count+1
-            tile1_cell[count] = [i,j]
-            tile2_cell[count] = [i,j]
-            tile1_distance[count] = [0,0]
-            tile2_distance[count] = [0,0]
-            xgrid_area[count] = dxo * dyo
-
-   rg.close()
-   print ('*** SUCCESS creating '+name+'.nc!') 
-
-   name = 'land_mosaic_tile1Xocean_mosaic_tile1'
-   rg = Dataset('output_files/' + name+'.nc','w')
-   rg.createDimension('string',255)
-   rg.createDimension('ncells',ni*nj-nl) # -1 is for a single land point
-   rg.createDimension('two',2)
-   contact = rg.createVariable('contact','c',('string',))
-   contact.standard_name = 'grid_contact_spec'
-   contact.contact_type = 'exchange'
-   contact.parent1_cell = 'tile1_cell'
-   contact.parent2_cell = 'tile2_cell'
-   contact.xgrid_area_field = 'xgrid_area'
-   contact.distant_to_parent1_centroid = 'tile1_distance'
-   contact.distant_to_parent2_centroid = 'tile2_distance'
-   tile1_cell = rg.createVariable('tile1_cell','f8',('ncells','two',))
-   tile1_cell.standard_name = 'parent_cell_indices_in_mosaic1'
-   tile2_cell = rg.createVariable('tile2_cell','f8',('ncells','two',))
-   tile2_cell.standard_name = 'parent_cell_indices_in_mosaic2'
-   xgrid_area = rg.createVariable('xgrid_area','f8',('ncells',))
-   xgrid_area.standard_name = 'exchange_grid_area'
-   xgrid_area.units = 'm2'
-   tile1_distance = rg.createVariable('tile1_distance','f8',('ncells','two'))
-   tile1_distance.standard_name = 'distance_from_parent1_cell_centroid'
-   tile2_distance = rg.createVariable('tile2_distance','f8',('ncells','two'))
-   tile2_distance.standard_name = 'distance_from_parent2_cell_centroid'
-   rg.grid_version = '0.2'
-   # Fill in data
-   contact[:] = '\000' * 255
-   contact[:37] = 'atmos_mosaic:tile1::land_mosaic:tile1'
-   for i in range(nl):
-      tile1_cell[i,:] = [ni,nj]
-      tile2_cell[i,:] = [ni,nj]
-   
-   xgrid_area[:] = dxo * dyo
-   count=-1
-   for j in range(nj):
-      for i in range(ni):
-        if Ocean_Depth[j,i]!=0:
-            count=count+1
-            tile1_cell[count] = [i,j]
-            tile2_cell[count] = [i,j]
-            tile1_distance[count] = [0,0]
-            tile2_distance[count] = [0,0]
-            xgrid_area[count] = dxo * dyo
-  
-   rg.close()
-   print ('*** SUCCESS creating '+name+'.nc!')
-
-
-   name = 'grid_spec' # sometimes grid_spec is called mosaic.nc
-   #name = 'mosaic' # sometimes grid_spec is called mosaic.nc
-   rg = Dataset('output_files/' + name+'.nc','w')
-   rg.createDimension('string',255)
-   rg.createDimension('nfile_aXo',1) # -1 is for a single land point
-   rg.createDimension('nfile_aXl',1) # -1 is for a single land point
-   rg.createDimension('nfile_lXo',1) # -1 is for a single land point
-   atm_mosaic_dir = rg.createVariable('atm_mosaic_dir','c',('string',))
-   atm_mosaic_dir.standard_name = 'directory_storing_atmosphere_mosaic'
-   atm_mosaic_file = rg.createVariable('atm_mosaic_file','c',('string',))
-   atm_mosaic_file.standard_name = 'atmosphere_mosaic_file_name'
-   atm_mosaic = rg.createVariable('atm_mosaic','c',('string',))
-   atm_mosaic.standard_name = 'atmosphere_mosaic_name'
-   lnd_mosaic_dir = rg.createVariable('lnd_mosaic_dir','c',('string',))
-   lnd_mosaic_dir.standard_name = 'directory_storing_land_mosaic'
-   lnd_mosaic_file = rg.createVariable('lnd_mosaic_file','c',('string',))
-   lnd_mosaic_file.standard_name = 'land_mosaic_file_name'
-   lnd_mosaic = rg.createVariable('lnd_mosaic','c',('string',))
-   lnd_mosaic.standard_name = 'land_mosaic_name'
-   ocn_mosaic_dir = rg.createVariable('ocn_mosaic_dir','c',('string',))
-   ocn_mosaic_dir.standard_name = 'directory_storing_ocean_mosaic'
-   ocn_mosaic_file = rg.createVariable('ocn_mosaic_file','c',('string',))
-   ocn_mosaic_file.standard_name = 'ocean_mosaic_file_name'
-   ocn_mosaic = rg.createVariable('ocn_mosaic','c',('string',))
-   ocn_mosaic.standard_name = 'ocean_mosaic_name'
-   ocn_topog_dir = rg.createVariable('ocn_topog_dir','c',('string',))
-   ocn_mosaic_dir.standard_name = 'directory_storing_ocean_topog'
-   ocn_topog_file = rg.createVariable('ocn_topog_file','c',('string',))
-   ocn_topog_file.standard_name = 'ocean_topog_file_name'
-   aXo_file = rg.createVariable('aXo_file','c',('nfile_aXo','string',))
-   aXo_file.standard_name = 'atmXocn_exchange_grid_file'
-   aXl_file = rg.createVariable('aXl_file','c',('nfile_aXl','string',))
-   aXl_file.standard_name = 'atmXlnd_exchange_grid_file'
-   lXo_file = rg.createVariable('lXo_file','c',('nfile_lXo','string',))
-   lXo_file.standard_name = 'lndXocn_exchange_grid_file'
-   #Global attributes
-   rg.grid_version = '0.2'
-   rg.code_version = "$Name:  $"
-   rg.history = "/net2/aja/workspace/MOM6-examples/ice_ocean_SIS2/OM4_025/preprocessing/fre_nctools/tools/make_quick_mosaic/make_quick_mosaic --input_mosaic ocean_mosaic.nc --ocean_topog ocean_topog.nc"
-   # Fill in data
-   atm_mosaic_dir[:] = '\000' * 255
-   atm_mosaic_dir[:2] = './'
-   atm_mosaic_file[:] = '\000' * 255
-   atm_mosaic_file[:15] = 'ocean_mosaic.nc'
-   atm_mosaic[:] = '\000' * 255
-   atm_mosaic[:12] = 'atmos_mosaic'
-   lnd_mosaic_dir[:] = '\000' * 255
-   lnd_mosaic_dir[:2] = './'
-   lnd_mosaic_file[:] = '\000' * 255
-   lnd_mosaic_file[:15] = 'ocean_mosaic.nc'
-   lnd_mosaic[:] = '\000' * 255
-   lnd_mosaic[:11] = 'land_mosaic'
-   ocn_mosaic_dir[:] = '\000' * 255
-   ocn_mosaic_dir[:2] = './'
-   ocn_mosaic_file[:] = '\000' * 255
-   ocn_mosaic_file[:15] = 'ocean_mosaic.nc'
-   ocn_mosaic[:] = '\000' * 255
-   ocn_mosaic[:12] = 'ocean_mosaic'
-   ocn_topog_dir[:] = '\000' * 255
-   ocn_topog_dir[:2] = './'
-   ocn_topog_file[:] = '\000' * 255
-   ocn_topog_file[:14] = 'ocean_topog.nc'
-   aXo_file[:,:] = '\000' * 255
-   aXo_file[:,:40] = 'atmos_mosaic_tile1Xocean_mosaic_tile1.nc'
-   aXl_file[:,:] = '\000' * 255
-   aXl_file[:,:39] = 'atmos_mosaic_tile1Xland_mosaic_tile1.nc'
-   lXo_file[:,:] = '\000' * 255
-   lXo_file[:,:39] = 'land_mosaic_tile1Xocean_mosaic_tile1.nc'
-   rg.close()
-   print ('*** SUCCESS creating '+name+'.nc!')
-
-def get_profile(t,i,j,var,depth,z,args,vname,take_mean = True):
-   '''
-   Get data (var), remove mask, smooth profile then interpolate to z grid.
-   '''
-   if take_mean:
-      data = np.mean(Dataset('WOA05_pottemp_salt.nc').variables[var][:,:,j,i], axis=0)
-      
-   else:
-      data = Dataset('WOA05_pottemp_salt.nc').variables[var][t,:,j,i]
-
-   # replace mask value with last good value
-   tmp = np.nonzero(data.mask==False)[0][-1]
-   data[tmp+1::] = data[tmp]
-   # smooth  
-   data = gaussian_filter(data,2) # filter std 2
-   # interpo
-   f1 = interp1d(depth, data)
-   if args.debug:
-      plt.figure()
-      plt.plot(data,-depth,'b',f1(z),-z,'rx')
-      plt.title(vname)
-      plt.savefig('PNG/'+vname+'.png')
-
-   return f1(z)
-
-def set_freezing_temp(T,S,z,y,args):
-    '''
-    Set the temp. in the upper 50 m to the surface freezing point, then smooth data
-    '''
-    d = np.nonzero(z<=50.)[0]
-    for k in range(len(d)):
-        for j in range(args.ny):
-           if y[j] <= (args.ISL + args.cshelf_lenght + args.slope_lenght):
-              T[0,k,j,:] = eos.tfreeze(S[0,k,j,:],1.0e5) 
-
-    for j in range(args.ny):
-      for i in range(args.nx):
-         T[0,d,j,i] = gaussian_filter(T[0,d,j,i],1) # filter std 1
-
-    # smooth T and S in the cross slope direction
-    #for k in range(args.nz):
-    #   for j in range(args.ny):
-    #       T[0,k,:,i] = gaussian_filter(T[0,k,:,i],2)
-    #       S[0,k,:,i] = gaussian_filter(T[0,k,:,i],2)
-
-    return T,S
-
-def make_ts(x,y,args):
-   '''
-   Extract T/S from WOA05 for a particulat lat. then interpolate results into ocean grid. 
-   '''
-   # climatology depth
-   depth = Dataset('WOA05_pottemp_salt.nc').variables['DEPTH'][:]
-   # model depth
-   z = np.linspace(0,args.max_depth,args.nz) # positive downward
-   # all values between -78 to - 60
-   # use sw.dist to find distance
-   # 176 lon (Ross Sea), July, southern wall conditions (-78)
-   i =  176; t = 6; j = 11
-   temp_south = get_profile(t,i,j,'PTEMP',depth,z,args,'TempSouth')
-   salt_south = get_profile(t,i,j,'SALT',depth,z,args,'SaltSouth')
-   # shelf break conditions (-72)
-   j = 17
-   temp_break = get_profile(t,i,j,'PTEMP',depth,z,args,'TempSlope')
-   salt_break = get_profile(t,i,j,'SALT',depth,z,args,'SaltSlope')
-   # northern wall conditions (-65)
-   j = 21
-   temp_north = get_profile(t,i,j,'PTEMP',depth,z,args,'TempNorth')
-   salt_north = get_profile(t,i,j,'SALT',depth,z,args,'SaltNorth')
-
-   # distace from southern wall to use in the interp.
-   #dist = [0,args.cshelf_lenght+args.slope_lenght*0.5,args.L,args.L]
-   dummy = args.ISL + args.cshelf_lenght
-   dist = [0, dummy, dummy+args.slope_lenght, args.L-50.,args.L]
-   # 3d fields
-   temp3D = np.zeros((1,args.nz,len(y),len(x)))
-   salt3D = np.zeros((1,args.nz,len(y),len(x)))
-
-   if args.homogeneous_ts:
-    dist = [0,args.max_depth]
-    f1 = interp1d(dist,[0, -2])
-    dummy_t = f1(z)
-    f1 = interp1d(dist,[34.,34.62])
-    dummy_s = f1(z)
-    sigma2 = eos.wright_eos(dummy_t,dummy_s,2.0e7)
-    # compute rho0/alpha/beta
-    alpha = eos.alpha_wright_eos(dummy_t,dummy_s,2.0e7)
-    beta = eos.beta_wright_eos(dummy_t,dummy_s,2.0e7)
-    Rho_T0_S0 = eos.wright_eos(0.,0.,2.0e7) + 0. # 0.017 is a correction factor
-    # compute linear eos
-    rho_lin = Rho_T0_S0 + alpha.mean()*dummy_t + beta.mean()*dummy_t
-    print 'sigma2 - rho_lin',sigma2 - rho_lin
-    plt.close('all')
-    plt.figure()
-    plt.plot(sigma2-1000.,-z,'k',rho_lin-1000,-z,'r')
-    plt.show()
-
-    for i in range(args.nx):
-       for j in range(args.ny):
-           temp3D[0,:,j,i] = dummy_t[:]
-           salt3D[0,:,j,i] = dummy_s[:]
-
-   else:
-     # distace from southern wall to use in the interp.
-     #dist = [0,args.cshelf_lenght+args.slope_lenght*0.5,args.L,args.L]
-     dummy = args.ISL + args.cshelf_lenght
-     dist = [0, dummy, dummy+args.slope_lenght, args.L-50.,args.L]
-     # horizontal interp
-     for k in range(args.nz):
-         #f1 = interp1d(dist, [temp_south[k],temp_break[k],temp_north[k], temp_north[k]])
-         f1 = interp1d(dist, [temp_south[k],temp_south[k],temp_north[k],temp_north[k], temp_north[k]])
-         dummy_t = f1(y)
-         #f1 = interp1d(dist, [salt_south[k],salt_break[k],salt_north[k], salt_north[k]])
-         f1 = interp1d(dist, [salt_south[k],salt_south[k],salt_north[k], salt_north[k], salt_north[k]])
-         dummy_s = f1(y)
-         for i in range(args.nx):
-            temp3D[0,k,:,i] = dummy_t[:]
-            salt3D[0,k,:,i] = dummy_s[:]
-
-   # set temp below 50 m to freezing point
-   if args.freeze_ic:
-      temp3D, salt3D = set_freezing_temp(temp3D,salt3D,z,y,args)
-
-   # compute sigma2
-   sigma2 = eos.wright_eos(temp3D,salt3D,2.0e7)
-   # compute rho0/alpha/beta
-   alpha = eos.alpha_wright_eos(temp3D,salt3D,2.0e7)
-   beta = eos.beta_wright_eos(temp3D,salt3D,2.0e7)
-   Rho_T0_S0 = eos.wright_eos(0.,0.,2.0e7) + 0.017 # 0.017 is a correction factor
-   
-   # compute linear eos
-   rho_lin = Rho_T0_S0 + alpha.mean()*temp3D + beta.mean()*salt3D
-
-   layers = Dataset('GOLD_IC.2010.11.15.nc').variables['Layer'][:] # used in the global run with sig2
-   if args.debug:
-      print 'alpha,beta,Rho_T0_S0',alpha.mean(),beta.mean(),Rho_T0_S0
-      print 'sigma2 - rho_lin',sigma2[0,:,0,0] - rho_lin[0,:,0,0]
-
-      plt.figure()
-      plt.contourf(y,-z,rho_lin[0,:,:,0])
-      plt.colorbar()
-      plt.contour(y,-z,rho_lin[0,:,:,0]-1000.,layers-1000,colors='k',linewidths=2)
-      plt.title('Density - 1000.')
-      plt.savefig('PNG/rho_section.png')
-  
- 
-      plt.figure()
-      plt.plot(sigma2[0,:,0,0]-1000.,-z,'b',rho_lin[0,:,0,0]-1000.,-z,'bx')
-      plt.plot(sigma2[0,:,args.ny/2.,0]-1000.,-z,'r',rho_lin[0,:,args.ny/2.,0]-1000.,-z,'rx')
-      plt.plot(sigma2[0,:,args.ny-1,0]-1000.,-z,'k',rho_lin[0,:,args.ny-1,0]-1000.,-z,'kx')
-      plt.title('Linear (dashed) vs. nonlinear EoS at south, center and north (b,r,k)')
-      plt.savefig('PNG/rho_profiles.png')
- 
-      # plot t - tfreeze at surface
-      tf = eos.tfreeze(salt3D[0,0,:,:],1.0e5) 
-      plt.figure()
-      plt.subplot(311)
-      plt.contourf(x,y,temp3D[0,0,:,:],np.linspace(temp3D[0,0,:,:].min(),temp3D[0,0,:,:].max(),50))
-      plt.colorbar()
-      plt.title('SST')
-      plt.subplot(312)
-      plt.contourf(x,y,tf,np.linspace(tf.min(),tf.max(),50))
-      plt.colorbar()
-      plt.title('Freezing temp. at surface')
-      plt.subplot(313)
-      plt.contourf(x,y,temp3D[0,0,:,:] - tf)
-      plt.colorbar()
-      plt.title('T - TFreeze')
-      plt.savefig('PNG/SST_and_Tfreeze.png')
-
-      #(S, T) = np.meshgrid(np.linspace(0.,40.,51), np.linspace(-2.5, 3.0, 51))
-      #r1 = eos.wright_eos(T,S,2.0e7)
-      #r2 = Rho_T0_S0 + alpha.mean()*T + beta.mean()*S
-
-      #plt.figure()
-      #CS1 = plt.contour(S,T,r1-1000,layers-1000,colors='b')
-      #plt.clabel(CS1, inline=1, fontsize=10)
-      #CS2 = plt.contour(S,T,r2-1000,layers-1000,colors='r')
-      #plt.clabel(CS2, inline=1, fontsize=10)
-      #plt.xlabel('Salt'); plt.ylabel('Temp')
-      #plt.grid()
-      #plt.show()
-
-   # create ncfiles
-
-   # vertical coord. (layers)
-   name = 'vertical_layers'
-   ncfile = Dataset('output_files/' + name+'.nc','w')
-   ncfile.createDimension('Layer',args.nz)
-   Layer = ncfile.createVariable('Layer',np.dtype('double').char,('Layer'))
-   Layer.units = 'kg/m^3'
-   Layer[:] = layers[:]
-
-   ncfile.close()
-   print ('*** SUCCESS creating '+name+'.nc!')
-   
-   # 1) The name of the z-space input file used to initialize
-   #  the layer thicknesses, temperatures and salinities.
-   name = 'ic_ts'
-   ncfile = Dataset('output_files/' + name+'.nc','w')
-   # create dimensions.
-   ncfile.createDimension('DEPTH',args.nz)
-   ncfile.createDimension('LAT',len(y))
-   ncfile.createDimension('LON',len(x))
-   ncfile.createDimension('TIME',1)
-
-   # create variables
-   LAT = ncfile.createVariable('LAT',np.dtype('double').char,('LAT'))
-   LAT.units = 'degrees_north'
-   LAT.long_name = 'h point nominal latitude'
-   LAT.cartesian_axis = 'Y'
-   LAT[:] = y[:]
-
-   LON = ncfile.createVariable('LON',np.dtype('double').char,('LON'))
-   LON.units = 'degrees_east'
-   LON.long_name = 'h point nominal longitude'
-   LON.cartesian_axis = 'X'
-   LON[:] = x[:]
-
-   TIME = ncfile.createVariable('TIME',np.dtype('double').char,('TIME'))
-   TIME.units = 'days since 0001-01-01 00:00:00'
-   TIME.calendar = 'noleap'
-   TIME.cartesian_axis = 'T'
-   TIME[0] = 0.0
-
-   DEPTH = ncfile.createVariable('DEPTH',np.dtype('double').char,('DEPTH'))
-   DEPTH.units = 'm'
-   DEPTH.direction = -1
-   DEPTH.cartesian_axis = 'Z'
-   DEPTH[:] = z[:]
-
-   PTEMP = ncfile.createVariable('PTEMP',np.dtype('float32').char,('TIME','DEPTH','LAT','LON'), fill_value = -1.e+34)
-   PTEMP.missing_value = -1.e+34
-   PTEMP[:] = temp3D[:] 
-
-   SALT = ncfile.createVariable('SALT',np.dtype('float32').char,('TIME','DEPTH','LAT','LON'), fill_value = -1.e+34)  
-   SALT.missing_value = -1.e+34
-   SALT[:] = salt3D[:]
-   ncfile.close()
-   print ('*** SUCCESS creating '+name+'.nc!')
-
-   # 2) The file from which the coordinate densities are read
-   #name = 'ts_ic_profile'
-   #ncfile = Dataset(name+'.nc','w')
-   # create dimensions.
-   #ncfile.createDimension('Layer',args.nz)
-
-   # create variables
-   #PTEMP = ncfile.createVariable('PTEMP',np.dtype('double').char,('Layer'))
-   #PTEMP.units = 'Celcius'
-   #PTEMP.long_name = 'Potential Temperature'
-   #PTEMP[:] = temp_int[:]
-
-   #SALT = ncfile.createVariable('SALT',np.dtype('double').char,('Layer'))
-   #SALT.units = 'PSU'
-   #SALT.long_name = 'Salinity'
-   #SALT[:] = salt_int[:]
-
-   #ncfile.close()
-   #print ('*** SUCCESS creating '+name+'.nc!')
-
-def make_wind(x,y,args):
-   # forcing parameters
-   nx = len(x); ny = len(y); nt =1 # time
-   Ly = args.L # domain size km
-   W = args.W # domain width km
-   u10_asf = args.u10_asf # def is -0.5  m/s
-   tau_asf = 0.05 # default is 0.075 # N/m^2
-   u10 = np.zeros((nt,ny,nx)) 
-   v10 = np.zeros((nt,ny,nx))
-   tau_x = np.zeros((nt,ny,nx)) # ice forcing
-   tau_y = np.zeros((nt,ny,nx))
-   
-   # Sin^2 wind profile
-   Lasf = 400.0 # km
-   for j in range(ny):
-         #tmp = np.pi*(y[j]-(Ly/2.0))/Lasf
-         tmp = np.pi*(y[j]/Ly)
-         u10[0,j,:] = u10_asf * np.sin(tmp)**2
-         tau_x[0,j,:] = tau_asf * np.sin(tmp)**2 
-   
-   
-   # create ncfile
-   # open a new netCDF file for writing.
-   # # used when forcing is applied in the atm
-   name = 'forcing_10'
-   ncfile = Dataset('output_files/' + name+'.nc','w')
-   # create dimensions.
-   ncfile.createDimension('LON',nx)
-   ncfile.createDimension('LAT',ny)
-   ncfile.createDimension('TIME',None)
-   # create variables
-   LON = ncfile.createVariable('LON',np.dtype('double').char,('LON'))
-   LON.units = 'km'
-   LON.long_name = 'h point nominal longitude'
-   LON.cartesian_axis = 'X'
-   LON[:] = x[:]
-
-   LAT = ncfile.createVariable('LAT',np.dtype('double').char,('LAT'))
-   LAT.units = 'km'
-   LAT.long_name = 'h point nominal latitude'
-   LAT.cartesian_axis = 'Y'
-   LAT[:] = y[:]
-
-   time = ncfile.createVariable('TIME',np.dtype('double').char,('TIME'))
-   time.long_name = 'time'
-   time.units = 'days since 0001-01-01 00:00:00'
-   time.cartesian_axis = 'T'
-   time.calendar_type = 'NOLEAP'
-   time.calendar = 'NOLEAP'
-   time.bounds = 'time_bounds'
-   time[0] = 0
-
-   u_10 = ncfile.createVariable('U_10',np.dtype('float32').char,('TIME','LAT','LON'))
-   u_10.long_name = 'U wind'
-   u_10.units = 'm/s'
-   u_10[:] = u10[:]
-
-   v_10 = ncfile.createVariable('V_10',np.dtype('float32').char,('TIME','LAT','LON'))
-   v_10.long_name = 'U wind'
-   v_10.units = 'm/s'
-   v_10[:] = v10[:]
-
-   ncfile.close()
-   print ('*** SUCCESS creating '+name+'.nc!')
-        
-   
-   
-   # used when forcing is applied in the sea ice
-   name = 'forcing'
-   ncfile = Dataset('output_files/' + name+'.nc','w')
-   # create dimensions.
-   ncfile.createDimension('xh',nx)
-   ncfile.createDimension('yh',ny)
-   ncfile.createDimension('xq',nx)
-   ncfile.createDimension('yq',ny)
-   ncfile.createDimension('time',None)
-   ncfile.createDimension('nv',2)
-
-   # create variables
-   xh = ncfile.createVariable('xh',np.dtype('double').char,('xh'))
-   xh.units = 'km'
-   xh.long_name = 'h point nominal longitude'
-   xh.cartesian_axis = 'X'
-   xh[:] = x[:]
-   
-   xq = ncfile.createVariable('xq',np.dtype('double').char,('xq'))
-   xq.units = 'km'
-   xq.long_name = 'q point nominal longitude'
-   xq.cartesian_axis = 'X'
-   xq[:] = x[:]
-
-   yh = ncfile.createVariable('yh',np.dtype('double').char,('yh'))
-   yh.units = 'km'
-   yh.long_name = 'h point nominal latitude'
-   yh.cartesian_axis = 'Y'
-   yh[:] = y[:]
-   
-   yq = ncfile.createVariable('yq',np.dtype('double').char,('yq'))
-   yq.units = 'km'
-   yq.long_name = 'q point nominal latitude'
-   yq.cartesian_axis = 'Y'
-   yq[:] = y[:]
-
-   time = ncfile.createVariable('time',np.dtype('double').char,('time'))
-   time.long_name = 'time'
-   time.units = 'days since 0001-01-01 00:00:00'
-   time.cartesian_axis = 'T'
-   time.calendar_type = 'NOLEAP'
-   time.calendar = 'NOLEAP'
-   time.bounds = 'time_bounds'
-   time[0] = 0
-
-   nv = ncfile.createVariable('nv',np.dtype('double').char,('nv'))   
-   nv.long_name = 'vertex number'
-   nv.units = 'none'
-   nv.cartesian_axis = 'N'
-   nv[:] = [1,2]
-
-   if args.coupled_run:
-     u_flux = ncfile.createVariable('u_flux',np.dtype('float32').char,('time', 'yh', 'xh'), fill_value = 1.e+20)
-     u_flux.units = 'Pa'
-     u_flux.missing_value = 1.e+20
-     u_flux.long_name = 'i-direction wind stress'
-     u_flux[:] = -tau_x[:] # change sign in ice
-
-     v_flux = ncfile.createVariable('v_flux',np.dtype('float32').char,('time', 'yh', 'xh'), fill_value = 1.e+20)
-     v_flux.units = 'Pa'
-     v_flux.missing_value = 1.e+20
-     v_flux.long_name = 'j-direction wind stress'
-     v_flux[:] = -tau_y[:] # change sign in ice
-
-   else:
-     taux = ncfile.createVariable('taux',np.dtype('float32').char,('time', 'yh', 'xq'), fill_value = 1.e+20)
-     taux.units = 'Pascal'
-     taux.missing_value = 1.e+20
-     taux.long_name = 'Zonal Wind Stress'
-     taux[:] = tau_x[:]   
-
-     tauy = ncfile.createVariable('tauy',np.dtype('float32').char,('time', 'yq', 'xh'), fill_value = 1.e+20)
-     tauy.units = 'Pascal'
-     tauy.missing_value = 1.e+20
-     tauy.long_name = 'Meridional Wind Stress'
-     tauy[:] = 0.0
-
-
-   ncfile.close()
-   print ('*** SUCCESS creating '+name+'.nc!')
-   
-   return
-
-def make_forcing(x,y,args):
-   # forcing parameters
-   Ly = args.L # domain size km
-   W = args.W # domain width km
-   CSL = args.cshelf_lenght  # km
-   Q0 = 10. # W/m^2
-   Qmax = 50.
-   Yt = 600.0  # km
-   Lasf = 400.0 # km
-   tau_acc = 0.2
-   tau_asf = -0.05 # default is -0.075 # N/m^2
-   katabatic_wind = 0.075 # def is 0.05 N/m2
-   sponge = 50.0 # km
-   # polynya salt and salt fluxes
-   major = 75.0
-   minor = 75.0
-   area = np.pi * major * minor * 0.5
-   print 'Polynya area is (km^2):', area
-   ISL = args.ISL
-   salt_flux = 0.0
-   heat_flux = 0.0
-   latent_flux = 0.0
-   #ice_form = ((np.abs(salt_flux)*3600*24) * area * 1.0e6* 1.0e3/34.) * 1.0e-3 / (area * 1.0e6) 
-   #print 'Sea ice formation (m/day)', ice_form
-   #ice_form = ice_form/area
-   nx = len(x); ny = len(y); nt =1 # time
-   tau_x = np.zeros((nt,ny,nx)) # ice forcing
-   tau_y = np.zeros((nt,ny,nx))
-   evaporation = np.zeros((nt,ny,nx))
-   salt = np.zeros((nt,ny,nx))
-   heat = np.zeros((nt,ny,nx))
-   latent = np.zeros((nt,ny,nx))
-   # core atm params and values
-   u10_asf = args.u10_asf # def is -0.5  m/s
-   v10_katabatic = 15.0 # m/s
-   t10_min = 250. # kelvin
-   t10_max = 270.
-   t10_polynya = 0.
-   u10 = np.zeros((nt,ny,nx)) 
-   v10 = np.zeros((nt,ny,nx))
-   t10 = np.ones((nt,ny,nx))* t10_min
-
-   # wind and heat
-   # x-dir
-   tmp1 = ISL + 100.
-   for j in range(ny):
-      if y[j] < tmp1:
-        tau_x[0,j,:] = 0.0
-        u10[0,j,:] = 0.0
-        heat[0,j,:] = -Q0
-      elif y[j] >= tmp1 and y[j] <= tmp1 + Lasf:
-         tmp = np.pi*(y[j]-tmp1)/Lasf
-         u10[0,j,:] = u10_asf * np.sin(tmp)**2
-         tau_x[0,j,:] = tau_asf * np.sin(tmp)**2 
-         heat[0,j,:] = -Q0 - (8 * Q0 * np.sin(tmp))
-      else:
-         tmp2 = (y[j] - tmp1 - Lasf)/(2.*(Ly-tmp1 - Lasf))
-         u10[0,j,:] = 0.0
-         tau_x[0,j,:] = tau_acc * np.sin(tmp2 * np.pi)**2
-         heat[0,j,:] = -Q0 
-        
-   # y-dir (decays linearly away from the ice shelf front)
-   # has a gaussian shape: tauy = tauy_max * np.exp(((x-W/2.)**2)/(2*W_v10))
-   W_v10 = 50000. # km
-   dummy = ISL + args.cshelf_lenght + args.slope_lenght
-   for i in range(nx):
-      for j in range(ny):
-         if y[j] < ISL:
-            tau_y[0,j,i] = katabatic_wind
-            v10[0,j,i] = v10_katabatic
-         elif y[j] <= dummy:
-            tmp =  np.exp((-(x[i]-W*0.5)**2)/(2*W_v10))
-            tau_y[0,j,i] = ((-katabatic_wind/(dummy)) * (y[j]) + katabatic_wind) * tmp
-            v10[0,j,i] = ((-v10_katabatic/(dummy)) * (y[j]) + v10_katabatic) * tmp
-
-   # read ocean's initial SST (in K)
-   T0 = Dataset('ic_ts.nc').variables['PTEMP'][0,1,:,0] + 273.
-   # T10 = T10 - 10 * np.exp(-(y[j]-ISL)/150.)
-   # e-folding scale is 150 km
-   efold = args.cshelf_lenght + args.slope_lenght
-   for j in range(ny):
-      if y[j]<=ISL:
-         t10[0,j,:] = 250. #T0[j] - 10. 
-         heat[0,j,:] = -100.
-      elif y[j]<=ISL + efold:
-         t10[0,j,:] = 270 - 20. * np.exp(-(y[j]-ISL)/100.)
-         heat[0,j,:] = -100. * np.exp(-(y[j]-ISL)/100.)
-      else:
-         t10[0,j,:] = 0.0
-         heat[0,j,:] = 0.0
-   
-   # evap, proxy for brine formation in polynyas
-   if t10_polynya > 0.:
-     for i in range(nx):
-       for j in range(ny):
-	 if (x[i] - W/2. >= -major and x[i] - W/2. <= major):
-	    if (y[j]-ISL >= 0.) and (y[j]-ISL <= (minor * np.abs((1-(x[i]-W/2.)**2/major**2)**(1/2.)))):
-	      evaporation[0,j,i] = salt_flux
-	      salt[0,j,i] = salt_flux
-	      heat[0,j,i] = heat_flux
-	      latent[0,j,i] = latent_flux
-	      t10[0,j,i] = t10_polynya
-
-   # set salt flux such that net buoynacy flux is zero
-   # B_heat = B_salt
-   cp = 3974.0 # J/(K kg)
-   rho0 = 1028.0; alpha = 0.11069/rho0; beta = 0.7906/rho0; g = 9.8
-   B_heat = heat[0,:,:] * g * alpha/ (rho0 * cp)
-   salt[0,:,:] = B_heat * rho0 / (beta * g)
-   print 'B_heat',B_heat.min(),B_heat.max()
-   print 'salt',salt.min(),salt.max()
-   # plots
-   if args.debug:
-
-      plt.figure()
-      u=u10[0,::5,::5]; v=v10[0,::5,::5]; mag = np.sqrt(u**2 + v**2)
-      plt.quiver(x[::5],y[::5],u, v, mag, cmap = plt.cm.seismic)
-      plt.colorbar()
-      plt.plot(x,np.ones(nx)*ISL,'k')
-      plt.plot(x,np.ones(nx)*(ISL+CSL),'k')
-      plt.title('Wind vel. at 10 m (m/s)')
-      plt.xlabel('x [km]'); plt.ylabel('y [km]')
-      plt.savefig('PNG/wind10m.png')
-
-      plt.figure()
-      plt.subplot(211)
-      plt.plot(y,u10[0,:,1])
-      plt.title('u10'); plt.xlabel('y [km]'); plt.ylabel('m/s')
-      plt.subplot(212)
-      plt.contourf(x,y,u10[0,:,:]); plt.colorbar()
-      plt.xlabel('x [km]'); plt.ylabel('y [km]')
-      plt.savefig('PNG/u10.png')
-
-      plt.figure()
-      plt.subplot(211)
-      plt.plot(y,v10[0,:,1])
-      plt.title('v10'); plt.xlabel('y [km]'); plt.ylabel('m/s')
-      plt.subplot(212)
-      plt.contourf(x,y,v10[0,:,:]); plt.colorbar()
-      plt.xlabel('x [km]'); plt.ylabel('y [km]')
-      plt.savefig('PNG/v10.png')
-
-      plt.figure()
-      plt.subplot(211)
-      plt.plot(y,tau_x[0,:,1])
-      plt.title('taux'); plt.xlabel('y [km]'); plt.ylabel('Pa')
-      plt.subplot(212)
-      plt.contourf(x,y,tau_x[0,:,:]); plt.colorbar()
-      plt.xlabel('x [km]'); plt.ylabel('y [km]')
-      plt.savefig('PNG/taux.png')
-
-      plt.figure()
-      plt.subplot(211)
-      plt.plot(y,tau_y[0,:,args.nx/2.])
-      plt.title('tauy'); plt.xlabel('y [km]'); plt.ylabel('Pa')
-      plt.subplot(212)
-      plt.contourf(x,y,tau_y[0,:,:]); plt.colorbar()
-      plt.xlabel('x [km]'); plt.ylabel('y [km]')
-      plt.savefig('PNG/tauy.png') 
-
-      plt.figure()
-      plt.subplot(211)
-      plt.plot(y,heat[0,:,1])
-      plt.title('Sensible Heat'); plt.xlabel('y [km]'); plt.ylabel('W/m^2')
-      plt.subplot(212)
-      plt.contourf(x,y,heat[0,:,:]); plt.colorbar()
-      plt.xlabel('x [km]'); plt.ylabel('y [km]')
-      plt.savefig('PNG/sensible_heat.png')
-
-      plt.figure()
-      plt.title('Salt flux kg/(m^2 s)')
-      plt.contourf(x,y,heat[0,:,:]); plt.colorbar()
-      plt.xlabel('x [km]'); plt.ylabel('y [km]')
-      plt.savefig('PNG/salt_flux.png')
-
-      plt.figure()
-      plt.subplot(211)
-      plt.plot(y,t10[0,:,1],'b',y,T0,'r')
-      plt.title('Atm temp at 10 m (b); Initial SST (r)'); plt.xlabel('y [km]'); plt.ylabel('K')
-      plt.subplot(212)
-      plt.contourf(x,y,t10[0,:,:]); plt.colorbar()
-      plt.xlabel('x [km]'); plt.ylabel('y [km]')
-      plt.savefig('PNG/t10.png')
-
-   # create ncfile
-   # open a new netCDF file for writing.
-   # # used when forcing is applied in the atm
-   name = 'forcing_10'
-   ncfile = Dataset('output_files/' + name+'.nc','w')
-   # create dimensions.
-   ncfile.createDimension('LON',nx)
-   ncfile.createDimension('LAT',ny)
-   ncfile.createDimension('TIME',None)
-   # create variables
-   LON = ncfile.createVariable('LON',np.dtype('double').char,('LON'))
-   LON.units = 'km'
-   LON.long_name = 'h point nominal longitude'
-   LON.cartesian_axis = 'X'
-   LON[:] = x[:]
-
-   LAT = ncfile.createVariable('LAT',np.dtype('double').char,('LAT'))
-   LAT.units = 'km'
-   LAT.long_name = 'h point nominal latitude'
-   LAT.cartesian_axis = 'Y'
-   LAT[:] = y[:]
-
-   time = ncfile.createVariable('TIME',np.dtype('double').char,('TIME'))
-   time.long_name = 'time'
-   time.units = 'days since 0001-01-01 00:00:00'
-   time.cartesian_axis = 'T'
-   time.calendar_type = 'NOLEAP'
-   time.calendar = 'NOLEAP'
-   time.bounds = 'time_bounds'
-   time[0] = 0
-
-   t_10 = ncfile.createVariable('T_10',np.dtype('float32').char,('TIME','LAT','LON')) 
-   t_10.long_name = 'Air Temperature'
-   t_10.units = 'Kelvin'
-   t_10[:] = t10[:]
-
-   u_10 = ncfile.createVariable('U_10',np.dtype('float32').char,('TIME','LAT','LON'))
-   u_10.long_name = 'U wind'
-   u_10.units = 'm/s'
-   u_10[:] = u10[:]
-
-   v_10 = ncfile.createVariable('V_10',np.dtype('float32').char,('TIME','LAT','LON'))
-   v_10.long_name = 'U wind'
-   v_10.units = 'm/s'
-   v_10[:] = v10[:]
-
-   ncfile.close()
-   print ('*** SUCCESS creating '+name+'.nc!')
-
-   # used when forcing is applied in the sea ice
-   name = 'forcing'
-   ncfile = Dataset('output_files/' + name+'.nc','w')
-   # create dimensions.
-   ncfile.createDimension('xh',nx)
-   ncfile.createDimension('yh',ny)
-   ncfile.createDimension('xq',nx)
-   ncfile.createDimension('yq',ny)
-   ncfile.createDimension('time',None)
-   ncfile.createDimension('nv',2)
-
-   # create variables
-   xh = ncfile.createVariable('xh',np.dtype('double').char,('xh'))
-   xh.units = 'km'
-   xh.long_name = 'h point nominal longitude'
-   xh.cartesian_axis = 'X'
-   xh[:] = x[:]
-   
-   xq = ncfile.createVariable('xq',np.dtype('double').char,('xq'))
-   xq.units = 'km'
-   xq.long_name = 'q point nominal longitude'
-   xq.cartesian_axis = 'X'
-   xq[:] = x[:]
-
-   yh = ncfile.createVariable('yh',np.dtype('double').char,('yh'))
-   yh.units = 'km'
-   yh.long_name = 'h point nominal latitude'
-   yh.cartesian_axis = 'Y'
-   yh[:] = y[:]
-   
-   yq = ncfile.createVariable('yq',np.dtype('double').char,('yq'))
-   yq.units = 'km'
-   yq.long_name = 'q point nominal latitude'
-   yq.cartesian_axis = 'Y'
-   yq[:] = y[:]
-
-   time = ncfile.createVariable('time',np.dtype('double').char,('time'))
-   time.long_name = 'time'
-   time.units = 'days since 0001-01-01 00:00:00'
-   time.cartesian_axis = 'T'
-   time.calendar_type = 'NOLEAP'
-   time.calendar = 'NOLEAP'
-   time.bounds = 'time_bounds'
-   time[0] = 0
-
-   nv = ncfile.createVariable('nv',np.dtype('double').char,('nv'))   
-   nv.long_name = 'vertex number'
-   nv.units = 'none'
-   nv.cartesian_axis = 'N'
-   nv[:] = [1,2]
-
-   if args.coupled_run:
-     u_flux = ncfile.createVariable('u_flux',np.dtype('float32').char,('time', 'yh', 'xh'), fill_value = 1.e+20)
-     u_flux.units = 'Pa'
-     u_flux.missing_value = 1.e+20
-     u_flux.long_name = 'i-direction wind stress'
-     u_flux[:] = -tau_x[:] # change sign in ice
-
-     v_flux = ncfile.createVariable('v_flux',np.dtype('float32').char,('time', 'yh', 'xh'), fill_value = 1.e+20)
-     v_flux.units = 'Pa'
-     v_flux.missing_value = 1.e+20
-     v_flux.long_name = 'j-direction wind stress'
-     v_flux[:] = -tau_y[:] # change sign in ice
-
-     t_flux = ncfile.createVariable('t_flux',np.dtype('float32').char,('time', 'yh', 'xh'), fill_value = 1.e+20)
-     t_flux.units = 'Watt meter-2'
-     t_flux.missing_value = 1.e+20
-     t_flux.long_name = 'Sensible heat flux'
-     t_flux[:] = -heat[:] # change sign in ice
-
-     # latent heat
-     lt = ncfile.createVariable('latent',np.dtype('float32').char,('time', 'yh', 'xh'), fill_value = 1.e+20)
-     lt.units = 'Watt meter-2'
-     lt.missing_value = 1.e+20
-     lt.long_name = 'Latent heat flux'
-     lt[:] = -latent # change sign in ice
-
-     salt_flux = ncfile.createVariable('salt_flux',np.dtype('float32').char,('time', 'yh', 'xh'), fill_value = 1.e+20)
-     salt_flux.units = 'kg/(m^2 s)'
-     salt_flux.missing_value = 1.e+20
-     salt_flux.long_name = 'salt flux'
-     salt_flux[:] = -salt[:] # + adds salt from ocean
-
-   else:
-     SW = ncfile.createVariable('SW',np.dtype('float32').char,('time', 'yh', 'xh'), fill_value = 1.e+20)
-     SW.units = 'Watt meter-2'
-     SW.missing_value = 1.e+20
-     SW.long_name = 'surface_net_downward_shortwave_flux'
-     SW[:] = 0.0
-
-     LW = ncfile.createVariable('LW',np.dtype('float32').char,('time', 'yh', 'xh'), fill_value = 1.e+20)
-     LW.units = 'Watt meter-2'
-     LW.missing_value = 1.e+20
-     LW.long_name = 'surface_net_downward_longwave_flux'
-     LW[:] = 0.0
-
-     latent = ncfile.createVariable('latent',np.dtype('float32').char,('time', 'yh', 'xh'), fill_value = 1.e+20)
-     latent.units = 'Watt meter-2'
-     latent.missing_value = 1.e+20
-     latent.long_name = 'Latent heat flux into ocean due to fusion and evaporation'
-     latent[:] = 0.0
-
-     sensible = ncfile.createVariable('sensible',np.dtype('float32').char,('time', 'yh', 'xh'), fill_value = 1.e+20)
-     sensible.units = 'Watt meter-2'
-     sensible.missing_value = 1.e+20
-     sensible.long_name = 'surface_downward_sensible_heat_flux'
-     sensible[:] = heat[:]
-
-     evap = ncfile.createVariable('evap',np.dtype('float32').char,('time', 'yh', 'xh'), fill_value = 1.e+20)
-     evap.units = 'kilogram meter-2 second-1'
-     evap.missing_value = 1.e+20
-     evap.long_name = 'Evaporation at ocean surface (usually negative)'
-     evap[:] = evaporation[:]
-
-     taux = ncfile.createVariable('taux',np.dtype('float32').char,('time', 'yh', 'xq'), fill_value = 1.e+20)
-     taux.units = 'Pascal'
-     taux.missing_value = 1.e+20
-     taux.long_name = 'Zonal Wind Stress'
-     taux[:] = tau_x[:]   
-
-     tauy = ncfile.createVariable('tauy',np.dtype('float32').char,('time', 'yq', 'xh'), fill_value = 1.e+20)
-     tauy.units = 'Pascal'
-     tauy.missing_value = 1.e+20
-     tauy.long_name = 'Meridional Wind Stress'
-     tauy[:] = 0.0
-
-     ustar = ncfile.createVariable('ustar',np.dtype('float32').char,('time', 'yh', 'xh'), fill_value = 1.e+20)
-     ustar.units = 'meter second-1'
-     ustar.missing_value = 1.e+20
-     ustar.long_name = 'Surface friction velocity'
-     ustar[:] = 0.0
-
-     SST = ncfile.createVariable('SST',np.dtype('float32').char,('time', 'yh', 'xh'), fill_value = -1.e+34)
-     SST.units = 'Celsius'
-     SST.missing_value = -1.e+34
-     SST.long_name = 'Sea Surface Temperature'
-     SST[:] = 0.0
-
-     SSS = ncfile.createVariable('SSS',np.dtype('float32').char,('time', 'yh', 'xh'), fill_value = -1.e+34)
-     SSS.units = 'PSU'
-     SSS.missing_value = -1.e+34
-     SSS.long_name = 'Sea Surface Salinity'
-     SSS[:] = 0.0
-
-   ncfile.close()
-   print ('*** SUCCESS creating '+name+'.nc!')
-   
-   return
-
-def make_topo(x,y,args):
-   # parameters
-   name = 'ocean_topog'
-   Hs = args.min_depth  # shelf's depth
-   x=x*1000  #Conversion to meters
-   y=y*1000  #Conversion to meters
-   nx = len(x); ny = len(y)
-   D = np.zeros((ny,nx))
-
-   #Adding a small Guassian bump/hill to bottom topography to break the symmetry
-   x0=(np.max(x)-np.min(x))/2.0
-   y0=(np.max(y)-np.min(y))/4.0
-   print x0
-   R=100*1000.0
-   H0=100.0
-   for j in range(ny):
-      for i in range(nx):
-	      #d=np.sqrt( ((x[i]-x0)**2)   + ((y[j]-y0)**2) ) #Gausian bump
-	      d=np.sqrt( ((x[i]-x0)**2) )  #Gausian hill
-              D[j,i] = Hs - (H0*np.exp(-(d/(R))**2))
-
-
-	
-   # to avoid sea ice formation under ice shelves,
-   # two topography files need to be constructed.
-   # The coupler topo is where the cavity is masked.
-
-   Dcoupler = D.copy()
-   #for j in range(ny):
-   #    if y[j]<= args.ISL:
-   #       Dcoupler[j,:] = 0.0
-
-   # 1) topography used in the coupler
-   # open a new netCDF file for writing.
-   name = 'ocean_topog'
-   ncfile = Dataset('output_files/' + name+'.nc','w')
-   # create dimensions.
-   ncfile.createDimension('nx',nx)
-   ncfile.createDimension('ny',ny)
-   ncfile.createDimension('ntiles',1)
- 
-   # create variables
-   nxx = ncfile.createVariable('nx',np.dtype('double').char,('nx'))
-   nxx.units = 'km'
-   nxx.description = 'x location of cell centers'
-   nxx.long_name = 'x location of cell centers'
-   nxx[:] = x[:]
-
-   nyy = ncfile.createVariable('ny',np.dtype('double').char,('ny'))
-   nyy.units = 'km'
-   nyy.description = 'y location of cell centers'
-   nyy.long_name = 'y location of cell centers'
-   nyy[:] = y[:]
-
-   depth = ncfile.createVariable('depth',np.dtype('float32').char,('ny','nx'))
-   depth.units = 'm'
-   depth.description = 'depth at h points'
-   depth.long_name = 'depth at h points'
-   depth[:,:] = Dcoupler[:,:]
-   ncfile.close()
-   print ('*** SUCCESS creating '+name+'.nc!')
-
-   # 2) topography used ny the ocean
-   # open a new netCDF file for writing.
-   name = 'topog'
-   ncfile = Dataset('output_files/' + name+'.nc','w')
-   # create dimensions.
-   ncfile.createDimension('nx',nx)
-   ncfile.createDimension('ny',ny)
-   ncfile.createDimension('ntiles',1)
-
-   # create variables
-   nxx = ncfile.createVariable('nx',np.dtype('double').char,('nx'))
-   nxx.units = 'km'
-   nxx.description = 'x location of cell centers'
-   nxx.long_name = 'x location of cell centers'
-   nxx[:] = x[:]
-
-   nyy = ncfile.createVariable('ny',np.dtype('double').char,('ny'))
-   nyy.units = 'km'
-   nyy.description = 'y location of cell centers'
-   nyy.long_name = 'y location of cell centers'
-   nyy[:] = y[:]
-
-   depth = ncfile.createVariable('depth',np.dtype('float32').char,('ny','nx'))
-   depth.units = 'm'
-   depth.description = 'depth at h points'
-   depth.long_name = 'depth at h points'
-   depth[:,:] = D[:,:]
-   ncfile.close()
-   print ('*** SUCCESS creating '+name+'.nc!')
- 
-   return Dcoupler
-
-# A helper function to use when writing strings in a netcdf file
-def set_string(variable, value):
-   """Sets "variable" to "value" padded with blanks where
-   "variable" is a netcdf variable object and "value" is a string."""
-   variable[:] = '\000' * variable.shape[0]
-   variable[:len(value)] = value
-   return
-
-# Invoke parseCommandLine(), the top-level prodedure
-if __name__ == '__main__': parseCommandLine()
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/Idealized_cartesian_grid.py b/tests/Iceberg_repository/Scripts_and_analysis/Idealized_cartesian_grid.py
deleted file mode 100644
index 6aa3510..0000000
--- a/tests/Iceberg_repository/Scripts_and_analysis/Idealized_cartesian_grid.py
+++ /dev/null
@@ -1,395 +0,0 @@
-
-# coding: utf-8
-
-# In[2]:
-
-import scipy.io.netcdf
-import numpy
-get_ipython().magic('pylab inline')
-
-
-# Model grid will have ni x nj h-point grid cells
-
-# In[3]:
-
-nj,ni = 40,240
-
-
-# A mosaic file has a supergrid of an integer refinement (e.g. 2*ni x 2*nj cells)
-
-# In[4]:
-
-snj, sni = 2*nj, 2*ni
-
-
-# Uniform resolution of the ocean model grid will be dxo x dyo
-
-# In[5]:
-
-dxo = 2.e3
-dyo = 2.e3
-
-
-# Using a supergrid refinement of 2, the grid lengths, area and coordinates are:
-
-# In[6]:
-
-dx = (0.5 * dxo) * numpy.ones((snj+1,sni))
-dy = (0.5 * dyo) * numpy.ones((snj,sni+1))
-area = (0.25 * (dxo * dyo)) * numpy.ones((snj,sni))
-x = numpy.zeros((snj+1,sni+1))
-x[:,1:] = numpy.cumsum( dx, axis=-1 )
-y = numpy.zeros((snj+1,sni+1))
-y[1:,:] = numpy.cumsum( dy, axis=-2 )
-
-
-# In[7]:
-
-# A helper function to use when writing strings in a netcdf file
-def set_string(variable, value):
-    """Sets "variable" to "value" padded with blanks where
-    "variable" is a netcdf variable object and "value" is a string."""
-    variable[:] = '\000' * variable.shape[0]
-    variable[:len(value)] = value
-
-
-# Create a netcdf3 horizontal ocean-grid file...
-
-# In[8]:
-
-rg = scipy.io.netcdf_file('ocean_hgrid.nc','w',version=2)
-
-
-# In[9]:
-
-rg.createDimension('nx',sni)
-rg.createDimension('ny',snj)
-rg.createDimension('nxp',sni+1)
-rg.createDimension('nyp',snj+1)
-rg.createDimension('string',255)
-
-
-# In[10]:
-
-dx_h = rg.createVariable('dx','f8',('nyp','nx',))
-dx_h.units = 'm'
-dy_h = rg.createVariable('dy','f8',('ny','nxp',))
-dy_h.units = 'm'
-area_h = rg.createVariable('area','f8',('ny','nx',))
-area_h.units = 'm2'
-x_h = rg.createVariable('x','f8',('nyp','nxp',))
-x_h.units = 'm'
-y_h = rg.createVariable('y','f8',('nyp','nxp',))
-y_h.units = 'm'
-tile = rg.createVariable('tile','c',('string',))
-
-
-# In[11]:
-
-dx_h[:,:] = dx[:,:]
-dy_h[:,:] = dy[:,:]
-area_h[:,:] = area[:,:]
-x_h[:,:] = x[:,:]
-y_h[:,:] = y[:,:]
-tile[:] = '\000' * 255
-tile[:5] = 'tile1'
-set_string(tile,'tile1')
-
-
-# In[12]:
-
-rg.close()
-
-
-# Create a netcdf3 ocean-mask file...
-
-# In[13]:
-
-rg = scipy.io.netcdf_file('ocean_mask.nc','w',version=2)
-rg.createDimension('nx',ni)
-rg.createDimension('ny',nj)
-mask = rg.createVariable('mask','f4',('ny','nx',))
-mask[:,:] = 1.
-rg.close()
-
-
-# Create a mosaic description for the above grid file...
-
-# In[14]:
-
-rg = scipy.io.netcdf_file('ocean_mosaic.nc','w',version=2)
-rg.createDimension('ntiles',1)
-rg.createDimension('string',255)
-mosaic = rg.createVariable('mosaic','c',('string',))
-mosaic.standard_name = 'grid_mosaic_spec'
-mosaic.children = 'contacts'
-mosaic.grid_descriptor = ''
-gridlocation = rg.createVariable('gridlocation','c',('string',))
-gridlocation.standard_name = 'grid_file_location'
-gridfiles = rg.createVariable('gridfiles','c',('ntiles','string',))
-gridtiles = rg.createVariable('gridtiles','c',('ntiles','string',))
-rg.grid_version = '0.2'
-# Fill in data
-mosaic[:] = '\000' * 255
-mosaic[:12] = 'ocean_mosaic'
-gridlocation[:] = '\000' * 255
-gridlocation[:2] = './'
-gridfiles[:] = '\000' * 255
-gridfiles[0,:14] = 'ocean_hgrid.nc'
-gridtiles[:] = '\000' * 255
-gridtiles[0,:5] = 'tile1'
-rg.close()
-
-
-# In[15]:
-
-get_ipython().system('pwd')
-
-
-# In[16]:
-
-# Fake a ocean_topog.nc file
-rg = scipy.io.netcdf_file('ocean_topog.nc','w',version=2)
-rg.createDimension('nx',ni)
-rg.createDimension('ny',nj)
-rg.createDimension('ntiles',1)
-depth = rg.createVariable('depth','f4',('ny','nx',))
-depth[:,:] = 1000.
-depth[-1,-1] =0
-rg.close()
-
-
-# In[17]:
-
-#fre_nctools/tools/make_quick_mosaic/make_quick_mosaic --input_mosaic ocean_mosaic.nc --ocean_topog ocean_topog.nc
-
-
-# In[18]:
-
-rg = scipy.io.netcdf_file('atmos_mosaic_tile1Xland_mosaic_tile1_BLAH.nc','w',version=2) # atmos_mosaic_tile1Xland_mosaic_tile1.nc
-rg.createDimension('string',255)
-rg.createDimension('ncells',1)
-rg.createDimension('two',2)
-contact = rg.createVariable('contact','c',('string',))
-contact.standard_name = 'grid_contact_spec'
-contact.contact_type = 'exchange'
-contact.parent1_cell = 'tile1_cell'
-contact.parent2_cell = 'tile2_cell'
-contact.xgrid_area_field = 'xgrid_area'
-contact.distant_to_parent1_centroid = 'tile1_distance'
-contact.distant_to_parent2_centroid = 'tile2_distance'
-tile1_cell = rg.createVariable('tile1_cell','f8',('ncells','two',))
-tile1_cell.standard_name = 'parent_cell_indices_in_mosaic1'
-tile2_cell = rg.createVariable('tile2_cell','f8',('ncells','two',))
-tile2_cell.standard_name = 'parent_cell_indices_in_mosaic2'
-xgrid_area = rg.createVariable('xgrid_area','f8',('ncells',))
-xgrid_area.standard_name = 'exchange_grid_area'
-xgrid_area.units = 'm2'
-tile1_distance = rg.createVariable('tile1_distance','f8',('ncells','two'))
-tile1_distance.standard_name = 'distance_from_parent1_cell_centroid'
-tile2_distance = rg.createVariable('tile2_distance','f8',('ncells','two'))
-tile2_distance.standard_name = 'distance_from_parent2_cell_centroid'
-rg.grid_version = '0.2'
-# Fill in data
-contact[:] = '\000' * 255
-contact[:37] = 'atmos_mosaic:tile1::land_mosaic:tile1'
-tile1_cell[:] = [ni,nj]
-tile2_cell[:] = [ni,nj]
-xgrid_area[:] = dxo * dyo
-tile1_distance[:] = 0.
-tile2_distance[:] = 0.
-rg.close()
-
-
-# In[19]:
-
-rg = scipy.io.netcdf_file('atmos_mosaic_tile1Xocean_mosaic_tile1_BLAH.nc','w',version=2) # atmos_mosaic_tile1Xocean_mosaic_tile1.nc
-rg.createDimension('string',255)
-rg.createDimension('ncells',ni*nj-1) # -1 is for a single land point
-rg.createDimension('two',2)
-contact = rg.createVariable('contact','c',('string',))
-contact.standard_name = 'grid_contact_spec'
-contact.contact_type = 'exchange'
-contact.parent1_cell = 'tile1_cell'
-contact.parent2_cell = 'tile2_cell'
-contact.xgrid_area_field = 'xgrid_area'
-contact.distant_to_parent1_centroid = 'tile1_distance'
-contact.distant_to_parent2_centroid = 'tile2_distance'
-tile1_cell = rg.createVariable('tile1_cell','f8',('ncells','two',))
-tile1_cell.standard_name = 'parent_cell_indices_in_mosaic1'
-tile2_cell = rg.createVariable('tile2_cell','f8',('ncells','two',))
-tile2_cell.standard_name = 'parent_cell_indices_in_mosaic2'
-xgrid_area = rg.createVariable('xgrid_area','f8',('ncells',))
-xgrid_area.standard_name = 'exchange_grid_area'
-xgrid_area.units = 'm2'
-tile1_distance = rg.createVariable('tile1_distance','f8',('ncells','two'))
-tile1_distance.standard_name = 'distance_from_parent1_cell_centroid'
-tile2_distance = rg.createVariable('tile2_distance','f8',('ncells','two'))
-tile2_distance.standard_name = 'distance_from_parent2_cell_centroid'
-rg.grid_version = '0.2'
-# Fill in data
-contact[:] = '\000' * 255
-contact[:37] = 'atmos_mosaic:tile1::land_mosaic:tile1'
-tile1_cell[:] = [ni,nj]
-tile2_cell[:] = [ni,nj]
-xgrid_area[:] = dxo * dyo
-for j in range(nj):
-    for i in range(ni):
-        if (i,j) != (ni-1,nj-1):
-            tile1_cell[i+ni*j] = [i,j]
-            tile2_cell[i+ni*j] = [i,j]
-            tile1_distance[i+ni*j] = [0,0]
-            tile2_distance[i+ni*j] = [0,0]
-            xgrid_area[i+ni*j] = dxo * dyo
-rg.close()
-
-
-# In[20]:
-
-rg = scipy.io.netcdf_file('land_mosaic_tile1Xocean_mosaic_tile1_BLAH.nc','w',version=2) # land_mosaic_tile1Xocean_mosaic_tile1.nc
-rg.createDimension('string',255)
-rg.createDimension('ncells',ni*nj-1) # -1 is for a single land point
-rg.createDimension('two',2)
-contact = rg.createVariable('contact','c',('string',))
-contact.standard_name = 'grid_contact_spec'
-contact.contact_type = 'exchange'
-contact.parent1_cell = 'tile1_cell'
-contact.parent2_cell = 'tile2_cell'
-contact.xgrid_area_field = 'xgrid_area'
-contact.distant_to_parent1_centroid = 'tile1_distance'
-contact.distant_to_parent2_centroid = 'tile2_distance'
-tile1_cell = rg.createVariable('tile1_cell','f8',('ncells','two',))
-tile1_cell.standard_name = 'parent_cell_indices_in_mosaic1'
-tile2_cell = rg.createVariable('tile2_cell','f8',('ncells','two',))
-tile2_cell.standard_name = 'parent_cell_indices_in_mosaic2'
-xgrid_area = rg.createVariable('xgrid_area','f8',('ncells',))
-xgrid_area.standard_name = 'exchange_grid_area'
-xgrid_area.units = 'm2'
-tile1_distance = rg.createVariable('tile1_distance','f8',('ncells','two'))
-tile1_distance.standard_name = 'distance_from_parent1_cell_centroid'
-tile2_distance = rg.createVariable('tile2_distance','f8',('ncells','two'))
-tile2_distance.standard_name = 'distance_from_parent2_cell_centroid'
-rg.grid_version = '0.2'
-# Fill in data
-contact[:] = '\000' * 255
-contact[:37] = 'atmos_mosaic:tile1::land_mosaic:tile1'
-tile1_cell[:] = [ni,nj]
-tile2_cell[:] = [ni,nj]
-xgrid_area[:] = dxo * dyo
-for j in range(nj):
-    for i in range(ni):
-        if (i,j) != (ni-1,nj-1):
-            tile1_cell[i+ni*j] = [i,j]
-            tile2_cell[i+ni*j] = [i,j]
-            tile1_distance[i+ni*j] = [0,0]
-            tile2_distance[i+ni*j] = [0,0]
-            xgrid_area[i+ni*j] = dxo * dyo
-rg.close()
-
-
-# In[24]:
-
-rg = scipy.io.netcdf_file('mosaic_BLAH.nc','w',version=2) # land_mosaic_tile1Xocean_mosaic_tile1.nc
-rg.createDimension('string',255)
-rg.createDimension('nfile_aXo',1) # -1 is for a single land point
-rg.createDimension('nfile_aXl',1) # -1 is for a single land point
-rg.createDimension('nfile_lXo',1) # -1 is for a single land point
-
-atm_mosaic_dir = rg.createVariable('atm_mosaic_dir','c',('string',))
-atm_mosaic_dir.standard_name = 'directory_storing_atmosphere_mosaic'
-
-atm_mosaic_file = rg.createVariable('atm_mosaic_file','c',('string',))
-atm_mosaic_file.standard_name = 'atmosphere_mosaic_file_name'
-
-atm_mosaic = rg.createVariable('atm_mosaic','c',('string',))
-atm_mosaic.standard_name = 'atmosphere_mosaic_name'
-
-lnd_mosaic_dir = rg.createVariable('lnd_mosaic_dir','c',('string',))
-lnd_mosaic_dir.standard_name = 'directory_storing_land_mosaic'
-
-lnd_mosaic_file = rg.createVariable('lnd_mosaic_file','c',('string',))
-lnd_mosaic_file.standard_name = 'land_mosaic_file_name'
-
-lnd_mosaic = rg.createVariable('lnd_mosaic','c',('string',))
-lnd_mosaic.standard_name = 'land_mosaic_name'
-
-ocn_mosaic_dir = rg.createVariable('ocn_mosaic_dir','c',('string',))
-ocn_mosaic_dir.standard_name = 'directory_storing_ocean_mosaic'
-
-ocn_mosaic_file = rg.createVariable('ocn_mosaic_file','c',('string',))
-ocn_mosaic_file.standard_name = 'ocean_mosaic_file_name'
-
-ocn_mosaic = rg.createVariable('ocn_mosaic','c',('string',))
-ocn_mosaic.standard_name = 'ocean_mosaic_name'
-
-
-ocn_topog_dir = rg.createVariable('ocn_topog_dir','c',('string',))
-ocn_mosaic_dir.standard_name = 'directory_storing_ocean_topog'
-
-ocn_topog_file = rg.createVariable('ocn_topog_file','c',('string',))
-ocn_topog_file.standard_name = 'ocean_topog_file_name'
-
-aXo_file = rg.createVariable('aXo_file','c',('string',))
-aXo_file.standard_name = 'atmXocn_exchange_grid_file'
-
-aXl_file = rg.createVariable('aXl_file','c',('string',))
-aXl_file.standard_name = 'atmXlnd_exchange_grid_file'
-
-lXo_file = rg.createVariable('lXo_file','c',('string',))
-lXo_file.standard_name = 'lndXocn_exchange_grid_file'
-
-#Global attributes
-rg.grid_version = '0.2'
-rg.code_version = "$Name:  $"
-rg.history = "/net2/aja/workspace/MOM6-examples/ice_ocean_SIS2/OM4_025/preprocessing/fre_nctools/tools/make_quick_mosaic/make_quick_mosaic --input_mosaic ocean_mosaic.nc --ocean_topog ocean_topog.nc"
-# Fill in data
-atm_mosaic_dir[:] = '\000' * 255
-atm_mosaic_dir[:2] = './'
-
-atm_mosaic_file[:] = '\000' * 255
-atm_mosaic_file[:15] = 'ocean_mosaic.nc'
-
-atm_mosaic[:] = '\000' * 255
-atm_mosaic[:12] = 'atmos_mosaic'
-
-lnd_mosaic_dir[:] = '\000' * 255
-lnd_mosaic_dir[:2] = './'
-
-lnd_mosaic_file[:] = '\000' * 255
-lnd_mosaic_file[:15] = 'ocean_mosaic.nc'
-
-lnd_mosaic[:] = '\000' * 255
-lnd_mosaic[:11] = 'land_mosaic'
-
-ocn_mosaic_dir[:] = '\000' * 255
-ocn_mosaic_dir[:2] = './'
-
-ocn_mosaic_file[:] = '\000' * 255
-ocn_mosaic_file[:15] = 'ocean_mosaic.nc'
-
-ocn_mosaic[:] = '\000' * 255
-ocn_mosaic[:12] = 'ocean_mosaic'
-
-ocn_topog_dir[:] = '\000' * 255
-ocn_topog_dir[:2] = './'
-
-ocn_topog_file[:] = '\000' * 255
-ocn_topog_file[:14] = 'ocean_topog.nc'
-
-aXo_file[:] = '\000' * 255
-aXo_file[:40] = 'atmos_mosaic_tile1Xocean_mosaic_tile1.nc'
-
-aXl_file[:] = '\000' * 255
-aXl_file[:39] = 'atmos_mosaic_tile1Xland_mosaic_tile1.nc'
-
-lXo_file[:] = '\000' * 255
-lXo_file[:39] = 'land_mosaic_tile1Xocean_mosaic_tile1.nc'
-
-rg.close()
-
-
-
-# In[ ]:
-
-
-
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/Weddell_Sea_initiation.sh b/tests/Iceberg_repository/Scripts_and_analysis/Weddell_Sea_initiation.sh
deleted file mode 100755
index 5c92e87..0000000
--- a/tests/Iceberg_repository/Scripts_and_analysis/Weddell_Sea_initiation.sh
+++ /dev/null
@@ -1 +0,0 @@
-./initialize_bergs_in_pattern.py -Make_icebergs_non_static_later=False -Ice_geometry_source=Weddell -Use_default_radius=True -Create_icebergs_bonds=False -break_some_bonds=False -plot_icebergs_positions=False
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/Weddell_sea_shelf_setup.py b/tests/Iceberg_repository/Scripts_and_analysis/Weddell_sea_shelf_setup.py
deleted file mode 100755
index ab2f704..0000000
--- a/tests/Iceberg_repository/Scripts_and_analysis/Weddell_sea_shelf_setup.py
+++ /dev/null
@@ -1,1398 +0,0 @@
-#!/usr/bin/env python
-
-#First import the netcdf4 library
-from netCDF4 import Dataset  # http://code.google.com/p/netcdf4-python/
-import numpy as np  # http://code.google.com/p/netcdf4-python/
-import matplotlib
-import math
-import os
-matplotlib.use("GTKAgg")
-from pylab import *
-#import matplotlib.pyplot as plt
-import pdb
-import netCDF4 as nc
-from scipy import interpolate
-from hexagon_area import Divide_hexagon_into_4_quadrants_old
-from hexagon_area import Hexagon_into_quadrants_using_triangles
-
-
-def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg):
-	
-	print 'Writing iceberg restart files...'
-	# To copy the global attributes of the netCDF file  
-
-	#Input and output files	
-	f=Dataset('input_files/icebergs.res.nc','r') # r is for read only
-	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w') # w if for creating a file
-
-	for attname in f.ncattrs():
-		    setattr(g,attname,getattr(f,attname))
-
-
-	# To copy the dimension of the netCDF file
-	for dimname,dim in f.dimensions.iteritems():
-		# if you want to make changes in the dimensions of the new file
-		# you should add your own conditions here before the creation of the dimension.
-		#g.createDimension(dimname,len(dim))
-		g.createDimension(dimname,Number_of_bergs)
-
-	# To copy the variables of the netCDF file
-
-	for varname,ncvar in f.variables.iteritems():
-		# if you want to make changes in the variables of the new file
-		# you should add your own conditions here before the creation of the variable.
-		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
-		#Proceed to copy the variable attributes
-		for attname in ncvar.ncattrs():  
-			setattr(var,attname,getattr(ncvar,attname))
-		#Finally copy the variable data to the new created variable
-		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
-		
-		if varname=='i':
-			var[:]=Number_of_bergs
-		
-		if varname=='iceberg_num':
-			for j in range(Number_of_bergs):
-				#var[j]=j+1
-				var[j]=iceberg_num[j]
-
-		if varname=='uvel' or varname=='vvel' or varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
-		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
-		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
-		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
-			var[:]=0
-
-		if varname=='mass_scaling':
-			var[:]=mass_scaling
-
-		if varname=='thickness':
-			for j in range(Number_of_bergs):
-				var[j]=thickness[j]
-		
-		if varname=='mass':
-			for j in range(Number_of_bergs):
-				var[j]=mass[j]
-
-		if varname=='width'  or varname=='length':
-			for j in range(Number_of_bergs):
-				var[j]=width[j]
-
-		if varname=='lon':
-			for j in range(Number_of_bergs):
-				var[j]=lon[j]
-
-		if varname=='lat':
-			for j in range(Number_of_bergs):
-				var[j]=lat[j]
-
-		if varname=='static_berg':
-			for j in range(Number_of_bergs):
-				var[j]=static_berg[j]
-
-
-	f.close()
-	g.close()
-
-	
-def Create_bond_restart_file(Number_of_bonds,first_berg_num,first_berg_ine,first_berg_jne,other_berg_ine,other_berg_jne,iceberg_num,other_berg_num,Ice_geometry_source):
-	#Creating the bond restart file
-
-	print 'Writing bond restart files...'
-	# To copy the global attributes of the netCDF file  
-
-	#Input and output files	
-	h=Dataset('input_files/bonds_iceberg.res.nc','r') # r is for read only
-	q=Dataset('output_files/' + Ice_geometry_source + '_bonds_iceberg.res.nc','w') # w if for creating a file
-
-	for attname in h.ncattrs():
-		    setattr(q,attname,getattr(h,attname))
-
-
-	# To copy the dimension of the netCDF file
-	for dimname,dim in h.dimensions.iteritems():
-		# if you want to make changes in the dimensions of the new file
-		# you should add your own conditions here before the creation of the dimension.
-		#g.createDimension(dimname,len(dim))
-		q.createDimension(dimname,Number_of_bonds)
-
-	# To copy the variables of the netCDF file
-
-	for varname,ncvar in h.variables.iteritems():
-		# if you want to make changes in the variables of the new file
-		# you should add your own conditions here before the creation of the variable.
-		var = q.createVariable(varname,ncvar.dtype,ncvar.dimensions)
-		#Proceed to copy the variable attributes
-		for attname in ncvar.ncattrs():  
-			setattr(var,attname,getattr(ncvar,attname))
-		#Finally copy the variable data to the new created variable
-		#var[:] = ncvar[0]
-		var[:] = 0.
-
-		if varname=='i':
-			var[:]=Number_of_bonds
-
-		if varname=='first_berg_num':
-			for j in range(Number_of_bonds):
-				var[j]=first_berg_num[j]
-
-		if varname=='first_berg_ine':
-			for j in range(Number_of_bonds):
-				var[j]=first_berg_ine[j]
-
-		if varname=='first_berg_jne':
-			for j in range(Number_of_bonds):
-				var[j]=first_berg_jne[j]
-
-		if varname=='other_berg_num':
-			for j in range(Number_of_bonds):
-				var[j]=other_berg_num[j]
-
-		if varname=='other_berg_ine':
-			for j in range(Number_of_bonds):
-				var[j]=other_berg_ine[j]
-
-		if varname=='other_berg_jne':
-			for j in range(Number_of_bonds):
-				var[j]=other_berg_jne[j]
-
-	h.close()
-	q.close()
-
-
-
-def Define_iceberg_thickness_and_mass(Number_of_bergs,dx_berg,dy_berg,h_ice_vec,xi,yi,rho_ice,Radius,x_ind_vec,y_ind_vec,h_ice,x,y,\
-		width,Interpolate_from_four_corners,element_area,element_type,Find_thickness_using_vector,static_berg):
-	thickness=[]
-	mass=[]
-	ny,nx=h_ice.shape
-	dx=x[1]-x[0]
-	grid_area=dx*dx
-	for berg_count in range(Number_of_bergs):
-		x_val=dx_berg[berg_count] ; y_val=dy_berg[berg_count]
-		R_ind=(abs(xi-x_val)+(abs(yi-y_val))).argmin()
-		i_val=floor(x_val/dx)
-		j_val=floor(y_val/dx)
-
-		#Interpolate thickness from 4 corners - possibly do this later, but I worry about when you are between a shelf and non shelf piece.
-		if Interpolate_from_four_corners==True:
-
-			x_cell=(x_val-x[i_val])/sqrt(grid_area)+0.5
-			y_cell=(y_val-y[j_val])/sqrt(grid_area)+0.5
-
-			mass_on_ocean=np.zeros([nx,ny,10])   #Setting up matrix to spread mass to ocean.  Note that I have used 10 points  so that I can ignore 0 and match with python numbering
-			mass_val=1.
-			mass_on_ocean=spread_mass_to_ocean(nx,ny,i_val,j_val,mass_on_ocean,x_cell,y_cell,element_area,mass_val,element_type,grid_area,static_berg[berg_count])
-			Th=0.
-			h=np.array([0,0,0,0,0,0,0,0,0,0])
-			if i_val>0 and j_val>0:
-				h[1]=h_ice[j_val-1,i_val-1]
-			if j_val>0:
-				h[2]=h_ice[j_val-1,i_val]
-			if j_val>0 and i_val<(nx-1):
-				h[3]=h_ice[j_val-1,i_val+1]
-			if i_val>0:
-				h[4]=h_ice[j_val,i_val-1]
-			if True:
-				h[5]=h_ice[j_val,i_val]
-			if i_val<(nx-1):
-				h[6]=h_ice[j_val,i_val+1]
-			if i_val>0 and j_val<(ny-1):
-				h[7]=h_ice[j_val+1,i_val-1]
-			if j_val<(ny-1):
-				h[8]=h_ice[j_val+1,i_val]
-			if i_val<(nx-1) and j_val<(ny-1):
-				h[9]=h_ice[j_val+1,i_val+1]
-			for k in range(1,10):
-				Th=Th+(mass_on_ocean[i_val,j_val,k]*h[k])
-				#print i_val,j_val,k,mass_on_ocean[i_val,j_val,k]
-			#if abs(Th-1)>0.0000001:
-			#	print 'Thickness',Th-1,i_val,j_val
-			#	test=0.
-			#	for k in range(1,10):
-			#		print k,mass_on_ocean[i_val,j_val,k], h[k]
-			#		test=test+(mass_on_ocean[i_val,j_val,k])
-			#	print test
-			#	halt
-				
-
-		elif Find_thickness_using_vector==True:
-			Th=h_ice_vec[R_ind][0]
-		else:#MP3
-			Th=h_ice[j_val,i_val]
-		thickness.append(Th)
-		#Check that all thicknesses are positive
-		if Th<=0:
-			print 'Thickness is less than or equal to zero,0!',i_val, j_val,x_val,y_val
-			halt
-		#mass.append(Th*rho_ice*element_area) 
-		mass.append(Th*rho_ice*(width[berg_count])**2) 
-		#if element_type=='square': 
-		#	mass.append(Th*rho_ice*((2*Radius)**2)) # For square elements
-		#else:
-		#	mass.append(Th*rho_ice*np.pi*(Radius**2))  #For circular elements
-	return [thickness, mass]
-
-def Create_distance_and_ice_mask_vector(x,y,ice_mask,h_ice,input_is_cartesian,R_earth,lat_ref,adjust_lat_ref):
-	N=len(x)  ; M = len(y)
-	x_min=np.min(x)  ;y_min=np.min(y)
-	count=-1
-	#R=np.zeros([N*M,1])
-	xi=np.zeros([N*M,1])
-	yi=np.zeros([N*M,1])
-	ice_mask_vec=np.zeros([N*M,1])
-	h_ice_vec=np.zeros([N*M,1])
-	x_ind_vec=np.zeros([N*M,1])
-	y_ind_vec=np.zeros([N*M,1])
-
-	#print N,M
-	for i in range(N):
-		for j in range(M):
-			count=count+1
-			if input_is_cartesian==True:
-				#R[count]=sqrt(((x[i]-x_min)**2) + ((y[j]-y_min)**2))
-				xi[count]=x[i]-x_min
-				yi[count]=y[j]-y_min
-			else:
-				#x and y are given in lon and lat
-				dlon=x[i]-x_min
-				dlat=y[j]-y_min
-				dy_dlat=(np.pi/180)*(R_earth)			
-				if adjust_lat_ref==True:
-					lat_ref=y[j]
-
-				dx_dlon=(np.pi/180)*(R_earth)*(np.cos(lat_ref*np.pi/180))
-				dx=dlon*dx_dlon
-				dy=dlat*dy_dlat
-				#R[count]=sqrt((dx**2)+(dy**2))
-				xi[count]=dx
-				yi[count]=dy
-			ice_mask_vec[count,0]=ice_mask[j,i]
-			h_ice_vec[count,0]=h_ice[j,i]
-			x_ind_vec[count,0]=i
-			y_ind_vec[count,0]=j
-			
-
-	ice_mask_vec[np.where(np.isnan(ice_mask_vec))]=0
-	#cNorm = mpl.colors.Normalize(vmin=-1., vmax=5.)
-	#plt.pcolor(x,y,ice_mask,norm=cNorm,cmap='jet')
-	#plt.scatter(x_temp, y_temp,c=ice_mask_vec[:,0],cmap='jet',norm=cNorm)
-	plt.show()
-
-	return [xi,yi, ice_mask_vec,h_ice_vec,x_ind_vec,y_ind_vec]
-
-
-def check_if_it_is_in_domain(x_val,y_val,x_min,x_max,y_min,y_max,input_is_cartesian,R_earth,lat_init,adjust_lat_ref,dx,dy):
-	point_is_in_domain=True
-	if input_is_cartesian==False:
-		dlat_dy=(180/np.pi)*(1/R_earth)
-		if adjust_lat_ref==True:
-			lat_ref=lat_init+(dlat_dy*y_val)
-		else:
-			lat_ref=y_max 
-		dlon_dx=(180/np.pi)*(1/R_earth)*(1/np.cos(lat_ref*np.pi/180))
-		x_val=(x_val*dlon_dx)
-		y_val=(y_val*dlat_dy)
-	
-	if (x_val >= (x_max-x_min+(dx))) or (x_val<= 0) or  (y_val >= (y_max-y_min+(dy))) or (y_val <= 0):
-		point_is_in_domain=False
-	#print 'x', x_val,  x_max
-	#print 'y', y_val,  y_max, floor(y_val/dx), floor(y_max/dx)
-	
-	return point_is_in_domain
-
-def check_if_it_is_ice(x_val,y_val,xi,yi,ice_mask_vec,ice_mask,input_is_cartesian,Find_thickness_using_vector,dx):
-	#R_val=np.sqrt(((x_val)**2) +((y_val)**2))
-	#R_ind=(abs(R-R_val)).argmin()
-	if Find_thickness_using_vector==True:
-		R_ind= (abs(x_val-xi) + abs(yi-y_val)).argmin()
-		if ice_mask_vec[R_ind]==1:
-			it_is_ice=True
-		else:
-			it_is_ice=False
-
-	else:
-		i_val=floor(x_val/dx)
-		j_val=floor(y_val/dx)
-		#print i_val,j_val,x_val,y_val
-		if ice_mask[j_val,i_val]==1.:
-			it_is_ice=True
-		else:
-			it_is_ice=False
-
-	return it_is_ice
-
-def calculate_element_area(element_type,Radius):
-	if element_type=='square':
-		element_area=(2*Radius)**2
-	elif element_type=='hexagon':
-		element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*(Radius)**2) #Area of hexagon around circle (used for packing)  
-		#Another derivation uses innner hexagon with two more triangles added, which is a 1/6 of the hexagon area each (two since there are 6, shared by 3 each)
-		#element_area=(4./3.)*H_i, where H_i=(3.*np.sqrt(3.)/2.)*((Radius)**2)  is the area of the inner hexagon (with sides equal to the radius)
-
-	return element_area
-
-def add_and_extra_boundary_berg(i,j,New_thickness,y_shift,x_shift,Nbh_thickness_value,Nbh_mass_value,New_mass,berg_count,dx_berg,dy_berg,\
-		iceberg_num,thickness,width,mass,static_berg,grid_area,rho_ice):
-	tol=0.0000000000001
-	if New_thickness[j,i]>1.+tol:
-		print 'The new thickness is too big!!!', i,j,  New_thickness[j,i]
-		halt
-	if ((Nbh_thickness_value-New_thickness[j,i])>tol):
-		y_val=y_shift[j]
-		x_val=x_shift[i]
-		if Nbh_thickness_value>0. and (abs(Nbh_thickness_value-1)<tol) and (Nbh_mass_value>New_mass[j,i]):
-			berg_count=berg_count+1
-			dx_berg.append(x_val)
-			dy_berg.append(y_val)
-			iceberg_num.append(berg_count)
-			width_val=np.sqrt((Nbh_thickness_value-New_thickness[j,i])*grid_area)
-			if Nbh_thickness_value-New_thickness[j,i]<0:
-				print 'Stop', Nbh_thickness_value, New_thickness[j,i],i,j
-			mass_val=Nbh_mass_value-New_mass[j,i]
-			thickness_val=mass_val/(width_val*width_val*rho_ice)
-			thickness.append(thickness_val)
-			width.append(width_val)
-			mass.append(mass_val)
-			static_berg.append(1.)
-	return [berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg]
-
-
-def add_extra_bergs_on_boundary(dx,dy,x,y,Number_of_bergs,element_area,rho_ice,X_min,X_max,Y_min,Y_max,input_is_cartesian,R_earth,lat_init,adjust_lat_ref,xi,yi,ice_mask_vec,ice_mask,\
-		iceberg_num,width,dx_berg,dy_berg,h_ice,element_type,Find_thickness_using_vector,static_berg,thickness,mass):
-	eps=0.000001
-	grid_area=dx*dy
-	Nx=len(x)  ; Ny=len(y)
-	x_shift=(x-np.min(x))+(dx/2) ; y_shift=(y-np.min(y))+(dy/2)
-
-	thickness_temp= [1. for i in range(Number_of_bergs)] ;
-	mass_temp= [element_area*rho_ice*1. for i in range(Number_of_bergs)] ;
-	New_area=regrid_iceberg_thickness(dy_berg,dx_berg,Number_of_bergs,thickness_temp,mass_temp,h_ice,x_shift,y_shift,rho_ice,element_type,static_berg,plot_outcome=False)
-	New_thickness=(New_area)/(rho_ice*grid_area)  #Should be equal to one everywhere where there is ice shelf.
-	New_mass=regrid_iceberg_thickness(dy_berg,dx_berg,Number_of_bergs,thickness,mass,h_ice,x_shift,y_shift,rho_ice,element_type,static_berg,plot_outcome=False)
-	berg_count=Number_of_bergs
-	
-	
-	#Vertical boundary
-	for i in np.array([0,Nx-1]):
-		#for j in range(Ny):
-		for j in range(1,Ny-1):
-			Nbh_mass_value=h_ice[j,i]*rho_ice*grid_area  #Neighbouring shelf value
-			if i==0:
-				Nbh_thickness_value=New_thickness[j,1]  #Neighbouring shelf value
-				#x_val=0+(eps*dx)
-			if i==Nx-1:
-				Nbh_thickness_value=New_thickness[j,Nx-2]  #Neighbouring shelf value
-				#x_val=x_shift[i]+(dx/2)-eps
-			[berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg]=add_and_extra_boundary_berg(i,j,New_thickness,y_shift,x_shift,\
-					Nbh_thickness_value,Nbh_mass_value,New_mass,berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg,grid_area,rho_ice)
-
-	##Horizontal boundary
-	for j in np.array([0,Ny-1]):
-		#for i in range(1,Nx-1):
-		for i in range(1,Nx-1):
-			Nbh_mass_value=h_ice[j,i]*rho_ice*grid_area  #Neighbouring shelf value
-			if j==0:
-				Nbh_thickness_value=New_thickness[1,i]  #Neighbouring shelf value
-				#y_val=0+(eps*dy)
-			if j==Ny-1:
-				Nbh_thickness_value=New_thickness[Ny-2,i]  #Neighbouring shelf value
-				#y_val=y_shift[j]+(dy/2)-eps
-			#Nbh_thickness_value=np.mean(New_thickness[range(1,Ny-1),i])  #Neighbouring shelf value
-			[berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg]=add_and_extra_boundary_berg(i,j,New_thickness,y_shift,x_shift,\
-					Nbh_thickness_value,Nbh_mass_value,New_mass,berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg,grid_area,rho_ice)
-
-	#Doing the corners seperately
-	for j in np.array([0,Ny-1]):
-		#for i in range(1,Nx-1):
-		for i in np.array([0,Nx-1]):
-			Nbh_mass_value=h_ice[j,i]*rho_ice*grid_area  #Neighbouring shelf value
-			if j==0 and i==0:
-				Nbh_thickness_value=New_thickness[1,1]  #Neighbouring shelf value
-			if j==0 and i==Nx-1:
-				Nbh_thickness_value=New_thickness[1,Nx-2]  #Neighbouring shelf value
-			if j==Ny-1 and i==0:
-				Nbh_thickness_value=New_thickness[Ny-2,1]  #Neighbouring shelf value
-			if j==Ny-1 and i==Nx-1:
-				Nbh_thickness_value=New_thickness[Ny-2,Nx-2]  #Neighbouring shelf value
-			[berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg]=add_and_extra_boundary_berg(i,j,New_thickness,y_shift,x_shift,\
-					Nbh_thickness_value,Nbh_mass_value,New_mass,berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg,grid_area,rho_ice)
-
-
-	Number_of_bergs=berg_count
-	
-	return [dx_berg, dy_berg,iceberg_num, width,Number_of_bergs,static_berg,thickness,mass]
-
-
-def remove_stationary_bergs(dx_berg, dy_berg,iceberg_num,width,Number_of_bergs,static_berg):
-	dx_berg_new=[]
-	dy_berg_new=[]
-	iceberg_num_new=[]
-	width_new=[]
-	static_berg_new=[]
-	for i in range(Number_of_bergs):
-		if static_berg[i]<0.5:
-			dx_berg_new.append(dx_berg[i])
-			dy_berg_new.append(dy_berg[i])
-			iceberg_num_new.append(iceberg_num[i])
-			width_new.append(width[i])
-			static_berg_new.append(static_berg[i])
-
-	Number_of_bergs_new=len(iceberg_num_new)
-	return [dx_berg_new, dy_berg_new,iceberg_num_new, width_new,Number_of_bergs_new,static_berg_new]
-
-def Create_icebergs(lon_init,lat_init,Radius,R_earth, x, y,ice_mask,h_ice,Convert_to_lat_lon,rho_ice,input_is_cartesian,\
-		element_type,scale_the_grid_to_lat_lon,lat_ref,adjust_lat_ref,Interpolate_from_four_corners,\
-		Fill_in_the_boundaries,set_all_bergs_static_by_default,break_some_bonds,Find_thickness_using_vector,Remove_stationary_bergs):
-	print 'Starting to create icebergs...'
-	dx_berg=[]  #x distance in cartesian of berg from lon_init
-	dy_berg=[]  #y distance in cartesian of berg from lat_init
-	dlon_berg=[] #x distance in lon of berg from lon_init
-	#dlat_berg=[] #y distance in lat of berg from lat_init
-	lon=[] #Longitude of iceberg
-	lat=[] #Latitude of iceberg
-	iceberg_num=[] #ID of iceberg
-	
-	element_area=calculate_element_area(element_type,Radius)
-	#width=np.sqrt(element_area)
-	width=[]
-	
-	#Create a vector of distances from a minimum point.
-	(xi,yi,ice_mask_vec,h_ice_vec,x_ind_vec,y_ind_vec)=Create_distance_and_ice_mask_vector(x,y,ice_mask,h_ice,input_is_cartesian,R_earth,lat_ref,adjust_lat_ref)
-	
-	#dx=x[1]-x[0]  ;dy=y[1]-y[0]
-	#X_min=np.min(x)-dx; X_max=np.max(x)+dx  #In lat lon or cartesian
-	#Y_min=np.min(y)-dy; Y_max=np.max(y)+dy  #In lat lon or cartesian
-	X_min=np.min(x); X_max=np.max(x)  #In lat lon or cartesian
-	Y_min=np.min(y); Y_max=np.max(y)  #In lat lon or cartesian
-
-	#N=2*int(ceil((R_max)/(2*Radius))+2)
-	
-	if element_type=='square':
-		#N=int(ceil((np.max(xi))/(2*Radius))+2) +2
-		#M=int(ceil((np.max(yi))/(2*Radius))+2) +2
-		N=int(ceil((X_max-X_min)/(Radius)))
-		M=int(ceil((Y_max-Y_min)/(Radius)))
-	else:
-		#N=int(ceil((np.max(xi))/(Radius/2))+2) +2
-		#M=int(ceil((np.max(yi))/((1/sqrt(3))*Radius/2))+2) +2
-		N=2*int(ceil((X_max-X_min)/(Radius)))
-		M=2*int(ceil((Y_max-Y_min)/(Radius)))
-	#N=10
-	#M=6
-	#MP4
-
- 	dx=x[1]-x[0]	
- 	dy=y[1]-y[0]
-	Lx=X_max+dx
-	Ly=Y_max+dx
-
-	berg_count=0
-	#for j in range(N):
-	for i in range(N):
-		if element_type=='square':
-			x_start=Radius
-			y_start=(Radius)
-			x_val=x_start+(2*i*Radius)
-
-		#Hexagonal	
-		else:   
-			y_start=(Radius)+(((i%2)*Radius))
-			x_start=((2/sqrt(3))*Radius)
-			x_val=x_start + (np.sqrt(3)*Radius*i)
-
-		for j in range(M):
-		#for i in range(M):
-			#x_val=x_start+(2*i*Radius)  ; y_val=y_start
-			y_val=y_start+(2*j*Radius)  ;# x_val=x_start + (np.sqrt(3)*Radius*i)
-			if check_if_it_is_in_domain(x_val,y_val,X_min,X_max,Y_min,Y_max,input_is_cartesian,R_earth,lat_init,adjust_lat_ref,dx,dy):
-			#if True:
-				#R_val=np.sqrt(((x_val-x0)**2) +((y_val-y0)**2))
-				if check_if_it_is_ice(x_val,y_val,xi,yi,ice_mask_vec,ice_mask,input_is_cartesian,Find_thickness_using_vector,dx):
-					#Don't allow points closer than R from the boundary (these are sorted out later)
-					#if abs(y_val-Ly)<Radius or  ((abs(x_val-Lx)<((2/sqrt(3))*Radius)) and element_type=='hexagon') or ((abs(x_val-Lx)<Radius) and element_type=='square'):
-					berg_count=berg_count+1
-					iceberg_num.append(berg_count)
-					dx_berg.append(x_val)
-					dy_berg.append(y_val)
-					width.append(np.sqrt(element_area))
-
-	Number_of_bergs=berg_count
-	print 'Icebergs created. Number of bergs = ', Number_of_bergs
-	
-	#Deciding if icebergs are static or not
-	static_berg = [0. for i in dx_berg]
-	if set_all_bergs_static_by_default==True:
-		static_berg = [1. for i in static_berg]
-	if break_some_bonds==True:
-		#static_berg =Change_static_berg_after_calving(Number_of_bergs,lat,lon, static_berg)
-		static_berg =Change_static_berg_after_calving(Number_of_bergs,dy_berg,dx_berg, static_berg)
-		static_berg=static_berg[0]
-		
-	if Remove_stationary_bergs is True:
-		Fill_in_the_boundaries=False
-		[dx_berg, dy_berg,iceberg_num, width,Number_of_bergs,static_berg]=remove_stationary_bergs(dx_berg, dy_berg,iceberg_num,\
-				width,Number_of_bergs,static_berg)
-		print 'After purge  Number of bergs = ', Number_of_bergs
-
-
-	#Defining the thickness of the icebergs
-	(thickness, mass)=Define_iceberg_thickness_and_mass(Number_of_bergs,dx_berg,dy_berg,h_ice_vec,xi,yi,rho_ice,Radius,x_ind_vec,y_ind_vec, h_ice,x,y,\
-			width,Interpolate_from_four_corners,element_area,element_type,Find_thickness_using_vector,static_berg)	
-
-	N_bergs_before_bd=Number_of_bergs
-	if Fill_in_the_boundaries==True and element_type=='hexagon':
-	 	[dx_berg, dy_berg,iceberg_num, width,Number_of_bergs,static_berg,thickness,mass]= add_extra_bergs_on_boundary(dx,dy,x,y,Number_of_bergs,element_area,rho_ice,X_min,X_max,Y_min,\
-				Y_max,input_is_cartesian,R_earth,lat_init,adjust_lat_ref,xi,yi,ice_mask_vec,ice_mask,iceberg_num,width,dx_berg,dy_berg,\
-				h_ice,element_type,Find_thickness_using_vector,static_berg,thickness,mass)
-		print 'Number of icebergs after accounting for boundaries = ', Number_of_bergs
-	
-
-
-	if Convert_to_lat_lon==True:
-		#Defining lon lat positions:
-		#dlat_berg=(180/np.pi)*(1/R_earth)*dy_berg
-		#dlon_berg=(180/np.pi)*(1/R_earth)*(1/cos(lat_init*np.pi/180))*dx_berg
-		for i in range(Number_of_bergs):
-			#Finding latittude
-			dlat_dy=(180/np.pi)*(1/R_earth)
-
-			lat.append(lat_init+(dlat_dy*dy_berg[i]))
-
-			#Finding longitude
-			if adjust_lat_ref==True:
-				lat_ref=lat_init+(dlat_dy*dy_berg[i])
-			dlon_dx=(180/np.pi)*(1/R_earth)*(1/np.cos(lat_ref*np.pi/180)) #Note that this depends on the latitude of the iceberg. Could approx this with lat_init.
-			lon.append(lon_init+(dlon_dx*dx_berg[i] ))
-
-			#dlon_berg.append(dlon_dx*dx_berg[i])
-			#lon.append(lon_init+dlon_berg[i])
-	else:
-		if scale_the_grid_to_lat_lon==True:
-			Scale_up=1./2000.
-			Radius=Radius*Scale_up
-			dx_berg = [(i*Scale_up) for i in dx_berg] ; dy_berg = [i*Scale_up for i in dy_berg] 
-			x=x*Scale_up ; y=y*Scale_up
-			dx=dx*Scale_up ;dy=dy*Scale_up
-		x=(x-np.min(x))+(dx/2) ; y=(y-np.min(y))+(dy/2)
-		lon=dx_berg  ; lat=dy_berg
-	
-	#Note that static_berg calculations used to be here, after the conversion. I have moved them. I hope that this does not affect answers.
-
-	return (Number_of_bergs,lon,lat,iceberg_num,dx_berg,dy_berg,thickness, mass,width,x,y,Radius,static_berg,N_bergs_before_bd)
-
-
-
-def Create_calving_event(lat1,lon1,lat2,lon2):
-	[R_calve, Calve_lon, Calve_lat]=get_calving_parameters()
-	
-	R1=np.sqrt((lon1-Calve_lon)**2+ (lat1-Calve_lat)**2)
-	R2=np.sqrt((lon2-Calve_lon)**2+ (lat2-Calve_lat)**2)
-
-	bond_broken=False
-	if ((R1 < R_calve)*(R2>R_calve) )  > 0.5 :
-		bond_broken=True
-	if ((R2 < R_calve)*(R1>R_calve) )  > 0.5 :
-		bond_broken=True
-
-	return bond_broken
-
-def get_calving_parameters():
-	#Calve_lat =20  
-	#Calve_lon=160
-	#R_calve=15
-	Calve_lat =20.2*2000  
-	Calve_lon=160*2000
-	R_calve=15*2000
-	#R_calve=1.*2000.
-	
-	return [R_calve, Calve_lon, Calve_lat]
-
-def Change_static_berg_after_calving(Number_of_bergs,lat,lon, static_berg):
-	[R_calve, Calve_lon, Calve_lat]=get_calving_parameters()
-	count=0.
-	for i in range(Number_of_bergs):
-		R1=np.sqrt((lon[i]-Calve_lon)**2+ (lat[i]-Calve_lat)**2)
-		#Making calved icebergs not be static.
-		if R1<R_calve:
-			count=count+1.
-			#print 'An iceberg is now static!'
-			static_berg[i]=0.
-	print 'Amount of unstatic icebergs after calving = ', count
-
-	return [static_berg]
-
-def find_max_number_of_bonds(first_berg_num,Number_of_bonds):
-	count=1
-	best_count=1
-	sorted_bonds=np.sort(first_berg_num)
-	for k in range(1,Number_of_bonds):
-		previous_berg=sorted_bonds[k-1]
-		print k, sorted_bonds[k]
-		if sorted_bonds[k] == sorted_bonds[k-1]:
-			count=count+1
-			best_count=max(count,best_count)
-		else:
-			count=1
-	Max_number_of_bonds=best_count
-	return Max_number_of_bonds
-
-def Define_iceberg_bonds(Number_of_bergs,iceberg_num,lat,lon,dx_berg, dy_berg,Radius,break_some_bonds,static_berg, Allow_bonds_for_static_iceberg\
-		,N_bergs_before_bd,Allow_bonds_with_boundary_bergs):
-	print 'Starting to create bonds...'
-	#Defining Bonds:
-	Bond=np.zeros((Number_of_bergs, Number_of_bergs))
-	bond_broken=False
-	first_berg_num=[]  # Initializing bond list first berg
-	first_berg_ine=[]  # Initializing bond list first berg
-	first_berg_jne=[]  # Initializing bond list first berg
-	first_berg_lat=[]  # Initializing bond list first berg
-	first_berg_lon=[]  # Initializing bond list first berg
-	other_berg_num=[]  # Initializing bond list other berg
-	other_berg_ine=[]  # Initializing bond list other berg
-	other_berg_jne=[]  # Initializing bond list other berg
-	other_berg_lat=[]  # Initializing bond list other berg
-	other_berg_lon=[]  # Initializing bond list other berg
-	bond_count=0
-	for i in range(Number_of_bergs):
-		if (static_berg[i]<0.5) or (Allow_bonds_for_static_iceberg is True):
-			#for j in range(Number_of_bergs):
-			for j in range(i):
-				if (static_berg[j]<0.5) or (Allow_bonds_for_static_iceberg is True):
-					if i!=j:
-						if ((i <N_bergs_before_bd) and (j <N_bergs_before_bd))  or (Allow_bonds_with_boundary_bergs is True):
-							R_dist=np.sqrt(((dx_berg[i]-dx_berg[j])**2) + ((dy_berg[i]-dy_berg[j])**2))
-							if break_some_bonds==True:
-								bond_broken=Create_calving_event(lat[i],lon[i],lat[j],lon[j])
-							if R_dist < (2.01*Radius) and (bond_broken==False):
-								bond_count=bond_count+2
-								#Connect bond in the first direction
-								first_berg_num.append(iceberg_num[i]);	first_berg_ine.append(999); 
-								other_berg_num.append(iceberg_num[j]); 	other_berg_ine.append(999);
-								first_berg_jne.append(999);first_berg_lat.append(lat[i]); first_berg_lon.append(lon[i])
-								other_berg_jne.append(999);other_berg_lat.append(lat[j]); other_berg_lon.append(lon[j])
-								#Connect bond in the other direction
-								first_berg_num.append(iceberg_num[j]);	first_berg_ine.append(999);
-								other_berg_num.append(iceberg_num[i]); 	other_berg_ine.append(999);
-								first_berg_jne.append(999);first_berg_lat.append(lat[j]); first_berg_lon.append(lon[j])
-								other_berg_jne.append(999);other_berg_lat.append(lat[i]); other_berg_lon.append(lon[i])
-	Number_of_bonds=bond_count
-	Max_number_of_bonds=find_max_number_of_bonds(first_berg_num,Number_of_bonds)
-	print 'Number of bonds created = ' , Number_of_bonds
-	print 'Maximum number of bonds = ' ,  Max_number_of_bonds
-
-	return [ Number_of_bonds, first_berg_num,first_berg_ine,first_berg_jne,first_berg_lat,first_berg_lon, other_berg_num,other_berg_ine, other_berg_jne,other_berg_lat,other_berg_lon]
-
-def load_ISOMIP_ice_geometry(filename,buffer_number):
-	with nc.Dataset(filename) as file:
-		ocean_mask = file.variables['openOceanMask'][:,:]
-		upperSurface = file.variables['upperSurface'][:,:]
-		lowerSurface = file.variables['lowerSurface'][:,:]
-		x = file.variables['x'][:]
-		y = file.variables['y'][:]
-
-	ice_mask=1-ocean_mask #one if it ice, zero if it is ocean
-	h_ice=upperSurface-lowerSurface #The ice thickness
-	M=ice_mask.shape
-
-	#Setting the boundaries to non-ice
-	A=np.arange(0,buffer_number)
-	B=np.arange(M[0]-buffer_number,M[0])
-	C=np.arange(M[1]-buffer_number,M[1])
-	ice_mask[A,:]=0; ice_mask[B,:]=0
-	ice_mask[:,A]=0; ice_mask[:,C]=0
-	
-	return [x,y,ice_mask,h_ice]
-
-
-def create_clipped_icethickness_file(h_ice,area,mass,grid_area,gravity):
-	#Creating clipped file
-        [ny, nx]= h_ice.shape ; 
-	
-	New_ice_thickness_filename='output_files/isomip_ice_shelf1_clipped.nc'
-        g=Dataset(New_ice_thickness_filename,'w') # w if for creating a file
-
-        g.createDimension('nx',nx)
-        g.createDimension('ny',ny)
-
-        thick_h=g.createVariable('thick','f8',('ny','nx'))
-        area_h=g.createVariable('area','f8',('ny','nx'))
-        p_surf_h=g.createVariable('p_surf','f8',('ny','nx'))
-
-        thick_h.units = 'm'
-        thick_h.standard_name = 'ice shelf thickness (clipped)'
-        area_h.units = 'm2'
-        area_h.standard_name = 'ice shelf area'
-        p_surf_h.units = 'Pa'
-        p_surf_h.standard_name = 'surface pressure due to ice shelf'
-
-	p_surf=(gravity*mass)/grid_area
-        g.variables['thick'][:]=h_ice
-        g.variables['area'][:]=area
-        g.variables['p_surf'][:]=p_surf
-        print 'Creating clipped ice file: ' , New_ice_thickness_filename
-        
-        g.sync()
-        g.close()
-
-
-def load_ISOMIP_reduced_ice_geometry(ice_filename,buffer_number,topog_filename):
-	with nc.Dataset(ice_filename) as file:
-		h_ice = file.variables['thick'][:,:]
-		area =  file.variables['area'][:,:]
-		M=h_ice.shape
-
-	y=np.linspace(1000,79000,M[0],endpoint=True)
-	#x=np.linspace(321000,799000,M[1],endpoint=True)
-	x=np.linspace(1000,479000,M[1],endpoint=True)
-	ice_mask=h_ice>0.
-
-
-	count=0. #MP1
-	#Setting the boundaries to non-ice
-	A=np.arange(0,buffer_number)
-	B=np.arange(M[0]-buffer_number,M[0])
-	C=np.arange(M[1]-buffer_number,M[1])
-	#if buffer_number>0:
-	ice_mask[A,:]=0; ice_mask[B,:]=0
-	ice_mask[:,A]=0; ice_mask[:,C]=0
-	
-	return [x,y,ice_mask,h_ice]
-
-def load_Weddel_ice_geometry(filename):
-	with nc.Dataset(filename) as file:
-		h_ice = file.variables['thickness'][:,:]
-		ice_mask = file.variables['icemask_grounded_and_shelves'][:,:]
-		x = file.variables['lon'][:]
-		y = file.variables['lat'][:]
-		ice_mask[np.where(ice_mask<-1)]=0.
-		
-		h_ice[np.where(np.isnan(h_ice))]=0.
-		ice_mask[np.where(np.isnan(ice_mask))]=0.
-
-		#ice_mask=1-ocean_mask #one if it ice, zero if it is ocean
-	
-	return [x,y,ice_mask,h_ice]
-
-def Select_just_one_berg(lon,lat,thickness,width,mass,iceberg_num,chosen_berg_num,static_berg):
-	print 'You have chosen to choose just one icebergs!!!'
-	for k in range(len(lat)):
-		if iceberg_num[k]==chosen_berg_num:
-			berg_ind=k
-	lon_temp=lon[berg_ind]; lon=[] ; lon.append(lon_temp)
-	lat_temp=lat[berg_ind]; lat=[] ; lat.append(lat_temp)
-	thickness_temp=thickness[berg_ind]; thickness=[] ; thickness.append(thickness_temp)
-	mass_temp=mass[berg_ind]; mass=[] ; mass.append(mass_temp)
-	width_temp=width[berg_ind]; width=[] ; width.append(width_temp)
-	static_berg_temp=static_berg[berg_ind]; static_berg=[] ; static_berg.append(static_berg_temp)
-	iceberg_num_temp=iceberg_num[berg_ind]; iceberg_num=[] ; iceberg_num.append(iceberg_num_temp)
-	Number_of_bergs=1
-	return [Number_of_bergs,lon,lat,thickness,width,mass,iceberg_num]
-
-def plotting_iceberg_positions(lat,lon,Number_of_bergs,R_earth,Radius,IA_scaling,Convert_to_lat_lon, \
-		plot_circles,h_ice,ice_mask,x,y,plot_ice_mask,plot_ice_thickness,thickness,plot_icebergs_positions,static_berg):
-	print 'Starting to plot...'	
-	Radius=Radius*IA_scaling
-	circ_ind=np.linspace(0,2*pi,100);
-
-	if plot_ice_mask==True:
-		cNorm = mpl.colors.Normalize(vmin=0., vmax=1.)
-		plt.pcolormesh(x,y,ice_mask,norm=cNorm)
-	elif plot_ice_thickness==True:
-		cNorm = mpl.colors.Normalize(vmin=0., vmax=1000.)
-		plt.pcolor(x,y,h_ice,cmap='jet',norm=cNorm)
-
-
-	if plot_icebergs_positions==True:
-		#plt.scatter(lon, lat,color='yellow')
-		#cNorm = mpl.colors.Normalize(vmin=0., vmax=1000.)
-		plt.scatter(lon, lat,c=thickness,norm=cNorm,cmap='jet',s=150)
-		cNorm = mpl.colors.Normalize(vmin=-1, vmax=1.)
-		#plt.scatter(lon, lat,c=static_berg,norm=cNorm,cmap='jet',s=150)
-
-	#plt.plot(lon, lat,'bo-',linewidth=5)
-	if plot_circles==True:
-		for k in range(Number_of_bergs):
-			if Convert_to_lat_lon==True:
-				dR_lat=(Radius/R_earth)*(180/np.pi)
-				dR_lon=(Radius/R_earth)*(180/np.pi)*(1/np.cos(lat[k]*np.pi/180))
-				plt.plot(lon[k]+(dR_lon*cos(circ_ind)),lat[k]+(dR_lat*sin(circ_ind)),'b');
-			else:
-				plt.plot(lon[k]+(Radius*cos(circ_ind)),lat[k]+(Radius*sin(circ_ind)),'b');
-
-
-
-	#plt.plot(lon, lat,'bo-')
-	if Convert_to_lat_lon==True:
-		plt.xlabel('longitude (deg)')
-		plt.ylabel('latitude (deg)')
-	else:
-		plt.xlabel('longitude (m)')
-		plt.ylabel('latitude (m)')
-	plt.title('Iceberg initial positions')
-	plt.grid(True)
- 	plt.colorbar()
-
-
-def plotting_iceberg_bonds(first_berg_lat,first_berg_lon,other_berg_lat,other_berg_lon,Number_of_bonds):
-
-	for k in range(Number_of_bonds):
-		x_bond=[]
-		y_bond=[]
-		x_bond.append(first_berg_lon[k])
-		x_bond.append(other_berg_lon[k])
-		y_bond.append(first_berg_lat[k])
-		y_bond.append(other_berg_lat[k])
-		plt.plot(x_bond, y_bond,'r',linewidth=5)
-
-
-def spread_mass_to_ocean(Nx,Ny,i,j,mass_on_ocean,x,y,Area,Mass,element_type,grid_area,static_berg):
-		#Note that the x,y coming into this routine are the position within a cell (from 0 to 1), with 0.5,0.5 being in the center of the cell.
-
-		#Initialize weights for each cell	
-		yDxL=0.  ; yDxC=0. ; yDxR=0. ; yCxL=0. ; yCxR=0. 
-		yUxL=0.  ; yUxC=0. ; yUxR=0. ; yCxC=1.
-
-		if element_type=='square':
-		#if True:
-			L = min(( (np.sqrt(Area)  / np.sqrt(grid_area))),1) ;  #Non dimensionalize element length by grid area. (This gives the non-dim length of the square)
-			xL=min(0.5, max(0., 0.5-(x/L)))
-			xR=min(0.5, max(0., (x/L)+(0.5-(1/L) )))
-			xC=max(0., 1.-(xL+xR))
-			yD=min(0.5, max(0., 0.5-(y/L)))
-			yU=min(0.5, max(0., (y/L)+(0.5-(1/L) )))
-			yC=max(0., 1.-(yD+yU))
-
-			yDxL=yD*xL#*grd%msk[i-1,j-1]
-			yDxC=yD*xC#*grd%msk[i  ,j-1]
-			yDxR=yD*xR#*grd%msk[i+1,j-1]
-			yCxL=yC*xL#*grd%msk[i-1,j  ]
-			yCxR=yC*xR#*grd%msk[i+1,j  ]
-			yUxL=yU*xL#*grd%msk[i-1,j+1]
-			yUxC=yU*xC#*grd%msk[i  ,j+1]
-			yUxR=yU*xR#*grd%msk(i+1,j+1]
-			yCxC=1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )
-
-		if element_type=='hexagon':
-		#if False:#element_type=='hexagon':
-			H = min(( (np.sqrt(Area/(2*sqrt(3)))  / np.sqrt(grid_area))),1) ;  #Non dimensionalize element length by grid area. (This gives the non-dim Apothen of the hexagon)
-			S=(2/np.sqrt(3))*H #Side of the hexagon
-			if S>0.5:
-				print 'Elements must be smaller than a whole gridcell', 'i.e.: S= ' , S , '>=0.5',i,j
-				halt
-
-			#Subtracting the position of the nearest corner from x,y
-			origin_x=1 ; origin_y=1
-			if x<0.5:
-				origin_x=0
-			if y<0.5:
-				origin_y=0
-
-			x0=(x-origin_x) #Position of the hexagon center, relative to origin at the nearest vertex
-			y0=(y-origin_y)
-			
-			#(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Divide_hexagon_into_4_quadrants_old(x0,y0,H)
-			(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Hexagon_into_quadrants_using_triangles(x0,y0,H,0.)
-			if min(min(Area_Q1,Area_Q2),min(Area_Q3, Area_Q4)) <0:
-				print 'Yolo'
-				print x0,y0,H
-				#print min(min(Area_Q1,Area_Q2),min(Area_Q3, Area_Q4))
-				print Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
-
-			Area_Q1=Area_Q1/Area_hex
-			Area_Q2=Area_Q2/Area_hex
-			Area_Q3=Area_Q3/Area_hex
-			Area_Q4=Area_Q4/Area_hex
-
-
-			#Now, you decide which quadrant belongs to which mass on ocean cell.
-			#Top right vertex
-			if x>=0.5 and y>= 0.5:
-				yUxR=Area_Q1
-				yUxC=Area_Q2
-				yCxC=Area_Q3
-				yCxR=Area_Q4
-			
-			#Top left vertex
-			if x<0.5 and y>= 0.5:
-				yUxC=Area_Q1
-				yUxL=Area_Q2
-				yCxL=Area_Q3
-				yCxC=Area_Q4
-			
-			#Bottom left vertex
-			if x<0.5 and y< 0.5:
-				yCxC=Area_Q1
-				yCxL=Area_Q2
-				yDxL=Area_Q3
-				yDxC=Area_Q4
-
-			#Bottom right vertex
-			if x>=0.5 and y< 0.5:
-				yCxR=Area_Q1
-				yCxC=Area_Q2
-				yDxC=Area_Q3
-				yDxR=Area_Q4
-
-			#if Sector<4 and Sector>-1:
-			#	print Sector
-				
-					
-			#Check that this is true
-			if abs(yCxC-(1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )))>0.001:
-				print 'All the mass is not being used!!!'
-				#print W1 , W2 , W3 , W4 , W5 , W6
-				#print Area_Upper, Area_Lower, Area_right, Area_left
-				print 'Areas: ',Area_hex,Area_hex*Area_Q1, Area_hex*Area_Q2, Area_hex*Area_Q3, Area_hex*Area_Q4
-				print 'x0=',x0, 'y0=',y0, 'H=', H
-				print 'Total area= ',(Area_Q1+Area_Q2+Area_Q3+Area_Q4)#, Sector
-				
-
-		#Accounting for masked points 
-		a=1. ; b=1. ; c=1. ; d=1.
-		if i==0:
-			a=0.;
-		if j==0: 
-			b=0.;
-		if i==Nx-1:
-			c=0;
-		if j==Ny-1:
-			d=0;
-
-		fraction_used= ((yDxL*a*b) + (yDxC*b) + (yDxR*b*c) +(yCxL*a) + (yCxR*c) + (yUxL*a*d) + (yUxC*d) + (yUxR*c*d) + (yCxC))
-		if static_berg>0.5:
-			fraction_used=1.
-
-		mass_on_ocean[i,j,1]=mass_on_ocean[i,j,1]+(a*b*yDxL*Mass/fraction_used)
-		mass_on_ocean[i,j,2]=mass_on_ocean[i,j,2]+(b*yDxC*Mass/fraction_used)
-		mass_on_ocean[i,j,3]=mass_on_ocean[i,j,3]+(b*c*yDxR*Mass/fraction_used)
-		mass_on_ocean[i,j,4]=mass_on_ocean[i,j,4]+(a*yCxL*Mass/fraction_used)
-		mass_on_ocean[i,j,5]=mass_on_ocean[i,j,5]+(yCxC*Mass/fraction_used)
-		mass_on_ocean[i,j,6]=mass_on_ocean[i,j,6]+(c*yCxR*Mass/fraction_used)
-		mass_on_ocean[i,j,7]=mass_on_ocean[i,j,7]+(a*d*yUxL*Mass/fraction_used)
-		mass_on_ocean[i,j,8]=mass_on_ocean[i,j,8]+(d*yUxC*Mass/fraction_used)
-		mass_on_ocean[i,j,9]=mass_on_ocean[i,j,9]+(c*d*yUxR*Mass/fraction_used)
-
-
-		return mass_on_ocean
-
-
-def calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x, y, Lx):
-
-	Lx_2=Lx/2.
-  
-	alpha=x2-x1
-	delta=y2-y1
-	beta=x4-x1
-	epsilon=y4-y1
-	gamma=(x3-x1)-(alpha+beta)
-	kappa=(y3-y1)-(delta+epsilon)
-
-	a=(kappa*beta-gamma*epsilon)
-	dx=np.mod(x-(x1-Lx_2),Lx)+(x1-Lx_2)-x1
-	dy=y-y1
-	b=(delta*beta-alpha*epsilon)-(kappa*dx-gamma*dy)
-	c=(alpha*dy-delta*dx)
-	
-	#print 'alpha,beta,gamma',alpha,beta,gamma
-	#print 'delta,epsilon,kappa',delta,epsilon,kappa
-	#print 'dx,dy',dx,dy
-	#print 'A,B,C,',a,b,c
-
-	if (abs(a)>1.e-12):
-		d=0.25*(b**2)-a*c
-		if (d>=0.):
-			yy1=-(0.5*b+sqrt(d))/a
-			yy2=-(0.5*b-sqrt(d))/a
-			if (abs(yy1-0.5).lt.abs(yy2-0.5)):
-				yj=yy1;
-			else:
-				yj=yy2;
-    		else:
-			print 'ERROR', halt
-	else:
-		if (b!=0.):
-			yj=-c/b
-		else:
-			yj=0.
-
-	a=(alpha+gamma*yj)
-	b=(delta+kappa*yj)
-	if (a!=0.):
-		xi=(dx-beta*yj)/a
-	elif (b!=0.):
-		xi=(dy-epsilon*yj)/b
-	else:
-		c=(epsilon*alpha-beta*delta)+(epsilon*gamma-beta*kappa)*yj
-		if (c!=0.):
-			xi=(epsilon*dx-beta*dy)/c
-		else:
-			print 'ERROR', halt2
-
-	return xi,yj
-
-
-
-def regrid_iceberg_thickness(lat,lon,Number_of_bergs,thickness,mass,h_ice,x,y,rho_ice,element_type,static_berg,plot_outcome=True):
-	Nx=len(x)  ; Ny=len(y)
-	dx=x[1]-x[0]    ;dy=y[1]-y[0]
-	New_mass=h_ice*0 #Initializing regrided field to zero
-	Area = [(mass[i]/(rho_ice*thickness[i])) for i in range(Number_of_bergs)] ;
-	grid_area=dx*dy #Assuming a regular grid
-	Orig_mass=h_ice*rho_ice*grid_area
-	
-	mass_on_ocean=np.zeros([Nx,Ny,10])   #Setting up matrix to spread mass to ocean.  Note that I have used 10 points  so that I can ignore 0 and match with python numbering
-	#mass_on_ocean=np.zeros([Nx,Ny])   #Setting up matrix to spread mass to ocean.
-	#Note: You may want to import the grid that the ocean model actually sees.
-	for berg_count in range(Number_of_bergs):  
-		x_val=lon[berg_count]  
-		y_val=lat[berg_count]
-		Area_val=Area[berg_count]
-		mass_val=mass[berg_count]
-
-		j_val=floor(y_val/dy)
-		i_val=floor(x_val/dx)
-		x_cell=(x_val-x[i_val])/sqrt(grid_area)+0.5
-		y_cell=(y_val-y[j_val])/sqrt(grid_area)+0.5
-		mass_on_ocean=spread_mass_to_ocean(Nx,Ny,i_val,j_val,mass_on_ocean,x_cell,y_cell,Area_val,mass_val,element_type,grid_area,static_berg[berg_count])
-
-	#Adding mass_onto_ocean
-	for i in range(1,Nx-1):
-		for j in range(1,Ny-1):
-			New_mass[j,i]=mass_on_ocean[i,j,5]  \
-					+  ( ( (mass_on_ocean[i-1,j-1,9]+mass_on_ocean[i+1,j+1,1])   \
-					+  (mass_on_ocean[i+1,j-1,7]+mass_on_ocean[i-1,j+1,3]) ) \
-					+   ( (mass_on_ocean[i-1,j  ,6]+mass_on_ocean[i+1,j  ,4])   \
-					+  (mass_on_ocean[i  ,j-1,8]+mass_on_ocean[i  ,j+1,2]) ) )
-	
-	#Adding mass to boundary cells
-	for j in range(1,Ny-1):
-		i=0
-		New_mass[j,i]=mass_on_ocean[i,j,5] +  mass_on_ocean[i+1,j+1,1] +  mass_on_ocean[i+1,j-1,7] \
-			+  mass_on_ocean[i+1,j  ,4] 	+  mass_on_ocean[i  ,j-1,8] + mass_on_ocean[i  ,j+1,2] 
-		i=Nx-1	
-		New_mass[j,i]=mass_on_ocean[i,j,5] +  mass_on_ocean[i-1,j-1,9] + mass_on_ocean[i-1,j+1,3] \
-					+   mass_on_ocean[i-1,j ,6] + mass_on_ocean[i ,j-1,8]+mass_on_ocean[i ,j+1,2]
-	
-	for i in range(1,Nx-1):
-		j=0
-		New_mass[j,i]=mass_on_ocean[i,j,5] +   mass_on_ocean[i+1,j+1,1] +  mass_on_ocean[i-1,j+1,3]  \
-				+  mass_on_ocean[i-1,j  ,6] + mass_on_ocean[i+1,j  ,4] +  mass_on_ocean[i  ,j+1,2]
-
-		j=Ny-1	
-		New_mass[j,i]=mass_on_ocean[i,j,5] +  mass_on_ocean[i-1,j-1,9] 	+  mass_on_ocean[i+1,j-1,7] + \
-				mass_on_ocean[i-1,j  ,6]+mass_on_ocean[i+1,j  ,4] +  mass_on_ocean[i  ,j-1,8]
-
-	#Corners
-	i=0 ;j=0
-	New_mass[j,i]=mass_on_ocean[i,j,5] + mass_on_ocean[i+1,j+1,1] + mass_on_ocean[i+1,j  ,4] + mass_on_ocean[i  ,j+1,2]  
-	i=0 ;j=Ny-1
-	New_mass[j,i]=mass_on_ocean[i,j,5] + mass_on_ocean[i+1,j-1,7] + mass_on_ocean[i+1,j  ,4] + mass_on_ocean[i  ,j-1,8]  
-	i=Nx-1; j=0
-	New_mass[j,i]=mass_on_ocean[i,j,5] + mass_on_ocean[i-1,j+1,3] + mass_on_ocean[i-1,j  ,6] + mass_on_ocean[i  ,j+1,2]
-	i=Nx-1; j=Ny-1	
-	New_mass[j,i]=mass_on_ocean[i,j,5] + mass_on_ocean[i-1,j-1,9] + mass_on_ocean[i-1,j  ,6] + mass_on_ocean[i  ,j-1,8]
-
-
-	if plot_outcome==True: #MP2
-		#print 'Warning: the interpolation scheme is not the same as the one used in the model'	
-		
-		#plot_data=(Orig_mass-New_mass)/Orig_mass
-		#cNorm = mpl.colors.Normalize(vmin=-.1, vmax=.1)
-		#vmax=np.max(abs(plot_data))
-		#plt.pcolormesh(x,y,plot_data,cmap='bwr',norm=cNorm)
-		#plt.title('Error between bergs and shelf')
-
-		#plot_data=h_ice
-		plot_data=New_mass
-		vmax=np.max(abs(plot_data))
-		cNorm = mpl.colors.Normalize(vmin=-vmax, vmax=vmax)
-		plt.pcolormesh(x,y,plot_data,cmap='jet',norm=cNorm)
-		plt.title('h_ice')
-
-		#plot_data=(New_mass-Orig_mass)/(rho_ice*grid_area)
-		#cNorm = mpl.colors.Normalize(vmin=-0.00000000001, vmax=0.00000000001)
-		#vmax=np.max(abs(plot_data))
-		#plt.pcolormesh(x,y,plot_data,cmap='bwr',norm=cNorm)
-
-		plt.colorbar()
-		#plt.xlim([min(x)-,max(x)])
-		#plt.ylim([min(y),max(y)])
-		#plt.show()
-
-	return New_mass
-
-def Switch_x_and_y_directions(lat,lon, A, B, C):
-	print 'Switching x and y directions!!!'
-	lat_new=[]
-	lon_new=[]
-	for i in range(len(lat)):
-		lat_new.append(lon[i])
-		lon_new.append(lat[i])
-	M=A.shape
-	A_new=np.zeros([M[1],M[0]])
-	B_new=np.zeros([M[1],M[0]])
-	C_new=np.zeros([M[1],M[0]])
-	for i in range(M[0]):
-		for j in range(M[1]):
-			A_new[j,i]=A[i,j]
-			B_new[j,i]=B[i,j]
-			C_new[j,i]=C[i,j]
-
-	return	[lat_new,lon_new,A_new,B_new, C_new]
-
-def interpolate_field_onto_new_grid(x,y,x_new,y_new,field):
-	xx, yy = np.meshgrid(x, y)
-	#f = interpolate.interp2d(x, y, field, kind='cubic')
-	f = interpolate.interp2d(x, y, field, kind='linear')
-	field_new = f(x_new, y_new)
-	return field_new
-
-def convert_input_to_catesian_coordinates(lon,lat,ice_mask,h_ice,R_earth,dx):
-	#Parameters
-	thickness_threshhold=0.01
-
-	lon_max=np.max(lon) ; lon_min=np.min(lon)
-	lat_max=np.max(lat) ; lat_min=np.min(lat)
-	lat_ref=np.mean(lat)
-
-	#Converting to cartesian grid
-        x=(np.pi/180)*R_earth*np.cos(lat_ref*np.pi/180.)*lon
-	y=(np.pi/180)*R_earth*lat
-	x=x-np.min(x)
-	y=y-np.min(y)
-	
-	#Creating regular grid
-	x_new=np.linspace(np.min(x), np.max(x), num=len(x))
-	y_new=np.linspace(np.min(y),np.max(y), num=len(y))
-	x_new=np.arange(np.min(x), np.max(x), step=dx)
-	y_new=np.arange(np.min(y), np.max(y), step=dx)
-
-	h_ice_new=interpolate_field_onto_new_grid(x,y,x_new,y_new,h_ice)
-	h_ice_new[np.where(h_ice_new<thickness_threshhold)]=0.
-	ice_mask_new=interpolate_field_onto_new_grid(x,y,x_new,y_new,ice_mask)
-	#ice_mask_new=np.round(ice_mask_new)
-	#print ice_mask_new[50,:]
-	
-	return [x_new,y_new,ice_mask_new,h_ice_new]
-
-####################################################################################################################################################
-##########################################################  Main Program   #########################################################################
-####################################################################################################################################################
-
-def main():
-
-	#Flags
-	save_restart_files=False
-	save_new_h_ice_file=True
-	Convert_to_lat_lon=False
-	input_is_cartesian=True
-
-	#Iceberg setup flags
-	only_choose_one_berg=False  ; chosen_berg_num=4564
-	scale_the_grid_to_lat_lon=False  #Remember to change this back when providing fields for Isomip
-	adjust_lat_ref=True
-	set_all_thicknesses_to_one=False   ; Th_prescribed=1.
-	Interpolate_from_four_corners=False
-	set_all_bergs_static_by_default=True
-	Find_thickness_using_vector=False
-	Switch_x_and_y_to_rotate_90=False
-	set_all_domain_to_ice=False
-
-	#Mass spreadng flags
-	Switch_regridding_element_type=False
-	Fill_in_the_boundaries=False
-	regrid_icebergs_onto_grid=True
-
-	#Plotting flags
-	plotting_bergs_over_grid=True
-	plot_circles=False
-	plot_ice_mask=True
-	plot_ice_thickness=True
-	plot_icebergs_positions=True
-
-	#Bond related flags
-	Create_icebergs_bonds=False
-	plot_bonds=True
-	break_some_bonds=False
-	Remove_stationary_bergs=False 
-	Allow_bonds_for_static_iceberg=False
-	Allow_bonds_with_boundary_bergs=False
-
-	element_type='square' 
-	#element_type='hexagon'
-
-	#Which experiment
-	#Ice_geometry_source='ISOMIP'   ; Convert_to_lat_lon=False       ; input_is_cartesian=True ; 
-	Ice_geometry_source='Weddell'     ; Convert_to_lat_lon=False        ; input_is_cartesian=False
-
-	ISOMIP_reduced=True  #Reduced uses 2X2 grid, not reduced uses 1X1 grid
-
-	ISOMIP_ice_geometry_filename='input_files/Isomip_ice_geometry.nc'
-	ISOMIP_reduced_ice_geometry_filename='input_files/isomip_ice_shelf1.nc'
-	Weddell_ice_geometry_filename='input_files/Bedmap2_gridded_subset_Weddell_Sea_Region.nc'
-	ISOMIP_topography_filename='input_files/Isomip_topog.nc'
-
-
-	#Parameters
-	thickness=100.
-	#Radius=0.25*1000
-	#Radius=sqrt(3)/2.*1000
-	#Radius=1.*1000
-	Radius=0.5*10000.  #Hexagon only valid for S<half gridcell.  (about 0.85 using 2km)
-	print 'Radius = ', Radius
-	rho_ice=850.
-	gravity=9.8
-	mass_scaling=1.
-	R_earth=6360.*1000.
-	buffer_number=0   #Number of buffer points on the sides of the domain
-
-	#Let interactive radius be different from radius for testing the model:
-	IA_scaling=1.#(1./2.)
-	Radius=Radius/IA_scaling
-
-	#Here we create the lons and lats for a tabular iceberg
-	#N= 5  # Number of rows in iceberg
-	#M= 4   # Number of columns in iceberg
-
-	if element_type=='square' and Interpolate_from_four_corners==True:
-		print 'Square packing with R dividing dx, works best with interpolation off.'
-
-	print 'Element type= ', element_type, ';  Switched_regridding= ', Switch_regridding_element_type
-	if break_some_bonds==True:
-		print 'Some bonds are being broken'
-
-	#####################################################################################
-	#####################################################################################
-
-	if  Ice_geometry_source=='ISOMIP':
-		if ISOMIP_reduced==False:
-			lon_init=0  ; lat_init=-70.  #latitude  of bottom left corner of iceberg
-			(x,y,ice_mask,h_ice)=load_ISOMIP_ice_geometry(ISOMIP_ice_geometry_filename,buffer_number)
-			ice_filename=ISOMIP_ice_geometry_filename
-		else:
-			lon_init=0  ; lat_init=-70.  #latitude  of bottom left corner of iceberg
-			(x,y,ice_mask,h_ice)=load_ISOMIP_reduced_ice_geometry(ISOMIP_reduced_ice_geometry_filename,buffer_number,ISOMIP_topography_filename)
-			ice_filename=ISOMIP_reduced_ice_geometry_filename
-		topog_filename=ISOMIP_topography_filename
-
-
-	if  Ice_geometry_source=='Weddell':
-		lon_init=-32.9  ; lat_init=-70.  #latitude  of bottom left corner of iceberg
-		(x,y,ice_mask,h_ice)=load_Weddel_ice_geometry(Weddell_ice_geometry_filename)
-		ice_filename=Weddell_ice_geometry_filename
-	
-	if input_is_cartesian is False:
-		dx=10000.
-		lat_grid=y ; lon_grid=x
-		(x,y,ice_mask,h_ice)=convert_input_to_catesian_coordinates(x,y,ice_mask,h_ice,R_earth,dx)
-		input_is_cartesian=True
-
-
-	if set_all_thicknesses_to_one==True:
-		print 'All thicknesses being set equal to 1'
-		if set_all_domain_to_ice is True:
-			ice_mask[:,:]=1.
-		h_ice[np.where(ice_mask>0.5)]=Th_prescribed
-
-	
-	lat_ref=np.max(y)
-	if (Convert_to_lat_lon==True)  and (input_is_cartesian==True):
-		lat_ref=lat_init
-		x=x-np.min(x)
-		y=y-np.min(y)
-		x=lon_init+((x/R_earth)*(180./np.pi)*(1/np.cos(lat_ref*np.pi/180.)))
-		y=lat_init+((y/R_earth)*(180./np.pi))
-		input_is_cartesian=False
-
-	#Define the positions,thickness, mass,  of the icebergs
-	(Number_of_bergs,lon,lat,iceberg_num,dx_berg, dy_berg,thickness,mass,width,x,y,Radius,static_berg,N_bergs_before_bd)= Create_icebergs(lon_init,lat_init,\
-			Radius,R_earth, x, y,ice_mask,h_ice,Convert_to_lat_lon,rho_ice,input_is_cartesian,element_type,scale_the_grid_to_lat_lon,lat_ref,adjust_lat_ref,\
-			Interpolate_from_four_corners,Fill_in_the_boundaries, set_all_bergs_static_by_default,break_some_bonds,Find_thickness_using_vector,Remove_stationary_bergs)
-
-	print 'Maximum thickness:', np.max(thickness), np.min(thickness)
-	#Define the positions of the iceberg bonds
-	if Create_icebergs_bonds==True:
-		(Number_of_bonds, first_berg_num,first_berg_ine,first_berg_jne,first_berg_lat,first_berg_lon, other_berg_num,other_berg_ine, other_berg_jne,other_berg_lat,other_berg_lon)=\
-				Define_iceberg_bonds(Number_of_bergs,iceberg_num,lat,lon,dx_berg, dy_berg,Radius,break_some_bonds,static_berg,Allow_bonds_for_static_iceberg\
-				,N_bergs_before_bd,Allow_bonds_with_boundary_bergs)
-
-	temp_mass=[mass[i]/thickness[i] for i in range(len(thickness))]
-	if only_choose_one_berg==True:
-		(Number_of_bergs,lon,lat,thickness,width,mass,iceberg_num)= Select_just_one_berg(lon,lat,thickness,width,mass,iceberg_num,chosen_berg_num,static_berg)
-
-
-	if regrid_icebergs_onto_grid==True:
-		if scale_the_grid_to_lat_lon==True:
-			print 'Regridding should be run with scale_the_grid_to_lat_lon off'
-		else:
-			if Switch_regridding_element_type==True:
-				if element_type=='square':
-					element_type='hexagon'
-				else:
-					element_type='square'
-			temp_thickness=[1. for i in thickness]
-			temp_mass=[mass[i]/(thickness[i]*rho_ice) for i in range(len(thickness))]
-			temp_rho_ice=1.
-			New_area=regrid_iceberg_thickness(lat,lon,Number_of_bergs,temp_thickness,temp_mass,h_ice,x,y,temp_rho_ice,element_type,static_berg,plot_outcome=False)
-			New_mass=regrid_iceberg_thickness(lat,lon,Number_of_bergs,thickness,mass,h_ice,x,y,rho_ice,element_type,static_berg,plot_outcome=False)
-		if save_new_h_ice_file==True:
-			grid_area=(x[1]-x[0])*(x[1]-x[0])
-			h_ice_new=New_mass*0
-			M=h_ice.shape
-			for j in range(M[0]):
-				for i in range(M[1]):
-					if New_area[j,i]>0:
-						h_ice_new[j,i]=New_mass[j,i]/(rho_ice*New_area[j,i])  
-
-	if Switch_x_and_y_to_rotate_90 is True:
-		[lat,lon, h_ice_new,New_area,New_mass]=Switch_x_and_y_directions(lat,lon, h_ice_new,New_area,New_mass)
-			
-
-	if save_restart_files==True:	
-		#Creating iceberg restart file
-		Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg)
-		
-		#Creating bond restart file
-		if Create_icebergs_bonds==True:
-			Create_bond_restart_file(Number_of_bonds,first_berg_num,first_berg_ine,first_berg_jne,other_berg_ine,other_berg_jne,iceberg_num,other_berg_num,Ice_geometry_source)
-			
-		if save_new_h_ice_file==True:
-			create_clipped_icethickness_file(h_ice_new,New_area,New_mass,grid_area,gravity)
-
-	# Plotting the positions and bonds of the newly formed formation
-	if plotting_bergs_over_grid==True:
-		plotting_iceberg_positions(lat,lon,Number_of_bergs,R_earth,Radius,IA_scaling,Convert_to_lat_lon,\
-				plot_circles,h_ice,ice_mask,x,y,plot_ice_mask,plot_ice_thickness,thickness,plot_icebergs_positions,static_berg)
-		if (plot_bonds==True) and (Create_icebergs_bonds):
-			plotting_iceberg_bonds(first_berg_lat,first_berg_lon,other_berg_lat,other_berg_lon,Number_of_bonds)
-
-
-	#field=New_mass/(rho_ice*grid_area)
-	#field=New_area/grid_area -1. 
-	#M=field.shape	
-	#print 'field',(field[M[0]-1,:])
-	#print 'field',(field[M[0]-2,:])
-	#print 'h_ice',h_ice_new[:,:]
-	#print 'h_ice-1',h_ice_new[:,:]-1.
-	plt.show()
-	print 'Script complete'
-
-
-
-if __name__ == '__main__':
-	main()
-	#sys.exit(main())
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/__pycache__/hexagon_area.cpython-38.pyc b/tests/Iceberg_repository/Scripts_and_analysis/__pycache__/hexagon_area.cpython-38.pyc
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diff --git a/tests/Iceberg_repository/Scripts_and_analysis/bergs_quickview.py b/tests/Iceberg_repository/Scripts_and_analysis/bergs_quickview.py
deleted file mode 100755
index e4a1d68..0000000
--- a/tests/Iceberg_repository/Scripts_and_analysis/bergs_quickview.py
+++ /dev/null
@@ -1,284 +0,0 @@
-#!/usr/bin/env python
-
-def bergs_yearday(bergs):
-	bergs=bergs_read(bergs,'year')
-	bergs=bergs_read(bergs,'day')
-	for b in xrange (0,len(bergs.berg)):
-		bergs.berg[b].yearday=bergs.berg[b].year+(bergs.berg[b].day/372)
-		#Note I have not included all the warnings about dimensions already existing.
-        return bergs
-
-
-def bergs_read(bergs,varname):
-	nc=bergs.nc
-	bergs_list=bergs.berg
-	var = nc.variables[varname][:]
-	for b in xrange (0,len(bergs.berg)):
-		k=[]
-		js=bergs.berg[b].js
-		je=bergs.berg[b].je
-		for l in xrange (0,len(js)):
-			temp=range(js[l],je[l]+1)
-			for i in xrange (0, len(temp)):
-				k.append(temp[i])
-			setattr(bergs.berg[b],varname,var[k])
-        return bergs
-
-
-def bergs_hash(year, day, x, y, m):
-	ilat=(90.+y)/180
-        ilon=(360 % x)/360;
-        iyear=np.floor(year);
-        iday=(day/372);
-        im=math.log(m,10)-7.9;
-        h=ilon+1e3*ilat+1e6*iday+1e9*iyear+1e12*im;
-        return h
-
-
-
-def bergs_open(filename):
-
-	#Creating a classes
-	class berg_handle:
-		def __init__(self,berg,nc):
-			self.berg=berg
-			self.nc=nc
-
-	class berg_type:
-		def __init__(self,hash):
-			self.hash=hash
-			self.year0=[]
-			self.day0=[]
-			self.lon0=[]
-			self.lat0=[]
-			self.mass0=[]
-			self.js=[]
-			self.je=[]
-			self.width=[]
-			self.lon=[]
-			self.lat=[]
-			self.year=[]
-			self.day=[]
-			self.uvel=[]
-			self.vvel=[]
-			self.uo=[]
-			self.vo=[]
-			self.ui=[]
-			self.ua=[]
-			self.vu=[]
-			self.mass_of_bits=[]
-			self.heat_density=[]
-			self.thickness=[]
-			self.length=[]
-			self.ssh_x=[]
-			self.ssh_y=[]
-			self.sst=[]
-			self.cn=[]
-			self.hi=[]
-			self.yearday=[]
-			self.iceberg_num=[]
-
-	#Importing the data
-	nc = Dataset(filename, mode='r')
-	lat = nc.variables['lat'][:]
-	N=len(lat)
-	js=np.where(lat>91)[0]
-	je=np.concatenate([js[1:]-1, np.array([N-1])])
-	lon = nc.variables['lon'][:]
-	year = nc.variables['year'][:]
-	day = nc.variables['day'][:]
-	#mass = nc.variables['mass'][:]
-	iceberg_num = nc.variables['iceberg_num'][:]
-
-	N=len(js)
-	h=np.zeros(N)
-	# Making a list of identifying hashes
-	k=0
-	for j in js+1:
-		#h[k]=bergs_hash(year[j], day[j],lon[j],lat[j],mass[j])
-		h[k]=iceberg_num[j]
-		k=k+1
-
-	#Creates a sorted array of unique elements of h
-	h=sorted(list(set(h)))
-
-	#Create a list of bergs, named by their hash values, h
-	berg=[]
-	for i in xrange (0,len(h)):
-		berg.append(berg_type(h[i]))
-
-	for i in xrange(0, len(js)):
-		j=js[i]+1
-		#l=np.where(h==bergs_hash(year[j], day[j],lon[j],lat[j],mass[j]))[0]
-		l=np.where(h==iceberg_num[j])[0]
-		berg[l].year0.append(year[j])
-		berg[l].day0.append(day[j])
-		berg[l].lon0.append(lon[j])
-		berg[l].lat0.append(lat[j])
-		#berg[l].mass0.append(mass[j])
-		berg[l].js.append(js[i]+2)
-		berg[l].je.append(je[i])
-
-	#Sort each segment
-	for i in xrange (0,len(h)):
-		yd=year[berg[i].js]+(day[berg[i].js]/373)
-		#Sort according to descending yd, and then pull out indicies for js, and je.
-		
-		berg[i].js=[berg[i].js[n] for n,_ in sorted(list(enumerate(yd)),reverse=True)]
-		berg[i].je=[berg[i].je[n] for n,_ in sorted(list(enumerate(yd)),reverse=True)]
-
-	bergs_handle=berg_handle(berg,nc)
-
-	return bergs_handle
-
-###############################################################################################
-#################################  Beginning of Script  #######################################
-###############################################################################################
-from netCDF4 import Dataset
-import numpy as np
-#from PIL import *
-import math
-import os
-import matplotlib
-matplotlib.use("GTKAgg")
-import matplotlib.pyplot as plt
-from pylab import *
-import pdb
-import argparse
-#This combination allows you to access the varibale imputted from the command line.
-import sys
-
-#Clear screen
-#os.system('clear')
-
-#This is a command which puts you into testing mode so that you can troubleshoot (like a breakpoint in matlab)
-#pdb.set_trace()
-
-#If no files are given at runtime, then use the files selected here:
-if len(sys.argv)==1:
-	Number_of_files=2  # How many files would you like to view?
-
-	#Choosing which files to use
-	#Weddel Sea Version
-	#fileroot='/home/aas/Iceberg_Project/Weddell_Sea/'
-	#dirname1='one_iceberg_testing_Verlet';
-	#dirname2='one_iceberg_testing_RK';
-	
-	#filename1=fileroot+dirname1+'/iceberg_trajectories.nc'
-	#filename2=fileroot+dirname2+'/iceberg_trajectories.nc'
-
-	#Other files
-	#filename1='/home/aas/Iceberg_Project/Test_data1/Quick_Global_RK15/iceberg_trajectories.nc';
-	#filename1= '/home/aas/Iceberg_Project/Weddell_Sea/one_iceberg_testing/iceberg_trajectories.nc'
-	filename1= '../Rolling/iceberg_trajectories.nc'
-
-else:
-	Number_of_files=len(sys.argv)-1
-	
-#Imput parameters
-berg_num=296190 #index of ic
-
-#Flags and on/off switches
-plot_timeseries=0
-plot_trajectory=1
-plot_bergsize=1
-fix_horizontal_scale=0
-plot_all_bergs=0  #plots all the icebergs and not just the one given by n
-plot_initial_size=0
-plot_size_at_start_and_finish_only=0
-short_form=1 #only looks up the lat / lon
-
-#Creating and filling up the bergs
-for loop in xrange(0,Number_of_files):
-	if len(sys.argv)==1:
-		if loop==0: filename=filename1
-		if loop==1: filename=filename2
-	else:
-		filename=sys.argv[loop+1]
-	print filename	
-
-	berg=[]; del berg
-	bergs=bergs_open(filename)
-	bergs=bergs_read(bergs,'width')
-	bergs=bergs_read(bergs,'length')
-	bergs=bergs_read(bergs,'lat')
-	bergs=bergs_read(bergs,'lon')
-	bergs=bergs_yearday(bergs)
-	
-	N=len(bergs.berg)
-	if plot_all_bergs==0:
-		N=1
-	for n in xrange (0, N):
-		if plot_all_bergs==0:
-			n=berg_num
-
-		#Loading variables
-		lon=bergs.berg[n].lon[:]
-		lat=bergs.berg[n].lat[:]
-		width=bergs.berg[n].width[:]
-		length=bergs.berg[n].length[:]
-		yearday=bergs.berg[n].yearday[:]
-
-		#Finding the index of the initial time
-		initial_time_ind=sorted(list(enumerate(yearday)),key=lambda x: x[0])[-1][0]
-		final_time_ind=sorted(list(enumerate(yearday)),key=lambda x: x[0])[0][0]
-
-###########################   Begining plotting  #################################
-
-		if plot_trajectory==1:
-			#plt.subplot(2,1,1)
-			if loop==0:
-				if n==1:
-					plt.plot(lon,lat,'ko-')
-				if n!=1:
-					plt.plot(lon,lat,'go-')
-			else:
-				plt.plot(lon,lat,'bo-')
-			plt.xlabel('longitude (deg)')
-			plt.ylabel('latitude (deg)')
-			plt.title('Iceberg trajectory')
-			plt.grid(True)
-			#savefig("test.png")
-
-			if plot_bergsize==1:
-				Radius_earth=6378.135*1000;
-				circ_ind=np.linspace(0,2*pi,100);
-				for k in xrange (0 ,len(lat)):
-    					L_eff=sqrt(((width[k]*length[k])/pi));
-					plt.plot(lon[k],lat[k],'bo',linewidth=5)
-				        #d_lat=(L_eff/Radius_earth)*(180/pi);
-					#d_lon=L_eff/(111.320*(10**(3))*cos(lat[k]*pi/180));
-				        d_lat=(L_eff/Radius_earth)*(180/pi);
-					d_lon=(L_eff/(Radius_earth*cos(lat[k]*pi/180)))*(180/pi);
-                                        if plot_size_at_start_and_finish_only==0:
-					        plt.plot(lon[k]+(d_lon*cos(circ_ind)),lat[k]+(d_lat*sin(circ_ind)),'b');
-					if k==initial_time_ind and plot_initial_size==1:
-						plt.plot(lon[k]+(d_lon*cos(circ_ind)),lat[k]+(d_lat*sin(circ_ind)),'r');
-					if k==final_time_ind:
-						plt.plot(lon[k]+(d_lon*cos(circ_ind)),lat[k]+(d_lat*sin(circ_ind)),'r');
-				
-			#Setting axes to have equal distance
-				if fix_horizontal_scale==1:
-					y_scale=(max(lat)-min(lat))*(Radius_earth*pi/180)
-					x_scale=(max(lon)-min(lon))*(111.320*(10**(3))*cos(np.mean(lat)/180*pi))
-					d=0.6*max(x_scale,y_scale)
-					d_lat=d*(180/(Radius_earth*pi))
-					d_lon=d/(111.320*(10**(3))*cos(np.mean(lat)*pi/180))
-					plt.xlim([((min(lon)+max(lon))/2)-d_lon,((min(lon)+max(lon))/2)+d_lon])
-					plt.ylim([((min(lat)+max(lat))/2)-d_lat,((min(lat)+max(lat))/2)+d_lat])
-	
-			plt.plot(lon[initial_time_ind],lat[initial_time_ind],'ro')
-plt.show()
-
-if plot_timeseries==1:
-	n=0
-	#plt.subplot(2,1,2)
-	plt.plot(yearday,lon,'ko-')
-	plt.xlabel('yearday')
-	plt.ylabel('lon (deg)')
-	plt.grid(True)
-	plt.savefig("test7.png")
-	plt.show()
-
-
-print 'Script complete'
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/calving_and_extract.py b/tests/Iceberg_repository/Scripts_and_analysis/calving_and_extract.py
deleted file mode 100644
index e4a9b62..0000000
--- a/tests/Iceberg_repository/Scripts_and_analysis/calving_and_extract.py
+++ /dev/null
@@ -1,126 +0,0 @@
-#from midas.rectgrid import *
-#from PIL import *
-import netCDF4 as nc
-import numpy as np
-import os
-import matplotlib as ml
-import matplotlib.pyplot as plt
-
-#These lines could be used to help select a subset of another data set. Not used for now.
-#sgrid_path = '/archive/gold/datasets/OM4_025/mosaic.v20140610.unpacked/ocean_hgrid.nc'
-#topog_path = '/archive/gold/datasets/OM4_025/mosaic.v20140610.unpacked/ocean_topog.nc'
-#calving_path = '/home/Alon.Stern/Iceberg_Project/Weddell_Sea/subsampling_calving/example_calving.nc'
-#sgrid=supergrid(file=sgrid_path,cyclic_x=True,tripolar_n=True)
-#grid=quadmesh(supergrid=sgrid)
-#location='Weddell'
-#xextent={'Weddell':(-85.,20.2)}
-#yextent={'Weddell':(grid.lath[0],-60.)}
-#subreg=grid.geo_region(x=xextent[location],y=yextent[location])
-#depth=nc.Dataset(topog_path).variables['depth'][subreg['y'],subreg['x']]
-#ny,nx=depth.shape
-#calving=nc.Dataset(calving_path).variables['CALVING']
-#calving_time=nc.Dataset(calving_path).variables['time']
-
-
-
-#Size of the domain
-nx=420
-ny=200
-
-R=3.
-x_pos_ind_1=200
-y_pos_ind_1=180
-
-x_pos_ind_2=400
-y_pos_ind_2=180
-
-Max_C=0.0058 #Maximum comes from the other calving flux file.
-
-#Defining the amount of calving
-calving=np.zeros((1,nx,ny))
-C=np.zeros((nx,ny))
-for i in xrange(0,nx):
-    for j in xrange(1,ny):
-        r_sq= (i-x_pos_ind_1)**2+(j-y_pos_ind_1)**2
-        if r_sq  < 3*(R**2):
-            C[i,j]=Max_C*np.exp(-(r_sq/(R**2))) 
-        r_sq= (i-x_pos_ind_2)**2+(j-y_pos_ind_2)**2 
-        if r_sq  < 3*(R**2):
-            C[i,j]=Max_C*np.exp(-(r_sq/(R**2)))
-   # calving[0,i,j]=C[i,j]
-
-
-
-#Creating the calving file
-fnam='calving_new.nc'
-f=nc.Dataset(fnam,'w',format='NETCDF3_CLASSIC')
-time=f.createDimension('time', None)
-yt=f.createDimension('yt',ny)
-xt=f.createDimension('xt',nx)
-
-yt=f.createVariable('yt','f4',('yt'))
-xt=f.createVariable('xt','f4',('xt'))
-CALVING=f.createVariable('CALVING','f4',('time','yt','xt'))
-time=f.createVariable('time','f4',('time'))
-
-CALVING.long_name = "frozen runoff" ;
-CALVING.units = "kg/(m^2*s)" ;
-CALVING.missing_value =-10000;# -1.e+34f ;
-CALVING.FillValue = -10000;#-1.e+34f ;
-CALVING.cell_methods = "time: mean" ;
-CALVING.time_avg_info = "average_T1,average_T2,average_DT" ;
-
-time.long_name = "time" ;
-time.units = "days since 1900-01-01 00:00:00" ;
-time.cartesian_axis = "T" ;
-time.calendar_type = "NOLEAP" ;
-time.calendar = "NOLEAP" ;
-time.bounds = "time_bounds" ;
-time.modulo = " " ;
-
-xt.long_name = "longitude" ;
-xt.units = "degrees_E" ;
-xt.cartesian_axis = "X" ;
-xt.edges = "xb" ;
-
-yt.long_name = "latitude" ;
-yt.units = "degrees_N" ;
-yt.cartesian_axis = "Y" ;
-yt.edges = "yb" ;
-
-f.filename = "19090101.ice_month.nc" ;
-f.title = "CM2G_LM3_1990_DYNCODE_pi-control_C2_25sep2012_test" ;
-f.grid_type = "regular" ;
-f.grid_tile = "N/A" ;
-f.history = "Mon Apr 22 14:33:03 2013: ncks -v time,xt,yt,CALVING 19090101.ice_month.nc example_calving.nc" ;
-f.NCO = "4.0.3" ;
-
-
-f.variables['time'][:]=0.
-#f.variables['yt'][:]=yn
-#f.variables['xt'][:]=xy
-f.variables['CALVING'][:]=calving
-
-print f.dimensions
-for dimobj in f.dimensions.values():
-    print dimobj
-f.sync()
-f.close()
-
-
-
-H = np.array([[1,2,3,4],[5,6,7,8],[9,10,11,12],[13,14,15,16]])  # added some commas and array creation code
-#H=np.zeros((nx,ny))
-H=C
-fig = plt.figure(figsize=(10, 10))
-ax = fig.add_subplot(111)
-ax.set_title('colorMap')
-plt.imshow(H)
-ax.set_aspect('equal')
-cax = fig.add_axes([0.12, 0.1, 0.78, 0.8])
-cax.get_xaxis().set_visible(False)
-cax.get_yaxis().set_visible(False)
-cax.patch.set_alpha(0)
-cax.set_frame_on(False)
-plt.colorbar(orientation='vertical')
-plt.show()
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/check_convergence.py b/tests/Iceberg_repository/Scripts_and_analysis/check_convergence.py
deleted file mode 100755
index 1f6fbd8..0000000
--- a/tests/Iceberg_repository/Scripts_and_analysis/check_convergence.py
+++ /dev/null
@@ -1,77 +0,0 @@
-#!/usr/bin/env python
-
-###############################################################################################
-from netCDF4 import Dataset
-import sys
-import argparse
-import numpy as np
-import os
-import numpy
-import netCDF4 as nc
-import matplotlib
-import matplotlib.pyplot as plt
-from pylab import *
-#import pdb
-#import argparse
-#This combination allows you to access the varibale imputted from the command line.
-#import sys
-
-
-def load_timeseries_data_from_file(filename,field):
-	print 'Loading data from file: ', filename	
-	with nc.Dataset(filename) as file:
-			data = file.variables[field][:]
-			Time = file.variables['time'][:]
-			x = file.variables['xq'][:]
-			y = file.variables['yh'][:]
-	
-	print 'Data size:' ,data.shape
-	
-	if len(data.shape)==3:
-		data=np.squeeze(np.sum(data,axis=1))  #Mean over first variable
-		data=np.squeeze(np.mean(data,axis=1))  #Mean over first variable
-	if len(data.shape)==4:
-			#data=np.squeeze(np.mean(data,axis=0))  #Mean over first variable
-			data=np.squeeze(np.sum(data,axis=1))  #Mean over first variable
-			data=np.squeeze(np.mean(data,axis=1))  #Mean over first variable
-			data=np.squeeze(np.mean(data,axis=1))  #Mean over first variable
-
-	return [data, Time,x,y]
-
-def plot_time_series_data(data,Time,field): 
-	print 'Starting to plot...'	
-	
-	plt.plot(Time,data)
-	plt.title(field)
-
-
-
-#Clear screen
-def main():
-
-	#os.system('clear')
-	parser = argparse.ArgumentParser()
-	parser.add_argument('--file', default=None, help='The input data file in NetCDF format.')
-	parser.add_argument('--field', default='u', help='The field to be viewed')
-	args = parser.parse_args()
-
-	filename=args.file
-	field=args.field
-
-	(time_series, Time) =load_timeseries_data_from_file(filename,field,x,y)
-
-	plot_time_series_data(time_series,Time, field)
-
-
-
-
-	plt.show()
-
-
-	print 'Script complete'
-
-
-
-if __name__ == '__main__':
-        main()
-        #sys.exit(main())
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/compare_Global_Quick_vs_Benchmark.py b/tests/Iceberg_repository/Scripts_and_analysis/compare_Global_Quick_vs_Benchmark.py
deleted file mode 100644
index 557e0dc..0000000
--- a/tests/Iceberg_repository/Scripts_and_analysis/compare_Global_Quick_vs_Benchmark.py
+++ /dev/null
@@ -1,121 +0,0 @@
-!I still need to write this code comparing the files. 
-
-
-from midas.rectgrid import *
-from PIL import *
-import netCDF4 as nc
-import numpy as np
-import os
-
-
-sgrid_path = '/archive/gold/datasets/OM4_025/mosaic.v20140610.unpacked/ocean_hgrid.nc'
-topog_path = '/archive/gold/datasets/OM4_025/mosaic.v20140610.unpacked/ocean_topog.nc'
-tideamp_path = '/archive/gold/datasets/OM4_025/INPUT/tidal_amplitude.v20140616.nc'
-seawifs_path = '/archive/gold/datasets/OM4_025/INPUT/seawifs_1998-2006_smoothed_2X.v20140629.nc'
-
-sgrid=supergrid(file=sgrid_path,cyclic_x=True,tripolar_n=True)
-grid=quadmesh(supergrid=sgrid)
-
-location='Weddell'
-xextent={'Weddell':(-85.,20.2)}
-yextent={'Weddell':(grid.lath[0],-60.)}
-
-subreg=grid.geo_region(x=xextent[location],y=yextent[location])
-h2=nc.Dataset(topog_path).variables['h2'][subreg['y'],subreg['x']]
-depth=nc.Dataset(topog_path).variables['depth'][subreg['y'],subreg['x']]
-tideamp=nc.Dataset(tideamp_path).variables['tideamp'][subreg['y'],subreg['x']]
-
-
-fnam='topog.nc'
-f=nc.Dataset(fnam,'w',format='NETCDF3_CLASSIC')
-
-ny,nx=depth.shape
-
-f.createDimension('ny',ny)
-f.createDimension('nx',nx)
-f.createDimension('ntiles',1)
-f.createVariable('depth','f8',('ny','nx'))
-f.createVariable('h2','f8',('ny','nx'))
-f.variables['depth'][:]=depth
-f.variables['h2'][:]=h2
-f.sync()
-f.close()
-
-
-fnam='tideamp.nc'
-f=nc.Dataset(fnam,'w',format='NETCDF3_CLASSIC')
-ny,nx=tideamp.shape
-f.createDimension('ny',ny)
-f.createDimension('nx',nx)
-f.createVariable('tideamp','f4',('ny','nx'))
-f.variables['tideamp'][:]=tideamp
-f.sync()
-f.close()
-
-
-fnam='ocean_hgrid.nc'
-f=nc.Dataset(fnam,'w',format='NETCDF3_CLASSIC')
-f.createDimension('ny',ny*2)
-f.createDimension('nx',nx*2)
-f.createDimension('nyp',ny*2+1)
-f.createDimension('nxp',nx*2+1)
-f.createDimension('string',255)
-f.createVariable('y','f8',('nyp','nxp'))
-f.createVariable('x','f8',('nyp','nxp'))
-f.createVariable('dy','f8',('ny','nxp'))
-f.createVariable('dx','f8',('nyp','nx'))
-f.createVariable('area','f8',('ny','nx'))
-f.createVariable('angle_dx','f8',('nyp','nxp'))
-f.createVariable('tile','S1',('string'))
-
-x_read=subreg['x']
-y_read=subreg['y']
-
-
-if x_read[-1] < x_read[0]:
-    ib=np.where(np.roll(x_read,shift=-1)<x_read)[0][0]
-    tmp = np.arange(x_read[0]*2,x_read[ib]*2+2)
-    x_read=np.concatenate((tmp,np.arange(x_read[ib+1]*2,x_read[-1]*2+3)))
-    y_read = np.arange(y_read[0]*2,y_read[-1]*2+3)    
-else:
-    x_read = np.arange(x_read[0]*2,x_read[-1]*2+3)
-    y_read = np.arange(y_read[0]*2,y_read[-1]*2+3)
-
-
-f.variables['y'].units='degrees'
-f.variables['x'].units='degrees'
-f.variables['dy'].units='meters'
-f.variables['dx'].units='meters'
-f.variables['area'].units='m2'
-f.variables['angle_dx'].units='degrees'
-
-yn=sgrid.y[y_read,:]
-yn=yn[:,x_read]
-f.variables['y'][:]=yn
-xn=sgrid.x[y_read,:]
-xn=xn[:,x_read]
-f.variables['x'][:]=xn
-dyn=sgrid.dy[y_read[:-1],:]
-dyn=dyn[:,x_read]
-f.variables['dy'][:]=dyn
-dxn=sgrid.dx[y_read,:]
-dxn=dxn[:,x_read[:-1]]
-f.variables['dx'][:]=dxn
-arean=sgrid.area[y_read[:-1],:]
-arean=arean[:,x_read[:-1]]
-f.variables['area'][:]=arean
-ang=sgrid.angle_dx[y_read,:]
-ang=ang[:,x_read]
-f.variables['angle_dx'][:]=ang
-f.variables['tile'][0] = 't'  ## This is stupid
-f.variables['tile'][1] = 'i'
-f.variables['tile'][2] = 'l'
-f.variables['tile'][3] = 'e'
-f.variables['tile'][4] = '1'
-f.sync()
-f.close()
-
-
-
-
-
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/copy_files_to_shelf_and_bergs.sh b/tests/Iceberg_repository/Scripts_and_analysis/copy_files_to_shelf_and_bergs.sh
deleted file mode 100755
index bc41d80..0000000
--- a/tests/Iceberg_repository/Scripts_and_analysis/copy_files_to_shelf_and_bergs.sh
+++ /dev/null
@@ -1,42 +0,0 @@
-#cp output_files/ISOMIP_icebergs.res.nc ../Bergs_cartesian_ISOMIP1_rho/INPUT/icebergs.res.nc
-#cp output_files/isomip_ice_shelf1_clipped.nc ../Shelf_cartesian_ISOMIP1_rho/INPUT/
-#cp output_files/isomip_ice_shelf1_clipped.nc ../Bergs_cartesian_ISOMIP1_rho/INPUT/
-
-#cp output_files/ISOMIP_icebergs.res.nc ../ISOMIP_ocean_ice/INPUT/icebergs.res.nc
-#cp output_files/ISOMIP_bonds_iceberg.res.nc ../ISOMIP_ocean_ice/INPUT/bonds_iceberg.res.nc
-#cp output_files/isomip_ice_shelf1_clipped.nc ../ISOMIP_ocean_ice/INPUT/isomip_ice_shelf1_clipped.nc
-
-#cp output_files/ISOMIP_icebergs.res.nc ../Tech_ISOMIP/INPUT/icebergs.res.nc
-#cp output_files/ISOMIP_bonds_iceberg.res.nc ../Tech_ISOMIP/INPUT/bonds_iceberg.res.nc
-#cp output_files/isomip_ice_shelf1_clipped.nc ../Tech_ISOMIP/INPUT/isomip_ice_shelf1_clipped.nc
-
-#cp output_files/ISOMIP_icebergs.res.nc ../Tech_ISOMIP//Bergs/Bond_drifting_Moving_berg_trimmed_shelf/INPUT/icebergs.res.nc
-#cp output_files/ISOMIP_bonds_iceberg.res.nc ../Tech_ISOMIP/Bergs/Bond_drifting_Moving_berg_trimmed_shelf/INPUT/bonds_iceberg.res.nc
-#cp output_files/isomip_ice_shelf1_clipped.nc ../Tech_ISOMIP/Bergs/Bond_drifting_Moving_berg_trimmed_shelf/INPUT/isomip_ice_shelf1_clipped.nc
-
-#cp output_files/ISOMIP_icebergs.res.nc ../Tech_ISOMIP//Bergs/Bond_drifting_Moving_berg_trimmed_shelf_larger_berg/INPUT/icebergs.res.nc
-#cp output_files/ISOMIP_bonds_iceberg.res.nc ../Tech_ISOMIP/Bergs/Bond_drifting_Moving_berg_trimmed_shelf_larger_berg/INPUT/bonds_iceberg.res.nc
-#cp output_files/isomip_ice_shelf1_clipped.nc ../Tech_ISOMIP/Bergs/Bond_drifting_Moving_berg_trimmed_shelf_larger_berg/INPUT/isomip_ice_shelf1_clipped.nc
-
-
-#cp output_files/ISOMIP_icebergs.res.nc ../Tech_ISOMIP/Bergs/Collapse_with_Bond_drifting_Moving_berg_trimmed_shelf_small_step_kd2/INPUT/icebergs.res.nc
-#cp output_files/ISOMIP_bonds_iceberg.res.nc ../Tech_ISOMIP/Bergs/Collapse_with_Bond_drifting_Moving_berg_trimmed_shelf_small_step_kd2/INPUT/bonds_iceberg.res.nc
-#cp output_files/isomip_ice_shelf1_clipped.nc ../Tech_ISOMIP/Bergs/Collapse_with_Bond_drifting_Moving_berg_trimmed_shelf_small_step_kd2/INPUT/isomip_ice_shelf1_clipped.nc
-
-
-#cp output_files/isomip_icebergs.res.nc ../tech_isomip/bergs/collapse_with_bond_drifting_moving_berg_trimmed_shelf_small_step_kd2_with_wind/input/icebergs.res.nc
-#cp output_files/isomip_bonds_iceberg.res.nc ../tech_isomip/bergs/collapse_with_bond_drifting_moving_berg_trimmed_shelf_small_step_kd2_with_wind/input/bonds_iceberg.res.nc
-#cp output_files/isomip_ice_shelf1_clipped.nc ../tech_isomip/bergs/collapse_with_bond_drifting_moving_berg_trimmed_shelf_small_step_kd2_with_wind/input/isomip_ice_shelf1_clipped.nc
-
-cp output_files/ISOMIP_icebergs.res.nc /lustre/f1/unswept/Alon.Stern/MOM6-examples_Alon/ice_ocean_SIS2/Tech_ISOMIP/Bergs/After_melt_bond_small_step/INPUT/icebergs.res.nc
-cp output_files/ISOMIP_bonds_iceberg.res.nc /lustre/f1/unswept/Alon.Stern/MOM6-examples_Alon/ice_ocean_SIS2/Tech_ISOMIP/Bergs/After_melt_bond_small_step/INPUT/bonds_iceberg.res.nc
-cp output_files/isomip_ice_shelf1_clipped.nc /lustre/f1/unswept/Alon.Stern/MOM6-examples_Alon/ice_ocean_SIS2/Tech_ISOMIP/Bergs/After_melt_bond_small_step/INPUT/isomip_ice_shelf1_clipped.nc
-
-#cp output_files/ISOMIP_icebergs.res.nc /lustre/f1/unswept/Alon.Stern/MOM6-examples_Alon/ice_ocean_SIS2/Tech_ISOMIP/Bergs/After_melt_Collapse_with_Bond_with_orientation/INPUT/icebergs.res.nc
-#cp output_files/ISOMIP_bonds_iceberg.res.nc /lustre/f1/unswept/Alon.Stern/MOM6-examples_Alon/ice_ocean_SIS2/Tech_ISOMIP/Bergs/After_melt_Collapse_with_Bond_with_orientation/INPUT/bonds_iceberg.res.nc
-#cp output_files/isomip_ice_shelf1_clipped.nc /lustre/f1/unswept/Alon.Stern/MOM6-examples_Alon/ice_ocean_SIS2/Tech_ISOMIP/Bergs/After_melt_Collapse_with_Bond_with_orientation/INPUT/isomip_ice_shelf1_clipped.nc
-
-#cp output_files/ISOMIP_icebergs.res.nc /lustre/f1/unswept/Alon.Stern/MOM6-examples_Alon/ice_ocean_SIS2/Tech_ISOMIP/Bergs/After_melt_Collapse_with_Bond_with_orientation/INPUT/icebergs.res.nc
-#cp output_files/ISOMIP_bonds_iceberg.res.nc /lustre/f1/unswept/Alon.Stern/MOM6-examples_Alon/ice_ocean_SIS2/Tech_ISOMIP/Bergs/After_melt_Collapse_with_Bond_with_orientation/INPUT/bonds_iceberg.res.nc
-#cp output_files/isomip_ice_shelf1_clipped.nc /lustre/f1/unswept/Alon.Stern/MOM6-examples_Alon/ice_ocean_SIS2/Tech_ISOMIP/Bergs/After_melt_Collapse_with_Bond_with_orientation/INPUT/isomip_ice_shelf1_clipped.nc
-
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/create_C3_env.sh b/tests/Iceberg_repository/Scripts_and_analysis/create_C3_env.sh
deleted file mode 100755
index e9aac87..0000000
--- a/tests/Iceberg_repository/Scripts_and_analysis/create_C3_env.sh
+++ /dev/null
@@ -1,14 +0,0 @@
-#This script creates a C3 environment
-
-mkdir build/intel
-cat << EOFA > build/intel/env
-module unload PrgEnv-pgi
-module unload PrgEnv-pathscale
-module unload PrgEnv-intel
-module unload PrgEnv-gnu
-module unload PrgEnv-cray
-module load PrgEnv-intel
-module unload netcdf
-module load cray-netcdf
-EOFA
-
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/create_berg_restart.py b/tests/Iceberg_repository/Scripts_and_analysis/create_berg_restart.py
deleted file mode 100755
index 27c4d5a..0000000
--- a/tests/Iceberg_repository/Scripts_and_analysis/create_berg_restart.py
+++ /dev/null
@@ -1,172 +0,0 @@
-#!/usr/bin/env python
-
-###############################################################################################
-from netCDF4 import Dataset
-import numpy as np
-import os
-#import matplotlib
-#import matplotlib.pyplot as plt
-#from pylab import *
-#import pdb
-#import argparse
-#This combination allows you to access the varibale imputted from the command line.
-#import sys
-
-#Clear screen
-os.system('clear')
-
-new_filename = 'output_files/icebergs_test.res.nc'
-
-f = Dataset(new_filename,'w', format='NETCDF3_CLASSIC')
-
-
-#Creating the calving file
-#f=nc.Dataset(fnam,'w',format='NETCDF3_CLASSIC')
-
-if True:
-	if True:
-
-		i=f.createDimension('i', None)
-		
-		i=f.createVariable('i','i')
-		#i=f.createVariable('i','i',('i'))
-
-		lon=f.createVariable('lon','d',('i'))
-		lon.long_name = "longitude" ;
-		lon.units = "degrees_E" ;
-		lon.checksum = "               0" ;
-
-		lat=f.createVariable('lat','d',('i'))
-		lat.long_name = "latitude" ;
-		lat.units = "degrees_N" ;
-		lat.checksum = "               0" ;
-
-		uvel=f.createVariable('uvel','d',('i'))
-		uvel.long_name = "zonal velocity" ;
-		uvel.units = "m/s" ;
-		uvel.checksum = "               0" ;
-
-		vvel=f.createVariable('vvel','d',('i'))
-		vvel.long_name = "meridional velocity" ;
-		vvel.units = "m/s" ;
-		vvel.checksum = "               0" ;
-
-		mass=f.createVariable('mass','d',('i'))
-		mass.long_name = "mass" ;
-		mass.units = "kg" ;
-		mass.checksum = "               0" ;
-
-		axn=f.createVariable('axn','d',('i'))
-		axn.long_name = "explicit zonal acceleration" ;
-		axn.units = "m/s^2" ;
-		axn.checksum = "               0" ;
-
-		ayn=f.createVariable('ayn','d',('i'))
-		ayn.long_name = "explicit meridional acceleration" ;
-		ayn.units = "m/s^2" ;
-		ayn.checksum = "               0" ;
-
-		bxn=f.createVariable('bxn','d',('i'))
-		bxn.long_name = "inplicit zonal acceleration" ;
-		bxn.units = "m/s^2" ;
-		bxn.checksum = "               0" ;
-
-		byn=f.createVariable('byn','d',('i'))
-		byn.long_name = "implicit meridional acceleration" ;
-		byn.units = "m/s^2" ;
-		byn.checksum = "               0" ;
-
-		ine=f.createVariable('ine','i',('i'))
-		ine.long_name = "i index" ;
-		ine.units = "none" ;
-		ine.packing = 0 ;
-		ine.checksum = "               0" ;
-
-		jne=f.createVariable('jne','i',('i'))
-		jne.long_name = "j index" ;
-		jne.units = "none" ;
-		jne.packing = 0 ;
-
-		thickness=f.createVariable('thickness','d',('i'))
-		thickness.long_name = "thickness" ;
-		thickness.units = "m" ;
-		thickness.checksum = "               0" ;
-
-		width=f.createVariable('width','d',('i'))
-		width.long_name = "width" ;
-		width.units = "m" ;
-		width.checksum = "               0" ;
-
-		length=f.createVariable('length','d',('i'))
-		length.long_name = "length" ;
-		length.units = "m" ;
-		length.checksum = "               0" ;
-
-		start_lon=f.createVariable('start_lon','d',('i'))
-		start_lon.long_name = "longitude of calving location" ;
-		start_lon.units = "degrees_E" ;
-		start_lon.checksum = "               0" ;
-
-		start_lat=f.createVariable('start_lat','d',('i'))
-		start_lat.long_name = "latitude of calving location" ;
-		start_lat.units = "degrees_N" ;
-		start_lat.checksum = "               0" ;
-
-		start_year=f.createVariable('start_year','i',('i'))
-		start_year.long_name = "calendar year of calving event" ;
-		start_year.units = "years" ;
-		start_year.packing = 0 ;
-		start_year.checksum = "               0" ;
-
-		iceberg_num=f.createVariable('iceberg_num','i',('i'))
-		iceberg_num.long_name = "identification of the iceberg" ;
-		iceberg_num.units = "dimensionless" ;
-		iceberg_num.packing = 0 ;
-		iceberg_num.checksum = "               0" ;
-
-		start_day=f.createVariable('start_day','d',('i'))
-		start_day.long_name = "year day of calving event" ;
-		start_day.units = "days" ;
-		start_day.checksum = "               0" ;
-
-		start_mass=f.createVariable('start_mass','d',('i'))
-		start_mass.long_name = "initial mass of calving berg" ;
-		start_mass.units = "kg" ;
-		start_mass.checksum = "               0" ;
-
-		mass_scaling=f.createVariable('mass_scaling','d',('i'))
-		mass_scaling.long_name = "scaling factor for mass of calving berg" ;
-		mass_scaling.units = "none" ;
-		mass_scaling.checksum = "               0" ;
-
-		mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
-		mass_of_bits.long_name = "mass of bergy bits" ;
-		mass_of_bits.units = "kg" ;
-		mass_of_bits.checksum = "               0" ;
-
-		heat_density=f.createVariable('heat_density','d',('i'))
-		heat_density.long_name = "heat density" ;
-		heat_density.units = "J/kg" ;
-		heat_density.checksum = "               0" ;
-
-		halo_berg=f.createVariable('halo_berg','d',('i'))
-		halo_berg.long_name = "halo_berg" ;
-		halo_berg.units = "dimensionless" ;
-		halo_berg.checksum = "               0" ;
-
-		static_berg=f.createVariable('static_berg','d',('i'))
-		static_berg.long_name = "static_berg" ;
-		static_berg.units = "dimensionless" ;
-		static_berg.checksum = "               0" ;
-
-print 'Created restart file: ' ,new_filename
-print 'Script complete'
-
-f.sync()
-f.close()
-
-
-
-
-
-print 'Script complete'
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/create_one_file.py b/tests/Iceberg_repository/Scripts_and_analysis/create_one_file.py
deleted file mode 100755
index 0c8bf5c..0000000
--- a/tests/Iceberg_repository/Scripts_and_analysis/create_one_file.py
+++ /dev/null
@@ -1,94 +0,0 @@
-#!/usr/bin/env python
-
-###############################################################################################
-from netCDF4 import Dataset
-import numpy as np
-import os
-import numpy
-import netCDF4 as nc
-#import matplotlib
-#import matplotlib.pyplot as plt
-#from pylab import *
-#import pdb
-#import argparse
-#This combination allows you to access the varibale imputted from the command line.
-#import sys
-
-#Clear screen
-def main():
-
-	os.system('clear')
-	input_geometry_filename='input_files/Isomip_ocean_geometry.nc'
-
-	#Flags
-	new_filename='output_files/one_file.nc'
-
-	#f=Dataset(input_geometry_filename,'r')
-	#g=Dataset(new_filename,'w') # w if for creating a file
-
-
-	with nc.Dataset(input_geometry_filename) as file:
-		
-
-		Depth = file.variables['D'][:,:]
-
-	M= Depth.shape
-	ny=M[0]
-	nx=M[1]
-	print nx,ny
-	
-	#Creating the topog file
-	#g=Dataset(new_filename,'w') # w if for creating a file
-	g=nc.Dataset(new_filename,'w',format='NETCDF3_CLASSIC')
-	
-
-	lat=g.createDimension('lat',ny)
-	lon=g.createDimension('lon',nx)
-	time=g.createDimension('time', None)
-
-	lat=g.createVariable('lat','f4',('lat'))
-	lon=g.createVariable('lon','f4',('lon'))
-	time=g.createVariable('time','f4',('time'))
-	one_var=g.createVariable('one_var','f4',('lat','lon'))
-
-	time.long_name = "time" ;
-	time.units = "days since 1900-01-01 00:00:00" ;
-	time.cartesian_axis = "T" ;
-	time.calendar_type = "NOLEAP" ;
-	time.calendar = "NOLEAP" ;
-	time.bounds = "time_bounds" ;
-	time.modulo = " " ;
-
-	lon.units = "degrees_E" ;
-	lon.cartesian_axis = "X" ;
-	#lon.edges = "xb" ;
-
-	#lat.long_name = "latitude" ;
-	lat.units = "degrees_N" ;
-	lat.cartesian_axis = "Y" ;
-	#lat.edges = "yb" ;
-
-	one_var.long_name="unnamed_variable"
-	one_var.units="m/s"
-	
-
-	
-	g.variables['one_var'][:]=1.
-	g.variables['lon'][:]=np.linspace(0.5,239.5,nx,endpoint=True)
-	g.variables['lat'][:]=np.linspace(0.5,39.5,ny,endpoint=True)
-	g.variables['time'][0]=1.
-
-	g.sync()
-	g.close()
-
-
-
-
-
-	print 'Script complete'
-
-
-
-if __name__ == '__main__':
-        main()
-        #sys.exit(main())
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/create_thickness_file.py b/tests/Iceberg_repository/Scripts_and_analysis/create_thickness_file.py
deleted file mode 100755
index a01754d..0000000
--- a/tests/Iceberg_repository/Scripts_and_analysis/create_thickness_file.py
+++ /dev/null
@@ -1,167 +0,0 @@
-#!/usr/bin/env python
-
-#First import the netcdf4 library
-from netCDF4 import Dataset  # http://code.google.com/p/netcdf4-python/
-import numpy as np  # http://code.google.com/p/netcdf4-python/
-import matplotlib
-import math
-import os
-matplotlib.use("GTKAgg")
-from pylab import *
-#import matplotlib.pyplot as plt
-import pdb
-import netCDF4 as nc
-from hexagon_area import Divide_hexagon_into_4_quadrants_old
-from hexagon_area import Hexagon_into_quadrants_using_triangles
-
-
-def load_ISOMIP_ice_geometry(filename):
-	with nc.Dataset(filename) as file:
-		ocean_mask = file.variables['openOceanMask'][:,:]
-		upperSurface = file.variables['upperSurface'][:,:]
-		lowerSurface = file.variables['lowerSurface'][:,:]
-		x = file.variables['x'][:]
-		y = file.variables['y'][:]
-
-	ice_mask=1-ocean_mask #one if it ice, zero if it is ocean
-	h_ice=upperSurface-lowerSurface #The ice thickness
-	M=ice_mask.shape
-
-	return [x,y,ice_mask,h_ice]
-
-def Switch_x_and_y_directions(lat,lon, A, B, C):
-        print 'Switching x and y directions!!!'
-        lat_new=[]
-        lon_new=[]
-        for i in range(len(lat)):
-                lat_new.append(lon[i])
-                lon_new.append(lat[i])
-        M=A.shape
-        A_new=np.zeros([M[1],M[0]])
-        B_new=np.zeros([M[1],M[0]])
-        C_new=np.zeros([M[1],M[0]])
-        for i in range(M[0]):
-                for j in range(M[1]):
-                        A_new[j,i]=A[i,j]
-                        B_new[j,i]=B[i,j]
-                        C_new[j,i]=C[i,j]
-
-        return  [lat_new,lon_new,A_new,B_new, C_new]
-
-
-def create_clipped_icethickness_file(h_ice,area,mass,grid_area,gravity,New_ice_thickness_filename):
-	#Creating clipped file
-        [ny, nx]= h_ice.shape ; 
-	
-        g=Dataset(New_ice_thickness_filename,'w') # w if for creating a file
-
-        g.createDimension('nx',nx)
-        g.createDimension('ny',ny)
-
-        thick_h=g.createVariable('thick','f8',('ny','nx'))
-        area_h=g.createVariable('area','f8',('ny','nx'))
-        p_surf_h=g.createVariable('p_surf','f8',('ny','nx'))
-
-        thick_h.units = 'm'
-        thick_h.standard_name = 'ice shelf thickness (clipped)'
-        area_h.units = 'm2'
-        area_h.standard_name = 'ice shelf area'
-        p_surf_h.units = 'Pa'
-        p_surf_h.standard_name = 'surface pressure due to ice shelf'
-
-	p_surf=(gravity*mass)/grid_area
-        g.variables['thick'][:]=h_ice
-        g.variables['area'][:]=area
-        g.variables['p_surf'][:]=p_surf
-        print 'Creating clipped ice file: ' , New_ice_thickness_filename
-        
-        g.sync()
-        g.close()
-
-
-def load_ISOMIP_reduced_ice_geometry(ice_filename,topog_filename):
-	with nc.Dataset(ice_filename) as file:
-		h_ice = file.variables['thick'][:,:]
-		area =  file.variables['area'][:,:]
-		M=h_ice.shape
-
-	y=np.linspace(1000,79000,M[0],endpoint=True)
-	#x=np.linspace(321000,799000,M[1],endpoint=True)
-	x=np.linspace(1000,479000,M[1],endpoint=True)
-	ice_mask=h_ice>0.
-	
-	return [x,y,ice_mask,h_ice]
-
-####################################################################################################################################################
-##########################################################  Main Program   #########################################################################
-####################################################################################################################################################
-
-def main():
-
-	#Flags
-	Switch_x_and_y_to_rotate_90=False
-
-
-	ISOMIP_ice_geometry_filename='input_files/Isomip_ice_geometry.nc'
-	ISOMIP_reduced_ice_geometry_filename='input_files/isomip_ice_shelf1.nc'
-	ISOMIP_reduced_ice_geometry_filename='output_files/isomip_ice_shelf1_clipped.nc'
-	Weddell_ice_geometry_filename='input_files/Bedmap2_gridded_subset_Weddell_Sea_Region.nc'
-	ISOMIP_topography_filename='input_files/Isomip_topog.nc'
-	Output_filename='output_files/isomip_ice_shelf1_new.nc'
-
-	(x,y,ice_mask,h_ice)=load_ISOMIP_reduced_ice_geometry(ISOMIP_reduced_ice_geometry_filename,ISOMIP_topography_filename)
-
-	#Parameters
-	rho_ice=850.
-	gravity=9.8
-
-
-	grid_area=(x[1]-x[0])*(x[1]-x[0])
-	New_area=h_ice*0.+grid_area
-	#New_area=ice_mask*grid_area
-	z_extra=0.00000000001
-	h_ice=h_ice+z_extra
-	#h_ice=(h_ice>0.)*0.00000000000001
-	New_mass=New_area*h_ice*rho_ice
-	h_ice=(0*h_ice)+z_extra
-	if Switch_x_and_y_to_rotate_90 is True:
-		lat=[];lon=[]
-		[lat,lon, h_ice,New_area,New_mass]=Switch_x_and_y_directions(lat,lon, h_ice,New_area,New_mass)
-		x_temp=x
-		x=y
-		y=x_temp
-	create_clipped_icethickness_file(h_ice,New_area,New_mass,grid_area,gravity,Output_filename)
-	
-
-
-	#Plotting the data
-	plot_data=(h_ice)
-        vmax=np.max(abs(plot_data))
-        cNorm = mpl.colors.Normalize(vmin=0., vmax=vmax)
-        plt.pcolormesh(x,y,plot_data,cmap='bwr',norm=cNorm)
-        plt.title('Ice geometry')
-	plt.colorbar()
-	
-
-	plt.show()
-	print 'Script complete'
-
-
-
-if __name__ == '__main__':
-	main()
-	#sys.exit(main())
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/filling_up_space.py b/tests/Iceberg_repository/Scripts_and_analysis/filling_up_space.py
deleted file mode 100755
index 0334a5f..0000000
--- a/tests/Iceberg_repository/Scripts_and_analysis/filling_up_space.py
+++ /dev/null
@@ -1,338 +0,0 @@
-#!/usr/bin/env python
-
-#First import the netcdf4 library
-from netCDF4 import Dataset  # http://code.google.com/p/netcdf4-python/
-import numpy as np  # http://code.google.com/p/netcdf4-python/
-import matplotlib
-import math
-import os
-matplotlib.use("GTKAgg")
-from pylab import *
-from scipy import interpolate
-#import matplotlib.pyplot as plt
-import argparse
-import pdb
-import netCDF4 as nc
-from hexagon_area import Divide_hexagon_into_4_quadrants_old
-from hexagon_area import Hexagon_into_quadrants_using_triangles
-
-
-
-def spread_mass_to_ocean(Nx,Ny,i,j,mass_on_ocean,x,y,Area,Mass,element_type,grid_area,static_berg,lat1, lat2, lat3, lat4, lon1, lon2, lon3, l):
-		#Using physical space
-
-		#Initialize weights for each cell	
-		yDxL=0.  ; yDxC=0. ; yDxR=0. ; yCxL=0. ; yCxR=0. 
-		yUxL=0.  ; yUxC=0. ; yUxR=0. ; yCxC=1.
-
-		if element_type=='square':
-		#if True:
-			L = min(( (np.sqrt(Area)  / np.sqrt(grid_area))),1) ;  #Non dimensionalize element length by grid area. (This gives the non-dim length of the square)
-			xL=min(0.5, max(0., 0.5-(x/L)))
-			xR=min(0.5, max(0., (x/L)+(0.5-(1/L) )))
-			xC=max(0., 1.-(xL+xR))
-			yD=min(0.5, max(0., 0.5-(y/L)))
-			yU=min(0.5, max(0., (y/L)+(0.5-(1/L) )))
-			yC=max(0., 1.-(yD+yU))
-
-			yDxL=yD*xL#*grd%msk[i-1,j-1]
-			yDxC=yD*xC#*grd%msk[i  ,j-1]
-			yDxR=yD*xR#*grd%msk[i+1,j-1]
-			yCxL=yC*xL#*grd%msk[i-1,j  ]
-			yCxR=yC*xR#*grd%msk[i+1,j  ]
-			yUxL=yU*xL#*grd%msk[i-1,j+1]
-			yUxC=yU*xC#*grd%msk[i  ,j+1]
-			yUxR=yU*xR#*grd%msk(i+1,j+1]
-			yCxC=1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )
-
-		if element_type=='hexagon':
-		#if False:#element_type=='hexagon':
-			H = min(( (np.sqrt(Area/(2*sqrt(3))) ;  #No longer no dimensionalizing, but rather using actual distances
-			S=(2/np.sqrt(3))*H #Side of the hexagon
-			grid_dist=1e15 #This should be changed to the minimum grid spacinge.
-			if S>0.5*(grid_dist):
-				print 'Elements must be smaller than a whole gridcell', 'i.e.: S= ' , S , '>=0.5',i,j
-				halt
-
-			#Subtracting the position of the nearest corner from x,y
-			#[origin_x, origin_y]=find_closest_corner(x,y,
-			origin_x=1 ; origin_y=1
-			if x<0.5:
-				origin_x=0
-			if y<0.5:
-				origin_y=0
-
-			x0=(x-origin_x) #Position of the hexagon center, relative to origin at the nearest vertex
-			y0=(y-origin_y)
-			
-			#(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Divide_hexagon_into_4_quadrants_old(x0,y0,H)
-			(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Hexagon_into_quadrants_using_triangles(x0,y0,H,0.)
-			if min(min(Area_Q1,Area_Q2),min(Area_Q3, Area_Q4)) <0:
-				print 'Yolo'
-				print x0,y0,H
-				#print min(min(Area_Q1,Area_Q2),min(Area_Q3, Area_Q4))
-				print Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
-
-			Area_Q1=Area_Q1/Area_hex
-			Area_Q2=Area_Q2/Area_hex
-			Area_Q3=Area_Q3/Area_hex
-			Area_Q4=Area_Q4/Area_hex
-
-			#Now, you decide which quadrant belongs to which mass on ocean cell.
-			#Top right vertex
-			if x>=0.5 and y>= 0.5:
-				yUxR=Area_Q1
-				yUxC=Area_Q2
-				yCxC=Area_Q3
-				yCxR=Area_Q4
-			
-			#Top left vertex
-			if x<0.5 and y>= 0.5:
-				yUxC=Area_Q1
-				yUxL=Area_Q2
-				yCxL=Area_Q3
-				yCxC=Area_Q4
-			
-			#Bottom left vertex
-			if x<0.5 and y< 0.5:
-				yCxC=Area_Q1
-				yCxL=Area_Q2
-				yDxL=Area_Q3
-				yDxC=Area_Q4
-
-			#Bottom right vertex
-			if x>=0.5 and y< 0.5:
-				yCxR=Area_Q1
-				yCxC=Area_Q2
-				yDxC=Area_Q3
-				yDxR=Area_Q4
-
-			#if Sector<4 and Sector>-1:
-			#	print Sector
-				
-					
-			#Check that this is true
-			if abs(yCxC-(1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )))>0.001:
-				print 'All the mass is not being used!!!'
-				#print W1 , W2 , W3 , W4 , W5 , W6
-				#print Area_Upper, Area_Lower, Area_right, Area_left
-				print 'Areas: ',Area_hex,Area_hex*Area_Q1, Area_hex*Area_Q2, Area_hex*Area_Q3, Area_hex*Area_Q4
-				print 'x0=',x0, 'y0=',y0, 'H=', H
-				print 'Total area= ',(Area_Q1+Area_Q2+Area_Q3+Area_Q4)#, Sector
-				
-
-		#Accounting for masked points 
-		a=1. ; b=1. ; c=1. ; d=1.
-		if i==0:
-			a=0.;
-		if j==0: 
-			b=0.;
-		if i==Nx-1:
-			c=0;
-		if j==Ny-1:
-			d=0;
-
-		fraction_used= ((yDxL*a*b) + (yDxC*b) + (yDxR*b*c) +(yCxL*a) + (yCxR*c) + (yUxL*a*d) + (yUxC*d) + (yUxR*c*d) + (yCxC))
-		if static_berg>0.5:
-			fraction_used=1.
-
-		mass_on_ocean[i,j,1]=mass_on_ocean[i,j,1]+(a*b*yDxL*Mass/fraction_used)
-		mass_on_ocean[i,j,2]=mass_on_ocean[i,j,2]+(b*yDxC*Mass/fraction_used)
-		mass_on_ocean[i,j,3]=mass_on_ocean[i,j,3]+(b*c*yDxR*Mass/fraction_used)
-		mass_on_ocean[i,j,4]=mass_on_ocean[i,j,4]+(a*yCxL*Mass/fraction_used)
-		mass_on_ocean[i,j,5]=mass_on_ocean[i,j,5]+(yCxC*Mass/fraction_used)
-		mass_on_ocean[i,j,6]=mass_on_ocean[i,j,6]+(c*yCxR*Mass/fraction_used)
-		mass_on_ocean[i,j,7]=mass_on_ocean[i,j,7]+(a*d*yUxL*Mass/fraction_used)
-		mass_on_ocean[i,j,8]=mass_on_ocean[i,j,8]+(d*yUxC*Mass/fraction_used)
-		mass_on_ocean[i,j,9]=mass_on_ocean[i,j,9]+(c*d*yUxR*Mass/fraction_used)
-
-
-		return mass_on_ocean
-
-
-def Create_icebergs(Radius, R_earth):
-	dx_berg=[]
-	dy_berg=[]
-	lat=[]
-	lon=[]
-	berg_count=0
-	
-	#Flags
-	adjust_lat_ref=True
-
-
-	#Developing some elements in cartesian coordinates:
-	lat_init=20.0 ; lon_init=0.0 #Starting point
-
-
-	for i in range(40):
-		x_start=Radius
-		y_start=(Radius)
-		x_val=x_start+(2*i*Radius)
-		for j in range(40):
-			y_val=y_start+(2*j*Radius)  ;# x_val=x_start + (np.sqrt(3)*Radius*i)
-
-			berg_count=berg_count+1
-			dx_berg.append(x_val)
-			dy_berg.append(y_val)
-
-	Number_of_bergs=berg_count
-
-	#Convert_to_lat_lon==True:
-	dlat_dy=(180/np.pi)*(1/R_earth)
-	#dlat_berg=(180/np.pi)*(1/R_earth)*dy_berg
-	#dlon_berg=(180/np.pi)*(1/R_earth)*(1/cos(lat_init*np.pi/180))*dx_berg
-	for i in range(Number_of_bergs):
-		#Finding latittude
-		lat.append(lat_init+(dlat_dy*dy_berg[i]))
-		#Finding longitude
-		if adjust_lat_ref==True:
-			lat_ref=lat_init+(dlat_dy*dy_berg[i])
-			#print lat_ref
-		dlon_dx=(180/np.pi)*(1/R_earth)*(1/np.cos(lat_ref*np.pi/180)) #Note that this depends on the latitude of the iceberg. Could approx this with lat_init.
-		lon.append(lon_init+(dlon_dx*dx_berg[i] ))
-
-	return [Number_of_bergs, lat, lon] 
-	
-def Create_lat_lon_grid(lat_min,lat_max,lon_min,lon_max, N_lat, N_lon):
-	grd_lat=np.linspace(lat_min,lat_max,N_lat)
-	grd_lon=np.linspace(lon_min,lon_max,N_lon)
-	field=np.zeros((N_lat,N_lon))
-
-	return [grd_lat, grd_lon, field]
-	
-def Projecting_to_local_cartesian(lat0, lon0, lat_corner, lon_corner, R_earth):
-	#Creates a local tangent plan around an iceberg at lat0, lon0
-	d_lat=(lat_corner-lat0)
-	d_lon=(lon_corner-lon0)
-
-	dy=R_earth*(np.pi/180.0)*d_lat
-	dx=R_earth*(np.pi/180.0)*cos(lat0*(np.pi/180))*d_lon
-	#dx=R_earth*(np.pi/180.0)*cos(lat_corner*(np.pi/180))*d_lon
-
-	return dy,dx
-
-
-def find_corners_of_cell(lat_berg,lon_berg,grd_lat,grd_lon):
-	j=np.sum(grd_lat<lat_berg)
-	i=np.sum(grd_lon<lon_berg)
-	print lat_berg,lon_berg
-	print grd_lat[j-1],  grd_lat[j]
-	print grd_lon[i-1],  grd_lon[i]
-	i1=i-1 ; j1=j-1
-	i2=i ; j2=j-1
-	i3=i   ; j3=j
-	i4=i-1   ; j4=j
-
-	return [j1,j2,j3,j4,i1,i2,i3,i4]
-
-def plot_grid_cell_and_point(lat_berg, lon_berg, lat1, lat2, lat3, lat4, lon1, lon2, lon3, lon4):
-	plt.plot(lon_berg,lat_berg,'o')
-	#plt.plot(np.array([lon1, lon2]), np.array([lat1, lat2]))
-	#plt.plot(np.array([lon2, lon3]), np.array([lat2, lat3]))
-	plt.plot(np.array([lon1, lon2, lon3, lon4, lon1]), np.array([lat1, lat2, lat3, lat4, lat1]))
-	plt.plot(lon1,lat1,'*r')
-	plt.plot(lon2,lat2,'*c')
-	plt.plot(lon4,lat3,'*g')
-	plt.plot(lon4,lat4,'*b')
-	eps_lat=(lat3-lat2)/2.
-	eps_lon=(lon2-lon1)/2.
-	#print 'lon:',  lon1,lon2, lon3, lon4
-	#print 'lat:', lat1,lat2, lat3, lat4
-	print eps_lat, eps_lon
-	plt.ylim([lat2-eps_lat, lat3+eps_lat])
-	plt.xlim([lon1-eps_lon, lon2+eps_lon])
-
-
-####################################################################################################################################################
-##########################################################  Main Program   #########################################################################
-####################################################################################################################################################
-
-def main():
-
-	#Parameters
-	R_earth=6360000.0
-	Radius=5000.0 #In meters
-
-	#Lat Lon Parameters
-	lat_min=20.0 ;	lat_max=50.0 ;	N_lat=5
-	lon_min=0.0  ;	lon_max=40.0 ;	N_lon=5
-	
-	
-	
-
-
-
-	#Defining Lat Lon
-	(grd_lat, grd_lon, field)= Create_lat_lon_grid(lat_min,lat_max,lon_min,lon_max, N_lat, N_lon)
-
-	#Creating Icebergs
-	#(Number_of_bergs, lat_berg, lon_berg)=Create_icebergs(Radius, R_earth)
-
-
-
-	lat_berg=32.0
-	lon_berg=22.2
-
-	#Finding grid index of cell of berg:
-	j1,j2,j3,j4,i1,i2,i3,i4	=find_corners_of_cell(lat_berg,lon_berg,grd_lat,grd_lon)
-	lat1=grd_lat[j1] ; lat2=grd_lat[j2]; lat3=grd_lat[j3]; lat4=grd_lat[j4]
-	lon1=grd_lon[i1] ; lon2=grd_lon[i2]; lon3=grd_lon[i3]; lon4=grd_lon[i4]
-	i_berg=i1 ;j_berg=j1 #Lower left point
-
-
-	#Converting points to tangent plane
-	(y_berg,x_berg)= Projecting_to_local_cartesian(lat_berg, lon_berg, lat_berg, lon_berg, R_earth)
-	(y1,x1)= Projecting_to_local_cartesian(lat_berg, lon_berg, lat1, lon1, R_earth)
-	(y2,x2)= Projecting_to_local_cartesian(lat_berg, lon_berg, lat2, lon2, R_earth)
-	(y3,x3)= Projecting_to_local_cartesian(lat_berg, lon_berg, lat3, lon3, R_earth)
-	(y4,x4)= Projecting_to_local_cartesian(lat_berg, lon_berg, lat4, lon4, R_earth)
-
-	#Normalization of the shape in tangent plane
-	#x_cell=(x_berg-x[i_val])/sqrt(grid_area)+0.5
-
-
-
-	#Plotting everything
-	plt.figure(figsize=(16,8))
-	plt.subplot(1,2,1)
-	plot_grid_cell_and_point(lat_berg,lon_berg, lat1, lat2, lat3, lat4, lon1, lon2, lon3, lon4)
-	plt.xlabel('lon') ; plt.ylabel('lat') ; 
-	plt.subplot(1,2,2)
-	plot_grid_cell_and_point(y_berg,x_berg, y1, y2, y3, y4, x1, x2, x3, x4)
-	plt.xlabel('x') ; plt.ylabel('y') ; 
-	print x1,x2,x3,x4
-	print y1,y2,y3,y4
-		
-
-
-
-
-
-	#Plotting berg positions
-	#plt.pcolor(grd_lon,grd_lat,field)
-	#plt.colorbar
-	#plt.scatter(lon_berg, lat_berg,c='red')
-
-	plt.show()
-	print 'Script complete'
-
-
-
-if __name__ == '__main__':
-	main()
-	#sys.exit(main())
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/flat_isomip_create.py b/tests/Iceberg_repository/Scripts_and_analysis/flat_isomip_create.py
deleted file mode 100755
index 9338dff..0000000
--- a/tests/Iceberg_repository/Scripts_and_analysis/flat_isomip_create.py
+++ /dev/null
@@ -1,71 +0,0 @@
-#!/usr/bin/env python
-
-###############################################################################################
-from netCDF4 import Dataset
-import numpy as np
-import os
-import numpy
-import netCDF4 as nc
-#import matplotlib
-#import matplotlib.pyplot as plt
-#from pylab import *
-#import pdb
-#import argparse
-#This combination allows you to access the varibale imputted from the command line.
-#import sys
-
-#Clear screen
-def main():
-
-	os.system('clear')
-	input_filename='input_files/isomip_ice_shelf1.nc'
-	new_filename='output_files/flat_isomip_ice_shelf1.nc'
-
-	#f=Dataset(input_geometry_filename,'r')
-	#g=Dataset(new_filename,'w') # w if for creating a file
-
-	rho_ice=850.
-
-	with nc.Dataset(input_filename) as file:
-		thick = file.variables['thick'][:,:]
-		area = file.variables['area'][:,:]
-		height = file.variables['height'][:,:]
-
-	M= thick.shape
-	ny=M[0]
-	nx=M[1]
-	print nx,ny
-	print thick.shape
-
-	#Setting thickness to a prescribed value
-	prescribed_thickness=1.
-	thick[np.where(thick>0)]=prescribed_thickness
-
-	
-	#Creating the file
-	g=Dataset(new_filename,'w') # w if for creating a file
-
-	yt=g.createDimension('yt',ny)
-	xt=g.createDimension('xt',nx)
-
-	thick_h=g.createVariable('thick','f4',('yt','xt'))
-	g.variables['thick'][:]=thick>0
-	thick_h=g.createVariable('area','f4',('yt','xt'))
-	g.variables['area'][:]=area
-	height_h=g.createVariable('height','f4',('yt','xt'))
-	g.variables['height'][:]=height
-
-	g.sync()
-	g.close()
-
-
-
-
-
-	print 'Script complete'
-
-
-
-if __name__ == '__main__':
-        main()
-        #sys.exit(main())
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/grid_cartesian_create.py b/tests/Iceberg_repository/Scripts_and_analysis/grid_cartesian_create.py
deleted file mode 100755
index 6aa3510..0000000
--- a/tests/Iceberg_repository/Scripts_and_analysis/grid_cartesian_create.py
+++ /dev/null
@@ -1,395 +0,0 @@
-
-# coding: utf-8
-
-# In[2]:
-
-import scipy.io.netcdf
-import numpy
-get_ipython().magic('pylab inline')
-
-
-# Model grid will have ni x nj h-point grid cells
-
-# In[3]:
-
-nj,ni = 40,240
-
-
-# A mosaic file has a supergrid of an integer refinement (e.g. 2*ni x 2*nj cells)
-
-# In[4]:
-
-snj, sni = 2*nj, 2*ni
-
-
-# Uniform resolution of the ocean model grid will be dxo x dyo
-
-# In[5]:
-
-dxo = 2.e3
-dyo = 2.e3
-
-
-# Using a supergrid refinement of 2, the grid lengths, area and coordinates are:
-
-# In[6]:
-
-dx = (0.5 * dxo) * numpy.ones((snj+1,sni))
-dy = (0.5 * dyo) * numpy.ones((snj,sni+1))
-area = (0.25 * (dxo * dyo)) * numpy.ones((snj,sni))
-x = numpy.zeros((snj+1,sni+1))
-x[:,1:] = numpy.cumsum( dx, axis=-1 )
-y = numpy.zeros((snj+1,sni+1))
-y[1:,:] = numpy.cumsum( dy, axis=-2 )
-
-
-# In[7]:
-
-# A helper function to use when writing strings in a netcdf file
-def set_string(variable, value):
-    """Sets "variable" to "value" padded with blanks where
-    "variable" is a netcdf variable object and "value" is a string."""
-    variable[:] = '\000' * variable.shape[0]
-    variable[:len(value)] = value
-
-
-# Create a netcdf3 horizontal ocean-grid file...
-
-# In[8]:
-
-rg = scipy.io.netcdf_file('ocean_hgrid.nc','w',version=2)
-
-
-# In[9]:
-
-rg.createDimension('nx',sni)
-rg.createDimension('ny',snj)
-rg.createDimension('nxp',sni+1)
-rg.createDimension('nyp',snj+1)
-rg.createDimension('string',255)
-
-
-# In[10]:
-
-dx_h = rg.createVariable('dx','f8',('nyp','nx',))
-dx_h.units = 'm'
-dy_h = rg.createVariable('dy','f8',('ny','nxp',))
-dy_h.units = 'm'
-area_h = rg.createVariable('area','f8',('ny','nx',))
-area_h.units = 'm2'
-x_h = rg.createVariable('x','f8',('nyp','nxp',))
-x_h.units = 'm'
-y_h = rg.createVariable('y','f8',('nyp','nxp',))
-y_h.units = 'm'
-tile = rg.createVariable('tile','c',('string',))
-
-
-# In[11]:
-
-dx_h[:,:] = dx[:,:]
-dy_h[:,:] = dy[:,:]
-area_h[:,:] = area[:,:]
-x_h[:,:] = x[:,:]
-y_h[:,:] = y[:,:]
-tile[:] = '\000' * 255
-tile[:5] = 'tile1'
-set_string(tile,'tile1')
-
-
-# In[12]:
-
-rg.close()
-
-
-# Create a netcdf3 ocean-mask file...
-
-# In[13]:
-
-rg = scipy.io.netcdf_file('ocean_mask.nc','w',version=2)
-rg.createDimension('nx',ni)
-rg.createDimension('ny',nj)
-mask = rg.createVariable('mask','f4',('ny','nx',))
-mask[:,:] = 1.
-rg.close()
-
-
-# Create a mosaic description for the above grid file...
-
-# In[14]:
-
-rg = scipy.io.netcdf_file('ocean_mosaic.nc','w',version=2)
-rg.createDimension('ntiles',1)
-rg.createDimension('string',255)
-mosaic = rg.createVariable('mosaic','c',('string',))
-mosaic.standard_name = 'grid_mosaic_spec'
-mosaic.children = 'contacts'
-mosaic.grid_descriptor = ''
-gridlocation = rg.createVariable('gridlocation','c',('string',))
-gridlocation.standard_name = 'grid_file_location'
-gridfiles = rg.createVariable('gridfiles','c',('ntiles','string',))
-gridtiles = rg.createVariable('gridtiles','c',('ntiles','string',))
-rg.grid_version = '0.2'
-# Fill in data
-mosaic[:] = '\000' * 255
-mosaic[:12] = 'ocean_mosaic'
-gridlocation[:] = '\000' * 255
-gridlocation[:2] = './'
-gridfiles[:] = '\000' * 255
-gridfiles[0,:14] = 'ocean_hgrid.nc'
-gridtiles[:] = '\000' * 255
-gridtiles[0,:5] = 'tile1'
-rg.close()
-
-
-# In[15]:
-
-get_ipython().system('pwd')
-
-
-# In[16]:
-
-# Fake a ocean_topog.nc file
-rg = scipy.io.netcdf_file('ocean_topog.nc','w',version=2)
-rg.createDimension('nx',ni)
-rg.createDimension('ny',nj)
-rg.createDimension('ntiles',1)
-depth = rg.createVariable('depth','f4',('ny','nx',))
-depth[:,:] = 1000.
-depth[-1,-1] =0
-rg.close()
-
-
-# In[17]:
-
-#fre_nctools/tools/make_quick_mosaic/make_quick_mosaic --input_mosaic ocean_mosaic.nc --ocean_topog ocean_topog.nc
-
-
-# In[18]:
-
-rg = scipy.io.netcdf_file('atmos_mosaic_tile1Xland_mosaic_tile1_BLAH.nc','w',version=2) # atmos_mosaic_tile1Xland_mosaic_tile1.nc
-rg.createDimension('string',255)
-rg.createDimension('ncells',1)
-rg.createDimension('two',2)
-contact = rg.createVariable('contact','c',('string',))
-contact.standard_name = 'grid_contact_spec'
-contact.contact_type = 'exchange'
-contact.parent1_cell = 'tile1_cell'
-contact.parent2_cell = 'tile2_cell'
-contact.xgrid_area_field = 'xgrid_area'
-contact.distant_to_parent1_centroid = 'tile1_distance'
-contact.distant_to_parent2_centroid = 'tile2_distance'
-tile1_cell = rg.createVariable('tile1_cell','f8',('ncells','two',))
-tile1_cell.standard_name = 'parent_cell_indices_in_mosaic1'
-tile2_cell = rg.createVariable('tile2_cell','f8',('ncells','two',))
-tile2_cell.standard_name = 'parent_cell_indices_in_mosaic2'
-xgrid_area = rg.createVariable('xgrid_area','f8',('ncells',))
-xgrid_area.standard_name = 'exchange_grid_area'
-xgrid_area.units = 'm2'
-tile1_distance = rg.createVariable('tile1_distance','f8',('ncells','two'))
-tile1_distance.standard_name = 'distance_from_parent1_cell_centroid'
-tile2_distance = rg.createVariable('tile2_distance','f8',('ncells','two'))
-tile2_distance.standard_name = 'distance_from_parent2_cell_centroid'
-rg.grid_version = '0.2'
-# Fill in data
-contact[:] = '\000' * 255
-contact[:37] = 'atmos_mosaic:tile1::land_mosaic:tile1'
-tile1_cell[:] = [ni,nj]
-tile2_cell[:] = [ni,nj]
-xgrid_area[:] = dxo * dyo
-tile1_distance[:] = 0.
-tile2_distance[:] = 0.
-rg.close()
-
-
-# In[19]:
-
-rg = scipy.io.netcdf_file('atmos_mosaic_tile1Xocean_mosaic_tile1_BLAH.nc','w',version=2) # atmos_mosaic_tile1Xocean_mosaic_tile1.nc
-rg.createDimension('string',255)
-rg.createDimension('ncells',ni*nj-1) # -1 is for a single land point
-rg.createDimension('two',2)
-contact = rg.createVariable('contact','c',('string',))
-contact.standard_name = 'grid_contact_spec'
-contact.contact_type = 'exchange'
-contact.parent1_cell = 'tile1_cell'
-contact.parent2_cell = 'tile2_cell'
-contact.xgrid_area_field = 'xgrid_area'
-contact.distant_to_parent1_centroid = 'tile1_distance'
-contact.distant_to_parent2_centroid = 'tile2_distance'
-tile1_cell = rg.createVariable('tile1_cell','f8',('ncells','two',))
-tile1_cell.standard_name = 'parent_cell_indices_in_mosaic1'
-tile2_cell = rg.createVariable('tile2_cell','f8',('ncells','two',))
-tile2_cell.standard_name = 'parent_cell_indices_in_mosaic2'
-xgrid_area = rg.createVariable('xgrid_area','f8',('ncells',))
-xgrid_area.standard_name = 'exchange_grid_area'
-xgrid_area.units = 'm2'
-tile1_distance = rg.createVariable('tile1_distance','f8',('ncells','two'))
-tile1_distance.standard_name = 'distance_from_parent1_cell_centroid'
-tile2_distance = rg.createVariable('tile2_distance','f8',('ncells','two'))
-tile2_distance.standard_name = 'distance_from_parent2_cell_centroid'
-rg.grid_version = '0.2'
-# Fill in data
-contact[:] = '\000' * 255
-contact[:37] = 'atmos_mosaic:tile1::land_mosaic:tile1'
-tile1_cell[:] = [ni,nj]
-tile2_cell[:] = [ni,nj]
-xgrid_area[:] = dxo * dyo
-for j in range(nj):
-    for i in range(ni):
-        if (i,j) != (ni-1,nj-1):
-            tile1_cell[i+ni*j] = [i,j]
-            tile2_cell[i+ni*j] = [i,j]
-            tile1_distance[i+ni*j] = [0,0]
-            tile2_distance[i+ni*j] = [0,0]
-            xgrid_area[i+ni*j] = dxo * dyo
-rg.close()
-
-
-# In[20]:
-
-rg = scipy.io.netcdf_file('land_mosaic_tile1Xocean_mosaic_tile1_BLAH.nc','w',version=2) # land_mosaic_tile1Xocean_mosaic_tile1.nc
-rg.createDimension('string',255)
-rg.createDimension('ncells',ni*nj-1) # -1 is for a single land point
-rg.createDimension('two',2)
-contact = rg.createVariable('contact','c',('string',))
-contact.standard_name = 'grid_contact_spec'
-contact.contact_type = 'exchange'
-contact.parent1_cell = 'tile1_cell'
-contact.parent2_cell = 'tile2_cell'
-contact.xgrid_area_field = 'xgrid_area'
-contact.distant_to_parent1_centroid = 'tile1_distance'
-contact.distant_to_parent2_centroid = 'tile2_distance'
-tile1_cell = rg.createVariable('tile1_cell','f8',('ncells','two',))
-tile1_cell.standard_name = 'parent_cell_indices_in_mosaic1'
-tile2_cell = rg.createVariable('tile2_cell','f8',('ncells','two',))
-tile2_cell.standard_name = 'parent_cell_indices_in_mosaic2'
-xgrid_area = rg.createVariable('xgrid_area','f8',('ncells',))
-xgrid_area.standard_name = 'exchange_grid_area'
-xgrid_area.units = 'm2'
-tile1_distance = rg.createVariable('tile1_distance','f8',('ncells','two'))
-tile1_distance.standard_name = 'distance_from_parent1_cell_centroid'
-tile2_distance = rg.createVariable('tile2_distance','f8',('ncells','two'))
-tile2_distance.standard_name = 'distance_from_parent2_cell_centroid'
-rg.grid_version = '0.2'
-# Fill in data
-contact[:] = '\000' * 255
-contact[:37] = 'atmos_mosaic:tile1::land_mosaic:tile1'
-tile1_cell[:] = [ni,nj]
-tile2_cell[:] = [ni,nj]
-xgrid_area[:] = dxo * dyo
-for j in range(nj):
-    for i in range(ni):
-        if (i,j) != (ni-1,nj-1):
-            tile1_cell[i+ni*j] = [i,j]
-            tile2_cell[i+ni*j] = [i,j]
-            tile1_distance[i+ni*j] = [0,0]
-            tile2_distance[i+ni*j] = [0,0]
-            xgrid_area[i+ni*j] = dxo * dyo
-rg.close()
-
-
-# In[24]:
-
-rg = scipy.io.netcdf_file('mosaic_BLAH.nc','w',version=2) # land_mosaic_tile1Xocean_mosaic_tile1.nc
-rg.createDimension('string',255)
-rg.createDimension('nfile_aXo',1) # -1 is for a single land point
-rg.createDimension('nfile_aXl',1) # -1 is for a single land point
-rg.createDimension('nfile_lXo',1) # -1 is for a single land point
-
-atm_mosaic_dir = rg.createVariable('atm_mosaic_dir','c',('string',))
-atm_mosaic_dir.standard_name = 'directory_storing_atmosphere_mosaic'
-
-atm_mosaic_file = rg.createVariable('atm_mosaic_file','c',('string',))
-atm_mosaic_file.standard_name = 'atmosphere_mosaic_file_name'
-
-atm_mosaic = rg.createVariable('atm_mosaic','c',('string',))
-atm_mosaic.standard_name = 'atmosphere_mosaic_name'
-
-lnd_mosaic_dir = rg.createVariable('lnd_mosaic_dir','c',('string',))
-lnd_mosaic_dir.standard_name = 'directory_storing_land_mosaic'
-
-lnd_mosaic_file = rg.createVariable('lnd_mosaic_file','c',('string',))
-lnd_mosaic_file.standard_name = 'land_mosaic_file_name'
-
-lnd_mosaic = rg.createVariable('lnd_mosaic','c',('string',))
-lnd_mosaic.standard_name = 'land_mosaic_name'
-
-ocn_mosaic_dir = rg.createVariable('ocn_mosaic_dir','c',('string',))
-ocn_mosaic_dir.standard_name = 'directory_storing_ocean_mosaic'
-
-ocn_mosaic_file = rg.createVariable('ocn_mosaic_file','c',('string',))
-ocn_mosaic_file.standard_name = 'ocean_mosaic_file_name'
-
-ocn_mosaic = rg.createVariable('ocn_mosaic','c',('string',))
-ocn_mosaic.standard_name = 'ocean_mosaic_name'
-
-
-ocn_topog_dir = rg.createVariable('ocn_topog_dir','c',('string',))
-ocn_mosaic_dir.standard_name = 'directory_storing_ocean_topog'
-
-ocn_topog_file = rg.createVariable('ocn_topog_file','c',('string',))
-ocn_topog_file.standard_name = 'ocean_topog_file_name'
-
-aXo_file = rg.createVariable('aXo_file','c',('string',))
-aXo_file.standard_name = 'atmXocn_exchange_grid_file'
-
-aXl_file = rg.createVariable('aXl_file','c',('string',))
-aXl_file.standard_name = 'atmXlnd_exchange_grid_file'
-
-lXo_file = rg.createVariable('lXo_file','c',('string',))
-lXo_file.standard_name = 'lndXocn_exchange_grid_file'
-
-#Global attributes
-rg.grid_version = '0.2'
-rg.code_version = "$Name:  $"
-rg.history = "/net2/aja/workspace/MOM6-examples/ice_ocean_SIS2/OM4_025/preprocessing/fre_nctools/tools/make_quick_mosaic/make_quick_mosaic --input_mosaic ocean_mosaic.nc --ocean_topog ocean_topog.nc"
-# Fill in data
-atm_mosaic_dir[:] = '\000' * 255
-atm_mosaic_dir[:2] = './'
-
-atm_mosaic_file[:] = '\000' * 255
-atm_mosaic_file[:15] = 'ocean_mosaic.nc'
-
-atm_mosaic[:] = '\000' * 255
-atm_mosaic[:12] = 'atmos_mosaic'
-
-lnd_mosaic_dir[:] = '\000' * 255
-lnd_mosaic_dir[:2] = './'
-
-lnd_mosaic_file[:] = '\000' * 255
-lnd_mosaic_file[:15] = 'ocean_mosaic.nc'
-
-lnd_mosaic[:] = '\000' * 255
-lnd_mosaic[:11] = 'land_mosaic'
-
-ocn_mosaic_dir[:] = '\000' * 255
-ocn_mosaic_dir[:2] = './'
-
-ocn_mosaic_file[:] = '\000' * 255
-ocn_mosaic_file[:15] = 'ocean_mosaic.nc'
-
-ocn_mosaic[:] = '\000' * 255
-ocn_mosaic[:12] = 'ocean_mosaic'
-
-ocn_topog_dir[:] = '\000' * 255
-ocn_topog_dir[:2] = './'
-
-ocn_topog_file[:] = '\000' * 255
-ocn_topog_file[:14] = 'ocean_topog.nc'
-
-aXo_file[:] = '\000' * 255
-aXo_file[:40] = 'atmos_mosaic_tile1Xocean_mosaic_tile1.nc'
-
-aXl_file[:] = '\000' * 255
-aXl_file[:39] = 'atmos_mosaic_tile1Xland_mosaic_tile1.nc'
-
-lXo_file[:] = '\000' * 255
-lXo_file[:39] = 'land_mosaic_tile1Xocean_mosaic_tile1.nc'
-
-rg.close()
-
-
-
-# In[ ]:
-
-
-
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/hexagon_area.py b/tests/Iceberg_repository/Scripts_and_analysis/hexagon_area.py
deleted file mode 100755
index 0315036..0000000
--- a/tests/Iceberg_repository/Scripts_and_analysis/hexagon_area.py
+++ /dev/null
@@ -1,1472 +0,0 @@
-#!/usr/bin/env python
-
-#First import the netcdf4 library
-from netCDF4 import Dataset  # http://code.google.com/p/netcdf4-python/
-import numpy as np  # http://code.google.com/p/netcdf4-python/
-import matplotlib
-import math
-import os
-matplotlib.use("tkagg")
-#from pylab import *
-#import matplotlib.pyplot as plt
-import pdb
-import netCDF4 as nc
-
-
-
-#######################
-
-def Divide_hexagon_into_4_quadrants_old(x0,y0,H):
-	S=(2/np.sqrt(3))*H
-	Area_hex=3*(np.sqrt(3)/2)*(S**2)  #Area of the hexagon (should be equal to Area/grid_area, since it is not dim)	 - check this
-	#print( 'y0,H',y0, H	
-	#Defining boundaries of hexagon, and if statements to see which side of the boundary you are on
-	W1= False ; W2=False ;W3=False ;W4=False ;W5=False ;W6=False ;H1=False ;V1=False ;V2=False
-	W1=(-y0<-np.sqrt(3)*(-x0) + ((np.sqrt(3)*(S))));#upper right
-	W2=(-y0<(H));#Top
-	W3=(-y0<np.sqrt(3)*(-x0) + ((np.sqrt(3)*(S))));#Upper left
-	W4=(-y0<np.sqrt(3)*(-x0) + (-(np.sqrt(3)*(S))));#Lower right
-	W5=(-y0>-H);#Bottom
-	W6=(-y0<-np.sqrt(3)*(-x0) + (-(np.sqrt(3)*(S))));#Lower left
-		
-
-	T1=(-x0<S) #Right
-	T2=(-y0<(H));#Top
-	T3= (-x0>-S) #Left
-	T4=(-y0>-H);#Bottom
-
-	H1=(y0<0);
-	V1=(x0<-(S/2));
-	V2=(x0<(S/2));
-	  
-	#Deciding if the origin is within the hexagon
-	#print( W1 , W2 , W3 , W4 , W5 , W6
-	#if In_hex:
-	#	print( In_hex
-		
-	#Calculating the area of the top and bottom half of the hexagon, 2 Cases for the majority above and below the y0=0 line
-	#(and two more for the hexagon totally above and below the y0=0 line)
-	if abs(y0)<H:
-		Trapesium=((np.sqrt(3)*H)-(abs(y0)/np.sqrt(3)))*(H-abs(y0));
-		if y0>=0:
-			Area_Lower=Trapesium;
-			Area_Upper=Area_hex-Trapesium;
-		else:
-			Area_Upper=Trapesium;
-			Area_Lower=Area_hex-Trapesium;
-	else:
-		if y0>=0:
-			Area_Lower=0.;
-			Area_Upper=Area_hex;
-		else: 
-			Area_Lower=Area_hex;
-			Area_Upper=0.;
-
-	#Calcularing Left and Right area of the hexagon, about the x0=0 line, 3 cases:
-	#(and two more for when the hexagon is totally to the left or right of the x0=0 line)
-	if abs(x0)<S:
-		if abs(x0)<S/2:
-			Rectangle=(abs(x0)*2*H);
-			Big_side =(Area_hex/2) +Rectangle;
-			Small_side=Area_hex-Big_side;
-		else:
-			Triangle=(np.sqrt(3))*((S-abs(x0))**2);
-			Small_side=Triangle;
-			Big_side=Area_hex-Small_side;
-		if x0>=0.:
-			Area_right=Big_side;
-			Area_left=Small_side;
-		else:
-			Area_right=Small_side;
-			Area_left=Big_side;
-	else:
-		if x0>=0.:
-			Area_right=Area_hex;
-			Area_left=0.;
-		else:
-			Area_right=0.;
-			Area_left=Area_hex;
-
-	In_hex= W1 & W2 & W3 & W4 & W5 & W6;
-	In_hex_box=T1 & T2 & T3 & T4
-	Area_Q1=0.; Area_Q2=0. ; Area_Q3=0.; Area_Q4=0.;
-	Sector=0
-	#if In_hex==False: #Then the hexagon is completely contained in the middle cell
-	if In_hex_box==False: #Then the hexagon is completely contained in the middle cell
-		Sector=-1
-		#mass_on_ocean[i,j,5]=mass_on_ocean[i,j,5]+Mass
-		if min(Area_Upper,Area_Lower)==0.:
-			Sector=-2
-			if Area_Upper==0.:
-				Area_Q3=Area_left;
-				Area_Q4=Area_right;
-			if Area_Lower==0.:
-				Area_Q1=Area_right;
-				Area_Q2=Area_left;
-
-		elif min(Area_right,Area_left)==0.:
-			Sector=-3
-			if Area_right==0.:
-				Area_Q2=Area_Upper;
-				Area_Q3=Area_Lower;
-		
-			if Area_left==0.:
-				Area_Q1=Area_Upper;
-				Area_Q4=Area_Lower;
-		
-
-		#yCxC=1.
-		#print( 'out of hex'
-
-	else:
-		#Determine which sector within the hexagon you are in. (sectors 1 to 6 go counter clockwise starting with top right)
-		if (H1==True):	#Bottom half
-			if V1:
-				#if W1==False:
-				if ((y0+(np.sqrt(3)*(x0+S)))<=0.):
-					Sector=1;
-				else:
-					Sector=2;
-			elif (V1==False) & (V2==True):
-				Sector=3;
-			else:  
-				#if (W3==True):
-				if ((y0-(np.sqrt(3)*(x0-S)))>=0.):
-					Sector=4;
-				else:
-					Sector=5;
-		else:  #Bottom half
-			if V1:
-				#if W6==False:
-				if ((y0 -(np.sqrt(3)*(x0+S)))>=0.):
-					Sector=10;
-				else:
-					Sector=9;
-			elif (V1==False) & (V2==True):
-				Sector=8;
-			else:  
-				#if (W4==True):
-				if ((y0+(np.sqrt(3)*(x0-S)))<=0.):
-					Sector=7;
-				else:
-					Sector=6;
-
-		#print( Sector
-
-		#If the hexagon is in Sector 1,3,4 or 6, then the intersetion of the hexagon and the corresponding sector forms a baby triangle
-		#If the hexagon is in Sector 2,5 then the intersetion of the hexagon and the corresponding sector forms a baby trapesoid
-		if Sector==2 or Sector==4  or Sector==7 or Sector==9:
-			Baby_triangle=(1/(2*np.sqrt(3)))*((-abs(y0)+(np.sqrt(3)*(S-abs(x0))))**2);
-		else:
-			#Baby_trap= (H-abs(y0)) * ((-H-abs(y0)+(2*np.sqrt(3)*(S-abs(x0))))/(2*np.sqrt(3)));  
-			Baby_trap=(H-abs(y0))*((S-abs(x0) - ((H+abs(y0))/(2*np.sqrt(3))))) ;
-
-		#Finally, we assign the correct areas in each quadrant (Q1,Q2,Q3,Q4), depending on which sector you are in.
-		C1=0.;C2=0.;C3=0.;C4=0.;
-
-		#Corner cases
-		if Sector==2:
-			Area_Q1=Baby_triangle;
-			Area_Q2=Area_Upper-Area_Q1
-			Area_Q3=Area_left-Area_Q2
-			Area_Q4=Area_right-Area_Q1
-
-		if Sector==4:
-			Area_Q2=Baby_triangle;
-			Area_Q1=Area_Upper-Area_Q2
-			Area_Q3=Area_left-Area_Q2
-			Area_Q4=Area_right-Area_Q1
-
-		if Sector==7:
-			Area_Q3=Baby_triangle;
-			Area_Q2=Area_left-Area_Q3
-			Area_Q1=Area_Upper-Area_Q2
-			Area_Q4=Area_right-Area_Q1
-
-		if Sector==9:
-			Area_Q4=Baby_triangle;
-			Area_Q1=Area_right-Area_Q4
-			Area_Q2=Area_Upper-Area_Q1
-			Area_Q3=Area_left-Area_Q2
-	
-		#Center cases
-		if Sector==3:
-			if x0<=0.:
-				Area_Q1=Baby_trap;
-				Area_Q2=Area_Upper-Area_Q1;
-				Area_Q3=Area_left-Area_Q2;
-				Area_Q4=Area_right-Area_Q1;
-			else:
-				Area_Q2=Baby_trap;
-				Area_Q1=Area_Upper-Area_Q2;
-				Area_Q3=Area_left-Area_Q2;
-				Area_Q4=Area_right-Area_Q1;
-			
-		if Sector==8:
-			if x0<=0.:
-				Area_Q4=Baby_trap;
-				Area_Q3=Area_Lower-Area_Q4;
-				Area_Q1=Area_right-Area_Q4;
-				Area_Q2=Area_Upper-Area_Q1;
-			else:
-				Area_Q3=Baby_trap;
-				Area_Q4=Area_Lower-Area_Q3;
-				Area_Q1=Area_right-Area_Q4;
-				Area_Q2=Area_Upper-Area_Q1;
-
-		#Outside triangle cases:
-		if Sector==1:
-			Area_Q1=0.;
-			Area_Q2=Area_Upper;
-			Area_Q4=Area_right;
-			Area_Q3=Area_left-Area_Q2;
-		
-		if Sector==5:
-			Area_Q2=0.;
-			Area_Q1=Area_Upper;
-			Area_Q3=Area_left;
-			Area_Q4=Area_Lower-Area_Q3;
-
-		if Sector==6:
-			Area_Q3=0.;
-			Area_Q2=Area_left;
-			Area_Q4=Area_Lower;
-			Area_Q1=Area_right-Area_Q4;
-		
-		if Sector==10:
-			Area_Q4=0.;
-			Area_Q3=Area_Lower;
-			Area_Q1=Area_right;
-			Area_Q2=Area_left-Area_Q3;
-
-		#print( x0,y0,Sector
-	return [Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4]
-
-
-
-def Hexagon_into_quadrants_using_triangles_across_lines(x0,y0,H,theta,	Px, Py, Qx, Qy, Rx, Ry, Sx, Sy ):
-	#In this routine, the hexagon is divided across lines PQ, RS.	 
-	#Length of side of Hexagon
-	S=(2/np.sqrt(3))*H;  
-
-	#Finding positions of corners
-	C1x=S		; C1y=0.  #Corner 1 (right)
-	C2x=H/np.sqrt(3.)  ; C2y=H;  #Corner 2 (top right)
-	C3x=-H/np.sqrt(3.) ; C3y=H;  #Corner 3 (top left)
-	C4x=-S		; C4y=0.; #Corner 4 (left)
-	C5x=-H/np.sqrt(3.) ; C5y=-H; #Corner 5 (bottom right)
-	C6x=H/np.sqrt(3.)  ; C6y=-H; #Corner 6 (bottom right)
-
-	#Finding positions of corners
-	[C1x,C1y]=rotate_and_translate(C1x,C1y,theta,x0,y0)
-	[C2x,C2y]=rotate_and_translate(C2x,C2y,theta,x0,y0)
-	[C3x,C3y]=rotate_and_translate(C3x,C3y,theta,x0,y0)
-	[C4x,C4y]=rotate_and_translate(C4x,C4y,theta,x0,y0)
-	[C5x,C5y]=rotate_and_translate(C5x,C5y,theta,x0,y0)
-	[C6x,C6y]=rotate_and_translate(C6x,C6y,theta,x0,y0)
-	 
-	#Area of Hexagon is the sum of the triangles
-	[T12_Area,T12_Q1,T12_Q2,T12_Q3,T12_Q4]=Triangle_divided_into_four_parts(x0,y0,C1x,C1y,C2x,C2y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T012
-	[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]=Triangle_divided_into_four_parts(x0,y0,C2x,C2y,C3x,C3y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
-	[T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4]=Triangle_divided_into_four_parts(x0,y0,C3x,C3y,C4x,C4y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T034
-	[T45_Area,T45_Q1,T45_Q2,T45_Q3,T45_Q4]=Triangle_divided_into_four_parts(x0,y0,C4x,C4y,C5x,C5y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
-	[T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4]=Triangle_divided_into_four_parts(x0,y0,C5x,C5y,C6x,C6y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
-	[T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4]=Triangle_divided_into_four_parts(x0,y0,C6x,C6y,C1x,C1y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
-	
-	#Area of Hexagon is the sum of the triangles
-	#print( '1:', Triangle_divided_into_four_parts(x0,y0,C1x,C1y,C2x,C2y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T012
-	#print( '1b:', Triangle_divided_into_four_quadrants(x0,y0,C1x,C1y,C2x,C2y); #T012
-	#print( '2', Triangle_divided_into_four_parts(x0,y0,C2x,C2y,C3x,C3y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
-	#print( '2b',Triangle_divided_into_four_quadrants(x0,y0,C2x,C2y,C3x,C3y); #T023
-	#print( '3:',Triangle_divided_into_four_parts(x0,y0,C3x,C3y,C4x,C4y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T034
-	#print( '3b',Triangle_divided_into_four_quadrants(x0,y0,C3x,C3y,C4x,C4y); #T034
-	#print( '4',Triangle_divided_into_four_parts(x0,y0,C4x,C4y,C5x,C5y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
-	#print( '4b:',Triangle_divided_into_four_quadrants(x0,y0,C4x,C4y,C5x,C5y); #T023
-	#print( '5', Triangle_divided_into_four_parts(x0,y0,C5x,C5y,C6x,C6y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
-	#print( '5b',Triangle_divided_into_four_quadrants(x0,y0,C5x,C5y,C6x,C6y); #T023
-	#print( '6:',Triangle_divided_into_four_parts(x0,y0,C6x,C6y,C1x,C1y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
-	#print( '6b',Triangle_divided_into_four_quadrants(x0,y0,C6x,C6y,C1x,C1y); #T023
-
-	#Summing up
-	Area_hex=T12_Area+T23_Area+T34_Area+T45_Area+T56_Area+T61_Area;
-	Area_Q1=T12_Q1+T23_Q1+T34_Q1+T45_Q1+T56_Q1+T61_Q1;
-	Area_Q2=T12_Q2+T23_Q2+T34_Q2+T45_Q2+T56_Q2+T61_Q2;
-	Area_Q3=T12_Q3+T23_Q3+T34_Q3+T45_Q3+T56_Q3+T61_Q3;
-	Area_Q4=T12_Q4+T23_Q4+T34_Q4+T45_Q4+T56_Q4+T61_Q4;
-	#Area_Q4=Area_hex-(Area_Q1+Area_Q2+Area_Q3)
-
-
-
-
-	#if  (abs(x0-(-0.186672393129))<0.00001)  and (abs(y0-(-0.436171))<0.00001):
-	#	print( 'Triangle 1,xo,y0',x0,y0 
-	#	print( 'Triangle 1H,S',H,S 
-	#	print( 'Triangle 1,Corners',C1x,C1y,C2x,C2y 
-	#	print( 'Triangle 1, Area full', T12_Area
-	#	print( 'Triangle 1, Area T1', T12_Q1
-	#	print( 'Triangle 1, Area T2', T12_Q2
-	#	print( 'Triangle 1, Area T3', T12_Q3
-	#	print( 'Triangle 1, Area T4', T12_Q4 
-	#	#print( 'Triangle 2',x0,y0,C2x,C2y,C3x,C3y,T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4
-	#	#print( 'Triangle 3',x0,y0,C3x,C3y,C4x,C4y,T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4 
-	#	#print( 'Triangle 4',x0,y0,C4x,C4y,C5x,C5y,T45_Area,T45_Q1,T45_Q2,T45_Q3,T45_Q4
-	#	#print( 'Triangle 5',x0,y0,C5x,C5y,C6x,C6y,T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4 
-	#	#print( 'Triangle 6',x0,y0,C6x,C6y,C1x,C1y,T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4
-
-	Area_Q1=max(Area_Q1,0.);
-	Area_Q2=max(Area_Q2,0.);
-	Area_Q3=max(Area_Q3,0.);
-	Area_Q4=max(Area_Q4,0.);
-
-
-	Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
-	if (abs(Error)>0.01):
-		print(	'diamonds, hex error, H,x0,y0, Error', H, x0 , y0, Error)
-		print( 'diamonds, hex error, Areas',Area_hex, (Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,	 Area_Q4)
-		print( 'Hexagon error is large!!')
-
-
-
-	#Adjust Areas so that the error is zero by subtracting the error from the largest sector.
-	if  (((Area_Q1>=Area_Q2) and (Area_Q1>=Area_Q3)) and (Area_Q1>=Area_Q4)):
-		#print( 'fix1',Error
-		Area_Q1=Area_Q1+Error
-	elif  (((Area_Q2>=Area_Q1) and (Area_Q2>=Area_Q3)) and (Area_Q2>=Area_Q4)):
-		#print( 'fix2', Error
-		Area_Q2=Area_Q2+Error
-	elif  (((Area_Q3>=Area_Q1) and (Area_Q3>=Area_Q2)) and (Area_Q3>=Area_Q4)):
-		#print( 'fix3',Error
-		Area_Q3=Area_Q3+Error
-	elif  (((Area_Q4>=Area_Q1) and (Area_Q4>=Area_Q2)) and (Area_Q4>=Area_Q3)):
-		#print( 'fix4',Error
-		Area_Q4=Area_Q4+Error
-	else:
-		print( 'There is some thing wrong with this hexagon. Something very wrong')
-
-	#Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
-	Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
-	if ((abs(Error)>0.01)):
-		print( 'The hexagon error is still too large!!!', Error)
-
-
-
-	return [Area_hex ,Area_Q1, Area_Q2, Area_Q3, Area_Q4]
-
-def Hexagon_into_quadrants_using_triangles(x0,y0,H,theta):
-		 
-	#Length of side of Hexagon
-	S=(2/np.sqrt(3))*H;  
-
-	#Finding positions of corners
-	C1x=S		; C1y=0.  #Corner 1 (right)
-	C2x=H/np.sqrt(3.)  ; C2y=H;  #Corner 2 (top right)
-	C3x=-H/np.sqrt(3.) ; C3y=H;  #Corner 3 (top left)
-	C4x=-S		; C4y=0.; #Corner 4 (left)
-	C5x=-H/np.sqrt(3.) ; C5y=-H; #Corner 5 (bottom right)
-	C6x=H/np.sqrt(3.)  ; C6y=-H; #Corner 6 (bottom right)
-
-	#Finding positions of corners
-	[C1x,C1y]=rotate_and_translate(C1x,C1y,theta,x0,y0)
-	[C2x,C2y]=rotate_and_translate(C2x,C2y,theta,x0,y0)
-	[C3x,C3y]=rotate_and_translate(C3x,C3y,theta,x0,y0)
-	[C4x,C4y]=rotate_and_translate(C4x,C4y,theta,x0,y0)
-	[C5x,C5y]=rotate_and_translate(C5x,C5y,theta,x0,y0)
-	[C6x,C6y]=rotate_and_translate(C6x,C6y,theta,x0,y0)
-	 
-	#Area of Hexagon is the sum of the triangles
-	[T12_Area,T12_Q1,T12_Q2,T12_Q3,T12_Q4]=Triangle_divided_into_four_quadrants(x0,y0,C1x,C1y,C2x,C2y); #T012
-	[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]=Triangle_divided_into_four_quadrants(x0,y0,C2x,C2y,C3x,C3y); #T023
-	[T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4]=Triangle_divided_into_four_quadrants(x0,y0,C3x,C3y,C4x,C4y); #T034
-	[T45_Area,T45_Q1,T45_Q2,T45_Q3,T45_Q4]=Triangle_divided_into_four_quadrants(x0,y0,C4x,C4y,C5x,C5y); #T023
-	[T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4]=Triangle_divided_into_four_quadrants(x0,y0,C5x,C5y,C6x,C6y); #T023
-	[T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4]=Triangle_divided_into_four_quadrants(x0,y0,C6x,C6y,C1x,C1y); #T023
-
-	#Summing up
-	Area_hex=T12_Area+T23_Area+T34_Area+T45_Area+T56_Area+T61_Area;
-	Area_Q1=T12_Q1+T23_Q1+T34_Q1+T45_Q1+T56_Q1+T61_Q1;
-	Area_Q2=T12_Q2+T23_Q2+T34_Q2+T45_Q2+T56_Q2+T61_Q2;
-	Area_Q3=T12_Q3+T23_Q3+T34_Q3+T45_Q3+T56_Q3+T61_Q3;
-	Area_Q4=T12_Q4+T23_Q4+T34_Q4+T45_Q4+T56_Q4+T61_Q4;
-	#Area_Q4=Area_hex-(Area_Q1+Area_Q2+Area_Q3)
-
-
-
-
-	#if  (abs(x0-(-0.186672393129))<0.00001)  and (abs(y0-(-0.436171))<0.00001):
-	#	print( 'Triangle 1,xo,y0',x0,y0 
-	#	print( 'Triangle 1H,S',H,S 
-	#	print( 'Triangle 1,Corners',C1x,C1y,C2x,C2y 
-	#	print( 'Triangle 1, Area full', T12_Area
-	#	print( 'Triangle 1, Area T1', T12_Q1
-	#	print( 'Triangle 1, Area T2', T12_Q2
-	#	print( 'Triangle 1, Area T3', T12_Q3
-	#	print( 'Triangle 1, Area T4', T12_Q4 
-	#	#print( 'Triangle 2',x0,y0,C2x,C2y,C3x,C3y,T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4
-	#	#print( 'Triangle 3',x0,y0,C3x,C3y,C4x,C4y,T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4 
-	#	#print( 'Triangle 4',x0,y0,C4x,C4y,C5x,C5y,T45_Area,T45_Q1,T45_Q2,T45_Q3,T45_Q4
-	#	#print( 'Triangle 5',x0,y0,C5x,C5y,C6x,C6y,T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4 
-	#	#print( 'Triangle 6',x0,y0,C6x,C6y,C1x,C1y,T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4
-
-	Area_Q1=max(Area_Q1,0.);
-	Area_Q2=max(Area_Q2,0.);
-	Area_Q3=max(Area_Q3,0.);
-	Area_Q4=max(Area_Q4,0.);
-
-
-	Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
-	if (abs(Error)>0.01):
-		print(	'diamonds, hex error, H,x0,y0, Error', H, x0 , y0, Error)
-		print( 'diamonds, hex error, Areas',Area_hex, (Area_Q1+Area_Q2 + Area_Q3+Area_Q4), Area_Q1,  Area_Q2 , Area_Q3,	 Area_Q4)
-		print( 'Hexagon error is large!!')
-
-
-
-	#Adjust Areas so that the error is zero by subtracting the error from the largest sector.
-	if  (((Area_Q1>=Area_Q2) and (Area_Q1>=Area_Q3)) and (Area_Q1>=Area_Q4)):
-		#print( 'fix1',Error
-		Area_Q1=Area_Q1+Error
-	elif  (((Area_Q2>=Area_Q1) and (Area_Q2>=Area_Q3)) and (Area_Q2>=Area_Q4)):
-		#print( 'fix2', Error
-		Area_Q2=Area_Q2+Error
-	elif  (((Area_Q3>=Area_Q1) and (Area_Q3>=Area_Q2)) and (Area_Q3>=Area_Q4)):
-		#print( 'fix3',Error
-		Area_Q3=Area_Q3+Error
-	elif  (((Area_Q4>=Area_Q1) and (Area_Q4>=Area_Q2)) and (Area_Q4>=Area_Q3)):
-		#print( 'fix4',Error
-		Area_Q4=Area_Q4+Error
-	else:
-		print( 'There is some thing wrong with this hexagon. Something very wrong')
-
-	#Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
-	Error=Area_hex-(Area_Q1+Area_Q2+Area_Q3+Area_Q4)
-	if ((abs(Error)>0.01)):
-		print( 'The hexagon error is still too large!!!', Error)
-
-
-
-	return [Area_hex ,Area_Q1, Area_Q2, Area_Q3, Area_Q4]
-
-
-def find_intersect_using_metric(Ax,Ay, Bx, By, Cx, Cy):
-	#Line AB
-	[AB_px, AB_py]=intercept_of_a_line(Ax,Ay,Bx,By,'x'); #x_intercept
-	[AB_qx, AB_qy]=intercept_of_a_line(Ax,Ay,Bx,By,'y'); #y_intercept
-	M_AB=point_in_interval_metric(Ax,Ay,Bx,By,AB_px,AB_py, AB_qx, AB_qy)
-	#Line AC
-	[AC_px, AC_py]=intercept_of_a_line(Ax,Ay,Cx,Cy,'x'); #x_intercept
-	[AC_qx, AC_qy]=intercept_of_a_line(Ax,Ay,Cx,Cy,'y'); #y_intercept
-	M_AC=point_in_interval_metric(Ax,Ay,Cx,Cy,AC_px, AC_py,AC_qx, AC_qy)
-	#Line AB
-	[BC_px, BC_py]=intercept_of_a_line(Bx,By,Cx,Cy,'x'); #x_intercept
-	[BC_qx, BC_qy]=intercept_of_a_line(Bx,By,Cx,Cy,'y'); #y_intercept
-	M_BC=point_in_interval_metric(Bx,By,Cx,Cy,BC_px,BC_py,BC_qx, BC_qy)
-
-	if M_AB<=min(M_BC, M_AC):
-		return AB_px, AB_py, AB_qx, AB_qy
-	elif M_AC<=min(M_BC, M_AB):
-		return AC_px, AC_py, AC_qx, AC_qy
-	elif M_BC<=min(M_AC, M_AB):
-		return BC_px, BC_py, BC_qx, BC_qy
-	else: 
-		print( 'You should not get here')
-		halt
-
-def find_intersect_using_metric_and_lines(Ax,Ay, Bx, By, Cx, Cy,Px, Py, Qx, Qy, Rx, Ry, Sx, Sy):
-	#Line AB
-	[AB_px, AB_py]=intercept_of_two_lines(Ax,Ay,Bx,By,Px, Py, Qx, Qy); #PQ_intercept
-	[AB_qx, AB_qy]=intercept_of_two_lines(Ax,Ay,Bx,By,Rx, Ry, Sx, Sy); #RS_intercept
-	M_AB=point_in_interval_metric(Ax,Ay,Bx,By,AB_px,AB_py, AB_qx, AB_qy)
-	#Line AC
-	[AC_px, AC_py]=intercept_of_two_lines(Ax,Ay,Cx,Cy,Px, Py, Qx, Qy); #PQ_intercept
-	[AC_qx, AC_qy]=intercept_of_two_lines(Ax,Ay,Cx,Cy, Rx, Ry, Sx, Sy); #RS_intercept
-	M_AC=point_in_interval_metric(Ax,Ay,Cx,Cy,AC_px, AC_py,AC_qx, AC_qy)
-	#Line AB
-	[BC_px, BC_py]=intercept_of_two_lines(Bx,By,Cx,Cy,Px, Py, Qx, Qy); #PQ_intercept
-	[BC_qx, BC_qy]=intercept_of_two_lines(Bx,By,Cx,Cy, Rx, Ry, Sx, Sy); #RS_intercept
-	M_BC=point_in_interval_metric(Bx,By,Cx,Cy,BC_px,BC_py,BC_qx, BC_qy)
-
-	if M_AB<=min(M_BC, M_AC):
-		return AB_px, AB_py, AB_qx, AB_qy
-	elif M_AC<=min(M_BC, M_AB):
-		return AC_px, AC_py, AC_qx, AC_qy
-	elif M_BC<=min(M_AC, M_AB):
-		return BC_px, BC_py, BC_qx, BC_qy
-	else: 
-		print( 'You should not get here')
-		halt
-
-
-def point_in_interval_metric(Ax,Ay,Bx,By,px,py,qx,qy):
-	metric=0.0
-	#print( 'Ax,Ay,Bx,By',Ax,Ay,Bx,By,px,py,qx,qy
-	#print( 'px,py,qx,qy',px,py,qx,qy
-
-	#Finds a metric for how close a point is to being inside an interval. If it is inside, then metric is equal to zero.
-	Mx1= max(px - max(Ax,Bx),0.)  #Zero is px <= max(Ax,Bx)
-	Mx2= max( min(Ax,Bx)-px ,0.)  #Zero is px <= max(Ax,Bx)
-	My1= max(py - max(Ay,By),0.)  #Zero is px <= max(Ax,Bx)
-	My2= max( min(Ay,By)-py ,0.)  #Zero is px <= max(Ax,Bx)
-	p_metric=abs(Mx1)+abs(Mx2)+abs(My1)+abs(My2)
-	#print( 'Mx1, Mx2, My1, My2', Mx1, Mx2, My1, My2 
-
-	#Finds a metric for how close a point is to being inside an interval. If it is inside, then metric is equal to zero.
-	Mx1= max(qx - max(Ax,Bx),0.)  #Zero is qx <= max(Ax,Bx)
-	Mx2= max( min(Ax,Bx)-qx ,0.)  #Zero is qx <= max(Ax,Bx)
-	My1= max(qy - max(Ay,By),0.)  #Zero is qx <= max(Ax,Bx)
-	My2= max( min(Ay,By)-qy ,0.)  #Zero is qx <= max(Ax,Bx)
-	q_metric=abs(Mx1)+abs(Mx2)+abs(My1)+abs(My2)
-
-	metric=p_metric+q_metric
-	return metric
-
-
-def Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy):
-	Area_key_quadrant=0.0 #Initializing
-	Area_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
-	#if Area_triangle==0.0:
-	#	Area_triangle=0.0 ; Area_Q1=0.0 ; Area_Q2=0.0; Area_Q3=0.0; Area_Q4= 0.0
-	#	return [Area_triangle, Area_Q1, Area_Q2 ,Area_Q3 ,Area_Q4]
-
-
-	#Calculating area across axes
-	[Area_Upper ,Area_Lower]=divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,'x');
-	[Area_Right ,Area_Left]=divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,'y');
-	 
-	#Decide if the origin is in the triangle
-	if point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.):	#Then you have to divide area 4 ways.
-		#Find a line in the triangle that cuts both axes in/on the trianlge
-		[px, py]=intercept_of_a_line(Ax,Ay,Bx,By,'x'); #x_intercept
-		[qx, qy]=intercept_of_a_line(Ax,Ay,Bx,By,'y'); #y_intercept
-		if (point_in_interval(Ax,Ay,Bx,By,px,py) & point_in_interval(Ax,Ay,Bx,By,qx,qy))==False:
-			[px, py]=intercept_of_a_line(Ax,Ay,Cx,Cy,'x'); #x_intercept
-			[qx, qy]=intercept_of_a_line(Ax,Ay,Cx,Cy,'y'); #y_intercept
-			if (point_in_interval(Ax,Ay,Cx,Cy,px,py) & point_in_interval(Ax,Ay,Cx,Cy,qx,qy))==False:
-				[px, py]=intercept_of_a_line(Bx,By,Cx,Cy,'x'); #x_intercept
-				[qx, qy]=intercept_of_a_line(Bx,By,Cx,Cy,'y'); #y_intercept
-				if (point_in_interval(Bx,By,Cx,Cy,px,py) & point_in_interval(Bx,By,Cx,Cy,qx,qy))==False:
-					#point_in_interval_metric
-					[px, py, qx, qy]= find_intersect_using_metric(Ax,Ay, Bx, By, Cx, Cy)
-					#print( 'Houston, we have a problem'
-					#plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy)
-					#halt
-
-		#Assigning quadrants. Key_quadrant is the quadrant with the baby triangle in it.
-		Area_key_quadrant=Area_of_triangle(px,py,qx,qy,0.,0.);
-		if Area_key_quadrant>0.0:
-			if px>=0. and qy>=0.: #First quadrant
-				Key_quadrant=1;
-			elif px<0. and qy>=0.:	#Second quadrant
-				Key_quadrant=2;
-			elif px<0. and qy<0.:
-				Key_quadrant=3;	 #Third quadrant
-			else:
-				Key_quadrant=4;	 #Forth quadrant
-	    
-	#if (point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.) is False) or (Area_key_quadrant==0):
-	if Area_key_quadrant==0:
-	#else:	#Then at least one quadrant is empty, and this can be used to find the areas in the other quadrant.  Assigning quadrants. Key_quadrant is the empty quadrant.
-		#print( 'Mother...'
-		#print( 'Ax, Ay',Ax,Ay
-		#print( 'Bx, By',Bx,By
-		#print( 'Cx, Cy',Cx,Cy
-		Area_key_quadrant=0;
-		if (((Ax>0. and Ay>0.) or (Bx>0. and By>0.) or (Cx>0. and Cy>0.))==False)  and (Area_Upper+Area_Right<=Area_triangle):
-		#if (((Ax>=0. and Ay>=0.) or (Bx>=0. and By>=0.) or (Cx>=0. and Cy>=0.))==False)  and (Area_Upper+Area_Right<=Area_triangle):
-			#No points land in this quadrant and triangle does not cross the quadrant
-			Key_quadrant=1;
-		elif  (((Ax<0. and Ay>0) or (Bx<0. and By>0.) or (Cx<0. and Cy>0.))==False)  and (Area_Upper+Area_Left<=Area_triangle):
-			#elif  (((Ax<0. and Ay>=0) or (Bx<0. and By>=0.) or (Cx<0. and Cy>=0.))==False)	 and (Area_Upper+Area_Left<=Area_triangle):
-			Key_quadrant=2;
-		elif (((Ax<0. and Ay<0.) or (Bx<0. and By<0.) or (Cx<0. and Cy<0.))==False) & (Area_Lower+Area_Left<=Area_triangle):
-			#elif (((Ax<0. and Ay<0.) or (Bx<0. and By<0.) or (Cx<0. and Cy<0.))==False) & (Area_Lower+Area_Left<=Area_triangle):
-			Key_quadrant=3;
-		else:
-			Key_quadrant=4;
-	
-	#Assign values to quadrants
-	if Key_quadrant==1:
-		Area_Q1=Area_key_quadrant;
-		Area_Q2=Area_Upper-Area_Q1;
-		Area_Q4=Area_Right-Area_Q1;
-		#Area_Q3=Area_Left-Area_Q2;
-		Area_Q3=Area_triangle-Area_Q1-Area_Q2-Area_Q4;
-	elif Key_quadrant==2:
-		Area_Q2=Area_key_quadrant;
-		Area_Q1=Area_Upper-Area_Q2;
-		Area_Q4=Area_Right-Area_Q1;
-		#Area_Q3=Area_Left-Area_Q2;
-		Area_Q3=Area_triangle-Area_Q1-Area_Q2-Area_Q4;
-	elif Key_quadrant==3:
-		Area_Q3=Area_key_quadrant;
-		Area_Q2=Area_Left-Area_Q3;
-		Area_Q1=Area_Upper-Area_Q2;
-		#Area_Q4=Area_Right-Area_Q1;
-		Area_Q4=Area_triangle-Area_Q1-Area_Q2-Area_Q3;
-	elif Key_quadrant==4:
-		Area_Q4=Area_key_quadrant;
-		Area_Q1=Area_Right-Area_Q4;
-		Area_Q2=Area_Upper-Area_Q1;
-		#Area_Q3=Area_Left-Area_Q2;
-		Area_Q3=Area_triangle-Area_Q1-Area_Q2-Area_Q4;
-	else:
-	    print( 'Help, I need somebody, help!')
-	    halt
-	
-	Area_Q1=max(Area_Q1,0.); 
-	Area_Q2=max(Area_Q2,0.);
-	Area_Q3=max(Area_Q3,0.);
-	Area_Q4=max(Area_Q4,0.); 
-
-	Error=abs(Area_Q1+Area_Q2+Area_Q3+Area_Q4-Area_triangle)
-	#Marker 1
-	if Error>1e-15:
-	#if True:
-		print( 'The triangles are not accurate enough. This is a problem!')
-		print( 'Triangle corners: ' ,Ax,Ay,Bx,By,Cx,Cy)
-		print( 'Error',Error)
-		print( 'Key_quadrant', Key_quadrant )
-		print( 'Area Key_quadrant', Area_key_quadrant )
-		print( 'Upper, Lower',Area_Upper ,Area_Lower)
-		print( 'Left, Right ', Area_Right ,Area_Left)
-		print( 'Point in triangle', point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.))
-		#plt.plot(np.array([Ax,Bx,Cx,Ax]),np.array([Ay, By, Cy,Ay]))
-		#plt.plot(np.array([-0.5,0.5]),np.array([0.,0.]),'k')
-		#plt.plot(np.array([0.,0.]),np.array([-0.5,0.5]),'k')
-		#plt.plot(0,0,'*')
-		#plt.show()
-		#halt
-		#return
-
-	return [Area_triangle, Area_Q1, Area_Q2 ,Area_Q3 ,Area_Q4]
-
-def find_quadrant_using_lines(x0 , y0 , Px, Py, Qx, Qy, Rx, Ry, Sx, Sy): #Finding "quadrant" of point using lines PQ, RS as axes.  (This assumes PQ is like the x axis and RS like the y axis)
-	#above_PQ=Point_above_line(x0,y0, Px, Py, Qx, Qy)
-	#above_RS=Point_above_line(x0,y0, Rx, Ry, Sx, Sy)
-	above_PQ=Above_on_below_line(x0,y0, Px, Py, Qx, Qy)
-	above_RS=Above_on_below_line(x0,y0, Rx, Ry, Sx, Sy)
-	if (above_PQ==1) and (above_RS==1):
-		quadrant=1
-	elif (above_PQ==1) and (above_RS==-1):
-		quadrant=2
-	elif (above_PQ==-1) and (above_RS==-1):
-		quadrant=3
-	elif (above_PQ==-1) and (above_RS==1):
-		quadrant=4
-	else:
-		#print( 'Point not in a quadrant!'
-		quadrant=0
-		#halt
-
-	return quadrant
-
-def Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy	):#Divides the triangle into 4 parts, across two intersecting lines. PQ, RS intersect at origin (for now)
-	Area_key_quadrant=0.0
-	Area_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
-	#if Area_triangle==0.0:
-	#	Area_triangle=0.0 ; Area_Q1=0.0 ; Area_Q2=0.0; Area_Q3=0.0; Area_Q4= 0.0
-	#	return [Area_triangle, Area_Q1, Area_Q2 ,Area_Q3 ,Area_Q4]
-
-
-	#Calculating area across axes
-	[Area_Upper ,Area_Lower]=divding_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy);
-	[Area_Right ,Area_Left] =divding_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Rx, Ry, Sx, Sy);
-	 
-	#Decide if the origin is in the triangle
-	if point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.):	#Then you have to divide area 4 ways.
-		#Find a line in the triangle that cuts both axes in/on the trianlge
-		[px, py]=intercept_of_two_lines(Ax,Ay,Bx,By,Px, Py, Qx, Qy); #PQ_intercept
-		[qx, qy]=intercept_of_two_lines(Ax,Ay,Bx,By,Rx, Ry, Sx, Sy); #RS_intercept
-		if (point_in_interval(Ax,Ay,Bx,By,px,py) & point_in_interval(Ax,Ay,Bx,By,qx,qy))==False:
-			[px, py]=intercept_of_two_lines(Ax,Ay,Cx,Cy,Px, Py, Qx, Qy); #PQ_intercept
-			[qx, qy]=intercept_of_two_lines(Ax,Ay,Cx,Cy,Rx, Ry, Sx, Sy); #RS_intercept
-			if (point_in_interval(Ax,Ay,Cx,Cy,px,py) & point_in_interval(Ax,Ay,Cx,Cy,qx,qy))==False:
-				[px, py]=intercept_of_two_lines(Bx,By,Cx,Cy,Px, Py, Qx, Qy); #PQ_intercept
-				[qx, qy]=intercept_of_two_lines(Bx,By,Cx,Cy,Rx, Ry, Sx, Sy); #RS_intercept
-				if (point_in_interval(Bx,By,Cx,Cy,px,py) & point_in_interval(Bx,By,Cx,Cy,qx,qy))==False:
-					#print( 'Houston, we have a problem'
-					[px, py, qx, qy]= find_intersect_using_metric_and_lines(Ax,Ay, Bx, By, Cx, Cy,Px, Py, Qx, Qy, Rx, Ry, Sx, Sy)
-					#plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy)
-					#halt
-
-		#Assigning quadrants. Key_quadrant is the quadrant with the baby triangle in it.
-		Area_key_quadrant=Area_of_triangle(px,py,qx,qy,0.,0.);
-		if px>=0. and qy>=0.: #First quadrant  (I think the zeros here are because the PQ, RS intersect at zero)
-			Key_quadrant=1;
-		elif px<0. and qy>=0.:	#Second quadrant
-			Key_quadrant=2;
-		elif px<0. and qy<0.:
-			Key_quadrant=3;	 #Third quadrant
-		else:
-			Key_quadrant=4;	 #Forth quadrant
-	    
-	if Area_key_quadrant==0:
-		#else:	#Then at least one quadrant is empty, and this can be used to find the areas in the other quadrant.  Assigning quadrants. Key_quadrant is the empty quadrant.
-		#print( 'Mother...'
-		#print( 'Ax, Ay',Ax,Ay
-		#print( 'Bx, By',Bx,By
-		#print( 'Cx, Cy',Cx,Cy
-		Area_key_quadrant=0;
-		#Finding which quadrant the triangle points fall in.
-		A_quad = find_quadrant_using_lines(Ax,Ay,Px, Py, Qx, Qy, Rx, Ry, Sx, Sy)
-		B_quad = find_quadrant_using_lines(Bx,By,Px, Py, Qx, Qy, Rx, Ry, Sx, Sy)
-		C_quad = find_quadrant_using_lines(Cx,Cy,Px, Py, Qx, Qy, Rx, Ry, Sx, Sy)
-		#print( 'A_quad, B_quad, C_quad',A_quad, B_quad, C_quad
-
-		if (((A_quad==1) or (B_quad==1) or (C_quad==1))==False)	 and (Area_Upper+Area_Right<=Area_triangle):
-			#No points land in this quadrant and triangle does not cross the quadrant
-			Key_quadrant=1;
-		elif  (((A_quad==2) or (B_quad==2) or (C_quad==2))==False)  and (Area_Upper+Area_Left<=Area_triangle):
-			Key_quadrant=2;
-		elif (((A_quad==3) or (B_quad==3) or (C_quad==3))==False) & (Area_Lower+Area_Left<=Area_triangle):
-			Key_quadrant=3;
-		else:
-			Key_quadrant=4;
-	
-		#print( Key_quadrant
-	#Assign values to quadrants
-	if Key_quadrant==1:
-		Area_Q1=Area_key_quadrant;
-		Area_Q2=Area_Upper-Area_Q1;
-		Area_Q4=Area_Right-Area_Q1;
-		#Area_Q3=Area_Left-Area_Q2;
-		Area_Q3=Area_triangle-Area_Q1-Area_Q2-Area_Q4;
-	elif Key_quadrant==2:
-		Area_Q2=Area_key_quadrant;
-		Area_Q1=Area_Upper-Area_Q2;
-		Area_Q4=Area_Right-Area_Q1;
-		#Area_Q3=Area_Left-Area_Q2;
-		Area_Q3=Area_triangle-Area_Q1-Area_Q2-Area_Q4;
-	elif Key_quadrant==3:
-		Area_Q3=Area_key_quadrant;
-		Area_Q2=Area_Left-Area_Q3;
-		Area_Q1=Area_Upper-Area_Q2;
-		#Area_Q4=Area_Right-Area_Q1;
-		Area_Q4=Area_triangle-Area_Q1-Area_Q2-Area_Q3;
-	elif Key_quadrant==4:
-		Area_Q4=Area_key_quadrant;
-		Area_Q1=Area_Right-Area_Q4;
-		Area_Q2=Area_Upper-Area_Q1;
-		#Area_Q3=Area_Left-Area_Q2;
-		Area_Q3=Area_triangle-Area_Q1-Area_Q2-Area_Q4;
-	else:
-	    print( 'Help, I need somebody, help!')
-	    halt
-	
-	Area_Q1=max(Area_Q1,0.); 
-	Area_Q2=max(Area_Q2,0.);
-	Area_Q3=max(Area_Q3,0.);
-	Area_Q4=max(Area_Q4,0.); 
-
-	Error=abs(Area_Q1+Area_Q2+Area_Q3+Area_Q4-Area_triangle)
-	if Error>1e-15:
-	#if True:
-		print( 'The triangles are not accurate enough. This is a problem!')
-		print( 'Triangle corners: ' ,Ax,Ay,Bx,By,Cx,Cy)
-		print( 'Error',Error)
-		print( 'Key_quadrant', Key_quadrant )
-		print( 'Area Key_quadrant', Area_key_quadrant )
-		print( 'Upper, Lower',Area_Upper ,Area_Lower)
-		print( 'Left, Right ', Area_Right ,Area_Left)
-		print( 'Point in triangle', point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.))
-		#return
-
-	return [Area_triangle, Area_Q1, Area_Q2 ,Area_Q3 ,Area_Q4]
-
-def divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1):
-	if axes1=='x':	#Use the y-coordinates for if statements to see which side of the line you are on
-		A0=Ay; B0=By;  C0=Cy;
-	if axes1=='y':	#Use the y-coordinates for if statements to see which side of the line you are on
-		A0=Ax; B0=Bx;  C0=Cx;
- 
-	#print( 'A0,B0,C0', A0,B0,C0
-	A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
-	if B0*C0>0.: #then B and C are on the same side	 (and non-zero)
-		#print( 'HHHH1'	
-		if A0*B0>=0.: #then all three on the the same side (if it equals zero, then A0=0 and the otehrs are not)
-			if (A0>0.)  or	(A0==0. and  B0>0.):
-				Area_positive= A_triangle;
-				Area_negative= 0.;
-			else:
-				Area_positive= 0.;
-				Area_negative= A_triangle;
-		else:  #A is on the opposite side to B and C
-			[Area_positive, Area_negative]=Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1);
-
-	elif B0*C0<0.: #then B and C are on the opposite sides
-		#print( 'HHHH2'	
-		if A0*B0>=0.:  #then C is all alone
-			[Area_positive, Area_negative]=Area_of_triangle_across_axes(Cx,Cy,Bx,By,Ax,Ay,axes1);
-		else: #then B is all alone
-			[Area_positive, Area_negative]=Area_of_triangle_across_axes(Bx,By,Cx,Cy,Ax,Ay,axes1);
-
-	else:  #This is the case when either B or C is equal to zero (or both), A0 could be zero too.
-		#print( 'HHHH3'	
-		if (A0==0. and B0==0. and C0==0.):
-			Area_positive= 0.;
-			Area_negative= 0.;
-		elif (A0*B0<0.)	 or  (A0*C0<0.):    #A, B are on opposite sides, and C is zero.	 OR  A, C are on opposite sides, and B is zero.
-			[Area_positive, Area_negative]=Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1);
-			#print( 'HHHH6'	
-		elif (A0*B0>0.) or (A0*C0>0.) or (abs(A0)>0. and (B0==0.) and (C0==0.)):
-			#print( 'HHHH7'	
-			if (A0>0.):
-				Area_positive= A_triangle;
-				Area_negative= 0.;
-			else:
-				Area_positive= 0.;
-				Area_negative= A_triangle;
-    
-		elif A0==0.:  #(Also, one of B,C is zero too)
-			#print( 'HHHH8'	
-			if B0>0. or C0>0.:
-				Area_positive= A_triangle;
-				Area_negative= 0.;
-			elif B0<0. or C0<0.:
-				Area_positive= 0.;
-				Area_negative= A_triangle;
-			else:
-				print( 'You should not get here1')
-				halt
-		else:
-			print( 'You should not get here2')
-			print( Ax,Ay,Bx,By,Cx,Cy)
-			halt
-	
-	return [Area_positive, Area_negative]
-
-def divding_triangle_across_line2(Ax,Ay,Bx,By,Cx,Cy,  Px, Py, Qx, Qy ):
-	A0= Above_on_below_line(Ax,Ay, Px, Py, Qx, Qy)
-	B0= Above_on_below_line(Bx,By, Px, Py, Qx, Qy)
-	C0= Above_on_below_line(Cx,Cy, Px, Py, Qx, Qy) 
-	
-	#print( 'A0,B0,C0', A0,B0,C0
-	#print( Px, Py, Qx, Qy
- 
-	A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
-	if B0*C0>0.: #then B and C are on the same side	 (and non-zero)
-		#print( 'GGG1'
-		if A0*B0>=0.: #then all three on the the same side (if it equals zero, then A0=0 and the otehrs are not)
-			if (A0>0.)  or	(A0==0. and  B0>0.):
-				Area_positive= A_triangle;
-				Area_negative= 0.;
-			else:
-				Area_positive= 0.;
-				Area_negative= A_triangle;
-		else:  #A is on the opposite side to B and C
-			[Area_positive, Area_negative]=Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy );
-
-	elif B0*C0<0.: #then B and C are on the opposite sides
-		#print( 'GGG2'
-		if A0*B0>=0.:  #then C is all alone
-			[Area_positive, Area_negative]=Area_of_triangle_across_line(Cx,Cy,Bx,By,Ax,Ay, Px, Py, Qx, Qy );
-		else: #then B is all alone
-			[Area_positive, Area_negative]=Area_of_triangle_across_line(Bx,By,Cx,Cy,Ax,Ay, Px, Py, Qx, Qy );
-
-	else:  #This is the case when either B or C is equal to zero (or both), A0 could be zero too.
-		#print( 'GGG3'
-		if (A0==0. and B0==0. and C0==0.):
-			Area_positive= 0.;
-			Area_negative= 0.;
-		elif (A0*B0<0.)	 or  (A0*C0<0.):    #A, B are on opposite sides, and C is zero.	 OR  A, C are on opposite sides, and B is zero.
-			[Area_positive, Area_negative]=Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy);
-			#print( 'GGG5', Area_positive, Area_negative
-		elif (A0*B0>0.) or (A0*C0>0.) or (abs(A0)>0. and (B0==0.) and (C0==0.)):
-			if (A0>0.):
-				Area_positive= A_triangle;
-				Area_negative= 0.;
-			else:
-				Area_positive= 0.;
-				Area_negative= A_triangle;
-    
-		elif A0==0.:  #(Also, one of B,C is zero too)
-			if B0>0. or C0>0.:
-				Area_positive= A_triangle;
-				Area_negative= 0.;
-			elif B0<0. or C0<0.:
-				Area_positive= 0.;
-				Area_negative= A_triangle;
-			else:
-				print( 'You should not get here1')
-				halt
-		else:
-			print( 'You should not get here2')
-			print( Ax,Ay,Bx,By,Cx,Cy)
-			halt
-	
-	return [Area_positive, Area_negative]
-
-
-def divding_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy,   Px, Py, Qx, Qy ):	 #Triangle is ABC, line is PQ
-	A0= Above_on_below_line(Ax,Ay, Px, Py, Qx, Qy)
-	B0= Above_on_below_line(Bx,By, Px, Py, Qx, Qy)
-	C0= Above_on_below_line(Cx,Cy, Px, Py, Qx, Qy) 
-	#print( 'BBB0', A0, B0, C0
-
-	A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
-	# B and C are on the same side of the line
-	#if (Point_above_line(Bx,By, Px, Py, Qx, Qy)==Point_above_line(Cx,Cy, Px, Py, Qx, Qy)) :
-	#if ((B0==C0) and (B0!=0))  or ((B0==0 or C0==0) and np.max(B0,C0)>0.5)	  :
-	if ((B0==C0) and (B0!=0))  or ((B0==0 or C0==0))   : #B and C on the same side or B or C is zero
-		#print( 'BBB1'
-		[Area_positive, Area_negative]=Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy);
-	else: #then B and C are on the opposite sides
-		#if Point_above_line(Ax,Ay, Px, Py, Qx, Qy)==Point_above_line(Bx,By, Px, Py, Qx, Qy):  #then C is all alone
-		if A0*B0>=0.:  #then C is all alone
-			#print( 'BBB2'
-			[Area_positive, Area_negative]=Area_of_triangle_across_line(Cx,Cy,Bx,By,Ax,Ay, Px, Py, Qx, Qy);
-		else: #then B is all alone
-			#print( 'BBB3'
-			[Area_positive, Area_negative]=Area_of_triangle_across_line(Bx,By,Cx,Cy,Ax,Ay, Px, Py, Qx, Qy);
-
-	return [Area_positive, Area_negative]
-
-
-def check_if_point_is_on_the_line(Ax,Ay,Bx,By,qx,qy,repeat_calculation=False):
-
-	tol=0.00000000000000;
-	dxc = qx - Ax;
-	dyc = qy - Ay;
- 
-	dxl = Bx - Ax;
-	dyl = By - Ay;
- 
-	cross = dxc * dyl - dyc * dxl;
-	
-	if abs(cross)<=tol:
-		point_is_on_line=True
-	else:
-		point_is_on_line=False
-
-	if repeat_calculation is False:
-		if point_is_on_line != check_if_point_is_on_the_line(Bx,By,Ax,Ay,qx,qy, True):
-			point_is_on_line=True
-
-	return point_is_on_line
-
-def intercept_of_a_line(Ax,Ay,Bx,By,axes1):
-	No_intercept_val=100000000000.; #Huge value used to make sure that the intercept is outside the triange in the parralel case. 
-	#No_intercept_val=np.NaN;
-	 
-	if axes1=='x': #x intercept
-		if (Ay==By)==False:
-			x0=Ax -(((Ax-Bx)/(Ay-By))*Ay);
-			y0=0.; 
-		else:
-			x0=No_intercept_val;
-			y0=No_intercept_val;
-	
-	if axes1=='y': #y intercept
-		if (Ax==Bx)==False:
-			x0=0.; 
-			y0=-(((Ay-By)/(Ax-Bx))*Ax)+Ay;	
-		else:
-			x0=No_intercept_val;
-			y0=No_intercept_val;
-	
-	return [x0, y0]
-
-def intercept_of_two_lines(Ax,Ay,Bx,By,Px,Py,Qx,Qy):
-	No_intercept_val=100000000000.; #Huge value used to make sure that the intercept is outside the triange in the parralel case. 
-	#No_intercept_val=np.NaN;
-
-	#One of the lines is actually a point:
-	if ((Ax==Bx) and (Ay==By)) or ((Px==Qx) and (Py==Qy)):
-		x0=No_intercept_val; y0=No_intercept_val;
-		halt6
-	else:
-		if (Ax==Bx):
-			(x0 , y0) =intercept_of_a_line(Px-Ax,Py,Qx-Ax,Qy,'y')
-			x0=Ax
-		#Here we check the other three directions to make code agree to machine precision with old version. The code could skip straight to the else.
-		elif (Px==Qx): 
-			(x0 , y0) =intercept_of_a_line(Ax-Px,Ay,Bx-Px,By,'y')
-			x0=Px
-		elif (Ay==By): 
-			(x0 , y0) =intercept_of_a_line(Px,Py-Ay,Qx,Qy-Ay,'x')
-			y0=Ay
-		elif (Py==Qy): 
-			(x0 , y0) =intercept_of_a_line(Ax,Ay-Py,Bx,By-Py,'x')
-			y0=Py
-		else:
-			m1=(Ay-By)/(Ax-Bx)
-			if (Px==Qx):
-				print( 'Stop2')
-				(x0 , y0) =intercept_of_a_line(Ax-Px,Ay,Bx-Px,By,'y')
-				x0=Px
-			else:
-				m2=(Py-Qy)/(Px-Qx)
-				if m1==m2:
-					print( 'Stop3')
-					x0=No_intercept_val;
-					y0=No_intercept_val;
-					halt2
-				else:
-					print( 'Stop4')
-					x0=(1/(m1-m2))*( (m1*Ax -Ay) -(m2*Px - Py))
-					y0=m1*(x0-Ax)+Ay
-	
-	return [x0, y0]
-
-
-def Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axis1):#In this fuction, A is the point on one side of the axis, and B,C are on the opposite sides
-	#print( 'Area_of_triangle_across_axes' ,Ax,Ay,Bx,By,Cx,Cy
-	A_triangle2=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
-	[pABx, pABy]=intercept_of_a_line(Ax,Ay,Bx,By,axis1);
-	[pACx, pACy]=intercept_of_a_line(Ax,Ay,Cx,Cy,axis1);
-	if axis1=='x':
-		A0=Ay; #Value used for if statements (deciding up/down vs left/right)
-	if axis1=='y':
-		A0=Ax; #Value used for if statements (deciding up/down vs left/right)
-	
-	#print( 'QQQ', Ax,Ay,pABx,pABy,pACx,pACy
-	A_half_triangle=Area_of_triangle(Ax,Ay,pABx,pABy,pACx,pACy);
-	if (A0>=0.):
-		Area_positive= A_half_triangle;
-		Area_negative= A_triangle2-A_half_triangle;
-
-	else:
-		Area_positive= A_triangle2-A_half_triangle;
-		Area_negative= A_half_triangle;
-
-	return [Area_positive, Area_negative]
-
-def Above_on_below_line(x,y,Px, Py, Qx, Qy): #If the point is above the line, then returns True, otherwise false
-	if Px==Qx:
-		if x>Px:
-			Point_above_line=1.0
-		elif x<Px:
-			Point_above_line=-1.0
-		else:
-			Point_above_line=0.0
-	else:
-		m=(Py-Qy)/(Px-Qx)
-		if y > m*(x-Px) + Py:
-			Point_above_line=1.0
-		elif y < m*(x-Px) + Py:
-			Point_above_line=-1.0
-		else:
-			Point_above_line=0.0
-
-	return Point_above_line
-
-def Point_above_line(x,y,Px, Py, Qx, Qy): #If the point is above the line, then returns True, otherwise false
-	if Px==Qx:
-		if x>=Px:
-			Point_above_line=True
-		else:
-			Point_above_line=False
-	else:
-		m=(Py-Qy)/(Px-Qx)
-		if y >= m*(x-Px) + Py:
-			Point_above_line=True
-		else:
-			Point_above_line=False
-
-	return Point_above_line
-
-
-def Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px,Py, Qx, Qy, debug=False):
-	#In this fuction, B and C are the same side of the line. (I think this works even if B and/or C are on the line too)
-	#A is unknown. PQ is the line.
-	#print( 'RRR Area_of_triangle_across_line' ,Ax,Ay,Bx,By,Cx,Cy
-	
-	if (Ax==Bx and Ay==By) or (Ax==Cx and Ay==Cy) or (Cx==Bx and Cy==By):
-		#print( 'AAA1'
-		Area_positive=0.0
-		Area_negative=0.0
-	else:
-		#print( 'AAA2'
-		A0= Above_on_below_line(Ax,Ay, Px, Py, Qx, Qy)
-		B0= Above_on_below_line(Bx,By, Px, Py, Qx, Qy)
-		C0= Above_on_below_line(Cx,Cy, Px, Py, Qx, Qy) 
-		A_triangle2=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
-
-		if check_if_point_is_on_the_line(Px,Py,Qx,Qy, Ax,Ay):  #Is point A on the line?
-			#print( 'AAA3'
-			#if Point_above_line(Bx,By, Px,Py, Qx, Qy) or Point_above_line(Cx,Cy, Px,Py, Qx, Qy):
-			if B0==1 or C0==1:
-				Area_positive= A_triangle2;
-				Area_negative= 0.0;
-			else:
-				Area_positive= 0.0;
-				Area_negative= A_triangle2;
-		else: #If A is not on the line
-			#If A is on the same side of the line as B and C
-			#All on the same side of the line
-			if ((A0==B0 and A0==C0)	 or (A0==B0 and C0==0) or (A0==C0 and B0==0)):	
-			#if Point_above_line(Ax,Ay, Px,Py, Qx, Qy) == Point_above_line( Bx,By, Px,Py, Qx, Qy)  and (Point_above_line(Ax,Ay,Px,Py,Qx,Qy)==Point_above_line(Cx,Cy,Px,Py,Qx,Qy)):	
-				#print( 'AAA4'
-				#if Point_above_line(Bx,By, Px,Py, Qx, Qy) or Point_above_line(Cx,Cy, Px,Py, Qx, Qy):
-				if A0==1 or C0==1:
-					Area_positive= A_triangle2;
-					Area_negative= 0.0;
-				else:
-					Area_positive= 0.0;
-					Area_negative= A_triangle2;
-			elif (C0==0 and B0==0 and (abs(A0)>0)):	 
-				if Point_above_line(Ax,Ay, Px,Py, Qx, Qy):
-					Area_positive= A_triangle2;
-					Area_negative= 0.0;
-				else:
-					Area_positive= 0.0;
-					Area_negative= A_triangle2;
-
-			else:  #If A is not on the same side of the line as B and C
-				#print( 'AAA5'
-				[pABx, pABy]=intercept_of_two_lines(Ax,Ay,Bx,By, Px, Py, Qx, Qy);
-				[pACx, pACy]=intercept_of_two_lines(Ax,Ay,Cx,Cy, Px, Py, Qx, Qy);
-				#print( 'Tri2', Ax,Ay,pABx,pABy,pACx,pACy
-				
-				A_half_triangle=Area_of_triangle(Ax,Ay,pABx,pABy,pACx,pACy);
-				if Point_above_line(Ax,Ay , Px,Py,Qx,Qy):
-					Area_positive= A_half_triangle;
-					Area_negative= A_triangle2-A_half_triangle;
-				else:
-					Area_positive= A_triangle2-A_half_triangle;
-					Area_negative= A_half_triangle;
-
-	return [Area_positive, Area_negative]
-
-def Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy):
-	Area	=   abs(    0.5*((Ax*(By-Cy))+(Bx*(Cy-Ay))+(Cx*(Ay-By))) );
-	return Area
-
-
-def point_in_interval(Ax,Ay,Bx,By,px,py):
-	point_is_in_interval=False
-	#print( 'NNN1'
-	if ((px <= max(Ax,Bx)) and (px >= min(Ax,Bx))):
-		#print( 'NNN2', 'py=', py,  'max=',max(Ay,By), 'XXX', (py - max(Ay,By))
-		if ((py <= max(Ay,By)) and (py >= min(Ay,By))):
-			##print( 'NNN3'
-			point_is_in_interval=True
-	return point_is_in_interval
-
-def rotate_and_translate(px,py,theta,x0,y0):
-	#This function takes a point px,py, and rotates it clockwise around the origin by theta degrees, and then translates by (x0,y0)
-	 px_temp = (np.cos(theta*np.pi/180.)*px) + (np.sin(theta*np.pi/180.)*py)
-	 py_temp = (-np.sin(theta*np.pi/180.)*px) + (np.cos(theta*np.pi/180.)*py)
-	 px= px_temp +x0
-	 py= py_temp +y0
-	 return [px,py]
-
-
-def point_in_triangle_old(Ax,Ay,Bx,By,Cx,Cy,qx,qy):
-	#if False:
-	if (Ax==qx and Ay==qy) or (Bx==qx and By==qy) or (Cx==qx and Cy==qy):  #Exclude the pathelogical case
-			point_is_in_triangle = 0.;
-	else:
-		if (check_if_point_is_on_the_line(Ax,Ay,Bx,By,qx,qy) or (check_if_point_is_on_the_line(Ax,Ay,Cx,Cy,qx,qy)) or (check_if_point_is_on_the_line(Bx,By,Cx,Cy,qx,qy))):
-			point_is_in_triangle = 0;
-		else:
-			#Compute vectors
-			v0x=Cx-Ax;
-			v1x=Bx-Ax;
-			v2x=qx-Ax;
-			v0y=Cy-Ay;
-			v1y=By-Ay;
-			v2y=qy-Ay;
-
-			#%Compute dot products
-			dot00 = (v0x*v0x)+(v0y*v0y);
-			dot01 = (v0x*v1x)+(v0y*v1y);
-			dot02 = (v0x*v2x)+(v0y*v2y);
-			dot11 = (v1x*v1x)+(v1y*v1y);
-			dot12 = (v1x*v2x)+(v1y*v2y);
-
-			#Compute barycentric coordinates
-			invDenom= 1 / ((dot00 * dot11) - (dot01*dot01));
-			u=((dot11*dot02)-(dot01*dot12))*invDenom;
-			v=((dot00*dot12)-(dot01*dot02))*invDenom;
-
-			point_is_in_triangle = (((u)>=0) & ((v)>=0) & ((u+v)<(1)));
-	return point_is_in_triangle
-
-
-
-def point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,qx,qy):
-	point_is_in_triangle = 0;
-
-	if (Ax==qx and Ay==qy) or (Bx==qx and By==qy) or (Cx==qx and Cy==qy):  #Exclude the pathelogical case
-			point_is_in_triangle = 0.;
-	else:
-		if (check_if_point_is_on_the_line(Ax,Ay,Bx,By,qx,qy) or (check_if_point_is_on_the_line(Ax,Ay,Cx,Cy,qx,qy)) or (check_if_point_is_on_the_line(Bx,By,Cx,Cy,qx,qy))):
-			point_is_in_triangle = 0;
-		else:
-			l0=(qx-Ax)*(By-Ay)-(qy-Ay)*(Bx-Ax)
-			l1=(qx-Bx)*(Cy-By)-(qy-By)*(Cx-Bx)
-			l2=(qx-Cx)*(Ay-Cy)-(qy-Cy)*(Ax-Cx)
-
-			p0=np.sign( l0);
-			p1=np.sign( l1);
-			p2=np.sign( l2);
-			if (l0 == 0.):
-				p0=0.
-			if (l1==0.):
-				p1=0.
-			if (l2==0.):
-				p2=0.
-			
-			if ( (abs(p0)+abs(p2))+(abs(p1)) == abs((p0+p2)+(p1)) ):
-				point_is_in_triangle = 1;
-	return point_is_in_triangle
-
-
-def roundoff(x,sig_fig):
-	x_roundoff=round(x*(10**(sig_fig)))/(10**(sig_fig))
-	#x_roundoff=(FLOAT (INT(x * (10.**sig_fig) + 0.5)) / (10.**sig_fig))
-	return x_roundoff
-
-
-
-def square_spreading_calculation(x,y,L):
-	xL=min(0.5, max(0., 0.5-(x/L)))
-	xR=min(0.5, max(0., (x/L)+(0.5-(1/L) )))
-	xC=max(0., 1.-(xL+xR))
-	yD=min(0.5, max(0., 0.5-(y/L)))
-	yU=min(0.5, max(0., (y/L)+(0.5-(1/L) )))
-	yC=max(0., 1.-(yD+yU))
-
-def plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy, Px=None, Py=None, Qx=None, Qy=None, Rx=None, Ry=None, Sx=None, Sy=None):
-	if Px is None:
-		Px=-1. ; Py=0. ; Qx=1. ; Qy=0. #x-axis 
-		Rx=0. ; Ry=-1. ; Sx=0. ; Sy=1. #y-axis 
-	plt.plot(np.array([Px, Qx]), np.array([Py, Qy]))
-	plt.plot(np.array([Rx, Sx]), np.array([Ry, Sy]))
-	plt.plot(np.array([Ax, Bx, Cx, Ax]), np.array([Ay, By, Cy, Ay]))
-	plt.plot(np.array([Ax, Bx, Cx, Ax]), np.array([Ay, By, Cy, Ay]),'8')
-	text(Ax,Ay,'A',fontsize=20)
-	text(Bx,By,'B',fontsize=20)
-	text(Cx,Cy,'C',fontsize=20)
-	plt.show()
-
-####################################################################################################################################################
-##########################################################  Main Program   #########################################################################
-####################################################################################################################################################
-
-def main():
-
-	#test_case='hexagon'
-	#test_case='triangle'
-	#test_case='square'
-	#test_case='point_in_triangle'
-	#test_case='line_intercept'
-	#test_case='Point_above_line'
-	#test_case='Triangle_across_line'
-	#test_case='Triangle_into_fours'
-	test_case='many_hexagons'
-
-	if test_case=='line_intercept':
-		Ax=1. ; Ay=1.5 ; Bx=1. ; By=-3.4 
-		Px=0.2; Py=-1.0; Qx=0.2; Qy=2.2
-		(x0,y0)=intercept_of_two_lines(Ax,Ay,Bx,By,Px,Py,Qx,Qy)
-		plt.plot( np.array([Ax, Bx])  , np.array([Ay, By]))
-		plt.plot(np.array([Px, Qx]), np.array([Py, Qy]))
-		plt.plot(x0,y0,'*')
-		#plt.plot(Ax,Ay,'*')
-		#plt.plot(Bx,By,'*')
-		#plt.plot(Px,Py,'*')
-		#plt.plot(Qx,Qy,'*')
-
-		print( 'x0, y0' , x0 , y0)
-		plt.show()
-
-
-	if test_case=='Triangle_across_line':
-		#y-axis
-		Px=0.0 ; Py=-1.0 ;Qx=0.0 ;Qy=1.0
-		axes1='y'
-
-		#x-axis
-		#Px=-1.0 ; Py=0.0 ;Qx=1.0 ;Qy=0.0
-		#axes1='x'
-
-		N=11 #Choose an odd number
-		count=0
-		for Ax in np.linspace(-0.5 , 0.5 , N):
-			for Ay in np.linspace(-0.5 , 0.5 , N):
-				for Bx in np.linspace(-0.5 , 0.5 , N):
-					for By in np.linspace(-0.5 , 0.5 , N):
-						for Cx in np.linspace(-0.5 , 0.5 , N):
-							for Cy in np.linspace(-0.5 , 0.5 , N):
-								count=count+1
-								if count>0:
-									x=divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1)
-									y=divding_triangle_across_line2(Ax,Ay,Bx,By,Cx,Cy, Px,Py, Qx, Qy)
-									#y=divding_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px,Py, Qx, Qy)
-									#if abs(x[0]-y[0])>0 or	 abs(x[1]-y[1])>0 or  abs(x[0]-z[0])>0 or  abs(x[1]-z[1])>0:
-									if abs(x[0]-y[0])>0 or	abs(x[1]-y[1])>0:
-										print( 'Broken!!!: ', 'Ax, Ay =', Ax, Ay, 'Bx, By =' , Bx, By, 'Cx, Cy =' ,Cx, Cy)
-										print( 'count', count)
-										print( x)
-										print( y)
-										plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy)
-										halt
-
-		print( 'Test Successful')
-
-
-
-	if test_case=='Triangle_into_fours':
-		Px=1. ; Py=0. ; Qx=2. ; Qy=0. #x-axis 
-		Rx=0. ; Ry=1. ; Sx=0. ; Sy=2. #y-axis 
-		
-		count=0
-		N=11 #Use an odd number
-		for Ax in np.linspace(-0.5 , 0.5 , N):
-			for Ay in np.linspace(-0.5 , 0.5 , N):
-				for Bx in np.linspace(-0.5 , 0.5 , N):
-					for By in np.linspace(-0.5 , 0.5 , N):
-						for Cx in np.linspace(-0.5 , 0.5 , N):
-							for Cy in np.linspace(-0.5 , 0.5 , N):
-								count=count+1
-								#print( count
-								if count>0:
-									x=Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy)
-									y=Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy )
-									Error=abs(x[1]+x[2]+x[3]+x[4]-x[0])
-									#if Error>1e-15:
-									if abs(x[0]-y[0])>0 or	abs(x[1]-y[1])>0 or abs(x[2]-y[2])>0 or	 abs(x[3]-y[3])>0 or  abs(x[4]-y[4])>0 :
-										print( 'Broken!!!: ', 'Ax, Ay =', Ax, Ay, 'Bx, By =' , Bx, By, 'Cx, Cy =' ,Cx, Cy)
-										print( 'count=', count)
-										#print( 'Error = ', Error
-										print( x)
-										#print( y
-										plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy)
-										halt
-
-		print( 'Triangle_into_fours Test Successful')
-
-		#[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]=Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy); 
-		#[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]= Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  )
-
-	if test_case=='Point_above_line':
-		x0=0.1 ;y0=0.3 ; Px=0.4; Py=-1.0; Qx=0.2; Qy=2.2
-		plt.plot(np.array([Px, Qx]), np.array([Py, Qy]))
-		plt.plot(x0,y0,'*')
-		print( Point_above_line(x0,y0,Px, Py, Qx, Qy))
-		plt.show()
-
-
-
-
-	if test_case=='many_hexagons':
-		Px=-1. ; Py=0. ; Qx=1. ; Qy=0. #x-axis 
-		Rx=0. ; Ry=-1. ; Sx=0. ; Sy=1. #y-axis 
-		N=101
-		theta=0.0
-		count=0
-		for x0 in np.linspace(-0.5 , 0.5 , N):
-			for y0 in np.linspace(-0.5 , 0.5 , N):
-				for H in np.linspace(0.0 , 0.5 , N):
-					count=count+1
-					#print( count
-					if count>0:
-						C5x=-H/np.sqrt(3.) ; C5y=-H; #Corner 5 (bottom right)
-						C6x=H/np.sqrt(3.)  ; C6y=-H; #Corner 6 (bottom right)
-						[C5x,C5y]=rotate_and_translate(C5x,C5y,theta,x0,y0)
-						[C6x,C6y]=rotate_and_translate(C6x,C6y,theta,x0,y0)
-						#x = Triangle_divided_into_four_parts(x0,y0,C5x,C5y,C6x,C6y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
-						#y = Triangle_divided_into_four_quadrants(x0,y0,C5x,C5y,C6x,C6y); #T023
-						#print( x
-						#print( y
-						#Ax=x0 ;  Ay=y0
-						#Bx=C5x ; By=C5y ;
-						#Cx=C6x ; Cy=C6y ;
-						#plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy)
-						#(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)=Hexagon_into_quadrants_using_triangles_across_lines(x0,y0,H,theta,  Px, Py, Qx, Qy, Rx, Ry, Sx, Sy )
-						#(Area_hexb, Area_Q1b, Area_Q2b, Area_Q3b, Area_Q4b)= Hexagon_into_quadrants_using_triangles(x0,y0,H,theta=0)
-						x=Hexagon_into_quadrants_using_triangles_across_lines(x0,y0,H,theta,  Px, Py, Qx, Qy, Rx, Ry, Sx, Sy )
-						y= Hexagon_into_quadrants_using_triangles(x0,y0,H,theta=0)
-						eps=1e-15
-						#eps=0.0
-						#if abs(Area_hex-Area_hexb)>eps or  abs(Area_Q1-Area_Q1b)>eps or abs(Area_Q2-Area_Q2b)>eps \
-						#		or  abs(Area_Q3-Area_Q3b)>eps or  abs(Area_Q4-Area_Q4b)>eps :
-						if abs(x[0]-y[0])>0 or	abs(x[1]-y[1])>0 or abs(x[2]-y[2])>0 or	 abs(x[3]-y[3])>0 or  abs(x[4]-y[4])>0 :
-							print( 'Broken!!!: ', x0, y0, H)
-							print( Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4) 
-							print( Area_hexb, Area_Q1b, Area_Q2b, Area_Q3b, Area_Q4b)
-							print( 'count=', count)
-							halt
-		
-		print( 'Many_Hexagons Test Successful')
-
-
-	if test_case=='hexagon':
-		H=1.
-		S=2.*H/np.sqrt(3.)
-		x0=0.
-		y0=0.
-		#(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Divide_hexagon_into_4_quadrants_old(x0,y0,H)
-		#print( x0,y0,H
-		#print( 'First version', Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
-		(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Hexagon_into_quadrants_using_triangles(x0,y0,H,theta=0)
-		print( 'Triangle version1',Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
-		(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Hexagon_into_quadrants_using_triangles(x0,y0,H,theta=90.)
-		print( 'Triangle version2',Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
-		
-		#print( 'Analysis'	
-		#print( 'sum of quadrants: ', (Area_Q1+Area_Q2+Area_Q3+Area_Q4)
-		print( 'Scaled areas: ')
-		print( (Area_Q1+Area_Q2+Area_Q3+Area_Q4)/Area_hex, Area_Q1/Area_hex, Area_Q2/Area_hex, Area_Q3/Area_hex, Area_Q4/Area_hex)
-		
-
-	elif test_case=='square':
-	 
-		x0=0.6999999999999
-		y0=0.3
-		L=0.6
-		square_spreading_calculation(x0,y0,L)
-
-	elif test_case=='triangle':
-		Ax=-0.5
-		Ay=-0.3 -((8./9.)/10.)
-		Bx=-0.277777777778
-		By= -0.5
-
-		Cx=0.5
-		Cy=0.3 +((8./9.)/10.)
-
-		[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]=Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy); #T023
-
-		#Px=1. ; Py=0. ; Qx=2. ; Qy=0.	
-		#Rx=0. ; Ry=1. ; Sx=0. ; Sy=2.	
-		#[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]= Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  )
-
-		print( 'Triangle 2: ',Ax,Ay,Bx,By,Cx,Cy)
-		print( 'Full',T23_Q1+T23_Q2+T23_Q3+T23_Q4)
-		print( 'Q1, Q2,Q3,Q4',T23_Q1,T23_Q2,T23_Q3,T23_Q4)
-		print( 'Full triangle area',T23_Area)
-		print( 'Error',(T23_Q1+T23_Q2+T23_Q3+T23_Q4-T23_Area))
-		
-		
-
-	elif test_case=='point_in_triangle':
-		Ax= -2.695732526092343E-012
-		Ay=0.204344508198090
-		Bx=-2.695750202346321E-012 
-		By= -8.433062639672301E-002
-		Cx=0.249999999997304
-		Cy=6.000694090068343E-002
-		print( 'Point in triangle', point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.))
-
-
-	print( 'Script complete')
-
-if __name__ == '__main__':
-	main()
-	#sys.exit(main())
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/hexagon_area.pyc b/tests/Iceberg_repository/Scripts_and_analysis/hexagon_area.pyc
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diff --git a/tests/Iceberg_repository/Scripts_and_analysis/iceshelf_geometry_create.py b/tests/Iceberg_repository/Scripts_and_analysis/iceshelf_geometry_create.py
deleted file mode 100755
index a819716..0000000
--- a/tests/Iceberg_repository/Scripts_and_analysis/iceshelf_geometry_create.py
+++ /dev/null
@@ -1,150 +0,0 @@
-#!/usr/bin/env python
-
-###############################################################################################
-from netCDF4 import Dataset
-import numpy as np
-import os
-import numpy
-import netCDF4 as nc
-import matplotlib
-import matplotlib.pyplot as plt
-from pylab import *
-#import pdb
-#import argparse
-#This combination allows you to access the varibale imputted from the command line.
-#import sys
-
-#Clear screen
-def main():
-
-	os.system('clear')
-	input_geometry_filename='input_files/Isomip_ocean_geometry.nc'
-	input_iceshelf_filename='input_files/Ocean1_3D_no_calving.nc'
-
-	new_filename='output_files/Ocean1_3D_no_calving_trimmed.nc'
-
-
-	#Parameters
-	rho_water=1028
-	rho_ice=918
-
-	#f=Dataset(input_geometry_filename,'r')
-	#g=Dataset(new_filename,'w') # w if for creating a file
-
-
-	with nc.Dataset(input_geometry_filename) as file:
-		Depth = file.variables['D'][:,:]
-	with nc.Dataset(input_iceshelf_filename) as file:
-		thick = file.variables['thick'][:,:]
-	with nc.Dataset(input_iceshelf_filename) as file:
-		area= file.variables['area'][:,:]
-
-
-
-	M=thick.shape
-	thick_orig=np.zeros((M[0],M[1]))
-	for i in range(M[0]):
-		for j in range(M[01]):
-			thick_orig[i,j]=thick[i,j]
-	
-	#Making ice shelf symetric
-	M=thick.shape
-	thick_tmp=thick
-	print M
-	for i in range(M[0]/2):
-		for j in range(M[1]):
-			i_sym=(M[0]-1-i)
-			if j==0:
-				print i, i_sym
-			thick_tmp[i,j]=((thick[i,j]+thick[i_sym,j])/2.)
-			thick_tmp[i_sym,j]=((thick[i,j]+thick[i_sym,j])/2.)
-	thick=thick_tmp
-
-	#Making draft increase going inwards
-	M=thick.shape
-	thick_tmp=thick
-	print M
-	for k in range(5):
-		#for i in range(M[0]/2):
-		#for i in range(M[0]/8):
-		for i in range(5):
-			#for j in range(M[1]):
-			for j in range(118):
-				i_sym=(M[0]-1-i)
-				if (thick_tmp[i,j]<thick_tmp[i+1,j]):
-					thick_tmp[i,j]=thick_tmp[i+1,j]
-					#thick_tmp[i,j]=((thick_tmp[i+1,j] +thick_tmp[i+2,j])/2)
-				thick_tmp[i_sym,j]=thick_tmp[i,j]
-
-		thick=thick_tmp
-	
-
-
-
-	draft=thick*(rho_water/rho_ice)
-
-	ocean_thick=Depth-draft
-	ocean_thick[np.where(ocean_thick<0)]=0.
-
-	#ocean_thick=draft
-	
-	subplot(4,1,1)
-	cNorm = mpl.colors.Normalize(vmin=0, vmax=10)
-	cmap='jet'
-	plt.pcolormesh(ocean_thick,norm=cNorm,cmap=cmap)
-	plt.colorbar()
-	
-	subplot(4,1,2)
-	cNorm = mpl.colors.Normalize(vmin=0, vmax=1000)
-	cmap='jet'
-	plt.pcolormesh(thick_orig,norm=cNorm,cmap=cmap)
-	plt.colorbar()
-
-
-	subplot(4,1,3)
-	cNorm = mpl.colors.Normalize(vmin=0, vmax=1000)
-	cmap='jet'
-	plt.pcolormesh(thick,norm=cNorm,cmap=cmap)
-	plt.colorbar()
-
-	subplot(4,1,4)
-	cNorm = mpl.colors.Normalize(vmin=0, vmax=10)
-	cmap='jet'
-	plt.pcolormesh(thick-thick_orig,norm=cNorm,cmap=cmap)
-	plt.colorbar()
-
-
-
-	ny=M[0]
-	nx=M[1]
-	print nx,ny
-
-
-	#Creating the topog file
-	g=Dataset(new_filename,'w') # w if for creating a file
-
-	yt=g.createDimension('yt',ny)
-	xt=g.createDimension('xt',nx)
-
-	thick_h=g.createVariable('thick','f4',('yt','xt'))
-	g.variables['thick'][:]=thick
-	area_h=g.createVariable('area','f4',('yt','xt'))
-	g.variables['area'][:]=area
-
-	print 'Writing file: ' , new_filename
-	
-	g.sync()
-	g.close()
-
-
-
-	plt.show()
-
-
-	print 'Script complete'
-
-
-
-if __name__ == '__main__':
-        main()
-        #sys.exit(main())
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/iceshelf_mass_file_create.py b/tests/Iceberg_repository/Scripts_and_analysis/iceshelf_mass_file_create.py
deleted file mode 100755
index b98e66d..0000000
--- a/tests/Iceberg_repository/Scripts_and_analysis/iceshelf_mass_file_create.py
+++ /dev/null
@@ -1,83 +0,0 @@
-#!/usr/bin/env python
-
-###############################################################################################
-from netCDF4 import Dataset
-import numpy as np
-import os
-import numpy
-import netCDF4 as nc
-#import matplotlib
-#import matplotlib.pyplot as plt
-#from pylab import *
-#import pdb
-#import argparse
-#This combination allows you to access the varibale imputted from the command line.
-#import sys
-
-#Clear screen
-def main():
-
-	os.system('clear')
-	input_filename='input_files/Isomip_ice_geometry.nc'
-	new_filename='output_files/ISOMIP_MIB.nc'
-
-	#f=Dataset(input_geometry_filename,'r')
-	#g=Dataset(new_filename,'w') # w if for creating a file
-
-	rho_ice=850.
-
-	with nc.Dataset(input_filename) as file:
-		ocean_mask = file.variables['openOceanMask'][:,:]
-		upperSurface = file.variables['upperSurface'][:,:]
-		lowerSurface = file.variables['lowerSurface'][:,:]
-		h_ice=upperSurface-lowerSurface
-		mass=h_ice*rho_ice
-		x = file.variables['x'][:]
-		y = file.variables['y'][:]
-
-
-	M= mass.shape
-	ny=M[0]
-	nx=M[1]
-	print nx,ny
-	print mass.shape
-
-	#subsampling data onto a grid half the size
-	MIB=np.zeros((ny/2,nx/2))
-	print MIB.shape
-	for i in range(0,nx,2):
-		for j in range(0,ny,2):
-			MIB[j/2,i/2]=mass[j,i]
-
-	
-	#Creating the topog file
-	g=Dataset(new_filename,'w') # w if for creating a file
-
-	time=g.createDimension('time',1)
-	yt=g.createDimension('yt',ny)
-	xt=g.createDimension('xt',nx)
-
-	mass_h=g.createVariable('mass','f4',('time','yt','xt'))
-	g.variables['mass'][:]=mass
-
-	#Creating subsampled version
-	yh=g.createDimension('yh',ny/2)
-	xh=g.createDimension('xh',nx/2)
-	MIB_h=g.createVariable('MIB','f4',('time','yh','xh'))
-	g.variables['MIB'][:]=MIB
-
-
-	g.sync()
-	g.close()
-
-
-
-
-
-	print 'Script complete'
-
-
-
-if __name__ == '__main__':
-        main()
-        #sys.exit(main())
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/movie_bergs_traj.py b/tests/Iceberg_repository/Scripts_and_analysis/movie_bergs_traj.py
deleted file mode 100755
index ec99778..0000000
--- a/tests/Iceberg_repository/Scripts_and_analysis/movie_bergs_traj.py
+++ /dev/null
@@ -1,283 +0,0 @@
-#!/usr/bin/env python
-
-def bergs_yearday(bergs):
-	bergs=bergs_read(bergs,'year')
-	bergs=bergs_read(bergs,'day')
-	for b in xrange (0,len(bergs.berg)):
-		bergs.berg[b].yearday=bergs.berg[b].year+(bergs.berg[b].day/372)
-		#Note I have not included all the warnings about dimensions already existing.
-        return bergs
-
-
-def bergs_read(bergs,varname):
-	nc=bergs.nc
-	bergs_list=bergs.berg
-	var = nc.variables[varname][:]
-	for b in xrange (0,len(bergs.berg)):
-		k=[]
-		js=bergs.berg[b].js
-		je=bergs.berg[b].je
-		for l in xrange (0,len(js)):
-			temp=range(js[l],je[l]+1)
-			for i in xrange (0, len(temp)):
-				k.append(temp[i])
-			setattr(bergs.berg[b],varname,var[k])
-        return bergs
-
-
-def bergs_hash(year, day, x, y, m):
-	ilat=(90.+y)/180
-        ilon=(360 % x)/360;
-        iyear=np.floor(year);
-        iday=(day/372);
-        im=math.log(m,10)-7.9;
-        h=ilon+1e3*ilat+1e6*iday+1e9*iyear+1e12*im;
-        return h
-
-
-
-def bergs_open(filename):
-
-	#Creating a classes
-	class berg_handle:
-		def __init__(self,berg,nc):
-			self.berg=berg
-			self.nc=nc
-
-	class berg_type:
-		def __init__(self,hash):
-			self.hash=hash
-			self.year0=[]
-			self.day0=[]
-			self.lon0=[]
-			self.lat0=[]
-			self.mass0=[]
-			self.js=[]
-			self.je=[]
-			self.width=[]
-			self.lon=[]
-			self.lat=[]
-			self.year=[]
-			self.day=[]
-			self.uvel=[]
-			self.vvel=[]
-			self.uo=[]
-			self.vo=[]
-			self.ui=[]
-			self.ua=[]
-			self.vu=[]
-			self.mass_of_bits=[]
-			self.heat_density=[]
-			self.thickness=[]
-			self.length=[]
-			self.ssh_x=[]
-			self.ssh_y=[]
-			self.sst=[]
-			self.cn=[]
-			self.hi=[]
-			self.yearday=[]
-			self.iceberg_num=[]
-
-	#Importing the data
-	nc = Dataset(filename, mode='r')
-	lat = nc.variables['lat'][:]
-	N=len(lat)
-	js=np.where(lat>91)[0]
-	je=np.concatenate([js[1:]-1, np.array([N-1])])
-	lon = nc.variables['lon'][:]
-	year = nc.variables['year'][:]
-	day = nc.variables['day'][:]
-	#mass = nc.variables['mass'][:]
-	iceberg_num = nc.variables['iceberg_num'][:]
-
-	N=len(js)
-	h=np.zeros(N)
-	# Making a list of identifying hashes
-	k=0
-	for j in js+1:
-		#h[k]=bergs_hash(year[j], day[j],lon[j],lat[j],mass[j])
-		h[k]=iceberg_num[j]
-		k=k+1
-
-	#Creates a sorted array of unique elements of h
-	h=sorted(list(set(h)))
-
-	#Create a list of bergs, named by their hash values, h
-	berg=[]
-	for i in xrange (0,len(h)):
-		berg.append(berg_type(h[i]))
-
-	for i in xrange(0, len(js)):
-		j=js[i]+1
-		#l=np.where(h==bergs_hash(year[j], day[j],lon[j],lat[j],mass[j]))[0]
-		l=np.where(h==iceberg_num[j])[0]
-		berg[l].year0.append(year[j])
-		berg[l].day0.append(day[j])
-		berg[l].lon0.append(lon[j])
-		berg[l].lat0.append(lat[j])
-		#berg[l].mass0.append(mass[j])
-		berg[l].js.append(js[i]+2)
-		berg[l].je.append(je[i])
-
-	#Sort each segment
-	for i in xrange (0,len(h)):
-		yd=year[berg[i].js]+(day[berg[i].js]/373)
-		#Sort according to descending yd, and then pull out indicies for js, and je.
-		
-		berg[i].js=[berg[i].js[n] for n,_ in sorted(list(enumerate(yd)),reverse=True)]
-		berg[i].je=[berg[i].je[n] for n,_ in sorted(list(enumerate(yd)),reverse=True)]
-
-	bergs_handle=berg_handle(berg,nc)
-
-	return bergs_handle
-
-###############################################################################################
-#################################  Beginning of Script  #######################################
-###############################################################################################
-from netCDF4 import Dataset
-import numpy as np
-#from PIL import *
-import math
-import os
-import matplotlib
-matplotlib.use("GTKAgg")
-import matplotlib.pyplot as plt
-from pylab import *
-import pdb
-import argparse
-#This combination allows you to access the varibale imputted from the command line.
-import sys
-
-#Clear screen
-#os.system('clear')
-
-#This is a command which puts you into testing mode so that you can troubleshoot (like a breakpoint in matlab)
-#pdb.set_trace()
-
-#If no files are given at runtime, then use the files selected here:
-if len(sys.argv)==1:
-	Number_of_files=2  # How many files would you like to view?
-
-	#Choosing which files to use
-	#Weddel Sea Version
-	fileroot='/home/aas/Iceberg_Project/Weddell_Sea/'
-	dirname1='one_iceberg_testing_Verlet';
-	dirname2='one_iceberg_testing_RK';
-	
-	filename1=fileroot+dirname1+'/iceberg_trajectories.nc'
-	filename2=fileroot+dirname2+'/iceberg_trajectories.nc'
-
-	#Other files
-	#filename1='/home/aas/Iceberg_Project/Test_data1/Quick_Global_RK15/iceberg_trajectories.nc';
-	#filename1= '/home/aas/Iceberg_Project/Weddell_Sea/one_iceberg_testing/iceberg_trajectories.nc'
-
-else:
-	Number_of_files=len(sys.argv)-1
-	
-#Imput parameters
-berg_num=0 #index of ic
-
-#Flags and on/off switches
-plot_timeseries=0
-plot_trajectory=1
-plot_bergsize=1
-fix_horizontal_scale=0
-plot_all_bergs=1  #plots all the icebergs and not just the one given by n
-plot_initial_size=0
-plot_size_at_start_and_finish_only=1
-short_form=1 #only looks up the lat / lon
-
-#Creating and filling up the bergs
-for loop in xrange(0,Number_of_files):
-	if len(sys.argv)==1:
-		if loop==0: filename=filename1
-		if loop==1: filename=filename2
-	else:
-		filename=sys.argv[loop+1]
-	print filename	
-
-	berg=[]; del berg
-	bergs=bergs_open(filename)
-	bergs=bergs_read(bergs,'width')
-	bergs=bergs_read(bergs,'length')
-	bergs=bergs_read(bergs,'lat')
-	bergs=bergs_read(bergs,'lon')
-	bergs=bergs_yearday(bergs)
-	
-	N=len(bergs.berg)
-	if plot_all_bergs==0:
-		N=1
-	for n in xrange (0, N):
-		if plot_all_bergs==0:
-			n=berg_num
-
-		#Loading variables
-		lon=bergs.berg[n].lon[:]
-		lat=bergs.berg[n].lat[:]
-		width=bergs.berg[n].width[:]
-		length=bergs.berg[n].length[:]
-		yearday=bergs.berg[n].yearday[:]
-
-		#Finding the index of the initial time
-		initial_time_ind=sorted(list(enumerate(yearday)),key=lambda x: x[0])[-1][0]
-		final_time_ind=sorted(list(enumerate(yearday)),key=lambda x: x[0])[0][0]
-
-###########################   Begining plotting  #################################
-
-		if plot_trajectory==1:
-			#plt.subplot(2,1,1)
-			if loop==0:
-				if n==1:
-					plt.plot(lon,lat,'ko-')
-				if n!=1:
-					plt.plot(lon,lat,'go-')
-			else:
-				plt.plot(lon,lat,'bo-')
-			plt.xlabel('longitude (deg)')
-			plt.ylabel('latitude (deg)')
-			plt.title('Iceberg trajectory')
-			plt.grid(True)
-			#savefig("test.png")
-
-			if plot_bergsize==1:
-				Radius_earth=6378.135*1000;
-				circ_ind=np.linspace(0,2*pi,100);
-				for k in xrange (0 ,len(lat)):
-    					L_eff=sqrt(((width[k]*length[k])/pi));
-					plt.plot(lon[k],lat[k],'bo',linewidth=5)
-				        #d_lat=(L_eff/Radius_earth)*(180/pi);
-					#d_lon=L_eff/(111.320*(10**(3))*cos(lat[k]*pi/180));
-				        d_lat=(L_eff/Radius_earth)*(180/pi);
-					d_lon=(L_eff/(Radius_earth*cos(lat[k]*pi/180)))*(180/pi);
-                                        if plot_size_at_start_and_finish_only==0:
-					        plt.plot(lon[k]+(d_lon*cos(circ_ind)),lat[k]+(d_lat*sin(circ_ind)),'b');
-					if k==initial_time_ind and plot_initial_size==1:
-						plt.plot(lon[k]+(d_lon*cos(circ_ind)),lat[k]+(d_lat*sin(circ_ind)),'r');
-					if k==final_time_ind:
-						plt.plot(lon[k]+(d_lon*cos(circ_ind)),lat[k]+(d_lat*sin(circ_ind)),'r');
-				
-			#Setting axes to have equal distance
-				if fix_horizontal_scale==1:
-					y_scale=(max(lat)-min(lat))*(Radius_earth*pi/180)
-					x_scale=(max(lon)-min(lon))*(111.320*(10**(3))*cos(np.mean(lat)/180*pi))
-					d=0.6*max(x_scale,y_scale)
-					d_lat=d*(180/(Radius_earth*pi))
-					d_lon=d/(111.320*(10**(3))*cos(np.mean(lat)*pi/180))
-					plt.xlim([((min(lon)+max(lon))/2)-d_lon,((min(lon)+max(lon))/2)+d_lon])
-					plt.ylim([((min(lat)+max(lat))/2)-d_lat,((min(lat)+max(lat))/2)+d_lat])
-	
-			plt.plot(lon[initial_time_ind],lat[initial_time_ind],'ro')
-plt.show()
-
-if plot_timeseries==1:
-	n=0
-	#plt.subplot(2,1,2)
-	plt.plot(yearday,lon,'ko-')
-	plt.xlabel('yearday')
-	plt.ylabel('lon (deg)')
-	plt.grid(True)
-	plt.savefig("test7.png")
-	plt.show()
-
-
-print 'Script complete'
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/old_bergs_quickview.py b/tests/Iceberg_repository/Scripts_and_analysis/old_bergs_quickview.py
deleted file mode 100755
index c67c638..0000000
--- a/tests/Iceberg_repository/Scripts_and_analysis/old_bergs_quickview.py
+++ /dev/null
@@ -1,268 +0,0 @@
-#!/usr/bin/env python
-
-def bergs_yearday(bergs):
-	bergs=bergs_read(bergs,'year')
-	bergs=bergs_read(bergs,'day')
-	for b in xrange (0,len(bergs.berg)):
-		bergs.berg[b].yearday=bergs.berg[b].year+(bergs.berg[b].day/372)
-		#Note I have not included all the warnings about dimensions already existing.
-        return bergs
-
-
-def bergs_read(bergs,varname):
-	nc=bergs.nc
-	bergs_list=bergs.berg
-	var = nc.variables[varname][:]
-	for b in xrange (0,len(bergs.berg)):
-		k=[]
-		js=bergs.berg[b].js
-		je=bergs.berg[b].je
-		for l in xrange (0,len(js)):
-			temp=range(js[l],je[l]+1)
-			for i in xrange (0, len(temp)):
-				k.append(temp[i])
-			setattr(bergs.berg[b],varname,var[k])
-        return bergs
-
-
-def bergs_hash(year, day, x, y, m):
-	ilat=(90.+y)/180
-        ilon=(360 % x)/360;
-        iyear=np.floor(year);
-        iday=(day/372);
-        im=math.log(m,10)-7.9;
-        h=ilon+1e3*ilat+1e6*iday+1e9*iyear+1e12*im;
-        return h
-
-
-
-def bergs_open(filename):
-
-	#Creating a classes
-	class berg_handle:
-		def __init__(self,berg,nc):
-			self.berg=berg
-			self.nc=nc
-
-	class berg_type:
-		def __init__(self,hash):
-			self.hash=hash
-			self.year0=[]
-			self.day0=[]
-			self.lon0=[]
-			self.lat0=[]
-			self.mass0=[]
-			self.js=[]
-			self.je=[]
-			self.width=[]
-			self.lon=[]
-			self.lat=[]
-			self.year=[]
-			self.day=[]
-			self.uvel=[]
-			self.vvel=[]
-			self.uo=[]
-			self.vo=[]
-			self.ui=[]
-			self.ua=[]
-			self.vu=[]
-			self.mass_of_bits=[]
-			self.heat_density=[]
-			self.thickness=[]
-			self.length=[]
-			self.ssh_x=[]
-			self.ssh_y=[]
-			self.sst=[]
-			self.cn=[]
-			self.hi=[]
-			self.yearday=[]
-
-	#Importing the data
-	nc = Dataset(filename, mode='r')
-	lat = nc.variables['lat'][:]
-	N=len(lat)
-	js=np.where(lat>91)[0]
-	je=np.concatenate([js[1:]-1, np.array([N-1])])
-	lon = nc.variables['lon'][:]
-	year = nc.variables['year'][:]
-	day = nc.variables['day'][:]
-	mass = nc.variables['mass'][:]
-
-	N=len(js)
-	h=np.zeros(N)
-	# Making a list of identifying hashes
-	k=0
-	for j in js+1:
-		h[k]=bergs_hash(year[j], day[j],lon[j],lat[j],mass[j])
-		k=k+1
-
-	#Creates a sorted array of unique elements of h
-	h=sorted(list(set(h)))
-
-	#Create a list of bergs, named by their hash values, h
-	berg=[]
-	for i in xrange (0,len(h)):
-		berg.append(berg_type(h[i]))
-
-	for i in xrange(0, len(js)):
-		j=js[i]+1
-		l=np.where(h==bergs_hash(year[j], day[j],lon[j],lat[j],mass[j]))[0]
-		berg[l].year0.append(year[j])
-		berg[l].day0.append(day[j])
-		berg[l].lon0.append(lon[j])
-		berg[l].lat0.append(lat[j])
-		berg[l].mass0.append(mass[j])
-		berg[l].js.append(js[i]+2)
-		berg[l].je.append(je[i])
-
-	#Sort each segment
-	for i in xrange (0,len(h)):
-		yd=year[berg[i].js]+(day[berg[i].js]/373)
-		#Sort according to descending yd, and then pull out indicies for js, and je.
-		
-		berg[i].js=[berg[i].js[n] for n,_ in sorted(list(enumerate(yd)),reverse=True)]
-		berg[i].je=[berg[i].je[n] for n,_ in sorted(list(enumerate(yd)),reverse=True)]
-
-	bergs_handle=berg_handle(berg,nc)
-
-	return bergs_handle
-
-###############################################################################################
-#################################  Beginning of Script  #######################################
-###############################################################################################
-from netCDF4 import Dataset
-import numpy as np
-#from PIL import *
-import math
-import os
-import matplotlib
-matplotlib.use("GTKAgg")
-import matplotlib.pyplot as plt
-from pylab import *
-import pdb
-import argparse
-#This combination allows you to access the varibale imputted from the command line.
-import sys
-
-#Clear screen
-#os.system('clear')
-
-#This is a command which puts you into testing mode so that you can troubleshoot (like a breakpoint in matlab)
-#pdb.set_trace()
-
-#If no files are given at runtime, then use the files selected here:
-if len(sys.argv)==1:
-	Number_of_files=2  # How many files would you like to view?
-
-	#Choosing which files to use
-	#Weddel Sea Version
-	fileroot='/home/aas/Iceberg_Project/Weddell_Sea/'
-	dirname1='one_iceberg_testing_Verlet';
-	dirname2='one_iceberg_testing_RK';
-	
-	filename1=fileroot+dirname1+'/iceberg_trajectories.nc'
-	filename2=fileroot+dirname2+'/iceberg_trajectories.nc'
-
-	#Other files
-	#filename1='/home/aas/Iceberg_Project/Test_data1/Quick_Global_RK15/iceberg_trajectories.nc';
-	#filename1= '/home/aas/Iceberg_Project/Weddell_Sea/one_iceberg_testing/iceberg_trajectories.nc'
-
-else:
-	Number_of_files=len(sys.argv)-1
-	
-#Imput parameters
-berg_num=0 #index of ic
-
-#Flags and on/off switches
-plot_timeseries=0
-plot_trajectory=1
-plot_bergsize=0
-fix_horizontal_scale=0
-plot_all_bergs=1  #plots all the icebergs and not just the one given by n
-
-
-#Creating and filling up the bergs
-for loop in xrange(0,Number_of_files):
-	if len(sys.argv)==1:
-		if loop==0: filename=filename1
-		if loop==1: filename=filename2
-	else:
-		filename=sys.argv[loop+1]
-	print filename	
-
-	berg=[]; del berg
-	bergs=bergs_open(filename)
-	bergs=bergs_read(bergs,'width')
-	bergs=bergs_read(bergs,'length')
-	bergs=bergs_read(bergs,'lat')
-	bergs=bergs_read(bergs,'lon')
-	bergs=bergs_yearday(bergs)
-	
-	N=len(bergs.berg)
-	if plot_all_bergs==0:
-		N=1
-	for n in xrange (0, N):
-		if plot_all_bergs==0:
-			n=berg_num
-
-		#Loading variables
-		lon=bergs.berg[n].lon[:]
-		lat=bergs.berg[n].lat[:]
-		width=bergs.berg[n].width[:]
-		length=bergs.berg[n].length[:]
-		yearday=bergs.berg[n].yearday[:]
-
-		#Finding the index of the initial time
-		initial_time_ind=sorted(list(enumerate(yearday)),key=lambda x: x[1])[0][0]
-
-###########################   Begining plotting  #################################
-
-		if plot_trajectory==1:
-			#plt.subplot(2,1,1)
-			if loop==0:
-				plt.plot(lon,lat,'ko-')
-			else:
-				plt.plot(lon,lat,'bo-')
-			plt.xlabel('longitude (deg)')
-			plt.ylabel('latitude (deg)')
-			plt.title('Iceberg trajectory')
-			plt.grid(True)
-			#savefig("test.png")
-
-			if plot_bergsize==1:
-				Radius_earth=6378.135*(10^(3));
-				circ_ind=np.linspace(0,2*pi,100);
-				for k in xrange (0 ,len(lat)):
-    					L_eff=sqrt(((width[k]*length[k])/pi));
-					plt.plot(lon[k],lat[k],'bo',linewidth=5)
-				        d_lat=(L_eff/Radius_earth)*(180/pi);
-					d_lon=L_eff/(111.320*(10**(3))*cos(lat[k]/180*pi));
-				        plt.plot(lon[k]+(d_lon*cos(circ_ind)),lat[k]+(d_lat*sin(circ_ind)),'b');
-					if k==initial_time_ind:
-						plt.plot(lon[k]+(d_lon*cos(circ_ind)),lat[k]+(d_lat*sin(circ_ind)),'r');
-				
-			#Setting axes to have equal distance
-				if fix_horizontal_scale==1:
-					y_scale=(max(lat)-min(lat))*(Radius_earth*pi/180)
-					x_scale=(max(lon)-min(lon))*(111.320*(10**(3))*cos(np.mean(lat)/180*pi))
-					d=0.6*max(x_scale,y_scale)
-					d_lat=d*(180/(Radius_earth*pi))
-					d_lon=d/(111.320*(10**(3))*cos(np.mean(lat)/180*pi))
-					plt.xlim([((min(lon)+max(lon))/2)-d_lon,((min(lon)+max(lon))/2)+d_lon])
-					plt.ylim([((min(lat)+max(lat))/2)-d_lat,((min(lat)+max(lat))/2)+d_lat])
-	
-			plt.plot(lon[initial_time_ind],lat[initial_time_ind],'ro')
-plt.show()
-
-if plot_timeseries==1:
-	n=0
-	#plt.subplot(2,1,2)
-	plt.plot(yearday,lon,'ko-')
-	plt.xlabel('yearday')
-	plt.ylabel('lon (deg)')
-	plt.grid(True)
-	plt.savefig("test7.png")
-	plt.show()
-
-
-print 'Script complete'
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/quick_benchmark_comparison.sh b/tests/Iceberg_repository/Scripts_and_analysis/quick_benchmark_comparison.sh
deleted file mode 100755
index 6f179c2..0000000
--- a/tests/Iceberg_repository/Scripts_and_analysis/quick_benchmark_comparison.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-echo "Difference between benchmark and quick test are:"
-cd ../
-diff Benchmark_Quick_Global_test/iceberg_trajectories.nc Quick_Global_test/iceberg_trajectories.nc
-
-echo "End of differences"
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/quick_plot.py b/tests/Iceberg_repository/Scripts_and_analysis/quick_plot.py
deleted file mode 100755
index 3d1f39b..0000000
--- a/tests/Iceberg_repository/Scripts_and_analysis/quick_plot.py
+++ /dev/null
@@ -1,205 +0,0 @@
-#!/usr/bin/env python
-
-#First import the netcdf4 library
-from netCDF4 import Dataset  # http://code.google.com/p/netcdf4-python/
-import numpy as np  # http://code.google.com/p/netcdf4-python/
-import matplotlib
-import math
-import os
-matplotlib.use("GTKAgg")
-from pylab import *
-#import matplotlib.pyplot as plt
-import pdb
-import netCDF4 as nc
-import sys
-import argparse
-
-
-def transpose_matrix(data):
-	M=data.shape
-	data_new=np.zeros([M[1],M[0]])
-	for i in range(M[0]):
-		for j in range(M[1]):
-			data_new[j,i]=data[i,j]
-	print 'After rotation' ,data.shape
-	return data_new
-
-def load_data_from_file(filename,field,dim_num,layer_number,rotated=None):
-	with nc.Dataset(filename) as file:
-		if dim_num==2:
-			data = file.variables[field][:]
-		if dim_num==3:
-			data = file.variables[field][:]
-		if dim_num==4:
-			data = file.variables[field][:]
-	
-	print 'Data size:' ,data.shape
-	
-	if len(data.shape)==3:
-		#data=np.squeeze(np.mean(data,axis=0))  #Mean over first variable
-		data=np.squeeze(data[-1,:,:])  #Final time
-	if len(data.shape)==4:
-			#data=np.squeeze(np.mean(data,axis=0))  #Mean over first variable
-			data=np.squeeze((data[-1,:,:,:]))  #Mean over first variable
-			data=np.squeeze(data[layer_number,:,:])#Layer choice over second 
-
-
-	if rotated=='rotated':
-		data=transpose_matrix(data)
-	return data
-
-def plot_data_field(data,field,vmin=None,vmax=None): 
-	print 'Starting to plot...'	
-	if vmin==None:
-		vmin=np.min(data)
-	else:
-		vmin=float(vmin)
-
-	if vmax==None:
-		vmax=np.max(data)
-	else:
-		vmax=float(vmax)
-	cmap='jet'
-	print vmin	
-	print vmax	
-
-	cNorm = mpl.colors.Normalize(vmin=vmin, vmax=vmax)
-	#cNorm = mpl.colors.Normalize(vmin=600, vmax=850)
-	plt.pcolormesh(data,norm=cNorm,cmap=cmap)
-	plt.colorbar()
-	plt.grid(True)
-	plt.title(field)
-
-def plot_operated_fields(data1,data2,field,operation,vmax_lim=None): 
-	print 'Starting to plot...'	
-
-	#Temp lines to subtract maximum
-	#temp_val=np.max(data1)
-	#data1=data1-temp_val ;	data2=data2-temp_val
-	
-	vmin=min(np.min(data1),np.min(data2))
-	vmax=max(np.max(data1),np.max(data2))
-	#vmin=-vmax
-
-	cmap='jet'
-	cNorm = mpl.colors.Normalize(vmin=vmin, vmax=vmax)
-
-	#Data from file 1:
-	plt.subplot(1,3,1)
-	plt.pcolormesh(data1,norm=cNorm,cmap=cmap)
-	plt.colorbar()
-	plt.title('File 1: ' + field)
-	#Data from file 2:
-	plt.subplot(1,3,2)
-	plt.pcolormesh(data2,norm=cNorm,cmap=cmap)
-	plt.colorbar()
-	plt.title('File 2: ' + field)
-
-
-	#Data from difference:
-	data3=data1-data2 #subtraction is the default
-	if operation=='divide':
-		data3=data1/data2
-	if operation=='relative':
-		data3=(data1-data2)/data1
-	if vmax_lim==None:
-		vmax=np.max(abs(data3))
-	else:
-		vmax=float(vmax_lim)
-	vmin=-vmax
-	cmap='bwr'
-	cNorm = mpl.colors.Normalize(vmin=vmin, vmax=vmax)
-	if operation=='divide':
-		cNorm = mpl.colors.Normalize(vmin=0, vmax=2)
-	if operation=='relative':
-		cNorm = mpl.colors.Normalize(vmin=-1, vmax=1)
-	plt.subplot(1,3,3)
-	plt.pcolormesh(data3,norm=cNorm,cmap=cmap)
-	plt.colorbar()
-	plt.title('Difference')
-	print 'Max/Min data3=', np.max(data3), np.min(data3)
-
-####################################################################################################################################################
-##########################################################  Main Program   #########################################################################
-####################################################################################################################################################
-
-def main():
-	parser = argparse.ArgumentParser()
-        parser.add_argument('--file1', default=None, help='The input data file1 in NetCDF format.')
-        parser.add_argument('--file2', default=None, help='The input data file2 in NetCDF format.')
-        parser.add_argument('--field', default=None, help='Feild to plot')
-        parser.add_argument('--field2', default=None, help='Feild to plot')
-        parser.add_argument('--operation',default=None, help='Operation betweeen fields')
-        parser.add_argument('--layer_number', default=0, help='Operation betweeen fields')
-        parser.add_argument('--dim_num', default=2, help='Number of dimensions of data')
-        parser.add_argument('--vmax', default=None, help='Maximum for plotting')
-        parser.add_argument('--vmin', default=None, help='Minimum for plotting')
-        parser.add_argument('--rotated', default=None, help='Minimum for plotting')
-	args = parser.parse_args()
-
-	#Converting input
-	field=args.field
-	field2=args.field
-	if args.field2 is not None:
-		field2=args.field2
-	layer_number=int(args.layer_number)
-	dim_num=int(args.dim_num)
-	operation=args.operation
-	filename1=args.file1
-	rotated=args.rotated
-	print 'File 1 = ' , filename1
-
-	#filename3='../../ocean_only/Alistair_ISOMIP/rho/ISOMIP_IC.nc'
-	#filename1='/lustre/f1/unswept/Alon.Stern/MOM6-examples_Alon/ocean_only/Alistair_ISOMIP/rho/ISOMIP.nc'
-
-	#if filename1==filename3:
-	#	print 'BOOM'
-	#else:
-	#	print 'NO'
-	plt.figure(figsize=(15,10))
-	#fig = plt.figure(1)
-
-	#Loading data from file1
-	data1=load_data_from_file(filename1,field,dim_num,layer_number,rotated)
-
-	if args.file2!=None:
-		filename2=args.file2
-		print 'File 2 = ' ,filename2
-		#Loading data from file1
-		data2=load_data_from_file(filename2,field2,dim_num,layer_number,rotated)
-
-		if operation=='subtract':
-			print 'Subtracting fields'
-			#data=data-data2
-			#operation='subtract'
-
-	if args.file2==None:
-		plot_data_field(data1,field,args.vmin,args.vmax)	
-	else:
-		plot_operated_fields(data1,data2,field,operation,args.vmax)	
-
-
-	#Plotting flags
-	#fig.set_size_inches(9,4.5)
-	plt.show()
-	print 'Script complete'
-
-
-
-if __name__ == '__main__':
-	main()
-	#sys.exit(main())
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/submit_to_queue.sh b/tests/Iceberg_repository/Scripts_and_analysis/submit_to_queue.sh
deleted file mode 100755
index bc0f32f..0000000
--- a/tests/Iceberg_repository/Scripts_and_analysis/submit_to_queue.sh
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/bin/csh -fx
-#PBS -N Tech_Bergs
-#PBS -l walltime=16:00:00
-#PBS -l size=128
-#PBS -S /bin/tcsh
-#PBS -r n
-#PBS -m ae
-#PBS -j oe
-#PBS -E
-#PBS -A gfdl_o
-
-#set compiler = intel
-
-
-module load totalview
-env
-pwd
-time aprun -n 128 ../../build/intel/ice_ocean_SIS2/repro/MOM6
-#date
-
-#time aprun ...
-
-#date
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/topog_file_create.py b/tests/Iceberg_repository/Scripts_and_analysis/topog_file_create.py
deleted file mode 100755
index 59ba3ad..0000000
--- a/tests/Iceberg_repository/Scripts_and_analysis/topog_file_create.py
+++ /dev/null
@@ -1,89 +0,0 @@
-#!/usr/bin/env python
-
-###############################################################################################
-from netCDF4 import Dataset
-import numpy as np
-import os
-import numpy
-import netCDF4 as nc
-#import matplotlib
-#import matplotlib.pyplot as plt
-#from pylab import *
-#import pdb
-#import argparse
-#This combination allows you to access the varibale imputted from the command line.
-#import sys
-
-#Clear screen
-def main():
-
-	os.system('clear')
-	input_geometry_filename='input_files/Isomip_ocean_geometry.nc'
-
-	#Flags
-	use_flat_bottom=True
-	use_side_walls=True
-
-	#Parameters
-	constant_depth=750.
-
-	if use_flat_bottom==True:
-		new_filename='output_files/topog_flat'
-	else:
-		new_filename='output_files/topog'
-	if use_side_walls==True:
-		new_filename=new_filename+'_boundaries'
-	new_filename=new_filename+'.nc'
-
-
-	#f=Dataset(input_geometry_filename,'r')
-	#g=Dataset(new_filename,'w') # w if for creating a file
-
-
-	with nc.Dataset(input_geometry_filename) as file:
-		Depth = file.variables['D'][:,:]
-
-	M= Depth.shape
-	ny=M[0]
-	nx=M[1]
-	print nx,ny
-
-	if use_flat_bottom==True:
-		Depth[:,:]=(Depth[:,:]*0.0)+constant_depth
-	if use_side_walls==True:
-		Depth[0,:]=0.0
-		Depth[ny-1,:]=0.0
-		Depth[:,0]=0.0
-		Depth[:,nx-1]=0.0
-	
-		Depth[ny-2,:]=0.0
-		Depth[ny-3,:]=0.0
-		Depth[ny-4,:]=0.0
-		Depth[ny-5,:]=0.0
-		Depth[ny-6,:]=0.0
-
-	#Creating the topog file
-	g=Dataset(new_filename,'w') # w if for creating a file
-
-	yt=g.createDimension('yt',ny)
-	xt=g.createDimension('xt',nx)
-
-	depth_h=g.createVariable('depth','f4',('yt','xt'))
-	g.variables['depth'][:]=Depth
-
-	print 'Writing file: ' , new_filename
-	
-	g.sync()
-	g.close()
-
-
-
-
-
-	print 'Script complete'
-
-
-
-if __name__ == '__main__':
-        main()
-        #sys.exit(main())
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/variables_comparison.sh b/tests/Iceberg_repository/Scripts_and_analysis/variables_comparison.sh
deleted file mode 100755
index 8e8619c..0000000
--- a/tests/Iceberg_repository/Scripts_and_analysis/variables_comparison.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-ncdump -v  VI ../ISOMIP_ocean_ice/Shelf/rho/00010101.ice_day.nc > a 
-ncdump -v  VI ../ISOMIP_ocean_ice/Bergs/rho/00010101.ice_day.nc > b
-diff a b > c
-more c
-
diff --git a/tests/Iceberg_repository/Scripts_and_analysis/write_restart_iceberg.py b/tests/Iceberg_repository/Scripts_and_analysis/write_restart_iceberg.py
deleted file mode 100755
index c170f52..0000000
--- a/tests/Iceberg_repository/Scripts_and_analysis/write_restart_iceberg.py
+++ /dev/null
@@ -1,424 +0,0 @@
-#!/usr/bin/env python
-
-#First import the netcdf4 library
-from netCDF4 import Dataset  # http://code.google.com/p/netcdf4-python/
-import numpy as np  # http://code.google.com/p/netcdf4-python/
-import matplotlib
-#import matplotlib.pyplot as plt
-import math
-import os
-matplotlib.use("GTKAgg")
-import matplotlib.pyplot as plt
-from pylab import *
-import pdb
-
-
-
-def Create_iceberg_restart_file(f,g,Number_of_bergs, Number_of_bonds,lon,lat,thickness,width,mass,mass_scaling,iceberg_num,make_icebergs_static):
-	
-	# To copy the global attributes of the netCDF file  
-
-	for attname in f.ncattrs():
-		    setattr(g,attname,getattr(f,attname))
-
-
-	# To copy the dimension of the netCDF file
-	for dimname,dim in f.dimensions.iteritems():
-		# if you want to make changes in the dimensions of the new file
-		# you should add your own conditions here before the creation of the dimension.
-		#g.createDimension(dimname,len(dim))
-		g.createDimension(dimname,Number_of_bergs)
-
-	# To copy the variables of the netCDF file
-
-	for varname,ncvar in f.variables.iteritems():
-		# if you want to make changes in the variables of the new file
-		# you should add your own conditions here before the creation of the variable.
-		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
-		#Proceed to copy the variable attributes
-		for attname in ncvar.ncattrs():  
-			setattr(var,attname,getattr(ncvar,attname))
-		#Finally copy the variable data to the new created variable
-		#var[:] = ncvar[0]  Remove this. Not sure what it does.
-		
-		if varname=='i':
-			var[:]=Number_of_bergs
-		
-		if varname=='iceberg_num':
-			for j in range(Number_of_bergs):
-				#var[j]=j+1
-				var[j]=iceberg_num[j]
-
-		if varname=='uvel' or varname=='vvel' or varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
-		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
-		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
-		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old' \
-		or varname=='static_berg':
-			var[:]=0
-
-		if varname=='mass_scaling':
-			var[:]=mass_scaling
-
-		if varname=='thickness':
-			var[:]=thickness
-		
-		if varname=='mass':
-			var[:]=mass
-
-		if varname=='width'  or varname=='length':
-			var[:]=width
-
-		if varname=='lon':
-			for j in range(Number_of_bergs):
-				var[j]=lon[j]
-
-		if varname=='lat':
-			for j in range(Number_of_bergs):
-				var[j]=lat[j]
-
-		if varname=='static_berg' and  make_icebergs_static==True:
-			for j in range(Number_of_bergs):
-				var[j]=1.
-
-	f.close()
-	g.close()
-
-
-def Create_bond_restart_file(q,h, Number_of_bonds,first_berg_num,first_berg_ine,first_berg_jne,other_berg_ine,other_berg_jne,iceberg_num,other_berg_num):
-	#Creating the bond restart file
-
-
-	# To copy the global attributes of the netCDF file  
-
-	for attname in h.ncattrs():
-		    setattr(q,attname,getattr(h,attname))
-
-
-	# To copy the dimension of the netCDF file
-	for dimname,dim in h.dimensions.iteritems():
-		# if you want to make changes in the dimensions of the new file
-		# you should add your own conditions here before the creation of the dimension.
-		#g.createDimension(dimname,len(dim))
-		q.createDimension(dimname,Number_of_bonds)
-
-	# To copy the variables of the netCDF file
-
-	for varname,ncvar in h.variables.iteritems():
-		# if you want to make changes in the variables of the new file
-		# you should add your own conditions here before the creation of the variable.
-		var = q.createVariable(varname,ncvar.dtype,ncvar.dimensions)
-		#Proceed to copy the variable attributes
-		for attname in ncvar.ncattrs():  
-			setattr(var,attname,getattr(ncvar,attname))
-		#Finally copy the variable data to the new created variable
-		#var[:] = ncvar[0]
-		var[:] = 0
-
-		if varname=='i':
-			var[:]=Number_of_bonds
-
-		if varname=='first_berg_num':
-			for j in range(Number_of_bonds):
-				var[j]=first_berg_num[j]
-
-		if varname=='first_berg_ine':
-			for j in range(Number_of_bonds):
-				var[j]=first_berg_ine[j]
-
-		if varname=='first_berg_jne':
-			for j in range(Number_of_bonds):
-				var[j]=first_berg_jne[j]
-
-		if varname=='other_berg_num':
-			for j in range(Number_of_bonds):
-				var[j]=other_berg_num[j]
-
-		if varname=='other_berg_ine':
-			for j in range(Number_of_bonds):
-				var[j]=other_berg_ine[j]
-
-		if varname=='other_berg_jne':
-			for j in range(Number_of_bonds):
-				var[j]=other_berg_jne[j]
-
-	h.close()
-	q.close()
-	
-	if Number_of_bonds==0:
-		print 'Warning: Iceberg bond files do not work for single icebergs (no bonds). Turn iceberg bonds off'
-
-def plotting_iceberg_positions_and_bonds(lat,lon,first_berg_lat,first_berg_lon,other_berg_lat,other_berg_lon,Number_of_bergs,Number_of_bonds,R_earth,Radius,IA_scaling,convert_to_lat_lon):
-
-	Radius=Radius*IA_scaling
-	circ_ind=np.linspace(0,2*pi,100);
-	for k in range(Number_of_bergs):
-		if convert_to_lat_lon==True:
-			dR_lat=(1/R_earth)*(180/np.pi)
-			dR_lon=(1/R_earth)*(180/np.pi)*(1/np.cos(lat[k]*np.pi/180))
-		else:
-			dR_lat=1 ; dR_lon=1
-
-		plt.plot(lon[k], lat[k],'bo-',linewidth=5)
-		plt.plot(lon[k]+(Radius*dR_lon*cos(circ_ind)),lat[k]+(Radius*dR_lat*sin(circ_ind)),'b');
-
-	for k in range(Number_of_bonds):
-		x_bond=[]
-		y_bond=[]
-		x_bond.append(first_berg_lon[k])
-		x_bond.append(other_berg_lon[k])
-		y_bond.append(first_berg_lat[k])
-		y_bond.append(other_berg_lat[k])
-		plt.plot(x_bond, y_bond,'r',linewidth=5)
-
-
-	#plt.plot(lon, lat,'bo-')
-	if convert_to_lat_lon==True:
-		plt.xlabel('longitude (deg)')
-		plt.ylabel('latitude (deg)')
-	else:
-		plt.xlabel('x (m)')
-		plt.ylabel('y (m)')
-	plt.title('Iceberg initial positions')
-	plt.grid(True)
-	plt.show()
-
-
-def calculate_element_area(element_type,Radius):
-        if element_type=='square':
-                element_area=(2*Radius)**2
-        elif element_type=='hexagon':
-                element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*(Radius)**2) #Area of hexagon around circle (used for packing)  
-                #Another derivation uses innner hexagon with two more triangles added, which is a 1/6 of the hexagon area each (two since there are 6, shared by 3 each)
-                #element_area=(4./3.)*H_i, where H_i=(3.*np.sqrt(3.)/2.)*((Radius)**2)  is the area of the inner hexagon (with sides equal to the radius)
-
-        return element_area
-
-
-def Define_iceberg_positions(N,M ,lon_init,lat_init,Radius,R_earth,convert_to_lat_lon,scale_the_grid_to_lat_lon,element_type, thickness,rho_ice):
-	dx_berg=[]  #x distance in cartesian of berg from lon_init
-	dy_berg=[]  #y distance in cartesian of berg from lat_init
-	dlon_berg=[] #x distance in lon of berg from lon_init
-	dlat_berg=[] #y distance in lat of berg from lat_init
-	lon=[] #Longitude of iceberg
-	lat=[] #Latitude of iceberg
-	iceberg_num=[] #ID of iceberg
-
-
-
-
-	berg_count=0
-	#for j in range(N):
-        for i in range(M):
-		if element_type=='square':
-			x_start=Radius+(2*Radius*i)
-                        y_start=(Radius)
-                        #y_start=(Radius)+(2*Radius*j)
-                else:
-                        #x_start=(Radius)+(((j%2)*Radius))
-                        #y_start=(Radius)+(np.sqrt(3)*Radius*j)
-                        y_start=(Radius)+(((i%2)*Radius))
-                        x_start=(Radius)+(np.sqrt(3)*Radius*i)
-
-		#for i in range(M):
-        	for j in range(N):
-                        #x_val=x_start+(2*i*Radius)  ; y_val=y_start
-                        y_val=y_start+(2*j*Radius)  ; x_val=x_start
-			berg_count=berg_count+1
-			iceberg_num.append(berg_count)
-			dx_berg.append(x_val)
-			dy_berg.append(y_val)
-
-	#Old version
-	#berg_count=0
-	#for j in range(M):
-	#	x_start=(j%2)*Radius
-	#	y_start=np.sqrt(3)*Radius*j
-	#	for i in range(N):
-	#		berg_count=berg_count+1
-	#		iceberg_num.append(berg_count)
-	#		dx_berg.append(x_start+(2*i*Radius))
-	#		dy_berg.append(y_start)
-
-	Number_of_bergs=berg_count
-
-	#Calculating iceberg properties (assuming constant thickness and area)
-	element_area=calculate_element_area(element_type,Radius)
-        width=np.sqrt(element_area)
-	thickness=thickness
-	mass=thickness*rho_ice*element_area
-
-	#Defining lon lat positions:
-	#dlat_berg=(180/np.pi)*(1/R_earth)*dy_berg
-	#dlon_berg=(180/np.pi)*(1/R_earth)*(1/cos(lat_init*np.pi/180))*dx_berg
-	if convert_to_lat_lon==True:
-		for i in range(Number_of_bergs):
-			#Finding latittude
-			dlat_dy=(180/np.pi)*(1/R_earth)
-			dlat_berg.append(dlat_dy*dy_berg[i])
-			lat.append(lat_init+dlat_berg[i])
-
-			#Finding longitude
-			dlon_dx=(180/np.pi)*(1/R_earth)*(1/np.cos(lat[i]*np.pi/180)) #Note that this depends on the latitude of the iceberg. Could approx this with lat_init.
-			dlon_berg.append(dlon_dx*dx_berg[i])
-			lon.append(lon_init+dlon_berg[i])
-	else:
-		if scale_the_grid_to_lat_lon==True:
-			Scale_up=1./2000.
-			Radius=Radius*Scale_up
-			dx_berg = [(i*Scale_up) for i in dx_berg] ; dy_berg = [i*Scale_up for i in dy_berg]
-			#x=x*Scale_up ; y=y*Scale_up
-			#dx=dx*Scale_up ;dy=dy*Scale_up
-		#x=(x-np.min(x))+(dx/2) ; y=(y-np.min(y))+(dy/2)
-
-		for i in range(Number_of_bergs):
-			lon.append(lon_init+dx_berg[i])
-			lat.append(lat_init+dy_berg[i])
-
-	return (Number_of_bergs,lon,lat,iceberg_num,dx_berg,dy_berg,Radius, width,mass)
-
-def Define_iceberg_bonds(Number_of_bergs,iceberg_num,lat,lon,dx_berg, dy_berg,Radius):
-	
-	#Defining Bonds:
-	Bond=np.zeros((Number_of_bergs, Number_of_bergs))
-	first_berg_num=[]  # Initializing bond list first berg
-	first_berg_ine=[]  # Initializing bond list first berg
-	first_berg_jne=[]  # Initializing bond list first berg
-	first_berg_lat=[]  # Initializing bond list first berg
-	first_berg_lon=[]  # Initializing bond list first berg
-	other_berg_num=[]  # Initializing bond list other berg
-	other_berg_ine=[]  # Initializing bond list other berg
-	other_berg_jne=[]  # Initializing bond list other berg
-	other_berg_lat=[]  # Initializing bond list other berg
-	other_berg_lon=[]  # Initializing bond list other berg
-	bond_count=0
-	for i in range(Number_of_bergs):
-		for j in range(Number_of_bergs):
-			if i!=j:
-				R_dist=np.sqrt(((dx_berg[i]-dx_berg[j])**2) + ((dy_berg[i]-dy_berg[j])**2))
-				if R_dist < (2.01*Radius):
-					bond_count=bond_count+1
-					Bond[i,j]=1 # This is not really used.
-					first_berg_num.append(iceberg_num[i])
-					first_berg_ine.append(999)
-					first_berg_jne.append(999)
-					other_berg_num.append(iceberg_num[j])
-					other_berg_ine.append(999)
-					other_berg_jne.append(999)
-					#Also get the lat lon of each for plotting
-					first_berg_lat.append(lat[i])
-					first_berg_lon.append(lon[i])
-					other_berg_lat.append(lat[j])
-					other_berg_lon.append(lon[j])
-	Number_of_bonds=bond_count
-
-	return [ Number_of_bonds, first_berg_num,first_berg_ine,first_berg_jne,first_berg_lat,first_berg_lon, other_berg_num,other_berg_ine, other_berg_jne,other_berg_lat,other_berg_lon]
-
-####################################################################################################################################################
-##########################################################  Main Program   #########################################################################
-####################################################################################################################################################
-
-
-def main():
-	# Read en existing NetCDF file and create a new one
-	# f is going to be the existing NetCDF file from where we want to import data
-	# and g is going to be the new file.
-
-	f=Dataset('input_files/icebergs.res.nc','r') # r is for read only
-	g=Dataset('output_files/New_icebergs.res.nc','w') # w if for creating a file
-					      # if the file exists it the file will be deleted to write on it
-
-	h=Dataset('input_files/bonds_iceberg.res.nc','r') # r is for read only
-	q=Dataset('output_files/New_bonds_iceberg.res.nc','w') # w if for creating a file
-
-	#Flags
-	save_restart_files=True
-	make_icebergs_static=False
-
-	#Parameters
-	thickness=1.
-	Radius=0.8*1000
-	rho_ice=850.
-	mass_scaling=1.
-	R_earth=6360.*1000.
-
-	#Derived quanities
-	#width=np.sqrt(np.pi*(Radius**2))
-	#mass=thickness*rho_ice*np.pi*(Radius**2)  
-	#width=2*Radius
-	#mass=thickness*rho_ice*((2*Radius)**2)  
-
-	#Let interactive radius be different from radius for testing the model:
-	IA_scaling=1.#(1./2.)
-	Radius=Radius/IA_scaling
-
-	#Here we create the lons and lats for a tabular iceberg
-	N=20  # Number of rows in iceberg
-	M=20   # Number of columns in iceberg
-	lon_init=-32.9  #longitude of bottom left corner of iceberg
-	lat_init=-70.  #latitude  of bottom left corner of iceberg
-	#x_init=100  #For ISOMIP Case
-	#y_init=3  #For ISOMIP Case
-	x_init=100*2000  #For ISOMIP Case
-	y_init=11*2000  #For ISOMIP Case
-	#x_init=354000.003288060  #
-	#y_init=33600.0000000000  #
-	#Experiment_name='Weddell'  ;  Convert_to_lat_lon=True     ; scale_the_grid_to_lat_lon=False
-	Experiment_name='ISOMIP'  ;  convert_to_lat_lon=False      ; scale_the_grid_to_lat_lon=False
-
-
-	#element_type='square' #'hexagonal'
-        element_type='hexagon'
-
-
-	#Defining lon_init, lat_init
-	if Experiment_name=='ISOMIP':
-		if convert_to_lat_lon==True:
-			lon_init=5  ; lat_init=-69.8  
-		else:
-			lon_init=x_init  ; lat_init=y_init
-
-	#Define the positions of the icebergs
-	(Number_of_bergs,lon,lat,iceberg_num,dx_berg, dy_berg,Radius,width,mass)\
-			= Define_iceberg_positions(N,M ,lon_init,lat_init,Radius,R_earth,convert_to_lat_lon,scale_the_grid_to_lat_lon,element_type, thickness,rho_ice)
-
-	#Define the positions of the iceberg bonds
-	(Number_of_bonds, first_berg_num,first_berg_ine,first_berg_jne,first_berg_lat,first_berg_lon, other_berg_num,other_berg_ine, other_berg_jne,other_berg_lat,other_berg_lon)=\
-			Define_iceberg_bonds(Number_of_bergs,iceberg_num,lat,lon,dx_berg, dy_berg,Radius)
-
-
-
-	#####################################################################################
-	#Creating iceberg restart file
-	Create_iceberg_restart_file(f,g,Number_of_bergs, Number_of_bonds,lon,lat,thickness,width,mass,mass_scaling,iceberg_num,make_icebergs_static)
-	
-	#Creating bond restart file
-	Create_bond_restart_file(q,h, Number_of_bonds,first_berg_num,first_berg_ine,first_berg_jne,other_berg_ine,other_berg_jne,iceberg_num,other_berg_num)
-
-	##################################################################################
-	
-	print 'Number of bergs created= ' , Number_of_bergs
-	print 'Number of Bonds created= ' , Number_of_bonds
-	plotting_iceberg_positions_and_bonds(lat,lon,first_berg_lat,first_berg_lon,other_berg_lat,other_berg_lon,Number_of_bergs,Number_of_bonds,R_earth,Radius,IA_scaling,convert_to_lat_lon)
-	# Plotting the positions and bonds of the newly formed formation
-
-	print 'Script complete'
-
-
-
-if __name__ == '__main__':
-	main()
-	#sys.exit(main())
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/tests/Iceberg_repository/setup_ISOMIP_calving.sh b/tests/Iceberg_repository/setup_ISOMIP_calving.sh
deleted file mode 100755
index 725891d..0000000
--- a/tests/Iceberg_repository/setup_ISOMIP_calving.sh
+++ /dev/null
@@ -1,54 +0,0 @@
-echo 'Beginning setup...'
-
-
-
-#Loading python libraries (its possible that not all of these are needed)
-module unload PrgEnv-intel/5.2.8
-module load PrgEnv-gnu/5.2.82
-module load python_scipy/0.17.0
-
-module load python
-module load python_netcdf4
-module load python_numpy
-module load python_pygtk
-module load python_matplotlib
-module load python_scipy/0.17.0
-
-
-
-git submodule init
-git submodule update
-
-cd ISOMIP_Calving/python_scripts
-mkdir -p output_files
-
-#Creating mosaic files using script
-echo 'Creating mosaic files...'
-./Create_mosaic.py -coupled_run -nx=240 -ny=40 -nz=36  -L=80.0 -W=480.0 
-echo 'Creating mosaic files complete'
-
-#Copying mosaic files to INPUT directory  (Files created by python script Create_mosaic)
-cp output_files/atmos_mosaic_tile1Xland_mosaic_tile1.nc ../INPUT/
-cp output_files/atmos_mosaic_tile1Xocean_mosaic_tile1.nc ../INPUT/
-cp output_files/land_mosaic_tile1Xocean_mosaic_tile1.nc ../INPUT/
-cp output_files/grid_spec.nc ../INPUT/
-cp output_files/ocean_hgrid.nc ../INPUT/
-cp output_files/ocean_mask.nc ../INPUT/
-cp output_files/ocean_mosaic.nc ../INPUT/
-cp output_files/ocean_topog.nc ../INPUT/
-cp output_files/topog.nc ../INPUT/
-
-#Creating iceberg and bond restart files, and ice shelf file
-echo 'Creating iceberg restart files...'
-./initialize_bergs_in_pattern.py -Make_icebergs_non_static_later=False -Run_plotting_subroutine=False
-echo 'Creating iceberg restart files complete'
-
-#Copying iceberg restarts and iceshelf file to INPUT directory  (Files created by python script initialize_bergs_in_pattern_Tech.py)
-cp output_files/ISOMIP_icebergs.res.nc ../INPUT/icebergs.res.nc
-cp output_files/ISOMIP_bonds_iceberg.res.nc ../INPUT/bonds_iceberg.res.nc
-cp output_files/ISOMIP_Ice_Shelf_clipped.nc ../INPUT/isomip_ice_shelf1_clipped.nc
-
-#Copying 3D_LAYER_WARM_TPY_IC.nc to INPUT
-cp input_files/3D_LAYER_WARM_TPY_IC.nc ../INPUT/
-cd ..
-echo 'Setup complete!'
diff --git a/tests/collision_tests/makeberg/RUN b/tests/collision_tests/makeberg/RUN
index ae7808f..dd66e2f 100755
--- a/tests/collision_tests/makeberg/RUN
+++ b/tests/collision_tests/makeberg/RUN
@@ -2,7 +2,7 @@
 
 rm ./output_files/Generic*
 
-./../../Iceberg_repository/Scripts_and_analysis/initialize_bergs_in_pattern.py \
+./initialize_bergs_in_pattern.py \
 	-set_all_bergs_static_by_default=False -Run_plotting_subroutine=False \
 	-break_some_bonds=False -Ice_geometry_source='Generic' \
 	-Generic_ice_geometry_filename='./testtabularberg.nc' \
diff --git a/tests/Iceberg_repository/hexagon_area.py b/tests/collision_tests/makeberg/hexagon_area.py
similarity index 96%
rename from tests/Iceberg_repository/hexagon_area.py
rename to tests/collision_tests/makeberg/hexagon_area.py
index 83d444d..5db6cec 100755
--- a/tests/Iceberg_repository/hexagon_area.py
+++ b/tests/collision_tests/makeberg/hexagon_area.py
@@ -19,7 +19,7 @@
 def Divide_hexagon_into_4_quadrants_old(x0,y0,H):
 	S=(2/sqrt(3))*H
 	Area_hex=3*(np.sqrt(3)/2)*(S**2)  #Area of the hexagon (should be equal to Area/grid_area, since it is not dim)	 - check this
-	#print 'y0,H',y0, H	
+	#print 'y0,H',y0, H
 	#Defining boundaries of hexagon, and if statements to see which side of the boundary you are on
 	W1= False ; W2=False ;W3=False ;W4=False ;W5=False ;W6=False ;H1=False ;V1=False ;V2=False
 	W1=(-y0<-sqrt(3)*(-x0) + ((sqrt(3)*(S))));#upper right
@@ -28,7 +28,7 @@ def Divide_hexagon_into_4_quadrants_old(x0,y0,H):
 	W4=(-y0<sqrt(3)*(-x0) + (-(sqrt(3)*(S))));#Lower right
 	W5=(-y0>-H);#Bottom
 	W6=(-y0<-sqrt(3)*(-x0) + (-(sqrt(3)*(S))));#Lower left
-		
+
 
 	T1=(-x0<S) #Right
 	T2=(-y0<(H));#Top
@@ -38,12 +38,12 @@ def Divide_hexagon_into_4_quadrants_old(x0,y0,H):
 	H1=(y0<0);
 	V1=(x0<-(S/2));
 	V2=(x0<(S/2));
-	  
+
 	#Deciding if the origin is within the hexagon
 	#print W1 , W2 , W3 , W4 , W5 , W6
 	#if In_hex:
 	#	print In_hex
-		
+
 	#Calculating the area of the top and bottom half of the hexagon, 2 Cases for the majority above and below the y0=0 line
 	#(and two more for the hexagon totally above and below the y0=0 line)
 	if abs(y0)<H:
@@ -58,7 +58,7 @@ def Divide_hexagon_into_4_quadrants_old(x0,y0,H):
 		if y0>=0:
 			Area_Lower=0.;
 			Area_Upper=Area_hex;
-		else: 
+		else:
 			Area_Lower=Area_hex;
 			Area_Upper=0.;
 
@@ -109,11 +109,11 @@ def Divide_hexagon_into_4_quadrants_old(x0,y0,H):
 			if Area_right==0.:
 				Area_Q2=Area_Upper;
 				Area_Q3=Area_Lower;
-		
+
 			if Area_left==0.:
 				Area_Q1=Area_Upper;
 				Area_Q4=Area_Lower;
-		
+
 
 		#yCxC=1.
 		#print 'out of hex'
@@ -129,7 +129,7 @@ def Divide_hexagon_into_4_quadrants_old(x0,y0,H):
 					Sector=2;
 			elif (V1==False) & (V2==True):
 				Sector=3;
-			else:  
+			else:
 				#if (W3==True):
 				if ((y0-(sqrt(3)*(x0-S)))>=0.):
 					Sector=4;
@@ -144,7 +144,7 @@ def Divide_hexagon_into_4_quadrants_old(x0,y0,H):
 					Sector=9;
 			elif (V1==False) & (V2==True):
 				Sector=8;
-			else:  
+			else:
 				#if (W4==True):
 				if ((y0+(sqrt(3)*(x0-S)))<=0.):
 					Sector=7;
@@ -158,7 +158,7 @@ def Divide_hexagon_into_4_quadrants_old(x0,y0,H):
 		if Sector==2 or Sector==4  or Sector==7 or Sector==9:
 			Baby_triangle=(1/(2*sqrt(3)))*((-abs(y0)+(sqrt(3)*(S-abs(x0))))**2);
 		else:
-			#Baby_trap= (H-abs(y0)) * ((-H-abs(y0)+(2*sqrt(3)*(S-abs(x0))))/(2*sqrt(3)));  
+			#Baby_trap= (H-abs(y0)) * ((-H-abs(y0)+(2*sqrt(3)*(S-abs(x0))))/(2*sqrt(3)));
 			Baby_trap=(H-abs(y0))*((S-abs(x0) - ((H+abs(y0))/(2*sqrt(3))))) ;
 
 		#Finally, we assign the correct areas in each quadrant (Q1,Q2,Q3,Q4), depending on which sector you are in.
@@ -188,7 +188,7 @@ def Divide_hexagon_into_4_quadrants_old(x0,y0,H):
 			Area_Q1=Area_right-Area_Q4
 			Area_Q2=Area_Upper-Area_Q1
 			Area_Q3=Area_left-Area_Q2
-	
+
 		#Center cases
 		if Sector==3:
 			if x0<=0.:
@@ -201,7 +201,7 @@ def Divide_hexagon_into_4_quadrants_old(x0,y0,H):
 				Area_Q1=Area_Upper-Area_Q2;
 				Area_Q3=Area_left-Area_Q2;
 				Area_Q4=Area_right-Area_Q1;
-			
+
 		if Sector==8:
 			if x0<=0.:
 				Area_Q4=Baby_trap;
@@ -220,7 +220,7 @@ def Divide_hexagon_into_4_quadrants_old(x0,y0,H):
 			Area_Q2=Area_Upper;
 			Area_Q4=Area_right;
 			Area_Q3=Area_left-Area_Q2;
-		
+
 		if Sector==5:
 			Area_Q2=0.;
 			Area_Q1=Area_Upper;
@@ -232,7 +232,7 @@ def Divide_hexagon_into_4_quadrants_old(x0,y0,H):
 			Area_Q2=Area_left;
 			Area_Q4=Area_Lower;
 			Area_Q1=Area_right-Area_Q4;
-		
+
 		if Sector==10:
 			Area_Q4=0.;
 			Area_Q3=Area_Lower;
@@ -245,9 +245,9 @@ def Divide_hexagon_into_4_quadrants_old(x0,y0,H):
 
 
 def Hexagon_into_quadrants_using_triangles_across_lines(x0,y0,H,theta,	Px, Py, Qx, Qy, Rx, Ry, Sx, Sy ):
-	#In this routine, the hexagon is divided across lines PQ, RS.	 
+	#In this routine, the hexagon is divided across lines PQ, RS.
 	#Length of side of Hexagon
-	S=(2/sqrt(3))*H;  
+	S=(2/sqrt(3))*H;
 
 	#Finding positions of corners
 	C1x=S		; C1y=0.  #Corner 1 (right)
@@ -264,7 +264,7 @@ def Hexagon_into_quadrants_using_triangles_across_lines(x0,y0,H,theta,	Px, Py, Q
 	[C4x,C4y]=rotate_and_translate(C4x,C4y,theta,x0,y0)
 	[C5x,C5y]=rotate_and_translate(C5x,C5y,theta,x0,y0)
 	[C6x,C6y]=rotate_and_translate(C6x,C6y,theta,x0,y0)
-	 
+
 	#Area of Hexagon is the sum of the triangles
 	[T12_Area,T12_Q1,T12_Q2,T12_Q3,T12_Q4]=Triangle_divided_into_four_parts(x0,y0,C1x,C1y,C2x,C2y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T012
 	[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]=Triangle_divided_into_four_parts(x0,y0,C2x,C2y,C3x,C3y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
@@ -272,7 +272,7 @@ def Hexagon_into_quadrants_using_triangles_across_lines(x0,y0,H,theta,	Px, Py, Q
 	[T45_Area,T45_Q1,T45_Q2,T45_Q3,T45_Q4]=Triangle_divided_into_four_parts(x0,y0,C4x,C4y,C5x,C5y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
 	[T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4]=Triangle_divided_into_four_parts(x0,y0,C5x,C5y,C6x,C6y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
 	[T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4]=Triangle_divided_into_four_parts(x0,y0,C6x,C6y,C1x,C1y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T023
-	
+
 	#Area of Hexagon is the sum of the triangles
 	#print '1:', Triangle_divided_into_four_parts(x0,y0,C1x,C1y,C2x,C2y, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  ); #T012
 	#print '1b:', Triangle_divided_into_four_quadrants(x0,y0,C1x,C1y,C2x,C2y); #T012
@@ -299,18 +299,18 @@ def Hexagon_into_quadrants_using_triangles_across_lines(x0,y0,H,theta,	Px, Py, Q
 
 
 	#if  (abs(x0-(-0.186672393129))<0.00001)  and (abs(y0-(-0.436171))<0.00001):
-	#	print 'Triangle 1,xo,y0',x0,y0 
-	#	print 'Triangle 1H,S',H,S 
-	#	print 'Triangle 1,Corners',C1x,C1y,C2x,C2y 
+	#	print 'Triangle 1,xo,y0',x0,y0
+	#	print 'Triangle 1H,S',H,S
+	#	print 'Triangle 1,Corners',C1x,C1y,C2x,C2y
 	#	print 'Triangle 1, Area full', T12_Area
 	#	print 'Triangle 1, Area T1', T12_Q1
 	#	print 'Triangle 1, Area T2', T12_Q2
 	#	print 'Triangle 1, Area T3', T12_Q3
-	#	print 'Triangle 1, Area T4', T12_Q4 
+	#	print 'Triangle 1, Area T4', T12_Q4
 	#	#print 'Triangle 2',x0,y0,C2x,C2y,C3x,C3y,T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4
-	#	#print 'Triangle 3',x0,y0,C3x,C3y,C4x,C4y,T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4 
+	#	#print 'Triangle 3',x0,y0,C3x,C3y,C4x,C4y,T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4
 	#	#print 'Triangle 4',x0,y0,C4x,C4y,C5x,C5y,T45_Area,T45_Q1,T45_Q2,T45_Q3,T45_Q4
-	#	#print 'Triangle 5',x0,y0,C5x,C5y,C6x,C6y,T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4 
+	#	#print 'Triangle 5',x0,y0,C5x,C5y,C6x,C6y,T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4
 	#	#print 'Triangle 6',x0,y0,C6x,C6y,C1x,C1y,T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4
 
 	Area_Q1=max(Area_Q1,0.);
@@ -353,9 +353,9 @@ def Hexagon_into_quadrants_using_triangles_across_lines(x0,y0,H,theta,	Px, Py, Q
 	return [Area_hex ,Area_Q1, Area_Q2, Area_Q3, Area_Q4]
 
 def Hexagon_into_quadrants_using_triangles(x0,y0,H,theta):
-		 
+
 	#Length of side of Hexagon
-	S=(2/sqrt(3))*H;  
+	S=(2/sqrt(3))*H;
 
 	#Finding positions of corners
 	C1x=S		; C1y=0.  #Corner 1 (right)
@@ -372,7 +372,7 @@ def Hexagon_into_quadrants_using_triangles(x0,y0,H,theta):
 	[C4x,C4y]=rotate_and_translate(C4x,C4y,theta,x0,y0)
 	[C5x,C5y]=rotate_and_translate(C5x,C5y,theta,x0,y0)
 	[C6x,C6y]=rotate_and_translate(C6x,C6y,theta,x0,y0)
-	 
+
 	#Area of Hexagon is the sum of the triangles
 	[T12_Area,T12_Q1,T12_Q2,T12_Q3,T12_Q4]=Triangle_divided_into_four_quadrants(x0,y0,C1x,C1y,C2x,C2y); #T012
 	[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]=Triangle_divided_into_four_quadrants(x0,y0,C2x,C2y,C3x,C3y); #T023
@@ -393,18 +393,18 @@ def Hexagon_into_quadrants_using_triangles(x0,y0,H,theta):
 
 
 	#if  (abs(x0-(-0.186672393129))<0.00001)  and (abs(y0-(-0.436171))<0.00001):
-	#	print 'Triangle 1,xo,y0',x0,y0 
-	#	print 'Triangle 1H,S',H,S 
-	#	print 'Triangle 1,Corners',C1x,C1y,C2x,C2y 
+	#	print 'Triangle 1,xo,y0',x0,y0
+	#	print 'Triangle 1H,S',H,S
+	#	print 'Triangle 1,Corners',C1x,C1y,C2x,C2y
 	#	print 'Triangle 1, Area full', T12_Area
 	#	print 'Triangle 1, Area T1', T12_Q1
 	#	print 'Triangle 1, Area T2', T12_Q2
 	#	print 'Triangle 1, Area T3', T12_Q3
-	#	print 'Triangle 1, Area T4', T12_Q4 
+	#	print 'Triangle 1, Area T4', T12_Q4
 	#	#print 'Triangle 2',x0,y0,C2x,C2y,C3x,C3y,T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4
-	#	#print 'Triangle 3',x0,y0,C3x,C3y,C4x,C4y,T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4 
+	#	#print 'Triangle 3',x0,y0,C3x,C3y,C4x,C4y,T34_Area,T34_Q1,T34_Q2,T34_Q3,T34_Q4
 	#	#print 'Triangle 4',x0,y0,C4x,C4y,C5x,C5y,T45_Area,T45_Q1,T45_Q2,T45_Q3,T45_Q4
-	#	#print 'Triangle 5',x0,y0,C5x,C5y,C6x,C6y,T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4 
+	#	#print 'Triangle 5',x0,y0,C5x,C5y,C6x,C6y,T56_Area,T56_Q1,T56_Q2,T56_Q3,T56_Q4
 	#	#print 'Triangle 6',x0,y0,C6x,C6y,C1x,C1y,T61_Area,T61_Q1,T61_Q2,T61_Q3,T61_Q4
 
 	Area_Q1=max(Area_Q1,0.);
@@ -467,7 +467,7 @@ def find_intersect_using_metric(Ax,Ay, Bx, By, Cx, Cy):
 		return AC_px, AC_py, AC_qx, AC_qy
 	elif M_BC<=min(M_AC, M_AB):
 		return BC_px, BC_py, BC_qx, BC_qy
-	else: 
+	else:
 		print ('You should not get here')
 		halt
 
@@ -491,7 +491,7 @@ def find_intersect_using_metric_and_lines(Ax,Ay, Bx, By, Cx, Cy,Px, Py, Qx, Qy,
 		return AC_px, AC_py, AC_qx, AC_qy
 	elif M_BC<=min(M_AC, M_AB):
 		return BC_px, BC_py, BC_qx, BC_qy
-	else: 
+	else:
 		print ('You should not get here')
 		halt
 
@@ -507,7 +507,7 @@ def point_in_interval_metric(Ax,Ay,Bx,By,px,py,qx,qy):
 	My1= max(py - max(Ay,By),0.)  #Zero is px <= max(Ax,Bx)
 	My2= max( min(Ay,By)-py ,0.)  #Zero is px <= max(Ax,Bx)
 	p_metric=abs(Mx1)+abs(Mx2)+abs(My1)+abs(My2)
-	#print 'Mx1, Mx2, My1, My2', Mx1, Mx2, My1, My2 
+	#print 'Mx1, Mx2, My1, My2', Mx1, Mx2, My1, My2
 
 	#Finds a metric for how close a point is to being inside an interval. If it is inside, then metric is equal to zero.
 	Mx1= max(qx - max(Ax,Bx),0.)  #Zero is qx <= max(Ax,Bx)
@@ -531,7 +531,7 @@ def Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy):
 	#Calculating area across axes
 	[Area_Upper ,Area_Lower]=divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,'x');
 	[Area_Right ,Area_Left]=divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,'y');
-	 
+
 	#Decide if the origin is in the triangle
 	if point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.):	#Then you have to divide area 4 ways.
 		#Find a line in the triangle that cuts both axes in/on the trianlge
@@ -561,7 +561,7 @@ def Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy):
 				Key_quadrant=3;	 #Third quadrant
 			else:
 				Key_quadrant=4;	 #Forth quadrant
-	    
+
 	#if (point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.) is False) or (Area_key_quadrant==0):
 	if Area_key_quadrant==0:
 	#else:	#Then at least one quadrant is empty, and this can be used to find the areas in the other quadrant.  Assigning quadrants. Key_quadrant is the empty quadrant.
@@ -582,7 +582,7 @@ def Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy):
 			Key_quadrant=3;
 		else:
 			Key_quadrant=4;
-	
+
 	#Assign values to quadrants
 	if Key_quadrant==1:
 		Area_Q1=Area_key_quadrant;
@@ -611,11 +611,11 @@ def Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy):
 	else:
 	    print( 'Help, I need somebody, help!')
 	    halt
-	
-	Area_Q1=max(Area_Q1,0.); 
+
+	Area_Q1=max(Area_Q1,0.);
 	Area_Q2=max(Area_Q2,0.);
 	Area_Q3=max(Area_Q3,0.);
-	Area_Q4=max(Area_Q4,0.); 
+	Area_Q4=max(Area_Q4,0.);
 
 	Error=abs(Area_Q1+Area_Q2+Area_Q3+Area_Q4-Area_triangle)
 	#Marker 1
@@ -625,7 +625,7 @@ def Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy):
 		print ('Triangle corners: ' ,Ax,Ay,Bx,By,Cx,Cy)
 		print ('Error',Error)
 		print ('Key_quadrant', Key_quadrant )
-		print ('Area Key_quadrant', Area_key_quadrant) 
+		print ('Area Key_quadrant', Area_key_quadrant)
 		print ('Upper, Lower',Area_Upper ,Area_Lower)
 		print ('Left, Right ', Area_Right ,Area_Left)
 		print ('Point in triangle', point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.))
@@ -670,7 +670,7 @@ def Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry,
 	#Calculating area across axes
 	[Area_Upper ,Area_Lower]=divding_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy);
 	[Area_Right ,Area_Left] =divding_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Rx, Ry, Sx, Sy);
-	 
+
 	#Decide if the origin is in the triangle
 	if point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,0.,0.):	#Then you have to divide area 4 ways.
 		#Find a line in the triangle that cuts both axes in/on the trianlge
@@ -698,7 +698,7 @@ def Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry,
 			Key_quadrant=3;	 #Third quadrant
 		else:
 			Key_quadrant=4;	 #Forth quadrant
-	    
+
 	if Area_key_quadrant==0:
 		#else:	#Then at least one quadrant is empty, and this can be used to find the areas in the other quadrant.  Assigning quadrants. Key_quadrant is the empty quadrant.
 		#print 'Mother...'
@@ -721,7 +721,7 @@ def Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry,
 			Key_quadrant=3;
 		else:
 			Key_quadrant=4;
-	
+
 		#print Key_quadrant
 	#Assign values to quadrants
 	if Key_quadrant==1:
@@ -751,11 +751,11 @@ def Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry,
 	else:
 	    print ('Help, I need somebody, help!')
 	    halt
-	
-	Area_Q1=max(Area_Q1,0.); 
+
+	Area_Q1=max(Area_Q1,0.);
 	Area_Q2=max(Area_Q2,0.);
 	Area_Q3=max(Area_Q3,0.);
-	Area_Q4=max(Area_Q4,0.); 
+	Area_Q4=max(Area_Q4,0.);
 
 	Error=abs(Area_Q1+Area_Q2+Area_Q3+Area_Q4-Area_triangle)
 	if Error>1e-15:
@@ -777,11 +777,11 @@ def divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1):
 		A0=Ay; B0=By;  C0=Cy;
 	if axes1=='y':	#Use the y-coordinates for if statements to see which side of the line you are on
 		A0=Ax; B0=Bx;  C0=Cx;
- 
+
 	#print 'A0,B0,C0', A0,B0,C0
 	A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
 	if B0*C0>0.: #then B and C are on the same side	 (and non-zero)
-		#print 'HHHH1'	
+		#print 'HHHH1'
 		if A0*B0>=0.: #then all three on the the same side (if it equals zero, then A0=0 and the otehrs are not)
 			if (A0>0.)  or	(A0==0. and  B0>0.):
 				Area_positive= A_triangle;
@@ -793,31 +793,31 @@ def divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1):
 			[Area_positive, Area_negative]=Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1);
 
 	elif B0*C0<0.: #then B and C are on the opposite sides
-		#print 'HHHH2'	
+		#print 'HHHH2'
 		if A0*B0>=0.:  #then C is all alone
 			[Area_positive, Area_negative]=Area_of_triangle_across_axes(Cx,Cy,Bx,By,Ax,Ay,axes1);
 		else: #then B is all alone
 			[Area_positive, Area_negative]=Area_of_triangle_across_axes(Bx,By,Cx,Cy,Ax,Ay,axes1);
 
 	else:  #This is the case when either B or C is equal to zero (or both), A0 could be zero too.
-		#print 'HHHH3'	
+		#print 'HHHH3'
 		if (A0==0. and B0==0. and C0==0.):
 			Area_positive= 0.;
 			Area_negative= 0.;
 		elif (A0*B0<0.)	 or  (A0*C0<0.):    #A, B are on opposite sides, and C is zero.	 OR  A, C are on opposite sides, and B is zero.
 			[Area_positive, Area_negative]=Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1);
-			#print 'HHHH6'	
+			#print 'HHHH6'
 		elif (A0*B0>0.) or (A0*C0>0.) or (abs(A0)>0. and (B0==0.) and (C0==0.)):
-			#print 'HHHH7'	
+			#print 'HHHH7'
 			if (A0>0.):
 				Area_positive= A_triangle;
 				Area_negative= 0.;
 			else:
 				Area_positive= 0.;
 				Area_negative= A_triangle;
-    
+
 		elif A0==0.:  #(Also, one of B,C is zero too)
-			#print 'HHHH8'	
+			#print 'HHHH8'
 			if B0>0. or C0>0.:
 				Area_positive= A_triangle;
 				Area_negative= 0.;
@@ -831,17 +831,17 @@ def divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1):
 			print ('You should not get here2')
 			print (Ax,Ay,Bx,By,Cx,Cy)
 			halt
-	
+
 	return [Area_positive, Area_negative]
 
 def divding_triangle_across_line2(Ax,Ay,Bx,By,Cx,Cy,  Px, Py, Qx, Qy ):
 	A0= Above_on_below_line(Ax,Ay, Px, Py, Qx, Qy)
 	B0= Above_on_below_line(Bx,By, Px, Py, Qx, Qy)
-	C0= Above_on_below_line(Cx,Cy, Px, Py, Qx, Qy) 
-	
+	C0= Above_on_below_line(Cx,Cy, Px, Py, Qx, Qy)
+
 	#print 'A0,B0,C0', A0,B0,C0
 	#print Px, Py, Qx, Qy
- 
+
 	A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
 	if B0*C0>0.: #then B and C are on the same side	 (and non-zero)
 		#print 'GGG1'
@@ -877,7 +877,7 @@ def divding_triangle_across_line2(Ax,Ay,Bx,By,Cx,Cy,  Px, Py, Qx, Qy ):
 			else:
 				Area_positive= 0.;
 				Area_negative= A_triangle;
-    
+
 		elif A0==0.:  #(Also, one of B,C is zero too)
 			if B0>0. or C0>0.:
 				Area_positive= A_triangle;
@@ -892,14 +892,14 @@ def divding_triangle_across_line2(Ax,Ay,Bx,By,Cx,Cy,  Px, Py, Qx, Qy ):
 			print ('You should not get here2')
 			print (Ax,Ay,Bx,By,Cx,Cy)
 			halt
-	
+
 	return [Area_positive, Area_negative]
 
 
 def divding_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy,   Px, Py, Qx, Qy ):	 #Triangle is ABC, line is PQ
 	A0= Above_on_below_line(Ax,Ay, Px, Py, Qx, Qy)
 	B0= Above_on_below_line(Bx,By, Px, Py, Qx, Qy)
-	C0= Above_on_below_line(Cx,Cy, Px, Py, Qx, Qy) 
+	C0= Above_on_below_line(Cx,Cy, Px, Py, Qx, Qy)
 	#print 'BBB0', A0, B0, C0
 
 	A_triangle=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
@@ -926,12 +926,12 @@ def check_if_point_is_on_the_line(Ax,Ay,Bx,By,qx,qy,repeat_calculation=False):
 	tol=0.00000000000000;
 	dxc = qx - Ax;
 	dyc = qy - Ay;
- 
+
 	dxl = Bx - Ax;
 	dyl = By - Ay;
- 
+
 	cross = dxc * dyl - dyc * dxl;
-	
+
 	if abs(cross)<=tol:
 		point_is_on_line=True
 	else:
@@ -944,29 +944,29 @@ def check_if_point_is_on_the_line(Ax,Ay,Bx,By,qx,qy,repeat_calculation=False):
 	return point_is_on_line
 
 def intercept_of_a_line(Ax,Ay,Bx,By,axes1):
-	No_intercept_val=100000000000.; #Huge value used to make sure that the intercept is outside the triange in the parralel case. 
+	No_intercept_val=100000000000.; #Huge value used to make sure that the intercept is outside the triange in the parralel case.
 	#No_intercept_val=np.NaN;
-	 
+
 	if axes1=='x': #x intercept
 		if (Ay==By)==False:
 			x0=Ax -(((Ax-Bx)/(Ay-By))*Ay);
-			y0=0.; 
+			y0=0.;
 		else:
 			x0=No_intercept_val;
 			y0=No_intercept_val;
-	
+
 	if axes1=='y': #y intercept
 		if (Ax==Bx)==False:
-			x0=0.; 
-			y0=-(((Ay-By)/(Ax-Bx))*Ax)+Ay;	
+			x0=0.;
+			y0=-(((Ay-By)/(Ax-Bx))*Ax)+Ay;
 		else:
 			x0=No_intercept_val;
 			y0=No_intercept_val;
-	
+
 	return [x0, y0]
 
 def intercept_of_two_lines(Ax,Ay,Bx,By,Px,Py,Qx,Qy):
-	No_intercept_val=100000000000.; #Huge value used to make sure that the intercept is outside the triange in the parralel case. 
+	No_intercept_val=100000000000.; #Huge value used to make sure that the intercept is outside the triange in the parralel case.
 	#No_intercept_val=np.NaN;
 
 	#One of the lines is actually a point:
@@ -978,13 +978,13 @@ def intercept_of_two_lines(Ax,Ay,Bx,By,Px,Py,Qx,Qy):
 			(x0 , y0) =intercept_of_a_line(Px-Ax,Py,Qx-Ax,Qy,'y')
 			x0=Ax
 		#Here we check the other three directions to make code agree to machine precision with old version. The code could skip straight to the else.
-		elif (Px==Qx): 
+		elif (Px==Qx):
 			(x0 , y0) =intercept_of_a_line(Ax-Px,Ay,Bx-Px,By,'y')
 			x0=Px
-		elif (Ay==By): 
+		elif (Ay==By):
 			(x0 , y0) =intercept_of_a_line(Px,Py-Ay,Qx,Qy-Ay,'x')
 			y0=Ay
-		elif (Py==Qy): 
+		elif (Py==Qy):
 			(x0 , y0) =intercept_of_a_line(Ax,Ay-Py,Bx,By-Py,'x')
 			y0=Py
 		else:
@@ -1004,7 +1004,7 @@ def intercept_of_two_lines(Ax,Ay,Bx,By,Px,Py,Qx,Qy):
 					print( 'Stop4')
 					x0=(1/(m1-m2))*( (m1*Ax -Ay) -(m2*Px - Py))
 					y0=m1*(x0-Ax)+Ay
-	
+
 	return [x0, y0]
 
 
@@ -1017,7 +1017,7 @@ def Area_of_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axis1):#In this fuction, A is
 		A0=Ay; #Value used for if statements (deciding up/down vs left/right)
 	if axis1=='y':
 		A0=Ax; #Value used for if statements (deciding up/down vs left/right)
-	
+
 	#print 'QQQ', Ax,Ay,pABx,pABy,pACx,pACy
 	A_half_triangle=Area_of_triangle(Ax,Ay,pABx,pABy,pACx,pACy);
 	if (A0>=0.):
@@ -1069,7 +1069,7 @@ def Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px,Py, Qx, Qy, debug=False):
 	#In this fuction, B and C are the same side of the line. (I think this works even if B and/or C are on the line too)
 	#A is unknown. PQ is the line.
 	#print 'RRR Area_of_triangle_across_line' ,Ax,Ay,Bx,By,Cx,Cy
-	
+
 	if (Ax==Bx and Ay==By) or (Ax==Cx and Ay==Cy) or (Cx==Bx and Cy==By):
 		#print 'AAA1'
 		Area_positive=0.0
@@ -1078,7 +1078,7 @@ def Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px,Py, Qx, Qy, debug=False):
 		#print 'AAA2'
 		A0= Above_on_below_line(Ax,Ay, Px, Py, Qx, Qy)
 		B0= Above_on_below_line(Bx,By, Px, Py, Qx, Qy)
-		C0= Above_on_below_line(Cx,Cy, Px, Py, Qx, Qy) 
+		C0= Above_on_below_line(Cx,Cy, Px, Py, Qx, Qy)
 		A_triangle2=Area_of_triangle(Ax,Ay,Bx,By,Cx,Cy);
 
 		if check_if_point_is_on_the_line(Px,Py,Qx,Qy, Ax,Ay):  #Is point A on the line?
@@ -1093,8 +1093,8 @@ def Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px,Py, Qx, Qy, debug=False):
 		else: #If A is not on the line
 			#If A is on the same side of the line as B and C
 			#All on the same side of the line
-			if ((A0==B0 and A0==C0)	 or (A0==B0 and C0==0) or (A0==C0 and B0==0)):	
-			#if Point_above_line(Ax,Ay, Px,Py, Qx, Qy) == Point_above_line( Bx,By, Px,Py, Qx, Qy)  and (Point_above_line(Ax,Ay,Px,Py,Qx,Qy)==Point_above_line(Cx,Cy,Px,Py,Qx,Qy)):	
+			if ((A0==B0 and A0==C0)	 or (A0==B0 and C0==0) or (A0==C0 and B0==0)):
+			#if Point_above_line(Ax,Ay, Px,Py, Qx, Qy) == Point_above_line( Bx,By, Px,Py, Qx, Qy)  and (Point_above_line(Ax,Ay,Px,Py,Qx,Qy)==Point_above_line(Cx,Cy,Px,Py,Qx,Qy)):
 				#print 'AAA4'
 				#if Point_above_line(Bx,By, Px,Py, Qx, Qy) or Point_above_line(Cx,Cy, Px,Py, Qx, Qy):
 				if A0==1 or C0==1:
@@ -1103,7 +1103,7 @@ def Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px,Py, Qx, Qy, debug=False):
 				else:
 					Area_positive= 0.0;
 					Area_negative= A_triangle2;
-			elif (C0==0 and B0==0 and (abs(A0)>0)):	 
+			elif (C0==0 and B0==0 and (abs(A0)>0)):
 				if Point_above_line(Ax,Ay, Px,Py, Qx, Qy):
 					Area_positive= A_triangle2;
 					Area_negative= 0.0;
@@ -1116,7 +1116,7 @@ def Area_of_triangle_across_line(Ax,Ay,Bx,By,Cx,Cy, Px,Py, Qx, Qy, debug=False):
 				[pABx, pABy]=intercept_of_two_lines(Ax,Ay,Bx,By, Px, Py, Qx, Qy);
 				[pACx, pACy]=intercept_of_two_lines(Ax,Ay,Cx,Cy, Px, Py, Qx, Qy);
 				#print 'Tri2', Ax,Ay,pABx,pABy,pACx,pACy
-				
+
 				A_half_triangle=Area_of_triangle(Ax,Ay,pABx,pABy,pACx,pACy);
 				if Point_above_line(Ax,Ay , Px,Py,Qx,Qy):
 					Area_positive= A_half_triangle;
@@ -1206,7 +1206,7 @@ def point_in_triangle(Ax,Ay,Bx,By,Cx,Cy,qx,qy):
 				p1=0.
 			if (l2==0.):
 				p2=0.
-			
+
 			if ( (abs(p0)+abs(p2))+(abs(p1)) == abs((p0+p2)+(p1)) ):
 				point_is_in_triangle = 1;
 	return point_is_in_triangle
@@ -1229,8 +1229,8 @@ def square_spreading_calculation(x,y,L):
 
 def plot_axes_and_triangel(Ax,Ay, Bx, By, Cx, Cy, Px=None, Py=None, Qx=None, Qy=None, Rx=None, Ry=None, Sx=None, Sy=None):
 	if Px is None:
-		Px=-1. ; Py=0. ; Qx=1. ; Qy=0. #x-axis 
-		Rx=0. ; Ry=-1. ; Sx=0. ; Sy=1. #y-axis 
+		Px=-1. ; Py=0. ; Qx=1. ; Qy=0. #x-axis
+		Rx=0. ; Ry=-1. ; Sx=0. ; Sy=1. #y-axis
 	plt.plot(np.array([Px, Qx]), np.array([Py, Qy]))
 	plt.plot(np.array([Rx, Sx]), np.array([Ry, Sy]))
 	plt.plot(np.array([Ax, Bx, Cx, Ax]), np.array([Ay, By, Cy, Ay]))
@@ -1257,7 +1257,7 @@ def main():
 	test_case='many_hexagons'
 
 	if test_case=='line_intercept':
-		Ax=1. ; Ay=1.5 ; Bx=1. ; By=-3.4 
+		Ax=1. ; Ay=1.5 ; Bx=1. ; By=-3.4
 		Px=0.2; Py=-1.0; Qx=0.2; Qy=2.2
 		(x0,y0)=intercept_of_two_lines(Ax,Ay,Bx,By,Px,Py,Qx,Qy)
 		plt.plot( np.array([Ax, Bx])  , np.array([Ay, By]))
@@ -1308,9 +1308,9 @@ def main():
 
 
 	if test_case=='Triangle_into_fours':
-		Px=1. ; Py=0. ; Qx=2. ; Qy=0. #x-axis 
-		Rx=0. ; Ry=1. ; Sx=0. ; Sy=2. #y-axis 
-		
+		Px=1. ; Py=0. ; Qx=2. ; Qy=0. #x-axis
+		Rx=0. ; Ry=1. ; Sx=0. ; Sy=2. #y-axis
+
 		count=0
 		N=11 #Use an odd number
 		for Ax in np.linspace(-0.5 , 0.5 , N):
@@ -1337,7 +1337,7 @@ def main():
 
 		print ('Triangle_into_fours Test Successful')
 
-		#[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]=Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy); 
+		#[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]=Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy);
 		#[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]= Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  )
 
 	if test_case=='Point_above_line':
@@ -1351,8 +1351,8 @@ def main():
 
 
 	if test_case=='many_hexagons':
-		Px=-1. ; Py=0. ; Qx=1. ; Qy=0. #x-axis 
-		Rx=0. ; Ry=-1. ; Sx=0. ; Sy=1. #y-axis 
+		Px=-1. ; Py=0. ; Qx=1. ; Qy=0. #x-axis
+		Rx=0. ; Ry=-1. ; Sx=0. ; Sy=1. #y-axis
 		N=101
 		theta=0.0
 		count=0
@@ -1388,7 +1388,7 @@ def main():
 							print (Area_hexb, Area_Q1b, Area_Q2b, Area_Q3b, Area_Q4b)
 							print ('count=', count)
 							halt
-		
+
 		print ('Many_Hexagons Test Successful')
 
 
@@ -1404,15 +1404,15 @@ def main():
 		print ('Triangle version1',Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
 		(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Hexagon_into_quadrants_using_triangles(x0,y0,H,theta=90.)
 		print ('Triangle version2',Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
-		
-		#print 'Analysis'	
+
+		#print 'Analysis'
 		#print 'sum of quadrants: ', (Area_Q1+Area_Q2+Area_Q3+Area_Q4)
 		print ('Scaled areas: ')
 		print( (Area_Q1+Area_Q2+Area_Q3+Area_Q4)/Area_hex, Area_Q1/Area_hex, Area_Q2/Area_hex, Area_Q3/Area_hex, Area_Q4/Area_hex)
-		
+
 
 	elif test_case=='square':
-	 
+
 		x0=0.6999999999999
 		y0=0.3
 		L=0.6
@@ -1429,8 +1429,8 @@ def main():
 
 		[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]=Triangle_divided_into_four_quadrants(Ax,Ay,Bx,By,Cx,Cy); #T023
 
-		#Px=1. ; Py=0. ; Qx=2. ; Qy=0.	
-		#Rx=0. ; Ry=1. ; Sx=0. ; Sy=2.	
+		#Px=1. ; Py=0. ; Qx=2. ; Qy=0.
+		#Rx=0. ; Ry=1. ; Sx=0. ; Sy=2.
 		#[T23_Area,T23_Q1,T23_Q2,T23_Q3,T23_Q4]= Triangle_divided_into_four_parts(Ax,Ay,Bx,By,Cx,Cy, Px, Py, Qx, Qy, Rx, Ry, Sx, Sy  )
 
 		print ('Triangle 2: ',Ax,Ay,Bx,By,Cx,Cy)
@@ -1438,13 +1438,13 @@ def main():
 		print ('Q1, Q2,Q3,Q4',T23_Q1,T23_Q2,T23_Q3,T23_Q4)
 		print ('Full triangle area',T23_Area)
 		print ('Error',(T23_Q1+T23_Q2+T23_Q3+T23_Q4-T23_Area))
-		
-		
+
+
 
 	elif test_case=='point_in_triangle':
 		Ax= -2.695732526092343E-012
 		Ay=0.204344508198090
-		Bx=-2.695750202346321E-012 
+		Bx=-2.695750202346321E-012
 		By= -8.433062639672301E-002
 		Cx=0.249999999997304
 		Cy=6.000694090068343E-002
@@ -1456,17 +1456,3 @@ def main():
 if __name__ == '__main__':
 	main()
 	#sys.exit(main())
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/tests/collision_tests/makeberg/hexagon_area.pyc b/tests/collision_tests/makeberg/hexagon_area.pyc
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diff --git a/tests/Iceberg_repository/Scripts_and_analysis/initialize_bergs_in_pattern.py b/tests/collision_tests/makeberg/initialize_bergs_in_pattern.py
similarity index 97%
rename from tests/Iceberg_repository/Scripts_and_analysis/initialize_bergs_in_pattern.py
rename to tests/collision_tests/makeberg/initialize_bergs_in_pattern.py
index 0008179..c9fc502 100755
--- a/tests/Iceberg_repository/Scripts_and_analysis/initialize_bergs_in_pattern.py
+++ b/tests/collision_tests/makeberg/initialize_bergs_in_pattern.py
@@ -1,5 +1,8 @@
 #!/usr/bin/env python
 
+## This is Alon Stern's 2016 code to generate iceberg and bond restart files
+## modified to add the collision test
+
 #First import the netcdf4 library
 from netCDF4 import Dataset  # http://code.google.com/p/netcdf4-python/
 import numpy as np  # http://code.google.com/p/netcdf4-python/
@@ -38,10 +41,10 @@ def parseCommandLine():
 	#Flags
 	parser.add_argument('-grounding_test', type='bool', default=False,
 		          help=''' old: displace 500 m S. new: get rid of SE element ''')
-        
+
 	parser.add_argument('-collision_test', type='bool', default=False,
 		          help=''' symmetry for berg around y=10 km ''')
-        
+
 	parser.add_argument('-save_restart_files', type='bool', default=True,
 		          help=''' Writes an iceberg restart file,  icebergs.res ''')
 
@@ -59,7 +62,7 @@ def parseCommandLine():
 		          help=''' When true, only one iceberg (with number chosen_berg_num) is written to icebergs.res. This is for debugging  ''')
 
 	parser.add_argument('-select_just_min_and_max_lat_berg', type='bool', default=False,
-		          help=''' When true, only the bergs with max and min lat are written to icebergs.res. This is for debugging  ''')        
+		          help=''' When true, only the bergs with max and min lat are written to icebergs.res. This is for debugging  ''')
 
 	parser.add_argument('-chosen_berg_num', type=int, default=1,
 		          help='''When only_choose_one_berg=True, then only the iceberg with this number is written to the icebergs.res file  ''')
@@ -137,7 +140,7 @@ def parseCommandLine():
 
 	parser.add_argument('-plot_h_ice_new', type='bool', default=True,
 		          help='''  The newly interpolated ice thickness is plotted under iceberg positions ''')
-	
+
 	parser.add_argument('-plot_bonds', type='bool', default=False,
 		          help=''' Bonds are plotted between the ice elements   ''')
 
@@ -224,17 +227,17 @@ def str2bool(string):
 
 		Value=None
 		return
-	
+
 	return Value
 
-	
+
 
 def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg):
-	
+
 	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
-	# To copy the global attributes of the netCDF file  
+	# To copy the global attributes of the netCDF file
 
-	#Input and output files	
+	#Input and output files
 	#Create Empty restart file. This is later read so that the attributes can be used.
 	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
 	create_empty_iceberg_restart_file(Empty_restart_filename)
@@ -263,14 +266,14 @@ def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,ma
 		# you should add your own conditions here before the creation of the variable.
 		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
 		#Proceed to copy the variable attributes
-		for attname in ncvar.ncattrs():  
+		for attname in ncvar.ncattrs():
 			setattr(var,attname,getattr(ncvar,attname))
 		#Finally copy the variable data to the new created variable
 		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
-		
+
 		if varname=='i':
 			var[:]=Number_of_bergs
-		
+
 		if varname=='iceberg_num':
 			for j in range(Number_of_bergs):
 				#var[j]=j+1
@@ -288,7 +291,7 @@ def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,ma
 		if varname=='thickness':
 			for j in range(Number_of_bergs):
 				var[j]=thickness[j]
-		
+
 		if varname=='mass':
 			for j in range(Number_of_bergs):
 				var[j]=mass[j]
@@ -314,19 +317,19 @@ def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,ma
 	g.close()
 
 
-	
+
 def Create_bond_restart_file(Number_of_bonds,first_berg_num,first_berg_ine,first_berg_jne,other_berg_ine,other_berg_jne,iceberg_num,other_berg_num,Ice_geometry_source):
 	#Creating the bond restart file
 
 	print 'Writing bond restart files with  ', Number_of_bonds, ' Bonds'
-	# To copy the global attributes of the netCDF file  
+	# To copy the global attributes of the netCDF file
 
-	#Input and output files	
+	#Input and output files
 	#Create Empty restart file. This is later read so that the attributes can be used.
 	Empty_bond_restart_filename='output_files/Empty_bonds_icebergs.res.nc'
 	create_empty_bond_restart_file(Empty_bond_restart_filename)
 	#Empty_bond_restart_filename='input_files/bonds_iceberg.res.nc'
-      
+
 	h=Dataset(Empty_bond_restart_filename,'r',format='NETCDF3_CLASSIC') # r is for read only
 	q=Dataset('output_files/' + Ice_geometry_source + '_bonds_iceberg.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
 
@@ -348,7 +351,7 @@ def Create_bond_restart_file(Number_of_bonds,first_berg_num,first_berg_ine,first
 		# you should add your own conditions here before the creation of the variable.
 		var = q.createVariable(varname,ncvar.dtype,ncvar.dimensions)
 		#Proceed to copy the variable attributes
-		for attname in ncvar.ncattrs():  
+		for attname in ncvar.ncattrs():
 			setattr(var,attname,getattr(ncvar,attname))
 		#Finally copy the variable data to the new created variable
 		#var[:] = ncvar[0]
@@ -510,7 +513,7 @@ def create_empty_iceberg_restart_file(Empty_restart_filename):
 	heat_density.long_name = "heat density" ;
 	heat_density.units = "J/kg" ;
 	heat_density.checksum = "               0" ;
-		
+
 	halo_berg=f.createVariable('halo_berg','d',('i'))
 	halo_berg.long_name = "halo_berg" ;
 	halo_berg.units = "dimensionless" ;
@@ -622,18 +625,18 @@ def Define_iceberg_thickness_and_mass(Number_of_bergs,dx_berg,dy_berg,rho_ice,Ra
 			#		test=test+(mass_on_ocean[i_val,j_val,k])
 			#	print test
 			#	halt
-				
 
-	
+
+
 		Th=h_ice[j_val,i_val]
 		thickness.append(Th)
 		#Check that all thicknesses are positive
 		if Th<=0:
 			print 'Thickness is less than or equal to zero,0!',i_val, j_val,x_val,y_val
 			halt
-		#mass.append(Th*rho_ice*element_area) 
-		mass.append(Th*rho_ice*(width[berg_count])**2) 
-		#if element_type=='square': 
+		#mass.append(Th*rho_ice*element_area)
+		mass.append(Th*rho_ice*(width[berg_count])**2)
+		#if element_type=='square':
 		#	mass.append(Th*rho_ice*((2*Radius)**2)) # For square elements
 		#else:
 		#	mass.append(Th*rho_ice*np.pi*(Radius**2))  #For circular elements
@@ -642,10 +645,10 @@ def Define_iceberg_thickness_and_mass(Number_of_bergs,dx_berg,dy_berg,rho_ice,Ra
 
 def check_if_it_is_in_domain(x_val,y_val,x_min,x_max,y_min,y_max,R_earth,lat_init,adjust_lat_ref,dx,dy):
 	point_is_in_domain=True
-	
+
 	if (x_val >= (x_max-x_min+(dx))) or (x_val<= 0) or  (y_val >= (y_max-y_min+(dy))) or (y_val <= 0):
 		point_is_in_domain=False
-	
+
 	return point_is_in_domain
 
 def check_if_it_is_ice(x_val,y_val,ice_mask,dx):
@@ -661,7 +664,7 @@ def calculate_element_area(element_type,Radius):
 	if element_type=='square':
 		element_area=(2*Radius)**2
 	elif element_type=='hexagon':
-		element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*(Radius)**2) #Area of hexagon around circle (used for packing)  
+		element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*(Radius)**2) #Area of hexagon around circle (used for packing)
 		#Another derivation uses innner hexagon with two more triangles added, which is a 1/6 of the hexagon area each (two since there are 6, shared by 3 each)
 		#element_area=(4./3.)*H_i, where H_i=(3.*np.sqrt(3.)/2.)*((Radius)**2)  is the area of the inner hexagon (with sides equal to the radius)
 
@@ -706,8 +709,8 @@ def add_extra_bergs_on_boundary(dx,dy,x,y,Number_of_bergs,element_area,rho_ice,X
 	New_thickness=(New_area)/(rho_ice*grid_area)  #Should be equal to one everywhere where there is ice shelf.
 	New_mass=regrid_iceberg_thickness(dy_berg,dx_berg,Number_of_bergs,thickness,mass,h_ice,x_shift,y_shift,rho_ice,element_type,static_berg,plot_outcome=False)
 	berg_count=Number_of_bergs
-	
-	
+
+
 	#Vertical boundary
 	for i in np.array([0,Nx-1]):
 		#for j in range(Ny):
@@ -755,7 +758,7 @@ def add_extra_bergs_on_boundary(dx,dy,x,y,Number_of_bergs,element_area,rho_ice,X
 
 
 	Number_of_bergs=berg_count
-	
+
 	return [dx_berg, dy_berg,iceberg_num, width,Number_of_bergs,static_berg,thickness,mass]
 
 
@@ -789,11 +792,11 @@ def Create_icebergs(lon_init,lat_init,Radius,R_earth, x, y,ice_mask,h_ice,Conver
 	lon=[] #Longitude of iceberg
 	lat=[] #Latitude of iceberg
 	iceberg_num=[] #ID of iceberg
-	
+
 	element_area=calculate_element_area(element_type,Radius)
 	#width=np.sqrt(element_area)
 	width=[]
-	
+
 	#dx=x[1]-x[0]  ;dy=y[1]-y[0]
 	#X_min=np.min(x)-dx; X_max=np.max(x)+dx  #In lat lon or cartesian
 	#Y_min=np.min(y)-dy; Y_max=np.max(y)+dy  #In lat lon or cartesian
@@ -801,7 +804,7 @@ def Create_icebergs(lon_init,lat_init,Radius,R_earth, x, y,ice_mask,h_ice,Conver
 	Y_min=np.min(y); Y_max=np.max(y)  #In lat lon or cartesian
 
 	#N=2*int(ceil((R_max)/(2*Radius))+2)
-	
+
 	if element_type=='square':
 		N=int(math.ceil((X_max-X_min)/(Radius)))
 		M=int(math.ceil((Y_max-Y_min)/(Radius)))
@@ -816,7 +819,7 @@ def Create_icebergs(lon_init,lat_init,Radius,R_earth, x, y,ice_mask,h_ice,Conver
 	#M=6
 	#MP4
 
- 	dx=x[1]-x[0]	
+ 	dx=x[1]-x[0]
  	dy=y[1]-y[0]
 	Lx=X_max+dx
 	Ly=Y_max+dx
@@ -829,8 +832,8 @@ def Create_icebergs(lon_init,lat_init,Radius,R_earth, x, y,ice_mask,h_ice,Conver
 			y_start=(Radius)
 			x_val=x_start+(2*i*Radius)
 
-		#Hexagonal	
-		else:   
+		#Hexagonal
+		else:
 			y_start=(Radius)+(((i%2)*Radius))
 			x_start=((2/np.sqrt(3))*Radius)
 			x_val=x_start + (np.sqrt(3)*Radius*i)
@@ -863,14 +866,14 @@ def Create_icebergs(lon_init,lat_init,Radius,R_earth, x, y,ice_mask,h_ice,Conver
                                                 dy_berg.append(y_val)
                                                 width.append(np.sqrt(element_area))
 
-                                               
+
 	#print 'dx_berg',dx_berg
 	#print 'dy_berg',dy_berg
 
 
 	Number_of_bergs=berg_count
-	
-	
+
+
 	#Deciding if icebergs are static or not
 	static_berg = [0. for i in dx_berg]
 	if set_all_bergs_static_by_default==True:
@@ -883,7 +886,7 @@ def Create_icebergs(lon_init,lat_init,Radius,R_earth, x, y,ice_mask,h_ice,Conver
 		#static_berg =Change_static_berg_after_calving(Number_of_bergs,lat,lon, static_berg)
 		static_berg =Change_static_berg_after_calving(Number_of_bergs,dy_berg,dx_berg, static_berg)
 		static_berg=static_berg[0]
-		
+
 	if Remove_stationary_bergs is True:
 		Fill_in_the_boundaries=False
 		[dx_berg, dy_berg,iceberg_num, width,Number_of_bergs,static_berg]=remove_stationary_bergs(dx_berg, dy_berg,iceberg_num,\
@@ -893,7 +896,7 @@ def Create_icebergs(lon_init,lat_init,Radius,R_earth, x, y,ice_mask,h_ice,Conver
 
 	#Defining the thickness of the icebergs
 	(thickness, mass)=Define_iceberg_thickness_and_mass(Number_of_bergs,dx_berg,dy_berg,rho_ice,Radius, h_ice,x,y,\
-			width,Interpolate_from_four_corners,element_area,element_type,static_berg)	
+			width,Interpolate_from_four_corners,element_area,element_type,static_berg)
 
 	N_bergs_before_bd=Number_of_bergs
 	if Fill_in_the_boundaries==True and element_type=='hexagon':
@@ -901,7 +904,7 @@ def Create_icebergs(lon_init,lat_init,Radius,R_earth, x, y,ice_mask,h_ice,Conver
 				Y_max,R_earth,lat_init,adjust_lat_ref,ice_mask,iceberg_num,width,dx_berg,dy_berg,\
 				h_ice,element_type,static_berg,thickness,mass)
 		print 'Number of icebergs after accounting for boundaries = ', Number_of_bergs
-	
+
         if collision_test:
                 for i in range(berg_count):
                         berg_count=berg_count+1
@@ -937,7 +940,7 @@ def Create_icebergs(lon_init,lat_init,Radius,R_earth, x, y,ice_mask,h_ice,Conver
 		if scale_the_grid_to_lat_lon==True:
 			Scale_up=1./2000.
 			Radius=Radius*Scale_up
-			dx_berg = [(i*Scale_up) for i in dx_berg] ; dy_berg = [i*Scale_up for i in dy_berg] 
+			dx_berg = [(i*Scale_up) for i in dx_berg] ; dy_berg = [i*Scale_up for i in dy_berg]
 			x=x*Scale_up ; y=y*Scale_up
 			dx=dx*Scale_up ;dy=dy*Scale_up
 		x=(x-np.min(x))+(dx/2) ; y=(y-np.min(y))+(dy/2)
@@ -946,9 +949,9 @@ def Create_icebergs(lon_init,lat_init,Radius,R_earth, x, y,ice_mask,h_ice,Conver
         if grounding_test:
                 for i in range(Number_of_bergs):
                         lat[i]=lat[i]-0.0 #500.0
-	
+
 	#Note that static_berg calculations used to be here, after the conversion. I have moved them. I hope that this does not affect answers.
-                        
+
         print 'Icebergs created. Number of bergs = ', Number_of_bergs
 	return (Number_of_bergs,lon,lat,iceberg_num,dx_berg,dy_berg,thickness, mass,width,x,y,Radius,static_berg,N_bergs_before_bd)
 
@@ -994,15 +997,15 @@ def Create_calving_event(lat1,lon1,lat2,lon2):
 	return bond_broken
 
 def get_calving_parameters():
-	#Calve_lat =20  
+	#Calve_lat =20
 	#Calve_lon=160
 	#R_calve=15
-	Calve_lat =20.2*2000  
+	Calve_lat =20.2*2000
 	Calve_lon=165*2000
 	R_calve=15*2000
 	R_long =18*2000
 	R_short =12*2000
-	
+
 	return [R_calve,  R_long, R_short, Calve_lon, Calve_lat]
 
 def Change_static_berg_after_calving(Number_of_bergs,lat,lon, static_berg):
@@ -1087,7 +1090,7 @@ def Define_iceberg_bonds(Number_of_bergs,iceberg_num,lat,lon,dx_berg, dy_berg,Ra
 							if R_dist < (2.01*Radius) and (bond_broken==False):
 								bond_count=bond_count+2
 								#Connect bond in the first direction
-								first_berg_num.append(iceberg_num[i]);	first_berg_ine.append(999); 
+								first_berg_num.append(iceberg_num[i]);	first_berg_ine.append(999);
 								other_berg_num.append(iceberg_num[j]); 	other_berg_ine.append(999);
 								first_berg_jne.append(999);first_berg_lat.append(lat[i]); first_berg_lon.append(lon[i])
 								other_berg_jne.append(999);other_berg_lat.append(lat[j]); other_berg_lon.append(lon[j])
@@ -1121,14 +1124,14 @@ def load_ISOMIP_ice_geometry(filename,buffer_number):
 	C=np.arange(M[1]-buffer_number,M[1])
 	ice_mask[A,:]=0; ice_mask[B,:]=0
 	ice_mask[:,A]=0; ice_mask[:,C]=0
-	
+
 	return [x,y,ice_mask,h_ice]
 
 
 def create_clipped_icethickness_file(h_ice,area,mass,grid_area,gravity,Ice_geometry_source):
 	#Creating clipped file
-        [ny, nx]= h_ice.shape ; 
-	
+        [ny, nx]= h_ice.shape ;
+
 	New_ice_thickness_filename='output_files/'+ Ice_geometry_source +'_Ice_Shelf_clipped.nc'
         g=Dataset(New_ice_thickness_filename,'w') # w if for creating a file
 
@@ -1151,7 +1154,7 @@ def create_clipped_icethickness_file(h_ice,area,mass,grid_area,gravity,Ice_geome
         g.variables['area'][:]=area
         g.variables['p_surf'][:]=p_surf
         print 'Creating clipped ice file: ' , New_ice_thickness_filename
-        
+
         g.sync()
         g.close()
 
@@ -1176,7 +1179,7 @@ def load_ISOMIP_reduced_ice_geometry(ice_filename,buffer_number):
 	#if buffer_number>0:
 	ice_mask[A,:]=0; ice_mask[B,:]=0
 	ice_mask[:,A]=0; ice_mask[:,C]=0
-	
+
 	return [x,y,ice_mask,h_ice]
 
 def load_generic_ice_geometry(filename):
@@ -1200,7 +1203,7 @@ def load_generic_ice_geometry(filename):
 		lon_init=x[0]-(dx/2.)
 		lat_init=y[0]-(dx/2.)
 		print 'Bottom corner = [ ', lon_init,' , ' , lat_init, ' dx = ' , dx
-	
+
 	return [x,y,ice_mask,h_ice,lon_init, lat_init]
 
 def load_Weddel_ice_geometry(filename):
@@ -1214,7 +1217,7 @@ def load_Weddel_ice_geometry(filename):
 		#ice_mask=1-ocean_mask #one if it ice, zero if it is ocean
 		h_ice[np.where(np.isnan(h_ice))]=0.
                 ice_mask[np.where(np.isnan(ice_mask))]=0.
-	
+
 	return [x,y,ice_mask,h_ice]
 
 def Select_just_one_berg(lon,lat,thickness,width,mass,iceberg_num,chosen_berg_num,static_berg):
@@ -1253,11 +1256,11 @@ def Select_just_min_and_max_lat_bergs(lon,lat,thickness,width,mass,iceberg_num,s
         static_berg=[static_berg[minnum],static_berg[maxnum]]
         iceberg_num=[iceberg_num[minnum],iceberg_num[maxnum]]
         Number_of_bergs=2
-	return [Number_of_bergs,lon,lat,thickness,width,mass,iceberg_num,static_berg]        
+	return [Number_of_bergs,lon,lat,thickness,width,mass,iceberg_num,static_berg]
 
 def plotting_iceberg_positions(lat,lon,Number_of_bergs,R_earth,Radius,IA_scaling,Convert_to_lat_lon, \
 		plot_circles,h_ice,ice_mask,x,y,plot_ice_mask,plot_ice_thickness,thickness,plot_icebergs_positions,static_berg,h_ice_new,plot_h_ice_new):
-	print 'Starting to plot...'	
+	print 'Starting to plot...'
 	Radius=Radius*IA_scaling
 	circ_ind=np.linspace(0,2*np.pi,100);
 
@@ -1326,8 +1329,8 @@ def plotting_iceberg_bonds(first_berg_lat,first_berg_lon,other_berg_lat,other_be
 def spread_mass_to_ocean(Nx,Ny,i,j,mass_on_ocean,x,y,Area,Mass,element_type,grid_area,static_berg):
 		#Note that the x,y coming into this routine are the position within a cell (from 0 to 1), with 0.5,0.5 being in the center of the cell.
 
-		#Initialize weights for each cell	
-		yDxL=0.  ; yDxC=0. ; yDxR=0. ; yCxL=0. ; yCxR=0. 
+		#Initialize weights for each cell
+		yDxL=0.  ; yDxC=0. ; yDxR=0. ; yCxL=0. ; yCxR=0.
 		yUxL=0.  ; yUxC=0. ; yUxR=0. ; yCxC=1.
 
 		if element_type=='square':
@@ -1367,7 +1370,7 @@ def spread_mass_to_ocean(Nx,Ny,i,j,mass_on_ocean,x,y,Area,Mass,element_type,grid
 
 			x0=(x-origin_x) #Position of the hexagon center, relative to origin at the nearest vertex
 			y0=(y-origin_y)
-			
+
 			#(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Divide_hexagon_into_4_quadrants_old(x0,y0,H)
 			(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Hexagon_into_quadrants_using_triangles(x0,y0,H,0.)
 			if min(min(Area_Q1,Area_Q2),min(Area_Q3, Area_Q4)) <0:
@@ -1389,14 +1392,14 @@ def spread_mass_to_ocean(Nx,Ny,i,j,mass_on_ocean,x,y,Area,Mass,element_type,grid
 				yUxC=Area_Q2
 				yCxC=Area_Q3
 				yCxR=Area_Q4
-			
+
 			#Top left vertex
 			if x<0.5 and y>= 0.5:
 				yUxC=Area_Q1
 				yUxL=Area_Q2
 				yCxL=Area_Q3
 				yCxC=Area_Q4
-			
+
 			#Bottom left vertex
 			if x<0.5 and y< 0.5:
 				yCxC=Area_Q1
@@ -1413,8 +1416,8 @@ def spread_mass_to_ocean(Nx,Ny,i,j,mass_on_ocean,x,y,Area,Mass,element_type,grid
 
 			#if Sector<4 and Sector>-1:
 			#	print Sector
-				
-					
+
+
 			#Check that this is true
 			if abs(yCxC-(1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )))>0.001:
 				print 'All the mass is not being used!!!'
@@ -1423,13 +1426,13 @@ def spread_mass_to_ocean(Nx,Ny,i,j,mass_on_ocean,x,y,Area,Mass,element_type,grid
 				print 'Areas: ',Area_hex,Area_hex*Area_Q1, Area_hex*Area_Q2, Area_hex*Area_Q3, Area_hex*Area_Q4
 				print 'x0=',x0, 'y0=',y0, 'H=', H
 				print 'Total area= ',(Area_Q1+Area_Q2+Area_Q3+Area_Q4)#, Sector
-				
 
-		#Accounting for masked points 
+
+		#Accounting for masked points
 		a=1. ; b=1. ; c=1. ; d=1.
 		if i==0:
 			a=0.;
-		if j==0: 
+		if j==0:
 			b=0.;
 		if i==Nx-1:
 			c=0;
@@ -1457,7 +1460,7 @@ def spread_mass_to_ocean(Nx,Ny,i,j,mass_on_ocean,x,y,Area,Mass,element_type,grid
 def calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x, y, Lx):
 
 	Lx_2=Lx/2.
-  
+
 	alpha=x2-x1
 	delta=y2-y1
 	beta=x4-x1
@@ -1470,7 +1473,7 @@ def calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x, y, Lx):
 	dy=y-y1
 	b=(delta*beta-alpha*epsilon)-(kappa*dx-gamma*dy)
 	c=(alpha*dy-delta*dx)
-	
+
 	#print 'alpha,beta,gamma',alpha,beta,gamma
 	#print 'delta,epsilon,kappa',delta,epsilon,kappa
 	#print 'dx,dy',dx,dy
@@ -1517,12 +1520,12 @@ def regrid_iceberg_thickness(lat,lon,Number_of_bergs,thickness,mass,h_ice,x,y,rh
 	Area = [(mass[i]/(rho_ice*thickness[i])) for i in range(Number_of_bergs)] ;
 	grid_area=dx*dy #Assuming a regular grid
 	Orig_mass=h_ice*rho_ice*grid_area
-	
+
 	mass_on_ocean=np.zeros([Nx,Ny,10])   #Setting up matrix to spread mass to ocean.  Note that I have used 10 points  so that I can ignore 0 and match with python numbering
 	#mass_on_ocean=np.zeros([Nx,Ny])   #Setting up matrix to spread mass to ocean.
 	#Note: You may want to import the grid that the ocean model actually sees.
-	for berg_count in range(Number_of_bergs):  
-		x_val=lon[berg_count]  
+	for berg_count in range(Number_of_bergs):
+		x_val=lon[berg_count]
 		y_val=lat[berg_count]
 		Area_val=Area[berg_count]
 		mass_val=mass[berg_count]
@@ -1558,39 +1561,39 @@ def regrid_iceberg_thickness(lat,lon,Number_of_bergs,thickness,mass,h_ice,x,y,rh
 					+  (mass_on_ocean[i+1,j-1,7]+mass_on_ocean[i-1,j+1,3]) ) \
 					+   ( (mass_on_ocean[i-1,j  ,6]+mass_on_ocean[i+1,j  ,4])   \
 					+  (mass_on_ocean[i  ,j-1,8]+mass_on_ocean[i  ,j+1,2]) ) )
-	
+
 	#Adding mass to boundary cells
 	for j in range(1,Ny-1):
 		i=0
 		New_mass[j,i]=mass_on_ocean[i,j,5] +  mass_on_ocean[i+1,j+1,1] +  mass_on_ocean[i+1,j-1,7] \
-			+  mass_on_ocean[i+1,j  ,4] 	+  mass_on_ocean[i  ,j-1,8] + mass_on_ocean[i  ,j+1,2] 
-		i=Nx-1	
+			+  mass_on_ocean[i+1,j  ,4] 	+  mass_on_ocean[i  ,j-1,8] + mass_on_ocean[i  ,j+1,2]
+		i=Nx-1
 		New_mass[j,i]=mass_on_ocean[i,j,5] +  mass_on_ocean[i-1,j-1,9] + mass_on_ocean[i-1,j+1,3] \
 					+   mass_on_ocean[i-1,j ,6] + mass_on_ocean[i ,j-1,8]+mass_on_ocean[i ,j+1,2]
-	
+
 	for i in range(1,Nx-1):
 		j=0
 		New_mass[j,i]=mass_on_ocean[i,j,5] +   mass_on_ocean[i+1,j+1,1] +  mass_on_ocean[i-1,j+1,3]  \
 				+  mass_on_ocean[i-1,j  ,6] + mass_on_ocean[i+1,j  ,4] +  mass_on_ocean[i  ,j+1,2]
 
-		j=Ny-1	
+		j=Ny-1
 		New_mass[j,i]=mass_on_ocean[i,j,5] +  mass_on_ocean[i-1,j-1,9] 	+  mass_on_ocean[i+1,j-1,7] + \
 				mass_on_ocean[i-1,j  ,6]+mass_on_ocean[i+1,j  ,4] +  mass_on_ocean[i  ,j-1,8]
 
 	#Corners
 	i=0 ;j=0
-	New_mass[j,i]=mass_on_ocean[i,j,5] + mass_on_ocean[i+1,j+1,1] + mass_on_ocean[i+1,j  ,4] + mass_on_ocean[i  ,j+1,2]  
+	New_mass[j,i]=mass_on_ocean[i,j,5] + mass_on_ocean[i+1,j+1,1] + mass_on_ocean[i+1,j  ,4] + mass_on_ocean[i  ,j+1,2]
 	i=0 ;j=Ny-1
-	New_mass[j,i]=mass_on_ocean[i,j,5] + mass_on_ocean[i+1,j-1,7] + mass_on_ocean[i+1,j  ,4] + mass_on_ocean[i  ,j-1,8]  
+	New_mass[j,i]=mass_on_ocean[i,j,5] + mass_on_ocean[i+1,j-1,7] + mass_on_ocean[i+1,j  ,4] + mass_on_ocean[i  ,j-1,8]
 	i=Nx-1; j=0
 	New_mass[j,i]=mass_on_ocean[i,j,5] + mass_on_ocean[i-1,j+1,3] + mass_on_ocean[i-1,j  ,6] + mass_on_ocean[i  ,j+1,2]
-	i=Nx-1; j=Ny-1	
+	i=Nx-1; j=Ny-1
 	New_mass[j,i]=mass_on_ocean[i,j,5] + mass_on_ocean[i-1,j-1,9] + mass_on_ocean[i-1,j  ,6] + mass_on_ocean[i  ,j-1,8]
 
 
 	if plot_outcome==True: #MP2
-		#print 'Warning: the interpolation scheme is not the same as the one used in the model'	
-		
+		#print 'Warning: the interpolation scheme is not the same as the one used in the model'
+
 		plot_data=(Orig_mass-New_mass)/Orig_mass
 		cNorm = mpl.colors.Normalize(vmin=-.1, vmax=.1)
 		vmax=np.max(abs(plot_data))
@@ -1654,7 +1657,7 @@ def convert_input_to_catesian_coordinates(lon,lat,ice_mask,h_ice,R_earth,dx):
         y=(np.pi/180)*R_earth*lat
         x=x-np.min(x)
         y=y-np.min(y)
-        
+
         #Creating regular grid
         x_new=np.linspace(np.min(x), np.max(x), num=len(x))
         y_new=np.linspace(np.min(y),np.max(y), num=len(y))
@@ -1666,7 +1669,7 @@ def convert_input_to_catesian_coordinates(lon,lat,ice_mask,h_ice,R_earth,dx):
         ice_mask_new=interpolate_field_onto_new_grid(x,y,x_new,y_new,ice_mask)
         #ice_mask_new=np.round(ice_mask_new)
         #print ice_mask_new[50,:]
-        
+
         return [x_new,y_new,ice_mask_new,h_ice_new]
 
 
@@ -1694,9 +1697,9 @@ def main(args):
 	Use_default_radius=args.Use_default_radius
 
 	#Static vs non-static flags
-	set_all_bergs_static_by_default=args.set_all_bergs_static_by_default 
-	set_some_bergs_static_by_default=args.set_some_bergs_static_by_default 
-	Make_icebergs_non_static_later=args.Make_icebergs_non_static_later 
+	set_all_bergs_static_by_default=args.set_all_bergs_static_by_default
+	set_some_bergs_static_by_default=args.set_some_bergs_static_by_default
+	Make_icebergs_non_static_later=args.Make_icebergs_non_static_later
 
 	#Mass spreadng flags
 	element_type=args.element_type
@@ -1744,9 +1747,9 @@ def main(args):
 
 	#Applying some special case flags
 	if Ice_geometry_source=='ISOMIP':
-		Convert_to_lat_lon=False       ; input_is_cartesian=True ; 
+		Convert_to_lat_lon=False       ; input_is_cartesian=True ;
 	if Ice_geometry_source=='Generic':
-		Convert_to_lat_lon=False       ; input_is_cartesian=True ; set_all_bergs_static_by_default=False ; Fill_in_the_boundaries=False ; Use_default_radius=True 
+		Convert_to_lat_lon=False       ; input_is_cartesian=True ; set_all_bergs_static_by_default=False ; Fill_in_the_boundaries=False ; Use_default_radius=True
 	if Ice_geometry_source=='Weddell':
 		Convert_to_lat_lon=False        ; input_is_cartesian=False
 
@@ -1776,7 +1779,7 @@ def main(args):
 		lon_init=-32.9  ; lat_init=-70.  #latitude  of bottom left corner of iceberg
 		(x,y,ice_mask,h_ice)=load_Weddel_ice_geometry(Weddell_ice_geometry_filename)
 		ice_filename=Weddell_ice_geometry_filename
-		Radius=0.5*10000. 
+		Radius=0.5*10000.
 
 	if  Ice_geometry_source=='Generic':
 		(x,y,ice_mask,h_ice, lon_init, lat_init)=load_generic_ice_geometry(Generic_ice_geometry_filename)
@@ -1800,7 +1803,7 @@ def main(args):
 		if element_type=='hexagon':
 			Radius= (np.sqrt(3)/2.) *(R_frac*dx)   #(S is < half the grid size)
 	print 'Radius set to R= ' , Radius
-	
+
 	lat_ref=np.max(y)
 	#Define the positions,thickness, mass,  of the icebergs
 	(Number_of_bergs,lon,lat,iceberg_num,dx_berg, dy_berg,thickness,mass,width,x,y,Radius,static_berg,N_bergs_before_bd)= Create_icebergs(lon_init,lat_init,\
@@ -1850,20 +1853,20 @@ def main(args):
 			for j in range(M[0]):
 				for i in range(M[1]):
 					if New_area[j,i]>0:
-						h_ice_new[j,i]=New_mass[j,i]/(rho_ice*New_area[j,i])  
+						h_ice_new[j,i]=New_mass[j,i]/(rho_ice*New_area[j,i])
 
 	if Switch_x_and_y_to_rotate_90 is True:
 		[lat,lon, h_ice_new,New_area,New_mass]=Switch_x_and_y_directions(lat,lon, h_ice_new,New_area,New_mass)
-			
 
-	if save_restart_files==True:	
+
+	if save_restart_files==True:
 		#Creating iceberg restart file
 		Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg)
-		
+
 		#Creating bond restart file
 		if Create_icebergs_bonds==True:
 			Create_bond_restart_file(Number_of_bonds,first_berg_num,first_berg_ine,first_berg_jne,other_berg_ine,other_berg_jne,iceberg_num,other_berg_num,Ice_geometry_source)
-			
+
 		if save_new_h_ice_file==True:
 			create_clipped_icethickness_file(h_ice_new,New_area,New_mass,grid_area,gravity,Ice_geometry_source)
 
@@ -1875,8 +1878,8 @@ def main(args):
 			plotting_iceberg_bonds(first_berg_lat,first_berg_lon,other_berg_lat,other_berg_lon,Number_of_bonds)
 
 	#field=New_mass/(rho_ice*grid_area)
-	field=New_area/grid_area -1. 
-	M=field.shape	
+	field=New_area/grid_area -1.
+	M=field.shape
 	#print 'field',(field[M[0]-1,:])
 	#print 'field',(field[M[0]-2,:])
 	#print 'h_ice',h_ice_new[:,:]
@@ -1891,17 +1894,3 @@ def main(args):
 	optCmdLineArgs=	parseCommandLine()
 	main(optCmdLineArgs)
 	#sys.exit(main())
-
-
-
-
-
-
-
-
-
-
-
-
-
-

From b4ce7ebf5b373c6fa21ab32f5845ce8459a21035 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Tue, 3 Jan 2023 13:24:04 -0500
Subject: [PATCH 336/361] Fixed calve_icebergs so that the random numbers for
 tidal drift are only calculated under the new scheme for interpolation of
 gridded fields to bergs (bergs%old_interp_flds_order=.false.). This prevents
 a crash in the OM4p5 basic regression test. Added a safeguard that makes sure
 only Verlet integration is allowed for MTS, DEM, and footloose

---
 src/icebergs.F90           | 19 +++++++++++--------
 src/icebergs_framework.F90 |  7 +++++++
 2 files changed, 18 insertions(+), 8 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 8bcf421..becc106 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -2525,7 +2525,7 @@ subroutine footloose_calving(bergs, time)
   real, save :: N_max, youngs, poisson, l_c, lw_c, B_c, exp_nlambda, rn
   real, save :: e1, drho, sigmay, lfootparam
   real :: foot_l,foot_mass, foot_area
-  type(randomNumberStream),save :: rns ! Random numbers for stochastic tidal parameterization
+  type(randomNumberStream),save :: rns ! Random numbers
   logical, save :: Visited=.false.
   integer :: grdi, grdj
   integer, dimension(8) :: seed
@@ -6324,6 +6324,9 @@ subroutine calve_icebergs(bergs)
   ! For convenience
   grd=>bergs%grd
 
+  rx = 0.
+  ry = 0.
+
   iNg=(grd%ieg-grd%isg+1) ! Total number of points globally in i direction
   jNg=(grd%jeg-grd%jsg+1) ! Total number of points globally in j direction
 
@@ -6438,14 +6441,14 @@ subroutine calve_icebergs(bergs)
             newberg%accum_bond_rotation=0.
           endif
 
-          !interpolate gridded variables to new iceberg
-          if (grd%tidal_drift>0.) then
-            call getRandomNumbers(rns, rx)
-            call getRandomNumbers(rns, ry)
-            rx = 2.*rx - 1.; ry = 2.*ry - 1.
-          endif
-
           if (.not. bergs%old_interp_flds_order) then
+            !interpolate gridded variables to new iceberg
+            if (grd%tidal_drift>0.) then
+              call getRandomNumbers(rns, rx)
+              call getRandomNumbers(rns, ry)
+              rx = 2.*rx - 1.; ry = 2.*ry - 1.
+            endif
+
             call interp_flds(grd, newberg%lon, newberg%lat, i, j, xi, yj, rx, ry, newberg%uo, newberg%vo, newberg%ui, &
               newberg%vi, newberg%ua, newberg%va, newberg%ssh_x, newberg%ssh_y, newberg%sst, newberg%sss, newberg%cn, &
               newberg%hi, newberg%od)
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 4be126f..0a36ce4 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -1539,6 +1539,13 @@ subroutine ice_bergs_framework_init(bergs, &
   !backwards compatibility
   if (.not. (bergs%mts .or. bergs%dem .or. bergs%fl_r>0.)) bergs%old_interp_flds_order=.true.
 
+  if (bergs%Runge_not_Verlet) then
+    if (bergs%mts .or. bergs%dem .or. bergs%fl_r>0.) then
+      call error_mesg('KID, ice_bergs_framework_init', &
+        'Runge_not_Verlet must be false to use MTS, DEM, or footloose!', FATAL)
+    endif
+  endif
+
   if (bergs%contact_distance>0) then
     dx_dlon=1; dy_dlat=1
     if (grd%grid_is_latlon) dy_dlat=pi_180*Rearth

From 5a5a1758c835ebed82b613957d5f0bd31a77f639 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Tue, 3 Jan 2023 16:43:51 -0500
Subject: [PATCH 337/361] Modified calve_icebergs so that new berg prev/old
 velocities and positions are not initialized unless using interactive
 icebergs. This has no impact except enabling the berg restart chksums to
 match the reference runs in the om4 regression tests (the regression tests
 pass either way, but this modification undoes a previous change that caused
 mismatch in the berg restart chksums only).

---
 src/icebergs.F90           | 58 ++++++++++++++++++++------------------
 src/icebergs_framework.F90 |  6 ++--
 2 files changed, 34 insertions(+), 30 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index becc106..d00f683 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -3082,26 +3082,28 @@ subroutine thermodynamics(bergs)
 
       !if footloose is based on length of foot, accumulate side mass loss on fl_k
       !note: this only works when bergs%use_operator_splitting=.true.
-      if (bergs%fl_use_l_scale .and. this%fl_k>=0) then
-        l_b3 = 3.*l_c*(lw_c*bergs%fl_youngs*B_c*(Tn**3.))**0.25 !child berg length x 3
-        if (L>l_b3) then !do not accumulate side made loss for sides < l_b3
-          fb = Tn*(1.-bergs%rho_bergs/rho_seawater) !freeboard
-          kd = Tn-fb !keel depth
-          if (W>l_b3) then
-            if (bergs%fl_l_scale_erosion_only) then
-              this%fl_k=this%fl_k + (dMe/fb - dMv/kd)/bergs%rho_bergs !horiz area from erosion - from buoy conv
-              if (this%fl_k<0) this%fl_k=0
-            else
-              this%fl_k= this%fl_k + (dMe + dMv)/Tn
-            endif
-          else
-            dMv_l=dMv*(Wn1 + W)/(2.*(Ln1 + W)) !mass loss from length from buoyant convection
-            dMe_l=dMe*(Wn+ Wn1)/(2.*(Ln+ Wn1)) !mass loss from length from erosion
-            if (bergs%fl_l_scale_erosion_only) then
-              this%fl_k=this%fl_k + (dMe_l/fb - dMv_l/kd)/bergs%rho_bergs
-              if (this%fl_k<0) this%fl_k=0
+      if (bergs%fl_r>0.) then
+        if (bergs%fl_use_l_scale .and. this%fl_k>=0) then
+          l_b3 = 3.*l_c*(lw_c*bergs%fl_youngs*B_c*(Tn**3.))**0.25 !child berg length x 3
+          if (L>l_b3) then !do not accumulate side made loss for sides < l_b3
+            fb = Tn*(1.-bergs%rho_bergs/rho_seawater) !freeboard
+            kd = Tn-fb !keel depth
+            if (W>l_b3) then
+              if (bergs%fl_l_scale_erosion_only) then
+                this%fl_k=this%fl_k + (dMe/fb - dMv/kd)/bergs%rho_bergs !horiz area from erosion - from buoy conv
+                if (this%fl_k<0) this%fl_k=0
+              else
+                this%fl_k= this%fl_k + (dMe + dMv)/Tn
+              endif
             else
-              this%fl_k= this%fl_k + (dMe_l + dMv_l)/Tn
+              dMv_l=dMv*(Wn1 + W)/(2.*(Ln1 + W)) !mass loss from length from buoyant convection
+              dMe_l=dMe*(Wn+ Wn1)/(2.*(Ln+ Wn1)) !mass loss from length from erosion
+              if (bergs%fl_l_scale_erosion_only) then
+                this%fl_k=this%fl_k + (dMe_l/fb - dMv_l/kd)/bergs%rho_bergs
+                if (this%fl_k<0) this%fl_k=0
+              else
+                this%fl_k= this%fl_k + (dMe_l + dMv_l)/Tn
+              endif
             endif
           endif
         endif
@@ -6374,14 +6376,16 @@ subroutine calve_icebergs(bergs)
           newberg%uvel=0.
           newberg%vvel=0.
           !--added by Alex:
-          newberg%uvel_prev=0.
-          newberg%vvel_prev=0.
-          newberg%uvel_old=0.
-          newberg%vvel_old=0.
-          newberg%lon_prev=newberg%lon
-          newberg%lat_prev=newberg%lat
-          newberg%lon_old=newberg%lon
-          newberg%lat_old=newberg%lat
+          if (bergs%interactive_icebergs_on) then
+            newberg%uvel_prev=0.
+            newberg%vvel_prev=0.
+            newberg%uvel_old=0.
+            newberg%vvel_old=0.
+            newberg%lon_prev=newberg%lon
+            newberg%lat_prev=newberg%lat
+            newberg%lon_old=newberg%lon
+            newberg%lat_old=newberg%lat
+          endif
           newberg%fl_k=0.
           !--added by Alon
           newberg%axn=0.
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 0a36ce4..749654a 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -635,7 +635,7 @@ module ice_bergs_framework
   real :: fl_bits_scale_t=0.9 !< For determining dimensions of FL bits berg; FL_bits thickness = fl_bits_scale_t * T
 
   !backwards compatibility
-  logical :: old_interp_flds_order=.false. !< Use old order of when to interpolate grid variables to bergs. Will be false if MTS, DEM, or footloose (.not. fl_r>0)
+  logical :: old_interp_flds_order=.false. !< Use old order of when to interpolate grid variables to bergs. Will be false if MTS, DEM, or footloose (fl_r>0)
 end type icebergs
 
 !> Read original restarts. Needs to be module global so can be public to icebergs_mod.
@@ -644,9 +644,9 @@ module ice_bergs_framework
 
 !> Version of file provided by CPP macro (usually set to git hash)
 #ifdef _FILE_VERSION
-character(len=128) :: version = _FILE_VERSION !< Version of file
+  character(len=128) :: version = _FILE_VERSION !< Version of file
 #else
-character(len=128) :: version = 'unknown' !< Version of file
+  character(len=128) :: version = 'unknown' !< Version of file
 #endif
 
 !> Set a value in the buffer at position (counter,n) after incrementing counter

From 8045fd45f953165d8d6964204ed2c54e655d6e99 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Tue, 3 Jan 2023 19:06:06 -0500
Subject: [PATCH 338/361] Cleaned up the footloose code, removing the old
 Poisson-based footloose calving approach (England et al., 2020) as well as
 several experimental features:

-removed fl_bits_scale_l, fl_bits_scale_w, and fl_bits_scale_t. Therefore, the representative size of binned footloose bergs is always set to the size of a freshly calved footloose child berg. (NOTE: THIS CHANGES THE CHKSUM FOR THE FOOTLOOSE TESTS. The chksums have been updated.)
-added option 'fl_init_child_xy_by_pe' to reproduce an old bug where under a certain combination of setup parameters, the position of a new footloose (FL) child berg along the parent perimeter would be random, but constant within each PE (e.g. all FL child bergs in PE 1 would always be initialized to +5 degrees from North, while all FL child bergs in PE 2 would always be initialized to +35 degrees from North, etc.). If fl_init_child_xy_be_pe=.false., then new FL child berg positions are assigned fully-randomly along the parent berg perimeter. The 'bug' is primarily kept for backwards compatibility, but compared to true randomness, is likely also slightly more computationally-efficient with negligible difference in the solution...
-Made nml fl_l_scale_erosion_only=.true. (footloose based on side erosion - melt to calculate foot size) the default footloose option, which also allowed me to remove it from the nml options because it is unnecessary.
-By removing the Poisson-based footloose calving (England et al., 2020), 'use_fl_l_scale' (Huth et al., 2022) became the default and this nml option was removed entirely because it is unnecessary. Consistently, all Poisson-based footloose calving variables were removed, including 'fl_r' and 'fl_r_s'.
-A new nml parameter 'footloose' was added to toggle footloose on and off (previously fl_r>0 accomplished this).
---
 .gitignore                                  |   3 +-
 src/icebergs.F90                            | 135 ++++-----------
 src/icebergs_framework.F90                  |  89 ++++------
 src/icebergs_io.F90                         |  27 +--
 tests/footloose_tests/README                |  20 +--
 tests/footloose_tests/RUN                   |   3 +
 tests/footloose_tests/RUN_FL_physical       |   4 -
 tests/footloose_tests/RUN_FL_poisson        |   4 -
 tests/footloose_tests/input_FL_physical.nml | 175 --------------------
 tests/footloose_tests/input_FL_poisson.nml  | 170 -------------------
 10 files changed, 86 insertions(+), 544 deletions(-)
 create mode 100755 tests/footloose_tests/RUN
 delete mode 100755 tests/footloose_tests/RUN_FL_physical
 delete mode 100755 tests/footloose_tests/RUN_FL_poisson
 delete mode 100644 tests/footloose_tests/input_FL_physical.nml
 delete mode 100644 tests/footloose_tests/input_FL_poisson.nml

diff --git a/.gitignore b/.gitignore
index cbab8f9..007fd81 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,4 @@
 CVS
 *~
-*core
\ No newline at end of file
+*core
+notes
\ No newline at end of file
diff --git a/src/icebergs.F90 b/src/icebergs.F90
index d00f683..25c0f94 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -54,6 +54,7 @@ module ice_bergs
 use ice_bergs_framework, only: mts
 use ice_bergs_framework, only: dem_tests_init
 use ice_bergs_framework, only: dem, save_bond_forces
+use ice_bergs_framework, only: footloose
 use ice_bergs_framework, only: orig_dem_moment_of_inertia, no_frac_first_ts
 use ice_bergs_framework, only: A68_test, A68_xdisp, A68_ydisp
 use ice_bergs_framework, only: set_constant_interaction_length_and_width, skip_first_outer_mts_step
@@ -188,7 +189,7 @@ subroutine debugwriteandstop(bergs)
   bergs%debug_write=.true.
   call record_posn(bergs)
   call move_all_trajectories(bergs)
-  call write_trajectory(bergs%trajectories, bergs%save_short_traj, bergs%save_fl_traj, bergs%fl_r, bergs%traj_name)
+  call write_trajectory(bergs%trajectories, bergs%save_short_traj, bergs%save_fl_traj, bergs%traj_name)
   if (save_bond_traj) call write_bond_trajectory(bergs%bond_trajectories, bergs%bond_traj_name)
   call mpp_sync()
   call error_mesg('KID', 'WRITE AND STOP!!!', FATAL)
@@ -2513,7 +2514,7 @@ end subroutine dump_locvel
 
 
 !> Footloose (FL) mechanism
-!> Based on England et al. (2020) Modeling the breakup of tabular icebergs. Sci. Adv.
+!> Based on Huth et al. (2022) Parameterizing Tabular-Iceberg Decay in an Ocean Model. JAMES.
 subroutine footloose_calving(bergs, time)
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
@@ -2522,7 +2523,7 @@ subroutine footloose_calving(bergs, time)
   type(iceberg), pointer :: this
   type(icebergs_gridded), pointer :: grd
   type(bond), pointer :: current_bond
-  real, save :: N_max, youngs, poisson, l_c, lw_c, B_c, exp_nlambda, rn
+  real, save :: N_max, youngs, poisson, l_c, lw_c, B_c, rn
   real, save :: e1, drho, sigmay, lfootparam
   real :: foot_l,foot_mass, foot_area
   type(randomNumberStream),save :: rns ! Random numbers
@@ -2549,7 +2550,6 @@ subroutine footloose_calving(bergs, time)
       N_max=0.0
     endif
 
-    !for fl_use_l_scale
     e1=exp(0.25*pi)
     drho=rho_seawater-bergs%rho_bergs
     sigmay=bergs%fl_strength*1000 !strength (Pa)
@@ -2560,7 +2560,6 @@ subroutine footloose_calving(bergs, time)
     l_c  = pi/(2.*sqrt(2.)) !for length-scale of child iceberg
     lw_c = 1./(gravity*rho_seawater) !for buoyancy length
     B_c  = youngs/(12.*(1.-poisson**2.)) !for bending stiffness
-    exp_nlambda=exp(-bergs%fl_r) !e^(-r*dt)
     seed = constructSeed(mpp_pe(),mpp_pe(),time) !Seed random numbers for Poisson distribution
     rns = initializeRandomNumberStream(seed)
     call getRandomNumbers(rns, rn)
@@ -2590,15 +2589,6 @@ subroutine footloose_calving(bergs, time)
         l_b3 = 3*l_b
 
         !---Determine k, the number of child bergs to calve via the footloose mechanism---!
-        !Bergs%fl_r is the average number of bergs to calve over the time increment
-        !given in seconds by bergs%fl_r_s. K is set according to a Poisson distribution
-        !or may be set directly equal to bergs%fl_r.
-        !England et al., 2020 used fl_r=4, fl_r_s= 86400 seconds (1 day), and daily
-        !timesteps, so that k (a whole number) gave the number of bergs to calve each
-        !timestep. Here, smaller timesteps are typically used, so k is scaled accordingly.
-        !Therefore, k is no longer a whole number, and is instead accumulated over time
-        !on this%fl_k. Then, floor(this%fl_k) child bergs are calved each timestep, after
-        !which, this number of child bergs is subtracted from this%fl_k
 
         !A max possible number of child bergs to calve, max_k, is set to prevent footloose
         !calving on very small icebergs or interior elements of bonded conglomerates:
@@ -2607,84 +2597,35 @@ subroutine footloose_calving(bergs, time)
             max_k=0          !no FL calving allowed for interior bergs
           else
             call max_k_for_edge_elements
+            call error_mesg('KID,footloose_calving', &
+              'Bonded footloose calving not yet fully implemented!', FATAL)
           endif
         else
           !non-bonded berg length must be greater than 3*(l_b) for FL calving. Set max_k accordingly.
-          if (bergs%fl_k_scale_by_perimeter>0) then
-            !the minimum length and width the parent berg can have after footloose
-            c = ceiling((L-l_b3)/l_b3); Lmin = L - c*l_b3;
-            c = ceiling((W-l_b3)/l_b3); Wmin = W - c*l_b3;
+          !the minimum length and width the parent berg can have after footloose
+          c = ceiling((L-l_b3)/l_b3); Lmin = L - c*l_b3;
+          c = ceiling((W-l_b3)/l_b3); Wmin = W - c*l_b3;
 
-            max_k = max(floor((L*W - Lmin*Wmin)/(l_b3*l_b)),0)
-          else
-            max_k = max(ceiling((L-l_b3)*W/(3*l_b**2.)),0)
-            if (L-max_k*3.*(l_b**2.)/W<=0.) max_k = max_k-1
-          endif
+          max_k = max(floor((L*W - Lmin*Wmin)/(l_b3*l_b)),0)
         endif
 
-        if (bergs%fl_use_l_scale) then
-          if (max_k==0) then
-            k=0
-          else
-            !here, fl_k is the accumulated foot area from erosion - side melt
-            foot_l = lfootparam*T/l_w
-            !this is the foot area needed to calve a single footloose berg
-            foot_area = foot_l * l_b3
-            foot_area = bergs%fl_l_scale * foot_area !option to scale the foot area needed to calve
-            k=floor(this%fl_k/foot_area)
-            if (k>max_k) k=max_k
-            this%fl_k=this%fl_k-k*foot_area
-          endif
+        if (max_k==0) then
+          k=0
         else
-          if (max_k==0) then
-            k=0
-            this%fl_k=0
-          else
-            ! If sea ice concentration is <=50%, generate footloose child bergs
-            IC=min(1.,grd%cn(grdi,grdj)+bergs%sicn_shift) !sea ice only known on grid when this routine is called
-            if (.not. IC>0.5) then
-
-              if (bergs%fl_use_poisson_distribution) then
-                k=0; pu=1.0
-                do while (pu >= exp_nlambda)
-                  call getRandomNumbers(rns, rn)
-                  pu=pu*rn
-                  k=k+1
-                enddo
-                k=k-1.0 !FL calving rate (per day or year)
-              else
-                k=bergs%fl_r
-              endif
-
-              if (bergs%iceberg_bonds_on) k=k*((N_max-N_bonds)/N_max) !reduce FL calve rate by number of bonds
-              k=k*(bergs%dt/bergs%fl_r_s) !scale k to dt
-              if (bergs%fl_k_scale_by_perimeter>0) then
-                if (c == 0) then
-                  !W not eligible for footloose, so only scale by length
-                  k = k * 2.*L/bergs%fl_k_scale_by_perimeter
-                else
-                  k = k * 2.*(L+W)/bergs%fl_k_scale_by_perimeter
-                endif
-              endif
-              this%fl_k=this%fl_k+k       !update fl_k
-            end if
-
-            k=floor(this%fl_k)
-          endif
-
-          if (k>max_k) then
-            k=max_k
-            this%fl_k=0.
-          else
-            this%fl_k=this%fl_k-k !save the remainder for the next timestep
-          endif
+          !here, fl_k is the accumulated foot area from erosion - side melt
+          foot_l = lfootparam*T/l_w
+          !this is the foot area needed to calve a single footloose berg
+          foot_area = foot_l * l_b3
+          k=floor(this%fl_k/foot_area)
+          if (k>max_k) k=max_k
+          this%fl_k=this%fl_k-k*foot_area
         endif
 
         !if there is footloose calving, create the new bergs and reduce length of parent berg
         if (k>0) then
 
           !new parent berg length (Ln) and width (Wn), and change in area (dA):
-          if (bergs%fl_k_scale_by_perimeter>0 .and. c>0) then
+          if (c>0) then
             !for scale by perimeter, both the length and width are reduced by ds
             ds = 0.5*( (L+W) - sqrt( (L+W)**2. - 4. * (l_b3*l_b*k) ) )
             Ln = L-ds; Wn=W-ds
@@ -2702,7 +2643,7 @@ subroutine footloose_calving(bergs, time)
 
           if (bergs%fl_style.eq.'new_bergs') then
             !calve and track footloose bergs
-            if (bergs%displace_fl_bergs .and. .not. bergs%fl_use_poisson_distribution) call getRandomNumbers(rns, rn)
+            if (bergs%displace_fl_bergs .and. .not. bergs%fl_init_child_xy_by_pe) call getRandomNumbers(rns, rn)
             call get_footloose_displacement
             call calve_fl_icebergs(bergs,this,k,l_b,fl_disp_x,fl_disp_y)
             bergs%nbergs_calved_fl=bergs%nbergs_calved_fl+1
@@ -2735,7 +2676,7 @@ subroutine footloose_calving(bergs, time)
 
       !Optionally, create a new berg from the FL bits if their mass exceeds a threshold
       if (this%mass_of_fl_bits*this%mass_scaling > bergs%new_berg_from_fl_bits_mass_thres) then
-        if (bergs%displace_fl_bergs .and. .not. bergs%fl_use_poisson_distribution) call getRandomNumbers(rns, rn)
+        if (bergs%displace_fl_bergs .and. .not. bergs%fl_init_child_xy_by_pe) call getRandomNumbers(rns, rn)
         call get_footloose_displacement
         k=floor(this%mass_of_fl_bits*this%mass_scaling/bergs%new_berg_from_fl_bits_mass_thres)
         call calve_fl_icebergs(bergs,this,k,l_b,fl_disp_x,fl_disp_y,berg_from_bits=.true.)
@@ -3082,28 +3023,20 @@ subroutine thermodynamics(bergs)
 
       !if footloose is based on length of foot, accumulate side mass loss on fl_k
       !note: this only works when bergs%use_operator_splitting=.true.
-      if (bergs%fl_r>0.) then
-        if (bergs%fl_use_l_scale .and. this%fl_k>=0) then
+      if (bergs%footloose) then
+        if (this%fl_k>=0) then
           l_b3 = 3.*l_c*(lw_c*bergs%fl_youngs*B_c*(Tn**3.))**0.25 !child berg length x 3
           if (L>l_b3) then !do not accumulate side made loss for sides < l_b3
             fb = Tn*(1.-bergs%rho_bergs/rho_seawater) !freeboard
             kd = Tn-fb !keel depth
             if (W>l_b3) then
-              if (bergs%fl_l_scale_erosion_only) then
-                this%fl_k=this%fl_k + (dMe/fb - dMv/kd)/bergs%rho_bergs !horiz area from erosion - from buoy conv
-                if (this%fl_k<0) this%fl_k=0
-              else
-                this%fl_k= this%fl_k + (dMe + dMv)/Tn
-              endif
+              this%fl_k=this%fl_k + (dMe/fb - dMv/kd)/bergs%rho_bergs !horiz area from erosion - from buoy conv
+              if (this%fl_k<0) this%fl_k=0
             else
               dMv_l=dMv*(Wn1 + W)/(2.*(Ln1 + W)) !mass loss from length from buoyant convection
               dMe_l=dMe*(Wn+ Wn1)/(2.*(Ln+ Wn1)) !mass loss from length from erosion
-              if (bergs%fl_l_scale_erosion_only) then
-                this%fl_k=this%fl_k + (dMe_l/fb - dMv_l/kd)/bergs%rho_bergs
-                if (this%fl_k<0) this%fl_k=0
-              else
-                this%fl_k= this%fl_k + (dMe_l + dMv_l)/Tn
-              endif
+              this%fl_k=this%fl_k + (dMe_l/fb - dMv_l/kd)/bergs%rho_bergs
+              if (this%fl_k<0) this%fl_k=0
             endif
           endif
         endif
@@ -3463,8 +3396,8 @@ subroutine fl_bits_dimensions(bergs,this,L_fl,W_fl,T_fl)
 
   l_w  = (lw_c*bergs%fl_youngs*B_c*(this%thickness**3.))**0.25  !buoyancy length
   l_b  = l_c*l_w !length of a freshly calved footloose child berg
-  L_fl = bergs%fl_bits_scale_l*3.*l_b; W_fl=bergs%fl_bits_scale_w*l_b
-  T_fl=bergs%fl_bits_scale_t*this%thickness
+  L_fl = 3.*l_b; W_fl = l_b
+  T_fl = this%thickness
   call rolling(bergs,T_fl,W_fl,L_fl)
 end subroutine fl_bits_dimensions
 
@@ -5533,7 +5466,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 
   call mpp_clock_begin(bergs%clock_fl1)
   ! Footloose mechanism part 1: calve the child icebergs
-  if (bergs%fl_r>0.) call footloose_calving(bergs, time)
+  if (bergs%footloose) call footloose_calving(bergs, time)
   call mpp_clock_end(bergs%clock_fl1)
 
   call mpp_clock_begin(bergs%clock_com2)
@@ -5561,7 +5494,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
 
   call mpp_clock_begin(bergs%clock_fl2)
   ! Footloose mechanism part 2:
-  if (bergs%fl_r>0.) then
+  if (bergs%footloose) then
     !delete any edge elements that have fully calved from the footloose mechanism
     if (bergs%iceberg_bonds_on) call delete_fully_fl_calved_edge_elements(bergs)
     !child bergs become interactive once they are out of contact range of any other
@@ -5599,7 +5532,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   if (sample_traj .or. bergs%writeandstop) call record_posn(bergs)
   if (write_traj .or. bergs%writeandstop) then
     call move_all_trajectories(bergs)
-    call write_trajectory(bergs%trajectories, bergs%save_short_traj, bergs%save_fl_traj, bergs%fl_r, bergs%traj_name)
+    call write_trajectory(bergs%trajectories, bergs%save_short_traj, bergs%save_fl_traj, bergs%traj_name)
     if (save_bond_traj) call write_bond_trajectory(bergs%bond_trajectories, bergs%bond_traj_name)
   endif
 
@@ -8276,7 +8209,7 @@ subroutine icebergs_end(bergs)
   call move_all_trajectories(bergs, delete_bergs=.true.)
 
   if (.not. bergs%ignore_traj) then
-    call write_trajectory(bergs%trajectories, bergs%save_short_traj, bergs%save_fl_traj, bergs%fl_r, bergs%traj_name)
+    call write_trajectory(bergs%trajectories, bergs%save_short_traj, bergs%save_fl_traj, bergs%traj_name)
     if (save_bond_traj) call write_bond_trajectory(bergs%bond_trajectories, bergs%bond_traj_name)
   endif
 
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 749654a..0a61f82 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -62,6 +62,7 @@ module ice_bergs_framework
 logical :: break_bonds_on_sub_steps=.false.
 logical :: skip_first_outer_mts_step=.false.
 logical :: no_frac_first_ts=.false.
+logical :: footloose=.false. !< Turn footloose calving on/off
 
 !Public params !Niki: write a subroutine to expose these
 public nclasses,buffer_width,buffer_width_traj,buffer_width_bond_traj
@@ -72,6 +73,7 @@ module ice_bergs_framework
 public dem, save_bond_forces, fracture_criterion, orig_dem_moment_of_inertia
 public short_step_mts_grounding, radius_based_drag
 public A68_test, A68_xdisp, A68_ydisp
+public footloose
 
 !Public types
 public icebergs_gridded, xyt, iceberg, icebergs, buffer, bond, bond_xyt
@@ -616,26 +618,17 @@ module ice_bergs_framework
   real :: constant_radius
   real :: ocean_drag_scale=1. !< Scaling factor for the ocean drag coefficients
   ! Footloose calving parameters
-  logical :: fl_use_poisson_distribution=.true. !< fl_r is (T) mean of Poisson distribution to determine k, or (F) k=fl_r
-  logical :: fl_use_perimeter=.false. !< scale number of footloose bergs to calve by perimeter of the parent berg
+  logical :: footloose=.false. !< Turn footloose calving on/off
+  logical :: fl_init_child_xy_by_pe=.true. !< True: position of a new footloose child berg along the parent perimeter is random, yet constant for each PE (old bug). False: fully-random.
   real :: fl_youngs=1.e8 !< Young's modulus for footloose calculations (Pa)
   real :: fl_strength=500. !< yield stress for footloose calculations (kPa)
-  logical :: fl_use_l_scale=.false. !< footloose based on side melt and/or erosion
-  real :: fl_l_scale=1. !< scaling factor for footloose based on side melt
-  logical :: fl_l_scale_erosion_only=.true. !< fl according to erosion - buoyant convection
-  real :: fl_r=0. !< footloose average number of bergs calved per fl_r_s
-  real :: fl_r_s=0. !< seconds over which fl_r footloose bergs calve
   logical :: displace_fl_bergs=.true. !< footloose berg positions are randomly assigned along edges of parent berg
   character(len=11) :: fl_style='new_bergs' !< Evolve footloose bergs individually as 'new_bergs', or as a group with size 'fl_bits'
   logical :: fl_bits_erosion_to_bergy_bits=.true. !< Erosion from footloose bits becomes bergy bits
-  real :: fl_k_scale_by_perimeter=0 !< If greater than 0, scales FL k by (berg perimeter (m))/(this scaling (m))
   real :: new_berg_from_fl_bits_mass_thres=huge(0.) ! Create a new berg from FL bits when mass_of_fl_bits exceeds this value
-  real :: fl_bits_scale_l=0.9 !< For determining dimensions of FL bits berg; FL_bits length    = fl_bits_scale_l * 3*l_b
-  real :: fl_bits_scale_w=0.9 !< For determining dimensions of FL bits berg; FL_bits width     = fl_bits_scale_w * 3*l_b
-  real :: fl_bits_scale_t=0.9 !< For determining dimensions of FL bits berg; FL_bits thickness = fl_bits_scale_t * T
 
   !backwards compatibility
-  logical :: old_interp_flds_order=.false. !< Use old order of when to interpolate grid variables to bergs. Will be false if MTS, DEM, or footloose (fl_r>0)
+  logical :: old_interp_flds_order=.false. !< Use old order of when to interpolate grid variables to bergs. Will be false if MTS, DEM, or footloose
 end type icebergs
 
 !> Read original restarts. Needs to be module global so can be public to icebergs_mod.
@@ -644,9 +637,9 @@ module ice_bergs_framework
 
 !> Version of file provided by CPP macro (usually set to git hash)
 #ifdef _FILE_VERSION
-  character(len=128) :: version = _FILE_VERSION !< Version of file
+character(len=128) :: version = _FILE_VERSION !< Version of file
 #else
-  character(len=128) :: version = 'unknown' !< Version of file
+character(len=128) :: version = 'unknown' !< Version of file
 #endif
 
 !> Set a value in the buffer at position (counter,n) after incrementing counter
@@ -834,24 +827,15 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: constant_length=0. ! If constant_interaction_LW, the constant length used. If zero in the nml, will be set to max initial L
 real :: constant_width=0. ! If constant_interaction_LW, the constant width used. If zero in the nml, will be set to max initial W
 real :: ocean_drag_scale=1. !< Scaling factor for the ocean drag coefficients
-! Footloose calving parameters [England et al (2020) Modeling the breakup of tabular icebergs. Sci. Adv.]
-logical :: fl_use_poisson_distribution=.true. ! fl_r is (T) mean of Poisson distribution to determine k, or (F) k=fl_r
-logical :: fl_use_perimeter=.false. ! scale number of footloose bergs to calve by perimeter of the parent berg
+! Footloose calving parameters
+!logical :: footloose=.false. !< Turn footloose calving on/off
+logical :: fl_init_child_xy_by_pe=.true. !< True: position of a new footloose child berg along the parent perimeter is random, yet constant for each PE (old bug). False: fully-random.
 real :: fl_youngs=1.e8 !< Young's modulus for footloose calculations (Pa)
 real :: fl_strength=500. !< yield stress for footloose calculations (kPa)
-logical :: fl_use_l_scale=.false. !< footloose based on side melt
-real :: fl_l_scale=1. !< scaling factor for footloose based on side melt and/or erosion
-logical :: fl_l_scale_erosion_only=.true. !< fl according to erosion - buoyant convection
-real :: fl_r=0. ! footloose average number of bergs calved per fl_r_s
-real :: fl_r_s=0. ! seconds over which fl_r footloose bergs calve
 logical :: displace_fl_bergs=.true. ! footloose berg positions are randomly assigned along edges of parent berg
 character(len=11) :: fl_style='new_bergs' ! Evolve footloose bergs individually as 'fl_bits', or as a group with size 'bergy_bits' or 'mean_size'
 logical :: fl_bits_erosion_to_bergy_bits=.true. ! Erosion from footloose bits becomes bergy bits
-real :: fl_k_scale_by_perimeter=0 ! If greater than 0, scales FL k by (berg perimeter (m))/(this scaling (m))
 real :: new_berg_from_fl_bits_mass_thres=huge(0.) ! Create a new berg from FL bits when mass_of_fl_bits exceeds this value
-real :: fl_bits_scale_l=0.9 ! For determining dimensions of FL bits berg; FL_bits length    = fl_bits_scale_l * 3*l_b
-real :: fl_bits_scale_w=0.9 ! For determining dimensions of FL bits berg; FL_bits width     = fl_bits_scale_w * l_b
-real :: fl_bits_scale_t=0.9 ! For determining dimensions of FL bits berg; FL_bits thickness = fl_bits_scale_t * T
 
 
 namelist /icebergs_nml/ verbose, budget, halo,  traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,traj_name,bond_traj_name,&
@@ -876,11 +860,11 @@ subroutine ice_bergs_framework_init(bergs, &
          debug_write,cdrag_grounding,h_to_init_grounding,frac_thres_scaling,frac_thres_n,frac_thres_t,save_bond_traj,&
          remove_unused_bergs,force_convergence,explicit_inner_mts,convergence_tolerance,dem,ignore_tangential_force,poisson,&
          dem_spring_coef,dem_damping_coef,dem_beam_test,constant_interaction_LW,constant_length,constant_width,&
-         fl_use_poisson_distribution, fl_use_perimeter, fl_r, fl_r_s,displace_fl_bergs,&
-         fl_style,fl_bits_erosion_to_bergy_bits,fl_k_scale_by_perimeter, save_fl_traj,&
-         new_berg_from_fl_bits_mass_thres,fl_bits_scale_l,fl_bits_scale_w,fl_bits_scale_t,separate_distrib_for_n_hemisphere,&
-         initial_mass_n, distribution_n, mass_scaling_n, initial_thickness_n, fl_use_l_scale, fl_l_scale,&
-         fl_l_scale_erosion_only, fl_youngs, fl_strength,  save_all_traj_year, save_nonfl_traj_by_class,&
+         fl_init_child_xy_by_pe, footloose,displace_fl_bergs,&
+         fl_style,fl_bits_erosion_to_bergy_bits, save_fl_traj,&
+         new_berg_from_fl_bits_mass_thres,separate_distrib_for_n_hemisphere,&
+         initial_mass_n, distribution_n, mass_scaling_n, initial_thickness_n,&
+         fl_youngs, fl_strength,  save_all_traj_year, save_nonfl_traj_by_class,&
          save_traj_by_class_start_mass_thres_n, save_traj_by_class_start_mass_thres_s,traj_area_thres_sntbc,&
          traj_area_thres_fl,tau_is_velocity, ocean_drag_scale, A68_test, &
          A68_xdisp,A68_ydisp,use_broken_bonds_for_substep_contact,print_fracture,&
@@ -1305,7 +1289,7 @@ subroutine ice_bergs_framework_init(bergs, &
 endif
 if (save_short_traj) buffer_width_traj=6 ! This is the length of the short buffer used for abrevated traj
 if (save_fl_traj) then
-  if (fl_r>0) then
+  if (footloose) then
     buffer_width_traj=buffer_width_traj+8+2
   else
     buffer_width_traj=buffer_width_traj+4+2
@@ -1510,37 +1494,26 @@ subroutine ice_bergs_framework_init(bergs, &
   endif
   bergs%ocean_drag_scale=ocean_drag_scale
   ! Footloose calving parameters
-  bergs%fl_use_poisson_distribution=fl_use_poisson_distribution
-  bergs%fl_use_perimeter=fl_use_perimeter
+  bergs%footloose=footloose
+  bergs%fl_init_child_xy_by_pe=fl_init_child_xy_by_pe
   bergs%fl_youngs=fl_youngs
   bergs%fl_strength=fl_strength
-  bergs%fl_use_l_scale=fl_use_l_scale
-  bergs%fl_l_scale=fl_l_scale
-  bergs%fl_l_scale_erosion_only=fl_l_scale_erosion_only
   bergs%new_berg_from_fl_bits_mass_thres=new_berg_from_fl_bits_mass_thres
-  bergs%fl_r=fl_r
-  bergs%fl_r_s=fl_r_s
   bergs%displace_fl_bergs=displace_fl_bergs
   bergs%fl_style=fl_style
   bergs%fl_bits_erosion_to_bergy_bits=fl_bits_erosion_to_bergy_bits
-  bergs%fl_k_scale_by_perimeter=fl_k_scale_by_perimeter
-  bergs%fl_bits_scale_l=fl_bits_scale_l
-  bergs%fl_bits_scale_w=fl_bits_scale_w
-  bergs%fl_bits_scale_t=fl_bits_scale_t
-  if (bergs%fl_use_l_scale) then
-    bergs%fl_use_perimeter=.true.
-    bergs%fl_k_scale_by_perimeter=1
-    if (.not. bergs%use_operator_splitting) then
-      call error_mesg('KID, ice_bergs_framework_init', &
-        'use_operator_splitting must be true when fl_use_l_scale=.true.', FATAL)
-    endif
+
+  if (bergs%footloose .and. .not. bergs%use_operator_splitting) then
+    call error_mesg('KID, ice_bergs_framework_init', &
+      'use_operator_splitting must be true to use footloose!', FATAL)
   endif
 
+
   !backwards compatibility
-  if (.not. (bergs%mts .or. bergs%dem .or. bergs%fl_r>0.)) bergs%old_interp_flds_order=.true.
+  if (.not. (bergs%mts .or. bergs%dem .or. bergs%footloose)) bergs%old_interp_flds_order=.true.
 
   if (bergs%Runge_not_Verlet) then
-    if (bergs%mts .or. bergs%dem .or. bergs%fl_r>0.) then
+    if (bergs%mts .or. bergs%dem .or. bergs%footloose) then
       call error_mesg('KID, ice_bergs_framework_init', &
         'Runge_not_Verlet must be false to use MTS, DEM, or footloose!', FATAL)
     endif
@@ -3848,14 +3821,13 @@ subroutine increase_ibuffer(old, num_bergs, width)
 end subroutine increase_ibuffer
 
 !> Packs a trajectory entry into a buffer
-subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj, save_fl_traj, fl_r)
+subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj, save_fl_traj)
   ! Arguments
   type(xyt), pointer :: traj !< Trajectory entry to pack
   type(buffer), pointer :: buff !< Buffer to pack entry into
   integer, intent(in) :: n !< Position in buffer to place entry
   logical, intent(in) :: save_short_traj !< If true, only use a subset of trajectory data
   logical, intent(in) :: save_fl_traj !< If true, save masses and footloose parameters
-  real, intent(in) :: fl_r !< If >0 and save_fl_traj, save footloose parameters
   ! Local variables
   integer :: counter ! Position in stack
   integer :: cnt, ij
@@ -3878,7 +3850,7 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj, save_fl_traj,
     call push_buffer_value(buff%data(:,n),counter,traj%mass_of_bits)
     call push_buffer_value(buff%data(:,n),counter,traj%uvel)
     call push_buffer_value(buff%data(:,n),counter,traj%vvel)
-    if (fl_r>0) then
+    if (footloose) then
       call push_buffer_value(buff%data(:,n),counter,traj%mass_scaling)
       call push_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bits)
       call push_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bergy_bits)
@@ -3937,14 +3909,13 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj, save_fl_traj,
 end subroutine pack_traj_into_buffer2
 
 !> Unpacks a trajectory entry from a buffer
-subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj, save_fl_traj, fl_r)
+subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj, save_fl_traj)
   ! Arguments
   type(xyt), pointer :: first !< Trajectory list
   type(buffer), pointer :: buff !< Buffer from which to unpack
   integer, intent(in) :: n !< Position in buffer to unpack
   logical, intent(in) :: save_short_traj !< If true, only use a subset of trajectory data
   logical, intent(in) :: save_fl_traj !< If true, save masses and footloose parameters
-  real, intent(in) :: fl_r !< If >0 and save_fl_traj, save footloose parameters
   ! Local variables
   type(xyt) :: traj
   integer :: counter ! Position in stack
@@ -3979,7 +3950,7 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj, save_fl_tra
     call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_bits)
     call pull_buffer_value(buff%data(:,n),counter,traj%uvel)
     call pull_buffer_value(buff%data(:,n),counter,traj%vvel)
-    if (fl_r>0) then
+    if (footloose) then
       call pull_buffer_value(buff%data(:,n),counter,traj%mass_scaling)
       call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bits)
       call pull_buffer_value(buff%data(:,n),counter,traj%mass_of_fl_bergy_bits)
@@ -5817,7 +5788,7 @@ subroutine record_posn(bergs)
           posn%mass_of_bits=this%mass_of_bits
           posn%uvel=this%uvel
           posn%vvel=this%vvel
-          if (bergs%fl_r>0) then
+          if (bergs%footloose) then
             posn%mass_scaling=this%mass_scaling
             posn%mass_of_fl_bits=this%mass_of_fl_bits
             posn%mass_of_fl_bergy_bits=this%mass_of_fl_bergy_bits
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index 267085c..1274513 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -40,11 +40,13 @@ module ice_bergs_io
 use ice_bergs_framework, only: force_all_pes_traj
 use ice_bergs_framework, only: check_for_duplicates_in_parallel
 use ice_bergs_framework, only: split_id, id_from_2_ints, generate_id
-! for MTS/DEM/fracture:
+! for MTS/DEM/fracture/footloose:
 use ice_bergs_framework, only: mts,save_bond_traj
 use ice_bergs_framework, only: push_bond_posn, append_bond_posn
 use ice_bergs_framework, only: pack_bond_traj_into_buffer2,unpack_bond_traj_from_buffer2
 use ice_bergs_framework, only: dem, fracture_criterion, iceberg_bonds_on
+use ice_bergs_framework, only: footloose
+
 
 implicit none ; private
 
@@ -233,7 +235,7 @@ subroutine write_restart(bergs, time_stamp)
    allocate(id_cnt(nbergs))
    allocate(id_ij(nbergs))
 
-   if (bergs%fl_r>0) then
+   if (bergs%footloose) then
      allocate(fl_k(nbergs))
      allocate(mass_of_fl_bits(nbergs))
      allocate(mass_of_fl_bergy_bits(nbergs))
@@ -302,7 +304,7 @@ subroutine write_restart(bergs, time_stamp)
   id = register_restart_field(bergs_restart,filename,'heat_density',heat_density, &
                                             longname='heat density',units='J/kg')
 
-  if (bergs%fl_r>0) then
+  if (bergs%footloose) then
     id = register_restart_field(bergs_restart,filename,'fl_k',fl_k,longname='footloose calving k',units='m')
     id = register_restart_field(bergs_restart,filename,'mass_of_fl_bits',mass_of_fl_bits, &
       longname='mass of footloose bits',units='kg')
@@ -371,7 +373,7 @@ subroutine write_restart(bergs, time_stamp)
       mass_of_bits(i) = this%mass_of_bits
       heat_density(i) = this%heat_density
 
-      if (bergs%fl_r>0) then
+      if (bergs%footloose) then
         fl_k(i) = this%fl_k
         mass_of_fl_bits(i) = this%mass_of_fl_bits
         mass_of_fl_bergy_bits(i) = this%mass_of_fl_bergy_bits
@@ -422,7 +424,7 @@ subroutine write_restart(bergs, time_stamp)
              static_berg,  &
              heat_density)
 
-  if (bergs%fl_r>0.) then
+  if (bergs%footloose) then
     deallocate(                   &
                  fl_k,            &
                  mass_of_fl_bits, &
@@ -1689,12 +1691,11 @@ subroutine read_ocean_depth(grd)
 end subroutine read_ocean_depth
 
 !> Write a trajectory-based diagnostics file
-subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r, traj_name)
+subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, traj_name)
 ! Arguments
 type(xyt), pointer :: trajectory !< An iceberg trajectory
 logical, intent(in) :: save_short_traj !< If true, record less data
 logical, intent(in) :: save_fl_traj !< If true, save masses and footloose data
-real, intent(in) :: fl_r !< If >0 and save_fl_traj, save footloose params
 character(len=70) :: traj_name !< name of trajectory file
 ! Local variables
 integer :: iret, ncid, i_dim, i
@@ -1752,7 +1753,7 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r, tra
            call increase_ibuffer(ibuffer_io, ntrajs_rcvd_io,buffer_width_traj)
            call mpp_recv(ibuffer_io%data, ntrajs_rcvd_io*buffer_width_traj,from_pe=from_pe, tag=COMM_TAG_12)
            do i=1, ntrajs_rcvd_io
-              call unpack_traj_from_buffer2(traj4io, ibuffer_io, i, save_short_traj, save_fl_traj, fl_r)
+              call unpack_traj_from_buffer2(traj4io, ibuffer_io, i, save_short_traj, save_fl_traj)
            enddo
        endif
      enddo
@@ -1760,7 +1761,7 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r, tra
      ! Pack and send trajectories to the root PE for this I/O tile
      do while (associated(trajectory))
        ntrajs_sent_io = ntrajs_sent_io +1
-       call pack_traj_into_buffer2(trajectory, obuffer_io, ntrajs_sent_io, save_short_traj, save_fl_traj, fl_r)
+       call pack_traj_into_buffer2(trajectory, obuffer_io, ntrajs_sent_io, save_short_traj, save_fl_traj)
        this => trajectory ! Need to keep pointer in order to free up the links memory
        trajectory => trajectory%next ! This will eventually result in trajectory => null()
        deallocate(this) ! Delete the link from memory
@@ -1830,7 +1831,7 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r, tra
         mbid = inq_varid(ncid, 'mass_of_bits')
         uvelid = inq_varid(ncid, 'uvel')
         vvelid = inq_varid(ncid, 'vvel')
-        if (fl_r>0) then
+        if (footloose) then
           msid = inq_varid(ncid, 'mass_scaling')
           mflbid = inq_varid(ncid, 'mass_of_fl_bits')
           mflbbid = inq_varid(ncid, 'mass_of_fl_bergy_bits')
@@ -1903,7 +1904,7 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r, tra
         mbid = def_var(ncid, 'mass_of_bits', NF_DOUBLE, i_dim)
         uvelid = def_var(ncid, 'uvel', NF_DOUBLE, i_dim)
         vvelid = def_var(ncid, 'vvel', NF_DOUBLE, i_dim)
-        if (fl_r>0) then
+        if (footloose) then
           msid = def_var(ncid, 'mass_scaling', NF_DOUBLE, i_dim)
           mflbid = def_var(ncid, 'mass_of_fl_bits', NF_DOUBLE, i_dim)
           mflbbid = def_var(ncid, 'mass_of_fl_bergy_bits', NF_DOUBLE, i_dim)
@@ -1985,7 +1986,7 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r, tra
         call put_att(ncid, uvelid, 'units', 'm/s')
         call put_att(ncid, vvelid, 'long_name', 'meridional spped')
         call put_att(ncid, vvelid, 'units', 'm/s')
-        if (fl_r>0) then
+        if (footloose) then
           call put_att(ncid, msid, 'long_name', 'mass_scaling')
           call put_att(ncid, msid, 'units', 'dimensionless')
           call put_att(ncid, mflbid, 'long_name', 'mass_of_fl_bits')
@@ -2105,7 +2106,7 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, fl_r, tra
         call put_double(ncid, mbid, i, this%mass_of_bits)
         call put_double(ncid, uvelid, i, this%uvel)
         call put_double(ncid, vvelid, i, this%vvel)
-        if (fl_r>0) then
+        if (footloose) then
           call put_double(ncid, msid, i, this%mass_scaling)
           call put_double(ncid, mflbid, i, this%mass_of_fl_bits)
           call put_double(ncid, mflbbid, i, this%mass_of_fl_bergy_bits)
diff --git a/tests/footloose_tests/README b/tests/footloose_tests/README
index 5bb4c4f..57c03e5 100644
--- a/tests/footloose_tests/README
+++ b/tests/footloose_tests/README
@@ -1,25 +1,11 @@
 Testing for footloose mechanism parameterization in (non-bonded mode only).
 
-"FL_poisson" tests a scheme similar to England et al 2020, where footloose child bergs are created according to a Poisson distribution.
+Tests the Huth et al 2022 scheme, where beam theory is used to determine when to calve footloose child bergs according to the size of the underwater foot on the parent berg, which is determined by tracking side melt and erosion over time.
 
-"FL_physical" tests the Huth et al 2022 scheme, where beam theory is used to determine when to calve footloose child bergs according to the size of the underwater foot on the parent berg, which is determined by tracking side melt and erosion over time.
-
-In both tests, we use the Huth et al 2022 footloose child berg binning scheme.
+This test uses the Huth et al 2022 footloose child berg binning scheme.
 
 1. Make the iceberg input files: cd makeberg; ./RUN; cd ..
-2. run the model: ./RUN_FL_poisson or ./RUN_FL_physical
+2. run the model: ./RUN
 3. animate the results:
 
-./animate_trajectories.py -fname="FL_poisson.nc"
-or
 ./animate_trajectories.py -fname="FL_physical.nc"
-
-
-!!for regression testing:
-Note the "write_restart berg" chksums in each of the .nml files that are called by the model run commands, and also printed below:
-
-FL_poisson:
-chksum=1239600118 chksum2=1239600118 chksum3=-1474195494 chksum4=-1474195494 chksum5=0 #=8
-
-FL_physical:
-chksum=-461793748 chksum2=-461793748 chksum3=-1042515716 chksum4=-1042515716 chksum5=0 #=12
diff --git a/tests/footloose_tests/RUN b/tests/footloose_tests/RUN
new file mode 100755
index 0000000..98b0f1b
--- /dev/null
+++ b/tests/footloose_tests/RUN
@@ -0,0 +1,3 @@
+rm FL_physical.nc
+rm FL_physical.nc.*
+srun -n4 ./../../build/bergs.x
\ No newline at end of file
diff --git a/tests/footloose_tests/RUN_FL_physical b/tests/footloose_tests/RUN_FL_physical
deleted file mode 100755
index c0fdd06..0000000
--- a/tests/footloose_tests/RUN_FL_physical
+++ /dev/null
@@ -1,4 +0,0 @@
-rm iceberg_trajectories.nc
-rm iceberg_trajectories.nc.*
-cp input_FL_physical.nml input.nml
-srun -n4 ./../../build/bergs.x
\ No newline at end of file
diff --git a/tests/footloose_tests/RUN_FL_poisson b/tests/footloose_tests/RUN_FL_poisson
deleted file mode 100755
index 6029355..0000000
--- a/tests/footloose_tests/RUN_FL_poisson
+++ /dev/null
@@ -1,4 +0,0 @@
-rm iceberg_trajectories.nc
-rm iceberg_trajectories.nc.*
-cp input_FL_poisson.nml input.nml
-srun -n4 ./../../build/bergs.x
\ No newline at end of file
diff --git a/tests/footloose_tests/input_FL_physical.nml b/tests/footloose_tests/input_FL_physical.nml
deleted file mode 100644
index 6b4d7f5..0000000
--- a/tests/footloose_tests/input_FL_physical.nml
+++ /dev/null
@@ -1,175 +0,0 @@
-!!KID, bergs_chksum: write_restart berg chksum=-461793748 chksum2=-461793748 chksum3=-1042515716 chksum4=-1042515716 chksum5=0 #=12
-
-
-&icebergs_driver_nml
-  ni=20 !number of elements, x direction
-  nj=20 !number of elements, y direction
-  ibdt=10.0 !1800.0 !86400.0 !seconds
-  ibuo=1.0 !ocean x velocity
-  ibvo=0.1 !ocean y velocity (if sin_test=true, will vary as ibvo*sin(y*2*pi/(4*gridres)) + gridres )
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibua=-1.0 !wind x velocity
-  ibuy=0.0  !wind y velocity
-  ibhrs=192 !total simulation hours
-  nmax=99999999 !max number of timesteps
-  saverestart=.true.
-  halo=3
-  debug=.false.
-  gridres=1000.
-  sst=-0.5
-  fl_test=.true.
-/
-
-
-&icebergs_nml
-
-    traj_name=FL_physical.nc
-    bond_traj_name=FL_physical_bonds.nc
-
-    !defaults given in parentheses:
-
-    fl_r=1        !(4) average number of footloose bergs to calve per fl_r_s seconds
-    fl_r_s=0  !(86400) time in s over which to calve, on average, fl_r footloose bergs
-    displace_fl_bergs=.true. !(T) randomly assign FL berg positions to sides of parent berg
-    fl_style='fl_bits' !'fl_bits' !('new_bergs'). Can also group FL bergs into 'fl_bits'
-    fl_youngs=1.e8 !Young's modulus for footloose calculations (Pa)
-    fl_strength=250. !yield stress for footloose calculations (kPa)
-    fl_use_l_scale=.true. !scaling factor for footloose based on side melt
-    fl_k_scale_by_perimeter=1 !If greater than 0, scales FL k by (berg perimeter (m))/(this scaling (m))
-    new_berg_from_fl_bits_mass_thres=3.e11  !Create a new berg from FL bits when mass_of_fl_bits exceeds this value
-    fl_l_scale_erosion_only=.true. !fl according to erosion - buoyant convection
-    fl_use_poisson_distribution=.false. !fl_r is (T) mean of Poisson distribution to determine k, or (F) k=fl_r
-    mts=.false. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=1 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
-    !contact_distance=0 !3.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    !contact_spring_coef=1.e-5!(default=spring_coeff) Berg spring coeff for collisions
-
-    halo=3 !(4) halo width
-    Lx=20000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.True. !(T) Point in cell can be found assuming regular Cartesian grid
-    !hexagonal_icebergs=.True. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    rho_bergs=850. ! (850) iceberg density
-    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=1.0 ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.true. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0.0 !4 !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.false.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.false.!.true.!.false. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors
-
-    verbose=.true. !(F) Be verbose to stderr
-    verbose_hrs=24 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !1 !(24) sampling period for trajectory storage
-    traj_write_hrs=24 ! (480) Period for writing sampled trajectories to disk
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    save_fl_traj=.true. !(T) True save masses and footloose parameters in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    length_for_manually_initialize_bonds=-1.e3!0.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/footloose_tests/input_FL_poisson.nml b/tests/footloose_tests/input_FL_poisson.nml
deleted file mode 100644
index feace6a..0000000
--- a/tests/footloose_tests/input_FL_poisson.nml
+++ /dev/null
@@ -1,170 +0,0 @@
-!!KID, bergs_chksum: write_restart berg chksum=1239600118 chksum2=1239600118 chksum3=-1474195494 chksum4=-1474195494 chksum5=0 #=8
-
-
-&icebergs_driver_nml
-  ni=20 !number of elements, x direction
-  nj=20 !number of elements, y direction
-  ibdt=10.0 !1800.0 !86400.0 !seconds
-  ibuo=0.1 !ocean x velocity
-  ibvo=0.05 !ocean y velocity (if sin_test=true, will vary as ibvo*sin(y*2*pi/(4*gridres)) + gridres )
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=192 !total simulation hours
-  nmax=99999999 !max number of timesteps
-  saverestart=.true.
-  halo=3
-  debug=.false.
-  gridres=1000.
-  sst=-2
-  !sin_test=.true.
-  fl_test=.true.
-/
-
-
-&icebergs_nml
-
-    traj_name=FL_poisson.nc
-    bond_traj_name=FL_poisson_bonds.nc
-    
-    !defaults given in parentheses:
-
-    fl_r=4        !(4) average number of footloose bergs to calve per fl_r_s seconds
-    fl_r_s=86400  !(86400) time in s over which to calve, on average, fl_r footloose bergs
-    displace_fl_bergs=.true. !(T) randomly assign FL berg positions to sides of parent berg
-    fl_style='fl_bits' !('new_bergs'). Can also group FL bergs into 'fl_bits'
-    new_berg_from_fl_bits_mass_thres=8.e11 !Create a new berg from FL bits when mass_of_fl_bits exceeds this value
-    fl_use_poisson_distribution=.true.
-
-    mts=.false. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=1 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
-    !contact_distance=0 !3.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    !contact_spring_coef=1.e-5!(default=spring_coeff) Berg spring coeff for collisions
-
-    halo=3 !(4) halo width
-    Lx=20000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.True. !(T) Point in cell can be found assuming regular Cartesian grid
-    !hexagonal_icebergs=.True. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    rho_bergs=850. ! (850) iceberg density
-    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=1.0 ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.true. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0.0 !4 !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.false.!.true.!.false. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors
-
-    verbose=.true. !(F) Be verbose to stderr
-    verbose_hrs=24 ! (24) Period between verbose messages
-    traj_sample_hrs=1 !1 !(24) sampling period for trajectory storage
-    traj_write_hrs=24 ! (480) Period for writing sampled trajectories to disk
-    budget=.false. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    save_fl_traj=.true. !(T) True save masses and footloose parameters in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    length_for_manually_initialize_bonds=-1.e3!0.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/

From f4d45dafb37834ceade81998f76596c6b6289843 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Wed, 4 Jan 2023 12:25:04 -0500
Subject: [PATCH 339/361] initialize some additional variables for new icebergs
 in calve_icebergs, for backwards compatibility in chksums when
 footloose=.true.

---
 src/icebergs.F90 | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 25c0f94..a0961e4 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -6309,7 +6309,8 @@ subroutine calve_icebergs(bergs)
           newberg%uvel=0.
           newberg%vvel=0.
           !--added by Alex:
-          if (bergs%interactive_icebergs_on) then
+          if (bergs%interactive_icebergs_on .or. footloose) then
+            !not needed? But provided for backwards compatibility:
             newberg%uvel_prev=0.
             newberg%vvel_prev=0.
             newberg%uvel_old=0.

From 5a863a837c0e78ffbf9bc3a769bfa5b654b25378 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Wed, 4 Jan 2023 16:11:08 -0500
Subject: [PATCH 340/361] Cleanup, conda environment, defaults, and
 verification: -Modified and cleaned up the makeberg and animation python
 scripts so that they can be used by a consistent conda environment, for which
 I added a .yml. -Changed several footloose defaults (e.g. fl_youngs and
 fl_strength) to match test E10_S.25 from Huth et al., 2022, Parameterizing
 Tabular-Iceberg Decay in an Ocean Model. Note I defaulted
 fl_init_child_xy_by_pe to false, but it must be true to exactly replicate the
 paper results. Note: At this point I have verified backwards compatibility of
 the footloose code within OM4, where testing this commit on test E10_S.25
 gives the same answer (i.e. chksums match) as when using the code from the
 paper. I tested a month of simulation, and a comprehensive set of
 new_berg_from_fl_bits_mass_thres+fl_stype=fl_bits, as well as
 fl_style=new_bergs, etc. Of course, some changes to the nml were necessary to
 reflect recent modifications since the commit used in the paper
 (be810d96d61c71e00f56f39fe0ea71260983b29e on branch solo-driver): adding
 footloose=.true. and fl_init_child_xy_by_pe=.true. (for backwards
 compatibility), and eliminating fl_use_l_scale, fl_l_scale_erosion_only,
 fl_r, fl_r_s, fl_k_scale_by_perimeter, fl_bits_scale_l, fl_bits_scale_w, and
 fl_bits_scale_t.

---
 src/icebergs.F90                              |    1 -
 src/icebergs_framework.F90                    |   22 +-
 tests/a68_test/makeberg/.gitignore            |    1 +
 tests/a68_test/makeberg/RUN                   |    6 +
 tests/a68_test/makeberg/hexagon_area.py       |    2 +-
 tests/a68_test/makeberg/hexagon_area.pyc      |  Bin 32612 -> 0 bytes
 tests/a68_test/makeberg/makeberg.py           |    8 +-
 tests/collision_tests/.gitignore              |    2 -
 .../animate_trajectories_1pe.py               |  175 -
 tests/collision_tests/input.nml               |  173 +
 tests/collision_tests/makeberg/.gitignore     |    1 +
 .../collision_tests/makeberg/hexagon_area.py  |    2 +-
 .../collision_tests/makeberg/hexagon_area.pyc |  Bin 30118 -> 0 bytes
 .../makeberg/initialize_bergs_in_pattern.py   | 3009 ++++++++---------
 tests/dem_cbeam_test/.gitignore               |    1 -
 tests/dem_cbeam_test/makeberg/makeberg.py     |  428 +--
 tests/dem_ground_frac_test/.gitignore         |    1 -
 .../dem_ground_frac_test/makeberg/makeberg.py |  416 +--
 tests/dem_ssbeam_test/.gitignore              |    1 -
 tests/dem_ssbeam_test/makeberg/makeberg.py    |  428 +--
 tests/footloose_tests/makeberg/makeberg.py    |  416 +--
 tests/iceberg_tests_env.yml                   |  229 ++
 22 files changed, 2774 insertions(+), 2548 deletions(-)
 create mode 100644 tests/a68_test/makeberg/.gitignore
 create mode 100755 tests/a68_test/makeberg/RUN
 delete mode 100644 tests/a68_test/makeberg/hexagon_area.pyc
 delete mode 100644 tests/collision_tests/.gitignore
 delete mode 100755 tests/collision_tests/animate_trajectories_1pe.py
 create mode 100644 tests/collision_tests/input.nml
 create mode 100644 tests/collision_tests/makeberg/.gitignore
 delete mode 100644 tests/collision_tests/makeberg/hexagon_area.pyc
 delete mode 100644 tests/dem_cbeam_test/.gitignore
 delete mode 100644 tests/dem_ground_frac_test/.gitignore
 delete mode 100644 tests/dem_ssbeam_test/.gitignore
 create mode 100644 tests/iceberg_tests_env.yml

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index a0961e4..a939940 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -6510,7 +6510,6 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b,fl_disp_x,fl_disp_y,berg_from_bit
   endif
 
   if (present(berg_from_bits)) then
-    !use scaling for fl_bits to calculate new berg T,L,W, and M. Also affects mass scaling.
     call fl_bits_dimensions(bergs,pberg,Lfl,Wfl,Tfl)
     cberg%length = Lfl; cberg%width = Wfl; cberg%thickness = Tfl
     cberg%mass = Tfl * Lfl * Wfl * bergs%rho_bergs
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 0a61f82..1afa5f6 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -262,7 +262,7 @@ module ice_bergs_framework
   real :: halo_berg
   real :: static_berg
   real :: mass_of_bits !< Mass of bergy bits (kg)
-  real :: mass_of_fl_bits !< Mass of footloose bits (kg)
+  real :: mass_of_fl_bits !< Mass (kg) of footloose bits (i.e. binned footloose child bergs)
   real :: mass_of_fl_bergy_bits !< Mass of bergy bits associated with the footloose bits (kg)
   real :: heat_density !< Heat density of berg (J/kg)
   real :: od !< Ocean depth
@@ -318,7 +318,7 @@ module ice_bergs_framework
   real :: start_mass !< Mass berg had when created (kg)
   real :: mass_scaling !< Multiplier to scale mass when interpreting berg as a cloud of bergs (nondim)
   real :: mass_of_bits !< Mass of bergy bits following berg (kg)
-  real :: mass_of_fl_bits !< Mass of footloose bergy bits following berg (kg)
+  real :: mass_of_fl_bits !< Mass of footloose bits (binned child bergs) following berg (kg)
   real :: mass_of_fl_bergy_bits !< Mass of bergy bits associated with the footloose bits (kg)
   real :: fl_k !< Cumulative number of footloose bergs to calve
   real :: heat_density !< Heat density of berg (J/kg)
@@ -619,13 +619,13 @@ module ice_bergs_framework
   real :: ocean_drag_scale=1. !< Scaling factor for the ocean drag coefficients
   ! Footloose calving parameters
   logical :: footloose=.false. !< Turn footloose calving on/off
-  logical :: fl_init_child_xy_by_pe=.true. !< True: position of a new footloose child berg along the parent perimeter is random, yet constant for each PE (old bug). False: fully-random.
-  real :: fl_youngs=1.e8 !< Young's modulus for footloose calculations (Pa)
-  real :: fl_strength=500. !< yield stress for footloose calculations (kPa)
+  logical :: fl_init_child_xy_by_pe=.false. !< True: position of a new footloose child berg along the parent perimeter is random, yet constant for each PE (old bug). False: fully-random.
+  real :: fl_youngs=1.e7 !< Young's modulus for footloose calculations (Pa)
+  real :: fl_strength=250. !< yield stress for footloose calculations (kPa)
   logical :: displace_fl_bergs=.true. !< footloose berg positions are randomly assigned along edges of parent berg
   character(len=11) :: fl_style='new_bergs' !< Evolve footloose bergs individually as 'new_bergs', or as a group with size 'fl_bits'
   logical :: fl_bits_erosion_to_bergy_bits=.true. !< Erosion from footloose bits becomes bergy bits
-  real :: new_berg_from_fl_bits_mass_thres=huge(0.) ! Create a new berg from FL bits when mass_of_fl_bits exceeds this value
+  real :: new_berg_from_fl_bits_mass_thres=1.e12 ! Create a new berg from FL bits when mass_of_fl_bits exceeds this value
 
   !backwards compatibility
   logical :: old_interp_flds_order=.false. !< Use old order of when to interpolate grid variables to bergs. Will be false if MTS, DEM, or footloose
@@ -635,7 +635,7 @@ module ice_bergs_framework
 !! \todo Remove when backward compatibility no longer needed
 logical :: orig_read=.false.
 
-!> Version of file provided by CPP macro (usually set to git hash)
+! Version of file provided by CPP macro (usually set to git hash)
 #ifdef _FILE_VERSION
 character(len=128) :: version = _FILE_VERSION !< Version of file
 #else
@@ -829,13 +829,13 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: ocean_drag_scale=1. !< Scaling factor for the ocean drag coefficients
 ! Footloose calving parameters
 !logical :: footloose=.false. !< Turn footloose calving on/off
-logical :: fl_init_child_xy_by_pe=.true. !< True: position of a new footloose child berg along the parent perimeter is random, yet constant for each PE (old bug). False: fully-random.
-real :: fl_youngs=1.e8 !< Young's modulus for footloose calculations (Pa)
-real :: fl_strength=500. !< yield stress for footloose calculations (kPa)
+logical :: fl_init_child_xy_by_pe=.false. !< True: position of a new footloose child berg along the parent perimeter is random, yet constant for each PE (old bug). False: fully-random.
+real :: fl_youngs=1.e7 !< Young's modulus for footloose calculations (Pa)
+real :: fl_strength=250. !< yield stress for footloose calculations (kPa)
 logical :: displace_fl_bergs=.true. ! footloose berg positions are randomly assigned along edges of parent berg
 character(len=11) :: fl_style='new_bergs' ! Evolve footloose bergs individually as 'fl_bits', or as a group with size 'bergy_bits' or 'mean_size'
 logical :: fl_bits_erosion_to_bergy_bits=.true. ! Erosion from footloose bits becomes bergy bits
-real :: new_berg_from_fl_bits_mass_thres=huge(0.) ! Create a new berg from FL bits when mass_of_fl_bits exceeds this value
+real :: new_berg_from_fl_bits_mass_thres=1.e12 ! Create a new berg from FL bits when mass_of_fl_bits exceeds this value
 
 
 namelist /icebergs_nml/ verbose, budget, halo,  traj_sample_hrs, initial_mass, traj_write_hrs, max_bonds, save_short_traj,traj_name,bond_traj_name,&
diff --git a/tests/a68_test/makeberg/.gitignore b/tests/a68_test/makeberg/.gitignore
new file mode 100644
index 0000000..ba0430d
--- /dev/null
+++ b/tests/a68_test/makeberg/.gitignore
@@ -0,0 +1 @@
+__pycache__/
\ No newline at end of file
diff --git a/tests/a68_test/makeberg/RUN b/tests/a68_test/makeberg/RUN
new file mode 100755
index 0000000..2cbc068
--- /dev/null
+++ b/tests/a68_test/makeberg/RUN
@@ -0,0 +1,6 @@
+rm ./output_files/Generic*
+
+# THIS IS THE BERG USED IN HUTH ET AL, 2022 OCEAN CURRENTS BREAK UP A TABULAR ICEBERG. SCIENCE ADVANCES:
+./makeberg.py -Convert_to_lat_lon=True -input_is_cartesian=False -element_type='square' -plot_circles=False -Create_icebergs_bonds=False -Generic_ice_geometry_filename='./../data/a68_experiment_berg_2020_12_09_gridded_ll_p0625_cropped.nc' -Ice_geometry_source='Generic' -set_all_thicknesses_to_one=True -Th_prescribed=200 -plot_ice_thickness=False -plot_circles=True -plot_h_ice_new=False -plot_ice_mask=True -plot_icebergs_positions=False -adjust_lat_ref=True -Interpolate_from_four_corners=False -Radius=1500 -lat_ref_grid_to_cartesian=-55.2 -uvel=0.22 -dx=500. -R_earth=6363827. -icethres=0.5 -displace_y=-0.1
+
+cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
diff --git a/tests/a68_test/makeberg/hexagon_area.py b/tests/a68_test/makeberg/hexagon_area.py
index 5db6cec..d1e2c01 100755
--- a/tests/a68_test/makeberg/hexagon_area.py
+++ b/tests/a68_test/makeberg/hexagon_area.py
@@ -825,7 +825,7 @@ def divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1):
 				Area_positive= 0.;
 				Area_negative= A_triangle;
 			else:
-				print 'You should not get here1'
+				print ('You should not get here1')
 				halt
 		else:
 			print ('You should not get here2')
diff --git a/tests/a68_test/makeberg/hexagon_area.pyc b/tests/a68_test/makeberg/hexagon_area.pyc
deleted file mode 100644
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diff --git a/tests/a68_test/makeberg/makeberg.py b/tests/a68_test/makeberg/makeberg.py
index 3db6dda..0a7224c 100755
--- a/tests/a68_test/makeberg/makeberg.py
+++ b/tests/a68_test/makeberg/makeberg.py
@@ -276,7 +276,7 @@ def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,ang_vel_in,uv
 
 
         # To copy the dimension of the netCDF file
-        for dimname,dim in f.dimensions.iteritems():
+        for dimname,dim in f.dimensions.items():
                 # if you want to make changes in the dimensions of the new file
                 # you should add your own conditions here before the creation of the dimension.
                 #g.createDimension(dimname,len(dim))
@@ -284,7 +284,7 @@ def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,ang_vel_in,uv
 
         # To copy the variables of the netCDF file
 
-        for varname,ncvar in f.variables.iteritems():
+        for varname,ncvar in f.variables.items():
                 # if you want to make changes in the variables of the new file
                 # you should add your own conditions here before the creation of the variable.
                 var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
@@ -373,7 +373,7 @@ def Create_bond_restart_file(Number_of_bonds,first_berg_num,first_berg_ine,first
 
 
         # To copy the dimension of the netCDF file
-        for dimname,dim in h.dimensions.iteritems():
+        for dimname,dim in h.dimensions.items():
                 # if you want to make changes in the dimensions of the new file
                 # you should add your own conditions here before the creation of the dimension.
                 #g.createDimension(dimname,len(dim))
@@ -381,7 +381,7 @@ def Create_bond_restart_file(Number_of_bonds,first_berg_num,first_berg_ine,first
 
         # To copy the variables of the netCDF file
 
-        for varname,ncvar in h.variables.iteritems():
+        for varname,ncvar in h.variables.items():
                 # if you want to make changes in the variables of the new file
                 # you should add your own conditions here before the creation of the variable.
                 var = q.createVariable(varname,ncvar.dtype,ncvar.dimensions)
diff --git a/tests/collision_tests/.gitignore b/tests/collision_tests/.gitignore
deleted file mode 100644
index 75188aa..0000000
--- a/tests/collision_tests/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
-results/
-input.nml
\ No newline at end of file
diff --git a/tests/collision_tests/animate_trajectories_1pe.py b/tests/collision_tests/animate_trajectories_1pe.py
deleted file mode 100755
index 19db84d..0000000
--- a/tests/collision_tests/animate_trajectories_1pe.py
+++ /dev/null
@@ -1,175 +0,0 @@
-#!/usr/bin/env python
-
-from netCDF4 import Dataset
-import pdb
-import netCDF4 as nc
-import numpy as np
-import matplotlib
-import math
-import os
-matplotlib.use("tkagg")
-from pylab import *
-import matplotlib.pyplot as plt
-from matplotlib.animation import FuncAnimation
-import argparse
-
-def parseCommandLine():
-    parser = argparse.ArgumentParser(description=
-    '''Generate animation of iceberg trajectories.''',
-    epilog='Written by Alex Huth, 2020')
-    parser.add_argument('-fname', type=str, default='iceberg_trajectories.nc.0000',
-                    help=''' provide filename to plot''')
-    optCmdLineArgs = parser.parse_args()
-    return optCmdLineArgs
-
-
-
-def main(args):
-    
-    print('reading file')
-
-    filename=args.fname
-    #filename = 'iceberg_trajectories.nc'
-    field = 'lon'
-    field2 = 'lat'
-
-    with nc.Dataset(filename) as file:
-        x = file.variables['lon'][:]/1.e3
-        y = file.variables['lat'][:]/1.e3
-        day = file.variables['day'][:]
-        hs = file.variables['halo_berg'][:]
-
-    #hs = hs+1
-    ud = np.unique(day)
-    t = ud[0]
-
-    print('unique hs',np.unique(hs))
-
-    # frame info
-    num_frames = len(ud)
-    movie_len = 5.0 #seconds
-    frame_len = 1000.0*movie_len/num_frames
-    
-    xmin = np.floor(min(min(x),min(y),-5))
-    xmax = np.ceil(max(max(x),max(y),25))
-    ymin = xmin
-    ymax = xmax
-
-    anim_running = True
-
-    def animate(i):
-
-        x1 = x[day == ud[i]]
-        y1 = y[day == ud[i]]
-        hstat = hs[day == ud[i]]
-        data = np.hstack((x1[:,np.newaxis],y1[:,np.newaxis]))
-
-        cstring=[]
-        for j in range(len(hstat)):
-            if (hstat[j]<0):
-                cstring.append("y")
-            elif (hstat[j]==0):                 
-                cstring.append("b")
-            elif (hstat[j]==1):
-                cstring.append("r")
-            elif (hstat[j]==2):
-                cstring.append("g")
-            elif (hstat[j]==3):
-                cstring.append("k")
-            elif (hstat[j]==4):
-                cstring.append("m")
-            else:
-                cstring.append("c")
-                                                           
-        scat.set_offsets(data)
-        scat.set_color(cstring)
-        scat.set_edgecolor('k')
-        
-        t = ud[i]
-        time_text.set_text('time = %.1f days' % t )        
-        return scat,time_text
-
-    def init():
-        scat.set_offsets([])
-        return scat,
-
-    def onClick(event):
-        global anim_running
-        if anim_running:
-            ani.event_source.stop()
-            anim_running = False
-        else:
-            ani.event_source.start()
-            anim_running = True       
-    
-    # Now we can do the plotting!
-    f = plt.figure(figsize=(5,5))
-    f.tight_layout()
-    ax1 = plt.subplot(111,xlim=(xmin, xmax), ylim=(ymin, ymax))
-    scat = ax1.scatter([],[],marker='o',s=60) 
-    #scat = ax1.scatter([],[],marker='o',facecolor='w',s=60,edgecolor='red')
-    time_text = ax1.text(0.02, 0.95, '', transform=ax1.transAxes)
-
-    # Change major ticks to show every 20.
-    ax1.xaxis.set_major_locator(MultipleLocator(5))
-    ax1.yaxis.set_major_locator(MultipleLocator(5))
-
-    ax1.xaxis.set_minor_locator(MultipleLocator(1))
-    ax1.yaxis.set_minor_locator(MultipleLocator(1))
-
-    # Turn grid on for both major and minor ticks and style minor slightly
-    # differently.
-    ax1.grid(which='major', color='#CCCCCC', linestyle=':')
-    ax1.grid(which='minor', color='#CCCCCC', linestyle=':')
-
-    ax1.set_xlabel('x (km)')
-    ax1.set_ylabel('y (km)')
-    ax1.set_title('Iceberg trajectory')
- 
-    f.canvas.mpl_connect('button_press_event', onClick)
-
-    ani = FuncAnimation(
-        f,animate,init_func=init,frames=num_frames,
-        interval=frame_len,blit=True,repeat=True)
-
-    print('time',t)
-
-    plt.plot([0,0],[0,20],'k-',lw=1)
-    plt.plot([10,10],[0,20],'k-',lw=1)
-    plt.plot([20,20],[0,20],'k-',lw=1)
-    plt.plot([0,0],[0,20],'k-',lw=1)
-    plt.plot([20,20],[0,20],'k-',lw=1)
-    plt.plot([0,0],[0,20],'k-',lw=1)
-    plt.plot([0,20],[10,10],'k-',lw=1)
-    plt.plot([0,20],[20,20],'k-',lw=1)
-    plt.plot([0,20],[0,0],'k-',lw=1)
-    plt.plot([0,20],[20,20],'k-',lw=1)
-
-    plt.plot([-2,-2],[-2,23],'b:',lw=1)
-    plt.plot([8,8],[-2,23],'b:',lw=1)
-    plt.plot([13,13],[-2,23],'b:',lw=1)
-    plt.plot([23,23],[-2,23],'b:',lw=1)
-    plt.plot([-2,23],[-2,-2],'b:',lw=1)
-    plt.plot([-2,23],[8,8],'b:',lw=1)
-    plt.plot([-2,23],[13,13],'b:',lw=1)
-    plt.plot([-2,23],[23,23],'b:',lw=1)      
- 
-    
-    plt.show()
-    #animation.save("iceberg_traj_animation.mp4")
-
-
-print('Script complete')
-
-if __name__ == '__main__':
-    optCmdLineArgs=	parseCommandLine()
-    anim_running = True
-    main(optCmdLineArgs)
-
-
-
-
-
-
-
-
diff --git a/tests/collision_tests/input.nml b/tests/collision_tests/input.nml
new file mode 100644
index 0000000..b51271c
--- /dev/null
+++ b/tests/collision_tests/input.nml
@@ -0,0 +1,173 @@
+!!KID, bergs_chksum: write_restart berg chksum=1560193269 chksum2=-1064844053 chksum3=-1070230468 chksum4=-1070230468 chksum5=0 #=16
+
+
+&icebergs_driver_nml
+  ni=20 !number of elements, x direction
+  nj=20 !number of elements, y direction
+  ibdt=3600.0 !seconds
+  ibuo=0.2 !ocean x velocity
+  ibvo=0.2 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibhrs=48 !total simulation hours
+  nmax=99999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.false.
+  collision_test=.true. !specific to the current test, must be true here
+/
+
+&icebergs_nml
+
+    traj_name=iKID.nc
+    bond_traj_name=iKID_bonds.nc
+
+    !defaults given in parentheses:
+    dem=.true.
+    poisson=0.3
+    dem_damping_coef=1.0
+    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
+    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
+    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
+    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5. A=L*W always works?
+    dem_spring_coef=4471.94
+    spring_coef=1.e-5 !if dem_spring_coef=5e6, r=1500, and hex pack?
+
+    explicit_inner_mts=.true.
+    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=60 !1 !30 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
+    contact_distance=1.75e3 !2.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
+    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
+    remove_unused_bergs=.false. !(T) remove unneeded bergs after PEs transfers
+    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
+    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
+
+    halo=3 !(4) halo width
+    Lx=20000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.True. !(T) Point in cell can be found assuming regular Cartesian grid
+    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    rho_bergs=850. ! (850) iceberg density
+    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0.4 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+    internal_bergs_for_drag=.false. !(F) True reduces side drag for bonded bergs in momentum eqn.
+
+    verbose=.true. !(F) Be verbose to stderr
+    verbose_hrs=24 ! (24) Period between verbose messages
+    traj_sample_hrs=0.5 !1 !(24) sampling period for trajectory storage
+    traj_write_hrs=-1 ! (480) Period for writing sampled trajectories to disk
+    budget=.true. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/
diff --git a/tests/collision_tests/makeberg/.gitignore b/tests/collision_tests/makeberg/.gitignore
new file mode 100644
index 0000000..ba0430d
--- /dev/null
+++ b/tests/collision_tests/makeberg/.gitignore
@@ -0,0 +1 @@
+__pycache__/
\ No newline at end of file
diff --git a/tests/collision_tests/makeberg/hexagon_area.py b/tests/collision_tests/makeberg/hexagon_area.py
index 5db6cec..d1e2c01 100755
--- a/tests/collision_tests/makeberg/hexagon_area.py
+++ b/tests/collision_tests/makeberg/hexagon_area.py
@@ -825,7 +825,7 @@ def divding_triangle_across_axes(Ax,Ay,Bx,By,Cx,Cy,axes1):
 				Area_positive= 0.;
 				Area_negative= A_triangle;
 			else:
-				print 'You should not get here1'
+				print ('You should not get here1')
 				halt
 		else:
 			print ('You should not get here2')
diff --git a/tests/collision_tests/makeberg/hexagon_area.pyc b/tests/collision_tests/makeberg/hexagon_area.pyc
deleted file mode 100644
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diff --git a/tests/collision_tests/makeberg/initialize_bergs_in_pattern.py b/tests/collision_tests/makeberg/initialize_bergs_in_pattern.py
index c9fc502..41d7dd2 100755
--- a/tests/collision_tests/makeberg/initialize_bergs_in_pattern.py
+++ b/tests/collision_tests/makeberg/initialize_bergs_in_pattern.py
@@ -22,821 +22,818 @@
 
 
 def parseCommandLine():
-	"""
-	Parse the command line positional and optional arguments.
-	This is the highest level procedure invoked from the very end of the script.
-	"""
+        """
+        Parse the command line positional and optional arguments.
+        This is the highest level procedure invoked from the very end of the script.
+        """
 
-	parser = argparse.ArgumentParser(description=
-	'''
-	Generate files for iceberg and bond restart files, matching given ice thickness fields.
-	''',
-	epilog='Written by Alon Stern, Dec. 2016.')
+        parser = argparse.ArgumentParser(description=
+        '''
+        Generate files for iceberg and bond restart files, matching given ice thickness fields.
+        ''',
+        epilog='Written by Alon Stern, Dec. 2016.')
 
-	#Adding an extra boolian type argument
-	#p = argparse.ArgumentParser()
-	parser.register('type','bool',str2bool) # add type keyword to registries
-	#p.add_argument('-b',type='bool')  # do not use 'type=bool'
+        #Adding an extra boolian type argument
+        #p = argparse.ArgumentParser()
+        parser.register('type','bool',str2bool) # add type keyword to registries
+        #p.add_argument('-b',type='bool')  # do not use 'type=bool'
 
-	#Flags
-	parser.add_argument('-grounding_test', type='bool', default=False,
-		          help=''' old: displace 500 m S. new: get rid of SE element ''')
+        #Flags
+        parser.add_argument('-grounding_test', type='bool', default=False,
+                          help=''' old: displace 500 m S. new: get rid of SE element ''')
 
-	parser.add_argument('-collision_test', type='bool', default=False,
-		          help=''' symmetry for berg around y=10 km ''')
+        parser.add_argument('-collision_test', type='bool', default=False,
+                          help=''' symmetry for berg around y=10 km ''')
 
-	parser.add_argument('-save_restart_files', type='bool', default=True,
-		          help=''' Writes an iceberg restart file,  icebergs.res ''')
+        parser.add_argument('-save_restart_files', type='bool', default=True,
+                          help=''' Writes an iceberg restart file,  icebergs.res ''')
 
-	parser.add_argument('-save_new_h_ice_file', type='bool', default=True,
-		          help=''' Writes a new gridded ice thickness file, which is what the ice thickness after the berg mass is interpolated back onto the grid''')
+        parser.add_argument('-save_new_h_ice_file', type='bool', default=True,
+                          help=''' Writes a new gridded ice thickness file, which is what the ice thickness after the berg mass is interpolated back onto the grid''')
 
-	parser.add_argument('-Convert_to_lat_lon', type='bool', default=False,
-		          help=''' Converts the iceberg positions to lat / lon coordinates  ''')
+        parser.add_argument('-Convert_to_lat_lon', type='bool', default=False,
+                          help=''' Converts the iceberg positions to lat / lon coordinates  ''')
 
-	parser.add_argument('-input_is_cartesian', type='bool', default=True,
-		          help=''' The positions in the ice thickness input file is given in cartesian coordiantes''')
+        parser.add_argument('-input_is_cartesian', type='bool', default=True,
+                          help=''' The positions in the ice thickness input file is given in cartesian coordiantes''')
 
-	#Iceberg setup flags
-	parser.add_argument('-only_choose_one_berg', type='bool', default=False,
-		          help=''' When true, only one iceberg (with number chosen_berg_num) is written to icebergs.res. This is for debugging  ''')
+        #Iceberg setup flags
+        parser.add_argument('-only_choose_one_berg', type='bool', default=False,
+                          help=''' When true, only one iceberg (with number chosen_berg_num) is written to icebergs.res. This is for debugging  ''')
 
-	parser.add_argument('-select_just_min_and_max_lat_berg', type='bool', default=False,
-		          help=''' When true, only the bergs with max and min lat are written to icebergs.res. This is for debugging  ''')
+        parser.add_argument('-select_just_min_and_max_lat_berg', type='bool', default=False,
+                          help=''' When true, only the bergs with max and min lat are written to icebergs.res. This is for debugging  ''')
 
-	parser.add_argument('-chosen_berg_num', type=int, default=1,
-		          help='''When only_choose_one_berg=True, then only the iceberg with this number is written to the icebergs.res file  ''')
+        parser.add_argument('-chosen_berg_num', type=int, default=1,
+                          help='''When only_choose_one_berg=True, then only the iceberg with this number is written to the icebergs.res file  ''')
 
-	parser.add_argument('-scale_the_grid_to_lat_lon', type='bool', default=False,
-		          help=''' This option scales dimensions by a fixed amount. Option should be removed   ''')
+        parser.add_argument('-scale_the_grid_to_lat_lon', type='bool', default=False,
+                          help=''' This option scales dimensions by a fixed amount. Option should be removed   ''')
 
-	parser.add_argument('-adjust_lat_ref', type='bool', default=True,
-		          help=''' This option is only used when Convert_to_lat_lon is true. If true, then the reference latitudes depends on iceberg position.\
-					  This still needs to be tested using lat lon test cases.''')
+        parser.add_argument('-adjust_lat_ref', type='bool', default=True,
+                          help=''' This option is only used when Convert_to_lat_lon is true. If true, then the reference latitudes depends on iceberg position.\
+                                          This still needs to be tested using lat lon test cases.''')
 
-	parser.add_argument('-set_all_thicknesses_to_one', type='bool', default=False,
-		          help=''' Sets all non-zero ice thickness to Th_prescibed (default 1), useful for debugging.  ''')
+        parser.add_argument('-set_all_thicknesses_to_one', type='bool', default=False,
+                          help=''' Sets all non-zero ice thickness to Th_prescibed (default 1), useful for debugging.  ''')
 
-	parser.add_argument('-Th_prescribed', type=float, default=1.0,
-		          help='''Prescibed ice thickness used when the flag set_all_thicknesses_to_one=True   ''')
+        parser.add_argument('-Th_prescribed', type=float, default=1.0,
+                          help='''Prescibed ice thickness used when the flag set_all_thicknesses_to_one=True   ''')
 
-	parser.add_argument('-Interpolate_from_four_corners', type='bool', default=True,
-		          help=''' The thickness of an iceberg is calcaulated from the 4 corners of the gridded thickness. When flag is false, the near thickness is used  ''')
+        parser.add_argument('-Interpolate_from_four_corners', type='bool', default=True,
+                          help=''' The thickness of an iceberg is calcaulated from the 4 corners of the gridded thickness. When flag is false, the near thickness is used  ''')
 
-	parser.add_argument('-Switch_x_and_y_to_rotate_90', type='bool', default=False,
-		          help=''' Rotates the whole domain by 90 degrees by switching lat and lon of icebergs.  ''')
+        parser.add_argument('-Switch_x_and_y_to_rotate_90', type='bool', default=False,
+                          help=''' Rotates the whole domain by 90 degrees by switching lat and lon of icebergs.  ''')
 
-	parser.add_argument('-set_all_domain_to_ice', type='bool', default=False,
-		          help=''' Sets the ice thickness = Th_prescibed (default 1) throughout the entire domain. Applied only when flag set_all_thicknesses_to_one=True   ''')
+        parser.add_argument('-set_all_domain_to_ice', type='bool', default=False,
+                          help=''' Sets the ice thickness = Th_prescibed (default 1) throughout the entire domain. Applied only when flag set_all_thicknesses_to_one=True   ''')
 
-	parser.add_argument('-Use_default_radius', type='bool', default=False,
-		          help=''' Calculates an appropriate ice element radius based on the ocean grid spacing.   ''')
+        parser.add_argument('-Use_default_radius', type='bool', default=False,
+                          help=''' Calculates an appropriate ice element radius based on the ocean grid spacing.   ''')
 
-	parser.add_argument('-Remove_stationary_bergs', type='bool', default=False,
-		          help=''' All stationary icebergs are removed.  ''')
+        parser.add_argument('-Remove_stationary_bergs', type='bool', default=False,
+                          help=''' All stationary icebergs are removed.  ''')
 
-	#Static vs non-static flags (These are needed for calving away from Static shelf)
-	parser.add_argument('-set_all_bergs_static_by_default', type='bool', default=True,
-			help='''Bergs are static unless instructed otherwise (e.g.: after applying calving)   ''')
+        #Static vs non-static flags (These are needed for calving away from Static shelf)
+        parser.add_argument('-set_all_bergs_static_by_default', type='bool', default=True,
+                        help='''Bergs are static unless instructed otherwise (e.g.: after applying calving)   ''')
 
-	parser.add_argument('-set_some_bergs_static_by_default', type='bool', default=False,
-		          help=''' Bergs in part of the domain are set to static by default (see subroutine for details)  ''')
+        parser.add_argument('-set_some_bergs_static_by_default', type='bool', default=False,
+                          help=''' Bergs in part of the domain are set to static by default (see subroutine for details)  ''')
 
-	parser.add_argument('-Make_icebergs_non_static_later', type='bool', default=True,
-			help=''' Run subroutine which makes some icebergs non-static later (eg: icebergs around calved tabular icebergs).  Note that bonds are \
-					only created for non_static, so by making bergs non_static later, it means they can move, but are not bonded.  ''')
+        parser.add_argument('-Make_icebergs_non_static_later', type='bool', default=True,
+                        help=''' Run subroutine which makes some icebergs non-static later (eg: icebergs around calved tabular icebergs).  Note that bonds are \
+                                        only created for non_static, so by making bergs non_static later, it means they can move, but are not bonded.  ''')
 
-	#Mass spreadng flags
-	parser.add_argument('-Switch_regridding_element_type', type='bool', default=False,
-		          help=''' When true, element shape is switched from hexagon to square (and visa versa) before regridding. Used in debugging to see if having \
-			  the wrond elemnt type makes a bid difference. Maybe this option should be removed(?)''')
+        #Mass spreadng flags
+        parser.add_argument('-Switch_regridding_element_type', type='bool', default=False,
+                          help=''' When true, element shape is switched from hexagon to square (and visa versa) before regridding. Used in debugging to see if having \
+                          the wrond elemnt type makes a bid difference. Maybe this option should be removed(?)''')
 
-	parser.add_argument('-Fill_in_the_boundaries', type='bool', default=True,
-		          help=''' Adds extra (static)  ice elements at the edges of the domain when the ice shelf extends right up until the boundaries of the domain.\
-					  Only used with hexagonal ice elements (for now).''')
+        parser.add_argument('-Fill_in_the_boundaries', type='bool', default=True,
+                          help=''' Adds extra (static)  ice elements at the edges of the domain when the ice shelf extends right up until the boundaries of the domain.\
+                                          Only used with hexagonal ice elements (for now).''')
 
-	parser.add_argument('-regrid_icebergs_onto_grid', type='bool', default=True,
-		          help=''' After icebergs have been defined, the iceberg mass is interpolated back onto the ocean grid  ''')
+        parser.add_argument('-regrid_icebergs_onto_grid', type='bool', default=True,
+                          help=''' After icebergs have been defined, the iceberg mass is interpolated back onto the ocean grid  ''')
 
-	parser.add_argument('-element_type', type=str, default='hexagon',
-			help='''Shape of element used in mass spreading. Options are: 'hexagon' or 'square'   ''')
+        parser.add_argument('-element_type', type=str, default='hexagon',
+                        help='''Shape of element used in mass spreading. Options are: 'hexagon' or 'square'   ''')
 
 
-	#Plotting flags - Only affect how the ice elements are plotted and does not affect files created by this script
-	parser.add_argument('-Run_plotting_subroutine', type='bool', default=True,
-		          help=''' Subrouting is run plots icebergs and ice thickness. All other plotting flags require this to be true.  ''')
+        #Plotting flags - Only affect how the ice elements are plotted and does not affect files created by this script
+        parser.add_argument('-Run_plotting_subroutine', type='bool', default=True,
+                          help=''' Subrouting is run plots icebergs and ice thickness. All other plotting flags require this to be true.  ''')
 
-	parser.add_argument('-plot_circles', type='bool', default=False,
-		          help=''' Circles are plotted to scale which show how large each ice element is. (Useful when converting to lat lon)  ''')
+        parser.add_argument('-plot_circles', type='bool', default=False,
+                          help=''' Circles are plotted to scale which show how large each ice element is. (Useful when converting to lat lon)  ''')
 
-	parser.add_argument('-plot_ice_mask', type='bool', default=False,
-		          help=''' The ice mask (showing where ice shelf is present) is plotted under iceberg positions. Option may be removed.  ''')
+        parser.add_argument('-plot_ice_mask', type='bool', default=False,
+                          help=''' The ice mask (showing where ice shelf is present) is plotted under iceberg positions. Option may be removed.  ''')
 
-	parser.add_argument('-plot_ice_thickness', type='bool', default=True,
-		          help=''' The ice thickness is plotted under iceberg positions   ''')
+        parser.add_argument('-plot_ice_thickness', type='bool', default=True,
+                          help=''' The ice thickness is plotted under iceberg positions   ''')
 
-	parser.add_argument('-plot_icebergs_positions', type='bool', default=True,
-		          help='''  Positions of ice elements are plotted  ''')
+        parser.add_argument('-plot_icebergs_positions', type='bool', default=True,
+                          help='''  Positions of ice elements are plotted  ''')
 
-	parser.add_argument('-plot_h_ice_new', type='bool', default=True,
-		          help='''  The newly interpolated ice thickness is plotted under iceberg positions ''')
+        parser.add_argument('-plot_h_ice_new', type='bool', default=True,
+                          help='''  The newly interpolated ice thickness is plotted under iceberg positions ''')
 
-	parser.add_argument('-plot_bonds', type='bool', default=False,
-		          help=''' Bonds are plotted between the ice elements   ''')
+        parser.add_argument('-plot_bonds', type='bool', default=False,
+                          help=''' Bonds are plotted between the ice elements   ''')
 
-	#Bond related flags
-	parser.add_argument('-Create_icebergs_bonds', type='bool', default=True,
-		          help=''' Bonds are created between icebergs  ''')
+        #Bond related flags
+        parser.add_argument('-Create_icebergs_bonds', type='bool', default=True,
+                          help=''' Bonds are created between icebergs  ''')
 
-	parser.add_argument('-break_some_bonds', type='bool', default=True,
-		          help=''' After the bonds have been set up, some are broken. This simulates a iceberg / ice shelf calving.\
-					  Note that this flag is also used to make a calving event even if bonds are not used since \
-					  the "calving" process also sets some icebergs to static and others to non-static''')
+        parser.add_argument('-break_some_bonds', type='bool', default=True,
+                          help=''' After the bonds have been set up, some are broken. This simulates a iceberg / ice shelf calving.\
+                                          Note that this flag is also used to make a calving event even if bonds are not used since \
+                                          the "calving" process also sets some icebergs to static and others to non-static''')
 
-	parser.add_argument('-Allow_bonds_for_static_iceberg', type='bool', default=False,
-		          help=''' If True then bonds are allowed for ice elements which are static.   ''')
+        parser.add_argument('-Allow_bonds_for_static_iceberg', type='bool', default=False,
+                          help=''' If True then bonds are allowed for ice elements which are static.   ''')
 
-	parser.add_argument('-Allow_bonds_with_boundary_bergs', type='bool', default=False,
-		          help=''' When true, bonds are allowed to form with elements close to the boundary. \
-					  When false, bonds are allowed for bergs closer with i,j < N_bergs_before_bd.\
-					  This option is a little confusing and might need to be removed (>)''')
+        parser.add_argument('-Allow_bonds_with_boundary_bergs', type='bool', default=False,
+                          help=''' When true, bonds are allowed to form with elements close to the boundary. \
+                                          When false, bonds are allowed for bergs closer with i,j < N_bergs_before_bd.\
+                                          This option is a little confusing and might need to be removed (>)''')
 
-	#Experimental setup flags
-	parser.add_argument('-Ice_geometry_source', type=str, default='ISOMIP',
-			help=''' Name of experiment which is being run. Options are 'ISOMIP', 'Generic' and 'Weddell'\
-					These experiments override some of the flags above and have standary input files  (see below).\
-					This will be made more general later so that ice thickness files are passed into the script with standarized formate through driver.\
-					''')
+        #Experimental setup flags
+        parser.add_argument('-Ice_geometry_source', type=str, default='ISOMIP',
+                        help=''' Name of experiment which is being run. Options are 'ISOMIP', 'Generic' and 'Weddell'\
+                                        These experiments override some of the flags above and have standary input files  (see below).\
+                                        This will be made more general later so that ice thickness files are passed into the script with standarized formate through driver.\
+                                        ''')
 
-	parser.add_argument('-ISOMIP_ice_geometry_filename', type=str, default='input_files/Isomip_ice_geometry.nc',
-			help=''' Ice thickness from the ISOMIP experiment, given on ice grid, rather than ocean grid.  ''')
+        parser.add_argument('-ISOMIP_ice_geometry_filename', type=str, default='input_files/Isomip_ice_geometry.nc',
+                        help=''' Ice thickness from the ISOMIP experiment, given on ice grid, rather than ocean grid.  ''')
 
-	parser.add_argument('-ISOMIP_reduced_ice_geometry_filename', type=str, default='input_files/Ocean1_3D_no_calving_trimmed.nc',
-			help=''' Ice thickness from ISOMIP experiment, given on ocean grid. Later all input files will be made to have this format\
-					(or to specify if they are on the ice grid, what format the ocean should have)''')
+        parser.add_argument('-ISOMIP_reduced_ice_geometry_filename', type=str, default='input_files/Ocean1_3D_no_calving_trimmed.nc',
+                        help=''' Ice thickness from ISOMIP experiment, given on ocean grid. Later all input files will be made to have this format\
+                                        (or to specify if they are on the ice grid, what format the ocean should have)''')
 
-	parser.add_argument('-Weddell_ice_geometry_filename', type=str, default='input_files/Bedmap2_gridded_subset_Weddell_Sea_Region.nc',
-			help='''  Ice thickness from the ice shelves in the Weddell Sea, given on ice grid, rather than ocean grid.  ''')
+        parser.add_argument('-Weddell_ice_geometry_filename', type=str, default='input_files/Bedmap2_gridded_subset_Weddell_Sea_Region.nc',
+                        help='''  Ice thickness from the ice shelves in the Weddell Sea, given on ice grid, rather than ocean grid.  ''')
 
-	parser.add_argument('-Generic_ice_geometry_filename', type=str, \
-			default='/lustre/f1/unswept/Alon.Stern/MOM6-examples_Alon/ice_ocean_SIS2/Drifting_tabular/python_scripts/output_files/Ice_shelf_file.nc',
-			help=''' Ice thickness used in a generic setup.   ''')
+        parser.add_argument('-Generic_ice_geometry_filename', type=str, \
+                        default='/lustre/f1/unswept/Alon.Stern/MOM6-examples_Alon/ice_ocean_SIS2/Drifting_tabular/python_scripts/output_files/Ice_shelf_file.nc',
+                        help=''' Ice thickness used in a generic setup.   ''')
 
 
-	parser.add_argument('-ISOMIP_reduced', type='bool', default=True,
-			help=''' Flag which specifies that we are using the reduced ISOMIP file (on the ocean grid), rather than geomety on the ice grid. \
-					Reduced uses 2X2 grid, not reduced uses 1X1 grid \
-					This should be made more general later.''')
+        parser.add_argument('-ISOMIP_reduced', type='bool', default=True,
+                        help=''' Flag which specifies that we are using the reduced ISOMIP file (on the ocean grid), rather than geomety on the ice grid. \
+                                        Reduced uses 2X2 grid, not reduced uses 1X1 grid \
+                                        This should be made more general later.''')
 
-	#Parameters
-	parser.add_argument('-Radius', type=float, default='850.0',
-			help='''Radius of ice element (m). This is overriden if Use_default_radius=True\
-					Note that Hexagon only valid if the Radius, S< half gridcell  (about 0.85 using 2km grid)''')
+        #Parameters
+        parser.add_argument('-Radius', type=float, default='850.0',
+                        help='''Radius of ice element (m). This is overriden if Use_default_radius=True\
+                                        Note that Hexagon only valid if the Radius, S< half gridcell  (about 0.85 using 2km grid)''')
 
-	parser.add_argument('-rho_ice', type=float, default=918.0,
-			help=''' Density of icebergs (kg/m^3)  ''')
+        parser.add_argument('-rho_ice', type=float, default=918.0,
+                        help=''' Density of icebergs (kg/m^3)  ''')
 
-	parser.add_argument('-gravity', type=float, default=9.8,
-			help=''' Gravitational acceleration  (m/s^2)''')
+        parser.add_argument('-gravity', type=float, default=9.8,
+                        help=''' Gravitational acceleration  (m/s^2)''')
 
-	parser.add_argument('-mass_scaling', type=float, default=1.0,
-			help=''' Number of icebergs represented by one ice element  ''')
+        parser.add_argument('-mass_scaling', type=float, default=1.0,
+                        help=''' Number of icebergs represented by one ice element  ''')
 
-	parser.add_argument('-R_earth', type=float, default=6360000.,
-			help=''' Radius of the earch (m) - used in Lat/Lon conversions.   ''')
+        parser.add_argument('-R_earth', type=float, default=6360000.,
+                        help=''' Radius of the earch (m) - used in Lat/Lon conversions.   ''')
 
-	parser.add_argument('-buffer_number', type=int, default=0,
-			help=''' Amount of points from the boundaries where ice thickness is set to zero for debugging. This should be removed.  ''')
+        parser.add_argument('-buffer_number', type=int, default=0,
+                        help=''' Amount of points from the boundaries where ice thickness is set to zero for debugging. This should be removed.  ''')
 
-	parser.add_argument('-IA_scaling', type=float, default=1.,
-			help='''  A scaling parameter which allows the interactive radius be different from radius for testing the bonds.\
-					(This has not been used in a long while, and perhaps should be removed)''')
+        parser.add_argument('-IA_scaling', type=float, default=1.,
+                        help='''  A scaling parameter which allows the interactive radius be different from radius for testing the bonds.\
+                                        (This has not been used in a long while, and perhaps should be removed)''')
 
-	optCmdLineArgs = parser.parse_args()
-	return optCmdLineArgs
+        optCmdLineArgs = parser.parse_args()
+        return optCmdLineArgs
 
 def str2bool(string):
-	if string.lower() in  ("yes", "true", "t", "1"):
-		Value=True
-	elif string.lower() in ("no", "false", "f", "0"):
-		Value=False
-	else:
-		print '**********************************************************************'
-		print 'The input variable ' ,str(string) ,  ' is not suitable for boolean conversion, using default'
-		print '**********************************************************************'
+        if string.lower() in  ("yes", "true", "t", "1"):
+                Value=True
+        elif string.lower() in ("no", "false", "f", "0"):
+                Value=False
+        else:
+                print ('**********************************************************************')
+                print ('The input variable ' ,str(string) ,  ' is not suitable for boolean conversion, using default')
+                print ('**********************************************************************')
 
-		Value=None
-		return
+                Value=None
+                return
 
-	return Value
+        return Value
 
 
 
 def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg):
 
-	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
-	# To copy the global attributes of the netCDF file
+        print ('Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..')
+        # To copy the global attributes of the netCDF file
 
-	#Input and output files
-	#Create Empty restart file. This is later read so that the attributes can be used.
-	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
-	create_empty_iceberg_restart_file(Empty_restart_filename)
-	#Empty_restart_filename='input_files/icebergs.res.nc'
+        #Input and output files
+        #Create Empty restart file. This is later read so that the attributes can be used.
+        Empty_restart_filename='output_files/Empty_icebergs.res.nc'
+        create_empty_iceberg_restart_file(Empty_restart_filename)
+        #Empty_restart_filename='input_files/icebergs.res.nc'
 
-	#Read empty restart file
-	f=Dataset(Empty_restart_filename,'r') # r is for read only
-	#Write a new restart file
-	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
+        #Read empty restart file
+        f=Dataset(Empty_restart_filename,'r') # r is for read only
+        #Write a new restart file
+        g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
 
-	for attname in f.ncattrs():
-		    setattr(g,attname,getattr(f,attname))
+        for attname in f.ncattrs():
+                    setattr(g,attname,getattr(f,attname))
 
 
-	# To copy the dimension of the netCDF file
-	for dimname,dim in f.dimensions.iteritems():
-		# if you want to make changes in the dimensions of the new file
-		# you should add your own conditions here before the creation of the dimension.
-		#g.createDimension(dimname,len(dim))
-		g.createDimension(dimname,Number_of_bergs)
+        # To copy the dimension of the netCDF file
+        for dimname,dim in f.dimensions.items():
+                # if you want to make changes in the dimensions of the new file
+                # you should add your own conditions here before the creation of the dimension.
+                #g.createDimension(dimname,len(dim))
+                g.createDimension(dimname,Number_of_bergs)
 
-	# To copy the variables of the netCDF file
+        # To copy the variables of the netCDF file
 
-	for varname,ncvar in f.variables.iteritems():
-		# if you want to make changes in the variables of the new file
-		# you should add your own conditions here before the creation of the variable.
-		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
-		#Proceed to copy the variable attributes
-		for attname in ncvar.ncattrs():
-			setattr(var,attname,getattr(ncvar,attname))
-		#Finally copy the variable data to the new created variable
-		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
+        for varname,ncvar in f.variables.items():
+                # if you want to make changes in the variables of the new file
+                # you should add your own conditions here before the creation of the variable.
+                var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
+                #Proceed to copy the variable attributes
+                for attname in ncvar.ncattrs():
+                        setattr(var,attname,getattr(ncvar,attname))
+                #Finally copy the variable data to the new created variable
+                #var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
 
-		if varname=='i':
-			var[:]=Number_of_bergs
+                if varname=='i':
+                        var[:]=Number_of_bergs
 
-		if varname=='iceberg_num':
-			for j in range(Number_of_bergs):
-				#var[j]=j+1
-				var[j]=iceberg_num[j]
+                if varname=='iceberg_num':
+                        for j in range(Number_of_bergs):
+                                #var[j]=j+1
+                                var[j]=iceberg_num[j]
 
-		if varname=='uvel' or varname=='vvel' or varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
-		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
-		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
-		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
-			var[:]=0
+                if varname=='uvel' or varname=='vvel' or varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
+                or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
+                or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
+                or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
+                        var[:]=0
 
-		if varname=='mass_scaling':
-			var[:]=mass_scaling
+                if varname=='mass_scaling':
+                        var[:]=mass_scaling
 
-		if varname=='thickness':
-			for j in range(Number_of_bergs):
-				var[j]=thickness[j]
+                if varname=='thickness':
+                        for j in range(Number_of_bergs):
+                                var[j]=thickness[j]
 
-		if varname=='mass':
-			for j in range(Number_of_bergs):
-				var[j]=mass[j]
+                if varname=='mass':
+                        for j in range(Number_of_bergs):
+                                var[j]=mass[j]
 
-		if varname=='width'  or varname=='length':
-			for j in range(Number_of_bergs):
-				var[j]=width[j]
+                if varname=='width'  or varname=='length':
+                        for j in range(Number_of_bergs):
+                                var[j]=width[j]
 
-		if varname=='lon':
-			for j in range(Number_of_bergs):
-				var[j]=lon[j]
+                if varname=='lon':
+                        for j in range(Number_of_bergs):
+                                var[j]=lon[j]
 
-		if varname=='lat':
-			for j in range(Number_of_bergs):
-				var[j]=lat[j]
+                if varname=='lat':
+                        for j in range(Number_of_bergs):
+                                var[j]=lat[j]
 
-		if varname=='static_berg':
-			for j in range(Number_of_bergs):
-				var[j]=static_berg[j]
+                if varname=='static_berg':
+                        for j in range(Number_of_bergs):
+                                var[j]=static_berg[j]
 
 
-	f.close()
-	g.close()
+        f.close()
+        g.close()
 
 
 
 def Create_bond_restart_file(Number_of_bonds,first_berg_num,first_berg_ine,first_berg_jne,other_berg_ine,other_berg_jne,iceberg_num,other_berg_num,Ice_geometry_source):
-	#Creating the bond restart file
+        #Creating the bond restart file
 
-	print 'Writing bond restart files with  ', Number_of_bonds, ' Bonds'
-	# To copy the global attributes of the netCDF file
+        print ('Writing bond restart files with  ', Number_of_bonds, ' Bonds')
+        # To copy the global attributes of the netCDF file
 
-	#Input and output files
-	#Create Empty restart file. This is later read so that the attributes can be used.
-	Empty_bond_restart_filename='output_files/Empty_bonds_icebergs.res.nc'
-	create_empty_bond_restart_file(Empty_bond_restart_filename)
-	#Empty_bond_restart_filename='input_files/bonds_iceberg.res.nc'
+        #Input and output files
+        #Create Empty restart file. This is later read so that the attributes can be used.
+        Empty_bond_restart_filename='output_files/Empty_bonds_icebergs.res.nc'
+        create_empty_bond_restart_file(Empty_bond_restart_filename)
+        #Empty_bond_restart_filename='input_files/bonds_iceberg.res.nc'
 
-	h=Dataset(Empty_bond_restart_filename,'r',format='NETCDF3_CLASSIC') # r is for read only
-	q=Dataset('output_files/' + Ice_geometry_source + '_bonds_iceberg.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
+        h=Dataset(Empty_bond_restart_filename,'r',format='NETCDF3_CLASSIC') # r is for read only
+        q=Dataset('output_files/' + Ice_geometry_source + '_bonds_iceberg.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
 
-	for attname in h.ncattrs():
-		    setattr(q,attname,getattr(h,attname))
+        for attname in h.ncattrs():
+                    setattr(q,attname,getattr(h,attname))
 
 
-	# To copy the dimension of the netCDF file
-	for dimname,dim in h.dimensions.iteritems():
-		# if you want to make changes in the dimensions of the new file
-		# you should add your own conditions here before the creation of the dimension.
-		#g.createDimension(dimname,len(dim))
-		q.createDimension(dimname,Number_of_bonds)
+        # To copy the dimension of the netCDF file
+        for dimname,dim in h.dimensions.items():
+                # if you want to make changes in the dimensions of the new file
+                # you should add your own conditions here before the creation of the dimension.
+                #g.createDimension(dimname,len(dim))
+                q.createDimension(dimname,Number_of_bonds)
 
-	# To copy the variables of the netCDF file
+        # To copy the variables of the netCDF file
 
-	for varname,ncvar in h.variables.iteritems():
-		# if you want to make changes in the variables of the new file
-		# you should add your own conditions here before the creation of the variable.
-		var = q.createVariable(varname,ncvar.dtype,ncvar.dimensions)
-		#Proceed to copy the variable attributes
-		for attname in ncvar.ncattrs():
-			setattr(var,attname,getattr(ncvar,attname))
-		#Finally copy the variable data to the new created variable
-		#var[:] = ncvar[0]
-		var[:] = 0.
+        for varname,ncvar in h.variables.items():
+                # if you want to make changes in the variables of the new file
+                # you should add your own conditions here before the creation of the variable.
+                var = q.createVariable(varname,ncvar.dtype,ncvar.dimensions)
+                #Proceed to copy the variable attributes
+                for attname in ncvar.ncattrs():
+                        setattr(var,attname,getattr(ncvar,attname))
+                #Finally copy the variable data to the new created variable
+                #var[:] = ncvar[0]
+                var[:] = 0.
 
-		if varname=='i':
-			var[:]=Number_of_bonds
+                if varname=='i':
+                        var[:]=Number_of_bonds
 
-		if varname=='first_berg_num':
-			for j in range(Number_of_bonds):
-				var[j]=first_berg_num[j]
+                if varname=='first_berg_num':
+                        for j in range(Number_of_bonds):
+                                var[j]=first_berg_num[j]
 
-		if varname=='first_berg_ine':
-			for j in range(Number_of_bonds):
-				var[j]=first_berg_ine[j]
+                if varname=='first_berg_ine':
+                        for j in range(Number_of_bonds):
+                                var[j]=first_berg_ine[j]
 
-		if varname=='first_berg_jne':
-			for j in range(Number_of_bonds):
-				var[j]=first_berg_jne[j]
+                if varname=='first_berg_jne':
+                        for j in range(Number_of_bonds):
+                                var[j]=first_berg_jne[j]
 
-		if varname=='other_berg_num':
-			for j in range(Number_of_bonds):
-				var[j]=other_berg_num[j]
+                if varname=='other_berg_num':
+                        for j in range(Number_of_bonds):
+                                var[j]=other_berg_num[j]
 
-		if varname=='other_berg_ine':
-			for j in range(Number_of_bonds):
-				var[j]=other_berg_ine[j]
+                if varname=='other_berg_ine':
+                        for j in range(Number_of_bonds):
+                                var[j]=other_berg_ine[j]
 
-		if varname=='other_berg_jne':
-			for j in range(Number_of_bonds):
-				var[j]=other_berg_jne[j]
+                if varname=='other_berg_jne':
+                        for j in range(Number_of_bonds):
+                                var[j]=other_berg_jne[j]
 
-	h.close()
-	q.close()
+        h.close()
+        q.close()
 
 
 def create_empty_iceberg_restart_file(Empty_restart_filename):
 
-	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
-
-	i=f.createDimension('i', None)
-	lon=f.createVariable('i','i')
-
-	lon=f.createVariable('lon','d',('i'))
-	lon.long_name = "longitude" ;
-	lon.units = "degrees_E" ;
-	lon.checksum = "               0" ;
-
-	lat=f.createVariable('lat','d',('i'))
-	lat.long_name = "latitude" ;
-	lat.units = "degrees_N" ;
-	lat.checksum = "               0" ;
-
-	uvel=f.createVariable('uvel','d',('i'))
-	uvel.long_name = "zonal velocity" ;
-	uvel.units = "m/s" ;
-	uvel.checksum = "               0" ;
-
-	vvel=f.createVariable('vvel','d',('i'))
-	vvel.long_name = "meridional velocity" ;
-	vvel.units = "m/s" ;
-	vvel.checksum = "               0" ;
-
-	mass=f.createVariable('mass','d',('i'))
-	mass.long_name = "mass" ;
-	mass.units = "kg" ;
-	mass.checksum = "               0" ;
-
-	axn=f.createVariable('axn','d',('i'))
-	axn.long_name = "explicit zonal acceleration" ;
-	axn.units = "m/s^2" ;
-	axn.checksum = "               0" ;
-
-	ayn=f.createVariable('ayn','d',('i'))
-	ayn.long_name = "explicit meridional acceleration" ;
-	ayn.units = "m/s^2" ;
-	ayn.checksum = "               0" ;
-
-	bxn=f.createVariable('bxn','d',('i'))
-	bxn.long_name = "inplicit zonal acceleration" ;
-	bxn.units = "m/s^2" ;
-	bxn.checksum = "               0" ;
-
-	byn=f.createVariable('byn','d',('i'))
-	byn.long_name = "implicit meridional acceleration" ;
-	byn.units = "m/s^2" ;
-	byn.checksum = "               0" ;
-
-	ine=f.createVariable('ine','i',('i'))
-	ine.long_name = "i index" ;
-	ine.units = "none" ;
-	ine.packing = 0 ;
-	ine.checksum = "               0" ;
-
-	jne=f.createVariable('jne','i',('i'))
-	jne.long_name = "j index" ;
-	jne.units = "none" ;
-	jne.packing = 0 ;
-	jne.checksum = "               0" ;
-
-	thickness=f.createVariable('thickness','d',('i'))
-	thickness.long_name = "thickness" ;
-	thickness.units = "m" ;
-	thickness.checksum = "               0" ;
-
-	width=f.createVariable('width','d',('i'))
-	width.long_name = "width" ;
-	width.units = "m" ;
-	width.checksum = "               0" ;
-
-	length=f.createVariable('length','d',('i'))
-	length.long_name = "length" ;
-	length.units = "m" ;
-	length.checksum = "               0" ;
-
-	start_lon=f.createVariable('start_lon','d',('i'))
-	start_lon.long_name = "longitude of calving location" ;
-	start_lon.units = "degrees_E" ;
-	start_lon.checksum = "               0" ;
-
-	start_lat=f.createVariable('start_lat','d',('i'))
-	start_lat.long_name = "latitude of calving location" ;
-	start_lat.units = "degrees_N" ;
-	start_lat.checksum = "               0" ;
-
-	start_year=f.createVariable('start_year','i',('i'))
-	start_year.long_name = "calendar year of calving event" ;
-	start_year.units = "years" ;
-	start_year.packing = 0 ;
-	start_year.checksum = "               0" ;
-
-	iceberg_num=f.createVariable('iceberg_num','i',('i'))
-	iceberg_num.long_name = "identification of the iceberg" ;
-	iceberg_num.units = "dimensionless" ;
-	iceberg_num.packing = 0 ;
-	iceberg_num.checksum = "               0" ;
-
-	start_day=f.createVariable('start_day','d',('i'))
-	start_day.long_name = "year day of calving event" ;
-	start_day.units = "days" ;
-	start_day.checksum = "               0" ;
-
-	start_mass=f.createVariable('start_mass','d',('i'))
-	start_mass.long_name = "initial mass of calving berg" ;
-	start_mass.units = "kg" ;
-	start_mass.checksum = "               0" ;
-
-	mass_scaling=f.createVariable('mass_scaling','d',('i'))
-	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
-	mass_scaling.units = "none" ;
-	mass_scaling.checksum = "               0" ;
-
-	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
-	mass_of_bits.long_name = "mass of bergy bits" ;
-	mass_of_bits.units = "kg" ;
-	mass_of_bits.checksum = "               0" ;
-
-	heat_density=f.createVariable('heat_density','d',('i'))
-	heat_density.long_name = "heat density" ;
-	heat_density.units = "J/kg" ;
-	heat_density.checksum = "               0" ;
-
-	halo_berg=f.createVariable('halo_berg','d',('i'))
-	halo_berg.long_name = "halo_berg" ;
-	halo_berg.units = "dimensionless" ;
-	halo_berg.checksum = "               0" ;
-
-	static_berg=f.createVariable('static_berg','d',('i'))
-	static_berg.long_name = "static_berg" ;
-	static_berg.units = "dimensionless" ;
-	static_berg.checksum = "               0" ;
-
-	f.sync()
-	f.close()
+        f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
+
+        i=f.createDimension('i', None)
+        lon=f.createVariable('i','i')
+
+        lon=f.createVariable('lon','d',('i'))
+        lon.long_name = "longitude" ;
+        lon.units = "degrees_E" ;
+        lon.checksum = "               0" ;
+
+        lat=f.createVariable('lat','d',('i'))
+        lat.long_name = "latitude" ;
+        lat.units = "degrees_N" ;
+        lat.checksum = "               0" ;
+
+        uvel=f.createVariable('uvel','d',('i'))
+        uvel.long_name = "zonal velocity" ;
+        uvel.units = "m/s" ;
+        uvel.checksum = "               0" ;
+
+        vvel=f.createVariable('vvel','d',('i'))
+        vvel.long_name = "meridional velocity" ;
+        vvel.units = "m/s" ;
+        vvel.checksum = "               0" ;
+
+        mass=f.createVariable('mass','d',('i'))
+        mass.long_name = "mass" ;
+        mass.units = "kg" ;
+        mass.checksum = "               0" ;
+
+        axn=f.createVariable('axn','d',('i'))
+        axn.long_name = "explicit zonal acceleration" ;
+        axn.units = "m/s^2" ;
+        axn.checksum = "               0" ;
+
+        ayn=f.createVariable('ayn','d',('i'))
+        ayn.long_name = "explicit meridional acceleration" ;
+        ayn.units = "m/s^2" ;
+        ayn.checksum = "               0" ;
+
+        bxn=f.createVariable('bxn','d',('i'))
+        bxn.long_name = "inplicit zonal acceleration" ;
+        bxn.units = "m/s^2" ;
+        bxn.checksum = "               0" ;
+
+        byn=f.createVariable('byn','d',('i'))
+        byn.long_name = "implicit meridional acceleration" ;
+        byn.units = "m/s^2" ;
+        byn.checksum = "               0" ;
+
+        ine=f.createVariable('ine','i',('i'))
+        ine.long_name = "i index" ;
+        ine.units = "none" ;
+        ine.packing = 0 ;
+        ine.checksum = "               0" ;
+
+        jne=f.createVariable('jne','i',('i'))
+        jne.long_name = "j index" ;
+        jne.units = "none" ;
+        jne.packing = 0 ;
+        jne.checksum = "               0" ;
+
+        thickness=f.createVariable('thickness','d',('i'))
+        thickness.long_name = "thickness" ;
+        thickness.units = "m" ;
+        thickness.checksum = "               0" ;
+
+        width=f.createVariable('width','d',('i'))
+        width.long_name = "width" ;
+        width.units = "m" ;
+        width.checksum = "               0" ;
+
+        length=f.createVariable('length','d',('i'))
+        length.long_name = "length" ;
+        length.units = "m" ;
+        length.checksum = "               0" ;
+
+        start_lon=f.createVariable('start_lon','d',('i'))
+        start_lon.long_name = "longitude of calving location" ;
+        start_lon.units = "degrees_E" ;
+        start_lon.checksum = "               0" ;
+
+        start_lat=f.createVariable('start_lat','d',('i'))
+        start_lat.long_name = "latitude of calving location" ;
+        start_lat.units = "degrees_N" ;
+        start_lat.checksum = "               0" ;
+
+        start_year=f.createVariable('start_year','i',('i'))
+        start_year.long_name = "calendar year of calving event" ;
+        start_year.units = "years" ;
+        start_year.packing = 0 ;
+        start_year.checksum = "               0" ;
+
+        iceberg_num=f.createVariable('iceberg_num','i',('i'))
+        iceberg_num.long_name = "identification of the iceberg" ;
+        iceberg_num.units = "dimensionless" ;
+        iceberg_num.packing = 0 ;
+        iceberg_num.checksum = "               0" ;
+
+        start_day=f.createVariable('start_day','d',('i'))
+        start_day.long_name = "year day of calving event" ;
+        start_day.units = "days" ;
+        start_day.checksum = "               0" ;
+
+        start_mass=f.createVariable('start_mass','d',('i'))
+        start_mass.long_name = "initial mass of calving berg" ;
+        start_mass.units = "kg" ;
+        start_mass.checksum = "               0" ;
+
+        mass_scaling=f.createVariable('mass_scaling','d',('i'))
+        mass_scaling.long_name = "scaling factor for mass of calving berg" ;
+        mass_scaling.units = "none" ;
+        mass_scaling.checksum = "               0" ;
+
+        mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
+        mass_of_bits.long_name = "mass of bergy bits" ;
+        mass_of_bits.units = "kg" ;
+        mass_of_bits.checksum = "               0" ;
+
+        heat_density=f.createVariable('heat_density','d',('i'))
+        heat_density.long_name = "heat density" ;
+        heat_density.units = "J/kg" ;
+        heat_density.checksum = "               0" ;
+
+        halo_berg=f.createVariable('halo_berg','d',('i'))
+        halo_berg.long_name = "halo_berg" ;
+        halo_berg.units = "dimensionless" ;
+        halo_berg.checksum = "               0" ;
+
+        static_berg=f.createVariable('static_berg','d',('i'))
+        static_berg.long_name = "static_berg" ;
+        static_berg.units = "dimensionless" ;
+        static_berg.checksum = "               0" ;
+
+        f.sync()
+        f.close()
 
 def create_empty_bond_restart_file(Empty_bond_restart_filename):
 
-	f = Dataset(Empty_bond_restart_filename,'w', format='NETCDF3_CLASSIC')
-
-	i=f.createDimension('i', None)
-	i=f.createVariable('i','i')
-
-	first_berg_ine=f.createVariable('first_berg_ine','i',('i'))
-	first_berg_ine.long_name = "iceberg ine of first berg in bond" ;
-	first_berg_ine.units = "dimensionless" ;
-	first_berg_ine.packing = 0 ;
-	first_berg_ine.checksum = "               0" ;
-
-	first_berg_jne=f.createVariable('first_berg_jne','i',('i'))
-	first_berg_jne.long_name = "iceberg jne of first berg in bond" ;
-	first_berg_jne.units = "dimensionless" ;
-	first_berg_jne.packing = 0 ;
-	first_berg_jne.checksum = "               0" ;
-
-	first_berg_num=f.createVariable('first_berg_num','i',('i'))
-	first_berg_num.long_name = "iceberg id first berg in bond" ;
-	first_berg_num.units = "dimensionless" ;
-	first_berg_num.packing = 0 ;
-	first_berg_num.checksum = "               0" ;
-
-	other_berg_ine=f.createVariable('other_berg_ine','i',('i'))
-	other_berg_ine.long_name = "iceberg ine of second berg in bond" ;
-	other_berg_ine.units = "dimensionless" ;
-	other_berg_ine.packing = 0 ;
-	other_berg_ine.checksum = "               0" ;
-
-	other_berg_jne=f.createVariable('other_berg_jne','i',('i'))
-	other_berg_jne.long_name = "iceberg jne of second berg in bond" ;
-	other_berg_jne.units = "dimensionless" ;
-	other_berg_jne.packing = 0 ;
-	other_berg_jne.checksum = "                0" ;
-
-	other_berg_num=f.createVariable('other_berg_num','i',('i'))
-	other_berg_num.long_name = "iceberg id second berg in bond" ;
-	other_berg_num.units = "dimensionless" ;
-	other_berg_num.packing = 0 ;
-	other_berg_num.checksum = "               0" ;
-
-	f.sync()
-	f.close()
+        f = Dataset(Empty_bond_restart_filename,'w', format='NETCDF3_CLASSIC')
+
+        i=f.createDimension('i', None)
+        i=f.createVariable('i','i')
+
+        first_berg_ine=f.createVariable('first_berg_ine','i',('i'))
+        first_berg_ine.long_name = "iceberg ine of first berg in bond" ;
+        first_berg_ine.units = "dimensionless" ;
+        first_berg_ine.packing = 0 ;
+        first_berg_ine.checksum = "               0" ;
+
+        first_berg_jne=f.createVariable('first_berg_jne','i',('i'))
+        first_berg_jne.long_name = "iceberg jne of first berg in bond" ;
+        first_berg_jne.units = "dimensionless" ;
+        first_berg_jne.packing = 0 ;
+        first_berg_jne.checksum = "               0" ;
+
+        first_berg_num=f.createVariable('first_berg_num','i',('i'))
+        first_berg_num.long_name = "iceberg id first berg in bond" ;
+        first_berg_num.units = "dimensionless" ;
+        first_berg_num.packing = 0 ;
+        first_berg_num.checksum = "               0" ;
+
+        other_berg_ine=f.createVariable('other_berg_ine','i',('i'))
+        other_berg_ine.long_name = "iceberg ine of second berg in bond" ;
+        other_berg_ine.units = "dimensionless" ;
+        other_berg_ine.packing = 0 ;
+        other_berg_ine.checksum = "               0" ;
+
+        other_berg_jne=f.createVariable('other_berg_jne','i',('i'))
+        other_berg_jne.long_name = "iceberg jne of second berg in bond" ;
+        other_berg_jne.units = "dimensionless" ;
+        other_berg_jne.packing = 0 ;
+        other_berg_jne.checksum = "                0" ;
+
+        other_berg_num=f.createVariable('other_berg_num','i',('i'))
+        other_berg_num.long_name = "iceberg id second berg in bond" ;
+        other_berg_num.units = "dimensionless" ;
+        other_berg_num.packing = 0 ;
+        other_berg_num.checksum = "               0" ;
+
+        f.sync()
+        f.close()
 
 def Define_iceberg_thickness_and_mass(Number_of_bergs,dx_berg,dy_berg,rho_ice,Radius,h_ice,x,y,\
-		width,Interpolate_from_four_corners,element_area,element_type,static_berg):
-	thickness=[]
-	mass=[]
-	ny,nx=h_ice.shape
-	dx=x[1]-x[0]
-	grid_area=dx*dx
-	for berg_count in range(Number_of_bergs):
-		x_val=dx_berg[berg_count] ; y_val=dy_berg[berg_count]
-		i_val=int(math.floor(x_val/dx))
-		j_val=int(math.floor(y_val/dx))
-
-		#Interpolate thickness from 4 corners - possibly do this later, but I worry about when you are between a shelf and non shelf piece.
-		if Interpolate_from_four_corners==True:
-
-			x_cell=(x_val-x[i_val])/np.sqrt(grid_area)+0.5
-			y_cell=(y_val-y[j_val])/np.sqrt(grid_area)+0.5
-
-			mass_on_ocean=np.zeros([nx,ny,10])   #Setting up matrix to spread mass to ocean.  Note that I have used 10 points  so that I can ignore 0 and match with python numbering
-			mass_val=1.
-			mass_on_ocean=spread_mass_to_ocean(nx,ny,i_val,j_val,mass_on_ocean,x_cell,y_cell,element_area,mass_val,element_type,grid_area,static_berg[berg_count])
-			Th=0.
-			h=np.array([0,0,0,0,0,0,0,0,0,0])
-			if i_val>0 and j_val>0:
-				h[1]=h_ice[j_val-1,i_val-1]
-			if j_val>0:
-				h[2]=h_ice[j_val-1,i_val]
-			if j_val>0 and i_val<(nx-1):
-				h[3]=h_ice[j_val-1,i_val+1]
-			if i_val>0:
-				h[4]=h_ice[j_val,i_val-1]
-			if True:
-				h[5]=h_ice[j_val,i_val]
-			if i_val<(nx-1):
-				h[6]=h_ice[j_val,i_val+1]
-			if i_val>0 and j_val<(ny-1):
-				h[7]=h_ice[j_val+1,i_val-1]
-			if j_val<(ny-1):
-				h[8]=h_ice[j_val+1,i_val]
-			if i_val<(nx-1) and j_val<(ny-1):
-				h[9]=h_ice[j_val+1,i_val+1]
-			for k in range(1,10):
-				Th=Th+(mass_on_ocean[i_val,j_val,k]*h[k])
-				#print i_val,j_val,k,mass_on_ocean[i_val,j_val,k]
-			#if abs(Th-1)>0.0000001:
-			#	print 'Thickness',Th-1,i_val,j_val
-			#	test=0.
-			#	for k in range(1,10):
-			#		print k,mass_on_ocean[i_val,j_val,k], h[k]
-			#		test=test+(mass_on_ocean[i_val,j_val,k])
-			#	print test
-			#	halt
-
-
-
-		Th=h_ice[j_val,i_val]
-		thickness.append(Th)
-		#Check that all thicknesses are positive
-		if Th<=0:
-			print 'Thickness is less than or equal to zero,0!',i_val, j_val,x_val,y_val
-			halt
-		#mass.append(Th*rho_ice*element_area)
-		mass.append(Th*rho_ice*(width[berg_count])**2)
-		#if element_type=='square':
-		#	mass.append(Th*rho_ice*((2*Radius)**2)) # For square elements
-		#else:
-		#	mass.append(Th*rho_ice*np.pi*(Radius**2))  #For circular elements
-	return [thickness, mass]
+                width,Interpolate_from_four_corners,element_area,element_type,static_berg):
+        thickness=[]
+        mass=[]
+        ny,nx=h_ice.shape
+        dx=x[1]-x[0]
+        grid_area=dx*dx
+        for berg_count in range(Number_of_bergs):
+                x_val=dx_berg[berg_count] ; y_val=dy_berg[berg_count]
+                i_val=int(math.floor(x_val/dx))
+                j_val=int(math.floor(y_val/dx))
+
+                #Interpolate thickness from 4 corners - possibly do this later, but I worry about when you are between a shelf and non shelf piece.
+                if Interpolate_from_four_corners==True:
+
+                        x_cell=(x_val-x[i_val])/np.sqrt(grid_area)+0.5
+                        y_cell=(y_val-y[j_val])/np.sqrt(grid_area)+0.5
+
+                        mass_on_ocean=np.zeros([nx,ny,10])   #Setting up matrix to spread mass to ocean.  Note that I have used 10 points  so that I can ignore 0 and match with python numbering
+                        mass_val=1.
+                        mass_on_ocean=spread_mass_to_ocean(nx,ny,i_val,j_val,mass_on_ocean,x_cell,y_cell,element_area,mass_val,element_type,grid_area,static_berg[berg_count])
+                        Th=0.
+                        h=np.array([0,0,0,0,0,0,0,0,0,0])
+                        if i_val>0 and j_val>0:
+                                h[1]=h_ice[j_val-1,i_val-1]
+                        if j_val>0:
+                                h[2]=h_ice[j_val-1,i_val]
+                        if j_val>0 and i_val<(nx-1):
+                                h[3]=h_ice[j_val-1,i_val+1]
+                        if i_val>0:
+                                h[4]=h_ice[j_val,i_val-1]
+                        if True:
+                                h[5]=h_ice[j_val,i_val]
+                        if i_val<(nx-1):
+                                h[6]=h_ice[j_val,i_val+1]
+                        if i_val>0 and j_val<(ny-1):
+                                h[7]=h_ice[j_val+1,i_val-1]
+                        if j_val<(ny-1):
+                                h[8]=h_ice[j_val+1,i_val]
+                        if i_val<(nx-1) and j_val<(ny-1):
+                                h[9]=h_ice[j_val+1,i_val+1]
+                        for k in range(1,10):
+                                Th=Th+(mass_on_ocean[i_val,j_val,k]*h[k])
+                                #print (i_val,j_val,k,mass_on_ocean[i_val,j_val,k])
+                        #if abs(Th-1)>0.0000001:
+                        #       print ('Thickness',Th-1,i_val,j_val)
+                        #       test=0.
+                        #       for k in range(1,10):
+                        #               print (k,mass_on_ocean[i_val,j_val,k], h[k])
+                        #               test=test+(mass_on_ocean[i_val,j_val,k])
+                        #       print (test)
+                        #       halt
+
+
+
+                Th=h_ice[j_val,i_val]
+                thickness.append(Th)
+                #Check that all thicknesses are positive
+                if Th<=0:
+                        print ('Thickness is less than or equal to zero,0!',i_val, j_val,x_val,y_val)
+                        halt
+                #mass.append(Th*rho_ice*element_area)
+                mass.append(Th*rho_ice*(width[berg_count])**2)
+                #if element_type=='square':
+                #       mass.append(Th*rho_ice*((2*Radius)**2)) # For square elements
+                #else:
+                #       mass.append(Th*rho_ice*np.pi*(Radius**2))  #For circular elements
+        return [thickness, mass]
 
 
 def check_if_it_is_in_domain(x_val,y_val,x_min,x_max,y_min,y_max,R_earth,lat_init,adjust_lat_ref,dx,dy):
-	point_is_in_domain=True
+        point_is_in_domain=True
 
-	if (x_val >= (x_max-x_min+(dx))) or (x_val<= 0) or  (y_val >= (y_max-y_min+(dy))) or (y_val <= 0):
-		point_is_in_domain=False
+        if (x_val >= (x_max-x_min+(dx))) or (x_val<= 0) or  (y_val >= (y_max-y_min+(dy))) or (y_val <= 0):
+                point_is_in_domain=False
 
-	return point_is_in_domain
+        return point_is_in_domain
 
 def check_if_it_is_ice(x_val,y_val,ice_mask,dx):
-	i_val=int(math.floor(x_val/dx))
-	j_val=int(math.floor(y_val/dx))
-	if ice_mask[j_val,i_val]==1.:
-		it_is_ice=True
-	else:
-		it_is_ice=False
-	return it_is_ice
+        i_val=int(math.floor(x_val/dx))
+        j_val=int(math.floor(y_val/dx))
+        if ice_mask[j_val,i_val]==1.:
+                it_is_ice=True
+        else:
+                it_is_ice=False
+        return it_is_ice
 
 def calculate_element_area(element_type,Radius):
-	if element_type=='square':
-		element_area=(2*Radius)**2
-	elif element_type=='hexagon':
-		element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*(Radius)**2) #Area of hexagon around circle (used for packing)
-		#Another derivation uses innner hexagon with two more triangles added, which is a 1/6 of the hexagon area each (two since there are 6, shared by 3 each)
-		#element_area=(4./3.)*H_i, where H_i=(3.*np.sqrt(3.)/2.)*((Radius)**2)  is the area of the inner hexagon (with sides equal to the radius)
+        if element_type=='square':
+                element_area=(2*Radius)**2
+        elif element_type=='hexagon':
+                element_area=(3.*np.sqrt(3.)/2.)*((4./3.)*(Radius)**2) #Area of hexagon around circle (used for packing)
+                #Another derivation uses innner hexagon with two more triangles added, which is a 1/6 of the hexagon area each (two since there are 6, shared by 3 each)
+                #element_area=(4./3.)*H_i, where H_i=(3.*np.sqrt(3.)/2.)*((Radius)**2)  is the area of the inner hexagon (with sides equal to the radius)
 
-	return element_area
+        return element_area
 
 def add_and_extra_boundary_berg(i,j,New_thickness,y_shift,x_shift,Nbh_thickness_value,Nbh_mass_value,New_mass,berg_count,dx_berg,dy_berg,\
-		iceberg_num,thickness,width,mass,static_berg,grid_area,rho_ice):
-	tol=0.0000000000001
-	if New_thickness[j,i]>1.+tol:
-		print 'The new thickness is too big!!!', i,j,  New_thickness[j,i]
-		halt
-	if ((Nbh_thickness_value-New_thickness[j,i])>tol):
-		y_val=y_shift[j]
-		x_val=x_shift[i]
-		if Nbh_thickness_value>0. and (abs(Nbh_thickness_value-1)<tol) and (Nbh_mass_value>New_mass[j,i]):
-			berg_count=berg_count+1
-			dx_berg.append(x_val)
-			dy_berg.append(y_val)
-			iceberg_num.append(berg_count)
-			width_val=np.sqrt((Nbh_thickness_value-New_thickness[j,i])*grid_area)
-			if Nbh_thickness_value-New_thickness[j,i]<0:
-				print 'Stop', Nbh_thickness_value, New_thickness[j,i],i,j
-			mass_val=Nbh_mass_value-New_mass[j,i]
-			thickness_val=mass_val/(width_val*width_val*rho_ice)
-			thickness.append(thickness_val)
-			width.append(width_val)
-			mass.append(mass_val)
-			static_berg.append(1.)
-	return [berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg]
+                iceberg_num,thickness,width,mass,static_berg,grid_area,rho_ice):
+        tol=0.0000000000001
+        if New_thickness[j,i]>1.+tol:
+                print ('The new thickness is too big!!!', i,j,  New_thickness[j,i])
+                halt
+        if ((Nbh_thickness_value-New_thickness[j,i])>tol):
+                y_val=y_shift[j]
+                x_val=x_shift[i]
+                if Nbh_thickness_value>0. and (abs(Nbh_thickness_value-1)<tol) and (Nbh_mass_value>New_mass[j,i]):
+                        berg_count=berg_count+1
+                        dx_berg.append(x_val)
+                        dy_berg.append(y_val)
+                        iceberg_num.append(berg_count)
+                        width_val=np.sqrt((Nbh_thickness_value-New_thickness[j,i])*grid_area)
+                        if Nbh_thickness_value-New_thickness[j,i]<0:
+                                print ('Stop', Nbh_thickness_value, New_thickness[j,i],i,j)
+                        mass_val=Nbh_mass_value-New_mass[j,i]
+                        thickness_val=mass_val/(width_val*width_val*rho_ice)
+                        thickness.append(thickness_val)
+                        width.append(width_val)
+                        mass.append(mass_val)
+                        static_berg.append(1.)
+        return [berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg]
 
 
 def add_extra_bergs_on_boundary(dx,dy,x,y,Number_of_bergs,element_area,rho_ice,X_min,X_max,Y_min,Y_max,R_earth,lat_init,adjust_lat_ref,ice_mask,\
-		iceberg_num,width,dx_berg,dy_berg,h_ice,element_type,static_berg,thickness,mass):
-	eps=0.000001
-	grid_area=dx*dy
-	Nx=len(x)  ; Ny=len(y)
-	x_shift=(x-np.min(x))+(dx/2) ; y_shift=(y-np.min(y))+(dy/2)
-
-	thickness_temp= [1. for i in range(Number_of_bergs)] ;
-	mass_temp= [element_area*rho_ice*1. for i in range(Number_of_bergs)] ;
-	New_area=regrid_iceberg_thickness(dy_berg,dx_berg,Number_of_bergs,thickness_temp,mass_temp,h_ice,x_shift,y_shift,rho_ice,element_type,static_berg,plot_outcome=False)
-	New_thickness=(New_area)/(rho_ice*grid_area)  #Should be equal to one everywhere where there is ice shelf.
-	New_mass=regrid_iceberg_thickness(dy_berg,dx_berg,Number_of_bergs,thickness,mass,h_ice,x_shift,y_shift,rho_ice,element_type,static_berg,plot_outcome=False)
-	berg_count=Number_of_bergs
-
-
-	#Vertical boundary
-	for i in np.array([0,Nx-1]):
-		#for j in range(Ny):
-		for j in range(1,Ny-1):
-			Nbh_mass_value=h_ice[j,i]*rho_ice*grid_area  #Neighbouring shelf value
-			if i==0:
-				Nbh_thickness_value=New_thickness[j,1]  #Neighbouring shelf value
-				#x_val=0+(eps*dx)
-			if i==Nx-1:
-				Nbh_thickness_value=New_thickness[j,Nx-2]  #Neighbouring shelf value
-				#x_val=x_shift[i]+(dx/2)-eps
-			[berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg]=add_and_extra_boundary_berg(i,j,New_thickness,y_shift,x_shift,\
-					Nbh_thickness_value,Nbh_mass_value,New_mass,berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg,grid_area,rho_ice)
-
-	##Horizontal boundary
-	for j in np.array([0,Ny-1]):
-		#for i in range(1,Nx-1):
-		for i in range(1,Nx-1):
-			Nbh_mass_value=h_ice[j,i]*rho_ice*grid_area  #Neighbouring shelf value
-			if j==0:
-				Nbh_thickness_value=New_thickness[1,i]  #Neighbouring shelf value
-				#y_val=0+(eps*dy)
-			if j==Ny-1:
-				Nbh_thickness_value=New_thickness[Ny-2,i]  #Neighbouring shelf value
-				#y_val=y_shift[j]+(dy/2)-eps
-			#Nbh_thickness_value=np.mean(New_thickness[range(1,Ny-1),i])  #Neighbouring shelf value
-			[berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg]=add_and_extra_boundary_berg(i,j,New_thickness,y_shift,x_shift,\
-					Nbh_thickness_value,Nbh_mass_value,New_mass,berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg,grid_area,rho_ice)
-
-	#Doing the corners seperately
-	for j in np.array([0,Ny-1]):
-		#for i in range(1,Nx-1):
-		for i in np.array([0,Nx-1]):
-			Nbh_mass_value=h_ice[j,i]*rho_ice*grid_area  #Neighbouring shelf value
-			if j==0 and i==0:
-				Nbh_thickness_value=New_thickness[1,1]  #Neighbouring shelf value
-			if j==0 and i==Nx-1:
-				Nbh_thickness_value=New_thickness[1,Nx-2]  #Neighbouring shelf value
-			if j==Ny-1 and i==0:
-				Nbh_thickness_value=New_thickness[Ny-2,1]  #Neighbouring shelf value
-			if j==Ny-1 and i==Nx-1:
-				Nbh_thickness_value=New_thickness[Ny-2,Nx-2]  #Neighbouring shelf value
-			[berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg]=add_and_extra_boundary_berg(i,j,New_thickness,y_shift,x_shift,\
-					Nbh_thickness_value,Nbh_mass_value,New_mass,berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg,grid_area,rho_ice)
-
-
-	Number_of_bergs=berg_count
-
-	return [dx_berg, dy_berg,iceberg_num, width,Number_of_bergs,static_berg,thickness,mass]
+                iceberg_num,width,dx_berg,dy_berg,h_ice,element_type,static_berg,thickness,mass):
+        eps=0.000001
+        grid_area=dx*dy
+        Nx=len(x)  ; Ny=len(y)
+        x_shift=(x-np.min(x))+(dx/2) ; y_shift=(y-np.min(y))+(dy/2)
+
+        thickness_temp= [1. for i in range(Number_of_bergs)] ;
+        mass_temp= [element_area*rho_ice*1. for i in range(Number_of_bergs)] ;
+        New_area=regrid_iceberg_thickness(dy_berg,dx_berg,Number_of_bergs,thickness_temp,mass_temp,h_ice,x_shift,y_shift,rho_ice,element_type,static_berg,plot_outcome=False)
+        New_thickness=(New_area)/(rho_ice*grid_area)  #Should be equal to one everywhere where there is ice shelf.
+        New_mass=regrid_iceberg_thickness(dy_berg,dx_berg,Number_of_bergs,thickness,mass,h_ice,x_shift,y_shift,rho_ice,element_type,static_berg,plot_outcome=False)
+        berg_count=Number_of_bergs
+
+
+        #Vertical boundary
+        for i in np.array([0,Nx-1]):
+                #for j in range(Ny):
+                for j in range(1,Ny-1):
+                        Nbh_mass_value=h_ice[j,i]*rho_ice*grid_area  #Neighbouring shelf value
+                        if i==0:
+                                Nbh_thickness_value=New_thickness[j,1]  #Neighbouring shelf value
+                                #x_val=0+(eps*dx)
+                        if i==Nx-1:
+                                Nbh_thickness_value=New_thickness[j,Nx-2]  #Neighbouring shelf value
+                                #x_val=x_shift[i]+(dx/2)-eps
+                        [berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg]=add_and_extra_boundary_berg(i,j,New_thickness,y_shift,x_shift,\
+                                        Nbh_thickness_value,Nbh_mass_value,New_mass,berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg,grid_area,rho_ice)
+
+        ##Horizontal boundary
+        for j in np.array([0,Ny-1]):
+                #for i in range(1,Nx-1):
+                for i in range(1,Nx-1):
+                        Nbh_mass_value=h_ice[j,i]*rho_ice*grid_area  #Neighbouring shelf value
+                        if j==0:
+                                Nbh_thickness_value=New_thickness[1,i]  #Neighbouring shelf value
+                                #y_val=0+(eps*dy)
+                        if j==Ny-1:
+                                Nbh_thickness_value=New_thickness[Ny-2,i]  #Neighbouring shelf value
+                                #y_val=y_shift[j]+(dy/2)-eps
+                        #Nbh_thickness_value=np.mean(New_thickness[range(1,Ny-1),i])  #Neighbouring shelf value
+                        [berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg]=add_and_extra_boundary_berg(i,j,New_thickness,y_shift,x_shift,\
+                                        Nbh_thickness_value,Nbh_mass_value,New_mass,berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg,grid_area,rho_ice)
+
+        #Doing the corners seperately
+        for j in np.array([0,Ny-1]):
+                #for i in range(1,Nx-1):
+                for i in np.array([0,Nx-1]):
+                        Nbh_mass_value=h_ice[j,i]*rho_ice*grid_area  #Neighbouring shelf value
+                        if j==0 and i==0:
+                                Nbh_thickness_value=New_thickness[1,1]  #Neighbouring shelf value
+                        if j==0 and i==Nx-1:
+                                Nbh_thickness_value=New_thickness[1,Nx-2]  #Neighbouring shelf value
+                        if j==Ny-1 and i==0:
+                                Nbh_thickness_value=New_thickness[Ny-2,1]  #Neighbouring shelf value
+                        if j==Ny-1 and i==Nx-1:
+                                Nbh_thickness_value=New_thickness[Ny-2,Nx-2]  #Neighbouring shelf value
+                        [berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg]=add_and_extra_boundary_berg(i,j,New_thickness,y_shift,x_shift,\
+                                        Nbh_thickness_value,Nbh_mass_value,New_mass,berg_count,dx_berg,dy_berg,iceberg_num,thickness,width,mass,static_berg,grid_area,rho_ice)
+
+
+        Number_of_bergs=berg_count
+
+        return [dx_berg, dy_berg,iceberg_num, width,Number_of_bergs,static_berg,thickness,mass]
 
 
 def remove_stationary_bergs(dx_berg, dy_berg,iceberg_num,width,Number_of_bergs,static_berg):
-	dx_berg_new=[]
-	dy_berg_new=[]
-	iceberg_num_new=[]
-	width_new=[]
-	static_berg_new=[]
-	for i in range(Number_of_bergs):
-		if static_berg[i]>0.5:
-		#if static_berg[i]<0.5:
-			dx_berg_new.append(dx_berg[i])
-			dy_berg_new.append(dy_berg[i])
-			iceberg_num_new.append(iceberg_num[i])
-			width_new.append(width[i])
-			static_berg_new.append(static_berg[i])
-
-	Number_of_bergs_new=len(iceberg_num_new)
-	return [dx_berg_new, dy_berg_new,iceberg_num_new, width_new,Number_of_bergs_new,static_berg_new]
+        dx_berg_new=[]
+        dy_berg_new=[]
+        iceberg_num_new=[]
+        width_new=[]
+        static_berg_new=[]
+        for i in range(Number_of_bergs):
+                if static_berg[i]>0.5:
+                #if static_berg[i]<0.5:
+                        dx_berg_new.append(dx_berg[i])
+                        dy_berg_new.append(dy_berg[i])
+                        iceberg_num_new.append(iceberg_num[i])
+                        width_new.append(width[i])
+                        static_berg_new.append(static_berg[i])
+
+        Number_of_bergs_new=len(iceberg_num_new)
+        return [dx_berg_new, dy_berg_new,iceberg_num_new, width_new,Number_of_bergs_new,static_berg_new]
 
 def Create_icebergs(lon_init,lat_init,Radius,R_earth, x, y,ice_mask,h_ice,Convert_to_lat_lon,rho_ice,\
-		element_type,scale_the_grid_to_lat_lon,lat_ref,adjust_lat_ref,Interpolate_from_four_corners,\
-		Fill_in_the_boundaries,set_all_bergs_static_by_default,break_some_bonds,Remove_stationary_bergs,\
+                element_type,scale_the_grid_to_lat_lon,lat_ref,adjust_lat_ref,Interpolate_from_four_corners,\
+                Fill_in_the_boundaries,set_all_bergs_static_by_default,break_some_bonds,Remove_stationary_bergs,\
                 set_some_bergs_static_by_default,collision_test,grounding_test):
-	print 'Starting to create icebergs...'
-	dx_berg=[]  #x distance in cartesian of berg from lon_init
-	dy_berg=[]  #y distance in cartesian of berg from lat_init
-	dlon_berg=[] #x distance in lon of berg from lon_init
-	#dlat_berg=[] #y distance in lat of berg from lat_init
-	lon=[] #Longitude of iceberg
-	lat=[] #Latitude of iceberg
-	iceberg_num=[] #ID of iceberg
-
-	element_area=calculate_element_area(element_type,Radius)
-	#width=np.sqrt(element_area)
-	width=[]
-
-	#dx=x[1]-x[0]  ;dy=y[1]-y[0]
-	#X_min=np.min(x)-dx; X_max=np.max(x)+dx  #In lat lon or cartesian
-	#Y_min=np.min(y)-dy; Y_max=np.max(y)+dy  #In lat lon or cartesian
-	X_min=np.min(x); X_max=np.max(x)  #In lat lon or cartesian
-	Y_min=np.min(y); Y_max=np.max(y)  #In lat lon or cartesian
-
-	#N=2*int(ceil((R_max)/(2*Radius))+2)
-
-	if element_type=='square':
-		N=int(math.ceil((X_max-X_min)/(Radius)))
-		M=int(math.ceil((Y_max-Y_min)/(Radius)))
-	else:
-
-                print 'X_max',X_max
-                print 'X_min',X_min
-                print 'Radius',Radius
-		N=2*int(math.ceil((X_max-X_min)/(Radius)))
-		M=2*int(math.ceil((Y_max-Y_min)/(Radius)))
-	#N=10
-	#M=6
-	#MP4
-
- 	dx=x[1]-x[0]
- 	dy=y[1]-y[0]
-	Lx=X_max+dx
-	Ly=Y_max+dx
-
-	berg_count=0
-	#for j in range(N):
-	for i in range(N):
-		if element_type=='square':
-			x_start=Radius
-			y_start=(Radius)
-			x_val=x_start+(2*i*Radius)
-
-		#Hexagonal
-		else:
-			y_start=(Radius)+(((i%2)*Radius))
-			x_start=((2/np.sqrt(3))*Radius)
-			x_val=x_start + (np.sqrt(3)*Radius*i)
+        print ('Starting to create icebergs...')
+        dx_berg=[]  #x distance in cartesian of berg from lon_init
+        dy_berg=[]  #y distance in cartesian of berg from lat_init
+        dlon_berg=[] #x distance in lon of berg from lon_init
+        #dlat_berg=[] #y distance in lat of berg from lat_init
+        lon=[] #Longitude of iceberg
+        lat=[] #Latitude of iceberg
+        iceberg_num=[] #ID of iceberg
+
+        element_area=calculate_element_area(element_type,Radius)
+        #width=np.sqrt(element_area)
+        width=[]
+
+        #dx=x[1]-x[0]  ;dy=y[1]-y[0]
+        #X_min=np.min(x)-dx; X_max=np.max(x)+dx  #In lat lon or cartesian
+        #Y_min=np.min(y)-dy; Y_max=np.max(y)+dy  #In lat lon or cartesian
+        X_min=np.min(x); X_max=np.max(x)  #In lat lon or cartesian
+        Y_min=np.min(y); Y_max=np.max(y)  #In lat lon or cartesian
+
+        #N=2*int(ceil((R_max)/(2*Radius))+2)
+
+        if element_type=='square':
+                N=int(math.ceil((X_max-X_min)/(Radius)))
+                M=int(math.ceil((Y_max-Y_min)/(Radius)))
+        else:
+
+                print ('X_max',X_max)
+                print ('X_min',X_min)
+                print ('Radius',Radius)
+                N=2*int(math.ceil((X_max-X_min)/(Radius)))
+                M=2*int(math.ceil((Y_max-Y_min)/(Radius)))
+
+        dx=x[1]-x[0]
+        dy=y[1]-y[0]
+        Lx=X_max+dx
+        Ly=Y_max+dx
+
+        berg_count=0
+        #for j in range(N):
+        for i in range(N):
+                if element_type=='square':
+                        x_start=Radius
+                        y_start=(Radius)
+                        x_val=x_start+(2*i*Radius)
+
+                #Hexagonal
+                else:
+                        y_start=(Radius)+(((i%2)*Radius))
+                        x_start=((2/np.sqrt(3))*Radius)
+                        x_val=x_start + (np.sqrt(3)*Radius*i)
 
                 if grounding_test:
                         for j in range(M):
@@ -867,272 +864,272 @@ def Create_icebergs(lon_init,lat_init,Radius,R_earth, x, y,ice_mask,h_ice,Conver
                                                 width.append(np.sqrt(element_area))
 
 
-	#print 'dx_berg',dx_berg
-	#print 'dy_berg',dy_berg
+        #print ('dx_berg',dx_berg)
+        #print ('dy_berg',dy_berg)
 
 
-	Number_of_bergs=berg_count
+        Number_of_bergs=berg_count
 
 
-	#Deciding if icebergs are static or not
-	static_berg = [0. for i in dx_berg]
-	if set_all_bergs_static_by_default==True:
-		static_berg = [1. for i in static_berg]
-	if set_some_bergs_static_by_default is True:
-		for i in range(len(dx_berg)):
-			if dx_berg[i]>Lx/2:
-				static_berg[i]=1.
-	if break_some_bonds==True:
-		#static_berg =Change_static_berg_after_calving(Number_of_bergs,lat,lon, static_berg)
-		static_berg =Change_static_berg_after_calving(Number_of_bergs,dy_berg,dx_berg, static_berg)
-		static_berg=static_berg[0]
+        #Deciding if icebergs are static or not
+        static_berg = [0. for i in dx_berg]
+        if set_all_bergs_static_by_default==True:
+                static_berg = [1. for i in static_berg]
+        if set_some_bergs_static_by_default is True:
+                for i in range(len(dx_berg)):
+                        if dx_berg[i]>Lx/2:
+                                static_berg[i]=1.
+        if break_some_bonds==True:
+                #static_berg =Change_static_berg_after_calving(Number_of_bergs,lat,lon, static_berg)
+                static_berg =Change_static_berg_after_calving(Number_of_bergs,dy_berg,dx_berg, static_berg)
+                static_berg=static_berg[0]
 
-	if Remove_stationary_bergs is True:
-		Fill_in_the_boundaries=False
-		[dx_berg, dy_berg,iceberg_num, width,Number_of_bergs,static_berg]=remove_stationary_bergs(dx_berg, dy_berg,iceberg_num,\
-				width,Number_of_bergs,static_berg)
-		print 'After purge  Number of bergs = ', Number_of_bergs
+        if Remove_stationary_bergs is True:
+                Fill_in_the_boundaries=False
+                [dx_berg, dy_berg,iceberg_num, width,Number_of_bergs,static_berg]=remove_stationary_bergs(dx_berg, dy_berg,iceberg_num,\
+                                width,Number_of_bergs,static_berg)
+                print ('After purge  Number of bergs = ', Number_of_bergs)
 
 
-	#Defining the thickness of the icebergs
-	(thickness, mass)=Define_iceberg_thickness_and_mass(Number_of_bergs,dx_berg,dy_berg,rho_ice,Radius, h_ice,x,y,\
-			width,Interpolate_from_four_corners,element_area,element_type,static_berg)
+        #Defining the thickness of the icebergs
+        (thickness, mass)=Define_iceberg_thickness_and_mass(Number_of_bergs,dx_berg,dy_berg,rho_ice,Radius, h_ice,x,y,\
+                        width,Interpolate_from_four_corners,element_area,element_type,static_berg)
 
-	N_bergs_before_bd=Number_of_bergs
-	if Fill_in_the_boundaries==True and element_type=='hexagon':
-	 	[dx_berg, dy_berg,iceberg_num, width,Number_of_bergs,static_berg,thickness,mass]= add_extra_bergs_on_boundary(dx,dy,x,y,Number_of_bergs,element_area,rho_ice,X_min,X_max,Y_min,\
-				Y_max,R_earth,lat_init,adjust_lat_ref,ice_mask,iceberg_num,width,dx_berg,dy_berg,\
-				h_ice,element_type,static_berg,thickness,mass)
-		print 'Number of icebergs after accounting for boundaries = ', Number_of_bergs
+        N_bergs_before_bd=Number_of_bergs
+        if Fill_in_the_boundaries==True and element_type=='hexagon':
+                [dx_berg, dy_berg,iceberg_num, width,Number_of_bergs,static_berg,thickness,mass]= add_extra_bergs_on_boundary(dx,dy,x,y,Number_of_bergs,element_area,rho_ice,X_min,X_max,Y_min,\
+                                Y_max,R_earth,lat_init,adjust_lat_ref,ice_mask,iceberg_num,width,dx_berg,dy_berg,\
+                                h_ice,element_type,static_berg,thickness,mass)
+                print ('Number of icebergs after accounting for boundaries = ', Number_of_bergs)
 
         if collision_test:
                 for i in range(berg_count):
                         berg_count=berg_count+1
-			iceberg_num.append(berg_count)
-			dx_berg.append(dx_berg[i])
-			dy_berg.append(20000.0-dy_berg[i])
-			width.append(width[i])
+                        iceberg_num.append(berg_count)
+                        dx_berg.append(dx_berg[i])
+                        dy_berg.append(20000.0-dy_berg[i])
+                        width.append(width[i])
                         thickness.append(thickness[i])
                         mass.append(mass[i])
                         static_berg.append(static_berg[i])
                 Number_of_bergs=berg_count
 
-	if Convert_to_lat_lon==True:
-		#Defining lon lat positions:
-		#dlat_berg=(180/np.pi)*(1/R_earth)*dy_berg
-		#dlon_berg=(180/np.pi)*(1/R_earth)*(1/np.cos(lat_init*np.pi/180))*dx_berg
-		for i in range(Number_of_bergs):
-			#Finding latittude
-			dlat_dy=(180/np.pi)*(1/R_earth)
-
-			lat.append(lat_init+(dlat_dy*dy_berg[i]))
-
-			#Finding longitude
-			if adjust_lat_ref==True:
-				lat_ref=lat_init+(dlat_dy*dy_berg[i])
-				#print lat_ref
-			dlon_dx=(180/np.pi)*(1/R_earth)*(1/np.cos(lat_ref*np.pi/180)) #Note that this depends on the latitude of the iceberg. Could approx this with lat_init.
-			lon.append(lon_init+(dlon_dx*dx_berg[i] ))
-
-			#dlon_berg.append(dlon_dx*dx_berg[i])
-			#lon.append(lon_init+dlon_berg[i])
-	else:
-		if scale_the_grid_to_lat_lon==True:
-			Scale_up=1./2000.
-			Radius=Radius*Scale_up
-			dx_berg = [(i*Scale_up) for i in dx_berg] ; dy_berg = [i*Scale_up for i in dy_berg]
-			x=x*Scale_up ; y=y*Scale_up
-			dx=dx*Scale_up ;dy=dy*Scale_up
-		x=(x-np.min(x))+(dx/2) ; y=(y-np.min(y))+(dy/2)
-		lon=dx_berg  ; lat=dy_berg
+        if Convert_to_lat_lon==True:
+                #Defining lon lat positions:
+                #dlat_berg=(180/np.pi)*(1/R_earth)*dy_berg
+                #dlon_berg=(180/np.pi)*(1/R_earth)*(1/np.cos(lat_init*np.pi/180))*dx_berg
+                for i in range(Number_of_bergs):
+                        #Finding latittude
+                        dlat_dy=(180/np.pi)*(1/R_earth)
+
+                        lat.append(lat_init+(dlat_dy*dy_berg[i]))
+
+                        #Finding longitude
+                        if adjust_lat_ref==True:
+                                lat_ref=lat_init+(dlat_dy*dy_berg[i])
+                                #print (lat_ref)
+                        dlon_dx=(180/np.pi)*(1/R_earth)*(1/np.cos(lat_ref*np.pi/180)) #Note that this depends on the latitude of the iceberg. Could approx this with lat_init.
+                        lon.append(lon_init+(dlon_dx*dx_berg[i] ))
+
+                        #dlon_berg.append(dlon_dx*dx_berg[i])
+                        #lon.append(lon_init+dlon_berg[i])
+        else:
+                if scale_the_grid_to_lat_lon==True:
+                        Scale_up=1./2000.
+                        Radius=Radius*Scale_up
+                        dx_berg = [(i*Scale_up) for i in dx_berg] ; dy_berg = [i*Scale_up for i in dy_berg]
+                        x=x*Scale_up ; y=y*Scale_up
+                        dx=dx*Scale_up ;dy=dy*Scale_up
+                x=(x-np.min(x))+(dx/2) ; y=(y-np.min(y))+(dy/2)
+                lon=dx_berg  ; lat=dy_berg
 
         if grounding_test:
                 for i in range(Number_of_bergs):
                         lat[i]=lat[i]-0.0 #500.0
 
-	#Note that static_berg calculations used to be here, after the conversion. I have moved them. I hope that this does not affect answers.
+        #Note that static_berg calculations used to be here, after the conversion. I have moved them. I hope that this does not affect answers.
 
-        print 'Icebergs created. Number of bergs = ', Number_of_bergs
-	return (Number_of_bergs,lon,lat,iceberg_num,dx_berg,dy_berg,thickness, mass,width,x,y,Radius,static_berg,N_bergs_before_bd)
+        print ('Icebergs created. Number of bergs = ', Number_of_bergs)
+        return (Number_of_bergs,lon,lat,iceberg_num,dx_berg,dy_berg,thickness, mass,width,x,y,Radius,static_berg,N_bergs_before_bd)
 
 
 
 def Create_calving_event(lat1,lon1,lat2,lon2):
-	[R_calve, R_long, R_short, Calve_lon, Calve_lat]=get_calving_parameters()
+        [R_calve, R_long, R_short, Calve_lon, Calve_lat]=get_calving_parameters()
 
-	#Circular calving from ice front
-	R1=np.sqrt((lon1-Calve_lon)**2+ (lat1-Calve_lat)**2)
-	R2=np.sqrt((lon2-Calve_lon)**2+ (lat2-Calve_lat)**2)
+        #Circular calving from ice front
+        R1=np.sqrt((lon1-Calve_lon)**2+ (lat1-Calve_lat)**2)
+        R2=np.sqrt((lon2-Calve_lon)**2+ (lat2-Calve_lat)**2)
 
-	#Iceberg splitting down the midde (length wise)
-	#R1=lat1
-	#R2=lat2
-	#R_calve=500*1000
-	#Iceberg splitting down the midde (width wise)
-	#R1=lon1
-	#R2=lon2
-	#R_calve=250*1000
+        #Iceberg splitting down the midde (length wise)
+        #R1=lat1
+        #R2=lat2
+        #R_calve=500*1000
+        #Iceberg splitting down the midde (width wise)
+        #R1=lon1
+        #R2=lon2
+        #R_calve=250*1000
 
-	#Circular Calving
-	bond_broken=False
-	if ((R1 < R_calve)*(R2>R_calve) )  > 0.5 :
-		bond_broken=True
-	if ((R2 < R_calve)*(R1>R_calve) )  > 0.5 :
-		bond_broken=True
+        #Circular Calving
+        bond_broken=False
+        if ((R1 < R_calve)*(R2>R_calve) )  > 0.5 :
+                bond_broken=True
+        if ((R2 < R_calve)*(R1>R_calve) )  > 0.5 :
+                bond_broken=True
 
 
 
-	#Rectabgular Calving
-	#R1_x=np.sqrt((lon1-Calve_lon)**2)
-	#R1_y=np.sqrt((lat1-Calve_lat)**2)
-	#R2_x=np.sqrt((lon2-Calve_lon)**2)
-	#R2_y=np.sqrt((lat2-Calve_lat)**2)
-	#bond_broken=False
-	#if ((R1_x<R_short)*(R1_y<R_long))*(1-((R2_x<R_short)*(R2_y<R_long)))  > 0.5 :
-	#	bond_broken=True
-	#if ((R2_x<R_short)*(R2_y<R_long))*(1-((R1_x<R_short)*(R1_y<R_long)))  > 0.5 :
-	#	bond_broken=True
+        #Rectabgular Calving
+        #R1_x=np.sqrt((lon1-Calve_lon)**2)
+        #R1_y=np.sqrt((lat1-Calve_lat)**2)
+        #R2_x=np.sqrt((lon2-Calve_lon)**2)
+        #R2_y=np.sqrt((lat2-Calve_lat)**2)
+        #bond_broken=False
+        #if ((R1_x<R_short)*(R1_y<R_long))*(1-((R2_x<R_short)*(R2_y<R_long)))  > 0.5 :
+        #       bond_broken=True
+        #if ((R2_x<R_short)*(R2_y<R_long))*(1-((R1_x<R_short)*(R1_y<R_long)))  > 0.5 :
+        #       bond_broken=True
 
 
-	return bond_broken
+        return bond_broken
 
 def get_calving_parameters():
-	#Calve_lat =20
-	#Calve_lon=160
-	#R_calve=15
-	Calve_lat =20.2*2000
-	Calve_lon=165*2000
-	R_calve=15*2000
-	R_long =18*2000
-	R_short =12*2000
+        #Calve_lat =20
+        #Calve_lon=160
+        #R_calve=15
+        Calve_lat =20.2*2000
+        Calve_lon=165*2000
+        R_calve=15*2000
+        R_long =18*2000
+        R_short =12*2000
 
-	return [R_calve,  R_long, R_short, Calve_lon, Calve_lat]
+        return [R_calve,  R_long, R_short, Calve_lon, Calve_lat]
 
 def Change_static_berg_after_calving(Number_of_bergs,lat,lon, static_berg):
-	[R_calve, R_long, R_short, Calve_lon, Calve_lat]=get_calving_parameters()
-	count=0.
-	for i in range(Number_of_bergs):
-		#R1=np.sqrt((lon[i]-Calve_lon)**2)
-		#R2=np.sqrt((lat[i]-Calve_lat)**2)
-		R1=np.sqrt((lon[i]-Calve_lon)**2+ (lat[i]-Calve_lat)**2)
-		#Making calved icebergs not be static.
-		#if R1<R_calve and (R2<1.6*R_calve):
-		#if R1<R_short and (R2<R_long):
-		if R1<R_calve:
-			count=count+1.
-			#print 'An iceberg is now static!'
-			static_berg[i]=0.
-	print 'Amount of unstatic icebergs after calving = ', count
-
-	return [static_berg]
+        [R_calve, R_long, R_short, Calve_lon, Calve_lat]=get_calving_parameters()
+        count=0.
+        for i in range(Number_of_bergs):
+                #R1=np.sqrt((lon[i]-Calve_lon)**2)
+                #R2=np.sqrt((lat[i]-Calve_lat)**2)
+                R1=np.sqrt((lon[i]-Calve_lon)**2+ (lat[i]-Calve_lat)**2)
+                #Making calved icebergs not be static.
+                #if R1<R_calve and (R2<1.6*R_calve):
+                #if R1<R_short and (R2<R_long):
+                if R1<R_calve:
+                        count=count+1.
+                        #print ('An iceberg is now static!')
+                        static_berg[i]=0.
+        print ('Amount of unstatic icebergs after calving = ', count)
+
+        return [static_berg]
 
 def Change_static_berg_after_bonding(Number_of_bergs,lat,lon, static_berg):
-	#For now, it just uses a bigger circle.
-	multiplier=1.2
-	[R_calve, R_long, R_short, Calve_lon, Calve_lat]=get_calving_parameters()
-	count=0.
-	for i in range(Number_of_bergs):
-		R1=np.sqrt((lon[i]-Calve_lon)**2+ (lat[i]-Calve_lat)**2)
-		#Making calved icebergs not be static.
-		#R1=np.sqrt((lon[i]-Calve_lon)**2)
-		#R2=np.sqrt((lat[i]-Calve_lat)**2)
-		#if R1<(multiplier*R_short) and (R2<(multiplier*R_long)):
-		if R1<(R_calve*multiplier):
-			count=count+1.
-			#print 'An iceberg is now static!'
-			static_berg[i]=0.
-	print 'Amount of unstatic icebergs after bonding and restatic= ', count
-
-	return [static_berg]
+        #For now, it just uses a bigger circle.
+        multiplier=1.2
+        [R_calve, R_long, R_short, Calve_lon, Calve_lat]=get_calving_parameters()
+        count=0.
+        for i in range(Number_of_bergs):
+                R1=np.sqrt((lon[i]-Calve_lon)**2+ (lat[i]-Calve_lat)**2)
+                #Making calved icebergs not be static.
+                #R1=np.sqrt((lon[i]-Calve_lon)**2)
+                #R2=np.sqrt((lat[i]-Calve_lat)**2)
+                #if R1<(multiplier*R_short) and (R2<(multiplier*R_long)):
+                if R1<(R_calve*multiplier):
+                        count=count+1.
+                        #print ('An iceberg is now static!')
+                        static_berg[i]=0.
+        print ('Amount of unstatic icebergs after bonding and restatic= ', count)
+
+        return [static_berg]
 
 def find_max_number_of_bonds(first_berg_num,Number_of_bonds):
-	count=1
-	best_count=1
-	sorted_bonds=np.sort(first_berg_num)
-	for k in range(1,Number_of_bonds):
-		previous_berg=sorted_bonds[k-1]
-		#print k, sorted_bonds[k]
-		if sorted_bonds[k] == sorted_bonds[k-1]:
-			count=count+1
-			best_count=max(count,best_count)
-		else:
-			count=1
-	Max_number_of_bonds=best_count
-	return Max_number_of_bonds
+        count=1
+        best_count=1
+        sorted_bonds=np.sort(first_berg_num)
+        for k in range(1,Number_of_bonds):
+                previous_berg=sorted_bonds[k-1]
+                #print (k, sorted_bonds[k])
+                if sorted_bonds[k] == sorted_bonds[k-1]:
+                        count=count+1
+                        best_count=max(count,best_count)
+                else:
+                        count=1
+        Max_number_of_bonds=best_count
+        return Max_number_of_bonds
 
 def Define_iceberg_bonds(Number_of_bergs,iceberg_num,lat,lon,dx_berg, dy_berg,Radius,break_some_bonds,static_berg, Allow_bonds_for_static_iceberg\
-		,N_bergs_before_bd,Allow_bonds_with_boundary_bergs):
-	print 'Starting to create bonds...'
-	#Defining Bonds:
-	Bond=np.zeros((Number_of_bergs, Number_of_bergs))
-	bond_broken=False
-	first_berg_num=[]  # Initializing bond list first berg
-	first_berg_ine=[]  # Initializing bond list first berg
-	first_berg_jne=[]  # Initializing bond list first berg
-	first_berg_lat=[]  # Initializing bond list first berg
-	first_berg_lon=[]  # Initializing bond list first berg
-	other_berg_num=[]  # Initializing bond list other berg
-	other_berg_ine=[]  # Initializing bond list other berg
-	other_berg_jne=[]  # Initializing bond list other berg
-	other_berg_lat=[]  # Initializing bond list other berg
-	other_berg_lon=[]  # Initializing bond list other berg
-	bond_count=0
-	for i in range(Number_of_bergs):
-		if (static_berg[i]<0.5) or (Allow_bonds_for_static_iceberg is True):
-			#for j in range(Number_of_bergs):
-			for j in range(i):
-				if (static_berg[j]<0.5) or (Allow_bonds_for_static_iceberg is True):
-					if i!=j:
-						if ((i <N_bergs_before_bd) and (j <N_bergs_before_bd))  or (Allow_bonds_with_boundary_bergs is True):
-							R_dist=np.sqrt(((dx_berg[i]-dx_berg[j])**2) + ((dy_berg[i]-dy_berg[j])**2))
-							if break_some_bonds==True:
-								bond_broken=Create_calving_event(lat[i],lon[i],lat[j],lon[j])
-							if R_dist < (2.01*Radius) and (bond_broken==False):
-								bond_count=bond_count+2
-								#Connect bond in the first direction
-								first_berg_num.append(iceberg_num[i]);	first_berg_ine.append(999);
-								other_berg_num.append(iceberg_num[j]); 	other_berg_ine.append(999);
-								first_berg_jne.append(999);first_berg_lat.append(lat[i]); first_berg_lon.append(lon[i])
-								other_berg_jne.append(999);other_berg_lat.append(lat[j]); other_berg_lon.append(lon[j])
-								#Connect bond in the other direction
-								first_berg_num.append(iceberg_num[j]);	first_berg_ine.append(999);
-								other_berg_num.append(iceberg_num[i]); 	other_berg_ine.append(999);
-								first_berg_jne.append(999);first_berg_lat.append(lat[j]); first_berg_lon.append(lon[j])
-								other_berg_jne.append(999);other_berg_lat.append(lat[i]); other_berg_lon.append(lon[i])
-	Number_of_bonds=bond_count
-	Max_number_of_bonds=find_max_number_of_bonds(first_berg_num,Number_of_bonds)
-	print 'Number of bonds created = ' , Number_of_bonds
-	print 'Maximum number of bonds = ' ,  Max_number_of_bonds
-
-	return [ Number_of_bonds, first_berg_num,first_berg_ine,first_berg_jne,first_berg_lat,first_berg_lon, other_berg_num,other_berg_ine, other_berg_jne,other_berg_lat,other_berg_lon]
+                ,N_bergs_before_bd,Allow_bonds_with_boundary_bergs):
+        print ('Starting to create bonds...')
+        #Defining Bonds:
+        Bond=np.zeros((Number_of_bergs, Number_of_bergs))
+        bond_broken=False
+        first_berg_num=[]  # Initializing bond list first berg
+        first_berg_ine=[]  # Initializing bond list first berg
+        first_berg_jne=[]  # Initializing bond list first berg
+        first_berg_lat=[]  # Initializing bond list first berg
+        first_berg_lon=[]  # Initializing bond list first berg
+        other_berg_num=[]  # Initializing bond list other berg
+        other_berg_ine=[]  # Initializing bond list other berg
+        other_berg_jne=[]  # Initializing bond list other berg
+        other_berg_lat=[]  # Initializing bond list other berg
+        other_berg_lon=[]  # Initializing bond list other berg
+        bond_count=0
+        for i in range(Number_of_bergs):
+                if (static_berg[i]<0.5) or (Allow_bonds_for_static_iceberg is True):
+                        #for j in range(Number_of_bergs):
+                        for j in range(i):
+                                if (static_berg[j]<0.5) or (Allow_bonds_for_static_iceberg is True):
+                                        if i!=j:
+                                                if ((i <N_bergs_before_bd) and (j <N_bergs_before_bd))  or (Allow_bonds_with_boundary_bergs is True):
+                                                        R_dist=np.sqrt(((dx_berg[i]-dx_berg[j])**2) + ((dy_berg[i]-dy_berg[j])**2))
+                                                        if break_some_bonds==True:
+                                                                bond_broken=Create_calving_event(lat[i],lon[i],lat[j],lon[j])
+                                                        if R_dist < (2.01*Radius) and (bond_broken==False):
+                                                                bond_count=bond_count+2
+                                                                #Connect bond in the first direction
+                                                                first_berg_num.append(iceberg_num[i]);  first_berg_ine.append(999);
+                                                                other_berg_num.append(iceberg_num[j]);  other_berg_ine.append(999);
+                                                                first_berg_jne.append(999);first_berg_lat.append(lat[i]); first_berg_lon.append(lon[i])
+                                                                other_berg_jne.append(999);other_berg_lat.append(lat[j]); other_berg_lon.append(lon[j])
+                                                                #Connect bond in the other direction
+                                                                first_berg_num.append(iceberg_num[j]);  first_berg_ine.append(999);
+                                                                other_berg_num.append(iceberg_num[i]);  other_berg_ine.append(999);
+                                                                first_berg_jne.append(999);first_berg_lat.append(lat[j]); first_berg_lon.append(lon[j])
+                                                                other_berg_jne.append(999);other_berg_lat.append(lat[i]); other_berg_lon.append(lon[i])
+        Number_of_bonds=bond_count
+        Max_number_of_bonds=find_max_number_of_bonds(first_berg_num,Number_of_bonds)
+        print ('Number of bonds created = ' , Number_of_bonds)
+        print ('Maximum number of bonds = ' ,  Max_number_of_bonds)
+
+        return [ Number_of_bonds, first_berg_num,first_berg_ine,first_berg_jne,first_berg_lat,first_berg_lon, other_berg_num,other_berg_ine, other_berg_jne,other_berg_lat,other_berg_lon]
 
 def load_ISOMIP_ice_geometry(filename,buffer_number):
-	with nc.Dataset(filename) as file:
-		ocean_mask = file.variables['openOceanMask'][:,:]
-		upperSurface = file.variables['upperSurface'][:,:]
-		lowerSurface = file.variables['lowerSurface'][:,:]
-		x = file.variables['x'][:]
-		y = file.variables['y'][:]
+        with nc.Dataset(filename) as file:
+                ocean_mask = file.variables['openOceanMask'][:,:]
+                upperSurface = file.variables['upperSurface'][:,:]
+                lowerSurface = file.variables['lowerSurface'][:,:]
+                x = file.variables['x'][:]
+                y = file.variables['y'][:]
 
-	ice_mask=1-ocean_mask #one if it ice, zero if it is ocean
-	h_ice=upperSurface-lowerSurface #The ice thickness
-	M=ice_mask.shape
+        ice_mask=1-ocean_mask #one if it ice, zero if it is ocean
+        h_ice=upperSurface-lowerSurface #The ice thickness
+        M=ice_mask.shape
 
-	#Setting the boundaries to non-ice
-	A=np.arange(0,buffer_number)
-	B=np.arange(M[0]-buffer_number,M[0])
-	C=np.arange(M[1]-buffer_number,M[1])
-	ice_mask[A,:]=0; ice_mask[B,:]=0
-	ice_mask[:,A]=0; ice_mask[:,C]=0
+        #Setting the boundaries to non-ice
+        A=np.arange(0,buffer_number)
+        B=np.arange(M[0]-buffer_number,M[0])
+        C=np.arange(M[1]-buffer_number,M[1])
+        ice_mask[A,:]=0; ice_mask[B,:]=0
+        ice_mask[:,A]=0; ice_mask[:,C]=0
 
-	return [x,y,ice_mask,h_ice]
+        return [x,y,ice_mask,h_ice]
 
 
 def create_clipped_icethickness_file(h_ice,area,mass,grid_area,gravity,Ice_geometry_source):
-	#Creating clipped file
+        #Creating clipped file
         [ny, nx]= h_ice.shape ;
 
-	New_ice_thickness_filename='output_files/'+ Ice_geometry_source +'_Ice_Shelf_clipped.nc'
+        New_ice_thickness_filename='output_files/'+ Ice_geometry_source +'_Ice_Shelf_clipped.nc'
         g=Dataset(New_ice_thickness_filename,'w') # w if for creating a file
 
         g.createDimension('nx',nx)
@@ -1149,94 +1146,94 @@ def create_clipped_icethickness_file(h_ice,area,mass,grid_area,gravity,Ice_geome
         p_surf_h.units = 'Pa'
         p_surf_h.standard_name = 'surface pressure due to ice shelf'
 
-	p_surf=(gravity*mass)/grid_area
+        p_surf=(gravity*mass)/grid_area
         g.variables['thick'][:]=h_ice
         g.variables['area'][:]=area
         g.variables['p_surf'][:]=p_surf
-        print 'Creating clipped ice file: ' , New_ice_thickness_filename
+        print ('Creating clipped ice file: ' , New_ice_thickness_filename)
 
         g.sync()
         g.close()
 
 
 def load_ISOMIP_reduced_ice_geometry(ice_filename,buffer_number):
-	with nc.Dataset(ice_filename) as file:
-		h_ice = file.variables['thick'][:,:]
-		area =  file.variables['area'][:,:]
-		M=h_ice.shape
+        with nc.Dataset(ice_filename) as file:
+                h_ice = file.variables['thick'][:,:]
+                area =  file.variables['area'][:,:]
+                M=h_ice.shape
 
-	y=np.linspace(1000,79000,M[0],endpoint=True)
-	#x=np.linspace(321000,799000,M[1],endpoint=True)
-	x=np.linspace(1000,479000,M[1],endpoint=True)
-	ice_mask=h_ice>0.
+        y=np.linspace(1000,79000,M[0],endpoint=True)
+        #x=np.linspace(321000,799000,M[1],endpoint=True)
+        x=np.linspace(1000,479000,M[1],endpoint=True)
+        ice_mask=h_ice>0.
 
 
-	count=0. #MP1
-	#Setting the boundaries to non-ice
-	A=np.arange(0,buffer_number)
-	B=np.arange(M[0]-buffer_number,M[0])
-	C=np.arange(M[1]-buffer_number,M[1])
-	#if buffer_number>0:
-	ice_mask[A,:]=0; ice_mask[B,:]=0
-	ice_mask[:,A]=0; ice_mask[:,C]=0
+        count=0. #MP1
+        #Setting the boundaries to non-ice
+        A=np.arange(0,buffer_number)
+        B=np.arange(M[0]-buffer_number,M[0])
+        C=np.arange(M[1]-buffer_number,M[1])
+        #if buffer_number>0:
+        ice_mask[A,:]=0; ice_mask[B,:]=0
+        ice_mask[:,A]=0; ice_mask[:,C]=0
 
-	return [x,y,ice_mask,h_ice]
+        return [x,y,ice_mask,h_ice]
 
 def load_generic_ice_geometry(filename):
-	print 'Loading from ' , filename
-	with nc.Dataset(filename) as file:
-		h_ice = file.variables['thick'][:]
-		area = file.variables['area'][:,:]
-		x = file.variables['lon'][:]
-		y = file.variables['lat'][:]
+        print ('Loading from ' , filename)
+        with nc.Dataset(filename) as file:
+                h_ice = file.variables['thick'][:]
+                area = file.variables['area'][:,:]
+                x = file.variables['lon'][:]
+                y = file.variables['lat'][:]
 
                # x = x.flatten('F')
                # y = y.flatten('F')
                 #h_ice = h_ice.flatten('F')
 
-		ice_mask=h_ice>0.
-		ice_mask[np.where(ice_mask<-1)]=0.
-		#ice_mask=1-ocean_mask #one if it ice, zero if it is ocean
-		h_ice[np.where(np.isnan(h_ice))]=0.
+                ice_mask=h_ice>0.
+                ice_mask[np.where(ice_mask<-1)]=0.
+                #ice_mask=1-ocean_mask #one if it ice, zero if it is ocean
+                h_ice[np.where(np.isnan(h_ice))]=0.
                 ice_mask[np.where(np.isnan(ice_mask))]=0.
-		dx=x[1]-x[0]
-		lon_init=x[0]-(dx/2.)
-		lat_init=y[0]-(dx/2.)
-		print 'Bottom corner = [ ', lon_init,' , ' , lat_init, ' dx = ' , dx
+                dx=x[1]-x[0]
+                lon_init=x[0]-(dx/2.)
+                lat_init=y[0]-(dx/2.)
+                print ('Bottom corner = [ ', lon_init,' , ' , lat_init, ' dx = ' , dx)
 
-	return [x,y,ice_mask,h_ice,lon_init, lat_init]
+        return [x,y,ice_mask,h_ice,lon_init, lat_init]
 
 def load_Weddel_ice_geometry(filename):
-	with nc.Dataset(filename) as file:
-		h_ice = file.variables['thickness'][:,:]
-		ice_mask = file.variables['icemask_grounded_and_shelves'][:,:]
-		x = file.variables['lon'][:]
-		y = file.variables['lat'][:]
-
-		ice_mask[np.where(ice_mask<-1)]=0.
-		#ice_mask=1-ocean_mask #one if it ice, zero if it is ocean
-		h_ice[np.where(np.isnan(h_ice))]=0.
+        with nc.Dataset(filename) as file:
+                h_ice = file.variables['thickness'][:,:]
+                ice_mask = file.variables['icemask_grounded_and_shelves'][:,:]
+                x = file.variables['lon'][:]
+                y = file.variables['lat'][:]
+
+                ice_mask[np.where(ice_mask<-1)]=0.
+                #ice_mask=1-ocean_mask #one if it ice, zero if it is ocean
+                h_ice[np.where(np.isnan(h_ice))]=0.
                 ice_mask[np.where(np.isnan(ice_mask))]=0.
 
-	return [x,y,ice_mask,h_ice]
+        return [x,y,ice_mask,h_ice]
 
 def Select_just_one_berg(lon,lat,thickness,width,mass,iceberg_num,chosen_berg_num,static_berg):
-	print 'You have chosen to choose just one icebergs!!!'
-	for k in range(len(lat)):
-		if iceberg_num[k]==chosen_berg_num:
-			berg_ind=k
-	lon_temp=lon[berg_ind]; lon=[] ; lon.append(lon_temp)
-	lat_temp=lat[berg_ind]; lat=[] ; lat.append(lat_temp)
-	thickness_temp=thickness[berg_ind]; thickness=[] ; thickness.append(thickness_temp)
-	mass_temp=mass[berg_ind]; mass=[] ; mass.append(mass_temp)
-	width_temp=width[berg_ind]; width=[] ; width.append(width_temp)
-	static_berg_temp=static_berg[berg_ind]; static_berg=[] ; static_berg.append(static_berg_temp)
-	iceberg_num_temp=iceberg_num[berg_ind]; iceberg_num=[] ; iceberg_num.append(iceberg_num_temp)
-	Number_of_bergs=1
-	return [Number_of_bergs,lon,lat,thickness,width,mass,iceberg_num]
+        print ('You have chosen to choose just one icebergs!!!')
+        for k in range(len(lat)):
+                if iceberg_num[k]==chosen_berg_num:
+                        berg_ind=k
+        lon_temp=lon[berg_ind]; lon=[] ; lon.append(lon_temp)
+        lat_temp=lat[berg_ind]; lat=[] ; lat.append(lat_temp)
+        thickness_temp=thickness[berg_ind]; thickness=[] ; thickness.append(thickness_temp)
+        mass_temp=mass[berg_ind]; mass=[] ; mass.append(mass_temp)
+        width_temp=width[berg_ind]; width=[] ; width.append(width_temp)
+        static_berg_temp=static_berg[berg_ind]; static_berg=[] ; static_berg.append(static_berg_temp)
+        iceberg_num_temp=iceberg_num[berg_ind]; iceberg_num=[] ; iceberg_num.append(iceberg_num_temp)
+        Number_of_bergs=1
+        return [Number_of_bergs,lon,lat,thickness,width,mass,iceberg_num]
 
 def Select_just_min_and_max_lat_bergs(lon,lat,thickness,width,mass,iceberg_num,static_berg):
-	print 'You have chosen to choose just two icebergs!!!'
+        print ('You have chosen to choose just two icebergs!!!')
         minlat = lat[1]
         maxlat = lat[1]
         minnum = iceberg_num[1]
@@ -1256,396 +1253,396 @@ def Select_just_min_and_max_lat_bergs(lon,lat,thickness,width,mass,iceberg_num,s
         static_berg=[static_berg[minnum],static_berg[maxnum]]
         iceberg_num=[iceberg_num[minnum],iceberg_num[maxnum]]
         Number_of_bergs=2
-	return [Number_of_bergs,lon,lat,thickness,width,mass,iceberg_num,static_berg]
+        return [Number_of_bergs,lon,lat,thickness,width,mass,iceberg_num,static_berg]
 
 def plotting_iceberg_positions(lat,lon,Number_of_bergs,R_earth,Radius,IA_scaling,Convert_to_lat_lon, \
-		plot_circles,h_ice,ice_mask,x,y,plot_ice_mask,plot_ice_thickness,thickness,plot_icebergs_positions,static_berg,h_ice_new,plot_h_ice_new):
-	print 'Starting to plot...'
-	Radius=Radius*IA_scaling
-	circ_ind=np.linspace(0,2*np.pi,100);
-
-
-
-	if plot_ice_mask==True:
-		cNorm = mpl.colors.Normalize(vmin=0., vmax=1.)
-		plt.pcolor(x,y,ice_mask,norm=cNorm)
-		plt.title('Ice mask')
-
-	elif plot_h_ice_new is True: # Ice thickness after interpolation
-		cNorm = mpl.colors.Normalize(vmin=np.min(h_ice_new), vmax=np.max(h_ice_new))
-		plt.pcolor(x,y,h_ice_new , norm=cNorm)
-		plt.title('New thickness')
-
-	elif plot_ice_thickness==True:
-		cNorm = mpl.colors.Normalize(vmin=0., vmax=1000.)
-		plt.pcolor(x,y,h_ice,cmap='jet',norm=cNorm)
-		plt.title('Old thickness')
-
-	if plot_icebergs_positions==True:
-		#variable=thickness
-		variable=static_berg
-		plt.scatter(lon, lat,color='yellow')
-		cNorm = mpl.colors.Normalize(vmin=0., vmax=np.max(variable))
-		plt.scatter(lon, lat,c=variable,norm=cNorm,cmap='jet',s=150)
-		#cNorm = mpl.colors.Normalize(vmin=-1, vmax=1.)
-		#plt.scatter(lon, lat,c=static_berg,norm=cNorm,cmap='jet',s=150)
-		#plt.title('Iceberg positions')
-
-	#plt.plot(lon, lat,'bo-',linewidth=5)
-	if plot_circles==True:
-		for k in range(Number_of_bergs):
-			if Convert_to_lat_lon==True:
-				dR_lat=(Radius/R_earth)*(180/np.pi)
-				dR_lon=(Radius/R_earth)*(180/np.pi)*(1/np.cos(lat[k]*np.pi/180))
-				plt.plot(lon[k]+(dR_lon*np.cos(circ_ind)),lat[k]+(dR_lat*np.sin(circ_ind)),'b');
-			else:
-				plt.plot(lon[k]+(Radius*np.cos(circ_ind)),lat[k]+(Radius*np.sin(circ_ind)),'b');
-
-
-
-	#plt.plot(lon, lat,'bo-')
-	if Convert_to_lat_lon==True:
-		plt.xlabel('longitude (deg)')
-		plt.ylabel('latitude (deg)')
-	else:
-		plt.xlabel('longitude (m)')
-		plt.ylabel('latitude (m)')
-	plt.colorbar()
-	plt.grid(True)
+                plot_circles,h_ice,ice_mask,x,y,plot_ice_mask,plot_ice_thickness,thickness,plot_icebergs_positions,static_berg,h_ice_new,plot_h_ice_new):
+        print ('Starting to plot...')
+        Radius=Radius*IA_scaling
+        circ_ind=np.linspace(0,2*np.pi,100);
+
+
+
+        if plot_ice_mask==True:
+                cNorm = mpl.colors.Normalize(vmin=0., vmax=1.)
+                plt.pcolor(x,y,ice_mask,norm=cNorm)
+                plt.title('Ice mask')
+
+        elif plot_h_ice_new is True: # Ice thickness after interpolation
+                cNorm = mpl.colors.Normalize(vmin=np.min(h_ice_new), vmax=np.max(h_ice_new))
+                plt.pcolor(x,y,h_ice_new , norm=cNorm)
+                plt.title('New thickness')
+
+        elif plot_ice_thickness==True:
+                cNorm = mpl.colors.Normalize(vmin=0., vmax=1000.)
+                plt.pcolor(x,y,h_ice,cmap='jet',norm=cNorm)
+                plt.title('Old thickness')
+
+        if plot_icebergs_positions==True:
+                #variable=thickness
+                variable=static_berg
+                plt.scatter(lon, lat,color='yellow')
+                cNorm = mpl.colors.Normalize(vmin=0., vmax=np.max(variable))
+                plt.scatter(lon, lat,c=variable,norm=cNorm,cmap='jet',s=150)
+                #cNorm = mpl.colors.Normalize(vmin=-1, vmax=1.)
+                #plt.scatter(lon, lat,c=static_berg,norm=cNorm,cmap='jet',s=150)
+                #plt.title('Iceberg positions')
+
+        #plt.plot(lon, lat,'bo-',linewidth=5)
+        if plot_circles==True:
+                for k in range(Number_of_bergs):
+                        if Convert_to_lat_lon==True:
+                                dR_lat=(Radius/R_earth)*(180/np.pi)
+                                dR_lon=(Radius/R_earth)*(180/np.pi)*(1/np.cos(lat[k]*np.pi/180))
+                                plt.plot(lon[k]+(dR_lon*np.cos(circ_ind)),lat[k]+(dR_lat*np.sin(circ_ind)),'b');
+                        else:
+                                plt.plot(lon[k]+(Radius*np.cos(circ_ind)),lat[k]+(Radius*np.sin(circ_ind)),'b');
+
+
+
+        #plt.plot(lon, lat,'bo-')
+        if Convert_to_lat_lon==True:
+                plt.xlabel('longitude (deg)')
+                plt.ylabel('latitude (deg)')
+        else:
+                plt.xlabel('longitude (m)')
+                plt.ylabel('latitude (m)')
+        plt.colorbar()
+        plt.grid(True)
 
 
 def plotting_iceberg_bonds(first_berg_lat,first_berg_lon,other_berg_lat,other_berg_lon,Number_of_bonds):
 
-	for k in range(Number_of_bonds):
-		x_bond=[]
-		y_bond=[]
-		x_bond.append(first_berg_lon[k])
-		x_bond.append(other_berg_lon[k])
-		y_bond.append(first_berg_lat[k])
-		y_bond.append(other_berg_lat[k])
-		plt.plot(x_bond, y_bond,'r',linewidth=5)
+        for k in range(Number_of_bonds):
+                x_bond=[]
+                y_bond=[]
+                x_bond.append(first_berg_lon[k])
+                x_bond.append(other_berg_lon[k])
+                y_bond.append(first_berg_lat[k])
+                y_bond.append(other_berg_lat[k])
+                plt.plot(x_bond, y_bond,'r',linewidth=5)
 
 
 def spread_mass_to_ocean(Nx,Ny,i,j,mass_on_ocean,x,y,Area,Mass,element_type,grid_area,static_berg):
-		#Note that the x,y coming into this routine are the position within a cell (from 0 to 1), with 0.5,0.5 being in the center of the cell.
-
-		#Initialize weights for each cell
-		yDxL=0.  ; yDxC=0. ; yDxR=0. ; yCxL=0. ; yCxR=0.
-		yUxL=0.  ; yUxC=0. ; yUxR=0. ; yCxC=1.
-
-		if element_type=='square':
-		#if True:
-			L = min(( (np.sqrt(Area)  / np.sqrt(grid_area))),1) ;  #Non dimensionalize element length by grid area. (This gives the non-dim length of the square)
-			xL=min(0.5, max(0., 0.5-(x/L)))
-			xR=min(0.5, max(0., (x/L)+(0.5-(1/L) )))
-			xC=max(0., 1.-(xL+xR))
-			yD=min(0.5, max(0., 0.5-(y/L)))
-			yU=min(0.5, max(0., (y/L)+(0.5-(1/L) )))
-			yC=max(0., 1.-(yD+yU))
-
-			yDxL=yD*xL#*grd%msk[i-1,j-1]
-			yDxC=yD*xC#*grd%msk[i  ,j-1]
-			yDxR=yD*xR#*grd%msk[i+1,j-1]
-			yCxL=yC*xL#*grd%msk[i-1,j  ]
-			yCxR=yC*xR#*grd%msk[i+1,j  ]
-			yUxL=yU*xL#*grd%msk[i-1,j+1]
-			yUxC=yU*xC#*grd%msk[i  ,j+1]
-			yUxR=yU*xR#*grd%msk(i+1,j+1]
-			yCxC=1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )
-
-		if element_type=='hexagon':
-		#if False:#element_type=='hexagon':
-			H = min(( (np.sqrt(Area/(2*np.sqrt(3)))  / np.sqrt(grid_area))),1) ;  #Non dimensionalize element length by grid area. (This gives the non-dim Apothen of the hexagon)
-			S=(2/np.sqrt(3))*H #Side of the hexagon
-			if S>0.5:
-				print 'Elements must be smaller than a whole gridcell', 'i.e.: S= ' , S , '>=0.5',i,j
-				halt
-
-			#Subtracting the position of the nearest corner from x,y
-			origin_x=1 ; origin_y=1
-			if x<0.5:
-				origin_x=0
-			if y<0.5:
-				origin_y=0
-
-			x0=(x-origin_x) #Position of the hexagon center, relative to origin at the nearest vertex
-			y0=(y-origin_y)
-
-			#(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Divide_hexagon_into_4_quadrants_old(x0,y0,H)
-			(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Hexagon_into_quadrants_using_triangles(x0,y0,H,0.)
-			if min(min(Area_Q1,Area_Q2),min(Area_Q3, Area_Q4)) <0:
-				print 'Yolo'
-				print x0,y0,H
-				#print min(min(Area_Q1,Area_Q2),min(Area_Q3, Area_Q4))
-				print Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4
-
-			Area_Q1=Area_Q1/Area_hex
-			Area_Q2=Area_Q2/Area_hex
-			Area_Q3=Area_Q3/Area_hex
-			Area_Q4=Area_Q4/Area_hex
-
-
-			#Now, you decide which quadrant belongs to which mass on ocean cell.
-			#Top right vertex
-			if x>=0.5 and y>= 0.5:
-				yUxR=Area_Q1
-				yUxC=Area_Q2
-				yCxC=Area_Q3
-				yCxR=Area_Q4
-
-			#Top left vertex
-			if x<0.5 and y>= 0.5:
-				yUxC=Area_Q1
-				yUxL=Area_Q2
-				yCxL=Area_Q3
-				yCxC=Area_Q4
-
-			#Bottom left vertex
-			if x<0.5 and y< 0.5:
-				yCxC=Area_Q1
-				yCxL=Area_Q2
-				yDxL=Area_Q3
-				yDxC=Area_Q4
-
-			#Bottom right vertex
-			if x>=0.5 and y< 0.5:
-				yCxR=Area_Q1
-				yCxC=Area_Q2
-				yDxC=Area_Q3
-				yDxR=Area_Q4
-
-			#if Sector<4 and Sector>-1:
-			#	print Sector
-
-
-			#Check that this is true
-			if abs(yCxC-(1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )))>0.001:
-				print 'All the mass is not being used!!!'
-				#print W1 , W2 , W3 , W4 , W5 , W6
-				#print Area_Upper, Area_Lower, Area_right, Area_left
-				print 'Areas: ',Area_hex,Area_hex*Area_Q1, Area_hex*Area_Q2, Area_hex*Area_Q3, Area_hex*Area_Q4
-				print 'x0=',x0, 'y0=',y0, 'H=', H
-				print 'Total area= ',(Area_Q1+Area_Q2+Area_Q3+Area_Q4)#, Sector
-
-
-		#Accounting for masked points
-		a=1. ; b=1. ; c=1. ; d=1.
-		if i==0:
-			a=0.;
-		if j==0:
-			b=0.;
-		if i==Nx-1:
-			c=0;
-		if j==Ny-1:
-			d=0;
-
-		fraction_used= ((yDxL*a*b) + (yDxC*b) + (yDxR*b*c) +(yCxL*a) + (yCxR*c) + (yUxL*a*d) + (yUxC*d) + (yUxR*c*d) + (yCxC))
-		if static_berg>0.5:
-			fraction_used=1.
-
-		mass_on_ocean[i,j,1]=mass_on_ocean[i,j,1]+(a*b*yDxL*Mass/fraction_used)
-		mass_on_ocean[i,j,2]=mass_on_ocean[i,j,2]+(b*yDxC*Mass/fraction_used)
-		mass_on_ocean[i,j,3]=mass_on_ocean[i,j,3]+(b*c*yDxR*Mass/fraction_used)
-		mass_on_ocean[i,j,4]=mass_on_ocean[i,j,4]+(a*yCxL*Mass/fraction_used)
-		mass_on_ocean[i,j,5]=mass_on_ocean[i,j,5]+(yCxC*Mass/fraction_used)
-		mass_on_ocean[i,j,6]=mass_on_ocean[i,j,6]+(c*yCxR*Mass/fraction_used)
-		mass_on_ocean[i,j,7]=mass_on_ocean[i,j,7]+(a*d*yUxL*Mass/fraction_used)
-		mass_on_ocean[i,j,8]=mass_on_ocean[i,j,8]+(d*yUxC*Mass/fraction_used)
-		mass_on_ocean[i,j,9]=mass_on_ocean[i,j,9]+(c*d*yUxR*Mass/fraction_used)
-
-
-		return mass_on_ocean
+                #Note that the x,y coming into this routine are the position within a cell (from 0 to 1), with 0.5,0.5 being in the center of the cell.
+
+                #Initialize weights for each cell
+                yDxL=0.  ; yDxC=0. ; yDxR=0. ; yCxL=0. ; yCxR=0.
+                yUxL=0.  ; yUxC=0. ; yUxR=0. ; yCxC=1.
+
+                if element_type=='square':
+                #if True:
+                        L = min(( (np.sqrt(Area)  / np.sqrt(grid_area))),1) ;  #Non dimensionalize element length by grid area. (This gives the non-dim length of the square)
+                        xL=min(0.5, max(0., 0.5-(x/L)))
+                        xR=min(0.5, max(0., (x/L)+(0.5-(1/L) )))
+                        xC=max(0., 1.-(xL+xR))
+                        yD=min(0.5, max(0., 0.5-(y/L)))
+                        yU=min(0.5, max(0., (y/L)+(0.5-(1/L) )))
+                        yC=max(0., 1.-(yD+yU))
+
+                        yDxL=yD*xL#*grd%msk[i-1,j-1]
+                        yDxC=yD*xC#*grd%msk[i  ,j-1]
+                        yDxR=yD*xR#*grd%msk[i+1,j-1]
+                        yCxL=yC*xL#*grd%msk[i-1,j  ]
+                        yCxR=yC*xR#*grd%msk[i+1,j  ]
+                        yUxL=yU*xL#*grd%msk[i-1,j+1]
+                        yUxC=yU*xC#*grd%msk[i  ,j+1]
+                        yUxR=yU*xR#*grd%msk(i+1,j+1]
+                        yCxC=1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )
+
+                if element_type=='hexagon':
+                #if False:#element_type=='hexagon':
+                        H = min(( (np.sqrt(Area/(2*np.sqrt(3)))  / np.sqrt(grid_area))),1) ;  #Non dimensionalize element length by grid area. (This gives the non-dim Apothen of the hexagon)
+                        S=(2/np.sqrt(3))*H #Side of the hexagon
+                        if S>0.5:
+                                print ('Elements must be smaller than a whole gridcell', 'i.e.: S= ' , S , '>=0.5',i,j)
+                                halt
+
+                        #Subtracting the position of the nearest corner from x,y
+                        origin_x=1 ; origin_y=1
+                        if x<0.5:
+                                origin_x=0
+                        if y<0.5:
+                                origin_y=0
+
+                        x0=(x-origin_x) #Position of the hexagon center, relative to origin at the nearest vertex
+                        y0=(y-origin_y)
+
+                        #(Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Divide_hexagon_into_4_quadrants_old(x0,y0,H)
+                        (Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)= Hexagon_into_quadrants_using_triangles(x0,y0,H,0.)
+                        if min(min(Area_Q1,Area_Q2),min(Area_Q3, Area_Q4)) <0:
+                                print ('Yolo')
+                                print (x0,y0,H)
+                                #print (min(min(Area_Q1,Area_Q2),min(Area_Q3, Area_Q4)))
+                                print (Area_hex, Area_Q1, Area_Q2, Area_Q3, Area_Q4)
+
+                        Area_Q1=Area_Q1/Area_hex
+                        Area_Q2=Area_Q2/Area_hex
+                        Area_Q3=Area_Q3/Area_hex
+                        Area_Q4=Area_Q4/Area_hex
+
+
+                        #Now, you decide which quadrant belongs to which mass on ocean cell.
+                        #Top right vertex
+                        if x>=0.5 and y>= 0.5:
+                                yUxR=Area_Q1
+                                yUxC=Area_Q2
+                                yCxC=Area_Q3
+                                yCxR=Area_Q4
+
+                        #Top left vertex
+                        if x<0.5 and y>= 0.5:
+                                yUxC=Area_Q1
+                                yUxL=Area_Q2
+                                yCxL=Area_Q3
+                                yCxC=Area_Q4
+
+                        #Bottom left vertex
+                        if x<0.5 and y< 0.5:
+                                yCxC=Area_Q1
+                                yCxL=Area_Q2
+                                yDxL=Area_Q3
+                                yDxC=Area_Q4
+
+                        #Bottom right vertex
+                        if x>=0.5 and y< 0.5:
+                                yCxR=Area_Q1
+                                yCxC=Area_Q2
+                                yDxC=Area_Q3
+                                yDxR=Area_Q4
+
+                        #if Sector<4 and Sector>-1:
+                        #       print (Sector)
+
+
+                        #Check that this is true
+                        if abs(yCxC-(1.-( ((yDxL+yUxR)+(yDxR+yUxL)) + ((yCxL+yCxR)+(yDxC+yUxC)) )))>0.001:
+                                print ('All the mass is not being used!!!')
+                                #print (W1 , W2 , W3 , W4 , W5 , W6)
+                                #print (Area_Upper, Area_Lower, Area_right, Area_left)
+                                print ('Areas: ',Area_hex,Area_hex*Area_Q1, Area_hex*Area_Q2, Area_hex*Area_Q3, Area_hex*Area_Q4)
+                                print ('x0=',x0, 'y0=',y0, 'H=', H)
+                                print ('Total area= ',(Area_Q1+Area_Q2+Area_Q3+Area_Q4))#, Sector
+
+
+                #Accounting for masked points
+                a=1. ; b=1. ; c=1. ; d=1.
+                if i==0:
+                        a=0.;
+                if j==0:
+                        b=0.;
+                if i==Nx-1:
+                        c=0;
+                if j==Ny-1:
+                        d=0;
+
+                fraction_used= ((yDxL*a*b) + (yDxC*b) + (yDxR*b*c) +(yCxL*a) + (yCxR*c) + (yUxL*a*d) + (yUxC*d) + (yUxR*c*d) + (yCxC))
+                if static_berg>0.5:
+                        fraction_used=1.
+
+                mass_on_ocean[i,j,1]=mass_on_ocean[i,j,1]+(a*b*yDxL*Mass/fraction_used)
+                mass_on_ocean[i,j,2]=mass_on_ocean[i,j,2]+(b*yDxC*Mass/fraction_used)
+                mass_on_ocean[i,j,3]=mass_on_ocean[i,j,3]+(b*c*yDxR*Mass/fraction_used)
+                mass_on_ocean[i,j,4]=mass_on_ocean[i,j,4]+(a*yCxL*Mass/fraction_used)
+                mass_on_ocean[i,j,5]=mass_on_ocean[i,j,5]+(yCxC*Mass/fraction_used)
+                mass_on_ocean[i,j,6]=mass_on_ocean[i,j,6]+(c*yCxR*Mass/fraction_used)
+                mass_on_ocean[i,j,7]=mass_on_ocean[i,j,7]+(a*d*yUxL*Mass/fraction_used)
+                mass_on_ocean[i,j,8]=mass_on_ocean[i,j,8]+(d*yUxC*Mass/fraction_used)
+                mass_on_ocean[i,j,9]=mass_on_ocean[i,j,9]+(c*d*yUxR*Mass/fraction_used)
+
+
+                return mass_on_ocean
 
 
 def calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x, y, Lx):
 
-	Lx_2=Lx/2.
-
-	alpha=x2-x1
-	delta=y2-y1
-	beta=x4-x1
-	epsilon=y4-y1
-	gamma=(x3-x1)-(alpha+beta)
-	kappa=(y3-y1)-(delta+epsilon)
-
-	a=(kappa*beta-gamma*epsilon)
-	dx=np.mod(x-(x1-Lx_2),Lx)+(x1-Lx_2)-x1
-	dy=y-y1
-	b=(delta*beta-alpha*epsilon)-(kappa*dx-gamma*dy)
-	c=(alpha*dy-delta*dx)
-
-	#print 'alpha,beta,gamma',alpha,beta,gamma
-	#print 'delta,epsilon,kappa',delta,epsilon,kappa
-	#print 'dx,dy',dx,dy
-	#print 'A,B,C,',a,b,c
-
-	if (abs(a)>1.e-12):
-		d=0.25*(b**2)-a*c
-		if (d>=0.):
-			yy1=-(0.5*b+np.sqrt(d))/a
-			yy2=-(0.5*b-np.sqrt(d))/a
-			if (abs(yy1-0.5).lt.abs(yy2-0.5)):
-				yj=yy1;
-			else:
-				yj=yy2;
-    		else:
-			print 'ERROR', halt
-	else:
-		if (b!=0.):
-			yj=-c/b
-		else:
-			yj=0.
-
-	a=(alpha+gamma*yj)
-	b=(delta+kappa*yj)
-	if (a!=0.):
-		xi=(dx-beta*yj)/a
-	elif (b!=0.):
-		xi=(dy-epsilon*yj)/b
-	else:
-		c=(epsilon*alpha-beta*delta)+(epsilon*gamma-beta*kappa)*yj
-		if (c!=0.):
-			xi=(epsilon*dx-beta*dy)/c
-		else:
-			print 'ERROR', halt2
-
-	return xi,yj
+        Lx_2=Lx/2.
+
+        alpha=x2-x1
+        delta=y2-y1
+        beta=x4-x1
+        epsilon=y4-y1
+        gamma=(x3-x1)-(alpha+beta)
+        kappa=(y3-y1)-(delta+epsilon)
+
+        a=(kappa*beta-gamma*epsilon)
+        dx=np.mod(x-(x1-Lx_2),Lx)+(x1-Lx_2)-x1
+        dy=y-y1
+        b=(delta*beta-alpha*epsilon)-(kappa*dx-gamma*dy)
+        c=(alpha*dy-delta*dx)
+
+        #print ('alpha,beta,gamma',alpha,beta,gamma)
+        #print ('delta,epsilon,kappa',delta,epsilon,kappa)
+        #print ('dx,dy',dx,dy)
+        #print ('A,B,C,',a,b,c)
+
+        if (abs(a)>1.e-12):
+                d=0.25*(b**2)-a*c
+                if (d>=0.):
+                        yy1=-(0.5*b+np.sqrt(d))/a
+                        yy2=-(0.5*b-np.sqrt(d))/a
+                        if (abs(yy1-0.5).lt.abs(yy2-0.5)):
+                                yj=yy1;
+                        else:
+                                yj=yy2;
+                else:
+                        print ('ERROR', halt)
+        else:
+                if (b!=0.):
+                        yj=-c/b
+                else:
+                        yj=0.
+
+        a=(alpha+gamma*yj)
+        b=(delta+kappa*yj)
+        if (a!=0.):
+                xi=(dx-beta*yj)/a
+        elif (b!=0.):
+                xi=(dy-epsilon*yj)/b
+        else:
+                c=(epsilon*alpha-beta*delta)+(epsilon*gamma-beta*kappa)*yj
+                if (c!=0.):
+                        xi=(epsilon*dx-beta*dy)/c
+                else:
+                        print ('ERROR', halt2)
+
+        return xi,yj
 
 
 
 def regrid_iceberg_thickness(lat,lon,Number_of_bergs,thickness,mass,h_ice,x,y,rho_ice,element_type,static_berg,plot_outcome=True):
-	Nx=len(x)  ; Ny=len(y)
-	dx=x[1]-x[0]    ;dy=y[1]-y[0]
-	New_mass=h_ice*0 #Initializing regrided field to zero
-	Area = [(mass[i]/(rho_ice*thickness[i])) for i in range(Number_of_bergs)] ;
-	grid_area=dx*dy #Assuming a regular grid
-	Orig_mass=h_ice*rho_ice*grid_area
-
-	mass_on_ocean=np.zeros([Nx,Ny,10])   #Setting up matrix to spread mass to ocean.  Note that I have used 10 points  so that I can ignore 0 and match with python numbering
-	#mass_on_ocean=np.zeros([Nx,Ny])   #Setting up matrix to spread mass to ocean.
-	#Note: You may want to import the grid that the ocean model actually sees.
-	for berg_count in range(Number_of_bergs):
-		x_val=lon[berg_count]
-		y_val=lat[berg_count]
-		Area_val=Area[berg_count]
-		mass_val=mass[berg_count]
-
-		j_val=int(math.floor(y_val/dy))
-		i_val=int(math.floor(x_val/dx))
-		x_cell=(x_val-x[i_val])/np.sqrt(grid_area)+0.5
-		y_cell=(y_val-y[j_val])/np.sqrt(grid_area)+0.5
-
-		#if plot_outcome==True:
-		#	print 'YOLO0', x_val-123626.65521,y_val
-		#	print 'YOLO1', x[i_val],y[j_val]
-		#	print 'YOLO2', x_cell,y_cell
-
-		#Using the same interpolation as in the model
-		#x1=x[i_val]-(dx/2.)   ; y1=y[j_val]-(dx/2.)
-		#x2=x[i_val]+(dx/2.) ; y2=y[j_val]-(dx/2.)
-		#x3=x[i_val]+(dx/2.) ; y3=y[j_val]+(dx/2.)
-		#x4=x[i_val]-(dx/2.) ; y4=y[j_val]+(dx/2.)
-		#[xi,yj]=calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x_val, y_val, Lx=100000000000000.)
-		#[x_cell,y_cell]=calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x_val, y_val, Lx=100000000000000.)
-		#print 'YOLO:x1,x2,x3,x4',x1,x2,x3,x4
-		#print 'YOLO:y1,y2,y3,y4',y1,y2,y3,y4
-		#print 'YOLO:xi,yj,x_cell,y_cell', xi,yj, x_cell,y_cell
-
-		mass_on_ocean=spread_mass_to_ocean(Nx,Ny,i_val,j_val,mass_on_ocean,x_cell,y_cell,Area_val,mass_val,element_type,grid_area,static_berg[berg_count])
-
-	#Adding mass_onto_ocean
-	for i in range(1,Nx-1):
-		for j in range(1,Ny-1):
-			New_mass[j,i]=mass_on_ocean[i,j,5]  \
-					+  ( ( (mass_on_ocean[i-1,j-1,9]+mass_on_ocean[i+1,j+1,1])   \
-					+  (mass_on_ocean[i+1,j-1,7]+mass_on_ocean[i-1,j+1,3]) ) \
-					+   ( (mass_on_ocean[i-1,j  ,6]+mass_on_ocean[i+1,j  ,4])   \
-					+  (mass_on_ocean[i  ,j-1,8]+mass_on_ocean[i  ,j+1,2]) ) )
-
-	#Adding mass to boundary cells
-	for j in range(1,Ny-1):
-		i=0
-		New_mass[j,i]=mass_on_ocean[i,j,5] +  mass_on_ocean[i+1,j+1,1] +  mass_on_ocean[i+1,j-1,7] \
-			+  mass_on_ocean[i+1,j  ,4] 	+  mass_on_ocean[i  ,j-1,8] + mass_on_ocean[i  ,j+1,2]
-		i=Nx-1
-		New_mass[j,i]=mass_on_ocean[i,j,5] +  mass_on_ocean[i-1,j-1,9] + mass_on_ocean[i-1,j+1,3] \
-					+   mass_on_ocean[i-1,j ,6] + mass_on_ocean[i ,j-1,8]+mass_on_ocean[i ,j+1,2]
-
-	for i in range(1,Nx-1):
-		j=0
-		New_mass[j,i]=mass_on_ocean[i,j,5] +   mass_on_ocean[i+1,j+1,1] +  mass_on_ocean[i-1,j+1,3]  \
-				+  mass_on_ocean[i-1,j  ,6] + mass_on_ocean[i+1,j  ,4] +  mass_on_ocean[i  ,j+1,2]
-
-		j=Ny-1
-		New_mass[j,i]=mass_on_ocean[i,j,5] +  mass_on_ocean[i-1,j-1,9] 	+  mass_on_ocean[i+1,j-1,7] + \
-				mass_on_ocean[i-1,j  ,6]+mass_on_ocean[i+1,j  ,4] +  mass_on_ocean[i  ,j-1,8]
-
-	#Corners
-	i=0 ;j=0
-	New_mass[j,i]=mass_on_ocean[i,j,5] + mass_on_ocean[i+1,j+1,1] + mass_on_ocean[i+1,j  ,4] + mass_on_ocean[i  ,j+1,2]
-	i=0 ;j=Ny-1
-	New_mass[j,i]=mass_on_ocean[i,j,5] + mass_on_ocean[i+1,j-1,7] + mass_on_ocean[i+1,j  ,4] + mass_on_ocean[i  ,j-1,8]
-	i=Nx-1; j=0
-	New_mass[j,i]=mass_on_ocean[i,j,5] + mass_on_ocean[i-1,j+1,3] + mass_on_ocean[i-1,j  ,6] + mass_on_ocean[i  ,j+1,2]
-	i=Nx-1; j=Ny-1
-	New_mass[j,i]=mass_on_ocean[i,j,5] + mass_on_ocean[i-1,j-1,9] + mass_on_ocean[i-1,j  ,6] + mass_on_ocean[i  ,j-1,8]
-
-
-	if plot_outcome==True: #MP2
-		#print 'Warning: the interpolation scheme is not the same as the one used in the model'
-
-		plot_data=(Orig_mass-New_mass)/Orig_mass
-		cNorm = mpl.colors.Normalize(vmin=-.1, vmax=.1)
-		vmax=np.max(abs(plot_data))
-		plt.pcolormesh(x,y,plot_data,cmap='bwr',norm=cNorm)
-		plt.title('Error between bergs and shelf')
-
-		#plot_data=(New_mass/New_thickness/rho_ice)
-		#vmax=np.max(abs(plot_data))
-		#cNorm = mpl.colors.Normalize(vmin=-vmax, vmax=vmax)
-		#plt.pcolormesh(x,y,plot_data,cmap='jet',norm=cNorm)
-		#plt.title('h_ice')
-
-		#plot_data=(New_mass-Orig_mass)/(rho_ice*grid_area)
-		#cNorm = mpl.colors.Normalize(vmin=-0.00000000001, vmax=0.00000000001)
-		#vmax=np.max(abs(plot_data))
-		#plt.pcolormesh(x,y,plot_data,cmap='bwr',norm=cNorm)
-
-		plt.colorbar()
-		#plt.xlim([min(x)-,max(x)])
-		#plt.ylim([min(y),max(y)])
-		#plt.show()
-
-	return New_mass
+        Nx=len(x)  ; Ny=len(y)
+        dx=x[1]-x[0]    ;dy=y[1]-y[0]
+        New_mass=h_ice*0 #Initializing regrided field to zero
+        Area = [(mass[i]/(rho_ice*thickness[i])) for i in range(Number_of_bergs)] ;
+        grid_area=dx*dy #Assuming a regular grid
+        Orig_mass=h_ice*rho_ice*grid_area
+
+        mass_on_ocean=np.zeros([Nx,Ny,10])   #Setting up matrix to spread mass to ocean.  Note that I have used 10 points  so that I can ignore 0 and match with python numbering
+        #mass_on_ocean=np.zeros([Nx,Ny])   #Setting up matrix to spread mass to ocean.
+        #Note: You may want to import the grid that the ocean model actually sees.
+        for berg_count in range(Number_of_bergs):
+                x_val=lon[berg_count]
+                y_val=lat[berg_count]
+                Area_val=Area[berg_count]
+                mass_val=mass[berg_count]
+
+                j_val=int(math.floor(y_val/dy))
+                i_val=int(math.floor(x_val/dx))
+                x_cell=(x_val-x[i_val])/np.sqrt(grid_area)+0.5
+                y_cell=(y_val-y[j_val])/np.sqrt(grid_area)+0.5
+
+                #if plot_outcome==True:
+                #       print ('YOLO0', x_val-123626.65521,y_val)
+                #       print ('YOLO1', x[i_val],y[j_val])
+                #       print ('YOLO2', x_cell,y_cell)
+
+                #Using the same interpolation as in the model
+                #x1=x[i_val]-(dx/2.)   ; y1=y[j_val]-(dx/2.)
+                #x2=x[i_val]+(dx/2.) ; y2=y[j_val]-(dx/2.)
+                #x3=x[i_val]+(dx/2.) ; y3=y[j_val]+(dx/2.)
+                #x4=x[i_val]-(dx/2.) ; y4=y[j_val]+(dx/2.)
+                #[xi,yj]=calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x_val, y_val, Lx=100000000000000.)
+                #[x_cell,y_cell]=calc_xiyj(x1, x2, x3, x4, y1, y2, y3, y4, x_val, y_val, Lx=100000000000000.)
+                #print ('YOLO:x1,x2,x3,x4',x1,x2,x3,x4)
+                #print ('YOLO:y1,y2,y3,y4',y1,y2,y3,y4)
+                #print ('YOLO:xi,yj,x_cell,y_cell', xi,yj, x_cell,y_cell)
+
+                mass_on_ocean=spread_mass_to_ocean(Nx,Ny,i_val,j_val,mass_on_ocean,x_cell,y_cell,Area_val,mass_val,element_type,grid_area,static_berg[berg_count])
+
+        #Adding mass_onto_ocean
+        for i in range(1,Nx-1):
+                for j in range(1,Ny-1):
+                        New_mass[j,i]=mass_on_ocean[i,j,5]  \
+                                        +  ( ( (mass_on_ocean[i-1,j-1,9]+mass_on_ocean[i+1,j+1,1])   \
+                                        +  (mass_on_ocean[i+1,j-1,7]+mass_on_ocean[i-1,j+1,3]) ) \
+                                        +   ( (mass_on_ocean[i-1,j  ,6]+mass_on_ocean[i+1,j  ,4])   \
+                                        +  (mass_on_ocean[i  ,j-1,8]+mass_on_ocean[i  ,j+1,2]) ) )
+
+        #Adding mass to boundary cells
+        for j in range(1,Ny-1):
+                i=0
+                New_mass[j,i]=mass_on_ocean[i,j,5] +  mass_on_ocean[i+1,j+1,1] +  mass_on_ocean[i+1,j-1,7] \
+                        +  mass_on_ocean[i+1,j  ,4]     +  mass_on_ocean[i  ,j-1,8] + mass_on_ocean[i  ,j+1,2]
+                i=Nx-1
+                New_mass[j,i]=mass_on_ocean[i,j,5] +  mass_on_ocean[i-1,j-1,9] + mass_on_ocean[i-1,j+1,3] \
+                                        +   mass_on_ocean[i-1,j ,6] + mass_on_ocean[i ,j-1,8]+mass_on_ocean[i ,j+1,2]
+
+        for i in range(1,Nx-1):
+                j=0
+                New_mass[j,i]=mass_on_ocean[i,j,5] +   mass_on_ocean[i+1,j+1,1] +  mass_on_ocean[i-1,j+1,3]  \
+                                +  mass_on_ocean[i-1,j  ,6] + mass_on_ocean[i+1,j  ,4] +  mass_on_ocean[i  ,j+1,2]
+
+                j=Ny-1
+                New_mass[j,i]=mass_on_ocean[i,j,5] +  mass_on_ocean[i-1,j-1,9]  +  mass_on_ocean[i+1,j-1,7] + \
+                                mass_on_ocean[i-1,j  ,6]+mass_on_ocean[i+1,j  ,4] +  mass_on_ocean[i  ,j-1,8]
+
+        #Corners
+        i=0 ;j=0
+        New_mass[j,i]=mass_on_ocean[i,j,5] + mass_on_ocean[i+1,j+1,1] + mass_on_ocean[i+1,j  ,4] + mass_on_ocean[i  ,j+1,2]
+        i=0 ;j=Ny-1
+        New_mass[j,i]=mass_on_ocean[i,j,5] + mass_on_ocean[i+1,j-1,7] + mass_on_ocean[i+1,j  ,4] + mass_on_ocean[i  ,j-1,8]
+        i=Nx-1; j=0
+        New_mass[j,i]=mass_on_ocean[i,j,5] + mass_on_ocean[i-1,j+1,3] + mass_on_ocean[i-1,j  ,6] + mass_on_ocean[i  ,j+1,2]
+        i=Nx-1; j=Ny-1
+        New_mass[j,i]=mass_on_ocean[i,j,5] + mass_on_ocean[i-1,j-1,9] + mass_on_ocean[i-1,j  ,6] + mass_on_ocean[i  ,j-1,8]
+
+
+        if plot_outcome==True: #MP2
+                #print ('Warning: the interpolation scheme is not the same as the one used in the model')
+
+                plot_data=(Orig_mass-New_mass)/Orig_mass
+                cNorm = mpl.colors.Normalize(vmin=-.1, vmax=.1)
+                vmax=np.max(abs(plot_data))
+                plt.pcolormesh(x,y,plot_data,cmap='bwr',norm=cNorm)
+                plt.title('Error between bergs and shelf')
+
+                #plot_data=(New_mass/New_thickness/rho_ice)
+                #vmax=np.max(abs(plot_data))
+                #cNorm = mpl.colors.Normalize(vmin=-vmax, vmax=vmax)
+                #plt.pcolormesh(x,y,plot_data,cmap='jet',norm=cNorm)
+                #plt.title('h_ice')
+
+                #plot_data=(New_mass-Orig_mass)/(rho_ice*grid_area)
+                #cNorm = mpl.colors.Normalize(vmin=-0.00000000001, vmax=0.00000000001)
+                #vmax=np.max(abs(plot_data))
+                #plt.pcolormesh(x,y,plot_data,cmap='bwr',norm=cNorm)
+
+                plt.colorbar()
+                #plt.xlim([min(x)-,max(x)])
+                #plt.ylim([min(y),max(y)])
+                #plt.show()
+
+        return New_mass
 
 def Switch_x_and_y_directions(lat,lon, A, B, C):
-	print 'Switching x and y directions!!!'
-	lat_new=[]
-	lon_new=[]
-	for i in range(len(lat)):
-		lat_new.append(lon[i])
-		lon_new.append(lat[i])
-	M=A.shape
-	A_new=np.zeros([M[1],M[0]])
-	B_new=np.zeros([M[1],M[0]])
-	C_new=np.zeros([M[1],M[0]])
-	for i in range(M[0]):
-		for j in range(M[1]):
-			A_new[j,i]=A[i,j]
-			B_new[j,i]=B[i,j]
-			C_new[j,i]=C[i,j]
-
-	return	[lat_new,lon_new,A_new,B_new, C_new]
+        print ('Switching x and y directions!!!')
+        lat_new=[]
+        lon_new=[]
+        for i in range(len(lat)):
+                lat_new.append(lon[i])
+                lon_new.append(lat[i])
+        M=A.shape
+        A_new=np.zeros([M[1],M[0]])
+        B_new=np.zeros([M[1],M[0]])
+        C_new=np.zeros([M[1],M[0]])
+        for i in range(M[0]):
+                for j in range(M[1]):
+                        A_new[j,i]=A[i,j]
+                        B_new[j,i]=B[i,j]
+                        C_new[j,i]=C[i,j]
+
+        return  [lat_new,lon_new,A_new,B_new, C_new]
 
 def interpolate_field_onto_new_grid(x,y,x_new,y_new,field):
         xx, yy = np.meshgrid(x, y)
         #f = interpolate.interp2d(x, y, field, kind='cubic')
-	f = interpolate.interp2d(x, y, field, kind='linear')
+        f = interpolate.interp2d(x, y, field, kind='linear')
         field_new = f(x_new, y_new)
         return field_new
 
 def convert_input_to_catesian_coordinates(lon,lat,ice_mask,h_ice,R_earth,dx):
-	#Parameters
+        #Parameters
         thickness_threshhold=0.01
 
         lon_max=np.max(lon) ; lon_min=np.min(lon)
@@ -1668,7 +1665,7 @@ def convert_input_to_catesian_coordinates(lon,lat,ice_mask,h_ice,R_earth,dx):
         h_ice_new[np.where(h_ice_new<thickness_threshhold)]=0.
         ice_mask_new=interpolate_field_onto_new_grid(x,y,x_new,y_new,ice_mask)
         #ice_mask_new=np.round(ice_mask_new)
-        #print ice_mask_new[50,:]
+        #print (ice_mask_new[50,:])
 
         return [x_new,y_new,ice_mask_new,h_ice_new]
 
@@ -1679,218 +1676,218 @@ def convert_input_to_catesian_coordinates(lon,lat,ice_mask,h_ice,R_earth,dx):
 
 def main(args):
 
-	#Flags
-	save_restart_files=args.save_restart_files
-	save_new_h_ice_file=args.save_new_h_ice_file
-	Convert_to_lat_lon=args.Convert_to_lat_lon
-	input_is_cartesian=args.input_is_cartesian
+        #Flags
+        save_restart_files=args.save_restart_files
+        save_new_h_ice_file=args.save_new_h_ice_file
+        Convert_to_lat_lon=args.Convert_to_lat_lon
+        input_is_cartesian=args.input_is_cartesian
 
-	#Iceberg setup flags
-	only_choose_one_berg=args.only_choose_one_berg  ; chosen_berg_num=args.chosen_berg_num
+        #Iceberg setup flags
+        only_choose_one_berg=args.only_choose_one_berg  ; chosen_berg_num=args.chosen_berg_num
         select_just_min_and_max_lat_berg=args.select_just_min_and_max_lat_berg
-	scale_the_grid_to_lat_lon=args.scale_the_grid_to_lat_lon
-	adjust_lat_ref=args.adjust_lat_ref
-	set_all_thicknesses_to_one=args.set_all_thicknesses_to_one   ; Th_prescribed=args.Th_prescribed
-	Interpolate_from_four_corners=args.Interpolate_from_four_corners
-	Switch_x_and_y_to_rotate_90=args.Switch_x_and_y_to_rotate_90
-	set_all_domain_to_ice=args.set_all_domain_to_ice
-	Use_default_radius=args.Use_default_radius
-
-	#Static vs non-static flags
-	set_all_bergs_static_by_default=args.set_all_bergs_static_by_default
-	set_some_bergs_static_by_default=args.set_some_bergs_static_by_default
-	Make_icebergs_non_static_later=args.Make_icebergs_non_static_later
-
-	#Mass spreadng flags
-	element_type=args.element_type
-	Switch_regridding_element_type=args.Switch_regridding_element_type
-	Fill_in_the_boundaries=args.Fill_in_the_boundaries
-	regrid_icebergs_onto_grid=args.regrid_icebergs_onto_grid
-
-	#Plotting flags
-	Run_plotting_subroutine=args.Run_plotting_subroutine
-	plot_circles=args.plot_circles
-	plot_ice_mask=args.plot_ice_mask
-	plot_ice_thickness=args.plot_ice_thickness
-	plot_icebergs_positions=args.plot_icebergs_positions
-	plot_h_ice_new=args.plot_h_ice_new
-	plot_bonds=args.plot_bonds
-
-	#Bond related flags
-	Create_icebergs_bonds=args.Create_icebergs_bonds
-	break_some_bonds=args.break_some_bonds
-	Remove_stationary_bergs=args.Remove_stationary_bergs
-	Allow_bonds_for_static_iceberg=args.Allow_bonds_for_static_iceberg
-	Allow_bonds_with_boundary_bergs=args.Allow_bonds_with_boundary_bergs
-
-
-	#Which experiment
-	Ice_geometry_source=args.Ice_geometry_source
-	ISOMIP_reduced=args.ISOMIP_reduced
-	ISOMIP_ice_geometry_filename=args.ISOMIP_ice_geometry_filename
-	ISOMIP_reduced_ice_geometry_filename=args.ISOMIP_reduced_ice_geometry_filename
-	Weddell_ice_geometry_filename=args.Weddell_ice_geometry_filename
-	Generic_ice_geometry_filename=args.Generic_ice_geometry_filename
+        scale_the_grid_to_lat_lon=args.scale_the_grid_to_lat_lon
+        adjust_lat_ref=args.adjust_lat_ref
+        set_all_thicknesses_to_one=args.set_all_thicknesses_to_one   ; Th_prescribed=args.Th_prescribed
+        Interpolate_from_four_corners=args.Interpolate_from_four_corners
+        Switch_x_and_y_to_rotate_90=args.Switch_x_and_y_to_rotate_90
+        set_all_domain_to_ice=args.set_all_domain_to_ice
+        Use_default_radius=args.Use_default_radius
+
+        #Static vs non-static flags
+        set_all_bergs_static_by_default=args.set_all_bergs_static_by_default
+        set_some_bergs_static_by_default=args.set_some_bergs_static_by_default
+        Make_icebergs_non_static_later=args.Make_icebergs_non_static_later
+
+        #Mass spreadng flags
+        element_type=args.element_type
+        Switch_regridding_element_type=args.Switch_regridding_element_type
+        Fill_in_the_boundaries=args.Fill_in_the_boundaries
+        regrid_icebergs_onto_grid=args.regrid_icebergs_onto_grid
+
+        #Plotting flags
+        Run_plotting_subroutine=args.Run_plotting_subroutine
+        plot_circles=args.plot_circles
+        plot_ice_mask=args.plot_ice_mask
+        plot_ice_thickness=args.plot_ice_thickness
+        plot_icebergs_positions=args.plot_icebergs_positions
+        plot_h_ice_new=args.plot_h_ice_new
+        plot_bonds=args.plot_bonds
+
+        #Bond related flags
+        Create_icebergs_bonds=args.Create_icebergs_bonds
+        break_some_bonds=args.break_some_bonds
+        Remove_stationary_bergs=args.Remove_stationary_bergs
+        Allow_bonds_for_static_iceberg=args.Allow_bonds_for_static_iceberg
+        Allow_bonds_with_boundary_bergs=args.Allow_bonds_with_boundary_bergs
+
+
+        #Which experiment
+        Ice_geometry_source=args.Ice_geometry_source
+        ISOMIP_reduced=args.ISOMIP_reduced
+        ISOMIP_ice_geometry_filename=args.ISOMIP_ice_geometry_filename
+        ISOMIP_reduced_ice_geometry_filename=args.ISOMIP_reduced_ice_geometry_filename
+        Weddell_ice_geometry_filename=args.Weddell_ice_geometry_filename
+        Generic_ice_geometry_filename=args.Generic_ice_geometry_filename
         collision_test=args.collision_test
         grounding_test=args.grounding_test
 
-	#Parameters
-	Radius=args.Radius
-	rho_ice=args.rho_ice
-	gravity=args.gravity
-	mass_scaling=args.mass_scaling
-	R_earth=args.R_earth
-	buffer_number=args.buffer_number
-
-	#Let interactive radius be different from radius for testing the model:
-	IA_scaling=args.IA_scaling
-
-	#Applying some special case flags
-	if Ice_geometry_source=='ISOMIP':
-		Convert_to_lat_lon=False       ; input_is_cartesian=True ;
-	if Ice_geometry_source=='Generic':
-		Convert_to_lat_lon=False       ; input_is_cartesian=True ; set_all_bergs_static_by_default=False ; Fill_in_the_boundaries=False ; Use_default_radius=True
-	if Ice_geometry_source=='Weddell':
-		Convert_to_lat_lon=False        ; input_is_cartesian=False
-
-	#Applying Warnings
-	if element_type=='square' and Interpolate_from_four_corners==True:
-		print 'Square packing with R dividing dx, works best with interpolation off.'
-
-	print 'Element type= ', element_type, ';  Switched_regridding= ', Switch_regridding_element_type
-	if break_some_bonds==True:
-		print 'Some bonds are being broken'
-
-	#####################################################################################
-	#####################################################################################
-	Radius=Radius/IA_scaling
-
-	if  Ice_geometry_source=='ISOMIP':
-		if ISOMIP_reduced==False:
-			lon_init=0  ; lat_init=-70.  #latitude  of bottom left corner of iceberg
-			(x,y,ice_mask,h_ice)=load_ISOMIP_ice_geometry(ISOMIP_ice_geometry_filename,buffer_number)
-			ice_filename=ISOMIP_ice_geometry_filename
-		else:
-			lon_init=0  ; lat_init=-70.  #latitude  of bottom left corner of iceberg
-			(x,y,ice_mask,h_ice)=load_ISOMIP_reduced_ice_geometry(ISOMIP_reduced_ice_geometry_filename,buffer_number)
-			ice_filename=ISOMIP_reduced_ice_geometry_filename
-
-	if  Ice_geometry_source=='Weddell':
-		lon_init=-32.9  ; lat_init=-70.  #latitude  of bottom left corner of iceberg
-		(x,y,ice_mask,h_ice)=load_Weddel_ice_geometry(Weddell_ice_geometry_filename)
-		ice_filename=Weddell_ice_geometry_filename
-		Radius=0.5*10000.
-
-	if  Ice_geometry_source=='Generic':
-		(x,y,ice_mask,h_ice, lon_init, lat_init)=load_generic_ice_geometry(Generic_ice_geometry_filename)
+        #Parameters
+        Radius=args.Radius
+        rho_ice=args.rho_ice
+        gravity=args.gravity
+        mass_scaling=args.mass_scaling
+        R_earth=args.R_earth
+        buffer_number=args.buffer_number
+
+        #Let interactive radius be different from radius for testing the model:
+        IA_scaling=args.IA_scaling
+
+        #Applying some special case flags
+        if Ice_geometry_source=='ISOMIP':
+                Convert_to_lat_lon=False       ; input_is_cartesian=True ;
+        if Ice_geometry_source=='Generic':
+                Convert_to_lat_lon=False       ; input_is_cartesian=True ; set_all_bergs_static_by_default=False ; Fill_in_the_boundaries=False ; Use_default_radius=True
+        if Ice_geometry_source=='Weddell':
+                Convert_to_lat_lon=False        ; input_is_cartesian=False
+
+        #Applying Warnings
+        if element_type=='square' and Interpolate_from_four_corners==True:
+                print ('Square packing with R dividing dx, works best with interpolation off.')
+
+        print ('Element type= ', element_type, ';  Switched_regridding= ', Switch_regridding_element_type)
+        if break_some_bonds==True:
+                print ('Some bonds are being broken')
+
+        #####################################################################################
+        #####################################################################################
+        Radius=Radius/IA_scaling
+
+        if  Ice_geometry_source=='ISOMIP':
+                if ISOMIP_reduced==False:
+                        lon_init=0  ; lat_init=-70.  #latitude  of bottom left corner of iceberg
+                        (x,y,ice_mask,h_ice)=load_ISOMIP_ice_geometry(ISOMIP_ice_geometry_filename,buffer_number)
+                        ice_filename=ISOMIP_ice_geometry_filename
+                else:
+                        lon_init=0  ; lat_init=-70.  #latitude  of bottom left corner of iceberg
+                        (x,y,ice_mask,h_ice)=load_ISOMIP_reduced_ice_geometry(ISOMIP_reduced_ice_geometry_filename,buffer_number)
+                        ice_filename=ISOMIP_reduced_ice_geometry_filename
+
+        if  Ice_geometry_source=='Weddell':
+                lon_init=-32.9  ; lat_init=-70.  #latitude  of bottom left corner of iceberg
+                (x,y,ice_mask,h_ice)=load_Weddel_ice_geometry(Weddell_ice_geometry_filename)
+                ice_filename=Weddell_ice_geometry_filename
+                Radius=0.5*10000.
+
+        if  Ice_geometry_source=='Generic':
+                (x,y,ice_mask,h_ice, lon_init, lat_init)=load_generic_ice_geometry(Generic_ice_geometry_filename)
 
         if input_is_cartesian is False:
                 dx=10000.
                 lat_grid=y ; lon_grid=x
                 (x,y,ice_mask,h_ice)=convert_input_to_catesian_coordinates(x,y,ice_mask,h_ice,R_earth,dx)
 
-	if set_all_thicknesses_to_one==True:
-		print 'All thicknesses being set equal to 1'
-		if set_all_domain_to_ice is True:
-			ice_mask[:,:]=1.
-		h_ice[np.where(ice_mask>0.5)]=Th_prescribed
-
-	if Use_default_radius is True:
-		dx=x[1]-x[0]  #This is used as the ocean grid size
-		R_frac=0.45
-		if element_type=='square':
-			Radius=R_frac*dx  #(less than half the grid size)
-		if element_type=='hexagon':
-			Radius= (np.sqrt(3)/2.) *(R_frac*dx)   #(S is < half the grid size)
-	print 'Radius set to R= ' , Radius
-
-	lat_ref=np.max(y)
-	#Define the positions,thickness, mass,  of the icebergs
-	(Number_of_bergs,lon,lat,iceberg_num,dx_berg, dy_berg,thickness,mass,width,x,y,Radius,static_berg,N_bergs_before_bd)= Create_icebergs(lon_init,lat_init,\
-			Radius,R_earth, x, y,ice_mask,h_ice,Convert_to_lat_lon,rho_ice,element_type,scale_the_grid_to_lat_lon,lat_ref,adjust_lat_ref,\
-			Interpolate_from_four_corners,Fill_in_the_boundaries, set_all_bergs_static_by_default,break_some_bonds,Remove_stationary_bergs,\
+        if set_all_thicknesses_to_one==True:
+                print ('All thicknesses being set equal to 1')
+                if set_all_domain_to_ice is True:
+                        ice_mask[:,:]=1.
+                h_ice[np.where(ice_mask>0.5)]=Th_prescribed
+
+        if Use_default_radius is True:
+                dx=x[1]-x[0]  #This is used as the ocean grid size
+                R_frac=0.45
+                if element_type=='square':
+                        Radius=R_frac*dx  #(less than half the grid size)
+                if element_type=='hexagon':
+                        Radius= (np.sqrt(3)/2.) *(R_frac*dx)   #(S is < half the grid size)
+        print ('Radius set to R= ' , Radius)
+
+        lat_ref=np.max(y)
+        #Define the positions,thickness, mass,  of the icebergs
+        (Number_of_bergs,lon,lat,iceberg_num,dx_berg, dy_berg,thickness,mass,width,x,y,Radius,static_berg,N_bergs_before_bd)= Create_icebergs(lon_init,lat_init,\
+                        Radius,R_earth, x, y,ice_mask,h_ice,Convert_to_lat_lon,rho_ice,element_type,scale_the_grid_to_lat_lon,lat_ref,adjust_lat_ref,\
+                        Interpolate_from_four_corners,Fill_in_the_boundaries, set_all_bergs_static_by_default,break_some_bonds,Remove_stationary_bergs,\
                         set_some_bergs_static_by_default,collision_test,grounding_test)
 
-	print 'Maximum thickness:', np.max(thickness), np.min(thickness)
-	#Define the positions of the iceberg bonds
-	if Create_icebergs_bonds==True:
-		(Number_of_bonds, first_berg_num,first_berg_ine,first_berg_jne,first_berg_lat,first_berg_lon, other_berg_num,other_berg_ine, other_berg_jne,other_berg_lat,other_berg_lon)=\
-				Define_iceberg_bonds(Number_of_bergs,iceberg_num,lat,lon,dx_berg, dy_berg,Radius,break_some_bonds,static_berg,Allow_bonds_for_static_iceberg\
-				,N_bergs_before_bd,Allow_bonds_with_boundary_bergs)
+        print ('Maximum thickness:', np.max(thickness), np.min(thickness))
+        #Define the positions of the iceberg bonds
+        if Create_icebergs_bonds==True:
+                (Number_of_bonds, first_berg_num,first_berg_ine,first_berg_jne,first_berg_lat,first_berg_lon, other_berg_num,other_berg_ine, other_berg_jne,other_berg_lat,other_berg_lon)=\
+                                Define_iceberg_bonds(Number_of_bergs,iceberg_num,lat,lon,dx_berg, dy_berg,Radius,break_some_bonds,static_berg,Allow_bonds_for_static_iceberg\
+                                ,N_bergs_before_bd,Allow_bonds_with_boundary_bergs)
 
-	if Make_icebergs_non_static_later is True:
-		Change_static_berg_after_bonding(Number_of_bergs,lat,lon, static_berg)
+        if Make_icebergs_non_static_later is True:
+                Change_static_berg_after_bonding(Number_of_bergs,lat,lon, static_berg)
 
 
-	temp_mass=[mass[i]/thickness[i] for i in range(len(thickness))]
-	if only_choose_one_berg==True:
-		(Number_of_bergs,lon,lat,thickness,width,mass,iceberg_num)= Select_just_one_berg(lon,lat,thickness,width,mass,iceberg_num,chosen_berg_num,static_berg)
+        temp_mass=[mass[i]/thickness[i] for i in range(len(thickness))]
+        if only_choose_one_berg==True:
+                (Number_of_bergs,lon,lat,thickness,width,mass,iceberg_num)= Select_just_one_berg(lon,lat,thickness,width,mass,iceberg_num,chosen_berg_num,static_berg)
 
         if select_just_min_and_max_lat_berg==True:
                 (Number_of_bergs,lon,lat,thickness,width,mass,iceberg_num,static_berg)=\
                         Select_just_min_and_max_lat_bergs(lon,lat,thickness,width,mass,iceberg_num,static_berg)
-                print 'Selected just min and max lat bergs. New number of bergs = ', Number_of_bergs
-
-
-	if regrid_icebergs_onto_grid==True:
-		if scale_the_grid_to_lat_lon==True:
-			print 'Regridding should be run with scale_the_grid_to_lat_lon off'
-		else:
-			if Switch_regridding_element_type==True:
-				if element_type=='square':
-					element_type='hexagon'
-				else:
-					element_type='square'
-			temp_thickness=[1. for i in thickness]
-			temp_mass=[mass[i]/(thickness[i]*rho_ice) for i in range(len(thickness))]
-			temp_rho_ice=1.
-			New_area=regrid_iceberg_thickness(lat,lon,Number_of_bergs,temp_thickness,temp_mass,h_ice,x,y,temp_rho_ice,element_type,static_berg,plot_outcome=False)
-			New_mass=regrid_iceberg_thickness(lat,lon,Number_of_bergs,thickness,mass,h_ice,x,y,rho_ice,element_type,static_berg,plot_outcome=False)
-		if save_new_h_ice_file==True:
-			grid_area=(x[1]-x[0])*(x[1]-x[0])
-			h_ice_new=New_mass*0
-			M=h_ice.shape
-			for j in range(M[0]):
-				for i in range(M[1]):
-					if New_area[j,i]>0:
-						h_ice_new[j,i]=New_mass[j,i]/(rho_ice*New_area[j,i])
-
-	if Switch_x_and_y_to_rotate_90 is True:
-		[lat,lon, h_ice_new,New_area,New_mass]=Switch_x_and_y_directions(lat,lon, h_ice_new,New_area,New_mass)
-
-
-	if save_restart_files==True:
-		#Creating iceberg restart file
-		Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg)
-
-		#Creating bond restart file
-		if Create_icebergs_bonds==True:
-			Create_bond_restart_file(Number_of_bonds,first_berg_num,first_berg_ine,first_berg_jne,other_berg_ine,other_berg_jne,iceberg_num,other_berg_num,Ice_geometry_source)
-
-		if save_new_h_ice_file==True:
-			create_clipped_icethickness_file(h_ice_new,New_area,New_mass,grid_area,gravity,Ice_geometry_source)
-
-	# Plotting the positions and bonds of the newly formed formation
-	if Run_plotting_subroutine==True:
-		plotting_iceberg_positions(lat,lon,Number_of_bergs,R_earth,Radius,IA_scaling,Convert_to_lat_lon,\
-				plot_circles,h_ice,ice_mask,x,y,plot_ice_mask,plot_ice_thickness,thickness,plot_icebergs_positions,static_berg,h_ice_new,plot_h_ice_new)
-		if (plot_bonds==True) and (Create_icebergs_bonds):
-			plotting_iceberg_bonds(first_berg_lat,first_berg_lon,other_berg_lat,other_berg_lon,Number_of_bonds)
-
-	#field=New_mass/(rho_ice*grid_area)
-	field=New_area/grid_area -1.
-	M=field.shape
-	#print 'field',(field[M[0]-1,:])
-	#print 'field',(field[M[0]-2,:])
-	#print 'h_ice',h_ice_new[:,:]
-	#print 'h_ice-1',h_ice_new[:,:]-1.
-	if Run_plotting_subroutine:
-		plt.show()
-	print 'Script complete'
+                print ('Selected just min and max lat bergs. New number of bergs = ', Number_of_bergs)
+
+
+        if regrid_icebergs_onto_grid==True:
+                if scale_the_grid_to_lat_lon==True:
+                        print ('Regridding should be run with scale_the_grid_to_lat_lon off')
+                else:
+                        if Switch_regridding_element_type==True:
+                                if element_type=='square':
+                                        element_type='hexagon'
+                                else:
+                                        element_type='square'
+                        temp_thickness=[1. for i in thickness]
+                        temp_mass=[mass[i]/(thickness[i]*rho_ice) for i in range(len(thickness))]
+                        temp_rho_ice=1.
+                        New_area=regrid_iceberg_thickness(lat,lon,Number_of_bergs,temp_thickness,temp_mass,h_ice,x,y,temp_rho_ice,element_type,static_berg,plot_outcome=False)
+                        New_mass=regrid_iceberg_thickness(lat,lon,Number_of_bergs,thickness,mass,h_ice,x,y,rho_ice,element_type,static_berg,plot_outcome=False)
+                if save_new_h_ice_file==True:
+                        grid_area=(x[1]-x[0])*(x[1]-x[0])
+                        h_ice_new=New_mass*0
+                        M=h_ice.shape
+                        for j in range(M[0]):
+                                for i in range(M[1]):
+                                        if New_area[j,i]>0:
+                                                h_ice_new[j,i]=New_mass[j,i]/(rho_ice*New_area[j,i])
+
+        if Switch_x_and_y_to_rotate_90 is True:
+                [lat,lon, h_ice_new,New_area,New_mass]=Switch_x_and_y_directions(lat,lon, h_ice_new,New_area,New_mass)
+
+
+        if save_restart_files==True:
+                #Creating iceberg restart file
+                Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg)
+
+                #Creating bond restart file
+                if Create_icebergs_bonds==True:
+                        Create_bond_restart_file(Number_of_bonds,first_berg_num,first_berg_ine,first_berg_jne,other_berg_ine,other_berg_jne,iceberg_num,other_berg_num,Ice_geometry_source)
+
+                if save_new_h_ice_file==True:
+                        create_clipped_icethickness_file(h_ice_new,New_area,New_mass,grid_area,gravity,Ice_geometry_source)
+
+        # Plotting the positions and bonds of the newly formed formation
+        if Run_plotting_subroutine==True:
+                plotting_iceberg_positions(lat,lon,Number_of_bergs,R_earth,Radius,IA_scaling,Convert_to_lat_lon,\
+                                plot_circles,h_ice,ice_mask,x,y,plot_ice_mask,plot_ice_thickness,thickness,plot_icebergs_positions,static_berg,h_ice_new,plot_h_ice_new)
+                if (plot_bonds==True) and (Create_icebergs_bonds):
+                        plotting_iceberg_bonds(first_berg_lat,first_berg_lon,other_berg_lat,other_berg_lon,Number_of_bonds)
+
+        #field=New_mass/(rho_ice*grid_area)
+        field=New_area/grid_area -1.
+        M=field.shape
+        #print ('field',(field[M[0]-1,:]))
+        #print ('field',(field[M[0]-2,:]))
+        #print ('h_ice',h_ice_new[:,:])
+        #print ('h_ice-1',h_ice_new[:,:]-1.)
+        if Run_plotting_subroutine:
+                plt.show()
+        print ('Script complete')
 
 
 
 if __name__ == '__main__':
-	optCmdLineArgs=	parseCommandLine()
-	main(optCmdLineArgs)
-	#sys.exit(main())
+        optCmdLineArgs= parseCommandLine()
+        main(optCmdLineArgs)
+        #sys.exit(main())
diff --git a/tests/dem_cbeam_test/.gitignore b/tests/dem_cbeam_test/.gitignore
deleted file mode 100644
index 68bcbc9..0000000
--- a/tests/dem_cbeam_test/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-results/
\ No newline at end of file
diff --git a/tests/dem_cbeam_test/makeberg/makeberg.py b/tests/dem_cbeam_test/makeberg/makeberg.py
index c213556..bbf24a8 100755
--- a/tests/dem_cbeam_test/makeberg/makeberg.py
+++ b/tests/dem_cbeam_test/makeberg/makeberg.py
@@ -20,236 +20,236 @@ def parseCommandLine():
 
 def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
 
-	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
-	# To copy the global attributes of the netCDF file
-
-	#Input and output files
-	#Create Empty restart file. This is later read so that the attributes can be used.
-	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
-	create_empty_iceberg_restart_file(Empty_restart_filename)
-	#Empty_restart_filename='input_files/icebergs.res.nc'
-
-	#Read empty restart file
-	f=Dataset(Empty_restart_filename,'r') # r is for read only
-	#Write a new restart file
-	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
-
-	for attname in f.ncattrs():
-		    setattr(g,attname,getattr(f,attname))
-
-
-	# To copy the dimension of the netCDF file
-	for dimname,dim in f.dimensions.iteritems():
-		# if you want to make changes in the dimensions of the new file
-		# you should add your own conditions here before the creation of the dimension.
-		#g.createDimension(dimname,len(dim))
-		g.createDimension(dimname,Number_of_bergs)
-
-	# To copy the variables of the netCDF file
-
-	for varname,ncvar in f.variables.iteritems():
-		# if you want to make changes in the variables of the new file
-		# you should add your own conditions here before the creation of the variable.
-		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
-		#Proceed to copy the variable attributes
-		for attname in ncvar.ncattrs():
-			setattr(var,attname,getattr(ncvar,attname))
-		#Finally copy the variable data to the new created variable
-		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
-
-		if varname=='i':
-			var[:]=Number_of_bergs
-
-		if varname=='iceberg_num':
-			for j in range(Number_of_bergs):
-				#var[j]=j+1
-				var[j]=iceberg_num[j]
-
-		if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
-		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
-		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
-		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
-			var[:]=0
+        print ('Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..')
+        # To copy the global attributes of the netCDF file
+
+        #Input and output files
+        #Create Empty restart file. This is later read so that the attributes can be used.
+        Empty_restart_filename='output_files/Empty_icebergs.res.nc'
+        create_empty_iceberg_restart_file(Empty_restart_filename)
+        #Empty_restart_filename='input_files/icebergs.res.nc'
+
+        #Read empty restart file
+        f=Dataset(Empty_restart_filename,'r') # r is for read only
+        #Write a new restart file
+        g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
+
+        for attname in f.ncattrs():
+                    setattr(g,attname,getattr(f,attname))
+
+
+        # To copy the dimension of the netCDF file
+        for dimname,dim in f.dimensions.items():
+                # if you want to make changes in the dimensions of the new file
+                # you should add your own conditions here before the creation of the dimension.
+                #g.createDimension(dimname,len(dim))
+                g.createDimension(dimname,Number_of_bergs)
+
+        # To copy the variables of the netCDF file
+
+        for varname,ncvar in f.variables.items():
+                # if you want to make changes in the variables of the new file
+                # you should add your own conditions here before the creation of the variable.
+                var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
+                #Proceed to copy the variable attributes
+                for attname in ncvar.ncattrs():
+                        setattr(var,attname,getattr(ncvar,attname))
+                #Finally copy the variable data to the new created variable
+                #var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
+
+                if varname=='i':
+                        var[:]=Number_of_bergs
+
+                if varname=='iceberg_num':
+                        for j in range(Number_of_bergs):
+                                #var[j]=j+1
+                                var[j]=iceberg_num[j]
+
+                if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
+                or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
+                or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
+                or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
+                        var[:]=0
 
                 if varname=='uvel':
-			for j in range(Number_of_bergs):
-				var[j]=uvel[j]
+                        for j in range(Number_of_bergs):
+                                var[j]=uvel[j]
 
                 if varname=='vvel':
-			for j in range(Number_of_bergs):
-				var[j]=vvel[j]
+                        for j in range(Number_of_bergs):
+                                var[j]=vvel[j]
 
-		if varname=='mass_scaling':
-			for j in range(Number_of_bergs):
-				var[j]=mass_scaling[j]
+                if varname=='mass_scaling':
+                        for j in range(Number_of_bergs):
+                                var[j]=mass_scaling[j]
 
-		if varname=='thickness':
-			for j in range(Number_of_bergs):
-				var[j]=thickness[j]
+                if varname=='thickness':
+                        for j in range(Number_of_bergs):
+                                var[j]=thickness[j]
 
-		if varname=='mass':
-			for j in range(Number_of_bergs):
-				var[j]=mass[j]
+                if varname=='mass':
+                        for j in range(Number_of_bergs):
+                                var[j]=mass[j]
 
-		if varname=='width'  or varname=='length':
-			for j in range(Number_of_bergs):
-				var[j]=width[j]
+                if varname=='width'  or varname=='length':
+                        for j in range(Number_of_bergs):
+                                var[j]=width[j]
 
-		if varname=='lon':
-			for j in range(Number_of_bergs):
-				var[j]=lon[j]
+                if varname=='lon':
+                        for j in range(Number_of_bergs):
+                                var[j]=lon[j]
 
-		if varname=='lat':
-			for j in range(Number_of_bergs):
-				var[j]=lat[j]
+                if varname=='lat':
+                        for j in range(Number_of_bergs):
+                                var[j]=lat[j]
 
-		if varname=='static_berg':
-			for j in range(Number_of_bergs):
-				var[j]=static_berg[j]
+                if varname=='static_berg':
+                        for j in range(Number_of_bergs):
+                                var[j]=static_berg[j]
 
 
-	f.close()
-	g.close()
+        f.close()
+        g.close()
 
 
 def create_empty_iceberg_restart_file(Empty_restart_filename):
 
-	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
-
-	i=f.createDimension('i', None)
-	lon=f.createVariable('i','i')
-
-	lon=f.createVariable('lon','d',('i'))
-	lon.long_name = "longitude" ;
-	lon.units = "degrees_E" ;
-	lon.checksum = "               0" ;
-
-	lat=f.createVariable('lat','d',('i'))
-	lat.long_name = "latitude" ;
-	lat.units = "degrees_N" ;
-	lat.checksum = "               0" ;
-
-	uvel=f.createVariable('uvel','d',('i'))
-	uvel.long_name = "zonal velocity" ;
-	uvel.units = "m/s" ;
-	uvel.checksum = "               0" ;
-
-	vvel=f.createVariable('vvel','d',('i'))
-	vvel.long_name = "meridional velocity" ;
-	vvel.units = "m/s" ;
-	vvel.checksum = "               0" ;
-
-	mass=f.createVariable('mass','d',('i'))
-	mass.long_name = "mass" ;
-	mass.units = "kg" ;
-	mass.checksum = "               0" ;
-
-	axn=f.createVariable('axn','d',('i'))
-	axn.long_name = "explicit zonal acceleration" ;
-	axn.units = "m/s^2" ;
-	axn.checksum = "               0" ;
-
-	ayn=f.createVariable('ayn','d',('i'))
-	ayn.long_name = "explicit meridional acceleration" ;
-	ayn.units = "m/s^2" ;
-	ayn.checksum = "               0" ;
-
-	bxn=f.createVariable('bxn','d',('i'))
-	bxn.long_name = "inplicit zonal acceleration" ;
-	bxn.units = "m/s^2" ;
-	bxn.checksum = "               0" ;
-
-	byn=f.createVariable('byn','d',('i'))
-	byn.long_name = "implicit meridional acceleration" ;
-	byn.units = "m/s^2" ;
-	byn.checksum = "               0" ;
-
-	ine=f.createVariable('ine','i',('i'))
-	ine.long_name = "i index" ;
-	ine.units = "none" ;
-	ine.packing = 0 ;
-	ine.checksum = "               0" ;
-
-	jne=f.createVariable('jne','i',('i'))
-	jne.long_name = "j index" ;
-	jne.units = "none" ;
-	jne.packing = 0 ;
-	jne.checksum = "               0" ;
-
-	thickness=f.createVariable('thickness','d',('i'))
-	thickness.long_name = "thickness" ;
-	thickness.units = "m" ;
-	thickness.checksum = "               0" ;
-
-	width=f.createVariable('width','d',('i'))
-	width.long_name = "width" ;
-	width.units = "m" ;
-	width.checksum = "               0" ;
-
-	length=f.createVariable('length','d',('i'))
-	length.long_name = "length" ;
-	length.units = "m" ;
-	length.checksum = "               0" ;
-
-	start_lon=f.createVariable('start_lon','d',('i'))
-	start_lon.long_name = "longitude of calving location" ;
-	start_lon.units = "degrees_E" ;
-	start_lon.checksum = "               0" ;
-
-	start_lat=f.createVariable('start_lat','d',('i'))
-	start_lat.long_name = "latitude of calving location" ;
-	start_lat.units = "degrees_N" ;
-	start_lat.checksum = "               0" ;
-
-	start_year=f.createVariable('start_year','i',('i'))
-	start_year.long_name = "calendar year of calving event" ;
-	start_year.units = "years" ;
-	start_year.packing = 0 ;
-	start_year.checksum = "               0" ;
-
-	iceberg_num=f.createVariable('iceberg_num','i',('i'))
-	iceberg_num.long_name = "identification of the iceberg" ;
-	iceberg_num.units = "dimensionless" ;
-	iceberg_num.packing = 0 ;
-	iceberg_num.checksum = "               0" ;
-
-	start_day=f.createVariable('start_day','d',('i'))
-	start_day.long_name = "year day of calving event" ;
-	start_day.units = "days" ;
-	start_day.checksum = "               0" ;
-
-	start_mass=f.createVariable('start_mass','d',('i'))
-	start_mass.long_name = "initial mass of calving berg" ;
-	start_mass.units = "kg" ;
-	start_mass.checksum = "               0" ;
-
-	mass_scaling=f.createVariable('mass_scaling','d',('i'))
-	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
-	mass_scaling.units = "none" ;
-	mass_scaling.checksum = "               0" ;
-
-	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
-	mass_of_bits.long_name = "mass of bergy bits" ;
-	mass_of_bits.units = "kg" ;
-	mass_of_bits.checksum = "               0" ;
-
-	heat_density=f.createVariable('heat_density','d',('i'))
-	heat_density.long_name = "heat density" ;
-	heat_density.units = "J/kg" ;
-	heat_density.checksum = "               0" ;
-
-	halo_berg=f.createVariable('halo_berg','d',('i'))
-	halo_berg.long_name = "halo_berg" ;
-	halo_berg.units = "dimensionless" ;
-	halo_berg.checksum = "               0" ;
-
-	static_berg=f.createVariable('static_berg','d',('i'))
-	static_berg.long_name = "static_berg" ;
-	static_berg.units = "dimensionless" ;
-	static_berg.checksum = "               0" ;
-
-	f.sync()
-	f.close()
+        f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
+
+        i=f.createDimension('i', None)
+        lon=f.createVariable('i','i')
+
+        lon=f.createVariable('lon','d',('i'))
+        lon.long_name = "longitude" ;
+        lon.units = "degrees_E" ;
+        lon.checksum = "               0" ;
+
+        lat=f.createVariable('lat','d',('i'))
+        lat.long_name = "latitude" ;
+        lat.units = "degrees_N" ;
+        lat.checksum = "               0" ;
+
+        uvel=f.createVariable('uvel','d',('i'))
+        uvel.long_name = "zonal velocity" ;
+        uvel.units = "m/s" ;
+        uvel.checksum = "               0" ;
+
+        vvel=f.createVariable('vvel','d',('i'))
+        vvel.long_name = "meridional velocity" ;
+        vvel.units = "m/s" ;
+        vvel.checksum = "               0" ;
+
+        mass=f.createVariable('mass','d',('i'))
+        mass.long_name = "mass" ;
+        mass.units = "kg" ;
+        mass.checksum = "               0" ;
+
+        axn=f.createVariable('axn','d',('i'))
+        axn.long_name = "explicit zonal acceleration" ;
+        axn.units = "m/s^2" ;
+        axn.checksum = "               0" ;
+
+        ayn=f.createVariable('ayn','d',('i'))
+        ayn.long_name = "explicit meridional acceleration" ;
+        ayn.units = "m/s^2" ;
+        ayn.checksum = "               0" ;
+
+        bxn=f.createVariable('bxn','d',('i'))
+        bxn.long_name = "inplicit zonal acceleration" ;
+        bxn.units = "m/s^2" ;
+        bxn.checksum = "               0" ;
+
+        byn=f.createVariable('byn','d',('i'))
+        byn.long_name = "implicit meridional acceleration" ;
+        byn.units = "m/s^2" ;
+        byn.checksum = "               0" ;
+
+        ine=f.createVariable('ine','i',('i'))
+        ine.long_name = "i index" ;
+        ine.units = "none" ;
+        ine.packing = 0 ;
+        ine.checksum = "               0" ;
+
+        jne=f.createVariable('jne','i',('i'))
+        jne.long_name = "j index" ;
+        jne.units = "none" ;
+        jne.packing = 0 ;
+        jne.checksum = "               0" ;
+
+        thickness=f.createVariable('thickness','d',('i'))
+        thickness.long_name = "thickness" ;
+        thickness.units = "m" ;
+        thickness.checksum = "               0" ;
+
+        width=f.createVariable('width','d',('i'))
+        width.long_name = "width" ;
+        width.units = "m" ;
+        width.checksum = "               0" ;
+
+        length=f.createVariable('length','d',('i'))
+        length.long_name = "length" ;
+        length.units = "m" ;
+        length.checksum = "               0" ;
+
+        start_lon=f.createVariable('start_lon','d',('i'))
+        start_lon.long_name = "longitude of calving location" ;
+        start_lon.units = "degrees_E" ;
+        start_lon.checksum = "               0" ;
+
+        start_lat=f.createVariable('start_lat','d',('i'))
+        start_lat.long_name = "latitude of calving location" ;
+        start_lat.units = "degrees_N" ;
+        start_lat.checksum = "               0" ;
+
+        start_year=f.createVariable('start_year','i',('i'))
+        start_year.long_name = "calendar year of calving event" ;
+        start_year.units = "years" ;
+        start_year.packing = 0 ;
+        start_year.checksum = "               0" ;
+
+        iceberg_num=f.createVariable('iceberg_num','i',('i'))
+        iceberg_num.long_name = "identification of the iceberg" ;
+        iceberg_num.units = "dimensionless" ;
+        iceberg_num.packing = 0 ;
+        iceberg_num.checksum = "               0" ;
+
+        start_day=f.createVariable('start_day','d',('i'))
+        start_day.long_name = "year day of calving event" ;
+        start_day.units = "days" ;
+        start_day.checksum = "               0" ;
+
+        start_mass=f.createVariable('start_mass','d',('i'))
+        start_mass.long_name = "initial mass of calving berg" ;
+        start_mass.units = "kg" ;
+        start_mass.checksum = "               0" ;
+
+        mass_scaling=f.createVariable('mass_scaling','d',('i'))
+        mass_scaling.long_name = "scaling factor for mass of calving berg" ;
+        mass_scaling.units = "none" ;
+        mass_scaling.checksum = "               0" ;
+
+        mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
+        mass_of_bits.long_name = "mass of bergy bits" ;
+        mass_of_bits.units = "kg" ;
+        mass_of_bits.checksum = "               0" ;
+
+        heat_density=f.createVariable('heat_density','d',('i'))
+        heat_density.long_name = "heat density" ;
+        heat_density.units = "J/kg" ;
+        heat_density.checksum = "               0" ;
+
+        halo_berg=f.createVariable('halo_berg','d',('i'))
+        halo_berg.long_name = "halo_berg" ;
+        halo_berg.units = "dimensionless" ;
+        halo_berg.checksum = "               0" ;
+
+        static_berg=f.createVariable('static_berg','d',('i'))
+        static_berg.long_name = "static_berg" ;
+        static_berg.units = "dimensionless" ;
+        static_berg.checksum = "               0" ;
+
+        f.sync()
+        f.close()
 
 
 def main(args):
@@ -318,6 +318,6 @@ def main(args):
 
 
 if __name__ == '__main__':
-    optCmdLineArgs=	parseCommandLine()
+    optCmdLineArgs=     parseCommandLine()
     anim_running = True
     main(optCmdLineArgs)
diff --git a/tests/dem_ground_frac_test/.gitignore b/tests/dem_ground_frac_test/.gitignore
deleted file mode 100644
index 68bcbc9..0000000
--- a/tests/dem_ground_frac_test/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-results/
\ No newline at end of file
diff --git a/tests/dem_ground_frac_test/makeberg/makeberg.py b/tests/dem_ground_frac_test/makeberg/makeberg.py
index a729381..1c50e07 100755
--- a/tests/dem_ground_frac_test/makeberg/makeberg.py
+++ b/tests/dem_ground_frac_test/makeberg/makeberg.py
@@ -8,56 +8,56 @@
 
 def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
 
-	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
-	# To copy the global attributes of the netCDF file
-
-	#Input and output files
-	#Create Empty restart file. This is later read so that the attributes can be used.
-	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
-	create_empty_iceberg_restart_file(Empty_restart_filename)
-	#Empty_restart_filename='input_files/icebergs.res.nc'
-
-	#Read empty restart file
-	f=Dataset(Empty_restart_filename,'r') # r is for read only
-	#Write a new restart file
-	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
-
-	for attname in f.ncattrs():
-		    setattr(g,attname,getattr(f,attname))
-
-
-	# To copy the dimension of the netCDF file
-	for dimname,dim in f.dimensions.iteritems():
-		# if you want to make changes in the dimensions of the new file
-		# you should add your own conditions here before the creation of the dimension.
-		#g.createDimension(dimname,len(dim))
-		g.createDimension(dimname,Number_of_bergs)
-
-	# To copy the variables of the netCDF file
-
-	for varname,ncvar in f.variables.iteritems():
-		# if you want to make changes in the variables of the new file
-		# you should add your own conditions here before the creation of the variable.
-		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
-		#Proceed to copy the variable attributes
-		for attname in ncvar.ncattrs():
-			setattr(var,attname,getattr(ncvar,attname))
-		#Finally copy the variable data to the new created variable
-		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
-
-		if varname=='i':
-			var[:]=Number_of_bergs
-
-		if varname=='iceberg_num':
-			for j in range(Number_of_bergs):
-				#var[j]=j+1
-				var[j]=iceberg_num[j]
-
-		if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
-		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
-		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
-		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
-			var[:]=0
+        print ('Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..')
+        # To copy the global attributes of the netCDF file
+
+        #Input and output files
+        #Create Empty restart file. This is later read so that the attributes can be used.
+        Empty_restart_filename='output_files/Empty_icebergs.res.nc'
+        create_empty_iceberg_restart_file(Empty_restart_filename)
+        #Empty_restart_filename='input_files/icebergs.res.nc'
+
+        #Read empty restart file
+        f=Dataset(Empty_restart_filename,'r') # r is for read only
+        #Write a new restart file
+        g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
+
+        for attname in f.ncattrs():
+                    setattr(g,attname,getattr(f,attname))
+
+
+        # To copy the dimension of the netCDF file
+        for dimname,dim in f.dimensions.items():
+                # if you want to make changes in the dimensions of the new file
+                # you should add your own conditions here before the creation of the dimension.
+                #g.createDimension(dimname,len(dim))
+                g.createDimension(dimname,Number_of_bergs)
+
+        # To copy the variables of the netCDF file
+
+        for varname,ncvar in f.variables.items():
+                # if you want to make changes in the variables of the new file
+                # you should add your own conditions here before the creation of the variable.
+                var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
+                #Proceed to copy the variable attributes
+                for attname in ncvar.ncattrs():
+                        setattr(var,attname,getattr(ncvar,attname))
+                #Finally copy the variable data to the new created variable
+                #var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
+
+                if varname=='i':
+                        var[:]=Number_of_bergs
+
+                if varname=='iceberg_num':
+                        for j in range(Number_of_bergs):
+                                #var[j]=j+1
+                                var[j]=iceberg_num[j]
+
+                if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
+                or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
+                or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
+                or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
+                        var[:]=0
 
                 if varname=='uvel':
                         var[:]=uvel
@@ -65,176 +65,176 @@ def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,ma
                 if varname=='vvel':
                         var[:]=vvel
 
-		if varname=='mass_scaling':
-			var[:]=mass_scaling
+                if varname=='mass_scaling':
+                        var[:]=mass_scaling
 
-		if varname=='thickness':
-			for j in range(Number_of_bergs):
-				var[j]=thickness[j]
+                if varname=='thickness':
+                        for j in range(Number_of_bergs):
+                                var[j]=thickness[j]
 
-		if varname=='mass':
-			for j in range(Number_of_bergs):
-				var[j]=mass[j]
+                if varname=='mass':
+                        for j in range(Number_of_bergs):
+                                var[j]=mass[j]
 
-		if varname=='width'  or varname=='length':
-			for j in range(Number_of_bergs):
-				var[j]=width[j]
+                if varname=='width'  or varname=='length':
+                        for j in range(Number_of_bergs):
+                                var[j]=width[j]
 
-		if varname=='lon':
-			for j in range(Number_of_bergs):
-				var[j]=lon[j]
+                if varname=='lon':
+                        for j in range(Number_of_bergs):
+                                var[j]=lon[j]
 
-		if varname=='lat':
-			for j in range(Number_of_bergs):
-				var[j]=lat[j]
+                if varname=='lat':
+                        for j in range(Number_of_bergs):
+                                var[j]=lat[j]
 
-		if varname=='static_berg':
-			for j in range(Number_of_bergs):
-				var[j]=static_berg[j]
+                if varname=='static_berg':
+                        for j in range(Number_of_bergs):
+                                var[j]=static_berg[j]
 
 
-	f.close()
-	g.close()
+        f.close()
+        g.close()
 
 
 def create_empty_iceberg_restart_file(Empty_restart_filename):
 
-	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
-
-	i=f.createDimension('i', None)
-	lon=f.createVariable('i','i')
-
-	lon=f.createVariable('lon','d',('i'))
-	lon.long_name = "longitude" ;
-	lon.units = "degrees_E" ;
-	lon.checksum = "               0" ;
-
-	lat=f.createVariable('lat','d',('i'))
-	lat.long_name = "latitude" ;
-	lat.units = "degrees_N" ;
-	lat.checksum = "               0" ;
-
-	uvel=f.createVariable('uvel','d',('i'))
-	uvel.long_name = "zonal velocity" ;
-	uvel.units = "m/s" ;
-	uvel.checksum = "               0" ;
-
-	vvel=f.createVariable('vvel','d',('i'))
-	vvel.long_name = "meridional velocity" ;
-	vvel.units = "m/s" ;
-	vvel.checksum = "               0" ;
-
-	mass=f.createVariable('mass','d',('i'))
-	mass.long_name = "mass" ;
-	mass.units = "kg" ;
-	mass.checksum = "               0" ;
-
-	axn=f.createVariable('axn','d',('i'))
-	axn.long_name = "explicit zonal acceleration" ;
-	axn.units = "m/s^2" ;
-	axn.checksum = "               0" ;
-
-	ayn=f.createVariable('ayn','d',('i'))
-	ayn.long_name = "explicit meridional acceleration" ;
-	ayn.units = "m/s^2" ;
-	ayn.checksum = "               0" ;
-
-	bxn=f.createVariable('bxn','d',('i'))
-	bxn.long_name = "inplicit zonal acceleration" ;
-	bxn.units = "m/s^2" ;
-	bxn.checksum = "               0" ;
-
-	byn=f.createVariable('byn','d',('i'))
-	byn.long_name = "implicit meridional acceleration" ;
-	byn.units = "m/s^2" ;
-	byn.checksum = "               0" ;
-
-	ine=f.createVariable('ine','i',('i'))
-	ine.long_name = "i index" ;
-	ine.units = "none" ;
-	ine.packing = 0 ;
-	ine.checksum = "               0" ;
-
-	jne=f.createVariable('jne','i',('i'))
-	jne.long_name = "j index" ;
-	jne.units = "none" ;
-	jne.packing = 0 ;
-	jne.checksum = "               0" ;
-
-	thickness=f.createVariable('thickness','d',('i'))
-	thickness.long_name = "thickness" ;
-	thickness.units = "m" ;
-	thickness.checksum = "               0" ;
-
-	width=f.createVariable('width','d',('i'))
-	width.long_name = "width" ;
-	width.units = "m" ;
-	width.checksum = "               0" ;
-
-	length=f.createVariable('length','d',('i'))
-	length.long_name = "length" ;
-	length.units = "m" ;
-	length.checksum = "               0" ;
-
-	start_lon=f.createVariable('start_lon','d',('i'))
-	start_lon.long_name = "longitude of calving location" ;
-	start_lon.units = "degrees_E" ;
-	start_lon.checksum = "               0" ;
-
-	start_lat=f.createVariable('start_lat','d',('i'))
-	start_lat.long_name = "latitude of calving location" ;
-	start_lat.units = "degrees_N" ;
-	start_lat.checksum = "               0" ;
-
-	start_year=f.createVariable('start_year','i',('i'))
-	start_year.long_name = "calendar year of calving event" ;
-	start_year.units = "years" ;
-	start_year.packing = 0 ;
-	start_year.checksum = "               0" ;
-
-	iceberg_num=f.createVariable('iceberg_num','i',('i'))
-	iceberg_num.long_name = "identification of the iceberg" ;
-	iceberg_num.units = "dimensionless" ;
-	iceberg_num.packing = 0 ;
-	iceberg_num.checksum = "               0" ;
-
-	start_day=f.createVariable('start_day','d',('i'))
-	start_day.long_name = "year day of calving event" ;
-	start_day.units = "days" ;
-	start_day.checksum = "               0" ;
-
-	start_mass=f.createVariable('start_mass','d',('i'))
-	start_mass.long_name = "initial mass of calving berg" ;
-	start_mass.units = "kg" ;
-	start_mass.checksum = "               0" ;
-
-	mass_scaling=f.createVariable('mass_scaling','d',('i'))
-	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
-	mass_scaling.units = "none" ;
-	mass_scaling.checksum = "               0" ;
-
-	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
-	mass_of_bits.long_name = "mass of bergy bits" ;
-	mass_of_bits.units = "kg" ;
-	mass_of_bits.checksum = "               0" ;
-
-	heat_density=f.createVariable('heat_density','d',('i'))
-	heat_density.long_name = "heat density" ;
-	heat_density.units = "J/kg" ;
-	heat_density.checksum = "               0" ;
-
-	halo_berg=f.createVariable('halo_berg','d',('i'))
-	halo_berg.long_name = "halo_berg" ;
-	halo_berg.units = "dimensionless" ;
-	halo_berg.checksum = "               0" ;
-
-	static_berg=f.createVariable('static_berg','d',('i'))
-	static_berg.long_name = "static_berg" ;
-	static_berg.units = "dimensionless" ;
-	static_berg.checksum = "               0" ;
-
-	f.sync()
-	f.close()
+        f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
+
+        i=f.createDimension('i', None)
+        lon=f.createVariable('i','i')
+
+        lon=f.createVariable('lon','d',('i'))
+        lon.long_name = "longitude" ;
+        lon.units = "degrees_E" ;
+        lon.checksum = "               0" ;
+
+        lat=f.createVariable('lat','d',('i'))
+        lat.long_name = "latitude" ;
+        lat.units = "degrees_N" ;
+        lat.checksum = "               0" ;
+
+        uvel=f.createVariable('uvel','d',('i'))
+        uvel.long_name = "zonal velocity" ;
+        uvel.units = "m/s" ;
+        uvel.checksum = "               0" ;
+
+        vvel=f.createVariable('vvel','d',('i'))
+        vvel.long_name = "meridional velocity" ;
+        vvel.units = "m/s" ;
+        vvel.checksum = "               0" ;
+
+        mass=f.createVariable('mass','d',('i'))
+        mass.long_name = "mass" ;
+        mass.units = "kg" ;
+        mass.checksum = "               0" ;
+
+        axn=f.createVariable('axn','d',('i'))
+        axn.long_name = "explicit zonal acceleration" ;
+        axn.units = "m/s^2" ;
+        axn.checksum = "               0" ;
+
+        ayn=f.createVariable('ayn','d',('i'))
+        ayn.long_name = "explicit meridional acceleration" ;
+        ayn.units = "m/s^2" ;
+        ayn.checksum = "               0" ;
+
+        bxn=f.createVariable('bxn','d',('i'))
+        bxn.long_name = "inplicit zonal acceleration" ;
+        bxn.units = "m/s^2" ;
+        bxn.checksum = "               0" ;
+
+        byn=f.createVariable('byn','d',('i'))
+        byn.long_name = "implicit meridional acceleration" ;
+        byn.units = "m/s^2" ;
+        byn.checksum = "               0" ;
+
+        ine=f.createVariable('ine','i',('i'))
+        ine.long_name = "i index" ;
+        ine.units = "none" ;
+        ine.packing = 0 ;
+        ine.checksum = "               0" ;
+
+        jne=f.createVariable('jne','i',('i'))
+        jne.long_name = "j index" ;
+        jne.units = "none" ;
+        jne.packing = 0 ;
+        jne.checksum = "               0" ;
+
+        thickness=f.createVariable('thickness','d',('i'))
+        thickness.long_name = "thickness" ;
+        thickness.units = "m" ;
+        thickness.checksum = "               0" ;
+
+        width=f.createVariable('width','d',('i'))
+        width.long_name = "width" ;
+        width.units = "m" ;
+        width.checksum = "               0" ;
+
+        length=f.createVariable('length','d',('i'))
+        length.long_name = "length" ;
+        length.units = "m" ;
+        length.checksum = "               0" ;
+
+        start_lon=f.createVariable('start_lon','d',('i'))
+        start_lon.long_name = "longitude of calving location" ;
+        start_lon.units = "degrees_E" ;
+        start_lon.checksum = "               0" ;
+
+        start_lat=f.createVariable('start_lat','d',('i'))
+        start_lat.long_name = "latitude of calving location" ;
+        start_lat.units = "degrees_N" ;
+        start_lat.checksum = "               0" ;
+
+        start_year=f.createVariable('start_year','i',('i'))
+        start_year.long_name = "calendar year of calving event" ;
+        start_year.units = "years" ;
+        start_year.packing = 0 ;
+        start_year.checksum = "               0" ;
+
+        iceberg_num=f.createVariable('iceberg_num','i',('i'))
+        iceberg_num.long_name = "identification of the iceberg" ;
+        iceberg_num.units = "dimensionless" ;
+        iceberg_num.packing = 0 ;
+        iceberg_num.checksum = "               0" ;
+
+        start_day=f.createVariable('start_day','d',('i'))
+        start_day.long_name = "year day of calving event" ;
+        start_day.units = "days" ;
+        start_day.checksum = "               0" ;
+
+        start_mass=f.createVariable('start_mass','d',('i'))
+        start_mass.long_name = "initial mass of calving berg" ;
+        start_mass.units = "kg" ;
+        start_mass.checksum = "               0" ;
+
+        mass_scaling=f.createVariable('mass_scaling','d',('i'))
+        mass_scaling.long_name = "scaling factor for mass of calving berg" ;
+        mass_scaling.units = "none" ;
+        mass_scaling.checksum = "               0" ;
+
+        mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
+        mass_of_bits.long_name = "mass of bergy bits" ;
+        mass_of_bits.units = "kg" ;
+        mass_of_bits.checksum = "               0" ;
+
+        heat_density=f.createVariable('heat_density','d',('i'))
+        heat_density.long_name = "heat density" ;
+        heat_density.units = "J/kg" ;
+        heat_density.checksum = "               0" ;
+
+        halo_berg=f.createVariable('halo_berg','d',('i'))
+        halo_berg.long_name = "halo_berg" ;
+        halo_berg.units = "dimensionless" ;
+        halo_berg.checksum = "               0" ;
+
+        static_berg=f.createVariable('static_berg','d',('i'))
+        static_berg.long_name = "static_berg" ;
+        static_berg.units = "dimensionless" ;
+        static_berg.checksum = "               0" ;
+
+        f.sync()
+        f.close()
 
 #-----------------------------------#
 #               Main                #
diff --git a/tests/dem_ssbeam_test/.gitignore b/tests/dem_ssbeam_test/.gitignore
deleted file mode 100644
index 68bcbc9..0000000
--- a/tests/dem_ssbeam_test/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-results/
\ No newline at end of file
diff --git a/tests/dem_ssbeam_test/makeberg/makeberg.py b/tests/dem_ssbeam_test/makeberg/makeberg.py
index 7ac6b92..45c1e93 100755
--- a/tests/dem_ssbeam_test/makeberg/makeberg.py
+++ b/tests/dem_ssbeam_test/makeberg/makeberg.py
@@ -18,236 +18,236 @@ def parseCommandLine():
 
 def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
 
-	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
-	# To copy the global attributes of the netCDF file
-
-	#Input and output files
-	#Create Empty restart file. This is later read so that the attributes can be used.
-	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
-	create_empty_iceberg_restart_file(Empty_restart_filename)
-	#Empty_restart_filename='input_files/icebergs.res.nc'
-
-	#Read empty restart file
-	f=Dataset(Empty_restart_filename,'r') # r is for read only
-	#Write a new restart file
-	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
-
-	for attname in f.ncattrs():
-		    setattr(g,attname,getattr(f,attname))
-
-
-	# To copy the dimension of the netCDF file
-	for dimname,dim in f.dimensions.iteritems():
-		# if you want to make changes in the dimensions of the new file
-		# you should add your own conditions here before the creation of the dimension.
-		#g.createDimension(dimname,len(dim))
-		g.createDimension(dimname,Number_of_bergs)
-
-	# To copy the variables of the netCDF file
-
-	for varname,ncvar in f.variables.iteritems():
-		# if you want to make changes in the variables of the new file
-		# you should add your own conditions here before the creation of the variable.
-		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
-		#Proceed to copy the variable attributes
-		for attname in ncvar.ncattrs():
-			setattr(var,attname,getattr(ncvar,attname))
-		#Finally copy the variable data to the new created variable
-		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
-
-		if varname=='i':
-			var[:]=Number_of_bergs
-
-		if varname=='iceberg_num':
-			for j in range(Number_of_bergs):
-				#var[j]=j+1
-				var[j]=iceberg_num[j]
-
-		if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
-		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
-		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
-		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
-			var[:]=0
+        print ('Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..')
+        # To copy the global attributes of the netCDF file
+
+        #Input and output files
+        #Create Empty restart file. This is later read so that the attributes can be used.
+        Empty_restart_filename='output_files/Empty_icebergs.res.nc'
+        create_empty_iceberg_restart_file(Empty_restart_filename)
+        #Empty_restart_filename='input_files/icebergs.res.nc'
+
+        #Read empty restart file
+        f=Dataset(Empty_restart_filename,'r') # r is for read only
+        #Write a new restart file
+        g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
+
+        for attname in f.ncattrs():
+                    setattr(g,attname,getattr(f,attname))
+
+
+        # To copy the dimension of the netCDF file
+        for dimname,dim in f.dimensions.items():
+                # if you want to make changes in the dimensions of the new file
+                # you should add your own conditions here before the creation of the dimension.
+                #g.createDimension(dimname,len(dim))
+                g.createDimension(dimname,Number_of_bergs)
+
+        # To copy the variables of the netCDF file
+
+        for varname,ncvar in f.variables.items():
+                # if you want to make changes in the variables of the new file
+                # you should add your own conditions here before the creation of the variable.
+                var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
+                #Proceed to copy the variable attributes
+                for attname in ncvar.ncattrs():
+                        setattr(var,attname,getattr(ncvar,attname))
+                #Finally copy the variable data to the new created variable
+                #var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
+
+                if varname=='i':
+                        var[:]=Number_of_bergs
+
+                if varname=='iceberg_num':
+                        for j in range(Number_of_bergs):
+                                #var[j]=j+1
+                                var[j]=iceberg_num[j]
+
+                if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
+                or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
+                or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
+                or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
+                        var[:]=0
 
                 if varname=='uvel':
-			for j in range(Number_of_bergs):
-				var[j]=uvel[j]
+                        for j in range(Number_of_bergs):
+                                var[j]=uvel[j]
 
                 if varname=='vvel':
-			for j in range(Number_of_bergs):
-				var[j]=vvel[j]
+                        for j in range(Number_of_bergs):
+                                var[j]=vvel[j]
 
-		if varname=='mass_scaling':
-			for j in range(Number_of_bergs):
-				var[j]=mass_scaling[j]
+                if varname=='mass_scaling':
+                        for j in range(Number_of_bergs):
+                                var[j]=mass_scaling[j]
 
-		if varname=='thickness':
-			for j in range(Number_of_bergs):
-				var[j]=thickness[j]
+                if varname=='thickness':
+                        for j in range(Number_of_bergs):
+                                var[j]=thickness[j]
 
-		if varname=='mass':
-			for j in range(Number_of_bergs):
-				var[j]=mass[j]
+                if varname=='mass':
+                        for j in range(Number_of_bergs):
+                                var[j]=mass[j]
 
-		if varname=='width'  or varname=='length':
-			for j in range(Number_of_bergs):
-				var[j]=width[j]
+                if varname=='width'  or varname=='length':
+                        for j in range(Number_of_bergs):
+                                var[j]=width[j]
 
-		if varname=='lon':
-			for j in range(Number_of_bergs):
-				var[j]=lon[j]
+                if varname=='lon':
+                        for j in range(Number_of_bergs):
+                                var[j]=lon[j]
 
-		if varname=='lat':
-			for j in range(Number_of_bergs):
-				var[j]=lat[j]
+                if varname=='lat':
+                        for j in range(Number_of_bergs):
+                                var[j]=lat[j]
 
-		if varname=='static_berg':
-			for j in range(Number_of_bergs):
-				var[j]=static_berg[j]
+                if varname=='static_berg':
+                        for j in range(Number_of_bergs):
+                                var[j]=static_berg[j]
 
 
-	f.close()
-	g.close()
+        f.close()
+        g.close()
 
 
 def create_empty_iceberg_restart_file(Empty_restart_filename):
 
-	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
-
-	i=f.createDimension('i', None)
-	lon=f.createVariable('i','i')
-
-	lon=f.createVariable('lon','d',('i'))
-	lon.long_name = "longitude" ;
-	lon.units = "degrees_E" ;
-	lon.checksum = "               0" ;
-
-	lat=f.createVariable('lat','d',('i'))
-	lat.long_name = "latitude" ;
-	lat.units = "degrees_N" ;
-	lat.checksum = "               0" ;
-
-	uvel=f.createVariable('uvel','d',('i'))
-	uvel.long_name = "zonal velocity" ;
-	uvel.units = "m/s" ;
-	uvel.checksum = "               0" ;
-
-	vvel=f.createVariable('vvel','d',('i'))
-	vvel.long_name = "meridional velocity" ;
-	vvel.units = "m/s" ;
-	vvel.checksum = "               0" ;
-
-	mass=f.createVariable('mass','d',('i'))
-	mass.long_name = "mass" ;
-	mass.units = "kg" ;
-	mass.checksum = "               0" ;
-
-	axn=f.createVariable('axn','d',('i'))
-	axn.long_name = "explicit zonal acceleration" ;
-	axn.units = "m/s^2" ;
-	axn.checksum = "               0" ;
-
-	ayn=f.createVariable('ayn','d',('i'))
-	ayn.long_name = "explicit meridional acceleration" ;
-	ayn.units = "m/s^2" ;
-	ayn.checksum = "               0" ;
-
-	bxn=f.createVariable('bxn','d',('i'))
-	bxn.long_name = "inplicit zonal acceleration" ;
-	bxn.units = "m/s^2" ;
-	bxn.checksum = "               0" ;
-
-	byn=f.createVariable('byn','d',('i'))
-	byn.long_name = "implicit meridional acceleration" ;
-	byn.units = "m/s^2" ;
-	byn.checksum = "               0" ;
-
-	ine=f.createVariable('ine','i',('i'))
-	ine.long_name = "i index" ;
-	ine.units = "none" ;
-	ine.packing = 0 ;
-	ine.checksum = "               0" ;
-
-	jne=f.createVariable('jne','i',('i'))
-	jne.long_name = "j index" ;
-	jne.units = "none" ;
-	jne.packing = 0 ;
-	jne.checksum = "               0" ;
-
-	thickness=f.createVariable('thickness','d',('i'))
-	thickness.long_name = "thickness" ;
-	thickness.units = "m" ;
-	thickness.checksum = "               0" ;
-
-	width=f.createVariable('width','d',('i'))
-	width.long_name = "width" ;
-	width.units = "m" ;
-	width.checksum = "               0" ;
-
-	length=f.createVariable('length','d',('i'))
-	length.long_name = "length" ;
-	length.units = "m" ;
-	length.checksum = "               0" ;
-
-	start_lon=f.createVariable('start_lon','d',('i'))
-	start_lon.long_name = "longitude of calving location" ;
-	start_lon.units = "degrees_E" ;
-	start_lon.checksum = "               0" ;
-
-	start_lat=f.createVariable('start_lat','d',('i'))
-	start_lat.long_name = "latitude of calving location" ;
-	start_lat.units = "degrees_N" ;
-	start_lat.checksum = "               0" ;
-
-	start_year=f.createVariable('start_year','i',('i'))
-	start_year.long_name = "calendar year of calving event" ;
-	start_year.units = "years" ;
-	start_year.packing = 0 ;
-	start_year.checksum = "               0" ;
-
-	iceberg_num=f.createVariable('iceberg_num','i',('i'))
-	iceberg_num.long_name = "identification of the iceberg" ;
-	iceberg_num.units = "dimensionless" ;
-	iceberg_num.packing = 0 ;
-	iceberg_num.checksum = "               0" ;
-
-	start_day=f.createVariable('start_day','d',('i'))
-	start_day.long_name = "year day of calving event" ;
-	start_day.units = "days" ;
-	start_day.checksum = "               0" ;
-
-	start_mass=f.createVariable('start_mass','d',('i'))
-	start_mass.long_name = "initial mass of calving berg" ;
-	start_mass.units = "kg" ;
-	start_mass.checksum = "               0" ;
-
-	mass_scaling=f.createVariable('mass_scaling','d',('i'))
-	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
-	mass_scaling.units = "none" ;
-	mass_scaling.checksum = "               0" ;
-
-	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
-	mass_of_bits.long_name = "mass of bergy bits" ;
-	mass_of_bits.units = "kg" ;
-	mass_of_bits.checksum = "               0" ;
-
-	heat_density=f.createVariable('heat_density','d',('i'))
-	heat_density.long_name = "heat density" ;
-	heat_density.units = "J/kg" ;
-	heat_density.checksum = "               0" ;
-
-	halo_berg=f.createVariable('halo_berg','d',('i'))
-	halo_berg.long_name = "halo_berg" ;
-	halo_berg.units = "dimensionless" ;
-	halo_berg.checksum = "               0" ;
-
-	static_berg=f.createVariable('static_berg','d',('i'))
-	static_berg.long_name = "static_berg" ;
-	static_berg.units = "dimensionless" ;
-	static_berg.checksum = "               0" ;
-
-	f.sync()
-	f.close()
+        f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
+
+        i=f.createDimension('i', None)
+        lon=f.createVariable('i','i')
+
+        lon=f.createVariable('lon','d',('i'))
+        lon.long_name = "longitude" ;
+        lon.units = "degrees_E" ;
+        lon.checksum = "               0" ;
+
+        lat=f.createVariable('lat','d',('i'))
+        lat.long_name = "latitude" ;
+        lat.units = "degrees_N" ;
+        lat.checksum = "               0" ;
+
+        uvel=f.createVariable('uvel','d',('i'))
+        uvel.long_name = "zonal velocity" ;
+        uvel.units = "m/s" ;
+        uvel.checksum = "               0" ;
+
+        vvel=f.createVariable('vvel','d',('i'))
+        vvel.long_name = "meridional velocity" ;
+        vvel.units = "m/s" ;
+        vvel.checksum = "               0" ;
+
+        mass=f.createVariable('mass','d',('i'))
+        mass.long_name = "mass" ;
+        mass.units = "kg" ;
+        mass.checksum = "               0" ;
+
+        axn=f.createVariable('axn','d',('i'))
+        axn.long_name = "explicit zonal acceleration" ;
+        axn.units = "m/s^2" ;
+        axn.checksum = "               0" ;
+
+        ayn=f.createVariable('ayn','d',('i'))
+        ayn.long_name = "explicit meridional acceleration" ;
+        ayn.units = "m/s^2" ;
+        ayn.checksum = "               0" ;
+
+        bxn=f.createVariable('bxn','d',('i'))
+        bxn.long_name = "inplicit zonal acceleration" ;
+        bxn.units = "m/s^2" ;
+        bxn.checksum = "               0" ;
+
+        byn=f.createVariable('byn','d',('i'))
+        byn.long_name = "implicit meridional acceleration" ;
+        byn.units = "m/s^2" ;
+        byn.checksum = "               0" ;
+
+        ine=f.createVariable('ine','i',('i'))
+        ine.long_name = "i index" ;
+        ine.units = "none" ;
+        ine.packing = 0 ;
+        ine.checksum = "               0" ;
+
+        jne=f.createVariable('jne','i',('i'))
+        jne.long_name = "j index" ;
+        jne.units = "none" ;
+        jne.packing = 0 ;
+        jne.checksum = "               0" ;
+
+        thickness=f.createVariable('thickness','d',('i'))
+        thickness.long_name = "thickness" ;
+        thickness.units = "m" ;
+        thickness.checksum = "               0" ;
+
+        width=f.createVariable('width','d',('i'))
+        width.long_name = "width" ;
+        width.units = "m" ;
+        width.checksum = "               0" ;
+
+        length=f.createVariable('length','d',('i'))
+        length.long_name = "length" ;
+        length.units = "m" ;
+        length.checksum = "               0" ;
+
+        start_lon=f.createVariable('start_lon','d',('i'))
+        start_lon.long_name = "longitude of calving location" ;
+        start_lon.units = "degrees_E" ;
+        start_lon.checksum = "               0" ;
+
+        start_lat=f.createVariable('start_lat','d',('i'))
+        start_lat.long_name = "latitude of calving location" ;
+        start_lat.units = "degrees_N" ;
+        start_lat.checksum = "               0" ;
+
+        start_year=f.createVariable('start_year','i',('i'))
+        start_year.long_name = "calendar year of calving event" ;
+        start_year.units = "years" ;
+        start_year.packing = 0 ;
+        start_year.checksum = "               0" ;
+
+        iceberg_num=f.createVariable('iceberg_num','i',('i'))
+        iceberg_num.long_name = "identification of the iceberg" ;
+        iceberg_num.units = "dimensionless" ;
+        iceberg_num.packing = 0 ;
+        iceberg_num.checksum = "               0" ;
+
+        start_day=f.createVariable('start_day','d',('i'))
+        start_day.long_name = "year day of calving event" ;
+        start_day.units = "days" ;
+        start_day.checksum = "               0" ;
+
+        start_mass=f.createVariable('start_mass','d',('i'))
+        start_mass.long_name = "initial mass of calving berg" ;
+        start_mass.units = "kg" ;
+        start_mass.checksum = "               0" ;
+
+        mass_scaling=f.createVariable('mass_scaling','d',('i'))
+        mass_scaling.long_name = "scaling factor for mass of calving berg" ;
+        mass_scaling.units = "none" ;
+        mass_scaling.checksum = "               0" ;
+
+        mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
+        mass_of_bits.long_name = "mass of bergy bits" ;
+        mass_of_bits.units = "kg" ;
+        mass_of_bits.checksum = "               0" ;
+
+        heat_density=f.createVariable('heat_density','d',('i'))
+        heat_density.long_name = "heat density" ;
+        heat_density.units = "J/kg" ;
+        heat_density.checksum = "               0" ;
+
+        halo_berg=f.createVariable('halo_berg','d',('i'))
+        halo_berg.long_name = "halo_berg" ;
+        halo_berg.units = "dimensionless" ;
+        halo_berg.checksum = "               0" ;
+
+        static_berg=f.createVariable('static_berg','d',('i'))
+        static_berg.long_name = "static_berg" ;
+        static_berg.units = "dimensionless" ;
+        static_berg.checksum = "               0" ;
+
+        f.sync()
+        f.close()
 
 
 def main(args):
@@ -315,6 +315,6 @@ def main(args):
 
 
 if __name__ == '__main__':
-    optCmdLineArgs=	parseCommandLine()
+    optCmdLineArgs=     parseCommandLine()
     anim_running = True
     main(optCmdLineArgs)
diff --git a/tests/footloose_tests/makeberg/makeberg.py b/tests/footloose_tests/makeberg/makeberg.py
index 10d0355..bb9b8ea 100755
--- a/tests/footloose_tests/makeberg/makeberg.py
+++ b/tests/footloose_tests/makeberg/makeberg.py
@@ -8,56 +8,56 @@
 
 def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,mass_scaling,iceberg_num,Ice_geometry_source,static_berg,uvel,vvel):
 
-	print 'Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..'
-	# To copy the global attributes of the netCDF file
-
-	#Input and output files
-	#Create Empty restart file. This is later read so that the attributes can be used.
-	Empty_restart_filename='output_files/Empty_icebergs.res.nc'
-	create_empty_iceberg_restart_file(Empty_restart_filename)
-	#Empty_restart_filename='input_files/icebergs.res.nc'
-
-	#Read empty restart file
-	f=Dataset(Empty_restart_filename,'r') # r is for read only
-	#Write a new restart file
-	g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
-
-	for attname in f.ncattrs():
-		    setattr(g,attname,getattr(f,attname))
-
-
-	# To copy the dimension of the netCDF file
-	for dimname,dim in f.dimensions.iteritems():
-		# if you want to make changes in the dimensions of the new file
-		# you should add your own conditions here before the creation of the dimension.
-		#g.createDimension(dimname,len(dim))
-		g.createDimension(dimname,Number_of_bergs)
-
-	# To copy the variables of the netCDF file
-
-	for varname,ncvar in f.variables.iteritems():
-		# if you want to make changes in the variables of the new file
-		# you should add your own conditions here before the creation of the variable.
-		var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
-		#Proceed to copy the variable attributes
-		for attname in ncvar.ncattrs():
-			setattr(var,attname,getattr(ncvar,attname))
-		#Finally copy the variable data to the new created variable
-		#var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
-
-		if varname=='i':
-			var[:]=Number_of_bergs
-
-		if varname=='iceberg_num':
-			for j in range(Number_of_bergs):
-				#var[j]=j+1
-				var[j]=iceberg_num[j]
-
-		if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
-		or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
-		or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
-		or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
-			var[:]=0
+        print ('Writing iceberg restart files, with ' , Number_of_bergs  , 'icebergs..')
+        # To copy the global attributes of the netCDF file
+
+        #Input and output files
+        #Create Empty restart file. This is later read so that the attributes can be used.
+        Empty_restart_filename='output_files/Empty_icebergs.res.nc'
+        create_empty_iceberg_restart_file(Empty_restart_filename)
+        #Empty_restart_filename='input_files/icebergs.res.nc'
+
+        #Read empty restart file
+        f=Dataset(Empty_restart_filename,'r') # r is for read only
+        #Write a new restart file
+        g=Dataset('output_files/' + Ice_geometry_source + '_icebergs.res.nc','w', format='NETCDF3_CLASSIC') # w if for creating a file
+
+        for attname in f.ncattrs():
+                    setattr(g,attname,getattr(f,attname))
+
+
+        # To copy the dimension of the netCDF file
+        for dimname,dim in f.dimensions.items():
+                # if you want to make changes in the dimensions of the new file
+                # you should add your own conditions here before the creation of the dimension.
+                #g.createDimension(dimname,len(dim))
+                g.createDimension(dimname,Number_of_bergs)
+
+        # To copy the variables of the netCDF file
+
+        for varname,ncvar in f.variables.items():
+                # if you want to make changes in the variables of the new file
+                # you should add your own conditions here before the creation of the variable.
+                var = g.createVariable(varname,ncvar.dtype,ncvar.dimensions)
+                #Proceed to copy the variable attributes
+                for attname in ncvar.ncattrs():
+                        setattr(var,attname,getattr(ncvar,attname))
+                #Finally copy the variable data to the new created variable
+                #var[:] = ncvar[0]  #I commented out this line because it was causing errors. I'm not sure if it is needed.
+
+                if varname=='i':
+                        var[:]=Number_of_bergs
+
+                if varname=='iceberg_num':
+                        for j in range(Number_of_bergs):
+                                #var[j]=j+1
+                                var[j]=iceberg_num[j]
+
+                if varname=='uvel_old' or varname=='vvel_old' or varname=='axn' or varname=='ayn'\
+                or varname=='bxn' or varname=='byn' or  varname=='halo_berg' or varname=='heat_density' or varname=='lon_old' or varname=='lat_old' \
+                or varname=='mass_of_bits' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' \
+                or varname=='start_lat' or varname=='start_mass' or  varname=='start_day' or varname=='start_year' or varname=='start_lon' or varname=='lat_old':\
+                        var[:]=0
 
                 if varname=='uvel':
                         var[:]=uvel
@@ -65,176 +65,176 @@ def Create_iceberg_restart_file(Number_of_bergs, lon,lat,thickness,width,mass,ma
                 if varname=='vvel':
                         var[:]=vvel
 
-		if varname=='mass_scaling':
-			var[:]=mass_scaling
+                if varname=='mass_scaling':
+                        var[:]=mass_scaling
 
-		if varname=='thickness':
-			for j in range(Number_of_bergs):
-				var[j]=thickness[j]
+                if varname=='thickness':
+                        for j in range(Number_of_bergs):
+                                var[j]=thickness[j]
 
-		if varname=='mass':
-			for j in range(Number_of_bergs):
-				var[j]=mass[j]
+                if varname=='mass':
+                        for j in range(Number_of_bergs):
+                                var[j]=mass[j]
 
-		if varname=='width'  or varname=='length':
-			for j in range(Number_of_bergs):
-				var[j]=width[j]
+                if varname=='width'  or varname=='length':
+                        for j in range(Number_of_bergs):
+                                var[j]=width[j]
 
-		if varname=='lon':
-			for j in range(Number_of_bergs):
-				var[j]=lon[j]
+                if varname=='lon':
+                        for j in range(Number_of_bergs):
+                                var[j]=lon[j]
 
-		if varname=='lat':
-			for j in range(Number_of_bergs):
-				var[j]=lat[j]
+                if varname=='lat':
+                        for j in range(Number_of_bergs):
+                                var[j]=lat[j]
 
-		if varname=='static_berg':
-			for j in range(Number_of_bergs):
-				var[j]=static_berg[j]
+                if varname=='static_berg':
+                        for j in range(Number_of_bergs):
+                                var[j]=static_berg[j]
 
 
-	f.close()
-	g.close()
+        f.close()
+        g.close()
 
 
 def create_empty_iceberg_restart_file(Empty_restart_filename):
 
-	f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
-
-	i=f.createDimension('i', None)
-	lon=f.createVariable('i','i')
-
-	lon=f.createVariable('lon','d',('i'))
-	lon.long_name = "longitude" ;
-	lon.units = "degrees_E" ;
-	lon.checksum = "               0" ;
-
-	lat=f.createVariable('lat','d',('i'))
-	lat.long_name = "latitude" ;
-	lat.units = "degrees_N" ;
-	lat.checksum = "               0" ;
-
-	uvel=f.createVariable('uvel','d',('i'))
-	uvel.long_name = "zonal velocity" ;
-	uvel.units = "m/s" ;
-	uvel.checksum = "               0" ;
-
-	vvel=f.createVariable('vvel','d',('i'))
-	vvel.long_name = "meridional velocity" ;
-	vvel.units = "m/s" ;
-	vvel.checksum = "               0" ;
-
-	mass=f.createVariable('mass','d',('i'))
-	mass.long_name = "mass" ;
-	mass.units = "kg" ;
-	mass.checksum = "               0" ;
-
-	axn=f.createVariable('axn','d',('i'))
-	axn.long_name = "explicit zonal acceleration" ;
-	axn.units = "m/s^2" ;
-	axn.checksum = "               0" ;
-
-	ayn=f.createVariable('ayn','d',('i'))
-	ayn.long_name = "explicit meridional acceleration" ;
-	ayn.units = "m/s^2" ;
-	ayn.checksum = "               0" ;
-
-	bxn=f.createVariable('bxn','d',('i'))
-	bxn.long_name = "inplicit zonal acceleration" ;
-	bxn.units = "m/s^2" ;
-	bxn.checksum = "               0" ;
-
-	byn=f.createVariable('byn','d',('i'))
-	byn.long_name = "implicit meridional acceleration" ;
-	byn.units = "m/s^2" ;
-	byn.checksum = "               0" ;
-
-	ine=f.createVariable('ine','i',('i'))
-	ine.long_name = "i index" ;
-	ine.units = "none" ;
-	ine.packing = 0 ;
-	ine.checksum = "               0" ;
-
-	jne=f.createVariable('jne','i',('i'))
-	jne.long_name = "j index" ;
-	jne.units = "none" ;
-	jne.packing = 0 ;
-	jne.checksum = "               0" ;
-
-	thickness=f.createVariable('thickness','d',('i'))
-	thickness.long_name = "thickness" ;
-	thickness.units = "m" ;
-	thickness.checksum = "               0" ;
-
-	width=f.createVariable('width','d',('i'))
-	width.long_name = "width" ;
-	width.units = "m" ;
-	width.checksum = "               0" ;
-
-	length=f.createVariable('length','d',('i'))
-	length.long_name = "length" ;
-	length.units = "m" ;
-	length.checksum = "               0" ;
-
-	start_lon=f.createVariable('start_lon','d',('i'))
-	start_lon.long_name = "longitude of calving location" ;
-	start_lon.units = "degrees_E" ;
-	start_lon.checksum = "               0" ;
-
-	start_lat=f.createVariable('start_lat','d',('i'))
-	start_lat.long_name = "latitude of calving location" ;
-	start_lat.units = "degrees_N" ;
-	start_lat.checksum = "               0" ;
-
-	start_year=f.createVariable('start_year','i',('i'))
-	start_year.long_name = "calendar year of calving event" ;
-	start_year.units = "years" ;
-	start_year.packing = 0 ;
-	start_year.checksum = "               0" ;
-
-	iceberg_num=f.createVariable('iceberg_num','i',('i'))
-	iceberg_num.long_name = "identification of the iceberg" ;
-	iceberg_num.units = "dimensionless" ;
-	iceberg_num.packing = 0 ;
-	iceberg_num.checksum = "               0" ;
-
-	start_day=f.createVariable('start_day','d',('i'))
-	start_day.long_name = "year day of calving event" ;
-	start_day.units = "days" ;
-	start_day.checksum = "               0" ;
-
-	start_mass=f.createVariable('start_mass','d',('i'))
-	start_mass.long_name = "initial mass of calving berg" ;
-	start_mass.units = "kg" ;
-	start_mass.checksum = "               0" ;
-
-	mass_scaling=f.createVariable('mass_scaling','d',('i'))
-	mass_scaling.long_name = "scaling factor for mass of calving berg" ;
-	mass_scaling.units = "none" ;
-	mass_scaling.checksum = "               0" ;
-
-	mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
-	mass_of_bits.long_name = "mass of bergy bits" ;
-	mass_of_bits.units = "kg" ;
-	mass_of_bits.checksum = "               0" ;
-
-	heat_density=f.createVariable('heat_density','d',('i'))
-	heat_density.long_name = "heat density" ;
-	heat_density.units = "J/kg" ;
-	heat_density.checksum = "               0" ;
-
-	halo_berg=f.createVariable('halo_berg','d',('i'))
-	halo_berg.long_name = "halo_berg" ;
-	halo_berg.units = "dimensionless" ;
-	halo_berg.checksum = "               0" ;
-
-	static_berg=f.createVariable('static_berg','d',('i'))
-	static_berg.long_name = "static_berg" ;
-	static_berg.units = "dimensionless" ;
-	static_berg.checksum = "               0" ;
-
-	f.sync()
-	f.close()
+        f = Dataset(Empty_restart_filename,'w', format='NETCDF3_CLASSIC')
+
+        i=f.createDimension('i', None)
+        lon=f.createVariable('i','i')
+
+        lon=f.createVariable('lon','d',('i'))
+        lon.long_name = "longitude" ;
+        lon.units = "degrees_E" ;
+        lon.checksum = "               0" ;
+
+        lat=f.createVariable('lat','d',('i'))
+        lat.long_name = "latitude" ;
+        lat.units = "degrees_N" ;
+        lat.checksum = "               0" ;
+
+        uvel=f.createVariable('uvel','d',('i'))
+        uvel.long_name = "zonal velocity" ;
+        uvel.units = "m/s" ;
+        uvel.checksum = "               0" ;
+
+        vvel=f.createVariable('vvel','d',('i'))
+        vvel.long_name = "meridional velocity" ;
+        vvel.units = "m/s" ;
+        vvel.checksum = "               0" ;
+
+        mass=f.createVariable('mass','d',('i'))
+        mass.long_name = "mass" ;
+        mass.units = "kg" ;
+        mass.checksum = "               0" ;
+
+        axn=f.createVariable('axn','d',('i'))
+        axn.long_name = "explicit zonal acceleration" ;
+        axn.units = "m/s^2" ;
+        axn.checksum = "               0" ;
+
+        ayn=f.createVariable('ayn','d',('i'))
+        ayn.long_name = "explicit meridional acceleration" ;
+        ayn.units = "m/s^2" ;
+        ayn.checksum = "               0" ;
+
+        bxn=f.createVariable('bxn','d',('i'))
+        bxn.long_name = "inplicit zonal acceleration" ;
+        bxn.units = "m/s^2" ;
+        bxn.checksum = "               0" ;
+
+        byn=f.createVariable('byn','d',('i'))
+        byn.long_name = "implicit meridional acceleration" ;
+        byn.units = "m/s^2" ;
+        byn.checksum = "               0" ;
+
+        ine=f.createVariable('ine','i',('i'))
+        ine.long_name = "i index" ;
+        ine.units = "none" ;
+        ine.packing = 0 ;
+        ine.checksum = "               0" ;
+
+        jne=f.createVariable('jne','i',('i'))
+        jne.long_name = "j index" ;
+        jne.units = "none" ;
+        jne.packing = 0 ;
+        jne.checksum = "               0" ;
+
+        thickness=f.createVariable('thickness','d',('i'))
+        thickness.long_name = "thickness" ;
+        thickness.units = "m" ;
+        thickness.checksum = "               0" ;
+
+        width=f.createVariable('width','d',('i'))
+        width.long_name = "width" ;
+        width.units = "m" ;
+        width.checksum = "               0" ;
+
+        length=f.createVariable('length','d',('i'))
+        length.long_name = "length" ;
+        length.units = "m" ;
+        length.checksum = "               0" ;
+
+        start_lon=f.createVariable('start_lon','d',('i'))
+        start_lon.long_name = "longitude of calving location" ;
+        start_lon.units = "degrees_E" ;
+        start_lon.checksum = "               0" ;
+
+        start_lat=f.createVariable('start_lat','d',('i'))
+        start_lat.long_name = "latitude of calving location" ;
+        start_lat.units = "degrees_N" ;
+        start_lat.checksum = "               0" ;
+
+        start_year=f.createVariable('start_year','i',('i'))
+        start_year.long_name = "calendar year of calving event" ;
+        start_year.units = "years" ;
+        start_year.packing = 0 ;
+        start_year.checksum = "               0" ;
+
+        iceberg_num=f.createVariable('iceberg_num','i',('i'))
+        iceberg_num.long_name = "identification of the iceberg" ;
+        iceberg_num.units = "dimensionless" ;
+        iceberg_num.packing = 0 ;
+        iceberg_num.checksum = "               0" ;
+
+        start_day=f.createVariable('start_day','d',('i'))
+        start_day.long_name = "year day of calving event" ;
+        start_day.units = "days" ;
+        start_day.checksum = "               0" ;
+
+        start_mass=f.createVariable('start_mass','d',('i'))
+        start_mass.long_name = "initial mass of calving berg" ;
+        start_mass.units = "kg" ;
+        start_mass.checksum = "               0" ;
+
+        mass_scaling=f.createVariable('mass_scaling','d',('i'))
+        mass_scaling.long_name = "scaling factor for mass of calving berg" ;
+        mass_scaling.units = "none" ;
+        mass_scaling.checksum = "               0" ;
+
+        mass_of_bits=f.createVariable('mass_of_bits','d',('i'))
+        mass_of_bits.long_name = "mass of bergy bits" ;
+        mass_of_bits.units = "kg" ;
+        mass_of_bits.checksum = "               0" ;
+
+        heat_density=f.createVariable('heat_density','d',('i'))
+        heat_density.long_name = "heat density" ;
+        heat_density.units = "J/kg" ;
+        heat_density.checksum = "               0" ;
+
+        halo_berg=f.createVariable('halo_berg','d',('i'))
+        halo_berg.long_name = "halo_berg" ;
+        halo_berg.units = "dimensionless" ;
+        halo_berg.checksum = "               0" ;
+
+        static_berg=f.createVariable('static_berg','d',('i'))
+        static_berg.long_name = "static_berg" ;
+        static_berg.units = "dimensionless" ;
+        static_berg.checksum = "               0" ;
+
+        f.sync()
+        f.close()
 
 
 
diff --git a/tests/iceberg_tests_env.yml b/tests/iceberg_tests_env.yml
new file mode 100644
index 0000000..cb8ad10
--- /dev/null
+++ b/tests/iceberg_tests_env.yml
@@ -0,0 +1,229 @@
+name: icebergs
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - conda-forge/linux-64::git-lfs==3.1.2=ha770c72_0
+  - conda-forge/linux-64::_libgcc_mutex==0.1=conda_forge
+  - conda-forge/linux-64::ca-certificates==2021.10.8=ha878542_0
+  - conda-forge/linux-64::ld_impl_linux-64==2.36.1=hea4e1c9_2
+  - conda-forge/linux-64::libgfortran4==7.5.0=h14aa051_20
+  - conda-forge/linux-64::libstdcxx-ng==11.2.0=he4da1e4_12
+  - conda-forge/linux-64::pandoc==2.17.1.1=ha770c72_0
+  - conda-forge/linux-64::libgfortran-ng==7.5.0=h14aa051_20
+  - conda-forge/linux-64::libgomp==11.2.0=h1d223b6_12
+  - conda-forge/linux-64::_openmp_mutex==4.5=1_gnu
+  - conda-forge/linux-64::libgcc-ng==11.2.0=h1d223b6_12
+  - conda-forge/linux-64::bzip2==1.0.8=h7f98852_4
+  - conda-forge/linux-64::c-ares==1.18.1=h7f98852_0
+  - conda-forge/linux-64::expat==2.4.4=h9c3ff4c_0
+  - conda-forge/linux-64::fribidi==1.0.10=h36c2ea0_0
+  - conda-forge/linux-64::geos==3.8.1=he1b5a44_0
+  - conda-forge/linux-64::giflib==5.2.1=h36c2ea0_2
+  - conda-forge/linux-64::gmp==6.2.1=h58526e2_0
+  - conda-forge/linux-64::icu==67.1=he1b5a44_0
+  - conda-forge/linux-64::jbig==2.1=h7f98852_2003
+  - conda-forge/linux-64::jpeg==9e=h7f98852_0
+  - conda-forge/linux-64::lerc==3.0=h9c3ff4c_0
+  - conda-forge/linux-64::libdeflate==1.10=h7f98852_0
+  - conda-forge/linux-64::libev==4.33=h516909a_1
+  - conda-forge/linux-64::libffi==3.4.2=h7f98852_5
+  - conda-forge/linux-64::libglu==9.0.0=he1b5a44_1001
+  - conda-forge/linux-64::libiconv==1.16=h516909a_0
+  - conda-forge/linux-64::libimagequant==2.17.0=h7f98852_1
+  - conda-forge/linux-64::libnsl==2.0.0=h7f98852_0
+  - conda-forge/linux-64::libopenblas==0.3.12=pthreads_hb3c22a3_1
+  - conda-forge/linux-64::libsodium==1.0.18=h36c2ea0_1
+  - conda-forge/linux-64::libuuid==2.32.1=h7f98852_1000
+  - conda-forge/linux-64::libwebp-base==1.2.2=h7f98852_1
+  - conda-forge/linux-64::libzlib==1.2.11=h36c2ea0_1013
+  - conda-forge/linux-64::lz4-c==1.9.3=h9c3ff4c_1
+  - conda-forge/linux-64::ncurses==6.3=h9c3ff4c_0
+  - conda-forge/linux-64::openssl==3.0.0=h7f98852_2
+  - conda-forge/linux-64::pthread-stubs==0.4=h36c2ea0_1001
+  - conda-forge/linux-64::tbb==2020.2=h4bd325d_4
+  - conda-forge/linux-64::xorg-kbproto==1.0.7=h7f98852_1002
+  - conda-forge/linux-64::xorg-libice==1.0.10=h7f98852_0
+  - conda-forge/linux-64::xorg-libxau==1.0.9=h7f98852_0
+  - conda-forge/linux-64::xorg-libxdmcp==1.1.3=h7f98852_0
+  - conda-forge/linux-64::xorg-renderproto==0.11.1=h7f98852_1002
+  - conda-forge/linux-64::xorg-xextproto==7.3.0=h7f98852_1002
+  - conda-forge/linux-64::xorg-xproto==7.0.31=h7f98852_1007
+  - conda-forge/linux-64::xz==5.2.5=h516909a_1
+  - conda-forge/linux-64::yaml==0.2.5=h7f98852_2
+  - conda-forge/linux-64::libblas==3.9.0=8_openblas
+  - conda-forge/linux-64::libedit==3.1.20191231=he28a2e2_2
+  - conda-forge/linux-64::libxcb==1.13=h7f98852_1004
+  - conda-forge/linux-64::readline==8.1=h46c0cb4_0
+  - conda-forge/linux-64::tk==8.6.12=h27826a3_0
+  - conda-forge/linux-64::xorg-fixesproto==5.0=h7f98852_1002
+  - conda-forge/linux-64::xorg-libsm==1.2.3=hd9c2040_1000
+  - conda-forge/linux-64::zeromq==4.3.4=h9c3ff4c_1
+  - conda-forge/linux-64::zlib==1.2.11=h36c2ea0_1013
+  - conda-forge/linux-64::zstd==1.5.2=ha95c52a_0
+  - conda-forge/linux-64::hdf4==4.2.15=h10796ff_3
+  - conda-forge/linux-64::hdf5==1.10.6=nompi_h3c11f04_101
+  - conda-forge/linux-64::krb5==1.19.2=h48eae69_3
+  - conda-forge/linux-64::libcblas==3.9.0=8_openblas
+  - conda-forge/linux-64::liblapack==3.9.0=8_openblas
+  - conda-forge/linux-64::libnghttp2==1.46.0=ha19adfc_0
+  - conda-forge/linux-64::libpng==1.6.37=h21135ba_2
+  - conda-forge/linux-64::libssh2==1.10.0=ha35d2d1_2
+  - conda-forge/linux-64::libtiff==4.3.0=h542a066_3
+  - conda-forge/linux-64::libxml2==2.9.10=h68273f3_2
+  - conda-forge/linux-64::mesalib==18.3.1=h590aaf7_0
+  - conda-forge/linux-64::sqlite==3.37.0=h9cd32fc_0
+  - conda-forge/linux-64::xorg-libx11==1.7.2=h7f98852_0
+  - conda-forge/linux-64::freetype==2.10.4=h0708190_1
+  - conda-forge/linux-64::lcms2==2.12=hddcbb42_0
+  - conda-forge/linux-64::libcurl==7.81.0=h494985f_0
+  - conda-forge/linux-64::libwebp==1.2.2=h3452ae3_0
+  - conda-forge/linux-64::openjpeg==2.4.0=hb52868f_1
+  - conda-forge/linux-64::python==3.8.12=h0744224_3_cpython
+  - conda-forge/linux-64::xorg-libxext==1.3.4=h7f98852_1
+  - conda-forge/linux-64::xorg-libxfixes==5.0.3=h7f98852_1004
+  - conda-forge/linux-64::xorg-libxrender==0.9.10=h7f98852_1003
+  - conda-forge/linux-64::xorg-libxt==1.2.1=h7f98852_2
+  - conda-forge/noarch::attrs==21.4.0=pyhd8ed1ab_0
+  - conda-forge/noarch::backcall==0.2.0=pyh9f0ad1d_0
+  - conda-forge/noarch::backports==1.0=py_2
+  - conda-forge/noarch::charset-normalizer==2.0.12=pyhd8ed1ab_0
+  - conda-forge/noarch::click==7.1.2=pyh9f0ad1d_0
+  - conda-forge/noarch::cloudpickle==2.0.0=pyhd8ed1ab_0
+  - conda-forge/noarch::colorama==0.4.4=pyh9f0ad1d_0
+  - conda-forge/linux-64::curl==7.81.0=h494985f_0
+  - conda-forge/noarch::cycler==0.11.0=pyhd8ed1ab_0
+  - conda-forge/noarch::decorator==5.1.1=pyhd8ed1ab_0
+  - conda-forge/noarch::defusedxml==0.7.1=pyhd8ed1ab_0
+  - conda-forge/noarch::entrypoints==0.4=pyhd8ed1ab_0
+  - conda-forge/noarch::executing==0.8.2=pyhd8ed1ab_0
+  - conda-forge/noarch::flit-core==3.6.0=pyhd8ed1ab_0
+  - conda-forge/linux-64::fontconfig==2.13.1=hba837de_1005
+  - conda-forge/noarch::fsspec==2022.1.0=pyhd8ed1ab_0
+  - conda-forge/noarch::heapdict==1.0.1=py_0
+  - conda-forge/noarch::idna==3.3=pyhd8ed1ab_0
+  - conda-forge/noarch::ipython_genutils==0.2.0=py_1
+  - conda-forge/noarch::json5==0.9.5=pyh9f0ad1d_0
+  - conda-forge/noarch::locket==0.2.0=py_2
+  - conda-forge/noarch::nest-asyncio==1.5.4=pyhd8ed1ab_0
+  - conda-forge/noarch::pandocfilters==1.5.0=pyhd8ed1ab_0
+  - conda-forge/noarch::parso==0.8.3=pyhd8ed1ab_0
+  - conda-forge/noarch::pickleshare==0.7.5=py_1003
+  - conda-forge/linux-64::proj==7.1.1=h966b41f_3
+  - conda-forge/noarch::prometheus_client==0.13.1=pyhd8ed1ab_0
+  - conda-forge/noarch::ptyprocess==0.7.0=pyhd3deb0d_0
+  - conda-forge/noarch::pure_eval==0.2.2=pyhd8ed1ab_0
+  - conda-forge/noarch::pycparser==2.21=pyhd8ed1ab_0
+  - conda-forge/noarch::pyparsing==3.0.7=pyhd8ed1ab_0
+  - conda-forge/noarch::pyshp==2.2.0=pyhd8ed1ab_0
+  - conda-forge/linux-64::python_abi==3.8=2_cp38
+  - conda-forge/noarch::pytz==2021.3=pyhd8ed1ab_0
+  - conda-forge/noarch::send2trash==1.8.0=pyhd8ed1ab_0
+  - conda-forge/noarch::six==1.16.0=pyh6c4a22f_0
+  - conda-forge/noarch::sortedcontainers==2.4.0=pyhd8ed1ab_0
+  - conda-forge/noarch::tblib==1.7.0=pyhd8ed1ab_0
+  - conda-forge/noarch::testpath==0.5.0=pyhd8ed1ab_0
+  - conda-forge/noarch::toolz==0.11.2=pyhd8ed1ab_0
+  - conda-forge/noarch::traitlets==5.1.1=pyhd8ed1ab_0
+  - conda-forge/noarch::typing==3.10.0.0=pyhd8ed1ab_0
+  - conda-forge/noarch::typing_extensions==4.1.1=pyha770c72_0
+  - conda-forge/noarch::webencodings==0.5.1=py_1
+  - conda-forge/noarch::websocket-client==1.2.3=pyhd8ed1ab_0
+  - conda-forge/noarch::wheel==0.37.1=pyhd8ed1ab_0
+  - conda-forge/linux-64::xorg-libxmu==1.1.3=h7f98852_0
+  - conda-forge/noarch::zipp==3.7.0=pyhd8ed1ab_1
+  - conda-forge/noarch::asttokens==2.0.5=pyhd8ed1ab_0
+  - conda-forge/noarch::babel==2.9.1=pyh44b312d_0
+  - conda-forge/linux-64::certifi==2021.10.8=py38h578d9bd_1
+  - conda-forge/linux-64::cffi==1.15.0=py38h3931269_0
+  - conda-forge/linux-64::cytoolz==0.11.2=py38h497a2fe_1
+  - conda-forge/linux-64::debugpy==1.5.1=py38h709712a_0
+  - conda-forge/noarch::docrep==0.2.7=py_0
+  - conda-forge/linux-64::future==0.18.2=py38h578d9bd_4
+  - conda-forge/linux-64::importlib-metadata==4.11.1=py38h578d9bd_0
+  - conda-forge/noarch::importlib_resources==5.4.0=pyhd8ed1ab_0
+  - conda-forge/linux-64::jedi==0.18.1=py38h578d9bd_0
+  - conda-forge/linux-64::jupyter_core==4.9.2=py38h578d9bd_0
+  - conda-forge/linux-64::kiwisolver==1.3.2=py38h1fd1430_1
+  - conda-forge/linux-64::libnetcdf==4.7.4=nompi_h56d31a8_107
+  - conda-forge/linux-64::markupsafe==2.0.1=py38h497a2fe_1
+  - conda-forge/noarch::matplotlib-inline==0.1.3=pyhd8ed1ab_0
+  - conda-forge/linux-64::mistune==0.8.4=py38h497a2fe_1005
+  - conda-forge/linux-64::msgpack-python==1.0.3=py38h1fd1430_0
+  - conda-forge/linux-64::numpy==1.18.1=py38h8854b6b_1
+  - conda-forge/linux-64::occt==7.4.0=h9121d39_3
+  - conda-forge/noarch::packaging==21.3=pyhd8ed1ab_0
+  - conda-forge/noarch::partd==1.2.0=pyhd8ed1ab_0
+  - conda-forge/noarch::pexpect==4.8.0=pyh9f0ad1d_2
+  - conda-forge/linux-64::pillow==9.0.1=py38he2f12e7_1
+  - conda-forge/linux-64::psutil==5.9.0=py38h497a2fe_0
+  - conda-forge/linux-64::pycosat==0.6.3=py38h497a2fe_1009
+  - conda-forge/linux-64::pyproj==2.6.1.post1=py38h56787f0_3
+  - conda-forge/linux-64::pyrsistent==0.18.1=py38h497a2fe_0
+  - conda-forge/linux-64::pysocks==1.7.1=py38h578d9bd_4
+  - conda-forge/noarch::python-dateutil==2.8.2=pyhd8ed1ab_0
+  - conda-forge/linux-64::pyyaml==6.0=py38h497a2fe_3
+  - conda-forge/linux-64::pyzmq==22.3.0=py38h2035c66_1
+  - conda-forge/linux-64::ruamel_yaml==0.15.80=py38h497a2fe_1006
+  - conda-forge/linux-64::setuptools==59.8.0=py38h578d9bd_0
+  - conda-forge/linux-64::sniffio==1.2.0=py38h578d9bd_2
+  - conda-forge/noarch::tomlkit==0.9.2=pyha770c72_0
+  - conda-forge/linux-64::tornado==6.1=py38h497a2fe_2
+  - conda-forge/noarch::tqdm==4.62.3=pyhd8ed1ab_0
+  - conda-forge/noarch::zict==2.0.0=py_0
+  - conda-forge/linux-64::anyio==3.5.0=py38h578d9bd_0
+  - conda-forge/linux-64::argon2-cffi-bindings==21.2.0=py38h497a2fe_1
+  - conda-forge/noarch::backports.functools_lru_cache==1.6.4=pyhd8ed1ab_0
+  - conda-forge/noarch::bleach==4.1.0=pyhd8ed1ab_0
+  - conda-forge/linux-64::bottleneck==1.3.2=py38hab2c0dc_2
+  - conda-forge/linux-64::brotlipy==0.7.0=py38h497a2fe_1003
+  - conda-forge/linux-64::cftime==1.5.0=py38hb5d20a5_0
+  - conda-forge/linux-64::conda-package-handling==1.7.3=py38h497a2fe_1
+  - defaults/linux-64::cryptography==36.0.0=py38h9ce1e76_0
+  - conda-forge/noarch::dask-core==2021.4.0=pyhd8ed1ab_0
+  - conda-forge/noarch::deprecation==2.1.0=pyh9f0ad1d_0
+  - conda-forge/linux-64::gmsh==4.6.0=hd134328_0
+  - conda-forge/linux-64::h5py==2.10.0=nompi_py38hafa665b_105
+  - conda-forge/noarch::jinja2==3.0.3=pyhd8ed1ab_0
+  - conda-forge/noarch::jsonschema==4.4.0=pyhd8ed1ab_0
+  - conda-forge/noarch::jupyter_client==7.1.2=pyhd8ed1ab_0
+  - conda-forge/linux-64::matplotlib-base==3.2.2=py38h5d868c9_1
+  - conda-forge/linux-64::netcdf-fortran==4.5.3=nompi_hfef6a68_101
+  - conda-forge/linux-64::pandas==1.0.1=py38hb3f55d8_0
+  - conda-forge/noarch::pip==22.0.3=pyhd8ed1ab_0
+  - conda-forge/noarch::pygments==2.11.2=pyhd8ed1ab_0
+  - conda-forge/linux-64::scipy==1.5.3=py38h828c644_0
+  - conda-forge/linux-64::shapely==1.7.1=py38ha11d057_1
+  - conda-forge/noarch::stack_data==0.2.0=pyhd8ed1ab_0
+  - conda-forge/linux-64::terminado==0.13.1=py38h578d9bd_0
+  - conda-forge/noarch::argon2-cffi==21.3.0=pyhd8ed1ab_0
+  - conda-forge/linux-64::bokeh==2.4.2=py38h578d9bd_0
+  - conda-forge/linux-64::cartopy==0.18.0=py38hc1e57b6_5
+  - conda-forge/linux-64::distributed==2021.4.1=py38h578d9bd_1
+  - conda-forge/linux-64::esmf==8.0.1=nompi_hcaa3220_2
+  - conda-forge/noarch::jupyter-packaging==0.11.1=pyhd8ed1ab_0
+  - conda-forge/noarch::jupyterlab_pygments==0.1.2=pyh9f0ad1d_0
+  - conda-forge/linux-64::matplotlib==3.2.2=1
+  - conda-forge/noarch::nbformat==5.1.3=pyhd8ed1ab_0
+  - conda-forge/linux-64::netcdf4==1.5.3=nompi_py38hfd55d45_105
+  - conda-forge/noarch::pyopenssl==22.0.0=pyhd8ed1ab_0
+  - conda-forge/noarch::wcwidth==0.2.5=pyh9f0ad1d_2
+  - conda-forge/noarch::xarray==0.17.0=pyhd8ed1ab_0
+  - conda-forge/noarch::cf_xarray==0.7.0=pyhd8ed1ab_0
+  - conda-forge/noarch::dask==2021.4.0=pyhd8ed1ab_0
+  - conda-forge/linux-64::esmpy==8.0.1=nompi_py38h5410a82_2
+  - conda-forge/noarch::nbclient==0.5.11=pyhd8ed1ab_0
+  - conda-forge/noarch::prompt-toolkit==3.0.27=pyha770c72_0
+  - conda-forge/noarch::urllib3==1.26.8=pyhd8ed1ab_1
+  - conda-forge/linux-64::ipython==8.0.1=py38h578d9bd_1
+  - conda-forge/linux-64::nbconvert==6.4.2=py38h578d9bd_0
+  - conda-forge/noarch::requests==2.27.1=pyhd8ed1ab_0
+  - conda-forge/noarch::xesmf==0.5.3=pyhd8ed1ab_0
+  - conda-forge/noarch::xgcm==0.5.1=py_0
+  - conda-forge/linux-64::ipykernel==6.9.1=py38he5a9106_0
+  - conda-forge/noarch::jupyter_server==1.13.5=pyhd8ed1ab_1
+  - conda-forge/noarch::jupyterlab_server==2.10.3=pyhd8ed1ab_0
+  - conda-forge/noarch::notebook==6.4.8=pyha770c72_0
+  - conda-forge/noarch::nbclassic==0.3.5=pyhd8ed1ab_0
+  - conda-forge/noarch::jupyterlab==3.0.14=pyhd8ed1ab_0
+prefix: /ncrc/home1/Alexander.Huth/miniconda3/envs/icebergs

From c89e750b6e6f8a69693a12f30702dde6f6821bab Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Wed, 4 Jan 2023 17:39:59 -0500
Subject: [PATCH 341/361] icebergs_driver and driver_data: Cleanup,
 documentation, and removal of unused features. Also cleaned-up corresponding
 tests .nmls.

---
 driver/driver_data.f90               | 353 +++++++++++++--------------
 driver/icebergs_driver.F90           | 178 +++-----------
 src/icebergs_framework.F90           |   2 +-
 tests/collision_tests/input.nml      |  17 +-
 tests/dem_cbeam_test/input.nml       |   5 +-
 tests/dem_ground_frac_test/input.nml |   3 +-
 tests/dem_ssbeam_test/input.nml      |  15 +-
 7 files changed, 211 insertions(+), 362 deletions(-)

diff --git a/driver/driver_data.f90 b/driver/driver_data.f90
index f68d3dc..e2d087c 100644
--- a/driver/driver_data.f90
+++ b/driver/driver_data.f90
@@ -17,6 +17,7 @@ module driver_data
 
 contains
 
+  !> Determine dimensions of A68 background grid
   subroutine a68_dims(data_dir,ni,nj)
     ! Arguments
     character(len=*) :: data_dir
@@ -37,6 +38,7 @@ subroutine a68_dims(data_dir,ni,nj)
     call handle_err(nf90_close(ncid))
   end subroutine a68_dims
 
+  !> Handle for errors
   subroutine handle_err(status)
     integer, intent (in) :: status
 
@@ -46,200 +48,181 @@ subroutine handle_err(status)
     end if
   end subroutine handle_err
 
-
+  !>Read in static (non-time-varying) fields, such as ocean depth.
+  !!If transient_a68_data_start_ind<=0, static wind,  ocean velocity, ssh are read in,
+  !!which can be useful for development instead of the respective time-varying
+  !!fields that are otherwise called by a68_prep_3d
   subroutine a68_prep(data_dir,mpp_domain,lon,lat,dx,dy,area,depth,uo,vo,tauxa,tauya,ssh,&
-    vert_int_ocean_vel,tau_is_velocity,Old_wrong_Rearth_and_SSH,REarth)
+    tau_is_velocity,REarth,transient_a68_data_start_ind)
     !mom_Rearth)
-  ! Arguments
-  character(len=*) :: data_dir
-  type(domain2D) :: mpp_domain
-  real :: lon(:,:) !< Longitude or position in x
-  real :: lat(:,:) !< Latitude or position in y
-  real :: dx(:,:) !< Length of northern edge of cell (m)
-  real :: dy(:,:) !< Length of eatern edge of cell (m)
-  real :: area(:,:) !< Area of cell (m2)
-  real :: depth(:,:) !< Depth of ocean (m)
-  real :: uo(:,:) !< Zonal ocean velocities (m/s)
-  real :: vo(:,:) !< Meridional ocean velocities (m/s)
-  real :: tauxa(:,:) !< Zonal wind stress (Pa)
-  real :: tauya(:,:) !< Meridional wind stress (Pa)
-  real :: ssh(:,:) !< Effective sea surface height (m)
-  logical :: Old_wrong_Rearth_and_SSH !< use Rearth=6.36e6 and SSH on B grid
-  logical :: mom_Rearth !< Use Rearth=6.378e6
-  logical :: vert_int_ocean_vel !< If true, use ocean velocity vertically-integrated over berg draft
-  logical :: tau_is_velocity !< If true, read in JRA-55 wind velocity (m/s), not ORAS5 stress (Pa)
-  real :: REarth
-  ! Local variables
-  character(len=1000) :: filename
-  real, parameter :: gres=0.125
-
-  !Grid specs: lon,lat,dx,dy,area
-  filename=trim(trim(data_dir)//'a68_experiment_ll_p125_grid.nc')
-  call read_a68_data(mpp_domain,filename,'longitude',lon)
-  lon=lon+360
-  call read_a68_data(mpp_domain,filename,'latitude',lat)
-
-  call haversine_dist_and_area(REarth,gres,lon,lat,dx,dy,area)
-
-  ! if (Old_wrong_Rearth_and_SSH) then
-  !   call read_a68_data(mpp_domain,filename,'dx_Rold',dx)
-  !   call read_a68_data(mpp_domain,filename,'dy_Rold',dy)
-  !   call read_a68_data(mpp_domain,filename,'area_Rold',area)
-  ! elseif (mom_Rearth) then
-  !   call read_a68_data(mpp_domain,filename,'dx_mom',dx)
-  !   call read_a68_data(mpp_domain,filename,'dy_mom',dy)
-  !   call read_a68_data(mpp_domain,filename,'area_mom',area)
-  ! else
-  !   call read_a68_data(mpp_domain,filename,'dx',dx)
-  !   call read_a68_data(mpp_domain,filename,'dy',dy)
-  !   call read_a68_data(mpp_domain,filename,'area',area)
-  ! endif
-
-  !Depth
-  filename=trim(trim(data_dir)//'a68_experiment_gebco_ll_p125.nc')
-  call read_a68_data(mpp_domain,filename,'elevation',depth)
-  depth=-depth !depth is negative in the data, but needs to be positive in the model
-
-  !Ocean velocity
-  !(vertically-integrated over draft of 200 m berg if vert_int_ocean_vel==true, otherwise, surface vel)
-  filename=trim(trim(data_dir)//'a68_experiment_ocean_surf_and_mean_vel_fixed_oras5_dec2020_ll_p125.nc')
-  !filename=trim(trim(data_dir)//'a68_experiment_ocean_test_vel.nc')
-
-  if (vert_int_ocean_vel) then
-    call read_a68_data(mpp_domain,filename,'uo_mean_over_berg_depth',uo)
-    call read_a68_data(mpp_domain,filename,'vo_mean_over_berg_depth',vo)
-  else
-    call read_a68_data(mpp_domain,filename,'uo',uo)
-    call read_a68_data(mpp_domain,filename,'vo',vo)
-  end if
-
-  if (tau_is_velocity) then
-  !Wind velocities -- note this is saved on tauxa and tauya, the wind stress variables.
-  !However, these variables are interpreted in the code as wind velocity if
-  !tau_is_velocity=.true. in the nml,
-    filename=trim(trim(data_dir)//'a68_experiment_wind_vel_jra55_dec2020_ll_p125.nc')
-    call read_a68_data(mpp_domain,filename,'ua',tauxa)
-    call read_a68_data(mpp_domain,filename,'va',tauya)
-  else
-    filename=trim(trim(data_dir)//'a68_experiment_wind_stress_oras5_dec2020_ll_p125.nc')
-    call read_a68_data(mpp_domain,filename,'taux',tauxa)
-    call read_a68_data(mpp_domain,filename,'tauy',tauya)
-  endif
-
-  !Effect sea surface height
-  filename=trim(trim(data_dir)//'a68_experiment_ssh_oras5_dec2020_ll_p125.nc')
-  if (Old_wrong_Rearth_and_SSH) then
-    call read_a68_data(mpp_domain,filename,'ssh_bgrid',ssh)
-  else
-    call read_a68_data(mpp_domain,filename,'SSH',ssh)
-  endif
-end subroutine a68_prep
-
-subroutine haversine_dist_and_area(REarth,gres,lon1,lat1,dx,dy,area)
-  !Arguments
-  real, intent(in) :: REarth    !Earth radius (m)
-  real, intent(in) :: gres      !grid resolution (degrees)
-  real, intent(in) :: lon1(:,:) !grid longitude
-  real, intent(in) :: lat1(:,:) !grid latitude
-  real, intent(out) :: dx(:,:)  !grid dx (m)
-  real, intent(out) :: dy(:,:)   !grid dy (m)
-  real, intent(out) :: area(:,:) !grid area (m^2)
-  ! Local variables
-  real, parameter :: pi_180=pi/180.
-  real, dimension(size(lon1,1),size(lon1,2)) :: lon2,lat2,p1,p2,dp,dm,a,c
-
-  !calculate dx
-  lon2=lon1-gres
-  lat2=lat1
-  p1 = lat1 * pi_180; p2 = lat2 * pi_180; dp = (lat2-lat1) * pi_180; dm = (lon2-lon1) * pi_180
-  a = sin(0.5*dp)**2. + cos(p1) * cos(p2) * sin(0.5*dm)**2.; c = 2. * atan2(sqrt(a), sqrt(1-a))
-  dx = REarth * c
-
-  !calculate dy
-  lat2=lat1-gres
-  lon2=lon1
-  p1 = lat1 * pi_180; p2 = lat2 * pi_180; dp = (lat2-lat1) * pi_180; dm = (lon2-lon1) * pi_180
-  a = sin(0.5*dp)**2. + cos(p1) * cos(p2) * sin(0.5*dm)**2.; c = 2. * atan2(sqrt(a), sqrt(1-a))
-  dy = REarth * c
-
-  !calculate area
-  area=pi_180*(REarth**2.)*abs(sin(lat1*pi_180)-sin(lat2*pi_180))*abs(gres)
-end subroutine haversine_dist_and_area
-
-
-!> Read ocean and atmospheric data for A68 experiment from file
-subroutine read_a68_data(domain,filename,var,field)
-  ! Arguments
-  type(domain2D) :: domain !< Parallel decomposition
-  character(len=*), intent(in) :: filename, var
-  real :: field(:,:)
-
-  call mpp_sync()
-  if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') 'icebergs_driver: Reading ',var
-  if (file_exist(filename)) then
-    if (field_exist(filename, var)) then
-      call read_data(filename, var, field, domain)
+    ! Arguments
+    character(len=*) :: data_dir
+    type(domain2D) :: mpp_domain
+    real :: lon(:,:) !< Longitude or position in x
+    real :: lat(:,:) !< Latitude or position in y
+    real :: dx(:,:) !< Length of northern edge of cell (m)
+    real :: dy(:,:) !< Length of eatern edge of cell (m)
+    real :: area(:,:) !< Area of cell (m2)
+    real :: depth(:,:) !< Depth of ocean (m)
+    real :: uo(:,:) !< Zonal ocean velocities (m/s)
+    real :: vo(:,:) !< Meridional ocean velocities (m/s)
+    real :: tauxa(:,:) !< Zonal wind stress (Pa)
+    real :: tauya(:,:) !< Meridional wind stress (Pa)
+    real :: ssh(:,:) !< Effective sea surface height (m)
+    logical :: Old_wrong_Rearth_and_SSH !< use Rearth=6.36e6 and SSH on B grid
+    logical :: mom_Rearth !< Use Rearth=6.378e6
+    logical :: tau_is_velocity !< If true, read in JRA-55 wind velocity (m/s), not ORAS5 stress (Pa)
+    real :: REarth
+    integer :: transient_a68_data_start_ind
+    ! Local variables
+    character(len=1000) :: filename
+    real, parameter :: gres=0.125
+
+    !Grid specs: lon,lat,dx,dy,area
+    filename=trim(trim(data_dir)//'a68_experiment_ll_p125_grid.nc')
+    call read_a68_data(mpp_domain,filename,'longitude',lon)
+    lon=lon+360
+    call read_a68_data(mpp_domain,filename,'latitude',lat)
+
+    call haversine_dist_and_area(REarth,gres,lon,lat,dx,dy,area)
+
+    !Depth
+    filename=trim(trim(data_dir)//'a68_experiment_gebco_ll_p125.nc')
+    call read_a68_data(mpp_domain,filename,'elevation',depth)
+    depth=-depth !depth is negative in the data, but needs to be positive in the model
+
+    if (transient_a68_data_start_ind<=0) then
+      !Ocean velocity
+      filename=trim(trim(data_dir)//'a68_experiment_ocean_surf_and_mean_vel_fixed_oras5_dec2020_ll_p125.nc')
+      call read_a68_data(mpp_domain,filename,'uo',uo)
+      call read_a68_data(mpp_domain,filename,'vo',vo)
+
+      if (tau_is_velocity) then
+        !Wind velocities -- note this is saved on tauxa and tauya, the wind stress variables.
+        !However, these variables are interpreted in the code as wind velocity if
+        !tau_is_velocity=.true. in the nml,
+        filename=trim(trim(data_dir)//'a68_experiment_wind_vel_jra55_dec2020_ll_p125.nc')
+        call read_a68_data(mpp_domain,filename,'ua',tauxa)
+        call read_a68_data(mpp_domain,filename,'va',tauya)
+      else
+        filename=trim(trim(data_dir)//'a68_experiment_wind_stress_oras5_dec2020_ll_p125.nc')
+        call read_a68_data(mpp_domain,filename,'taux',tauxa)
+        call read_a68_data(mpp_domain,filename,'tauy',tauya)
+      endif
+
+      !Effect sea surface height
+      filename=trim(trim(data_dir)//'a68_experiment_ssh_oras5_dec2020_ll_p125.nc')
+      call read_a68_data(mpp_domain,filename,'SSH',ssh)
+    endif
+  end subroutine a68_prep
+
+  !> Haversine distance and area
+  subroutine haversine_dist_and_area(REarth,gres,lon1,lat1,dx,dy,area)
+    !Arguments
+    real, intent(in) :: REarth    !Earth radius (m)
+    real, intent(in) :: gres      !grid resolution (degrees)
+    real, intent(in) :: lon1(:,:) !grid longitude
+    real, intent(in) :: lat1(:,:) !grid latitude
+    real, intent(out) :: dx(:,:)  !grid dx (m)
+    real, intent(out) :: dy(:,:)   !grid dy (m)
+    real, intent(out) :: area(:,:) !grid area (m^2)
+    ! Local variables
+    real, parameter :: pi_180=pi/180.
+    real, dimension(size(lon1,1),size(lon1,2)) :: lon2,lat2,p1,p2,dp,dm,a,c
+
+    !calculate dx
+    lon2=lon1-gres
+    lat2=lat1
+    p1 = lat1 * pi_180; p2 = lat2 * pi_180; dp = (lat2-lat1) * pi_180; dm = (lon2-lon1) * pi_180
+    a = sin(0.5*dp)**2. + cos(p1) * cos(p2) * sin(0.5*dm)**2.; c = 2. * atan2(sqrt(a), sqrt(1-a))
+    dx = REarth * c
+
+    !calculate dy
+    lat2=lat1-gres
+    lon2=lon1
+    p1 = lat1 * pi_180; p2 = lat2 * pi_180; dp = (lat2-lat1) * pi_180; dm = (lon2-lon1) * pi_180
+    a = sin(0.5*dp)**2. + cos(p1) * cos(p2) * sin(0.5*dm)**2.; c = 2. * atan2(sqrt(a), sqrt(1-a))
+    dy = REarth * c
+
+    !calculate area
+    area=pi_180*(REarth**2.)*abs(sin(lat1*pi_180)-sin(lat2*pi_180))*abs(gres)
+  end subroutine haversine_dist_and_area
+
+
+  !> Read in data for A68 experiment from file
+  subroutine read_a68_data(domain,filename,var,field)
+    ! Arguments
+    type(domain2D) :: domain !< Parallel decomposition
+    character(len=*), intent(in) :: filename, var
+    real :: field(:,:)
+
+    call mpp_sync()
+    if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') 'icebergs_driver: Reading ',var
+    if (file_exist(filename)) then
+      if (field_exist(filename, var)) then
+        call read_data(filename, var, field, domain)
+      else
+        if (mpp_pe().eq.mpp_root_pe()) then
+          call error_mesg('icebergs_driver:','Variable missing in file!', FATAL)
+        endif
+      endif
     else
       if (mpp_pe().eq.mpp_root_pe()) then
-        call error_mesg('icebergs_driver:','Variable missing in file!', FATAL)
+        call error_mesg('icebergs_driver:','File for variable not found!', FATAL)
       endif
     endif
-  else
-    if (mpp_pe().eq.mpp_root_pe()) then
-      call error_mesg('icebergs_driver:','File for variable not found!', FATAL)
-    endif
-  endif
-  call mpp_sync()
-end subroutine read_a68_data
-
-subroutine a68_prep_3d(data_dir,mpp_domain,tauxa_hr,tauya_hr,uo_hr,vo_hr,ssh_hr)
-  ! Arguments
-  character(len=*) :: data_dir
-
-  type(domain2D) :: mpp_domain
-  real :: tauxa_hr(:,:,:) !< Zonal jra55 wind velocity (m/s, hourly)
-  real :: tauya_hr(:,:,:) !< Meridional jra55 wind velocity (m/s, hourly)
-  real :: uo_hr(:,:,:) !< Zonal OSCAR ocean surface velocity (m/s, hourly)
-  real :: vo_hr(:,:,:) !< Meridional OSCAR ocean surface velocity (m/s, hourly)
-  real :: ssh_hr(:,:,:) !< Effective sea surface height (m, hourly)
-  ! Local variables
-  character(len=1000) :: filename
-
-  !filename=trim(trim(data_dir)//'a68_experiment_wind_vel_jra55_dec2020_HOURLY_ll_p125.nc')
-  filename=trim(trim(data_dir)//'a68_experiment_wind_vel_ncep_10m_dec2020_HOURLY_ll_p125.nc')
-  call read_a68_data_3d(mpp_domain,filename,'ua',tauxa_hr)
-  call read_a68_data_3d(mpp_domain,filename,'va',tauya_hr)
-
-  filename=trim(trim(data_dir)//'a68_experiment_ocean_surf_vel_oscar_dec2020_HOURLY_ll_p125.nc')
-  call read_a68_data_3d(mpp_domain,filename,'uo',uo_hr)
-  call read_a68_data_3d(mpp_domain,filename,'vo',vo_hr)
-
-  filename=trim(trim(data_dir)//'a68_experiment_ssh_duacs_dec2020_HOURLY_ll_p125.nc')
-  call read_a68_data_3d(mpp_domain,filename,'SSH',ssh_hr)
-end subroutine a68_prep_3d
-
-subroutine read_a68_data_3d(domain,filename,var,field)
-  ! Arguments
-  type(domain2D) :: domain !< Parallel decomposition
-  character(len=*), intent(in) :: filename, var
-  real :: field(:,:,:)
-
-  call mpp_sync()
-  if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') 'icebergs_driver: Reading ',var
-  if (file_exist(filename)) then
-    if (field_exist(filename, var)) then
-      call read_data(filename, var, field, domain)
+    call mpp_sync()
+  end subroutine read_a68_data
+
+  !> Wrapper to read in time-varying A68 data
+  subroutine a68_prep_3d(data_dir,mpp_domain,tauxa_hr,tauya_hr,uo_hr,vo_hr,ssh_hr)
+    ! Arguments
+    character(len=*) :: data_dir
+
+    type(domain2D) :: mpp_domain
+    real :: tauxa_hr(:,:,:) !< Zonal jra55 wind velocity (m/s, hourly)
+    real :: tauya_hr(:,:,:) !< Meridional jra55 wind velocity (m/s, hourly)
+    real :: uo_hr(:,:,:) !< Zonal OSCAR ocean surface velocity (m/s, hourly)
+    real :: vo_hr(:,:,:) !< Meridional OSCAR ocean surface velocity (m/s, hourly)
+    real :: ssh_hr(:,:,:) !< Effective sea surface height (m, hourly)
+    ! Local variables
+    character(len=1000) :: filename
+
+    filename=trim(trim(data_dir)//'a68_experiment_wind_vel_ncep_10m_dec2020_HOURLY_ll_p125.nc')
+    call read_a68_data_3d(mpp_domain,filename,'ua',tauxa_hr)
+    call read_a68_data_3d(mpp_domain,filename,'va',tauya_hr)
+
+    filename=trim(trim(data_dir)//'a68_experiment_ocean_surf_vel_oscar_dec2020_HOURLY_ll_p125.nc')
+    call read_a68_data_3d(mpp_domain,filename,'uo',uo_hr)
+    call read_a68_data_3d(mpp_domain,filename,'vo',vo_hr)
+
+    filename=trim(trim(data_dir)//'a68_experiment_ssh_duacs_dec2020_HOURLY_ll_p125.nc')
+    call read_a68_data_3d(mpp_domain,filename,'SSH',ssh_hr)
+  end subroutine a68_prep_3d
+
+  !> Read in time-varying A68 data
+  subroutine read_a68_data_3d(domain,filename,var,field)
+    ! Arguments
+    type(domain2D) :: domain !< Parallel decomposition
+    character(len=*), intent(in) :: filename, var
+    real :: field(:,:,:)
+
+    call mpp_sync()
+    if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') 'icebergs_driver: Reading ',var
+    if (file_exist(filename)) then
+      if (field_exist(filename, var)) then
+        call read_data(filename, var, field, domain)
+      else
+        if (mpp_pe().eq.mpp_root_pe()) then
+          call error_mesg('icebergs_driver:','Variable missing in file!', FATAL)
+        endif
+      endif
     else
       if (mpp_pe().eq.mpp_root_pe()) then
-        call error_mesg('icebergs_driver:','Variable missing in file!', FATAL)
+        call error_mesg('icebergs_driver:','File for variable not found!', FATAL)
       endif
     endif
-  else
-    if (mpp_pe().eq.mpp_root_pe()) then
-      call error_mesg('icebergs_driver:','File for variable not found!', FATAL)
-    endif
-  endif
-  call mpp_sync()
-end subroutine read_a68_data_3d
+    call mpp_sync()
+  end subroutine read_a68_data_3d
 
 end module driver_data
diff --git a/driver/icebergs_driver.F90 b/driver/icebergs_driver.F90
index eeef73c..b5e9fae 100644
--- a/driver/icebergs_driver.F90
+++ b/driver/icebergs_driver.F90
@@ -58,15 +58,9 @@ program icebergs_driver
 logical :: debug=.true. !< If true, do some debugging
 logical :: saverestart=.false. !< If true, save a berg restart file at the end
 logical :: collision_test=.false.
-logical :: chaotic_test=.false.
-logical :: grounding_test=.false.
 logical :: big_grounding_test=.false.
-logical :: dem_test_contact=.false.
 logical :: a68_test=.false.
-logical :: vert_int_ocean_vel=.false.
 logical :: tau_is_velocity=.true.
-logical :: reverse_a68_forcings=.false.
-logical :: sin_test=.false.
 logical :: fl_test=.false.
 character(len=1000) :: data_dir = 'data/'
 integer :: transient_a68_data_start_ind=0 !<set to .gt. 0 to use the hourly JRA-55 wind data for the A68
@@ -82,18 +76,15 @@ program icebergs_driver
 real :: gridres=1.e3
 real :: bump_depth=0
 real :: sst=-2
-logical :: Old_wrong_Rearth_and_SSH=.false. !< use Rearth=6.36e6 and SSH on B grid
 real :: REarth=6.378e6
-!logical :: mom_Rearth=.false. !< Use Rearth=6.378e6
-logical :: no_wind=.false.
 integer :: ibhrs=2
 integer :: nmax = 2000000000 !<max number of iteration
 integer :: write_time_inc=1
 namelist /icebergs_driver_nml/ debug, ni, nj, halo, ibhrs, ibdt, ibuo, ibvo, nmax, &
-  saverestart,ibui,ibvi,collision_test,chaotic_test,grounding_test,&
-  gridres,write_time_inc,bump_depth, sst, a68_test, data_dir, vert_int_ocean_vel,&
-  reverse_a68_forcings,sin_test,fl_test,tau_is_velocity,transient_a68_data_start_ind,ibua,ibuy,&
-  Old_wrong_Rearth_and_SSH,no_wind,REarth,big_grounding_test,dem_test_contact !mom_Rearth
+  saverestart,ibui,ibvi,collision_test,&
+  gridres,write_time_inc,bump_depth, sst, a68_test, data_dir,&
+  fl_test,tau_is_velocity,transient_a68_data_start_ind,ibua,ibuy,&
+  REarth,big_grounding_test
 ! For loops
 integer :: isc !< Start of i-index for computational domain (used for loops)
 integer :: iec !< End of i-index for computational domain (used for loops)
@@ -119,7 +110,7 @@ program icebergs_driver
 real, allocatable :: sin_rot(:,:) !< Sine of angle of grid orientation
 real, allocatable :: depth(:,:) !< Depth of ocean (m)
 ! Work variables
-integer :: i,j, dit
+integer :: i,j
 real, allocatable :: coord(:) !< One dimensional coordinate for initializing diagnostics
 
 ! For icebergs_run
@@ -140,7 +131,6 @@ program icebergs_driver
 real, dimension(:,:), pointer :: mass_berg !< Mass of bergs (kg)
 real, dimension(:,:), pointer  :: ustar_berg !< Friction velocity on base of bergs (m/s)
 real, dimension(:,:), pointer :: area_berg !< Area of bergs (m2)
-!grounding_test
 real :: a,bx,by,c,xc,yc !gaussian params
 !grounding/collision tests
 real :: mid
@@ -254,24 +244,14 @@ program icebergs_driver
 ! area_berg = !Area of bergs (m2)
 
 if (a68_test) then
-  if (Old_wrong_Rearth_and_SSH) REarth=6360000.
   call mpp_sync()
-  call a68_prep(data_dir,mpp_domain,lon,lat,dx,dy,area,depth,uo,vo,tauxa,tauya,ssh,vert_int_ocean_vel,tau_is_velocity,Old_wrong_Rearth_and_SSH,REarth)
-  !mom_Rearth)
+  !note some of these fields will be replaced if transient_a68_data_start_ind>0 (transient instead of static fields)
+  call a68_prep(data_dir,mpp_domain,lon,lat,dx,dy,area,depth,uo,vo,tauxa,tauya,ssh,tau_is_velocity,REarth,&
+    transient_a68_data_start_ind)
   call mpp_sync()
-  if (no_wind) then
-    tauxa=0.0; tauya=0.0
-  endif
-  !where (lon<(-37.6+360.))
-  !  depth=depth+1000.
-  !end where
   wet=1.0
   cos_rot=1.0
   sin_rot=0.0
-  if (reverse_a68_forcings) then
-    uo=-uo; vo=-vo
-    tauxa=-tauxa; tauya=-tauya
-  endif
 
   if (transient_a68_data_start_ind>0) then
     if (.not. (ibdt==3600.0 .or. ibdt==1800.0)) then
@@ -286,19 +266,11 @@ program icebergs_driver
     allocate( vo_hr(isd:ied,jsd:jed,744) )
     allocate( ssh_hr(isd:ied,jsd:jed,744) )
     call a68_prep_3d(data_dir,mpp_domain,tauxa_hr,tauya_hr,uo_hr,vo_hr,ssh_hr)
-    if (reverse_a68_forcings) then
-      tauxa_hr=-tauxa_hr; tauya_hr=-tauya_hr
-      uo_hr=-uo_hr; vo_hr=-vo_hr
-      ssh_hr=-ssh_hr
-      dit=-1
-    else
-      dit=1
-    endif
-    if (no_wind) then
-      tauxa_hr=0.0; tauya_hr=0.0
-    endif
   endif
 else
+  !non-A68 tests
+  transient_a68_data_start_ind=0
+
   do j = jsd, jed
     do i = isd, ied
       lon(i,j) = gridres*real(i)
@@ -313,14 +285,6 @@ program icebergs_driver
     enddo
   enddo
 
-  if (chaotic_test) then
-    !assign land cells at the N and S portions of the domain.
-    !input.nml: set coastal drift parameter to prevent grounding
-    do j=jsd,jed; do i=isd,ied
-      if (lat(i,j)<=0.0+2*gridres .or. lat(i,j)>=1000.e3-2*gridres) wet(i,j)=0.0
-    enddo;enddo
-  endif
-
   if (big_grounding_test) then
     lat(:,:)=lat(:,:)-0.45 !-25000.1
     lon(:,:)=lon(:,:)-0.45
@@ -342,19 +306,15 @@ program icebergs_driver
     depth = 1000.0-depth
   endif
 
-   if (dem_test_contact) then
-    lat(:,:)=lat(:,:)-0.45 !-25000.1
-    lon(:,:)=lon(:,:)-0.45
-    !assign land cells at the N and S portions of the domain.
-    !input.nml: set coastal drift parameter to prevent grounding
-    do j=jsd,jed; do i=isd,ied
-      if (lat(i,j)<=(-5.e3) .or. lat(i,j)>=(220.e3)) wet(i,j)=0.0
-    enddo;enddo
+  if (fl_test) then
+    where(lon>10000) vo=-vo
+  endif
 
-    mid=50.e3
+  if (collision_test) then
+    mid=10.e3
 
     do j=jsd,jed; do i=isd,ied
-      if (lon(i,j)>65 .or. lat(i,j)==mid) then
+      if (lon(i,j)>mid .or. lon(i,j)<=0.0 .or. lat(i,j)==mid) then
         vo(i,j)=0.0
       else
         if (lat(i,j)>mid) then
@@ -363,38 +323,10 @@ program icebergs_driver
           vo(i,j)=ibvo
         endif
       endif
-  enddo;enddo
-
-
-  endif
-
-  if (grounding_test) then
-    lat(:,:)=lat(:,:)-15000.0
-    !assign land cells at the N and S portions of the domain.
-    !input.nml: set coastal drift parameter to prevent grounding
-    do j=jsd,jed; do i=isd,ied
-      if (lat(i,j)<=0.0+2*gridres .or. lat(i,j)>=30.e3-2*gridres) wet(i,j)=0.0
     enddo;enddo
-
-    !introduce gaussian bump to bathymetry
-    a = 1000.0-bump_depth !max height(m)
-    c = 2.5e3; !controls width
-    bx = 15.e3; by = 15.e3
-    do j=jsd,jed; do i=isd,ied
-      xc=lon(i,j)-(gridres/2.); yc=lat(i,j)-(gridres/2.) !define at cell centers
-      depth(i,j)=a*exp(-((xc-bx)*(xc-bx)/(2.*c*c)+(yc-by)*(yc-by)/(2.*c*c)))
-    enddo; enddo
-    print *,'min, max depth',minval(depth(:,:)),maxval(depth(:,:))
-    depth = 1000.0-depth
   endif
 endif
 
-if (sin_test) vo = vo * sin(lat*2*pi/(20.0*gridres) + gridres)
-
-if (fl_test) then
-  where(lon>10000) vo=-vo
-endif
-
 call set_calendar_type(THIRTY_DAY_MONTHS)
 
 if (transient_a68_data_start_ind==355) then
@@ -411,54 +343,6 @@ program icebergs_driver
                    cos_rot(isc-1:iec+1,jsc-1:jec+1), sin_rot(isc-1:iec+1,jsc-1:jec+1), &
                    depth(isc:iec,jsc:jec), fractional_area=.false.)
 
-if (collision_test .or. grounding_test) then
-  if (grounding_test) then
-    mid=15.e3
-  else
-    mid=10.e3
-  endif
-
-  do j=jsd,jed; do i=isd,ied
-    if (lon(i,j)>mid .or. lon(i,j)<=0.0 .or. lat(i,j)==mid) then
-      vo(i,j)=0.0
-      ! if (grounding_test .and. lon(i,j)>mid+5.e3) then
-      !   if (lat(i,j)>mid) then
-      !     vo(i,j)=+ibvo
-      !   else
-      !     vo(i,j)=-ibvo
-      !   endif
-      ! endif
-
-    else
-      if (lat(i,j)>mid) then
-        vo(i,j)=-ibvo
-      else
-        vo(i,j)=ibvo
-      endif
-    endif
-  enddo;enddo
-endif
-
-if (chaotic_test) then
-  do j=jsd,jed; do i=isd,ied
-    if (lat(i,j)==500.e3 .or. lon(i,j)==500.e3) then
-      vo(i,j)=0.0
-    elseif (lon(i,j)>500.e3) then
-      if (lat(i,j)>500.e3) then
-        vo(i,j)=0.5*ibvo
-      else
-        vo(i,j)=-0.5*ibvo
-      endif
-    else
-      if (lat(i,j)>500.e3) then
-        vo(i,j)=-ibvo
-      else
-        vo(i,j)=ibvo
-      endif
-    endif
-  enddo;enddo
-endif
-
 ns = 1 !timestep counter
 if (transient_a68_data_start_ind>0) ns2 = 1
 
@@ -484,17 +368,17 @@ program icebergs_driver
   if (transient_a68_data_start_ind>0) then
 
     if ((ibdt==3600.0) .or. (mod(ns2,1.)==0)) then
-      tauxa=tauxa_hr(:,:,transient_a68_data_start_ind+dit*(int(ns2)-1))
-      tauya=tauya_hr(:,:,transient_a68_data_start_ind+dit*(int(ns2)-1))
-      uo=uo_hr(:,:,transient_a68_data_start_ind+dit*(int(ns2)-1))
-      vo=vo_hr(:,:,transient_a68_data_start_ind+dit*(int(ns2)-1))
-      ssh=ssh_hr(:,:,transient_a68_data_start_ind+dit*(int(ns2)-1))
+      tauxa=tauxa_hr(:,:,transient_a68_data_start_ind+(int(ns2)-1))
+      tauya=tauya_hr(:,:,transient_a68_data_start_ind+(int(ns2)-1))
+      uo=uo_hr(:,:,transient_a68_data_start_ind+(int(ns2)-1))
+      vo=vo_hr(:,:,transient_a68_data_start_ind+(int(ns2)-1))
+      ssh=ssh_hr(:,:,transient_a68_data_start_ind+(int(ns2)-1))
     else
-      tauxa=0.5*(tauxa+tauxa_hr(:,:,transient_a68_data_start_ind+dit*(int(ceiling(ns2))-1)))
-      tauya=0.5*(tauya+tauya_hr(:,:,transient_a68_data_start_ind+dit*(int(ceiling(ns2))-1)))
-      uo=0.5*(uo+uo_hr(:,:,transient_a68_data_start_ind+dit*(int(ceiling(ns2))-1)))
-      vo=0.5*(vo+vo_hr(:,:,transient_a68_data_start_ind+dit*(int(ceiling(ns2))-1)))
-      ssh=ssh_hr(:,:,transient_a68_data_start_ind+dit*(int(ns2)-1))
+      tauxa=0.5*(tauxa+tauxa_hr(:,:,transient_a68_data_start_ind+(int(ceiling(ns2))-1)))
+      tauya=0.5*(tauya+tauya_hr(:,:,transient_a68_data_start_ind+(int(ceiling(ns2))-1)))
+      uo=0.5*(uo+uo_hr(:,:,transient_a68_data_start_ind+(int(ceiling(ns2))-1)))
+      vo=0.5*(vo+vo_hr(:,:,transient_a68_data_start_ind+(int(ceiling(ns2))-1)))
+      ssh=ssh_hr(:,:,transient_a68_data_start_ind+(int(ns2)-1))
     endif
   endif
 
@@ -532,11 +416,11 @@ program icebergs_driver
   write(*,'(a,i5)')' Saving after timestep   ',ns-1
   print *,' ns2   ',ns2
   if (mod(ns2,1.)==0) then
-    print *,'transient_a68_data_start_ind+dit*(int(ns2)-1)',&
-      transient_a68_data_start_ind+dit*(int(ns2)-1)
+    print *,'transient_a68_data_start_ind+(int(ns2)-1)',&
+      transient_a68_data_start_ind+(int(ns2)-1)
   else
-    print *,'transient_a68_data_start_ind+dit*(int(ceiling(ns2))-1))',&
-      transient_a68_data_start_ind+dit*(int(ceiling(ns2))-1)
+    print *,'transient_a68_data_start_ind+(int(ceiling(ns2))-1))',&
+      transient_a68_data_start_ind+(int(ceiling(ns2))-1)
   endif
   write(*,'(a)')' Restart time is:'
   write(*,'(a,i5,a,i5,a,i5)')' year',iyr,'  month ',imon,'  day   ',iday
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 1afa5f6..dcd97e2 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -635,7 +635,7 @@ module ice_bergs_framework
 !! \todo Remove when backward compatibility no longer needed
 logical :: orig_read=.false.
 
-! Version of file provided by CPP macro (usually set to git hash)
+!> Version of file provided by CPP macro (usually set to git hash)
 #ifdef _FILE_VERSION
 character(len=128) :: version = _FILE_VERSION !< Version of file
 #else
diff --git a/tests/collision_tests/input.nml b/tests/collision_tests/input.nml
index b51271c..c806ac5 100644
--- a/tests/collision_tests/input.nml
+++ b/tests/collision_tests/input.nml
@@ -1,5 +1,4 @@
-!!KID, bergs_chksum: write_restart berg chksum=1560193269 chksum2=-1064844053 chksum3=-1070230468 chksum4=-1070230468 chksum5=0 #=16
-
+!!KID, bergs_chksum: write_restart berg chksum=-1441819690 chksum2=-1441819690 chksum3=1124700946 chksum4=1124700946 chksum5=0 #=16
 
 &icebergs_driver_nml
   ni=20 !number of elements, x direction
@@ -19,20 +18,10 @@
 
 &icebergs_nml
 
-    traj_name=iKID.nc
-    bond_traj_name=iKID_bonds.nc
+    traj_name=MTS_KID.nc
+    bond_traj_name=MTS_KID_bonds.nc
 
     !defaults given in parentheses:
-    dem=.true.
-    poisson=0.3
-    dem_damping_coef=1.0
-    !a dem_spring_coef equivalent to the spring_coef (k) used for non-DEM would be:
-    !E=k*rho_bergs*2*sqrt(3)*(radius**2). If rho_bergs=850, radius=389.71 m, k=1.e-5, then E=4471.94
-    !if square packing, use A=4*(radius**2) instead of A=2*sqrt(3)*(radius**2)
-    !E=34000 for square packing with 1000 m radius, rho_bergs=850, and k=1.e-5. A=L*W always works?
-    dem_spring_coef=4471.94
-    spring_coef=1.e-5 !if dem_spring_coef=5e6, r=1500, and hex pack?
-
     explicit_inner_mts=.true.
     mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
     mts_sub_steps=60 !1 !30 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
diff --git a/tests/dem_cbeam_test/input.nml b/tests/dem_cbeam_test/input.nml
index c90bc74..5088968 100644
--- a/tests/dem_cbeam_test/input.nml
+++ b/tests/dem_cbeam_test/input.nml
@@ -24,9 +24,6 @@
   saverestart=.true.
   halo=3
   debug=.true.
-  collision_test=.false.
-  grounding_test=.false.
-  bump_depth=9999.0 !(m) depth of top of gaussian bump below sea level
   gridres=15000
 /
 
@@ -56,7 +53,7 @@
     remove_unused_bergs=.false. !(T) remove unneeded bergs after PEs transfers
 
 
-    fracture_criterion='none' !('none') 'strain_rate','strain','stress',or 'none'
+    fracture_criterion='none' !('none') or 'stress'
     !here, try setting scaling 1.0 if force_convergence=.false., 0.5 if force_convergence=.true.
     frac_thres_scaling = 1.0 !(1) scales frac_thres_n and frac_thres_t
     frac_thres_n = 0. !1.e7  !normal fracture strain threshold
diff --git a/tests/dem_ground_frac_test/input.nml b/tests/dem_ground_frac_test/input.nml
index 0525a05..7e76e72 100644
--- a/tests/dem_ground_frac_test/input.nml
+++ b/tests/dem_ground_frac_test/input.nml
@@ -24,7 +24,6 @@
   saverestart=.true.
   halo=3
   debug=.true.
-  collision_test=.false.
   big_grounding_test=.true.
   bump_depth=50.!(m) depth of top of gaussian bump below sea level
 /
@@ -66,7 +65,7 @@
     cdrag_grounding=1.e4
     h_to_init_grounding=0 !0 !200.0
     ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
-    remove_unused_bergs=.true.!.false. !(T) remove unneeded bergs after PEs transfers
+    remove_unused_bergs=.true. !(T) remove unneeded bergs after PEs transfers
 
     fracture_criterion='stress' !('none')
     frac_thres_scaling = 1
diff --git a/tests/dem_ssbeam_test/input.nml b/tests/dem_ssbeam_test/input.nml
index 14a455b..d79512b 100644
--- a/tests/dem_ssbeam_test/input.nml
+++ b/tests/dem_ssbeam_test/input.nml
@@ -15,13 +15,10 @@
   ibvi=0.0 !ice y velocity
   ibhrs=200 !total simulation hours
   write_time_inc = 1 !600 !increment at which time is written to screen
-  nmax=10 !1200  !max number of timesteps
+  nmax=10 !max number of timesteps
   saverestart=.true.
   halo=3
   debug=.true.
-  collision_test=.false.
-  grounding_test=.false.
-  bump_depth=9999.0 !(m) depth of top of gaussian bump below sea level
   gridres=15000
 /
 
@@ -36,7 +33,7 @@
     dem_spring_coef=1.e9 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
 
     mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=1e5 !20 !00  !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
+    mts_sub_steps=1e5 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
 
     force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
     convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
@@ -45,16 +42,16 @@
     contact_spring_coef=1.e-8 !(default=spring_coeff) Berg spring coeff for collisions
     debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
     cdrag_grounding=3.16e6 !friction drag param
-    h_to_init_grounding=200.0 !300.0 !150.0 !300.
+    h_to_init_grounding=200.0
     ewsame=.false. !(F) set T if periodic and 2 PEs along the x (zonal) direction
     remove_unused_bergs=.false. !(T) remove unneeded bergs after PEs transfers
 
 
-    fracture_criterion='none' !('none') 'strain_rate','strain','stress',or 'none'
+    fracture_criterion='none' !('none') or 'stress'
     !here, try setting scaling 1.0 if force_convergence=.false., 0.5 if force_convergence=.true.
     frac_thres_scaling = 1.0 !(1) scales frac_thres_n and frac_thres_t
-    frac_thres_n = 0. !1.e7  !normal fracture strain threshold
-    frac_thres_t = 0. !5.e7 !tangential fracture strain threshold
+    frac_thres_n = 0. !normal fracture strain threshold
+    frac_thres_t = 0. !tangential fracture strain threshold
 
     halo=3 !(4) halo width
     Lx=300.e3 ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)

From cdd773a12bf708ea6a4f5dbf57ee2037a5eba574 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Wed, 4 Jan 2023 19:21:09 -0500
Subject: [PATCH 342/361] Removed non-DEM breaking of bonds. Previous attempts
 to account for bond-breaking without DEM-mode was not fully-successful
 because without DEM torque and shear terms, 'strings' of bonded particles one
 layer thick would tend to bend unphysically without breaking. Furthermore,
 the physical basis for non-DEM fracture was lacking compared to DEM-mode
 fracture, anyway. Therefore, I removed all code related to non-DEM fracture,
 which substantially simplifies much of the code. For example, this eliminated
 6 variables (rotation, n_frac_var, n_strain_rate, accum_bond_rotation,
 lon_prev, lat_prev).

---
 src/icebergs.F90           |  43 +---
 src/icebergs_framework.F90 | 472 +++----------------------------------
 src/icebergs_io.F90        | 166 +------------
 3 files changed, 40 insertions(+), 641 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index a939940..c720aa1 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -49,8 +49,7 @@ module ice_bergs
 use ice_bergs_framework, only: quad_interp_from_agrid
 use ice_bergs_framework, only: save_bond_traj
 use ice_bergs_framework, only: orig_bond_length
-use ice_bergs_framework, only: update_and_break_bonds,break_bonds_dem,assign_n_bonds,reset_bond_rotation
-use ice_bergs_framework, only: update_bond_angles
+use ice_bergs_framework, only: break_bonds_dem,assign_n_bonds
 use ice_bergs_framework, only: mts
 use ice_bergs_framework, only: dem_tests_init
 use ice_bergs_framework, only: dem, save_bond_forces
@@ -1879,15 +1878,6 @@ subroutine accel_explicit_inner_mts(bergs, berg, i, j, xi, yj, lat, uvel, vvel,
         if (berg%start_lon==bergs%dem_tests_end_lon) then
           F_y = F_y - 1.5e10/3.
         endif
-      elseif (bergs%dem_beam_test==3) then
-        !Angular velocity test (starting element has constant rot=-pi/2)
-        if (berg%start_lon==bergs%dem_tests_start_lon) then
-          T=0.0; T_d=0.0
-        endif
-      elseif (bergs%dem_beam_test==4) then
-        if (berg%start_lon==bergs%dem_tests_start_lon) then
-          F_y=0.0; Fd_y=0.0
-        endif
       endif
     endif
 
@@ -5441,7 +5431,6 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   call mpp_clock_begin(bergs%clock_mom)
 
   if (.not.bergs%Static_icebergs) then
-    if (bergs%iceberg_bonds_on .and. (.not. bergs%dem)) call reset_bond_rotation(bergs)
 
     if (bergs%mts) then
       call evolve_icebergs_mts(bergs)
@@ -6315,8 +6304,6 @@ subroutine calve_icebergs(bergs)
             newberg%vvel_prev=0.
             newberg%uvel_old=0.
             newberg%vvel_old=0.
-            newberg%lon_prev=newberg%lon
-            newberg%lat_prev=newberg%lat
             newberg%lon_old=newberg%lon
             newberg%lat_old=newberg%lat
           endif
@@ -6372,13 +6359,6 @@ subroutine calve_icebergs(bergs)
             newberg%ang_vel=0.; newberg%ang_accel=0.; newberg%rot=0.
           endif
 
-          if (bergs%fracture_criterion .ne. 'none' .and. (.not. bergs%dem)) then
-            if (.not. allocations_done) then
-              if (.not. allocated(newberg%accum_bond_rotation)) allocate(newberg%accum_bond_rotation)
-            endif
-            newberg%accum_bond_rotation=0.
-          endif
-
           if (.not. bergs%old_interp_flds_order) then
             !interpolate gridded variables to new iceberg
             if (grd%tidal_drift>0.) then
@@ -6530,8 +6510,6 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b,fl_disp_x,fl_disp_y,berg_from_bit
 
   cberg%start_lon    = cberg%lon
   cberg%start_lat    = cberg%lat
-  cberg%lon_prev     = pberg%lon_prev + fl_disp_x
-  cberg%lat_prev     = pberg%lat_prev + fl_disp_y
   cberg%lon_old      = pberg%lon_old  + fl_disp_x
   cberg%lat_old      = pberg%lat_old  + fl_disp_y
   cberg%start_day    = bergs%current_yearday
@@ -6591,11 +6569,6 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b,fl_disp_x,fl_disp_y,berg_from_bit
     cberg%ang_vel=0.; cberg%ang_accel=0.; cberg%rot=0.
   endif
 
-  if (bergs%fracture_criterion .ne. 'none' .and. (.not. bergs%dem)) then
-    allocate(cberg%accum_bond_rotation)
-    cberg%accum_bond_rotation=0.
-  endif
-
   call add_new_berg_to_list(bergs%list(cberg%ine,cberg%jne)%first, cberg)
 end subroutine calve_fl_icebergs
 
@@ -6773,16 +6746,7 @@ subroutine evolve_icebergs_mts(bergs)
 
     enddo
 
-    !  print *,'iters',ii
-
-    if (.not. bergs%dem) then
-      call update_bond_angles(bergs)
-      call update_and_break_bonds(bergs)
-    else
-      if (.not. break_bonds_on_sub_steps) then
-        call break_bonds_dem(bergs)
-      endif
-    endif
+    if (bergs%dem .and. (.not. break_bonds_on_sub_steps)) call break_bonds_dem(bergs)
 
     !PART 2: X_0 and V_0, before fast sub-steps
     !X_0=X_n (no change)
@@ -6792,7 +6756,6 @@ subroutine evolve_icebergs_mts(bergs)
       berg=>bergs%list(grdi,grdj)%first
       do while (associated(berg)) ! loop over all bergs
         if (berg%static_berg .lt. 0.5 .and. berg%conglom_id.ne.0) then
-          berg%lat_prev = berg%lat; berg%lon_prev = berg%lon
           berg%uvel=berg%uvel_prev; berg%vvel=berg%vvel_prev
 
           berg%uvel = berg%uvel + dt_2*(berg%axn+berg%bxn)
@@ -7085,7 +7048,7 @@ subroutine evolve_icebergs_mts(bergs)
       enddo ! loop over all bergs
     enddo; enddo ! update 'old' velocities
 
-    if (.not. bergs%use_broken_bonds_for_substep_contact) then
+    if (bergs%dem .and. .not. bergs%use_broken_bonds_for_substep_contact) then
       if (break_bonds_on_sub_steps .and. bergs%bond_break_detected) call break_bonds_dem(bergs)
     endif
   enddo ! loop over sub-steps
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index dcd97e2..0affce1 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -18,7 +18,7 @@ module ice_bergs_framework
 
 implicit none ; private
 
-integer :: buffer_width=36 ! This should be a parameter
+integer :: buffer_width=34 ! This should be a parameter
 integer :: buffer_width_traj=32 ! This should be a parameter
 integer :: buffer_width_bond_traj=11 !This should be a parameter
 integer, parameter :: nclasses=10 ! Number of ice bergs classes
@@ -57,7 +57,6 @@ module ice_bergs_framework
 real :: A68_xdisp=0. !< longitude of the SW corner of the grounding zone in the A68 test case
 real :: A68_ydisp=0. !< latitude of the SW corner of the grounding zone in the A68 test case
 logical :: rev_mind=.false. !< Alterate option for staggering the 3x3 cells used for quadratic mapping of ocean depth to particles
-character(len=11) :: fracture_criterion='none' !<'stress' or 'none'. In non-dem-mode, 'strain_rate' and 'strain' are also options.
 logical :: orig_dem_moment_of_inertia=.false. !< Use Potyondy & Cundall,2004 torque from relative particle rotation (rather than Wang, 2020)
 logical :: break_bonds_on_sub_steps=.false.
 logical :: skip_first_outer_mts_step=.false.
@@ -70,7 +69,7 @@ module ice_bergs_framework
 public ignore_ij_restart, use_slow_find,generate_test_icebergs,old_bug_rotated_weights,budget
 public orig_read, force_all_pes_traj
 public mts,save_bond_traj,ewsame,iceberg_bonds_on
-public dem, save_bond_forces, fracture_criterion, orig_dem_moment_of_inertia
+public dem, save_bond_forces, orig_dem_moment_of_inertia
 public short_step_mts_grounding, radius_based_drag
 public A68_test, A68_xdisp, A68_ydisp
 public footloose
@@ -103,7 +102,7 @@ module ice_bergs_framework
 public split_id, id_from_2_ints, generate_id, cij_from_old_id, convert_old_id
 public update_latlon,set_conglom_ids,transfer_mts_bergs,quad_interp_from_agrid
 public pack_bond_traj_into_buffer2, unpack_bond_traj_from_buffer2, push_bond_posn, append_bond_posn
-public update_and_break_bonds,break_bonds_dem,assign_n_bonds,reset_bond_rotation,update_bond_angles
+public break_bonds_dem,assign_n_bonds
 public orig_bond_length
 public dem_tests_init
 public set_constant_interaction_length_and_width
@@ -294,8 +293,6 @@ module ice_bergs_framework
   ! State variables (specific to the iceberg, needed for restarts)
   real :: lon !< Longitude of berg (degree N or unit of grid coordinate)
   real :: lat !< Latitude of berg (degree E or unit of grid coordinate)
-  real :: lon_prev !< Previous timestep longitude of berg
-  real :: lat_prev !< Previous timestep latitude of berg
   real :: uvel !< Zonal velocity of berg (m/s)
   real :: vvel !< Meridional velocity of berg (m/s)
   real :: mass !< Mass of berg (kg)
@@ -355,8 +352,6 @@ module ice_bergs_framework
   integer, allocatable :: conglom_id !<ID for a conglomerate
   ! If iceberg_bonds_on
   integer, allocatable :: n_bonds
-  ! If frac
-  real, allocatable :: accum_bond_rotation
   ! For DEM-mode
   real, allocatable :: ang_vel !< Angular velocity
   real, allocatable :: ang_accel !< Angular acceleration
@@ -373,15 +368,8 @@ module ice_bergs_framework
   integer :: other_berg_jne
   real :: length
   type(bond_xyt), pointer :: bond_trajectory=>null()
-  ! Fracture parameters:
-  !The following are accumulated over all timesteps, unless fracture_criterion=='strain_rate',
-  !in which case the following correspond to only the most recent timestep and units are s^(-1)
-  real, allocatable :: rotation !radians (non-dem only)
-  real, allocatable :: rel_rotation !<non-dem: relative to the mean of all bonds for a berg. dem: relative to other particle
-  ! non-dem-mode fracture:
-  real, allocatable :: n_frac_var !<normal stress or strain
-  real, allocatable :: n_strain_rate !<for fracture_criterion=='strain_rate' only
   ! For DEM-mode
+  real, allocatable :: rel_rotation !<rotation relative to other particle
   real, allocatable :: tangd1 !< Accumulated tangential displacement, x-component (m)
   real, allocatable :: tangd2 !< Accumulated tangential displacement, y-component (m)
   real, allocatable :: nstress !< Normal stress (Pa)
@@ -409,12 +397,8 @@ module ice_bergs_framework
   integer(kind=8) :: id1 !<ID of first berg
   integer(kind=8) :: id2 !<ID of second berg
   type(bond_xyt), pointer :: next=>null() !< Next link in list
-  real, allocatable :: rotation !radians (non-dem only)
-  real, allocatable :: rel_rotation !<non-dem: relative to the mean of all bonds for a berg. dem: relative to other particle
-  ! non-dem-mode fracture:
-  real, allocatable :: n_frac_var !<normal stress or strain
-  real, allocatable :: n_strain_rate !<for fracture_criterion=='strain_rate' only
   ! For DEM-mode
+  real, allocatable :: rel_rotation !<Rotation relative to other particle
   real, allocatable :: tangd1 !< Accumulated tangential displacement, x-component (m)
   real, allocatable :: tangd2 !< Accumulated tangential displacement, y-component (m)
   real, allocatable :: nstress
@@ -462,9 +446,9 @@ module ice_bergs_framework
   real :: contact_spring_coef !<Spring coefficient for berg collisions -Alex
   real :: cdrag_grounding=0.0 !< Drag coefficient against ocean bottom
   real :: h_to_init_grounding
-  character(len=11) :: fracture_criterion='none' !<'stress' or 'none'. In non-dem-mode, 'strain_rate' and 'strain' are also options.
-  real :: frac_thres_n=0.0 !normal fracture strain threshold
-  real :: frac_thres_t=0.0 !tangential fracture strain threshold
+  character(len=11) :: fracture_criterion='none' !< For DEM-mode. Options are 'stress' or 'none'.
+  real :: frac_thres_n=0.0 !normal fracture stress threshold
+  real :: frac_thres_t=0.0 !tangential fracture stress threshold
   logical :: debug_write=.false. !< Sets traj_sample_hours=traj_write_hours & includes halo bergs in write
   real :: bond_coef !< Spring constant for iceberg bonds
   real :: radial_damping_coef !< Coefficient for relative iceberg motion damping (radial component) -Alon
@@ -713,8 +697,8 @@ subroutine ice_bergs_framework_init(bergs, &
 real :: contact_spring_coef=0. !Spring coef for berg collisions (is set to spring_coef if not specified)
 real :: cdrag_grounding=0.0 ! Drag coefficient against ocean bottom
 real :: h_to_init_grounding=100.0
-real :: frac_thres_n=0.0 !normal fracture strain threshold
-real :: frac_thres_t=0.0 !tangential fracture strain threshold
+real :: frac_thres_n=0.0 !normal fracture stress threshold
+real :: frac_thres_t=0.0 !tangential fracture stress threshold
 real :: frac_thres_scaling=1.0 !scaling factor for frac_thres_n and frac_thres_t, useful for tuning
 logical :: debug_write=.false. !Sets traj_sample_hours=traj_write_hours & includes halo bergs in write
 real :: bond_coef=1.e-8 ! Spring constant for iceberg bonds - not being used right now
@@ -814,6 +798,7 @@ subroutine ice_bergs_framework_init(bergs, &
 integer(kind=8) :: debug_iceberg_with_id = -1 ! If positive, monitors a berg with this id
 ! DEM-mode parameters
 !logical :: dem=.false. !if T, run in DEM-mode with angular terms, variable stiffness, etc
+character(len=11) :: fracture_criterion='none' !< For DEM-mode. Options are 'stress' or 'none'.
 logical :: use_grounding_torque=.false.
 logical :: ignore_tangential_force=.false.
 real :: poisson=0.3 ! Poisson's ratio
@@ -1301,14 +1286,6 @@ subroutine ice_bergs_framework_init(bergs, &
   buffer_width=buffer_width+3+(max_bonds*6)
   buffer_width_traj=buffer_width_traj+3
   buffer_width_bond_traj=buffer_width_bond_traj+6
-elseif (fracture_criterion .ne. 'none') then
-  buffer_width=buffer_width+1+(max_bonds*3)
-  buffer_width_traj=buffer_width_traj+1
-  buffer_width_bond_traj=buffer_width_bond_traj+3
-  if (fracture_criterion .eq. 'strain_rate') then
-    buffer_width=buffer_width+(max_bonds*1)
-    buffer_width_bond_traj=buffer_width_bond_traj+1
-  endif
 endif
 
 if (iceberg_bonds_on) then
@@ -2396,16 +2373,12 @@ subroutine mts_pack_in_dir(bergs, nbergs_to_send, dir)
               berg%conglom_id=current_conglom_id+2
             case ("w")
               berg%lon=berg%lon-pfix; berg%conglom_id=4
-              berg%lon_prev=berg%lon_prev-pfix
               call pack_berg_into_buffer2(berg, bergs%obuffer_w, nbergs_to_send, bergs%max_bonds)
               berg%lon=berg%lon+pfix; berg%conglom_id=current_conglom_id+8
-              berg%lon_prev=berg%lon_prev+pfix
             case ("e")
               berg%lon=berg%lon-pfix; berg%conglom_id=8
-              berg%lon_prev=berg%lon_prev-pfix
               call pack_berg_into_buffer2(berg, bergs%obuffer_e, nbergs_to_send, bergs%max_bonds)
               berg%lon=berg%lon+pfix; berg%conglom_id=current_conglom_id+4
-              berg%lon_prev=berg%lon_prev+pfix
             end select
             berg%halo_berg=current_halo_id
           endif
@@ -2445,13 +2418,13 @@ recursive subroutine mts_mark_and_pack_halo_and_congloms(bergs, berg, dir, nberg
 
     select case (dir)
     case ("e")
-      berg%conglom_id=8;                    berg%lon=berg%lon-pfix; berg%lon_prev=berg%lon_prev-pfix
+      berg%conglom_id=8;                    berg%lon=berg%lon-pfix;
       call pack_berg_into_buffer2(berg,bergs%obuffer_e, nbergs_to_send, bergs%max_bonds)
-      berg%conglom_id=current_conglom_id+4; berg%lon=berg%lon+pfix; berg%lon_prev=berg%lon_prev+pfix
+      berg%conglom_id=current_conglom_id+4; berg%lon=berg%lon+pfix;
     case ("w")
-      berg%conglom_id=4;                    berg%lon=berg%lon-pfix; berg%lon_prev=berg%lon_prev-pfix
+      berg%conglom_id=4;                    berg%lon=berg%lon-pfix;
       call pack_berg_into_buffer2(berg,bergs%obuffer_w, nbergs_to_send, bergs%max_bonds)
-      berg%conglom_id=current_conglom_id+8; berg%lon=berg%lon+pfix; berg%lon_prev=berg%lon_prev+pfix
+      berg%conglom_id=current_conglom_id+8; berg%lon=berg%lon+pfix;
     case ("n")
       berg%conglom_id=1
       call pack_berg_into_buffer2(berg,bergs%obuffer_n, nbergs_to_send, bergs%max_bonds)
@@ -2577,16 +2550,12 @@ recursive subroutine mts_pack_contact_bergs(bergs, berg, dir, pfix, nbergs_to_se
                 other_berg%conglom_id=current_conglom_id+2
               case ("w")
                 other_berg%lon=other_berg%lon-pfix; other_berg%conglom_id=4
-                other_berg%lon_prev=other_berg%lon_prev-pfix
                 call pack_berg_into_buffer2(other_berg,bergs%obuffer_w, nbergs_to_send, bergs%max_bonds)
                 other_berg%lon=other_berg%lon+pfix; other_berg%conglom_id=current_conglom_id+8
-                other_berg%lon_prev=other_berg%lon_prev+pfix
               case ("e")
                 other_berg%lon=other_berg%lon-pfix; other_berg%conglom_id=8
-                other_berg%lon_prev=other_berg%lon_prev-pfix
                 call pack_berg_into_buffer2(other_berg,bergs%obuffer_e, nbergs_to_send, bergs%max_bonds)
                 other_berg%lon=other_berg%lon+pfix; other_berg%conglom_id=current_conglom_id+4
-                other_berg%lon_prev=other_berg%lon_prev+pfix
               end select
               other_berg%halo_berg=current_halo_id
             endif
@@ -3305,8 +3274,6 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
   counter = 0
   call push_buffer_value(buff%data(:,n), counter, berg%lon)
   call push_buffer_value(buff%data(:,n), counter, berg%lat)
-  call push_buffer_value(buff%data(:,n), counter, berg%lon_prev)
-  call push_buffer_value(buff%data(:,n), counter, berg%lat_prev)
   call push_buffer_value(buff%data(:,n), counter, berg%uvel)
   call push_buffer_value(buff%data(:,n), counter, berg%vvel)
   call push_buffer_value(buff%data(:,n), counter, berg%uvel_prev)
@@ -3369,8 +3336,6 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
     call push_buffer_value(buff%data(:,n), counter, berg%ang_vel)
     call push_buffer_value(buff%data(:,n), counter, berg%ang_accel)
     call push_buffer_value(buff%data(:,n), counter, berg%rot)
-  elseif (fracture_criterion .ne. 'none') then
-    call push_buffer_value(buff%data(:,n), counter, berg%accum_bond_rotation)
   endif
 
   if (max_bonds .gt. 0) then
@@ -3391,13 +3356,6 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
           call push_buffer_value(buff%data(:,n), counter, current_bond%sstress)
           call push_buffer_value(buff%data(:,n), counter, current_bond%rel_rotation)
           call push_buffer_value(buff%data(:,n), counter, current_bond%broken)
-        elseif (fracture_criterion .ne. 'none') then
-          call push_buffer_value(buff%data(:,n), counter, current_bond%rotation)
-          call push_buffer_value(buff%data(:,n), counter, current_bond%rel_rotation)
-          call push_buffer_value(buff%data(:,n), counter, current_bond%n_frac_var)
-          if (fracture_criterion .eq. 'strain_rate') then
-            call push_buffer_value(buff%data(:,n), counter, current_bond%n_strain_rate)
-          endif
         endif
 
         current_bond=>current_bond%next_bond
@@ -3415,15 +3373,7 @@ subroutine pack_berg_into_buffer2(berg, buff, n, max_bonds_in)
           call push_buffer_value(buff%data(:,n), counter, 0)
           call push_buffer_value(buff%data(:,n), counter, 0)
           call push_buffer_value(buff%data(:,n), counter, 0)
-        elseif (fracture_criterion .ne. 'none') then
-          call push_buffer_value(buff%data(:,n), counter, 0)
-          call push_buffer_value(buff%data(:,n), counter, 0)
-          call push_buffer_value(buff%data(:,n), counter, 0)
-          if (fracture_criterion .eq. 'strain_rate') then
-            call push_buffer_value(buff%data(:,n), counter, 0)
-          endif
         endif
-
       endif
     enddo
   endif
@@ -3554,25 +3504,15 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
   force_app = .false.
   if(present(force_append)) force_app = force_append
 
-  if (mts) then
-    allocate(localberg%axn_fast,localberg%ayn_fast,localberg%bxn_fast,localberg%byn_fast,localberg%conglom_id)
-  endif
+  if (mts) allocate(localberg%axn_fast,localberg%ayn_fast,localberg%bxn_fast,localberg%byn_fast,localberg%conglom_id)
 
-  if (iceberg_bonds_on) then
-    allocate(localberg%n_bonds)
-  endif
+  if (iceberg_bonds_on) allocate(localberg%n_bonds)
 
-  if (dem) then
-    allocate(localberg%ang_vel,localberg%ang_accel,localberg%rot)
-  elseif (fracture_criterion .ne. 'none') then
-    allocate(localberg%accum_bond_rotation)
-  endif
+  if (dem) allocate(localberg%ang_vel,localberg%ang_accel,localberg%rot)
 
   counter = 0
   call pull_buffer_value(buff%data(:,n), counter, localberg%lon)
   call pull_buffer_value(buff%data(:,n), counter, localberg%lat)
-  call pull_buffer_value(buff%data(:,n), counter, localberg%lon_prev)
-  call pull_buffer_value(buff%data(:,n), counter, localberg%lat_prev)
   call pull_buffer_value(buff%data(:,n), counter, localberg%uvel)
   call pull_buffer_value(buff%data(:,n), counter, localberg%vvel)
   call pull_buffer_value(buff%data(:,n), counter, localberg%uvel_prev)
@@ -3635,8 +3575,6 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
     call pull_buffer_value(buff%data(:,n), counter, localberg%ang_vel)
     call pull_buffer_value(buff%data(:,n), counter, localberg%ang_accel)
     call pull_buffer_value(buff%data(:,n), counter, localberg%rot)
-  elseif (fracture_criterion .ne. 'none') then
-    call pull_buffer_value(buff%data(:,n), counter, localberg%accum_bond_rotation)
   endif
 
   !These quantities no longer need to be passed between processors
@@ -3763,13 +3701,6 @@ subroutine unpack_berg_from_buffer2(bergs, buff, n, grd, force_append, max_bonds
           call pull_buffer_value(buff%data(:,n), counter, current_bond%sstress)
           call pull_buffer_value(buff%data(:,n), counter, current_bond%rel_rotation)
           call pull_buffer_value(buff%data(:,n), counter, current_bond%broken)
-        elseif (fracture_criterion .ne. 'none') then
-          call pull_buffer_value(buff%data(:,n), counter, current_bond%rotation)
-          call pull_buffer_value(buff%data(:,n), counter, current_bond%rel_rotation)
-          call pull_buffer_value(buff%data(:,n), counter, current_bond%n_frac_var)
-          if (fracture_criterion .eq. 'strain_rate') then
-            call pull_buffer_value(buff%data(:,n), counter, current_bond%n_strain_rate)
-          endif
         endif
       endif
     enddo
@@ -3900,10 +3831,7 @@ subroutine pack_traj_into_buffer2(traj, buff, n, save_short_traj, save_fl_traj)
       call push_buffer_value(buff%data(:,n), counter, traj%ang_vel)
       call push_buffer_value(buff%data(:,n), counter, traj%ang_accel)
       call push_buffer_value(buff%data(:,n), counter, traj%rot)
-    elseif (fracture_criterion .ne. 'none') then
-      call push_buffer_value(buff%data(:,n), counter, traj%accum_bond_rotation)
     endif
-
   endif
 
 end subroutine pack_traj_into_buffer2
@@ -3929,11 +3857,7 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj, save_fl_tra
     allocate(traj%n_bonds)
   endif
 
-  if (dem) then
-    allocate(traj%ang_vel,traj%ang_accel,traj%rot)
-  elseif (fracture_criterion .ne. 'none') then
-    allocate(traj%accum_bond_rotation)
-  endif
+  if (dem) allocate(traj%ang_vel,traj%ang_accel,traj%rot)
 
   counter = 0
   call pull_buffer_value(buff%data(:,n),counter,traj%lon)
@@ -4000,8 +3924,6 @@ subroutine unpack_traj_from_buffer2(first, buff, n, save_short_traj, save_fl_tra
       call pull_buffer_value(buff%data(:,n), counter, traj%ang_vel)
       call pull_buffer_value(buff%data(:,n), counter, traj%ang_accel)
       call pull_buffer_value(buff%data(:,n), counter, traj%rot)
-    elseif (fracture_criterion .ne. 'none') then
-      call pull_buffer_value(buff%data(:,n), counter, traj%accum_bond_rotation)
     endif
   endif
   call append_posn(first, traj)
@@ -4044,13 +3966,6 @@ subroutine pack_bond_traj_into_buffer2(bond_traj, buff, n)
     call push_buffer_value(buff%data(:,n),counter,bond_traj%sstress)
     call push_buffer_value(buff%data(:,n),counter,bond_traj%rel_rotation)
     call push_buffer_value(buff%data(:,n),counter,bond_traj%broken)
-  elseif (fracture_criterion.ne.'none') then
-    call push_buffer_value(buff%data(:,n),counter,bond_traj%rotation)
-    call push_buffer_value(buff%data(:,n),counter,bond_traj%rel_rotation)
-    call push_buffer_value(buff%data(:,n),counter,bond_traj%n_frac_var)
-    if (fracture_criterion.eq.'strain_rate') then
-      call push_buffer_value(buff%data(:,n),counter,bond_traj%n_strain_rate)
-    endif
   endif
 
 end subroutine pack_bond_traj_into_buffer2
@@ -4066,14 +3981,7 @@ subroutine unpack_bond_traj_from_buffer2(first, buff, n)
   integer :: counter ! Position in stack
   integer :: cnt1, ij1, cnt2, ij2
 
-  if (dem) then
-    allocate(bond_traj%tangd1,bond_traj%tangd2,bond_traj%nstress,bond_traj%sstress,bond_traj%rel_rotation)
-  elseif (fracture_criterion.ne.'none') then
-    allocate(bond_traj%rotation,bond_traj%rel_rotation,bond_traj%n_frac_var)
-    if (fracture_criterion.eq.'strain_rate') then
-      allocate(bond_traj%n_strain_rate)
-    endif
-  endif
+  if (dem) allocate(bond_traj%tangd1,bond_traj%tangd2,bond_traj%nstress,bond_traj%sstress,bond_traj%rel_rotation)
 
   counter = 0
   call pull_buffer_value(buff%data(:,n),counter,bond_traj%lon)
@@ -4097,13 +4005,6 @@ subroutine unpack_bond_traj_from_buffer2(first, buff, n)
     call pull_buffer_value(buff%data(:,n),counter,bond_traj%sstress)
     call pull_buffer_value(buff%data(:,n),counter,bond_traj%rel_rotation)
     call pull_buffer_value(buff%data(:,n),counter,bond_traj%broken)
-  elseif (fracture_criterion.ne.'none') then
-    call pull_buffer_value(buff%data(:,n),counter,bond_traj%rotation)
-    call pull_buffer_value(buff%data(:,n),counter,bond_traj%rel_rotation)
-    call pull_buffer_value(buff%data(:,n),counter,bond_traj%n_frac_var)
-    if (fracture_criterion.eq.'strain_rate') then
-      call pull_buffer_value(buff%data(:,n),counter,bond_traj%n_strain_rate)
-    endif
   endif
 
   call append_bond_posn(first, bond_traj)
@@ -4571,11 +4472,8 @@ subroutine create_iceberg(berg, bergvals)
     berg%n_bonds=0
   endif
 
-  if (dem) then
-    allocate(berg%ang_vel,berg%ang_accel,berg%rot)
-  elseif (fracture_criterion .ne. 'none') then
-    allocate(berg%accum_bond_rotation)
-  endif
+  if (dem) allocate(berg%ang_vel,berg%ang_accel,berg%rot)
+
   berg=bergvals
   berg%prev=>null()
   berg%next=>null()
@@ -4815,269 +4713,8 @@ subroutine dem_tests_init(bergs)
   bergs%dem_tests_start_lon=minlon; bergs%dem_tests_end_lon=maxlon
 
   print *,'pe,dem tests start lon,dem tests end lon',mpp_pe(),minlon,maxlon
-
-  if (bergs%dem_beam_test>=3) then
-    do grdj=grd%jsd,grd%jed ; do grdi=grd%isd,grd%ied !loop over all cells
-      this=>bergs%list(grdi,grdj)%first
-      do while (associated(this)) ! loop over all bergs in cell
-        if (bergs%dem_beam_test==3) then
-          if (this%start_lon==minlon) this%rot=-pi/2.
-        elseif (bergs%dem_beam_test==4) then
-          if (this%start_lon==maxlon) then
-            this%vvel=-40.0
-            this%vvel_old=-40.0
-            this%vvel_prev=-40.0
-          endif
-        endif
-        this=>this%next
-      enddo
-    enddo;enddo
-  endif
-
 end subroutine dem_tests_init
 
-!> Set the accumulated bond rotation to zero for all bergs
-subroutine reset_bond_rotation(bergs)
-type(icebergs), pointer :: bergs !< Container for all types and memory
-type(iceberg), pointer :: this, other_berg
-type(bond) , pointer :: current_bond
-type(icebergs_gridded), pointer :: grd
-integer :: grdi, grdj
-
-if (.not. bergs%fracture_criterion=='strain_rate') return
-
-  grd=>bergs%grd
-  do grdj=grd%jsd,grd%jed ; do grdi=grd%isd,grd%ied !loop over all cells
-    this=>bergs%list(grdi,grdj)%first
-    do while (associated(this)) ! loop over all bergs in cell
-      this%accum_bond_rotation=0.0
-      current_bond=>this%first_bond
-      do while (associated(current_bond)) ! loop over all bonds
-        current_bond%rotation=0.0
-        current_bond=>current_bond%next_bond
-      enddo
-      this=>this%next
-    enddo
-  enddo;enddo
-end subroutine reset_bond_rotation
-
-!>Saves rotation of bond on each bond, and accumulates the rotation of all bonds connected to a particle
-!!onto the particle.
-subroutine update_bond_angles(bergs)
-type(icebergs), pointer :: bergs !< Container for all types and memory
-type(iceberg), pointer :: this, other_berg
-type(icebergs_gridded), pointer :: grd
-integer :: grdi, grdj
-type(bond) , pointer :: current_bond
-real :: dx_dlon1,dx_dlon2,dx_dlon,dy_dlat,lat_ref,b1_u,b1_v,b2_u,b2_v
-real :: dxa,dya,dxb,dyb,vr1,vr2
-real :: angular_momentum,moment_of_inertia,tangent_velocity
-real :: cross_b1b2,dot_b1b2,angle
-
-  if (bergs%fracture_criterion=='none') return
-
-  grd=>bergs%grd
-
-  if (.not. bergs%grd%grid_is_latlon) then
-    dx_dlon=1.0; dy_dlat=1.0
-  else
-    dy_dlat=pi_180*Rearth
-  endif
-
-  do grdj=grd%jsd,grd%jed ; do grdi=grd%isd,grd%ied !loop over all cells
-    this=>bergs%list(grdi,grdj)%first
-    do while (associated(this)) ! loop over all bergs in cell
-      if (this%conglom_id>0) then
-        current_bond=>this%first_bond
-        if (associated(current_bond)) then
-
-          do while (associated(current_bond)) ! loop over all bonds
-            other_berg=>current_bond%other_berg
-            if (associated(other_berg)) then
-
-              !relative coords from previous cycle
-              if (bergs%grd%grid_is_latlon) then
-                lat_ref=0.5*(this%lat_prev+other_berg%lat_prev); dx_dlon=pi_180*Rearth*cos(lat_ref*pi_180)
-              endif
-              dxa=(other_berg%lon_prev-this%lon_prev)*dx_dlon;   dya=(other_berg%lat_prev-this%lat_prev)*dy_dlat
-
-              !relative coords from current cycle
-              if (bergs%grd%grid_is_latlon) then
-                lat_ref=0.5*(this%lat+other_berg%lat);         dx_dlon=pi_180*Rearth*cos(lat_ref*pi_180)
-              endif
-              dxb=(other_berg%lon-this%lon)*dx_dlon;           dyb=(other_berg%lat-this%lat)*dy_dlat
-
-              current_bond%length=sqrt(dxb*dxb+dyb*dyb) !update bond length
-
-              cross_b1b2=dxa*dyb-dya*dxb !([dxa dya 0] x [dxb dyb 0]) . [0 0 1]
-              dot_b1b2 = dxa*dxb+dya*dyb ![dxa dya] . [dxa dxb]
-              angle = atan2(cross_b1b2,dot_b1b2)
-
-              current_bond%rotation=current_bond%rotation+angle
-            endif
-            current_bond=>current_bond%next_bond
-          enddo !loop over all bonds
-        endif
-      endif
-      this=>this%next
-    enddo ! loop over all bergs in cell
-  enddo; enddo !loop over all cells
-end subroutine update_bond_angles
-
-
-!> For each berg element, calculates the average rotation rate of all bonds connected to a particle. Bonds are
-!! then broken based on their individual rotation rate compared to the average rotation rates accumulated on
-!! the berg elements that the bonds connect, and based on the rate of bond stretching (normal strain-rate).
-!! Alternatively, bonds can be broken based on the total accumulated relative rotation and normal strain (not rates).
-subroutine update_and_break_bonds(bergs)
-  type(icebergs), pointer :: bergs !< Container for all types and memory
-  type(iceberg), pointer :: other_berg, this
-  type(icebergs_gridded), pointer :: grd
-  integer :: grdi, grdj
-  type(bond) , pointer :: current_bond,other_bond,kick_the_bucket
-  real :: frac_thres_n,frac_thres_t,spring_coef
-  real :: inv_dt, rdenom, mean_denom, R1, R2, n_frac_var, BondEetot
-
-  frac_thres_n=bergs%frac_thres_n; frac_thres_t=bergs%frac_thres_t
-  if (frac_thres_n<=0.0 .and. frac_thres_t<=0.0) return !all fracture ignored
-  if (frac_thres_n<=0.0) frac_thres_n=huge(1.0) !no fracture from normal strain
-  if (frac_thres_t<=0.0) frac_thres_t=huge(1.0) !no fracture from bond rotation
-
-  if (bergs%fracture_criterion=='strain_rate') then
-    inv_dt=1.0/bergs%dt
-  elseif (bergs%fracture_criterion=='strain' .or. bergs%fracture_criterion=='stress') then
-    inv_dt=1.0
-  else
-    return
-  endif
-
-  if (bergs%hexagonal_icebergs) then
-    rdenom=1./(2.*sqrt(3.))
-  else
-    if (bergs%iceberg_bonds_on) then
-      rdenom=1./4.
-    else
-      rdenom=1./pi
-    endif
-  endif
-
-  grd=>bergs%grd
-
-  !1. accumulate bond rotation/rotation-rate to the berg element
-  do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
-    this=>bergs%list(grdi,grdj)%first
-    do while (associated(this)) ! loop over all bergs
-      this%accum_bond_rotation=0.0
-      current_bond=>this%first_bond
-      do while (associated(current_bond)) ! loop over all bonds
-        current_bond%rotation=current_bond%rotation*inv_dt
-        this%accum_bond_rotation=this%accum_bond_rotation+current_bond%rotation
-        current_bond=>current_bond%next_bond
-      enddo
-      this=>this%next
-    enddo
-  enddo;enddo
-
-  !2. Compare rotation/rotation-rate of each bond to the berg-based mean w/o the bond it in
-  do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied !loop over cells
-    this=>bergs%list(grdi,grdj)%first
-    do while (associated(this)) ! loop over all bergs
-      if (this%conglom_id>0 .and. this%n_bonds>1) then
-        R1=sqrt(this%length*this%width*rdenom)
-        if (this%n_bonds>1) mean_denom=1.0/(this%n_bonds-1)
-
-        !2. Bond updates: normal strain/strain-rate, and relative rotation/rotation-rate
-        current_bond=>this%first_bond
-        do while (associated(current_bond)) ! loop over all bonds
-          other_berg=>current_bond%other_berg
-          if (.not. associated(other_berg)) &
-            call error_mesg('KID,update_and_break_bonds','other_berg not associated!' ,FATAL)
-          R2=sqrt(other_berg%length*other_berg%width*rdenom)
-
-          !the relative rotation (or rotation-rate) of the current bond relative to the mean
-          !rotation (or rotation-rate) of bonds on the parent berg, where the current bond is
-          !excluded from the mean.
-          if (this%n_bonds>1) then
-            current_bond%rel_rotation = current_bond%rotation-&
-              (this%accum_bond_rotation-current_bond%rotation)*mean_denom
-          else
-            current_bond%rel_rotation = 0.0
-          endif
-
-          !normal strain or strain-rate: note original length is taken as the sum of the
-          !radii (calculated according to area) of the two bergs the bond connects.
-          if (bergs%fracture_criterion=='strain_rate') then
-            n_frac_var=current_bond%length/(R1+R2) - 1.0
-            current_bond%n_strain_rate=(n_frac_var-current_bond%n_frac_var)*inv_dt
-            current_bond%n_frac_var=n_frac_var
-            n_frac_var=current_bond%n_strain_rate
-          elseif (bergs%fracture_criterion=='strain') then
-            n_frac_var=current_bond%length/(R1+R2) - 1.0
-            current_bond%n_frac_var=n_frac_var
-          elseif (bergs%fracture_criterion=='stress') then
-            n_frac_var=(current_bond%length-(R1+R2))*min(this%mass,other_berg%mass)*&
-              (bergs%spring_coef)/(min(this%thickness,other_berg%thickness)*(R1+R2))
-            current_bond%rel_rotation = current_bond%rel_rotation*R1*min(this%mass,other_berg%mass)*&
-              bergs%spring_coef/(min(this%thickness,other_berg%thickness)*(R1+R2))
-            current_bond%n_frac_var=n_frac_var
-          endif
-
-        !mark bond and matching bond on other_berg as fractured
-        if (abs(current_bond%rel_rotation)>frac_thres_t.or.n_frac_var>frac_thres_n) then
-          current_bond%other_id=-1
-
-          !mark matching bond on other_berg
-          other_bond=>other_berg%first_bond
-          do while (associated(other_bond)) ! loop over all bonds
-            if (other_bond%other_id.eq.this%id) other_bond%other_id=-1
-            other_bond=>other_bond%next_bond
-          enddo
-        endif
-        current_bond=>current_bond%next_bond
-      enddo
-    endif
-    this=>this%next
-  enddo
-enddo; enddo
-
-  !4. final cleanup
-  do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
-    this=>bergs%list(grdi,grdj)%first
-    do while (associated(this)) ! loop over all bergs
-      current_bond=>this%first_bond
-      do while (associated(current_bond)) ! loop over all bonds
-        if (current_bond%other_id==-1) then
-          if (grdj>=grd%jsc .and. grdj<=grd%jec .and. grdi>=grd%isc .and. grdi<=grd%iec) then
-            if (bergs%fracture_criterion=='strain_rate') then
-              n_frac_var=current_bond%n_strain_rate
-            else
-              n_frac_var=current_bond%n_frac_var
-            endif
-            if (abs(current_bond%rel_rotation)>frac_thres_t.and.n_frac_var>frac_thres_n) then
-              print *,'angle and n_frac_var break',current_bond%rel_rotation,n_frac_var,this%id
-            elseif (abs(current_bond%rel_rotation)>frac_thres_t) then
-              print *,'angle break',current_bond%rel_rotation,n_frac_var,this%id
-            elseif (n_frac_var>frac_thres_n) then
-              print *,'n_frac_var break',current_bond%rel_rotation,n_frac_var,this%id
-            else
-              print *,'break due to bond match',current_bond%rel_rotation,n_frac_var,this%id
-            endif
-          endif
-          this%accum_bond_rotation=this%accum_bond_rotation-current_bond%rotation
-          this%n_bonds=this%n_bonds-1
-          kick_the_bucket=>current_bond
-          current_bond=>current_bond%next_bond
-          call delete_bond_from_list(this,kick_the_bucket)
-        else
-          current_bond=>current_bond%next_bond
-        endif
-      enddo
-      this=>this%next
-    enddo
-  enddo;enddo
-
-end subroutine update_and_break_bonds
-
 !> DEM-style fracture
 subroutine break_bonds_dem(bergs)
   type(icebergs), pointer :: bergs !< Container for all types and memory
@@ -5096,8 +4733,8 @@ subroutine break_bonds_dem(bergs)
   frac_thres_n=bergs%frac_thres_n; frac_thres_t=bergs%frac_thres_t
 
   if (frac_thres_n<=0.0 .and. frac_thres_t<=0.0) return !all fracture ignored
-  if (frac_thres_n<=0.0) frac_thres_n=huge(1.0) !no fracture from normal strain
-  if (frac_thres_t<=0.0) frac_thres_t=huge(1.0) !no fracture from bond rotation
+  if (frac_thres_n<=0.0) frac_thres_n=huge(1.0) !no fracture from normal stress
+  if (frac_thres_t<=0.0) frac_thres_t=huge(1.0) !no fracture from tangential stress
   grd=>bergs%grd
   do grdj = grd%jsd,grd%jed ; do grdi = grd%isd,grd%ied
     this=>bergs%list(grdi,grdj)%first
@@ -5217,13 +4854,6 @@ subroutine form_a_bond(berg, other_id, other_berg_ine, other_berg_jne, other_ber
       allocate(new_bond%F_x, new_bond%F_y, new_bond%Fd_x, new_bond%Fd_y, new_bond%T, new_bond%T_d)
       new_bond%F_x=0.; new_bond%F_y=0.; new_bond%Fd_x=0.; new_bond%Fd_y=0.; new_bond%T=0.; new_bond%T_d=0.
     endif
-  elseif (fracture_criterion.ne.'none') then
-    allocate(new_bond%rotation,new_bond%rel_rotation,new_bond%n_frac_var)
-    new_bond%rotation=0.; new_bond%rel_rotation=0.; new_bond%n_frac_var=0.
-    if (fracture_criterion.eq.'strain_rate') then
-      allocate(new_bond%n_strain_rate)
-      new_bond%n_strain_rate=0.
-    endif
   endif
 
   new_bond%other_id=other_id
@@ -5507,7 +5137,7 @@ subroutine update_latlon(bergs)
   ! Local variables
   type(icebergs_gridded), pointer :: grd
   type(iceberg), pointer :: berg
-  real :: dlon, dlat,dlon2,dlat2,xi,yj,Lx
+  real :: dlon, dlat,xi,yj,Lx
   integer :: grdi,grdj
   logical :: lret
 
@@ -5526,16 +5156,12 @@ subroutine update_latlon(bergs)
             !already been corrected (if needed), as the scheme below would fail.
             dlon = berg%lon - berg%lon_old
             dlat = berg%lat - berg%lat_old
-            dlon2 = berg%lon - berg%lon_prev
-            dlat2 = berg%lat - berg%lat_prev
 
             berg%lon=bilin(grd, grd%lon, berg%ine, berg%jne, berg%xi, berg%yj)
             berg%lat=bilin(grd, grd%lat, berg%ine, berg%jne, berg%xi, berg%yj)
 
             berg%lon_old = berg%lon-dlon
             berg%lat_old = berg%lat-dlat
-            berg%lon_prev = berg%lon-dlon2
-            berg%lat_prev = berg%lat-dlat2
 
             !need to update local positon in cell from updated global coords, due to roundoff
             lret=pos_within_cell(grd, berg%lon, berg%lat, berg%ine, berg%jne, berg%xi, berg%yj)
@@ -5734,20 +5360,9 @@ subroutine record_posn(bergs)
     allocate(posn%n_bonds)
   endif
 
-  if (dem) then
-    allocate(posn%ang_vel,posn%ang_accel,posn%rot)
-  elseif (fracture_criterion .ne. 'none') then
-    allocate(posn%accum_bond_rotation)
-  endif
+  if (dem) allocate(posn%ang_vel,posn%ang_accel,posn%rot)
 
-  if (save_bond_traj) then
-    if (dem) then
-      allocate(bond_posn%tangd1,bond_posn%tangd2,bond_posn%nstress,bond_posn%sstress,bond_posn%rel_rotation)
-    elseif (fracture_criterion.ne.'none') then
-      allocate(bond_posn%rotation,bond_posn%rel_rotation,bond_posn%n_frac_var)
-      if (fracture_criterion.eq.'strain_rate') allocate(bond_posn%n_strain_rate)
-    endif
-  endif
+  if (save_bond_traj .and. dem) allocate(bond_posn%tangd1,bond_posn%tangd2,bond_posn%nstress,bond_posn%sstress,bond_posn%rel_rotation)
 
   area_thres=bergs%traj_area_thres*1.e6 ! convert from km^2 to m^2
   area_thres2=bergs%traj_area_thres_sntbc*1.e6
@@ -5838,8 +5453,6 @@ subroutine record_posn(bergs)
             posn%ang_vel=this%ang_vel
             posn%ang_accel=this%ang_accel
             posn%rot=this%rot
-          elseif (fracture_criterion .ne. 'none') then
-            posn%accum_bond_rotation=this%accum_bond_rotation
           endif
         endif
 
@@ -5873,11 +5486,6 @@ subroutine record_posn(bergs)
                 bond_posn%nstress=current_bond%nstress
                 bond_posn%sstress=current_bond%sstress
                 bond_posn%rel_rotation=current_bond%rel_rotation
-              elseif (fracture_criterion.ne.'none') then
-                bond_posn%rotation=current_bond%rotation
-                bond_posn%rel_rotation=current_bond%rel_rotation
-                bond_posn%n_frac_var=current_bond%n_frac_var
-                if (fracture_criterion.eq.'strain_rate') bond_posn%n_strain_rate=current_bond%n_strain_rate
               endif
 
               call push_bond_posn(current_bond%bond_trajectory, bond_posn)
@@ -5911,11 +5519,7 @@ subroutine push_posn(trajectory, posn_vals)
     allocate(new_posn%n_bonds)
   endif
 
-  if (dem) then
-    allocate(new_posn%ang_vel,new_posn%ang_accel,new_posn%rot)
-  elseif (fracture_criterion .ne. 'none') then
-    allocate(new_posn%accum_bond_rotation)
-  endif
+  if (dem) allocate(new_posn%ang_vel,new_posn%ang_accel,new_posn%rot)
 
   new_posn=posn_vals
   new_posn%next=>trajectory
@@ -5933,12 +5537,7 @@ subroutine push_bond_posn(bond_trajectory, bond_posn_vals)
 
   allocate(new_bond_posn)
 
-  if (dem) then
-    allocate(new_bond_posn%tangd1,new_bond_posn%tangd2,new_bond_posn%nstress,new_bond_posn%sstress,new_bond_posn%rel_rotation)
-  elseif (fracture_criterion.ne.'none') then
-    allocate(new_bond_posn%rotation,new_bond_posn%rel_rotation,new_bond_posn%n_frac_var)
-    if (fracture_criterion.eq.'strain_rate') allocate(new_bond_posn%n_strain_rate)
-  endif
+  if (dem) allocate(new_bond_posn%tangd1,new_bond_posn%tangd2,new_bond_posn%nstress,new_bond_posn%sstress,new_bond_posn%rel_rotation)
 
   new_bond_posn=bond_posn_vals
   new_bond_posn%next=>bond_trajectory
@@ -5965,11 +5564,7 @@ subroutine append_posn(trajectory, posn_vals)
     allocate(new_posn%n_bonds)
   endif
 
-  if (dem) then
-    allocate(new_posn%ang_vel,new_posn%ang_accel,new_posn%rot)
-  elseif (fracture_criterion .ne. 'none' .and. (.not. dem)) then
-    allocate(new_posn%accum_bond_rotation)
-  endif
+  if (dem) allocate(new_posn%ang_vel,new_posn%ang_accel,new_posn%rot)
 
   new_posn=posn_vals
   new_posn%next=>null()
@@ -5997,12 +5592,7 @@ subroutine append_bond_posn(bond_trajectory, bond_posn_vals)
 
   allocate(new_bond_posn)
 
-  if (dem) then
-    allocate(new_bond_posn%tangd1,new_bond_posn%tangd2,new_bond_posn%nstress,new_bond_posn%sstress,new_bond_posn%rel_rotation)
-  elseif (fracture_criterion.ne.'none') then
-    allocate(new_bond_posn%rotation,new_bond_posn%rel_rotation,new_bond_posn%n_frac_var)
-    if (fracture_criterion.eq.'strain_rate') allocate(new_bond_posn%n_strain_rate)
-  endif
+  if (dem) allocate(new_bond_posn%tangd1,new_bond_posn%tangd2,new_bond_posn%nstress,new_bond_posn%sstress,new_bond_posn%rel_rotation)
 
   new_bond_posn=bond_posn_vals
   new_bond_posn%next=>null()
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index 1274513..e9c4cd2 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -44,7 +44,7 @@ module ice_bergs_io
 use ice_bergs_framework, only: mts,save_bond_traj
 use ice_bergs_framework, only: push_bond_posn, append_bond_posn
 use ice_bergs_framework, only: pack_bond_traj_into_buffer2,unpack_bond_traj_from_buffer2
-use ice_bergs_framework, only: dem, fracture_criterion, iceberg_bonds_on
+use ice_bergs_framework, only: dem, iceberg_bonds_on
 use ice_bergs_framework, only: footloose
 
 
@@ -161,17 +161,11 @@ subroutine write_restart(bergs, time_stamp)
                                    ang_vel,      &
                                    ang_accel,    &
                                    rot,          &
-                                   lon_prev,     &
-                                   lat_prev,     &
-                                   accum_bond_rotation, &
                                    tangd1,       &
                                    tangd2,       &
                                    nstress,      &
                                    sstress,      &
-                                   rotation,     &
-                                   rel_rotation, &
-                                   n_frac_var,   &
-                                   n_strain_rate
+                                   rel_rotation
 
 integer, allocatable, dimension(:) :: ine,              &
                                       jne,              &
@@ -251,10 +245,6 @@ subroutine write_restart(bergs, time_stamp)
      allocate(ang_vel(nbergs))
      allocate(ang_accel(nbergs))
      allocate(rot(nbergs))
-   elseif (fracture_criterion.ne.'none') then
-     allocate(lon_prev(nbergs))
-     allocate(lat_prev(nbergs))
-     allocate(accum_bond_rotation(nbergs))
    endif
 
   filename = trim("icebergs.res.nc")
@@ -330,11 +320,6 @@ subroutine write_restart(bergs, time_stamp)
       longname='dem angular acceleration',units='rad/s^2')
     id = register_restart_field(bergs_restart,filename,'rot',rot,&
       longname='dem accumulated rotation',units='rad')
-  elseif (fracture_criterion.ne.'none') then
-    id = register_restart_field(bergs_restart,filename,'lon_prev',lon_prev,longname='previous longitude',units='degrees_E')
-    id = register_restart_field(bergs_restart,filename,'lat_prev',lat_prev,longname='previous latitude',units='degrees_N')
-    id = register_restart_field(bergs_restart,filename,'accum_bond_rotation',accum_bond_rotation,&
-      longname='accumulated bond rotation',units='rad')
   endif
 
   !Checking if any icebergs are static in order to decide whether to save static_berg
@@ -389,10 +374,6 @@ subroutine write_restart(bergs, time_stamp)
         ang_vel(i) = this%ang_vel
         ang_accel(i) = this%ang_accel
         rot(i) = this%rot
-      elseif (fracture_criterion.ne.'none') then
-        lon_prev(i) = this%lon_prev
-        lat_prev(i) = this%lat_prev
-        accum_bond_rotation(i) = this%accum_bond_rotation
       endif
       this=>this%next
     enddo
@@ -442,11 +423,6 @@ subroutine write_restart(bergs, time_stamp)
              ang_vel,      &
              ang_accel,    &
              rot)
-  elseif (fracture_criterion.ne.'none') then
-    deallocate(            &
-             lon_prev,     &
-             lat_prev,     &
-             accum_bond_rotation)
   endif
 
   deallocate(           &
@@ -482,13 +458,6 @@ subroutine write_restart(bergs, time_stamp)
     allocate(sstress(nbonds))
     allocate(rel_rotation(nbonds))
     allocate(broken(nbonds))
-  elseif (fracture_criterion.ne.'none') then
-    allocate(rotation(nbonds))
-    allocate(rel_rotation(nbonds))
-    allocate(n_frac_var(nbonds))
-    if (fracture_criterion.eq.'strain_rate') then
-      allocate(n_strain_rate(nbonds))
-    endif
   endif
 
   call get_instance_filename("bonds_iceberg.res.nc", filename_bonds)
@@ -522,17 +491,6 @@ subroutine write_restart(bergs, time_stamp)
       longname='relative rotation',units='rad')
      id = register_restart_field(bergs_bond_restart,filename_bonds,'broken',broken,&
       longname='broken status',units='none')
-  elseif (fracture_criterion.ne.'none') then
-    id = register_restart_field(bergs_bond_restart,filename_bonds,'rotation',rotation,&
-      longname='rotation',units='rad')
-    id = register_restart_field(bergs_bond_restart,filename_bonds,'rel_rotation',rel_rotation,&
-      longname='relative rotation',units='rad')
-    id = register_restart_field(bergs_bond_restart,filename_bonds,'n_frac_var',n_frac_var,&
-      longname='normal fracture variable',units='dimensionless/s^-1/Pa/J')
-    if (fracture_criterion.eq.'strain_rate') then
-      id = register_restart_field(bergs_bond_restart,filename_bonds,'n_strain_rate',n_strain_rate,&
-        longname='normal strain-rate',units='1/seconds')
-    endif
   endif
 
   ! Write variables
@@ -558,13 +516,6 @@ subroutine write_restart(bergs, time_stamp)
           sstress(i)=current_bond%sstress
           rel_rotation(i)=current_bond%rel_rotation
           broken(i)=current_bond%broken
-        elseif (fracture_criterion.ne.'none') then
-          rotation(i)=current_bond%rotation
-          rel_rotation(i)=current_bond%rel_rotation
-          n_frac_var(i)=current_bond%n_frac_var
-          if (fracture_criterion.eq.'strain_rate') then
-            n_strain_rate(i)=current_bond%n_strain_rate
-          endif
         endif
 
         current_bond=>current_bond%next_bond
@@ -593,14 +544,6 @@ subroutine write_restart(bergs, time_stamp)
              sstress,               &
              rel_rotation,          &
              broken)
-  elseif (fracture_criterion.ne.'none') then
-    deallocate(                     &
-             rotation,              &
-             rel_rotation,          &
-             n_frac_var)
-    if (fracture_criterion.eq.'strain_rate') then
-      deallocate(n_strain_rate)
-    endif
   endif
 
   call nullify_domain()
@@ -704,10 +647,7 @@ subroutine read_restart_bergs(bergs,Time)
                                    byn_fast,     &
                                    ang_vel,      &
                                    ang_accel,    &
-                                   rot,          &
-                                   lon_prev,     &
-                                   lat_prev,     &
-                                   accum_bond_rotation
+                                   rot
 
 integer, allocatable, dimension(:) :: ine,        &
                                       jne,        &
@@ -796,10 +736,6 @@ subroutine read_restart_bergs(bergs,Time)
        allocate(ang_vel(nbergs_in_file))
        allocate(ang_accel(nbergs_in_file))
        allocate(rot(nbergs_in_file))
-     elseif (fracture_criterion.ne.'none') then
-       allocate(lon_prev(nbergs_in_file))
-       allocate(lat_prev(nbergs_in_file))
-       allocate(accum_bond_rotation(nbergs_in_file))
      endif
 
      call read_unlimited_axis(filename,'lon',lon,domain=grd%domain)
@@ -846,18 +782,11 @@ subroutine read_restart_bergs(bergs,Time)
        call read_real_vector(filename,'ang_vel'  ,ang_vel  ,grd%domain,value_if_not_in_file=0.)
        call read_real_vector(filename,'ang_accel',ang_accel,grd%domain,value_if_not_in_file=0.)
        call read_real_vector(filename,'rot'      ,rot      ,grd%domain,value_if_not_in_file=0.)
-     elseif (fracture_criterion.ne.'none') then
-       call read_real_vector(filename,'lon_prev',lon_prev,grd%domain,value_if_not_in_file=0.)
-       call read_real_vector(filename,'lat_prev',lat_prev,grd%domain,value_if_not_in_file=0.)
-       call read_real_vector(filename,'accum_bond_rotation',accum_bond_rotation,grd%domain,value_if_not_in_file=0.)
      endif
   elseif (bergs%require_restart) then
      stop 'read_restart_bergs, RESTART NOT FOUND!'
   endif
 
-   if (all(lon_prev.eq.0)) lon_prev=lon
-   if (all(lat_prev.eq.0)) lat_prev=lat
-
   ! Find approx outer bounds for tile
   lon0=minval( grd%lon(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
   lon1=maxval( grd%lon(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
@@ -899,8 +828,6 @@ subroutine read_restart_bergs(bergs,Time)
       localberg%vvel_old=vvel(k) !Alon
       localberg%lon_old=lon(k) !Alon
       localberg%lat_old=lat(k) !Alon
-      localberg%lon_prev=lon(k)
-      localberg%lat_prev=lat(k)
       localberg%bxn=bxn(k) !Alon
       localberg%byn=byn(k) !Alon
       localberg%thickness=thickness(k)
@@ -937,10 +864,6 @@ subroutine read_restart_bergs(bergs,Time)
        localberg%ang_vel  =ang_vel(k)
        localberg%ang_accel=ang_accel(k)
        localberg%rot      =rot(k)
-     elseif (fracture_criterion.ne.'none') then
-       localberg%lon_prev=lon_prev(k)
-       localberg%lat_prev=lat_prev(k)
-       localberg%accum_bond_rotation=accum_bond_rotation(k)
      endif
 
       if (really_debug) lres=is_point_in_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, explain=.true.)
@@ -1002,11 +925,6 @@ subroutine read_restart_bergs(bergs,Time)
                ang_vel,      &
                ang_accel,    &
                rot)
-    elseif (fracture_criterion.ne.'none') then
-      deallocate(            &
-               lon_prev,     &
-               lat_prev,     &
-               accum_bond_rotation)
     endif
 
     if (replace_iceberg_num) then
@@ -1112,8 +1030,6 @@ subroutine generate_bergs(bergs,Time)
     allocate(localberg%ang_vel)
     allocate(localberg%ang_accel)
     allocate(localberg%rot)
-  elseif (fracture_criterion.ne.'none') then
-    allocate(localberg%accum_bond_rotation)
   endif
 
   do j=grd%jsc,grd%jec; do i=grd%isc,grd%iec
@@ -1152,8 +1068,6 @@ subroutine generate_bergs(bergs,Time)
       localberg%byn=0. !Alon
       localberg%uvel_prev=0. !Alon
       localberg%vvel_prev=0. !Alon
-      localberg%lon_prev=0.
-      localberg%lat_prev=0.
 
       if (mts) then
         localberg%axn_fast=0.
@@ -1165,8 +1079,6 @@ subroutine generate_bergs(bergs,Time)
         localberg%ang_vel=0.
         localberg%ang_accel=0.
         localberg%rot=0.
-      elseif (fracture_criterion.ne.'none') then
-        localberg%accum_bond_rotation=0.
       endif
 
       !Berg A
@@ -1267,10 +1179,7 @@ subroutine read_restart_bonds(bergs,Time)
                                       tangd2,           &
                                       nstress,          &
                                       sstress,          &
-                                      rotation,         &
-                                      rel_rotation,     &
-                                      n_frac_var,       &
-                                      n_strain_rate
+                                      rel_rotation
 integer(kind=8), allocatable, dimension(:) :: first_id,   &
                                               other_id
 !integer, allocatable, dimension(:,:) :: iceberg_counter_grd
@@ -1316,13 +1225,6 @@ subroutine read_restart_bonds(bergs,Time)
       allocate(sstress(nbonds_in_file))
       allocate(rel_rotation(nbonds_in_file))
       allocate(broken(nbonds_in_file))
-    elseif (fracture_criterion.ne.'none') then
-      allocate(rotation(nbonds_in_file))
-      allocate(rel_rotation(nbonds_in_file))
-      allocate(n_frac_var(nbonds_in_file))
-      if (fracture_criterion.eq.'strain_rate') then
-        allocate(n_strain_rate(nbonds_in_file))
-      endif
     endif
 
     call read_unlimited_axis(filename,'first_id_cnt',id_cnt,domain=grd%domain)
@@ -1348,13 +1250,6 @@ subroutine read_restart_bonds(bergs,Time)
       call read_real_vector(filename,'sstress',sstress,grd%domain,value_if_not_in_file=0.)
       call read_real_vector(filename,'rel_rotation',rel_rotation,grd%domain,value_if_not_in_file=0.)
       call read_int_vector(filename,'broken',broken,grd%domain,value_if_not_in_file=0)
-    elseif (fracture_criterion.ne.'none') then
-      call read_real_vector(filename,'rotation',rotation,grd%domain,value_if_not_in_file=0.)
-      call read_real_vector(filename,'rel_rotation',rel_rotation,grd%domain,value_if_not_in_file=0.)
-      call read_real_vector(filename,'n_frac_var',n_frac_var,grd%domain,value_if_not_in_file=0.)
-      if (fracture_criterion.eq.'strain_rate') then
-        call read_real_vector(filename,'n_strain_rate',n_strain_rate,grd%domain,value_if_not_in_file=0.)
-      endif
     endif
 
     number_first_bonds_matched=0
@@ -1459,13 +1354,6 @@ subroutine read_restart_bonds(bergs,Time)
               current_bond%sstress=sstress(k)
               current_bond%rel_rotation=rel_rotation(k)
               current_bond%broken=broken(k)
-            elseif (fracture_criterion.ne.'none') then
-              current_bond%rotation=rotation(k)
-              current_bond%rel_rotation=rel_rotation(k)
-              current_bond%n_frac_var=n_frac_var(k)
-              if (fracture_criterion.eq.'strain_rate') then
-                current_bond%n_strain_rate=n_strain_rate(k)
-              endif
             endif
 
             !Counting number of bonds where the first bond is in the computational domain
@@ -1532,14 +1420,6 @@ subroutine read_restart_bonds(bergs,Time)
                sstress,               &
                rel_rotation,          &
                broken)
-    elseif (fracture_criterion.ne.'none') then
-      deallocate(                     &
-               rotation,              &
-               rel_rotation,          &
-               n_frac_var)
-      if (fracture_criterion.eq.'strain_rate') then
-        deallocate(n_strain_rate)
-      endif
     endif
   endif
 
@@ -1705,7 +1585,7 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, traj_name
 integer :: cnid, hiid, hsid
 integer :: mid, smid, did, wid, lid, mbid, mflbid, mflbbid, hdid, nbid, odid, flkid
 integer :: axnid,aynid,bxnid,bynid,axnfid,aynfid,bxnfid,bynfid, msid
-integer :: avid, aaid, rid, abrid
+integer :: avid, aaid, rid
 character(len=70) :: filename
 character(len=7) :: pe_name
 type(xyt), pointer :: this, next
@@ -1880,8 +1760,6 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, traj_name
           avid = inq_varid(ncid, 'ang_vel')
           aaid = inq_varid(ncid, 'ang_accel')
           rid  = inq_varid(ncid, 'rot')
-        elseif (fracture_criterion .ne. 'none') then
-          abrid = inq_varid(ncid, 'accum_bond_rotation')
         endif
 
       endif
@@ -1953,8 +1831,6 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, traj_name
           avid = def_var(ncid, 'ang_vel', NF_DOUBLE, i_dim)
           aaid = def_var(ncid, 'ang_accel', NF_DOUBLE, i_dim)
           rid  = def_var(ncid, 'rot', NF_DOUBLE, i_dim)
-        elseif (fracture_criterion .ne. 'none') then
-          abrid = def_var(ncid, 'accum_bond_rotation', NF_DOUBLE, i_dim)
         endif
       endif
 
@@ -2072,9 +1948,6 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, traj_name
           call put_att(ncid, aaid, 'units', 'rad/s^2')
           call put_att(ncid, rid, 'long_name', 'accumulated rotation')
           call put_att(ncid, rid, 'units', 'rad')
-        elseif (fracture_criterion .ne. 'none') then
-          call put_att(ncid, abrid, 'long_name', 'accumulated bond rotation')
-          call put_att(ncid, abrid, 'units', 'radians')
         endif
       endif
     endif
@@ -2155,8 +2028,6 @@ subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, traj_name
           call put_double(ncid, avid, i, this%ang_vel)
           call put_double(ncid, aaid, i, this%ang_accel)
           call put_double(ncid, rid,  i, this%rot)
-        elseif (fracture_criterion .ne. 'none') then
-          call put_double(ncid, abrid, i, this%accum_bond_rotation)
         endif
 
       endif
@@ -2182,7 +2053,7 @@ subroutine write_bond_trajectory(trajectory, bond_traj_name)
 ! Local variables
 integer :: iret, ncid, i_dim, i
 integer :: lonid, latid, yearid, dayid, lenid,n1id, n2id
-integer :: rotid,rrotid,nsid,nsrid, brid
+integer :: rrotid,brid
 integer :: idcnt1_id, idcnt2_id, idij1_id, idij2_id
 integer :: td1id,td2id,dnsid,dssid
 character(len=70) :: filename
@@ -2304,12 +2175,6 @@ subroutine write_bond_trajectory(trajectory, bond_traj_name)
         td1id = inq_varid(ncid, 'tangd1');  td2id = inq_varid(ncid, 'tangd2')
         dnsid = inq_varid(ncid, 'nstress'); dssid = inq_varid(ncid, 'sstress')
         rrotid = inq_varid(ncid, 'rel_rotation'); brid = inq_varid(ncid, 'broken')
-      elseif (fracture_criterion.ne.'none') then
-        rotid = inq_varid(ncid, 'rotation');    rrotid = inq_varid(ncid, 'rel_rotation')
-        nsid = inq_varid(ncid, 'n_frac_var')
-        if (fracture_criterion.eq.'strain_rate') then
-          nsrid = inq_varid(ncid, 'n_strain_rate')
-        endif
       endif
 
     else
@@ -2331,12 +2196,6 @@ subroutine write_bond_trajectory(trajectory, bond_traj_name)
         dnsid = def_var(ncid, 'nstress', NF_DOUBLE, i_dim); dssid = def_var(ncid, 'sstress', NF_DOUBLE, i_dim)
         rrotid = def_var(ncid, 'rel_rotation', NF_DOUBLE, i_dim)
         brid = def_var(ncid, 'broken', NF_INT, i_dim)
-      elseif (fracture_criterion.ne.'none') then
-        rotid = def_var(ncid, 'rotation', NF_DOUBLE, i_dim); rrotid = def_var(ncid, 'rel_rotation', NF_DOUBLE, i_dim)
-        nsid = def_var(ncid, 'n_frac_var', NF_DOUBLE, i_dim)
-        if (fracture_criterion.eq.'strain_rate') then
-          nsrid = def_var(ncid, 'n_strain_rate', NF_DOUBLE, i_dim)
-        endif
       endif
 
       ! Attributes
@@ -2368,13 +2227,6 @@ subroutine write_bond_trajectory(trajectory, bond_traj_name)
         call put_att(ncid, dssid, 'long_name', 'shear stress');  call put_att(ncid, dssid, 'units', 'Pa')
         call put_att(ncid, rrotid, 'long_name', 'relative rotation');      call put_att(ncid, rrotid, 'units', 'rad')
         call put_att(ncid, brid, 'long_name', 'broken status');      call put_att(ncid, brid, 'units', 'none')
-      elseif (fracture_criterion.ne.'none') then
-        call put_att(ncid, rotid, 'long_name', 'rotation');                call put_att(ncid, rotid, 'units', 'rad')
-        call put_att(ncid, rrotid, 'long_name', 'relative rotation');      call put_att(ncid, rrotid, 'units', 'rad')
-        call put_att(ncid, nsid, 'long_name', 'normal fracture variable'); call put_att(ncid, nsid, 'units', 'varies')
-        if (fracture_criterion.eq.'strain_rate') then
-          call put_att(ncid, nsrid, 'long_name', 'normal strain-rate'); call put_att(ncid, nsrid, 'units', '1/seconds')
-        endif
       endif
     endif
 
@@ -2405,12 +2257,6 @@ subroutine write_bond_trajectory(trajectory, bond_traj_name)
         call put_double(ncid,td1id,i,this%tangd1);  call put_double(ncid,td2id,i,this%tangd2)
         call put_double(ncid,dnsid,i,this%nstress); call put_double(ncid,dssid,i,this%sstress)
         call put_double(ncid,rrotid,i,this%rel_rotation); call put_int(ncid,brid,i,this%broken)
-      elseif (fracture_criterion.ne.'none') then
-        call put_double(ncid,rotid,i,this%rotation);  call put_double(ncid,rrotid,i,this%rel_rotation)
-        call put_double(ncid,nsid,i,this%n_frac_var)
-        if (fracture_criterion.eq.'strain_rate') then
-          call put_double(ncid,nsrid,i,this%n_strain_rate)
-        endif
       endif
 
       next=>this%next

From 3002ee72e84b586b1d3da10e5cf63db0e272ac3c Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Thu, 5 Jan 2023 13:31:12 -0500
Subject: [PATCH 343/361] Some further cleanup of A68, simplifying the read-in
 of data

---
 driver/driver_data.F90         | 184 +++++++++++++++++++++++++++++++++
 driver/driver_data.f90         |  94 +++++------------
 driver/icebergs_driver.F90     |  22 ++--
 tests/a68_test/data/.gitignore |   3 +-
 tests/a68_test/long_run.nml    |  11 +-
 5 files changed, 225 insertions(+), 89 deletions(-)
 create mode 100644 driver/driver_data.F90

diff --git a/driver/driver_data.F90 b/driver/driver_data.F90
new file mode 100644
index 0000000..b60b015
--- /dev/null
+++ b/driver/driver_data.F90
@@ -0,0 +1,184 @@
+module driver_data
+
+use fms_mod, only : read_data
+use fms_mod, only : file_exist
+use fms_mod, only : field_exist
+use fms_mod, only : error_mesg
+use fms_mod, only : FATAL
+use mpp_domains_mod, only : domain2D
+use mpp_mod, only : mpp_pe
+use mpp_mod, only : mpp_root_pe
+use mpp_mod, only: mpp_sync
+use constants_mod, only: pi
+use netcdf
+!include 'netcdf.inc'
+
+implicit none
+
+contains
+
+  !> Determine dimensions of A68 background grid
+  subroutine a68_dims(data_dir,ni,nj)
+    ! Arguments
+    character(len=*) :: data_dir
+    integer, intent(out):: ni,nj
+    ! Local variables
+    character(len=1000):: infile
+    integer(kind=4) :: ncid
+    integer :: status
+
+    infile=trim(trim(data_dir)//'a68_experiment_ll_p125_grid.nc')
+
+    !Open netCDF file
+    call handle_err(nf90_open(infile, nf90_nowrite, ncid))
+    !Inquire about the dimensions
+    call handle_err(nf90_inquire_dimension(ncid,1,len=nj))
+    call handle_err(nf90_inquire_dimension(ncid,2,len=ni))
+    !Close netCDF file
+    call handle_err(nf90_close(ncid))
+  end subroutine a68_dims
+
+  !> Handle for errors
+  subroutine handle_err(status)
+    integer, intent (in) :: status
+
+    if(status /= nf90_noerr) then
+      print *, trim(nf90_strerror(status))
+      stop "Stopped"
+    end if
+  end subroutine handle_err
+
+  !>A68 grid setup
+  subroutine a68_prep(data_dir,mpp_domain,lon,lat,dx,dy,area,REarth)
+    ! Arguments
+    character(len=*) :: data_dir
+    type(domain2D) :: mpp_domain
+    real :: lon(:,:) !< Longitude or position in x
+    real :: lat(:,:) !< Latitude or position in y
+    real :: dx(:,:) !< Length of northern edge of cell (m)
+    real :: dy(:,:) !< Length of eatern edge of cell (m)
+    real :: area(:,:) !< Area of cell (m2)
+    real :: REarth
+    ! Local variables
+    character(len=1000) :: filename
+    real, parameter :: gres=0.125
+
+    !Grid specs: lon,lat,dx,dy,area
+    filename=trim(trim(data_dir)//'a68_experiment_ll_p125_grid.nc')
+    call read_a68_data(mpp_domain,filename,'longitude',lon)
+    lon=lon+360
+    call read_a68_data(mpp_domain,filename,'latitude',lat)
+
+    call haversine_dist_and_area(REarth,gres,lon,lat,dx,dy,area)
+  end subroutine a68_prep
+
+  !> Haversine distance and area
+  subroutine haversine_dist_and_area(REarth,gres,lon1,lat1,dx,dy,area)
+    ! Arguments
+    real, intent(in) :: REarth    !Earth radius (m)
+    real, intent(in) :: gres      !grid resolution (degrees)
+    real, intent(in) :: lon1(:,:) !grid longitude
+    real, intent(in) :: lat1(:,:) !grid latitude
+    real, intent(out) :: dx(:,:)  !grid dx (m)
+    real, intent(out) :: dy(:,:)   !grid dy (m)
+    real, intent(out) :: area(:,:) !grid area (m^2)
+    ! Local variables
+    real, parameter :: pi_180=pi/180.
+    real, dimension(size(lon1,1),size(lon1,2)) :: lon2,lat2,p1,p2,dp,dm,a,c
+
+    !calculate dx
+    lon2=lon1-gres
+    lat2=lat1
+    p1 = lat1 * pi_180; p2 = lat2 * pi_180; dp = (lat2-lat1) * pi_180; dm = (lon2-lon1) * pi_180
+    a = sin(0.5*dp)**2. + cos(p1) * cos(p2) * sin(0.5*dm)**2.; c = 2. * atan2(sqrt(a), sqrt(1-a))
+    dx = REarth * c
+
+    !calculate dy
+    lat2=lat1-gres
+    lon2=lon1
+    p1 = lat1 * pi_180; p2 = lat2 * pi_180; dp = (lat2-lat1) * pi_180; dm = (lon2-lon1) * pi_180
+    a = sin(0.5*dp)**2. + cos(p1) * cos(p2) * sin(0.5*dm)**2.; c = 2. * atan2(sqrt(a), sqrt(1-a))
+    dy = REarth * c
+
+    !calculate area
+    area=pi_180*(REarth**2.)*abs(sin(lat1*pi_180)-sin(lat2*pi_180))*abs(gres)
+  end subroutine haversine_dist_and_area
+
+
+  !> Read in static (not time-varying) data for A68 experiment from file
+  subroutine read_a68_data(domain,filename,var,field)
+    ! Arguments
+    type(domain2D) :: domain !< Parallel decomposition
+    character(len=*), intent(in) :: filename, var
+    real :: field(:,:)
+
+    call mpp_sync()
+    if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') 'icebergs_driver: Reading ',var
+    if (file_exist(filename)) then
+      if (field_exist(filename, var)) then
+        call read_data(filename, var, field, domain)
+      else
+        if (mpp_pe().eq.mpp_root_pe()) then
+          call error_mesg('icebergs_driver:','Variable missing in file!', FATAL)
+        endif
+      endif
+    else
+      if (mpp_pe().eq.mpp_root_pe()) then
+        call error_mesg('icebergs_driver:','File for variable not found!', FATAL)
+      endif
+    endif
+    call mpp_sync()
+  end subroutine read_a68_data
+
+  !> Calls read_a68_data for wind velocity, ocean velocity, and ssh
+  subroutine a68_prep_3d(data_dir,mpp_domain,tauxa_hr,tauya_hr,uo_hr,vo_hr,ssh_hr)
+    ! Arguments
+    character(len=*) :: data_dir
+
+    type(domain2D) :: mpp_domain
+    real :: tauxa_hr(:,:,:) !< Zonal jra55 wind velocity (m/s, hourly)
+    real :: tauya_hr(:,:,:) !< Meridional jra55 wind velocity (m/s, hourly)
+    real :: uo_hr(:,:,:) !< Zonal OSCAR ocean surface velocity (m/s, hourly)
+    real :: vo_hr(:,:,:) !< Meridional OSCAR ocean surface velocity (m/s, hourly)
+    real :: ssh_hr(:,:,:) !< Effective sea surface height (m, hourly)
+    ! Local variables
+    character(len=1000) :: filename
+
+    filename=trim(trim(data_dir)//'a68_experiment_wind_vel_ncep_10m_dec2020_HOURLY_ll_p125.nc')
+    call read_a68_data_3d(mpp_domain,filename,'ua',tauxa_hr)
+    call read_a68_data_3d(mpp_domain,filename,'va',tauya_hr)
+
+    filename=trim(trim(data_dir)//'a68_experiment_ocean_surf_vel_oscar_dec2020_HOURLY_ll_p125.nc')
+    call read_a68_data_3d(mpp_domain,filename,'uo',uo_hr)
+    call read_a68_data_3d(mpp_domain,filename,'vo',vo_hr)
+
+    filename=trim(trim(data_dir)//'a68_experiment_ssh_duacs_dec2020_HOURLY_ll_p125.nc')
+    call read_a68_data_3d(mpp_domain,filename,'SSH',ssh_hr)
+  end subroutine a68_prep_3d
+
+  !> Read in time-varying A68 data
+  subroutine read_a68_data_3d(domain,filename,var,field)
+    ! Arguments
+    type(domain2D) :: domain !< Parallel decomposition
+    character(len=*), intent(in) :: filename, var
+    real :: field(:,:,:)
+
+    call mpp_sync()
+    if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') 'icebergs_driver: Reading ',var
+    if (file_exist(filename)) then
+      if (field_exist(filename, var)) then
+        call read_data(filename, var, field, domain)
+      else
+        if (mpp_pe().eq.mpp_root_pe()) then
+          call error_mesg('icebergs_driver:','Variable missing in file!', FATAL)
+        endif
+      endif
+    else
+      if (mpp_pe().eq.mpp_root_pe()) then
+        call error_mesg('icebergs_driver:','File for variable not found!', FATAL)
+      endif
+    endif
+    call mpp_sync()
+  end subroutine read_a68_data_3d
+
+end module driver_data
diff --git a/driver/driver_data.f90 b/driver/driver_data.f90
index e2d087c..37061b1 100644
--- a/driver/driver_data.f90
+++ b/driver/driver_data.f90
@@ -17,28 +17,28 @@ module driver_data
 
 contains
 
-  !> Determine dimensions of A68 background grid
+!> Determine dimensions of A68 background grid
   subroutine a68_dims(data_dir,ni,nj)
-    ! Arguments
+! Arguments
     character(len=*) :: data_dir
     integer, intent(out):: ni,nj
-    ! Local variables
+! Local variables
     character(len=1000):: infile
     integer(kind=4) :: ncid
     integer :: status
 
     infile=trim(trim(data_dir)//'a68_experiment_ll_p125_grid.nc')
 
-    !Open netCDF file
+!Open netCDF file
     call handle_err(nf90_open(infile, nf90_nowrite, ncid))
-    !Inquire about the dimensions
+!Inquire about the dimensions
     call handle_err(nf90_inquire_dimension(ncid,1,len=nj))
     call handle_err(nf90_inquire_dimension(ncid,2,len=ni))
-    !Close netCDF file
+!Close netCDF file
     call handle_err(nf90_close(ncid))
   end subroutine a68_dims
 
-  !> Handle for errors
+!> Handle for errors
   subroutine handle_err(status)
     integer, intent (in) :: status
 
@@ -48,14 +48,9 @@ subroutine handle_err(status)
     end if
   end subroutine handle_err
 
-  !>Read in static (non-time-varying) fields, such as ocean depth.
-  !!If transient_a68_data_start_ind<=0, static wind,  ocean velocity, ssh are read in,
-  !!which can be useful for development instead of the respective time-varying
-  !!fields that are otherwise called by a68_prep_3d
-  subroutine a68_prep(data_dir,mpp_domain,lon,lat,dx,dy,area,depth,uo,vo,tauxa,tauya,ssh,&
-    tau_is_velocity,REarth,transient_a68_data_start_ind)
-    !mom_Rearth)
-    ! Arguments
+!>A68 grid setup
+  subroutine a68_prep(data_dir,mpp_domain,lon,lat,dx,dy,area,REarth)
+! Arguments
     character(len=*) :: data_dir
     type(domain2D) :: mpp_domain
     real :: lon(:,:) !< Longitude or position in x
@@ -63,62 +58,23 @@ subroutine a68_prep(data_dir,mpp_domain,lon,lat,dx,dy,area,depth,uo,vo,tauxa,tau
     real :: dx(:,:) !< Length of northern edge of cell (m)
     real :: dy(:,:) !< Length of eatern edge of cell (m)
     real :: area(:,:) !< Area of cell (m2)
-    real :: depth(:,:) !< Depth of ocean (m)
-    real :: uo(:,:) !< Zonal ocean velocities (m/s)
-    real :: vo(:,:) !< Meridional ocean velocities (m/s)
-    real :: tauxa(:,:) !< Zonal wind stress (Pa)
-    real :: tauya(:,:) !< Meridional wind stress (Pa)
-    real :: ssh(:,:) !< Effective sea surface height (m)
-    logical :: Old_wrong_Rearth_and_SSH !< use Rearth=6.36e6 and SSH on B grid
-    logical :: mom_Rearth !< Use Rearth=6.378e6
-    logical :: tau_is_velocity !< If true, read in JRA-55 wind velocity (m/s), not ORAS5 stress (Pa)
     real :: REarth
-    integer :: transient_a68_data_start_ind
-    ! Local variables
+! Local variables
     character(len=1000) :: filename
     real, parameter :: gres=0.125
 
-    !Grid specs: lon,lat,dx,dy,area
+!Grid specs: lon,lat,dx,dy,area
     filename=trim(trim(data_dir)//'a68_experiment_ll_p125_grid.nc')
     call read_a68_data(mpp_domain,filename,'longitude',lon)
     lon=lon+360
     call read_a68_data(mpp_domain,filename,'latitude',lat)
 
     call haversine_dist_and_area(REarth,gres,lon,lat,dx,dy,area)
-
-    !Depth
-    filename=trim(trim(data_dir)//'a68_experiment_gebco_ll_p125.nc')
-    call read_a68_data(mpp_domain,filename,'elevation',depth)
-    depth=-depth !depth is negative in the data, but needs to be positive in the model
-
-    if (transient_a68_data_start_ind<=0) then
-      !Ocean velocity
-      filename=trim(trim(data_dir)//'a68_experiment_ocean_surf_and_mean_vel_fixed_oras5_dec2020_ll_p125.nc')
-      call read_a68_data(mpp_domain,filename,'uo',uo)
-      call read_a68_data(mpp_domain,filename,'vo',vo)
-
-      if (tau_is_velocity) then
-        !Wind velocities -- note this is saved on tauxa and tauya, the wind stress variables.
-        !However, these variables are interpreted in the code as wind velocity if
-        !tau_is_velocity=.true. in the nml,
-        filename=trim(trim(data_dir)//'a68_experiment_wind_vel_jra55_dec2020_ll_p125.nc')
-        call read_a68_data(mpp_domain,filename,'ua',tauxa)
-        call read_a68_data(mpp_domain,filename,'va',tauya)
-      else
-        filename=trim(trim(data_dir)//'a68_experiment_wind_stress_oras5_dec2020_ll_p125.nc')
-        call read_a68_data(mpp_domain,filename,'taux',tauxa)
-        call read_a68_data(mpp_domain,filename,'tauy',tauya)
-      endif
-
-      !Effect sea surface height
-      filename=trim(trim(data_dir)//'a68_experiment_ssh_oras5_dec2020_ll_p125.nc')
-      call read_a68_data(mpp_domain,filename,'SSH',ssh)
-    endif
   end subroutine a68_prep
 
-  !> Haversine distance and area
+!> Haversine distance and area
   subroutine haversine_dist_and_area(REarth,gres,lon1,lat1,dx,dy,area)
-    !Arguments
+! Arguments
     real, intent(in) :: REarth    !Earth radius (m)
     real, intent(in) :: gres      !grid resolution (degrees)
     real, intent(in) :: lon1(:,:) !grid longitude
@@ -126,32 +82,32 @@ subroutine haversine_dist_and_area(REarth,gres,lon1,lat1,dx,dy,area)
     real, intent(out) :: dx(:,:)  !grid dx (m)
     real, intent(out) :: dy(:,:)   !grid dy (m)
     real, intent(out) :: area(:,:) !grid area (m^2)
-    ! Local variables
+! Local variables
     real, parameter :: pi_180=pi/180.
     real, dimension(size(lon1,1),size(lon1,2)) :: lon2,lat2,p1,p2,dp,dm,a,c
 
-    !calculate dx
+!calculate dx
     lon2=lon1-gres
     lat2=lat1
     p1 = lat1 * pi_180; p2 = lat2 * pi_180; dp = (lat2-lat1) * pi_180; dm = (lon2-lon1) * pi_180
     a = sin(0.5*dp)**2. + cos(p1) * cos(p2) * sin(0.5*dm)**2.; c = 2. * atan2(sqrt(a), sqrt(1-a))
     dx = REarth * c
 
-    !calculate dy
+!calculate dy
     lat2=lat1-gres
     lon2=lon1
     p1 = lat1 * pi_180; p2 = lat2 * pi_180; dp = (lat2-lat1) * pi_180; dm = (lon2-lon1) * pi_180
     a = sin(0.5*dp)**2. + cos(p1) * cos(p2) * sin(0.5*dm)**2.; c = 2. * atan2(sqrt(a), sqrt(1-a))
     dy = REarth * c
 
-    !calculate area
+!calculate area
     area=pi_180*(REarth**2.)*abs(sin(lat1*pi_180)-sin(lat2*pi_180))*abs(gres)
   end subroutine haversine_dist_and_area
 
 
-  !> Read in data for A68 experiment from file
+!> Read in static (not time-varying) data for A68 experiment from file
   subroutine read_a68_data(domain,filename,var,field)
-    ! Arguments
+! Arguments
     type(domain2D) :: domain !< Parallel decomposition
     character(len=*), intent(in) :: filename, var
     real :: field(:,:)
@@ -174,9 +130,9 @@ subroutine read_a68_data(domain,filename,var,field)
     call mpp_sync()
   end subroutine read_a68_data
 
-  !> Wrapper to read in time-varying A68 data
+!> Calls read_a68_data for wind velocity, ocean velocity, and ssh
   subroutine a68_prep_3d(data_dir,mpp_domain,tauxa_hr,tauya_hr,uo_hr,vo_hr,ssh_hr)
-    ! Arguments
+! Arguments
     character(len=*) :: data_dir
 
     type(domain2D) :: mpp_domain
@@ -185,7 +141,7 @@ subroutine a68_prep_3d(data_dir,mpp_domain,tauxa_hr,tauya_hr,uo_hr,vo_hr,ssh_hr)
     real :: uo_hr(:,:,:) !< Zonal OSCAR ocean surface velocity (m/s, hourly)
     real :: vo_hr(:,:,:) !< Meridional OSCAR ocean surface velocity (m/s, hourly)
     real :: ssh_hr(:,:,:) !< Effective sea surface height (m, hourly)
-    ! Local variables
+! Local variables
     character(len=1000) :: filename
 
     filename=trim(trim(data_dir)//'a68_experiment_wind_vel_ncep_10m_dec2020_HOURLY_ll_p125.nc')
@@ -200,9 +156,9 @@ subroutine a68_prep_3d(data_dir,mpp_domain,tauxa_hr,tauya_hr,uo_hr,vo_hr,ssh_hr)
     call read_a68_data_3d(mpp_domain,filename,'SSH',ssh_hr)
   end subroutine a68_prep_3d
 
-  !> Read in time-varying A68 data
+!> Read in time-varying A68 data
   subroutine read_a68_data_3d(domain,filename,var,field)
-    ! Arguments
+! Arguments
     type(domain2D) :: domain !< Parallel decomposition
     character(len=*), intent(in) :: filename, var
     real :: field(:,:,:)
diff --git a/driver/icebergs_driver.F90 b/driver/icebergs_driver.F90
index b5e9fae..787dd80 100644
--- a/driver/icebergs_driver.F90
+++ b/driver/icebergs_driver.F90
@@ -60,7 +60,6 @@ program icebergs_driver
 logical :: collision_test=.false.
 logical :: big_grounding_test=.false.
 logical :: a68_test=.false.
-logical :: tau_is_velocity=.true.
 logical :: fl_test=.false.
 character(len=1000) :: data_dir = 'data/'
 integer :: transient_a68_data_start_ind=0 !<set to .gt. 0 to use the hourly JRA-55 wind data for the A68
@@ -83,7 +82,7 @@ program icebergs_driver
 namelist /icebergs_driver_nml/ debug, ni, nj, halo, ibhrs, ibdt, ibuo, ibvo, nmax, &
   saverestart,ibui,ibvi,collision_test,&
   gridres,write_time_inc,bump_depth, sst, a68_test, data_dir,&
-  fl_test,tau_is_velocity,transient_a68_data_start_ind,ibua,ibuy,&
+  fl_test,transient_a68_data_start_ind,ibua,ibuy,&
   REarth,big_grounding_test
 ! For loops
 integer :: isc !< Start of i-index for computational domain (used for loops)
@@ -223,8 +222,8 @@ program icebergs_driver
 vo = ibvo !meridonal ocean velocities (m/s)
 ui = ibui !zonal ice velocities (m/s)
 vi = ibvi !meridonal ice velocities (m/s)
-tauxa = ibua !zonal wind velocity (m/s) or stress (Pa) if tau_is_velocity=.false,
-tauya = ibuy !meridonal wind velocity (m/s) or stress (Pa) if tau_is_velocity=.false,
+tauxa = ibua !zonal wind velocity (m/s)
+tauya = ibuy !meridonal wind velocity (m/s)
 ssh = 0.0 !eff sea-surf height
 sstemp = sst !sea surface temperature (C or K; if K, will automatically adjust to C)
 cn = 0.0 !sea-ice concentration (nondim)
@@ -245,9 +244,8 @@ program icebergs_driver
 
 if (a68_test) then
   call mpp_sync()
-  !note some of these fields will be replaced if transient_a68_data_start_ind>0 (transient instead of static fields)
-  call a68_prep(data_dir,mpp_domain,lon,lat,dx,dy,area,depth,uo,vo,tauxa,tauya,ssh,tau_is_velocity,REarth,&
-    transient_a68_data_start_ind)
+  !grid setup
+  call a68_prep(data_dir,mpp_domain,lon,lat,dx,dy,area,REarth)
   call mpp_sync()
   wet=1.0
   cos_rot=1.0
@@ -258,14 +256,16 @@ program icebergs_driver
       call error_mesg('icebergs_driver:', &
       'in order to use transient_a68_data_start_ind>0, timestep must be 30 min or 1 hr', FATAL)
     endif
-    if (.not. tau_is_velocity) call error_mesg('icebergs_driver:', &
-      'tau_is_velocity must be true if transient_a68_data_start_ind>-1', FATAL)
     allocate( tauxa_hr(isd:ied,jsd:jed,739) )
     allocate( tauya_hr(isd:ied,jsd:jed,739) )
     allocate( uo_hr(isd:ied,jsd:jed,744) )
     allocate( vo_hr(isd:ied,jsd:jed,744) )
     allocate( ssh_hr(isd:ied,jsd:jed,744) )
+    !read in time-varying wind velocity, ocean velocity, and ssh
     call a68_prep_3d(data_dir,mpp_domain,tauxa_hr,tauya_hr,uo_hr,vo_hr,ssh_hr)
+  else
+    call error_mesg('icebergs_driver:', &
+      'must set transient_a68_data_start_ind (i.e. start date index) to greater than zero!', FATAL)
   endif
 else
   !non-A68 tests
@@ -286,7 +286,7 @@ program icebergs_driver
   enddo
 
   if (big_grounding_test) then
-    lat(:,:)=lat(:,:)-0.45 !-25000.1
+    lat(:,:)=lat(:,:)-0.45
     lon(:,:)=lon(:,:)-0.45
     !assign land cells at the N and S portions of the domain.
     !input.nml: set coastal drift parameter to prevent grounding
@@ -297,7 +297,7 @@ program icebergs_driver
     !introduce gaussian bump to bathymetry
     a = 1000.0-bump_depth !max height(m)
     c = 5e3; !controls width
-    bx = 63.e3; by = 60.e3 !50.e3
+    bx = 63.e3; by = 60.e3
     do j=jsd,jed; do i=isd,ied
       xc=lon(i,j)-(gridres/2.); yc=lat(i,j)-(gridres/2.) !define at cell centers
       depth(i,j)=a*exp(-((xc-bx)*(xc-bx)/(2.*c*c)+(yc-by)*(yc-by)/(2.*c*c)))
diff --git a/tests/a68_test/data/.gitignore b/tests/a68_test/data/.gitignore
index e143a14..994796a 100644
--- a/tests/a68_test/data/.gitignore
+++ b/tests/a68_test/data/.gitignore
@@ -2,4 +2,5 @@
 a68_experiment_ocean_surf_vel_oscar_dec2020_HOURLY_ll_p125.nc
 a68_experiment_ssh_duacs_dec2020_HOURLY_ll_p125.nc
 a68_experiment_wind_vel_ncep_10m_dec2020_HOURLY_ll_p125.nc
-split_script.sh
\ No newline at end of file
+split_script.sh
+old/
\ No newline at end of file
diff --git a/tests/a68_test/long_run.nml b/tests/a68_test/long_run.nml
index f872eef..5566d06 100644
--- a/tests/a68_test/long_run.nml
+++ b/tests/a68_test/long_run.nml
@@ -3,15 +3,9 @@
 
 &icebergs_driver_nml
   a68_test=.true.
-  vert_int_ocean_vel=.false.!.true.
   !specify your data dir (ocean currents, winds, etc)
   data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68_test/data/'
-  Old_wrong_Rearth_and_SSH=.false.
-  !mom_Rearth=.true.
   Rearth=<re>
-  !6363827 !6.378e6
-  no_wind=.false.
-  tau_is_velocity=.true.!.false.
   ibdt=1800.0 !seconds
   ibuo=0.0 !ocean x velocity
   ibvo=0.0 !ocean y velocity
@@ -23,8 +17,9 @@
   saverestart=.true.!.false.
   halo=3
   debug=.true.
-  reverse_a68_forcings=.false.
-  transient_a68_data_start_ind=206 !330 !static=0, dec09_1PM=206, dec13_5PM=305, dec14_1PM=326, dec14_5PM=330
+
+  !if non-zero, use time-varying ocean currents, winds, and sea-surface height:
+  transient_a68_data_start_ind=206 !206=dec09_1PM=206
 /
 
 &icebergs_nml

From 42481026b263b421232216876515201aab0aab70 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Thu, 5 Jan 2023 13:58:26 -0500
Subject: [PATCH 344/361] doxygen fix?

---
 src/icebergs_framework.F90 | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 0affce1..574769b 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -619,7 +619,6 @@ module ice_bergs_framework
 !! \todo Remove when backward compatibility no longer needed
 logical :: orig_read=.false.
 
-!> Version of file provided by CPP macro (usually set to git hash)
 #ifdef _FILE_VERSION
 character(len=128) :: version = _FILE_VERSION !< Version of file
 #else

From 338e8b226fc7a3d19e0669d53d297780c1ee469d Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Thu, 5 Jan 2023 14:06:30 -0500
Subject: [PATCH 345/361] more doxy comments

---
 src/icebergs_framework.F90 | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 574769b..896c1fb 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -501,8 +501,8 @@ module ice_bergs_framework
   logical :: only_interactive_forces=.False. !< Icebergs only feel interactive forces, and not ocean, wind...
   logical :: halo_debugging=.False. !< Use for debugging halos (remove when its working)
   logical :: save_short_traj=.True. !< True saves only lon,lat,time,id in iceberg_trajectory.nc
-  character(len=70) :: traj_name='iceberg_trajectories.nc'
-  character(len=70) :: bond_traj_name='bond_trajectories.nc'
+  character(len=70) :: traj_name='iceberg_trajectories.nc' !< Name of output particle trajectory file
+  character(len=70) :: bond_traj_name='bond_trajectories.nc' !< Name of output bond trajectory file
   logical :: save_fl_traj=.True. ! True saves short traj, plus masses and footloose parameters in iceberg_trajectory.nc
   real :: save_all_traj_year=huge(0.0) ! Year at which all trajectories (for all berg areas) are saved
   logical :: save_nonfl_traj_by_class=.false. ! Save non-footloose trajectories based on initial mass class
@@ -619,6 +619,7 @@ module ice_bergs_framework
 !! \todo Remove when backward compatibility no longer needed
 logical :: orig_read=.false.
 
+!> Version of file provided by CPP macro (usually set to git hash)
 #ifdef _FILE_VERSION
 character(len=128) :: version = _FILE_VERSION !< Version of file
 #else
@@ -757,8 +758,8 @@ subroutine ice_bergs_framework_init(bergs, &
 logical :: only_interactive_forces=.False. ! Icebergs only feel interactive forces, and not ocean, wind...
 logical :: halo_debugging=.False. ! Use for debugging halos (remove when its working)
 logical :: save_short_traj=.True. ! True saves only lon,lat,time,id in iceberg_trajectory.nc
-character(len=70) :: traj_name='iceberg_trajectories.nc'
-character(len=70) :: bond_traj_name='bond_trajectories.nc'
+character(len=70) :: traj_name='iceberg_trajectories.nc' !< Name of output particle trajectory file
+character(len=70) :: bond_traj_name='bond_trajectories.nc' !< Name of output bond trajectory file
 logical :: save_fl_traj=.True. ! True saves short traj, plus masses and footloose parameters in iceberg_trajectory.nc
 real :: save_all_traj_year=huge(0.0) ! Year at which all trajectories (for all berg areas) are saved
 logical :: save_nonfl_traj_by_class=.false. ! Save non-footloose trajectories based on initial mass class

From cb1c2bc48a988c78d995e3f2713a5b33ec9dacdc Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Thu, 5 Jan 2023 16:26:10 -0500
Subject: [PATCH 346/361] docs: update CPP ifdef logic to set "file version"

doxygen is mishandling the CPP #ifdef logic and mishandling differently
on different platforms (possible dependence on the version of /lib/cpp).
The form of #ifdef A #else B #endif allowed doxygen to see two
declarations of a variable.  Refactoring the logic to #ifdef A #endif
seems to fix the problem.
---
 src/icebergs.F90           | 8 ++++----
 src/icebergs_framework.F90 | 9 ++++-----
 src/icebergs_io.F90        | 8 ++++----
 3 files changed, 12 insertions(+), 13 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index c720aa1..5715e7a 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -85,11 +85,11 @@ module ice_bergs
 real, parameter :: Cd_iv=0.9 !< (Vertical) Drag coefficient between bergs and sea-ice
 !TOM> no horizontal drag for sea ice! real, parameter :: Cd_ih=0.0012 !< (Horizontal) Drag coefficient between bergs and sea-ice
 
-#ifdef _FILE_VERSION
-character(len=128) :: version = _FILE_VERSION !< Version of file
-#else
-character(len=128) :: version = 'unknown' !< Version of file
+#ifndef _FILE_VERSION
+! Version of file provided can be set to git hash via a CPP macro but if not set we use 'unknown'
+#define _FILE_VERSION 'unknown'
 #endif
+character(len=128) :: version = _FILE_VERSION !< Version of file
 
 contains
 
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 896c1fb..38859ad 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -619,12 +619,11 @@ module ice_bergs_framework
 !! \todo Remove when backward compatibility no longer needed
 logical :: orig_read=.false.
 
-!> Version of file provided by CPP macro (usually set to git hash)
-#ifdef _FILE_VERSION
-character(len=128) :: version = _FILE_VERSION !< Version of file
-#else
-character(len=128) :: version = 'unknown' !< Version of file
+#ifndef _FILE_VERSION
+! Version of file provided can be set to git hash via a CPP macro but if not set we use 'unknown'
+#define _FILE_VERSION 'unknown'
 #endif
+character(len=128) :: version = _FILE_VERSION !< Version of file
 
 !> Set a value in the buffer at position (counter,n) after incrementing counter
 interface push_buffer_value
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index e9c4cd2..6ab8151 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -69,11 +69,11 @@ module ice_bergs_io
 integer :: clock_trw,clock_trp
 integer :: clock_btrw,clock_btrp !bond trajectories
 
-#ifdef _FILE_VERSION
-  character(len=128) :: version = _FILE_VERSION
-#else
-  character(len=128) :: version = 'unknown'
+#ifndef _FILE_VERSION
+! Version of file provided can be set to git hash via a CPP macro but if not set we use 'unknown'
+#define _FILE_VERSION 'unknown'
 #endif
+character(len=128) :: version = _FILE_VERSION !< Version of file
 
 contains
 

From 796d5919b956e03bbff669cc49f01eee5b9b4077 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Thu, 12 Jan 2023 16:52:18 +0000
Subject: [PATCH 347/361] Added script to download data for the a68_test.
 Simplified the conda environment tests/iceberg_env.yml. Edited some READMEs.

---
 tests/README                         |  25 +++
 tests/a68_test/.gitignore            |   5 +-
 tests/a68_test/README                |  10 +-
 tests/a68_test/data/.gitignore       |   6 -
 tests/a68_test/data/recombine_nc.sh  |  12 --
 tests/a68_test/get_data.sh           |   6 +
 tests/dem_cbeam_test/makeberg/README |   2 -
 tests/iceberg_env.yml                |  16 ++
 tests/iceberg_tests_env.yml          | 229 ---------------------------
 9 files changed, 56 insertions(+), 255 deletions(-)
 create mode 100644 tests/README
 delete mode 100644 tests/a68_test/data/.gitignore
 delete mode 100644 tests/a68_test/data/recombine_nc.sh
 create mode 100755 tests/a68_test/get_data.sh
 delete mode 100644 tests/dem_cbeam_test/makeberg/README
 create mode 100644 tests/iceberg_env.yml
 delete mode 100644 tests/iceberg_tests_env.yml

diff --git a/tests/README b/tests/README
new file mode 100644
index 0000000..997c61d
--- /dev/null
+++ b/tests/README
@@ -0,0 +1,25 @@
+These directories contain test cases for the updates to the iceberg module described in the following publications:
+
+[1] Huth, A., Adcroft, A., & Sergienko, O. (2022). Parameterizing Tabular-Iceberg Decay in an Ocean Model. Journal of Advances in Modeling Earth Systems, 14(3), e2021MS002869. doi:10.1029/2021MS002869
+
+[2] Huth, A., Adcroft, A., Sergienko, O., & Khan, N. (2022). Ocean currents break up a tabular iceberg. Science Advances, 8(42), eabq6974. doi:10.1126/sciadv.abq6974
+
+
+Test descriptions:
+
+footloose_tests/: Breakup of two icebergs via the footloose mechanism, as described in [1]
+
+collision_tests/: Two bonded-particle icebergs collide using either the original Kinematic Icebergs Dynamics (KID) bonded-particle model, KID with multiple-time-stepping (MTS), or the "improved" KID (iKID) that includes MTS with parallel-bond-style discrete element method (DEM) sub-steps (see [2]).
+
+dem_cbeam_test/ and dem_ssbeam_test/: check whether iKID can match analytical solutions for beam bending
+
+dem_ground_frac_test/: An iKID iceberg grounds and breaks into pieces
+
+a68_test/: iKID simulation of the two rift-calving breakups of iceberg A68a in December 2020, from [2]
+
+
+Each test contains python scripts to create the initial iceberg configuration (restart files) and to plot the results.
+To build an appropriate conda environment:
+
+conda env create --name icebergs --file=iceberg_env.yml
+conda activate icebergs
\ No newline at end of file
diff --git a/tests/a68_test/.gitignore b/tests/a68_test/.gitignore
index 3ca2294..9df8bdc 100644
--- a/tests/a68_test/.gitignore
+++ b/tests/a68_test/.gitignore
@@ -1 +1,4 @@
-input.nml
\ No newline at end of file
+input.nml
+orig_data/
+data/
+a68a_data.tar.gz
\ No newline at end of file
diff --git a/tests/a68_test/README b/tests/a68_test/README
index f770f07..029d2f6 100644
--- a/tests/a68_test/README
+++ b/tests/a68_test/README
@@ -1,11 +1,11 @@
 TO RUN THE EXPERIMENT IN THE PAPER:
+Huth, A., A. Adcroft, O. Sergienko, and N. Khan, 2022: Ocean currents break up a tabular iceberg. Science Advances, 8(42), eabq6974. doi:10.1126/sciadv.abq6974.
 
-I. Make the iceberg input files:
-   cd makeberg; ./RUN_for_paper; cd ..
+I. Download the data
+   ./get_data.sh
 
-II. Some quick processing of the hourly data
-   cd data; source recombine_nc.sh; cd ..
-   (note that the recombine_nc.sh requires cdo or nco -- edit it accordingly)
+II. Make the iceberg input files:
+   cd makeberg; ./RUN; cd ..
 
 III. The full run from the paper:
    ./long_run_for_paper.sh
diff --git a/tests/a68_test/data/.gitignore b/tests/a68_test/data/.gitignore
deleted file mode 100644
index 994796a..0000000
--- a/tests/a68_test/data/.gitignore
+++ /dev/null
@@ -1,6 +0,0 @@
-!*.nc
-a68_experiment_ocean_surf_vel_oscar_dec2020_HOURLY_ll_p125.nc
-a68_experiment_ssh_duacs_dec2020_HOURLY_ll_p125.nc
-a68_experiment_wind_vel_ncep_10m_dec2020_HOURLY_ll_p125.nc
-split_script.sh
-old/
\ No newline at end of file
diff --git a/tests/a68_test/data/recombine_nc.sh b/tests/a68_test/data/recombine_nc.sh
deleted file mode 100644
index 46e25ee..0000000
--- a/tests/a68_test/data/recombine_nc.sh
+++ /dev/null
@@ -1,12 +0,0 @@
-
-#using cdo
-cdo mergetime ./split_files/ocean*.nc a68_experiment_ocean_surf_vel_oscar_dec2020_HOURLY_ll_p125.nc
-cdo mergetime ./split_files/ssh*.nc a68_experiment_ssh_duacs_dec2020_HOURLY_ll_p125.nc
-cdo mergetime ./split_files/wind*.nc a68_experiment_wind_vel_ncep_10m_dec2020_HOURLY_ll_p125.nc
-
-#using ncrcat (nco)
-#ncrcat ./split_files/ocean00000?.nc a68_experiment_ocean_surf_vel_oscar_dec2020_HOURLY_ll_p125.nc
-#ncrcat ./split_files/ssh00000?.nc a68_experiment_ssh_duacs_dec2020_HOURLY_ll_p125.nc
-#ncrcat ./split_files/wind00000?.nc a68_experiment_wind_vel_ncep_10m_dec2020_HOURLY_ll_p125.nc
-
-ln -s a68_experiment_ocean_surf_vel_oscar_dec2020_HOURLY_ll_p125.nc ../../../postprocessing/data/a68_experiment_ocean_surf_vel_oscar_dec2020_HOURLY_ll_p125.nc
diff --git a/tests/a68_test/get_data.sh b/tests/a68_test/get_data.sh
new file mode 100755
index 0000000..4dd5315
--- /dev/null
+++ b/tests/a68_test/get_data.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+#download and extract data for the A68a experiment from the GFDL FTP server:
+wget ftp://ftp.gfdl.noaa.gov/perm/Alexander.Huth/a68a_data.tar.gz
+tar -xvf a68a_data.tar.gz
+rm a68a_data.tar.gz
diff --git a/tests/dem_cbeam_test/makeberg/README b/tests/dem_cbeam_test/makeberg/README
deleted file mode 100644
index 9a03aec..0000000
--- a/tests/dem_cbeam_test/makeberg/README
+++ /dev/null
@@ -1,2 +0,0 @@
-RUN makes a 30x3 element conglomerate berg. The leftmost column of elements are static. The rightmost column will be assigned an additional shear force during the model run. This is the cantilever beam test from Section 3.2 of Wang 2020 "A scale-invariant bonded particle model for simulating large deformation and failure of continua"
-
diff --git a/tests/iceberg_env.yml b/tests/iceberg_env.yml
new file mode 100644
index 0000000..457788e
--- /dev/null
+++ b/tests/iceberg_env.yml
@@ -0,0 +1,16 @@
+name: icebergs
+channels:
+  - conda-forge
+dependencies:
+  - pip=22.0.3=pyhd8ed1ab_0
+  - pip:
+    - pyproj==2.6.1.post1
+  - python=3.8.12
+  - netcdf4=1.5.3
+  - matplotlib=3.2.2
+  - xarray=0.17.0
+  - cartopy = 0.18.0
+  - scipy = 1.5.3
+  - esmf=8.0.1=nompi_hcaa3220_2
+  - esmpy=8.0.1=nompi_py38h5410a82_2
+  - numpy=1.18.1=py38h8854b6b_1
\ No newline at end of file
diff --git a/tests/iceberg_tests_env.yml b/tests/iceberg_tests_env.yml
deleted file mode 100644
index cb8ad10..0000000
--- a/tests/iceberg_tests_env.yml
+++ /dev/null
@@ -1,229 +0,0 @@
-name: icebergs
-channels:
-  - conda-forge
-  - defaults
-dependencies:
-  - conda-forge/linux-64::git-lfs==3.1.2=ha770c72_0
-  - conda-forge/linux-64::_libgcc_mutex==0.1=conda_forge
-  - conda-forge/linux-64::ca-certificates==2021.10.8=ha878542_0
-  - conda-forge/linux-64::ld_impl_linux-64==2.36.1=hea4e1c9_2
-  - conda-forge/linux-64::libgfortran4==7.5.0=h14aa051_20
-  - conda-forge/linux-64::libstdcxx-ng==11.2.0=he4da1e4_12
-  - conda-forge/linux-64::pandoc==2.17.1.1=ha770c72_0
-  - conda-forge/linux-64::libgfortran-ng==7.5.0=h14aa051_20
-  - conda-forge/linux-64::libgomp==11.2.0=h1d223b6_12
-  - conda-forge/linux-64::_openmp_mutex==4.5=1_gnu
-  - conda-forge/linux-64::libgcc-ng==11.2.0=h1d223b6_12
-  - conda-forge/linux-64::bzip2==1.0.8=h7f98852_4
-  - conda-forge/linux-64::c-ares==1.18.1=h7f98852_0
-  - conda-forge/linux-64::expat==2.4.4=h9c3ff4c_0
-  - conda-forge/linux-64::fribidi==1.0.10=h36c2ea0_0
-  - conda-forge/linux-64::geos==3.8.1=he1b5a44_0
-  - conda-forge/linux-64::giflib==5.2.1=h36c2ea0_2
-  - conda-forge/linux-64::gmp==6.2.1=h58526e2_0
-  - conda-forge/linux-64::icu==67.1=he1b5a44_0
-  - conda-forge/linux-64::jbig==2.1=h7f98852_2003
-  - conda-forge/linux-64::jpeg==9e=h7f98852_0
-  - conda-forge/linux-64::lerc==3.0=h9c3ff4c_0
-  - conda-forge/linux-64::libdeflate==1.10=h7f98852_0
-  - conda-forge/linux-64::libev==4.33=h516909a_1
-  - conda-forge/linux-64::libffi==3.4.2=h7f98852_5
-  - conda-forge/linux-64::libglu==9.0.0=he1b5a44_1001
-  - conda-forge/linux-64::libiconv==1.16=h516909a_0
-  - conda-forge/linux-64::libimagequant==2.17.0=h7f98852_1
-  - conda-forge/linux-64::libnsl==2.0.0=h7f98852_0
-  - conda-forge/linux-64::libopenblas==0.3.12=pthreads_hb3c22a3_1
-  - conda-forge/linux-64::libsodium==1.0.18=h36c2ea0_1
-  - conda-forge/linux-64::libuuid==2.32.1=h7f98852_1000
-  - conda-forge/linux-64::libwebp-base==1.2.2=h7f98852_1
-  - conda-forge/linux-64::libzlib==1.2.11=h36c2ea0_1013
-  - conda-forge/linux-64::lz4-c==1.9.3=h9c3ff4c_1
-  - conda-forge/linux-64::ncurses==6.3=h9c3ff4c_0
-  - conda-forge/linux-64::openssl==3.0.0=h7f98852_2
-  - conda-forge/linux-64::pthread-stubs==0.4=h36c2ea0_1001
-  - conda-forge/linux-64::tbb==2020.2=h4bd325d_4
-  - conda-forge/linux-64::xorg-kbproto==1.0.7=h7f98852_1002
-  - conda-forge/linux-64::xorg-libice==1.0.10=h7f98852_0
-  - conda-forge/linux-64::xorg-libxau==1.0.9=h7f98852_0
-  - conda-forge/linux-64::xorg-libxdmcp==1.1.3=h7f98852_0
-  - conda-forge/linux-64::xorg-renderproto==0.11.1=h7f98852_1002
-  - conda-forge/linux-64::xorg-xextproto==7.3.0=h7f98852_1002
-  - conda-forge/linux-64::xorg-xproto==7.0.31=h7f98852_1007
-  - conda-forge/linux-64::xz==5.2.5=h516909a_1
-  - conda-forge/linux-64::yaml==0.2.5=h7f98852_2
-  - conda-forge/linux-64::libblas==3.9.0=8_openblas
-  - conda-forge/linux-64::libedit==3.1.20191231=he28a2e2_2
-  - conda-forge/linux-64::libxcb==1.13=h7f98852_1004
-  - conda-forge/linux-64::readline==8.1=h46c0cb4_0
-  - conda-forge/linux-64::tk==8.6.12=h27826a3_0
-  - conda-forge/linux-64::xorg-fixesproto==5.0=h7f98852_1002
-  - conda-forge/linux-64::xorg-libsm==1.2.3=hd9c2040_1000
-  - conda-forge/linux-64::zeromq==4.3.4=h9c3ff4c_1
-  - conda-forge/linux-64::zlib==1.2.11=h36c2ea0_1013
-  - conda-forge/linux-64::zstd==1.5.2=ha95c52a_0
-  - conda-forge/linux-64::hdf4==4.2.15=h10796ff_3
-  - conda-forge/linux-64::hdf5==1.10.6=nompi_h3c11f04_101
-  - conda-forge/linux-64::krb5==1.19.2=h48eae69_3
-  - conda-forge/linux-64::libcblas==3.9.0=8_openblas
-  - conda-forge/linux-64::liblapack==3.9.0=8_openblas
-  - conda-forge/linux-64::libnghttp2==1.46.0=ha19adfc_0
-  - conda-forge/linux-64::libpng==1.6.37=h21135ba_2
-  - conda-forge/linux-64::libssh2==1.10.0=ha35d2d1_2
-  - conda-forge/linux-64::libtiff==4.3.0=h542a066_3
-  - conda-forge/linux-64::libxml2==2.9.10=h68273f3_2
-  - conda-forge/linux-64::mesalib==18.3.1=h590aaf7_0
-  - conda-forge/linux-64::sqlite==3.37.0=h9cd32fc_0
-  - conda-forge/linux-64::xorg-libx11==1.7.2=h7f98852_0
-  - conda-forge/linux-64::freetype==2.10.4=h0708190_1
-  - conda-forge/linux-64::lcms2==2.12=hddcbb42_0
-  - conda-forge/linux-64::libcurl==7.81.0=h494985f_0
-  - conda-forge/linux-64::libwebp==1.2.2=h3452ae3_0
-  - conda-forge/linux-64::openjpeg==2.4.0=hb52868f_1
-  - conda-forge/linux-64::python==3.8.12=h0744224_3_cpython
-  - conda-forge/linux-64::xorg-libxext==1.3.4=h7f98852_1
-  - conda-forge/linux-64::xorg-libxfixes==5.0.3=h7f98852_1004
-  - conda-forge/linux-64::xorg-libxrender==0.9.10=h7f98852_1003
-  - conda-forge/linux-64::xorg-libxt==1.2.1=h7f98852_2
-  - conda-forge/noarch::attrs==21.4.0=pyhd8ed1ab_0
-  - conda-forge/noarch::backcall==0.2.0=pyh9f0ad1d_0
-  - conda-forge/noarch::backports==1.0=py_2
-  - conda-forge/noarch::charset-normalizer==2.0.12=pyhd8ed1ab_0
-  - conda-forge/noarch::click==7.1.2=pyh9f0ad1d_0
-  - conda-forge/noarch::cloudpickle==2.0.0=pyhd8ed1ab_0
-  - conda-forge/noarch::colorama==0.4.4=pyh9f0ad1d_0
-  - conda-forge/linux-64::curl==7.81.0=h494985f_0
-  - conda-forge/noarch::cycler==0.11.0=pyhd8ed1ab_0
-  - conda-forge/noarch::decorator==5.1.1=pyhd8ed1ab_0
-  - conda-forge/noarch::defusedxml==0.7.1=pyhd8ed1ab_0
-  - conda-forge/noarch::entrypoints==0.4=pyhd8ed1ab_0
-  - conda-forge/noarch::executing==0.8.2=pyhd8ed1ab_0
-  - conda-forge/noarch::flit-core==3.6.0=pyhd8ed1ab_0
-  - conda-forge/linux-64::fontconfig==2.13.1=hba837de_1005
-  - conda-forge/noarch::fsspec==2022.1.0=pyhd8ed1ab_0
-  - conda-forge/noarch::heapdict==1.0.1=py_0
-  - conda-forge/noarch::idna==3.3=pyhd8ed1ab_0
-  - conda-forge/noarch::ipython_genutils==0.2.0=py_1
-  - conda-forge/noarch::json5==0.9.5=pyh9f0ad1d_0
-  - conda-forge/noarch::locket==0.2.0=py_2
-  - conda-forge/noarch::nest-asyncio==1.5.4=pyhd8ed1ab_0
-  - conda-forge/noarch::pandocfilters==1.5.0=pyhd8ed1ab_0
-  - conda-forge/noarch::parso==0.8.3=pyhd8ed1ab_0
-  - conda-forge/noarch::pickleshare==0.7.5=py_1003
-  - conda-forge/linux-64::proj==7.1.1=h966b41f_3
-  - conda-forge/noarch::prometheus_client==0.13.1=pyhd8ed1ab_0
-  - conda-forge/noarch::ptyprocess==0.7.0=pyhd3deb0d_0
-  - conda-forge/noarch::pure_eval==0.2.2=pyhd8ed1ab_0
-  - conda-forge/noarch::pycparser==2.21=pyhd8ed1ab_0
-  - conda-forge/noarch::pyparsing==3.0.7=pyhd8ed1ab_0
-  - conda-forge/noarch::pyshp==2.2.0=pyhd8ed1ab_0
-  - conda-forge/linux-64::python_abi==3.8=2_cp38
-  - conda-forge/noarch::pytz==2021.3=pyhd8ed1ab_0
-  - conda-forge/noarch::send2trash==1.8.0=pyhd8ed1ab_0
-  - conda-forge/noarch::six==1.16.0=pyh6c4a22f_0
-  - conda-forge/noarch::sortedcontainers==2.4.0=pyhd8ed1ab_0
-  - conda-forge/noarch::tblib==1.7.0=pyhd8ed1ab_0
-  - conda-forge/noarch::testpath==0.5.0=pyhd8ed1ab_0
-  - conda-forge/noarch::toolz==0.11.2=pyhd8ed1ab_0
-  - conda-forge/noarch::traitlets==5.1.1=pyhd8ed1ab_0
-  - conda-forge/noarch::typing==3.10.0.0=pyhd8ed1ab_0
-  - conda-forge/noarch::typing_extensions==4.1.1=pyha770c72_0
-  - conda-forge/noarch::webencodings==0.5.1=py_1
-  - conda-forge/noarch::websocket-client==1.2.3=pyhd8ed1ab_0
-  - conda-forge/noarch::wheel==0.37.1=pyhd8ed1ab_0
-  - conda-forge/linux-64::xorg-libxmu==1.1.3=h7f98852_0
-  - conda-forge/noarch::zipp==3.7.0=pyhd8ed1ab_1
-  - conda-forge/noarch::asttokens==2.0.5=pyhd8ed1ab_0
-  - conda-forge/noarch::babel==2.9.1=pyh44b312d_0
-  - conda-forge/linux-64::certifi==2021.10.8=py38h578d9bd_1
-  - conda-forge/linux-64::cffi==1.15.0=py38h3931269_0
-  - conda-forge/linux-64::cytoolz==0.11.2=py38h497a2fe_1
-  - conda-forge/linux-64::debugpy==1.5.1=py38h709712a_0
-  - conda-forge/noarch::docrep==0.2.7=py_0
-  - conda-forge/linux-64::future==0.18.2=py38h578d9bd_4
-  - conda-forge/linux-64::importlib-metadata==4.11.1=py38h578d9bd_0
-  - conda-forge/noarch::importlib_resources==5.4.0=pyhd8ed1ab_0
-  - conda-forge/linux-64::jedi==0.18.1=py38h578d9bd_0
-  - conda-forge/linux-64::jupyter_core==4.9.2=py38h578d9bd_0
-  - conda-forge/linux-64::kiwisolver==1.3.2=py38h1fd1430_1
-  - conda-forge/linux-64::libnetcdf==4.7.4=nompi_h56d31a8_107
-  - conda-forge/linux-64::markupsafe==2.0.1=py38h497a2fe_1
-  - conda-forge/noarch::matplotlib-inline==0.1.3=pyhd8ed1ab_0
-  - conda-forge/linux-64::mistune==0.8.4=py38h497a2fe_1005
-  - conda-forge/linux-64::msgpack-python==1.0.3=py38h1fd1430_0
-  - conda-forge/linux-64::numpy==1.18.1=py38h8854b6b_1
-  - conda-forge/linux-64::occt==7.4.0=h9121d39_3
-  - conda-forge/noarch::packaging==21.3=pyhd8ed1ab_0
-  - conda-forge/noarch::partd==1.2.0=pyhd8ed1ab_0
-  - conda-forge/noarch::pexpect==4.8.0=pyh9f0ad1d_2
-  - conda-forge/linux-64::pillow==9.0.1=py38he2f12e7_1
-  - conda-forge/linux-64::psutil==5.9.0=py38h497a2fe_0
-  - conda-forge/linux-64::pycosat==0.6.3=py38h497a2fe_1009
-  - conda-forge/linux-64::pyproj==2.6.1.post1=py38h56787f0_3
-  - conda-forge/linux-64::pyrsistent==0.18.1=py38h497a2fe_0
-  - conda-forge/linux-64::pysocks==1.7.1=py38h578d9bd_4
-  - conda-forge/noarch::python-dateutil==2.8.2=pyhd8ed1ab_0
-  - conda-forge/linux-64::pyyaml==6.0=py38h497a2fe_3
-  - conda-forge/linux-64::pyzmq==22.3.0=py38h2035c66_1
-  - conda-forge/linux-64::ruamel_yaml==0.15.80=py38h497a2fe_1006
-  - conda-forge/linux-64::setuptools==59.8.0=py38h578d9bd_0
-  - conda-forge/linux-64::sniffio==1.2.0=py38h578d9bd_2
-  - conda-forge/noarch::tomlkit==0.9.2=pyha770c72_0
-  - conda-forge/linux-64::tornado==6.1=py38h497a2fe_2
-  - conda-forge/noarch::tqdm==4.62.3=pyhd8ed1ab_0
-  - conda-forge/noarch::zict==2.0.0=py_0
-  - conda-forge/linux-64::anyio==3.5.0=py38h578d9bd_0
-  - conda-forge/linux-64::argon2-cffi-bindings==21.2.0=py38h497a2fe_1
-  - conda-forge/noarch::backports.functools_lru_cache==1.6.4=pyhd8ed1ab_0
-  - conda-forge/noarch::bleach==4.1.0=pyhd8ed1ab_0
-  - conda-forge/linux-64::bottleneck==1.3.2=py38hab2c0dc_2
-  - conda-forge/linux-64::brotlipy==0.7.0=py38h497a2fe_1003
-  - conda-forge/linux-64::cftime==1.5.0=py38hb5d20a5_0
-  - conda-forge/linux-64::conda-package-handling==1.7.3=py38h497a2fe_1
-  - defaults/linux-64::cryptography==36.0.0=py38h9ce1e76_0
-  - conda-forge/noarch::dask-core==2021.4.0=pyhd8ed1ab_0
-  - conda-forge/noarch::deprecation==2.1.0=pyh9f0ad1d_0
-  - conda-forge/linux-64::gmsh==4.6.0=hd134328_0
-  - conda-forge/linux-64::h5py==2.10.0=nompi_py38hafa665b_105
-  - conda-forge/noarch::jinja2==3.0.3=pyhd8ed1ab_0
-  - conda-forge/noarch::jsonschema==4.4.0=pyhd8ed1ab_0
-  - conda-forge/noarch::jupyter_client==7.1.2=pyhd8ed1ab_0
-  - conda-forge/linux-64::matplotlib-base==3.2.2=py38h5d868c9_1
-  - conda-forge/linux-64::netcdf-fortran==4.5.3=nompi_hfef6a68_101
-  - conda-forge/linux-64::pandas==1.0.1=py38hb3f55d8_0
-  - conda-forge/noarch::pip==22.0.3=pyhd8ed1ab_0
-  - conda-forge/noarch::pygments==2.11.2=pyhd8ed1ab_0
-  - conda-forge/linux-64::scipy==1.5.3=py38h828c644_0
-  - conda-forge/linux-64::shapely==1.7.1=py38ha11d057_1
-  - conda-forge/noarch::stack_data==0.2.0=pyhd8ed1ab_0
-  - conda-forge/linux-64::terminado==0.13.1=py38h578d9bd_0
-  - conda-forge/noarch::argon2-cffi==21.3.0=pyhd8ed1ab_0
-  - conda-forge/linux-64::bokeh==2.4.2=py38h578d9bd_0
-  - conda-forge/linux-64::cartopy==0.18.0=py38hc1e57b6_5
-  - conda-forge/linux-64::distributed==2021.4.1=py38h578d9bd_1
-  - conda-forge/linux-64::esmf==8.0.1=nompi_hcaa3220_2
-  - conda-forge/noarch::jupyter-packaging==0.11.1=pyhd8ed1ab_0
-  - conda-forge/noarch::jupyterlab_pygments==0.1.2=pyh9f0ad1d_0
-  - conda-forge/linux-64::matplotlib==3.2.2=1
-  - conda-forge/noarch::nbformat==5.1.3=pyhd8ed1ab_0
-  - conda-forge/linux-64::netcdf4==1.5.3=nompi_py38hfd55d45_105
-  - conda-forge/noarch::pyopenssl==22.0.0=pyhd8ed1ab_0
-  - conda-forge/noarch::wcwidth==0.2.5=pyh9f0ad1d_2
-  - conda-forge/noarch::xarray==0.17.0=pyhd8ed1ab_0
-  - conda-forge/noarch::cf_xarray==0.7.0=pyhd8ed1ab_0
-  - conda-forge/noarch::dask==2021.4.0=pyhd8ed1ab_0
-  - conda-forge/linux-64::esmpy==8.0.1=nompi_py38h5410a82_2
-  - conda-forge/noarch::nbclient==0.5.11=pyhd8ed1ab_0
-  - conda-forge/noarch::prompt-toolkit==3.0.27=pyha770c72_0
-  - conda-forge/noarch::urllib3==1.26.8=pyhd8ed1ab_1
-  - conda-forge/linux-64::ipython==8.0.1=py38h578d9bd_1
-  - conda-forge/linux-64::nbconvert==6.4.2=py38h578d9bd_0
-  - conda-forge/noarch::requests==2.27.1=pyhd8ed1ab_0
-  - conda-forge/noarch::xesmf==0.5.3=pyhd8ed1ab_0
-  - conda-forge/noarch::xgcm==0.5.1=py_0
-  - conda-forge/linux-64::ipykernel==6.9.1=py38he5a9106_0
-  - conda-forge/noarch::jupyter_server==1.13.5=pyhd8ed1ab_1
-  - conda-forge/noarch::jupyterlab_server==2.10.3=pyhd8ed1ab_0
-  - conda-forge/noarch::notebook==6.4.8=pyha770c72_0
-  - conda-forge/noarch::nbclassic==0.3.5=pyhd8ed1ab_0
-  - conda-forge/noarch::jupyterlab==3.0.14=pyhd8ed1ab_0
-prefix: /ncrc/home1/Alexander.Huth/miniconda3/envs/icebergs

From 66637d698913e3cc73b0145a6d9026ef310164c0 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Wed, 18 Jan 2023 16:30:29 -0500
Subject: [PATCH 348/361] removed redundant file

---
 build/mkmkf            |   2 +-
 driver/driver_data.f90 | 184 -----------------------------------------
 2 files changed, 1 insertion(+), 185 deletions(-)
 delete mode 100644 driver/driver_data.f90

diff --git a/build/mkmkf b/build/mkmkf
index bb29be6..6aa5125 100644
--- a/build/mkmkf
+++ b/build/mkmkf
@@ -1,3 +1,3 @@
 rm -f path_names
-../../mkmf/bin/list_paths ../../FMS/{mpp,diag_manager,time_manager,include,memutils,constants,platform,fms,random_numbers,mosaic,exchange} ../src/ ../driver/ ../tests/collision_test/
+../../mkmf/bin/list_paths ../../FMS/{mpp,diag_manager,time_manager,include,memutils,constants,platform,fms,random_numbers,mosaic,exchange} ../src/ ../driver/
 ../../mkmf/bin/mkmf -t ../../mkmf/templates/ncrc-intel.mk -c "-Duse_libMPI -Duse_netCDF" -p bergs.x path_names
\ No newline at end of file
diff --git a/driver/driver_data.f90 b/driver/driver_data.f90
deleted file mode 100644
index 37061b1..0000000
--- a/driver/driver_data.f90
+++ /dev/null
@@ -1,184 +0,0 @@
-module driver_data
-
-use fms_mod, only : read_data
-use fms_mod, only : file_exist
-use fms_mod, only : field_exist
-use fms_mod, only : error_mesg
-use fms_mod, only : FATAL
-use mpp_domains_mod, only : domain2D
-use mpp_mod, only : mpp_pe
-use mpp_mod, only : mpp_root_pe
-use mpp_mod, only: mpp_sync
-use constants_mod, only: pi
-use netcdf
-!include 'netcdf.inc'
-
-implicit none
-
-contains
-
-!> Determine dimensions of A68 background grid
-  subroutine a68_dims(data_dir,ni,nj)
-! Arguments
-    character(len=*) :: data_dir
-    integer, intent(out):: ni,nj
-! Local variables
-    character(len=1000):: infile
-    integer(kind=4) :: ncid
-    integer :: status
-
-    infile=trim(trim(data_dir)//'a68_experiment_ll_p125_grid.nc')
-
-!Open netCDF file
-    call handle_err(nf90_open(infile, nf90_nowrite, ncid))
-!Inquire about the dimensions
-    call handle_err(nf90_inquire_dimension(ncid,1,len=nj))
-    call handle_err(nf90_inquire_dimension(ncid,2,len=ni))
-!Close netCDF file
-    call handle_err(nf90_close(ncid))
-  end subroutine a68_dims
-
-!> Handle for errors
-  subroutine handle_err(status)
-    integer, intent (in) :: status
-
-    if(status /= nf90_noerr) then
-      print *, trim(nf90_strerror(status))
-      stop "Stopped"
-    end if
-  end subroutine handle_err
-
-!>A68 grid setup
-  subroutine a68_prep(data_dir,mpp_domain,lon,lat,dx,dy,area,REarth)
-! Arguments
-    character(len=*) :: data_dir
-    type(domain2D) :: mpp_domain
-    real :: lon(:,:) !< Longitude or position in x
-    real :: lat(:,:) !< Latitude or position in y
-    real :: dx(:,:) !< Length of northern edge of cell (m)
-    real :: dy(:,:) !< Length of eatern edge of cell (m)
-    real :: area(:,:) !< Area of cell (m2)
-    real :: REarth
-! Local variables
-    character(len=1000) :: filename
-    real, parameter :: gres=0.125
-
-!Grid specs: lon,lat,dx,dy,area
-    filename=trim(trim(data_dir)//'a68_experiment_ll_p125_grid.nc')
-    call read_a68_data(mpp_domain,filename,'longitude',lon)
-    lon=lon+360
-    call read_a68_data(mpp_domain,filename,'latitude',lat)
-
-    call haversine_dist_and_area(REarth,gres,lon,lat,dx,dy,area)
-  end subroutine a68_prep
-
-!> Haversine distance and area
-  subroutine haversine_dist_and_area(REarth,gres,lon1,lat1,dx,dy,area)
-! Arguments
-    real, intent(in) :: REarth    !Earth radius (m)
-    real, intent(in) :: gres      !grid resolution (degrees)
-    real, intent(in) :: lon1(:,:) !grid longitude
-    real, intent(in) :: lat1(:,:) !grid latitude
-    real, intent(out) :: dx(:,:)  !grid dx (m)
-    real, intent(out) :: dy(:,:)   !grid dy (m)
-    real, intent(out) :: area(:,:) !grid area (m^2)
-! Local variables
-    real, parameter :: pi_180=pi/180.
-    real, dimension(size(lon1,1),size(lon1,2)) :: lon2,lat2,p1,p2,dp,dm,a,c
-
-!calculate dx
-    lon2=lon1-gres
-    lat2=lat1
-    p1 = lat1 * pi_180; p2 = lat2 * pi_180; dp = (lat2-lat1) * pi_180; dm = (lon2-lon1) * pi_180
-    a = sin(0.5*dp)**2. + cos(p1) * cos(p2) * sin(0.5*dm)**2.; c = 2. * atan2(sqrt(a), sqrt(1-a))
-    dx = REarth * c
-
-!calculate dy
-    lat2=lat1-gres
-    lon2=lon1
-    p1 = lat1 * pi_180; p2 = lat2 * pi_180; dp = (lat2-lat1) * pi_180; dm = (lon2-lon1) * pi_180
-    a = sin(0.5*dp)**2. + cos(p1) * cos(p2) * sin(0.5*dm)**2.; c = 2. * atan2(sqrt(a), sqrt(1-a))
-    dy = REarth * c
-
-!calculate area
-    area=pi_180*(REarth**2.)*abs(sin(lat1*pi_180)-sin(lat2*pi_180))*abs(gres)
-  end subroutine haversine_dist_and_area
-
-
-!> Read in static (not time-varying) data for A68 experiment from file
-  subroutine read_a68_data(domain,filename,var,field)
-! Arguments
-    type(domain2D) :: domain !< Parallel decomposition
-    character(len=*), intent(in) :: filename, var
-    real :: field(:,:)
-
-    call mpp_sync()
-    if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') 'icebergs_driver: Reading ',var
-    if (file_exist(filename)) then
-      if (field_exist(filename, var)) then
-        call read_data(filename, var, field, domain)
-      else
-        if (mpp_pe().eq.mpp_root_pe()) then
-          call error_mesg('icebergs_driver:','Variable missing in file!', FATAL)
-        endif
-      endif
-    else
-      if (mpp_pe().eq.mpp_root_pe()) then
-        call error_mesg('icebergs_driver:','File for variable not found!', FATAL)
-      endif
-    endif
-    call mpp_sync()
-  end subroutine read_a68_data
-
-!> Calls read_a68_data for wind velocity, ocean velocity, and ssh
-  subroutine a68_prep_3d(data_dir,mpp_domain,tauxa_hr,tauya_hr,uo_hr,vo_hr,ssh_hr)
-! Arguments
-    character(len=*) :: data_dir
-
-    type(domain2D) :: mpp_domain
-    real :: tauxa_hr(:,:,:) !< Zonal jra55 wind velocity (m/s, hourly)
-    real :: tauya_hr(:,:,:) !< Meridional jra55 wind velocity (m/s, hourly)
-    real :: uo_hr(:,:,:) !< Zonal OSCAR ocean surface velocity (m/s, hourly)
-    real :: vo_hr(:,:,:) !< Meridional OSCAR ocean surface velocity (m/s, hourly)
-    real :: ssh_hr(:,:,:) !< Effective sea surface height (m, hourly)
-! Local variables
-    character(len=1000) :: filename
-
-    filename=trim(trim(data_dir)//'a68_experiment_wind_vel_ncep_10m_dec2020_HOURLY_ll_p125.nc')
-    call read_a68_data_3d(mpp_domain,filename,'ua',tauxa_hr)
-    call read_a68_data_3d(mpp_domain,filename,'va',tauya_hr)
-
-    filename=trim(trim(data_dir)//'a68_experiment_ocean_surf_vel_oscar_dec2020_HOURLY_ll_p125.nc')
-    call read_a68_data_3d(mpp_domain,filename,'uo',uo_hr)
-    call read_a68_data_3d(mpp_domain,filename,'vo',vo_hr)
-
-    filename=trim(trim(data_dir)//'a68_experiment_ssh_duacs_dec2020_HOURLY_ll_p125.nc')
-    call read_a68_data_3d(mpp_domain,filename,'SSH',ssh_hr)
-  end subroutine a68_prep_3d
-
-!> Read in time-varying A68 data
-  subroutine read_a68_data_3d(domain,filename,var,field)
-! Arguments
-    type(domain2D) :: domain !< Parallel decomposition
-    character(len=*), intent(in) :: filename, var
-    real :: field(:,:,:)
-
-    call mpp_sync()
-    if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') 'icebergs_driver: Reading ',var
-    if (file_exist(filename)) then
-      if (field_exist(filename, var)) then
-        call read_data(filename, var, field, domain)
-      else
-        if (mpp_pe().eq.mpp_root_pe()) then
-          call error_mesg('icebergs_driver:','Variable missing in file!', FATAL)
-        endif
-      endif
-    else
-      if (mpp_pe().eq.mpp_root_pe()) then
-        call error_mesg('icebergs_driver:','File for variable not found!', FATAL)
-      endif
-    endif
-    call mpp_sync()
-  end subroutine read_a68_data_3d
-
-end module driver_data

From a7c0676940be6e18e50887df984d170ef926d4cb Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Fri, 3 Mar 2023 11:36:09 -0500
Subject: [PATCH 349/361] Replaced type(real) with real in iceberg.F90
 subroutine calve_fl_icebergs. Added a .nml that was missing from the
 footloose test in previous commits. A few empty, but necessary, directories
 were missing from the test cases in previous commits, so modified the
 makeberg run files to create these directories.

---
 src/icebergs.F90                        |   8 +-
 tests/a68_test/makeberg/RUN             |   3 +
 tests/collision_tests/.gitignore        |   1 +
 tests/collision_tests/input.nml         | 162 ------------------------
 tests/collision_tests/makeberg/RUN      |   4 +
 tests/dem_cbeam_test/makeberg/RUN       |   3 +
 tests/dem_ground_frac_test/makeberg/RUN |   3 +
 tests/dem_ssbeam_test/makeberg/RUN      |   3 +
 tests/footloose_tests/makeberg/RUN      |   4 +-
 9 files changed, 24 insertions(+), 167 deletions(-)
 create mode 100644 tests/collision_tests/.gitignore
 delete mode 100644 tests/collision_tests/input.nml

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 5715e7a..62223bd 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -6410,10 +6410,10 @@ subroutine calve_fl_icebergs(bergs,pberg,k,l_b,fl_disp_x,fl_disp_y,berg_from_bit
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
   type(iceberg), pointer :: pberg !< Parent berg
-  type(real),intent(in) :: k !< Number of child bergs to calve
-  type(real),intent(in) :: l_b !< The width, and 1/3 the length, of a child berg
-  type(real) :: fl_disp_x !< Child berg x-displacement from parent berg
-  type(real) :: fl_disp_y !< Child berg x-displacement from parent berg
+  real,intent(in) :: k !< Number of child bergs to calve
+  real,intent(in) :: l_b !< The width, and 1/3 the length, of a child berg
+  real :: fl_disp_x !< Child berg x-displacement from parent berg
+  real :: fl_disp_y !< Child berg x-displacement from parent berg
   logical, optional, intent(in) :: berg_from_bits !< True to create new berg from footloose bits
   ! Local variables
   type(iceberg) :: cberg ! The new child berg
diff --git a/tests/a68_test/makeberg/RUN b/tests/a68_test/makeberg/RUN
index 2cbc068..c2d37d8 100755
--- a/tests/a68_test/makeberg/RUN
+++ b/tests/a68_test/makeberg/RUN
@@ -1,3 +1,6 @@
+mkdir output_files
+mkdir ./../INPUT
+mkdir ./../RESTART
 rm ./output_files/Generic*
 
 # THIS IS THE BERG USED IN HUTH ET AL, 2022 OCEAN CURRENTS BREAK UP A TABULAR ICEBERG. SCIENCE ADVANCES:
diff --git a/tests/collision_tests/.gitignore b/tests/collision_tests/.gitignore
new file mode 100644
index 0000000..3ca2294
--- /dev/null
+++ b/tests/collision_tests/.gitignore
@@ -0,0 +1 @@
+input.nml
\ No newline at end of file
diff --git a/tests/collision_tests/input.nml b/tests/collision_tests/input.nml
deleted file mode 100644
index c806ac5..0000000
--- a/tests/collision_tests/input.nml
+++ /dev/null
@@ -1,162 +0,0 @@
-!!KID, bergs_chksum: write_restart berg chksum=-1441819690 chksum2=-1441819690 chksum3=1124700946 chksum4=1124700946 chksum5=0 #=16
-
-&icebergs_driver_nml
-  ni=20 !number of elements, x direction
-  nj=20 !number of elements, y direction
-  ibdt=3600.0 !seconds
-  ibuo=0.2 !ocean x velocity
-  ibvo=0.2 !ocean y velocity
-  ibui=0.0 !ice x velocity
-  ibvi=0.0 !ice y velocity
-  ibhrs=48 !total simulation hours
-  nmax=99999999 !max number of timesteps
-  saverestart=.true.
-  halo=3
-  debug=.false.
-  collision_test=.true. !specific to the current test, must be true here
-/
-
-&icebergs_nml
-
-    traj_name=MTS_KID.nc
-    bond_traj_name=MTS_KID_bonds.nc
-
-    !defaults given in parentheses:
-    explicit_inner_mts=.true.
-    mts=.true. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
-    mts_sub_steps=60 !1 !30 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
-    contact_distance=1.75e3 !2.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
-    contact_spring_coef=1.e-7!(default=spring_coeff) Berg spring coeff for collisions
-    debug_write=.false. !(F)sets traj_sample_hours=traj_write_hours & includes halo bergs in write
-    remove_unused_bergs=.false. !(T) remove unneeded bergs after PEs transfers
-    force_convergence=.true. !(F) experimental MTS convergence scheme to better conserve momentum during collisions
-    convergence_tolerance=1e-8 !(1.e-8) tolerance for the MTS force_convergence scheme
-
-    halo=3 !(4) halo width
-    Lx=20000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
-    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
-    grid_is_regular=.True. !(T) Point in cell can be found assuming regular Cartesian grid
-    hexagonal_icebergs=.true. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
-    Static_icebergs=.False. ! (T) True=icebergs do no move
-
-    rho_bergs=850. ! (850) iceberg density
-    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
-    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
-    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
-    tangental_damping_coef=2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
-    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
-    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
-    bergy_bit_erosion_fraction=0. ! (0.) Fraction of erosion melt flux to divert to bergy bits
-    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
-    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
-    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
-    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
-    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
-    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
-    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
-    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
-    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
-    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
-    add_weight_to_ocean=.true. ! (T) Add weight of icebergs + bits to ocean
-    passive_mode=.false. ! (F) Add weight of icebergs + bits to ocean
-    time_average_weight=.false. ! (F) Time average the weight on the ocean
-    speed_limit=0. ! (0.) CFL speed limit for a berg
-    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
-    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
-    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
-    coastal_drift=0.4 !(0.)Vel added to currents to cause bergs to drift away from land cells
-    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
-    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
-    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
-    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
-    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
-    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
-    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
-    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
-    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
-    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
-    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
-    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
-    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
-    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
-    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
-    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
-    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
-    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
-    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
-    set_melt_rates_to_zero=.true.!(F)For testing, thermodyn is run, but all melt rates=0
-
-    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
-    interactive_icebergs_on=.true. ! (F) Turn on/off interactions between icebergs
-    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
-    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
-    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
-    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
-    max_bonds=6 ! (6) Max # of bonds passed between processors
-    internal_bergs_for_drag=.false. !(F) True reduces side drag for bonded bergs in momentum eqn.
-
-    verbose=.true. !(F) Be verbose to stderr
-    verbose_hrs=24 ! (24) Period between verbose messages
-    traj_sample_hrs=0.5 !1 !(24) sampling period for trajectory storage
-    traj_write_hrs=-1 ! (480) Period for writing sampled trajectories to disk
-    budget=.true. !(T) Calculate budgets
-    debug=.false. !(F) Turn on debugging
-    really_debug=.false. !(F) Turn on debugging
-    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
-    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
-
-    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
-    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
-    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
-
-    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
-    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
-    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
-    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
-    length_for_manually_initialize_bonds=800.0 !(1e3)Dist b/w bergs to init bonds manually
-    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
-    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
-    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
-    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
-    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
-    orig_read=.false. !(F) Legacy option that does nothing
-    read_old_restarts=.false. ! (F) Legacy option that does nothing
-
-    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
-    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
-    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
-    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
-    do_unit_tests=.true. !(F) Conduct some unit tests
-    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
-
-    ! Mass thresholds between iceberg classes (kg):
-    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
-    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-
-    ! Fraction of calving to apply to this class (non-dim):
-    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
-    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
-
-    ! Ratio between effective and real iceberg mass (non-dim):
-    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
-    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
-
-    ! Total thickness of newly calved bergs (m):
-    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
-    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
-
-/
-
-&diag_manager_nml
-/
-
- &fms_io_nml
-         fms_netcdf_restart=.false.
-         threading_read='multi'
-/
-
- &fms_nml
-       clock_grain='MODULE'
-       domains_stack_size = 2000000
-       clock_flags='SYNC'
-/
diff --git a/tests/collision_tests/makeberg/RUN b/tests/collision_tests/makeberg/RUN
index dd66e2f..7c8292c 100755
--- a/tests/collision_tests/makeberg/RUN
+++ b/tests/collision_tests/makeberg/RUN
@@ -1,3 +1,7 @@
+mkdir output_files
+mkdir ./../INPUT
+mkdir ./../RESTART
+
 ./makeberg.py
 
 rm ./output_files/Generic*
diff --git a/tests/dem_cbeam_test/makeberg/RUN b/tests/dem_cbeam_test/makeberg/RUN
index 9456794..4f0942a 100755
--- a/tests/dem_cbeam_test/makeberg/RUN
+++ b/tests/dem_cbeam_test/makeberg/RUN
@@ -1,3 +1,6 @@
+mkdir output_files
+mkdir ./../INPUT
+mkdir ./../RESTART
 rm ./output_files/Generic*
 ./makeberg.py -t=1
 cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
diff --git a/tests/dem_ground_frac_test/makeberg/RUN b/tests/dem_ground_frac_test/makeberg/RUN
index 520d671..ec3fc16 100755
--- a/tests/dem_ground_frac_test/makeberg/RUN
+++ b/tests/dem_ground_frac_test/makeberg/RUN
@@ -1,3 +1,6 @@
+mkdir output_files
+mkdir ./../INPUT
+mkdir ./../RESTART
 rm ./output_files/Generic*
 ./makeberg.py
 cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
diff --git a/tests/dem_ssbeam_test/makeberg/RUN b/tests/dem_ssbeam_test/makeberg/RUN
index 9456794..4f0942a 100755
--- a/tests/dem_ssbeam_test/makeberg/RUN
+++ b/tests/dem_ssbeam_test/makeberg/RUN
@@ -1,3 +1,6 @@
+mkdir output_files
+mkdir ./../INPUT
+mkdir ./../RESTART
 rm ./output_files/Generic*
 ./makeberg.py -t=1
 cp ./output_files/Generic_icebergs.res.nc ./../INPUT/icebergs.res.nc
diff --git a/tests/footloose_tests/makeberg/RUN b/tests/footloose_tests/makeberg/RUN
index 750e29e..d52ee05 100755
--- a/tests/footloose_tests/makeberg/RUN
+++ b/tests/footloose_tests/makeberg/RUN
@@ -1,4 +1,6 @@
-
+mkdir output_files
+mkdir ./../INPUT
+mkdir ./../RESTART
 rm ./output_files/Generic*
 ./makeberg.py
 

From 738b131f0274aea3e51a74b564303f3440c90650 Mon Sep 17 00:00:00 2001
From: Uriel Ramirez <uriel.ramirez@noaa.gov>
Date: Mon, 20 Mar 2023 17:12:19 -0400
Subject: [PATCH 350/361] initial icebergs_io removal

---
 src/icebergs.F90           |    5 -
 src/icebergs_fms2io.F90    | 2496 ++++++++++++++++++++++++++++++++++++
 src/icebergs_fmsio.F90     | 2496 ++++++++++++++++++++++++++++++++++++
 src/icebergs_framework.F90 |    8 +-
 src/icebergs_io.F90        | 2493 +----------------------------------
 5 files changed, 4997 insertions(+), 2501 deletions(-)
 create mode 100644 src/icebergs_fms2io.F90
 create mode 100644 src/icebergs_fmsio.F90

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 62223bd..64f95fd 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -4,11 +4,7 @@ module ice_bergs
 ! This file is part of NOAA-GFDL/icebergs. See LICENSE.md for the license.
 
 use constants_mod, only: pi, omega, HLF
-use fms_mod, only: open_namelist_file, check_nml_error, close_file
-use fms_mod, only: field_exist, get_global_att_value
 use fms_mod, only: stdlog, stderr, error_mesg, FATAL, WARNING
-use fms_mod, only: write_version_number, read_data, write_data, file_exist
-use mosaic_mod, only: get_mosaic_ntiles, get_mosaic_ncontacts
 use mpp_mod, only: mpp_npes, mpp_pe, mpp_root_pe, mpp_sum, mpp_min, mpp_max, NULL_PE
 use mpp_mod, only: mpp_send, mpp_recv, mpp_sync_self, mpp_chksum, mpp_sync
 use mpp_mod, only: mpp_clock_begin, mpp_clock_end, mpp_clock_id
@@ -17,7 +13,6 @@ module ice_bergs
 use random_numbers_mod, only: constructSeed
 use mpp_mod, only: mpp_gather
 use fms_mod, only: clock_flag_default
-use fms_io_mod, only: get_instance_filename
 use mpp_domains_mod, only: domain2D, mpp_update_domains, mpp_define_domains
 use mpp_parameter_mod, only: CGRID_NE, BGRID_NE, CORNER, AGRID
 use mpp_domains_mod, only: mpp_get_compute_domain, mpp_get_data_domain
diff --git a/src/icebergs_fms2io.F90 b/src/icebergs_fms2io.F90
new file mode 100644
index 0000000..58587fd
--- /dev/null
+++ b/src/icebergs_fms2io.F90
@@ -0,0 +1,2496 @@
+!> Handles reading/writing of restart files and trajectory-based diagnostic files
+module ice_bergs_fms2io
+
+! This file is part of NOAA-GFDL/icebergs. See LICENSE.md for the license.
+
+use mpp_domains_mod, only: domain2D
+use mpp_domains_mod, only: mpp_domain_is_tile_root_pe,mpp_get_domain_tile_root_pe
+use mpp_domains_mod, only: mpp_get_tile_pelist,mpp_get_tile_npes,mpp_get_io_domain,mpp_get_tile_id
+
+use mpp_mod, only: mpp_npes, mpp_pe, mpp_root_pe, mpp_sum, mpp_min, mpp_max, NULL_PE
+use mpp_mod, only: mpp_send, mpp_recv, mpp_gather, mpp_chksum, mpp_sync_self
+use mpp_mod, only: COMM_TAG_11, COMM_TAG_12, COMM_TAG_13, COMM_TAG_14
+
+use fms_mod, only: stdlog, stderr, error_mesg, FATAL, WARNING, NOTE
+use fms_mod, only: field_exist, file_exist, read_data, write_data
+
+use fms_io_mod, only: get_instance_filename
+use fms_io_mod, only : save_restart, restart_file_type, free_restart_type, set_meta_global
+use fms_io_mod, only : register_restart_axis, register_restart_field, set_domain, nullify_domain
+use fms_io_mod, only : read_unlimited_axis =>read_compressed, field_exist, get_field_size
+
+use mpp_mod,    only : mpp_clock_begin, mpp_clock_end, mpp_clock_id
+use mpp_mod,    only : CLOCK_COMPONENT, CLOCK_SUBCOMPONENT, CLOCK_LOOP
+use fms_mod,    only : clock_flag_default
+
+use time_manager_mod, only: time_type, get_date, get_time, set_date, operator(-)
+
+use ice_bergs_framework, only: icebergs_gridded, xyt, bond_xyt, iceberg, icebergs, buffer, bond
+use ice_bergs_framework, only: pack_traj_into_buffer2,unpack_traj_from_buffer2
+use ice_bergs_framework, only: find_cell,find_cell_by_search,count_bergs,is_point_in_cell,pos_within_cell,append_posn
+use ice_bergs_framework, only: count_bonds, form_a_bond, find_individual_iceberg
+use ice_bergs_framework, only: push_posn
+use ice_bergs_framework, only: add_new_berg_to_list,destroy_iceberg
+use ice_bergs_framework, only: increase_ibuffer,grd_chksum2,grd_chksum3
+use ice_bergs_framework, only: sum_mass,sum_heat,bilin
+!params !Niki: write a subroutine to get these
+use ice_bergs_framework, only: nclasses, buffer_width, buffer_width_traj, buffer_width_bond_traj
+use ice_bergs_framework, only: verbose, really_debug, debug, restart_input_dir,make_calving_reproduce
+use ice_bergs_framework, only: ignore_ij_restart, use_slow_find,generate_test_icebergs,print_berg
+use ice_bergs_framework, only: force_all_pes_traj
+use ice_bergs_framework, only: check_for_duplicates_in_parallel
+use ice_bergs_framework, only: split_id, id_from_2_ints, generate_id
+! for MTS/DEM/fracture/footloose:
+use ice_bergs_framework, only: mts,save_bond_traj
+use ice_bergs_framework, only: push_bond_posn, append_bond_posn
+use ice_bergs_framework, only: pack_bond_traj_into_buffer2,unpack_bond_traj_from_buffer2
+use ice_bergs_framework, only: dem, iceberg_bonds_on
+use ice_bergs_framework, only: footloose
+
+
+implicit none ; private
+
+include 'netcdf.inc'
+
+public ice_bergs_io_init
+public read_restart_bergs, write_restart, write_trajectory, write_bond_trajectory
+public read_restart_calving, read_restart_bonds
+public read_ocean_depth
+
+!Local Vars
+integer, parameter :: file_format_major_version=0
+integer, parameter :: file_format_minor_version=1
+!I/O vars
+type(domain2d), pointer, save :: io_domain=>NULL()
+integer, save :: io_tile_id(1), io_tile_root_pe, io_npes
+integer, allocatable,save :: io_tile_pelist(:)
+logical :: is_io_tile_root_pe = .true.
+
+integer :: clock_trw,clock_trp
+integer :: clock_btrw,clock_btrp !bond trajectories
+
+#ifndef _FILE_VERSION
+! Version of file provided can be set to git hash via a CPP macro but if not set we use 'unknown'
+#define _FILE_VERSION 'unknown'
+#endif
+character(len=128) :: version = _FILE_VERSION !< Version of file
+
+contains
+
+!> Initialize parallel i/o
+subroutine ice_bergs_io_init(bergs, io_layout)
+type(icebergs), pointer :: bergs !< Icebergs container
+integer, intent(in) :: io_layout(2) !< Decomposition of i/o processors
+
+integer :: np
+integer :: stdlogunit, stderrunit
+
+  ! Get the stderr and stdlog unit numbers
+  stderrunit=stderr()
+  stdlogunit=stdlog()
+  write(stdlogunit,*) "ice_bergs_framework: "//trim(version)
+
+  !I/O layout init
+  io_tile_id=-1
+  io_domain => mpp_get_io_domain(bergs%grd%domain)
+  if(associated(io_domain)) then
+     io_tile_id = mpp_get_tile_id(io_domain)
+     is_io_tile_root_pe = mpp_domain_is_tile_root_pe(io_domain)
+     io_tile_root_pe = mpp_get_domain_tile_root_pe(io_domain)
+     np=mpp_get_tile_npes(io_domain)
+     allocate(io_tile_pelist(np))
+     call mpp_get_tile_pelist(io_domain,io_tile_pelist)
+     io_npes = io_layout(1)*io_layout(2)
+  endif
+
+  clock_trw=mpp_clock_id( 'Icebergs-traj write', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+  clock_trp=mpp_clock_id( 'Icebergs-traj prepare', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+  clock_btrw=mpp_clock_id( 'Iceberg-bonds-traj write', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+  clock_btrp=mpp_clock_id( 'Iceberg-bonds-traj prepare', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+
+end subroutine ice_bergs_io_init
+
+!> Write an iceberg restart file
+subroutine write_restart(bergs, time_stamp)
+! Arguments
+type(icebergs), pointer :: bergs !< Icebergs container
+character(len=*), intent(in), optional :: time_stamp !< Timestamp for restart file
+
+! Local variables
+type(bond), pointer :: current_bond
+integer :: i,j,id
+character(len=35) :: filename
+character(len=35) :: filename_bonds
+type(iceberg), pointer :: this=>NULL()
+integer :: stderrunit
+!I/O vars
+type(restart_file_type) :: bergs_restart
+type(restart_file_type) :: bergs_bond_restart
+type(restart_file_type) :: calving_restart
+integer :: nbergs, nbonds
+integer :: n_static_bergs
+logical :: check_bond_quality
+type(icebergs_gridded), pointer :: grd
+real, allocatable, dimension(:) :: lon,          &
+                                   lat,          &
+                                   uvel,         &
+                                   vvel,         &
+                                   mass,         &
+                                   axn,          &
+                                   ayn,          &
+                                   bxn,          &
+                                   byn,          &
+                                   thickness,    &
+                                   width,        &
+                                   length,       &
+                                   fl_k,         &
+                                   start_lon,    &
+                                   start_lat,    &
+                                   start_day,    &
+                                   start_mass,   &
+                                   mass_scaling, &
+                                   mass_of_bits, &
+                                   mass_of_fl_bits, &
+                                   mass_of_fl_bergy_bits, &
+                                   static_berg,  &
+                                   heat_density, &
+                                   axn_fast,     &
+                                   ayn_fast,     &
+                                   bxn_fast,     &
+                                   byn_fast,     &
+                                   ang_vel,      &
+                                   ang_accel,    &
+                                   rot,          &
+                                   tangd1,       &
+                                   tangd2,       &
+                                   nstress,      &
+                                   sstress,      &
+                                   rel_rotation
+
+integer, allocatable, dimension(:) :: ine,              &
+                                      jne,              &
+                                      id_cnt,           &
+                                      id_ij,            &
+                                      start_year,       &
+                                      first_id_cnt,     &
+                                      other_id_cnt,     &
+                                      first_id_ij,      &
+                                      other_id_ij,      &
+                                      first_berg_jne,         &
+                                      first_berg_ine,         &
+                                      other_berg_jne,         &
+                                      other_berg_ine,         &
+                                      broken
+
+
+integer :: grdi, grdj
+
+! Get the stderr unit number
+ stderrunit=stderr()
+
+
+  ! For convenience
+  grd=>bergs%grd
+
+  !First add the bergs on the io_tile_root_pe (if any) to the I/O list
+  nbergs = 0
+  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this))
+      nbergs = nbergs +1
+      this=>this%next
+    enddo
+  enddo ; enddo
+
+   allocate(lon(nbergs))
+   allocate(lat(nbergs))
+   allocate(uvel(nbergs))
+   allocate(vvel(nbergs))
+   allocate(mass(nbergs))
+   allocate(axn(nbergs))    !Alon
+   allocate(ayn(nbergs))    !Alon
+   allocate(bxn(nbergs)) !Alon
+   allocate(byn(nbergs)) !Alon
+   allocate(thickness(nbergs))
+   allocate(width(nbergs))
+   allocate(length(nbergs))
+   allocate(start_lon(nbergs))
+   allocate(start_lat(nbergs))
+   allocate(start_day(nbergs))
+   allocate(start_mass(nbergs))
+   allocate(mass_scaling(nbergs))
+   allocate(mass_of_bits(nbergs))
+   allocate(heat_density(nbergs))
+   allocate(static_berg(nbergs))
+
+   allocate(ine(nbergs))
+   allocate(jne(nbergs))
+   allocate(start_year(nbergs))
+   allocate(id_cnt(nbergs))
+   allocate(id_ij(nbergs))
+
+   if (bergs%footloose) then
+     allocate(fl_k(nbergs))
+     allocate(mass_of_fl_bits(nbergs))
+     allocate(mass_of_fl_bergy_bits(nbergs))
+   end if
+
+   if (mts) then
+     allocate(axn_fast(nbergs))
+     allocate(ayn_fast(nbergs))
+     allocate(bxn_fast(nbergs))
+     allocate(byn_fast(nbergs))
+   endif
+   if (dem) then
+     allocate(ang_vel(nbergs))
+     allocate(ang_accel(nbergs))
+     allocate(rot(nbergs))
+   endif
+
+  filename = trim("icebergs.res.nc")
+  call set_domain(bergs%grd%domain)
+  call register_restart_axis(bergs_restart,filename,'i',nbergs)
+  call set_meta_global(bergs_restart,'file_format_major_version',ival=(/file_format_major_version/))
+  call set_meta_global(bergs_restart,'file_format_minor_version',ival=(/file_format_minor_version/))
+  call set_meta_global(bergs_restart,'time_axis',ival=(/0/))
+
+  !Now start writing in the io_tile_root_pe if there are any bergs in the I/O list
+
+  ! Define Variables
+  id = register_restart_field(bergs_restart,filename,'lon',lon,longname='longitude',units='degrees_E')
+  id = register_restart_field(bergs_restart,filename,'lat',lat,longname='latitude',units='degrees_N')
+  id = register_restart_field(bergs_restart,filename,'uvel',uvel,longname='zonal velocity',units='m/s')
+  id = register_restart_field(bergs_restart,filename,'vvel',vvel,longname='meridional velocity',units='m/s')
+  id = register_restart_field(bergs_restart,filename,'mass',mass,longname='mass',units='kg')
+  if (.not. bergs%Runge_not_Verlet) then
+    id = register_restart_field(bergs_restart,filename,'axn',axn,longname='explicit zonal acceleration',units='m/s^2')
+    id = register_restart_field(bergs_restart,filename,'ayn',ayn,longname='explicit meridional acceleration',units='m/s^2')
+    id = register_restart_field(bergs_restart,filename,'bxn',bxn,longname='implicit zonal acceleration',units='m/s^2')
+    id = register_restart_field(bergs_restart,filename,'byn',byn,longname='implicit meridional acceleration',units='m/s^2')
+  endif
+  id = register_restart_field(bergs_restart,filename,'ine',ine,longname='i index',units='none')
+  id = register_restart_field(bergs_restart,filename,'jne',jne,longname='j index',units='none')
+  id = register_restart_field(bergs_restart,filename,'thickness',thickness,longname='thickness',units='m')
+  id = register_restart_field(bergs_restart,filename,'width',width,longname='width',units='m')
+  id = register_restart_field(bergs_restart,filename,'length',length,longname='length',units='m')
+  id = register_restart_field(bergs_restart,filename,'start_lon',start_lon, &
+                                            longname='longitude of calving location',units='degrees_E')
+  id = register_restart_field(bergs_restart,filename,'start_lat',start_lat, &
+                                            longname='latitude of calving location',units='degrees_N')
+  id = register_restart_field(bergs_restart,filename,'start_year',start_year, &
+                                            longname='calendar year of calving event', units='years')
+  id = register_restart_field(bergs_restart,filename,'id_cnt',id_cnt, &
+                                            longname='counter component of iceberg id', units='dimensionless')
+  id = register_restart_field(bergs_restart,filename,'id_ij',id_ij, &
+                                            longname='position component of iceberg id', units='dimensionless')
+  id = register_restart_field(bergs_restart,filename,'start_day',start_day, &
+                                            longname='year day of calving event',units='days')
+  id = register_restart_field(bergs_restart,filename,'start_mass',start_mass, &
+                                            longname='initial mass of calving berg',units='kg')
+  id = register_restart_field(bergs_restart,filename,'mass_scaling',mass_scaling, &
+                                            longname='scaling factor for mass of calving berg',units='none')
+  id = register_restart_field(bergs_restart,filename,'mass_of_bits',mass_of_bits, &
+                                            longname='mass of bergy bits',units='kg')
+  id = register_restart_field(bergs_restart,filename,'heat_density',heat_density, &
+                                            longname='heat density',units='J/kg')
+
+  if (bergs%footloose) then
+    id = register_restart_field(bergs_restart,filename,'fl_k',fl_k,longname='footloose calving k',units='m')
+    id = register_restart_field(bergs_restart,filename,'mass_of_fl_bits',mass_of_fl_bits, &
+      longname='mass of footloose bits',units='kg')
+    id = register_restart_field(bergs_restart,filename,'mass_of_fl_bergy_bits',mass_of_fl_bergy_bits, &
+      longname='mass of bergy bits associated with footloose bits',units='kg')
+   end if
+
+  if (mts) then
+    id = register_restart_field(bergs_restart,filename,'axn_fast',axn_fast,&
+      longname='sub-step explicit zonal acceleration',units='m/s^2')
+    id = register_restart_field(bergs_restart,filename,'ayn_fast',ayn_fast,&
+      longname='sub-step explicit meridional acceleration',units='m/s^2')
+    id = register_restart_field(bergs_restart,filename,'bxn_fast',bxn_fast,&
+      longname='sub-step implicit zonal acceleration',units='m/s^2')
+    id = register_restart_field(bergs_restart,filename,'byn_fast',byn_fast,&
+      longname='sub-step implicit meridional acceleration',units='m/s^2')
+  endif
+
+  if (dem) then
+    id = register_restart_field(bergs_restart,filename,'ang_vel',ang_vel,&
+      longname='dem angular velocity',units='rad/s')
+    id = register_restart_field(bergs_restart,filename,'ang_accel',ang_accel,&
+      longname='dem angular acceleration',units='rad/s^2')
+    id = register_restart_field(bergs_restart,filename,'rot',rot,&
+      longname='dem accumulated rotation',units='rad')
+  endif
+
+  !Checking if any icebergs are static in order to decide whether to save static_berg
+  n_static_bergs = 0
+  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this))
+      n_static_bergs=n_static_bergs+this%static_berg
+      this=>this%next
+    enddo
+  enddo ; enddo
+  call mpp_sum(n_static_bergs)
+  if (n_static_bergs .gt. 0) &
+    id = register_restart_field(bergs_restart,filename,'static_berg',static_berg, &
+                                              longname='static_berg',units='dimensionless')
+
+  ! Write variables
+
+  i = 0
+  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
+    this=>bergs%list(grdi,grdj)%first
+    do while(associated(this))
+      i = i + 1
+      lon(i) = this%lon; lat(i) = this%lat
+      uvel(i) = this%uvel; vvel(i) = this%vvel
+      ine(i) = this%ine; jne(i) = this%jne
+      mass(i) = this%mass; thickness(i) = this%thickness
+      axn(i) = this%axn; ayn(i) = this%ayn !Added by Alon
+      bxn(i) = this%bxn; byn(i) = this%byn !Added by Alon
+      width(i) = this%width; length(i) = this%length
+      start_lon(i) = this%start_lon; start_lat(i) = this%start_lat
+      start_year(i) = this%start_year; start_day(i) = this%start_day
+      start_mass(i) = this%start_mass; mass_scaling(i) = this%mass_scaling
+      static_berg(i) = this%static_berg
+      call split_id(this%id, id_cnt(i), id_ij(i))
+      mass_of_bits(i) = this%mass_of_bits
+      heat_density(i) = this%heat_density
+
+      if (bergs%footloose) then
+        fl_k(i) = this%fl_k
+        mass_of_fl_bits(i) = this%mass_of_fl_bits
+        mass_of_fl_bergy_bits(i) = this%mass_of_fl_bergy_bits
+      end if
+
+      if (mts) then
+        axn_fast(i) = this%axn_fast
+        ayn_fast(i) = this%ayn_fast
+        bxn_fast(i) = this%bxn_fast
+        byn_fast(i) = this%byn_fast
+      endif
+      if (dem) then
+        ang_vel(i) = this%ang_vel
+        ang_accel(i) = this%ang_accel
+        rot(i) = this%rot
+      endif
+      this=>this%next
+    enddo
+  enddo ; enddo
+
+
+  call save_restart(bergs_restart, time_stamp)
+  call free_restart_type(bergs_restart)
+
+  deallocate(              &
+             lon,          &
+             lat,          &
+             uvel,         &
+             vvel,         &
+             mass,         &
+             axn,          &
+             ayn,          &
+             bxn,          &
+             byn,          &
+             thickness,    &
+             width,        &
+             length,       &
+             start_lon,    &
+             start_lat,    &
+             start_day,    &
+             start_mass,   &
+             mass_scaling, &
+             mass_of_bits, &
+             static_berg,  &
+             heat_density)
+
+  if (bergs%footloose) then
+    deallocate(                   &
+                 fl_k,            &
+                 mass_of_fl_bits, &
+                 mass_of_fl_bergy_bits)
+  end if
+  if (mts) then
+    deallocate(            &
+             axn_fast,     &
+             ayn_fast,     &
+             bxn_fast,     &
+             byn_fast)
+  endif
+  if (dem) then
+    deallocate(            &
+             ang_vel,      &
+             ang_accel,    &
+             rot)
+  endif
+
+  deallocate(           &
+             ine,       &
+             jne,       &
+             id_cnt,    &
+             id_ij,     &
+             start_year )
+
+  call nullify_domain()
+
+!########## Creating bond restart file ######################
+
+  !Allocating restart memory for bond related variables.
+  nbonds=0
+  if (bergs%iceberg_bonds_on) then
+    check_bond_quality=.true.
+    call count_bonds(bergs, nbonds,check_bond_quality)
+
+  allocate(first_id_cnt(nbonds))
+  allocate(other_id_cnt(nbonds))
+  allocate(first_id_ij(nbonds))
+  allocate(other_id_ij(nbonds))
+  allocate(first_berg_ine(nbonds))
+  allocate(first_berg_jne(nbonds))
+  allocate(other_berg_ine(nbonds))
+  allocate(other_berg_jne(nbonds))
+
+  if (dem) then
+    allocate(tangd1(nbonds))
+    allocate(tangd2(nbonds))
+    allocate(nstress(nbonds))
+    allocate(sstress(nbonds))
+    allocate(rel_rotation(nbonds))
+    allocate(broken(nbonds))
+  endif
+
+  call get_instance_filename("bonds_iceberg.res.nc", filename_bonds)
+  call set_domain(bergs%grd%domain)
+  call register_restart_axis(bergs_bond_restart,filename,'i',nbonds)
+  call set_meta_global(bergs_bond_restart,'file_format_major_version',ival=(/file_format_major_version/))
+  call set_meta_global(bergs_bond_restart,'file_format_minor_version',ival=(/file_format_minor_version/))
+  call set_meta_global(bergs_bond_restart,'time_axis',ival=(/0/))
+
+  !Now start writing in the io_tile_root_pe if there are any bergs in the I/O list
+
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'first_berg_ine',first_berg_ine,longname='iceberg ine of first berg in bond',units='dimensionless')
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'first_berg_jne',first_berg_jne,longname='iceberg jne of first berg in bond',units='dimensionless')
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'first_id_cnt',first_id_cnt,longname='counter component of iceberg id first berg in bond',units='dimensionless')
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'first_id_ij',first_id_ij,longname='position component of iceberg id first berg in bond',units='dimensionless')
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'other_berg_ine',other_berg_ine,longname='iceberg ine of second berg in bond',units='dimensionless')
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'other_berg_jne',other_berg_jne,longname='iceberg jne of second berg in bond',units='dimensionless')
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'other_id_cnt',other_id_cnt,longname='counter component of iceberg id second berg in bond',units='dimensionless')
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'other_id_ij',other_id_ij,longname='position component of iceberg id second berg in bond',units='dimensionless')
+
+  if (dem) then
+    id = register_restart_field(bergs_bond_restart,filename_bonds,'tangd1',tangd1,&
+      longname='zonal tangential displacement',units='m')
+    id = register_restart_field(bergs_bond_restart,filename_bonds,'tangd2',tangd2,&
+      longname='meridional tangential displacement',units='m')
+    id = register_restart_field(bergs_bond_restart,filename_bonds,'nstress',nstress,&
+      longname='normal stress',units='Pa')
+    id = register_restart_field(bergs_bond_restart,filename_bonds,'sstress',sstress,&
+      longname='shear stress',units='Pa')
+    id = register_restart_field(bergs_bond_restart,filename_bonds,'rel_rotation',rel_rotation,&
+      longname='relative rotation',units='rad')
+     id = register_restart_field(bergs_bond_restart,filename_bonds,'broken',broken,&
+      longname='broken status',units='none')
+  endif
+
+  ! Write variables
+
+  i = 0
+  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
+    this=>bergs%list(grdi,grdj)%first
+    do while(associated(this)) !Loops over all bergs
+      current_bond=>this%first_bond
+      do while (associated(current_bond)) ! loop over all bonds
+        i = i + 1
+        first_berg_ine(i)=this%ine
+        first_berg_jne(i)=this%jne
+        call split_id( this%id, first_id_cnt(i), first_id_ij(i) )
+        call split_id( current_bond%other_id, other_id_cnt(i), other_id_ij(i) )
+        other_berg_ine(i)=current_bond%other_berg%ine
+        other_berg_jne(i)=current_bond%other_berg%jne
+
+        if (dem) then
+          tangd1(i)=current_bond%tangd1
+          tangd2(i)=current_bond%tangd2
+          nstress(i)=current_bond%nstress
+          sstress(i)=current_bond%sstress
+          rel_rotation(i)=current_bond%rel_rotation
+          broken(i)=current_bond%broken
+        endif
+
+        current_bond=>current_bond%next_bond
+      enddo !End of loop over bonds
+      this=>this%next
+    enddo!End of loop over bergs
+  enddo; enddo !End of loop over grid
+
+  call save_restart(bergs_bond_restart, time_stamp)
+  call free_restart_type(bergs_bond_restart)
+
+
+  deallocate(first_id_cnt,          &
+             other_id_cnt,          &
+             first_id_ij,           &
+             other_id_ij,           &
+             first_berg_ine,        &
+             first_berg_jne,        &
+             other_berg_ine,        &
+             other_berg_jne)
+  if (dem) then
+    deallocate(                     &
+             tangd1,                &
+             tangd2,                &
+             nstress,               &
+             sstress,               &
+             rel_rotation,          &
+             broken)
+  endif
+
+  call nullify_domain()
+  endif
+
+  ! Write stored ice
+  filename='calving.res.nc'
+  if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(stderrunit,'(2a)') 'KID, write_restart: writing ',filename
+  call grd_chksum3(bergs%grd, bergs%grd%stored_ice, 'write stored_ice')
+  call grd_chksum2(bergs%grd, bergs%grd%stored_heat, 'write stored_heat')
+  if (bergs%tau_calving>0.) then
+    call grd_chksum2(bergs%grd, bergs%grd%rmean_calving, 'write mean calving')
+    call grd_chksum2(bergs%grd, bergs%grd%rmean_calving_hflx, 'write mean calving_hflx')
+  endif
+
+  call set_domain(bergs%grd%domain)
+  id = register_restart_field(calving_restart,filename,'stored_ice',bergs%grd%stored_ice,longname='STORED_ICE',units='none')
+  id = register_restart_field(calving_restart,filename,'stored_heat',bergs%grd%stored_heat,longname='STORED_HEAT',units='none')
+  id = register_restart_field(calving_restart,filename,'iceberg_counter_grd',bergs%grd%iceberg_counter_grd,longname='ICEBERG_COUNTER_GRD',units='none')
+  if (bergs%tau_calving>0.) then
+    id = register_restart_field(calving_restart,filename,'rmean_calving',bergs%grd%rmean_calving,longname='RMEAN_CALVING',units='none')
+    id = register_restart_field(calving_restart,filename,'rmean_calving_hflx',bergs%grd%rmean_calving_hflx,longname='RMEAN_CALVING_HFLX',units='none')
+  endif
+
+  call save_restart(calving_restart, time_stamp)
+  call free_restart_type(calving_restart)
+
+end subroutine write_restart
+
+!> Find the last berg in a linked list.
+function last_berg(berg)
+! Arguments
+type(iceberg), pointer :: berg !< Pointer to an iceberg
+type(iceberg), pointer :: last_berg
+! Local variables
+
+  last_berg=>berg
+  do while (associated(last_berg%next))
+    last_berg=>last_berg%next
+  enddo
+
+end function last_berg
+
+!> Read a real value from a file and optionally return a default value if variable is missing
+real function get_real_from_file(ncid, varid, k, value_if_not_in_file)
+integer, intent(in) :: ncid !< file id
+integer, intent(in) :: varid !< variable id
+integer, intent(in) :: k !< index
+real, optional :: value_if_not_in_file !< default value, if variable missing in file
+
+if (varid<1.and.present(value_if_not_in_file)) then
+  get_real_from_file=value_if_not_in_file
+else
+  get_real_from_file=get_double(ncid, ncid, k)
+endif
+end function get_real_from_file
+
+!> Read an iceberg restart file
+subroutine read_restart_bergs(bergs,Time)
+! Arguments
+type(icebergs), pointer :: bergs !< Icebergs container
+type(time_type), intent(in) :: Time !< Model time
+! Local variables
+integer :: k, siz(4), nbergs_in_file, nbergs_read
+logical :: lres, found_restart, found, replace_iceberg_num
+logical :: explain
+logical :: multiPErestart  ! Not needed with new restart read; currently kept for compatibility
+real :: lon0, lon1, lat0, lat1
+real :: pos_is_good, pos_is_good_all_pe
+character(len=53) :: filename, filename_base
+type(icebergs_gridded), pointer :: grd
+type(iceberg) :: localberg ! NOT a pointer but an actual local variable
+integer :: stderrunit, i, j, cnt, ij
+
+real, allocatable, dimension(:) :: lon,          &
+                                   lat,          &
+                                   uvel,         &
+                                   vvel,         &
+                                   mass,         &
+                                   axn,          &
+                                   ayn,          &
+                                   bxn,          &
+                                   byn,          &
+                                   thickness,    &
+                                   width,        &
+                                   length,       &
+                                   fl_k,         &
+                                   start_lon,    &
+                                   start_lat,    &
+                                   start_day,    &
+                                   start_mass,   &
+                                   mass_scaling, &
+                                   mass_of_bits, &
+                                   mass_of_fl_bits, &
+                                   mass_of_fl_bergy_bits, &
+                                   static_berg,  &
+                                   heat_density, &
+                                   axn_fast,     &
+                                   ayn_fast,     &
+                                   bxn_fast,     &
+                                   byn_fast,     &
+                                   ang_vel,      &
+                                   ang_accel,    &
+                                   rot
+
+integer, allocatable, dimension(:) :: ine,        &
+                                      jne,        &
+                                      iceberg_num,&
+                                      id_cnt,     &
+                                      id_ij,      &
+                                      start_year
+
+!integer, allocatable, dimension(:,:) :: iceberg_counter_grd
+
+  ! Get the stderr unit number
+  stderrunit=stderr()
+
+  ! For convenience
+  grd=>bergs%grd
+
+  ! Zero out nbergs_in_file
+  nbergs_in_file = 0
+
+  filename_base=trim(restart_input_dir)//'icebergs.res.nc'
+
+  found_restart = find_restart_file(filename_base, filename, multiPErestart, io_tile_id(1))
+
+  if (found_restart) then
+     filename = filename_base
+     call get_field_size(filename,'i',siz, field_found=found, domain=bergs%grd%domain)
+     nbergs_in_file = siz(1)
+
+     replace_iceberg_num = field_exist(filename, 'iceberg_num') ! True if using 32-bit iceberg_num in restart file
+     allocate(lon(nbergs_in_file))
+     allocate(lat(nbergs_in_file))
+     allocate(uvel(nbergs_in_file))
+     allocate(vvel(nbergs_in_file))
+     allocate(mass(nbergs_in_file))
+     allocate(axn(nbergs_in_file)) !Alon
+     allocate(ayn(nbergs_in_file)) !Alon
+     allocate(bxn(nbergs_in_file)) !Alon
+     allocate(byn(nbergs_in_file)) !Alon
+     allocate(thickness(nbergs_in_file))
+     allocate(width(nbergs_in_file))
+     allocate(length(nbergs_in_file))
+     allocate(fl_k(nbergs_in_file))
+     allocate(start_lon(nbergs_in_file))
+     allocate(start_lat(nbergs_in_file))
+     allocate(start_day(nbergs_in_file))
+     allocate(start_mass(nbergs_in_file))
+     allocate(mass_scaling(nbergs_in_file))
+     allocate(mass_of_bits(nbergs_in_file))
+     allocate(mass_of_fl_bits(nbergs_in_file))
+     allocate(mass_of_fl_bergy_bits(nbergs_in_file))
+     allocate(static_berg(nbergs_in_file))
+     allocate(heat_density(nbergs_in_file))
+     allocate(ine(nbergs_in_file))
+     allocate(jne(nbergs_in_file))
+     allocate(start_year(nbergs_in_file))
+     if (replace_iceberg_num) then
+       call error_mesg('read_restart_bergs', "Calculating new iceberg ID's", WARNING)
+       allocate(iceberg_num(nbergs_in_file))
+     else
+       allocate(id_cnt(nbergs_in_file))
+       allocate(id_ij(nbergs_in_file))
+     endif
+
+      if (iceberg_bonds_on) then
+        allocate(localberg%n_bonds)
+        localberg%n_bonds=0.
+      end if
+
+      if (mts) then
+        allocate(localberg%axn_fast)
+        allocate(localberg%ayn_fast)
+        allocate(localberg%bxn_fast)
+        allocate(localberg%byn_fast)
+        allocate(localberg%conglom_id)
+        localberg%conglom_id=0.
+
+       allocate(axn_fast(nbergs_in_file))
+       allocate(ayn_fast(nbergs_in_file))
+       allocate(bxn_fast(nbergs_in_file))
+       allocate(byn_fast(nbergs_in_file))
+     endif
+     if (dem) then
+       allocate(localberg%ang_vel)
+       allocate(localberg%ang_accel)
+       allocate(localberg%rot)
+       allocate(ang_vel(nbergs_in_file))
+       allocate(ang_accel(nbergs_in_file))
+       allocate(rot(nbergs_in_file))
+     endif
+
+     call read_unlimited_axis(filename,'lon',lon,domain=grd%domain)
+     call read_unlimited_axis(filename,'lat',lat,domain=grd%domain)
+     call read_unlimited_axis(filename,'uvel',uvel,domain=grd%domain)
+     call read_unlimited_axis(filename,'vvel',vvel,domain=grd%domain)
+     call read_unlimited_axis(filename,'mass',mass,domain=grd%domain)
+     call read_real_vector(filename,'axn',axn,grd%domain,value_if_not_in_file=0.)
+     call read_real_vector(filename,'ayn',ayn,grd%domain,value_if_not_in_file=0.)
+     call read_real_vector(filename,'bxn',bxn,grd%domain,value_if_not_in_file=0.)
+     call read_real_vector(filename,'byn',byn,grd%domain,value_if_not_in_file=0.)
+     call read_unlimited_axis(filename,'thickness',thickness,domain=grd%domain)
+     call read_unlimited_axis(filename,'width',width,domain=grd%domain)
+     call read_unlimited_axis(filename,'length',length,domain=grd%domain)
+     call read_real_vector(filename,'fl_k',fl_k,grd%domain,value_if_not_in_file=0.)
+     call read_unlimited_axis(filename,'start_lon',start_lon,domain=grd%domain)
+     call read_unlimited_axis(filename,'start_lat',start_lat,domain=grd%domain)
+     call read_unlimited_axis(filename,'start_day',start_day,domain=grd%domain)
+     call read_unlimited_axis(filename,'start_mass',start_mass,domain=grd%domain)
+     call read_unlimited_axis(filename,'mass_scaling',mass_scaling,domain=grd%domain)
+     call read_real_vector(filename,'mass_of_bits',mass_of_bits,domain=grd%domain,value_if_not_in_file=0.)
+     call read_real_vector(filename,'mass_of_fl_bits',mass_of_fl_bits,domain=grd%domain,value_if_not_in_file=0.)
+     call read_real_vector(filename,'mass_of_fl_bergy_bits',mass_of_fl_bergy_bits,domain=grd%domain,value_if_not_in_file=0.)
+     call read_real_vector(filename,'heat_density',heat_density,domain=grd%domain,value_if_not_in_file=0.)
+     call read_unlimited_axis(filename,'ine',ine,domain=grd%domain)
+     call read_unlimited_axis(filename,'jne',jne,domain=grd%domain)
+     call read_unlimited_axis(filename,'start_year',start_year,domain=grd%domain)
+     if (replace_iceberg_num) then
+       call read_int_vector(filename,'iceberg_num',iceberg_num,grd%domain,value_if_not_in_file=-1)
+     else
+       call read_int_vector(filename,'id_cnt',id_cnt,grd%domain)
+       call read_int_vector(filename,'id_ij',id_ij,grd%domain)
+     endif
+     call read_real_vector(filename,'static_berg',static_berg,grd%domain,value_if_not_in_file=0.)
+
+     if (mts) then
+       call read_real_vector(filename,'axn_fast',axn_fast,grd%domain,value_if_not_in_file=0.)
+       call read_real_vector(filename,'ayn_fast',ayn_fast,grd%domain,value_if_not_in_file=0.)
+       call read_real_vector(filename,'bxn_fast',bxn_fast,grd%domain,value_if_not_in_file=0.)
+       call read_real_vector(filename,'byn_fast',byn_fast,grd%domain,value_if_not_in_file=0.)
+     endif
+
+     if (dem) then
+       call read_real_vector(filename,'ang_vel'  ,ang_vel  ,grd%domain,value_if_not_in_file=0.)
+       call read_real_vector(filename,'ang_accel',ang_accel,grd%domain,value_if_not_in_file=0.)
+       call read_real_vector(filename,'rot'      ,rot      ,grd%domain,value_if_not_in_file=0.)
+     endif
+  elseif (bergs%require_restart) then
+     stop 'read_restart_bergs, RESTART NOT FOUND!'
+  endif
+
+  ! Find approx outer bounds for tile
+  lon0=minval( grd%lon(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
+  lon1=maxval( grd%lon(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
+  lat0=minval( grd%lat(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
+  lat1=maxval( grd%lat(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
+
+  do k=1, nbergs_in_file
+    localberg%lon=lon(k)
+    localberg%lat=lat(k)
+    if (.not. ignore_ij_restart) then ! read i,j position and avoid the "find" step
+      localberg%ine=ine(k)
+      localberg%jne=jne(k)
+      if ( localberg%ine>=grd%isc .and. localberg%ine<=grd%iec .and. &
+         localberg%jne>=grd%jsc .and.localberg%jne<=grd%jec ) then
+        lres=.true.
+      else
+        lres=.false.
+      endif
+    else ! i,j are not available from the file so we search the grid to find out if we reside on this PE
+      if (use_slow_find) then
+        lres=find_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
+      else
+        lres=find_cell_by_search(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
+      endif
+    endif
+    if (really_debug) then
+      write(stderrunit,'(a,i8,a,2f9.4,a,i8)') 'KID, read_restart_bergs: berg ',k,' is at ',localberg%lon,localberg%lat,&
+           & ' on PE ',mpp_pe()
+      write(stderrunit,*) 'KID, read_restart_bergs: lres = ',lres
+    endif
+
+    if (lres) then ! true if we reside on this PE grid
+      localberg%uvel=uvel(k)
+      localberg%vvel=vvel(k)
+      localberg%mass=mass(k)
+      localberg%axn=axn(k) !Alon
+      localberg%ayn=ayn(k) !Alon
+      localberg%uvel_old=uvel(k) !Alon
+      localberg%vvel_old=vvel(k) !Alon
+      localberg%lon_old=lon(k) !Alon
+      localberg%lat_old=lat(k) !Alon
+      localberg%bxn=bxn(k) !Alon
+      localberg%byn=byn(k) !Alon
+      localberg%thickness=thickness(k)
+      localberg%width=width(k)
+      localberg%length=length(k)
+      localberg%fl_k=fl_k(k)
+      localberg%start_lon=start_lon(k)
+      localberg%start_lat=start_lat(k)
+      localberg%start_year=start_year(k)
+      if (replace_iceberg_num) then
+        localberg%id = generate_id(grd, localberg%ine, localberg%jne)
+      else
+        localberg%id=id_from_2_ints(id_cnt(k), id_ij(k))
+      endif
+      localberg%start_day=start_day(k)
+      localberg%start_mass=start_mass(k)
+      localberg%mass_scaling=mass_scaling(k)
+      localberg%mass_of_bits=mass_of_bits(k)
+      localberg%mass_of_fl_bits=mass_of_fl_bits(k)
+      localberg%mass_of_fl_bergy_bits=mass_of_fl_bergy_bits(k)
+      localberg%halo_berg=0.
+      localberg%static_berg=static_berg(k)
+      localberg%heat_density=heat_density(k)
+      localberg%first_bond=>null()
+
+     if (mts) then
+       localberg%axn_fast=axn_fast(k)
+       localberg%ayn_fast=ayn_fast(k)
+       localberg%bxn_fast=bxn_fast(k)
+       localberg%byn_fast=byn_fast(k)
+     endif
+
+     if (dem) then
+       localberg%ang_vel  =ang_vel(k)
+       localberg%ang_accel=ang_accel(k)
+       localberg%rot      =rot(k)
+     endif
+
+      if (really_debug) lres=is_point_in_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, explain=.true.)
+      lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
+      !call add_new_berg_to_list(bergs%first, localberg)
+
+      if (bergs%grd%area(localberg%ine,localberg%jne) .ne. 0)  then
+        call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg)
+      else
+        if (mpp_pe().eq.mpp_root_pe()) then
+          print * , 'Grounded iceberg: ', lat(k),lon(k), localberg%id
+          call error_mesg('KID, read_restart_bergs', 'Iceberg not added because it is grounded', WARNING)
+        endif
+       endif
+
+      if (really_debug) call print_berg(stderrunit, bergs%list(localberg%ine,localberg%jne)%first, 'read_restart_bergs, add_new_berg_to_list')
+    elseif (multiPErestart .and. io_tile_id(1) .lt. 0) then
+      call error_mesg('KID, read_restart_bergs', 'berg in PE file was not on PE!', FATAL)
+    endif
+  enddo
+
+  if (found_restart) then
+    deallocate(lon,          &
+               lat,          &
+               uvel,         &
+               vvel,         &
+               mass,         &
+               axn,          &
+               ayn,          &
+               bxn,          &
+               byn,          &
+               thickness,    &
+               width,        &
+               length,       &
+               fl_k,         &
+               start_lon,    &
+               start_lat,    &
+               start_day,    &
+               start_mass,   &
+               mass_scaling, &
+               mass_of_bits, &
+               mass_of_fl_bits, &
+               mass_of_fl_bergy_bits, &
+               static_berg,  &
+               heat_density, &
+               ine,          &
+               jne,          &
+               start_year )
+
+    if (mts) then
+      deallocate(            &
+               axn_fast,     &
+               ayn_fast,     &
+               bxn_fast,     &
+               byn_fast)
+    endif
+    if (dem) then
+      deallocate(            &
+               ang_vel,      &
+               ang_accel,    &
+               rot)
+    endif
+
+    if (replace_iceberg_num) then
+      deallocate(iceberg_num)
+    else
+      deallocate(id_cnt)
+      deallocate(id_ij)
+    endif
+
+    ! This block only works for IO_LAYOUT=1,1 or 0,0 but not for arbitrary layouts.
+    ! I'm commenting this out until we find a way to implement the same sorts of checks
+    ! that work for all i/o layouts. -AJA
+    !Checking the total number of icebergs read from the restart file.
+    !nbergs_read=count_bergs(bergs)
+    !call mpp_sum(nbergs_read)
+    !if (mpp_pe().eq.mpp_root_pe()) then
+    !  write(*,'(a,i8,a,i8,a)') 'KID, read_restart_bergs: Number of Icebergs in restart file=',nbergs_in_file,' Number of Icebergs read=', nbergs_read
+    !  if (nbergs_read .gt. nbergs_in_file) then
+    !    call error_mesg('KID, read_restart_bergs', 'More icebergs read than exist in restart file.', FATAL)
+    !  elseif (nbergs_read .lt. nbergs_in_file) then
+    !    if (bergs%ignore_missing_restart_bergs) then
+    !      call error_mesg('KID, read_restart_bergs', 'Some Icebergs from restart file were not found (ignore_missing flag is on)', WARNING)
+    !    else
+    !      call error_mesg('KID, read_restart_bergs', 'Some Icebergs from restart file were not found', FATAL)
+    !    endif
+    !  elseif (nbergs_read .eq. nbergs_in_file) then
+    !    write(*,'(a,i8,a,i8,a)') 'KID, read_restart_bergs: Number of icebergs read (#',nbergs_read,') matches the number of icebergs in the file'
+    !  endif
+    !endif
+
+  elseif(.not. found_restart .and. bergs%nbergs_start==0 .and. generate_test_icebergs) then
+    call generate_bergs(bergs,Time)
+  endif
+
+  call check_for_duplicates_in_parallel(bergs)
+
+  bergs%floating_mass_start=sum_mass(bergs)
+  call mpp_sum( bergs%floating_mass_start )
+  bergs%icebergs_mass_start=sum_mass(bergs,justbergs=.true.)
+  call mpp_sum( bergs%icebergs_mass_start )
+  bergs%bergy_mass_start=sum_mass(bergs,justbits=.true.)
+  call mpp_sum( bergs%bergy_mass_start )
+  bergs%fl_bits_mass_start=sum_mass(bergs,justflbits=.true.)
+  call mpp_sum( bergs%fl_bits_mass_start )
+  if (mpp_pe().eq.mpp_root_pe().and.verbose) write(*,'(a)') 'KID, read_restart_bergs: completed'
+
+end subroutine read_restart_bergs
+
+!> Read a vector of reals from file and use a default value if variable is missing
+subroutine read_real_vector(filename, varname, values, domain, value_if_not_in_file)
+  character(len=*), intent(in)  :: filename !< Name of file to read from
+  character(len=*), intent(in)  :: varname !< Name of variable to read
+  real,             intent(out) :: values(:) !< Returned vector of reals
+  type(domain2D),   intent(in)  :: domain !< Parallel decomposition
+  real, optional,   intent(in)  :: value_if_not_in_file !< Value to use if variable is not in file
+
+  if (present(value_if_not_in_file).and..not.field_exist(filename, varname)) then
+    values(:)=value_if_not_in_file
+  else
+    call read_unlimited_axis(filename,varname,values,domain=domain)
+  endif
+end subroutine read_real_vector
+
+!> Read a vector of integers from file and use a default value if variable is missing
+subroutine read_int_vector(filename, varname, values, domain, value_if_not_in_file)
+  character(len=*),  intent(in)  :: filename !< Name of file to read from
+  character(len=*),  intent(in)  :: varname !< Name of variable to read
+  integer,           intent(out) :: values(:) !< Returned vector of integers
+  type(domain2D),    intent(in)  :: domain !< Parallel decomposition
+  integer, optional, intent(in)  :: value_if_not_in_file !< Value to use if variable is not in file
+
+  if (present(value_if_not_in_file).and..not.field_exist(filename, varname)) then
+    values(:)=value_if_not_in_file
+  else
+    call read_unlimited_axis(filename,varname,values,domain=domain)
+  endif
+end subroutine read_int_vector
+
+!> Generate bergs for the purpose of debugging
+subroutine generate_bergs(bergs,Time)
+! Arguments
+type(icebergs), pointer :: bergs !< Icebergs container
+type(time_type), intent(in) :: Time !< Model time
+! Local variables
+type(icebergs_gridded), pointer :: grd
+integer :: i,j
+type(iceberg) :: localberg ! NOT a pointer but an actual local variable
+integer :: iyr, imon, iday, ihr, imin, isec
+logical :: lres
+
+  ! For convenience
+  grd=>bergs%grd
+
+  call get_date(Time, iyr, imon, iday, ihr, imin, isec)
+
+  if (mts) then
+    allocate(localberg%axn_fast)
+    allocate(localberg%ayn_fast)
+    allocate(localberg%bxn_fast)
+    allocate(localberg%byn_fast)
+  endif
+  if (dem) then
+    allocate(localberg%ang_vel)
+    allocate(localberg%ang_accel)
+    allocate(localberg%rot)
+  endif
+
+  do j=grd%jsc,grd%jec; do i=grd%isc,grd%iec
+    if (grd%msk(i,j)>0. .and. abs(grd%latc(i,j))>80.0) then
+      if (max(grd%lat(i,j),grd%lat(i-1,j),grd%lat(i,j-1),grd%lat(i-1,j-1))>89.999) cycle ! Cannot use this at Pole cells
+      localberg%xi=-999.
+      localberg%yj=-999.
+      localberg%ine=i
+      localberg%jne=j
+      localberg%lon=grd%lonc(i,j)
+      localberg%lat=grd%latc(i,j)
+      localberg%lon_old=localberg%lon
+      localberg%lat_old=localberg%lat
+      localberg%mass=bergs%initial_mass_s(1)
+      localberg%thickness=bergs%initial_thickness_s(1)
+      localberg%width=bergs%initial_width_s(1)
+      localberg%length=bergs%initial_length_s(1)
+      localberg%fl_k=0.
+      localberg%start_lon=localberg%lon
+      localberg%start_lat=localberg%lat
+      localberg%start_year=iyr
+      localberg%start_day=float(iday)+(float(ihr)+float(imin)/60.)/24.
+      localberg%start_mass=localberg%mass
+      localberg%mass_scaling=bergs%mass_scaling_s(1)
+      localberg%mass_of_bits=0.
+      localberg%mass_of_fl_bits=0.
+      localberg%mass_of_fl_bergy_bits=0.
+      localberg%halo_berg=0.
+      localberg%static_berg=0.
+      localberg%heat_density=0.
+      localberg%axn=0. !Alon
+      localberg%ayn=0. !Alon
+      localberg%uvel_old=0. !Alon
+      localberg%vvel_old=0. !Alon
+      localberg%bxn=0. !Alon
+      localberg%byn=0. !Alon
+      localberg%uvel_prev=0. !Alon
+      localberg%vvel_prev=0. !Alon
+
+      if (mts) then
+        localberg%axn_fast=0.
+        localberg%ayn_fast=0.
+        localberg%bxn_fast=0.
+        localberg%byn_fast=0.
+      endif
+      if (dem) then
+        localberg%ang_vel=0.
+        localberg%ang_accel=0.
+        localberg%rot=0.
+      endif
+
+      !Berg A
+      call loc_set_berg_pos(grd, 0.9, 0.5, 1., 0., localberg)
+      localberg%id = generate_id(grd, i, j)
+      call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
+      !Berg B
+      call loc_set_berg_pos(grd, 0.1, 0.5, -1., 0., localberg)
+      localberg%id = generate_id(grd, i, j)
+      call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
+      !Berg C
+      call loc_set_berg_pos(grd, 0.5, 0.9, 0., 1., localberg)
+      localberg%id = generate_id(grd, i, j)
+      call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
+      !Berg D
+      call loc_set_berg_pos(grd, 0.5, 0.1, 0., -1., localberg)
+      localberg%id = generate_id(grd, i, j)
+      call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
+    endif
+  enddo; enddo
+
+  bergs%nbergs_start=count_bergs(bergs)
+  call mpp_sum(bergs%nbergs_start)
+  if (mpp_pe().eq.mpp_root_pe()) &
+    write(*,'(a,i8,a)') 'KID, generate_bergs: ',bergs%nbergs_start,' were generated'
+
+end subroutine generate_bergs
+
+!> For generating bergs for debugging, assign initial berg positions and velocities
+subroutine loc_set_berg_pos(grd, xi, yj, uvel, vvel, berg)
+  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+  real, intent(in) :: xi !< Non-dimensional x-position within cell to give berg
+  real, intent(in) :: yj !< Non-dimensional y-position within cell to give berg
+  real, intent(in) :: uvel !< Zonal velocity to give berg
+  real, intent(in) :: vvel !< Meridional velocity to give berg
+  type(iceberg), intent(inout) :: berg !< An iceberg
+  integer :: i, j
+  logical :: lres
+  i = berg%ine ; j = berg%jne
+  if (max(grd%lat(i,j),grd%lat(i-1,j),grd%lat(i,j-1),grd%lat(i-1,j-1))>89.999) then
+    berg%lon=grd%lonc(i,j)
+    berg%lat=grd%latc(i,j)
+    berg%xi=0.5 ; berg%yj=0.5
+  else
+    berg%lon=bilin(grd, grd%lon, i, j, xi, yj)
+    berg%lat=bilin(grd, grd%lat, i, j, xi, yj)
+    berg%xi=xi ; berg%yj=yj
+  endif
+  berg%uvel=uvel ; berg%vvel=vvel
+  berg%lon_old=berg%lon ; berg%lat_old=berg%lat
+  berg%start_lon=berg%lon ; berg%start_lat=berg%lat
+  lres=pos_within_cell(grd, berg%lon, berg%lat, berg%ine, berg%jne, berg%xi, berg%yj)
+  if (.not. lres) then
+    lres=pos_within_cell(grd, berg%lon, berg%lat, berg%ine, berg%jne, berg%xi, berg%yj, explain=.true.)
+    write(0,*) lres, i, j, xi, yj, uvel, vvel
+    write(0,*) lres, berg%ine, berg%jne, berg%xi, berg%yj
+    write(0,*) 'bx=',berg%lon, 'gx=',grd%lon(i-1,j-1), grd%lon(i,j-1), grd%lon(i,j), grd%lon(i-1,j),'cx=', grd%lonc(i,j)
+    write(0,*) 'by=',berg%lat, 'gy=',grd%lat(i-1,j-1), grd%lat(i,j-1), grd%lat(i,j), grd%lat(i-1,j),'cy=', grd%latc(i,j)
+    stop 'generate_bergs, loc_set_berg_pos(): VERY FATAL!'
+  endif
+end subroutine loc_set_berg_pos
+
+!> Read bond restart file
+subroutine read_restart_bonds(bergs,Time)
+! Arguments
+type(icebergs), pointer :: bergs !< Icebergs container
+type(time_type), intent(in) :: Time !< Model time
+! Local variables
+integer :: k, siz(4), nbonds_in_file
+logical :: lres, found_restart, found
+logical :: first_berg_found, second_berg_found
+logical :: multiPErestart  ! Not needed with new restart read; currently kept for compatibility
+real :: lon0, lon1, lat0, lat1
+character(len=53) :: filename, filename_base
+type(icebergs_gridded), pointer :: grd
+type(iceberg) :: localberg ! NOT a pointer but an actual local variable
+type(iceberg) , pointer :: this, first_berg, second_berg
+type(bond) , pointer :: current_bond
+integer :: stderrunit
+integer :: number_first_bonds_matched !How many first bond bergs found on pe
+integer :: number_second_bonds_matched !How many second bond bergs found on pe
+integer :: number_perfect_bonds ! How many complete bonds formed
+integer :: number_partial_bonds ! How many either complete/partial bonds formed.
+integer :: number_perfect_bonds_with_first_on_pe ! How many bonds with first bond on the compuational domain
+integer :: all_pe_number_perfect_bonds, all_pe_number_partial_bonds
+integer :: all_pe_number_first_bonds_matched, all_pe_number_second_bonds_matched
+integer :: all_pe_number_perfect_bonds_with_first_on_pe
+integer :: ine, jne
+logical :: search_data_domain
+real :: berg_found, berg_found_all_pe
+integer, allocatable, dimension(:) :: id_cnt, id_ij,    &
+                                      first_berg_jne,   &
+                                      first_berg_ine,   &
+                                      other_berg_jne,   &
+                                      other_berg_ine,   &
+                                      broken
+real, allocatable, dimension(:) ::    tangd1,           &
+                                      tangd2,           &
+                                      nstress,          &
+                                      sstress,          &
+                                      rel_rotation
+integer(kind=8), allocatable, dimension(:) :: first_id,   &
+                                              other_id
+!integer, allocatable, dimension(:,:) :: iceberg_counter_grd
+
+  ! Get the stderr unit number
+  stderrunit=stderr()
+
+  ! For convenience
+  grd=>bergs%grd
+
+  ! Zero out nbergs_in_file
+  nbonds_in_file = 0
+  all_pe_number_perfect_bonds=0
+
+  filename_base=trim(restart_input_dir)//'bonds_iceberg.res.nc'
+
+  found_restart = find_restart_file(filename_base, filename, multiPErestart, io_tile_id(1))
+  call error_mesg('read_restart_bonds_bergs_new', 'Using icebergs bond restart read', NOTE)
+
+  filename = filename_base
+  call get_field_size(filename,'i',siz, field_found=found, domain=bergs%grd%domain)
+  nbonds_in_file = siz(1)
+
+    if (mpp_pe() .eq. mpp_root_pe()) then
+      write(stderrunit,*)  'KID, bond read restart : ','Number of bonds in file',  nbonds_in_file
+    endif
+
+  if (nbonds_in_file .gt. 0) then
+
+    allocate(first_id(nbonds_in_file))
+    allocate(other_id(nbonds_in_file))
+    allocate(id_cnt(nbonds_in_file))
+    allocate(id_ij(nbonds_in_file))
+    allocate(first_berg_jne(nbonds_in_file))
+    allocate(first_berg_ine(nbonds_in_file))
+    allocate(other_berg_ine(nbonds_in_file))
+    allocate(other_berg_jne(nbonds_in_file))
+
+    if (dem) then
+      allocate(tangd1(nbonds_in_file))
+      allocate(tangd2(nbonds_in_file))
+      allocate(nstress(nbonds_in_file))
+      allocate(sstress(nbonds_in_file))
+      allocate(rel_rotation(nbonds_in_file))
+      allocate(broken(nbonds_in_file))
+    endif
+
+    call read_unlimited_axis(filename,'first_id_cnt',id_cnt,domain=grd%domain)
+    call read_unlimited_axis(filename,'first_id_ij',id_ij,domain=grd%domain)
+    do k=1, nbonds_in_file
+      first_id(k) = id_from_2_ints( id_cnt(k), id_ij(k) )
+    enddo
+    call read_unlimited_axis(filename,'other_id_cnt',id_cnt,domain=grd%domain)
+    call read_unlimited_axis(filename,'other_id_ij',id_ij,domain=grd%domain)
+    do k=1, nbonds_in_file
+      other_id(k) = id_from_2_ints( id_cnt(k), id_ij(k) )
+    enddo
+    deallocate(id_cnt, id_ij)
+    call read_unlimited_axis(filename,'first_berg_jne',first_berg_jne,domain=grd%domain)
+    call read_unlimited_axis(filename,'first_berg_ine',first_berg_ine,domain=grd%domain)
+    call read_unlimited_axis(filename,'other_berg_jne',other_berg_jne,domain=grd%domain)
+    call read_unlimited_axis(filename,'other_berg_ine',other_berg_ine,domain=grd%domain)
+
+    if (dem) then
+      call read_real_vector(filename,'tangd1',tangd1,grd%domain,value_if_not_in_file=0.)
+      call read_real_vector(filename,'tangd2',tangd2,grd%domain,value_if_not_in_file=0.)
+      call read_real_vector(filename,'nstress',nstress,grd%domain,value_if_not_in_file=0.)
+      call read_real_vector(filename,'sstress',sstress,grd%domain,value_if_not_in_file=0.)
+      call read_real_vector(filename,'rel_rotation',rel_rotation,grd%domain,value_if_not_in_file=0.)
+      call read_int_vector(filename,'broken',broken,grd%domain,value_if_not_in_file=0)
+    endif
+
+    number_first_bonds_matched=0
+    number_second_bonds_matched=0
+    number_perfect_bonds=0
+    number_partial_bonds=0
+    number_perfect_bonds_with_first_on_pe=0
+
+    do k=1, nbonds_in_file
+
+       ! If i,j in restart files are not good, then we find the berg position of the bond addresses manually:
+       if (ignore_ij_restart) then
+         !Finding first iceberg in bond
+         ine=999 ; jne=999 ; berg_found=0.0 ; search_data_domain=.true.
+         call find_individual_iceberg(bergs,first_id(k), ine, jne,berg_found,search_data_domain)
+         berg_found_all_pe=berg_found
+         call mpp_sum(berg_found_all_pe)
+         if (berg_found_all_pe .gt. 0.5) then
+             first_berg_ine(k)=ine
+             first_berg_jne(k)=jne
+         else
+           print * , 'First bond berg not located: ', first_id(k),berg_found, mpp_pe(),ine, jne
+           call error_mesg('read_restart_bonds_bergs_new', 'First iceberg in bond not found on any pe', FATAL)
+         endif
+         !else
+
+         !Finding other iceberg other iceberg
+         ine=999 ; jne=999 ; berg_found=0.0 ; search_data_domain =.true.
+         call find_individual_iceberg(bergs,other_id(k), ine, jne, berg_found,search_data_domain)
+         berg_found_all_pe=berg_found
+         call mpp_sum(berg_found_all_pe)
+         if (berg_found_all_pe .gt. 0.5) then
+           !if (berg_found_all_pe .gt. 1.5) then
+           !  call error_mesg('read_restart_bonds_bergs_new', 'Other iceberg bond found on more than one pe', FATAL)
+           !else
+             other_berg_ine(k)=ine
+             other_berg_jne(k)=jne
+           !endif
+         else
+          call error_mesg('read_restart_bonds_bergs_new', 'Other iceberg in bond not found on any pe', FATAL)
+         endif
+         if (berg_found_all_pe .lt. 0.5) then
+                 print * , 'First bond berg not located: ', other_id(k),berg_found, mpp_pe(),ine, jne
+             call error_mesg('read_restart_bonds_bergs_new', 'First bond iceberg not located', FATAL)
+         endif
+       endif
+
+      ! Decide whether the first iceberg is on the processeor
+      if ( (first_berg_ine(k)>=grd%isd) .and. (first_berg_ine(k)<=grd%ied) .and. &
+        (first_berg_jne(k)>=grd%jsd) .and. (first_berg_jne(k)<=grd%jed) ) then
+        number_first_bonds_matched=number_first_bonds_matched+1
+
+        ! Search for the first berg, which the bond belongs to
+        first_berg_found=.false.
+        first_berg=>null()
+        this=>bergs%list(first_berg_ine(k),first_berg_jne(k))%first
+        do while(associated(this))
+          if (this%id == first_id(k)) then
+            first_berg_found=.true.
+            first_berg=>this
+            !if (first_berg%halo_berg.gt.0.5) print *, 'bonding halo berg:', first_id(k),  first_berg_ine(k),first_berg_jne(k) ,grd%isc, grd%iec, mpp_pe()
+            this=>null()
+          else
+            this=>this%next
+          endif
+        enddo
+
+        ! Decide whether the second iceberg is on the processeor (data domain)
+        second_berg_found=.false.
+        !if ( other_berg_ine(k)>=grd%isc-1 .and. other_berg_ine(k)<=grd%iec+1 .and. &
+        !  other_berg_jne(k)>=grd%jsc-1 .and.other_berg_jne(k)<=grd%jec+1 ) then
+        if ( (other_berg_ine(k)>=grd%isd) .and. (other_berg_ine(k)<=grd%ied) .and. &
+          (other_berg_jne(k)>=grd%jsd) .and.(other_berg_jne(k)<=grd%jed) ) then
+          number_second_bonds_matched=number_second_bonds_matched+1
+
+          ! Search for the second berg, which the bond belongs to
+          second_berg=>null()
+          this=>bergs%list(other_berg_ine(k),other_berg_jne(k))%first
+          do while(associated(this))
+            if (this%id == other_id(k)) then
+              second_berg_found=.true.
+              second_berg=>this
+              this=>null()
+            else
+              this=>this%next
+            endif
+          enddo
+        endif
+
+        if (first_berg_found) then
+          number_partial_bonds=number_partial_bonds+1
+          if (second_berg_found) then
+            call form_a_bond(first_berg, other_id(k), other_berg_ine(k), other_berg_jne(k),  second_berg)
+            number_perfect_bonds=number_perfect_bonds+1
+
+            current_bond=>first_berg%first_bond
+
+            if (dem) then
+              current_bond%tangd1=tangd1(k)
+              current_bond%tangd2=tangd2(k)
+              current_bond%nstress=nstress(k)
+              current_bond%sstress=sstress(k)
+              current_bond%rel_rotation=rel_rotation(k)
+              current_bond%broken=broken(k)
+            endif
+
+            !Counting number of bonds where the first bond is in the computational domain
+            if ( (first_berg_ine(k)>=grd%isc) .and. (first_berg_ine(k)<=grd%iec) .and. &
+              (first_berg_jne(k)>=grd%jsc) .and. (first_berg_jne(k)<=grd%jec) ) then
+               number_perfect_bonds_with_first_on_pe=number_perfect_bonds_with_first_on_pe+1
+            endif
+
+          else
+            !print *, 'Forming a bond of the second type', mpp_pe(), first_id(k),  other_id(k)
+            !call form_a_bond(first_berg, other_id(k), other_berg_ine(k),other_berg_jne(k))
+          endif
+        else
+          write(stderrunit,*) 'KID, bond read restart : ','Not enough partial bonds formed', k, mpp_pe(), nbonds_in_file
+          call error_mesg('read_restart_bonds_bergs_new', 'Failure with reading bonds: First bond not found on pe', FATAL)
+        endif
+      endif
+    enddo
+
+    !Analyse how many bonds were created and take appropriate action
+    all_pe_number_perfect_bonds=number_perfect_bonds
+    all_pe_number_perfect_bonds_with_first_on_pe=number_perfect_bonds_with_first_on_pe
+    all_pe_number_partial_bonds=number_partial_bonds
+    all_pe_number_first_bonds_matched=number_first_bonds_matched
+    all_pe_number_second_bonds_matched=number_second_bonds_matched
+    call mpp_sum(all_pe_number_perfect_bonds)
+    call mpp_sum(all_pe_number_partial_bonds)
+    call mpp_sum(all_pe_number_perfect_bonds_with_first_on_pe)
+
+    if (all_pe_number_partial_bonds .lt. nbonds_in_file) then
+      write(stderrunit,*) 'KID, bond read restart : ','Not enough partial bonds formed', all_pe_number_partial_bonds , nbonds_in_file
+      call error_mesg('read_restart_bonds_bergs_new', 'Not enough partial bonds formed', FATAL)
+    endif
+
+    if (all_pe_number_perfect_bonds .lt. nbonds_in_file) then
+      call mpp_sum(all_pe_number_first_bonds_matched)
+      call mpp_sum(all_pe_number_second_bonds_matched)
+      write(stderrunit,*)  'KID, bond read restart : ','Warning, some bonds are not fully formed',  all_pe_number_first_bonds_matched , nbonds_in_file
+      write(stderrunit,*)  'KID, bond read restart : ','Number of first and second bonds matched:', all_pe_number_second_bonds_matched , nbonds_in_file
+      call error_mesg('read_restart_bonds_bergs_new', 'Not enough perfect bonds formed', NOTE)
+    endif
+
+    if (all_pe_number_perfect_bonds_with_first_on_pe .ne. nbonds_in_file) then
+      call mpp_sum(all_pe_number_first_bonds_matched)
+      call mpp_sum(all_pe_number_second_bonds_matched)
+      write(stderrunit,*)  'KID, bond read restart : ','Warning, # bonds with first bond on computational domain, does not match file',  all_pe_number_first_bonds_matched , nbonds_in_file
+      write(stderrunit,*)  'KID, bond read restart : ','Computational bond, first second:', all_pe_number_second_bonds_matched , nbonds_in_file
+      call error_mesg('read_restart_bonds_bergs_new', 'Computational perfect bonds do not match those in file', NOTE)
+    endif
+
+    deallocate(               &
+            first_id,         &
+            other_id,         &
+            first_berg_ine,   &
+            first_berg_jne,   &
+            other_berg_ine,   &
+            other_berg_jne )
+
+    if (dem) then
+      deallocate(                     &
+               tangd1,                &
+               tangd2,                &
+               nstress,               &
+               sstress,               &
+               rel_rotation,          &
+               broken)
+    endif
+  endif
+
+  if (mpp_pe() .eq. mpp_root_pe()) then
+    write(stderrunit,*)  'KID, bond read restart : ','Number of bonds (including halos)',  all_pe_number_perfect_bonds
+    write(stderrunit,*)  'KID, bond read restart : ','Number of true bonds created',  all_pe_number_perfect_bonds_with_first_on_pe
+  endif
+
+end subroutine read_restart_bonds
+
+!> Reading calving and gridded restart data
+subroutine read_restart_calving(bergs)
+use random_numbers_mod, only: initializeRandomNumberStream, getRandomNumbers, randomNumberStream
+! Arguments
+type(icebergs), pointer :: bergs !< Icebergs container
+! Local variables
+integer :: k,i,j
+character(len=37) :: filename, actual_filename
+type(icebergs_gridded), pointer :: grd
+real, allocatable, dimension(:,:) :: randnum
+type(randomNumberStream) :: rns
+
+  ! For convenience
+  grd=>bergs%grd
+
+  ! Read stored ice
+  filename=trim(restart_input_dir)//'calving.res.nc'
+  if (file_exist(filename)) then
+    if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') &
+     'KID, read_restart_calving: reading ',filename
+    call read_data(filename, 'stored_ice', grd%stored_ice, grd%domain)
+    if (field_exist(filename, 'stored_heat')) then
+      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+       'KID, read_restart_calving: reading stored_heat from restart file.'
+      call read_data(filename, 'stored_heat', grd%stored_heat, grd%domain)
+    else
+      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+     'KID, read_restart_calving: stored_heat WAS NOT FOUND in the file. Setting to 0.'
+      grd%stored_heat(:,:)=0.
+    endif
+    if (field_exist(filename, 'rmean_calving')) then
+      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+       'KID, read_restart_calving: reading rmean_calving from restart file.'
+      call read_data(filename, 'rmean_calving', grd%rmean_calving, grd%domain)
+      grd%rmean_calving_initialized=.true.
+    else
+      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+     'KID, read_restart_calving: rmean_calving WAS NOT FOUND in the file. Setting to 0.'
+    endif
+    if (field_exist(filename, 'rmean_calving_hflx')) then
+      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+       'KID, read_restart_calving: reading rmean_calving_hflx from restart file.'
+      call read_data(filename, 'rmean_calving_hflx', grd%rmean_calving_hflx, grd%domain)
+      grd%rmean_calving_hflx_initialized=.true.
+    else
+      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+     'KID, read_restart_calving: rmean_calving_hflx WAS NOT FOUND in the file. Setting to 0.'
+    endif
+    if (field_exist(filename, 'iceberg_counter_grd')) then
+      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+       'KID, read_restart_calving: reading iceberg_counter_grd from restart file.'
+      call read_data(filename, 'iceberg_counter_grd', grd%iceberg_counter_grd, grd%domain)
+    else
+      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+     'KID, read_restart_calving: iceberg_counter_grd WAS NOT FOUND in the file. Setting to 0.'
+      grd%iceberg_counter_grd(:,:) = 0
+    endif
+    bergs%restarted=.true.
+  else
+    if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+     'KID, read_restart_calving: initializing stored ice to random numbers'
+    if ( make_calving_reproduce ) then
+       allocate(randnum(1,nclasses))
+       do j=grd%jsc, grd%jec
+          do i=grd%isc, grd%iec
+             rns=initializeRandomNumberStream(i+10000*j)
+             call getRandomNumbers(rns,randnum(1,:))
+             do k=1, nclasses
+               if (grd%lat(i,j)<0.) then
+                 grd%stored_ice(i,j,k)=randnum(1,k) * grd%msk(i,j) * bergs%initial_mass_s(k) * bergs%mass_scaling_s(k)
+               else
+                 grd%stored_ice(i,j,k)=randnum(1,k) * grd%msk(i,j) * bergs%initial_mass_n(k) * bergs%mass_scaling_n(k)
+               endif
+             end do
+          end do
+       end do
+    else
+       allocate(randnum(grd%jsc:grd%jec,nclasses))
+       do i=grd%isc, grd%iec
+          rns = initializeRandomNumberStream(i)
+          call getRandomNumbers(rns,randnum)
+          do k=1, nclasses
+            where (grd%lat(i,grd%jsc:grd%jec)<0.)
+             grd%stored_ice(i,grd%jsc:grd%jec,k) = randnum(:,k) * grd%msk(i,grd%jsc:grd%jec) * &
+               & bergs%initial_mass_s(k) * bergs%mass_scaling_s(k)
+           elsewhere
+             grd%stored_ice(i,grd%jsc:grd%jec,k) = randnum(:,k) * grd%msk(i,grd%jsc:grd%jec) * &
+               & bergs%initial_mass_n(k) * bergs%mass_scaling_n(k)
+           end where
+          end do
+       end do
+    end if
+    deallocate(randnum)
+  endif
+
+  call grd_chksum3(bergs%grd, bergs%grd%stored_ice, 'read_restart_calving, stored_ice')
+  call grd_chksum2(bergs%grd, bergs%grd%stored_heat, 'read_restart_calving, stored_heat')
+  call grd_chksum2(bergs%grd, bergs%grd%rmean_calving, 'read_restart_calving, rmean_calving')
+  call grd_chksum2(bergs%grd, bergs%grd%rmean_calving_hflx, 'read_restart_calving, rmean_calving_hflx')
+
+  bergs%stored_start=sum( grd%stored_ice(grd%isc:grd%iec,grd%jsc:grd%jec,:) )
+  bergs%rmean_calving_start=sum( grd%rmean_calving(grd%isc:grd%iec,grd%jsc:grd%jec) )
+  bergs%rmean_calving_hflx_start=sum( grd%rmean_calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec) )
+  call mpp_sum( bergs%stored_start )
+  bergs%stored_heat_start=sum( grd%stored_heat(grd%isc:grd%iec,grd%jsc:grd%jec) )
+  call mpp_sum( bergs%stored_heat_start )
+  bergs%floating_heat_start=sum_heat(bergs)
+  call mpp_sum( bergs%floating_heat_start )
+
+end subroutine read_restart_calving
+
+!> Read ocean depth from file
+subroutine read_ocean_depth(grd)
+! Arguments
+type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+! Local variables
+character(len=37) :: filename
+
+  ! Read stored ice
+  filename=trim(restart_input_dir)//'topog.nc'
+  if (file_exist(filename)) then
+    if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') &
+     'KID, read_ocean_depth: reading ',filename
+    if (field_exist(filename, 'depth')) then
+      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+       'KID, read_ocean_depth: reading depth from topog file.'
+      call read_data(filename, 'depth', grd%ocean_depth, grd%domain)
+    else
+      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+     'KID, read_ocean_depth: depth WAS NOT FOUND in the file. Setting to 0.'
+      !grd%ocean_depth(:,:)=0.
+    endif
+  else
+    if (mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+     'KID, read_ocean_depth: Ocean depth file (topog.nc) not present)'
+  endif
+
+  !call grd_chksum2(bergs%grd, bergs%grd%ocean_depth, 'read_ocean_depth, ocean_depth')
+end subroutine read_ocean_depth
+
+!> Write a trajectory-based diagnostics file
+subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, traj_name)
+! Arguments
+type(xyt), pointer :: trajectory !< An iceberg trajectory
+logical, intent(in) :: save_short_traj !< If true, record less data
+logical, intent(in) :: save_fl_traj !< If true, save masses and footloose data
+character(len=70) :: traj_name !< name of trajectory file
+! Local variables
+integer :: iret, ncid, i_dim, i
+integer :: lonid, latid, yearid, dayid, uvelid, vvelid, idcntid, idijid
+integer :: uvelpid,vvelpid
+integer :: uoid, void, uiid, viid, uaid, vaid, sshxid, sshyid, sstid, sssid
+integer :: cnid, hiid, hsid
+integer :: mid, smid, did, wid, lid, mbid, mflbid, mflbbid, hdid, nbid, odid, flkid
+integer :: axnid,aynid,bxnid,bynid,axnfid,aynfid,bxnfid,bynfid, msid
+integer :: avid, aaid, rid
+character(len=70) :: filename
+character(len=7) :: pe_name
+type(xyt), pointer :: this, next
+integer :: stderrunit, cnt, ij
+!I/O vars
+type(xyt), pointer :: traj4io=>null()
+integer :: from_pe,np
+type(buffer), pointer :: obuffer_io=>null(), ibuffer_io=>null()
+logical :: io_is_in_append_mode
+integer :: ntrajs_sent_io,ntrajs_rcvd_io
+
+  ! Get the stderr unit number
+  stderrunit=stderr()
+  traj4io=>null()
+  obuffer_io=>null()
+  ibuffer_io=>null()
+
+  !Assemble the list of trajectories from all pes in this I/O tile
+  call mpp_clock_begin(clock_trp)
+
+  !First add the trajs on the io_tile_root_pe (if any) to the I/O list
+  if(is_io_tile_root_pe .OR. force_all_pes_traj ) then
+     if(associated(trajectory)) then
+        this=>trajectory
+        do while (associated(this))
+           call append_posn(traj4io, this)
+           this=>this%next
+        enddo
+        trajectory => null()
+     endif
+  endif
+
+  if(.NOT. force_all_pes_traj ) then
+
+  !Now gather and append the bergs from all pes in the io_tile to the list on corresponding io_tile_root_pe
+  ntrajs_sent_io =0
+  ntrajs_rcvd_io =0
+
+  if(is_io_tile_root_pe) then
+     !Receive trajs from all pes in this I/O tile !FRAGILE!SCARY!
+     do np=2,size(io_tile_pelist) ! Note: np starts from 2 to exclude self
+        from_pe=io_tile_pelist(np)
+        call mpp_recv(ntrajs_rcvd_io, glen=1, from_pe=from_pe, tag=COMM_TAG_11)
+        if (ntrajs_rcvd_io .gt. 0) then
+           call increase_ibuffer(ibuffer_io, ntrajs_rcvd_io,buffer_width_traj)
+           call mpp_recv(ibuffer_io%data, ntrajs_rcvd_io*buffer_width_traj,from_pe=from_pe, tag=COMM_TAG_12)
+           do i=1, ntrajs_rcvd_io
+              call unpack_traj_from_buffer2(traj4io, ibuffer_io, i, save_short_traj, save_fl_traj)
+           enddo
+       endif
+     enddo
+  else
+     ! Pack and send trajectories to the root PE for this I/O tile
+     do while (associated(trajectory))
+       ntrajs_sent_io = ntrajs_sent_io +1
+       call pack_traj_into_buffer2(trajectory, obuffer_io, ntrajs_sent_io, save_short_traj, save_fl_traj)
+       this => trajectory ! Need to keep pointer in order to free up the links memory
+       trajectory => trajectory%next ! This will eventually result in trajectory => null()
+       deallocate(this) ! Delete the link from memory
+     enddo
+
+     call mpp_send(ntrajs_sent_io, plen=1, to_pe=io_tile_root_pe, tag=COMM_TAG_11)
+     if (ntrajs_sent_io .gt. 0) then
+        call mpp_send(obuffer_io%data, ntrajs_sent_io*buffer_width_traj, to_pe=io_tile_root_pe, tag=COMM_TAG_12)
+     endif
+  endif
+  call mpp_sync_self()
+  endif !.NOT. force_all_pes_traj
+
+  call mpp_clock_end(clock_trp)
+
+  !Now start writing in the io_tile_root_pe if there are any bergs in the I/O list
+  call mpp_clock_begin(clock_trw)
+
+  if((force_all_pes_traj .OR. is_io_tile_root_pe) .AND. associated(traj4io)) then
+
+    !call get_instance_filename("iceberg_trajectories.nc", filename)
+    call get_instance_filename(traj_name, filename)
+    if(io_tile_id(1) .ge. 0 .AND. .NOT. force_all_pes_traj) then !io_tile_root_pes write
+       if(io_npes .gt. 1) then !attach tile_id  to filename only if there is more than one I/O pe
+          if (io_tile_id(1)<10000) then
+             write(filename,'(A,".",I4.4)') trim(filename), io_tile_id(1)
+          else
+             write(filename,'(A,".",I6.6)') trim(filename), io_tile_id(1)
+          endif
+       endif
+    else !All pes write, attach pe# to filename
+       if (mpp_npes()<10000) then
+          write(filename,'(A,".",I4.4)') trim(filename), mpp_pe()
+       else
+          write(filename,'(A,".",I6.6)') trim(filename), mpp_pe()
+       endif
+    endif
+
+    io_is_in_append_mode = .false.
+    iret = nf_create(filename, NF_NOCLOBBER, ncid)
+    if (iret .ne. NF_NOERR) then
+      iret = nf_open(filename, NF_WRITE, ncid)
+      io_is_in_append_mode = .true.
+      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_trajectory: nf_open failed'
+    endif
+    if (verbose) then
+      if (io_is_in_append_mode) then
+        write(*,'(2a)') 'KID, write_trajectory: appending to ',filename
+      else
+        write(*,'(2a)') 'KID, write_trajectory: creating ',filename
+      endif
+    endif
+
+    if (io_is_in_append_mode) then
+      iret = nf_inq_dimid(ncid, 'i', i_dim)
+      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_trajectory: nf_inq_dimid i failed'
+      lonid = inq_varid(ncid, 'lon')
+      latid = inq_varid(ncid, 'lat')
+      yearid = inq_varid(ncid, 'year')
+      dayid = inq_varid(ncid, 'day')
+      idcntid = inq_varid(ncid, 'id_cnt')
+      idijid = inq_varid(ncid, 'id_ij')
+      if (save_fl_traj) then
+        mid = inq_varid(ncid, 'mass')
+        smid = inq_varid(ncid, 'start_mass')
+        did = inq_varid(ncid, 'thickness')
+        mbid = inq_varid(ncid, 'mass_of_bits')
+        uvelid = inq_varid(ncid, 'uvel')
+        vvelid = inq_varid(ncid, 'vvel')
+        if (footloose) then
+          msid = inq_varid(ncid, 'mass_scaling')
+          mflbid = inq_varid(ncid, 'mass_of_fl_bits')
+          mflbbid = inq_varid(ncid, 'mass_of_fl_bergy_bits')
+          flkid = inq_varid(ncid, 'fl_k')
+        endif
+      endif
+      if (.not.save_short_traj) then
+        !uvelid = inq_varid(ncid, 'uvel')
+        !vvelid = inq_varid(ncid, 'vvel')
+        uvelpid = inq_varid(ncid, 'uvel_prev')
+        vvelpid = inq_varid(ncid, 'vvel_prev')
+        uoid = inq_varid(ncid, 'uo')
+        void = inq_varid(ncid, 'vo')
+        uiid = inq_varid(ncid, 'ui')
+        viid = inq_varid(ncid, 'vi')
+        uaid = inq_varid(ncid, 'ua')
+        vaid = inq_varid(ncid, 'va')
+        hdid = inq_varid(ncid, 'heat_density')
+        wid = inq_varid(ncid, 'width')
+        lid = inq_varid(ncid, 'length')
+        sshxid = inq_varid(ncid, 'ssh_x')
+        sshyid = inq_varid(ncid, 'ssh_y')
+        sstid = inq_varid(ncid, 'sst')
+        sssid = inq_varid(ncid, 'sss')
+        cnid = inq_varid(ncid, 'cn')
+        hiid = inq_varid(ncid, 'hi')
+        axnid = inq_varid(ncid, 'axn')
+        aynid = inq_varid(ncid, 'ayn')
+        bxnid = inq_varid(ncid, 'bxn')
+        bynid = inq_varid(ncid, 'byn')
+        hsid = inq_varid(ncid, 'halo_berg')
+        odid = inq_varid(ncid, 'od')
+
+        if (mts) then
+          axnfid = inq_varid(ncid, 'axn_fast')
+          aynfid = inq_varid(ncid, 'ayn_fast')
+          bxnfid = inq_varid(ncid, 'bxn_fast')
+          bynfid = inq_varid(ncid, 'byn_fast')
+        endif
+
+        if (iceberg_bonds_on) then
+          nbid = inq_varid(ncid, 'n_bonds')
+        end if
+
+        if (dem) then
+          avid = inq_varid(ncid, 'ang_vel')
+          aaid = inq_varid(ncid, 'ang_accel')
+          rid  = inq_varid(ncid, 'rot')
+        endif
+
+      endif
+    else
+      ! Dimensions
+      iret = nf_def_dim(ncid, 'i', NF_UNLIMITED, i_dim)
+      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_trajectory: nf_def_dim i failed'
+
+      ! Variables
+      lonid = def_var(ncid, 'lon', NF_DOUBLE, i_dim)
+      latid = def_var(ncid, 'lat', NF_DOUBLE, i_dim)
+      yearid = def_var(ncid, 'year', NF_INT, i_dim)
+      dayid = def_var(ncid, 'day', NF_DOUBLE, i_dim)
+      idcntid = def_var(ncid, 'id_cnt', NF_INT, i_dim)
+      idijid = def_var(ncid, 'id_ij', NF_INT, i_dim)
+      if (save_fl_traj) then
+        mid = def_var(ncid, 'mass', NF_DOUBLE, i_dim)
+        smid = def_var(ncid, 'start_mass', NF_DOUBLE, i_dim)
+        did = def_var(ncid, 'thickness', NF_DOUBLE, i_dim)
+        mbid = def_var(ncid, 'mass_of_bits', NF_DOUBLE, i_dim)
+        uvelid = def_var(ncid, 'uvel', NF_DOUBLE, i_dim)
+        vvelid = def_var(ncid, 'vvel', NF_DOUBLE, i_dim)
+        if (footloose) then
+          msid = def_var(ncid, 'mass_scaling', NF_DOUBLE, i_dim)
+          mflbid = def_var(ncid, 'mass_of_fl_bits', NF_DOUBLE, i_dim)
+          mflbbid = def_var(ncid, 'mass_of_fl_bergy_bits', NF_DOUBLE, i_dim)
+          flkid = def_var(ncid, 'fl_k', NF_DOUBLE, i_dim)
+        endif
+      endif
+      if (.not. save_short_traj) then
+        !uvelid = def_var(ncid, 'uvel', NF_DOUBLE, i_dim)
+        !vvelid = def_var(ncid, 'vvel', NF_DOUBLE, i_dim)
+        uvelpid = def_var(ncid, 'uvel_prev', NF_DOUBLE, i_dim)
+        vvelpid = def_var(ncid, 'vvel_prev', NF_DOUBLE, i_dim)
+        uoid = def_var(ncid, 'uo', NF_DOUBLE, i_dim)
+        void = def_var(ncid, 'vo', NF_DOUBLE, i_dim)
+        uiid = def_var(ncid, 'ui', NF_DOUBLE, i_dim)
+        viid = def_var(ncid, 'vi', NF_DOUBLE, i_dim)
+        uaid = def_var(ncid, 'ua', NF_DOUBLE, i_dim)
+        vaid = def_var(ncid, 'va', NF_DOUBLE, i_dim)
+        hdid = def_var(ncid, 'heat_density', NF_DOUBLE, i_dim)
+        wid = def_var(ncid, 'width', NF_DOUBLE, i_dim)
+        lid = def_var(ncid, 'length', NF_DOUBLE, i_dim)
+        sshxid = def_var(ncid, 'ssh_x', NF_DOUBLE, i_dim)
+        sshyid = def_var(ncid, 'ssh_y', NF_DOUBLE, i_dim)
+        sstid = def_var(ncid, 'sst', NF_DOUBLE, i_dim)
+        sssid = def_var(ncid, 'sss', NF_DOUBLE, i_dim)
+        cnid = def_var(ncid, 'cn', NF_DOUBLE, i_dim)
+        hiid = def_var(ncid, 'hi', NF_DOUBLE, i_dim)
+        axnid = def_var(ncid, 'axn', NF_DOUBLE, i_dim)
+        aynid = def_var(ncid, 'ayn', NF_DOUBLE, i_dim)
+        bxnid = def_var(ncid, 'bxn', NF_DOUBLE, i_dim)
+        bynid = def_var(ncid, 'byn', NF_DOUBLE, i_dim)
+        hsid = def_var(ncid, 'halo_berg', NF_DOUBLE, i_dim)
+        odid = def_var(ncid, 'od', NF_DOUBLE, i_dim)
+
+        if (mts) then
+          axnfid = def_var(ncid, 'axn_fast', NF_DOUBLE, i_dim)
+          aynfid = def_var(ncid, 'ayn_fast', NF_DOUBLE, i_dim)
+          bxnfid = def_var(ncid, 'bxn_fast', NF_DOUBLE, i_dim)
+          bynfid = def_var(ncid, 'byn_fast', NF_DOUBLE, i_dim)
+        endif
+
+        if (iceberg_bonds_on) then
+          nbid = def_var(ncid, 'n_bonds', NF_INT, i_dim)
+        end if
+
+        if (dem) then
+          avid = def_var(ncid, 'ang_vel', NF_DOUBLE, i_dim)
+          aaid = def_var(ncid, 'ang_accel', NF_DOUBLE, i_dim)
+          rid  = def_var(ncid, 'rot', NF_DOUBLE, i_dim)
+        endif
+      endif
+
+      ! Attributes
+      iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_major_version', NF_INT, 1, 0)
+      iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_minor_version', NF_INT, 1, 1)
+      call put_att(ncid, lonid, 'long_name', 'longitude')
+      call put_att(ncid, lonid, 'units', 'degrees_E')
+      call put_att(ncid, latid, 'long_name', 'latitude')
+      call put_att(ncid, latid, 'units', 'degrees_N')
+      call put_att(ncid, yearid, 'long_name', 'year')
+      call put_att(ncid, yearid, 'units', 'years')
+      call put_att(ncid, dayid, 'long_name', 'year day')
+      call put_att(ncid, dayid, 'units', 'days')
+      call put_att(ncid, idcntid, 'long_name', 'counter component of iceberg id')
+      call put_att(ncid, idcntid, 'units', 'dimensionless')
+      call put_att(ncid, idijid, 'long_name', 'position component of iceberg id')
+      call put_att(ncid, idijid, 'units', 'dimensionless')
+      if (save_fl_traj) then
+        call put_att(ncid, mid, 'long_name', 'mass')
+        call put_att(ncid, mid, 'units', 'kg')
+        call put_att(ncid, smid, 'long_name', 'start_mass')
+        call put_att(ncid, smid, 'units', 'kg')
+        call put_att(ncid, did, 'long_name', 'thickness')
+        call put_att(ncid, did, 'units', 'm')
+        call put_att(ncid, mbid, 'long_name', 'mass_of_bits')
+        call put_att(ncid, mbid, 'units', 'kg')
+        call put_att(ncid, uvelid, 'long_name', 'zonal spped')
+        call put_att(ncid, uvelid, 'units', 'm/s')
+        call put_att(ncid, vvelid, 'long_name', 'meridional spped')
+        call put_att(ncid, vvelid, 'units', 'm/s')
+        if (footloose) then
+          call put_att(ncid, msid, 'long_name', 'mass_scaling')
+          call put_att(ncid, msid, 'units', 'dimensionless')
+          call put_att(ncid, mflbid, 'long_name', 'mass_of_fl_bits')
+          call put_att(ncid, mflbid, 'units', 'kg')
+          call put_att(ncid, mflbbid, 'long_name', 'mass_of_fl_bergy_bits')
+          call put_att(ncid, mflbbid, 'units', 'kg')
+          call put_att(ncid, flkid, 'long_name', 'footloose calving k')
+          call put_att(ncid, flkid, 'units', 'none')
+        endif
+      endif
+      if (.not. save_short_traj) then
+        ! call put_att(ncid, uvelid, 'long_name', 'zonal spped')
+        ! call put_att(ncid, uvelid, 'units', 'm/s')
+        ! call put_att(ncid, vvelid, 'long_name', 'meridional spped')
+        ! call put_att(ncid, vvelid, 'units', 'm/s')
+        call put_att(ncid, uoid, 'long_name', 'ocean zonal spped')
+        call put_att(ncid, uoid, 'units', 'm/s')
+        call put_att(ncid, void, 'long_name', 'ocean meridional spped')
+        call put_att(ncid, void, 'units', 'm/s')
+        call put_att(ncid, uiid, 'long_name', 'ice zonal spped')
+        call put_att(ncid, uiid, 'units', 'm/s')
+        call put_att(ncid, viid, 'long_name', 'ice meridional spped')
+        call put_att(ncid, viid, 'units', 'm/s')
+        call put_att(ncid, uaid, 'long_name', 'atmos zonal spped')
+        call put_att(ncid, uaid, 'units', 'm/s')
+        call put_att(ncid, vaid, 'long_name', 'atmos meridional spped')
+        call put_att(ncid, vaid, 'units', 'm/s')
+        call put_att(ncid, hdid, 'long_name', 'heat_density')
+        call put_att(ncid, hdid, 'units', 'J/kg')
+        call put_att(ncid, wid, 'long_name', 'width')
+        call put_att(ncid, wid, 'units', 'm')
+        call put_att(ncid, lid, 'long_name', 'length')
+        call put_att(ncid, lid, 'units', 'm')
+        call put_att(ncid, sshxid, 'long_name', 'sea surface height gradient_x')
+        call put_att(ncid, sshxid, 'units', 'non-dim')
+        call put_att(ncid, sshyid, 'long_name', 'sea surface height gradient_y')
+        call put_att(ncid, sshyid, 'units', 'non-dim')
+        call put_att(ncid, sstid, 'long_name', 'sea surface temperature')
+        call put_att(ncid, sstid, 'units', 'degrees_C')
+        call put_att(ncid, sssid, 'long_name', 'sea surface salinity')
+        call put_att(ncid, sssid, 'units', 'psu')
+        call put_att(ncid, cnid, 'long_name', 'sea ice concentration')
+        call put_att(ncid, cnid, 'units', 'none')
+        call put_att(ncid, hiid, 'long_name', 'sea ice thickness')
+        call put_att(ncid, hiid, 'units', 'm')
+        call put_att(ncid, axnid, 'long_name', 'explicit zonal acceleration')
+        call put_att(ncid, axnid, 'units', 'm')
+        call put_att(ncid, aynid, 'long_name', 'explicit meridional acceleration')
+        call put_att(ncid, aynid, 'units', 'm')
+        call put_att(ncid, bxnid, 'long_name', 'implicit zonal acceleration')
+        call put_att(ncid, bxnid, 'units', 'm')
+        call put_att(ncid, bynid, 'long_name', 'implicit meridional acceleration')
+        call put_att(ncid, bynid, 'units', 'm')
+        call put_att(ncid, hsid, 'long_name', 'halo status')
+        call put_att(ncid, hsid, 'units', 'non-dim')
+        call put_att(ncid, odid, 'long_name', 'ocean_depth')
+        call put_att(ncid, odid, 'units', 'm')
+
+        if (mts) then
+          call put_att(ncid, uvelpid, 'long_name', 'zonal speed mts')
+          call put_att(ncid, uvelpid, 'units', 'm/s')
+          call put_att(ncid, vvelpid, 'long_name', 'meridional speed mts')
+          call put_att(ncid, vvelpid, 'units', 'm/s')
+          call put_att(ncid, axnfid, 'long_name', 'explicit fast step zonal acceleration')
+          call put_att(ncid, axnfid, 'units', 'm')
+          call put_att(ncid, aynfid, 'long_name', 'explicit fast step meridional acceleration')
+          call put_att(ncid, aynfid, 'units', 'm')
+          call put_att(ncid, bxnfid, 'long_name', 'implicit fast step zonal acceleration')
+          call put_att(ncid, bxnfid, 'units', 'm')
+          call put_att(ncid, bynfid, 'long_name', 'implicit fast step meridional acceleration')
+          call put_att(ncid, bynfid, 'units', 'm')
+        endif
+
+        if (iceberg_bonds_on) then
+          call put_att(ncid, nbid, 'long_name', 'number of bonds')
+          call put_att(ncid, nbid, 'units', 'dimensionless')
+        end if
+
+        if (dem) then
+          call put_att(ncid, avid, 'long_name', 'angular velocity')
+          call put_att(ncid, avid, 'units', 'rad/s')
+          call put_att(ncid, aaid, 'long_name', 'angular acceleration')
+          call put_att(ncid, aaid, 'units', 'rad/s^2')
+          call put_att(ncid, rid, 'long_name', 'accumulated rotation')
+          call put_att(ncid, rid, 'units', 'rad')
+        endif
+      endif
+    endif
+
+    ! End define mode
+    iret = nf_enddef(ncid)
+
+    ! Write variables
+    this=>traj4io
+    if (io_is_in_append_mode) then
+      iret = nf_inq_dimlen(ncid, i_dim, i)
+      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_trajectory: nf_inq_dimlen i failed'
+    else
+      i = 0
+    endif
+    do while (associated(this))
+      i=i+1
+      call put_double(ncid, lonid, i, this%lon)
+      call put_double(ncid, latid, i, this%lat)
+      call put_int(ncid, yearid, i, this%year)
+      call put_double(ncid, dayid, i, this%day)
+      call split_id(this%id, cnt, ij)
+      call put_int(ncid, idcntid, i, cnt)
+      call put_int(ncid, idijid, i, ij)
+      if (save_fl_traj) then
+        call put_double(ncid, mid, i, this%mass)
+        call put_double(ncid, smid, i, this%start_mass)
+        call put_double(ncid, did, i, this%thickness)
+        call put_double(ncid, mbid, i, this%mass_of_bits)
+        call put_double(ncid, uvelid, i, this%uvel)
+        call put_double(ncid, vvelid, i, this%vvel)
+        if (footloose) then
+          call put_double(ncid, msid, i, this%mass_scaling)
+          call put_double(ncid, mflbid, i, this%mass_of_fl_bits)
+          call put_double(ncid, mflbbid, i, this%mass_of_fl_bergy_bits)
+          call put_double(ncid, flkid, i, this%fl_k)
+        endif
+      endif
+      if (.not. save_short_traj) then
+        ! call put_double(ncid, uvelid, i, this%uvel)
+        ! call put_double(ncid, vvelid, i, this%vvel)
+        call put_double(ncid, uvelpid, i, this%uvel_prev)
+        call put_double(ncid, vvelpid, i, this%vvel_prev)
+        call put_double(ncid, uoid, i, this%uo)
+        call put_double(ncid, void, i, this%vo)
+        call put_double(ncid, uiid, i, this%ui)
+        call put_double(ncid, viid, i, this%vi)
+        call put_double(ncid, uaid, i, this%ua)
+        call put_double(ncid, vaid, i, this%va)
+        call put_double(ncid, hdid, i, this%heat_density)
+        call put_double(ncid, wid, i, this%width)
+        call put_double(ncid, lid, i, this%length)
+        call put_double(ncid, sshxid, i, this%ssh_x)
+        call put_double(ncid, sshyid, i, this%ssh_y)
+        call put_double(ncid, sstid, i, this%sst)
+        call put_double(ncid, sssid, i, this%sss)
+        call put_double(ncid, cnid, i, this%cn)
+        call put_double(ncid, hiid, i, this%hi)
+        call put_double(ncid, axnid, i, this%axn)
+        call put_double(ncid, aynid, i, this%ayn)
+        call put_double(ncid, bxnid, i, this%bxn)
+        call put_double(ncid, bynid, i, this%byn)
+        call put_double(ncid, hsid, i, this%halo_berg)
+        call put_double(ncid, odid, i, this%od)
+
+        if (mts) then
+          call put_double(ncid, axnfid, i, this%axn_fast)
+          call put_double(ncid, aynfid, i, this%ayn_fast)
+          call put_double(ncid, bxnfid, i, this%bxn_fast)
+          call put_double(ncid, bynfid, i, this%byn_fast)
+        endif
+
+        if (iceberg_bonds_on) then
+          call put_int(ncid, nbid, i, this%n_bonds)
+        end if
+
+        if (dem) then
+          call put_double(ncid, avid, i, this%ang_vel)
+          call put_double(ncid, aaid, i, this%ang_accel)
+          call put_double(ncid, rid,  i, this%rot)
+        endif
+
+      endif
+      next=>this%next
+      deallocate(this)
+      this=>next
+    enddo
+
+    ! Finish up
+    iret = nf_close(ncid)
+    if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_trajectory: nf_close failed',mpp_pe(),filename
+
+  endif !(is_io_tile_root_pe .AND. associated(traj4io))
+  call mpp_clock_end(clock_trw)
+
+end subroutine write_trajectory
+
+!> Write a trajectory-based diagnostics file for bonds
+subroutine write_bond_trajectory(trajectory, bond_traj_name)
+! Arguments
+type(bond_xyt), pointer :: trajectory !< An iceberg bond trajectory
+character(len=70) :: bond_traj_name !<file name of bond trajectories
+! Local variables
+integer :: iret, ncid, i_dim, i
+integer :: lonid, latid, yearid, dayid, lenid,n1id, n2id
+integer :: rrotid,brid
+integer :: idcnt1_id, idcnt2_id, idij1_id, idij2_id
+integer :: td1id,td2id,dnsid,dssid
+character(len=70) :: filename
+character(len=7) :: pe_name
+type(bond_xyt), pointer :: this, next
+integer :: stderrunit, cnt, ij
+!I/O vars
+type(bond_xyt), pointer :: traj4io=>null()
+integer :: ntrajs_sent_io,ntrajs_rcvd_io
+integer :: from_pe,np
+type(buffer), pointer :: obuffer_io=>null(), ibuffer_io=>null()
+logical :: io_is_in_append_mode
+
+  stderrunit=stderr()  ! Get the stderr unit number
+  traj4io=>null()
+  ibuffer_io=>null(); obuffer_io=>null()
+
+  !Assemble the list of trajectories from all pes in this I/O tile
+  call mpp_clock_begin(clock_btrp)
+
+  !First add the trajs on the io_tile_root_pe (if any) to the I/O list
+  if(is_io_tile_root_pe .OR. force_all_pes_traj ) then
+    if(associated(trajectory)) then
+      this=>trajectory
+      do while (associated(this))
+        call append_bond_posn(traj4io, this)
+        this=>this%next
+      enddo
+      trajectory => null()
+    endif
+  endif
+
+  if(.NOT. force_all_pes_traj ) then
+    !Now gather and append the bergs from all pes in the io_tile to the list on corresponding io_tile_root_pe
+    ntrajs_sent_io =0; ntrajs_rcvd_io =0
+
+    if(is_io_tile_root_pe) then
+      !Receive trajs from all pes in this I/O tile !FRAGILE!SCARY!
+      do np=2,size(io_tile_pelist) ! Note: np starts from 2 to exclude self
+        from_pe=io_tile_pelist(np)
+        call mpp_recv(ntrajs_rcvd_io, glen=1, from_pe=from_pe, tag=COMM_TAG_11)
+        if (ntrajs_rcvd_io .gt. 0) then
+          call increase_ibuffer(ibuffer_io, ntrajs_rcvd_io,buffer_width_bond_traj)
+          call mpp_recv(ibuffer_io%data, ntrajs_rcvd_io*buffer_width_bond_traj,from_pe=from_pe, tag=COMM_TAG_12)
+          do i=1, ntrajs_rcvd_io
+            call unpack_bond_traj_from_buffer2(traj4io, ibuffer_io, i)
+          enddo
+        endif
+      enddo
+    else
+      ! Pack and send trajectories to the root PE for this I/O tile
+      do while (associated(trajectory))
+        ntrajs_sent_io = ntrajs_sent_io +1
+        call pack_bond_traj_into_buffer2(trajectory, obuffer_io, ntrajs_sent_io)
+        this => trajectory ! Need to keep pointer in order to free up the links memory
+        trajectory => trajectory%next ! This will eventually result in trajectory => null()
+        deallocate(this) ! Delete the link from memory
+      enddo
+
+      call mpp_send(ntrajs_sent_io, plen=1, to_pe=io_tile_root_pe, tag=COMM_TAG_11)
+      if (ntrajs_sent_io .gt. 0) then
+        call mpp_send(obuffer_io%data, ntrajs_sent_io*buffer_width_bond_traj, to_pe=io_tile_root_pe, tag=COMM_TAG_12)
+      endif
+    endif
+  endif !.NOT. force_all_pes_traj
+
+  call mpp_clock_end(clock_btrp)
+
+  !Now start writing in the io_tile_root_pe if there are any bergs in the I/O list
+  call mpp_clock_begin(clock_btrw)
+
+  if((force_all_pes_traj .OR. is_io_tile_root_pe) .AND. associated(traj4io)) then
+
+    !call get_instance_filename("bond_trajectories.nc", filename)
+    call get_instance_filename(bond_traj_name, filename)
+    if(io_tile_id(1) .ge. 0 .AND. .NOT. force_all_pes_traj) then !io_tile_root_pes write
+      if(io_npes .gt. 1) then !attach tile_id  to filename only if there is more than one I/O pe
+        if (io_tile_id(1)<10000) then
+          write(filename,'(A,".",I4.4)') trim(filename), io_tile_id(1)
+        else
+          write(filename,'(A,".",I6.6)') trim(filename), io_tile_id(1)
+        endif
+      endif
+    else !All pes write, attach pe# to filename
+      if (mpp_npes()<10000) then
+        write(filename,'(A,".",I4.4)') trim(filename), mpp_pe()
+      else
+        write(filename,'(A,".",I6.6)') trim(filename), mpp_pe()
+      endif
+    endif
+
+    io_is_in_append_mode = .false.
+    iret = nf_create(filename, NF_NOCLOBBER, ncid)
+    if (iret .ne. NF_NOERR) then
+      iret = nf_open(filename, NF_WRITE, ncid)
+      io_is_in_append_mode = .true.
+      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_bond_trajectory: nf_open failed'
+    endif
+    if (verbose) then
+      if (io_is_in_append_mode) then
+        write(*,'(2a)') 'KID, write_bond_trajectory: appending to ',filename
+      else
+        write(*,'(2a)') 'KID, write_bond_trajectory: creating ',filename
+      endif
+    endif
+
+    if (io_is_in_append_mode) then
+      iret = nf_inq_dimid(ncid, 'i', i_dim)
+      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_bond_trajectory: nf_inq_dimid i failed'
+      lonid = inq_varid(ncid, 'lon');         latid = inq_varid(ncid, 'lat')
+      yearid = inq_varid(ncid, 'year');       dayid = inq_varid(ncid, 'day')
+      lenid = inq_varid(ncid, 'length');
+      n1id = inq_varid(ncid, 'n1');           n2id = inq_varid(ncid, 'n2')
+
+      idcnt1_id = inq_varid(ncid, 'id_cnt1'); idij1_id = inq_varid(ncid, 'id_ij1')
+      idcnt2_id = inq_varid(ncid, 'id_cnt2'); idij2_id = inq_varid(ncid, 'id_ij2')
+
+      if (dem) then
+        td1id = inq_varid(ncid, 'tangd1');  td2id = inq_varid(ncid, 'tangd2')
+        dnsid = inq_varid(ncid, 'nstress'); dssid = inq_varid(ncid, 'sstress')
+        rrotid = inq_varid(ncid, 'rel_rotation'); brid = inq_varid(ncid, 'broken')
+      endif
+
+    else
+      ! Dimensions
+      iret = nf_def_dim(ncid, 'i', NF_UNLIMITED, i_dim)
+      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_bond_trajectory: nf_def_dim i failed'
+
+      ! Variables
+      lonid = def_var(ncid, 'lon', NF_DOUBLE, i_dim);      latid = def_var(ncid, 'lat', NF_DOUBLE, i_dim)
+      yearid = def_var(ncid, 'year', NF_INT, i_dim);       dayid = def_var(ncid, 'day', NF_DOUBLE, i_dim)
+      lenid = def_var(ncid, 'length', NF_DOUBLE, i_dim);
+      n1id = def_var(ncid, 'n1', NF_DOUBLE, i_dim);        n2id = def_var(ncid, 'n2', NF_DOUBLE, i_dim)
+
+      idcnt1_id = def_var(ncid, 'id_cnt1', NF_INT, i_dim); idij1_id = def_var(ncid, 'id_ij1', NF_INT, i_dim)
+      idcnt2_id = def_var(ncid, 'id_cnt2', NF_INT, i_dim); idij2_id = def_var(ncid, 'id_ij2', NF_INT, i_dim)
+
+      if (dem) then
+        td1id = def_var(ncid, 'tangd1',  NF_DOUBLE, i_dim); td2id = def_var(ncid, 'tangd2',  NF_DOUBLE, i_dim)
+        dnsid = def_var(ncid, 'nstress', NF_DOUBLE, i_dim); dssid = def_var(ncid, 'sstress', NF_DOUBLE, i_dim)
+        rrotid = def_var(ncid, 'rel_rotation', NF_DOUBLE, i_dim)
+        brid = def_var(ncid, 'broken', NF_INT, i_dim)
+      endif
+
+      ! Attributes
+      iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_major_version', NF_INT, 1, 0)
+      iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_minor_version', NF_INT, 1, 1)
+      call put_att(ncid, lonid, 'long_name', 'longitude');    call put_att(ncid, lonid, 'units', 'degrees_E')
+      call put_att(ncid, latid, 'long_name', 'latitude');     call put_att(ncid, latid, 'units', 'degrees_N')
+      call put_att(ncid, yearid, 'long_name', 'year');        call put_att(ncid, yearid, 'units', 'years')
+      call put_att(ncid, dayid, 'long_name', 'year day');     call put_att(ncid, dayid, 'units', 'days')
+      call put_att(ncid, lenid, 'long_name', 'length');       call put_att(ncid, lenid, 'units', 'm')
+      call put_att(ncid, n1id, 'long_name', 'unit vector 1'); call put_att(ncid, n1id, 'units', 'non-dim')
+      call put_att(ncid, n2id, 'long_name', 'unit vector 2'); call put_att(ncid, n2id, 'units', 'non-dim')
+
+      call put_att(ncid, idcnt1_id, 'long_name', 'counter component of first connected iceberg id')
+      call put_att(ncid, idcnt1_id, 'units', 'dimensionless')
+      call put_att(ncid, idij1_id, 'long_name', 'position component of first connected iceberg id')
+      call put_att(ncid, idij1_id, 'units', 'dimensionless')
+      call put_att(ncid, idcnt2_id, 'long_name', 'counter component of second connected iceberg id')
+      call put_att(ncid, idcnt2_id, 'units', 'dimensionless')
+      call put_att(ncid, idij2_id, 'long_name', 'position component of second connected iceberg id')
+      call put_att(ncid, idij2_id, 'units', 'dimensionless')
+
+      if (dem) then
+        call put_att(ncid, td1id, 'long_name', 'zonal tangential displacement')
+        call put_att(ncid, td1id, 'units', 'm')
+        call put_att(ncid, td2id, 'long_name', 'meridional tangential displacement')
+        call put_att(ncid, td2id, 'units', 'm')
+        call put_att(ncid, dnsid, 'long_name', 'normal stress'); call put_att(ncid, dnsid, 'units', 'Pa')
+        call put_att(ncid, dssid, 'long_name', 'shear stress');  call put_att(ncid, dssid, 'units', 'Pa')
+        call put_att(ncid, rrotid, 'long_name', 'relative rotation');      call put_att(ncid, rrotid, 'units', 'rad')
+        call put_att(ncid, brid, 'long_name', 'broken status');      call put_att(ncid, brid, 'units', 'none')
+      endif
+    endif
+
+    ! End define mode
+    iret = nf_enddef(ncid)
+
+    ! Write variables
+    this=>traj4io
+    if (io_is_in_append_mode) then
+      iret = nf_inq_dimlen(ncid, i_dim, i)
+      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_bond_trajectory: nf_inq_dimlen i failed'
+    else
+      i = 0
+    endif
+    do while (associated(this))
+      i=i+1
+      call put_double(ncid, lonid, i, this%lon);    call put_double(ncid, latid, i, this%lat)
+      call put_int(ncid, yearid, i, this%year);     call put_double(ncid, dayid, i, this%day)
+      call put_double(ncid, lenid, i, this%length);
+      call put_double(ncid, n1id, i, this%n1);      call put_double(ncid, n2id, i, this%n2)
+
+      call split_id(this%id1, cnt, ij)
+      call put_int(ncid, idcnt1_id, i, cnt);        call put_int(ncid, idij1_id, i, ij)
+      call split_id(this%id2, cnt, ij)
+      call put_int(ncid, idcnt2_id, i, cnt);        call put_int(ncid, idij2_id, i, ij)
+
+      if (dem) then
+        call put_double(ncid,td1id,i,this%tangd1);  call put_double(ncid,td2id,i,this%tangd2)
+        call put_double(ncid,dnsid,i,this%nstress); call put_double(ncid,dssid,i,this%sstress)
+        call put_double(ncid,rrotid,i,this%rel_rotation); call put_int(ncid,brid,i,this%broken)
+      endif
+
+      next=>this%next
+      deallocate(this)
+      this=>next
+    enddo
+
+    ! Finish up
+    iret = nf_close(ncid)
+    if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_bond_trajectory: nf_close failed',mpp_pe(),filename
+
+  endif !(is_io_tile_root_pe .AND. associated(traj4io))
+  call mpp_clock_end(clock_btrw)
+
+end subroutine write_bond_trajectory
+
+!> Returns netcdf id of variable
+integer function inq_var(ncid, var, unsafe)
+! Arguments
+integer, intent(in) :: ncid !< Handle to netcdf file
+character(len=*), intent(in) :: var !< Name of variable
+logical, optional, intent(in) :: unsafe !< If present and true, do not fail if variable is not in file
+! Local variables
+integer :: iret
+integer :: stderrunit
+logical :: unsafely=.false.
+
+  if(present(unsafe)) unsafely=unsafe
+  ! Get the stderr unit number
+  stderrunit=stderr()
+
+  iret=nf_inq_varid(ncid, var, inq_var)
+  if (iret .ne. NF_NOERR) then
+    if (.not. unsafely) then
+      write(stderrunit,*) 'KID, inq_var: nf_inq_varid ',var,' failed'
+      call error_mesg('KID, inq_var', 'netcdf function returned a failure!', FATAL)
+    else
+      inq_var=-1
+    endif
+  endif
+
+end function inq_var
+
+!> Define a netcdf variable
+integer function def_var(ncid, var, ntype, idim)
+! Arguments
+integer, intent(in) :: ncid !< Handle to netcdf file
+character(len=*), intent(in) :: var !< Name of variable
+integer, intent(in) :: ntype !< Netcdf type of variable
+integer, intent(in) :: idim !< Length of vector
+! Local variables
+integer :: iret
+integer :: stderrunit
+
+  ! Get the stderr unit number
+  stderrunit=stderr()
+
+  iret = nf_def_var(ncid, var, ntype, 1, idim, def_var)
+  if (iret .ne. NF_NOERR) then
+    call error_mesg('KID, def_var', nf_strerror(iret), FATAL)
+  endif
+
+end function def_var
+
+!> Returns id of variable
+integer function inq_varid(ncid, var)
+! Arguments
+integer, intent(in) :: ncid !< Handle to netcdf file
+character(len=*), intent(in) :: var !< Name of variable
+! Local variables
+integer :: iret
+integer :: stderrunit
+
+  ! Get the stderr unit number
+  stderrunit=stderr()
+
+  iret = nf_inq_varid(ncid, var, inq_varid)
+  if (iret .ne. NF_NOERR) then
+    write(stderrunit,*) 'KID, inq_varid: nf_inq_varid failed for ',trim(var)
+    call error_mesg('KID, inq_varid', 'netcdf function returned a failure!', FATAL)
+  endif
+
+end function inq_varid
+
+!> Add a string attribute to a netcdf variable
+subroutine put_att(ncid, id, att, attval)
+! Arguments
+integer, intent(in) :: ncid !< Handle to netcdf file
+integer, intent(in) :: id !< Netcdf id of variable
+character(len=*), intent(in) :: att !< Name of attribute
+character(len=*), intent(in) :: attval !< Value of attribute
+! Local variables
+integer :: vallen, iret
+integer :: stderrunit
+
+  ! Get the stderr unit number
+  stderrunit=stderr()
+
+  vallen=len_trim(attval)
+  iret = nf_put_att_text(ncid, id, att, vallen, attval)
+  if (iret .ne. NF_NOERR) then
+    write(stderrunit,*) 'KID, put_att: nf_put_att_text failed adding', &
+      trim(att),' = ',trim(attval)
+    call error_mesg('KID, put_att', 'netcdf function returned a failure!', FATAL)
+  endif
+
+end subroutine put_att
+
+!> Read a real from a netcdf file
+real function get_double(ncid, id, i)
+! Arguments
+integer, intent(in) :: ncid !< Handle to netcdf file
+integer, intent(in) :: id !< Netcdf id of variable
+integer, intent(in) :: i !< Index to read
+! Local variables
+integer :: iret
+integer :: stderrunit
+
+  ! Get the stderr unit number
+  stderrunit=stderr()
+
+  iret=nf_get_var1_double(ncid, id, i, get_double)
+  if (iret .ne. NF_NOERR) then
+    write(stderrunit,*) 'KID, get_double: nf_get_var1_double failed reading'
+    call error_mesg('KID, get_double', 'netcdf function returned a failure!', FATAL)
+  endif
+
+end function get_double
+
+!> Read an integer from a netcdf file
+integer function get_int(ncid, id, i)
+! Arguments
+integer, intent(in) :: ncid !< Handle to netcdf file
+integer, intent(in) :: id !< Netcdf id of variable
+integer, intent(in) :: i !< Index to read
+! Local variables
+integer :: iret
+integer :: stderrunit
+
+  ! Get the stderr unit number
+  stderrunit=stderr()
+
+  iret=nf_get_var1_int(ncid, id, i, get_int)
+  if (iret .ne. NF_NOERR) then
+    write(stderrunit,*) 'KID, get_int: nf_get_var1_int failed reading'
+    call error_mesg('KID, get_int', 'netcdf function returned a failure!', FATAL)
+  endif
+
+end function get_int
+
+!> Write a real to a netcdf file
+subroutine put_double(ncid, id, i, val)
+! Arguments
+integer, intent(in) :: ncid !< Handle to netcdf file
+integer, intent(in) :: id !< Netcdf id of variable
+integer, intent(in) :: i !< Index of position to write
+real, intent(in) :: val !< Value to write
+! Local variables
+integer :: iret
+integer :: stderrunit
+
+  ! Get the stderr unit number
+  stderrunit=stderr()
+
+  iret = nf_put_vara_double(ncid, id, i, 1, val)
+  if (iret .ne. NF_NOERR) then
+    write(stderrunit,*) 'KID, put_double: nf_put_vara_double failed writing'
+    call error_mesg('KID, put_double', 'netcdf function returned a failure!', FATAL)
+  endif
+
+end subroutine put_double
+
+!> Write an integer to a netcdf file
+subroutine put_int(ncid, id, i, val)
+! Arguments
+integer, intent(in) :: ncid !< Handle to netcdf file
+integer, intent(in) :: id !< Netcdf id of variable
+integer, intent(in) :: i !< Index of position to write
+integer, intent(in) :: val !< Value to write
+! Local variables
+integer :: iret
+integer :: stderrunit
+
+  ! Get the stderr unit number
+  stderrunit=stderr()
+
+  iret = nf_put_vara_int(ncid, id, i, 1, val)
+  if (iret .ne. NF_NOERR) then
+    write(stderrunit,*) 'KID, put_int: nf_put_vara_int failed writing'
+    call error_mesg('KID, put_int', 'netcdf function returned a failure!', FATAL)
+  endif
+
+end subroutine put_int
+
+!> True is a restart file can be found
+logical function find_restart_file(filename, actual_file, multiPErestart, tile_id)
+  character(len=*), intent(in) :: filename !< Base-name of restart file
+  character(len=*), intent(out) :: actual_file !< Actual name of file, if found
+  logical, intent(out) :: multiPErestart !< True if found, false otherwise
+  integer, intent(in) :: tile_id !< Parallel tile number of file
+
+  character(len=6) :: pe_name
+
+  find_restart_file = .false.
+
+  ! If running as ensemble, add the ensemble id string to the filename
+  call get_instance_filename(filename, actual_file)
+
+  ! Prefer combined restart files.
+  inquire(file=actual_file,exist=find_restart_file)
+  if (find_restart_file) return
+
+  ! Uncombined restart
+  if(tile_id .ge. 0) then
+    write(actual_file,'(A,".",I4.4)') trim(actual_file), tile_id
+  else
+  if (mpp_npes()>10000) then
+     write(pe_name,'(a,i6.6)' )'.', mpp_pe()
+  else
+     write(pe_name,'(a,i4.4)' )'.', mpp_pe()
+  endif
+  actual_file=trim(actual_file)//trim(pe_name)
+  endif
+  inquire(file=actual_file,exist=find_restart_file)
+  if (find_restart_file) then
+     multiPErestart=.true.
+     return
+  endif
+
+  ! No file found, Reset all return parameters
+  find_restart_file=.false.
+  actual_file = ''
+  multiPErestart=.false.
+
+end function find_restart_file
+
+end module
diff --git a/src/icebergs_fmsio.F90 b/src/icebergs_fmsio.F90
new file mode 100644
index 0000000..479e59c
--- /dev/null
+++ b/src/icebergs_fmsio.F90
@@ -0,0 +1,2496 @@
+!> Handles reading/writing of restart files and trajectory-based diagnostic files
+module ice_bergs_fmsio
+#ifdef use_depreciated_io
+! This file is part of NOAA-GFDL/icebergs. See LICENSE.md for the license.
+
+use mpp_domains_mod, only: domain2D
+use mpp_domains_mod, only: mpp_domain_is_tile_root_pe,mpp_get_domain_tile_root_pe
+use mpp_domains_mod, only: mpp_get_tile_pelist,mpp_get_tile_npes,mpp_get_io_domain,mpp_get_tile_id
+
+use mpp_mod, only: mpp_npes, mpp_pe, mpp_root_pe, mpp_sum, mpp_min, mpp_max, NULL_PE
+use mpp_mod, only: mpp_send, mpp_recv, mpp_gather, mpp_chksum, mpp_sync_self
+use mpp_mod, only: COMM_TAG_11, COMM_TAG_12, COMM_TAG_13, COMM_TAG_14
+
+use fms_mod, only: stdlog, stderr, error_mesg, FATAL, WARNING, NOTE
+use fms_mod, only: field_exist, file_exist, read_data, write_data
+
+use fms_io_mod, only: get_instance_filename
+use fms_io_mod, only : save_restart, restart_file_type, free_restart_type, set_meta_global
+use fms_io_mod, only : register_restart_axis, register_restart_field, set_domain, nullify_domain
+use fms_io_mod, only : read_unlimited_axis =>read_compressed, field_exist, get_field_size
+
+use mpp_mod,    only : mpp_clock_begin, mpp_clock_end, mpp_clock_id
+use mpp_mod,    only : CLOCK_COMPONENT, CLOCK_SUBCOMPONENT, CLOCK_LOOP
+use fms_mod,    only : clock_flag_default
+
+use time_manager_mod, only: time_type, get_date, get_time, set_date, operator(-)
+
+use ice_bergs_framework, only: icebergs_gridded, xyt, bond_xyt, iceberg, icebergs, buffer, bond
+use ice_bergs_framework, only: pack_traj_into_buffer2,unpack_traj_from_buffer2
+use ice_bergs_framework, only: find_cell,find_cell_by_search,count_bergs,is_point_in_cell,pos_within_cell,append_posn
+use ice_bergs_framework, only: count_bonds, form_a_bond, find_individual_iceberg
+use ice_bergs_framework, only: push_posn
+use ice_bergs_framework, only: add_new_berg_to_list,destroy_iceberg
+use ice_bergs_framework, only: increase_ibuffer,grd_chksum2,grd_chksum3
+use ice_bergs_framework, only: sum_mass,sum_heat,bilin
+!params !Niki: write a subroutine to get these
+use ice_bergs_framework, only: nclasses, buffer_width, buffer_width_traj, buffer_width_bond_traj
+use ice_bergs_framework, only: verbose, really_debug, debug, restart_input_dir,make_calving_reproduce
+use ice_bergs_framework, only: ignore_ij_restart, use_slow_find,generate_test_icebergs,print_berg
+use ice_bergs_framework, only: force_all_pes_traj
+use ice_bergs_framework, only: check_for_duplicates_in_parallel
+use ice_bergs_framework, only: split_id, id_from_2_ints, generate_id
+! for MTS/DEM/fracture/footloose:
+use ice_bergs_framework, only: mts,save_bond_traj
+use ice_bergs_framework, only: push_bond_posn, append_bond_posn
+use ice_bergs_framework, only: pack_bond_traj_into_buffer2,unpack_bond_traj_from_buffer2
+use ice_bergs_framework, only: dem, iceberg_bonds_on
+use ice_bergs_framework, only: footloose
+
+
+implicit none ; private
+
+include 'netcdf.inc'
+
+public ice_bergs_io_init
+public read_restart_bergs, write_restart, write_trajectory, write_bond_trajectory
+public read_restart_calving, read_restart_bonds
+public read_ocean_depth
+
+!Local Vars
+integer, parameter :: file_format_major_version=0
+integer, parameter :: file_format_minor_version=1
+!I/O vars
+type(domain2d), pointer, save :: io_domain=>NULL()
+integer, save :: io_tile_id(1), io_tile_root_pe, io_npes
+integer, allocatable,save :: io_tile_pelist(:)
+logical :: is_io_tile_root_pe = .true.
+
+integer :: clock_trw,clock_trp
+integer :: clock_btrw,clock_btrp !bond trajectories
+
+#ifndef _FILE_VERSION
+! Version of file provided can be set to git hash via a CPP macro but if not set we use 'unknown'
+#define _FILE_VERSION 'unknown'
+#endif
+character(len=128) :: version = _FILE_VERSION !< Version of file
+
+contains
+
+!> Initialize parallel i/o
+subroutine ice_bergs_io_init(bergs, io_layout)
+type(icebergs), pointer :: bergs !< Icebergs container
+integer, intent(in) :: io_layout(2) !< Decomposition of i/o processors
+
+integer :: np
+integer :: stdlogunit, stderrunit
+
+  ! Get the stderr and stdlog unit numbers
+  stderrunit=stderr()
+  stdlogunit=stdlog()
+  write(stdlogunit,*) "ice_bergs_framework: "//trim(version)
+
+  !I/O layout init
+  io_tile_id=-1
+  io_domain => mpp_get_io_domain(bergs%grd%domain)
+  if(associated(io_domain)) then
+     io_tile_id = mpp_get_tile_id(io_domain)
+     is_io_tile_root_pe = mpp_domain_is_tile_root_pe(io_domain)
+     io_tile_root_pe = mpp_get_domain_tile_root_pe(io_domain)
+     np=mpp_get_tile_npes(io_domain)
+     allocate(io_tile_pelist(np))
+     call mpp_get_tile_pelist(io_domain,io_tile_pelist)
+     io_npes = io_layout(1)*io_layout(2)
+  endif
+
+  clock_trw=mpp_clock_id( 'Icebergs-traj write', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+  clock_trp=mpp_clock_id( 'Icebergs-traj prepare', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+  clock_btrw=mpp_clock_id( 'Iceberg-bonds-traj write', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+  clock_btrp=mpp_clock_id( 'Iceberg-bonds-traj prepare', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
+
+end subroutine ice_bergs_io_init
+
+!> Write an iceberg restart file
+subroutine write_restart(bergs, time_stamp)
+! Arguments
+type(icebergs), pointer :: bergs !< Icebergs container
+character(len=*), intent(in), optional :: time_stamp !< Timestamp for restart file
+
+! Local variables
+type(bond), pointer :: current_bond
+integer :: i,j,id
+character(len=35) :: filename
+character(len=35) :: filename_bonds
+type(iceberg), pointer :: this=>NULL()
+integer :: stderrunit
+!I/O vars
+type(restart_file_type) :: bergs_restart
+type(restart_file_type) :: bergs_bond_restart
+type(restart_file_type) :: calving_restart
+integer :: nbergs, nbonds
+integer :: n_static_bergs
+logical :: check_bond_quality
+type(icebergs_gridded), pointer :: grd
+real, allocatable, dimension(:) :: lon,          &
+                                   lat,          &
+                                   uvel,         &
+                                   vvel,         &
+                                   mass,         &
+                                   axn,          &
+                                   ayn,          &
+                                   bxn,          &
+                                   byn,          &
+                                   thickness,    &
+                                   width,        &
+                                   length,       &
+                                   fl_k,         &
+                                   start_lon,    &
+                                   start_lat,    &
+                                   start_day,    &
+                                   start_mass,   &
+                                   mass_scaling, &
+                                   mass_of_bits, &
+                                   mass_of_fl_bits, &
+                                   mass_of_fl_bergy_bits, &
+                                   static_berg,  &
+                                   heat_density, &
+                                   axn_fast,     &
+                                   ayn_fast,     &
+                                   bxn_fast,     &
+                                   byn_fast,     &
+                                   ang_vel,      &
+                                   ang_accel,    &
+                                   rot,          &
+                                   tangd1,       &
+                                   tangd2,       &
+                                   nstress,      &
+                                   sstress,      &
+                                   rel_rotation
+
+integer, allocatable, dimension(:) :: ine,              &
+                                      jne,              &
+                                      id_cnt,           &
+                                      id_ij,            &
+                                      start_year,       &
+                                      first_id_cnt,     &
+                                      other_id_cnt,     &
+                                      first_id_ij,      &
+                                      other_id_ij,      &
+                                      first_berg_jne,         &
+                                      first_berg_ine,         &
+                                      other_berg_jne,         &
+                                      other_berg_ine,         &
+                                      broken
+
+
+integer :: grdi, grdj
+
+! Get the stderr unit number
+ stderrunit=stderr()
+
+
+  ! For convenience
+  grd=>bergs%grd
+
+  !First add the bergs on the io_tile_root_pe (if any) to the I/O list
+  nbergs = 0
+  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this))
+      nbergs = nbergs +1
+      this=>this%next
+    enddo
+  enddo ; enddo
+
+   allocate(lon(nbergs))
+   allocate(lat(nbergs))
+   allocate(uvel(nbergs))
+   allocate(vvel(nbergs))
+   allocate(mass(nbergs))
+   allocate(axn(nbergs))    !Alon
+   allocate(ayn(nbergs))    !Alon
+   allocate(bxn(nbergs)) !Alon
+   allocate(byn(nbergs)) !Alon
+   allocate(thickness(nbergs))
+   allocate(width(nbergs))
+   allocate(length(nbergs))
+   allocate(start_lon(nbergs))
+   allocate(start_lat(nbergs))
+   allocate(start_day(nbergs))
+   allocate(start_mass(nbergs))
+   allocate(mass_scaling(nbergs))
+   allocate(mass_of_bits(nbergs))
+   allocate(heat_density(nbergs))
+   allocate(static_berg(nbergs))
+
+   allocate(ine(nbergs))
+   allocate(jne(nbergs))
+   allocate(start_year(nbergs))
+   allocate(id_cnt(nbergs))
+   allocate(id_ij(nbergs))
+
+   if (bergs%footloose) then
+     allocate(fl_k(nbergs))
+     allocate(mass_of_fl_bits(nbergs))
+     allocate(mass_of_fl_bergy_bits(nbergs))
+   end if
+
+   if (mts) then
+     allocate(axn_fast(nbergs))
+     allocate(ayn_fast(nbergs))
+     allocate(bxn_fast(nbergs))
+     allocate(byn_fast(nbergs))
+   endif
+   if (dem) then
+     allocate(ang_vel(nbergs))
+     allocate(ang_accel(nbergs))
+     allocate(rot(nbergs))
+   endif
+
+  filename = trim("icebergs.res.nc")
+  call set_domain(bergs%grd%domain)
+  call register_restart_axis(bergs_restart,filename,'i',nbergs)
+  call set_meta_global(bergs_restart,'file_format_major_version',ival=(/file_format_major_version/))
+  call set_meta_global(bergs_restart,'file_format_minor_version',ival=(/file_format_minor_version/))
+  call set_meta_global(bergs_restart,'time_axis',ival=(/0/))
+
+  !Now start writing in the io_tile_root_pe if there are any bergs in the I/O list
+
+  ! Define Variables
+  id = register_restart_field(bergs_restart,filename,'lon',lon,longname='longitude',units='degrees_E')
+  id = register_restart_field(bergs_restart,filename,'lat',lat,longname='latitude',units='degrees_N')
+  id = register_restart_field(bergs_restart,filename,'uvel',uvel,longname='zonal velocity',units='m/s')
+  id = register_restart_field(bergs_restart,filename,'vvel',vvel,longname='meridional velocity',units='m/s')
+  id = register_restart_field(bergs_restart,filename,'mass',mass,longname='mass',units='kg')
+  if (.not. bergs%Runge_not_Verlet) then
+    id = register_restart_field(bergs_restart,filename,'axn',axn,longname='explicit zonal acceleration',units='m/s^2')
+    id = register_restart_field(bergs_restart,filename,'ayn',ayn,longname='explicit meridional acceleration',units='m/s^2')
+    id = register_restart_field(bergs_restart,filename,'bxn',bxn,longname='implicit zonal acceleration',units='m/s^2')
+    id = register_restart_field(bergs_restart,filename,'byn',byn,longname='implicit meridional acceleration',units='m/s^2')
+  endif
+  id = register_restart_field(bergs_restart,filename,'ine',ine,longname='i index',units='none')
+  id = register_restart_field(bergs_restart,filename,'jne',jne,longname='j index',units='none')
+  id = register_restart_field(bergs_restart,filename,'thickness',thickness,longname='thickness',units='m')
+  id = register_restart_field(bergs_restart,filename,'width',width,longname='width',units='m')
+  id = register_restart_field(bergs_restart,filename,'length',length,longname='length',units='m')
+  id = register_restart_field(bergs_restart,filename,'start_lon',start_lon, &
+                                            longname='longitude of calving location',units='degrees_E')
+  id = register_restart_field(bergs_restart,filename,'start_lat',start_lat, &
+                                            longname='latitude of calving location',units='degrees_N')
+  id = register_restart_field(bergs_restart,filename,'start_year',start_year, &
+                                            longname='calendar year of calving event', units='years')
+  id = register_restart_field(bergs_restart,filename,'id_cnt',id_cnt, &
+                                            longname='counter component of iceberg id', units='dimensionless')
+  id = register_restart_field(bergs_restart,filename,'id_ij',id_ij, &
+                                            longname='position component of iceberg id', units='dimensionless')
+  id = register_restart_field(bergs_restart,filename,'start_day',start_day, &
+                                            longname='year day of calving event',units='days')
+  id = register_restart_field(bergs_restart,filename,'start_mass',start_mass, &
+                                            longname='initial mass of calving berg',units='kg')
+  id = register_restart_field(bergs_restart,filename,'mass_scaling',mass_scaling, &
+                                            longname='scaling factor for mass of calving berg',units='none')
+  id = register_restart_field(bergs_restart,filename,'mass_of_bits',mass_of_bits, &
+                                            longname='mass of bergy bits',units='kg')
+  id = register_restart_field(bergs_restart,filename,'heat_density',heat_density, &
+                                            longname='heat density',units='J/kg')
+
+  if (bergs%footloose) then
+    id = register_restart_field(bergs_restart,filename,'fl_k',fl_k,longname='footloose calving k',units='m')
+    id = register_restart_field(bergs_restart,filename,'mass_of_fl_bits',mass_of_fl_bits, &
+      longname='mass of footloose bits',units='kg')
+    id = register_restart_field(bergs_restart,filename,'mass_of_fl_bergy_bits',mass_of_fl_bergy_bits, &
+      longname='mass of bergy bits associated with footloose bits',units='kg')
+   end if
+
+  if (mts) then
+    id = register_restart_field(bergs_restart,filename,'axn_fast',axn_fast,&
+      longname='sub-step explicit zonal acceleration',units='m/s^2')
+    id = register_restart_field(bergs_restart,filename,'ayn_fast',ayn_fast,&
+      longname='sub-step explicit meridional acceleration',units='m/s^2')
+    id = register_restart_field(bergs_restart,filename,'bxn_fast',bxn_fast,&
+      longname='sub-step implicit zonal acceleration',units='m/s^2')
+    id = register_restart_field(bergs_restart,filename,'byn_fast',byn_fast,&
+      longname='sub-step implicit meridional acceleration',units='m/s^2')
+  endif
+
+  if (dem) then
+    id = register_restart_field(bergs_restart,filename,'ang_vel',ang_vel,&
+      longname='dem angular velocity',units='rad/s')
+    id = register_restart_field(bergs_restart,filename,'ang_accel',ang_accel,&
+      longname='dem angular acceleration',units='rad/s^2')
+    id = register_restart_field(bergs_restart,filename,'rot',rot,&
+      longname='dem accumulated rotation',units='rad')
+  endif
+
+  !Checking if any icebergs are static in order to decide whether to save static_berg
+  n_static_bergs = 0
+  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this))
+      n_static_bergs=n_static_bergs+this%static_berg
+      this=>this%next
+    enddo
+  enddo ; enddo
+  call mpp_sum(n_static_bergs)
+  if (n_static_bergs .gt. 0) &
+    id = register_restart_field(bergs_restart,filename,'static_berg',static_berg, &
+                                              longname='static_berg',units='dimensionless')
+
+  ! Write variables
+
+  i = 0
+  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
+    this=>bergs%list(grdi,grdj)%first
+    do while(associated(this))
+      i = i + 1
+      lon(i) = this%lon; lat(i) = this%lat
+      uvel(i) = this%uvel; vvel(i) = this%vvel
+      ine(i) = this%ine; jne(i) = this%jne
+      mass(i) = this%mass; thickness(i) = this%thickness
+      axn(i) = this%axn; ayn(i) = this%ayn !Added by Alon
+      bxn(i) = this%bxn; byn(i) = this%byn !Added by Alon
+      width(i) = this%width; length(i) = this%length
+      start_lon(i) = this%start_lon; start_lat(i) = this%start_lat
+      start_year(i) = this%start_year; start_day(i) = this%start_day
+      start_mass(i) = this%start_mass; mass_scaling(i) = this%mass_scaling
+      static_berg(i) = this%static_berg
+      call split_id(this%id, id_cnt(i), id_ij(i))
+      mass_of_bits(i) = this%mass_of_bits
+      heat_density(i) = this%heat_density
+
+      if (bergs%footloose) then
+        fl_k(i) = this%fl_k
+        mass_of_fl_bits(i) = this%mass_of_fl_bits
+        mass_of_fl_bergy_bits(i) = this%mass_of_fl_bergy_bits
+      end if
+
+      if (mts) then
+        axn_fast(i) = this%axn_fast
+        ayn_fast(i) = this%ayn_fast
+        bxn_fast(i) = this%bxn_fast
+        byn_fast(i) = this%byn_fast
+      endif
+      if (dem) then
+        ang_vel(i) = this%ang_vel
+        ang_accel(i) = this%ang_accel
+        rot(i) = this%rot
+      endif
+      this=>this%next
+    enddo
+  enddo ; enddo
+
+
+  call save_restart(bergs_restart, time_stamp)
+  call free_restart_type(bergs_restart)
+
+  deallocate(              &
+             lon,          &
+             lat,          &
+             uvel,         &
+             vvel,         &
+             mass,         &
+             axn,          &
+             ayn,          &
+             bxn,          &
+             byn,          &
+             thickness,    &
+             width,        &
+             length,       &
+             start_lon,    &
+             start_lat,    &
+             start_day,    &
+             start_mass,   &
+             mass_scaling, &
+             mass_of_bits, &
+             static_berg,  &
+             heat_density)
+
+  if (bergs%footloose) then
+    deallocate(                   &
+                 fl_k,            &
+                 mass_of_fl_bits, &
+                 mass_of_fl_bergy_bits)
+  end if
+  if (mts) then
+    deallocate(            &
+             axn_fast,     &
+             ayn_fast,     &
+             bxn_fast,     &
+             byn_fast)
+  endif
+  if (dem) then
+    deallocate(            &
+             ang_vel,      &
+             ang_accel,    &
+             rot)
+  endif
+
+  deallocate(           &
+             ine,       &
+             jne,       &
+             id_cnt,    &
+             id_ij,     &
+             start_year )
+
+  call nullify_domain()
+
+!########## Creating bond restart file ######################
+
+  !Allocating restart memory for bond related variables.
+  nbonds=0
+  if (bergs%iceberg_bonds_on) then
+    check_bond_quality=.true.
+    call count_bonds(bergs, nbonds,check_bond_quality)
+
+  allocate(first_id_cnt(nbonds))
+  allocate(other_id_cnt(nbonds))
+  allocate(first_id_ij(nbonds))
+  allocate(other_id_ij(nbonds))
+  allocate(first_berg_ine(nbonds))
+  allocate(first_berg_jne(nbonds))
+  allocate(other_berg_ine(nbonds))
+  allocate(other_berg_jne(nbonds))
+
+  if (dem) then
+    allocate(tangd1(nbonds))
+    allocate(tangd2(nbonds))
+    allocate(nstress(nbonds))
+    allocate(sstress(nbonds))
+    allocate(rel_rotation(nbonds))
+    allocate(broken(nbonds))
+  endif
+
+  call get_instance_filename("bonds_iceberg.res.nc", filename_bonds)
+  call set_domain(bergs%grd%domain)
+  call register_restart_axis(bergs_bond_restart,filename,'i',nbonds)
+  call set_meta_global(bergs_bond_restart,'file_format_major_version',ival=(/file_format_major_version/))
+  call set_meta_global(bergs_bond_restart,'file_format_minor_version',ival=(/file_format_minor_version/))
+  call set_meta_global(bergs_bond_restart,'time_axis',ival=(/0/))
+
+  !Now start writing in the io_tile_root_pe if there are any bergs in the I/O list
+
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'first_berg_ine',first_berg_ine,longname='iceberg ine of first berg in bond',units='dimensionless')
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'first_berg_jne',first_berg_jne,longname='iceberg jne of first berg in bond',units='dimensionless')
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'first_id_cnt',first_id_cnt,longname='counter component of iceberg id first berg in bond',units='dimensionless')
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'first_id_ij',first_id_ij,longname='position component of iceberg id first berg in bond',units='dimensionless')
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'other_berg_ine',other_berg_ine,longname='iceberg ine of second berg in bond',units='dimensionless')
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'other_berg_jne',other_berg_jne,longname='iceberg jne of second berg in bond',units='dimensionless')
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'other_id_cnt',other_id_cnt,longname='counter component of iceberg id second berg in bond',units='dimensionless')
+  id = register_restart_field(bergs_bond_restart,filename_bonds,'other_id_ij',other_id_ij,longname='position component of iceberg id second berg in bond',units='dimensionless')
+
+  if (dem) then
+    id = register_restart_field(bergs_bond_restart,filename_bonds,'tangd1',tangd1,&
+      longname='zonal tangential displacement',units='m')
+    id = register_restart_field(bergs_bond_restart,filename_bonds,'tangd2',tangd2,&
+      longname='meridional tangential displacement',units='m')
+    id = register_restart_field(bergs_bond_restart,filename_bonds,'nstress',nstress,&
+      longname='normal stress',units='Pa')
+    id = register_restart_field(bergs_bond_restart,filename_bonds,'sstress',sstress,&
+      longname='shear stress',units='Pa')
+    id = register_restart_field(bergs_bond_restart,filename_bonds,'rel_rotation',rel_rotation,&
+      longname='relative rotation',units='rad')
+     id = register_restart_field(bergs_bond_restart,filename_bonds,'broken',broken,&
+      longname='broken status',units='none')
+  endif
+
+  ! Write variables
+
+  i = 0
+  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
+    this=>bergs%list(grdi,grdj)%first
+    do while(associated(this)) !Loops over all bergs
+      current_bond=>this%first_bond
+      do while (associated(current_bond)) ! loop over all bonds
+        i = i + 1
+        first_berg_ine(i)=this%ine
+        first_berg_jne(i)=this%jne
+        call split_id( this%id, first_id_cnt(i), first_id_ij(i) )
+        call split_id( current_bond%other_id, other_id_cnt(i), other_id_ij(i) )
+        other_berg_ine(i)=current_bond%other_berg%ine
+        other_berg_jne(i)=current_bond%other_berg%jne
+
+        if (dem) then
+          tangd1(i)=current_bond%tangd1
+          tangd2(i)=current_bond%tangd2
+          nstress(i)=current_bond%nstress
+          sstress(i)=current_bond%sstress
+          rel_rotation(i)=current_bond%rel_rotation
+          broken(i)=current_bond%broken
+        endif
+
+        current_bond=>current_bond%next_bond
+      enddo !End of loop over bonds
+      this=>this%next
+    enddo!End of loop over bergs
+  enddo; enddo !End of loop over grid
+
+  call save_restart(bergs_bond_restart, time_stamp)
+  call free_restart_type(bergs_bond_restart)
+
+
+  deallocate(first_id_cnt,          &
+             other_id_cnt,          &
+             first_id_ij,           &
+             other_id_ij,           &
+             first_berg_ine,        &
+             first_berg_jne,        &
+             other_berg_ine,        &
+             other_berg_jne)
+  if (dem) then
+    deallocate(                     &
+             tangd1,                &
+             tangd2,                &
+             nstress,               &
+             sstress,               &
+             rel_rotation,          &
+             broken)
+  endif
+
+  call nullify_domain()
+  endif
+
+  ! Write stored ice
+  filename='calving.res.nc'
+  if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(stderrunit,'(2a)') 'KID, write_restart: writing ',filename
+  call grd_chksum3(bergs%grd, bergs%grd%stored_ice, 'write stored_ice')
+  call grd_chksum2(bergs%grd, bergs%grd%stored_heat, 'write stored_heat')
+  if (bergs%tau_calving>0.) then
+    call grd_chksum2(bergs%grd, bergs%grd%rmean_calving, 'write mean calving')
+    call grd_chksum2(bergs%grd, bergs%grd%rmean_calving_hflx, 'write mean calving_hflx')
+  endif
+
+  call set_domain(bergs%grd%domain)
+  id = register_restart_field(calving_restart,filename,'stored_ice',bergs%grd%stored_ice,longname='STORED_ICE',units='none')
+  id = register_restart_field(calving_restart,filename,'stored_heat',bergs%grd%stored_heat,longname='STORED_HEAT',units='none')
+  id = register_restart_field(calving_restart,filename,'iceberg_counter_grd',bergs%grd%iceberg_counter_grd,longname='ICEBERG_COUNTER_GRD',units='none')
+  if (bergs%tau_calving>0.) then
+    id = register_restart_field(calving_restart,filename,'rmean_calving',bergs%grd%rmean_calving,longname='RMEAN_CALVING',units='none')
+    id = register_restart_field(calving_restart,filename,'rmean_calving_hflx',bergs%grd%rmean_calving_hflx,longname='RMEAN_CALVING_HFLX',units='none')
+  endif
+
+  call save_restart(calving_restart, time_stamp)
+  call free_restart_type(calving_restart)
+
+end subroutine write_restart
+
+!> Find the last berg in a linked list.
+function last_berg(berg)
+! Arguments
+type(iceberg), pointer :: berg !< Pointer to an iceberg
+type(iceberg), pointer :: last_berg
+! Local variables
+
+  last_berg=>berg
+  do while (associated(last_berg%next))
+    last_berg=>last_berg%next
+  enddo
+
+end function last_berg
+
+!> Read a real value from a file and optionally return a default value if variable is missing
+real function get_real_from_file(ncid, varid, k, value_if_not_in_file)
+integer, intent(in) :: ncid !< file id
+integer, intent(in) :: varid !< variable id
+integer, intent(in) :: k !< index
+real, optional :: value_if_not_in_file !< default value, if variable missing in file
+
+if (varid<1.and.present(value_if_not_in_file)) then
+  get_real_from_file=value_if_not_in_file
+else
+  get_real_from_file=get_double(ncid, ncid, k)
+endif
+end function get_real_from_file
+
+!> Read an iceberg restart file
+subroutine read_restart_bergs(bergs,Time)
+! Arguments
+type(icebergs), pointer :: bergs !< Icebergs container
+type(time_type), intent(in) :: Time !< Model time
+! Local variables
+integer :: k, siz(4), nbergs_in_file, nbergs_read
+logical :: lres, found_restart, found, replace_iceberg_num
+logical :: explain
+logical :: multiPErestart  ! Not needed with new restart read; currently kept for compatibility
+real :: lon0, lon1, lat0, lat1
+real :: pos_is_good, pos_is_good_all_pe
+character(len=53) :: filename, filename_base
+type(icebergs_gridded), pointer :: grd
+type(iceberg) :: localberg ! NOT a pointer but an actual local variable
+integer :: stderrunit, i, j, cnt, ij
+
+real, allocatable, dimension(:) :: lon,          &
+                                   lat,          &
+                                   uvel,         &
+                                   vvel,         &
+                                   mass,         &
+                                   axn,          &
+                                   ayn,          &
+                                   bxn,          &
+                                   byn,          &
+                                   thickness,    &
+                                   width,        &
+                                   length,       &
+                                   fl_k,         &
+                                   start_lon,    &
+                                   start_lat,    &
+                                   start_day,    &
+                                   start_mass,   &
+                                   mass_scaling, &
+                                   mass_of_bits, &
+                                   mass_of_fl_bits, &
+                                   mass_of_fl_bergy_bits, &
+                                   static_berg,  &
+                                   heat_density, &
+                                   axn_fast,     &
+                                   ayn_fast,     &
+                                   bxn_fast,     &
+                                   byn_fast,     &
+                                   ang_vel,      &
+                                   ang_accel,    &
+                                   rot
+
+integer, allocatable, dimension(:) :: ine,        &
+                                      jne,        &
+                                      iceberg_num,&
+                                      id_cnt,     &
+                                      id_ij,      &
+                                      start_year
+
+!integer, allocatable, dimension(:,:) :: iceberg_counter_grd
+
+  ! Get the stderr unit number
+  stderrunit=stderr()
+
+  ! For convenience
+  grd=>bergs%grd
+
+  ! Zero out nbergs_in_file
+  nbergs_in_file = 0
+
+  filename_base=trim(restart_input_dir)//'icebergs.res.nc'
+
+  found_restart = find_restart_file(filename_base, filename, multiPErestart, io_tile_id(1))
+
+  if (found_restart) then
+     filename = filename_base
+     call get_field_size(filename,'i',siz, field_found=found, domain=bergs%grd%domain)
+     nbergs_in_file = siz(1)
+
+     replace_iceberg_num = field_exist(filename, 'iceberg_num') ! True if using 32-bit iceberg_num in restart file
+     allocate(lon(nbergs_in_file))
+     allocate(lat(nbergs_in_file))
+     allocate(uvel(nbergs_in_file))
+     allocate(vvel(nbergs_in_file))
+     allocate(mass(nbergs_in_file))
+     allocate(axn(nbergs_in_file)) !Alon
+     allocate(ayn(nbergs_in_file)) !Alon
+     allocate(bxn(nbergs_in_file)) !Alon
+     allocate(byn(nbergs_in_file)) !Alon
+     allocate(thickness(nbergs_in_file))
+     allocate(width(nbergs_in_file))
+     allocate(length(nbergs_in_file))
+     allocate(fl_k(nbergs_in_file))
+     allocate(start_lon(nbergs_in_file))
+     allocate(start_lat(nbergs_in_file))
+     allocate(start_day(nbergs_in_file))
+     allocate(start_mass(nbergs_in_file))
+     allocate(mass_scaling(nbergs_in_file))
+     allocate(mass_of_bits(nbergs_in_file))
+     allocate(mass_of_fl_bits(nbergs_in_file))
+     allocate(mass_of_fl_bergy_bits(nbergs_in_file))
+     allocate(static_berg(nbergs_in_file))
+     allocate(heat_density(nbergs_in_file))
+     allocate(ine(nbergs_in_file))
+     allocate(jne(nbergs_in_file))
+     allocate(start_year(nbergs_in_file))
+     if (replace_iceberg_num) then
+       call error_mesg('read_restart_bergs', "Calculating new iceberg ID's", WARNING)
+       allocate(iceberg_num(nbergs_in_file))
+     else
+       allocate(id_cnt(nbergs_in_file))
+       allocate(id_ij(nbergs_in_file))
+     endif
+
+      if (iceberg_bonds_on) then
+        allocate(localberg%n_bonds)
+        localberg%n_bonds=0.
+      end if
+
+      if (mts) then
+        allocate(localberg%axn_fast)
+        allocate(localberg%ayn_fast)
+        allocate(localberg%bxn_fast)
+        allocate(localberg%byn_fast)
+        allocate(localberg%conglom_id)
+        localberg%conglom_id=0.
+
+       allocate(axn_fast(nbergs_in_file))
+       allocate(ayn_fast(nbergs_in_file))
+       allocate(bxn_fast(nbergs_in_file))
+       allocate(byn_fast(nbergs_in_file))
+     endif
+     if (dem) then
+       allocate(localberg%ang_vel)
+       allocate(localberg%ang_accel)
+       allocate(localberg%rot)
+       allocate(ang_vel(nbergs_in_file))
+       allocate(ang_accel(nbergs_in_file))
+       allocate(rot(nbergs_in_file))
+     endif
+
+     call read_unlimited_axis(filename,'lon',lon,domain=grd%domain)
+     call read_unlimited_axis(filename,'lat',lat,domain=grd%domain)
+     call read_unlimited_axis(filename,'uvel',uvel,domain=grd%domain)
+     call read_unlimited_axis(filename,'vvel',vvel,domain=grd%domain)
+     call read_unlimited_axis(filename,'mass',mass,domain=grd%domain)
+     call read_real_vector(filename,'axn',axn,grd%domain,value_if_not_in_file=0.)
+     call read_real_vector(filename,'ayn',ayn,grd%domain,value_if_not_in_file=0.)
+     call read_real_vector(filename,'bxn',bxn,grd%domain,value_if_not_in_file=0.)
+     call read_real_vector(filename,'byn',byn,grd%domain,value_if_not_in_file=0.)
+     call read_unlimited_axis(filename,'thickness',thickness,domain=grd%domain)
+     call read_unlimited_axis(filename,'width',width,domain=grd%domain)
+     call read_unlimited_axis(filename,'length',length,domain=grd%domain)
+     call read_real_vector(filename,'fl_k',fl_k,grd%domain,value_if_not_in_file=0.)
+     call read_unlimited_axis(filename,'start_lon',start_lon,domain=grd%domain)
+     call read_unlimited_axis(filename,'start_lat',start_lat,domain=grd%domain)
+     call read_unlimited_axis(filename,'start_day',start_day,domain=grd%domain)
+     call read_unlimited_axis(filename,'start_mass',start_mass,domain=grd%domain)
+     call read_unlimited_axis(filename,'mass_scaling',mass_scaling,domain=grd%domain)
+     call read_real_vector(filename,'mass_of_bits',mass_of_bits,domain=grd%domain,value_if_not_in_file=0.)
+     call read_real_vector(filename,'mass_of_fl_bits',mass_of_fl_bits,domain=grd%domain,value_if_not_in_file=0.)
+     call read_real_vector(filename,'mass_of_fl_bergy_bits',mass_of_fl_bergy_bits,domain=grd%domain,value_if_not_in_file=0.)
+     call read_real_vector(filename,'heat_density',heat_density,domain=grd%domain,value_if_not_in_file=0.)
+     call read_unlimited_axis(filename,'ine',ine,domain=grd%domain)
+     call read_unlimited_axis(filename,'jne',jne,domain=grd%domain)
+     call read_unlimited_axis(filename,'start_year',start_year,domain=grd%domain)
+     if (replace_iceberg_num) then
+       call read_int_vector(filename,'iceberg_num',iceberg_num,grd%domain,value_if_not_in_file=-1)
+     else
+       call read_int_vector(filename,'id_cnt',id_cnt,grd%domain)
+       call read_int_vector(filename,'id_ij',id_ij,grd%domain)
+     endif
+     call read_real_vector(filename,'static_berg',static_berg,grd%domain,value_if_not_in_file=0.)
+
+     if (mts) then
+       call read_real_vector(filename,'axn_fast',axn_fast,grd%domain,value_if_not_in_file=0.)
+       call read_real_vector(filename,'ayn_fast',ayn_fast,grd%domain,value_if_not_in_file=0.)
+       call read_real_vector(filename,'bxn_fast',bxn_fast,grd%domain,value_if_not_in_file=0.)
+       call read_real_vector(filename,'byn_fast',byn_fast,grd%domain,value_if_not_in_file=0.)
+     endif
+
+     if (dem) then
+       call read_real_vector(filename,'ang_vel'  ,ang_vel  ,grd%domain,value_if_not_in_file=0.)
+       call read_real_vector(filename,'ang_accel',ang_accel,grd%domain,value_if_not_in_file=0.)
+       call read_real_vector(filename,'rot'      ,rot      ,grd%domain,value_if_not_in_file=0.)
+     endif
+  elseif (bergs%require_restart) then
+     stop 'read_restart_bergs, RESTART NOT FOUND!'
+  endif
+
+  ! Find approx outer bounds for tile
+  lon0=minval( grd%lon(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
+  lon1=maxval( grd%lon(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
+  lat0=minval( grd%lat(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
+  lat1=maxval( grd%lat(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
+
+  do k=1, nbergs_in_file
+    localberg%lon=lon(k)
+    localberg%lat=lat(k)
+    if (.not. ignore_ij_restart) then ! read i,j position and avoid the "find" step
+      localberg%ine=ine(k)
+      localberg%jne=jne(k)
+      if ( localberg%ine>=grd%isc .and. localberg%ine<=grd%iec .and. &
+         localberg%jne>=grd%jsc .and.localberg%jne<=grd%jec ) then
+        lres=.true.
+      else
+        lres=.false.
+      endif
+    else ! i,j are not available from the file so we search the grid to find out if we reside on this PE
+      if (use_slow_find) then
+        lres=find_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
+      else
+        lres=find_cell_by_search(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
+      endif
+    endif
+    if (really_debug) then
+      write(stderrunit,'(a,i8,a,2f9.4,a,i8)') 'KID, read_restart_bergs: berg ',k,' is at ',localberg%lon,localberg%lat,&
+           & ' on PE ',mpp_pe()
+      write(stderrunit,*) 'KID, read_restart_bergs: lres = ',lres
+    endif
+
+    if (lres) then ! true if we reside on this PE grid
+      localberg%uvel=uvel(k)
+      localberg%vvel=vvel(k)
+      localberg%mass=mass(k)
+      localberg%axn=axn(k) !Alon
+      localberg%ayn=ayn(k) !Alon
+      localberg%uvel_old=uvel(k) !Alon
+      localberg%vvel_old=vvel(k) !Alon
+      localberg%lon_old=lon(k) !Alon
+      localberg%lat_old=lat(k) !Alon
+      localberg%bxn=bxn(k) !Alon
+      localberg%byn=byn(k) !Alon
+      localberg%thickness=thickness(k)
+      localberg%width=width(k)
+      localberg%length=length(k)
+      localberg%fl_k=fl_k(k)
+      localberg%start_lon=start_lon(k)
+      localberg%start_lat=start_lat(k)
+      localberg%start_year=start_year(k)
+      if (replace_iceberg_num) then
+        localberg%id = generate_id(grd, localberg%ine, localberg%jne)
+      else
+        localberg%id=id_from_2_ints(id_cnt(k), id_ij(k))
+      endif
+      localberg%start_day=start_day(k)
+      localberg%start_mass=start_mass(k)
+      localberg%mass_scaling=mass_scaling(k)
+      localberg%mass_of_bits=mass_of_bits(k)
+      localberg%mass_of_fl_bits=mass_of_fl_bits(k)
+      localberg%mass_of_fl_bergy_bits=mass_of_fl_bergy_bits(k)
+      localberg%halo_berg=0.
+      localberg%static_berg=static_berg(k)
+      localberg%heat_density=heat_density(k)
+      localberg%first_bond=>null()
+
+     if (mts) then
+       localberg%axn_fast=axn_fast(k)
+       localberg%ayn_fast=ayn_fast(k)
+       localberg%bxn_fast=bxn_fast(k)
+       localberg%byn_fast=byn_fast(k)
+     endif
+
+     if (dem) then
+       localberg%ang_vel  =ang_vel(k)
+       localberg%ang_accel=ang_accel(k)
+       localberg%rot      =rot(k)
+     endif
+
+      if (really_debug) lres=is_point_in_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, explain=.true.)
+      lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
+      !call add_new_berg_to_list(bergs%first, localberg)
+
+      if (bergs%grd%area(localberg%ine,localberg%jne) .ne. 0)  then
+        call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg)
+      else
+        if (mpp_pe().eq.mpp_root_pe()) then
+          print * , 'Grounded iceberg: ', lat(k),lon(k), localberg%id
+          call error_mesg('KID, read_restart_bergs', 'Iceberg not added because it is grounded', WARNING)
+        endif
+       endif
+
+      if (really_debug) call print_berg(stderrunit, bergs%list(localberg%ine,localberg%jne)%first, 'read_restart_bergs, add_new_berg_to_list')
+    elseif (multiPErestart .and. io_tile_id(1) .lt. 0) then
+      call error_mesg('KID, read_restart_bergs', 'berg in PE file was not on PE!', FATAL)
+    endif
+  enddo
+
+  if (found_restart) then
+    deallocate(lon,          &
+               lat,          &
+               uvel,         &
+               vvel,         &
+               mass,         &
+               axn,          &
+               ayn,          &
+               bxn,          &
+               byn,          &
+               thickness,    &
+               width,        &
+               length,       &
+               fl_k,         &
+               start_lon,    &
+               start_lat,    &
+               start_day,    &
+               start_mass,   &
+               mass_scaling, &
+               mass_of_bits, &
+               mass_of_fl_bits, &
+               mass_of_fl_bergy_bits, &
+               static_berg,  &
+               heat_density, &
+               ine,          &
+               jne,          &
+               start_year )
+
+    if (mts) then
+      deallocate(            &
+               axn_fast,     &
+               ayn_fast,     &
+               bxn_fast,     &
+               byn_fast)
+    endif
+    if (dem) then
+      deallocate(            &
+               ang_vel,      &
+               ang_accel,    &
+               rot)
+    endif
+
+    if (replace_iceberg_num) then
+      deallocate(iceberg_num)
+    else
+      deallocate(id_cnt)
+      deallocate(id_ij)
+    endif
+
+    ! This block only works for IO_LAYOUT=1,1 or 0,0 but not for arbitrary layouts.
+    ! I'm commenting this out until we find a way to implement the same sorts of checks
+    ! that work for all i/o layouts. -AJA
+    !Checking the total number of icebergs read from the restart file.
+    !nbergs_read=count_bergs(bergs)
+    !call mpp_sum(nbergs_read)
+    !if (mpp_pe().eq.mpp_root_pe()) then
+    !  write(*,'(a,i8,a,i8,a)') 'KID, read_restart_bergs: Number of Icebergs in restart file=',nbergs_in_file,' Number of Icebergs read=', nbergs_read
+    !  if (nbergs_read .gt. nbergs_in_file) then
+    !    call error_mesg('KID, read_restart_bergs', 'More icebergs read than exist in restart file.', FATAL)
+    !  elseif (nbergs_read .lt. nbergs_in_file) then
+    !    if (bergs%ignore_missing_restart_bergs) then
+    !      call error_mesg('KID, read_restart_bergs', 'Some Icebergs from restart file were not found (ignore_missing flag is on)', WARNING)
+    !    else
+    !      call error_mesg('KID, read_restart_bergs', 'Some Icebergs from restart file were not found', FATAL)
+    !    endif
+    !  elseif (nbergs_read .eq. nbergs_in_file) then
+    !    write(*,'(a,i8,a,i8,a)') 'KID, read_restart_bergs: Number of icebergs read (#',nbergs_read,') matches the number of icebergs in the file'
+    !  endif
+    !endif
+
+  elseif(.not. found_restart .and. bergs%nbergs_start==0 .and. generate_test_icebergs) then
+    call generate_bergs(bergs,Time)
+  endif
+
+  call check_for_duplicates_in_parallel(bergs)
+
+  bergs%floating_mass_start=sum_mass(bergs)
+  call mpp_sum( bergs%floating_mass_start )
+  bergs%icebergs_mass_start=sum_mass(bergs,justbergs=.true.)
+  call mpp_sum( bergs%icebergs_mass_start )
+  bergs%bergy_mass_start=sum_mass(bergs,justbits=.true.)
+  call mpp_sum( bergs%bergy_mass_start )
+  bergs%fl_bits_mass_start=sum_mass(bergs,justflbits=.true.)
+  call mpp_sum( bergs%fl_bits_mass_start )
+  if (mpp_pe().eq.mpp_root_pe().and.verbose) write(*,'(a)') 'KID, read_restart_bergs: completed'
+
+end subroutine read_restart_bergs
+
+!> Read a vector of reals from file and use a default value if variable is missing
+subroutine read_real_vector(filename, varname, values, domain, value_if_not_in_file)
+  character(len=*), intent(in)  :: filename !< Name of file to read from
+  character(len=*), intent(in)  :: varname !< Name of variable to read
+  real,             intent(out) :: values(:) !< Returned vector of reals
+  type(domain2D),   intent(in)  :: domain !< Parallel decomposition
+  real, optional,   intent(in)  :: value_if_not_in_file !< Value to use if variable is not in file
+
+  if (present(value_if_not_in_file).and..not.field_exist(filename, varname)) then
+    values(:)=value_if_not_in_file
+  else
+    call read_unlimited_axis(filename,varname,values,domain=domain)
+  endif
+end subroutine read_real_vector
+
+!> Read a vector of integers from file and use a default value if variable is missing
+subroutine read_int_vector(filename, varname, values, domain, value_if_not_in_file)
+  character(len=*),  intent(in)  :: filename !< Name of file to read from
+  character(len=*),  intent(in)  :: varname !< Name of variable to read
+  integer,           intent(out) :: values(:) !< Returned vector of integers
+  type(domain2D),    intent(in)  :: domain !< Parallel decomposition
+  integer, optional, intent(in)  :: value_if_not_in_file !< Value to use if variable is not in file
+
+  if (present(value_if_not_in_file).and..not.field_exist(filename, varname)) then
+    values(:)=value_if_not_in_file
+  else
+    call read_unlimited_axis(filename,varname,values,domain=domain)
+  endif
+end subroutine read_int_vector
+
+!> Generate bergs for the purpose of debugging
+subroutine generate_bergs(bergs,Time)
+! Arguments
+type(icebergs), pointer :: bergs !< Icebergs container
+type(time_type), intent(in) :: Time !< Model time
+! Local variables
+type(icebergs_gridded), pointer :: grd
+integer :: i,j
+type(iceberg) :: localberg ! NOT a pointer but an actual local variable
+integer :: iyr, imon, iday, ihr, imin, isec
+logical :: lres
+
+  ! For convenience
+  grd=>bergs%grd
+
+  call get_date(Time, iyr, imon, iday, ihr, imin, isec)
+
+  if (mts) then
+    allocate(localberg%axn_fast)
+    allocate(localberg%ayn_fast)
+    allocate(localberg%bxn_fast)
+    allocate(localberg%byn_fast)
+  endif
+  if (dem) then
+    allocate(localberg%ang_vel)
+    allocate(localberg%ang_accel)
+    allocate(localberg%rot)
+  endif
+
+  do j=grd%jsc,grd%jec; do i=grd%isc,grd%iec
+    if (grd%msk(i,j)>0. .and. abs(grd%latc(i,j))>80.0) then
+      if (max(grd%lat(i,j),grd%lat(i-1,j),grd%lat(i,j-1),grd%lat(i-1,j-1))>89.999) cycle ! Cannot use this at Pole cells
+      localberg%xi=-999.
+      localberg%yj=-999.
+      localberg%ine=i
+      localberg%jne=j
+      localberg%lon=grd%lonc(i,j)
+      localberg%lat=grd%latc(i,j)
+      localberg%lon_old=localberg%lon
+      localberg%lat_old=localberg%lat
+      localberg%mass=bergs%initial_mass_s(1)
+      localberg%thickness=bergs%initial_thickness_s(1)
+      localberg%width=bergs%initial_width_s(1)
+      localberg%length=bergs%initial_length_s(1)
+      localberg%fl_k=0.
+      localberg%start_lon=localberg%lon
+      localberg%start_lat=localberg%lat
+      localberg%start_year=iyr
+      localberg%start_day=float(iday)+(float(ihr)+float(imin)/60.)/24.
+      localberg%start_mass=localberg%mass
+      localberg%mass_scaling=bergs%mass_scaling_s(1)
+      localberg%mass_of_bits=0.
+      localberg%mass_of_fl_bits=0.
+      localberg%mass_of_fl_bergy_bits=0.
+      localberg%halo_berg=0.
+      localberg%static_berg=0.
+      localberg%heat_density=0.
+      localberg%axn=0. !Alon
+      localberg%ayn=0. !Alon
+      localberg%uvel_old=0. !Alon
+      localberg%vvel_old=0. !Alon
+      localberg%bxn=0. !Alon
+      localberg%byn=0. !Alon
+      localberg%uvel_prev=0. !Alon
+      localberg%vvel_prev=0. !Alon
+
+      if (mts) then
+        localberg%axn_fast=0.
+        localberg%ayn_fast=0.
+        localberg%bxn_fast=0.
+        localberg%byn_fast=0.
+      endif
+      if (dem) then
+        localberg%ang_vel=0.
+        localberg%ang_accel=0.
+        localberg%rot=0.
+      endif
+
+      !Berg A
+      call loc_set_berg_pos(grd, 0.9, 0.5, 1., 0., localberg)
+      localberg%id = generate_id(grd, i, j)
+      call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
+      !Berg B
+      call loc_set_berg_pos(grd, 0.1, 0.5, -1., 0., localberg)
+      localberg%id = generate_id(grd, i, j)
+      call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
+      !Berg C
+      call loc_set_berg_pos(grd, 0.5, 0.9, 0., 1., localberg)
+      localberg%id = generate_id(grd, i, j)
+      call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
+      !Berg D
+      call loc_set_berg_pos(grd, 0.5, 0.1, 0., -1., localberg)
+      localberg%id = generate_id(grd, i, j)
+      call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
+    endif
+  enddo; enddo
+
+  bergs%nbergs_start=count_bergs(bergs)
+  call mpp_sum(bergs%nbergs_start)
+  if (mpp_pe().eq.mpp_root_pe()) &
+    write(*,'(a,i8,a)') 'KID, generate_bergs: ',bergs%nbergs_start,' were generated'
+
+end subroutine generate_bergs
+
+!> For generating bergs for debugging, assign initial berg positions and velocities
+subroutine loc_set_berg_pos(grd, xi, yj, uvel, vvel, berg)
+  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+  real, intent(in) :: xi !< Non-dimensional x-position within cell to give berg
+  real, intent(in) :: yj !< Non-dimensional y-position within cell to give berg
+  real, intent(in) :: uvel !< Zonal velocity to give berg
+  real, intent(in) :: vvel !< Meridional velocity to give berg
+  type(iceberg), intent(inout) :: berg !< An iceberg
+  integer :: i, j
+  logical :: lres
+  i = berg%ine ; j = berg%jne
+  if (max(grd%lat(i,j),grd%lat(i-1,j),grd%lat(i,j-1),grd%lat(i-1,j-1))>89.999) then
+    berg%lon=grd%lonc(i,j)
+    berg%lat=grd%latc(i,j)
+    berg%xi=0.5 ; berg%yj=0.5
+  else
+    berg%lon=bilin(grd, grd%lon, i, j, xi, yj)
+    berg%lat=bilin(grd, grd%lat, i, j, xi, yj)
+    berg%xi=xi ; berg%yj=yj
+  endif
+  berg%uvel=uvel ; berg%vvel=vvel
+  berg%lon_old=berg%lon ; berg%lat_old=berg%lat
+  berg%start_lon=berg%lon ; berg%start_lat=berg%lat
+  lres=pos_within_cell(grd, berg%lon, berg%lat, berg%ine, berg%jne, berg%xi, berg%yj)
+  if (.not. lres) then
+    lres=pos_within_cell(grd, berg%lon, berg%lat, berg%ine, berg%jne, berg%xi, berg%yj, explain=.true.)
+    write(0,*) lres, i, j, xi, yj, uvel, vvel
+    write(0,*) lres, berg%ine, berg%jne, berg%xi, berg%yj
+    write(0,*) 'bx=',berg%lon, 'gx=',grd%lon(i-1,j-1), grd%lon(i,j-1), grd%lon(i,j), grd%lon(i-1,j),'cx=', grd%lonc(i,j)
+    write(0,*) 'by=',berg%lat, 'gy=',grd%lat(i-1,j-1), grd%lat(i,j-1), grd%lat(i,j), grd%lat(i-1,j),'cy=', grd%latc(i,j)
+    stop 'generate_bergs, loc_set_berg_pos(): VERY FATAL!'
+  endif
+end subroutine loc_set_berg_pos
+
+!> Read bond restart file
+subroutine read_restart_bonds(bergs,Time)
+! Arguments
+type(icebergs), pointer :: bergs !< Icebergs container
+type(time_type), intent(in) :: Time !< Model time
+! Local variables
+integer :: k, siz(4), nbonds_in_file
+logical :: lres, found_restart, found
+logical :: first_berg_found, second_berg_found
+logical :: multiPErestart  ! Not needed with new restart read; currently kept for compatibility
+real :: lon0, lon1, lat0, lat1
+character(len=53) :: filename, filename_base
+type(icebergs_gridded), pointer :: grd
+type(iceberg) :: localberg ! NOT a pointer but an actual local variable
+type(iceberg) , pointer :: this, first_berg, second_berg
+type(bond) , pointer :: current_bond
+integer :: stderrunit
+integer :: number_first_bonds_matched !How many first bond bergs found on pe
+integer :: number_second_bonds_matched !How many second bond bergs found on pe
+integer :: number_perfect_bonds ! How many complete bonds formed
+integer :: number_partial_bonds ! How many either complete/partial bonds formed.
+integer :: number_perfect_bonds_with_first_on_pe ! How many bonds with first bond on the compuational domain
+integer :: all_pe_number_perfect_bonds, all_pe_number_partial_bonds
+integer :: all_pe_number_first_bonds_matched, all_pe_number_second_bonds_matched
+integer :: all_pe_number_perfect_bonds_with_first_on_pe
+integer :: ine, jne
+logical :: search_data_domain
+real :: berg_found, berg_found_all_pe
+integer, allocatable, dimension(:) :: id_cnt, id_ij,    &
+                                      first_berg_jne,   &
+                                      first_berg_ine,   &
+                                      other_berg_jne,   &
+                                      other_berg_ine,   &
+                                      broken
+real, allocatable, dimension(:) ::    tangd1,           &
+                                      tangd2,           &
+                                      nstress,          &
+                                      sstress,          &
+                                      rel_rotation
+integer(kind=8), allocatable, dimension(:) :: first_id,   &
+                                              other_id
+!integer, allocatable, dimension(:,:) :: iceberg_counter_grd
+
+  ! Get the stderr unit number
+  stderrunit=stderr()
+
+  ! For convenience
+  grd=>bergs%grd
+
+  ! Zero out nbergs_in_file
+  nbonds_in_file = 0
+  all_pe_number_perfect_bonds=0
+
+  filename_base=trim(restart_input_dir)//'bonds_iceberg.res.nc'
+
+  found_restart = find_restart_file(filename_base, filename, multiPErestart, io_tile_id(1))
+  call error_mesg('read_restart_bonds_bergs_new', 'Using icebergs bond restart read', NOTE)
+
+  filename = filename_base
+  call get_field_size(filename,'i',siz, field_found=found, domain=bergs%grd%domain)
+  nbonds_in_file = siz(1)
+
+    if (mpp_pe() .eq. mpp_root_pe()) then
+      write(stderrunit,*)  'KID, bond read restart : ','Number of bonds in file',  nbonds_in_file
+    endif
+
+  if (nbonds_in_file .gt. 0) then
+
+    allocate(first_id(nbonds_in_file))
+    allocate(other_id(nbonds_in_file))
+    allocate(id_cnt(nbonds_in_file))
+    allocate(id_ij(nbonds_in_file))
+    allocate(first_berg_jne(nbonds_in_file))
+    allocate(first_berg_ine(nbonds_in_file))
+    allocate(other_berg_ine(nbonds_in_file))
+    allocate(other_berg_jne(nbonds_in_file))
+
+    if (dem) then
+      allocate(tangd1(nbonds_in_file))
+      allocate(tangd2(nbonds_in_file))
+      allocate(nstress(nbonds_in_file))
+      allocate(sstress(nbonds_in_file))
+      allocate(rel_rotation(nbonds_in_file))
+      allocate(broken(nbonds_in_file))
+    endif
+
+    call read_unlimited_axis(filename,'first_id_cnt',id_cnt,domain=grd%domain)
+    call read_unlimited_axis(filename,'first_id_ij',id_ij,domain=grd%domain)
+    do k=1, nbonds_in_file
+      first_id(k) = id_from_2_ints( id_cnt(k), id_ij(k) )
+    enddo
+    call read_unlimited_axis(filename,'other_id_cnt',id_cnt,domain=grd%domain)
+    call read_unlimited_axis(filename,'other_id_ij',id_ij,domain=grd%domain)
+    do k=1, nbonds_in_file
+      other_id(k) = id_from_2_ints( id_cnt(k), id_ij(k) )
+    enddo
+    deallocate(id_cnt, id_ij)
+    call read_unlimited_axis(filename,'first_berg_jne',first_berg_jne,domain=grd%domain)
+    call read_unlimited_axis(filename,'first_berg_ine',first_berg_ine,domain=grd%domain)
+    call read_unlimited_axis(filename,'other_berg_jne',other_berg_jne,domain=grd%domain)
+    call read_unlimited_axis(filename,'other_berg_ine',other_berg_ine,domain=grd%domain)
+
+    if (dem) then
+      call read_real_vector(filename,'tangd1',tangd1,grd%domain,value_if_not_in_file=0.)
+      call read_real_vector(filename,'tangd2',tangd2,grd%domain,value_if_not_in_file=0.)
+      call read_real_vector(filename,'nstress',nstress,grd%domain,value_if_not_in_file=0.)
+      call read_real_vector(filename,'sstress',sstress,grd%domain,value_if_not_in_file=0.)
+      call read_real_vector(filename,'rel_rotation',rel_rotation,grd%domain,value_if_not_in_file=0.)
+      call read_int_vector(filename,'broken',broken,grd%domain,value_if_not_in_file=0)
+    endif
+
+    number_first_bonds_matched=0
+    number_second_bonds_matched=0
+    number_perfect_bonds=0
+    number_partial_bonds=0
+    number_perfect_bonds_with_first_on_pe=0
+
+    do k=1, nbonds_in_file
+
+       ! If i,j in restart files are not good, then we find the berg position of the bond addresses manually:
+       if (ignore_ij_restart) then
+         !Finding first iceberg in bond
+         ine=999 ; jne=999 ; berg_found=0.0 ; search_data_domain=.true.
+         call find_individual_iceberg(bergs,first_id(k), ine, jne,berg_found,search_data_domain)
+         berg_found_all_pe=berg_found
+         call mpp_sum(berg_found_all_pe)
+         if (berg_found_all_pe .gt. 0.5) then
+             first_berg_ine(k)=ine
+             first_berg_jne(k)=jne
+         else
+           print * , 'First bond berg not located: ', first_id(k),berg_found, mpp_pe(),ine, jne
+           call error_mesg('read_restart_bonds_bergs_new', 'First iceberg in bond not found on any pe', FATAL)
+         endif
+         !else
+
+         !Finding other iceberg other iceberg
+         ine=999 ; jne=999 ; berg_found=0.0 ; search_data_domain =.true.
+         call find_individual_iceberg(bergs,other_id(k), ine, jne, berg_found,search_data_domain)
+         berg_found_all_pe=berg_found
+         call mpp_sum(berg_found_all_pe)
+         if (berg_found_all_pe .gt. 0.5) then
+           !if (berg_found_all_pe .gt. 1.5) then
+           !  call error_mesg('read_restart_bonds_bergs_new', 'Other iceberg bond found on more than one pe', FATAL)
+           !else
+             other_berg_ine(k)=ine
+             other_berg_jne(k)=jne
+           !endif
+         else
+          call error_mesg('read_restart_bonds_bergs_new', 'Other iceberg in bond not found on any pe', FATAL)
+         endif
+         if (berg_found_all_pe .lt. 0.5) then
+                 print * , 'First bond berg not located: ', other_id(k),berg_found, mpp_pe(),ine, jne
+             call error_mesg('read_restart_bonds_bergs_new', 'First bond iceberg not located', FATAL)
+         endif
+       endif
+
+      ! Decide whether the first iceberg is on the processeor
+      if ( (first_berg_ine(k)>=grd%isd) .and. (first_berg_ine(k)<=grd%ied) .and. &
+        (first_berg_jne(k)>=grd%jsd) .and. (first_berg_jne(k)<=grd%jed) ) then
+        number_first_bonds_matched=number_first_bonds_matched+1
+
+        ! Search for the first berg, which the bond belongs to
+        first_berg_found=.false.
+        first_berg=>null()
+        this=>bergs%list(first_berg_ine(k),first_berg_jne(k))%first
+        do while(associated(this))
+          if (this%id == first_id(k)) then
+            first_berg_found=.true.
+            first_berg=>this
+            !if (first_berg%halo_berg.gt.0.5) print *, 'bonding halo berg:', first_id(k),  first_berg_ine(k),first_berg_jne(k) ,grd%isc, grd%iec, mpp_pe()
+            this=>null()
+          else
+            this=>this%next
+          endif
+        enddo
+
+        ! Decide whether the second iceberg is on the processeor (data domain)
+        second_berg_found=.false.
+        !if ( other_berg_ine(k)>=grd%isc-1 .and. other_berg_ine(k)<=grd%iec+1 .and. &
+        !  other_berg_jne(k)>=grd%jsc-1 .and.other_berg_jne(k)<=grd%jec+1 ) then
+        if ( (other_berg_ine(k)>=grd%isd) .and. (other_berg_ine(k)<=grd%ied) .and. &
+          (other_berg_jne(k)>=grd%jsd) .and.(other_berg_jne(k)<=grd%jed) ) then
+          number_second_bonds_matched=number_second_bonds_matched+1
+
+          ! Search for the second berg, which the bond belongs to
+          second_berg=>null()
+          this=>bergs%list(other_berg_ine(k),other_berg_jne(k))%first
+          do while(associated(this))
+            if (this%id == other_id(k)) then
+              second_berg_found=.true.
+              second_berg=>this
+              this=>null()
+            else
+              this=>this%next
+            endif
+          enddo
+        endif
+
+        if (first_berg_found) then
+          number_partial_bonds=number_partial_bonds+1
+          if (second_berg_found) then
+            call form_a_bond(first_berg, other_id(k), other_berg_ine(k), other_berg_jne(k),  second_berg)
+            number_perfect_bonds=number_perfect_bonds+1
+
+            current_bond=>first_berg%first_bond
+
+            if (dem) then
+              current_bond%tangd1=tangd1(k)
+              current_bond%tangd2=tangd2(k)
+              current_bond%nstress=nstress(k)
+              current_bond%sstress=sstress(k)
+              current_bond%rel_rotation=rel_rotation(k)
+              current_bond%broken=broken(k)
+            endif
+
+            !Counting number of bonds where the first bond is in the computational domain
+            if ( (first_berg_ine(k)>=grd%isc) .and. (first_berg_ine(k)<=grd%iec) .and. &
+              (first_berg_jne(k)>=grd%jsc) .and. (first_berg_jne(k)<=grd%jec) ) then
+               number_perfect_bonds_with_first_on_pe=number_perfect_bonds_with_first_on_pe+1
+            endif
+
+          else
+            !print *, 'Forming a bond of the second type', mpp_pe(), first_id(k),  other_id(k)
+            !call form_a_bond(first_berg, other_id(k), other_berg_ine(k),other_berg_jne(k))
+          endif
+        else
+          write(stderrunit,*) 'KID, bond read restart : ','Not enough partial bonds formed', k, mpp_pe(), nbonds_in_file
+          call error_mesg('read_restart_bonds_bergs_new', 'Failure with reading bonds: First bond not found on pe', FATAL)
+        endif
+      endif
+    enddo
+
+    !Analyse how many bonds were created and take appropriate action
+    all_pe_number_perfect_bonds=number_perfect_bonds
+    all_pe_number_perfect_bonds_with_first_on_pe=number_perfect_bonds_with_first_on_pe
+    all_pe_number_partial_bonds=number_partial_bonds
+    all_pe_number_first_bonds_matched=number_first_bonds_matched
+    all_pe_number_second_bonds_matched=number_second_bonds_matched
+    call mpp_sum(all_pe_number_perfect_bonds)
+    call mpp_sum(all_pe_number_partial_bonds)
+    call mpp_sum(all_pe_number_perfect_bonds_with_first_on_pe)
+
+    if (all_pe_number_partial_bonds .lt. nbonds_in_file) then
+      write(stderrunit,*) 'KID, bond read restart : ','Not enough partial bonds formed', all_pe_number_partial_bonds , nbonds_in_file
+      call error_mesg('read_restart_bonds_bergs_new', 'Not enough partial bonds formed', FATAL)
+    endif
+
+    if (all_pe_number_perfect_bonds .lt. nbonds_in_file) then
+      call mpp_sum(all_pe_number_first_bonds_matched)
+      call mpp_sum(all_pe_number_second_bonds_matched)
+      write(stderrunit,*)  'KID, bond read restart : ','Warning, some bonds are not fully formed',  all_pe_number_first_bonds_matched , nbonds_in_file
+      write(stderrunit,*)  'KID, bond read restart : ','Number of first and second bonds matched:', all_pe_number_second_bonds_matched , nbonds_in_file
+      call error_mesg('read_restart_bonds_bergs_new', 'Not enough perfect bonds formed', NOTE)
+    endif
+
+    if (all_pe_number_perfect_bonds_with_first_on_pe .ne. nbonds_in_file) then
+      call mpp_sum(all_pe_number_first_bonds_matched)
+      call mpp_sum(all_pe_number_second_bonds_matched)
+      write(stderrunit,*)  'KID, bond read restart : ','Warning, # bonds with first bond on computational domain, does not match file',  all_pe_number_first_bonds_matched , nbonds_in_file
+      write(stderrunit,*)  'KID, bond read restart : ','Computational bond, first second:', all_pe_number_second_bonds_matched , nbonds_in_file
+      call error_mesg('read_restart_bonds_bergs_new', 'Computational perfect bonds do not match those in file', NOTE)
+    endif
+
+    deallocate(               &
+            first_id,         &
+            other_id,         &
+            first_berg_ine,   &
+            first_berg_jne,   &
+            other_berg_ine,   &
+            other_berg_jne )
+
+    if (dem) then
+      deallocate(                     &
+               tangd1,                &
+               tangd2,                &
+               nstress,               &
+               sstress,               &
+               rel_rotation,          &
+               broken)
+    endif
+  endif
+
+  if (mpp_pe() .eq. mpp_root_pe()) then
+    write(stderrunit,*)  'KID, bond read restart : ','Number of bonds (including halos)',  all_pe_number_perfect_bonds
+    write(stderrunit,*)  'KID, bond read restart : ','Number of true bonds created',  all_pe_number_perfect_bonds_with_first_on_pe
+  endif
+
+end subroutine read_restart_bonds
+
+!> Reading calving and gridded restart data
+subroutine read_restart_calving(bergs)
+use random_numbers_mod, only: initializeRandomNumberStream, getRandomNumbers, randomNumberStream
+! Arguments
+type(icebergs), pointer :: bergs !< Icebergs container
+! Local variables
+integer :: k,i,j
+character(len=37) :: filename, actual_filename
+type(icebergs_gridded), pointer :: grd
+real, allocatable, dimension(:,:) :: randnum
+type(randomNumberStream) :: rns
+
+  ! For convenience
+  grd=>bergs%grd
+
+  ! Read stored ice
+  filename=trim(restart_input_dir)//'calving.res.nc'
+  if (file_exist(filename)) then
+    if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') &
+     'KID, read_restart_calving: reading ',filename
+    call read_data(filename, 'stored_ice', grd%stored_ice, grd%domain)
+    if (field_exist(filename, 'stored_heat')) then
+      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+       'KID, read_restart_calving: reading stored_heat from restart file.'
+      call read_data(filename, 'stored_heat', grd%stored_heat, grd%domain)
+    else
+      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+     'KID, read_restart_calving: stored_heat WAS NOT FOUND in the file. Setting to 0.'
+      grd%stored_heat(:,:)=0.
+    endif
+    if (field_exist(filename, 'rmean_calving')) then
+      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+       'KID, read_restart_calving: reading rmean_calving from restart file.'
+      call read_data(filename, 'rmean_calving', grd%rmean_calving, grd%domain)
+      grd%rmean_calving_initialized=.true.
+    else
+      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+     'KID, read_restart_calving: rmean_calving WAS NOT FOUND in the file. Setting to 0.'
+    endif
+    if (field_exist(filename, 'rmean_calving_hflx')) then
+      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+       'KID, read_restart_calving: reading rmean_calving_hflx from restart file.'
+      call read_data(filename, 'rmean_calving_hflx', grd%rmean_calving_hflx, grd%domain)
+      grd%rmean_calving_hflx_initialized=.true.
+    else
+      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+     'KID, read_restart_calving: rmean_calving_hflx WAS NOT FOUND in the file. Setting to 0.'
+    endif
+    if (field_exist(filename, 'iceberg_counter_grd')) then
+      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+       'KID, read_restart_calving: reading iceberg_counter_grd from restart file.'
+      call read_data(filename, 'iceberg_counter_grd', grd%iceberg_counter_grd, grd%domain)
+    else
+      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+     'KID, read_restart_calving: iceberg_counter_grd WAS NOT FOUND in the file. Setting to 0.'
+      grd%iceberg_counter_grd(:,:) = 0
+    endif
+    bergs%restarted=.true.
+  else
+    if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+     'KID, read_restart_calving: initializing stored ice to random numbers'
+    if ( make_calving_reproduce ) then
+       allocate(randnum(1,nclasses))
+       do j=grd%jsc, grd%jec
+          do i=grd%isc, grd%iec
+             rns=initializeRandomNumberStream(i+10000*j)
+             call getRandomNumbers(rns,randnum(1,:))
+             do k=1, nclasses
+               if (grd%lat(i,j)<0.) then
+                 grd%stored_ice(i,j,k)=randnum(1,k) * grd%msk(i,j) * bergs%initial_mass_s(k) * bergs%mass_scaling_s(k)
+               else
+                 grd%stored_ice(i,j,k)=randnum(1,k) * grd%msk(i,j) * bergs%initial_mass_n(k) * bergs%mass_scaling_n(k)
+               endif
+             end do
+          end do
+       end do
+    else
+       allocate(randnum(grd%jsc:grd%jec,nclasses))
+       do i=grd%isc, grd%iec
+          rns = initializeRandomNumberStream(i)
+          call getRandomNumbers(rns,randnum)
+          do k=1, nclasses
+            where (grd%lat(i,grd%jsc:grd%jec)<0.)
+             grd%stored_ice(i,grd%jsc:grd%jec,k) = randnum(:,k) * grd%msk(i,grd%jsc:grd%jec) * &
+               & bergs%initial_mass_s(k) * bergs%mass_scaling_s(k)
+           elsewhere
+             grd%stored_ice(i,grd%jsc:grd%jec,k) = randnum(:,k) * grd%msk(i,grd%jsc:grd%jec) * &
+               & bergs%initial_mass_n(k) * bergs%mass_scaling_n(k)
+           end where
+          end do
+       end do
+    end if
+    deallocate(randnum)
+  endif
+
+  call grd_chksum3(bergs%grd, bergs%grd%stored_ice, 'read_restart_calving, stored_ice')
+  call grd_chksum2(bergs%grd, bergs%grd%stored_heat, 'read_restart_calving, stored_heat')
+  call grd_chksum2(bergs%grd, bergs%grd%rmean_calving, 'read_restart_calving, rmean_calving')
+  call grd_chksum2(bergs%grd, bergs%grd%rmean_calving_hflx, 'read_restart_calving, rmean_calving_hflx')
+
+  bergs%stored_start=sum( grd%stored_ice(grd%isc:grd%iec,grd%jsc:grd%jec,:) )
+  bergs%rmean_calving_start=sum( grd%rmean_calving(grd%isc:grd%iec,grd%jsc:grd%jec) )
+  bergs%rmean_calving_hflx_start=sum( grd%rmean_calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec) )
+  call mpp_sum( bergs%stored_start )
+  bergs%stored_heat_start=sum( grd%stored_heat(grd%isc:grd%iec,grd%jsc:grd%jec) )
+  call mpp_sum( bergs%stored_heat_start )
+  bergs%floating_heat_start=sum_heat(bergs)
+  call mpp_sum( bergs%floating_heat_start )
+
+end subroutine read_restart_calving
+
+!> Read ocean depth from file
+subroutine read_ocean_depth(grd)
+! Arguments
+type(icebergs_gridded), pointer :: grd !< Container for gridded fields
+! Local variables
+character(len=37) :: filename
+
+  ! Read stored ice
+  filename=trim(restart_input_dir)//'topog.nc'
+  if (file_exist(filename)) then
+    if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') &
+     'KID, read_ocean_depth: reading ',filename
+    if (field_exist(filename, 'depth')) then
+      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+       'KID, read_ocean_depth: reading depth from topog file.'
+      call read_data(filename, 'depth', grd%ocean_depth, grd%domain)
+    else
+      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+     'KID, read_ocean_depth: depth WAS NOT FOUND in the file. Setting to 0.'
+      !grd%ocean_depth(:,:)=0.
+    endif
+  else
+    if (mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
+     'KID, read_ocean_depth: Ocean depth file (topog.nc) not present)'
+  endif
+
+  !call grd_chksum2(bergs%grd, bergs%grd%ocean_depth, 'read_ocean_depth, ocean_depth')
+end subroutine read_ocean_depth
+
+!> Write a trajectory-based diagnostics file
+subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, traj_name)
+! Arguments
+type(xyt), pointer :: trajectory !< An iceberg trajectory
+logical, intent(in) :: save_short_traj !< If true, record less data
+logical, intent(in) :: save_fl_traj !< If true, save masses and footloose data
+character(len=70) :: traj_name !< name of trajectory file
+! Local variables
+integer :: iret, ncid, i_dim, i
+integer :: lonid, latid, yearid, dayid, uvelid, vvelid, idcntid, idijid
+integer :: uvelpid,vvelpid
+integer :: uoid, void, uiid, viid, uaid, vaid, sshxid, sshyid, sstid, sssid
+integer :: cnid, hiid, hsid
+integer :: mid, smid, did, wid, lid, mbid, mflbid, mflbbid, hdid, nbid, odid, flkid
+integer :: axnid,aynid,bxnid,bynid,axnfid,aynfid,bxnfid,bynfid, msid
+integer :: avid, aaid, rid
+character(len=70) :: filename
+character(len=7) :: pe_name
+type(xyt), pointer :: this, next
+integer :: stderrunit, cnt, ij
+!I/O vars
+type(xyt), pointer :: traj4io=>null()
+integer :: from_pe,np
+type(buffer), pointer :: obuffer_io=>null(), ibuffer_io=>null()
+logical :: io_is_in_append_mode
+integer :: ntrajs_sent_io,ntrajs_rcvd_io
+
+  ! Get the stderr unit number
+  stderrunit=stderr()
+  traj4io=>null()
+  obuffer_io=>null()
+  ibuffer_io=>null()
+
+  !Assemble the list of trajectories from all pes in this I/O tile
+  call mpp_clock_begin(clock_trp)
+
+  !First add the trajs on the io_tile_root_pe (if any) to the I/O list
+  if(is_io_tile_root_pe .OR. force_all_pes_traj ) then
+     if(associated(trajectory)) then
+        this=>trajectory
+        do while (associated(this))
+           call append_posn(traj4io, this)
+           this=>this%next
+        enddo
+        trajectory => null()
+     endif
+  endif
+
+  if(.NOT. force_all_pes_traj ) then
+
+  !Now gather and append the bergs from all pes in the io_tile to the list on corresponding io_tile_root_pe
+  ntrajs_sent_io =0
+  ntrajs_rcvd_io =0
+
+  if(is_io_tile_root_pe) then
+     !Receive trajs from all pes in this I/O tile !FRAGILE!SCARY!
+     do np=2,size(io_tile_pelist) ! Note: np starts from 2 to exclude self
+        from_pe=io_tile_pelist(np)
+        call mpp_recv(ntrajs_rcvd_io, glen=1, from_pe=from_pe, tag=COMM_TAG_11)
+        if (ntrajs_rcvd_io .gt. 0) then
+           call increase_ibuffer(ibuffer_io, ntrajs_rcvd_io,buffer_width_traj)
+           call mpp_recv(ibuffer_io%data, ntrajs_rcvd_io*buffer_width_traj,from_pe=from_pe, tag=COMM_TAG_12)
+           do i=1, ntrajs_rcvd_io
+              call unpack_traj_from_buffer2(traj4io, ibuffer_io, i, save_short_traj, save_fl_traj)
+           enddo
+       endif
+     enddo
+  else
+     ! Pack and send trajectories to the root PE for this I/O tile
+     do while (associated(trajectory))
+       ntrajs_sent_io = ntrajs_sent_io +1
+       call pack_traj_into_buffer2(trajectory, obuffer_io, ntrajs_sent_io, save_short_traj, save_fl_traj)
+       this => trajectory ! Need to keep pointer in order to free up the links memory
+       trajectory => trajectory%next ! This will eventually result in trajectory => null()
+       deallocate(this) ! Delete the link from memory
+     enddo
+
+     call mpp_send(ntrajs_sent_io, plen=1, to_pe=io_tile_root_pe, tag=COMM_TAG_11)
+     if (ntrajs_sent_io .gt. 0) then
+        call mpp_send(obuffer_io%data, ntrajs_sent_io*buffer_width_traj, to_pe=io_tile_root_pe, tag=COMM_TAG_12)
+     endif
+  endif
+  call mpp_sync_self()
+  endif !.NOT. force_all_pes_traj
+
+  call mpp_clock_end(clock_trp)
+
+  !Now start writing in the io_tile_root_pe if there are any bergs in the I/O list
+  call mpp_clock_begin(clock_trw)
+
+  if((force_all_pes_traj .OR. is_io_tile_root_pe) .AND. associated(traj4io)) then
+
+    !call get_instance_filename("iceberg_trajectories.nc", filename)
+    call get_instance_filename(traj_name, filename)
+    if(io_tile_id(1) .ge. 0 .AND. .NOT. force_all_pes_traj) then !io_tile_root_pes write
+       if(io_npes .gt. 1) then !attach tile_id  to filename only if there is more than one I/O pe
+          if (io_tile_id(1)<10000) then
+             write(filename,'(A,".",I4.4)') trim(filename), io_tile_id(1)
+          else
+             write(filename,'(A,".",I6.6)') trim(filename), io_tile_id(1)
+          endif
+       endif
+    else !All pes write, attach pe# to filename
+       if (mpp_npes()<10000) then
+          write(filename,'(A,".",I4.4)') trim(filename), mpp_pe()
+       else
+          write(filename,'(A,".",I6.6)') trim(filename), mpp_pe()
+       endif
+    endif
+
+    io_is_in_append_mode = .false.
+    iret = nf_create(filename, NF_NOCLOBBER, ncid)
+    if (iret .ne. NF_NOERR) then
+      iret = nf_open(filename, NF_WRITE, ncid)
+      io_is_in_append_mode = .true.
+      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_trajectory: nf_open failed'
+    endif
+    if (verbose) then
+      if (io_is_in_append_mode) then
+        write(*,'(2a)') 'KID, write_trajectory: appending to ',filename
+      else
+        write(*,'(2a)') 'KID, write_trajectory: creating ',filename
+      endif
+    endif
+
+    if (io_is_in_append_mode) then
+      iret = nf_inq_dimid(ncid, 'i', i_dim)
+      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_trajectory: nf_inq_dimid i failed'
+      lonid = inq_varid(ncid, 'lon')
+      latid = inq_varid(ncid, 'lat')
+      yearid = inq_varid(ncid, 'year')
+      dayid = inq_varid(ncid, 'day')
+      idcntid = inq_varid(ncid, 'id_cnt')
+      idijid = inq_varid(ncid, 'id_ij')
+      if (save_fl_traj) then
+        mid = inq_varid(ncid, 'mass')
+        smid = inq_varid(ncid, 'start_mass')
+        did = inq_varid(ncid, 'thickness')
+        mbid = inq_varid(ncid, 'mass_of_bits')
+        uvelid = inq_varid(ncid, 'uvel')
+        vvelid = inq_varid(ncid, 'vvel')
+        if (footloose) then
+          msid = inq_varid(ncid, 'mass_scaling')
+          mflbid = inq_varid(ncid, 'mass_of_fl_bits')
+          mflbbid = inq_varid(ncid, 'mass_of_fl_bergy_bits')
+          flkid = inq_varid(ncid, 'fl_k')
+        endif
+      endif
+      if (.not.save_short_traj) then
+        !uvelid = inq_varid(ncid, 'uvel')
+        !vvelid = inq_varid(ncid, 'vvel')
+        uvelpid = inq_varid(ncid, 'uvel_prev')
+        vvelpid = inq_varid(ncid, 'vvel_prev')
+        uoid = inq_varid(ncid, 'uo')
+        void = inq_varid(ncid, 'vo')
+        uiid = inq_varid(ncid, 'ui')
+        viid = inq_varid(ncid, 'vi')
+        uaid = inq_varid(ncid, 'ua')
+        vaid = inq_varid(ncid, 'va')
+        hdid = inq_varid(ncid, 'heat_density')
+        wid = inq_varid(ncid, 'width')
+        lid = inq_varid(ncid, 'length')
+        sshxid = inq_varid(ncid, 'ssh_x')
+        sshyid = inq_varid(ncid, 'ssh_y')
+        sstid = inq_varid(ncid, 'sst')
+        sssid = inq_varid(ncid, 'sss')
+        cnid = inq_varid(ncid, 'cn')
+        hiid = inq_varid(ncid, 'hi')
+        axnid = inq_varid(ncid, 'axn')
+        aynid = inq_varid(ncid, 'ayn')
+        bxnid = inq_varid(ncid, 'bxn')
+        bynid = inq_varid(ncid, 'byn')
+        hsid = inq_varid(ncid, 'halo_berg')
+        odid = inq_varid(ncid, 'od')
+
+        if (mts) then
+          axnfid = inq_varid(ncid, 'axn_fast')
+          aynfid = inq_varid(ncid, 'ayn_fast')
+          bxnfid = inq_varid(ncid, 'bxn_fast')
+          bynfid = inq_varid(ncid, 'byn_fast')
+        endif
+
+        if (iceberg_bonds_on) then
+          nbid = inq_varid(ncid, 'n_bonds')
+        end if
+
+        if (dem) then
+          avid = inq_varid(ncid, 'ang_vel')
+          aaid = inq_varid(ncid, 'ang_accel')
+          rid  = inq_varid(ncid, 'rot')
+        endif
+
+      endif
+    else
+      ! Dimensions
+      iret = nf_def_dim(ncid, 'i', NF_UNLIMITED, i_dim)
+      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_trajectory: nf_def_dim i failed'
+
+      ! Variables
+      lonid = def_var(ncid, 'lon', NF_DOUBLE, i_dim)
+      latid = def_var(ncid, 'lat', NF_DOUBLE, i_dim)
+      yearid = def_var(ncid, 'year', NF_INT, i_dim)
+      dayid = def_var(ncid, 'day', NF_DOUBLE, i_dim)
+      idcntid = def_var(ncid, 'id_cnt', NF_INT, i_dim)
+      idijid = def_var(ncid, 'id_ij', NF_INT, i_dim)
+      if (save_fl_traj) then
+        mid = def_var(ncid, 'mass', NF_DOUBLE, i_dim)
+        smid = def_var(ncid, 'start_mass', NF_DOUBLE, i_dim)
+        did = def_var(ncid, 'thickness', NF_DOUBLE, i_dim)
+        mbid = def_var(ncid, 'mass_of_bits', NF_DOUBLE, i_dim)
+        uvelid = def_var(ncid, 'uvel', NF_DOUBLE, i_dim)
+        vvelid = def_var(ncid, 'vvel', NF_DOUBLE, i_dim)
+        if (footloose) then
+          msid = def_var(ncid, 'mass_scaling', NF_DOUBLE, i_dim)
+          mflbid = def_var(ncid, 'mass_of_fl_bits', NF_DOUBLE, i_dim)
+          mflbbid = def_var(ncid, 'mass_of_fl_bergy_bits', NF_DOUBLE, i_dim)
+          flkid = def_var(ncid, 'fl_k', NF_DOUBLE, i_dim)
+        endif
+      endif
+      if (.not. save_short_traj) then
+        !uvelid = def_var(ncid, 'uvel', NF_DOUBLE, i_dim)
+        !vvelid = def_var(ncid, 'vvel', NF_DOUBLE, i_dim)
+        uvelpid = def_var(ncid, 'uvel_prev', NF_DOUBLE, i_dim)
+        vvelpid = def_var(ncid, 'vvel_prev', NF_DOUBLE, i_dim)
+        uoid = def_var(ncid, 'uo', NF_DOUBLE, i_dim)
+        void = def_var(ncid, 'vo', NF_DOUBLE, i_dim)
+        uiid = def_var(ncid, 'ui', NF_DOUBLE, i_dim)
+        viid = def_var(ncid, 'vi', NF_DOUBLE, i_dim)
+        uaid = def_var(ncid, 'ua', NF_DOUBLE, i_dim)
+        vaid = def_var(ncid, 'va', NF_DOUBLE, i_dim)
+        hdid = def_var(ncid, 'heat_density', NF_DOUBLE, i_dim)
+        wid = def_var(ncid, 'width', NF_DOUBLE, i_dim)
+        lid = def_var(ncid, 'length', NF_DOUBLE, i_dim)
+        sshxid = def_var(ncid, 'ssh_x', NF_DOUBLE, i_dim)
+        sshyid = def_var(ncid, 'ssh_y', NF_DOUBLE, i_dim)
+        sstid = def_var(ncid, 'sst', NF_DOUBLE, i_dim)
+        sssid = def_var(ncid, 'sss', NF_DOUBLE, i_dim)
+        cnid = def_var(ncid, 'cn', NF_DOUBLE, i_dim)
+        hiid = def_var(ncid, 'hi', NF_DOUBLE, i_dim)
+        axnid = def_var(ncid, 'axn', NF_DOUBLE, i_dim)
+        aynid = def_var(ncid, 'ayn', NF_DOUBLE, i_dim)
+        bxnid = def_var(ncid, 'bxn', NF_DOUBLE, i_dim)
+        bynid = def_var(ncid, 'byn', NF_DOUBLE, i_dim)
+        hsid = def_var(ncid, 'halo_berg', NF_DOUBLE, i_dim)
+        odid = def_var(ncid, 'od', NF_DOUBLE, i_dim)
+
+        if (mts) then
+          axnfid = def_var(ncid, 'axn_fast', NF_DOUBLE, i_dim)
+          aynfid = def_var(ncid, 'ayn_fast', NF_DOUBLE, i_dim)
+          bxnfid = def_var(ncid, 'bxn_fast', NF_DOUBLE, i_dim)
+          bynfid = def_var(ncid, 'byn_fast', NF_DOUBLE, i_dim)
+        endif
+
+        if (iceberg_bonds_on) then
+          nbid = def_var(ncid, 'n_bonds', NF_INT, i_dim)
+        end if
+
+        if (dem) then
+          avid = def_var(ncid, 'ang_vel', NF_DOUBLE, i_dim)
+          aaid = def_var(ncid, 'ang_accel', NF_DOUBLE, i_dim)
+          rid  = def_var(ncid, 'rot', NF_DOUBLE, i_dim)
+        endif
+      endif
+
+      ! Attributes
+      iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_major_version', NF_INT, 1, 0)
+      iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_minor_version', NF_INT, 1, 1)
+      call put_att(ncid, lonid, 'long_name', 'longitude')
+      call put_att(ncid, lonid, 'units', 'degrees_E')
+      call put_att(ncid, latid, 'long_name', 'latitude')
+      call put_att(ncid, latid, 'units', 'degrees_N')
+      call put_att(ncid, yearid, 'long_name', 'year')
+      call put_att(ncid, yearid, 'units', 'years')
+      call put_att(ncid, dayid, 'long_name', 'year day')
+      call put_att(ncid, dayid, 'units', 'days')
+      call put_att(ncid, idcntid, 'long_name', 'counter component of iceberg id')
+      call put_att(ncid, idcntid, 'units', 'dimensionless')
+      call put_att(ncid, idijid, 'long_name', 'position component of iceberg id')
+      call put_att(ncid, idijid, 'units', 'dimensionless')
+      if (save_fl_traj) then
+        call put_att(ncid, mid, 'long_name', 'mass')
+        call put_att(ncid, mid, 'units', 'kg')
+        call put_att(ncid, smid, 'long_name', 'start_mass')
+        call put_att(ncid, smid, 'units', 'kg')
+        call put_att(ncid, did, 'long_name', 'thickness')
+        call put_att(ncid, did, 'units', 'm')
+        call put_att(ncid, mbid, 'long_name', 'mass_of_bits')
+        call put_att(ncid, mbid, 'units', 'kg')
+        call put_att(ncid, uvelid, 'long_name', 'zonal spped')
+        call put_att(ncid, uvelid, 'units', 'm/s')
+        call put_att(ncid, vvelid, 'long_name', 'meridional spped')
+        call put_att(ncid, vvelid, 'units', 'm/s')
+        if (footloose) then
+          call put_att(ncid, msid, 'long_name', 'mass_scaling')
+          call put_att(ncid, msid, 'units', 'dimensionless')
+          call put_att(ncid, mflbid, 'long_name', 'mass_of_fl_bits')
+          call put_att(ncid, mflbid, 'units', 'kg')
+          call put_att(ncid, mflbbid, 'long_name', 'mass_of_fl_bergy_bits')
+          call put_att(ncid, mflbbid, 'units', 'kg')
+          call put_att(ncid, flkid, 'long_name', 'footloose calving k')
+          call put_att(ncid, flkid, 'units', 'none')
+        endif
+      endif
+      if (.not. save_short_traj) then
+        ! call put_att(ncid, uvelid, 'long_name', 'zonal spped')
+        ! call put_att(ncid, uvelid, 'units', 'm/s')
+        ! call put_att(ncid, vvelid, 'long_name', 'meridional spped')
+        ! call put_att(ncid, vvelid, 'units', 'm/s')
+        call put_att(ncid, uoid, 'long_name', 'ocean zonal spped')
+        call put_att(ncid, uoid, 'units', 'm/s')
+        call put_att(ncid, void, 'long_name', 'ocean meridional spped')
+        call put_att(ncid, void, 'units', 'm/s')
+        call put_att(ncid, uiid, 'long_name', 'ice zonal spped')
+        call put_att(ncid, uiid, 'units', 'm/s')
+        call put_att(ncid, viid, 'long_name', 'ice meridional spped')
+        call put_att(ncid, viid, 'units', 'm/s')
+        call put_att(ncid, uaid, 'long_name', 'atmos zonal spped')
+        call put_att(ncid, uaid, 'units', 'm/s')
+        call put_att(ncid, vaid, 'long_name', 'atmos meridional spped')
+        call put_att(ncid, vaid, 'units', 'm/s')
+        call put_att(ncid, hdid, 'long_name', 'heat_density')
+        call put_att(ncid, hdid, 'units', 'J/kg')
+        call put_att(ncid, wid, 'long_name', 'width')
+        call put_att(ncid, wid, 'units', 'm')
+        call put_att(ncid, lid, 'long_name', 'length')
+        call put_att(ncid, lid, 'units', 'm')
+        call put_att(ncid, sshxid, 'long_name', 'sea surface height gradient_x')
+        call put_att(ncid, sshxid, 'units', 'non-dim')
+        call put_att(ncid, sshyid, 'long_name', 'sea surface height gradient_y')
+        call put_att(ncid, sshyid, 'units', 'non-dim')
+        call put_att(ncid, sstid, 'long_name', 'sea surface temperature')
+        call put_att(ncid, sstid, 'units', 'degrees_C')
+        call put_att(ncid, sssid, 'long_name', 'sea surface salinity')
+        call put_att(ncid, sssid, 'units', 'psu')
+        call put_att(ncid, cnid, 'long_name', 'sea ice concentration')
+        call put_att(ncid, cnid, 'units', 'none')
+        call put_att(ncid, hiid, 'long_name', 'sea ice thickness')
+        call put_att(ncid, hiid, 'units', 'm')
+        call put_att(ncid, axnid, 'long_name', 'explicit zonal acceleration')
+        call put_att(ncid, axnid, 'units', 'm')
+        call put_att(ncid, aynid, 'long_name', 'explicit meridional acceleration')
+        call put_att(ncid, aynid, 'units', 'm')
+        call put_att(ncid, bxnid, 'long_name', 'implicit zonal acceleration')
+        call put_att(ncid, bxnid, 'units', 'm')
+        call put_att(ncid, bynid, 'long_name', 'implicit meridional acceleration')
+        call put_att(ncid, bynid, 'units', 'm')
+        call put_att(ncid, hsid, 'long_name', 'halo status')
+        call put_att(ncid, hsid, 'units', 'non-dim')
+        call put_att(ncid, odid, 'long_name', 'ocean_depth')
+        call put_att(ncid, odid, 'units', 'm')
+
+        if (mts) then
+          call put_att(ncid, uvelpid, 'long_name', 'zonal speed mts')
+          call put_att(ncid, uvelpid, 'units', 'm/s')
+          call put_att(ncid, vvelpid, 'long_name', 'meridional speed mts')
+          call put_att(ncid, vvelpid, 'units', 'm/s')
+          call put_att(ncid, axnfid, 'long_name', 'explicit fast step zonal acceleration')
+          call put_att(ncid, axnfid, 'units', 'm')
+          call put_att(ncid, aynfid, 'long_name', 'explicit fast step meridional acceleration')
+          call put_att(ncid, aynfid, 'units', 'm')
+          call put_att(ncid, bxnfid, 'long_name', 'implicit fast step zonal acceleration')
+          call put_att(ncid, bxnfid, 'units', 'm')
+          call put_att(ncid, bynfid, 'long_name', 'implicit fast step meridional acceleration')
+          call put_att(ncid, bynfid, 'units', 'm')
+        endif
+
+        if (iceberg_bonds_on) then
+          call put_att(ncid, nbid, 'long_name', 'number of bonds')
+          call put_att(ncid, nbid, 'units', 'dimensionless')
+        end if
+
+        if (dem) then
+          call put_att(ncid, avid, 'long_name', 'angular velocity')
+          call put_att(ncid, avid, 'units', 'rad/s')
+          call put_att(ncid, aaid, 'long_name', 'angular acceleration')
+          call put_att(ncid, aaid, 'units', 'rad/s^2')
+          call put_att(ncid, rid, 'long_name', 'accumulated rotation')
+          call put_att(ncid, rid, 'units', 'rad')
+        endif
+      endif
+    endif
+
+    ! End define mode
+    iret = nf_enddef(ncid)
+
+    ! Write variables
+    this=>traj4io
+    if (io_is_in_append_mode) then
+      iret = nf_inq_dimlen(ncid, i_dim, i)
+      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_trajectory: nf_inq_dimlen i failed'
+    else
+      i = 0
+    endif
+    do while (associated(this))
+      i=i+1
+      call put_double(ncid, lonid, i, this%lon)
+      call put_double(ncid, latid, i, this%lat)
+      call put_int(ncid, yearid, i, this%year)
+      call put_double(ncid, dayid, i, this%day)
+      call split_id(this%id, cnt, ij)
+      call put_int(ncid, idcntid, i, cnt)
+      call put_int(ncid, idijid, i, ij)
+      if (save_fl_traj) then
+        call put_double(ncid, mid, i, this%mass)
+        call put_double(ncid, smid, i, this%start_mass)
+        call put_double(ncid, did, i, this%thickness)
+        call put_double(ncid, mbid, i, this%mass_of_bits)
+        call put_double(ncid, uvelid, i, this%uvel)
+        call put_double(ncid, vvelid, i, this%vvel)
+        if (footloose) then
+          call put_double(ncid, msid, i, this%mass_scaling)
+          call put_double(ncid, mflbid, i, this%mass_of_fl_bits)
+          call put_double(ncid, mflbbid, i, this%mass_of_fl_bergy_bits)
+          call put_double(ncid, flkid, i, this%fl_k)
+        endif
+      endif
+      if (.not. save_short_traj) then
+        ! call put_double(ncid, uvelid, i, this%uvel)
+        ! call put_double(ncid, vvelid, i, this%vvel)
+        call put_double(ncid, uvelpid, i, this%uvel_prev)
+        call put_double(ncid, vvelpid, i, this%vvel_prev)
+        call put_double(ncid, uoid, i, this%uo)
+        call put_double(ncid, void, i, this%vo)
+        call put_double(ncid, uiid, i, this%ui)
+        call put_double(ncid, viid, i, this%vi)
+        call put_double(ncid, uaid, i, this%ua)
+        call put_double(ncid, vaid, i, this%va)
+        call put_double(ncid, hdid, i, this%heat_density)
+        call put_double(ncid, wid, i, this%width)
+        call put_double(ncid, lid, i, this%length)
+        call put_double(ncid, sshxid, i, this%ssh_x)
+        call put_double(ncid, sshyid, i, this%ssh_y)
+        call put_double(ncid, sstid, i, this%sst)
+        call put_double(ncid, sssid, i, this%sss)
+        call put_double(ncid, cnid, i, this%cn)
+        call put_double(ncid, hiid, i, this%hi)
+        call put_double(ncid, axnid, i, this%axn)
+        call put_double(ncid, aynid, i, this%ayn)
+        call put_double(ncid, bxnid, i, this%bxn)
+        call put_double(ncid, bynid, i, this%byn)
+        call put_double(ncid, hsid, i, this%halo_berg)
+        call put_double(ncid, odid, i, this%od)
+
+        if (mts) then
+          call put_double(ncid, axnfid, i, this%axn_fast)
+          call put_double(ncid, aynfid, i, this%ayn_fast)
+          call put_double(ncid, bxnfid, i, this%bxn_fast)
+          call put_double(ncid, bynfid, i, this%byn_fast)
+        endif
+
+        if (iceberg_bonds_on) then
+          call put_int(ncid, nbid, i, this%n_bonds)
+        end if
+
+        if (dem) then
+          call put_double(ncid, avid, i, this%ang_vel)
+          call put_double(ncid, aaid, i, this%ang_accel)
+          call put_double(ncid, rid,  i, this%rot)
+        endif
+
+      endif
+      next=>this%next
+      deallocate(this)
+      this=>next
+    enddo
+
+    ! Finish up
+    iret = nf_close(ncid)
+    if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_trajectory: nf_close failed',mpp_pe(),filename
+
+  endif !(is_io_tile_root_pe .AND. associated(traj4io))
+  call mpp_clock_end(clock_trw)
+
+end subroutine write_trajectory
+
+!> Write a trajectory-based diagnostics file for bonds
+subroutine write_bond_trajectory(trajectory, bond_traj_name)
+! Arguments
+type(bond_xyt), pointer :: trajectory !< An iceberg bond trajectory
+character(len=70) :: bond_traj_name !<file name of bond trajectories
+! Local variables
+integer :: iret, ncid, i_dim, i
+integer :: lonid, latid, yearid, dayid, lenid,n1id, n2id
+integer :: rrotid,brid
+integer :: idcnt1_id, idcnt2_id, idij1_id, idij2_id
+integer :: td1id,td2id,dnsid,dssid
+character(len=70) :: filename
+character(len=7) :: pe_name
+type(bond_xyt), pointer :: this, next
+integer :: stderrunit, cnt, ij
+!I/O vars
+type(bond_xyt), pointer :: traj4io=>null()
+integer :: ntrajs_sent_io,ntrajs_rcvd_io
+integer :: from_pe,np
+type(buffer), pointer :: obuffer_io=>null(), ibuffer_io=>null()
+logical :: io_is_in_append_mode
+
+  stderrunit=stderr()  ! Get the stderr unit number
+  traj4io=>null()
+  ibuffer_io=>null(); obuffer_io=>null()
+
+  !Assemble the list of trajectories from all pes in this I/O tile
+  call mpp_clock_begin(clock_btrp)
+
+  !First add the trajs on the io_tile_root_pe (if any) to the I/O list
+  if(is_io_tile_root_pe .OR. force_all_pes_traj ) then
+    if(associated(trajectory)) then
+      this=>trajectory
+      do while (associated(this))
+        call append_bond_posn(traj4io, this)
+        this=>this%next
+      enddo
+      trajectory => null()
+    endif
+  endif
+
+  if(.NOT. force_all_pes_traj ) then
+    !Now gather and append the bergs from all pes in the io_tile to the list on corresponding io_tile_root_pe
+    ntrajs_sent_io =0; ntrajs_rcvd_io =0
+
+    if(is_io_tile_root_pe) then
+      !Receive trajs from all pes in this I/O tile !FRAGILE!SCARY!
+      do np=2,size(io_tile_pelist) ! Note: np starts from 2 to exclude self
+        from_pe=io_tile_pelist(np)
+        call mpp_recv(ntrajs_rcvd_io, glen=1, from_pe=from_pe, tag=COMM_TAG_11)
+        if (ntrajs_rcvd_io .gt. 0) then
+          call increase_ibuffer(ibuffer_io, ntrajs_rcvd_io,buffer_width_bond_traj)
+          call mpp_recv(ibuffer_io%data, ntrajs_rcvd_io*buffer_width_bond_traj,from_pe=from_pe, tag=COMM_TAG_12)
+          do i=1, ntrajs_rcvd_io
+            call unpack_bond_traj_from_buffer2(traj4io, ibuffer_io, i)
+          enddo
+        endif
+      enddo
+    else
+      ! Pack and send trajectories to the root PE for this I/O tile
+      do while (associated(trajectory))
+        ntrajs_sent_io = ntrajs_sent_io +1
+        call pack_bond_traj_into_buffer2(trajectory, obuffer_io, ntrajs_sent_io)
+        this => trajectory ! Need to keep pointer in order to free up the links memory
+        trajectory => trajectory%next ! This will eventually result in trajectory => null()
+        deallocate(this) ! Delete the link from memory
+      enddo
+
+      call mpp_send(ntrajs_sent_io, plen=1, to_pe=io_tile_root_pe, tag=COMM_TAG_11)
+      if (ntrajs_sent_io .gt. 0) then
+        call mpp_send(obuffer_io%data, ntrajs_sent_io*buffer_width_bond_traj, to_pe=io_tile_root_pe, tag=COMM_TAG_12)
+      endif
+    endif
+  endif !.NOT. force_all_pes_traj
+
+  call mpp_clock_end(clock_btrp)
+
+  !Now start writing in the io_tile_root_pe if there are any bergs in the I/O list
+  call mpp_clock_begin(clock_btrw)
+
+  if((force_all_pes_traj .OR. is_io_tile_root_pe) .AND. associated(traj4io)) then
+
+    !call get_instance_filename("bond_trajectories.nc", filename)
+    call get_instance_filename(bond_traj_name, filename)
+    if(io_tile_id(1) .ge. 0 .AND. .NOT. force_all_pes_traj) then !io_tile_root_pes write
+      if(io_npes .gt. 1) then !attach tile_id  to filename only if there is more than one I/O pe
+        if (io_tile_id(1)<10000) then
+          write(filename,'(A,".",I4.4)') trim(filename), io_tile_id(1)
+        else
+          write(filename,'(A,".",I6.6)') trim(filename), io_tile_id(1)
+        endif
+      endif
+    else !All pes write, attach pe# to filename
+      if (mpp_npes()<10000) then
+        write(filename,'(A,".",I4.4)') trim(filename), mpp_pe()
+      else
+        write(filename,'(A,".",I6.6)') trim(filename), mpp_pe()
+      endif
+    endif
+
+    io_is_in_append_mode = .false.
+    iret = nf_create(filename, NF_NOCLOBBER, ncid)
+    if (iret .ne. NF_NOERR) then
+      iret = nf_open(filename, NF_WRITE, ncid)
+      io_is_in_append_mode = .true.
+      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_bond_trajectory: nf_open failed'
+    endif
+    if (verbose) then
+      if (io_is_in_append_mode) then
+        write(*,'(2a)') 'KID, write_bond_trajectory: appending to ',filename
+      else
+        write(*,'(2a)') 'KID, write_bond_trajectory: creating ',filename
+      endif
+    endif
+
+    if (io_is_in_append_mode) then
+      iret = nf_inq_dimid(ncid, 'i', i_dim)
+      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_bond_trajectory: nf_inq_dimid i failed'
+      lonid = inq_varid(ncid, 'lon');         latid = inq_varid(ncid, 'lat')
+      yearid = inq_varid(ncid, 'year');       dayid = inq_varid(ncid, 'day')
+      lenid = inq_varid(ncid, 'length');
+      n1id = inq_varid(ncid, 'n1');           n2id = inq_varid(ncid, 'n2')
+
+      idcnt1_id = inq_varid(ncid, 'id_cnt1'); idij1_id = inq_varid(ncid, 'id_ij1')
+      idcnt2_id = inq_varid(ncid, 'id_cnt2'); idij2_id = inq_varid(ncid, 'id_ij2')
+
+      if (dem) then
+        td1id = inq_varid(ncid, 'tangd1');  td2id = inq_varid(ncid, 'tangd2')
+        dnsid = inq_varid(ncid, 'nstress'); dssid = inq_varid(ncid, 'sstress')
+        rrotid = inq_varid(ncid, 'rel_rotation'); brid = inq_varid(ncid, 'broken')
+      endif
+
+    else
+      ! Dimensions
+      iret = nf_def_dim(ncid, 'i', NF_UNLIMITED, i_dim)
+      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_bond_trajectory: nf_def_dim i failed'
+
+      ! Variables
+      lonid = def_var(ncid, 'lon', NF_DOUBLE, i_dim);      latid = def_var(ncid, 'lat', NF_DOUBLE, i_dim)
+      yearid = def_var(ncid, 'year', NF_INT, i_dim);       dayid = def_var(ncid, 'day', NF_DOUBLE, i_dim)
+      lenid = def_var(ncid, 'length', NF_DOUBLE, i_dim);
+      n1id = def_var(ncid, 'n1', NF_DOUBLE, i_dim);        n2id = def_var(ncid, 'n2', NF_DOUBLE, i_dim)
+
+      idcnt1_id = def_var(ncid, 'id_cnt1', NF_INT, i_dim); idij1_id = def_var(ncid, 'id_ij1', NF_INT, i_dim)
+      idcnt2_id = def_var(ncid, 'id_cnt2', NF_INT, i_dim); idij2_id = def_var(ncid, 'id_ij2', NF_INT, i_dim)
+
+      if (dem) then
+        td1id = def_var(ncid, 'tangd1',  NF_DOUBLE, i_dim); td2id = def_var(ncid, 'tangd2',  NF_DOUBLE, i_dim)
+        dnsid = def_var(ncid, 'nstress', NF_DOUBLE, i_dim); dssid = def_var(ncid, 'sstress', NF_DOUBLE, i_dim)
+        rrotid = def_var(ncid, 'rel_rotation', NF_DOUBLE, i_dim)
+        brid = def_var(ncid, 'broken', NF_INT, i_dim)
+      endif
+
+      ! Attributes
+      iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_major_version', NF_INT, 1, 0)
+      iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_minor_version', NF_INT, 1, 1)
+      call put_att(ncid, lonid, 'long_name', 'longitude');    call put_att(ncid, lonid, 'units', 'degrees_E')
+      call put_att(ncid, latid, 'long_name', 'latitude');     call put_att(ncid, latid, 'units', 'degrees_N')
+      call put_att(ncid, yearid, 'long_name', 'year');        call put_att(ncid, yearid, 'units', 'years')
+      call put_att(ncid, dayid, 'long_name', 'year day');     call put_att(ncid, dayid, 'units', 'days')
+      call put_att(ncid, lenid, 'long_name', 'length');       call put_att(ncid, lenid, 'units', 'm')
+      call put_att(ncid, n1id, 'long_name', 'unit vector 1'); call put_att(ncid, n1id, 'units', 'non-dim')
+      call put_att(ncid, n2id, 'long_name', 'unit vector 2'); call put_att(ncid, n2id, 'units', 'non-dim')
+
+      call put_att(ncid, idcnt1_id, 'long_name', 'counter component of first connected iceberg id')
+      call put_att(ncid, idcnt1_id, 'units', 'dimensionless')
+      call put_att(ncid, idij1_id, 'long_name', 'position component of first connected iceberg id')
+      call put_att(ncid, idij1_id, 'units', 'dimensionless')
+      call put_att(ncid, idcnt2_id, 'long_name', 'counter component of second connected iceberg id')
+      call put_att(ncid, idcnt2_id, 'units', 'dimensionless')
+      call put_att(ncid, idij2_id, 'long_name', 'position component of second connected iceberg id')
+      call put_att(ncid, idij2_id, 'units', 'dimensionless')
+
+      if (dem) then
+        call put_att(ncid, td1id, 'long_name', 'zonal tangential displacement')
+        call put_att(ncid, td1id, 'units', 'm')
+        call put_att(ncid, td2id, 'long_name', 'meridional tangential displacement')
+        call put_att(ncid, td2id, 'units', 'm')
+        call put_att(ncid, dnsid, 'long_name', 'normal stress'); call put_att(ncid, dnsid, 'units', 'Pa')
+        call put_att(ncid, dssid, 'long_name', 'shear stress');  call put_att(ncid, dssid, 'units', 'Pa')
+        call put_att(ncid, rrotid, 'long_name', 'relative rotation');      call put_att(ncid, rrotid, 'units', 'rad')
+        call put_att(ncid, brid, 'long_name', 'broken status');      call put_att(ncid, brid, 'units', 'none')
+      endif
+    endif
+
+    ! End define mode
+    iret = nf_enddef(ncid)
+
+    ! Write variables
+    this=>traj4io
+    if (io_is_in_append_mode) then
+      iret = nf_inq_dimlen(ncid, i_dim, i)
+      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_bond_trajectory: nf_inq_dimlen i failed'
+    else
+      i = 0
+    endif
+    do while (associated(this))
+      i=i+1
+      call put_double(ncid, lonid, i, this%lon);    call put_double(ncid, latid, i, this%lat)
+      call put_int(ncid, yearid, i, this%year);     call put_double(ncid, dayid, i, this%day)
+      call put_double(ncid, lenid, i, this%length);
+      call put_double(ncid, n1id, i, this%n1);      call put_double(ncid, n2id, i, this%n2)
+
+      call split_id(this%id1, cnt, ij)
+      call put_int(ncid, idcnt1_id, i, cnt);        call put_int(ncid, idij1_id, i, ij)
+      call split_id(this%id2, cnt, ij)
+      call put_int(ncid, idcnt2_id, i, cnt);        call put_int(ncid, idij2_id, i, ij)
+
+      if (dem) then
+        call put_double(ncid,td1id,i,this%tangd1);  call put_double(ncid,td2id,i,this%tangd2)
+        call put_double(ncid,dnsid,i,this%nstress); call put_double(ncid,dssid,i,this%sstress)
+        call put_double(ncid,rrotid,i,this%rel_rotation); call put_int(ncid,brid,i,this%broken)
+      endif
+
+      next=>this%next
+      deallocate(this)
+      this=>next
+    enddo
+
+    ! Finish up
+    iret = nf_close(ncid)
+    if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_bond_trajectory: nf_close failed',mpp_pe(),filename
+
+  endif !(is_io_tile_root_pe .AND. associated(traj4io))
+  call mpp_clock_end(clock_btrw)
+
+end subroutine write_bond_trajectory
+
+!> Returns netcdf id of variable
+integer function inq_var(ncid, var, unsafe)
+! Arguments
+integer, intent(in) :: ncid !< Handle to netcdf file
+character(len=*), intent(in) :: var !< Name of variable
+logical, optional, intent(in) :: unsafe !< If present and true, do not fail if variable is not in file
+! Local variables
+integer :: iret
+integer :: stderrunit
+logical :: unsafely=.false.
+
+  if(present(unsafe)) unsafely=unsafe
+  ! Get the stderr unit number
+  stderrunit=stderr()
+
+  iret=nf_inq_varid(ncid, var, inq_var)
+  if (iret .ne. NF_NOERR) then
+    if (.not. unsafely) then
+      write(stderrunit,*) 'KID, inq_var: nf_inq_varid ',var,' failed'
+      call error_mesg('KID, inq_var', 'netcdf function returned a failure!', FATAL)
+    else
+      inq_var=-1
+    endif
+  endif
+
+end function inq_var
+
+!> Define a netcdf variable
+integer function def_var(ncid, var, ntype, idim)
+! Arguments
+integer, intent(in) :: ncid !< Handle to netcdf file
+character(len=*), intent(in) :: var !< Name of variable
+integer, intent(in) :: ntype !< Netcdf type of variable
+integer, intent(in) :: idim !< Length of vector
+! Local variables
+integer :: iret
+integer :: stderrunit
+
+  ! Get the stderr unit number
+  stderrunit=stderr()
+
+  iret = nf_def_var(ncid, var, ntype, 1, idim, def_var)
+  if (iret .ne. NF_NOERR) then
+    call error_mesg('KID, def_var', nf_strerror(iret), FATAL)
+  endif
+
+end function def_var
+
+!> Returns id of variable
+integer function inq_varid(ncid, var)
+! Arguments
+integer, intent(in) :: ncid !< Handle to netcdf file
+character(len=*), intent(in) :: var !< Name of variable
+! Local variables
+integer :: iret
+integer :: stderrunit
+
+  ! Get the stderr unit number
+  stderrunit=stderr()
+
+  iret = nf_inq_varid(ncid, var, inq_varid)
+  if (iret .ne. NF_NOERR) then
+    write(stderrunit,*) 'KID, inq_varid: nf_inq_varid failed for ',trim(var)
+    call error_mesg('KID, inq_varid', 'netcdf function returned a failure!', FATAL)
+  endif
+
+end function inq_varid
+
+!> Add a string attribute to a netcdf variable
+subroutine put_att(ncid, id, att, attval)
+! Arguments
+integer, intent(in) :: ncid !< Handle to netcdf file
+integer, intent(in) :: id !< Netcdf id of variable
+character(len=*), intent(in) :: att !< Name of attribute
+character(len=*), intent(in) :: attval !< Value of attribute
+! Local variables
+integer :: vallen, iret
+integer :: stderrunit
+
+  ! Get the stderr unit number
+  stderrunit=stderr()
+
+  vallen=len_trim(attval)
+  iret = nf_put_att_text(ncid, id, att, vallen, attval)
+  if (iret .ne. NF_NOERR) then
+    write(stderrunit,*) 'KID, put_att: nf_put_att_text failed adding', &
+      trim(att),' = ',trim(attval)
+    call error_mesg('KID, put_att', 'netcdf function returned a failure!', FATAL)
+  endif
+
+end subroutine put_att
+
+!> Read a real from a netcdf file
+real function get_double(ncid, id, i)
+! Arguments
+integer, intent(in) :: ncid !< Handle to netcdf file
+integer, intent(in) :: id !< Netcdf id of variable
+integer, intent(in) :: i !< Index to read
+! Local variables
+integer :: iret
+integer :: stderrunit
+
+  ! Get the stderr unit number
+  stderrunit=stderr()
+
+  iret=nf_get_var1_double(ncid, id, i, get_double)
+  if (iret .ne. NF_NOERR) then
+    write(stderrunit,*) 'KID, get_double: nf_get_var1_double failed reading'
+    call error_mesg('KID, get_double', 'netcdf function returned a failure!', FATAL)
+  endif
+
+end function get_double
+
+!> Read an integer from a netcdf file
+integer function get_int(ncid, id, i)
+! Arguments
+integer, intent(in) :: ncid !< Handle to netcdf file
+integer, intent(in) :: id !< Netcdf id of variable
+integer, intent(in) :: i !< Index to read
+! Local variables
+integer :: iret
+integer :: stderrunit
+
+  ! Get the stderr unit number
+  stderrunit=stderr()
+
+  iret=nf_get_var1_int(ncid, id, i, get_int)
+  if (iret .ne. NF_NOERR) then
+    write(stderrunit,*) 'KID, get_int: nf_get_var1_int failed reading'
+    call error_mesg('KID, get_int', 'netcdf function returned a failure!', FATAL)
+  endif
+
+end function get_int
+
+!> Write a real to a netcdf file
+subroutine put_double(ncid, id, i, val)
+! Arguments
+integer, intent(in) :: ncid !< Handle to netcdf file
+integer, intent(in) :: id !< Netcdf id of variable
+integer, intent(in) :: i !< Index of position to write
+real, intent(in) :: val !< Value to write
+! Local variables
+integer :: iret
+integer :: stderrunit
+
+  ! Get the stderr unit number
+  stderrunit=stderr()
+
+  iret = nf_put_vara_double(ncid, id, i, 1, val)
+  if (iret .ne. NF_NOERR) then
+    write(stderrunit,*) 'KID, put_double: nf_put_vara_double failed writing'
+    call error_mesg('KID, put_double', 'netcdf function returned a failure!', FATAL)
+  endif
+
+end subroutine put_double
+
+!> Write an integer to a netcdf file
+subroutine put_int(ncid, id, i, val)
+! Arguments
+integer, intent(in) :: ncid !< Handle to netcdf file
+integer, intent(in) :: id !< Netcdf id of variable
+integer, intent(in) :: i !< Index of position to write
+integer, intent(in) :: val !< Value to write
+! Local variables
+integer :: iret
+integer :: stderrunit
+
+  ! Get the stderr unit number
+  stderrunit=stderr()
+
+  iret = nf_put_vara_int(ncid, id, i, 1, val)
+  if (iret .ne. NF_NOERR) then
+    write(stderrunit,*) 'KID, put_int: nf_put_vara_int failed writing'
+    call error_mesg('KID, put_int', 'netcdf function returned a failure!', FATAL)
+  endif
+
+end subroutine put_int
+
+!> True is a restart file can be found
+logical function find_restart_file(filename, actual_file, multiPErestart, tile_id)
+  character(len=*), intent(in) :: filename !< Base-name of restart file
+  character(len=*), intent(out) :: actual_file !< Actual name of file, if found
+  logical, intent(out) :: multiPErestart !< True if found, false otherwise
+  integer, intent(in) :: tile_id !< Parallel tile number of file
+
+  character(len=6) :: pe_name
+
+  find_restart_file = .false.
+
+  ! If running as ensemble, add the ensemble id string to the filename
+  call get_instance_filename(filename, actual_file)
+
+  ! Prefer combined restart files.
+  inquire(file=actual_file,exist=find_restart_file)
+  if (find_restart_file) return
+
+  ! Uncombined restart
+  if(tile_id .ge. 0) then
+    write(actual_file,'(A,".",I4.4)') trim(actual_file), tile_id
+  else
+  if (mpp_npes()>10000) then
+     write(pe_name,'(a,i6.6)' )'.', mpp_pe()
+  else
+     write(pe_name,'(a,i4.4)' )'.', mpp_pe()
+  endif
+  actual_file=trim(actual_file)//trim(pe_name)
+  endif
+  inquire(file=actual_file,exist=find_restart_file)
+  if (find_restart_file) then
+     multiPErestart=.true.
+     return
+  endif
+
+  ! No file found, Reset all return parameters
+  find_restart_file=.false.
+  actual_file = ''
+  multiPErestart=.false.
+
+end function find_restart_file
+#endif
+end module
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index 38859ad..c9b5e0e 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -653,7 +653,7 @@ subroutine ice_bergs_framework_init(bergs, &
 use mpp_mod, only: mpp_clock_begin, mpp_clock_end, mpp_clock_id, input_nml_file
 use mpp_mod, only: CLOCK_COMPONENT, CLOCK_SUBCOMPONENT, CLOCK_LOOP
 
-use fms_mod, only: open_namelist_file, check_nml_error, close_file
+use fms_mod, only: check_nml_error
 use fms_mod, only: clock_flag_default
 
 use diag_manager_mod, only: register_diag_field, register_static_field, send_data
@@ -876,13 +876,7 @@ subroutine ice_bergs_framework_init(bergs, &
 
 ! Read namelist parameters
  !write(stderrunit,*) 'KID: reading namelist'
-#ifdef INTERNAL_FILE_NML
   read (input_nml_file, nml=icebergs_nml, iostat=ierr)
-#else
-  iunit = open_namelist_file()
-  read  (iunit, icebergs_nml,iostat=ierr)
-  call close_file (iunit)
-#endif
   ierr = check_nml_error(ierr,'icebergs_nml')
 
   if (really_debug) debug=.true. ! One implies the other...
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index 6ab8151..28fb88a 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -1,2496 +1,11 @@
 !> Handles reading/writing of restart files and trajectory-based diagnostic files
 module ice_bergs_io
-
 ! This file is part of NOAA-GFDL/icebergs. See LICENSE.md for the license.
 
-use mpp_domains_mod, only: domain2D
-use mpp_domains_mod, only: mpp_domain_is_tile_root_pe,mpp_get_domain_tile_root_pe
-use mpp_domains_mod, only: mpp_get_tile_pelist,mpp_get_tile_npes,mpp_get_io_domain,mpp_get_tile_id
-
-use mpp_mod, only: mpp_npes, mpp_pe, mpp_root_pe, mpp_sum, mpp_min, mpp_max, NULL_PE
-use mpp_mod, only: mpp_send, mpp_recv, mpp_gather, mpp_chksum, mpp_sync_self
-use mpp_mod, only: COMM_TAG_11, COMM_TAG_12, COMM_TAG_13, COMM_TAG_14
-
-use fms_mod, only: stdlog, stderr, error_mesg, FATAL, WARNING, NOTE
-use fms_mod, only: field_exist, file_exist, read_data, write_data
-
-use fms_io_mod, only: get_instance_filename
-use fms_io_mod, only : save_restart, restart_file_type, free_restart_type, set_meta_global
-use fms_io_mod, only : register_restart_axis, register_restart_field, set_domain, nullify_domain
-use fms_io_mod, only : read_unlimited_axis =>read_compressed, field_exist, get_field_size
-
-use mpp_mod,    only : mpp_clock_begin, mpp_clock_end, mpp_clock_id
-use mpp_mod,    only : CLOCK_COMPONENT, CLOCK_SUBCOMPONENT, CLOCK_LOOP
-use fms_mod,    only : clock_flag_default
-
-use time_manager_mod, only: time_type, get_date, get_time, set_date, operator(-)
-
-use ice_bergs_framework, only: icebergs_gridded, xyt, bond_xyt, iceberg, icebergs, buffer, bond
-use ice_bergs_framework, only: pack_traj_into_buffer2,unpack_traj_from_buffer2
-use ice_bergs_framework, only: find_cell,find_cell_by_search,count_bergs,is_point_in_cell,pos_within_cell,append_posn
-use ice_bergs_framework, only: count_bonds, form_a_bond, find_individual_iceberg
-use ice_bergs_framework, only: push_posn
-use ice_bergs_framework, only: add_new_berg_to_list,destroy_iceberg
-use ice_bergs_framework, only: increase_ibuffer,grd_chksum2,grd_chksum3
-use ice_bergs_framework, only: sum_mass,sum_heat,bilin
-!params !Niki: write a subroutine to get these
-use ice_bergs_framework, only: nclasses, buffer_width, buffer_width_traj, buffer_width_bond_traj
-use ice_bergs_framework, only: verbose, really_debug, debug, restart_input_dir,make_calving_reproduce
-use ice_bergs_framework, only: ignore_ij_restart, use_slow_find,generate_test_icebergs,print_berg
-use ice_bergs_framework, only: force_all_pes_traj
-use ice_bergs_framework, only: check_for_duplicates_in_parallel
-use ice_bergs_framework, only: split_id, id_from_2_ints, generate_id
-! for MTS/DEM/fracture/footloose:
-use ice_bergs_framework, only: mts,save_bond_traj
-use ice_bergs_framework, only: push_bond_posn, append_bond_posn
-use ice_bergs_framework, only: pack_bond_traj_into_buffer2,unpack_bond_traj_from_buffer2
-use ice_bergs_framework, only: dem, iceberg_bonds_on
-use ice_bergs_framework, only: footloose
-
-
-implicit none ; private
-
-include 'netcdf.inc'
-
-public ice_bergs_io_init
-public read_restart_bergs, write_restart, write_trajectory, write_bond_trajectory
-public read_restart_calving, read_restart_bonds
-public read_ocean_depth
-
-!Local Vars
-integer, parameter :: file_format_major_version=0
-integer, parameter :: file_format_minor_version=1
-!I/O vars
-type(domain2d), pointer, save :: io_domain=>NULL()
-integer, save :: io_tile_id(1), io_tile_root_pe, io_npes
-integer, allocatable,save :: io_tile_pelist(:)
-logical :: is_io_tile_root_pe = .true.
-
-integer :: clock_trw,clock_trp
-integer :: clock_btrw,clock_btrp !bond trajectories
-
-#ifndef _FILE_VERSION
-! Version of file provided can be set to git hash via a CPP macro but if not set we use 'unknown'
-#define _FILE_VERSION 'unknown'
+#ifdef use_depreciated_io
+  use ice_bergs_fmsio
+#else
+  use ice_bergs_fms2io
 #endif
-character(len=128) :: version = _FILE_VERSION !< Version of file
-
-contains
-
-!> Initialize parallel i/o
-subroutine ice_bergs_io_init(bergs, io_layout)
-type(icebergs), pointer :: bergs !< Icebergs container
-integer, intent(in) :: io_layout(2) !< Decomposition of i/o processors
-
-integer :: np
-integer :: stdlogunit, stderrunit
-
-  ! Get the stderr and stdlog unit numbers
-  stderrunit=stderr()
-  stdlogunit=stdlog()
-  write(stdlogunit,*) "ice_bergs_framework: "//trim(version)
-
-  !I/O layout init
-  io_tile_id=-1
-  io_domain => mpp_get_io_domain(bergs%grd%domain)
-  if(associated(io_domain)) then
-     io_tile_id = mpp_get_tile_id(io_domain)
-     is_io_tile_root_pe = mpp_domain_is_tile_root_pe(io_domain)
-     io_tile_root_pe = mpp_get_domain_tile_root_pe(io_domain)
-     np=mpp_get_tile_npes(io_domain)
-     allocate(io_tile_pelist(np))
-     call mpp_get_tile_pelist(io_domain,io_tile_pelist)
-     io_npes = io_layout(1)*io_layout(2)
-  endif
-
-  clock_trw=mpp_clock_id( 'Icebergs-traj write', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
-  clock_trp=mpp_clock_id( 'Icebergs-traj prepare', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
-  clock_btrw=mpp_clock_id( 'Iceberg-bonds-traj write', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
-  clock_btrp=mpp_clock_id( 'Iceberg-bonds-traj prepare', flags=clock_flag_default, grain=CLOCK_SUBCOMPONENT )
-
-end subroutine ice_bergs_io_init
-
-!> Write an iceberg restart file
-subroutine write_restart(bergs, time_stamp)
-! Arguments
-type(icebergs), pointer :: bergs !< Icebergs container
-character(len=*), intent(in), optional :: time_stamp !< Timestamp for restart file
-
-! Local variables
-type(bond), pointer :: current_bond
-integer :: i,j,id
-character(len=35) :: filename
-character(len=35) :: filename_bonds
-type(iceberg), pointer :: this=>NULL()
-integer :: stderrunit
-!I/O vars
-type(restart_file_type) :: bergs_restart
-type(restart_file_type) :: bergs_bond_restart
-type(restart_file_type) :: calving_restart
-integer :: nbergs, nbonds
-integer :: n_static_bergs
-logical :: check_bond_quality
-type(icebergs_gridded), pointer :: grd
-real, allocatable, dimension(:) :: lon,          &
-                                   lat,          &
-                                   uvel,         &
-                                   vvel,         &
-                                   mass,         &
-                                   axn,          &
-                                   ayn,          &
-                                   bxn,          &
-                                   byn,          &
-                                   thickness,    &
-                                   width,        &
-                                   length,       &
-                                   fl_k,         &
-                                   start_lon,    &
-                                   start_lat,    &
-                                   start_day,    &
-                                   start_mass,   &
-                                   mass_scaling, &
-                                   mass_of_bits, &
-                                   mass_of_fl_bits, &
-                                   mass_of_fl_bergy_bits, &
-                                   static_berg,  &
-                                   heat_density, &
-                                   axn_fast,     &
-                                   ayn_fast,     &
-                                   bxn_fast,     &
-                                   byn_fast,     &
-                                   ang_vel,      &
-                                   ang_accel,    &
-                                   rot,          &
-                                   tangd1,       &
-                                   tangd2,       &
-                                   nstress,      &
-                                   sstress,      &
-                                   rel_rotation
-
-integer, allocatable, dimension(:) :: ine,              &
-                                      jne,              &
-                                      id_cnt,           &
-                                      id_ij,            &
-                                      start_year,       &
-                                      first_id_cnt,     &
-                                      other_id_cnt,     &
-                                      first_id_ij,      &
-                                      other_id_ij,      &
-                                      first_berg_jne,         &
-                                      first_berg_ine,         &
-                                      other_berg_jne,         &
-                                      other_berg_ine,         &
-                                      broken
-
-
-integer :: grdi, grdj
-
-! Get the stderr unit number
- stderrunit=stderr()
-
-
-  ! For convenience
-  grd=>bergs%grd
-
-  !First add the bergs on the io_tile_root_pe (if any) to the I/O list
-  nbergs = 0
-  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
-    this=>bergs%list(grdi,grdj)%first
-    do while (associated(this))
-      nbergs = nbergs +1
-      this=>this%next
-    enddo
-  enddo ; enddo
-
-   allocate(lon(nbergs))
-   allocate(lat(nbergs))
-   allocate(uvel(nbergs))
-   allocate(vvel(nbergs))
-   allocate(mass(nbergs))
-   allocate(axn(nbergs))    !Alon
-   allocate(ayn(nbergs))    !Alon
-   allocate(bxn(nbergs)) !Alon
-   allocate(byn(nbergs)) !Alon
-   allocate(thickness(nbergs))
-   allocate(width(nbergs))
-   allocate(length(nbergs))
-   allocate(start_lon(nbergs))
-   allocate(start_lat(nbergs))
-   allocate(start_day(nbergs))
-   allocate(start_mass(nbergs))
-   allocate(mass_scaling(nbergs))
-   allocate(mass_of_bits(nbergs))
-   allocate(heat_density(nbergs))
-   allocate(static_berg(nbergs))
-
-   allocate(ine(nbergs))
-   allocate(jne(nbergs))
-   allocate(start_year(nbergs))
-   allocate(id_cnt(nbergs))
-   allocate(id_ij(nbergs))
-
-   if (bergs%footloose) then
-     allocate(fl_k(nbergs))
-     allocate(mass_of_fl_bits(nbergs))
-     allocate(mass_of_fl_bergy_bits(nbergs))
-   end if
-
-   if (mts) then
-     allocate(axn_fast(nbergs))
-     allocate(ayn_fast(nbergs))
-     allocate(bxn_fast(nbergs))
-     allocate(byn_fast(nbergs))
-   endif
-   if (dem) then
-     allocate(ang_vel(nbergs))
-     allocate(ang_accel(nbergs))
-     allocate(rot(nbergs))
-   endif
-
-  filename = trim("icebergs.res.nc")
-  call set_domain(bergs%grd%domain)
-  call register_restart_axis(bergs_restart,filename,'i',nbergs)
-  call set_meta_global(bergs_restart,'file_format_major_version',ival=(/file_format_major_version/))
-  call set_meta_global(bergs_restart,'file_format_minor_version',ival=(/file_format_minor_version/))
-  call set_meta_global(bergs_restart,'time_axis',ival=(/0/))
-
-  !Now start writing in the io_tile_root_pe if there are any bergs in the I/O list
-
-  ! Define Variables
-  id = register_restart_field(bergs_restart,filename,'lon',lon,longname='longitude',units='degrees_E')
-  id = register_restart_field(bergs_restart,filename,'lat',lat,longname='latitude',units='degrees_N')
-  id = register_restart_field(bergs_restart,filename,'uvel',uvel,longname='zonal velocity',units='m/s')
-  id = register_restart_field(bergs_restart,filename,'vvel',vvel,longname='meridional velocity',units='m/s')
-  id = register_restart_field(bergs_restart,filename,'mass',mass,longname='mass',units='kg')
-  if (.not. bergs%Runge_not_Verlet) then
-    id = register_restart_field(bergs_restart,filename,'axn',axn,longname='explicit zonal acceleration',units='m/s^2')
-    id = register_restart_field(bergs_restart,filename,'ayn',ayn,longname='explicit meridional acceleration',units='m/s^2')
-    id = register_restart_field(bergs_restart,filename,'bxn',bxn,longname='implicit zonal acceleration',units='m/s^2')
-    id = register_restart_field(bergs_restart,filename,'byn',byn,longname='implicit meridional acceleration',units='m/s^2')
-  endif
-  id = register_restart_field(bergs_restart,filename,'ine',ine,longname='i index',units='none')
-  id = register_restart_field(bergs_restart,filename,'jne',jne,longname='j index',units='none')
-  id = register_restart_field(bergs_restart,filename,'thickness',thickness,longname='thickness',units='m')
-  id = register_restart_field(bergs_restart,filename,'width',width,longname='width',units='m')
-  id = register_restart_field(bergs_restart,filename,'length',length,longname='length',units='m')
-  id = register_restart_field(bergs_restart,filename,'start_lon',start_lon, &
-                                            longname='longitude of calving location',units='degrees_E')
-  id = register_restart_field(bergs_restart,filename,'start_lat',start_lat, &
-                                            longname='latitude of calving location',units='degrees_N')
-  id = register_restart_field(bergs_restart,filename,'start_year',start_year, &
-                                            longname='calendar year of calving event', units='years')
-  id = register_restart_field(bergs_restart,filename,'id_cnt',id_cnt, &
-                                            longname='counter component of iceberg id', units='dimensionless')
-  id = register_restart_field(bergs_restart,filename,'id_ij',id_ij, &
-                                            longname='position component of iceberg id', units='dimensionless')
-  id = register_restart_field(bergs_restart,filename,'start_day',start_day, &
-                                            longname='year day of calving event',units='days')
-  id = register_restart_field(bergs_restart,filename,'start_mass',start_mass, &
-                                            longname='initial mass of calving berg',units='kg')
-  id = register_restart_field(bergs_restart,filename,'mass_scaling',mass_scaling, &
-                                            longname='scaling factor for mass of calving berg',units='none')
-  id = register_restart_field(bergs_restart,filename,'mass_of_bits',mass_of_bits, &
-                                            longname='mass of bergy bits',units='kg')
-  id = register_restart_field(bergs_restart,filename,'heat_density',heat_density, &
-                                            longname='heat density',units='J/kg')
-
-  if (bergs%footloose) then
-    id = register_restart_field(bergs_restart,filename,'fl_k',fl_k,longname='footloose calving k',units='m')
-    id = register_restart_field(bergs_restart,filename,'mass_of_fl_bits',mass_of_fl_bits, &
-      longname='mass of footloose bits',units='kg')
-    id = register_restart_field(bergs_restart,filename,'mass_of_fl_bergy_bits',mass_of_fl_bergy_bits, &
-      longname='mass of bergy bits associated with footloose bits',units='kg')
-   end if
-
-  if (mts) then
-    id = register_restart_field(bergs_restart,filename,'axn_fast',axn_fast,&
-      longname='sub-step explicit zonal acceleration',units='m/s^2')
-    id = register_restart_field(bergs_restart,filename,'ayn_fast',ayn_fast,&
-      longname='sub-step explicit meridional acceleration',units='m/s^2')
-    id = register_restart_field(bergs_restart,filename,'bxn_fast',bxn_fast,&
-      longname='sub-step implicit zonal acceleration',units='m/s^2')
-    id = register_restart_field(bergs_restart,filename,'byn_fast',byn_fast,&
-      longname='sub-step implicit meridional acceleration',units='m/s^2')
-  endif
-
-  if (dem) then
-    id = register_restart_field(bergs_restart,filename,'ang_vel',ang_vel,&
-      longname='dem angular velocity',units='rad/s')
-    id = register_restart_field(bergs_restart,filename,'ang_accel',ang_accel,&
-      longname='dem angular acceleration',units='rad/s^2')
-    id = register_restart_field(bergs_restart,filename,'rot',rot,&
-      longname='dem accumulated rotation',units='rad')
-  endif
-
-  !Checking if any icebergs are static in order to decide whether to save static_berg
-  n_static_bergs = 0
-  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
-    this=>bergs%list(grdi,grdj)%first
-    do while (associated(this))
-      n_static_bergs=n_static_bergs+this%static_berg
-      this=>this%next
-    enddo
-  enddo ; enddo
-  call mpp_sum(n_static_bergs)
-  if (n_static_bergs .gt. 0) &
-    id = register_restart_field(bergs_restart,filename,'static_berg',static_berg, &
-                                              longname='static_berg',units='dimensionless')
-
-  ! Write variables
-
-  i = 0
-  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
-    this=>bergs%list(grdi,grdj)%first
-    do while(associated(this))
-      i = i + 1
-      lon(i) = this%lon; lat(i) = this%lat
-      uvel(i) = this%uvel; vvel(i) = this%vvel
-      ine(i) = this%ine; jne(i) = this%jne
-      mass(i) = this%mass; thickness(i) = this%thickness
-      axn(i) = this%axn; ayn(i) = this%ayn !Added by Alon
-      bxn(i) = this%bxn; byn(i) = this%byn !Added by Alon
-      width(i) = this%width; length(i) = this%length
-      start_lon(i) = this%start_lon; start_lat(i) = this%start_lat
-      start_year(i) = this%start_year; start_day(i) = this%start_day
-      start_mass(i) = this%start_mass; mass_scaling(i) = this%mass_scaling
-      static_berg(i) = this%static_berg
-      call split_id(this%id, id_cnt(i), id_ij(i))
-      mass_of_bits(i) = this%mass_of_bits
-      heat_density(i) = this%heat_density
-
-      if (bergs%footloose) then
-        fl_k(i) = this%fl_k
-        mass_of_fl_bits(i) = this%mass_of_fl_bits
-        mass_of_fl_bergy_bits(i) = this%mass_of_fl_bergy_bits
-      end if
-
-      if (mts) then
-        axn_fast(i) = this%axn_fast
-        ayn_fast(i) = this%ayn_fast
-        bxn_fast(i) = this%bxn_fast
-        byn_fast(i) = this%byn_fast
-      endif
-      if (dem) then
-        ang_vel(i) = this%ang_vel
-        ang_accel(i) = this%ang_accel
-        rot(i) = this%rot
-      endif
-      this=>this%next
-    enddo
-  enddo ; enddo
-
-
-  call save_restart(bergs_restart, time_stamp)
-  call free_restart_type(bergs_restart)
-
-  deallocate(              &
-             lon,          &
-             lat,          &
-             uvel,         &
-             vvel,         &
-             mass,         &
-             axn,          &
-             ayn,          &
-             bxn,          &
-             byn,          &
-             thickness,    &
-             width,        &
-             length,       &
-             start_lon,    &
-             start_lat,    &
-             start_day,    &
-             start_mass,   &
-             mass_scaling, &
-             mass_of_bits, &
-             static_berg,  &
-             heat_density)
-
-  if (bergs%footloose) then
-    deallocate(                   &
-                 fl_k,            &
-                 mass_of_fl_bits, &
-                 mass_of_fl_bergy_bits)
-  end if
-  if (mts) then
-    deallocate(            &
-             axn_fast,     &
-             ayn_fast,     &
-             bxn_fast,     &
-             byn_fast)
-  endif
-  if (dem) then
-    deallocate(            &
-             ang_vel,      &
-             ang_accel,    &
-             rot)
-  endif
-
-  deallocate(           &
-             ine,       &
-             jne,       &
-             id_cnt,    &
-             id_ij,     &
-             start_year )
-
-  call nullify_domain()
-
-!########## Creating bond restart file ######################
-
-  !Allocating restart memory for bond related variables.
-  nbonds=0
-  if (bergs%iceberg_bonds_on) then
-    check_bond_quality=.true.
-    call count_bonds(bergs, nbonds,check_bond_quality)
-
-  allocate(first_id_cnt(nbonds))
-  allocate(other_id_cnt(nbonds))
-  allocate(first_id_ij(nbonds))
-  allocate(other_id_ij(nbonds))
-  allocate(first_berg_ine(nbonds))
-  allocate(first_berg_jne(nbonds))
-  allocate(other_berg_ine(nbonds))
-  allocate(other_berg_jne(nbonds))
-
-  if (dem) then
-    allocate(tangd1(nbonds))
-    allocate(tangd2(nbonds))
-    allocate(nstress(nbonds))
-    allocate(sstress(nbonds))
-    allocate(rel_rotation(nbonds))
-    allocate(broken(nbonds))
-  endif
-
-  call get_instance_filename("bonds_iceberg.res.nc", filename_bonds)
-  call set_domain(bergs%grd%domain)
-  call register_restart_axis(bergs_bond_restart,filename,'i',nbonds)
-  call set_meta_global(bergs_bond_restart,'file_format_major_version',ival=(/file_format_major_version/))
-  call set_meta_global(bergs_bond_restart,'file_format_minor_version',ival=(/file_format_minor_version/))
-  call set_meta_global(bergs_bond_restart,'time_axis',ival=(/0/))
-
-  !Now start writing in the io_tile_root_pe if there are any bergs in the I/O list
-
-  id = register_restart_field(bergs_bond_restart,filename_bonds,'first_berg_ine',first_berg_ine,longname='iceberg ine of first berg in bond',units='dimensionless')
-  id = register_restart_field(bergs_bond_restart,filename_bonds,'first_berg_jne',first_berg_jne,longname='iceberg jne of first berg in bond',units='dimensionless')
-  id = register_restart_field(bergs_bond_restart,filename_bonds,'first_id_cnt',first_id_cnt,longname='counter component of iceberg id first berg in bond',units='dimensionless')
-  id = register_restart_field(bergs_bond_restart,filename_bonds,'first_id_ij',first_id_ij,longname='position component of iceberg id first berg in bond',units='dimensionless')
-  id = register_restart_field(bergs_bond_restart,filename_bonds,'other_berg_ine',other_berg_ine,longname='iceberg ine of second berg in bond',units='dimensionless')
-  id = register_restart_field(bergs_bond_restart,filename_bonds,'other_berg_jne',other_berg_jne,longname='iceberg jne of second berg in bond',units='dimensionless')
-  id = register_restart_field(bergs_bond_restart,filename_bonds,'other_id_cnt',other_id_cnt,longname='counter component of iceberg id second berg in bond',units='dimensionless')
-  id = register_restart_field(bergs_bond_restart,filename_bonds,'other_id_ij',other_id_ij,longname='position component of iceberg id second berg in bond',units='dimensionless')
-
-  if (dem) then
-    id = register_restart_field(bergs_bond_restart,filename_bonds,'tangd1',tangd1,&
-      longname='zonal tangential displacement',units='m')
-    id = register_restart_field(bergs_bond_restart,filename_bonds,'tangd2',tangd2,&
-      longname='meridional tangential displacement',units='m')
-    id = register_restart_field(bergs_bond_restart,filename_bonds,'nstress',nstress,&
-      longname='normal stress',units='Pa')
-    id = register_restart_field(bergs_bond_restart,filename_bonds,'sstress',sstress,&
-      longname='shear stress',units='Pa')
-    id = register_restart_field(bergs_bond_restart,filename_bonds,'rel_rotation',rel_rotation,&
-      longname='relative rotation',units='rad')
-     id = register_restart_field(bergs_bond_restart,filename_bonds,'broken',broken,&
-      longname='broken status',units='none')
-  endif
-
-  ! Write variables
-
-  i = 0
-  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
-    this=>bergs%list(grdi,grdj)%first
-    do while(associated(this)) !Loops over all bergs
-      current_bond=>this%first_bond
-      do while (associated(current_bond)) ! loop over all bonds
-        i = i + 1
-        first_berg_ine(i)=this%ine
-        first_berg_jne(i)=this%jne
-        call split_id( this%id, first_id_cnt(i), first_id_ij(i) )
-        call split_id( current_bond%other_id, other_id_cnt(i), other_id_ij(i) )
-        other_berg_ine(i)=current_bond%other_berg%ine
-        other_berg_jne(i)=current_bond%other_berg%jne
-
-        if (dem) then
-          tangd1(i)=current_bond%tangd1
-          tangd2(i)=current_bond%tangd2
-          nstress(i)=current_bond%nstress
-          sstress(i)=current_bond%sstress
-          rel_rotation(i)=current_bond%rel_rotation
-          broken(i)=current_bond%broken
-        endif
-
-        current_bond=>current_bond%next_bond
-      enddo !End of loop over bonds
-      this=>this%next
-    enddo!End of loop over bergs
-  enddo; enddo !End of loop over grid
-
-  call save_restart(bergs_bond_restart, time_stamp)
-  call free_restart_type(bergs_bond_restart)
-
-
-  deallocate(first_id_cnt,          &
-             other_id_cnt,          &
-             first_id_ij,           &
-             other_id_ij,           &
-             first_berg_ine,        &
-             first_berg_jne,        &
-             other_berg_ine,        &
-             other_berg_jne)
-  if (dem) then
-    deallocate(                     &
-             tangd1,                &
-             tangd2,                &
-             nstress,               &
-             sstress,               &
-             rel_rotation,          &
-             broken)
-  endif
-
-  call nullify_domain()
-  endif
-
-  ! Write stored ice
-  filename='calving.res.nc'
-  if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(stderrunit,'(2a)') 'KID, write_restart: writing ',filename
-  call grd_chksum3(bergs%grd, bergs%grd%stored_ice, 'write stored_ice')
-  call grd_chksum2(bergs%grd, bergs%grd%stored_heat, 'write stored_heat')
-  if (bergs%tau_calving>0.) then
-    call grd_chksum2(bergs%grd, bergs%grd%rmean_calving, 'write mean calving')
-    call grd_chksum2(bergs%grd, bergs%grd%rmean_calving_hflx, 'write mean calving_hflx')
-  endif
-
-  call set_domain(bergs%grd%domain)
-  id = register_restart_field(calving_restart,filename,'stored_ice',bergs%grd%stored_ice,longname='STORED_ICE',units='none')
-  id = register_restart_field(calving_restart,filename,'stored_heat',bergs%grd%stored_heat,longname='STORED_HEAT',units='none')
-  id = register_restart_field(calving_restart,filename,'iceberg_counter_grd',bergs%grd%iceberg_counter_grd,longname='ICEBERG_COUNTER_GRD',units='none')
-  if (bergs%tau_calving>0.) then
-    id = register_restart_field(calving_restart,filename,'rmean_calving',bergs%grd%rmean_calving,longname='RMEAN_CALVING',units='none')
-    id = register_restart_field(calving_restart,filename,'rmean_calving_hflx',bergs%grd%rmean_calving_hflx,longname='RMEAN_CALVING_HFLX',units='none')
-  endif
-
-  call save_restart(calving_restart, time_stamp)
-  call free_restart_type(calving_restart)
-
-end subroutine write_restart
-
-!> Find the last berg in a linked list.
-function last_berg(berg)
-! Arguments
-type(iceberg), pointer :: berg !< Pointer to an iceberg
-type(iceberg), pointer :: last_berg
-! Local variables
-
-  last_berg=>berg
-  do while (associated(last_berg%next))
-    last_berg=>last_berg%next
-  enddo
-
-end function last_berg
-
-!> Read a real value from a file and optionally return a default value if variable is missing
-real function get_real_from_file(ncid, varid, k, value_if_not_in_file)
-integer, intent(in) :: ncid !< file id
-integer, intent(in) :: varid !< variable id
-integer, intent(in) :: k !< index
-real, optional :: value_if_not_in_file !< default value, if variable missing in file
-
-if (varid<1.and.present(value_if_not_in_file)) then
-  get_real_from_file=value_if_not_in_file
-else
-  get_real_from_file=get_double(ncid, ncid, k)
-endif
-end function get_real_from_file
-
-!> Read an iceberg restart file
-subroutine read_restart_bergs(bergs,Time)
-! Arguments
-type(icebergs), pointer :: bergs !< Icebergs container
-type(time_type), intent(in) :: Time !< Model time
-! Local variables
-integer :: k, siz(4), nbergs_in_file, nbergs_read
-logical :: lres, found_restart, found, replace_iceberg_num
-logical :: explain
-logical :: multiPErestart  ! Not needed with new restart read; currently kept for compatibility
-real :: lon0, lon1, lat0, lat1
-real :: pos_is_good, pos_is_good_all_pe
-character(len=53) :: filename, filename_base
-type(icebergs_gridded), pointer :: grd
-type(iceberg) :: localberg ! NOT a pointer but an actual local variable
-integer :: stderrunit, i, j, cnt, ij
-
-real, allocatable, dimension(:) :: lon,          &
-                                   lat,          &
-                                   uvel,         &
-                                   vvel,         &
-                                   mass,         &
-                                   axn,          &
-                                   ayn,          &
-                                   bxn,          &
-                                   byn,          &
-                                   thickness,    &
-                                   width,        &
-                                   length,       &
-                                   fl_k,         &
-                                   start_lon,    &
-                                   start_lat,    &
-                                   start_day,    &
-                                   start_mass,   &
-                                   mass_scaling, &
-                                   mass_of_bits, &
-                                   mass_of_fl_bits, &
-                                   mass_of_fl_bergy_bits, &
-                                   static_berg,  &
-                                   heat_density, &
-                                   axn_fast,     &
-                                   ayn_fast,     &
-                                   bxn_fast,     &
-                                   byn_fast,     &
-                                   ang_vel,      &
-                                   ang_accel,    &
-                                   rot
-
-integer, allocatable, dimension(:) :: ine,        &
-                                      jne,        &
-                                      iceberg_num,&
-                                      id_cnt,     &
-                                      id_ij,      &
-                                      start_year
-
-!integer, allocatable, dimension(:,:) :: iceberg_counter_grd
-
-  ! Get the stderr unit number
-  stderrunit=stderr()
-
-  ! For convenience
-  grd=>bergs%grd
-
-  ! Zero out nbergs_in_file
-  nbergs_in_file = 0
-
-  filename_base=trim(restart_input_dir)//'icebergs.res.nc'
-
-  found_restart = find_restart_file(filename_base, filename, multiPErestart, io_tile_id(1))
-
-  if (found_restart) then
-     filename = filename_base
-     call get_field_size(filename,'i',siz, field_found=found, domain=bergs%grd%domain)
-     nbergs_in_file = siz(1)
-
-     replace_iceberg_num = field_exist(filename, 'iceberg_num') ! True if using 32-bit iceberg_num in restart file
-     allocate(lon(nbergs_in_file))
-     allocate(lat(nbergs_in_file))
-     allocate(uvel(nbergs_in_file))
-     allocate(vvel(nbergs_in_file))
-     allocate(mass(nbergs_in_file))
-     allocate(axn(nbergs_in_file)) !Alon
-     allocate(ayn(nbergs_in_file)) !Alon
-     allocate(bxn(nbergs_in_file)) !Alon
-     allocate(byn(nbergs_in_file)) !Alon
-     allocate(thickness(nbergs_in_file))
-     allocate(width(nbergs_in_file))
-     allocate(length(nbergs_in_file))
-     allocate(fl_k(nbergs_in_file))
-     allocate(start_lon(nbergs_in_file))
-     allocate(start_lat(nbergs_in_file))
-     allocate(start_day(nbergs_in_file))
-     allocate(start_mass(nbergs_in_file))
-     allocate(mass_scaling(nbergs_in_file))
-     allocate(mass_of_bits(nbergs_in_file))
-     allocate(mass_of_fl_bits(nbergs_in_file))
-     allocate(mass_of_fl_bergy_bits(nbergs_in_file))
-     allocate(static_berg(nbergs_in_file))
-     allocate(heat_density(nbergs_in_file))
-     allocate(ine(nbergs_in_file))
-     allocate(jne(nbergs_in_file))
-     allocate(start_year(nbergs_in_file))
-     if (replace_iceberg_num) then
-       call error_mesg('read_restart_bergs', "Calculating new iceberg ID's", WARNING)
-       allocate(iceberg_num(nbergs_in_file))
-     else
-       allocate(id_cnt(nbergs_in_file))
-       allocate(id_ij(nbergs_in_file))
-     endif
-
-      if (iceberg_bonds_on) then
-        allocate(localberg%n_bonds)
-        localberg%n_bonds=0.
-      end if
-
-      if (mts) then
-        allocate(localberg%axn_fast)
-        allocate(localberg%ayn_fast)
-        allocate(localberg%bxn_fast)
-        allocate(localberg%byn_fast)
-        allocate(localberg%conglom_id)
-        localberg%conglom_id=0.
-
-       allocate(axn_fast(nbergs_in_file))
-       allocate(ayn_fast(nbergs_in_file))
-       allocate(bxn_fast(nbergs_in_file))
-       allocate(byn_fast(nbergs_in_file))
-     endif
-     if (dem) then
-       allocate(localberg%ang_vel)
-       allocate(localberg%ang_accel)
-       allocate(localberg%rot)
-       allocate(ang_vel(nbergs_in_file))
-       allocate(ang_accel(nbergs_in_file))
-       allocate(rot(nbergs_in_file))
-     endif
-
-     call read_unlimited_axis(filename,'lon',lon,domain=grd%domain)
-     call read_unlimited_axis(filename,'lat',lat,domain=grd%domain)
-     call read_unlimited_axis(filename,'uvel',uvel,domain=grd%domain)
-     call read_unlimited_axis(filename,'vvel',vvel,domain=grd%domain)
-     call read_unlimited_axis(filename,'mass',mass,domain=grd%domain)
-     call read_real_vector(filename,'axn',axn,grd%domain,value_if_not_in_file=0.)
-     call read_real_vector(filename,'ayn',ayn,grd%domain,value_if_not_in_file=0.)
-     call read_real_vector(filename,'bxn',bxn,grd%domain,value_if_not_in_file=0.)
-     call read_real_vector(filename,'byn',byn,grd%domain,value_if_not_in_file=0.)
-     call read_unlimited_axis(filename,'thickness',thickness,domain=grd%domain)
-     call read_unlimited_axis(filename,'width',width,domain=grd%domain)
-     call read_unlimited_axis(filename,'length',length,domain=grd%domain)
-     call read_real_vector(filename,'fl_k',fl_k,grd%domain,value_if_not_in_file=0.)
-     call read_unlimited_axis(filename,'start_lon',start_lon,domain=grd%domain)
-     call read_unlimited_axis(filename,'start_lat',start_lat,domain=grd%domain)
-     call read_unlimited_axis(filename,'start_day',start_day,domain=grd%domain)
-     call read_unlimited_axis(filename,'start_mass',start_mass,domain=grd%domain)
-     call read_unlimited_axis(filename,'mass_scaling',mass_scaling,domain=grd%domain)
-     call read_real_vector(filename,'mass_of_bits',mass_of_bits,domain=grd%domain,value_if_not_in_file=0.)
-     call read_real_vector(filename,'mass_of_fl_bits',mass_of_fl_bits,domain=grd%domain,value_if_not_in_file=0.)
-     call read_real_vector(filename,'mass_of_fl_bergy_bits',mass_of_fl_bergy_bits,domain=grd%domain,value_if_not_in_file=0.)
-     call read_real_vector(filename,'heat_density',heat_density,domain=grd%domain,value_if_not_in_file=0.)
-     call read_unlimited_axis(filename,'ine',ine,domain=grd%domain)
-     call read_unlimited_axis(filename,'jne',jne,domain=grd%domain)
-     call read_unlimited_axis(filename,'start_year',start_year,domain=grd%domain)
-     if (replace_iceberg_num) then
-       call read_int_vector(filename,'iceberg_num',iceberg_num,grd%domain,value_if_not_in_file=-1)
-     else
-       call read_int_vector(filename,'id_cnt',id_cnt,grd%domain)
-       call read_int_vector(filename,'id_ij',id_ij,grd%domain)
-     endif
-     call read_real_vector(filename,'static_berg',static_berg,grd%domain,value_if_not_in_file=0.)
-
-     if (mts) then
-       call read_real_vector(filename,'axn_fast',axn_fast,grd%domain,value_if_not_in_file=0.)
-       call read_real_vector(filename,'ayn_fast',ayn_fast,grd%domain,value_if_not_in_file=0.)
-       call read_real_vector(filename,'bxn_fast',bxn_fast,grd%domain,value_if_not_in_file=0.)
-       call read_real_vector(filename,'byn_fast',byn_fast,grd%domain,value_if_not_in_file=0.)
-     endif
-
-     if (dem) then
-       call read_real_vector(filename,'ang_vel'  ,ang_vel  ,grd%domain,value_if_not_in_file=0.)
-       call read_real_vector(filename,'ang_accel',ang_accel,grd%domain,value_if_not_in_file=0.)
-       call read_real_vector(filename,'rot'      ,rot      ,grd%domain,value_if_not_in_file=0.)
-     endif
-  elseif (bergs%require_restart) then
-     stop 'read_restart_bergs, RESTART NOT FOUND!'
-  endif
-
-  ! Find approx outer bounds for tile
-  lon0=minval( grd%lon(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
-  lon1=maxval( grd%lon(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
-  lat0=minval( grd%lat(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
-  lat1=maxval( grd%lat(grd%isc-1:grd%iec,grd%jsc-1:grd%jec) )
-
-  do k=1, nbergs_in_file
-    localberg%lon=lon(k)
-    localberg%lat=lat(k)
-    if (.not. ignore_ij_restart) then ! read i,j position and avoid the "find" step
-      localberg%ine=ine(k)
-      localberg%jne=jne(k)
-      if ( localberg%ine>=grd%isc .and. localberg%ine<=grd%iec .and. &
-         localberg%jne>=grd%jsc .and.localberg%jne<=grd%jec ) then
-        lres=.true.
-      else
-        lres=.false.
-      endif
-    else ! i,j are not available from the file so we search the grid to find out if we reside on this PE
-      if (use_slow_find) then
-        lres=find_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
-      else
-        lres=find_cell_by_search(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne)
-      endif
-    endif
-    if (really_debug) then
-      write(stderrunit,'(a,i8,a,2f9.4,a,i8)') 'KID, read_restart_bergs: berg ',k,' is at ',localberg%lon,localberg%lat,&
-           & ' on PE ',mpp_pe()
-      write(stderrunit,*) 'KID, read_restart_bergs: lres = ',lres
-    endif
-
-    if (lres) then ! true if we reside on this PE grid
-      localberg%uvel=uvel(k)
-      localberg%vvel=vvel(k)
-      localberg%mass=mass(k)
-      localberg%axn=axn(k) !Alon
-      localberg%ayn=ayn(k) !Alon
-      localberg%uvel_old=uvel(k) !Alon
-      localberg%vvel_old=vvel(k) !Alon
-      localberg%lon_old=lon(k) !Alon
-      localberg%lat_old=lat(k) !Alon
-      localberg%bxn=bxn(k) !Alon
-      localberg%byn=byn(k) !Alon
-      localberg%thickness=thickness(k)
-      localberg%width=width(k)
-      localberg%length=length(k)
-      localberg%fl_k=fl_k(k)
-      localberg%start_lon=start_lon(k)
-      localberg%start_lat=start_lat(k)
-      localberg%start_year=start_year(k)
-      if (replace_iceberg_num) then
-        localberg%id = generate_id(grd, localberg%ine, localberg%jne)
-      else
-        localberg%id=id_from_2_ints(id_cnt(k), id_ij(k))
-      endif
-      localberg%start_day=start_day(k)
-      localberg%start_mass=start_mass(k)
-      localberg%mass_scaling=mass_scaling(k)
-      localberg%mass_of_bits=mass_of_bits(k)
-      localberg%mass_of_fl_bits=mass_of_fl_bits(k)
-      localberg%mass_of_fl_bergy_bits=mass_of_fl_bergy_bits(k)
-      localberg%halo_berg=0.
-      localberg%static_berg=static_berg(k)
-      localberg%heat_density=heat_density(k)
-      localberg%first_bond=>null()
-
-     if (mts) then
-       localberg%axn_fast=axn_fast(k)
-       localberg%ayn_fast=ayn_fast(k)
-       localberg%bxn_fast=bxn_fast(k)
-       localberg%byn_fast=byn_fast(k)
-     endif
-
-     if (dem) then
-       localberg%ang_vel  =ang_vel(k)
-       localberg%ang_accel=ang_accel(k)
-       localberg%rot      =rot(k)
-     endif
-
-      if (really_debug) lres=is_point_in_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, explain=.true.)
-      lres=pos_within_cell(grd, localberg%lon, localberg%lat, localberg%ine, localberg%jne, localberg%xi, localberg%yj)
-      !call add_new_berg_to_list(bergs%first, localberg)
-
-      if (bergs%grd%area(localberg%ine,localberg%jne) .ne. 0)  then
-        call add_new_berg_to_list(bergs%list(localberg%ine,localberg%jne)%first, localberg)
-      else
-        if (mpp_pe().eq.mpp_root_pe()) then
-          print * , 'Grounded iceberg: ', lat(k),lon(k), localberg%id
-          call error_mesg('KID, read_restart_bergs', 'Iceberg not added because it is grounded', WARNING)
-        endif
-       endif
-
-      if (really_debug) call print_berg(stderrunit, bergs%list(localberg%ine,localberg%jne)%first, 'read_restart_bergs, add_new_berg_to_list')
-    elseif (multiPErestart .and. io_tile_id(1) .lt. 0) then
-      call error_mesg('KID, read_restart_bergs', 'berg in PE file was not on PE!', FATAL)
-    endif
-  enddo
-
-  if (found_restart) then
-    deallocate(lon,          &
-               lat,          &
-               uvel,         &
-               vvel,         &
-               mass,         &
-               axn,          &
-               ayn,          &
-               bxn,          &
-               byn,          &
-               thickness,    &
-               width,        &
-               length,       &
-               fl_k,         &
-               start_lon,    &
-               start_lat,    &
-               start_day,    &
-               start_mass,   &
-               mass_scaling, &
-               mass_of_bits, &
-               mass_of_fl_bits, &
-               mass_of_fl_bergy_bits, &
-               static_berg,  &
-               heat_density, &
-               ine,          &
-               jne,          &
-               start_year )
-
-    if (mts) then
-      deallocate(            &
-               axn_fast,     &
-               ayn_fast,     &
-               bxn_fast,     &
-               byn_fast)
-    endif
-    if (dem) then
-      deallocate(            &
-               ang_vel,      &
-               ang_accel,    &
-               rot)
-    endif
-
-    if (replace_iceberg_num) then
-      deallocate(iceberg_num)
-    else
-      deallocate(id_cnt)
-      deallocate(id_ij)
-    endif
-
-    ! This block only works for IO_LAYOUT=1,1 or 0,0 but not for arbitrary layouts.
-    ! I'm commenting this out until we find a way to implement the same sorts of checks
-    ! that work for all i/o layouts. -AJA
-    !Checking the total number of icebergs read from the restart file.
-    !nbergs_read=count_bergs(bergs)
-    !call mpp_sum(nbergs_read)
-    !if (mpp_pe().eq.mpp_root_pe()) then
-    !  write(*,'(a,i8,a,i8,a)') 'KID, read_restart_bergs: Number of Icebergs in restart file=',nbergs_in_file,' Number of Icebergs read=', nbergs_read
-    !  if (nbergs_read .gt. nbergs_in_file) then
-    !    call error_mesg('KID, read_restart_bergs', 'More icebergs read than exist in restart file.', FATAL)
-    !  elseif (nbergs_read .lt. nbergs_in_file) then
-    !    if (bergs%ignore_missing_restart_bergs) then
-    !      call error_mesg('KID, read_restart_bergs', 'Some Icebergs from restart file were not found (ignore_missing flag is on)', WARNING)
-    !    else
-    !      call error_mesg('KID, read_restart_bergs', 'Some Icebergs from restart file were not found', FATAL)
-    !    endif
-    !  elseif (nbergs_read .eq. nbergs_in_file) then
-    !    write(*,'(a,i8,a,i8,a)') 'KID, read_restart_bergs: Number of icebergs read (#',nbergs_read,') matches the number of icebergs in the file'
-    !  endif
-    !endif
-
-  elseif(.not. found_restart .and. bergs%nbergs_start==0 .and. generate_test_icebergs) then
-    call generate_bergs(bergs,Time)
-  endif
-
-  call check_for_duplicates_in_parallel(bergs)
-
-  bergs%floating_mass_start=sum_mass(bergs)
-  call mpp_sum( bergs%floating_mass_start )
-  bergs%icebergs_mass_start=sum_mass(bergs,justbergs=.true.)
-  call mpp_sum( bergs%icebergs_mass_start )
-  bergs%bergy_mass_start=sum_mass(bergs,justbits=.true.)
-  call mpp_sum( bergs%bergy_mass_start )
-  bergs%fl_bits_mass_start=sum_mass(bergs,justflbits=.true.)
-  call mpp_sum( bergs%fl_bits_mass_start )
-  if (mpp_pe().eq.mpp_root_pe().and.verbose) write(*,'(a)') 'KID, read_restart_bergs: completed'
-
-end subroutine read_restart_bergs
-
-!> Read a vector of reals from file and use a default value if variable is missing
-subroutine read_real_vector(filename, varname, values, domain, value_if_not_in_file)
-  character(len=*), intent(in)  :: filename !< Name of file to read from
-  character(len=*), intent(in)  :: varname !< Name of variable to read
-  real,             intent(out) :: values(:) !< Returned vector of reals
-  type(domain2D),   intent(in)  :: domain !< Parallel decomposition
-  real, optional,   intent(in)  :: value_if_not_in_file !< Value to use if variable is not in file
-
-  if (present(value_if_not_in_file).and..not.field_exist(filename, varname)) then
-    values(:)=value_if_not_in_file
-  else
-    call read_unlimited_axis(filename,varname,values,domain=domain)
-  endif
-end subroutine read_real_vector
-
-!> Read a vector of integers from file and use a default value if variable is missing
-subroutine read_int_vector(filename, varname, values, domain, value_if_not_in_file)
-  character(len=*),  intent(in)  :: filename !< Name of file to read from
-  character(len=*),  intent(in)  :: varname !< Name of variable to read
-  integer,           intent(out) :: values(:) !< Returned vector of integers
-  type(domain2D),    intent(in)  :: domain !< Parallel decomposition
-  integer, optional, intent(in)  :: value_if_not_in_file !< Value to use if variable is not in file
-
-  if (present(value_if_not_in_file).and..not.field_exist(filename, varname)) then
-    values(:)=value_if_not_in_file
-  else
-    call read_unlimited_axis(filename,varname,values,domain=domain)
-  endif
-end subroutine read_int_vector
-
-!> Generate bergs for the purpose of debugging
-subroutine generate_bergs(bergs,Time)
-! Arguments
-type(icebergs), pointer :: bergs !< Icebergs container
-type(time_type), intent(in) :: Time !< Model time
-! Local variables
-type(icebergs_gridded), pointer :: grd
-integer :: i,j
-type(iceberg) :: localberg ! NOT a pointer but an actual local variable
-integer :: iyr, imon, iday, ihr, imin, isec
-logical :: lres
-
-  ! For convenience
-  grd=>bergs%grd
-
-  call get_date(Time, iyr, imon, iday, ihr, imin, isec)
-
-  if (mts) then
-    allocate(localberg%axn_fast)
-    allocate(localberg%ayn_fast)
-    allocate(localberg%bxn_fast)
-    allocate(localberg%byn_fast)
-  endif
-  if (dem) then
-    allocate(localberg%ang_vel)
-    allocate(localberg%ang_accel)
-    allocate(localberg%rot)
-  endif
-
-  do j=grd%jsc,grd%jec; do i=grd%isc,grd%iec
-    if (grd%msk(i,j)>0. .and. abs(grd%latc(i,j))>80.0) then
-      if (max(grd%lat(i,j),grd%lat(i-1,j),grd%lat(i,j-1),grd%lat(i-1,j-1))>89.999) cycle ! Cannot use this at Pole cells
-      localberg%xi=-999.
-      localberg%yj=-999.
-      localberg%ine=i
-      localberg%jne=j
-      localberg%lon=grd%lonc(i,j)
-      localberg%lat=grd%latc(i,j)
-      localberg%lon_old=localberg%lon
-      localberg%lat_old=localberg%lat
-      localberg%mass=bergs%initial_mass_s(1)
-      localberg%thickness=bergs%initial_thickness_s(1)
-      localberg%width=bergs%initial_width_s(1)
-      localberg%length=bergs%initial_length_s(1)
-      localberg%fl_k=0.
-      localberg%start_lon=localberg%lon
-      localberg%start_lat=localberg%lat
-      localberg%start_year=iyr
-      localberg%start_day=float(iday)+(float(ihr)+float(imin)/60.)/24.
-      localberg%start_mass=localberg%mass
-      localberg%mass_scaling=bergs%mass_scaling_s(1)
-      localberg%mass_of_bits=0.
-      localberg%mass_of_fl_bits=0.
-      localberg%mass_of_fl_bergy_bits=0.
-      localberg%halo_berg=0.
-      localberg%static_berg=0.
-      localberg%heat_density=0.
-      localberg%axn=0. !Alon
-      localberg%ayn=0. !Alon
-      localberg%uvel_old=0. !Alon
-      localberg%vvel_old=0. !Alon
-      localberg%bxn=0. !Alon
-      localberg%byn=0. !Alon
-      localberg%uvel_prev=0. !Alon
-      localberg%vvel_prev=0. !Alon
-
-      if (mts) then
-        localberg%axn_fast=0.
-        localberg%ayn_fast=0.
-        localberg%bxn_fast=0.
-        localberg%byn_fast=0.
-      endif
-      if (dem) then
-        localberg%ang_vel=0.
-        localberg%ang_accel=0.
-        localberg%rot=0.
-      endif
-
-      !Berg A
-      call loc_set_berg_pos(grd, 0.9, 0.5, 1., 0., localberg)
-      localberg%id = generate_id(grd, i, j)
-      call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
-      !Berg B
-      call loc_set_berg_pos(grd, 0.1, 0.5, -1., 0., localberg)
-      localberg%id = generate_id(grd, i, j)
-      call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
-      !Berg C
-      call loc_set_berg_pos(grd, 0.5, 0.9, 0., 1., localberg)
-      localberg%id = generate_id(grd, i, j)
-      call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
-      !Berg D
-      call loc_set_berg_pos(grd, 0.5, 0.1, 0., -1., localberg)
-      localberg%id = generate_id(grd, i, j)
-      call add_new_berg_to_list(bergs%list(i,j)%first, localberg)
-    endif
-  enddo; enddo
-
-  bergs%nbergs_start=count_bergs(bergs)
-  call mpp_sum(bergs%nbergs_start)
-  if (mpp_pe().eq.mpp_root_pe()) &
-    write(*,'(a,i8,a)') 'KID, generate_bergs: ',bergs%nbergs_start,' were generated'
-
-end subroutine generate_bergs
-
-!> For generating bergs for debugging, assign initial berg positions and velocities
-subroutine loc_set_berg_pos(grd, xi, yj, uvel, vvel, berg)
-  type(icebergs_gridded), pointer :: grd !< Container for gridded fields
-  real, intent(in) :: xi !< Non-dimensional x-position within cell to give berg
-  real, intent(in) :: yj !< Non-dimensional y-position within cell to give berg
-  real, intent(in) :: uvel !< Zonal velocity to give berg
-  real, intent(in) :: vvel !< Meridional velocity to give berg
-  type(iceberg), intent(inout) :: berg !< An iceberg
-  integer :: i, j
-  logical :: lres
-  i = berg%ine ; j = berg%jne
-  if (max(grd%lat(i,j),grd%lat(i-1,j),grd%lat(i,j-1),grd%lat(i-1,j-1))>89.999) then
-    berg%lon=grd%lonc(i,j)
-    berg%lat=grd%latc(i,j)
-    berg%xi=0.5 ; berg%yj=0.5
-  else
-    berg%lon=bilin(grd, grd%lon, i, j, xi, yj)
-    berg%lat=bilin(grd, grd%lat, i, j, xi, yj)
-    berg%xi=xi ; berg%yj=yj
-  endif
-  berg%uvel=uvel ; berg%vvel=vvel
-  berg%lon_old=berg%lon ; berg%lat_old=berg%lat
-  berg%start_lon=berg%lon ; berg%start_lat=berg%lat
-  lres=pos_within_cell(grd, berg%lon, berg%lat, berg%ine, berg%jne, berg%xi, berg%yj)
-  if (.not. lres) then
-    lres=pos_within_cell(grd, berg%lon, berg%lat, berg%ine, berg%jne, berg%xi, berg%yj, explain=.true.)
-    write(0,*) lres, i, j, xi, yj, uvel, vvel
-    write(0,*) lres, berg%ine, berg%jne, berg%xi, berg%yj
-    write(0,*) 'bx=',berg%lon, 'gx=',grd%lon(i-1,j-1), grd%lon(i,j-1), grd%lon(i,j), grd%lon(i-1,j),'cx=', grd%lonc(i,j)
-    write(0,*) 'by=',berg%lat, 'gy=',grd%lat(i-1,j-1), grd%lat(i,j-1), grd%lat(i,j), grd%lat(i-1,j),'cy=', grd%latc(i,j)
-    stop 'generate_bergs, loc_set_berg_pos(): VERY FATAL!'
-  endif
-end subroutine loc_set_berg_pos
-
-!> Read bond restart file
-subroutine read_restart_bonds(bergs,Time)
-! Arguments
-type(icebergs), pointer :: bergs !< Icebergs container
-type(time_type), intent(in) :: Time !< Model time
-! Local variables
-integer :: k, siz(4), nbonds_in_file
-logical :: lres, found_restart, found
-logical :: first_berg_found, second_berg_found
-logical :: multiPErestart  ! Not needed with new restart read; currently kept for compatibility
-real :: lon0, lon1, lat0, lat1
-character(len=53) :: filename, filename_base
-type(icebergs_gridded), pointer :: grd
-type(iceberg) :: localberg ! NOT a pointer but an actual local variable
-type(iceberg) , pointer :: this, first_berg, second_berg
-type(bond) , pointer :: current_bond
-integer :: stderrunit
-integer :: number_first_bonds_matched !How many first bond bergs found on pe
-integer :: number_second_bonds_matched !How many second bond bergs found on pe
-integer :: number_perfect_bonds ! How many complete bonds formed
-integer :: number_partial_bonds ! How many either complete/partial bonds formed.
-integer :: number_perfect_bonds_with_first_on_pe ! How many bonds with first bond on the compuational domain
-integer :: all_pe_number_perfect_bonds, all_pe_number_partial_bonds
-integer :: all_pe_number_first_bonds_matched, all_pe_number_second_bonds_matched
-integer :: all_pe_number_perfect_bonds_with_first_on_pe
-integer :: ine, jne
-logical :: search_data_domain
-real :: berg_found, berg_found_all_pe
-integer, allocatable, dimension(:) :: id_cnt, id_ij,    &
-                                      first_berg_jne,   &
-                                      first_berg_ine,   &
-                                      other_berg_jne,   &
-                                      other_berg_ine,   &
-                                      broken
-real, allocatable, dimension(:) ::    tangd1,           &
-                                      tangd2,           &
-                                      nstress,          &
-                                      sstress,          &
-                                      rel_rotation
-integer(kind=8), allocatable, dimension(:) :: first_id,   &
-                                              other_id
-!integer, allocatable, dimension(:,:) :: iceberg_counter_grd
-
-  ! Get the stderr unit number
-  stderrunit=stderr()
-
-  ! For convenience
-  grd=>bergs%grd
-
-  ! Zero out nbergs_in_file
-  nbonds_in_file = 0
-  all_pe_number_perfect_bonds=0
-
-  filename_base=trim(restart_input_dir)//'bonds_iceberg.res.nc'
-
-  found_restart = find_restart_file(filename_base, filename, multiPErestart, io_tile_id(1))
-  call error_mesg('read_restart_bonds_bergs_new', 'Using icebergs bond restart read', NOTE)
-
-  filename = filename_base
-  call get_field_size(filename,'i',siz, field_found=found, domain=bergs%grd%domain)
-  nbonds_in_file = siz(1)
-
-    if (mpp_pe() .eq. mpp_root_pe()) then
-      write(stderrunit,*)  'KID, bond read restart : ','Number of bonds in file',  nbonds_in_file
-    endif
-
-  if (nbonds_in_file .gt. 0) then
-
-    allocate(first_id(nbonds_in_file))
-    allocate(other_id(nbonds_in_file))
-    allocate(id_cnt(nbonds_in_file))
-    allocate(id_ij(nbonds_in_file))
-    allocate(first_berg_jne(nbonds_in_file))
-    allocate(first_berg_ine(nbonds_in_file))
-    allocate(other_berg_ine(nbonds_in_file))
-    allocate(other_berg_jne(nbonds_in_file))
-
-    if (dem) then
-      allocate(tangd1(nbonds_in_file))
-      allocate(tangd2(nbonds_in_file))
-      allocate(nstress(nbonds_in_file))
-      allocate(sstress(nbonds_in_file))
-      allocate(rel_rotation(nbonds_in_file))
-      allocate(broken(nbonds_in_file))
-    endif
-
-    call read_unlimited_axis(filename,'first_id_cnt',id_cnt,domain=grd%domain)
-    call read_unlimited_axis(filename,'first_id_ij',id_ij,domain=grd%domain)
-    do k=1, nbonds_in_file
-      first_id(k) = id_from_2_ints( id_cnt(k), id_ij(k) )
-    enddo
-    call read_unlimited_axis(filename,'other_id_cnt',id_cnt,domain=grd%domain)
-    call read_unlimited_axis(filename,'other_id_ij',id_ij,domain=grd%domain)
-    do k=1, nbonds_in_file
-      other_id(k) = id_from_2_ints( id_cnt(k), id_ij(k) )
-    enddo
-    deallocate(id_cnt, id_ij)
-    call read_unlimited_axis(filename,'first_berg_jne',first_berg_jne,domain=grd%domain)
-    call read_unlimited_axis(filename,'first_berg_ine',first_berg_ine,domain=grd%domain)
-    call read_unlimited_axis(filename,'other_berg_jne',other_berg_jne,domain=grd%domain)
-    call read_unlimited_axis(filename,'other_berg_ine',other_berg_ine,domain=grd%domain)
-
-    if (dem) then
-      call read_real_vector(filename,'tangd1',tangd1,grd%domain,value_if_not_in_file=0.)
-      call read_real_vector(filename,'tangd2',tangd2,grd%domain,value_if_not_in_file=0.)
-      call read_real_vector(filename,'nstress',nstress,grd%domain,value_if_not_in_file=0.)
-      call read_real_vector(filename,'sstress',sstress,grd%domain,value_if_not_in_file=0.)
-      call read_real_vector(filename,'rel_rotation',rel_rotation,grd%domain,value_if_not_in_file=0.)
-      call read_int_vector(filename,'broken',broken,grd%domain,value_if_not_in_file=0)
-    endif
-
-    number_first_bonds_matched=0
-    number_second_bonds_matched=0
-    number_perfect_bonds=0
-    number_partial_bonds=0
-    number_perfect_bonds_with_first_on_pe=0
-
-    do k=1, nbonds_in_file
-
-       ! If i,j in restart files are not good, then we find the berg position of the bond addresses manually:
-       if (ignore_ij_restart) then
-         !Finding first iceberg in bond
-         ine=999 ; jne=999 ; berg_found=0.0 ; search_data_domain=.true.
-         call find_individual_iceberg(bergs,first_id(k), ine, jne,berg_found,search_data_domain)
-         berg_found_all_pe=berg_found
-         call mpp_sum(berg_found_all_pe)
-         if (berg_found_all_pe .gt. 0.5) then
-             first_berg_ine(k)=ine
-             first_berg_jne(k)=jne
-         else
-           print * , 'First bond berg not located: ', first_id(k),berg_found, mpp_pe(),ine, jne
-           call error_mesg('read_restart_bonds_bergs_new', 'First iceberg in bond not found on any pe', FATAL)
-         endif
-         !else
-
-         !Finding other iceberg other iceberg
-         ine=999 ; jne=999 ; berg_found=0.0 ; search_data_domain =.true.
-         call find_individual_iceberg(bergs,other_id(k), ine, jne, berg_found,search_data_domain)
-         berg_found_all_pe=berg_found
-         call mpp_sum(berg_found_all_pe)
-         if (berg_found_all_pe .gt. 0.5) then
-           !if (berg_found_all_pe .gt. 1.5) then
-           !  call error_mesg('read_restart_bonds_bergs_new', 'Other iceberg bond found on more than one pe', FATAL)
-           !else
-             other_berg_ine(k)=ine
-             other_berg_jne(k)=jne
-           !endif
-         else
-          call error_mesg('read_restart_bonds_bergs_new', 'Other iceberg in bond not found on any pe', FATAL)
-         endif
-         if (berg_found_all_pe .lt. 0.5) then
-                 print * , 'First bond berg not located: ', other_id(k),berg_found, mpp_pe(),ine, jne
-             call error_mesg('read_restart_bonds_bergs_new', 'First bond iceberg not located', FATAL)
-         endif
-       endif
-
-      ! Decide whether the first iceberg is on the processeor
-      if ( (first_berg_ine(k)>=grd%isd) .and. (first_berg_ine(k)<=grd%ied) .and. &
-        (first_berg_jne(k)>=grd%jsd) .and. (first_berg_jne(k)<=grd%jed) ) then
-        number_first_bonds_matched=number_first_bonds_matched+1
-
-        ! Search for the first berg, which the bond belongs to
-        first_berg_found=.false.
-        first_berg=>null()
-        this=>bergs%list(first_berg_ine(k),first_berg_jne(k))%first
-        do while(associated(this))
-          if (this%id == first_id(k)) then
-            first_berg_found=.true.
-            first_berg=>this
-            !if (first_berg%halo_berg.gt.0.5) print *, 'bonding halo berg:', first_id(k),  first_berg_ine(k),first_berg_jne(k) ,grd%isc, grd%iec, mpp_pe()
-            this=>null()
-          else
-            this=>this%next
-          endif
-        enddo
-
-        ! Decide whether the second iceberg is on the processeor (data domain)
-        second_berg_found=.false.
-        !if ( other_berg_ine(k)>=grd%isc-1 .and. other_berg_ine(k)<=grd%iec+1 .and. &
-        !  other_berg_jne(k)>=grd%jsc-1 .and.other_berg_jne(k)<=grd%jec+1 ) then
-        if ( (other_berg_ine(k)>=grd%isd) .and. (other_berg_ine(k)<=grd%ied) .and. &
-          (other_berg_jne(k)>=grd%jsd) .and.(other_berg_jne(k)<=grd%jed) ) then
-          number_second_bonds_matched=number_second_bonds_matched+1
-
-          ! Search for the second berg, which the bond belongs to
-          second_berg=>null()
-          this=>bergs%list(other_berg_ine(k),other_berg_jne(k))%first
-          do while(associated(this))
-            if (this%id == other_id(k)) then
-              second_berg_found=.true.
-              second_berg=>this
-              this=>null()
-            else
-              this=>this%next
-            endif
-          enddo
-        endif
-
-        if (first_berg_found) then
-          number_partial_bonds=number_partial_bonds+1
-          if (second_berg_found) then
-            call form_a_bond(first_berg, other_id(k), other_berg_ine(k), other_berg_jne(k),  second_berg)
-            number_perfect_bonds=number_perfect_bonds+1
-
-            current_bond=>first_berg%first_bond
-
-            if (dem) then
-              current_bond%tangd1=tangd1(k)
-              current_bond%tangd2=tangd2(k)
-              current_bond%nstress=nstress(k)
-              current_bond%sstress=sstress(k)
-              current_bond%rel_rotation=rel_rotation(k)
-              current_bond%broken=broken(k)
-            endif
-
-            !Counting number of bonds where the first bond is in the computational domain
-            if ( (first_berg_ine(k)>=grd%isc) .and. (first_berg_ine(k)<=grd%iec) .and. &
-              (first_berg_jne(k)>=grd%jsc) .and. (first_berg_jne(k)<=grd%jec) ) then
-               number_perfect_bonds_with_first_on_pe=number_perfect_bonds_with_first_on_pe+1
-            endif
-
-          else
-            !print *, 'Forming a bond of the second type', mpp_pe(), first_id(k),  other_id(k)
-            !call form_a_bond(first_berg, other_id(k), other_berg_ine(k),other_berg_jne(k))
-          endif
-        else
-          write(stderrunit,*) 'KID, bond read restart : ','Not enough partial bonds formed', k, mpp_pe(), nbonds_in_file
-          call error_mesg('read_restart_bonds_bergs_new', 'Failure with reading bonds: First bond not found on pe', FATAL)
-        endif
-      endif
-    enddo
-
-    !Analyse how many bonds were created and take appropriate action
-    all_pe_number_perfect_bonds=number_perfect_bonds
-    all_pe_number_perfect_bonds_with_first_on_pe=number_perfect_bonds_with_first_on_pe
-    all_pe_number_partial_bonds=number_partial_bonds
-    all_pe_number_first_bonds_matched=number_first_bonds_matched
-    all_pe_number_second_bonds_matched=number_second_bonds_matched
-    call mpp_sum(all_pe_number_perfect_bonds)
-    call mpp_sum(all_pe_number_partial_bonds)
-    call mpp_sum(all_pe_number_perfect_bonds_with_first_on_pe)
-
-    if (all_pe_number_partial_bonds .lt. nbonds_in_file) then
-      write(stderrunit,*) 'KID, bond read restart : ','Not enough partial bonds formed', all_pe_number_partial_bonds , nbonds_in_file
-      call error_mesg('read_restart_bonds_bergs_new', 'Not enough partial bonds formed', FATAL)
-    endif
-
-    if (all_pe_number_perfect_bonds .lt. nbonds_in_file) then
-      call mpp_sum(all_pe_number_first_bonds_matched)
-      call mpp_sum(all_pe_number_second_bonds_matched)
-      write(stderrunit,*)  'KID, bond read restart : ','Warning, some bonds are not fully formed',  all_pe_number_first_bonds_matched , nbonds_in_file
-      write(stderrunit,*)  'KID, bond read restart : ','Number of first and second bonds matched:', all_pe_number_second_bonds_matched , nbonds_in_file
-      call error_mesg('read_restart_bonds_bergs_new', 'Not enough perfect bonds formed', NOTE)
-    endif
-
-    if (all_pe_number_perfect_bonds_with_first_on_pe .ne. nbonds_in_file) then
-      call mpp_sum(all_pe_number_first_bonds_matched)
-      call mpp_sum(all_pe_number_second_bonds_matched)
-      write(stderrunit,*)  'KID, bond read restart : ','Warning, # bonds with first bond on computational domain, does not match file',  all_pe_number_first_bonds_matched , nbonds_in_file
-      write(stderrunit,*)  'KID, bond read restart : ','Computational bond, first second:', all_pe_number_second_bonds_matched , nbonds_in_file
-      call error_mesg('read_restart_bonds_bergs_new', 'Computational perfect bonds do not match those in file', NOTE)
-    endif
-
-    deallocate(               &
-            first_id,         &
-            other_id,         &
-            first_berg_ine,   &
-            first_berg_jne,   &
-            other_berg_ine,   &
-            other_berg_jne )
-
-    if (dem) then
-      deallocate(                     &
-               tangd1,                &
-               tangd2,                &
-               nstress,               &
-               sstress,               &
-               rel_rotation,          &
-               broken)
-    endif
-  endif
-
-  if (mpp_pe() .eq. mpp_root_pe()) then
-    write(stderrunit,*)  'KID, bond read restart : ','Number of bonds (including halos)',  all_pe_number_perfect_bonds
-    write(stderrunit,*)  'KID, bond read restart : ','Number of true bonds created',  all_pe_number_perfect_bonds_with_first_on_pe
-  endif
-
-end subroutine read_restart_bonds
-
-!> Reading calving and gridded restart data
-subroutine read_restart_calving(bergs)
-use random_numbers_mod, only: initializeRandomNumberStream, getRandomNumbers, randomNumberStream
-! Arguments
-type(icebergs), pointer :: bergs !< Icebergs container
-! Local variables
-integer :: k,i,j
-character(len=37) :: filename, actual_filename
-type(icebergs_gridded), pointer :: grd
-real, allocatable, dimension(:,:) :: randnum
-type(randomNumberStream) :: rns
-
-  ! For convenience
-  grd=>bergs%grd
-
-  ! Read stored ice
-  filename=trim(restart_input_dir)//'calving.res.nc'
-  if (file_exist(filename)) then
-    if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') &
-     'KID, read_restart_calving: reading ',filename
-    call read_data(filename, 'stored_ice', grd%stored_ice, grd%domain)
-    if (field_exist(filename, 'stored_heat')) then
-      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
-       'KID, read_restart_calving: reading stored_heat from restart file.'
-      call read_data(filename, 'stored_heat', grd%stored_heat, grd%domain)
-    else
-      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
-     'KID, read_restart_calving: stored_heat WAS NOT FOUND in the file. Setting to 0.'
-      grd%stored_heat(:,:)=0.
-    endif
-    if (field_exist(filename, 'rmean_calving')) then
-      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
-       'KID, read_restart_calving: reading rmean_calving from restart file.'
-      call read_data(filename, 'rmean_calving', grd%rmean_calving, grd%domain)
-      grd%rmean_calving_initialized=.true.
-    else
-      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
-     'KID, read_restart_calving: rmean_calving WAS NOT FOUND in the file. Setting to 0.'
-    endif
-    if (field_exist(filename, 'rmean_calving_hflx')) then
-      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
-       'KID, read_restart_calving: reading rmean_calving_hflx from restart file.'
-      call read_data(filename, 'rmean_calving_hflx', grd%rmean_calving_hflx, grd%domain)
-      grd%rmean_calving_hflx_initialized=.true.
-    else
-      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
-     'KID, read_restart_calving: rmean_calving_hflx WAS NOT FOUND in the file. Setting to 0.'
-    endif
-    if (field_exist(filename, 'iceberg_counter_grd')) then
-      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
-       'KID, read_restart_calving: reading iceberg_counter_grd from restart file.'
-      call read_data(filename, 'iceberg_counter_grd', grd%iceberg_counter_grd, grd%domain)
-    else
-      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
-     'KID, read_restart_calving: iceberg_counter_grd WAS NOT FOUND in the file. Setting to 0.'
-      grd%iceberg_counter_grd(:,:) = 0
-    endif
-    bergs%restarted=.true.
-  else
-    if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
-     'KID, read_restart_calving: initializing stored ice to random numbers'
-    if ( make_calving_reproduce ) then
-       allocate(randnum(1,nclasses))
-       do j=grd%jsc, grd%jec
-          do i=grd%isc, grd%iec
-             rns=initializeRandomNumberStream(i+10000*j)
-             call getRandomNumbers(rns,randnum(1,:))
-             do k=1, nclasses
-               if (grd%lat(i,j)<0.) then
-                 grd%stored_ice(i,j,k)=randnum(1,k) * grd%msk(i,j) * bergs%initial_mass_s(k) * bergs%mass_scaling_s(k)
-               else
-                 grd%stored_ice(i,j,k)=randnum(1,k) * grd%msk(i,j) * bergs%initial_mass_n(k) * bergs%mass_scaling_n(k)
-               endif
-             end do
-          end do
-       end do
-    else
-       allocate(randnum(grd%jsc:grd%jec,nclasses))
-       do i=grd%isc, grd%iec
-          rns = initializeRandomNumberStream(i)
-          call getRandomNumbers(rns,randnum)
-          do k=1, nclasses
-            where (grd%lat(i,grd%jsc:grd%jec)<0.)
-             grd%stored_ice(i,grd%jsc:grd%jec,k) = randnum(:,k) * grd%msk(i,grd%jsc:grd%jec) * &
-               & bergs%initial_mass_s(k) * bergs%mass_scaling_s(k)
-           elsewhere
-             grd%stored_ice(i,grd%jsc:grd%jec,k) = randnum(:,k) * grd%msk(i,grd%jsc:grd%jec) * &
-               & bergs%initial_mass_n(k) * bergs%mass_scaling_n(k)
-           end where
-          end do
-       end do
-    end if
-    deallocate(randnum)
-  endif
-
-  call grd_chksum3(bergs%grd, bergs%grd%stored_ice, 'read_restart_calving, stored_ice')
-  call grd_chksum2(bergs%grd, bergs%grd%stored_heat, 'read_restart_calving, stored_heat')
-  call grd_chksum2(bergs%grd, bergs%grd%rmean_calving, 'read_restart_calving, rmean_calving')
-  call grd_chksum2(bergs%grd, bergs%grd%rmean_calving_hflx, 'read_restart_calving, rmean_calving_hflx')
-
-  bergs%stored_start=sum( grd%stored_ice(grd%isc:grd%iec,grd%jsc:grd%jec,:) )
-  bergs%rmean_calving_start=sum( grd%rmean_calving(grd%isc:grd%iec,grd%jsc:grd%jec) )
-  bergs%rmean_calving_hflx_start=sum( grd%rmean_calving_hflx(grd%isc:grd%iec,grd%jsc:grd%jec) )
-  call mpp_sum( bergs%stored_start )
-  bergs%stored_heat_start=sum( grd%stored_heat(grd%isc:grd%iec,grd%jsc:grd%jec) )
-  call mpp_sum( bergs%stored_heat_start )
-  bergs%floating_heat_start=sum_heat(bergs)
-  call mpp_sum( bergs%floating_heat_start )
-
-end subroutine read_restart_calving
-
-!> Read ocean depth from file
-subroutine read_ocean_depth(grd)
-! Arguments
-type(icebergs_gridded), pointer :: grd !< Container for gridded fields
-! Local variables
-character(len=37) :: filename
-
-  ! Read stored ice
-  filename=trim(restart_input_dir)//'topog.nc'
-  if (file_exist(filename)) then
-    if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') &
-     'KID, read_ocean_depth: reading ',filename
-    if (field_exist(filename, 'depth')) then
-      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
-       'KID, read_ocean_depth: reading depth from topog file.'
-      call read_data(filename, 'depth', grd%ocean_depth, grd%domain)
-    else
-      if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
-     'KID, read_ocean_depth: depth WAS NOT FOUND in the file. Setting to 0.'
-      !grd%ocean_depth(:,:)=0.
-    endif
-  else
-    if (mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
-     'KID, read_ocean_depth: Ocean depth file (topog.nc) not present)'
-  endif
-
-  !call grd_chksum2(bergs%grd, bergs%grd%ocean_depth, 'read_ocean_depth, ocean_depth')
-end subroutine read_ocean_depth
-
-!> Write a trajectory-based diagnostics file
-subroutine write_trajectory(trajectory, save_short_traj, save_fl_traj, traj_name)
-! Arguments
-type(xyt), pointer :: trajectory !< An iceberg trajectory
-logical, intent(in) :: save_short_traj !< If true, record less data
-logical, intent(in) :: save_fl_traj !< If true, save masses and footloose data
-character(len=70) :: traj_name !< name of trajectory file
-! Local variables
-integer :: iret, ncid, i_dim, i
-integer :: lonid, latid, yearid, dayid, uvelid, vvelid, idcntid, idijid
-integer :: uvelpid,vvelpid
-integer :: uoid, void, uiid, viid, uaid, vaid, sshxid, sshyid, sstid, sssid
-integer :: cnid, hiid, hsid
-integer :: mid, smid, did, wid, lid, mbid, mflbid, mflbbid, hdid, nbid, odid, flkid
-integer :: axnid,aynid,bxnid,bynid,axnfid,aynfid,bxnfid,bynfid, msid
-integer :: avid, aaid, rid
-character(len=70) :: filename
-character(len=7) :: pe_name
-type(xyt), pointer :: this, next
-integer :: stderrunit, cnt, ij
-!I/O vars
-type(xyt), pointer :: traj4io=>null()
-integer :: from_pe,np
-type(buffer), pointer :: obuffer_io=>null(), ibuffer_io=>null()
-logical :: io_is_in_append_mode
-integer :: ntrajs_sent_io,ntrajs_rcvd_io
-
-  ! Get the stderr unit number
-  stderrunit=stderr()
-  traj4io=>null()
-  obuffer_io=>null()
-  ibuffer_io=>null()
-
-  !Assemble the list of trajectories from all pes in this I/O tile
-  call mpp_clock_begin(clock_trp)
-
-  !First add the trajs on the io_tile_root_pe (if any) to the I/O list
-  if(is_io_tile_root_pe .OR. force_all_pes_traj ) then
-     if(associated(trajectory)) then
-        this=>trajectory
-        do while (associated(this))
-           call append_posn(traj4io, this)
-           this=>this%next
-        enddo
-        trajectory => null()
-     endif
-  endif
-
-  if(.NOT. force_all_pes_traj ) then
-
-  !Now gather and append the bergs from all pes in the io_tile to the list on corresponding io_tile_root_pe
-  ntrajs_sent_io =0
-  ntrajs_rcvd_io =0
-
-  if(is_io_tile_root_pe) then
-     !Receive trajs from all pes in this I/O tile !FRAGILE!SCARY!
-     do np=2,size(io_tile_pelist) ! Note: np starts from 2 to exclude self
-        from_pe=io_tile_pelist(np)
-        call mpp_recv(ntrajs_rcvd_io, glen=1, from_pe=from_pe, tag=COMM_TAG_11)
-        if (ntrajs_rcvd_io .gt. 0) then
-           call increase_ibuffer(ibuffer_io, ntrajs_rcvd_io,buffer_width_traj)
-           call mpp_recv(ibuffer_io%data, ntrajs_rcvd_io*buffer_width_traj,from_pe=from_pe, tag=COMM_TAG_12)
-           do i=1, ntrajs_rcvd_io
-              call unpack_traj_from_buffer2(traj4io, ibuffer_io, i, save_short_traj, save_fl_traj)
-           enddo
-       endif
-     enddo
-  else
-     ! Pack and send trajectories to the root PE for this I/O tile
-     do while (associated(trajectory))
-       ntrajs_sent_io = ntrajs_sent_io +1
-       call pack_traj_into_buffer2(trajectory, obuffer_io, ntrajs_sent_io, save_short_traj, save_fl_traj)
-       this => trajectory ! Need to keep pointer in order to free up the links memory
-       trajectory => trajectory%next ! This will eventually result in trajectory => null()
-       deallocate(this) ! Delete the link from memory
-     enddo
-
-     call mpp_send(ntrajs_sent_io, plen=1, to_pe=io_tile_root_pe, tag=COMM_TAG_11)
-     if (ntrajs_sent_io .gt. 0) then
-        call mpp_send(obuffer_io%data, ntrajs_sent_io*buffer_width_traj, to_pe=io_tile_root_pe, tag=COMM_TAG_12)
-     endif
-  endif
-  call mpp_sync_self()
-  endif !.NOT. force_all_pes_traj
-
-  call mpp_clock_end(clock_trp)
-
-  !Now start writing in the io_tile_root_pe if there are any bergs in the I/O list
-  call mpp_clock_begin(clock_trw)
-
-  if((force_all_pes_traj .OR. is_io_tile_root_pe) .AND. associated(traj4io)) then
-
-    !call get_instance_filename("iceberg_trajectories.nc", filename)
-    call get_instance_filename(traj_name, filename)
-    if(io_tile_id(1) .ge. 0 .AND. .NOT. force_all_pes_traj) then !io_tile_root_pes write
-       if(io_npes .gt. 1) then !attach tile_id  to filename only if there is more than one I/O pe
-          if (io_tile_id(1)<10000) then
-             write(filename,'(A,".",I4.4)') trim(filename), io_tile_id(1)
-          else
-             write(filename,'(A,".",I6.6)') trim(filename), io_tile_id(1)
-          endif
-       endif
-    else !All pes write, attach pe# to filename
-       if (mpp_npes()<10000) then
-          write(filename,'(A,".",I4.4)') trim(filename), mpp_pe()
-       else
-          write(filename,'(A,".",I6.6)') trim(filename), mpp_pe()
-       endif
-    endif
-
-    io_is_in_append_mode = .false.
-    iret = nf_create(filename, NF_NOCLOBBER, ncid)
-    if (iret .ne. NF_NOERR) then
-      iret = nf_open(filename, NF_WRITE, ncid)
-      io_is_in_append_mode = .true.
-      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_trajectory: nf_open failed'
-    endif
-    if (verbose) then
-      if (io_is_in_append_mode) then
-        write(*,'(2a)') 'KID, write_trajectory: appending to ',filename
-      else
-        write(*,'(2a)') 'KID, write_trajectory: creating ',filename
-      endif
-    endif
-
-    if (io_is_in_append_mode) then
-      iret = nf_inq_dimid(ncid, 'i', i_dim)
-      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_trajectory: nf_inq_dimid i failed'
-      lonid = inq_varid(ncid, 'lon')
-      latid = inq_varid(ncid, 'lat')
-      yearid = inq_varid(ncid, 'year')
-      dayid = inq_varid(ncid, 'day')
-      idcntid = inq_varid(ncid, 'id_cnt')
-      idijid = inq_varid(ncid, 'id_ij')
-      if (save_fl_traj) then
-        mid = inq_varid(ncid, 'mass')
-        smid = inq_varid(ncid, 'start_mass')
-        did = inq_varid(ncid, 'thickness')
-        mbid = inq_varid(ncid, 'mass_of_bits')
-        uvelid = inq_varid(ncid, 'uvel')
-        vvelid = inq_varid(ncid, 'vvel')
-        if (footloose) then
-          msid = inq_varid(ncid, 'mass_scaling')
-          mflbid = inq_varid(ncid, 'mass_of_fl_bits')
-          mflbbid = inq_varid(ncid, 'mass_of_fl_bergy_bits')
-          flkid = inq_varid(ncid, 'fl_k')
-        endif
-      endif
-      if (.not.save_short_traj) then
-        !uvelid = inq_varid(ncid, 'uvel')
-        !vvelid = inq_varid(ncid, 'vvel')
-        uvelpid = inq_varid(ncid, 'uvel_prev')
-        vvelpid = inq_varid(ncid, 'vvel_prev')
-        uoid = inq_varid(ncid, 'uo')
-        void = inq_varid(ncid, 'vo')
-        uiid = inq_varid(ncid, 'ui')
-        viid = inq_varid(ncid, 'vi')
-        uaid = inq_varid(ncid, 'ua')
-        vaid = inq_varid(ncid, 'va')
-        hdid = inq_varid(ncid, 'heat_density')
-        wid = inq_varid(ncid, 'width')
-        lid = inq_varid(ncid, 'length')
-        sshxid = inq_varid(ncid, 'ssh_x')
-        sshyid = inq_varid(ncid, 'ssh_y')
-        sstid = inq_varid(ncid, 'sst')
-        sssid = inq_varid(ncid, 'sss')
-        cnid = inq_varid(ncid, 'cn')
-        hiid = inq_varid(ncid, 'hi')
-        axnid = inq_varid(ncid, 'axn')
-        aynid = inq_varid(ncid, 'ayn')
-        bxnid = inq_varid(ncid, 'bxn')
-        bynid = inq_varid(ncid, 'byn')
-        hsid = inq_varid(ncid, 'halo_berg')
-        odid = inq_varid(ncid, 'od')
-
-        if (mts) then
-          axnfid = inq_varid(ncid, 'axn_fast')
-          aynfid = inq_varid(ncid, 'ayn_fast')
-          bxnfid = inq_varid(ncid, 'bxn_fast')
-          bynfid = inq_varid(ncid, 'byn_fast')
-        endif
-
-        if (iceberg_bonds_on) then
-          nbid = inq_varid(ncid, 'n_bonds')
-        end if
-
-        if (dem) then
-          avid = inq_varid(ncid, 'ang_vel')
-          aaid = inq_varid(ncid, 'ang_accel')
-          rid  = inq_varid(ncid, 'rot')
-        endif
-
-      endif
-    else
-      ! Dimensions
-      iret = nf_def_dim(ncid, 'i', NF_UNLIMITED, i_dim)
-      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_trajectory: nf_def_dim i failed'
-
-      ! Variables
-      lonid = def_var(ncid, 'lon', NF_DOUBLE, i_dim)
-      latid = def_var(ncid, 'lat', NF_DOUBLE, i_dim)
-      yearid = def_var(ncid, 'year', NF_INT, i_dim)
-      dayid = def_var(ncid, 'day', NF_DOUBLE, i_dim)
-      idcntid = def_var(ncid, 'id_cnt', NF_INT, i_dim)
-      idijid = def_var(ncid, 'id_ij', NF_INT, i_dim)
-      if (save_fl_traj) then
-        mid = def_var(ncid, 'mass', NF_DOUBLE, i_dim)
-        smid = def_var(ncid, 'start_mass', NF_DOUBLE, i_dim)
-        did = def_var(ncid, 'thickness', NF_DOUBLE, i_dim)
-        mbid = def_var(ncid, 'mass_of_bits', NF_DOUBLE, i_dim)
-        uvelid = def_var(ncid, 'uvel', NF_DOUBLE, i_dim)
-        vvelid = def_var(ncid, 'vvel', NF_DOUBLE, i_dim)
-        if (footloose) then
-          msid = def_var(ncid, 'mass_scaling', NF_DOUBLE, i_dim)
-          mflbid = def_var(ncid, 'mass_of_fl_bits', NF_DOUBLE, i_dim)
-          mflbbid = def_var(ncid, 'mass_of_fl_bergy_bits', NF_DOUBLE, i_dim)
-          flkid = def_var(ncid, 'fl_k', NF_DOUBLE, i_dim)
-        endif
-      endif
-      if (.not. save_short_traj) then
-        !uvelid = def_var(ncid, 'uvel', NF_DOUBLE, i_dim)
-        !vvelid = def_var(ncid, 'vvel', NF_DOUBLE, i_dim)
-        uvelpid = def_var(ncid, 'uvel_prev', NF_DOUBLE, i_dim)
-        vvelpid = def_var(ncid, 'vvel_prev', NF_DOUBLE, i_dim)
-        uoid = def_var(ncid, 'uo', NF_DOUBLE, i_dim)
-        void = def_var(ncid, 'vo', NF_DOUBLE, i_dim)
-        uiid = def_var(ncid, 'ui', NF_DOUBLE, i_dim)
-        viid = def_var(ncid, 'vi', NF_DOUBLE, i_dim)
-        uaid = def_var(ncid, 'ua', NF_DOUBLE, i_dim)
-        vaid = def_var(ncid, 'va', NF_DOUBLE, i_dim)
-        hdid = def_var(ncid, 'heat_density', NF_DOUBLE, i_dim)
-        wid = def_var(ncid, 'width', NF_DOUBLE, i_dim)
-        lid = def_var(ncid, 'length', NF_DOUBLE, i_dim)
-        sshxid = def_var(ncid, 'ssh_x', NF_DOUBLE, i_dim)
-        sshyid = def_var(ncid, 'ssh_y', NF_DOUBLE, i_dim)
-        sstid = def_var(ncid, 'sst', NF_DOUBLE, i_dim)
-        sssid = def_var(ncid, 'sss', NF_DOUBLE, i_dim)
-        cnid = def_var(ncid, 'cn', NF_DOUBLE, i_dim)
-        hiid = def_var(ncid, 'hi', NF_DOUBLE, i_dim)
-        axnid = def_var(ncid, 'axn', NF_DOUBLE, i_dim)
-        aynid = def_var(ncid, 'ayn', NF_DOUBLE, i_dim)
-        bxnid = def_var(ncid, 'bxn', NF_DOUBLE, i_dim)
-        bynid = def_var(ncid, 'byn', NF_DOUBLE, i_dim)
-        hsid = def_var(ncid, 'halo_berg', NF_DOUBLE, i_dim)
-        odid = def_var(ncid, 'od', NF_DOUBLE, i_dim)
-
-        if (mts) then
-          axnfid = def_var(ncid, 'axn_fast', NF_DOUBLE, i_dim)
-          aynfid = def_var(ncid, 'ayn_fast', NF_DOUBLE, i_dim)
-          bxnfid = def_var(ncid, 'bxn_fast', NF_DOUBLE, i_dim)
-          bynfid = def_var(ncid, 'byn_fast', NF_DOUBLE, i_dim)
-        endif
-
-        if (iceberg_bonds_on) then
-          nbid = def_var(ncid, 'n_bonds', NF_INT, i_dim)
-        end if
-
-        if (dem) then
-          avid = def_var(ncid, 'ang_vel', NF_DOUBLE, i_dim)
-          aaid = def_var(ncid, 'ang_accel', NF_DOUBLE, i_dim)
-          rid  = def_var(ncid, 'rot', NF_DOUBLE, i_dim)
-        endif
-      endif
-
-      ! Attributes
-      iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_major_version', NF_INT, 1, 0)
-      iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_minor_version', NF_INT, 1, 1)
-      call put_att(ncid, lonid, 'long_name', 'longitude')
-      call put_att(ncid, lonid, 'units', 'degrees_E')
-      call put_att(ncid, latid, 'long_name', 'latitude')
-      call put_att(ncid, latid, 'units', 'degrees_N')
-      call put_att(ncid, yearid, 'long_name', 'year')
-      call put_att(ncid, yearid, 'units', 'years')
-      call put_att(ncid, dayid, 'long_name', 'year day')
-      call put_att(ncid, dayid, 'units', 'days')
-      call put_att(ncid, idcntid, 'long_name', 'counter component of iceberg id')
-      call put_att(ncid, idcntid, 'units', 'dimensionless')
-      call put_att(ncid, idijid, 'long_name', 'position component of iceberg id')
-      call put_att(ncid, idijid, 'units', 'dimensionless')
-      if (save_fl_traj) then
-        call put_att(ncid, mid, 'long_name', 'mass')
-        call put_att(ncid, mid, 'units', 'kg')
-        call put_att(ncid, smid, 'long_name', 'start_mass')
-        call put_att(ncid, smid, 'units', 'kg')
-        call put_att(ncid, did, 'long_name', 'thickness')
-        call put_att(ncid, did, 'units', 'm')
-        call put_att(ncid, mbid, 'long_name', 'mass_of_bits')
-        call put_att(ncid, mbid, 'units', 'kg')
-        call put_att(ncid, uvelid, 'long_name', 'zonal spped')
-        call put_att(ncid, uvelid, 'units', 'm/s')
-        call put_att(ncid, vvelid, 'long_name', 'meridional spped')
-        call put_att(ncid, vvelid, 'units', 'm/s')
-        if (footloose) then
-          call put_att(ncid, msid, 'long_name', 'mass_scaling')
-          call put_att(ncid, msid, 'units', 'dimensionless')
-          call put_att(ncid, mflbid, 'long_name', 'mass_of_fl_bits')
-          call put_att(ncid, mflbid, 'units', 'kg')
-          call put_att(ncid, mflbbid, 'long_name', 'mass_of_fl_bergy_bits')
-          call put_att(ncid, mflbbid, 'units', 'kg')
-          call put_att(ncid, flkid, 'long_name', 'footloose calving k')
-          call put_att(ncid, flkid, 'units', 'none')
-        endif
-      endif
-      if (.not. save_short_traj) then
-        ! call put_att(ncid, uvelid, 'long_name', 'zonal spped')
-        ! call put_att(ncid, uvelid, 'units', 'm/s')
-        ! call put_att(ncid, vvelid, 'long_name', 'meridional spped')
-        ! call put_att(ncid, vvelid, 'units', 'm/s')
-        call put_att(ncid, uoid, 'long_name', 'ocean zonal spped')
-        call put_att(ncid, uoid, 'units', 'm/s')
-        call put_att(ncid, void, 'long_name', 'ocean meridional spped')
-        call put_att(ncid, void, 'units', 'm/s')
-        call put_att(ncid, uiid, 'long_name', 'ice zonal spped')
-        call put_att(ncid, uiid, 'units', 'm/s')
-        call put_att(ncid, viid, 'long_name', 'ice meridional spped')
-        call put_att(ncid, viid, 'units', 'm/s')
-        call put_att(ncid, uaid, 'long_name', 'atmos zonal spped')
-        call put_att(ncid, uaid, 'units', 'm/s')
-        call put_att(ncid, vaid, 'long_name', 'atmos meridional spped')
-        call put_att(ncid, vaid, 'units', 'm/s')
-        call put_att(ncid, hdid, 'long_name', 'heat_density')
-        call put_att(ncid, hdid, 'units', 'J/kg')
-        call put_att(ncid, wid, 'long_name', 'width')
-        call put_att(ncid, wid, 'units', 'm')
-        call put_att(ncid, lid, 'long_name', 'length')
-        call put_att(ncid, lid, 'units', 'm')
-        call put_att(ncid, sshxid, 'long_name', 'sea surface height gradient_x')
-        call put_att(ncid, sshxid, 'units', 'non-dim')
-        call put_att(ncid, sshyid, 'long_name', 'sea surface height gradient_y')
-        call put_att(ncid, sshyid, 'units', 'non-dim')
-        call put_att(ncid, sstid, 'long_name', 'sea surface temperature')
-        call put_att(ncid, sstid, 'units', 'degrees_C')
-        call put_att(ncid, sssid, 'long_name', 'sea surface salinity')
-        call put_att(ncid, sssid, 'units', 'psu')
-        call put_att(ncid, cnid, 'long_name', 'sea ice concentration')
-        call put_att(ncid, cnid, 'units', 'none')
-        call put_att(ncid, hiid, 'long_name', 'sea ice thickness')
-        call put_att(ncid, hiid, 'units', 'm')
-        call put_att(ncid, axnid, 'long_name', 'explicit zonal acceleration')
-        call put_att(ncid, axnid, 'units', 'm')
-        call put_att(ncid, aynid, 'long_name', 'explicit meridional acceleration')
-        call put_att(ncid, aynid, 'units', 'm')
-        call put_att(ncid, bxnid, 'long_name', 'implicit zonal acceleration')
-        call put_att(ncid, bxnid, 'units', 'm')
-        call put_att(ncid, bynid, 'long_name', 'implicit meridional acceleration')
-        call put_att(ncid, bynid, 'units', 'm')
-        call put_att(ncid, hsid, 'long_name', 'halo status')
-        call put_att(ncid, hsid, 'units', 'non-dim')
-        call put_att(ncid, odid, 'long_name', 'ocean_depth')
-        call put_att(ncid, odid, 'units', 'm')
-
-        if (mts) then
-          call put_att(ncid, uvelpid, 'long_name', 'zonal speed mts')
-          call put_att(ncid, uvelpid, 'units', 'm/s')
-          call put_att(ncid, vvelpid, 'long_name', 'meridional speed mts')
-          call put_att(ncid, vvelpid, 'units', 'm/s')
-          call put_att(ncid, axnfid, 'long_name', 'explicit fast step zonal acceleration')
-          call put_att(ncid, axnfid, 'units', 'm')
-          call put_att(ncid, aynfid, 'long_name', 'explicit fast step meridional acceleration')
-          call put_att(ncid, aynfid, 'units', 'm')
-          call put_att(ncid, bxnfid, 'long_name', 'implicit fast step zonal acceleration')
-          call put_att(ncid, bxnfid, 'units', 'm')
-          call put_att(ncid, bynfid, 'long_name', 'implicit fast step meridional acceleration')
-          call put_att(ncid, bynfid, 'units', 'm')
-        endif
-
-        if (iceberg_bonds_on) then
-          call put_att(ncid, nbid, 'long_name', 'number of bonds')
-          call put_att(ncid, nbid, 'units', 'dimensionless')
-        end if
-
-        if (dem) then
-          call put_att(ncid, avid, 'long_name', 'angular velocity')
-          call put_att(ncid, avid, 'units', 'rad/s')
-          call put_att(ncid, aaid, 'long_name', 'angular acceleration')
-          call put_att(ncid, aaid, 'units', 'rad/s^2')
-          call put_att(ncid, rid, 'long_name', 'accumulated rotation')
-          call put_att(ncid, rid, 'units', 'rad')
-        endif
-      endif
-    endif
-
-    ! End define mode
-    iret = nf_enddef(ncid)
-
-    ! Write variables
-    this=>traj4io
-    if (io_is_in_append_mode) then
-      iret = nf_inq_dimlen(ncid, i_dim, i)
-      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_trajectory: nf_inq_dimlen i failed'
-    else
-      i = 0
-    endif
-    do while (associated(this))
-      i=i+1
-      call put_double(ncid, lonid, i, this%lon)
-      call put_double(ncid, latid, i, this%lat)
-      call put_int(ncid, yearid, i, this%year)
-      call put_double(ncid, dayid, i, this%day)
-      call split_id(this%id, cnt, ij)
-      call put_int(ncid, idcntid, i, cnt)
-      call put_int(ncid, idijid, i, ij)
-      if (save_fl_traj) then
-        call put_double(ncid, mid, i, this%mass)
-        call put_double(ncid, smid, i, this%start_mass)
-        call put_double(ncid, did, i, this%thickness)
-        call put_double(ncid, mbid, i, this%mass_of_bits)
-        call put_double(ncid, uvelid, i, this%uvel)
-        call put_double(ncid, vvelid, i, this%vvel)
-        if (footloose) then
-          call put_double(ncid, msid, i, this%mass_scaling)
-          call put_double(ncid, mflbid, i, this%mass_of_fl_bits)
-          call put_double(ncid, mflbbid, i, this%mass_of_fl_bergy_bits)
-          call put_double(ncid, flkid, i, this%fl_k)
-        endif
-      endif
-      if (.not. save_short_traj) then
-        ! call put_double(ncid, uvelid, i, this%uvel)
-        ! call put_double(ncid, vvelid, i, this%vvel)
-        call put_double(ncid, uvelpid, i, this%uvel_prev)
-        call put_double(ncid, vvelpid, i, this%vvel_prev)
-        call put_double(ncid, uoid, i, this%uo)
-        call put_double(ncid, void, i, this%vo)
-        call put_double(ncid, uiid, i, this%ui)
-        call put_double(ncid, viid, i, this%vi)
-        call put_double(ncid, uaid, i, this%ua)
-        call put_double(ncid, vaid, i, this%va)
-        call put_double(ncid, hdid, i, this%heat_density)
-        call put_double(ncid, wid, i, this%width)
-        call put_double(ncid, lid, i, this%length)
-        call put_double(ncid, sshxid, i, this%ssh_x)
-        call put_double(ncid, sshyid, i, this%ssh_y)
-        call put_double(ncid, sstid, i, this%sst)
-        call put_double(ncid, sssid, i, this%sss)
-        call put_double(ncid, cnid, i, this%cn)
-        call put_double(ncid, hiid, i, this%hi)
-        call put_double(ncid, axnid, i, this%axn)
-        call put_double(ncid, aynid, i, this%ayn)
-        call put_double(ncid, bxnid, i, this%bxn)
-        call put_double(ncid, bynid, i, this%byn)
-        call put_double(ncid, hsid, i, this%halo_berg)
-        call put_double(ncid, odid, i, this%od)
-
-        if (mts) then
-          call put_double(ncid, axnfid, i, this%axn_fast)
-          call put_double(ncid, aynfid, i, this%ayn_fast)
-          call put_double(ncid, bxnfid, i, this%bxn_fast)
-          call put_double(ncid, bynfid, i, this%byn_fast)
-        endif
-
-        if (iceberg_bonds_on) then
-          call put_int(ncid, nbid, i, this%n_bonds)
-        end if
-
-        if (dem) then
-          call put_double(ncid, avid, i, this%ang_vel)
-          call put_double(ncid, aaid, i, this%ang_accel)
-          call put_double(ncid, rid,  i, this%rot)
-        endif
-
-      endif
-      next=>this%next
-      deallocate(this)
-      this=>next
-    enddo
-
-    ! Finish up
-    iret = nf_close(ncid)
-    if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_trajectory: nf_close failed',mpp_pe(),filename
-
-  endif !(is_io_tile_root_pe .AND. associated(traj4io))
-  call mpp_clock_end(clock_trw)
-
-end subroutine write_trajectory
-
-!> Write a trajectory-based diagnostics file for bonds
-subroutine write_bond_trajectory(trajectory, bond_traj_name)
-! Arguments
-type(bond_xyt), pointer :: trajectory !< An iceberg bond trajectory
-character(len=70) :: bond_traj_name !<file name of bond trajectories
-! Local variables
-integer :: iret, ncid, i_dim, i
-integer :: lonid, latid, yearid, dayid, lenid,n1id, n2id
-integer :: rrotid,brid
-integer :: idcnt1_id, idcnt2_id, idij1_id, idij2_id
-integer :: td1id,td2id,dnsid,dssid
-character(len=70) :: filename
-character(len=7) :: pe_name
-type(bond_xyt), pointer :: this, next
-integer :: stderrunit, cnt, ij
-!I/O vars
-type(bond_xyt), pointer :: traj4io=>null()
-integer :: ntrajs_sent_io,ntrajs_rcvd_io
-integer :: from_pe,np
-type(buffer), pointer :: obuffer_io=>null(), ibuffer_io=>null()
-logical :: io_is_in_append_mode
-
-  stderrunit=stderr()  ! Get the stderr unit number
-  traj4io=>null()
-  ibuffer_io=>null(); obuffer_io=>null()
-
-  !Assemble the list of trajectories from all pes in this I/O tile
-  call mpp_clock_begin(clock_btrp)
-
-  !First add the trajs on the io_tile_root_pe (if any) to the I/O list
-  if(is_io_tile_root_pe .OR. force_all_pes_traj ) then
-    if(associated(trajectory)) then
-      this=>trajectory
-      do while (associated(this))
-        call append_bond_posn(traj4io, this)
-        this=>this%next
-      enddo
-      trajectory => null()
-    endif
-  endif
-
-  if(.NOT. force_all_pes_traj ) then
-    !Now gather and append the bergs from all pes in the io_tile to the list on corresponding io_tile_root_pe
-    ntrajs_sent_io =0; ntrajs_rcvd_io =0
-
-    if(is_io_tile_root_pe) then
-      !Receive trajs from all pes in this I/O tile !FRAGILE!SCARY!
-      do np=2,size(io_tile_pelist) ! Note: np starts from 2 to exclude self
-        from_pe=io_tile_pelist(np)
-        call mpp_recv(ntrajs_rcvd_io, glen=1, from_pe=from_pe, tag=COMM_TAG_11)
-        if (ntrajs_rcvd_io .gt. 0) then
-          call increase_ibuffer(ibuffer_io, ntrajs_rcvd_io,buffer_width_bond_traj)
-          call mpp_recv(ibuffer_io%data, ntrajs_rcvd_io*buffer_width_bond_traj,from_pe=from_pe, tag=COMM_TAG_12)
-          do i=1, ntrajs_rcvd_io
-            call unpack_bond_traj_from_buffer2(traj4io, ibuffer_io, i)
-          enddo
-        endif
-      enddo
-    else
-      ! Pack and send trajectories to the root PE for this I/O tile
-      do while (associated(trajectory))
-        ntrajs_sent_io = ntrajs_sent_io +1
-        call pack_bond_traj_into_buffer2(trajectory, obuffer_io, ntrajs_sent_io)
-        this => trajectory ! Need to keep pointer in order to free up the links memory
-        trajectory => trajectory%next ! This will eventually result in trajectory => null()
-        deallocate(this) ! Delete the link from memory
-      enddo
-
-      call mpp_send(ntrajs_sent_io, plen=1, to_pe=io_tile_root_pe, tag=COMM_TAG_11)
-      if (ntrajs_sent_io .gt. 0) then
-        call mpp_send(obuffer_io%data, ntrajs_sent_io*buffer_width_bond_traj, to_pe=io_tile_root_pe, tag=COMM_TAG_12)
-      endif
-    endif
-  endif !.NOT. force_all_pes_traj
-
-  call mpp_clock_end(clock_btrp)
-
-  !Now start writing in the io_tile_root_pe if there are any bergs in the I/O list
-  call mpp_clock_begin(clock_btrw)
-
-  if((force_all_pes_traj .OR. is_io_tile_root_pe) .AND. associated(traj4io)) then
-
-    !call get_instance_filename("bond_trajectories.nc", filename)
-    call get_instance_filename(bond_traj_name, filename)
-    if(io_tile_id(1) .ge. 0 .AND. .NOT. force_all_pes_traj) then !io_tile_root_pes write
-      if(io_npes .gt. 1) then !attach tile_id  to filename only if there is more than one I/O pe
-        if (io_tile_id(1)<10000) then
-          write(filename,'(A,".",I4.4)') trim(filename), io_tile_id(1)
-        else
-          write(filename,'(A,".",I6.6)') trim(filename), io_tile_id(1)
-        endif
-      endif
-    else !All pes write, attach pe# to filename
-      if (mpp_npes()<10000) then
-        write(filename,'(A,".",I4.4)') trim(filename), mpp_pe()
-      else
-        write(filename,'(A,".",I6.6)') trim(filename), mpp_pe()
-      endif
-    endif
-
-    io_is_in_append_mode = .false.
-    iret = nf_create(filename, NF_NOCLOBBER, ncid)
-    if (iret .ne. NF_NOERR) then
-      iret = nf_open(filename, NF_WRITE, ncid)
-      io_is_in_append_mode = .true.
-      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_bond_trajectory: nf_open failed'
-    endif
-    if (verbose) then
-      if (io_is_in_append_mode) then
-        write(*,'(2a)') 'KID, write_bond_trajectory: appending to ',filename
-      else
-        write(*,'(2a)') 'KID, write_bond_trajectory: creating ',filename
-      endif
-    endif
-
-    if (io_is_in_append_mode) then
-      iret = nf_inq_dimid(ncid, 'i', i_dim)
-      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_bond_trajectory: nf_inq_dimid i failed'
-      lonid = inq_varid(ncid, 'lon');         latid = inq_varid(ncid, 'lat')
-      yearid = inq_varid(ncid, 'year');       dayid = inq_varid(ncid, 'day')
-      lenid = inq_varid(ncid, 'length');
-      n1id = inq_varid(ncid, 'n1');           n2id = inq_varid(ncid, 'n2')
-
-      idcnt1_id = inq_varid(ncid, 'id_cnt1'); idij1_id = inq_varid(ncid, 'id_ij1')
-      idcnt2_id = inq_varid(ncid, 'id_cnt2'); idij2_id = inq_varid(ncid, 'id_ij2')
-
-      if (dem) then
-        td1id = inq_varid(ncid, 'tangd1');  td2id = inq_varid(ncid, 'tangd2')
-        dnsid = inq_varid(ncid, 'nstress'); dssid = inq_varid(ncid, 'sstress')
-        rrotid = inq_varid(ncid, 'rel_rotation'); brid = inq_varid(ncid, 'broken')
-      endif
-
-    else
-      ! Dimensions
-      iret = nf_def_dim(ncid, 'i', NF_UNLIMITED, i_dim)
-      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_bond_trajectory: nf_def_dim i failed'
-
-      ! Variables
-      lonid = def_var(ncid, 'lon', NF_DOUBLE, i_dim);      latid = def_var(ncid, 'lat', NF_DOUBLE, i_dim)
-      yearid = def_var(ncid, 'year', NF_INT, i_dim);       dayid = def_var(ncid, 'day', NF_DOUBLE, i_dim)
-      lenid = def_var(ncid, 'length', NF_DOUBLE, i_dim);
-      n1id = def_var(ncid, 'n1', NF_DOUBLE, i_dim);        n2id = def_var(ncid, 'n2', NF_DOUBLE, i_dim)
-
-      idcnt1_id = def_var(ncid, 'id_cnt1', NF_INT, i_dim); idij1_id = def_var(ncid, 'id_ij1', NF_INT, i_dim)
-      idcnt2_id = def_var(ncid, 'id_cnt2', NF_INT, i_dim); idij2_id = def_var(ncid, 'id_ij2', NF_INT, i_dim)
-
-      if (dem) then
-        td1id = def_var(ncid, 'tangd1',  NF_DOUBLE, i_dim); td2id = def_var(ncid, 'tangd2',  NF_DOUBLE, i_dim)
-        dnsid = def_var(ncid, 'nstress', NF_DOUBLE, i_dim); dssid = def_var(ncid, 'sstress', NF_DOUBLE, i_dim)
-        rrotid = def_var(ncid, 'rel_rotation', NF_DOUBLE, i_dim)
-        brid = def_var(ncid, 'broken', NF_INT, i_dim)
-      endif
-
-      ! Attributes
-      iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_major_version', NF_INT, 1, 0)
-      iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_minor_version', NF_INT, 1, 1)
-      call put_att(ncid, lonid, 'long_name', 'longitude');    call put_att(ncid, lonid, 'units', 'degrees_E')
-      call put_att(ncid, latid, 'long_name', 'latitude');     call put_att(ncid, latid, 'units', 'degrees_N')
-      call put_att(ncid, yearid, 'long_name', 'year');        call put_att(ncid, yearid, 'units', 'years')
-      call put_att(ncid, dayid, 'long_name', 'year day');     call put_att(ncid, dayid, 'units', 'days')
-      call put_att(ncid, lenid, 'long_name', 'length');       call put_att(ncid, lenid, 'units', 'm')
-      call put_att(ncid, n1id, 'long_name', 'unit vector 1'); call put_att(ncid, n1id, 'units', 'non-dim')
-      call put_att(ncid, n2id, 'long_name', 'unit vector 2'); call put_att(ncid, n2id, 'units', 'non-dim')
-
-      call put_att(ncid, idcnt1_id, 'long_name', 'counter component of first connected iceberg id')
-      call put_att(ncid, idcnt1_id, 'units', 'dimensionless')
-      call put_att(ncid, idij1_id, 'long_name', 'position component of first connected iceberg id')
-      call put_att(ncid, idij1_id, 'units', 'dimensionless')
-      call put_att(ncid, idcnt2_id, 'long_name', 'counter component of second connected iceberg id')
-      call put_att(ncid, idcnt2_id, 'units', 'dimensionless')
-      call put_att(ncid, idij2_id, 'long_name', 'position component of second connected iceberg id')
-      call put_att(ncid, idij2_id, 'units', 'dimensionless')
-
-      if (dem) then
-        call put_att(ncid, td1id, 'long_name', 'zonal tangential displacement')
-        call put_att(ncid, td1id, 'units', 'm')
-        call put_att(ncid, td2id, 'long_name', 'meridional tangential displacement')
-        call put_att(ncid, td2id, 'units', 'm')
-        call put_att(ncid, dnsid, 'long_name', 'normal stress'); call put_att(ncid, dnsid, 'units', 'Pa')
-        call put_att(ncid, dssid, 'long_name', 'shear stress');  call put_att(ncid, dssid, 'units', 'Pa')
-        call put_att(ncid, rrotid, 'long_name', 'relative rotation');      call put_att(ncid, rrotid, 'units', 'rad')
-        call put_att(ncid, brid, 'long_name', 'broken status');      call put_att(ncid, brid, 'units', 'none')
-      endif
-    endif
-
-    ! End define mode
-    iret = nf_enddef(ncid)
-
-    ! Write variables
-    this=>traj4io
-    if (io_is_in_append_mode) then
-      iret = nf_inq_dimlen(ncid, i_dim, i)
-      if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_bond_trajectory: nf_inq_dimlen i failed'
-    else
-      i = 0
-    endif
-    do while (associated(this))
-      i=i+1
-      call put_double(ncid, lonid, i, this%lon);    call put_double(ncid, latid, i, this%lat)
-      call put_int(ncid, yearid, i, this%year);     call put_double(ncid, dayid, i, this%day)
-      call put_double(ncid, lenid, i, this%length);
-      call put_double(ncid, n1id, i, this%n1);      call put_double(ncid, n2id, i, this%n2)
-
-      call split_id(this%id1, cnt, ij)
-      call put_int(ncid, idcnt1_id, i, cnt);        call put_int(ncid, idij1_id, i, ij)
-      call split_id(this%id2, cnt, ij)
-      call put_int(ncid, idcnt2_id, i, cnt);        call put_int(ncid, idij2_id, i, ij)
-
-      if (dem) then
-        call put_double(ncid,td1id,i,this%tangd1);  call put_double(ncid,td2id,i,this%tangd2)
-        call put_double(ncid,dnsid,i,this%nstress); call put_double(ncid,dssid,i,this%sstress)
-        call put_double(ncid,rrotid,i,this%rel_rotation); call put_int(ncid,brid,i,this%broken)
-      endif
-
-      next=>this%next
-      deallocate(this)
-      this=>next
-    enddo
-
-    ! Finish up
-    iret = nf_close(ncid)
-    if (iret .ne. NF_NOERR) write(stderrunit,*) 'KID, write_bond_trajectory: nf_close failed',mpp_pe(),filename
-
-  endif !(is_io_tile_root_pe .AND. associated(traj4io))
-  call mpp_clock_end(clock_btrw)
-
-end subroutine write_bond_trajectory
-
-!> Returns netcdf id of variable
-integer function inq_var(ncid, var, unsafe)
-! Arguments
-integer, intent(in) :: ncid !< Handle to netcdf file
-character(len=*), intent(in) :: var !< Name of variable
-logical, optional, intent(in) :: unsafe !< If present and true, do not fail if variable is not in file
-! Local variables
-integer :: iret
-integer :: stderrunit
-logical :: unsafely=.false.
-
-  if(present(unsafe)) unsafely=unsafe
-  ! Get the stderr unit number
-  stderrunit=stderr()
-
-  iret=nf_inq_varid(ncid, var, inq_var)
-  if (iret .ne. NF_NOERR) then
-    if (.not. unsafely) then
-      write(stderrunit,*) 'KID, inq_var: nf_inq_varid ',var,' failed'
-      call error_mesg('KID, inq_var', 'netcdf function returned a failure!', FATAL)
-    else
-      inq_var=-1
-    endif
-  endif
-
-end function inq_var
-
-!> Define a netcdf variable
-integer function def_var(ncid, var, ntype, idim)
-! Arguments
-integer, intent(in) :: ncid !< Handle to netcdf file
-character(len=*), intent(in) :: var !< Name of variable
-integer, intent(in) :: ntype !< Netcdf type of variable
-integer, intent(in) :: idim !< Length of vector
-! Local variables
-integer :: iret
-integer :: stderrunit
-
-  ! Get the stderr unit number
-  stderrunit=stderr()
-
-  iret = nf_def_var(ncid, var, ntype, 1, idim, def_var)
-  if (iret .ne. NF_NOERR) then
-    call error_mesg('KID, def_var', nf_strerror(iret), FATAL)
-  endif
-
-end function def_var
-
-!> Returns id of variable
-integer function inq_varid(ncid, var)
-! Arguments
-integer, intent(in) :: ncid !< Handle to netcdf file
-character(len=*), intent(in) :: var !< Name of variable
-! Local variables
-integer :: iret
-integer :: stderrunit
-
-  ! Get the stderr unit number
-  stderrunit=stderr()
-
-  iret = nf_inq_varid(ncid, var, inq_varid)
-  if (iret .ne. NF_NOERR) then
-    write(stderrunit,*) 'KID, inq_varid: nf_inq_varid failed for ',trim(var)
-    call error_mesg('KID, inq_varid', 'netcdf function returned a failure!', FATAL)
-  endif
-
-end function inq_varid
-
-!> Add a string attribute to a netcdf variable
-subroutine put_att(ncid, id, att, attval)
-! Arguments
-integer, intent(in) :: ncid !< Handle to netcdf file
-integer, intent(in) :: id !< Netcdf id of variable
-character(len=*), intent(in) :: att !< Name of attribute
-character(len=*), intent(in) :: attval !< Value of attribute
-! Local variables
-integer :: vallen, iret
-integer :: stderrunit
-
-  ! Get the stderr unit number
-  stderrunit=stderr()
-
-  vallen=len_trim(attval)
-  iret = nf_put_att_text(ncid, id, att, vallen, attval)
-  if (iret .ne. NF_NOERR) then
-    write(stderrunit,*) 'KID, put_att: nf_put_att_text failed adding', &
-      trim(att),' = ',trim(attval)
-    call error_mesg('KID, put_att', 'netcdf function returned a failure!', FATAL)
-  endif
-
-end subroutine put_att
-
-!> Read a real from a netcdf file
-real function get_double(ncid, id, i)
-! Arguments
-integer, intent(in) :: ncid !< Handle to netcdf file
-integer, intent(in) :: id !< Netcdf id of variable
-integer, intent(in) :: i !< Index to read
-! Local variables
-integer :: iret
-integer :: stderrunit
-
-  ! Get the stderr unit number
-  stderrunit=stderr()
-
-  iret=nf_get_var1_double(ncid, id, i, get_double)
-  if (iret .ne. NF_NOERR) then
-    write(stderrunit,*) 'KID, get_double: nf_get_var1_double failed reading'
-    call error_mesg('KID, get_double', 'netcdf function returned a failure!', FATAL)
-  endif
-
-end function get_double
-
-!> Read an integer from a netcdf file
-integer function get_int(ncid, id, i)
-! Arguments
-integer, intent(in) :: ncid !< Handle to netcdf file
-integer, intent(in) :: id !< Netcdf id of variable
-integer, intent(in) :: i !< Index to read
-! Local variables
-integer :: iret
-integer :: stderrunit
-
-  ! Get the stderr unit number
-  stderrunit=stderr()
-
-  iret=nf_get_var1_int(ncid, id, i, get_int)
-  if (iret .ne. NF_NOERR) then
-    write(stderrunit,*) 'KID, get_int: nf_get_var1_int failed reading'
-    call error_mesg('KID, get_int', 'netcdf function returned a failure!', FATAL)
-  endif
-
-end function get_int
-
-!> Write a real to a netcdf file
-subroutine put_double(ncid, id, i, val)
-! Arguments
-integer, intent(in) :: ncid !< Handle to netcdf file
-integer, intent(in) :: id !< Netcdf id of variable
-integer, intent(in) :: i !< Index of position to write
-real, intent(in) :: val !< Value to write
-! Local variables
-integer :: iret
-integer :: stderrunit
-
-  ! Get the stderr unit number
-  stderrunit=stderr()
-
-  iret = nf_put_vara_double(ncid, id, i, 1, val)
-  if (iret .ne. NF_NOERR) then
-    write(stderrunit,*) 'KID, put_double: nf_put_vara_double failed writing'
-    call error_mesg('KID, put_double', 'netcdf function returned a failure!', FATAL)
-  endif
-
-end subroutine put_double
-
-!> Write an integer to a netcdf file
-subroutine put_int(ncid, id, i, val)
-! Arguments
-integer, intent(in) :: ncid !< Handle to netcdf file
-integer, intent(in) :: id !< Netcdf id of variable
-integer, intent(in) :: i !< Index of position to write
-integer, intent(in) :: val !< Value to write
-! Local variables
-integer :: iret
-integer :: stderrunit
-
-  ! Get the stderr unit number
-  stderrunit=stderr()
-
-  iret = nf_put_vara_int(ncid, id, i, 1, val)
-  if (iret .ne. NF_NOERR) then
-    write(stderrunit,*) 'KID, put_int: nf_put_vara_int failed writing'
-    call error_mesg('KID, put_int', 'netcdf function returned a failure!', FATAL)
-  endif
-
-end subroutine put_int
-
-!> True is a restart file can be found
-logical function find_restart_file(filename, actual_file, multiPErestart, tile_id)
-  character(len=*), intent(in) :: filename !< Base-name of restart file
-  character(len=*), intent(out) :: actual_file !< Actual name of file, if found
-  logical, intent(out) :: multiPErestart !< True if found, false otherwise
-  integer, intent(in) :: tile_id !< Parallel tile number of file
-
-  character(len=6) :: pe_name
-
-  find_restart_file = .false.
-
-  ! If running as ensemble, add the ensemble id string to the filename
-  call get_instance_filename(filename, actual_file)
-
-  ! Prefer combined restart files.
-  inquire(file=actual_file,exist=find_restart_file)
-  if (find_restart_file) return
-
-  ! Uncombined restart
-  if(tile_id .ge. 0) then
-    write(actual_file,'(A,".",I4.4)') trim(actual_file), tile_id
-  else
-  if (mpp_npes()>10000) then
-     write(pe_name,'(a,i6.6)' )'.', mpp_pe()
-  else
-     write(pe_name,'(a,i4.4)' )'.', mpp_pe()
-  endif
-  actual_file=trim(actual_file)//trim(pe_name)
-  endif
-  inquire(file=actual_file,exist=find_restart_file)
-  if (find_restart_file) then
-     multiPErestart=.true.
-     return
-  endif
-
-  ! No file found, Reset all return parameters
-  find_restart_file=.false.
-  actual_file = ''
-  multiPErestart=.false.
-
-end function find_restart_file
 
 end module

From 6938cf5714ccf034c90e4bbc4f166adc1a4f8454 Mon Sep 17 00:00:00 2001
From: Uriel Ramirez <uriel.ramirez@noaa.gov>
Date: Thu, 23 Mar 2023 14:50:00 -0400
Subject: [PATCH 351/361] Use fms2_io in icebergs_fms2_io instead of fms_io

---
 src/icebergs_fms2io.F90 | 856 ++++++++++++++++++++++++++--------------
 1 file changed, 563 insertions(+), 293 deletions(-)

diff --git a/src/icebergs_fms2io.F90 b/src/icebergs_fms2io.F90
index 58587fd..40e78b8 100644
--- a/src/icebergs_fms2io.F90
+++ b/src/icebergs_fms2io.F90
@@ -10,14 +10,17 @@ module ice_bergs_fms2io
 use mpp_mod, only: mpp_npes, mpp_pe, mpp_root_pe, mpp_sum, mpp_min, mpp_max, NULL_PE
 use mpp_mod, only: mpp_send, mpp_recv, mpp_gather, mpp_chksum, mpp_sync_self
 use mpp_mod, only: COMM_TAG_11, COMM_TAG_12, COMM_TAG_13, COMM_TAG_14
+use mpp_mod, only: mpp_get_current_pelist
 
-use fms_mod, only: stdlog, stderr, error_mesg, FATAL, WARNING, NOTE
-use fms_mod, only: field_exist, file_exist, read_data, write_data
+use fms_mod, only: stdlog, stderr, error_mesg, FATAL, WARNING, NOTE, lowercase
 
-use fms_io_mod, only: get_instance_filename
-use fms_io_mod, only : save_restart, restart_file_type, free_restart_type, set_meta_global
-use fms_io_mod, only : register_restart_axis, register_restart_field, set_domain, nullify_domain
-use fms_io_mod, only : read_unlimited_axis =>read_compressed, field_exist, get_field_size
+use fms2_io_mod, only: get_instance_filename
+use fms2_io_mod, only: FmsNetcdfDomainFile_t, open_file, close_file, read_restart, fms2_io_write_restart => write_restart
+use fms2_io_mod, only: variable_exists, get_dimension_size, get_num_dimensions, get_dimension_names
+use fms2_io_mod, only: get_variable_attribute, variable_att_exists, write_data, read_data
+use fms2_io_mod, only: register_unlimited_compressed_axis, register_axis, register_restart_field, register_variable_attribute
+use fms2_io_mod, only: register_global_attribute, register_field
+use fms2_io_mod, only: get_global_io_domain_indices, unlimited
 
 use mpp_mod,    only : mpp_clock_begin, mpp_clock_end, mpp_clock_id
 use mpp_mod,    only : CLOCK_COMPONENT, CLOCK_SUBCOMPONENT, CLOCK_LOOP
@@ -75,6 +78,12 @@ module ice_bergs_fms2io
 #endif
 character(len=128) :: version = _FILE_VERSION !< Version of file
 
+interface register_restart_field_wrap
+  module procedure :: register_restart_field_wrap_1d
+  module procedure :: register_restart_field_wrap_2d
+  module procedure :: register_restart_field_wrap_3d
+end interface
+
 contains
 
 !> Initialize parallel i/o
@@ -124,9 +133,6 @@ subroutine write_restart(bergs, time_stamp)
 type(iceberg), pointer :: this=>NULL()
 integer :: stderrunit
 !I/O vars
-type(restart_file_type) :: bergs_restart
-type(restart_file_type) :: bergs_bond_restart
-type(restart_file_type) :: calving_restart
 integer :: nbergs, nbonds
 integer :: n_static_bergs
 logical :: check_bond_quality
@@ -184,6 +190,11 @@ subroutine write_restart(bergs, time_stamp)
 
 
 integer :: grdi, grdj
+type(FmsNetcdfDomainFile_t) :: fileobj         !< Fms2_io fileobj
+integer :: global_nbergs
+character(len=8), dimension(4) :: dim_names_4d
+character(len=8), dimension(3) :: dim_names_3d
+character(len=1), dimension(1) :: dim_names_1d
 
 ! Get the stderr unit number
  stderrunit=stderr()
@@ -247,97 +258,6 @@ subroutine write_restart(bergs, time_stamp)
      allocate(rot(nbergs))
    endif
 
-  filename = trim("icebergs.res.nc")
-  call set_domain(bergs%grd%domain)
-  call register_restart_axis(bergs_restart,filename,'i',nbergs)
-  call set_meta_global(bergs_restart,'file_format_major_version',ival=(/file_format_major_version/))
-  call set_meta_global(bergs_restart,'file_format_minor_version',ival=(/file_format_minor_version/))
-  call set_meta_global(bergs_restart,'time_axis',ival=(/0/))
-
-  !Now start writing in the io_tile_root_pe if there are any bergs in the I/O list
-
-  ! Define Variables
-  id = register_restart_field(bergs_restart,filename,'lon',lon,longname='longitude',units='degrees_E')
-  id = register_restart_field(bergs_restart,filename,'lat',lat,longname='latitude',units='degrees_N')
-  id = register_restart_field(bergs_restart,filename,'uvel',uvel,longname='zonal velocity',units='m/s')
-  id = register_restart_field(bergs_restart,filename,'vvel',vvel,longname='meridional velocity',units='m/s')
-  id = register_restart_field(bergs_restart,filename,'mass',mass,longname='mass',units='kg')
-  if (.not. bergs%Runge_not_Verlet) then
-    id = register_restart_field(bergs_restart,filename,'axn',axn,longname='explicit zonal acceleration',units='m/s^2')
-    id = register_restart_field(bergs_restart,filename,'ayn',ayn,longname='explicit meridional acceleration',units='m/s^2')
-    id = register_restart_field(bergs_restart,filename,'bxn',bxn,longname='implicit zonal acceleration',units='m/s^2')
-    id = register_restart_field(bergs_restart,filename,'byn',byn,longname='implicit meridional acceleration',units='m/s^2')
-  endif
-  id = register_restart_field(bergs_restart,filename,'ine',ine,longname='i index',units='none')
-  id = register_restart_field(bergs_restart,filename,'jne',jne,longname='j index',units='none')
-  id = register_restart_field(bergs_restart,filename,'thickness',thickness,longname='thickness',units='m')
-  id = register_restart_field(bergs_restart,filename,'width',width,longname='width',units='m')
-  id = register_restart_field(bergs_restart,filename,'length',length,longname='length',units='m')
-  id = register_restart_field(bergs_restart,filename,'start_lon',start_lon, &
-                                            longname='longitude of calving location',units='degrees_E')
-  id = register_restart_field(bergs_restart,filename,'start_lat',start_lat, &
-                                            longname='latitude of calving location',units='degrees_N')
-  id = register_restart_field(bergs_restart,filename,'start_year',start_year, &
-                                            longname='calendar year of calving event', units='years')
-  id = register_restart_field(bergs_restart,filename,'id_cnt',id_cnt, &
-                                            longname='counter component of iceberg id', units='dimensionless')
-  id = register_restart_field(bergs_restart,filename,'id_ij',id_ij, &
-                                            longname='position component of iceberg id', units='dimensionless')
-  id = register_restart_field(bergs_restart,filename,'start_day',start_day, &
-                                            longname='year day of calving event',units='days')
-  id = register_restart_field(bergs_restart,filename,'start_mass',start_mass, &
-                                            longname='initial mass of calving berg',units='kg')
-  id = register_restart_field(bergs_restart,filename,'mass_scaling',mass_scaling, &
-                                            longname='scaling factor for mass of calving berg',units='none')
-  id = register_restart_field(bergs_restart,filename,'mass_of_bits',mass_of_bits, &
-                                            longname='mass of bergy bits',units='kg')
-  id = register_restart_field(bergs_restart,filename,'heat_density',heat_density, &
-                                            longname='heat density',units='J/kg')
-
-  if (bergs%footloose) then
-    id = register_restart_field(bergs_restart,filename,'fl_k',fl_k,longname='footloose calving k',units='m')
-    id = register_restart_field(bergs_restart,filename,'mass_of_fl_bits',mass_of_fl_bits, &
-      longname='mass of footloose bits',units='kg')
-    id = register_restart_field(bergs_restart,filename,'mass_of_fl_bergy_bits',mass_of_fl_bergy_bits, &
-      longname='mass of bergy bits associated with footloose bits',units='kg')
-   end if
-
-  if (mts) then
-    id = register_restart_field(bergs_restart,filename,'axn_fast',axn_fast,&
-      longname='sub-step explicit zonal acceleration',units='m/s^2')
-    id = register_restart_field(bergs_restart,filename,'ayn_fast',ayn_fast,&
-      longname='sub-step explicit meridional acceleration',units='m/s^2')
-    id = register_restart_field(bergs_restart,filename,'bxn_fast',bxn_fast,&
-      longname='sub-step implicit zonal acceleration',units='m/s^2')
-    id = register_restart_field(bergs_restart,filename,'byn_fast',byn_fast,&
-      longname='sub-step implicit meridional acceleration',units='m/s^2')
-  endif
-
-  if (dem) then
-    id = register_restart_field(bergs_restart,filename,'ang_vel',ang_vel,&
-      longname='dem angular velocity',units='rad/s')
-    id = register_restart_field(bergs_restart,filename,'ang_accel',ang_accel,&
-      longname='dem angular acceleration',units='rad/s^2')
-    id = register_restart_field(bergs_restart,filename,'rot',rot,&
-      longname='dem accumulated rotation',units='rad')
-  endif
-
-  !Checking if any icebergs are static in order to decide whether to save static_berg
-  n_static_bergs = 0
-  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
-    this=>bergs%list(grdi,grdj)%first
-    do while (associated(this))
-      n_static_bergs=n_static_bergs+this%static_berg
-      this=>this%next
-    enddo
-  enddo ; enddo
-  call mpp_sum(n_static_bergs)
-  if (n_static_bergs .gt. 0) &
-    id = register_restart_field(bergs_restart,filename,'static_berg',static_berg, &
-                                              longname='static_berg',units='dimensionless')
-
-  ! Write variables
-
   i = 0
   do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
     this=>bergs%list(grdi,grdj)%first
@@ -379,9 +299,120 @@ subroutine write_restart(bergs, time_stamp)
     enddo
   enddo ; enddo
 
+  filename = "RESTART/"//trim("icebergs.res.nc")
+  dim_names_1d(1) = "i"
+  if (.not. open_file(fileobj, filename, "overwrite", bergs%grd%domain, is_restart=.true.)) &
+    call error_mesg('write_icebegrs_restart', "Error opening the icebergs restart file to write", FATAL)
+
+  call register_unlimited_compressed_axis(fileobj, dim_names_1d(1), nbergs)
+  call register_global_attribute(fileobj,"file_format_major_version", file_format_major_version)
+  call register_global_attribute(fileobj,"file_format_minor_version", file_format_minor_version)
+  call register_global_attribute(fileobj,"time_axis", 0)
+
+  !Now start writing in the io_tile_root_pe if there are any bergs in the I/O list
+
+  ! Define Variables
+  call register_restart_field_wrap(fileobj,'lon',lon, &
+                                   dim_names_1d,longname='longitude',units='degrees_E')
+  call register_restart_field_wrap(fileobj,'lat',lat, &
+                                   dim_names_1d,longname='latitude',units='degrees_N')
+  call register_restart_field_wrap(fileobj,'uvel',uvel, &
+                                   dim_names_1d,longname='zonal velocity',units='m/s')
+  call register_restart_field_wrap(fileobj,'vvel',vvel, &
+                                   dim_names_1d,longname='meridional velocity',units='m/s')
+  call register_restart_field_wrap(fileobj,'mass',mass, &
+                                   dim_names_1d,longname='mass',units='kg')
+  if (.not. bergs%Runge_not_Verlet) then
+    call register_restart_field_wrap(fileobj,'axn',axn, &
+                                    dim_names_1d,longname='explicit zonal acceleration',units='m/s^2')
+    call register_restart_field_wrap(fileobj,'ayn',ayn, &
+                                    dim_names_1d,longname='explicit meridional acceleration',units='m/s^2')
+    call register_restart_field_wrap(fileobj,'bxn',bxn, &
+                                    dim_names_1d,longname='implicit zonal acceleration',units='m/s^2')
+    call register_restart_field_wrap(fileobj,'byn',byn, &
+                                    dim_names_1d,longname='implicit meridional acceleration',units='m/s^2')
+  endif
+  call register_restart_field_wrap(fileobj,'ine',ine, &
+                                   dim_names_1d,longname='i index',units='none')
+  call register_restart_field_wrap(fileobj,'jne',jne, &
+                                   dim_names_1d,longname='j index',units='none')
+  call register_restart_field_wrap(fileobj,'thickness',thickness, &
+                                   dim_names_1d,longname='thickness',units='m')
+  call register_restart_field_wrap(fileobj,'width',width, &
+                                   dim_names_1d,longname='width',units='m')
+  call register_restart_field_wrap(fileobj,'length',length, &
+                                   dim_names_1d,longname='length',units='m')
+  call register_restart_field_wrap(fileobj,'start_lon',start_lon, &
+                                   dim_names_1d,longname='longitude of calving location',units='degrees_E')
+  call register_restart_field_wrap(fileobj,'start_lat',start_lat, &
+                                   dim_names_1d,longname='latitude of calving location',units='degrees_N')
+  call register_restart_field_wrap(fileobj,'start_year',start_year, &
+                                   dim_names_1d,longname='calendar year of calving event', units='years')
+  call register_restart_field_wrap(fileobj,'id_cnt',id_cnt, &
+                                   dim_names_1d,longname='counter component of iceberg id', units='dimensionless')
+  call register_restart_field_wrap(fileobj,'id_ij',id_ij, &
+                                   dim_names_1d,longname='position component of iceberg id', units='dimensionless')
+  call register_restart_field_wrap(fileobj,'start_day',start_day, &
+                                   dim_names_1d,longname='year day of calving event',units='days')
+  call register_restart_field_wrap(fileobj,'start_mass',start_mass, &
+                                   dim_names_1d,longname='initial mass of calving berg',units='kg')
+  call register_restart_field_wrap(fileobj,'mass_scaling',mass_scaling, &
+                                   dim_names_1d,longname='scaling factor for mass of calving berg',units='none')
+  call register_restart_field_wrap(fileobj,'mass_of_bits',mass_of_bits, &
+                                   dim_names_1d,longname='mass of bergy bits',units='kg')
+  call register_restart_field_wrap(fileobj,'heat_density',heat_density, &
+                                   dim_names_1d,longname='heat density',units='J/kg')
+
+  if (bergs%footloose) then
+    call register_restart_field_wrap(fileobj,'fl_k',fl_k, &
+                                    dim_names_1d,longname='footloose calving k',units='m')
+    call register_restart_field_wrap(fileobj,'mass_of_fl_bits',mass_of_fl_bits, &
+                                    dim_names_1d,longname='mass of footloose bits',units='kg')
+    call register_restart_field_wrap(fileobj,'mass_of_fl_bergy_bits',mass_of_fl_bergy_bits, &
+                                    dim_names_1d,longname='mass of bergy bits associated with footloose bits',units='kg')
+   end if
+
+  if (mts) then
+    call register_restart_field_wrap(fileobj,'axn_fast',axn_fast,&
+                                     dim_names_1d,longname='sub-step explicit zonal acceleration',units='m/s^2')
+    call register_restart_field_wrap(fileobj,'ayn_fast',ayn_fast,&
+                                     dim_names_1d,longname='sub-step explicit meridional acceleration',units='m/s^2')
+    call register_restart_field_wrap(fileobj,'bxn_fast',bxn_fast,&
+                                     dim_names_1d,longname='sub-step implicit zonal acceleration',units='m/s^2')
+    call register_restart_field_wrap(fileobj,'byn_fast',byn_fast,&
+                                     dim_names_1d,longname='sub-step implicit meridional acceleration',units='m/s^2')
+  endif
+
+  if (dem) then
+    call register_restart_field_wrap(fileobj,'ang_vel',ang_vel,&
+                                     dim_names_1d,longname='dem angular velocity',units='rad/s')
+    call register_restart_field_wrap(fileobj,'ang_accel',ang_accel,&
+                                     dim_names_1d,longname='dem angular acceleration',units='rad/s^2')
+    call register_restart_field_wrap(fileobj,'rot',rot,&
+                                     dim_names_1d,longname='dem accumulated rotation',units='rad')
+  endif
+
+  !Checking if any icebergs are static in order to decide whether to save static_berg
+  n_static_bergs = 0
+  do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
+    this=>bergs%list(grdi,grdj)%first
+    do while (associated(this))
+      n_static_bergs=n_static_bergs+this%static_berg
+      this=>this%next
+    enddo
+  enddo ; enddo
+  call mpp_sum(n_static_bergs)
+  if (n_static_bergs .gt. 0) &
+    call register_restart_field_wrap(fileobj,'static_berg',static_berg, &
+                                     dim_names_1d,longname='static_berg',units='dimensionless')
+
+  call register_field(fileobj, "i", "int")
+  call fms2_io_write_restart(fileobj)
+
+  call get_dimension_size(fileobj, "i", global_nbergs)
+  call write_data(fileobj, "i", global_nbergs)
 
-  call save_restart(bergs_restart, time_stamp)
-  call free_restart_type(bergs_restart)
+  call close_file(fileobj)
 
   deallocate(              &
              lon,          &
@@ -432,8 +463,6 @@ subroutine write_restart(bergs, time_stamp)
              id_ij,     &
              start_year )
 
-  call nullify_domain()
-
 !########## Creating bond restart file ######################
 
   !Allocating restart memory for bond related variables.
@@ -460,41 +489,6 @@ subroutine write_restart(bergs, time_stamp)
     allocate(broken(nbonds))
   endif
 
-  call get_instance_filename("bonds_iceberg.res.nc", filename_bonds)
-  call set_domain(bergs%grd%domain)
-  call register_restart_axis(bergs_bond_restart,filename,'i',nbonds)
-  call set_meta_global(bergs_bond_restart,'file_format_major_version',ival=(/file_format_major_version/))
-  call set_meta_global(bergs_bond_restart,'file_format_minor_version',ival=(/file_format_minor_version/))
-  call set_meta_global(bergs_bond_restart,'time_axis',ival=(/0/))
-
-  !Now start writing in the io_tile_root_pe if there are any bergs in the I/O list
-
-  id = register_restart_field(bergs_bond_restart,filename_bonds,'first_berg_ine',first_berg_ine,longname='iceberg ine of first berg in bond',units='dimensionless')
-  id = register_restart_field(bergs_bond_restart,filename_bonds,'first_berg_jne',first_berg_jne,longname='iceberg jne of first berg in bond',units='dimensionless')
-  id = register_restart_field(bergs_bond_restart,filename_bonds,'first_id_cnt',first_id_cnt,longname='counter component of iceberg id first berg in bond',units='dimensionless')
-  id = register_restart_field(bergs_bond_restart,filename_bonds,'first_id_ij',first_id_ij,longname='position component of iceberg id first berg in bond',units='dimensionless')
-  id = register_restart_field(bergs_bond_restart,filename_bonds,'other_berg_ine',other_berg_ine,longname='iceberg ine of second berg in bond',units='dimensionless')
-  id = register_restart_field(bergs_bond_restart,filename_bonds,'other_berg_jne',other_berg_jne,longname='iceberg jne of second berg in bond',units='dimensionless')
-  id = register_restart_field(bergs_bond_restart,filename_bonds,'other_id_cnt',other_id_cnt,longname='counter component of iceberg id second berg in bond',units='dimensionless')
-  id = register_restart_field(bergs_bond_restart,filename_bonds,'other_id_ij',other_id_ij,longname='position component of iceberg id second berg in bond',units='dimensionless')
-
-  if (dem) then
-    id = register_restart_field(bergs_bond_restart,filename_bonds,'tangd1',tangd1,&
-      longname='zonal tangential displacement',units='m')
-    id = register_restart_field(bergs_bond_restart,filename_bonds,'tangd2',tangd2,&
-      longname='meridional tangential displacement',units='m')
-    id = register_restart_field(bergs_bond_restart,filename_bonds,'nstress',nstress,&
-      longname='normal stress',units='Pa')
-    id = register_restart_field(bergs_bond_restart,filename_bonds,'sstress',sstress,&
-      longname='shear stress',units='Pa')
-    id = register_restart_field(bergs_bond_restart,filename_bonds,'rel_rotation',rel_rotation,&
-      longname='relative rotation',units='rad')
-     id = register_restart_field(bergs_bond_restart,filename_bonds,'broken',broken,&
-      longname='broken status',units='none')
-  endif
-
-  ! Write variables
-
   i = 0
   do grdj = bergs%grd%jsc,bergs%grd%jec ; do grdi = bergs%grd%isc,bergs%grd%iec
     this=>bergs%list(grdi,grdj)%first
@@ -524,9 +518,51 @@ subroutine write_restart(bergs, time_stamp)
     enddo!End of loop over bergs
   enddo; enddo !End of loop over grid
 
-  call save_restart(bergs_bond_restart, time_stamp)
-  call free_restart_type(bergs_bond_restart)
+  filename = "RESTART/"//trim("bonds_iceberg.res.nc")
+  if (open_file(fileobj, filename, "overwrite", bergs%grd%domain, is_restart=.true.)) &
+    call error_mesg('write_icebegrs_restart', "Error opening the bonds icebergs restart file to write", FATAL)
+
+  call register_unlimited_compressed_axis(fileobj,'i',nbonds)
+  call register_global_attribute(fileobj,'file_format_major_version',file_format_major_version)
+  call register_global_attribute(fileobj,'file_format_minor_version',file_format_minor_version)
+  call register_global_attribute(fileobj,'time_axis',0)
 
+  !Now start writing in the io_tile_root_pe if there are any bergs in the I/O list
+
+  call register_restart_field_wrap(fileobj,'first_berg_ine',first_berg_ine, &
+                                   dim_names_1d,longname='iceberg ine of first berg in bond',units='dimensionless')
+  call register_restart_field_wrap(fileobj,'first_berg_jne',first_berg_jne, &
+                                   dim_names_1d,longname='iceberg jne of first berg in bond',units='dimensionless')
+  call register_restart_field_wrap(fileobj,'first_id_cnt',first_id_cnt, &
+                                   dim_names_1d,longname='counter component of iceberg id first berg in bond',units='dimensionless')
+  call register_restart_field_wrap(fileobj,'first_id_ij',first_id_ij, &
+                                   dim_names_1d,longname='position component of iceberg id first berg in bond',units='dimensionless')
+  call register_restart_field_wrap(fileobj,'other_berg_ine',other_berg_ine, &
+                                   dim_names_1d,longname='iceberg ine of second berg in bond',units='dimensionless')
+  call register_restart_field_wrap(fileobj,'other_berg_jne',other_berg_jne, &
+                                   dim_names_1d,longname='iceberg jne of second berg in bond',units='dimensionless')
+  call register_restart_field_wrap(fileobj,'other_id_cnt',other_id_cnt, &
+                                   dim_names_1d,longname='counter component of iceberg id second berg in bond',units='dimensionless')
+  call register_restart_field_wrap(fileobj,'other_id_ij',other_id_ij, &
+                                   dim_names_1d,longname='position component of iceberg id second berg in bond',units='dimensionless')
+
+  if (dem) then
+    call register_restart_field_wrap(fileobj,'tangd1',tangd1,&
+                                     dim_names_1d,longname='zonal tangential displacement',units='m')
+    call register_restart_field_wrap(fileobj,'tangd2',tangd2,&
+                                     dim_names_1d,longname='meridional tangential displacement',units='m')
+    call register_restart_field_wrap(fileobj,'nstress',nstress,&
+                                     dim_names_1d,longname='normal stress',units='Pa')
+    call register_restart_field_wrap(fileobj,'sstress',sstress,&
+                                     dim_names_1d,longname='shear stress',units='Pa')
+    call register_restart_field_wrap(fileobj,'rel_rotation',rel_rotation,&
+                                     dim_names_1d,longname='relative rotation',units='rad')
+    call register_restart_field_wrap(fileobj,'broken',broken,&
+                                     dim_names_1d,longname='broken status',units='none')
+  endif
+
+  call fms2_io_write_restart(fileobj)
+  call close_file(fileobj)
 
   deallocate(first_id_cnt,          &
              other_id_cnt,          &
@@ -545,12 +581,10 @@ subroutine write_restart(bergs, time_stamp)
              rel_rotation,          &
              broken)
   endif
-
-  call nullify_domain()
   endif
 
   ! Write stored ice
-  filename='calving.res.nc'
+  filename="RESTART/"//trim("calving.res.nc")
   if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(stderrunit,'(2a)') 'KID, write_restart: writing ',filename
   call grd_chksum3(bergs%grd, bergs%grd%stored_ice, 'write stored_ice')
   call grd_chksum2(bergs%grd, bergs%grd%stored_heat, 'write stored_heat')
@@ -559,18 +593,41 @@ subroutine write_restart(bergs, time_stamp)
     call grd_chksum2(bergs%grd, bergs%grd%rmean_calving_hflx, 'write mean calving_hflx')
   endif
 
-  call set_domain(bergs%grd%domain)
-  id = register_restart_field(calving_restart,filename,'stored_ice',bergs%grd%stored_ice,longname='STORED_ICE',units='none')
-  id = register_restart_field(calving_restart,filename,'stored_heat',bergs%grd%stored_heat,longname='STORED_HEAT',units='none')
-  id = register_restart_field(calving_restart,filename,'iceberg_counter_grd',bergs%grd%iceberg_counter_grd,longname='ICEBERG_COUNTER_GRD',units='none')
+  dim_names_4d = (/"xaxis_1", "yaxis_1", "zaxis_1", "Time   "/)
+  dim_names_3d = (/"xaxis_1", "yaxis_1", "Time   "/)
+
+  if (.not. open_file(fileobj, filename, "overwrite", bergs%grd%domain, is_restart=.true.)) &
+    call error_mesg('write_icebegrs_restart', "Error opening the calving restart file to write", FATAL)
+
+  call register_axis(fileobj, "xaxis_1", "x")
+  call register_axis(fileobj, "yaxis_1", "y")
+  call register_axis(fileobj, "zaxis_1", size(bergs%grd%stored_ice, 3))
+  call register_axis(fileobj, "Time", unlimited)
+
+  call register_restart_field_wrap(fileobj,'stored_ice',bergs%grd%stored_ice, &
+                                   dim_names_4d,longname='STORED_ICE',units='none', &
+                                   is_domain_decomposed=.true.)
+  call register_restart_field_wrap(fileobj,'stored_heat',bergs%grd%stored_heat,&
+                                   dim_names_3d,longname='STORED_HEAT',units='none', &
+                                   is_domain_decomposed=.true.)
+
+  call register_restart_field_wrap(fileobj,'iceberg_counter_grd', bergs%grd%iceberg_counter_grd, &
+                                   dim_names_3d,longname='ICEBERG_COUNTER_GRD',units='none', &
+                                   is_domain_decomposed=.true.)
+
   if (bergs%tau_calving>0.) then
-    id = register_restart_field(calving_restart,filename,'rmean_calving',bergs%grd%rmean_calving,longname='RMEAN_CALVING',units='none')
-    id = register_restart_field(calving_restart,filename,'rmean_calving_hflx',bergs%grd%rmean_calving_hflx,longname='RMEAN_CALVING_HFLX',units='none')
+    call register_restart_field_wrap(fileobj,'rmean_calving',bergs%grd%rmean_calving, &
+                                     dim_names_3d,longname='RMEAN_CALVING',units='none', &
+                                     is_domain_decomposed=.true.)
+    call register_restart_field_wrap(fileobj,'rmean_calving_hflx',bergs%grd%rmean_calving_hflx, &
+                                     dim_names_3d,longname='RMEAN_CALVING_HFLX',units='none', &
+                                     is_domain_decomposed=.true.)
   endif
 
-  call save_restart(calving_restart, time_stamp)
-  call free_restart_type(calving_restart)
-
+  call write_axis_metadata(fileobj)
+  call fms2_io_write_restart(fileobj)
+  call write_axis_data(fileobj, size(bergs%grd%stored_ice, 3))
+  call close_file(fileobj)
 end subroutine write_restart
 
 !> Find the last berg in a linked list.
@@ -610,10 +667,9 @@ subroutine read_restart_bergs(bergs,Time)
 integer :: k, siz(4), nbergs_in_file, nbergs_read
 logical :: lres, found_restart, found, replace_iceberg_num
 logical :: explain
-logical :: multiPErestart  ! Not needed with new restart read; currently kept for compatibility
 real :: lon0, lon1, lat0, lat1
 real :: pos_is_good, pos_is_good_all_pe
-character(len=53) :: filename, filename_base
+character(len=53) :: filename
 type(icebergs_gridded), pointer :: grd
 type(iceberg) :: localberg ! NOT a pointer but an actual local variable
 integer :: stderrunit, i, j, cnt, ij
@@ -656,6 +712,9 @@ subroutine read_restart_bergs(bergs,Time)
                                       id_ij,      &
                                       start_year
 
+type(FmsNetcdfDomainFile_t) :: fileobj !< Fms2_io fileobj
+character(len=1), dimension(1) :: dim_names_1d
+
 !integer, allocatable, dimension(:,:) :: iceberg_counter_grd
 
   ! Get the stderr unit number
@@ -667,16 +726,15 @@ subroutine read_restart_bergs(bergs,Time)
   ! Zero out nbergs_in_file
   nbergs_in_file = 0
 
-  filename_base=trim(restart_input_dir)//'icebergs.res.nc'
+  filename=trim(restart_input_dir)//'icebergs.res.nc'
 
-  found_restart = find_restart_file(filename_base, filename, multiPErestart, io_tile_id(1))
+  found_restart = open_file(fileobj, filename, "read", bergs%grd%domain, is_restart=.true.)
 
   if (found_restart) then
-     filename = filename_base
-     call get_field_size(filename,'i',siz, field_found=found, domain=bergs%grd%domain)
+     call get_dimension_size(fileobj, 'i', siz(1))
      nbergs_in_file = siz(1)
 
-     replace_iceberg_num = field_exist(filename, 'iceberg_num') ! True if using 32-bit iceberg_num in restart file
+     replace_iceberg_num = variable_exists(fileobj, 'iceberg_num') ! True if using 32-bit iceberg_num in restart file
      allocate(lon(nbergs_in_file))
      allocate(lat(nbergs_in_file))
      allocate(uvel(nbergs_in_file))
@@ -703,6 +761,19 @@ subroutine read_restart_bergs(bergs,Time)
      allocate(ine(nbergs_in_file))
      allocate(jne(nbergs_in_file))
      allocate(start_year(nbergs_in_file))
+
+     !Set initial values to zero if argument is_optional is .true.
+     axn = 0
+     ayn = 0
+     bxn = 0
+     byn = 0
+     fl_k = 0
+     mass_of_bits = 0
+     mass_of_fl_bits = 0
+     mass_of_fl_bergy_bits = 0
+     heat_density = 0
+     static_berg = 0
+
      if (replace_iceberg_num) then
        call error_mesg('read_restart_bergs', "Calculating new iceberg ID's", WARNING)
        allocate(iceberg_num(nbergs_in_file))
@@ -738,51 +809,56 @@ subroutine read_restart_bergs(bergs,Time)
        allocate(rot(nbergs_in_file))
      endif
 
-     call read_unlimited_axis(filename,'lon',lon,domain=grd%domain)
-     call read_unlimited_axis(filename,'lat',lat,domain=grd%domain)
-     call read_unlimited_axis(filename,'uvel',uvel,domain=grd%domain)
-     call read_unlimited_axis(filename,'vvel',vvel,domain=grd%domain)
-     call read_unlimited_axis(filename,'mass',mass,domain=grd%domain)
-     call read_real_vector(filename,'axn',axn,grd%domain,value_if_not_in_file=0.)
-     call read_real_vector(filename,'ayn',ayn,grd%domain,value_if_not_in_file=0.)
-     call read_real_vector(filename,'bxn',bxn,grd%domain,value_if_not_in_file=0.)
-     call read_real_vector(filename,'byn',byn,grd%domain,value_if_not_in_file=0.)
-     call read_unlimited_axis(filename,'thickness',thickness,domain=grd%domain)
-     call read_unlimited_axis(filename,'width',width,domain=grd%domain)
-     call read_unlimited_axis(filename,'length',length,domain=grd%domain)
-     call read_real_vector(filename,'fl_k',fl_k,grd%domain,value_if_not_in_file=0.)
-     call read_unlimited_axis(filename,'start_lon',start_lon,domain=grd%domain)
-     call read_unlimited_axis(filename,'start_lat',start_lat,domain=grd%domain)
-     call read_unlimited_axis(filename,'start_day',start_day,domain=grd%domain)
-     call read_unlimited_axis(filename,'start_mass',start_mass,domain=grd%domain)
-     call read_unlimited_axis(filename,'mass_scaling',mass_scaling,domain=grd%domain)
-     call read_real_vector(filename,'mass_of_bits',mass_of_bits,domain=grd%domain,value_if_not_in_file=0.)
-     call read_real_vector(filename,'mass_of_fl_bits',mass_of_fl_bits,domain=grd%domain,value_if_not_in_file=0.)
-     call read_real_vector(filename,'mass_of_fl_bergy_bits',mass_of_fl_bergy_bits,domain=grd%domain,value_if_not_in_file=0.)
-     call read_real_vector(filename,'heat_density',heat_density,domain=grd%domain,value_if_not_in_file=0.)
-     call read_unlimited_axis(filename,'ine',ine,domain=grd%domain)
-     call read_unlimited_axis(filename,'jne',jne,domain=grd%domain)
-     call read_unlimited_axis(filename,'start_year',start_year,domain=grd%domain)
+     call register_restart_field(fileobj,'lon',lon,dim_names_1d)
+     call register_restart_field(fileobj,'lat',lat,dim_names_1d)
+     call register_restart_field(fileobj,'uvel',uvel,dim_names_1d)
+     call register_restart_field(fileobj,'vvel',vvel,dim_names_1d)
+     call register_restart_field(fileobj,'mass',mass,dim_names_1d)
+     call register_restart_field(fileobj,'axn',axn,dim_names_1d,is_optional=.true.)
+     call register_restart_field(fileobj,'ayn',ayn,dim_names_1d,is_optional=.true.)
+     call register_restart_field(fileobj,'bxn',bxn,dim_names_1d,is_optional=.true.)
+     call register_restart_field(fileobj,'byn',byn,dim_names_1d,is_optional=.true.)
+     call register_restart_field(fileobj,'thickness',thickness,dim_names_1d)
+     call register_restart_field(fileobj,'width',width,dim_names_1d)
+     call register_restart_field(fileobj,'length',length,dim_names_1d)
+     call register_restart_field(fileobj,'fl_k',fl_k,dim_names_1d,is_optional=.true.)
+     call register_restart_field(fileobj,'start_lon',start_lon,dim_names_1d)
+     call register_restart_field(fileobj,'start_lat',start_lat,dim_names_1d)
+     call register_restart_field(fileobj,'start_day',start_day,dim_names_1d)
+     call register_restart_field(fileobj,'start_mass',start_mass,dim_names_1d)
+     call register_restart_field(fileobj,'mass_scaling',mass_scaling,dim_names_1d)
+     call register_restart_field(fileobj,'mass_of_bits',mass_of_bits,dim_names_1d,is_optional=.true.)
+     call register_restart_field(fileobj,'mass_of_fl_bits',mass_of_fl_bits,dim_names_1d,is_optional=.true.)
+     call register_restart_field(fileobj,'mass_of_fl_bergy_bits',mass_of_fl_bergy_bits,dim_names_1d,is_optional=.true.)
+     call register_restart_field(fileobj,'heat_density',heat_density,dim_names_1d,is_optional=.true.)
+     call register_restart_field(fileobj,'ine',ine,dim_names_1d)
+     call register_restart_field(fileobj,'jne',jne,dim_names_1d)
+     call register_restart_field(fileobj,'start_year',start_year,dim_names_1d)
      if (replace_iceberg_num) then
-       call read_int_vector(filename,'iceberg_num',iceberg_num,grd%domain,value_if_not_in_file=-1)
+       iceberg_num = -1
+       call register_restart_field(fileobj,'iceberg_num',iceberg_num,dim_names_1d,is_optional=.true.)
      else
-       call read_int_vector(filename,'id_cnt',id_cnt,grd%domain)
-       call read_int_vector(filename,'id_ij',id_ij,grd%domain)
+       call register_restart_field(fileobj,'id_cnt',id_cnt,dim_names_1d)
+       call register_restart_field(fileobj,'id_ij',id_ij,dim_names_1d)
      endif
-     call read_real_vector(filename,'static_berg',static_berg,grd%domain,value_if_not_in_file=0.)
+     call register_restart_field(fileobj,'static_berg',static_berg,dim_names_1d,is_optional=.true.)
 
      if (mts) then
-       call read_real_vector(filename,'axn_fast',axn_fast,grd%domain,value_if_not_in_file=0.)
-       call read_real_vector(filename,'ayn_fast',ayn_fast,grd%domain,value_if_not_in_file=0.)
-       call read_real_vector(filename,'bxn_fast',bxn_fast,grd%domain,value_if_not_in_file=0.)
-       call read_real_vector(filename,'byn_fast',byn_fast,grd%domain,value_if_not_in_file=0.)
+       axn_fast = 0; ayn_fast = 0; bxn_fast = 0; byn_fast = 0;
+       call register_restart_field(fileobj,'axn_fast',axn_fast,dim_names_1d,is_optional=.true.)
+       call register_restart_field(fileobj,'ayn_fast',ayn_fast,dim_names_1d,is_optional=.true.)
+       call register_restart_field(fileobj,'bxn_fast',bxn_fast,dim_names_1d,is_optional=.true.)
+       call register_restart_field(fileobj,'byn_fast',byn_fast,dim_names_1d,is_optional=.true.)
      endif
 
      if (dem) then
-       call read_real_vector(filename,'ang_vel'  ,ang_vel  ,grd%domain,value_if_not_in_file=0.)
-       call read_real_vector(filename,'ang_accel',ang_accel,grd%domain,value_if_not_in_file=0.)
-       call read_real_vector(filename,'rot'      ,rot      ,grd%domain,value_if_not_in_file=0.)
+       ang_vel = 0; ang_accel = 0; rot = 0;
+       call register_restart_field(fileobj,'ang_vel'  ,ang_vel  ,dim_names_1d,is_optional=.true.)
+       call register_restart_field(fileobj,'ang_accel',ang_accel,dim_names_1d,is_optional=.true.)
+       call register_restart_field(fileobj,'rot'      ,rot      ,dim_names_1d,is_optional=.true.)
      endif
+      call read_restart(fileobj)
+      call close_file(fileobj)
   elseif (bergs%require_restart) then
      stop 'read_restart_bergs, RESTART NOT FOUND!'
   endif
@@ -880,8 +956,6 @@ subroutine read_restart_bergs(bergs,Time)
        endif
 
       if (really_debug) call print_berg(stderrunit, bergs%list(localberg%ine,localberg%jne)%first, 'read_restart_bergs, add_new_berg_to_list')
-    elseif (multiPErestart .and. io_tile_id(1) .lt. 0) then
-      call error_mesg('KID, read_restart_bergs', 'berg in PE file was not on PE!', FATAL)
     endif
   enddo
 
@@ -973,36 +1047,6 @@ subroutine read_restart_bergs(bergs,Time)
 
 end subroutine read_restart_bergs
 
-!> Read a vector of reals from file and use a default value if variable is missing
-subroutine read_real_vector(filename, varname, values, domain, value_if_not_in_file)
-  character(len=*), intent(in)  :: filename !< Name of file to read from
-  character(len=*), intent(in)  :: varname !< Name of variable to read
-  real,             intent(out) :: values(:) !< Returned vector of reals
-  type(domain2D),   intent(in)  :: domain !< Parallel decomposition
-  real, optional,   intent(in)  :: value_if_not_in_file !< Value to use if variable is not in file
-
-  if (present(value_if_not_in_file).and..not.field_exist(filename, varname)) then
-    values(:)=value_if_not_in_file
-  else
-    call read_unlimited_axis(filename,varname,values,domain=domain)
-  endif
-end subroutine read_real_vector
-
-!> Read a vector of integers from file and use a default value if variable is missing
-subroutine read_int_vector(filename, varname, values, domain, value_if_not_in_file)
-  character(len=*),  intent(in)  :: filename !< Name of file to read from
-  character(len=*),  intent(in)  :: varname !< Name of variable to read
-  integer,           intent(out) :: values(:) !< Returned vector of integers
-  type(domain2D),    intent(in)  :: domain !< Parallel decomposition
-  integer, optional, intent(in)  :: value_if_not_in_file !< Value to use if variable is not in file
-
-  if (present(value_if_not_in_file).and..not.field_exist(filename, varname)) then
-    values(:)=value_if_not_in_file
-  else
-    call read_unlimited_axis(filename,varname,values,domain=domain)
-  endif
-end subroutine read_int_vector
-
 !> Generate bergs for the purpose of debugging
 subroutine generate_bergs(bergs,Time)
 ! Arguments
@@ -1150,7 +1194,6 @@ subroutine read_restart_bonds(bergs,Time)
 integer :: k, siz(4), nbonds_in_file
 logical :: lres, found_restart, found
 logical :: first_berg_found, second_berg_found
-logical :: multiPErestart  ! Not needed with new restart read; currently kept for compatibility
 real :: lon0, lon1, lat0, lat1
 character(len=53) :: filename, filename_base
 type(icebergs_gridded), pointer :: grd
@@ -1182,6 +1225,8 @@ subroutine read_restart_bonds(bergs,Time)
                                       rel_rotation
 integer(kind=8), allocatable, dimension(:) :: first_id,   &
                                               other_id
+type(FmsNetcdfDomainFile_t) :: fileobj !< Fms2_io fileobj
+character(len=1) :: dim_names_1d(1)
 !integer, allocatable, dimension(:,:) :: iceberg_counter_grd
 
   ! Get the stderr unit number
@@ -1194,14 +1239,15 @@ subroutine read_restart_bonds(bergs,Time)
   nbonds_in_file = 0
   all_pe_number_perfect_bonds=0
 
-  filename_base=trim(restart_input_dir)//'bonds_iceberg.res.nc'
+  filename=trim(restart_input_dir)//'bonds_iceberg.res.nc'
 
-  found_restart = find_restart_file(filename_base, filename, multiPErestart, io_tile_id(1))
+  found_restart = open_file(fileobj, filename, "read", bergs%grd%domain, is_restart=.true.)
   call error_mesg('read_restart_bonds_bergs_new', 'Using icebergs bond restart read', NOTE)
 
-  filename = filename_base
-  call get_field_size(filename,'i',siz, field_found=found, domain=bergs%grd%domain)
-  nbonds_in_file = siz(1)
+  if (found_restart) then
+   call get_dimension_size(fileobj,'i',siz(1))
+   nbonds_in_file = siz(1)
+  endif
 
     if (mpp_pe() .eq. mpp_root_pe()) then
       write(stderrunit,*)  'KID, bond read restart : ','Number of bonds in file',  nbonds_in_file
@@ -1226,32 +1272,35 @@ subroutine read_restart_bonds(bergs,Time)
       allocate(rel_rotation(nbonds_in_file))
       allocate(broken(nbonds_in_file))
     endif
-
-    call read_unlimited_axis(filename,'first_id_cnt',id_cnt,domain=grd%domain)
-    call read_unlimited_axis(filename,'first_id_ij',id_ij,domain=grd%domain)
+    dim_names_1d = "i"
+    call register_restart_field(fileobj,'first_id_cnt',id_cnt,dim_names_1d)
+    call register_restart_field(fileobj,'first_id_ij',id_ij,dim_names_1d)
     do k=1, nbonds_in_file
       first_id(k) = id_from_2_ints( id_cnt(k), id_ij(k) )
     enddo
-    call read_unlimited_axis(filename,'other_id_cnt',id_cnt,domain=grd%domain)
-    call read_unlimited_axis(filename,'other_id_ij',id_ij,domain=grd%domain)
+    call register_restart_field(fileobj,'other_id_cnt',id_cnt,dim_names_1d)
+    call register_restart_field(fileobj,'other_id_ij',id_ij,dim_names_1d)
     do k=1, nbonds_in_file
       other_id(k) = id_from_2_ints( id_cnt(k), id_ij(k) )
     enddo
     deallocate(id_cnt, id_ij)
-    call read_unlimited_axis(filename,'first_berg_jne',first_berg_jne,domain=grd%domain)
-    call read_unlimited_axis(filename,'first_berg_ine',first_berg_ine,domain=grd%domain)
-    call read_unlimited_axis(filename,'other_berg_jne',other_berg_jne,domain=grd%domain)
-    call read_unlimited_axis(filename,'other_berg_ine',other_berg_ine,domain=grd%domain)
+    call register_restart_field(fileobj,'first_berg_jne',first_berg_jne,dim_names_1d)
+    call register_restart_field(fileobj,'first_berg_ine',first_berg_ine,dim_names_1d)
+    call register_restart_field(fileobj,'other_berg_jne',other_berg_jne,dim_names_1d)
+    call register_restart_field(fileobj,'other_berg_ine',other_berg_ine,dim_names_1d)
 
     if (dem) then
-      call read_real_vector(filename,'tangd1',tangd1,grd%domain,value_if_not_in_file=0.)
-      call read_real_vector(filename,'tangd2',tangd2,grd%domain,value_if_not_in_file=0.)
-      call read_real_vector(filename,'nstress',nstress,grd%domain,value_if_not_in_file=0.)
-      call read_real_vector(filename,'sstress',sstress,grd%domain,value_if_not_in_file=0.)
-      call read_real_vector(filename,'rel_rotation',rel_rotation,grd%domain,value_if_not_in_file=0.)
-      call read_int_vector(filename,'broken',broken,grd%domain,value_if_not_in_file=0)
+      tangd1 = 0; tangd2 = 0; nstress = 0; sstress = 0; rel_rotation = 0; broken = 0;
+      call register_restart_field(fileobj,'tangd1',tangd1,dim_names_1d,is_optional=.true.)
+      call register_restart_field(fileobj,'tangd2',tangd2,dim_names_1d,is_optional=.true.)
+      call register_restart_field(fileobj,'nstress',nstress,dim_names_1d,is_optional=.true.)
+      call register_restart_field(fileobj,'sstress',sstress,dim_names_1d,is_optional=.true.)
+      call register_restart_field(fileobj,'rel_rotation',rel_rotation,dim_names_1d,is_optional=.true.)
+      call register_restart_field(fileobj,'broken',broken,dim_names_1d,is_optional=.true.)
     endif
 
+    call read_restart(fileobj)
+    call close_file(fileobj)
     number_first_bonds_matched=0
     number_second_bonds_matched=0
     number_perfect_bonds=0
@@ -1441,53 +1490,56 @@ subroutine read_restart_calving(bergs)
 type(icebergs_gridded), pointer :: grd
 real, allocatable, dimension(:,:) :: randnum
 type(randomNumberStream) :: rns
+type(FmsNetcdfDomainFile_t) :: fileobj !< Fms2_io fileobj
 
   ! For convenience
   grd=>bergs%grd
 
   ! Read stored ice
   filename=trim(restart_input_dir)//'calving.res.nc'
-  if (file_exist(filename)) then
+  if (open_file(fileobj, filename, "read", grd%domain)) then
+    call register_axis_wrapper(fileobj)
     if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') &
      'KID, read_restart_calving: reading ',filename
-    call read_data(filename, 'stored_ice', grd%stored_ice, grd%domain)
-    if (field_exist(filename, 'stored_heat')) then
+    call read_data(fileobj, 'stored_ice', grd%stored_ice)
+    if (variable_exists(fileobj, 'stored_heat')) then
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
        'KID, read_restart_calving: reading stored_heat from restart file.'
-      call read_data(filename, 'stored_heat', grd%stored_heat, grd%domain)
+      call read_data(fileobj, 'stored_heat', grd%stored_heat)
     else
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
      'KID, read_restart_calving: stored_heat WAS NOT FOUND in the file. Setting to 0.'
       grd%stored_heat(:,:)=0.
     endif
-    if (field_exist(filename, 'rmean_calving')) then
+    if (variable_exists(fileobj,'rmean_calving')) then
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
        'KID, read_restart_calving: reading rmean_calving from restart file.'
-      call read_data(filename, 'rmean_calving', grd%rmean_calving, grd%domain)
+      call read_data(fileobj, 'rmean_calving', grd%rmean_calving)
       grd%rmean_calving_initialized=.true.
     else
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
      'KID, read_restart_calving: rmean_calving WAS NOT FOUND in the file. Setting to 0.'
     endif
-    if (field_exist(filename, 'rmean_calving_hflx')) then
+    if (variable_exists(fileobj, 'rmean_calving_hflx')) then
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
        'KID, read_restart_calving: reading rmean_calving_hflx from restart file.'
-      call read_data(filename, 'rmean_calving_hflx', grd%rmean_calving_hflx, grd%domain)
+      call read_data(fileobj, 'rmean_calving_hflx', grd%rmean_calving_hflx)
       grd%rmean_calving_hflx_initialized=.true.
     else
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
      'KID, read_restart_calving: rmean_calving_hflx WAS NOT FOUND in the file. Setting to 0.'
     endif
-    if (field_exist(filename, 'iceberg_counter_grd')) then
+    if (variable_exists(fileobj, 'iceberg_counter_grd')) then
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
        'KID, read_restart_calving: reading iceberg_counter_grd from restart file.'
-      call read_data(filename, 'iceberg_counter_grd', grd%iceberg_counter_grd, grd%domain)
+      call read_data(fileobj, 'iceberg_counter_grd', grd%iceberg_counter_grd)
     else
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
      'KID, read_restart_calving: iceberg_counter_grd WAS NOT FOUND in the file. Setting to 0.'
       grd%iceberg_counter_grd(:,:) = 0
     endif
     bergs%restarted=.true.
+    call close_file(fileobj)
   else
     if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
      'KID, read_restart_calving: initializing stored ice to random numbers'
@@ -1547,21 +1599,23 @@ subroutine read_ocean_depth(grd)
 type(icebergs_gridded), pointer :: grd !< Container for gridded fields
 ! Local variables
 character(len=37) :: filename
-
+type(FmsNetcdfDomainFile_t) :: fileobj !< Fms2_io fileobj
   ! Read stored ice
   filename=trim(restart_input_dir)//'topog.nc'
-  if (file_exist(filename)) then
+  if (open_file(fileobj, filename, "read", grd%domain)) then
     if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') &
      'KID, read_ocean_depth: reading ',filename
-    if (field_exist(filename, 'depth')) then
+    call register_axis_wrapper(fileobj)
+    if (variable_exists(fileobj, "depth")) then
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
        'KID, read_ocean_depth: reading depth from topog file.'
-      call read_data(filename, 'depth', grd%ocean_depth, grd%domain)
+      call read_data(fileobj, 'depth', grd%ocean_depth)
     else
       if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
      'KID, read_ocean_depth: depth WAS NOT FOUND in the file. Setting to 0.'
       !grd%ocean_depth(:,:)=0.
     endif
+    call close_file(fileobj)
   else
     if (mpp_pe().eq.mpp_root_pe()) write(*,'(a)') &
      'KID, read_ocean_depth: Ocean depth file (topog.nc) not present)'
@@ -2451,46 +2505,262 @@ subroutine put_int(ncid, id, i, val)
 
 end subroutine put_int
 
-!> True is a restart file can be found
-logical function find_restart_file(filename, actual_file, multiPErestart, tile_id)
-  character(len=*), intent(in) :: filename !< Base-name of restart file
-  character(len=*), intent(out) :: actual_file !< Actual name of file, if found
-  logical, intent(out) :: multiPErestart !< True if found, false otherwise
-  integer, intent(in) :: tile_id !< Parallel tile number of file
-
-  character(len=6) :: pe_name
+!> Wrapper for fms_io register_restart_field
+subroutine register_restart_field_wrap_1d(fileobj, varname, vdata, dimensions, &
+                                          longname, units, is_domain_decomposed)
+  type(FmsNetcdfDomainFile_t), intent(inout) :: fileobj              !< Fms2_io fileobj
+  character(len=*),            intent(in)    :: varname              !< Name of the variable
+  class(*),                    intent(in)    :: vdata(:)             !< Variable data
+  character(len=*),            intent(in)    :: dimensions(:)        !< Names of variable dimensions
+  character(len=*),            intent(in)    :: longname             !< Longname of the variable
+  character(len=*),            intent(in)    :: units                !< Units of the variable
+  logical, optional,           intent(in)    :: is_domain_decomposed !< .True. if the variable is
+                                                                     !! domain decomposed
+
+  integer(8)           :: chksum_val !< Calculated checksum
+  integer, allocatable :: all_pe(:)  !< List of pes in the current pelist
+  character(len=32)    :: chksum     !< Checksum as a character
+  logical              :: do_chksum  !< .True. if it is needed to write checksums
+
+  call register_restart_field(fileobj, varname, vdata, dimensions)
+
+  do_chksum = .true.
+  if (present(is_domain_decomposed)) then
+    do_chksum = .not. is_domain_decomposed
+  endif
 
-  find_restart_file = .false.
+  !! The checksum for domain decomposed variables is calculated inside the `write_restart` call
+  if (do_chksum) then
+    allocate(all_pe(mpp_npes()))
+    call mpp_get_current_pelist(all_pe)
 
-  ! If running as ensemble, add the ensemble id string to the filename
-  call get_instance_filename(filename, actual_file)
+    select type (vdata)
+    type is (real)
+      chksum_val = mpp_chksum(vdata, all_pe)
+    type is (integer)
+      chksum_val = mpp_chksum(vdata, all_pe)
+      call register_variable_attribute(fileobj, varname, "packing", int(0))
+    end select
 
-  ! Prefer combined restart files.
-  inquire(file=actual_file,exist=find_restart_file)
-  if (find_restart_file) return
+    chksum = ""
+    write(chksum, "(Z16)") chksum_val
 
-  ! Uncombined restart
-  if(tile_id .ge. 0) then
-    write(actual_file,'(A,".",I4.4)') trim(actual_file), tile_id
+    call add_variable_metadata(fileobj, varname, longname, units, chksum=chksum)
   else
-  if (mpp_npes()>10000) then
-     write(pe_name,'(a,i6.6)' )'.', mpp_pe()
+    call add_variable_metadata(fileobj, varname, longname, units)
+  endif
+
+end subroutine register_restart_field_wrap_1d
+
+!> Wrapper for fms_io register_restart_field
+subroutine register_restart_field_wrap_2d(fileobj, varname, vdata, dimensions, &
+                                          longname, units, is_domain_decomposed)
+  type(FmsNetcdfDomainFile_t), intent(inout) :: fileobj              !< Fms2_io fileobj
+  character(len=*),            intent(in)    :: varname              !< Name of the variable
+  class(*),                    intent(in)    :: vdata(:,:)           !< Variable data
+  character(len=*),            intent(in)    :: dimensions(:)        !< Names of variable dimensions
+  character(len=*),            intent(in)    :: longname             !< Longname of the variable
+  character(len=*),            intent(in)    :: units                !< Units of the variable
+  logical, optional,           intent(in)    :: is_domain_decomposed !< .True. if the variable is
+                                                                     !! domain decomposed
+
+  integer(8)           :: chksum_val !< Calculated checksum
+  integer, allocatable :: all_pe(:)  !< List of pes in the current pelist
+  character(len=32)    :: chksum     !< Checksum as a character
+  logical              :: do_chksum  !< .True. if it is needed to write checksums
+
+  call register_restart_field(fileobj, varname, vdata, dimensions)
+
+  do_chksum = .true.
+  if (present(is_domain_decomposed)) then
+    do_chksum = .not. is_domain_decomposed
+  endif
+
+  !! The checksum for domain decomposed variables is calculated inside the `write_restart` call
+  if (do_chksum) then
+    allocate(all_pe(mpp_npes()))
+    call mpp_get_current_pelist(all_pe)
+
+    select type (vdata)
+    type is (real)
+      chksum_val = mpp_chksum(vdata, all_pe)
+    type is (integer)
+      chksum_val = mpp_chksum(vdata, all_pe)
+      call register_variable_attribute(fileobj, varname, "packing", int(0))
+    end select
+
+    chksum = ""
+    write(chksum, "(Z16)") chksum_val
+
+    call add_variable_metadata(fileobj, varname, longname, units, chksum=chksum)
   else
-     write(pe_name,'(a,i4.4)' )'.', mpp_pe()
+    call add_variable_metadata(fileobj, varname, longname, units)
   endif
-  actual_file=trim(actual_file)//trim(pe_name)
+
+end subroutine register_restart_field_wrap_2d
+
+!> Wrapper for fms_io register_restart_field
+subroutine register_restart_field_wrap_3d(fileobj, varname, vdata, dimensions, &
+                                          longname, units, is_domain_decomposed)
+  type(FmsNetcdfDomainFile_t), intent(inout) :: fileobj              !< Fms2_io fileobj
+  character(len=*),            intent(in)    :: varname              !< Name of the variable
+  class(*),                    intent(in)    :: vdata(:,:,:)         !< Variable data
+  character(len=*),            intent(in)    :: dimensions(:)        !< Names of variable dimensions
+  character(len=*),            intent(in)    :: longname             !< Longname of the variable
+  character(len=*),            intent(in)    :: units                !< Units of the variable
+  logical, optional,           intent(in)    :: is_domain_decomposed !< .True. if the variable is
+                                                                     !! domain decomposed
+
+  integer(8)           :: chksum_val !< Calculated checksum
+  integer, allocatable :: all_pe(:)  !< List of pes in the current pelist
+  character(len=32)    :: chksum     !< Checksum as a character
+  logical              :: do_chksum  !< .True. if it is needed to write checksums
+
+  call register_restart_field(fileobj, varname, vdata, dimensions)
+
+  do_chksum = .true.
+  if (present(is_domain_decomposed)) then
+    do_chksum = .not. is_domain_decomposed
   endif
-  inquire(file=actual_file,exist=find_restart_file)
-  if (find_restart_file) then
-     multiPErestart=.true.
-     return
+
+  !! The checksum for domain decomposed variables is calculated inside the `write_restart` call
+  if (do_chksum) then
+    allocate(all_pe(mpp_npes()))
+    call mpp_get_current_pelist(all_pe)
+
+    select type (vdata)
+    type is (real)
+      chksum_val = mpp_chksum(vdata, all_pe)
+    type is (integer)
+      chksum_val = mpp_chksum(vdata, all_pe)
+      call register_variable_attribute(fileobj, varname, "packing", int(0))
+    end select
+
+    chksum = ""
+    write(chksum, "(Z16)") chksum_val
+
+    call add_variable_metadata(fileobj, varname, longname, units, chksum=chksum)
+  else
+    call add_variable_metadata(fileobj, varname, longname, units)
+  endif
+end subroutine register_restart_field_wrap_3d
+
+!> Writes out some variable meta_data
+subroutine add_variable_metadata(fileobj, varname, longname, units, chksum)
+  type(FmsNetcdfDomainFile_t), intent(inout)          :: fileobj   !< Fms2_io fileobj
+  character(len=*),            intent(in)             :: varname   !< Name of the variable
+  character(len=*),            intent(in)             :: longname  !< Longname of the variable
+  character(len=*),            intent(in)             :: units     !< Units of the variable
+  character(len=*),            intent(in),  optional  :: chksum    !< Checksum as a character
+
+  call register_variable_attribute(fileobj, varname, "long_name", trim(longname), &
+                                   str_len=len_trim(longname))
+  call register_variable_attribute(fileobj, varname, "units", trim(units), &
+                                   str_len=len_trim(units))
+  if (present(chksum)) then
+    call register_variable_attribute(fileobj, varname, "checksum", chksum, str_len=32)
   endif
+end subroutine add_variable_metadata
+
+!> Writes out the dummy axis_data
+subroutine write_axis_data(fileobj, z_size)
+  type(FmsNetcdfDomainFile_t), intent(inout)          :: fileobj   !< Fms2_io fileobj
+  integer,                     intent(in)             :: z_size    !< Size of the z dimension
+
+  integer, dimension(:), allocatable :: buffer !< Buffer with axis data
+  integer :: is, ie !< Starting and Ending indices for data
+  integer :: i !< For do loops
+
+  call get_global_io_domain_indices(fileobj, "xaxis_1", is, ie, indices=buffer)
+  call write_data(fileobj, "xaxis_1", buffer)
+  deallocate(buffer)
+
+  call get_global_io_domain_indices(fileobj, "yaxis_1", is, ie, indices=buffer)
+  call write_data(fileobj, "yaxis_1", buffer)
+  deallocate(buffer)
+
+  allocate(buffer(z_size))
+  buffer = (/ (i, i=1,z_size)/)
+  call write_data(fileobj, "zaxis_1", buffer)
+
+  call write_data(fileobj, "Time", 1)
+
+end subroutine write_axis_data
+
+!> Writes out the dummy axis_metadata
+subroutine write_axis_metadata(fileobj)
+  type(FmsNetcdfDomainFile_t), intent(inout)          :: fileobj   !< Fms2_io fileobj
+
+  !< Register the dimensions as variables too
+  call register_field(fileobj, "xaxis_1", "double", (/"xaxis_1"/))
+  call register_field(fileobj, "yaxis_1", "double", (/"yaxis_1"/))
+  call register_field(fileobj, "zaxis_1", "double", (/"zaxis_1"/))
+  call register_field(fileobj, "Time", "double", (/"Time"/))
+
+  call register_variable_attribute(fileobj, "xaxis_1", "long_name", "xaxis_1", str_len=7)
+  call register_variable_attribute(fileobj, "xaxis_1", "cartesian_axis", "X", str_len=1)
+  call register_variable_attribute(fileobj, "xaxis_1", "units", "none", str_len=4)
+
+  call register_variable_attribute(fileobj, "yaxis_1", "long_name", "yaxis_1", str_len=7)
+  call register_variable_attribute(fileobj, "yaxis_1", "cartesian_axis", "Y", str_len=1)
+  call register_variable_attribute(fileobj, "yaxis_1", "units", "none", str_len=4)
+
+  call register_variable_attribute(fileobj, "zaxis_1", "long_name", "zaxis_1", str_len=7)
+  call register_variable_attribute(fileobj, "zaxis_1", "cartesian_axis", "Z", str_len=1)
+  call register_variable_attribute(fileobj, "zaxis_1", "units", "none", str_len=4)
+
+  call register_variable_attribute(fileobj, "Time", "long_name", "Time", str_len=4)
+  call register_variable_attribute(fileobj, "Time", "cartesian_axis", "T", str_len=1)
+  call register_variable_attribute(fileobj, "Time", "units", "time level", str_len=10)
+
+end subroutine
+
+!> Wrapper for fms2_io register_axis calls when reading domain decomposed files
+subroutine register_axis_wrapper(fileobj)
+  type(FmsNetcdfDomainFile_t), intent(inout)          :: fileobj   !< Fms2_io fileobj
+
+    character(len=20), dimension(:), allocatable :: file_dim_names !< Array of dimension names
+    integer :: i                    !< For do loops
+    integer :: dim_size             !< Size of the dimension
+    integer :: ndims                !< Number of dimensions in the file
+    logical :: is_domain_decomposed !< Flag indication if domain decomposed
+    character(len=1) :: buffer      !< string buffer
+
+    ndims = get_num_dimensions(fileobj)
+    allocate(file_dim_names(ndims))
+
+    call get_dimension_names(fileobj, file_dim_names)
+
+    !< When reading fms2_io requires that the domain decomposed dimensions ("x" and "y") are
+    !! registered so that fms2_io knows that they are domain decomposed
+    do i = 1, ndims
+       is_domain_decomposed = .false.
+
+       !< Check if the dimension is also a variable
+       if (variable_exists(fileobj, file_dim_names(i))) then
+
+          !< If the variable exists look for the "cartesian_axis" or "axis" variable attribute
+          if (variable_att_exists(fileobj, file_dim_names(i), "axis")) then
+              call get_variable_attribute(fileobj, file_dim_names(i), "axis", buffer)
+
+              !< If the attribute exists and it is "x" or "y" register it as a domain decomposed dimension
+              if (lowercase(buffer) .eq. "x" .or. lowercase(buffer) .eq. "y" ) then
+                  is_domain_decomposed = .true.
+                  call register_axis(fileobj, file_dim_names(i), buffer)
+              endif
+
+          else if (variable_att_exists(fileobj, file_dim_names(i), "cartesian_axis")) then
+              call get_variable_attribute(fileobj, file_dim_names(i), "cartesian_axis", buffer)
 
-  ! No file found, Reset all return parameters
-  find_restart_file=.false.
-  actual_file = ''
-  multiPErestart=.false.
+              !< If the attribute exists and it "x" or "y" register it as a domain decomposed dimension
+              if (lowercase(buffer) .eq. "x" .or. lowercase(buffer) .eq. "y" ) then
+                  is_domain_decomposed = .true.
+                  call register_axis(fileobj, file_dim_names(i), buffer)
+              endif
 
-end function find_restart_file
+          endif !< If variable attribute exists
+       endif !< If variable exists
+   enddo
+end subroutine register_axis_wrapper
 
 end module

From 2b7865308a826b5ea2d65d73a83629e0db215c3f Mon Sep 17 00:00:00 2001
From: Uriel Ramirez <uriel.ramirez@noaa.gov>
Date: Fri, 24 Mar 2023 09:09:09 -0400
Subject: [PATCH 352/361] attempt to fix the doxygen ci

---
 src/icebergs_fms2io.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/icebergs_fms2io.F90 b/src/icebergs_fms2io.F90
index 40e78b8..2d785f9 100644
--- a/src/icebergs_fms2io.F90
+++ b/src/icebergs_fms2io.F90
@@ -2691,7 +2691,7 @@ end subroutine write_axis_data
 subroutine write_axis_metadata(fileobj)
   type(FmsNetcdfDomainFile_t), intent(inout)          :: fileobj   !< Fms2_io fileobj
 
-  !< Register the dimensions as variables too
+  ! Register the dimensions as variables too
   call register_field(fileobj, "xaxis_1", "double", (/"xaxis_1"/))
   call register_field(fileobj, "yaxis_1", "double", (/"yaxis_1"/))
   call register_field(fileobj, "zaxis_1", "double", (/"zaxis_1"/))

From c29245058e8b9f7a1ef771d8c09cc4774814d7e6 Mon Sep 17 00:00:00 2001
From: Uriel Ramirez <uriel.ramirez@noaa.gov>
Date: Mon, 27 Mar 2023 12:30:18 -0400
Subject: [PATCH 353/361] fix for ensemble runs

---
 src/icebergs_fms2io.F90 | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/icebergs_fms2io.F90 b/src/icebergs_fms2io.F90
index 2d785f9..56c1b2d 100644
--- a/src/icebergs_fms2io.F90
+++ b/src/icebergs_fms2io.F90
@@ -1497,7 +1497,9 @@ subroutine read_restart_calving(bergs)
 
   ! Read stored ice
   filename=trim(restart_input_dir)//'calving.res.nc'
-  if (open_file(fileobj, filename, "read", grd%domain)) then
+  ! The call to get_instance_filename is required because this is not read in as a restart file
+  call get_instance_filename(filename, actual_filename)
+  if (open_file(fileobj, actual_filename, "read", grd%domain)) then
     call register_axis_wrapper(fileobj)
     if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') &
      'KID, read_restart_calving: reading ',filename

From c17de023d3e6035e1d4766e183f86d5897f99468 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Mon, 26 Jun 2023 15:18:23 -0400
Subject: [PATCH 354/361] Patched FMS2-branch to work with FMS1

- Added missing #ifdef to avoid compilation errors when using an older FMS
- Changed "use_deprecated_io" to "USE_FMS2_IO"
  - The word "deprecated" has a limited lifetime (consider what to use when
    FMS2 is replaced).
  - Backwards compatibility requires that no macros are needed to use
    FMS1. That is, the new stuff can use -DUSE_FMS2_IO but the old stuff
    should not be require any changes.
---
 src/icebergs_fms2io.F90 | 2 ++
 src/icebergs_fmsio.F90  | 4 +++-
 src/icebergs_io.F90     | 2 +-
 3 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/icebergs_fms2io.F90 b/src/icebergs_fms2io.F90
index 56c1b2d..cd3bbe0 100644
--- a/src/icebergs_fms2io.F90
+++ b/src/icebergs_fms2io.F90
@@ -1,5 +1,6 @@
 !> Handles reading/writing of restart files and trajectory-based diagnostic files
 module ice_bergs_fms2io
+#ifdef USE_FMS2_IO
 
 ! This file is part of NOAA-GFDL/icebergs. See LICENSE.md for the license.
 
@@ -2765,4 +2766,5 @@ subroutine register_axis_wrapper(fileobj)
    enddo
 end subroutine register_axis_wrapper
 
+#endif
 end module
diff --git a/src/icebergs_fmsio.F90 b/src/icebergs_fmsio.F90
index 479e59c..38b320d 100644
--- a/src/icebergs_fmsio.F90
+++ b/src/icebergs_fmsio.F90
@@ -1,6 +1,7 @@
 !> Handles reading/writing of restart files and trajectory-based diagnostic files
 module ice_bergs_fmsio
-#ifdef use_depreciated_io
+#ifndef USE_FMS2_IO
+
 ! This file is part of NOAA-GFDL/icebergs. See LICENSE.md for the license.
 
 use mpp_domains_mod, only: domain2D
@@ -2492,5 +2493,6 @@ logical function find_restart_file(filename, actual_file, multiPErestart, tile_i
   multiPErestart=.false.
 
 end function find_restart_file
+
 #endif
 end module
diff --git a/src/icebergs_io.F90 b/src/icebergs_io.F90
index 28fb88a..1049f0b 100644
--- a/src/icebergs_io.F90
+++ b/src/icebergs_io.F90
@@ -2,7 +2,7 @@
 module ice_bergs_io
 ! This file is part of NOAA-GFDL/icebergs. See LICENSE.md for the license.
 
-#ifdef use_depreciated_io
+#ifndef USE_FMS2_IO
   use ice_bergs_fmsio
 #else
   use ice_bergs_fms2io

From 16c6772c88ab216a52b4a390dc8a8033c8798857 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Tue, 27 Jun 2023 17:07:57 -0400
Subject: [PATCH 355/361] Added build file for fms2. Added missing input.nml
 for the footloose test. Slight fix to icebergs_driver where mpp_exit was
 called too early.

---
 build/README.md                  |  21 +---
 build/mkmkf_fms2                 |   3 +
 driver/icebergs_driver.F90       |   4 +-
 tests/footloose_tests/.gitignore |   1 -
 tests/footloose_tests/input.nml  | 171 +++++++++++++++++++++++++++++++
 5 files changed, 181 insertions(+), 19 deletions(-)
 create mode 100644 build/mkmkf_fms2
 create mode 100644 tests/footloose_tests/input.nml

diff --git a/build/README.md b/build/README.md
index c3f26c4..1ae7745 100644
--- a/build/README.md
+++ b/build/README.md
@@ -1,23 +1,12 @@
-To create list of files to compile:
-
-
-#rm -f path_names
-
+To create a `Makefile` (for FMS2):
 ```
-../../mkmf/bin/list_paths ../../FMS/{mpp,diag_manager,time_manager,include,memutils,constants,platform,fms,random_numbers,mosaic,exchange} ../src/ ../driver/
+source mkmkf_fms2
 ```
-To create a `Makefile`:
+Or for FMS1:
 ```
-../../mkmf/bin/mkmf -t ../../mkmf/templates/ncrc-gnu.mk -c "-Duse_libMPI -Duse_netCDF" -p bergs.x path_names
-
-
-##../../mkmf/bin/mkmf -t ../../mkmf/templates/ncrc-intel.mk -c "-Duse_libMPI -Duse_netCDF" -p bergs.x path_names
+mkmkf
 ```
-To compile a "debug" executable:
+Then, to compile a "debug" executable:
 ```
-make DEBUG=1 -j
-#or
 source mkcmd
-#source mkcmd runs the following:
-#make NETCDF=3 DEBUG=1 bergs.x -j
 ```
diff --git a/build/mkmkf_fms2 b/build/mkmkf_fms2
new file mode 100644
index 0000000..84932e2
--- /dev/null
+++ b/build/mkmkf_fms2
@@ -0,0 +1,3 @@
+rm -f path_names
+../../mkmf/bin/list_paths  ../src/ ../driver/
+../../mkmf/bin/mkmf -t ../../mkmf/templates/ncrc-intel.mk -c "-Duse_libMPI -Duse_netCDF -Duse_fms2_io -I../../../build/fms2" -p bergs.x -l '-L../../../build/fms2 -lfms' path_names
\ No newline at end of file
diff --git a/driver/icebergs_driver.F90 b/driver/icebergs_driver.F90
index 787dd80..125f3b8 100644
--- a/driver/icebergs_driver.F90
+++ b/driver/icebergs_driver.F90
@@ -440,9 +440,9 @@ program icebergs_driver
   write(*,*) 'Simulation finished in ', (time_finish - time_begin)/60., 'minutes'
 end if
 
-call mpp_exit()
-
 !Deallocate all memory and disassociated pointer
 call icebergs_end(bergs)
 
+call mpp_exit()
+
 end program icebergs_driver
diff --git a/tests/footloose_tests/.gitignore b/tests/footloose_tests/.gitignore
index 3ca2294..e69de29 100644
--- a/tests/footloose_tests/.gitignore
+++ b/tests/footloose_tests/.gitignore
@@ -1 +0,0 @@
-input.nml
\ No newline at end of file
diff --git a/tests/footloose_tests/input.nml b/tests/footloose_tests/input.nml
new file mode 100644
index 0000000..452cbf5
--- /dev/null
+++ b/tests/footloose_tests/input.nml
@@ -0,0 +1,171 @@
+!!KID, bergs_chksum: write_restart berg chksum=-330632313 chksum2=-330632313 chksum3=-1023714556 chksum4=-1023714556 chksum5=0 #=12
+
+
+&icebergs_driver_nml
+  ni=20 !number of elements, x direction
+  nj=20 !number of elements, y direction
+  ibdt=10.0 !1800.0 !86400.0 !seconds
+  ibuo=1.0 !ocean x velocity
+  ibvo=0.1 !ocean y velocity
+  ibui=0.0 !ice x velocity
+  ibvi=0.0 !ice y velocity
+  ibua=-1.0 !wind x velocity
+  ibuy=0.0  !wind y velocity
+  ibhrs=192 !total simulation hours
+  nmax=99999999 !max number of timesteps
+  saverestart=.true.
+  halo=3
+  debug=.false.
+  gridres=1000.
+  sst=-0.5
+  fl_test=.true.
+/
+
+
+&icebergs_nml
+
+    traj_name=FL_physical.nc
+    bond_traj_name=FL_physical_bonds.nc
+
+    !defaults given in parentheses:
+    footloose=.true. !(F) Turn footloose calving on/off
+    displace_fl_bergs=.true. !(T) randomly assign FL berg positions to sides of parent berg
+    fl_style='fl_bits' !'fl_bits' !('new_bergs'). Can also group FL bergs into 'fl_bits'
+    fl_youngs=1.e8 !Young's modulus for footloose calculations (Pa)
+    fl_strength=250. !yield stress for footloose calculations (kPa)
+    new_berg_from_fl_bits_mass_thres=3.e11  !Create a new berg from FL bits when mass_of_fl_bits exceeds this value
+    fl_init_child_xy_by_pe=.false. !(F) True: position of a new footloose child berg along the parent perimeter is random, yet constant for each PE (old bug). False: fully-random.
+
+    mts=.false. !(F) for using the Multiple Time Stepping Velocity Verlet scheme
+    mts_sub_steps=1 !(-1) # of mts sub-steps (-1=automatically determine # from spring const)
+    !contact_distance=0 !3.e3 !(0) unbonded bergs contact at max(contact_dist,sum of their radii)
+    !contact_spring_coef=1.e-5!(default=spring_coeff) Berg spring coeff for collisions
+
+    halo=3 !(4) halo width
+    Lx=20000. ! (360.) Length of X-domain. For periodicity (use a huge number for non-periodic)
+    grid_is_latlon=.false. !(T) 'T'=lat/lon grid, uses earth radius to convert to distance
+    grid_is_regular=.True. !(T) Point in cell can be found assuming regular Cartesian grid
+    !hexagonal_icebergs=.True. !(F)'T'=bergs are rectangles,'F'=bergs are hex (for mass spread)
+    Static_icebergs=.False. ! (T) True=icebergs do no move
+
+    rho_bergs=850. ! (850) iceberg density
+    spring_coef=1.e-5 !(1.e-8) Spring const for berg interactions (dflt~highest stable value)
+    bond_coef=1.e-8 ! (1.e-8) Spring const for berg bonds - not being used right now
+    radial_damping_coef=1.e-4 ! (1.e-4) Coeff for rel berg motion damping (radial component)
+    tangental_damping_coef=2.e-5 !(2.e-5) Coeff for rel berg motion damping (tangential comp.)
+    critical_interaction_damping_on=.true. !(T) Sets damping on rel berg vel to crit val
+    LoW_ratio=1.5 ! (1.5) Initial ratio L/W for newly calved icebergs
+    bergy_bit_erosion_fraction=1.0 ! (0.) Fraction of erosion melt flux to divert to bergy bits
+    sicn_shift=0. ! (0) Shift of sea-ice concent. in erosion flux modulation (0<sicn_shift<1)
+    u_override=0.0 ! (0) Overrides the u velocity of icebergs (for ocean testing)
+    v_override=0.0 ! (0) Overrides the v velocity of icebergs (for ocean testing)
+    initial_orientation=-0. !(0)berg orient. rel. to this angle (degrees). for hex. mass spread.
+    utide_icebergs=0. ! (0.) Tidal speeds, set to zero for now.
+    ustar_icebergs_bg=0.0 !(0.001)Bckgrnd u_star under bergs.Should relate to ocean boundlayr
+    cdrag_icebergs = 1.5e-3 ! (1.5e-3) Momentum Drag coef, taken from Holland and Jenkins 1999
+    Gamma_T_3EQ=0.022 ! (0.022) Non-dimensional heat-transfer coefficient
+    const_gamma=.false. ! (T) 'T' = constant heat transfer coeff, used to calc salt transfer
+    use_operator_splitting=.true. ! (T) Use 1st order operator splitting for thermodynamics
+    add_weight_to_ocean=.false. ! (T) Add weight of icebergs + bits to ocean
+    passive_mode=.true. ! (F) Add weight of icebergs + bits to ocean
+    time_average_weight=.false. ! (F) Time average the weight on the ocean
+    speed_limit=0. ! (0.) CFL speed limit for a berg
+    tau_calving=0. ! (0.) Time scale (yrs) for smoothing out calving field
+    tip_parameter=0. !(0.)For override berg rolling crit ratio (0.=get param from rhoi&rhoo)
+    grounding_fraction=0. ! (0.) Fraction of water column depth at which grounding occurs
+    coastal_drift=0.0 !4 !(0.)Vel added to currents to cause bergs to drift away from land cells
+    tidal_drift=0. !(0.)Amp of stoch. tidal vel added to currents to cause random berg drift
+    Runge_not_Verlet=.false. !(T) True=Runge Kutta, False=Verlet.
+    use_mixed_melting=.false.!(F) 'T' partly determ. melt frm 3eq model(uses BergParams&Bond #)
+    apply_thickness_cutoff_to_gridded_melt=.true.!(F)Prevnt melt for Ho < melt_cuttoff on grid
+    apply_thickness_cutoff_to_bergs_melt=.true. !(F)Prevnt melt for Ho < melt_cuttoff on bergs
+    melt_cutoff=10.0 ! (-1.0) Min ocean thickness for melting to occur (no apply for vals < 0)
+    allow_bergs_to_roll=.true. !.true. ! (T) Allows bergs toroll over when rolling conditions are met
+    use_updated_rolling_scheme=.true. !(F) Use corrected Rolling Scheme
+    pass_fields_to_ocean_model=.False. !(F) Prep berg area,mass,ustar  to pass to ocean model
+    use_mixed_layer_salinity_for_thermo=.False.!(F)'T'=use ocean salinity in 3&2 eq. melt model
+    find_melt_using_spread_mass=.False. !(F)'T'=calc ice mass loss before & after spread_mass
+    Use_three_equation_model=.false. !(T)If using iceshelf-type thermodyn, use 3 eq. melt model
+    melt_icebergs_as_ice_shelf=.False. ! (F)  Uses iceshelf type thermodynamics
+    Iceberg_melt_without_decay=.False. !(F)Berg melt flx to ocean w/out berg decay/shape change
+    add_iceberg_thickness_to_SSH=.False. ! (F) Adds the iceberg contribution to SSH.
+    override_iceberg_velocities=.False. ! (F) Allows setting a fixed vel for non-static bergs
+    use_f_plane=.false. ! (F) Flag to use a f-plane for the rotation
+    lat_ref=0. ! (0) Reference latitude for f-plane (when this option is on)
+    rotate_icebergs_for_mass_spreading=.true. !(T) Hex bergs rotate for mass spread
+    set_melt_rates_to_zero=.false.!(F)For testing, thermodyn is run, but all melt rates=0
+
+    iceberg_bonds_on=.true. ! (F) True=Allow icebergs to have bonds, False=don't allow.
+    interactive_icebergs_on=.false.!.true.!.false. ! (F) Turn on/off interactions between icebergs
+    only_interactive_forces=.false. !(F)Bergs only feel interactive forces, not ocean, wind...
+    use_new_predictive_corrective =.true. ! (F) Flag to use Bob's pred-corr berg scheme
+    input_freq_distribution=.false. !(F)input dist is: 'T' freq dist or 'F' mass dist
+    use_old_spreading=.false. !(T)spreads berg mass as if  berg is 1 grid cell wide (for rect)
+    max_bonds=6 ! (6) Max # of bonds passed between processors
+
+    verbose=.true. !(F) Be verbose to stderr
+    verbose_hrs=24 ! (24) Period between verbose messages
+    traj_sample_hrs=1 !1 !(24) sampling period for trajectory storage
+    traj_write_hrs=24 ! (480) Period for writing sampled trajectories to disk
+    budget=.false. !(T) Calculate budgets
+    debug=.false. !(F) Turn on debugging
+    really_debug=.false. !(F) Turn on debugging
+    halo_debugging=.false. ! (F) Use for debugging halos (remove when its working)
+    debug_iceberg_with_id = -1  ! If positive, monitors a berg with this id
+
+    parallel_reprod=.true. !(T) Reproduce across different PE decompositions
+    save_short_traj=.false. ! (T) True saves only lon,lat,time,id in iceberg_trajectory.nc
+    save_fl_traj=.true. !(T) True save masses and footloose parameters in iceberg_trajectory.nc
+    ignore_traj=.false. ! (F) If true, then model does not track trajectory data at all
+
+    ignore_missing_restart_bergs=.False. !(F) 'T'=ignore missing bergs in restart
+    require_restart=.true. !(F) 'T'=fail if the restart file is not present at start
+    use_slow_find=.true. !(T) Use slow, but robust, find_cell for reading restarts
+    manually_initialize_bonds=.true. ! (F) True= Bonds are initialize manually.
+    length_for_manually_initialize_bonds=-1.e3!0.0 !(1e3)Dist b/w bergs to init bonds manually
+    ignore_ij_restart=.true. !(F) ign. cell from restart,useful for restart on diff grid
+    generate_test_icebergs=.false. ! (F) Create ergs in absence of a restart file
+    fix_restart_dates=.true. !(T) Post-restart, check bergs created before curr model date
+    restart_input_dir='INPUT/' !('INPUT'/) Directory to look for restart files
+    read_ocean_depth_from_file=.false. ! (F) If true, ocean depth is read from a file.
+    orig_read=.false. !(F) Legacy option that does nothing
+    read_old_restarts=.false. ! (F) Legacy option that does nothing
+
+    use_roundoff_fix=.true. !(T) fix roundoff discrp btwn is_point_in_cell & pos_within_cell
+    old_bug_rotated_weights=.false. !(F) Skip offcenter wght rotation for rot. halo updates
+    make_calving_reproduce=.true. !Make  calving.res.nc reprod. across pe cnt changes
+    old_bug_bilin=.false. !(T) 'T' use inverted bilinear function,'F' gives correct answer
+    do_unit_tests=.true. !(F) Conduct some unit tests
+    force_all_pes_traj=.false. !(F) Force all pes write traj files regardless of io_layout
+
+    ! Mass thresholds between iceberg classes (kg):
+    !( 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11 )
+    initial_mass=8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+
+    ! Fraction of calving to apply to this class (non-dim):
+    !( (/0.24 ,0.12 ,0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.03/) )
+    distribution=0.0, 0.99, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
+
+    ! Ratio between effective and real iceberg mass (non-dim):
+    !( (/2000, 200, 50, 20, 10, 5, 2, 1, 1, 1/) )
+    mass_scaling=1, 1, 1, 1, 1, 1, 1, 1, 1, 1
+
+    ! Total thickness of newly calved bergs (m):
+    !( (/40., 67., 133., 175., 250., 250., 250., 250., 250., 250./) )
+    initial_thickness=40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+
+/
+
+&diag_manager_nml
+/
+
+ &fms_io_nml
+         fms_netcdf_restart=.false.
+         threading_read='multi'
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = 2000000
+       clock_flags='SYNC'
+/

From 3997659da95c33fafc51c9f7ac08461e1d48c32b Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Tue, 25 Jul 2023 15:22:01 -0400
Subject: [PATCH 356/361] Avoids type ambiguity for variable/function

Gnu compiler was complaining with "Derived type 'buffer' is used as an actual argument ..."
for a one character variable being passed to class(*) in FMS2. It turns out the compiler
was seeing the function 'buffer' in the "use" statements above. Renaming the variable
avoids the ambiguity.

Thanks to @marshallward for figuring out the cause.
---
 src/icebergs_fms2io.F90 | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/icebergs_fms2io.F90 b/src/icebergs_fms2io.F90
index cd3bbe0..19ab78a 100644
--- a/src/icebergs_fms2io.F90
+++ b/src/icebergs_fms2io.F90
@@ -2727,7 +2727,7 @@ subroutine register_axis_wrapper(fileobj)
     integer :: dim_size             !< Size of the dimension
     integer :: ndims                !< Number of dimensions in the file
     logical :: is_domain_decomposed !< Flag indication if domain decomposed
-    character(len=1) :: buffer      !< string buffer
+    character(len=1) :: cbuffer      !< string buffer
 
     ndims = get_num_dimensions(fileobj)
     allocate(file_dim_names(ndims))
@@ -2744,21 +2744,21 @@ subroutine register_axis_wrapper(fileobj)
 
           !< If the variable exists look for the "cartesian_axis" or "axis" variable attribute
           if (variable_att_exists(fileobj, file_dim_names(i), "axis")) then
-              call get_variable_attribute(fileobj, file_dim_names(i), "axis", buffer)
+              call get_variable_attribute(fileobj, file_dim_names(i), "axis", cbuffer)
 
               !< If the attribute exists and it is "x" or "y" register it as a domain decomposed dimension
-              if (lowercase(buffer) .eq. "x" .or. lowercase(buffer) .eq. "y" ) then
+              if (lowercase(cbuffer) .eq. "x" .or. lowercase(cbuffer) .eq. "y" ) then
                   is_domain_decomposed = .true.
-                  call register_axis(fileobj, file_dim_names(i), buffer)
+                  call register_axis(fileobj, file_dim_names(i), cbuffer)
               endif
 
           else if (variable_att_exists(fileobj, file_dim_names(i), "cartesian_axis")) then
-              call get_variable_attribute(fileobj, file_dim_names(i), "cartesian_axis", buffer)
+              call get_variable_attribute(fileobj, file_dim_names(i), "cartesian_axis", cbuffer)
 
               !< If the attribute exists and it "x" or "y" register it as a domain decomposed dimension
-              if (lowercase(buffer) .eq. "x" .or. lowercase(buffer) .eq. "y" ) then
+              if (lowercase(cbuffer) .eq. "x" .or. lowercase(cbuffer) .eq. "y" ) then
                   is_domain_decomposed = .true.
-                  call register_axis(fileobj, file_dim_names(i), buffer)
+                  call register_axis(fileobj, file_dim_names(i), cbuffer)
               endif
 
           endif !< If variable attribute exists

From bbb92de831e8178f2323109a0de9e2898556a451 Mon Sep 17 00:00:00 2001
From: Alistair Adcroft <Alistair.Adcroft@noaa.gov>
Date: Tue, 25 Jul 2023 15:48:07 -0400
Subject: [PATCH 357/361] Renamed write_restart to write_restart_bergs

Another namespace ambiguity: FMS2 PR tried to rename write_restart() from
FMS2 to fms2_io_write_restart() to avoid collision with the subroutine
write_restart() in icebergs_fms2io.F90. However, the nVidia compiler was
complaining. Better solution is to simply rename the colliding subroutine
in the iceberg modules.
---
 src/icebergs.F90        |  4 ++--
 src/icebergs_fms2io.F90 | 14 +++++++-------
 src/icebergs_fmsio.F90  |  8 ++++----
 3 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 64f95fd..ebff51c 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -55,7 +55,7 @@ module ice_bergs
 use ice_bergs_framework, only: break_bonds_on_sub_steps
 use ice_bergs_framework, only: short_step_mts_grounding, radius_based_drag
 
-use ice_bergs_io,        only: ice_bergs_io_init, write_restart, write_trajectory, write_bond_trajectory
+use ice_bergs_io,        only: ice_bergs_io_init, write_restart_bergs, write_trajectory, write_bond_trajectory
 use ice_bergs_io,        only: read_restart_bergs, read_restart_calving
 use ice_bergs_io,        only: read_restart_bonds
 use ice_bergs_io,        only: read_ocean_depth
@@ -8142,7 +8142,7 @@ subroutine icebergs_save_restart(bergs, time_stamp)
 
   call mpp_clock_begin(bergs%clock_iow)
   call bergs_chksum(bergs, 'write_restart bergs')
-  call write_restart(bergs, time_stamp)
+  call write_restart_bergs(bergs, time_stamp)
   call mpp_clock_end(bergs%clock_iow)
 
 end subroutine icebergs_save_restart
diff --git a/src/icebergs_fms2io.F90 b/src/icebergs_fms2io.F90
index 19ab78a..844b660 100644
--- a/src/icebergs_fms2io.F90
+++ b/src/icebergs_fms2io.F90
@@ -16,7 +16,7 @@ module ice_bergs_fms2io
 use fms_mod, only: stdlog, stderr, error_mesg, FATAL, WARNING, NOTE, lowercase
 
 use fms2_io_mod, only: get_instance_filename
-use fms2_io_mod, only: FmsNetcdfDomainFile_t, open_file, close_file, read_restart, fms2_io_write_restart => write_restart
+use fms2_io_mod, only: FmsNetcdfDomainFile_t, open_file, close_file, read_restart, write_restart
 use fms2_io_mod, only: variable_exists, get_dimension_size, get_num_dimensions, get_dimension_names
 use fms2_io_mod, only: get_variable_attribute, variable_att_exists, write_data, read_data
 use fms2_io_mod, only: register_unlimited_compressed_axis, register_axis, register_restart_field, register_variable_attribute
@@ -57,7 +57,7 @@ module ice_bergs_fms2io
 include 'netcdf.inc'
 
 public ice_bergs_io_init
-public read_restart_bergs, write_restart, write_trajectory, write_bond_trajectory
+public read_restart_bergs, write_restart_bergs, write_trajectory, write_bond_trajectory
 public read_restart_calving, read_restart_bonds
 public read_ocean_depth
 
@@ -121,7 +121,7 @@ subroutine ice_bergs_io_init(bergs, io_layout)
 end subroutine ice_bergs_io_init
 
 !> Write an iceberg restart file
-subroutine write_restart(bergs, time_stamp)
+subroutine write_restart_bergs(bergs, time_stamp)
 ! Arguments
 type(icebergs), pointer :: bergs !< Icebergs container
 character(len=*), intent(in), optional :: time_stamp !< Timestamp for restart file
@@ -408,7 +408,7 @@ subroutine write_restart(bergs, time_stamp)
                                      dim_names_1d,longname='static_berg',units='dimensionless')
 
   call register_field(fileobj, "i", "int")
-  call fms2_io_write_restart(fileobj)
+  call write_restart(fileobj)
 
   call get_dimension_size(fileobj, "i", global_nbergs)
   call write_data(fileobj, "i", global_nbergs)
@@ -562,7 +562,7 @@ subroutine write_restart(bergs, time_stamp)
                                      dim_names_1d,longname='broken status',units='none')
   endif
 
-  call fms2_io_write_restart(fileobj)
+  call write_restart(fileobj)
   call close_file(fileobj)
 
   deallocate(first_id_cnt,          &
@@ -626,10 +626,10 @@ subroutine write_restart(bergs, time_stamp)
   endif
 
   call write_axis_metadata(fileobj)
-  call fms2_io_write_restart(fileobj)
+  call write_restart(fileobj)
   call write_axis_data(fileobj, size(bergs%grd%stored_ice, 3))
   call close_file(fileobj)
-end subroutine write_restart
+end subroutine write_restart_bergs
 
 !> Find the last berg in a linked list.
 function last_berg(berg)
diff --git a/src/icebergs_fmsio.F90 b/src/icebergs_fmsio.F90
index 38b320d..1b1a3f4 100644
--- a/src/icebergs_fmsio.F90
+++ b/src/icebergs_fmsio.F90
@@ -54,7 +54,7 @@ module ice_bergs_fmsio
 include 'netcdf.inc'
 
 public ice_bergs_io_init
-public read_restart_bergs, write_restart, write_trajectory, write_bond_trajectory
+public read_restart_bergs, write_restart_bergs, write_trajectory, write_bond_trajectory
 public read_restart_calving, read_restart_bonds
 public read_ocean_depth
 
@@ -112,7 +112,7 @@ subroutine ice_bergs_io_init(bergs, io_layout)
 end subroutine ice_bergs_io_init
 
 !> Write an iceberg restart file
-subroutine write_restart(bergs, time_stamp)
+subroutine write_restart_bergs(bergs, time_stamp)
 ! Arguments
 type(icebergs), pointer :: bergs !< Icebergs container
 character(len=*), intent(in), optional :: time_stamp !< Timestamp for restart file
@@ -552,7 +552,7 @@ subroutine write_restart(bergs, time_stamp)
 
   ! Write stored ice
   filename='calving.res.nc'
-  if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(stderrunit,'(2a)') 'KID, write_restart: writing ',filename
+  if (verbose.and.mpp_pe().eq.mpp_root_pe()) write(stderrunit,'(2a)') 'KID, write_restart_bergs: writing ',filename
   call grd_chksum3(bergs%grd, bergs%grd%stored_ice, 'write stored_ice')
   call grd_chksum2(bergs%grd, bergs%grd%stored_heat, 'write stored_heat')
   if (bergs%tau_calving>0.) then
@@ -572,7 +572,7 @@ subroutine write_restart(bergs, time_stamp)
   call save_restart(calving_restart, time_stamp)
   call free_restart_type(calving_restart)
 
-end subroutine write_restart
+end subroutine write_restart_bergs
 
 !> Find the last berg in a linked list.
 function last_berg(berg)

From 9c8266d37ce8fcd3087a29136894bf4789f3bd76 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Wed, 10 Jan 2024 13:08:10 -0500
Subject: [PATCH 358/361] fixed noted units of calving

---
 src/icebergs.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index ebff51c..c228aef 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -5076,7 +5076,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   ! Arguments
   type(icebergs), pointer :: bergs !< Container for all types and memory
   type(time_type), intent(in) :: time !< Model time
-  real, dimension(:,:), intent(inout) :: calving !< Calving (kg/s). This field is updated with melt by bergs.
+  real, dimension(:,:), intent(inout) :: calving !< Calving (kg m-2 s-1). This field is updated with melt by bergs.
   real, dimension(:,:), intent(inout) :: calving_hflx !< Calving heat flux (W/m2)
   real, dimension(:,:), intent(in) :: uo !< Ocean zonal velocity (m/s)
   real, dimension(:,:), intent(in) :: vo !< Ocean meridional velocity (m/s)

From 89cf3e63fde1ddbc613eecbff528178be4a89a47 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Fri, 2 Feb 2024 11:22:09 -0500
Subject: [PATCH 359/361] Use masked-out SST to determine units of SST,
 preventing an error where some PEs erroneously trigger (or not) a K to C SST
 conversion due to unrealistic SST values under ice shelves (which occur on
 zero-thickness ocean surface layers and are unused otherwise)

---
 src/icebergs.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index c228aef..7a896fe 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -5337,7 +5337,7 @@ subroutine icebergs_run(bergs, time, calving, uo, vo, ui, vi, tauxa, tauya, ssh,
   endif
 
   call mpp_update_domains(grd%ssh, grd%domain)
-  max_SST = maxval(sst(:,:))
+  max_SST = maxval(sst(:,:) * grd%msk(grd%isc:grd%iec,grd%jsc:grd%jec))
   if (max_SST > 120.0) then ! The input sst is in degrees Kelvin, otherwise the water would be boiling.
     grd%sst(grd%isc:grd%iec,grd%jsc:grd%jec) = sst(:,:)-273.15 ! Note convert from Kelvin to Celsius
   else  ! The input sst is already in degrees Celsius.

From 9d77ef15f2ab647ddce47521ddf0e228e1bfe423 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Wed, 7 Feb 2024 13:50:17 -0500
Subject: [PATCH 360/361] Several miscellaneous updates: Modified the icebergs
 driver and driver_data modules to be FMS2-compatible; updated the default
 solo-mode make commands and build environment for gaea c5; updated the
 namelist file for the a68a test case so that the data directory will properly
 be assigned on any system by default; fixed an allocation error for the
 iceberg bond trajectory 'broken' (which saves whether a bond is broken or
 not); fixed a boolean error in icebergs_fms2io.F90 that was preventing
 iceberg bonds from being written. All solo-mode tests passed.

---
 build/a68_dims__genmod.f90   |  12 --
 build/env                    |  28 +++--
 build/handle_err__genmod.f90 |  10 --
 build/mkmkf                  |   8 +-
 build/mkmkf_fms2             |   4 +-
 driver/driver_data.F90       | 187 ++--------------------------
 driver/driver_data_fms.F90   | 185 ++++++++++++++++++++++++++++
 driver/driver_data_fms2.F90  | 229 +++++++++++++++++++++++++++++++++++
 driver/icebergs_driver.F90   |  10 +-
 src/icebergs_fms2io.F90      |   2 +-
 src/icebergs_framework.F90   |  13 +-
 tests/a68_test/long_run.nml  |   6 +-
 12 files changed, 462 insertions(+), 232 deletions(-)
 delete mode 100644 build/a68_dims__genmod.f90
 delete mode 100644 build/handle_err__genmod.f90
 create mode 100644 driver/driver_data_fms.F90
 create mode 100644 driver/driver_data_fms2.F90

diff --git a/build/a68_dims__genmod.f90 b/build/a68_dims__genmod.f90
deleted file mode 100644
index 3e781da..0000000
--- a/build/a68_dims__genmod.f90
+++ /dev/null
@@ -1,12 +0,0 @@
-        !COMPILER-GENERATED INTERFACE MODULE: Fri Oct  1 13:21:29 2021
-        ! This source file is for reference only and may not completely
-        ! represent the generated interface used by the compiler.
-        MODULE A68_DIMS__genmod
-          INTERFACE 
-            SUBROUTINE A68_DIMS(DATA_DIR,NI,NJ)
-              CHARACTER(LEN=1000) :: DATA_DIR
-              INTEGER(KIND=4), INTENT(OUT) :: NI
-              INTEGER(KIND=4), INTENT(OUT) :: NJ
-            END SUBROUTINE A68_DIMS
-          END INTERFACE 
-        END MODULE A68_DIMS__genmod
diff --git a/build/env b/build/env
index 8dd47c1..c751803 100644
--- a/build/env
+++ b/build/env
@@ -1,16 +1,18 @@
-#source /opt/modules/default/etc/modules.sh
-module use -a /ncrc/home2/fms/local/modulefiles
-setenv MODULEPATH /usw/eslogin/modulefiles-c4:/sw/eslogin-c4/modulefiles:/opt/cray/pe/ari/modulefiles:/opt/cray/ari/modulefiles:/opt/cray/pe/modulefiles:/opt/cray/modulefiles:/opt/modulefiles:/sw/common/modulefiles
-#module unload PrgEnv-pgi PrgEnv-intel PrgEnv-gnu darshan; module load PrgEnv-gnu; module unload netcdf gcc; module load gcc/7.3.0 cray-hdf5 cray-netcdf
-
-module unload PrgEnv-pgi
-module unload PrgEnv-pathscale
-module unload PrgEnv-intel
-module unload PrgEnv-gnu
-module unload PrgEnv-cray
+#module unload PrgEnv-pgi
+#module unload PrgEnv-pathscale
+#module unload PrgEnv-intel
+#module unload PrgEnv-gnu
+#module unload PrgEnv-cray
 
 module load PrgEnv-intel
-module swap intel intel/18.0.6.288
-module unload netcdf
+module load intel-classic/2022.0.2
+#module swap intel intel/18.0.6.288
+#module load intel
+#module unload netcdf
+module load cray-hdf5
 module load cray-netcdf
-module load cray-hdf5
\ No newline at end of file
+
+module switch cray-libsci/22.10.1.2
+#module load cray-hdf5/1.12.1.3
+#module load cray-netcdf/4.8.1.3
+#module load cray-hdf5
diff --git a/build/handle_err__genmod.f90 b/build/handle_err__genmod.f90
deleted file mode 100644
index 0dd846d..0000000
--- a/build/handle_err__genmod.f90
+++ /dev/null
@@ -1,10 +0,0 @@
-        !COMPILER-GENERATED INTERFACE MODULE: Fri Oct  1 13:21:29 2021
-        ! This source file is for reference only and may not completely
-        ! represent the generated interface used by the compiler.
-        MODULE HANDLE_ERR__genmod
-          INTERFACE 
-            SUBROUTINE HANDLE_ERR(STATUS)
-              INTEGER(KIND=4), INTENT(IN) :: STATUS
-            END SUBROUTINE HANDLE_ERR
-          END INTERFACE 
-        END MODULE HANDLE_ERR__genmod
diff --git a/build/mkmkf b/build/mkmkf
index 6aa5125..595590d 100644
--- a/build/mkmkf
+++ b/build/mkmkf
@@ -1,3 +1,7 @@
+# rm -f path_names
+# ../../mkmf/bin/list_paths ../../FMS/{mpp,diag_manager,time_manager,include,memutils,constants,platform,fms,random_numbers,mosaic,exchange} ../src/ ../driver/
+# ../../mkmf/bin/mkmf -t ../../mkmf/templates/ncrc-intel.mk -c "-Duse_libMPI -Duse_netCDF" -p bergs.x path_names
+
 rm -f path_names
-../../mkmf/bin/list_paths ../../FMS/{mpp,diag_manager,time_manager,include,memutils,constants,platform,fms,random_numbers,mosaic,exchange} ../src/ ../driver/
-../../mkmf/bin/mkmf -t ../../mkmf/templates/ncrc-intel.mk -c "-Duse_libMPI -Duse_netCDF" -p bergs.x path_names
\ No newline at end of file
+../../mkmf/bin/list_paths -l ../src/ ../driver/
+../../mkmf/bin/mkmf -t ../../mkmf/templates/ncrc-intel.mk -o "-I../../../build/fms" -p bergs.x -l '-L../../../build/fms -lfms' -c "-Duse_libMPI -Duse_netCDF -I../../../build/fms" path_names
\ No newline at end of file
diff --git a/build/mkmkf_fms2 b/build/mkmkf_fms2
index 84932e2..58877cd 100644
--- a/build/mkmkf_fms2
+++ b/build/mkmkf_fms2
@@ -1,3 +1,3 @@
 rm -f path_names
-../../mkmf/bin/list_paths  ../src/ ../driver/
-../../mkmf/bin/mkmf -t ../../mkmf/templates/ncrc-intel.mk -c "-Duse_libMPI -Duse_netCDF -Duse_fms2_io -I../../../build/fms2" -p bergs.x -l '-L../../../build/fms2 -lfms' path_names
\ No newline at end of file
+../../mkmf/bin/list_paths -l ../src/ ../driver/
+../../mkmf/bin/mkmf -t ../../mkmf/templates/ncrc-intel.mk -o "-I../../../build/fms2" -p bergs.x -l '-L../../../build/fms2 -lfms' -c "-Duse_libMPI -Duse_netCDF -DUSE_FMS2_IO -I../../../build/fms2" path_names
\ No newline at end of file
diff --git a/driver/driver_data.F90 b/driver/driver_data.F90
index b60b015..12fa0ab 100644
--- a/driver/driver_data.F90
+++ b/driver/driver_data.F90
@@ -1,184 +1,11 @@
+!> Handles reading/writing of restart files and trajectory-based diagnostic files
 module driver_data
+! This file is part of NOAA-GFDL/icebergs. See LICENSE.md for the license.
 
-use fms_mod, only : read_data
-use fms_mod, only : file_exist
-use fms_mod, only : field_exist
-use fms_mod, only : error_mesg
-use fms_mod, only : FATAL
-use mpp_domains_mod, only : domain2D
-use mpp_mod, only : mpp_pe
-use mpp_mod, only : mpp_root_pe
-use mpp_mod, only: mpp_sync
-use constants_mod, only: pi
-use netcdf
-!include 'netcdf.inc'
-
-implicit none
-
-contains
-
-  !> Determine dimensions of A68 background grid
-  subroutine a68_dims(data_dir,ni,nj)
-    ! Arguments
-    character(len=*) :: data_dir
-    integer, intent(out):: ni,nj
-    ! Local variables
-    character(len=1000):: infile
-    integer(kind=4) :: ncid
-    integer :: status
-
-    infile=trim(trim(data_dir)//'a68_experiment_ll_p125_grid.nc')
-
-    !Open netCDF file
-    call handle_err(nf90_open(infile, nf90_nowrite, ncid))
-    !Inquire about the dimensions
-    call handle_err(nf90_inquire_dimension(ncid,1,len=nj))
-    call handle_err(nf90_inquire_dimension(ncid,2,len=ni))
-    !Close netCDF file
-    call handle_err(nf90_close(ncid))
-  end subroutine a68_dims
-
-  !> Handle for errors
-  subroutine handle_err(status)
-    integer, intent (in) :: status
-
-    if(status /= nf90_noerr) then
-      print *, trim(nf90_strerror(status))
-      stop "Stopped"
-    end if
-  end subroutine handle_err
-
-  !>A68 grid setup
-  subroutine a68_prep(data_dir,mpp_domain,lon,lat,dx,dy,area,REarth)
-    ! Arguments
-    character(len=*) :: data_dir
-    type(domain2D) :: mpp_domain
-    real :: lon(:,:) !< Longitude or position in x
-    real :: lat(:,:) !< Latitude or position in y
-    real :: dx(:,:) !< Length of northern edge of cell (m)
-    real :: dy(:,:) !< Length of eatern edge of cell (m)
-    real :: area(:,:) !< Area of cell (m2)
-    real :: REarth
-    ! Local variables
-    character(len=1000) :: filename
-    real, parameter :: gres=0.125
-
-    !Grid specs: lon,lat,dx,dy,area
-    filename=trim(trim(data_dir)//'a68_experiment_ll_p125_grid.nc')
-    call read_a68_data(mpp_domain,filename,'longitude',lon)
-    lon=lon+360
-    call read_a68_data(mpp_domain,filename,'latitude',lat)
-
-    call haversine_dist_and_area(REarth,gres,lon,lat,dx,dy,area)
-  end subroutine a68_prep
-
-  !> Haversine distance and area
-  subroutine haversine_dist_and_area(REarth,gres,lon1,lat1,dx,dy,area)
-    ! Arguments
-    real, intent(in) :: REarth    !Earth radius (m)
-    real, intent(in) :: gres      !grid resolution (degrees)
-    real, intent(in) :: lon1(:,:) !grid longitude
-    real, intent(in) :: lat1(:,:) !grid latitude
-    real, intent(out) :: dx(:,:)  !grid dx (m)
-    real, intent(out) :: dy(:,:)   !grid dy (m)
-    real, intent(out) :: area(:,:) !grid area (m^2)
-    ! Local variables
-    real, parameter :: pi_180=pi/180.
-    real, dimension(size(lon1,1),size(lon1,2)) :: lon2,lat2,p1,p2,dp,dm,a,c
-
-    !calculate dx
-    lon2=lon1-gres
-    lat2=lat1
-    p1 = lat1 * pi_180; p2 = lat2 * pi_180; dp = (lat2-lat1) * pi_180; dm = (lon2-lon1) * pi_180
-    a = sin(0.5*dp)**2. + cos(p1) * cos(p2) * sin(0.5*dm)**2.; c = 2. * atan2(sqrt(a), sqrt(1-a))
-    dx = REarth * c
-
-    !calculate dy
-    lat2=lat1-gres
-    lon2=lon1
-    p1 = lat1 * pi_180; p2 = lat2 * pi_180; dp = (lat2-lat1) * pi_180; dm = (lon2-lon1) * pi_180
-    a = sin(0.5*dp)**2. + cos(p1) * cos(p2) * sin(0.5*dm)**2.; c = 2. * atan2(sqrt(a), sqrt(1-a))
-    dy = REarth * c
-
-    !calculate area
-    area=pi_180*(REarth**2.)*abs(sin(lat1*pi_180)-sin(lat2*pi_180))*abs(gres)
-  end subroutine haversine_dist_and_area
-
-
-  !> Read in static (not time-varying) data for A68 experiment from file
-  subroutine read_a68_data(domain,filename,var,field)
-    ! Arguments
-    type(domain2D) :: domain !< Parallel decomposition
-    character(len=*), intent(in) :: filename, var
-    real :: field(:,:)
-
-    call mpp_sync()
-    if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') 'icebergs_driver: Reading ',var
-    if (file_exist(filename)) then
-      if (field_exist(filename, var)) then
-        call read_data(filename, var, field, domain)
-      else
-        if (mpp_pe().eq.mpp_root_pe()) then
-          call error_mesg('icebergs_driver:','Variable missing in file!', FATAL)
-        endif
-      endif
-    else
-      if (mpp_pe().eq.mpp_root_pe()) then
-        call error_mesg('icebergs_driver:','File for variable not found!', FATAL)
-      endif
-    endif
-    call mpp_sync()
-  end subroutine read_a68_data
-
-  !> Calls read_a68_data for wind velocity, ocean velocity, and ssh
-  subroutine a68_prep_3d(data_dir,mpp_domain,tauxa_hr,tauya_hr,uo_hr,vo_hr,ssh_hr)
-    ! Arguments
-    character(len=*) :: data_dir
-
-    type(domain2D) :: mpp_domain
-    real :: tauxa_hr(:,:,:) !< Zonal jra55 wind velocity (m/s, hourly)
-    real :: tauya_hr(:,:,:) !< Meridional jra55 wind velocity (m/s, hourly)
-    real :: uo_hr(:,:,:) !< Zonal OSCAR ocean surface velocity (m/s, hourly)
-    real :: vo_hr(:,:,:) !< Meridional OSCAR ocean surface velocity (m/s, hourly)
-    real :: ssh_hr(:,:,:) !< Effective sea surface height (m, hourly)
-    ! Local variables
-    character(len=1000) :: filename
-
-    filename=trim(trim(data_dir)//'a68_experiment_wind_vel_ncep_10m_dec2020_HOURLY_ll_p125.nc')
-    call read_a68_data_3d(mpp_domain,filename,'ua',tauxa_hr)
-    call read_a68_data_3d(mpp_domain,filename,'va',tauya_hr)
-
-    filename=trim(trim(data_dir)//'a68_experiment_ocean_surf_vel_oscar_dec2020_HOURLY_ll_p125.nc')
-    call read_a68_data_3d(mpp_domain,filename,'uo',uo_hr)
-    call read_a68_data_3d(mpp_domain,filename,'vo',vo_hr)
-
-    filename=trim(trim(data_dir)//'a68_experiment_ssh_duacs_dec2020_HOURLY_ll_p125.nc')
-    call read_a68_data_3d(mpp_domain,filename,'SSH',ssh_hr)
-  end subroutine a68_prep_3d
-
-  !> Read in time-varying A68 data
-  subroutine read_a68_data_3d(domain,filename,var,field)
-    ! Arguments
-    type(domain2D) :: domain !< Parallel decomposition
-    character(len=*), intent(in) :: filename, var
-    real :: field(:,:,:)
-
-    call mpp_sync()
-    if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') 'icebergs_driver: Reading ',var
-    if (file_exist(filename)) then
-      if (field_exist(filename, var)) then
-        call read_data(filename, var, field, domain)
-      else
-        if (mpp_pe().eq.mpp_root_pe()) then
-          call error_mesg('icebergs_driver:','Variable missing in file!', FATAL)
-        endif
-      endif
-    else
-      if (mpp_pe().eq.mpp_root_pe()) then
-        call error_mesg('icebergs_driver:','File for variable not found!', FATAL)
-      endif
-    endif
-    call mpp_sync()
-  end subroutine read_a68_data_3d
+#ifndef USE_FMS2_IO
+  use driver_data_fms
+#else
+  use driver_data_fms2
+#endif
 
 end module driver_data
diff --git a/driver/driver_data_fms.F90 b/driver/driver_data_fms.F90
new file mode 100644
index 0000000..b0a09bc
--- /dev/null
+++ b/driver/driver_data_fms.F90
@@ -0,0 +1,185 @@
+module driver_data_fms
+#ifndef USE_FMS2_IO
+
+use fms_mod, only : read_data
+use fms_mod, only : file_exist
+use fms_mod, only : field_exist
+use fms_mod, only : error_mesg
+use fms_mod, only : FATAL
+use mpp_domains_mod, only : domain2D
+use mpp_mod, only : mpp_pe
+use mpp_mod, only : mpp_root_pe
+use mpp_mod, only: mpp_sync
+use constants_mod, only: pi
+use netcdf
+!include 'netcdf.inc'
+
+implicit none
+
+contains
+
+  !> Determine dimensions of A68 background grid
+  subroutine a68_dims(data_dir,ni,nj)
+    ! Arguments
+    character(len=*) :: data_dir
+    integer, intent(out):: ni,nj
+    ! Local variables
+    character(len=1000):: infile
+    integer(kind=4) :: ncid
+    integer :: status
+
+    infile=trim(trim(data_dir)//'a68_experiment_ll_p125_grid.nc')
+
+    !Open netCDF file
+    call handle_err(nf90_open(infile, nf90_nowrite, ncid))
+    !Inquire about the dimensions
+    call handle_err(nf90_inquire_dimension(ncid,1,len=nj))
+    call handle_err(nf90_inquire_dimension(ncid,2,len=ni))
+    !Close netCDF file
+    call handle_err(nf90_close(ncid))
+  end subroutine a68_dims
+
+  !> Handle for errors
+  subroutine handle_err(status)
+    integer, intent (in) :: status
+
+    if(status /= nf90_noerr) then
+      print *, trim(nf90_strerror(status))
+      stop "Stopped"
+    end if
+  end subroutine handle_err
+
+  !>A68 grid setup
+  subroutine a68_prep(data_dir,mpp_domain,lon,lat,dx,dy,area,REarth)
+    ! Arguments
+    character(len=*) :: data_dir
+    type(domain2D) :: mpp_domain
+    real :: lon(:,:) !< Longitude or position in x
+    real :: lat(:,:) !< Latitude or position in y
+    real :: dx(:,:) !< Length of northern edge of cell (m)
+    real :: dy(:,:) !< Length of eatern edge of cell (m)
+    real :: area(:,:) !< Area of cell (m2)
+    real :: REarth
+    ! Local variables
+    character(len=1000) :: filename
+    real, parameter :: gres=0.125
+
+    !Grid specs: lon,lat,dx,dy,area
+    filename=trim(trim(data_dir)//'a68_experiment_ll_p125_grid.nc')
+    call read_a68_data(mpp_domain,filename,'longitude',lon)
+    lon=lon+360
+    call read_a68_data(mpp_domain,filename,'latitude',lat)
+
+    call haversine_dist_and_area(REarth,gres,lon,lat,dx,dy,area)
+  end subroutine a68_prep
+
+  !> Haversine distance and area
+  subroutine haversine_dist_and_area(REarth,gres,lon1,lat1,dx,dy,area)
+    ! Arguments
+    real, intent(in) :: REarth    !Earth radius (m)
+    real, intent(in) :: gres      !grid resolution (degrees)
+    real, intent(in) :: lon1(:,:) !grid longitude
+    real, intent(in) :: lat1(:,:) !grid latitude
+    real, intent(out) :: dx(:,:)  !grid dx (m)
+    real, intent(out) :: dy(:,:)   !grid dy (m)
+    real, intent(out) :: area(:,:) !grid area (m^2)
+    ! Local variables
+    real, parameter :: pi_180=pi/180.
+    real, dimension(size(lon1,1),size(lon1,2)) :: lon2,lat2,p1,p2,dp,dm,a,c
+
+    !calculate dx
+    lon2=lon1-gres
+    lat2=lat1
+    p1 = lat1 * pi_180; p2 = lat2 * pi_180; dp = (lat2-lat1) * pi_180; dm = (lon2-lon1) * pi_180
+    a = sin(0.5*dp)**2. + cos(p1) * cos(p2) * sin(0.5*dm)**2.; c = 2. * atan2(sqrt(a), sqrt(1-a))
+    dx = REarth * c
+
+    !calculate dy
+    lat2=lat1-gres
+    lon2=lon1
+    p1 = lat1 * pi_180; p2 = lat2 * pi_180; dp = (lat2-lat1) * pi_180; dm = (lon2-lon1) * pi_180
+    a = sin(0.5*dp)**2. + cos(p1) * cos(p2) * sin(0.5*dm)**2.; c = 2. * atan2(sqrt(a), sqrt(1-a))
+    dy = REarth * c
+
+    !calculate area
+    area=pi_180*(REarth**2.)*abs(sin(lat1*pi_180)-sin(lat2*pi_180))*abs(gres)
+  end subroutine haversine_dist_and_area
+
+
+  !> Read in static (not time-varying) data for A68 experiment from file
+  subroutine read_a68_data(domain,filename,var,field)
+    ! Arguments
+    type(domain2D) :: domain !< Parallel decomposition
+    character(len=*), intent(in) :: filename, var
+    real :: field(:,:)
+
+    call mpp_sync()
+    if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') 'icebergs_driver: Reading ',var
+    if (file_exist(filename)) then
+      if (field_exist(filename, var)) then
+        call read_data(filename, var, field, domain)
+      else
+        if (mpp_pe().eq.mpp_root_pe()) then
+          call error_mesg('icebergs_driver:','Variable missing in file!', FATAL)
+        endif
+      endif
+    else
+      if (mpp_pe().eq.mpp_root_pe()) then
+        call error_mesg('icebergs_driver:','File for variable not found!', FATAL)
+      endif
+    endif
+    call mpp_sync()
+  end subroutine read_a68_data
+
+  !> Calls read_a68_data for wind velocity, ocean velocity, and ssh
+  subroutine a68_prep_3d(data_dir,mpp_domain,tauxa_hr,tauya_hr,uo_hr,vo_hr,ssh_hr)
+    ! Arguments
+    character(len=*) :: data_dir
+
+    type(domain2D) :: mpp_domain
+    real :: tauxa_hr(:,:,:) !< Zonal jra55 wind velocity (m/s, hourly)
+    real :: tauya_hr(:,:,:) !< Meridional jra55 wind velocity (m/s, hourly)
+    real :: uo_hr(:,:,:) !< Zonal OSCAR ocean surface velocity (m/s, hourly)
+    real :: vo_hr(:,:,:) !< Meridional OSCAR ocean surface velocity (m/s, hourly)
+    real :: ssh_hr(:,:,:) !< Effective sea surface height (m, hourly)
+    ! Local variables
+    character(len=1000) :: filename
+
+    filename=trim(trim(data_dir)//'a68_experiment_wind_vel_ncep_10m_dec2020_HOURLY_ll_p125.nc')
+    call read_a68_data_3d(mpp_domain,filename,'ua',tauxa_hr)
+    call read_a68_data_3d(mpp_domain,filename,'va',tauya_hr)
+
+    filename=trim(trim(data_dir)//'a68_experiment_ocean_surf_vel_oscar_dec2020_HOURLY_ll_p125.nc')
+    call read_a68_data_3d(mpp_domain,filename,'uo',uo_hr)
+    call read_a68_data_3d(mpp_domain,filename,'vo',vo_hr)
+
+    filename=trim(trim(data_dir)//'a68_experiment_ssh_duacs_dec2020_HOURLY_ll_p125.nc')
+    call read_a68_data_3d(mpp_domain,filename,'SSH',ssh_hr)
+  end subroutine a68_prep_3d
+
+  !> Read in time-varying A68 data
+  subroutine read_a68_data_3d(domain,filename,var,field)
+    ! Arguments
+    type(domain2D) :: domain !< Parallel decomposition
+    character(len=*), intent(in) :: filename, var
+    real :: field(:,:,:)
+
+    call mpp_sync()
+    if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') 'icebergs_driver: Reading ',var
+    if (file_exist(filename)) then
+      if (field_exist(filename, var)) then
+        call read_data(filename, var, field, domain)
+      else
+        if (mpp_pe().eq.mpp_root_pe()) then
+          call error_mesg('icebergs_driver:','Variable missing in file!', FATAL)
+        endif
+      endif
+    else
+      if (mpp_pe().eq.mpp_root_pe()) then
+        call error_mesg('icebergs_driver:','File for variable not found!', FATAL)
+      endif
+    endif
+    call mpp_sync()
+  end subroutine read_a68_data_3d
+#endif
+end module driver_data_fms
diff --git a/driver/driver_data_fms2.F90 b/driver/driver_data_fms2.F90
new file mode 100644
index 0000000..462cb8b
--- /dev/null
+++ b/driver/driver_data_fms2.F90
@@ -0,0 +1,229 @@
+module driver_data_fms2
+#ifdef USE_FMS2_IO
+
+use fms2_io_mod, only : read_data
+use fms2_io_mod, only : variable_exists
+use fms2_io_mod, only: get_instance_filename
+use fms2_io_mod, only: open_file
+use fms2_io_mod, only: get_num_dimensions, register_axis, get_dimension_names, get_dimension_size
+use fms2_io_mod, only: FmsNetcdfDomainFile_t
+use fms_mod, only : error_mesg, lowercase
+use fms_mod, only : FATAL
+use mpp_domains_mod, only : domain2D
+use mpp_mod, only : mpp_pe
+use mpp_mod, only : mpp_root_pe
+use mpp_mod, only: mpp_sync
+use constants_mod, only: pi
+use netcdf
+!include 'netcdf.inc'
+
+implicit none
+
+contains
+
+  !> Determine dimensions of A68 background grid
+  subroutine a68_dims(data_dir,ni,nj)
+    ! Arguments
+    character(len=*) :: data_dir
+    integer, intent(out):: ni,nj
+    ! Local variables
+    character(len=1000):: infile
+    integer(kind=4) :: ncid
+    integer :: status
+
+    infile=trim(trim(data_dir)//'a68_experiment_ll_p125_grid.nc')
+
+    !Open netCDF file
+    call handle_err(nf90_open(infile, nf90_nowrite, ncid))
+    !Inquire about the dimensions
+    call handle_err(nf90_inquire_dimension(ncid,1,len=nj))
+    call handle_err(nf90_inquire_dimension(ncid,2,len=ni))
+    !Close netCDF file
+    call handle_err(nf90_close(ncid))
+  end subroutine a68_dims
+
+  !> Handle for errors
+  subroutine handle_err(status)
+    integer, intent (in) :: status
+
+    if(status /= nf90_noerr) then
+      print *, trim(nf90_strerror(status))
+      stop "Stopped"
+    end if
+  end subroutine handle_err
+
+  !>A68 grid setup
+  subroutine a68_prep(data_dir,mpp_domain,lon,lat,dx,dy,area,REarth)
+    ! Arguments
+    character(len=*) :: data_dir
+    type(domain2D) :: mpp_domain
+    real :: lon(:,:) !< Longitude or position in x
+    real :: lat(:,:) !< Latitude or position in y
+    real :: dx(:,:) !< Length of northern edge of cell (m)
+    real :: dy(:,:) !< Length of eatern edge of cell (m)
+    real :: area(:,:) !< Area of cell (m2)
+    real :: REarth
+    ! Local variables
+    character(len=1000) :: filename
+    real, parameter :: gres=0.125
+
+    !Grid specs: lon,lat,dx,dy,area
+    filename=trim(trim(data_dir)//'a68_experiment_ll_p125_grid.nc')
+    call read_a68_data(mpp_domain,filename,'longitude',lon)
+    lon=lon+360
+    call read_a68_data(mpp_domain,filename,'latitude',lat)
+
+    call haversine_dist_and_area(REarth,gres,lon,lat,dx,dy,area)
+  end subroutine a68_prep
+
+  !> Haversine distance and area
+  subroutine haversine_dist_and_area(REarth,gres,lon1,lat1,dx,dy,area)
+    ! Arguments
+    real, intent(in) :: REarth    !Earth radius (m)
+    real, intent(in) :: gres      !grid resolution (degrees)
+    real, intent(in) :: lon1(:,:) !grid longitude
+    real, intent(in) :: lat1(:,:) !grid latitude
+    real, intent(out) :: dx(:,:)  !grid dx (m)
+    real, intent(out) :: dy(:,:)   !grid dy (m)
+    real, intent(out) :: area(:,:) !grid area (m^2)
+    ! Local variables
+    real, parameter :: pi_180=pi/180.
+    real, dimension(size(lon1,1),size(lon1,2)) :: lon2,lat2,p1,p2,dp,dm,a,c
+
+    !calculate dx
+    lon2=lon1-gres
+    lat2=lat1
+    p1 = lat1 * pi_180; p2 = lat2 * pi_180; dp = (lat2-lat1) * pi_180; dm = (lon2-lon1) * pi_180
+    a = sin(0.5*dp)**2. + cos(p1) * cos(p2) * sin(0.5*dm)**2.; c = 2. * atan2(sqrt(a), sqrt(1-a))
+    dx = REarth * c
+
+    !calculate dy
+    lat2=lat1-gres
+    lon2=lon1
+    p1 = lat1 * pi_180; p2 = lat2 * pi_180; dp = (lat2-lat1) * pi_180; dm = (lon2-lon1) * pi_180
+    a = sin(0.5*dp)**2. + cos(p1) * cos(p2) * sin(0.5*dm)**2.; c = 2. * atan2(sqrt(a), sqrt(1-a))
+    dy = REarth * c
+
+    !calculate area
+    area=pi_180*(REarth**2.)*abs(sin(lat1*pi_180)-sin(lat2*pi_180))*abs(gres)
+  end subroutine haversine_dist_and_area
+
+
+  !> Read in static (not time-varying) data for A68 experiment from file
+  subroutine read_a68_data(domain,filename,var,field)
+    ! Arguments
+    type(domain2D) :: domain !< Parallel decomposition
+    character(len=*), intent(in) :: filename, var
+    character(len=120) :: actual_filename
+    real :: field(:,:)
+    type(FmsNetcdfDomainFile_t) :: fileobj !< Fms2_io fileobj
+
+    call mpp_sync()
+
+    if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') 'icebergs_driver: Reading ',var
+    call get_instance_filename(filename, actual_filename)
+    if (open_file(fileobj, trim(actual_filename), "read", domain)) then
+      call register_axis_wrapper_a68(fileobj)
+      if (variable_exists(fileobj, var)) then
+        call read_data(fileobj, var, field)
+        !call read_data(actual_filename, var, field, domain)
+      else
+        if (mpp_pe().eq.mpp_root_pe()) then
+          call error_mesg('icebergs_driver:','Variable missing in file!', FATAL)
+        endif
+      endif
+    else
+      if (mpp_pe().eq.mpp_root_pe()) then
+        call error_mesg('icebergs_driver:','File for variable not found!', FATAL)
+      endif
+    endif
+    call mpp_sync()
+  end subroutine read_a68_data
+
+  !> Calls read_a68_data for wind velocity, ocean velocity, and ssh
+  subroutine a68_prep_3d(data_dir,mpp_domain,tauxa_hr,tauya_hr,uo_hr,vo_hr,ssh_hr)
+    ! Arguments
+    character(len=*) :: data_dir
+
+    type(domain2D) :: mpp_domain
+    real :: tauxa_hr(:,:,:) !< Zonal jra55 wind velocity (m/s, hourly)
+    real :: tauya_hr(:,:,:) !< Meridional jra55 wind velocity (m/s, hourly)
+    real :: uo_hr(:,:,:) !< Zonal OSCAR ocean surface velocity (m/s, hourly)
+    real :: vo_hr(:,:,:) !< Meridional OSCAR ocean surface velocity (m/s, hourly)
+    real :: ssh_hr(:,:,:) !< Effective sea surface height (m, hourly)
+    ! Local variables
+    character(len=1000) :: filename
+
+    filename=trim(trim(data_dir)//'a68_experiment_wind_vel_ncep_10m_dec2020_HOURLY_ll_p125.nc')
+    call read_a68_data_3d(mpp_domain,filename,'ua',tauxa_hr)
+    call read_a68_data_3d(mpp_domain,filename,'va',tauya_hr)
+
+    filename=trim(trim(data_dir)//'a68_experiment_ocean_surf_vel_oscar_dec2020_HOURLY_ll_p125.nc')
+    call read_a68_data_3d(mpp_domain,filename,'uo',uo_hr)
+    call read_a68_data_3d(mpp_domain,filename,'vo',vo_hr)
+
+    filename=trim(trim(data_dir)//'a68_experiment_ssh_duacs_dec2020_HOURLY_ll_p125.nc')
+    call read_a68_data_3d(mpp_domain,filename,'SSH',ssh_hr)
+  end subroutine a68_prep_3d
+
+  !> Read in time-varying A68 data
+  subroutine read_a68_data_3d(domain,filename,var,field)
+    ! Arguments
+    type(domain2D) :: domain !< Parallel decomposition
+    character(len=*), intent(in) :: filename, var
+    character(len=120) :: actual_filename
+    real :: field(:,:,:)
+    type(FmsNetcdfDomainFile_t) :: fileobj !< Fms2_io fileobj
+
+    call mpp_sync()
+    if (mpp_pe().eq.mpp_root_pe()) write(*,'(2a)') 'icebergs_driver: Reading ',var
+    call get_instance_filename(filename, actual_filename)
+    if (open_file(fileobj, trim(actual_filename), "read", domain)) then
+      call register_axis_wrapper_a68(fileobj)
+      if (variable_exists(fileobj, var)) then
+        call read_data(fileobj, var, field)
+        !call read_data(actual_filename, var, field, domain)
+      else
+        if (mpp_pe().eq.mpp_root_pe()) then
+          call error_mesg('icebergs_driver:','Variable missing in file!', FATAL)
+        endif
+      endif
+    else
+      if (mpp_pe().eq.mpp_root_pe()) then
+        call error_mesg('icebergs_driver:','File for variable not found!', FATAL)
+      endif
+    endif
+    call mpp_sync()
+  end subroutine read_a68_data_3d
+
+  !> Wrapper for fms2_io register_axis calls when reading domain decomposed files
+subroutine register_axis_wrapper_a68(fileobj)
+  type(FmsNetcdfDomainFile_t), intent(inout)          :: fileobj   !< Fms2_io fileobj
+
+  character(len=20), dimension(:), allocatable :: file_dim_names !< Array of dimension names
+  integer :: i                    !< For do loops
+  integer :: dim_size             !< Size of the dimension
+  integer :: ndims                !< Number of dimensions in the file
+
+  ndims = get_num_dimensions(fileobj)
+  allocate(file_dim_names(ndims))
+
+  call get_dimension_names(fileobj, file_dim_names)
+
+  !< When reading fms2_io requires that the domain decomposed dimensions ("x" and "y") are
+  !! registered so that fms2_io knows that they are domain decomposed
+  do i = 1, ndims
+    if (lowercase(file_dim_names(i)) .eq. 'lon') then
+      call register_axis(fileobj, file_dim_names(i), "x")
+    elseif (lowercase(file_dim_names(i)) .eq. 'lat') then
+      call register_axis(fileobj, file_dim_names(i), "y")
+    elseif (lowercase(file_dim_names(i)) .eq. 'time') then
+      call get_dimension_size(fileobj, file_dim_names(i), dim_size)
+      call register_axis(fileobj, file_dim_names(i), dim_size)
+    endif
+  enddo
+
+  deallocate(file_dim_names)
+end subroutine register_axis_wrapper_a68
+#endif
+end module driver_data_fms2
diff --git a/driver/icebergs_driver.F90 b/driver/icebergs_driver.F90
index 125f3b8..2e17027 100644
--- a/driver/icebergs_driver.F90
+++ b/driver/icebergs_driver.F90
@@ -3,8 +3,7 @@ program icebergs_driver
 use constants_mod, only: pi
 use fms_mod, only : fms_init
 use fms_mod, only : fms_end
-use fms_mod, only : open_namelist_file
-use fms_mod, only : close_file
+use fms_mod, only : check_nml_error
 use fms_mod, only : error_mesg
 use fms_mod, only : FATAL
 use mpp_domains_mod, only : mpp_define_layout
@@ -19,6 +18,7 @@ program icebergs_driver
 use mpp_mod, only : mpp_root_pe
 use mpp_mod, only: mpp_sync
 use mpp_mod, only: mpp_exit
+use mpp_mod, only: input_nml_file
 use time_manager_mod, only : time_type
 use time_manager_mod, only : set_date
 use time_manager_mod, only : set_calendar_type
@@ -76,6 +76,7 @@ program icebergs_driver
 real :: bump_depth=0
 real :: sst=-2
 real :: REarth=6.378e6
+integer :: ierr
 integer :: ibhrs=2
 integer :: nmax = 2000000000 !<max number of iteration
 integer :: write_time_inc=1
@@ -138,9 +139,8 @@ program icebergs_driver
 call fms_init()
 
 ! Read run-time parameters
-nmunit = open_namelist_file(file='input.nml')
-read(nmunit, nml=icebergs_driver_nml)
-call close_file(nmunit)
+read(input_nml_file, nml=icebergs_driver_nml, iostat=ierr)
+ierr = check_nml_error(ierr,'icebergs_driver_nml')
 
 if (a68_test) then
   call a68_dims(data_dir,ni,nj)
diff --git a/src/icebergs_fms2io.F90 b/src/icebergs_fms2io.F90
index 844b660..ddc97f2 100644
--- a/src/icebergs_fms2io.F90
+++ b/src/icebergs_fms2io.F90
@@ -520,7 +520,7 @@ subroutine write_restart_bergs(bergs, time_stamp)
   enddo; enddo !End of loop over grid
 
   filename = "RESTART/"//trim("bonds_iceberg.res.nc")
-  if (open_file(fileobj, filename, "overwrite", bergs%grd%domain, is_restart=.true.)) &
+  if (.not. open_file(fileobj, filename, "overwrite", bergs%grd%domain, is_restart=.true.)) &
     call error_mesg('write_icebegrs_restart', "Error opening the bonds icebergs restart file to write", FATAL)
 
   call register_unlimited_compressed_axis(fileobj,'i',nbonds)
diff --git a/src/icebergs_framework.F90 b/src/icebergs_framework.F90
index c9b5e0e..c327135 100644
--- a/src/icebergs_framework.F90
+++ b/src/icebergs_framework.F90
@@ -3974,7 +3974,8 @@ subroutine unpack_bond_traj_from_buffer2(first, buff, n)
   integer :: counter ! Position in stack
   integer :: cnt1, ij1, cnt2, ij2
 
-  if (dem) allocate(bond_traj%tangd1,bond_traj%tangd2,bond_traj%nstress,bond_traj%sstress,bond_traj%rel_rotation)
+  if (dem) allocate(bond_traj%tangd1,bond_traj%tangd2,bond_traj%nstress,&
+                    bond_traj%sstress,bond_traj%rel_rotation,bond_traj%broken)
 
   counter = 0
   call pull_buffer_value(buff%data(:,n),counter,bond_traj%lon)
@@ -5355,7 +5356,8 @@ subroutine record_posn(bergs)
 
   if (dem) allocate(posn%ang_vel,posn%ang_accel,posn%rot)
 
-  if (save_bond_traj .and. dem) allocate(bond_posn%tangd1,bond_posn%tangd2,bond_posn%nstress,bond_posn%sstress,bond_posn%rel_rotation)
+  if (save_bond_traj .and. dem) allocate(bond_posn%tangd1,bond_posn%tangd2,bond_posn%nstress,&
+                                         bond_posn%sstress,bond_posn%rel_rotation,bond_posn%broken)
 
   area_thres=bergs%traj_area_thres*1.e6 ! convert from km^2 to m^2
   area_thres2=bergs%traj_area_thres_sntbc*1.e6
@@ -5479,6 +5481,7 @@ subroutine record_posn(bergs)
                 bond_posn%nstress=current_bond%nstress
                 bond_posn%sstress=current_bond%sstress
                 bond_posn%rel_rotation=current_bond%rel_rotation
+                bond_posn%broken=current_bond%broken
               endif
 
               call push_bond_posn(current_bond%bond_trajectory, bond_posn)
@@ -5530,7 +5533,8 @@ subroutine push_bond_posn(bond_trajectory, bond_posn_vals)
 
   allocate(new_bond_posn)
 
-  if (dem) allocate(new_bond_posn%tangd1,new_bond_posn%tangd2,new_bond_posn%nstress,new_bond_posn%sstress,new_bond_posn%rel_rotation)
+  if (dem) allocate(new_bond_posn%tangd1,new_bond_posn%tangd2,new_bond_posn%nstress,&
+                    new_bond_posn%sstress,new_bond_posn%rel_rotation,new_bond_posn%broken)
 
   new_bond_posn=bond_posn_vals
   new_bond_posn%next=>bond_trajectory
@@ -5585,7 +5589,8 @@ subroutine append_bond_posn(bond_trajectory, bond_posn_vals)
 
   allocate(new_bond_posn)
 
-  if (dem) allocate(new_bond_posn%tangd1,new_bond_posn%tangd2,new_bond_posn%nstress,new_bond_posn%sstress,new_bond_posn%rel_rotation)
+  if (dem) allocate(new_bond_posn%tangd1,new_bond_posn%tangd2,new_bond_posn%nstress,&
+                    new_bond_posn%sstress,new_bond_posn%rel_rotation,new_bond_posn%broken)
 
   new_bond_posn=bond_posn_vals
   new_bond_posn%next=>null()
diff --git a/tests/a68_test/long_run.nml b/tests/a68_test/long_run.nml
index 5566d06..2aa3ff7 100644
--- a/tests/a68_test/long_run.nml
+++ b/tests/a68_test/long_run.nml
@@ -4,7 +4,7 @@
 &icebergs_driver_nml
   a68_test=.true.
   !specify your data dir (ocean currents, winds, etc)
-  data_dir='/lustre/f2/dev/gfdl/Alexander.Huth/MOM6-examples/src/icebergs/tests/a68_test/data/'
+  data_dir='./data/'
   Rearth=<re>
   ibdt=1800.0 !seconds
   ibuo=0.0 !ocean x velocity
@@ -148,8 +148,8 @@
 
     verbose=.false. !(F) Be verbose to stderr
     verbose_hrs=1! (24) Period between verbose messages
-    traj_sample_hrs=0!1 !(24) sampling period for trajectory storage
-    traj_write_hrs=0!6 !(480) Period for writing sampled trajectories to disk
+    traj_sample_hrs=1 !(24) sampling period for trajectory storage
+    traj_write_hrs=6 !(480) Period for writing sampled trajectories to disk
     save_bond_traj=.false. !(F) If T, saves bond trajectories in a separate file
     budget=.false. !(T) Calculate budgets
     debug=.false. !(F) Turn on debugging

From 4abac9e6ce52dcf9fd7b9b9420e81199fbff69a6 Mon Sep 17 00:00:00 2001
From: alex-huth <alexander.huth@noaa.gov>
Date: Mon, 15 Apr 2024 11:17:09 -0400
Subject: [PATCH 361/361] fixed heat budget

---
 src/icebergs.F90 | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/src/icebergs.F90 b/src/icebergs.F90
index 7a896fe..6c1fee7 100644
--- a/src/icebergs.F90
+++ b/src/icebergs.F90
@@ -6156,6 +6156,7 @@ subroutine accumulate_calving(bergs)
   ! Local variables
   type(icebergs_gridded), pointer :: grd
   real :: remaining_dist_s, remaining_dist_n, net_calving_used
+  real, dimension(bergs%grd%isd:bergs%grd%ied,bergs%grd%jsd:bergs%grd%jed) :: remaining_dist
   integer :: k, i, j
   logical, save :: first_call=.true.
   integer :: stderrunit
@@ -6203,20 +6204,20 @@ subroutine accumulate_calving(bergs)
     call error_mesg('KID, accumulate_calving', 'calving is OVER distributed!', WARNING)
   endif
   where (grd%lat<0.)
-    grd%tmp=remaining_dist_s
+    remaining_dist=remaining_dist_s
   elsewhere
-    grd%tmp=remaining_dist_n
+    remaining_dist=remaining_dist_n
   end where
-  net_calving_used=sum( grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec) *(1.-grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec)))
+  net_calving_used=sum( grd%calving(grd%isc:grd%iec,grd%jsc:grd%jec)*(1.-remaining_dist(grd%isc:grd%iec,grd%jsc:grd%jec)) )
   bergs%net_calving_used=bergs%net_calving_used+net_calving_used*bergs%dt
   ! Remove the calving accounted for by accumulation
-  grd%calving(:,:)=grd%calving(:,:)*grd%tmp(:,:)
+  grd%calving(:,:)=grd%calving(:,:)*remaining_dist(:,:)
 
   ! Do the same for heat (no separate classes needed)
-  grd%calving_hflx(:,:)=grd%calving_hflx(:,:)*grd%tmp(:,:)
-  grd%tmp(:,:)=bergs%dt*grd%calving_hflx(:,:)*grd%area(:,:)*(1.-grd%tmp(:,:))
+  grd%tmp(:,:)=bergs%dt*grd%calving_hflx(:,:)*grd%area(:,:)*(1.-remaining_dist(:,:))
   bergs%net_incoming_calving_heat_used=bergs%net_incoming_calving_heat_used+sum( grd%tmp(grd%isc:grd%iec,grd%jsc:grd%jec) )
-  grd%stored_heat(:,:)=grd%stored_heat(:,:)+grd%tmp(:,:) ! +=bergs%dt*grd%calving_hflx(:,:)*grd%area(:,:)*(1.-remaining_dist)
+  grd%stored_heat(:,:)=grd%stored_heat(:,:)+grd%tmp(:,:) ! +=bergs%dt*grd%calving_hflx(:,:)*grd%area(:,:)*(1.-remaining_dist(:,:))
+  grd%calving_hflx(:,:)=grd%calving_hflx(:,:)*remaining_dist(:,:)
 
 end subroutine accumulate_calving